
#NAME
PARCLIP_METTL3_Ping2014_hg19_CDS_m3_run2.txt

#BEAR
!!a"""ccc"""cccooooooccc]ccca22e	chr1:149824115-149824361(+)$1	246	125	157	15.3185
fff!!ggggggg[bboooooobbgggggggff	chr9:131708677-131708896(-)$1	219	113	145	12.8981
==========[a[cccnnnnnccc]a]=====	chr12:49663284-49663505(+)$1	221	84	116	12.3207
======####cccbboooooobb]ccc22===	chr16:58197871-58198091(-)$1	220	90	122	14.5442
[a!!ccc"""eeeeeooooooeeeee22ccc2	chr19:16528692-16528920(-)$1	228	124	156	14.5261
c!!bb"""bb"""bboooooobb22bb333bb	chr1:151554058-151554282(+)$1	224	63	95	12.1208
eeeee!!eeeee[bboooooobb]eeeeeeee	chr4:10078923-10079144(-)$1	221	147	179	11.8458
fff"""ccc!!cccrrrrrrrrrccc22ccc3	chr17:76210305-76210526(+)$1	221	136	168	12.1720
!!ffffff!!a[cccooooooccc]a22ffff	chrX:48674837-48675060(+)$1	223	10	42	15.9162
ncccdddd!!eeeeeooooooeeeee22dddd	chr6:123319009-123319238(+)$1	229	85	117	12.8845
GG:ccc####eeeeeooooooeeeee4444cc	chr15:41020808-41021091(+)$1	283	35	67	11.6169
cc[bb[dddd!!cccooooooccc]ddddbb]	chr5:180651351-180651586(+)$1	235	118	150	13.3659
b"""eeeee[bbcccooooooccc]bb]eeee	chr18:33693988-33694215(-)$1	227	144	176	13.9087
4444cccgggggggbboooooobb]ggggggg	chr1:210015528-210015752(+)$1	224	98	130	10.9992
!!iiiiiiiii[cccooooooccc7777777i	chr17:2227972-2228199(-)$1	227	40	72	11.8677
eeee!!bb[ffffffooooooffffff22bb2	chr17:34854121-34854346(+)$1	225	147	179	11.7792
ddffffff"""bbccclllccc]bb333ffff	chr14:91928417-91928656(-)$1	239	80	112	9.3645
iiiiiiii[ggggggglllggggggg22iiii	chr1:36213502-36213722(-)$1	220	3	35	10.4068
ddddddd[ccc[cccooooooccc333cccdd	chr5:179224913-179225140(-)$1	227	57	89	14.6693
bb[eeeee[ccccccooooooccc]ccceeee	chr16:2498757-2498985(+)$1	228	54	86	14.1777
===eeeee!!ccc[aooooooa]ccc22eeee	chr17:40452594-40452835(+)$1	241	125	157	15.2120
ccc!!ddddccc[a[ccclllccc]a333ccc	chr1:32797183-32797409(+)$1	226	117	149	11.3442
A:ggggggg!!cccrrrrrrrrrccc22gggg	chr1:43148229-43148478(+)$1	249	210	242	10.3823
[iiiiiiiii"""bbrrrrrrrrrbb22iiii	chr2:232323694-232323913(-)$1	219	135	167	11.0535
==========!!cccpppppppccc333====	chr1:206782681-206782910(-)$1	229	45	77	11.5542
eeggggggg####a[ccclllccc]a333ggg	chr9:139749424-139749658(-)$1	234	20	52	12.1591
hhhhhh[eeeeecccooooooccc]eeeee]h	chr8:41844916-41845146(-)$1	230	189	221	12.7414
ee!!eeeee!!ddddoooooodddd22eeeee	chr6:31627553-31627777(-)$1	224	72	104	13.6142
dd[cccccc[a[ddddoooooodddd22a]cc	chr6:116579717-116579946(-)$1	229	53	85	13.2243
ggggg$$$$$eeeeeooooooeeeeegggggg	chr5:180218618-180218847(-)$1	229	115	147	12.4143
==========!!cccooooooccc]=======	chr16:75140310-75140536(+)$1	226	132	164	16.5445
hhhheeeee[ccc[aooooooa]ccc]eeeee	chrX:53458265-53458490(-)$1	225	103	135	13.1396
c[eeeee"""acccpppppppccc]a333eee	chr9:131046765-131047003(+)$1	238	120	152	10.9823
d"""dddd!!a!!bboooooobb22a22dddd	chr2:74273716-74273940(+)$1	224	160	192	14.3478
eeeeeeeee[ddddoooooodddd]eeeeeee	chr12:57038524-57038750(-)$1	226	74	106	11.3142
cbb!!dddd"""cccooooooccc22dddd22	chr9:139360318-139360540(-)$1	222	26	58	13.7797
hhbb:a[ccc!!cccooooooccc333ccc]a	chr1:150418691-150418912(+)$1	221	147	179	13.8636
d"""dddd[bb[cccooooooccc22bb]ddd	chr2:219130013-219130234(-)$1	221	90	122	13.5020
bccc!!a[ddddrrrrrrrrrdddda22ccc]	chr11:62361225-62361454(-)$1	229	130	162	10.0963
fff[dddd[ffffffooooooffffff]dddd	chr14:21969784-21970011(+)$1	227	161	193	12.0561
b[eeeee"""cccrrrrrrrrrccc4444eee	chr6:44233035-44233258(-)$1	223	79	111	11.6303
2ccccccffffff[aooooooaffffff]ccc	chr1:225965558-225965782(+)$1	224	162	194	11.8344
f!!aggggggg[bboooooobbggggggg]a2	chr11:134014750-134014975(+)$1	225	9	41	11.6680
eeee!!ccc!!a[ddddllldddd]a22ccce	chr15:41021961-41022239(+)$1	278	24	56	11.0517
ddd!!bb$$$$$cccooooooccc4444bb22	chr1:40218538-40218770(+)$1	232	90	122	13.7133
gggggffffff[cccooooooccc]ffffffG	chr16:66785320-66785544(-)$1	224	170	202	13.0800
dffffffccc!!ccc[aooooooa]cccccc5	chr6:26198986-26199246(-)$1	260	25	57	11.0929
fffff:ccc[eeeeeooooooeeeee333ccc	chr1:37980159-37980392(-)$1	233	193	225	12.7771
eeeedddd!!eeeeeooooooeeeee22dddd	chr19:42858692-42858918(+)$1	226	104	136	13.4286
ddd[ccc####ddddooooooddddccc]ddd	chr1:149832446-149832697(-)$1	251	135	167	13.3213
iiiiiiii[bb[cccoooooocccbb]iiiii	chr1:82456284-82456539(+)$1	255	53	85	14.6646
eee[cccddddddddoooooodddd333dddd	chr6:26027119-26027380(-)$1	261	154	186	13.4479
c[a####dddd[cccooooooccc]dddd333	chr3:9506197-9506424(+)$1	227	76	108	14.1576
b[ffffff[bb[ddddooooooddddbb]fff	chr19:42373032-42373272(+)$1	240	72	104	10.4209

#otherMatches

#Seq PSSM
CGCAAGUCGACCGGCGGCAAGGCCCCGAGGAA	chr1:149824115-149824361(+)$1	246	125	157	15.3185
GCCUUGGUGUGGUCCUACCCUGGCUGCACCGG	chr9:131708677-131708896(-)$1	219	113	145	12.8981
UUGGGGGAGGAGAUGAUUCCUUCAACACCUUC	chr12:49663284-49663505(+)$1	221	84	116	12.3207
UCCAGUGGUCUCACGGCAGCACGAUGAAGACU	chr16:58197871-58198091(-)$1	220	90	122	14.5442
ACAUGGUCCCGCCUUCGGAGAGAGGCACGCCC	chr19:16528692-16528920(-)$1	228	124	156	14.5261
UUAGGAUAUCCAAGCCGCCUAGCCCGAAGCCC	chr1:151554058-151554282(+)$1	224	63	95	12.1208
UCCGGUGGCAUGGACAUGAUGGUGUAUGUUUG	chr4:10078923-10079144(-)$1	221	147	179	11.8458
GGACCACCGCAUCUCUACAUUCAAGAACUGGC	chr17:76210305-76210526(+)$1	221	136	168	12.1720
GGGUGCUCCUCUCUGUGCUUCCAGUGCUGAGU	chrX:48674837-48675060(+)$1	223	10	42	15.9162
UGCGGGCUAGGAAGUUUCAUCACUUUGAGGCC	chr6:123319009-123319238(+)$1	229	85	117	12.8845
GAAACAAAUUGCUCAUCUGCCUGAGUUCUGUG	chr15:41020808-41021091(+)$1	283	35	67	11.6169
ggaggagguugaggaagaggaUCUAGACCCCG	chr5:180651351-180651586(+)$1	235	118	150	13.3659
GCCUAGCAAUUGGUAUAUAUCUACAUAUUUGU	chr18:33693988-33694215(-)$1	227	144	176	13.9087
GAACCUACUACCCCUGGACUCACAUGGGGUAG	chr1:210015528-210015752(+)$1	224	98	130	10.9992
AAAUUCCUAAAUAGCUUCUUUGCUUUUGUCCU	chr17:2227972-2228199(-)$1	227	40	72	11.8677
CAGGGGCCAGAGGCGGAUUAUUGCCUCCAGGA	chr17:34854121-34854346(+)$1	225	147	179	11.7792
UCCAUUUUGAGGAAUCACAGAUAUCGAAGAGA	chr14:91928417-91928656(-)$1	239	80	112	9.3645
ACAAUGACUGACAUUUGUAAAAUGUUUUGUUA	chr1:36213502-36213722(-)$1	220	3	35	10.4068
GUCCGGCUCUUCCAGAUCUUCCUGAAAAAGGC	chr5:179224913-179225140(-)$1	227	57	89	14.6693
CCAGGAAGUGGGCUCCACCCUGAGACCCCUUC	chr16:2498757-2498985(+)$1	228	54	86	14.1777
GGCUCUCGUGCAGGUGUGAGAAGUUGGCCGAG	chr17:40452594-40452835(+)$1	241	125	157	15.2120
AAUGCUGCCGCACGCACCUGGGGUCCAAAUGC	chr1:32797183-32797409(+)$1	226	117	149	11.3442
CAGCCCAGCAGCGGAACCGUUAGCCGGAGCUG	chr1:43148229-43148478(+)$1	249	210	242	10.3823
ACUGGUUUGAAAGUCUUUGGCAAUGAAAUUAA	chr2:232323694-232323913(-)$1	219	135	167	11.0535
UCUAGAAGAUUGGCUUUUUGGUAGUAGUGUUU	chr1:206782681-206782910(-)$1	229	45	77	11.5542
CAGUGGGUACCUUGUGGGUUCCCCUCCCCUGC	chr9:139749424-139749658(-)$1	234	20	52	12.1591
CUGUUUUUCUUCUAAAAUGUGUUACGAAGGCA	chr8:41844916-41845146(-)$1	230	189	221	12.7414
GUGGCUGGCUACCUCGCCCUUGGGGCCGCCGG	chr6:31627553-31627777(-)$1	224	72	104	13.6142
GGUGCGCCGGGACUGUGAGACGACAGGCUGUG	chr6:116579717-116579946(-)$1	229	53	85	13.2243
GCUGGCUACCGGGGUAUUGUCACCUUCCAGUU	chr5:180218618-180218847(-)$1	229	115	147	12.4143
GGGCUUGCUUGCUGACUCCUCUCAAAGGUGAG	chr16:75140310-75140536(+)$1	226	132	164	16.5445
AUCCGGCUGGAUGGGGCCAUUCGUAUGCAGCC	chrX:53458265-53458490(-)$1	225	103	135	13.1396
AGGAGAUCUCCCAGUUCGUAUCUGAGUAAGUU	chr9:131046765-131047003(+)$1	238	120	152	10.9823
AAUGCCCUGACUACCUCGAGUGGCUGGAGGGG	chr2:74273716-74273940(+)$1	224	160	192	14.3478
UACUGGAUUCUGGUGCACCAAUCAAAAUUCCU	chr12:57038524-57038750(-)$1	226	74	106	11.3142
CGAUUUUGCCUACGGCACCUACCGCAGCAAUU	chr9:139360318-139360540(-)$1	222	26	58	13.7797
UAUGAAGCACAAUACAAAGAAGUAAAAGUGGU	chr1:150418691-150418912(+)$1	221	147	179	13.8636
GCCAUCUAUGACCUGGCUACGCAGACUCUUAG	chr2:219130013-219130234(-)$1	221	90	122	13.5020
GGCUGAGAGGUAGAGGGUGGAUGCCCAGGGCA	chr11:62361225-62361454(-)$1	229	130	162	10.0963
AUUCUUGCACUUGGGCCCGACCUCGAGAGCGA	chr14:21969784-21970011(+)$1	227	161	193	12.0561
cUCUGCCAAGCGGACCCGCAACCCGGAAAGGC	chr6:44233035-44233258(-)$1	223	79	111	11.6303
CGCUGGCGGGGCCGCUGCUUUGGGCCCCAGCC	chr1:225965558-225965782(+)$1	224	162	194	11.8344
GGAGAGUGAGGGCCACCCCCGGCCUCACUACA	chr11:134014750-134014975(+)$1	225	9	41	11.6680
UGGCAGCAUUAAGGCUUUUGGAGUGUCUAUGG	chr15:41021961-41022239(+)$1	278	24	56	11.0517
UUCUUCCUGACAUGUGACAAGACAGACUGGCU	chr1:40218538-40218770(+)$1	232	90	122	13.7133
Cggucgggccgggccguggggggcgcggccuc	chr16:66785320-66785544(-)$1	224	170	202	13.0800
UGCAGCUGGCCAUCCGCAACGACGAGGAGCUA	chr6:26198986-26199246(-)$1	260	25	57	11.0929
GCCCCAAGCCCGGCCGCGCUAGGCCGUUUGUU	chr1:37980159-37980392(-)$1	233	193	225	12.7771
CAGUCGGACCGCAGCCUCAUAGCUGCCUUCUG	chr19:42858692-42858918(+)$1	226	104	136	13.4286
CGGAUCUCUGGCCUCAUUUACGAGGAGACCCG	chr1:149832446-149832697(-)$1	251	135	167	13.3213
GAAGAUGAUGCUAUUGUGGCAGAUGCUUCAUC	chr1:82456284-82456539(+)$1	255	53	85	14.6646
GGAUGUGGUUUACGCGCUCAAGCGUCAAGGAC	chr6:26027119-26027380(-)$1	261	154	186	13.4479
GUCGAAAUGGAUACAGCCUCAUGUUUUCACCA	chr3:9506197-9506424(+)$1	227	76	108	14.1576
CACAGCGCGGCACCUGUACCUCCGGGGUGGCG	chr19:42373032-42373272(+)$1	240	72	104	10.4209

#DB
..(...(((...(((......))).))))..)	chr1:149824115-149824361(+)$1	1	125	157	15.3185
(((..(((((((.((......)))))))))))	chr9:131708677-131708896(-)$1	1	113	145	12.8981
((((((((((.(.(((.....))).).)))))	chr12:49663284-49663505(+)$1	1	84	116	12.3207
((((((....(((((......)).)))..)))	chr16:58197871-58198091(-)$1	1	90	122	14.5442
.(..(((...(((((......)))))..))).	chr19:16528692-16528920(-)$1	1	124	156	14.5261
(..((...((...((......))..))...))	chr1:151554058-151554282(+)$1	1	63	95	12.1208
(((((..(((((.((......)).))))))))	chr4:10078923-10079144(-)$1	1	147	179	11.8458
(((...(((..(((.........)))..))).	chr17:76210305-76210526(+)$1	1	136	168	12.1720
..((((((..(.(((......))).)..))))	chrX:48674837-48675060(+)$1	1	10	42	15.9162
.)))((((..(((((......)))))..))))	chr6:123319009-123319238(+)$1	1	85	117	12.8845
((.(((....(((((......)))))....))	chr15:41020808-41021091(+)$1	1	35	67	11.6169
((.((.((((..(((......))).)))))).	chr5:180651351-180651586(+)$1	1	118	150	13.3659
(...(((((.(((((......))).)).))))	chr18:33693988-33694215(-)$1	1	144	176	13.9087
....)))(((((((((......)).)))))))	chr1:210015528-210015752(+)$1	1	98	130	10.9992
..(((((((((.(((......))).......)	chr17:2227972-2228199(-)$1	1	40	72	11.8677
((((..((.((((((......))))))..)).	chr17:34854121-34854346(+)$1	1	147	179	11.7792
((((((((...(((((...))).))...))))	chr14:91928417-91928656(-)$1	1	80	112	9.3645
((((((((.(((((((...)))))))..))))	chr1:36213502-36213722(-)$1	1	3	35	10.4068
)))((((.(((.(((......)))...)))))	chr5:179224913-179225140(-)$1	1	57	89	14.6693
((.(((((.((((((......))).)))))))	chr16:2498757-2498985(+)$1	1	54	86	14.1777
)))(((((..(((.(......).)))..))))	chr17:40452594-40452835(+)$1	1	125	157	15.2120
(((..(((((((.(.(((...))).)...)))	chr1:32797183-32797409(+)$1	1	117	149	11.3442
).(((((((..(((.........)))..))))	chr1:43148229-43148478(+)$1	1	210	242	10.3823
.(((((((((...((.........))..))))	chr2:232323694-232323913(-)$1	1	135	167	11.0535
((((((((((..(((.......)))...))))	chr1:206782681-206782910(-)$1	1	45	77	11.5542
(((((((((....(.(((...))).)...)))	chr9:139749424-139749658(-)$1	1	20	52	12.1591
((((((.((((((((......))).))))).)	chr8:41844916-41845146(-)$1	1	189	221	12.7414
((..(((((..((((......))))..)))))	chr6:31627553-31627777(-)$1	1	72	104	13.6142
((.((((((.(.((((......))))..).))	chr6:116579717-116579946(-)$1	1	53	85	13.2243
(((((.....(((((......)))))))))))	chr5:180218618-180218847(-)$1	1	115	147	12.4143
((((((((((..(((......))).)))))))	chr16:75140310-75140536(+)$1	1	132	164	16.5445
))))(((((.(((.(......).))).)))))	chrX:53458265-53458490(-)$1	1	103	135	13.1396
(.(((((...((((.......))).)...)))	chr9:131046765-131047003(+)$1	1	120	152	10.9823
(...((((..(..((......))..)..))))	chr2:74273716-74273940(+)$1	1	160	192	14.3478
))))(((((.((((......)))).)))))((	chr12:57038524-57038750(-)$1	1	74	106	11.3142
)((..((((...(((......)))..))))..	chr9:139360318-139360540(-)$1	1	26	58	13.7797
)))).(.(((..(((......)))...))).)	chr1:150418691-150418912(+)$1	1	147	179	13.8636
(...((((.((.(((......)))..)).)))	chr2:219130013-219130234(-)$1	1	90	122	13.5020
((((..(.((((.........)))))..))).	chr11:62361225-62361454(-)$1	1	130	162	10.0963
(((.((((.((((((......)))))).))))	chr14:21969784-21970011(+)$1	1	161	193	12.0561
(.(((((...(((.........)))....)))	chr6:44233035-44233258(-)$1	1	79	111	11.6303
.)))(((((((((.(......))))))).)))	chr1:225965558-225965782(+)$1	1	162	194	11.8344
(..((((((((.((......))))))))).).	chr11:134014750-134014975(+)$1	1	9	41	11.6680
((((..(((..(.((((...)))).)..))))	chr15:41021961-41022239(+)$1	1	24	56	11.0517
(((..((.....(((......)))....))..	chr1:40218538-40218770(+)$1	1	90	122	13.7133
)))))((((((.(((......))).)))))))	chr16:66785320-66785544(-)$1	1	170	202	13.0800
((((((((((..(((.(......).)))))).	chr6:26198986-26199246(-)$1	1	25	57	11.0929
))))).(((.(((((......)))))...)))	chr1:37980159-37980392(-)$1	1	193	225	12.7771
))))((((..(((((......)))))..))))	chr19:42858692-42858918(+)$1	1	104	136	13.4286
(((.(((....((((......))))))).)))	chr1:149832446-149832697(-)$1	1	135	167	13.3213
((((((((.((.(((......))))).)))))	chr1:82456284-82456539(+)$1	1	53	85	14.6646
(((.(((((((((((......))))...))))	chr6:26027119-26027380(-)$1	1	154	186	13.4479
(.(....((((.(((......))).))))...	chr3:9506197-9506424(+)$1	1	76	108	14.1576
(.((((((.((.((((......)))))).)))	chr19:42373032-42373272(+)$1	1	72	104	10.4209

#PSSM
e : 0.14	d : 0.14	c : 0.11	f : 0.09	= : 0.09	b : 0.09	! : 0.05	h : 0.05	[ : 0.03	i : 0.03	g : 0.03	n : 0.01	G : 0.01	4 : 0.01	A : 0.01	2 : 0.01	
e : 0.14	! : 0.09	f : 0.09	= : 0.09	c : 0.09	d : 0.09	[ : 0.07	" : 0.05	i : 0.05	h : 0.05	b : 0.03	g : 0.03	a : 0.01	G : 0.01	4 : 0.01	: : 0.01	
f : 0.14	e : 0.14	= : 0.09	! : 0.07	c : 0.07	i : 0.07	g : 0.07	[ : 0.05	" : 0.05	d : 0.05	a : 0.03	h : 0.03	b : 0.03	: : 0.01	4 : 0.01	
e : 0.16	! : 0.11	" : 0.09	f : 0.09	c : 0.09	= : 0.07	i : 0.07	g : 0.07	b : 0.05	[ : 0.05	h : 0.03	4 : 0.01	d : 0.01	a : 0.01	# : 0.01	
e : 0.16	! : 0.12	c : 0.12	d : 0.11	f : 0.09	g : 0.09	= : 0.07	i : 0.07	" : 0.03	b : 0.03	h : 0.01	: : 0.01	# : 0.01	
d : 0.14	e : 0.14	c : 0.12	f : 0.09	g : 0.07	= : 0.07	! : 0.07	i : 0.07	" : 0.05	[ : 0.01	h : 0.01	$ : 0.01	a : 0.01	b : 0.01	: : 0.01	# : 0.01	
c : 0.18	d : 0.16	e : 0.14	f : 0.09	g : 0.07	i : 0.07	= : 0.05	# : 0.05	b : 0.03	[ : 0.03	" : 0.01	! : 0.01	$ : 0.01	a : 0.01	
d : 0.18	e : 0.14	c : 0.12	g : 0.09	f : 0.09	" : 0.07	i : 0.07	= : 0.05	# : 0.05	[ : 0.03	$ : 0.03	b : 0.01	
c : 0.14	[ : 0.12	e : 0.11	d : 0.11	g : 0.09	! : 0.09	" : 0.07	= : 0.05	# : 0.05	i : 0.03	$ : 0.03	f : 0.03	b : 0.01	
! : 0.16	" : 0.11	[ : 0.09	c : 0.09	g : 0.07	# : 0.07	b : 0.07	d : 0.07	f : 0.07	= : 0.05	e : 0.03	i : 0.03	$ : 0.03	
! : 0.16	e : 0.14	c : 0.12	" : 0.09	g : 0.07	a : 0.07	b : 0.07	f : 0.07	d : 0.07	# : 0.03	[ : 0.01	i : 0.01	$ : 0.01	
[ : 0.18	c : 0.16	e : 0.14	! : 0.11	d : 0.09	" : 0.07	g : 0.05	f : 0.05	a : 0.03	b : 0.03	# : 0.01	$ : 0.01	
c : 0.46	e : 0.11	d : 0.11	[ : 0.09	f : 0.05	" : 0.03	g : 0.03	b : 0.03	# : 0.01	! : 0.01	r : 0.01	
c : 0.42	b : 0.12	d : 0.12	e : 0.11	[ : 0.05	g : 0.03	f : 0.03	a : 0.03	r : 0.03	
c : 0.37	b : 0.12	e : 0.11	d : 0.11	r : 0.07	a : 0.05	f : 0.03	[ : 0.03	o : 0.03	g : 0.01	p : 0.01	
o : 0.68	r : 0.09	c : 0.07	d : 0.05	p : 0.03	b : 0.01	g : 0.01	[ : 0.01	
o : 0.74	r : 0.09	l : 0.03	c : 0.03	p : 0.03	n : 0.01	d : 0.01	a : 0.01	
o : 0.75	r : 0.09	l : 0.05	c : 0.03	p : 0.03	n : 0.01	
o : 0.75	r : 0.09	l : 0.09	p : 0.03	n : 0.01	
o : 0.75	r : 0.09	l : 0.05	p : 0.03	n : 0.01	c : 0.01	g : 0.01	
o : 0.72	r : 0.09	l : 0.03	p : 0.03	d : 0.03	n : 0.01	c : 0.01	g : 0.01	b : 0.01	
c : 0.38	b : 0.11	e : 0.11	d : 0.11	r : 0.07	o : 0.07	a : 0.05	f : 0.03	g : 0.01	p : 0.01	
c : 0.40	d : 0.14	b : 0.11	e : 0.11	r : 0.05	f : 0.05	] : 0.05	g : 0.03	o : 0.01	
c : 0.48	d : 0.14	e : 0.11	g : 0.05	f : 0.05	] : 0.03	2 : 0.03	b : 0.03	r : 0.01	a : 0.01	
] : 0.31	c : 0.12	e : 0.12	d : 0.11	2 : 0.07	g : 0.05	f : 0.05	b : 0.05	3 : 0.03	7 : 0.01	4 : 0.01	
c : 0.16	e : 0.16	a : 0.14	3 : 0.09	g : 0.07	b : 0.07	d : 0.07	f : 0.07	2 : 0.05	4 : 0.03	7 : 0.01	= : 0.01	
2 : 0.25	3 : 0.16	c : 0.09	g : 0.07	b : 0.07	f : 0.07	] : 0.05	e : 0.05	4 : 0.05	d : 0.05	7 : 0.01	= : 0.01	
2 : 0.27	3 : 0.14	c : 0.11	e : 0.09	g : 0.07	4 : 0.05	d : 0.05	= : 0.03	] : 0.03	b : 0.03	f : 0.03	7 : 0.01	i : 0.01	
e : 0.14	d : 0.14	c : 0.12	g : 0.09	3 : 0.09	] : 0.07	= : 0.05	f : 0.05	i : 0.05	a : 0.03	2 : 0.03	4 : 0.03	7 : 0.01	b : 0.01	
c : 0.18	e : 0.18	d : 0.14	g : 0.09	= : 0.07	f : 0.07	b : 0.05	i : 0.05	3 : 0.03	] : 0.03	2 : 0.01	4 : 0.01	7 : 0.01	
c : 0.18	e : 0.16	d : 0.14	f : 0.09	= : 0.07	g : 0.07	2 : 0.05	b : 0.05	i : 0.05	] : 0.03	7 : 0.01	a : 0.01	3 : 0.01	
e : 0.20	d : 0.14	2 : 0.09	c : 0.09	f : 0.07	= : 0.07	g : 0.07	i : 0.07	3 : 0.03	] : 0.03	b : 0.01	h : 0.01	a : 0.01	G : 0.01	5 : 0.01	

#score	686.3195235631742
#seq	54
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_CDS_m2_run2.txt

#BEAR
eeeeemmmmeeeee	chr4:144459923-144460161(+)$1	238	105	119	10.7270
eeeeemmmmeeeee	chr12:101701987-101702212(+)$1	225	95	109	10.7270
eeeeemmmmeeeee	chr3:63898217-63898439(+)$1	222	126	140	10.7270
eeeeennnnneeee	chr6:36564618-36564841(+)$1	223	184	198	9.5073
eeeeemmmmeeeee	chr5:865513-865755(-)$1	242	32	46	10.7270
eeeeellleeeeed	chr15:40998302-40998551(-)$1	249	114	128	9.2919
eeeeellleeeee]	chr1:32800508-32800744(-)$1	236	3	17	9.2273
deeeeellleeeee	chr19:50311852-50312075(+)$1	223	183	197	9.2917
eeeeemmmmeeeee	chr15:41001160-41001400(+)$1	240	51	65	10.7270
eeeeeooooooeee	chr4:119613034-119613323(-)$1	289	200	214	9.6077
eeeeemmmmeeeee	chr19:50534226-50534446(+)$1	220	4	18	10.7270
[eeeeellleeeee	chr16:632909-633134(+)$1	225	50	64	9.2561
[eeeeellleeeee	chr20:48808037-48808256(+)$1	219	62	76	9.2561
eeeeennnnneeee	chr5:98129055-98129285(+)$1	230	103	117	9.5073
eeeeemmmmeeeee	chr12:101693700-101693924(+)$1	224	52	66	10.7270
eeeeellleeeee]	chr4:186064480-186064699(+)$1	219	41	55	9.2273
eeeeemmmmeeeee	chr19:581398-581630(+)$1	232	2	16	10.7270
eeeeeooooooeee	chr1:1413986-1414216(+)$1	230	207	221	9.6077
eeeeemmmmeeeee	chr4:71863727-71863954(+)$1	227	107	121	10.7270
eeeeemmmmeeeee	chr3:121500534-121500767(-)$1	233	161	175	10.7270
eeeeeooooooeee	chr11:66206049-66206278(-)$1	229	97	111	9.6077
deeeeellleeeee	chr14:23240160-23240382(+)$1	222	164	178	9.2917
eeeeemmmmeeeee	chr1:165667589-165667811(-)$1	222	171	185	10.7270
eeeeennnnneeee	chr19:13879742-13879962(+)$1	220	129	143	9.5073
eeeeemmmmeeeee	chr12:112842959-112843190(-)$1	231	64	78	10.7270
eeeeemmmmeeeee	chr14:21969771-21970147(-)$1	376	279	293	10.7270
eeeeeooooooeee	chr14:21968545-21968916(-)$1	371	79	93	9.6077
[eeeeellleeeee	chr5:175665430-175665670(+)$1	240	150	164	9.2561
eeeeemmmmeeeee	chr12:111856209-111856441(+)$1	232	97	111	10.7270
eeeeeooooooeee	chr3:183899736-183899960(+)$1	224	152	166	9.6077
eeeeeooooooeee	chr16:29819813-29820033(+)$1	220	71	85	9.6077
eeeeennnnneeee	chr11:94731446-94731676(+)$1	230	120	134	9.5073
eeeeennnnneeee	chr1:247151334-247151563(-)$1	229	84	98	9.5073
eeeeennnnneeee	chr1:39906650-39906885(+)$1	235	136	150	9.5073
eeeeemmmmeeeee	chr2:176957737-176957960(+)$1	223	157	171	10.7270
eeeeemmmmeeeee	chr15:41001158-41001404(-)$1	246	120	134	10.7270
eeeeennnnneeee	chr14:21967587-21967814(+)$1	227	191	205	9.5073
eeeeemmmmeeeee	chr14:21969023-21969364(-)$1	341	149	163	10.7270
eeeeennnnneeee	chr14:99976950-99977172(+)$1	222	189	203	9.5073
eeeeemmmmeeeee	chr10:103577478-103577710(-)$1	232	170	184	10.7270
eeeeennnnneeee	chr10:103912050-103912277(+)$1	227	13	27	9.5073
eeeeeooooooeee	chr11:497893-498113(+)$1	220	154	168	9.6077
eeeeemmmmeeeee	chr1:245021413-245021638(-)$1	225	184	198	10.7270
eeeeemmmmeeeee	chr3:170858103-170858323(+)$1	220	161	175	10.7270
eeeeennnnneeee	chr19:36633512-36633732(+)$1	220	90	104	9.5073
eeeeellleeeee]	chr8:146015119-146015357(-)$1	238	4	18	9.2273
eeeeemmmmeeeee	chr16:28074419-28074647(+)$1	228	27	41	10.7270
eeeeellleeeeed	chr15:40990896-40991120(+)$1	224	190	204	9.2919
eeeeemmmmeeeee	chr14:21967348-21967599(-)$1	251	58	72	10.7270
eeeeeooooooeee	chr4:119621622-119621888(-)$1	266	147	161	9.6077
eeeeemmmmeeeee	chrX:70517127-70517370(+)$1	243	27	41	10.7270
eeeeemmmmeeeee	chr5:159437463-159437684(+)$1	221	156	170	10.7270
eeeeemmmmeeeee	chr4:119618239-119618571(-)$1	332	190	204	10.7270
eeeeeooooooeee	chr4:119606601-119606855(-)$1	254	68	82	9.6077
eeeeeooooooeee	chr8:101724891-101725116(-)$1	225	4	18	9.6077
eeeeemmmmeeeee	chr6:31595837-31596061(+)$1	224	129	143	10.7270
eeeeemmmmeeeee	chrX:23748849-23749068(-)$1	219	4	18	10.7270
eeeeemmmmeeeee	chr2:231931676-231931899(+)$1	223	138	152	10.7270
eeeeemmmmeeeee	chr22:38201468-38201696(-)$1	228	97	111	10.7270
eee[ammmma]eee	chr20:36611802-36612022(-)$1	220	143	157	8.5928

#otherMatches

#Seq PSSM
ACUGCUGAUGUAGU	chr4:144459923-144460161(+)$1	238	105	119	10.7270
GUGGUACAGACUGC	chr12:101701987-101702212(+)$1	225	95	109	10.7270
gcggccgcggccgc	chr3:63898217-63898439(+)$1	222	126	140	10.7270
CUACAGGAUAUGUG	chr6:36564618-36564841(+)$1	223	184	198	9.5073
ACGUGGGGUCAUGU	chr5:865513-865755(-)$1	242	32	46	10.7270
CCGCCUUUGGUGGA	chr15:40998302-40998551(-)$1	249	114	128	9.2919
AGGGGGAGCCCCUG	chr1:32800508-32800744(-)$1	236	3	17	9.2273
GGCCCGCAACGGGU	chr19:50311852-50312075(+)$1	223	183	197	9.2917
CGCUUUUUUAGGUG	chr15:41001160-41001400(+)$1	240	51	65	10.7270
ACAAAAUUAAAUUU	chr4:119613034-119613323(-)$1	289	200	214	9.6077
GAAGGGAGGCUUUC	chr19:50534226-50534446(+)$1	220	4	18	10.7270
GGGCGCCCUGUGCC	chr16:632909-633134(+)$1	225	50	64	9.2561
CGGGCUUCGAGCCC	chr20:48808037-48808256(+)$1	219	62	76	9.2561
GCACCUCCUUGGUG	chr5:98129055-98129285(+)$1	230	103	117	9.5073
CUCUUGAGAAAGAG	chr12:101693700-101693924(+)$1	224	52	66	10.7270
UCACCAUGGGUGAU	chr4:186064480-186064699(+)$1	219	41	55	9.2273
GGCCGACCCCGGCC	chr19:581398-581630(+)$1	232	2	16	10.7270
CUGGGUGUGGUCCC	chr1:1413986-1414216(+)$1	230	207	221	9.6077
GGGAAGUGGUUCCU	chr4:71863727-71863954(+)$1	227	107	121	10.7270
AUGUCAGAAGACAU	chr3:121500534-121500767(-)$1	233	161	175	10.7270
GGUCGGCGGUGUGA	chr11:66206049-66206278(-)$1	229	97	111	9.6077
GCGUGUUGUACAUG	chr14:23240160-23240382(+)$1	222	164	178	9.2917
CGAGAAAGCUUUCG	chr1:165667589-165667811(-)$1	222	171	185	10.7270
CCCCUCAGAAAGGG	chr19:13879742-13879962(+)$1	220	129	143	9.5073
AUUUUACCAAAAAU	chr12:112842959-112843190(-)$1	231	64	78	10.7270
UCUCUUGGAAGGGA	chr14:21969771-21970147(-)$1	376	279	293	10.7270
CCACUUUAUGCAGU	chr14:21968545-21968916(-)$1	371	79	93	9.6077
ucgcggaggccgcg	chr5:175665430-175665670(+)$1	240	150	164	9.2561
AGCUCUGAGGAGCU	chr12:111856209-111856441(+)$1	232	97	111	10.7270
AGCUGAUGUCACAG	chr3:183899736-183899960(+)$1	224	152	166	9.6077
CCUCAGAAAUGUGA	chr16:29819813-29820033(+)$1	220	71	85	9.6077
UUGUGGACCACAUG	chr11:94731446-94731676(+)$1	230	120	134	9.5073
GAUAUGAAAGAUGU	chr1:247151334-247151563(-)$1	229	84	98	9.5073
GCAUUGAUGAGGUG	chr1:39906650-39906885(+)$1	235	136	150	9.5073
GCCGUUGUAGCGGC	chr2:176957737-176957960(+)$1	223	157	171	10.7270
CUGGGUCUUCCCAG	chr15:41001158-41001404(-)$1	246	120	134	10.7270
AAACUUUUACAGUU	chr14:21967587-21967814(+)$1	227	191	205	9.5073
CAUGUUUCCACAUG	chr14:21969023-21969364(-)$1	341	149	163	10.7270
UUGUUUUUUUAACA	chr14:99976950-99977172(+)$1	222	189	203	9.5073
UUCUGUCCUCGGGA	chr10:103577478-103577710(-)$1	232	170	184	10.7270
GCGCCCGCGCGGCG	chr10:103912050-103912277(+)$1	227	13	27	9.5073
GUUGCUUAUCUGUA	chr11:497893-498113(+)$1	220	154	168	9.6077
CAACUGUGCAGUUG	chr1:245021413-245021638(-)$1	225	184	198	10.7270
GCUGCUUCCGCAGC	chr3:170858103-170858323(+)$1	220	161	175	10.7270
UCCGGCAGUUCCGG	chr19:36633512-36633732(+)$1	220	90	104	9.5073
CUGCAGCCUGUGGA	chr8:146015119-146015357(-)$1	238	4	18	9.2273
UUCCUGAAGAGGAA	chr16:28074419-28074647(+)$1	228	27	41	10.7270
UCUACCUAGUGGAA	chr15:40990896-40991120(+)$1	224	190	204	9.2919
GGUAAUCUGUUAUC	chr14:21967348-21967599(-)$1	251	58	72	10.7270
GAGGUGCUGCAAUC	chr4:119621622-119621888(-)$1	266	147	161	9.6077
UCUUUAUUUGAAGA	chrX:70517127-70517370(+)$1	243	27	41	10.7270
GCUGGCCCUCCAGU	chr5:159437463-159437684(+)$1	221	156	170	10.7270
GUUAGUUCUCUGAU	chr4:119618239-119618571(-)$1	332	190	204	10.7270
UCCCUCCCACAGGG	chr4:119606601-119606855(-)$1	254	68	82	9.6077
UUUGUGACUUAACA	chr8:101724891-101725116(-)$1	225	4	18	9.6077
UGGUGGCAGUACCA	chr6:31595837-31596061(+)$1	224	129	143	10.7270
UAGUUUCUUGGCUA	chrX:23748849-23749068(-)$1	219	4	18	10.7270
UACUGGAGUCGGUA	chr2:231931676-231931899(+)$1	223	138	152	10.7270
GGCCCGCUUGGGCU	chr22:38201468-38201696(-)$1	228	97	111	10.7270
GCUGCUCAAGGAGC	chr20:36611802-36612022(-)$1	220	143	157	8.5928

#DB
(((((....)))))	chr4:144459923-144460161(+)$1	1	105	119	10.7270
(((((....)))))	chr12:101701987-101702212(+)$1	1	95	109	10.7270
(((((....)))))	chr3:63898217-63898439(+)$1	1	126	140	10.7270
(((((.....))))	chr6:36564618-36564841(+)$1	1	184	198	9.5073
(((((....)))))	chr5:865513-865755(-)$1	1	32	46	10.7270
(((((...)))))(	chr15:40998302-40998551(-)$1	1	114	128	9.2919
(((((...))))).	chr1:32800508-32800744(-)$1	1	3	17	9.2273
)(((((...)))))	chr19:50311852-50312075(+)$1	1	183	197	9.2917
(((((....)))))	chr15:41001160-41001400(+)$1	1	51	65	10.7270
(((((......)))	chr4:119613034-119613323(-)$1	1	200	214	9.6077
(((((....)))))	chr19:50534226-50534446(+)$1	1	4	18	10.7270
.(((((...)))))	chr16:632909-633134(+)$1	1	50	64	9.2561
.(((((...)))))	chr20:48808037-48808256(+)$1	1	62	76	9.2561
(((((.....))))	chr5:98129055-98129285(+)$1	1	103	117	9.5073
(((((....)))))	chr12:101693700-101693924(+)$1	1	52	66	10.7270
(((((...))))).	chr4:186064480-186064699(+)$1	1	41	55	9.2273
(((((....)))))	chr19:581398-581630(+)$1	1	2	16	10.7270
(((((......)))	chr1:1413986-1414216(+)$1	1	207	221	9.6077
(((((....)))))	chr4:71863727-71863954(+)$1	1	107	121	10.7270
(((((....)))))	chr3:121500534-121500767(-)$1	1	161	175	10.7270
(((((......)))	chr11:66206049-66206278(-)$1	1	97	111	9.6077
((((((...)))))	chr14:23240160-23240382(+)$1	1	164	178	9.2917
(((((....)))))	chr1:165667589-165667811(-)$1	1	171	185	10.7270
(((((.....))))	chr19:13879742-13879962(+)$1	1	129	143	9.5073
(((((....)))))	chr12:112842959-112843190(-)$1	1	64	78	10.7270
(((((....)))))	chr14:21969771-21970147(-)$1	1	279	293	10.7270
(((((......)))	chr14:21968545-21968916(-)$1	1	79	93	9.6077
.(((((...)))))	chr5:175665430-175665670(+)$1	1	150	164	9.2561
(((((....)))))	chr12:111856209-111856441(+)$1	1	97	111	10.7270
(((((......)))	chr3:183899736-183899960(+)$1	1	152	166	9.6077
(((((......)))	chr16:29819813-29820033(+)$1	1	71	85	9.6077
(((((.....))))	chr11:94731446-94731676(+)$1	1	120	134	9.5073
(((((.....))))	chr1:247151334-247151563(-)$1	1	84	98	9.5073
(((((.....))))	chr1:39906650-39906885(+)$1	1	136	150	9.5073
(((((....)))))	chr2:176957737-176957960(+)$1	1	157	171	10.7270
(((((....)))))	chr15:41001158-41001404(-)$1	1	120	134	10.7270
(((((.....))))	chr14:21967587-21967814(+)$1	1	191	205	9.5073
(((((....)))))	chr14:21969023-21969364(-)$1	1	149	163	10.7270
(((((.....))))	chr14:99976950-99977172(+)$1	1	189	203	9.5073
(((((....)))))	chr10:103577478-103577710(-)$1	1	170	184	10.7270
(((((.....))))	chr10:103912050-103912277(+)$1	1	13	27	9.5073
(((((......)))	chr11:497893-498113(+)$1	1	154	168	9.6077
(((((....)))))	chr1:245021413-245021638(-)$1	1	184	198	10.7270
(((((....)))))	chr3:170858103-170858323(+)$1	1	161	175	10.7270
(((((.....))))	chr19:36633512-36633732(+)$1	1	90	104	9.5073
(((((...))))).	chr8:146015119-146015357(-)$1	1	4	18	9.2273
(((((....)))))	chr16:28074419-28074647(+)$1	1	27	41	10.7270
(((((...)))))(	chr15:40990896-40991120(+)$1	1	190	204	9.2919
(((((....)))))	chr14:21967348-21967599(-)$1	1	58	72	10.7270
(((((......)))	chr4:119621622-119621888(-)$1	1	147	161	9.6077
(((((....)))))	chrX:70517127-70517370(+)$1	1	27	41	10.7270
(((((....)))))	chr5:159437463-159437684(+)$1	1	156	170	10.7270
(((((....)))))	chr4:119618239-119618571(-)$1	1	190	204	10.7270
(((((......)))	chr4:119606601-119606855(-)$1	1	68	82	9.6077
(((((......)))	chr8:101724891-101725116(-)$1	1	4	18	9.6077
(((((....)))))	chr6:31595837-31596061(+)$1	1	129	143	10.7270
(((((....)))))	chrX:23748849-23749068(-)$1	1	4	18	10.7270
(((((....)))))	chr2:231931676-231931899(+)$1	1	138	152	10.7270
(((((....)))))	chr22:38201468-38201696(-)$1	1	97	111	10.7270
(((.(....).)))	chr20:36611802-36612022(-)$1	1	143	157	8.5928

#PSSM
e : 0.91	[ : 0.05	d : 0.03	
e : 1.00	
e : 1.00	
e : 0.98	[ : 0.01	
e : 0.98	a : 0.01	
m : 0.49	n : 0.16	o : 0.16	l : 0.08	e : 0.08	
m : 0.49	n : 0.16	l : 0.16	o : 0.16	
m : 0.49	n : 0.16	l : 0.16	o : 0.16	
m : 0.49	n : 0.16	o : 0.16	e : 0.08	l : 0.08	
e : 0.65	n : 0.16	o : 0.16	a : 0.01	
e : 0.81	o : 0.16	] : 0.01	
e : 1.00	
e : 1.00	
e : 0.91	] : 0.05	d : 0.03	

#score	603.4446691690043
#seq	60
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_CDS_m2_run1.txt

#BEAR
f[ccc!!eeeeeddddmmmmdddd22eeeeeccc	chr4:85710869-85711154(-)$1	285	169	203	11.8967
e!!ffffff[ddddoooooodddd22ffffff22	chr6:43305053-43305282(-)$1	229	141	175	14.0087
cccdddd"""ddddoooooodddd22dddd]ccc	chr10:35318431-35318652(-)$1	221	113	147	15.5898
a[dddd$$$$$ddddnnnnndddd333dddd]ag	chr10:34620135-34620357(-)$1	222	136	170	17.1796
[hhhhhhhh!!ddddnnnnnddddhhhhhhhhee	chr10:105781300-105781570(+)$1	270	23	57	13.1019
dddd"""bb!!ddddnnnnndddd22bb4444dd	chr14:75265998-75266225(+)$1	227	26	60	15.0167
""ggggggg!!ddddoooooodddd22ggggggg	chr10:27431227-27431468(-)$1	241	14	48	16.1167
ccc[dddd[a[ddddoooooodddd]a]ddddcc	chr19:52693272-52693493(+)$1	221	186	220	14.2230
$$$$ccc"""ddddoooooodddd55555cccee	chr19:10791599-10791870(+)$1	271	19	53	11.4854
:iiiiiiiii[ddddnnnnndddd22iiiiiiii	chr1:172558706-172558925(+)$1	219	107	141	16.3708
e[eeeee####ddddnnnnndddd333eeeee44	chr21:45475504-45475727(+)$1	223	24	58	18.1992
ccc!!dddd!!ddddnnnnndddd]dddd22ccc	chr14:50360671-50360897(+)$1	226	39	73	14.9911
[bb[gggggggddddnnnnndddd]ggggggg33	chr14:91939487-91939739(-)$1	252	84	118	15.3721
ggggg[ccc"""cccnnnnnccccccggggggg2	chrX:53577770-53578022(-)$1	252	138	172	13.8487
c[ccc[ccc!!ddddnnnnndddd333ccc]ccc	chr5:145522939-145523177(-)$1	238	5	39	18.2668
:dddddddd!!ddddnnnnndddd22dddd]ddd	chr1:36213495-36213760(-)$1	265	0	34	15.0112
###ccc$$$$$ddddlllddddccceeeeeeeee	chr5:137750731-137750963(+)$1	232	130	164	11.7086
ddd"""bb"""cccoooooocccbb333dddd]f	chr22:41739452-41739673(+)$1	221	42	76	12.4133
d!!a[dddd[a[ddddllldddd]a22dddda22	chr18:18571064-18571289(-)$1	225	117	151	12.2175
!!eeeee[a!!ddddoooooodddd22a]eeeee	chr16:28856011-28856223(-)$1	212	160	194	15.7686
zddddcccccceeeeellleeeee333ccc]ccc	chr2:73677815-73678034(+)$1	219	133	167	11.0220
[bb[dddd!!eeeeennnnneeeee22dddd]bb	chr11:250739-250961(+)$1	222	83	117	12.6056
=========[ddddoooooodddd]=========	chr1:145497321-145497542(+)$1	221	49	83	15.4355
:ccceeeee"""cccooooooccc333eeeee]c	chr13:37453378-37453591(-)$1	213	90	124	13.7298
:dddd!!cccddddoooooodddd22cccdddd:	chr17:4851527-4851773(-)$1	246	72	106	12.6438
c[a[bbiiiiiiiiinnnnniiiiiiiii4444b	chr2:15760239-15760454(+)$1	215	105	139	11.2971
eeeee"""dddd[ddddllldddd22dddd]eee	chr9:6013672-6013896(-)$1	224	186	220	11.9202
iiiiiii[bb"""bbnnnnnbb333bb]iiiiii	chr20:57242984-57243201(+)$1	217	72	106	11.2369
e[ffffff"""ddddnnnnndddd333ffffff]	chr3:133368570-133368790(-)$1	220	12	46	17.0782
hhhhhhhh"""ddddnnnnndddd]hhhhhhhh2	chr15:35275259-35275478(-)$1	219	53	87	13.9466
ccc####ccc[ddddoooooodddd]cccccc]f	chr7:127224388-127224606(-)$1	218	158	192	14.2122
=========="""ddddllldddd22========	chr16:66761576-66761794(-)$1	218	108	142	14.1093
b[ggggggg[ddddoooooodddd]gggggggbb	chr17:40010513-40010943(-)$1	430	154	188	14.1986
cc[dddd!!a[ddddnnnnndddd]a22dddd]c	chr20:57015972-57016194(+)$1	222	30	64	16.0825
###cccxxxxxxxxxxxxxxxccc333ccc]a]a	chr1:212273945-212274170(+)$1	225	74	108	11.7002
"""ffffff!!ddddnnnnndddd22ffffff33	chr5:16764271-16764492(-)$1	221	76	110	16.5634
fffeeeee####cccnnnnnccc4444eeeee33	chr6:43307753-43307965(-)$1	212	43	77	14.6317
:ggggggg"""ddddoooooodddd]gggggggf	chr7:72883749-72883985(-)$1	236	87	121	14.9746
iiii[bb$$$$$cccooooooccc333bb]iiii	chr17:45757313-45757585(+)$1	272	223	257	13.2188
f!!eeeeeccc[cccooooooccc]ccc]eeeee	chr3:135870744-135870982(-)$1	238	58	92	11.8777
###dddd[a[eeeeennnnneeeee]adddd444	chr6:26204935-26205203(+)$1	268	135	169	13.3664
ggggg####eeeeeooooooeeeee4444ggggg	chr19:37004775-37005054(-)$1	279	90	124	12.5808
Ceeeee####a[cccnnnnnccc]a333eeeeee	chr13:41932889-41933103(+)$1	214	106	140	13.5983
ff[ccc$$$$$ddddnnnnndddd55555ccc]f	chr1:120483189-120483413(-)$1	224	54	88	12.8201
ffffeeeee!!ddddnnnnndddd]eeeee]fff	chr22:42042924-42043183(+)$1	259	212	246	14.9875
[ggggggg!!eeeeennnnneeeee]ggggggg]	chr19:32844966-32845219(+)$1	253	69	103	13.9758
b[eeeee[cccddddnnnnndddd22ccc]eeee	chr15:90170183-90170417(+)$1	234	188	222	16.0723
b!!ffffff!!ddddooooooddddffffff22b	chr7:129680773-129680986(-)$1	213	44	78	12.8758
""cccxxxxxxxxxxxxxxxccc4444ggggggg	chrM:6328-6557(+)$1	229	155	189	10.8221

#otherMatches

#Seq PSSM
UCAUUGAGGGACAGUGGCAUCAUUUGGUCCUGGU	chr4:85710869-85711154(-)$1	285	169	203	11.8967
AAAUGUAGUUCCCUGGAGUUGGGGCCAUUACAGC	chr6:43305053-43305282(-)$1	229	141	175	14.0087
GCUACAUCGGAUGUAUACAGAUAUGAGUGUCAGC	chr10:35318431-35318652(-)$1	221	113	147	15.5898
CGUUGGAGAGUCUGCAGACCGCAGUUGCCGAGGU	chr10:34620135-34620357(-)$1	222	136	170	17.1796
UGAAAAAUUGCUUAGUUGAUCUGAAAUUUUUUUA	chr10:105781300-105781570(+)$1	270	23	57	13.1019
CUUUGGAUAGAUAUCGGGAUGAUAGAUGGAGAGA	chr14:75265998-75266225(+)$1	227	26	60	15.0167
UUGGAAAUUAGAAAAUUUACUUUUUGCAAUUUCC	chr10:27431227-27431468(-)$1	241	14	48	16.1167
GCGGAGGGGUACCUGGGGGCACGGGCGGCCCUCG	chr19:52693272-52693493(+)$1	221	186	220	14.2230
AGAAGGCAGUAGUGAGCACACACUCCAUGGCCGG	chr19:10791599-10791870(+)$1	271	19	53	11.4854
AUUCUUCUUCAUUACCUGAAGUAAAAGAAGAAGA	chr1:172558706-172558925(+)$1	219	107	141	16.3708
GUGCUGUGCAUGGAGGGUCUUUCCCAGAUAGUCU	chr21:45475504-45475727(+)$1	223	24	58	18.1992
UCGUAGUGGACUGCGCCGACCGCGACCGCAUCGA	chr14:50360671-50360897(+)$1	226	39	73	14.9911
UGGAGGAGCAGUCCAGCUUAUGGGCCUGCUUCGA	chr14:91939487-91939739(-)$1	252	84	118	15.3721
CUCUGCUAUUCUCCGAAGCCCGGGUACAGAGGGA	chrX:53577770-53578022(-)$1	252	138	172	13.8487
GUGGAUUCUAUAGAUGAAAUGUCUCUCAGGUUCC	chr5:145522939-145523177(-)$1	238	5	39	18.2668
UAGCUUAAAUAUUGCAAAUAGCAACUUUUGUGGU	chr1:36213495-36213760(-)$1	265	0	34	15.0112
AAGUGUGCAAAGGGACAGUCCCACGAACCAGAGA	chr5:137750731-137750963(+)$1	232	130	164	11.7086
CCGGAGCUCGGAGGACCAGACCUGGAAGCGGAUC	chr22:41739452-41739673(+)$1	221	42	76	12.4133
AAUCUAUUGAAGAGGCAAAGUCUGUGGCAAUGUG	chr18:18571064-18571289(-)$1	225	117	151	12.2175
GAGGAGACCCCAGUCAUCGUAGGCUCUGCUCUCU	chr16:28856011-28856223(-)$1	212	160	194	15.7686
CAGAGAAGCCUGGUAGUUUCUACCAACAGGUCUU	chr2:73677815-73678034(+)$1	219	133	167	11.0220
AGCCCAGCUUCUGAGGAAAAUUCAGUUGUUGUGC	chr11:250739-250961(+)$1	222	83	117	12.6056
UUUUCUGUUCCUCUACUACCAGGGCAACAGGGAG	chr1:145497321-145497542(+)$1	221	49	83	15.4355
CGCUGGAGUGCUGUGAGUUCCCAUUUGGCUCCAA	chr13:37453378-37453591(-)$1	213	90	124	13.7298
AGUAGCAGCGCCAUGGCCGGGUGGAACGCCUACA	chr17:4851527-4851773(-)$1	246	72	106	12.6438
CUGCCACUUUGCAUUCUUUCGAUGUAAAGAAACU	chr2:15760239-15760454(+)$1	215	105	139	11.2971
UGGUUAUCGAGCCUCUUAUUAAGACUGCUUCAGC	chr9:6013672-6013896(-)$1	224	186	220	11.9202
UGGCCGGAUUAAGCAGAAGAUGAAAGAAUUGGCC	chr20:57242984-57243201(+)$1	217	72	106	11.2369
UGCGGUUUUAGUGGCAGAAAGCUAGAUAAACUGA	chr3:133368570-133368790(-)$1	220	12	46	17.0782
GAGAGGCAUCAACUAACUCAUAGUCUGCCUUUUA	chr15:35275259-35275478(-)$1	219	53	87	13.9466
CUUGGAGCUUAGGUUAGAAGAGACCCGAGAAGCC	chr7:127224388-127224606(-)$1	218	158	192	14.2122
CUGGCUCUCCAAGGACCCAGGGUCGGGGAGGGCC	chr16:66761576-66761794(-)$1	218	108	142	14.1093
CAUUCUUUUGGACUAACAGAAGUCAAAGGGAAGC	chr17:40010513-40010943(-)$1	430	154	188	14.1986
CAAAGACAGAAACACCAAUAGUGUCUAAGUCUCU	chr20:57015972-57016194(+)$1	222	30	64	16.0825
UGAAACAAAAGUGUGUGAAGAGUUGUAACUGUGU	chr1:212273945-212274170(+)$1	225	74	108	11.7002
CAAUGAGGACUUCAAGUCUAUUGGCAUCCUCGAC	chr5:16764271-16764492(-)$1	221	76	110	16.5634
UCUUUUGGGAAAUUCAGCUGGAAGAAGCCAGAAA	chr6:43307753-43307965(-)$1	212	43	77	14.6317
CAUCACUGCAAAGACCACACAGUCUCUGGUGAUG	chr7:72883749-72883985(-)$1	236	87	121	14.9746
UUCUCACAGAAAAUGAGAAAACAUGGAGUAAGGA	chr17:45757313-45757585(+)$1	272	223	257	13.2188
UUACUGAGUGUUGAGGAAGUACUCCGCAGCUUAG	chr3:135870744-135870982(-)$1	238	58	92	11.8777
AUUCGUGAUGCUGUGACUUACACGGAGCACGCCA	chr6:26204935-26205203(+)$1	268	135	169	13.3664
UGUGGGAAAGCUUUCAGCCAAAAGUCACAUCACA	chr19:37004775-37005054(-)$1	279	90	124	12.5808
UUUGGACACAGCUGAUAGAUUCAUCAAUUCCAAA	chr13:41932889-41933103(+)$1	214	106	140	13.5983
CAUGUGUUGAUGGGAUUAACUCCUUCUCUUGCUU	chr1:120483189-120483413(-)$1	224	54	88	12.8201
gugucgcccaggcuggagugcaguggggcgaaca	chr22:42042924-42043183(+)$1	259	212	246	14.9875
GGGCGCGAAGGAAUGGAUGAUGUUUAUCGUGCUG	chr19:32844966-32845219(+)$1	253	69	103	13.9758
AUAAAGAAGUUGGAUGCCUGGUCCCAAGCCUCUU	chr15:90170183-90170417(+)$1	234	188	222	16.0723
CUCUUUGAAAUGGGCAGGUAAGCCCUUUGAGCUG	chr7:129680773-129680986(-)$1	213	44	78	12.8758
CUACUUCUCCUAUCUCUCCCAGUCCUAGCUGCUG	chrM:6328-6557(+)$1	229	155	189	10.8221

#DB
(.(((..(((((((((....))))..))))))))	chr4:85710869-85711154(-)$1	1	169	203	11.8967
(..((((((.((((......))))..))))))..	chr6:43305053-43305282(-)$1	1	141	175	14.0087
(((((((...((((......))))..)))).)))	chr10:35318431-35318652(-)$1	1	113	147	15.5898
(.((((.....((((.....))))...)))).))	chr10:34620135-34620357(-)$1	1	136	170	17.1796
.((((((((..((((.....))))))))))))))	chr10:105781300-105781570(+)$1	1	23	57	13.1019
((((...((..((((.....))))..))....))	chr14:75265998-75266225(+)$1	1	26	60	15.0167
..(((((((..((((......))))..)))))))	chr10:27431227-27431468(-)$1	1	14	48	16.1167
(((.((((.(.((((......)))).).))))))	chr19:52693272-52693493(+)$1	1	186	220	14.2230
....(((...((((......)))).....)))))	chr19:10791599-10791870(+)$1	1	19	53	11.4854
.(((((((((.((((.....))))..))))))))	chr1:172558706-172558925(+)$1	1	107	141	16.3708
(.(((((....((((.....))))...)))))..	chr21:45475504-45475727(+)$1	1	24	58	18.1992
(((..((((..((((.....)))).))))..)))	chr14:50360671-50360897(+)$1	1	39	73	14.9911
.((.(((((((((((.....)))).)))))))..	chr14:91939487-91939739(-)$1	1	84	118	15.3721
(((((.(((...(((.....))))))))))))).	chrX:53577770-53578022(-)$1	1	138	172	13.8487
(.(((.(((..((((.....))))...))).)))	chr5:145522939-145523177(-)$1	1	5	39	18.2668
.((((((((..((((.....))))..)))).)))	chr1:36213495-36213760(-)$1	1	0	34	15.0112
...(((.....((((...))))))))))))))))	chr5:137750731-137750963(+)$1	1	130	164	11.7086
(((...((...(((......)))))...)))).)	chr22:41739452-41739673(+)$1	1	42	76	12.4133
(..(.((((.(.((((...)))).)..)))))..	chr18:18571064-18571289(-)$1	1	117	151	12.2175
..(((((.(..((((......))))..).)))))	chr16:28856011-28856223(-)$1	1	160	194	15.7686
.))))(((((((((((...)))))...))).)))	chr2:73677815-73678034(+)$1	1	133	167	11.0220
.((.((((..(((((.....)))))..)))).))	chr11:250739-250961(+)$1	1	83	117	12.6056
(((((((((.((((......)))).)))))))))	chr1:145497321-145497542(+)$1	1	49	83	15.4355
.((((((((...(((......)))...))))).)	chr13:37453378-37453591(-)$1	1	90	124	13.7298
.((((..(((((((......))))..))))))).	chr17:4851527-4851773(-)$1	1	72	106	12.6438
(.(.(((((((((((.....)))))))))....)	chr2:15760239-15760454(+)$1	1	105	139	11.2971
(((((...((((.((((...))))..)))).)))	chr9:6013672-6013896(-)$1	1	186	220	11.9202
(((((((.((...((.....))...)).))))))	chr20:57242984-57243201(+)$1	1	72	106	11.2369
(.((((((...((((.....))))...)))))).	chr3:133368570-133368790(-)$1	1	12	46	17.0782
((((((((...((((.....)))).)))))))).	chr15:35275259-35275478(-)$1	1	53	87	13.9466
(((....(((.((((......)))).)))))).)	chr7:127224388-127224606(-)$1	1	158	192	14.2122
((((((((((...((((...))))..))))))))	chr16:66761576-66761794(-)$1	1	108	142	14.1093
(.(((((((.((((......)))).)))))))))	chr17:40010513-40010943(-)$1	1	154	188	14.1986
((.((((..(.((((.....)))).)..)))).)	chr20:57015972-57016194(+)$1	1	30	64	16.0825
...(((...............)))...))).).)	chr1:212273945-212274170(+)$1	1	74	108	11.7002
...((((((..((((.....))))..))))))..	chr5:16764271-16764492(-)$1	1	76	110	16.5634
((((((((....(((.....)))....)))))..	chr6:43307753-43307965(-)$1	1	43	77	14.6317
.(((((((...((((......)))).)))))))(	chr7:72883749-72883985(-)$1	1	87	121	14.9746
((((.((.....(((......)))...)).))))	chr17:45757313-45757585(+)$1	1	223	257	13.2188
(..((((((((.(((......))).))).)))))	chr3:135870744-135870982(-)$1	1	58	92	11.8777
...((((.(.(((((.....))))).)))))...	chr6:26204935-26205203(+)$1	1	135	169	13.3664
(((((....(((((......)))))....)))))	chr19:37004775-37005054(-)$1	1	90	124	12.5808
((((((....(.(((.....))).)...)))))(	chr13:41932889-41933103(+)$1	1	106	140	13.5983
((.(((.....((((.....)))).....))).)	chr1:120483189-120483413(-)$1	1	54	88	12.8201
(((((((((..((((.....)))).))))).)))	chr22:42042924-42043183(+)$1	1	212	246	14.9875
.(((((((..(((((.....))))).))))))).	chr19:32844966-32845219(+)$1	1	69	103	13.9758
(.(((((.(((((((.....))))..))).))))	chr15:90170183-90170417(+)$1	1	188	222	16.0723
(..((((((..((((......))))))))))..)	chr7:129680773-129680986(-)$1	1	44	78	12.8758
..(((...............)))....)))))))	chrM:6328-6557(+)$1	1	155	189	10.8221

#PSSM
c : 0.14	f : 0.10	: : 0.10	e : 0.08	[ : 0.08	d : 0.06	" : 0.06	# : 0.06	b : 0.06	g : 0.04	= : 0.04	i : 0.04	a : 0.02	$ : 0.02	! : 0.02	z : 0.02	h : 0.02	C : 0.02	
[ : 0.16	c : 0.12	! : 0.10	d : 0.10	g : 0.08	" : 0.06	i : 0.06	# : 0.06	f : 0.06	h : 0.04	b : 0.04	= : 0.04	e : 0.04	$ : 0.02	
c : 0.16	d : 0.12	g : 0.12	e : 0.10	! : 0.08	i : 0.06	# : 0.06	f : 0.06	h : 0.04	b : 0.04	= : 0.04	[ : 0.04	$ : 0.02	a : 0.02	" : 0.02	
d : 0.16	c : 0.14	e : 0.14	g : 0.12	f : 0.10	[ : 0.08	i : 0.06	h : 0.04	= : 0.04	$ : 0.02	! : 0.02	" : 0.02	a : 0.02	# : 0.02	
d : 0.18	e : 0.18	c : 0.14	g : 0.14	f : 0.08	h : 0.04	" : 0.04	i : 0.04	[ : 0.04	= : 0.04	! : 0.02	b : 0.02	# : 0.02	
d : 0.18	e : 0.16	g : 0.10	c : 0.10	f : 0.08	" : 0.06	! : 0.04	h : 0.04	i : 0.04	[ : 0.04	= : 0.04	b : 0.04	# : 0.04	x : 0.02	
d : 0.16	e : 0.14	g : 0.10	f : 0.08	c : 0.08	$ : 0.06	i : 0.06	# : 0.06	! : 0.04	h : 0.04	" : 0.04	b : 0.04	= : 0.04	x : 0.04	
e : 0.10	g : 0.10	d : 0.10	c : 0.10	f : 0.08	$ : 0.08	[ : 0.08	" : 0.06	# : 0.06	h : 0.04	b : 0.04	i : 0.04	= : 0.04	x : 0.04	! : 0.02	
c : 0.14	" : 0.12	$ : 0.08	# : 0.08	d : 0.08	e : 0.06	f : 0.06	g : 0.06	! : 0.06	b : 0.04	i : 0.04	a : 0.04	= : 0.04	x : 0.04	h : 0.02	[ : 0.02	
! : 0.24	" : 0.16	[ : 0.10	c : 0.10	$ : 0.08	# : 0.06	e : 0.04	a : 0.04	i : 0.04	x : 0.04	g : 0.02	d : 0.02	b : 0.02	= : 0.02	
! : 0.20	" : 0.16	d : 0.14	e : 0.10	$ : 0.08	[ : 0.08	c : 0.06	# : 0.04	a : 0.04	x : 0.04	g : 0.02	i : 0.02	
d : 0.61	e : 0.12	" : 0.08	[ : 0.06	x : 0.04	c : 0.02	i : 0.02	# : 0.02	$ : 0.02	
d : 0.63	c : 0.14	e : 0.10	" : 0.04	x : 0.04	i : 0.02	[ : 0.02	
d : 0.67	c : 0.14	e : 0.10	x : 0.04	i : 0.02	b : 0.02	
d : 0.55	o : 0.16	c : 0.12	e : 0.08	x : 0.04	i : 0.02	b : 0.02	
n : 0.48	o : 0.34	d : 0.08	x : 0.04	l : 0.02	e : 0.02	
n : 0.48	o : 0.34	l : 0.06	d : 0.04	x : 0.04	m : 0.02	
n : 0.48	o : 0.34	l : 0.10	x : 0.04	m : 0.02	
n : 0.48	o : 0.34	l : 0.08	x : 0.04	m : 0.02	d : 0.02	
n : 0.48	o : 0.34	d : 0.04	l : 0.04	x : 0.04	m : 0.02	e : 0.02	
d : 0.55	o : 0.18	c : 0.10	e : 0.10	i : 0.02	b : 0.02	x : 0.02	
d : 0.67	c : 0.18	e : 0.10	i : 0.02	b : 0.02	
d : 0.65	c : 0.20	e : 0.10	i : 0.02	3 : 0.02	
d : 0.63	c : 0.12	e : 0.10	] : 0.04	4 : 0.04	b : 0.02	i : 0.02	3 : 0.02	
2 : 0.22	3 : 0.18	] : 0.16	d : 0.12	e : 0.08	5 : 0.04	c : 0.04	a : 0.04	4 : 0.04	h : 0.02	b : 0.02	i : 0.02	
2 : 0.30	3 : 0.20	] : 0.10	4 : 0.06	h : 0.04	5 : 0.04	g : 0.04	c : 0.04	e : 0.04	d : 0.02	= : 0.02	i : 0.02	b : 0.02	a : 0.02	f : 0.02	
3 : 0.20	2 : 0.10	g : 0.10	d : 0.08	c : 0.08	e : 0.06	f : 0.06	4 : 0.06	h : 0.04	b : 0.04	a : 0.04	5 : 0.04	i : 0.04	= : 0.04	
d : 0.16	g : 0.14	c : 0.14	e : 0.12	f : 0.08	h : 0.04	b : 0.04	] : 0.04	5 : 0.04	i : 0.04	3 : 0.04	= : 0.04	a : 0.02	2 : 0.02	4 : 0.02	
d : 0.22	e : 0.14	g : 0.14	c : 0.12	f : 0.08	i : 0.06	h : 0.04	4 : 0.04	5 : 0.04	] : 0.04	= : 0.04	b : 0.02	
d : 0.22	e : 0.18	g : 0.16	c : 0.12	f : 0.08	h : 0.04	4 : 0.04	i : 0.04	= : 0.04	] : 0.04	2 : 0.02	
e : 0.18	d : 0.16	g : 0.16	] : 0.14	f : 0.08	c : 0.06	i : 0.06	h : 0.04	4 : 0.04	= : 0.04	2 : 0.02	
e : 0.18	c : 0.16	g : 0.16	d : 0.10	f : 0.08	4 : 0.06	i : 0.06	] : 0.04	h : 0.04	a : 0.04	= : 0.04	2 : 0.02	
e : 0.16	c : 0.12	g : 0.12	] : 0.12	2 : 0.06	d : 0.06	i : 0.06	4 : 0.06	3 : 0.06	b : 0.04	= : 0.04	f : 0.04	a : 0.02	h : 0.02	
c : 0.16	e : 0.16	f : 0.10	2 : 0.08	g : 0.08	b : 0.08	i : 0.06	3 : 0.06	d : 0.04	4 : 0.04	= : 0.04	] : 0.04	: : 0.02	a : 0.02	

#score	686.3728024135553
#seq	49
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_UTR_m3_run2.txt

#BEAR
b[eeeee"""aooooooa333eeeeebb	chr17:1421768-1422188(-)$1	420	388	416	12.5171
ggggggg[bb[aooooooa333bb]ggg	chr5:112353877-112354278(+)$1	401	245	273	13.2452
ggggggga[cccnnnnnccc]a]ggggg	chrX:147031984-147032264(+)$1	280	79	107	10.4849
:eeeee"""bboooooobb333eeeee:	chr7:138521867-138522204(-)$1	337	38	66	11.5828
'bb[gggggggoooooogggggggbb22	chr12:4461753-4462216(+)$1	463	113	141	11.9809
ccc[a!!ddddoooooodddd]a]ccc]	chr8:141541636-141542021(-)$1	385	250	278	13.4849
:ggggggg[bboooooobb22ggggggg	chr5:126171845-126172329(+)$1	484	14	42	13.5582
gggggg[ddddoooooodddd]gggggg	chr8:117858380-117858653(-)$1	273	78	106	14.0461
""ccc!!ddddoooooodddd22ccc44	chr6:13621906-13622223(-)$1	317	245	273	13.2681
ddd[cccddddoooooodddd]cccddd	chr7:4808635-4808968(+)$1	333	145	173	11.9688
##ccc"""cccooooooccc22ccc===	chr3:185347469-185347923(+)$1	454	159	187	14.5630
ee####eeeeeooooooeeeee22eeee	chr1:179324009-179324423(+)$1	414	327	355	11.3485
====="""ddddmmmmdddd333=====	chr6:72012689-72012959(+)$1	270	172	200	11.0363
cciiiiiiiiiooooooiiiiiiiii]c	chr1:9642613-9642882(+)$1	269	185	213	15.0553
cc"""ffffffooooooffffff333cc	chr17:5287454-5287827(+)$1	373	87	115	11.3190
b[ggggggg[ccclllccc333gggggg	chr5:130536975-130537248(+)$1	273	218	246	11.2521
"""dddd[cccooooooccc22dddd44	chr11:92626096-92626399(+)$1	303	185	213	12.6657
eeiiiiiiiiiooooooiiiiiiiii::	chr20:48569804-48570126(+)$1	322	192	220	12.8263
iiiiiii[cccooooooccciiiiiiii	chr3:30734279-30734599(+)$1	320	274	302	15.3329
[bb[dddd[bboooooobb22ddddbb]	chr2:242385556-242385870(+)$1	314	101	129	11.6174
!a[dddd!!bboooooobb22dddd]a3	chr3:42253123-42253437(+)$1	314	241	269	12.4304
hh!!ccc[abboooooobb]a]ccc22h	chr17:41846449-41846836(-)$1	387	150	178	12.8421
[bb[bb!!cccooooooccc22bb]bb]	chr16:30676529-30676822(+)$1	293	146	174	12.6095
[ggggggg!!ccclllccc22ggggggg	chr2:202902312-202902573(+)$1	261	141	169	10.9468
!ffffff"""aooooooa333ffffff]	chr11:64895167-64895426(-)$1	259	171	199	12.9126
cc[==========mmmm==========c	chr20:2125629-2126071(+)$1	442	226	254	12.0070
b[ccc[eeeeeooooooeeeee]ccc]b	chr14:105236285-105236591(-)$1	306	268	296	12.0464
ffffff[bbbboooooobb]bb]fffff	chr16:31123341-31123713(+)$1	372	47	75	10.6062
$$ggggggg[ccclllccc333gggggg	chr22:19429494-19429752(-)$1	258	205	233	11.0324
iiiiiii####bbmmmmbb333iiiiii	chr1:2334888-2335249(+)$1	361	242	270	10.9677
iii[eeeeebboooooobb4444eeeee	chr3:52003208-52003446(-)$1	238	24	52	13.1373
[a[a[dddd[aooooooa]dddd]aa]e	chr7:129472344-129472686(-)$1	342	163	191	12.3412
eeee!!eeeeeooooooeeeee333eee	chr18:29128547-29128831(+)$1	284	142	170	11.8263
#ccc[a[ddddoooooodddd]accc44	chr8:42027490-42027786(+)$1	296	56	84	13.0974
=============mmmm===========	chr1:64125556-64126010(+)$1	454	404	432	12.4027
hhhhhhhhcccooooooccc333hhhhh	chr11:47491599-47491857(-)$1	258	32	60	12.7868
hhhh"""ddddoooooodddd22hhhhh	chr7:64169163-64169420(+)$1	257	222	250	12.2532
ggggg[eeeeeooooooeeeee]ggggg	chr16:9211930-9212272(+)$1	342	234	262	13.1373
dd$$$$$ddddoooooodddd22dddd]	chrX:133904468-133904730(-)$1	262	46	74	11.2774
=========[aooooooa]=========	chr16:57462226-57462497(-)$1	271	50	78	15.8634
##iiiiiiiiiooooooiiiiiiiii]d	chr7:115898334-115898653(+)$1	319	102	130	15.0943
[==========mmmm==========bb]	chr17:54942586-54942913(+)$1	327	275	303	11.4008
:============lll============	chr2:169629523-169629777(+)$1	254	199	227	12.1869
ii!!ccc[cccooooooccc]ccc22ii	chr12:44193102-44193342(-)$1	240	203	231	13.6815
[===========mmmm===========]	chr10:126310289-126310665(-)$1	376	329	357	12.4943
hhhhhhhh[bboooooobb]hhhhhhhh	chr1:78411993-78412381(-)$1	388	52	80	11.1363
ddd[gggggggooooooggggggg]ddd	chr2:75882766-75883098(+)$1	332	46	74	12.8189
FF===========mmmm===========	chr10:857203-857447(-)$1	244	25	53	11.2008
gggggg[ddddoooooodddd]gggggg	chrX:31139319-31139591(-)$1	272	177	205	14.0461
""===========mmmm===========	chr11:113146048-113146401(+)$1	353	242	270	12.3988
ee$$$$$ddddoooooodddd333eeee	chr11:85669869-85670197(-)$1	328	268	296	11.8857
bb[==========lll==========]b	chr1:200828494-200828780(+)$1	286	224	252	12.0569
d==========oooooo==========h	chr17:48940013-48940346(-)$1	333	256	284	15.7484
:eeeee!!cccooooooccc]eeeeedd	chr20:18469785-18470087(-)$1	302	76	104	11.6784
:ggggggg!!aooooooa22ggggggg:	chr20:48568765-48569168(+)$1	403	140	168	12.4365
adddd!!ddddoooooodddd22dddd]	chrX:105921812-105922130(+)$1	318	200	228	12.0904
gggggg"""bboooooobb333gggggg	chr3:52289200-52289645(-)$1	445	313	341	15.3428
iiiiiii!!bboooooobb4444iiiii	chr2:192288793-192289175(+)$1	382	126	154	15.4778

#otherMatches

#Seq PSSM
GAGGAUGUCCCUGGUCUGUUCCAUCCCC	chr17:1421768-1422188(-)$1	420	388	416	12.5171
UGAAGGCACAACGUAAAAGGAAUGAGCU	chr5:112353877-112354278(+)$1	401	245	273	13.2452
AACAGAUUGGAUUUUAUGUUGACAUUUG	chrX:147031984-147032264(+)$1	280	79	107	10.4849
AUAGUAACAUUAACAACAAGAAUACUAA	chr7:138521867-138522204(-)$1	337	38	66	11.5828
UGCAUCAAAAUCUAACCAUUUUGAGCCU	chr12:4461753-4462216(+)$1	463	113	141	11.9809
AUUGAUGGGCUCAAACUAGCUGUGAAUC	chr8:141541636-141542021(-)$1	385	250	278	13.4849
GAAUACUGUGAUCUAUUUCUUUAGUAUU	chr5:126171845-126172329(+)$1	484	14	42	13.5582
AAAGUUCUAGCUUAAGUGUUGAAACUUU	chr8:117858380-117858653(-)$1	273	78	106	14.0461
UUGUUUCCUGUUUAACUACAGAUGACUU	chr6:13621906-13622223(-)$1	317	245	273	13.2681
UCUGUCCAGGGAGAAACCCCUCGGAAGA	chr7:4808635-4808968(+)$1	333	145	173	11.9688
GUGAGAAAACUUUGCCUGGUCCCUCUAG	chr3:185347469-185347923(+)$1	454	159	187	14.5630
UGCACAACAGUAUUGUAAUUGUAAUGGA	chr1:179324009-179324423(+)$1	414	327	355	11.3485
uauaacaacuauugacauagcauuuaua	chr6:72012689-72012959(+)$1	270	172	200	11.0363
CUAAAUUAAAUCAUGCUAUUUAAUUUAA	chr1:9642613-9642882(+)$1	269	185	213	15.0553
GAAAGCCAGUUAGUUAGAAUUGGAAAUC	chr17:5287454-5287827(+)$1	373	87	115	11.3190
gaggucaggaguucuagaccagccugac	chr5:130536975-130537248(+)$1	273	218	246	11.2521
AUCCACUUCUUUUUUAUGAGUCAGUGUU	chr11:92626096-92626399(+)$1	303	185	213	12.6657
GCUGCAAGUGCUACCUCGCGCUUGUACA	chr20:48569804-48570126(+)$1	322	192	220	12.8263
UUUUGACUACCUUAUCUGGUGUUAAGAU	chr3:30734279-30734599(+)$1	320	274	302	15.3329
UUCUCUAAAUAUGGAAUUAGAUUAGGAU	chr2:242385556-242385870(+)$1	314	101	129	11.6174
UAGUUGAAACUGUAGAAAGGGUCAGGUU	chr3:42253123-42253437(+)$1	314	241	269	12.4304
CCCGAUGGCCCACGGCAGGAGGUGUGUG	chr17:41846449-41846836(-)$1	387	150	178	12.8421
CGCCGGCCGUCUCCUUUGGCUCCCUGCA	chr16:30676529-30676822(+)$1	293	146	174	12.6095
UCCAUAUGCUGACCCUGUCUCUGUGUGG	chr2:202902312-202902573(+)$1	261	141	169	10.9468
AGGCGGGCAGCACUGAGGGACCCUGCCC	chr11:64895167-64895426(-)$1	259	171	199	12.9126
GAAGGGGCAAUGCUCUUGUGUUGUCCCU	chr20:2125629-2126071(+)$1	442	226	254	12.0070
GUCAGCCAGCCGCCCUGGGCUGUCUGUC	chr14:105236285-105236591(-)$1	306	268	296	12.0464
CAGGAGACUCAAGCCUCUGAAGCCUCCU	chr16:31123341-31123713(+)$1	372	47	75	10.6062
gagcccaggaguucgagaccagccuggg	chr22:19429494-19429752(-)$1	258	205	233	11.0324
UUCUUAACUACCAUGAUUGCUUUUGAGG	chr1:2334888-2335249(+)$1	361	242	270	10.9677
GGGUGGGCUGCCUGCCUGCUCUGAGCUC	chr3:52003208-52003446(-)$1	238	24	52	13.1373
UGUGAGCAGUGCCAUGACUCUGCCCCUU	chr7:129472344-129472686(-)$1	342	163	191	12.3412
UUUCUAAAUGAUUUUCUUUGUUCCUGAA	chr18:29128547-29128831(+)$1	284	142	170	11.8263
CUGGAGUAGAGGGCCGACUCUUCCCAUG	chr8:42027490-42027786(+)$1	296	56	84	13.0974
UUUAGAAAGAAAAACAAUUUUUUUUUUA	chr1:64125556-64126010(+)$1	454	404	432	12.4027
GGUUGGGGAGGCGCUGUUCUGAAUCCCA	chr11:47491599-47491857(-)$1	258	32	60	12.7868
UCUACACAUAAGAUAAUUUAUACUGGAG	chr7:64169163-64169420(+)$1	257	222	250	12.2532
AGACCAUUGCAAAUCAGUGUAAGGGUUU	chr16:9211930-9212272(+)$1	342	234	262	13.1373
UUAAUAUGCAGAUUUGCCUGCUGGAAUC	chrX:133904468-133904730(-)$1	262	46	74	11.2774
GCAUGUCUUGUAAAGAGAGGGGAUGUGC	chr16:57462226-57462497(-)$1	271	50	78	15.8634
uacaggugugggagccaccaugccugac	chr7:115898334-115898653(+)$1	319	102	130	15.0943
UGACUUGUGUUUUAAAAUACAAGUUGUC	chr17:54942586-54942913(+)$1	327	275	303	11.4008
CAAAGUUGCCUGAACAUUGGGCGGUUUU	chr2:169629523-169629777(+)$1	254	199	227	12.1869
UUAAUAGAUGUGGGAGGAUAACUAGAGA	chr12:44193102-44193342(-)$1	240	203	231	13.6815
UUUUGCUCGUCUUCAUGGACGAGUGAAC	chr10:126310289-126310665(-)$1	376	329	357	12.4943
GAUUUUGAUUCAUUUAAGGUUUAAAAUC	chr1:78411993-78412381(-)$1	388	52	80	11.1363
uuuauuaauauguaggaauguuaagaaa	chr2:75882766-75883098(+)$1	332	46	74	12.8189
AGUACAAGAGCUAGUAGUAGUUUUUGUA	chr10:857203-857447(-)$1	244	25	53	11.2008
UGCUCAUUUGAGAACUGUCAGCUGAGUG	chrX:31139319-31139591(-)$1	272	177	205	14.0461
UCUCCUUUUUGUAGGUUUAUAGAAAGGG	chr11:113146048-113146401(+)$1	353	242	270	12.3988
GGGACUAGUUUAUAGGAGAACGUAUCAA	chr11:85669869-85670197(-)$1	328	268	296	11.8857
UGUAAAAAAAUUUCACAGAUUUUUUUCC	chr1:200828494-200828780(+)$1	286	224	252	12.0569
GGCUGAUUUUUUUUUAUAAAAAUUGGCA	chr17:48940013-48940346(-)$1	333	256	284	15.7484
AAACAUGACUGAAAGUCCAGAGUGUUAG	chr20:18469785-18470087(-)$1	302	76	104	11.6784
CGGUCGAGUUCGUAUUGGUUCUCGGCUA	chr20:48568765-48569168(+)$1	403	140	168	12.4365
CCUUAGCUUGCUCAGCUGCAAAAUAAGC	chrX:105921812-105922130(+)$1	318	200	228	12.0904
CAGGAAAAUGAUUGUAUUUGAGUUCCUG	chr3:52289200-52289645(-)$1	445	313	341	15.3428
UGAUGUGUUCUUCCUUUAGUCAUCAUGU	chr2:192288793-192289175(+)$1	382	126	154	15.4778

#DB
(.(((((...(......)...)))))))	chr17:1421768-1422188(-)$1	1	388	416	12.5171
(((((((.((.(......)...)).)))	chr5:112353877-112354278(+)$1	1	245	273	13.2452
((((((((.(((.....))).).)))))	chrX:147031984-147032264(+)$1	1	79	107	10.4849
.(((((...((......))...))))).	chr7:138521867-138522204(-)$1	1	38	66	11.5828
.((.(((((((......)))))))))..	chr12:4461753-4462216(+)$1	1	113	141	11.9809
(((.(..((((......)))).).))).	chr8:141541636-141542021(-)$1	1	250	278	13.4849
.(((((((.((......))..)))))))	chr5:126171845-126172329(+)$1	1	14	42	13.5582
((((((.((((......)))).))))))	chr8:117858380-117858653(-)$1	1	78	106	14.0461
..(((..((((......))))..)))..	chr6:13621906-13622223(-)$1	1	245	273	13.2681
(((.(((((((......)))).))))))	chr7:4808635-4808968(+)$1	1	145	173	11.9688
..(((...(((......)))..))))))	chr3:185347469-185347923(+)$1	1	159	187	14.5630
((....(((((......)))))..))))	chr1:179324009-179324423(+)$1	1	327	355	11.3485
(((((...((((....))))...)))))	chr6:72012689-72012959(+)$1	1	172	200	11.0363
(((((((((((......))))))))).)	chr1:9642613-9642882(+)$1	1	185	213	15.0553
((...((((((......))))))...))	chr17:5287454-5287827(+)$1	1	87	115	11.3190
(.(((((((.(((...)))...))))))	chr5:130536975-130537248(+)$1	1	218	246	11.2521
...((((.(((......)))..))))..	chr11:92626096-92626399(+)$1	1	185	213	12.6657
))(((((((((......)))))))))..	chr20:48569804-48570126(+)$1	1	192	220	12.8263
(((((((.(((......)))))))))))	chr3:30734279-30734599(+)$1	1	274	302	15.3329
.((.((((.((......))..)))))).	chr2:242385556-242385870(+)$1	1	101	129	11.6174
.(.((((..((......))..)))).).	chr3:42253123-42253437(+)$1	1	241	269	12.4304
((..(((.(((......)).).)))..)	chr17:41846449-41846836(-)$1	1	150	178	12.8421
.((.((..(((......)))..)).)).	chr16:30676529-30676822(+)$1	1	146	174	12.6095
.(((((((..(((...)))..)))))))	chr2:202902312-202902573(+)$1	1	141	169	10.9468
.((((((...(......)...)))))).	chr11:64895167-64895426(-)$1	1	171	199	12.9126
((.((((((((((....)))))))))))	chr20:2125629-2126071(+)$1	1	226	254	12.0070
(.(((.(((((......))))).))).)	chr14:105236285-105236591(-)$1	1	268	296	12.0464
((((((.((((......)).)).)))))	chr16:31123341-31123713(+)$1	1	47	75	10.6062
..(((((((.(((...)))...))))))	chr22:19429494-19429752(-)$1	1	205	233	11.0324
(((((((....((....))...))))))	chr1:2334888-2335249(+)$1	1	242	270	10.9677
(((.(((((((......))....)))))	chr3:52003208-52003446(-)$1	1	24	52	13.1373
.(.(.((((.(......).)))).)).)	chr7:129472344-129472686(-)$1	1	163	191	12.3412
((((..(((((......)))))...)))	chr18:29128547-29128831(+)$1	1	142	170	11.8263
.(((.(.((((......)))).))))..	chr8:42027490-42027786(+)$1	1	56	84	13.0974
(((((((((((((....)))))))))))	chr1:64125556-64126010(+)$1	1	404	432	12.4027
(((((((((((......)))...)))))	chr11:47491599-47491857(-)$1	1	32	60	12.7868
((((...((((......))))..)))))	chr7:64169163-64169420(+)$1	1	222	250	12.2532
(((((.(((((......))))).)))))	chr16:9211930-9212272(+)$1	1	234	262	13.1373
((.....((((......))))..)))).	chrX:133904468-133904730(-)$1	1	46	74	11.2774
(((((((((.(......).)))))))))	chr16:57462226-57462497(-)$1	1	50	78	15.8634
..(((((((((......))))))))).)	chr7:115898334-115898653(+)$1	1	102	130	15.0943
.((((((((((....)))))))))))).	chr17:54942586-54942913(+)$1	1	275	303	11.4008
.((((((((((((...))))))))))))	chr2:169629523-169629777(+)$1	1	199	227	12.1869
((..(((.(((......))).)))..))	chr12:44193102-44193342(-)$1	1	203	231	13.6815
.(((((((((((....))))))))))).	chr10:126310289-126310665(-)$1	1	329	357	12.4943
((((((((.((......)).))))))))	chr1:78411993-78412381(-)$1	1	52	80	11.1363
(((.(((((((......))))))).)))	chr2:75882766-75883098(+)$1	1	46	74	12.8189
(((((((((((((....)))))))))))	chr10:857203-857447(-)$1	1	25	53	11.2008
((((((.((((......)))).))))))	chrX:31139319-31139591(-)$1	1	177	205	14.0461
..(((((((((((....)))))))))))	chr11:113146048-113146401(+)$1	1	242	270	12.3988
((.....((((......))))...))))	chr11:85669869-85670197(-)$1	1	268	296	11.8857
((.((((((((((...)))))))))).)	chr1:200828494-200828780(+)$1	1	224	252	12.0569
)((((((((((......))))))))))(	chr17:48940013-48940346(-)$1	1	256	284	15.7484
.(((((..(((......))).)))))((	chr20:18469785-18470087(-)$1	1	76	104	11.6784
.(((((((..(......)..))))))).	chr20:48568765-48569168(+)$1	1	140	168	12.4365
(((((..((((......))))..)))).	chrX:105921812-105922130(+)$1	1	200	228	12.0904
((((((...((......))...))))))	chr3:52289200-52289645(-)$1	1	313	341	15.3428
(((((((..((......))....)))))	chr2:192288793-192289175(+)$1	1	126	154	15.4778

#PSSM
g : 0.10	[ : 0.10	: : 0.08	i : 0.08	b : 0.06	c : 0.06	d : 0.06	e : 0.06	h : 0.06	" : 0.05	# : 0.05	= : 0.05	! : 0.03	' : 0.01	f : 0.01	$ : 0.01	F : 0.01	a : 0.01	
g : 0.15	= : 0.12	e : 0.10	c : 0.08	i : 0.08	b : 0.06	d : 0.06	h : 0.06	[ : 0.05	" : 0.05	# : 0.03	a : 0.03	f : 0.03	$ : 0.01	F : 0.01	
g : 0.18	= : 0.15	i : 0.12	c : 0.08	e : 0.06	[ : 0.06	b : 0.05	d : 0.05	h : 0.05	" : 0.03	! : 0.03	f : 0.03	$ : 0.03	# : 0.01	
g : 0.18	= : 0.18	[ : 0.12	i : 0.10	e : 0.06	c : 0.06	d : 0.05	h : 0.05	! : 0.03	f : 0.03	$ : 0.03	# : 0.01	" : 0.01	a : 0.01	
g : 0.22	= : 0.18	c : 0.10	i : 0.10	e : 0.06	d : 0.06	" : 0.03	f : 0.03	[ : 0.03	h : 0.03	$ : 0.03	a : 0.01	# : 0.01	b : 0.01	! : 0.01	
g : 0.20	= : 0.17	i : 0.10	e : 0.06	! : 0.06	d : 0.06	c : 0.05	" : 0.05	f : 0.05	[ : 0.03	h : 0.03	$ : 0.03	# : 0.01	b : 0.01	a : 0.01	
= : 0.17	g : 0.15	e : 0.10	i : 0.10	" : 0.08	! : 0.08	[ : 0.06	d : 0.06	c : 0.05	f : 0.03	h : 0.03	$ : 0.03	
d : 0.20	= : 0.17	g : 0.12	" : 0.10	[ : 0.08	e : 0.08	! : 0.06	i : 0.05	h : 0.03	a : 0.01	f : 0.01	b : 0.01	# : 0.01	
d : 0.20	= : 0.17	c : 0.12	e : 0.08	" : 0.06	[ : 0.06	g : 0.06	! : 0.06	i : 0.05	b : 0.03	f : 0.01	a : 0.01	# : 0.01	
b : 0.18	d : 0.18	= : 0.15	c : 0.13	e : 0.06	[ : 0.06	i : 0.05	" : 0.03	g : 0.03	! : 0.03	f : 0.01	# : 0.01	
c : 0.18	d : 0.18	b : 0.17	= : 0.15	a : 0.08	e : 0.06	i : 0.05	g : 0.03	[ : 0.01	f : 0.01	# : 0.01	
o : 0.74	= : 0.12	c : 0.06	a : 0.01	d : 0.01	b : 0.01	m : 0.01	
o : 0.75	= : 0.10	m : 0.05	c : 0.05	n : 0.01	b : 0.01	
o : 0.75	m : 0.13	l : 0.08	n : 0.01	
o : 0.75	m : 0.13	l : 0.08	n : 0.01	
o : 0.75	m : 0.12	l : 0.08	n : 0.01	= : 0.01	
o : 0.75	m : 0.08	= : 0.06	c : 0.05	n : 0.01	d : 0.01	
c : 0.18	b : 0.18	d : 0.18	= : 0.15	a : 0.08	e : 0.06	i : 0.05	g : 0.03	o : 0.01	f : 0.01	
c : 0.18	b : 0.18	d : 0.18	= : 0.15	e : 0.06	i : 0.05	3 : 0.03	g : 0.03	] : 0.03	a : 0.01	f : 0.01	2 : 0.01	
d : 0.20	= : 0.17	3 : 0.13	c : 0.13	2 : 0.08	e : 0.06	i : 0.05	] : 0.05	g : 0.03	4 : 0.03	f : 0.01	
d : 0.18	3 : 0.17	= : 0.17	2 : 0.12	e : 0.06	i : 0.06	] : 0.05	g : 0.05	4 : 0.03	f : 0.01	a : 0.01	b : 0.01	h : 0.01	
= : 0.17	3 : 0.15	2 : 0.12	e : 0.10	] : 0.10	g : 0.08	i : 0.06	d : 0.05	f : 0.03	4 : 0.03	a : 0.01	b : 0.01	c : 0.01	h : 0.01	
g : 0.17	= : 0.17	2 : 0.08	i : 0.08	] : 0.06	c : 0.06	3 : 0.06	d : 0.06	e : 0.05	b : 0.03	a : 0.03	f : 0.03	4 : 0.03	h : 0.01	
g : 0.20	= : 0.18	c : 0.12	i : 0.10	d : 0.08	e : 0.06	3 : 0.05	h : 0.05	b : 0.03	] : 0.03	f : 0.03	2 : 0.01	
= : 0.18	g : 0.17	c : 0.12	e : 0.10	i : 0.10	d : 0.08	] : 0.05	h : 0.05	3 : 0.03	f : 0.03	b : 0.01	a : 0.01	2 : 0.01	
g : 0.18	= : 0.18	e : 0.12	i : 0.10	d : 0.08	b : 0.06	c : 0.06	h : 0.05	2 : 0.03	f : 0.03	3 : 0.01	] : 0.01	a : 0.01	
g : 0.18	= : 0.17	e : 0.08	d : 0.08	] : 0.08	b : 0.06	i : 0.06	4 : 0.05	h : 0.05	2 : 0.03	c : 0.03	f : 0.03	: : 0.01	a : 0.01	
g : 0.17	] : 0.13	= : 0.12	e : 0.08	h : 0.08	d : 0.06	i : 0.06	b : 0.05	: : 0.05	4 : 0.05	c : 0.05	2 : 0.01	3 : 0.01	f : 0.01	

#score	732.8556929812397
#seq	58
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_CDS_m1_run1.txt

#BEAR
[dddduuuuuuuuuuuudddd]bb	chr2:208477911-208478131(-)$1	220	172	196	20.8115
:dddduuuuuuuuuuuudddd:::	chr1:150550633-150550855(-)$1	222	53	77	17.6858
eeeee^^^^^^^^^^^^^^^^^^^	chr1:32158274-32158497(-)$1	223	61	85	18.4362
dd[ccctttttttttttccc]ddd	chr1:17355109-17355330(-)$1	221	164	188	18.9499
eeeeevvvvvvvvvvvvveeeee2	chr8:107738407-107738637(+)$1	230	72	96	21.6834
[acccuuuuuuuuuuuuccc]a]g	chr1:213145856-213146080(+)$1	224	130	154	21.4149
dd[bbuuuuuuuuuuuubb]dddd	chr14:71479755-71479985(+)$1	230	113	137	20.0838
fffffyyyyyyyyyyyyyyyyfff	chr3:107466727-107466942(+)$1	215	163	187	20.8671
[ddddtttttttttttddddccce	chr12:130830256-130830476(+)$1	220	146	170	18.5481
fffff^^^^^^^^^^^^^^^^^^^	chr12:121204004-121204224(-)$1	220	117	141	17.8179
bdddduuuuuuuuuuuudddd]bb	chr1:16255451-16255672(+)$1	221	162	186	20.4845
eeeeettttttttttteeeeefff	chr11:3727601-3727824(-)$1	223	148	172	19.2792
eeeee^^^^^^^^^^^^^^^^^^^	chr11:108383754-108383974(-)$1	220	80	104	18.4362
fffffxxxxxxxxxxxxxxxffff	chr18:2762108-2762327(+)$1	219	59	83	18.0888
fffff^^^^^^^^^^^^^^^^^^f	chr17:5317300-5317521(-)$1	221	83	107	17.5700
fffffvvvvvvvvvvvvvffffff	chr19:2050711-2050931(-)$1	220	93	117	20.3721
hhhhhwwwwwwwwwwwwwwhhhhh	chr1:211529655-211529885(+)$1	230	31	55	18.2890
bb[bbuuuuuuuuuuuubbbb]bb	chr4:71892293-71892519(+)$1	226	113	137	19.2303
eeeee^^^^^^^^^^^^^^^^^^^	chr11:62297055-62297283(-)$1	228	106	130	18.4362
dddd^^^^^^^^^^^^^^^^^^^^	chr9:33886801-33887028(+)$1	227	40	64	17.7368
fffff^^^^^^^^^^^^^^^^^^f	chr10:119798408-119798638(-)$1	230	2	26	17.5700
[dddd^^^^^^^^^^^^^^^^^^^	chr7:141443325-141443551(+)$1	226	33	57	17.8975
fffffftttttttttttffffff3	chr18:12686185-12686409(-)$1	224	174	198	18.2872
eeeeeyyyyyyyyyyyyyyyyeee	chr16:30720775-30720999(+)$1	224	83	107	21.7399
=====wwwwwwwwwwwwww=====	chr12:49460333-49460558(-)$1	225	131	155	20.6946
eeeeeyyyyyyyyyyyyyyyyeee	chrM:13320-13542(+)$1	222	94	118	21.7399
hhhhhvvvvvvvvvvvvvhhhhhh	chr11:108383063-108383287(-)$1	224	157	181	18.1306
eeeee^^^^^^^^^^^^^^^^^^e	chrX:118724911-118725141(-)$1	230	168	192	18.2434
dddyyyyyyyyyyyyyyyydddd:	chr15:62210321-62210556(-)$1	235	59	83	19.3316
eeeeeuuuuuuuuuuuueeeeedd	chr10:1087092-1087322(-)$1	230	75	99	21.7027
eeeeeuuuuuuuuuuuueeeee22	chr3:112066317-112066537(+)$1	220	60	84	21.7035
ee[bbuuuuuuuuuuuubb]eeee	chr1:179991859-179992084(+)$1	225	94	118	20.7790
dddd^^^^^^^^^^^^^^^^^^^^	chr10:11504681-11504900(-)$1	219	180	204	17.7368
bdddduuuuuuuuuuuudddd]bb	chr6:163984461-163984682(+)$1	221	121	145	20.4845
eeeee^^^^^^^^^^^^^^^^^^^	chrM:9936-10162(+)$1	226	160	184	18.4362
fffff^^^^^^^^^^^^^^^^^^^	chr1:65871457-65871687(+)$1	230	46	70	17.8179
eeeeeuuuuuuuuuuuueeeee44	chr4:367491-367711(+)$1	220	131	155	22.1721
eeeeeuuuuuuuuuuuueeeee:b	chr3:53326401-53326625(-)$1	224	96	120	21.0374
gggggxxxxxxxxxxxxxxxgggg	chr9:112899885-112900108(+)$1	223	143	167	18.3303
ddddwwwwwwwwwwwwwwdddd:h	chr11:124637154-124637379(-)$1	225	90	114	19.0411
fffffuuuuuuuuuuuuffffff:	chr6:7584036-7584257(+)$1	221	58	82	19.8961
eeeewwwwwwwwwwwwwweeeee:	chr6:30712075-30712293(-)$1	218	52	76	20.3977
dd[ccctttttttttttccc]ddd	chr19:52724243-52724464(+)$1	221	11	35	18.9499
eeeeettttttttttteeeee444	chr2:211018731-211018961(-)$1	230	140	164	19.9530
eecccuuuuuuuuuuuuccc]eee	chr7:6066452-6066678(-)$1	226	29	53	21.6987
cccwwwwwwwwwwwwwwccc4444	chr10:99219355-99219573(-)$1	218	15	39	20.0335
cc[bbyyyyyyyyyyyyyyyybb]	chr1:91402952-91403172(-)$1	220	88	112	20.3931
eeeeevvvvvvvvvvvvveeeee]	chr7:139060760-139060984(+)$1	224	20	44	21.8571
:dddduuuuuuuuuuuudddd:::	chr14:54944697-54944918(-)$1	221	64	88	17.6858
c[ccc^^^^^^^^^^^^^^^^^^^	chrY:2847239-2847456(+)$1	217	144	168	17.8572
fffff^^^^^^^^^^^^^^^^^^^	chr3:160149429-160149653(+)$1	224	91	115	17.8179
gg[bbtttttttttttbb]ggggg	chr10:5808466-5808684(-)$1	218	108	132	17.9967
hhhhhuuuuuuuuuuuuhhhhhhh	chr3:167414709-167414930(-)$1	221	155	179	17.8782
""cccuuuuuuuuuuuuccc]eee	chr6:26156645-26156869(+)$1	224	28	52	21.1157
::cccuuuuuuuuuuuuccc:ggg	chr16:69727760-69727986(+)$1	226	48	72	18.3493
fffffftttttttttttffffffc	chr5:89757012-89757229(-)$1	217	94	118	18.1397
ddcccwwwwwwwwwwwwwwccc::	chr12:90035939-90036158(-)$1	219	182	206	19.4294
iiii^^^^^^^^^^^^^^^^^^^^	chr7:142991708-142991927(+)$1	219	166	190	17.6949
eeeeettttttttttteeeee]dd	chr10:91066624-91066842(+)$1	218	51	75	19.4241
fffffuuuuuuuuuuuuffffffd	chr2:225653738-225653963(-)$1	225	180	204	20.4419
eeeeevvvvvvvvvvvvveeeee:	chr11:77034248-77034470(-)$1	222	44	68	21.1115
!dddduuuuuuuuuuuudddd22d	chr3:98309402-98309624(-)$1	222	116	140	20.6349
eeeeettttttttttteeeee22c	chr6:26199677-26199898(+)$1	221	98	122	19.3103
eeeeevvvvvvvvvvvvveeeee4	chrX:129201230-129201452(-)$1	222	81	105	21.9000
eeeeettttttttttteeeee]gg	chr6:12120902-12121120(+)$1	218	73	97	19.5367
d[cccwwwwwwwwwwwwwwccc22	chr2:89156980-89157210(-)$1	230	95	119	20.5661
eeeewwwwwwwwwwwwwweeeee:	chr11:65623343-65623560(-)$1	217	37	61	20.3977
[ddddwwwwwwwwwwwwwwdddd]	chr8:105509985-105510205(-)$1	220	33	57	20.6527
eeeewwwwwwwwwwwwwweeeee]	chr3:39185129-39185355(-)$1	226	23	47	21.1433
!ddddyyyyyyyyyyyyyyyyddd	chr7:127569261-127569482(+)$1	221	173	197	20.8944
fffff^^^^^^^^^^^^^^^^^^f	chr1:90399287-90399508(+)$1	221	85	109	17.5700
fffffftttttttttttffffff]	chr21:34925645-34925865(+)$1	220	48	72	18.2348
ee[ccctttttttttttccceeee	chr7:6185138-6185368(+)$1	230	138	162	19.5873
!!cccuuuuuuuuuuuuccc22ab	chr19:47207479-47207709(-)$1	230	66	90	21.1089

#otherMatches

#Seq PSSM
UCAGACACUGGAACAUCUCUGUAG	chr2:208477911-208478131(-)$1	220	172	196	20.8115
GCUGCAUCGAACCAUUAGCAGAAA	chr1:150550633-150550855(-)$1	222	53	77	17.6858
CCCUGAUCCCUUGUUCCCUACUCC	chr1:32158274-32158497(-)$1	223	61	85	18.4362
GACACCAACCUCAAUAAGGUCUCA	chr1:17355109-17355330(-)$1	221	164	188	18.9499
UCUCUGGUAUGGGAAAAAAGGGAG	chr8:107738407-107738637(+)$1	230	72	96	21.6834
GAAACUACUUUCACCACGUUGUGC	chr1:213145856-213146080(+)$1	224	130	154	21.4149
GUGGAUUGGCAUUAACUUUGACAG	chr14:71479755-71479985(+)$1	230	113	137	20.0838
GGCCUUUUUAAAAUGCUUUUUAGG	chr3:107466727-107466942(+)$1	215	163	187	20.8671
AUGUUAAAGAAUCAAAAACAGGUA	chr12:130830256-130830476(+)$1	220	146	170	18.5481
CCAUUUACUUUAUUGCCACUCCUC	chr12:121204004-121204224(-)$1	220	117	141	17.8179
CCAGGAAGCACCUCAAGCCUGAGC	chr1:16255451-16255672(+)$1	221	162	186	20.4845
AGGUGAAGUUCUAACCCACCUUUU	chr11:3727601-3727824(-)$1	223	148	172	19.2792
AAUGUAUAUACCGCACACAGAUAA	chr11:108383754-108383974(-)$1	220	80	104	18.4362
AGCUGUUUCAAAUGUUCGCUCAGU	chr18:2762108-2762327(+)$1	219	59	83	18.0888
GAGAGAUUUUUCACCAGUUCCACC	chr17:5317300-5317521(-)$1	221	83	107	17.5700
AAACCAGCCGAACUUCAGGGUUUC	chr19:2050711-2050931(-)$1	220	93	117	20.3721
ACCUAUUAUGUUUAUCUUUUAGGU	chr1:211529655-211529885(+)$1	230	31	55	18.2890
GUGCCUAUCUUAACACUGGAUGUU	chr4:71892293-71892519(+)$1	226	113	137	19.2303
GCAUGAAUAUACAGACGCACAAAA	chr11:62297055-62297283(-)$1	228	106	130	18.4362
GUCUCAUUUAUUAGCAUUUCAUUU	chr9:33886801-33887028(+)$1	227	40	64	17.7368
GAUCUGAUAAACUUAACAAUGGGG	chr10:119798408-119798638(-)$1	230	2	26	17.5700
AGCCCUGAAUCGUGUGCACUUACU	chr7:141443325-141443551(+)$1	226	33	57	17.8975
AGUAGCAGUAUAUCAUAGUUACUC	chr18:12686185-12686409(-)$1	224	174	198	18.2872
GGCUUGAGGAAAAGCGCAAAAAAG	chr16:30720775-30720999(+)$1	224	83	107	21.7399
GUGUAUUCUGUCACCUCUCUGCAU	chr12:49460333-49460558(-)$1	225	131	155	20.6946
GGAGGACUACUCAAAACCAUACCU	chrM:13320-13542(+)$1	222	94	118	21.7399
AGUCAGGAAGUAAAAUAAUGGCUG	chr11:108383063-108383287(-)$1	224	157	181	18.1306
CCUGCCCCAAGCACCACAUCACAG	chrX:118724911-118725141(-)$1	230	168	192	18.2434
ACAUAUCUUUUAAAAAACUUGUAU	chr15:62210321-62210556(-)$1	235	59	83	19.3316
UGGUGAAAUUAAGAUAACGCCAUG	chr10:1087092-1087322(-)$1	230	75	99	21.7027
ACAGAUCAUAUUUAUUUUUUGUCC	chr3:112066317-112066537(+)$1	220	60	84	21.7035
GACAGAAAAAAAAUCAACUCUUGA	chr1:179991859-179992084(+)$1	225	94	118	20.7790
GGUCAGAAGUUAGUUAUACAUACA	chr10:11504681-11504900(-)$1	219	180	204	17.7368
AGACAAAUACAGACCGCUGUCAUG	chr6:163984461-163984682(+)$1	221	121	145	20.4845
UAGCCUUACUACUAAUAAUUAUUA	chrM:9936-10162(+)$1	226	160	184	18.4362
AGAGGCCACUCAAAAUAGUUUUAC	chr1:65871457-65871687(+)$1	230	46	70	17.8179
UGAAUAAACAUAAGAAAAUUCAUA	chr4:367491-367711(+)$1	220	131	155	22.1721
UCAGUCCCACUCUGCCAGCUGAAG	chr3:53326401-53326625(-)$1	224	96	120	21.0374
GGCAUCCAAUGAGACAACCAAUGC	chr9:112899885-112900108(+)$1	223	143	167	18.3303
GCUUAUUUUUACAUUUCCAAGCGA	chr11:124637154-124637379(-)$1	225	90	114	19.0411
GCUUUCAGUACAGAAGAGAAGCAU	chr6:7584036-7584257(+)$1	221	58	82	19.8961
CCGGCCCCCUCCACCAUCCCGGGA	chr6:30712075-30712293(-)$1	218	52	76	20.3977
ACCAGCAACCUGAAGAAGCUAGUG	chr19:52724243-52724464(+)$1	221	11	35	18.9499
UGUAGAUAAAGUACAACUACAAAA	chr2:211018731-211018961(-)$1	230	140	164	19.9530
AAACGUUCUUCUAACUUUGUAUUU	chr7:6066452-6066678(-)$1	226	29	53	21.6987
GAUUUCUCAAGCUAUAUAUCUAAG	chr10:99219355-99219573(-)$1	218	15	39	20.0335
UUGAUGUAUCAGCCACAAAAAAUG	chr1:91402952-91403172(-)$1	220	88	112	20.3931
AAUGUUAUUAACUCUUCUAUAUUA	chr7:139060760-139060984(+)$1	224	20	44	21.8571
AGACCUAACUGAAGAAUGGUUACG	chr14:54944697-54944918(-)$1	221	64	88	17.6858
AACUUGAAAACACAUAUAAAAACA	chrY:2847239-2847456(+)$1	217	144	168	17.8572
CCAGAUUCUAUAACAAAUCAAAUU	chr3:160149429-160149653(+)$1	224	91	115	17.8179
UGCGCACAAUGUAGCAGCACAAGG	chr10:5808466-5808684(-)$1	218	108	132	17.9967
UUUAAGUUAUACAAUUGUUAAAUA	chr3:167414709-167414930(-)$1	221	155	179	17.8782
CCGUGAAGAAGAAGGCCCGCAAGU	chr6:26156645-26156869(+)$1	224	28	52	21.1157
CAGUCGGAAUCAUCACAGACCCCC	chr16:69727760-69727986(+)$1	226	48	72	18.3493
GGCACUUCAAUACCUUUGGUGCUG	chr5:89757012-89757229(-)$1	217	94	118	18.1397
UGGGCCUUUCUUUUUAUCAGCCUC	chr12:90035939-90036158(-)$1	219	182	206	19.4294
GGUGGGAAAAAUUGACAUGUAAAU	chr7:142991708-142991927(+)$1	219	166	190	17.6949
UCAUCUGAAGAAAGCUGAUGAGGC	chr10:91066624-91066842(+)$1	218	51	75	19.4241
GAGGUUAGACCAAAAUUAUCUCAU	chr2:225653738-225653963(-)$1	225	180	204	20.4419
UGCUAUUUUUCUCCUUUCUAGCAU	chr11:77034248-77034470(-)$1	222	44	68	21.1115
ACUACAGAUACUUUGAAGUAGAAG	chr3:98309402-98309624(-)$1	222	116	140	20.6349
GUUUAUUUAUCAUGCCUGAACCUG	chr6:26199677-26199898(+)$1	221	98	122	19.3103
CACUCAGCUCGUUCUCCAGAGUGU	chrX:129201230-129201452(-)$1	222	81	105	21.9000
UCAAGAGAAUGCCAAACUUGAACA	chr6:12120902-12121120(+)$1	218	73	97	19.5367
UGCUGAAUAACUUCUAUCCCAGAG	chr2:89156980-89157210(-)$1	230	95	119	20.5661
ACGACCCCUACGCCACCUUUGUCA	chr11:65623343-65623560(-)$1	217	37	61	20.3977
AAGCAAAUCCUCCAACUGCUGCUG	chr8:105509985-105510205(-)$1	220	33	57	20.6527
GGUCCCUACUUUCCCACUGGCCAA	chr3:39185129-39185355(-)$1	226	23	47	21.1433
CCACAUACCCUCCUUUCCCCCUGU	chr7:127569261-127569482(+)$1	221	173	197	20.8944
CCAGUACACCAAUGAUCAAUAAAA	chr1:90399287-90399508(+)$1	221	85	109	17.5700
CUUCGGUUGUGACUGUCCCGGAGC	chr21:34925645-34925865(+)$1	220	48	72	18.2348
GCUACAUAAAAGUAAGCUGUGCAG	chr7:6185138-6185368(+)$1	230	138	162	19.5873
UAGCACCACCGAACUCCUGCCUCG	chr19:47207479-47207709(-)$1	230	66	90	21.1089

#DB
.((((............)))).))	chr2:208477911-208478131(-)$1	1	172	196	20.8115
.((((............))))...	chr1:150550633-150550855(-)$1	1	53	77	17.6858
(((((...................	chr1:32158274-32158497(-)$1	1	61	85	18.4362
((.(((...........))).)))	chr1:17355109-17355330(-)$1	1	164	188	18.9499
(((((.............))))).	chr8:107738407-107738637(+)$1	1	72	96	21.6834
.((((............))).).)	chr1:213145856-213146080(+)$1	1	130	154	21.4149
((.((............)).))))	chr14:71479755-71479985(+)$1	1	113	137	20.0838
(((((................)))	chr3:107466727-107466942(+)$1	1	163	187	20.8671
.((((...........))))))))	chr12:130830256-130830476(+)$1	1	146	170	18.5481
(((((...................	chr12:121204004-121204224(-)$1	1	117	141	17.8179
(((((............)))).))	chr1:16255451-16255672(+)$1	1	162	186	20.4845
(((((...........)))))(((	chr11:3727601-3727824(-)$1	1	148	172	19.2792
(((((...................	chr11:108383754-108383974(-)$1	1	80	104	18.4362
(((((...............))))	chr18:2762108-2762327(+)$1	1	59	83	18.0888
(((((..................)	chr17:5317300-5317521(-)$1	1	83	107	17.5700
(((((.............))))))	chr19:2050711-2050931(-)$1	1	93	117	20.3721
(((((..............)))))	chr1:211529655-211529885(+)$1	1	31	55	18.2890
((.((............)))).))	chr4:71892293-71892519(+)$1	1	113	137	19.2303
(((((...................	chr11:62297055-62297283(-)$1	1	106	130	18.4362
((((....................	chr9:33886801-33887028(+)$1	1	40	64	17.7368
(((((..................)	chr10:119798408-119798638(-)$1	1	2	26	17.5700
.((((...................	chr7:141443325-141443551(+)$1	1	33	57	17.8975
((((((...........)))))).	chr18:12686185-12686409(-)$1	1	174	198	18.2872
(((((................)))	chr16:30720775-30720999(+)$1	1	83	107	21.7399
(((((..............)))))	chr12:49460333-49460558(-)$1	1	131	155	20.6946
(((((................)))	chrM:13320-13542(+)$1	1	94	118	21.7399
(((((.............))))))	chr11:108383063-108383287(-)$1	1	157	181	18.1306
(((((..................)	chrX:118724911-118725141(-)$1	1	168	192	18.2434
(((................)))).	chr15:62210321-62210556(-)$1	1	59	83	19.3316
(((((............)))))))	chr10:1087092-1087322(-)$1	1	75	99	21.7027
(((((............)))))..	chr3:112066317-112066537(+)$1	1	60	84	21.7035
((.((............)).))))	chr1:179991859-179992084(+)$1	1	94	118	20.7790
((((....................	chr10:11504681-11504900(-)$1	1	180	204	17.7368
(((((............)))).))	chr6:163984461-163984682(+)$1	1	121	145	20.4845
(((((...................	chrM:9936-10162(+)$1	1	160	184	18.4362
(((((...................	chr1:65871457-65871687(+)$1	1	46	70	17.8179
(((((............)))))..	chr4:367491-367711(+)$1	1	131	155	22.1721
(((((............))))).(	chr3:53326401-53326625(-)$1	1	96	120	21.0374
(((((...............))))	chr9:112899885-112900108(+)$1	1	143	167	18.3303
((((..............)))).(	chr11:124637154-124637379(-)$1	1	90	114	19.0411
(((((............)))))).	chr6:7584036-7584257(+)$1	1	58	82	19.8961
((((..............))))).	chr6:30712075-30712293(-)$1	1	52	76	20.3977
((.(((...........))).)))	chr19:52724243-52724464(+)$1	1	11	35	18.9499
(((((...........)))))...	chr2:211018731-211018961(-)$1	1	140	164	19.9530
(((((............))).)))	chr7:6066452-6066678(-)$1	1	29	53	21.6987
(((..............)))....	chr10:99219355-99219573(-)$1	1	15	39	20.0335
((.((................)).	chr1:91402952-91403172(-)$1	1	88	112	20.3931
(((((.............))))).	chr7:139060760-139060984(+)$1	1	20	44	21.8571
.((((............))))...	chr14:54944697-54944918(-)$1	1	64	88	17.6858
(.(((...................	chrY:2847239-2847456(+)$1	1	144	168	17.8572
(((((...................	chr3:160149429-160149653(+)$1	1	91	115	17.8179
((.((...........)).)))))	chr10:5808466-5808684(-)$1	1	108	132	17.9967
(((((............)))))))	chr3:167414709-167414930(-)$1	1	155	179	17.8782
..(((............))).)))	chr6:26156645-26156869(+)$1	1	28	52	21.1157
..(((............))).(((	chr16:69727760-69727986(+)$1	1	48	72	18.3493
((((((...........)))))))	chr5:89757012-89757229(-)$1	1	94	118	18.1397
))(((..............)))..	chr12:90035939-90036158(-)$1	1	182	206	19.4294
((((....................	chr7:142991708-142991927(+)$1	1	166	190	17.6949
(((((...........))))).))	chr10:91066624-91066842(+)$1	1	51	75	19.4241
(((((............)))))))	chr2:225653738-225653963(-)$1	1	180	204	20.4419
(((((.............))))).	chr11:77034248-77034470(-)$1	1	44	68	21.1115
.((((............))))..)	chr3:98309402-98309624(-)$1	1	116	140	20.6349
(((((...........)))))..)	chr6:26199677-26199898(+)$1	1	98	122	19.3103
(((((.............))))).	chrX:129201230-129201452(-)$1	1	81	105	21.9000
(((((...........))))).))	chr6:12120902-12121120(+)$1	1	73	97	19.5367
(.(((..............)))..	chr2:89156980-89157210(-)$1	1	95	119	20.5661
((((..............))))).	chr11:65623343-65623560(-)$1	1	37	61	20.3977
.((((..............)))).	chr8:105509985-105510205(-)$1	1	33	57	20.6527
((((..............))))).	chr3:39185129-39185355(-)$1	1	23	47	21.1433
.((((................)))	chr7:127569261-127569482(+)$1	1	173	197	20.8944
(((((..................)	chr1:90399287-90399508(+)$1	1	85	109	17.5700
((((((...........)))))).	chr21:34925645-34925865(+)$1	1	48	72	18.2348
((.(((...........)))))))	chr7:6185138-6185368(+)$1	1	138	162	19.5873
..(((............)))..))	chr19:47207479-47207709(-)$1	1	66	90	21.1089

#PSSM
e : 0.35	f : 0.18	d : 0.12	[ : 0.06	: : 0.04	b : 0.04	h : 0.04	c : 0.04	! : 0.04	g : 0.02	= : 0.01	" : 0.01	i : 0.01	
e : 0.35	d : 0.24	f : 0.18	h : 0.04	g : 0.02	c : 0.02	[ : 0.02	a : 0.01	b : 0.01	= : 0.01	" : 0.01	: : 0.01	i : 0.01	! : 0.01	
e : 0.31	d : 0.18	f : 0.18	c : 0.12	[ : 0.10	h : 0.04	= : 0.01	g : 0.01	i : 0.01	
e : 0.31	f : 0.18	d : 0.17	c : 0.14	b : 0.06	h : 0.04	= : 0.01	y : 0.01	g : 0.01	w : 0.01	i : 0.01	
e : 0.27	f : 0.18	c : 0.14	d : 0.13	b : 0.06	w : 0.06	h : 0.04	^ : 0.04	= : 0.01	y : 0.01	g : 0.01	
u : 0.28	^ : 0.21	w : 0.13	t : 0.09	v : 0.08	y : 0.08	c : 0.04	f : 0.04	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	t : 0.17	w : 0.13	v : 0.08	y : 0.08	x : 0.02	
u : 0.28	^ : 0.21	w : 0.13	t : 0.08	v : 0.08	y : 0.08	e : 0.06	x : 0.02	d : 0.01	b : 0.01	
^ : 0.21	c : 0.12	e : 0.12	w : 0.12	d : 0.09	v : 0.08	y : 0.08	f : 0.06	b : 0.05	x : 0.02	h : 0.01	
^ : 0.21	e : 0.21	c : 0.12	d : 0.10	y : 0.08	f : 0.08	w : 0.06	b : 0.04	x : 0.02	h : 0.02	] : 0.01	
^ : 0.21	e : 0.21	c : 0.14	d : 0.13	f : 0.08	y : 0.06	h : 0.04	] : 0.02	x : 0.02	b : 0.01	= : 0.01	g : 0.01	
e : 0.24	^ : 0.21	d : 0.13	f : 0.09	] : 0.06	y : 0.06	c : 0.04	h : 0.04	g : 0.02	b : 0.01	= : 0.01	4 : 0.01	: : 0.01	2 : 0.01	
e : 0.22	^ : 0.21	f : 0.12	d : 0.09	] : 0.08	c : 0.04	h : 0.04	g : 0.04	2 : 0.04	: : 0.02	4 : 0.02	a : 0.01	= : 0.01	b : 0.01	
^ : 0.21	e : 0.17	f : 0.12	d : 0.10	b : 0.06	: : 0.06	2 : 0.05	g : 0.05	h : 0.04	4 : 0.04	] : 0.01	c : 0.01	= : 0.01	a : 0.01	
^ : 0.16	: : 0.10	d : 0.10	e : 0.10	f : 0.09	b : 0.08	g : 0.06	] : 0.06	h : 0.05	4 : 0.05	2 : 0.04	c : 0.02	3 : 0.01	= : 0.01	

#score	1446.7604118105335
#seq	74
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_CDS_m1_run1.txt

#BEAR
iiiiiiiiiuuuuuuuuuuuuiiiiii	chr1:110882610-110882831(+)$1	221	101	128	24.2169
fff[cccwwwwwwwwwwwwwwccc]ff	chr17:65941791-65942012(+)$1	221	55	82	22.0573
c"""dddduuuuuuuuuuuudddd]cc	chrX:118370527-118370754(+)$1	227	101	128	23.5841
dddd[bbvvvvvvvvvvvvvbb]dddd	chr7:5567369-5567606(-)$1	237	207	234	21.6264
iiiiiiiiivvvvvvvvvvvvviiiii	chr19:8528385-8528634(+)$1	249	4	31	23.9313
::gggggggtttttttttttggggggg	chr9:130674695-130674923(-)$1	228	0	27	22.7174
!!dddd[bbvvvvvvvvvvvvvbb]dd	chr6:170893340-170893573(-)$1	233	67	94	22.5441
:ffffffvvvvvvvvvvvvvffffff:	chr12:53342857-53343109(+)$1	252	73	100	20.7242
ggg:eeeeevvvvvvvvvvvvveeeee	chr17:7403954-7404178(+)$1	224	55	82	22.1980
:ggggggguuuuuuuuuuuuggggggg	chr1:183520113-183520344(+)$1	231	91	118	22.8694
iiiiiiiiiuuuuuuuuuuuuiiiiii	chr14:32562399-32562631(+)$1	232	10	37	24.2169
d"""eeeeettttttttttteeeee]d	chrX:31198463-31198682(-)$1	219	134	161	23.7529
eee!!bb[bbtttttttttttbb22bb	chr14:92548620-92548851(-)$1	231	58	85	20.5350
b[bb[ddddtttttttttttdddd]bb	chr1:3800120-3800368(-)$1	248	103	130	23.6798
dddeeeeeattttttttttta]eeeee	chr17:7760282-7760517(-)$1	235	35	62	23.5968
ffff!!cccwwwwwwwwwwwwwwccc2	chr1:47110750-47110981(-)$1	231	123	150	21.4760
e"""eeeeevvvvvvvvvvvvveeeee	chr1:892489-892711(-)$1	222	135	162	23.4051
eee[eeeeeuuuuuuuuuuuueeeeee	chr8:37555235-37555454(+)$1	219	62	89	23.0332
&&bb[cccvvvvvvvvvvvvvccc]bb	chr17:35634736-35634980(-)$1	244	46	73	22.8527
iiiiiiiiiuuuuuuuuuuuuiiiiii	chr11:73789452-73789678(-)$1	226	67	94	24.2169
cccfffffftttttttttttffffff4	chr1:235505336-235505558(+)$1	222	180	207	23.5375
ggggg[cccuuuuuuuuuuuuccc]gg	chr16:53738011-53738233(-)$1	222	78	105	24.4811
:ccc[ddddtttttttttttdddd]cc	chr10:120818780-120818999(-)$1	219	64	91	23.6256
c####cccvvvvvvvvvvvvvccc444	chr5:67593240-67593479(+)$1	239	18	45	24.2810
d####ddddtttttttttttdddd444	chr16:2816076-2816300(+)$1	224	75	102	24.0045
""gggggggtttttttttttggggggg	chr19:47570589-47570813(-)$1	224	16	43	24.5016
cccfffffftttttttttttffffff]	chr3:12650174-12650394(-)$1	220	143	170	23.5575
f!!eeeeeattttttttttta]eeeee	chr5:140956980-140957200(-)$1	220	131	158	24.1161
ddd"""ccctttttttttttccc]ddd	chr17:33463937-33464178(-)$1	241	189	216	23.9240
EEcccddddtttttttttttdddd]cc	chr1:36213502-36213722(-)$1	220	76	103	22.2984
dddd[ddddtttttttttttdddd]dd	chr22:38897037-38897263(-)$1	226	39	66	23.6658
ffffff[bbtttttttttttbb333ff	chr14:21968955-21969371(-)$1	416	224	251	22.8760
dddd[bbbbuuuuuuuuuuuubb]bb]	chr9:135982003-135982226(-)$1	223	92	119	21.9243
$$$$$ddddvvvvvvvvvvvvvdddd8	chr3:9489553-9489776(+)$1	223	114	141	22.1874
:eeeee!!attttttttttta22eeee	chr19:39943999-39944224(+)$1	225	20	47	22.4699
:bbfffffftttttttttttffffff]	chr7:92354958-92355198(-)$1	240	183	210	22.5069
:ccc[dddduuuuuuuuuuuuddddcc	chr17:37648946-37649174(+)$1	228	157	184	23.0860
EEEeeeeeuuuuuuuuuuuueeeeecc	chr6:31627553-31627777(-)$1	224	25	52	20.1896
fff!!cccuuuuuuuuuuuuccc22ff	chr6:32947605-32947854(+)$1	249	194	221	23.1398
c[dddd[bbuuuuuuuuuuuubb]ddd	chr21:34944794-34945019(+)$1	225	100	127	22.6106
!!gggggggtttttttttttggggggg	chr11:129999889-130000113(+)$1	224	130	157	24.5650
dddd[bbvvvvvvvvvvvvvbb]dddd	chr19:58805749-58805975(+)$1	226	49	76	21.6264
""ccc[ccctttttttttttccc]ccc	chr3:185639768-185639998(-)$1	230	112	139	24.6069
bb:ffffffuuuuuuuuuuuuffffff	chr18:24126883-24127109(-)$1	226	134	161	22.0255
#hhhhhhhhuuuuuuuuuuuuhhhhhh	chr17:1579454-1579689(-)$1	235	145	172	21.3058
b!!ddddvvvvvvvvvvvvvdddd]bb	chr14:23538694-23538924(-)$1	230	132	159	22.5785
=========ttttttttttt=======	chr1:150939477-150939714(-)$1	237	91	118	24.9011
d[gggggggtttttttttttggggggg	chr15:40998302-40998577(-)$1	275	216	243	24.3880
=========uuuuuuuuuuuu======	chr14:21971351-21971618(+)$1	267	200	227	24.7204
ffffffyyyyyyyyyyyyyyyyfffff	chr11:8737034-8737270(+)$1	236	36	63	20.1380
f[gggggggvvvvvvvvvvvvvggggg	chr8:41844916-41845146(-)$1	230	98	125	23.9578
cdddd[ccctttttttttttccc]ddd	chr4:1834488-1834711(-)$1	223	79	106	23.6576
cc"""ddddtttttttttttdddd]cc	chr17:42478655-42478885(-)$1	230	71	98	24.3758
gggggggwwwwwwwwwwwwwwgggggg	chr11:70181574-70181800(+)$1	226	112	139	22.4042
$$$$$ddddtttttttttttddddddd	chr10:5945027-5945247(+)$1	220	179	206	22.9552
ffbb[ddddtttttttttttdddd]bb	chr1:36056209-36056458(-)$1	249	64	91	23.3879
=========ttttttttttt=======	chr17:16285276-16285540(+)$1	264	108	135	24.9011
gggg[cccuuuuuuuuuuuuccc333g	chr15:52645985-52646217(-)$1	232	3	30	23.9709
:::ffffffuuuuuuuuuuuuffffff	chr1:11297892-11298119(-)$1	227	167	194	20.7945
dddd!!cccwwwwwwwwwwwwwwccc2	chr21:33036052-33036278(+)$1	226	36	63	21.4301
f[bbeeeeevvvvvvvvvvvvveeeee	chr12:6601404-6601627(-)$1	223	74	101	22.9264
$$$$dddduuuuuuuuuuuudddd444	chr19:13246490-13246725(+)$1	235	134	161	22.4474
dd[fffffftttttttttttffffff3	chr1:171553057-171553289(+)$1	232	137	164	23.4205
!!bb[cccwwwwwwwwwwwwwwcccbb	chr19:10262078-10262302(-)$1	224	149	176	22.2031
]bbfffffftttttttttttffffff:	chr22:42981784-42982026(-)$1	242	185	212	22.0741

#otherMatches

#Seq PSSM
CGGGCGGCCAAGCAUGCCAGAGGCCGC	chr1:110882610-110882831(+)$1	221	101	128	24.2169
UCGUGUCCAAAGUCCAUCACAGACUCG	chr17:65941791-65942012(+)$1	221	55	82	22.0573
CAAAGGCCGCAAAUUCUACGGGCCCGG	chrX:118370527-118370754(+)$1	227	101	128	23.5841
GUCCACCGCAAAUGCUUCUAGGCGGAC	chr7:5567369-5567606(-)$1	237	207	234	21.6264
UAAGUAUCGUCUAGUUACUUAUUGGUA	chr19:8528385-8528634(+)$1	249	4	31	23.9313
GUGUCCAGCUCCGGCCAAAUGCUGGGC	chr9:130674695-130674923(-)$1	228	0	27	22.7174
GCCGCCCGCUCUCCUUCCUGCUGCAGG	chr6:170893340-170893573(-)$1	233	67	94	22.5441
CCUGUCCUUUCUCUCUCCCCGGACAGC	chr12:53342857-53343109(+)$1	252	73	100	20.7242
CACAGCCGGCCAUCCUAAAGCCCCGGC	chr17:7403954-7404178(+)$1	224	55	82	22.1980
UCUCUCAGCAACGUCAUCCUCUGAGAG	chr1:183520113-183520344(+)$1	231	91	118	22.8694
UGAACUAGUUCAUGGGUAUAUAUUAGU	chr14:32562399-32562631(+)$1	232	10	37	24.2169
UUUCUGGUCGAGUUGCAAAAGGCCAUA	chrX:31198463-31198682(-)$1	219	134	161	23.7529
UGGAACGAGUGUUAGAAGCAAAUGAUG	chr14:92548620-92548851(-)$1	231	58	85	20.5350
GUCUGGGGUUUGUAGAUUCUGCUUGGG	chr1:3800120-3800368(-)$1	248	103	130	23.6798
AGCGCGCCCGACAGCAGCUAGAGGCGC	chr17:7760282-7760517(-)$1	235	35	62	23.5968
ACUUCACUGCACUUAUAAAUAUUCAGG	chr1:47110750-47110981(-)$1	231	123	150	21.4760
UCCUGCAGGAGAAUGACCAGAGCCUGC	chr1:892489-892711(-)$1	222	135	162	23.4051
GGCGCCGGUGUCUCCCUACAAGCCGGG	chr8:37555235-37555454(+)$1	219	62	89	23.0332
AUCAUGUGUUCUCUAUUAAUUCGCUUG	chr17:35634736-35634980(-)$1	244	46	73	22.8527
UUUGGGCUGGAGCUUUGAGAACAGCCU	chr11:73789452-73789678(-)$1	226	67	94	24.2169
AGUGAAGCUUUUUACCCGCCAGCUUUU	chr1:235505336-235505558(+)$1	222	180	207	23.5375
GGAGCCCGACAUACCUUAGCUUCGCGC	chr16:53738011-53738233(-)$1	222	78	105	24.4811
AACCAUUGAUAAUUUAAUUUUCAAAGG	chr10:120818780-120818999(-)$1	219	64	91	23.6256
CAUUGUGUCAUAAACAAAACAGCAACU	chr5:67593240-67593479(+)$1	239	18	45	24.2810
CGAUCCAGGUCCAGAACCCCCCUGAUA	chr16:2816076-2816300(+)$1	224	75	102	24.0045
GUGGGCCCCAGCAGUUCCAAGGGGUCU	chr19:47570589-47570813(-)$1	224	16	43	24.5016
CUUUUAUCCAAGGAAGAUAGGGAUGAG	chr3:12650174-12650394(-)$1	220	143	170	23.5575
UCUUGGUCCGAAAUGACUAUGAGGCCA	chr5:140956980-140957200(-)$1	220	131	158	24.1161
CAGAAAAUCGCAAGUCACAAGAUGCUG	chr17:33463937-33464178(-)$1	241	189	216	23.9240
CUGAGCCUUCACUUCCCAUAGAGGAUU	chr1:36213502-36213722(-)$1	220	76	103	22.2984
UUGCGUAAAAAAAAGUGGGAUUUGAGU	chr22:38897037-38897263(-)$1	226	39	66	23.6658
CCUGGCAGCAAAGACCACACGCCAAGC	chr14:21968955-21969371(-)$1	416	224	251	22.8760
AGUGCCGGAUCCUCAAGAACUUCUCGU	chr9:135982003-135982226(-)$1	223	92	119	21.9243
CUAAAUACCCCAAAACCAAAAAGGUAA	chr3:9489553-9489776(+)$1	223	114	141	22.1874
GCGGGCAGUGAGAAAGAAGAAGAGCCU	chr19:39943999-39944224(+)$1	225	20	47	22.4699
CAGCAGCGGACAAAUAAAACUCGCUGA	chr7:92354958-92355198(-)$1	240	183	210	22.5069
ACCUAUGGCCAAGUAUAUAAAGCCAAG	chr17:37648946-37649174(+)$1	228	157	184	23.0860
AUUUGGGGGCCCAUUACACACCCCAGC	chr6:31627553-31627777(-)$1	224	25	52	20.1896
AAACCCAGAAGAGAUUGAGAUUGAUUU	chr6:32947605-32947854(+)$1	249	194	221	23.1398
GCCAGCCGUACUAUUCACAACACUGCU	chr21:34944794-34945019(+)$1	225	100	127	22.6106
UUGGCUGUUGACCCAGAAAAGGCGGCC	chr11:129999889-130000113(+)$1	224	130	157	24.5650
GACUCAGAACAUAACUCCAGCUUAGUC	chr19:58805749-58805975(+)$1	226	49	76	21.6264
UUGAUGGGCGUAGGAUCAGAGUUGAUU	chr3:185639768-185639998(-)$1	230	112	139	24.6069
CGCUGGGGAACACUUACAUCCUCCCCA	chr18:24126883-24127109(-)$1	226	134	161	22.0255
AAGUUGCUCAUCUUGGCAUUGGAGCGG	chr17:1579454-1579689(-)$1	235	145	172	21.3058
GAAAACAGACCUGAAAAUGAUGUUCCA	chr14:23538694-23538924(-)$1	230	132	159	22.5785
CCUGGUUUGCCAAUUACAUCCGAGCUG	chr1:150939477-150939714(-)$1	237	91	118	24.9011
GAAAUAUUAAAUCAACAAAAUAAUAUU	chr15:40998302-40998577(-)$1	275	216	243	24.3880
UUUCUGCCACAGCACCCAUCAUGGCAG	chr14:21971351-21971618(+)$1	267	200	227	24.7204
AGCCAGGAAAGAGAGAGAAAGGCUGGC	chr11:8737034-8737270(+)$1	236	36	63	20.1380
UGUCUUGGUACAAAAGAACAAAACCGA	chr8:41844916-41845146(-)$1	230	98	125	23.9578
CGUUUUUCCAAAUUAUUUGAGGAUGAG	chr4:1834488-1834711(-)$1	223	79	106	23.6576
GGAAGUGGUCCCAUGUUCAAACCAACC	chr17:42478655-42478885(-)$1	230	71	98	24.3758
AUGAACGAAGAACAUAAUAAACGUUUA	chr11:70181574-70181800(+)$1	226	112	139	22.4042
UUAAAAGUAUUUGUAAAUGUUGCUGCU	chr10:5945027-5945247(+)$1	220	179	206	22.9552
CAGGGUGCCCUCACUCACUUGGCAGCC	chr1:36056209-36056458(-)$1	249	64	91	23.3879
CUCUUUCUGACUACAACAUCCAGAAGG	chr17:16285276-16285540(+)$1	264	108	135	24.9011
UAGGAACCAAGUGAGAAGAAGGUACCU	chr15:52645985-52646217(-)$1	232	3	30	23.9709
GUAGCAUGAACCCUGCCUUUGUCAUGC	chr1:11297892-11298119(-)$1	227	167	194	20.7945
CACUUUUCUUAAAGGAAAGUAAUGGAC	chr21:33036052-33036278(+)$1	226	36	63	21.4301
UGUAUCCGAAAGAGGAAAAUGGUUGGA	chr12:6601404-6601627(-)$1	223	74	101	22.9264
AAGAUGGCCAAGUUCUCCACGCCGGAC	chr19:13246490-13246725(+)$1	235	134	161	22.4474
GCCAAGGCACAAUCCGGUCUUGCCUUU	chr1:171553057-171553289(+)$1	232	137	164	23.4205
CGUCACCCAAAAAAAUGCACCAGGGGA	chr19:10262078-10262302(-)$1	224	149	176	22.2031
GCCUCUGUGACCACGCAGCCCACAGAA	chr22:42981784-42982026(-)$1	242	185	212	22.0741

#DB
(((((((((............))))))	chr1:110882610-110882831(+)$1	1	101	128	24.2169
(((.(((..............))).))	chr17:65941791-65942012(+)$1	1	55	82	22.0573
(...((((............)))).))	chrX:118370527-118370754(+)$1	1	101	128	23.5841
((((.((.............)).))))	chr7:5567369-5567606(-)$1	1	207	234	21.6264
(((((((((.............)))))	chr19:8528385-8528634(+)$1	1	4	31	23.9313
..(((((((...........)))))))	chr9:130674695-130674923(-)$1	1	0	27	22.7174
..((((.((.............)).))	chr6:170893340-170893573(-)$1	1	67	94	22.5441
.((((((.............)))))).	chr12:53342857-53343109(+)$1	1	73	100	20.7242
))).(((((.............)))))	chr17:7403954-7404178(+)$1	1	55	82	22.1980
.(((((((............)))))))	chr1:183520113-183520344(+)$1	1	91	118	22.8694
(((((((((............))))))	chr14:32562399-32562631(+)$1	1	10	37	24.2169
(...(((((...........))))).)	chrX:31198463-31198682(-)$1	1	134	161	23.7529
(((..((.((...........))..))	chr14:92548620-92548851(-)$1	1	58	85	20.5350
(.((.((((...........)))).))	chr1:3800120-3800368(-)$1	1	103	130	23.6798
(((((((((...........).)))))	chr17:7760282-7760517(-)$1	1	35	62	23.5968
((((..(((..............))).	chr1:47110750-47110981(-)$1	1	123	150	21.4760
(...(((((.............)))))	chr1:892489-892711(-)$1	1	135	162	23.4051
(((.(((((............))))))	chr8:37555235-37555454(+)$1	1	62	89	23.0332
..((.(((.............))).))	chr17:35634736-35634980(-)$1	1	46	73	22.8527
(((((((((............))))))	chr11:73789452-73789678(-)$1	1	67	94	24.2169
(((((((((...........)))))).	chr1:235505336-235505558(+)$1	1	180	207	23.5375
(((((.(((............))).))	chr16:53738011-53738233(-)$1	1	78	105	24.4811
.(((.((((...........)))).))	chr10:120818780-120818999(-)$1	1	64	91	23.6256
(....(((.............)))...	chr5:67593240-67593479(+)$1	1	18	45	24.2810
(....((((...........))))...	chr16:2816076-2816300(+)$1	1	75	102	24.0045
..(((((((...........)))))))	chr19:47570589-47570813(-)$1	1	16	43	24.5016
(((((((((...........)))))).	chr3:12650174-12650394(-)$1	1	143	170	23.5575
(..((((((...........).)))))	chr5:140956980-140957200(-)$1	1	131	158	24.1161
(((...(((...........))).)))	chr17:33463937-33464178(-)$1	1	189	216	23.9240
(((((((((...........)))).))	chr1:36213502-36213722(-)$1	1	76	103	22.2984
((((.((((...........)))).))	chr22:38897037-38897263(-)$1	1	39	66	23.6658
((((((.((...........))...))	chr14:21968955-21969371(-)$1	1	224	251	22.8760
((((.((((............)).)).	chr9:135982003-135982226(-)$1	1	92	119	21.9243
.....((((.............)))).	chr3:9489553-9489776(+)$1	1	114	141	22.1874
.(((((..(...........)..))))	chr19:39943999-39944224(+)$1	1	20	47	22.4699
.((((((((...........)))))).	chr7:92354958-92355198(-)$1	1	183	210	22.5069
.(((.((((............))))))	chr17:37648946-37649174(+)$1	1	157	184	23.0860
((((((((............)))))((	chr6:31627553-31627777(-)$1	1	25	52	20.1896
(((..(((............)))..))	chr6:32947605-32947854(+)$1	1	194	221	23.1398
(.((((.((............)).)))	chr21:34944794-34945019(+)$1	1	100	127	22.6106
..(((((((...........)))))))	chr11:129999889-130000113(+)$1	1	130	157	24.5650
((((.((.............)).))))	chr19:58805749-58805975(+)$1	1	49	76	21.6264
..(((.(((...........))).)))	chr3:185639768-185639998(-)$1	1	112	139	24.6069
)).((((((............))))))	chr18:24126883-24127109(-)$1	1	134	161	22.0255
.((((((((............))))))	chr17:1579454-1579689(-)$1	1	145	172	21.3058
(..((((.............)))).))	chr14:23538694-23538924(-)$1	1	132	159	22.5785
(((((((((...........)))))))	chr1:150939477-150939714(-)$1	1	91	118	24.9011
(.(((((((...........)))))))	chr15:40998302-40998577(-)$1	1	216	243	24.3880
(((((((((............))))))	chr14:21971351-21971618(+)$1	1	200	227	24.7204
((((((................)))))	chr11:8737034-8737270(+)$1	1	36	63	20.1380
(.(((((((.............)))))	chr8:41844916-41845146(-)$1	1	98	125	23.9578
)((((.(((...........))).)))	chr4:1834488-1834711(-)$1	1	79	106	23.6576
((...((((...........)))).))	chr17:42478655-42478885(-)$1	1	71	98	24.3758
(((((((..............))))))	chr11:70181574-70181800(+)$1	1	112	139	22.4042
.....((((...........)))))))	chr10:5945027-5945247(+)$1	1	179	206	22.9552
))((.((((...........)))).))	chr1:36056209-36056458(-)$1	1	64	91	23.3879
(((((((((...........)))))))	chr17:16285276-16285540(+)$1	1	108	135	24.9011
((((.(((............)))...)	chr15:52645985-52646217(-)$1	1	3	30	23.9709
...((((((............))))))	chr1:11297892-11298119(-)$1	1	167	194	20.7945
((((..(((..............))).	chr21:33036052-33036278(+)$1	1	36	63	21.4301
(.(((((((.............)))))	chr12:6601404-6601627(-)$1	1	74	101	22.9264
....((((............))))...	chr19:13246490-13246725(+)$1	1	134	161	22.4474
((.((((((...........)))))).	chr1:171553057-171553289(+)$1	1	137	164	23.4205
..((.(((..............)))))	chr19:10262078-10262302(-)$1	1	149	176	22.2031
.))((((((...........)))))).	chr22:42981784-42982026(-)$1	1	185	212	22.0741

#PSSM
d : 0.16	f : 0.13	: : 0.12	c : 0.10	i : 0.06	g : 0.06	! : 0.04	e : 0.04	b : 0.04	$ : 0.04	= : 0.04	" : 0.03	E : 0.03	& : 0.01	# : 0.01	] : 0.01	
d : 0.13	f : 0.10	" : 0.07	! : 0.07	g : 0.07	[ : 0.07	c : 0.07	i : 0.06	e : 0.04	$ : 0.04	b : 0.04	= : 0.04	: : 0.03	# : 0.03	E : 0.03	& : 0.01	h : 0.01	
d : 0.15	g : 0.15	b : 0.10	f : 0.09	c : 0.09	i : 0.06	" : 0.06	e : 0.04	$ : 0.04	= : 0.04	# : 0.03	! : 0.03	: : 0.03	E : 0.01	h : 0.01	[ : 0.01	
f : 0.16	d : 0.13	g : 0.13	" : 0.07	b : 0.07	i : 0.06	e : 0.06	c : 0.06	$ : 0.04	= : 0.04	[ : 0.03	! : 0.03	# : 0.03	: : 0.01	h : 0.01	
[ : 0.16	f : 0.15	e : 0.13	g : 0.12	d : 0.09	i : 0.06	! : 0.06	c : 0.04	= : 0.04	# : 0.03	" : 0.03	$ : 0.03	h : 0.01	
d : 0.23	f : 0.15	e : 0.13	g : 0.10	c : 0.09	i : 0.06	b : 0.06	[ : 0.04	= : 0.04	! : 0.03	" : 0.01	h : 0.01	
d : 0.20	c : 0.18	f : 0.12	e : 0.12	g : 0.10	i : 0.06	b : 0.06	[ : 0.04	= : 0.04	! : 0.01	h : 0.01	y : 0.01	
d : 0.18	c : 0.16	e : 0.12	f : 0.10	g : 0.09	i : 0.06	v : 0.06	b : 0.06	= : 0.04	w : 0.03	[ : 0.01	! : 0.01	h : 0.01	y : 0.01	
d : 0.15	f : 0.10	u : 0.09	v : 0.09	c : 0.09	g : 0.07	b : 0.07	e : 0.07	i : 0.06	w : 0.04	a : 0.04	= : 0.04	h : 0.01	y : 0.01	
t : 0.41	u : 0.27	v : 0.20	w : 0.07	b : 0.01	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
t : 0.43	u : 0.27	v : 0.20	w : 0.07	y : 0.01	
u : 0.18	d : 0.16	v : 0.13	f : 0.09	w : 0.07	g : 0.07	c : 0.07	b : 0.04	a : 0.04	e : 0.03	= : 0.03	t : 0.01	y : 0.01	
d : 0.18	c : 0.13	f : 0.12	v : 0.10	b : 0.09	g : 0.09	i : 0.04	e : 0.04	w : 0.04	= : 0.04	] : 0.03	2 : 0.01	h : 0.01	y : 0.01	
d : 0.20	c : 0.15	f : 0.13	e : 0.12	g : 0.10	i : 0.06	b : 0.06	= : 0.04	] : 0.03	w : 0.03	3 : 0.01	2 : 0.01	h : 0.01	
d : 0.23	f : 0.13	e : 0.13	c : 0.10	g : 0.10	] : 0.07	i : 0.06	= : 0.04	2 : 0.03	3 : 0.03	b : 0.01	h : 0.01	
] : 0.18	f : 0.13	e : 0.13	d : 0.12	g : 0.10	i : 0.06	c : 0.06	4 : 0.04	= : 0.04	2 : 0.03	3 : 0.03	b : 0.01	h : 0.01	
f : 0.18	c : 0.13	d : 0.13	g : 0.12	e : 0.10	b : 0.10	i : 0.06	4 : 0.04	= : 0.04	] : 0.01	h : 0.01	3 : 0.01	
d : 0.13	g : 0.13	c : 0.10	e : 0.10	f : 0.09	b : 0.09	i : 0.06	4 : 0.06	] : 0.04	= : 0.04	: : 0.03	2 : 0.03	8 : 0.01	h : 0.01	3 : 0.01	

#score	1495.9834245491566
#seq	65
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_CDS_m2_run2.txt

#BEAR
""eeeee[cccqqqqqqqqccc]eeeeed	chr17:34893429-34893666(+)$1	237	144	173	8.5661
ddd"""ffffffooooooffffffddddf	chr11:33163074-33163311(-)$1	237	128	157	9.6701
eeeee"""ddddnnnnndddd333eeeee	chr6:64289828-64290064(+)$1	236	204	233	10.7070
eeeee"""cccpppppppccc333eeeee	chr1:63884952-63885186(+)$1	234	123	152	9.9367
fffff$$$$$cccnnnnnccc22ffffff	chr4:108829724-108829954(+)$1	230	174	203	9.2640
$$$$ccc[ccclllccc]ccc333fffff	chr9:86584253-86584496(-)$1	243	193	222	8.3533
ccc[bb[eeeeeooooooeeeee]bb333	chr7:94166789-94167016(+)$1	227	38	67	9.8413
eeeebb"""cccooooooccc]bb333ee	chr5:14758562-14758791(-)$1	229	175	204	11.7909
ccc[ccc[cccqqqqqqqqccc]ccc]cc	chr8:38961084-38961386(+)$1	302	133	162	9.0501
ggggggg!!cccooooooccc>>>>>>>>	chr2:188361596-188361823(-)$1	227	115	144	11.2942
gggggggcccqqqqqqqqccc333ggggg	chr5:131008402-131008634(-)$1	232	126	155	9.6775
!ggggggg!!ddddllldddd22gggggg	chr5:86705034-86705269(-)$1	235	24	53	9.2688
ccddddffffffooooooffffff]dddd	chr6:170105105-170105331(+)$1	226	10	39	9.0080
:bb!!ccc!!bboooooobb22ccc22bb	chr1:28177069-28177295(+)$1	226	120	149	8.3972
eeee!!eeeeeccclllccc]eeeee]ee	chr8:62574384-62574646(-)$1	262	150	179	8.2875
=============mmmm============	chr19:18390706-18390940(-)$1	234	65	94	8.9198
============mmmm============>	chr7:112423936-112424159(-)$1	223	73	102	8.7033
[ffffff"""cccnnnnnccc]ffffff]	chr11:62291708-62291936(-)$1	228	154	183	9.2380
ddd!!ccc[cccnnnnncccccc]dddd:	chr13:45010577-45010808(-)$1	231	116	145	9.0988
ee####cccrrrrrrrrrccc22eeeee]	chr15:64458148-64458407(-)$1	259	21	50	10.9569
ddd[ccc!!cccooooooccc22cccddd	chr2:38523149-38523459(-)$1	310	194	223	13.6195
$$eeeee!!cccooooooccc]eeeee55	chrM:14381-14653(-)$1	272	209	238	10.7193
eeeee!!cccqqqqqqqqccc22eeeeef	chr2:198256869-198257170(-)$1	301	93	122	9.8237
eeeee"""bbrrrrrrrrrbb333eeeee	chr14:62203523-62203750(+)$1	227	59	88	10.4032
###eeeee[cccooooooccc333eeeee	chr4:123814223-123814474(+)$1	251	202	231	13.3997
e[dddd"""ddddnnnnndddd333dddd	chr2:128521990-128522277(-)$1	287	86	115	9.4949
biiiiiiiiirrrrrrrrriiiiiiiii]	chr6:122777572-122777804(-)$1	232	118	147	9.2298
!!ccc!!eeeeemmmmeeeee22ccc444	chr18:54278163-54278397(-)$1	234	122	151	8.3687
[ccc[gggggggooooooggggggg4444	chr7:91743055-91743284(-)$1	229	81	110	11.0557
eee[ccc!!cccooooooccc22ccc]ee	chr5:134192921-134193147(+)$1	226	144	173	14.0764
eeeee!!cccqqqqqqqqccc22eeeeeb	chr9:123367816-123368090(-)$1	274	166	195	9.6294
:ffffff!!cccooooooccc22ffffff	chr5:134235167-134235401(+)$1	234	1	30	11.5265
!!ccc[cccddddnnnnndddd]ccc]cc	chr9:19096605-19096838(-)$1	233	163	192	9.2336
dd####cccrrrrrrrrrccc333dddd]	chrX:48435824-48436083(+)$1	259	118	147	11.0150
d[bb[ccc[bboooooobb]ccc]bb]dd	chr1:68947115-68947340(-)$1	225	141	170	8.8843
dddiiiiiiiiiooooooiiiiiiiii::	chr2:242276798-242277025(+)$1	227	196	225	9.3807
c[ccc!!ddddoooooodddd22ccc]cc	chr12:69995124-69995392(+)$1	268	13	42	11.4974
b"""bb[eeeeeooooooeeeee]bb444	chr19:11256947-11257172(-)$1	225	126	155	9.6142
ddd[ccc!!ddddnnnnndddd]cccddd	chr5:92956669-92956901(-)$1	232	37	66	9.3745
c[dddd[eeeeeooooooeeeee]dddd]	chr1:93298970-93299204(+)$1	234	35	64	10.0673
ddd[ddddddddnnnnndddd22dddd]d	chr2:182766402-182766665(+)$1	263	152	181	8.4864
cc[eeeee[cccooooooccc333eeeee	chr2:38522989-38523244(-)$1	255	74	103	13.3983
ff[ccc"""bb[aooooooabb]cccfff	chr17:29551989-29552215(+)$1	226	53	82	9.8107

#otherMatches

#Seq PSSM
AUUAGUCUUCCUAGGAAUCGGACGAUUAG	chr17:34893429-34893666(+)$1	237	144	173	8.5661
UCAGUAUUGCAGCAUUCACUGUAGUGAUA	chr11:33163074-33163311(-)$1	237	128	157	9.6701
GUUUCAAAGAUUCCAACGGUCAUAGAAAC	chr6:64289828-64290064(+)$1	236	204	233	10.7070
CCAAGUACAUGAAAAAUCCAUUCUCUUGG	chr1:63884952-63885186(+)$1	234	123	152	9.9367
GAAGAUGCUUGGAUAAUUUCUUUUCUUUG	chr4:108829724-108829954(+)$1	230	174	203	9.2640
UUUUAUAGUGUGAAGCAGUAUUCUGGAAA	chr9:86584253-86584496(-)$1	243	193	222	8.3533
GCCUGUAGAUGGGUCCUGUUGUCAACCUC	chr7:94166789-94167016(+)$1	227	38	67	9.8413
CGCCGCCUUUCCUUUCAUGGACGCAAUGG	chr5:14758562-14758791(-)$1	229	175	204	11.7909
GAUUUUUUUAACCUUCUUUUUGCAAAUGU	chr8:38961084-38961386(+)$1	302	133	162	9.0501
UAUUUUCACUCGACAGUGCGAAGAAUUUA	chr2:188361596-188361823(-)$1	227	115	144	11.2942
AAGAUGCUCUGAACUUCAAGAAACGCAUC	chr5:131008402-131008634(-)$1	232	126	155	9.6775
UUCACAAAAUUUAACAUUUAACAUUUGUG	chr5:86705034-86705269(-)$1	235	24	53	9.2688
GCACAUAAGAGUCCACAAGCUCUUCAUGU	chr6:170105105-170105331(+)$1	226	10	39	9.0080
AGACUGCCCUGGCUCUUUCCUAGGCCUUC	chr1:28177069-28177295(+)$1	226	120	149	8.3972
UUAUUUUAUAGGUAAUUUGCAUUGUAUAU	chr8:62574384-62574646(-)$1	262	150	179	8.2875
uuuuuuuuuuuucuuuGGAAGAGAGAAGA	chr19:18390706-18390940(-)$1	234	65	94	8.9198
UUCAGUCGUUUUUGCUGGAAUGAUUGAGC	chr7:112423936-112424159(-)$1	223	73	102	8.7033
GGAUGUCAAAGGUAAAAAGCCAGAUAUUG	chr11:62291708-62291936(-)$1	228	154	183	9.2380
UUCUUGUCAUCCUUGCUGGGGACUGAAAA	chr13:45010577-45010808(-)$1	231	116	145	9.0988
UUUUAAACAACUAGAUAAUGUAUAAAUCA	chr15:64458148-64458407(-)$1	259	21	50	10.9569
CAUACCACAGGUAUUGAAGCCCCUGGGUG	chr2:38523149-38523459(-)$1	310	194	223	13.6195
GUAUCCUGAGGCAUGGGGGUCAGGGGUUG	chrM:14381-14653(-)$1	272	209	238	10.7193
AACGAUGAUAAGAACACCUAUAUUCGUUA	chr2:198256869-198257170(-)$1	301	93	122	9.8237
UACCAAUUUCUCUUGUUUUGACAGUGGUA	chr14:62203523-62203750(+)$1	227	59	88	10.4032
AGAAACUGUAUCAUCAAAGAUUUUCAGUU	chr4:123814223-123814474(+)$1	251	202	231	13.3997
AUAUGUUAGAGAUGUACUGUCUGCCGCAU	chr2:128521990-128522277(-)$1	287	86	115	9.4949
UCUCUUUACUAAUGAUCAAAGUGAAGAGU	chr6:122777572-122777804(-)$1	232	118	147	9.2298
UACUUUUAUUGGUACUCCAGUCCAGGCAA	chr18:54278163-54278397(-)$1	234	122	151	8.3687
UGAGAAAGAAUUUAAACUGAUUCUUAUAA	chr7:91743055-91743284(-)$1	229	81	110	11.0557
CAGGUGUUCCAGUGAUGCCUGACACAAUU	chr5:134192921-134193147(+)$1	226	144	173	14.0764
UUCAGAAGUUAUUCUUCCAACACCUGAAG	chr9:123367816-123368090(-)$1	274	166	195	9.6294
UUUCUUUCAGGUAUAGAAGCCAAGAAGAA	chr5:134235167-134235401(+)$1	234	1	30	11.5265
UCAAGUAAGGAAAAAUAAUUUCAUUUUCU	chr9:19096605-19096838(-)$1	233	163	192	9.2336
UAUAGUAUAUCAACCUUUUGUUUUUAAAU	chrX:48435824-48436083(+)$1	259	118	147	11.0150
UAAUGCGUAUGAUUUCCCGAAUGAGUCAA	chr1:68947115-68947340(-)$1	225	141	170	8.8843
GUGUAUUUUAAUAUAAGAAUUAAGAUAAU	chr2:242276798-242277025(+)$1	227	196	225	9.3807
UUUCUAGCAAAGUUGUGUUUGAAAGAUAC	chr12:69995124-69995392(+)$1	268	13	42	11.4974
AGUUUCACAUCUGUGACGGGAUGGGACAA	chr19:11256947-11257172(-)$1	225	126	155	9.6142
CUGGUAACCGAAUGUGUUGUUCUUUGCAG	chr5:92956669-92956901(-)$1	232	37	66	9.3745
AGACGACGAGGUACUGUCACCUUUUUGUG	chr1:93298970-93299204(+)$1	234	35	64	10.0673
CAAGUCUCCGGGACGCCCCUGCAGAGAAU	chr2:182766402-182766665(+)$1	263	152	181	8.4864
AGGUGUCUCAUCAUGCCAGAUUAAAGACA	chr2:38522989-38523244(-)$1	255	74	103	13.3983
ACUCAAAUAAGUGUUUAUUCCUCUUGGUU	chr17:29551989-29552215(+)$1	226	53	82	9.8107

#DB
..(((((.(((........))).))))))	chr17:34893429-34893666(+)$1	1	144	173	8.5661
(((...((((((......)))))))))))	chr11:33163074-33163311(-)$1	1	128	157	9.6701
(((((...((((.....))))...)))))	chr6:64289828-64290064(+)$1	1	204	233	10.7070
(((((...(((.......)))...)))))	chr1:63884952-63885186(+)$1	1	123	152	9.9367
(((((.....(((.....)))..))))))	chr4:108829724-108829954(+)$1	1	174	203	9.2640
....(((.(((...))).)))...)))))	chr9:86584253-86584496(-)$1	1	193	222	8.3533
(((.((.(((((......))))).))...	chr7:94166789-94167016(+)$1	1	38	67	9.8413
((((((...(((......))).))...))	chr5:14758562-14758791(-)$1	1	175	204	11.7909
(((.(((.(((........))).))).))	chr8:38961084-38961386(+)$1	1	133	162	9.0501
(((((((..(((......)))........	chr2:188361596-188361823(-)$1	1	115	144	11.2942
((((((((((........)))...)))))	chr5:131008402-131008634(-)$1	1	126	155	9.6775
.(((((((..((((...))))..))))))	chr5:86705034-86705269(-)$1	1	24	53	9.2688
((((((((((((......)))))).))))	chr6:170105105-170105331(+)$1	1	10	39	9.0080
.((..(((..((......))..)))..))	chr1:28177069-28177295(+)$1	1	120	149	8.3972
((((..((((((((...))).))))).))	chr8:62574384-62574646(-)$1	1	150	179	8.2875
(((((((((((((....))))))))))))	chr19:18390706-18390940(-)$1	1	65	94	8.9198
((((((((((((....)))))))))))).	chr7:112423936-112424159(-)$1	1	73	102	8.7033
.((((((...(((.....))).)))))).	chr11:62291708-62291936(-)$1	1	154	183	9.2380
(((..(((.(((.....)))))).)))).	chr13:45010577-45010808(-)$1	1	116	145	9.0988
((....(((.........)))..))))).	chr15:64458148-64458407(-)$1	1	21	50	10.9569
(((.(((..(((......)))..))))))	chr2:38523149-38523459(-)$1	1	194	223	13.6195
..(((((..(((......))).)))))..	chrM:14381-14653(-)$1	1	209	238	10.7193
(((((..(((........)))..)))))(	chr2:198256869-198257170(-)$1	1	93	122	9.8237
(((((...((.........))...)))))	chr14:62203523-62203750(+)$1	1	59	88	10.4032
...(((((.(((......)))...)))))	chr4:123814223-123814474(+)$1	1	202	231	13.3997
(.((((...((((.....))))...))))	chr2:128521990-128522277(-)$1	1	86	115	9.4949
((((((((((.........))))))))).	chr6:122777572-122777804(-)$1	1	118	147	9.2298
..(((..(((((....)))))..)))...	chr18:54278163-54278397(-)$1	1	122	151	8.3687
.(((.(((((((......)))))))....	chr7:91743055-91743284(-)$1	1	81	110	11.0557
(((.(((..(((......)))..))).))	chr5:134192921-134193147(+)$1	1	144	173	14.0764
(((((..(((........)))..)))))(	chr9:123367816-123368090(-)$1	1	166	195	9.6294
.((((((..(((......)))..))))))	chr5:134235167-134235401(+)$1	1	1	30	11.5265
..(((.(((((((.....)))).))).))	chr9:19096605-19096838(-)$1	1	163	192	9.2336
((....(((.........)))...)))).	chrX:48435824-48436083(+)$1	1	118	147	11.0150
(.((.(((.((......)).))).)).))	chr1:68947115-68947340(-)$1	1	141	170	8.8843
)))(((((((((......)))))))))..	chr2:242276798-242277025(+)$1	1	196	225	9.3807
(.(((..((((......))))..))).))	chr12:69995124-69995392(+)$1	1	13	42	11.4974
(...((.(((((......))))).))...	chr19:11256947-11257172(-)$1	1	126	155	9.6142
(((.(((..((((.....)))).))))))	chr5:92956669-92956901(-)$1	1	37	66	9.3745
(.((((.(((((......))))).)))).	chr1:93298970-93299204(+)$1	1	35	64	10.0673
(((.((((((((.....))))..)))).)	chr2:182766402-182766665(+)$1	1	152	181	8.4864
((.(((((.(((......)))...)))))	chr2:38522989-38523244(-)$1	1	74	103	13.3983
((.(((...((.(......))).))))))	chr17:29551989-29552215(+)$1	1	53	82	9.8107

#PSSM
e : 0.23	d : 0.18	c : 0.13	! : 0.06	f : 0.04	$ : 0.04	g : 0.04	: : 0.04	= : 0.04	[ : 0.04	b : 0.04	" : 0.02	# : 0.02	
e : 0.20	d : 0.16	c : 0.11	f : 0.09	[ : 0.09	g : 0.06	" : 0.04	$ : 0.04	= : 0.04	! : 0.04	b : 0.02	# : 0.02	i : 0.02	
e : 0.23	d : 0.20	c : 0.13	f : 0.06	g : 0.06	# : 0.06	b : 0.04	= : 0.04	[ : 0.04	$ : 0.02	i : 0.02	" : 0.02	
e : 0.25	[ : 0.13	c : 0.11	f : 0.06	g : 0.06	d : 0.06	" : 0.04	! : 0.04	= : 0.04	# : 0.04	i : 0.04	$ : 0.02	b : 0.02	
e : 0.20	c : 0.20	d : 0.09	f : 0.06	b : 0.06	g : 0.06	! : 0.06	= : 0.04	# : 0.04	i : 0.04	[ : 0.04	" : 0.02	
c : 0.20	! : 0.11	e : 0.09	" : 0.09	g : 0.09	d : 0.09	b : 0.06	= : 0.04	f : 0.04	# : 0.04	i : 0.04	$ : 0.02	[ : 0.02	
c : 0.25	" : 0.13	e : 0.11	f : 0.09	g : 0.09	! : 0.09	[ : 0.06	= : 0.04	i : 0.04	$ : 0.02	d : 0.02	
c : 0.20	" : 0.16	e : 0.16	! : 0.13	[ : 0.06	f : 0.04	g : 0.04	= : 0.04	i : 0.04	d : 0.04	$ : 0.02	
c : 0.23	! : 0.18	e : 0.11	" : 0.09	[ : 0.09	d : 0.06	f : 0.04	= : 0.04	i : 0.04	$ : 0.02	b : 0.02	g : 0.02	
c : 0.37	d : 0.13	e : 0.11	b : 0.06	f : 0.04	! : 0.04	= : 0.04	r : 0.04	i : 0.04	$ : 0.02	" : 0.02	g : 0.02	
c : 0.34	d : 0.16	e : 0.11	r : 0.09	q : 0.06	b : 0.06	f : 0.04	= : 0.04	g : 0.02	i : 0.02	
c : 0.27	d : 0.13	q : 0.11	e : 0.09	r : 0.09	f : 0.04	= : 0.04	o : 0.04	p : 0.02	l : 0.02	b : 0.02	g : 0.02	i : 0.02	[ : 0.02	
o : 0.41	q : 0.11	d : 0.09	r : 0.09	n : 0.06	c : 0.06	m : 0.04	p : 0.02	l : 0.02	= : 0.02	a : 0.02	
o : 0.44	n : 0.18	q : 0.11	r : 0.09	m : 0.06	p : 0.02	l : 0.02	d : 0.02	c : 0.02	
o : 0.44	n : 0.18	q : 0.11	r : 0.09	m : 0.06	l : 0.04	p : 0.02	c : 0.02	
o : 0.44	n : 0.18	q : 0.11	r : 0.09	m : 0.06	l : 0.04	p : 0.02	c : 0.02	
o : 0.44	n : 0.18	q : 0.11	r : 0.09	l : 0.04	p : 0.02	c : 0.02	m : 0.02	= : 0.02	e : 0.02	
o : 0.39	q : 0.11	n : 0.11	d : 0.09	r : 0.09	c : 0.04	= : 0.04	p : 0.02	] : 0.02	e : 0.02	b : 0.02	
c : 0.44	d : 0.16	e : 0.09	q : 0.04	f : 0.04	b : 0.04	= : 0.04	r : 0.04	g : 0.02	i : 0.02	o : 0.02	
c : 0.48	d : 0.16	e : 0.09	f : 0.04	b : 0.04	= : 0.04	i : 0.04	g : 0.02	] : 0.02	a : 0.02	
c : 0.48	d : 0.16	e : 0.09	f : 0.04	= : 0.04	b : 0.04	i : 0.04	2 : 0.02	] : 0.02	g : 0.02	
2 : 0.27	3 : 0.18	c : 0.09	e : 0.09	] : 0.06	d : 0.06	f : 0.04	= : 0.04	i : 0.04	> : 0.02	g : 0.02	b : 0.02	
2 : 0.25	3 : 0.20	] : 0.11	e : 0.11	f : 0.06	c : 0.06	= : 0.04	i : 0.04	b : 0.02	> : 0.02	g : 0.02	
3 : 0.20	c : 0.20	e : 0.13	f : 0.11	] : 0.11	g : 0.04	= : 0.04	i : 0.04	b : 0.02	> : 0.02	d : 0.02	
e : 0.25	c : 0.20	d : 0.11	f : 0.09	b : 0.06	g : 0.06	3 : 0.04	= : 0.04	i : 0.04	> : 0.02	] : 0.02	
e : 0.25	c : 0.18	d : 0.16	f : 0.09	b : 0.06	g : 0.04	= : 0.04	i : 0.04	3 : 0.02	> : 0.02	2 : 0.02	4 : 0.02	
e : 0.23	d : 0.20	] : 0.13	f : 0.11	4 : 0.06	3 : 0.04	g : 0.04	= : 0.04	i : 0.04	> : 0.02	2 : 0.02	
e : 0.27	d : 0.20	f : 0.11	c : 0.06	4 : 0.06	g : 0.04	= : 0.04	3 : 0.02	> : 0.02	b : 0.02	5 : 0.02	i : 0.02	: : 0.02	] : 0.02	
e : 0.18	d : 0.16	f : 0.13	] : 0.11	c : 0.06	4 : 0.06	> : 0.04	g : 0.04	b : 0.04	: : 0.04	3 : 0.02	= : 0.02	5 : 0.02	

#score	432.1407283544649
#seq	43
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_UTR_m3_run1.txt

#BEAR
fffffooooooffff	chr15:72877560-72877822(+)$1	262	135	150	10.8753
fffffooooooffff	chr17:80576862-80577079(-)$1	217	52	67	10.8753
gggggoooooogggg	chr19:49464553-49464769(+)$1	216	68	83	10.5363
#ddddoooooodddd	chr12:93803647-93803868(-)$1	221	46	61	10.1097
fffffooooooffff	chr8:101534112-101534333(-)$1	221	20	35	10.8753
eeeeeooooooeeee	chr3:176740107-176740332(-)$1	225	195	210	12.0715
a[cccooooooccca	chr3:98235318-98235548(-)$1	230	44	59	10.3064
c[cccooooooccc]	chr7:123324447-123324673(-)$1	226	85	100	10.4320
%ddddoooooodddd	chr3:44636848-44637078(-)$1	230	121	136	9.4845
ddcccooooooccc2	chr5:41918551-41918776(+)$1	225	99	114	10.0432
[ddddoooooodddd	chr7:73644009-73644239(+)$1	230	21	36	10.2807
eddddoooooodddd	chrX:62569290-62569516(-)$1	226	155	170	10.4216
gggggoooooogggg	chr17:73773799-73774029(-)$1	230	5	20	10.5363
""cccooooooccc]	chr2:74330278-74330502(+)$1	224	165	180	10.1874
eeeeeooooooeeee	chr2:173460734-173460957(+)$1	223	173	188	12.0715
eeeeeooooooeeee	chr21:34809243-34809469(+)$1	226	195	210	12.0715
a[cccooooooccca	chr12:129278046-129278269(-)$1	223	187	202	10.3064
[ddddoooooodddd	chr11:64083926-64084156(+)$1	230	109	124	10.2807
eeeeeooooooeeee	chr7:139255260-139255490(-)$1	230	59	74	12.0715
eeeeeooooooeeee	chr4:40427277-40427498(-)$1	221	158	173	12.0715
fffffooooooffff	chr19:12574314-12574537(-)$1	223	56	71	10.8753
fffffooooooffff	chr15:75219106-75219326(-)$1	220	5	20	10.8753
eeeeeooooooeeee	chr19:21366742-21366973(+)$1	231	27	42	12.0715
gggggoooooogggg	chr1:78414307-78414525(-)$1	218	172	187	10.5363
fffffooooooffff	chr12:121136879-121137101(+)$1	222	40	55	10.8753
eeeeeooooooeeee	chr1:35447364-35447584(-)$1	220	110	125	12.0715
ee[bboooooobb]e	chr22:38879810-38880040(-)$1	230	99	114	9.6205
eeeeeooooooeeee	chr1:225590809-225591031(-)$1	222	202	217	12.0715
b[cccoooooocccb	chr9:25676955-25677177(-)$1	222	81	96	9.8115
eeeeeooooooeeee	chr3:124684558-124684788(-)$1	230	186	201	12.0715
eeeeeooooooeeee	chr6:107017342-107017595(+)$1	253	11	26	12.0715
fffffooooooffff	chrX:100881782-100882003(+)$1	221	51	66	10.8753
[ddddoooooodddd	chr15:74890338-74890568(+)$1	230	169	184	10.2807
dddddoooooodddd	chr6:149731016-149731236(+)$1	220	99	114	10.1290
fffffooooooffff	chr16:84157160-84157390(-)$1	230	124	139	10.8753
eeeeeooooooeeee	chr5:112349522-112349741(+)$1	219	22	37	12.0715
eeeeeooooooeeee	chr10:112657961-112658181(+)$1	220	199	214	12.0715
eeeeeooooooeeee	chr10:70451843-70452079(+)$1	236	209	224	12.0715
eee[aooooooaeee	chr13:25907609-25907839(+)$1	230	28	43	11.3543
fffffooooooffff	chr17:61889222-61889452(+)$1	230	24	39	10.8753
fffffooooooffff	chr19:40029654-40029874(-)$1	220	150	165	10.8753
eeeeeooooooeeee	chr19:4045125-4045338(-)$1	213	0	15	12.0715
eeeeeooooooeeee	chr11:72549503-72549733(-)$1	230	147	162	12.0715
eeeeeooooooeeee	chr1:33066257-33066487(+)$1	230	43	58	12.0715
fffffooooooffff	chr17:28853217-28853435(+)$1	218	124	139	10.8753
eeeeeooooooeeee	chr11:16777541-16777771(+)$1	230	202	217	12.0715
cccccooooooccc]	chr13:79173423-79173649(-)$1	226	157	172	10.3213
c[cccooooooccc]	chr9:112933930-112934160(+)$1	230	116	131	10.4320
fffffooooooffff	chr21:34809673-34809899(+)$1	226	95	110	10.8753
ddcccooooooccc3	chr20:43571093-43571311(-)$1	218	116	131	10.2499
eeeeeooooooeeee	chr1:150549357-150549584(-)$1	227	76	91	12.0715
eeeeeooooooeeee	chr3:195777303-195777528(-)$1	225	61	76	12.0715
!ddddoooooodddd	chr12:31539536-31539766(-)$1	230	158	173	10.2447
eeeeeooooooeeee	chr1:192548368-192548591(+)$1	223	88	103	12.0715
fff[aooooooa]ff	chr16:30615086-30615307(-)$1	221	22	37	10.3836
eeeeeooooooeeee	chr17:80559277-80559500(+)$1	223	124	139	12.0715
fffffooooooffff	chr3:179504457-179504687(+)$1	230	140	155	10.8753
eeeeeooooooeeee	chr12:117154487-117154707(-)$1	220	158	173	12.0715
eeeeeooooooeeee	chr9:4586035-4586280(+)$1	245	205	220	12.0715

#otherMatches

#Seq PSSM
UAUUUUACUUCAAAU	chr15:72877560-72877822(+)$1	262	135	150	10.8753
AAACACUUCACUGUU	chr17:80576862-80577079(-)$1	217	52	67	10.8753
gugugagccaccaug	chr19:49464553-49464769(+)$1	216	68	83	10.5363
AUAUUUAAAUUGAUA	chr12:93803647-93803868(-)$1	221	46	61	10.1097
UGAAGUACUUUUUUC	chr8:101534112-101534333(-)$1	221	20	35	10.8753
UUGAAUUCUGUUUUA	chr3:176740107-176740332(-)$1	225	195	210	12.0715
GAGCAAGAAACUGCC	chr3:98235318-98235548(-)$1	230	44	59	10.3064
ugaGUGGGAAGACUG	chr7:123324447-123324673(-)$1	226	85	100	10.4320
uggcauuaaauuguc	chr3:44636848-44637078(-)$1	230	121	136	9.4845
AUUAAUCCUAUUUAU	chr5:41918551-41918776(+)$1	225	99	114	10.0432
AGCUGAUUAAACAGU	chr7:73644009-73644239(+)$1	230	21	36	10.2807
AGCUGAAUACACAGU	chrX:62569290-62569516(-)$1	226	155	170	10.4216
UAGUAGUAAAAUGCU	chr17:73773799-73774029(-)$1	230	5	20	10.5363
GCAGGUCACAUCCUA	chr2:74330278-74330502(+)$1	224	165	180	10.1874
UUGAACAUAUUUUUA	chr2:173460734-173460957(+)$1	223	173	188	12.0715
UUUUUUUUCUUAAAG	chr21:34809243-34809469(+)$1	226	195	210	12.0715
GAGUCAUUUGAGACC	chr12:129278046-129278269(-)$1	223	187	202	10.3064
CAAUAACACUAUAUU	chr11:64083926-64084156(+)$1	230	109	124	10.2807
GUGUUUGUAGUGAUA	chr7:139255260-139255490(-)$1	230	59	74	12.0715
CCAUGUAUCAUCAUG	chr4:40427277-40427498(-)$1	221	158	173	12.0715
gugugagccaccaca	chr19:12574314-12574537(-)$1	223	56	71	10.8753
auCAUACAUCAGUGA	chr15:75219106-75219326(-)$1	220	5	20	10.8753
UUAUUAAACAAAAUA	chr19:21366742-21366973(+)$1	231	27	42	12.0715
GUUUUUGGUUUAAAA	chr1:78414307-78414525(-)$1	218	172	187	10.5363
AAGGGGUGGGAUUCU	chr12:121136879-121137101(+)$1	222	40	55	10.8753
UGUUACCAGUAUAAU	chr1:35447364-35447584(-)$1	220	110	125	12.0715
GUAAUCAUAAAAUAA	chr22:38879810-38880040(-)$1	230	99	114	9.6205
UUGUAUUAACUUACA	chr1:225590809-225591031(-)$1	222	202	217	12.0715
AUGCCUGUCUUGGCU	chr9:25676955-25677177(-)$1	222	81	96	9.8115
CUGGCGUUCUAGUCA	chr3:124684558-124684788(-)$1	230	186	201	12.0715
ucccaaaaugcuggg	chr6:107017342-107017595(+)$1	253	11	26	12.0715
GCUGGGUGAAGCCAG	chrX:100881782-100882003(+)$1	221	51	66	10.8753
ACUGGACAGUACUGG	chr15:74890338-74890568(+)$1	230	169	184	10.2807
UGUCCCAUUAUGGAU	chr6:149731016-149731236(+)$1	220	99	114	10.1290
UUAUUGAUAGAAAUA	chr16:84157160-84157390(-)$1	230	124	139	10.8753
CAAUAAUAGUAUAUU	chr5:112349522-112349741(+)$1	219	22	37	12.0715
UCCUUUCUUUCAAGG	chr10:112657961-112658181(+)$1	220	199	214	12.0715
UGCUAGAAAAUUGGC	chr10:70451843-70452079(+)$1	236	209	224	12.0715
ACAACCUUACAGUGU	chr13:25907609-25907839(+)$1	230	28	43	11.3543
GUGGCUCCAAUGUCA	chr17:61889222-61889452(+)$1	230	24	39	10.8753
UUUUAUAAAAUUGAG	chr19:40029654-40029874(-)$1	220	150	165	10.8753
GCUUGAACACCCAGG	chr19:4045125-4045338(-)$1	213	0	15	12.0715
GAGGGGGGCAGCCCU	chr11:72549503-72549733(-)$1	230	147	162	12.0715
AGAGAUACCUUUUUC	chr1:33066257-33066487(+)$1	230	43	58	12.0715
UUUCAUUUCACUGAA	chr17:28853217-28853435(+)$1	218	124	139	10.8753
UCACACCUGUUUGUG	chr11:16777541-16777771(+)$1	230	202	217	12.0715
CCUGAAAUGUCUCAC	chr13:79173423-79173649(-)$1	226	157	172	10.3213
AAAAUGUUUAGAUUC	chr9:112933930-112934160(+)$1	230	116	131	10.4320
UAAGAUUUUGUUUUU	chr21:34809673-34809899(+)$1	226	95	110	10.8753
CCCAGUGCCUUCUGU	chr20:43571093-43571311(-)$1	218	116	131	10.2499
AGUCAUAGAAUUGAU	chr1:150549357-150549584(-)$1	227	76	91	12.0715
GGGAGCAGUGUCUUC	chr3:195777303-195777528(-)$1	225	61	76	12.0715
AGGGUCUAAUCACCC	chr12:31539536-31539766(-)$1	230	158	173	10.2447
UCCCUGGCUGAAGGG	chr1:192548368-192548591(+)$1	223	88	103	12.0715
UCUGUCCACACAGGG	chr16:30615086-30615307(-)$1	221	22	37	10.3836
UAUCAACUCUGUGGU	chr17:80559277-80559500(+)$1	223	124	139	12.0715
AUGGUGGUCUAAUUG	chr3:179504457-179504687(+)$1	230	140	155	10.8753
AGAAACCCAGCUUUC	chr12:117154487-117154707(-)$1	220	158	173	12.0715
auUAUUUUCAUAUAA	chr9:4586035-4586280(+)$1	245	205	220	12.0715

#DB
(((((......))))	chr15:72877560-72877822(+)$1	1	135	150	10.8753
(((((......))))	chr17:80576862-80577079(-)$1	1	52	67	10.8753
(((((......))))	chr19:49464553-49464769(+)$1	1	68	83	10.5363
.((((......))))	chr12:93803647-93803868(-)$1	1	46	61	10.1097
(((((......))))	chr8:101534112-101534333(-)$1	1	20	35	10.8753
(((((......))))	chr3:176740107-176740332(-)$1	1	195	210	12.0715
(.(((......))))	chr3:98235318-98235548(-)$1	1	44	59	10.3064
(.(((......))).	chr7:123324447-123324673(-)$1	1	85	100	10.4320
.((((......))))	chr3:44636848-44637078(-)$1	1	121	136	9.4845
(((((......))).	chr5:41918551-41918776(+)$1	1	99	114	10.0432
.((((......))))	chr7:73644009-73644239(+)$1	1	21	36	10.2807
(((((......))))	chrX:62569290-62569516(-)$1	1	155	170	10.4216
(((((......))))	chr17:73773799-73774029(-)$1	1	5	20	10.5363
..(((......))).	chr2:74330278-74330502(+)$1	1	165	180	10.1874
(((((......))))	chr2:173460734-173460957(+)$1	1	173	188	12.0715
(((((......))))	chr21:34809243-34809469(+)$1	1	195	210	12.0715
(.(((......))))	chr12:129278046-129278269(-)$1	1	187	202	10.3064
.((((......))))	chr11:64083926-64084156(+)$1	1	109	124	10.2807
(((((......))))	chr7:139255260-139255490(-)$1	1	59	74	12.0715
(((((......))))	chr4:40427277-40427498(-)$1	1	158	173	12.0715
(((((......))))	chr19:12574314-12574537(-)$1	1	56	71	10.8753
(((((......))))	chr15:75219106-75219326(-)$1	1	5	20	10.8753
(((((......))))	chr19:21366742-21366973(+)$1	1	27	42	12.0715
(((((......))))	chr1:78414307-78414525(-)$1	1	172	187	10.5363
(((((......))))	chr12:121136879-121137101(+)$1	1	40	55	10.8753
(((((......))))	chr1:35447364-35447584(-)$1	1	110	125	12.0715
((.((......)).)	chr22:38879810-38880040(-)$1	1	99	114	9.6205
(((((......))))	chr1:225590809-225591031(-)$1	1	202	217	12.0715
(.(((......))))	chr9:25676955-25677177(-)$1	1	81	96	9.8115
(((((......))))	chr3:124684558-124684788(-)$1	1	186	201	12.0715
(((((......))))	chr6:107017342-107017595(+)$1	1	11	26	12.0715
(((((......))))	chrX:100881782-100882003(+)$1	1	51	66	10.8753
.((((......))))	chr15:74890338-74890568(+)$1	1	169	184	10.2807
)((((......))))	chr6:149731016-149731236(+)$1	1	99	114	10.1290
(((((......))))	chr16:84157160-84157390(-)$1	1	124	139	10.8753
(((((......))))	chr5:112349522-112349741(+)$1	1	22	37	12.0715
(((((......))))	chr10:112657961-112658181(+)$1	1	199	214	12.0715
(((((......))))	chr10:70451843-70452079(+)$1	1	209	224	12.0715
(((.(......))))	chr13:25907609-25907839(+)$1	1	28	43	11.3543
(((((......))))	chr17:61889222-61889452(+)$1	1	24	39	10.8753
(((((......))))	chr19:40029654-40029874(-)$1	1	150	165	10.8753
(((((......))))	chr19:4045125-4045338(-)$1	1	0	15	12.0715
(((((......))))	chr11:72549503-72549733(-)$1	1	147	162	12.0715
(((((......))))	chr1:33066257-33066487(+)$1	1	43	58	12.0715
(((((......))))	chr17:28853217-28853435(+)$1	1	124	139	10.8753
(((((......))))	chr11:16777541-16777771(+)$1	1	202	217	12.0715
(((((......))).	chr13:79173423-79173649(-)$1	1	157	172	10.3213
(.(((......))).	chr9:112933930-112934160(+)$1	1	116	131	10.4320
(((((......))))	chr21:34809673-34809899(+)$1	1	95	110	10.8753
(((((......))).	chr20:43571093-43571311(-)$1	1	116	131	10.2499
(((((......))))	chr1:150549357-150549584(-)$1	1	76	91	12.0715
(((((......))))	chr3:195777303-195777528(-)$1	1	61	76	12.0715
.((((......))))	chr12:31539536-31539766(-)$1	1	158	173	10.2447
(((((......))))	chr1:192548368-192548591(+)$1	1	88	103	12.0715
(((.(......).))	chr16:30615086-30615307(-)$1	1	22	37	10.3836
(((((......))))	chr17:80559277-80559500(+)$1	1	124	139	12.0715
(((((......))))	chr3:179504457-179504687(+)$1	1	140	155	10.8753
(((((......))))	chr12:117154487-117154707(-)$1	1	158	173	12.0715
(((((......))))	chr9:4586035-4586280(+)$1	1	205	220	12.0715

#PSSM
e : 0.44	f : 0.23	g : 0.05	c : 0.05	d : 0.05	[ : 0.05	a : 0.03	# : 0.01	% : 0.01	" : 0.01	b : 0.01	! : 0.01	
e : 0.42	f : 0.23	d : 0.16	[ : 0.08	g : 0.05	" : 0.01	c : 0.01	
e : 0.40	f : 0.23	c : 0.15	d : 0.13	g : 0.05	[ : 0.01	
e : 0.38	f : 0.22	c : 0.15	d : 0.13	g : 0.05	[ : 0.03	b : 0.01	
e : 0.38	f : 0.22	c : 0.15	d : 0.13	g : 0.05	a : 0.03	b : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
e : 0.38	f : 0.22	c : 0.15	d : 0.13	g : 0.05	a : 0.03	b : 0.01	
e : 0.40	f : 0.22	c : 0.15	d : 0.13	g : 0.05	b : 0.01	] : 0.01	
e : 0.40	f : 0.23	c : 0.15	d : 0.13	g : 0.05	] : 0.01	
e : 0.42	f : 0.23	d : 0.13	] : 0.06	g : 0.05	a : 0.03	2 : 0.01	b : 0.01	3 : 0.01	

#score	655.3150341325892
#seq	59
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_UTR_m1_run2.txt

#BEAR
eeee!!ccctttttttttttccc22eee	chr3:88103788-88104009(-)$1	221	98	126	23.0569
d[ggggggguuuuuuuuuuuuggggggg	chr5:32354385-32354635(-)$1	250	155	183	24.8475
eeffffffvvvvvvvvvvvvvffffff]	chr1:6245136-6245368(-)$1	232	14	42	24.1949
ccc[eeeeevvvvvvvvvvvvveeeee]	chr1:227847269-227847520(+)$1	251	94	122	24.7123
fffffffffwwwwwwwwwwwwwwfffff	chr10:93043830-93044061(+)$1	231	91	119	23.0819
dddd[cccwwwwwwwwwwwwwwcccddd	chr1:31405073-31405301(-)$1	228	34	62	22.6320
ccc!!cccxxxxxxxxxxxxxxxccc]c	chr13:79888149-79888379(-)$1	230	69	97	18.6726
dddd[eeeeettttttttttteeeee]d	chr15:75759512-75759800(-)$1	288	214	242	23.0031
FFF:eeeeettttttttttteeeeefff	chr15:41673013-41673245(+)$1	232	91	119	21.1571
eeeeeeeeexxxxxxxxxxxxxxxeeee	chr17:57771974-57772216(+)$1	242	43	71	19.0247
"a[fffffftttttttttttffffff]a	chr6:17616076-17616347(-)$1	271	29	57	22.4933
eee!!ddddtttttttttttddddeeee	chr11:32998548-32998809(+)$1	261	118	146	22.5098
ggggggggguuuuuuuuuuuuggggggg	chr16:19513018-19513256(-)$1	238	29	57	24.9497
ffff!!ccctttttttttttccc22fff	chr18:57570375-57570604(+)$1	229	66	94	22.8495
HHHffffffuuuuuuuuuuuuffffff:	chr16:70608320-70608558(+)$1	238	62	90	21.5101
[ffffffwwwwwwwwwwwwwwffffff]	chr21:38123463-38123700(-)$1	237	173	201	23.4938
eeee[dddduuuuuuuuuuuuddddeee	chr10:112045937-112046165(+)$1	228	39	67	24.0784
e[ffffffvvvvvvvvvvvvvffffff]	chr1:218505277-218505521(+)$1	244	58	86	24.2351
f!!bb!!bbuuuuuuuuuuuubb22bb]	chr1:67875750-67875970(-)$1	220	110	138	22.4924
gggggggyyyyyyyyyyyyyyyyggggg	chr15:42706120-42706361(-)$1	241	143	171	22.4701
eeee"""avvvvvvvvvvvvva333eee	chr5:71502617-71502828(+)$1	211	22	50	24.1487
ddd[fffffftttttttttttffffff]	chr8:81432027-81432272(+)$1	245	182	210	22.4641
gggggggxxxxxxxxxxxxxxxgggggg	chr15:64977966-64978202(+)$1	236	30	58	19.3780
dffffff[attttttttttta]ffffff	chr16:24836799-24837053(+)$1	254	185	213	23.1869
qccceeeeevvvvvvvvvvvvveeeee:	chr10:65382714-65383015(+)$1	301	209	237	22.8156
[ffffffwwwwwwwwwwwwwwffffff]	chr4:42112902-42113153(-)$1	251	214	242	23.4938
gggggggwwwwwwwwwwwwwwggggggg	chr6:86318791-86319003(-)$1	212	26	54	23.7193
[bbgggggggtttttttttttggggggg	chr5:81571567-81571791(-)$1	224	98	126	22.4369
###eeeeevvvvvvvvvvvvveeeeegg	chr14:34903871-34904100(-)$1	229	17	45	24.4833
ffff[cccvvvvvvvvvvvvvccc]fff	chr1:185265881-185266110(-)$1	229	194	222	24.2548
::ggggggguuuuuuuuuuuuggggggg	chr7:138983989-138984244(+)$1	255	15	43	22.8586
eeee[cccwwwwwwwwwwwwwwccc]ee	chr7:25162392-25162618(-)$1	226	25	53	23.6407
$$$$eeeeeuuuuuuuuuuuueeeee55	chr18:19447319-19447560(+)$1	241	199	227	22.3910
dddd[cccvvvvvvvvvvvvvccc]ddd	chr1:27107624-27107857(+)$1	233	87	115	23.2553
!!ggggggguuuuuuuuuuuuggggggg	chr19:1257810-1258036(+)$1	226	101	129	25.0098
ffdddd[bbuuuuuuuuuuuubb]dddd	chr20:42090842-42091094(+)$1	252	151	179	22.7163
fff!!dddduuuuuuuuuuuudddd444	chr17:45760832-45761055(+)$1	223	113	141	23.5652
eccc!!bbvvvvvvvvvvvvvbb22ccc	chr12:124499555-124499800(+)$1	245	205	233	22.7590
eeeeeeeeeettttttttttteeeee22	chr3:152182185-152182408(+)$1	223	159	187	23.1483
ffffeeeeeuuuuuuuuuuuueeeee:G	chr1:120457491-120457729(-)$1	238	143	171	23.5448
ffccc[cccuuuuuuuuuuuuccc]ccc	chr6:17609077-17609300(+)$1	223	54	82	24.1837
=========wwwwwwwwwwwwww=====	chr6:150132334-150132562(+)$1	228	149	177	23.7324
#eeeee[bbtttttttttttbb]eeeee	chr3:160218647-160218877(-)$1	230	96	124	22.8071
heeeee[bbtttttttttttbb]eeeee	chr4:177250264-177250496(+)$1	232	91	119	22.6367
[gggggggvvvvvvvvvvvvvggggggg	chr4:57259921-57260155(-)$1	234	3	31	24.5962
ccggggggguuuuuuuuuuuuggggggg	chr17:20904771-20905007(-)$1	236	127	155	24.7951
ee!!eeeeewwwwwwwwwwwwwweeeee	chrX:37698257-37698496(-)$1	239	159	187	23.9664
==========ttttttttttt=======	chr21:43408306-43408575(-)$1	269	196	224	23.1298
bb[ffffffuuuuuuuuuuuuffffffb	chr1:67877089-67877320(-)$1	231	194	222	23.4984
eeee[eeeeettttttttttteeeee]e	chr6:64292298-64292513(+)$1	215	148	176	23.7617
[iiiiiiiiitttttttttttiiiiiii	chr3:67061207-67061437(+)$1	230	51	79	22.5297
=========wwwwwwwwwwwwww=====	chr14:77802622-77802862(-)$1	240	163	191	23.7324
eeee[ddddvvvvvvvvvvvvvdddd]e	chr15:58246602-58246832(-)$1	230	72	100	23.4106
iiibb!!bbuuuuuuuuuuuubb22bb]	chr10:129895409-129895637(-)$1	228	91	119	22.4767
d[eeeeexxxxxxxxxxxxxxxeeeee]	chr1:47843501-47843735(+)$1	234	159	187	19.5488
e"""eeeeeuuuuuuuuuuuueeeee33	chr12:89983753-89983986(-)$1	233	24	52	25.1363
ffff[dddduuuuuuuuuuuuddddfff	chr2:32536436-32536704(+)$1	268	39	67	23.8710
eee[eeeeevvvvvvvvvvvvveeeeee	chr8:30535551-30535837(-)$1	286	104	132	24.7556
dddd[eeeeettttttttttteeeeedd	chr12:98928318-98928548(+)$1	230	70	98	22.7778
ggggeeeeexxxxxxxxxxxxxxxeeee	chr10:858330-858567(-)$1	237	62	90	19.1198
[eeeeeyyyyyyyyyyyyyyyyeeeee]	chrX:135293106-135293327(+)$1	221	172	200	22.5385
!ffffffbbtttttttttttbb]fffff	chr12:65090555-65090782(+)$1	227	30	58	22.4087
f"""eeeeeuuuuuuuuuuuueeeee33	chr10:5807549-5807784(-)$1	235	32	60	25.0725

#otherMatches

#Seq PSSM
UGAAUACUAAUUUCGAACCAUAGCUUUC	chr3:88103788-88104009(-)$1	221	98	126	23.0569
UUCAGUAAAAUCAUAUUCAAAUUUAUUG	chr5:32354385-32354635(-)$1	250	155	183	24.8475
AACCAUGAUUAUUAACUAAGUUUGUGGC	chr1:6245136-6245368(-)$1	232	14	42	24.1949
GCUAAGUUUAUGAAAAAGAUGCAGACUC	chr1:227847269-227847520(+)$1	251	94	122	24.7123
GGGCUAGAUACUUUUUUUUUUUAAUCUG	chr10:93043830-93044061(+)$1	231	91	119	23.0819
AGCAUGAGAAAAAAAAAUCCAACUCUGC	chr1:31405073-31405301(-)$1	228	34	62	22.6320
GUGUAUGUCCAAAUUAUUUAUAAGCAGU	chr13:79888149-79888379(-)$1	230	69	97	18.6726
UUCAUUUUGUAUUUAAUAUCAAUGGACU	chr15:75759512-75759800(-)$1	288	214	242	23.0031
cACCAAAUGUACUUCUUAUUCAUUUUAU	chr15:41673013-41673245(+)$1	232	91	119	21.1571
UCACUGAGUGUACAGAAGAGAGAAAUUC	chr17:57771974-57772216(+)$1	242	43	71	19.0247
UGGUGUUGUACUCAAUUUUAACAACAGC	chr6:17616076-17616347(-)$1	271	29	57	22.4933
ACUAUUUUCCCUAUCGCAAAGAAAAGUA	chr11:32998548-32998809(+)$1	261	118	146	22.5098
GGGUUGCUGGCCUCACACUUGCAGCAGC	chr16:19513018-19513256(-)$1	238	29	57	24.9497
UGAUUCGGUUUAUACAUAUUACCUUGUU	chr18:57570375-57570604(+)$1	229	66	94	22.8495
gucAUAAAuucuuguuuuuuuguuuguu	chr16:70608320-70608558(+)$1	238	62	90	21.5101
CAAGUCUACCAAAAUAAACUAAGACUUU	chr21:38123463-38123700(-)$1	237	173	201	23.4938
GAUUUGCUUCCAUUUUCCUACAGGCAGU	chr10:112045937-112046165(+)$1	228	39	67	24.0784
UUUUAUUUCCUUUCauuuauuaaauaau	chr1:218505277-218505521(+)$1	244	58	86	24.2351
CAAAGGAAUGAGAAAUAGGAAGUUACUA	chr1:67875750-67875970(-)$1	220	110	138	22.4924
UAGUAUAAAUCUUUUUGUGUACCUAUGC	chr15:42706120-42706361(-)$1	241	143	171	22.4701
GAAUAAUGAUACCUCCCACCCCUUGAUU	chr5:71502617-71502828(+)$1	211	22	50	24.1487
uuuuuauuaauuuuauuuuuUUUAAUAC	chr8:81432027-81432272(+)$1	245	182	210	22.4641
CUGGUGGACUCCUGUGGCUACCCCAUCA	chr15:64977966-64978202(+)$1	236	30	58	19.3780
CUGAGCAUCUUUGGGAUCUUGUUGCUCA	chr16:24836799-24837053(+)$1	254	185	213	23.1869
AACUGCACUUUUUCACAUUCACAGUGCU	chr10:65382714-65383015(+)$1	301	209	237	22.8156
UUUUGCAUCUUUCUAAUUCAUUGUAAAU	chr4:42112902-42113153(-)$1	251	214	242	23.4938
UCUAUUUUAAGGAGAGAAAUUAAAUAGA	chr6:86318791-86319003(-)$1	212	26	54	23.7193
CUCAUCCUGUGGAAUAAGAAAAUGGGAU	chr5:81571567-81571791(-)$1	224	98	126	22.4369
CAUUUUAAUUGCCUUCUAUUUUUAAAAC	chr14:34903871-34904100(-)$1	229	17	45	24.4833
CUUACAUCUGAAAUAAGGAAUGAUAUAA	chr1:185265881-185266110(-)$1	229	194	222	24.2548
UCUAAAUGGUAUAAGCUUCAUCCAUUUA	chr7:138983989-138984244(+)$1	255	15	43	22.8586
CAGAAACAAAACUGUAGAACUGUGUAUU	chr7:25162392-25162618(-)$1	226	25	53	23.6407
UGGUCAAAUUAUGCAUAAGAUAUUUGUA	chr18:19447319-19447560(+)$1	241	199	227	22.3910
UGUGUGUGGUUUAUUGUUGUACAUUCAC	chr1:27107624-27107857(+)$1	233	87	115	23.2553
AUUUUCCUUCAUUUCUUUAACAAGGAGA	chr19:1257810-1258036(+)$1	226	101	129	25.0098
GAGAAGUGAAUUAACCUUACAUCCCUUU	chr20:42090842-42091094(+)$1	252	151	179	22.7163
UUGCAAACAGGAUAAAUUAAAUGUUCAA	chr17:45760832-45761055(+)$1	223	113	141	23.5652
gcuaaaugauuuccgaguuuccagcuag	chr12:124499555-124499800(+)$1	245	205	233	22.7590
GAUAUUAGAAUAAAAUUUAUUUUCUACU	chr3:152182185-152182408(+)$1	223	159	187	23.1483
CAGGCUUCUGCCAUAUCCAUGAGAAGAU	chr1:120457491-120457729(-)$1	238	143	171	23.5448
ACCUGAAGUUUUCAAAUCCAUACUGCAG	chr6:17609077-17609300(+)$1	223	54	82	24.1837
GUAAGCUGUGUCCUAGUUCUUGAACAGU	chr6:150132334-150132562(+)$1	228	149	177	23.7324
CAUGAGGUAAAUCUACAGCAUAGUUCAU	chr3:160218647-160218877(-)$1	230	96	124	22.8071
UGUGGUAUGcuuuccauuuacaaaccac	chr4:177250264-177250496(+)$1	232	91	119	22.6367
UUGGUAUAUAGUCUCGCAUAUUAUAUUA	chr4:57259921-57260155(-)$1	234	3	31	24.5962
uggucucugccauaaauaguacagagau	chr17:20904771-20905007(-)$1	236	127	155	24.7951
AAUAAAGGAGUUUAAUGCAGUGAUCUUU	chrX:37698257-37698496(-)$1	239	159	187	23.9664
AAAGAAUGUAAAAUGUUUUAAUAUAUUC	chr21:43408306-43408575(-)$1	269	196	224	23.1298
CAUAUGAACUAUUGACCCAUUGUUCAUU	chr1:67877089-67877320(-)$1	231	194	222	23.4984
AAGAGUUCAAAGAGUUAUGAGUUGAAGU	chr6:64292298-64292513(+)$1	215	148	176	23.7617
AGAAUGUAUGUAGCACUUUCCUAUAUAU	chr3:67061207-67061437(+)$1	230	51	79	22.5297
AUGUACCUGAUUUUUUUAGGCCCCAGGU	chr14:77802622-77802862(-)$1	240	163	191	23.7324
UUUCUUUUACCCAUAAAUAACAUGAAUG	chr15:58246602-58246832(-)$1	230	72	100	23.4106
GAGGGAGAGAUCUGACAAAUACUGCCCA	chr10:129895409-129895637(-)$1	228	91	119	22.4767
AUGAGAUUUAAAAUCUUAAAAUGUUUCU	chr1:47843501-47843735(+)$1	234	159	187	19.5488
ACUGUUUAAUUUUUAAAAUUUUUGAAAA	chr12:89983753-89983986(-)$1	233	24	52	25.1363
GGGAAGAUGGCAGUGGUAAAACAUUUCC	chr2:32536436-32536704(+)$1	268	39	67	23.8710
agguggauucaaauacaucaaaaguccc	chr8:30535551-30535837(-)$1	286	104	132	24.7556
CUUAUGUUUUUACAAUUCUCCAAAACUA	chr12:98928318-98928548(+)$1	230	70	98	22.7778
ACUCUGCUUUUUUUUUUUUUUUUUAAGU	chr10:858330-858567(-)$1	237	62	90	19.1198
GAUUUCCACCUACCGCUUACCUGAAAUG	chrX:135293106-135293327(+)$1	221	172	200	22.5385
UAACUUCUCUUUUGUACAUUGAUGAGGU	chr12:65090555-65090782(+)$1	227	30	58	22.4087
CCAAACUGGCUUUUUUUUUUUCUAGUGA	chr10:5807549-5807784(-)$1	235	32	60	25.0725

#DB
((((..(((...........)))..)))	chr3:88103788-88104009(-)$1	1	98	126	23.0569
(.(((((((............)))))))	chr5:32354385-32354635(-)$1	1	155	183	24.8475
((((((((.............)))))).	chr1:6245136-6245368(-)$1	1	14	42	24.1949
(((.(((((.............))))).	chr1:227847269-227847520(+)$1	1	94	122	24.7123
(((((((((..............)))))	chr10:93043830-93044061(+)$1	1	91	119	23.0819
((((.(((..............))))))	chr1:31405073-31405301(-)$1	1	34	62	22.6320
(((..(((...............))).)	chr13:79888149-79888379(-)$1	1	69	97	18.6726
((((.(((((...........))))).)	chr15:75759512-75759800(-)$1	1	214	242	23.0031
(((.(((((...........)))))(((	chr15:41673013-41673245(+)$1	1	91	119	21.1571
))))(((((...............))))	chr17:57771974-57772216(+)$1	1	43	71	19.0247
.(.((((((...........)))))).)	chr6:17616076-17616347(-)$1	1	29	57	22.4933
(((..((((...........))))))))	chr11:32998548-32998809(+)$1	1	118	146	22.5098
))(((((((............)))))))	chr16:19513018-19513256(-)$1	1	29	57	24.9497
((((..(((...........)))..)))	chr18:57570375-57570604(+)$1	1	66	94	22.8495
(((((((((............)))))).	chr16:70608320-70608558(+)$1	1	62	90	21.5101
.((((((..............)))))).	chr21:38123463-38123700(-)$1	1	173	201	23.4938
((((.((((............)))))))	chr10:112045937-112046165(+)$1	1	39	67	24.0784
(.((((((.............)))))).	chr1:218505277-218505521(+)$1	1	58	86	24.2351
(..((..((............))..)).	chr1:67875750-67875970(-)$1	1	110	138	22.4924
(((((((................)))))	chr15:42706120-42706361(-)$1	1	143	171	22.4701
((((...(.............)...)))	chr5:71502617-71502828(+)$1	1	22	50	24.1487
(((.((((((...........)))))).	chr8:81432027-81432272(+)$1	1	182	210	22.4641
(((((((...............))))))	chr15:64977966-64978202(+)$1	1	30	58	19.3780
)((((((.(...........).))))))	chr16:24836799-24837053(+)$1	1	185	213	23.1869
.)))(((((.............))))).	chr10:65382714-65383015(+)$1	1	209	237	22.8156
.((((((..............)))))).	chr4:42112902-42113153(-)$1	1	214	242	23.4938
(((((((..............)))))))	chr6:86318791-86319003(-)$1	1	26	54	23.7193
.(((((((((...........)))))))	chr5:81571567-81571791(-)$1	1	98	126	22.4369
...(((((.............)))))))	chr14:34903871-34904100(-)$1	1	17	45	24.4833
((((.(((.............))).)))	chr1:185265881-185266110(-)$1	1	194	222	24.2548
..(((((((............)))))))	chr7:138983989-138984244(+)$1	1	15	43	22.8586
((((.(((..............))).))	chr7:25162392-25162618(-)$1	1	25	53	23.6407
....(((((............)))))..	chr18:19447319-19447560(+)$1	1	199	227	22.3910
((((.(((.............))).)))	chr1:27107624-27107857(+)$1	1	87	115	23.2553
..(((((((............)))))))	chr19:1257810-1258036(+)$1	1	101	129	25.0098
((((((.((............)).))))	chr20:42090842-42091094(+)$1	1	151	179	22.7163
(((..((((............))))...	chr17:45760832-45761055(+)$1	1	113	141	23.5652
((((..((.............))..)))	chr12:124499555-124499800(+)$1	1	205	233	22.7590
((((((((((...........)))))..	chr3:152182185-152182408(+)$1	1	159	187	23.1483
))))(((((............))))).)	chr1:120457491-120457729(-)$1	1	143	171	23.5448
))(((.(((............))).)))	chr6:17609077-17609300(+)$1	1	54	82	24.1837
(((((((((..............)))))	chr6:150132334-150132562(+)$1	1	149	177	23.7324
.(((((.((...........)).)))))	chr3:160218647-160218877(-)$1	1	96	124	22.8071
)(((((.((...........)).)))))	chr4:177250264-177250496(+)$1	1	91	119	22.6367
.(((((((.............)))))))	chr4:57259921-57260155(-)$1	1	3	31	24.5962
))(((((((............)))))))	chr17:20904771-20905007(-)$1	1	127	155	24.7951
((..(((((..............)))))	chrX:37698257-37698496(-)$1	1	159	187	23.9664
((((((((((...........)))))))	chr21:43408306-43408575(-)$1	1	196	224	23.1298
((.((((((............)))))))	chr1:67877089-67877320(-)$1	1	194	222	23.4984
((((.(((((...........))))).)	chr6:64292298-64292513(+)$1	1	148	176	23.7617
.(((((((((...........)))))))	chr3:67061207-67061437(+)$1	1	51	79	22.5297
(((((((((..............)))))	chr14:77802622-77802862(-)$1	1	163	191	23.7324
((((.((((.............)))).)	chr15:58246602-58246832(-)$1	1	72	100	23.4106
(((((..((............))..)).	chr10:129895409-129895637(-)$1	1	91	119	22.4767
(.(((((...............))))).	chr1:47843501-47843735(+)$1	1	159	187	19.5488
(...(((((............)))))..	chr12:89983753-89983986(-)$1	1	24	52	25.1363
((((.((((............)))))))	chr2:32536436-32536704(+)$1	1	39	67	23.8710
(((.(((((.............))))))	chr8:30535551-30535837(-)$1	1	104	132	24.7556
((((.(((((...........)))))))	chr12:98928318-98928548(+)$1	1	70	98	22.7778
))))(((((...............))))	chr10:858330-858567(-)$1	1	62	90	19.1198
.(((((................))))).	chrX:135293106-135293327(+)$1	1	172	200	22.5385
.((((((((...........)).)))))	chr12:65090555-65090782(+)$1	1	30	58	22.4087
(...(((((............)))))..	chr10:5807549-5807784(-)$1	1	32	60	25.0725

#PSSM
e : 0.23	f : 0.15	d : 0.12	[ : 0.09	g : 0.07	c : 0.04	= : 0.04	# : 0.03	! : 0.03	F : 0.01	" : 0.01	H : 0.01	q : 0.01	: : 0.01	$ : 0.01	h : 0.01	b : 0.01	i : 0.01	
e : 0.23	f : 0.19	g : 0.09	c : 0.07	d : 0.07	[ : 0.04	= : 0.04	! : 0.03	b : 0.03	i : 0.03	" : 0.03	F : 0.01	a : 0.01	H : 0.01	# : 0.01	: : 0.01	$ : 0.01	
e : 0.22	f : 0.19	g : 0.15	d : 0.09	c : 0.07	= : 0.04	[ : 0.03	! : 0.03	i : 0.03	" : 0.03	F : 0.01	H : 0.01	b : 0.01	# : 0.01	$ : 0.01	
f : 0.22	e : 0.20	g : 0.17	d : 0.07	! : 0.06	[ : 0.04	c : 0.04	= : 0.04	b : 0.03	" : 0.03	: : 0.01	$ : 0.01	i : 0.01	
e : 0.26	f : 0.17	g : 0.15	[ : 0.15	! : 0.09	= : 0.04	b : 0.03	" : 0.01	d : 0.01	c : 0.01	i : 0.01	
e : 0.31	f : 0.17	g : 0.15	d : 0.09	! : 0.07	c : 0.07	= : 0.04	" : 0.01	[ : 0.01	i : 0.01	
e : 0.26	f : 0.17	g : 0.15	c : 0.12	d : 0.07	[ : 0.04	= : 0.04	! : 0.03	" : 0.01	b : 0.01	i : 0.01	y : 0.01	
e : 0.25	c : 0.12	g : 0.11	f : 0.11	b : 0.11	d : 0.07	w : 0.04	= : 0.04	y : 0.03	x : 0.03	a : 0.01	[ : 0.01	i : 0.01	
e : 0.23	v : 0.12	g : 0.09	b : 0.09	f : 0.07	w : 0.07	d : 0.07	c : 0.04	x : 0.04	= : 0.04	y : 0.03	a : 0.01	i : 0.01	
u : 0.28	v : 0.19	t : 0.14	w : 0.14	x : 0.07	e : 0.06	y : 0.03	f : 0.01	g : 0.01	= : 0.01	i : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	t : 0.26	v : 0.19	w : 0.14	x : 0.07	y : 0.03	
u : 0.28	v : 0.19	w : 0.14	t : 0.12	x : 0.07	b : 0.04	c : 0.03	y : 0.03	e : 0.01	f : 0.01	d : 0.01	a : 0.01	
e : 0.15	g : 0.12	f : 0.12	b : 0.11	w : 0.09	c : 0.07	x : 0.07	v : 0.06	d : 0.06	y : 0.03	a : 0.01	] : 0.01	= : 0.01	i : 0.01	
e : 0.23	g : 0.14	f : 0.14	c : 0.11	d : 0.07	w : 0.06	b : 0.06	x : 0.04	] : 0.04	y : 0.01	3 : 0.01	= : 0.01	i : 0.01	
e : 0.28	f : 0.17	g : 0.15	c : 0.09	2 : 0.07	d : 0.07	= : 0.04	x : 0.03	3 : 0.01	] : 0.01	i : 0.01	
e : 0.33	f : 0.17	g : 0.15	2 : 0.07	d : 0.07	c : 0.04	] : 0.04	= : 0.04	3 : 0.01	i : 0.01	
e : 0.36	f : 0.23	g : 0.15	d : 0.06	c : 0.04	= : 0.04	b : 0.03	] : 0.01	4 : 0.01	i : 0.01	
e : 0.23	f : 0.22	g : 0.17	] : 0.07	d : 0.06	= : 0.04	b : 0.03	c : 0.03	3 : 0.03	5 : 0.01	4 : 0.01	2 : 0.01	: : 0.01	i : 0.01	
e : 0.20	g : 0.17	] : 0.15	f : 0.11	d : 0.07	c : 0.04	= : 0.04	: : 0.03	3 : 0.03	a : 0.01	5 : 0.01	4 : 0.01	2 : 0.01	G : 0.01	b : 0.01	i : 0.01	

#score	1453.2247850404997
#seq	63
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_CDS_m3_run1.txt

#BEAR
f!!eeeee[cccooooooccceeeee]f	chr13:31835020-31835240(+)$1	220	148	176	9.1112
dddd!!a[ddddmmmmdddd]a22dddd	chrX:53432085-53432318(-)$1	233	171	199	11.1087
eee$$$$$ddddmmmmddddeeeee]cc	chr10:5784255-5784485(+)$1	230	61	89	10.2884
eee!!bb!!cccooooooccc22bb]ee	chr11:14900671-14900891(-)$1	220	43	71	9.7778
!!dddd"""cccmmmmcccdddd22fff	chrX:118603652-118603880(+)$1	228	171	199	10.9204
(ccc[a!!ddddmmmmdddd22a]ccc3	chr1:24022233-24022469(+)$1	236	140	168	11.4449
ee"""bb[ddddllldddd22bb]eeee	chr15:101114276-101114499(-)$1	223	181	209	9.2715
fffffddddcccmmmmccc22dddd]ff	chr10:60560548-60560905(+)$1	357	196	224	9.3999
ccc!!ccc[ccclllccc]ccc]ccc22	chr5:135510104-135510325(+)$1	221	17	45	10.7148
eee[bb"""cccmmmmcccbb]eeeeed	chr19:1393159-1393380(+)$1	221	31	59	10.7665
""dddd!!ddddmmmmdddd22dddd22	chr14:32560723-32560945(+)$1	222	165	193	11.2075
iii[ccceeeeellleeeee4444ccc]	chr5:87502860-87503092(-)$1	232	37	65	9.2192
gggg####ddddmmmmdddd22gggggg	chr3:150906077-150906298(+)$1	221	47	75	11.4682
fffffccc[ddddllldddd]ccc4444	chr19:44500256-44500478(+)$1	222	104	132	9.3889
###dddd!!cccnnnnncccdddd4444	chr1:20981842-20982070(-)$1	228	46	74	9.0625
cc!!ccc[eeeeemmmmeeeee]ccc22	chr3:141923498-141923721(-)$1	223	164	192	9.0334
[ccc[bb[ddddmmmmdddd]bb]cccb	chr9:126128449-126128668(+)$1	219	54	82	10.1727
cc!!ccc[cccbbmmmmbb]cccccc22	chr1:153635473-153635703(+)$1	230	39	67	9.1535
#ccc[ggggggglllggggggg]ccc44	chr1:245023634-245023867(-)$1	233	147	175	8.9789
eeee[bb[ddddmmmmddddbb]eeeee	chr3:9710358-9710578(+)$1	220	117	145	10.1308
!eeeee"""cccnnnnnccceeeee22b	chr8:26221182-26221401(+)$1	219	152	180	8.8448
ddd$$$$$ddddmmmmdddd]dddd]ff	chr8:30332195-30332471(+)$1	276	203	231	10.3098
hheeeee[ddddmmmmdddd4444eeee	chr17:57812624-57812844(+)$1	220	16	44	10.7340
ee!!ccc[eeeeellleeeeeccc]eee	chr2:20508172-20508391(-)$1	219	68	96	8.5900
ddd[ccc[ccclllcccccc22dddd33	chr14:100820683-100820910(-)$1	227	89	117	9.6626
ddddccc!!cccmmmmccc]ccc>>>>>	chr1:160314444-160314668(+)$1	224	89	117	11.0051
iiiiiiiiiccclllccc]iiiiiiiii	chr6:105526279-105526502(-)$1	223	155	183	9.7111
eee"""cccooooooccc333eeeee33	chr11:47819249-47819473(-)$1	224	174	202	8.9049
cc!!ccc[ddddllldddd]ccc22ccc	chr19:41198770-41198996(-)$1	226	71	99	10.2601
eee[a"""ddddmmmmdddd]a]eeeee	chr4:25929847-25930067(+)$1	220	111	139	11.7629
cc"""gggggggooooooggggggg22c	chr10:38241757-38241985(-)$1	228	85	113	8.6951
fffffbba[cccmmmmccc]a333bb22	chr3:52726842-52727073(+)$1	231	195	223	10.6857
"eeeee!!ddddmmmmdddd333eeeee	chr17:4846416-4846638(+)$1	222	61	89	11.7564
eeeeea"""ccclllccc333a]eeeee	chr12:98927329-98927552(+)$1	223	107	135	11.2080
bdddd[a[ddddmmmmdddd]adddd33	chr7:99091069-99091303(-)$1	234	179	207	11.3545
bb"""ddddcccmmmmccc4444dddd3	chr2:170355960-170356180(+)$1	220	126	154	11.1605
##==========mmmm==========55	chr12:15813517-15813743(-)$1	226	15	43	9.6975
ggggg####cccooooooccc4444ggg	chr16:2813163-2813384(+)$1	221	17	45	10.9414
$cccdddd[cccnnnnnccc22dddd44	chr1:90049077-90049307(+)$1	230	137	165	8.6567
=========cccmmmmccc]========	chr2:32526383-32526605(+)$1	222	16	44	11.8916
dd[ccc"""a[bbmmmmbb]a333ccc]	chrX:107977016-107977257(-)$1	241	142	170	9.6690
ccc!!a[eeeeemmmmeeeee]a22ccc	chr16:74660288-74660529(+)$1	241	84	112	9.6429
feeeee####bbmmmmbb333eeeee]f	chr2:18113478-18113697(+)$1	219	175	203	9.5532
a"""ccc[ddddlllddddccc333a22	chr8:135524637-135524862(-)$1	225	94	122	10.7243
dddd####ddddmmmmdddd4444dddd	chr10:32115149-32115377(-)$1	228	150	178	11.7435
dd$$$$$eeeeemmmmeeeeedddd444	chr22:19471285-19471506(+)$1	221	139	167	9.0484
&dddd####cccooooooccc22dddd7	chr1:11345837-11346063(+)$1	226	158	186	9.3708
d!!dddd!!cccmmmmcccdddddddd:	chr19:16344300-16344521(+)$1	221	87	115	10.1926
ccc!!ccc[cccmmmmccc]ccc22ccc	chr20:17948600-17948820(-)$1	220	27	55	11.5040
c[ccc!!a[cccooooooccca22cccc	chr1:43240376-43240599(+)$1	223	45	73	10.1842
dddddcccddddmmmmdddd22ccc]dd	chr1:2520323-2520550(+)$1	227	113	141	10.2942
E===========mmmm===========:	chr17:39537910-39538149(-)$1	239	17	45	9.1547
ff[a[bb!!cccmmmmccc]bb]a]fff	chr15:65369890-65370112(+)$1	222	113	141	10.6904
dd!!ccc!!cccmmmmccccccdddd33	chr10:60560679-60560903(-)$1	224	131	159	12.7107
cc[iiiiiiiiimmmmiiiiiiiii]cc	chr10:30611293-30611516(-)$1	223	127	155	10.2287
ffffff"""cccmmmmcccffffff]cc	chr12:54062857-54063079(-)$1	222	177	205	10.1773
ggggggg!!cccmmmmccc333gggggg	chr2:9618361-9618584(+)$1	223	183	211	12.2115
ddd!!bb!!ddddllldddd333bb22d	chr4:17841705-17841926(+)$1	221	63	91	10.1592
eeeee####cccmmmmccc4444eeeee	chr6:105526497-105526719(-)$1	222	177	205	12.3480
dd[ccc[eeeeemmmmeeeee333ccc]	chr9:88207446-88207674(-)$1	228	53	81	10.3356
ggggccc[cccooooooccc]ccc]ggg	chr10:91162791-91163030(+)$1	239	19	47	9.8649
cc[dddd!!ccclllccc]dddd]ccc5	chr6:105526213-105526480(+)$1	267	107	135	9.5807
a!!eeeee[cccmmmmccceeeee22a2	chr12:133682872-133683091(+)$1	219	161	189	10.2436
dd[eeeee[cccmmmmccc333eeeee]	chr3:150281225-150281446(+)$1	221	70	98	11.5719
cdddd####ccclllccc4444dddd]c	chr3:15062260-15062480(+)$1	220	116	144	11.1262

#otherMatches

#Seq PSSM
GUAUCCAGACUUUGCUGCAGGCUGGGCC	chr13:31835020-31835240(+)$1	220	148	176	9.1112
GUGGGAGUCCUAAGCCUAGGUCAGCCAC	chrX:53432085-53432318(-)$1	233	171	199	11.1087
AUGCUGCUGAAGUAUCCUUCCGUGAUCC	chr10:5784255-5784485(+)$1	230	61	89	10.2884
AUGCAACCUCUGAAGAUGCAGUUGUACG	chr11:14900671-14900891(-)$1	220	43	71	9.7778
CAAGAGAACCCAGUUUUGGCUCUACUUU	chrX:118603652-118603880(+)$1	228	171	199	10.9204
GGCCAUGCGCUGGUUCCAGCAGAAGGUA	chr1:24022233-24022469(+)$1	236	140	168	11.4449
GAUUUGCUUGAGCUUCUCAUCGCCUCCA	chr15:101114276-101114499(-)$1	223	181	209	9.2715
GUUUCCUGUGCCAAAAGGCAGACAGUGG	chr10:60560548-60560905(+)$1	357	196	224	9.3999
GCAUAUUUGUACAGAGUAGGAACUGCAA	chr5:135510104-135510325(+)$1	221	17	45	10.7148
GUGGGCAGGCGGGUCUUCGGCACACUCC	chr19:1393159-1393380(+)$1	221	31	59	10.7665
UAUAAAUACUUUACCAAGAGCUUUUAAC	chr14:32560723-32560945(+)$1	222	165	193	11.2075
CAUUGUGUAUAGCUCCUAUAAAUUUAUU	chr5:87502860-87503092(-)$1	232	37	65	9.2192
UAUUUUUAAUCUGUAGAGAUGUGGUGAA	chr3:150906077-150906298(+)$1	221	47	75	11.4682
AUCAUAAAUAACUCUCAGUUCUUUGAAA	chr19:44500256-44500478(+)$1	222	104	132	9.3889
ACGCUCAUCGUGGCUGACACUGAGAACC	chr1:20981842-20982070(-)$1	228	46	74	9.0625
AAUAAUUCUCUUCUUAUGAAGGUAAUCU	chr3:141923498-141923721(-)$1	223	164	192	9.0334
AGGUUCCGGUGCGACUGCGCGGGCACCG	chr9:126128449-126128668(+)$1	219	54	82	10.1727
GACUGUGUGUACUCUAAAGUUGCCACUC	chr1:153635473-153635703(+)$1	230	39	67	9.1535
ACAAUGGAGAGUUUUGCUUUUCUUUGGG	chr1:245023634-245023867(-)$1	233	147	175	8.9789
CAGGUGAAUGUUGAACAGCAUCCUCUGA	chr3:9710358-9710578(+)$1	220	117	145	10.1308
AUGACUAGAGACUAUUUGUCAGUCAAAA	chr8:26221182-26221401(+)$1	219	152	180	8.8448
AUAAAAUGAGACAAAAGUCUGUAUGCUU	chr8:30332195-30332471(+)$1	276	203	231	10.3098
AGAGAAUAAGCAUAAAUGUUAGAAAUUC	chr17:57812624-57812844(+)$1	220	16	44	10.7340
GCCUCUCCAACUGAAGUAGUUGAGCGCU	chr2:20508172-20508391(-)$1	219	68	96	8.5900
AUGCAUGUAGGUCACCUCAUUCCAUUUA	chr14:100820683-100820910(-)$1	227	89	117	9.6626
GGAGAGGAAGAUAUAUAUCCCCUUAAAU	chr1:160314444-160314668(+)$1	224	89	117	11.0051
GCUGAGGAGGUAGACUACAUUCCUUAGC	chr6:105526279-105526502(-)$1	223	155	183	9.7111
ACAGCCUUAUUAGUUUAAUCAUGUUUUA	chr11:47819249-47819473(-)$1	224	174	202	8.9049
UGAUGGAGACAGAGACUGUGUCCUGCAG	chr19:41198770-41198996(-)$1	226	71	99	10.2601
CUGGAAUUGUUCAAGAGGAUGUGCAGCC	chr4:25929847-25930067(+)$1	220	111	139	11.7629
UGUAAAGAAUGUAAGAAAAUAUUUUACC	chr10:38241757-38241985(-)$1	228	85	113	8.6951
CCUUUCCCAGGCUGAUGCUCGACAGGUA	chr3:52726842-52727073(+)$1	231	195	223	10.6857
CGGGUGCUUCUGGUUCCAGACAAUACCU	chr17:4846416-4846638(+)$1	222	61	89	11.7564
UCACUCACUACCUUAGGUCUAGAAGUGG	chr12:98927329-98927552(+)$1	223	107	135	11.2080
gcagaucauuugagaucaggaguuugaa	chr7:99091069-99091303(-)$1	234	179	207	11.3545
CUGCCAGUCCCAUAUUUGGAGUUGAUUA	chr2:170355960-170356180(+)$1	220	126	154	11.1605
GCUAAGGUAAAAAUAGUUUUGUUUUAUA	chr12:15813517-15813743(-)$1	226	15	43	9.6975
GACCCCUUCUAGACAUAGCUGCUCAGGG	chr16:2813163-2813384(+)$1	221	17	45	10.9414
UGGAUGCUGAGGAGUUCCCUGAAGCAAU	chr1:90049077-90049307(+)$1	230	137	165	8.6567
AUGAGUAUCUUGAUUUCAAUGAUAUUUA	chr2:32526383-32526605(+)$1	222	16	44	11.8916
GGGACAGAAUGACAACAGUGAGUAUGUG	chrX:107977016-107977257(-)$1	241	142	170	9.6690
GGAGCAGAUUGGAUUUCCAGUGUCAUCC	chr16:74660288-74660529(+)$1	241	84	112	9.6429
UUGUGGUGAGCGAUCCUGACUCCACAGA	chr2:18113478-18113697(+)$1	219	175	203	9.5532
CACAGGCAGCGGUGGCCGCGCUCCAGGA	chr8:135524637-135524862(-)$1	225	94	122	10.7243
GUAUUUCUUCUCUUUGGAGAUUUUAUAC	chr10:32115149-32115377(-)$1	228	150	178	11.7435
CCGCCUAUGAAGACAUCUUCAGGGAUGA	chr22:19471285-19471506(+)$1	221	139	167	9.0484
GGCCACACACUGCACCAUCAGCCUGGCA	chr1:11345837-11346063(+)$1	226	158	186	9.3708
GUCAAGUUCGAGAUCCCUUACUUCACUA	chr19:16344300-16344521(+)$1	221	87	115	10.1926
CGGGACCUUAGCCCCAGCUCAGGCGCCG	chr20:17948600-17948820(-)$1	220	27	55	11.5040
UCACAGAGAUGCCAACCUGCACCAUGUA	chr1:43240376-43240599(+)$1	223	45	73	10.1842
CCUGGGCAUCUCUGCGGAGGUCUGUGCC	chr1:2520323-2520550(+)$1	227	113	141	10.2942
UGGGGGGCCAGCAGCAGCUGGCUCUCUU	chr17:39537910-39538149(-)$1	239	17	45	9.1547
GCUGGAGUUUCGUGGCCGACCUGCCGCA	chr15:65369890-65370112(+)$1	222	113	141	10.6904
CCACUGUCUGCCUUUUGGCACAGGAAAC	chr10:60560679-60560903(-)$1	224	131	159	12.7107
GUCAUCUUUUUUCUCCAGAGAAGAUCAC	chr10:30611293-30611516(-)$1	223	127	155	10.2287
UCUGAUAUGCUUUCCAAAGGUCAGAAAA	chr12:54062857-54063079(-)$1	222	177	205	10.1773
UAUGUUACAGCAAACUUGCAUUUAAUAU	chr2:9618361-9618584(+)$1	223	183	211	12.2115
GGUGACCAAGCUGAAGCAGCACAGGAUG	chr4:17841705-17841926(+)$1	221	63	91	10.1592
CUGCCCUAGCCUCCUGAGGAAACGGUGG	chr6:105526497-105526719(-)$1	222	177	205	12.3480
AGAAAUCAUUUCUCAAGAAGUUCAGUUG	chr9:88207446-88207674(-)$1	228	53	81	10.3356
UUUACCGAAGAAAAGGCUCUGUGGAUAA	chr10:91162791-91163030(+)$1	239	19	47	9.8649
CUAAGGAAUGUAGUCUACCUCCUCAGCC	chr6:105526213-105526480(+)$1	267	107	135	9.5807
GAUAAAGCCUUCAGCCGGAGCUUUUCCC	chr12:133682872-133683091(+)$1	219	161	189	10.2436
UUGCAGCUUCUAAAGAUGGCACAGCUGG	chr3:150281225-150281446(+)$1	221	70	98	11.5719
ACCGGAACCGCUGUCAGUUUUGCCGGCU	chr3:15062260-15062480(+)$1	220	116	144	11.1262

#DB
(..(((((.(((......)))))))).)	chr13:31835020-31835240(+)$1	1	148	176	9.1112
((((..(.((((....)))).)..))))	chrX:53432085-53432318(-)$1	1	171	199	11.1087
(((.....((((....))))))))).))	chr10:5784255-5784485(+)$1	1	61	89	10.2884
(((..((..(((......)))..)).))	chr11:14900671-14900891(-)$1	1	43	71	9.7778
..((((...(((....)))))))..)))	chrX:118603652-118603880(+)$1	1	171	199	10.9204
.(((.(..((((....))))..).))).	chr1:24022233-24022469(+)$1	1	140	168	11.4449
((...((.((((...))))..)).))))	chr15:101114276-101114499(-)$1	1	181	209	9.2715
((((((((((((....)))..)))).))	chr10:60560548-60560905(+)$1	1	196	224	9.3999
(((..(((.(((...))).))).)))..	chr5:135510104-135510325(+)$1	1	17	45	10.7148
(((.((...(((....))))).))))))	chr19:1393159-1393380(+)$1	1	31	59	10.7665
..((((..((((....))))..))))..	chr14:32560723-32560945(+)$1	1	165	193	11.2075
(((.((((((((...)))))....))).	chr5:87502860-87503092(-)$1	1	37	65	9.2192
((((....((((....))))..))))))	chr3:150906077-150906298(+)$1	1	47	75	11.4682
((((((((.((((...)))).)))....	chr19:44500256-44500478(+)$1	1	104	132	9.3889
...((((..(((.....)))))))....	chr1:20981842-20982070(-)$1	1	46	74	9.0625
((..(((.(((((....))))).)))..	chr3:141923498-141923721(-)$1	1	164	192	9.0334
.(((.((.((((....)))).)).))))	chr9:126128449-126128668(+)$1	1	54	82	10.1727
((..(((.(((((....)).))))))..	chr1:153635473-153635703(+)$1	1	39	67	9.1535
.(((.(((((((...))))))).)))..	chr1:245023634-245023867(-)$1	1	147	175	8.9789
((((.((.((((....)))))).)))))	chr3:9710358-9710578(+)$1	1	117	145	10.1308
.(((((...(((.....))))))))..)	chr8:26221182-26221401(+)$1	1	152	180	8.8448
(((.....((((....)))).)))).))	chr8:30332195-30332471(+)$1	1	203	231	10.3098
(((((((.((((....))))....))))	chr17:57812624-57812844(+)$1	1	16	44	10.7340
((..(((.(((((...)))))))).)))	chr2:20508172-20508391(-)$1	1	68	96	8.5900
(((.(((.(((...))))))..))))..	chr14:100820683-100820910(-)$1	1	89	117	9.6626
(((((((..(((....))).))).....	chr1:160314444-160314668(+)$1	1	89	117	11.0051
((((((((((((...))).)))))))))	chr6:105526279-105526502(-)$1	1	155	183	9.7111
(((...(((......)))...)))))..	chr11:47819249-47819473(-)$1	1	174	202	8.9049
((..(((.((((...)))).)))..)))	chr19:41198770-41198996(-)$1	1	71	99	10.2601
(((.(...((((....)))).).)))))	chr4:25929847-25930067(+)$1	1	111	139	11.7629
((...(((((((......)))))))..)	chr10:38241757-38241985(-)$1	1	85	113	8.6951
((((((((.(((....))).)...))..	chr3:52726842-52727073(+)$1	1	195	223	10.6857
.(((((..((((....))))...)))))	chr17:4846416-4846638(+)$1	1	61	89	11.7564
((((((...(((...)))...).)))))	chr12:98927329-98927552(+)$1	1	107	135	11.2080
(((((.(.((((....)))).)))))..	chr7:99091069-99091303(-)$1	1	179	207	11.3545
((...(((((((....)))....)))).	chr2:170355960-170356180(+)$1	1	126	154	11.1605
..((((((((((....))))))))))..	chr12:15813517-15813743(-)$1	1	15	43	9.6975
(((((....(((......)))....)))	chr16:2813163-2813384(+)$1	1	17	45	10.9414
.(((((((.(((.....)))..))))..	chr1:90049077-90049307(+)$1	1	137	165	8.6567
((((((((((((....))).))))))))	chr2:32526383-32526605(+)$1	1	16	44	11.8916
((.(((...(.((....)).)...))).	chrX:107977016-107977257(-)$1	1	142	170	9.6690
(((..(.(((((....))))).)..)))	chr16:74660288-74660529(+)$1	1	84	112	9.6429
((((((....((....))...))))).)	chr2:18113478-18113697(+)$1	1	175	203	9.5532
(...(((.((((...)))))))...)..	chr8:135524637-135524862(-)$1	1	94	122	10.7243
((((....((((....))))....))))	chr10:32115149-32115377(-)$1	1	150	178	11.7435
((.....(((((....)))))))))...	chr22:19471285-19471506(+)$1	1	139	167	9.0484
.((((....(((......)))..)))).	chr1:11345837-11346063(+)$1	1	158	186	9.3708
(..((((..(((....))))))))))).	chr19:16344300-16344521(+)$1	1	87	115	10.1926
(((..(((.(((....))).)))..)))	chr20:17948600-17948820(-)$1	1	27	55	11.5040
(.(((..(.(((......))))..))))	chr1:43240376-43240599(+)$1	1	45	73	10.1842
((((((((((((....))))..))).))	chr1:2520323-2520550(+)$1	1	113	141	10.2942
((((((((((((....))))))))))).	chr17:39537910-39538149(-)$1	1	17	45	9.1547
((.(.((..(((....))).)).).)))	chr15:65369890-65370112(+)$1	1	113	141	10.6904
((..(((..(((....))))))))))..	chr10:60560679-60560903(-)$1	1	131	159	12.7107
((.(((((((((....))))))))).))	chr10:30611293-30611516(-)$1	1	127	155	10.2287
((((((...(((....))))))))).))	chr12:54062857-54063079(-)$1	1	177	205	10.1773
(((((((..(((....)))...))))))	chr2:9618361-9618584(+)$1	1	183	211	12.2115
(((..((..((((...))))...))..)	chr4:17841705-17841926(+)$1	1	63	91	10.1592
(((((....(((....)))....)))))	chr6:105526497-105526719(-)$1	1	177	205	12.3480
((.(((.(((((....)))))...))).	chr9:88207446-88207674(-)$1	1	53	81	10.3356
(((((((.(((......))).))).)))	chr10:91162791-91163030(+)$1	1	19	47	9.8649
((.((((..(((...))).)))).))).	chr6:105526213-105526480(+)$1	1	107	135	9.5807
(..(((((.(((....))))))))..).	chr12:133682872-133683091(+)$1	1	161	189	10.2436
((.(((((.(((....)))...))))).	chr3:150281225-150281446(+)$1	1	70	98	11.5719
(((((....(((...)))....)))).)	chr3:15062260-15062480(+)$1	1	116	144	11.1262

#PSSM
d : 0.20	c : 0.16	e : 0.15	f : 0.10	g : 0.06	# : 0.04	! : 0.03	" : 0.03	i : 0.03	b : 0.03	a : 0.03	( : 0.01	[ : 0.01	h : 0.01	$ : 0.01	= : 0.01	& : 0.01	E : 0.01	
d : 0.23	e : 0.20	c : 0.20	f : 0.07	! : 0.06	g : 0.06	" : 0.03	i : 0.03	# : 0.03	= : 0.03	h : 0.01	b : 0.01	[ : 0.01	
d : 0.18	e : 0.18	! : 0.12	c : 0.12	[ : 0.09	" : 0.06	f : 0.06	g : 0.06	= : 0.04	i : 0.03	# : 0.01	$ : 0.01	
d : 0.18	e : 0.15	! : 0.15	c : 0.10	" : 0.07	f : 0.06	[ : 0.06	g : 0.06	$ : 0.04	= : 0.04	i : 0.03	a : 0.01	
c : 0.20	d : 0.15	e : 0.13	! : 0.09	[ : 0.07	" : 0.06	f : 0.06	$ : 0.04	= : 0.04	# : 0.03	i : 0.03	g : 0.03	b : 0.01	a : 0.01	
c : 0.24	b : 0.12	d : 0.12	e : 0.10	# : 0.09	$ : 0.04	a : 0.04	g : 0.04	= : 0.04	! : 0.03	i : 0.03	" : 0.03	[ : 0.01	f : 0.01	
c : 0.23	b : 0.10	" : 0.10	# : 0.10	d : 0.09	e : 0.06	! : 0.06	$ : 0.04	g : 0.04	= : 0.04	a : 0.03	i : 0.03	[ : 0.03	
[ : 0.20	! : 0.18	e : 0.10	" : 0.10	# : 0.10	c : 0.07	d : 0.04	= : 0.04	$ : 0.03	g : 0.03	i : 0.03	a : 0.03	
d : 0.29	[ : 0.13	! : 0.13	" : 0.09	e : 0.09	# : 0.07	c : 0.06	= : 0.04	g : 0.03	i : 0.03	
c : 0.49	d : 0.29	e : 0.09	g : 0.03	= : 0.03	o : 0.01	a : 0.01	# : 0.01	i : 0.01	
c : 0.49	d : 0.29	e : 0.09	g : 0.03	= : 0.03	o : 0.01	[ : 0.01	b : 0.01	i : 0.01	
c : 0.44	d : 0.29	e : 0.09	b : 0.04	g : 0.03	o : 0.03	= : 0.03	l : 0.01	i : 0.01	
m : 0.56	l : 0.16	o : 0.12	n : 0.04	d : 0.03	e : 0.03	b : 0.03	
m : 0.61	l : 0.21	o : 0.12	n : 0.04	
m : 0.61	l : 0.20	o : 0.12	n : 0.04	c : 0.01	
m : 0.61	o : 0.10	c : 0.10	d : 0.04	l : 0.04	n : 0.04	e : 0.01	g : 0.01	
c : 0.35	d : 0.29	o : 0.10	e : 0.07	n : 0.04	m : 0.04	= : 0.03	g : 0.01	b : 0.01	i : 0.01	
c : 0.41	d : 0.29	o : 0.09	e : 0.09	b : 0.04	= : 0.03	g : 0.01	i : 0.01	
c : 0.40	d : 0.29	e : 0.09	] : 0.04	3 : 0.04	b : 0.03	g : 0.03	= : 0.03	i : 0.01	4 : 0.01	
d : 0.29	c : 0.20	] : 0.12	e : 0.10	3 : 0.07	4 : 0.04	2 : 0.03	g : 0.03	i : 0.03	= : 0.03	b : 0.01	f : 0.01	
c : 0.18	e : 0.12	2 : 0.12	] : 0.10	3 : 0.10	4 : 0.09	d : 0.06	b : 0.04	= : 0.04	g : 0.03	i : 0.03	a : 0.03	f : 0.01	
c : 0.15	2 : 0.12	e : 0.10	d : 0.10	4 : 0.10	3 : 0.10	a : 0.07	b : 0.06	= : 0.04	] : 0.03	g : 0.03	i : 0.03	f : 0.01	
d : 0.20	e : 0.12	c : 0.12	] : 0.10	4 : 0.09	3 : 0.09	2 : 0.06	g : 0.04	= : 0.04	a : 0.03	b : 0.03	i : 0.03	f : 0.01	
e : 0.20	d : 0.20	c : 0.12	2 : 0.09	] : 0.06	4 : 0.06	3 : 0.06	g : 0.04	= : 0.04	b : 0.03	i : 0.03	> : 0.01	a : 0.01	f : 0.01	
e : 0.21	d : 0.21	c : 0.18	2 : 0.07	b : 0.04	g : 0.04	4 : 0.04	] : 0.04	= : 0.04	i : 0.03	> : 0.01	3 : 0.01	f : 0.01	
c : 0.21	e : 0.20	d : 0.16	] : 0.10	g : 0.06	2 : 0.06	4 : 0.04	= : 0.04	f : 0.03	> : 0.01	i : 0.01	b : 0.01	a : 0.01	
c : 0.20	e : 0.16	2 : 0.13	d : 0.09	4 : 0.07	f : 0.06	g : 0.06	3 : 0.06	] : 0.04	= : 0.03	> : 0.01	i : 0.01	5 : 0.01	a : 0.01	
c : 0.13	e : 0.13	2 : 0.10	f : 0.09	3 : 0.09	d : 0.07	4 : 0.07	] : 0.06	g : 0.06	b : 0.03	5 : 0.03	: : 0.03	> : 0.01	i : 0.01	= : 0.01	7 : 0.01	

#score	668.7862645529365
#seq	65
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_CDS_m1_run1.txt

#BEAR
ggeeeee"""bboooooobb4444eeee	chr1:236966677-236966964(+)$1	287	141	169	16.0573
gggg[bba[cccooooooccc]a]bbgg	chr4:10100618-10100865(-)$1	247	8	36	14.8107
#eeeee####cccmmmmccc4444eeee	chr10:113941415-113941655(-)$1	240	135	163	11.3749
%%dddd!!ddddoooooodddd]ddddc	chr7:105733313-105733593(-)$1	280	133	161	11.6749
!!eeeee!!cccooooooccc22eeeee	chrX:148564464-148564705(-)$1	241	181	209	16.4191
b22cccccccccooooooccc22cccGG	chr1:110527580-110527820(+)$1	240	79	107	12.7670
a[dddd[bbcccooooooccc]bb333d	chr16:88802558-88802798(-)$1	240	196	224	13.9341
ccdddd####bboooooobb4444dddd	chr1:65690340-65690580(+)$1	240	13	41	15.8530
c"""dddd[cccoooooocccdddd333	chr17:55183270-55183559(+)$1	289	20	48	14.3972
dd####bb[cccooooooccc333bb33	chr4:139966093-139966333(+)$1	240	175	203	14.9622
ccc[bb"""cccnnnnnccc333bbccc	chr19:11144021-11144261(+)$1	240	91	119	11.3171
==dddd"""cccnnnnnccc4444dddd	chr8:95538928-95539168(-)$1	240	177	205	12.3848
a[ggggggg[bboooooobbggggggg]	chr17:12893343-12893583(+)$1	240	40	68	13.6191
ggggggg!!cccooooooccc>>>>>>>	chr5:176638936-176639216(+)$1	280	54	82	14.9488
ddddcccccc[aooooooaccc>>>>>>	chr19:45912188-45912428(+)$1	240	6	34	12.9009
b!!dddd!!cccooooooccc22dddd2	chr6:43167610-43167850(+)$1	240	119	147	15.8726
==bb[ccc!!bboooooobb22ccc]bb	chr17:21205431-21205671(+)$1	240	165	193	13.5745
b!!ccc!!ddddoooooodddd22ccc2	chr1:150970533-150970773(-)$1	240	140	168	13.4345
:eeeee[a[cccooooooccc]a]eeee	chr11:105948448-105948688(+)$1	240	8	36	15.0261
dddffffffcccooooooccc333ffff	chr12:105536848-105537088(+)$1	240	106	134	14.5809
[dddd$$$$$bboooooobb4444dddd	chr16:24582097-24582337(+)$1	240	165	193	14.7908
gg[eeeee[cccooooooccc]eeeee]	chr19:47227975-47228215(-)$1	240	40	68	15.4556
FFffffff[cccooooooccc]ffffff	chr2:69556742-69556982(-)$1	240	209	237	13.2663
hhhhhh"""cccooooooccc]hhhhhh	chr22:44892811-44893051(-)$1	240	28	56	13.7203
dddd[ccc[cccoooooocccccc]ddd	chr2:120979447-120979687(-)$1	240	162	190	14.5960
c[bb[ccc!!bboooooobb4444ccc]	chr11:64621798-64622038(-)$1	240	173	201	15.2100
dddd[a[eeeeeooooooeeeee]addd	chr1:109177654-109177894(+)$1	240	80	108	11.7082
ggggggccc[aooooooa]ccc22gggg	chr22:20074672-20074912(+)$1	240	54	82	12.6915
======"""cccooooooccc=======	chr6:53785369-53785649(+)$1	280	9	37	16.3680
======####bboooooobb22======	chr15:44853124-44853366(+)$1	242	149	177	15.6408
"""ccc####ccclllccc4444cccbb	chr21:28209862-28210104(-)$1	242	82	110	11.0901
ddd[dddd[cccooooooccc]dddddd	chr1:202858095-202858335(-)$1	240	186	214	14.4410
ddeeeee!!cccooooooccc333eeee	chr17:58144879-58145119(-)$1	240	133	161	16.6204
eeee"""a[ddddoooooodddd]a444	chr11:61179217-61179457(-)$1	240	157	185	11.6554
eee[ccc"""bboooooobb333ccc]e	chr5:98209252-98209492(-)$1	240	46	74	15.9206
ggeeeee"""bboooooobbeeeee]gg	chr15:100246894-100247134(+)$1	240	169	197	14.4773
gggeeeee[cccooooooccceeeee::	chr13:113883666-113883906(+)$1	240	51	79	12.9723
##eeeee"""bboooooobb22eeeee3	chr10:27462033-27462273(+)$1	240	32	60	15.2721
eeeebb"""bboooooobb]bb]eeeee	chr19:18557095-18557335(-)$1	240	1	29	11.3707
d"""ccc!!cccooooooccc]ccc333	chr13:46104759-46104999(+)$1	240	190	218	16.0833
gg[ccc####bboooooobb4444ccc]	chr14:68264684-68264924(-)$1	240	62	90	16.4725
###dddd!!cccooooooccc22dddd3	chr16:8948940-8949180(-)$1	240	16	44	16.0634
bbffffff[cccooooooccc]ffffff	chr2:33817125-33817372(-)$1	247	171	199	13.6809
eeffffff[a[aooooooa]a]ffffff	chr2:10799196-10799436(-)$1	240	186	214	12.6709
ddggggggg[bboooooobbggggggg]	chr1:214816513-214816753(+)$1	240	75	103	13.3340
ccceeeee[cccooooooccc]eeeee:	chr13:96282176-96282456(-)$1	280	72	100	14.2530
gg[ccc"""ddddnnnnndddd333ccc	chr19:19453525-19453771(+)$1	246	60	88	10.3345
ggggggg!!cccooooooccc22ggggg	chr14:24705098-24705338(+)$1	240	87	115	16.2221
!!dddd[eeeeeooooooeeeee4444d	chr4:17816396-17816636(+)$1	240	22	50	12.3310
:ffffff!!cccooooooccc22fffff	chr11:65386296-65386549(+)$1	253	57	85	14.2297
$$$ccc####bboooooobb4444ccc2	chr11:10789516-10789756(+)$1	240	94	122	15.7575
gdddd!!eeeeeooooooeeeee22ddd	chr19:44571236-44571476(+)$1	240	150	178	11.5719
f!!eeeee!!cccnnnnnccc22eeeee	chr10:103565721-103565961(-)$1	240	198	226	11.3236
!ddddccc[cccooooooccc]ccc]dd	chr1:78046611-78046851(-)$1	240	68	96	15.3728

#otherMatches

#Seq PSSM
GCGGGAGAAGCUAAACGAAGAACACUUC	chr1:236966677-236966964(+)$1	287	141	169	16.0573
CACGUGGCCCUGGCCCGGCAGUGACCUG	chr4:10100618-10100865(-)$1	247	8	36	14.8107
UUGGUACAAUAGAUGUUUCUUAUCUGCC	chr10:113941415-113941655(-)$1	240	135	163	11.3749
AAGAAGAAAGCAGUACUGUGUUACUUUG	chr7:105733313-105733593(-)$1	280	133	161	11.6749
CUUCAGACAUCCCUCAGUGGAAUUCUGA	chrX:148564464-148564705(-)$1	241	181	209	16.4191
cgggccggccggGGAAUGUCGAUGCCUG	chr1:110527580-110527820(+)$1	240	79	107	12.7670
UGGGGCUGGAGCACACCCGCUACCCCUG	chr16:88802558-88802798(-)$1	240	196	224	13.9341
AUGGUUUUGCACAGAAAAGUUUUUAACC	chr1:65690340-65690580(+)$1	240	13	41	15.8530
CUAUUCUCCAGCAAAUCAGCUGAGGUGU	chr17:55183270-55183559(+)$1	289	20	48	14.3972
CAAGGAGCCAAGAUUCCCCUUAUUGUGU	chr4:139966093-139966333(+)$1	240	175	203	14.9622
GGCAUGUUCGACCAGAAGUCCUCCAGCC	chr19:11144021-11144261(+)$1	240	91	119	11.3171
ACGUAUCAUCUUCUCUUAAGUUAAAUGC	chr8:95538928-95539168(-)$1	240	177	205	12.3848
GAGCUCGGGUCGACGCUCCGCCUGAGUC	chr17:12893343-12893583(+)$1	240	40	68	13.6191
GGAGGGGCGGGAUGAGUUUCCAGAGCAU	chr5:176638936-176639216(+)$1	280	54	82	14.9488
UCUGCCCCCUACGAAGAAGAGGAAAAAA	chr19:45912188-45912428(+)$1	240	6	34	12.9009
GUGCUCUGCUGCCUGGGAGCAAAAGAGA	chr6:43167610-43167850(+)$1	240	119	147	15.8726
GGGGUCCUAGGUGCAUAGGCAGAGGCCC	chr17:21205431-21205671(+)$1	240	165	193	13.5745
GAGUCAUUCCCUGGGCAAGGGGCCUGGA	chr1:150970533-150970773(-)$1	240	140	168	13.4345
GGUUCUGCUUGGUGCCAUCCAUGGAGGG	chr11:105948448-105948688(+)$1	240	8	36	15.0261
GCAUUUAGAGUCCUAUGAGAUACUUCUG	chr12:105536848-105537088(+)$1	240	106	134	14.5809
GAUUAAAACGAUGGAAGAAUAUAAUAAU	chr16:24582097-24582337(+)$1	240	165	193	14.7908
UUGGCUGUGGCUAUGGGCAGCAACAGUG	chr19:47227975-47228215(-)$1	240	40	68	15.4556
GUGGGUAAUAGGUAAAAUUCUCUUAUCC	chr2:69556742-69556982(-)$1	240	209	237	13.2663
CUUCCUUGUGUCUCGACUGACUGGGGAG	chr22:44892811-44893051(-)$1	240	28	56	13.7203
AGUUAAAUAUUGAUAUGCCAGAUUAAAC	chr2:120979447-120979687(-)$1	240	162	190	14.5960
CGAGCUGCCUGCCGACCUGCCCCCGCAC	chr11:64621798-64622038(-)$1	240	173	201	15.2100
GGUCUGGAGCUUAUGAACAAGUUGUGAU	chr1:109177654-109177894(+)$1	240	80	108	11.7082
CUUUGUGCCCCCAAAAAGAGGCGAACAG	chr22:20074672-20074912(+)$1	240	54	82	12.6915
ACAUGAAACGCAAUUCCCUGCUUAUGUG	chr6:53785369-53785649(+)$1	280	9	37	16.3680
CCAUGAAAGAUGAUCUGGCAGAUUAUGG	chr15:44853124-44853366(+)$1	242	149	177	15.6408
GUUACAAAAAAAGAAGCUUGAAGUGUCU	chr21:28209862-28210104(-)$1	242	82	110	11.0901
CGGCUCCCGGGUGCUGCAGCCAGGGACC	chr1:202858095-202858335(-)$1	240	186	214	14.4410
CAGAGUGAACCUGCAUGAAGGGAACACU	chr17:58144879-58145119(-)$1	240	133	161	16.6204
CUGUCUUCAUGGCAUCGAAGCCAAGUCC	chr11:61179217-61179457(-)$1	240	157	185	11.6554
UUGGAUUAUUUUGUUACAGAUUAGAUGC	chr5:98209252-98209492(-)$1	240	46	74	15.9206
AGCCUGCUCUGGUGCCUUCCGUAGGUUU	chr15:100246894-100247134(+)$1	240	169	197	14.4773
AGUAGAAUUCAUAAGUAAAUGGUUCUCC	chr13:113883666-113883906(+)$1	240	51	79	12.9723
AGUCGGGAACUCCAUACCGAACUCCGAA	chr10:27462033-27462273(+)$1	240	32	60	15.2721
GGUCCUUCCAGCCUCCACUCAGUGGCCC	chr19:18557095-18557335(-)$1	240	1	29	11.3707
UGCCCUCUUGGUUAUUUCACCUGAGUAG	chr13:46104759-46104999(+)$1	240	190	218	16.0833
AGAAGCCAAAGCAAGAAAGUCAGAGCUG	chr14:68264684-68264924(-)$1	240	62	90	16.4725
CCAGUGGAAGGCGACGAGGUCACCUAUA	chr16:8948940-8949180(-)$1	240	16	44	16.0634
UCUGGGGAUGUGACCAAGCGCCUUCUCA	chr2:33817125-33817372(-)$1	247	171	199	13.6809
GUGUGUGUAUGUGUCAUGAGAAAUACAC	chr2:10799196-10799436(-)$1	240	186	214	12.6709
UGAGCUGGAAGUAGCACGACUCCAGCUA	chr1:214816513-214816753(+)$1	240	75	103	13.3340
AUUUUCUGUUGCAACAGAGUAUCAGAAA	chr13:96282176-96282456(-)$1	280	72	100	14.2530
UGACUGUGAUGCACUCCAUGCAGGCCGG	chr19:19453525-19453771(+)$1	246	60	88	10.3345
GCUCAGGCACAGGCUCUUCUGACUUUGA	chr14:24705098-24705338(+)$1	240	87	115	16.2221
UGACUGUAGUUAAAUAAAUAAUUUCAUC	chr4:17816396-17816636(+)$1	240	22	50	12.3310
UGGGGCUGGGGGUGAUGUUCUGAGGCCC	chr11:65386296-65386549(+)$1	253	57	85	14.2297
GUUUCUAUAGGAAAAGCGUCAUCAAGAU	chr11:10789516-10789756(+)$1	240	94	122	15.7575
UGAAUCUUGAUAUAAUUUUAUCAuuauu	chr19:44571236-44571476(+)$1	240	150	178	11.5719
AGUAGGACUUGCAGAAAUUGCUUGUUCU	chr10:103565721-103565961(-)$1	240	198	226	11.3236
CUCUGACAAAAGCCUUGUCUUAUGUGCA	chr1:78046611-78046851(-)$1	240	68	96	15.3728

#DB
))(((((...((......))....))))	chr1:236966677-236966964(+)$1	1	141	169	16.0573
((((.(((.(((......))).).))))	chr4:10100618-10100865(-)$1	1	8	36	14.8107
.(((((....(((....)))....))))	chr10:113941415-113941655(-)$1	1	135	163	11.3749
..((((..((((......)))).)))))	chr7:105733313-105733593(-)$1	1	133	161	11.6749
..(((((..(((......)))..)))))	chrX:148564464-148564705(-)$1	1	181	209	16.4191
)..)))((((((......)))..)))))	chr1:110527580-110527820(+)$1	1	79	107	12.7670
(.((((.(((((......))).))...)	chr16:88802558-88802798(-)$1	1	196	224	13.9341
((((((....((......))....))))	chr1:65690340-65690580(+)$1	1	13	41	15.8530
(...((((.(((......)))))))...	chr17:55183270-55183559(+)$1	1	20	48	14.3972
((....((.(((......)))...))..	chr4:139966093-139966333(+)$1	1	175	203	14.9622
(((.((...(((.....)))...)))))	chr19:11144021-11144261(+)$1	1	91	119	11.3171
))((((...(((.....)))....))))	chr8:95538928-95539168(-)$1	1	177	205	12.3848
(.(((((((.((......))))))))).	chr17:12893343-12893583(+)$1	1	40	68	13.6191
(((((((..(((......))).......	chr5:176638936-176639216(+)$1	1	54	82	14.9488
((((((((((.(......))))......	chr19:45912188-45912428(+)$1	1	6	34	12.9009
(..((((..(((......)))..)))).	chr6:43167610-43167850(+)$1	1	119	147	15.8726
((((.(((..((......))..))).))	chr17:21205431-21205671(+)$1	1	165	193	13.5745
(..(((..((((......))))..))).	chr1:150970533-150970773(-)$1	1	140	168	13.4345
.(((((.(.(((......))).).))))	chr11:105948448-105948688(+)$1	1	8	36	15.0261
((((((((((((......)))...))))	chr12:105536848-105537088(+)$1	1	106	134	14.5809
.((((.....((......))....))))	chr16:24582097-24582337(+)$1	1	165	193	14.7908
((.(((((.(((......))).))))).	chr19:47227975-47228215(-)$1	1	40	68	15.4556
))((((((.(((......))).))))))	chr2:69556742-69556982(-)$1	1	209	237	13.2663
((((((...(((......))).))))))	chr22:44892811-44893051(-)$1	1	28	56	13.7203
((((.(((.(((......)))))).)))	chr2:120979447-120979687(-)$1	1	162	190	14.5960
(.((.(((..((......))....))).	chr11:64621798-64622038(-)$1	1	173	201	15.2100
((((.(.(((((......))))).))))	chr1:109177654-109177894(+)$1	1	80	108	11.7082
(((((((((.(......).)))..))))	chr22:20074672-20074912(+)$1	1	54	82	12.6915
((((((...(((......))))))))))	chr6:53785369-53785649(+)$1	1	9	37	16.3680
((((((....((......))..))))))	chr15:44853124-44853366(+)$1	1	149	177	15.6408
...(((....(((...)))....)))))	chr21:28209862-28210104(-)$1	1	82	110	11.0901
(((.((((.(((......))).))))))	chr1:202858095-202858335(-)$1	1	186	214	14.4410
(((((((..(((......)))...))))	chr17:58144879-58145119(-)$1	1	133	161	16.6204
((((...(.((((......)))).)...	chr11:61179217-61179457(-)$1	1	157	185	11.6554
(((.(((...((......))...))).)	chr5:98209252-98209492(-)$1	1	46	74	15.9206
(((((((...((......))))))).))	chr15:100246894-100247134(+)$1	1	169	197	14.4773
)))(((((.(((......))))))))..	chr13:113883666-113883906(+)$1	1	51	79	12.9723
..(((((...((......))..))))).	chr10:27462033-27462273(+)$1	1	32	60	15.2721
((((((...((......)).)).)))))	chr19:18557095-18557335(-)$1	1	1	29	11.3707
(...(((..(((......))).)))...	chr13:46104759-46104999(+)$1	1	190	218	16.0833
((.(((....((......))....))).	chr14:68264684-68264924(-)$1	1	62	90	16.4725
...((((..(((......)))..)))).	chr16:8948940-8949180(-)$1	1	16	44	16.0634
))((((((.(((......))).))))))	chr2:33817125-33817372(-)$1	1	171	199	13.6809
))((((((.(.(......).).))))))	chr2:10799196-10799436(-)$1	1	186	214	12.6709
(((((((((.((......))))))))).	chr1:214816513-214816753(+)$1	1	75	103	13.3340
)))(((((.(((......))).))))).	chr13:96282176-96282456(-)$1	1	72	100	14.2530
((.(((...((((.....))))...)))	chr19:19453525-19453771(+)$1	1	60	88	10.3345
(((((((..(((......)))..)))))	chr14:24705098-24705338(+)$1	1	87	115	16.2221
..((((.(((((......)))))....)	chr4:17816396-17816636(+)$1	1	22	50	12.3310
.((((((..(((......)))..)))))	chr11:65386296-65386549(+)$1	1	57	85	14.2297
...(((....((......))....))).	chr11:10789516-10789756(+)$1	1	94	122	15.7575
)((((..(((((......)))))..)))	chr19:44571236-44571476(+)$1	1	150	178	11.5719
(..(((((..(((.....)))..)))))	chr10:103565721-103565961(-)$1	1	198	226	11.3236
.(((((((.(((......))).))).))	chr1:78046611-78046851(-)$1	1	68	96	15.3728

#PSSM
g : 0.20	d : 0.16	c : 0.09	b : 0.07	= : 0.07	e : 0.07	# : 0.05	! : 0.05	a : 0.03	: : 0.03	% : 0.01	[ : 0.01	F : 0.01	h : 0.01	" : 0.01	$ : 0.01	f : 0.01	
d : 0.20	g : 0.18	e : 0.11	! : 0.09	= : 0.07	[ : 0.05	c : 0.05	" : 0.05	# : 0.03	% : 0.01	2 : 0.01	F : 0.01	h : 0.01	b : 0.01	f : 0.01	$ : 0.01	
d : 0.24	e : 0.18	g : 0.12	f : 0.07	" : 0.05	! : 0.05	[ : 0.05	# : 0.03	c : 0.03	b : 0.03	= : 0.03	2 : 0.01	h : 0.01	$ : 0.01	
e : 0.24	d : 0.24	g : 0.11	c : 0.11	f : 0.09	[ : 0.05	" : 0.03	b : 0.03	= : 0.03	# : 0.01	h : 0.01	
d : 0.22	e : 0.20	c : 0.16	[ : 0.09	g : 0.09	f : 0.09	b : 0.03	= : 0.03	# : 0.01	h : 0.01	" : 0.01	
c : 0.24	e : 0.20	d : 0.16	g : 0.09	f : 0.09	b : 0.05	= : 0.03	# : 0.01	$ : 0.01	h : 0.01	a : 0.01	" : 0.01	! : 0.01	
e : 0.16	c : 0.16	" : 0.12	# : 0.11	f : 0.09	[ : 0.07	d : 0.07	g : 0.07	! : 0.05	b : 0.03	$ : 0.01	
" : 0.18	! : 0.18	c : 0.12	e : 0.12	# : 0.11	f : 0.07	a : 0.05	b : 0.03	d : 0.03	g : 0.03	$ : 0.01	
[ : 0.25	! : 0.20	" : 0.18	# : 0.11	c : 0.05	e : 0.05	d : 0.03	g : 0.03	b : 0.01	f : 0.01	$ : 0.01	
c : 0.51	# : 0.11	" : 0.07	d : 0.07	[ : 0.05	! : 0.05	e : 0.05	$ : 0.01	b : 0.01	a : 0.01	
c : 0.55	b : 0.25	d : 0.07	e : 0.05	[ : 0.03	a : 0.01	
c : 0.55	b : 0.24	d : 0.07	e : 0.05	a : 0.03	o : 0.03	
o : 0.87	c : 0.05	n : 0.03	d : 0.03	
o : 0.88	n : 0.07	m : 0.01	l : 0.01	
o : 0.88	n : 0.07	m : 0.01	l : 0.01	
o : 0.88	n : 0.07	m : 0.01	l : 0.01	
o : 0.88	n : 0.07	m : 0.01	c : 0.01	
o : 0.85	c : 0.07	n : 0.03	a : 0.01	b : 0.01	
c : 0.55	b : 0.25	d : 0.05	e : 0.05	a : 0.03	] : 0.01	o : 0.01	
c : 0.57	b : 0.24	d : 0.07	e : 0.05	] : 0.03	4 : 0.01	
c : 0.51	4 : 0.16	d : 0.07	e : 0.07	2 : 0.05	3 : 0.03	g : 0.03	b : 0.01	a : 0.01	
] : 0.22	2 : 0.18	4 : 0.16	d : 0.09	3 : 0.09	e : 0.09	c : 0.05	g : 0.03	> : 0.01	= : 0.01	b : 0.01	
4 : 0.16	2 : 0.16	e : 0.14	3 : 0.11	c : 0.07	d : 0.05	f : 0.05	a : 0.03	] : 0.03	g : 0.03	> : 0.03	= : 0.03	b : 0.01	h : 0.01	
4 : 0.16	e : 0.14	c : 0.12	d : 0.09	] : 0.07	3 : 0.07	f : 0.07	g : 0.05	2 : 0.05	b : 0.03	> : 0.03	= : 0.03	h : 0.01	
e : 0.22	c : 0.18	d : 0.14	f : 0.09	g : 0.07	b : 0.05	3 : 0.03	> : 0.03	a : 0.03	= : 0.03	h : 0.01	] : 0.01	4 : 0.01	2 : 0.01	
e : 0.20	d : 0.18	c : 0.16	f : 0.09	g : 0.07	3 : 0.05	] : 0.05	b : 0.03	> : 0.03	= : 0.03	4 : 0.03	h : 0.01	
d : 0.20	e : 0.18	g : 0.11	c : 0.11	f : 0.09	3 : 0.07	> : 0.03	b : 0.03	= : 0.03	4 : 0.03	G : 0.01	h : 0.01	] : 0.01	: : 0.01	
d : 0.18	e : 0.14	3 : 0.09	] : 0.09	f : 0.09	g : 0.07	c : 0.05	2 : 0.05	> : 0.03	b : 0.03	= : 0.03	: : 0.03	G : 0.01	h : 0.01	4 : 0.01	

#score	756.8810913579899
#seq	54
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_CDS_m1_run1.txt

#BEAR
fffffwwwwwwwwwwwwwwffff	chr16:23570763-23571017(+)$1	254	154	177	21.7777
Icccvvvvvvvvvvvvvccc:ee	chrX:135956225-135956548(-)$1	323	153	176	21.1913
!!cccyyyyyyyyyyyyyyyycc	chr11:63743596-63744089(+)$1	493	402	425	19.4073
##bbvvvvvvvvvvvvvbb333c	chr22:36141874-36142119(-)$1	245	94	117	22.4158
fffffuuuuuuuuuuuuffffff	chr17:7403878-7404267(+)$1	389	9	32	22.7164
"ddddwwwwwwwwwwwwwwdddd	chr10:28906509-28906779(+)$1	270	62	85	22.0424
eeeeewwwwwwwwwwwwwweeee	chr15:72499367-72499718(-)$1	351	229	252	21.9788
eeeeewwwwwwwwwwwwwweeee	chr15:68582020-68582288(+)$1	268	205	228	21.9788
======ttttttttttt======	chr17:16285703-16286138(+)$1	435	140	163	22.5659
!ddddvvvvvvvvvvvvvdddd2	chr6:44217311-44217665(+)$1	354	56	79	24.0551
eddddtttttttttttdddd22e	chr16:31202640-31203058(+)$1	418	106	129	21.4029
""ddddtttttttttttdddd22	chr12:6647190-6647627(+)$1	437	178	201	22.3849
ddcccuuuuuuuuuuuuccc]dd	chr19:9677294-9677575(-)$1	281	78	101	23.0485
bbccctttttttttttcccdddd	chr11:14535108-14535345(-)$1	237	186	209	21.4876
:dddduuuuuuuuuuuudddd::	chr9:33036536-33036787(+)$1	251	115	138	20.3328
ggddddtttttttttttdddd22	chr19:59067981-59068214(-)$1	233	32	55	22.2814
""cccwwwwwwwwwwwwwwccc3	chr10:129907185-129907508(-)$1	323	114	137	22.6264
!!ddddtttttttttttdddd22	chr12:57038902-57039237(-)$1	335	187	210	22.4961
ggggggtttttttttttgggggg	chr17:8283013-8283304(-)$1	291	16	39	22.1303
fffffuuuuuuuuuuuuffffff	chr1:113471694-113472056(-)$1	362	199	222	22.7164
e[cccvvvvvvvvvvvvvccc]e	chr1:28169608-28169857(+)$1	249	77	100	24.3671
fffffftttttttttttffffff	chr19:34710213-34710578(+)$1	365	6	29	21.7457
:ddddvvvvvvvvvvvvvdddd:	chr6:34212922-34213247(+)$1	325	205	228	22.0215
ceeeeettttttttttteeeee2	chrX:153297841-153298077(-)$1	236	2	25	21.9462
"""ccctttttttttttccc]==	chr17:66038209-66038569(+)$1	360	179	202	22.8100
hhhhhvvvvvvvvvvvvvhhhhh	chr6:26056399-26056779(-)$1	380	338	361	21.8112
eeeeevvvvvvvvvvvvveeeee	chr4:30724511-30724806(+)$1	295	89	112	23.7475
!ddddvvvvvvvvvvvvvdddd]	chr15:65892044-65892325(-)$1	281	95	118	24.1997
""cccvvvvvvvvvvvvvccc44	chr19:10505618-10505913(-)$1	295	203	226	24.4430
ggggggtttttttttttgggggg	chr11:62327653-62328026(-)$1	373	106	129	22.1303
d[ddddtttttttttttdddddd	chr7:149189899-149190157(-)$1	258	121	144	22.0251
eeeeeettttttttttteeeee3	chr9:86586696-86587180(-)$1	484	289	312	22.1463
:dddduuuuuuuuuuuudddd::	chr19:40741803-40742111(-)$1	308	179	202	20.3328
[ddddvvvvvvvvvvvvvdddd]	chr19:29698657-29698929(-)$1	272	102	125	24.1842
e!!awwwwwwwwwwwwwwa22ee	chr20:5095663-5096102(-)$1	439	122	145	21.5206
eeeeevvvvvvvvvvvvveeeee	chr1:182353668-182353927(-)$1	259	104	127	23.7475
eeeeevvvvvvvvvvvvveeeee	chr21:34926227-34926668(+)$1	441	416	439	23.7475
edddduuuuuuuuuuuudddd]e	chr16:30545897-30546164(-)$1	267	38	61	23.2531
ggggguuuuuuuuuuuugggggg	chrX:24024484-24024917(-)$1	433	45	68	23.1976
ffffvvvvvvvvvvvvvffffff	chr3:101311445-101311677(+)$1	232	99	122	22.8202
eeeeevvvvvvvvvvvvveeeee	chr19:36727829-36728249(+)$1	420	396	419	23.7475
ffffvvvvvvvvvvvvvffffff	chr4:109546183-109546499(+)$1	316	233	256	22.8202
f[ddddtttttttttttdddd]f	chr1:225147755-225147999(+)$1	244	113	136	22.5304
$cccvvvvvvvvvvvvvcccfff	chr6:24777349-24777589(+)$1	240	118	141	23.3352
fffffftttttttttttffffff	chr19:50001073-50001403(+)$1	330	210	233	21.7457
iiiwwwwwwwwwwwwwwiiiiii	chr19:33202662-33202901(+)$1	239	178	201	21.2624
ff[bbtttttttttttbb22fff	chr22:21224582-21224872(+)$1	290	127	150	20.3359
b[ccctttttttttttcccbb]b	chr19:49377030-49377268(+)$1	238	49	72	21.3676
gggbbuuuuuuuuuuuubb]ggg	chr19:59059311-59059647(+)$1	336	161	184	22.4514
"ddddvvvvvvvvvvvvvdddd5	chr9:136216346-136216655(+)$1	309	134	157	23.3326
cccbbvvvvvvvvvvvvvbb]cc	chr9:125639653-125639948(-)$1	295	96	119	22.9047
cddddtttttttttttdddd]cc	chr8:54965130-54965416(-)$1	286	18	41	21.6955
##cccuuuuuuuuuuuuccc444	chr16:56468571-56468841(-)$1	270	97	120	23.6614
fffffwwwwwwwwwwwwwwffff	chr2:242572734-242573013(-)$1	279	159	182	21.7777
=====uuuuuuuuuuuu======	chr18:47016756-47017022(-)$1	266	70	93	23.5312
eeeeevvvvvvvvvvvvveeeee	chr8:145140922-145141187(+)$1	265	145	168	23.7475
ggggggtttttttttttgggggg	chr1:24021049-24021381(+)$1	332	293	316	22.1303
edddduuuuuuuuuuuudddd>>	chr16:29706012-29706308(+)$1	296	124	147	22.8531
a[cccwwwwwwwwwwwwwwccc]	chr1:115260427-115260911(-)$1	484	112	135	22.5324
gggggvvvvvvvvvvvvvggggg	chr1:22408114-22408387(+)$1	273	35	58	24.0029
fffffuuuuuuuuuuuuffffff	chr3:180321957-180322183(+)$1	226	185	208	22.7164
!eeeeettttttttttteeeee]	chr3:52027565-52027953(-)$1	388	300	323	22.2936
""ccctttttttttttccc333g	chr9:134321701-134322006(+)$1	305	8	31	22.5080
fffffwwwwwwwwwwwwwwffff	chr10:62551805-62552147(+)$1	342	1	24	21.7777
=====vvvvvvvvvvvvv=====	chr18:19208977-19209476(+)$1	499	180	203	24.2036
i[ddddtttttttttttdddd33	chr5:154336619-154336872(+)$1	253	20	43	22.7877
ggcccvvvvvvvvvvvvvccc33	chr3:52027883-52028242(-)$1	359	45	68	24.5347
fffffuuuuuuuuuuuuffffff	chr3:12880747-12881085(-)$1	338	19	42	22.7164
[ddddvvvvvvvvvvvvvdddd2	chr20:54973922-54974234(+)$1	312	44	67	24.0395
f[cccuuuuuuuuuuuucccfff	chr16:3282360-3282589(-)$1	229	97	120	23.6356
==[bbuuuuuuuuuuuubb]===	chr10:27415539-27415778(-)$1	239	36	59	22.5368

#otherMatches

#Seq PSSM
CAGUAAACACACCCAAAGAUGCU	chr16:23570763-23571017(+)$1	254	154	177	21.7777
GUGAUUCCUACAGCAGUUCAAGC	chrX:135956225-135956548(-)$1	323	153	176	21.1913
AAUCUAUUUAAACUUUACUUCAG	chr11:63743596-63744089(+)$1	493	402	425	19.4073
CAGCCGACCCCUACCAUGCCCUU	chr22:36141874-36142119(-)$1	245	94	117	22.4158
AUUUCUCUAUCAUCCCUGAGAUG	chr17:7403878-7404267(+)$1	389	9	32	22.7164
UUCUUUAAUUACAGGCAUCAAGA	chr10:28906509-28906779(+)$1	270	62	85	22.0424
GCCUGUCAUCUGUGCUACUCAGG	chr15:72499367-72499718(-)$1	351	229	252	21.9788
GUGCUGAUCCCAAUGCCAAAGCA	chr15:68582020-68582288(+)$1	268	205	228	21.9788
UUUCUGACUACAACAUCCAGAAA	chr17:16285703-16286138(+)$1	435	140	163	22.5659
UUUGCUUCUUUAAAACUUGUGAU	chr6:44217311-44217665(+)$1	354	56	79	24.0551
GAGGCCGUAUUAAUUAGCCUGGC	chr16:31202640-31203058(+)$1	418	106	129	21.4029
AAGAGGAAGAGAGAGACCCUCAC	chr12:6647190-6647627(+)$1	437	178	201	22.3849
GUUGAUCAGUCACAUCUUCAGGC	chr19:9677294-9677575(-)$1	281	78	101	23.0485
AGCUCGUACUUACUUGGAGAGAC	chr11:14535108-14535345(-)$1	237	186	209	21.4876
UUGACAACCGAACCAUCGUCAUC	chr9:33036536-33036787(+)$1	251	115	138	20.3328
CUCUCUUUUCUUUUCCUGGAGCC	chr19:59067981-59068214(-)$1	233	32	55	22.2814
AUCCUAAAAAGAGGUCAGAAGGC	chr10:129907185-129907508(-)$1	323	114	137	22.6264
ACGUCCAGUUUGAUGAGGGACUA	chr12:57038902-57039237(-)$1	335	187	210	22.4961
UUCAAAUAUUUGUUACUUUUGAA	chr17:8283013-8283304(-)$1	291	16	39	22.1303
GAGCUUUCAUUUCCAUCGGCUUC	chr1:113471694-113472056(-)$1	362	199	222	22.7164
CCCUGGCUUAGAACCUGACAGAG	chr1:28169608-28169857(+)$1	249	77	100	24.3671
AGCACAAUAGCAACAUCUGUGCU	chr19:34710213-34710578(+)$1	365	6	29	21.7457
UGGCACGCCCUACUCCACUGCCC	chr6:34212922-34213247(+)$1	325	205	228	22.0215
CUCUGCUCACUUGUUCUGCAGAC	chrX:153297841-153298077(-)$1	236	2	25	21.9462
UCCCAGCAUUCAUUUCUCUGUUG	chr17:66038209-66038569(+)$1	360	179	202	22.8100
UGUGGAGAAAAACAACAGCCGUA	chr6:26056399-26056779(-)$1	380	338	361	21.8112
CUCCCUGAUUGUCAAGGUGGGAG	chr4:30724511-30724806(+)$1	295	89	112	23.7475
GAGGGUCACUGCGACAUUCCCUA	chr15:65892044-65892325(-)$1	281	95	118	24.1997
UCACUAAGAUUAAGGUAGGGUCC	chr19:10505618-10505913(-)$1	295	203	226	24.4430
UGUGUUGGAUGAAUUUAAGCGCA	chr11:62327653-62328026(-)$1	373	106	129	22.1303
UCUCCCAGAUUGAACAAGGGAAG	chr7:149189899-149190157(-)$1	258	121	144	22.0251
CGAGGACCACCUCCCCCUCCUCC	chr9:86586696-86587180(-)$1	484	289	312	22.1463
GCCUGCCCUUCUACAACCAGGAC	chr19:40741803-40742111(-)$1	308	179	202	20.3328
AAUCGAAAUCAAGUUAUCCGAUA	chr19:29698657-29698929(-)$1	272	102	125	24.1842
ACACUUAAAAUACUACUUGGCUC	chr20:5095663-5096102(-)$1	439	122	145	21.5206
GGCACCAGUACCACAUCCGUGCC	chr1:182353668-182353927(-)$1	259	104	127	23.7475
GGAGGAGAAAAAGAAGUACCUCC	chr21:34926227-34926668(+)$1	441	416	439	23.7475
CUUAGUUUCCAUCCCCUCUAGUG	chr16:30545897-30546164(-)$1	267	38	61	23.2531
UUUUCUUCUGAAUGCAUGGAAGU	chrX:24024484-24024917(-)$1	433	45	68	23.1976
GGGAGCGAAAUAUAAAAUCUCAU	chr3:101311445-101311677(+)$1	232	99	122	22.8202
CCCAUGAAAGCCUUGAAAGUGGG	chr19:36727829-36728249(+)$1	420	396	419	23.7475
UGACUUUUUUUUUUUCUGUUGUA	chr4:109546183-109546499(+)$1	316	233	256	22.8202
AGUAUAAUUCAACAACAUAUGGU	chr1:225147755-225147999(+)$1	244	113	136	22.5304
CUACAUAAUGAAUCCCAGUAUGA	chr6:24777349-24777589(+)$1	240	118	141	23.3352
CACCUGUCCCCCUGCUUCAGGUG	chr19:50001073-50001403(+)$1	330	210	233	21.7457
UAGUAAGAAAAAGCCAUUUGUAG	chr19:33202662-33202901(+)$1	239	178	201	21.2624
ACAUCAAUAGCAUUAAGAGCGUG	chr22:21224582-21224872(+)$1	290	127	150	20.3359
AAGCUGUAAAGAAAGAAGCUCAC	chr19:49377030-49377268(+)$1	238	49	72	21.3676
GAGCACAUUCUGCGCUUUGCCUC	chr19:59059311-59059647(+)$1	336	161	184	22.4514
GAGCCAUCCUCUAUAAGCGGCUG	chr9:136216346-136216655(+)$1	309	134	157	23.3326
ACAGCAAAUACAAGACUAGCAUG	chr9:125639653-125639948(-)$1	295	96	119	22.9047
AUAUCAUUAGUAACAAGAUAUUC	chr8:54965130-54965416(-)$1	286	18	41	21.6955
CAGUAUCCAUAUAUUCCUGCACA	chr16:56468571-56468841(-)$1	270	97	120	23.6614
UUCUCCUCUAAGCACACCCGAGA	chr2:242572734-242573013(-)$1	279	159	182	21.7777
AAAUGACUCAUCAUCUCCAUUUU	chr18:47016756-47017022(-)$1	266	70	93	23.5312
CCCCAUUCUGCCUCCUUCUGGGG	chr8:145140922-145141187(+)$1	265	145	168	23.7475
AUGUGGUAUGUUGGUGUUCACAU	chr1:24021049-24021381(+)$1	332	293	316	22.1303
GGGCAGCCUUUCUUCGAUGCCAU	chr16:29706012-29706308(+)$1	296	124	147	22.8531
CAUUGACUAACCACAUCCACAAA	chr1:115260427-115260911(-)$1	484	112	135	22.5324
AGUUGUCCUGUCCCAUUUUAACU	chr1:22408114-22408387(+)$1	273	35	58	24.0029
uuuuguuuuuauuaauuuaaaaa	chr3:180321957-180322183(+)$1	226	185	208	22.7164
UGAGGCAGGAUUUGUUAGCCUCU	chr3:52027565-52027953(-)$1	388	300	323	22.2936
CUUGACCUUCAGAACCUCAUACG	chr9:134321701-134322006(+)$1	305	8	31	22.5080
UUCAGGUAGCUAUUAAAAACUGA	chr10:62551805-62552147(+)$1	342	1	24	21.7777
UUGUUUAUGUCAGUUUUUAAUAA	chr18:19208977-19209476(+)$1	499	180	203	24.2036
ACAUUGACUUUGUAAACUAAUUU	chr5:154336619-154336872(+)$1	253	20	43	22.7877
CAGGGAGAGACUUGGGGACCCAC	chr3:52027883-52028242(-)$1	359	45	68	24.5347
CACAGACGCUAACCCACCUGUGU	chr3:12880747-12881085(-)$1	338	19	42	22.7164
UCUGGAUUUAAUUGUUCACCAGU	chr20:54973922-54974234(+)$1	312	44	67	24.0395
GCUUGGAUCCUACUCAACAACUC	chr16:3282360-3282589(-)$1	229	97	120	23.6356
GUUAUUUGGAAAAUUGUGUCACU	chr10:27415539-27415778(-)$1	239	36	59	22.5368

#DB
(((((..............))))	chr16:23570763-23571017(+)$1	1	154	177	21.7777
((((.............))).((	chrX:135956225-135956548(-)$1	1	153	176	21.1913
..(((................))	chr11:63743596-63744089(+)$1	1	402	425	19.4073
..((.............))...)	chr22:36141874-36142119(-)$1	1	94	117	22.4158
(((((............))))))	chr17:7403878-7404267(+)$1	1	9	32	22.7164
.((((..............))))	chr10:28906509-28906779(+)$1	1	62	85	22.0424
(((((..............))))	chr15:72499367-72499718(-)$1	1	229	252	21.9788
(((((..............))))	chr15:68582020-68582288(+)$1	1	205	228	21.9788
((((((...........))))))	chr17:16285703-16286138(+)$1	1	140	163	22.5659
.((((.............)))).	chr6:44217311-44217665(+)$1	1	56	79	24.0551
(((((...........))))..)	chr16:31202640-31203058(+)$1	1	106	129	21.4029
..((((...........))))..	chr12:6647190-6647627(+)$1	1	178	201	22.3849
(((((............))).))	chr19:9677294-9677575(-)$1	1	78	101	23.0485
))(((...........)))((((	chr11:14535108-14535345(-)$1	1	186	209	21.4876
.((((............))))..	chr9:33036536-33036787(+)$1	1	115	138	20.3328
((((((...........))))..	chr19:59067981-59068214(-)$1	1	32	55	22.2814
..(((..............))).	chr10:129907185-129907508(-)$1	1	114	137	22.6264
..((((...........))))..	chr12:57038902-57039237(-)$1	1	187	210	22.4961
((((((...........))))))	chr17:8283013-8283304(-)$1	1	16	39	22.1303
(((((............))))))	chr1:113471694-113472056(-)$1	1	199	222	22.7164
(.(((.............))).)	chr1:28169608-28169857(+)$1	1	77	100	24.3671
((((((...........))))))	chr19:34710213-34710578(+)$1	1	6	29	21.7457
.((((.............)))).	chr6:34212922-34213247(+)$1	1	205	228	22.0215
((((((...........))))).	chrX:153297841-153298077(-)$1	1	2	25	21.9462
...(((...........))).))	chr17:66038209-66038569(+)$1	1	179	202	22.8100
(((((.............)))))	chr6:26056399-26056779(-)$1	1	338	361	21.8112
(((((.............)))))	chr4:30724511-30724806(+)$1	1	89	112	23.7475
.((((.............)))).	chr15:65892044-65892325(-)$1	1	95	118	24.1997
..(((.............)))..	chr19:10505618-10505913(-)$1	1	203	226	24.4430
((((((...........))))))	chr11:62327653-62328026(-)$1	1	106	129	22.1303
(.((((...........))))))	chr7:149189899-149190157(-)$1	1	121	144	22.0251
((((((...........))))).	chr9:86586696-86587180(-)$1	1	289	312	22.1463
.((((............))))..	chr19:40741803-40742111(-)$1	1	179	202	20.3328
.((((.............)))).	chr19:29698657-29698929(-)$1	1	102	125	24.1842
(..(..............)..))	chr20:5095663-5096102(-)$1	1	122	145	21.5206
(((((.............)))))	chr1:182353668-182353927(-)$1	1	104	127	23.7475
(((((.............)))))	chr21:34926227-34926668(+)$1	1	416	439	23.7475
(((((............)))).)	chr16:30545897-30546164(-)$1	1	38	61	23.2531
(((((............))))))	chrX:24024484-24024917(-)$1	1	45	68	23.1976
((((.............))))))	chr3:101311445-101311677(+)$1	1	99	122	22.8202
(((((.............)))))	chr19:36727829-36728249(+)$1	1	396	419	23.7475
((((.............))))))	chr4:109546183-109546499(+)$1	1	233	256	22.8202
(.((((...........)))).)	chr1:225147755-225147999(+)$1	1	113	136	22.5304
.(((.............))))))	chr6:24777349-24777589(+)$1	1	118	141	23.3352
((((((...........))))))	chr19:50001073-50001403(+)$1	1	210	233	21.7457
(((..............))))))	chr19:33202662-33202901(+)$1	1	178	201	21.2624
((.((...........))..)))	chr22:21224582-21224872(+)$1	1	127	150	20.3359
(.(((...........))))).)	chr19:49377030-49377268(+)$1	1	49	72	21.3676
(((((............)).)))	chr19:59059311-59059647(+)$1	1	161	184	22.4514
.((((.............)))).	chr9:136216346-136216655(+)$1	1	134	157	23.3326
(((((.............)).))	chr9:125639653-125639948(-)$1	1	96	119	22.9047
(((((...........)))).))	chr8:54965130-54965416(-)$1	1	18	41	21.6955
..(((............)))...	chr16:56468571-56468841(-)$1	1	97	120	23.6614
(((((..............))))	chr2:242572734-242573013(-)$1	1	159	182	21.7777
(((((............))))))	chr18:47016756-47017022(-)$1	1	70	93	23.5312
(((((.............)))))	chr8:145140922-145141187(+)$1	1	145	168	23.7475
((((((...........))))))	chr1:24021049-24021381(+)$1	1	293	316	22.1303
(((((............))))..	chr16:29706012-29706308(+)$1	1	124	147	22.8531
(.(((..............))).	chr1:115260427-115260911(-)$1	1	112	135	22.5324
(((((.............)))))	chr1:22408114-22408387(+)$1	1	35	58	24.0029
(((((............))))))	chr3:180321957-180322183(+)$1	1	185	208	22.7164
.(((((...........))))).	chr3:52027565-52027953(-)$1	1	300	323	22.2936
..(((...........)))...)	chr9:134321701-134322006(+)$1	1	8	31	22.5080
(((((..............))))	chr10:62551805-62552147(+)$1	1	1	24	21.7777
(((((.............)))))	chr18:19208977-19209476(+)$1	1	180	203	24.2036
(.((((...........))))..	chr5:154336619-154336872(+)$1	1	20	43	22.7877
(((((.............)))..	chr3:52027883-52028242(-)$1	1	45	68	24.5347
(((((............))))))	chr3:12880747-12881085(-)$1	1	19	42	22.7164
.((((.............)))).	chr20:54973922-54974234(+)$1	1	44	67	24.0395
(.(((............))))))	chr16:3282360-3282589(-)$1	1	97	120	23.6356
((.((............)).)))	chr10:27415539-27415778(-)$1	1	36	59	22.5368

#PSSM
f : 0.19	e : 0.18	g : 0.11	" : 0.09	! : 0.07	= : 0.05	: : 0.04	c : 0.04	# : 0.02	d : 0.02	b : 0.02	[ : 0.02	i : 0.02	I : 0.01	h : 0.01	$ : 0.01	a : 0.01	
d : 0.19	f : 0.16	e : 0.14	g : 0.11	[ : 0.09	" : 0.07	= : 0.05	c : 0.04	! : 0.04	# : 0.02	b : 0.01	h : 0.01	i : 0.01	
d : 0.26	c : 0.21	f : 0.15	e : 0.14	g : 0.08	= : 0.04	[ : 0.02	b : 0.01	" : 0.01	h : 0.01	! : 0.01	i : 0.01	
d : 0.26	c : 0.21	f : 0.15	e : 0.14	b : 0.07	g : 0.07	= : 0.04	h : 0.01	a : 0.01	w : 0.01	
d : 0.26	c : 0.18	e : 0.14	f : 0.12	v : 0.07	g : 0.07	b : 0.05	= : 0.04	w : 0.02	h : 0.01	
v : 0.32	u : 0.21	w : 0.14	t : 0.08	d : 0.08	g : 0.04	e : 0.04	f : 0.02	y : 0.01	= : 0.01	c : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.30	u : 0.21	w : 0.14	y : 0.01	
v : 0.32	t : 0.22	u : 0.21	w : 0.14	c : 0.04	d : 0.02	y : 0.01	b : 0.01	
v : 0.25	d : 0.16	w : 0.12	c : 0.12	f : 0.11	b : 0.05	g : 0.05	e : 0.04	= : 0.02	y : 0.01	i : 0.01	
d : 0.25	c : 0.16	w : 0.11	f : 0.11	e : 0.11	g : 0.07	b : 0.05	= : 0.04	y : 0.01	h : 0.01	a : 0.01	i : 0.01	2 : 0.01	
d : 0.28	f : 0.15	c : 0.15	e : 0.14	g : 0.07	= : 0.04	3 : 0.02	2 : 0.02	b : 0.02	] : 0.02	y : 0.01	h : 0.01	i : 0.01	
d : 0.25	f : 0.19	e : 0.14	g : 0.08	c : 0.07	= : 0.05	] : 0.05	3 : 0.02	2 : 0.02	: : 0.01	y : 0.01	h : 0.01	i : 0.01	b : 0.01	4 : 0.01	
f : 0.19	e : 0.16	d : 0.14	g : 0.08	c : 0.07	= : 0.07	3 : 0.05	2 : 0.05	] : 0.05	: : 0.02	4 : 0.02	h : 0.01	i : 0.01	> : 0.01	
f : 0.21	e : 0.16	g : 0.09	2 : 0.08	= : 0.07	c : 0.05	d : 0.05	3 : 0.05	] : 0.05	: : 0.04	4 : 0.02	h : 0.01	i : 0.01	b : 0.01	5 : 0.01	> : 0.01	

#score	1602.7532070846785
#seq	71
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_UTR_m2_run2.txt

#BEAR
occc]eeeeecccooooooccc::iiiiiiiii	chr9:129598138-129598361(+)$1	223	102	135	12.0805
gggggggggggggooooooggggggg22ggggg	chr20:13280020-13280240(+)$1	220	92	125	14.8283
ee[a[bb!!ddddoooooodddd333bbaeeee	chr3:122143836-122144056(-)$1	220	129	162	12.2430
==========[ddddmmmmdddd]=========	chr5:79773019-79773244(+)$1	225	150	183	12.6371
ggggggg"""cccoooooocccggggggg::::	chr1:110135422-110135644(+)$1	222	178	211	11.8992
ggggggg[ccc[bbnnnnnbb22cccggggggg	chr17:7481173-7481424(+)$1	251	29	62	12.0387
eee[ggggggg[cccmmmmccc]gggggggeee	chr5:139625492-139625714(-)$1	222	179	212	10.6667
iiiii####ddddooooooddddiiiiiiiiid	chr14:55515198-55515421(+)$1	223	31	64	14.8955
:==============mmmm==============	chr10:104573462-104573687(+)$1	225	185	218	13.4306
==========[bbpppppppbb333========	chr6:31590433-31590662(+)$1	229	10	43	11.9110
======$$$$$cccnnnnnccc===========	chr19:810744-810985(+)$1	241	193	226	13.8296
hhh[iiiiiiiiirrrrrrrrriiiiiiiii22	chr10:62629758-62629979(-)$1	221	109	142	11.5165
ffffbbgggggggooooooggggggg]bbdddd	chr19:49993937-49994181(+)$1	244	75	108	12.1867
dd####gggggggooooooggggggg666666d	chr20:42275589-42275811(+)$1	222	144	177	11.1214
============ssssssssss===========	chr22:41488417-41488639(+)$1	222	109	142	11.9628
c[ccc!!bb!!bboooooobb4444bb22ccc]	chr17:31268376-31268600(+)$1	224	103	136	13.9445
[ccc"""bb[cccooooooccc22bb]ccc]bb	chr7:140420721-140420947(-)$1	226	166	199	13.4680
"==========[bbnnnnnbb==========33	chr2:87001821-87002042(+)$1	221	107	140	14.8713
ccca[ffffffbboooooobb]ffffff]a888	chr22:38363573-38363797(+)$1	224	124	157	11.0499
=============oooooo==============	chr6:109484879-109485098(+)$1	219	57	90	17.9879
==========!!bbnnnnnbb22==========	chr6:15521162-15521388(+)$1	226	82	115	14.7187
b==============mmmm==============	chr3:184299884-184300106(+)$1	222	162	195	14.2125
h[ggggggg!!bboooooobb666666gggggg	chr5:77782623-77782854(-)$1	231	16	49	12.7229
"ffffff"""cccooooooccc22ffffff333	chr6:30593989-30594208(+)$1	219	157	190	13.9221
bb"""iiiiiiiiinnnnniiiiiiiii]bb]g	chrX:46920410-46920630(+)$1	220	60	93	12.3431
==========!!ccclllccc22==========	chr4:110971505-110971726(-)$1	221	44	77	14.1944
$$$dddd"""cccooooooccc]dddd4444ii	chr9:84198737-84198963(-)$1	226	92	125	13.0259
g!!eeeee!!cccrrrrrrrrrccc4444eeee	chrX:103436249-103436478(+)$1	229	31	64	10.0898
gggggg[ffffffooooooffffff333ggggg	chr5:172756380-172756612(-)$1	232	77	110	13.6430
ggggggg"""cccnnnnncccggggggg=====	chr10:43680399-43680633(+)$1	234	196	229	13.2602
ffff"""ccc[bboooooobb]ccc4444ffff	chr20:5171960-5172185(+)$1	225	8	41	13.7287
c[eeeeeccc[bboooooobbccc4444eeeee	chr19:50000458-50000698(+)$1	240	187	220	13.5363
b[a[a!!gggggggnnnnnggggggg22a]a]b	chr6:150464212-150464434(+)$1	222	167	200	11.5633
ddd[a[eeeeebboooooobb4444eeeeea]d	chr2:74688567-74688793(-)$1	226	167	200	12.6772
a!!ggggggg[bblllbb]ggggggg]aa]eee	chr10:43881560-43881786(-)$1	226	171	204	10.4229
:eeeee!!bb[bboooooobb]bb333eeeee:	chr11:128837186-128837407(-)$1	221	49	82	11.3262
gggggggccc[bboooooobbccc22ggggggg	chr19:1390785-1391006(+)$1	221	48	81	14.6856
!bb[eeeee[cccooooooccc]eeeeebb22b	chr7:2702744-2702965(+)$1	221	168	201	11.9701
gggccc!!eeeeeooooooeeeeeccc]ggggg	chr8:81432908-81433132(+)$1	224	92	125	13.0545
c[ccc[gggggggooooooggggggg]ccc]cc	chr19:7682997-7683220(+)$1	223	82	115	14.5870
bb!!ccc!!ddddoooooodddd]ccc]bbccc	chr11:59569617-59569841(+)$1	224	69	102	12.6387
::===========oooooo===========:dd	chr1:167386487-167386710(+)$1	223	123	156	14.0444
====[dddd[cccooooooccc333dddd]===	chr5:122950746-122950971(+)$1	225	17	50	14.6236
c!!ccc####ddddmmmmdddd333cccccc22	chr20:45314285-45314511(-)$1	226	139	172	10.1155
bb[iiiiiiiii[ammmmaiiiiiiiii]bb]b	chr5:177022330-177022549(+)$1	219	53	86	11.6847
"dddd"""bb[ccclllcccbb333dddd333e	chr14:21927184-21927409(-)$1	225	150	183	10.0839
cciiiiiiiii[bbnnnnnbb22iiiiiiiii2	chr5:154195568-154195806(+)$1	238	200	233	13.1442
=============oooooo=============:	chr6:7610311-7610533(+)$1	222	119	152	17.0208
ggggggg"""cccooooooccc333ggggggg:	chr14:73566294-73566519(+)$1	225	149	182	15.6450
eeeee!!bbddddoooooodddd]bb22eeeee	chr10:73576849-73577082(-)$1	233	114	147	11.1970
ffffff"""ddddooooooddddffffffccco	chr1:214526351-214526570(-)$1	219	42	75	11.7790
ca[ccc[ccc[bboooooobb]cccccc]a]cc	chr17:79993795-79994025(-)$1	230	30	63	14.3365

#otherMatches

#Seq PSSM
UAUUACUCCUACUAAUUUCAGUACUAAGGUGGU	chr9:129598138-129598361(+)$1	223	102	135	12.0805
UGGGAUGAGGUGGAGGACGCUGCCUCUGGUUCU	chr20:13280020-13280240(+)$1	220	92	125	14.8283
GGCGCAGCCACUGCAAAACUAGUCAACUCCCAU	chr3:122143836-122144056(-)$1	220	129	162	12.2430
UUUUUCAUUAUAGAACAUCUUUUUUAGUGAAAG	chr5:79773019-79773244(+)$1	225	150	183	12.6371
AUUGGAAAGUUCUGCAAUAAGAUUCUAGUUCUC	chr1:110135422-110135644(+)$1	222	178	211	11.8992
CUAGCAGAGUUUUGAUUACCACUGACCUGCUGG	chr17:7481173-7481424(+)$1	251	29	62	12.0387
CUCCUGCCCCUCCCAUUCCUGGUGGGGGCAGAG	chr5:139625492-139625714(-)$1	222	179	212	10.6667
AAGAACAGAAAGCACAAAGGUUUUUCUUUUCUU	chr14:55515198-55515421(+)$1	223	31	64	14.8955
AUGAUAGGUUGGUAGGGGCUUGUUGAUCUGUCA	chr10:104573462-104573687(+)$1	225	185	218	13.4306
AGUUUCUGUUAUGGUCUGUACAGGGGACAGAGA	chr6:31590433-31590662(+)$1	229	10	43	11.9110
UAAAGAGAAAUCAGUUUACCUGUUUUUAAAAAA	chr19:810744-810985(+)$1	241	193	226	13.8296
CACACCUGCCAUGGGAUGUUAAUGUGGCAGGGG	chr10:62629758-62629979(-)$1	221	109	142	11.5165
GCCUGCUAUCUGUCACCCAACAGGUAUGCUGCC	chr19:49993937-49994181(+)$1	244	75	108	12.1867
AGCUCUGGAAGGUAUAUGCAUCUUCUGUAAUAC	chr20:42275589-42275811(+)$1	222	144	177	11.1214
GGGAGGAGGUGAGUGUCUCUUGUCGCCUCCUCC	chr22:41488417-41488639(+)$1	222	109	142	11.9628
cuggccuguuucauuuauuuguauuaucugccu	chr17:31268376-31268600(+)$1	224	103	136	13.9445
CCGGCCAGCCGAGUUCAUUCUCCAGCACCGUGA	chr7:140420721-140420947(-)$1	226	166	199	13.4680
AUUUUAAACUACAGAUGGACUUGGUUUGAGGGA	chr2:87001821-87002042(+)$1	221	107	140	14.8713
GGACGAGCUCAUCAUCACCGACUGAGCUGGAGU	chr22:38363573-38363797(+)$1	224	124	157	11.0499
UUUUUUUUUGUACAAGAAAGUAUAGAGGAAGAG	chr6:109484879-109485098(+)$1	219	57	90	17.9879
UUUUUUGGUGCUGUUGGCUACUUUAUCAAAAAA	chr6:15521162-15521388(+)$1	226	82	115	14.7187
ugugugugugugugugugugcgcgcgcgcgcgc	chr3:184299884-184300106(+)$1	222	162	195	14.2125
AAAGAGGCUGGAGGAGCCACUGGACAAAGCUUC	chr5:77782623-77782854(-)$1	231	16	49	12.7229
AUAAAGCUCUACUGUCUCUGGUUUGCUUUGGGC	chr6:30593989-30594208(+)$1	219	157	190	13.9221
UACCCCAAAAUGUAUUUGCUACAUUUUGUUGUU	chrX:46920410-46920630(+)$1	220	60	93	12.3431
UUUUGUUCAGUUGCCCCGGGCUUUUGAACAGAA	chr4:110971505-110971726(-)$1	221	44	77	14.1944
GAUUGAGGAACGGAAUCUGCCGACUCACAUGAC	chr9:84198737-84198963(-)$1	226	92	125	13.0259
AAAUAGAGCAUAGUAACUGUAUCUAAAUUCUCU	chrX:103436249-103436478(+)$1	229	31	64	10.0898
GGGAAGAGGCGCUCCAAGCGGCGCCCAACUUUC	chr5:172756380-172756612(-)$1	232	77	110	13.6430
GCUUGUUUUUUGAGAGAAUCAAAUGAGUUUACU	chr10:43680399-43680633(+)$1	234	196	229	13.2602
AAAUGCACACUUUUUAUAUAAUGUGACCAGUUU	chr20:5171960-5172185(+)$1	225	8	41	13.7287
UUGCCCUGCCUGCAUCUAAGUGGCUUCUGGGGC	chr19:50000458-50000698(+)$1	240	187	220	13.5363
ggcgcACGGGUUUUCUUCCAAAGCCCCCGGGGU	chr6:150464212-150464434(+)$1	222	167	200	11.5633
GGAGCACUCCACCACUAUGGGCAUCUGGAGGGU	chr2:74688567-74688793(-)$1	226	167	200	12.6772
CAAUACUAAUACUGUAGGAAUUGGUGAGGCCUU	chr10:43881560-43881786(-)$1	226	171	204	10.4229
CGAGUUUAGAUUGUCAUUUCAUUCCAUAACUCU	chr11:128837186-128837407(-)$1	221	49	82	11.3262
CGGGGGUGGCGUCUGACCCGAGCCCGGCCUCCG	chr19:1390785-1391006(+)$1	221	48	81	14.6856
CGCAUGGCUCUUCCUCCCAGAGCAGCCGGCAGC	chr7:2702744-2702965(+)$1	221	168	201	11.9701
UGAGAAGCUUUAUUAUUCUAUAAAUUCUUCAGG	chr8:81432908-81433132(+)$1	224	92	125	13.0545
UGAGUCCAGUCCUGCUGUGGGGGCUGAGCUGGG	chr19:7682997-7683220(+)$1	223	82	115	14.5870
CUCACUGAAUUCUUAUCAUGGAAACAGCAGCAG	chr11:59569617-59569841(+)$1	224	69	102	12.6387
UAGAAAGUAAUUAGCUCUGUAAUUAUUUUCAGG	chr1:167386487-167386710(+)$1	223	123	156	14.0444
UUGUUGCAUCACUAUGUGAAGUACUGUGUUGCA	chr5:122950746-122950971(+)$1	225	17	50	14.6236
GUUCCUUGGCACCCUGUUGGGuauuggguacuu	chr20:45314285-45314511(-)$1	226	139	172	10.1155
CAAGAGCUUCUUUGAAGCCAAGAAGCUUGUGUA	chr5:177022330-177022549(+)$1	219	53	86	11.6847
UGAGGUCUUACGAAUUUUUCUACUUUCUUUUUG	chr14:21927184-21927409(-)$1	225	150	183	10.0839
CAGUCUGGUGCCUGCCCCACAUUGUACCGGACA	chr5:154195568-154195806(+)$1	238	200	233	13.1442
AAGAUUUUGUUUCCAAGUAGAAAUGAAAUCUUA	chr6:7610311-7610533(+)$1	222	119	152	17.0208
AGAGACACACAUAAGGUAGUAUUCUUGUCUUUU	chr14:73566294-73566519(+)$1	225	149	182	15.6450
AUGCACUGGAGGUCUUUUAGCCUGCCCUUGCAU	chr10:73576849-73577082(-)$1	233	114	147	11.1970
guccuugaUUGCCCCCUUUGGUAAAGGACAACU	chr1:214526351-214526570(-)$1	219	42	75	11.7790
GAAAGAUGGGCGGCAGCCUCCUUCCUCUAUGCC	chr17:79993795-79994025(-)$1	230	30	63	14.3365

#DB
.))).)))))(((......)))..(((((((((	chr9:129598138-129598361(+)$1	1	102	135	12.0805
(((((((((((((......)))))))..)))))	chr20:13280020-13280240(+)$1	1	92	125	14.8283
((.(.((..((((......))))...)))))))	chr3:122143836-122144056(-)$1	1	129	162	12.2430
((((((((((.((((....)))).)))))))))	chr5:79773019-79773244(+)$1	1	150	183	12.6371
(((((((...(((......))))))))))....	chr1:110135422-110135644(+)$1	1	178	211	11.8992
(((((((.(((.((.....))..))))))))))	chr17:7481173-7481424(+)$1	1	29	62	12.0387
(((.(((((((.(((....))).))))))))))	chr5:139625492-139625714(-)$1	1	179	212	10.6667
(((((....((((......))))))))))))))	chr14:55515198-55515421(+)$1	1	31	64	14.8955
.((((((((((((((....))))))))))))))	chr10:104573462-104573687(+)$1	1	185	218	13.4306
((((((((((.((.......))...))))))))	chr6:31590433-31590662(+)$1	1	10	43	11.9110
((((((.....(((.....))))))))))))))	chr19:810744-810985(+)$1	1	193	226	13.8296
(((.(((((((((.........)))))))))..	chr10:62629758-62629979(-)$1	1	109	142	11.5165
))))(((((((((......))))))).))((((	chr19:49993937-49994181(+)$1	1	75	108	12.1867
((....(((((((......)))))))......)	chr20:42275589-42275811(+)$1	1	144	177	11.1214
((((((((((((..........)))))))))))	chr22:41488417-41488639(+)$1	1	109	142	11.9628
(.(((..((..((......))....))..))).	chr17:31268376-31268600(+)$1	1	103	136	13.9445
.(((...((.(((......)))..)).))).))	chr7:140420721-140420947(-)$1	1	166	199	13.4680
.((((((((((.((.....))))))))))))..	chr2:87001821-87002042(+)$1	1	107	140	14.8713
((((.((((((((......)).)))))).)...	chr22:38363573-38363797(+)$1	1	124	157	11.0499
(((((((((((((......))))))))))))))	chr6:109484879-109485098(+)$1	1	57	90	17.9879
((((((((((..((.....))..))))))))))	chr6:15521162-15521388(+)$1	1	82	115	14.7187
)((((((((((((((....))))))))))))))	chr3:184299884-184300106(+)$1	1	162	195	14.2125
(.(((((((..((......))......))))))	chr5:77782623-77782854(-)$1	1	16	49	12.7229
.((((((...(((......)))..))))))...	chr6:30593989-30594208(+)$1	1	157	190	13.9221
((...(((((((((.....))))))))).)).)	chrX:46920410-46920630(+)$1	1	60	93	12.3431
((((((((((..(((...)))..))))))))))	chr4:110971505-110971726(-)$1	1	44	77	14.1944
...((((...(((......))).))))....))	chr9:84198737-84198963(-)$1	1	92	125	13.0259
(..(((((..(((.........)))....))))	chrX:103436249-103436478(+)$1	1	31	64	10.0898
((((((.((((((......))))))...)))))	chr5:172756380-172756612(-)$1	1	77	110	13.6430
(((((((...(((.....)))))))))))))))	chr10:43680399-43680633(+)$1	1	196	229	13.2602
((((...(((.((......)).)))....))))	chr20:5171960-5172185(+)$1	1	8	41	13.7287
(.((((((((.((......)))))....)))))	chr19:50000458-50000698(+)$1	1	187	220	13.5363
(.(.(..(((((((.....)))))))..).).)	chr6:150464212-150464434(+)$1	1	167	200	11.5633
(((.(.(((((((......))....)))))).)	chr2:74688567-74688793(-)$1	1	167	200	12.6772
(..(((((((.((...)).))))))).)).)))	chr10:43881560-43881786(-)$1	1	171	204	10.4229
.(((((..((.((......)).))...))))).	chr11:128837186-128837407(-)$1	1	49	82	11.3262
((((((((((.((......)))))..)))))))	chr19:1390785-1391006(+)$1	1	48	81	14.6856
.((.(((((.(((......))).)))))))..)	chr7:2702744-2702965(+)$1	1	168	201	11.9701
((((((..(((((......)))))))).)))))	chr8:81432908-81433132(+)$1	1	92	125	13.0545
(.(((.(((((((......))))))).))).))	chr19:7682997-7683220(+)$1	1	82	115	14.5870
((..(((..((((......)))).))).)))))	chr11:59569617-59569841(+)$1	1	69	102	12.6387
..(((((((((((......))))))))))).((	chr1:167386487-167386710(+)$1	1	123	156	14.0444
((((.((((.(((......)))...)))).)))	chr5:122950746-122950971(+)$1	1	17	50	14.6236
(..(((....((((....))))...))))))..	chr20:45314285-45314511(-)$1	1	139	172	10.1155
((.(((((((((.(....)))))))))).)).)	chr5:177022330-177022549(+)$1	1	53	86	11.6847
.((((...((.(((...)))))...))))...)	chr14:21927184-21927409(-)$1	1	150	183	10.0839
(((((((((((.((.....))..))))))))).	chr5:154195568-154195806(+)$1	1	200	233	13.1442
(((((((((((((......))))))))))))).	chr6:7610311-7610533(+)$1	1	119	152	17.0208
(((((((...(((......)))...))))))).	chr14:73566294-73566519(+)$1	1	149	182	15.6450
(((((..((((((......)))).))..)))))	chr10:73576849-73577082(-)$1	1	114	147	11.1970
((((((...((((......))))))))))(((.	chr1:214526351-214526570(-)$1	1	42	75	11.7790
((.(((.(((.((......)).)))))).).))	chr17:79993795-79994025(-)$1	1	30	63	14.3365

#PSSM
g : 0.17	= : 0.17	c : 0.13	b : 0.09	e : 0.05	: : 0.05	f : 0.05	" : 0.05	h : 0.03	d : 0.03	o : 0.01	i : 0.01	[ : 0.01	$ : 0.01	a : 0.01	! : 0.01	
= : 0.23	g : 0.15	[ : 0.09	c : 0.07	e : 0.07	f : 0.07	b : 0.07	d : 0.05	! : 0.05	i : 0.01	h : 0.01	$ : 0.01	: : 0.01	a : 0.01	
= : 0.24	g : 0.17	c : 0.09	e : 0.07	f : 0.07	! : 0.07	[ : 0.05	i : 0.03	d : 0.03	h : 0.01	# : 0.01	" : 0.01	$ : 0.01	a : 0.01	b : 0.01	
= : 0.24	g : 0.17	c : 0.13	[ : 0.09	f : 0.07	e : 0.07	i : 0.05	a : 0.03	d : 0.03	# : 0.01	" : 0.01	! : 0.01	
= : 0.23	g : 0.19	c : 0.11	e : 0.09	i : 0.07	[ : 0.05	" : 0.05	f : 0.03	d : 0.03	a : 0.03	] : 0.01	b : 0.01	# : 0.01	
= : 0.23	g : 0.19	e : 0.09	i : 0.07	c : 0.07	! : 0.05	" : 0.05	f : 0.05	b : 0.03	# : 0.03	d : 0.03	[ : 0.03	
g : 0.23	= : 0.21	e : 0.09	! : 0.09	i : 0.07	" : 0.07	# : 0.03	f : 0.03	d : 0.03	[ : 0.03	b : 0.01	$ : 0.01	c : 0.01	
= : 0.21	g : 0.15	" : 0.13	e : 0.07	! : 0.07	i : 0.07	c : 0.07	b : 0.05	# : 0.03	f : 0.03	[ : 0.01	$ : 0.01	d : 0.01	
= : 0.21	g : 0.15	" : 0.11	c : 0.09	b : 0.09	e : 0.07	i : 0.07	! : 0.05	# : 0.03	f : 0.03	$ : 0.01	d : 0.01	
= : 0.21	g : 0.13	d : 0.09	" : 0.09	c : 0.09	i : 0.07	e : 0.05	! : 0.05	[ : 0.05	f : 0.03	b : 0.03	$ : 0.01	# : 0.01	
c : 0.21	[ : 0.17	= : 0.13	g : 0.11	d : 0.11	i : 0.07	! : 0.07	f : 0.03	e : 0.03	$ : 0.01	
c : 0.23	b : 0.21	d : 0.13	= : 0.11	g : 0.09	[ : 0.07	i : 0.05	! : 0.03	f : 0.01	e : 0.01	
b : 0.28	c : 0.26	d : 0.13	g : 0.09	= : 0.09	i : 0.03	s : 0.01	f : 0.01	e : 0.01	[ : 0.01	
o : 0.59	b : 0.07	c : 0.07	d : 0.03	= : 0.03	r : 0.03	p : 0.01	s : 0.01	i : 0.01	n : 0.01	g : 0.01	l : 0.01	a : 0.01	
o : 0.59	n : 0.15	c : 0.03	= : 0.03	r : 0.03	l : 0.03	m : 0.03	d : 0.01	p : 0.01	s : 0.01	
o : 0.59	n : 0.15	m : 0.11	l : 0.05	r : 0.03	p : 0.01	s : 0.01	
o : 0.59	n : 0.15	m : 0.11	r : 0.03	l : 0.03	p : 0.01	s : 0.01	b : 0.01	
o : 0.59	n : 0.15	m : 0.11	r : 0.03	p : 0.01	s : 0.01	l : 0.01	b : 0.01	c : 0.01	
o : 0.59	n : 0.13	m : 0.07	c : 0.05	r : 0.03	p : 0.01	s : 0.01	] : 0.01	d : 0.01	a : 0.01	
c : 0.24	b : 0.24	d : 0.13	g : 0.11	= : 0.09	r : 0.03	i : 0.03	p : 0.01	s : 0.01	f : 0.01	e : 0.01	
b : 0.28	c : 0.23	d : 0.13	g : 0.11	= : 0.09	r : 0.03	i : 0.03	s : 0.01	f : 0.01	e : 0.01	
c : 0.23	g : 0.13	d : 0.13	= : 0.11	2 : 0.07	] : 0.07	b : 0.03	r : 0.03	4 : 0.03	i : 0.03	s : 0.01	6 : 0.01	f : 0.01	e : 0.01	
g : 0.15	= : 0.15	d : 0.11	2 : 0.11	3 : 0.09	c : 0.09	] : 0.05	i : 0.05	4 : 0.03	f : 0.03	: : 0.01	6 : 0.01	b : 0.01	e : 0.01	
= : 0.19	g : 0.17	3 : 0.11	c : 0.11	i : 0.09	] : 0.05	f : 0.05	4 : 0.03	2 : 0.03	e : 0.03	: : 0.01	6 : 0.01	d : 0.01	b : 0.01	
= : 0.21	g : 0.17	3 : 0.13	i : 0.11	c : 0.11	f : 0.07	4 : 0.05	b : 0.03	6 : 0.01	d : 0.01	2 : 0.01	e : 0.01	
= : 0.23	g : 0.19	i : 0.11	c : 0.09	3 : 0.05	b : 0.05	f : 0.05	d : 0.05	4 : 0.05	e : 0.03	6 : 0.01	2 : 0.01	
= : 0.23	i : 0.11	g : 0.11	] : 0.07	c : 0.07	2 : 0.05	f : 0.05	d : 0.05	4 : 0.05	b : 0.03	6 : 0.03	3 : 0.03	e : 0.03	
= : 0.23	g : 0.13	i : 0.11	2 : 0.07	c : 0.07	4 : 0.07	f : 0.05	e : 0.05	b : 0.03	] : 0.03	d : 0.03	6 : 0.01	3 : 0.01	a : 0.01	
= : 0.24	g : 0.17	i : 0.07	] : 0.07	e : 0.07	a : 0.05	b : 0.05	c : 0.05	4 : 0.05	f : 0.03	d : 0.03	6 : 0.01	2 : 0.01	
= : 0.24	g : 0.15	e : 0.11	c : 0.09	i : 0.07	b : 0.07	] : 0.05	a : 0.03	f : 0.03	: : 0.01	d : 0.01	6 : 0.01	4 : 0.01	3 : 0.01	
= : 0.24	g : 0.13	e : 0.13	i : 0.07	c : 0.07	] : 0.05	: : 0.03	3 : 0.03	b : 0.03	a : 0.03	d : 0.01	6 : 0.01	8 : 0.01	4 : 0.01	f : 0.01	2 : 0.01	
= : 0.23	g : 0.13	e : 0.13	c : 0.09	i : 0.07	] : 0.07	2 : 0.05	3 : 0.05	d : 0.03	: : 0.01	6 : 0.01	b : 0.01	8 : 0.01	f : 0.01	
= : 0.21	g : 0.13	e : 0.13	d : 0.09	: : 0.07	b : 0.07	2 : 0.05	c : 0.05	i : 0.03	3 : 0.03	] : 0.01	8 : 0.01	f : 0.01	o : 0.01	

#score	674.5690731940795
#seq	52
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_CDS_m1_run2.txt

#BEAR
gggg[a[a[bb!!bboooooobbbba]a]gggggg	chr3:121500534-121500767(-)$1	233	98	133	11.7481
"eeeee!!ccc[ddddooooooddddccc333eee	chr20:44569742-44569964(+)$1	222	36	71	11.9554
[ggggggg!!bb[cccnnnnnccc]bb4444gggg	chr15:43677895-43678133(+)$1	238	13	48	16.9059
f"""bb"""ccc[ddddllldddd]ccc4444bb2	chr9:100983324-100983562(-)$1	238	149	184	10.8846
%%%%%ggggggg[cccnnnnnccc]gggggggccc	chr1:27250524-27250748(+)$1	224	173	208	12.9947
ggggeeeeebb!!bboooooobb22bb]eeeeecc	chr20:18523697-18523916(+)$1	219	57	92	11.6088
GGG:ccc[cccbbcccnnnnnccc]bb]ccc333c	chr17:74077955-74078176(-)$1	221	32	67	13.6383
cceeeee!!bb[cccooooooccc]bb]eeeee22	chr8:145138289-145138509(+)$1	220	17	52	13.1705
fffff"""bb[eeeeennnnneeeeebbffffff]	chr18:5433813-5434042(-)$1	229	169	204	12.0807
[bb[ccc[ccc!!cccnnnnncccccc]ccc]bb]	chr8:146015119-146015357(-)$1	238	84	119	15.6055
d[dddd"""bb!!cccnnnnnccc]bb333dddd]	chr19:50302914-50303145(+)$1	231	32	67	17.3482
bbeeeee[cccddddnnnnndddd]ccc333eeee	chr19:3984099-3984352(-)$1	253	145	180	12.6660
!dddd[eeeee"""bbnnnnnbb333eeeee333d	chr17:76067068-76067300(+)$1	232	68	103	14.5078
f[dddd[eeeee[cccnnnnnccceeeeedddd33	chr3:183273314-183273536(-)$1	222	67	102	14.0774
c[eeeee[ccc[ccc[aooooooa]cccccc]eee	chrX:129139083-129139310(+)$1	227	12	47	12.1160
&&eeeee"""dddd[annnnna]dddd]eeeeecc	chr8:37553408-37553637(+)$1	229	192	227	13.3831
####bb"""gggggggnnnnnggggggg333bb]b	chr7:99998646-99998874(+)$1	228	179	214	14.7414
]ccceeeee####cccnnnnnccc4444eeeeegg	chr2:55277167-55277440(-)$1	273	192	227	15.5456
b####eeeee[a[cccnnnnnccc]a333eeeee5	chr1:16785320-16785556(+)$1	236	133	168	15.4603
##eeeee[bb[bbcccnnnnnccc]bb]bb]eeee	chr16:53967816-53968083(+)$1	267	67	102	15.0287
ff[ccc$$$$$eeeeennnnneeeeecccffffff	chr19:45648706-45648930(+)$1	224	79	114	12.2886
=========="""cccnnnnnccc22=========	chr17:17067875-17068105(+)$1	230	189	224	16.9738
eeee"""iiiiiiiiinnnnniiiiiiiiieeeee	chr7:100876089-100876310(-)$1	221	81	116	14.5493
e[bb[dddd"""ddddnnnnndddd333dddd22b	chr1:212553181-212553400(-)$1	219	100	135	12.7777
[dddd####bb[ddddnnnnndddd]bb22dddd]	chr19:38886276-38886503(+)$1	227	31	66	13.8945
gbb[ccc!!bb"""bbnnnnnbb333bb22ccc]b	chr17:43226582-43226816(+)$1	234	99	134	15.7371
)))dddd"""ccccccnnnnnccc]ccc22dddd0	chr20:51871854-51872081(+)$1	227	79	114	14.7004
!!eeeee"""bb[bb[aooooooa]bb22bb]eee	chr1:52879534-52879756(+)$1	222	78	113	11.6401
ccc!!ccc[bb[ddddnnnnndddd]bbccc22cc	chr14:21979166-21979466(-)$1	300	200	235	13.5566
:ffffff[ccc"""bbnnnnnbb333ccc]fffff	chr14:21967348-21967599(-)$1	251	82	117	14.6492
eeeee####bb!!ddddoooooodddd22bb333e	chr19:10671789-10672015(-)$1	226	160	195	10.2555
"eeeee[a!!ccc[bbnnnnnbbccc22a]eeeee	chr22:50304103-50304344(-)$1	241	93	128	15.1362
c####cccccc!!cccnnnnnccc22ccc22ccc2	chr2:86307911-86308132(-)$1	221	43	78	16.2498
ee[eeeee[ccc!!bbnnnnnbb22ccceeeee33	chr14:21971532-21971810(-)$1	278	15	50	15.5549
22bbdddd[ccc[cccnnnnnccc]ccc333dddd	chr10:35841973-35842197(+)$1	224	59	94	14.6012
ddd!!ccc[cccacccooooooccc]a]cccccc]	chr19:7991996-7992224(-)$1	228	125	160	12.1799
b!!a============nnnnn============]a	chr16:53843950-53844207(+)$1	257	14	49	15.8257
gggggg[dddd"""bbnnnnnbb4444dddd]ggg	chr10:135085262-135085481(-)$1	219	144	179	14.6400
ee[bb[ccc####cccnnnnnccc4444cccbb]e	chr1:161337525-161337751(+)$1	226	24	59	15.2586
!!eeeee!!ddddcccaooooooa]ccc]dddd22	chr9:136242701-136242931(-)$1	230	80	115	11.9027
fffff####bb[bbbbnnnnnbb22bb]bb22fff	chr19:50534226-50534446(+)$1	220	35	70	14.1100
ffff!!bb[ddddcccnnnnnccc]dddd]bb]ff	chr16:29818819-29819047(+)$1	228	114	149	13.9557
ffffff[a####cccooooooccc4444a]fffff	chr14:21971242-21971467(+)$1	225	107	142	12.8477
ggggccc"""a[bbbbnnnnnbb]bb]a4444ccc	chr12:69633310-69633542(+)$1	232	154	189	14.9877
ffff!!bb[ddddcccnnnnnccc]dddd]bb]ff	chr16:29818911-29819136(+)$1	225	22	57	13.9557
""dddd!!ccc"""bbnnnnnbb22ccc]dddd22	chr1:149822849-149823099(+)$1	250	195	230	15.7342
!!dddd[a[gggggggnnnnnggggggg333a]dd	chr19:50063822-50064049(-)$1	227	17	52	14.8317
===!!ccc[gggggggnnnnnggggggg]ccc22=	chr4:119621611-119621894(+)$1	283	143	178	14.4692
ffggggggg!!ccc[annnnna]ccc]ggggggg:	chr14:81744874-81745093(-)$1	219	106	141	13.4345
ffff"""bb[bb[cccnnnnnccc]bb]bb]ffff	chr14:103988609-103988909(-)$1	300	116	151	14.8397
b####ccceeeee[bbnnnnnbb]eeeee]ccc22	chr8:37555793-37556017(+)$1	224	26	61	13.1364
::ccc[a[dddd[cccnnnnnccc]dddda]ccc:	chr4:5720955-5721188(+)$1	233	23	58	12.4803
####bb####bb[cccnnnnnccc]bbbb22gggg	chr9:100773507-100773759(+)$1	252	144	179	16.0943
ccceeeee[ccc!!bbnnnnnbb22ccceeeee]c	chr8:145017935-145018155(+)$1	220	35	70	15.2861

#otherMatches

#Seq PSSM
GGCGAGGACUCCAAGAACUCACUGAUGCACGCCGA	chr3:121500534-121500767(-)$1	233	98	133	11.7481
ACUGCUCCGCUCUCAGCUCAUCCUGAAGCUUCGGC	chr20:44569742-44569964(+)$1	222	36	71	11.9554
UGGGAGAGUUACUAGGUAUUUUCUUGUUUUCCUUU	chr15:43677895-43678133(+)$1	238	13	48	16.9059
UGGAGCUGGUGCGGCACAAAGUGCGGCAGAUCGCG	chr9:100983324-100983562(-)$1	238	149	184	10.8846
CUUCAGAAGAAAAGCUCACCUGGCCUUUCUUUGGC	chr1:27250524-27250748(+)$1	224	173	208	12.9947
GAGCGGAGUCAGAGGAGGGGCCCGAUGUGCUCCGG	chr20:18523697-18523916(+)$1	219	57	92	11.6088
CAGCCCCUGCCCACCUUCAGCAGGAUGAGGCCCUG	chr17:74077955-74078176(-)$1	221	32	67	13.6383
CUGGCUUGAACGGACGAUGCGGUCAGUAGGGCUGG	chr8:145138289-145138509(+)$1	220	17	52	13.1705
UUGUGCCUUGAUGGGAGAGUGUCCCGCACACAACC	chr18:5433813-5434042(-)$1	229	169	204	12.0807
UGCUGGCCGCAAAGUGGGUCUCAUUGCUGCCCGCC	chr8:146015119-146015357(-)$1	238	84	119	15.6055
GGAGCAAUGCCAAGCAGAUCGUGUCGGAGAUGCUG	chr19:50302914-50303145(+)$1	231	32	67	17.3482
GCCCGGGCCGGGGAGACACGCUUCACUGAUACCCG	chr19:3984099-3984352(-)$1	253	145	180	12.6660
ACUUCCCCCUUUCCCACACUUUGUUCAAGGGCAUG	chr17:76067068-76067300(+)$1	232	68	103	14.5078
CUGACACUUGGGCGCUCCUUCAGUCUCGAUGUUGA	chr3:183273314-183273536(-)$1	222	67	102	14.0774
UGUGUAAAAGGUGAUUGAAGCAGCUGUCCCUGUUA	chrX:129139083-129139310(+)$1	227	12	47	12.1160
UCUUGCCACCGGCGGACCCCCUGCGCCAGGCGAAC	chr8:37553408-37553637(+)$1	229	192	227	13.3831
UUUCGCAGAUGAGGGGCAGGCCCCCUUACACGCUG	chr7:99998646-99998874(+)$1	228	179	214	14.7414
GUCCGCGGCCCCAGUGCCCACCGCCCCUGCCGCCG	chr2:55277167-55277440(-)$1	273	192	227	15.5456
ACGAAGCCCUCCUCAGCUGGCCUGUGUUUGGGGCA	chr1:16785320-16785556(+)$1	236	133	168	15.4603
UCAUUUCUUGUAGACAAAUGCUGUGCUUCAUGAAG	chr16:53967816-53968083(+)$1	267	67	102	15.0287
GGGUGCAGAACGGGGCCCCCAGCCCCGCACCCAGC	chr19:45648706-45648930(+)$1	224	79	114	12.2886
CUGCAGGGUCAGGCACAGCAGGUGGAGACCCUGCA	chr17:17067875-17068105(+)$1	230	189	224	16.9738
CUGGACUGGACUGGGGUCGUCCUCCGGUCCCCAGG	chr7:100876089-100876310(-)$1	221	81	116	14.5493
GUAGUGAGGACUUCAGCGCCAUUGAUUACCUCCUC	chr1:212553181-212553400(-)$1	219	100	135	12.7777
GGGUCCCCCAGCGGCACUACCUGCCCCUUUGACCG	chr19:38886276-38886503(+)$1	227	31	66	13.8945
AGGAGGACAGUAGGUGGCAAUCGAGAGCGUUCCCC	chr17:43226582-43226816(+)$1	234	99	134	15.7371
CCGAGCUGGGUCCCCUGAAGGAGGAGGAGAAGCUG	chr20:51871854-51872081(+)$1	227	79	114	14.7004
UCGCUCUCCCACACUGCGCUACAGGAGGAGUAGGA	chr1:52879534-52879756(+)$1	222	78	113	11.6401
GGUGAGGCACUGGGCUGUUGGGGCCGAGGCUCAAC	chr14:21979166-21979466(-)$1	300	200	235	13.5566
AGGUUGGUGUCAAAGGAAAUCCCCAAGGCUUCAAC	chr14:21967348-21967599(-)$1	251	82	117	14.6492
GGCAGGAGAAGGUGGGUACUGGGGCCUGACUGGAC	chr19:10671789-10672015(-)$1	226	160	195	10.2555
AGGAGUGCUUGGACUCGGCGUGAUUUUUGGACUCU	chr22:50304103-50304344(-)$1	241	93	128	15.1362
CAGUCGCCUAGGAGACCAGAUGUUUACUAAUGGCC	chr2:86307911-86308132(-)$1	221	43	78	16.2498
ACAGAGUUAGGAUUUACCACUUAUUUUCAGUUCAC	chr14:21971532-21971810(-)$1	278	15	50	15.5549
GGCCUCCAAGGUGUGGGAUGACCAGGCUGUAUGGA	chr10:35841973-35842197(+)$1	224	59	94	14.6012
GGCCUCCAGCACCGAGCAGAUUCUCUGAGUGUGGU	chr19:7991996-7992224(-)$1	228	125	160	12.1799
uuuguauucucuuauuggaaaaauaagagaguguc	chr16:53843950-53844207(+)$1	257	14	49	15.8257
GCCGCUGCAUCAUGGCGGGCAGCAUUGGGUGAGGC	chr10:135085262-135085481(-)$1	219	144	179	14.6400
GAAUCCUAUGAGAGGGGACAGUCCAAAGAUAGAAU	chr1:161337525-161337751(+)$1	226	24	59	15.2586
CCGCCGUCGCCAUGGGCCAGAACGACCUGAUGGGC	chr9:136242701-136242931(-)$1	230	80	115	11.9027
UUCCCACAGCCCUGCCAGCCGGGAACACGGAGGGG	chr19:50534226-50534446(+)$1	220	35	70	14.1100
GAAGAACCAUGCCUGCGAGAUGUGUGGCAAGGCCU	chr16:29818819-29819047(+)$1	228	114	149	13.9557
UUCAGAAGGCUCUCUAUCUCCAGAUCAACAUCUGA	chr14:21971242-21971467(+)$1	225	107	142	12.8477
UGUCGGCGAAGAGUUCAACCAGGUACGUGAGAGCC	chr12:69633310-69633542(+)$1	232	154	189	14.9877
GAAGAACCAUGCCUGCGAGAUGUGUGGCAAGGCCU	chr16:29818911-29819136(+)$1	225	22	57	13.9557
AGAGUCACCACAAGGCAAAGGGCAAGUGAGGCUGA	chr1:149822849-149823099(+)$1	250	195	230	15.7342
AUCAGCUCUGAGGGCUGCAGAGGUCUUCCCUGUGC	chr19:50063822-50064049(-)$1	227	17	52	14.8317
UCUCUGGUGUGGUUCUGGGGAGGGGUUGGACCUUG	chr4:119621611-119621894(+)$1	283	143	178	14.4692
CAGUGACCUCUGCUCGUUUUCCCAGCUGGGUCACC	chr14:81744874-81745093(-)$1	219	106	141	13.4345
GCUUCCCGGCCGAGGACGAGUUCCCCGACCUGAGC	chr14:103988609-103988909(-)$1	300	116	151	14.8397
CGACAAGCGCUUCGCCACCUCGGAGGAGCUGCUCA	chr8:37555793-37556017(+)$1	224	26	61	13.1364
ACGACACUCAAAAUCUGCUCAAGAAUUUGGAGUCU	chr4:5720955-5721188(+)$1	233	23	58	12.4803
acgaugaagUCAGUGAGGAGGUCAGUGCAGCUGUU	chr9:100773507-100773759(+)$1	252	144	179	16.0943
GUCCCCUGCGCCAGUGCCACACAGCGGCCAGGGUG	chr8:145017935-145018155(+)$1	220	35	70	15.2861

#DB
((((.(.(.((..((......))))).).))))))	chr3:121500534-121500767(-)$1	1	98	133	11.7481
.(((((..(((.((((......)))))))...)))	chr20:44569742-44569964(+)$1	1	36	71	11.9554
.(((((((..((.(((.....))).))....))))	chr15:43677895-43678133(+)$1	1	13	48	16.9059
(...((...(((.((((...)))).)))....)).	chr9:100983324-100983562(-)$1	1	149	184	10.8846
.....(((((((.(((.....))).))))))))))	chr1:27250524-27250748(+)$1	1	173	208	12.9947
))))(((((((..((......))..)).)))))((	chr20:18523697-18523916(+)$1	1	57	92	11.6088
(((.(((.((((((((.....))).)).)))...)	chr17:74077955-74078176(-)$1	1	32	67	13.6383
(((((((..((.(((......))).)).)))))..	chr8:145138289-145138509(+)$1	1	17	52	13.1705
(((((...((.(((((.....))))))))))))).	chr18:5433813-5434042(-)$1	1	169	204	12.0807
.((.(((.(((..(((.....)))))).))).)).	chr8:146015119-146015357(-)$1	1	84	119	15.6055
(.((((...((..(((.....))).))...)))).	chr19:50302914-50303145(+)$1	1	32	67	17.3482
))(((((.(((((((.....)))).)))...))))	chr19:3984099-3984352(-)$1	1	145	180	12.6660
.((((.(((((...((.....))...)))))...)	chr17:76067068-76067300(+)$1	1	68	103	14.5078
(.((((.(((((.(((.....))))))))))))..	chr3:183273314-183273536(-)$1	1	67	102	14.0774
(.(((((.(((.(((.(......).)))))).)))	chrX:129139083-129139310(+)$1	1	12	47	12.1160
..(((((...((((.(.....).)))).)))))))	chr8:37553408-37553637(+)$1	1	192	227	13.3831
....((...(((((((.....)))))))...)).)	chr7:99998646-99998874(+)$1	1	179	214	14.7414
.)))(((((....(((.....)))....)))))((	chr2:55277167-55277440(-)$1	1	192	227	15.5456
(....(((((.(.(((.....))).)...))))).	chr1:16785320-16785556(+)$1	1	133	168	15.4603
..(((((.((.(((((.....))).)).)).))))	chr16:53967816-53968083(+)$1	1	67	102	15.0287
((.(((.....(((((.....))))))))))))))	chr19:45648706-45648930(+)$1	1	79	114	12.2886
((((((((((...(((.....)))..)))))))))	chr17:17067875-17068105(+)$1	1	189	224	16.9738
((((...(((((((((.....))))))))))))))	chr7:100876089-100876310(-)$1	1	81	116	14.5493
(.((.((((...((((.....))))...))))..)	chr1:212553181-212553400(-)$1	1	100	135	12.7777
.((((....((.((((.....)))).))..)))).	chr19:38886276-38886503(+)$1	1	31	66	13.8945
(((.(((..((...((.....))...))..))).)	chr17:43226582-43226816(+)$1	1	99	134	15.7371
...((((...((((((.....))).)))..)))).	chr20:51871854-51872081(+)$1	1	79	114	14.7004
..(((((...((.((.(......).))..)).)))	chr1:52879534-52879756(+)$1	1	78	113	11.6401
(((..(((.((.((((.....)))).)))))..))	chr14:21979166-21979466(-)$1	1	200	235	13.5566
.((((((.(((...((.....))...))).)))))	chr14:21967348-21967599(-)$1	1	82	117	14.6492
(((((....((..((((......))))..))...)	chr19:10671789-10672015(-)$1	1	160	195	10.2555
.(((((.(..(((.((.....)))))..).)))))	chr22:50304103-50304344(-)$1	1	93	128	15.1362
(....((((((..(((.....)))..)))..))).	chr2:86307911-86308132(-)$1	1	43	78	16.2498
((.(((((.(((..((.....))..))))))))..	chr14:21971532-21971810(-)$1	1	15	50	15.5549
..))((((.(((.(((.....))).)))...))))	chr10:35841973-35842197(+)$1	1	59	94	14.6012
(((..(((.(((((((......))).).)))))).	chr19:7991996-7992224(-)$1	1	125	160	12.1799
(..(((((((((((((.....)))))))))))).)	chr16:53843950-53844207(+)$1	1	14	49	15.8257
((((((.((((...((.....))....)))).)))	chr10:135085262-135085481(-)$1	1	144	179	14.6400
((.((.(((....(((.....)))....))))).)	chr1:161337525-161337751(+)$1	1	24	59	15.2586
..(((((..((((((((......).))).))))..	chr9:136242701-136242931(-)$1	1	80	115	11.9027
(((((....((.((((.....))..)).))..)))	chr19:50534226-50534446(+)$1	1	35	70	14.1100
((((..((.(((((((.....))).)))).)).))	chr16:29818819-29819047(+)$1	1	114	149	13.9557
((((((.(....(((......)))....).)))))	chr14:21971242-21971467(+)$1	1	107	142	12.8477
))))(((...(.((((.....)).)).)....)))	chr12:69633310-69633542(+)$1	1	154	189	14.9877
((((..((.(((((((.....))).)))).)).))	chr16:29818911-29819136(+)$1	1	22	57	13.9557
..((((..(((...((.....))..))).))))..	chr1:149822849-149823099(+)$1	1	195	230	15.7342
..((((.(.(((((((.....)))))))...).))	chr19:50063822-50064049(-)$1	1	17	52	14.8317
(((..(((.(((((((.....))))))).)))..)	chr4:119621611-119621894(+)$1	1	143	178	14.4692
))(((((((..(((.(.....).))).))))))).	chr14:81744874-81745093(-)$1	1	106	141	13.4345
((((...((.((.(((.....))).)).)).))))	chr14:103988609-103988909(-)$1	1	116	151	14.8397
(....((((((((.((.....)).))))).)))..	chr8:37555793-37556017(+)$1	1	26	61	13.1364
..(((.(.((((.(((.....))).))))).))).	chr4:5720955-5721188(+)$1	1	23	58	12.4803
....((....((.(((.....))).))))..))))	chr9:100773507-100773759(+)$1	1	144	179	16.0943
((((((((.(((..((.....))..)))))))).)	chr8:145017935-145018155(+)$1	1	35	70	15.2861

#PSSM
f : 0.18	g : 0.09	c : 0.09	e : 0.09	b : 0.07	! : 0.07	" : 0.05	[ : 0.05	# : 0.05	d : 0.03	= : 0.03	: : 0.03	% : 0.01	G : 0.01	& : 0.01	] : 0.01	) : 0.01	2 : 0.01	
f : 0.16	e : 0.11	# : 0.11	g : 0.09	c : 0.07	[ : 0.07	! : 0.07	b : 0.05	d : 0.05	" : 0.03	= : 0.03	% : 0.01	G : 0.01	& : 0.01	) : 0.01	2 : 0.01	: : 0.01	
e : 0.20	f : 0.12	d : 0.12	g : 0.11	# : 0.09	b : 0.07	c : 0.07	[ : 0.05	= : 0.03	" : 0.01	% : 0.01	G : 0.01	) : 0.01	! : 0.01	
e : 0.24	f : 0.12	d : 0.12	g : 0.11	# : 0.09	c : 0.05	b : 0.05	! : 0.05	[ : 0.03	" : 0.01	% : 0.01	: : 0.01	= : 0.01	a : 0.01	
e : 0.25	d : 0.14	c : 0.11	! : 0.09	b : 0.07	f : 0.07	g : 0.05	# : 0.05	[ : 0.03	= : 0.03	" : 0.03	% : 0.01	
e : 0.25	c : 0.18	d : 0.12	g : 0.07	b : 0.05	" : 0.05	[ : 0.05	# : 0.05	= : 0.03	f : 0.03	! : 0.03	a : 0.01	
e : 0.24	c : 0.18	[ : 0.11	" : 0.11	# : 0.07	g : 0.05	d : 0.05	! : 0.03	= : 0.03	b : 0.03	$ : 0.01	f : 0.01	a : 0.01	
" : 0.14	e : 0.12	[ : 0.12	c : 0.11	! : 0.09	a : 0.07	# : 0.07	g : 0.05	d : 0.05	b : 0.05	= : 0.03	$ : 0.01	i : 0.01	
[ : 0.18	c : 0.16	" : 0.12	e : 0.11	! : 0.09	# : 0.09	b : 0.05	d : 0.05	g : 0.03	= : 0.03	$ : 0.01	i : 0.01	
c : 0.24	b : 0.20	" : 0.09	d : 0.09	g : 0.07	e : 0.07	# : 0.07	! : 0.05	= : 0.03	$ : 0.01	i : 0.01	[ : 0.01	
c : 0.27	b : 0.24	d : 0.11	g : 0.07	[ : 0.05	e : 0.05	# : 0.05	" : 0.03	$ : 0.01	i : 0.01	= : 0.01	a : 0.01	! : 0.01	
c : 0.14	[ : 0.12	" : 0.12	! : 0.11	b : 0.11	d : 0.11	g : 0.07	e : 0.07	# : 0.05	a : 0.01	i : 0.01	= : 0.01	
[ : 0.18	d : 0.16	! : 0.14	c : 0.11	" : 0.11	b : 0.07	e : 0.05	g : 0.05	# : 0.03	i : 0.01	a : 0.01	= : 0.01	
c : 0.46	d : 0.14	b : 0.09	" : 0.09	g : 0.05	e : 0.03	[ : 0.03	! : 0.03	i : 0.01	= : 0.01	
c : 0.44	b : 0.25	d : 0.12	g : 0.05	e : 0.03	[ : 0.03	i : 0.01	= : 0.01	
c : 0.38	b : 0.20	d : 0.11	o : 0.07	g : 0.05	e : 0.03	[ : 0.03	a : 0.03	n : 0.01	i : 0.01	= : 0.01	
n : 0.79	o : 0.11	a : 0.05	d : 0.03	
n : 0.79	o : 0.18	l : 0.01	
n : 0.79	o : 0.18	l : 0.01	
n : 0.79	o : 0.18	l : 0.01	
n : 0.77	o : 0.18	d : 0.03	
c : 0.38	b : 0.24	o : 0.11	d : 0.09	g : 0.05	e : 0.03	a : 0.03	i : 0.01	= : 0.01	
c : 0.40	b : 0.24	d : 0.11	o : 0.07	g : 0.05	e : 0.03	] : 0.03	i : 0.01	= : 0.01	
c : 0.44	d : 0.14	2 : 0.09	3 : 0.05	a : 0.05	g : 0.05	e : 0.03	] : 0.03	b : 0.01	i : 0.01	= : 0.01	4 : 0.01	
] : 0.35	2 : 0.12	d : 0.11	e : 0.07	c : 0.07	4 : 0.07	3 : 0.05	g : 0.05	b : 0.03	i : 0.01	= : 0.01	
c : 0.22	b : 0.20	d : 0.11	g : 0.07	e : 0.07	3 : 0.07	4 : 0.07	] : 0.05	a : 0.03	2 : 0.03	i : 0.01	= : 0.01	
c : 0.25	b : 0.25	d : 0.09	g : 0.07	4 : 0.07	] : 0.05	e : 0.05	3 : 0.03	= : 0.03	i : 0.01	2 : 0.01	a : 0.01	
c : 0.24	] : 0.16	g : 0.09	b : 0.09	4 : 0.07	d : 0.07	3 : 0.05	e : 0.05	2 : 0.05	a : 0.03	= : 0.03	i : 0.01	
c : 0.18	e : 0.16	3 : 0.11	d : 0.09	2 : 0.09	] : 0.07	b : 0.07	4 : 0.05	g : 0.03	= : 0.03	a : 0.03	f : 0.01	i : 0.01	
e : 0.14	c : 0.12	3 : 0.11	] : 0.11	d : 0.09	b : 0.09	2 : 0.09	g : 0.05	4 : 0.05	f : 0.03	= : 0.03	i : 0.01	a : 0.01	
e : 0.18	c : 0.16	d : 0.14	3 : 0.09	f : 0.07	b : 0.07	g : 0.05	4 : 0.05	] : 0.05	2 : 0.05	= : 0.03	
e : 0.20	d : 0.14	c : 0.11	g : 0.09	f : 0.09	3 : 0.07	] : 0.07	b : 0.07	4 : 0.03	= : 0.03	2 : 0.03	a : 0.01	
e : 0.25	c : 0.12	d : 0.12	f : 0.11	g : 0.09	b : 0.07	3 : 0.05	2 : 0.05	] : 0.05	= : 0.03	
e : 0.14	c : 0.14	f : 0.14	g : 0.11	2 : 0.11	3 : 0.09	d : 0.09	] : 0.09	b : 0.03	= : 0.01	
e : 0.16	c : 0.12	f : 0.12	2 : 0.11	g : 0.09	] : 0.09	d : 0.05	b : 0.05	3 : 0.03	= : 0.03	: : 0.03	5 : 0.01	0 : 0.01	a : 0.01	

#score	758.0044306109035
#seq	54
#width	35
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_CDS_m1_run1.txt

#BEAR
eee:ggggggguuuuuuuuuuuugggggggBB{	chr13:42144675-42144876(-)$1	201	40	73	19.9086
iiiiii[acccuuuuuuuuuuuuccc333a]ii	chr4:24550499-24550700(-)$1	201	45	78	25.9275
eee"""eeeeettttttttttteeeeeeeeeed	chr6:119300501-119300702(-)$1	201	126	159	21.8067
::cccddddwwwwwwwwwwwwwwdddd]cccdd	chr10:76784776-76784977(+)$1	201	38	71	21.4017
DDccc[acccvvvvvvvvvvvvvccc]a]cccd	chr16:27483092-27483293(-)$1	201	9	42	23.7438
b[eeeeebbwwwwwwwwwwwwwwbb]eeeee22	chr17:2341337-2341538(-)$1	201	39	72	22.4031
==========^^^^^^^^^^^^^^^^^^^====	chr15:89843440-89843641(+)$1	201	3	36	18.8148
ccc!!ffffffyyyyyyyyyyyyyyyyffffff	chr4:42077645-42077846(+)$1	201	47	80	21.0540
++++++++cccuuuuuuuuuuuuccc333eeee	chr3:183585664-183585865(-)$1	201	34	67	20.4637
dddd[a[ccctttttttttttcccaddddccc5	chr19:36594653-36594854(+)$1	201	43	76	21.4967
eeee[addddvvvvvvvvvvvvvdddd]a]eee	chr9:134322477-134322678(+)$1	201	31	64	24.4201
dd!!bb[cccwwwwwwwwwwwwwwccc]bb]dd	chr15:91448528-91448729(+)$1	201	7	40	24.6705
fff"""ddddvvvvvvvvvvvvvdddd]fffff	chr12:62960047-62960248(+)$1	201	56	89	24.1818
c!!hhhhhhhhuuuuuuuuuuuuhhhhhhhh33	chr18:56031421-56031622(+)$1	201	12	45	21.7172
b[ffffff!!bbtttttttttttbb22ffffff	chr20:13763648-13763849(-)$1	201	147	180	20.1078
b[hhhhhhhhvvvvvvvvvvvvvhhhhhhhh]b	chr12:114362459-114362660(-)$1	201	72	105	21.9838
ddd!!ddddwwwwwwwwwwwwwwdddd22dddd	chr6:146231585-146231786(-)$1	201	87	120	23.2116
!a!!ddddxxxxxxxxxxxxxxxdddd22a22e	chr12:21628312-21628513(-)$1	201	66	99	19.1207
b!!ccc[cccvvvvvvvvvvvvvccc]ccc22b	chr1:110560469-110560670(+)$1	201	78	111	25.2005
[iiiiiiiiivvvvvvvvvvvvviiiiiiiii]	chr1:45472360-45472561(-)$1	201	15	48	25.2814
"bbgggggggtttttttttttggggggg]bbcc	chr4:25265303-25265504(+)$1	201	96	129	20.9988
eeeeffffffuuuuuuuuuuuuffffff]eeee	chr19:34916801-34917002(+)$1	201	66	99	22.9859
bb[gggggggvvvvvvvvvvvvvggggggg]bb	chr17:47004280-47004481(+)$1	201	78	111	24.3149
ccc[ffffffattttttttttta]ffffff22c	chr3:151085907-151086108(+)$1	201	11	44	22.2750
ee!!fffffftttttttttttffffff22eeee	chr21:37744630-37744831(+)$1	201	51	84	21.5179
!!cccbb[bbvvvvvvvvvvvvvbb]bb]ccc3	chr12:121448611-121448812(-)$1	201	93	126	23.5524
gggggg[cccvvvvvvvvvvvvvcccggggggg	chr4:87720189-87720390(+)$1	201	14	47	26.0144
cc[bb!!cccwwwwwwwwwwwwwwccc333bb]	chr5:145878054-145878255(+)$1	201	93	126	24.8603
gggggggyyyyyyyyyyyyyyyygggggggddd	chr4:68385043-68385244(-)$1	201	134	167	22.1492
fff$$$$$ddddtttttttttttddddffffff	chr1:207941033-207941234(+)$1	201	80	113	20.0694
ff"""eeeee^^^^^^^^^^^^^^^^^^^eeee	chr1:154232341-154232542(+)$1	201	97	130	17.8481
ccc[ffffff^^^^^^^^^^^^^^^^^^^^^ff	chr7:80456660-80456861(-)$1	201	120	153	17.4096
eeee!!eeeeettttttttttteeeee22eeee	chr6:146269316-146269517(-)$1	201	104	137	22.1968
eee$$$$$ccctttttttttttccc4444eeee	chr19:39292365-39292566(-)$1	201	74	107	22.7180
dd[bb!!bbyyyyyyyyyyyyyyyybb22bb]d	chr17:3937396-3937597(-)$1	201	123	156	21.8567
cccgggggggtttttttttttggggggg]ccc3	chr2:25039477-25039678(+)$1	201	148	181	22.1197
[bb!!eeeeevvvvvvvvvvvvveeeeebba]d	chr1:156286919-156287120(-)$1	201	20	53	23.5581
gggggg[ddddyyyyyyyyyyyyyyyydddd99	chr19:4013121-4013322(+)$1	201	6	39	19.6763
!ccc[a[cccwwwwwwwwwwwwwwccc]a]ccc	chr17:26943330-26943531(-)$1	201	148	181	25.4922
[eeeee[cccxxxxxxxxxxxxxxxccc]eeee	chr9:86300857-86301058(-)$1	201	38	71	20.5656
ccc!!a[cccvvvvvvvvvvvvvccca22ccc]	chr20:31015898-31016099(+)$1	201	101	134	26.6280
EEiiiiiiiiiuuuuuuuuuuuuiiiiiiiii:	chr12:48060722-48060923(-)$1	201	167	200	21.8046
[ccc"""cccwwwwwwwwwwwwwwcccccc]ii	chr4:1730280-1730481(+)$1	201	125	158	25.2477
iiiiiiiiyyyyyyyyyyyyyyyyiiiiiiiii	chr11:57576735-57576936(+)$1	201	4	37	23.1388
ffffff[ccc^^^^^^^^^^^^^^^^^^^^^^^	chr9:97897672-97897873(-)$1	201	40	73	17.5640
ee!!bb^^^^^^^^^^^^^^^^^^^bb22eeee	chr13:113170740-113170941(-)$1	201	17	50	17.6937
Ddddd"""bbvvvvvvvvvvvvvbb]ddddfff	chr6:36842402-36842603(-)$1	201	10	43	22.1137
eeeee!!cccwwwwwwwwwwwwwwccc]eeeee	chr15:73862455-73862656(-)$1	201	164	197	25.0148
!!a[bb[ddddvvvvvvvvvvvvvddddbb]a2	chr14:100809564-100809765(-)$1	201	10	43	22.9702
=====bbcccwwwwwwwwwwwwwwccc]bb]==	chr8:145140203-145140404(+)$1	201	154	187	24.6980
ddd"""eeeeettttttttttteeeeedddd33	chr12:72291560-72291761(+)$1	201	131	164	21.5980
e[eeeeecccvvvvvvvvvvvvvccc]eeeee3	chr18:13012904-13013105(+)$1	201	142	175	25.1104
eeee[bb!!ccctttttttttttccc22bbeee	chr2:230661335-230661536(-)$1	201	52	85	21.9412
a[gggggggxxxxxxxxxxxxxxxggggggg]a	chr8:144658513-144658714(-)$1	201	167	200	20.5649
b!!ffffffuuuuuuuuuuuuffffff22bb22	chr10:127413873-127414074(+)$1	201	102	135	20.9313
ffffff[cccuuuuuuuuuuuucccffffff]c	chr3:197602509-197602710(+)$1	201	51	84	23.9748

#otherMatches

#Seq PSSM
CAUGCCCACUCUCAGUUCUGCAUGAGUGGGGAC	chr13:42144675-42144876(-)$1	201	40	73	19.9086
UAUUUUGUAGGAAAUUGAUGAAGCCUGUAAGAG	chr4:24550499-24550700(-)$1	201	45	78	25.9275
UCAGACUCUUCGGUUUGAAUUAGAAGAUGAAGG	chr6:119300501-119300702(-)$1	201	126	159	21.8067
GAGCCCUUUGACAACUCAGAUGAAGAGAGGCCA	chr10:76784776-76784977(+)$1	201	38	71	21.4017
CCGGCUGGAGAACCCUACUCACCCUCGCCGCCC	chr16:27483092-27483293(-)$1	201	9	42	23.7438
GUUUCAGGUUCCCAAAGUAACGUACACUGAAUU	chr17:2341337-2341538(-)$1	201	39	72	22.4031
UUUUGGCUUUCAAAAAUUUUAGCUAUUAAAAGG	chr15:89843440-89843641(+)$1	201	3	36	18.8148
GCCACAGAUCUGGGAUUAGGUAAAGUAAGAUUU	chr4:42077645-42077846(+)$1	201	47	80	21.0540
AACAAAAAUGCGGAUUCAGAAAAGCACCCAGGA	chr3:183585664-183585865(-)$1	201	34	67	20.4637
GCAGUGAGCUUCCCAGCCCCUAGCCCUGUGGAA	chr19:36594653-36594854(+)$1	201	43	76	21.4967
UGGAACGAGGCUCUUUUCCCCUUCCUCAGCUCC	chr9:134322477-134322678(+)$1	201	31	64	24.4201
AGAACCAUGAGAUUAUCAGCCAUAUCAAGGACU	chr15:91448528-91448729(+)$1	201	7	40	24.6705
GGAAUGGGUAGCCUUGAAUUAUGUGCCGUUUGC	chr12:62960047-62960248(+)$1	201	56	89	24.1818
CCUCAGUAUACAUAAAAUUUCAGGUGUAUUGUU	chr18:56031421-56031622(+)$1	201	12	45	21.7172
GAUCGAAAAGUCAAAAUUGACAAGAGAUUUCGA	chr20:13763648-13763849(-)$1	201	147	180	20.1078
AUGAUACUUGUUACUUUCUUAUCCAGGUGUUUU	chr12:114362459-114362660(-)$1	201	72	105	21.9838
GAUCUCACAGAAGCUCCAUUAAGUGUGCAAUCU	chr6:146231585-146231786(-)$1	201	87	120	23.2116
AUGAGUAAAUCCAUGGAAAAUUAUUACCAAGAG	chr12:21628312-21628513(-)$1	201	66	99	19.1207
GUUCCUUUCUUUUCUUCCAGCAUGGAUGGGUUC	chr1:110560469-110560670(+)$1	201	78	111	25.2005
GAUGAUGGGGGACCUAUUCAUUACCCCAUUAUG	chr1:45472360-45472561(-)$1	201	15	48	25.2814
UCCUUAUUAAAAUAGCUGCAAUUGAUAAUGGUC	chr4:25265303-25265504(+)$1	201	96	129	20.9988
GAAGCCUGAAUAUGUGGUAUUUUUCAGGUCUUU	chr19:34916801-34917002(+)$1	201	66	99	22.9859
UACCAGUCCCUCUUGAUGCGCCUGGGACUGAUA	chr17:47004280-47004481(+)$1	201	78	111	24.3149
UCCAAUCCCCCUUUCCUAGCUUGUGGGGAUGCG	chr3:151085907-151086108(+)$1	201	11	44	22.2750
UGGAAAUGGAAAAGUCACAAAUCCGUUCACAGU	chr21:37744630-37744831(+)$1	201	51	84	21.5179
AAUGAGCAUGAACAAGAUGGCAACGAGCUUCAG	chr12:121448611-121448812(-)$1	201	93	126	23.5524
UUUGAGUACAAAAAUGAAGAAAAUGUUUCAAAU	chr4:87720189-87720390(+)$1	201	14	47	26.0144
AAAGCAAUUGAAAAGAUGAAAGACCGAGAAGCC	chr5:145878054-145878255(+)$1	201	93	126	24.8603
GCUGAUGAAGAAUUUUACUUAUCCGUUGGCUCA	chr4:68385043-68385244(-)$1	201	134	167	22.1492
UGUUUUCCAGUGUCGACUUCUUCCACUACAAAA	chr1:207941033-207941234(+)$1	201	80	113	20.0694
CCAUUUCCCACACCCACUACUCCGCUGACUGGG	chr1:154232341-154232542(+)$1	201	97	130	17.8481
AGUAAGUGUUaaaaaaaaaaaaaaaaaaaaaaa	chr7:80456660-80456861(-)$1	201	120	153	17.4096
AGGCUGGUAAGGCAAAAUUUUACUUAUAUGCUU	chr6:146269316-146269517(-)$1	201	104	137	22.1968
UUGACUUUGCCCAUCGCCUCUCGGCCUUCCAGA	chr19:39292365-39292566(-)$1	201	74	107	22.7180
UCGGCCAGUUAAUUAUCCGUCUUUUGCCAGCAG	chr17:3937396-3937597(-)$1	201	123	156	21.8567
AGAUUGCUGUAUAAGGACCUCACAGCAACUCUU	chr2:25039477-25039678(+)$1	201	148	181	22.1197
AGUACUUUGAUUAUAAAACCAGUUCAGAACCCA	chr1:156286919-156287120(-)$1	201	20	53	23.5581
CGGCCCCUGGACCCCCUGACCAUGCACUCCACC	chr19:4013121-4013322(+)$1	201	6	39	19.6763
CCCUGAUGAUAGAAAAAUGGGAGAGUCUUGAGG	chr17:26943330-26943531(-)$1	201	148	181	25.4922
GUUGAUAUUUGCUGGAAAAAUUUUGAAAGAUCA	chr9:86300857-86301058(-)$1	201	38	71	20.5656
GUGGAGAGCUGUGGGUCUAAUGAAGCCAGCACU	chr20:31015898-31016099(+)$1	201	101	134	26.6280
UCUAUGAAAGUUUUCCCAUGUUUAUUUUUGUAC	chr12:48060722-48060923(-)$1	201	167	200	21.8046
GCAGUGAGGCCCAGCCCCCAGAAAGCCCUGAGA	chr4:1730280-1730481(+)$1	201	125	158	25.2477
UACUAGGUAAACAUGCUAUUCCUAACUUGGUAA	chr11:57576735-57576936(+)$1	201	4	37	23.1388
UUUCAGUGAGCCAUUUCUGUUUAAAAUUUUGUU	chr9:97897672-97897873(-)$1	201	40	73	17.5640
GAAUACUAUCAACUUGUCUUCUGCUGUUAUCCC	chr13:113170740-113170941(-)$1	201	17	50	17.6937
CGGAAGUAGCAAUUACUAGACAAGCAUUCCGCC	chr6:36842402-36842603(-)$1	201	10	43	22.1137
CGGUAAGAGCAUCCCUACAAAAUAGCUGUACUG	chr15:73862455-73862656(-)$1	201	164	197	25.0148
CACGUGUAAAAAUACUUUUUCUCAUUUUCAGGG	chr14:100809564-100809765(-)$1	201	10	43	22.9702
UGGCCCUGCCCCACAAUACCCACCGGUAAGAGG	chr8:145140203-145140404(+)$1	201	154	187	24.6980
CGAGGUUAAGAGAUUAUAGAAGUCUUAUCGGUA	chr12:72291560-72291761(+)$1	201	131	164	21.5980
UCAUUUUCUGGAGUACUAUAGGGCAGUAAAAUU	chr18:13012904-13013105(+)$1	201	142	175	25.1104
UGAGUGCCUUGUAGAAAUCCGUAGCAUAGUCUC	chr2:230661335-230661536(-)$1	201	52	85	21.9412
UGGGCAGGGAAGGACAGUGAGGUACUCUGCUGA	chr8:144658513-144658714(-)$1	201	167	200	20.5649
UCAAAAGGCAAUUCUUUCCAAGUUUUUAUAUUA	chr10:127413873-127414074(+)$1	201	102	135	20.9313
CAUUUCAGCCUAAAUUAACAAUGGCGAAAUGCA	chr3:197602509-197602710(+)$1	201	51	84	23.9748

#DB
))).(((((((............)))))))((.	chr13:42144675-42144876(-)$1	1	40	73	19.9086
((((((.((((............)))...).))	chr4:24550499-24550700(-)$1	1	45	78	25.9275
(((...(((((...........))))))))))(	chr6:119300501-119300702(-)$1	1	126	159	21.8067
..(((((((..............)))).)))((	chr10:76784776-76784977(+)$1	1	38	71	21.4017
(((((.((((.............))).).)))(	chr16:27483092-27483293(-)$1	1	9	42	23.7438
(.(((((((..............)).)))))..	chr17:2341337-2341538(-)$1	1	39	72	22.4031
((((((((((...................))))	chr15:89843440-89843641(+)$1	1	3	36	18.8148
(((..((((((................))))))	chr4:42077645-42077846(+)$1	1	47	80	21.0540
........(((............)))...))))	chr3:183585664-183585865(-)$1	1	34	67	20.4637
((((.(.(((...........))))))))))).	chr19:36594653-36594854(+)$1	1	43	76	21.4967
((((.(((((.............)))).).)))	chr9:134322477-134322678(+)$1	1	31	64	24.4201
((..((.(((..............))).)).))	chr15:91448528-91448729(+)$1	1	7	40	24.6705
(((...((((.............)))).)))))	chr12:62960047-62960248(+)$1	1	56	89	24.1818
(..((((((((............))))))))..	chr18:56031421-56031622(+)$1	1	12	45	21.7172
(.((((((..((...........))..))))))	chr20:13763648-13763849(-)$1	1	147	180	20.1078
(.((((((((.............)))))))).)	chr12:114362459-114362660(-)$1	1	72	105	21.9838
(((..((((..............))))..))))	chr6:146231585-146231786(-)$1	1	87	120	23.2116
.(..((((...............))))..)..)	chr12:21628312-21628513(-)$1	1	66	99	19.1207
(..(((.(((.............))).)))..)	chr1:110560469-110560670(+)$1	1	78	111	25.2005
.(((((((((.............))))))))).	chr1:45472360-45472561(-)$1	1	15	48	25.2814
.(((((((((...........))))))).))))	chr4:25265303-25265504(+)$1	1	96	129	20.9988
((((((((((............)))))).))))	chr19:34916801-34917002(+)$1	1	66	99	22.9859
((.(((((((.............))))))).))	chr17:47004280-47004481(+)$1	1	78	111	24.3149
(((.(((((((...........).))))))..)	chr3:151085907-151086108(+)$1	1	11	44	22.2750
((..((((((...........))))))..))))	chr21:37744630-37744831(+)$1	1	51	84	21.5179
..(((((.((.............)).)).))).	chr12:121448611-121448812(-)$1	1	93	126	23.5524
((((((.(((.............))))))))))	chr4:87720189-87720390(+)$1	1	14	47	26.0144
((.((..(((..............)))...)).	chr5:145878054-145878255(+)$1	1	93	126	24.8603
(((((((................))))))))))	chr4:68385043-68385244(-)$1	1	134	167	22.1492
(((.....((((...........))))))))))	chr1:207941033-207941234(+)$1	1	80	113	20.0694
((...(((((...................))))	chr1:154232341-154232542(+)$1	1	97	130	17.8481
(((.((((((.....................))	chr7:80456660-80456861(-)$1	1	120	153	17.4096
((((..(((((...........)))))..))))	chr6:146269316-146269517(-)$1	1	104	137	22.1968
(((.....(((...........)))....))))	chr19:39292365-39292566(-)$1	1	74	107	22.7180
((.((..((................))..)).)	chr17:3937396-3937597(-)$1	1	123	156	21.8567
((((((((((...........))))))).))).	chr2:25039477-25039678(+)$1	1	148	181	22.1197
.((..(((((.............)))))))).)	chr1:156286919-156287120(-)$1	1	20	53	23.5581
((((((.((((................))))..	chr19:4013121-4013322(+)$1	1	6	39	19.6763
.(((.(.(((..............))).).)))	chr17:26943330-26943531(-)$1	1	148	181	25.4922
.(((((.(((...............))).))))	chr9:86300857-86301058(-)$1	1	38	71	20.5656
(((..(.(((.............))))..))).	chr20:31015898-31016099(+)$1	1	101	134	26.6280
))(((((((((............))))))))).	chr12:48060722-48060923(-)$1	1	167	200	21.8046
.(((...(((..............)))))).))	chr4:1730280-1730481(+)$1	1	125	158	25.2477
((((((((................)))))))))	chr11:57576735-57576936(+)$1	1	4	37	23.1388
((((((.(((.......................	chr9:97897672-97897873(-)$1	1	40	73	17.5640
((..((...................))..))))	chr13:113170740-113170941(-)$1	1	17	50	17.6937
(((((...((.............)).))))(((	chr6:36842402-36842603(-)$1	1	10	43	22.1137
(((((..(((..............))).)))))	chr15:73862455-73862656(-)$1	1	164	197	25.0148
..(.((.((((.............)))))).).	chr14:100809564-100809765(-)$1	1	10	43	22.9702
((((((((((..............))).)).))	chr8:145140203-145140404(+)$1	1	154	187	24.6980
(((...(((((...........)))))))))..	chr12:72291560-72291761(+)$1	1	131	164	21.5980
(.((((((((.............))).))))).	chr18:13012904-13013105(+)$1	1	142	175	25.1104
((((.((..(((...........)))..)))))	chr2:230661335-230661536(-)$1	1	52	85	21.9412
(.(((((((...............))))))).)	chr8:144658513-144658714(-)$1	1	167	200	20.5649
(..((((((............))))))..))..	chr10:127413873-127414074(+)$1	1	102	135	20.9313
((((((.(((............))))))))).)	chr3:197602509-197602710(+)$1	1	51	84	23.9748

#PSSM
e : 0.19	c : 0.12	b : 0.10	d : 0.08	f : 0.08	! : 0.07	[ : 0.07	g : 0.05	i : 0.03	D : 0.03	= : 0.03	: : 0.01	+ : 0.01	" : 0.01	E : 0.01	a : 0.01	
e : 0.19	c : 0.14	d : 0.10	[ : 0.08	f : 0.08	! : 0.08	i : 0.05	b : 0.05	g : 0.05	= : 0.03	: : 0.01	D : 0.01	+ : 0.01	a : 0.01	E : 0.01	
e : 0.19	c : 0.17	! : 0.12	f : 0.08	i : 0.07	d : 0.07	g : 0.07	[ : 0.05	= : 0.03	b : 0.03	+ : 0.01	h : 0.01	" : 0.01	a : 0.01	
e : 0.14	! : 0.14	g : 0.12	c : 0.10	i : 0.07	" : 0.07	f : 0.07	[ : 0.05	= : 0.03	d : 0.03	h : 0.03	b : 0.03	$ : 0.03	: : 0.01	+ : 0.01	
g : 0.14	f : 0.14	" : 0.08	! : 0.08	b : 0.08	i : 0.07	c : 0.07	e : 0.07	[ : 0.07	= : 0.03	h : 0.03	d : 0.03	$ : 0.03	+ : 0.01	
f : 0.16	g : 0.14	b : 0.10	" : 0.08	e : 0.08	i : 0.07	a : 0.07	! : 0.07	d : 0.05	h : 0.03	$ : 0.03	[ : 0.01	= : 0.01	+ : 0.01	c : 0.01	
[ : 0.21	e : 0.12	f : 0.12	g : 0.10	d : 0.08	i : 0.05	b : 0.05	! : 0.05	h : 0.03	$ : 0.03	" : 0.03	a : 0.01	= : 0.01	+ : 0.01	^ : 0.01	
c : 0.26	d : 0.12	f : 0.12	g : 0.08	e : 0.08	i : 0.05	b : 0.03	h : 0.03	$ : 0.03	a : 0.01	= : 0.01	+ : 0.01	[ : 0.01	y : 0.01	^ : 0.01	" : 0.01	! : 0.01	
c : 0.32	d : 0.12	f : 0.10	g : 0.08	e : 0.08	b : 0.07	h : 0.03	! : 0.03	i : 0.03	y : 0.03	= : 0.01	x : 0.01	^ : 0.01	
c : 0.33	e : 0.08	f : 0.08	d : 0.08	g : 0.07	w : 0.05	y : 0.05	h : 0.03	x : 0.03	i : 0.03	b : 0.03	= : 0.01	! : 0.01	^ : 0.01	u : 0.01	
v : 0.23	w : 0.16	^ : 0.08	c : 0.07	t : 0.07	e : 0.05	x : 0.05	u : 0.05	y : 0.05	d : 0.05	g : 0.01	f : 0.01	h : 0.01	b : 0.01	a : 0.01	i : 0.01	
v : 0.24	t : 0.16	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	b : 0.01	d : 0.01	c : 0.01	
v : 0.24	t : 0.21	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	
v : 0.24	t : 0.21	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	
v : 0.24	t : 0.21	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	
v : 0.24	t : 0.21	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	
v : 0.24	t : 0.21	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	
v : 0.24	t : 0.21	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	
v : 0.24	t : 0.21	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	
v : 0.24	t : 0.21	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	
v : 0.24	t : 0.21	w : 0.16	u : 0.14	^ : 0.08	y : 0.08	x : 0.05	
v : 0.24	w : 0.16	t : 0.14	u : 0.12	^ : 0.08	y : 0.08	x : 0.05	g : 0.03	f : 0.03	c : 0.01	
v : 0.24	w : 0.16	u : 0.08	^ : 0.08	y : 0.08	e : 0.05	c : 0.05	t : 0.05	x : 0.05	f : 0.05	g : 0.03	a : 0.01	
c : 0.19	d : 0.10	w : 0.10	g : 0.08	^ : 0.08	e : 0.07	b : 0.07	y : 0.07	f : 0.05	h : 0.03	i : 0.03	x : 0.03	] : 0.01	v : 0.01	
c : 0.28	d : 0.12	g : 0.10	^ : 0.08	e : 0.07	b : 0.07	f : 0.07	y : 0.05	i : 0.05	h : 0.03	a : 0.01	x : 0.01	
c : 0.26	d : 0.14	g : 0.10	f : 0.08	e : 0.07	^ : 0.07	] : 0.05	i : 0.05	y : 0.03	h : 0.03	b : 0.03	2 : 0.01	4 : 0.01	
d : 0.16	g : 0.12	c : 0.12	e : 0.08	f : 0.08	^ : 0.07	] : 0.05	i : 0.05	b : 0.05	3 : 0.03	y : 0.03	h : 0.03	2 : 0.03	4 : 0.01	a : 0.01	
2 : 0.16	g : 0.12	] : 0.12	f : 0.10	d : 0.08	e : 0.07	^ : 0.07	3 : 0.05	c : 0.05	i : 0.05	h : 0.03	a : 0.01	b : 0.01	4 : 0.01	
2 : 0.14	] : 0.10	f : 0.10	g : 0.08	b : 0.08	e : 0.07	^ : 0.07	d : 0.07	3 : 0.05	c : 0.05	i : 0.05	a : 0.03	h : 0.03	4 : 0.01	
e : 0.21	c : 0.14	b : 0.14	f : 0.10	g : 0.08	d : 0.07	i : 0.05	a : 0.03	] : 0.03	h : 0.03	^ : 0.03	= : 0.01	3 : 0.01	
e : 0.24	c : 0.12	] : 0.10	f : 0.10	d : 0.07	b : 0.07	2 : 0.05	i : 0.05	h : 0.03	g : 0.03	^ : 0.03	B : 0.01	= : 0.01	a : 0.01	
e : 0.23	c : 0.12	f : 0.10	i : 0.08	2 : 0.08	] : 0.08	d : 0.07	= : 0.03	3 : 0.03	b : 0.03	B : 0.01	g : 0.01	9 : 0.01	^ : 0.01	a : 0.01	
e : 0.21	d : 0.14	f : 0.10	3 : 0.08	c : 0.07	i : 0.05	2 : 0.05	b : 0.05	] : 0.05	= : 0.03	{ : 0.01	5 : 0.01	g : 0.01	9 : 0.01	: : 0.01	^ : 0.01	a : 0.01	

#score	1250.092150771032
#seq	56
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_CDS_m1_run2.txt

#BEAR
ggg!!cccqqqqqqqqccc22gg	chr21:34924782-34924995(+)$1	213	39	62	16.5160
bb[eeeeeqqqqqqqqeeeee]b	chr15:75212653-75212883(-)$1	230	121	144	13.5957
fffeeeeeqqqqqqqqeeeee22	chr4:39905555-39905809(-)$1	254	170	193	13.8233
gggggg[aqqqqqqqqa]ggggg	chr17:56082183-56082413(-)$1	230	38	61	14.8303
:gggggggqqqqqqqqggggggg	chr5:162868170-162868393(+)$1	223	150	173	14.1335
c!!eeeeeqqqqqqqqeeeee22	chr20:17930869-17931115(-)$1	246	70	93	14.3880
d####cccqqqqqqqqccc7777	chr1:62914072-62914305(+)$1	233	140	163	14.5683
========qqqqqqqq=======	chr17:27614376-27614612(-)$1	236	148	171	15.9218
f####cccqqqqqqqqccc4444	chr1:28564259-28564470(+)$1	211	90	113	16.7908
fffff[bbqqqqqqqqbbfffff	chr15:35271812-35272045(-)$1	233	136	159	14.0665
ccc!!cccqqqqqqqqcccccc]	chr5:138661765-138662023(+)$1	258	187	210	16.4640
ddddddddqqqqqqqqdddd22d	chr1:16255782-16256028(+)$1	246	112	135	14.4704
ee"""cccqqqqqqqqccc333e	chr17:76219646-76219877(+)$1	231	120	143	16.9716
:eeeeebbqqqqqqqqbb]eeee	chr8:101721319-101721551(-)$1	232	94	117	13.6916
dddd[cccqqqqqqqqccc]ddd	chr1:28527127-28527395(-)$1	268	131	154	15.5645
!!a!!cccqqqqqqqqccc22a2	chr12:50152946-50153194(+)$1	248	99	122	16.7245
ccc!!cccqqqqqqqqcccccc3	chr2:176042863-176043127(-)$1	264	107	130	16.5535
[ccc[cccqqqqqqqqcccccc]	chr13:25670763-25671001(+)$1	238	65	88	16.1904
========qqqqqqqq=======	chr17:45757867-45758131(+)$1	264	192	215	15.9218
====[cccqqqqqqqqccc====	chr2:61712811-61713088(-)$1	277	147	170	16.6685
eeee[abbqqqqqqqqbb]a]ee	chr1:40034394-40034629(-)$1	235	71	94	15.1361
gga!!cccqqqqqqqqccc22a]	chr8:29921239-29921462(-)$1	223	171	194	16.6259
eee[ddddqqqqqqqqdddd]ee	chr5:133541535-133541791(-)$1	256	175	198	14.9952
#bb[ddddqqqqqqqqdddd]bb	chr1:62905381-62905641(+)$1	260	139	162	14.2426
!!a[ddddqqqqqqqqdddda22	chr3:149682868-149683101(-)$1	233	202	225	15.3553
FFccc[bbqqqqqqqqbb]ccc:	chr6:17646197-17646426(-)$1	229	172	195	13.2638
ddd!!cccrrrrrrrrrccc333	chr10:126630965-126631204(+)$1	239	171	194	10.1192
h####cccqqqqqqqqccc]hhh	chr7:135611987-135612198(-)$1	211	174	197	15.5794
$$$$ddddqqqqqqqqdddd444	chr17:45755577-45755812(+)$1	235	191	214	14.9703
$$$$ddddqqqqqqqqdddd444	chr2:44547253-44547476(-)$1	223	165	188	14.9703
"""eeeeeqqqqqqqqeeeee44	chr1:193060647-193060921(+)$1	274	147	170	14.7012
$$$$$cccqqqqqqqqccc6666	chr14:45583933-45584179(+)$1	246	148	171	14.1528
bbffffffqqqqqqqqffffff]	chr8:33357805-33358040(+)$1	235	123	146	13.3179
dddd[cccqqqqqqqqccc]ddd	chr3:170584102-170584331(-)$1	229	123	146	15.5645
dccc!!bbqqqqqqqqbbccc22	chr21:34948696-34948919(+)$1	223	37	60	15.5409
fffff[bbqqqqqqqqbb]ffff	chr15:66791589-66791854(-)$1	265	228	251	14.1690
ff[bb[bbqqqqqqqqbb]bb]f	chr6:74228958-74229194(-)$1	236	144	167	13.7128
dccc[cccqqqqqqqqccc]ccc	chr1:16259427-16259654(+)$1	227	118	141	16.0829
eeeeecccqqqqqqqqccc]eee	chr13:23911421-23911654(-)$1	233	122	145	15.5246
####ddddqqqqqqqqddddccc	chr17:43005431-43005651(+)$1	220	184	207	15.1816
ddd[ddddqqqqqqqqdddd]dd	chrX:135954347-135954603(-)$1	256	60	83	14.8247
dddd!!bbqqqqqqqqbb22ddd	chr6:32944448-32944671(+)$1	223	23	46	14.6445
========qqqqqqqq=======	chr17:27614235-27614466(-)$1	231	2	25	15.9218
eeee!!bbqqqqqqqqbbeeeee	chr20:40033402-40033631(-)$1	229	125	148	15.0598
$$ffffffqqqqqqqqfffffff	chr6:163990400-163990676(+)$1	276	230	253	13.3213
dddd[cccqqqqqqqqcccdddd	chr11:33308799-33309032(+)$1	233	59	82	15.3901
iiii[cccqqqqqqqqccc]iii	chr17:44159743-44159972(-)$1	229	130	153	16.3781
:gggggggqqqqqqqqggggggg	chr2:61483906-61484157(-)$1	251	7	30	14.1335
eee[a[bbqqqqqqqqbba]eee	chr1:16261159-16261400(+)$1	241	63	86	15.2639
[gggggggqqqqqqqqggggggg	chr19:40478309-40478534(+)$1	225	111	134	15.0939
dd!!ddddqqqqqqqqdddd22d	chr8:101721636-101721872(-)$1	236	43	66	15.1536
ff####bbqqqqqqqqbb22fff	chr19:37239037-37239275(-)$1	238	172	195	14.8686
ddd"""bbqqqqqqqqbb22ddd	chr1:16256575-16256838(+)$1	263	46	69	14.8811
"ccc[cccqqqqqqqqcccccc3	chr1:16256114-16256333(+)$1	219	122	145	16.2799
========qqqqqqqq=======	chr18:57569925-57570168(+)$1	243	81	104	15.9218
!bb!!cccqqqqqqqqccc22bb	chrX:71493679-71493922(-)$1	243	140	163	15.5727
eee[ddddqqqqqqqqdddd>>>	chr3:39449997-39450227(+)$1	230	82	105	14.7515
eeeee[bbqqqqqqqqbbeeeee	chr1:113241286-113241511(+)$1	225	125	148	14.6548
:ccc!!bbqqqqqqqqbb4444c	chr3:98234506-98234728(-)$1	222	173	196	14.9571
ddddddddqqqqqqqqdddd22d	chr1:16255832-16256071(+)$1	239	62	85	14.4704
eee[ddddqqqqqqqqddddeee	chr8:101718831-101719063(-)$1	232	123	146	14.8304
ggg!!cccqqqqqqqqcccgggg	chr10:103546121-103546347(-)$1	226	177	200	16.4808

#otherMatches

#Seq PSSM
AUACUCUGCUGCUGACCGGUCUA	chr21:34924782-34924995(+)$1	213	39	62	16.5160
UUGACAUUGCUACUUGAGUGUGA	chr15:75212653-75212883(-)$1	230	121	144	13.5957
GAAUGGUUGAGUGUAAAACUACU	chr4:39905555-39905809(-)$1	254	170	193	13.8233
GCUUUGGAUUAAGGAUUGUGGAG	chr17:56082183-56082413(-)$1	230	38	61	14.8303
AACUUGCCACUUGAAAGGUAAGU	chr5:162868170-162868393(+)$1	223	150	173	14.1335
UCUAGGAGGUAGAUGACUUCUUU	chr20:17930869-17931115(-)$1	246	70	93	14.3880
GGAGAAGAUAAAUAUUUCUGUGA	chr1:62914072-62914305(+)$1	233	140	163	14.5683
CUAUACCAAUUCCAAAUGGUGUG	chr17:27614376-27614612(-)$1	236	148	171	15.9218
CACAGAGUAGAGAACAACUGGCA	chr1:28564259-28564470(+)$1	211	90	113	16.7908
GUUUUGCAUCAUAAACUGAGAAC	chr15:35271812-35272045(-)$1	233	136	159	14.0665
CCUCAUUAUCAGAAAUUAAAGGU	chr5:138661765-138662023(+)$1	258	187	210	16.4640
CUGGACAGACUUAAUACUGUUGC	chr1:16255782-16256028(+)$1	246	112	135	14.4704
UGUUUCAACUGUGCUCUUGUUUU	chr17:76219646-76219877(+)$1	231	120	143	16.9716
CUGCAGACUCAGAACCGUGCUGC	chr8:101721319-101721551(-)$1	232	94	117	13.6916
ACAGAGCAGCAUCUGAUGCCCUG	chr1:28527127-28527395(-)$1	268	131	154	15.5645
CUUUUUGAUACUCAACUCAUUAU	chr12:50152946-50153194(+)$1	248	99	122	16.7245
UGUAACAAAUUACUGCUUGACAU	chr2:176042863-176043127(-)$1	264	107	130	16.5535
GGUCGCAAAGUAUUUGUUGGACA	chr13:25670763-25671001(+)$1	238	65	88	16.1904
CUUUCUUCUACUUCCUGGAGGAG	chr17:45757867-45758131(+)$1	264	192	215	15.9218
GAUGCUGUUUUUGAAUGCACAUU	chr2:61712811-61713088(-)$1	277	147	170	16.6685
CCGUGCACAAAAGAAAGUAGAAC	chr1:40034394-40034629(-)$1	235	71	94	15.1361
UUCUGUGGUGUUAUGUCCAGUGU	chr8:29921239-29921462(-)$1	223	171	194	16.6259
UAAGGUAAUUUCAAUUUUAUGUU	chr5:133541535-133541791(-)$1	256	175	198	14.9952
UGGGAUUUGAAGAAAAAAAUGCC	chr1:62905381-62905641(+)$1	260	139	162	14.2426
UUCUAGUAUUUGCUUCUAUUGUU	chr3:149682868-149683101(-)$1	233	202	225	15.3553
ACAGUAGAUUAGUAUUUCAGCUU	chr6:17646197-17646426(-)$1	229	172	195	13.2638
UAUGUGUCGUGCCCAAAGACCUA	chr10:126630965-126631204(+)$1	239	171	194	10.1192
UAAACCCAGUUAAGCAUGGAAGA	chr7:135611987-135612198(-)$1	211	174	197	15.5794
GAACGUACACCGUUGAGUAUACA	chr17:45755577-45755812(+)$1	235	191	214	14.9703
AAGUGUUUGAUUCUAAGAAUUGU	chr2:44547253-44547476(-)$1	223	165	188	14.9703
CUACUAAAUAAAUCAUUUUAGAC	chr1:193060647-193060921(+)$1	274	147	170	14.7012
AUUAUGGACAAUAUUAUCCUCCC	chr14:45583933-45584179(+)$1	246	148	171	14.1528
GUGUAAGGUUUGGAUCCCUUGCU	chr8:33357805-33358040(+)$1	235	123	146	13.3179
GAUUAGUCAAGAUGAAGAUGAAU	chr3:170584102-170584331(-)$1	229	123	146	15.5645
AUGGAAGCGCUUACCAGCCCAGC	chr21:34948696-34948919(+)$1	223	37	60	15.5409
AGAAUUUUUUUAAAGUGACAUUU	chr15:66791589-66791854(-)$1	265	228	251	14.1690
AUUAAUAAUUCUAGGUUUCUUUA	chr6:74228958-74229194(-)$1	236	144	167	13.7128
GGCAUCCUGGAAACUGAGGCUGC	chr1:16259427-16259654(+)$1	227	118	141	16.0829
UGAUAUGCUAGAACGUGCAGUGU	chr13:23911421-23911654(-)$1	233	122	145	15.5246
UGGCAGGGGGAGGAGGCCCUUUC	chr17:43005431-43005651(+)$1	220	184	207	15.1816
AAGAGAGAUAACUAGUUUUCAUU	chrX:135954347-135954603(-)$1	256	60	83	14.8247
GUGGUCGCCCCAUCAAGCCCCCA	chr6:32944448-32944671(+)$1	223	23	46	14.6445
CUAUACCAAUUCCAAAUGGUGUG	chr17:27614235-27614466(-)$1	231	2	25	15.9218
CAUGUUCCUCUCCCCUGGUAUGG	chr20:40033402-40033631(-)$1	229	125	148	15.0598
AUUGGGAAUGAUAACUUUUCCAC	chr6:163990400-163990676(+)$1	276	230	253	13.3213
GGCCCAUUCUUCAACAAGUGGCC	chr11:33308799-33309032(+)$1	233	59	82	15.3901
UCUGAGGUGAAGACAGAUCAUGG	chr17:44159743-44159972(-)$1	229	130	153	16.3781
uuaauauauuuucauuuauauua	chr2:61483906-61484157(-)$1	251	7	30	14.1335
AUCAGCGCCAAGAUCAGCCAGAU	chr1:16261159-16261400(+)$1	241	63	86	15.2639
AGGCUGUGGAUCAGAAUACAGCC	chr19:40478309-40478534(+)$1	225	111	134	15.0939
CUCAGCGCAAAGAAGAGCGCCAG	chr8:101721636-101721872(-)$1	236	43	66	15.1536
CACACUGGCGAGAAACCCUAUGA	chr19:37239037-37239275(-)$1	238	172	195	14.8686
CCUAUUCUAACAUAACAGUCAGG	chr1:16256575-16256838(+)$1	263	46	69	14.8811
AGUUACCGAAAACAAAUGGAACA	chr1:16256114-16256333(+)$1	219	122	145	16.2799
GGGGACUCCUUCAAAAGAGUUUU	chr18:57569925-57570168(+)$1	243	81	104	15.9218
AAGGAAUCCCUCAUCUGGUGACU	chrX:71493679-71493922(-)$1	243	140	163	15.5727
CUUCUGCCCUCACUUAGGCAUCU	chr3:39449997-39450227(+)$1	230	82	105	14.7515
GUGACAUGCUGUUCCACAGUCAC	chr1:113241286-113241511(+)$1	225	125	148	14.6548
UGAUGUGCCUUUCCUUGCCUAAA	chr3:98234506-98234728(-)$1	222	173	196	14.9571
CUGGACAGACUUAAUACUGUUGC	chr1:16255832-16256071(+)$1	239	62	85	14.4704
CUGCAGGAGUUCGCAAUCCUCAG	chr8:101718831-101719063(-)$1	232	123	146	14.8304
ACUGCACCUUGUGAAUGGUAGUU	chr10:103546121-103546347(-)$1	226	177	200	16.4808

#DB
(((..(((........)))..))	chr21:34924782-34924995(+)$1	1	39	62	16.5160
((.(((((........))))).)	chr15:75212653-75212883(-)$1	1	121	144	13.5957
((((((((........)))))..	chr4:39905555-39905809(-)$1	1	170	193	13.8233
((((((.(........).)))))	chr17:56082183-56082413(-)$1	1	38	61	14.8303
.(((((((........)))))))	chr5:162868170-162868393(+)$1	1	150	173	14.1335
(..(((((........)))))..	chr20:17930869-17931115(-)$1	1	70	93	14.3880
(....(((........)))....	chr1:62914072-62914305(+)$1	1	140	163	14.5683
((((((((........)))))))	chr17:27614376-27614612(-)$1	1	148	171	15.9218
(....(((........)))....	chr1:28564259-28564470(+)$1	1	90	113	16.7908
(((((.((........)))))))	chr15:35271812-35272045(-)$1	1	136	159	14.0665
(((..(((........)))))).	chr5:138661765-138662023(+)$1	1	187	210	16.4640
((((((((........))))..)	chr1:16255782-16256028(+)$1	1	112	135	14.4704
((...(((........)))...)	chr17:76219646-76219877(+)$1	1	120	143	16.9716
.(((((((........)).))))	chr8:101721319-101721551(-)$1	1	94	117	13.6916
((((.(((........))).)))	chr1:28527127-28527395(-)$1	1	131	154	15.5645
..(..(((........)))..).	chr12:50152946-50153194(+)$1	1	99	122	16.7245
(((..(((........)))))).	chr2:176042863-176043127(-)$1	1	107	130	16.5535
.(((.(((........)))))).	chr13:25670763-25671001(+)$1	1	65	88	16.1904
((((((((........)))))))	chr17:45757867-45758131(+)$1	1	192	215	15.9218
((((.(((........)))))))	chr2:61712811-61713088(-)$1	1	147	170	16.6685
((((.(((........)).).))	chr1:40034394-40034629(-)$1	1	71	94	15.1361
(((..(((........)))..).	chr8:29921239-29921462(-)$1	1	171	194	16.6259
(((.((((........)))).))	chr5:133541535-133541791(-)$1	1	175	198	14.9952
.((.((((........)))).))	chr1:62905381-62905641(+)$1	1	139	162	14.2426
..(.((((........)))))..	chr3:149682868-149683101(-)$1	1	202	225	15.3553
))(((.((........)).))).	chr6:17646197-17646426(-)$1	1	172	195	13.2638
(((..(((.........)))...	chr10:126630965-126631204(+)$1	1	171	194	10.1192
(....(((........))).)))	chr7:135611987-135612198(-)$1	1	174	197	15.5794
....((((........))))...	chr17:45755577-45755812(+)$1	1	191	214	14.9703
....((((........))))...	chr2:44547253-44547476(-)$1	1	165	188	14.9703
...(((((........)))))..	chr1:193060647-193060921(+)$1	1	147	170	14.7012
.....(((........)))....	chr14:45583933-45584179(+)$1	1	148	171	14.1528
((((((((........)))))).	chr8:33357805-33358040(+)$1	1	123	146	13.3179
((((.(((........))).)))	chr3:170584102-170584331(-)$1	1	123	146	15.5645
((((..((........)))))..	chr21:34948696-34948919(+)$1	1	37	60	15.5409
(((((.((........)).))))	chr15:66791589-66791854(-)$1	1	228	251	14.1690
((.((.((........)).)).)	chr6:74228958-74229194(-)$1	1	144	167	13.7128
((((.(((........))).)))	chr1:16259427-16259654(+)$1	1	118	141	16.0829
((((((((........))).)))	chr13:23911421-23911654(-)$1	1	122	145	15.5246
....((((........)))))))	chr17:43005431-43005651(+)$1	1	184	207	15.1816
(((.((((........)))).))	chrX:135954347-135954603(-)$1	1	60	83	14.8247
((((..((........))..)))	chr6:32944448-32944671(+)$1	1	23	46	14.6445
((((((((........)))))))	chr17:27614235-27614466(-)$1	1	2	25	15.9218
((((..((........)))))))	chr20:40033402-40033631(-)$1	1	125	148	15.0598
..((((((........)))))))	chr6:163990400-163990676(+)$1	1	230	253	13.3213
((((.(((........)))))))	chr11:33308799-33309032(+)$1	1	59	82	15.3901
((((.(((........))).)))	chr17:44159743-44159972(-)$1	1	130	153	16.3781
.(((((((........)))))))	chr2:61483906-61484157(-)$1	1	7	30	14.1335
(((.(.((........))).)))	chr1:16261159-16261400(+)$1	1	63	86	15.2639
.(((((((........)))))))	chr19:40478309-40478534(+)$1	1	111	134	15.0939
((..((((........))))..)	chr8:101721636-101721872(-)$1	1	43	66	15.1536
((....((........))..)))	chr19:37239037-37239275(-)$1	1	172	195	14.8686
(((...((........))..)))	chr1:16256575-16256838(+)$1	1	46	69	14.8811
.(((.(((........)))))).	chr1:16256114-16256333(+)$1	1	122	145	16.2799
((((((((........)))))))	chr18:57569925-57570168(+)$1	1	81	104	15.9218
.((..(((........)))..))	chrX:71493679-71493922(-)$1	1	140	163	15.5727
(((.((((........))))...	chr3:39449997-39450227(+)$1	1	82	105	14.7515
(((((.((........)))))))	chr1:113241286-113241511(+)$1	1	125	148	14.6548
.(((..((........))....)	chr3:98234506-98234728(-)$1	1	173	196	14.9571
((((((((........))))..)	chr1:16255832-16256071(+)$1	1	62	85	14.4704
(((.((((........)))))))	chr8:101718831-101719063(-)$1	1	123	146	14.8304
(((..(((........)))))))	chr10:103546121-103546347(-)$1	1	177	200	16.4808

#PSSM
d : 0.20	e : 0.14	f : 0.09	= : 0.08	g : 0.06	: : 0.06	$ : 0.06	c : 0.04	! : 0.04	b : 0.03	[ : 0.03	# : 0.03	" : 0.03	F : 0.01	h : 0.01	i : 0.01	
d : 0.16	e : 0.16	g : 0.11	c : 0.11	f : 0.08	= : 0.08	b : 0.06	# : 0.06	$ : 0.06	! : 0.04	F : 0.01	" : 0.01	i : 0.01	
d : 0.14	e : 0.14	c : 0.12	g : 0.09	f : 0.08	# : 0.08	= : 0.08	a : 0.04	$ : 0.04	[ : 0.03	! : 0.03	" : 0.03	b : 0.03	i : 0.01	
! : 0.14	e : 0.14	[ : 0.11	d : 0.09	c : 0.09	# : 0.08	= : 0.08	g : 0.06	f : 0.06	$ : 0.04	" : 0.03	b : 0.01	i : 0.01	
! : 0.19	d : 0.19	[ : 0.14	e : 0.11	g : 0.06	# : 0.06	= : 0.06	f : 0.06	" : 0.03	c : 0.01	$ : 0.01	b : 0.01	a : 0.01	
c : 0.35	d : 0.19	[ : 0.09	e : 0.08	g : 0.06	= : 0.06	! : 0.06	f : 0.03	a : 0.01	# : 0.01	" : 0.01	
c : 0.35	b : 0.22	d : 0.19	e : 0.06	= : 0.06	g : 0.04	f : 0.03	[ : 0.01	
c : 0.35	b : 0.22	d : 0.19	e : 0.06	= : 0.06	g : 0.04	f : 0.03	a : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
c : 0.33	b : 0.22	d : 0.19	e : 0.06	= : 0.06	g : 0.04	f : 0.03	a : 0.01	r : 0.01	
c : 0.35	b : 0.22	d : 0.19	e : 0.06	= : 0.06	g : 0.04	f : 0.03	] : 0.01	
c : 0.37	d : 0.19	e : 0.09	] : 0.08	g : 0.06	= : 0.06	f : 0.04	2 : 0.04	a : 0.01	4 : 0.01	
d : 0.20	2 : 0.11	e : 0.11	c : 0.11	] : 0.11	g : 0.08	= : 0.08	f : 0.06	4 : 0.03	7 : 0.01	3 : 0.01	a : 0.01	6 : 0.01	b : 0.01	
e : 0.16	c : 0.12	2 : 0.11	g : 0.08	= : 0.08	f : 0.08	d : 0.08	4 : 0.06	] : 0.06	3 : 0.03	7 : 0.01	a : 0.01	h : 0.01	6 : 0.01	b : 0.01	i : 0.01	> : 0.01	
e : 0.12	2 : 0.11	c : 0.11	g : 0.09	d : 0.09	= : 0.08	4 : 0.08	f : 0.08	] : 0.03	3 : 0.03	a : 0.03	b : 0.03	7 : 0.01	h : 0.01	6 : 0.01	i : 0.01	> : 0.01	
d : 0.14	e : 0.14	g : 0.09	2 : 0.08	= : 0.08	f : 0.08	4 : 0.06	] : 0.06	b : 0.04	3 : 0.04	c : 0.04	7 : 0.01	: : 0.01	h : 0.01	6 : 0.01	i : 0.01	> : 0.01	

#score	933.9184934205417
#seq	62
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_CDS_m2_run2.txt

#BEAR
ddddwwwwwwwwwwwwwwdddd::	chrM:13365-13608(+)$1	243	8	32	19.2481
bb[ddddtttttttttttdddd]b	chr16:31202192-31202450(+)$1	258	126	150	21.8628
ceeeeeuuuuuuuuuuuueeeee]	chr17:43175734-43175962(+)$1	228	181	205	22.9261
==[ddddtttttttttttdddd]=	chr6:43483667-43483903(-)$1	236	154	178	22.6362
gggggggtttttttttttgggggg	chr2:109405281-109405509(+)$1	228	60	84	22.4939
ifffffftttttttttttffffff	chr17:1563963-1564206(-)$1	243	46	70	21.9768
ccc!!bbtttttttttttbb22cc	chr19:30106093-30106334(+)$1	241	187	211	21.3005
ccc[ccctttttttttttccc]cc	chr7:2403971-2404202(+)$1	231	124	148	22.9034
:eeeeettttttttttteeeee:b	chr17:4787605-4787837(+)$1	232	12	36	19.3429
d[bbcccuuuuuuuuuuuuccc]b	chr1:155903430-155903682(-)$1	252	152	176	22.1131
d!!cccvvvvvvvvvvvvvccc22	chr3:167761106-167761349(-)$1	243	43	67	23.1032
[fffffftttttttttttffffff	chr19:8553622-8553857(+)$1	235	169	193	21.9980
dcccxxxxxxxxxxxxxxxccc]d	chr10:129910106-129910358(-)$1	252	80	104	16.8865
ffffffuuuuuuuuuuuuffffff	chr19:39979153-39979383(+)$1	230	90	114	22.6864
####bbvvvvvvvvvvvvvbb333	chr3:47777419-47777657(-)$1	238	28	52	22.0281
c!!ddddtttttttttttdddd22	chr19:50000449-50000685(+)$1	236	140	164	22.2941
gggggggtttttttttttgggggg	chr1:78429656-78429907(-)$1	251	180	204	22.4939
++dddduuuuuuuuuuuudddd33	chrM:13461-13706(+)$1	245	115	139	22.0803
gggggggtttttttttttgggggg	chr1:44118730-44118962(+)$1	232	43	67	22.4939
eeeeevvvvvvvvvvvvveeeee]	chr1:155823423-155823652(-)$1	229	89	113	22.3340
ccc[ccctttttttttttccc]cc	chr6:13364952-13365182(-)$1	230	149	173	22.9034
gggggggtttttttttttgggggg	chr2:62069156-62069393(-)$1	237	58	82	22.4939
eeeeewwwwwwwwwwwwwweeeee	chr17:76415569-76415808(+)$1	239	206	230	21.3288
%%dddduuuuuuuuuuuudddd66	chr20:34309596-34309825(-)$1	229	24	48	20.9277
:eeeeevvvvvvvvvvvvveeeee	chr3:9482072-9482321(+)$1	249	174	198	21.6686
c[cccwwwwwwwwwwwwwwccc]c	chr17:27246071-27246297(-)$1	226	33	57	22.1710
ddddccctttttttttttccc555	chr10:99141404-99141633(-)$1	229	75	99	20.3925
!cccwwwwwwwwwwwwwwccc22e	chr3:57646395-57646624(-)$1	229	140	164	21.2945
e!!ccctttttttttttccc]eee	chr7:26236912-26237150(-)$1	238	64	88	21.7479
ffffffuuuuuuuuuuuuffffff	chrM:8019-8242(+)$1	223	53	77	22.6864
dd!!bbwwwwwwwwwwwwwwbb22	chr15:90167461-90167710(+)$1	249	199	223	20.5100
eeeeevvvvvvvvvvvvveeeeec	chr16:14042049-14042273(+)$1	224	11	35	22.3272
======vvvvvvvvvvvvv=====	chr8:145748272-145748496(+)$1	224	181	205	23.1225
:eeeeeuuuuuuuuuuuueeeeeE	chr9:33166851-33167075(-)$1	224	171	195	21.1171
cccddddtttttttttttdddd]c	chr14:70855193-70855421(-)$1	228	120	144	22.5373
ccc[bbtttttttttttbb]cccE	chr16:11940478-11940707(-)$1	229	13	37	19.9796
ffffffuuuuuuuuuuuuffffff	chrX:64748085-64748304(-)$1	219	94	118	22.6864
+++cccuuuuuuuuuuuuccc>>>	chr6:26031909-26032139(-)$1	230	180	204	21.1143
ggggggvvvvvvvvvvvvvggggg	chr10:75056699-75056921(-)$1	222	180	204	23.0754
ffffffuuuuuuuuuuuuffffff	chrM:7944-8173(+)$1	229	128	152	22.6864
ggggggvvvvvvvvvvvvvggggg	chr13:41766333-41766556(-)$1	223	87	111	23.0754
bbbbyyyyyyyyyyyyyyyybb]b	chr17:48829451-48829709(+)$1	258	198	222	18.9218
dd!!ccctttttttttttccc22d	chr10:103559073-103559300(-)$1	227	146	170	22.6417
ffffffwwwwwwwwwwwwwwffff	chr10:62551654-62551908(+)$1	254	151	175	21.0596
dddddduuuuuuuuuuuudddd]d	chrM:14957-15211(+)$1	254	16	40	22.9765
eeee[awwwwwwwwwwwwwwa]ee	chr16:2816186-2816430(+)$1	244	120	144	21.1907
!ddddvvvvvvvvvvvvvdddd22	chr18:32920258-32920493(-)$1	235	175	199	22.3645
!fffffftttttttttttffffff	chr7:99694837-99695068(-)$1	231	57	81	22.0322
dd[ddddtttttttttttdddd]d	chr19:5653289-5653520(+)$1	231	53	77	22.3224
gggggggtttttttttttgggggg	chr19:40321015-40321247(-)$1	232	128	152	22.4939
ggggggwwwwwwwwwwwwwwgggg	chr9:95027677-95027926(-)$1	249	16	40	21.6962
ggggggyyyyyyyyyyyyyyyygg	chr20:57485740-57485968(+)$1	228	59	83	20.0876
:ccc[bbtttttttttttbb]ccc	chr19:33870488-33870715(+)$1	227	100	124	20.8345
ffffffuuuuuuuuuuuuffffff	chrX:71493547-71493786(-)$1	239	156	180	22.6864
dddddduuuuuuuuuuuudddd]d	chr5:138650265-138650504(+)$1	239	164	188	22.9765
ddddwwwwwwwwwwwwwwdddd44	chrX:47087885-47088127(+)$1	242	84	108	21.0926
iiiiiiwwwwwwwwwwwwwwiiii	chr8:48798421-48798654(-)$1	233	170	194	21.4355
ddyyyyyyyyyyyyyyyydddd]e	chr1:45981255-45981486(-)$1	231	198	222	19.8113
eeeeewwwwwwwwwwwwwweeeee	chr2:190339334-190339562(+)$1	228	3	27	21.3288

#otherMatches

#Seq PSSM
UCAUCCACAACCUUAACAAUGAAC	chrM:13365-13608(+)$1	243	8	32	19.2481
GGAGGCUAUGAUCGAGGCGGCUAC	chr16:31202192-31202450(+)$1	258	126	150	21.8628
UGCAGGUAAAACUGUCUUCCUGUA	chr17:43175734-43175962(+)$1	228	181	205	22.9261
CGCCUGCGCGAGGAAGAAGUAGAC	chr6:43483667-43483903(-)$1	236	154	178	22.6362
UUCAUCGUUAAAAUAUUCUGAUGA	chr2:109405281-109405509(+)$1	228	60	84	22.4939
UGGCAGGAUAUCACCUCACCUGCU	chr17:1563963-1564206(-)$1	243	46	70	21.9768
CCUGUGAAUUCUUUGCCGUCUAAG	chr19:30106093-30106334(+)$1	241	187	211	21.3005
GAAAUUCAAGCAAAUUCAGAGAUU	chr7:2403971-2404202(+)$1	231	124	148	22.9034
GACUGAUACUUUUCCUUUCGGUAC	chr17:4787605-4787837(+)$1	232	12	36	19.3429
CUGCUCCUUCAGGAGCCUUGGAUG	chr1:155903430-155903682(-)$1	252	152	176	22.1131
GGAGCUAAAGAAACAGCACAGUGA	chr3:167761106-167761349(-)$1	243	43	67	23.1032
UGUUAACCAUUUUAAUUUGUUGGC	chr19:8553622-8553857(+)$1	235	169	193	21.9980
UGGUGCAAAACAAACACAAACUAA	chr10:129910106-129910358(-)$1	252	80	104	16.8865
CCGCUGGCGGCUUUCAAACAGCGG	chr19:39979153-39979383(+)$1	230	90	114	22.6864
UUUUCAUCCUCAGAACAAUUGUUU	chr3:47777419-47777657(-)$1	238	28	52	22.0281
GAACCUCAGAAGAAAGAAGGGGAA	chr19:50000449-50000685(+)$1	236	140	164	22.2941
UUUUCAUUUUUUGUUUUUAUGGAA	chr1:78429656-78429907(-)$1	251	180	204	22.4939
AUCGCUACCUCCCUGACAAGCGCC	chrM:13461-13706(+)$1	245	115	139	22.0803
uauauuauuuuauaCUCUUAAUGU	chr1:44118730-44118962(+)$1	232	43	67	22.4939
CUGUAAGAAGAGAAGAACUACAGU	chr1:155823423-155823652(-)$1	229	89	113	22.3340
GCCCCGCCUACCUGAUCAGCGAGG	chr6:13364952-13365182(-)$1	230	149	173	22.9034
AAAUGUACCAGGAUAAAUUACAUU	chr2:62069156-62069393(-)$1	237	58	82	22.4939
CUCUCAGCACGAUUUUCCCGAGAG	chr17:76415569-76415808(+)$1	239	206	230	21.3288
AGGCAGAAAAAAACAGAGCUGCAG	chr20:34309596-34309825(-)$1	229	24	48	20.9277
CAGUGCAGAUGUACAGAACGCGCU	chr3:9482072-9482321(+)$1	249	174	198	21.6686
GUGACUAUUGCCCUCUCCUGUUUC	chr17:27246071-27246297(-)$1	226	33	57	22.1710
CACCUCCCUCGCUUUUUUGGAACU	chr10:99141404-99141633(-)$1	229	75	99	20.3925
AAUAUCUUAUAUCUCAAUUGUCUC	chr3:57646395-57646624(-)$1	229	140	164	21.2945
GAAAGGUAAUGAGGGAUCCUGCAA	chr7:26236912-26237150(-)$1	238	64	88	21.7479
UGAGCUGUCCCCACAUUAGGCUUA	chrM:8019-8242(+)$1	223	53	77	22.6864
CCUCCUCCACCCCCUUCUAAAGUU	chr15:90167461-90167710(+)$1	249	199	223	20.5100
GUUAAGAACAUCGCAGAAUUAGCA	chr16:14042049-14042273(+)$1	224	11	35	22.3272
CCCAGCAACCCGCCUUCUAGCUGG	chr8:145748272-145748496(+)$1	224	181	205	23.1225
AGGCGCCUCCUCCCAGCCGCGCCC	chr9:33166851-33167075(-)$1	224	171	195	21.1171
UGGGACAGAUCAGCAGUAUGUCUC	chr14:70855193-70855421(-)$1	228	120	144	22.5373
UCCCUCCAAACUCUAAAGAAGGAA	chr16:11940478-11940707(-)$1	229	13	37	19.9796
GCGUGGAAUAACCCGUCCCCACGU	chrX:64748085-64748304(-)$1	219	94	118	22.6864
UUGCGCCAUCCAUGCUAAGCGAGU	chr6:26031909-26032139(-)$1	230	180	204	21.1143
GAAUAAUUCCUUCCuuuguuuauu	chr10:75056699-75056921(-)$1	222	180	204	23.0754
UGAGCUGUCCCCACAUUAGGCUUA	chrM:7944-8173(+)$1	229	128	152	22.6864
CUGAAUGGGACUUAGAUGGAUUCA	chr13:41766333-41766556(-)$1	223	87	111	23.0754
UGGCAUAGAAAAAGUAUAAAGCUC	chr17:48829451-48829709(+)$1	258	198	222	18.9218
UGCAGCACCCUCUUUAAAUGCCAC	chr10:103559073-103559300(-)$1	227	146	170	22.6417
UUUCAGGUAGCUAUUAAAAACUGA	chr10:62551654-62551908(+)$1	254	151	175	21.0596
GCUGAAUCAUCCGCUACCUUCACG	chrM:14957-15211(+)$1	254	16	40	22.9765
AACGCCACCAGUAACCCGCCGUCG	chr16:2816186-2816430(+)$1	244	120	144	21.1907
GUUUGUUGCCAUCCUACCCAAAGA	chr18:32920258-32920493(-)$1	235	175	199	22.3645
CCAGGCAACAUCAACAUCUGUCUG	chr7:99694837-99695068(-)$1	231	57	81	22.0322
UUUCAGGCCAAAAAUGAACCUGUG	chr19:5653289-5653520(+)$1	231	53	77	22.3224
CAUGGUUAUGAUGACGACAACCAU	chr19:40321015-40321247(-)$1	232	128	152	22.4939
CAUGCUAUAUAAAUUAACUCAGUA	chr9:95027677-95027926(-)$1	249	16	40	21.6962
GGACACUGAGAACAUCCGCCGUGU	chr20:57485740-57485968(+)$1	228	59	83	20.0876
AGGACAGUAGACCUCACCCUUUCC	chr19:33870488-33870715(+)$1	227	100	124	20.8345
CUGGGCACCCUCUUUAAGGCCUAG	chrX:71493547-71493786(-)$1	239	156	180	22.6864
GAGUUUGAAAUACCUUUAAAACAU	chr5:138650265-138650504(+)$1	239	164	188	22.9765
UUCCAUAUUUGCACUAAAGGAGAU	chrX:47087885-47088127(+)$1	242	84	108	21.0926
AUAAACUGUuuuuuuuguuuguuu	chr8:48798421-48798654(-)$1	233	170	194	21.4355
uuuuuuuuuuuuuuuuuugagaug	chr1:45981255-45981486(-)$1	231	198	222	19.8113
CUCUUGGCAUUUACAAUAAAAGGG	chr2:190339334-190339562(+)$1	228	3	27	21.3288

#DB
((((..............))))..	chrM:13365-13608(+)$1	1	8	32	19.2481
((.((((...........)))).)	chr16:31202192-31202450(+)$1	1	126	150	21.8628
((((((............))))).	chr17:43175734-43175962(+)$1	1	181	205	22.9261
((.((((...........)))).)	chr6:43483667-43483903(-)$1	1	154	178	22.6362
(((((((...........))))))	chr2:109405281-109405509(+)$1	1	60	84	22.4939
)((((((...........))))))	chr17:1563963-1564206(-)$1	1	46	70	21.9768
(((..((...........))..))	chr19:30106093-30106334(+)$1	1	187	211	21.3005
(((.(((...........))).))	chr7:2403971-2404202(+)$1	1	124	148	22.9034
.(((((...........))))).(	chr17:4787605-4787837(+)$1	1	12	36	19.3429
(.(((((............))).)	chr1:155903430-155903682(-)$1	1	152	176	22.1131
(..(((.............)))..	chr3:167761106-167761349(-)$1	1	43	67	23.1032
.((((((...........))))))	chr19:8553622-8553857(+)$1	1	169	193	21.9980
((((...............))).)	chr10:129910106-129910358(-)$1	1	80	104	16.8865
((((((............))))))	chr19:39979153-39979383(+)$1	1	90	114	22.6864
....((.............))...	chr3:47777419-47777657(-)$1	1	28	52	22.0281
(..((((...........))))..	chr19:50000449-50000685(+)$1	1	140	164	22.2941
(((((((...........))))))	chr1:78429656-78429907(-)$1	1	180	204	22.4939
..((((............))))..	chrM:13461-13706(+)$1	1	115	139	22.0803
(((((((...........))))))	chr1:44118730-44118962(+)$1	1	43	67	22.4939
(((((.............))))).	chr1:155823423-155823652(-)$1	1	89	113	22.3340
(((.(((...........))).))	chr6:13364952-13365182(-)$1	1	149	173	22.9034
(((((((...........))))))	chr2:62069156-62069393(-)$1	1	58	82	22.4939
(((((..............)))))	chr17:76415569-76415808(+)$1	1	206	230	21.3288
..((((............))))..	chr20:34309596-34309825(-)$1	1	24	48	20.9277
.(((((.............)))))	chr3:9482072-9482321(+)$1	1	174	198	21.6686
(.(((..............))).)	chr17:27246071-27246297(-)$1	1	33	57	22.1710
(((((((...........)))...	chr10:99141404-99141633(-)$1	1	75	99	20.3925
.(((..............)))..)	chr3:57646395-57646624(-)$1	1	140	164	21.2945
(..(((...........))).)))	chr7:26236912-26237150(-)$1	1	64	88	21.7479
((((((............))))))	chrM:8019-8242(+)$1	1	53	77	22.6864
((..((..............))..	chr15:90167461-90167710(+)$1	1	199	223	20.5100
(((((.............)))))(	chr16:14042049-14042273(+)$1	1	11	35	22.3272
((((((.............)))))	chr8:145748272-145748496(+)$1	1	181	205	23.1225
.(((((............))))))	chr9:33166851-33167075(-)$1	1	171	195	21.1171
(((((((...........)))).)	chr14:70855193-70855421(-)$1	1	120	144	22.5373
(((.((...........)).)))(	chr16:11940478-11940707(-)$1	1	13	37	19.9796
((((((............))))))	chrX:64748085-64748304(-)$1	1	94	118	22.6864
...(((............)))...	chr6:26031909-26032139(-)$1	1	180	204	21.1143
((((((.............)))))	chr10:75056699-75056921(-)$1	1	180	204	23.0754
((((((............))))))	chrM:7944-8173(+)$1	1	128	152	22.6864
((((((.............)))))	chr13:41766333-41766556(-)$1	1	87	111	23.0754
((((................)).)	chr17:48829451-48829709(+)$1	1	198	222	18.9218
((..(((...........)))..)	chr10:103559073-103559300(-)$1	1	146	170	22.6417
((((((..............))))	chr10:62551654-62551908(+)$1	1	151	175	21.0596
((((((............)))).)	chrM:14957-15211(+)$1	1	16	40	22.9765
((((.(..............).))	chr16:2816186-2816430(+)$1	1	120	144	21.1907
.((((.............))))..	chr18:32920258-32920493(-)$1	1	175	199	22.3645
.((((((...........))))))	chr7:99694837-99695068(-)$1	1	57	81	22.0322
((.((((...........)))).)	chr19:5653289-5653520(+)$1	1	53	77	22.3224
(((((((...........))))))	chr19:40321015-40321247(-)$1	1	128	152	22.4939
((((((..............))))	chr9:95027677-95027926(-)$1	1	16	40	21.6962
((((((................))	chr20:57485740-57485968(+)$1	1	59	83	20.0876
.(((.((...........)).)))	chr19:33870488-33870715(+)$1	1	100	124	20.8345
((((((............))))))	chrX:71493547-71493786(-)$1	1	156	180	22.6864
((((((............)))).)	chr5:138650265-138650504(+)$1	1	164	188	22.9765
((((..............))))..	chrX:47087885-47088127(+)$1	1	84	108	21.0926
((((((..............))))	chr8:48798421-48798654(-)$1	1	170	194	21.4355
((................)))).)	chr1:45981255-45981486(-)$1	1	198	222	19.8113
(((((..............)))))	chr2:190339334-190339562(+)$1	1	3	27	21.3288

#PSSM
d : 0.20	g : 0.15	c : 0.13	f : 0.10	e : 0.10	: : 0.06	! : 0.05	b : 0.03	= : 0.03	i : 0.03	+ : 0.03	[ : 0.01	# : 0.01	% : 0.01	
d : 0.16	e : 0.15	g : 0.15	f : 0.15	c : 0.13	! : 0.05	b : 0.03	= : 0.03	[ : 0.03	+ : 0.03	# : 0.01	% : 0.01	i : 0.01	
e : 0.15	g : 0.15	f : 0.15	c : 0.15	d : 0.13	! : 0.08	[ : 0.05	b : 0.03	# : 0.01	= : 0.01	+ : 0.01	i : 0.01	y : 0.01	
d : 0.22	e : 0.15	g : 0.15	f : 0.15	c : 0.11	! : 0.05	[ : 0.05	b : 0.03	# : 0.01	= : 0.01	i : 0.01	y : 0.01	
d : 0.16	g : 0.15	f : 0.15	c : 0.15	e : 0.13	w : 0.05	b : 0.05	y : 0.03	[ : 0.03	! : 0.01	x : 0.01	= : 0.01	i : 0.01	
d : 0.15	g : 0.15	f : 0.15	c : 0.13	w : 0.10	b : 0.08	e : 0.06	v : 0.05	y : 0.03	x : 0.01	= : 0.01	a : 0.01	i : 0.01	
u : 0.20	w : 0.18	v : 0.15	d : 0.08	g : 0.08	c : 0.08	f : 0.05	t : 0.05	y : 0.05	b : 0.03	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.37	u : 0.22	w : 0.18	v : 0.15	y : 0.05	x : 0.01	
t : 0.32	u : 0.22	w : 0.18	v : 0.15	y : 0.05	e : 0.01	x : 0.01	c : 0.01	b : 0.01	
d : 0.22	f : 0.13	w : 0.13	c : 0.11	v : 0.10	e : 0.08	g : 0.08	b : 0.05	y : 0.03	u : 0.01	x : 0.01	
d : 0.22	c : 0.18	e : 0.13	f : 0.13	g : 0.11	w : 0.08	b : 0.05	y : 0.03	= : 0.01	] : 0.01	
d : 0.22	c : 0.18	f : 0.15	e : 0.13	g : 0.13	b : 0.05	] : 0.03	2 : 0.01	= : 0.01	a : 0.01	y : 0.01	i : 0.01	
d : 0.22	e : 0.15	f : 0.15	g : 0.13	c : 0.10	2 : 0.05	] : 0.05	b : 0.03	3 : 0.01	5 : 0.01	= : 0.01	> : 0.01	y : 0.01	i : 0.01	
] : 0.18	e : 0.15	g : 0.15	f : 0.15	2 : 0.10	c : 0.08	: : 0.03	3 : 0.03	6 : 0.01	5 : 0.01	= : 0.01	> : 0.01	4 : 0.01	i : 0.01	
g : 0.15	f : 0.15	c : 0.11	e : 0.11	d : 0.08	b : 0.06	2 : 0.06	] : 0.03	= : 0.03	3 : 0.03	E : 0.03	: : 0.01	6 : 0.01	5 : 0.01	> : 0.01	4 : 0.01	i : 0.01	

#score	1283.003743984557
#seq	59
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_CDS_m2_run2.txt

#BEAR
[aiiiiiiiii[ddddllldddd]iiiiiiiii]a]	chr4:17813839-17814079(+)$1	240	91	127	13.4215
hhhh"""ccc!!abboooooobb]a22ccc22hhhh	chr15:91474836-91475076(-)$1	240	180	216	14.9703
========$$$$$ddddllldddd22==========	chr3:53269052-53269292(-)$1	240	7	43	13.5979
"""dddd[ccc!!bboooooobb22ccc]dddd444	chr8:61749382-61749622(+)$1	240	187	223	15.9911
bb:===============lll===============	chr16:4475770-4476010(+)$1	240	138	174	14.3696
===========[cccooooooccc]===========	chr11:86662775-86663015(-)$1	240	152	188	19.6753
!bb============rrrrrrrrr============	chr14:74961530-74961770(+)$1	240	174	210	14.2188
========="""cccmmmmccc333===========	chr17:74077712-74077952(-)$1	240	4	40	15.6736
ff!!ccc[ccc!!bboooooobb333cccccc4444	chr6:7566563-7566803(+)$1	240	35	71	17.5851
'eeeee!!ccc!!bboooooobb22ccc]eeeee55	chr10:43292031-43292271(+)$1	240	126	162	14.0075
eeeeddddgggggggooooooggggggg333dddd]	chr11:77812053-77812293(-)$1	240	43	79	14.3209
bb[hhhhhhhh[cccooooooccc22hhhhhhhh22	chr20:57244366-57244606(+)$1	240	3	39	13.7013
:===========[bboooooobb]===========:	chr9:125047357-125047597(+)$1	240	7	43	17.2238
gggggggggggg!!aooooooa22ggggggg]gggg	chr2:32626529-32626769(+)$1	240	165	201	16.0244
[bb!!ccc[ccccccooooooccc22ccc]ccc22b	chr6:43738685-43738925(+)$1	240	4	40	15.9616
ccc[===========oooooo===========]ccc	chr2:234749253-234749493(-)$1	240	57	93	18.2969
bb[eeeeebb"""bboooooobb333bb]eeeee]b	chr19:44514668-44514908(+)$1	240	119	155	15.2895
ddd[a"""a[eeeeeooooooeeeeea]a]dddd]d	chr10:43883155-43883395(-)$1	240	49	85	13.1360
f[dddd[eeeee[bboooooobb]eeeee]ddddff	chr3:183396865-183397105(+)$1	240	92	128	12.8316
fffggggggg[ddddoooooodddd]ggggggg]ff	chr11:60689354-60689594(+)$1	240	35	71	14.7119
ggg"""dddd[cccbboooooobb]ccc333dddd2	chr9:136272039-136272279(-)$1	240	134	170	13.9987
gggg[ffffff[cccoooooocccffffff22gggg	chr6:52381399-52381639(-)$1	240	49	85	14.8852
iiiiii[ccc"""bboooooobb333ccciiiiiii	chr16:11931801-11932041(-)$1	240	150	186	18.9695
bb[a!!ffffff[cccnnnnnccc]ffffff22a]b	chr9:125935914-125936154(-)$1	240	54	90	11.0353
dddd"""ccc[cccbboooooobb]ccc]ccc]ddd	chr16:67914882-67915122(+)$1	240	38	74	14.2872
+==========eeeeellleeeee]==========3	chr14:75472509-75472749(+)$1	240	183	219	13.3544
e:ggggggg!!ddddoooooodddd]gggggggFFF	chr17:33951400-33951685(+)$1	285	190	226	12.9407
#eeeee[ccc!!cccooooooccc22ccc]eeeee4	chr10:79767418-79767658(-)$1	240	21	57	16.8595
eeeeeee!!ccc[bboooooobb333ccc22eeeee	chr17:76802157-76802397(-)$1	240	40	76	15.6073
b[eeeee$$$$$cccooooooccc]eeeee333bb2	chrX:40498224-40498464(-)$1	240	71	107	14.6919
===[aa[ccc!!cccmmmmcccccc]a]a]======	chr17:73887189-73887429(-)$1	240	178	214	13.7531
++ggggggg"""cccooooooccc333ggggggghh	chr2:105883786-105884026(-)$1	240	106	142	17.0123
""iiiiiiiii[cccooooooccciiiiiiiii444	chr3:141906461-141906701(-)$1	240	55	91	18.6396
cc[ggggggg[ccc[annnnna]ccc22ggggggg]	chr1:212241858-212242101(+)$1	243	183	219	12.5242
[ffffff==========mmmm==========22fff	chr10:11997202-11997442(-)$1	240	190	226	12.5642
c"""ffffff"""cccmmmmccc4444ffffffccc	chr6:13364824-13365098(-)$1	274	148	184	11.7657
========"""eeeeellleeeee333=========	chr8:124448640-124448880(+)$1	240	198	234	14.2173
dd!!eeeee####bboooooobb333eeeee333dd	chr2:47132574-47132814(-)$1	240	181	217	16.4704
dd"""bb[gggggggooooooggggggg]bb333dd	chr17:19842942-19843182(-)$1	240	140	176	14.8617
!dddd"""ccc[cccooooooccc]ccc333dddd2	chr8:48962358-48962598(+)$1	240	168	204	16.3602
=====ccc####cccooooooccc4444ccc22===	chrX:49029636-49029876(+)$1	240	155	191	18.0345
cc[iiiiiiiiirrrrrrrrriiiiiiiii22ccc]	chrX:71495939-71496179(-)$1	240	164	200	12.9240
ddd"""ccc####cccmmmmccc4444ccc>>>>>>	chr17:46154256-46154496(-)$1	240	104	140	11.8820
""eeeeeccc[ddddoooooodddd333ccc22eee	chr1:155232906-155233146(-)$1	240	74	110	14.8780
::::===========oooooo===========ccc#	chr20:36685890-36686130(+)$1	240	24	60	13.9264
"""ccc!!gggggggoooooogggggggccc333dd	chr22:50356598-50356838(+)$1	240	130	166	16.2962
$$$ccc[cccbb[aooooooa]bb]ccc]cccdddd	chr10:3824100-3824340(-)$1	240	109	145	13.4953

#otherMatches

#Seq PSSM
AGGGUAAUAGAAUUUGCAGCAAAGUUUGUUACCUCA	chr4:17813839-17814079(+)$1	240	91	127	13.4215
GGAUGCCGCCUUCUGAAGACACAUGUUGGUCAGUUC	chr15:91474836-91475076(-)$1	240	180	216	14.9703
UUUACCCAGAAUGCAGGCUCCUUGGAUGGGUGGGGG	chr3:53269052-53269292(-)$1	240	7	43	13.5979
AGGUAAAUGCACAAGAAAGUCCUGAUGCCUUUAAAA	chr8:61749382-61749622(+)$1	240	187	223	15.9911
GUUGCUGGUGGUUGUGGGGACCCCGCGGCUGCCGGC	chr16:4475770-4476010(+)$1	240	138	174	14.3696
UUGGAAUGGCCAGCUCCAUUUGGUGGGUUAUUCUGA	chr11:86662775-86663015(-)$1	240	152	188	19.6753
GUGAUGACUGGUGACUCUGGGAUUGUCACCAGUUGU	chr14:74961530-74961770(+)$1	240	174	210	14.2188
GCACAGGGAGAUGCUCAGGGGCCAGUCCCUGUGUCU	chr17:74077712-74077952(-)$1	240	4	40	15.6736
UUCAUUCACAGAUACGCAUGAGUCAACUGGAAGUUA	chr6:7566563-7566803(+)$1	240	35	71	17.5851
AGUUGGAAGAAGACAGUGAAAUGGAUUUGCCAGCAU	chr10:43292031-43292271(+)$1	240	126	162	14.0075
UUCCUUCAGAAAAGAAAAACCUCUUUUUAAUUGGAU	chr11:77812053-77812293(-)$1	240	43	79	14.3209
CGUGCAGGCCCUGCCGAGCCGGGCCCGGGCCUGCUC	chr20:57244366-57244606(+)$1	240	3	39	13.7013
accUGAAUcugaauuagauaggacuuagauuugggg	chr9:125047357-125047597(+)$1	240	7	43	17.2238
UGUGAGUUUGUUUUAGUAGUAUUUAAUAGAUGUUAC	chr2:32626529-32626769(+)$1	240	165	201	16.0244
GCUAGCUCGGGCCGGGAGGAGCCGCAGCCggaggag	chr6:43738685-43738925(+)$1	240	4	40	15.9616
GUUGCUCGUGCCAUCACGAGGGAUGGCACGAGGGAC	chr2:234749253-234749493(-)$1	240	57	93	18.2969
CAUGCGUGGUAAGGAAUUCAGUCAGAGCUCAUGUCU	chr19:44514668-44514908(+)$1	240	119	155	15.2895
CCUGACAAGUGUCCAUGAUGCUGGGCCCUGAGGGAG	chr10:43883155-43883395(-)$1	240	49	85	13.1360
CUCUGUUAUGAUCCUGCAACAAGUAUCAUCACAGGG	chr3:183396865-183397105(+)$1	240	92	128	12.8316
GCCUGAAGCUUGUCAUCUUCCUGGCCGGCUUCGUGG	chr11:60689354-60689594(+)$1	240	35	71	14.7119
UGGGAGAGCAUGGCCCGAGACAGGCGCCCCCUGCUG	chr9:136272039-136272279(-)$1	240	134	170	13.9987
CCCAGAGUAUUUCCUUCCCCCAGGGAUGCUGAUGGG	chr6:52381399-52381639(-)$1	240	49	85	14.8852
cuuugccagcaucugagaccccaaaagcugcagagu	chr16:11931801-11932041(-)$1	240	150	186	18.9695
GUGUGGUGUAAUGAGGAUUGGCCUGGUUGCAAAAGG	chr9:125935914-125936154(-)$1	240	54	90	11.0353
GCUAGCAGGAGGGGCUUCAGAUAGAUUCAUCCAUGG	chr16:67914882-67915122(+)$1	240	38	74	14.2872
CAUGAAGAUUAUGUUUCUAAAAUAUUGAUUUUUAUC	chr14:75472509-75472749(+)$1	240	183	219	13.3544
AUCGGGAGGCUCAGAGGUCAGUCUGUUUUCCUGGCU	chr17:33951400-33951685(+)$1	285	190	226	12.9407
AUCAUUCUUCCAGAUGUUACAAUCCAGAACAGUGAG	chr10:79767418-79767658(-)$1	240	21	57	16.8595
GUGGAGGGCGACCGGCAAUGACCUCCGUCCACCUCC	chr17:76802157-76802397(-)$1	240	40	76	15.6073
UCCCUUGCUAUAGGCCUUCAUGCCCCGAGGACUAGC	chrX:40498224-40498464(-)$1	240	71	107	14.6919
UGCGCGCGUCAGACCACUCGGUGACACUGGGCGUCU	chr17:73887189-73887429(-)$1	240	178	214	13.7531
AAUGGUGGUCUUGUGCACACCCACUGUGCCGCCAGC	chr2:105883786-105884026(-)$1	240	106	142	17.0123
GAUUUUGUGCUGUUGUGUUUUCAAGGUGCAAAAGGC	chr3:141906461-141906701(-)$1	240	55	91	18.6396
CCAGGUAAGAUAUUAGUCAUUCAAAUUCUCUUACCA	chr1:212241858-212242101(+)$1	243	183	219	12.5242
UUGUUUCCUUGUAUAUUUUCAGGUAUAUAAGCUGAA	chr10:11997202-11997442(-)$1	240	190	226	12.5642
UGAGCCUUCUGCAGGGGAUGUCCACAGAGAGGGAAG	chr6:13364824-13365098(-)$1	274	148	184	11.7657
GAGGUGAGGACAUUCAAGAUGGAUUUACUUAUUUUC	chr8:124448640-124448880(+)$1	240	198	234	14.2173
ACUAUGCUGAAUUUGCAAAAUCACUGCAGUAGAUGU	chr2:47132574-47132814(-)$1	240	181	217	16.4704
AUGAUUUUAUAUGACAAGUGAGUUAUAUUGAUAGAU	chr17:19842942-19843182(-)$1	240	140	176	14.8617
UCCAGUGGGAUGGUAAGUUAAUAUAGUCAUUUUGGU	chr8:48962358-48962598(+)$1	240	168	204	16.3602
CUUGUUGAGAGAGGAAACCACUCCAAAAUCGUCGCA	chrX:49029636-49029876(+)$1	240	155	191	18.0345
GGUGUGUUUGUAAGUAUCUUAUAUAAAUAUUUCCGU	chrX:71495939-71496179(-)$1	240	164	200	12.9240
UUUACACCAGAAAGCUGGCGGGCACUAUGGGGAAAA	chr17:46154256-46154496(-)$1	240	104	140	11.8820
CGCCCGCCUUCGGGCUGAGCCGCCCAACAAGUUGUG	chr1:155232906-155233146(-)$1	240	74	110	14.8780
UACUUUCUCUUUUGUCUAGCAACAGAAGAGAAGAAA	chr20:36685890-36686130(+)$1	240	24	60	13.9264
ACCCUGAUGACGUGGCCAGCACCACGUCCAGCAGCG	chr22:50356598-50356838(+)$1	240	130	166	16.2962
CGAGCUUUUGUUACAACUUAGAGACCAACAGCCUGA	chr10:3824100-3824340(-)$1	240	109	145	13.4953

#DB
.((((((((((.((((...)))).))))))))).).	chr4:17813839-17814079(+)$1	1	91	127	13.4215
((((...(((..(((......)).)..)))..))))	chr15:91474836-91475076(-)$1	1	180	216	14.9703
((((((((.....((((...))))..))))))))))	chr3:53269052-53269292(-)$1	1	7	43	13.5979
...((((.(((..((......))..))).))))...	chr8:61749382-61749622(+)$1	1	187	223	15.9911
)).(((((((((((((((...)))))))))))))))	chr16:4475770-4476010(+)$1	1	138	174	14.3696
(((((((((((.(((......))).)))))))))))	chr11:86662775-86663015(-)$1	1	152	188	19.6753
.((((((((((((((.........))))))))))))	chr14:74961530-74961770(+)$1	1	174	210	14.2188
(((((((((...(((....)))...)))))))))))	chr17:74077712-74077952(-)$1	1	4	40	15.6736
((..(((.(((..((......))...))))))....	chr6:7566563-7566803(+)$1	1	35	71	17.5851
.(((((..(((..((......))..))).)))))..	chr10:43292031-43292271(+)$1	1	126	162	14.0075
(((((((((((((((......)))))))...)))).	chr11:77812053-77812293(-)$1	1	43	79	14.3209
((.((((((((.(((......)))..))))))))..	chr20:57244366-57244606(+)$1	1	3	39	13.7013
.(((((((((((.((......)).))))))))))).	chr9:125047357-125047597(+)$1	1	7	43	17.2238
((((((((((((..(......)..))))))).))))	chr2:32626529-32626769(+)$1	1	165	201	16.0244
.((..(((.((((((......)))..))).)))..)	chr6:43738685-43738925(+)$1	1	4	40	15.9616
(((.(((((((((((......))))))))))).)))	chr2:234749253-234749493(-)$1	1	57	93	18.2969
((.(((((((...((......))...)).))))).)	chr19:44514668-44514908(+)$1	1	119	155	15.2895
(((.(...(.(((((......)))))).).)))).)	chr10:43883155-43883395(-)$1	1	49	85	13.1360
(.((((.(((((.((......)).))))).))))))	chr3:183396865-183397105(+)$1	1	92	128	12.8316
((((((((((.((((......)))).))))))).))	chr11:60689354-60689594(+)$1	1	35	71	14.7119
(((...((((.(((((......)).)))...)))).	chr9:136272039-136272279(-)$1	1	134	170	13.9987
((((.((((((.(((......)))))))))..))))	chr6:52381399-52381639(-)$1	1	49	85	14.8852
((((((.(((...((......))...))))))))))	chr16:11931801-11932041(-)$1	1	150	186	18.9695
((.(..((((((.(((.....))).))))))..).)	chr9:125935914-125936154(-)$1	1	54	90	11.0353
((((...(((.(((((......)).))).))).)))	chr16:67914882-67915122(+)$1	1	38	74	14.2872
.(((((((((((((((...))))).)))))))))).	chr14:75472509-75472749(+)$1	1	183	219	13.3544
).(((((((..((((......)))).))))))))))	chr17:33951400-33951685(+)$1	1	190	226	12.9407
.(((((.(((..(((......)))..))).))))).	chr10:79767418-79767658(-)$1	1	21	57	16.8595
))(((((..(((.((......))...)))..)))))	chr17:76802157-76802397(-)$1	1	40	76	15.6073
(.(((((.....(((......))).)))))...)).	chrX:40498224-40498464(-)$1	1	71	107	14.6919
(((.((.(((..(((....)))))).).).))))))	chr17:73887189-73887429(-)$1	1	178	214	13.7531
..(((((((...(((......)))...)))))))))	chr2:105883786-105884026(-)$1	1	106	142	17.0123
..(((((((((.(((......))))))))))))...	chr3:141906461-141906701(-)$1	1	55	91	18.6396
((.(((((((.(((.(.....).)))..))))))).	chr1:212241858-212242101(+)$1	1	183	219	12.5242
.((((((((((((((((....))))))))))..)))	chr10:11997202-11997442(-)$1	1	190	226	12.5642
(...((((((...(((....)))....)))))))))	chr6:13364824-13365098(-)$1	1	148	184	11.7657
((((((((...(((((...)))))...)))))))))	chr8:124448640-124448880(+)$1	1	198	234	14.2173
((..(((((....((......))...)))))...))	chr2:47132574-47132814(-)$1	1	181	217	16.4704
((...((.(((((((......))))))).))...))	chr17:19842942-19843182(-)$1	1	140	176	14.8617
.((((...(((.(((......))).)))...)))).	chr8:48962358-48962598(+)$1	1	168	204	16.3602
((((((((....(((......)))....)))..)))	chrX:49029636-49029876(+)$1	1	155	191	18.0345
((.(((((((((.........)))))))))..))).	chrX:71495939-71496179(-)$1	1	164	200	12.9240
(((...(((....(((....)))....)))......	chr17:46154256-46154496(-)$1	1	104	140	11.8820
..((((((((.((((......))))...)))..)))	chr1:155232906-155233146(-)$1	1	74	110	14.8780
....(((((((((((......)))))))))))(((.	chr20:36685890-36686130(+)$1	1	24	60	13.9264
...(((..(((((((......))))))))))...))	chr22:50356598-50356838(+)$1	1	130	166	16.2962
...(((.(((((.(......).)).))).)))))))	chr10:3824100-3824340(-)$1	1	109	145	13.4953

#PSSM
= : 0.12	b : 0.10	d : 0.10	" : 0.08	c : 0.08	[ : 0.06	f : 0.06	e : 0.06	g : 0.06	! : 0.04	: : 0.04	+ : 0.04	h : 0.02	' : 0.02	i : 0.02	# : 0.02	$ : 0.02	
= : 0.17	b : 0.12	d : 0.12	" : 0.10	e : 0.08	f : 0.06	g : 0.06	c : 0.06	[ : 0.04	: : 0.04	a : 0.02	h : 0.02	i : 0.02	+ : 0.02	$ : 0.02	
= : 0.17	e : 0.12	[ : 0.10	g : 0.10	d : 0.10	" : 0.08	i : 0.06	: : 0.04	b : 0.04	! : 0.04	f : 0.04	h : 0.02	c : 0.02	$ : 0.02	
= : 0.19	e : 0.14	g : 0.12	i : 0.08	d : 0.08	" : 0.08	! : 0.06	[ : 0.06	h : 0.04	c : 0.04	a : 0.02	f : 0.02	: : 0.02	
= : 0.23	e : 0.14	" : 0.10	g : 0.10	i : 0.08	d : 0.08	c : 0.06	! : 0.04	a : 0.04	f : 0.04	h : 0.02	[ : 0.02	
= : 0.21	e : 0.14	" : 0.12	c : 0.10	g : 0.10	i : 0.08	d : 0.06	f : 0.06	h : 0.02	! : 0.02	a : 0.02	b : 0.02	
= : 0.21	g : 0.10	e : 0.10	[ : 0.10	" : 0.08	c : 0.08	f : 0.08	i : 0.06	d : 0.06	! : 0.04	h : 0.02	b : 0.02	
= : 0.23	c : 0.21	g : 0.10	i : 0.06	[ : 0.06	! : 0.06	e : 0.06	f : 0.06	d : 0.04	" : 0.04	h : 0.02	$ : 0.02	
c : 0.25	= : 0.19	g : 0.17	i : 0.06	f : 0.06	$ : 0.04	e : 0.04	h : 0.02	[ : 0.02	b : 0.02	a : 0.02	d : 0.02	! : 0.02	" : 0.02	# : 0.02	
c : 0.27	= : 0.17	g : 0.12	i : 0.06	" : 0.06	f : 0.06	# : 0.06	$ : 0.04	h : 0.02	b : 0.02	[ : 0.02	e : 0.02	d : 0.02	! : 0.02	
= : 0.17	c : 0.12	" : 0.12	[ : 0.10	! : 0.08	g : 0.08	i : 0.06	# : 0.06	$ : 0.04	e : 0.04	f : 0.04	h : 0.02	b : 0.02	
[ : 0.12	! : 0.12	= : 0.12	" : 0.10	c : 0.10	g : 0.08	e : 0.08	d : 0.06	# : 0.06	$ : 0.04	f : 0.02	i : 0.02	b : 0.02	
c : 0.31	= : 0.10	[ : 0.10	d : 0.08	! : 0.08	g : 0.06	" : 0.06	e : 0.06	# : 0.04	a : 0.02	$ : 0.02	r : 0.02	
c : 0.38	b : 0.21	d : 0.10	= : 0.10	g : 0.06	e : 0.06	! : 0.02	r : 0.02	a : 0.02	
c : 0.31	b : 0.25	d : 0.10	= : 0.10	g : 0.06	e : 0.06	a : 0.02	[ : 0.02	r : 0.02	o : 0.02	
o : 0.65	c : 0.06	d : 0.04	= : 0.04	r : 0.04	m : 0.04	b : 0.04	e : 0.04	a : 0.02	
o : 0.70	m : 0.08	l : 0.06	= : 0.04	r : 0.04	n : 0.04	d : 0.02	
o : 0.70	m : 0.10	l : 0.08	r : 0.04	n : 0.04	= : 0.02	
o : 0.70	l : 0.10	m : 0.10	r : 0.04	n : 0.04	
o : 0.70	m : 0.06	l : 0.04	r : 0.04	c : 0.04	n : 0.04	e : 0.04	d : 0.02	
o : 0.68	c : 0.08	d : 0.04	r : 0.04	n : 0.04	e : 0.04	l : 0.02	m : 0.02	a : 0.02	
c : 0.31	b : 0.21	d : 0.10	= : 0.08	g : 0.06	e : 0.06	a : 0.04	o : 0.04	r : 0.02	i : 0.02	] : 0.02	
c : 0.29	b : 0.27	d : 0.10	= : 0.08	g : 0.06	e : 0.06	r : 0.02	3 : 0.02	2 : 0.02	] : 0.02	i : 0.02	
c : 0.27	3 : 0.12	] : 0.08	d : 0.08	= : 0.08	2 : 0.06	g : 0.06	e : 0.06	b : 0.06	4 : 0.04	r : 0.02	i : 0.02	
] : 0.17	3 : 0.17	2 : 0.12	= : 0.12	g : 0.08	i : 0.06	d : 0.06	4 : 0.06	e : 0.04	c : 0.04	a : 0.02	f : 0.02	
= : 0.19	3 : 0.17	c : 0.14	2 : 0.10	g : 0.08	i : 0.06	e : 0.06	] : 0.06	4 : 0.06	f : 0.04	
c : 0.23	= : 0.21	g : 0.12	i : 0.06	e : 0.06	3 : 0.06	4 : 0.06	2 : 0.04	a : 0.04	f : 0.04	h : 0.02	b : 0.02	
c : 0.27	= : 0.23	g : 0.14	i : 0.06	e : 0.06	f : 0.06	] : 0.04	h : 0.02	b : 0.02	2 : 0.02	4 : 0.02	3 : 0.02	
= : 0.23	c : 0.21	] : 0.12	g : 0.10	i : 0.06	3 : 0.06	e : 0.06	f : 0.06	a : 0.04	h : 0.02	
= : 0.23	c : 0.17	g : 0.10	] : 0.10	i : 0.08	e : 0.08	3 : 0.06	f : 0.06	d : 0.02	h : 0.02	2 : 0.02	b : 0.02	
= : 0.25	c : 0.14	g : 0.10	2 : 0.08	e : 0.08	3 : 0.08	i : 0.06	d : 0.06	f : 0.04	h : 0.02	b : 0.02	> : 0.02	
= : 0.23	2 : 0.14	d : 0.12	c : 0.08	e : 0.08	g : 0.08	3 : 0.08	i : 0.06	h : 0.02	] : 0.02	f : 0.02	> : 0.02	
= : 0.19	d : 0.14	g : 0.12	e : 0.08	2 : 0.08	3 : 0.08	i : 0.06	c : 0.06	h : 0.04	] : 0.04	4 : 0.02	f : 0.02	> : 0.02	
= : 0.21	d : 0.14	e : 0.10	g : 0.08	c : 0.08	4 : 0.06	3 : 0.06	] : 0.04	h : 0.04	2 : 0.02	i : 0.02	a : 0.02	F : 0.02	b : 0.02	f : 0.02	> : 0.02	
= : 0.21	d : 0.17	c : 0.08	4 : 0.06	g : 0.06	] : 0.06	f : 0.06	e : 0.06	h : 0.04	2 : 0.04	a : 0.02	5 : 0.02	i : 0.02	F : 0.02	b : 0.02	> : 0.02	
= : 0.17	d : 0.12	] : 0.08	4 : 0.08	2 : 0.08	b : 0.06	f : 0.06	h : 0.04	g : 0.04	c : 0.04	e : 0.04	5 : 0.02	: : 0.02	i : 0.02	3 : 0.02	F : 0.02	> : 0.02	# : 0.02	

#score	701.2458010596592
#seq	47
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_UTR_m3_run2.txt

#BEAR
ggggggbbnnnnnbb]gggggg	chr1:94353449-94353672(-)$1	223	5	27	11.5143
$$$eeeeennnnneeeee333c	chr4:76570335-76570560(-)$1	225	56	78	10.6946
!!ffffffnnnnnffffff]cc	chr1:91966634-91966867(+)$1	233	197	219	10.8181
"ccc[cccnnnnncccccc444	chr12:46579904-46580157(-)$1	253	44	66	11.4338
:iiiiiiiiillliiiiiiiii	chr3:24019516-24019738(+)$1	222	197	219	9.8090
========nnnnn=========	chr22:38880894-38881125(-)$1	231	75	97	15.0549
=========lll==========	chr2:74442271-74442500(+)$1	229	74	96	12.2415
========nnnnn=========	chr3:32523918-32524139(-)$1	221	120	142	15.0549
=========lll==========	chrX:10415751-10415986(-)$1	235	160	182	12.2415
ffff[cccnnnnnccc]fffff	chr5:133937819-133938040(-)$1	221	190	212	10.7533
eeeee[bbnnnnnbb333eeee	chr10:96371052-96371284(+)$1	232	172	194	9.5580
========nnnnn=========	chr15:49419249-49419477(-)$1	228	44	66	15.0549
========nnnnn=========	chr8:11184399-11184628(+)$1	229	148	170	15.0549
i$$$$$bbnnnnnbbiiiiiii	chr2:37333708-37333939(-)$1	231	19	41	10.9359
iiiiiiiiimmmmiiiiiiiii	chr12:98943464-98943685(+)$1	221	139	161	10.0025
eeee[cccnnnnnccc]eeeee	chr3:196658191-196658417(+)$1	226	118	140	10.4782
iiiiiiiimmmmiiiiiiiiig	chr14:35550414-35550649(+)$1	235	117	139	9.8207
$$$eeeeennnnneeeee]fff	chr12:111157794-111158035(-)$1	241	184	206	10.0198
iiiiiiiinnnnniiiiiiiii	chr10:96372662-96372884(+)$1	222	24	46	14.2001
========mmmm==========	chr4:90165744-90165967(-)$1	223	159	181	10.9748
!gggggggnnnnngggggggff	chr8:9635357-9635608(+)$1	251	197	219	12.4092
iiiiiiiinnnnniiiiiiiii	chr6:149979231-149979455(-)$1	224	172	194	14.2001
iiiiiiiiimmmmiiiiiiiii	chr19:52516839-52517065(-)$1	226	175	197	10.0025
bb[eeeeennnnneeeee333b	chr22:38686961-38687201(-)$1	240	77	99	10.5249
[ffffffannnnna]ffffffe	chr19:41830428-41830661(+)$1	233	202	224	10.1107
========mmmm==========	chr12:122714664-122714890(-)$1	226	163	185	10.9748
fgggggggnnnnnggggggg00	chr1:28864683-28864909(+)$1	226	68	90	11.3400
$$ffffffnnnnnffffff333	chr13:37596936-37597163(-)$1	227	48	70	10.6284
d[bb[cccnnnnnccc]bb]dd	chr2:73799816-73800039(+)$1	223	64	86	10.1782
=========lll==========	chr1:23411979-23412200(-)$1	221	155	177	12.2415
c"""ddddnnnnndddd333cc	chr17:10584245-10584470(-)$1	225	80	102	10.3739
c[aeeeeennnnneeeee]a]c	chr3:184086198-184086425(+)$1	227	42	64	10.7732
gggg[cccnnnnncccgggggg	chr19:37238462-37238688(-)$1	226	189	211	12.2995
"gggggggnnnnnggggggg66	chr6:105528432-105528662(+)$1	230	88	110	11.6431
eee"""bbnnnnnbbeeeee]d	chr8:1905955-1906179(+)$1	224	127	149	9.6148
hhh!!cccnnnnnccc333hhh	chr6:11582638-11582859(+)$1	221	140	162	10.6346
ii[eeeeennnnneeeee22ii	chr7:141357283-141357512(-)$1	229	65	87	11.1414
b"""ddddnnnnndddd333bb	chr10:96370139-96370365(+)$1	226	3	25	9.8000
========nnnnn=========	chr14:70839171-70839392(-)$1	221	147	169	15.0549
=========lll==========	chr8:124826344-124826574(+)$1	230	8	30	12.2415
==========lll=========	chr1:10368408-10368646(+)$1	238	136	158	12.1926
diiiiiiiiillliiiiiiiii	chr1:212793649-212793871(+)$1	222	172	194	10.6098
ffff[cccnnnnnccc]fffff	chr5:153436395-153436617(+)$1	222	19	41	10.7533
iiiiiiiinnnnniiiiiiiii	chr2:128064849-128065079(-)$1	230	36	58	14.2001
##ffffffnnnnnffffff444	chr17:47371886-47372112(-)$1	226	185	207	10.7401
[gggggggnnnnnggggggg33	chr11:58388178-58388407(+)$1	229	159	181	12.8477
:iiiiiiiiillliiiiiiiii	chr17:1324034-1324263(-)$1	229	172	194	9.8090
ccceeeeennnnneeeee]ccc	chr4:78087125-78087347(+)$1	222	72	94	10.4349
b[ffffffnnnnnffffff]bb	chr5:179203389-179203624(+)$1	235	74	96	10.0849
==========lll=========	chr6:24777113-24777341(+)$1	228	79	101	12.1926
========mmmm==========	chr6:89322114-89322335(-)$1	221	17	39	10.9748

#otherMatches

#Seq PSSM
AGUAAAAUGUGUAAUAUUUAUU	chr1:94353449-94353672(-)$1	223	5	27	11.5143
UUUGAUGUGAAAAGCAUCUUUG	chr4:76570335-76570560(-)$1	225	56	78	10.6946
UCCUGGCGCUUCCUGUCAGUGG	chr1:91966634-91966867(+)$1	233	197	219	10.8181
CAGUUCCACACUUUGGACUUAG	chr12:46579904-46580157(-)$1	253	44	66	11.4338
ACAUGUACAUAAUAUGUAUGUG	chr3:24019516-24019738(+)$1	222	197	219	9.8090
UUAUAUUGACCUGCAGUGUAAA	chr22:38880894-38881125(-)$1	231	75	97	15.0549
UUAAUCAGACUUUCUGAUUAAA	chr2:74442271-74442500(+)$1	229	74	96	12.2415
AGAGUUUUGACUUGGGACUCUA	chr3:32523918-32524139(-)$1	221	120	142	15.0549
CACGUGGCCAAAGGUCAUGUGA	chrX:10415751-10415986(-)$1	235	160	182	12.2415
GCCCCAAAUAGAUUUUAGGGCA	chr5:133937819-133938040(-)$1	221	190	212	10.7533
AGUAUACUACCAAAGAAAGUAC	chr10:96371052-96371284(+)$1	232	172	194	9.5580
GCAAAUAAGUUGGUUAUUUGCU	chr15:49419249-49419477(-)$1	228	44	66	15.0549
UACUAUAACUUUCUUAUGGUAU	chr8:11184399-11184628(+)$1	229	148	170	15.0549
gccaccgcgcccagccUCAUCU	chr2:37333708-37333939(-)$1	231	19	41	10.9359
AGAAAGACUUGUAGGUCUUUCU	chr12:98943464-98943685(+)$1	221	139	161	10.0025
UCUCCAAGUGAGUCUUAGAGAG	chr3:196658191-196658417(+)$1	226	118	140	10.4782
uauuuuaaauuauuaaaGUAUC	chr14:35550414-35550649(+)$1	235	117	139	9.8207
ACCAGUUUAUACAGAACUCACA	chr12:111157794-111158035(-)$1	241	184	206	10.0198
GGUGUACAGGGAUUGUAUAUUU	chr10:96372662-96372884(+)$1	222	24	46	14.2001
GUGACAGCUUCAGCUGUCAUAU	chr4:90165744-90165967(-)$1	223	159	181	10.9748
UUAUUUUUUCAAUGAAGGUGAG	chr8:9635357-9635608(+)$1	251	197	219	12.4092
UGUGGAAAGCUAAUUUUUACAC	chr6:149979231-149979455(-)$1	224	172	194	14.2001
auaaaaauaaaauuguuuuugu	chr19:52516839-52517065(-)$1	226	175	197	10.0025
CCAUGGAGACUGCUUCCAGAAG	chr22:38686961-38687201(-)$1	240	77	99	10.5249
AUGAGAGCUGUCUGUCUCUUAC	chr19:41830428-41830661(+)$1	233	202	224	10.1107
UUAGUUUCUCAUGGAAUUAAUU	chr12:122714664-122714890(-)$1	226	163	185	10.9748
CAUGGCUCACUCAGAGCUAUAU	chr1:28864683-28864909(+)$1	226	68	90	11.3400
uguuuuuguuuuuuAAAAAAUU	chr13:37596936-37597163(-)$1	227	48	70	10.6284
UGGACCGACUUGAUCGUUUGGC	chr2:73799816-73800039(+)$1	223	64	86	10.1782
GGGACCCAGAGGCUGGGUCCCU	chr1:23411979-23412200(-)$1	221	155	177	12.2415
GAAACUGUCUCGCAUAGGAGCC	chr17:10584245-10584470(-)$1	225	80	102	10.3739
CGCCUGUGAAAGACACAGUGGG	chr3:184086198-184086425(+)$1	227	42	64	10.7732
guggcgcuaucucggcucacug	chr19:37238462-37238688(-)$1	226	189	211	12.2995
UUCCUUGCCUUAUGUGAGGAUU	chr6:105528432-105528662(+)$1	230	88	110	11.6431
AUGUUUCAGUCAAUGUAUUAUC	chr8:1905955-1906179(+)$1	224	127	149	9.6148
UUUUUCUUUUUCCAAGUAUGAA	chr6:11582638-11582859(+)$1	221	140	162	10.6346
GCCAGGUGUGAAUUACUUAUGU	chr7:141357283-141357512(-)$1	229	65	87	11.1414
cgucacugcacuccagucuagc	chr10:96370139-96370365(+)$1	226	3	25	9.8000
AGUGAGAAGAGCAUUUUUACUU	chr14:70839171-70839392(-)$1	221	147	169	15.0549
CUGUGUUUGAGGUAAAUGCAGU	chr8:124826344-124826574(+)$1	230	8	30	12.2415
UGCUUGAAGAUUGUCUUUGAGU	chr1:10368408-10368646(+)$1	238	136	158	12.1926
GAGCCUGGGUGGUACCCAGGCU	chr1:212793649-212793871(+)$1	222	172	194	10.6098
UCUACCAAUUACCUUGAUAGAA	chr5:153436395-153436617(+)$1	222	19	41	10.7533
AAGAGGGAAAGUAUUUCUCUUG	chr2:128064849-128065079(-)$1	230	36	58	14.2001
AUUGAGUCAGAUAGGCUCAUUC	chr17:47371886-47372112(-)$1	226	185	207	10.7401
CUUCUCCUUUCAUGGGAGAGAC	chr11:58388178-58388407(+)$1	229	159	181	12.8477
uuuaaaaaaaaauuuuuuuuGG	chr17:1324034-1324263(-)$1	229	172	194	9.8090
UCUAUUUGUUAUUCAGAUCAGA	chr4:78087125-78087347(+)$1	222	72	94	10.4349
UUUGCCACCCCAAGUGGUAUGU	chr5:179203389-179203624(+)$1	235	74	96	10.0849
AAACCAGUUUUAGAAAUUGGUU	chr6:24777113-24777341(+)$1	228	79	101	12.1926
UUUUUUUUAAAAAAAGAAAGUU	chr6:89322114-89322335(-)$1	221	17	39	10.9748

#DB
((((((((.....)).))))))	chr1:94353449-94353672(-)$1	1	5	27	11.5143
...(((((.....)))))...)	chr4:76570335-76570560(-)$1	1	56	78	10.6946
..((((((.....)))))).))	chr1:91966634-91966867(+)$1	1	197	219	10.8181
.(((.(((.....))))))...	chr12:46579904-46580157(-)$1	1	44	66	11.4338
.(((((((((...)))))))))	chr3:24019516-24019738(+)$1	1	197	219	9.8090
((((((((.....)))))))))	chr22:38880894-38881125(-)$1	1	75	97	15.0549
(((((((((...))))))))))	chr2:74442271-74442500(+)$1	1	74	96	12.2415
((((((((.....)))))))))	chr3:32523918-32524139(-)$1	1	120	142	15.0549
(((((((((...))))))))))	chrX:10415751-10415986(-)$1	1	160	182	12.2415
((((.(((.....))).)))))	chr5:133937819-133938040(-)$1	1	190	212	10.7533
(((((.((.....))...))))	chr10:96371052-96371284(+)$1	1	172	194	9.5580
((((((((.....)))))))))	chr15:49419249-49419477(-)$1	1	44	66	15.0549
((((((((.....)))))))))	chr8:11184399-11184628(+)$1	1	148	170	15.0549
(.....((.....)))))))))	chr2:37333708-37333939(-)$1	1	19	41	10.9359
(((((((((....)))))))))	chr12:98943464-98943685(+)$1	1	139	161	10.0025
((((.(((.....))).)))))	chr3:196658191-196658417(+)$1	1	118	140	10.4782
((((((((....)))))))))(	chr14:35550414-35550649(+)$1	1	117	139	9.8207
...(((((.....))))).)))	chr12:111157794-111158035(-)$1	1	184	206	10.0198
((((((((.....)))))))))	chr10:96372662-96372884(+)$1	1	24	46	14.2001
((((((((....))))))))))	chr4:90165744-90165967(-)$1	1	159	181	10.9748
.(((((((.....)))))))))	chr8:9635357-9635608(+)$1	1	197	219	12.4092
((((((((.....)))))))))	chr6:149979231-149979455(-)$1	1	172	194	14.2001
(((((((((....)))))))))	chr19:52516839-52517065(-)$1	1	175	197	10.0025
((.(((((.....)))))...)	chr22:38686961-38687201(-)$1	1	77	99	10.5249
.(((((((.....).)))))))	chr19:41830428-41830661(+)$1	1	202	224	10.1107
((((((((....))))))))))	chr12:122714664-122714890(-)$1	1	163	185	10.9748
((((((((.....)))))))..	chr1:28864683-28864909(+)$1	1	68	90	11.3400
..((((((.....))))))...	chr13:37596936-37597163(-)$1	1	48	70	10.6284
(.((.(((.....))).)).))	chr2:73799816-73800039(+)$1	1	64	86	10.1782
(((((((((...))))))))))	chr1:23411979-23412200(-)$1	1	155	177	12.2415
(...((((.....))))...))	chr17:10584245-10584470(-)$1	1	80	102	10.3739
(.((((((.....))))).).)	chr3:184086198-184086425(+)$1	1	42	64	10.7732
((((.(((.....)))))))))	chr19:37238462-37238688(-)$1	1	189	211	12.2995
.(((((((.....)))))))..	chr6:105528432-105528662(+)$1	1	88	110	11.6431
(((...((.....))))))).)	chr8:1905955-1906179(+)$1	1	127	149	9.6148
(((..(((.....)))...)))	chr6:11582638-11582859(+)$1	1	140	162	10.6346
((.(((((.....)))))..))	chr7:141357283-141357512(-)$1	1	65	87	11.1414
(...((((.....))))...))	chr10:96370139-96370365(+)$1	1	3	25	9.8000
((((((((.....)))))))))	chr14:70839171-70839392(-)$1	1	147	169	15.0549
(((((((((...))))))))))	chr8:124826344-124826574(+)$1	1	8	30	12.2415
((((((((((...)))))))))	chr1:10368408-10368646(+)$1	1	136	158	12.1926
)(((((((((...)))))))))	chr1:212793649-212793871(+)$1	1	172	194	10.6098
((((.(((.....))).)))))	chr5:153436395-153436617(+)$1	1	19	41	10.7533
((((((((.....)))))))))	chr2:128064849-128065079(-)$1	1	36	58	14.2001
..((((((.....))))))...	chr17:47371886-47372112(-)$1	1	185	207	10.7401
.(((((((.....)))))))..	chr11:58388178-58388407(+)$1	1	159	181	12.8477
.(((((((((...)))))))))	chr17:1324034-1324263(-)$1	1	172	194	9.8090
((((((((.....))))).)))	chr4:78087125-78087347(+)$1	1	72	94	10.4349
(.((((((.....)))))).))	chr5:179203389-179203624(+)$1	1	74	96	10.0849
((((((((((...)))))))))	chr6:24777113-24777341(+)$1	1	79	101	12.1926
((((((((....))))))))))	chr6:89322114-89322335(-)$1	1	17	39	10.9748

#PSSM
= : 0.27	i : 0.15	$ : 0.05	f : 0.05	e : 0.05	b : 0.05	c : 0.05	g : 0.03	! : 0.03	" : 0.03	: : 0.03	[ : 0.03	d : 0.03	h : 0.01	# : 0.01	
= : 0.27	i : 0.19	g : 0.11	$ : 0.07	f : 0.05	e : 0.05	[ : 0.05	c : 0.03	" : 0.03	! : 0.01	b : 0.01	h : 0.01	# : 0.01	
= : 0.27	i : 0.17	f : 0.13	g : 0.11	$ : 0.05	e : 0.05	c : 0.03	[ : 0.03	" : 0.03	b : 0.01	a : 0.01	h : 0.01	
= : 0.27	i : 0.17	e : 0.15	f : 0.13	g : 0.11	" : 0.05	c : 0.01	$ : 0.01	b : 0.01	! : 0.01	
= : 0.27	i : 0.17	e : 0.13	[ : 0.11	g : 0.09	f : 0.09	d : 0.03	$ : 0.01	" : 0.01	! : 0.01	
= : 0.27	i : 0.17	c : 0.13	e : 0.11	g : 0.09	f : 0.09	d : 0.03	[ : 0.01	$ : 0.01	" : 0.01	
= : 0.27	i : 0.17	c : 0.13	e : 0.11	f : 0.09	b : 0.07	g : 0.07	d : 0.03	
= : 0.27	i : 0.17	c : 0.13	e : 0.11	b : 0.07	f : 0.07	g : 0.07	d : 0.03	a : 0.01	
n : 0.70	= : 0.11	i : 0.09	m : 0.07	
n : 0.70	m : 0.11	l : 0.07	i : 0.05	= : 0.03	
n : 0.70	l : 0.17	m : 0.11	
n : 0.70	l : 0.17	m : 0.11	
n : 0.70	= : 0.13	l : 0.09	m : 0.03	i : 0.01	
= : 0.27	i : 0.17	c : 0.13	e : 0.11	b : 0.07	f : 0.07	g : 0.07	d : 0.03	a : 0.01	
= : 0.27	i : 0.17	c : 0.13	e : 0.11	b : 0.07	f : 0.07	g : 0.07	d : 0.03	] : 0.01	
= : 0.27	i : 0.19	e : 0.13	c : 0.13	f : 0.09	g : 0.07	d : 0.03	] : 0.01	3 : 0.01	
= : 0.27	i : 0.19	e : 0.13	g : 0.11	f : 0.09	] : 0.07	3 : 0.03	d : 0.03	c : 0.01	
= : 0.27	i : 0.19	e : 0.15	f : 0.13	g : 0.11	3 : 0.07	c : 0.01	b : 0.01	
= : 0.27	i : 0.19	f : 0.13	g : 0.11	3 : 0.09	e : 0.05	] : 0.05	c : 0.01	b : 0.01	2 : 0.01	
= : 0.27	i : 0.19	g : 0.11	3 : 0.09	f : 0.07	] : 0.05	e : 0.05	4 : 0.03	a : 0.01	h : 0.01	2 : 0.01	c : 0.01	
= : 0.27	i : 0.21	f : 0.09	3 : 0.07	c : 0.05	g : 0.03	4 : 0.03	e : 0.03	] : 0.03	b : 0.03	0 : 0.01	d : 0.01	6 : 0.01	h : 0.01	
= : 0.27	i : 0.19	c : 0.09	f : 0.07	g : 0.05	e : 0.05	b : 0.05	4 : 0.03	3 : 0.03	d : 0.03	0 : 0.01	6 : 0.01	h : 0.01	

#score	586.7452724783883
#seq	51
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_CDS_m1_run1.txt

#BEAR
ggggyyyyyyyyyyyyyyyygggggg	chr18:48581134-48581356(+)$1	222	137	163	22.0517
hhhhhhhuuuuuuuuuuuuhhhhhhh	chr17:1579454-1579689(-)$1	235	147	173	21.5722
dd"""bbuuuuuuuuuuuubb4444d	chr18:28602247-28602471(-)$1	224	56	82	23.0078
!!eeeeeuuuuuuuuuuuueeeee33	chr13:45826965-45827185(+)$1	220	179	205	24.3345
b[ddddwwwwwwwwwwwwwwdddd33	chr15:42982409-42982629(+)$1	220	34	60	23.0563
ggggggguuuuuuuuuuuuggggggg	chr11:11373734-11373962(-)$1	228	81	107	24.2563
f[bb[avvvvvvvvvvvvva]bbfff	chr17:26659130-26659359(-)$1	229	80	106	22.8965
cc[cccvvvvvvvvvvvvvccc]ccc	chr2:121746740-121746974(+)$1	234	159	185	24.1771
fffa[bbvvvvvvvvvvvvvbb]a]f	chr17:76455136-76455363(+)$1	227	37	63	23.5450
hhhhh[awwwwwwwwwwwwwwa]hhh	chr5:180670694-180670914(-)$1	220	46	72	21.6644
gggggggvvvvvvvvvvvvvgggggg	chr2:43798792-43799017(-)$1	225	177	203	24.2242
c[eeeeettttttttttteeeee]cc	chr17:37580794-37581019(-)$1	225	21	47	22.0221
ddddddvvvvvvvvvvvvvdddd]dd	chr20:4837582-4837820(-)$1	238	71	97	22.4738
fff[cccvvvvvvvvvvvvvcccfff	chr5:109120406-109120629(+)$1	223	174	200	24.1080
"ffffffuuuuuuuuuuuuffffff3	chr8:38184206-38184429(-)$1	223	105	131	23.6585
eeee[bbuuuuuuuuuuuubb]eeee	chr10:60573553-60573773(-)$1	220	2	28	23.2514
###ddddvvvvvvvvvvvvvddddee	chr17:73897710-73897931(-)$1	221	46	72	23.5652
!!cccyyyyyyyyyyyyyyyyccc22	chr3:50098819-50099042(+)$1	223	77	103	22.3166
:fffffftttttttttttffffffcc	chr19:38126942-38127163(-)$1	221	57	83	20.6930
gggggggtttttttttttggggggg:	chr2:98419092-98419324(-)$1	232	84	110	21.4564
a[eeeeettttttttttteeeee]a3	chr22:20229741-20229964(-)$1	223	74	100	22.1934
[ccccccvvvvvvvvvvvvvccc444	chr16:2813880-2814107(+)$1	227	16	42	24.6445
'ffffffvvvvvvvvvvvvvffffff	chr12:49440414-49440633(-)$1	219	15	41	22.6695
Fffffffuuuuuuuuuuuuffffffe	chr7:4796578-4796799(+)$1	221	67	93	22.8305
ccc[cccuuuuuuuuuuuuccc]ccc	chr17:34937816-34938039(+)$1	223	72	98	24.6930
ffff[bbvvvvvvvvvvvvvbbffff	chr11:63672266-63672493(+)$1	227	27	53	23.2416
eeeeewwwwwwwwwwwwwweeeee::	chr6:13620414-13620637(+)$1	223	79	105	20.0824
ddddcccwwwwwwwwwwwwwwccc]d	chr11:118277572-118277814(+)$1	242	179	205	22.7006
!!cccxxxxxxxxxxxxxxxcccccc	chrM:11559-11780(+)$1	221	100	126	19.5336
[bbyyyyyyyyyyyyyyyybb]ffff	chr17:38421146-38421377(+)$1	231	162	188	20.0183
iiii[ccctttttttttttccc]iii	chr7:33066379-33066601(-)$1	222	34	60	23.6607
ddddcccwwwwwwwwwwwwwwccc]d	chr11:35640752-35640984(+)$1	232	159	185	22.7006
gggg[bbtttttttttttbb]ggggg	chr3:9792662-9792882(-)$1	220	89	115	22.5031
ddddddduuuuuuuuuuuuddddFFF	chr16:30456141-30456370(-)$1	229	73	99	21.8910
"""ddddvvvvvvvvvvvvvdddd]e	chr10:5496332-5496553(+)$1	221	117	143	23.9301
##eeeeewwwwwwwwwwwwwweeeee	chr19:47503641-47503861(+)$1	220	73	99	22.5062
gggg[ccctttttttttttccc]ggg	chr2:33817051-33817281(-)$1	230	195	221	23.6670
g[fffffftttttttttttffffff]	chr16:449582-449826(+)$1	244	110	136	22.0057
:fffffftttttttttttffffffcc	chrX:138867300-138867526(-)$1	226	9	35	20.6930
iiiyyyyyyyyyyyyyyyyiiiiiii	chr7:149561218-149561437(-)$1	219	139	165	21.2366
Bffffffvvvvvvvvvvvvvffffff	chr21:46703281-46703504(-)$1	223	176	202	22.3122
ff"""bbwwwwwwwwwwwwwwbb333	chr12:48367834-48368061(-)$1	227	141	167	22.6006
!!cccwwwwwwwwwwwwwwccc]eee	chr1:225611569-225611801(-)$1	232	7	33	23.3608
!!ddddvvvvvvvvvvvvvdddd333	chr2:47388762-47388984(-)$1	222	147	173	24.0969
iiiiiiiuuuuuuuuuuuuiiiiiii	chrM:7762-7986(-)$1	224	88	114	24.3622
iiii[ccctttttttttttccciiii	chr1:178411904-178412125(+)$1	221	169	195	23.5857
###bbyyyyyyyyyyyyyyyybb333	chr1:156237204-156237435(-)$1	231	189	215	21.4712
iiiiiiiuuuuuuuuuuuuiiiiiii	chr1:233515052-233515279(+)$1	227	52	78	24.3622
!a[dddduuuuuuuuuuuudddda22	chr3:93803059-93803283(+)$1	224	192	218	23.8573
e"""cccuuuuuuuuuuuuccc]eee	chr6:26156667-26156907(+)$1	240	4	30	24.5946
ffff[bbuuuuuuuuuuuubb]ffff	chr16:29818007-29818229(+)$1	222	85	111	23.3005
====cccuuuuuuuuuuuuccc>>>>	chr12:49219395-49219625(+)$1	230	27	53	23.9214
!!eeeeeuuuuuuuuuuuueeeee22	chr8:20073824-20074044(+)$1	220	39	65	23.8917
dddd[ccctttttttttttccc]ddd	chr6:30614178-30614400(+)$1	222	109	135	22.3264
eeeyyyyyyyyyyyyyyyyeeeee33	chrX:53240929-53241148(-)$1	219	14	40	20.8761
e"""cccuuuuuuuuuuuuccc]eee	chr6:26156593-26156821(+)$1	228	78	104	24.5946
GGeeeeevvvvvvvvvvvvveeeee:	chr22:32081401-32081632(-)$1	231	176	202	21.4249
gggg[bbvvvvvvvvvvvvvbb]ggg	chr10:60588485-60588732(-)$1	247	192	218	24.1157
ee[dddduuuuuuuuuuuudddd]ee	chr2:170668144-170668366(+)$1	222	131	157	23.4598
gggg[bbwwwwwwwwwwwwwwbb22g	chr17:7678553-7678772(-)$1	219	114	140	22.5461
hhhhhhwwwwwwwwwwwwwwhhhhhh	chr5:179249865-179250088(+)$1	223	74	100	21.2129
hhh[cccwwwwwwwwwwwwwwccc]h	chr16:69404346-69404569(-)$1	223	188	214	22.7520
"""ddddvvvvvvvvvvvvvdddd33	chr11:62299892-62300131(-)$1	239	172	198	24.2842
ffffcccvvvvvvvvvvvvvccc333	chr12:27066835-27067055(-)$1	220	103	129	24.6666
##cccwwwwwwwwwwwwwwccceeee	chr5:40767535-40767768(-)$1	233	137	163	23.0383
ggggyyyyyyyyyyyyyyyygggggg	chr8:27667737-27667956(-)$1	219	166	192	22.0517
ccc!!ccctttttttttttccc]ccc	chr19:14574576-14574798(+)$1	222	124	150	23.2520
"""dddduuuuuuuuuuuudddd333	chrX:24483551-24483771(+)$1	220	99	125	24.5369
"""dddduuuuuuuuuuuudddd333	chr16:23634274-23634494(-)$1	220	68	94	24.5369
c[ddddwwwwwwwwwwwwwwdddd]c	chr4:57873004-57873239(+)$1	235	185	211	22.9924

#otherMatches

#Seq PSSM
AGAGACAUACAGCACCCCAGCUCUGU	chr18:48581134-48581356(+)$1	222	137	163	22.0517
GUUGCUCAUCUUGGCAUUGGAGCGGC	chr17:1579454-1579689(-)$1	235	147	173	21.5722
CAUACGCGCCUGAAAUACAGCAUUUU	chr18:28602247-28602471(-)$1	224	56	82	23.0078
UCAUUCUUUUCUGUAUCAUAGAGUCU	chr13:45826965-45827185(+)$1	220	179	205	24.3345
GCUGGCAGCAAACAUUCCAGGCCAAU	chr15:42982409-42982629(+)$1	220	34	60	23.0563
CAUUGAAUUAGAUCCACGUUUCAAUG	chr11:11373734-11373962(-)$1	228	81	107	24.2563
GCGGACUUUAUUCUUUCCUGACCCUU	chr17:26659130-26659359(-)$1	229	80	106	22.8965
UGAACAAAAAUAACAUGCCUGUGCAG	chr2:121746740-121746974(+)$1	234	159	185	24.1771
UCGCAGUAGACCUCGUAGAAGCGGAC	chr17:76455136-76455363(+)$1	227	37	63	23.5450
GUGCUAGUUUCUCUAAGCCAUCCAGU	chr5:180670694-180670914(-)$1	220	46	72	21.6644
AUUUCCCAUCAGAAGGCAUAGGGAAG	chr2:43798792-43799017(-)$1	225	177	203	24.2242
UCCCCAGUUUCUCGAUCUUUGGGCAU	chr17:37580794-37581019(-)$1	225	21	47	22.0221
AACAUUAUAAAAAAAUACAGAUGCUU	chr20:4837582-4837820(-)$1	238	71	97	22.4738
AUCACAGGAACUGCAAAAGACUGGGU	chr5:109120406-109120629(+)$1	223	174	200	24.1080
AAUUUCUACACCAAACCAGAGAAAUG	chr8:38184206-38184429(-)$1	223	105	131	23.6585
AGUGUGCAUAAAACACAACGCUCACU	chr10:60573553-60573773(-)$1	220	2	28	23.2514
UUUGUGCCCCGAGUCCCCCUGCACGU	chr17:73897710-73897931(-)$1	221	46	72	23.5652
UCAUCUGACUGCUACAUAUAUGAUUC	chr3:50098819-50099042(+)$1	223	77	103	22.3166
UGGACUUGAAGAACAAGAAAGUCCUC	chr19:38126942-38127163(-)$1	221	57	83	20.6930
UUUGAAGUAAAUACAGACCUUCAAAA	chr2:98419092-98419324(-)$1	232	84	110	21.4564
AGGCUCAACGACAACCCCUGGGUGUG	chr22:20229741-20229964(-)$1	223	74	100	22.1934
CGAGUCCUAUGUUGAAAUCUGGAAUG	chr16:2813880-2814107(+)$1	227	16	42	24.6445
UCUUUUCCACCUCACACCCUGAGAAG	chr12:49440414-49440633(-)$1	219	15	41	22.6695
UCUUUGAACCGUUACUUUAUCAAAGU	chr7:4796578-4796799(+)$1	221	67	93	22.8305
AUAGACGAAAAAAUAAGUGUGUGUGU	chr17:34937816-34938039(+)$1	223	72	98	24.6930
CGCCCACAACAUCAGCAGCAGUGGUG	chr11:63672266-63672493(+)$1	227	27	53	23.2416
AAGGCAACAAGCAGCACAAGCCUUCA	chr6:13620414-13620637(+)$1	223	79	105	20.0824
GAGCCUGAAAAAAAUAGUCAAUAGUG	chr11:118277572-118277814(+)$1	242	179	205	22.7006
CAUUCUCAUCCAAACCCCCUGAAGCU	chrM:11559-11780(+)$1	221	100	126	19.5336
UAGCACCUCCUCCACCCACCUCGGCC	chr17:38421146-38421377(+)$1	231	162	188	20.0183
AAGAAUGAAAACUAAUUAAUUAAUUU	chr7:33066379-33066601(-)$1	222	34	60	23.6607
CACGCUGGCUGCCCAACCUCACGGAC	chr11:35640752-35640984(+)$1	232	159	185	22.7006
UGGAAGUACUUGCGCACGGCCUCCAG	chr3:9792662-9792882(-)$1	220	89	115	22.5031
CCAAACCGUUAGGAACCCAGGUUGCU	chr16:30456141-30456370(-)$1	229	73	99	21.8910
AAAGAGCACCCUGAUGUUCAGCUUCU	chr10:5496332-5496553(+)$1	221	117	143	23.9301
AUCAUUGAACUCUUUAUCCAGCAGUG	chr19:47503641-47503861(+)$1	220	73	99	22.5062
AAACUGACCAUGGUUUUUUGUUUGUU	chr2:33817051-33817281(-)$1	230	195	221	23.6670
GCUGCCCCAGGAACCAUAAGGGGUGA	chr16:449582-449826(+)$1	244	110	136	22.0057
UUGUGCUUUAUUUUUCUCAGUAUAUU	chrX:138867300-138867526(-)$1	226	9	35	20.6930
CAGAACCUCCGCUGCUUCCCUGGAGG	chr7:149561218-149561437(-)$1	219	139	165	21.2366
UGUACUCCCAGGACAAGCACGAGUAC	chr21:46703281-46703504(-)$1	223	176	202	22.3122
AGAGGGCAAUAGCAGGUUCACGUACA	chr12:48367834-48368061(-)$1	227	141	167	22.6006
CAGGUUAAUUAUAGAAAAUGCCAAGU	chr1:225611569-225611801(-)$1	232	7	33	23.3608
AUUCUUCACUUUGAUUUUUAAGAUAA	chr2:47388762-47388984(-)$1	222	147	173	24.0969
CCAUUGGUGGCCAAUUGAUUUGAUGG	chrM:7762-7986(-)$1	224	88	114	24.3622
GUCAACAUCCCCACUGCCAGUGUGAC	chr1:178411904-178412125(+)$1	221	169	195	23.5857
GUUCCUCUUUUCUCUUCCACUGGCUU	chr1:156237204-156237435(-)$1	231	189	215	21.4712
GGGGAGGCCAGCAGCCCACCCUCCCU	chr1:233515052-233515279(+)$1	227	52	78	24.3622
CCUGGAGGGAAAUCAAUAGCUCUGCU	chr3:93803059-93803283(+)$1	224	192	218	23.8573
UCCCGUGAAGAAGAAGGCCCGCAAGU	chr6:26156667-26156907(+)$1	240	4	30	24.5946
UGGGCGGCCUCAUGAACUCCUUCCCG	chr16:29818007-29818229(+)$1	222	85	111	23.3005
AUUCUCCACUCCCACCCCAGGAUCUC	chr12:49219395-49219625(+)$1	230	27	53	23.9214
CGCUUUAAAACUCAUAACCUAAAGAU	chr8:20073824-20074044(+)$1	220	39	65	23.8917
GGAGAAGCCCAUGCACACAGCUCCUC	chr6:30614178-30614400(+)$1	222	109	135	22.3264
ACCUCUUUGCCUCUGUUUUGGUGACA	chrX:53240929-53241148(-)$1	219	14	40	20.8761
UCCCGUGAAGAAGAAGGCCCGCAAGU	chr6:26156593-26156821(+)$1	228	78	104	24.5946
uggguuuuuuuuuuuuuuuuGGACCU	chr22:32081401-32081632(-)$1	231	176	202	21.4249
UCUUCGGUUUUUAUUUAGUUCUAGAG	chr10:60588485-60588732(-)$1	247	192	218	24.1157
CCAAUUUUUUAUUCAUUUUAAAUAGG	chr2:170668144-170668366(+)$1	222	131	157	23.4598
CCACAGGGCCUUCUAAAAAUACUGAG	chr17:7678553-7678772(-)$1	219	114	140	22.5461
GUCUUUUAAACAAUCUAGAUGAGGAC	chr5:179249865-179250088(+)$1	223	74	100	21.2129
GCCUUGGCCCUUCUCCCAUAACCAUG	chr16:69404346-69404569(-)$1	223	188	214	22.7520
GAAGGUCCAGAUGUUCAUAUGACUCU	chr11:62299892-62300131(-)$1	239	172	198	24.2842
CUCUACCUAUUUCCACAGUUGGUACA	chr12:27066835-27067055(-)$1	220	103	129	24.6666
UUAGCCUUUUGAAACAUAUGCUGCAG	chr5:40767535-40767768(-)$1	233	137	163	23.0383
AAUAACUGUUUAUUCCAAAAUAUUUA	chr8:27667737-27667956(-)$1	219	166	192	22.0517
CCGGAGGCUCAUCCCCAAUGCCACGG	chr19:14574576-14574798(+)$1	222	124	150	23.2520
CUCUCCAUCAAACAAUUCCUGGACUU	chrX:24483551-24483771(+)$1	220	99	125	24.5369
GAAAGUGAAAAGCAAGUACUACUGAA	chr16:23634274-23634494(-)$1	220	68	94	24.5369
ACAGGCUCAAUAGGAAACAUGUUUAU	chr4:57873004-57873239(+)$1	235	185	211	22.9924

#DB
((((................))))))	chr18:48581134-48581356(+)$1	1	137	163	22.0517
(((((((............)))))))	chr17:1579454-1579689(-)$1	1	147	173	21.5722
((...((............))....)	chr18:28602247-28602471(-)$1	1	56	82	23.0078
..(((((............)))))..	chr13:45826965-45827185(+)$1	1	179	205	24.3345
(.((((..............))))..	chr15:42982409-42982629(+)$1	1	34	60	23.0563
(((((((............)))))))	chr11:11373734-11373962(-)$1	1	81	107	24.2563
(.((.(.............).)))))	chr17:26659130-26659359(-)$1	1	80	106	22.8965
((.(((.............))).)))	chr2:121746740-121746974(+)$1	1	159	185	24.1771
((((.((.............)).).)	chr17:76455136-76455363(+)$1	1	37	63	23.5450
(((((.(..............).)))	chr5:180670694-180670914(-)$1	1	46	72	21.6644
(((((((.............))))))	chr2:43798792-43799017(-)$1	1	177	203	24.2242
(.(((((...........))))).))	chr17:37580794-37581019(-)$1	1	21	47	22.0221
((((((.............)))).))	chr20:4837582-4837820(-)$1	1	71	97	22.4738
(((.(((.............))))))	chr5:109120406-109120629(+)$1	1	174	200	24.1080
.((((((............)))))).	chr8:38184206-38184429(-)$1	1	105	131	23.6585
((((.((............)).))))	chr10:60573553-60573773(-)$1	1	2	28	23.2514
...((((.............))))))	chr17:73897710-73897931(-)$1	1	46	72	23.5652
..(((................)))..	chr3:50098819-50099042(+)$1	1	77	103	22.3166
.((((((...........))))))((	chr19:38126942-38127163(-)$1	1	57	83	20.6930
(((((((...........))))))).	chr2:98419092-98419324(-)$1	1	84	110	21.4564
(.(((((...........))))).).	chr22:20229741-20229964(-)$1	1	74	100	22.1934
.((((((.............)))...	chr16:2813880-2814107(+)$1	1	16	42	24.6445
.((((((.............))))))	chr12:49440414-49440633(-)$1	1	15	41	22.6695
(((((((............))))))(	chr7:4796578-4796799(+)$1	1	67	93	22.8305
(((.(((............))).)))	chr17:34937816-34938039(+)$1	1	72	98	24.6930
((((.((.............))))))	chr11:63672266-63672493(+)$1	1	27	53	23.2416
(((((..............)))))..	chr6:13620414-13620637(+)$1	1	79	105	20.0824
(((((((..............))).)	chr11:118277572-118277814(+)$1	1	179	205	22.7006
..(((...............))))))	chrM:11559-11780(+)$1	1	100	126	19.5336
.((................)).))))	chr17:38421146-38421377(+)$1	1	162	188	20.0183
((((.(((...........))).)))	chr7:33066379-33066601(-)$1	1	34	60	23.6607
(((((((..............))).)	chr11:35640752-35640984(+)$1	1	159	185	22.7006
((((.((...........)).)))))	chr3:9792662-9792882(-)$1	1	89	115	22.5031
)))((((............)))))))	chr16:30456141-30456370(-)$1	1	73	99	21.8910
...((((.............)))).)	chr10:5496332-5496553(+)$1	1	117	143	23.9301
..(((((..............)))))	chr19:47503641-47503861(+)$1	1	73	99	22.5062
((((.(((...........))).)))	chr2:33817051-33817281(-)$1	1	195	221	23.6670
(.((((((...........)))))).	chr16:449582-449826(+)$1	1	110	136	22.0057
.((((((...........))))))((	chrX:138867300-138867526(-)$1	1	9	35	20.6930
(((................)))))))	chr7:149561218-149561437(-)$1	1	139	165	21.2366
)((((((.............))))))	chr21:46703281-46703504(-)$1	1	176	202	22.3122
((...((..............))...	chr12:48367834-48368061(-)$1	1	141	167	22.6006
..(((..............))).)))	chr1:225611569-225611801(-)$1	1	7	33	23.3608
..((((.............))))...	chr2:47388762-47388984(-)$1	1	147	173	24.0969
(((((((............)))))))	chrM:7762-7986(-)$1	1	88	114	24.3622
((((.(((...........)))))))	chr1:178411904-178412125(+)$1	1	169	195	23.5857
...((................))...	chr1:156237204-156237435(-)$1	1	189	215	21.4712
(((((((............)))))))	chr1:233515052-233515279(+)$1	1	52	78	24.3622
.(.((((............)))))..	chr3:93803059-93803283(+)$1	1	192	218	23.8573
(...(((............))).)))	chr6:26156667-26156907(+)$1	1	4	30	24.5946
((((.((............)).))))	chr16:29818007-29818229(+)$1	1	85	111	23.3005
(((((((............)))....	chr12:49219395-49219625(+)$1	1	27	53	23.9214
..(((((............)))))..	chr8:20073824-20074044(+)$1	1	39	65	23.8917
((((.(((...........))).)))	chr6:30614178-30614400(+)$1	1	109	135	22.3264
(((................)))))..	chrX:53240929-53241148(-)$1	1	14	40	20.8761
(...(((............))).)))	chr6:26156593-26156821(+)$1	1	78	104	24.5946
))(((((.............))))).	chr22:32081401-32081632(-)$1	1	176	202	21.4249
((((.((.............)).)))	chr10:60588485-60588732(-)$1	1	192	218	24.1157
((.((((............)))).))	chr2:170668144-170668366(+)$1	1	131	157	23.4598
((((.((..............))..)	chr17:7678553-7678772(-)$1	1	114	140	22.5461
((((((..............))))))	chr5:179249865-179250088(+)$1	1	74	100	21.2129
(((.(((..............))).)	chr16:69404346-69404569(-)$1	1	188	214	22.7520
...((((.............))))..	chr11:62299892-62300131(-)$1	1	172	198	24.2842
(((((((.............)))...	chr12:27066835-27067055(-)$1	1	103	129	24.6666
..(((..............)))))))	chr5:40767535-40767768(-)$1	1	137	163	23.0383
((((................))))))	chr8:27667737-27667956(-)$1	1	166	192	22.0517
(((..(((...........))).)))	chr19:14574576-14574798(+)$1	1	124	150	23.2520
...((((............))))...	chrX:24483551-24483771(+)$1	1	99	125	24.5369
...((((............))))...	chr16:23634274-23634494(-)$1	1	68	94	24.5369
(.((((..............)))).)	chr4:57873004-57873239(+)$1	1	185	211	22.9924

#PSSM
g : 0.14	! : 0.10	f : 0.10	d : 0.08	e : 0.08	c : 0.07	" : 0.07	i : 0.07	h : 0.05	# : 0.05	: : 0.02	[ : 0.02	b : 0.01	a : 0.01	' : 0.01	F : 0.01	B : 0.01	= : 0.01	G : 0.01	
f : 0.17	g : 0.12	d : 0.08	! : 0.08	[ : 0.08	" : 0.08	i : 0.07	h : 0.05	c : 0.05	e : 0.05	# : 0.05	b : 0.01	a : 0.01	= : 0.01	G : 0.01	
f : 0.17	g : 0.12	e : 0.12	" : 0.11	d : 0.11	c : 0.10	i : 0.07	h : 0.05	[ : 0.04	b : 0.02	# : 0.02	= : 0.01	
d : 0.21	f : 0.14	g : 0.12	e : 0.11	c : 0.08	" : 0.05	i : 0.05	h : 0.04	[ : 0.04	y : 0.04	b : 0.02	a : 0.01	= : 0.01	! : 0.01	
c : 0.21	d : 0.17	[ : 0.17	e : 0.10	f : 0.10	y : 0.07	h : 0.04	g : 0.04	" : 0.02	i : 0.02	b : 0.01	! : 0.01	
c : 0.22	d : 0.17	b : 0.12	y : 0.10	f : 0.10	e : 0.08	g : 0.04	w : 0.04	h : 0.02	i : 0.02	a : 0.01	[ : 0.01	x : 0.01	
c : 0.21	b : 0.12	d : 0.11	y : 0.10	f : 0.10	e : 0.08	w : 0.08	v : 0.05	g : 0.04	i : 0.02	h : 0.01	a : 0.01	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	y : 0.10	t : 0.08	c : 0.07	x : 0.01	f : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	t : 0.17	y : 0.10	x : 0.01	
u : 0.28	v : 0.24	w : 0.18	y : 0.10	t : 0.08	e : 0.02	f : 0.02	g : 0.01	x : 0.01	b : 0.01	
v : 0.18	c : 0.17	w : 0.14	d : 0.10	e : 0.08	b : 0.07	f : 0.07	y : 0.05	i : 0.04	g : 0.02	h : 0.01	a : 0.01	x : 0.01	
c : 0.22	d : 0.17	b : 0.10	e : 0.10	w : 0.10	f : 0.10	g : 0.07	i : 0.04	h : 0.02	] : 0.02	y : 0.02	
c : 0.28	d : 0.17	e : 0.11	b : 0.10	f : 0.10	g : 0.08	] : 0.04	i : 0.04	h : 0.02	4 : 0.01	a : 0.01	
d : 0.17	] : 0.17	e : 0.14	f : 0.14	c : 0.11	g : 0.08	b : 0.05	i : 0.05	h : 0.02	4 : 0.01	> : 0.01	
f : 0.17	e : 0.15	g : 0.11	c : 0.11	d : 0.08	3 : 0.08	i : 0.07	] : 0.05	h : 0.04	4 : 0.02	a : 0.02	F : 0.01	> : 0.01	2 : 0.01	
3 : 0.14	f : 0.14	e : 0.12	g : 0.11	c : 0.10	] : 0.08	i : 0.07	2 : 0.05	h : 0.04	4 : 0.02	d : 0.02	a : 0.01	: : 0.01	F : 0.01	> : 0.01	
3 : 0.17	e : 0.14	g : 0.11	f : 0.11	c : 0.11	d : 0.07	i : 0.07	h : 0.05	2 : 0.04	: : 0.04	4 : 0.01	F : 0.01	] : 0.01	> : 0.01	

#score	1604.1208974275955
#seq	70
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_CDS_m3_run1.txt

#BEAR
cc[ccc[cccbbmmmmbb]ccc]ccc	chr20:34241893-34242114(-)$1	221	165	191	10.5886
d####gggggggmmmmggggggg]dd	chr20:49508961-49509274(-)$1	313	237	263	9.9092
ggggggg[ddddmmmmdddd22gggg	chr12:98927838-98928077(+)$1	239	157	183	11.2344
iiiiiibb[bbmmmmbbbb22iiiii	chr14:56763436-56763669(+)$1	233	120	146	10.3659
iiiiiii!!cccmmmmccc22iiiii	chr13:37581043-37581308(+)$1	265	188	214	14.9448
::==========mmmm==========	chr13:34404753-34404997(+)$1	244	129	155	10.9399
e!!eeeee!!bbmmmmbb22eeeee2	chr2:85850722-85850948(+)$1	226	29	55	11.0461
a[ccc[a!!cccmmmmccc22a]ccc	chrX:70519794-70520030(+)$1	236	118	144	13.7109
b[dddd"""cccmmmmccc333dddd	chr10:105137945-105138184(+)$1	239	66	92	13.3069
ggggg[ccccccmmmmccc22cccgg	chr8:146017276-146017625(-)$1	349	44	70	13.0461
Ieeeee"""cccmmmmccc4444eee	chr19:44679062-44679291(+)$1	229	185	211	12.6499
ggggggg[ddddmmmmdddd22gggg	chr14:24679770-24680010(-)$1	240	111	137	11.2344
========[cccmmmmccc=======	chr13:41705205-41705443(-)$1	238	80	106	14.1423
iiiii####cccmmmmccc22iiiii	chr22:42052863-42053114(+)$1	251	209	235	14.9742
ffffff####bbmmmmbb4444ffff	chr18:669013-669271(+)$1	258	41	67	11.5540
[eeeee!!ddddmmmmddddeeeee]	chr6:17600728-17600956(+)$1	228	155	181	10.2930
eeee$$$$$ccclllccc4444eeee	chrX:71495325-71495566(-)$1	241	211	237	10.1770
bb"""ccc!!bbmmmmbb22ccc444	chr6:146121182-146121427(-)$1	245	17	43	10.8171
=====!!a!!bbmmmmbb22a22===	chr1:226173055-226173291(-)$1	236	50	76	13.3005
::gggggggcccmmmmccc]gggggg	chr2:136615425-136615649(-)$1	224	30	56	10.8164
[eeeee[a[cccmmmmccc333a]ee	chr19:49119047-49119296(-)$1	249	44	70	14.0431
======[a[a[ammmma]a]a]====	chr12:57626108-57626452(+)$1	344	227	253	13.1351
$$$eeeee!!ccclllccc22eeeee	chr2:29001674-29001905(+)$1	231	120	146	9.7919
"bb!!ccc[cccmmmmccc]ccc22b	chr8:146015684-146015954(-)$1	270	40	66	11.2833
iiiiiii!!cccmmmmccciiiiiii	chr20:470380-470611(-)$1	231	8	34	14.0130
e[eeeee!!cccmmmmccc22eeeee	chr5:179135933-179136161(+)$1	228	75	101	13.4266
::==========mmmm==========	chr5:149748266-149748514(+)$1	248	85	111	10.9399
==$$$$$cccooooooccc333====	chr11:33743878-33744107(-)$1	229	11	37	10.1199
!!eeeee!!ccclllccc]eeeeecc	chr6:26197138-26197379(-)$1	241	17	43	9.9191
cc[ccc!!ddddmmmmdddd333ccc	chr17:40717853-40718136(+)$1	283	4	30	11.2069
i[eeeee!!cccmmmmccc22eeeee	chr1:224558884-224559122(+)$1	238	103	129	13.6400
""eeeee!!cccmmmmccc]eeeee4	chr15:35273585-35273831(-)$1	246	90	116	12.7605
hhhhhhh"""bbmmmmbb333hhhhh	chr4:79856215-79856440(-)$1	225	6	32	11.4675
hhhhh"""ddddmmmmdddd333hhh	chr14:55510840-55511104(+)$1	264	152	178	10.5144
iiiiiia[ddddllldddd]a]iiii	chr15:63447761-63447985(-)$1	224	110	136	9.5828
gggggg"""cccmmmmccc333gggg	chr11:62362788-62363027(-)$1	239	10	36	15.1966
ccc[dddd!!bbmmmmbb22dddd]c	chr1:24082358-24082588(+)$1	230	74	100	10.3484
iiiiiii"""bbmmmmbb]iiiiiii	chr15:59934261-59934500(-)$1	239	2	28	13.1271
========[bboooooobb22=====	chr1:26231054-26231280(-)$1	226	18	44	10.9970
ga!!dddd[cccmmmmcccdddd22a	chr12:125397908-125398143(-)$1	235	82	108	10.5160
iiiiiiiiicccmmmmccc]iiiiii	chr1:235652372-235652598(-)$1	226	44	70	13.5607
eeee[gggggggmmmmggggggg22e	chr9:72873918-72874157(+)$1	239	1	27	10.0872
GG==========mmmm==========	chr17:29663590-29663813(+)$1	223	21	47	11.7777
eeeee!!bbcccmmmmccc]bb22ee	chr7:50513332-50513584(-)$1	252	3	29	10.7292
ffffff####bbmmmmbb4444ffff	chr5:10258131-10258381(+)$1	250	112	138	11.5540
[===========lll===========	chr22:42046729-42046980(+)$1	251	210	236	11.2287
eeeeccc"""bbmmmmbb333ccc]e	chr6:87969959-87970198(+)$1	239	91	117	12.8180
[eeeee"""cccmmmmccc333eeee	chr17:61908654-61908886(+)$1	232	33	59	14.5872
[eeeee!!a!!ammmma22a22eeee	chr1:25549683-25549917(-)$1	234	36	62	11.6016
ggggggg!!bboooooobb]gggggg	chr11:64888099-64888351(-)$1	252	64	90	9.8037
"dddd####cccmmmmcccdddd444	chr18:77733702-77733936(-)$1	234	82	108	11.4757
d[ccc####cccmmmmccc333ccc]	chr2:10584525-10584757(-)$1	232	15	41	14.1828
:ggggggg[cccmmmmccc]gggggg	chr18:55278773-55279033(-)$1	260	222	248	12.2716
"a[dddd!!cccmmmmccc22dddd]	chr8:30541527-30541758(-)$1	231	97	123	12.7049
ggggg[bb[cccmmmmccc333bbgg	chr20:60768505-60768735(+)$1	230	59	85	13.1237

#otherMatches

#Seq PSSM
UUACUUGAAAGGGCUACCAUUUGAAG	chr20:34241893-34242114(-)$1	221	165	191	10.5886
ACCCAGCUUCUUUGAAGAGAAGCCUG	chr20:49508961-49509274(-)$1	313	237	263	9.9092
GGCUGAAGGAUUGCAAAAUUAAUUUA	chr12:98927838-98928077(+)$1	239	157	183	11.2344
UUGUGGCCACGUGCACGGGUACCACA	chr14:56763436-56763669(+)$1	233	120	146	10.3659
AAUAUUCCCACUCAUGGGUUAGAAUG	chr13:37581043-37581308(+)$1	265	188	214	14.9448
AAGAAGGAAGGUCUGAAUCUUCCUUC	chr13:34404753-34404997(+)$1	244	129	155	10.9399
UUCACCCUUCCCUACAGGCCGGGGUU	chr2:85850722-85850948(+)$1	226	29	55	11.0461
GUCGCCGAUACUAAUAAGUUGCAGUG	chrX:70519794-70520030(+)$1	236	118	144	13.7109
GUUAUUACCAGGAUGACCUACGAGUA	chr10:105137945-105138184(+)$1	239	66	92	13.3069
CGGGCUGGCGGGGGUACCCGGGCCGC	chr8:146017276-146017625(-)$1	349	44	70	13.0461
GACUCAUAUAUGcauacauuccuuga	chr19:44679062-44679291(+)$1	229	185	211	12.6499
CAUUUCUCGGCCUAUGGGCUUUGGAG	chr14:24679770-24680010(-)$1	240	111	137	11.2344
GAUGUGGCAUAUCUCAAUGGCUAUAU	chr13:41705205-41705443(-)$1	238	80	106	14.1423
AGUUGAAAAUCUUAUUAGAAACAGCU	chr22:42052863-42053114(+)$1	251	209	235	14.9742
UUUUGACAAUUCUACAGAUUAUUCAG	chr18:669013-669271(+)$1	258	41	67	11.5540
GGCUCCGGUGCAGAGCUGCAGGAGCA	chr6:17600728-17600956(+)$1	228	155	181	10.2930
GCAGCCCUAUGGUAUCCAAAUACUGU	chrX:71495325-71495566(-)$1	241	211	237	10.1770
UGAAUGGAAAUUUGCUGACAUCCUAA	chr6:146121182-146121427(-)$1	245	17	43	10.8171
UUAUUUUUUUCCCUCAGGUUAUUGAU	chr1:226173055-226173291(-)$1	236	50	76	13.3005
ccagcuUGAAAGACAGCUUCUUAGGC	chr2:136615425-136615649(-)$1	224	30	56	10.8164
GCUGGGCGCCAGAUCCCUGUCUCACC	chr19:49119047-49119296(-)$1	249	44	70	14.0431
UUGACUACGCCCGCAUGAGAGAGGUU	chr12:57626108-57626452(+)$1	344	227	253	13.1351
CCAUUUGUUUGCUAUUGGCUUAUAAA	chr2:29001674-29001905(+)$1	231	120	146	9.7919
GGGGAGGUGGGGGUGCUCUGACCGAC	chr8:146015684-146015954(-)$1	270	40	66	11.2833
uuuaaaaauuaauuuuuuauuuuGAA	chr20:470380-470611(-)$1	231	8	34	14.0130
AUGUGGUGGUGCCUAUGUGAAACUGC	chr5:179135933-179136161(+)$1	228	75	101	13.4266
UUCUUUCUGGGAAGUCUCCCAGGAAG	chr5:149748266-149748514(+)$1	248	85	111	10.9399
CCUUCUUGGCCUUCCAGCCCUUGGUU	chr11:33743878-33744107(-)$1	229	11	37	10.1199
CCACCGUUACCGGCCCGGCACGGUGG	chr6:26197138-26197379(-)$1	241	17	43	9.9191
GGAGUCUCCAGUGGGUACUGCCUGAC	chr17:40717853-40718136(+)$1	283	4	30	11.2069
CAUUAUGGUGCCGAGUGGUAACAUGG	chr1:224558884-224559122(+)$1	238	103	129	13.6400
AAAGUUUCCGAUCUCCAUCUAAACUG	chr15:35273585-35273831(-)$1	246	90	116	12.7605
GUUUAUUUUAUCUAAUGAGACAGUAA	chr4:79856215-79856440(-)$1	225	6	32	11.4675
CCUUCUUCUAUGAAAUUAUAUCUGAA	chr14:55510840-55511104(+)$1	264	152	178	10.5144
AGGUUGUUCAACAGUGUUGUGCCAGC	chr15:63447761-63447985(-)$1	224	110	136	9.5828
GGGAGCCUCAGUGCUGAUUUCUGCUC	chr11:62362788-62363027(-)$1	239	10	36	15.1966
UGCGGCUUCAGGACGCCCGAGAGCAG	chr1:24082358-24082588(+)$1	230	74	100	10.3484
AACGUUUCACGGUAUUUCUAAAUGUU	chr15:59934261-59934500(-)$1	239	2	28	13.1271
AAGUGAUUGCAUGUUUUUGAAAAUCA	chr1:26231054-26231280(-)$1	226	18	44	10.9970
GCAAGACCAUCACCCUUGAGGUCGAG	chr12:125397908-125398143(-)$1	235	82	108	10.5160
AUAGGUGCUCAUGGCUGUGAAGUGCC	chr1:235652372-235652598(-)$1	226	44	70	13.5607
GUGGAUGGGCGCUUGGGCGCCUGGGC	chr9:72873918-72874157(+)$1	239	1	27	10.0872
AUGuuuuuuuuuuuaaaaaaaaaaau	chr17:29663590-29663813(+)$1	223	21	47	11.7777
UCCUUAACUUCUAAAUGGGUAGGUGA	chr7:50513332-50513584(-)$1	252	3	29	10.7292
GAUGGCUGAGAUUGCUGUGAAUGCCG	chr5:10258131-10258381(+)$1	250	112	138	11.5540
AGUUUACGGAGCAGCGCUUUGUAAAU	chr22:42046729-42046980(+)$1	251	210	236	11.2287
UUCAUCUAGAGGCAGACCACGGGAUU	chr6:87969959-87970198(+)$1	239	91	117	12.8180
UUAUCAUGGCUACUAAUAGGAUUGAU	chr17:61908654-61908886(+)$1	232	33	59	14.5872
AUGAUGAUGCAGAUAUCGACUACAUU	chr1:25549683-25549917(-)$1	234	36	62	11.6016
CUUCUCCAGGUGGCCAAACAGGAGAA	chr11:64888099-64888351(-)$1	252	64	90	9.8037
ACAAGCACAUCAUGAUUGACUUGGGG	chr18:77733702-77733936(-)$1	234	82	108	11.4757
UGGGAGACAUUCUAAAGAAACAUCUG	chr2:10584525-10584757(-)$1	232	15	41	14.1828
UUGUUUUGUAUACAUUUAUUUAAAAC	chr18:55278773-55279033(-)$1	260	222	248	12.2716
ACGUCAAAGGCAUCUAUGCAGUUGGG	chr8:30541527-30541758(-)$1	231	97	123	12.7049
AGCCCAGCCGGCUACUGCCACAGCGG	chr20:60768505-60768735(+)$1	230	59	85	13.1237

#DB
((.(((.(((((....)).))).)))	chr20:34241893-34242114(-)$1	1	165	191	10.5886
(....(((((((....))))))).))	chr20:49508961-49509274(-)$1	1	237	263	9.9092
(((((((.((((....))))..))))	chr12:98927838-98928077(+)$1	1	157	183	11.2344
((((((((.((....))))..)))))	chr14:56763436-56763669(+)$1	1	120	146	10.3659
(((((((..(((....)))..)))))	chr13:37581043-37581308(+)$1	1	188	214	14.9448
..((((((((((....))))))))))	chr13:34404753-34404997(+)$1	1	129	155	10.9399
(..(((((..((....))..))))).	chr2:85850722-85850948(+)$1	1	29	55	11.0461
(.(((.(..(((....)))..).)))	chrX:70519794-70520030(+)$1	1	118	144	13.7109
(.((((...(((....)))...))))	chr10:105137945-105138184(+)$1	1	66	92	13.3069
(((((.((((((....)))..)))))	chr8:146017276-146017625(-)$1	1	44	70	13.0461
)(((((...(((....)))....)))	chr19:44679062-44679291(+)$1	1	185	211	12.6499
(((((((.((((....))))..))))	chr14:24679770-24680010(-)$1	1	111	137	11.2344
((((((((.(((....))))))))))	chr13:41705205-41705443(-)$1	1	80	106	14.1423
(((((....(((....)))..)))))	chr22:42052863-42053114(+)$1	1	209	235	14.9742
((((((....((....))....))))	chr18:669013-669271(+)$1	1	41	67	11.5540
.(((((..((((....))))))))).	chr6:17600728-17600956(+)$1	1	155	181	10.2930
((((.....(((...)))....))))	chrX:71495325-71495566(-)$1	1	211	237	10.1770
((...(((..((....))..)))...	chr6:146121182-146121427(-)$1	1	17	43	10.8171
(((((..(..((....))..)..)))	chr1:226173055-226173291(-)$1	1	50	76	13.3005
..((((((((((....))).))))))	chr2:136615425-136615649(-)$1	1	30	56	10.8164
.(((((.(.(((....)))...).))	chr19:49119047-49119296(-)$1	1	44	70	14.0431
((((((.(.(.(....).).).))))	chr12:57626108-57626452(+)$1	1	227	253	13.1351
...(((((..(((...)))..)))))	chr2:29001674-29001905(+)$1	1	120	146	9.7919
.((..(((.(((....))).)))..)	chr8:146015684-146015954(-)$1	1	40	66	11.2833
(((((((..(((....))))))))))	chr20:470380-470611(-)$1	1	8	34	14.0130
(.(((((..(((....)))..)))))	chr5:179135933-179136161(+)$1	1	75	101	13.4266
..((((((((((....))))))))))	chr5:149748266-149748514(+)$1	1	85	111	10.9399
((.....(((......)))...))))	chr11:33743878-33744107(-)$1	1	11	37	10.1199
..(((((..(((...))).)))))))	chr6:26197138-26197379(-)$1	1	17	43	9.9191
((.(((..((((....))))...)))	chr17:40717853-40718136(+)$1	1	4	30	11.2069
(.(((((..(((....)))..)))))	chr1:224558884-224559122(+)$1	1	103	129	13.6400
..(((((..(((....))).))))).	chr15:35273585-35273831(-)$1	1	90	116	12.7605
(((((((...((....))...)))))	chr4:79856215-79856440(-)$1	1	6	32	11.4675
(((((...((((....))))...)))	chr14:55510840-55511104(+)$1	1	152	178	10.5144
(((((((.((((...)))).).))))	chr15:63447761-63447985(-)$1	1	110	136	9.5828
((((((...(((....)))...))))	chr11:62362788-62363027(-)$1	1	10	36	15.1966
(((.((((..((....))..)))).)	chr1:24082358-24082588(+)$1	1	74	100	10.3484
(((((((...((....)).)))))))	chr15:59934261-59934500(-)$1	1	2	28	13.1271
((((((((.((......))..)))))	chr1:26231054-26231280(-)$1	1	18	44	10.9970
((..((((.(((....)))))))..)	chr12:125397908-125398143(-)$1	1	82	108	10.5160
((((((((((((....))).))))))	chr1:235652372-235652598(-)$1	1	44	70	13.5607
((((.(((((((....)))))))..)	chr9:72873918-72874157(+)$1	1	1	27	10.0872
((((((((((((....))))))))))	chr17:29663590-29663813(+)$1	1	21	47	11.7777
(((((..(((((....))).))..))	chr7:50513332-50513584(-)$1	1	3	29	10.7292
((((((....((....))....))))	chr5:10258131-10258381(+)$1	1	112	138	11.5540
.(((((((((((...)))))))))))	chr22:42046729-42046980(+)$1	1	210	236	11.2287
(((((((...((....))...))).)	chr6:87969959-87970198(+)$1	1	91	117	12.8180
.(((((...(((....)))...))))	chr17:61908654-61908886(+)$1	1	33	59	14.5872
.(((((..(..(....)..)..))))	chr1:25549683-25549917(-)$1	1	36	62	11.6016
(((((((..((......)).))))))	chr11:64888099-64888351(-)$1	1	64	90	9.8037
.((((....(((....)))))))...	chr18:77733702-77733936(-)$1	1	82	108	11.4757
(.(((....(((....)))...))).	chr2:10584525-10584757(-)$1	1	15	41	14.1828
.(((((((.(((....))).))))))	chr18:55278773-55279033(-)$1	1	222	248	12.2716
.(.((((..(((....)))..)))).	chr8:30541527-30541758(-)$1	1	97	123	12.7049
(((((.((.(((....)))...))))	chr20:60768505-60768735(+)$1	1	59	85	13.1237

#PSSM
i : 0.14	g : 0.12	e : 0.10	= : 0.09	[ : 0.09	: : 0.07	" : 0.07	c : 0.05	d : 0.03	b : 0.03	f : 0.03	h : 0.03	a : 0.01	I : 0.01	$ : 0.01	! : 0.01	G : 0.01	
e : 0.16	g : 0.12	i : 0.12	= : 0.10	[ : 0.09	c : 0.05	: : 0.05	! : 0.03	f : 0.03	b : 0.03	h : 0.03	a : 0.03	# : 0.01	$ : 0.01	" : 0.01	G : 0.01	d : 0.01	
e : 0.23	g : 0.14	= : 0.14	i : 0.12	[ : 0.05	c : 0.05	! : 0.03	d : 0.03	f : 0.03	$ : 0.03	h : 0.03	# : 0.01	" : 0.01	b : 0.01	
e : 0.27	g : 0.14	= : 0.14	i : 0.12	c : 0.07	d : 0.05	f : 0.03	! : 0.03	h : 0.03	# : 0.01	" : 0.01	$ : 0.01	[ : 0.01	
e : 0.21	g : 0.14	= : 0.14	i : 0.12	c : 0.09	d : 0.09	f : 0.03	$ : 0.03	h : 0.03	# : 0.01	" : 0.01	! : 0.01	[ : 0.01	
e : 0.20	g : 0.14	= : 0.12	i : 0.10	c : 0.09	d : 0.07	[ : 0.05	# : 0.05	f : 0.03	$ : 0.03	! : 0.03	h : 0.01	" : 0.01	
g : 0.12	= : 0.10	e : 0.10	" : 0.09	# : 0.09	! : 0.09	i : 0.07	c : 0.07	[ : 0.05	d : 0.05	b : 0.03	a : 0.03	$ : 0.03	h : 0.01	
! : 0.21	" : 0.14	= : 0.10	c : 0.09	# : 0.09	g : 0.07	[ : 0.05	b : 0.05	a : 0.05	e : 0.03	d : 0.03	$ : 0.01	i : 0.01	
! : 0.25	[ : 0.16	" : 0.12	d : 0.10	# : 0.09	= : 0.07	c : 0.05	g : 0.05	$ : 0.01	i : 0.01	b : 0.01	a : 0.01	
c : 0.50	d : 0.10	! : 0.10	= : 0.07	b : 0.05	" : 0.05	g : 0.03	# : 0.03	a : 0.01	
c : 0.49	b : 0.23	d : 0.10	= : 0.07	g : 0.03	[ : 0.01	o : 0.01	! : 0.01	
c : 0.49	b : 0.18	d : 0.10	= : 0.07	o : 0.05	g : 0.03	a : 0.03	m : 0.01	
m : 0.85	l : 0.07	o : 0.05	c : 0.01	
m : 0.85	l : 0.09	o : 0.05	
m : 0.85	l : 0.09	o : 0.05	
m : 0.83	o : 0.05	c : 0.03	b : 0.01	l : 0.01	d : 0.01	= : 0.01	
c : 0.50	b : 0.20	d : 0.10	= : 0.07	g : 0.03	a : 0.03	o : 0.03	
c : 0.50	b : 0.23	d : 0.10	= : 0.07	g : 0.03	] : 0.01	2 : 0.01	
c : 0.47	d : 0.10	2 : 0.09	= : 0.07	] : 0.05	b : 0.05	4 : 0.05	g : 0.03	3 : 0.03	a : 0.01	
2 : 0.25	3 : 0.16	] : 0.16	d : 0.12	= : 0.09	4 : 0.07	g : 0.03	i : 0.03	c : 0.01	e : 0.01	a : 0.01	
2 : 0.23	3 : 0.20	g : 0.09	= : 0.09	e : 0.07	4 : 0.07	c : 0.05	a : 0.05	i : 0.05	d : 0.05	b : 0.01	
3 : 0.16	e : 0.12	i : 0.10	= : 0.10	c : 0.09	g : 0.09	2 : 0.07	4 : 0.07	d : 0.07	] : 0.03	a : 0.01	h : 0.01	b : 0.01	
e : 0.18	g : 0.14	= : 0.14	i : 0.12	d : 0.09	c : 0.09	] : 0.03	f : 0.03	2 : 0.03	3 : 0.03	4 : 0.01	a : 0.01	h : 0.01	b : 0.01	
e : 0.20	= : 0.16	i : 0.12	c : 0.10	g : 0.10	2 : 0.07	d : 0.05	] : 0.03	f : 0.03	4 : 0.03	h : 0.03	b : 0.01	
e : 0.21	= : 0.16	g : 0.14	i : 0.12	c : 0.09	d : 0.05	2 : 0.05	f : 0.03	4 : 0.03	h : 0.03	] : 0.03	
e : 0.20	= : 0.16	g : 0.14	i : 0.12	c : 0.09	] : 0.05	4 : 0.05	d : 0.03	f : 0.03	h : 0.03	2 : 0.01	b : 0.01	a : 0.01	

#score	656.5900388580238
#seq	55
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_CDS_m1_run2.txt

#BEAR
dddffffff!!ddddnnnnndddd22ffffff22	chr12:49093473-49093717(-)$1	244	206	240	11.7197
gg:ffffff"""cccnnnnnccc333ffffffEE	chr6:43480451-43480679(-)$1	228	161	195	10.9007
iccc[ffffff[cccooooooccc]ffffffccc	chr17:80014102-80014323(+)$1	221	69	103	11.9004
:::eeeee[a[cccooooooccc333a]eeeeeh	chr16:29872421-29872648(-)$1	227	60	94	9.5316
dd[ccc!!bb!!cccmmmmccc22bb22cccddd	chr5:37314202-37314437(-)$1	235	164	198	10.2849
dd[ccc!!bb!!cccooooooccc]bb22cccdd	chr5:175816253-175816492(+)$1	239	161	195	12.5343
dddd!!bbccc!!bbnnnnnbb333ccc]bb22d	chr17:34171004-34171238(+)$1	234	64	98	12.8201
dddd[cccccc[bbnnnnnbbccc22cccddddh	chr19:13059434-13059676(+)$1	242	79	113	11.1711
d####a[ccc!!cccooooooccc333ccca333	chr22:39262644-39262868(-)$1	224	61	95	14.9713
gggggccc!!bbcccnnnnnccc]bbccc]gggg	chr9:99180021-99180249(-)$1	228	152	186	13.2783
ccc"""iiiiiiiiinnnnniiiiiiiiiccc]d	chr20:25397673-25397893(+)$1	220	88	122	13.9123
eeee"""ccc!!ddddoooooodddd]ccc333e	chrX:47001642-47001893(-)$1	251	104	138	11.4894
lffffffeeeeecccnnnnnccc22eeeee:iii	chr10:62547860-62548102(+)$1	242	85	119	11.2801
##iiiiiiiii"""annnnna333iiiiiiiii5	chr2:70314908-70315136(+)$1	228	15	49	13.4852
g[bb"""ccc!!cccnnnnnccc22cccbb]ggg	chr6:27100202-27100428(-)$1	226	177	211	15.1632
======!!bb!!bboooooobb333bb22=====	chr1:33241512-33241761(-)$1	249	13	47	12.4530
ccc[ccc[gggggggnnnnnggggggg]ccc]cc	chr19:13246224-13246487(+)$1	263	130	164	13.2021
ggccc####bb[bbnnnnnbb]bb333ccc]ggg	chr19:46190634-46190997(-)$1	363	156	190	11.7161
ee!!ccc!!bb!!bbnnnnnbb22bb]ccc4444	chr6:136599025-136599249(-)$1	224	58	92	12.6929
eeee[bb!!a[ddddnnnnndddda]bb]eeeee	chr16:2814288-2814566(+)$1	278	77	111	11.6340
dddd[a[cccddddccclllccc]dddd22ccc]	chr20:2443640-2443914(-)$1	274	73	107	9.7990
!bb####bb!!ddddoooooodddd333bbbb22	chr16:2049631-2049858(-)$1	227	92	126	10.6781
hhhh===========lll===========bb[dd	chr7:23338869-23339090(+)$1	221	106	140	10.3370
e####ccc[ccccccooooooccc]cccccc333	chr19:19033424-19033664(+)$1	240	102	136	13.5596
d!!ggggggg[eeeeellleeeee]ggggggg22	chr2:176043801-176044038(-)$1	237	159	193	9.8685
eee####ccc!!cccbboooooobb]ccc22ccc	chr9:106875514-106875738(+)$1	224	170	204	9.5458
eeee[eeeee!!cccmmmmccc4444eeeee22e	chr17:61890598-61890827(+)$1	229	30	64	10.4469
fffbb[ccc!!ddddoooooodddd22ccc]bb3	chr1:229625601-229625827(-)$1	226	142	176	10.6443
ffff!!cccffffffnnnnnffffff22ccc22f	chr5:98128892-98129128(+)$1	236	96	130	11.2707
ebb[ccc[ccc[cccnnnnnccc]ccc]ccc22b	chr10:75542053-75542279(+)$1	226	119	153	14.0541
[eeeee[ccc"""cccmmmmccc333ccceeeee	chr16:28845588-28845815(+)$1	227	176	210	11.4885
!!cccccc[bb[cccnnnnnccc22bb]ccc]cc	chr12:131357026-131357269(+)$1	243	111	145	14.5748
ccc[a[dddd[ddddnnnnndddddddd]a]ccc	chr1:226549570-226549795(-)$1	225	185	219	11.7633
:iiiiiiiii!!cccnnnnnccc4444iiiiiii	chr14:39645216-39645451(+)$1	235	191	225	14.7582
a[============[bblllbb]===========	chr14:96010230-96010481(+)$1	251	106	140	10.9901
=!!eeeee!!a[cccmmmmccc]a]eeeee]===	chr11:124501137-124501368(+)$1	231	92	126	10.6005
$$dddd!!cccddddnnnnndddd]cccdddd33	chr16:47117358-47117603(-)$1	245	76	110	12.2509
ccccc####eeeeeooooooeeeee4444ccc]c	chr10:12240631-12240865(+)$1	234	88	122	10.9025
c[ccc[ddddbb[bbnnnnnbbbb22dddd]ccc	chr5:137089468-137089703(-)$1	235	51	85	10.8387
eeee!!a[bb!!ccclllccc]bb]a22eeeeec	chr20:49509815-49510037(-)$1	222	68	102	10.8211
hh[ccc[ccc"""ccclllccccccccchhhhhh	chr17:55927231-55927477(-)$1	246	164	198	10.9745
dddd"""ccc!!addddllldddd]a22cccddd	chr19:39868051-39868296(+)$1	245	53	87	10.9046
[ccc[iiiiiiiii!!annnnna22iiiiiiiii	chr16:28502734-28502955(-)$1	221	122	156	11.3820
ffff[dddd[a[cccooooooccc]a333dddd2	chr10:28970242-28970467(+)$1	225	5	39	12.1599
ffffffccc[a[cccnnnnnccc]a]ccc22fff	chr17:71281677-71281901(-)$1	224	116	150	13.3325
gccc!!eeeee[cccnnnnnccc]eeeee]ccc3	chr14:104381360-104381596(-)$1	236	116	150	13.9386
bb[bb"""bb[ddddnnnnndddd]bbbb]bb33	chr8:94746305-94746527(-)$1	222	96	130	11.2731
eeeeeaccc[eeeeennnnneeeee]ccc]a]ee	chr16:56487140-56487374(+)$1	234	129	163	11.4931
ee"""ggggggga[annnnna]a]ggggggg]ee	chr2:150435975-150436197(-)$1	222	26	60	13.1967
cc[bb[eeeeeddddnnnnndddd333eeeee22	chr19:9958606-9958834(+)$1	228	170	204	12.4530
===========[cccmmmmccc333=========	chr1:155226384-155226657(-)$1	273	21	55	12.8927
a[cccffffff[cccnnnnnccc]ffffff]ccc	chr19:47290592-47290822(-)$1	230	29	63	13.3186
eedddd"""ccc[bbnnnnnbb22ccc22ddddd	chr22:39928324-39928558(-)$1	234	73	107	11.3187
##ccc[eeeee[cccnnnnnccceeeee]ccchh	chr18:77748261-77748486(-)$1	225	18	52	12.9913
cc[eeeee[ccc[bboooooobb]ccc]eeeee]	chr12:57037144-57037384(-)$1	240	99	133	10.5940
[a[bb!!gggggggnnnnnggggggg22bb]a]f	chr19:51301220-51301479(-)$1	259	122	156	10.8299
!!eeeee[ccc[cccnnnnnccc22ccceeeee2	chr19:3783752-3783977(-)$1	225	157	191	14.3851

#otherMatches

#Seq PSSM
GAGGUUGUGGUUUGUGGUGGACAAUACAUAAUAG	chr12:49093473-49093717(-)$1	244	206	240	11.7197
GACUGUCCACACUGCGCAUGGUAAGCUGGGCAAG	chr6:43480451-43480679(-)$1	228	161	195	10.9007
UUGUUCUUGGAGCUGGAGCCACAGGUCCGAGACA	chr17:80014102-80014323(+)$1	221	69	103	11.9004
UCUUCCAGGAACCCGGUUUGGGGCCAUGCUGGAC	chr16:29872421-29872648(-)$1	227	60	94	9.5316
AUACCAUUAAUACUAUGUUUGGAUUUUUUGGAUG	chr5:37314202-37314437(-)$1	235	164	198	10.2849
CGCACCCGGAUCGCCGCCCAGGGUUUCACGGUCG	chr5:175816253-175816492(+)$1	239	161	195	12.5343
CCAUCCCCCUAGGCCGUGGAGGAUAUAGAGGUCG	chr17:34171004-34171238(+)$1	234	64	98	12.8201
UAUGAGACGAUGCUGACGGAGAUCAUGUCCAUGG	chr19:13059434-13059676(+)$1	242	79	113	11.1711
AGCGAGAGCGUCCUGCGUACACAGAUCCGCCACA	chr22:39262644-39262868(-)$1	224	61	95	14.9713
GGGGCGAGAACGCACACAACGUGACGCUCAGCCC	chr9:99180021-99180249(-)$1	228	152	186	13.2783
CGAAGUGAUUUGAUACCAACUAUCAAAUUUCGAC	chr20:25397673-25397893(+)$1	220	88	122	13.9123
AGGCCAAUGGCCUUCCCAUCAUGGAAUCCAACUG	chrX:47001642-47001893(-)$1	251	104	138	11.4894
UGCCAGAGCUUUUGGAAUACCUAUCAGAGUAUAU	chr10:62547860-62548102(+)$1	242	85	119	11.2801
CGGCUUCUUAUGCACGGAAAGGAAGUAGGAAGCA	chr2:70314908-70315136(+)$1	228	15	49	13.4852
GGAGAUCCAGACGGCCGUGCGCCUGCUGCUGCCU	chr6:27100202-27100428(-)$1	226	177	211	15.1632
GGUUUUCUUGCAGUCCCACCACCAUCAUUAAAAU	chr1:33241512-33241761(-)$1	249	13	47	12.4530
AUCAUGGAGAAGGGCACCGAGUUCUUCCUCAAGG	chr19:13246224-13246487(+)$1	263	130	164	13.2021
CCUGCGGAACCCGCUCAUCGCCGGCAAGUAGGGG	chr19:46190634-46190997(-)$1	363	156	190	11.7161
UGUUGGAAAUGGAUCUAGUCGAUACAGUCCUUCU	chr6:136599025-136599249(-)$1	224	58	92	12.6929
UGUGUCUUUGACUCUUGAUCAGAGCCAGUCACAG	chr16:2814288-2814566(+)$1	278	77	111	11.6340
AGCCGCUGCAGCUGCUGCCACAGCCAGUAUUGCC	chr20:2443640-2443914(-)$1	274	73	107	9.7990
CGGAGAAGCCAGGCACCACAUUGCCACAGCCCCC	chr16:2049631-2049858(-)$1	227	92	126	10.6781
GGCCGGGCGGCCGUGUGGCGCGGCUGCUCGCCCC	chr7:23338869-23339090(+)$1	221	106	140	10.3370
CAUUAUCAUCUUCACCAACACGUGCAAGUGAGCG	chr19:19033424-19033664(+)$1	240	102	136	13.5596
AAAUUUAUUGGUGCAGGUGCUGCAACAGUAGGAG	chr2:176043801-176044038(-)$1	237	159	193	9.8685
AAGAAGCUCUAGAAGCUGUAAAAAGACUUAAAGA	chr9:106875514-106875738(+)$1	224	170	204	9.5458
UAUGAUGUGGCACGAGACAUUGAUACCCACACGC	chr17:61890598-61890827(+)$1	229	30	64	10.4469
UUAAAUUACAAAGCAAUAAUAUGUUGAGUAUUUU	chr1:229625601-229625827(-)$1	226	142	176	10.6443
GCGGCAGGUGGGUCGCUACCUGACCCUUGCCAUC	chr5:98128892-98129128(+)$1	236	96	130	11.2707
UUCCUCGAUUGUGCCGCGAGGGCUCAGGUGACCG	chr10:75542053-75542279(+)$1	226	119	153	14.0541
GAGGCUGCCAAGGGCCUACUGGCAGGUGGAGCUU	chr16:28845588-28845815(+)$1	227	176	210	11.4885
GAUGGCUGCGCAGGGAGAGCCCCAGGUCCAGUUC	chr12:131357026-131357269(+)$1	243	111	145	14.5748
CUUAUGUGCUGUCAGAUUACCUGGGGCAGACAAG	chr1:226549570-226549795(-)$1	225	185	219	11.7633
AUGUUGGUUUGAACAAAACCUGUGAUAAAAUCAA	chr14:39645216-39645451(+)$1	235	191	225	14.7582
GAGUUUGUAGGGGGCUGUGACAUUCUUCUGCAGA	chr14:96010230-96010481(+)$1	251	106	140	10.9901
UGCCGGAGAAUGAUGCAGCUAUGAGCUUUGAAGC	chr11:124501137-124501368(+)$1	231	92	126	10.6005
CCUCCUCAUUAUGAACUGUUUUCACUAAGGGACA	chr16:47117358-47117603(-)$1	245	76	110	12.2509
CCUCAGAAUGUGAAGGAUUAUUUACUCGAUGAUG	chr10:12240631-12240865(+)$1	234	88	122	10.9025
ACUGCGUGGUGGUGGUGAAUCCCCAGACCAAGCG	chr5:137089468-137089703(-)$1	235	51	85	10.8387
CCUGCUGCAGCUGCCACAGGCCCUCCCCCAGGUA	chr20:49509815-49510037(-)$1	222	68	102	10.8211
CCGUGGUGGGCUGAGGGUGCCUCCCCCAGGCUGG	chr17:55927231-55927477(-)$1	246	164	198	10.9745
GCCUGUGUCCUCCCAUCCAGGAUGUGCUGGAAGG	chr19:39868051-39868296(+)$1	245	53	87	10.9046
GCGCGCAUUGGAAGAACGCGGUGGGCUUCUGGUG	chr16:28502734-28502955(-)$1	221	122	156	11.3820
UGAGCUCAGCGCCUGCUUCUCUAGACUUCUUGAU	chr10:28970242-28970467(+)$1	225	5	39	12.1599
GUGGGCAGCAGCGGCCCCCAGCCCCGGCUCAGCC	chr17:71281677-71281901(-)$1	224	116	150	13.3325
ACUACACCAAAGUUUACCAGGAGAUUUGGAUAGG	chr14:104381360-104381596(-)$1	236	116	150	13.9386
AGAGCAUUUCCGGAGACCACCUCCAGAGCAUUUU	chr8:94746305-94746527(-)$1	222	96	130	11.2731
AUGAACUUGGACUUCCAUGAGAAGUAUAAUGAUU	chr16:56487140-56487374(+)$1	234	129	163	11.4931
UCUCUUCAGGCUCUCGAACAGUGUGGCCUGAUGA	chr2:150435975-150436197(-)$1	222	26	60	13.1967
UCAGCCAAGGCCAGGGGAGACCUGGGUGCCUUCA	chr19:9958606-9958834(+)$1	228	170	204	12.4530
ACCAGUGGAGAAGCUGAGGAGCCCCUCUUCACUG	chr1:155226384-155226657(-)$1	273	21	55	12.8927
GCGCUCGGAGUGGGCUUGGCGCUGGCUCUGCAGC	chr19:47290592-47290822(-)$1	230	29	63	13.3186
GGUGAAACGGCCCCGGAAGACGAAGGCAAUUCAG	chr22:39928324-39928558(-)$1	234	73	107	11.3187
GAGGGGCCGGCUGAGCCCACCUCGCUGGGCCCUC	chr18:77748261-77748486(-)$1	225	18	52	12.9913
GUGUUUGCUGGUGUUGGUGAGAGGACCCGUGAAG	chr12:57037144-57037384(-)$1	240	99	133	10.5940
GUUUGAGCUGCAUUCAGGAAGUGCGGGACAUGGU	chr19:51301220-51301479(-)$1	259	122	156	10.8299
AUGGUGGAGGUGCUGCCACCCAGAGGCCCCACCC	chr19:3783752-3783977(-)$1	225	157	191	14.3851

#DB
(((((((((..((((.....))))..))))))..	chr12:49093473-49093717(-)$1	1	206	240	11.7197
)).((((((...(((.....)))...))))))))	chr6:43480451-43480679(-)$1	1	161	195	10.9007
)(((.((((((.(((......))).)))))))))	chr17:80014102-80014323(+)$1	1	69	103	11.9004
...(((((.(.(((......)))...).)))))(	chr16:29872421-29872648(-)$1	1	60	94	9.5316
((.(((..((..(((....)))..))..))))))	chr5:37314202-37314437(-)$1	1	164	198	10.2849
((.(((..((..(((......))).))..)))))	chr5:175816253-175816492(+)$1	1	161	195	12.5343
((((..(((((..((.....))...))).))..)	chr17:34171004-34171238(+)$1	1	64	98	12.8201
((((.((((((.((.....)))))..)))))))(	chr19:13059434-13059676(+)$1	1	79	113	11.1711
(....(.(((..(((......)))...))))...	chr22:39262644-39262868(-)$1	1	61	95	14.9713
((((((((..(((((.....))).))))).))))	chr9:99180021-99180249(-)$1	1	152	186	13.2783
(((...(((((((((.....)))))))))))).)	chr20:25397673-25397893(+)$1	1	88	122	13.9123
((((...(((..((((......)))).)))...)	chrX:47001642-47001893(-)$1	1	104	138	11.4894
.))))))((((((((.....)))..))))).(((	chr10:62547860-62548102(+)$1	1	85	119	11.2801
..(((((((((...(.....)...))))))))).	chr2:70314908-70315136(+)$1	1	15	49	13.4852
(.((...(((..(((.....)))..))))).)))	chr6:27100202-27100428(-)$1	1	177	211	15.1632
((((((..((..((......))...))..)))))	chr1:33241512-33241761(-)$1	1	13	47	12.4530
(((.(((.(((((((.....))))))).))).))	chr19:13246224-13246487(+)$1	1	130	164	13.2021
(((((....((.((.....)).))...))).)))	chr19:46190634-46190997(-)$1	1	156	190	11.7161
((..(((..((..((.....))..)).)))....	chr6:136599025-136599249(-)$1	1	58	92	12.6929
((((.((..(.((((.....))))).)).)))))	chr16:2814288-2814566(+)$1	1	77	111	11.6340
((((.(.((((((((((...))).))))..))).	chr20:2443640-2443914(-)$1	1	73	107	9.7990
.((....((..((((......))))...))))..	chr16:2049631-2049858(-)$1	1	92	126	10.6781
))))(((((((((((...)))))))))))((.((	chr7:23338869-23339090(+)$1	1	106	140	10.3370
(....(((.((((((......))).))))))...	chr19:19033424-19033664(+)$1	1	102	136	13.5596
(..(((((((.(((((...))))).)))))))..	chr2:176043801-176044038(-)$1	1	159	193	9.8685
(((....(((..(((((......)).)))..)))	chr9:106875514-106875738(+)$1	1	170	204	9.5458
((((.(((((..(((....)))....)))))..)	chr17:61890598-61890827(+)$1	1	30	64	10.4469
(((((.(((..((((......))))..))).)).	chr1:229625601-229625827(-)$1	1	142	176	10.6443
((((..(((((((((.....))))))..)))..)	chr5:98128892-98129128(+)$1	1	96	130	11.2707
(((.(((.(((.(((.....))).))).)))..)	chr10:75542053-75542279(+)$1	1	119	153	14.0541
.(((((.(((...(((....)))...))))))))	chr16:28845588-28845815(+)$1	1	176	210	11.4885
..((((((.((.(((.....)))..)).))).))	chr12:131357026-131357269(+)$1	1	111	145	14.5748
(((.(.((((.((((.....)))))))).).)))	chr1:226549570-226549795(-)$1	1	185	219	11.7633
.(((((((((..(((.....)))....)))))))	chr14:39645216-39645451(+)$1	1	191	225	14.7582
(.((((((((((((.((...)).)))))))))))	chr14:96010230-96010481(+)$1	1	106	140	10.9901
(..(((((..(.(((....))).).))))).)))	chr11:124501137-124501368(+)$1	1	92	126	10.6005
..((((..(((((((.....)))).)))))))..	chr16:47117358-47117603(-)$1	1	76	110	12.2509
(((((....(((((......)))))....))).)	chr10:12240631-12240865(+)$1	1	88	122	10.9025
(.(((.((((((.((.....))))..)))).)))	chr5:137089468-137089703(-)$1	1	51	85	10.8387
((((..(.((..(((...))).)).)..))))))	chr20:49509815-49510037(-)$1	1	68	102	10.8211
((.(((.(((...(((...)))))))))))))))	chr17:55927231-55927477(-)$1	1	164	198	10.9745
((((...(((..(((((...)))).)..))))))	chr19:39868051-39868296(+)$1	1	53	87	10.9046
.(((.(((((((((..(.....)..)))))))))	chr16:28502734-28502955(-)$1	1	122	156	11.3820
((((.((((.(.(((......))).)...)))).	chr10:28970242-28970467(+)$1	1	5	39	12.1599
(((((((((.(.(((.....))).).)))..)))	chr17:71281677-71281901(-)$1	1	116	150	13.3325
((((..(((((.(((.....))).))))).))).	chr14:104381360-104381596(-)$1	1	116	150	13.9386
((.((...((.((((.....)))).)))).))..	chr8:94746305-94746527(-)$1	1	96	130	11.2731
(((((((((.(((((.....))))).))).).))	chr16:56487140-56487374(+)$1	1	129	163	11.4931
((...((((((((.(.....).).))))))).))	chr2:150435975-150436197(-)$1	1	26	60	13.1967
((.((.(((((((((.....))))...)))))..	chr19:9958606-9958834(+)$1	1	170	204	12.4530
(((((((((((.(((....)))...)))))))))	chr1:155226384-155226657(-)$1	1	21	55	12.8927
(.(((((((((.(((.....))).)))))).)))	chr19:47290592-47290822(-)$1	1	29	63	13.3186
))((((...(((.((.....))..)))..))))(	chr22:39928324-39928558(-)$1	1	73	107	11.3187
..(((.(((((.(((.....)))))))).)))))	chr18:77748261-77748486(-)$1	1	18	52	12.9913
((.(((((.(((.((......)).))).))))).	chr12:57037144-57037384(-)$1	1	99	133	10.5940
.(.((..(((((((.....)))))))..)).).)	chr19:51301220-51301479(-)$1	1	122	156	10.8299
..(((((.(((.(((.....)))..)))))))).	chr19:3783752-3783977(-)$1	1	157	191	14.3851

#PSSM
e : 0.19	d : 0.15	c : 0.12	g : 0.08	f : 0.07	= : 0.05	! : 0.05	[ : 0.05	: : 0.03	# : 0.03	h : 0.03	a : 0.03	i : 0.01	l : 0.01	$ : 0.01	b : 0.01	
e : 0.17	c : 0.15	d : 0.12	f : 0.08	# : 0.07	[ : 0.07	! : 0.07	g : 0.05	b : 0.05	= : 0.03	h : 0.03	: : 0.01	i : 0.01	$ : 0.01	a : 0.01	
c : 0.21	e : 0.14	d : 0.12	[ : 0.12	f : 0.08	b : 0.05	= : 0.05	! : 0.05	: : 0.03	# : 0.03	i : 0.03	g : 0.01	h : 0.01	" : 0.01	
c : 0.21	e : 0.17	f : 0.10	d : 0.10	b : 0.08	# : 0.07	= : 0.05	[ : 0.05	g : 0.03	" : 0.03	i : 0.03	! : 0.01	h : 0.01	
c : 0.21	[ : 0.12	e : 0.10	" : 0.08	f : 0.07	! : 0.07	# : 0.07	= : 0.07	b : 0.07	g : 0.03	i : 0.03	d : 0.03	a : 0.01	
c : 0.17	f : 0.10	e : 0.10	! : 0.08	" : 0.08	[ : 0.08	= : 0.07	# : 0.07	a : 0.05	i : 0.05	d : 0.05	g : 0.03	b : 0.01	
c : 0.19	e : 0.14	f : 0.08	! : 0.08	" : 0.08	[ : 0.07	i : 0.07	# : 0.07	= : 0.05	d : 0.05	b : 0.03	g : 0.03	a : 0.01	
c : 0.28	e : 0.14	! : 0.10	f : 0.07	i : 0.07	[ : 0.07	= : 0.05	g : 0.05	d : 0.05	b : 0.03	# : 0.03	" : 0.03	
c : 0.29	b : 0.10	e : 0.08	f : 0.07	[ : 0.07	! : 0.07	i : 0.07	g : 0.07	= : 0.05	d : 0.05	# : 0.03	" : 0.01	
c : 0.28	b : 0.14	e : 0.10	! : 0.08	i : 0.07	g : 0.07	f : 0.05	= : 0.05	[ : 0.05	a : 0.03	d : 0.03	" : 0.01	
! : 0.24	c : 0.14	e : 0.10	[ : 0.08	b : 0.08	" : 0.05	f : 0.05	i : 0.05	g : 0.05	= : 0.05	a : 0.05	d : 0.01	
[ : 0.22	! : 0.22	d : 0.15	" : 0.07	c : 0.07	e : 0.07	g : 0.05	b : 0.03	i : 0.03	= : 0.03	f : 0.01	
c : 0.42	d : 0.17	b : 0.05	" : 0.05	e : 0.05	[ : 0.05	! : 0.03	i : 0.03	g : 0.03	= : 0.03	a : 0.03	f : 0.01	
c : 0.45	d : 0.19	b : 0.14	e : 0.05	i : 0.03	g : 0.03	= : 0.03	" : 0.01	f : 0.01	[ : 0.01	
c : 0.45	d : 0.17	b : 0.08	o : 0.05	n : 0.05	a : 0.03	e : 0.03	i : 0.01	g : 0.01	= : 0.01	f : 0.01	[ : 0.01	! : 0.01	
n : 0.54	o : 0.19	m : 0.07	c : 0.05	d : 0.03	l : 0.03	b : 0.03	e : 0.01	! : 0.01	
n : 0.54	o : 0.21	m : 0.08	l : 0.07	b : 0.03	c : 0.01	d : 0.01	a : 0.01	
n : 0.56	o : 0.22	l : 0.12	m : 0.08	
n : 0.56	o : 0.22	m : 0.08	l : 0.08	= : 0.01	c : 0.01	
n : 0.50	o : 0.22	c : 0.10	l : 0.05	b : 0.03	= : 0.01	e : 0.01	m : 0.01	g : 0.01	
c : 0.36	o : 0.17	b : 0.14	d : 0.12	e : 0.05	a : 0.03	g : 0.03	i : 0.01	= : 0.01	f : 0.01	n : 0.01	
c : 0.45	d : 0.15	b : 0.12	] : 0.05	e : 0.05	o : 0.03	g : 0.03	i : 0.01	3 : 0.01	= : 0.01	f : 0.01	n : 0.01	
c : 0.38	d : 0.17	3 : 0.07	b : 0.07	2 : 0.05	e : 0.05	g : 0.03	] : 0.03	a : 0.03	i : 0.01	= : 0.01	o : 0.01	4 : 0.01	f : 0.01	
d : 0.17	2 : 0.14	] : 0.14	3 : 0.12	c : 0.12	b : 0.07	e : 0.07	g : 0.03	= : 0.03	4 : 0.03	i : 0.01	f : 0.01	a : 0.01	
] : 0.17	3 : 0.15	2 : 0.14	d : 0.08	b : 0.07	c : 0.07	e : 0.07	g : 0.05	i : 0.03	a : 0.03	= : 0.03	4 : 0.03	f : 0.03	
c : 0.15	3 : 0.12	b : 0.12	2 : 0.07	e : 0.07	g : 0.07	] : 0.07	f : 0.05	i : 0.05	d : 0.05	= : 0.05	4 : 0.05	a : 0.05	
c : 0.26	2 : 0.10	b : 0.08	3 : 0.08	e : 0.08	f : 0.07	i : 0.05	g : 0.05	d : 0.05	= : 0.05	] : 0.03	4 : 0.03	a : 0.01	
c : 0.29	2 : 0.14	e : 0.10	] : 0.08	f : 0.07	i : 0.07	d : 0.05	= : 0.05	b : 0.03	3 : 0.03	g : 0.03	4 : 0.01	
c : 0.31	e : 0.15	f : 0.07	2 : 0.07	] : 0.07	i : 0.07	b : 0.07	= : 0.05	g : 0.03	d : 0.03	4 : 0.01	h : 0.01	3 : 0.01	
c : 0.28	e : 0.17	b : 0.08	d : 0.08	f : 0.07	] : 0.07	i : 0.05	= : 0.05	2 : 0.05	g : 0.03	a : 0.01	h : 0.01	
c : 0.22	e : 0.14	] : 0.14	b : 0.07	d : 0.07	f : 0.05	g : 0.05	i : 0.05	= : 0.05	a : 0.03	2 : 0.03	3 : 0.01	: : 0.01	4 : 0.01	h : 0.01	
c : 0.19	e : 0.12	d : 0.10	2 : 0.07	g : 0.07	i : 0.07	= : 0.07	] : 0.07	f : 0.05	3 : 0.05	b : 0.05	4 : 0.01	[ : 0.01	h : 0.01	a : 0.01	
c : 0.15	2 : 0.14	e : 0.14	d : 0.12	3 : 0.08	i : 0.07	= : 0.07	g : 0.05	] : 0.05	h : 0.03	E : 0.01	4 : 0.01	b : 0.01	f : 0.01	
c : 0.15	d : 0.12	2 : 0.10	3 : 0.10	e : 0.10	h : 0.07	= : 0.07	g : 0.05	i : 0.05	f : 0.05	] : 0.03	E : 0.01	5 : 0.01	4 : 0.01	b : 0.01	

#score	682.7743610258327
#seq	57
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_CDS_m2_run2.txt

#BEAR
ggggggg[aooooooa]gggggggd	chr10:43882460-43882810(-)$1	350	154	179	12.8665
:ccceeeeeooooooeeeee]cccc	chr17:49237279-49237542(+)$1	263	210	235	12.3968
==========nnnnn==========	chr6:160163058-160163278(+)$1	220	159	184	9.0283
ddd[eeeeeooooooeeeee]dddd	chr1:93299001-93299317(+)$1	316	7	32	12.6569
b[a[eeeeeooooooeeeeeabb]a	chr5:180669073-180669425(-)$1	352	254	279	12.7242
FFddddcccooooooccc]ddddff	chr16:449302-449580(+)$1	278	235	260	11.1223
c!!ffffffooooooffffff22cc	chr10:79795268-79795548(+)$1	280	238	263	12.4286
!ccc[a[bboooooobb]acccddd	chr19:8520261-8520526(+)$1	265	26	51	12.7039
c[a[eeeeeooooooeeeeea]ccc	chr12:49524980-49525230(-)$1	250	143	168	13.6249
""gggggggooooooggggggg555	chr10:85910364-85910736(+)$1	372	271	296	11.4757
==========lll===========3	chr14:102548004-102548258(-)$1	254	63	88	9.4326
cc!!eeeeeooooooeeeee22ccc	chr7:26236863-26237149(-)$1	286	32	57	13.5196
c[gggggggoooooogggggggccc	chr22:18185001-18185252(+)$1	251	131	156	13.3570
cc"""ddddoooooodddd]ccc22	chr19:30500095-30500349(+)$1	254	194	219	12.6039
###ddddbboooooobb22dddd44	chr7:44873941-44874261(-)$1	320	112	137	12.3487
b[dddd[bboooooobb]dddd]bb	chr19:14199779-14200065(-)$1	286	71	96	11.7971
!!ccc[cccooooooccc]ccc22b	chr19:42375318-42375581(+)$1	263	173	198	12.8954
gggggg[bboooooobb]ggggggg	chr12:49580015-49580335(-)$1	320	293	318	13.1563
ee[ffffffooooooffffff]eee	chr1:202300914-202301166(-)$1	252	68	93	11.6572
ddddeeeeeooooooeeeee>>>>>	chr16:11650266-11650560(-)$1	294	135	160	12.1900
[ccc!!cccoooooocccccceeee	chr1:93307222-93307575(+)$1	353	101	126	12.6488
ccgggggggooooooggggggg777	chr8:30655100-30655335(-)$1	235	63	88	12.0268
""==========lll==========	chr10:74804667-74804901(-)$1	234	165	190	9.4139
dddd[ddddoooooodddddddd33	chr11:62339955-62340314(-)$1	359	282	307	12.1452
c"""eeeeeooooooeeeee22ccc	chr8:101932728-101933033(-)$1	305	180	205	13.5425
gggdddd[aooooooa]dddd]ggg	chr17:39846256-39846541(+)$1	285	10	35	12.3726
!!ccc[ddddoooooodddd]ccc6	chr16:47487823-47488104(-)$1	281	79	104	11.0087
cc!!eeeeeooooooeeeee4444c	chr22:19035913-19036171(-)$1	258	195	220	13.9987
a$$$$$cccooooooccc4444a22	chr22:21965045-21965320(+)$1	275	93	118	12.0025
gg]bbddddooooooddddffffff	chr19:40478291-40478562(+)$1	271	150	175	10.9128
c[dddd[bboooooobbdddd]ccc	chr8:22880254-22880576(-)$1	322	211	236	12.6322
!bb!!ddddoooooodddd4444bb	chr1:25669351-25669636(+)$1	285	119	144	12.0573
::gggggggoooooogggggggddd	chr7:33054138-33054473(-)$1	335	94	119	10.9960
ffffffcccooooooccc]ffffff	chr15:69747408-69747726(+)$1	318	116	141	11.7293
ccgggggggooooooggggggg:FF	chr7:5569065-5569394(-)$1	329	267	292	11.4505
gggg[ddddoooooodddd333ggg	chr6:74228554-74229051(-)$1	497	65	90	12.9596
ddddeeeeeooooooeeeee>>>>>	chr3:141463912-141464211(+)$1	299	31	56	12.1900
c!!ffffffooooooffffff22cc	chr3:23959830-23960159(+)$1	329	22	47	12.4286
eeeee!!bboooooobb]eeeee]e	chr4:174253072-174253350(-)$1	278	242	267	12.3536
ddd[eeeeeooooooeeeee]dddd	chr1:93298858-93299104(+)$1	246	150	175	12.6569
$$$ffffffooooooffffff333e	chr4:100870379-100870643(-)$1	264	196	221	12.1657
cc!!cccbboooooobb]ccc22cc	chr17:79826501-79826904(-)$1	403	123	148	13.1620
fccc!!cccooooooccc22ccc33	chr7:107398848-107399166(+)$1	318	54	79	12.9109
eeee[a[bboooooobb]aeeeee:	chr6:32945818-32946062(+)$1	244	193	218	11.2545
d!!ffffffooooooffffff4444	chr15:52843940-52844317(-)$1	377	163	188	12.7854
fffffddddooooooddddffffff	chr3:180321957-180322183(+)$1	226	124	149	11.3752
ddd"""cccooooooccc333dddd	chr2:70314865-70315216(+)$1	351	156	181	12.3228
iiiii!!bboooooobb22iiiiii	chr17:74732960-74733237(-)$1	277	134	159	12.6780
bb[ccccccooooooccc]cccbbi	chr4:174254655-174254910(-)$1	255	15	40	12.0746
eeee[ddddooooooddddeeeee2	chrX:100646642-100646910(+)$1	268	129	154	11.6856
d"""eeeeeooooooeeeee333dd	chr3:169700852-169701129(+)$1	277	231	256	13.7097
###ddddbboooooobb]dddd333	chr14:23794355-23794603(+)$1	248	104	129	13.1676
ggggeeeeeooooooeeeee:cccg	chr12:57032861-57033191(-)$1	330	204	229	12.3639
ggggg!!bboooooobb]ggggggg	chr20:376760-377161(+)$1	401	35	60	13.2067
bbgggggggoooooogggggggA}F	chr2:3623306-3623569(+)$1	263	181	206	10.9271
hhh[ccc[aooooooaccchhhhhh	chr8:28608229-28608573(+)$1	344	209	234	11.0878
eeeee!!bboooooobbeeeee333	chr22:41320323-41320586(+)$1	263	91	116	13.0439
[a[ddddbboooooobb4444dddd	chr19:18684398-18684654(+)$1	256	18	43	12.3079
[bb[eeeeeooooooeeeee]bb]a	chr3:128890188-128890423(-)$1	235	182	207	12.4681
####eeeeeooooooeeeeedddd]	chr6:11094426-11094677(+)$1	251	115	140	13.0827
fffccc[bboooooobb]ccc]fff	chr17:5336512-5336759(-)$1	247	13	38	12.1931
cc!!ccc[aooooooaccccccagg	chr19:12841605-12841913(-)$1	308	104	129	13.2184

#otherMatches

#Seq PSSM
CAGGCCUGGAAAGGAUGAGGCCUGG	chr10:43882460-43882810(-)$1	350	154	179	12.8665
ugugcuaggcucucuucuagacacu	chr17:49237279-49237542(+)$1	263	210	235	12.3968
CCUUUUGAUUGUUAAAAUCAAAAGG	chr6:160163058-160163278(+)$1	220	159	184	9.0283
CGACGAGGUACUGUCACCUUUUUGU	chr1:93299001-93299317(+)$1	316	7	32	12.6569
AAGUAGCUGCUCACUUAGCUCUGGG	chr5:180669073-180669425(-)$1	352	254	279	12.7242
UUUCCCCCCAGCAAAGGGAGGGGCC	chr16:449302-449580(+)$1	278	235	260	11.1223
UCCUGAAGACCUAUUUUUUCAAUAG	chr10:79795268-79795548(+)$1	280	238	263	12.4286
GUGAAGGAGAACGACCUGCUCAGAA	chr19:8520261-8520526(+)$1	265	26	51	12.7039
CACUAUGGUGAGUAAGCCGUGCGGC	chr12:49524980-49525230(-)$1	250	143	168	13.6249
CGUAAGUAAUGCUUUUUAUUUAACA	chr10:85910364-85910736(+)$1	372	271	296	11.4757
AAAUCUUUGUAAUAUGAGGAUUUUA	chr14:102548004-102548258(-)$1	254	63	88	9.4326
AGAUUAAAUGCUAAAGUUUACCCUU	chr7:26236863-26237149(-)$1	286	32	57	13.5196
UCAUUCAGCAAGGUGGCUGGGUAUG	chr22:18185001-18185252(+)$1	251	131	156	13.3570
GCAUAUAAUUUGAACAUUAAGCAUU	chr19:30500095-30500349(+)$1	254	194	219	12.6039
ACAUCCACAAAUCUCUGAUUGGAAA	chr7:44873941-44874261(-)$1	320	112	137	12.3487
GAGUGGACCCCCUGCGGACCGCACC	chr19:14199779-14200065(-)$1	286	71	96	11.7971
CUGGGucucuuuuuugagucucuug	chr19:42375318-42375581(+)$1	263	173	198	12.8954
UUGAAAUAAUGCUUUUUUUUUCAAA	chr12:49580015-49580335(-)$1	320	293	318	13.1563
UCCUCUUUAGGCUGAUGAGGAAGAG	chr1:202300914-202301166(-)$1	252	68	93	11.6572
GGGCAUGAAUCCUCCUUCGUAUUAU	chr16:11650266-11650560(-)$1	294	135	160	12.1900
UGGAACCGUCCCAAAAUGUCCCUUG	chr1:93307222-93307575(+)$1	353	101	126	12.6488
AGGUGCGUUAUCCAGAACGCAUUAC	chr8:30655100-30655335(-)$1	235	63	88	12.0268
AAGAGAUGUGUAUGCUGCAUAUUUU	chr10:74804667-74804901(-)$1	234	165	190	9.4139
CCUUCGGUUCUGAGAAACCAAGGCC	chr11:62339955-62340314(-)$1	359	282	307	12.1452
UCCCACAAAUAGUUUUUUGUUUACG	chr8:101932728-101933033(-)$1	305	180	205	13.5425
AUUGUUAGCGGAAGGGGUGAUAAAU	chr17:39846256-39846541(+)$1	285	10	35	12.3726
AUGGAGAUUCUCAAAUGGAUGUCCU	chr16:47487823-47488104(-)$1	281	79	104	11.0087
GCAAGUUCAUGUGUCUGGACCCAGG	chr22:19035913-19036171(-)$1	258	195	220	13.9987
CUUCCAGGACAACCCUCCAUAUGAU	chr22:21965045-21965320(+)$1	275	93	118	12.0025
CCAUCGUGGGCUCUACCACAGGUGU	chr19:40478291-40478562(+)$1	271	150	175	10.9128
CCUUGUACACGAUGCUGAUAAAGUG	chr8:22880254-22880576(-)$1	322	211	236	12.6322
UUAUCAUAGAUGCAGCUGUUAUUUA	chr1:25669351-25669636(+)$1	285	119	144	12.0573
UAGAAGUAGCCAACUCUAUUUUACA	chr7:33054138-33054473(-)$1	335	94	119	10.9960
ACAUUGGGAGCCUCAUCUGCAAUGU	chr15:69747408-69747726(+)$1	318	116	141	11.7293
GCGGGAGGCAAGGGCGCUUUCUCUG	chr7:5569065-5569394(-)$1	329	267	292	11.4505
GAGUUGACAGGGAUAUGUCUUUGCU	chr6:74228554-74229051(-)$1	497	65	90	12.9596
GAGUUCAGUGUUUAAAUUGAAAUAU	chr3:141463912-141464211(+)$1	299	31	56	12.1900
GUAUUAGUGACAAGCCAUUGAGUCU	chr3:23959830-23960159(+)$1	329	22	47	12.4286
UAUAGCUGAUAAGAUUCUCUGUAGA	chr4:174253072-174253350(-)$1	278	242	267	12.3536
CGACGAGGUACUGUCACCUUUUUGU	chr1:93298858-93299104(+)$1	246	150	175	12.6569
GAGUACCUCACCGCAGAGGUAAAUG	chr4:100870379-100870643(-)$1	264	196	221	12.1657
CUCACCAUCAAGAAGGACUGGAAGG	chr17:79826501-79826904(-)$1	403	123	148	13.1620
CUAUAAUCAGCCACAUGAGGAUAUU	chr7:107398848-107399166(+)$1	318	54	79	12.9109
AUCGAGGCCGAGCUGGGGCCGAUGA	chr6:32945818-32946062(+)$1	244	193	218	11.2545
GUUGCUAGCAAGCUGGCUGGCUGAU	chr15:52843940-52844317(-)$1	377	163	188	12.7854
GGUGACAUCAUUCGAGGUGAUUAGU	chr3:180321957-180322183(+)$1	226	124	149	11.3752
CUCGGAGGGGAAUUGUCCGGAGAGA	chr2:70314865-70315216(+)$1	351	156	181	12.3228
GGGACCGCUACACCAAGGAGUCCCG	chr17:74732960-74733237(-)$1	277	134	159	12.6780
GCCAGCGCCCGCCCUGGCAGCUGCG	chr4:174254655-174254910(-)$1	255	15	40	12.0746
GGCUAUGGUGGGCAAACUAAGCCGA	chrX:100646642-100646910(+)$1	268	129	154	11.6856
GUUUUUAGAAAGAUGUUUGAUGCCU	chr3:169700852-169701129(+)$1	277	231	256	13.7097
CGGGCUAGAGCGACAUCAUGGUAUU	chr14:23794355-23794603(+)$1	248	104	129	13.1676
GUCUCAGCCAUUCCAGGUUGCUGAG	chr12:57032861-57033191(-)$1	330	204	229	12.3639
GGGUUCUGGGUAGGACCUGACCCUU	chr20:376760-377161(+)$1	401	35	60	13.2067
CGCUCCCUCGGCUGGGAGGGAGGUU	chr2:3623306-3623569(+)$1	263	181	206	10.9271
GGUUCCUAGGCAUUGCAGGACCUUG	chr8:28608229-28608573(+)$1	344	209	234	11.0878
AUGUCCAUGACACUCCAGACAUGCC	chr22:41320323-41320586(+)$1	263	91	116	13.0439
ACACUGCCAGUAAUAUGGUCCGCAG	chr19:18684398-18684654(+)$1	256	18	43	12.3079
GUGAGCACAUGCAACUGUGUAUAGC	chr3:128890188-128890423(-)$1	235	182	207	12.4681
CCAAGAUGUGGCACAGCGUCGGGCU	chr6:11094426-11094677(+)$1	251	115	140	13.0827
UUUCUUCUCAGGUUGGACAAGAAGA	chr17:5336512-5336759(-)$1	247	13	38	12.1931
GUGACGAUGAUAAAACUCGGCCCCU	chr19:12841605-12841913(-)$1	308	104	129	13.2184

#DB
(((((((.(......).)))))))(	chr10:43882460-43882810(-)$1	1	154	179	12.8665
.((((((((......))))).)))(	chr17:49237279-49237542(+)$1	1	210	235	12.3968
((((((((((.....))))))))))	chr6:160163058-160163278(+)$1	1	159	184	9.0283
(((.(((((......))))).))))	chr1:93299001-93299317(+)$1	1	7	32	12.6569
(.(.(((((......)))))))).)	chr5:180669073-180669425(-)$1	1	254	279	12.7242
))(((((((......))).))))((	chr16:449302-449580(+)$1	1	235	260	11.1223
(..((((((......))))))..))	chr10:79795268-79795548(+)$1	1	238	263	12.4286
.(((.(.((......)).)))))))	chr19:8520261-8520526(+)$1	1	26	51	12.7039
(.(.(((((......)))))).)))	chr12:49524980-49525230(-)$1	1	143	168	13.6249
..(((((((......)))))))...	chr10:85910364-85910736(+)$1	1	271	296	11.4757
((((((((((...))))))))))).	chr14:102548004-102548258(-)$1	1	63	88	9.4326
((..(((((......)))))..)))	chr7:26236863-26237149(-)$1	1	32	57	13.5196
(.(((((((......))))))))))	chr22:18185001-18185252(+)$1	1	131	156	13.3570
((...((((......)))).)))..	chr19:30500095-30500349(+)$1	1	194	219	12.6039
...((((((......))..))))..	chr7:44873941-44874261(-)$1	1	112	137	12.3487
(.((((.((......)).)))).))	chr19:14199779-14200065(-)$1	1	71	96	11.7971
..(((.(((......))).)))..)	chr19:42375318-42375581(+)$1	1	173	198	12.8954
((((((.((......)).)))))))	chr12:49580015-49580335(-)$1	1	293	318	13.1563
((.((((((......)))))).)))	chr1:202300914-202301166(-)$1	1	68	93	11.6572
(((((((((......))))).....	chr16:11650266-11650560(-)$1	1	135	160	12.1900
.(((..(((......))))))))))	chr1:93307222-93307575(+)$1	1	101	126	12.6488
(((((((((......)))))))...	chr8:30655100-30655335(-)$1	1	63	88	12.0268
..((((((((((...))))))))))	chr10:74804667-74804901(-)$1	1	165	190	9.4139
((((.((((......))))))))..	chr11:62339955-62340314(-)$1	1	282	307	12.1452
(...(((((......)))))..)))	chr8:101932728-101933033(-)$1	1	180	205	13.5425
(((((((.(......).)))).)))	chr17:39846256-39846541(+)$1	1	10	35	12.3726
..(((.((((......)))).))).	chr16:47487823-47488104(-)$1	1	79	104	11.0087
((..(((((......)))))....)	chr22:19035913-19036171(-)$1	1	195	220	13.9987
(.....(((......)))....)..	chr22:21965045-21965320(+)$1	1	93	118	12.0025
)).))((((......))))((((((	chr19:40478291-40478562(+)$1	1	150	175	10.9128
(.((((.((......)))))).)))	chr8:22880254-22880576(-)$1	1	211	236	12.6322
.((..((((......))))....))	chr1:25669351-25669636(+)$1	1	119	144	12.0573
..(((((((......)))))))(((	chr7:33054138-33054473(-)$1	1	94	119	10.9960
(((((((((......))).))))))	chr15:69747408-69747726(+)$1	1	116	141	11.7293
))(((((((......))))))).))	chr7:5569065-5569394(-)$1	1	267	292	11.4505
((((.((((......))))...)))	chr6:74228554-74229051(-)$1	1	65	90	12.9596
(((((((((......))))).....	chr3:141463912-141464211(+)$1	1	31	56	12.1900
(..((((((......))))))..))	chr3:23959830-23960159(+)$1	1	22	47	12.4286
(((((..((......)).))))).)	chr4:174253072-174253350(-)$1	1	242	267	12.3536
(((.(((((......))))).))))	chr1:93298858-93299104(+)$1	1	150	175	12.6569
...((((((......))))))...)	chr4:100870379-100870643(-)$1	1	196	221	12.1657
((..(((((......)).)))..))	chr17:79826501-79826904(-)$1	1	123	148	13.1620
((((..(((......)))..)))..	chr7:107398848-107399166(+)$1	1	54	79	12.9109
((((.(.((......)).)))))).	chr6:32945818-32946062(+)$1	1	193	218	11.2545
(..((((((......))))))....	chr15:52843940-52844317(-)$1	1	163	188	12.7854
)))))((((......))))((((((	chr3:180321957-180322183(+)$1	1	124	149	11.3752
(((...(((......)))...))))	chr2:70314865-70315216(+)$1	1	156	181	12.3228
(((((..((......))..))))))	chr17:74732960-74733237(-)$1	1	134	159	12.6780
((.((((((......))).))))))	chr4:174254655-174254910(-)$1	1	15	40	12.0746
((((.((((......))))))))).	chrX:100646642-100646910(+)$1	1	129	154	11.6856
(...(((((......)))))...))	chr3:169700852-169701129(+)$1	1	231	256	13.7097
...((((((......)).))))...	chr14:23794355-23794603(+)$1	1	104	129	13.1676
))))(((((......))))).((((	chr12:57032861-57033191(-)$1	1	204	229	12.3639
(((((..((......)).)))))))	chr20:376760-377161(+)$1	1	35	60	13.2067
))(((((((......)))))))).)	chr2:3623306-3623569(+)$1	1	181	206	10.9271
(((.(((.(......))))))))))	chr8:28608229-28608573(+)$1	1	209	234	11.0878
(((((..((......)))))))...	chr22:41320323-41320586(+)$1	1	91	116	13.0439
.(.((((((......))....))))	chr19:18684398-18684654(+)$1	1	18	43	12.3079
.((.(((((......))))).)).)	chr3:128890188-128890423(-)$1	1	182	207	12.4681
....(((((......))))))))).	chr6:11094426-11094677(+)$1	1	115	140	13.0827
((((((.((......)).))).)))	chr17:5336512-5336759(-)$1	1	13	38	12.1931
((..(((.(......))))))))))	chr19:12841605-12841913(-)$1	1	104	129	13.2184

#PSSM
c : 0.20	d : 0.12	g : 0.11	e : 0.08	b : 0.06	! : 0.06	f : 0.06	# : 0.04	[ : 0.04	: : 0.03	= : 0.03	" : 0.03	F : 0.01	a : 0.01	$ : 0.01	i : 0.01	h : 0.01	
c : 0.17	g : 0.11	d : 0.09	[ : 0.08	! : 0.08	e : 0.08	" : 0.06	b : 0.06	# : 0.04	f : 0.04	= : 0.03	$ : 0.03	F : 0.01	: : 0.01	i : 0.01	h : 0.01	a : 0.01	
g : 0.19	d : 0.14	! : 0.11	c : 0.09	e : 0.06	= : 0.04	" : 0.04	# : 0.04	[ : 0.04	f : 0.04	a : 0.03	$ : 0.03	b : 0.03	] : 0.01	i : 0.01	h : 0.01	
g : 0.17	d : 0.16	c : 0.12	f : 0.11	[ : 0.09	! : 0.08	" : 0.06	e : 0.06	= : 0.04	$ : 0.01	b : 0.01	i : 0.01	# : 0.01	
e : 0.25	g : 0.14	d : 0.11	f : 0.11	c : 0.11	[ : 0.08	= : 0.04	! : 0.04	" : 0.03	$ : 0.01	b : 0.01	i : 0.01	
e : 0.22	d : 0.22	g : 0.12	f : 0.09	! : 0.09	c : 0.08	= : 0.04	a : 0.03	[ : 0.03	$ : 0.01	" : 0.01	
e : 0.22	d : 0.19	c : 0.17	g : 0.11	[ : 0.09	f : 0.08	! : 0.06	= : 0.04	
e : 0.22	b : 0.22	c : 0.12	d : 0.12	g : 0.09	f : 0.08	[ : 0.06	= : 0.04	
e : 0.22	b : 0.22	c : 0.12	d : 0.12	g : 0.09	f : 0.08	a : 0.06	= : 0.04	
o : 0.93	= : 0.04	d : 0.01	
o : 0.95	n : 0.01	l : 0.01	= : 0.01	
o : 0.95	n : 0.01	l : 0.01	= : 0.01	
o : 0.95	l : 0.03	n : 0.01	
o : 0.95	n : 0.01	= : 0.01	l : 0.01	
o : 0.95	n : 0.01	= : 0.01	l : 0.01	
e : 0.22	b : 0.22	c : 0.12	d : 0.11	g : 0.09	f : 0.08	a : 0.06	= : 0.04	o : 0.01	
e : 0.22	b : 0.22	c : 0.16	d : 0.12	g : 0.09	f : 0.08	= : 0.04	] : 0.03	
e : 0.24	c : 0.16	d : 0.16	] : 0.14	g : 0.11	f : 0.08	= : 0.04	2 : 0.03	4 : 0.01	
e : 0.25	d : 0.19	g : 0.14	f : 0.08	c : 0.08	] : 0.06	= : 0.04	2 : 0.04	a : 0.03	4 : 0.03	3 : 0.01	
e : 0.29	g : 0.14	d : 0.12	f : 0.12	c : 0.11	= : 0.04	4 : 0.04	3 : 0.03	] : 0.01	2 : 0.01	i : 0.01	h : 0.01	
g : 0.14	c : 0.14	d : 0.12	f : 0.12	] : 0.08	4 : 0.06	e : 0.06	= : 0.04	3 : 0.04	a : 0.03	2 : 0.03	> : 0.03	i : 0.01	: : 0.01	h : 0.01	
d : 0.16	g : 0.14	c : 0.14	2 : 0.08	] : 0.08	e : 0.08	4 : 0.06	= : 0.04	f : 0.04	3 : 0.04	b : 0.03	> : 0.03	i : 0.01	h : 0.01	
c : 0.16	d : 0.16	g : 0.08	e : 0.08	2 : 0.06	f : 0.06	3 : 0.06	= : 0.04	b : 0.04	4 : 0.04	> : 0.03	a : 0.03	5 : 0.01	] : 0.01	7 : 0.01	: : 0.01	i : 0.01	A : 0.01	h : 0.01	
c : 0.17	d : 0.12	g : 0.09	f : 0.08	3 : 0.08	e : 0.06	= : 0.04	] : 0.04	2 : 0.04	4 : 0.04	b : 0.04	> : 0.03	5 : 0.01	7 : 0.01	F : 0.01	i : 0.01	} : 0.01	h : 0.01	
c : 0.16	d : 0.12	g : 0.09	f : 0.08	3 : 0.08	e : 0.06	2 : 0.04	b : 0.04	= : 0.03	a : 0.03	4 : 0.03	> : 0.03	F : 0.03	i : 0.03	5 : 0.01	7 : 0.01	6 : 0.01	: : 0.01	h : 0.01	] : 0.01	

#score	758.7071634566404
#seq	62
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_UTR_m2_run1.txt

#BEAR
dd!!dddd[ddddoooooodddd22dddd333	chr17:44833631-44833847(+)$1	216	38	70	13.3058
!!ffffff!!ddddoooooodddd22ffffff	chr12:19672157-19672375(+)$1	218	114	146	13.1232
####bb[ffffffooooooffffffbbbb]ad	chr7:99171427-99171649(+)$1	222	87	119	12.9233
[ggggggg!!ddddoooooodddd22gggggg	chr1:32663305-32663522(+)$1	217	23	55	14.0691
dddccc[bb[ddddoooooodddd]bb333cc	chr2:155310113-155310345(+)$1	232	33	65	12.2912
bb[eeeee!!cccooooooccc22eeeee]bb	chr7:8127527-8127794(+)$1	267	105	137	13.3205
=========fffffflllffffff4444====	chr2:164460925-164461146(-)$1	221	24	56	10.7371
f[ffffff[ddddoooooodddd22ffffff]	chr18:43707991-43708224(+)$1	233	42	74	14.0296
hhh[bb[ffffffooooooffffff22bbhhh	chr4:160280842-160281057(+)$1	215	44	76	11.9880
###gggggggrrrrrrrrrggggggg]ggggg	chr1:61924768-61925003(+)$1	235	191	223	10.8130
ffff!!ccc[cccooooooccc]ccc]fffff	chr12:104382221-104382451(+)$1	230	68	100	14.7978
=========[a[aooooooaa==========:	chr10:75008058-75008283(-)$1	225	165	197	15.2735
[ggggggg[ddddooooooddddgggggggbb	chr15:25582836-25583067(-)$1	231	178	210	14.7623
ggg[ccc####bboooooobb333ccc]gggg	chr16:53524951-53525167(+)$1	216	95	127	14.4977
!!ccc[ffffffooooooffffff22ccc22e	chr8:67772237-67772460(+)$1	223	20	52	12.4180
fffff$$$$$cccooooooccc]ffffff22e	chr12:132569675-132569905(+)$1	230	126	158	13.4410
####cccccc[bboooooobb]ccc4444ccc	chr4:41956207-41956428(+)$1	221	154	186	14.0939
#ccc$$$$$ddddoooooodddd22ccc22cc	chr19:36936045-36936260(-)$1	215	128	160	13.6217
ffffcccffffffooooooffffff]ccc]ff	chr11:76262110-76262350(+)$1	240	61	93	13.6733
dddd"""ffffffooooooffffff333dddd	chr1:31782874-31783104(+)$1	230	160	192	13.3542
====[bb!!a[bboooooobb]a4444bb]==	chr8:65494542-65494763(+)$1	221	165	197	14.2235
ff!!dddd!!cccoooooocccdddd4444ff	chr16:1415510-1415740(-)$1	230	76	108	14.1615
ccc"""ccc[cccooooooccc]ccc]ccc]f	chr7:123323170-123323419(-)$1	249	97	129	15.1340
ffffffffff!!aooooooa22ffffff4444	chr12:53906776-53907005(-)$1	229	5	37	12.8317
c[eeeee[bb[bboooooobb22bb]eeeee]	chr3:48282509-48282731(+)$1	222	104	136	11.4598
fff[bb"""ddddoooooodddd]bb]fffff	chr3:49757257-49757480(-)$1	223	40	72	13.6281
ff[bb[ccc[cccooooooccc]ccc]bbfff	chr1:151024167-151024395(-)$1	228	83	115	14.1419
[===========ddddllldddd22=======	chr14:104164561-104164791(-)$1	230	21	53	11.4995
======[a!!cccrrrrrrrrrccc22a]===	chr14:65398868-65399098(+)$1	230	185	217	11.7276
eeee===========mmmm===========dd	chr8:104081309-104081525(+)$1	216	10	42	10.3038
!!bb!!gggggggooooooggggggg]bb22h	chr17:8785030-8785251(-)$1	221	54	86	13.6649
eeee"""ffffffooooooffffff]eeeee:	chr7:99667515-99667738(-)$1	223	107	139	12.4491
a[ggggggg[cccrrrrrrrrrcccggggggg	chr19:4360932-4361162(-)$1	230	151	183	11.1745
b[ccc!!ffffffooooooffffff]ccc]bb	chr15:41028258-41028488(-)$1	230	56	88	14.0121
eee!!ddddddddoooooodddd]dddd4444	chr16:603470-603688(+)$1	218	58	90	12.7382
ggggggg"""ddddnnnnndddd22ggggggg	chr12:105764585-105764810(+)$1	225	188	220	10.9781
!!ggggggg[cccoooooocccggggggg]cc	chr9:34086325-34086544(-)$1	219	40	72	16.0010
:::gggggggcccooooooccc22ggggggg:	chr10:94414317-94414547(+)$1	230	156	188	11.1822
c####dddd[cccooooooccc]dddd22ccc	chr3:40575439-40575666(+)$1	227	63	95	13.4132
::===========oooooo===========::	chr15:23812892-23813116(+)$1	224	156	188	12.0905
ggg####bb[cccoooooocccbb333ggggg	chr3:114098993-114099209(-)$1	216	21	53	15.0693
==========cccmmmmccc]===========	chr19:22273772-22274012(+)$1	240	40	72	11.0512
dd[ffffff!!bboooooobb22ffffff]dd	chr10:112772938-112773160(+)$1	222	78	110	12.8516
b"""ccc!!ddddooooooddddccc4444bb	chr12:112460652-112460871(+)$1	219	14	46	14.6807
ddccca!!ffffffooooooffffff22a]cc	chr3:57611882-57612113(-)$1	231	20	52	12.4158
========[ddddoooooodddd333======	chr11:63391952-63392181(-)$1	229	46	78	16.6324
"""gggggggrrrrrrrrrggggggg333bbc	chr7:1581815-1582056(+)$1	241	116	148	10.6078
e!!ffffff!!aooooooa]ffffff22eeee	chr19:33469482-33469712(-)$1	230	76	108	12.4969
=========!!bboooooobb22=========	chr1:84702885-84703097(+)$1	212	173	205	15.4876
eeeee####ddddoooooodddd22eeeee]a	chr19:47278503-47278723(-)$1	220	80	112	13.6298
d[dddd"""ddddoooooodddddddd]dddd	chr17:4172546-4172771(-)$1	225	59	91	12.5954
FFFffffffddddoooooodddd333ffffff	chr2:61245732-61245957(+)$1	225	3	35	12.9794

#otherMatches

#Seq PSSM
UCACUGGGUAUUUGGUUAAAGGUCUCCCACAA	chr17:44833631-44833847(+)$1	216	38	70	13.3058
CCAGAGGAAUUGUUAAUAAAAGCACCUUCUUU	chr12:19672157-19672375(+)$1	218	114	146	13.1232
AAUUCACAUGGGAAUAAAAUUCCAUUGCUGCA	chr7:99171427-99171649(+)$1	222	87	119	12.9233
UGGCUCUGCUAAUAGUAAAUUGUUUUCAGGGC	chr1:32663305-32663522(+)$1	217	23	55	14.0691
gcccaucacaugcccuagaagguaagucccau	chr2:155310113-155310345(+)$1	232	33	65	12.2912
ACUACUUUCAGUUCAAUAAAACCUAGAGUUGU	chr7:8127527-8127794(+)$1	267	105	137	13.3205
UCUUUUUUUGAAUGUCAUGCAUUUCGUAAGAA	chr2:164460925-164461146(-)$1	221	24	56	10.7371
CCUGUAGGAUAGCAUUGAAGCUGAACUUACAA	chr18:43707991-43708224(+)$1	233	42	74	14.0296
CAUUGUCAAUUAUGCAUUUGUAAUUUUACAUG	chr4:160280842-160281057(+)$1	215	44	76	11.9880
uuuucuuugGGAACUGAAGUCAGAGGCACGAA	chr1:61924768-61925003(+)$1	235	191	223	10.8130
CUUUGAAGUGCCUUGCAUCAGGGAUUAGGAGC	chr12:104382221-104382451(+)$1	230	68	100	14.7978
CUUGCUUUGAGACUUUGAUGCCAGGGCAGGUU	chr10:75008058-75008283(-)$1	225	165	197	15.2735
UACAAGCUAUAGCUAAUGUGCUGAGCUUGUGC	chr15:25582836-25583067(-)$1	231	178	210	14.7623
UUUGUUAUAUAGGGAUCAACCAGCUAAGAAAA	chr16:53524951-53525167(+)$1	216	95	127	14.4977
GUUUAAGAAGAAACCGUAUUUUUCCAUGAUAA	chr8:67772237-67772460(+)$1	223	20	52	12.4180
UAAAGACGCUGCGAAUUGACGCCUUUUAUAAU	chr12:132569675-132569905(+)$1	230	126	158	13.4410
UUUUCUUGGCAUGUUAAAUCAAGCUUAAAAAG	chr4:41956207-41956428(+)$1	221	154	186	14.0939
UAGCAAUCCUUGACACUUUUCAAUAGCUUUUA	chr19:36936045-36936260(-)$1	215	128	160	13.6217
AAAAGUUCAUUUACAGUUCUAAAUGUAAUGUU	chr11:76262110-76262350(+)$1	240	61	93	13.6733
ACCCACCAUUUAUGUUAAAAUAGAUUAAGGGU	chr1:31782874-31783104(+)$1	230	160	192	13.3542
GGGAGGUGGAGUUGGGAUGGAGUAUGGAUGUC	chr8:65494542-65494763(+)$1	221	165	197	14.2235
GUUUAUCUAGUAGUAAGACCUAGGAUUUUUAC	chr16:1415510-1415740(-)$1	230	76	108	14.1615
UGUUUCAUAUUUAUAAUGCUAAUUAUCAUACC	chr7:123323170-123323419(-)$1	249	97	129	15.1340
CCUACCCCAGAAUGAGAAAAGGCUGGGGAGAG	chr12:53906776-53907005(-)$1	229	5	37	12.8317
CACACGGUGCUGCUACCUCGUUUGCUUCGUGC	chr3:48282509-48282731(+)$1	222	104	136	11.4598
GCGAACCACCUUAAGAUAGUGAGAGUCUGCCU	chr3:49757257-49757480(-)$1	223	40	72	13.6281
AGAGAGAAGCAGUAGAUACACUCCUUAUCCUC	chr1:151024167-151024395(-)$1	228	83	115	14.1419
CGUCUGAGGCCUGCCCCCUGGGCUGGGGCCUC	chr14:104164561-104164791(-)$1	230	21	53	11.4995
UUUUCUGCUUAGACUUACUUAUUCUUUGAGGA	chr14:65398868-65399098(+)$1	230	185	217	11.7276
AGGGGAAUGGUGUAAACAUUUAUACUGUUUUG	chr8:104081309-104081525(+)$1	216	10	42	10.3038
GGGCCAUCAGUGGACGAAGUCGCUGGAGCAAC	chr17:8785030-8785251(-)$1	221	54	86	13.6649
GAAGUGCACUAUUAAACAGAAUAGUUUUUCAG	chr7:99667515-99667738(-)$1	223	107	139	12.4491
CUCCCGGGCCUGCUGUCAGCUUGCAGCCCGGG	chr19:4360932-4361162(-)$1	230	151	183	11.1745
UUGCUGGUGAGGUGGAUGAACUUCAAAGCUAU	chr15:41028258-41028488(-)$1	230	56	88	14.0121
GGGCAGGGGCUGUGCACAGACGGACCCCCCAC	chr16:603470-603688(+)$1	218	58	90	12.7382
CCUUAUUCUAUUUAUAACUUAAGAUGAUAAGG	chr12:105764585-105764810(+)$1	225	188	220	10.9781
UACUAUUGCUAGACCCUCUUCUGUAAUGGGUA	chr9:34086325-34086544(-)$1	219	40	72	16.0010
UAUUUUUCACUUGUUGCCCCAAAUGUGAAAGC	chr10:94414317-94414547(+)$1	230	156	188	11.1822
AUAGCUAGAUGUUUCUUUUAACUUUUAUUUCG	chr3:40575439-40575666(+)$1	227	63	95	13.4132
aauuauauauauaaaaauauauauguauaaga	chr15:23812892-23813116(+)$1	224	156	188	12.0905
UGGAUCCAGCGCCAAGCCGGGCCUUCCCUGCC	chr3:114098993-114099209(-)$1	216	21	53	15.0693
UUAAUUUUAGUUAAAUGUAAGUUAAAAUUAAA	chr19:22273772-22274012(+)$1	240	40	72	11.0512
AUAUAAUUAAUCACUAUUUUGUAUAAUUACAU	chr10:112772938-112773160(+)$1	222	78	110	12.8516
CAGGUGGCUGGUGAAAUGACACCUCAGAAGGA	chr12:112460652-112460871(+)$1	219	14	46	14.6807
AUUAUCCUCUAAAUAACCAAAUUUAGUUGUAU	chr3:57611882-57612113(-)$1	231	20	52	12.4158
UUUAAAAGCAAUUUUUGAUAGUUUUUCUUUUA	chr11:63391952-63392181(-)$1	229	46	78	16.6324
CAGUUUGAUACUGUAAAUCUAUCAGAGCAGAG	chr7:1581815-1582056(+)$1	241	116	148	10.6078
ACUAAUUUUAAGGAUUGACAAGAGUUUAUUUU	chr19:33469482-33469712(-)$1	230	76	108	12.4969
UUGAUUAUUACAAUUUAGUUUUCAGUAAUCAA	chr1:84702885-84703097(+)$1	212	173	205	15.4876
CCCAGCACCCUCCAGGACAGGAGAUCUGGGAU	chr19:47278503-47278723(-)$1	220	80	112	13.6298
AUUUGACAUAAUGUUGCUUCAUUUCAGUUUUU	chr17:4172546-4172771(-)$1	225	59	91	12.5954
AGAUAGGUGUGAUUCAAAUGUCAAAUCACCUA	chr2:61245732-61245957(+)$1	225	3	35	12.9794

#DB
((..((((.((((......))))..))))...	chr17:44833631-44833847(+)$1	1	38	70	13.3058
..((((((..((((......))))..))))))	chr12:19672157-19672375(+)$1	1	114	146	13.1232
....((.((((((......)))))))))).))	chr7:99171427-99171649(+)$1	1	87	119	12.9233
.(((((((..((((......))))..))))))	chr1:32663305-32663522(+)$1	1	23	55	14.0691
((((((.((.((((......)))).))...))	chr2:155310113-155310345(+)$1	1	33	65	12.2912
((.(((((..(((......)))..))))).))	chr7:8127527-8127794(+)$1	1	105	137	13.3205
(((((((((((((((...))))))....))))	chr2:164460925-164461146(-)$1	1	24	56	10.7371
(.((((((.((((......))))..)))))).	chr18:43707991-43708224(+)$1	1	42	74	14.0296
(((.((.((((((......))))))..)))))	chr4:160280842-160281057(+)$1	1	44	76	11.9880
...(((((((.........))))))).)))))	chr1:61924768-61925003(+)$1	1	191	223	10.8130
((((..(((.(((......))).))).)))))	chr12:104382221-104382451(+)$1	1	68	100	14.7978
(((((((((.(.(......)))))))))))).	chr10:75008058-75008283(-)$1	1	165	197	15.2735
.(((((((.((((......)))))))))))))	chr15:25582836-25583067(-)$1	1	178	210	14.7623
(((.(((....((......))...))).))))	chr16:53524951-53525167(+)$1	1	95	127	14.4977
..(((.((((((......))))))..)))..)	chr8:67772237-67772460(+)$1	1	20	52	12.4180
(((((.....(((......))).))))))..)	chr12:132569675-132569905(+)$1	1	126	158	13.4410
....((((((.((......)).)))....)))	chr4:41956207-41956428(+)$1	1	154	186	14.0939
.(((.....((((......))))..)))..))	chr19:36936045-36936260(-)$1	1	128	160	13.6217
(((((((((((((......)))))).))).))	chr11:76262110-76262350(+)$1	1	61	93	13.6733
((((...((((((......))))))...))))	chr1:31782874-31783104(+)$1	1	160	192	13.3542
((((.((..(.((......)).)....)).))	chr8:65494542-65494763(+)$1	1	165	197	14.2235
((..((((..(((......)))))))....))	chr16:1415510-1415740(-)$1	1	76	108	14.1615
(((...(((.(((......))).))).))).)	chr7:123323170-123323419(-)$1	1	97	129	15.1340
((((((((((..(......)..))))))....	chr12:53906776-53907005(-)$1	1	5	37	12.8317
(.(((((.((.((......))..)).))))).	chr3:48282509-48282731(+)$1	1	104	136	11.4598
(((.((...((((......)))).)).)))))	chr3:49757257-49757480(-)$1	1	40	72	13.6281
((.((.(((.(((......))).))).)))))	chr1:151024167-151024395(-)$1	1	83	115	14.1419
.(((((((((((((((...))))..)))))))	chr14:104164561-104164791(-)$1	1	21	53	11.4995
((((((.(..(((.........)))..).)))	chr14:65398868-65399098(+)$1	1	185	217	11.7276
))))(((((((((((....)))))))))))((	chr8:104081309-104081525(+)$1	1	10	42	10.3038
..((..(((((((......))))))).))..)	chr17:8785030-8785251(-)$1	1	54	86	13.6649
((((...((((((......)))))).))))).	chr7:99667515-99667738(-)$1	1	107	139	12.4491
(.(((((((.(((.........))))))))))	chr19:4360932-4361162(-)$1	1	151	183	11.1745
(.(((..((((((......)))))).))).))	chr15:41028258-41028488(-)$1	1	56	88	14.0121
(((..((((((((......)))).))))....	chr16:603470-603688(+)$1	1	58	90	12.7382
(((((((...((((.....))))..)))))))	chr12:105764585-105764810(+)$1	1	188	220	10.9781
..(((((((.(((......)))))))))).))	chr9:34086325-34086544(-)$1	1	40	72	16.0010
...((((((((((......)))..))))))).	chr10:94414317-94414547(+)$1	1	156	188	11.1822
(....((((.(((......))).))))..)))	chr3:40575439-40575666(+)$1	1	63	95	13.4132
..(((((((((((......)))))))))))..	chr15:23812892-23813116(+)$1	1	156	188	12.0905
(((....((.(((......)))))...)))))	chr3:114098993-114099209(-)$1	1	21	53	15.0693
(((((((((((((....))).)))))))))))	chr19:22273772-22274012(+)$1	1	40	72	11.0512
((.((((((..((......))..)))))).))	chr10:112772938-112773160(+)$1	1	78	110	12.8516
(...(((..((((......)))))))....))	chr12:112460652-112460871(+)$1	1	14	46	14.6807
((((((..((((((......))))))..).))	chr3:57611882-57612113(-)$1	1	20	52	12.4158
((((((((.((((......))))...))))))	chr11:63391952-63392181(-)$1	1	46	78	16.6324
...(((((((.........)))))))...))(	chr7:1581815-1582056(+)$1	1	116	148	10.6078
(..((((((..(......).))))))..))))	chr19:33469482-33469712(-)$1	1	76	108	12.4969
(((((((((..((......))..)))))))))	chr1:84702885-84703097(+)$1	1	173	205	15.4876
(((((....((((......))))..))))).)	chr19:47278503-47278723(-)$1	1	80	112	13.6298
(.((((...((((......)))))))).))))	chr17:4172546-4172771(-)$1	1	59	91	12.5954
(((((((((((((......))))...))))))	chr2:61245732-61245957(+)$1	1	3	35	12.9794

#PSSM
f : 0.15	= : 0.13	d : 0.11	e : 0.09	! : 0.07	# : 0.07	[ : 0.05	b : 0.05	g : 0.05	c : 0.05	: : 0.03	h : 0.01	a : 0.01	" : 0.01	F : 0.01	
= : 0.15	f : 0.13	d : 0.09	! : 0.09	g : 0.09	[ : 0.09	# : 0.07	e : 0.07	c : 0.03	: : 0.03	" : 0.03	b : 0.01	h : 0.01	F : 0.01	
= : 0.17	f : 0.13	g : 0.13	c : 0.09	e : 0.09	# : 0.07	! : 0.05	d : 0.05	[ : 0.05	" : 0.03	h : 0.01	b : 0.01	: : 0.01	F : 0.01	
f : 0.17	= : 0.17	g : 0.15	c : 0.09	e : 0.09	# : 0.07	! : 0.05	[ : 0.05	d : 0.03	" : 0.03	b : 0.03	
= : 0.17	g : 0.15	c : 0.15	f : 0.13	b : 0.07	d : 0.05	e : 0.05	! : 0.05	" : 0.05	# : 0.03	$ : 0.01	[ : 0.01	
= : 0.17	g : 0.15	f : 0.11	d : 0.09	c : 0.09	b : 0.07	! : 0.05	" : 0.05	e : 0.03	[ : 0.03	$ : 0.03	# : 0.03	a : 0.01	
g : 0.17	= : 0.15	f : 0.13	c : 0.13	d : 0.07	[ : 0.07	" : 0.07	e : 0.03	$ : 0.03	! : 0.03	# : 0.03	b : 0.01	
f : 0.24	g : 0.15	= : 0.15	d : 0.07	c : 0.07	! : 0.05	" : 0.05	b : 0.03	# : 0.03	$ : 0.03	e : 0.01	[ : 0.01	a : 0.01	
f : 0.23	! : 0.13	= : 0.13	g : 0.11	[ : 0.07	c : 0.07	b : 0.05	" : 0.05	# : 0.03	$ : 0.03	d : 0.03	
d : 0.21	f : 0.19	[ : 0.17	! : 0.15	g : 0.07	= : 0.07	# : 0.01	$ : 0.01	c : 0.01	a : 0.01	b : 0.01	" : 0.01	
d : 0.28	c : 0.24	f : 0.17	! : 0.07	[ : 0.05	= : 0.05	r : 0.03	a : 0.01	# : 0.01	g : 0.01	
d : 0.28	c : 0.24	f : 0.17	b : 0.11	= : 0.05	r : 0.03	[ : 0.01	! : 0.01	g : 0.01	a : 0.01	
d : 0.30	c : 0.24	f : 0.15	b : 0.11	r : 0.03	a : 0.03	o : 0.03	= : 0.03	g : 0.01	
o : 0.75	d : 0.09	r : 0.07	f : 0.03	= : 0.01	m : 0.01	
o : 0.82	r : 0.07	f : 0.01	d : 0.01	= : 0.01	n : 0.01	m : 0.01	
o : 0.82	r : 0.07	m : 0.03	l : 0.01	d : 0.01	n : 0.01	
o : 0.82	r : 0.07	l : 0.03	m : 0.03	n : 0.01	
o : 0.82	r : 0.07	l : 0.03	m : 0.01	n : 0.01	c : 0.01	
o : 0.78	r : 0.07	f : 0.03	l : 0.01	m : 0.01	n : 0.01	c : 0.01	a : 0.01	
d : 0.24	c : 0.21	f : 0.15	b : 0.11	o : 0.07	g : 0.05	a : 0.03	r : 0.03	= : 0.03	] : 0.01	
d : 0.30	f : 0.19	c : 0.19	b : 0.11	g : 0.05	r : 0.03	= : 0.03	a : 0.01	2 : 0.01	] : 0.01	
d : 0.30	f : 0.19	c : 0.19	= : 0.07	2 : 0.07	g : 0.05	] : 0.03	r : 0.03	3 : 0.01	
d : 0.32	f : 0.21	2 : 0.09	] : 0.09	g : 0.07	= : 0.07	c : 0.05	3 : 0.01	a : 0.01	b : 0.01	
f : 0.24	2 : 0.15	c : 0.13	d : 0.11	g : 0.09	= : 0.09	3 : 0.05	b : 0.03	] : 0.03	4 : 0.01	
f : 0.21	2 : 0.17	c : 0.15	g : 0.11	= : 0.09	d : 0.07	3 : 0.05	4 : 0.03	b : 0.03	] : 0.01	e : 0.01	
g : 0.15	f : 0.11	c : 0.11	= : 0.11	d : 0.09	2 : 0.09	] : 0.07	3 : 0.07	b : 0.05	4 : 0.05	e : 0.03	
= : 0.13	f : 0.11	g : 0.11	] : 0.11	4 : 0.09	c : 0.09	d : 0.07	e : 0.07	2 : 0.07	3 : 0.05	b : 0.03	
f : 0.15	g : 0.15	= : 0.13	b : 0.09	c : 0.09	e : 0.07	4 : 0.07	3 : 0.05	2 : 0.05	d : 0.03	] : 0.03	a : 0.01	
g : 0.17	= : 0.15	f : 0.13	b : 0.09	e : 0.09	4 : 0.09	c : 0.07	d : 0.05	3 : 0.03	2 : 0.03	] : 0.01	a : 0.01	
= : 0.17	] : 0.15	g : 0.15	f : 0.11	2 : 0.07	4 : 0.07	e : 0.07	c : 0.05	3 : 0.03	d : 0.03	h : 0.01	b : 0.01	
f : 0.15	= : 0.15	g : 0.13	c : 0.11	b : 0.09	d : 0.07	2 : 0.05	e : 0.05	] : 0.03	4 : 0.03	3 : 0.01	a : 0.01	h : 0.01	: : 0.01	
f : 0.15	c : 0.13	= : 0.13	g : 0.11	d : 0.09	b : 0.07	: : 0.07	e : 0.05	] : 0.03	h : 0.03	4 : 0.03	3 : 0.01	a : 0.01	

#score	683.8499751001522
#seq	52
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_UTR_m1_run2.txt

#BEAR
========ttttttttttt==========	chr14:64152249-64152474(-)$1	225	57	86	24.4037
!!ddddyyyyyyyyyyyyyyyydddd444	chr18:51823035-51823284(+)$1	249	106	135	24.9007
gggggyyyyyyyyyyyyyyyyggggggg:	chr15:83686768-83687012(-)$1	244	195	224	24.4245
hhhhhhhyyyyyyyyyyyyyyyyhhhhhh	chr11:123494863-123495088(+)$1	225	101	130	22.6900
=======xxxxxxxxxxxxxxx=======	chr7:36493262-36493484(+)$1	222	60	89	22.8673
iiiiiiiwwwwwwwwwwwwwwiiiiiiii	chr2:20449570-20449796(-)$1	226	76	105	25.4298
####dddduuuuuuuuuuuudddd4444d	chr1:1499249-1499480(-)$1	231	91	120	24.9701
d!!cccxxxxxxxxxxxxxxxccc22ddd	chr12:29657674-29657900(-)$1	226	147	176	21.0529
iiiiiiiwwwwwwwwwwwwwwiiiiiiii	chr11:27519392-27519710(-)$1	318	233	262	25.4298
dd"""ccctttttttttttccc22ddddg	chr7:75956109-75956386(-)$1	277	229	258	22.3170
!bb####bbtttttttttttbb4444bb2	chr17:38326964-38327203(+)$1	239	143	172	21.4339
c"""ddddvvvvvvvvvvvvvdddd333c	chr2:183642176-183642433(+)$1	257	110	139	24.6530
=======wwwwwwwwwwwwww========	chr13:98119614-98119843(+)$1	229	32	61	25.9041
gggggyyyyyyyyyyyyyyyyggggggg]	chr1:29474174-29474482(-)$1	308	50	79	25.5123
"""fffffftttttttttttffffff333	chr2:28616090-28616331(+)$1	241	54	83	22.1236
dddd[cccuuuuuuuuuuuuccc333ddd	chr14:35592583-35592810(+)$1	227	188	217	24.6799
[a[eeeeeuuuuuuuuuuuueeeeea]bb	chrX:76762456-76762684(-)$1	228	36	65	23.7931
ee[ddddxxxxxxxxxxxxxxxdddd333	chr22:33256416-33256647(+)$1	231	147	176	21.2953
"ccc!!bbvvvvvvvvvvvvvbb22ccc3	chr12:8928912-8929161(+)$1	249	152	181	23.3074
========uuuuuuuuuuuu=========	chr21:15744758-15745016(-)$1	258	47	76	26.5462
iiiiiiiivvvvvvvvvvvvviiiiiiii	chr12:92536821-92537051(-)$1	230	25	54	25.0528
dddd[cccwwwwwwwwwwwwwwcccdddd	chr1:26159090-26159312(+)$1	222	181	210	22.7119
========vvvvvvvvvvvvv========	chr3:86995709-86995948(-)$1	239	104	133	25.5821
======[auuuuuuuuuuuua]=======	chr2:152331758-152332009(+)$1	251	212	241	26.8591
[bb!!cccuuuuuuuuuuuuccc]bb]cc	chr12:104742412-104742762(+)$1	350	144	173	24.6460
fggggggguuuuuuuuuuuuggggggg33	chr6:28125787-28126041(+)$1	254	90	119	25.2832
!ccc!!ccctttttttttttccc22ccc2	chr11:27517900-27518185(-)$1	285	158	187	23.2796
eeeeyyyyyyyyyyyyyyyyeeeee22==	chr1:205686558-205686851(-)$1	293	254	283	23.1198
ggggbbxxxxxxxxxxxxxxxbb]ggggg	chr1:220987476-220987726(+)$1	250	9	38	20.7686
eeffffffvvvvvvvvvvvvvffffff77	chr7:2704184-2704475(+)$1	291	73	102	20.8763
=========ttttttttttt=========	chr16:72817368-72817599(-)$1	231	79	108	24.4899
!!bb!!bbuuuuuuuuuuuubb]bb22cc	chr2:28639405-28639664(+)$1	259	141	170	23.8307
"""ddddwwwwwwwwwwwwwwdddd333e	chr3:179305881-179306117(+)$1	236	57	86	24.7805
$$$$cccwwwwwwwwwwwwwwccc4444e	chr5:76369139-76369411(-)$1	272	60	89	23.9905
ggggdddduuuuuuuuuuuudddd]gggg	chr9:35099896-35100135(-)$1	239	123	152	25.1396
iiiiiiiwwwwwwwwwwwwwwiiiiiiii	chr7:87834498-87834723(-)$1	225	139	168	25.4298
f!!a!!ccctttttttttttccc22a444	chr1:244870623-244870851(+)$1	228	158	187	23.8804
gggggggyyyyyyyyyyyyyyyygggggg	chr16:69735137-69735367(+)$1	230	180	209	25.4185
gggggggyyyyyyyyyyyyyyyygggggg	chr8:128753224-128753653(+)$1	429	257	286	25.4185
ggg[dddduuuuuuuuuuuudddd]gggg	chr2:27002066-27002336(+)$1	270	192	221	25.2284
dd!!cccyyyyyyyyyyyyyyyyccc22d	chr12:104743652-104743921(+)$1	269	105	134	24.7970
hhhh[cccuuuuuuuuuuuuccc333hhh	chr6:36064871-36065096(+)$1	225	49	78	24.7349
ggg[dddduuuuuuuuuuuudddd]gggg	chr12:104742650-104742950(+)$1	300	84	113	25.2284
!!cccyyyyyyyyyyyyyyyyccc22fff	chr18:12793549-12793772(-)$1	223	37	66	24.7816
gggggyyyyyyyyyyyyyyyyggggggg3	chr8:66516212-66516436(-)$1	224	17	46	25.6057
b!!eeeeevvvvvvvvvvvvveeeee22b	chr8:97622245-97622490(+)$1	245	70	99	22.8548
d!!ddddwwwwwwwwwwwwwwdddddddd	chr17:18112494-18112747(+)$1	253	196	225	23.4561
ff:eeeeeyyyyyyyyyyyyyyyyeeeee	chr7:44919506-44919740(-)$1	234	119	148	21.4809
fffffyyyyyyyyyyyyyyyyffffff44	chr15:42824952-42825180(+)$1	228	103	132	23.5255
gggggggxxxxxxxxxxxxxxxggggggg	chr12:104743840-104744112(+)$1	272	207	236	21.8133
ddd!!cccvvvvvvvvvvvvvcccdddd]	chr17:26653871-26654109(+)$1	238	83	112	23.4766
gg!!ddddtttttttttttdddd333ggg	chr4:177251731-177251984(+)$1	253	124	153	23.6949
"""ddddwwwwwwwwwwwwwwdddd22gg	chr4:57897191-57897423(-)$1	232	162	191	24.4054
dd[bb[bbuuuuuuuuuuuubb]bb]ddd	chr2:96851467-96851715(-)$1	248	164	193	22.6742
cc!!ddddvvvvvvvvvvvvvdddd22cc	chr6:35801981-35802209(-)$1	228	98	127	24.0440
hhh!!cccattttttttttta]ccc22hh	chr1:28177480-28177739(+)$1	259	15	44	23.5681
g[eeeeewwwwwwwwwwwwwweeeee22g	chr6:116597757-116597991(-)$1	234	44	73	23.5498
cggggggguuuuuuuuuuuuggggggg33	chr17:26654683-26654906(+)$1	223	57	86	25.3736
fff[dddduuuuuuuuuuuuddddfffff	chr5:142657696-142657923(-)$1	227	118	147	23.5946
ggggddddvvvvvvvvvvvvvdddd5555	chr1:47842721-47842944(+)$1	223	16	45	21.1906
========ttttttttttt==========	chr21:34729704-34729952(+)$1	248	128	157	24.4037

#otherMatches

#Seq PSSM
GCCUGUGUAUUUGAACUACAUACAGGUAU	chr14:64152249-64152474(-)$1	225	57	86	24.4037
uuucaauaaauauauuuuucauuugauuc	chr18:51823035-51823284(+)$1	249	106	135	24.9007
UUAGCAUUAUAAUACAUCUUGGCUAAAUA	chr15:83686768-83687012(-)$1	244	195	224	24.4245
UUUUAUCACUCAUCUACCCCAAAGAUAAA	chr11:123494863-123495088(+)$1	225	101	130	22.6900
UAUUUUUUCUUGUGCauauuauaaaaaua	chr7:36493262-36493484(+)$1	222	60	89	22.8673
UGUACAUUUACAAGCGGCCUUAUGUACAU	chr2:20449570-20449796(-)$1	226	76	105	25.4298
GAAUAGGUGUCAAAUGCUAAACCUUUUAU	chr1:1499249-1499480(-)$1	231	91	120	24.9701
AUGCUUAAAAAUUUAAUGGAAAAGACUGA	chr12:29657674-29657900(-)$1	226	147	176	21.0529
AUGUAAUUGAUAGCAUUACUUAUUACAUC	chr11:27519392-27519710(-)$1	318	233	262	25.4298
AUGUAGCUGUCGUACAUUGAGCAAAUAAA	chr7:75956109-75956386(-)$1	277	229	258	22.3170
GUUUCUUGCUCUCUCUCCCUGCCUUUAAA	chr17:38326964-38327203(+)$1	239	143	172	21.4339
UAUCUACAUAAAUGUCUAAGUUGUAUAAA	chr2:183642176-183642433(+)$1	257	110	139	24.6530
GCUACAGUUGCCAUCACCUUUCUGUGGUA	chr13:98119614-98119843(+)$1	229	32	61	25.9041
GCAGUAACCCAUAGGAAAUAAACUGUAGA	chr1:29474174-29474482(-)$1	308	50	79	25.5123
UUUGGCCCUGUCUGAAAUCGGGGGUCCCC	chr2:28616090-28616331(+)$1	241	54	83	22.1236
UGUGAGGAACACUAUUCAACUCCCAACAC	chr14:35592583-35592810(+)$1	227	188	217	24.6799
GGCAAUUAUUAAAUCAAAAUUAAUUCAUC	chrX:76762456-76762684(-)$1	228	36	65	23.7931
AGCACCCUCUCUUCCCUAUCAUGGGUCAU	chr22:33256416-33256647(+)$1	231	147	176	21.2953
UUAUGAGAGAGAAUGUAUAUAUCAAAUAU	chr12:8928912-8929161(+)$1	249	152	181	23.3074
UUCCUCAUAUUUAGUUUUGAAUGAGGAAA	chr21:15744758-15745016(-)$1	258	47	76	26.5462
AUGAACUGGUGUAAAUUUGUACAGUUCAU	chr12:92536821-92537051(-)$1	230	25	54	25.0528
CCAGGCCCUUGACUGCUCCUUUGGGCUGG	chr1:26159090-26159312(+)$1	222	181	210	22.7119
GGAUGAACCACACAUUAAAAUGUUCAUUC	chr3:86995709-86995948(-)$1	239	104	133	25.5821
GAUAAAGGUGUUUAUAUUUUUGUUUGUUG	chr2:152331758-152332009(+)$1	251	212	241	26.8591
GGGUUGAAUUUUUUUCUUUUUUCUCCAUG	chr12:104742412-104742762(+)$1	350	144	173	24.6460
AAUAAUAAGGCCUUUUUUUAUUAUUAUUU	chr6:28125787-28126041(+)$1	254	90	119	25.2832
ACCAUAGAAAAAUACAGUCAUUCAUUGGC	chr11:27517900-27518185(-)$1	285	158	187	23.2796
AUAUUUCCUUCUCUAAAUAUAUAUGUAUC	chr1:205686558-205686851(-)$1	293	254	283	23.1198
AAUUCUGUGGAGGAGAAGAAAAGUGAUUC	chr1:220987476-220987726(+)$1	250	9	38	20.7686
GCCAUGGCUGUAUGUACUGUCGCUGUGUU	chr7:2704184-2704475(+)$1	291	73	102	20.8763
GAAAAAUUUAAUACAUCUAGGAAUUUUUU	chr16:72817368-72817599(-)$1	231	79	108	24.4899
UUAUUCCAUUUAUUUUAGUUUGUGUUUAC	chr2:28639405-28639664(+)$1	259	141	170	23.8307
UUUAACUGGCUCUAUAAAUUAAGUUUGUG	chr3:179305881-179306117(+)$1	236	57	86	24.7805
AAAAACAACACCCCAAAAUCCUGUCACCU	chr5:76369139-76369411(-)$1	272	60	89	23.9905
GGAGUCUGGGAACAAGGAAGCAGAUUUUC	chr9:35099896-35100135(-)$1	239	123	152	25.1396
UUUUAUCAAGAGAGCUUAACAGAUAAAAA	chr7:87834498-87834723(-)$1	225	139	168	25.4298
AGAAGAAAGGAAUAUAUGAACUUAAUGAG	chr1:244870623-244870851(+)$1	228	158	187	23.8804
ACUAUUUCCAAAAACACAUAAACAAAUAG	chr16:69735137-69735367(+)$1	230	180	209	25.4185
UAAAUGUAAAUAACUUUAAUAAAACGUUU	chr8:128753224-128753653(+)$1	429	257	286	25.4185
cuguggccuuagugccuucuggccccagc	chr2:27002066-27002336(+)$1	270	192	221	25.2284
GACCAUAUUCAGuuuuauuuauuuauuuu	chr12:104743652-104743921(+)$1	269	105	134	24.7970
CAUUUCUUGAAAGGAUCCCAAAGCCCAGU	chr6:36064871-36065096(+)$1	225	49	78	24.7349
AACUGUCCUGCAGCUGAAAUGGACUGUUC	chr12:104742650-104742950(+)$1	300	84	113	25.2284
AGAGCUCAAUUUGAAAAAUCUGUUACUAA	chr18:12793549-12793772(-)$1	223	37	66	24.7816
GAAAGUAUUUUGGUUUGUUUUCUUUCAUU	chr8:66516212-66516436(-)$1	224	17	46	25.6057
UUCCACUUUGUAUAAAUUUUUAAGUGUCA	chr8:97622245-97622490(+)$1	245	70	99	22.8548
UCAUCCUCAUGUCAUCCUUCUAGGAAGGC	chr17:18112494-18112747(+)$1	253	196	225	23.4561
ACAACUUUAAUUUCGUACACCCUAAAAGU	chr7:44919506-44919740(-)$1	234	119	148	21.4809
ACACACUCUUUCUCUUACCCUUGUGUAUU	chr15:42824952-42825180(+)$1	228	103	132	23.5255
AAGGCAUUAAUAAUAUCCACGUGUGCCUU	chr12:104743840-104744112(+)$1	272	207	236	21.8133
GUGUCAGGAACCAUGUCAAACCCUCACCU	chr17:26653871-26654109(+)$1	238	83	112	23.4766
UUAAAGAAGUCUCAUAAUGUUCUACAAAG	chr4:177251731-177251984(+)$1	253	124	153	23.6949
AAAUACUUUUUAUCACAACACAGUACAUA	chr4:57897191-57897423(-)$1	232	162	191	24.4054
UCCGAUUGUAUAGAAAACACCAUUUUGAU	chr2:96851467-96851715(-)$1	248	164	193	22.6742
AGCUUUUUCUUUACCUUACCCAAAAUUCU	chr6:35801981-35802209(-)$1	228	98	127	24.0440
UAGCUAGGCUUUUCUCUUUUGUCCUUCCU	chr1:28177480-28177739(+)$1	259	15	44	23.5681
UGGCAUAUUUGUCUUCCUUUUUAUGCAUG	chr6:116597757-116597991(-)$1	234	44	73	23.5498
CUUUCAGUCAAAUGGAUUAAACUGGAAAA	chr17:26654683-26654906(+)$1	223	57	86	25.3736
UUAUCACAGUAAUUUUAAAAUGUGUAAAA	chr5:142657696-142657923(-)$1	227	118	147	23.5946
CCCUCUAGUAAUCACAACAUUUUAGGAUU	chr1:47842721-47842944(+)$1	223	16	45	21.1906
GCUGuuuuuuuuuuuuuuugagacagucu	chr21:34729704-34729952(+)$1	248	128	157	24.4037

#DB
((((((((...........))))))))))	chr14:64152249-64152474(-)$1	1	57	86	24.4037
..((((................))))...	chr18:51823035-51823284(+)$1	1	106	135	24.9007
(((((................))))))).	chr15:83686768-83687012(-)$1	1	195	224	24.4245
(((((((................))))))	chr11:123494863-123495088(+)$1	1	101	130	22.6900
(((((((...............)))))))	chr7:36493262-36493484(+)$1	1	60	89	22.8673
(((((((..............))))))))	chr2:20449570-20449796(-)$1	1	76	105	25.4298
....((((............))))....)	chr1:1499249-1499480(-)$1	1	91	120	24.9701
(..(((...............)))..)))	chr12:29657674-29657900(-)$1	1	147	176	21.0529
(((((((..............))))))))	chr11:27519392-27519710(-)$1	1	233	262	25.4298
((...(((...........)))..)))))	chr7:75956109-75956386(-)$1	1	229	258	22.3170
.((....((...........))....)).	chr17:38326964-38327203(+)$1	1	143	172	21.4339
(...((((.............))))...)	chr2:183642176-183642433(+)$1	1	110	139	24.6530
(((((((..............))))))))	chr13:98119614-98119843(+)$1	1	32	61	25.9041
(((((................))))))).	chr1:29474174-29474482(-)$1	1	50	79	25.5123
...((((((...........))))))...	chr2:28616090-28616331(+)$1	1	54	83	22.1236
((((.(((............)))...)))	chr14:35592583-35592810(+)$1	1	188	217	24.6799
.(.(((((............)))))).))	chrX:76762456-76762684(-)$1	1	36	65	23.7931
((.((((...............))))...	chr22:33256416-33256647(+)$1	1	147	176	21.2953
.(((..((.............))..))).	chr12:8928912-8929161(+)$1	1	152	181	23.3074
((((((((............)))))))))	chr21:15744758-15745016(-)$1	1	47	76	26.5462
((((((((.............))))))))	chr12:92536821-92537051(-)$1	1	25	54	25.0528
((((.(((..............)))))))	chr1:26159090-26159312(+)$1	1	181	210	22.7119
((((((((.............))))))))	chr3:86995709-86995948(-)$1	1	104	133	25.5821
((((((.(............).)))))))	chr2:152331758-152332009(+)$1	1	212	241	26.8591
.((..(((............))).)).))	chr12:104742412-104742762(+)$1	1	144	173	24.6460
((((((((............)))))))..	chr6:28125787-28126041(+)$1	1	90	119	25.2832
.(((..(((...........)))..))).	chr11:27517900-27518185(-)$1	1	158	187	23.2796
((((................)))))..))	chr1:205686558-205686851(-)$1	1	254	283	23.1198
((((((...............)).)))))	chr1:220987476-220987726(+)$1	1	9	38	20.7686
((((((((.............))))))..	chr7:2704184-2704475(+)$1	1	73	102	20.8763
(((((((((...........)))))))))	chr16:72817368-72817599(-)$1	1	79	108	24.4899
..((..((............)).))..))	chr2:28639405-28639664(+)$1	1	141	170	23.8307
...((((..............))))...)	chr3:179305881-179306117(+)$1	1	57	86	24.7805
....(((..............)))....)	chr5:76369139-76369411(-)$1	1	60	89	23.9905
((((((((............)))).))))	chr9:35099896-35100135(-)$1	1	123	152	25.1396
(((((((..............))))))))	chr7:87834498-87834723(-)$1	1	139	168	25.4298
(..(..(((...........)))..)...	chr1:244870623-244870851(+)$1	1	158	187	23.8804
(((((((................))))))	chr16:69735137-69735367(+)$1	1	180	209	25.4185
(((((((................))))))	chr8:128753224-128753653(+)$1	1	257	286	25.4185
(((.((((............)))).))))	chr2:27002066-27002336(+)$1	1	192	221	25.2284
((..(((................)))..)	chr12:104743652-104743921(+)$1	1	105	134	24.7970
((((.(((............)))...)))	chr6:36064871-36065096(+)$1	1	49	78	24.7349
(((.((((............)))).))))	chr12:104742650-104742950(+)$1	1	84	113	25.2284
..(((................)))..)))	chr18:12793549-12793772(-)$1	1	37	66	24.7816
(((((................))))))).	chr8:66516212-66516436(-)$1	1	17	46	25.6057
(..(((((.............)))))..)	chr8:97622245-97622490(+)$1	1	70	99	22.8548
(..((((..............))))))))	chr17:18112494-18112747(+)$1	1	196	225	23.4561
)).(((((................)))))	chr7:44919506-44919740(-)$1	1	119	148	21.4809
(((((................))))))..	chr15:42824952-42825180(+)$1	1	103	132	23.5255
(((((((...............)))))))	chr12:104743840-104744112(+)$1	1	207	236	21.8133
(((..(((.............))))))).	chr17:26653871-26654109(+)$1	1	83	112	23.4766
((..((((...........))))...)))	chr4:177251731-177251984(+)$1	1	124	153	23.6949
...((((..............))))..))	chr4:57897191-57897423(-)$1	1	162	191	24.4054
((.((.((............)).)).)))	chr2:96851467-96851715(-)$1	1	164	193	22.6742
((..((((.............))))..))	chr6:35801981-35802209(-)$1	1	98	127	24.0440
(((..((((...........).)))..))	chr1:28177480-28177739(+)$1	1	15	44	23.5681
(.(((((..............)))))..)	chr6:116597757-116597991(-)$1	1	44	73	23.5498
((((((((............)))))))..	chr17:26654683-26654906(+)$1	1	57	86	25.3736
(((.((((............)))))))))	chr5:142657696-142657923(-)$1	1	118	147	23.5946
((((((((.............))))....	chr1:47842721-47842944(+)$1	1	16	45	21.1906
((((((((...........))))))))))	chr21:34729704-34729952(+)$1	1	128	157	24.4037

#PSSM
g : 0.21	= : 0.13	d : 0.13	! : 0.08	f : 0.08	i : 0.06	" : 0.06	h : 0.04	c : 0.04	e : 0.04	[ : 0.03	# : 0.01	$ : 0.01	b : 0.01	
g : 0.22	= : 0.13	! : 0.11	d : 0.09	i : 0.06	" : 0.06	h : 0.04	e : 0.04	c : 0.04	f : 0.04	b : 0.03	# : 0.01	a : 0.01	$ : 0.01	[ : 0.01	
g : 0.21	= : 0.13	! : 0.11	" : 0.08	d : 0.06	i : 0.06	h : 0.04	b : 0.04	[ : 0.04	c : 0.04	f : 0.04	e : 0.03	# : 0.01	$ : 0.01	: : 0.01	
g : 0.18	= : 0.13	d : 0.11	! : 0.09	e : 0.08	i : 0.06	c : 0.06	f : 0.04	[ : 0.04	h : 0.03	# : 0.03	" : 0.03	b : 0.03	$ : 0.01	a : 0.01	
d : 0.22	= : 0.13	g : 0.13	! : 0.11	i : 0.06	c : 0.06	e : 0.06	f : 0.04	[ : 0.04	b : 0.03	h : 0.01	" : 0.01	# : 0.01	y : 0.01	
d : 0.22	c : 0.16	= : 0.13	y : 0.09	g : 0.08	i : 0.06	e : 0.06	! : 0.06	f : 0.03	h : 0.01	# : 0.01	b : 0.01	[ : 0.01	
d : 0.21	c : 0.18	= : 0.11	y : 0.11	g : 0.08	i : 0.06	e : 0.06	b : 0.04	x : 0.03	f : 0.03	h : 0.01	# : 0.01	[ : 0.01	
y : 0.18	w : 0.14	d : 0.14	c : 0.14	= : 0.08	x : 0.08	b : 0.06	e : 0.04	f : 0.03	g : 0.03	i : 0.01	a : 0.01	
u : 0.24	y : 0.19	w : 0.16	v : 0.14	x : 0.08	t : 0.06	c : 0.03	b : 0.01	f : 0.01	= : 0.01	a : 0.01	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	t : 0.16	w : 0.16	v : 0.14	x : 0.08	
u : 0.24	y : 0.19	w : 0.16	v : 0.14	t : 0.09	x : 0.08	= : 0.03	c : 0.01	d : 0.01	
y : 0.18	w : 0.16	v : 0.14	d : 0.09	c : 0.09	x : 0.08	= : 0.06	b : 0.04	e : 0.03	a : 0.03	g : 0.03	f : 0.01	
d : 0.19	c : 0.16	= : 0.09	y : 0.09	g : 0.08	b : 0.08	i : 0.06	e : 0.06	x : 0.04	f : 0.04	] : 0.03	w : 0.01	
d : 0.22	c : 0.18	= : 0.13	g : 0.09	y : 0.08	i : 0.06	e : 0.06	f : 0.04	b : 0.03	] : 0.03	2 : 0.01	4 : 0.01	
d : 0.21	= : 0.13	g : 0.13	c : 0.11	i : 0.06	2 : 0.06	e : 0.06	f : 0.04	3 : 0.04	] : 0.03	b : 0.03	h : 0.01	4 : 0.01	y : 0.01	
d : 0.16	g : 0.14	= : 0.13	2 : 0.08	e : 0.08	i : 0.06	f : 0.06	4 : 0.04	3 : 0.04	c : 0.04	b : 0.04	] : 0.04	h : 0.01	
g : 0.19	= : 0.13	2 : 0.11	d : 0.09	3 : 0.08	i : 0.06	f : 0.06	4 : 0.04	c : 0.04	e : 0.04	a : 0.03	h : 0.01	b : 0.01	] : 0.01	5 : 0.01	
g : 0.21	= : 0.13	2 : 0.13	d : 0.11	4 : 0.06	i : 0.06	3 : 0.06	f : 0.06	h : 0.03	] : 0.03	c : 0.03	b : 0.01	e : 0.01	5 : 0.01	
g : 0.19	= : 0.14	d : 0.11	3 : 0.09	4 : 0.08	c : 0.08	i : 0.06	h : 0.04	2 : 0.04	b : 0.03	f : 0.03	7 : 0.01	e : 0.01	5 : 0.01	
g : 0.18	= : 0.14	d : 0.11	3 : 0.09	i : 0.06	c : 0.06	4 : 0.04	h : 0.04	e : 0.04	2 : 0.03	] : 0.03	b : 0.03	f : 0.03	: : 0.01	7 : 0.01	5 : 0.01	

#score	1461.7772110850658
#seq	61
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_UTR_m3_run1.txt

#BEAR
gggggqqqqqqqqggggg	chr10:98745159-98745408(+)$1	249	164	182	13.8560
e!!bbqqqqqqqqbbeee	chr20:48740969-48741213(-)$1	244	181	199	13.8129
eeeeeqqqqqqqqeeeee	chr1:45975761-45976004(+)$1	243	66	84	14.8831
eeeeeqqqqqqqqeeeee	chr13:79888496-79888719(-)$1	223	98	116	14.8831
gggggqqqqqqqqggggg	chr2:85280675-85280907(+)$1	232	174	192	13.8560
!!cccqqqqqqqqcccgg	chr11:47487764-47488000(-)$1	236	150	168	14.3426
eeeeeqqqqqqqqeeeee	chr1:28608235-28608456(+)$1	221	136	154	14.8831
$$cccqqqqqqqqccc44	chr14:62214671-62214909(+)$1	238	73	91	13.7052
eeeeeqqqqqqqqeeeee	chr19:58119467-58119690(+)$1	223	86	104	14.8831
ffcccqqqqqqqqccc22	chr3:197553753-197553980(+)$1	227	6	24	13.7139
eeeeeqqqqqqqqeeeee	chr12:44190774-44191000(-)$1	226	185	203	14.8831
!!cccqqqqqqqqccc22	chr6:135357418-135357659(-)$1	241	88	106	14.1547
!!cccqqqqqqqqccc22	chr5:126172576-126172811(+)$1	235	193	211	14.1547
eeeeeqqqqqqqqeeeee	chr12:98994842-98995099(+)$1	257	186	204	14.8831
eeeeeqqqqqqqqeeeee	chr4:158091577-158091801(+)$1	224	199	217	14.8831
[a[bbqqqqqqqqbba]d	chr2:220084424-220084652(-)$1	228	179	197	13.2354
!!cccqqqqqqqqccc33	chr15:83659346-83659569(+)$1	223	199	217	14.5119
"""bbqqqqqqqqbb444	chr10:30306080-30306309(-)$1	229	201	219	13.1878
eeeeeqqqqqqqqeeeee	chr5:59893612-59893835(-)$1	223	184	202	14.8831
eeeeeqqqqqqqqeeeee	chr19:36882931-36883156(-)$1	225	95	113	14.8831
iiiiiqqqqqqqqiiiii	chr12:30887842-30888072(-)$1	230	112	130	13.6436
fffffqqqqqqqqfffff	chr10:115670825-115671051(+)$1	226	84	102	13.4637
ddcccqqqqqqqqccchh	chr14:78182073-78182308(+)$1	235	124	142	13.4292
fffffqqqqqqqqfffff	chr19:17971924-17972154(+)$1	230	196	214	13.4637
eddddqqqqqqqqdddd:	chr12:56431411-56431633(+)$1	222	126	144	12.8111
eeeeeqqqqqqqqeeeee	chr2:61709420-61709679(-)$1	259	17	35	14.8831
eeeeeqqqqqqqqeeeee	chr10:122668098-122668350(+)$1	252	141	159	14.8831
!ddddqqqqqqqqdddd2	chrX:62569011-62569230(-)$1	219	74	92	13.8794
fffffqqqqqqqqfffff	chr3:129369504-129369730(-)$1	226	108	126	13.4637
c[cccqqqqqqqqccc]c	chr12:111158216-111158487(-)$1	271	29	47	14.0213
eeeeeqqqqqqqqeeeee	chr10:86277031-86277253(+)$1	222	84	102	14.8831
!ddddqqqqqqqqdddd2	chr6:47592056-47592286(+)$1	230	172	190	13.8794
:ddddqqqqqqqqddddg	chr16:9210714-9210941(+)$1	227	134	152	12.6878
fffffqqqqqqqqfffff	chr5:112214187-112214432(-)$1	245	40	58	13.4637
!!cccqqqqqqqqccc22	chr20:43708486-43708730(+)$1	244	134	152	14.1547
!!cccqqqqqqqqccc]d	chr17:42269101-42269338(-)$1	237	54	72	14.3339
!!cccqqqqqqqqccc]d	chr17:75484263-75484503(+)$1	240	63	81	14.3339
gggggqqqqqqqqggggg	chrX:134496679-134496905(+)$1	226	32	50	13.8560
[ddddqqqqqqqqddddc	chr1:100984923-100985144(+)$1	221	82	100	13.8507
ii[bbqqqqqqqqbb333	chr12:46754155-46754386(-)$1	231	157	175	13.3286
eeeeeqqqqqqqqeeeee	chr3:71019786-71020018(-)$1	232	60	78	14.8831
fffffqqqqqqqqfffff	chr13:42816502-42816729(+)$1	227	137	155	13.4637
gggggqqqqqqqqggggg	chr14:60752652-60752880(+)$1	228	8	26	13.8560
[ddddqqqqqqqqdddd3	chr7:135614200-135614452(-)$1	252	95	113	14.0276
cc!!aqqqqqqqqa22cc	chr17:48823847-48824098(+)$1	251	178	196	12.8182
dddddqqqqqqqqdddd4	chr3:120045204-120045425(-)$1	221	171	189	13.6292
cc[bbqqqqqqqqbb]cc	chr6:79645562-79645789(-)$1	227	85	103	12.9301
fffffqqqqqqqqfffff	chr12:69995154-69995392(+)$1	238	55	73	13.4637
eeeeeqqqqqqqqeeeee	chr22:18209777-18210004(+)$1	227	193	211	14.8831
[ddddqqqqqqqqdddd]	chr2:70315952-70316205(+)$1	253	186	204	13.9623
eeeeeqqqqqqqqeeeee	chr10:99227917-99228161(-)$1	244	20	38	14.8831
"""bbqqqqqqqqbb444	chr1:36319968-36320198(+)$1	230	116	134	13.1878
eeeeeqqqqqqqqeeeee	chr19:4044989-4045225(-)$1	236	217	235	14.8831
!!cccqqqqqqqqccc]d	chr2:85548258-85548476(-)$1	218	120	138	14.3339
eeeeeqqqqqqqqeeeee	chr9:130864619-130864843(+)$1	224	19	37	14.8831
fffffqqqqqqqqfffff	chr5:79773108-79773349(+)$1	241	95	113	13.4637
!ddddqqqqqqqqdddd2	chr8:64099331-64099577(+)$1	246	89	107	13.8794
eeeeeqqqqqqqqeeeee	chr12:54405177-54405408(+)$1	231	37	55	14.8831
""cccqqqqqqqqccc33	chr7:92237532-92237770(-)$1	238	197	215	14.3052
eeeeeqqqqqqqqeeeee	chr3:185635222-185635501(-)$1	279	238	256	14.8831
###bbqqqqqqqqbbddd	chr19:45593893-45594139(+)$1	246	136	154	13.0246
eeeeeqqqqqqqqeeeee	chr13:23903686-23903913(-)$1	227	43	61	14.8831
eeeeeqqqqqqqqeeeee	chr3:101485522-101485747(+)$1	225	99	117	14.8831
eeeeeqqqqqqqqeeeee	chr1:100548580-100548814(+)$1	234	70	88	14.8831
eee[aqqqqqqqqa]eee	chr14:60749550-60749779(+)$1	229	86	104	14.2896
fff[aqqqqqqqqa]fff	chr5:33458626-33458858(+)$1	232	64	82	13.3297
dd[bbqqqqqqqqbb]dd	chr19:10781551-10781774(+)$1	223	157	175	12.9685
$$cccqqqqqqqqcccdd	chr3:155655565-155655801(+)$1	236	46	64	13.6068
"ddddqqqqqqqqddddd	chr13:113832006-113832248(-)$1	242	110	128	13.7624
eeeeeqqqqqqqqeeeee	chr10:1063676-1063905(+)$1	229	140	158	14.8831
fffffqqqqqqqqfffff	chr17:29109981-29110225(-)$1	244	87	105	13.4637
fffffqqqqqqqqfffff	chr17:25639659-25639881(+)$1	222	81	99	13.4637
[ddddqqqqqqqqdddd]	chr9:79000637-79000929(-)$1	292	158	176	13.9623
dd[bbqqqqqqqqbb]dd	chr5:179044916-179045160(-)$1	244	26	44	12.9685

#otherMatches

#Seq PSSM
AUCUGCCCACGAACAGAU	chr10:98745159-98745408(+)$1	249	164	182	13.8560
AACCUCCUGCUCAAGUCU	chr20:48740969-48741213(-)$1	244	181	199	13.8129
auauaguaagcaguaugu	chr1:45975761-45976004(+)$1	243	66	84	14.8831
AGUACUUUUUUAUGUACU	chr13:79888496-79888719(-)$1	223	98	116	14.8831
UUUAUGAAUAUUAAUGAA	chr2:85280675-85280907(+)$1	232	174	192	13.8560
CCUGUUUUGAUUUGCAAA	chr11:47487764-47488000(-)$1	236	150	168	14.3426
GUGGGUCUGAGUCCCCAC	chr1:28608235-28608456(+)$1	221	136	154	14.8831
CAAUGUUUGAUUUUAUGC	chr14:62214671-62214909(+)$1	238	73	91	13.7052
GAAGCAUUUUUUAGCUUC	chr19:58119467-58119690(+)$1	223	86	104	14.8831
UUGCCUUUGAUACGGUUA	chr3:197553753-197553980(+)$1	227	6	24	13.7139
UGUAGAAAGACAACUACA	chr12:44190774-44191000(-)$1	226	185	203	14.8831
UUAGUUGAUACGUAUUUU	chr6:135357418-135357659(-)$1	241	88	106	14.1547
CAGUUUUGCUUUUGAUAA	chr5:126172576-126172811(+)$1	235	193	211	14.1547
UCUCUGGUCCUCAAGAGA	chr12:98994842-98995099(+)$1	257	186	204	14.8831
CUGUUAUUCCAACAGCAG	chr4:158091577-158091801(+)$1	224	199	217	14.8831
UUGCCAUCUUUUAGGAUG	chr2:220084424-220084652(-)$1	228	179	197	13.2354
UUAACUCUGUACUGUUCA	chr15:83659346-83659569(+)$1	223	199	217	14.5119
UAUUAUCUAUUUUUAUUU	chr10:30306080-30306309(-)$1	229	201	219	13.1878
CCACAGCUGCUAAUGUGG	chr5:59893612-59893835(-)$1	223	184	202	14.8831
ucuugacauccaccaaga	chr19:36882931-36883156(-)$1	225	95	113	14.8831
CUUGACUACCUCAUUAAG	chr12:30887842-30888072(-)$1	230	112	130	13.6436
AUGUGGUAUUACACACAU	chr10:115670825-115671051(+)$1	226	84	102	13.4637
AAAUCAUAUUAUAGAUGG	chr14:78182073-78182308(+)$1	235	124	142	13.4292
UGGGUCGCUGCCUGCCCA	chr19:17971924-17972154(+)$1	230	196	214	13.4637
UUAGGUACAAAAUCCUAC	chr12:56431411-56431633(+)$1	222	126	144	12.8111
AUGCAUCAAUUCUUGCAU	chr2:61709420-61709679(-)$1	259	17	35	14.8831
CCAGGGAAUCUGACCUGG	chr10:122668098-122668350(+)$1	252	141	159	14.8831
AGCGCCCGUUCCAGCGUC	chrX:62569011-62569230(-)$1	219	74	92	13.8794
CUUGGCCGCACUUUUAAG	chr3:129369504-129369730(-)$1	226	108	126	13.4637
UGAUACAAACCACUGUGA	chr12:111158216-111158487(-)$1	271	29	47	14.0213
GUUUCUAAUAACUGAGAC	chr10:86277031-86277253(+)$1	222	84	102	14.8831
AUAUAAAUAAGAAUGUGC	chr6:47592056-47592286(+)$1	230	172	190	13.8794
UGAGGCCAUCUUCCCUUG	chr16:9210714-9210941(+)$1	227	134	152	12.6878
AUGUUGCCUUGGAAACAU	chr5:112214187-112214432(-)$1	245	40	58	13.4637
UAGCCUGGAUAAUGGUGU	chr20:43708486-43708730(+)$1	244	134	152	14.1547
UUUAUUUUUGCAUAUGUA	chr17:42269101-42269338(-)$1	237	54	72	14.3339
GAGGAGAAAGGCGUCCGG	chr17:75484263-75484503(+)$1	240	63	81	14.3339
AAGAUUUUAUAAUAUUUU	chrX:134496679-134496905(+)$1	226	32	50	13.8560
GAGGAGCGUUACAUCCUG	chr1:100984923-100985144(+)$1	221	82	100	13.8507
GUACCAUGAAUUAGGAGC	chr12:46754155-46754386(-)$1	231	157	175	13.3286
AGUAACCCUUCCCUUAUU	chr3:71019786-71020018(-)$1	232	60	78	14.8831
GACAACGUGAGUUUUGUU	chr13:42816502-42816729(+)$1	227	137	155	13.4637
UGUGGAAAGUAACCCACA	chr14:60752652-60752880(+)$1	228	8	26	13.8560
CCUAGCUAAUUUAUUAGA	chr7:135614200-135614452(-)$1	252	95	113	14.0276
UCGGGACAGAGAACAAGA	chr17:48823847-48824098(+)$1	251	178	196	12.8182
caccugaggucagggguu	chr3:120045204-120045425(-)$1	221	171	189	13.6292
AUGCAUAAUUCUUUGAAU	chr6:79645562-79645789(-)$1	227	85	103	12.9301
UAUCCUUAAGUUUGGAUA	chr12:69995154-69995392(+)$1	238	55	73	13.4637
UUUGUAGAACUUGAUGAA	chr22:18209777-18210004(+)$1	227	193	211	14.8831
UAAGCUUUUCCCUGUUUU	chr2:70315952-70316205(+)$1	253	186	204	13.9623
ACCGGACAUGAAACUGGU	chr10:99227917-99228161(-)$1	244	20	38	14.8831
CUUUGGCAAUAAACAUUU	chr1:36319968-36320198(+)$1	230	116	134	13.1878
CUCUGCAUGGGCCCAGAG	chr19:4044989-4045225(-)$1	236	217	235	14.8831
UUAGUCUUAUAAUACUUU	chr2:85548258-85548476(-)$1	218	120	138	14.3339
UGUCUUGCAGCAUGGAUA	chr9:130864619-130864843(+)$1	224	19	37	14.8831
AUGUGCCAUAUUACAUAU	chr5:79773108-79773349(+)$1	241	95	113	13.4637
AGUGGUAAAGGCUCCACC	chr8:64099331-64099577(+)$1	246	89	107	13.8794
UUUAUGGUAGCAGAUAAA	chr12:54405177-54405408(+)$1	231	37	55	14.8831
UUCUCAAUUUUAGGAGUU	chr7:92237532-92237770(-)$1	238	197	215	14.3052
CAGUCUAAAUUUUGACUG	chr3:185635222-185635501(-)$1	279	238	256	14.8831
UUUCCUGAAGACCGGGGC	chr19:45593893-45594139(+)$1	246	136	154	13.0246
AAGGGGAAUUAAGUCUUU	chr13:23903686-23903913(-)$1	227	43	61	14.8831
GCUAUUUAAAACUAUGGC	chr3:101485522-101485747(+)$1	225	99	117	14.8831
GUCCUAAAUUUUCAGGAC	chr1:100548580-100548814(+)$1	234	70	88	14.8831
UGAGCAUUUGUUAGAUCA	chr14:60749550-60749779(+)$1	229	86	104	14.2896
UCAUGAACUCAGCCCUGG	chr5:33458626-33458858(+)$1	232	64	82	13.3297
UUAUCCAACACAAGAGGA	chr19:10781551-10781774(+)$1	223	157	175	12.9685
AAUCUACGGCUUAAGAGC	chr3:155655565-155655801(+)$1	236	46	64	13.6068
CAUGGCAUGUUCUUCAUU	chr13:113832006-113832248(-)$1	242	110	128	13.7624
CUGAAGUUACAUGUUCAG	chr10:1063676-1063905(+)$1	229	140	158	14.8831
UGCAGAGAAUGAGCUGCA	chr17:29109981-29110225(-)$1	244	87	105	13.4637
UUUGCUGUAAAGUGCAAG	chr17:25639659-25639881(+)$1	222	81	99	13.4637
CUUGAAAGAAACCUCAAU	chr9:79000637-79000929(-)$1	292	158	176	13.9623
UUCGUAAGGUUCGGCAAG	chr5:179044916-179045160(-)$1	244	26	44	12.9685

#DB
(((((........)))))	chr10:98745159-98745408(+)$1	1	164	182	13.8560
(..((........)))))	chr20:48740969-48741213(-)$1	1	181	199	13.8129
(((((........)))))	chr1:45975761-45976004(+)$1	1	66	84	14.8831
(((((........)))))	chr13:79888496-79888719(-)$1	1	98	116	14.8831
(((((........)))))	chr2:85280675-85280907(+)$1	1	174	192	13.8560
..(((........)))))	chr11:47487764-47488000(-)$1	1	150	168	14.3426
(((((........)))))	chr1:28608235-28608456(+)$1	1	136	154	14.8831
..(((........)))..	chr14:62214671-62214909(+)$1	1	73	91	13.7052
(((((........)))))	chr19:58119467-58119690(+)$1	1	86	104	14.8831
(((((........)))..	chr3:197553753-197553980(+)$1	1	6	24	13.7139
(((((........)))))	chr12:44190774-44191000(-)$1	1	185	203	14.8831
..(((........)))..	chr6:135357418-135357659(-)$1	1	88	106	14.1547
..(((........)))..	chr5:126172576-126172811(+)$1	1	193	211	14.1547
(((((........)))))	chr12:98994842-98995099(+)$1	1	186	204	14.8831
(((((........)))))	chr4:158091577-158091801(+)$1	1	199	217	14.8831
.(.((........))).)	chr2:220084424-220084652(-)$1	1	179	197	13.2354
..(((........)))..	chr15:83659346-83659569(+)$1	1	199	217	14.5119
...((........))...	chr10:30306080-30306309(-)$1	1	201	219	13.1878
(((((........)))))	chr5:59893612-59893835(-)$1	1	184	202	14.8831
(((((........)))))	chr19:36882931-36883156(-)$1	1	95	113	14.8831
(((((........)))))	chr12:30887842-30888072(-)$1	1	112	130	13.6436
(((((........)))))	chr10:115670825-115671051(+)$1	1	84	102	13.4637
))(((........)))((	chr14:78182073-78182308(+)$1	1	124	142	13.4292
(((((........)))))	chr19:17971924-17972154(+)$1	1	196	214	13.4637
)((((........)))).	chr12:56431411-56431633(+)$1	1	126	144	12.8111
(((((........)))))	chr2:61709420-61709679(-)$1	1	17	35	14.8831
(((((........)))))	chr10:122668098-122668350(+)$1	1	141	159	14.8831
.((((........)))).	chrX:62569011-62569230(-)$1	1	74	92	13.8794
(((((........)))))	chr3:129369504-129369730(-)$1	1	108	126	13.4637
(.(((........))).)	chr12:111158216-111158487(-)$1	1	29	47	14.0213
(((((........)))))	chr10:86277031-86277253(+)$1	1	84	102	14.8831
.((((........)))).	chr6:47592056-47592286(+)$1	1	172	190	13.8794
.((((........))))(	chr16:9210714-9210941(+)$1	1	134	152	12.6878
(((((........)))))	chr5:112214187-112214432(-)$1	1	40	58	13.4637
..(((........)))..	chr20:43708486-43708730(+)$1	1	134	152	14.1547
..(((........))).)	chr17:42269101-42269338(-)$1	1	54	72	14.3339
..(((........))).)	chr17:75484263-75484503(+)$1	1	63	81	14.3339
(((((........)))))	chrX:134496679-134496905(+)$1	1	32	50	13.8560
.((((........)))))	chr1:100984923-100985144(+)$1	1	82	100	13.8507
((.((........))...	chr12:46754155-46754386(-)$1	1	157	175	13.3286
(((((........)))))	chr3:71019786-71020018(-)$1	1	60	78	14.8831
(((((........)))))	chr13:42816502-42816729(+)$1	1	137	155	13.4637
(((((........)))))	chr14:60752652-60752880(+)$1	1	8	26	13.8560
.((((........)))).	chr7:135614200-135614452(-)$1	1	95	113	14.0276
((..(........)..))	chr17:48823847-48824098(+)$1	1	178	196	12.8182
(((((........)))).	chr3:120045204-120045425(-)$1	1	171	189	13.6292
((.((........)).))	chr6:79645562-79645789(-)$1	1	85	103	12.9301
(((((........)))))	chr12:69995154-69995392(+)$1	1	55	73	13.4637
(((((........)))))	chr22:18209777-18210004(+)$1	1	193	211	14.8831
.((((........)))).	chr2:70315952-70316205(+)$1	1	186	204	13.9623
(((((........)))))	chr10:99227917-99228161(-)$1	1	20	38	14.8831
...((........))...	chr1:36319968-36320198(+)$1	1	116	134	13.1878
(((((........)))))	chr19:4044989-4045225(-)$1	1	217	235	14.8831
..(((........))).)	chr2:85548258-85548476(-)$1	1	120	138	14.3339
(((((........)))))	chr9:130864619-130864843(+)$1	1	19	37	14.8831
(((((........)))))	chr5:79773108-79773349(+)$1	1	95	113	13.4637
.((((........)))).	chr8:64099331-64099577(+)$1	1	89	107	13.8794
(((((........)))))	chr12:54405177-54405408(+)$1	1	37	55	14.8831
..(((........)))..	chr7:92237532-92237770(-)$1	1	197	215	14.3052
(((((........)))))	chr3:185635222-185635501(-)$1	1	238	256	14.8831
...((........)))))	chr19:45593893-45594139(+)$1	1	136	154	13.0246
(((((........)))))	chr13:23903686-23903913(-)$1	1	43	61	14.8831
(((((........)))))	chr3:101485522-101485747(+)$1	1	99	117	14.8831
(((((........)))))	chr1:100548580-100548814(+)$1	1	70	88	14.8831
(((.(........).)))	chr14:60749550-60749779(+)$1	1	86	104	14.2896
(((.(........).)))	chr5:33458626-33458858(+)$1	1	64	82	13.3297
((.((........)).))	chr19:10781551-10781774(+)$1	1	157	175	12.9685
..(((........)))))	chr3:155655565-155655801(+)$1	1	46	64	13.6068
.((((........)))))	chr13:113832006-113832248(-)$1	1	110	128	13.7624
(((((........)))))	chr10:1063676-1063905(+)$1	1	140	158	14.8831
(((((........)))))	chr17:29109981-29110225(-)$1	1	87	105	13.4637
(((((........)))))	chr17:25639659-25639881(+)$1	1	81	99	13.4637
.((((........)))).	chr9:79000637-79000929(-)$1	1	158	176	13.9623
((.((........)).))	chr5:179044916-179045160(-)$1	1	26	44	12.9685

#PSSM
e : 0.35	! : 0.14	f : 0.14	[ : 0.06	g : 0.05	" : 0.05	d : 0.05	c : 0.04	$ : 0.02	i : 0.02	: : 0.01	# : 0.01	
e : 0.32	d : 0.18	f : 0.14	! : 0.12	g : 0.05	" : 0.04	$ : 0.02	i : 0.02	c : 0.02	a : 0.01	[ : 0.01	# : 0.01	
e : 0.32	c : 0.18	d : 0.14	f : 0.13	[ : 0.06	g : 0.05	! : 0.02	" : 0.02	i : 0.01	# : 0.01	
e : 0.31	c : 0.18	d : 0.14	b : 0.12	f : 0.12	g : 0.05	[ : 0.02	i : 0.01	! : 0.01	
e : 0.31	c : 0.18	d : 0.14	b : 0.12	f : 0.12	g : 0.05	a : 0.04	i : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.31	c : 0.18	d : 0.14	b : 0.12	f : 0.12	g : 0.05	a : 0.04	i : 0.01	
e : 0.31	c : 0.18	d : 0.14	b : 0.12	f : 0.12	g : 0.05	] : 0.02	i : 0.01	2 : 0.01	
e : 0.33	c : 0.18	d : 0.16	f : 0.13	g : 0.05	] : 0.04	4 : 0.02	a : 0.01	i : 0.01	3 : 0.01	2 : 0.01	
e : 0.33	d : 0.20	f : 0.13	g : 0.06	] : 0.06	2 : 0.05	4 : 0.04	3 : 0.04	c : 0.02	i : 0.01	h : 0.01	
e : 0.33	f : 0.13	d : 0.12	2 : 0.09	g : 0.08	4 : 0.05	3 : 0.05	c : 0.05	] : 0.02	i : 0.01	h : 0.01	: : 0.01	

#score	1039.0715210519152
#seq	74
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_CDS_m2_run2.txt

#BEAR
eeee####cccooooooccc333eeeee	chr19:37618918-37619139(+)$1	221	161	189	14.6700
"""hhhhhhhhoooooohhhhhhhh444	chr5:148886548-148886772(-)$1	224	56	84	11.0337
dd[a[ffffffooooooffffff333a]	chr1:82456547-82456774(+)$1	227	36	64	12.0677
eeeee!!ddddoooooodddd333eeee	chr14:21868962-21869185(-)$1	223	142	170	14.1604
gg[ccc[ddddooooooddddcccgggg	chr12:110781032-110781251(+)$1	219	75	103	14.0217
======"""bboooooobb=========	chr19:50154039-50154263(+)$1	224	40	68	15.2640
"cccbb[ddddoooooodddd]bb22cc	chrM:15552-15783(+)$1	231	151	179	12.8908
[ccc[bb!!bboooooobb]bbccc]ee	chr2:74435703-74435919(+)$1	216	128	156	12.8839
$$$dddd!!bboooooobbdddd]gggg	chr14:21699018-21699238(-)$1	220	78	106	11.9775
gggg]bbddddooooooddddffffff[	chr19:40478310-40478534(+)$1	224	129	157	12.4657
==========[ccclllccc4444====	chr1:222800928-222801151(+)$1	223	77	105	10.5654
eeee!!eeeeeooooooeeeeeeeeee:	chr16:18853500-18853718(-)$1	218	127	155	11.5284
eee"""eeeeeooooooeeeee4444ee	chr19:34887127-34887345(+)$1	218	24	52	12.8769
========!!cccmmmmccc22======	chr11:67256744-67256964(+)$1	220	156	184	10.3021
$$$$bb[ddddoooooodddd]bb22ff	chr20:61537155-61537377(-)$1	222	48	76	12.2830
eeee"""ddddooooooddddeeeee]f	chr5:76349754-76349977(+)$1	223	116	144	13.6476
=============mmmm===========	chr14:94528815-94529042(-)$1	227	58	86	11.1361
bb[bb!!ddddoooooodddd22bb]bb	chr14:102505908-102506129(+)$1	221	182	210	12.2295
"bb[ccc[cccooooooccc]cccbbdd	chr19:42792972-42793193(+)$1	221	88	116	12.8808
cc$$$$$ddddooooooddddcccccc:	chr10:103899606-103899816(+)$1	210	172	200	11.8476
eee!!bb[cccooooooccc]bb22eee	chr7:99697186-99697404(-)$1	218	44	72	13.3771
g[ccc"""cccooooooccc]cccgggg	chr13:42873585-42873802(+)$1	217	148	176	14.6569
h!!iiiiiiiiinnnnniiiiiiiii22	chr17:61882410-61882634(+)$1	224	180	208	9.5184
===========oooooo===========	chr4:24556256-24556476(-)$1	220	84	112	15.7303
[eeeee!!cccooooooccc]eeeee]a	chr11:43964598-43964815(+)$1	217	81	109	13.8373
iiiiiddddbboooooobb]dddd]iii	chr1:76260099-76260319(+)$1	220	89	117	12.7620
dddd[ffffffooooooffffffdddd]	chr12:49420586-49420806(-)$1	220	9	37	10.7693
ff[bb"""cccooooooccc22bb]fff	chr16:46617403-46617624(-)$1	221	50	78	13.2678
iiiiii[ddddoooooodddd22iiiii	chr11:3744470-3744693(-)$1	223	55	83	14.4917
:ddddbb[cccooooooccc333bb]dd	chr10:129899648-129899873(-)$1	225	136	164	12.0752
gggggg[a[bboooooobbaggggggg3	chr6:56354199-56354419(-)$1	220	14	42	13.6610
cc]dddd:cccoooooocccffffff[b	chr1:155450126-155450347(-)$1	221	121	149	10.8417
""ffffff[bboooooobb]ffffff22	chr12:6604195-6604405(+)$1	210	139	167	11.7762
eee!!bb[cccooooooccc]bbeeeee	chr10:70728641-70728857(+)$1	216	31	59	13.5890
eeee"""ddddoooooodddd]eeeee:	chr16:28187119-28187341(-)$1	222	29	57	13.1041
d!!bb[bb[bboooooobb]bb]bbddd	chr19:39216349-39216577(+)$1	228	70	98	11.3682
===========oooooo===========	chr10:27448551-27448769(+)$1	218	45	73	15.7303
####ccc[cccooooooccc]ccc22ee	chr5:110439489-110439709(+)$1	220	182	210	14.0596
==========bbmmmmbb]=========	chr5:56218860-56219071(-)$1	211	154	182	9.8343
##iiiiiiiiiooooooiiiiiiiii44	chr19:34832931-34833156(+)$1	225	188	216	14.6311
$$$$gggggggooooooggggggg4444	chr13:33110271-33110492(-)$1	221	174	202	13.0043
ff[ccc[ddddoooooodddd22ccc]f	chr19:47767943-47768168(+)$1	225	20	48	13.4210
[ffffffddddoooooodddd]ffffff	chr12:6635198-6635423(+)$1	225	17	45	12.6654
eeee####cccooooooccc333eeeee	chr12:133779711-133779929(+)$1	218	7	35	14.6700
eee[cccddddoooooodddd]ccc]ee	chr19:6415748-6415968(-)$1	220	170	198	13.7619
eeee!!eeeeeooooooeeeeeeeeeeB	chr11:764295-764510(+)$1	215	33	61	11.5256
eeeee[bb!!aooooooa22bbeeeeea	chr9:35061921-35062144(-)$1	223	52	80	11.7468
==[ccc!!cccooooooccc]ccc====	chr1:153640876-153641093(-)$1	217	180	208	15.2602
==========bbmmmmbb22========	chr13:110434417-110434637(-)$1	220	82	110	9.3399
============mmmm============	chr1:151271309-151271529(-)$1	220	178	206	11.1516
ffffgggggggooooooggggggg>>>>	chr11:108043699-108043923(-)$1	224	160	188	12.1182
[ffffffddddoooooodddd333ffff	chr5:112878068-112878288(+)$1	220	182	210	13.1812
:dddd[bb[bboooooobb]bb333ddd	chr1:29486793-29487003(-)$1	210	79	107	10.8419

#otherMatches

#Seq PSSM
GUGGAAAGAUGUUUAGUCAUGGCUCACA	chr19:37618918-37619139(+)$1	221	161	189	14.6700
UUUAACCCUUGAACCUAUAGGGGUUUCC	chr5:148886548-148886772(-)$1	224	56	84	11.0337
AGAGACUCUCCCUAUCCGGAGAGCAGCC	chr1:82456547-82456774(+)$1	227	36	64	12.0677
UGGUAUAUGGGUAAGACCCCAACUUACC	chr14:21868962-21869185(-)$1	223	142	170	14.1604
UGACAGAUGGCCUGCCUGCCACUGCACU	chr12:110781032-110781251(+)$1	219	75	103	14.0217
GGAGGCAAAGGCCCUGACCGCCUCUCUC	chr19:50154039-50154263(+)$1	224	40	68	15.2640
ACUAAGCCAAUCACUUUAUUGACUCCUA	chrM:15552-15783(+)$1	231	151	179	12.8908
AAUAAUCAAGCGAACUGGUAGGUAUAUC	chr2:74435703-74435919(+)$1	216	128	156	12.8839
UACGGGUCAGUAACAGAACACCCUUCUC	chr14:21699018-21699238(-)$1	220	78	106	11.9775
AGCCAUCGUGGGCUCUACCACAGGUGUG	chr19:40478310-40478534(+)$1	224	129	157	12.4657
UUCUGCAGCUACAGAUUCUGAGAAAGCU	chr1:222800928-222801151(+)$1	223	77	105	10.5654
CAAGCCAAAGAAACUUCUCUUUCUUGGA	chr16:18853500-18853718(-)$1	218	127	155	11.5284
cuuuUUAAAUGUUCUUUCAUUUUGCCAA	chr19:34887127-34887345(+)$1	218	24	52	12.8769
UCAUCUUCCACAUGGAGAUGCUGAAGGU	chr11:67256744-67256964(+)$1	220	156	184	10.3021
AGCAGCACGCCGUCGUGGGCGAGCGAUC	chr20:61537155-61537377(-)$1	222	48	76	12.2830
CAUCCUGGCAGUGAUACCUGUGAUGGCU	chr5:76349754-76349977(+)$1	223	116	144	13.6476
GUUUUUUUACUUUUAAGGAAGUGGGAAA	chr14:94528815-94529042(-)$1	227	58	86	11.1361
GGAGGAUGCCAUAUUGCUGGUGGCCCCC	chr14:102505908-102506129(+)$1	221	182	210	12.2295
UUGCAGCCCAGACACUCCUGAGCUCAGA	chr19:42792972-42793193(+)$1	221	88	116	12.8808
AGGAAGAACUUCAAAAAGAGUCUGGGCC	chr10:103899606-103899816(+)$1	210	172	200	11.8476
GGGAACAGGUGGCUCUGUAUGUGGACCU	chr7:99697186-99697404(-)$1	218	44	72	13.3771
AUCUAAUGCUUCAGAUAAAGAUAGUGAU	chr13:42873585-42873802(+)$1	217	148	176	14.6569
GUAUUAUUGGUUAUCUAAACUAAUAACC	chr17:61882410-61882634(+)$1	224	180	208	9.5184
GAAGAGGAAGAGGGAGAUCUUCUUCUUU	chr4:24556256-24556476(-)$1	220	84	112	15.7303
GAGGAGAAGGCCAAGAAGUCGUUCCUGC	chr11:43964598-43964815(+)$1	217	81	109	13.8373
AAAUAGGUGGAUCCUUUUCAUACCUUAU	chr1:76260099-76260319(+)$1	220	89	117	12.7620
AGUGCGCUGGAAGCGGCUUCGGCUGCUG	chr12:49420586-49420806(-)$1	220	9	37	10.7693
CACAGGACUUCUUAGAUGAACAUUAUGA	chr16:46617403-46617624(-)$1	221	50	78	13.2678
GAGAUGAAGAUUCCCUUGUUUCACAUUU	chr11:3744470-3744693(-)$1	223	55	83	14.4917
AGCUCCCAGCCUAAGGUGGCAGAGGAGA	chr10:129899648-129899873(-)$1	225	136	164	12.0752
CCAUGAAGCUUGGAGUAAACUUAUGGAG	chr6:56354199-56354419(-)$1	220	14	42	13.6610
GUAUGUGUGUCUCUAGUGACCUUUUGUC	chr1:155450126-155450347(-)$1	221	121	149	10.8417
AUCAGUAUGUUGUGCAAGAGGUACUGUC	chr12:6604195-6604405(+)$1	210	139	167	11.7762
AUACUAUGUAGGCUUGUUUGGAUUAUUC	chr10:70728641-70728857(+)$1	216	31	59	13.5890
CUUUAUCCGGAACAAGCUCUGCAAAGUU	chr16:28187119-28187341(-)$1	222	29	57	13.1041
CCUGAAGCAGUAUGAACGCAGCAUCGUG	chr19:39216349-39216577(+)$1	228	70	98	11.3682
AUGGUUAUUUUGAUGAAGAGAUGGCUGU	chr10:27448551-27448769(+)$1	218	45	73	15.7303
UUAAAAGUCAAUUUUUUUUGUCUUCUGG	chr5:110439489-110439709(+)$1	220	182	210	14.0596
GUAAACUUGAGGGGAGCUAUCAGGUUUG	chr5:56218860-56219071(-)$1	211	154	182	9.8343
UCCCAGCAGCCAGCGCAGGCUGUUGGAG	chr19:34832931-34833156(+)$1	225	188	216	14.6311
CCCAGUUUGAACUAUCAUUUAAACAUUC	chr13:33110271-33110492(-)$1	221	174	202	13.0043
CGAGGCAGGGCCGAGCUGCCUGGGCUGC	chr19:47767943-47768168(+)$1	225	20	48	13.4210
GUGGCUUCCUUCCCCUAGAGGAAAGCCA	chr12:6635198-6635423(+)$1	225	17	45	12.6654
UUGAAAUCACAGCUCAUUGUACAUCAGA	chr12:133779711-133779929(+)$1	218	7	35	14.6700
CGGAGGGCAGGCCCUGUUCUGUCCCCCC	chr19:6415748-6415968(-)$1	220	170	198	13.7619
UCUUUCCGUUGGUUGCACAACGAGGACC	chr11:764295-764510(+)$1	215	33	61	11.5256
CCCUCAUGGAUGGCCUAAAGCAGAGGGC	chr9:35061921-35062144(-)$1	223	52	80	11.7468
UGUCUUCCAGAAAUGUCUCUAAAGCAGU	chr1:153640876-153641093(-)$1	217	180	208	15.2602
CUCCUGGGGCCGGACCCGAAGCCUCGGG	chr13:110434417-110434637(-)$1	220	82	110	9.3399
CAGCGCAAUUUUGUGCAAAGUUGUGCUG	chr1:151271309-151271529(-)$1	220	178	206	11.1516
GAAGCUCAGGCAUCCAAGUCUGAGAAUU	chr11:108043699-108043923(-)$1	224	160	188	12.1182
AAGUAUAGUUUAAUUCAAAACGUAUGUA	chr5:112878068-112878288(+)$1	220	182	210	13.1812
CGGCCCACGGCGAGAUGGCAGUUACGGU	chr1:29486793-29487003(-)$1	210	79	107	10.8419

#DB
((((....(((......)))...)))))	chr19:37618918-37619139(+)$1	1	161	189	14.6700
...((((((((......))))))))...	chr5:148886548-148886772(-)$1	1	56	84	11.0337
((.(.((((((......))))))...).	chr1:82456547-82456774(+)$1	1	36	64	12.0677
(((((..((((......))))...))))	chr14:21868962-21869185(-)$1	1	142	170	14.1604
((.(((.((((......)))))))))))	chr12:110781032-110781251(+)$1	1	75	103	14.0217
((((((...((......)))))))))))	chr19:50154039-50154263(+)$1	1	40	68	15.2640
.(((((.((((......)))).))..))	chrM:15552-15783(+)$1	1	151	179	12.8908
.(((.((..((......)).))))).))	chr2:74435703-74435919(+)$1	1	128	156	12.8839
...((((..((......)))))).))))	chr14:21699018-21699238(-)$1	1	78	106	11.9775
)))).))((((......))))((((((.	chr19:40478310-40478534(+)$1	1	129	157	12.4657
((((((((((.(((...)))....))))	chr1:222800928-222801151(+)$1	1	77	105	10.5654
((((..(((((......)))))))))).	chr16:18853500-18853718(-)$1	1	127	155	11.5284
(((...(((((......)))))....))	chr19:34887127-34887345(+)$1	1	24	52	12.8769
((((((((..(((....)))..))))))	chr11:67256744-67256964(+)$1	1	156	184	10.3021
....((.((((......)))).))..))	chr20:61537155-61537377(-)$1	1	48	76	12.2830
((((...((((......))))))))).)	chr5:76349754-76349977(+)$1	1	116	144	13.6476
(((((((((((((....)))))))))))	chr14:94528815-94529042(-)$1	1	58	86	11.1361
((.((..((((......))))..)).))	chr14:102505908-102506129(+)$1	1	182	210	12.2295
.((.(((.(((......))).)))))))	chr19:42792972-42793193(+)$1	1	88	116	12.8808
((.....((((......)))))))))).	chr10:103899606-103899816(+)$1	1	172	200	11.8476
(((..((.(((......))).))..)))	chr7:99697186-99697404(-)$1	1	44	72	13.3771
(.(((...(((......))).)))))))	chr13:42873585-42873802(+)$1	1	148	176	14.6569
(..(((((((((.....)))))))))..	chr17:61882410-61882634(+)$1	1	180	208	9.5184
(((((((((((......)))))))))))	chr4:24556256-24556476(-)$1	1	84	112	15.7303
.(((((..(((......))).))))).)	chr11:43964598-43964815(+)$1	1	81	109	13.8373
(((((((((((......)).)))).)))	chr1:76260099-76260319(+)$1	1	89	117	12.7620
((((.((((((......)))))))))).	chr12:49420586-49420806(-)$1	1	9	37	10.7693
((.((...(((......)))..)).)))	chr16:46617403-46617624(-)$1	1	50	78	13.2678
((((((.((((......))))..)))))	chr11:3744470-3744693(-)$1	1	55	83	14.4917
.((((((.(((......)))...)).))	chr10:129899648-129899873(-)$1	1	136	164	12.0752
((((((.(.((......)))))))))).	chr6:56354199-56354419(-)$1	1	14	42	13.6610
)).)))).(((......)))((((((.(	chr1:155450126-155450347(-)$1	1	121	149	10.8417
..((((((.((......)).))))))..	chr12:6604195-6604405(+)$1	1	139	167	11.7762
(((..((.(((......))).)))))))	chr10:70728641-70728857(+)$1	1	31	59	13.5890
((((...((((......)))).))))).	chr16:28187119-28187341(-)$1	1	29	57	13.1041
(..((.((.((......)).)).)))))	chr19:39216349-39216577(+)$1	1	70	98	11.3682
(((((((((((......)))))))))))	chr10:27448551-27448769(+)$1	1	45	73	15.7303
....(((.(((......))).)))..))	chr5:110439489-110439709(+)$1	1	182	210	14.0596
((((((((((((....)).)))))))))	chr5:56218860-56219071(-)$1	1	154	182	9.8343
..(((((((((......)))))))))..	chr19:34832931-34833156(+)$1	1	188	216	14.6311
....(((((((......)))))))....	chr13:33110271-33110492(-)$1	1	174	202	13.0043
((.(((.((((......))))..))).)	chr19:47767943-47768168(+)$1	1	20	48	13.4210
.((((((((((......)))).))))))	chr12:6635198-6635423(+)$1	1	17	45	12.6654
((((....(((......)))...)))))	chr12:133779711-133779929(+)$1	1	7	35	14.6700
(((.(((((((......)))).))).))	chr19:6415748-6415968(-)$1	1	170	198	13.7619
((((..(((((......))))))))))(	chr11:764295-764510(+)$1	1	33	61	11.5256
(((((.((..(......)..))))))))	chr9:35061921-35062144(-)$1	1	52	80	11.7468
((.(((..(((......))).)))))))	chr1:153640876-153641093(-)$1	1	180	208	15.2602
((((((((((((....))..))))))))	chr13:110434417-110434637(-)$1	1	82	110	9.3399
((((((((((((....))))))))))))	chr1:151271309-151271529(-)$1	1	178	206	11.1516
(((((((((((......)))))))....	chr11:108043699-108043923(-)$1	1	160	188	12.1182
.((((((((((......))))...))))	chr5:112878068-112878288(+)$1	1	182	210	13.1812
.((((.((.((......)).))...)))	chr1:29486793-29487003(-)$1	1	79	107	10.8419

#PSSM
e : 0.22	= : 0.18	" : 0.07	g : 0.07	[ : 0.07	d : 0.05	$ : 0.05	f : 0.05	c : 0.03	i : 0.03	: : 0.03	# : 0.03	b : 0.01	h : 0.01	
e : 0.24	= : 0.18	f : 0.09	d : 0.07	c : 0.07	g : 0.05	$ : 0.05	" : 0.03	b : 0.03	! : 0.03	i : 0.03	# : 0.03	[ : 0.01	
e : 0.24	= : 0.16	[ : 0.11	$ : 0.07	f : 0.07	c : 0.05	i : 0.05	d : 0.05	g : 0.03	! : 0.03	" : 0.01	b : 0.01	] : 0.01	# : 0.01	
e : 0.16	= : 0.16	c : 0.11	d : 0.09	i : 0.07	f : 0.07	$ : 0.05	b : 0.05	g : 0.03	[ : 0.03	! : 0.03	h : 0.01	a : 0.01	" : 0.01	# : 0.01	
= : 0.16	c : 0.13	b : 0.09	d : 0.07	! : 0.07	i : 0.07	[ : 0.05	e : 0.05	" : 0.05	g : 0.05	f : 0.05	# : 0.03	h : 0.01	] : 0.01	$ : 0.01	
= : 0.16	b : 0.13	c : 0.11	f : 0.09	" : 0.09	! : 0.07	d : 0.05	i : 0.05	g : 0.05	[ : 0.05	# : 0.03	h : 0.01	$ : 0.01	e : 0.01	
b : 0.15	= : 0.15	[ : 0.11	f : 0.09	" : 0.09	! : 0.07	d : 0.05	e : 0.05	c : 0.05	# : 0.03	i : 0.03	g : 0.03	h : 0.01	$ : 0.01	
d : 0.28	= : 0.15	[ : 0.09	! : 0.07	f : 0.05	" : 0.05	e : 0.05	b : 0.05	# : 0.03	i : 0.03	g : 0.03	h : 0.01	a : 0.01	: : 0.01	
d : 0.28	c : 0.22	= : 0.13	! : 0.07	[ : 0.07	e : 0.05	f : 0.03	i : 0.03	g : 0.03	h : 0.01	" : 0.01	
d : 0.26	c : 0.22	b : 0.15	= : 0.13	e : 0.05	f : 0.03	! : 0.03	i : 0.03	g : 0.03	h : 0.01	
d : 0.26	c : 0.24	b : 0.18	= : 0.07	e : 0.05	f : 0.03	i : 0.03	g : 0.03	h : 0.01	[ : 0.01	a : 0.01	
o : 0.86	c : 0.03	= : 0.03	b : 0.03	i : 0.01	
o : 0.86	m : 0.05	c : 0.03	= : 0.01	n : 0.01	
o : 0.86	m : 0.09	c : 0.01	n : 0.01	
o : 0.86	m : 0.09	l : 0.01	n : 0.01	
o : 0.86	m : 0.09	l : 0.01	n : 0.01	
o : 0.86	m : 0.03	b : 0.03	l : 0.01	n : 0.01	= : 0.01	
c : 0.26	d : 0.26	b : 0.18	= : 0.07	e : 0.05	f : 0.03	i : 0.03	g : 0.03	h : 0.01	a : 0.01	
c : 0.26	d : 0.26	b : 0.15	= : 0.07	e : 0.05	f : 0.03	i : 0.03	g : 0.03	2 : 0.03	h : 0.01	] : 0.01	
d : 0.28	c : 0.26	= : 0.11	] : 0.09	e : 0.05	f : 0.03	i : 0.03	g : 0.03	2 : 0.03	h : 0.01	a : 0.01	
d : 0.30	= : 0.13	] : 0.13	f : 0.07	b : 0.07	3 : 0.05	e : 0.05	g : 0.05	2 : 0.03	i : 0.03	h : 0.01	4 : 0.01	
= : 0.13	c : 0.11	b : 0.11	3 : 0.09	f : 0.09	] : 0.09	e : 0.09	2 : 0.09	g : 0.05	d : 0.03	i : 0.03	h : 0.01	4 : 0.01	
c : 0.15	= : 0.15	3 : 0.11	f : 0.11	e : 0.11	b : 0.09	2 : 0.05	g : 0.05	d : 0.03	4 : 0.03	i : 0.03	h : 0.01	] : 0.01	
e : 0.16	c : 0.16	= : 0.15	b : 0.11	3 : 0.07	f : 0.07	i : 0.05	g : 0.05	4 : 0.03	d : 0.03	h : 0.01	] : 0.01	2 : 0.01	
e : 0.18	= : 0.18	f : 0.09	g : 0.07	2 : 0.07	c : 0.07	b : 0.07	i : 0.05	3 : 0.03	4 : 0.03	] : 0.03	h : 0.01	d : 0.01	> : 0.01	
e : 0.20	= : 0.18	f : 0.11	g : 0.07	] : 0.07	i : 0.07	4 : 0.05	2 : 0.05	d : 0.05	c : 0.03	3 : 0.01	b : 0.01	> : 0.01	
e : 0.24	= : 0.18	f : 0.09	d : 0.09	g : 0.07	4 : 0.05	] : 0.05	c : 0.03	2 : 0.03	i : 0.03	a : 0.01	b : 0.01	[ : 0.01	> : 0.01	
= : 0.18	e : 0.16	f : 0.11	d : 0.07	4 : 0.05	g : 0.05	: : 0.05	] : 0.03	b : 0.03	2 : 0.03	a : 0.03	i : 0.03	c : 0.01	[ : 0.01	3 : 0.01	B : 0.01	> : 0.01	

#score	672.5051687123638
#seq	53
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_CDS_m3_run1.txt

#BEAR
eeeeooooooeeeee	chr2:96852457-96852697(-)$1	240	14	29	11.2358
ggggooooooggggg	chr16:22092020-22092316(+)$1	296	38	53	10.1472
eebboooooobb]ee	chr3:179052053-179052293(+)$1	240	203	218	10.5357
ddddooooooddddf	chr4:77969378-77969618(-)$1	240	198	213	10.6804
[cccooooooccc]c	chr1:78097630-78097870(-)$1	240	161	176	10.0510
dd[aooooooa]ddd	chr12:99117368-99117608(+)$1	240	99	114	10.3059
eeeeooooooeeeee	chr14:50074268-50074508(+)$1	240	86	101	11.2358
ffffoooooofffff	chr5:149360846-149361086(+)$1	240	192	207	9.9998
ee[aooooooaeeee	chr6:53787389-53787629(+)$1	240	67	82	11.0484
ffffoooooofffff	chr6:30309523-30309763(+)$1	240	111	126	9.9998
eeeeooooooeeeee	chr20:49194870-49195110(+)$1	240	172	187	11.2358
eeeeooooooeeeee	chr8:38961049-38961289(+)$1	240	16	31	11.2358
ffffoooooofffff	chr3:93802889-93803129(+)$1	240	63	78	9.9998
ccccoooooocccff	chr17:17163562-17163802(-)$1	240	85	100	10.1784
eeeeooooooeeeee	chr6:166796195-166796435(-)$1	240	41	56	11.2358
f[bboooooobb]ff	chr7:127014556-127014796(-)$1	240	10	25	9.9424
eeeeooooooeeeee	chr13:77657189-77657429(-)$1	240	91	106	11.2358
[cccooooooccc]d	chr19:6751180-6751432(+)$1	252	199	214	10.0445
eeeeooooooeeeee	chr5:38964853-38965093(-)$1	240	87	102	11.2358
ddddoooooodddd2	chr22:50216947-50217187(-)$1	240	166	181	10.4198
ddddooooooddddd	chr2:20453599-20453839(-)$1	240	188	203	10.5833
ggggooooooggggg	chr20:39832137-39832377(-)$1	240	16	31	10.1472
ddddoooooodddd]	chr13:41381373-41381613(+)$1	240	107	122	10.7134
f[bboooooobb]ff	chr4:113538805-113539045(-)$1	240	155	170	9.9424
ee[aooooooa]eee	chr17:27237223-27237463(-)$1	240	221	236	10.8619
ffffoooooofffff	chr6:127648063-127648303(-)$1	240	172	187	9.9998
ddddoooooodddd:	chr1:114308444-114308724(-)$1	280	229	244	9.6722
eeeeooooooeeeee	chr12:110924115-110924355(+)$1	240	106	121	11.2358
ee[aooooooa]eee	chr19:44470094-44470334(+)$1	240	222	237	10.8619
""bboooooobbfff	chr13:39586155-39586395(-)$1	240	170	185	9.5404
ddddoooooodddd:	chr12:118476019-118476259(-)$1	240	200	215	9.6722
ddddoooooodddd]	chr16:28187196-28187443(-)$1	247	138	153	10.7134
g[bboooooobb]gg	chrX:16857890-16858130(+)$1	240	132	147	9.9404
ddddooooooddddi	chrX:48340728-48340968(+)$1	240	74	89	10.6203
ddddoooooodddd]	chr10:30602718-30602958(-)$1	240	43	58	10.7134
ddddoooooodddd:	chr15:81046570-81046853(+)$1	283	267	282	9.6722
ddbboooooobb]dd	chr8:26223764-26224004(+)$1	240	199	214	10.0607
[cccooooooccc22	chr22:41832681-41832921(-)$1	240	218	233	9.6072
eeeeooooooeeeee	chr13:108862985-108863225(-)$1	240	148	163	11.2358
eeeeooooooeeeee	chr6:146126827-146127067(-)$1	240	164	179	11.2358
c[bboooooobb]cc	chr19:10940878-10941118(+)$1	240	181	196	9.7674
eeeeooooooeeeee	chr10:112661170-112661410(-)$1	240	28	43	11.2358
ffffoooooofffff	chr9:133577522-133577762(+)$1	240	197	212	9.9998
ddddoooooodddd]	chr1:220311222-220311462(+)$1	240	166	181	10.7134
ddddoooooodddd]	chr4:88370234-88370474(+)$1	240	95	110	10.7134
eeeeooooooeeeee	chr16:14678106-14678346(-)$1	240	26	41	11.2358
e[bboooooobbeee	chr19:50985746-50985986(+)$1	240	4	19	10.4942
ddddooooooddddd	chr6:43141702-43141942(+)$1	240	89	104	10.5833
ffffoooooofffff	chr10:75884130-75884370(-)$1	240	222	237	9.9998
eebboooooobb]ee	chr17:79990572-79990930(+)$1	358	332	347	10.5357
ggggooooooggggg	chr8:91643793-91644033(-)$1	240	85	100	10.1472
ffffoooooofffff	chr1:229771443-229771685(+)$1	242	4	19	9.9998
ffbboooooobb]ff	chr13:39262819-39263059(+)$1	240	15	30	9.8826
:cccoooooocccdd	chr21:33038661-33038909(+)$1	248	104	119	9.1157
eeeeooooooeeeee	chr20:55091900-55092140(+)$1	240	76	91	11.2358
eeeeooooooeeeee	chr6:112021284-112021524(-)$1	240	72	87	11.2358
ddddooooooddddd	chr6:116599955-116600195(-)$1	240	99	114	10.5833

#otherMatches

#Seq PSSM
UCAGCUUAACCUGAU	chr2:96852457-96852697(-)$1	240	14	29	11.2358
UUUACAUCAAUGAAG	chr16:22092020-22092316(+)$1	296	38	53	10.1472
UCCUUUUUUUGGAGA	chr3:179052053-179052293(+)$1	240	203	218	10.5357
GGGACAUGCUUCCCC	chr4:77969378-77969618(-)$1	240	198	213	10.6804
CUCAAAAUAAUGGAA	chr1:78097630-78097870(-)$1	240	161	176	10.0510
GGUACAGUACUUUCU	chr12:99117368-99117608(+)$1	240	99	114	10.3059
CUUUGCUUAAAAAGC	chr14:50074268-50074508(+)$1	240	86	101	11.2358
UUGGUGGAAUCCAGG	chr5:149360846-149361086(+)$1	240	192	207	9.9998
CCACACCCAGGGGAG	chr6:53787389-53787629(+)$1	240	67	82	11.0484
GAGGGUUUCACCUCA	chr6:30309523-30309763(+)$1	240	111	126	9.9998
CUUUCUUUUCAAAGU	chr20:49194870-49195110(+)$1	240	172	187	11.2358
AAUAUGGCAUUAUUU	chr8:38961049-38961289(+)$1	240	16	31	11.2358
AGAUACUAACAUCUC	chr3:93802889-93803129(+)$1	240	63	78	9.9998
GGUGAAUAAGCACAG	chr17:17163562-17163802(-)$1	240	85	100	10.1784
GACCACUCGGGGUCU	chr6:166796195-166796435(-)$1	240	41	56	11.2358
GAAGUUGCACCUACA	chr7:127014556-127014796(-)$1	240	10	25	9.9424
UUCUGCCUUAGGAGA	chr13:77657189-77657429(-)$1	240	91	106	11.2358
CCGGACGGACCCGCU	chr19:6751180-6751432(+)$1	252	199	214	10.0445
GCUUCAUUUUAGGCA	chr5:38964853-38965093(-)$1	240	87	102	11.2358
GAGGAACAUCCCUCC	chr22:50216947-50217187(-)$1	240	166	181	10.4198
GCCAAUUACGUGGUU	chr2:20453599-20453839(-)$1	240	188	203	10.5833
CUGGCAAUGUCCAGC	chr20:39832137-39832377(-)$1	240	16	31	10.1472
GUUCUACCAUGGACU	chr13:41381373-41381613(+)$1	240	107	122	10.7134
AAAAAGCAUCUUAUU	chr4:113538805-113539045(-)$1	240	155	170	9.9424
UGCGCAUGUACACAC	chr17:27237223-27237463(-)$1	240	221	236	10.8619
AUUAUGCAUUUGAUU	chr6:127648063-127648303(-)$1	240	172	187	9.9998
UUCUAUAAAGAGAAA	chr1:114308444-114308724(-)$1	280	229	244	9.6722
GUACAUGCACGUACU	chr12:110924115-110924355(+)$1	240	106	121	11.2358
GGGAGAAAAAUGCUA	chr19:44470094-44470334(+)$1	240	222	237	10.8619
CAGCAGGUAAGCAGC	chr13:39586155-39586395(-)$1	240	170	185	9.5404
AGACAUGGAGGUCUG	chr12:118476019-118476259(-)$1	240	200	215	9.6722
CGGAACAAGCUCUGC	chr16:28187196-28187443(-)$1	247	138	153	10.7134
UGCAAAUGGCUGAAG	chrX:16857890-16858130(+)$1	240	132	147	9.9404
ACCAGCUGGAUGGUC	chrX:48340728-48340968(+)$1	240	74	89	10.6203
UGUAAUAAUCUAUAG	chr10:30602718-30602958(-)$1	240	43	58	10.7134
AUCAAAGAGCUGAUG	chr15:81046570-81046853(+)$1	283	267	282	9.6722
AAAGAAACAACUAUU	chr8:26223764-26224004(+)$1	240	199	214	10.0607
AGCCUCGCAUGGCCC	chr22:41832681-41832921(-)$1	240	218	233	9.6072
ACUUGAGCAAAAGUG	chr13:108862985-108863225(-)$1	240	148	163	11.2358
UGUCCCAAAUGACAU	chr6:146126827-146127067(-)$1	240	164	179	11.2358
GCCAACCCCCUGCCC	chr19:10940878-10941118(+)$1	240	181	196	9.7674
UUCUCAUUGAAGGAA	chr10:112661170-112661410(-)$1	240	28	43	11.2358
UUCAGUGGGAUGGAG	chr9:133577522-133577762(+)$1	240	197	212	9.9998
AGAACUAUUAUUCUU	chr1:220311222-220311462(+)$1	240	166	181	10.7134
UCCUGUUUCUGGGAA	chr4:88370234-88370474(+)$1	240	95	110	10.7134
AGAUGAUGAAAUCUC	chr16:14678106-14678346(-)$1	240	26	41	11.2358
CAUGCAGCCCCAGGG	chr19:50985746-50985986(+)$1	240	4	19	10.4942
UUUGAAGAGACAGAU	chr6:43141702-43141942(+)$1	240	89	104	10.5833
UGCUAUUUCAGGUAA	chr10:75884130-75884370(-)$1	240	222	237	9.9998
CCCUGUGGGGAGAGG	chr17:79990572-79990930(+)$1	358	332	347	10.5357
UCUACUCUUCUAGAU	chr8:91643793-91644033(-)$1	240	85	100	10.1472
UACUAAACUCAGUGG	chr1:229771443-229771685(+)$1	242	4	19	9.9998
GGUCAGUCUCGGCCC	chr13:39262819-39263059(+)$1	240	15	30	9.8826
UACCAGUGCAGGUCC	chr21:33038661-33038909(+)$1	248	104	119	9.1157
CUAUCUUUUUGUAGA	chr20:55091900-55092140(+)$1	240	76	91	11.2358
CUGCCGCCUAGUAGU	chr6:112021284-112021524(-)$1	240	72	87	11.2358
AUGUUAAGGUACAUA	chr6:116599955-116600195(-)$1	240	99	114	10.5833

#DB
((((......)))))	chr2:96852457-96852697(-)$1	1	14	29	11.2358
((((......)))))	chr16:22092020-22092316(+)$1	1	38	53	10.1472
((((......)).))	chr3:179052053-179052293(+)$1	1	203	218	10.5357
((((......)))))	chr4:77969378-77969618(-)$1	1	198	213	10.6804
.(((......))).)	chr1:78097630-78097870(-)$1	1	161	176	10.0510
((.(......).)))	chr12:99117368-99117608(+)$1	1	99	114	10.3059
((((......)))))	chr14:50074268-50074508(+)$1	1	86	101	11.2358
((((......)))))	chr5:149360846-149361086(+)$1	1	192	207	9.9998
((.(......)))))	chr6:53787389-53787629(+)$1	1	67	82	11.0484
((((......)))))	chr6:30309523-30309763(+)$1	1	111	126	9.9998
((((......)))))	chr20:49194870-49195110(+)$1	1	172	187	11.2358
((((......)))))	chr8:38961049-38961289(+)$1	1	16	31	11.2358
((((......)))))	chr3:93802889-93803129(+)$1	1	63	78	9.9998
)(((......)))((	chr17:17163562-17163802(-)$1	1	85	100	10.1784
((((......)))))	chr6:166796195-166796435(-)$1	1	41	56	11.2358
(.((......)).))	chr7:127014556-127014796(-)$1	1	10	25	9.9424
((((......)))))	chr13:77657189-77657429(-)$1	1	91	106	11.2358
.(((......))).)	chr19:6751180-6751432(+)$1	1	199	214	10.0445
((((......)))))	chr5:38964853-38965093(-)$1	1	87	102	11.2358
((((......)))).	chr22:50216947-50217187(-)$1	1	166	181	10.4198
((((......))))(	chr2:20453599-20453839(-)$1	1	188	203	10.5833
((((......)))))	chr20:39832137-39832377(-)$1	1	16	31	10.1472
((((......)))).	chr13:41381373-41381613(+)$1	1	107	122	10.7134
(.((......)).))	chr4:113538805-113539045(-)$1	1	155	170	9.9424
((.(......).)))	chr17:27237223-27237463(-)$1	1	221	236	10.8619
((((......)))))	chr6:127648063-127648303(-)$1	1	172	187	9.9998
((((......)))).	chr1:114308444-114308724(-)$1	1	229	244	9.6722
((((......)))))	chr12:110924115-110924355(+)$1	1	106	121	11.2358
((.(......).)))	chr19:44470094-44470334(+)$1	1	222	237	10.8619
..((......)))))	chr13:39586155-39586395(-)$1	1	170	185	9.5404
((((......)))).	chr12:118476019-118476259(-)$1	1	200	215	9.6722
((((......)))).	chr16:28187196-28187443(-)$1	1	138	153	10.7134
(.((......)).))	chrX:16857890-16858130(+)$1	1	132	147	9.9404
((((......))))(	chrX:48340728-48340968(+)$1	1	74	89	10.6203
((((......)))).	chr10:30602718-30602958(-)$1	1	43	58	10.7134
((((......)))).	chr15:81046570-81046853(+)$1	1	267	282	9.6722
((((......)).))	chr8:26223764-26224004(+)$1	1	199	214	10.0607
.(((......)))..	chr22:41832681-41832921(-)$1	1	218	233	9.6072
((((......)))))	chr13:108862985-108863225(-)$1	1	148	163	11.2358
((((......)))))	chr6:146126827-146127067(-)$1	1	164	179	11.2358
(.((......)).))	chr19:10940878-10941118(+)$1	1	181	196	9.7674
((((......)))))	chr10:112661170-112661410(-)$1	1	28	43	11.2358
((((......)))))	chr9:133577522-133577762(+)$1	1	197	212	9.9998
((((......)))).	chr1:220311222-220311462(+)$1	1	166	181	10.7134
((((......)))).	chr4:88370234-88370474(+)$1	1	95	110	10.7134
((((......)))))	chr16:14678106-14678346(-)$1	1	26	41	11.2358
(.((......)))))	chr19:50985746-50985986(+)$1	1	4	19	10.4942
((((......))))(	chr6:43141702-43141942(+)$1	1	89	104	10.5833
((((......)))))	chr10:75884130-75884370(-)$1	1	222	237	9.9998
((((......)).))	chr17:79990572-79990930(+)$1	1	332	347	10.5357
((((......)))))	chr8:91643793-91644033(-)$1	1	85	100	10.1472
((((......)))))	chr1:229771443-229771685(+)$1	1	4	19	9.9998
((((......)).))	chr13:39262819-39263059(+)$1	1	15	30	9.8826
.(((......)))((	chr21:33038661-33038909(+)$1	1	104	119	9.1157
((((......)))))	chr20:55091900-55092140(+)$1	1	76	91	11.2358
((((......)))))	chr6:112021284-112021524(-)$1	1	72	87	11.2358
((((......))))(	chr6:116599955-116600195(-)$1	1	99	114	10.5833

#PSSM
e : 0.35	d : 0.28	f : 0.17	g : 0.07	[ : 0.05	c : 0.03	" : 0.01	: : 0.01	
e : 0.33	d : 0.28	f : 0.14	c : 0.08	[ : 0.08	g : 0.05	" : 0.01	
e : 0.24	d : 0.24	b : 0.17	f : 0.12	c : 0.08	[ : 0.07	g : 0.05	
e : 0.24	d : 0.24	b : 0.17	f : 0.12	c : 0.08	a : 0.07	g : 0.05	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
e : 0.24	d : 0.24	b : 0.17	f : 0.12	c : 0.08	a : 0.07	g : 0.05	
e : 0.26	d : 0.24	b : 0.17	f : 0.12	c : 0.08	g : 0.05	] : 0.05	
e : 0.31	d : 0.26	] : 0.14	f : 0.14	c : 0.08	g : 0.05	
e : 0.35	d : 0.29	f : 0.21	g : 0.07	] : 0.03	2 : 0.01	c : 0.01	
e : 0.35	f : 0.22	d : 0.12	] : 0.08	g : 0.07	: : 0.05	c : 0.03	2 : 0.03	i : 0.01	

#score	596.5144013043937
#seq	57
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_UTR_m1_run2.txt

#BEAR
#eeeeewwwwwwwwwwwwwweee	chr7:44618654-44618877(-)$1	223	62	85	21.8907
======xxxxxxxxxxxxxxx==	chr12:92537389-92537610(-)$1	221	138	161	18.1904
eeeeevvvvvvvvvvvvveeeee	chr1:234742058-234742292(-)$1	234	152	175	21.7683
======wwwwwwwwwwwwww===	chr13:98119614-98119852(+)$1	238	33	56	22.6434
ee[ddddtttttttttttdddd]	chr2:217069868-217070102(+)$1	234	19	42	21.2517
ddd[ccctttttttttttccc]d	chr3:41281598-41281844(+)$1	246	62	85	21.7951
cc[cccuuuuuuuuuuuuccc22	chr7:44867470-44867733(-)$1	263	42	65	22.9630
gg!!bbwwwwwwwwwwwwwwbb]	chr5:71501660-71501988(+)$1	328	292	315	21.5675
[eeeeeyyyyyyyyyyyyyyyye	chr14:50085309-50085551(-)$1	242	112	135	21.3561
fffffvvvvvvvvvvvvvfffff	chr10:124923435-124923727(+)$1	292	175	198	21.3099
ggg[ccctttttttttttcccgg	chr15:77338334-77338607(-)$1	273	235	258	22.4167
iiiiiiitttttttttttiiiii	chr19:39327205-39327432(-)$1	227	131	154	21.8295
hhh[bbvvvvvvvvvvvvvbbhh	chr8:41368214-41368472(+)$1	258	208	231	21.2433
"fffffftttttttttttfffff	chrX:47495607-47495844(-)$1	237	169	192	20.8944
e"""bbuuuuuuuuuuuubb333	chr8:10753593-10753816(-)$1	223	117	140	22.5315
gggggguuuuuuuuuuuuggggg	chr11:92625054-92625284(+)$1	230	45	68	23.1280
ggggggvvvvvvvvvvvvvgggg	chr6:144150771-144150998(+)$1	227	167	190	22.9797
ffffffuuuuuuuuuuuufffff	chr8:67834132-67834354(-)$1	222	136	159	22.1093
gggggggtttttttttttggggg	chr10:74034843-74035066(+)$1	223	198	221	21.7674
!!dddduuuuuuuuuuuudddd]	chr1:173859372-173859601(+)$1	229	27	50	22.5956
e[ddddvvvvvvvvvvvvvdddd	chr4:83276373-83276622(-)$1	249	45	68	22.2035
[eeeeeyyyyyyyyyyyyyyyye	chr12:111158136-111158407(-)$1	271	145	168	21.3561
iiiiiiitttttttttttiiiii	chr3:14239697-14239945(+)$1	248	194	217	21.8295
ggggggvvvvvvvvvvvvvgggg	chr7:75958535-75958782(-)$1	247	44	67	22.9797
gggggggtttttttttttggggg	chr18:673269-673499(+)$1	230	10	33	21.7674
ffffffyyyyyyyyyyyyyyyyf	chr10:5498832-5499072(+)$1	240	155	178	20.8766
b!!cccvvvvvvvvvvvvvccc2	chr22:26888021-26888258(-)$1	237	78	101	22.7186
ddddyyyyyyyyyyyyyyyyddd	chr11:33730493-33730769(-)$1	276	46	69	20.6218
""ddddyyyyyyyyyyyyyyyyd	chr12:6601333-6601613(-)$1	280	86	109	21.0232
eeeeewwwwwwwwwwwwwweeee	chr17:26654415-26654656(+)$1	241	15	38	21.7313
eeeebbvvvvvvvvvvvvvbb]e	chr9:130507064-130507302(-)$1	238	146	169	22.2165
ffffffuuuuuuuuuuuufffff	chr10:21781553-21781782(-)$1	229	40	63	22.1093
dd[cccuuuuuuuuuuuuccc]d	chr2:219103305-219103546(+)$1	241	185	208	23.0585
a!!bbvvvvvvvvvvvvvbb22a	chr22:29696274-29696501(+)$1	227	71	94	21.2230
:ddddwwwwwwwwwwwwwwdddd	chrX:24024652-24024914(-)$1	262	231	254	20.3245
"""cccvvvvvvvvvvvvvccc2	chr3:38531507-38531741(+)$1	234	170	193	22.7772
eeeeeyyyyyyyyyyyyyyyyee	chr12:109540581-109540832(+)$1	251	22	45	21.4992
$ddddvvvvvvvvvvvvvdddd4	chr7:103008459-103008688(+)$1	229	81	104	21.2004
d!!cccuuuuuuuuuuuuccc22	chr14:70795792-70796020(-)$1	228	149	172	23.0457
ggggggxxxxxxxxxxxxxxxgg	chr13:21721469-21721696(+)$1	227	10	33	17.9440
[eeeeewwwwwwwwwwwwwweee	chr10:70742698-70742923(+)$1	225	176	199	21.9939
=======ttttttttttt=====	chr7:26251621-26251850(+)$1	229	60	83	22.3756
ffffffwwwwwwwwwwwwwwfff	chr14:73742039-73742263(-)$1	224	198	221	21.4025
bbyyyyyyyyyyyyyyyybb===	chr2:48027111-48027384(+)$1	273	187	210	19.0395
'''cccvvvvvvvvvvvvvccc9	chr4:83345817-83346053(-)$1	236	149	172	20.2984
GGGcccuuuuuuuuuuuuccc::	chr21:34889758-34889986(-)$1	228	38	61	19.7103
!eeeeevvvvvvvvvvvvveeee	chr19:44515158-44515385(+)$1	227	89	112	22.5760
::ddddvvvvvvvvvvvvvdddd	chr18:649742-649969(-)$1	227	69	92	20.1360
eeeeewwwwwwwwwwwwwweeee	chr5:41918314-41918538(+)$1	224	77	100	21.7313
eee!!bbtttttttttttbb22e	chr5:71505039-71505307(+)$1	268	108	131	21.1307
======vvvvvvvvvvvvv====	chr15:78461274-78461497(+)$1	223	108	131	23.3288
b:ddddwwwwwwwwwwwwwwddd	chr12:57927653-57927882(-)$1	229	15	38	20.2976
eeee[bbtttttttttttbb]ee	chr12:53808433-53808681(+)$1	248	211	234	21.3549
c"""bbyyyyyyyyyyyyyyyyb	chr20:32676017-32676288(-)$1	271	155	178	20.6195
fffffvvvvvvvvvvvvvfffff	chr19:37001898-37002150(-)$1	252	63	86	21.3099
======uuuuuuuuuuuu=====	chr22:40731014-40731253(+)$1	239	8	31	23.6098
eeeeeyyyyyyyyyyyyyyyyee	chr2:55199728-55199951(-)$1	223	3	26	21.4992
gggggguuuuuuuuuuuuggggg	chr20:11906966-11907187(+)$1	221	189	212	23.1280
dddd[bbtttttttttttbb]dd	chr7:40172279-40172507(-)$1	228	25	48	20.8332
ii[cccuuuuuuuuuuuuccc]i	chr5:68473945-68474173(+)$1	228	95	118	23.5144
ffffffuuuuuuuuuuuufffff	chr1:150547894-150548147(-)$1	253	115	138	22.1093
gggggggtttttttttttggggg	chr20:55982992-55983222(+)$1	230	8	31	21.7674
ddddddvvvvvvvvvvvvvdddd	chr6:4133754-4134027(-)$1	273	113	136	21.8871
ggggggxxxxxxxxxxxxxxxgg	chr1:203770315-203770541(+)$1	226	96	119	17.9440
h!!ddddtttttttttttdddd7	chr1:145442161-145442474(+)$1	313	143	166	20.5280

#otherMatches

#Seq PSSM
GAGUGAUUUUCCUCUGUUUUUCA	chr7:44618654-44618877(-)$1	223	62	85	21.8907
GUUGUUAUUGUUAACCUUUUCGG	chr12:92537389-92537610(-)$1	221	138	161	18.1904
AGUUGGUUACAUAAGAUACAAUU	chr1:234742058-234742292(-)$1	234	152	175	21.7683
CUACAGUUGCCAUCACCUUUCUG	chr13:98119614-98119852(+)$1	238	33	56	22.6434
AAGUGUGUUGUUCUUGUUCACAG	chr2:217069868-217070102(+)$1	234	19	42	21.2517
UUUGUAUAAAAUAGACAAAUAGA	chr3:41281598-41281844(+)$1	246	62	85	21.7951
CUUCAAAAAAUAUACUAAUUGCU	chr7:44867470-44867733(-)$1	263	42	65	22.9630
UUAACUGAAGCAAAUACCAAAGC	chr5:71501660-71501988(+)$1	328	292	315	21.5675
AGGGAAAAUAAAUACAGUGAUAU	chr14:50085309-50085551(-)$1	242	112	135	21.3561
AAUCAGUUUUGACCUUGAUGAUU	chr10:124923435-124923727(+)$1	292	175	198	21.3099
CAACAUAUUAUUUUUCAUUAUUU	chr15:77338334-77338607(-)$1	273	235	258	22.4167
UUUUUGUUUUUGUUAUUUGCAAA	chr19:39327205-39327432(-)$1	227	131	154	21.8295
UAGUGUGUCUGCAUUUUCAACCU	chr8:41368214-41368472(+)$1	258	208	231	21.2433
GCCAAGGAAGAAUCACACCCUUG	chrX:47495607-47495844(-)$1	237	169	192	20.8944
GCAUCGUUUCAAUCGCAUCGUAU	chr8:10753593-10753816(-)$1	223	117	140	22.5315
AAGUUGGCUUUGUUCAUAUAGCU	chr11:92625054-92625284(+)$1	230	45	68	23.1280
AAAGGUGGUUAUAUUGUAAGCUU	chr6:144150771-144150998(+)$1	227	167	190	22.9797
UUUGGCUAACUUUUAAUUGCUGA	chr8:67834132-67834354(-)$1	222	136	159	22.1093
GUGGUUGGAAAACUGAGGCAGCC	chr10:74034843-74035066(+)$1	223	198	221	21.7674
GAAAACUGUAUUUAUUUUGUUUG	chr1:173859372-173859601(+)$1	229	27	50	22.5956
UUCUAACACUUGUUUUAUUUUAG	chr4:83276373-83276622(-)$1	249	45	68	22.2035
GACAAAGCCAUUCUUUUAAAUAU	chr12:111158136-111158407(-)$1	271	145	168	21.3561
CUGAUUUUUCUUUUCUUUAAAUU	chr3:14239697-14239945(+)$1	248	194	217	21.8295
UUUUGCCAAAAUACCACUAGUGG	chr7:75958535-75958782(-)$1	247	44	67	22.9797
GUAUGUGCAUUUCAAUCCCACGU	chr18:673269-673499(+)$1	230	10	33	21.7674
GACUGUUUGUUUAUAAAUGUGUA	chr10:5498832-5499072(+)$1	240	155	178	20.8766
GAACUUUAAGGACCUCAUUGAGA	chr22:26888021-26888258(-)$1	237	78	101	22.7186
CAGCCUCCUGCUAACUCCUAGCU	chr11:33730493-33730769(-)$1	276	46	69	20.6218
AAGUAGAAUGUUCGCUGAUGACC	chr12:6601333-6601613(-)$1	280	86	109	21.0232
AGCAGGACCAGACCAGAAACUGC	chr17:26654415-26654656(+)$1	241	15	38	21.7313
GCCAGCUCCAGCCUCCCGUGCGU	chr9:130507064-130507302(-)$1	238	146	169	22.2165
UGCACAAACUUUUUUUAAUGUGU	chr10:21781553-21781782(-)$1	229	40	63	22.1093
UUUGAAAAAUACUUCCAAUUCCA	chr2:219103305-219103546(+)$1	241	185	208	23.0585
CUUCCUUCUUUUAAAAAUGGUUG	chr22:29696274-29696501(+)$1	227	71	94	21.2230
AGGCCCAUAAAGCACUCUUGGCC	chrX:24024652-24024914(-)$1	262	231	254	20.3245
AAUGAAUAAUUAAGUUAAUUUCU	chr3:38531507-38531741(+)$1	234	170	193	22.7772
UAAGAUUCUGUUUUUUGUUUUUC	chr12:109540581-109540832(+)$1	251	22	45	21.4992
CUAACCUUAUAUAGACUUGUUAA	chr7:103008459-103008688(+)$1	229	81	104	21.2004
UCUCUGUCUUAUAACAAUCAGUU	chr14:70795792-70796020(-)$1	228	149	172	23.0457
AAAUUCUAUUUACUAUUUGUUGA	chr13:21721469-21721696(+)$1	227	10	33	17.9440
GUGAGUUCACCUGUCUUUAUACU	chr10:70742698-70742923(+)$1	225	176	199	21.9939
UUUUCUUUUUCUUAAAACAGGAA	chr7:26251621-26251850(+)$1	229	60	83	22.3756
CUCUUGACCUCGGAUAACAAUAA	chr14:73742039-73742263(-)$1	224	198	221	21.4025
UCACCAAAGCCUAUCAACGAAUG	chr2:48027111-48027384(+)$1	273	187	210	19.0395
AUUAGUUUUCUUUGUUUUUACUU	chr4:83345817-83346053(-)$1	236	149	172	20.2984
UCUGAUUUCUUUGUUCUUGUCUU	chr21:34889758-34889986(-)$1	228	38	61	19.7103
AUCCAUCAGCGAAUCCACAGUGG	chr19:44515158-44515385(+)$1	227	89	112	22.5760
UACCUUAAAAAAAAAAAAAAAGG	chr18:649742-649969(-)$1	227	69	92	20.1360
ACUGAUAACUGCCCUCUUUUCAG	chr5:41918314-41918538(+)$1	224	77	100	21.7313
ACUCCUCUCUCUUGUUCUGAAUG	chr5:71505039-71505307(+)$1	268	108	131	21.1307
AAUGGACACCACAUGAACCUCUG	chr15:78461274-78461497(+)$1	223	108	131	23.3288
CAGCUGGAAGCAACAAAGAACAG	chr12:57927653-57927882(-)$1	229	15	38	20.2976
UGAUGCCUUUUGGACCUUGGGAU	chr12:53808433-53808681(+)$1	248	211	234	21.3549
AUCAGUGCCUCUUAUGUAAUUAA	chr20:32676017-32676288(-)$1	271	155	178	20.6195
UUAAAUAUAUUAAUUUCUUUUAA	chr19:37001898-37002150(-)$1	252	63	86	21.3099
AAGUGUUUUUUUUUUCUUAUACU	chr22:40731014-40731253(+)$1	239	8	31	23.6098
GAAAAAAAAAAAAAAAAGCCCUU	chr2:55199728-55199951(-)$1	223	3	26	21.4992
UACUGUAUUUUUAAUGUAACAGU	chr20:11906966-11907187(+)$1	221	189	212	23.1280
ACUUGCAACAUUUAGCUCUGGAA	chr7:40172279-40172507(-)$1	228	25	48	20.8332
UUUGGUUAAUAAAACAAUACUCA	chr5:68473945-68474173(+)$1	228	95	118	23.5144
GGGGGCAAUGUGUCAAAAGUCCC	chr1:150547894-150548147(-)$1	253	115	138	22.1093
GAGGUGCCACCAGCACCCGUGCC	chr20:55982992-55983222(+)$1	230	8	31	21.7674
CAGCUGCACAUGAAUAGAACAGC	chr6:4133754-4134027(-)$1	273	113	136	21.8871
UAGGUAAUCUUUUUAAAAACAUA	chr1:203770315-203770541(+)$1	226	96	119	17.9440
GUCUUCAUAAAAGCCCUUUGAAC	chr1:145442161-145442474(+)$1	313	143	166	20.5280

#DB
.(((((..............)))	chr7:44618654-44618877(-)$1	1	62	85	21.8907
((((((...............))	chr12:92537389-92537610(-)$1	1	138	161	18.1904
(((((.............)))))	chr1:234742058-234742292(-)$1	1	152	175	21.7683
((((((..............)))	chr13:98119614-98119852(+)$1	1	33	56	22.6434
((.((((...........)))).	chr2:217069868-217070102(+)$1	1	19	42	21.2517
(((.(((...........))).)	chr3:41281598-41281844(+)$1	1	62	85	21.7951
((.(((............)))..	chr7:44867470-44867733(-)$1	1	42	65	22.9630
((..((..............)).	chr5:71501660-71501988(+)$1	1	292	315	21.5675
.(((((................)	chr14:50085309-50085551(-)$1	1	112	135	21.3561
(((((.............)))))	chr10:124923435-124923727(+)$1	1	175	198	21.3099
(((.(((...........)))))	chr15:77338334-77338607(-)$1	1	235	258	22.4167
(((((((...........)))))	chr19:39327205-39327432(-)$1	1	131	154	21.8295
(((.((.............))))	chr8:41368214-41368472(+)$1	1	208	231	21.2433
.((((((...........)))))	chrX:47495607-47495844(-)$1	1	169	192	20.8944
(...((............))...	chr8:10753593-10753816(-)$1	1	117	140	22.5315
((((((............)))))	chr11:92625054-92625284(+)$1	1	45	68	23.1280
((((((.............))))	chr6:144150771-144150998(+)$1	1	167	190	22.9797
((((((............)))))	chr8:67834132-67834354(-)$1	1	136	159	22.1093
(((((((...........)))))	chr10:74034843-74035066(+)$1	1	198	221	21.7674
..((((............)))).	chr1:173859372-173859601(+)$1	1	27	50	22.5956
(.((((.............))))	chr4:83276373-83276622(-)$1	1	45	68	22.2035
.(((((................)	chr12:111158136-111158407(-)$1	1	145	168	21.3561
(((((((...........)))))	chr3:14239697-14239945(+)$1	1	194	217	21.8295
((((((.............))))	chr7:75958535-75958782(-)$1	1	44	67	22.9797
(((((((...........)))))	chr18:673269-673499(+)$1	1	10	33	21.7674
((((((................)	chr10:5498832-5499072(+)$1	1	155	178	20.8766
(..(((.............))).	chr22:26888021-26888258(-)$1	1	78	101	22.7186
((((................)))	chr11:33730493-33730769(-)$1	1	46	69	20.6218
..((((................)	chr12:6601333-6601613(-)$1	1	86	109	21.0232
(((((..............))))	chr17:26654415-26654656(+)$1	1	15	38	21.7313
((((((.............)).)	chr9:130507064-130507302(-)$1	1	146	169	22.2165
((((((............)))))	chr10:21781553-21781782(-)$1	1	40	63	22.1093
((.(((............))).)	chr2:219103305-219103546(+)$1	1	185	208	23.0585
(..((.............))..)	chr22:29696274-29696501(+)$1	1	71	94	21.2230
.((((..............))))	chrX:24024652-24024914(-)$1	1	231	254	20.3245
...(((.............))).	chr3:38531507-38531741(+)$1	1	170	193	22.7772
(((((................))	chr12:109540581-109540832(+)$1	1	22	45	21.4992
.((((.............)))).	chr7:103008459-103008688(+)$1	1	81	104	21.2004
(..(((............)))..	chr14:70795792-70796020(-)$1	1	149	172	23.0457
((((((...............))	chr13:21721469-21721696(+)$1	1	10	33	17.9440
.(((((..............)))	chr10:70742698-70742923(+)$1	1	176	199	21.9939
(((((((...........)))))	chr7:26251621-26251850(+)$1	1	60	83	22.3756
((((((..............)))	chr14:73742039-73742263(-)$1	1	198	221	21.4025
((................)))))	chr2:48027111-48027384(+)$1	1	187	210	19.0395
...(((.............))).	chr4:83345817-83346053(-)$1	1	149	172	20.2984
((((((............)))..	chr21:34889758-34889986(-)$1	1	38	61	19.7103
.(((((.............))))	chr19:44515158-44515385(+)$1	1	89	112	22.5760
..((((.............))))	chr18:649742-649969(-)$1	1	69	92	20.1360
(((((..............))))	chr5:41918314-41918538(+)$1	1	77	100	21.7313
(((..((...........))..)	chr5:71505039-71505307(+)$1	1	108	131	21.1307
((((((.............))))	chr15:78461274-78461497(+)$1	1	108	131	23.3288
).((((..............)))	chr12:57927653-57927882(-)$1	1	15	38	20.2976
((((.((...........)).))	chr12:53808433-53808681(+)$1	1	211	234	21.3549
(...((................)	chr20:32676017-32676288(-)$1	1	155	178	20.6195
(((((.............)))))	chr19:37001898-37002150(-)$1	1	63	86	21.3099
((((((............)))))	chr22:40731014-40731253(+)$1	1	8	31	23.6098
(((((................))	chr2:55199728-55199951(-)$1	1	3	26	21.4992
((((((............)))))	chr20:11906966-11907187(+)$1	1	189	212	23.1280
((((.((...........)).))	chr7:40172279-40172507(-)$1	1	25	48	20.8332
((.(((............))).)	chr5:68473945-68474173(+)$1	1	95	118	23.5144
((((((............)))))	chr1:150547894-150548147(-)$1	1	115	138	22.1093
(((((((...........)))))	chr20:55982992-55983222(+)$1	1	8	31	21.7674
((((((.............))))	chr6:4133754-4134027(-)$1	1	113	136	21.8871
((((((...............))	chr1:203770315-203770541(+)$1	1	96	119	17.9440
(..((((...........)))).	chr1:145442161-145442474(+)$1	1	143	166	20.5280

#PSSM
e : 0.16	g : 0.16	f : 0.10	d : 0.09	= : 0.07	[ : 0.04	i : 0.04	" : 0.04	b : 0.04	c : 0.03	h : 0.03	! : 0.03	: : 0.03	# : 0.01	a : 0.01	$ : 0.01	' : 0.01	G : 0.01	
e : 0.21	g : 0.16	f : 0.12	d : 0.10	= : 0.07	! : 0.07	" : 0.06	i : 0.04	: : 0.03	c : 0.01	h : 0.01	[ : 0.01	b : 0.01	' : 0.01	G : 0.01	
e : 0.20	d : 0.16	g : 0.15	f : 0.12	= : 0.07	! : 0.07	[ : 0.06	" : 0.04	i : 0.03	h : 0.01	y : 0.01	' : 0.01	G : 0.01	
e : 0.18	d : 0.18	g : 0.13	c : 0.12	f : 0.12	= : 0.07	[ : 0.04	! : 0.03	i : 0.03	" : 0.03	b : 0.01	y : 0.01	
e : 0.15	d : 0.15	c : 0.15	g : 0.13	f : 0.12	b : 0.09	= : 0.07	i : 0.03	y : 0.03	[ : 0.03	! : 0.01	
c : 0.15	g : 0.13	d : 0.12	b : 0.12	f : 0.09	e : 0.07	= : 0.07	v : 0.07	y : 0.06	w : 0.04	i : 0.03	
v : 0.26	u : 0.20	w : 0.13	y : 0.13	x : 0.04	g : 0.04	b : 0.04	d : 0.03	c : 0.03	i : 0.03	f : 0.01	= : 0.01	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.26	t : 0.21	u : 0.20	w : 0.13	y : 0.13	x : 0.04	
v : 0.18	w : 0.13	y : 0.12	c : 0.10	f : 0.09	b : 0.09	g : 0.07	d : 0.06	x : 0.04	i : 0.03	= : 0.03	e : 0.01	
c : 0.15	d : 0.12	y : 0.12	b : 0.12	g : 0.10	w : 0.09	f : 0.09	e : 0.06	x : 0.04	= : 0.04	i : 0.03	
d : 0.15	c : 0.15	y : 0.10	f : 0.10	g : 0.10	e : 0.09	= : 0.07	x : 0.04	b : 0.04	i : 0.03	2 : 0.03	] : 0.03	3 : 0.01	
d : 0.16	g : 0.15	e : 0.13	f : 0.10	= : 0.09	y : 0.07	] : 0.06	2 : 0.06	c : 0.04	i : 0.03	b : 0.01	h : 0.01	3 : 0.01	: : 0.01	
e : 0.20	d : 0.15	g : 0.15	f : 0.12	= : 0.09	2 : 0.06	] : 0.04	i : 0.04	h : 0.01	3 : 0.01	a : 0.01	4 : 0.01	9 : 0.01	: : 0.01	b : 0.01	7 : 0.01	

#score	1402.865442308842
#seq	65
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_CDS_m2_run2.txt

#BEAR
iiiiiiiiiqqqqqqqqiiiiiiii	chr2:113331082-113331283(+)$1	201	64	89	14.4130
####eeeeeqqqqqqqqeeeee22e	chr19:39911375-39911576(+)$1	201	130	155	16.1573
22bbeeeeeqqqqqqqqeeeeeGGG	chr6:90410340-90410541(-)$1	201	169	194	11.9312
eeee[ddddqqqqqqqqdddd22ee	chr4:25418075-25418276(+)$1	201	126	151	14.2749
ffff!!cccqqqqqqqqccc22fff	chr2:37341787-37341988(-)$1	201	17	42	14.1393
c$$$$$cccqqqqqqqqccc22ccc	chr17:3721567-3721768(-)$1	201	84	109	14.3692
ffffffcccqqqqqqqqccc]ffff	chr13:113909226-113909427(+)$1	201	24	49	13.7150
bb!!eeeeerrrrrrrrreeeee44	chr3:152554550-152554751(+)$1	201	63	88	10.2650
####eeeeeqqqqqqqqeeeee22e	chr19:39911336-39911537(+)$1	201	169	194	16.1573
=========qqqqqqqq========	chr6:150001269-150001470(-)$1	201	155	180	15.1364
::gggggggqqqqqqqqgggggggD	chr20:40083210-40083411(-)$1	201	87	112	12.0763
ddd[eeeeeqqqqqqqqeeeee]dd	chr9:98240279-98240480(-)$1	201	157	182	14.9626
a"""eeeeeqqqqqqqqeeeee333	chr18:657808-658009(+)$1	201	113	138	16.7948
d]cccddddqqqqqqqqdddd::ee	chr22:31332868-31333069(-)$1	201	126	151	11.8837
####eeeeesssssssssseeeee3	chr19:49952528-49952729(-)$1	201	29	54	10.0064
!!ccc[cccqqqqqqqqccc]ccc2	chr1:86142857-86143058(-)$1	201	62	87	15.0206
b[gggggggqqqqqqqqggggggg4	chr12:106827443-106827644(+)$1	201	133	158	14.5215
iiiiiiiiiqqqqqqqqiiiiiiii	chr2:24046090-24046291(-)$1	201	158	183	14.4130
eeeaeeeeeqqqqqqqqeeeee333	chr1:200817230-200817431(+)$1	201	118	143	15.7583
###a[ddddqqqqqqqqdddd]a22	chr2:201722394-201722595(-)$1	201	43	68	15.1448
=========qqqqqqqq========	chr18:21098786-21098987(+)$1	201	4	29	15.1364
#ccc!!cccqqqqqqqqccc22ccc	chr1:43828591-43828792(+)$1	201	90	115	15.1374
[eeeee[bbqqqqqqqqbb]eeeee	chr1:92518023-92518224(+)$1	201	2	27	13.7245
::ccc[cccqqqqqqqqccc]cccB	chr1:24085936-24086137(+)$1	201	4	29	12.5326
""ccc[cccqqqqqqqqccc]ccc2	chr14:92620636-92620837(+)$1	201	81	106	15.1608
ccc!!ddddqqqqqqqqdddd22cc	chrX:133927799-133928000(-)$1	201	137	162	14.9690
%%%eeeeerrrrrrrrreeeeeccc	chr16:30997716-30997917(+)$1	201	118	143	9.0488
dddd[ddddqqqqqqqqdddd333d	chr17:76087453-76087654(+)$1	201	123	148	14.5478
[eeeee[bbqqqqqqqqbbeeeeed	chr10:6154186-6154387(+)$1	201	121	146	13.8351
eeeee[cccqqqqqqqqccceeeee	chr17:56581713-56581914(-)$1	201	64	89	14.6528
eeee!!cccqqqqqqqqccc]eeee	chr3:169497034-169497235(+)$1	201	101	126	14.6391
eeee####aqqqqqqqqa4444eee	chr18:29100976-29101177(+)$1	201	55	80	13.4686
:bb[eeeeeqqqqqqqqeeeee]bb	chr19:58049537-58049738(+)$1	201	125	150	14.1569
"""eeeeerrrrrrrrreeeee22g	chr20:37193907-37194108(+)$1	201	15	40	10.7326
:ccc[ddddqqqqqqqqdddd22cc	chr9:33053046-33053247(-)$1	201	64	89	14.0955
cc####cccrrrrrrrrrccc22cc	chr20:47628449-47628650(+)$1	201	164	189	9.9167
##gggggggqqqqqqqqggggggg]	chr6:7211783-7211984(+)$1	201	96	121	14.9148
c"""ddddrrrrrrrrrdddd4444	chr13:77581441-77581642(-)$1	201	3	28	10.2356
::cccddddqqqqqqqqdddd]ccc	chr15:28499469-28499670(-)$1	201	102	127	13.0710
ff[ccc[bbqqqqqqqqbb22cccf	chrX:70757722-70757923(+)$1	201	159	184	12.7582
d$$$$$cccqqqqqqqqccc66666	chr2:29158317-29158518(+)$1	201	78	103	12.2884
eeeee[cccqqqqqqqqccceeeee	chr13:32910577-32910778(+)$1	201	9	34	14.6528
$$$$$ddddqqqqqqqqdddd333c	chr19:34904589-34904790(+)$1	201	82	107	15.1242
::bb!!cccqqqqqqqqccc22bb:	chr6:56426033-56426234(-)$1	201	152	177	11.6618
ccc[eeeeeqqqqqqqqeeeee]cc	chr12:133266825-133267026(+)$1	201	93	118	15.7202
cc[eeeeerrrrrrrrreeeee]cc	chr3:184048958-184049159(+)$1	201	93	118	10.3878
]bbffffffqqqqqqqqffffffcc	chr6:86324768-86324969(-)$1	201	155	180	12.7033
eeee[ddddqqqqqqqqdddd333e	chr22:50875389-50875590(+)$1	201	73	98	14.8977
####eeeeeqqqqqqqqeeeee]cc	chr19:18420175-18420376(-)$1	201	126	151	16.4388
"""bb!!bbqqqqqqqqbb]bb444	chr20:47888099-47888300(-)$1	201	33	58	13.5540
++gggggggqqqqqqqqggggggg]	chr1:78432655-78432856(-)$1	201	143	168	13.6479
ddd[ccc[aqqqqqqqqa]ccc]dd	chr13:114188428-114188629(+)$1	201	103	128	13.6701
ddddeeeeeqqqqqqqqeeeee>>>	chr20:62221706-62221907(-)$1	201	141	166	14.3805
""eeeeesssssssssseeeee444	chr5:132223484-132223685(-)$1	201	95	120	9.8952
fff[eeeeeqqqqqqqqeeeee]ff	chr14:90451430-90451631(+)$1	201	119	144	15.0685
####eeeeesssssssssseeeee4	chr11:66043496-66043697(+)$1	201	99	124	9.9601
ffffff[bbqqqqqqqqbb]fffff	chr6:52148087-52148288(-)$1	201	128	153	12.4375
bb[ffffffqqqqqqqqffffffbb	chr13:49050786-49050987(+)$1	201	155	180	12.6716

#otherMatches

#Seq PSSM
UAAGGCCUCUUGGGAACGAGGCUUU	chr2:113331082-113331283(+)$1	201	64	89	14.4130
AUCCCUGAGUCCCAGCCCUCAGCCC	chr19:39911375-39911576(+)$1	201	130	155	16.1573
CAGCCUAGGUAAAAUAUUCUAGCAC	chr6:90410340-90410541(-)$1	201	169	194	11.9312
CUGGGACUUAUUCUACAAGGUAACU	chr4:25418075-25418276(+)$1	201	126	151	14.2749
AAGUAAAGAUUGGAGACUUUGGACU	chr2:37341787-37341988(-)$1	201	17	42	14.1393
AGCAGCUCAGACUCAGAUGAAAUGG	chr17:3721567-3721768(-)$1	201	84	109	14.3692
UUUGCUUCCCAUUCAGAGGAUAGUG	chr13:113909226-113909427(+)$1	201	24	49	13.7150
CAAAUUUGCAAUCCAAGAGUGAAGA	chr3:152554550-152554751(+)$1	201	63	88	10.2650
AUCCCUGAGUCCCAGCCCUCAGCCC	chr19:39911336-39911537(+)$1	201	169	194	16.1573
AUGGGUAGUUCGUCUAUAUUAUUCA	chr6:150001269-150001470(-)$1	201	155	180	15.1364
ACUUUUGGCAGAAAUGGGCUAAAAU	chr20:40083210-40083411(-)$1	201	87	112	12.0763
CCAUGCUCCUGGGGGCUGGAGUUUG	chr9:98240279-98240480(-)$1	201	157	182	14.9626
CAUGCAGGCGCGCUACAGCCUGAGA	chr18:657808-658009(+)$1	201	113	138	16.7948
UGAACCCUGAUCCUGAACAGGACCG	chr22:31332868-31333069(-)$1	201	126	151	11.8837
cccgcuaggccccuucuucccuaga	chr19:49952528-49952729(-)$1	201	29	54	10.0064
GUUGAAAGCCUACAUUCGCUCUCAG	chr1:86142857-86143058(-)$1	201	62	87	15.0206
GAAUUUGUUUCCAUCUCAACAAAUC	chr12:106827443-106827644(+)$1	201	133	158	14.5215
AAGAAGGUACUCUAAACUACUUUUU	chr2:24046090-24046291(-)$1	201	158	183	14.4130
GAGCAUUGAAGAAGAACUUAAUAUA	chr1:200817230-200817431(+)$1	201	118	143	15.7583
UUUGAACUAUUGGGACUUAGUACUU	chr2:201722394-201722595(-)$1	201	43	68	15.1448
CAUUUAGAACAAAGGAAUUUUGAAU	chr18:21098786-21098987(+)$1	201	4	29	15.1364
CAGCAGCAGAUGAGACCCUGAGGCU	chr1:43828591-43828792(+)$1	201	90	115	15.1374
UAACAAAAAAGUUUUAAUUAUUGUU	chr1:92518023-92518224(+)$1	201	2	27	13.7245
ACUGGGGGUGUGUCUAAGCCGCCAC	chr1:24085936-24086137(+)$1	201	4	29	12.5326
AGCUUGAAGGGAAAGAACUUGAAGA	chr14:92620636-92620837(+)$1	201	81	106	15.1608
UAUGAGCCGUCACAGCCUGGUAAGU	chrX:133927799-133928000(-)$1	201	137	162	14.9690
AGGUCACCCCUUCUACAGGUGAGUG	chr16:30997716-30997917(+)$1	201	118	143	9.0488
GUGAAGGACCCAUCCCAGUCCCAGU	chr17:76087453-76087654(+)$1	201	123	148	14.5478
CGACGCCACAGAGAAAGGUGUGUCC	chr10:6154186-6154387(+)$1	201	121	146	13.8351
GGGCUUCCAAGUGUUAGUGGAGUCU	chr17:56581713-56581914(-)$1	201	64	89	14.6528
CCUUAUGAGGCGGAGAACUCCGGGG	chr3:169497034-169497235(+)$1	201	101	126	14.6391
AAUCUAAUCUUAUUUAUGUCAUGAU	chr18:29100976-29101177(+)$1	201	55	80	13.4686
AGACUUCUUGAGCACCAGAGAAUUC	chr19:58049537-58049738(+)$1	201	125	150	14.1569
UAACAUUUCAUGUAGCAAGAUGAUA	chr20:37193907-37194108(+)$1	201	15	40	10.7326
CCUGAGCACUUUGUGGUGUGCAACA	chr9:33053046-33053247(-)$1	201	64	89	14.0955
GGCCUCGGGUUCGUUUUUCCCCACC	chr20:47628449-47628650(+)$1	201	164	189	9.9167
GGAGUUUGUUUGCAAGUAUGGACUG	chr6:7211783-7211984(+)$1	201	96	121	14.9148
GCCACCCAUCUGUACUUUGGGAGAU	chr13:77581441-77581642(-)$1	201	3	28	10.2356
AAAGACCUUAUUAAUACGGGGAUCU	chr15:28499469-28499670(-)$1	201	102	127	13.0710
GGGCAGUACAAGCUUACGUCUCUGC	chrX:70757722-70757923(+)$1	201	159	184	12.7582
CAAACUAGGAAUGUAAACCUUAUAA	chr2:29158317-29158518(+)$1	201	78	103	12.2884
CAGUUAUUUAUUACCCCAGAAGCUG	chr13:32910577-32910778(+)$1	201	9	34	14.6528
GAAGACCAUAAUUAAAAGUGGAGAU	chr19:34904589-34904790(+)$1	201	82	107	15.1242
GGAAGACAUGAaagagaauggauua	chr6:56426033-56426234(-)$1	201	152	177	11.6618
AGAAGUCUGGAUGUCGGUGGGCCUC	chr12:133266825-133267026(+)$1	201	93	118	15.7202
AGGGUCCUAAAAAGGUGGGGACGCU	chr3:184048958-184049159(+)$1	201	93	118	10.3878
GUCGUGGGGCUGCUCCUCCCCGCGG	chr6:86324768-86324969(-)$1	201	155	180	12.7033
AGGGUGCUUUCCCUAACGAGCUGUC	chr22:50875389-50875590(+)$1	201	73	98	14.8977
aagccucaguuuccccucugagagg	chr19:18420175-18420376(-)$1	201	126	151	16.4388
CCACCAAGAGCUAGAAAUCAGGCCA	chr20:47888099-47888300(-)$1	201	33	58	13.5540
AAGUUUUGAAAACAUGAUCAAAACA	chr1:78432655-78432856(-)$1	201	143	168	13.6479
GCCUUUAUCUUCUUAAUGUUAACGG	chr13:114188428-114188629(+)$1	201	103	128	13.6701
GGCCUCCCCGCUGCUCGGGGGAUAC	chr20:62221706-62221907(-)$1	201	141	166	14.3805
CAGGAAUCCAAAUCCCCAUUCCCUA	chr5:132223484-132223685(-)$1	201	95	120	9.8952
AGAAGGUAACAGAACUUUUACuauu	chr14:90451430-90451631(+)$1	201	119	144	15.0685
AUGGCUGCUGAAAUCAAAAAGCGGA	chr11:66043496-66043697(+)$1	201	99	124	9.9601
UGACAACCAAUACCGGCUGAUUGUC	chr6:52148087-52148288(-)$1	201	128	153	12.4375
CGCUUUGAUAUUGAAGGAUCAGAUG	chr13:49050786-49050987(+)$1	201	155	180	12.6716

#DB
(((((((((........))))))))	chr2:113331082-113331283(+)$1	1	64	89	14.4130
....(((((........)))))..)	chr19:39911375-39911576(+)$1	1	130	155	16.1573
..))(((((........))))))))	chr6:90410340-90410541(-)$1	1	169	194	11.9312
((((.((((........))))..))	chr4:25418075-25418276(+)$1	1	126	151	14.2749
((((..(((........)))..)))	chr2:37341787-37341988(-)$1	1	17	42	14.1393
(.....(((........)))..)))	chr17:3721567-3721768(-)$1	1	84	109	14.3692
(((((((((........))).))))	chr13:113909226-113909427(+)$1	1	24	49	13.7150
((..(((((.........)))))..	chr3:152554550-152554751(+)$1	1	63	88	10.2650
....(((((........)))))..)	chr19:39911336-39911537(+)$1	1	169	194	16.1573
(((((((((........))))))))	chr6:150001269-150001470(-)$1	1	155	180	15.1364
..(((((((........))))))))	chr20:40083210-40083411(-)$1	1	87	112	12.0763
(((.(((((........))))).))	chr9:98240279-98240480(-)$1	1	157	182	14.9626
(...(((((........)))))...	chr18:657808-658009(+)$1	1	113	138	16.7948
).)))((((........))))..((	chr22:31332868-31333069(-)$1	1	126	151	11.8837
....(((((..........))))).	chr19:49952528-49952729(-)$1	1	29	54	10.0064
..(((.(((........))).))).	chr1:86142857-86143058(-)$1	1	62	87	15.0206
(.(((((((........))))))).	chr12:106827443-106827644(+)$1	1	133	158	14.5215
(((((((((........))))))))	chr2:24046090-24046291(-)$1	1	158	183	14.4130
(((((((((........)))))...	chr1:200817230-200817431(+)$1	1	118	143	15.7583
...(.((((........)))).)..	chr2:201722394-201722595(-)$1	1	43	68	15.1448
(((((((((........))))))))	chr18:21098786-21098987(+)$1	1	4	29	15.1364
.(((..(((........)))..)))	chr1:43828591-43828792(+)$1	1	90	115	15.1374
.(((((.((........)).)))))	chr1:92518023-92518224(+)$1	1	2	27	13.7245
..(((.(((........))).)))(	chr1:24085936-24086137(+)$1	1	4	29	12.5326
..(((.(((........))).))).	chr14:92620636-92620837(+)$1	1	81	106	15.1608
(((..((((........))))..))	chrX:133927799-133928000(-)$1	1	137	162	14.9690
...(((((.........))))))))	chr16:30997716-30997917(+)$1	1	118	143	9.0488
((((.((((........))))...)	chr17:76087453-76087654(+)$1	1	123	148	14.5478
.(((((.((........))))))))	chr10:6154186-6154387(+)$1	1	121	146	13.8351
(((((.(((........))))))))	chr17:56581713-56581914(-)$1	1	64	89	14.6528
((((..(((........))).))))	chr3:169497034-169497235(+)$1	1	101	126	14.6391
((((....(........)....)))	chr18:29100976-29101177(+)$1	1	55	80	13.4686
.((.(((((........))))).))	chr19:58049537-58049738(+)$1	1	125	150	14.1569
...(((((.........)))))..)	chr20:37193907-37194108(+)$1	1	15	40	10.7326
.(((.((((........))))..))	chr9:33053046-33053247(-)$1	1	64	89	14.0955
((....(((.........)))..))	chr20:47628449-47628650(+)$1	1	164	189	9.9167
..(((((((........))))))).	chr6:7211783-7211984(+)$1	1	96	121	14.9148
(...((((.........))))....	chr13:77581441-77581642(-)$1	1	3	28	10.2356
..(((((((........)))).)))	chr15:28499469-28499670(-)$1	1	102	127	13.0710
((.(((.((........))..))))	chrX:70757722-70757923(+)$1	1	159	184	12.7582
(.....(((........))).....	chr2:29158317-29158518(+)$1	1	78	103	12.2884
(((((.(((........))))))))	chr13:32910577-32910778(+)$1	1	9	34	14.6528
.....((((........))))...)	chr19:34904589-34904790(+)$1	1	82	107	15.1242
..((..(((........)))..)).	chr6:56426033-56426234(-)$1	1	152	177	11.6618
(((.(((((........))))).))	chr12:133266825-133267026(+)$1	1	93	118	15.7202
((.(((((.........))))).))	chr3:184048958-184049159(+)$1	1	93	118	10.3878
.))((((((........))))))((	chr6:86324768-86324969(-)$1	1	155	180	12.7033
((((.((((........))))...)	chr22:50875389-50875590(+)$1	1	73	98	14.8977
....(((((........))))).))	chr19:18420175-18420376(-)$1	1	126	151	16.4388
...((..((........)).))...	chr20:47888099-47888300(-)$1	1	33	58	13.5540
..(((((((........))))))).	chr1:78432655-78432856(-)$1	1	143	168	13.6479
(((.(((.(........).))).))	chr13:114188428-114188629(+)$1	1	103	128	13.6701
(((((((((........)))))...	chr20:62221706-62221907(-)$1	1	141	166	14.3805
..(((((..........)))))...	chr5:132223484-132223685(-)$1	1	95	120	9.8952
(((.(((((........))))).))	chr14:90451430-90451631(+)$1	1	119	144	15.0685
....(((((..........))))).	chr11:66043496-66043697(+)$1	1	99	124	9.9601
((((((.((........)).)))))	chr6:52148087-52148288(-)$1	1	128	153	12.4375
((.((((((........))))))))	chr13:49050786-49050987(+)$1	1	155	180	12.6716

#PSSM
# : 0.13	e : 0.12	c : 0.10	: : 0.10	d : 0.10	f : 0.08	" : 0.06	b : 0.05	i : 0.03	= : 0.03	[ : 0.03	2 : 0.01	a : 0.01	! : 0.01	% : 0.01	$ : 0.01	] : 0.01	+ : 0.01	
e : 0.15	# : 0.12	" : 0.10	c : 0.10	f : 0.08	b : 0.06	: : 0.06	d : 0.06	$ : 0.05	i : 0.03	= : 0.03	2 : 0.01	] : 0.01	! : 0.01	[ : 0.01	% : 0.01	+ : 0.01	
e : 0.17	c : 0.15	# : 0.12	b : 0.06	f : 0.06	g : 0.06	d : 0.06	" : 0.06	$ : 0.05	[ : 0.05	i : 0.03	= : 0.03	! : 0.01	% : 0.01	
e : 0.20	c : 0.13	# : 0.10	f : 0.08	[ : 0.08	g : 0.06	b : 0.05	$ : 0.05	i : 0.03	! : 0.03	= : 0.03	" : 0.03	a : 0.03	d : 0.03	
e : 0.37	c : 0.12	[ : 0.08	! : 0.08	f : 0.06	g : 0.06	$ : 0.05	i : 0.03	= : 0.03	# : 0.03	d : 0.01	b : 0.01	
e : 0.34	d : 0.17	! : 0.08	[ : 0.08	f : 0.06	g : 0.06	i : 0.03	$ : 0.03	= : 0.03	# : 0.03	c : 0.03	
e : 0.31	c : 0.24	d : 0.17	g : 0.06	[ : 0.06	i : 0.03	= : 0.03	f : 0.03	# : 0.01	! : 0.01	
e : 0.29	c : 0.22	d : 0.17	b : 0.08	g : 0.06	i : 0.03	= : 0.03	f : 0.03	# : 0.01	[ : 0.01	s : 0.01	
e : 0.24	c : 0.22	d : 0.15	b : 0.08	g : 0.06	r : 0.06	i : 0.03	= : 0.03	a : 0.03	f : 0.03	s : 0.01	
q : 0.84	r : 0.10	s : 0.05	
q : 0.84	r : 0.10	s : 0.05	
q : 0.84	r : 0.10	s : 0.05	
q : 0.84	r : 0.10	s : 0.05	
q : 0.84	r : 0.10	s : 0.05	
q : 0.84	r : 0.10	s : 0.05	
q : 0.84	r : 0.10	s : 0.05	
q : 0.84	r : 0.10	s : 0.05	
e : 0.25	c : 0.20	d : 0.17	b : 0.08	g : 0.06	i : 0.03	r : 0.03	= : 0.03	s : 0.03	a : 0.03	f : 0.03	
e : 0.27	c : 0.22	d : 0.17	b : 0.08	g : 0.06	i : 0.03	= : 0.03	s : 0.03	f : 0.03	4 : 0.01	] : 0.01	
e : 0.32	c : 0.24	d : 0.17	g : 0.06	] : 0.05	i : 0.03	= : 0.03	f : 0.03	4 : 0.01	2 : 0.01	
e : 0.37	d : 0.17	2 : 0.08	] : 0.08	g : 0.06	f : 0.05	i : 0.03	= : 0.03	c : 0.03	4 : 0.01	6 : 0.01	b : 0.01	
e : 0.39	2 : 0.13	c : 0.08	f : 0.06	g : 0.06	3 : 0.05	i : 0.03	= : 0.03	] : 0.03	4 : 0.03	: : 0.01	6 : 0.01	b : 0.01	
e : 0.15	c : 0.13	2 : 0.12	] : 0.12	f : 0.08	3 : 0.08	g : 0.06	4 : 0.05	i : 0.03	= : 0.03	G : 0.01	: : 0.01	a : 0.01	6 : 0.01	b : 0.01	> : 0.01	
c : 0.25	e : 0.17	3 : 0.08	2 : 0.06	f : 0.06	4 : 0.06	g : 0.06	b : 0.05	i : 0.03	= : 0.03	d : 0.03	G : 0.01	6 : 0.01	> : 0.01	
c : 0.20	e : 0.17	4 : 0.10	f : 0.08	d : 0.06	3 : 0.05	2 : 0.05	i : 0.03	= : 0.03	b : 0.03	] : 0.03	G : 0.01	D : 0.01	B : 0.01	g : 0.01	6 : 0.01	: : 0.01	> : 0.01	

#score	787.0378761085017
#seq	58
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_UTR_m2_run1.txt

#BEAR
!!===========mmmm===========4444	chr1:115249133-115249356(-)$1	223	148	180	15.7913
c!!==========nnnnn==========333c	chr15:50792076-50792298(+)$1	222	14	46	16.2548
Cbb!!iiiiiiiiinnnnniiiiiiiii22bb	chr17:5287062-5287286(-)$1	224	104	136	11.9922
===========ssssssssss===========	chr1:225589785-225590014(-)$1	229	153	185	13.0220
====iiiiiiiiillliiiiiiiii333====	chr2:65497827-65498056(+)$1	229	138	170	14.9299
d####==========mmmm==========22d	chr18:77897866-77898087(+)$1	221	109	141	15.0368
e[ggggggg[cccnnnnnccc]ggggggg]ee	chr5:72205651-72205882(+)$1	231	190	222	12.2453
eeeee============lll============	chr12:79982765-79982987(-)$1	222	152	184	14.6279
==========[cccmmmmccc]==========	chr2:32531043-32531273(+)$1	230	64	96	15.2983
gccc!!ccc[cccooooooccc]ccc22ccc]	chr1:225977527-225977752(+)$1	225	167	199	14.5990
=========[cccooooooccc]=========	chr4:71896335-71896568(+)$1	233	70	102	18.4844
ffff!!eeeee[aooooooa22eeeeefffff	chr5:114949191-114949421(-)$1	230	65	97	10.9466
##ggggggg!!eeeeellleeeee]ggggggg	chr5:114951690-114951920(-)$1	230	129	161	11.0892
##bb!!ccc[cccooooooccc]ccc22bb44	chr1:68167232-68167464(-)$1	232	157	189	14.3854
###cccgggggggooooooggggggg4444cc	chr19:36729531-36729760(+)$1	229	90	122	15.2182
f[bb!!==========mmmm==========22	chr1:23635361-23635584(-)$1	223	153	185	14.2531
c!!bbdddd[cccoooooocccdddd]bbccc	chr5:76736548-76736772(-)$1	224	17	49	11.9079
:===========rrrrrrrrr===========	chr1:203769557-203769790(+)$1	233	11	43	14.5725
gggggccccccbboooooobb]ccc22ccc22	chr21:28209349-28209572(-)$1	223	151	183	12.3296
iiiiiiii[ddddoooooodddd]iiiiiiii	chr21:15745505-15745734(-)$1	229	151	183	15.0064
[bb####bb[cccooooooccc]bb333bb]h	chr5:158584540-158584756(-)$1	216	111	143	13.5911
&============oooooo============]	chr3:186503933-186504155(+)$1	222	19	51	18.5800
eee"""gggggggooooooggggggg4444ee	chr6:86318183-86318413(-)$1	230	74	106	15.1855
(bbbb"""eeeeeooooooeeeee333bb444	chr2:192554790-192555013(+)$1	223	65	97	12.3585
eeee[bb[eeeeeooooooeeeee]bb22eee	chr12:124496452-124496671(+)$1	219	164	196	10.9883
cc!!==========nnnnn==========ccc	chr3:180632396-180632622(+)$1	226	151	183	15.8125
[dddd"""eeeeeooooooeeeee22ddddcc	chr19:36727174-36727392(+)$1	218	113	145	11.1164
eeeee!!ccccccooooooccc]ccceeeee:	chr20:4681319-4681540(+)$1	221	38	70	11.9717
cc[bb[a[eeeeeooooooeeeeea]bbcccc	chr2:20401211-20401432(-)$1	221	24	56	12.0711
bccc!!gggggggrrrrrrrrrgggggggccc	chr7:99639182-99639406(+)$1	224	89	121	11.4998
[===========[bbmmmmbb===========	chr12:69968697-69968933(+)$1	236	81	113	14.6385
eeee"""a[ddddoooooodddd]a333eeee	chr8:42027721-42027945(+)$1	224	112	144	12.8131
$$$ccc[ccccccooooooccc]cccccc666	chr12:76739450-76739682(-)$1	232	173	205	12.2252
iiii!!==========lll==========444	chr20:34238145-34238378(-)$1	233	42	74	16.9546
========!!cccmmmmccc============	chr1:35649730-35649973(-)$1	243	16	48	14.9116
d####===========lll===========22	chr12:27156099-27156328(-)$1	229	6	38	16.1959
ggggggg####cccmmmmccc4444ggggggg	chr1:111489930-111490162(-)$1	232	162	194	11.1258
============rrrrrrrrr===========	chr12:95695899-95696128(+)$1	229	129	161	15.6654
===[ffffff[bboooooobbffffff]====	chr8:82614068-82614290(-)$1	222	56	88	12.5589
ff[============mmmm============]	chr14:70236975-70237201(+)$1	226	70	102	15.8275
iiiiiiiii[cccooooooccc]iiiiiiiii	chr3:10191905-10192141(+)$1	236	105	137	17.1372
ggggggggggggggnnnnnggggggg22gggg	chr8:440863-441090(-)$1	227	12	44	12.2357
eeee!!iiiiiiiiillliiiiiiiii333ee	chr4:140394905-140395133(+)$1	228	1	33	14.0034
====!!gggggggooooooggggggg======	chr10:13251537-13251765(+)$1	228	54	86	17.1674
bba!!eeeeecccooooooccc22eeeee22a	chr17:30327165-30327401(+)$1	236	138	170	11.9107
=========ggggggglllggggggg4444==	chr13:25908569-25908805(+)$1	236	167	199	14.1132
"""==========qqqqqqqq==========3	chr11:33001533-33001753(+)$1	220	35	67	13.8534
iiiiiii"""ddddnnnnndddd4444iiiii	chrX:84528084-84528312(+)$1	228	79	111	12.0285
c:===========oooooo===========::	chr8:86393400-86393630(+)$1	230	154	186	15.6372

#otherMatches

#Seq PSSM
CAAUAUUCUCAUUUGAGAAUGAGGAUGUCUCA	chr1:115249133-115249356(-)$1	223	148	180	15.7913
ACUAGUAUUCUCACAUAUUGAGAAUAUUCAUU	chr15:50792076-50792298(+)$1	222	14	46	16.2548
UCAUCAUUAAUUCACUUCAUGAAUUGGUUUUG	chr17:5287062-5287286(-)$1	224	104	136	11.9922
AACUGAAGGGGUUAAAGUCGUUUCUUUUAGUU	chr1:225589785-225590014(-)$1	229	153	185	13.0220
AUGCAUUUAAAUUUGGGAUUUGGGUGGAGUAU	chr2:65497827-65498056(+)$1	229	138	170	14.9299
CUCUAUCUUUAGGUAGAAAUAUUUGGAGGAUG	chr18:77897866-77898087(+)$1	221	109	141	15.0368
AAGUUGAAAAAUGAUUGCUAUAUUUCAAUGUU	chr5:72205651-72205882(+)$1	231	190	222	12.2453
AUUCCCAAUUACAGUCUCUAAGAUUGUAAUUG	chr12:79982765-79982987(-)$1	222	152	184	14.6279
AGauauauauuuauauuuauacauauauauuu	chr2:32531043-32531273(+)$1	230	64	96	15.2983
UUUGAAUCUAGUUUUCAGUGAUCAGAAGCAGC	chr1:225977527-225977752(+)$1	225	167	199	14.5990
GUUCUAAAAAGAUGuaauaaucauuuuagaau	chr4:71896335-71896568(+)$1	233	70	102	18.4844
AGUUAAAUAGGACAAAGCAGGCCCUAUGACUA	chr5:114949191-114949421(-)$1	230	65	97	10.9466
UGUUGGGAGGGAUGUACAAUGCAUAUUCCCAA	chr5:114951690-114951920(-)$1	230	129	161	11.0892
UAUGGAAAGAAUAAAAGCAUGUACUUCACAGC	chr1:68167232-68167464(-)$1	232	157	189	14.3854
UGUAAUAUGaaauuaaucuauuuuauuaaaau	chr19:36729531-36729760(+)$1	229	90	122	15.2182
UCUCAAAUGUUUUUAUAAUGAUAAAAAUAUCA	chr1:23635361-23635584(-)$1	223	153	185	14.2531
GCAGGCCUAUGAACGCAACUUCUGGGACCCAU	chr5:76736548-76736772(-)$1	224	17	49	11.9079
UGAAAAAGAAAUACUGCCUUAAUUUCUUUUUC	chr1:203769557-203769790(+)$1	233	11	43	14.5725
UUUGACCAGCACUGUUUAUGGCUGCUAUGGUU	chr21:28209349-28209572(-)$1	223	151	183	12.3296
CAGUUCUUACUAAAUUGUAUUAGCAGGAGCUG	chr21:15745505-15745734(-)$1	229	151	183	15.0064
AUCAUGGCUACAGGUAGAACUGGGGAGGGGGG	chr5:158584540-158584756(-)$1	216	111	143	13.5911
CUCCAAAAUGGAUCAAAAUGUUUGUUUUGGAU	chr3:186503933-186504155(+)$1	222	19	51	18.5800
AAUUGUGUUUUAUUUAUCCGUAGAAUUUAUAU	chr6:86318183-86318413(-)$1	230	74	106	15.1855
AACCUGUUAUUUCCAAUCAGAAAUUGAAGUUA	chr2:192554790-192555013(+)$1	223	65	97	12.3585
AUGAAAUAACAGUCUUGUAACUGUAGUAAUCA	chr12:124496452-124496671(+)$1	219	164	196	10.9883
CAUUACUCAUUUUGCCUCACAAAGUGAGUUGG	chr3:180632396-180632622(+)$1	226	151	183	15.8125
UCAAGAAAUUUUUACUGGAGAGAAACCUUGUG	chr19:36727174-36727392(+)$1	218	113	145	11.1164
UGGGAAUGGUGCCCUUGGAGGCAACCUCCCAU	chr20:4681319-4681540(+)$1	221	38	70	11.9717
GCUCCUGUGGCCCCACCCUGGGCCCUGGGCUG	chr2:20401211-20401432(-)$1	221	24	56	12.0711
UGAGUCAUGGUAAAACAAUAAAUUAUCAUCUC	chr7:99639182-99639406(+)$1	224	89	121	11.4998
AAAAUGAAGAUGCAAGUGCUUCAUUUUCAUUU	chr12:69968697-69968933(+)$1	236	81	113	14.6385
ccuaaaucucugaauaaaaucagugcuguagg	chr8:42027721-42027945(+)$1	224	112	144	12.8131
UUCAGUCUACUUAGGAAAAUAGCGUAACUUUA	chr12:76739450-76739682(-)$1	232	173	205	12.2252
UUGUUUGAAGAUGAAAGUCUUUUAUCUUUUUU	chr20:34238145-34238378(-)$1	233	42	74	16.9546
GAUGUUAGCAGUUUAUUGACCUAAUAUUUGUA	chr1:35649730-35649973(-)$1	243	16	48	14.9116
UCUUAUUGAAUUUUCUGUGGGGAAAUUUAGAU	chr12:27156099-27156328(-)$1	229	6	38	16.1959
AAUUUUAUAUAAUCCAAAGGUAUUUUAGAAUU	chr1:111489930-111490162(-)$1	232	162	194	11.1258
GAAGAAUUAGAGUUUAAUAAUUUUUAAUUCUU	chr12:95695899-95696128(+)$1	229	129	161	15.6654
UUUGUUUGUGUGACUAUAUUCCAUAGAGAAGA	chr8:82614068-82614290(-)$1	222	56	88	12.5589
GAAUACAAGUGUGGUAAAUGCCAUGUUUGUAC	chr14:70236975-70237201(+)$1	226	70	102	15.8275
AUGGAUGUAUAAUACAUCCAUUCUACAUCCGU	chr3:10191905-10192141(+)$1	236	105	137	17.1372
UAAUAGAACAGGUUUACUUGAUCUGUCAUCUG	chr8:440863-441090(-)$1	227	12	44	12.2357
GGGAUAAGAAGGCAUAGAAUGUUUUCUGGUUC	chr4:140394905-140395133(+)$1	228	1	33	14.0034
AGGUAAACAGAGAGCUAUGUUUCUGUAUCUUU	chr10:13251537-13251765(+)$1	228	54	86	17.1674
GCAGUUCCCUAUUUUGUUUAAUGAAGGGAUAU	chr17:30327165-30327401(+)$1	236	138	170	11.9107
GCAUUUUAGGUUUUUUAAAGAAAAAUUAUUUU	chr13:25908569-25908805(+)$1	236	167	199	14.1132
CUUGGUUGUGCAUUAACUUACAUGUAUAAUUU	chr11:33001533-33001753(+)$1	220	35	67	13.8534
AUAAGAAUCAGUUCCUUGAGAAUAAAUUUUUU	chrX:84528084-84528312(+)$1	228	79	111	12.0285
UGUUGUAAUUUAAUGACUUUUGAAUUACAGAG	chr8:86393400-86393630(+)$1	230	154	186	15.6372

#DB
..(((((((((((....)))))))))))....	chr1:115249133-115249356(-)$1	1	148	180	15.7913
(..((((((((((.....))))))))))...)	chr15:50792076-50792298(+)$1	1	14	46	16.2548
(((..(((((((((.....)))))))))..))	chr17:5287062-5287286(-)$1	1	104	136	11.9922
(((((((((((..........)))))))))))	chr1:225589785-225590014(-)$1	1	153	185	13.0220
(((((((((((((...)))))))))...))))	chr2:65497827-65498056(+)$1	1	138	170	14.9299
(....((((((((((....))))))))))..)	chr18:77897866-77898087(+)$1	1	109	141	15.0368
(.(((((((.(((.....))).))))))).))	chr5:72205651-72205882(+)$1	1	190	222	12.2453
)))))((((((((((((...))))))))))))	chr12:79982765-79982987(-)$1	1	152	184	14.6279
((((((((((.(((....))).))))))))))	chr2:32531043-32531273(+)$1	1	64	96	15.2983
((((..(((.(((......))).)))..))).	chr1:225977527-225977752(+)$1	1	167	199	14.5990
(((((((((.(((......))).)))))))))	chr4:71896335-71896568(+)$1	1	70	102	18.4844
((((..(((((.(......)..))))))))))	chr5:114949191-114949421(-)$1	1	65	97	10.9466
..(((((((..(((((...))))).)))))))	chr5:114951690-114951920(-)$1	1	129	161	11.0892
..((..(((.(((......))).)))..))..	chr1:68167232-68167464(-)$1	1	157	189	14.3854
...((((((((((......)))))))....))	chr19:36729531-36729760(+)$1	1	90	122	15.2182
(.((..((((((((((....))))))))))..	chr1:23635361-23635584(-)$1	1	153	185	14.2531
(..((((((.(((......))))))).)))))	chr5:76736548-76736772(-)$1	1	17	49	11.9079
.(((((((((((.........)))))))))))	chr1:203769557-203769790(+)$1	1	11	43	14.5725
(((((((((((((......)).)))..)))..	chr21:28209349-28209572(-)$1	1	151	183	12.3296
((((((((.((((......)))).))))))))	chr21:15745505-15745734(-)$1	1	151	183	15.0064
.((....((.(((......))).))...)).)	chr5:158584540-158584756(-)$1	1	111	143	13.5911
.((((((((((((......)))))))))))).	chr3:186503933-186504155(+)$1	1	19	51	18.5800
(((...(((((((......)))))))....))	chr6:86318183-86318413(-)$1	1	74	106	15.1855
.((((...(((((......)))))...))...	chr2:192554790-192555013(+)$1	1	65	97	12.3585
((((.((.(((((......))))).))..)))	chr12:124496452-124496671(+)$1	1	164	196	10.9883
((..((((((((((.....)))))))))))))	chr3:180632396-180632622(+)$1	1	151	183	15.8125
.((((...(((((......)))))..))))))	chr19:36727174-36727392(+)$1	1	113	145	11.1164
(((((..((((((......))).)))))))).	chr20:4681319-4681540(+)$1	1	38	70	11.9717
((.((.(.(((((......)))))).))))))	chr2:20401211-20401432(-)$1	1	24	56	12.0711
)(((..(((((((.........))))))))))	chr7:99639182-99639406(+)$1	1	89	121	11.4998
.(((((((((((.((....)))))))))))))	chr12:69968697-69968933(+)$1	1	81	113	14.6385
((((...(.((((......)))).)...))))	chr8:42027721-42027945(+)$1	1	112	144	12.8131
...(((.((((((......))).))))))...	chr12:76739450-76739682(-)$1	1	173	205	12.2252
((((..((((((((((...))))))))))...	chr20:34238145-34238378(-)$1	1	42	74	16.9546
((((((((..(((....)))))))))))))))	chr1:35649730-35649973(-)$1	1	16	48	14.9116
(....(((((((((((...)))))))))))..	chr12:27156099-27156328(-)$1	1	6	38	16.1959
(((((((....(((....)))....)))))))	chr1:111489930-111490162(-)$1	1	162	194	11.1258
((((((((((((.........)))))))))))	chr12:95695899-95696128(+)$1	1	129	161	15.6654
(((.((((((.((......)))))))).))))	chr8:82614068-82614290(-)$1	1	56	88	12.5589
((.((((((((((((....)))))))))))).	chr14:70236975-70237201(+)$1	1	70	102	15.8275
(((((((((.(((......))).)))))))))	chr3:10191905-10192141(+)$1	1	105	137	17.1372
((((((((((((((.....)))))))..))))	chr8:440863-441090(-)$1	1	12	44	12.2357
((((..(((((((((...)))))))))...))	chr4:140394905-140395133(+)$1	1	1	33	14.0034
((((..(((((((......)))))))))))))	chr10:13251537-13251765(+)$1	1	54	86	17.1674
(((..((((((((......)))..)))))..)	chr17:30327165-30327401(+)$1	1	138	170	11.9107
((((((((((((((((...)))))))....))	chr13:25908569-25908805(+)$1	1	167	199	14.1132
...((((((((((........)))))))))).	chr11:33001533-33001753(+)$1	1	35	67	13.8534
(((((((...((((.....))))....)))))	chrX:84528084-84528312(+)$1	1	79	111	12.0285
).(((((((((((......)))))))))))..	chr8:86393400-86393630(+)$1	1	154	186	15.6372

#PSSM
= : 0.18	e : 0.14	c : 0.10	g : 0.08	i : 0.08	f : 0.06	# : 0.06	[ : 0.06	d : 0.04	b : 0.04	! : 0.02	C : 0.02	: : 0.02	& : 0.02	( : 0.02	$ : 0.02	" : 0.02	
= : 0.24	e : 0.12	# : 0.10	b : 0.08	c : 0.08	i : 0.08	! : 0.06	g : 0.06	[ : 0.04	f : 0.04	d : 0.02	$ : 0.02	" : 0.02	: : 0.02	
= : 0.28	e : 0.12	b : 0.10	g : 0.10	i : 0.08	! : 0.06	# : 0.06	c : 0.04	[ : 0.04	f : 0.02	d : 0.02	$ : 0.02	a : 0.02	" : 0.02	
= : 0.32	g : 0.10	e : 0.10	b : 0.10	c : 0.08	i : 0.08	! : 0.06	# : 0.06	f : 0.02	" : 0.02	d : 0.02	[ : 0.02	
= : 0.30	! : 0.20	g : 0.10	i : 0.08	# : 0.06	b : 0.06	e : 0.04	c : 0.04	" : 0.04	[ : 0.02	d : 0.02	f : 0.02	
= : 0.36	! : 0.18	i : 0.10	g : 0.08	" : 0.08	c : 0.06	d : 0.02	# : 0.02	b : 0.02	[ : 0.02	f : 0.02	e : 0.02	
= : 0.40	g : 0.16	i : 0.12	c : 0.06	" : 0.06	e : 0.04	d : 0.02	# : 0.02	b : 0.02	! : 0.02	a : 0.02	[ : 0.02	f : 0.02	
= : 0.40	g : 0.14	i : 0.10	c : 0.10	" : 0.06	e : 0.04	[ : 0.04	d : 0.02	b : 0.02	a : 0.02	# : 0.02	f : 0.02	
= : 0.38	g : 0.14	e : 0.12	c : 0.10	i : 0.08	[ : 0.04	d : 0.02	b : 0.02	! : 0.02	# : 0.02	f : 0.02	" : 0.02	
= : 0.34	[ : 0.14	e : 0.12	g : 0.12	i : 0.06	c : 0.06	! : 0.04	d : 0.04	# : 0.02	f : 0.02	" : 0.02	
= : 0.32	c : 0.24	g : 0.12	e : 0.10	i : 0.06	d : 0.06	[ : 0.04	! : 0.02	# : 0.02	
= : 0.30	c : 0.26	g : 0.12	e : 0.10	i : 0.06	d : 0.06	b : 0.04	s : 0.02	[ : 0.02	
c : 0.26	= : 0.24	g : 0.12	e : 0.10	i : 0.06	d : 0.06	r : 0.04	b : 0.04	s : 0.02	a : 0.02	[ : 0.02	
o : 0.46	= : 0.14	r : 0.06	m : 0.04	n : 0.04	i : 0.04	c : 0.04	g : 0.04	s : 0.02	l : 0.02	e : 0.02	b : 0.02	q : 0.02	d : 0.02	
o : 0.46	n : 0.12	= : 0.12	m : 0.08	r : 0.06	s : 0.02	l : 0.02	e : 0.02	b : 0.02	i : 0.02	g : 0.02	q : 0.02	
o : 0.46	m : 0.14	n : 0.12	= : 0.08	r : 0.06	l : 0.04	s : 0.02	e : 0.02	g : 0.02	q : 0.02	
o : 0.46	m : 0.16	n : 0.12	l : 0.10	r : 0.06	s : 0.02	i : 0.02	= : 0.02	q : 0.02	
o : 0.46	n : 0.12	m : 0.12	l : 0.12	r : 0.06	= : 0.02	s : 0.02	i : 0.02	c : 0.02	q : 0.02	
o : 0.46	l : 0.10	n : 0.08	m : 0.08	c : 0.08	r : 0.06	= : 0.04	i : 0.04	s : 0.02	q : 0.02	
c : 0.26	= : 0.18	e : 0.10	g : 0.10	i : 0.06	r : 0.06	b : 0.06	d : 0.06	s : 0.02	l : 0.02	a : 0.02	m : 0.02	q : 0.02	
= : 0.24	c : 0.24	e : 0.10	g : 0.10	i : 0.06	r : 0.06	b : 0.06	d : 0.06	s : 0.02	2 : 0.02	q : 0.02	
= : 0.34	c : 0.18	e : 0.10	g : 0.10	i : 0.06	] : 0.06	d : 0.06	2 : 0.02	r : 0.02	4 : 0.02	f : 0.02	
= : 0.36	g : 0.14	] : 0.14	e : 0.12	d : 0.08	i : 0.06	c : 0.02	4 : 0.02	f : 0.02	2 : 0.02	
= : 0.38	g : 0.14	e : 0.12	c : 0.10	i : 0.08	] : 0.04	4 : 0.04	d : 0.02	b : 0.02	f : 0.02	2 : 0.02	
= : 0.38	g : 0.14	i : 0.10	c : 0.10	e : 0.04	] : 0.04	a : 0.04	4 : 0.04	d : 0.02	b : 0.02	3 : 0.02	2 : 0.02	f : 0.02	
= : 0.38	g : 0.18	i : 0.08	3 : 0.08	c : 0.08	e : 0.04	2 : 0.04	d : 0.02	b : 0.02	] : 0.02	f : 0.02	4 : 0.02	
= : 0.40	i : 0.08	3 : 0.08	g : 0.08	2 : 0.08	4 : 0.08	e : 0.06	b : 0.04	] : 0.02	d : 0.02	c : 0.02	f : 0.02	
= : 0.40	i : 0.08	3 : 0.08	g : 0.08	2 : 0.08	4 : 0.06	b : 0.06	c : 0.04	e : 0.04	f : 0.02	d : 0.02	] : 0.02	
= : 0.40	g : 0.10	4 : 0.08	c : 0.08	b : 0.08	i : 0.06	e : 0.06	3 : 0.04	2 : 0.04	f : 0.02	d : 0.02	
= : 0.34	4 : 0.12	c : 0.12	2 : 0.06	g : 0.06	i : 0.06	e : 0.06	3 : 0.04	b : 0.04	] : 0.02	f : 0.02	d : 0.02	6 : 0.02	
= : 0.30	c : 0.14	e : 0.12	2 : 0.10	4 : 0.08	g : 0.06	i : 0.06	3 : 0.02	b : 0.02	f : 0.02	] : 0.02	6 : 0.02	: : 0.02	
= : 0.24	c : 0.14	e : 0.10	4 : 0.08	] : 0.06	g : 0.06	2 : 0.06	i : 0.06	: : 0.04	b : 0.02	d : 0.02	f : 0.02	h : 0.02	6 : 0.02	a : 0.02	3 : 0.02	

#score	686.1715143759142
#seq	49
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_CDS_m3_run2.txt

#BEAR
eeeeemmmmeeeee::	chr10:126100462-126100686(-)$1	224	9	25	10.4530
eeeeellleeeee]cc	chr19:3980485-3980757(-)$1	272	171	187	9.3401
eeeeemmmmeeeee]c	chr4:1746601-1746836(+)$1	235	8	24	11.8012
eeeeeooooooeeeee	chr1:32800342-32800565(-)$1	223	10	26	9.2898
eeeeeooooooeeeee	chr19:50881527-50881744(+)$1	217	41	57	9.2898
eeeeemmmmeeeee44	chr19:40739708-40739931(-)$1	223	157	173	11.6383
eeeeellleeeee]cc	chr5:137089380-137089613(-)$1	233	22	38	9.3401
eeeooooooeeeee]h	chr1:19635003-19635232(-)$1	229	56	72	9.3702
eeeeeooooooeeeee	chr17:26890348-26890571(-)$1	223	21	37	9.2898
eeeeemmmmeeeee::	chr17:80016408-80016637(-)$1	229	8	24	10.4530
eeeeeooooooeeeee	chr5:130495041-130495298(-)$1	257	42	58	9.2898
eeeeemmmmeeeeeDD	chr2:176972168-176972390(+)$1	222	189	205	9.8906
eeeennnnneeeee]b	chr20:33871929-33872150(-)$1	221	14	30	9.1660
eeeeellleeeeeeee	chr16:2094581-2094825(-)$1	244	97	113	9.8086
eeeeemmmmeeeee]b	chr12:122989972-122990222(-)$1	250	221	237	11.7338
eeeennnnneeeee]d	chr20:49508733-49509004(-)$1	271	60	76	9.1420
eeeeemmmmeeeee::	chr1:27269128-27269355(+)$1	227	89	105	10.4530
eeeeemmmmeeeee33	chr19:13879595-13879845(+)$1	250	94	110	11.7465
eeeee4444eeeee]b	chr19:2271291-2271533(+)$1	242	188	204	9.4299
eeeeemmmmeeeee:d	chr1:205687420-205687685(-)$1	265	110	126	10.9072
eeeeemmmmeeeee44	chr11:10821901-10822124(-)$1	223	47	63	11.6383
eeeeemmmmeeeee]b	chr7:27182750-27182972(+)$1	222	138	154	11.7338
eeeennnnneeeee]c	chr1:26231054-26231317(-)$1	263	163	179	9.2334
eeeooooooeeeee]c	chr12:131357319-131357556(+)$1	237	60	76	9.7415
eeeeemmmmeeeee::	chr1:242035332-242035574(+)$1	242	146	162	10.4530
eeeeemmmmeeeee::	chr20:54956479-54956700(-)$1	221	195	211	10.4530
eeeeeooooooeeeee	chr4:186097015-186097237(-)$1	222	169	185	9.2898
eeeeemmmmeeeee22	chr12:49666861-49667112(+)$1	251	61	77	11.2905
eeeeemmmmeeeee:F	chr22:42076185-42076413(-)$1	228	21	37	10.5963
eeeennnnneeeee]b	chr16:30078804-30079029(+)$1	225	195	211	9.1660
eeeeeooooooeeeee	chr12:54577372-54577600(-)$1	228	36	52	9.2898
eeeeemmmmeeeeecc	chrX:24229062-24229293(+)$1	231	110	126	11.3075
eeeeemmmmeeeee]c	chr5:148724998-148725253(+)$1	255	105	121	11.8012
eeeeemmmmeeeeecc	chr17:4578105-4578326(-)$1	221	157	173	11.3075
eeeeemmmmeeeee::	chr17:34171004-34171238(+)$1	234	125	141	10.4530
eeeeemmmmeeeee]e	chr14:94545365-94545593(-)$1	228	95	111	11.6928
eeeeemmmmeeeee22	chr18:43666999-43667226(-)$1	227	25	41	11.2905
eeeooooooeeeee33	chr19:40329573-40329887(-)$1	314	202	218	9.6869
eeeeemmmmeeeee]a	chr10:43883127-43883356(-)$1	229	43	59	11.8449
[eeeeellleeeee]b	chr7:5568836-5569066(-)$1	230	209	225	9.7411
eeeeemmmmeeeee00	chr13:100617825-100618049(-)$1	224	173	189	10.9086
eeeeeooooooeeeee	chr19:13226023-13226248(-)$1	225	27	43	9.2898
eeeeemmmmeeeee]b	chr7:75687198-75687440(+)$1	242	174	190	11.7338
eeeeemmmmeeeee]b	chr19:10363153-10363386(+)$1	233	3	19	11.7338
eeeeemmmmeeeee:d	chr19:39963956-39964215(+)$1	259	45	61	10.9072
eeeeemmmmeeeeedd	chr16:67913433-67913665(+)$1	232	102	118	11.1161
eeeeemmmmeeeee]c	chr3:56716688-56716908(-)$1	220	113	129	11.8012
eeeooooooeeeee]d	chr7:105733377-105733598(-)$1	221	38	54	9.6500
eeeeemmmmeeeee::	chr10:74326347-74326594(-)$1	247	64	80	10.4530
eeeeellleeeeeddd	chr5:154173630-154173852(+)$1	222	46	62	9.2269
!eeeeellleeeee33	chr6:52137019-52137247(-)$1	228	62	78	9.7585
eeeeemmmmeeeee::	chr3:64007942-64008165(-)$1	223	202	218	10.4530
eeeeemmmmeeeee::	chr8:37555971-37556196(+)$1	225	205	221	10.4530
eeeeemmmmeeeee44	chr3:50326176-50326407(-)$1	231	47	63	11.6383
eeeeemmmmeeeee:e	chr8:145150982-145151226(+)$1	244	113	129	10.8903
eeeeemmmmeeeeedd	chr16:69355052-69355273(+)$1	221	142	158	11.1161
eeeeeooooooeeeee	chr1:155180036-155180269(+)$1	233	173	189	9.2898
feeeeellleeeee33	chr19:984346-984570(+)$1	224	62	78	9.7471

#otherMatches

#Seq PSSM
GUGGCUUCUGCUACAU	chr10:126100462-126100686(-)$1	224	9	25	10.4530
CCUGAAGGUCAGGAUC	chr19:3980485-3980757(-)$1	272	171	187	9.3401
AGGCCCUUGGGCCUGC	chr4:1746601-1746836(+)$1	235	8	24	11.8012
GGGGGAGGUCCCCCCC	chr1:32800342-32800565(-)$1	223	10	26	9.2898
GGUCCGUGGUGGGGCC	chr19:50881527-50881744(+)$1	217	41	57	9.2898
UCUGCCCACGCAGAGG	chr19:40739708-40739931(-)$1	223	157	173	11.6383
CUCCAAUGUGGAGGAG	chr5:137089380-137089613(-)$1	233	22	38	9.3401
gcucuaauaggucacu	chr1:19635003-19635232(-)$1	229	56	72	9.3702
UUGCCCCCAGAGGCAG	chr17:26890348-26890571(-)$1	223	21	37	9.2898
AAGGCUUCAGCUUUGG	chr17:80016408-80016637(-)$1	229	8	24	10.4530
GGCCUGAAUAAGGGUU	chr5:130495041-130495298(-)$1	257	42	58	9.2898
gccccggcgggggcgg	chr2:176972168-176972390(+)$1	222	189	205	9.8906
GAGUCAAGAGCUCCGG	chr20:33871929-33872150(-)$1	221	14	30	9.1660
UGCAGCGACUGCGGGC	chr16:2094581-2094825(-)$1	244	97	113	9.8086
GCUAGCACUCUAGCUU	chr12:122989972-122990222(-)$1	250	221	237	11.7338
CUUUCUAACAAAGUAU	chr20:49508733-49509004(-)$1	271	60	76	9.1420
GGGCAGACCUGCCCAA	chr1:27269128-27269355(+)$1	227	89	105	10.4530
GGUGGGCACCUACCAG	chr19:13879595-13879845(+)$1	250	94	110	11.7465
GAGGGAAUAGUCAGAG	chr19:2271291-2271533(+)$1	242	188	204	9.4299
GUGGGUCGCCCCACAG	chr1:205687420-205687685(-)$1	265	110	126	10.9072
CUGUCACUAGAUAGAA	chr11:10821901-10822124(-)$1	223	47	63	11.6383
UCGCUGCCGGGCGAGG	chr7:27182750-27182972(+)$1	222	138	154	11.7338
GUAGGUAAUCUAUUUG	chr1:26231054-26231317(-)$1	263	163	179	9.2334
GCUUGUAUUGGUUGGU	chr12:131357319-131357556(+)$1	237	60	76	9.7415
GAGUGUAAGCACUCCA	chr1:242035332-242035574(+)$1	242	146	162	10.4530
AGCAGAGAACUGCUAC	chr20:54956479-54956700(-)$1	221	195	211	10.4530
CUGUCAAGACAGGCGG	chr4:186097015-186097237(-)$1	222	169	185	9.2898
CCGUGAGGACAUGGCU	chr12:49666861-49667112(+)$1	251	61	77	11.2905
GAUAUUUUUAUGUCCC	chr22:42076185-42076413(-)$1	228	21	37	10.5963
GGACGUGAGGUUUGAG	chr16:30078804-30079029(+)$1	225	195	211	9.1660
UCUACAAUCCCGUGGA	chr12:54577372-54577600(-)$1	228	36	52	9.2898
GCAGAUCCAUUUGUUC	chrX:24229062-24229293(+)$1	231	110	126	11.3075
UGGCCGUACGGUCGCU	chr5:148724998-148725253(+)$1	255	105	121	11.8012
GCCUCUGGAGAGGCCC	chr17:4578105-4578326(-)$1	221	157	173	11.3075
CCCCAAAAGUGGGGAU	chr17:34171004-34171238(+)$1	234	125	141	10.4530
GUUUGUUCCCAGGCCG	chr14:94545365-94545593(-)$1	228	95	111	11.6928
UAGGCUGUUGCUUACC	chr18:43666999-43667226(-)$1	227	25	41	11.2905
UCGUUGGUCCGGUGAG	chr19:40329573-40329887(-)$1	314	202	218	9.6869
GAGGUGAAGGCUUUGU	chr10:43883127-43883356(-)$1	229	43	59	11.8449
GAGCACCCCGUGCUGC	chr7:5568836-5569066(-)$1	230	209	225	9.7411
CCAGGACCCCUUGGUU	chr13:100617825-100618049(-)$1	224	173	189	10.9086
CCUAGAGGUGCCUGGG	chr19:13226023-13226248(-)$1	225	27	43	9.2898
AUGAUCUGCGUCAUUG	chr7:75687198-75687440(+)$1	242	174	190	11.7338
GCUCCAGGAGGGGCGG	chr19:10363153-10363386(+)$1	233	3	19	11.7338
CUAGGGGGACCUAGAG	chr19:39963956-39964215(+)$1	259	45	61	10.9072
AGCCGCUCACGGCUCC	chr16:67913433-67913665(+)$1	232	102	118	11.1161
GGGCGCGGCCGCCCUG	chr3:56716688-56716908(-)$1	220	113	129	11.8012
CACUUUUUUGUGGUUG	chr7:105733377-105733598(-)$1	221	38	54	9.6500
UCUGCUUUGGCAGAAC	chr10:74326347-74326594(-)$1	247	64	80	10.4530
UUUGGCUACCGAAAGU	chr5:154173630-154173852(+)$1	222	46	62	9.2269
GUCCUGACACAGGAGU	chr6:52137019-52137247(-)$1	228	62	78	9.7585
UUAGUAUAGGCUAAAA	chr3:64007942-64008165(-)$1	223	202	218	10.4530
GCUGGGAUACCAGUAA	chr8:37555971-37556196(+)$1	225	205	221	10.4530
UGUUUACGAGGACAUG	chr3:50326176-50326407(-)$1	231	47	63	11.6383
CCGCCACCUGGUGGGC	chr8:145150982-145151226(+)$1	244	113	129	10.8903
UGAGAAAAAUCUCAUA	chr16:69355052-69355273(+)$1	221	142	158	11.1161
CCCAGUAUCCCUUGGG	chr1:155180036-155180269(+)$1	233	173	189	9.2898
GCUGCAUCGUGUGGGA	chr19:984346-984570(+)$1	224	62	78	9.7471

#DB
(((((....)))))..	chr10:126100462-126100686(-)$1	1	9	25	10.4530
(((((...))))).))	chr19:3980485-3980757(-)$1	1	171	187	9.3401
(((((....))))).)	chr4:1746601-1746836(+)$1	1	8	24	11.8012
(((((......)))))	chr1:32800342-32800565(-)$1	1	10	26	9.2898
(((((......)))))	chr19:50881527-50881744(+)$1	1	41	57	9.2898
(((((....)))))..	chr19:40739708-40739931(-)$1	1	157	173	11.6383
(((((...))))).))	chr5:137089380-137089613(-)$1	1	22	38	9.3401
(((......))))).)	chr1:19635003-19635232(-)$1	1	56	72	9.3702
(((((......)))))	chr17:26890348-26890571(-)$1	1	21	37	9.2898
(((((....)))))..	chr17:80016408-80016637(-)$1	1	8	24	10.4530
(((((......)))))	chr5:130495041-130495298(-)$1	1	42	58	9.2898
(((((....)))))))	chr2:176972168-176972390(+)$1	1	189	205	9.8906
((((.....))))).)	chr20:33871929-33872150(-)$1	1	14	30	9.1660
(((((...))))))))	chr16:2094581-2094825(-)$1	1	97	113	9.8086
(((((....))))).)	chr12:122989972-122990222(-)$1	1	221	237	11.7338
((((.....))))).)	chr20:49508733-49509004(-)$1	1	60	76	9.1420
(((((....)))))..	chr1:27269128-27269355(+)$1	1	89	105	10.4530
(((((....)))))..	chr19:13879595-13879845(+)$1	1	94	110	11.7465
)))))....))))).)	chr19:2271291-2271533(+)$1	1	188	204	9.4299
(((((....))))).(	chr1:205687420-205687685(-)$1	1	110	126	10.9072
(((((....)))))..	chr11:10821901-10822124(-)$1	1	47	63	11.6383
(((((....))))).)	chr7:27182750-27182972(+)$1	1	138	154	11.7338
((((.....))))).)	chr1:26231054-26231317(-)$1	1	163	179	9.2334
(((......))))).)	chr12:131357319-131357556(+)$1	1	60	76	9.7415
(((((....)))))..	chr1:242035332-242035574(+)$1	1	146	162	10.4530
(((((....)))))..	chr20:54956479-54956700(-)$1	1	195	211	10.4530
(((((......)))))	chr4:186097015-186097237(-)$1	1	169	185	9.2898
(((((....)))))..	chr12:49666861-49667112(+)$1	1	61	77	11.2905
(((((....))))).(	chr22:42076185-42076413(-)$1	1	21	37	10.5963
((((.....))))).)	chr16:30078804-30079029(+)$1	1	195	211	9.1660
(((((......)))))	chr12:54577372-54577600(-)$1	1	36	52	9.2898
(((((....)))))))	chrX:24229062-24229293(+)$1	1	110	126	11.3075
(((((....))))).)	chr5:148724998-148725253(+)$1	1	105	121	11.8012
(((((....)))))))	chr17:4578105-4578326(-)$1	1	157	173	11.3075
(((((....)))))..	chr17:34171004-34171238(+)$1	1	125	141	10.4530
(((((....))))).)	chr14:94545365-94545593(-)$1	1	95	111	11.6928
(((((....)))))..	chr18:43666999-43667226(-)$1	1	25	41	11.2905
(((......)))))..	chr19:40329573-40329887(-)$1	1	202	218	9.6869
(((((....))))).)	chr10:43883127-43883356(-)$1	1	43	59	11.8449
.(((((...))))).)	chr7:5568836-5569066(-)$1	1	209	225	9.7411
(((((....)))))..	chr13:100617825-100618049(-)$1	1	173	189	10.9086
(((((......)))))	chr19:13226023-13226248(-)$1	1	27	43	9.2898
(((((....))))).)	chr7:75687198-75687440(+)$1	1	174	190	11.7338
(((((....))))).)	chr19:10363153-10363386(+)$1	1	3	19	11.7338
(((((....))))).(	chr19:39963956-39964215(+)$1	1	45	61	10.9072
(((((....)))))))	chr16:67913433-67913665(+)$1	1	102	118	11.1161
(((((....))))).)	chr3:56716688-56716908(-)$1	1	113	129	11.8012
(((......))))).)	chr7:105733377-105733598(-)$1	1	38	54	9.6500
(((((....)))))..	chr10:74326347-74326594(-)$1	1	64	80	10.4530
(((((...))))))))	chr5:154173630-154173852(+)$1	1	46	62	9.2269
.(((((...)))))..	chr6:52137019-52137247(-)$1	1	62	78	9.7585
(((((....)))))..	chr3:64007942-64008165(-)$1	1	202	218	10.4530
(((((....)))))..	chr8:37555971-37556196(+)$1	1	205	221	10.4530
(((((....)))))..	chr3:50326176-50326407(-)$1	1	47	63	11.6383
(((((....))))).(	chr8:145150982-145151226(+)$1	1	113	129	10.8903
(((((....)))))))	chr16:69355052-69355273(+)$1	1	142	158	11.1161
(((((......)))))	chr1:155180036-155180269(+)$1	1	173	189	9.2898
((((((...)))))..	chr19:984346-984570(+)$1	1	62	78	9.7471

#PSSM
e : 0.94	[ : 0.01	! : 0.01	f : 0.01	
e : 1.00	
e : 1.00	
e : 0.93	o : 0.06	
e : 0.86	o : 0.06	n : 0.06	
m : 0.58	o : 0.20	l : 0.06	n : 0.06	e : 0.05	4 : 0.01	
m : 0.58	o : 0.20	l : 0.12	n : 0.06	4 : 0.01	
m : 0.58	o : 0.20	l : 0.12	n : 0.06	4 : 0.01	
m : 0.58	o : 0.20	e : 0.06	n : 0.06	l : 0.05	4 : 0.01	
e : 0.86	o : 0.13	
e : 0.86	o : 0.13	
e : 1.00	
e : 1.00	
e : 0.94	] : 0.03	d : 0.01	
] : 0.31	: : 0.22	e : 0.15	c : 0.06	3 : 0.06	4 : 0.05	d : 0.05	2 : 0.03	D : 0.01	0 : 0.01	
e : 0.18	: : 0.15	c : 0.15	b : 0.13	d : 0.12	3 : 0.06	4 : 0.05	2 : 0.03	h : 0.01	D : 0.01	F : 0.01	a : 0.01	0 : 0.01	

#score	604.0130383438709
#seq	58
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_CDS_m1_run1.txt

#BEAR
[hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr11:9609927-9610170(+)$1	243	32	60	22.8665
ccc[ddddwwwwwwwwwwwwwwdddd]c	chr7:120446601-120446848(-)$1	247	196	224	23.1415
!gggggggvvvvvvvvvvvvvggggggg	chr5:137902609-137902925(-)$1	316	243	271	24.8824
c"""eeeeeuuuuuuuuuuuueeeee]c	chrM:10161-10421(+)$1	260	136	164	25.0640
ddd!!ddddvvvvvvvvvvvvvdddd]d	chr4:57871400-57871706(+)$1	306	48	76	24.3756
dffffffwwwwwwwwwwwwwwffffff:	chr2:61473358-61473703(-)$1	345	224	252	20.3539
[ccc[eeeeettttttttttteeeee]c	chr17:65144645-65144881(-)$1	236	15	43	24.5254
ff[dddd[auuuuuuuuuuuuaddddff	chr13:23907458-23907788(-)$1	330	35	63	23.9582
[ccc[eeeeettttttttttteeeee]c	chr2:26607811-26608080(+)$1	269	164	192	24.5254
ff[ffffffuuuuuuuuuuuuffffff]	chr16:14758748-14759016(+)$1	268	232	260	23.3225
gggggg[bbuuuuuuuuuuuubb]gggg	chr17:57751964-57752239(+)$1	275	211	239	24.3398
dd[ffffffuuuuuuuuuuuuffffffd	chr1:156280256-156280553(-)$1	297	80	108	23.3103
cc[ffffffyyyyyyyyyyyyyyyyfff	chr17:21101988-21102219(-)$1	231	37	65	20.7252
gggg[ddddyyyyyyyyyyyyyyyyddd	chr12:120903391-120903639(-)$1	248	4	32	21.3588
bbdddd!!bbtttttttttttbb22ddd	chr3:160239534-160239788(-)$1	254	101	129	21.8021
eeee[eeeeettttttttttteeeeeee	chr16:30409913-30410143(+)$1	230	199	227	23.5504
h[bb[dddduuuuuuuuuuuudddd]bb	chr7:803358-803597(+)$1	239	60	88	23.4685
iiiiiiiiivvvvvvvvvvvvviiiiii	chr1:100515378-100515657(+)$1	279	213	241	25.4598
!!bb!!cccuuuuuuuuuuuuccc22bb	chr17:29162134-29162366(+)$1	232	150	178	24.4544
"""cccbbauuuuuuuuuuuua]bb]cc	chr1:43161757-43161981(+)$1	224	16	44	24.0618
nccceeeeevvvvvvvvvvvvveeeee:	chr8:77617907-77618147(+)$1	240	166	194	23.0442
[hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr17:40010528-40010787(-)$1	259	82	110	22.8665
ccc!!eeeeettttttttttteeeee22	chr10:129901353-129901589(-)$1	236	176	204	23.9758
b[ccc[cccuuuuuuuuuuuuccc]ccc	chr12:116675325-116675551(-)$1	226	44	72	25.1151
ccc[eeeeettttttttttteeeee]cc	chr16:28847963-28848197(+)$1	234	105	133	23.7224
====="""bbtttttttttttbb22===	chr12:58144941-58145208(-)$1	267	202	230	23.6460
dddd"""ccctttttttttttccc]ddd	chrX:135290594-135290838(+)$1	244	176	204	23.7085
===!!eeeeettttttttttteeeee22	chrX:40547650-40547881(-)$1	231	22	50	24.1995
DDggggggguuuuuuuuuuuuggggggg	chr22:29182206-29182438(+)$1	232	203	231	22.9429
[dddd[ddddtttttttttttdddd]dd	chr2:170663456-170663682(+)$1	226	103	131	23.1968
ddd####ccctttttttttttccc333d	chr15:78770559-78770783(+)$1	224	104	132	24.2077
f####cccvvvvvvvvvvvvvccc4444	chr17:38450595-38450845(+)$1	250	98	126	24.6271
eee!!ddddyyyyyyyyyyyyyyyyddd	chr7:120428551-120428826(-)$1	275	135	163	21.1188
''ggggggguuuuuuuuuuuuggggggg	chrX:154444707-154444957(+)$1	250	70	98	23.9503
++++eeeeeuuuuuuuuuuuueeeeeii	chrX:118603742-118604054(+)$1	312	40	68	22.3441
gggggg!!bbtttttttttttbb22ggg	chr15:48460733-48461071(-)$1	338	82	110	23.3963
cc"""dddduuuuuuuuuuuudddd333	chr6:44216242-44216479(+)$1	237	94	122	24.8045
ggggg[cccvvvvvvvvvvvvvcccggg	chr13:31232135-31232381(+)$1	246	22	50	25.3500
eeeeeyyyyyyyyyyyyyyyyeeeeegg	chr5:37310567-37310893(-)$1	326	129	157	20.6284
""aaeeeeevvvvvvvvvvvvveeeee]	chr1:147090867-147091106(+)$1	239	165	193	24.7920
&&&ddddwwwwwwwwwwwwwwdddd]ee	chr9:6481923-6482160(+)$1	237	104	132	20.3698
eeeeeeeevvvvvvvvvvvvveeeee]e	chr1:45480986-45481226(+)$1	240	90	118	24.0511
=========uuuuuuuuuuuu=======	chr4:74017100-74017340(-)$1	240	24	52	25.9096
iiiiiiiiivvvvvvvvvvvvviiiiii	chr2:145157030-145157318(-)$1	288	138	166	25.4598
ccc!!ddddtttttttttttdddd]ccc	chr16:19088536-19088788(+)$1	252	138	166	23.5879
g!!ffffffvvvvvvvvvvvvvffffff	chr1:214794001-214794250(+)$1	249	108	136	23.7372
iiiiiiiiiuuuuuuuuuuuuiiiiiii	chr3:180666907-180667183(+)$1	276	57	85	25.4612
ggggggcccvvvvvvvvvvvvvccc444	chr10:74813150-74813415(-)$1	265	35	63	25.1035
iiiiiiiiitttttttttttiiiiiiii	chr18:2750267-2750514(+)$1	247	58	86	23.9319
ccc[ddddvvvvvvvvvvvvvdddd]cc	chr11:85347038-85347298(+)$1	260	58	86	24.2546
=========vvvvvvvvvvvvv======	chr1:91973718-91974018(+)$1	300	15	43	25.8465
eee"""cccuuuuuuuuuuuuccc]eee	chr6:26156479-26156731(+)$1	252	190	218	24.9146
[ccc!!cccvvvvvvvvvvvvvcccccc	chrX:99888827-99889107(-)$1	280	221	249	25.5731
!!ccc!!bbvvvvvvvvvvvvvbb22cc	chr1:91989499-91989758(+)$1	259	182	210	24.3545
eeeee!!bbvvvvvvvvvvvvvbb22ee	chr7:151859621-151859854(-)$1	233	31	59	23.3656
eee!!cccyyyyyyyyyyyyyyyyccce	chr2:237995685-237995961(+)$1	276	116	144	21.7925
''eeeeewwwwwwwwwwwwwweeeeegg	chr1:14107520-14107751(+)$1	231	150	178	21.6205
!!ccc[ccctttttttttttccc]ccc4	chr19:59060666-59060912(+)$1	246	92	120	24.1828
[ddddeeeeettttttttttteeeee33	chr12:49719476-49719700(+)$1	224	55	83	23.7820
=========wwwwwwwwwwwwww=====	chr22:29176864-29177131(+)$1	267	68	96	24.1670
[dddd[ccctttttttttttccc4444d	chr1:197069460-197069689(-)$1	229	108	136	23.5991
d[bb"""ccctttttttttttcccbb]d	chr12:49428541-49428818(-)$1	277	75	103	23.2775
"""gggggggtttttttttttggggggg	chr5:41907737-41907979(+)$1	242	66	94	24.2121
:ccc[cccvvvvvvvvvvvvvccc]ccc	chr8:28385253-28385492(+)$1	239	93	121	24.0506

#otherMatches

#Seq PSSM
CUAGGAAUAAUACCUUGUUUUCUAUUUU	chr11:9609927-9610170(+)$1	243	32	60	22.8665
GAUGUUCCAAACAGGCCCACCAGGAAGA	chr7:120446601-120446848(-)$1	247	196	224	23.1415
ACCAAUGUGGUUAAUAUGUAGACGUUGG	chr5:137902609-137902925(-)$1	316	243	271	24.8824
AAACAACUAACCUGCCACUAAUAGUUAU	chrM:10161-10421(+)$1	260	136	164	25.0640
AACAGAAUGUUGCACUAAAUUUCAUUGG	chr4:57871400-57871706(+)$1	306	48	76	24.3756
UGCUUAUAAAAACAAUAAAUGGUGAGUU	chr2:61473358-61473703(-)$1	345	224	252	20.3539
UCAGUUAAACUUUCUCUGUAUGUUUGUC	chr17:65144645-65144881(-)$1	236	15	43	24.5254
UAAGCAUUGGAAAAUUUGGAACAUGCUA	chr13:23907458-23907788(-)$1	330	35	63	23.9582
UUAUGGUUGGAACAGCUUUUGCCAACAG	chr2:26607811-26608080(+)$1	269	164	192	24.5254
UGAGAGAAAGAUCCUCUUUUAUUUCUCA	chr16:14758748-14759016(+)$1	268	232	260	23.3225
CUUGUUGCUGAGGUUGAAAAAAGAAACA	chr17:57751964-57752239(+)$1	275	211	239	24.3398
ACACCCAGGAGAACUGUGAGACCUGGGG	chr1:156280256-156280553(-)$1	297	80	108	23.3103
UCUCCCUUUCCUGCCCCCUCCAUCAAAA	chr17:21101988-21102219(-)$1	231	37	65	20.7252
AGCACUAACUCCAAACGUUUUUUUUGUU	chr12:120903391-120903639(-)$1	248	4	32	21.3588
CACAGUCUGGGCCCUCUCUUACCUUACU	chr3:160239534-160239788(-)$1	254	101	129	21.8021
GCUGCGGCCACAUAACCCACCUGGCCCA	chr16:30409913-30410143(+)$1	230	199	227	23.5504
CAGUCUCUGACUUGUAACCUCCAGGCAC	chr7:803358-803597(+)$1	239	60	88	23.4685
CUCCAAAAUCUCUUCUUCUUCAGUUUUG	chr1:100515378-100515657(+)$1	279	213	241	25.4598
ACUCUAGAAGAAAGACAGCAAUUUAUGA	chr17:29162134-29162366(+)$1	232	150	178	24.4544
UAUCCAAGCUAAAAUAAUAUUGACUCUG	chr1:43161757-43161981(+)$1	224	16	44	24.0618
GUUCAGCCACUCCUCACCAGCAUGGCUU	chr8:77617907-77618147(+)$1	240	166	194	23.0442
ACUGUUUAUAAUCCUGAGCUUGAUAAAU	chr17:40010528-40010787(-)$1	259	82	110	22.8665
UGUAAUUGGCAGCAGGAGACAGCCAAGA	chr10:129901353-129901589(-)$1	236	176	204	23.9758
GAACUCACGGGAAUCAAAUGGCGUAGGU	chr12:116675325-116675551(-)$1	226	44	72	25.1151
CAGCUCCCCUUCCACCCCCCGGGGAACU	chr16:28847963-28848197(+)$1	234	105	133	23.7224
CAGCCGAAACGAUCAAGGUGAGUGGGGU	chr12:58144941-58145208(-)$1	267	202	230	23.6460
AGUGUGCUGGAUGCAAGAACCCCAUCAC	chrX:135290594-135290838(+)$1	244	176	204	23.7085
UAGAGACCGUAGUACUUAGAAAUGGUAG	chrX:40547650-40547881(-)$1	231	22	50	24.1995
AGACGGGUGUAAUAAUAUCUCCACCUGU	chr22:29182206-29182438(+)$1	232	203	231	22.9429
CAGACCUGCUAAUACUUUUCAAGUAAGU	chr2:170663456-170663682(+)$1	226	103	131	23.1968
AAUGGAAACAUACCUUAAAGCUGUGAAA	chr15:78770559-78770783(+)$1	224	104	132	24.2077
UGAACUUCCCACCUUAUACCAGAAAUCA	chr17:38450595-38450845(+)$1	250	98	126	24.6271
CAUGGCAAACAGCUUUAAUACACACUUU	chr7:120428551-120428826(-)$1	275	135	163	21.1188
AGUUGUGGCAAAGGAGAAAUGGCCACAG	chrX:154444707-154444957(+)$1	250	70	98	23.9503
UUCAAAGAUAAAUACAAGCAGAUCUUCC	chrX:118603742-118604054(+)$1	312	40	68	22.3441
AAUCUACAGGAAGUAAGAAGGCCAAUAG	chr15:48460733-48461071(-)$1	338	82	110	23.3963
CUUUUGUAAUUAAUGAGAUUUUUAUUUU	chr6:44216242-44216479(+)$1	237	94	122	24.8045
AUUUGUGGACAUAAGUUUUCCAUCCCAA	chr13:31232135-31232381(+)$1	246	22	50	25.3500
UCUCUUAUCAACUGCUACAUCAGAGAUA	chr5:37310567-37310893(-)$1	326	129	157	20.6284
CACCGGGAGCGCUCCUUACAAACUCUCA	chr1:147090867-147091106(+)$1	239	165	193	24.7920
AUUGUCCCUUCUAAUCAUUAUGGACCCA	chr9:6481923-6482160(+)$1	237	104	132	20.3698
GGGCCAUGGGCUUUAUCCUGACAUGGAC	chr1:45480986-45481226(+)$1	240	90	118	24.0511
caaaauauuauaauuuuaaaaaauauuu	chr4:74017100-74017340(-)$1	240	24	52	25.9096
UUAUUGACUAUACGUUGGAAAAAGUCAA	chr2:145157030-145157318(-)$1	288	138	166	25.4598
CCUCGACCAUGAUGCAGAAUUGGUAGGG	chr16:19088536-19088788(+)$1	252	138	166	23.5879
CAUCUAAUUCUCAAAGAACUCCAAUUAG	chr1:214794001-214794250(+)$1	249	108	136	23.7372
UAUUUGGAAGAAUGAUUAAAGUUUUGAG	chr3:180666907-180667183(+)$1	276	57	85	25.4612
UUCCUAAAGUUCUCUGUAUUUUCUUUUC	chr10:74813150-74813415(-)$1	265	35	63	25.1035
CUCUCCUCUUUUGUUUUGUUAGGGGAGA	chr18:2750267-2750514(+)$1	247	58	86	23.9319
ACCGUUCCACUGCCACCAAAAGGAAGGG	chr11:85347038-85347298(+)$1	260	58	86	24.2546
AACAGUUUUUACAAUCUAUCUUAGAAUU	chr1:91973718-91974018(+)$1	300	15	43	25.8465
ACUCCCGUGAAGAAGAAGGCCCGCAAGU	chr6:26156479-26156731(+)$1	252	190	218	24.9146
UGCCUCAGAGAAAAGAGCAGAGUCUGGC	chrX:99888827-99889107(-)$1	280	221	249	25.5731
CUCCCAAGUUAACAAGUGAUAUACAAGG	chr1:91989499-91989758(+)$1	259	182	210	24.3545
ugaUGAUGCAGAAUCCACCAAGGCUCCA	chr7:151859621-151859854(-)$1	233	31	59	23.3656
UGGUCAGCUUCUAGCUUUAUAUUUGCUC	chr2:237995685-237995961(+)$1	276	116	144	21.7925
GGAAACAUUCAACAAAAACUUUGUUUGC	chr1:14107520-14107751(+)$1	231	150	178	21.6205
AACCUGUGCUUAUGGCUCUUGCGGAGGG	chr19:59060666-59060912(+)$1	246	92	120	24.1828
UGUUCGGGCCUCUGCAUAUUUGGCCCCC	chr12:49719476-49719700(+)$1	224	55	83	23.7820
CAGUUGUCCAGUAAGAAAGAAAAGGAUA	chr22:29176864-29177131(+)$1	267	68	96	24.1670
AAUAGCACCAUAAAAAUUCAGGUAUUUC	chr1:197069460-197069689(-)$1	229	108	136	23.5991
GCUCACUUGGUUCUCCCCUCUCCAGACC	chr12:49428541-49428818(-)$1	277	75	103	23.2775
GGUGAAGUAAUCCUCAUGUUUUUAUUUC	chr5:41907737-41907979(+)$1	242	66	94	24.2121
UUAGUGGCGUGUGUUUUGUUGGCCUCUA	chr8:28385253-28385492(+)$1	239	93	121	24.0506

#DB
.((((((((.............))))))	chr11:9609927-9610170(+)$1	1	32	60	22.8665
(((.((((..............)))).)	chr7:120446601-120446848(-)$1	1	196	224	23.1415
.(((((((.............)))))))	chr5:137902609-137902925(-)$1	1	243	271	24.8824
(...(((((............))))).)	chrM:10161-10421(+)$1	1	136	164	25.0640
(((..((((.............)))).)	chr4:57871400-57871706(+)$1	1	48	76	24.3756
)((((((..............)))))).	chr2:61473358-61473703(-)$1	1	224	252	20.3539
.(((.(((((...........))))).)	chr17:65144645-65144881(-)$1	1	15	43	24.5254
((.((((.(............)))))))	chr13:23907458-23907788(-)$1	1	35	63	23.9582
.(((.(((((...........))))).)	chr2:26607811-26608080(+)$1	1	164	192	24.5254
((.((((((............)))))).	chr16:14758748-14759016(+)$1	1	232	260	23.3225
((((((.((............)).))))	chr17:57751964-57752239(+)$1	1	211	239	24.3398
((.((((((............)))))))	chr1:156280256-156280553(-)$1	1	80	108	23.3103
((.((((((................)))	chr17:21101988-21102219(-)$1	1	37	65	20.7252
((((.((((................)))	chr12:120903391-120903639(-)$1	1	4	32	21.3588
((((((..((...........))..)))	chr3:160239534-160239788(-)$1	1	101	129	21.8021
((((.(((((...........)))))))	chr16:30409913-30410143(+)$1	1	199	227	23.5504
(.((.((((............)))).))	chr7:803358-803597(+)$1	1	60	88	23.4685
(((((((((.............))))))	chr1:100515378-100515657(+)$1	1	213	241	25.4598
..((..(((............)))..))	chr17:29162134-29162366(+)$1	1	150	178	24.4544
...((((((............).)).))	chr1:43161757-43161981(+)$1	1	16	44	24.0618
.)))(((((.............))))).	chr8:77617907-77618147(+)$1	1	166	194	23.0442
.((((((((.............))))))	chr17:40010528-40010787(-)$1	1	82	110	22.8665
(((..(((((...........)))))..	chr10:129901353-129901589(-)$1	1	176	204	23.9758
(.(((.(((............))).)))	chr12:116675325-116675551(-)$1	1	44	72	25.1151
(((.(((((...........))))).))	chr16:28847963-28848197(+)$1	1	105	133	23.7224
(((((...((...........))..)))	chr12:58144941-58145208(-)$1	1	202	230	23.6460
((((...(((...........))).)))	chrX:135290594-135290838(+)$1	1	176	204	23.7085
(((..(((((...........)))))..	chrX:40547650-40547881(-)$1	1	22	50	24.1995
))(((((((............)))))))	chr22:29182206-29182438(+)$1	1	203	231	22.9429
.((((.((((...........)))).))	chr2:170663456-170663682(+)$1	1	103	131	23.1968
(((....(((...........)))...)	chr15:78770559-78770783(+)$1	1	104	132	24.2077
(....(((.............)))....	chr17:38450595-38450845(+)$1	1	98	126	24.6271
(((..((((................)))	chr7:120428551-120428826(-)$1	1	135	163	21.1188
..(((((((............)))))))	chrX:154444707-154444957(+)$1	1	70	98	23.9503
....(((((............)))))))	chrX:118603742-118604054(+)$1	1	40	68	22.3441
((((((..((...........))..)))	chr15:48460733-48461071(-)$1	1	82	110	23.3963
((...((((............))))...	chr6:44216242-44216479(+)$1	1	94	122	24.8045
(((((.(((.............))))))	chr13:31232135-31232381(+)$1	1	22	50	25.3500
(((((................)))))))	chr5:37310567-37310893(-)$1	1	129	157	20.6284
..(((((((.............))))).	chr1:147090867-147091106(+)$1	1	165	193	24.7920
...((((..............)))).))	chr9:6481923-6482160(+)$1	1	104	132	20.3698
((((((((.............))))).)	chr1:45480986-45481226(+)$1	1	90	118	24.0511
(((((((((............)))))))	chr4:74017100-74017340(-)$1	1	24	52	25.9096
(((((((((.............))))))	chr2:145157030-145157318(-)$1	1	138	166	25.4598
(((..((((...........)))).)))	chr16:19088536-19088788(+)$1	1	138	166	23.5879
(..((((((.............))))))	chr1:214794001-214794250(+)$1	1	108	136	23.7372
(((((((((............)))))))	chr3:180666907-180667183(+)$1	1	57	85	25.4612
(((((((((.............)))...	chr10:74813150-74813415(-)$1	1	35	63	25.1035
(((((((((...........))))))))	chr18:2750267-2750514(+)$1	1	58	86	23.9319
(((.((((.............)))).))	chr11:85347038-85347298(+)$1	1	58	86	24.2546
(((((((((.............))))))	chr1:91973718-91974018(+)$1	1	15	43	25.8465
(((...(((............))).)))	chr6:26156479-26156731(+)$1	1	190	218	24.9146
.(((..(((.............))))))	chrX:99888827-99889107(-)$1	1	221	249	25.5731
..(((..((.............))..))	chr1:91989499-91989758(+)$1	1	182	210	24.3545
(((((..((.............))..))	chr7:151859621-151859854(-)$1	1	31	59	23.3656
(((..(((................))))	chr2:237995685-237995961(+)$1	1	116	144	21.7925
..(((((..............)))))))	chr1:14107520-14107751(+)$1	1	150	178	21.6205
..(((.(((...........))).))).	chr19:59060666-59060912(+)$1	1	92	120	24.1828
.(((((((((...........)))))..	chr12:49719476-49719700(+)$1	1	55	83	23.7820
(((((((((..............)))))	chr22:29176864-29177131(+)$1	1	68	96	24.1670
.((((.(((...........)))....)	chr1:197069460-197069689(-)$1	1	108	136	23.5991
(.((...(((...........))))).)	chr12:49428541-49428818(-)$1	1	75	103	23.2775
...(((((((...........)))))))	chr5:41907737-41907979(+)$1	1	66	94	24.2121
.(((.(((.............))).)))	chr8:28385253-28385492(+)$1	1	93	121	24.0506

#PSSM
[ : 0.12	c : 0.12	e : 0.10	d : 0.09	g : 0.09	= : 0.07	! : 0.06	i : 0.06	f : 0.04	" : 0.04	b : 0.03	' : 0.03	h : 0.01	n : 0.01	D : 0.01	+ : 0.01	& : 0.01	: : 0.01	
c : 0.18	d : 0.10	e : 0.10	g : 0.09	= : 0.07	" : 0.06	i : 0.06	! : 0.06	f : 0.04	[ : 0.04	h : 0.03	' : 0.03	b : 0.01	D : 0.01	# : 0.01	+ : 0.01	& : 0.01	
c : 0.20	g : 0.12	e : 0.12	d : 0.10	= : 0.07	" : 0.06	[ : 0.06	i : 0.06	b : 0.04	h : 0.03	f : 0.01	# : 0.01	+ : 0.01	a : 0.01	& : 0.01	! : 0.01	
g : 0.14	c : 0.14	d : 0.10	! : 0.09	f : 0.07	e : 0.07	i : 0.06	= : 0.06	[ : 0.04	" : 0.04	b : 0.04	h : 0.03	# : 0.03	+ : 0.01	a : 0.01	
e : 0.14	d : 0.12	g : 0.12	! : 0.12	[ : 0.09	f : 0.07	i : 0.06	c : 0.06	= : 0.06	" : 0.06	h : 0.03	# : 0.03	
e : 0.20	d : 0.17	g : 0.10	f : 0.07	[ : 0.07	i : 0.06	! : 0.06	c : 0.06	" : 0.06	= : 0.04	h : 0.03	# : 0.01	y : 0.01	
e : 0.20	d : 0.17	c : 0.17	f : 0.07	g : 0.06	! : 0.06	i : 0.06	" : 0.04	= : 0.04	h : 0.03	[ : 0.01	b : 0.01	# : 0.01	y : 0.01	
c : 0.21	e : 0.18	d : 0.14	g : 0.06	f : 0.06	b : 0.06	i : 0.06	w : 0.04	= : 0.04	h : 0.03	! : 0.03	[ : 0.01	" : 0.01	y : 0.01	
e : 0.17	c : 0.17	d : 0.10	b : 0.09	v : 0.07	w : 0.06	f : 0.06	i : 0.06	g : 0.04	= : 0.04	h : 0.03	a : 0.03	y : 0.03	
v : 0.29	u : 0.25	e : 0.09	w : 0.07	y : 0.07	t : 0.07	b : 0.04	c : 0.04	d : 0.01	g : 0.01	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	t : 0.29	u : 0.25	w : 0.07	y : 0.07	
v : 0.29	u : 0.25	t : 0.21	w : 0.07	y : 0.07	c : 0.03	e : 0.01	d : 0.01	i : 0.01	
v : 0.21	e : 0.18	c : 0.15	d : 0.09	g : 0.06	b : 0.06	y : 0.06	f : 0.04	w : 0.03	a : 0.03	i : 0.03	= : 0.01	
e : 0.21	c : 0.20	d : 0.14	b : 0.09	g : 0.06	f : 0.06	y : 0.06	i : 0.06	h : 0.03	= : 0.03	] : 0.01	w : 0.01	
e : 0.21	c : 0.17	d : 0.14	g : 0.06	f : 0.06	y : 0.06	i : 0.06	2 : 0.04	b : 0.04	= : 0.04	h : 0.03	] : 0.03	4 : 0.01	
e : 0.21	d : 0.12	2 : 0.09	g : 0.07	] : 0.07	c : 0.07	f : 0.06	i : 0.06	y : 0.04	= : 0.04	h : 0.03	b : 0.03	4 : 0.03	3 : 0.01	
e : 0.21	d : 0.10	g : 0.10	] : 0.09	c : 0.09	f : 0.07	i : 0.06	= : 0.06	2 : 0.04	4 : 0.04	h : 0.03	3 : 0.03	b : 0.01	
c : 0.15	g : 0.14	] : 0.10	f : 0.09	e : 0.09	d : 0.07	i : 0.07	= : 0.06	3 : 0.04	4 : 0.04	h : 0.03	b : 0.03	2 : 0.03	
c : 0.18	d : 0.15	g : 0.14	e : 0.09	i : 0.07	= : 0.06	f : 0.04	4 : 0.04	h : 0.03	: : 0.03	] : 0.03	b : 0.03	2 : 0.03	3 : 0.03	

#score	1517.791957794752
#seq	64
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_CDS_m3_run1.txt

#BEAR
cc!!cccooooooccc]cc	chr1:173776467-173776707(-)$1	240	80	99	12.3203
''ccc[aooooooa]ccc8	chr5:81571793-81572033(-)$1	240	139	158	10.1822
eeeecccooooooccc]ee	chr11:46680895-46681135(+)$1	240	126	145	12.0472
g!!ddddoooooodddd22	chr8:119122593-119122833(-)$1	240	12	31	10.8913
ffccc[bboooooobb]cc	chr17:5336526-5336766(-)$1	240	21	40	9.3304
Fffffffooooooffffff	chr2:54150410-54150650(-)$1	240	195	214	10.3337
#ffffffooooooffffff	chr6:34213124-34213364(+)$1	240	134	153	10.7597
eeeecccoooooocccFFF	chrX:70756051-70756291(+)$1	240	89	108	10.6570
b"""cccooooooccc333	chr11:60658153-60658393(-)$1	240	85	104	12.1796
ddd[cccooooooccc]dd	chr3:182605294-182605534(+)$1	240	64	83	11.9466
""cccbboooooobb4444	chr17:39983730-39983970(-)$1	240	179	198	11.4184
ccc[cccooooooccc]cc	chr5:76342233-76342473(+)$1	240	21	40	12.1902
dd[ddddoooooodddd]d	chr11:62348480-62348727(-)$1	247	36	55	10.9096
gggggggoooooogggggg	chr20:20617934-20618174(-)$1	240	57	76	11.5341
"""ddddoooooodddd22	chr5:43502387-43502627(-)$1	240	72	91	10.8400
b"""cccooooooccc22b	chr11:69458598-69458838(+)$1	240	117	136	11.4675
fff!!bboooooobb]fff	chr5:72798690-72798930(+)$1	240	208	227	11.1417
gggggggoooooogggggg	chr2:27263486-27263726(+)$1	240	23	42	11.5341
ee[ddddoooooodddd33	chr19:18423368-18423608(-)$1	240	3	22	11.1795
[a[ddddoooooodddd]a	chr9:79117217-79117457(+)$1	240	66	85	11.1032
eeeee[aooooooa]eeee	chr4:87685674-87685914(+)$1	240	196	215	11.2421
gggggggoooooogggggg	chr4:56819295-56819535(+)$1	240	187	206	11.5341
gggggggoooooogggggg	chr11:62344557-62344838(-)$1	281	117	136	11.5341
[dddd!!aooooooa22dd	chr19:38055997-38056237(-)$1	240	170	189	9.5935
!ffffffooooooffffff	chr1:202302524-202302764(-)$1	240	138	157	10.8194
f####bboooooobb4444	chr1:62916484-62916726(+)$1	242	74	93	11.1977
:ffffffooooooffffff	chr2:85769938-85770178(+)$1	240	143	162	9.7799
ggggg[aooooooaggggg	chr6:44219449-44219689(+)$1	240	210	229	11.8006
dddd[bboooooobbdddd	chr19:58268100-58268340(+)$1	240	199	218	10.7828
ebbddddoooooodddd>>	chr12:72025965-72026205(-)$1	240	137	156	10.0601
"""ddddoooooodddd]c	chr19:30500106-30500346(+)$1	240	185	204	11.1700
eeeecccooooooccc]ee	chr2:191300868-191301108(+)$1	240	66	85	12.0472
eeeee[aooooooaeeeee	chr19:42373670-42373910(+)$1	240	131	150	11.2134
cbb!!bboooooobb22bb	chr19:14203260-14203500(-)$1	240	200	219	9.9601
iiiiiiiooooooiiiiii	chr3:194140543-194140783(-)$1	240	2	21	11.3626
'ffffffooooooffffff	chr11:62348918-62349278(-)$1	360	164	183	10.2348
fff[cccooooooccc]ff	chr1:53699171-53699411(-)$1	240	171	190	12.0945
ccc[bboooooobb]cccc	chr10:124921783-124922023(+)$1	240	5	24	9.1054
=====[aooooooa=====	chr21:34931511-34931751(+)$1	240	96	115	11.9872
[ddddbboooooobb]ddd	chr11:62348556-62348975(-)$1	419	79	98	10.8727
eeeecccooooooccc22e	chr11:94917483-94917723(-)$1	240	212	231	11.7316
d[eeeeeooooooeeeee]	chr1:214791881-214792121(+)$1	240	13	32	10.6007
&&&&cccoooooocccggg	chr20:47587730-47587973(+)$1	243	21	40	9.7617
ddd[cccooooooccc]dd	chr11:18330416-18330656(-)$1	240	134	153	11.9466
####cccooooooccc]dd	chr11:82959025-82959265(+)$1	240	186	205	12.1594
cceeeeeooooooeeeee5	chr20:50342319-50342559(-)$1	240	11	30	9.8045
ddd[cccooooooccc]dd	chr2:178096525-178096765(-)$1	240	99	118	11.9466
eeee[bboooooobb]eee	chr11:10821615-10821865(-)$1	250	227	246	11.1147
fffff[aooooooa]ffff	chr2:148709897-148710139(-)$1	242	46	65	11.0503
dddddddoooooodddd]d	chr12:57180929-57181171(+)$1	242	144	163	10.7218
dddd[bboooooobbdddd	chr5:94005815-94006056(+)$1	241	207	226	10.7828
gggggggoooooogggggg	chr17:16455270-16455510(-)$1	240	7	26	11.5341
eee!!bboooooobbeeee	chr19:3976160-3976400(-)$1	240	46	65	11.2399

#otherMatches

#Seq PSSM
CCUUCUGCAUAAACAGUGG	chr1:173776467-173776707(-)$1	240	80	99	12.3203
UUCAUAUGCCAAAAAAUGU	chr5:81571793-81572033(-)$1	240	139	158	10.1822
CCCCACCAUCCCAGGUAGG	chr11:46680895-46681135(+)$1	240	126	145	12.0472
CCUGAGUCUGGAUACUUUA	chr8:119122593-119122833(-)$1	240	12	31	10.8913
UUCUUCUCAGGUUGGACAA	chr17:5336526-5336766(-)$1	240	21	40	9.3304
GAGUUUAUUUUUUUGAACU	chr2:54150410-54150650(-)$1	240	195	214	10.3337
CCCUAGUCCCCGUACUAGG	chr6:34213124-34213364(+)$1	240	134	153	10.7597
GAGCCAGACAAUACUGGUG	chrX:70756051-70756291(+)$1	240	89	108	10.6570
GAGACAGGAGAGGCUGAGC	chr11:60658153-60658393(-)$1	240	85	104	12.1796
AAUUUCUCUUUCUAGACAU	chr3:182605294-182605534(+)$1	240	64	83	11.9466
CUUGAGGGCAAAACCAAUG	chr17:39983730-39983970(-)$1	240	179	198	11.4184
GAAGGCCAAAAUAGGCAUU	chr5:76342233-76342473(+)$1	240	21	40	12.1902
GCUCGGCACCCAGGCUGUG	chr11:62348480-62348727(-)$1	247	36	55	10.9096
AGAAUCAAGAUACUGGUUU	chr20:20617934-20618174(-)$1	240	57	76	11.5341
GGAUGGAUCUGUUUUCAAA	chr5:43502387-43502627(-)$1	240	72	91	10.8400
CAUCCGCAAACACGCGCAG	chr11:69458598-69458838(+)$1	240	117	136	11.4675
UCUGACUAGUUUAAGGAGA	chr5:72798690-72798930(+)$1	240	208	227	11.1417
AGCUUUCAUCCCCGAAAGU	chr2:27263486-27263726(+)$1	240	23	42	11.5341
GUGGUCCAUCUCAGGGCAG	chr19:18423368-18423608(-)$1	240	3	22	11.1795
GAUUAUUGUUUGAAAUGCU	chr9:79117217-79117457(+)$1	240	66	85	11.1032
UGUCACGGUACUGUUUGAC	chr4:87685674-87685914(+)$1	240	196	215	11.2421
UCCUUUUUAUUUUAGAAGG	chr4:56819295-56819535(+)$1	240	187	206	11.5341
GCUGGAUGGUCGAGUCCGG	chr11:62344557-62344838(-)$1	281	117	136	11.5341
UAAGGAAUGUGGAAAGGCC	chr19:38055997-38056237(-)$1	240	170	189	9.5935
UGAUUCUGCUGGAAGGAUU	chr1:202302524-202302764(-)$1	240	138	157	10.8194
CAAAGUUACUGAAGAGAAG	chr1:62916484-62916726(+)$1	242	74	93	11.1977
CCUCUCAGAAGAGUGAGAG	chr2:85769938-85770178(+)$1	240	143	162	9.7799
GGAGCACAAUUAGGGCUUC	chr6:44219449-44219689(+)$1	240	210	229	11.8006
ggccucaaacuccugggcu	chr19:58268100-58268340(+)$1	240	199	218	10.7828
AUGAUCUGACACAAGAUAA	chr12:72025965-72026205(-)$1	240	137	156	10.0601
AUAUAAUUUGAACAUUAAG	chr19:30500106-30500346(+)$1	240	185	204	11.1700
UUGUGUUAAGAUAAACAAC	chr2:191300868-191301108(+)$1	240	66	85	12.0472
UCUGGACAGAAUCGCCGGA	chr19:42373670-42373910(+)$1	240	131	150	11.2134
CCUCAAAUCCAUUUUAAAG	chr19:14203260-14203500(-)$1	240	200	219	9.9601
UGACAGUAUACCAGCUGUU	chr3:194140543-194140783(-)$1	240	2	21	11.3626
GUCCCAGCACAGCCUGGGA	chr11:62348918-62349278(-)$1	360	164	183	10.2348
CCUCCUCCUGACCGAGUGG	chr1:53699171-53699411(-)$1	240	171	190	12.0945
UUGAGUAUUUGGACCCAAG	chr10:124921783-124922023(+)$1	240	5	24	9.1054
GAGGAAGAAGAACCUCCUU	chr21:34931511-34931751(+)$1	240	96	115	11.9872
UGGCCCUGAUGCAGGAGGU	chr11:62348556-62348975(-)$1	419	79	98	10.8727
UGGAUAUGUAAAAAUGAUU	chr11:94917483-94917723(-)$1	240	212	231	11.7316
UCUUGGGUCCUUUUCUAAC	chr1:214791881-214792121(+)$1	240	13	32	10.6007
UCAAUGCAAUCAAGCAAUA	chr20:47587730-47587973(+)$1	243	21	40	9.7617
UACUCGAUCCUUCUUGUGU	chr11:18330416-18330656(-)$1	240	134	153	11.9466
cuuuggacuugaauccugg	chr11:82959025-82959265(+)$1	240	186	205	12.1594
UUCAUUUCCCACCAAAUGU	chr20:50342319-50342559(-)$1	240	11	30	9.8045
AAGUUGACAAUUAUCAUUU	chr2:178096525-178096765(-)$1	240	99	118	11.9466
AGGUAAGAGAAUGCUGACU	chr11:10821615-10821865(-)$1	250	227	246	11.1147
GUGACCGAACUAGCAGUUG	chr2:148709897-148710139(-)$1	242	46	65	11.0503
UGGCAGACUACAUUUUGAC	chr12:57180929-57181171(+)$1	242	144	163	10.7218
UGGUUGUUUUUAUGCACCa	chr5:94005815-94006056(+)$1	241	207	226	10.7828
UAUAUGUGGGAAAGCAUAU	chr17:16455270-16455510(-)$1	240	7	26	11.5341
AGGCAGCAGACACGCCCUC	chr19:3976160-3976400(-)$1	240	46	65	11.2399

#DB
((..(((......))).))	chr1:173776467-173776707(-)$1	1	80	99	12.3203
..(((.(......).))).	chr5:81571793-81572033(-)$1	1	139	158	10.1822
(((((((......))).))	chr11:46680895-46681135(+)$1	1	126	145	12.0472
(..((((......))))..	chr8:119122593-119122833(-)$1	1	12	31	10.8913
(((((.((......)).))	chr17:5336526-5336766(-)$1	1	21	40	9.3304
)((((((......))))))	chr2:54150410-54150650(-)$1	1	195	214	10.3337
.((((((......))))))	chr6:34213124-34213364(+)$1	1	134	153	10.7597
))))(((......))))))	chrX:70756051-70756291(+)$1	1	89	108	10.6570
(...(((......)))...	chr11:60658153-60658393(-)$1	1	85	104	12.1796
(((.(((......))).))	chr3:182605294-182605534(+)$1	1	64	83	11.9466
..(((((......))....	chr17:39983730-39983970(-)$1	1	179	198	11.4184
(((.(((......))).))	chr5:76342233-76342473(+)$1	1	21	40	12.1902
((.((((......)))).)	chr11:62348480-62348727(-)$1	1	36	55	10.9096
(((((((......))))))	chr20:20617934-20618174(-)$1	1	57	76	11.5341
...((((......))))..	chr5:43502387-43502627(-)$1	1	72	91	10.8400
(...(((......)))..)	chr11:69458598-69458838(+)$1	1	117	136	11.4675
(((..((......)).)))	chr5:72798690-72798930(+)$1	1	208	227	11.1417
(((((((......))))))	chr2:27263486-27263726(+)$1	1	23	42	11.5341
((.((((......))))..	chr19:18423368-18423608(-)$1	1	3	22	11.1795
.(.((((......)))).)	chr9:79117217-79117457(+)$1	1	66	85	11.1032
(((((.(......).))))	chr4:87685674-87685914(+)$1	1	196	215	11.2421
(((((((......))))))	chr4:56819295-56819535(+)$1	1	187	206	11.5341
(((((((......))))))	chr11:62344557-62344838(-)$1	1	117	136	11.5341
.((((..(......)..))	chr19:38055997-38056237(-)$1	1	170	189	9.5935
.((((((......))))))	chr1:202302524-202302764(-)$1	1	138	157	10.8194
(....((......))....	chr1:62916484-62916726(+)$1	1	74	93	11.1977
.((((((......))))))	chr2:85769938-85770178(+)$1	1	143	162	9.7799
(((((.(......))))))	chr6:44219449-44219689(+)$1	1	210	229	11.8006
((((.((......))))))	chr19:58268100-58268340(+)$1	1	199	218	10.7828
(((((((......))))..	chr12:72025965-72026205(-)$1	1	137	156	10.0601
...((((......)))).)	chr19:30500106-30500346(+)$1	1	185	204	11.1700
(((((((......))).))	chr2:191300868-191301108(+)$1	1	66	85	12.0472
(((((.(......))))))	chr19:42373670-42373910(+)$1	1	131	150	11.2134
(((..((......))..))	chr19:14203260-14203500(-)$1	1	200	219	9.9601
(((((((......))))))	chr3:194140543-194140783(-)$1	1	2	21	11.3626
.((((((......))))))	chr11:62348918-62349278(-)$1	1	164	183	10.2348
(((.(((......))).))	chr1:53699171-53699411(-)$1	1	171	190	12.0945
(((.((......)).))))	chr10:124921783-124922023(+)$1	1	5	24	9.1054
(((((.(......))))))	chr21:34931511-34931751(+)$1	1	96	115	11.9872
.((((((......)).)))	chr11:62348556-62348975(-)$1	1	79	98	10.8727
(((((((......)))..)	chr11:94917483-94917723(-)$1	1	212	231	11.7316
(.(((((......))))).	chr1:214791881-214792121(+)$1	1	13	32	10.6007
....(((......))))))	chr20:47587730-47587973(+)$1	1	21	40	9.7617
(((.(((......))).))	chr11:18330416-18330656(-)$1	1	134	153	11.9466
....(((......))).))	chr11:82959025-82959265(+)$1	1	186	205	12.1594
(((((((......))))).	chr20:50342319-50342559(-)$1	1	11	30	9.8045
(((.(((......))).))	chr2:178096525-178096765(-)$1	1	99	118	11.9466
((((.((......)).)))	chr11:10821615-10821865(-)$1	1	227	246	11.1147
(((((.(......).))))	chr2:148709897-148710139(-)$1	1	46	65	11.0503
(((((((......)))).)	chr12:57180929-57181171(+)$1	1	144	163	10.7218
((((.((......))))))	chr5:94005815-94006056(+)$1	1	207	226	10.7828
(((((((......))))))	chr17:16455270-16455510(-)$1	1	7	26	11.5341
(((..((......))))))	chr19:3976160-3976400(-)$1	1	46	65	11.2399

#PSSM
e : 0.18	d : 0.15	g : 0.13	c : 0.09	f : 0.09	" : 0.05	[ : 0.05	' : 0.03	# : 0.03	b : 0.03	F : 0.01	! : 0.01	: : 0.01	i : 0.01	= : 0.01	& : 0.01	
e : 0.16	f : 0.16	d : 0.16	g : 0.11	" : 0.09	c : 0.07	# : 0.03	b : 0.03	' : 0.01	! : 0.01	a : 0.01	i : 0.01	= : 0.01	[ : 0.01	& : 0.01	
e : 0.18	f : 0.15	d : 0.15	g : 0.11	c : 0.09	" : 0.07	[ : 0.05	! : 0.03	# : 0.03	b : 0.03	i : 0.01	= : 0.01	& : 0.01	
d : 0.22	e : 0.16	f : 0.11	[ : 0.11	g : 0.11	! : 0.07	c : 0.05	" : 0.03	# : 0.03	i : 0.01	= : 0.01	& : 0.01	
c : 0.32	d : 0.18	f : 0.11	g : 0.11	e : 0.07	! : 0.05	[ : 0.05	# : 0.01	i : 0.01	b : 0.01	= : 0.01	
c : 0.26	b : 0.18	d : 0.15	[ : 0.13	f : 0.09	g : 0.09	e : 0.03	! : 0.01	i : 0.01	
c : 0.26	b : 0.18	d : 0.15	a : 0.11	f : 0.09	g : 0.09	e : 0.03	! : 0.01	i : 0.01	o : 0.01	
o : 0.96	b : 0.01	a : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.98	b : 0.01	
c : 0.26	b : 0.18	d : 0.15	a : 0.11	f : 0.09	g : 0.09	o : 0.03	e : 0.03	i : 0.01	
c : 0.26	b : 0.18	d : 0.15	g : 0.11	f : 0.09	] : 0.07	e : 0.05	a : 0.01	i : 0.01	= : 0.01	
c : 0.30	d : 0.18	f : 0.11	g : 0.11	e : 0.09	] : 0.05	4 : 0.03	2 : 0.03	b : 0.01	i : 0.01	= : 0.01	
d : 0.20	] : 0.18	f : 0.13	g : 0.13	e : 0.11	2 : 0.07	c : 0.03	4 : 0.03	F : 0.01	3 : 0.01	i : 0.01	= : 0.01	
e : 0.15	f : 0.15	d : 0.15	g : 0.13	c : 0.09	2 : 0.07	] : 0.07	3 : 0.03	4 : 0.03	F : 0.01	> : 0.01	b : 0.01	i : 0.01	= : 0.01	
d : 0.18	f : 0.15	e : 0.13	g : 0.13	c : 0.09	2 : 0.03	3 : 0.03	4 : 0.03	b : 0.03	8 : 0.01	F : 0.01	a : 0.01	> : 0.01	i : 0.01	= : 0.01	] : 0.01	5 : 0.01	

#score	586.7561734479111
#seq	53
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_UTR_m1_run2.txt

#BEAR
ccacccccc[ccclllcccccc]ccc]a333ccc	chr7:99708808-99709037(-)$1	229	2	36	11.8299
============oooooo============gggg	chr12:46753347-46753573(-)$1	226	110	144	17.1939
d!!==========oooooo==========22ddd	chr14:90752613-90752833(-)$1	220	183	217	17.4819
eeee[ccc[ddddooooooddddccc22eeeee2	chr19:34844510-34844729(+)$1	219	113	147	13.9292
========####cccmmmmccc===========:	chr12:46753026-46753291(-)$1	265	15	49	12.9649
ddddiiiiiiiiiooooooiiiiiiiii]dddd:	chr9:135138921-135139137(-)$1	216	0	34	15.1686
ff[ddddbb!!bboooooobb22bb]ddddffff	chr1:8414838-8415069(-)$1	231	173	207	12.4767
ddd!!ccceeeeeooooooeeeee]cccdddd]d	chr15:91503495-91503714(+)$1	219	46	80	13.1273
b!!eeeee"""bboooooobb4444eeeee22bb	chr21:46225523-46225741(-)$1	218	60	94	12.9862
==========!!bbnnnnnbb22==========5	chr3:120114869-120115095(-)$1	226	17	51	13.3600
eeee[dddd[cccoooooocccddddeeeee]cc	chr5:118861552-118861771(+)$1	219	104	138	13.8235
dddd!!cccddddoooooodddd]ccc]dddd44	chr17:36895806-36896027(-)$1	221	43	77	14.4537
g"""ccc[a[cccooooooccc]a]ccc333ggg	chr19:46268667-46268891(-)$1	224	159	193	16.6332
adddd[gggggggooooooggggggg333dddd:	chrX:135045082-135045302(-)$1	220	105	139	14.6140
rrrgggggggcccooooooccc:ggggggg!!a[	chr2:54096502-54096725(-)$1	223	74	108	13.4370
effffff[bbcccooooooccc]bb22ffffff:	chr12:49082994-49083216(-)$1	222	13	47	12.8486
ggggg[bb[ddddooooooddddbb]ggggggg2	chr2:25044560-25044783(+)$1	223	109	143	14.8068
=====!!a"""bboooooobba22==========	chr6:30684630-30684856(-)$1	226	186	220	17.3682
#dddd"""eeeeeooooooeeeee333dddd22f	chr6:1395194-1395424(+)$1	230	115	149	13.0805
c[ggggggg[cccnnnnncccggggggg22ccc]	chr17:76968322-76968542(-)$1	220	44	78	12.3875
=========ddddoooooodddd4444=======	chr3:15137583-15137822(-)$1	239	15	49	17.0388
ccc"""bb!!cccooooooccc22bbccc333ff	chr8:95892810-95893036(-)$1	226	90	124	16.0941
=============oooooo==============c	chr3:33425431-33425650(+)$1	219	103	137	18.7656
d!!bb$$$$$cccooooooccc4444bb22dddd	chr1:40218518-40218740(+)$1	222	112	146	13.5860
ddd!!bb[a[cccooooooccc]a]bb]dddd]g	chr15:75094851-75095076(+)$1	225	25	59	15.0884
fffff"""ccc!!aooooooa22ccc333fffff	chr4:174243742-174243961(+)$1	219	109	143	13.7133
dd"""bbffffffooooooffffff333bb4444	chr21:28217556-28217788(-)$1	232	69	103	13.6762
:ccc[dddd[cccooooooccc]dddd22ccccc	chr6:33739222-33739435(-)$1	213	96	130	13.6487
iiiiiiiii"""cccmmmmccciiiiiiiiihhh	chr19:15358810-15359027(-)$1	217	77	111	11.7964
dddd!!gggggggooooooggggggg333dddd5	chr12:4413187-4413420(+)$1	233	166	200	15.1912
[ccc"""ffffffooooooffffff333cccbb2	chr2:242168346-242168560(-)$1	214	24	58	14.3705
ffff"""ccccccooooooccc]cccffffff]b	chr19:55858798-55859030(+)$1	232	144	178	15.1423
eeee"""ffffffooooooffffff333eeeee6	chr1:181059196-181059428(+)$1	232	67	101	13.9537
eee####bb[cccooooooccc]bbeeeee4444	chrX:15349893-15350128(-)$1	235	20	54	15.4964
c[ddddbb[ddddoooooodddd]bb]ddddccc	chr16:70398411-70398627(+)$1	216	68	102	13.4600
ggggg[dddd[bboooooobb22ddddggggggg	chr17:78443605-78443837(-)$1	232	107	141	13.6962
:ccc!!gggggggooooooggggggg22ccc::c	chr19:32875325-32875570(+)$1	245	36	70	12.8435
====gggggggbboooooobb]ggggggg22===	chr17:40733595-40733818(-)$1	223	29	63	15.7493
!!===========nnnnn===========22bb:	chr5:137683187-137683412(+)$1	225	17	51	13.4324
gggggccc[ddddoooooodddd]ccc>>>>>>>	chr21:34793822-34794032(+)$1	210	125	159	13.6404
eee"""bb!!cccooooooccc22bb]eeeee]a	chr22:21801407-21801631(+)$1	224	77	111	15.6467
=======bb[ddddmmmmdddd]bb22=======	chr2:25961053-25961272(-)$1	219	12	46	11.5035
========="""annnnna333==========::	chr20:32699889-32700113(-)$1	224	2	36	13.2759
==========[bbnnnnnbb]==========hhh	chr6:75964562-75964779(-)$1	217	114	148	13.0876
ccc==========oooooo==========]cccG	chr4:17635380-17635601(+)$1	221	132	166	17.4948
!!ccc[bb[ddddoooooodddd]bbcccccc::	chr4:2834000-2834224(+)$1	224	140	174	13.0374
iiiiiii[ddddaooooooa]ddddiiiiiiiii	chr15:40759399-40759613(+)$1	214	149	183	15.4605
fffff[bb[ddddooooooddddbb]ffffffff	chr7:156765183-156765408(+)$1	225	30	64	12.9696
cca[==========nnnnn==========]a]cc	chr7:99017049-99017272(-)$1	223	128	162	14.1886
=========="""ccclllccc]==========d	chr22:20113924-20114146(+)$1	222	119	153	14.0063
"""ccc[ccc[bboooooobbccc22ccc4444c	chr17:61668003-61668220(+)$1	217	17	51	14.5391
[ccc!!gggggggooooooggggggg]ccc]eee	chr10:99236519-99236747(-)$1	228	72	106	15.6098
=========[cccooooooccc]==========5	chr6:36891856-36892078(+)$1	222	152	186	18.6722

#otherMatches

#Seq PSSM
ucccugcacaccagccugggugacagagcaagac	chr7:99708808-99709037(-)$1	229	2	36	11.8299
AUUUAUCGUACGUCACAGUGUAUGGUGAAUAUAU	chr12:46753347-46753573(-)$1	226	110	144	17.1939
UCCUUCAUAAAUGAGAAGGUAUUUAUGAAAUGAG	chr14:90752613-90752833(-)$1	220	183	217	17.4819
AGCCAGCUGCUGUCCAUGUGCAGAGCAAGGCUGC	chr19:34844510-34844729(+)$1	219	113	147	13.9292
AAGGGCCAGAAAUGUGGAGACAUGGUUUUUGUUA	chr12:46753026-46753291(-)$1	265	15	49	12.9649
CAGCCUAGCUUGGAAUAAGCUGAGUUAGUGCUGG	chr9:135138921-135139137(-)$1	216	0	34	15.1686
ACAUCCAGAAAGCUUCCCUGCAAUCUUGGGGUUU	chr1:8414838-8415069(-)$1	231	173	207	12.4767
UAUUAUCAUUCUGAAGCCACAGAACUGAAUGAAG	chr15:91503495-91503714(+)$1	219	46	80	13.1273
CUUGAAAUCUUGCUGAAAUGUUCUCAUUUCCUGU	chr21:46225523-46225741(-)$1	218	60	94	12.9862
uuuaauauuuuauuuuCUUGACUAGGUAUUAAGC	chr3:120114869-120115095(-)$1	226	17	51	13.3600
CUGCCAGGCGUGUGUUACAGCAGUUUGCAGAUAA	chr5:118861552-118861771(+)$1	219	104	138	13.8235
GGAGUUGGAAGUUGGCUCUGACUCUCCUCUCUCU	chr17:36895806-36896027(-)$1	221	43	77	14.4537
GACAUUGGUGCUGAAGACGCAGGGACAGGAAUGG	chr19:46268667-46268891(-)$1	224	159	193	16.6332
cggucuuuugggacuggcuucCCAAAUAUGAUUU	chrX:135045082-135045302(-)$1	220	105	139	14.6140
UUAAGCGGUCUGCUACAGUGUAACUUUCUUACCA	chr2:54096502-54096725(-)$1	223	74	108	13.4370
GAGAUUUUCAUGUUGUAUCACACUGUCAAGUUUU	chr12:49082994-49083216(-)$1	222	13	47	12.8486
CUUGCCACUGUGACAAAGUUCACGUAGCAGGUCU	chr2:25044560-25044783(+)$1	223	109	143	14.8068
GCAUAUUUUCAGGUGAAUUCCAUUUAUGCUAUUU	chr6:30684630-30684856(-)$1	226	186	220	17.3682
CCUGCAGGCUCCCACAUGAGGGAGAGGGCAGACU	chr6:1395194-1395424(+)$1	230	115	149	13.0805
GCUGCUGCCCAGGAGCGACCUGGCGGUGCCCAGC	chr17:76968322-76968542(-)$1	220	44	78	12.3875
UUUCUUUCUUAGGGCUCCUCCUACUCCAGAGAGG	chr3:15137583-15137822(-)$1	239	15	49	17.0388
GUCCUUUCUAAAUUCCUCCAUUGUGAGAUAAGGA	chr8:95892810-95893036(-)$1	226	90	124	16.0941
AGUACCUGUGGCCAUGAGAGGCUGCGGGUACUGG	chr3:33425431-33425650(+)$1	219	103	137	18.7656
CUUCCUGACAUGUGACAAGACAGACUGGCUGGAU	chr1:40218518-40218740(+)$1	222	112	146	13.5860
UGGGCCUGUGGGGACUGAACCUGGAAGAUCAUGG	chr15:75094851-75095076(+)$1	225	25	59	15.0884
CUGACUGAGGUAAGACUUUCCAAGCCCUUGUUAG	chr4:174243742-174243961(+)$1	219	109	143	13.7133
GGAAAGCGGCUCCGAGCCAGGGGCUAUUGCAAAG	chr21:28217556-28217788(-)$1	232	69	103	13.6762
UGCGAGAAGCCUCUCCAGCGAGUCUUCCCCGUGU	chr6:33739222-33739435(-)$1	213	96	130	13.6487
CCCCUGAGGAACUGCAUCUGCGUUUCAGGGGCUU	chr19:15358810-15359027(-)$1	217	77	111	11.7964
UAAUUGAUUUUCUAGUUCAAGAAGAUAAUAUUGG	chr12:4413187-4413420(+)$1	233	166	200	15.1912
UGCCAGAGCGCCUCAGCACAGGUGUCAGGGUGCA	chr2:242168346-242168560(-)$1	214	24	58	14.3705
CUGGAAUGGGGUUGGUUUGGACACCCCCAGGGAU	chr19:55858798-55859030(+)$1	232	144	178	15.1423
UAAGUUUGUCUUGUGGCAUUAAGACUAUUUUGCU	chr1:181059196-181059428(+)$1	232	67	101	13.9537
GAGGACACAUCUCUUAACUGGGUUGCUCUAAGAA	chrX:15349893-15350128(-)$1	235	20	54	15.4964
ACUGGUAAAACAGCUGCCUUUGUCUUAGCCAUGC	chr16:70398411-70398627(+)$1	216	68	102	13.4600
UCUGGAGCUGUGCUGCACUGCUUCAGCCCAGAGG	chr17:78443605-78443837(-)$1	232	107	141	13.6962
AAGGUCGGUGCGCUCUUCUGUGCACCAUCCUCAC	chr19:32875325-32875570(+)$1	245	36	70	12.8435
UUCUCCCCAUCCCACUUAAGGUGAUGGGGCAAGG	chr17:40733595-40733818(-)$1	223	29	63	15.7493
UCAAGAGGAGGGCACCAAGUUUUCCUUUUUUCUA	chr5:137683187-137683412(+)$1	225	17	51	13.4324
AUUCUGCCUGGGUGACAAUGCCUUGGUUUCAACA	chr21:34793822-34794032(+)$1	210	125	159	13.6404
GGAACAGGUGCUGGGGGUGCAGAUCCCUCCCUCC	chr22:21801407-21801631(+)$1	224	77	111	15.6467
ACAUGGUGAUAGGCAGGGGCCUUUCCUACCAUGU	chr2:25961053-25961272(-)$1	219	12	46	11.5035
CGCCUGCGCCUUGGCGAGCUCUGCGCAGGCGCAU	chr20:32699889-32700113(-)$1	224	2	36	13.2759
UAUGUACAUGAUAAAUUAUAAUAUGUAUAUGGUU	chr6:75964562-75964779(-)$1	217	114	148	13.0876
UGUUUGUAUUAAUGGACAGGUUAGUGCAAUGCAA	chr4:17635380-17635601(+)$1	221	132	166	17.4948
UAGGCGCCAGGGGAAGAUGCCCCAGGGCCCCUCU	chr4:2834000-2834224(+)$1	224	140	174	13.0374
UCCUAUCUGUACCAAAGAGGAGUAUGGUGGGAGA	chr15:40759399-40759613(+)$1	214	149	183	15.4605
CUGUAAGUCUGUUCAUUUUAACAACAUACAGggc	chr7:156765183-156765408(+)$1	225	30	64	12.9696
UGCUCGCUGCUCCCAGGAAGGGGGUGGCGUGACA	chr7:99017049-99017272(-)$1	223	128	162	14.1886
ACAGGUGCUUCCUGGGGAGCCCUGAGCACUUGUC	chr22:20113924-20114146(+)$1	222	119	153	14.0063
GAAAGUUGGCUGUUUCCUUGCGCUCUGCUCCUAC	chr17:61668003-61668220(+)$1	217	17	51	14.5391
UGAUGGAUGGGGAAAAGGAUCCCCGUAAUCUUCU	chr10:99236519-99236747(-)$1	228	72	106	15.6098
AGGCAGCACUGCUCUCGUCAGCUGUGUUGCCUUU	chr6:36891856-36892078(+)$1	222	152	186	18.6722

#DB
(((((((((.(((...)))))).))).)...)))	chr7:99708808-99709037(-)$1	1	2	36	11.8299
((((((((((((......))))))))))))((((	chr12:46753347-46753573(-)$1	1	110	144	17.1939
(..((((((((((......))))))))))..)))	chr14:90752613-90752833(-)$1	1	183	217	17.4819
((((.(((.((((......)))))))..))))).	chr19:34844510-34844729(+)$1	1	113	147	13.9292
((((((((....(((....)))))))))))))).	chr12:46753026-46753291(-)$1	1	15	49	12.9649
(((((((((((((......))))))))).)))).	chr9:135138921-135139137(-)$1	1	0	34	15.1686
((.((((((..((......))..)).))))))))	chr1:8414838-8415069(-)$1	1	173	207	12.4767
(((..((((((((......))))).))))))).)	chr15:91503495-91503714(+)$1	1	46	80	13.1273
(..(((((...((......))....)))))..))	chr21:46225523-46225741(-)$1	1	60	94	12.9862
((((((((((..((.....))..)))))))))).	chr3:120114869-120115095(-)$1	1	17	51	13.3600
((((.((((.(((......)))))))))))).))	chr5:118861552-118861771(+)$1	1	104	138	13.8235
((((..(((((((......)))).))).))))..	chr17:36895806-36896027(-)$1	1	43	77	14.4537
(...(((.(.(((......))).).)))...)))	chr19:46268667-46268891(-)$1	1	159	193	16.6332
)((((.(((((((......)))))))...)))).	chrX:135045082-135045302(-)$1	1	105	139	14.6140
...)))))))(((......))).(((((((..(.	chr2:54096502-54096725(-)$1	1	74	108	13.4370
)((((((.(((((......))).))..)))))).	chr12:49082994-49083216(-)$1	1	13	47	12.8486
(((((.((.((((......)))))).))))))).	chr2:25044560-25044783(+)$1	1	109	143	14.8068
(((((..(...((......)))..))))))))))	chr6:30684630-30684856(-)$1	1	186	220	17.3682
.((((...(((((......)))))...))))..)	chr6:1395194-1395424(+)$1	1	115	149	13.0805
(.(((((((.(((.....))))))))))..))).	chr17:76968322-76968542(-)$1	1	44	78	12.3875
(((((((((((((......))))....)))))))	chr3:15137583-15137822(-)$1	1	15	49	17.0388
(((...((..(((......)))..)))))...))	chr8:95892810-95893036(-)$1	1	90	124	16.0941
(((((((((((((......))))))))))))))(	chr3:33425431-33425650(+)$1	1	103	137	18.7656
(..((.....(((......)))....))..))))	chr1:40218518-40218740(+)$1	1	112	146	13.5860
(((..((.(.(((......))).).)).)))).)	chr15:75094851-75095076(+)$1	1	25	59	15.0884
(((((...(((..(......)..)))...)))))	chr4:174243742-174243961(+)$1	1	109	143	13.7133
((...((((((((......))))))...))....	chr21:28217556-28217788(-)$1	1	69	103	13.6762
.(((.((((.(((......))).))))..)))((	chr6:33739222-33739435(-)$1	1	96	130	13.6487
(((((((((...(((....)))))))))))))))	chr19:15358810-15359027(-)$1	1	77	111	11.7964
((((..(((((((......)))))))...)))).	chr12:4413187-4413420(+)$1	1	166	200	15.1912
.(((...((((((......))))))...))))).	chr2:242168346-242168560(-)$1	1	24	58	14.3705
((((...((((((......))).))))))))).)	chr19:55858798-55859030(+)$1	1	144	178	15.1423
((((...((((((......))))))...))))).	chr1:181059196-181059428(+)$1	1	67	101	13.9537
(((....((.(((......))).)))))))....	chrX:15349893-15350128(-)$1	1	20	54	15.4964
(.((((((.((((......)))).)).)))))))	chr16:70398411-70398627(+)$1	1	68	102	13.4600
(((((.((((.((......))..)))))))))))	chr17:78443605-78443837(-)$1	1	107	141	13.6962
.(((..(((((((......)))))))..)))..(	chr19:32875325-32875570(+)$1	1	36	70	12.8435
(((((((((((((......)).)))))))..)))	chr17:40733595-40733818(-)$1	1	29	63	15.7493
..(((((((((((.....)))))))))))..)).	chr5:137683187-137683412(+)$1	1	17	51	13.4324
((((((((.((((......)))).))).......	chr21:34793822-34794032(+)$1	1	125	159	13.6404
(((...((..(((......)))..)).))))).)	chr22:21801407-21801631(+)$1	1	77	111	15.6467
(((((((((.((((....)))).))..)))))))	chr2:25961053-25961272(-)$1	1	12	46	11.5035
(((((((((...(.....)...))))))))))..	chr20:32699889-32700113(-)$1	1	2	36	13.2759
((((((((((.((.....)).))))))))))(((	chr6:75964562-75964779(-)$1	1	114	148	13.0876
(((((((((((((......)))))))))).))))	chr4:17635380-17635601(+)$1	1	132	166	17.4948
..(((.((.((((......)))).))))))))..	chr4:2834000-2834224(+)$1	1	140	174	13.0374
(((((((.(((((......).)))))))))))))	chr15:40759399-40759613(+)$1	1	149	183	15.4605
(((((.((.((((......)))))).))))))((	chr7:156765183-156765408(+)$1	1	30	64	12.9696
(((.((((((((((.....)))))))))).).))	chr7:99017049-99017272(-)$1	1	128	162	14.1886
((((((((((...(((...))).))))))))))(	chr22:20113924-20114146(+)$1	1	119	153	14.0063
...(((.(((.((......)))))..)))....)	chr17:61668003-61668220(+)$1	1	17	51	14.5391
.(((..(((((((......))))))).))).)))	chr10:99236519-99236747(-)$1	1	72	106	15.6098
(((((((((.(((......))).)))))))))).	chr6:36891856-36892078(+)$1	1	152	186	18.6722

#PSSM
= : 0.22	d : 0.15	c : 0.11	e : 0.11	f : 0.07	g : 0.07	: : 0.03	i : 0.03	[ : 0.03	! : 0.03	b : 0.01	a : 0.01	r : 0.01	# : 0.01	" : 0.01	
= : 0.22	c : 0.15	d : 0.15	! : 0.09	e : 0.09	f : 0.09	g : 0.05	" : 0.03	[ : 0.03	i : 0.03	r : 0.01	
= : 0.24	d : 0.15	c : 0.13	e : 0.09	f : 0.07	g : 0.07	! : 0.05	" : 0.05	a : 0.03	i : 0.03	[ : 0.01	r : 0.01	
= : 0.28	c : 0.13	d : 0.13	g : 0.09	e : 0.07	" : 0.07	f : 0.07	! : 0.03	i : 0.03	b : 0.01	# : 0.01	[ : 0.01	
= : 0.28	! : 0.11	g : 0.11	" : 0.11	c : 0.07	d : 0.07	[ : 0.05	i : 0.05	f : 0.05	e : 0.01	b : 0.01	# : 0.01	
= : 0.26	" : 0.13	c : 0.11	! : 0.09	[ : 0.09	d : 0.07	i : 0.05	g : 0.05	b : 0.03	e : 0.01	f : 0.01	$ : 0.01	# : 0.01	
= : 0.26	b : 0.15	g : 0.13	c : 0.11	" : 0.09	d : 0.07	i : 0.05	e : 0.01	f : 0.01	! : 0.01	$ : 0.01	# : 0.01	[ : 0.01	
= : 0.24	b : 0.16	c : 0.13	g : 0.13	[ : 0.07	d : 0.05	f : 0.05	i : 0.03	" : 0.03	e : 0.01	a : 0.01	$ : 0.01	
= : 0.22	g : 0.13	[ : 0.11	c : 0.09	b : 0.07	d : 0.07	f : 0.05	i : 0.03	e : 0.03	" : 0.03	a : 0.03	! : 0.03	# : 0.01	$ : 0.01	
d : 0.18	[ : 0.16	= : 0.16	g : 0.11	" : 0.07	! : 0.05	c : 0.05	f : 0.05	e : 0.03	# : 0.01	i : 0.01	b : 0.01	$ : 0.01	
c : 0.28	d : 0.18	= : 0.11	" : 0.09	g : 0.09	f : 0.05	[ : 0.05	! : 0.03	e : 0.03	# : 0.01	i : 0.01	
c : 0.26	d : 0.18	b : 0.13	= : 0.11	g : 0.07	f : 0.05	" : 0.05	e : 0.03	! : 0.03	# : 0.01	i : 0.01	
c : 0.30	d : 0.16	b : 0.15	= : 0.09	g : 0.07	f : 0.05	e : 0.03	a : 0.03	o : 0.01	i : 0.01	! : 0.01	" : 0.01	
o : 0.77	n : 0.07	c : 0.05	l : 0.01	b : 0.01	a : 0.01	d : 0.01	= : 0.01	
o : 0.79	n : 0.11	c : 0.05	l : 0.01	m : 0.01	
o : 0.79	n : 0.11	m : 0.05	l : 0.01	c : 0.01	
o : 0.79	n : 0.11	m : 0.05	c : 0.01	l : 0.01	
o : 0.79	n : 0.11	m : 0.05	c : 0.01	l : 0.01	
o : 0.77	c : 0.03	= : 0.03	m : 0.03	n : 0.03	d : 0.01	a : 0.01	b : 0.01	l : 0.01	
c : 0.32	d : 0.16	b : 0.15	= : 0.11	g : 0.07	f : 0.05	e : 0.03	i : 0.01	o : 0.01	3 : 0.01	a : 0.01	
c : 0.32	d : 0.16	b : 0.13	= : 0.11	g : 0.07	f : 0.05	e : 0.03	] : 0.03	i : 0.01	a : 0.01	3 : 0.01	
c : 0.32	d : 0.18	= : 0.13	g : 0.09	2 : 0.07	f : 0.05	e : 0.03	i : 0.01	4 : 0.01	a : 0.01	] : 0.01	3 : 0.01	
] : 0.18	d : 0.18	= : 0.16	2 : 0.13	g : 0.11	f : 0.05	i : 0.03	e : 0.03	4 : 0.03	: : 0.01	c : 0.01	
= : 0.22	g : 0.13	b : 0.11	c : 0.09	d : 0.07	] : 0.07	4 : 0.05	2 : 0.05	f : 0.05	i : 0.03	e : 0.03	a : 0.03	
= : 0.24	b : 0.18	g : 0.13	c : 0.11	d : 0.07	] : 0.05	4 : 0.05	f : 0.05	i : 0.03	3 : 0.01	2 : 0.01	
= : 0.24	c : 0.15	g : 0.13	b : 0.09	3 : 0.07	i : 0.05	] : 0.05	d : 0.05	2 : 0.05	e : 0.03	4 : 0.03	
= : 0.24	c : 0.13	3 : 0.13	] : 0.07	2 : 0.07	g : 0.07	i : 0.05	d : 0.05	e : 0.05	b : 0.03	f : 0.03	4 : 0.01	
= : 0.28	c : 0.11	3 : 0.11	g : 0.09	e : 0.07	2 : 0.05	i : 0.05	d : 0.05	f : 0.05	] : 0.03	a : 0.01	b : 0.01	> : 0.01	
= : 0.28	e : 0.11	d : 0.11	c : 0.11	3 : 0.09	g : 0.07	f : 0.05	2 : 0.05	i : 0.03	] : 0.01	b : 0.01	> : 0.01	
= : 0.20	d : 0.16	e : 0.11	2 : 0.09	c : 0.09	f : 0.07	3 : 0.05	g : 0.05	i : 0.03	] : 0.03	b : 0.01	> : 0.01	4 : 0.01	
= : 0.18	d : 0.16	c : 0.11	f : 0.09	2 : 0.07	e : 0.07	3 : 0.05	g : 0.05	4 : 0.05	i : 0.03	! : 0.01	> : 0.01	a : 0.01	] : 0.01	
= : 0.18	d : 0.15	c : 0.11	f : 0.09	g : 0.07	e : 0.07	4 : 0.05	2 : 0.03	] : 0.03	h : 0.03	b : 0.03	! : 0.01	3 : 0.01	: : 0.01	> : 0.01	i : 0.01	
= : 0.16	c : 0.13	d : 0.09	f : 0.09	g : 0.07	] : 0.07	4 : 0.07	e : 0.05	b : 0.05	: : 0.05	h : 0.03	a : 0.01	2 : 0.01	> : 0.01	i : 0.01	
c : 0.15	: : 0.13	f : 0.09	g : 0.07	d : 0.07	= : 0.07	2 : 0.05	5 : 0.05	4 : 0.05	b : 0.03	h : 0.03	[ : 0.01	] : 0.01	6 : 0.01	> : 0.01	a : 0.01	G : 0.01	i : 0.01	e : 0.01	

#score	763.8493402278017
#seq	53
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_UTR_m2_run2.txt

#BEAR
cc[==========oooooo==========ccc5	chr5:135518017-135518252(+)$1	235	59	92	18.3987
===!!ccc[ddddooooooddddccc=======	chr19:45166105-45166330(+)$1	225	176	209	16.1403
iiiii####ddddooooooddddiiiiiiiiie	chr14:55515050-55515307(+)$1	257	179	212	16.4348
feeeee####cccooooooccc4444eeeee44	chr9:112140432-112140689(-)$1	257	28	61	14.6463
d####iiiiiiiiinnnnniiiiiiiii333dd	chr8:38070519-38070741(+)$1	222	160	193	12.9413
a[ccc[ddddcccooooooccc]ddddccc]a:	chr14:69926111-69926322(+)$1	211	9	42	13.1733
c[bb[eeeee[bboooooobbeeeee]bb]ccc	chr14:34902713-34902938(-)$1	225	121	154	13.4295
GGG===========oooooo===========::	chr5:36182892-36183106(+)$1	214	40	73	14.8341
=============nnnnn==============:	chr1:10367931-10368159(+)$1	228	73	106	15.7907
=====[dddd[bboooooobb]dddd22=====	chr5:134194479-134194751(+)$1	272	18	51	15.5813
d!!gggggggcccooooooccc22ggggggg22	chr3:133308274-133308501(+)$1	227	168	201	15.7746
##dddd[a[ddddoooooodddd]a]dddd444	chr22:41325646-41325870(+)$1	224	140	173	12.8353
#iiiiiiiiicccooooooccc333iiiiiiii	chr1:227844349-227844584(+)$1	235	108	141	18.4459
gggggg!!bb[bboooooobb]bb]gggggggf	chr2:85548808-85549064(-)$1	256	146	179	15.3310
eeeee[ccc[cccooooooccc]ccc]eeeee:	chr1:11082862-11083094(+)$1	232	155	188	13.9111
E==========bboooooobb]==========:	chr2:170495096-170495330(+)$1	234	159	192	18.1791
iiiiiiii!!cccooooooccc333iiiiiiii	chr14:35180398-35180612(-)$1	214	43	76	18.7404
eeee[a[bb[cccooooooccc]bb]a]eeeee	chr6:116597867-116598078(-)$1	211	93	126	13.6778
:===========rrrrrrrrr===========:	chrX:131208584-131208830(+)$1	246	47	80	14.0976
iiiiiiiii!!bboooooobb22iiiiiiiii:	chr12:22840867-22841099(+)$1	232	158	191	17.7875
ggg[bbgggggggooooooggggggg333bb]g	chr11:32126499-32126722(+)$1	223	125	158	14.7059
ggggggbb[cccooooooccc]bb]ggggggg:	chr6:53132345-53132595(-)$1	250	1	34	13.5332
===[bb!!eeeeeooooooeeeee]bb]=====	chr8:28203267-28203497(-)$1	230	30	63	14.6480
========eeeeemmmmeeeee333========	chr10:98984026-98984261(-)$1	235	62	95	12.7776
iiiieeeee[cccooooooccc]eeeee4444i	chr17:18112313-18112535(+)$1	222	176	209	14.9932
ccc[gggggggbboooooobb]ggggggg]ccc	chr1:154556559-154556784(-)$1	225	132	165	16.2441
ggiiiiiiiii[ddddlllddddiiiiiiiii:	chr1:178887557-178887806(+)$1	249	96	129	12.3190
e[gggggggddddoooooodddd22ggggggg]	chr7:135611827-135612068(-)$1	241	88	121	15.1218
eeeee[a[eeeeeooooooeeeee]a]eeeeec	chr1:244870816-244871067(+)$1	251	114	147	13.0930
ccggggggg!!bboooooobb22ggggggg]cc	chr11:10818994-10819227(-)$1	233	53	86	16.4254
========"""ddddnnnnndddd4444=====	chr10:62553846-62554077(+)$1	231	193	226	12.2025
eee"""a!!bbbboooooobb]bb22a333eee	chr11:47487615-47487838(-)$1	223	102	135	13.8726
eiiiiiiiii[bbnnnnnbbiiiiiiiii]eee	chr8:95893129-95893359(-)$1	230	47	80	13.4386
c[===========mmmm===========]ccc:	chr17:27587557-27587785(-)$1	228	5	38	14.0124
ccddddgggggggooooooggggggg]dddd]c	chr17:20905479-20905709(-)$1	230	78	111	13.6945
========"""bboooooobb]==========:	chr1:38422821-38423046(-)$1	225	2	35	19.2396
========"""bboooooobb==========::	chr1:85111956-85112213(-)$1	257	152	185	18.1358
ggggga[iiiiiiiiillliiiiiiiii]a]gg	chr1:67877192-67877417(-)$1	225	66	99	13.1026
cc[eeeee!!cccooooooccc22eeeee]ccc	chrX:102930375-102930598(-)$1	223	182	215	14.7095
::===========oooooo===========:::	chr8:12942702-12942927(-)$1	225	72	105	14.7499
bb[==========oooooo==========]bbd	chr2:196601545-196601771(+)$1	226	48	81	17.8843
===========rrrrrrrrr============:	chr10:61549570-61549805(-)$1	235	159	192	15.2368
====!!ccc!!bboooooobb4444ccc333==	chr5:32603131-32603387(+)$1	256	41	74	17.1098
ccc$$$$$eeeeeooooooeeeee333ccc]gg	chr10:129896558-129896773(-)$1	215	153	186	13.0762
c!!eeeee"""bboooooobb4444eeeee]cc	chr16:83845468-83845691(+)$1	223	177	210	15.2552
[ggggggg!!cccooooooccc22ggggggg]c	chr7:94296686-94296908(+)$1	222	18	51	16.7572
===========ssssssssss============	chrX:107965224-107965435(-)$1	211	149	182	13.8647
cc[a[ccc[ddddoooooodddd]ccc]a]ccc	chr21:46226224-46226474(-)$1	250	1	34	14.4506
[============ppppppp============]	chr2:219459977-219460225(+)$1	248	122	155	13.8444
===========qqqqqqqq===========ggg	chr6:11579492-11579727(+)$1	235	91	124	13.6447

#otherMatches

#Seq PSSM
UGUAUUUUGAAAUUCACUUAUUUUAAAAUCGAA	chr5:135518017-135518252(+)$1	235	59	92	18.3987
CAGCAUCUGCAGCCAGCAAGCUGGGACUGGCAG	chr19:45166105-45166330(+)$1	225	176	209	16.1403
AAGAACAGAAAGCACAAAGGUUUUUCUUUUCUU	chr14:55515050-55515307(+)$1	257	179	212	16.4348
CUGAUGUUAAUUUAUUCUAAGAACACCAUCAUU	chr9:112140432-112140689(-)$1	257	28	61	14.6463
AUACUGACUUUGGACUGAAUUCAAAGUUUUCUU	chr8:38070519-38070741(+)$1	222	160	193	12.9413
GUUCUAGGCUUUCCUUCAAGAACAGUCAGAUCA	chr14:69926111-69926322(+)$1	211	9	42	13.1733
CAAGUAAUAUAUAUGUGUUUAAUAUUUUUAGAG	chr14:34902713-34902938(-)$1	225	121	154	13.4295
AGCUUUUAAAAUGACUUGCUUUGUUUUAGAAAG	chr5:36182892-36183106(+)$1	214	40	73	14.8341
AAUGUGAUGAAUGGGAAUUGUUUAUUACAUUGA	chr1:10367931-10368159(+)$1	228	73	106	15.7907
GGAAGAAAAUGAGUAGUAUCUGGUUUAAUUUUU	chr5:134194479-134194751(+)$1	272	18	51	15.5813
CAGACUUGCUACUGGCAAGAGUGAAGCAAGUGG	chr3:133308274-133308501(+)$1	227	168	201	15.7746
AAGCUGUGUGUGAUCUUACUCAUUCUCAGCCAU	chr22:41325646-41325870(+)$1	224	140	173	12.8353
UAAGAUAAUACAGUAGCUUUUGAAAUGUUAUUU	chr1:227844349-227844584(+)$1	235	108	141	18.4459
GGCUUUUAUGAGAUACAUUUCCCACAAAGUCCA	chr2:85548808-85549064(-)$1	256	146	179	15.3310
UGGACUUGUCAAGUGAAUUCUUUGCAUGUUCAA	chr1:11082862-11083094(+)$1	232	155	188	13.9111
CAUAUCCAAAGUCCAUUUAGAGUUUUGGGUGUU	chr2:170495096-170495330(+)$1	234	159	192	18.1791
UAUGGCAAACACAUGCUUUUGUAUCUUGUCAUA	chr14:35180398-35180612(-)$1	214	43	76	18.7404
UACUGUGAAAUUGCUCUGACAAAUUGGAAGUGU	chr6:116597867-116598078(-)$1	211	93	126	13.6778
GUGGGGAGGUGUAAAUAAGUCAUACCUUCUUAA	chrX:131208584-131208830(+)$1	246	47	80	14.0976
AGGAAAUUAAAAAUGUAAUUUAAUAAUUUCCUA	chr12:22840867-22841099(+)$1	232	158	191	17.7875
UUUGUUUGUUUUUCUAUUAAAAAGCAAUCAAGA	chr11:32126499-32126722(+)$1	223	125	158	14.7059
AGAUAUUCUUGGAACCACUCAUGACAUAUCUUA	chr6:53132345-53132595(-)$1	250	1	34	13.5332
gaaagcaauuuuguaauuucagagaguguuuug	chr8:28203267-28203497(-)$1	230	30	63	14.6480
AACUGCUUAGAAGCCCCUUUCUCUAGAGCAGUU	chr10:98984026-98984261(-)$1	235	62	95	12.7776
AGUUAGACUUGCCACGUUGGGUCAGUUUUAGAA	chr17:18112313-18112535(+)$1	222	176	209	14.9932
CCCAUCCUGCACUUUAGCCAGCUGCAGGGCGGG	chr1:154556559-154556784(-)$1	225	132	165	16.2441
UAAGCUGGAAGAUGUUUUUGAUACUUUCGGCUC	chr1:178887557-178887806(+)$1	249	96	129	12.3190
GUGUGGAAGCUGCAAACAAGUAGGCCUUUUAUU	chr7:135611827-135612068(-)$1	241	88	121	15.1218
UGCUUGUAAUAUUUUUAAUAAUGUGAGGAGUAC	chr1:244870816-244871067(+)$1	251	114	147	13.0930
UCAAAUAUUUUAGGAGUAUCUUUAAUGUUUAGA	chr11:10818994-10819227(-)$1	233	53	86	16.4254
UUUUCCUGUAGUUGGAACUACUAAAAUUUAGGA	chr10:62553846-62554077(+)$1	231	193	226	12.2025
GCUUUUCUUACCUAAUCACAGAGUUUGUGUAGU	chr11:47487615-47487838(-)$1	223	102	135	13.8726
CUUGAAUUUCUACAAAUGGUGAAAUUUAAUGUU	chr8:95893129-95893359(-)$1	230	47	80	13.4386
UGUUUUUACAAAUAACAGUUUGUAGGGAAAAUA	chr17:27587557-27587785(-)$1	228	5	38	14.0124
AAUUACUGAGUUUAUACAGAAAUUUAGGUAACU	chr17:20905479-20905709(-)$1	230	78	111	13.6945
UGGGCUGUGUUGGAAUGGGCCUGCAGCCCAACA	chr1:38422821-38423046(-)$1	225	2	35	19.2396
AGAUGAUACUCUGGAAAAACAUGUCAUUUCAUU	chr1:85111956-85112213(-)$1	257	152	185	18.1358
UAAAAGAAACUUUUAUGUUAUAAGAGUUACUUU	chr1:67877192-67877417(-)$1	225	66	99	13.1026
AGUGUGCCUUUCAUGUUACUGGUUGGUAUUCUG	chrX:102930375-102930598(-)$1	223	182	215	14.7095
GUGUUUGUUGCUGGCUGAAUGGCAAUAGAUGUC	chr8:12942702-12942927(-)$1	225	72	105	14.7499
AGUGAUUUAGAUAUCUAUCUAUCUAGAUUUCUG	chr2:196601545-196601771(+)$1	226	48	81	17.8843
AUAAUUGAUAAUGUGAAUUUUUGUUAAUUGUUC	chr10:61549570-61549805(-)$1	235	159	192	15.2368
UGAAAUCUAUUACCUACAUGUUUUCUAGUUGUU	chr5:32603131-32603387(+)$1	256	41	74	17.1098
ACUCUAUCUGGCAGCCCGAUGCCACCCAGUACA	chr10:129896558-129896773(-)$1	215	153	186	13.0762
GCCACUGUCUUGUGUCAGAACUUUUACAGUACA	chr16:83845468-83845691(+)$1	223	177	210	15.2552
AGAGGAGUCUAACGGUGAAGUUUCACUUUUCAU	chr7:94296686-94296908(+)$1	222	18	51	16.7572
GGAAGGAAGGUAUGAUCUGGAAUCUUUUUUCCG	chrX:107965224-107965435(-)$1	211	149	182	13.8647
AUUGGUGUUUCCCGCAGUGGGGAUGCAGCUGUU	chr21:46226224-46226474(-)$1	250	1	34	14.4506
UGGAGGGCUGGGUUCUGCUCACUCAGUCuuuuu	chr2:219459977-219460225(+)$1	248	122	155	13.8444
cucauguaguuauugugaggauuacgugagauu	chr6:11579492-11579727(+)$1	235	91	124	13.6447

#DB
((.((((((((((......))))))))))))).	chr5:135518017-135518252(+)$1	1	59	92	18.3987
(((..(((.((((......))))))))))))))	chr19:45166105-45166330(+)$1	1	176	209	16.1403
(((((....((((......)))))))))))))(	chr14:55515050-55515307(+)$1	1	179	212	16.4348
((((((....(((......)))....)))))..	chr9:112140432-112140689(-)$1	1	28	61	14.6463
(....(((((((((.....)))))))))...))	chr8:38070519-38070741(+)$1	1	160	193	12.9413
(.(((.(((((((......))).))))))).).	chr14:69926111-69926322(+)$1	1	9	42	13.1733
(.((.(((((.((......))))))).)).)))	chr14:34902713-34902938(-)$1	1	121	154	13.4295
((((((((((((((......)))))))))))..	chr5:36182892-36183106(+)$1	1	40	73	14.8341
(((((((((((((.....)))))))))))))).	chr1:10367931-10368159(+)$1	1	73	106	15.7907
(((((.((((.((......)).))))..)))))	chr5:134194479-134194751(+)$1	1	18	51	15.5813
(..((((((((((......)))..)))))))..	chr3:133308274-133308501(+)$1	1	168	201	15.7746
..((((.(.((((......)))).).))))...	chr22:41325646-41325870(+)$1	1	140	173	12.8353
.((((((((((((......)))...))))))))	chr1:227844349-227844584(+)$1	1	108	141	18.4459
((((((..((.((......)).)).)))))))(	chr2:85548808-85549064(-)$1	1	146	179	15.3310
(((((.(((.(((......))).))).))))).	chr1:11082862-11083094(+)$1	1	155	188	13.9111
)((((((((((((......)).)))))))))).	chr2:170495096-170495330(+)$1	1	159	192	18.1791
((((((((..(((......)))...))))))))	chr14:35180398-35180612(-)$1	1	43	76	18.7404
((((.(.((.(((......))).)).).)))))	chr6:116597867-116598078(-)$1	1	93	126	13.6778
.(((((((((((.........))))))))))).	chrX:131208584-131208830(+)$1	1	47	80	14.0976
(((((((((..((......))..))))))))).	chr12:22840867-22841099(+)$1	1	158	191	17.7875
(((.(((((((((......)))))))...)).)	chr11:32126499-32126722(+)$1	1	125	158	14.7059
((((((((.(((......))).)).))))))).	chr6:53132345-53132595(-)$1	1	1	34	13.5332
(((.((..(((((......))))).)).)))))	chr8:28203267-28203497(-)$1	1	30	63	14.6480
(((((((((((((....)))))...))))))))	chr10:98984026-98984261(-)$1	1	62	95	12.7776
(((((((((.(((......))).)))))....)	chr17:18112313-18112535(+)$1	1	176	209	14.9932
(((.(((((((((......)).))))))).)))	chr1:154556559-154556784(-)$1	1	132	165	16.2441
))(((((((((.((((...))))))))))))).	chr1:178887557-178887806(+)$1	1	96	129	12.3190
(.(((((((((((......))))..))))))).	chr7:135611827-135612068(-)$1	1	88	121	15.1218
(((((.(.(((((......))))).).)))))(	chr1:244870816-244871067(+)$1	1	114	147	13.0930
(((((((((..((......))..))))))).))	chr11:10818994-10819227(-)$1	1	53	86	16.4254
((((((((...((((.....))))....)))))	chr10:62553846-62554077(+)$1	1	193	226	12.2025
(((...(..((((......)).))..)...)))	chr11:47487615-47487838(-)$1	1	102	135	13.8726
((((((((((.((.....))))))))))).)))	chr8:95893129-95893359(-)$1	1	47	80	13.4386
(.(((((((((((....))))))))))).))).	chr17:27587557-27587785(-)$1	1	5	38	14.0124
(((((((((((((......))))))).)))).)	chr17:20905479-20905709(-)$1	1	78	111	13.6945
((((((((...((......)).)))))))))).	chr1:38422821-38423046(-)$1	1	2	35	19.2396
((((((((...((......))))))))))))..	chr1:85111956-85112213(-)$1	1	152	185	18.1358
((((((.(((((((((...))))))))).).))	chr1:67877192-67877417(-)$1	1	66	99	13.1026
((.(((((..(((......)))..))))).)))	chrX:102930375-102930598(-)$1	1	182	215	14.7095
..(((((((((((......)))))))))))...	chr8:12942702-12942927(-)$1	1	72	105	14.7499
((.((((((((((......)))))))))).))(	chr2:196601545-196601771(+)$1	1	48	81	17.8843
(((((((((((.........)))))))))))).	chr10:61549570-61549805(-)$1	1	159	192	15.2368
((((..(((..((......))....)))...))	chr5:32603131-32603387(+)$1	1	41	74	17.1098
(((.....(((((......)))))...))).))	chr10:129896558-129896773(-)$1	1	153	186	13.0762
(..(((((...((......))....))))).))	chr16:83845468-83845691(+)$1	1	177	210	15.2552
.(((((((..(((......)))..))))))).)	chr7:94296686-94296908(+)$1	1	18	51	16.7572
(((((((((((..........))))))))))))	chrX:107965224-107965435(-)$1	1	149	182	13.8647
((.(.(((.((((......)))).))).).)))	chr21:46226224-46226474(-)$1	1	1	34	14.4506
.((((((((((((.......)))))))))))).	chr2:219459977-219460225(+)$1	1	122	155	13.8444
(((((((((((........)))))))))))(((	chr6:11579492-11579727(+)$1	1	91	124	13.6447

#PSSM
= : 0.23	c : 0.19	e : 0.12	g : 0.10	i : 0.08	d : 0.04	# : 0.04	: : 0.04	[ : 0.04	f : 0.02	a : 0.02	G : 0.02	E : 0.02	b : 0.02	
= : 0.30	c : 0.14	i : 0.12	g : 0.12	e : 0.10	[ : 0.08	# : 0.04	! : 0.04	G : 0.02	: : 0.02	b : 0.02	
= : 0.34	i : 0.14	g : 0.14	e : 0.10	[ : 0.08	c : 0.06	! : 0.04	d : 0.04	# : 0.02	b : 0.02	G : 0.02	
= : 0.36	i : 0.14	g : 0.14	e : 0.12	[ : 0.06	d : 0.04	! : 0.02	# : 0.02	c : 0.02	b : 0.02	" : 0.02	$ : 0.02	a : 0.02	
= : 0.34	g : 0.16	i : 0.12	e : 0.12	[ : 0.06	! : 0.04	d : 0.04	b : 0.04	# : 0.02	c : 0.02	" : 0.02	$ : 0.02	
= : 0.32	g : 0.14	i : 0.12	e : 0.10	[ : 0.08	c : 0.04	d : 0.04	a : 0.04	b : 0.04	# : 0.02	" : 0.02	! : 0.02	$ : 0.02	
= : 0.32	g : 0.14	i : 0.12	c : 0.08	e : 0.08	[ : 0.06	# : 0.04	d : 0.04	! : 0.04	a : 0.04	b : 0.02	$ : 0.02	
= : 0.32	i : 0.14	g : 0.14	c : 0.08	e : 0.08	! : 0.06	# : 0.04	d : 0.04	b : 0.04	a : 0.02	[ : 0.02	$ : 0.02	
= : 0.23	i : 0.12	e : 0.12	g : 0.12	[ : 0.08	! : 0.08	" : 0.08	# : 0.04	d : 0.04	b : 0.04	c : 0.04	
= : 0.23	d : 0.14	! : 0.12	i : 0.10	e : 0.10	g : 0.08	" : 0.08	[ : 0.06	b : 0.04	# : 0.02	c : 0.02	
= : 0.23	c : 0.21	d : 0.10	[ : 0.08	e : 0.08	" : 0.08	i : 0.06	! : 0.06	g : 0.06	b : 0.02	
b : 0.25	c : 0.21	= : 0.16	d : 0.12	e : 0.08	i : 0.04	g : 0.04	[ : 0.02	r : 0.02	s : 0.02	q : 0.02	
b : 0.25	c : 0.19	= : 0.14	d : 0.14	e : 0.08	i : 0.04	r : 0.04	g : 0.04	o : 0.02	s : 0.02	q : 0.02	
o : 0.72	i : 0.04	n : 0.04	r : 0.04	m : 0.04	d : 0.04	= : 0.02	s : 0.02	p : 0.02	q : 0.02	
o : 0.74	n : 0.06	r : 0.04	m : 0.04	d : 0.04	i : 0.02	s : 0.02	p : 0.02	q : 0.02	
o : 0.74	n : 0.08	r : 0.04	m : 0.04	d : 0.02	i : 0.02	s : 0.02	p : 0.02	q : 0.02	
o : 0.74	n : 0.08	r : 0.04	m : 0.04	l : 0.04	s : 0.02	p : 0.02	q : 0.02	
o : 0.74	n : 0.08	r : 0.04	l : 0.04	e : 0.02	= : 0.02	s : 0.02	p : 0.02	q : 0.02	
o : 0.72	n : 0.04	= : 0.04	r : 0.04	l : 0.04	c : 0.02	e : 0.02	b : 0.02	s : 0.02	p : 0.02	q : 0.02	
b : 0.25	c : 0.21	= : 0.12	d : 0.12	e : 0.08	i : 0.04	r : 0.04	g : 0.04	o : 0.02	n : 0.02	s : 0.02	p : 0.02	
b : 0.23	c : 0.21	= : 0.18	d : 0.14	e : 0.08	i : 0.06	g : 0.04	r : 0.02	s : 0.02	
= : 0.23	c : 0.19	d : 0.14	] : 0.14	e : 0.10	i : 0.06	2 : 0.04	g : 0.04	4 : 0.04	
= : 0.27	d : 0.16	2 : 0.10	] : 0.08	e : 0.08	4 : 0.06	i : 0.06	3 : 0.06	b : 0.06	g : 0.06	
= : 0.27	i : 0.12	e : 0.10	2 : 0.08	b : 0.08	g : 0.08	4 : 0.06	d : 0.06	3 : 0.06	c : 0.04	] : 0.04	
= : 0.27	i : 0.12	g : 0.12	4 : 0.08	3 : 0.08	] : 0.08	c : 0.06	e : 0.06	d : 0.04	2 : 0.04	a : 0.02	b : 0.02	
= : 0.30	g : 0.18	i : 0.16	c : 0.08	e : 0.08	4 : 0.04	d : 0.04	] : 0.04	b : 0.02	a : 0.02	2 : 0.02	3 : 0.02	
= : 0.32	i : 0.16	g : 0.14	e : 0.08	] : 0.08	d : 0.04	a : 0.04	3 : 0.04	c : 0.04	2 : 0.02	b : 0.02	4 : 0.02	
= : 0.32	i : 0.16	g : 0.14	e : 0.12	c : 0.06	] : 0.06	d : 0.04	3 : 0.04	b : 0.02	2 : 0.02	4 : 0.02	
= : 0.36	g : 0.14	i : 0.12	e : 0.12	3 : 0.08	c : 0.04	d : 0.04	] : 0.04	b : 0.02	4 : 0.02	a : 0.02	
= : 0.32	] : 0.12	g : 0.12	i : 0.10	e : 0.10	c : 0.08	3 : 0.06	d : 0.04	b : 0.02	4 : 0.02	a : 0.02	
= : 0.27	c : 0.12	e : 0.12	g : 0.12	i : 0.10	] : 0.10	3 : 0.04	4 : 0.04	b : 0.04	d : 0.02	: : 0.02	
= : 0.25	c : 0.16	g : 0.12	i : 0.10	e : 0.10	4 : 0.06	: : 0.06	] : 0.06	d : 0.02	a : 0.02	2 : 0.02	b : 0.02	
: : 0.27	c : 0.18	= : 0.14	e : 0.08	g : 0.08	i : 0.06	4 : 0.04	d : 0.04	] : 0.04	5 : 0.02	2 : 0.02	f : 0.02	

#score	752.295786323882
#seq	50
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_CDS_m2_run2.txt

#BEAR
efffffftttttttttttffffff	chr4:147227017-147227240(-)$1	223	6	30	21.3667
###dddduuuuuuuuuuuuddddg	chr2:43805588-43805807(-)$1	219	115	139	23.7072
""cccxxxxxxxxxxxxxxxccc3	chr6:150004073-150004296(-)$1	223	16	40	18.1016
d"""ddddtttttttttttdddd7	chr17:42745479-42745705(-)$1	226	144	168	21.2504
a[eeeeettttttttttteeeeea	chr1:154524468-154524697(-)$1	229	192	216	23.0320
d[ddddyyyyyyyyyyyyyyyydd	chr4:175223132-175223360(+)$1	228	105	129	21.2430
bb[dddduuuuuuuuuuuudddd]	chr1:111490615-111490839(-)$1	224	197	221	23.1471
deeeeevvvvvvvvvvvvveeeee	chr12:11244697-11244920(-)$1	223	91	115	23.1433
""eeeeeuuuuuuuuuuuueeeee	chr5:10411528-10411748(+)$1	220	157	181	24.4860
gffffffuuuuuuuuuuuufffff	chr2:9683259-9683484(-)$1	225	148	172	22.7518
a[eeeeeuuuuuuuuuuuueeeee	chr12:102154934-102155158(-)$1	224	103	127	24.4308
####cccuuuuuuuuuuuuccc44	chr1:179990003-179990231(+)$1	228	115	139	23.3516
eeeeewwwwwwwwwwwwwweeeee	chr13:108882147-108882368(+)$1	221	165	189	22.1160
ccc[ddddtttttttttttdddd]	chr11:32637455-32637690(+)$1	235	30	54	21.9013
d!!ddddtttttttttttdddd22	chr15:48591305-48591524(-)$1	219	29	53	21.9555
!ffffffuuuuuuuuuuuufffff	chrM:5373-5608(+)$1	235	186	210	22.9358
hhhhhyyyyyyyyyyyyyyyyhhh	chr16:58577197-58577414(-)$1	217	120	144	19.9430
gggggggvvvvvvvvvvvvvgggg	chr20:5974193-5974410(+)$1	217	165	189	22.4551
ddddddduuuuuuuuuuuudddd:	chr11:32635793-32636015(+)$1	222	70	94	22.0785
g[fffffftttttttttttfffff	chr3:154012997-154013228(-)$1	231	72	96	21.5756
[ccc[bbuuuuuuuuuuuubb]cc	chr17:17158135-17158359(-)$1	224	115	139	22.2456
iii!!bbtttttttttttbb22ii	chr1:186413240-186413464(+)$1	224	17	41	20.7506
$$$ddddtttttttttttdddd44	chr19:44612249-44612475(-)$1	226	40	64	21.7481
"ffffffyyyyyyyyyyyyyyyyf	chrX:53654597-53654816(-)$1	219	145	169	20.3497
eeeeewwwwwwwwwwwwwweeeee	chr12:88547998-88548216(+)$1	218	152	176	22.1160
!!ddddyyyyyyyyyyyyyyyydd	chr6:80626367-80626595(-)$1	228	116	140	21.5328
ggggggguuuuuuuuuuuuggggg	chr1:114248599-114248820(-)$1	221	111	135	23.3309
ddddcccuuuuuuuuuuuuccc]d	chr19:9677207-9677426(-)$1	219	178	202	22.8641
e[eeeeevvvvvvvvvvvvveeee	chr4:122737874-122738100(-)$1	226	136	160	23.3226
ggggggguuuuuuuuuuuuggggg	chr1:54269533-54269754(-)$1	221	35	59	23.3309
ffffffvvvvvvvvvvvvvfffff	chr5:133295549-133295778(-)$1	229	108	132	21.8940
""cccyyyyyyyyyyyyyyyyccc	chr9:127912069-127912294(-)$1	225	95	119	21.7689
:ffffffuuuuuuuuuuuufffff	chr3:196666125-196666346(-)$1	221	150	174	21.9453
ffffffbbtttttttttttbb]ff	chr1:227841937-227842160(+)$1	223	186	210	20.5548
d[bb[avvvvvvvvvvvvva]bb]	chr1:19948519-19948742(+)$1	223	133	157	21.4778
!ffffffwwwwwwwwwwwwwwfff	chr19:3976161-3976388(-)$1	227	150	174	21.0189
::eeeeeuuuuuuuuuuuueeeee	chr14:60611599-60611823(-)$1	224	102	126	22.4089
:ddddwwwwwwwwwwwwwwddddh	chr2:74392249-74392468(-)$1	219	10	34	20.4177
ee[ddddtttttttttttdddd]e	chr10:121596329-121596552(-)$1	223	51	75	22.1126
d!!dddduuuuuuuuuuuudddd3	chr7:140036984-140037205(-)$1	221	49	73	23.7293
b:eeeeevvvvvvvvvvvvveeee	chr4:56225413-56225641(+)$1	228	96	120	22.0625
:::ddddvvvvvvvvvvvvvdddd	chr2:37428758-37428986(-)$1	228	155	179	19.7077
!!eeeeeuuuuuuuuuuuueeeee	chr17:2310228-2310449(-)$1	221	62	86	24.5623
a[eeeeevvvvvvvvvvvvveeee	chr6:64286739-64286959(+)$1	220	128	152	23.4615
eee[ccctttttttttttccceee	chr1:154557365-154557585(-)$1	220	66	90	22.4608
i[eeeeeuuuuuuuuuuuueeeee	chr15:49935584-49935812(+)$1	228	84	108	24.3840
gggggwwwwwwwwwwwwwwggggg	chr17:29221621-29221846(-)$1	225	168	192	21.6588
i!!cccwwwwwwwwwwwwwwccci	chr20:20617935-20618169(-)$1	234	135	159	22.0091
ggggggguuuuuuuuuuuuggggg	chr5:176637950-176638177(+)$1	227	149	173	23.3309
!!ddddvvvvvvvvvvvvvdddd]	chr8:124042767-124042988(-)$1	221	51	75	23.1415
###ddddtttttttttttdddd33	chr11:43964956-43965177(+)$1	221	184	208	22.4271
""eeeeevvvvvvvvvvvvveeee	chr16:29822244-29822463(+)$1	219	151	175	23.5167
a[eeeeettttttttttteeeee]	chr3:41267080-41267315(+)$1	235	86	110	23.1990
beeeeevvvvvvvvvvvvveeeee	chr1:225590903-225591126(-)$1	223	151	175	23.0642
ggggggguuuuuuuuuuuuggggg	chr1:100573098-100573317(-)$1	219	133	157	23.3309
::cccyyyyyyyyyyyyyyyyccc	chr10:5772394-5772619(+)$1	225	194	218	19.6918
ddddyyyyyyyyyyyyyyyydddd	chrM:11620-11843(+)$1	223	70	94	20.8946
eeeeewwwwwwwwwwwwwweeeee	chr5:61875222-61875443(+)$1	221	102	126	22.1160
iiiiiiiitttttttttttiiiii	chr19:30503350-30503576(+)$1	226	148	172	21.3980
fffyyyyyyyyyyyyyyyyfffff	chr8:124358763-124358984(-)$1	221	193	217	20.2385
""eeeeeuuuuuuuuuuuueeeee	chr8:95886689-95886906(-)$1	217	165	189	24.4860
dd:dddduuuuuuuuuuuudddd:	chr6:97339027-97339247(-)$1	220	137	161	21.1767
eeeeewwwwwwwwwwwwwweeeee	chr10:88939826-88940051(+)$1	225	12	36	22.1160
hhh[ccctttttttttttccc444	chr6:149983118-149983341(-)$1	223	80	104	21.4292
gggggggtttttttttttgggggg	chr6:87967638-87967860(+)$1	222	126	150	21.9303
BB:eeeeettttttttttteeeee	chr1:220197639-220197858(-)$1	219	190	214	19.9256
ffffffvvvvvvvvvvvvvfffff	chr5:133723980-133724204(+)$1	224	93	117	21.8940

#otherMatches

#Seq PSSM
UGCAUUAUUUAUAAACACUAAUGC	chr4:147227017-147227240(-)$1	223	6	30	21.3667
UUAAGACUAUGUUUCACCCGUCUG	chr2:43805588-43805807(-)$1	219	115	139	23.7072
AAUGUACUCAAAUCUCAUCAGCAG	chr6:150004073-150004296(-)$1	223	16	40	18.1016
CACUCUUCUAGACGAAUAUGAAGU	chr17:42745479-42745705(-)$1	226	144	168	21.2504
GUGGAGGAUGCUGGCCUCCCUCCC	chr1:154524468-154524697(-)$1	229	192	216	23.0320
UUUUACCUCAUACUCACCUUAUGU	chr4:175223132-175223360(+)$1	228	105	129	21.2430
AGGUGCUGAGAGAGAAAGAAGCAG	chr1:111490615-111490839(-)$1	224	197	221	23.1471
CAUGAUAACUUUUCUACCCAUCAU	chr12:11244697-11244920(-)$1	223	91	115	23.1433
UUUUUGGUUUUUUUGUUCUCCAAA	chr5:10411528-10411748(+)$1	220	157	181	24.4860
AUCUACAGACUUCAACACAUGUAG	chr2:9683259-9683484(-)$1	225	148	172	22.7518
CUCUUAUUUUUAUUAUCUCAUGAG	chr12:102154934-102155158(-)$1	224	103	127	24.4308
AAAAUCCUAUCAGUUAUAUGGAAA	chr1:179990003-179990231(+)$1	228	115	139	23.3516
CUACAGAAAAAUCUCUCAGUGUAG	chr13:108882147-108882368(+)$1	221	165	189	22.1160
CAUCUAUAAUUAUUUCCUCUAUAA	chr11:32637455-32637690(+)$1	235	30	54	21.9013
AAUUAAGAAAGACAAAUCCUUACC	chr15:48591305-48591524(-)$1	219	29	53	21.9555
AGUUGCAAUACUUAAUUUCUGCAA	chrM:5373-5608(+)$1	235	186	210	22.9358
guuugacagauaguagauacccaa	chr16:58577197-58577414(-)$1	217	120	144	19.9430
AUCUCUUUUGUAAUAAUUUCAGGA	chr20:5974193-5974410(+)$1	217	165	189	22.4551
AGUUGUAUUUGUUUUAUUUUACAU	chr11:32635793-32636015(+)$1	222	70	94	22.0785
UUAAAAUUUAAUUCUCUUUAAUUU	chr3:154012997-154013228(-)$1	231	72	96	21.5756
UCAUUACAAGAUAUGGCAAGUCGU	chr17:17158135-17158359(-)$1	224	115	139	22.2456
UAUGAGUUCCCCACCUUUAUAGAU	chr1:186413240-186413464(+)$1	224	17	41	20.7506
AAGGUUUUUCUCCAACAUGAACAU	chr19:44612249-44612475(-)$1	226	40	64	21.7481
UGCUUUGCACAGAAUUUAAUACUC	chrX:53654597-53654816(-)$1	219	145	169	20.3497
AGACAAUUCCAUAAGUACAUGUCU	chr12:88547998-88548216(+)$1	218	152	176	22.1160
ACUUCUACAUUCGGACAUACAAAG	chr6:80626367-80626595(-)$1	228	116	140	21.5328
UUCUUACAUCGACUUUUCCGUGAG	chr1:114248599-114248820(-)$1	221	111	135	23.3309
UUCACUGUUUCUUCACACCUAGUU	chr19:9677207-9677426(-)$1	219	178	202	22.8641
UUGGUGCUUUUUCUUGUUUUGCAC	chr4:122737874-122738100(-)$1	226	136	160	23.3226
aaaaaauuaaauaauauGUGUUUU	chr1:54269533-54269754(-)$1	221	35	59	23.3309
UCACAUAUUUCUACCCCAAAUGUG	chr5:133295549-133295778(-)$1	229	108	132	21.8940
UUGUUCAUAUCAACAACUUAAAAC	chr9:127912069-127912294(-)$1	225	95	119	21.7689
AAGUGGUGACAUAAAGAAAAUCAU	chr3:196666125-196666346(-)$1	221	150	174	21.9453
GCUGGGGCCUUGACAAUUUGCACU	chr1:227841937-227842160(+)$1	223	186	210	20.5548
UCUGUCUUUUCAACAUAAUGUCAU	chr1:19948519-19948742(+)$1	223	133	157	21.4778
UAAUUUUAACAAACGCAUUAAGAG	chr19:3976161-3976388(-)$1	227	150	174	21.0189
CUUCUUAUUUUAAAAUCUUUAAGA	chr14:60611599-60611823(-)$1	224	102	126	22.4089
AUGGUACUAAUAUUAAAAAGCCAA	chr2:74392249-74392468(-)$1	219	10	34	20.4177
GCAGAAGGUGGAUUAUGACUUCAG	chr10:121596329-121596552(-)$1	223	51	75	22.1126
CUUUCAGUAUUUAGUGUCUCUGAU	chr7:140036984-140037205(-)$1	221	49	73	23.7293
CAGAUAUUUUUCCCACUUUUAUAU	chr4:56225413-56225641(+)$1	228	96	120	22.0625
CUCUCUGAUUCCAUACAUUCCAGA	chr2:37428758-37428986(-)$1	228	155	179	19.7077
UCAGAGGACCUGGCUCCUCCCUCU	chr17:2310228-2310449(-)$1	221	62	86	24.5623
CGACCUUAAACAAAUUUAUAGAGG	chr6:64286739-64286959(+)$1	220	128	152	23.4615
GCCACGGAAUGAAUUGUCCCGGGU	chr1:154557365-154557585(-)$1	220	66	90	22.4608
ACAGAGGGCAAUAUGACAAUCUUU	chr15:49935584-49935812(+)$1	228	84	108	24.3840
CAGGUAUUCAAUUAUACUAGCUUG	chr17:29221621-29221846(-)$1	225	168	192	21.6588
UUAACAAACAUCUACAAACCUGUA	chr20:20617935-20618169(-)$1	234	135	159	22.0091
UAUUGAACCAGACUACAAAUUCAG	chr5:176637950-176638177(+)$1	227	149	173	23.3309
CCACCUUUUAUUUCCCUGUGGGUC	chr8:124042767-124042988(-)$1	221	51	75	23.1415
ACUCCAUGCCCUUGUCCGAUGGUU	chr11:43964956-43965177(+)$1	221	184	208	22.4271
AUCGUGUUCCUGUGUCCCCUGCAU	chr16:29822244-29822463(+)$1	219	151	175	23.5167
GUGUUGUUUUAUGCCAUUACAACU	chr3:41267080-41267315(+)$1	235	86	110	23.1990
CUGCAAUUCCAGCUGCCAUUUGCA	chr1:225590903-225591126(-)$1	223	151	175	23.0642
GGUUUGUUUUAAAAAUUUUAUAGA	chr1:100573098-100573317(-)$1	219	133	157	23.3309
UUUCCAAGAAUUGUACAAGGCGGA	chr10:5772394-5772619(+)$1	225	194	218	19.6918
GGCGCAGUCAUUCUCAUAAUCGCC	chrM:11620-11843(+)$1	223	70	94	20.8946
UCUUUUAUUAUUACUCCACAAAGA	chr5:61875222-61875443(+)$1	221	102	126	22.1160
UUUAAUCUGAAAAGUCAUAAGAUU	chr19:30503350-30503576(+)$1	226	148	172	21.3980
UUGAAAAAAUAAAAAGUGCUAACC	chr8:124358763-124358984(-)$1	221	193	217	20.2385
UAAcauggauucuaacaaaugugu	chr8:95886689-95886906(-)$1	217	165	189	24.4860
GGACUGCUGAGAAAAUAAUGCAGG	chr6:97339027-97339247(-)$1	220	137	161	21.1767
UCUGAUUAAAGCCCAGAUUUCAGA	chr10:88939826-88940051(+)$1	225	12	36	22.1160
UGGUGCUGAUGAAAUAAAAGCUCA	chr6:149983118-149983341(-)$1	223	80	104	21.4292
CUGGUGUGACUAACUUUAAUACCA	chr6:87967638-87967860(+)$1	222	126	150	21.9303
CUCCUGCUGAACAGAUGAAAGCAG	chr1:220197639-220197858(-)$1	219	190	214	19.9256
UGAUGUAUCUUCUAUCUUAACAUC	chr5:133723980-133724204(+)$1	224	93	117	21.8940

#DB
(((((((...........))))))	chr4:147227017-147227240(-)$1	1	6	30	21.3667
...((((............)))))	chr2:43805588-43805807(-)$1	1	115	139	23.7072
..(((...............))).	chr6:150004073-150004296(-)$1	1	16	40	18.1016
(...((((...........)))).	chr17:42745479-42745705(-)$1	1	144	168	21.2504
(.(((((...........))))))	chr1:154524468-154524697(-)$1	1	192	216	23.0320
(.((((................))	chr4:175223132-175223360(+)$1	1	105	129	21.2430
((.((((............)))).	chr1:111490615-111490839(-)$1	1	197	221	23.1471
)(((((.............)))))	chr12:11244697-11244920(-)$1	1	91	115	23.1433
..(((((............)))))	chr5:10411528-10411748(+)$1	1	157	181	24.4860
)((((((............)))))	chr2:9683259-9683484(-)$1	1	148	172	22.7518
(.(((((............)))))	chr12:102154934-102155158(-)$1	1	103	127	24.4308
....(((............)))..	chr1:179990003-179990231(+)$1	1	115	139	23.3516
(((((..............)))))	chr13:108882147-108882368(+)$1	1	165	189	22.1160
(((.((((...........)))).	chr11:32637455-32637690(+)$1	1	30	54	21.9013
(..((((...........))))..	chr15:48591305-48591524(-)$1	1	29	53	21.9555
.((((((............)))))	chrM:5373-5608(+)$1	1	186	210	22.9358
(((((................)))	chr16:58577197-58577414(-)$1	1	120	144	19.9430
(((((((.............))))	chr20:5974193-5974410(+)$1	1	165	189	22.4551
)))((((............)))).	chr11:32635793-32636015(+)$1	1	70	94	22.0785
(.((((((...........)))))	chr3:154012997-154013228(-)$1	1	72	96	21.5756
.(((.((............)).))	chr17:17158135-17158359(-)$1	1	115	139	22.2456
(((..((...........))..))	chr1:186413240-186413464(+)$1	1	17	41	20.7506
...((((...........))))..	chr19:44612249-44612475(-)$1	1	40	64	21.7481
.((((((................)	chrX:53654597-53654816(-)$1	1	145	169	20.3497
(((((..............)))))	chr12:88547998-88548216(+)$1	1	152	176	22.1160
..((((................))	chr6:80626367-80626595(-)$1	1	116	140	21.5328
(((((((............)))))	chr1:114248599-114248820(-)$1	1	111	135	23.3309
(((((((............))).)	chr19:9677207-9677426(-)$1	1	178	202	22.8641
(.(((((.............))))	chr4:122737874-122738100(-)$1	1	136	160	23.3226
(((((((............)))))	chr1:54269533-54269754(-)$1	1	35	59	23.3309
((((((.............)))))	chr5:133295549-133295778(-)$1	1	108	132	21.8940
..(((................)))	chr9:127912069-127912294(-)$1	1	95	119	21.7689
.((((((............)))))	chr3:196666125-196666346(-)$1	1	150	174	21.9453
((((((((...........)).))	chr1:227841937-227842160(+)$1	1	186	210	20.5548
(.((.(.............).)).	chr1:19948519-19948742(+)$1	1	133	157	21.4778
.((((((..............)))	chr19:3976161-3976388(-)$1	1	150	174	21.0189
..(((((............)))))	chr14:60611599-60611823(-)$1	1	102	126	22.4089
.((((..............))))(	chr2:74392249-74392468(-)$1	1	10	34	20.4177
((.((((...........)))).)	chr10:121596329-121596552(-)$1	1	51	75	22.1126
(..((((............)))).	chr7:140036984-140037205(-)$1	1	49	73	23.7293
).(((((.............))))	chr4:56225413-56225641(+)$1	1	96	120	22.0625
...((((.............))))	chr2:37428758-37428986(-)$1	1	155	179	19.7077
..(((((............)))))	chr17:2310228-2310449(-)$1	1	62	86	24.5623
(.(((((.............))))	chr6:64286739-64286959(+)$1	1	128	152	23.4615
(((.(((...........))))))	chr1:154557365-154557585(-)$1	1	66	90	22.4608
(.(((((............)))))	chr15:49935584-49935812(+)$1	1	84	108	24.3840
(((((..............)))))	chr17:29221621-29221846(-)$1	1	168	192	21.6588
(..(((..............))))	chr20:20617935-20618169(-)$1	1	135	159	22.0091
(((((((............)))))	chr5:176637950-176638177(+)$1	1	149	173	23.3309
..((((.............)))).	chr8:124042767-124042988(-)$1	1	51	75	23.1415
...((((...........))))..	chr11:43964956-43965177(+)$1	1	184	208	22.4271
..(((((.............))))	chr16:29822244-29822463(+)$1	1	151	175	23.5167
(.(((((...........))))).	chr3:41267080-41267315(+)$1	1	86	110	23.1990
)(((((.............)))))	chr1:225590903-225591126(-)$1	1	151	175	23.0642
(((((((............)))))	chr1:100573098-100573317(-)$1	1	133	157	23.3309
..(((................)))	chr10:5772394-5772619(+)$1	1	194	218	19.6918
((((................))))	chrM:11620-11843(+)$1	1	70	94	20.8946
(((((..............)))))	chr5:61875222-61875443(+)$1	1	102	126	22.1160
((((((((...........)))))	chr19:30503350-30503576(+)$1	1	148	172	21.3980
(((................)))))	chr8:124358763-124358984(-)$1	1	193	217	20.2385
..(((((............)))))	chr8:95886689-95886906(-)$1	1	165	189	24.4860
)).((((............)))).	chr6:97339027-97339247(-)$1	1	137	161	21.1767
(((((..............)))))	chr10:88939826-88940051(+)$1	1	12	36	22.1160
(((.(((...........)))...	chr6:149983118-149983341(-)$1	1	80	104	21.4292
(((((((...........))))))	chr6:87967638-87967860(+)$1	1	126	150	21.9303
)).(((((...........)))))	chr1:220197639-220197858(-)$1	1	190	214	19.9256
((((((.............)))))	chr5:133723980-133724204(+)$1	1	93	117	21.8940

#PSSM
d : 0.14	g : 0.13	e : 0.11	" : 0.08	! : 0.07	: : 0.07	a : 0.05	i : 0.05	f : 0.05	# : 0.04	b : 0.04	h : 0.02	c : 0.01	[ : 0.01	$ : 0.01	B : 0.01	
f : 0.14	[ : 0.13	e : 0.11	g : 0.10	" : 0.08	! : 0.08	d : 0.07	: : 0.05	# : 0.04	c : 0.02	h : 0.02	i : 0.02	b : 0.01	$ : 0.01	B : 0.01	
e : 0.28	f : 0.16	d : 0.10	g : 0.10	c : 0.07	# : 0.04	! : 0.04	: : 0.04	[ : 0.02	h : 0.02	i : 0.02	" : 0.01	$ : 0.01	b : 0.01	
e : 0.28	d : 0.23	f : 0.14	g : 0.10	c : 0.07	[ : 0.04	" : 0.01	# : 0.01	h : 0.01	! : 0.01	b : 0.01	i : 0.01	y : 0.01	
e : 0.28	d : 0.23	f : 0.14	c : 0.11	g : 0.10	[ : 0.02	y : 0.02	h : 0.01	! : 0.01	i : 0.01	
d : 0.22	e : 0.22	f : 0.14	w : 0.08	g : 0.08	c : 0.07	y : 0.07	b : 0.02	x : 0.01	a : 0.01	i : 0.01	
e : 0.19	d : 0.17	f : 0.10	y : 0.10	w : 0.10	v : 0.08	g : 0.08	c : 0.05	b : 0.04	x : 0.01	i : 0.01	
u : 0.31	v : 0.17	t : 0.16	y : 0.11	w : 0.11	d : 0.02	x : 0.01	f : 0.01	b : 0.01	i : 0.01	e : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	t : 0.25	v : 0.17	y : 0.11	w : 0.11	x : 0.01	
u : 0.31	v : 0.17	y : 0.11	w : 0.11	t : 0.08	d : 0.05	e : 0.02	c : 0.02	f : 0.01	x : 0.01	b : 0.01	g : 0.01	
e : 0.22	d : 0.19	f : 0.11	y : 0.10	v : 0.08	g : 0.08	c : 0.05	b : 0.04	w : 0.02	x : 0.01	a : 0.01	i : 0.01	
e : 0.28	d : 0.22	f : 0.11	g : 0.10	c : 0.08	y : 0.08	b : 0.02	2 : 0.01	] : 0.01	w : 0.01	i : 0.01	
e : 0.29	d : 0.22	f : 0.13	g : 0.10	c : 0.08	y : 0.04	] : 0.02	h : 0.01	2 : 0.01	b : 0.01	i : 0.01	4 : 0.01	
e : 0.29	d : 0.19	f : 0.14	g : 0.10	c : 0.07	4 : 0.04	i : 0.02	] : 0.02	2 : 0.01	h : 0.01	y : 0.01	b : 0.01	3 : 0.01	
e : 0.28	f : 0.16	g : 0.11	d : 0.07	] : 0.07	3 : 0.04	4 : 0.04	c : 0.04	i : 0.04	h : 0.02	: : 0.02	7 : 0.01	a : 0.01	2 : 0.01	

#score	1483.5089293574806
#seq	67
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_UTR_m2_run1.txt

#BEAR
gggg[ddddooooooddddgggggg	chr22:22115523-22115778(-)$1	255	62	87	13.3186
======!!aooooooa22=======	chr11:73583878-73584137(-)$1	259	73	98	13.8302
ddgggggggooooooggggggg>>>	chr10:73577027-73577257(-)$1	230	82	107	12.6951
hhhh!!cccooooooccc22hhhhh	chr12:4411517-4411782(+)$1	265	33	58	12.8274
=========oooooo==========	chr4:120976704-120976931(-)$1	227	49	74	14.5083
ff!!eeeeeooooooeeeee22fff	chr13:42806404-42806633(+)$1	229	91	116	12.9758
###bb[cccoooooocccbb333gg	chrX:119389658-119389889(+)$1	231	133	158	13.8383
ee!!a[cccooooooccc]a4444e	chr12:49047607-49047862(-)$1	255	15	40	14.8966
ffff[ddddoooooodddd]fffff	chr17:40995097-40995406(+)$1	309	246	271	12.4824
d"""ccc[aooooooa]ccc22ddd	chr12:104327639-104327879(+)$1	240	172	197	13.2581
ddgggggggooooooggggggg]dd	chr1:159998804-159999075(-)$1	271	72	97	13.2447
fffff[cccooooooccc22fffff	chr12:54679685-54679945(+)$1	260	44	69	13.5558
gggg####bboooooobb4444ggg	chr6:97594060-97594349(-)$1	289	179	204	11.5604
[ddddddddoooooodddd4444dd	chr5:158584874-158585142(-)$1	268	72	97	12.4883
fffffffffooooooffffff]fff	chr1:95712325-95712562(+)$1	237	126	151	12.2254
c[gggggggooooooggggggg]cc	chr9:95012041-95012310(-)$1	269	25	50	13.8887
$eeeeecccooooooccc]eeeee3	chr8:17088993-17089298(-)$1	305	247	272	13.3005
eeebb[cccooooooccc]bb:ggg	chr15:76209513-76209789(+)$1	276	199	224	12.1030
e"""eeeeeooooooeeeee]eeee	chr1:27202550-27202791(-)$1	241	151	176	13.2781
gggggg[bboooooobb]ggggggg	chr1:169433635-169433907(-)$1	272	87	112	13.0700
dd"""ddddoooooodddd4444dd	chr18:56997741-56997993(-)$1	252	6	31	13.3228
""bb!!bboooooobb]bb333===	chr19:37308963-37309219(+)$1	256	174	199	11.2957
eeee!!cccooooooccc22eeeee	chr5:112337163-112337387(+)$1	224	67	92	13.9613
a"""eeeeeooooooeeeee4444a	chr3:24018958-24019255(+)$1	297	144	169	13.4776
"""bb!!bboooooobb22bb333f	chr17:2588576-2588834(+)$1	258	145	170	12.2950
e[gggggggooooooggggggg]ee	chr1:112309832-112310065(+)$1	233	176	201	13.7844
"a[ffffffooooooffffff]a33	chr3:47122305-47122548(-)$1	243	81	106	12.8728
eeeeea[bboooooobb22a]eeee	chr4:75972424-75972651(+)$1	227	16	41	12.3476
ccc[eeeeeooooooeeeee]ccc3	chr17:26674144-26674410(-)$1	266	32	57	13.4469
cccffffffooooooffffff]ccc	chr19:21305010-21305253(+)$1	243	149	174	12.7894
!!cccacccooooooccc]a]ccce	chr17:4848859-4849111(-)$1	252	52	77	14.4805
ccc"""cccooooooccc333ccc]	chr1:229458784-229459094(-)$1	310	82	107	15.3511
"ccc!!cccooooooccc22cccee	chr6:143748422-143748648(-)$1	226	19	44	14.5237
eeeee[cccooooooccc]eeeee]	chr2:27845365-27845670(+)$1	305	100	125	13.6922
ggggddddoooooodddd4444ggg	chr6:44414654-44415094(+)$1	440	165	190	11.9566
cc!!ccc[aooooooaccccccagg	chr19:12841675-12841963(-)$1	288	154	179	13.9219
ggggggg[aooooooa]ggggggg:	chr19:811776-812080(+)$1	304	172	197	12.7726
iiiiiiiiiooooooiiiiiiiii:	chr20:48569841-48570090(+)$1	249	157	182	12.8273
gga[eeeeeooooooeeeee]aggg	chr16:75665619-75665846(-)$1	227	116	141	13.3984
cc[ffffffooooooffffff22cc	chr15:81269180-81269420(-)$1	240	153	178	12.6470
ccc!!ddddoooooodddd22ccc=	chrX:153292453-153292690(-)$1	237	6	31	13.6331
b!!eeeeeaooooooa]eeeee22b	chr7:141360936-141361171(-)$1	235	12	37	12.2265
eeee!!cccooooooccc22eeeee	chr19:39440829-39441068(-)$1	239	118	143	13.9613
ccc!!ddddoooooodddd333ccc	chr5:134120024-134120262(+)$1	238	30	55	14.2396
"""ffffffooooooffffff]ccc	chr19:18679951-18680201(+)$1	250	6	31	13.0192
dddd!!cccooooooccc]dddddd	chrX:110931355-110931606(+)$1	251	105	130	12.8092
[bb[eeeeeooooooeeeee]bb]c	chrX:70279496-70279760(-)$1	264	170	195	12.1430
b[ccc[cccooooooccc333ccc]	chr10:102122735-102122986(+)$1	251	54	79	14.8739
ee!!cccbboooooobb]ccc22ee	chr1:165697097-165697375(-)$1	278	49	74	12.6910
=========oooooo==========	chr2:197705655-197705906(-)$1	251	58	83	14.5083
cc####cccooooooccc333ccc2	chr19:10800149-10800381(+)$1	232	89	114	15.0484
cccffffffooooooffffffffff	chr15:67494316-67494741(-)$1	425	251	276	12.3484
eee[a!!bboooooobb22a]eeee	chr16:58439675-58439944(+)$1	269	19	44	12.9470
fff[eeeeeooooooeeeeefffff	chr12:12273313-12273545(-)$1	232	10	35	12.4715
"ccc[ddddoooooodddd]ccc]h	chr12:104169330-104169577(-)$1	247	176	201	12.9953
ccc!!ddddoooooodddd22ccc]	chr6:34253167-34253473(-)$1	306	113	138	13.6305
b[gggggggooooooggggggg]bb	chr2:135714025-135714291(+)$1	266	107	132	13.0295
eee"""cccooooooccc333eeee	chr11:9192161-9192391(-)$1	230	65	90	14.8524

#otherMatches

#Seq PSSM
GGACUCUGUCCUGACACAGGUCCUC	chr22:22115523-22115778(-)$1	255	62	87	13.3186
CUAAAACAUGGGGAGAGUUUUUGGA	chr11:73583878-73584137(-)$1	259	73	98	13.8302
CAGAAACCACAGCAUUGGUUUUUUU	chr10:73577027-73577257(-)$1	230	82	107	12.6951
GAGAUCCUCAUCUUGGAGCUUUUUC	chr12:4411517-4411782(+)$1	265	33	58	12.8274
UGUUUGCGGCUUAACUUGUAAAUAA	chr4:120976704-120976931(-)$1	227	49	74	14.5083
CUGAGGAAGAACUUGCUUUUAAAGG	chr13:42806404-42806633(+)$1	229	91	116	12.9758
UAAUCUGCUAGUCCAAGCGAACAGC	chrX:119389658-119389889(+)$1	231	133	158	13.8383
GAACCCACUUCUAUUAGUUGAUAGU	chr12:49047607-49047862(-)$1	255	15	40	14.8966
ACACCUAGCCACCCUGUUGUGUGUC	chr17:40995097-40995406(+)$1	309	246	271	12.4824
GGUACCAUAGCCAAAUCUGGGACAA	chr12:104327639-104327879(+)$1	240	172	197	13.2581
AUGUUUGUGGUCCUACACAAACUAU	chr1:159998804-159999075(-)$1	271	72	97	13.2447
AAUAGCAGGUGGAACCCUAACUAUU	chr12:54679685-54679945(+)$1	260	44	69	13.5558
GAGGCAAGUUAACAAAGAAAACCCU	chr6:97594060-97594349(-)$1	289	179	204	11.5604
GAAGGGGUGGGUGGGCACUUGGGCC	chr5:158584874-158585142(-)$1	268	72	97	12.4883
AAAUAGCAGUGUUUUUUGUUGUUUU	chr1:95712325-95712562(+)$1	237	126	151	12.2254
AUUUUUCUGCAGUUUUAGAGGACUG	chr9:95012041-95012310(-)$1	269	25	50	13.8887
AUAGAAAGCAUUAAAGCUGUUUUGC	chr8:17088993-17089298(-)$1	305	247	272	13.3005
AAGACAUCAACUCACUGAAGUAGGU	chr15:76209513-76209789(+)$1	276	199	224	12.1030
AUUCUAUAUUCAAAUGUAUAUUUUG	chr1:27202550-27202791(-)$1	241	151	176	13.2781
UUAUCUUGAAAAGAAUCUAGAUAGG	chr1:169433635-169433907(-)$1	272	87	112	13.0700
AUAACGUAAACACACUUGCCCUCAU	chr18:56997741-56997993(-)$1	252	6	31	13.3228
CUGAUCAGUAAUUUCUUUCCUAUAU	chr19:37308963-37309219(+)$1	256	174	199	11.2957
UAUUUUGAAAGUGAAUUCUUAAUGU	chr5:112337163-112337387(+)$1	224	67	92	13.9613
CUCCCUGAUAGACCAAUCAGCUGUG	chr3:24018958-24019255(+)$1	297	144	169	13.4776
UAAGAGUUCACUGAAGAUAUUGACA	chr17:2588576-2588834(+)$1	258	145	170	12.2950
AUAUUUAAACAUUGCUUUAGAUUUU	chr1:112309832-112310065(+)$1	233	176	201	13.7844
GCAUUCUGUGAAGAAACAGGAAGAU	chr3:47122305-47122548(-)$1	243	81	106	12.8728
GUCCACUGCUUUACUGUCUGUUGGA	chr4:75972424-75972651(+)$1	227	16	41	12.3476
UGGAUUGAUGACUAAGUCAAGCUAC	chr17:26674144-26674410(-)$1	266	32	57	13.4469
GCUGAAUUUAAAGAGAAAUUCUggc	chr19:21305010-21305253(+)$1	243	149	174	12.7894
CCAGGGCUGGAUGGACAGACACCUC	chr17:4848859-4849111(-)$1	252	52	77	14.4805
UUAAAACUCCAGACAGAGAUAUAAU	chr1:229458784-229459094(-)$1	310	82	107	15.3511
AGGGUAUCCACAGCAGGAAGUCCCC	chr6:143748422-143748648(-)$1	226	19	44	14.5237
UUUAAUGGGUUAUUUCUCUUUGAGG	chr2:27845365-27845670(+)$1	305	100	125	13.6922
GUGCCUGCAAACCAGCAGCUAUGUA	chr6:44414654-44415094(+)$1	440	165	190	11.9566
GUGACGAUGAUAAAACUCGGCCCCU	chr19:12841675-12841963(-)$1	288	154	179	13.9219
GCCCCCGCGUCCUGUCCCGGGGGCU	chr19:811776-812080(+)$1	304	172	197	12.7726
UGCAAGUGCUACCUCGCGCUUGUAC	chr20:48569841-48570090(+)$1	249	157	182	12.8273
CCGGGUUUAUGAAAUUGGACGCCAG	chr16:75665619-75665846(-)$1	227	116	141	13.3984
UGAGCUGGGAGGUGCUUCAGUAGUG	chr15:81269180-81269420(-)$1	240	153	178	12.6470
GCCUUGGCGGUUUAUCGCCCUGGCA	chrX:153292453-153292690(-)$1	237	6	31	13.6331
GAGGGCAGCUUACGUGUUUGUCAAC	chr7:141360936-141361171(-)$1	235	12	37	12.2265
CGGCUAUCGCGGCGACGGCUGCCGG	chr19:39440829-39441068(-)$1	239	118	143	13.9613
GGCAUGGCUAUGAAAAGCCCACGCC	chr5:134120024-134120262(+)$1	238	30	55	14.2396
AGAAGUCUUGAGACGGAGGCUGGCC	chr19:18679951-18680201(+)$1	250	6	31	13.0192
AUUCACAGGUUUUCUCCUAGAAUCU	chrX:110931355-110931606(+)$1	251	105	130	12.8092
GGUGAGAGUAAGUUAACUUUGGUGC	chrX:70279496-70279760(-)$1	264	170	195	12.1430
AAGCAAGGGCAAGAACCCAAGUGCC	chr10:102122735-102122986(+)$1	251	54	79	14.8739
ACGAGCCGCCACCAAGCAGGCAGGU	chr1:165697097-165697375(-)$1	278	49	74	12.6910
CUAUUUUUACAAUAUUGAAAAUAGG	chr2:197705655-197705906(-)$1	251	58	83	14.5083
AGUUUUUGCAGUUCAGUAUCCCUCU	chr19:10800149-10800381(+)$1	232	89	114	15.0484
CCUCUCUACUGAGUUGUGGGGGAUA	chr15:67494316-67494741(-)$1	425	251	276	12.3484
CUGGGCCCAUUAGACUGUUUGCAGG	chr16:58439675-58439944(+)$1	269	19	44	12.9470
GGACGAAGGGCUUUGUUUUCUCUAG	chr12:12273313-12273545(-)$1	232	10	35	12.4715
CGCCAUCAGGGUGUAUUGGAGGCUG	chr12:104169330-104169577(-)$1	247	176	201	12.9953
CAGAGCUGACCUCAUUCAGGCUUGA	chr6:34253167-34253473(-)$1	306	113	138	13.6305
UGAGGGAGGGAAGGGCUUUCUUGGU	chr2:135714025-135714291(+)$1	266	107	132	13.0295
AGAGAAAGCAAUUGAGCUGCGUCUG	chr11:9192161-9192391(-)$1	230	65	90	14.8524

#DB
((((.((((......))))))))))	chr22:22115523-22115778(-)$1	1	62	87	13.3186
((((((..(......)..)))))))	chr11:73583878-73584137(-)$1	1	73	98	13.8302
(((((((((......)))))))...	chr10:73577027-73577257(-)$1	1	82	107	12.6951
((((..(((......)))..)))))	chr12:4411517-4411782(+)$1	1	33	58	12.8274
(((((((((......))))))))))	chr4:120976704-120976931(-)$1	1	49	74	14.5083
((..(((((......)))))..)))	chr13:42806404-42806633(+)$1	1	91	116	12.9758
...((.(((......)))))...))	chrX:119389658-119389889(+)$1	1	133	158	13.8383
((..(.(((......))).)....)	chr12:49047607-49047862(-)$1	1	15	40	14.8966
((((.((((......)))).)))))	chr17:40995097-40995406(+)$1	1	246	271	12.4824
(...(((.(......).)))..)))	chr12:104327639-104327879(+)$1	1	172	197	13.2581
(((((((((......))))))).))	chr1:159998804-159999075(-)$1	1	72	97	13.2447
(((((.(((......)))..)))))	chr12:54679685-54679945(+)$1	1	44	69	13.5558
((((....((......))....)))	chr6:97594060-97594349(-)$1	1	179	204	11.5604
.((((((((......))))....))	chr5:158584874-158585142(-)$1	1	72	97	12.4883
(((((((((......)))))).)))	chr1:95712325-95712562(+)$1	1	126	151	12.2254
(.(((((((......))))))).))	chr9:95012041-95012310(-)$1	1	25	50	13.8887
.((((((((......))).))))).	chr8:17088993-17089298(-)$1	1	247	272	13.3005
)))((.(((......))).)).(((	chr15:76209513-76209789(+)$1	1	199	224	12.1030
(...(((((......))))).))))	chr1:27202550-27202791(-)$1	1	151	176	13.2781
((((((.((......)).)))))))	chr1:169433635-169433907(-)$1	1	87	112	13.0700
((...((((......))))....))	chr18:56997741-56997993(-)$1	1	6	31	13.3228
..((..((......)).))...)))	chr19:37308963-37309219(+)$1	1	174	199	11.2957
((((..(((......)))..)))))	chr5:112337163-112337387(+)$1	1	67	92	13.9613
(...(((((......)))))....)	chr3:24018958-24019255(+)$1	1	144	169	13.4776
...((..((......))..))...)	chr17:2588576-2588834(+)$1	1	145	170	12.2950
(.(((((((......))))))).))	chr1:112309832-112310065(+)$1	1	176	201	13.7844
.(.((((((......)))))).)..	chr3:47122305-47122548(-)$1	1	81	106	12.8728
((((((.((......))..).))))	chr4:75972424-75972651(+)$1	1	16	41	12.3476
(((.(((((......))))).))).	chr17:26674144-26674410(-)$1	1	32	57	13.4469
(((((((((......)))))).)))	chr19:21305010-21305253(+)$1	1	149	174	12.7894
..(((((((......))).).))))	chr17:4848859-4849111(-)$1	1	52	77	14.4805
(((...(((......)))...))).	chr1:229458784-229459094(-)$1	1	82	107	15.3511
.(((..(((......)))..)))))	chr6:143748422-143748648(-)$1	1	19	44	14.5237
(((((.(((......))).))))).	chr2:27845365-27845670(+)$1	1	100	125	13.6922
((((((((......))))....)))	chr6:44414654-44415094(+)$1	1	165	190	11.9566
((..(((.(......))))))))))	chr19:12841675-12841963(-)$1	1	154	179	13.9219
(((((((.(......).))))))).	chr19:811776-812080(+)$1	1	172	197	12.7726
(((((((((......))))))))).	chr20:48569841-48570090(+)$1	1	157	182	12.8273
))(.(((((......))))).)(((	chr16:75665619-75665846(-)$1	1	116	141	13.3984
((.((((((......))))))..))	chr15:81269180-81269420(-)$1	1	153	178	12.6470
(((..((((......))))..)))(	chrX:153292453-153292690(-)$1	1	6	31	13.6331
(..((((((......).)))))..)	chr7:141360936-141361171(-)$1	1	12	37	12.2265
((((..(((......)))..)))))	chr19:39440829-39441068(-)$1	1	118	143	13.9613
(((..((((......))))...)))	chr5:134120024-134120262(+)$1	1	30	55	14.2396
...((((((......)))))).)))	chr19:18679951-18680201(+)$1	1	6	31	13.0192
((((..(((......))).))))))	chrX:110931355-110931606(+)$1	1	105	130	12.8092
.((.(((((......))))).)).)	chrX:70279496-70279760(-)$1	1	170	195	12.1430
(.(((.(((......)))...))).	chr10:102122735-102122986(+)$1	1	54	79	14.8739
((..(((((......)).)))..))	chr1:165697097-165697375(-)$1	1	49	74	12.6910
(((((((((......))))))))))	chr2:197705655-197705906(-)$1	1	58	83	14.5083
((....(((......)))...))).	chr19:10800149-10800381(+)$1	1	89	114	15.0484
)))((((((......))))))((((	chr15:67494316-67494741(-)$1	1	251	276	12.3484
(((.(..((......))..).))))	chr16:58439675-58439944(+)$1	1	19	44	12.9470
(((.(((((......))))))))))	chr12:12273313-12273545(-)$1	1	10	35	12.4715
.(((.((((......)))).))).)	chr12:104169330-104169577(-)$1	1	176	201	12.9953
(((..((((......))))..))).	chr6:34253167-34253473(-)$1	1	113	138	13.6305
(.(((((((......))))))).))	chr2:135714025-135714291(+)$1	1	107	132	13.0295
(((...(((......)))...))))	chr11:9192161-9192391(-)$1	1	65	90	14.8524

#PSSM
e : 0.18	c : 0.18	g : 0.10	" : 0.10	d : 0.08	f : 0.08	= : 0.05	b : 0.05	[ : 0.03	h : 0.01	# : 0.01	$ : 0.01	a : 0.01	! : 0.01	i : 0.01	
c : 0.20	e : 0.17	g : 0.10	" : 0.10	d : 0.08	f : 0.08	[ : 0.06	= : 0.05	! : 0.03	h : 0.01	# : 0.01	a : 0.01	i : 0.01	b : 0.01	
c : 0.18	g : 0.17	e : 0.13	" : 0.10	! : 0.08	f : 0.06	= : 0.05	# : 0.03	d : 0.03	b : 0.03	[ : 0.03	h : 0.01	i : 0.01	a : 0.01	
g : 0.17	f : 0.13	! : 0.12	" : 0.10	e : 0.10	[ : 0.08	b : 0.06	c : 0.06	= : 0.05	d : 0.03	h : 0.01	i : 0.01	# : 0.01	
e : 0.18	! : 0.15	g : 0.12	f : 0.12	c : 0.08	[ : 0.05	= : 0.05	b : 0.05	" : 0.05	a : 0.03	# : 0.03	d : 0.03	i : 0.01	
d : 0.15	e : 0.15	! : 0.13	g : 0.12	[ : 0.10	f : 0.10	= : 0.05	c : 0.05	# : 0.03	a : 0.03	" : 0.03	i : 0.01	
c : 0.32	d : 0.15	e : 0.13	g : 0.10	f : 0.10	! : 0.05	= : 0.03	[ : 0.03	# : 0.01	b : 0.01	i : 0.01	
c : 0.27	d : 0.15	e : 0.13	f : 0.10	b : 0.10	g : 0.08	[ : 0.05	= : 0.03	! : 0.01	# : 0.01	i : 0.01	
c : 0.27	d : 0.13	e : 0.12	b : 0.10	f : 0.10	a : 0.08	g : 0.08	= : 0.03	o : 0.03	i : 0.01	
o : 0.98	b : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 0.96	b : 0.01	d : 0.01	
c : 0.27	d : 0.15	e : 0.12	f : 0.10	b : 0.10	a : 0.08	g : 0.08	= : 0.03	o : 0.01	i : 0.01	
c : 0.29	d : 0.15	e : 0.12	b : 0.10	f : 0.10	g : 0.08	] : 0.06	= : 0.03	2 : 0.01	i : 0.01	
c : 0.31	d : 0.15	e : 0.13	g : 0.10	f : 0.10	2 : 0.06	= : 0.03	b : 0.03	] : 0.03	i : 0.01	
d : 0.13	2 : 0.13	e : 0.13	g : 0.12	] : 0.10	f : 0.10	3 : 0.06	= : 0.05	c : 0.05	b : 0.03	4 : 0.03	i : 0.01	
e : 0.17	g : 0.13	2 : 0.12	f : 0.10	3 : 0.10	a : 0.06	4 : 0.06	= : 0.05	b : 0.05	c : 0.05	] : 0.03	i : 0.01	d : 0.01	
f : 0.15	g : 0.13	3 : 0.12	] : 0.12	4 : 0.10	e : 0.08	2 : 0.06	c : 0.06	= : 0.05	b : 0.03	h : 0.01	i : 0.01	d : 0.01	
c : 0.17	e : 0.15	g : 0.13	4 : 0.10	2 : 0.06	3 : 0.06	f : 0.06	] : 0.06	= : 0.05	h : 0.01	: : 0.01	i : 0.01	a : 0.01	d : 0.01	b : 0.01	
c : 0.20	e : 0.13	g : 0.12	f : 0.10	= : 0.06	4 : 0.06	] : 0.06	2 : 0.05	3 : 0.03	d : 0.03	a : 0.03	> : 0.01	h : 0.01	i : 0.01	b : 0.01	
c : 0.20	e : 0.18	g : 0.15	f : 0.10	d : 0.08	= : 0.06	4 : 0.03	3 : 0.03	] : 0.03	> : 0.01	h : 0.01	i : 0.01	2 : 0.01	b : 0.01	
e : 0.18	g : 0.13	f : 0.12	c : 0.10	= : 0.08	d : 0.08	] : 0.06	3 : 0.05	h : 0.03	: : 0.03	b : 0.03	> : 0.01	a : 0.01	2 : 0.01	

#score	769.9415558980124
#seq	58
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_CDS_m2_run1.txt

#BEAR
%bb!!eeeeeooooooeeeee333bb3	chr2:242179377-242179597(-)$1	220	141	168	11.5288
!!hhhhhhhhoooooohhhhhhhh333	chr6:7585958-7586189(+)$1	231	26	53	13.1209
ggggg!!cccoooooocccggggggg5	chr19:44376892-44377119(-)$1	227	49	76	14.6970
ii[ccc[a[annnnna]a]ccc]iiii	chr7:158482420-158482644(-)$1	224	126	153	9.8061
####a!!cccooooooccc22a333cc	chrX:13790897-13791119(-)$1	222	105	132	15.6996
ff[bb!!cccooooooccc22bb]fff	chr6:31603654-31603884(+)$1	230	131	158	14.0473
[ccc"""cccooooooccc4444ccc]	chr18:13681974-13682196(-)$1	222	89	116	15.1161
========rrrrrrrrr==========	chr17:7404265-7404496(+)$1	231	170	197	9.6073
"ccc[eeeeeooooooeeeeeccc333	chr12:15793537-15793762(-)$1	225	40	67	13.0171
!!hhhhhhhhoooooohhhhhhhh22e	chr4:57265262-57265496(-)$1	234	64	91	12.2664
fffff"""bboooooobb333ffffff	chr4:187628084-187628317(-)$1	233	90	117	12.4047
eee[ccc[bboooooobb]ccceeeee	chr9:123421610-123421832(-)$1	222	63	90	12.2895
========[aooooooa]=========	chr1:119618873-119619094(-)$1	221	165	192	14.7459
ddd[ccccccooooooccc4444ccc]	chr2:74386139-74386361(-)$1	222	154	181	14.2903
eebbbb[cccooooooccc]bb22bb]	chr5:37351251-37351483(-)$1	232	128	155	12.9263
ee!!ccccccooooooccc22ccc555	chr6:160176389-160176615(+)$1	226	3	30	12.7631
"""bb[ddddoooooodddd]bb]eee	chr5:71494456-71494686(+)$1	230	155	182	12.8138
"dddd!!cccooooooccc22dddd33	chr17:57663458-57663677(+)$1	219	154	181	14.3182
==========oooooo===========	chr1:24080625-24080842(+)$1	217	176	203	14.8712
""ccc[ddddoooooodddd]ccc22b	chr5:145537191-145537410(-)$1	219	102	129	13.4250
eeee!!ddddoooooodddd22eeeee	chr8:64099668-64099891(+)$1	223	32	59	12.4612
eeeebb[cccooooooccc]bb:eeee	chr19:37241205-37241427(-)$1	222	139	166	12.0685
!iiiiiiiiiooooooiiiiiiiii22	chr5:32420065-32420304(-)$1	239	166	193	14.7182
:ggggggg[aooooooa]ggggggg::	chr13:53254017-53254248(+)$1	231	178	205	11.2522
=======cccmmmmccc4444======	chrX:41055459-41055704(+)$1	245	45	72	9.5930
dd!!ccc[bboooooobb]ccc22ddd	chr16:24801366-24801586(+)$1	220	89	116	12.2718
ggggg!!cccnnnnnccc4444ggggg	chr13:100211587-100211809(+)$1	222	72	99	10.4741
ee[bb!!cccooooooccc]bbeeeee	chrX:153197423-153197652(-)$1	229	193	220	13.7505
hhhhh!!cccooooooccc22hhhhhh	chrX:74295127-74295349(-)$1	222	14	41	13.2990
fffff[ddddooooooddddffffff2	chrX:118716516-118716739(+)$1	223	157	184	12.0584
ffff!!ddddoooooodddd22fffff	chr5:79285890-79286111(-)$1	221	25	52	12.3913
ffffffddddoooooodddd333ffff	chr10:115639269-115639491(+)$1	222	128	155	12.3966
b[a[ffffffooooooffffff]a]bb	chr6:123130298-123130525(+)$1	227	143	170	11.3150
dahhhhhhhhoooooohhhhhhhh]a]	chr3:4358767-4358987(+)$1	220	94	121	12.0859
d[ccc!!cccooooooccccccdddd:	chr1:156025085-156025307(+)$1	222	172	199	13.4656
###gggggggooooooggggggg>>>>	chr7:102944784-102945013(+)$1	229	30	57	13.5550
!!dddd[cccoooooocccdddd22dd	chr1:109302516-109302738(+)$1	222	50	77	13.1221
$ggggggg[aooooooa]ggggggg33	chr10:121652251-121652475(+)$1	224	183	210	14.4263
!!cccbb[bboooooobb]bb]ccc22	chr1:19948518-19948742(+)$1	224	89	116	12.1628
iiiiiiccc[ammmmaccc333iiiii	chr3:182605315-182605536(+)$1	221	63	90	10.6340
ffbb"""cccooooooccc]bb333ff	chr5:14758570-14758791(-)$1	221	177	204	14.0866
d!!ccc[cccoooooocccccc333dd	chr5:179688658-179688881(-)$1	223	113	140	15.0099
[bbgggggggooooooggggggg]bb2	chr5:110097203-110097424(+)$1	221	187	214	13.3050
ccc[ccc[bboooooobb]ccc]ccc]	chr5:32415070-32415296(-)$1	226	168	195	13.1881
$$$gggggggooooooggggggg4444	chr13:33110271-33110492(-)$1	221	175	202	13.9181
eeeee!!cccooooooccc22eeeeeD	chr1:226549571-226549791(-)$1	220	3	30	12.7652
ggggggddddoooooodddd]gggggg	chr3:52723102-52723322(+)$1	220	178	205	13.4745
cc[ccc[cccooooooccc]ccc]ccc	chr1:77627218-77627439(-)$1	221	65	92	14.8832
dddgggggggooooooggggggg]ddd	chr5:82868242-82868463(+)$1	221	24	51	13.0459
##bb!!ddddoooooodddd22bb333	chr12:48468055-48468286(-)$1	231	193	220	13.3616

#otherMatches

#Seq PSSM
CGCAAGGUGCGCGACAGCACUGGAGCA	chr2:242179377-242179597(-)$1	220	141	168	11.5288
cucgggaucucgcuccggaucucgcuc	chr6:7585958-7586189(+)$1	231	26	53	13.1209
UCAUGCUGGGGAGAAACCCUAUGAAUG	chr19:44376892-44377119(-)$1	227	49	76	14.6970
AAGAAGAGGUAAAUAGGUAUUUGUUUU	chr7:158482420-158482644(-)$1	224	126	153	9.8061
AAUUCUUACACAUAAAUGUUUGCCAGA	chrX:13790897-13791119(-)$1	222	105	132	15.6996
GGAGGCUUCCGCCCUGGGACACCCUCA	chr6:31603654-31603884(+)$1	230	131	158	14.0473
UAGAAGCUGAAACCUAUCAACACUCUU	chr18:13681974-13682196(-)$1	222	89	116	15.1161
GGAGGCGUGGUACCAAGACGUCUCUGU	chr17:7404265-7404496(+)$1	231	170	197	9.6073
UUGUGCCAAAUAACAUUUUGGAUAUUG	chr12:15793537-15793762(-)$1	225	40	67	13.0171
AAGAAUUGUUCUUGUAGAUGAUUCAAU	chr4:57265262-57265496(-)$1	234	64	91	12.2664
GAUGUUAAUGACAACCCACCUACAUUU	chr4:187628084-187628317(-)$1	233	90	117	12.4047
GUUAUCAGGGGCUUCACUGUGAAACCU	chr9:123421610-123421832(-)$1	222	63	90	12.2895
UUAUUUGAGGAAAAAAUGUUGAAUGGU	chr1:119618873-119619094(-)$1	221	165	192	14.7459
CCAUGUUGAUUUCUGUGUCCUGUGACU	chr2:74386139-74386361(-)$1	222	154	181	14.2903
CACUGAUAAUGGCAGAAUUUUCUUGGC	chr5:37351251-37351483(-)$1	232	128	155	12.9263
CCAACAGCUCAGAGGAGAGAACUGGCA	chr6:160176389-160176615(+)$1	226	3	30	12.7631
AACAGCAACUUGCCACAGUUCCUCUUC	chr5:71494456-71494686(+)$1	230	155	182	12.8138
AAUCACAAUCAAAACAGAUAUUGAUCU	chr17:57663458-57663677(+)$1	219	154	181	14.3182
ACUGGGUGGCUUGGCUGCUACUCAGUG	chr1:24080625-24080842(+)$1	217	176	203	14.8712
AUACCCAUCUAAAUUAAGGUAGGUUUG	chr5:145537191-145537410(-)$1	219	102	129	13.4250
GGUGUUGUACCUGUCAGUGCUUCACCU	chr8:64099668-64099891(+)$1	223	32	59	12.4612
UCAUACUGGGGAAAAGCCCUGUGCAUG	chr19:37241205-37241427(-)$1	222	139	166	12.0685
CCAGUAGCUGCUCACACAGUUACUGCU	chr5:32420065-32420304(-)$1	239	166	193	14.7182
AAAAGUUGGAGGGAGAUGCAGCUUUAA	chr13:53254017-53254248(+)$1	231	178	205	11.2522
ACUGUUCGUCAGGUGGCACAGGAGCAG	chrX:41055459-41055704(+)$1	245	45	72	9.5930
GUAUGAAUGGCACUUCCCUUUCUCACC	chr16:24801366-24801586(+)$1	220	89	116	12.2718
CUGCAGUUUAUUUCUUAAUCUAUGCAG	chr13:100211587-100211809(+)$1	222	72	99	10.4741
UGAGACCGGCUGAGUUGCCUUCCAGGU	chrX:153197423-153197652(-)$1	229	193	220	13.7505
UUUUCACCUGAGCAGACAGACGGGAGC	chrX:74295127-74295349(-)$1	222	14	41	13.2990
UUAAUAUGUUUAUAUUAGCAAUUGAAU	chrX:118716516-118716739(+)$1	223	157	184	12.0584
UGUAUGUAAACUGUUUUUUGAUUAUAG	chr5:79285890-79286111(-)$1	221	25	52	12.3913
GCCAUAAUGAAUAAUAUCAUAUAUGUG	chr10:115639269-115639491(+)$1	222	128	155	12.3966
UGUAACAUGUGAUAAGACAUGUAAGGC	chr6:123130298-123130525(+)$1	227	143	170	11.3150
acaggaauaaaccaacuuauuucucgu	chr3:4358767-4358987(+)$1	220	94	121	12.0859
GAUCCCAAGGGGGCGACCUGGACCCCA	chr1:156025085-156025307(+)$1	222	172	199	13.4656
UUUUUUUUGGUUUCCUUUAAAAAUUGU	chr7:102944784-102945013(+)$1	229	30	57	13.5550
UCUAGAUGUAACUAUAUGCUUUGUUUU	chr1:109302516-109302738(+)$1	222	50	77	13.1221
GGCCUCCCUGCUCUUACCGGGAGGUAA	chr10:121652251-121652475(+)$1	224	183	210	14.4263
UUAGGAAUUGUUUUCUCACUUACCUUC	chr1:19948518-19948742(+)$1	224	89	116	12.1628
GUAUGACAGCGUGUACCUGACUUUAUA	chr3:182605315-182605536(+)$1	221	63	90	10.6340
CCGCCUUUCCUUUCAUGGACGCAAUGG	chr5:14758570-14758791(-)$1	221	177	204	14.0866
GCUGGAUCAUGAAAGAAUGUCCUACCU	chr5:179688658-179688881(-)$1	223	113	140	15.0099
UUGGUGCUGUUAUAAUACAGUACACAC	chr5:110097203-110097424(+)$1	221	187	214	13.3050
GUGCCAUCCUAUACUCAGAGUGCUACU	chr5:32415070-32415296(-)$1	226	168	195	13.1881
CCAGUUUGAACUAUCAUUUAAACAUUC	chr13:33110271-33110492(-)$1	221	175	202	13.9181
UCAGGUUUGGGCAAAACUACCCCUGAU	chr1:226549571-226549791(-)$1	220	3	30	12.7652
UCUGAUAGUCACUGAAGACUGAUUAGA	chr3:52723102-52723322(+)$1	220	178	205	13.4745
AUUGAUACUUGCCAAGGAGCAUCCAUG	chr1:77627218-77627439(-)$1	221	65	92	14.8832
CAGCUUCUUUUCUGCUGGAGAAGACUG	chr5:82868242-82868463(+)$1	221	24	51	13.0459
CAUAUAACUACAUUUUUAGUCCUAAUA	chr12:48468055-48468286(-)$1	231	193	220	13.3616

#DB
.((..(((((......)))))...)).	chr2:242179377-242179597(-)$1	1	141	168	11.5288
..((((((((......))))))))...	chr6:7585958-7586189(+)$1	1	26	53	13.1209
(((((..(((......)))))))))).	chr19:44376892-44377119(-)$1	1	49	76	14.6970
((.(((.(.(.....).).))).))))	chr7:158482420-158482644(-)$1	1	126	153	9.8061
....(..(((......)))..)...))	chrX:13790897-13791119(-)$1	1	105	132	15.6996
((.((..(((......)))..)).)))	chr6:31603654-31603884(+)$1	1	131	158	14.0473
.(((...(((......)))....))).	chr18:13681974-13682196(-)$1	1	89	116	15.1161
((((((((.........))))))))))	chr17:7404265-7404496(+)$1	1	170	197	9.6073
.(((.(((((......))))))))...	chr12:15793537-15793762(-)$1	1	40	67	13.0171
..((((((((......))))))))..)	chr4:57265262-57265496(-)$1	1	64	91	12.2664
(((((...((......))...))))))	chr4:187628084-187628317(-)$1	1	90	117	12.4047
(((.(((.((......)).))))))))	chr9:123421610-123421832(-)$1	1	63	90	12.2895
((((((((.(......).)))))))))	chr1:119618873-119619094(-)$1	1	165	192	14.7459
(((.((((((......)))....))).	chr2:74386139-74386361(-)$1	1	154	181	14.2903
((((((.(((......))).))..)).	chr5:37351251-37351483(-)$1	1	128	155	12.9263
((..((((((......)))..)))...	chr6:160176389-160176615(+)$1	1	3	30	12.7631
...((.((((......)))).)).)))	chr5:71494456-71494686(+)$1	1	155	182	12.8138
.((((..(((......)))..))))..	chr17:57663458-57663677(+)$1	1	154	181	14.3182
((((((((((......)))))))))))	chr1:24080625-24080842(+)$1	1	176	203	14.8712
..(((.((((......)))).)))..)	chr5:145537191-145537410(-)$1	1	102	129	13.4250
((((..((((......))))..)))))	chr8:64099668-64099891(+)$1	1	32	59	12.4612
))))((.(((......))).)).((((	chr19:37241205-37241427(-)$1	1	139	166	12.0685
.(((((((((......)))))))))..	chr5:32420065-32420304(-)$1	1	166	193	14.7182
.(((((((.(......).)))))))..	chr13:53254017-53254248(+)$1	1	178	205	11.2522
((((((((((....)))....))))))	chrX:41055459-41055704(+)$1	1	45	72	9.5930
((..(((.((......)).)))..)))	chr16:24801366-24801586(+)$1	1	89	116	12.2718
(((((..(((.....)))....)))))	chr13:100211587-100211809(+)$1	1	72	99	10.4741
((.((..(((......))).)))))))	chrX:153197423-153197652(-)$1	1	193	220	13.7505
(((((..(((......)))..))))))	chrX:74295127-74295349(-)$1	1	14	41	13.2990
(((((.((((......)))))))))).	chrX:118716516-118716739(+)$1	1	157	184	12.0584
((((..((((......))))..)))))	chr5:79285890-79286111(-)$1	1	25	52	12.3913
((((((((((......))))...))))	chr10:115639269-115639491(+)$1	1	128	155	12.3966
(.(.((((((......)))))).).))	chr6:123130298-123130525(+)$1	1	143	170	11.3150
((((((((((......)))))))).).	chr3:4358767-4358987(+)$1	1	94	121	12.0859
(.(((..(((......)))))))))).	chr1:156025085-156025307(+)$1	1	172	199	13.4656
...(((((((......)))))))....	chr7:102944784-102945013(+)$1	1	30	57	13.5550
..((((.(((......)))))))..))	chr1:109302516-109302738(+)$1	1	50	77	13.1221
.(((((((.(......).)))))))..	chr10:121652251-121652475(+)$1	1	183	210	14.4263
..(((((.((......)).)).)))..	chr1:19948518-19948742(+)$1	1	89	116	12.1628
(((((((((.(....))))...)))))	chr3:182605315-182605536(+)$1	1	63	90	10.6340
((((...(((......))).))...))	chr5:14758570-14758791(-)$1	1	177	204	14.0866
(..(((.(((......))))))...))	chr5:179688658-179688881(-)$1	1	113	140	15.0099
.(((((((((......))))))).)).	chr5:110097203-110097424(+)$1	1	187	214	13.3050
(((.(((.((......)).))).))).	chr5:32415070-32415296(-)$1	1	168	195	13.1881
...(((((((......)))))))....	chr13:33110271-33110492(-)$1	1	175	202	13.9181
(((((..(((......)))..)))))(	chr1:226549571-226549791(-)$1	1	3	30	12.7652
((((((((((......)))).))))))	chr3:52723102-52723322(+)$1	1	178	205	13.4745
((.(((.(((......))).))).)))	chr1:77627218-77627439(-)$1	1	65	92	14.8832
((((((((((......))))))).)))	chr5:82868242-82868463(+)$1	1	24	51	13.0459
..((..((((......))))..))...	chr12:48468055-48468286(-)$1	1	193	220	13.3616

#PSSM
e : 0.14	f : 0.12	d : 0.12	! : 0.10	= : 0.08	" : 0.08	g : 0.06	# : 0.06	i : 0.04	[ : 0.04	$ : 0.04	c : 0.04	% : 0.02	: : 0.02	h : 0.02	b : 0.02	
e : 0.14	f : 0.12	! : 0.10	g : 0.10	c : 0.08	= : 0.08	d : 0.08	i : 0.06	# : 0.06	b : 0.04	" : 0.04	[ : 0.04	h : 0.02	a : 0.02	$ : 0.02	
c : 0.12	b : 0.10	g : 0.10	h : 0.08	[ : 0.08	= : 0.08	f : 0.08	e : 0.08	d : 0.08	! : 0.06	# : 0.04	i : 0.04	" : 0.02	a : 0.02	$ : 0.02	
g : 0.18	c : 0.16	b : 0.12	h : 0.08	= : 0.08	f : 0.08	[ : 0.08	! : 0.06	e : 0.06	d : 0.04	i : 0.04	# : 0.02	
c : 0.21	g : 0.18	b : 0.10	! : 0.08	h : 0.08	= : 0.08	f : 0.08	" : 0.04	d : 0.04	i : 0.04	a : 0.02	[ : 0.02	e : 0.02	
! : 0.23	c : 0.16	g : 0.14	= : 0.08	h : 0.06	" : 0.06	b : 0.06	[ : 0.06	e : 0.04	i : 0.04	f : 0.04	d : 0.02	
! : 0.18	d : 0.16	[ : 0.12	c : 0.12	g : 0.12	= : 0.08	h : 0.06	" : 0.06	e : 0.04	i : 0.02	f : 0.02	b : 0.02	
c : 0.40	d : 0.16	g : 0.12	[ : 0.08	h : 0.06	= : 0.06	e : 0.04	a : 0.02	" : 0.02	i : 0.02	f : 0.02	
c : 0.40	d : 0.16	b : 0.10	[ : 0.08	g : 0.08	h : 0.06	e : 0.04	r : 0.02	= : 0.02	i : 0.02	f : 0.02	
c : 0.38	d : 0.16	b : 0.10	a : 0.08	g : 0.08	h : 0.06	e : 0.04	r : 0.02	= : 0.02	i : 0.02	f : 0.02	[ : 0.02	
o : 0.90	n : 0.04	r : 0.02	m : 0.02	a : 0.02	
o : 0.90	n : 0.04	m : 0.04	r : 0.02	
o : 0.90	n : 0.04	m : 0.04	r : 0.02	
o : 0.90	n : 0.04	m : 0.04	r : 0.02	
o : 0.90	n : 0.04	r : 0.02	c : 0.02	m : 0.02	
o : 0.90	a : 0.04	c : 0.04	r : 0.02	
c : 0.40	d : 0.16	b : 0.10	g : 0.08	h : 0.06	a : 0.06	e : 0.04	] : 0.02	r : 0.02	= : 0.02	i : 0.02	f : 0.02	
c : 0.38	d : 0.16	b : 0.10	g : 0.08	h : 0.06	] : 0.06	e : 0.04	= : 0.04	a : 0.02	i : 0.02	4 : 0.02	f : 0.02	
c : 0.36	d : 0.16	g : 0.12	] : 0.10	h : 0.06	= : 0.06	e : 0.04	4 : 0.04	3 : 0.02	i : 0.02	f : 0.02	
d : 0.18	g : 0.14	c : 0.12	2 : 0.12	] : 0.10	4 : 0.08	h : 0.06	= : 0.06	e : 0.04	3 : 0.04	i : 0.02	f : 0.02	b : 0.02	
2 : 0.18	g : 0.14	c : 0.14	b : 0.10	4 : 0.08	h : 0.06	= : 0.06	3 : 0.06	] : 0.06	e : 0.04	f : 0.04	i : 0.02	d : 0.02	
c : 0.19	g : 0.16	b : 0.12	h : 0.08	= : 0.08	3 : 0.06	4 : 0.06	f : 0.06	2 : 0.06	d : 0.04	a : 0.02	i : 0.02	] : 0.02	e : 0.02	
g : 0.18	3 : 0.10	c : 0.10	h : 0.08	= : 0.08	e : 0.08	] : 0.06	b : 0.06	f : 0.06	d : 0.06	4 : 0.04	2 : 0.04	i : 0.04	: : 0.02	
c : 0.14	g : 0.10	] : 0.10	e : 0.10	3 : 0.08	h : 0.08	= : 0.08	f : 0.08	i : 0.06	2 : 0.06	d : 0.04	a : 0.02	> : 0.02	4 : 0.02	b : 0.02	
3 : 0.12	e : 0.12	g : 0.10	f : 0.10	c : 0.10	= : 0.08	d : 0.08	b : 0.06	i : 0.06	2 : 0.06	] : 0.04	5 : 0.02	h : 0.02	> : 0.02	4 : 0.02	
f : 0.12	e : 0.12	3 : 0.10	c : 0.10	d : 0.10	b : 0.08	= : 0.08	2 : 0.08	g : 0.06	i : 0.04	5 : 0.02	: : 0.02	h : 0.02	a : 0.02	> : 0.02	4 : 0.02	
3 : 0.12	e : 0.12	f : 0.10	] : 0.10	= : 0.08	2 : 0.08	d : 0.08	5 : 0.04	i : 0.04	c : 0.04	b : 0.04	: : 0.04	g : 0.04	h : 0.02	> : 0.02	4 : 0.02	D : 0.02	

#score	648.2966502192623
#seq	50
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_UTR_m3_run1.txt

#BEAR
fffffqqqqqqqqfffff	chr1:229457139-229457358(-)$1	219	42	60	13.8302
!!cccqqqqqqqqccc22	chr20:32890982-32891211(-)$1	229	40	58	14.2023
eeeeeqqqqqqqqeeeee	chr19:37046912-37047131(-)$1	219	84	102	13.9126
eeeeeqqqqqqqqeeeee	chr17:27401740-27401970(-)$1	230	202	220	13.9126
ffcccqqqqqqqqccc22	chr17:37077626-37077856(+)$1	230	155	173	13.9859
b[cccqqqqqqqqccc]b	chr12:96661451-96661682(+)$1	231	44	62	13.7420
c:cccqqqqqqqqccccc	chr2:169626068-169626301(+)$1	233	81	99	12.9712
e!!bbqqqqqqqqbb333	chr3:196074497-196074727(-)$1	230	76	94	13.6851
f[cccqqqqqqqqccc33	chr1:89301335-89301553(+)$1	218	34	52	14.5122
=====qqqqqqqq=====	chr1:222839028-222839258(+)$1	230	76	94	14.4430
ee[bbqqqqqqqqbb]ee	chr17:56430543-56430769(+)$1	226	6	24	13.5636
[ddddqqqqqqqqdddd]	chr3:156865736-156865966(-)$1	230	155	173	13.8838
EEcccqqqqqqqqcccff	chr20:34309603-34309818(-)$1	215	149	167	12.1122
fffffqqqqqqqqfffff	chr17:40994372-40994598(+)$1	226	149	167	13.8302
eeeeeqqqqqqqqeeeee	chr3:38525097-38525316(+)$1	219	41	59	13.9126
"ddddqqqqqqqqddddg	chr7:123180606-123180825(-)$1	219	13	31	13.7285
d[cccqqqqqqqqcccdd	chr14:35344269-35344489(+)$1	220	150	168	13.9659
fffffqqqqqqqqfffff	chr15:39889410-39889647(+)$1	237	38	56	13.8302
fffffqqqqqqqqfffff	chr1:115314993-115315213(-)$1	220	54	72	13.8302
=====qqqqqqqq=====	chr1:171562215-171562422(+)$1	207	18	36	14.4430
gg[bbqqqqqqqqbb]gg	chr8:11667088-11667309(+)$1	221	49	67	13.6476
iiiiiqqqqqqqqiiiii	chr17:78227091-78227328(+)$1	237	198	216	14.1268
cc[bbqqqqqqqqbbccc	chr1:244219626-244219847(+)$1	221	83	101	13.3294
!!cccqqqqqqqqcccbb	chr1:33324006-33324236(+)$1	230	64	82	13.7798
eeeeeqqqqqqqqeeeee	chr1:87210356-87210586(+)$1	230	173	191	13.9126
"ddddqqqqqqqqdddd]	chr3:141165326-141165550(+)$1	224	148	166	13.7891
[ddddqqqqqqqqdddd]	chr7:86988884-86989106(+)$1	222	196	214	13.8838
"ddddqqqqqqqqdddd3	chr15:68483634-68483843(+)$1	209	113	131	13.8414
iiiiiqqqqqqqqiiiii	chr17:18709273-18709490(+)$1	217	85	103	14.1268
fffffqqqqqqqqfffff	chr11:62608993-62609273(-)$1	280	39	57	13.8302
eeeeeqqqqqqqqeeeee	chr12:57392650-57392870(-)$1	220	37	55	13.9126
d[cccqqqqqqqqcccdd	chr15:25583935-25584165(-)$1	230	208	226	13.9659
gggggqqqqqqqqggggg	chr12:69233594-69233816(+)$1	222	57	75	14.1824
ddcccqqqqqqqqccc22	chr14:104378562-104378802(-)$1	240	55	73	13.8091
=====qqqqqqqq=====	chr3:150348080-150348298(+)$1	218	48	66	14.4430
gggggqqqqqqqqggggg	chr6:24703717-24703947(+)$1	230	181	199	14.1824
gggggqqqqqqqqggggg	chr15:52873843-52874062(-)$1	219	115	133	14.1824
!!cccqqqqqqqqccc44	chr8:103219804-103220050(-)$1	246	85	103	14.4160
eeeeeqqqqqqqqeeeee	chr17:72199725-72199947(+)$1	222	128	146	13.9126
+ddddqqqqqqqqdddd>	chr1:226332800-226333029(-)$1	229	176	194	12.7335
fffffqqqqqqqqfffff	chr8:141572525-141572743(-)$1	218	178	196	13.8302
g!!bbqqqqqqqqbb444	chr16:24835187-24835452(+)$1	265	37	55	13.4937
dddbbqqqqqqqqbb]dd	chr19:46386996-46387216(-)$1	220	27	45	13.0061
iiiiiqqqqqqqqiiiii	chr20:11905075-11905300(+)$1	225	180	198	14.1268
ggg[aqqqqqqqqa]ggg	chr5:114951126-114951338(-)$1	212	119	137	13.8992
eeeeeqqqqqqqqeeeee	chr11:77376312-77376545(-)$1	233	132	150	13.9126
!ddddqqqqqqqqdddd3	chr19:23924715-23924935(-)$1	220	124	142	13.9233
!ddddqqqqqqqqdddd2	chr12:69237810-69238029(+)$1	219	84	102	13.7119
eeeeeqqqqqqqqeeeee	chr3:52014917-52015133(+)$1	216	68	86	13.9126
!!cccqqqqqqqqccc]d	chr1:2238363-2238594(+)$1	231	48	66	14.2681
eeeeeqqqqqqqqeeeee	chr5:72207423-72207654(+)$1	231	4	22	13.9126
d[cccqqqqqqqqccc22	chr7:139790172-139790396(-)$1	224	187	205	13.9542
fffffqqqqqqqqfffff	chr20:47729924-47730149(-)$1	225	87	105	13.8302
fff[aqqqqqqqqa]fff	chr2:135206773-135207003(+)$1	230	159	177	13.6570
fffffqqqqqqqqfffff	chr4:177249604-177249823(+)$1	219	174	192	13.8302
==[bbqqqqqqqqbb22=	chr7:95036240-95036463(-)$1	223	124	142	13.2581
#ddddqqqqqqqqdddd3	chr20:57608528-57608758(-)$1	230	97	115	13.7935
gggggqqqqqqqqggggg	chrX:67752916-67753134(+)$1	218	64	82	14.1824
iiiiiqqqqqqqqiiiii	chr1:227843508-227843730(+)$1	222	56	74	14.1268
eeeeeqqqqqqqqeeeee	chr4:78639278-78639508(-)$1	230	21	39	13.9126
"ddddqqqqqqqqddddb	chr2:101885768-101885997(+)$1	229	150	168	13.3910
ee[bbqqqqqqqqbb]ee	chr13:41132899-41133115(-)$1	216	31	49	13.5636
fffffqqqqqqqqfffff	chr1:113666921-113667151(+)$1	230	165	183	13.8302
ff[bbqqqqqqqqbb]ff	chr4:6709981-6710203(-)$1	222	15	33	13.4932
fffffqqqqqqqqfffff	chr9:74969421-74969651(-)$1	230	118	136	13.8302
[ddddqqqqqqqqdddd]	chr8:25272570-25272790(-)$1	220	94	112	13.8838
!ddddqqqqqqqqddddf	chr8:22471614-22471836(+)$1	222	77	95	13.7899
fffffqqqqqqqqfffff	chr8:74236421-74236647(+)$1	226	142	160	13.8302
eeeeeqqqqqqqqeeeee	chr17:56051393-56051626(-)$1	233	46	64	13.9126

#otherMatches

#Seq PSSM
UAUAAGAUCCUUAUUAUA	chr1:229457139-229457358(-)$1	219	42	60	13.8302
ACGCGCAUAUCCCUGCUC	chr20:32890982-32891211(-)$1	229	40	58	14.2023
gaauuccCUGACCAAUUC	chr19:37046912-37047131(-)$1	219	84	102	13.9126
GCCCUCUCACCCCAGGGC	chr17:27401740-27401970(-)$1	230	202	220	13.9126
AUUUGCCUCUGUCCAAAC	chr17:37077626-37077856(+)$1	230	155	173	13.9859
UUUACUUUCAAUUGUAUA	chr12:96661451-96661682(+)$1	231	44	62	13.7420
GCUCCUGCUCCAUGGAUG	chr2:169626068-169626301(+)$1	233	81	99	12.9712
GGACCAAACUCAAGGAAA	chr3:196074497-196074727(-)$1	230	76	94	13.6851
ACUAUGCAUUCAAAUGAA	chr1:89301335-89301553(+)$1	218	34	52	14.5122
UUGAGCCAAACAAUUCAA	chr1:222839028-222839258(+)$1	230	76	94	14.4430
CUUUCUUCUUGUUGGCGG	chr17:56430543-56430769(+)$1	226	6	24	13.5636
CAGGUUCAAUUGUACUUU	chr3:156865736-156865966(-)$1	230	155	173	13.8838
UUGGAAGAGUAAGUCCAG	chr20:34309603-34309818(-)$1	215	149	167	12.1122
GGUUGCCUUUUCCCAGCC	chr17:40994372-40994598(+)$1	226	149	167	13.8302
UGGGAUUCGUUUUUCCCG	chr3:38525097-38525316(+)$1	219	41	59	13.9126
AGAGUGCAAGAAGGCUCC	chr7:123180606-123180825(-)$1	219	13	31	13.7285
GACCGCCUCUCUCCGGCC	chr14:35344269-35344489(+)$1	220	150	168	13.9659
AAGAAUUGUUGGuuuuuu	chr15:39889410-39889647(+)$1	237	38	56	13.8302
GAGCUGUUUAUAAAGUUC	chr1:115314993-115315213(-)$1	220	54	72	13.8302
CUUUGCAAUUUUCUGGGG	chr1:171562215-171562422(+)$1	207	18	36	14.4430
UUUGUUCCAAUAUAUUAA	chr8:11667088-11667309(+)$1	221	49	67	13.6476
uagaauacaagauuuuua	chr17:78227091-78227328(+)$1	237	198	216	14.1268
UCGCUACAUAACAAGGAA	chr1:244219626-244219847(+)$1	221	83	101	13.3294
UCGCCUUAAAGAUGGUAC	chr1:33324006-33324236(+)$1	230	64	82	13.7798
UGCAGUUUUAUAGUUGUA	chr1:87210356-87210586(+)$1	230	173	191	13.9126
AUUAUGAGGAGCAAUAGA	chr3:141165326-141165550(+)$1	224	148	166	13.7891
GAAUGGUUAUGUAUAUUG	chr7:86988884-86989106(+)$1	222	196	214	13.8838
GUUACCUGUUUAUGUAGA	chr15:68483634-68483843(+)$1	209	113	131	13.8414
GAAAUAAUUGUUAGUUUU	chr17:18709273-18709490(+)$1	217	85	103	14.1268
aucaguuuaauaucugau	chr11:62608993-62609273(-)$1	280	39	57	13.8302
AGUUGUUGACGUCUAACU	chr12:57392650-57392870(-)$1	220	37	55	13.9126
AUCACUUUUGCUUGUGUU	chr15:25583935-25584165(-)$1	230	208	226	13.9659
AUAUAUUUCUAACUAUAU	chr12:69233594-69233816(+)$1	222	57	75	14.1824
ACUGAGCCACCCAUCAUU	chr14:104378562-104378802(-)$1	240	55	73	13.8091
AAAAAAAGAGAUCUUUUU	chr3:150348080-150348298(+)$1	218	48	66	14.4430
acugguuugggUUUUAGU	chr6:24703717-24703947(+)$1	230	181	199	14.1824
ACAAGUCUUUAAUUUUGU	chr15:52873843-52874062(-)$1	219	115	133	14.1824
AUGCAAAAAUAAAUGCUU	chr8:103219804-103220050(-)$1	246	85	103	14.4160
GUGUCUCUAGGGUGAUAC	chr17:72199725-72199947(+)$1	222	128	146	13.9126
AGCAGUGCUUAAUUUGUG	chr1:226332800-226333029(-)$1	229	176	194	12.7335
UUGCCAUCCAUGAGGUGA	chr8:141572525-141572743(-)$1	218	178	196	13.8302
ACAGCUAUUCUCUGCACA	chr16:24835187-24835452(+)$1	265	37	55	13.4937
UGCCACCUCUAUCUGUGU	chr19:46386996-46387216(-)$1	220	27	45	13.0061
CUUUUUCCCCAUUAAAAG	chr20:11905075-11905300(+)$1	225	180	198	14.1268
UAACAGGUAGAAAUAUUA	chr5:114951126-114951338(-)$1	212	119	137	13.8992
AGCCCUGGGAUUUGGGUU	chr11:77376312-77376545(-)$1	233	132	150	13.9126
AUGGACUAACAUUUCUAG	chr19:23924715-23924935(-)$1	220	124	142	13.9233
UAUUAAAAUUGUCUGAUU	chr12:69237810-69238029(+)$1	219	84	102	13.7119
GCAAGACUUCCACCUUGU	chr3:52014917-52015133(+)$1	216	68	86	13.9126
CCCCAACUACAGCUGGAG	chr1:2238363-2238594(+)$1	231	48	66	14.2681
UAAUAGUUUUGAAUGUUG	chr5:72207423-72207654(+)$1	231	4	22	13.9126
UUGAUUACCUUAUAUCCC	chr7:139790172-139790396(-)$1	224	187	205	13.9542
AAAUUUUUUUGUUAAUUU	chr20:47729924-47730149(-)$1	225	87	105	13.8302
GCAGGAGAGAGACCGUGU	chr2:135206773-135207003(+)$1	230	159	177	13.6570
UCCAUUAUUCUUUAUGGA	chr4:177249604-177249823(+)$1	219	174	192	13.8302
UUUUGGAAAAACACACUA	chr7:95036240-95036463(-)$1	223	124	142	13.2581
CGUUUUCCUACUUAAAUU	chr20:57608528-57608758(-)$1	230	97	115	13.7935
GGUUGGGGAAUAGCAAUU	chrX:67752916-67753134(+)$1	218	64	82	14.1824
UACUGAAUAAAAGUGGUA	chr1:227843508-227843730(+)$1	222	56	74	14.1268
AUUACCUUUUUUUGUAAU	chr4:78639278-78639508(-)$1	230	21	39	13.9126
UGUGAUUUAGUUUUUACA	chr2:101885768-101885997(+)$1	229	150	168	13.3910
UUCUUGGUUAAAAAAAAA	chr13:41132899-41133115(-)$1	216	31	49	13.5636
ACAUCACUACUUCGAUGU	chr1:113666921-113667151(+)$1	230	165	183	13.8302
GGAAAUAUAACUUUUGUC	chr4:6709981-6710203(-)$1	222	15	33	13.4932
AAGCAUUCAGUUUUGCUU	chr9:74969421-74969651(-)$1	230	118	136	13.8302
UUUCAAUGUGUGCUGGAU	chr8:25272570-25272790(-)$1	220	94	112	13.8838
AUCAGCCUUCCCCCUGAG	chr8:22471614-22471836(+)$1	222	77	95	13.7899
GUGCCUUGAAUUUGGUAU	chr8:74236421-74236647(+)$1	226	142	160	13.8302
UGGCAAGAUGAAAUGCCA	chr17:56051393-56051626(-)$1	233	46	64	13.9126

#DB
(((((........)))))	chr1:229457139-229457358(-)$1	1	42	60	13.8302
..(((........)))..	chr20:32890982-32891211(-)$1	1	40	58	14.2023
(((((........)))))	chr19:37046912-37047131(-)$1	1	84	102	13.9126
(((((........)))))	chr17:27401740-27401970(-)$1	1	202	220	13.9126
(((((........)))..	chr17:37077626-37077856(+)$1	1	155	173	13.9859
(.(((........))).)	chr12:96661451-96661682(+)$1	1	44	62	13.7420
).(((........)))((	chr2:169626068-169626301(+)$1	1	81	99	12.9712
(..((........))...	chr3:196074497-196074727(-)$1	1	76	94	13.6851
(.(((........)))..	chr1:89301335-89301553(+)$1	1	34	52	14.5122
(((((........)))))	chr1:222839028-222839258(+)$1	1	76	94	14.4430
((.((........)).))	chr17:56430543-56430769(+)$1	1	6	24	13.5636
.((((........)))).	chr3:156865736-156865966(-)$1	1	155	173	13.8838
))(((........)))((	chr20:34309603-34309818(-)$1	1	149	167	12.1122
(((((........)))))	chr17:40994372-40994598(+)$1	1	149	167	13.8302
(((((........)))))	chr3:38525097-38525316(+)$1	1	41	59	13.9126
.((((........)))))	chr7:123180606-123180825(-)$1	1	13	31	13.7285
(.(((........)))))	chr14:35344269-35344489(+)$1	1	150	168	13.9659
(((((........)))))	chr15:39889410-39889647(+)$1	1	38	56	13.8302
(((((........)))))	chr1:115314993-115315213(-)$1	1	54	72	13.8302
(((((........)))))	chr1:171562215-171562422(+)$1	1	18	36	14.4430
((.((........)).))	chr8:11667088-11667309(+)$1	1	49	67	13.6476
(((((........)))))	chr17:78227091-78227328(+)$1	1	198	216	14.1268
((.((........)))))	chr1:244219626-244219847(+)$1	1	83	101	13.3294
..(((........)))))	chr1:33324006-33324236(+)$1	1	64	82	13.7798
(((((........)))))	chr1:87210356-87210586(+)$1	1	173	191	13.9126
.((((........)))).	chr3:141165326-141165550(+)$1	1	148	166	13.7891
.((((........)))).	chr7:86988884-86989106(+)$1	1	196	214	13.8838
.((((........)))).	chr15:68483634-68483843(+)$1	1	113	131	13.8414
(((((........)))))	chr17:18709273-18709490(+)$1	1	85	103	14.1268
(((((........)))))	chr11:62608993-62609273(-)$1	1	39	57	13.8302
(((((........)))))	chr12:57392650-57392870(-)$1	1	37	55	13.9126
(.(((........)))))	chr15:25583935-25584165(-)$1	1	208	226	13.9659
(((((........)))))	chr12:69233594-69233816(+)$1	1	57	75	14.1824
(((((........)))..	chr14:104378562-104378802(-)$1	1	55	73	13.8091
(((((........)))))	chr3:150348080-150348298(+)$1	1	48	66	14.4430
(((((........)))))	chr6:24703717-24703947(+)$1	1	181	199	14.1824
(((((........)))))	chr15:52873843-52874062(-)$1	1	115	133	14.1824
..(((........)))..	chr8:103219804-103220050(-)$1	1	85	103	14.4160
(((((........)))))	chr17:72199725-72199947(+)$1	1	128	146	13.9126
.((((........)))).	chr1:226332800-226333029(-)$1	1	176	194	12.7335
(((((........)))))	chr8:141572525-141572743(-)$1	1	178	196	13.8302
(..((........))...	chr16:24835187-24835452(+)$1	1	37	55	13.4937
(((((........)).))	chr19:46386996-46387216(-)$1	1	27	45	13.0061
(((((........)))))	chr20:11905075-11905300(+)$1	1	180	198	14.1268
(((.(........).)))	chr5:114951126-114951338(-)$1	1	119	137	13.8992
(((((........)))))	chr11:77376312-77376545(-)$1	1	132	150	13.9126
.((((........)))).	chr19:23924715-23924935(-)$1	1	124	142	13.9233
.((((........)))).	chr12:69237810-69238029(+)$1	1	84	102	13.7119
(((((........)))))	chr3:52014917-52015133(+)$1	1	68	86	13.9126
..(((........))).)	chr1:2238363-2238594(+)$1	1	48	66	14.2681
(((((........)))))	chr5:72207423-72207654(+)$1	1	4	22	13.9126
(.(((........)))..	chr7:139790172-139790396(-)$1	1	187	205	13.9542
(((((........)))))	chr20:47729924-47730149(-)$1	1	87	105	13.8302
(((.(........).)))	chr2:135206773-135207003(+)$1	1	159	177	13.6570
(((((........)))))	chr4:177249604-177249823(+)$1	1	174	192	13.8302
((.((........))..)	chr7:95036240-95036463(-)$1	1	124	142	13.2581
.((((........)))).	chr20:57608528-57608758(-)$1	1	97	115	13.7935
(((((........)))))	chrX:67752916-67753134(+)$1	1	64	82	14.1824
(((((........)))))	chr1:227843508-227843730(+)$1	1	56	74	14.1268
(((((........)))))	chr4:78639278-78639508(-)$1	1	21	39	13.9126
.((((........)))))	chr2:101885768-101885997(+)$1	1	150	168	13.3910
((.((........)).))	chr13:41132899-41133115(-)$1	1	31	49	13.5636
(((((........)))))	chr1:113666921-113667151(+)$1	1	165	183	13.8302
((.((........)).))	chr4:6709981-6710203(-)$1	1	15	33	13.4932
(((((........)))))	chr9:74969421-74969651(-)$1	1	118	136	13.8302
.((((........)))).	chr8:25272570-25272790(-)$1	1	94	112	13.8838
.((((........)))))	chr8:22471614-22471836(+)$1	1	77	95	13.7899
(((((........)))))	chr8:74236421-74236647(+)$1	1	142	160	13.8302
(((((........)))))	chr17:56051393-56051626(-)$1	1	46	64	13.9126

#PSSM
f : 0.21	e : 0.20	! : 0.10	g : 0.10	d : 0.07	= : 0.05	" : 0.05	i : 0.05	[ : 0.04	c : 0.02	b : 0.01	E : 0.01	+ : 0.01	# : 0.01	
f : 0.20	d : 0.20	e : 0.18	! : 0.08	g : 0.08	[ : 0.07	= : 0.05	i : 0.05	: : 0.01	E : 0.01	c : 0.01	
c : 0.18	d : 0.18	f : 0.17	e : 0.15	[ : 0.08	g : 0.07	i : 0.05	= : 0.04	! : 0.02	
c : 0.18	d : 0.17	f : 0.15	e : 0.15	b : 0.13	i : 0.05	g : 0.05	= : 0.04	[ : 0.02	
c : 0.18	d : 0.17	f : 0.15	e : 0.15	b : 0.13	i : 0.05	g : 0.05	= : 0.04	a : 0.02	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.18	d : 0.17	f : 0.15	e : 0.15	b : 0.13	i : 0.05	g : 0.05	= : 0.04	a : 0.02	
c : 0.18	d : 0.17	f : 0.15	e : 0.15	b : 0.13	i : 0.05	g : 0.05	= : 0.04	] : 0.02	
c : 0.20	f : 0.17	d : 0.17	e : 0.15	] : 0.07	g : 0.07	i : 0.05	= : 0.04	3 : 0.01	4 : 0.01	2 : 0.01	
d : 0.21	f : 0.20	e : 0.18	g : 0.08	2 : 0.07	i : 0.05	= : 0.04	] : 0.02	c : 0.02	3 : 0.02	4 : 0.02	b : 0.01	
f : 0.21	e : 0.18	g : 0.10	2 : 0.07	3 : 0.07	= : 0.05	] : 0.05	d : 0.05	i : 0.05	b : 0.04	c : 0.02	4 : 0.02	> : 0.01	

#score	954.3746075971848
#seq	69
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_UTR_m3_run1.txt

#BEAR
===uuuuuuuuuuuu=====	chr14:96852472-96852696(+)$1	224	66	86	22.7310
:ccctttttttttttcccgg	chr18:32720787-32721017(+)$1	230	30	50	21.3038
fffftttttttttttfffff	chr9:133513114-133513342(+)$1	228	29	49	21.8213
gggvvvvvvvvvvvvvgggg	chr1:24999040-24999271(+)$1	231	19	39	22.8635
dddvvvvvvvvvvvvvdddd	chr6:36936051-36936273(-)$1	222	45	65	22.5685
ggguuuuuuuuuuuuggggg	chr18:10552274-10552507(+)$1	233	10	30	22.8849
eeeettttttttttteeeee	chr11:27519339-27519564(-)$1	225	49	69	22.4038
ddduuuuuuuuuuuuddddD	chr1:205686184-205686406(-)$1	222	197	217	21.5593
ddduuuuuuuuuuuudddd:	chr6:89790459-89790686(+)$1	227	81	101	21.8259
ddddtttttttttttdddd]	chr12:4410310-4410541(+)$1	231	114	134	22.2476
eeeuuuuuuuuuuuueeeee	chr7:29035153-29035380(-)$1	227	160	180	22.8726
fffuuuuuuuuuuuufffff	chr16:19513434-19513658(-)$1	224	147	167	22.2848
====ttttttttttt=====	chr6:56971621-56971850(+)$1	229	165	185	22.1284
ddddtttttttttttdddd:	chr10:59954636-59954862(-)$1	226	122	142	21.2962
hhhvvvvvvvvvvvvvhhhh	chr12:54633582-54633803(-)$1	221	184	204	21.5690
gggvvvvvvvvvvvvvgggg	chr1:234742736-234742953(-)$1	217	11	31	22.8635
iiiitttttttttttiiiii	chr12:8927682-8927903(+)$1	221	162	182	21.9071
eeevvvvvvvvvvvvveeee	chr11:68381563-68381786(+)$1	223	36	56	22.8397
hhhuuuuuuuuuuuuhhhhh	chr2:42806199-42806421(+)$1	222	168	188	21.3711
[bbuuuuuuuuuuuubb]gg	chr19:7978940-7979167(+)$1	227	191	211	21.5267
eeeuuuuuuuuuuuueeeee	chr11:17395154-17395374(+)$1	220	55	75	22.8726
ddduuuuuuuuuuuudddd4	chr1:156707022-156707245(-)$1	223	193	213	22.6014
fffuuuuuuuuuuuufffff	chr10:116621654-116621875(+)$1	221	149	169	22.2848
ggguuuuuuuuuuuuggggg	chr18:48701442-48701663(-)$1	221	22	42	22.8849
!ccctttttttttttccccc	chrX:23802427-23802673(+)$1	246	129	149	22.2892
ggggtttttttttttggggg	chr15:34376126-34376350(-)$1	224	78	98	22.2772
eeevvvvvvvvvvvvveeee	chr11:121178397-121178619(+)$1	222	200	220	22.8397
eeeettttttttttteeeee	chr11:125526893-125527122(+)$1	229	1	21	22.4038
ddduuuuuuuuuuuudddd2	chr10:17757100-17757331(+)$1	231	156	176	22.5270
ccwwwwwwwwwwwwwwccc:	chr5:134193829-134194059(+)$1	230	113	133	19.8636
f[attttttttttta]ffff	chr4:109734817-109735041(-)$1	224	181	201	21.4243
fffftttttttttttfffff	chr3:44794655-44794887(-)$1	232	97	117	21.8213
ggguuuuuuuuuuuuggggg	chr14:61180503-61180730(-)$1	227	169	189	22.8849
[ccctttttttttttccc33	chr17:1421208-1421428(+)$1	220	29	49	22.2238
gggvvvvvvvvvvvvvgggg	chr1:38268939-38269164(-)$1	225	60	80	22.8635
eeeuuuuuuuuuuuueeeee	chr2:109302202-109302426(+)$1	224	31	51	22.8726
eeeettttttttttteeeee	chr11:82972416-82972640(-)$1	224	30	50	22.4038
dddvvvvvvvvvvvvvdddd	chr13:30340843-30341069(-)$1	226	4	24	22.5685
hhhvvvvvvvvvvvvvhhhh	chr1:109178143-109178369(+)$1	226	122	142	21.5690
fffftttttttttttfffff	chrX:53405476-53405698(-)$1	222	24	44	21.8213
fffftttttttttttfffff	chr17:5335866-5336088(+)$1	222	123	143	21.8213
fffwwwwwwwwwwwwwwfff	chr1:54291452-54291674(-)$1	222	13	33	20.4982
ddduuuuuuuuuuuudddd]	chr14:37147799-37148021(+)$1	222	74	94	22.7772
ddduuuuuuuuuuuudddd3	chr7:140036984-140037206(-)$1	222	54	74	22.7084
ggggtttttttttttggggg	chr7:28863740-28863967(+)$1	227	126	146	22.2772
eeeettttttttttteeeee	chr2:10923848-10924067(-)$1	219	3	23	22.4038
ddddtttttttttttdddd2	chr1:67469658-67469880(-)$1	222	4	24	21.9974
ddddtttttttttttdddd:	chr11:27516204-27516428(-)$1	224	184	204	21.2962
"bbtttttttttttbb333d	chr6:71570413-71570638(+)$1	225	128	148	19.6951
gggvvvvvvvvvvvvvgggg	chr9:125609188-125609423(-)$1	235	8	28	22.8635
ddduuuuuuuuuuuudddd:	chr12:54630649-54630882(-)$1	233	56	76	21.8259
fffftttttttttttfffff	chr5:96372686-96372908(+)$1	222	43	63	21.8213
hhhwwwwwwwwwwwwwwhhh	chr7:120428106-120428330(-)$1	224	140	160	19.9124
eeevvvvvvvvvvvvveeee	chr5:150647405-150647627(+)$1	222	36	56	22.8397
dddvvvvvvvvvvvvvdddd	chr12:72180402-72180628(+)$1	226	108	128	22.5685
cwwwwwwwwwwwwwwccc]d	chr20:10619360-10619590(-)$1	230	113	133	20.0717
ddduuuuuuuuuuuudddd]	chr13:73330172-73330398(+)$1	226	102	122	22.7772
eeevvvvvvvvvvvvveeee	chr12:97311315-97311537(+)$1	222	96	116	22.8397
fffftttttttttttfffff	chr13:25908917-25909148(+)$1	231	45	65	21.8213
eeeuuuuuuuuuuuueeeee	chr17:58522919-58523143(-)$1	224	57	77	22.8726
ddduuuuuuuuuuuudddd:	chr10:112772391-112772614(+)$1	223	11	31	21.8259
fffuuuuuuuuuuuufffff	chr12:88589561-88589784(+)$1	223	161	181	22.2848
eeeettttttttttteeeee	chr21:18937999-18938222(+)$1	223	90	110	22.4038
cccuuuuuuuuuuuuccc::	chr12:54424401-54424628(+)$1	227	15	35	20.7130
ggguuuuuuuuuuuuggggg	chr18:48606593-48606813(+)$1	220	90	110	22.8849
ccctttttttttttcccccc	chr4:57259658-57259880(-)$1	222	98	118	21.4043
dddwwwwwwwwwwwwwwddd	chr4:120980145-120980369(-)$1	224	157	177	20.7440

#otherMatches

#Seq PSSM
AUUUAUAUUACUAAUAAUGG	chr14:96852472-96852696(+)$1	224	66	86	22.7310
AAAGGGAAACAGAUACUUGA	chr18:32720787-32721017(+)$1	230	30	50	21.3038
UUUUAAAACAAAACAAAAAA	chr9:133513114-133513342(+)$1	228	29	49	21.8213
UUUUUAUGGUUCCUUUAAAU	chr1:24999040-24999271(+)$1	231	19	39	22.8635
GCCACCAUCAUGUCUAGGCC	chr6:36936051-36936273(-)$1	222	45	65	22.5685
ACCCUUCCUGCCCACGGUGA	chr18:10552274-10552507(+)$1	233	10	30	22.8849
AAUACAUAUUCUUAAUAUUU	chr11:27519339-27519564(-)$1	225	49	69	22.4038
CACACCCUACCCCGAGUGCC	chr1:205686184-205686406(-)$1	222	197	217	21.5593
CCACCCUAUCUUCACUGGCU	chr6:89790459-89790686(+)$1	227	81	101	21.8259
UCUAUACUUCUCCUUUGGAC	chr12:4410310-4410541(+)$1	231	114	134	22.2476
GUUUACUACAAAAUUAACAU	chr7:29035153-29035380(-)$1	227	160	180	22.8726
ggcauucaaaucuaggucag	chr16:19513434-19513658(-)$1	224	147	167	22.2848
UUAAAUCUUCUCUUAUUAGU	chr6:56971621-56971850(+)$1	229	165	185	22.1284
AACAGUUUUAUAUUAUGUUG	chr10:59954636-59954862(-)$1	226	122	142	21.2962
UGUCAAAAAUUAUACUGCAU	chr12:54633582-54633803(-)$1	221	184	204	21.5690
GGGGAAAUUGCAACCAUCCU	chr1:234742736-234742953(-)$1	217	11	31	22.8635
CUUAUUUAGUAGUAUUGAGU	chr12:8927682-8927903(+)$1	221	162	182	21.9071
UUUAAAAGUAGAAAUCAAAA	chr11:68381563-68381786(+)$1	223	36	56	22.8397
ACGUUUUAAGUCUUGUGUUU	chr2:42806199-42806421(+)$1	222	168	188	21.3711
UCUCUCCUGCCUCCCAGCCU	chr19:7978940-7979167(+)$1	227	191	211	21.5267
cauagcacaaccaugauggg	chr11:17395154-17395374(+)$1	220	55	75	22.8726
CCCAGCACACUCUCAGGGAC	chr1:156707022-156707245(-)$1	223	193	213	22.6014
UCAGAAACCAUUGAAUGAAU	chr10:116621654-116621875(+)$1	221	149	169	22.2848
UAUGUUCCCAAAUCUGUGCU	chr18:48701442-48701663(-)$1	221	22	42	22.8849
AUCAGAAACCCACUAUGAUA	chrX:23802427-23802673(+)$1	246	129	149	22.2892
AUGAACUACUAUACAUUAUG	chr15:34376126-34376350(-)$1	224	78	98	22.2772
UUAAUAAUACCAAGACUAAG	chr11:121178397-121178619(+)$1	222	200	220	22.8397
AGGAAGAGUAUAGUGUCCUG	chr11:125526893-125527122(+)$1	229	1	21	22.4038
AGGUAAUUAUACUAUCCUUU	chr10:17757100-17757331(+)$1	231	156	176	22.5270
ACUUACUUUUCUCCCUGUGA	chr5:134193829-134194059(+)$1	230	113	133	19.8636
UCCUUAUCUUAUGUGAAGAU	chr4:109734817-109735041(-)$1	224	181	201	21.4243
GUGUUCAUUAAAAUCACAuu	chr3:44794655-44794887(-)$1	232	97	117	21.8213
UUGCCGAUAGCCAACCAAUG	chr14:61180503-61180730(-)$1	227	169	189	22.8849
ACAUACAGCUGGAAAAUGGA	chr17:1421208-1421428(+)$1	220	29	49	22.2238
aggaguucagaaucagccug	chr1:38268939-38269164(-)$1	225	60	80	22.8635
UAUUUAUUAAAUAUUAUGCU	chr2:109302202-109302426(+)$1	224	31	51	22.8726
GGUUGAAUAUUUGUAAACCA	chr11:82972416-82972640(-)$1	224	30	50	22.4038
AACUAAUAAAUCAAGUGUUC	chr13:30340843-30341069(-)$1	226	4	24	22.5685
ACAGCAUUGUAUAAAGUGUG	chr1:109178143-109178369(+)$1	226	122	142	21.5690
UGAGCUCAGCCUUUACUCAU	chrX:53405476-53405698(-)$1	222	24	44	21.8213
AUUGAAACUUUUAAACAAUA	chr17:5335866-5336088(+)$1	222	123	143	21.8213
AGUGAUACAUGUCCCUGACU	chr1:54291452-54291674(-)$1	222	13	33	20.4982
UGCUUGUGUGGAAAUGCAAA	chr14:37147799-37148021(+)$1	222	74	94	22.7772
CAGUAUUUAGUGUCUCUGAU	chr7:140036984-140037206(-)$1	222	54	74	22.7084
GCAUGUUUUUUAAAAAUGUU	chr7:28863740-28863967(+)$1	227	126	146	22.2772
GGUUUUUUUUAAUGUGAUCC	chr2:10923848-10924067(-)$1	219	3	23	22.4038
CUUUUAAAAUUUUAUGAAGA	chr1:67469658-67469880(-)$1	222	4	24	21.9974
CUACUUUUAAAAUUUGUGGU	chr11:27516204-27516428(-)$1	224	184	204	21.2962
UGUUGUUAUGAUGUGCUUAA	chr6:71570413-71570638(+)$1	225	128	148	19.6951
ACCUGCCAACCUUAUUGGUA	chr9:125609188-125609423(-)$1	235	8	28	22.8635
UUUGUGUCAUUAAUGAAAGA	chr12:54630649-54630882(-)$1	233	56	76	21.8259
ACGCUGUGUAUGUAUGUGUA	chr5:96372686-96372908(+)$1	222	43	63	21.8213
AUGCUAAAUAAAUUAUAUAU	chr7:120428106-120428330(-)$1	224	140	160	19.9124
CCCCUGUUACAAUGAAGGGG	chr5:150647405-150647627(+)$1	222	36	56	22.8397
UCAUACAUACUUUACUUGAA	chr12:72180402-72180628(+)$1	226	108	128	22.5685
UUCCUUUUUAUUUAUAUGUA	chr20:10619360-10619590(-)$1	230	113	133	20.0717
UUAUAAAUCAACUUUUAAAA	chr13:73330172-73330398(+)$1	226	102	122	22.7772
GUGUCAAUUUAAAUUCUACA	chr12:97311315-97311537(+)$1	222	96	116	22.8397
UAACUUUUGUAAAAUGUUAC	chr13:25908917-25909148(+)$1	231	45	65	21.8213
CUGCCCCCCACCCCUCAGUU	chr17:58522919-58523143(-)$1	224	57	77	22.8726
UCCACAAAACUAACAGGAUA	chr10:112772391-112772614(+)$1	223	11	31	21.8259
CAAUUAAAAAUAAUUUUGAG	chr12:88589561-88589784(+)$1	223	161	181	22.2848
UGUUACUAGCCUCAAAAUAC	chr21:18937999-18938222(+)$1	223	90	110	22.4038
UCCAAUUUCAAAAAAGGAAA	chr12:54424401-54424628(+)$1	227	15	35	20.7130
GUACUCUUGAUUACUUACAA	chr18:48606593-48606813(+)$1	220	90	110	22.8849
AGAUUCUUAAUAUUUCUCCA	chr4:57259658-57259880(-)$1	222	98	118	21.4043
UGGUACAUGCUUUCUAUCCA	chr4:120980145-120980369(-)$1	224	157	177	20.7440

#DB
(((............)))))	chr14:96852472-96852696(+)$1	1	66	86	22.7310
.(((...........)))((	chr18:32720787-32721017(+)$1	1	30	50	21.3038
((((...........)))))	chr9:133513114-133513342(+)$1	1	29	49	21.8213
(((.............))))	chr1:24999040-24999271(+)$1	1	19	39	22.8635
(((.............))))	chr6:36936051-36936273(-)$1	1	45	65	22.5685
(((............)))))	chr18:10552274-10552507(+)$1	1	10	30	22.8849
((((...........)))))	chr11:27519339-27519564(-)$1	1	49	69	22.4038
(((............)))))	chr1:205686184-205686406(-)$1	1	197	217	21.5593
(((............)))).	chr6:89790459-89790686(+)$1	1	81	101	21.8259
((((...........)))).	chr12:4410310-4410541(+)$1	1	114	134	22.2476
(((............)))))	chr7:29035153-29035380(-)$1	1	160	180	22.8726
(((............)))))	chr16:19513434-19513658(-)$1	1	147	167	22.2848
((((...........)))))	chr6:56971621-56971850(+)$1	1	165	185	22.1284
((((...........)))).	chr10:59954636-59954862(-)$1	1	122	142	21.2962
(((.............))))	chr12:54633582-54633803(-)$1	1	184	204	21.5690
(((.............))))	chr1:234742736-234742953(-)$1	1	11	31	22.8635
((((...........)))))	chr12:8927682-8927903(+)$1	1	162	182	21.9071
(((.............))))	chr11:68381563-68381786(+)$1	1	36	56	22.8397
(((............)))))	chr2:42806199-42806421(+)$1	1	168	188	21.3711
.((............)).))	chr19:7978940-7979167(+)$1	1	191	211	21.5267
(((............)))))	chr11:17395154-17395374(+)$1	1	55	75	22.8726
(((............)))).	chr1:156707022-156707245(-)$1	1	193	213	22.6014
(((............)))))	chr10:116621654-116621875(+)$1	1	149	169	22.2848
(((............)))))	chr18:48701442-48701663(-)$1	1	22	42	22.8849
.(((...........)))))	chrX:23802427-23802673(+)$1	1	129	149	22.2892
((((...........)))))	chr15:34376126-34376350(-)$1	1	78	98	22.2772
(((.............))))	chr11:121178397-121178619(+)$1	1	200	220	22.8397
((((...........)))))	chr11:125526893-125527122(+)$1	1	1	21	22.4038
(((............)))).	chr10:17757100-17757331(+)$1	1	156	176	22.5270
((..............))).	chr5:134193829-134194059(+)$1	1	113	133	19.8636
(.(...........).))))	chr4:109734817-109735041(-)$1	1	181	201	21.4243
((((...........)))))	chr3:44794655-44794887(-)$1	1	97	117	21.8213
(((............)))))	chr14:61180503-61180730(-)$1	1	169	189	22.8849
.(((...........)))..	chr17:1421208-1421428(+)$1	1	29	49	22.2238
(((.............))))	chr1:38268939-38269164(-)$1	1	60	80	22.8635
(((............)))))	chr2:109302202-109302426(+)$1	1	31	51	22.8726
((((...........)))))	chr11:82972416-82972640(-)$1	1	30	50	22.4038
(((.............))))	chr13:30340843-30341069(-)$1	1	4	24	22.5685
(((.............))))	chr1:109178143-109178369(+)$1	1	122	142	21.5690
((((...........)))))	chrX:53405476-53405698(-)$1	1	24	44	21.8213
((((...........)))))	chr17:5335866-5336088(+)$1	1	123	143	21.8213
(((..............)))	chr1:54291452-54291674(-)$1	1	13	33	20.4982
(((............)))).	chr14:37147799-37148021(+)$1	1	74	94	22.7772
(((............)))).	chr7:140036984-140037206(-)$1	1	54	74	22.7084
((((...........)))))	chr7:28863740-28863967(+)$1	1	126	146	22.2772
((((...........)))))	chr2:10923848-10924067(-)$1	1	3	23	22.4038
((((...........)))).	chr1:67469658-67469880(-)$1	1	4	24	21.9974
((((...........)))).	chr11:27516204-27516428(-)$1	1	184	204	21.2962
.((...........))...)	chr6:71570413-71570638(+)$1	1	128	148	19.6951
(((.............))))	chr9:125609188-125609423(-)$1	1	8	28	22.8635
(((............)))).	chr12:54630649-54630882(-)$1	1	56	76	21.8259
((((...........)))))	chr5:96372686-96372908(+)$1	1	43	63	21.8213
(((..............)))	chr7:120428106-120428330(-)$1	1	140	160	19.9124
(((.............))))	chr5:150647405-150647627(+)$1	1	36	56	22.8397
(((.............))))	chr12:72180402-72180628(+)$1	1	108	128	22.5685
(..............))).)	chr20:10619360-10619590(-)$1	1	113	133	20.0717
(((............)))).	chr13:73330172-73330398(+)$1	1	102	122	22.7772
(((.............))))	chr12:97311315-97311537(+)$1	1	96	116	22.8397
((((...........)))))	chr13:25908917-25909148(+)$1	1	45	65	21.8213
(((............)))))	chr17:58522919-58523143(-)$1	1	57	77	22.8726
(((............)))).	chr10:112772391-112772614(+)$1	1	11	31	21.8259
(((............)))))	chr12:88589561-88589784(+)$1	1	161	181	22.2848
((((...........)))))	chr21:18937999-18938222(+)$1	1	90	110	22.4038
(((............)))..	chr12:54424401-54424628(+)$1	1	15	35	20.7130
(((............)))))	chr18:48606593-48606813(+)$1	1	90	110	22.8849
(((...........)))(((	chr4:57259658-57259880(-)$1	1	98	118	21.4043
(((..............)))	chr4:120980145-120980369(-)$1	1	157	177	20.7440

#PSSM
d : 0.25	e : 0.19	f : 0.16	g : 0.14	h : 0.05	c : 0.05	= : 0.02	[ : 0.02	: : 0.01	i : 0.01	! : 0.01	" : 0.01	
d : 0.25	e : 0.19	f : 0.14	g : 0.14	c : 0.08	h : 0.05	= : 0.02	b : 0.02	i : 0.01	[ : 0.01	w : 0.01	
d : 0.25	e : 0.19	f : 0.14	g : 0.14	c : 0.07	h : 0.05	= : 0.02	b : 0.02	w : 0.02	i : 0.01	a : 0.01	
u : 0.35	v : 0.19	f : 0.08	e : 0.07	w : 0.07	d : 0.05	c : 0.04	t : 0.04	g : 0.02	= : 0.01	i : 0.01	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
t : 0.37	u : 0.35	v : 0.19	w : 0.07	
u : 0.35	t : 0.32	v : 0.19	w : 0.07	a : 0.01	b : 0.01	c : 0.01	
v : 0.19	d : 0.19	f : 0.13	e : 0.13	c : 0.08	g : 0.08	w : 0.05	= : 0.02	b : 0.02	i : 0.01	h : 0.01	] : 0.01	
d : 0.23	e : 0.19	f : 0.14	g : 0.14	c : 0.10	h : 0.04	w : 0.04	= : 0.02	i : 0.01	b : 0.01	3 : 0.01	
d : 0.25	e : 0.19	f : 0.16	g : 0.14	c : 0.10	h : 0.05	= : 0.02	i : 0.01	] : 0.01	3 : 0.01	
d : 0.25	e : 0.19	g : 0.17	f : 0.16	h : 0.05	c : 0.04	= : 0.02	3 : 0.02	i : 0.01	] : 0.01	: : 0.01	
e : 0.19	g : 0.17	f : 0.16	: : 0.10	d : 0.08	h : 0.05	] : 0.04	= : 0.02	c : 0.02	2 : 0.02	3 : 0.02	D : 0.01	i : 0.01	4 : 0.01	

#score	1478.1191336898476
#seq	67
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_CDS_m1_run2.txt

#BEAR
dddddddd!!a!!bbnnnnnbb]a22dddd]d	chr1:6285064-6285340(-)$1	276	70	102	12.0877
ee!!gggggggddddnnnnndddd22gggggg	chr19:50185168-50185421(+)$1	253	140	172	13.5594
ccc]ccc::bb[cccnnnnnccc]bbccc[ee	chr12:132561944-132562174(+)$1	230	87	119	11.4303
hhhhh[a[a!!cccooooooccc22a]a]hhh	chr14:23057836-23058083(-)$1	247	182	214	11.5080
ddd[ccc"""ddddannnnna]dddd22ccc]	chr16:89347357-89347597(-)$1	240	168	200	12.7345
!!eeeee[ccc[ccclllccc]ccceeeee]g	chr17:38560377-38560607(-)$1	230	89	121	10.5072
bb[ggggggg"""ddddllldddd333ggggg	chr10:33209107-33209335(-)$1	228	151	183	10.7788
ddd####eeeeecccooooooccc]eeeee]d	chr15:75693089-75693317(-)$1	228	109	141	10.5222
gggggg####eeeeennnnneeeee4444ggg	chr6:26205034-26205267(+)$1	233	108	140	12.7322
gggggg[ccc!!cccmmmmccc]cccgggggg	chr2:230911188-230911416(-)$1	228	102	134	11.2770
bbb:dddd[ccccccnnnnnccc]ccc]dddd	chr5:149826274-149826501(-)$1	227	153	185	12.6143
f"""bb[ccc[ddddnnnnndddd]ccc]bb5	chrX:114882188-114882413(+)$1	225	73	105	11.9950
cc===========rrrrrrrrr==========	chr16:27503609-27503833(-)$1	224	95	127	9.9887
dddeeeeeccc[cccnnnnnccc]ccc]eeee	chr7:48015827-48016061(-)$1	234	130	162	14.3128
++++++ccc"""cccnnnnnccc333ccc22d	chr19:41257191-41257416(+)$1	225	163	195	11.9554
gggggg[bb[a[ccc[allla]ccca]bbggg	chr9:34635589-34635817(-)$1	228	22	54	11.1321
b[dddd[bb"""cccoooooocccbbdddd]b	chr22:24479128-24479352(+)$1	224	62	94	10.6785
ee[dddd$$$$$cccnnnnnccc4444dddd]	chr19:4431953-4432193(+)$1	240	29	61	14.3113
===========[ccclllccc]==========	chr12:105536887-105537119(+)$1	232	121	153	12.4016
[bb!!==========oooooo==========]	chr7:98527700-98527923(+)$1	223	79	111	12.1299
ggggg!!ccc!!ddddmmmmdddd]ccc333g	chr19:38873895-38874144(+)$1	249	109	141	10.5485
hhhhhhh"""a[cccnnnnnccc]ahhhhhhh	chr19:36545821-36546048(+)$1	227	107	139	13.6097
::ccc[dddd!!cccnnnnncccdddd]ccc:	chr19:59058642-59058875(+)$1	233	119	151	11.4673
bb!!===========nnnnn===========]	chr1:1158524-1158764(-)$1	240	182	214	14.8896
hhhhhhhh####cccnnnnnccc]hhhhhhhh	chr10:93751827-93752079(+)$1	252	34	66	13.0596
[dddd"""ccc[aooooooa]ccc333dddd2	chr16:30775480-30775733(+)$1	253	168	200	10.8911
##dddd[ccc!!cccmmmmccc]cccdddd33	chr5:179048220-179048449(-)$1	229	127	159	10.3064
dd"""ffffff[cccooooooccc4444ffff	chr2:10263525-10263752(+)$1	227	48	80	11.0223
ddd[a!!ccc"""ccclllccc22ccc22a]d	chr21:45103101-45103331(+)$1	230	124	156	11.2870
=====[eeeee!!bbnnnnnbb22eeeee]==	chr10:106074945-106075164(-)$1	219	33	65	11.8378
cc"""a[ccc!!cccnnnnnccc]ccc]accc	chr15:89803908-89804138(+)$1	230	62	94	15.9642
ffeeeee!!ccccccnnnnnccc333ccc22e	chr9:106896725-106896954(+)$1	229	71	103	14.4545
ccc!!==========nnnnn==========22	chr17:58040102-58040339(-)$1	237	124	156	14.6751
fffff####ffffffnnnnnffffff4444ff	chr10:104809370-104809597(+)$1	227	176	208	11.0025
"dddd[ccc!!ddddnnnnndddd]cccdddd	chr1:186375230-186375467(+)$1	237	72	104	13.3132
!bb[a"""ccc[cccnnnnnccc]ccc333a]	chr16:23690412-23690637(+)$1	225	179	211	15.7769
iiiiiibb"""ddddnnnnndddd22bb]iii	chr2:61717767-61718001(-)$1	234	158	190	13.3834
dd!!dddd[ffffffnnnnnffffff]dddd2	chr19:40331236-40331465(-)$1	229	92	124	11.1293
::ccc[dddd!!cccnnnnncccdddd]ccc:	chr19:59058682-59058910(+)$1	228	79	111	11.4673
"""dddd[gggggggnnnnnggggggg]dddd	chr1:33282691-33282918(-)$1	227	183	215	12.4245
ff::ggggggg[cccnnnnnccc]gggggggb	chr22:35799144-35799373(+)$1	229	113	145	12.7059
eee[dddd[bb[cccnnnnnccc]bb]dddd]	chr2:73476138-73476371(+)$1	233	102	134	13.5744
ee####bb"""ddddnnnnndddd22bb22ee	chr19:2271805-2272039(+)$1	234	58	90	12.4612
gggggg####a[cccnnnnnccc]a22ggggg	chr12:53646697-53646923(+)$1	226	143	175	15.8776
ddddeeeee[ddddannnnna]dddd]eeeee	chr22:30403100-30403344(+)$1	244	183	215	11.4941
Fccc[eeeee[ddddnnnnndddd]eeeeecc	chr22:41572393-41572630(+)$1	237	166	198	11.8801
:iiiiiiiii"""cccmmmmccc22iiiiiii	chr1:168260404-168260633(+)$1	229	1	33	10.7815
eeee"""ccc!!cccnnnnnccc22ccc22ee	chr3:131221645-131221874(-)$1	229	4	36	15.1574
gggggg[accc[cccnnnnncccccc]a]ggg	chr19:54967748-54967990(+)$1	242	18	50	15.6725
e"""ffffff[ddddnnnnndddd]ffffff4	chr9:95032074-95032313(-)$1	239	63	95	11.7712
ffff[a[a[ccccccnnnnnccc22ccc]aa]	chr1:46810541-46810771(+)$1	230	56	88	14.7375
!!ggggggg####cccmmmmccc4444ggggg	chr7:2411380-2411605(+)$1	225	19	51	11.6100

#otherMatches

#Seq PSSM
GAUUCUUCCGCGAUCGAACAGAAGAAGAAGAA	chr1:6285064-6285340(-)$1	276	70	102	12.0877
GCAAGGUCAUCGGGGUGAGUCUCCAGGGUGGC	chr19:50185168-50185421(+)$1	253	140	172	13.5594
GGUGGUUCAGCAGAAACUCAUUCAGCAGCAGG	chr12:132561944-132562174(+)$1	230	87	119	11.4303
UCUUUUCUCUCGGGCUUCAUCUCUUGUGUGGG	chr14:23057836-23058083(-)$1	247	182	214	11.5080
GAGAAGUUUGCCUGCUUGUCGCCAGGGUACUA	chr16:89347357-89347597(-)$1	240	168	200	12.7345
ACCAGGUCAGAGAAAGGUUUUGUUUACUUGCU	chr17:38560377-38560607(-)$1	230	89	121	10.5072
AUUGGAGAUGAGGUAUGUUGUAUAAAGCAUUU	chr10:33209107-33209335(-)$1	228	151	183	10.7788
CCAAAGGAGCGAGCCACAGAGGGCAUUGCUAU	chr15:75693089-75693317(-)$1	228	109	141	10.5222
CUGAAGAGACAGGGACGCACUCUUUACGGCUU	chr6:26205034-26205267(+)$1	233	108	140	12.7322
UGUGCUGCUGAAGUACCUGUGCGCAGAGUACG	chr2:230911188-230911416(-)$1	228	102	134	11.2770
GGAUGGCUGGGUGGUAGAAAACCUGCUGGGCU	chr5:149826274-149826501(-)$1	227	153	185	12.6143
UCCAGCCAGGCUGUAUAAACUAUGACCUUGUG	chrX:114882188-114882413(+)$1	225	73	105	11.9950
CCUCUAUGUCCUGAACUCAAUGCAGGAUGUGG	chr16:27503609-27503833(-)$1	224	95	127	9.9887
CAUGGGGUAACGGUCAUGCCGAUGGUUAACCC	chr7:48015827-48016061(-)$1	234	130	162	14.3128
CAACAACCUCAAUGAGAAGAUCAAGAAGGAUG	chr19:41257191-41257416(+)$1	225	163	195	11.9554
GGAUGGUGGAGUACGGCCGGGGCGUCAUCCCA	chr9:34635589-34635817(-)$1	228	22	54	11.1321
UCCAGAAGGAACUGGCUGCAUCCACCUCUGAA	chr22:24479128-24479352(+)$1	224	62	94	10.6785
AGAAACUGAAGGCCAAGGAGUGGGACGAGUUC	chr19:4431953-4432193(+)$1	240	29	61	14.3113
AAUUUUAAAUGAGGUAACAUCAUAUUUGAGAU	chr12:105536887-105537119(+)$1	232	121	153	12.4016
UAGCUGUGAUAUUUGAUGUUGCAAGUAUCAUC	chr7:98527700-98527923(+)$1	223	79	111	12.1299
CCCGGCAGCUGGAGAUGAUCGUCUGAGCCCCC	chr19:38873895-38874144(+)$1	249	109	141	10.5485
CCUCUGUCAUGGCGGGAGUUCCGGCGCGGAGG	chr19:36545821-36546048(+)$1	227	107	139	13.6097
UGGUGAACGUACUGUCUAUUGCAACGUACACA	chr19:59058642-59058875(+)$1	233	119	151	11.4673
Cugugugugcgcgcguguguuguguguacaug	chr1:1158524-1158764(-)$1	240	182	214	14.8896
UUUUUUCUUAUUAGGAUCCACCUCAGAAAAAG	chr10:93751827-93752079(+)$1	252	34	66	13.0596
GCCUCAGACCGCCUACAGCGCCGGGUGGAGGA	chr16:30775480-30775733(+)$1	253	168	200	10.8911
UGUUGAACUUGAAUCAGAAGAUGAAGUCAAAU	chr5:179048220-179048449(-)$1	229	127	159	10.3064
CGCUUUGUCAUCUUCCCCAUCGAGUACCAUGA	chr2:10263525-10263752(+)$1	227	48	80	11.0223
CCUUUGAGGACACAGGGCCCCUUCUCCAGGUG	chr21:45103101-45103331(+)$1	230	124	156	11.2870
UGGUGCUCCGGCCGCUCAGUGCCCCUGGAUCG	chr10:106074945-106075164(-)$1	219	33	65	11.8378
CACUUAGGAGACGUAAGAUAUACACUUGUUGU	chr15:89803908-89804138(+)$1	230	62	94	15.9642
CAAGGUUGCCUUGGGAAAUACCUGGAAAGAAA	chr9:106896725-106896954(+)$1	229	71	103	14.4545
GUCAAACUUGUUAUGCAGCAUAUAACAGGUAG	chr17:58040102-58040339(-)$1	237	124	156	14.6751
UUAGAAGAUGUGAUUGAAGAAAUCAUCAAAUC	chr10:104809370-104809597(+)$1	227	176	208	11.0025
CGAUGAGUCAGCUGAAGAAAUCAGGGACCAUU	chr1:186375230-186375467(+)$1	237	72	104	13.3132
CGUAGGAUUCCACGGCUUUUUCGAGGACAACG	chr16:23690412-23690637(+)$1	225	179	211	15.7769
CUUGAUAGAAAAGUACAUGUUACUCCCUAAUC	chr2:61717767-61718001(-)$1	234	158	190	13.3834
GUGGUCGUGGAGGCCGAGGGGGCUUUGGCGGG	chr19:40331236-40331465(-)$1	229	92	124	11.1293
UGGUGAACGUACUGUCUAUUGCAACGUACACA	chr19:59058682-59058910(+)$1	228	79	111	11.4673
GUGAUUUUGAGCCCCAUUACGGGGUUCUAAGU	chr1:33282691-33282918(-)$1	227	183	215	12.4245
GAUCUGGCCAGCUUUGAUGAGGACCUGGCCGA	chr22:35799144-35799373(+)$1	229	113	145	12.7059
CUUUGCUGACAGGGACAUGUUCUGUGCUGGCC	chr2:73476138-73476371(+)$1	233	102	134	13.5744
CAAACGCAUUAACUGGCGAACAGUGCUGAGUG	chr19:2271805-2272039(+)$1	234	58	90	12.4612
AGGUCAAAUUGCCAUCCUCUAUGUCUGUGGCC	chr12:53646697-53646923(+)$1	226	143	175	15.8776
GGAGACCUUUCUGACGUGGAGUUCGGUAAGGU	chr22:30403100-30403344(+)$1	244	183	215	11.4941
GGUGAGCUCCGCAGGGUUGUUCUGAGGGGCCA	chr22:41572393-41572630(+)$1	237	166	198	11.8801
UUCCAGUCCUAAAGAUUAGUGUCACAGGGUUG	chr1:168260404-168260633(+)$1	229	1	33	10.7815
CCCGGAGUUCAUUGUAAAACGCACCGGAAGUG	chr3:131221645-131221874(-)$1	229	4	36	15.1574
GGGGGCUGGAGACGCCUGUCGCGCUCACUGCC	chr19:54967748-54967990(+)$1	242	18	50	15.6725
AAUUUACAAAGCAGUGCCCAGCUGGUUUGUGC	chr9:95032074-95032313(-)$1	239	63	95	11.7712
UGGUGCACUGGUCAAUAACUUUGCUGCCUGGG	chr1:46810541-46810771(+)$1	230	56	88	14.7375
UUUUUUAAACAGGGUGUUGUCACAAAUUUUGA	chr7:2411380-2411605(+)$1	225	19	51	11.6100

#DB
((((((((..(..((.....)).)..)))).)	chr1:6285064-6285340(-)$1	1	70	102	12.0877
((..(((((((((((.....))))..))))))	chr19:50185168-50185421(+)$1	1	140	172	13.5594
))).)))..((.(((.....))).))(((.((	chr12:132561944-132562174(+)$1	1	87	119	11.4303
(((((.(.(..(((......)))..).).)))	chr14:23057836-23058083(-)$1	1	182	214	11.5080
(((.(((...(((((.....).))))..))).	chr16:89347357-89347597(-)$1	1	168	200	12.7345
..(((((.(((.(((...))).)))))))).)	chr17:38560377-38560607(-)$1	1	89	121	10.5072
((.(((((((...((((...))))...)))))	chr10:33209107-33209335(-)$1	1	151	183	10.7788
(((....((((((((......))).))))).)	chr15:75693089-75693317(-)$1	1	109	141	10.5222
((((((....(((((.....)))))....)))	chr6:26205034-26205267(+)$1	1	108	140	12.7322
((((((.(((..(((....))).)))))))))	chr2:230911188-230911416(-)$1	1	102	134	11.2770
))).((((.((((((.....))).))).))))	chr5:149826274-149826501(-)$1	1	153	185	12.6143
(...((.(((.((((.....)))).))).)).	chrX:114882188-114882413(+)$1	1	73	105	11.9950
))(((((((((((.........))))))))))	chr16:27503609-27503833(-)$1	1	95	127	9.9887
)))((((((((.(((.....))).))).))))	chr7:48015827-48016061(-)$1	1	130	162	14.3128
......(((...(((.....)))...)))..)	chr19:41257191-41257416(+)$1	1	163	195	11.9554
((((((.((.(.(((.(...).)))).)))))	chr9:34635589-34635817(-)$1	1	22	54	11.1321
(.((((.((...(((......))))))))).)	chr22:24479128-24479352(+)$1	1	62	94	10.6785
((.((((.....(((.....)))....)))).	chr19:4431953-4432193(+)$1	1	29	61	14.3113
(((((((((((.(((...))).))))))))))	chr12:105536887-105537119(+)$1	1	121	153	12.4016
.((..((((((((((......)))))))))).	chr7:98527700-98527923(+)$1	1	79	111	12.1299
(((((..(((..((((....)))).)))...)	chr19:38873895-38874144(+)$1	1	109	141	10.5485
(((((((...(.(((.....))).))))))))	chr19:36545821-36546048(+)$1	1	107	139	13.6097
..(((.((((..(((.....))))))).))).	chr19:59058642-59058875(+)$1	1	119	151	11.4673
((..(((((((((((.....))))))))))).	chr1:1158524-1158764(-)$1	1	182	214	14.8896
((((((((....(((.....))).))))))))	chr10:93751827-93752079(+)$1	1	34	66	13.0596
.((((...(((.(......).)))...)))).	chr16:30775480-30775733(+)$1	1	168	200	10.8911
..((((.(((..(((....))).)))))))..	chr5:179048220-179048449(-)$1	1	127	159	10.3064
((...((((((.(((......)))....))))	chr2:10263525-10263752(+)$1	1	48	80	11.0223
(((.(..(((...(((...)))..)))..).)	chr21:45103101-45103331(+)$1	1	124	156	11.2870
(((((.(((((..((.....))..))))).))	chr10:106074945-106075164(-)$1	1	33	65	11.8378
((...(.(((..(((.....))).))).))))	chr15:89803908-89804138(+)$1	1	62	94	15.9642
(((((((..((((((.....)))...)))..)	chr9:106896725-106896954(+)$1	1	71	103	14.4545
(((..((((((((((.....))))))))))..	chr17:58040102-58040339(-)$1	1	124	156	14.6751
(((((....((((((.....))))))....))	chr10:104809370-104809597(+)$1	1	176	208	11.0025
.((((.(((..((((.....)))).)))))))	chr1:186375230-186375467(+)$1	1	72	104	13.3132
.((.(...(((.(((.....))).)))...).	chr16:23690412-23690637(+)$1	1	179	211	15.7769
((((((((...((((.....))))..)).)))	chr2:61717767-61718001(-)$1	1	158	190	13.3834
((..((((.((((((.....)))))).)))).	chr19:40331236-40331465(-)$1	1	92	124	11.1293
..(((.((((..(((.....))))))).))).	chr19:59058682-59058910(+)$1	1	79	111	11.4673
...((((.(((((((.....))))))).))))	chr1:33282691-33282918(-)$1	1	183	215	12.4245
))..(((((((.(((.....))).)))))))(	chr22:35799144-35799373(+)$1	1	113	145	12.7059
(((.((((.((.(((.....))).)).)))).	chr2:73476138-73476371(+)$1	1	102	134	13.5744
((....((...((((.....))))..))..))	chr19:2271805-2272039(+)$1	1	58	90	12.4612
((((((....(.(((.....))).)..)))))	chr12:53646697-53646923(+)$1	1	143	175	15.8776
(((((((((.(((((.....).)))).)))))	chr22:30403100-30403344(+)$1	1	183	215	11.4941
)(((.(((((.((((.....)))).)))))))	chr22:41572393-41572630(+)$1	1	166	198	11.8801
.(((((((((...(((....)))..)))))))	chr1:168260404-168260633(+)$1	1	1	33	10.7815
((((...(((..(((.....)))..)))..))	chr3:131221645-131221874(-)$1	1	4	36	15.1574
((((((.((((.(((.....)))))).).)))	chr19:54967748-54967990(+)$1	1	18	50	15.6725
(...((((((.((((.....)))).)))))).	chr9:95032074-95032313(-)$1	1	63	95	11.7712
((((.(.(.((((((.....)))..))).)).	chr1:46810541-46810771(+)$1	1	56	88	14.7375
..(((((((....(((....)))....)))))	chr7:2411380-2411605(+)$1	1	19	51	11.6100

#PSSM
d : 0.15	e : 0.11	g : 0.11	f : 0.09	c : 0.07	b : 0.07	h : 0.05	! : 0.05	: : 0.05	= : 0.03	[ : 0.03	" : 0.03	+ : 0.01	# : 0.01	i : 0.01	F : 0.01	
d : 0.19	g : 0.11	e : 0.09	c : 0.09	b : 0.09	f : 0.07	h : 0.05	" : 0.05	! : 0.03	= : 0.03	: : 0.03	i : 0.03	+ : 0.01	[ : 0.01	# : 0.01	
d : 0.19	g : 0.13	c : 0.09	" : 0.09	e : 0.07	! : 0.05	h : 0.05	b : 0.05	= : 0.05	[ : 0.03	f : 0.03	i : 0.03	+ : 0.01	: : 0.01	# : 0.01	
d : 0.15	g : 0.15	! : 0.09	[ : 0.07	e : 0.07	" : 0.07	h : 0.05	= : 0.05	c : 0.05	# : 0.03	: : 0.03	f : 0.03	i : 0.03	] : 0.01	+ : 0.01	
d : 0.19	g : 0.19	c : 0.07	e : 0.07	= : 0.07	h : 0.05	" : 0.05	# : 0.03	! : 0.03	a : 0.03	f : 0.03	i : 0.03	[ : 0.03	b : 0.01	+ : 0.01	
g : 0.17	d : 0.15	[ : 0.09	e : 0.09	= : 0.09	# : 0.05	" : 0.05	c : 0.03	! : 0.03	h : 0.03	f : 0.03	a : 0.03	i : 0.03	b : 0.01	+ : 0.01	
d : 0.15	[ : 0.15	e : 0.11	= : 0.09	g : 0.07	c : 0.07	# : 0.07	" : 0.05	! : 0.03	h : 0.03	f : 0.03	b : 0.03	a : 0.01	i : 0.01	
c : 0.17	d : 0.11	e : 0.09	= : 0.09	g : 0.07	" : 0.07	b : 0.07	[ : 0.05	# : 0.05	f : 0.03	a : 0.03	: : 0.01	$ : 0.01	h : 0.01	! : 0.01	i : 0.01	
c : 0.26	g : 0.09	= : 0.09	" : 0.07	e : 0.07	# : 0.07	[ : 0.07	! : 0.03	b : 0.03	d : 0.03	f : 0.03	: : 0.01	a : 0.01	$ : 0.01	i : 0.01	
c : 0.28	" : 0.11	= : 0.09	g : 0.07	# : 0.07	f : 0.07	! : 0.05	e : 0.05	b : 0.03	[ : 0.03	d : 0.03	$ : 0.01	i : 0.01	
! : 0.17	c : 0.15	" : 0.13	= : 0.09	a : 0.07	g : 0.05	e : 0.05	[ : 0.05	f : 0.05	b : 0.03	d : 0.03	# : 0.03	$ : 0.01	
[ : 0.24	! : 0.17	d : 0.17	" : 0.09	c : 0.07	= : 0.07	e : 0.03	# : 0.03	f : 0.03	$ : 0.01	g : 0.01	
c : 0.51	d : 0.19	= : 0.07	" : 0.05	! : 0.03	f : 0.03	e : 0.01	a : 0.01	g : 0.01	# : 0.01	
c : 0.57	d : 0.21	= : 0.05	b : 0.03	f : 0.03	e : 0.01	r : 0.01	o : 0.01	g : 0.01	
c : 0.55	d : 0.17	= : 0.05	b : 0.03	o : 0.03	a : 0.03	f : 0.03	e : 0.01	r : 0.01	g : 0.01	
n : 0.67	o : 0.11	c : 0.05	l : 0.03	d : 0.03	m : 0.03	r : 0.01	[ : 0.01	
n : 0.67	o : 0.11	m : 0.09	l : 0.05	d : 0.01	r : 0.01	a : 0.01	
n : 0.67	o : 0.11	l : 0.09	m : 0.09	r : 0.01	
n : 0.67	o : 0.11	m : 0.09	l : 0.05	c : 0.03	r : 0.01	
n : 0.67	o : 0.09	c : 0.09	m : 0.05	l : 0.03	r : 0.01	a : 0.01	
c : 0.49	d : 0.17	o : 0.07	a : 0.05	b : 0.03	= : 0.03	f : 0.03	e : 0.01	r : 0.01	] : 0.01	g : 0.01	
c : 0.53	d : 0.17	] : 0.09	= : 0.05	b : 0.03	f : 0.03	e : 0.01	r : 0.01	g : 0.01	
c : 0.51	d : 0.21	= : 0.09	] : 0.05	2 : 0.03	f : 0.03	e : 0.01	g : 0.01	
d : 0.24	] : 0.19	c : 0.17	2 : 0.11	= : 0.09	3 : 0.03	4 : 0.03	f : 0.03	a : 0.01	e : 0.01	g : 0.01	
c : 0.19	2 : 0.15	] : 0.11	= : 0.09	d : 0.07	3 : 0.07	b : 0.05	4 : 0.05	e : 0.03	a : 0.03	f : 0.03	g : 0.03	h : 0.01	
c : 0.24	2 : 0.09	= : 0.09	d : 0.07	e : 0.07	3 : 0.07	4 : 0.07	b : 0.05	f : 0.05	a : 0.03	h : 0.03	g : 0.03	i : 0.01	
c : 0.24	] : 0.11	d : 0.09	4 : 0.09	= : 0.09	g : 0.07	e : 0.07	2 : 0.03	3 : 0.03	h : 0.03	b : 0.03	i : 0.01	f : 0.01	
c : 0.15	d : 0.13	g : 0.11	] : 0.11	e : 0.09	= : 0.09	4 : 0.05	b : 0.05	a : 0.03	2 : 0.03	h : 0.03	3 : 0.01	i : 0.01	f : 0.01	
d : 0.19	g : 0.11	c : 0.11	e : 0.11	] : 0.09	= : 0.09	2 : 0.05	4 : 0.03	3 : 0.03	h : 0.03	f : 0.03	b : 0.01	a : 0.01	i : 0.01	
d : 0.19	g : 0.17	e : 0.09	= : 0.09	c : 0.07	2 : 0.07	h : 0.05	3 : 0.03	f : 0.03	a : 0.03	i : 0.03	[ : 0.01	b : 0.01	] : 0.01	4 : 0.01	
g : 0.17	d : 0.13	] : 0.09	e : 0.09	c : 0.09	= : 0.09	h : 0.05	2 : 0.05	f : 0.05	3 : 0.03	a : 0.03	i : 0.03	b : 0.01	
g : 0.19	d : 0.13	] : 0.13	e : 0.11	h : 0.05	= : 0.05	2 : 0.05	b : 0.03	: : 0.03	f : 0.03	c : 0.03	i : 0.03	5 : 0.01	3 : 0.01	4 : 0.01	

#score	648.8933255882755
#seq	52
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_CDS_m3_run1.txt

#BEAR
gggggg7777777ffffff:	chr16:56504358-56504587(+)$1	229	37	57	12.7819
]eeeee7777777dddd]bb	chr5:154310969-154311190(-)$1	221	94	114	13.0908
mdddd88888888bbeeeee	chr11:102272771-102273001(-)$1	230	134	154	14.5211
dddd>>>>>>>>>>>>>>dd	chr2:230723580-230723804(-)$1	224	87	107	12.9775
meeeee7777777hhhhhhh	chr3:56657399-56657622(-)$1	223	101	121	12.5840
d]dddd7777777ccc]fff	chr13:49086770-49087000(-)$1	230	145	165	13.9368
peeeee7777777eeeee::	chr17:27613571-27613802(-)$1	231	202	222	10.8474
b]ccc88888888=======	chr5:171295625-171295855(-)$1	230	118	138	15.5268
gggggg7777777ggggggg	chr11:13736019-13736239(+)$1	220	172	192	14.3583
ffffff7777777dddd333	chr16:4848012-4848242(-)$1	230	151	171	13.2378
b>>>>>>>>>>>>ggggggg	chr1:6341210-6341440(-)$1	230	100	120	13.9843
]eeeee7777777ffffff:	chr6:7395198-7395428(+)$1	230	48	68	12.8603
ddd]bb88888888cccfff	chr2:171906523-171906753(-)$1	230	74	94	14.1569
ppdddd7777777bb]ccc]	chr6:13639721-13639943(-)$1	222	102	122	12.0161
>>>>>>>>>>>>>ggggggg	chr5:80600720-80600950(+)$1	230	204	224	14.2467
ffff999999999ggggggg	chr15:52874269-52874499(-)$1	230	53	73	14.2289
ee]ccc88888888gggggg	chr7:40102541-40102765(+)$1	224	177	197	14.8456
>>>>>>>>>>>>>=======	chr6:160109096-160109319(-)$1	223	99	119	14.1353
dddd999999999ccc333a	chr13:103309320-103309550(+)$1	230	140	160	14.3772
ccc0000000000ccchhhh	chr6:84644237-84644460(+)$1	223	120	140	14.5975
33dddd7777777eeeee]c	chr11:118243863-118244093(+)$1	230	191	211	13.9730
]eeeee7777777bb333cc	chr10:126517897-126518127(+)$1	230	183	203	13.8328
ldddd88888888ddddeee	chr3:142151478-142151697(-)$1	219	157	177	14.6017
dddd999999999ddddiii	chr7:86823967-86824192(+)$1	225	163	183	13.9655
oodddd7777777ccc]ggg	chr9:114694510-114694729(+)$1	219	108	128	13.9452
2dddd88888888ffffff3	chr3:184039301-184039538(+)$1	237	135	155	15.3063
eeee>>>>>>>>>>>>eeee	chr4:106196298-106196528(+)$1	230	34	54	13.5642
iiiiii7777777iiiiiii	chr11:78270522-78270752(-)$1	230	83	103	13.6337
ggggg88888888dddd22c	chr2:219677015-219677245(+)$1	230	35	55	14.7655
dddd0000000000bb22ee	chr2:109086332-109086555(+)$1	223	84	104	14.5244
eeee0000000000eeeee:	chr5:77334847-77335077(-)$1	230	208	228	14.1298
>>>>>>>>>>>>>ggggggg	chr19:50902534-50902764(+)$1	230	67	87	14.2467
eeeee88888888ccc]ddd	chr3:112251462-112251692(-)$1	230	118	138	15.1233
dd22bb7777777eeeee]f	chr6:80744705-80744932(+)$1	227	82	102	12.9409
ffffbb7777777ffffff=	chr16:58587599-58587819(-)$1	220	106	126	13.3631
deeeee666666ffffff33	chr16:69726576-69726806(+)$1	230	46	66	10.8093
dddd999999999iiiiiii	chr2:15737467-15737694(+)$1	227	135	155	14.4275
gggggg666666eeeeeggg	chr2:228388498-228388721(+)$1	223	151	171	10.7183
ffffff666666dddd333c	chr13:28846069-28846296(+)$1	227	99	119	10.4633
eeee0000000000bbhhhh	chr12:94654329-94654559(+)$1	230	93	113	14.5666
22ccc88888888ffffff:	chr11:18317494-18317724(-)$1	230	141	161	14.1913
>>>>>>>>>>>>>hhhhhhh	chr6:135358232-135358462(-)$1	230	150	170	12.8950
eeeee>>>>>>>>>>>>>>b	chr6:82924080-82924310(-)$1	230	79	99	12.3306
66dddd7777777bb]gggg	chr3:49764955-49765185(-)$1	230	85	105	13.4372
ffff0000000000bb]ddd	chr19:39334567-39334791(-)$1	224	95	115	14.1150
>>>>>>>>>>>>>iiiiiii	chr18:67531531-67531755(-)$1	224	201	221	14.0517
c]ccc88888888ggggggg	chr5:36985723-36985953(+)$1	230	116	136	15.8772
mmmmbb7777777eeeee]d	chr22:43032731-43032952(-)$1	221	107	127	11.0954
>>>>>>>>>>>>>ccc]hhh	chr5:36177233-36177463(+)$1	230	100	120	13.6129
dddd999999999dddd:cc	chr7:105135498-105135728(-)$1	230	126	146	12.6669
ffffff7777777bb22ccc	chr11:34485649-34485873(+)$1	224	174	194	12.8839
55dddd7777777ffffffd	chrX:76938618-76938841(-)$1	223	186	206	12.3796
dddd>>>>>>>>>>>ggggg	chr2:20885284-20885515(-)$1	231	37	57	14.4132
cccc>>>>>>>>>>>>ccc2	chr10:97599386-97599611(+)$1	225	150	170	13.4047
22dddd666666ggggggg:	chr9:96326616-96326859(+)$1	243	62	82	10.4960
22ccc88888888dddd22e	chr6:407468-407693(+)$1	225	126	146	14.5355
eeee]a7777777ggggggg	chr19:2041027-2041257(-)$1	230	105	125	14.5555
gggggg7777777ccciiii	chr15:78882822-78883047(+)$1	225	143	163	14.2389
eeee>>>>>>>>>>>>ccc]	chr12:93212979-93213209(-)$1	230	159	179	13.8550
gg]ccc7777777ggggggg	chr16:24560221-24560451(+)$1	230	207	227	14.2799
ffff999999999ffffff:	chr19:24309867-24310097(+)$1	230	208	228	12.6525
4dddd88888888ggggggg	chr6:74304682-74304912(-)$1	230	201	221	16.1978
hhhhhh7777777ccc333d	chr17:17158135-17158359(-)$1	224	162	182	12.5466

#otherMatches

#Seq PSSM
CAGGUUUUAUGAGAAAGCUG	chr16:56504358-56504587(+)$1	229	37	57	12.7819
CCAGUAACAAAAGGUUGCUA	chr5:154310969-154311190(-)$1	221	94	114	13.0908
AGUUGCCUCAGACUCCAGUA	chr11:102272771-102273001(-)$1	230	134	154	14.5211
AGGAAAAGAUCAGAACAAGG	chr2:230723580-230723804(-)$1	224	87	107	12.9775
AGUAUGCAGCAAUUUUCAUU	chr3:56657399-56657622(-)$1	223	101	121	12.5840
GUCAGCAUAAAGCUCAUUGA	chr13:49086770-49087000(-)$1	230	145	165	13.9368
UUUUUAUCUAUCCUUCAAAU	chr17:27613571-27613802(-)$1	231	202	222	10.8474
GAUGACACUAUUUUGAUUUG	chr5:171295625-171295855(-)$1	230	118	138	15.5268
UGAUAUCUACCUCAGGAUGA	chr11:13736019-13736239(+)$1	220	172	192	14.3583
UGCAGCCCAACUCCACCAAG	chr16:4848012-4848242(-)$1	230	151	171	13.2378
UCAUCACCAUCUCGGGACGC	chr1:6341210-6341440(-)$1	230	100	120	13.9843
UUUACAGCUAGUGCCUUAGA	chr6:7395198-7395428(+)$1	230	48	68	12.8603
CUGUGAUCUCAGACGGCAAA	chr2:171906523-171906753(-)$1	230	74	94	14.1569
UAUCCACAAUUUAGCAUCAG	chr6:13639721-13639943(-)$1	222	102	122	12.0161
AGAUUAAAAAGACAAGCGGC	chr5:80600720-80600950(+)$1	230	204	224	14.2467
UCUAGAAAGUCAAUGGAGGU	chr15:52874269-52874499(-)$1	230	53	73	14.2289
AUUGGUGGGAAUUGGGAGAG	chr7:40102541-40102765(+)$1	224	177	197	14.8456
GUCAUAUCAAUCAUAGCAUU	chr6:160109096-160109319(-)$1	223	99	119	14.1353
GCAGCAAAGAUAAGGAAAAA	chr13:103309320-103309550(+)$1	230	140	160	14.3772
ACUCAUGAUACGAGGCUUUU	chr6:84644237-84644460(+)$1	223	120	140	14.5975
AUGCUUCCCUAUCCUGAAGA	chr11:118243863-118244093(+)$1	230	191	211	13.9730
GUCUUGCCCAAAAGCUUUUA	chr10:126517897-126518127(+)$1	230	183	203	13.8328
CGAGCAAAAAUGAACCAGCA	chr3:142151478-142151697(-)$1	219	157	177	14.6017
GACAACACUAACAGGUACUG	chr7:86823967-86824192(+)$1	225	163	183	13.9655
AUUCAACUCAGGGGUGUCCA	chr9:114694510-114694729(+)$1	219	108	128	13.9452
AGUGGAAAUUCAUGAGCCUA	chr3:184039301-184039538(+)$1	237	135	155	15.3063
UCUGUCAACUCUUAUUCUGC	chr4:106196298-106196528(+)$1	230	34	54	13.5642
UCAGGACAGUGGCUUUGUAC	chr11:78270522-78270752(-)$1	230	83	103	13.6337
UUUAUGACUCGACUGGACCA	chr2:219677015-219677245(+)$1	230	35	55	14.7655
AAAAGAAGGAAACAGUUACU	chr2:109086332-109086555(+)$1	223	84	104	14.5244
UAGGUAAAUAUUAAUUCUCA	chr5:77334847-77335077(-)$1	230	208	228	14.1298
UCCACUUCCUUCCCUUCCCC	chr19:50902534-50902764(+)$1	230	67	87	14.2467
AUGACUACACAAGACACUUC	chr3:112251462-112251692(-)$1	230	118	138	15.1233
UUACCGGAACGAAAUAGCUU	chr6:80744705-80744932(+)$1	227	82	102	12.9409
UAUGCAAUUUCCACAUCAUU	chr16:58587599-58587819(-)$1	220	106	126	13.3631
UAUGCAAAUGCAGUGUGAAU	chr16:69726576-69726806(+)$1	230	46	66	10.8093
UUGUAAAUUGAUAUUUCCUU	chr2:15737467-15737694(+)$1	227	135	155	14.4275
UCUUUGAAUCUUUGUAGGGA	chr2:228388498-228388721(+)$1	223	151	171	10.7183
UCAAAAUAAUAAUCCAUUGG	chr13:28846069-28846296(+)$1	227	99	119	10.4633
UGUUUGCCUCCUUCCUAACC	chr12:94654329-94654559(+)$1	230	93	113	14.5666
CCAUCUCCUCUUGUGUCUCU	chr11:18317494-18317724(-)$1	230	141	161	14.1913
UAUCAGAAUUAACAGGAUCU	chr6:135358232-135358462(-)$1	230	150	170	12.8950
UUGUGACUUUUUAACUCAUG	chr6:82924080-82924310(-)$1	230	79	99	12.3306
CUGGGGUUUCAGGUGUACCA	chr3:49764955-49765185(-)$1	230	85	105	13.4372
GGCUGAUAUCUAUUCUGGCU	chr19:39334567-39334791(-)$1	224	95	115	14.1150
UUUAAGCUUAUUCUUGACAU	chr18:67531531-67531755(-)$1	224	201	221	14.0517
AACAUGGCAUUAAAUCUGAU	chr5:36985723-36985953(+)$1	230	116	136	15.8772
AUAUGGUGCUCUUCCCAGUC	chr22:43032731-43032952(-)$1	221	107	127	11.0954
UCAACUACCUCCAACACCUA	chr5:36177233-36177463(+)$1	230	100	120	13.6129
UCCAAAUACUUAAGGUGAGU	chr7:105135498-105135728(-)$1	230	126	146	12.6669
UUCUCCUUGUCAAUGCCUGC	chr11:34485649-34485873(+)$1	224	174	194	12.8839
AGGAUAAGCGUAAUUCUUCU	chrX:76938618-76938841(-)$1	223	186	206	12.3796
UGAGAACCACAUACUGCAGU	chr2:20885284-20885515(-)$1	231	37	57	14.4132
GCAUCAAGUAGAAGAAUGCA	chr10:97599386-97599611(+)$1	225	150	170	13.4047
AGGGCCCCCAGCCACUCUGA	chr9:96326616-96326859(+)$1	243	62	82	10.4960
AUGAAAAAUGUCAAGAUGAG	chr6:407468-407693(+)$1	225	126	146	14.5355
GACUGGGCCCACAUCUCCUG	chr19:2041027-2041257(-)$1	230	105	125	14.5555
UGAUGUCCGUGAGGUCUGUG	chr15:78882822-78883047(+)$1	225	143	163	14.2389
UUACUUCUGUCUCUCUAAGU	chr12:93212979-93213209(-)$1	230	159	179	13.8550
UUUUGAUGACAGCUCAGUUG	chr16:24560221-24560451(+)$1	230	207	227	14.2799
AGAUAAUUCAUACUGGAGAG	chr19:24309867-24310097(+)$1	230	208	228	12.6525
UGUCUUUUUUUAAUUGUACU	chr6:74304682-74304912(-)$1	230	201	221	16.1978
GGCAGAGAAAUACGUUCUGC	chr17:17158135-17158359(-)$1	224	162	182	12.5466

#DB
)))))).......)))))).	chr16:56504358-56504587(+)$1	1	37	57	12.7819
.))))).......)))).))	chr5:154310969-154311190(-)$1	1	94	114	13.0908
.))))........)))))))	chr11:102272771-102273001(-)$1	1	134	154	14.5211
))))..............))	chr2:230723580-230723804(-)$1	1	87	107	12.9775
.))))).......)))))))	chr3:56657399-56657622(-)$1	1	101	121	12.5840
).)))).......))).)))	chr13:49086770-49087000(-)$1	1	145	165	13.9368
.))))).......)))))..	chr17:27613571-27613802(-)$1	1	202	222	10.8474
).)))........)))))))	chr5:171295625-171295855(-)$1	1	118	138	15.5268
)))))).......)))))))	chr11:13736019-13736239(+)$1	1	172	192	14.3583
)))))).......))))...	chr16:4848012-4848242(-)$1	1	151	171	13.2378
)............)))))))	chr1:6341210-6341440(-)$1	1	100	120	13.9843
.))))).......)))))).	chr6:7395198-7395428(+)$1	1	48	68	12.8603
))).))........))))))	chr2:171906523-171906753(-)$1	1	74	94	14.1569
..)))).......)).))).	chr6:13639721-13639943(-)$1	1	102	122	12.0161
.............)))))))	chr5:80600720-80600950(+)$1	1	204	224	14.2467
)))).........)))))))	chr15:52874269-52874499(-)$1	1	53	73	14.2289
)).)))........))))))	chr7:40102541-40102765(+)$1	1	177	197	14.8456
.............)))))))	chr6:160109096-160109319(-)$1	1	99	119	14.1353
)))).........)))...)	chr13:103309320-103309550(+)$1	1	140	160	14.3772
)))..........)))))))	chr6:84644237-84644460(+)$1	1	120	140	14.5975
..)))).......))))).)	chr11:118243863-118244093(+)$1	1	191	211	13.9730
.))))).......))...))	chr10:126517897-126518127(+)$1	1	183	203	13.8328
.))))........)))))))	chr3:142151478-142151697(-)$1	1	157	177	14.6017
)))).........)))))))	chr7:86823967-86824192(+)$1	1	163	183	13.9655
..)))).......))).)))	chr9:114694510-114694729(+)$1	1	108	128	13.9452
.))))........)))))).	chr3:184039301-184039538(+)$1	1	135	155	15.3063
))))............))))	chr4:106196298-106196528(+)$1	1	34	54	13.5642
)))))).......)))))))	chr11:78270522-78270752(-)$1	1	83	103	13.6337
)))))........))))..)	chr2:219677015-219677245(+)$1	1	35	55	14.7655
))))..........))..))	chr2:109086332-109086555(+)$1	1	84	104	14.5244
))))..........))))).	chr5:77334847-77335077(-)$1	1	208	228	14.1298
.............)))))))	chr19:50902534-50902764(+)$1	1	67	87	14.2467
)))))........))).)))	chr3:112251462-112251692(-)$1	1	118	138	15.1233
))..)).......))))).)	chr6:80744705-80744932(+)$1	1	82	102	12.9409
)))))).......))))))(	chr16:58587599-58587819(-)$1	1	106	126	13.3631
))))))......))))))..	chr16:69726576-69726806(+)$1	1	46	66	10.8093
)))).........)))))))	chr2:15737467-15737694(+)$1	1	135	155	14.4275
))))))......))))))))	chr2:228388498-228388721(+)$1	1	151	171	10.7183
))))))......))))...)	chr13:28846069-28846296(+)$1	1	99	119	10.4633
))))..........))))))	chr12:94654329-94654559(+)$1	1	93	113	14.5666
..)))........)))))).	chr11:18317494-18317724(-)$1	1	141	161	14.1913
.............)))))))	chr6:135358232-135358462(-)$1	1	150	170	12.8950
)))))..............)	chr6:82924080-82924310(-)$1	1	79	99	12.3306
..)))).......)).))))	chr3:49764955-49765185(-)$1	1	85	105	13.4372
))))..........)).)))	chr19:39334567-39334791(-)$1	1	95	115	14.1150
.............)))))))	chr18:67531531-67531755(-)$1	1	201	221	14.0517
).)))........)))))))	chr5:36985723-36985953(+)$1	1	116	136	15.8772
....)).......))))).)	chr22:43032731-43032952(-)$1	1	107	127	11.0954
.............))).)))	chr5:36177233-36177463(+)$1	1	100	120	13.6129
)))).........)))).((	chr7:105135498-105135728(-)$1	1	126	146	12.6669
)))))).......))..)))	chr11:34485649-34485873(+)$1	1	174	194	12.8839
..)))).......)))))))	chrX:76938618-76938841(-)$1	1	186	206	12.3796
))))...........)))))	chr2:20885284-20885515(-)$1	1	37	57	14.4132
))))............))).	chr10:97599386-97599611(+)$1	1	150	170	13.4047
..))))......))))))).	chr9:96326616-96326859(+)$1	1	62	82	10.4960
..)))........))))..)	chr6:407468-407693(+)$1	1	126	146	14.5355
)))).).......)))))))	chr19:2041027-2041257(-)$1	1	105	125	14.5555
)))))).......)))))))	chr15:78882822-78883047(+)$1	1	143	163	14.2389
))))............))).	chr12:93212979-93213209(-)$1	1	159	179	13.8550
)).))).......)))))))	chr16:24560221-24560451(+)$1	1	207	227	14.2799
)))).........)))))).	chr19:24309867-24310097(+)$1	1	208	228	12.6525
.))))........)))))))	chr6:74304682-74304912(-)$1	1	201	221	16.1978
)))))).......)))...)	chr17:17158135-17158359(-)$1	1	162	182	12.5466

#PSSM
d : 0.17	e : 0.12	f : 0.11	g : 0.09	> : 0.09	2 : 0.06	] : 0.04	m : 0.04	c : 0.04	p : 0.03	b : 0.03	3 : 0.01	l : 0.01	o : 0.01	i : 0.01	6 : 0.01	5 : 0.01	4 : 0.01	h : 0.01	
e : 0.22	d : 0.20	f : 0.11	> : 0.11	g : 0.09	] : 0.04	2 : 0.04	c : 0.03	p : 0.01	3 : 0.01	o : 0.01	i : 0.01	6 : 0.01	m : 0.01	5 : 0.01	h : 0.01	
d : 0.30	e : 0.20	f : 0.11	> : 0.11	c : 0.09	g : 0.07	] : 0.03	i : 0.01	2 : 0.01	m : 0.01	h : 0.01	
d : 0.28	e : 0.20	c : 0.11	f : 0.11	> : 0.11	g : 0.07	] : 0.01	0 : 0.01	i : 0.01	2 : 0.01	m : 0.01	h : 0.01	
> : 0.19	d : 0.17	e : 0.12	c : 0.09	9 : 0.09	g : 0.07	0 : 0.07	b : 0.06	f : 0.04	i : 0.01	] : 0.01	h : 0.01	
> : 0.20	8 : 0.15	d : 0.11	e : 0.09	9 : 0.09	0 : 0.07	g : 0.06	b : 0.06	f : 0.04	c : 0.03	i : 0.01	a : 0.01	h : 0.01	
7 : 0.36	> : 0.20	8 : 0.19	9 : 0.09	0 : 0.07	6 : 0.06	
7 : 0.36	> : 0.20	8 : 0.19	9 : 0.09	0 : 0.07	6 : 0.06	
7 : 0.36	> : 0.20	8 : 0.19	9 : 0.09	0 : 0.07	6 : 0.06	
7 : 0.36	> : 0.20	8 : 0.19	9 : 0.09	0 : 0.07	6 : 0.06	
7 : 0.36	> : 0.20	8 : 0.19	9 : 0.09	0 : 0.07	6 : 0.06	
7 : 0.36	> : 0.20	8 : 0.19	9 : 0.09	0 : 0.07	6 : 0.06	
7 : 0.36	> : 0.20	8 : 0.19	9 : 0.09	0 : 0.07	f : 0.01	e : 0.01	d : 0.01	g : 0.01	
g : 0.15	f : 0.12	d : 0.12	c : 0.12	> : 0.09	b : 0.07	e : 0.07	0 : 0.06	i : 0.04	h : 0.03	= : 0.03	8 : 0.03	
g : 0.17	c : 0.14	f : 0.12	d : 0.12	b : 0.12	> : 0.09	e : 0.09	i : 0.04	h : 0.03	= : 0.03	
g : 0.19	c : 0.14	f : 0.12	d : 0.12	e : 0.11	> : 0.07	i : 0.04	b : 0.04	h : 0.03	= : 0.03	] : 0.03	3 : 0.01	2 : 0.01	
g : 0.20	f : 0.12	e : 0.12	d : 0.11	] : 0.07	h : 0.06	c : 0.06	3 : 0.06	i : 0.06	> : 0.03	= : 0.03	2 : 0.03	
g : 0.23	f : 0.15	e : 0.12	h : 0.07	3 : 0.07	i : 0.07	c : 0.06	2 : 0.04	> : 0.03	= : 0.03	d : 0.03	] : 0.01	: : 0.01	
g : 0.23	f : 0.14	c : 0.09	e : 0.07	h : 0.07	3 : 0.07	i : 0.07	d : 0.04	] : 0.04	= : 0.03	2 : 0.03	b : 0.01	: : 0.01	> : 0.01	
g : 0.22	: : 0.11	d : 0.09	c : 0.09	e : 0.07	h : 0.07	i : 0.07	f : 0.04	= : 0.04	3 : 0.04	b : 0.03	] : 0.03	a : 0.01	2 : 0.01	

#score	856.9278296137032
#seq	63
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_CDS_m3_run2.txt

#BEAR
eeeeooooooeeee	chr17:1554668-1554946(-)$1	278	127	141	10.8897
[cccooooooccc]	chr22:26829707-26829927(+)$1	220	111	125	10.2445
ddddoooooodddd	chr7:127729589-127729820(+)$1	231	133	147	11.0490
eeeeooooooeeee	chr7:135612347-135612610(-)$1	263	16	30	10.8897
ddddoooooodddd	chr10:5803178-5803406(+)$1	228	75	89	11.0490
eeeeooooooeeee	chrX:41082471-41082695(+)$1	224	132	146	10.8897
ddddoooooodddd	chr11:3797084-3797314(-)$1	230	95	109	11.0490
e[bboooooobb]e	chr12:77203409-77203639(+)$1	230	184	198	9.6249
ddddoooooodddd	chr11:86519479-86519711(+)$1	232	136	150	11.0490
eeeeooooooeeee	chr1:6285064-6285340(-)$1	276	182	196	10.8897
ddddoooooodddd	chr12:6636874-6637109(+)$1	235	57	71	11.0490
ggggoooooogggg	chr22:22221556-22221782(-)$1	226	136	150	9.9249
cc[aooooooa]cc	chr13:96705349-96705597(-)$1	248	225	239	10.3507
bcccooooooccc]	chr19:48954341-48954582(+)$1	241	39	53	9.8582
ddddoooooodddd	chr2:190339334-190339562(+)$1	228	61	75	11.0490
eeeeooooooeeee	chr12:57627260-57627490(+)$1	230	60	74	10.8897
e[bboooooobbee	chr22:41924464-41924695(+)$1	231	198	212	9.7700
ggggoooooogggg	chr1:35658081-35658331(-)$1	250	185	199	9.9249
ff[aooooooa]ff	chr12:57908978-57909210(+)$1	232	208	222	9.7945
ddddoooooodddd	chr17:75209454-75209674(+)$1	220	165	179	11.0490
eeeeooooooeeee	chr2:230911083-230911311(-)$1	228	69	83	10.8897
ddddoooooodddd	chr17:8108565-8108801(-)$1	236	189	203	11.0490
eeeeooooooeeee	chr19:54966543-54966790(+)$1	247	53	67	10.8897
eeeeooooooeeee	chr1:892189-892417(-)$1	228	164	178	10.8897
ddddoooooodddd	chr3:128598442-128598668(+)$1	226	162	176	11.0490
eeeeooooooeeee	chr18:54293505-54293739(-)$1	234	82	96	10.8897
eeeeooooooeeee	chr15:77240705-77240930(+)$1	225	73	87	10.8897
ddddoooooodddd	chr7:44608629-44608855(-)$1	226	122	136	11.0490
!cccooooooccc2	chr1:226549570-226549791(-)$1	221	9	23	10.0333
ddddoooooodddd	chr16:87902720-87902945(-)$1	225	140	154	11.0490
ddddoooooodddd	chr17:4925538-4925763(+)$1	225	75	89	11.0490
!!bboooooobb]d	chr22:35660668-35660897(+)$1	229	157	171	9.5028
ddddoooooodddd	chr12:113596655-113596897(-)$1	242	93	107	11.0490
eeeeooooooeeee	chr17:30687628-30687872(+)$1	244	167	181	10.8897
[cccoooooocccc	chr10:75506535-75506802(+)$1	267	180	194	10.2514
ggggoooooogggg	chr17:43013426-43013673(-)$1	247	92	106	9.9249
!abboooooobb]a	chr22:38699103-38699329(-)$1	226	154	168	9.2057
e[bboooooobb]e	chr3:197009462-197009691(-)$1	229	126	140	9.6249
ddddoooooodddd	chr17:38324071-38324301(+)$1	230	108	122	11.0490
ee[aooooooa]ee	chr9:95050035-95050274(-)$1	239	200	214	10.8976
cc[aooooooa]cc	chr19:40331236-40331465(-)$1	229	206	220	10.3507
ddddoooooodddd	chrX:114882188-114882413(+)$1	225	115	129	11.0490
ddddoooooodddd	chr16:23690412-23690637(+)$1	225	81	95	11.0490
ggggoooooogggg	chr2:113404585-113404824(+)$1	239	34	48	9.9249
ddddoooooodddd	chr17:1585172-1585397(-)$1	225	64	78	11.0490
eeeeooooooeeee	chr1:113460461-113460699(-)$1	238	107	121	10.8897
[a[aooooooa]a]	chr5:65440173-65440403(+)$1	230	212	226	10.1879
eeeeooooooeeee	chr10:88233574-88233799(-)$1	225	163	177	10.8897
a[bboooooobb]a	chr17:45735809-45736040(+)$1	231	29	43	9.1282
ddddoooooodddd	chr19:45888984-45889209(-)$1	225	44	58	11.0490
e!!aooooooa22e	chr1:113460145-113460367(-)$1	222	124	138	10.1076
hhhaooooooa]hh	chr2:37439003-37439243(-)$1	240	55	69	9.6619
[cccooooooccc]	chr12:7075511-7075745(-)$1	234	129	143	10.2445
eeeeooooooeeee	chrM:14396-14648(-)$1	252	89	103	10.8897
ddddoooooodddd	chr5:145849164-145849392(+)$1	228	1	15	11.0490
!cccooooooccc2	chr20:57485316-57485543(+)$1	227	196	210	10.0333
ccbboooooobb]c	chr9:125673984-125674212(-)$1	228	23	37	9.2870
eeeeooooooeeee	chr16:2814252-2814482(+)$1	230	22	36	10.8897
dcccooooooccc]	chr3:185641610-185641849(-)$1	239	166	180	10.3578
[cccoooooocccc	chr1:67891766-67892001(-)$1	235	142	156	10.2514
ddddoooooodddd	chr22:30975737-30975983(-)$1	246	185	199	11.0490
ddddoooooodddd	chrM:15456-15711(+)$1	255	143	157	11.0490
cc[aooooooa]cc	chr1:150939783-150940023(-)$1	240	134	148	10.3507
eeeaooooooa]ee	chr1:156290638-156290864(-)$1	226	162	176	10.9394
ee[aooooooa]ee	chr19:49497052-49497278(+)$1	226	12	26	10.8976
ecccooooooccce	chrX:70756000-70756241(+)$1	241	143	157	10.5836
eeeeooooooeeee	chr5:133292426-133292667(-)$1	241	214	228	10.8897
dd[aooooooa]dd	chr10:106074945-106075164(-)$1	219	92	106	10.8828

#otherMatches

#Seq PSSM
CUCAGCCCAAUGAG	chr17:1554668-1554946(-)$1	278	127	141	10.8897
AGGGAGCAGCCCCG	chr22:26829707-26829927(+)$1	220	111	125	10.2445
GGAGAAACAGUUCC	chr7:127729589-127729820(+)$1	231	133	147	11.0490
UGGUAUGGAAACCA	chr7:135612347-135612610(-)$1	263	16	30	10.8897
GUGGAUUCAACUGC	chr10:5803178-5803406(+)$1	228	75	89	11.0490
CAGCUGAUCCGCUG	chrX:41082471-41082695(+)$1	224	132	146	10.8897
UUUGGAACCACAAA	chr11:3797084-3797314(-)$1	230	95	109	11.0490
UCGGACAUACCUCA	chr12:77203409-77203639(+)$1	230	184	198	9.6249
GCCCAGCCAGGGGC	chr11:86519479-86519711(+)$1	232	136	150	11.0490
GGUCAAGGUGGACC	chr1:6285064-6285340(-)$1	276	182	196	10.8897
AUUCCCUUUAGAAU	chr12:6636874-6637109(+)$1	235	57	71	11.0490
UCGUACAUCGGCGA	chr22:22221556-22221782(-)$1	226	136	150	9.9249
GGCGCGCUGCCACC	chr13:96705349-96705597(-)$1	248	225	239	10.3507
GCCCAUGAUGGGGA	chr19:48954341-48954582(+)$1	241	39	53	9.8582
GGAGGAUAAGCUUU	chr2:190339334-190339562(+)$1	228	61	75	11.0490
ACAGCUGCUACUGU	chr12:57627260-57627490(+)$1	230	60	74	10.8897
CGUGUGCCAUCAGU	chr22:41924464-41924695(+)$1	231	198	212	9.7700
CCGCCAAGCAGCGG	chr1:35658081-35658331(-)$1	250	185	199	9.9249
GAAGACCUAACAUC	chr12:57908978-57909210(+)$1	232	208	222	9.7945
GGUUGGAGGGAGCC	chr17:75209454-75209674(+)$1	220	165	179	11.0490
AAACCUGUGUGUUU	chr2:230911083-230911311(-)$1	228	69	83	10.8897
GCUUUGCUAUGAGC	chr17:8108565-8108801(-)$1	236	189	203	11.0490
CAUGAAAGAGUAUG	chr19:54966543-54966790(+)$1	247	53	67	10.8897
GGCAGCUGGGUGCC	chr1:892189-892417(-)$1	228	164	178	10.8897
CCGCGAACCGGCGG	chr3:128598442-128598668(+)$1	226	162	176	11.0490
UUCAGUUCUAUGAG	chr18:54293505-54293739(-)$1	234	82	96	10.8897
UGUUGAGAAAGACA	chr15:77240705-77240930(+)$1	225	73	87	10.8897
GCAGGGUGAGCUGC	chr7:44608629-44608855(-)$1	226	122	136	11.0490
UUGGGCAAAACUAC	chr1:226549570-226549791(-)$1	221	9	23	10.0333
UGCUCAAGGAGGCA	chr16:87902720-87902945(-)$1	225	140	154	11.0490
CCUGAAGAUGCAGG	chr17:4925538-4925763(+)$1	225	75	89	11.0490
AGGAAGAAAGUCAG	chr22:35660668-35660897(+)$1	229	157	171	9.5028
CUGCAGCGUGGUGG	chr12:113596655-113596897(-)$1	242	93	107	11.0490
GAUUGCUUAAAAUC	chr17:30687628-30687872(+)$1	244	167	181	10.8897
AGCCUACAAUGGCC	chr10:75506535-75506802(+)$1	267	180	194	10.2514
GCCCGAUGGAGGGU	chr17:43013426-43013673(-)$1	247	92	106	9.9249
AGAGCAAGUUCUAC	chr22:38699103-38699329(-)$1	226	154	168	9.2057
UAGCCCUAGUGUAG	chr3:197009462-197009691(-)$1	229	126	140	9.6249
GGAAUGAACCUUCC	chr17:38324071-38324301(+)$1	230	108	122	11.0490
AGGUAUGUUGGGUU	chr9:95050035-95050274(-)$1	239	200	214	10.8976
gUGGUAAGAUUGGC	chr19:40331236-40331465(-)$1	229	206	220	10.3507
AUCUAACAGAAGAU	chrX:114882188-114882413(+)$1	225	115	129	11.0490
GGCAAGAUUGUGCC	chr16:23690412-23690637(+)$1	225	81	95	11.0490
UGGGCUCUGUCUUA	chr2:113404585-113404824(+)$1	239	34	48	9.9249
GGUCAAUGUGGAUU	chr17:1585172-1585397(-)$1	225	64	78	11.0490
GCCAACGGACUGGC	chr1:113460461-113460699(-)$1	238	107	121	10.8897
GGGGGAGGGGCGCG	chr5:65440173-65440403(+)$1	230	212	226	10.1879
CAGUAAGUGAACUG	chr10:88233574-88233799(-)$1	225	163	177	10.8897
acugUAUAUUCAUU	chr17:45735809-45736040(+)$1	231	29	43	9.1282
CGCCAUCUGCGGCG	chr19:45888984-45889209(-)$1	225	44	58	11.0490
GCUUUUUGCUAUAC	chr1:113460145-113460367(-)$1	222	124	138	10.1076
UUCCAGAAACGUGA	chr2:37439003-37439243(-)$1	240	55	69	9.6619
GCUGAACCUACAGG	chr12:7075511-7075745(-)$1	234	129	143	10.2445
GGUGUGUUAUUAUU	chrM:14396-14648(-)$1	252	89	103	10.8897
GCAGCUUCACCUGC	chr5:145849164-145849392(+)$1	228	1	15	11.0490
GUAAAUUUACUUAA	chr20:57485316-57485543(+)$1	227	196	210	10.0333
UCCACUUUUAUGAG	chr9:125673984-125674212(-)$1	228	23	37	9.2870
CAGGCCAAAUCCUG	chr16:2814252-2814482(+)$1	230	22	36	10.8897
UGGUCCCAUUGCCG	chr3:185641610-185641849(-)$1	239	166	180	10.3578
ACUUGAAGAAAAGG	chr1:67891766-67892001(-)$1	235	142	156	10.2514
GGAGAUUACGUUCC	chr22:30975737-30975983(-)$1	246	185	199	11.0490
CCUAACAAACUAGG	chrM:15456-15711(+)$1	255	143	157	11.0490
UGCCUCUGAUGUCA	chr1:150939783-150940023(-)$1	240	134	148	10.3507
UGUCAAGAUGGUAC	chr1:156290638-156290864(-)$1	226	162	176	10.9394
GAACCAUCGAGAUC	chr19:49497052-49497278(+)$1	226	12	26	10.8976
CCAGACAAUACUGG	chrX:70756000-70756241(+)$1	241	143	157	10.5836
AGAGGUGAGUCUCU	chr5:133292426-133292667(-)$1	241	214	228	10.8897
CCGCGCCGAUGGGG	chr10:106074945-106075164(-)$1	219	92	106	10.8828

#DB
((((......))))	chr17:1554668-1554946(-)$1	1	127	141	10.8897
.(((......))).	chr22:26829707-26829927(+)$1	1	111	125	10.2445
((((......))))	chr7:127729589-127729820(+)$1	1	133	147	11.0490
((((......))))	chr7:135612347-135612610(-)$1	1	16	30	10.8897
((((......))))	chr10:5803178-5803406(+)$1	1	75	89	11.0490
((((......))))	chrX:41082471-41082695(+)$1	1	132	146	10.8897
((((......))))	chr11:3797084-3797314(-)$1	1	95	109	11.0490
(.((......)).)	chr12:77203409-77203639(+)$1	1	184	198	9.6249
((((......))))	chr11:86519479-86519711(+)$1	1	136	150	11.0490
((((......))))	chr1:6285064-6285340(-)$1	1	182	196	10.8897
((((......))))	chr12:6636874-6637109(+)$1	1	57	71	11.0490
((((......))))	chr22:22221556-22221782(-)$1	1	136	150	9.9249
((.(......).))	chr13:96705349-96705597(-)$1	1	225	239	10.3507
((((......))).	chr19:48954341-48954582(+)$1	1	39	53	9.8582
((((......))))	chr2:190339334-190339562(+)$1	1	61	75	11.0490
((((......))))	chr12:57627260-57627490(+)$1	1	60	74	10.8897
(.((......))))	chr22:41924464-41924695(+)$1	1	198	212	9.7700
((((......))))	chr1:35658081-35658331(-)$1	1	185	199	9.9249
((.(......).))	chr12:57908978-57909210(+)$1	1	208	222	9.7945
((((......))))	chr17:75209454-75209674(+)$1	1	165	179	11.0490
((((......))))	chr2:230911083-230911311(-)$1	1	69	83	10.8897
((((......))))	chr17:8108565-8108801(-)$1	1	189	203	11.0490
((((......))))	chr19:54966543-54966790(+)$1	1	53	67	10.8897
((((......))))	chr1:892189-892417(-)$1	1	164	178	10.8897
((((......))))	chr3:128598442-128598668(+)$1	1	162	176	11.0490
((((......))))	chr18:54293505-54293739(-)$1	1	82	96	10.8897
((((......))))	chr15:77240705-77240930(+)$1	1	73	87	10.8897
((((......))))	chr7:44608629-44608855(-)$1	1	122	136	11.0490
.(((......))).	chr1:226549570-226549791(-)$1	1	9	23	10.0333
((((......))))	chr16:87902720-87902945(-)$1	1	140	154	11.0490
((((......))))	chr17:4925538-4925763(+)$1	1	75	89	11.0490
..((......)).)	chr22:35660668-35660897(+)$1	1	157	171	9.5028
((((......))))	chr12:113596655-113596897(-)$1	1	93	107	11.0490
((((......))))	chr17:30687628-30687872(+)$1	1	167	181	10.8897
.(((......))))	chr10:75506535-75506802(+)$1	1	180	194	10.2514
((((......))))	chr17:43013426-43013673(-)$1	1	92	106	9.9249
.(((......)).)	chr22:38699103-38699329(-)$1	1	154	168	9.2057
(.((......)).)	chr3:197009462-197009691(-)$1	1	126	140	9.6249
((((......))))	chr17:38324071-38324301(+)$1	1	108	122	11.0490
((.(......).))	chr9:95050035-95050274(-)$1	1	200	214	10.8976
((.(......).))	chr19:40331236-40331465(-)$1	1	206	220	10.3507
((((......))))	chrX:114882188-114882413(+)$1	1	115	129	11.0490
((((......))))	chr16:23690412-23690637(+)$1	1	81	95	11.0490
((((......))))	chr2:113404585-113404824(+)$1	1	34	48	9.9249
((((......))))	chr17:1585172-1585397(-)$1	1	64	78	11.0490
((((......))))	chr1:113460461-113460699(-)$1	1	107	121	10.8897
.(.(......).).	chr5:65440173-65440403(+)$1	1	212	226	10.1879
((((......))))	chr10:88233574-88233799(-)$1	1	163	177	10.8897
(.((......)).)	chr17:45735809-45736040(+)$1	1	29	43	9.1282
((((......))))	chr19:45888984-45889209(-)$1	1	44	58	11.0490
(..(......)..)	chr1:113460145-113460367(-)$1	1	124	138	10.1076
((((......).))	chr2:37439003-37439243(-)$1	1	55	69	9.6619
.(((......))).	chr12:7075511-7075745(-)$1	1	129	143	10.2445
((((......))))	chrM:14396-14648(-)$1	1	89	103	10.8897
((((......))))	chr5:145849164-145849392(+)$1	1	1	15	11.0490
.(((......))).	chr20:57485316-57485543(+)$1	1	196	210	10.0333
((((......)).)	chr9:125673984-125674212(-)$1	1	23	37	9.2870
((((......))))	chr16:2814252-2814482(+)$1	1	22	36	10.8897
((((......))).	chr3:185641610-185641849(-)$1	1	166	180	10.3578
.(((......))))	chr1:67891766-67892001(-)$1	1	142	156	10.2514
((((......))))	chr22:30975737-30975983(-)$1	1	185	199	11.0490
((((......))))	chrM:15456-15711(+)$1	1	143	157	11.0490
((.(......).))	chr1:150939783-150940023(-)$1	1	134	148	10.3507
((((......).))	chr1:156290638-156290864(-)$1	1	162	176	10.9394
((.(......).))	chr19:49497052-49497278(+)$1	1	12	26	10.8976
)(((......)))(	chrX:70756000-70756241(+)$1	1	143	157	10.5836
((((......))))	chr5:133292426-133292667(-)$1	1	214	228	10.8897
((.(......).))	chr10:106074945-106075164(-)$1	1	92	106	10.8828

#PSSM
e : 0.35	d : 0.33	[ : 0.07	g : 0.05	c : 0.05	! : 0.05	b : 0.01	f : 0.01	a : 0.01	h : 0.01	
d : 0.32	e : 0.27	c : 0.19	[ : 0.05	g : 0.05	! : 0.02	a : 0.02	f : 0.01	h : 0.01	
d : 0.30	e : 0.25	c : 0.13	[ : 0.11	b : 0.10	g : 0.05	! : 0.01	h : 0.01	
d : 0.30	e : 0.23	a : 0.16	c : 0.13	b : 0.10	g : 0.05	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
d : 0.30	e : 0.23	a : 0.16	c : 0.13	b : 0.10	g : 0.05	
d : 0.30	e : 0.23	] : 0.14	c : 0.13	b : 0.10	g : 0.05	2 : 0.01	
d : 0.32	e : 0.29	c : 0.17	] : 0.08	g : 0.05	f : 0.01	a : 0.01	2 : 0.01	h : 0.01	
e : 0.35	d : 0.33	c : 0.08	] : 0.07	g : 0.05	2 : 0.02	a : 0.02	f : 0.01	h : 0.01	

#score	718.3893158326593
#seq	68
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_UTR_m3_run2.txt

#BEAR
iiiiiiii[acccmmmmccc]a]iiiiiiii	chr11:82692473-82692752(-)$1	279	1	32	10.3618
ffffff"""cccoooooocccffffffffff	chr2:62451625-62451851(+)$1	226	25	56	14.0802
fff####eeeeeooooooeeeee22ffffff	chr19:24312333-24312558(+)$1	225	184	215	13.6335
cccddddeeeeeooooooeeeee4444dddd	chr4:142151248-142151462(+)$1	214	70	101	12.4052
$$$ccc!!ddddoooooodddd]ccc22ggg	chr5:61684456-61684684(-)$1	228	132	163	14.0835
!!eeeee!!ddddnnnnndddd333eeeee2	chr4:113190195-113190415(+)$1	220	107	138	10.7170
[eeeee####ddddllldddd4444eeeee]	chr15:75136592-75136825(-)$1	233	187	218	10.0290
ffff"""eeeeeooooooeeeee22ffffff	chr7:99637897-99638116(+)$1	219	164	195	13.7694
fffiiiiiiiiiooooooiiiiiiiiidddd	chr7:105889024-105889254(-)$1	230	112	143	13.6856
!ccc[bb[ddddoooooodddd]bb]cccff	chr3:179305794-179306025(+)$1	231	133	164	13.5113
ffffff####cccnnnnnccc22ffffff]d	chr3:130737374-130737594(-)$1	220	60	91	10.4859
ccc$$$$$ddddoooooodddd22cccdddd	chr13:27641160-27641377(-)$1	217	168	199	13.4140
!ggggggg!!bboooooobb22ggggggg]d	chr9:135564800-135565032(+)$1	232	125	156	14.0656
[ggggggg[ddddnnnnndddd]ggggggg]	chr19:39875370-39875591(+)$1	221	75	106	11.4215
fffdddd[ddddoooooodddd]dddd]fff	chr10:105787096-105787336(+)$1	240	54	85	13.1051
ffffff"""cccnnnnnccc333ffffff]a	chr8:146034098-146034319(+)$1	221	35	66	11.0318
cc==========oooooo==========:::	chr3:40575995-40576216(+)$1	221	122	153	12.6097
cc[===========mmmm===========]c	chr22:29696145-29696367(+)$1	222	84	115	11.0923
cffffff!!cccooooooccc]ffffff]cc	chr6:97592677-97592890(-)$1	213	2	33	14.0338
ddd[ccc[a[bboooooobb]a]ccc333dd	chr5:137088470-137088693(-)$1	223	124	155	13.4550
iiiiiiieeeeeooooooeeeee4444iiii	chr7:99637435-99637657(+)$1	222	122	153	14.2515
[eeeee!!ddddoooooodddd22eeeeebb	chr12:51214475-51214705(+)$1	230	82	113	13.7618
ffffffbb[bboooooobb]bb333ffffff	chr11:118395300-118395516(+)$1	216	177	208	11.0430
ff[ccc"""ddddmmmmdddd]ccc]fffff	chr10:58117150-58117380(-)$1	230	53	84	10.0244
f[bb!!ffffffooooooffffffbbfffff	chr12:4382996-4383218(+)$1	222	107	138	11.2113
gggggggeeeeeooooooeeeee]ggggggg	chr1:6478216-6478439(+)$1	223	119	150	14.1954
===============lll=============	chr3:178736366-178736595(-)$1	229	149	180	11.9284
dddddd"""cccooooooccc>>>>>>>>>>	chr4:103538026-103538256(+)$1	230	96	127	11.7574
"bb[ddddddddoooooodddd4444ddddb	chr19:47567435-47567665(-)$1	230	56	87	12.6688
ccc[ccceeeeeooooooeeeee]ccc]ccc	chr7:140422915-140423137(-)$1	222	115	146	14.0102
ggggg!!eeeeeooooooeeeee22gggggg	chrX:23720909-23721133(-)$1	224	126	157	14.3792
h!!bb!!a[cccooooooccc]a22bb4444	chr10:104847924-104848145(-)$1	221	55	86	13.3685
hhhhhhhh[cccooooooccc333hhhhhhh	chr1:40888412-40888637(+)$1	225	67	98	12.0680
!!ccc[ccc[bboooooobb]cccccc]eee	chr5:133723980-133724205(+)$1	225	59	90	13.3693
e!!ffffff!!aooooooa]ffffff22eee	chr19:33469482-33469712(-)$1	230	76	107	11.8232
ggg[ccc"""bboooooobb22cccgggggg	chr19:36486929-36487156(+)$1	227	153	184	14.2104
ccc$$$$$ddddoooooodddd]cccdddd3	chr16:67672304-67672527(+)$1	223	113	144	13.3367
###dddd[a[bboooooobb]adddd22bb]	chr1:153779036-153779257(-)$1	221	74	105	11.5616
b[ggggggg[bboooooobbggggggg]bb:	chr19:7087790-7088012(+)$1	222	75	106	12.5626
bb!!ccceeeeeooooooeeeee]ccc22bb	chr1:156692773-156693019(-)$1	246	69	100	12.7323
Effffff!!cccooooooccc22ffffff::	chr16:69730440-69730647(+)$1	207	74	105	11.4851
iiiiii!!eeeeennnnneeeee]iiiiiii	chr18:51907016-51907235(+)$1	219	3	34	11.1117
a[==========oooooo==========]a:	chr4:15071385-15071606(+)$1	221	133	164	14.6260
[bb[ccc[ddddoooooodddd22cccbbcc	chr4:119631661-119631882(+)$1	221	74	105	14.0555
#eeeee!!ddddoooooodddd]eeeee333	chr10:63422655-63422872(-)$1	217	142	173	13.9002
=========[bboooooobb333========	chr17:47788702-47788924(-)$1	222	104	135	15.5223
!!ffffff!!bboooooobb333ffffff55	chr18:48573480-48573707(+)$1	227	77	108	12.4838
hhhhh"""ddddoooooodddd4444hhhhh	chr8:104455082-104455309(+)$1	227	60	91	13.4208
======="""bbmmmmbb]===========4	chr17:65343367-65343590(-)$1	223	140	171	10.0926
ff"""gggggggoooooogggggggffffff	chr12:69236617-69236859(+)$1	242	57	88	13.4683
c[ccc"""ddddoooooodddd22cccccc:	chr14:21899772-21900001(-)$1	229	37	68	14.5028

#otherMatches

#Seq PSSM
CUCUGUGGUGCGUAUUGACGACCCCAUGGAG	chr11:82692473-82692752(-)$1	279	1	32	10.3618
GUAACAUAUGUUAAAUAAAACUGUUAUUUUU	chr2:62451625-62451851(+)$1	226	25	56	14.0802
guacacuuuuaguuauuuuuaaauuuacaau	chr19:24312333-24312558(+)$1	225	184	215	13.6335
GGAGGCAGAAUAUUCAGUUGUUCUUUUUGCC	chr4:142151248-142151462(+)$1	214	70	101	12.4052
AUUGUAUAAAGAUGUUACUCUUCUAUUUACU	chr5:61684456-61684684(-)$1	228	132	163	14.0835
UUGACUUUAAUUGAUAUACAGUAUUAAGUUU	chr4:113190195-113190415(+)$1	220	107	138	10.7170
GUCCUGCCUAGCGUCCAGCGUCUUCUAGGAG	chr15:75136592-75136825(-)$1	233	187	218	10.0290
CAGCAAGCACUCAUUAAGGAGUGAGGCUGAG	chr7:99637897-99638116(+)$1	219	164	195	13.7694
CAUUAAUUAAUCCCUCUUGAUUGAUUAUAUC	chr7:105889024-105889254(-)$1	230	112	143	13.6856
UUUUUUAAAGCUUUAACUGGCUCUAUAAAUU	chr3:179305794-179306025(+)$1	231	133	164	13.5113
UCUGUUAGAAACCCUGAAGGUGAAACAGACC	chr3:130737374-130737594(-)$1	220	60	91	10.4859
GAGUUCCUGGUAAUCACAUACUUGUUCACAU	chr13:27641160-27641377(-)$1	217	168	199	13.4140
CUUAAGUUGAAGCCAAGACUAAAAUUUAAUG	chr9:135564800-135565032(+)$1	232	125	156	14.0656
UGUUAUUUUUAGAUACAUUUUAUGAAUAACU	chr19:39875370-39875591(+)$1	221	75	106	11.4215
uguauGGUUGUAAAUUCAUACACUUAUCACA	chr10:105787096-105787336(+)$1	240	54	85	13.1051
GCCCGGGUCUUCGUGCAGAACCAUUGGGCAC	chr8:146034098-146034319(+)$1	221	35	66	11.0318
auuuuggcuaucuguggugauggccagaUCU	chr3:40575995-40576216(+)$1	221	122	153	12.6097
UAUUUAUAAUGUUGGCCACAACAUUAUGAUU	chr22:29696145-29696367(+)$1	222	84	115	11.0923
CCAAAGGAGAUUGAUAAAGAUACCUUUGAGA	chr6:97592677-97592890(-)$1	213	2	33	14.0338
GACCUUGGUCGUUUUUAUACUAGCAAAAUGU	chr5:137088470-137088693(-)$1	223	124	155	13.4550
AGAAUUUAAUAAAAGGCAUUAUUUGAAAAGU	chr7:99637435-99637657(+)$1	222	122	153	14.2515
AGUGGUACCUUUAUAAGAAAAGUGACUGCCA	chr12:51214475-51214705(+)$1	230	82	113	13.7618
UGGGUCCUGAAUUCACCUUGAGAAAGACCCA	chr11:118395300-118395516(+)$1	216	177	208	11.0430
uucccacuuucuguuuucggauuggagaaga	chr10:58117150-58117380(-)$1	230	53	84	10.0244
GAGGUCAGGGGAACGCUCUCCCCUCCCCUUC	chr12:4382996-4383218(+)$1	222	107	138	11.2113
UCUGCUCUAGGCAGAAAAGCCUAGGAGUGGA	chr1:6478216-6478439(+)$1	223	119	150	14.1954
UAAGAUUCUUUAGAUAAAAUCUAAAGAAUUU	chr3:178736366-178736595(-)$1	229	149	180	11.9284
CUGACCACAGCAUCAUUUUGCAUUCAAAUUA	chr4:103538026-103538256(+)$1	230	96	127	11.7574
AAUAUGUAUAUAAUGAACUGUAUUUUUACAA	chr19:47567435-47567665(-)$1	230	56	87	12.6688
AGGCGGAGUGCGAGCUGCUGCACAUCCUCCU	chr7:140422915-140423137(-)$1	222	115	146	14.0102
cuuauggagcauugccaugugcuagauaggc	chrX:23720909-23721133(-)$1	224	126	157	14.3792
GUAUGUUAGGGUAUUAAAACUGUUUCACCAG	chr10:104847924-104848145(-)$1	221	55	86	13.3685
CCUUCAGUAGGAUCUGGCUCCGUGGCUGGAG	chr1:40888412-40888637(+)$1	225	67	98	12.0680
UAGAUAUCCUUCAGAAUCGAUGGAGUCCAAC	chr5:133723980-133724205(+)$1	225	59	90	13.3693
ACUAAUUUUAAGGAUUGACAAGAGUUUAUUU	chr19:33469482-33469712(-)$1	230	76	107	11.8232
UCUAUCACCCUGGUUGAUCAACUGAAGACCC	chr19:36486929-36487156(+)$1	227	153	184	14.2104
GCAAAUUAAGUUACCACAGACUCUGUAGUGU	chr16:67672304-67672527(+)$1	223	113	144	13.3367
UGCCGAGAUGUUAUAACAAGGACUCGUUCAU	chr1:153779036-153779257(-)$1	221	74	105	11.5616
AUGGACAUACGUACUCAAACUGUGUUUUUCA	chr19:7087790-7088012(+)$1	222	75	106	12.5626
UCCCAUGGAAGGGGAAAGCCUUCACGUCAGA	chr1:156692773-156693019(-)$1	246	69	100	12.7323
UAAUUGUUAUUAUUUUCCUAGGCGCAAUUUC	chr16:69730440-69730647(+)$1	207	74	105	11.4851
GUUAUGUUAUUUCUUGUUGAAAUUUAUAAUU	chr18:51907016-51907235(+)$1	219	3	34	11.1117
CGUUUUUUAUUUUUUUCUAAAUAAAAAGAGA	chr4:15071385-15071606(+)$1	221	133	164	14.6260
CUUCAGCUAAUUACAAAGGAUUUUGCUAAUU	chr4:119631661-119631882(+)$1	221	74	105	14.0555
CGCCGCAAUCUCGGCCGAGAGAAGCGGCCCC	chr10:63422655-63422872(-)$1	217	142	173	13.9002
AUGAAGCCCCUCUUCCCCGGCAUGGGCUUCA	chr17:47788702-47788924(-)$1	222	104	135	15.5223
AAGGAGAAAAAAGAUGAAUUGGAUUCUUUAA	chr18:48573480-48573707(+)$1	227	77	108	12.4838
UUUGUUACUUUUGAUUUGAGAACUCUACAAA	chr8:104455082-104455309(+)$1	227	60	91	13.4208
UGAGCAUAUCUGUGACCACAUGUUUACUUUA	chr17:65343367-65343590(-)$1	223	140	171	10.0926
CUUUUAAUUGUUCUGACAGAUAGUUGGGGAU	chr12:69236617-69236859(+)$1	242	57	88	13.4683
GACAAUCUGACAUGCACUUGUUUCUUGCCUC	chr14:21899772-21900001(-)$1	229	37	68	14.5028

#DB
((((((((.((((....))).).))))))))	chr11:82692473-82692752(-)$1	1	1	32	10.3618
((((((...(((......)))))))))))))	chr2:62451625-62451851(+)$1	1	25	56	14.0802
(((....(((((......)))))..))))))	chr19:24312333-24312558(+)$1	1	184	215	13.6335
)))(((((((((......)))))....))))	chr4:142151248-142151462(+)$1	1	70	101	12.4052
...(((..((((......)))).)))..)))	chr5:61684456-61684684(-)$1	1	132	163	14.0835
..(((((..((((.....))))...))))).	chr4:113190195-113190415(+)$1	1	107	138	10.7170
.(((((....((((...))))....))))).	chr15:75136592-75136825(-)$1	1	187	218	10.0290
((((...(((((......)))))..))))))	chr7:99637897-99638116(+)$1	1	164	195	13.7694
)))(((((((((......)))))))))((((	chr7:105889024-105889254(-)$1	1	112	143	13.6856
.(((.((.((((......)))).)).)))))	chr3:179305794-179306025(+)$1	1	133	164	13.5113
((((((....(((.....)))..)))))).)	chr3:130737374-130737594(-)$1	1	60	91	10.4859
(((.....((((......))))..)))))))	chr13:27641160-27641377(-)$1	1	168	199	13.4140
.(((((((..((......))..))))))).)	chr9:135564800-135565032(+)$1	1	125	156	14.0656
.(((((((.((((.....)))).))))))).	chr19:39875370-39875591(+)$1	1	75	106	11.4215
(((((((.((((......)))).)))).)))	chr10:105787096-105787336(+)$1	1	54	85	13.1051
((((((...(((.....)))...)))))).)	chr8:146034098-146034319(+)$1	1	35	66	11.0318
))((((((((((......))))))))))...	chr3:40575995-40576216(+)$1	1	122	153	12.6097
((.(((((((((((....))))))))))).)	chr22:29696145-29696367(+)$1	1	84	115	11.0923
(((((((..(((......))).)))))).))	chr6:97592677-97592890(-)$1	1	2	33	14.0338
(((.(((.(.((......)).).)))...))	chr5:137088470-137088693(-)$1	1	124	155	13.4550
((((((((((((......)))))....))))	chr7:99637435-99637657(+)$1	1	122	153	14.2515
.(((((..((((......))))..)))))))	chr12:51214475-51214705(+)$1	1	82	113	13.7618
((((((((.((......)).))...))))))	chr11:118395300-118395516(+)$1	1	177	208	11.0430
((.(((...((((....)))).))).)))))	chr10:58117150-58117380(-)$1	1	53	84	10.0244
(.((..((((((......)))))))))))))	chr12:4382996-4383218(+)$1	1	107	138	11.2113
((((((((((((......))))).)))))))	chr1:6478216-6478439(+)$1	1	119	150	14.1954
(((((((((((((((...)))))))))))))	chr3:178736366-178736595(-)$1	1	149	180	11.9284
((((((...(((......)))..........	chr4:103538026-103538256(+)$1	1	96	127	11.7574
.((.((((((((......))))....)))))	chr19:47567435-47567665(-)$1	1	56	87	12.6688
(((.((((((((......))))).))).)))	chr7:140422915-140423137(-)$1	1	115	146	14.0102
(((((..(((((......)))))..))))))	chrX:23720909-23721133(-)$1	1	126	157	14.3792
(..((..(.(((......))).)..))....	chr10:104847924-104848145(-)$1	1	55	86	13.3685
((((((((.(((......)))...)))))))	chr1:40888412-40888637(+)$1	1	67	98	12.0680
..(((.(((.((......)).)))))).)))	chr5:133723980-133724205(+)$1	1	59	90	13.3693
(..((((((..(......).))))))..)))	chr19:33469482-33469712(-)$1	1	76	107	11.8232
(((.(((...((......))..)))))))))	chr19:36486929-36487156(+)$1	1	153	184	14.2104
(((.....((((......)))).))))))).	chr16:67672304-67672527(+)$1	1	113	144	13.3367
...((((.(.((......)).)))))..)).	chr1:153779036-153779257(-)$1	1	74	105	11.5616
(.(((((((.((......))))))))).)).	chr19:7087790-7088012(+)$1	1	75	106	12.5626
((..((((((((......))))).)))..))	chr1:156692773-156693019(-)$1	1	69	100	12.7323
(((((((..(((......)))..))))))..	chr16:69730440-69730647(+)$1	1	74	105	11.4851
((((((..(((((.....))))).)))))))	chr18:51907016-51907235(+)$1	1	3	34	11.1117
(.((((((((((......)))))))))).).	chr4:15071385-15071606(+)$1	1	133	164	14.6260
.((.(((.((((......))))..)))))))	chr4:119631661-119631882(+)$1	1	74	105	14.0555
.(((((..((((......)))).)))))...	chr10:63422655-63422872(-)$1	1	142	173	13.9002
(((((((((.((......))...))))))))	chr17:47788702-47788924(-)$1	1	104	135	15.5223
..((((((..((......))...))))))..	chr18:48573480-48573707(+)$1	1	77	108	12.4838
(((((...((((......))))....)))))	chr8:104455082-104455309(+)$1	1	60	91	13.4208
(((((((...((....)).))))))))))).	chr17:65343367-65343590(-)$1	1	140	171	10.0926
((...(((((((......)))))))))))))	chr12:69236617-69236859(+)$1	1	57	88	13.4683
(.(((...((((......))))..)))))).	chr14:21899772-21900001(-)$1	1	37	68	14.5028

#PSSM
f : 0.21	c : 0.15	! : 0.09	[ : 0.07	i : 0.05	g : 0.05	= : 0.05	h : 0.05	d : 0.03	# : 0.03	b : 0.03	$ : 0.01	" : 0.01	e : 0.01	E : 0.01	a : 0.01	
f : 0.23	c : 0.13	! : 0.09	g : 0.09	[ : 0.07	i : 0.05	e : 0.05	= : 0.05	b : 0.05	d : 0.03	h : 0.03	$ : 0.01	# : 0.01	
f : 0.21	c : 0.13	g : 0.11	= : 0.09	e : 0.07	i : 0.05	b : 0.05	! : 0.05	[ : 0.03	d : 0.03	h : 0.03	$ : 0.01	# : 0.01	" : 0.01	
f : 0.17	= : 0.11	c : 0.09	g : 0.09	[ : 0.09	i : 0.07	d : 0.07	e : 0.07	$ : 0.03	b : 0.03	h : 0.03	# : 0.01	! : 0.01	" : 0.01	
c : 0.17	f : 0.15	= : 0.11	d : 0.09	g : 0.09	i : 0.07	e : 0.07	" : 0.03	$ : 0.03	h : 0.03	# : 0.01	[ : 0.01	! : 0.01	b : 0.01	
f : 0.15	c : 0.13	= : 0.11	d : 0.09	g : 0.09	i : 0.07	e : 0.07	" : 0.05	! : 0.05	$ : 0.03	# : 0.01	b : 0.01	h : 0.01	[ : 0.01	
" : 0.13	! : 0.11	= : 0.11	c : 0.11	g : 0.09	f : 0.09	d : 0.07	i : 0.05	# : 0.05	b : 0.03	$ : 0.03	e : 0.01	h : 0.01	
" : 0.15	e : 0.15	! : 0.13	[ : 0.09	= : 0.09	g : 0.07	f : 0.05	i : 0.03	# : 0.03	$ : 0.03	b : 0.01	d : 0.01	a : 0.01	h : 0.01	c : 0.01	
d : 0.21	e : 0.17	" : 0.11	[ : 0.09	! : 0.09	= : 0.09	# : 0.03	a : 0.03	f : 0.03	g : 0.03	i : 0.01	c : 0.01	
d : 0.27	e : 0.17	c : 0.13	[ : 0.09	= : 0.07	! : 0.05	# : 0.03	" : 0.03	a : 0.01	i : 0.01	b : 0.01	f : 0.01	g : 0.01	
d : 0.29	b : 0.19	c : 0.17	e : 0.17	= : 0.07	i : 0.01	f : 0.01	! : 0.01	g : 0.01	
d : 0.29	c : 0.17	e : 0.17	b : 0.17	= : 0.07	i : 0.01	o : 0.01	f : 0.01	a : 0.01	g : 0.01	
o : 0.78	d : 0.07	c : 0.03	= : 0.03	n : 0.01	e : 0.01	m : 0.01	
o : 0.78	n : 0.09	m : 0.05	= : 0.03	d : 0.01	
o : 0.78	n : 0.09	m : 0.07	l : 0.01	= : 0.01	
o : 0.78	n : 0.09	m : 0.07	l : 0.03	
o : 0.78	n : 0.09	m : 0.05	l : 0.03	b : 0.01	
o : 0.76	n : 0.07	c : 0.03	d : 0.03	b : 0.03	m : 0.01	l : 0.01	
d : 0.29	c : 0.17	e : 0.17	b : 0.17	= : 0.07	i : 0.01	f : 0.01	a : 0.01	] : 0.01	g : 0.01	
d : 0.29	c : 0.17	e : 0.17	b : 0.15	= : 0.09	] : 0.03	i : 0.01	f : 0.01	g : 0.01	
d : 0.29	e : 0.17	c : 0.13	= : 0.09	] : 0.07	3 : 0.05	2 : 0.03	f : 0.03	g : 0.03	i : 0.01	b : 0.01	
d : 0.25	e : 0.17	= : 0.09	2 : 0.07	3 : 0.07	a : 0.05	f : 0.05	] : 0.05	g : 0.03	4 : 0.01	i : 0.01	b : 0.01	> : 0.01	c : 0.01	
e : 0.17	] : 0.15	3 : 0.11	2 : 0.11	= : 0.09	f : 0.07	4 : 0.05	g : 0.05	c : 0.05	i : 0.01	> : 0.01	a : 0.01	d : 0.01	
f : 0.15	2 : 0.15	c : 0.11	= : 0.11	4 : 0.09	g : 0.07	] : 0.07	3 : 0.05	i : 0.03	d : 0.03	b : 0.01	> : 0.01	e : 0.01	
c : 0.21	f : 0.13	= : 0.11	4 : 0.09	g : 0.09	2 : 0.07	i : 0.05	3 : 0.03	b : 0.03	d : 0.03	e : 0.03	> : 0.01	h : 0.01	
f : 0.21	c : 0.17	g : 0.11	= : 0.11	4 : 0.07	e : 0.07	i : 0.05	] : 0.03	d : 0.03	b : 0.03	> : 0.01	h : 0.01	
f : 0.23	c : 0.13	g : 0.11	= : 0.11	e : 0.07	i : 0.05	2 : 0.05	d : 0.05	4 : 0.03	h : 0.03	3 : 0.01	> : 0.01	b : 0.01	
f : 0.23	= : 0.11	d : 0.09	g : 0.09	2 : 0.07	e : 0.07	] : 0.07	i : 0.05	c : 0.03	h : 0.03	3 : 0.01	> : 0.01	4 : 0.01	b : 0.01	
f : 0.23	g : 0.11	d : 0.09	e : 0.09	= : 0.07	i : 0.05	c : 0.05	b : 0.05	] : 0.03	3 : 0.03	h : 0.03	: : 0.01	> : 0.01	4 : 0.01	2 : 0.01	
f : 0.17	d : 0.11	g : 0.09	e : 0.07	] : 0.07	c : 0.07	b : 0.07	i : 0.05	= : 0.05	: : 0.03	h : 0.03	> : 0.01	4 : 0.01	a : 0.01	3 : 0.01	5 : 0.01	
f : 0.17	d : 0.11	: : 0.09	g : 0.07	c : 0.07	i : 0.05	] : 0.05	b : 0.05	= : 0.03	4 : 0.03	h : 0.03	e : 0.03	3 : 0.03	2 : 0.01	a : 0.01	> : 0.01	5 : 0.01	

#score	649.9272264907238
#seq	51
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_UTR_m3_run2.txt

#BEAR
ccc[cccqqqqqqqqcccccc	chr14:67801391-67801612(+)$1	221	49	70	15.1533
eee!!bbqqqqqqqqbbeeee	chr3:3171689-3171908(+)$1	219	104	125	13.9862
====cccqqqqqqqqccc]==	chr20:35240713-35240939(+)$1	226	150	171	15.7162
[ffffffqqqqqqqqffffff	chr21:17251659-17251887(+)$1	228	120	141	13.8658
dd"""bbqqqqqqqqbb]ddd	chr17:72741861-72742080(+)$1	219	178	199	13.5302
d####bbqqqqqqqqbb333d	chr4:10075902-10076123(-)$1	221	50	71	14.0790
gggggggqqqqqqqqgggggg	chr22:41996782-41997014(-)$1	232	161	182	15.4212
gg!!cccqqqqqqqqccc333	chr4:41958726-41958952(+)$1	226	61	82	16.0748
[a[ddddqqqqqqqqdddd]a	chr1:10697888-10698111(-)$1	223	167	188	15.1781
a[eeeeeqqqqqqqqeeeee]	chr8:57074213-57074444(-)$1	231	146	167	14.6916
ggggcccqqqqqqqqccc::G	chr2:70131419-70131649(+)$1	230	142	163	12.9252
!!eeeeeqqqqqqqqeeeee2	chr3:156424293-156424523(+)$1	230	40	61	14.6736
gggggggqqqqqqqqgggggg	chr1:91381666-91381884(-)$1	218	18	39	15.4212
ff[ddddqqqqqqqqddddff	chr1:167992212-167992434(+)$1	222	178	199	14.7392
fff[cccqqqqqqqqccc22f	chr3:108269953-108270179(-)$1	226	167	188	14.8737
cc[ddddqqqqqqqqdddd]c	chr18:29204001-29204223(-)$1	222	164	185	15.1439
ee[ddddqqqqqqqqdddd]e	chr6:42975684-42975903(+)$1	219	141	162	14.8511
====cccqqqqqqqqccc333	chr18:60794974-60795217(-)$1	243	49	70	15.8620
hffffffqqqqqqqqffffff	chr1:151097746-151097973(+)$1	227	105	126	13.6214
bb!!cccqqqqqqqqccc22b	chr10:61552487-61552707(-)$1	220	152	173	14.6719
b!!ddddqqqqqqqqdddd22	chr10:63853425-63853646(+)$1	221	20	41	14.8724
++eeeeeqqqqqqqqeeeeeb	chr6:119498495-119498727(-)$1	232	65	86	12.9431
gggggggqqqqqqqqgggggg	chr19:16472331-16472554(-)$1	223	28	49	15.4212
"""ddddqqqqqqqqdddd33	chr14:96998613-96998832(+)$1	219	65	86	15.3495
:ccc[bbqqqqqqqqbb]ccc	chr5:14508667-14508885(+)$1	218	19	40	13.1225
%%%%cccqqqqqqqqccceee	chr17:27871692-27871910(+)$1	218	121	142	12.7078
cccddddqqqqqqqqdddd55	chr1:89300084-89300314(+)$1	230	153	174	13.1170
ccc[cccqqqqqqqqccc]cc	chr6:83877019-83877241(-)$1	222	8	29	15.2578
::eeeeeqqqqqqqqeeeeee	chr19:2072929-2073159(-)$1	230	43	64	12.4879
gggggggqqqqqqqqgggggg	chr5:112349724-112349947(+)$1	223	195	216	15.4212
gggggggqqqqqqqqgggggg	chr19:44980579-44980809(-)$1	230	123	144	15.4212
gggggggqqqqqqqqgggggg	chr9:86276090-86276311(-)$1	221	184	205	15.4212
gggggggqqqqqqqqgggggg	chr16:22345141-22345360(+)$1	219	155	176	15.4212
!!a[cccqqqqqqqqccc]a2	chr3:140692724-140692946(+)$1	222	132	153	15.4750
gggggggqqqqqqqqgggggg	chr2:65313891-65314111(-)$1	220	185	206	15.4212
eeeeebbqqqqqqqqbb]eee	chr1:115250186-115250416(-)$1	230	150	171	13.7777
g[eeeeeqqqqqqqqeeeee]	chr20:49369809-49370041(+)$1	232	47	68	14.7803
!!eeeeeqqqqqqqqeeeeei	chr2:198338907-198339133(+)$1	226	55	76	14.8072
$$$ddddqqqqqqqqdddd44	chr12:98929225-98929443(+)$1	218	28	49	14.4266
c"""cccqqqqqqqqccc]cc	chr9:87636439-87636669(+)$1	230	71	92	15.4877
[ffffffqqqqqqqqffffff	chr6:28400472-28400692(-)$1	220	57	78	13.8658
ff[ddddqqqqqqqqdddd]f	chr2:87004553-87004773(+)$1	220	52	73	14.9907
gggggggqqqqqqqqgggggg	chr5:14509291-14509516(+)$1	225	6	27	15.4212
ff!!cccqqqqqqqqccc]ff	chr15:69740464-69740694(+)$1	230	24	45	15.3891
iiiiiiiqqqqqqqqiiiiii	chr3:196311697-196311923(+)$1	226	12	33	15.2998
ff[ddddqqqqqqqqdddd]f	chr11:61569665-61569895(-)$1	230	123	144	14.9907
:ccc[bbqqqqqqqqbb]ccc	chr17:29222163-29222388(+)$1	225	196	217	13.1225
hhhhhbbqqqqqqqqbb]hhh	chr5:118872080-118872298(+)$1	218	112	133	13.0744
bb!!bbaqqqqqqqqa]bb22	chr1:166823441-166823666(+)$1	225	109	130	13.3144
ee[ddddqqqqqqqqdddd]e	chr8:38827471-38827694(+)$1	223	91	112	14.8511
d[eeeeeqqqqqqqqeeeee]	chr3:39133025-39133255(+)$1	230	12	33	14.5280
gggggggqqqqqqqqgggggg	chr1:111727063-111727293(-)$1	230	178	199	15.4212
h!!ddddqqqqqqqqddddhh	chr2:135926770-135926992(+)$1	222	154	175	14.7173
=======qqqqqqqq======	chr7:56078768-56078992(-)$1	224	62	83	15.5380
iiiiiiiqqqqqqqqiiiiii	chr8:27142832-27143054(-)$1	222	122	143	15.2998

#otherMatches

#Seq PSSM
AGAUCUGAAAUACUCCAGUUU	chr14:67801391-67801612(+)$1	221	49	70	15.1533
CAGUAGCAUUACAAAGCCUGU	chr3:3171689-3171908(+)$1	219	104	125	13.9862
GUGCGUGGUCCAUAGCACAGU	chr20:35240713-35240939(+)$1	226	150	171	15.7162
GAAACAAAAUUGAUGUUGUUU	chr21:17251659-17251887(+)$1	228	120	141	13.8658
CCCAUCUCCCAAAUAAGUGGG	chr17:72741861-72742080(+)$1	219	178	199	13.5302
GAAUCACUGGUAAAUGUUGGC	chr4:10075902-10076123(-)$1	221	50	71	14.0790
GGAUGCUGUUUCCUAAGCGUC	chr22:41996782-41997014(-)$1	232	161	182	15.4212
AAUAUACAAAAAAAGGUAAUC	chr4:41958726-41958952(+)$1	226	61	82	16.0748
UAGUUAAUUUAACAUUUGAGU	chr1:10697888-10698111(-)$1	223	167	188	15.1781
UAUUUUUUUAUCCAUAGAAAA	chr8:57074213-57074444(-)$1	231	146	167	14.6916
GAAAAUCUUAUUUAUGAUAUA	chr2:70131419-70131649(+)$1	230	142	163	12.9252
CAUUGGCAUGAAAUGGCCAAC	chr3:156424293-156424523(+)$1	230	40	61	14.6736
GUUUGAGACUGUUCACUCAAA	chr1:91381666-91381884(-)$1	218	18	39	15.4212
CUUAUAGUCAGUAUUUUGUGG	chr1:167992212-167992434(+)$1	222	178	199	14.7392
UGAAUCUCAGUAUAUAGACAU	chr3:108269953-108270179(-)$1	226	167	188	14.8737
UUUUGGAUGAAUUUUUCCACA	chr18:29204001-29204223(-)$1	222	164	185	15.1439
AGGAGCAAAACCUUCUGCUAC	chr6:42975684-42975903(+)$1	219	141	162	14.8511
AUGCCCUUAAAUCAUAGGAAA	chr18:60794974-60795217(-)$1	243	49	70	15.8620
UUAAAUAUACUUCUUUAUUUA	chr1:151097746-151097973(+)$1	227	105	126	13.6214
GCUUCACUAUCCAUUGUGUUG	chr10:61552487-61552707(-)$1	220	152	173	14.6719
GUAUUGCUUUUGUUUGCAGGU	chr10:63853425-63853646(+)$1	221	20	41	14.8724
AUAGCACUUAAUUUUGUGUUU	chr6:119498495-119498727(-)$1	232	65	86	12.9431
UUUGUCUCCUUUUAAAGGCAA	chr19:16472331-16472554(-)$1	223	28	49	15.4212
ACCGAUGAAAUUUUACAUCUA	chr14:96998613-96998832(+)$1	219	65	86	15.3495
ACAGAGCUGCAAGCUGCGCUG	chr5:14508667-14508885(+)$1	218	19	40	13.1225
UCCUGCUUUUCCUAUAGUCAG	chr17:27871692-27871910(+)$1	218	121	142	12.7078
GAUCCAGAUUUUAUAUUGGCA	chr1:89300084-89300314(+)$1	230	153	174	13.1170
UGUAACCAAGGACUAGGUCAC	chr6:83877019-83877241(-)$1	222	8	29	15.2578
CACUUCCACUUUCCAGGAGGC	chr19:2072929-2073159(-)$1	230	43	64	12.4879
GACCCAGCAGCUACUUUGGGU	chr5:112349724-112349947(+)$1	223	195	216	15.4212
UUAAUAGCUAUAAACUUAUUA	chr19:44980579-44980809(-)$1	230	123	144	15.4212
AAUACUCUUAAAGCUGAGUAU	chr9:86276090-86276311(-)$1	221	184	205	15.4212
CAUUCUCAUAAUAAAGAGAGU	chr16:22345141-22345360(+)$1	219	155	176	15.4212
GUUAUCUAUUAAAUCAGAAAU	chr3:140692724-140692946(+)$1	222	132	153	15.4750
UUACCAAUAGUUAUUUUGGUG	chr2:65313891-65314111(-)$1	220	185	206	15.4212
GAAAUGUCAUAAAUUACUGUU	chr1:115250186-115250416(-)$1	230	150	171	13.7777
AAAACCAAUAGAUCCUGGUUA	chr20:49369809-49370041(+)$1	232	47	68	14.7803
UCACCUUACCUGAAAGAGGUU	chr2:198338907-198339133(+)$1	226	55	76	14.8072
AUAUGUGUCCAUCUUUGCAGC	chr12:98929225-98929443(+)$1	218	28	49	14.4266
UACUUCUUCAUCCAUAGACAC	chr9:87636439-87636669(+)$1	230	71	92	15.4877
uucuuccauuacucaggaaga	chr6:28400472-28400692(-)$1	220	57	78	13.8658
AUUUUGCUCAUGACUGCAGUA	chr2:87004553-87004773(+)$1	220	52	73	14.9907
GAUUGUGGAGCAGUACACAGU	chr5:14509291-14509516(+)$1	225	6	27	15.4212
UUAAGGAAGACUAUAUCUAGA	chr15:69740464-69740694(+)$1	230	24	45	15.3891
UGCAGCUAUUUUAAAAGUUGU	chr3:196311697-196311923(+)$1	226	12	33	15.2998
UUUGGGGACAUAAAGCCUCUG	chr11:61569665-61569895(-)$1	230	123	144	14.9907
UGGUGAAUUAUAUUUUUAACC	chr17:29222163-29222388(+)$1	225	196	217	13.1225
UUUCAGAUGAAGAUUUCAUGG	chr5:118872080-118872298(+)$1	218	112	133	13.0744
CACUGACUUAAUUAUGAUCUA	chr1:166823441-166823666(+)$1	225	109	130	13.3144
AGAGGAAGCUACCUAUUCUAU	chr8:38827471-38827694(+)$1	223	91	112	14.8511
UCAUGUUUUCCUAUUAACAUU	chr3:39133025-39133255(+)$1	230	12	33	14.5280
GAUGGGACUUGAAAUUCCCAU	chr1:111727063-111727293(-)$1	230	178	199	15.4212
AGCCUAUAAUUUCACAUAGUU	chr2:135926770-135926992(+)$1	222	154	175	14.7173
AGAGUUUUGUGAUCUGAAUUC	chr7:56078768-56078992(-)$1	224	62	83	15.5380
ggaacuuuuguguaugaguuu	chr8:27142832-27143054(-)$1	222	122	143	15.2998

#DB
(((.(((........))))))	chr14:67801391-67801612(+)$1	1	49	70	15.1533
(((..((........))))))	chr3:3171689-3171908(+)$1	1	104	125	13.9862
(((((((........))).))	chr20:35240713-35240939(+)$1	1	150	171	15.7162
.((((((........))))))	chr21:17251659-17251887(+)$1	1	120	141	13.8658
((...((........)).)))	chr17:72741861-72742080(+)$1	1	178	199	13.5302
(....((........))...)	chr4:10075902-10076123(-)$1	1	50	71	14.0790
(((((((........))))))	chr22:41996782-41997014(-)$1	1	161	182	15.4212
((..(((........)))...	chr4:41958726-41958952(+)$1	1	61	82	16.0748
.(.((((........)))).)	chr1:10697888-10698111(-)$1	1	167	188	15.1781
(.(((((........))))).	chr8:57074213-57074444(-)$1	1	146	167	14.6916
))))(((........)))..)	chr2:70131419-70131649(+)$1	1	142	163	12.9252
..(((((........))))).	chr3:156424293-156424523(+)$1	1	40	61	14.6736
(((((((........))))))	chr1:91381666-91381884(-)$1	1	18	39	15.4212
((.((((........))))))	chr1:167992212-167992434(+)$1	1	178	199	14.7392
(((.(((........)))..)	chr3:108269953-108270179(-)$1	1	167	188	14.8737
((.((((........)))).)	chr18:29204001-29204223(-)$1	1	164	185	15.1439
((.((((........)))).)	chr6:42975684-42975903(+)$1	1	141	162	14.8511
(((((((........)))...	chr18:60794974-60795217(-)$1	1	49	70	15.8620
)((((((........))))))	chr1:151097746-151097973(+)$1	1	105	126	13.6214
((..(((........)))..)	chr10:61552487-61552707(-)$1	1	152	173	14.6719
(..((((........))))..	chr10:63853425-63853646(+)$1	1	20	41	14.8724
..(((((........))))))	chr6:119498495-119498727(-)$1	1	65	86	12.9431
(((((((........))))))	chr19:16472331-16472554(-)$1	1	28	49	15.4212
...((((........))))..	chr14:96998613-96998832(+)$1	1	65	86	15.3495
.(((.((........)).)))	chr5:14508667-14508885(+)$1	1	19	40	13.1225
....(((........))))))	chr17:27871692-27871910(+)$1	1	121	142	12.7078
(((((((........))))..	chr1:89300084-89300314(+)$1	1	153	174	13.1170
(((.(((........))).))	chr6:83877019-83877241(-)$1	1	8	29	15.2578
..(((((........)))))(	chr19:2072929-2073159(-)$1	1	43	64	12.4879
(((((((........))))))	chr5:112349724-112349947(+)$1	1	195	216	15.4212
(((((((........))))))	chr19:44980579-44980809(-)$1	1	123	144	15.4212
(((((((........))))))	chr9:86276090-86276311(-)$1	1	184	205	15.4212
(((((((........))))))	chr16:22345141-22345360(+)$1	1	155	176	15.4212
..(.(((........))).).	chr3:140692724-140692946(+)$1	1	132	153	15.4750
(((((((........))))))	chr2:65313891-65314111(-)$1	1	185	206	15.4212
(((((((........)).)))	chr1:115250186-115250416(-)$1	1	150	171	13.7777
(.(((((........))))).	chr20:49369809-49370041(+)$1	1	47	68	14.7803
..(((((........))))))	chr2:198338907-198339133(+)$1	1	55	76	14.8072
...((((........))))..	chr12:98929225-98929443(+)$1	1	28	49	14.4266
(...(((........))).))	chr9:87636439-87636669(+)$1	1	71	92	15.4877
.((((((........))))))	chr6:28400472-28400692(-)$1	1	57	78	13.8658
((.((((........)))).)	chr2:87004553-87004773(+)$1	1	52	73	14.9907
(((((((........))))))	chr5:14509291-14509516(+)$1	1	6	27	15.4212
((..(((........))).))	chr15:69740464-69740694(+)$1	1	24	45	15.3891
(((((((........))))))	chr3:196311697-196311923(+)$1	1	12	33	15.2998
((.((((........)))).)	chr11:61569665-61569895(-)$1	1	123	144	14.9907
.(((.((........)).)))	chr17:29222163-29222388(+)$1	1	196	217	13.1225
(((((((........)).)))	chr5:118872080-118872298(+)$1	1	112	133	13.0744
((..(((........).))..	chr1:166823441-166823666(+)$1	1	109	130	13.3144
((.((((........)))).)	chr8:38827471-38827694(+)$1	1	91	112	14.8511
(.(((((........))))).	chr3:39133025-39133255(+)$1	1	12	33	14.5280
(((((((........))))))	chr1:111727063-111727293(-)$1	1	178	199	15.4212
(..((((........))))))	chr2:135926770-135926992(+)$1	1	154	175	14.7173
(((((((........))))))	chr7:56078768-56078992(-)$1	1	62	83	15.5380
(((((((........))))))	chr8:27142832-27143054(-)$1	1	122	143	15.2998

#PSSM
g : 0.23	c : 0.09	f : 0.09	e : 0.07	= : 0.05	[ : 0.05	d : 0.05	! : 0.05	h : 0.05	b : 0.05	: : 0.05	i : 0.03	a : 0.01	+ : 0.01	" : 0.01	% : 0.01	$ : 0.01	
g : 0.21	f : 0.14	c : 0.10	! : 0.09	e : 0.07	= : 0.05	[ : 0.05	b : 0.03	" : 0.03	i : 0.03	d : 0.01	# : 0.01	a : 0.01	+ : 0.01	% : 0.01	: : 0.01	$ : 0.01	h : 0.01	
g : 0.20	e : 0.16	[ : 0.12	! : 0.10	c : 0.09	f : 0.07	= : 0.05	" : 0.05	i : 0.03	# : 0.01	% : 0.01	a : 0.01	$ : 0.01	h : 0.01	
d : 0.21	g : 0.20	e : 0.14	! : 0.09	[ : 0.07	= : 0.05	f : 0.05	" : 0.03	c : 0.03	i : 0.03	# : 0.01	% : 0.01	h : 0.01	
c : 0.21	d : 0.21	g : 0.18	e : 0.14	f : 0.05	[ : 0.03	i : 0.03	! : 0.01	" : 0.01	# : 0.01	h : 0.01	b : 0.01	= : 0.01	
c : 0.21	d : 0.21	g : 0.18	b : 0.14	e : 0.12	f : 0.05	i : 0.03	= : 0.01	
c : 0.21	d : 0.21	g : 0.18	b : 0.12	e : 0.12	f : 0.05	i : 0.03	a : 0.01	= : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.21	d : 0.21	g : 0.18	b : 0.12	e : 0.12	f : 0.05	i : 0.03	a : 0.01	= : 0.01	
c : 0.21	d : 0.21	g : 0.18	b : 0.12	e : 0.12	f : 0.05	i : 0.03	] : 0.01	= : 0.01	
c : 0.21	d : 0.21	g : 0.18	e : 0.14	] : 0.09	f : 0.05	i : 0.03	3 : 0.01	b : 0.01	= : 0.01	
d : 0.23	e : 0.18	g : 0.18	] : 0.09	c : 0.05	f : 0.05	3 : 0.05	2 : 0.03	i : 0.03	: : 0.01	h : 0.01	b : 0.01	= : 0.01	
e : 0.18	g : 0.18	] : 0.10	c : 0.09	f : 0.09	3 : 0.07	2 : 0.07	= : 0.03	i : 0.03	h : 0.03	d : 0.01	: : 0.01	5 : 0.01	a : 0.01	4 : 0.01	
g : 0.18	f : 0.14	c : 0.10	e : 0.10	2 : 0.07	3 : 0.05	] : 0.05	i : 0.05	= : 0.03	d : 0.03	b : 0.03	h : 0.03	a : 0.01	G : 0.01	5 : 0.01	4 : 0.01	

#score	805.4461807783748
#seq	55
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_UTR_m1_run2.txt

#BEAR
ffffffuuuuuuuuuuuufff	chrX:46741263-46741503(+)$1	240	92	113	21.5882
!!eeeeettttttttttteee	chr16:21667064-21667286(+)$1	222	132	153	22.5179
[bbddddvvvvvvvvvvvvvd	chr9:79002022-79002246(-)$1	224	77	98	21.7730
:eeeeeuuuuuuuuuuuueee	chr11:10328462-10328692(+)$1	230	116	137	20.8206
ccc[ccctttttttttttccc	chr19:36114742-36114972(+)$1	230	116	137	22.4286
eeeeevvvvvvvvvvvvveee	chr11:33766214-33766444(-)$1	230	109	130	21.2923
=======vvvvvvvvvvvvv=	chr11:108344775-108344995(-)$1	220	150	171	22.7268
gggggggwwwwwwwwwwwwww	chrX:102930675-102930909(-)$1	234	190	211	20.8313
::eeeeettttttttttteee	chr16:58553709-58553932(+)$1	223	52	73	20.4901
gggggggvvvvvvvvvvvvvg	chr3:33431574-33431794(-)$1	220	100	121	22.5923
::eeeeettttttttttteee	chr16:89351694-89351913(-)$1	219	81	102	20.4901
%%eeeeettttttttttteee	chr7:92237463-92237689(-)$1	226	24	45	21.2539
bb[ayyyyyyyyyyyyyyyya	chr11:57585554-57585785(+)$1	231	78	99	18.6239
ggggggguuuuuuuuuuuugg	chr14:81941896-81942117(-)$1	221	73	94	22.4356
=======yyyyyyyyyyyyyy	chr17:56081931-56082158(-)$1	227	9	30	19.8157
"""dddduuuuuuuuuuuudd	chr8:70579999-70580223(-)$1	224	94	115	22.0225
!a[ddddvvvvvvvvvvvvvd	chr17:37074998-37075217(+)$1	219	176	197	22.3117
ffffffuuuuuuuuuuuufff	chr16:88941198-88941419(-)$1	221	110	131	21.5882
!!cccwwwwwwwwwwwwwwcc	chr14:24759752-24759976(-)$1	224	33	54	21.0772
[fffffftttttttttttfff	chr13:52605524-52605747(+)$1	223	28	49	22.3276
cc"""bbuuuuuuuuuuuubb	chr10:70451909-70452132(+)$1	223	124	145	21.4786
[ffffffuuuuuuuuuuuuff	chr18:9402077-9402302(+)$1	225	160	181	22.4479
""bbccctttttttttttccc	chr6:116599323-116599545(-)$1	222	69	90	22.0827
ffffffvvvvvvvvvvvvvff	chr10:85912047-85912272(+)$1	225	176	197	22.3284
ggggggguuuuuuuuuuuugg	chr5:167978204-167978429(-)$1	225	7	28	22.4356
:fffffftttttttttttfff	chr10:59952985-59953211(-)$1	226	89	110	21.3616
iiiddddtttttttttttddd	chr11:105878763-105878993(-)$1	230	104	125	21.6780
ffffffvvvvvvvvvvvvvff	chr1:15987735-15987955(+)$1	220	103	124	22.3284
ccc[ccctttttttttttccc	chr2:242275374-242275604(+)$1	230	188	209	22.4286
ggggggguuuuuuuuuuuugg	chr5:98129623-98129853(+)$1	230	27	48	22.4356
Jfffffftttttttttttfff	chrX:103439283-103439503(+)$1	220	9	30	20.7671
cccccvvvvvvvvvvvvvccc	chrX:23851479-23851705(-)$1	226	173	194	21.5212
((eeeeettttttttttteee	chr2:152976841-152977066(-)$1	225	43	64	21.1897
ddd!!bbuuuuuuuuuuuubb	chr19:11833721-11833951(-)$1	230	27	48	21.1153
eee[bbvvvvvvvvvvvvvbb	chr17:2586146-2586368(+)$1	222	127	148	21.4803
###ddddvvvvvvvvvvvvvd	chr7:76825430-76825653(-)$1	223	103	124	22.2167
cccddddvvvvvvvvvvvvvd	chr4:103716942-103717166(-)$1	224	195	216	21.9450
!!eeeeevvvvvvvvvvvvve	chr2:105881263-105881488(-)$1	225	146	167	22.7796
[fffffftttttttttttfff	chr17:53471265-53471485(-)$1	220	172	193	22.3276
iiiiiiivvvvvvvvvvvvvi	chr5:87502861-87503089(-)$1	228	147	168	22.4440
###ddddvvvvvvvvvvvvvd	chr4:186317927-186318149(+)$1	222	29	50	22.2167
ffffffuuuuuuuuuuuufff	chr21:46323248-46323478(-)$1	230	76	97	21.5882
+fffffftttttttttttfff	chr17:5083132-5083354(-)$1	222	95	116	21.6795
=======vvvvvvvvvvvvv=	chr1:68942018-68942241(-)$1	223	142	163	22.7268
hhhhhhhvvvvvvvvvvvvvh	chr7:7273834-7274064(+)$1	230	185	206	20.6767
g####bbuuuuuuuuuuuubb	chr11:44265713-44265935(+)$1	222	161	182	21.5254
!!eeeeewwwwwwwwwwwwww	chr6:163992621-163992845(+)$1	224	184	205	21.0238
ff[cccuuuuuuuuuuuuccc	chr14:77977056-77977286(-)$1	230	96	117	21.8240
::eeeeettttttttttteee	chr15:62145635-62145865(-)$1	230	134	155	20.4901
ffffccctttttttttttccc	chr17:55757291-55757516(+)$1	225	124	145	22.3642
ggg!!bbuuuuuuuuuuuubb	chr8:130854281-130854511(-)$1	230	30	51	21.8610
g!!ddddtttttttttttddd	chr10:94414601-94414825(+)$1	224	95	116	21.8139
####ccctttttttttttccc	chr17:16245748-16245978(-)$1	230	177	198	22.5290
iiiiiiitttttttttttiii	chrX:48436016-48436238(+)$1	222	3	24	22.0620
::cccwwwwwwwwwwwwwwcc	chr11:63395818-63396048(-)$1	230	80	101	19.0494
gggggggtttttttttttggg	chr11:33378268-33378489(+)$1	221	41	62	22.2347
ggeeeeevvvvvvvvvvvvve	chr1:230415206-230415425(+)$1	219	69	90	22.5258
:eeeeeuuuuuuuuuuuueee	chr3:49060567-49060776(+)$1	209	139	160	20.8206
ggggg[attttttttttta]g	chr13:31719703-31719933(-)$1	230	92	113	22.6203
ffff[bbwwwwwwwwwwwwww	chr16:9211876-9212106(+)$1	230	180	201	20.3418
ffffffwwwwwwwwwwwwwwf	chr4:100802535-100802756(-)$1	221	99	120	21.0372
gggggggtttttttttttggg	chr8:38709163-38709384(+)$1	221	43	64	22.2347
[bb!!bbwwwwwwwwwwwwww	chr3:101043881-101044111(-)$1	230	170	191	20.1940
ffffffuuuuuuuuuuuufff	chr9:125609547-125609782(-)$1	235	68	89	21.5882
eeeeeyyyyyyyyyyyyyyyy	chr2:29404766-29404996(+)$1	230	98	119	19.0717
eeeeewwwwwwwwwwwwwwee	chr22:46239634-46239854(+)$1	220	152	173	20.5580
ee"""bbuuuuuuuuuuuubb	chr19:53116538-53116768(-)$1	230	190	211	21.3115
%ddddvvvvvvvvvvvvvddd	chr10:93806449-93806672(-)$1	223	133	154	20.2469
%bb[ccctttttttttttccc	chr1:155916681-155916902(-)$1	221	141	162	21.6882
eeeeevvvvvvvvvvvvveee	chr2:219758379-219758596(+)$1	217	113	134	21.2923
!!eeeeettttttttttteee	chr4:38702285-38702507(+)$1	222	119	140	22.5179
gffffffvvvvvvvvvvvvvf	chr3:101369540-101369770(-)$1	230	58	79	22.4209
###ddddtttttttttttddd	chr10:11376684-11376914(+)$1	230	57	78	21.7896

#otherMatches

#Seq PSSM
GGAGAUGUUAAUUUAAAAAUU	chrX:46741263-46741503(+)$1	240	92	113	21.5882
UCUUUCUGUUAUUAUUCAAGA	chr16:21667064-21667286(+)$1	222	132	153	22.5179
CAUGCUUCAACUAUUAAAUUA	chr9:79002022-79002246(-)$1	224	77	98	21.7730
CUUUCCAAAACCUAAAGAGGA	chr11:10328462-10328692(+)$1	230	116	137	20.8206
UUAUGCACUAAAUUUCCAUGU	chr19:36114742-36114972(+)$1	230	116	137	22.4286
aaaugacaauaauaaacccau	chr11:33766214-33766444(-)$1	230	109	130	21.2923
UCUCUUCCACUUCCAAUUAUG	chr11:108344775-108344995(-)$1	220	150	171	22.7268
AAUGUAUAUACCUGAAAACCC	chrX:102930675-102930909(-)$1	234	190	211	20.8313
AUGGCCCCAAGGUCUGCAGGG	chr16:58553709-58553932(+)$1	223	52	73	20.4901
ACCUUUCUAAUGAGCUGUAUG	chr3:33431574-33431794(-)$1	220	100	121	22.5923
AAGAAACGAAAUCCAAUAGUU	chr16:89351694-89351913(-)$1	219	81	102	20.4901
AAAGGUAUGUAAACAAAUUAU	chr7:92237463-92237689(-)$1	226	24	45	21.2539
GAUCUCUCUUGUCCUCUUCUG	chr11:57585554-57585785(+)$1	231	78	99	18.6239
GUUUCACAUAAUUACACACGU	chr14:81941896-81942117(-)$1	221	73	94	22.4356
AAUUGCUUUGCUUUUUAAACC	chr17:56081931-56082158(-)$1	227	9	30	19.8157
CAACAGUUACUCCAUCUAUGC	chr8:70579999-70580223(-)$1	224	94	115	22.0225
ACUGAAGCCUUCUUCUGCCAC	chr17:37074998-37075217(+)$1	219	176	197	22.3117
UGGUAAUAAACGAGAUGUUUG	chr16:88941198-88941419(-)$1	221	110	131	21.5882
CUGCUGUGUGUCCGUGGUGAG	chr14:24759752-24759976(-)$1	224	33	54	21.0772
ACAGUCAAGAGGUGGGACUGA	chr13:52605524-52605747(+)$1	223	28	49	22.3276
UCCAACAUCUUCCAAUCAUUG	chr10:70451909-70452132(+)$1	223	124	145	21.4786
UAUAAGCCACAUUUCUAAAGU	chr18:9402077-9402302(+)$1	225	160	181	22.4479
AUGCUGUUCUGGAAUAUCACA	chr6:116599323-116599545(-)$1	222	69	90	22.0827
CAUAUUUAAAUGUUCCGGUAA	chr10:85912047-85912272(+)$1	225	176	197	22.3284
GAUAAUGAAAAUGAGUGUACA	chr5:167978204-167978429(-)$1	225	7	28	22.4356
UGGAAAGAUUGUACUUACUUU	chr10:59952985-59953211(-)$1	226	89	110	21.3616
acugCACUAGAUCACUUUGUG	chr11:105878763-105878993(-)$1	230	104	125	21.6780
UUCACCCAAACUUUUAGCAGG	chr1:15987735-15987955(+)$1	220	103	124	22.3284
CAUAAAUUUAUAGAUAGUGUU	chr2:242275374-242275604(+)$1	230	188	209	22.4286
GAUUGUAUCAAUUUUGUUUUG	chr5:98129623-98129853(+)$1	230	27	48	22.4356
GAGUACUCUCACUUAACAAGU	chrX:103439283-103439503(+)$1	220	9	30	20.7671
AGAACUCCUCAUUCUCAUGUU	chrX:23851479-23851705(-)$1	226	173	194	21.5212
CUGAAAAUAUUAAAACUUUUU	chr2:152976841-152977066(-)$1	225	43	64	21.1897
GGAAAGCCAUCAGUCAUCAGC	chr19:11833721-11833951(-)$1	230	27	48	21.1153
AGUCCUGGGUUUUUGAAAAAG	chr17:2586146-2586368(+)$1	222	127	148	21.4803
UUAAUUCCUUCAGCACUUUAG	chr7:76825430-76825653(-)$1	223	103	124	22.2167
AUCUGUGACUCCUCCACUUCC	chr4:103716942-103717166(-)$1	224	195	216	21.9450
CAGACCUUUUUCCCCUCAUUA	chr2:105881263-105881488(-)$1	225	146	167	22.7796
AUUACUUUCCCAUUCACUAGG	chr17:53471265-53471485(-)$1	220	172	193	22.3276
AGAUCUGUUUGUGUCACCUUU	chr5:87502861-87503089(-)$1	228	147	168	22.4440
CCAGCGGUCUUUAAAUUCUCC	chr4:186317927-186318149(+)$1	222	29	50	22.2167
CCAUCGACCUGUACUAUCUGA	chr21:46323248-46323478(-)$1	230	76	97	21.5882
agugguuuccaacuuuuuaau	chr17:5083132-5083354(-)$1	222	95	116	21.6795
UAUAUGUAUGUGUUUUUAAAA	chr1:68942018-68942241(-)$1	223	142	163	22.7268
UCUCAGCUAUUUAGUAUUUUG	chr7:7273834-7274064(+)$1	230	185	206	20.6767
ACAGAGGGAGAGAACAAGGCC	chr11:44265713-44265935(+)$1	222	161	182	21.5254
GGUGGUUGUCAAGAAACAAAA	chr6:163992621-163992845(+)$1	224	184	205	21.0238
UUUGUAUCCAUCAAGUAUUAC	chr14:77977056-77977286(-)$1	230	96	117	21.8240
CAGUCUAAUAAAAAAAUCUGG	chr15:62145635-62145865(-)$1	230	134	155	20.4901
UCAGGUGGAACUUUAGCACAC	chr17:55757291-55757516(+)$1	225	124	145	22.3642
AAAUUGAUCUUUUUUCUUUUC	chr8:130854281-130854511(-)$1	230	30	51	21.8610
UCUAUAAUUUAUAUUCUUUUG	chr10:94414601-94414825(+)$1	224	95	116	21.8139
GCCAGUCGAUUAAUAGCAGAU	chr17:16245748-16245978(-)$1	230	177	198	22.5290
UUUAAAUUUUUUCUGCCUAUU	chrX:48436016-48436238(+)$1	222	3	24	22.0620
AAGACUAACUGAAAAUGAUGU	chr11:63395818-63396048(-)$1	230	80	101	19.0494
UGCUACACUAGUUUGCCAUGU	chr11:33378268-33378489(+)$1	221	41	62	22.2347
AUGUUUCUUAAACUUUCCGCG	chr1:230415206-230415425(+)$1	219	69	90	22.5258
UAUACACUUCUCCCAUUUUGU	chr3:49060567-49060776(+)$1	209	139	160	20.8206
AGUGCGAGUCAACACCCAUGG	chr13:31719703-31719933(-)$1	230	92	113	22.6203
UAAUUUAUUCUAUCAUAUUAU	chr16:9211876-9212106(+)$1	230	180	201	20.3418
GUACAAUCACUAACUUUCCUU	chr4:100802535-100802756(-)$1	221	99	120	21.0372
UUCUGACUUUAUCCUGUUGUU	chr8:38709163-38709384(+)$1	221	43	64	22.2347
UGUCCUCAUAACUUUAACAAA	chr3:101043881-101044111(-)$1	230	170	191	20.1940
UAAGAUUUUAAAAUUGCUAUU	chr9:125609547-125609782(-)$1	235	68	89	21.5882
GUUAUCUUCUUAAAAACCAUU	chr2:29404766-29404996(+)$1	230	98	119	19.0717
GUGCAUUUAAAGAAUAUAUUG	chr22:46239634-46239854(+)$1	220	152	173	20.5580
UCAUACCUUGCAUAUCAUUGG	chr19:53116538-53116768(-)$1	230	190	211	21.3115
UGCAGCUACUGCUUACAACUG	chr10:93806449-93806672(-)$1	223	133	154	20.2469
UCAGUGGAACCCUUGCCCCCA	chr1:155916681-155916902(-)$1	221	141	162	21.6882
cucucuuugcggcacucuggg	chr2:219758379-219758596(+)$1	217	113	134	21.2923
UAAGACUGAAUGGGUAAAGGU	chr4:38702285-38702507(+)$1	222	119	140	22.5179
ACUGUACUGAAUUUAAAACCG	chr3:101369540-101369770(-)$1	230	58	79	22.4209
UUUCCUCUCCACACCCACGAG	chr10:11376684-11376914(+)$1	230	57	78	21.7896

#DB
((((((............)))	chrX:46741263-46741503(+)$1	1	92	113	21.5882
..(((((...........)))	chr16:21667064-21667286(+)$1	1	132	153	22.5179
.((((((.............)	chr9:79002022-79002246(-)$1	1	77	98	21.7730
.(((((............)))	chr11:10328462-10328692(+)$1	1	116	137	20.8206
(((.(((...........)))	chr19:36114742-36114972(+)$1	1	116	137	22.4286
(((((.............)))	chr11:33766214-33766444(-)$1	1	109	130	21.2923
(((((((.............)	chr11:108344775-108344995(-)$1	1	150	171	22.7268
(((((((..............	chrX:102930675-102930909(-)$1	1	190	211	20.8313
..(((((...........)))	chr16:58553709-58553932(+)$1	1	52	73	20.4901
(((((((.............)	chr3:33431574-33431794(-)$1	1	100	121	22.5923
..(((((...........)))	chr16:89351694-89351913(-)$1	1	81	102	20.4901
..(((((...........)))	chr7:92237463-92237689(-)$1	1	24	45	21.2539
((.(................)	chr11:57585554-57585785(+)$1	1	78	99	18.6239
(((((((............))	chr14:81941896-81942117(-)$1	1	73	94	22.4356
(((((((..............	chr17:56081931-56082158(-)$1	1	9	30	19.8157
...((((............))	chr8:70579999-70580223(-)$1	1	94	115	22.0225
.(.((((.............)	chr17:37074998-37075217(+)$1	1	176	197	22.3117
((((((............)))	chr16:88941198-88941419(-)$1	1	110	131	21.5882
..(((..............))	chr14:24759752-24759976(-)$1	1	33	54	21.0772
.((((((...........)))	chr13:52605524-52605747(+)$1	1	28	49	22.3276
((...((............))	chr10:70451909-70452132(+)$1	1	124	145	21.4786
.((((((............))	chr18:9402077-9402302(+)$1	1	160	181	22.4479
..(((((...........)))	chr6:116599323-116599545(-)$1	1	69	90	22.0827
((((((.............))	chr10:85912047-85912272(+)$1	1	176	197	22.3284
(((((((............))	chr5:167978204-167978429(-)$1	1	7	28	22.4356
.((((((...........)))	chr10:59952985-59953211(-)$1	1	89	110	21.3616
)))((((...........)))	chr11:105878763-105878993(-)$1	1	104	125	21.6780
((((((.............))	chr1:15987735-15987955(+)$1	1	103	124	22.3284
(((.(((...........)))	chr2:242275374-242275604(+)$1	1	188	209	22.4286
(((((((............))	chr5:98129623-98129853(+)$1	1	27	48	22.4356
(((((((...........)))	chrX:103439283-103439503(+)$1	1	9	30	20.7671
(((((.............)))	chrX:23851479-23851705(-)$1	1	173	194	21.5212
..(((((...........)))	chr2:152976841-152977066(-)$1	1	43	64	21.1897
(((..((............))	chr19:11833721-11833951(-)$1	1	27	48	21.1153
(((.((.............))	chr17:2586146-2586368(+)$1	1	127	148	21.4803
...((((.............)	chr7:76825430-76825653(-)$1	1	103	124	22.2167
)))((((.............)	chr4:103716942-103717166(-)$1	1	195	216	21.9450
..(((((.............)	chr2:105881263-105881488(-)$1	1	146	167	22.7796
.((((((...........)))	chr17:53471265-53471485(-)$1	1	172	193	22.3276
(((((((.............)	chr5:87502861-87503089(-)$1	1	147	168	22.4440
...((((.............)	chr4:186317927-186318149(+)$1	1	29	50	22.2167
((((((............)))	chr21:46323248-46323478(-)$1	1	76	97	21.5882
.((((((...........)))	chr17:5083132-5083354(-)$1	1	95	116	21.6795
(((((((.............)	chr1:68942018-68942241(-)$1	1	142	163	22.7268
(((((((.............)	chr7:7273834-7274064(+)$1	1	185	206	20.6767
(....((............))	chr11:44265713-44265935(+)$1	1	161	182	21.5254
..(((((..............	chr6:163992621-163992845(+)$1	1	184	205	21.0238
((.(((............)))	chr14:77977056-77977286(-)$1	1	96	117	21.8240
..(((((...........)))	chr15:62145635-62145865(-)$1	1	134	155	20.4901
(((((((...........)))	chr17:55757291-55757516(+)$1	1	124	145	22.3642
(((..((............))	chr8:130854281-130854511(-)$1	1	30	51	21.8610
(..((((...........)))	chr10:94414601-94414825(+)$1	1	95	116	21.8139
....(((...........)))	chr17:16245748-16245978(-)$1	1	177	198	22.5290
(((((((...........)))	chrX:48436016-48436238(+)$1	1	3	24	22.0620
..(((..............))	chr11:63395818-63396048(-)$1	1	80	101	19.0494
(((((((...........)))	chr11:33378268-33378489(+)$1	1	41	62	22.2347
))(((((.............)	chr1:230415206-230415425(+)$1	1	69	90	22.5258
.(((((............)))	chr3:49060567-49060776(+)$1	1	139	160	20.8206
(((((.(...........).)	chr13:31719703-31719933(-)$1	1	92	113	22.6203
((((.((..............	chr16:9211876-9212106(+)$1	1	180	201	20.3418
((((((..............)	chr4:100802535-100802756(-)$1	1	99	120	21.0372
(((((((...........)))	chr8:38709163-38709384(+)$1	1	43	64	22.2347
.((..((..............	chr3:101043881-101044111(-)$1	1	170	191	20.1940
((((((............)))	chr9:125609547-125609782(-)$1	1	68	89	21.5882
(((((................	chr2:29404766-29404996(+)$1	1	98	119	19.0717
(((((..............))	chr22:46239634-46239854(+)$1	1	152	173	20.5580
((...((............))	chr19:53116538-53116768(-)$1	1	190	211	21.3115
.((((.............)))	chr10:93806449-93806672(-)$1	1	133	154	20.2469
.((.(((...........)))	chr1:155916681-155916902(-)$1	1	141	162	21.6882
(((((.............)))	chr2:219758379-219758596(+)$1	1	113	134	21.2923
..(((((...........)))	chr4:38702285-38702507(+)$1	1	119	140	22.5179
(((((((.............)	chr3:101369540-101369770(-)$1	1	58	79	22.4209
...((((...........)))	chr10:11376684-11376914(+)$1	1	57	78	21.7896

#PSSM
g : 0.17	f : 0.13	: : 0.09	! : 0.08	e : 0.08	[ : 0.06	c : 0.06	# : 0.05	= : 0.04	% : 0.04	i : 0.04	" : 0.02	b : 0.01	J : 0.01	( : 0.01	d : 0.01	+ : 0.01	h : 0.01	
f : 0.23	g : 0.13	e : 0.10	! : 0.08	c : 0.06	# : 0.06	b : 0.05	: : 0.05	= : 0.04	i : 0.04	" : 0.02	d : 0.02	% : 0.01	a : 0.01	( : 0.01	h : 0.01	
e : 0.23	f : 0.21	g : 0.12	c : 0.08	# : 0.06	b : 0.05	= : 0.04	[ : 0.04	" : 0.04	i : 0.04	d : 0.02	h : 0.01	! : 0.01	
f : 0.21	e : 0.21	d : 0.13	g : 0.10	[ : 0.05	c : 0.05	= : 0.04	! : 0.04	" : 0.02	i : 0.02	# : 0.02	a : 0.01	b : 0.01	h : 0.01	
e : 0.21	f : 0.19	d : 0.13	c : 0.13	g : 0.10	= : 0.04	! : 0.04	" : 0.02	i : 0.02	y : 0.01	b : 0.01	h : 0.01	# : 0.01	[ : 0.01	
f : 0.19	e : 0.16	d : 0.12	b : 0.10	c : 0.09	g : 0.09	v : 0.05	= : 0.04	w : 0.04	y : 0.02	i : 0.02	h : 0.01	[ : 0.01	
e : 0.13	d : 0.12	u : 0.09	v : 0.09	g : 0.09	f : 0.09	b : 0.09	c : 0.08	w : 0.05	= : 0.04	y : 0.02	i : 0.02	h : 0.01	a : 0.01	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
t : 0.34	v : 0.27	u : 0.23	w : 0.10	y : 0.04	
v : 0.21	e : 0.15	u : 0.13	f : 0.12	c : 0.10	w : 0.10	d : 0.05	y : 0.04	g : 0.02	i : 0.01	a : 0.01	
v : 0.17	f : 0.16	e : 0.16	c : 0.13	b : 0.08	w : 0.06	g : 0.06	d : 0.06	y : 0.04	i : 0.01	] : 0.01	
f : 0.19	e : 0.19	d : 0.13	c : 0.13	g : 0.09	b : 0.08	w : 0.05	= : 0.02	y : 0.02	i : 0.02	a : 0.01	h : 0.01	

#score	1575.728547289115
#seq	73
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_UTR_m2_run2.txt

#BEAR
""ddddqqqqqqqqdddd22ee	chr1:179814516-179814740(-)$1	224	48	70	15.6698
ffddddqqqqqqqqdddd]fff	chr14:70497003-70497224(+)$1	221	186	208	15.2394
"""cccqqqqqqqqccc22ccc	chr1:155224944-155225163(-)$1	219	162	184	15.8078
!eeeeeqqqqqqqqeeeeeddd	chr2:37429385-37429607(+)$1	222	183	205	15.3473
""ddddqqqqqqqqdddd22ee	chr5:167981476-167981704(-)$1	228	77	99	15.6698
==ddddqqqqqqqqdddd]===	chr10:119040924-119041147(-)$1	223	89	111	15.9620
"eeeeeqqqqqqqqeeeee333	chr12:124498592-124498810(+)$1	218	76	98	16.2151
ffffffqqqqqqqqffffff]c	chr5:96372822-96373051(+)$1	229	180	202	14.3841
!eeeeeqqqqqqqqeeeee22g	chr1:202102537-202102763(-)$1	226	26	48	15.7397
[eeeeeqqqqqqqqeeeee]dd	chr4:39522873-39523097(-)$1	224	67	89	15.6356
[eeeeeqqqqqqqqeeeee]ff	chr4:140432038-140432264(-)$1	226	65	87	15.7002
ffffffqqqqqqqqffffff]d	chr4:78638969-78639190(-)$1	221	53	75	14.2642
dddcccqqqqqqqqccc4444d	chr12:8250104-8250330(+)$1	226	170	192	15.3279
ffffffqqqqqqqqffffffbb	chr8:1952359-1952586(+)$1	227	110	132	13.7213
c[ddddqqqqqqqqdddd]ccc	chrX:150577141-150577379(+)$1	238	31	53	15.8150
eeeebbqqqqqqqqbb]eeeee	chrX:23803913-23804134(+)$1	221	72	94	13.9478
f!!cccqqqqqqqqccc]ffff	chr16:19514228-19514451(-)$1	223	187	209	15.4995
"""cccqqqqqqqqccc22ccc	chr5:74893930-74894156(+)$1	226	23	45	15.8078
ggggggqqqqqqqqggggggg:	chr10:14944437-14944659(+)$1	222	104	126	14.1091
ggggggqqqqqqqqggggggg:	chr10:35860442-35860667(+)$1	225	121	143	14.1091
ccccccqqqqqqqqccc]ccc]	chr7:131177839-131178063(+)$1	224	83	105	15.3998
ffddddqqqqqqqqdddd22ff	chr13:27262018-27262240(+)$1	222	16	38	15.2026
ffffffqqqqqqqqffffff77	chr1:162495069-162495292(+)$1	223	143	165	13.1519
[eeeeeqqqqqqqqeeeeeccc	chr14:75600053-75600290(-)$1	237	194	216	15.8329
bb[cccqqqqqqqqcccbbeee	chr6:7402779-7403007(+)$1	228	168	190	14.0412
"""cccqqqqqqqqccc]====	chr19:21241465-21241694(+)$1	229	31	53	16.1560
ffffffqqqqqqqqffffff44	chr3:113163643-113163865(-)$1	222	167	189	14.4002
eee[bbqqqqqqqqbb]eeeee	chr12:27477675-27477907(+)$1	232	117	139	13.8262
====bbqqqqqqqqbb]=====	chr1:163325195-163325417(+)$1	222	110	132	14.5151
======qqqqqqqq========	chr1:207968410-207968633(+)$1	223	61	83	15.6027
iiddddqqqqqqqqdddd4444	chr13:42810047-42810274(+)$1	227	68	90	15.7661
!!ddddqqqqqqqqdddd22a]	chr4:79847688-79847907(-)$1	219	177	199	15.8561
a[ddddqqqqqqqqdddd]acc	chr13:39611348-39611575(-)$1	227	78	100	15.7823
###cccqqqqqqqqccc22ccc	chr21:34901113-34901332(-)$1	219	184	206	15.6632
ffffffqqqqqqqqffffffcc	chrX:135044876-135045097(-)$1	221	41	63	14.3499
!eeeeeqqqqqqqqeeeee22d	chr19:8028167-8028396(-)$1	229	124	146	15.6640
b[ddddqqqqqqqqddddbb22	chr14:93695183-93695408(+)$1	225	155	177	14.3997
ffffffqqqqqqqqffffff]b	chr10:6157640-6157864(+)$1	224	39	61	14.0983
dddd[aqqqqqqqqadddd]cc	chr16:56548467-56548690(-)$1	223	171	193	14.7246
ee[cccqqqqqqqqccceeeee	chr3:32523196-32523418(-)$1	222	84	106	15.4488
!eeeeeqqqqqqqqeeeee22c	chr1:33146864-33147087(+)$1	223	75	97	15.7839
d[ddddqqqqqqqqdddd]ddd	chr9:72324819-72325044(-)$1	225	188	210	15.1543
###cccqqqqqqqqccc333gg	chr4:107269014-107269236(+)$1	222	62	84	16.1236
e!!cccqqqqqqqqccc22eee	chr1:23635131-23635352(-)$1	221	187	209	15.3612
eeecccqqqqqqqqccc22eee	chr3:194123313-194123535(-)$1	222	50	72	15.2326
[eeeeeqqqqqqqqeeeeeccc	chr6:133852016-133852239(+)$1	223	160	182	15.8329
cc[cccqqqqqqqqccc]ccc3	chr17:47375111-47375341(-)$1	230	77	99	15.6076
!eeeeeqqqqqqqqeeeee22d	chr5:180001747-180001967(+)$1	220	105	127	15.6640
cc[cccqqqqqqqqccc]ccc:	chrX:70795212-70795434(+)$1	222	54	76	14.6339
======qqqqqqqq========	chr12:101019712-101019932(+)$1	220	144	166	15.6027
g[ddddqqqqqqqqdddd]ggg	chr10:98985190-98985410(-)$1	220	126	148	15.7945
==[cccqqqqqqqqccc=====	chr18:9588641-9588867(-)$1	226	46	68	16.1026
iiiiiiqqqqqqqqiiiiiiii	chr13:53268161-53268387(+)$1	226	175	197	15.0887
ee[cccqqqqqqqqccceeeee	chr8:11667167-11667400(+)$1	233	77	99	15.4488
c[ddddqqqqqqqqddddccc2	chr16:51170564-51170787(-)$1	223	114	136	15.3303
ceeeeeqqqqqqqqeeeee22c	chr2:32248957-32249188(-)$1	231	165	187	15.5470
ccccccqqqqqqqqccc]ccc]	chr1:172411728-172411951(-)$1	223	5	27	15.3998
[eeeeeqqqqqqqqeeeeeccc	chr4:110631486-110631715(-)$1	229	14	36	15.8329
!!ddddqqqqqqqqdddd]fff	chr1:203765501-203765724(+)$1	223	173	195	15.7437
d[ddddqqqqqqqqdddd333d	chr2:135816311-135816540(+)$1	229	34	56	15.9276
:eeeeeqqqqqqqqeeeee:ii	chr3:63819551-63819778(-)$1	227	71	93	13.6619
:eeeeeqqqqqqqqeeeeefff	chr11:94905591-94905813(-)$1	222	80	102	14.3793
====[aqqqqqqqqa]======	chr17:5377124-5377347(-)$1	223	41	63	15.2882

#otherMatches

#Seq PSSM
UUUUGCAGUUUUGAGUAGUAUG	chr1:179814516-179814740(-)$1	224	48	70	15.6698
GAAGAAAGACUUUAUUCUCUCU	chr14:70497003-70497224(+)$1	221	186	208	15.2394
CCCUCCUCACUCCUGGACCGGC	chr1:155224944-155225163(-)$1	219	162	184	15.8078
cuugaggucaggaguucgagac	chr2:37429385-37429607(+)$1	222	183	205	15.3473
CAUGAAUUCAGAGUUUCAAACA	chr5:167981476-167981704(-)$1	228	77	99	15.6698
GGGGAGAAAAGUUAUUCCACUU	chr10:119040924-119041147(-)$1	223	89	111	15.9620
gauagugauuaagugcuaugaa	chr12:124498592-124498810(+)$1	218	76	98	16.2151
UCAUAAUCUGUCUUUUGUGAAA	chr5:96372822-96373051(+)$1	229	180	202	14.3841
GAACUCAGCAUGGGGGGUUGGU	chr1:202102537-202102763(-)$1	226	26	48	15.7397
GUUGAUGUCAAUGAAUCAAGAA	chr4:39522873-39523097(-)$1	224	67	89	15.6356
UUGCAUCAAUAGCAGUGUGUAG	chr4:140432038-140432264(-)$1	226	65	87	15.7002
GUUGCAGGAAGGUGUGUAAUUG	chr4:78638969-78639190(-)$1	221	53	75	14.2642
AAUUCCUGAAAAAUGGAAAAUG	chr12:8250104-8250330(+)$1	226	170	192	15.3279
ACAUUUUACUUUUCAAGUGUGU	chr8:1952359-1952586(+)$1	227	110	132	13.7213
uuaaaaauaaauuauuuucagg	chrX:150577141-150577379(+)$1	238	31	53	15.8150
UAGAUGACAACCUCCAUUCUAU	chrX:23803913-23804134(+)$1	221	72	94	13.9478
CACCAUGCAAUCCAGUGAGGCU	chr16:19514228-19514451(-)$1	223	187	209	15.4995
AUAAUCCUUCCUCAGAUGAUGU	chr5:74893930-74894156(+)$1	226	23	45	15.8078
AAUAUUUUUUUCCUAAUGUUAA	chr10:14944437-14944659(+)$1	222	104	126	14.1091
CAUGAUGAUGAAUAGUUAUGUU	chr10:35860442-35860667(+)$1	225	121	143	14.1091
UGGACCAGUUCUAAGGUAUCAC	chr7:131177839-131178063(+)$1	224	83	105	15.3998
GUUCUCAGGAUGGAGAGAACAC	chr13:27262018-27262240(+)$1	222	16	38	15.2026
UCCCAGUUACUUCUUUGGGGUA	chr1:162495069-162495292(+)$1	223	143	165	13.1519
gaguaucuuuuugugugcuaau	chr14:75600053-75600290(-)$1	237	194	216	15.8329
GGUAAGUUCAGAUUUUUCCCUC	chr6:7402779-7403007(+)$1	228	168	190	14.0412
ACACCUUAUUGCACAGGAGAGC	chr19:21241465-21241694(+)$1	229	31	53	16.1560
CUUUCUUUUUUCUUGGGAAGUC	chr3:113163643-113163865(-)$1	222	167	189	14.4002
UUUCCCAUAUUUCAGGUGAAUA	chr12:27477675-27477907(+)$1	232	117	139	13.8262
UUUUCUAUUUAGAAAGAAAAGU	chr1:163325195-163325417(+)$1	222	110	132	14.5151
GAAGCAGAUAAUGGUGUUUUUU	chr1:207968410-207968633(+)$1	223	61	83	15.6027
GAUGUAUUUUAGUUUGCAGGAU	chr13:42810047-42810274(+)$1	227	68	90	15.7661
UUCCUACUCUUCACUGGGUUUG	chr4:79847688-79847907(-)$1	219	177	199	15.8561
GUGGAGUCUUUUUCCUCCUCAG	chr13:39611348-39611575(-)$1	227	78	100	15.7823
CACCCACAUUACUAUGGAAGCC	chr21:34901113-34901332(-)$1	219	184	206	15.6632
AGGUUUUUCUCCGUGAAUCUUA	chrX:135044876-135045097(-)$1	221	41	63	14.3499
CACAAGUGUUUGUCUUUGUCUG	chr19:8028167-8028396(-)$1	229	124	146	15.6640
CUAGUUUUCUUAUUGACUGUAU	chr14:93695183-93695408(+)$1	225	155	177	14.3997
UUUUUAAUAUAGUAUAAAAAUC	chr10:6157640-6157864(+)$1	224	39	61	14.0983
CUGAUGUUUCUCUUCUCAGCAU	chr16:56548467-56548690(-)$1	223	171	193	14.7246
UGGAUCUCUUAGUUGGUCACUU	chr3:32523196-32523418(-)$1	222	84	106	15.4488
AACAAAAAGUAGACUUUGUAAA	chr1:33146864-33147087(+)$1	223	75	97	15.7839
ACCAUGUAAAAUACCAUGAUAU	chr9:72324819-72325044(-)$1	225	188	210	15.1543
UAAUAAUUUAUUUUUUAGCAGG	chr4:107269014-107269236(+)$1	222	62	84	16.1236
AUAGUCAUUUAACAGACCUUAU	chr1:23635131-23635352(-)$1	221	187	209	15.3612
UGUACAUUCAGCAUUGUAAAUA	chr3:194123313-194123535(-)$1	222	50	72	15.2326
AUUACAUCUAAAUUUGUAAGUC	chr6:133852016-133852239(+)$1	223	160	182	15.8329
CAGAAAUUUUCUUCUUUGUGUA	chr17:47375111-47375341(-)$1	230	77	99	15.6076
UUUCUUUUUAAAUUGAGAACAU	chr5:180001747-180001967(+)$1	220	105	127	15.6640
CAGUGUACCUUUUAACAGUGUA	chrX:70795212-70795434(+)$1	222	54	76	14.6339
UUAAGGGAUGGUGACUUUAAAA	chr12:101019712-101019932(+)$1	220	144	166	15.6027
AAAGAAUUUAUAGCUUUUCUGG	chr10:98985190-98985410(-)$1	220	126	148	15.7945
AGGUGCCUCACAUCGCACUGUU	chr18:9588641-9588867(-)$1	226	46	68	16.1026
AAGUGCAAAGAGCAGUGCUUCA	chr13:53268161-53268387(+)$1	226	175	197	15.0887
UGUGGAAAAGAAGGUCCCGCUG	chr8:11667167-11667400(+)$1	233	77	99	15.4488
CUAUAUCCAGUUUAAUAUGAAU	chr16:51170564-51170787(-)$1	223	114	136	15.3303
CUUUAACUUUGUUUUUAAAAUG	chr2:32248957-32249188(-)$1	231	165	187	15.5470
CAGAGACAAAUUCAUCUAUUGU	chr1:172411728-172411951(-)$1	223	5	27	15.3998
ugcagugagcugagauugcacu	chr4:110631486-110631715(-)$1	229	14	36	15.8329
GGUUCUGGACCUUGAGAAAGAG	chr1:203765501-203765724(+)$1	223	173	195	15.7437
AUUUUAAGUUUAUGUAGAUGCU	chr2:135816311-135816540(+)$1	229	34	56	15.9276
GUAAAAUACUCUGUUUUUAAGU	chr3:63819551-63819778(-)$1	227	71	93	13.6619
ACUGAAAUGCCAAAUUCAGCUA	chr11:94905591-94905813(-)$1	222	80	102	14.3793
UAGCAGUAGGAAUUCAGCUAUA	chr17:5377124-5377347(-)$1	223	41	63	15.2882

#DB
..((((........))))..))	chr1:179814516-179814740(-)$1	1	48	70	15.6698
((((((........)))).)))	chr14:70497003-70497224(+)$1	1	186	208	15.2394
...(((........)))..)))	chr1:155224944-155225163(-)$1	1	162	184	15.8078
.(((((........))))))))	chr2:37429385-37429607(+)$1	1	183	205	15.3473
..((((........))))..))	chr5:167981476-167981704(-)$1	1	77	99	15.6698
((((((........)))).)))	chr10:119040924-119041147(-)$1	1	89	111	15.9620
.(((((........)))))...	chr12:124498592-124498810(+)$1	1	76	98	16.2151
((((((........)))))).)	chr5:96372822-96373051(+)$1	1	180	202	14.3841
.(((((........)))))..)	chr1:202102537-202102763(-)$1	1	26	48	15.7397
.(((((........))))).))	chr4:39522873-39523097(-)$1	1	67	89	15.6356
.(((((........))))).))	chr4:140432038-140432264(-)$1	1	65	87	15.7002
((((((........)))))).)	chr4:78638969-78639190(-)$1	1	53	75	14.2642
((((((........)))....)	chr12:8250104-8250330(+)$1	1	170	192	15.3279
((((((........))))))((	chr8:1952359-1952586(+)$1	1	110	132	13.7213
(.((((........)))).)))	chrX:150577141-150577379(+)$1	1	31	53	15.8150
((((((........)).)))))	chrX:23803913-23804134(+)$1	1	72	94	13.9478
(..(((........))).))))	chr16:19514228-19514451(-)$1	1	187	209	15.4995
...(((........)))..)))	chr5:74893930-74894156(+)$1	1	23	45	15.8078
((((((........))))))).	chr10:14944437-14944659(+)$1	1	104	126	14.1091
((((((........))))))).	chr10:35860442-35860667(+)$1	1	121	143	14.1091
((((((........))).))).	chr7:131177839-131178063(+)$1	1	83	105	15.3998
((((((........))))..))	chr13:27262018-27262240(+)$1	1	16	38	15.2026
((((((........))))))..	chr1:162495069-162495292(+)$1	1	143	165	13.1519
.(((((........))))))))	chr14:75600053-75600290(-)$1	1	194	216	15.8329
((.(((........))))))))	chr6:7402779-7403007(+)$1	1	168	190	14.0412
...(((........))).))))	chr19:21241465-21241694(+)$1	1	31	53	16.1560
((((((........))))))..	chr3:113163643-113163865(-)$1	1	167	189	14.4002
(((.((........)).)))))	chr12:27477675-27477907(+)$1	1	117	139	13.8262
((((((........)).)))))	chr1:163325195-163325417(+)$1	1	110	132	14.5151
((((((........))))))))	chr1:207968410-207968633(+)$1	1	61	83	15.6027
((((((........))))....	chr13:42810047-42810274(+)$1	1	68	90	15.7661
..((((........))))..).	chr4:79847688-79847907(-)$1	1	177	199	15.8561
(.((((........)))).)))	chr13:39611348-39611575(-)$1	1	78	100	15.7823
...(((........)))..)))	chr21:34901113-34901332(-)$1	1	184	206	15.6632
((((((........))))))((	chrX:135044876-135045097(-)$1	1	41	63	14.3499
.(((((........)))))..)	chr19:8028167-8028396(-)$1	1	124	146	15.6640
(.((((........))))))..	chr14:93695183-93695408(+)$1	1	155	177	14.3997
((((((........)))))).)	chr10:6157640-6157864(+)$1	1	39	61	14.0983
((((.(........))))).))	chr16:56548467-56548690(-)$1	1	171	193	14.7246
((.(((........))))))))	chr3:32523196-32523418(-)$1	1	84	106	15.4488
.(((((........)))))..)	chr1:33146864-33147087(+)$1	1	75	97	15.7839
(.((((........)))).)))	chr9:72324819-72325044(-)$1	1	188	210	15.1543
...(((........)))...))	chr4:107269014-107269236(+)$1	1	62	84	16.1236
(..(((........)))..)))	chr1:23635131-23635352(-)$1	1	187	209	15.3612
((((((........)))..)))	chr3:194123313-194123535(-)$1	1	50	72	15.2326
.(((((........))))))))	chr6:133852016-133852239(+)$1	1	160	182	15.8329
((.(((........))).))).	chr17:47375111-47375341(-)$1	1	77	99	15.6076
.(((((........)))))..)	chr5:180001747-180001967(+)$1	1	105	127	15.6640
((.(((........))).))).	chrX:70795212-70795434(+)$1	1	54	76	14.6339
((((((........))))))))	chr12:101019712-101019932(+)$1	1	144	166	15.6027
(.((((........)))).)))	chr10:98985190-98985410(-)$1	1	126	148	15.7945
((.(((........))))))))	chr18:9588641-9588867(-)$1	1	46	68	16.1026
((((((........))))))))	chr13:53268161-53268387(+)$1	1	175	197	15.0887
((.(((........))))))))	chr8:11667167-11667400(+)$1	1	77	99	15.4488
(.((((........))))))).	chr16:51170564-51170787(-)$1	1	114	136	15.3303
((((((........)))))..)	chr2:32248957-32249188(-)$1	1	165	187	15.5470
((((((........))).))).	chr1:172411728-172411951(-)$1	1	5	27	15.3998
.(((((........))))))))	chr4:110631486-110631715(-)$1	1	14	36	15.8329
..((((........)))).)))	chr1:203765501-203765724(+)$1	1	173	195	15.7437
(.((((........))))...)	chr2:135816311-135816540(+)$1	1	34	56	15.9276
.(((((........))))).((	chr3:63819551-63819778(-)$1	1	71	93	13.6619
.(((((........)))))(((	chr11:94905591-94905813(-)$1	1	80	102	14.3793
((((.(........).))))))	chr17:5377124-5377347(-)$1	1	41	63	15.2882

#PSSM
f : 0.15	! : 0.11	c : 0.11	" : 0.09	= : 0.09	e : 0.09	[ : 0.07	d : 0.06	g : 0.04	b : 0.03	i : 0.03	# : 0.03	: : 0.03	a : 0.01	
e : 0.30	f : 0.14	[ : 0.11	= : 0.09	" : 0.07	! : 0.06	c : 0.06	d : 0.03	g : 0.03	i : 0.03	# : 0.03	b : 0.01	
d : 0.26	e : 0.26	f : 0.11	[ : 0.09	= : 0.06	" : 0.04	! : 0.03	g : 0.03	c : 0.03	# : 0.03	i : 0.01	
c : 0.26	d : 0.25	e : 0.23	f : 0.11	= : 0.06	g : 0.03	[ : 0.01	i : 0.01	
c : 0.26	d : 0.23	e : 0.22	f : 0.11	b : 0.04	g : 0.03	= : 0.03	[ : 0.03	i : 0.01	
c : 0.26	d : 0.23	e : 0.22	f : 0.11	b : 0.04	g : 0.03	= : 0.03	a : 0.03	i : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.26	d : 0.23	e : 0.22	f : 0.11	b : 0.04	g : 0.03	= : 0.03	a : 0.03	i : 0.01	
c : 0.26	d : 0.25	e : 0.22	f : 0.11	b : 0.04	g : 0.03	= : 0.03	i : 0.01	] : 0.01	
c : 0.26	d : 0.25	e : 0.22	f : 0.11	] : 0.04	= : 0.04	g : 0.03	i : 0.01	
e : 0.28	d : 0.25	f : 0.11	] : 0.09	2 : 0.07	= : 0.07	g : 0.03	4 : 0.01	b : 0.01	3 : 0.01	i : 0.01	
e : 0.28	2 : 0.14	f : 0.12	] : 0.11	= : 0.09	c : 0.07	4 : 0.03	g : 0.03	b : 0.03	3 : 0.03	d : 0.01	i : 0.01	
c : 0.19	f : 0.17	2 : 0.14	= : 0.11	e : 0.11	3 : 0.04	] : 0.04	g : 0.04	d : 0.03	4 : 0.03	a : 0.01	b : 0.01	i : 0.01	: : 0.01	
c : 0.23	e : 0.14	= : 0.11	f : 0.09	2 : 0.09	g : 0.06	d : 0.04	] : 0.04	4 : 0.04	3 : 0.03	i : 0.03	b : 0.01	7 : 0.01	a : 0.01	
c : 0.20	e : 0.14	d : 0.12	= : 0.11	f : 0.09	g : 0.04	: : 0.04	] : 0.04	3 : 0.03	b : 0.03	4 : 0.03	2 : 0.03	i : 0.03	7 : 0.01	

#score	958.3993692445606
#seq	63
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_CDS_m3_run1.txt

#BEAR
dd[bb!!cccnnnnnccc22bb]d	chr10:101489318-101489558(-)$1	240	2	26	11.4496
a[ccceeeeennnnneeeee]ccc	chr1:100176332-100176572(-)$1	240	113	137	12.0048
fffff[ddddnnnnndddd22fff	chr14:53327043-53327283(-)$1	240	158	182	12.5341
e"""eeeeeooooooeeeee4444	chr1:113655013-113655253(+)$1	240	128	152	8.3113
ff[ccc!!ddddllldddd22ccc	chr4:76407651-76407891(-)$1	240	59	83	7.9717
cc"""ddddannnnna]ddddccc	chr19:7690785-7691025(-)$1	240	140	164	12.5791
:ggggggg[annnnna]ggggggg	chr14:69350807-69351047(-)$1	240	84	108	11.0323
eeeee!!cccnnnnnccceeeeeJ	chr19:3983145-3983385(-)$1	240	59	83	10.2373
c[ccc[ddddnnnnnddddccc]c	chr4:1696402-1696642(-)$1	240	142	166	13.0069
dccc####bbnnnnnbb4444ccc	chr17:34173828-34174071(+)$1	243	173	197	11.3868
c[ccc[ddddnnnnndddd22ccc	chr2:86279932-86280172(-)$1	240	212	236	13.4455
ffff"""cccnnnnnccc22ffff	chr12:14923831-14924071(-)$1	240	117	141	12.1970
###gggggggnnnnngggggggdd	chr14:59113338-59113578(+)$1	240	102	126	11.5895
gggggggcccnnnnnccc]ggggg	chr17:62495976-62496217(-)$1	241	10	34	12.3304
ceeeee[cccnnnnnccc22eeee	chr11:64787813-64788053(+)$1	240	116	140	11.4906
ccc!!eeeeennnnneeeeeccc]	chr14:102486245-102486485(+)$1	240	197	221	12.1145
==========nnnnn=========	chr11:43343521-43343761(+)$1	240	98	122	12.6738
gggggg[cccnnnnnccc]ggggg	chr22:50962711-50962951(-)$1	240	212	236	12.4340
b[bb[eeeeennnnneeeee]bb]	chr14:50360528-50360768(+)$1	240	214	238	10.9875
=========oooooo=========	chr1:95364906-95365146(-)$1	240	54	78	9.0315
dd####ddddnnnnndddd4444d	chr1:90058265-90058505(+)$1	240	17	41	13.0763
b!!gggggggnnnnnggggggg22	chr5:162943518-162943758(+)$1	240	20	44	11.5283
eee[ccc!!annnnna22ccc]ee	chr8:37555889-37556169(+)$1	280	206	230	10.8955
c[ffffff[annnnna]ffffff]	chr16:71807106-71807357(-)$1	251	19	43	10.8349
ffff!!eeeeellleeeee333ff	chr3:156271379-156271619(-)$1	240	67	91	7.6486
eeee[eeeeennnnneeeee]eee	chr3:28381917-28382157(-)$1	240	129	153	11.3059
ccc!!addddnnnnndddd]a22c	chr18:43698139-43698379(+)$1	240	134	158	12.9337
b####ddddannnnna]dddd333	chr22:39909628-39909868(+)$1	240	150	174	12.5487
dddd"""cccnnnnnccc333ddd	chr17:7218962-7219242(-)$1	280	41	65	12.4212
d[bb####bbnnnnnbbbb]dddd	chr19:5691462-5691702(+)$1	240	135	159	10.0015
eeee!!ddddoooooodddd]eee	chr17:4849873-4850125(-)$1	252	44	68	8.6721
==========nnnnn=========	chr9:115030235-115030475(-)$1	240	2	26	12.6738
ff!!ccc[bbnnnnnbbcccffff	chr17:18110052-18110292(+)$1	240	175	199	10.7597
:ccc[ddddoooooodddd22ccc	chr1:112999821-113000061(+)$1	240	190	214	8.4834
fffff[ddddnnnnndddd]ffff	chr7:26232051-26232291(-)$1	240	47	71	12.3504
dddd"""cccooooooccc22ddd	chr2:219508416-219508656(-)$1	240	117	141	8.3669
!!ccc[ddddnnnnndddd]ccc2	chr12:121855427-121855667(+)$1	240	3	27	13.0748
ee[a!!ddddnnnnndddd22a33	chr2:230910512-230910752(-)$1	240	119	143	13.4686
hhh!!bbcccnnnnnccc]bb22h	chr14:45414411-45414693(-)$1	282	51	75	10.3653
:ccc!!ddddnnnnndddd22ccc	chr14:91937113-91937353(-)$1	240	144	168	12.5942
dd[eeeee[annnnna]eeeeedd	chr6:31498559-31498799(-)$1	240	97	121	11.0605
b[dddd[cccnnnnnccc]dddd]	chr10:112362244-112362484(+)$1	240	107	131	11.2950
ff[bb[ddddnnnnnddddbb]ff	chr19:7083323-7083563(+)$1	240	77	101	11.7322
hhhhhhddddnnnnndddd]hhhh	chr7:27839569-27839809(+)$1	240	143	167	10.8283
ccc[a[ddddnnnnndddd]a]cc	chr18:55217918-55218158(-)$1	240	139	163	13.3471
e####eeeeennnnneeeee4444	chr2:109400132-109400372(+)$1	240	109	133	12.1511
d####ddddoooooodddd22ddd	chr6:44220928-44221168(+)$1	240	165	189	9.1759
fffffbbcccnnnnnccc]bb]ff	chr6:30619095-30619335(+)$1	240	108	132	10.6207
$$$$ccc[bbnnnnnbb]ccc]dd	chr1:16268338-16268578(-)$1	240	139	163	9.9553
ffffffddddnnnnndddd]ffff	chr8:145152124-145152364(+)$1	240	199	223	11.9780
!!a[ffffffnnnnnffffff]af	chr9:71395154-71395394(+)$1	240	57	81	10.4234
:iiiiiiiiinnnnniiiiiiiii	chr6:109321692-109321932(-)$1	240	31	55	11.1695
!!dddd[cccnnnnnccc]dddd]	chr19:55966928-55967168(-)$1	240	18	42	11.4261

#otherMatches

#Seq PSSM
GGUUGAGUGUGGGUAGCAGCCAUU	chr10:101489318-101489558(-)$1	240	2	26	11.4496
UGAUUCAUGGAAAACCUAUGCAAU	chr1:100176332-100176572(-)$1	240	113	137	12.0048
CCAAGAUGAGAUUUAUUCAAGCUU	chr14:53327043-53327283(-)$1	240	158	182	12.5341
CGCACUGGUGCCAUGGCCAGAUUA	chr1:113655013-113655253(+)$1	240	128	152	8.3113
UAUAUUAGGCAUGAAAUGUAAGAU	chr4:76407651-76407891(-)$1	240	59	83	7.9717
GUACAGUCCCUCAAUGUGGACGCC	chr19:7690785-7691025(-)$1	240	140	164	12.5791
ACCCUUCAACAACUGGAUGGAGGG	chr14:69350807-69351047(-)$1	240	84	108	11.0323
GGCUCCUGUCCCCCUGACGAGUCC	chr19:3983145-3983385(-)$1	240	59	83	10.2373
GUAAGUACUUUGGAUAAGUCUUUC	chr4:1696402-1696642(-)$1	240	142	166	13.0069
AGAGUUUUGCCUGCUGCUUUCCUC	chr17:34173828-34174071(+)$1	243	173	197	11.3868
UCUACAGAGGCUUCACCUUGGGUA	chr2:86279932-86280172(-)$1	240	212	236	13.4455
UGCUGCGGGACAAUAUCCAAGGCA	chr12:14923831-14924071(-)$1	240	117	141	12.1970
GAAUGUGGGGCUGUACCCCGCGCC	chr14:59113338-59113578(+)$1	240	102	126	11.5895
CUGGUAAUCCAACAGGGACUUACC	chr17:62495976-62496217(-)$1	241	10	34	12.3304
CAGGACCUGCCUGGAGCACUGUCC	chr11:64787813-64788053(+)$1	240	116	140	11.4906
UCUUACAGCUGUCGAAGCUGGGGU	chr14:102486245-102486485(+)$1	240	197	221	12.1145
UAAGACUUUACCAGAUGAAGUCUU	chr11:43343521-43343761(+)$1	240	98	122	12.6738
GUCCUGGCUUUUGUCAAGGCAGGG	chr22:50962711-50962951(-)$1	240	212	236	12.4340
GAUGAGGCUCGCCAGGAGCUGCAC	chr14:50360528-50360768(+)$1	240	214	238	10.9875
UUUAUUUUUAACUUAAAAGAUGGG	chr1:95364906-95365146(-)$1	240	54	78	9.0315
GCCACCAAAAACCUAUUUUACCAG	chr1:90058265-90058505(+)$1	240	17	41	13.0763
GGAUUCCUAUUCUGUAUGGGGAAG	chr5:162943518-162943758(+)$1	240	20	44	11.5283
GGCCGUGCCGUCCCUCCCCACAGC	chr8:37555889-37556169(+)$1	280	206	230	10.8955
ACUAGUUUGAAAUUGUGAAGCUGC	chr16:71807106-71807357(-)$1	251	19	43	10.8349
GGCAUAUGGAUCUUAUUCAGUCUG	chr3:156271379-156271619(-)$1	240	67	91	7.6486
AAUAUAUUCAGGAGAUGAAUCUGU	chr3:28381917-28382157(-)$1	240	129	153	11.3059
GCUAGCUAGGUAAUUCUUAUGACA	chr18:43698139-43698379(+)$1	240	134	158	12.9337
CCUCUUGGACUAUGUGAUCCGCCC	chr22:39909628-39909868(+)$1	240	150	174	12.5487
CCCCUCUUCAUGCACUGAUUUGGG	chr17:7218962-7219242(-)$1	280	41	65	12.4212
CCGCCAUGAGGAAAGCUGCUGCCA	chr19:5691462-5691702(+)$1	240	135	159	10.0015
GGUCAAGUUUUUACGUGAAUGGGC	chr17:4849873-4850125(-)$1	252	44	68	8.6721
UUUCUUAGAAAUGGCUUCUGAGGA	chr9:115030235-115030475(-)$1	240	2	26	12.6738
CCCUGCUCUGAAACCCAAGCGGUC	chr17:18110052-18110292(+)$1	240	175	199	10.7597
UACUUUUGCCUACCAGCAGCUAGU	chr1:112999821-113000061(+)$1	240	190	214	8.4834
GGAAAUCAAAGUAAGUUUGUUUUC	chr7:26232051-26232291(-)$1	240	47	71	12.3504
CAGACCAGAUUCACCCAUCCCUCU	chr2:219508416-219508656(-)$1	240	117	141	8.3669
GACUGAAGGUGAAGGACCUGCGGC	chr12:121855427-121855667(+)$1	240	3	27	13.0748
CACGUACGCUGGCCUGGCGGUCAU	chr2:230910512-230910752(-)$1	240	119	143	13.4686
UUUGAAGCUGUUUGCCAGACUGAA	chr14:45414411-45414693(-)$1	282	51	75	10.3653
GGCCUCGAAGCAUGCUUUCUUGGC	chr14:91937113-91937353(-)$1	240	144	168	12.5942
UGGCCAGAGCAGGCCGGUUUGGCA	chr6:31498559-31498799(-)$1	240	97	121	11.0605
GAGAGUGAGAGGGGUUCUGGCUCA	chr10:112362244-112362484(+)$1	240	107	131	11.2950
UCAUACAGGGGAGUACCCUUACGA	chr19:7083323-7083563(+)$1	240	77	101	11.7322
AGUUUGGUACUCCUUGUAUGUAAA	chr7:27839569-27839809(+)$1	240	143	167	10.8283
GACCCUGAGCUGUCCGCUCUGUGU	chr18:55217918-55218158(-)$1	240	139	163	13.3471
UAGUAUUUGGGUUUGUUAAGGAUG	chr2:109400132-109400372(+)$1	240	109	133	12.1511
CGCAUGAUCAAGCUAGGUCUAGGU	chr6:44220928-44221168(+)$1	240	165	189	9.1759
UUUUGCGGUUCUACAAGCGUGACA	chr6:30619095-30619335(+)$1	240	108	132	10.6207
UUUAAGGAUGGAUGGCACCCUGGA	chr1:16268338-16268578(-)$1	240	139	163	9.9553
GCCUCUCUUCAUCUGGAAGAAGAG	chr8:145152124-145152364(+)$1	240	199	223	11.9780
CAGUGACACUUCGCCGGUGUUCCA	chr9:71395154-71395394(+)$1	240	57	81	10.4234
AUUAGAAUAAUCUUUUUGUUUUAA	chr6:109321692-109321932(-)$1	240	31	55	11.1695
CACGGUGCCCGAGCUGGGGACUGA	chr19:55966928-55967168(-)$1	240	18	42	11.4261

#DB
((.((..(((.....)))..)).)	chr10:101489318-101489558(-)$1	1	2	26	11.4496
(.((((((((.....))))).)))	chr1:100176332-100176572(-)$1	1	113	137	12.0048
(((((.((((.....))))..)))	chr14:53327043-53327283(-)$1	1	158	182	12.5341
(...(((((......)))))....	chr1:113655013-113655253(+)$1	1	128	152	8.3113
((.(((..((((...))))..)))	chr4:76407651-76407891(-)$1	1	59	83	7.9717
((...(((((.....).)))))))	chr19:7690785-7691025(-)$1	1	140	164	12.5791
.(((((((.(.....).)))))))	chr14:69350807-69351047(-)$1	1	84	108	11.0323
(((((..(((.....)))))))))	chr19:3983145-3983385(-)$1	1	59	83	10.2373
(.(((.((((.....))))))).)	chr4:1696402-1696642(-)$1	1	142	166	13.0069
((((....((.....))....)))	chr17:34173828-34174071(+)$1	1	173	197	11.3868
(.(((.((((.....))))..)))	chr2:86279932-86280172(-)$1	1	212	236	13.4455
((((...(((.....)))..))))	chr12:14923831-14924071(-)$1	1	117	141	12.1970
...(((((((.....)))))))))	chr14:59113338-59113578(+)$1	1	102	126	11.5895
((((((((((.....))).)))))	chr17:62495976-62496217(-)$1	1	10	34	12.3304
)(((((.(((.....)))..))))	chr11:64787813-64788053(+)$1	1	116	140	11.4906
(((..(((((.....)))))))).	chr14:102486245-102486485(+)$1	1	197	221	12.1145
((((((((((.....)))))))))	chr11:43343521-43343761(+)$1	1	98	122	12.6738
((((((.(((.....))).)))))	chr22:50962711-50962951(-)$1	1	212	236	12.4340
(.((.(((((.....))))).)).	chr14:50360528-50360768(+)$1	1	214	238	10.9875
(((((((((......)))))))))	chr1:95364906-95365146(-)$1	1	54	78	9.0315
((....((((.....))))....)	chr1:90058265-90058505(+)$1	1	17	41	13.0763
(..(((((((.....)))))))..	chr5:162943518-162943758(+)$1	1	20	44	11.5283
(((.(((..(.....)..))).))	chr8:37555889-37556169(+)$1	1	206	230	10.8955
(.((((((.(.....).)))))).	chr16:71807106-71807357(-)$1	1	19	43	10.8349
((((..(((((...)))))...))	chr3:156271379-156271619(-)$1	1	67	91	7.6486
((((.(((((.....))))).)))	chr3:28381917-28382157(-)$1	1	129	153	11.3059
(((..(((((.....)))).)..)	chr18:43698139-43698379(+)$1	1	134	158	12.9337
(....(((((.....).))))...	chr22:39909628-39909868(+)$1	1	150	174	12.5487
((((...(((.....)))...)))	chr17:7218962-7219242(-)$1	1	41	65	12.4212
(.((....((.....)))).))))	chr19:5691462-5691702(+)$1	1	135	159	10.0015
((((..((((......)))).)))	chr17:4849873-4850125(-)$1	1	44	68	8.6721
((((((((((.....)))))))))	chr9:115030235-115030475(-)$1	1	2	26	12.6738
((..(((.((.....)))))))))	chr17:18110052-18110292(+)$1	1	175	199	10.7597
.(((.((((......))))..)))	chr1:112999821-113000061(+)$1	1	190	214	8.4834
(((((.((((.....)))).))))	chr7:26232051-26232291(-)$1	1	47	71	12.3504
((((...(((......)))..)))	chr2:219508416-219508656(-)$1	1	117	141	8.3669
..(((.((((.....)))).))).	chr12:121855427-121855667(+)$1	1	3	27	13.0748
((.(..((((.....))))..)..	chr2:230910512-230910752(-)$1	1	119	143	13.4686
(((..(((((.....))).))..)	chr14:45414411-45414693(-)$1	1	51	75	10.3653
.(((..((((.....))))..)))	chr14:91937113-91937353(-)$1	1	144	168	12.5942
((.(((((.(.....).)))))))	chr6:31498559-31498799(-)$1	1	97	121	11.0605
(.((((.(((.....))).)))).	chr10:112362244-112362484(+)$1	1	107	131	11.2950
((.((.((((.....)))))).))	chr19:7083323-7083563(+)$1	1	77	101	11.7322
((((((((((.....)))).))))	chr7:27839569-27839809(+)$1	1	143	167	10.8283
(((.(.((((.....)))).).))	chr18:55217918-55218158(-)$1	1	139	163	13.3471
(....(((((.....)))))....	chr2:109400132-109400372(+)$1	1	109	133	12.1511
(....((((......))))..)))	chr6:44220928-44221168(+)$1	1	165	189	9.1759
((((((((((.....))).)).))	chr6:30619095-30619335(+)$1	1	108	132	10.6207
....(((.((.....)).))).))	chr1:16268338-16268578(-)$1	1	139	163	9.9553
((((((((((.....)))).))))	chr8:145152124-145152364(+)$1	1	199	223	11.9780
..(.((((((.....)))))).))	chr9:71395154-71395394(+)$1	1	57	81	10.4234
.(((((((((.....)))))))))	chr6:109321692-109321932(-)$1	1	31	55	11.1695
..((((.(((.....))).)))).	chr19:55966928-55967168(-)$1	1	18	42	11.4261

#PSSM
f : 0.16	d : 0.15	c : 0.15	e : 0.13	: : 0.07	b : 0.07	= : 0.05	! : 0.05	g : 0.03	h : 0.03	a : 0.01	# : 0.01	$ : 0.01	
f : 0.16	[ : 0.13	c : 0.13	e : 0.11	d : 0.09	# : 0.07	! : 0.07	g : 0.05	= : 0.05	h : 0.03	" : 0.01	$ : 0.01	i : 0.01	
c : 0.18	f : 0.13	[ : 0.09	e : 0.09	# : 0.09	d : 0.07	g : 0.05	= : 0.05	" : 0.03	b : 0.03	! : 0.03	h : 0.03	$ : 0.01	a : 0.01	i : 0.01	
c : 0.15	f : 0.13	g : 0.09	e : 0.09	b : 0.07	! : 0.07	# : 0.07	d : 0.07	= : 0.05	[ : 0.05	" : 0.03	a : 0.01	h : 0.01	$ : 0.01	i : 0.01	
c : 0.15	! : 0.13	f : 0.11	# : 0.11	g : 0.09	e : 0.07	" : 0.07	= : 0.05	[ : 0.05	b : 0.03	d : 0.03	h : 0.01	a : 0.01	i : 0.01	
e : 0.15	[ : 0.13	! : 0.11	d : 0.11	g : 0.09	c : 0.07	# : 0.05	" : 0.05	= : 0.05	f : 0.05	b : 0.03	a : 0.01	h : 0.01	i : 0.01	
d : 0.33	e : 0.15	g : 0.07	[ : 0.07	! : 0.05	" : 0.05	= : 0.05	c : 0.05	# : 0.03	f : 0.03	b : 0.03	i : 0.01	
d : 0.33	c : 0.22	e : 0.15	g : 0.05	= : 0.05	! : 0.03	# : 0.03	f : 0.03	[ : 0.03	i : 0.01	
d : 0.35	c : 0.22	e : 0.13	b : 0.07	[ : 0.05	= : 0.05	g : 0.03	! : 0.01	f : 0.01	i : 0.01	
d : 0.28	c : 0.22	e : 0.11	a : 0.11	o : 0.07	b : 0.07	g : 0.03	= : 0.03	f : 0.01	i : 0.01	
n : 0.84	o : 0.11	d : 0.01	e : 0.01	
n : 0.84	o : 0.11	d : 0.01	l : 0.01	
n : 0.84	o : 0.11	l : 0.03	
n : 0.84	o : 0.11	l : 0.03	
n : 0.84	o : 0.11	l : 0.01	e : 0.01	
d : 0.30	c : 0.20	e : 0.13	a : 0.11	b : 0.07	= : 0.05	g : 0.03	o : 0.03	f : 0.01	i : 0.01	
d : 0.32	c : 0.22	e : 0.13	] : 0.09	b : 0.07	= : 0.05	g : 0.03	2 : 0.01	f : 0.01	i : 0.01	
d : 0.35	c : 0.24	e : 0.15	g : 0.05	= : 0.05	f : 0.03	4 : 0.01	2 : 0.01	b : 0.01	] : 0.01	i : 0.01	
d : 0.35	e : 0.16	] : 0.11	c : 0.07	2 : 0.05	g : 0.05	= : 0.05	f : 0.03	4 : 0.01	3 : 0.01	b : 0.01	i : 0.01	
2 : 0.20	e : 0.15	] : 0.13	d : 0.09	g : 0.09	c : 0.07	= : 0.05	b : 0.05	4 : 0.03	f : 0.03	3 : 0.03	i : 0.01	
2 : 0.15	f : 0.11	d : 0.09	g : 0.09	c : 0.09	b : 0.07	] : 0.07	4 : 0.07	e : 0.05	= : 0.05	3 : 0.03	a : 0.03	h : 0.01	i : 0.01	
c : 0.18	f : 0.11	] : 0.11	d : 0.11	g : 0.09	e : 0.09	4 : 0.05	= : 0.05	b : 0.03	3 : 0.03	2 : 0.03	a : 0.01	h : 0.01	i : 0.01	
c : 0.18	f : 0.16	d : 0.16	e : 0.09	4 : 0.05	g : 0.05	= : 0.05	2 : 0.05	] : 0.03	3 : 0.03	b : 0.01	h : 0.01	a : 0.01	i : 0.01	
c : 0.18	d : 0.16	f : 0.16	] : 0.09	e : 0.07	g : 0.05	= : 0.05	4 : 0.03	2 : 0.03	3 : 0.03	h : 0.03	J : 0.01	i : 0.01	

#score	597.9778998735432
#seq	53
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_UTR_m2_run1.txt

#BEAR
ddd[bbtttttttttttbbdddd	chr19:41096958-41097186(+)$1	228	49	72	20.6474
hheeeeettttttttttteeeee	chr3:69126937-69127158(-)$1	221	137	160	21.3123
c:eeeeettttttttttteeeee	chr21:33104063-33104287(-)$1	224	112	135	20.7525
fff[bbyyyyyyyyyyyyyyyyb	chr12:51102217-51102442(+)$1	225	13	36	19.5873
ccccccvvvvvvvvvvvvvccc]	chr7:27788036-27788272(+)$1	236	149	172	23.0117
fffffwwwwwwwwwwwwwwffff	chr19:3976160-3976388(-)$1	228	152	175	21.4050
fffffwwwwwwwwwwwwwwffff	chr17:48814249-48814487(+)$1	238	35	58	21.4050
ffffyyyyyyyyyyyyyyyyfff	chr17:26918704-26918955(-)$1	251	183	206	20.8842
eeeeevvvvvvvvvvvvveeeee	chr1:110032616-110032840(+)$1	224	61	84	22.3995
eeeeewwwwwwwwwwwwwweeee	chr19:2430493-2430721(-)$1	228	199	222	21.9385
[eeeeewwwwwwwwwwwwwweee	chr19:41800362-41800585(+)$1	223	79	102	21.9404
ffffffuuuuuuuuuuuufffff	chr17:73895581-73895812(-)$1	231	4	27	22.2596
!!cccattttttttttta]ccc2	chr19:46119961-46120189(-)$1	228	124	147	22.5092
'ddddwwwwwwwwwwwwwwdddd	chr12:46760952-46761182(-)$1	230	162	185	21.1921
fffffwwwwwwwwwwwwwwffff	chr7:97481400-97481624(-)$1	224	191	214	21.4050
iiiiixxxxxxxxxxxxxxxiii	chr19:1269277-1269501(+)$1	224	10	33	17.6855
[bb[bbuuuuuuuuuuuubb]bb	chr9:95050307-95050529(-)$1	222	27	50	21.5351
ff[ccctttttttttttccc]ff	chr19:10216979-10217202(+)$1	223	168	191	21.7718
ffffffvvvvvvvvvvvvvffff	chr12:49719772-49720016(+)$1	244	129	152	21.9748
C:cccvvvvvvvvvvvvvcccbb	chr6:91296632-91296862(-)$1	230	42	65	20.2322
eeeeebbtttttttttttbb]ee	chr7:150731384-150731605(+)$1	221	40	63	21.0923
[eeeeevvvvvvvvvvvvveeee	chr6:42627413-42627639(+)$1	226	45	68	22.9089
hh[cccuuuuuuuuuuuuccc44	chr14:24658559-24658787(-)$1	228	132	155	23.0671
bb[cccuuuuuuuuuuuuccc]b	chr22:45599737-45599963(-)$1	226	146	169	22.7652
###ddddtttttttttttdddd2	chrX:57002866-57003106(-)$1	240	75	98	21.2224
deeeeettttttttttteeeee3	chr12:49719530-49719767(+)$1	237	5	28	21.3783
eeeddddtttttttttttdddd]	chrX:20252774-20253027(-)$1	253	29	52	21.3790
!!cccvvvvvvvvvvvvvccc22	chr19:46055234-46055458(-)$1	224	16	39	22.7379
[eeeeettttttttttteeeee]	chr7:131241183-131241411(-)$1	228	120	143	21.6876
!!cccvvvvvvvvvvvvvccc]f	chr1:150293900-150294124(+)$1	224	166	189	23.1397
$cccyyyyyyyyyyyyyyyyccc	chr10:94297098-94297318(-)$1	220	43	66	21.2784
[cccwwwwwwwwwwwwwwccc]b	chr17:74731060-74731313(-)$1	253	53	76	21.7017
dd[cccuuuuuuuuuuuuccc]d	chr21:44299502-44299724(-)$1	222	11	34	23.2598
!cccwwwwwwwwwwwwwwccc]c	chr10:116622008-116622231(+)$1	223	96	119	21.9274
dd[cccvvvvvvvvvvvvvcccd	chrX:70504148-70504395(+)$1	247	177	200	22.7531
ffffffuuuuuuuuuuuufffff	chr10:129896264-129896497(-)$1	233	112	135	22.2596
dddccctttttttttttccc]dd	chr14:53417162-53417391(-)$1	229	107	130	21.6619
eeeeyyyyyyyyyyyyyyyyeee	chr5:137495672-137495903(-)$1	231	206	229	21.2404
!!ddddwwwwwwwwwwwwwwddd	chr6:86322348-86322588(-)$1	240	128	151	21.8017
!!cccxxxxxxxxxxxxxxxccc	chr1:100598306-100598531(-)$1	225	145	168	18.3033
!bb[bbwwwwwwwwwwwwwwbb]	chrX:119763735-119763958(-)$1	223	36	59	20.4854
!!eeeeettttttttttteeeee	chr19:2271719-2271951(+)$1	232	139	162	22.0400
g[dddduuuuuuuuuuuuddddg	chr15:64979759-64979985(-)$1	226	51	74	22.9323
dddcccuuuuuuuuuuuuccc::	chr4:41266026-41266261(+)$1	235	180	203	21.3981
gggggguuuuuuuuuuuuggggg	chr7:148516602-148516825(-)$1	223	148	171	22.8254
gggggguuuuuuuuuuuuggggg	chr10:33468585-33468814(-)$1	229	139	162	22.8254
gggggggtttttttttttggggg	chr7:102950693-102950913(+)$1	220	177	200	21.2928
ceeeeeuuuuuuuuuuuueeeee	chr1:224605942-224606162(-)$1	220	132	155	23.0417
ccc[ccctttttttttttccccc	chr3:15106616-15106840(-)$1	224	73	96	22.1726
ddddwwwwwwwwwwwwwwdddd:	chr19:45922257-45922482(-)$1	225	201	224	20.1457
cc"""bbtttttttttttbb]cc	chr1:8921156-8921377(-)$1	221	176	199	20.7135
d[dddduuuuuuuuuuuuddddd	chr10:93272203-93272428(+)$1	225	14	37	22.7430
$$$ccctttttttttttccc444	chr13:75923272-75923500(-)$1	228	52	75	21.2729
::ddddvvvvvvvvvvvvvdddd	chr16:23701310-23701535(+)$1	225	94	117	20.5254
[eeeeeuuuuuuuuuuuueeeee	chr17:62496686-62496940(-)$1	254	163	186	23.2713
=======ttttttttttt=====	chr5:145890508-145890735(+)$1	227	62	85	21.6684
##eeeeettttttttttteeeee	chr1:113161447-113161672(-)$1	225	117	140	21.7897
ggggggvvvvvvvvvvvvvgggg	chr19:45882916-45883142(-)$1	226	75	98	22.4998
ffffyyyyyyyyyyyyyyyyfff	chr16:24826484-24826711(+)$1	227	13	36	20.8842
$$ddddvvvvvvvvvvvvvdddd	chr6:43588427-43588655(-)$1	228	125	148	22.1734
[cccyyyyyyyyyyyyyyyyccc	chr20:36662096-36662338(+)$1	242	97	120	21.5626
ddddddvvvvvvvvvvvvvdddd	chr6:83906959-83907180(+)$1	221	83	106	22.2243
!!dddduuuuuuuuuuuudddd2	chr2:228419150-228419373(+)$1	223	145	168	23.0037

#otherMatches

#Seq PSSM
UGGGCCAGACCUCCGACGGCCAC	chr19:41096958-41097186(+)$1	228	49	72	20.6474
CUGGAACCAUGUAAAGAAGUUCC	chr3:69126937-69127158(-)$1	221	137	160	21.3123
CCGCCCGCCUCGCCGCUUCGGGC	chr21:33104063-33104287(-)$1	224	112	135	20.7525
AAUUGCUGUGUUUUCUGUGUCUG	chr12:51102217-51102442(+)$1	225	13	36	19.5873
GCCCAUGUCAUCUUUCAAAAUGU	chr7:27788036-27788272(+)$1	236	149	172	23.0117
AUUUUAACAAACGCAUUAAGAGG	chr19:3976160-3976388(-)$1	228	152	175	21.4050
AGCAAUUUUUUAAGUACCUUUGU	chr17:48814249-48814487(+)$1	238	35	58	21.4050
GUCCCUCACCCAGAAACCCAGGA	chr17:26918704-26918955(-)$1	251	183	206	20.8842
GGAGGGGACAUCUGACGACCUCC	chr1:110032616-110032840(+)$1	224	61	84	22.3995
GUGGGUUUUUUUAAGGCUUUCUA	chr19:2430493-2430721(-)$1	228	199	222	21.9385
CUCACCAAUUCCUGCCCGCAGGU	chr19:41800362-41800585(+)$1	223	79	102	21.9404
CACUCCUGCUGCCUCCCUGGAGU	chr17:73895581-73895812(-)$1	231	4	27	22.2596
ACAGACGGCAAUGAACAGAUCUC	chr19:46119961-46120189(-)$1	228	124	147	22.5092
CAAUGUAUACCUAUCAUUUUAUU	chr12:46760952-46761182(-)$1	230	162	185	21.1921
CUGUAGUCAUUUAUGUUCAUGCA	chr7:97481400-97481624(-)$1	224	191	214	21.4050
CCGGCGGAAGCGUAUAUAAGGCC	chr19:1269277-1269501(+)$1	224	10	33	17.6855
CGGGUACAAUUAAAGAUAUAGUU	chr9:95050307-95050529(-)$1	222	27	50	21.5351
CGCUGACCCUUUGUCUCUCGUCG	chr19:10216979-10217202(+)$1	223	168	191	21.7718
GUUUCCAGGAGCUAAGAAGGGAG	chr12:49719772-49720016(+)$1	244	129	152	21.9748
AACCGGAAGUGUAGUGGGCGGGG	chr6:91296632-91296862(-)$1	230	42	65	20.2322
CGUGGCCAAGUACACAAGGGACC	chr7:150731384-150731605(+)$1	221	40	63	21.0923
GACAAUUCGUUACAUGUAUAUUG	chr6:42627413-42627639(+)$1	226	45	68	22.9089
UCCGGUAUAUCUAUGUUAACCUC	chr14:24658559-24658787(-)$1	228	132	155	23.0671
UGGUGGCUAGUGACAAAACCAAC	chr22:45599737-45599963(-)$1	226	146	169	22.7652
ACAAGUUUUUCUCUACCUAACUG	chrX:57002866-57003106(-)$1	240	75	98	21.2224
CGGGCCUCUGCAUAUUUGGCCCC	chr12:49719530-49719767(+)$1	237	5	28	21.3783
CUUCAUUUAACUUUAACUGAUGU	chrX:20252774-20253027(-)$1	253	29	52	21.3790
AAUCAUUGUACCUUCCCUUGAGA	chr19:46055234-46055458(-)$1	224	16	39	22.7379
AGCGGCAGGGAGGAAGAGCCGCC	chr7:131241183-131241411(-)$1	228	120	143	21.6876
AGGGUAAUUCCAGUCCGCGCCAC	chr1:150293900-150294124(+)$1	224	166	189	23.1397
AUCCAGCCAUCAAGAGAAUAGGA	chr10:94297098-94297318(-)$1	220	43	66	21.2784
UUCUUUCUUUUCAAACCUAGAUG	chr17:74731060-74731313(-)$1	253	53	76	21.7017
GUGGGGUAUACGUCAUCUCUCGG	chr21:44299502-44299724(-)$1	222	11	34	23.2598
UGAGAACCUUUUUCCCCCCUCUC	chr10:116622008-116622231(+)$1	223	96	119	21.9274
guugccagacaaaacaccgggca	chrX:70504148-70504395(+)$1	247	177	200	22.7531
UCUCUGUGUUCCCCAAAUCAGAG	chr10:129896264-129896497(-)$1	233	112	135	22.2596
GGCUCUGGACGGGAUAAGGAUGC	chr14:53417162-53417391(-)$1	229	107	130	21.6619
CAAGGACCCUUAUGUUACUACUU	chr5:137495672-137495903(-)$1	231	206	229	21.2404
UACGGGACAUUGAACUAAUACUU	chr6:86322348-86322588(-)$1	240	128	151	21.8017
GAGGCAGCGAGCCAACAUGAGCC	chr1:100598306-100598531(-)$1	225	145	168	18.3033
CCUGGCGCUCCCCACCUUUAGCG	chrX:119763735-119763958(-)$1	223	36	59	20.4854
GACGCCAAACGCAUUAACUGGCG	chr19:2271719-2271951(+)$1	232	139	162	22.0400
GCGCUGGGAGUGUAGAAGUGGCC	chr15:64979759-64979985(-)$1	226	51	74	22.9323
UGUGCCUCACAAUUCUUUGGCUA	chr4:41266026-41266261(+)$1	235	180	203	21.3981
GUGCCUAAUUAUUGCAGAGGGUA	chr7:148516602-148516825(-)$1	223	148	171	22.8254
UUUGGAAACUGAGCGAAAUCCAA	chr10:33468585-33468814(-)$1	229	139	162	22.8254
UUUGUGAAUCAUCCACUGUUGCA	chr7:102950693-102950913(+)$1	220	177	200	21.2928
AUAUCACAAUACCAAACUUGAUA	chr1:224605942-224606162(-)$1	220	132	155	23.0417
AGCUAGUCCUUUCUCGUCGCUGC	chr3:15106616-15106840(-)$1	224	73	96	22.1726
GAGGAAAUGCAGCUAAAACCUCA	chr19:45922257-45922482(-)$1	225	201	224	20.1457
GCCCAAGUCAUUGUUUUUCUCGC	chr1:8921156-8921377(-)$1	221	176	199	20.7135
UCUGUCUCAAAACACUUUGACAA	chr10:93272203-93272428(+)$1	225	14	37	22.7430
CUUCCUGUAGGUUGAUGAGGUAA	chr13:75923272-75923500(-)$1	228	52	75	21.2729
CUGGUGCCCUCCUCACUCCCACC	chr16:23701310-23701535(+)$1	225	94	117	20.5254
UCUUUACACCUAAUAACAUAAAG	chr17:62496686-62496940(-)$1	254	163	186	23.2713
ACUCCAAGAAAACCCGAGUUGGG	chr5:145890508-145890735(+)$1	227	62	85	21.6684
AGGCUGUGUGAGAAUUUGGCAGC	chr1:113161447-113161672(-)$1	225	117	140	21.7897
CUGCUGACACCAUCUCUCCCAGC	chr19:45882916-45883142(-)$1	226	75	98	22.4998
AGUCUCCAUUUGUUCCCUAUGAC	chr16:24826484-24826711(+)$1	227	13	36	20.8842
CUGAGUUCCCCAUCCUACCACUC	chr6:43588427-43588655(-)$1	228	125	148	22.1734
GAGACCCAUCCCCUCCCCCUUCU	chr20:36662096-36662338(+)$1	242	97	120	21.5626
UGGGAAAAAAAAAAUCUAAUUCU	chr6:83906959-83907180(+)$1	221	83	106	22.2243
GAUCUUAGCUUUAAACACAAGAG	chr2:228419150-228419373(+)$1	223	145	168	23.0037

#DB
(((.((...........))))))	chr19:41096958-41097186(+)$1	1	49	72	20.6474
(((((((...........)))))	chr3:69126937-69127158(-)$1	1	137	160	21.3123
).(((((...........)))))	chr21:33104063-33104287(-)$1	1	112	135	20.7525
(((.((................)	chr12:51102217-51102442(+)$1	1	13	36	19.5873
((((((.............))).	chr7:27788036-27788272(+)$1	1	149	172	23.0117
(((((..............))))	chr19:3976160-3976388(-)$1	1	152	175	21.4050
(((((..............))))	chr17:48814249-48814487(+)$1	1	35	58	21.4050
((((................)))	chr17:26918704-26918955(-)$1	1	183	206	20.8842
(((((.............)))))	chr1:110032616-110032840(+)$1	1	61	84	22.3995
(((((..............))))	chr19:2430493-2430721(-)$1	1	199	222	21.9385
.(((((..............)))	chr19:41800362-41800585(+)$1	1	79	102	21.9404
((((((............)))))	chr17:73895581-73895812(-)$1	1	4	27	22.2596
..((((...........).))).	chr19:46119961-46120189(-)$1	1	124	147	22.5092
.((((..............))))	chr12:46760952-46761182(-)$1	1	162	185	21.1921
(((((..............))))	chr7:97481400-97481624(-)$1	1	191	214	21.4050
(((((...............)))	chr19:1269277-1269501(+)$1	1	10	33	17.6855
.((.((............)).))	chr9:95050307-95050529(-)$1	1	27	50	21.5351
((.(((...........))).))	chr19:10216979-10217202(+)$1	1	168	191	21.7718
((((((.............))))	chr12:49719772-49720016(+)$1	1	129	152	21.9748
(.(((.............)))((	chr6:91296632-91296862(-)$1	1	42	65	20.2322
(((((((...........)).))	chr7:150731384-150731605(+)$1	1	40	63	21.0923
.(((((.............))))	chr6:42627413-42627639(+)$1	1	45	68	22.9089
((.(((............)))..	chr14:24658559-24658787(-)$1	1	132	155	23.0671
((.(((............))).)	chr22:45599737-45599963(-)$1	1	146	169	22.7652
...((((...........)))).	chrX:57002866-57003106(-)$1	1	75	98	21.2224
((((((...........))))).	chr12:49719530-49719767(+)$1	1	5	28	21.3783
(((((((...........)))).	chrX:20252774-20253027(-)$1	1	29	52	21.3790
..(((.............)))..	chr19:46055234-46055458(-)$1	1	16	39	22.7379
.(((((...........))))).	chr7:131241183-131241411(-)$1	1	120	143	21.6876
..(((.............))).)	chr1:150293900-150294124(+)$1	1	166	189	23.1397
.(((................)))	chr10:94297098-94297318(-)$1	1	43	66	21.2784
.(((..............))).)	chr17:74731060-74731313(-)$1	1	53	76	21.7017
((.(((............))).)	chr21:44299502-44299724(-)$1	1	11	34	23.2598
.(((..............))).)	chr10:116622008-116622231(+)$1	1	96	119	21.9274
((.(((.............))))	chrX:70504148-70504395(+)$1	1	177	200	22.7531
((((((............)))))	chr10:129896264-129896497(-)$1	1	112	135	22.2596
((((((...........))).))	chr14:53417162-53417391(-)$1	1	107	130	21.6619
((((................)))	chr5:137495672-137495903(-)$1	1	206	229	21.2404
..((((..............)))	chr6:86322348-86322588(-)$1	1	128	151	21.8017
..(((...............)))	chr1:100598306-100598531(-)$1	1	145	168	18.3033
.((.((..............)).	chrX:119763735-119763958(-)$1	1	36	59	20.4854
..(((((...........)))))	chr19:2271719-2271951(+)$1	1	139	162	22.0400
(.((((............)))))	chr15:64979759-64979985(-)$1	1	51	74	22.9323
)))(((............)))..	chr4:41266026-41266261(+)$1	1	180	203	21.3981
((((((............)))))	chr7:148516602-148516825(-)$1	1	148	171	22.8254
((((((............)))))	chr10:33468585-33468814(-)$1	1	139	162	22.8254
(((((((...........)))))	chr7:102950693-102950913(+)$1	1	177	200	21.2928
((((((............)))))	chr1:224605942-224606162(-)$1	1	132	155	23.0417
(((.(((...........)))))	chr3:15106616-15106840(-)$1	1	73	96	22.1726
((((..............)))).	chr19:45922257-45922482(-)$1	1	201	224	20.1457
((...((...........)).))	chr1:8921156-8921377(-)$1	1	176	199	20.7135
(.((((............)))))	chr10:93272203-93272428(+)$1	1	14	37	22.7430
...(((...........)))...	chr13:75923272-75923500(-)$1	1	52	75	21.2729
..((((.............))))	chr16:23701310-23701535(+)$1	1	94	117	20.5254
.(((((............)))))	chr17:62496686-62496940(-)$1	1	163	186	23.2713
(((((((...........)))))	chr5:145890508-145890735(+)$1	1	62	85	21.6684
..(((((...........)))))	chr1:113161447-113161672(-)$1	1	117	140	21.7897
((((((.............))))	chr19:45882916-45883142(-)$1	1	75	98	22.4998
((((................)))	chr16:24826484-24826711(+)$1	1	13	36	20.8842
..((((.............))))	chr6:43588427-43588655(-)$1	1	125	148	22.1734
.(((................)))	chr20:36662096-36662338(+)$1	1	97	120	21.5626
((((((.............))))	chr6:83906959-83907180(+)$1	1	83	106	22.2243
..((((............)))).	chr2:228419150-228419373(+)$1	1	145	168	23.0037

#PSSM
f : 0.15	d : 0.14	! : 0.14	[ : 0.11	c : 0.07	e : 0.07	g : 0.07	$ : 0.04	h : 0.03	# : 0.03	' : 0.01	i : 0.01	C : 0.01	b : 0.01	: : 0.01	= : 0.01	
e : 0.17	f : 0.15	d : 0.12	c : 0.11	! : 0.11	g : 0.06	: : 0.04	b : 0.04	h : 0.03	# : 0.03	[ : 0.03	$ : 0.03	i : 0.01	= : 0.01	
e : 0.23	d : 0.19	c : 0.17	f : 0.14	[ : 0.07	g : 0.06	b : 0.03	i : 0.01	# : 0.01	" : 0.01	$ : 0.01	= : 0.01	
c : 0.28	e : 0.22	d : 0.17	f : 0.12	[ : 0.07	g : 0.06	i : 0.01	" : 0.01	= : 0.01	
c : 0.23	e : 0.20	d : 0.15	f : 0.09	y : 0.07	b : 0.06	g : 0.06	w : 0.04	i : 0.01	" : 0.01	= : 0.01	
e : 0.15	c : 0.15	d : 0.14	w : 0.12	b : 0.09	y : 0.07	v : 0.06	g : 0.06	f : 0.04	x : 0.03	a : 0.01	= : 0.01	
u : 0.22	v : 0.19	w : 0.17	t : 0.11	y : 0.09	e : 0.06	x : 0.03	b : 0.03	d : 0.03	g : 0.01	c : 0.01	= : 0.01	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
t : 0.28	u : 0.22	v : 0.19	w : 0.17	y : 0.09	x : 0.03	
u : 0.22	v : 0.19	t : 0.17	w : 0.17	y : 0.09	c : 0.04	x : 0.03	e : 0.03	b : 0.01	a : 0.01	
c : 0.20	e : 0.14	v : 0.12	w : 0.12	y : 0.09	d : 0.09	b : 0.06	g : 0.04	f : 0.03	x : 0.03	] : 0.01	= : 0.01	
c : 0.25	d : 0.17	e : 0.17	y : 0.09	f : 0.09	g : 0.06	w : 0.04	b : 0.04	x : 0.03	= : 0.01	
c : 0.25	e : 0.20	d : 0.19	f : 0.12	] : 0.07	g : 0.06	y : 0.01	i : 0.01	b : 0.01	4 : 0.01	= : 0.01	
e : 0.22	d : 0.20	f : 0.14	c : 0.12	] : 0.07	g : 0.06	b : 0.04	4 : 0.03	y : 0.01	i : 0.01	2 : 0.01	: : 0.01	= : 0.01	
e : 0.19	d : 0.15	f : 0.15	c : 0.09	b : 0.07	g : 0.07	] : 0.06	2 : 0.06	4 : 0.03	: : 0.03	i : 0.01	3 : 0.01	= : 0.01	

#score	1366.909463932237
#seq	63
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_UTR_m2_run2.txt

#BEAR
gg!!accc"""cccnnnnncccccc]a22ggggggg]ee	chr9:133762447-133762648(+)$1	201	65	104	11.8377
eeeggggggg"""cccoooooocccgggggggeeeeebb	chr1:22050709-22050910(-)$1	201	95	134	14.0013
"""ffffff!!eeeeeooooooeeeee4444ffffff33	chr2:29397241-29397442(+)$1	201	18	57	14.6113
%%%%dddd!!a"""bboooooobb22a22ddddgggggg	chr15:78833129-78833330(+)$1	201	36	75	11.0658
a[ffffff"""eeeeeooooooeeeee>>>>>>>>>>>>	chr6:170159876-170160077(+)$1	201	93	132	11.2151
eeeee[ffffffbb[aooooooa]bb22ffffff]eeee	chr16:27472241-27472442(-)$1	201	157	196	11.8289
####ggggggg[ddddoooooodddd333ggggggg444	chr15:52517054-52517255(-)$1	201	37	76	17.6550
!!bb[bb[ffffff[aooooooa]ffffff]bb]bb]dd	chr8:48869832-48870033(-)$1	201	44	83	11.2313
ffffff!!a"""eeeeennnnneeeee22a22ffffffa	chr22:46758091-46758292(-)$1	201	40	79	11.4628
cc!!============oooooo============]ccc]	chr11:1010896-1011097(+)$1	201	138	177	15.9975
[ccc[ffffff[bb[aooooooa]bb]ffffff]ccccc	chr19:5895215-5895416(-)$1	201	38	77	13.3350
hhggggggg[ddddcccnnnnnccc4444dddd]ggggg	chr16:22345337-22345538(+)$1	201	28	67	12.5409
eeeee[dddd"""a[cccmmmmccca333ddddeeeeec	chr9:90264776-90264977(+)$1	201	94	133	11.0191
========[gggggggmmmmggggggg]===========	chr5:148884482-148884683(-)$1	201	113	152	11.8258
!!ccc[ccc!!eeeeennnnneeeee333cccccc22ee	chr17:65734152-65734353(+)$1	201	115	154	13.3417
gggccc!!ccc"""cccnnnnnccc333ccc333ccc]g	chr17:79801161-79801362(-)$1	201	75	114	14.2281
####ffffff[ccc[bblllbb]ccc]ffffffdddd]c	chr16:30064481-30064682(+)$1	201	29	68	11.1069
dd####dddd[cccnnnnncccdddd333dddd22ccc]	chr15:23033258-23033459(-)$1	201	106	145	10.4137
dbbeeeeebb"""cccooooooccc333bb]eeeee]bb	chr16:1715994-1716195(+)$1	201	136	175	13.6104
!!a[==========lll==========22a22bb]bb]b	chr10:89623542-89623743(+)$1	201	150	189	11.2617
dd"""===========oooooo===========dddd::	chr7:105192025-105192226(+)$1	201	134	173	13.3965
"""bb"""gggggggooooooggggggg333bb22bb]e	chr10:74113930-74114131(-)$1	201	153	192	12.3335
####ccc$$$$$ccc[bbmmmmbbccc4444cccfffff	chr8:38684623-38684824(+)$1	201	57	96	10.7239
=========bb!!ccclllccc22bb4444=========	chr11:790885-791086(-)$1	201	75	114	13.1236
####dddd!!bb!!ccclllccc22bb333ddddbb444	chr7:138982520-138982721(+)$1	201	49	88	11.4311
c"""eeeeecccccc!!ccclllccc22ccc]ccc]eee	chr15:75659805-75660006(-)$1	201	141	180	10.7776
g!!ggggggg!!bb[cccnnnnnccc]bbggggggg333	chr5:43613005-43613206(+)$1	201	74	113	12.8184
[============ddddnnnnndddd]============	chr7:99015819-99016020(+)$1	201	103	142	14.8638
!ggggggg!!bb[arrrrrrrrra]bb22ggggggg22f	chr19:15221143-15221344(+)$1	201	118	157	11.5074
[ccc[cccccc!!ccc[cccmmmmccc22ccc]ccc]cc	chr5:154195029-154195230(+)$1	201	149	188	10.4957
ccccffffff!!ddddoooooodddd22ffffff22ccc	chr1:185278457-185278658(-)$1	201	15	54	14.4897
ggg[ccc[bb!!ddddllldddd]bb]cccgggggggbb	chr10:75012169-75012370(-)$1	201	155	194	11.2774
cc!!ffffffccccccnnnnnccc]ccc]ffffff22cc	chr16:2757801-2758002(+)$1	201	25	64	12.4734
b####ffffff!!bboooooobb]ffffff]bb]dddd2	chr16:24826373-24826574(+)$1	201	128	167	11.1954
[ffffff[a[a[ddddoooooodddd]aaffffff333b	chr1:1189483-1189684(-)$1	201	83	122	14.8377
========ccc[cccooooooccc]ccc]==========	chrX:154306934-154307135(+)$1	201	162	201	15.1003
=!!bb!!ccc"""ddddmmmmdddd4444cccbb]====	chr19:47113820-47114021(+)$1	201	135	174	13.0529
####iiiiiiiiicccooooooccc]iiiiiiiii22bb	chr3:184019317-184019518(+)$1	201	22	61	15.6032
c!!ffffff"""ddddrrrrrrrrrddddffffff22cc	chr12:56633385-56633586(-)$1	201	5	44	11.3824
###eeeeea[ddddrrrrrrrrrdddd22a]eeeee333	chr2:242203907-242204108(-)$1	201	84	123	11.8880
c"""a[ffffff[cccoooooocccffffffa]ccc:::	chr3:15262285-15262486(+)$1	201	72	111	11.8542
[ccc[ffffff[ddddooooooddddffffff]cccbb:	chr20:57253942-57254143(+)$1	201	75	114	12.7209
ddd"""dddd"""eeeeellleeeee333dddd]dddd:	chr3:54798262-54798463(+)$1	201	127	166	10.3720
!eeeee[a[bb[ddddoooooodddd]bba]eeeeeccc	chr5:34911757-34911958(-)$1	201	56	95	13.0142
"""ccc[dddd!!ddddnnnnndddd22dddd22ccc==	chr18:2728425-2728626(+)$1	201	72	111	12.9897
iiiiiii####ccc!!cccmmmmccc333ccciiiiiii	chr17:80349506-80349707(-)$1	201	82	121	12.3014
ggggg[bb[a!!ddddoooooodddd22abb]ggggggg	chr16:15695840-15696041(-)$1	201	142	181	14.6362
[ffffff!!bb"""cccnnnnnccc]bb22ffffff]cc	chr16:74487002-74487203(-)$1	201	132	171	12.0495
ggg####dddd[ddddnnnnndddd]ddddggggggg55	chr2:25042699-25042900(+)$1	201	142	181	10.4934
!!bb[a[ccc[bb!!cccnnnnnccc22bb]ccc]a]bb	chr19:12825857-12826058(-)$1	201	146	185	11.6082
[ccc!!dddd!!ddddnnnnndddd]dddd]cccbb===	chr17:66511175-66511376(+)$1	201	76	115	11.8675
####ccc$$$$$ddddnnnnndddd4444ccc4444fff	chr2:135815590-135815791(+)$1	201	111	150	13.7949
cc"""eeeee"""cccpppppppccc333eeeee]ccc]	chr16:31049235-31049436(+)$1	201	143	182	11.3757
c[iiiiiiiii[ddddmmmmddddiiiiiiiii]ccc::	chr9:136209792-136209993(-)$1	201	117	156	10.2354

#otherMatches

#Seq PSSM
GCCGCCCCUGAGGCUUCACGCCGGGAGAAGCCACCUUCC	chr9:133762447-133762648(+)$1	201	65	104	11.8377
gCACUGUGCAGACUCAGCAUUAUGGUGCACAGCUCCUUG	chr1:22050709-22050910(-)$1	201	95	134	14.0013
CAACUUCUGCUUCUUCCCAAAAGGAGAUUAACAGAAGAA	chr2:29397241-29397442(+)$1	201	18	57	14.6113
CUCAGGAGUUCGGUACGUGAAAGUUAGCUCUCCCGGAGG	chr15:78833129-78833330(+)$1	201	36	75	11.0658
GGGUCAGUUACUGAAGAGUUACCUUCAAAACACUAAACU	chr6:170159876-170160077(+)$1	201	93	132	11.2151
GUGGGAUACACCUUGCAGAAUAGGGAUCGGUGUGCCCCG	chr16:27472241-27472442(-)$1	201	157	196	11.8289
GACAGAGAUGAUAGAUUUUCUUAUCUUCCUUAUUUUGCA	chr15:52517054-52517255(-)$1	201	37	76	17.6550
UUACAGACAUCUUUAGUUUUUUCCAGAGAUUUCGGUUUG	chr8:48869832-48870033(-)$1	201	44	83	11.2313
CAGGGCAGUGCAGCACUAGGCAGGUGUGAGGAGCCCUGC	chr22:46758091-46758292(-)$1	201	40	79	11.4628
CCUUGGUGUGUGGCCGUCCUGGUGGCUGCACACCUGGCG	chr11:1010896-1011097(+)$1	201	138	177	15.9975
UGUGAGUCCCUUUAGGUCCUGGUGUGUGGGGACACACCU	chr19:5895215-5895416(-)$1	201	38	77	13.3350
UUUGUAAACUUAAUGCCAACAAGGUCUAAGUUAUGUUUA	chr16:22345337-22345538(+)$1	201	28	67	12.5409
CGGCUAUUACUCUGUGGCCAAAGCCCUUUGUGAAGCCGG	chr9:90264776-90264977(+)$1	201	94	133	11.0191
UUAUUUUGCAUGUUAAUGCUUUAGCAUUUAAAAUGGAAA	chr5:148884482-148884683(-)$1	201	113	152	11.8258
UGUUAAUAUGGAGUCAGUUUUUGACUAUAGUAUAAAUUC	chr17:65734152-65734353(+)$1	201	115	154	13.3417
CCCGGCACAGGCCUGGGCCUUCCCCUUCCCUCAAGCCAG	chr17:79801161-79801362(-)$1	201	75	114	14.2281
GUGAAUUGCCCGCGGCCCGAGGGUGCAGGUGAUGGGUGC	chr16:30064481-30064682(+)$1	201	29	68	11.1069
GGAAAUGAGAGUGAAUAAGUCAUCUCUAACCUCUCCCAG	chr15:23033258-23033459(-)$1	201	106	145	10.4137
CGAUCGUGCCCAAGGUCCUUCCACCCCAGGCCACGAGUC	chr16:1715994-1716195(+)$1	201	136	175	13.6104
GGCACCUCCCGCUCCUGGAGCGGGGGGGAGAAgcggcgg	chr10:89623542-89623743(+)$1	201	150	189	11.2617
UAUGUCUUUUAAGAUAUGACUUUGUUUUAAAAGUACUGU	chr7:105192025-105192226(+)$1	201	134	173	13.3965
ACCCACCCCAGUCCGCCGCCUCGGACUGUCCUGAAGCCG	chr10:74113930-74114131(-)$1	201	153	192	12.3335
CUCAGGAUGAAGGGGCAGUGAUCUCCCAGAUUUCAGACA	chr8:38684623-38684824(+)$1	201	57	96	10.7239
GCGGGCAUUGGGACCAGUGUGGAGCCUGAGGGUGCCUGC	chr11:790885-791086(-)$1	201	75	114	13.1236
GAAAUCUCAGUGACUGCCCAGCAAGCAAAGGAGACGAAA	chr7:138982520-138982721(+)$1	201	49	88	11.4311
GAGAACCUGUCCAGGUGAGGAACCCUGUCCUAGGGCCAG	chr15:75659805-75660006(-)$1	201	141	180	10.7776
GUCUCCUGCUGGUGUUCAGAACUUGGUCAAGCAGGGUUU	chr5:43613005-43613206(+)$1	201	74	113	12.8184
AAGUACCACUCCUAGGCCAGGCGCCUCAGGAGUGGUGCU	chr7:99015819-99016020(+)$1	201	103	142	14.8638
CCUGGAGCAGCGAGGCCAGGGUACAUGAAGCUUCAGAGC	chr19:15221143-15221344(+)$1	201	118	157	11.5074
GCUCACUCUCCAAUUGACCCGCCUGGGAACAAGGGAUGA	chr5:154195029-154195230(+)$1	201	149	188	10.4957
CCAAAUUUAUAAGGAAAAAUGAUUCCCAAUGGAUAUUUG	chr1:185278457-185278658(-)$1	201	15	54	14.4897
GCCACCGCGAGACGUUCCGGGCGGUCACGGGGCUCGGGA	chr10:75012169-75012370(-)$1	201	155	194	11.2774
ACCUCGCAGAGCUCCUGACAAAGGCGGCUUCUGCGUCGU	chr16:2757801-2758002(+)$1	201	25	64	12.4734
UCCAUUUGUUCCCUAUGACUUUAUGAACAGCAGUACUUC	chr16:24826373-24826574(+)$1	201	128	167	11.1954
AGAGCCAGCAGGGGCUGUUUCGGGCCGCGUGGCUCCCCG	chr1:1189483-1189684(-)$1	201	83	122	14.8377
AUUAUUUUGAUUUAUUUUAUUAUGUAUUAAAAGUAAUGA	chrX:154306934-154307135(+)$1	201	162	201	15.1003
UAAACCGGGCAAUAUUGUGUUCAGUUCAAGCUGUGAAGA	chr19:47113820-47114021(+)$1	201	135	174	13.0529
AUCAUCUCCGUUUUGGCCAUGACCAUGAGUGGGGAGCGU	chr3:184019317-184019518(+)$1	201	22	61	15.6032
CACCUUCUUACUCCCUGGACCUAGAAGGGGAGAAGAGGC	chr12:56633385-56633586(-)$1	201	5	44	11.3824
CCAGUUGCCACUCUAAAUUCAGAAGAGGAGAGCGACCCU	chr2:242203907-242204108(-)$1	201	84	123	11.8880
CCACCUCCAGUGAGAGCACAUUUUCCACUGGGCGCUAAU	chr3:15262285-15262486(+)$1	201	72	111	11.8542
AGGAGGCCUAGCAGGGCAGGCUCCCUCUGGGCAUCCCUG	chr20:57253942-57254143(+)$1	201	75	114	12.7209
GGGCCCUGGGAAAGAGGCUAAGCUUUACCCCCAUCCCCA	chr3:54798262-54798463(+)$1	201	127	166	10.3720
UUCGAAUGUGUUACCAAGGUUAUGGUUACCCUUUGAUGC	chr5:34911757-34911958(-)$1	201	56	95	13.0142
AGUUAUAGAAAAUGGAACAGCUUUCCCAUUUCAGGUGGA	chr18:2728425-2728626(+)$1	201	72	111	12.9897
AAGGGCCAGGGUCCGAGUGUCCUCACCAAGGAGGCUCUU	chr17:80349506-80349707(-)$1	201	82	121	12.3014
CAAGACCUACGGCCACAGCAGCGUGGAGGAGCUCUUGGG	chr16:15695840-15696041(-)$1	201	142	181	14.6362
CAGGUAGAGCCACCUUGACCACCAAAGGAACUACCUAUC	chr16:74487002-74487203(-)$1	201	132	171	12.0495
GGCCAUUGGGGAAGGUGGCUAGCUUAUCCCGCCCCUUCA	chr2:25042699-25042900(+)$1	201	142	181	10.4934
UCUGGAAGUGCGGAUUGACAGGCUCAUCCCCCACAUGCA	chr19:12825857-12826058(-)$1	201	146	185	11.6082
UCUGCAGAGGUUAGUGGCUCAUACUUCCUCCCAGGAGCU	chr17:66511175-66511376(+)$1	201	76	115	11.8675
ACCUCUAUUUUCCAGCCCUUUGCUGCAUUUGGCACAUUU	chr2:135815590-135815791(+)$1	201	111	150	13.7949
GCCCGCAGGGGCAGGUAAUCCCAACCCAACCCUGAGCCU	chr16:31049235-31049436(+)$1	201	143	182	11.3757
UGAGAGGGGUCCUGGGGUGUUUCAGACCCUUCUGGGCAU	chr9:136209792-136209993(-)$1	201	117	156	10.2354

#DB
((..((((...(((.....)))))).)..))))))).))	chr9:133762447-133762648(+)$1	1	65	104	11.8377
)))(((((((...(((......))))))))))(((((((	chr1:22050709-22050910(-)$1	1	95	134	14.0013
...((((((..(((((......)))))....))))))..	chr2:29397241-29397442(+)$1	1	18	57	14.6113
....((((..(...((......))..)..))))))))))	chr15:78833129-78833330(+)$1	1	36	75	11.0658
(.((((((...(((((......)))))............	chr6:170159876-170160077(+)$1	1	93	132	11.2151
(((((.((((((((.(......).))..)))))).))))	chr16:27472241-27472442(-)$1	1	157	196	11.8289
....(((((((.((((......))))...)))))))...	chr15:52517054-52517255(-)$1	1	37	76	17.6550
..((.((.((((((.(......).)))))).)).)).))	chr8:48869832-48870033(-)$1	1	44	83	11.2313
((((((..(...(((((.....)))))..)..)))))))	chr22:46758091-46758292(-)$1	1	40	79	11.4628
((..((((((((((((......)))))))))))).))).	chr11:1010896-1011097(+)$1	1	138	177	15.9975
.(((.((((((.((.(......).)).)))))).)))))	chr19:5895215-5895416(-)$1	1	38	77	13.3350
(((((((((.(((((((.....)))....)))).)))))	chr16:22345337-22345538(+)$1	1	28	67	12.5409
(((((.((((...(.(((....))))...))))))))))	chr9:90264776-90264977(+)$1	1	94	133	11.0191
((((((((.(((((((....))))))).)))))))))))	chr5:148884482-148884683(-)$1	1	113	152	11.8258
..(((.(((..(((((.....)))))...))))))..))	chr17:65734152-65734353(+)$1	1	115	154	13.3417
((((((..(((...(((.....)))...)))...))).)	chr17:79801161-79801362(-)$1	1	75	114	14.2281
....((((((.(((.((...)).))).)))))))))).)	chr16:30064481-30064682(+)$1	1	29	68	11.1069
((....((((.(((.....)))))))...))))..))).	chr15:23033258-23033459(-)$1	1	106	145	10.4137
((((((((((...(((......)))...)).))))).))	chr16:1715994-1716195(+)$1	1	136	175	13.6104
..(.((((((((((...))))))))))..)..)).)).)	chr10:89623542-89623743(+)$1	1	150	189	11.2617
((...(((((((((((......)))))))))))))))..	chr7:105192025-105192226(+)$1	1	134	173	13.3965
...((...(((((((......)))))))...))..)).)	chr10:74113930-74114131(-)$1	1	153	192	12.3335
....(((.....(((.((....)))))....))))))))	chr8:38684623-38684824(+)$1	1	57	96	10.7239
(((((((((((..(((...)))..))....)))))))))	chr11:790885-791086(-)$1	1	75	114	13.1236
....((((..((..(((...)))..))...))))))...	chr7:138982520-138982721(+)$1	1	49	88	11.4311
(...(((((((((((..(((...)))..))).))).)))	chr15:75659805-75660006(-)$1	1	141	180	10.7776
(..(((((((..((.(((.....))).)))))))))...	chr5:43613005-43613206(+)$1	1	74	113	12.8184
.((((((((((((((((.....)))).))))))))))))	chr7:99015819-99016020(+)$1	1	103	142	14.8638
.(((((((..((.(.........).))..)))))))..)	chr19:15221143-15221344(+)$1	1	118	157	11.5074
.(((.((((((..(((.(((....)))..))).))).))	chr5:154195029-154195230(+)$1	1	149	188	10.4957
((((((((((..((((......))))..))))))..)))	chr1:185278457-185278658(-)$1	1	15	54	14.4897
(((.(((.((..((((...)))).)).))))))))))))	chr10:75012169-75012370(-)$1	1	155	194	11.2774
((..((((((((((((.....))).))).))))))..))	chr16:2757801-2758002(+)$1	1	25	64	12.4734
(....((((((..((......)).)))))).)).)))).	chr16:24826373-24826574(+)$1	1	128	167	11.1954
.((((((.(.(.((((......)))).))))))))...)	chr1:1189483-1189684(-)$1	1	83	122	14.8377
(((((((((((.(((......))).))).))))))))))	chrX:154306934-154307135(+)$1	1	162	201	15.1003
(..((..(((...((((....))))....))))).))))	chr19:47113820-47114021(+)$1	1	135	174	13.0529
....((((((((((((......))).)))))))))..))	chr3:184019317-184019518(+)$1	1	22	61	15.6032
(..((((((...((((.........))))))))))..))	chr12:56633385-56633586(-)$1	1	5	44	11.3824
...((((((.((((.........))))..).)))))...	chr2:242203907-242204108(-)$1	1	84	123	11.8880
(...(.((((((.(((......)))))))))).)))...	chr3:15262285-15262486(+)$1	1	72	111	11.8542
.(((.((((((.((((......)))))))))).))))).	chr20:57253942-57254143(+)$1	1	75	114	12.7209
(((...((((...(((((...)))))...)))).)))).	chr3:54798262-54798463(+)$1	1	127	166	10.3720
.(((((.(.((.((((......)))).))).))))))))	chr5:34911757-34911958(-)$1	1	56	95	13.0142
...(((.((((..((((.....))))..))))..)))))	chr18:2728425-2728626(+)$1	1	72	111	12.9897
(((((((....(((..(((....)))...))))))))))	chr17:80349506-80349707(-)$1	1	82	121	12.3014
(((((.((.(..((((......))))..))).)))))))	chr16:15695840-15696041(-)$1	1	142	181	14.6362
.((((((..((...(((.....))).))..)))))).))	chr16:74487002-74487203(-)$1	1	132	171	12.0495
(((....((((.((((.....)))).)))))))))))..	chr2:25042699-25042900(+)$1	1	142	181	10.4934
..((.(.(((.((..(((.....)))..)).))).).))	chr19:12825857-12826058(-)$1	1	146	185	11.6082
.(((..((((..((((.....)))).)))).))))))))	chr17:66511175-66511376(+)$1	1	76	115	11.8675
....(((.....((((.....))))....)))....)))	chr2:135815590-135815791(+)$1	1	111	150	13.7949
((...(((((...(((.......)))...))))).))).	chr16:31049235-31049436(+)$1	1	143	182	11.3757
(.(((((((((.((((....))))))))))))).)))..	chr9:136209792-136209993(-)$1	1	117	156	10.2354

#PSSM
c : 0.14	# : 0.12	[ : 0.12	g : 0.11	! : 0.11	= : 0.07	d : 0.07	e : 0.05	" : 0.05	% : 0.01	a : 0.01	f : 0.01	h : 0.01	b : 0.01	i : 0.01	
# : 0.14	c : 0.14	! : 0.12	g : 0.11	" : 0.09	e : 0.07	= : 0.07	f : 0.05	d : 0.05	[ : 0.03	% : 0.01	h : 0.01	b : 0.01	i : 0.01	
# : 0.16	" : 0.12	! : 0.11	c : 0.11	g : 0.11	e : 0.07	f : 0.07	= : 0.07	b : 0.05	i : 0.03	% : 0.01	a : 0.01	d : 0.01	
# : 0.16	c : 0.14	f : 0.11	g : 0.09	e : 0.09	" : 0.09	b : 0.07	= : 0.07	! : 0.05	[ : 0.03	i : 0.03	% : 0.01	
f : 0.16	g : 0.11	e : 0.11	= : 0.11	c : 0.11	[ : 0.09	# : 0.05	" : 0.05	i : 0.05	a : 0.03	d : 0.03	b : 0.03	! : 0.01	
f : 0.22	c : 0.12	= : 0.12	g : 0.09	[ : 0.09	e : 0.09	i : 0.05	d : 0.03	# : 0.03	" : 0.03	! : 0.03	b : 0.01	a : 0.01	
f : 0.24	= : 0.12	c : 0.11	d : 0.11	g : 0.09	e : 0.07	! : 0.05	i : 0.05	[ : 0.05	b : 0.03	" : 0.01	# : 0.01	
f : 0.20	d : 0.14	= : 0.12	c : 0.09	g : 0.09	e : 0.07	[ : 0.05	! : 0.05	$ : 0.03	i : 0.03	" : 0.01	a : 0.01	# : 0.01	b : 0.01	
f : 0.20	d : 0.11	c : 0.11	g : 0.09	= : 0.09	! : 0.07	a : 0.05	[ : 0.05	" : 0.03	b : 0.03	$ : 0.03	e : 0.03	i : 0.03	# : 0.01	
f : 0.16	d : 0.11	c : 0.11	g : 0.09	! : 0.09	b : 0.09	" : 0.07	= : 0.07	[ : 0.05	$ : 0.03	i : 0.03	# : 0.01	a : 0.01	e : 0.01	
" : 0.18	! : 0.12	f : 0.11	c : 0.09	b : 0.09	= : 0.07	d : 0.07	g : 0.05	[ : 0.05	a : 0.03	$ : 0.03	i : 0.03	# : 0.01	
" : 0.20	! : 0.16	[ : 0.14	c : 0.11	= : 0.07	e : 0.05	f : 0.05	b : 0.05	d : 0.03	g : 0.03	$ : 0.03	i : 0.01	
d : 0.25	" : 0.16	c : 0.14	! : 0.09	e : 0.07	b : 0.07	= : 0.07	g : 0.03	[ : 0.03	f : 0.01	i : 0.01	
d : 0.31	c : 0.27	e : 0.09	b : 0.07	" : 0.05	= : 0.05	a : 0.03	g : 0.03	! : 0.03	f : 0.01	
c : 0.27	d : 0.27	[ : 0.11	e : 0.09	n : 0.03	b : 0.03	= : 0.03	g : 0.03	r : 0.03	! : 0.03	l : 0.01	
c : 0.27	d : 0.27	e : 0.09	a : 0.05	o : 0.05	n : 0.03	b : 0.03	= : 0.03	! : 0.03	r : 0.03	g : 0.01	l : 0.01	[ : 0.01	
o : 0.38	c : 0.14	n : 0.12	l : 0.05	d : 0.05	r : 0.05	e : 0.03	m : 0.03	b : 0.03	! : 0.01	[ : 0.01	p : 0.01	
o : 0.38	n : 0.24	c : 0.11	l : 0.07	m : 0.05	r : 0.05	= : 0.01	b : 0.01	e : 0.01	p : 0.01	
o : 0.38	n : 0.27	m : 0.09	l : 0.09	c : 0.05	r : 0.05	= : 0.01	p : 0.01	
o : 0.38	n : 0.24	m : 0.11	c : 0.09	l : 0.05	r : 0.05	= : 0.01	d : 0.01	p : 0.01	
o : 0.38	n : 0.24	m : 0.09	c : 0.07	r : 0.05	l : 0.03	d : 0.03	g : 0.01	b : 0.01	= : 0.01	p : 0.01	
o : 0.33	n : 0.14	c : 0.11	d : 0.11	m : 0.07	r : 0.05	g : 0.03	e : 0.03	b : 0.03	= : 0.01	l : 0.01	p : 0.01	
d : 0.27	c : 0.22	e : 0.09	b : 0.05	a : 0.05	= : 0.05	r : 0.05	g : 0.03	n : 0.03	m : 0.03	] : 0.01	2 : 0.01	l : 0.01	p : 0.01	
c : 0.31	d : 0.27	e : 0.09	] : 0.09	= : 0.05	b : 0.03	g : 0.03	2 : 0.03	a : 0.01	m : 0.01	r : 0.01	
c : 0.31	d : 0.25	e : 0.09	b : 0.07	= : 0.05	] : 0.05	2 : 0.03	f : 0.03	g : 0.03	r : 0.01	i : 0.01	
d : 0.20	c : 0.18	b : 0.11	] : 0.09	e : 0.09	g : 0.05	f : 0.05	= : 0.05	4 : 0.05	3 : 0.03	2 : 0.01	a : 0.01	i : 0.01	
3 : 0.16	] : 0.12	2 : 0.11	f : 0.07	4 : 0.07	c : 0.07	d : 0.07	g : 0.05	e : 0.05	= : 0.05	b : 0.05	a : 0.03	i : 0.03	
2 : 0.24	3 : 0.18	4 : 0.11	f : 0.11	= : 0.05	b : 0.05	c : 0.05	d : 0.05	g : 0.03	i : 0.03	> : 0.01	] : 0.01	a : 0.01	
3 : 0.16	2 : 0.14	f : 0.14	4 : 0.11	= : 0.07	b : 0.07	d : 0.07	c : 0.05	] : 0.03	a : 0.03	i : 0.03	g : 0.01	> : 0.01	
f : 0.20	d : 0.14	c : 0.14	g : 0.09	= : 0.09	a : 0.07	4 : 0.05	b : 0.05	3 : 0.03	i : 0.03	> : 0.01	2 : 0.01	e : 0.01	
f : 0.18	g : 0.12	d : 0.12	] : 0.12	c : 0.12	= : 0.11	4 : 0.03	2 : 0.03	i : 0.03	> : 0.01	3 : 0.01	b : 0.01	e : 0.01	
f : 0.18	c : 0.14	g : 0.12	d : 0.12	= : 0.11	e : 0.07	b : 0.05	2 : 0.03	] : 0.03	i : 0.03	> : 0.01	3 : 0.01	a : 0.01	
f : 0.18	g : 0.12	d : 0.11	= : 0.11	e : 0.09	b : 0.09	c : 0.09	] : 0.05	i : 0.05	> : 0.01	3 : 0.01	2 : 0.01	4 : 0.01	
g : 0.14	f : 0.14	c : 0.14	e : 0.11	] : 0.11	= : 0.09	d : 0.05	2 : 0.05	b : 0.03	i : 0.03	> : 0.01	3 : 0.01	4 : 0.01	
g : 0.16	c : 0.16	f : 0.12	] : 0.11	e : 0.09	= : 0.07	d : 0.07	b : 0.05	2 : 0.05	i : 0.03	> : 0.01	4 : 0.01	
c : 0.18	g : 0.16	e : 0.11	b : 0.09	= : 0.09	2 : 0.09	f : 0.07	d : 0.07	> : 0.01	] : 0.01	3 : 0.01	i : 0.01	a : 0.01	4 : 0.01	
c : 0.16	] : 0.11	= : 0.11	g : 0.09	2 : 0.09	e : 0.07	f : 0.07	d : 0.07	b : 0.05	3 : 0.05	4 : 0.03	> : 0.01	: : 0.01	i : 0.01	
c : 0.18	= : 0.12	b : 0.11	e : 0.09	3 : 0.07	] : 0.07	g : 0.05	d : 0.05	f : 0.05	: : 0.05	4 : 0.03	> : 0.01	2 : 0.01	i : 0.01	5 : 0.01	
c : 0.16	b : 0.12	= : 0.12	e : 0.09	: : 0.09	g : 0.07	3 : 0.05	] : 0.05	f : 0.05	4 : 0.03	> : 0.01	d : 0.01	a : 0.01	2 : 0.01	i : 0.01	5 : 0.01	

#score	675.6779699449278
#seq	54
#width	39
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_CDS_m3_run1.txt

#BEAR
ff[ddddddddmmmmdddd22ddddfff	chr10:89530608-89530864(-)$1	256	17	45	12.7846
iiiiii[ddddllldddd]iiiiiiiii	chr6:159187938-159188174(-)$1	236	49	77	11.2028
!!bb!!eeeeemmmmeeeee333bb22d	chr19:44738872-44739198(+)$1	326	94	122	11.8446
ffff"""ddddmmmmdddd]ffffff22	chr17:7403878-7404267(+)$1	389	352	380	13.1872
a[eeeee[cccmmmmccc333eeeee]a	chr19:13888877-13889169(+)$1	292	112	140	10.7201
d[dddd[ddddmmmmdddd]dddd]ddd	chr6:34735603-34735874(+)$1	271	170	198	11.9611
[ccc!!eeeeemmmmeeeee22ccc]ee	chr12:57626399-57626726(+)$1	327	30	58	12.7139
:ffffffddddmmmmdddd22ffffff:	chr5:149825071-149825347(-)$1	276	232	260	11.0341
eeeccceeeeemmmmeeeee333ccc::	chr6:27861315-27861658(+)$1	343	252	280	10.3453
ggggg!!ddddmmmmdddd4444ggggg	chr22:32894223-32894639(+)$1	416	33	61	14.9379
ddd"""ddddammmma]dddddddd22e	chr9:130211459-130211741(-)$1	282	81	109	10.5431
ffff!!ddddnnnnndddd333ffffff	chr19:9949015-9949342(+)$1	327	292	320	11.1211
fff"""eeeeemmmmeeeee22ffffff	chr17:8285360-8285733(-)$1	373	196	224	12.3443
!!bb"""ddddmmmmdddd4444bb333	chr1:22408114-22408387(+)$1	273	127	155	14.3386
bb####eeeeellleeeee333bb333a	chr3:184428864-184429222(-)$1	358	57	85	10.9623
!!eeeeeddddmmmmdddd333eeeeec	chr1:3697566-3697871(-)$1	305	216	244	13.8510
=====bbddddmmmmdddd22bb]====	chr1:24305112-24305407(-)$1	295	209	237	13.1443
c[iiiiiiiiimmmmiiiiiiiii]ccc	chr17:79478955-79479268(-)$1	313	24	52	10.1491
ggggg!!a[bbmmmmbb]a22ggggggg	chr5:149823704-149823970(-)$1	266	72	100	10.5475
eeeddddddddmmmmdddd22dddd]ee	chr16:47487823-47488104(-)$1	281	19	47	12.5974
c$$$$$eeeeellleeeee333ccc]cc	chr1:118483390-118483619(+)$1	229	110	138	11.0235
ea!!bb[ddddmmmmddddbb22a]eee	chr9:134321701-134322006(+)$1	305	183	211	11.2483
ccddddeeeeemmmmeeeee]dddd]cc	chr5:180669073-180669425(-)$1	352	320	348	10.8532
gggggg[ddddllldddd]gggggggcc	chr6:34212922-34213247(+)$1	325	255	283	10.9695
dddd"""ddddmmmmdddd333dddd]d	chr15:89174102-89174456(+)$1	354	264	292	14.4883
[gggggggddddllldddd]ggggggg]	chr21:34923284-34923600(+)$1	316	170	198	11.1925
gg[ccc[ddddmmmmdddd]ccc]gggg	chr3:185639698-185639973(-)$1	275	27	55	13.6379
ddccccccddddllldddd333ccc]cc	chr19:10368813-10369078(+)$1	265	168	196	12.2544
ggggg!!ddddmmmmdddd22ggggggg	chr18:19321585-19321813(+)$1	228	190	218	14.8013
ffffff[ddddmmmmdddd]ffffff:c	chr6:31593752-31594039(+)$1	287	198	226	11.6371
cc"""eeeeemmmmeeeee333ccc]dd	chr1:52250051-52250320(+)$1	269	108	136	11.2530
ffff!!eeeeemmmmeeeeeffffffcc	chr19:45404184-45404461(+)$1	277	109	137	11.3195
!eeeee[ddddmmmmddddeeeee]ccc	chr15:72492714-72493096(-)$1	382	33	61	12.2040
=======ddddmmmmdddd]========	chr7:26232770-26233093(-)$1	323	231	259	14.1385
ffffff!!cccmmmmccc333ffffff4	chr1:225147755-225147999(+)$1	244	31	59	11.1590
ffff"""ddddmmmmdddd4444fffff	chr11:63743596-63744089(+)$1	493	98	126	14.5327
cc$$$$$ddddllldddd4444cccccc	chr12:6646649-6647025(+)$1	376	332	360	11.6756
b[ccc[eeeeemmmmeeeee]ccc]bb:	chr5:130498178-130498467(-)$1	289	3	31	10.4459
[dddd!!ddddmmmmdddd22dddd]bb	chr19:54711165-54711600(+)$1	435	37	65	13.6229
[dddd!!ddddmmmmdddd4444dddd]	chr1:24019019-24019291(+)$1	272	175	203	13.9372
[bb"""eeeeemmmmeeeee333bb]a]	chr10:135123575-135123881(+)$1	306	216	244	12.5819
ggg[a!!eeeeellleeeee22aggggg	chr4:24572232-24572570(-)$1	338	181	209	11.0329
ffff####cccmmmmccc4444ffffff	chr1:28863163-28863507(+)$1	344	287	315	11.7023
dd[ccc[ddddmmmmddddccc]dddd]	chr12:112844450-112844794(-)$1	344	236	264	12.2455
==####eeeeemmmmeeeee]=======	chr8:74893326-74893729(+)$1	403	124	152	12.6791
$dddd!!ddddmmmmdddd22dddd333	chr10:79795268-79795548(+)$1	280	193	221	13.7811
bbeeeeeddddmmmmdddd]eeeee]bb	chr3:141463912-141464211(+)$1	299	93	121	11.4293
=====####ccclllccc333=======	chr5:79283978-79284225(-)$1	247	34	62	10.8068
bb[cccccc[ammmmaccc22ccc]bb]	chr19:40478291-40478562(+)$1	271	224	252	10.3420
dddccc[ddddmmmmdddd]ccc22ddd	chr10:73058872-73059281(+)$1	409	220	248	11.9933
!!ccc[ccccccmmmmccc22ccc]ccc	chr1:43162226-43162562(+)$1	336	109	137	10.1740
hhh[a"""ddddllldddd333a]hhhh	chr9:125639653-125639948(-)$1	295	182	210	11.7473

#otherMatches

#Seq PSSM
GGAGUAUAAUUGGUAGAUUUAAUACCUU	chr10:89530608-89530864(-)$1	256	17	45	12.7846
UGCUUAAUGUUACAGACGCUGAGCAGCG	chr6:159187938-159188174(-)$1	236	49	77	11.2028
CAGGUGUCUUCAGGGGAAGAGUUCCCAG	chr19:44738872-44739198(+)$1	326	94	122	11.8446
GGGCCUUGAGUGGGugcuuuguccuuag	chr17:7403878-7404267(+)$1	389	352	380	13.1872
CCUCCUCCAAGACACCUUCCUGAGGACG	chr19:13888877-13889169(+)$1	292	112	140	10.7201
CGUAAGUUUAAACUUUUAAUCUUAAGGG	chr6:34735603-34735874(+)$1	271	170	198	11.9611
UGGGCAGGCCUCUCCGGGCCCUCCCCAG	chr12:57626399-57626726(+)$1	327	30	58	12.7139
AGCACGUGCUGUGCCCAGUGGAUGUGCA	chr5:149825071-149825347(-)$1	276	232	260	11.0341
CACGCCGUGUCCGAGGGCACAAAGGCCG	chr6:27861315-27861658(+)$1	343	252	280	10.3453
UCCCGCCUUCCUCCAGGAAUUAUCGGGG	chr22:32894223-32894639(+)$1	416	33	61	14.9379
UCAGGAAUCUCUUCUGCAGAUUGAGGUG	chr9:130211459-130211741(-)$1	282	81	109	10.5431
CCUGGAGCUGAUCAACGGUGAGCAGGGC	chr19:9949015-9949342(+)$1	327	292	320	11.1211
CUUCCCCUCUUUCCAAAGAGCUGAGACA	chr17:8285360-8285733(-)$1	373	196	224	12.3443
AUGAUUGGUGGAGAACCAUAUACUCUUG	chr1:22408114-22408387(+)$1	273	127	155	14.3386
CUAAAACCUCUggaggaggaggaggagg	chr3:184428864-184429222(-)$1	358	57	85	10.9623
CUGACGCCAGGGCCGCCUGUCCGCGUUU	chr1:3697566-3697871(-)$1	305	216	244	13.8510
CCUUUCUUCAGAUGGCUGAUUAGUGAGG	chr1:24305112-24305407(-)$1	295	209	237	13.1443
GCCGCGGGGCUCCUGGGUUCUGCGUUGC	chr17:79478955-79479268(-)$1	313	24	52	10.1491
CCUCUGACAGCACUCGCAGGAAGGGGGG	chr5:149823704-149823970(-)$1	266	72	100	10.5475
UGCUUGUUUCUUUUAGGAAUCACAGUGC	chr16:47487823-47488104(-)$1	281	19	47	12.5974
GGAAUACAAGAUACUCUUGAGGCAGAGG	chr1:118483390-118483619(+)$1	229	110	138	11.0235
GGGAGAUGGAGCCCCCUCCUCGGCAUGU	chr9:134321701-134322006(+)$1	305	183	211	11.2483
GGCUGGUUUCCCAGGGGAGAUCCAGUCC	chr5:180669073-180669425(-)$1	352	320	348	10.8532
GGGGGUGCUGGCCCCCAGGAUUCCCCCA	chr6:34212922-34213247(+)$1	325	255	283	10.9695
AGAAACAAGACAGUGGUUUGAAUUCUGG	chr15:89174102-89174456(+)$1	354	264	292	14.4883
GAGUUGCCUGGGCAGCCUGUGGCAACUG	chr21:34923284-34923600(+)$1	316	170	198	11.1925
GAUGUAUGUAACAAUUUAUUUACCUUUU	chr3:185639698-185639973(-)$1	275	27	55	13.6379
CACUGACCGUCAAGCUGGCCCAGGUACA	chr19:10368813-10369078(+)$1	265	168	196	12.2544
AAGCCGCGGCCACCUGGCCAGGGCUUGC	chr18:19321585-19321813(+)$1	228	190	218	14.8013
UUAAGGGUCAAGAAUUUGGAUCUUGAAA	chr6:31593752-31594039(+)$1	287	198	226	11.6371
AUUAAUUGUUCCAAAACAGGCUAUAGUG	chr1:52250051-52250320(+)$1	269	108	136	11.2530
GGUUGGCAACGGUAACGUUGGGCCAGGC	chr19:45404184-45404461(+)$1	277	109	137	11.3195
CGCCCUGAGGGUACUUCCUGGGGCCUCG	chr15:72492714-72493096(-)$1	382	33	61	12.2040
UAAAAAUUGAGGUUAUUCAGAUUUUUGU	chr7:26232770-26233093(-)$1	323	231	259	14.1385
UGUGGAAUUACUAUGGUAUUAUUUACAG	chr1:225147755-225147999(+)$1	244	31	59	11.1590
AGGAAUUGGCCGUUGGGCUUACCUCCUG	chr11:63743596-63744089(+)$1	493	98	126	14.5327
CCAAAUAUGAUGACAUCAAGAAGGUGGU	chr12:6646649-6647025(+)$1	376	332	360	11.6756
auguaguuacugcucaguaaauacuugu	chr5:130498178-130498467(-)$1	289	3	31	10.4459
UGCGGUAGCUGGGGUUAGCGUCCGUUUC	chr19:54711165-54711600(+)$1	435	37	65	13.6229
CGAGCAGCCAAGGUGUUGGAGCAGCUCA	chr1:24019019-24019291(+)$1	272	175	203	13.9372
GGUAGGGAGCCGCCAGGCUCAGCACGUG	chr10:135123575-135123881(+)$1	306	216	244	12.5819
GCUGCAAUGAGUGUGGCUCAGAGAGUUG	chr4:24572232-24572570(-)$1	338	181	209	11.0329
GGGGUCAUGGUUCUUACCCAAUUCCCCA	chr1:28863163-28863507(+)$1	344	287	315	11.7023
GGGGCAAGGUGAGAGUACCUGUGCUUGG	chr12:112844450-112844794(-)$1	344	236	264	12.2455
UACACAAAAUAAUGCUAUUUCUGAAAGU	chr8:74893326-74893729(+)$1	403	124	152	12.6791
AACAUAGACUUGCAAGAGUAGGUGUCUU	chr10:79795268-79795548(+)$1	280	193	221	13.7811
UGGGGAGAAUGUAAUCAUUCCUUCCACA	chr3:141463912-141464211(+)$1	299	93	121	11.4293
AGUAGUUUUAGAGUAUCUUUUCUACUUU	chr5:79283978-79284225(-)$1	247	34	62	10.8068
CCAUGUGCUAGGCAGCAGCAAACAAGGC	chr19:40478291-40478562(+)$1	271	224	252	10.3420
GGCAGCCUCCUGAUGGGGAUGUUUGGCC	chr10:73058872-73059281(+)$1	409	220	248	11.9933
AGGUCCUGGUGGUGUUCCAGUUCAAGGC	chr1:43162226-43162562(+)$1	336	109	137	10.1740
CAGGAAGAGCUUGAAAAGUAAGUGUUGA	chr9:125639653-125639948(-)$1	295	182	210	11.7473

#DB
((.((((((((....))))..)))))))	chr10:89530608-89530864(-)$1	1	17	45	12.7846
((((((.((((...)))).)))))))))	chr6:159187938-159188174(-)$1	1	49	77	11.2028
..((..(((((....)))))...))..)	chr19:44738872-44739198(+)$1	1	94	122	11.8446
((((...((((....)))).))))))..	chr17:7403878-7404267(+)$1	1	352	380	13.1872
(.(((((.(((....)))...))))).)	chr19:13888877-13889169(+)$1	1	112	140	10.7201
(.((((.((((....)))).)))).)))	chr6:34735603-34735874(+)$1	1	170	198	11.9611
.(((..(((((....)))))..))).))	chr12:57626399-57626726(+)$1	1	30	58	12.7139
.((((((((((....))))..)))))).	chr5:149825071-149825347(-)$1	1	232	260	11.0341
)))((((((((....)))))...)))..	chr6:27861315-27861658(+)$1	1	252	280	10.3453
(((((..((((....))))....)))))	chr22:32894223-32894639(+)$1	1	33	61	14.9379
(((...(((((....).))))))))..)	chr9:130211459-130211741(-)$1	1	81	109	10.5431
((((..((((.....))))...))))))	chr19:9949015-9949342(+)$1	1	292	320	11.1211
(((...(((((....)))))..))))))	chr17:8285360-8285733(-)$1	1	196	224	12.3443
..((...((((....))))....))...	chr1:22408114-22408387(+)$1	1	127	155	14.3386
((....(((((...)))))...))...)	chr3:184428864-184429222(-)$1	1	57	85	10.9623
..(((((((((....))))...))))))	chr1:3697566-3697871(-)$1	1	216	244	13.8510
(((((((((((....))))..)).))))	chr1:24305112-24305407(-)$1	1	209	237	13.1443
(.(((((((((....))))))))).)))	chr17:79478955-79479268(-)$1	1	24	52	10.1491
(((((..(.((....)).)..)))))))	chr5:149823704-149823970(-)$1	1	72	100	10.5475
(((((((((((....))))..)))).))	chr16:47487823-47488104(-)$1	1	19	47	12.5974
(.....(((((...)))))...))).))	chr1:118483390-118483619(+)$1	1	110	138	11.0235
((..((.((((....))))))..).)))	chr9:134321701-134322006(+)$1	1	183	211	11.2483
(((((((((((....))))).)))).))	chr5:180669073-180669425(-)$1	1	320	348	10.8532
((((((.((((...)))).)))))))((	chr6:34212922-34213247(+)$1	1	255	283	10.9695
((((...((((....))))...)))).)	chr15:89174102-89174456(+)$1	1	264	292	14.4883
.(((((((((((...)))).))))))).	chr21:34923284-34923600(+)$1	1	170	198	11.1925
((.(((.((((....)))).))).))))	chr3:185639698-185639973(-)$1	1	27	55	13.6379
))((((((((((...))))...))).))	chr19:10368813-10369078(+)$1	1	168	196	12.2544
(((((..((((....))))..)))))))	chr18:19321585-19321813(+)$1	1	190	218	14.8013
((((((.((((....)))).)))))).(	chr6:31593752-31594039(+)$1	1	198	226	11.6371
((...(((((....)))))...))).))	chr1:52250051-52250320(+)$1	1	108	136	11.2530
((((..(((((....)))))))))))((	chr19:45404184-45404461(+)$1	1	109	137	11.3195
.(((((.((((....))))))))).)))	chr15:72492714-72493096(-)$1	1	33	61	12.2040
(((((((((((....)))).))))))))	chr7:26232770-26233093(-)$1	1	231	259	14.1385
((((((..(((....)))...)))))).	chr1:225147755-225147999(+)$1	1	31	59	11.1590
((((...((((....))))....)))))	chr11:63743596-63744089(+)$1	1	98	126	14.5327
((.....((((...))))....))))))	chr12:6646649-6647025(+)$1	1	332	360	11.6756
(.(((.(((((....))))).))).)).	chr5:130498178-130498467(-)$1	1	3	31	10.4459
.((((..((((....))))..)))).))	chr19:54711165-54711600(+)$1	1	37	65	13.6229
.((((..((((....))))....)))).	chr1:24019019-24019291(+)$1	1	175	203	13.9372
.((...(((((....)))))...)).).	chr10:135123575-135123881(+)$1	1	216	244	12.5819
(((.(..(((((...)))))..))))))	chr4:24572232-24572570(-)$1	1	181	209	11.0329
((((....(((....)))....))))))	chr1:28863163-28863507(+)$1	1	287	315	11.7023
((.(((.((((....))))))).)))).	chr12:112844450-112844794(-)$1	1	236	264	12.2455
((....(((((....))))).)))))))	chr8:74893326-74893729(+)$1	1	124	152	12.6791
.((((..((((....))))..))))...	chr10:79795268-79795548(+)$1	1	193	221	13.7811
(((((((((((....)))).))))).))	chr3:141463912-141464211(+)$1	1	93	121	11.4293
(((((....(((...)))...)))))))	chr5:79283978-79284225(-)$1	1	34	62	10.8068
((.((((((.(....))))..))).)).	chr19:40478291-40478562(+)$1	1	224	252	10.3420
((((((.((((....)))).)))..)))	chr10:73058872-73059281(+)$1	1	220	248	11.9933
..(((.((((((....)))..))).)))	chr1:43162226-43162562(+)$1	1	109	137	10.1740
(((.(...((((...))))...).))))	chr9:125639653-125639948(-)$1	1	182	210	11.7473

#PSSM
f : 0.17	d : 0.11	g : 0.11	! : 0.09	[ : 0.09	c : 0.09	b : 0.07	= : 0.07	e : 0.05	i : 0.01	a : 0.01	: : 0.01	$ : 0.01	h : 0.01	
f : 0.19	d : 0.15	g : 0.13	! : 0.07	[ : 0.07	c : 0.07	b : 0.07	= : 0.07	e : 0.05	i : 0.01	$ : 0.01	a : 0.01	h : 0.01	
f : 0.17	d : 0.15	e : 0.11	g : 0.11	[ : 0.07	c : 0.07	b : 0.05	= : 0.05	i : 0.03	# : 0.03	$ : 0.03	! : 0.01	" : 0.01	h : 0.01	
c : 0.17	d : 0.15	f : 0.15	g : 0.09	e : 0.07	" : 0.07	= : 0.05	i : 0.03	b : 0.03	# : 0.03	$ : 0.03	[ : 0.03	! : 0.01	
" : 0.15	c : 0.15	d : 0.13	g : 0.09	! : 0.07	e : 0.07	f : 0.05	# : 0.05	= : 0.05	i : 0.03	$ : 0.03	a : 0.03	b : 0.01	
! : 0.21	" : 0.15	c : 0.11	e : 0.09	d : 0.07	# : 0.07	f : 0.05	i : 0.03	b : 0.03	$ : 0.03	g : 0.03	[ : 0.03	= : 0.01	
e : 0.28	[ : 0.17	! : 0.15	" : 0.09	d : 0.07	c : 0.05	# : 0.03	f : 0.01	b : 0.01	i : 0.01	g : 0.01	= : 0.01	$ : 0.01	
d : 0.53	e : 0.24	c : 0.05	# : 0.03	[ : 0.01	i : 0.01	a : 0.01	g : 0.01	! : 0.01	" : 0.01	
d : 0.59	e : 0.24	c : 0.09	i : 0.01	[ : 0.01	# : 0.01	
d : 0.59	e : 0.24	c : 0.09	i : 0.01	b : 0.01	[ : 0.01	
d : 0.55	e : 0.23	c : 0.09	a : 0.03	n : 0.01	i : 0.01	b : 0.01	m : 0.01	
m : 0.76	l : 0.09	d : 0.05	c : 0.03	n : 0.01	e : 0.01	
m : 0.78	l : 0.19	n : 0.01	
m : 0.78	l : 0.19	n : 0.01	
m : 0.76	l : 0.09	d : 0.05	e : 0.05	n : 0.01	
d : 0.57	e : 0.24	c : 0.07	a : 0.03	i : 0.01	b : 0.01	m : 0.01	
d : 0.57	e : 0.24	c : 0.11	] : 0.01	i : 0.01	b : 0.01	
d : 0.59	e : 0.24	c : 0.11	i : 0.01	] : 0.01	
d : 0.53	e : 0.24	3 : 0.05	] : 0.03	4 : 0.03	c : 0.03	i : 0.01	a : 0.01	
e : 0.21	3 : 0.21	2 : 0.19	] : 0.15	4 : 0.11	i : 0.03	d : 0.01	b : 0.01	g : 0.01	c : 0.01	
3 : 0.26	2 : 0.24	4 : 0.11	f : 0.05	] : 0.05	c : 0.05	i : 0.03	d : 0.03	g : 0.03	e : 0.03	b : 0.01	= : 0.01	
3 : 0.21	d : 0.13	4 : 0.11	c : 0.11	f : 0.09	2 : 0.07	g : 0.07	e : 0.05	= : 0.05	i : 0.03	b : 0.01	
c : 0.19	d : 0.15	f : 0.15	e : 0.07	4 : 0.07	g : 0.07	3 : 0.05	= : 0.05	i : 0.03	b : 0.03	a : 0.03	2 : 0.01	] : 0.01	
d : 0.19	f : 0.17	c : 0.17	g : 0.11	b : 0.07	e : 0.07	] : 0.05	= : 0.05	i : 0.03	a : 0.01	2 : 0.01	
d : 0.17	f : 0.17	] : 0.13	g : 0.13	c : 0.11	= : 0.07	b : 0.05	e : 0.05	i : 0.01	3 : 0.01	2 : 0.01	h : 0.01	
f : 0.19	] : 0.17	g : 0.13	d : 0.09	c : 0.09	= : 0.07	e : 0.05	3 : 0.05	2 : 0.03	b : 0.03	i : 0.01	h : 0.01	
c : 0.17	f : 0.13	g : 0.11	d : 0.09	e : 0.07	= : 0.07	b : 0.07	2 : 0.05	3 : 0.05	] : 0.03	: : 0.03	i : 0.01	a : 0.01	h : 0.01	
c : 0.21	f : 0.09	d : 0.09	g : 0.09	] : 0.09	e : 0.07	= : 0.07	: : 0.05	a : 0.03	3 : 0.03	b : 0.03	i : 0.01	2 : 0.01	4 : 0.01	h : 0.01	

#score	627.2428359794307
#seq	52
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_UTR_m3_run1.txt

#BEAR
g[eeeeeqqqqqqqqeeeeegg	chr16:53524850-53525076(+)$1	226	125	147	15.4608
"""ddddqqqqqqqqdddd333	chr20:10286992-10287217(+)$1	225	93	115	15.1076
fffffffqqqqqqqqffffff:	chr7:12273536-12273763(+)$1	227	85	107	13.7634
gggggggqqqqqqqqggggggg	chr1:93307873-93308099(-)$1	226	71	93	16.1422
d!!ddddqqqqqqqqdddd22d	chr5:96110099-96110322(+)$1	223	102	124	13.9827
b[eeeeeqqqqqqqqeeeee]b	chr3:89530535-89530777(+)$1	242	125	147	14.8849
iiiiiiiqqqqqqqqiiiiiii	chr5:173386636-173386873(+)$1	237	191	213	16.2120
bb[ddddqqqqqqqqdddd]bb	chr2:70166103-70166328(+)$1	225	166	188	13.4423
dddd[bbqqqqqqqqbbddddd	chr1:77557544-77557792(-)$1	248	47	69	13.3594
gggggggqqqqqqqqggggggg	chr8:81433121-81433345(+)$1	224	123	145	16.1422
$$$$cccqqqqqqqqccc]ccc	chr10:102121512-102121756(+)$1	244	202	224	14.6672
:ffffffqqqqqqqqffffffc	chr1:67874284-67874552(-)$1	268	115	137	13.7601
$$eeeeeqqqqqqqqeeeee55	chr2:189876386-189876616(+)$1	230	177	199	13.4922
cc[ddddqqqqqqqqddddccc	chr5:56217661-56217899(-)$1	238	186	208	14.2098
ccc[cccqqqqqqqqccc]ccc	chr12:76423389-76423727(-)$1	338	35	57	15.2211
gggggggqqqqqqqqggggggg	chr2:153616659-153616889(+)$1	230	182	204	16.1422
ffffffaqqqqqqqqa]fffff	chrX:12842088-12842332(+)$1	244	12	34	14.5363
f[eeeeeqqqqqqqqeeeeeff	chr5:72877201-72877431(+)$1	230	180	202	14.9850
!!eeeeeqqqqqqqqeeeee22	chr17:60022573-60022796(-)$1	223	145	167	15.3398
eee[cccqqqqqqqqccceeee	chr7:131173354-131173585(+)$1	231	185	207	14.8857
iiiiiiiqqqqqqqqiiiiiii	chr1:28607763-28608022(+)$1	259	84	106	16.2120
!!a[cccqqqqqqqqccca22h	chr10:61550296-61550518(-)$1	222	148	170	15.2194
"ffffffqqqqqqqqffffff3	chr2:96851557-96851841(-)$1	284	13	35	15.1421
eee[cccqqqqqqqqccc]eee	chr12:107366316-107366634(+)$1	318	181	203	14.9619
gggggggqqqqqqqqggggggg	chr2:208630104-208630332(-)$1	228	13	35	16.1422
!bb!!bbqqqqqqqqbb22bb2	chr2:61276051-61276281(+)$1	230	23	45	13.5355
=======qqqqqqqq=======	chr7:128409554-128409790(+)$1	236	206	228	16.7042
gggggggqqqqqqqqggggggg	chr20:31437311-31437548(+)$1	237	73	95	16.1422
ggg!!bbqqqqqqqqbb22ggg	chr15:31667002-31667229(+)$1	227	79	101	15.0210
gggggggqqqqqqqqggggggg	chrX:150575718-150575977(+)$1	259	139	161	16.1422
ddd!!bbqqqqqqqqbb333dd	chr1:204372711-204372947(-)$1	236	181	203	14.0511
eeeebbaqqqqqqqqa]bb]ee	chr6:64290777-64291176(+)$1	399	95	117	13.5127
gggggggqqqqqqqqggggggg	chr5:159503418-159503645(-)$1	227	185	207	16.1422
f[eeeeeqqqqqqqqeeeee33	chrX:46739394-46739620(+)$1	226	92	114	15.5261
iiiiiiiqqqqqqqqiiiiiii	chr8:59360068-59360318(+)$1	250	185	207	16.2120
===!!bbqqqqqqqqbb22===	chr9:89559686-89559964(-)$1	278	45	67	15.3409
!!eeeeeqqqqqqqqeeeee44	chr12:54631265-54631538(-)$1	273	172	194	15.5305
###ddddqqqqqqqqdddd333	chr2:179380430-179380657(+)$1	227	103	125	14.9899
=======qqqqqqqq=======	chr11:86520850-86521073(+)$1	223	57	79	16.7042
=======qqqqqqqq=======	chr3:51431620-51431886(+)$1	266	62	84	16.7042
b[eeeeeqqqqqqqqeeeee]b	chr2:207939809-207940037(-)$1	228	124	146	14.8849
Hffffffqqqqqqqqffffff:	chr12:72317704-72317961(+)$1	257	80	102	13.2885
####cccqqqqqqqqccc4444	chr7:50512341-50512609(-)$1	268	134	156	15.4482
gggg[bbqqqqqqqqbb]gggg	chr2:204301872-204302093(-)$1	221	129	151	15.4652
gggggggqqqqqqqqggggggg	chr8:92097506-92097727(+)$1	221	163	185	16.1422
====[bbqqqqqqqqbb=====	chr15:69732978-69733207(+)$1	229	34	56	15.9405
ffff[bbqqqqqqqqbbfffff	chr7:63985320-63985561(-)$1	241	151	173	14.3816
=======qqqqqqqq=======	chr2:68406665-68406916(-)$1	251	160	182	16.7042
bffffffqqqqqqqqffffff]	chr10:102122136-102122396(+)$1	260	187	209	14.6741
!ffffffqqqqqqqqffffff]	chr1:6583184-6583413(-)$1	229	117	139	15.0751
ffeeeeeqqqqqqqqeeeee22	chr5:78982294-78982522(+)$1	228	132	154	14.7975
="""cccqqqqqqqqccc22==	chr5:143538060-143538298(-)$1	238	129	151	15.5447
gggggggqqqqqqqqggggggg	chr7:86509204-86509432(-)$1	228	194	216	16.1422
!!a[cccqqqqqqqqccc]a22	chr2:191556976-191557223(+)$1	247	62	84	15.6451
====[bbqqqqqqqqbb]====	chr1:244869912-244870134(+)$1	222	176	198	15.8579
iiiiiiiqqqqqqqqiiiiiii	chr3:195778364-195778594(-)$1	230	39	61	16.2120
$$$ddddqqqqqqqqddddddd	chr2:48602576-48602848(+)$1	272	183	205	13.4346
iiiiiiiqqqqqqqqiiiiiii	chr3:48014995-48015228(-)$1	233	149	171	16.2120
[dddd[aqqqqqqqqa]dddd2	chr6:107474240-107474483(-)$1	243	207	229	13.9753
gggggggqqqqqqqqggggggg	chr11:102102538-102102773(+)$1	235	59	81	16.1422
%%eeeeeqqqqqqqqeeeee88	chr8:90945817-90946072(-)$1	255	33	55	13.1719
hffffffqqqqqqqqffffff9	chr7:20453703-20453930(+)$1	227	110	132	13.9659

#otherMatches

#Seq PSSM
GCUUUUAUAUUUUUUUAAAAUG	chr16:53524850-53525076(+)$1	226	125	147	15.4608
UCUUGAGUUUCAUUUUUCAUUU	chr20:10286992-10287217(+)$1	225	93	115	15.1076
AAAAUAAAAAAAAAGUUAUUUU	chr7:12273536-12273763(+)$1	227	85	107	13.7634
UAAACUUGAUAUACAAGGUUUA	chr1:93307873-93308099(-)$1	226	71	93	16.1422
CAAUUUUUUAUUAUCAAAAAGG	chr5:96110099-96110322(+)$1	223	102	124	13.9827
ACUAUUUUCUUUUUUAGGUACU	chr3:89530535-89530777(+)$1	242	125	147	14.8849
auauuuuuaaaauuuaaaguau	chr5:173386636-173386873(+)$1	237	191	213	16.2120
CUUUUUUCCCCCCCCAAAAUAG	chr2:70166103-70166328(+)$1	225	166	188	13.4423
GUGAAGACAUUAAAUucucacu	chr1:77557544-77557792(-)$1	248	47	69	13.3594
GUAACUAAAUUAUGCUAGUUAU	chr8:81433121-81433345(+)$1	224	123	145	16.1422
aacaucCAAAAAAAGGGAAGGA	chr10:102121512-102121756(+)$1	244	202	224	14.6672
AAAAUACCAUGAUUAGUAUUUC	chr1:67874284-67874552(-)$1	268	115	137	13.7601
AUCUUGUCAACCAGUGCAAGUG	chr2:189876386-189876616(+)$1	230	177	199	13.4922
CUAUAAACAUGCAUUUUUAAGU	chr5:56217661-56217899(-)$1	238	186	208	14.2098
UCAAGAAGACUUUUAUUUAUGA	chr12:76423389-76423727(-)$1	338	35	57	15.2211
GAAUAUUUAAUUUUUGAUAUUC	chr2:153616659-153616889(+)$1	230	182	204	16.1422
UCUGGCCAAAAACAGGAGCCAG	chrX:12842088-12842332(+)$1	244	12	34	14.5363
AAGAUUUUGUAAUGCGAAUCUC	chr5:72877201-72877431(+)$1	230	180	202	14.9850
UUUUUUUUUUAAAUUAAAGAUU	chr17:60022573-60022796(-)$1	223	145	167	15.3398
GUCCAGUGGUAUACAACUGACA	chr7:131173354-131173585(+)$1	231	185	207	14.8857
GGGCAGCCUGAGGCUGUUGCCC	chr1:28607763-28608022(+)$1	259	84	106	16.2120
CUGAUAGAACAAACACUACUCU	chr10:61550296-61550518(-)$1	222	148	170	15.2194
UGAAUUUGUACAAAGAAAUUUC	chr2:96851557-96851841(-)$1	284	13	35	15.1421
UUUCAUGUUUAAUUUCAUAAAA	chr12:107366316-107366634(+)$1	318	181	203	14.9619
UUUUCUUCCUCUUCUGAGAAAG	chr2:208630104-208630332(-)$1	228	13	35	16.1422
CUGGUUACAUUUUAUUAUACAC	chr2:61276051-61276281(+)$1	230	23	45	13.5355
AGUUGCUAUAGGUCCAGCAACU	chr7:128409554-128409790(+)$1	236	206	228	16.7042
GAAUGGGGAUUGUAUCCCAUUU	chr20:31437311-31437548(+)$1	237	73	95	16.1422
GUUGGCUGUUUCCAAAGAGAGC	chr15:31667002-31667229(+)$1	227	79	101	15.0210
ACUAUGUUAAAUAACAUAUGGU	chrX:150575718-150575977(+)$1	259	139	161	16.1422
AGACAGGUAAAAGUUCCAUUUC	chr1:204372711-204372947(-)$1	236	181	203	14.0511
UGUUGCCUUUGUCUUGUGCAAA	chr6:64290777-64291176(+)$1	399	95	117	13.5127
UAUAGGGGUGCCCUACUCUAUA	chr5:159503418-159503645(-)$1	227	185	207	16.1422
GCUAAAAGUUUAUUAUUUUAAU	chrX:46739394-46739620(+)$1	226	92	114	15.5261
UCUGAAUAUAGACAAAUUUGGA	chr8:59360068-59360318(+)$1	250	185	207	16.2120
UGCCAUGGUGUUGAACAAUGCA	chr9:89559686-89559964(-)$1	278	45	67	15.3409
GAGAAGCAGUCAUUAGCUUUGU	chr12:54631265-54631538(-)$1	273	172	194	15.5305
UCCAAAAUUUUCACUUUUUUUC	chr2:179380430-179380657(+)$1	227	103	125	14.9899
UUUUCAGUGUGCUUUCUGGGAG	chr11:86520850-86521073(+)$1	223	57	79	16.7042
UUUUUUUUAAACGAUGAGAAGG	chr3:51431620-51431886(+)$1	266	62	84	16.7042
UUGGUAUAUUGUAAGAUAUCUA	chr2:207939809-207940037(-)$1	228	124	146	14.8849
UGUAAUUUUAAAAUUAAUUGCU	chr12:72317704-72317961(+)$1	257	80	102	13.2885
UGUUACCUCUUUUAUGGUUUUU	chr7:50512341-50512609(-)$1	268	134	156	15.4482
AAAAUGUACCCGCUAACCUUUU	chr2:204301872-204302093(-)$1	221	129	151	15.4652
auuuaaaaauauuuauuuaGAU	chr8:92097506-92097727(+)$1	221	163	185	16.1422
GUUAAGUCUUCAUGUGCUAACA	chr15:69732978-69733207(+)$1	229	34	56	15.9405
uucuucaaaaaugcaugagaaa	chr7:63985320-63985561(-)$1	241	151	173	14.3816
GCUGGAAGAAAAACAUUUUGGU	chr2:68406665-68406916(-)$1	251	160	182	16.7042
UCCUUUGUGUGUAUUCAGAGGC	chr10:102122136-102122396(+)$1	260	187	209	14.6741
CAGUCUGUUAUGGGUCAGAUUA	chr1:6583184-6583413(-)$1	229	117	139	15.0751
UUUGUAUGAUGUCAAAUGCAAU	chr5:78982294-78982522(+)$1	228	132	154	14.7975
UUUUCAGUAUAGUUUUUGUUAA	chr5:143538060-143538298(-)$1	238	129	151	15.5447
UAGGUUAUCUUCUCUUGAUUUA	chr7:86509204-86509432(-)$1	228	194	216	16.1422
UUCCAAUAUUUAUCCAUUCGUU	chr2:191556976-191557223(+)$1	247	62	84	15.6451
UUUUAUGUACCAUGUCAGAAAG	chr1:244869912-244870134(+)$1	222	176	198	15.8579
AUGGGAACUGCCUCUUUCCUGU	chr3:195778364-195778594(-)$1	230	39	61	16.2120
CUGAUCAGAAAUACAUGAUGUG	chr2:48602576-48602848(+)$1	272	183	205	13.4346
UUUGAAAUUUGUUUUUUUCAAA	chr3:48014995-48015228(-)$1	233	149	171	16.2120
AUGCAAUGAAGAGAAAAUGUAA	chr6:107474240-107474483(-)$1	243	207	229	13.9753
GCCCUUCAAUUUGGAGGAGGGC	chr11:102102538-102102773(+)$1	235	59	81	16.1422
ccuagucuguggcuugacuguu	chr8:90945817-90946072(-)$1	255	33	55	13.1719
UUUCUUAUAAAGAUUUGAGAGC	chr7:20453703-20453930(+)$1	227	110	132	13.9659

#DB
(.(((((........)))))))	chr16:53524850-53525076(+)$1	1	125	147	15.4608
...((((........))))...	chr20:10286992-10287217(+)$1	1	93	115	15.1076
)((((((........)))))).	chr7:12273536-12273763(+)$1	1	85	107	13.7634
(((((((........)))))))	chr1:93307873-93308099(-)$1	1	71	93	16.1422
(..((((........))))..)	chr5:96110099-96110322(+)$1	1	102	124	13.9827
(.(((((........))))).)	chr3:89530535-89530777(+)$1	1	125	147	14.8849
(((((((........)))))))	chr5:173386636-173386873(+)$1	1	191	213	16.2120
((.((((........)))).))	chr2:70166103-70166328(+)$1	1	166	188	13.4423
((((.((........))))))(	chr1:77557544-77557792(-)$1	1	47	69	13.3594
(((((((........)))))))	chr8:81433121-81433345(+)$1	1	123	145	16.1422
....(((........))).)))	chr10:102121512-102121756(+)$1	1	202	224	14.6672
.((((((........))))))(	chr1:67874284-67874552(-)$1	1	115	137	13.7601
..(((((........)))))..	chr2:189876386-189876616(+)$1	1	177	199	13.4922
((.((((........)))))))	chr5:56217661-56217899(-)$1	1	186	208	14.2098
(((.(((........))).)))	chr12:76423389-76423727(-)$1	1	35	57	15.2211
(((((((........)))))))	chr2:153616659-153616889(+)$1	1	182	204	16.1422
(((((((........).)))))	chrX:12842088-12842332(+)$1	1	12	34	14.5363
(.(((((........)))))))	chr5:72877201-72877431(+)$1	1	180	202	14.9850
..(((((........)))))..	chr17:60022573-60022796(-)$1	1	145	167	15.3398
(((.(((........)))))))	chr7:131173354-131173585(+)$1	1	185	207	14.8857
(((((((........)))))))	chr1:28607763-28608022(+)$1	1	84	106	16.2120
..(.(((........))))..)	chr10:61550296-61550518(-)$1	1	148	170	15.2194
.((((((........)))))).	chr2:96851557-96851841(-)$1	1	13	35	15.1421
(((.(((........))).)))	chr12:107366316-107366634(+)$1	1	181	203	14.9619
(((((((........)))))))	chr2:208630104-208630332(-)$1	1	13	35	16.1422
.((..((........))..)).	chr2:61276051-61276281(+)$1	1	23	45	13.5355
(((((((........)))))))	chr7:128409554-128409790(+)$1	1	206	228	16.7042
(((((((........)))))))	chr20:31437311-31437548(+)$1	1	73	95	16.1422
(((..((........))..)))	chr15:31667002-31667229(+)$1	1	79	101	15.0210
(((((((........)))))))	chrX:150575718-150575977(+)$1	1	139	161	16.1422
(((..((........))...))	chr1:204372711-204372947(-)$1	1	181	203	14.0511
(((((((........).)).))	chr6:64290777-64291176(+)$1	1	95	117	13.5127
(((((((........)))))))	chr5:159503418-159503645(-)$1	1	185	207	16.1422
(.(((((........)))))..	chrX:46739394-46739620(+)$1	1	92	114	15.5261
(((((((........)))))))	chr8:59360068-59360318(+)$1	1	185	207	16.2120
(((..((........))..)))	chr9:89559686-89559964(-)$1	1	45	67	15.3409
..(((((........)))))..	chr12:54631265-54631538(-)$1	1	172	194	15.5305
...((((........))))...	chr2:179380430-179380657(+)$1	1	103	125	14.9899
(((((((........)))))))	chr11:86520850-86521073(+)$1	1	57	79	16.7042
(((((((........)))))))	chr3:51431620-51431886(+)$1	1	62	84	16.7042
(.(((((........))))).)	chr2:207939809-207940037(-)$1	1	124	146	14.8849
(((((((........)))))).	chr12:72317704-72317961(+)$1	1	80	102	13.2885
....(((........)))....	chr7:50512341-50512609(-)$1	1	134	156	15.4482
((((.((........)).))))	chr2:204301872-204302093(-)$1	1	129	151	15.4652
(((((((........)))))))	chr8:92097506-92097727(+)$1	1	163	185	16.1422
((((.((........)))))))	chr15:69732978-69733207(+)$1	1	34	56	15.9405
((((.((........)))))))	chr7:63985320-63985561(-)$1	1	151	173	14.3816
(((((((........)))))))	chr2:68406665-68406916(-)$1	1	160	182	16.7042
(((((((........)))))).	chr10:102122136-102122396(+)$1	1	187	209	14.6741
.((((((........)))))).	chr1:6583184-6583413(-)$1	1	117	139	15.0751
(((((((........)))))..	chr5:78982294-78982522(+)$1	1	132	154	14.7975
(...(((........)))..))	chr5:143538060-143538298(-)$1	1	129	151	15.5447
(((((((........)))))))	chr7:86509204-86509432(-)$1	1	194	216	16.1422
..(.(((........))).)..	chr2:191556976-191557223(+)$1	1	62	84	15.6451
((((.((........)).))))	chr1:244869912-244870134(+)$1	1	176	198	15.8579
(((((((........)))))))	chr3:195778364-195778594(-)$1	1	39	61	16.2120
...((((........)))))))	chr2:48602576-48602848(+)$1	1	183	205	13.4346
(((((((........)))))))	chr3:48014995-48015228(-)$1	1	149	171	16.2120
.((((.(........).)))).	chr6:107474240-107474483(-)$1	1	207	229	13.9753
(((((((........)))))))	chr11:102102538-102102773(+)$1	1	59	81	16.1422
..(((((........)))))..	chr8:90945817-90946072(-)$1	1	33	55	13.1719
(((((((........)))))).	chr7:20453703-20453930(+)$1	1	110	132	13.9659

#PSSM
g : 0.20	= : 0.12	f : 0.09	! : 0.09	i : 0.08	b : 0.06	d : 0.04	$ : 0.04	e : 0.04	" : 0.03	c : 0.03	# : 0.03	: : 0.01	H : 0.01	[ : 0.01	% : 0.01	h : 0.01	
g : 0.19	f : 0.16	= : 0.11	[ : 0.08	! : 0.08	i : 0.08	d : 0.04	$ : 0.04	e : 0.04	" : 0.03	b : 0.03	c : 0.03	# : 0.03	% : 0.01	
e : 0.20	g : 0.19	f : 0.14	= : 0.11	i : 0.08	d : 0.04	" : 0.03	[ : 0.03	$ : 0.03	a : 0.03	# : 0.03	! : 0.01	c : 0.01	b : 0.01	
e : 0.17	g : 0.17	f : 0.14	d : 0.12	= : 0.09	i : 0.08	[ : 0.08	! : 0.06	$ : 0.01	# : 0.01	" : 0.01	
e : 0.16	g : 0.16	f : 0.12	c : 0.12	d : 0.11	i : 0.08	[ : 0.08	! : 0.06	= : 0.06	b : 0.01	
e : 0.16	g : 0.16	b : 0.16	f : 0.12	c : 0.12	d : 0.09	i : 0.08	= : 0.06	[ : 0.01	
e : 0.16	g : 0.16	b : 0.14	c : 0.12	f : 0.11	d : 0.09	i : 0.08	= : 0.06	a : 0.04	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.16	g : 0.16	b : 0.14	c : 0.12	f : 0.11	d : 0.09	i : 0.08	= : 0.06	a : 0.04	
e : 0.16	g : 0.16	b : 0.14	c : 0.12	f : 0.11	d : 0.09	i : 0.08	= : 0.06	] : 0.04	
e : 0.16	g : 0.16	f : 0.14	d : 0.12	c : 0.12	i : 0.08	= : 0.08	2 : 0.04	] : 0.03	3 : 0.01	b : 0.01	
e : 0.17	g : 0.17	f : 0.14	d : 0.12	= : 0.09	i : 0.08	] : 0.06	2 : 0.06	a : 0.01	3 : 0.01	b : 0.01	4 : 0.01	
e : 0.19	g : 0.19	f : 0.14	= : 0.11	i : 0.08	3 : 0.04	2 : 0.04	d : 0.04	c : 0.04	] : 0.03	b : 0.01	4 : 0.01	a : 0.01	
g : 0.20	f : 0.16	= : 0.12	2 : 0.08	i : 0.08	d : 0.06	3 : 0.04	c : 0.04	e : 0.04	] : 0.03	b : 0.03	4 : 0.03	5 : 0.01	8 : 0.01	
g : 0.20	= : 0.12	i : 0.08	2 : 0.08	3 : 0.06	d : 0.06	c : 0.06	b : 0.04	f : 0.04	e : 0.04	: : 0.03	4 : 0.03	] : 0.03	5 : 0.01	h : 0.01	8 : 0.01	9 : 0.01	

#score	938.7823296664577
#seq	62
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_CDS_m2_run2.txt

#BEAR
eeeee[cccooooooccc]eeeee	chr1:31426684-31426903(-)$1	219	8	32	13.8776
ddgggggggooooooggggggg22	chr1:213186511-213186729(-)$1	218	175	199	12.1868
""bb[ddddoooooodddd]bb]e	chr5:71494530-71494749(+)$1	219	82	106	12.4859
iii####bboooooobb333iiii	chr14:51111488-51111709(-)$1	221	6	30	13.3557
===========lll==========	chr12:6632033-6632254(+)$1	221	7	31	9.1788
###ffffffooooooffffff333	chr17:57724710-57724920(+)$1	210	37	61	11.2461
ggg####bboooooobb333gggg	chr8:23294561-23294778(-)$1	217	30	54	13.3128
:dddd[cccooooooccc22dddd	chr1:115282254-115282464(-)$1	210	80	104	12.7599
####eeeeeooooooeeeee4444	chr19:36728104-36728331(+)$1	227	59	83	12.0356
e!!ffffffooooooffffff22e	chr2:73676971-73677197(+)$1	226	158	182	10.9075
[ccc[ddddoooooodddd333cc	chr2:24468934-24469153(-)$1	219	157	181	13.8069
!dddd[aooooooadddd22bb]c	chr16:2817741-2817967(+)$1	226	7	31	10.0419
ccc"""cccooooooccc333ccc	chr1:114308624-114308843(-)$1	219	118	142	15.0158
=========oooooo=========	chr19:34945260-34945478(+)$1	218	91	115	13.6204
ggggg[cccooooooccc]ggggg	chr1:155449453-155449681(-)$1	228	3	27	14.2377
eee"""cccnnnnnccc333eeee	chr2:242099761-242099979(+)$1	218	170	194	9.7541
gggg!!cccooooooccc22gggg	chr15:23012311-23012537(-)$1	226	20	44	14.6981
=========oooooo=========	chr6:56918710-56918931(+)$1	221	130	154	13.6204
eeeee[cccooooooccc333eee	chr19:53856443-53856664(+)$1	221	42	66	14.6166
h[dddd[bboooooobb333dddd	chr1:23637427-23637648(-)$1	221	29	53	12.1975
ggggg!!bboooooobb22ggggg	chr6:111654284-111654506(-)$1	222	103	127	12.5114
$$$$$ddddoooooodddd22fff	chr4:187535251-187535471(-)$1	220	140	164	12.0882
fff!!ddddooooooddddfffff	chr1:21219957-21220180(-)$1	223	175	199	12.6485
!bb!!ddddoooooodddd22bb2	chr10:101515326-101515546(+)$1	220	9	33	12.5444
eeea[ddddoooooodddd]a777	chr12:49426694-49426911(-)$1	217	46	70	11.6025
ccc[eeeeeooooooeeeee]ccc	chr8:48752525-48752746(-)$1	221	141	165	12.2171
cc[ffffffooooooffffff]cc	chr12:98927329-98927552(+)$1	223	195	219	11.1598
:dddd[cccooooooccc]ddddg	chr9:80336232-80336457(-)$1	225	180	204	12.4353
eeeee[cccooooooccc]eeeee	chr2:71582761-71582985(+)$1	224	127	151	13.8776
:dddd[cccooooooccc333ddd	chr1:197073992-197074223(-)$1	231	121	145	13.3240
eeeee[cccooooooccc22eeee	chr10:119042972-119043189(-)$1	217	171	195	14.1456
=========oooooo=========	chr4:24556256-24556476(-)$1	220	86	110	13.6204
ddd[eeeeeooooooeeeee]ddd	chr2:145157477-145157695(-)$1	218	80	104	11.9240
fffff!!bboooooobb22fffff	chr1:91404489-91404710(-)$1	221	90	114	11.2527
e[ddddcccooooooccc]dddd2	chr18:55274447-55274664(-)$1	217	130	154	13.0745
d:ccc[cccooooooccc]ccc::	chr6:87968455-87968674(+)$1	219	136	160	10.7935
fff"""cccooooooccc333fff	chr17:29663698-29663921(+)$1	223	7	31	14.3716
hhhhhhcccooooooccceeeeel	chr1:27106504-27106723(+)$1	219	114	138	11.7640
ccc!!ddddoooooodddd]ccc6	chr3:41274800-41275018(+)$1	218	13	37	13.2773
ccc!!cccaooooooa]ccc]ccc	chr20:49509685-49509904(-)$1	219	25	49	13.2443
eeee!!cccooooooccc]eeeee	chr2:232320622-232320839(-)$1	217	125	149	14.1866
ddd[eeeeeooooooeeeee]ddd	chr12:111168306-111168525(-)$1	219	21	45	11.9240
eee!!ddddoooooodddd]eeee	chr1:229738284-229738501(-)$1	217	79	103	13.7138
"ccc!!cccooooooccc]ccc33	chr1:90058443-90058664(+)$1	221	153	177	14.3897
eeeeeddddoooooodddd]eeee	chr5:125939327-125939546(+)$1	219	68	92	13.0951
[cccddddoooooodddd22ccc3	chr8:17611428-17611647(-)$1	219	63	87	11.8671
bbgggggggooooooggggggg==	chr21:34931963-34932179(+)$1	216	102	126	12.2223
eeeee[cccooooooccc]eeeee	chrX:70776797-70777014(+)$1	217	163	187	13.8776
g[bb[ddddoooooodddd]bbgg	chr19:41800424-41800642(+)$1	218	80	104	12.5521
dddd[ddddoooooodddd]dddd	chr4:17841705-17841926(+)$1	221	105	129	12.9736
dddd[ddddoooooodddddddde	chr4:187584353-187584578(-)$1	225	19	43	12.5614
ggg!!ddddoooooodddd]gggg	chr17:33951469-33951687(+)$1	218	127	151	13.8760
d$$$$$cccooooooccc333ddd	chr8:67576649-67576874(-)$1	225	132	156	13.6116

#otherMatches

#Seq PSSM
GCUUUUUUCUCUCUUGAAUGAAGU	chr1:31426684-31426903(-)$1	219	8	32	13.8776
AGUUCCAGUACUGUAACUGGAGAC	chr1:213186511-213186729(-)$1	218	175	199	12.1868
ACAGCAACUUGCCACAGUUCCUCU	chr5:71494530-71494749(+)$1	219	82	106	12.4859
GGAAAUUUGACUAACCAUGGUUCU	chr14:51111488-51111709(-)$1	221	6	30	13.3557
GUACCCCAGGCCCUGUUUGGGGUG	chr12:6632033-6632254(+)$1	221	7	31	9.1788
UUUGUUUUUAGCUGGGAAAACUCU	chr17:57724710-57724920(+)$1	210	37	61	11.2461
UGACUCCUGAUAUGCCGUACUUGG	chr8:23294561-23294778(-)$1	217	30	54	13.3128
CAGAACGUCAAGCUAGACUUUUCU	chr1:115282254-115282464(-)$1	210	80	104	12.7599
GAAAGCUUUCAGCCAGAAGUCACA	chr19:36728104-36728331(+)$1	227	59	83	12.0356
UGCCAGGUACUCAUAUACCUGAAG	chr2:73676971-73677197(+)$1	226	158	182	10.9075
UGAGUAAUAUUAAAUUAUUUUUCU	chr2:24468934-24469153(-)$1	219	157	181	13.8069
CCAGAACACCACCGUCUGCCCCAA	chr16:2817741-2817967(+)$1	226	7	31	10.0419
UGCAUCAGAACUUAAUCUACAGCA	chr1:114308624-114308843(-)$1	219	118	142	15.0158
UGGCAGGGAACAUUAUUCCUGCUA	chr19:34945260-34945478(+)$1	218	91	115	13.6204
AAGAAACUGUUGAAUCAGAUUCUU	chr1:155449453-155449681(-)$1	228	3	27	14.2377
AGUAUAUUCAGGGAGAGGCAGCUA	chr2:242099761-242099979(+)$1	218	170	194	9.7541
AAAUUACGAGUUUUAUUGAUAUUU	chr15:23012311-23012537(-)$1	226	20	44	14.6981
AGAGAUUAGCUAACAUUAAUUUCU	chr6:56918710-56918931(+)$1	221	130	154	13.6204
AUACUGGAGAAAAACCUUACAAGU	chr19:53856443-53856664(+)$1	221	42	66	14.6166
AAUCAGAGUCUUGAAGCAAACUGA	chr1:23637427-23637648(-)$1	221	29	53	12.1975
AUCACUUUAUCCUUCUAUUGUGAU	chr6:111654284-111654506(-)$1	222	103	127	12.5114
UUGGGACAAAAUAAAUUGUAUAUU	chr4:187535251-187535471(-)$1	220	140	164	12.0882
GUGCAAGUUCCCUACAACUCACUU	chr1:21219957-21220180(-)$1	223	175	199	12.6485
CCAUUUAAUAACAUAAUUAUCUGU	chr10:101515326-101515546(+)$1	220	9	33	12.5444
CAUCUUCAGCAGAGUCUGAUGUCA	chr12:49426694-49426911(-)$1	217	46	70	11.6025
AUUCUCAUGUGGAUUCAUGAUAAU	chr8:48752525-48752746(-)$1	221	141	165	12.2171
CUAUUUUAAAAGUAAUUGAAGAAG	chr12:98927329-98927552(+)$1	223	195	219	11.1598
AUCCUCCAGUUGAACCUGAAGGAG	chr9:80336232-80336457(-)$1	225	180	204	12.4353
GCUGUCGACAGUUACGUCAACAGU	chr2:71582761-71582985(+)$1	224	127	151	13.8776
AUCCAAUCUAUGUUCAGAAAAUGG	chr1:197073992-197074223(-)$1	231	121	145	13.3240
GCCUUAGCUAAAUCAGGUGAAAGG	chr10:119042972-119043189(-)$1	217	171	195	14.1456
AGAGGAAGAGGGAGAUCUUCUUCU	chr4:24556256-24556476(-)$1	220	86	110	13.6204
GUAUGUCUGAACAGACAGGCUUAC	chr2:145157477-145157695(-)$1	218	80	104	11.9240
AAGAAGCUAGUUCAUUAAAUUCUU	chr1:91404489-91404710(-)$1	221	90	114	11.2527
UAGAAGGUGGUGCCACACUCUUCA	chr18:55274447-55274664(-)$1	217	130	154	13.0745
GACAAUGUUAUACAAAACUUUGAA	chr6:87968455-87968674(+)$1	219	136	160	10.7935
UACUUUAGAACAACAUCUUAUGUG	chr17:29663698-29663921(+)$1	223	7	31	14.3716
CCGAGAGCAUUUGCCUGCCUGUCC	chr1:27106504-27106723(+)$1	219	114	138	11.7640
UCCUUUUUAAUUUUCUAGGUGGAA	chr3:41274800-41275018(+)$1	218	13	37	13.2773
GAAAAUGUCUAUAGUGUGCACUUC	chr20:49509685-49509904(-)$1	219	25	49	13.2443
GAAGGAAGCGUGAGUGCUGCUUCC	chr2:232320622-232320839(-)$1	217	125	149	14.1866
CAGAAAGCAACUACCUGUUUCUUG	chr12:111168306-111168525(-)$1	219	21	45	11.9240
GGUCCGUCUCCAAGAAGACAGCUA	chr1:229738284-229738501(-)$1	217	79	103	13.7138
UGUUGACUUAAAGAAAAGAGACCC	chr1:90058443-90058664(+)$1	221	153	177	14.3897
CUGUCUUUGGAAACGCAAACGACA	chr5:125939327-125939546(+)$1	219	68	92	13.0951
AGUUUAAUAAACUCAUUACUAGCC	chr8:17611428-17611647(-)$1	219	63	87	11.8671
CAAUUUGCCCUCAGAGGUAAGUAG	chr21:34931963-34932179(+)$1	216	102	126	12.2223
ACUGUUUAUUAUAAUAUGUGCAGU	chrX:70776797-70777014(+)$1	217	163	187	13.8776
GAUGUCCUGAUCCAGCAGGCCACC	chr19:41800424-41800642(+)$1	218	80	104	12.5521
ACUACUUUCCAAAAUGAAGAUGGU	chr4:17841705-17841926(+)$1	221	105	129	12.9736
gguccagaucgaggcauuugaucc	chr4:187584353-187584578(-)$1	225	19	43	12.5614
AGGCUCAGAGGUCAGUCUGUUUUC	chr17:33951469-33951687(+)$1	218	127	151	13.8760
CGAUACGGGUUUCCUCCUAAAGAG	chr8:67576649-67576874(-)$1	225	132	156	13.6116

#DB
(((((.(((......))).)))))	chr1:31426684-31426903(-)$1	1	8	32	13.8776
(((((((((......)))))))..	chr1:213186511-213186729(-)$1	1	175	199	12.1868
..((.((((......)))).)).)	chr5:71494530-71494749(+)$1	1	82	106	12.4859
(((....((......))...))))	chr14:51111488-51111709(-)$1	1	6	30	13.3557
(((((((((((...))))))))))	chr12:6632033-6632254(+)$1	1	7	31	9.1788
...((((((......))))))...	chr17:57724710-57724920(+)$1	1	37	61	11.2461
(((....((......))...))))	chr8:23294561-23294778(-)$1	1	30	54	13.3128
.((((.(((......)))..))))	chr1:115282254-115282464(-)$1	1	80	104	12.7599
....(((((......)))))....	chr19:36728104-36728331(+)$1	1	59	83	12.0356
(..((((((......))))))..)	chr2:73676971-73677197(+)$1	1	158	182	10.9075
.(((.((((......))))...))	chr2:24468934-24469153(-)$1	1	157	181	13.8069
.((((.(......)))))..)).)	chr16:2817741-2817967(+)$1	1	7	31	10.0419
(((...(((......)))...)))	chr1:114308624-114308843(-)$1	1	118	142	15.0158
(((((((((......)))))))))	chr19:34945260-34945478(+)$1	1	91	115	13.6204
(((((.(((......))).)))))	chr1:155449453-155449681(-)$1	1	3	27	14.2377
(((...(((.....)))...))))	chr2:242099761-242099979(+)$1	1	170	194	9.7541
((((..(((......)))..))))	chr15:23012311-23012537(-)$1	1	20	44	14.6981
(((((((((......)))))))))	chr6:56918710-56918931(+)$1	1	130	154	13.6204
(((((.(((......)))...)))	chr19:53856443-53856664(+)$1	1	42	66	14.6166
(.((((.((......))...))))	chr1:23637427-23637648(-)$1	1	29	53	12.1975
(((((..((......))..)))))	chr6:111654284-111654506(-)$1	1	103	127	12.5114
.....((((......))))..)))	chr4:187535251-187535471(-)$1	1	140	164	12.0882
(((..((((......)))))))))	chr1:21219957-21220180(-)$1	1	175	199	12.6485
.((..((((......))))..)).	chr10:101515326-101515546(+)$1	1	9	33	12.5444
((((.((((......)))).)...	chr12:49426694-49426911(-)$1	1	46	70	11.6025
(((.(((((......))))).)))	chr8:48752525-48752746(-)$1	1	141	165	12.2171
((.((((((......)))))).))	chr12:98927329-98927552(+)$1	1	195	219	11.1598
.((((.(((......))).))))(	chr9:80336232-80336457(-)$1	1	180	204	12.4353
(((((.(((......))).)))))	chr2:71582761-71582985(+)$1	1	127	151	13.8776
.((((.(((......)))...)))	chr1:197073992-197074223(-)$1	1	121	145	13.3240
(((((.(((......)))..))))	chr10:119042972-119043189(-)$1	1	171	195	14.1456
(((((((((......)))))))))	chr4:24556256-24556476(-)$1	1	86	110	13.6204
(((.(((((......))))).)))	chr2:145157477-145157695(-)$1	1	80	104	11.9240
(((((..((......))..)))))	chr1:91404489-91404710(-)$1	1	90	114	11.2527
(.(((((((......))).)))).	chr18:55274447-55274664(-)$1	1	130	154	13.0745
).(((.(((......))).)))..	chr6:87968455-87968674(+)$1	1	136	160	10.7935
(((...(((......)))...)))	chr17:29663698-29663921(+)$1	1	7	31	14.3716
))))))(((......)))(((((.	chr1:27106504-27106723(+)$1	1	114	138	11.7640
(((..((((......)))).))).	chr3:41274800-41275018(+)$1	1	13	37	13.2773
(((..((((......).))).)))	chr20:49509685-49509904(-)$1	1	25	49	13.2443
((((..(((......))).)))))	chr2:232320622-232320839(-)$1	1	125	149	14.1866
(((.(((((......))))).)))	chr12:111168306-111168525(-)$1	1	21	45	11.9240
(((..((((......)))).))))	chr1:229738284-229738501(-)$1	1	79	103	13.7138
.(((..(((......))).)))..	chr1:90058443-90058664(+)$1	1	153	177	14.3897
(((((((((......)))).))))	chr5:125939327-125939546(+)$1	1	68	92	13.0951
.(((((((......))))..))).	chr8:17611428-17611647(-)$1	1	63	87	11.8671
))(((((((......)))))))((	chr21:34931963-34932179(+)$1	1	102	126	12.2223
(((((.(((......))).)))))	chrX:70776797-70777014(+)$1	1	163	187	13.8776
(.((.((((......)))).))))	chr19:41800424-41800642(+)$1	1	80	104	12.5521
((((.((((......)))).))))	chr4:17841705-17841926(+)$1	1	105	129	12.9736
((((.((((......)))))))))	chr4:187584353-187584578(-)$1	1	19	43	12.5614
(((..((((......)))).))))	chr17:33951469-33951687(+)$1	1	127	151	13.8760
(.....(((......)))...)))	chr8:67576649-67576874(-)$1	1	132	156	13.6116

#PSSM
e : 0.22	d : 0.13	g : 0.11	c : 0.09	= : 0.07	: : 0.05	f : 0.05	" : 0.03	# : 0.03	[ : 0.03	! : 0.03	h : 0.03	i : 0.01	$ : 0.01	b : 0.01	
e : 0.18	d : 0.16	c : 0.15	g : 0.09	= : 0.07	[ : 0.05	f : 0.05	# : 0.03	$ : 0.03	b : 0.03	" : 0.01	i : 0.01	! : 0.01	: : 0.01	h : 0.01	
e : 0.18	d : 0.18	c : 0.15	g : 0.13	= : 0.07	b : 0.05	f : 0.05	# : 0.03	$ : 0.03	i : 0.01	! : 0.01	[ : 0.01	h : 0.01	
d : 0.15	e : 0.13	! : 0.11	g : 0.09	= : 0.07	f : 0.07	c : 0.07	# : 0.05	" : 0.05	[ : 0.05	b : 0.03	$ : 0.03	a : 0.01	h : 0.01	
e : 0.18	! : 0.16	d : 0.13	[ : 0.11	g : 0.07	= : 0.07	f : 0.07	" : 0.05	# : 0.03	$ : 0.03	c : 0.01	h : 0.01	
d : 0.30	[ : 0.20	! : 0.09	= : 0.07	e : 0.07	f : 0.05	" : 0.05	g : 0.03	# : 0.03	h : 0.01	c : 0.01	$ : 0.01	
c : 0.37	d : 0.26	= : 0.07	e : 0.07	f : 0.05	g : 0.03	# : 0.03	! : 0.03	a : 0.01	[ : 0.01	
c : 0.37	d : 0.26	b : 0.09	= : 0.07	e : 0.07	f : 0.05	g : 0.03	o : 0.01	
c : 0.35	d : 0.24	b : 0.09	= : 0.07	e : 0.07	f : 0.05	g : 0.03	o : 0.03	a : 0.01	
o : 0.96	= : 0.01	n : 0.01	
o : 0.96	= : 0.01	n : 0.01	
o : 0.96	l : 0.01	n : 0.01	
o : 0.96	l : 0.01	n : 0.01	
o : 0.94	l : 0.01	a : 0.01	n : 0.01	
o : 0.92	d : 0.03	= : 0.01	c : 0.01	
c : 0.35	d : 0.28	b : 0.09	= : 0.07	e : 0.07	f : 0.05	g : 0.03	a : 0.01	
c : 0.35	d : 0.28	b : 0.09	= : 0.07	e : 0.07	f : 0.05	g : 0.03	] : 0.01	
c : 0.35	d : 0.28	3 : 0.07	= : 0.07	e : 0.07	f : 0.05	g : 0.03	2 : 0.03	
d : 0.24	] : 0.16	3 : 0.16	2 : 0.13	e : 0.09	= : 0.07	f : 0.05	g : 0.03	c : 0.01	
3 : 0.18	e : 0.16	] : 0.15	2 : 0.13	f : 0.09	g : 0.07	= : 0.07	d : 0.05	c : 0.05	
e : 0.16	g : 0.13	d : 0.11	3 : 0.11	f : 0.09	= : 0.07	] : 0.07	c : 0.07	b : 0.05	2 : 0.03	i : 0.01	4 : 0.01	a : 0.01	
e : 0.18	d : 0.18	g : 0.13	c : 0.13	b : 0.07	= : 0.07	f : 0.07	3 : 0.03	i : 0.01	4 : 0.01	2 : 0.01	7 : 0.01	] : 0.01	
e : 0.18	d : 0.18	c : 0.13	g : 0.11	= : 0.09	f : 0.07	2 : 0.03	] : 0.03	3 : 0.03	i : 0.01	4 : 0.01	b : 0.01	7 : 0.01	: : 0.01	
e : 0.22	g : 0.13	d : 0.13	c : 0.11	= : 0.09	f : 0.07	2 : 0.05	3 : 0.05	i : 0.01	4 : 0.01	7 : 0.01	: : 0.01	l : 0.01	6 : 0.01	

#score	675.6865738579017
#seq	53
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_UTR_m3_run1.txt

#BEAR
h!!iiiiiiiii[ddddoooooodddd333iiiiiiiii4	chr2:131809116-131809356(-)$1	240	148	188	19.4352
c!!==========####bblllbb22==========22cc	chr19:40316021-40316261(-)$1	240	175	215	16.5367
[eeeee[dddd####cccnnnnnccc4444dddd22eeee	chr15:55651035-55651275(-)$1	240	58	98	12.9005
iiiiiiiii[bb"""cccooooooccc333bb]iiiiiii	chr11:60658153-60658393(-)$1	240	74	114	20.7665
:iiiiiiiii$$$$$ddddmmmmdddd4444iiiiiiiii	chr5:126888171-126888411(+)$1	240	197	237	19.4949
===========zzzzzzzzzzzzzzzzz===========]	chr1:100549595-100549835(-)$1	240	100	140	16.3269
!ccc[bb[ccc$$$$$cccmmmmccc4444ccc]bb]ccc	chr13:24879691-24879933(+)$1	242	155	195	15.3106
========[ccceeeeebbmmmmbb]eeeee]ccc]====	chr2:169727775-169728015(-)$1	240	172	212	14.6438
ffffff[bb[bb"""cccooooooccc333bb]bb]ffff	chr12:67707327-67707567(+)$1	240	38	78	14.8941
=======ffffff!!cccooooooccc]ffffff22====	chr22:47073075-47073315(+)$1	240	51	91	16.5320
"ccc[ccccccccc[ddddmmmmdddd333ccc22ccc]c	chr8:18387700-18387940(-)$1	240	9	49	15.6253
$================oooooo================5	chr11:105969142-105969382(+)$1	240	84	124	19.2649
d]cccccc[ccc####ddddllldddd4444ccc]ccc::	chr20:60550097-60550337(-)$1	240	104	144	14.0059
[bb[ccc[eeeee!!cccooooooccc22eeeeeccc]bb	chr2:97476669-97476909(+)$1	240	20	60	13.4622
========&&&&&&&ddddoooooodddd4444=======	chr21:35476675-35476915(+)$1	240	133	173	16.3462
+iiiiiiiiibb!!ddddnnnnndddd333bb22iiiiii	chr1:150192400-150192644(-)$1	244	76	116	17.4313
==========="""eeeeeooooooeeeee4444======	chr13:27642629-27642869(-)$1	240	137	177	19.7368
!!a[ffffff"""eeeeeooooooeeeee333ffffff]a	chr15:82334427-82334667(-)$1	240	35	75	14.0073
[ggggggg"""ccc[ddddmmmmdddd]ccc333gggggg	chr7:33045923-33046163(+)$1	240	37	77	17.1170
iiiiiiiii[dddd[ddddnnnnndddd]dddd]iiiiii	chrX:46740792-46741034(+)$1	242	4	44	15.8628
gggggggccc$$$$$eeeeellleeeeeccc]ggggggg:	chr2:12882589-12882829(+)$1	240	120	160	13.7557
======####ccc"""ccclllccc4444ccc4444====	chr5:72877416-72877656(+)$1	240	63	103	18.5622
ddd[ccc[ffffffddddnnnnndddd4444ffffffccc	chr1:84701132-84701374(+)$1	242	159	199	12.4035
iiiiiiiii"""bb[ddddnnnnndddd]bb22iiiiiii	chr2:26613330-26613570(+)$1	240	155	195	16.8984
=========[iiiiiiiiimmmmiiiiiiiii333=====	chrX:44971455-44971695(+)$1	240	116	156	18.5820
iiiiiiiii$$$$$ffffffooooooffffffiiiiiiii	chr14:51189666-51189906(-)$1	240	81	121	15.0505
===================oooooo===============	chr8:67476304-67476544(-)$1	240	92	132	20.5791
cc!!ggggggg####cccqqqqqqqqccc4444ggggggg	chrX:37590334-37590574(+)$1	240	38	78	14.0490
==========!!eeeeeooooooeeeee22==========	chr1:68168779-68169019(-)$1	240	7	47	19.2446
ggg[ggggggg####ddddmmmmdddd4444ggggggg22	chr19:21303205-21303445(+)$1	240	46	86	18.3501
dddd!!=============mmmm=============]ddd	chr14:35179672-35179912(-)$1	240	176	216	16.1549
e!!ccc!!ccc[gggggggooooooggggggg]ccc]ccc	chrX:37591241-37591481(+)$1	240	45	85	13.6308
:iiiiiiiii$$$$$ddddmmmmdddd4444iiiiiiiii	chr5:126888327-126888567(+)$1	240	41	81	19.4949
+=========="""cccqqqqqqqqccc22==========	chr5:143538103-143538352(-)$1	249	173	213	16.6857
#=============!!cccmmmmccc=============e	chr1:35649879-35650126(-)$1	247	163	203	20.2366
dd[iiiiiiiii####ccclllccc4444iiiiiiiii]d	chr4:95586025-95586265(+)$1	240	62	102	19.0148
============"""ddddmmmmdddd=============	chr12:105197416-105197656(-)$1	240	5	45	21.8523
=========[dddd[ddddmmmmdddd]dddd22======	chr10:97071719-97071965(-)$1	246	79	119	17.4925
c==========####ddddmmmmdddd333==========	chr6:159054571-159054811(+)$1	240	172	212	22.7990
===!!iiiiiiiiillliiiiiiiii4444==========	chr1:67877375-67877615(-)$1	240	111	151	15.5116
c============"""cccmmmmccc22============	chr1:224346497-224346737(+)$1	240	79	119	20.8455
::=============ddddmmmmdddd22===========	chr6:96056411-96056651(+)$1	240	148	188	18.3239
dd[dddd"""ccc"""cccmmmmccc333ccc4444dddd	chr5:175934404-175934644(+)$1	240	176	216	14.6280
b[ggggggg!!ccc[cccooooooccc]ccc333gggggg	chr10:35858072-35858317(+)$1	245	146	186	17.2350
gggggggiiiiiiiiiddddllldddd333iiiiiiiii:	chr15:44063868-44064108(+)$1	240	42	82	17.5409
===========xxxxxxxxxxxxxxx==============	chr22:40727546-40727786(+)$1	240	103	143	16.8192
d[iiiiiiiii[eeeeeooooooeeeee]iiiiiiiii]d	chr9:86276342-86276582(-)$1	240	16	56	17.1425

#otherMatches

#Seq PSSM
UGUUUUUAUAUGUCUUUAUUGGAAAAGUCCUAUGUAAAAC	chr2:131809116-131809356(-)$1	240	148	188	19.4352
CCCCCCUCACCCCAGGACCCUAGGAGGGGGUGGGGGCAGG	chr19:40316021-40316261(-)$1	240	175	215	16.5367
GGCACAAAGAGGCAAACUAAGCAAGUCAAAUUCUAAUGUG	chr15:55651035-55651275(-)$1	240	58	98	12.9005
GCAGUUCCUGUGAGACAGGAGAGGCUGAGCCAAGGGAACU	chr11:60658153-60658393(-)$1	240	74	114	20.7665
AUUAUUUUUGUAUAAUACUGUUCAGUACUUCCAAGAAUAA	chr5:126888171-126888411(+)$1	240	197	237	19.4949
GUAAGAAAGAAUCUUUGCUAAUUUUUUUUUUUUUUUUACG	chr1:100549595-100549835(-)$1	240	100	140	16.3269
AGAAAAGAUGACAUAACAUUUUGAUGAAUUUCACCUAUUC	chr13:24879691-24879933(+)$1	242	155	195	15.3106
uacaugugcacaaugugcagguuuguuacauauguauaca	chr2:169727775-169728015(-)$1	240	172	212	14.6438
UUUUCUUAAUGCCAGUGUGAAUUUGCAGAUGUUUUCAGAA	chr12:67707327-67707567(+)$1	240	38	78	14.8941
AGCGUCUGGCGGGGACAGCUAGUAUUGACUUGCCCAGGAC	chr22:47073075-47073315(+)$1	240	51	91	16.5320
AGUAUAUCAGGGCAUCCCAGGAUUGGGUACUGUAUCCUAG	chr8:18387700-18387940(-)$1	240	9	49	15.6253
UAGUAAAAGaaaaaaauuugaauguuuuuuuuuuuuauuu	chr11:105969142-105969382(+)$1	240	84	124	19.2649
UUUGUACCUAUUUUUUUAUUACAAAUAUACUAAUUGGUUC	chr20:60550097-60550337(-)$1	240	104	144	14.0059
AAGGUCCAUGUUGGUCCUUCCACUGGGUGCAGCAGGAGCU	chr2:97476669-97476909(+)$1	240	20	60	13.4622
CUUUUAGGGAAAGACUUGGUCAACUCUAAUAUAUCUAGAA	chr21:35476675-35476915(+)$1	240	133	173	16.3462
UAGAGGUGAUCCAGGAAUCUUUAGUUUGAAGGCAGUUACC	chr1:150192400-150192644(-)$1	244	76	116	17.4313
CUGGUAGAGUCUAAGUAUUAUAUGAAGUGCCCAUGAUUCU	chr13:27642629-27642869(-)$1	240	137	177	19.7368
AUGGAGAUUUUAUAGGUUCAGACAAAUCUUCUAGAUCUGC	chr15:82334427-82334667(-)$1	240	35	75	14.0073
cgugauccgcccaccuuggccucccaaaguguugggauua	chr7:33045923-33046163(+)$1	240	37	77	17.1170
UUUGAUCACAAUUUACAAAUGAUCUUUGCAAAUAGUGGUC	chrX:46740792-46741034(+)$1	242	4	44	15.8628
CCUCUCCCCUAUUUUUUAAGUACCUUGGAGGAGGAGAGGU	chr2:12882589-12882829(+)$1	240	120	160	13.7557
UAUGUUCCAGUAAGGGUAUUAAGUAAAAAUUAAAUAAACG	chr5:72877416-72877656(+)$1	240	63	103	18.5622
ACAGUGCUCCAUUUUAUUUUGUUGGUGUUUCAGAUGGGCA	chr1:84701132-84701374(+)$1	242	159	199	12.4035
GAAAUGAGUCACGGCACUAACUCAUGGUUCUAUACUCAUU	chr2:26613330-26613570(+)$1	240	155	195	16.8984
auauauauuuuauauauacuuauguauguauauauaauau	chrX:44971455-44971695(+)$1	240	116	156	18.5820
UGAAGUUUGAGAUCUGAUGAGAAUGGUUGUUAUAAACUUU	chr14:51189666-51189906(-)$1	240	81	121	15.0505
AAGGAAGGAUAGAAAGUUGCACUACUAAUUUUUUGUUUUU	chr8:67476304-67476544(-)$1	240	92	132	20.5791
AGCUAGGUUGUCCUAUUGGCAUAAAACAAACCAGCAACUU	chrX:37590334-37590574(+)$1	240	38	78	14.0490
GAAACAUGCUCUUUUACCUAACAGUAAACAAGUAUGUUUU	chr1:68168779-68169019(-)$1	240	7	47	19.2446
GGGGUUAACUUAUAAUAUUGAGUGGUGCAUGAGGUUGGUG	chr19:21303205-21303445(+)$1	240	46	86	18.3501
GCUAAUUAGUAAAAUAUUGAAGGCAAUAUUUUACUGCUAG	chr14:35179672-35179912(-)$1	240	176	216	16.1549
AUGAGCUUUCGUUGACUGCUUCUCUGCAGUCGUUGAUGCU	chrX:37591241-37591481(+)$1	240	45	85	13.6308
AUUAUUUUUGUAUAAUACUGUUCAGUACUUCCAAGAAUAA	chr5:126888327-126888567(+)$1	240	41	81	19.4949
UCAUUUGUCUUUUUCAGUAUAGUUUUUGUUAAGGCAAAUG	chr5:143538103-143538352(-)$1	249	173	213	16.6857
UUUAUGGAUGUUAGCAGUUUAUUGACCUAAUAUUUGUAAA	chr1:35649879-35650126(-)$1	247	163	203	20.2366
AAGAUUUUUUAUCAAAAUGUGUCAUGCCAGUAAGAGAUGU	chr4:95586025-95586265(+)$1	240	62	102	19.0148
GCCCGUUGACUUACGCUUUUAAAAAAGAAGUUGGUGGGUU	chr12:105197416-105197656(-)$1	240	5	45	21.8523
GAGGAAAGGUAACUCUGAUCUCAGUUACAGUUUUUUUUUC	chr10:97071719-97071965(-)$1	246	79	119	17.4925
UUUGUUUUAAAAACCUUGUAAAUAUGAAUGUUUAAGACAA	chr6:159054571-159054811(+)$1	240	172	212	22.7990
AGUGAAGGAAUUUUUAAAAAAUUUUUAAGAAUUGUUUGUC	chr1:67877375-67877615(-)$1	240	111	151	15.5116
UUGAGGGAAGCUUUUUAAUAUUAGUUUCAAGCUUUCCUUA	chr1:224346497-224346737(+)$1	240	79	119	20.8455
cagugucugugggggauugguuccaguuaccccuauagau	chr6:96056411-96056651(+)$1	240	148	188	18.3239
CCUGGGCUCCUUAGCCCACAAUAGUGUAAUAAAAGUGCCC	chr5:175934404-175934644(+)$1	240	176	216	14.6280
CGUCAAGCUGCCUGGAUGAGCGCCCAUGCAGCAAGGCUUG	chr10:35858072-35858317(+)$1	245	146	186	17.2350
uagccauacaguugcuaccauacuggucacggcagCUGUA	chr15:44063868-44064108(+)$1	240	42	82	17.5409
uuuuuuuuuuuuuuuuuuuuuuuuuCAAAAAAAAAAGUCC	chr22:40727546-40727786(+)$1	240	103	143	16.8192
GUGGAGUACAGUAAGAUGUGUGGGUUUUUCUGUAUUUUUC	chr9:86276342-86276582(-)$1	240	16	56	17.1425

#DB
(..(((((((((.((((......))))...))))))))).	chr2:131809116-131809356(-)$1	1	148	188	19.4352
(..((((((((((....((...))..))))))))))..))	chr19:40316021-40316261(-)$1	1	175	215	16.5367
.(((((.((((....(((.....)))....))))..))))	chr15:55651035-55651275(-)$1	1	58	98	12.9005
(((((((((.((...(((......)))...)).)))))))	chr11:60658153-60658393(-)$1	1	74	114	20.7665
.(((((((((.....((((....))))....)))))))))	chr5:126888171-126888411(+)$1	1	197	237	19.4949
(((((((((((.................))))))))))).	chr1:100549595-100549835(-)$1	1	100	140	16.3269
.(((.((.(((.....(((....)))....))).)).)))	chr13:24879691-24879933(+)$1	1	155	195	15.3106
((((((((.((((((((((....)).))))).))).))))	chr2:169727775-169728015(-)$1	1	172	212	14.6438
((((((.((.((...(((......)))...)).)).))))	chr12:67707327-67707567(+)$1	1	38	78	14.8941
(((((((((((((..(((......))).))))))..))))	chr22:47073075-47073315(+)$1	1	51	91	16.5320
.(((.(((((((((.((((....))))...)))..))).)	chr8:18387700-18387940(-)$1	1	9	49	15.6253
.((((((((((((((((......)))))))))))))))).	chr11:105969142-105969382(+)$1	1	84	124	19.2649
).)))(((.(((....((((...))))....))).)))..	chr20:60550097-60550337(-)$1	1	104	144	14.0059
.((.(((.(((((..(((......)))..)))))))).))	chr2:97476669-97476909(+)$1	1	20	60	13.4622
((((((((.......((((......))))....)))))))	chr21:35476675-35476915(+)$1	1	133	173	16.3462
.(((((((((((..((((.....))))...))..))))))	chr1:150192400-150192644(-)$1	1	76	116	17.4313
(((((((((((...(((((......)))))....))))))	chr13:27642629-27642869(-)$1	1	137	177	19.7368
..(.((((((...(((((......)))))...)))))).)	chr15:82334427-82334667(-)$1	1	35	75	14.0073
.(((((((...(((.((((....)))).)))...))))))	chr7:33045923-33046163(+)$1	1	37	77	17.1170
(((((((((.((((.((((.....)))).)))).))))))	chrX:46740792-46741034(+)$1	1	4	44	15.8628
((((((((((.....(((((...)))))))).))))))).	chr2:12882589-12882829(+)$1	1	120	160	13.7557
((((((....(((...(((...)))....)))....))))	chr5:72877416-72877656(+)$1	1	63	103	18.5622
(((.(((.((((((((((.....))))....)))))))))	chr1:84701132-84701374(+)$1	1	159	199	12.4035
(((((((((...((.((((.....)))).))..)))))))	chr2:26613330-26613570(+)$1	1	155	195	16.8984
(((((((((.(((((((((....)))))))))...)))))	chrX:44971455-44971695(+)$1	1	116	156	18.5820
(((((((((.....((((((......))))))))))))))	chr14:51189666-51189906(-)$1	1	81	121	15.0505
(((((((((((((((((((......)))))))))))))))	chr8:67476304-67476544(-)$1	1	92	132	20.5791
((..(((((((....(((........)))....)))))))	chrX:37590334-37590574(+)$1	1	38	78	14.0490
((((((((((..(((((......)))))..))))))))))	chr1:68168779-68169019(-)$1	1	7	47	19.2446
(((.(((((((....((((....))))....)))))))..	chr19:21303205-21303445(+)$1	1	46	86	18.3501
((((..(((((((((((((....))))))))))))).)))	chr14:35179672-35179912(-)$1	1	176	216	16.1549
(..(((..(((.(((((((......))))))).))).)))	chrX:37591241-37591481(+)$1	1	45	85	13.6308
.(((((((((.....((((....))))....)))))))))	chr5:126888327-126888567(+)$1	1	41	81	19.4949
.((((((((((...(((........)))..))))))))))	chr5:143538103-143538352(-)$1	1	173	213	16.6857
.(((((((((((((..(((....)))))))))))))))))	chr1:35649879-35650126(-)$1	1	163	203	20.2366
((.(((((((((....(((...)))....))))))))).)	chr4:95586025-95586265(+)$1	1	62	102	19.0148
((((((((((((...((((....)))))))))))))))))	chr12:105197416-105197656(-)$1	1	5	45	21.8523
(((((((((.((((.((((....)))).))))..))))))	chr10:97071719-97071965(-)$1	1	79	119	17.4925
)((((((((((....((((....))))...))))))))))	chr6:159054571-159054811(+)$1	1	172	212	22.7990
(((..(((((((((...)))))))))....))))))))))	chr1:67877375-67877615(-)$1	1	111	151	15.5116
)((((((((((((...(((....)))..))))))))))))	chr1:224346497-224346737(+)$1	1	79	119	20.8455
..(((((((((((((((((....))))..)))))))))))	chr6:96056411-96056651(+)$1	1	148	188	18.3239
((.((((...(((...(((....)))...)))....))))	chr5:175934404-175934644(+)$1	1	176	216	14.6280
(.(((((((..(((.(((......))).)))...))))))	chr10:35858072-35858317(+)$1	1	146	186	17.2350
)))))))(((((((((((((...))))...))))))))).	chr15:44063868-44064108(+)$1	1	42	82	17.5409
(((((((((((...............))))))))))))))	chr22:40727546-40727786(+)$1	1	103	143	16.8192
(.(((((((((.(((((......))))).))))))))).)	chr9:86276342-86276582(-)$1	1	16	56	17.1425

#PSSM
= : 0.27	d : 0.12	c : 0.08	i : 0.08	[ : 0.06	: : 0.06	g : 0.06	! : 0.04	+ : 0.04	h : 0.02	f : 0.02	" : 0.02	$ : 0.02	e : 0.02	# : 0.02	b : 0.02	
= : 0.38	i : 0.14	! : 0.08	g : 0.08	d : 0.08	c : 0.06	[ : 0.04	e : 0.02	f : 0.02	] : 0.02	b : 0.02	: : 0.02	
= : 0.40	i : 0.17	g : 0.10	! : 0.08	c : 0.06	d : 0.04	[ : 0.04	e : 0.02	f : 0.02	b : 0.02	a : 0.02	
= : 0.40	i : 0.21	c : 0.08	[ : 0.08	g : 0.08	! : 0.04	d : 0.04	e : 0.02	f : 0.02	
= : 0.40	i : 0.21	g : 0.12	c : 0.08	[ : 0.04	f : 0.04	! : 0.04	e : 0.02	d : 0.02	
= : 0.40	i : 0.23	g : 0.12	c : 0.10	f : 0.04	e : 0.02	b : 0.02	! : 0.02	d : 0.02	
= : 0.40	i : 0.23	g : 0.12	c : 0.08	[ : 0.04	b : 0.02	f : 0.02	# : 0.02	! : 0.02	d : 0.02	
= : 0.38	i : 0.25	g : 0.08	[ : 0.06	c : 0.06	f : 0.04	d : 0.02	b : 0.02	# : 0.02	! : 0.02	" : 0.02	
= : 0.34	i : 0.25	c : 0.08	f : 0.06	g : 0.06	[ : 0.04	" : 0.04	d : 0.02	b : 0.02	e : 0.02	& : 0.02	# : 0.02	
= : 0.29	i : 0.17	c : 0.12	[ : 0.10	f : 0.06	" : 0.06	g : 0.04	d : 0.02	e : 0.02	& : 0.02	# : 0.02	$ : 0.02	! : 0.02	
= : 0.27	c : 0.14	i : 0.12	$ : 0.08	d : 0.06	b : 0.06	" : 0.06	f : 0.04	g : 0.04	! : 0.04	e : 0.02	& : 0.02	
= : 0.17	c : 0.14	i : 0.10	$ : 0.10	# : 0.08	" : 0.08	b : 0.06	f : 0.04	d : 0.04	[ : 0.04	z : 0.02	e : 0.02	& : 0.02	! : 0.02	x : 0.02	
= : 0.14	# : 0.12	" : 0.12	$ : 0.10	c : 0.10	e : 0.08	i : 0.06	f : 0.04	d : 0.04	[ : 0.02	z : 0.02	& : 0.02	! : 0.02	b : 0.02	g : 0.02	x : 0.02	
" : 0.17	# : 0.14	$ : 0.10	= : 0.10	e : 0.08	d : 0.06	! : 0.06	c : 0.06	i : 0.06	z : 0.02	& : 0.02	f : 0.02	b : 0.02	g : 0.02	x : 0.02	
# : 0.14	" : 0.12	[ : 0.12	e : 0.10	$ : 0.08	= : 0.08	d : 0.06	! : 0.06	i : 0.04	z : 0.02	& : 0.02	f : 0.02	g : 0.02	c : 0.02	l : 0.02	x : 0.02	
d : 0.31	c : 0.17	e : 0.12	# : 0.06	= : 0.06	" : 0.06	i : 0.04	z : 0.02	$ : 0.02	f : 0.02	g : 0.02	! : 0.02	l : 0.02	x : 0.02	
d : 0.36	c : 0.29	e : 0.12	= : 0.06	# : 0.02	z : 0.02	i : 0.02	f : 0.02	g : 0.02	l : 0.02	x : 0.02	
d : 0.34	c : 0.27	o : 0.08	e : 0.06	b : 0.04	i : 0.04	= : 0.04	z : 0.02	f : 0.02	g : 0.02	q : 0.02	x : 0.02	
d : 0.29	o : 0.21	c : 0.12	n : 0.06	b : 0.04	e : 0.04	i : 0.04	= : 0.04	q : 0.04	z : 0.02	f : 0.02	g : 0.02	x : 0.02	
m : 0.34	o : 0.29	n : 0.10	l : 0.06	d : 0.04	q : 0.04	z : 0.02	e : 0.02	f : 0.02	i : 0.02	x : 0.02	
m : 0.34	o : 0.31	l : 0.12	n : 0.10	q : 0.04	z : 0.02	i : 0.02	x : 0.02	
m : 0.34	o : 0.31	l : 0.12	n : 0.10	q : 0.04	z : 0.02	i : 0.02	x : 0.02	
m : 0.34	o : 0.31	n : 0.10	l : 0.06	c : 0.04	q : 0.04	b : 0.02	z : 0.02	i : 0.02	x : 0.02	
d : 0.29	o : 0.23	c : 0.14	e : 0.06	b : 0.04	= : 0.04	n : 0.04	i : 0.04	q : 0.04	z : 0.02	x : 0.02	
d : 0.34	c : 0.25	o : 0.10	e : 0.08	= : 0.04	i : 0.04	q : 0.04	2 : 0.02	z : 0.02	b : 0.02	x : 0.02	
d : 0.36	c : 0.23	e : 0.10	= : 0.06	4 : 0.04	i : 0.04	2 : 0.02	z : 0.02	] : 0.02	o : 0.02	q : 0.02	g : 0.02	x : 0.02	
d : 0.36	c : 0.14	= : 0.12	e : 0.12	4 : 0.10	z : 0.02	i : 0.02	f : 0.02	g : 0.02	2 : 0.02	3 : 0.02	
4 : 0.21	3 : 0.17	= : 0.14	e : 0.12	] : 0.08	2 : 0.06	d : 0.06	c : 0.04	z : 0.02	i : 0.02	f : 0.02	g : 0.02	
4 : 0.21	= : 0.19	3 : 0.17	2 : 0.08	c : 0.08	e : 0.06	] : 0.06	f : 0.04	d : 0.04	i : 0.02	g : 0.02	
= : 0.21	4 : 0.21	3 : 0.17	c : 0.10	e : 0.06	i : 0.06	f : 0.04	d : 0.04	2 : 0.04	b : 0.02	g : 0.02	
= : 0.29	4 : 0.17	c : 0.14	i : 0.10	b : 0.08	d : 0.06	e : 0.04	f : 0.04	3 : 0.02	g : 0.02	
= : 0.29	i : 0.14	c : 0.10	d : 0.06	b : 0.06	f : 0.06	4 : 0.06	3 : 0.06	] : 0.04	g : 0.04	e : 0.02	2 : 0.02	
= : 0.29	i : 0.14	4 : 0.10	c : 0.08	] : 0.06	f : 0.06	2 : 0.06	3 : 0.06	d : 0.04	g : 0.04	e : 0.02	
= : 0.31	i : 0.19	c : 0.06	f : 0.06	2 : 0.06	4 : 0.06	3 : 0.06	g : 0.06	] : 0.04	d : 0.02	b : 0.02	e : 0.02	
= : 0.36	i : 0.23	g : 0.10	2 : 0.06	c : 0.06	b : 0.04	f : 0.04	4 : 0.04	] : 0.02	3 : 0.02	
= : 0.38	i : 0.23	g : 0.10	c : 0.08	2 : 0.04	] : 0.04	f : 0.04	4 : 0.04	b : 0.02	
= : 0.40	i : 0.23	g : 0.10	] : 0.06	f : 0.06	c : 0.06	2 : 0.02	e : 0.02	d : 0.02	
= : 0.40	i : 0.23	c : 0.10	g : 0.10	f : 0.04	d : 0.04	2 : 0.02	e : 0.02	] : 0.02	
= : 0.40	i : 0.19	c : 0.08	] : 0.08	g : 0.08	d : 0.04	e : 0.02	f : 0.02	: : 0.02	b : 0.02	2 : 0.02	
= : 0.34	i : 0.14	c : 0.10	d : 0.08	: : 0.06	g : 0.06	e : 0.04	4 : 0.02	] : 0.02	f : 0.02	5 : 0.02	b : 0.02	a : 0.02	2 : 0.02	

#score	802.5862967074872
#seq	47
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_UTR_m1_run2.txt

#BEAR
eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr11:115046615-115046876(-)$1	261	106	140	37.5152
$ffffff^^^^^^^^^^^^^^^^^^^^^ffffff	chr12:53910117-53910339(-)$1	222	96	130	34.9784
ee[eeeee^^^^^^^^^^^^^^^^^^^eeeee]e	chr5:79774110-79774331(+)$1	221	64	98	34.7884
"""eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^	chr16:47116603-47116850(-)$1	247	96	130	36.9304
e[cccccc^^^^^^^^^^^^^^^^^^^ccc22cc	chr22:40725114-40725336(+)$1	222	93	127	34.9694
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ff	chr11:110036547-110036789(+)$1	242	105	139	37.0212
eeeee^^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr12:51636696-51636955(+)$1	259	127	161	36.9356
eee[dddd^^^^^^^^^^^^^^^^^^^^^^^^^^	chr20:21491747-21491974(-)$1	227	81	115	36.4016
ccc[ccc^^^^^^^^^^^^^^^^^^^^^cccccc	chr3:86994292-86994511(-)$1	219	172	206	36.3819
!!dddd^^^^^^^^^^^^^^^^^^^^^dddd333	chr17:76220371-76220589(+)$1	218	95	129	35.7347
^^^^^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chr19:52516817-52517038(-)$1	221	93	127	35.3045
ggggggg^^^^^^^^^^^^^^^^^^^^^gggggg	chr3:113163743-113163982(-)$1	239	94	128	36.4661
dddd!!ccc^^^^^^^^^^^^^^^^^^ccc22dd	chr1:230974058-230974283(-)$1	225	97	131	33.0636
dddddddd^^^^^^^^^^^^^^^^^^^dddd:gg	chr9:33047005-33047237(-)$1	232	103	137	33.2075
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^hh	chr17:38784292-38784513(-)$1	221	161	195	36.7504
========^^^^^^^^^^^^^^^^^^^^======	chr4:15690591-15690815(+)$1	224	28	62	36.6991
::ffffff^^^^^^^^^^^^^^^^^^^^ffffff	chr8:71023374-71023609(-)$1	235	184	218	32.7529
eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr6:56968573-56968808(+)$1	235	97	131	37.5152
iiiiiiii^^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:153946684-153946920(-)$1	236	100	134	37.0677
iiiiiiii^^^^^^^^^^^^^^^^^^^iiiiiii	chr4:76404960-76405183(-)$1	223	24	58	35.1719
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ff	chr5:134193530-134193759(+)$1	229	23	57	37.0212
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ff	chr11:27517170-27517417(-)$1	247	114	148	37.0212
eeeee^^^^^^^^^^^^^^^^^^^^^^^eeeee2	chr1:214524242-214524471(-)$1	229	101	135	36.1364
d"""eeeee^^^^^^^^^^^^^^^^^^eeeee]d	chr5:162946073-162946294(+)$1	221	16	50	33.1943
==[eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:172461767-172461991(+)$1	224	31	65	37.0394
iiiiiiii^^^^^^^^^^^^^^^^^^^^^^iiii	chr11:110038625-110038846(+)$1	221	160	194	36.8482
ggggggg^^^^^^^^^^^^^^^^^^^^^^^gggg	chr1:167391972-167392212(+)$1	240	92	126	37.2258
d"""eeeee^^^^^^^^^^^^^^^^^^eeeee33	chr1:245014982-245015206(-)$1	224	36	70	33.4762
gggggccc^^^^^^^^^^^^^^^^^^ccc333gg	chr3:196555191-196555420(+)$1	229	178	212	34.3358
fff!!ccc^^^^^^^^^^^^^^^^^^^^^^^^^^	chr19:53738191-53738418(-)$1	227	82	116	36.7387
!dddd^^^^^^^^^^^^^^^^^^^^^^dddd22c	chr13:41506325-41506547(-)$1	222	83	117	35.1611
ggggg[bb^^^^^^^^^^^^^^^^^^^^bbgggg	chr16:15959805-15960027(-)$1	222	91	125	35.4915
hhhhh[bb^^^^^^^^^^^^^^^^^^^bb]hhhh	chr19:39221081-39221304(+)$1	223	4	38	32.6107
dddddddd^^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:173871674-173871909(+)$1	235	150	184	36.0855
=====[bb^^^^^^^^^^^^^^^^^^^^bb]===	chr2:20449742-20449962(-)$1	220	63	97	35.8277
hhhhhhhh^^^^^^^^^^^^^^^^^^^^hhhhhh	chr2:198415971-198416216(+)$1	245	203	237	32.4264
========^^^^^^^^^^^^^^^^^^========	chr10:89730424-89730653(+)$1	229	19	53	34.4092
hhhh[ccc^^^^^^^^^^^^^^^^^^^^ccc]hh	chr9:14084685-14084920(-)$1	235	188	222	34.9747
dd^^^^^^^^^^^^^^^^^^^^^^^^^dddd:::	chr12:57607001-57607234(-)$1	233	59	93	32.2810
dddd^^^^^^^^^^^^^^^^^^^^^^^dddd]ff	chr11:77032900-77033129(-)$1	229	102	136	35.0486
iiiiiiii^^^^^^^^^^^^^^^^^^^^^^^^^^	chr4:25367391-25367615(+)$1	224	30	64	37.0677
[ffffff^^^^^^^^^^^^^^^^^^^^ffffff]	chr3:69069389-69069624(-)$1	235	107	141	34.3931
"bb^^^^^^^^^^^^^^^^^^^^^^^^^^^bb33	chr13:50592156-50592382(-)$1	226	30	64	36.4169
#eeeee^^^^^^^^^^^^^^^^^^^^^eeeee44	chr7:66105207-66105430(+)$1	223	113	147	35.6156
========^^^^^^^^^^^^^^^^^^^^======	chr6:131908282-131908512(-)$1	230	121	155	36.6991
ddd[dddd^^^^^^^^^^^^^^^^^^^^^ddddd	chr14:100744159-100744385(+)$1	226	96	130	34.9794
gggggggbb^^^^^^^^^^^^^^^^^^bb]gggg	chr22:40728731-40728955(+)$1	224	91	125	33.2959
b[ggggggg^^^^^^^^^^^^^^^^^^ggggggg	chr17:55197985-55198212(+)$1	227	90	124	33.2853
dddd^^^^^^^^^^^^^^^^^^^^^^^^^^dddd	chr11:62566583-62566812(-)$1	229	98	132	36.2851
iiiiiiii^^^^^^^^^^^^^^^^^^^^iiiiii	chr7:92086808-92087037(+)$1	229	1	35	36.0851
ggggggg^^^^^^^^^^^^^^^^^^^^^^ggggg	chr11:96085977-96086212(-)$1	235	105	139	36.8940
iiii[ccc^^^^^^^^^^^^^^^^^^^ccc]iii	chr11:107375508-107375726(-)$1	218	12	46	35.6217
dd[eeeee^^^^^^^^^^^^^^^^^^^eeeee]d	chr4:107269474-107269709(+)$1	235	94	128	34.6751
eeffffff^^^^^^^^^^^^^^^^^^^^^^^^^^	chr13:36876146-36876374(-)$1	228	68	102	36.1492
hhhhhhhh^^^^^^^^^^^^^^^^^^^^hhhhhh	chr2:178095003-178095221(-)$1	218	120	154	32.4264
iiiiiiii^^^^^^^^^^^^^^^^^^^iiiiiii	chr8:145978745-145978970(-)$1	225	102	136	35.1719
b[eeeee^^^^^^^^^^^^^^^^^^^^^^^^^ee	chr4:31145135-31145363(+)$1	228	121	155	36.9331
""eeeee^^^^^^^^^^^^^^^^^^^^eeeee33	chr9:96440969-96441189(+)$1	220	176	210	35.6589
fffff[bb^^^^^^^^^^^^^^^^^^^^^bb]ff	chr1:162498071-162498296(+)$1	225	91	125	34.9199
:::eeeee^^^^^^^^^^^^^^^^^^^^eeeeeC	chr13:21950161-21950416(-)$1	255	126	160	31.3986
::ffffff^^^^^^^^^^^^^^^^^^^ffffff:	chr12:49521485-49521710(-)$1	225	119	153	30.9700
cc!!dddd^^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:97284925-97285141(+)$1	216	13	47	36.6406
ffff[ccc^^^^^^^^^^^^^^^^^^ccc]ffff	chr17:29701084-29701311(+)$1	227	56	90	32.9662
##dddd^^^^^^^^^^^^^^^^^^^^^dddd22d	chr1:217781445-217781672(-)$1	227	144	178	34.8400
^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd]hh	chr4:96086987-96087207(-)$1	220	64	98	34.7701
cc[dddd^^^^^^^^^^^^^^^^^^^^ddddccc	chr6:146120558-146120778(-)$1	220	7	41	34.9191

#otherMatches

#Seq PSSM
UAGACUCUUUUCCUUCCCUUUUCUGUUCUAGUUU	chr11:115046615-115046876(-)$1	261	106	140	37.5152
GAGUUCUAAUUCUUUUUCAUCUAUUUGCAGAGCU	chr12:53910117-53910339(-)$1	222	96	130	34.9784
UAUAAGUAUAAAUUUAAAUGAACUAAUUACUUUU	chr5:79774110-79774331(+)$1	221	64	98	34.7884
CUUGAUUUUUCUUUACAUUCCUUUUAUUUUUCCU	chr16:47116603-47116850(-)$1	247	96	130	36.9304
GCUGCGCACUACAUUUACUUCUUUAUCUGCAAGU	chr22:40725114-40725336(+)$1	222	93	127	34.9694
AUUUAAACUUUUUUUUUUUAACAUUUCCUUUUUA	chr11:110036547-110036789(+)$1	242	105	139	37.0212
GCACUUCUCCCCACUCGUCAUCUUUUAACUAGUG	chr12:51636696-51636955(+)$1	259	127	161	36.9356
uuuuugCGUUUUCCCCUGCUUUCUUCCUUUCUCU	chr20:21491747-21491974(-)$1	227	81	115	36.4016
UUGCUGUUUCUUACCUAGACUCUCUUUUACACAA	chr3:86994292-86994511(-)$1	219	172	206	36.3819
GUGGCCUAAAUCCUUUUUAAAUGACUUGGCUCGA	chr17:76220371-76220589(+)$1	218	95	129	35.7347
aacucugccaaccacuuuucuccuaucaguauaa	chr19:52516817-52517038(-)$1	221	93	127	35.3045
UAAGGGUUUUUUUUAUUAAUACAUUUUUACCUUU	chr3:113163743-113163982(-)$1	239	94	128	36.4661
AACUCACCUCAACCCCUCAUCAUCUCCAGGAAAG	chr1:230974058-230974283(-)$1	225	97	131	33.0636
CUACCCUUUCUUUUUUUAUAUAUUUUUAAGGUAU	chr9:33047005-33047237(-)$1	232	103	137	33.2075
CCAUCCUUAUUGUAUAGAAAAAAAAUUACUUUUU	chr17:38784292-38784513(-)$1	221	161	195	36.7504
guaguauuuuucuauguuauauuuaaaugguacu	chr4:15690591-15690815(+)$1	224	28	62	36.6991
CUUCAUGAUACUGGUAAUUUAUAAUAAUUCGUGA	chr8:71023374-71023609(-)$1	235	184	218	32.7529
AGCACCCAUUUUUAAAUCUACUUUUCUUCCUUAU	chr6:56968573-56968808(+)$1	235	97	131	37.5152
UUAUUUCUCACUCAAAACUUAUUUCCCCUCAACC	chr1:153946684-153946920(-)$1	236	100	134	37.0677
aaagaagguaaaaaacucucaacaaucccuucuu	chr4:76404960-76405183(-)$1	223	24	58	35.1719
ACAUUUAUUUCCCUUUCAGUUUAUUUUCCUUCCU	chr5:134193530-134193759(+)$1	229	23	57	37.0212
uucuuuuuucuuuuuuuuAAUAAAAUCUACCAGU	chr11:27517170-27517417(-)$1	247	114	148	37.0212
CACUUUUUCUUUUCUUUACCUACCCUAUGAGUGC	chr1:214524242-214524471(-)$1	229	101	135	36.1364
UAAUAAUGGGCCUUGUAAGUCUUUUCACCAUUCA	chr5:162946073-162946294(+)$1	221	16	50	33.1943
AGCCAUCUCAACAGAAUCGCACCAAACUAUACUU	chr5:172461767-172461991(+)$1	224	31	65	37.0394
UAUUUGAACAUUCGCCAAAUUUUACAUUUAUUUA	chr11:110038625-110038846(+)$1	221	160	194	36.8482
GGAAAAGCUUUACUUUAUCUCUUUCCUUCCCUUU	chr1:167391972-167392212(+)$1	240	92	126	37.2258
UGAGAUAGCUAUGAGAAAACUAAAACUGCUAUGA	chr1:245014982-245015206(-)$1	224	36	70	33.4762
UGGUCUGCAUAACCUGAAUGAAAGAAGCAAAUGA	chr3:196555191-196555420(+)$1	229	178	212	34.3358
CAGUUAUAUUUCUACAUGCCUUUUUUUCUACAUA	chr19:53738191-53738418(-)$1	227	82	116	36.7387
GGGGUUGCAUACAAAGAUAACAUAUAUAUCCAAC	chr13:41506325-41506547(-)$1	222	83	117	35.1611
UUGCAAGAGUCCAUUUUCCAUUUUUAAAUCUGCA	chr16:15959805-15960027(-)$1	222	91	125	35.4915
UAUUCUGAUUGAUUUUUUUUCUUGGUUUCUGGAU	chr19:39221081-39221304(+)$1	223	4	38	32.6107
CCACCUCCCCCUCUUUCCCUUUACCGAAAAAAAA	chr1:173871674-173871909(+)$1	235	150	184	36.0855
AUUGGACUGAGAUAUUUGGUUACCAUGGAGGCCA	chr2:20449742-20449962(-)$1	220	63	97	35.8277
UAAUUGCUUACAGAUUAUACCUCAUAUUAGCAAU	chr2:198415971-198416216(+)$1	245	203	237	32.4264
AGAUGUUUCUCUUCAAAAAUCAUCUUAAACAUUU	chr10:89730424-89730653(+)$1	229	19	53	34.4092
GCAGGUCUUGCACGCCCCUCCCUUACCCAGAACU	chr9:14084685-14084920(-)$1	235	188	222	34.9747
Cuuuuuuucuuucuuuuuuuuuuuuuuggccuuu	chr12:57607001-57607234(-)$1	233	59	93	32.2810
UUUCUUUCCUUUUCUAAUUUUUUAUAUGAAAUAA	chr11:77032900-77033129(-)$1	229	102	136	35.0486
GGAAUAGUUAUCCCCAAAACAAAACAAAAAGAGA	chr4:25367391-25367615(+)$1	224	30	64	37.0677
UUUCUUACAUUUCUUUUACCUAUUUUUUGAGAAU	chr3:69069389-69069624(-)$1	235	107	141	34.3931
ACUGAAAAAUAAAAUAUUUCAAGCACACAAAGAA	chr13:50592156-50592382(-)$1	226	30	64	36.4169
UUAUAUUUUGUUUUACUCCUCACUCCUGUAUAUU	chr7:66105207-66105430(+)$1	223	113	147	35.6156
AAAUCUCUUGGUAGAUUUUCAGAAUAAUAGAGAU	chr6:131908282-131908512(-)$1	230	121	155	36.6991
GGGACUUCUUUUCACAUUCUUAUAAAUAUGAAGC	chr14:100744159-100744385(+)$1	226	96	130	34.9794
AUAGCAGGAUAACUUUAAAAAACAUUUUCUUUGC	chr22:40728731-40728955(+)$1	224	91	125	33.2959
UUGAGAGGGUUUCUUUUACUUCAAAAUCUUUCUU	chr17:55197985-55198212(+)$1	227	90	124	33.2853
Gucuuucucccuuuucucccucauuuuucuagau	chr11:62566583-62566812(-)$1	229	98	132	36.2851
AAUAUAAUGAAAUAUAUUUUGAACUUAAAUUAUA	chr7:92086808-92087037(+)$1	229	1	35	36.0851
UAUUUAUUUUUAUCCAUAGCUUUUUCCAUAUAAG	chr11:96085977-96086212(-)$1	235	105	139	36.8940
UUCUGUCCCCCGCAUUAAUGACUCUCAGGAAGGA	chr11:107375508-107375726(-)$1	218	12	46	35.6217
AGCAGCUAUCCUUUUUUUUUUUAAUUCUAGCUUC	chr4:107269474-107269709(+)$1	235	94	128	34.6751
AUGGAAAGCUGCCAAUUACCUAUAUGUAUGUUCU	chr13:36876146-36876374(-)$1	228	68	102	36.1492
UUAGCUCUGGCAAAAAAAAAAAAUUUUAAGAGCU	chr2:178095003-178095221(-)$1	218	120	154	32.4264
AAAAAUAUAUAUAUACUACUUCUGAUCAUAUUUU	chr8:145978745-145978970(-)$1	225	102	136	35.1719
uuuuCAGAACAAGACCACUAUUAUUAACUAACUU	chr4:31145135-31145363(+)$1	228	121	155	36.9331
CCuuuuauuauuauuauuuuuuuCUUUUAAGAAC	chr9:96440969-96441189(+)$1	220	176	210	35.6589
AAACAUUGCCUUUCCUACACAUUCCUCAUCAUUG	chr1:162498071-162498296(+)$1	225	91	125	34.9199
UUUCAACAUUUUUAAUAACUUUUUUUAUUGUUGG	chr13:21950161-21950416(-)$1	255	126	160	31.3986
CUCAAAGUAAAGUCAUUAACAUCAAAAGCUUUGU	chr12:49521485-49521710(-)$1	225	119	153	30.9700
GGCUAGCAAUCUUAUCUAUUGUCAUGUCUUACUA	chr1:97284925-97285141(+)$1	216	13	47	36.6406
UUCAAACGUAAUAGCAUUAAGAAGAUCGUGUGAA	chr17:29701084-29701311(+)$1	227	56	90	32.9662
UAAGAGUUCCAAUUUGUGCUGCUAUUUCUCUGAU	chr1:217781445-217781672(-)$1	227	144	178	34.8400
UUUAUAAUUUUCUUAUUCUCACUUUUUUUUCAUU	chr4:96086987-96087207(-)$1	220	64	98	34.7701
UUAGUGCUUCCCUAUACAAUUGUUAAUGCACAAA	chr6:146120558-146120778(-)$1	220	7	41	34.9191

#DB
(((((.............................	chr11:115046615-115046876(-)$1	1	106	140	37.5152
.((((((.....................))))))	chr12:53910117-53910339(-)$1	1	96	130	34.9784
((.(((((...................))))).)	chr5:79774110-79774331(+)$1	1	64	98	34.7884
...(((((..........................	chr16:47116603-47116850(-)$1	1	96	130	36.9304
(.((((((...................)))..))	chr22:40725114-40725336(+)$1	1	93	127	34.9694
................................))	chr11:110036547-110036789(+)$1	1	105	139	37.0212
(((((.........................))))	chr12:51636696-51636955(+)$1	1	127	161	36.9356
(((.((((..........................	chr20:21491747-21491974(-)$1	1	81	115	36.4016
(((.(((.....................))))))	chr3:86994292-86994511(-)$1	1	172	206	36.3819
..((((.....................))))...	chr17:76220371-76220589(+)$1	1	95	129	35.7347
...........................)))))))	chr19:52516817-52517038(-)$1	1	93	127	35.3045
(((((((.....................))))))	chr3:113163743-113163982(-)$1	1	94	128	36.4661
((((..(((..................)))..))	chr1:230974058-230974283(-)$1	1	97	131	33.0636
))))((((...................)))).((	chr9:33047005-33047237(-)$1	1	103	137	33.2075
................................))	chr17:38784292-38784513(-)$1	1	161	195	36.7504
((((((((....................))))))	chr4:15690591-15690815(+)$1	1	28	62	36.6991
..((((((....................))))))	chr8:71023374-71023609(-)$1	1	184	218	32.7529
(((((.............................	chr6:56968573-56968808(+)$1	1	97	131	37.5152
((((((((..........................	chr1:153946684-153946920(-)$1	1	100	134	37.0677
((((((((...................)))))))	chr4:76404960-76405183(-)$1	1	24	58	35.1719
................................))	chr5:134193530-134193759(+)$1	1	23	57	37.0212
................................))	chr11:27517170-27517417(-)$1	1	114	148	37.0212
(((((.......................))))).	chr1:214524242-214524471(-)$1	1	101	135	36.1364
(...(((((..................))))).)	chr5:162946073-162946294(+)$1	1	16	50	33.1943
((.(((((..........................	chr5:172461767-172461991(+)$1	1	31	65	37.0394
((((((((......................))))	chr11:110038625-110038846(+)$1	1	160	194	36.8482
(((((((.......................))))	chr1:167391972-167392212(+)$1	1	92	126	37.2258
(...(((((..................)))))..	chr1:245014982-245015206(-)$1	1	36	70	33.4762
((((((((..................)))...))	chr3:196555191-196555420(+)$1	1	178	212	34.3358
(((..(((..........................	chr19:53738191-53738418(-)$1	1	82	116	36.7387
.((((......................))))..)	chr13:41506325-41506547(-)$1	1	83	117	35.1611
(((((.((....................))))))	chr16:15959805-15960027(-)$1	1	91	125	35.4915
(((((.((...................)).))))	chr19:39221081-39221304(+)$1	1	4	38	32.6107
((((((((..........................	chr1:173871674-173871909(+)$1	1	150	184	36.0855
(((((.((....................)).)))	chr2:20449742-20449962(-)$1	1	63	97	35.8277
((((((((....................))))))	chr2:198415971-198416216(+)$1	1	203	237	32.4264
((((((((..................))))))))	chr10:89730424-89730653(+)$1	1	19	53	34.4092
((((.(((....................))).))	chr9:14084685-14084920(-)$1	1	188	222	34.9747
((.........................))))...	chr12:57607001-57607234(-)$1	1	59	93	32.2810
((((.......................)))).))	chr11:77032900-77033129(-)$1	1	102	136	35.0486
((((((((..........................	chr4:25367391-25367615(+)$1	1	30	64	37.0677
.((((((....................)))))).	chr3:69069389-69069624(-)$1	1	107	141	34.3931
.((...........................))..	chr13:50592156-50592382(-)$1	1	30	64	36.4169
.(((((.....................)))))..	chr7:66105207-66105430(+)$1	1	113	147	35.6156
((((((((....................))))))	chr6:131908282-131908512(-)$1	1	121	155	36.6991
(((.((((.....................)))))	chr14:100744159-100744385(+)$1	1	96	130	34.9794
(((((((((..................)).))))	chr22:40728731-40728955(+)$1	1	91	125	33.2959
(.(((((((..................)))))))	chr17:55197985-55198212(+)$1	1	90	124	33.2853
((((..........................))))	chr11:62566583-62566812(-)$1	1	98	132	36.2851
((((((((....................))))))	chr7:92086808-92087037(+)$1	1	1	35	36.0851
(((((((......................)))))	chr11:96085977-96086212(-)$1	1	105	139	36.8940
((((.(((...................))).)))	chr11:107375508-107375726(-)$1	1	12	46	35.6217
((.(((((...................))))).)	chr4:107269474-107269709(+)$1	1	94	128	34.6751
((((((((..........................	chr13:36876146-36876374(-)$1	1	68	102	36.1492
((((((((....................))))))	chr2:178095003-178095221(-)$1	1	120	154	32.4264
((((((((...................)))))))	chr8:145978745-145978970(-)$1	1	102	136	35.1719
(.(((((.........................))	chr4:31145135-31145363(+)$1	1	121	155	36.9331
..(((((....................)))))..	chr9:96440969-96441189(+)$1	1	176	210	35.6589
(((((.((.....................)).))	chr1:162498071-162498296(+)$1	1	91	125	34.9199
...(((((....................)))))(	chr13:21950161-21950416(-)$1	1	126	160	31.3986
..((((((...................)))))).	chr12:49521485-49521710(-)$1	1	119	153	30.9700
((..((((..........................	chr1:97284925-97285141(+)$1	1	13	47	36.6406
((((.(((..................))).))))	chr17:29701084-29701311(+)$1	1	56	90	32.9662
..((((.....................))))..)	chr1:217781445-217781672(-)$1	1	144	178	34.8400
...........................)))).))	chr4:96086987-96087207(-)$1	1	64	98	34.7701
((.((((....................)))))))	chr6:146120558-146120778(-)$1	1	7	41	34.9191

#PSSM
d : 0.15	e : 0.12	i : 0.10	^ : 0.09	g : 0.09	= : 0.07	h : 0.06	" : 0.04	c : 0.04	: : 0.04	f : 0.04	! : 0.03	# : 0.03	b : 0.03	$ : 0.01	[ : 0.01	
d : 0.13	e : 0.12	i : 0.10	^ : 0.09	g : 0.09	f : 0.07	= : 0.07	" : 0.06	h : 0.06	[ : 0.04	c : 0.04	: : 0.04	! : 0.01	b : 0.01	# : 0.01	
d : 0.13	e : 0.12	f : 0.12	^ : 0.10	g : 0.10	i : 0.10	[ : 0.06	= : 0.06	h : 0.06	" : 0.04	c : 0.03	b : 0.01	: : 0.01	! : 0.01	
e : 0.18	d : 0.13	^ : 0.12	f : 0.10	g : 0.10	i : 0.10	= : 0.06	h : 0.06	[ : 0.04	" : 0.03	! : 0.03	c : 0.01	
e : 0.21	^ : 0.15	d : 0.13	g : 0.10	f : 0.09	i : 0.09	= : 0.06	h : 0.04	[ : 0.04	c : 0.03	! : 0.03	
^ : 0.22	e : 0.15	d : 0.12	c : 0.10	i : 0.09	f : 0.07	g : 0.07	[ : 0.06	= : 0.04	h : 0.03	! : 0.01	
^ : 0.27	e : 0.13	c : 0.12	d : 0.09	i : 0.09	f : 0.07	g : 0.07	b : 0.06	= : 0.04	h : 0.03	
^ : 0.40	e : 0.10	c : 0.10	i : 0.09	d : 0.07	b : 0.07	= : 0.04	f : 0.04	h : 0.03	g : 0.01	
^ : 0.92	e : 0.03	c : 0.01	b : 0.01	g : 0.01	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.95	c : 0.03	= : 0.01	
^ : 0.57	d : 0.12	e : 0.09	c : 0.07	g : 0.03	i : 0.03	b : 0.03	f : 0.03	= : 0.01	
^ : 0.36	e : 0.12	d : 0.12	c : 0.10	f : 0.06	b : 0.06	g : 0.04	= : 0.04	i : 0.04	h : 0.03	
^ : 0.31	d : 0.13	e : 0.12	c : 0.07	f : 0.06	g : 0.06	= : 0.04	i : 0.04	b : 0.04	] : 0.04	h : 0.03	3 : 0.01	
^ : 0.24	d : 0.15	e : 0.13	g : 0.10	f : 0.07	i : 0.06	= : 0.04	h : 0.04	2 : 0.03	c : 0.03	] : 0.03	b : 0.03	3 : 0.01	
^ : 0.24	e : 0.13	g : 0.10	f : 0.07	i : 0.07	2 : 0.06	= : 0.06	] : 0.06	h : 0.04	c : 0.03	3 : 0.03	: : 0.03	d : 0.03	b : 0.01	
^ : 0.16	f : 0.15	g : 0.13	h : 0.09	i : 0.07	e : 0.06	3 : 0.06	= : 0.06	] : 0.04	c : 0.04	d : 0.04	2 : 0.03	: : 0.01	4 : 0.01	
^ : 0.16	g : 0.13	f : 0.12	d : 0.09	h : 0.09	i : 0.07	c : 0.06	3 : 0.06	= : 0.06	e : 0.04	: : 0.03	2 : 0.01	] : 0.01	4 : 0.01	C : 0.01	

#score	2328.0906515914157
#seq	66
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_UTR_m3_run2.txt

#BEAR
hhhhhh!!bbqqqqqqqqbb22hhhhhh	chr21:43409451-43409672(-)$1	221	151	179	13.7460
ddddccc!!aqqqqqqqqa22ccc:bbc	chr3:185634636-185634866(-)$1	230	39	67	13.9915
hhhhhh!!bbqqqqqqqqbb]hhhhhhh	chr9:34087551-34087780(-)$1	229	190	218	13.9229
d[bb"""cccqqqqqqqqccc4444bb]	chr6:74225594-74225836(-)$1	242	101	129	15.9117
ddd[bb[cccqqqqqqqqccc22bb]dd	chr22:24761499-24761724(+)$1	225	65	93	14.5310
cc"""eeeeeqqqqqqqqeeeee4444c	chr2:196602053-196602274(+)$1	221	22	50	17.2794
eeeee[ddddqqqqqqqqdddd]eeeee	chr12:109548438-109548668(+)$1	230	14	42	14.6192
:ccc"""cccqqqqqqqqccc4444ccc	chr18:72912699-72912924(-)$1	225	152	180	16.0463
dd!!ffffffqqqqqqqqffffff22dd	chr10:64566450-64566678(+)$1	228	34	62	15.9589
eeee!!ddddqqqqqqqqdddd4444ee	chr19:41777997-41778228(+)$1	231	36	64	15.6831
[dddd[bbbbqqqqqqqqbb]bb22ddd	chr16:3073996-3074222(+)$1	226	143	171	15.0393
gg!!eeeeeaqqqqqqqqa]eeeee22g	chr13:111291420-111291657(+)$1	237	123	151	15.9832
bccc!!ddddqqqqqqqqdddd22ccc2	chr14:64855015-64855248(+)$1	233	140	168	15.3626
[ccc[bb[bbqqqqqqqqbb]bbccc33	chr19:10265236-10265474(-)$1	238	134	162	16.4038
fffffeeeeeqqqqqqqqeeeee00000	chr1:229643931-229644166(-)$1	235	70	98	14.0576
###dddd!!aqqqqqqqqa22dddd444	chr17:17714342-17714566(+)$1	224	72	100	15.3789
fff!!eeeeeqqqqqqqqeeeeefffff	chr19:54382494-54382712(-)$1	218	11	39	15.8576
[ccc[eeeeeqqqqqqqqeeeee22ccc	chr9:95032074-95032313(-)$1	239	144	172	16.6476
dd"""eeeeeqqqqqqqqeeeee4444d	chrX:134166949-134167179(+)$1	230	107	135	16.9186
e!!gggggggqqqqqqqqgggggggeee	chrX:99884203-99884429(-)$1	226	105	133	15.8158
ddd[ffffffqqqqqqqqffffff22dd	chr4:38701108-38701339(+)$1	231	200	228	15.5913
%%ffffffbbqqqqqqqqbb]ffffff4	chr18:57571196-57571448(+)$1	252	144	172	14.8807
gggccc[cccqqqqqqqqcccccc:ggg	chr7:26240103-26240332(-)$1	229	24	52	14.9894
!bb!!eeeeeqqqqqqqqeeeee22bb2	chr19:30106093-30106334(+)$1	241	101	129	15.9546
bb[dddd[bbqqqqqqqqbb]ddddbb]	chr18:54293505-54293739(-)$1	234	52	80	15.2729
========[aqqqqqqqqa]========	chr19:1009762-1009993(-)$1	231	136	164	16.5913
dddd[eeeeeqqqqqqqqeeeee]dddd	chrX:23802422-23802650(+)$1	228	58	86	15.5018
ffff"""cccqqqqqqqqcccffffff:	chr1:85784667-85784896(-)$1	229	112	140	14.9745
eeee####bbqqqqqqqqbb22eeeee:	chr16:28109422-28109652(-)$1	230	27	55	15.0190
####ffffffqqqqqqqqffffffeeee	chr5:162871432-162871663(+)$1	231	201	229	15.8872
ccc!!eeeeeqqqqqqqqeeeee22ccc	chr19:1434978-1435206(+)$1	228	88	116	16.8405
ccc[bbddddqqqqqqqqdddd4444bb	chr5:151170434-151170705(+)$1	271	66	94	15.3058
ff"""eeeeeqqqqqqqqeeeee]ffff	chr6:18264627-18264854(-)$1	227	147	175	16.1888
cccc####bbqqqqqqqqbbccc22ccc	chr12:57909958-57910187(+)$1	229	117	145	16.8864
[ccc[bb[bbqqqqqqqqbb]bb]ccc]	chr11:62648368-62648598(+)$1	230	184	212	16.4307
!eeeee[cccqqqqqqqqccc]eeeee2	chr7:42956900-42957143(-)$1	243	27	55	15.5655
ccc!!bb[bbqqqqqqqqbb22bb22cc	chrX:135951508-135951747(-)$1	239	160	188	16.1383
ff####ddddqqqqqqqqdddd333fff	chr2:184026172-184026397(+)$1	225	87	115	16.0807
::eeeee[bbqqqqqqqqbb333eeeee	chr8:22879940-22880166(-)$1	226	14	42	14.3761
====ffffffqqqqqqqqffffff4444	chr1:113454941-113455171(-)$1	230	189	217	16.5764
#bbeeeeebbqqqqqqqqbb]eeeee33	chrX:23803948-23804191(+)$1	243	33	61	16.2019
ddd[ccc[bbqqqqqqqqbbcccdddd8	chr12:10998353-10998577(-)$1	224	81	109	15.4987
bb[dddd[bbqqqqqqqqbb]dddd]bb	chr16:23692138-23692390(+)$1	252	181	209	15.2097
((((ffffffqqqqqqqqffffff333e	chr5:33459758-33459991(+)$1	233	142	170	13.9939
ffff####bbqqqqqqqqbbffffffcc	chr19:33872241-33872464(+)$1	223	108	136	16.1017
####ffffffqqqqqqqqffffff4444	chr3:37032456-37032684(-)$1	228	125	153	16.7437
=iiiiiiiiiqqqqqqqqiiiiiiiii:	chr5:126172499-126172728(+)$1	229	95	123	15.2678
b"""ffffffqqqqqqqqffffffbb]g	chr3:23962159-23962435(+)$1	276	79	107	15.4486
c!!bb[ddddqqqqqqqqddddbb]ccc	chr3:184035018-184035255(+)$1	237	203	231	14.9912
ff!!ffffffqqqqqqqqffffff]fff	chr3:9482072-9482321(+)$1	249	72	100	15.9971
:iiiiiiiiiqqqqqqqqiiiiiiiii:	chr12:76441417-76441647(-)$1	230	87	115	14.3880

#otherMatches

#Seq PSSM
UUUUAAAAGCCAACUACUGUCAUUAAGA	chr21:43409451-43409672(-)$1	221	151	179	13.7460
AGGCUGUUUCUUAAAGGUGUUACAAGGG	chr3:185634636-185634866(-)$1	230	39	67	13.9915
GGGAAGUUGGUGUCACUUCCCCUUCCCA	chr9:34087551-34087780(-)$1	229	190	218	13.9229
AAUAGAUGGCCAAUAGAUGCCCUGAUAA	chr6:74225594-74225836(-)$1	242	101	129	15.9117
GGCAUCUGUGACUCCCACCACCCGAAGC	chr22:24761499-24761724(+)$1	225	65	93	14.5310
GAAUUUUGGUAUAUaucaaucaaucaau	chr2:196602053-196602274(+)$1	221	22	50	17.2794
GAAGAGGAGAAAAGGGAAUUUUGUCUUU	chr12:109548438-109548668(+)$1	230	14	42	14.6192
AAGAAGUAGCACGUAAUGGCUUUUAUCU	chr18:72912699-72912924(-)$1	225	152	180	16.0463
GUAAUUCUGUAUUUUCUAACGGGAAGAU	chr10:64566450-64566678(+)$1	228	34	62	15.9589
CCUGAAGCUUCUCAACUCAAGCCAGACA	chr19:41777997-41778228(+)$1	231	36	64	15.6831
UGGACACCACUUCUUAAUGUCGGGGGUC	chr16:3073996-3074222(+)$1	226	143	171	15.0393
GGUGGGGAGCUCUGAGACGCCUCCUGUC	chr13:111291420-111291657(+)$1	237	123	151	15.9832
CAGAAAUCCUGAACGGGAAGGAGAUCUC	chr14:64855015-64855248(+)$1	233	140	168	15.3626
ACAGUGAUGAGCAGCCCAUCUUCCUGAC	chr19:10265236-10265474(-)$1	238	134	162	16.4038
CGCGCCAUCUCUUCCCUUAGGUGUUUAA	chr1:229643931-229644166(-)$1	235	70	98	14.0576
GUCCGUGUCCUCAGCUCUGUCCACGCUU	chr17:17714342-17714566(+)$1	224	72	100	15.3789
CGUGCCCCGCGAGGCUGGGCGGGACGCU	chr19:54382494-54382712(-)$1	218	11	39	15.8576
CUGGUGAGCAGUAAGAUGUGUUUCUUCA	chr9:95032074-95032313(-)$1	239	144	172	16.6476
GGCUCCUGUUACACACUGGACAGACCAC	chrX:134166949-134167179(+)$1	230	107	135	16.9186
CUACUGAUGUUCUGUGAUACAUCAGGUU	chrX:99884203-99884429(-)$1	226	105	133	15.8158
AUUGUGUUAACAGUUCAUUUAACAAAGA	chr4:38701108-38701339(+)$1	231	200	228	15.5913
UUUAGAUGGAAAAUUACCUCACAUCUGU	chr18:57571196-57571448(+)$1	252	144	172	14.8807
AGCGGCAGUUCUCACUACAGCGCCAGGA	chr7:26240103-26240332(-)$1	229	24	52	14.9894
UUUAUUUCCUACAUUUACGGGAGCAAAU	chr19:30106093-30106334(+)$1	241	101	129	15.9546
UGUGGGCCAUGUUUGAGGAUUGCCCCAG	chr18:54293505-54293739(-)$1	234	52	80	15.2729
GCGCCUCGGGCAUAGGGACGUGGGGUGC	chr19:1009762-1009993(-)$1	231	136	164	16.5913
GAUCCUUUACACAAUAAAGUAGAUGAUC	chrX:23802422-23802650(+)$1	228	58	86	15.5018
GAAAGAUACUAUCACAUAAGUUUUCCUC	chr1:85784667-85784896(-)$1	229	112	140	14.9745
GUGUGUGGCCAGGUACUAGGAGGCACCA	chr16:28109422-28109652(-)$1	230	27	55	15.0190
ACACCUUCAUAACUAUGAAUGAAGCUGC	chr5:162871432-162871663(+)$1	231	201	229	15.8872
GGACUGAGGUUUUUAAAUAUUUCUUUCU	chr19:1434978-1435206(+)$1	228	88	116	16.8405
AUUCGCCAUGUUGAUGCUCAUGCCACGC	chr5:151170434-151170705(+)$1	271	66	94	15.3058
CCCGCGCGCCUUCUCCUCGGCGUCGGCC	chr6:18264627-18264854(-)$1	227	147	175	16.1888
AAGCCACAGCAGAUACAAGCGCUGAUGG	chr12:57909958-57910187(+)$1	229	117	145	16.8864
GAGAAGCAGCCGAUGAACGCGGCGUCUG	chr11:62648368-62648598(+)$1	230	184	212	16.4307
UAAAGUAUGUUUUGUUUUGCAGACUUUU	chr7:42956900-42957143(-)$1	243	27	55	15.5655
UAUAAGGAGUAUGUUAAAAUGACCAGAU	chrX:135951508-135951747(-)$1	239	160	188	16.1383
AUUAUGGUCUUUUAAUUUAGAUAGUAUU	chr2:184026172-184026397(+)$1	225	87	115	16.0807
CUGGUUUACCUUUUUUCUGGAAAAAGCC	chr8:22879940-22880166(-)$1	226	14	42	14.3761
GAAAACAUUUCUUCUCCCAAAUGUCUAU	chr1:113454941-113455171(-)$1	230	189	217	16.5764
GCUGUAGAUGACAACCUCCAUUCUAUUU	chrX:23803948-23804191(+)$1	243	33	61	16.2019
GGUCAUAACUCUUUCUUCAGUAUACCAA	chr12:10998353-10998577(-)$1	224	81	109	15.4987
GGUGCUGAGCAAGAAAGGGCACAGUUUC	chr16:23692138-23692390(+)$1	252	181	209	15.2097
CAUGUUCUCCUUUGAGGUGGAGAAGGAG	chr5:33459758-33459991(+)$1	233	142	170	13.9939
CUAUAGAGCCAGGAGACAGGAUAGGGGU	chr19:33872241-33872464(+)$1	223	108	136	16.1017
AACAUGAGAAUGCCACCUUUUUUAAAAC	chr3:37032456-37032684(-)$1	228	125	153	16.7437
GGUGGAGGGAGGGAAGGGUUUCUCUAUU	chr5:126172499-126172728(+)$1	229	95	123	15.2678
UAAAUUUCUUCACAAAAAAAGAAAAGAU	chr3:23962159-23962435(+)$1	276	79	107	15.4486
AAUGAUGAUCCCUUCCCAGAUCUCCUAC	chr3:184035018-184035255(+)$1	237	203	231	14.9912
UCCCUCUGAAGCACAGAAUUUAGAUGAG	chr3:9482072-9482321(+)$1	249	72	100	15.9971
CUGAAUUUAACUGUAUUUUUAAAUUUAA	chr12:76441417-76441647(-)$1	230	87	115	14.3880

#DB
((((((..((........))..))))))	chr21:43409451-43409672(-)$1	1	151	179	13.7460
))))(((..(........)..))).(((	chr3:185634636-185634866(-)$1	1	39	67	13.9915
((((((..((........)).)))))))	chr9:34087551-34087780(-)$1	1	190	218	13.9229
(.((...(((........)))....)).	chr6:74225594-74225836(-)$1	1	101	129	15.9117
(((.((.(((........)))..)).))	chr22:24761499-24761724(+)$1	1	65	93	14.5310
((...(((((........)))))....)	chr2:196602053-196602274(+)$1	1	22	50	17.2794
(((((.((((........)))).)))))	chr12:109548438-109548668(+)$1	1	14	42	14.6192
.(((...(((........)))....)))	chr18:72912699-72912924(-)$1	1	152	180	16.0463
((..((((((........))))))..))	chr10:64566450-64566678(+)$1	1	34	62	15.9589
((((..((((........))))....))	chr19:41777997-41778228(+)$1	1	36	64	15.6831
.((((.((((........)).))..)))	chr16:3073996-3074222(+)$1	1	143	171	15.0393
((..((((((........).)))))..)	chr13:111291420-111291657(+)$1	1	123	151	15.9832
((((..((((........))))..))).	chr14:64855015-64855248(+)$1	1	140	168	15.3626
.(((.((.((........)).)))))..	chr19:10265236-10265474(-)$1	1	134	162	16.4038
((((((((((........))))).....	chr1:229643931-229644166(-)$1	1	70	98	14.0576
...((((..(........)..))))...	chr17:17714342-17714566(+)$1	1	72	100	15.3789
(((..(((((........))))))))))	chr19:54382494-54382712(-)$1	1	11	39	15.8576
.(((.(((((........)))))..)))	chr9:95032074-95032313(-)$1	1	144	172	16.6476
((...(((((........)))))....)	chrX:134166949-134167179(+)$1	1	107	135	16.9186
(..(((((((........))))))))))	chrX:99884203-99884429(-)$1	1	105	133	15.8158
(((.((((((........))))))..))	chr4:38701108-38701339(+)$1	1	200	228	15.5913
..((((((((........)).)))))).	chr18:57571196-57571448(+)$1	1	144	172	14.8807
)))(((.(((........)))))).(((	chr7:26240103-26240332(-)$1	1	24	52	14.9894
.((..(((((........)))))..)).	chr19:30106093-30106334(+)$1	1	101	129	15.9546
((.((((.((........)).)))))).	chr18:54293505-54293739(-)$1	1	52	80	15.2729
((((((((.(........).))))))))	chr19:1009762-1009993(-)$1	1	136	164	16.5913
((((.(((((........))))).))))	chrX:23802422-23802650(+)$1	1	58	86	15.5018
((((...(((........))))))))).	chr1:85784667-85784896(-)$1	1	112	140	14.9745
((((....((........))..))))).	chr16:28109422-28109652(-)$1	1	27	55	15.0190
....((((((........))))))))))	chr5:162871432-162871663(+)$1	1	201	229	15.8872
(((..(((((........)))))..)))	chr19:1434978-1435206(+)$1	1	88	116	16.8405
(((.((((((........))))....))	chr5:151170434-151170705(+)$1	1	66	94	15.3058
((...(((((........))))).))))	chr6:18264627-18264854(-)$1	1	147	175	16.1888
((((....((........)))))..)))	chr12:57909958-57910187(+)$1	1	117	145	16.8864
.(((.((.((........)).)).))).	chr11:62648368-62648598(+)$1	1	184	212	16.4307
.(((((.(((........))).))))).	chr7:42956900-42957143(-)$1	1	27	55	15.5655
(((..((.((........))..))..))	chrX:135951508-135951747(-)$1	1	160	188	16.1383
((....((((........))))...)))	chr2:184026172-184026397(+)$1	1	87	115	16.0807
..(((((.((........))...)))))	chr8:22879940-22880166(-)$1	1	14	42	14.3761
((((((((((........))))))....	chr1:113454941-113455171(-)$1	1	189	217	16.5764
.(((((((((........)).)))))..	chrX:23803948-23804191(+)$1	1	33	61	16.2019
(((.(((.((........))))))))).	chr12:10998353-10998577(-)$1	1	81	109	15.4987
((.((((.((........)).)))).))	chr16:23692138-23692390(+)$1	1	181	209	15.2097
....((((((........))))))...)	chr5:33459758-33459991(+)$1	1	142	170	13.9939
((((....((........))))))))))	chr19:33872241-33872464(+)$1	1	108	136	16.1017
....((((((........))))))....	chr3:37032456-37032684(-)$1	1	125	153	16.7437
)(((((((((........))))))))).	chr5:126172499-126172728(+)$1	1	95	123	15.2678
(...((((((........)))))))).)	chr3:23962159-23962435(+)$1	1	79	107	15.4486
(..((.((((........)))))).)))	chr3:184035018-184035255(+)$1	1	203	231	14.9912
((..((((((........)))))).)))	chr3:9482072-9482321(+)$1	1	72	100	15.9971
.(((((((((........))))))))).	chr12:76441417-76441647(-)$1	1	87	115	14.3880

#PSSM
d : 0.15	f : 0.13	c : 0.11	e : 0.07	[ : 0.07	b : 0.07	# : 0.07	: : 0.05	= : 0.05	h : 0.03	g : 0.03	! : 0.03	% : 0.01	( : 0.01	
c : 0.19	d : 0.15	f : 0.13	e : 0.07	b : 0.07	# : 0.05	h : 0.03	g : 0.03	! : 0.03	= : 0.03	i : 0.03	[ : 0.01	% : 0.01	: : 0.01	( : 0.01	" : 0.01	
c : 0.17	d : 0.11	e : 0.09	! : 0.09	f : 0.09	" : 0.07	# : 0.07	b : 0.05	h : 0.03	[ : 0.03	= : 0.03	i : 0.03	g : 0.01	( : 0.01	
c : 0.13	! : 0.13	d : 0.11	e : 0.11	[ : 0.07	" : 0.07	f : 0.07	# : 0.05	h : 0.03	b : 0.03	= : 0.03	i : 0.03	g : 0.01	( : 0.01	
f : 0.19	" : 0.11	! : 0.11	e : 0.09	d : 0.07	[ : 0.07	# : 0.07	c : 0.05	b : 0.05	h : 0.03	i : 0.03	g : 0.01	= : 0.01	
e : 0.25	f : 0.17	b : 0.09	# : 0.07	c : 0.05	" : 0.05	[ : 0.05	d : 0.05	h : 0.03	! : 0.03	i : 0.03	g : 0.01	= : 0.01	
e : 0.23	d : 0.17	f : 0.17	b : 0.07	" : 0.05	[ : 0.05	# : 0.05	! : 0.03	c : 0.03	i : 0.03	g : 0.01	= : 0.01	
e : 0.21	f : 0.17	[ : 0.13	c : 0.11	d : 0.11	! : 0.07	# : 0.05	i : 0.03	b : 0.01	g : 0.01	= : 0.01	
b : 0.29	e : 0.19	f : 0.15	c : 0.11	d : 0.11	! : 0.03	i : 0.03	g : 0.01	[ : 0.01	
b : 0.29	e : 0.17	f : 0.15	c : 0.11	d : 0.11	a : 0.07	i : 0.03	g : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
b : 0.29	e : 0.17	f : 0.15	c : 0.11	d : 0.11	a : 0.07	i : 0.03	g : 0.01	
b : 0.29	e : 0.17	f : 0.15	c : 0.11	d : 0.11	2 : 0.03	] : 0.03	i : 0.03	g : 0.01	
e : 0.19	f : 0.17	] : 0.15	c : 0.15	d : 0.11	2 : 0.09	i : 0.03	g : 0.01	= : 0.01	3 : 0.01	
e : 0.21	f : 0.21	d : 0.17	2 : 0.07	c : 0.07	b : 0.05	4 : 0.03	i : 0.03	h : 0.01	g : 0.01	= : 0.01	] : 0.01	3 : 0.01	
e : 0.25	f : 0.21	b : 0.09	c : 0.07	4 : 0.07	d : 0.05	h : 0.03	2 : 0.03	3 : 0.03	i : 0.03	] : 0.01	g : 0.01	= : 0.01	
f : 0.23	4 : 0.11	e : 0.11	2 : 0.11	d : 0.07	c : 0.05	b : 0.05	] : 0.05	h : 0.03	i : 0.03	0 : 0.01	g : 0.01	= : 0.01	3 : 0.01	
4 : 0.15	2 : 0.15	e : 0.13	d : 0.09	f : 0.09	c : 0.05	h : 0.03	: : 0.03	b : 0.03	3 : 0.03	i : 0.03	] : 0.03	0 : 0.01	g : 0.01	= : 0.01	
c : 0.15	4 : 0.13	e : 0.13	f : 0.13	b : 0.09	2 : 0.07	d : 0.05	h : 0.03	] : 0.03	i : 0.03	0 : 0.01	g : 0.01	= : 0.01	3 : 0.01	
c : 0.17	e : 0.13	b : 0.11	d : 0.11	f : 0.11	4 : 0.09	3 : 0.05	h : 0.03	i : 0.03	2 : 0.01	0 : 0.01	g : 0.01	= : 0.01	] : 0.01	
c : 0.17	d : 0.11	e : 0.11	4 : 0.07	f : 0.07	: : 0.07	] : 0.05	g : 0.05	2 : 0.05	h : 0.03	3 : 0.03	b : 0.03	0 : 0.01	= : 0.01	8 : 0.01	

#score	794.0516382051459
#seq	51
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_UTR_m1_run2.txt

#BEAR
bb!!eeeee[a[bboooooobb]a]eeeee22bbc	chr11:69467962-69468246(+)$1	284	23	58	14.3597
===gggggggeeeeennnnneeeee333ggggggg	chr5:112352281-112352521(+)$1	240	187	222	11.4875
======"""eeeeeooooooeeeee==========	chr17:40353330-40353570(-)$1	240	166	201	15.4001
eeee####bb!!bboooooobb]bb333eeeee::	chr5:89808235-89808475(+)$1	240	34	69	13.2533
fffff####bb[bboooooobbbb333ffffff::	chr20:32441989-32442234(+)$1	245	170	205	12.7097
gg!!dddd[a[cccooooooccc]a]dddd]gggg	chr7:26241304-26241544(+)$1	240	44	79	15.6986
$$$ggggggg[cccooooooccc]ggggggg22cc	chr17:8371254-8371494(+)$1	240	36	71	15.8464
ddd[ccc!!ffffffooooooffffffccc]dddd	chr2:86790365-86790605(-)$1	240	3	38	12.1168
eeee"""ccc[cccnnnnnccc]ccc333eeeee]	chr22:44890267-44890507(-)$1	240	176	211	11.3580
""ddddeeeee[bboooooobb]eeeee333dddd	chr1:35899029-35899269(-)$1	240	34	69	14.0210
$$$ggggggg!!bboooooobb22ggggggg333b	chr6:149826324-149826564(-)$1	240	90	125	16.2340
c[ccc"""a[ddddoooooodddd]a]cccccc22	chr3:113438190-113438432(-)$1	242	88	123	14.5109
[eeeee[gggggggooooooggggggg]eeeee]c	chr6:109688317-109688561(-)$1	244	45	80	14.6409
[ffffff[ccc!!bbnnnnnbb22ccc]ffffff]	chr1:153932027-153932267(-)$1	240	52	87	10.7284
g"""ccc$$$$$bboooooobb4444cccgggggg	chr16:19089989-19090229(+)$1	240	199	234	16.0999
ccccc!!ddddcccooooooccc]ddddccc9999	chr5:130728778-130729018(+)$1	240	114	149	12.0788
eeggggggg"""bboooooobb333ggggggg:::	chr10:35860165-35860405(+)$1	240	198	233	14.5845
hhhhhh!!ccccccooooooccc]ccc]hhhhhhh	chrX:24004808-24005056(-)$1	248	189	224	14.0460
Giiiiiiiii!!a!!annnnna22a22iiiiiiii	chr20:3209657-3209897(-)$1	240	106	141	11.5621
hhhhhh!!ccccccooooooccc4444ccc333hh	chr17:21218378-21218618(+)$1	240	86	121	15.5382
e[ddddccc[ddddoooooodddd22ccc333ddd	chr17:7129001-7129248(-)$1	247	144	179	13.6930
!!dddd$$$$$cccooooooccc4444dddd22cc	chr5:137497651-137497891(-)$1	240	42	77	14.7120
ddddccc"""ddddoooooodddd4444ccc]ddd	chr17:4269481-4269721(-)$1	240	86	121	14.2506
ii[eeeee[a"""bbnnnnnbb333a]eeeeeiii	chr12:58190267-58190507(+)$1	240	130	165	12.2958
gggg!!bbffffffooooooffffff]bb22gggg	chr8:19687851-19688091(+)$1	240	175	210	13.0231
eddddffffff[bboooooobb]ffffff4444dd	chr8:66621245-66621524(+)$1	279	37	72	13.5071
bccc[eeeee!!bboooooobbeeeee]ccc]bbg	chr7:148951602-148951842(+)$1	240	67	102	14.3949
!!iiiiiiiii[bbmmmmbb333iiiiiiiii333	chr2:70167649-70167889(+)$1	240	165	200	11.3178
ccc[dddd"""ddddoooooodddd333ddddccc	chr1:230400926-230401171(+)$1	245	162	197	13.2130
ggggg!!dddd!!ccclllccc22dddd]gggggg	chr5:159520739-159520979(-)$1	240	6	41	11.0514
ccc[eeeee[ddddoooooodddd333eeeee]cc	chr22:21304556-21304796(+)$1	240	193	228	14.4846
cc"""bb"""a[bboooooobb]a333bb]ccc44	chr22:30423578-30423818(+)$1	240	44	79	16.0217
!=============oooooo=============]f	chr8:101715126-101715367(-)$1	241	126	161	17.0152
dd"""iiiiiiiiiooooooiiiiiiiii333ddd	chr13:96232496-96232736(-)$1	240	2	37	15.6149
iiiii[bb"""cccooooooccc333bb]iiiiii	chr11:60658228-60658468(-)$1	240	153	188	16.3826
ccc[ccc[bb!!bboooooobb22bb]cccccc:D	chr4:120415494-120415734(+)$1	240	153	188	13.6186
ccc"""dddd[cccooooooccc]dddd333ccce	chr3:44967492-44967732(-)$1	240	116	151	14.9123
cc[dddd####cccooooooccc333dddd22ccc	chr1:1190515-1190755(-)$1	240	50	85	15.9949
ddgggggggdddd[aooooooa]dddd]ggggggg	chr17:34958349-34958589(+)$1	240	178	213	13.8484
ffffff[bb!!cccooooooccc]bb]ffffff44	chr19:56185839-56186079(+)$1	240	46	81	14.0103
==========="""bbmmmmbb333==========	chr1:233520364-233520604(+)$1	240	44	79	12.4173
!ggggggg[eeeeeooooooeeeeeggggggg22d	chr5:130727803-130728073(+)$1	270	167	202	14.4496
ggggg[eeeee[bbaooooooa]bb]eeeeegggg	chr12:6776327-6776567(-)$1	240	117	152	14.0086
ggggggg####cccooooooccc22gggggggfff	chr16:87732324-87732564(-)$1	240	22	57	16.6308
ggg"""dddd[cccnnnnnccc]dddd]ggggggg	chr17:41844267-41844507(-)$1	240	98	133	11.5665
[ggggggg####cccmmmmccc333gggggggddd	chr3:169805516-169805756(-)$1	240	91	126	12.5963
ffcccggggggg[aooooooagggggggeeeeell	chr17:78443257-78443497(-)$1	240	168	203	13.9082
ff[bb!!gggggggooooooggggggg]bb]ffff	chr19:36149533-36149775(+)$1	242	38	73	14.0082
cc!!gggggggrrrrrrrrrggggggg]ccc22dd	chr1:101441649-101441889(+)$1	240	138	173	10.8379
!!ffffffffffffooooooffffff333ffffff	chr16:731922-732162(+)$1	240	121	156	12.9070
d"""dddd!!ddddoooooodddd]dddd4444dd	chr14:75369700-75370011(+)$1	311	256	291	13.3855
hhhhh!!gggggggooooooggggggg]hhhhhhh	chr8:90792220-90792460(+)$1	240	84	119	13.8490
fff[ggggggg[bboooooobb]gggggggfffff	chr22:43562531-43562800(-)$1	269	52	87	15.7192

#otherMatches

#Seq PSSM
GGCCGCAGCUCCAUUUUCUUAUUGCGCUGCUACCG	chr11:69467962-69468246(+)$1	284	23	58	14.3597
AGAGCAAAGUUAAUUAUAAAAAUUAGACAUUUUGC	chr5:112352281-112352521(+)$1	240	187	222	11.4875
UGUGUCUUAAGAGUGGCUGGACUUUGACAUGUGGC	chr17:40353330-40353570(-)$1	240	166	201	15.4001
CAAAUCAUUCUUGCUUAACUGCUGAUCUUUUGUAA	chr5:89808235-89808475(+)$1	240	34	69	13.2533
AUUAAUUUUCAUACUUUGCUGUUGUGUUUAAUCUA	chr20:32441989-32442234(+)$1	245	170	205	12.7097
UCCCGGCUCCCUCCCCCUUCGGAUGUGGCUUGAGC	chr7:26241304-26241544(+)$1	240	44	79	15.6986
AUUGCCUGAGAUAUUUGUAUAUAACUUGGGCUUUG	chr17:8371254-8371494(+)$1	240	36	71	15.8464
AGUGCCGCCGCUCCCUACUCUGGGGGUUGGGACUA	chr2:86790365-86790605(-)$1	240	3	38	12.1168
UCCACCUUGGACUUGGAAGAAGCCCACAUUGGAGA	chr22:44890267-44890507(-)$1	240	176	211	11.3580
UCACCCUGGCCCUGUUCCACCAUGGUUAUCUGGGU	chr1:35899029-35899269(-)$1	240	34	69	14.0210
GAUUAUGGUCUUUAGAUUAAUACUGAUUAUAUAGA	chr6:149826324-149826564(-)$1	240	90	125	16.2340
UAUGCCUAUGAGUCAGUAAAGACUGAAGUAAUGUC	chr3:113438190-113438432(-)$1	242	88	123	14.5109
GCAUUUAGAUAACUAUUAAAGGUUGUUAAGAUGAA	chr6:109688317-109688561(-)$1	244	45	80	14.6409
GGACAGGUCAUAAACCUAGAGUCAGUGUCCUGUUG	chr1:153932027-153932267(-)$1	240	52	87	10.7284
AGAUUGGCCAAGCAGAACUAUGAAGUCCAUCAAGU	chr16:19089989-19090229(+)$1	240	199	234	16.0999
AAAGGAACAGGGAUCACUUUAUCUUCUGCCUUCAU	chr5:130728778-130729018(+)$1	240	114	149	12.0788
AGCCUGUGCCCUGGAUUCUACCUCUGUAUAGGAAA	chr10:35860165-35860405(+)$1	240	198	233	14.5845
GUAAGAAAUAGAAUUAUAAUGUUACUGGUUUUAUC	chrX:24004808-24005056(-)$1	248	189	224	14.0460
CUUCAUCGAGCAGAACUUGGUGGCCGCCUUGGUGA	chr20:3209657-3209897(-)$1	240	106	141	11.5621
CUGCCCAUCCCGGGUCCUUUCCCUGAUGGGUUGGG	chr17:21218378-21218618(+)$1	240	86	121	15.5382
UGCCUGGGCUCAGCCUACCAGCUGCUGCCAUACAG	chr17:7129001-7129248(-)$1	247	144	179	13.6930
UAUCUCUGUUUCAGCUCUGUCUGUAGUGAGGAUCA	chr5:137497651-137497891(-)$1	240	42	77	14.7120
CAGCCCGGGCCCUCGGCAGGGAGGAUGACGGAGCU	chr17:4269481-4269721(-)$1	240	86	121	14.2506
UUACUUUUAGCUCUGGACAUCAUUACAAAAAGGAA	chr12:58190267-58190507(+)$1	240	130	165	12.2958
GGAGAGCUGGGAGUUGCUCUAUUCCCUAGAAUUCC	chr8:19687851-19688091(+)$1	240	175	210	13.0231
ACAAUGAGCUGCGAAAAGACUCCUGGUUCCCCUGU	chr8:66621245-66621524(+)$1	279	37	72	13.5071
UGGAAGAAGAGUCCAGGCCAGGUCUUCAUCCUGCU	chr7:148951602-148951842(+)$1	240	67	102	14.3949
AUAAAUGUGGAACUUGAUAGAUCUCUAUAUUUUUA	chr2:70167649-70167889(+)$1	240	165	200	11.3178
AUGUCACAAUGCUGGGGGAAACCAGGUAUGUGCAU	chr1:230400926-230401171(+)$1	245	162	197	13.2130
GACAGAAGUCAAGUGUGAAGCAAAUGGUGCUGUUC	chr5:159520739-159520979(-)$1	240	6	41	11.0514
ggagugcaguggcgcaaucucgccuuccugcaguc	chr22:21304556-21304796(+)$1	240	193	228	14.4846
GCAGCUCUUAGCUCUUUUUUGAUCGAUGAAGCACU	chr22:30423578-30423818(+)$1	240	44	79	16.0217
AUGUCAGUUCUGUUUUAAGUAACAGAAUUGAUAAC	chr8:101715126-101715367(-)$1	241	126	161	17.0152
UUUCAUUCCUGAGCAGAAGAGCUUGGGGAAAUGAA	chr13:96232496-96232736(-)$1	240	2	37	15.6149
UUCCUGUGAGACAGGAGAGGCUGAGCCAAGGGAAC	chr11:60658228-60658468(-)$1	240	153	188	16.3826
ACCAUCUCAUGACUUUAUACAGGAAUCGGAGGUAA	chr4:120415494-120415734(+)$1	240	153	188	13.6186
UAACUCGCAAAGCAAUUGCCUGCCUUGUACUUUAU	chr3:44967492-44967732(-)$1	240	116	151	14.9123
CAGCAGGCCAACCGGCACCACGGACUCCUGGGUGG	chr1:1190515-1190755(-)$1	240	50	85	15.9949
AUUCCAGUUCUGCGGCCCAGACGGCAGAAACUGGA	chr17:34958349-34958589(+)$1	240	178	213	13.8484
GGACCACAGCUCUGUUCCUUCGGCCUCUGGUCCUC	chr19:56185839-56186079(+)$1	240	46	81	14.0103
gugcauguauguuggcgugugugugugugcaugca	chr1:233520364-233520604(+)$1	240	44	79	12.4173
CACAAGCACAAUGAUCAUUUUUAUUUGUUUGUUUG	chr5:130727803-130728073(+)$1	270	167	202	14.4496
CCUCUUGUUCUAUUCUUGCCUGCAAAAGAACAGAG	chr12:6776327-6776567(-)$1	240	117	152	14.0086
GGGGCGGAAAAUGGCUCUCACCAGGCUGCUCUCGG	chr16:87732324-87732564(-)$1	240	22	57	16.6308
CUUAACAAGAUUUAGCUCUUAGUUCUUCAAGUAAA	chr17:41844267-41844507(-)$1	240	98	133	11.5665
UAUUUGUUGUGUCUGUAUUCAGUGAAGUAAAUUGA	chr3:169805516-169805756(-)$1	240	91	126	12.5963
CCGGCGACACUGACACCUGAGCAGUGUCCAGAACC	chr17:78443257-78443497(-)$1	240	168	203	13.9082
CUGUCCUCCAUCCUUCUCCCAGGAUGGUGAAGGGG	chr19:36149533-36149775(+)$1	242	38	73	14.0082
GCAGAAAUGGUUGUGACAGUGCUGUUUGGCUUUUU	chr1:101441649-101441889(+)$1	240	138	173	10.8379
GAGCUUUUUUCUCAGGUGGAUGAGAAGAGGAAGGU	chr16:731922-732162(+)$1	240	121	156	12.9070
UUGAGCUUUUCAGUUAAGUUGCUGUAAGCACCUGG	chr14:75369700-75370011(+)$1	311	256	291	13.3855
UGUUUAAUAGAACUUGAACCAGUUUUGAGAACAUU	chr8:90792220-90792460(+)$1	240	84	119	13.8490
UCUAGCCCCUGGAGGGCCUGUUGCAGGGGCAGGGC	chr22:43562531-43562800(-)$1	269	52	87	15.7192

#DB
((..(((((.(.((......)).).)))))..)))	chr11:69467962-69468246(+)$1	1	23	58	14.3597
(((((((((((((((.....)))))...)))))))	chr5:112352281-112352521(+)$1	1	187	222	11.4875
((((((...(((((......)))))))))))))))	chr17:40353330-40353570(-)$1	1	166	201	15.4001
((((....((..((......)).))...)))))..	chr5:89808235-89808475(+)$1	1	34	69	13.2533
(((((....((.((......))))...))))))..	chr20:32441989-32442234(+)$1	1	170	205	12.7097
((..((((.(.(((......))).).)))).))))	chr7:26241304-26241544(+)$1	1	44	79	15.6986
...(((((((.(((......))).)))))))..))	chr17:8371254-8371494(+)$1	1	36	71	15.8464
(((.(((..((((((......))))))))).))))	chr2:86790365-86790605(-)$1	1	3	38	12.1168
((((...(((.(((.....))).)))...))))).	chr22:44890267-44890507(-)$1	1	176	211	11.3580
..(((((((((.((......)).)))))...))))	chr1:35899029-35899269(-)$1	1	34	69	14.0210
...(((((((..((......))..)))))))...)	chr6:149826324-149826564(-)$1	1	90	125	16.2340
(.(((...(.((((......)))).).))))))..	chr3:113438190-113438432(-)$1	1	88	123	14.5109
.(((((.(((((((......))))))).))))).)	chr6:109688317-109688561(-)$1	1	45	80	14.6409
.((((((.(((..((.....))..))).)))))).	chr1:153932027-153932267(-)$1	1	52	87	10.7284
(...(((.....((......))....)))))))))	chr16:19089989-19090229(+)$1	1	199	234	16.0999
(((((..(((((((......))).)))))))....	chr5:130728778-130729018(+)$1	1	114	149	12.0788
))(((((((...((......))...)))))))...	chr10:35860165-35860405(+)$1	1	198	233	14.5845
((((((..((((((......))).))).)))))))	chrX:24004808-24005056(-)$1	1	189	224	14.0460
((((((((((..(..(.....)..)..))))))))	chr20:3209657-3209897(-)$1	1	106	141	11.5621
((((((..((((((......)))....)))...))	chr17:21218378-21218618(+)$1	1	86	121	15.5382
(.(((((((.((((......))))..)))...)))	chr17:7129001-7129248(-)$1	1	144	179	13.6930
..((((.....(((......)))....))))..))	chr5:137497651-137497891(-)$1	1	42	77	14.7120
(((((((...((((......))))....))).)))	chr17:4269481-4269721(-)$1	1	86	121	14.2506
((.(((((.(...((.....))...).))))))))	chr12:58190267-58190507(+)$1	1	130	165	12.2958
((((..((((((((......)))))).))..))))	chr8:19687851-19688091(+)$1	1	175	210	13.0231
(((((((((((.((......)).))))))....))	chr8:66621245-66621524(+)$1	1	37	72	13.5071
((((.(((((..((......))))))).))).))(	chr7:148951602-148951842(+)$1	1	67	102	14.3949
..(((((((((.((....))...)))))))))...	chr2:70167649-70167889(+)$1	1	165	200	11.3178
(((.((((...((((......))))...)))))))	chr1:230400926-230401171(+)$1	1	162	197	13.2130
(((((..((((..(((...)))..)))).))))))	chr5:159520739-159520979(-)$1	1	6	41	11.0514
(((.(((((.((((......))))...))))).))	chr22:21304556-21304796(+)$1	1	193	228	14.4846
((...((...(.((......)).)...)).)))..	chr22:30423578-30423818(+)$1	1	44	79	16.0217
.(((((((((((((......))))))))))))).)	chr8:101715126-101715367(-)$1	1	126	161	17.0152
((...(((((((((......)))))))))...)))	chr13:96232496-96232736(-)$1	1	2	37	15.6149
(((((.((...(((......)))...)).))))))	chr11:60658228-60658468(-)$1	1	153	188	16.3826
(((.(((.((..((......))..)).)))))).)	chr4:120415494-120415734(+)$1	1	153	188	13.6186
(((...((((.(((......))).))))...))))	chr3:44967492-44967732(-)$1	1	116	151	14.9123
((.((((....(((......)))...))))..)))	chr1:1190515-1190755(-)$1	1	50	85	15.9949
(((((((((((((.(......).)))).)))))))	chr17:34958349-34958589(+)$1	1	178	213	13.8484
((((((.((..(((......))).)).))))))..	chr19:56185839-56186079(+)$1	1	46	81	14.0103
(((((((((((...((....))...))))))))))	chr1:233520364-233520604(+)$1	1	44	79	12.4173
.(((((((.(((((......))))))))))))..)	chr5:130727803-130728073(+)$1	1	167	202	14.4496
(((((.(((((.(((......).)).)))))))))	chr12:6776327-6776567(-)$1	1	117	152	14.0086
(((((((....(((......)))..)))))))(((	chr16:87732324-87732564(-)$1	1	22	57	16.6308
(((...((((.(((.....))).)))).)))))))	chr17:41844267-41844507(-)$1	1	98	133	11.5665
.(((((((....(((....)))...))))))))))	chr3:169805516-169805756(-)$1	1	91	126	12.5963
)))))(((((((.(......))))))))(((((..	chr17:78443257-78443497(-)$1	1	168	203	13.9082
((.((..(((((((......))))))).)).))))	chr19:36149533-36149775(+)$1	1	38	73	14.0082
((..(((((((.........))))))).)))..))	chr1:101441649-101441889(+)$1	1	138	173	10.8379
..((((((((((((......))))))...))))))	chr16:731922-732162(+)$1	1	121	156	12.9070
(...((((..((((......)))).))))....))	chr14:75369700-75370011(+)$1	1	256	291	13.3855
(((((..(((((((......))))))).)))))))	chr8:90792220-90792460(+)$1	1	84	119	13.8490
(((.(((((((.((......)).))))))))))))	chr22:43562531-43562800(-)$1	1	52	87	15.7192

#PSSM
c : 0.16	g : 0.13	e : 0.09	f : 0.09	d : 0.09	! : 0.09	= : 0.05	[ : 0.05	h : 0.05	b : 0.03	$ : 0.03	i : 0.03	" : 0.01	G : 0.01	
c : 0.16	g : 0.15	f : 0.11	d : 0.09	= : 0.07	e : 0.07	" : 0.05	h : 0.05	i : 0.05	! : 0.05	$ : 0.03	[ : 0.03	b : 0.01	
g : 0.16	c : 0.15	d : 0.11	f : 0.09	= : 0.07	" : 0.07	! : 0.05	e : 0.05	h : 0.05	i : 0.05	[ : 0.05	$ : 0.03	
g : 0.20	d : 0.11	" : 0.11	[ : 0.09	e : 0.07	f : 0.07	c : 0.07	! : 0.05	= : 0.05	h : 0.05	i : 0.05	b : 0.01	
g : 0.22	d : 0.15	c : 0.13	" : 0.09	e : 0.07	f : 0.07	= : 0.05	h : 0.05	i : 0.05	# : 0.01	! : 0.01	[ : 0.01	b : 0.01	
g : 0.20	d : 0.13	e : 0.09	! : 0.09	c : 0.07	" : 0.07	f : 0.07	= : 0.05	i : 0.05	# : 0.03	h : 0.03	[ : 0.03	b : 0.01	
g : 0.20	e : 0.11	d : 0.11	! : 0.11	c : 0.09	" : 0.05	f : 0.05	i : 0.05	b : 0.05	# : 0.03	[ : 0.03	= : 0.03	$ : 0.01	
g : 0.24	d : 0.13	e : 0.11	" : 0.07	# : 0.07	! : 0.05	i : 0.05	b : 0.05	c : 0.03	[ : 0.03	$ : 0.03	f : 0.03	= : 0.03	
g : 0.20	e : 0.09	" : 0.09	c : 0.09	# : 0.07	d : 0.07	b : 0.05	[ : 0.05	i : 0.05	f : 0.05	! : 0.03	$ : 0.03	= : 0.03	a : 0.01	
g : 0.16	e : 0.09	d : 0.09	" : 0.09	[ : 0.07	f : 0.07	c : 0.07	b : 0.05	i : 0.05	# : 0.05	a : 0.03	$ : 0.03	= : 0.03	! : 0.03	
d : 0.15	! : 0.11	g : 0.11	e : 0.09	[ : 0.09	f : 0.07	" : 0.07	c : 0.05	# : 0.05	a : 0.03	$ : 0.03	i : 0.03	= : 0.03	b : 0.01	
c : 0.24	[ : 0.15	! : 0.13	d : 0.13	g : 0.07	e : 0.05	f : 0.05	" : 0.05	$ : 0.01	= : 0.01	i : 0.01	# : 0.01	r : 0.01	
b : 0.26	c : 0.26	d : 0.13	e : 0.05	f : 0.05	g : 0.05	! : 0.03	" : 0.03	a : 0.01	= : 0.01	i : 0.01	[ : 0.01	r : 0.01	
b : 0.30	c : 0.28	d : 0.11	e : 0.05	f : 0.05	g : 0.05	! : 0.01	= : 0.01	i : 0.01	[ : 0.01	" : 0.01	a : 0.01	r : 0.01	
o : 0.71	b : 0.05	n : 0.03	c : 0.03	a : 0.03	e : 0.01	f : 0.01	! : 0.01	m : 0.01	d : 0.01	r : 0.01	
o : 0.79	n : 0.09	m : 0.03	a : 0.01	c : 0.01	b : 0.01	r : 0.01	
o : 0.79	n : 0.11	m : 0.05	l : 0.01	r : 0.01	
o : 0.79	n : 0.11	m : 0.05	l : 0.01	r : 0.01	
o : 0.79	n : 0.11	m : 0.03	b : 0.01	l : 0.01	r : 0.01	
o : 0.79	n : 0.07	c : 0.07	b : 0.01	m : 0.01	r : 0.01	
b : 0.28	c : 0.28	d : 0.09	o : 0.07	g : 0.07	e : 0.05	f : 0.03	n : 0.01	3 : 0.01	= : 0.01	i : 0.01	a : 0.01	
b : 0.28	c : 0.28	d : 0.11	g : 0.09	e : 0.05	f : 0.05	a : 0.05	3 : 0.01	= : 0.01	i : 0.01	
c : 0.20	] : 0.18	d : 0.11	2 : 0.09	g : 0.09	3 : 0.09	e : 0.07	f : 0.05	b : 0.01	4 : 0.01	= : 0.01	i : 0.01	
d : 0.15	] : 0.11	2 : 0.11	g : 0.11	3 : 0.11	e : 0.09	f : 0.07	b : 0.05	4 : 0.05	a : 0.03	i : 0.03	c : 0.01	= : 0.01	
3 : 0.16	g : 0.15	d : 0.11	e : 0.09	b : 0.07	f : 0.07	4 : 0.07	] : 0.05	c : 0.05	a : 0.03	2 : 0.03	i : 0.03	= : 0.01	
g : 0.22	3 : 0.15	d : 0.11	f : 0.07	4 : 0.07	e : 0.05	= : 0.05	c : 0.05	] : 0.03	a : 0.03	2 : 0.03	i : 0.03	b : 0.03	
g : 0.22	3 : 0.15	d : 0.15	] : 0.09	e : 0.07	c : 0.07	= : 0.05	4 : 0.05	f : 0.03	i : 0.03	2 : 0.01	b : 0.01	
] : 0.16	g : 0.15	d : 0.13	c : 0.11	e : 0.09	3 : 0.09	= : 0.05	f : 0.05	i : 0.05	b : 0.05	4 : 0.01	
g : 0.18	c : 0.18	e : 0.13	d : 0.09	f : 0.07	3 : 0.07	= : 0.05	i : 0.05	b : 0.05	h : 0.03	] : 0.03	
g : 0.22	e : 0.15	c : 0.15	f : 0.07	d : 0.07	3 : 0.07	= : 0.05	i : 0.05	h : 0.03	4 : 0.03	2 : 0.01	] : 0.01	b : 0.01	
g : 0.20	e : 0.13	c : 0.13	f : 0.09	3 : 0.09	2 : 0.05	= : 0.05	] : 0.05	i : 0.05	h : 0.03	d : 0.03	4 : 0.03	
g : 0.22	e : 0.11	f : 0.11	2 : 0.09	3 : 0.07	c : 0.07	= : 0.05	d : 0.05	i : 0.05	h : 0.03	] : 0.03	4 : 0.03	9 : 0.01	
g : 0.15	f : 0.13	d : 0.11	c : 0.11	e : 0.07	2 : 0.07	= : 0.05	3 : 0.05	i : 0.05	b : 0.03	h : 0.03	4 : 0.03	9 : 0.01	: : 0.01	] : 0.01	
d : 0.16	g : 0.15	c : 0.11	f : 0.09	: : 0.07	h : 0.05	i : 0.05	b : 0.03	= : 0.03	3 : 0.03	2 : 0.03	] : 0.03	4 : 0.03	e : 0.01	9 : 0.01	l : 0.01	
d : 0.18	g : 0.16	c : 0.13	f : 0.09	: : 0.05	h : 0.05	i : 0.05	= : 0.03	] : 0.03	4 : 0.03	b : 0.01	2 : 0.01	9 : 0.01	3 : 0.01	D : 0.01	e : 0.01	l : 0.01	

#score	735.9232145854771
#seq	53
#width	35
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_CDS_m2_run2.txt

#BEAR
:eeeee!!cccqqqqqqqqccc22eeeeec	chr19:12790370-12790596(-)$1	226	124	154	16.9488
ddd####ddddqqqqqqqqdddd4444ddd	chr17:39846293-39846520(+)$1	227	166	196	16.8712
fffff!!ddddqqqqqqqqddddffffff:	chr8:22471524-22471751(+)$1	227	161	191	15.4627
eeee[ccccccqqqqqqqqccc333cccee	chr22:36912653-36912899(-)$1	246	104	134	18.0942
ffff[bb[cccqqqqqqqqccc333bb22f	chr17:38151397-38151636(+)$1	239	37	67	17.1608
cc####eeeeeqqqqqqqqeeeeeccceee	chr2:170413650-170413890(-)$1	240	83	113	17.5142
eee[a[eeeeeqqqqqqqqeeeee22a]ee	chr19:59059357-59059594(+)$1	237	163	193	17.3395
gg!!bb!!cccqqqqqqqqccc]bb22ggg	chr13:73336038-73336258(-)$1	220	32	62	17.3727
ggggg[eeeeeqqqqqqqqeeeee4444gg	chr4:41263672-41263911(+)$1	239	163	193	18.0187
Gdddd[eeeeeqqqqqqqqeeeee]ddddD	chr1:43826345-43826570(+)$1	225	85	115	15.1886
cc!!ddddcccqqqqqqqqccc22ddddcc	chr19:41269421-41269645(+)$1	224	139	169	17.2136
ffffff[ddddqqqqqqqqdddd]ffffff	chr17:45730003-45730221(+)$1	218	147	177	15.9786
e[eeeee[cccqqqqqqqqccc]eeeee]e	chr12:57882756-57882980(+)$1	224	177	207	18.1453
dd[ccc[ddddqqqqqqqqdddd]ccc]dd	chr12:120884456-120884681(+)$1	225	120	150	16.7469
[ggggggg[bbqqqqqqqqbbggggggg33	chr19:1091725-1091947(-)$1	222	12	42	17.4430
c[ccc[eeeeeqqqqqqqqeeeee]ccccc	chr19:48981649-48981873(+)$1	224	114	144	17.7137
cc"""dddd[aqqqqqqqqa]ddddccc]b	chr1:154184916-154185184(-)$1	268	197	227	16.9039
iiiiiiii[bbqqqqqqqqbb]iiiiiiii	chr11:64534576-64534807(-)$1	231	180	210	17.5818
[ccc"""ddddqqqqqqqqdddd]ccc>>>	chr4:71555675-71555903(+)$1	228	71	101	16.9250
ccccc[bb!!aqqqqqqqqa22bbccc]cc	chr1:78430259-78430485(-)$1	226	144	174	15.8874
ffeeeee[cccqqqqqqqqccc]eeeee::	chr16:30779534-30779758(+)$1	224	120	150	16.0767
deeeeeeeeeeqqqqqqqqeeeee]eeeee	chr22:38054894-38055134(+)$1	240	109	139	16.8250
fff####bb[aqqqqqqqqabbffffffcc	chr4:77969464-77969692(-)$1	228	52	82	15.9549
gggg!!eeeeeqqqqqqqqeeeee333ggg	chr17:76993169-76993396(-)$1	227	89	119	18.3918
"""a!!eeeeeqqqqqqqqeeeee22a333	chr19:33072122-33072340(+)$1	218	79	109	18.0579
[bb[a[eeeeeqqqqqqqqeeeeea]bbdd	chr1:151371972-151372221(+)$1	249	205	235	16.3109
gg!!ddddcccqqqqqqqqccc]dddd22g	chr19:59061648-59061878(+)$1	230	78	108	17.4617
ddd[gggggggqqqqqqqqggggggg]ddd	chr16:249082-249304(-)$1	222	92	122	16.9360
[eeeee"""bbqqqqqqqqbb22eeeee]a	chr20:32267603-32267845(-)$1	242	55	85	16.7411
c!!eeeee!!aqqqqqqqqa22eeeee22c	chr10:70496607-70496834(+)$1	227	194	224	17.3072
cc"""ffffffqqqqqqqqffffff333cc	chr17:72205241-72205492(+)$1	251	204	234	16.6903
eeeee####bbqqqqqqqqbb4444eeeee	chr12:58145348-58145572(-)$1	224	11	41	16.8340
c[eeeee!!bbqqqqqqqqbb22eeeee]c	chr17:77808869-77809117(-)$1	248	215	245	17.0174
##ccc[eeeeeqqqqqqqqeeeee]ccc]f	chr3:53262006-53262243(-)$1	237	75	105	17.5952
eeeee"""cccqqqqqqqqccc4444eeee	chr1:226178853-226179111(-)$1	258	175	205	18.2120
h!!dddd[cccqqqqqqqqccc]dddd22h	chr1:62907137-62907379(+)$1	242	59	89	17.0335
ee!!ccc[cccqqqqqqqqcccccc333ee	chr19:39663457-39663688(+)$1	231	116	146	18.2034
===####ddddqqqqqqqqdddd22=====	chr1:234519421-234519648(+)$1	227	37	67	18.0061
a"""gggggggqqqqqqqqggggggg333a	chr1:93299070-93299315(+)$1	245	189	219	18.2762
ggggggccc[aqqqqqqqqa]ccc22gggg	chr7:75694140-75694365(+)$1	225	68	98	17.4586
##iiiiiiiiiqqqqqqqqiiiiiiiii>>	chr1:62913016-62913260(+)$1	244	133	163	17.8389
!!bb####cccqqqqqqqqccc22bb22a]	chr10:35467966-35468199(+)$1	233	125	155	17.0853
::iiiiiiiiiqqqqqqqqiiiiiiiiibb	chr22:39713461-39713695(-)$1	234	109	139	15.8063
b####dddd[aqqqqqqqqadddd4444bb	chr22:19164036-19164274(-)$1	238	87	117	16.6553
:==========qqqqqqqq==========:	chr10:79795214-79795463(+)$1	249	201	231	17.3010
c!!eeeee!!aqqqqqqqqa22eeeee22c	chr10:70496645-70496876(+)$1	231	156	186	17.3072
iiiiiii[cccqqqqqqqqccc]iiiiiii	chr5:179247993-179248220(+)$1	227	15	45	18.9376
gggg!!eeeeeqqqqqqqqeeeee22gggg	chr12:120636863-120637101(-)$1	238	25	55	17.8271
eeeee"""cccqqqqqqqqccc333eeeee	chr17:76219691-76219920(+)$1	229	72	102	18.4973
e[ffffffcccqqqqqqqqccc]ffffffe	chr17:62499451-62499683(-)$1	232	139	169	16.8107
:ggggggg[bbqqqqqqqqbb]gggggggE	chrX:153669350-153669573(+)$1	223	142	172	15.4457
c[ffffffcccqqqqqqqqccc22ffffff	chr6:27100098-27100320(-)$1	222	155	185	16.8139
======"""bbqqqqqqqqbb333======	chrX:48791943-48792171(-)$1	228	112	142	18.5569
bbccc[eeeeeqqqqqqqqeeeee]ccc]b	chr4:185618754-185618980(-)$1	226	173	203	17.0297
f[a[gggggggqqqqqqqqggggggg]a22	chr2:28002280-28002508(+)$1	228	168	198	17.5012
F:iiiiiiiiiqqqqqqqqiiiiiiiii:d	chr1:156203333-156203555(+)$1	222	64	94	15.8155
dddd[a[ddddqqqqqqqqdddd]addddG	chr12:122243872-122244095(+)$1	223	96	126	15.6570
cciiiiiiiiiqqqqqqqqiiiiiiiii]c	chr1:151288369-151288591(-)$1	222	180	210	18.3592
d[dddd!!cccqqqqqqqqccc22dddd]d	chr21:30433562-30433801(-)$1	239	8	38	17.2949
gggggg!!cccqqqqqqqqcccggggggg3	chr20:2641060-2641306(-)$1	246	81	111	18.6344
===========qqqqqqqq===========	chr3:32544002-32544229(-)$1	227	156	186	19.0506
=======[cccqqqqqqqqccc]=======	chr3:186505214-186505450(+)$1	236	178	208	19.5008

#otherMatches

#Seq PSSM
AUUCUGGACCAGAUGGUGAUGGAGCAGAAC	chr19:12790370-12790596(-)$1	226	124	154	16.9488
UGAUUUGUGCCUCUCUGCUGGCAAAUCUCA	chr17:39846293-39846520(+)$1	227	166	196	16.8712
UUGGCUAUCAGCCUUCCCCCUGAGCCAGCC	chr8:22471524-22471751(+)$1	227	161	191	15.4627
GAGGACGACAUGGAUAAGAAUGAAAUCGCC	chr22:36912653-36912899(-)$1	246	104	134	18.0942
GGACAGGAAACCUAGCCAAGUUCAACCAGG	chr17:38151397-38151636(+)$1	239	37	67	17.1608
ACUUAAAUCAACUAUGUUAUUGAUGUCAGA	chr2:170413650-170413890(-)$1	240	83	113	17.5142
ACAGCCCUUUUGCUUUCUAAGAAGUUGGUG	chr19:59059357-59059594(+)$1	237	163	193	17.3395
AUCAGGCCGAAUCUCCUACUUUUCCAUAUC	chr13:73336038-73336258(-)$1	220	32	62	17.3727
CAUGGCCUUUAAAUAACUCUAGAGAUUUUU	chr4:41263672-41263911(+)$1	239	163	193	18.0187
CCAUGAUGUUCGGGUAGCAGAACACCAUGU	chr1:43826345-43826570(+)$1	225	85	115	15.1886
CUGUCCAUGCUUUUCAAUCAGUAAGUGGGG	chr19:41269421-41269645(+)$1	224	139	169	17.2136
CUUUGACAUCUAAAGAUCCAGAUAUCAAGG	chr17:45730003-45730221(+)$1	218	147	177	15.9786
UCAGGCCUCACUGUCAUUUGUGUGGCUUUA	chr12:57882756-57882980(+)$1	224	177	207	18.1453
CUACGCGCCGUGGACACAGACGGGGUGGAG	chr12:120884456-120884681(+)$1	225	120	150	16.7469
GUGCAGGCCAGCACACUCUCUGUCUGCAGA	chr19:1091725-1091947(-)$1	222	12	42	17.4430
GGCCGAGUGGUGGAGGGAAACCACAUGGUG	chr19:48981649-48981873(+)$1	224	114	144	17.7137
GCACUCAUUGAUACCCUUUUGGAUGGCUAU	chr1:154184916-154185184(-)$1	268	197	227	16.9039
GCUUGGGUGAGUGGGGGUUCUGGCCCAAGU	chr11:64534576-64534807(-)$1	231	180	210	17.5818
UCGUGAAGUUCGUAAAGAAGAGCAACGUUA	chr4:71555675-71555903(+)$1	228	71	101	16.9250
AAGGGAUAGAUGUAAGUAAAAAUACCCAUU	chr1:78430259-78430485(-)$1	226	144	174	15.8874
GGGGCCCAGGGCCCUUCCUCCCGGGGCCGA	chr16:30779534-30779758(+)$1	224	120	150	16.0767
UCGCGCGCCUCGGCUUCGGGGGGCUGCGCG	chr22:38054894-38055134(+)$1	240	109	139	16.8250
UCUCCAAGGACAACAGCAAGCCAGAAGUGC	chr4:77969464-77969692(-)$1	228	52	82	15.9549
ACCUGACCCUGUCAGACAGUGGGGACAAGG	chr17:76993169-76993396(-)$1	227	89	119	18.3918
AGAGGCUGGCCGAGCUGCAGGCCAAACACG	chr19:33072122-33072340(+)$1	218	79	109	18.0579
UACAGAGGUCCAAUCACGCGGACCCAGUAA	chr1:151371972-151372221(+)$1	249	205	235	16.3109
AUUCCUGCUUGGCCCAGGACAAGGCAGACG	chr19:59061648-59061878(+)$1	230	78	108	17.4617
CAUCCAGUUUUCAGCAGCAAAAGCUGCGUG	chr16:249082-249304(-)$1	222	92	122	16.9360
ACCCCCACAGGUGUGAAAUCCCCGGGGGAG	chr20:32267603-32267845(-)$1	242	55	85	16.7411
ACAGGUAAAUCUUUAAUAUGUCUUAUUAUU	chr10:70496607-70496834(+)$1	227	194	224	17.3072
CCGGUGAGUGAGCCUGAAGUCACUUCAGGG	chr17:72205241-72205492(+)$1	251	204	234	16.6903
ACUCUGUAAGCGACUUUUGGUGAUAGGAGU	chr12:58145348-58145572(-)$1	224	11	41	16.8340
CGCCCAGCCCCACCUGCCCGGACCUGGGGG	chr17:77808869-77809117(-)$1	248	215	245	17.0174
CAGGUGGUCCUGAAGAGCAAGGAUGACCAG	chr3:53262006-53262243(-)$1	237	75	105	17.5952
UUUCACUUUCGUUCCCAAUUGAUCUUUGAG	chr1:226178853-226179111(-)$1	258	175	205	18.2120
ACUGUGAGAAGAGAGAAAACUUGUUACCAU	chr1:62907137-62907379(+)$1	242	59	89	17.0335
GCAAAGGUGCCAAAGAUGGGGCCCUCACGC	chr19:39663457-39663688(+)$1	231	116	146	18.2034
UUUCCAACAGAUAAAAUAUUUUGAUAAAAG	chr1:234519421-234519648(+)$1	227	37	67	18.0061
AAAUUGUGCUUGGGAAGCAAAGCACAUGGU	chr1:93299070-93299315(+)$1	245	189	219	18.2762
UGUUCCUUCGUUAAGUCACAGGAAACGGAA	chr7:75694140-75694365(+)$1	225	68	98	17.4586
AUGAGCUUUCCAAAGUAGAGGAGAGUUCUG	chr1:62913016-62913260(+)$1	244	133	163	17.8389
GCCUGGUGUUCCCAAGAUUGAAGAAGAGAG	chr10:35467966-35468199(+)$1	233	125	155	17.0853
CACCCAUGGUGGUUGUGGGCAUUGUGGGCU	chr22:39713461-39713695(-)$1	234	109	139	15.8063
CAUGAACCCUCUGAUCACUGGGGUCUUCGG	chr22:19164036-19164274(-)$1	238	87	117	16.6553
GGCAUGAUUUAUGAUUCCCUGGAUUAUGCA	chr10:79795214-79795463(+)$1	249	201	231	17.3010
ACAGGUAAAUCUUUAAUAUGUCUUAUUAUU	chr10:70496645-70496876(+)$1	231	156	186	17.3072
UUCUGCUGCAGCCCCGAGCCUGAGGCGGAA	chr5:179247993-179248220(+)$1	227	15	45	18.9376
UGCCCGUCUCCCUCUUCCUGGAGAAUGGUG	chr12:120636863-120637101(-)$1	238	25	55	17.8271
AGAUGUUUCAACUGUGCUCUUGUUUUGUCU	chr17:76219691-76219920(+)$1	229	72	102	18.4973
UGUAAUGAAAAGGGUUUUAUUUGUCAUUGG	chr17:62499451-62499683(-)$1	232	139	169	16.8107
ACAUCAUCAUGGAGAACGGCAAGGUGGUGG	chrX:153669350-153669573(+)$1	223	142	172	15.4457
ACACCAGCGCUAAGUAAACAGUGAGUUGGU	chr6:27100098-27100320(-)$1	222	155	185	16.8139
CAUGGCAACCACAUUGAGAUGCAGGCCAUG	chrX:48791943-48792171(-)$1	228	112	142	18.5569
GGAAACGGUAACUCCAAUUUUACUUUUUAC	chr4:185618754-185618980(-)$1	226	173	203	17.0297
CAUGGAAUCACUGCCUCCUGUGAUUUGAAG	chr2:28002280-28002508(+)$1	228	168	198	17.5012
UCUUUCCUCCUUUCUCUUCAGGAGGAAAUC	chr1:156203333-156203555(+)$1	222	64	94	15.8155
UCCGUCAUGGGCAACAUUAUCCACGUGGAG	chr12:122243872-122244095(+)$1	223	96	126	15.6570
UACAUCCACAUGGAUGAGGAUGUGGGUGAU	chr1:151288369-151288591(-)$1	222	180	210	18.3592
GACUUUCUUUCCAUUGCUUGAAUAAAAGAC	chr21:30433562-30433801(-)$1	239	8	38	17.2949
UGUGAUUGAGUGUUUGAAGAUUGUCACACG	chr20:2641060-2641306(-)$1	246	81	111	18.6344
CCCGGGCUGGGGAGCGGGGUCUGGCCCGGG	chr3:32544002-32544229(-)$1	227	156	186	19.0506
UUAAAAAUCUACCAAAAGUUAGCUUUUUGG	chr3:186505214-186505450(+)$1	236	178	208	19.5008

#DB
.(((((..(((........)))..)))))(	chr19:12790370-12790596(-)$1	1	124	154	16.9488
(((....((((........))))....)))	chr17:39846293-39846520(+)$1	1	166	196	16.8712
(((((..((((........)))))))))).	chr8:22471524-22471751(+)$1	1	161	191	15.4627
((((.((((((........)))...)))))	chr22:36912653-36912899(-)$1	1	104	134	18.0942
((((.((.(((........)))...))..)	chr17:38151397-38151636(+)$1	1	37	67	17.1608
((....(((((........)))))))))))	chr2:170413650-170413890(-)$1	1	83	113	17.5142
(((.(.(((((........)))))..).))	chr19:59059357-59059594(+)$1	1	163	193	17.3395
((..((..(((........))).))..)))	chr13:73336038-73336258(-)$1	1	32	62	17.3727
(((((.(((((........)))))....))	chr4:41263672-41263911(+)$1	1	163	193	18.0187
(((((.(((((........))))).))))(	chr1:43826345-43826570(+)$1	1	85	115	15.1886
((..(((((((........)))..))))))	chr19:41269421-41269645(+)$1	1	139	169	17.2136
((((((.((((........)))).))))))	chr17:45730003-45730221(+)$1	1	147	177	15.9786
(.(((((.(((........))).))))).)	chr12:57882756-57882980(+)$1	1	177	207	18.1453
((.(((.((((........)))).))).))	chr12:120884456-120884681(+)$1	1	120	150	16.7469
.(((((((.((........)))))))))..	chr19:1091725-1091947(-)$1	1	12	42	17.4430
(.(((.(((((........))))).)))))	chr19:48981649-48981873(+)$1	1	114	144	17.7137
((...((((.(........).))))))).)	chr1:154184916-154185184(-)$1	1	197	227	16.9039
((((((((.((........)).))))))))	chr11:64534576-64534807(-)$1	1	180	210	17.5818
.(((...((((........)))).)))...	chr4:71555675-71555903(+)$1	1	71	101	16.9250
(((((.((..(........)..))))).))	chr1:78430259-78430485(-)$1	1	144	174	15.8874
))(((((.(((........))).)))))..	chr16:30779534-30779758(+)$1	1	120	150	16.0767
(((((((((((........))))).)))))	chr22:38054894-38055134(+)$1	1	109	139	16.8250
(((....((.(........)))))))))))	chr4:77969464-77969692(-)$1	1	52	82	15.9549
((((..(((((........)))))...)))	chr17:76993169-76993396(-)$1	1	89	119	18.3918
...(..(((((........)))))..)...	chr19:33072122-33072340(+)$1	1	79	109	18.0579
.((.(.(((((........)))))).))))	chr1:151371972-151372221(+)$1	1	205	235	16.3109
((..(((((((........))).))))..)	chr19:59061648-59061878(+)$1	1	78	108	17.4617
(((.(((((((........))))))).)))	chr16:249082-249304(-)$1	1	92	122	16.9360
.(((((...((........))..))))).)	chr20:32267603-32267845(-)$1	1	55	85	16.7411
(..(((((..(........)..)))))..)	chr10:70496607-70496834(+)$1	1	194	224	17.3072
((...((((((........))))))...))	chr17:72205241-72205492(+)$1	1	204	234	16.6903
(((((....((........))....)))))	chr12:58145348-58145572(-)$1	1	11	41	16.8340
(.(((((..((........))..))))).)	chr17:77808869-77809117(-)$1	1	215	245	17.0174
..(((.(((((........))))).))).)	chr3:53262006-53262243(-)$1	1	75	105	17.5952
(((((...(((........)))....))))	chr1:226178853-226179111(-)$1	1	175	205	18.2120
(..((((.(((........))).))))..)	chr1:62907137-62907379(+)$1	1	59	89	17.0335
((..(((.(((........))))))...))	chr19:39663457-39663688(+)$1	1	116	146	18.2034
(((....((((........))))..)))))	chr1:234519421-234519648(+)$1	1	37	67	18.0061
(...(((((((........)))))))...)	chr1:93299070-93299315(+)$1	1	189	219	18.2762
(((((((((.(........).)))..))))	chr7:75694140-75694365(+)$1	1	68	98	17.4586
..(((((((((........)))))))))..	chr1:62913016-62913260(+)$1	1	133	163	17.8389
..((....(((........)))..))..).	chr10:35467966-35468199(+)$1	1	125	155	17.0853
..(((((((((........)))))))))((	chr22:39713461-39713695(-)$1	1	109	139	15.8063
(....((((.(........)))))....))	chr22:19164036-19164274(-)$1	1	87	117	16.6553
.((((((((((........)))))))))).	chr10:79795214-79795463(+)$1	1	201	231	17.3010
(..(((((..(........)..)))))..)	chr10:70496645-70496876(+)$1	1	156	186	17.3072
(((((((.(((........))).)))))))	chr5:179247993-179248220(+)$1	1	15	45	18.9376
((((..(((((........)))))..))))	chr12:120636863-120637101(-)$1	1	25	55	17.8271
(((((...(((........)))...)))))	chr17:76219691-76219920(+)$1	1	72	102	18.4973
(.(((((((((........))).)))))))	chr17:62499451-62499683(-)$1	1	139	169	16.8107
.(((((((.((........)).))))))))	chrX:153669350-153669573(+)$1	1	142	172	15.4457
(.(((((((((........)))..))))))	chr6:27100098-27100320(-)$1	1	155	185	16.8139
((((((...((........))...))))))	chrX:48791943-48792171(-)$1	1	112	142	18.5569
(((((.(((((........))))).))).)	chr4:185618754-185618980(-)$1	1	173	203	17.0297
(.(.(((((((........))))))).)..	chr2:28002280-28002508(+)$1	1	168	198	17.5012
(.(((((((((........))))))))).(	chr1:156203333-156203555(+)$1	1	64	94	15.8155
((((.(.((((........)))).))))))	chr12:122243872-122244095(+)$1	1	96	126	15.6570
(((((((((((........))))))))).)	chr1:151288369-151288591(-)$1	1	180	210	18.3592
(.((((..(((........)))..)))).)	chr21:30433562-30433801(-)$1	1	8	38	17.2949
((((((..(((........)))))))))).	chr20:2641060-2641306(-)$1	1	81	111	18.6344
(((((((((((........)))))))))))	chr3:32544002-32544229(-)$1	1	156	186	19.0506
(((((((.(((........))).)))))))	chr3:186505214-186505450(+)$1	1	178	208	19.5008

#PSSM
c : 0.17	e : 0.12	g : 0.11	d : 0.09	f : 0.09	: : 0.06	[ : 0.06	= : 0.06	i : 0.03	# : 0.03	b : 0.03	G : 0.01	" : 0.01	h : 0.01	a : 0.01	! : 0.01	F : 0.01	
e : 0.14	g : 0.14	c : 0.11	[ : 0.11	d : 0.08	f : 0.08	= : 0.08	! : 0.06	# : 0.04	i : 0.03	" : 0.03	b : 0.03	: : 0.03	
e : 0.17	! : 0.11	g : 0.11	f : 0.09	i : 0.09	d : 0.08	c : 0.08	= : 0.08	" : 0.06	# : 0.03	b : 0.03	[ : 0.01	a : 0.01	
e : 0.19	g : 0.11	c : 0.09	i : 0.09	# : 0.08	f : 0.08	[ : 0.06	! : 0.06	d : 0.06	= : 0.06	" : 0.04	a : 0.01	b : 0.01	
e : 0.17	g : 0.12	# : 0.09	c : 0.09	i : 0.09	d : 0.08	f : 0.06	= : 0.06	[ : 0.04	" : 0.04	! : 0.04	a : 0.03	b : 0.01	
e : 0.12	[ : 0.12	g : 0.11	# : 0.09	d : 0.09	i : 0.09	! : 0.06	f : 0.06	= : 0.06	c : 0.04	" : 0.04	b : 0.03	a : 0.01	
e : 0.27	i : 0.09	! : 0.08	# : 0.08	d : 0.08	g : 0.08	" : 0.08	c : 0.04	[ : 0.04	f : 0.04	= : 0.04	b : 0.03	
e : 0.22	d : 0.17	[ : 0.11	! : 0.08	g : 0.08	i : 0.08	" : 0.06	f : 0.04	c : 0.03	b : 0.03	# : 0.03	= : 0.03	
c : 0.32	e : 0.19	d : 0.14	! : 0.06	i : 0.06	[ : 0.04	g : 0.04	" : 0.03	= : 0.03	b : 0.01	f : 0.01	# : 0.01	
c : 0.30	e : 0.19	d : 0.11	b : 0.11	[ : 0.06	i : 0.06	! : 0.04	g : 0.04	= : 0.03	f : 0.01	
c : 0.30	e : 0.19	d : 0.11	b : 0.11	a : 0.11	i : 0.06	g : 0.04	= : 0.03	f : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.30	e : 0.19	d : 0.11	b : 0.11	a : 0.11	i : 0.06	g : 0.04	= : 0.03	f : 0.01	
c : 0.30	e : 0.19	d : 0.12	b : 0.12	i : 0.06	2 : 0.04	g : 0.04	] : 0.03	= : 0.03	f : 0.01	
c : 0.32	e : 0.19	d : 0.14	2 : 0.08	g : 0.06	i : 0.06	] : 0.03	= : 0.03	b : 0.01	f : 0.01	4 : 0.01	3 : 0.01	
e : 0.22	d : 0.14	] : 0.12	2 : 0.11	g : 0.09	i : 0.08	3 : 0.06	f : 0.03	4 : 0.03	c : 0.03	= : 0.03	b : 0.01	
e : 0.29	2 : 0.09	g : 0.09	i : 0.09	f : 0.06	3 : 0.06	] : 0.06	d : 0.06	4 : 0.04	= : 0.04	b : 0.03	c : 0.03	
e : 0.11	f : 0.09	g : 0.09	i : 0.09	4 : 0.08	c : 0.08	2 : 0.08	] : 0.08	d : 0.08	3 : 0.06	= : 0.06	b : 0.03	a : 0.03	
e : 0.16	c : 0.14	d : 0.09	g : 0.09	i : 0.09	f : 0.08	2 : 0.08	= : 0.08	4 : 0.06	3 : 0.04	b : 0.03	] : 0.01	
e : 0.17	c : 0.14	d : 0.09	i : 0.09	f : 0.08	g : 0.08	= : 0.08	3 : 0.06	4 : 0.04	b : 0.03	a : 0.03	2 : 0.03	] : 0.03	
e : 0.16	g : 0.11	d : 0.09	2 : 0.09	i : 0.09	f : 0.08	c : 0.08	= : 0.08	3 : 0.06	] : 0.04	4 : 0.03	> : 0.01	b : 0.01	a : 0.01	
e : 0.14	] : 0.12	g : 0.11	d : 0.09	2 : 0.09	c : 0.08	= : 0.08	f : 0.06	3 : 0.04	i : 0.03	> : 0.03	: : 0.03	b : 0.03	a : 0.01	
c : 0.16	e : 0.16	d : 0.09	g : 0.09	f : 0.06	b : 0.06	= : 0.06	: : 0.04	3 : 0.04	i : 0.03	> : 0.03	a : 0.03	D : 0.01	h : 0.01	] : 0.01	E : 0.01	2 : 0.01	G : 0.01	

#score	1069.6297982425451
#seq	62
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_CDS_m3_run2.txt

#BEAR
""cccqqqqqqqqccc	chr19:53453768-53453987(-)$1	219	42	58	13.5984
iiiiiqqqqqqqqiii	chr13:31713051-31713274(-)$1	223	176	192	13.1708
eeeeeqqqqqqqqeee	chr8:21832151-21832381(+)$1	230	147	163	14.0397
fffffqqqqqqqqfff	chr14:60616715-60616940(-)$1	225	34	50	12.6947
eeeeeqqqqqqqqeee	chr12:46245708-46245934(+)$1	226	74	90	14.0397
eeeeeqqqqqqqqeee	chr18:72589165-72589383(+)$1	218	6	22	14.0397
fffffqqqqqqqqfff	chr6:42985780-42986012(+)$1	232	210	226	12.6947
eeeeeqqqqqqqqeee	chr12:133779120-133779341(+)$1	221	164	180	14.0397
%ddddqqqqqqqqddd	chr11:27389786-27390008(-)$1	222	77	93	13.0804
:ddddqqqqqqqqddd	chr2:171853112-171853342(-)$1	230	54	70	12.6488
eeeeeqqqqqqqqeee	chr7:104742399-104742619(+)$1	220	84	100	14.0397
d[cccqqqqqqqqccc	chr17:72862564-72862786(-)$1	222	36	52	13.4745
eeeeeqqqqqqqqeee	chr7:77407904-77408129(+)$1	225	174	190	14.0397
:ddddqqqqqqqqddd	chr8:131130685-131130906(-)$1	221	105	121	12.6488
###bbqqqqqqqqbb4	chr17:41246548-41246781(-)$1	233	142	158	12.3794
!!cccqqqqqqqqccc	chr5:138661798-138662017(+)$1	219	157	173	13.7753
eeeeeqqqqqqqqeee	chr19:9721429-9721655(-)$1	226	44	60	14.0397
!!cccqqqqqqqqccc	chr17:65927972-65928196(+)$1	224	160	176	13.7753
b[cccqqqqqqqqccc	chr7:128632026-128632244(-)$1	218	96	112	13.2923
eeeeeqqqqqqqqeee	chr1:193060686-193060917(+)$1	231	111	127	14.0397
fffffqqqqqqqqfff	chr1:35656862-35657081(-)$1	219	85	101	12.6947
=====qqqqqqqq===	chr5:133535959-133536185(-)$1	226	20	36	13.4029
$ddddqqqqqqqqddd	chr14:75537547-75537766(+)$1	219	10	26	13.4765
(ddddqqqqqqqqddd	chr12:69158457-69158683(+)$1	226	47	63	13.0189
eeeeeqqqqqqqqeee	chr9:35060924-35061144(-)$1	220	38	54	14.0397
iiiiiqqqqqqqqiii	chr15:55488937-55489155(-)$1	218	95	111	13.1708
fffffqqqqqqqqfff	chr15:52893202-52893422(-)$1	220	199	215	12.6947
b[cccqqqqqqqqccc	chr9:130742265-130742491(-)$1	226	162	178	13.2923
eeeeeqqqqqqqqeee	chr7:64388954-64389184(+)$1	230	173	189	14.0397
ee[bbqqqqqqqqbbe	chr18:48702867-48703085(-)$1	218	37	53	12.9072
&&cccqqqqqqqqccc	chr3:160149418-160149655(+)$1	237	192	208	12.3304
##cccqqqqqqqqccc	chr5:65309289-65309514(+)$1	225	60	76	13.5576
ddd[aqqqqqqqqa]d	chr3:129389823-129390047(-)$1	224	169	185	13.1013
eeeeeqqqqqqqqeee	chr2:86831810-86832040(-)$1	230	194	210	14.0397
ee[bbqqqqqqqqbb]	chr3:182576951-182577174(+)$1	223	172	188	12.6994
[ddddqqqqqqqqddd	chr6:82933079-82933302(-)$1	223	172	188	13.6796
:ddddqqqqqqqqddd	chr8:145011047-145011267(-)$1	220	65	81	12.6488
[ddddqqqqqqqqddd	chrX:41027311-41027532(+)$1	221	144	160	13.6796
!ddddqqqqqqqqddd	chr8:103850876-103851100(-)$1	224	143	159	13.7343
gggggqqqqqqqqggg	chr3:196650242-196650467(+)$1	225	129	145	13.2367
"""bbqqqqqqqqbbe	chr3:131181551-131181781(-)$1	230	64	80	12.6710
eecccqqqqqqqqccc	chr5:145616871-145617092(+)$1	221	155	171	13.7136
ddd[aqqqqqqqqa]d	chr9:32542003-32542234(-)$1	231	8	24	13.1013
dddddqqqqqqqqddd	chr10:123727069-123727291(-)$1	222	57	73	13.4505
eeeeeqqqqqqqqeee	chr6:33287407-33287632(-)$1	225	134	150	14.0397
fffffqqqqqqqqfff	chr8:117868350-117868580(-)$1	230	184	200	12.6947
!ddddqqqqqqqqddd	chr15:56993011-56993240(-)$1	229	179	195	13.7343
fffffqqqqqqqqfff	chr3:142747114-142747330(+)$1	216	33	49	12.6947
d!!bbqqqqqqqqbb2	chr20:44511534-44511753(+)$1	219	155	171	12.2531
eeeeeqqqqqqqqeee	chr11:32953989-32954201(+)$1	212	97	113	14.0397
eeeeeqqqqqqqqeee	chr13:60240826-60241051(-)$1	225	170	186	14.0397
gggggqqqqqqqqggg	chr6:33255115-33255336(-)$1	221	196	212	13.2367
eeeeeqqqqqqqqeee	chr1:151372061-151372280(+)$1	219	122	138	14.0397
eeeeeqqqqqqqqeee	chr9:19286747-19286974(+)$1	227	52	68	14.0397
eeeeeqqqqqqqqeee	chr2:73961564-73961789(-)$1	225	96	112	14.0397
eee[aqqqqqqqqaee	chr7:92764628-92764849(-)$1	221	140	156	13.7221
eeebbqqqqqqqqbb2	chr3:112251460-112251692(-)$1	232	101	117	12.5831
d[cccqqqqqqqqccc	chr2:219411567-219411785(-)$1	218	113	129	13.4745
gggggqqqqqqqqggg	chr1:53676304-53676534(+)$1	230	191	207	13.2367
gg[bbqqqqqqqqbbg	chr3:121527717-121527940(-)$1	223	95	111	12.5457
!ddddqqqqqqqqddd	chr14:103363539-103363759(+)$1	220	190	206	13.7343
[ddddqqqqqqqqddd	chr6:24657971-24658197(-)$1	226	190	206	13.6796
eeeeeqqqqqqqqeee	chr8:144902736-144902958(-)$1	222	61	77	14.0397
""cccqqqqqqqqccc	chr18:54285149-54285369(-)$1	220	158	174	13.5984
!!cccqqqqqqqqccc	chr17:26646210-26646440(+)$1	230	94	110	13.7753
"ddddqqqqqqqqddd	chr13:29246384-29246617(+)$1	233	21	37	13.6630

#otherMatches

#Seq PSSM
AAUUCAUACUGGAGAG	chr19:53453768-53453987(-)$1	219	42	58	13.5984
UUAAACUAUAGACuuu	chr13:31713051-31713274(-)$1	223	176	192	13.1708
UUGGGUCAUAUUUCCC	chr8:21832151-21832381(+)$1	230	147	163	14.0397
GGGUUUUUUUAAUGGC	chr14:60616715-60616940(-)$1	225	34	50	12.6947
CUUUUAAAUGGGAGAA	chr12:46245708-46245934(+)$1	226	74	90	14.0397
UGUGAUAGAAGUUUCA	chr18:72589165-72589383(+)$1	218	6	22	14.0397
CUGUUGAAGCAAUGAU	chr6:42985780-42986012(+)$1	232	210	226	12.6947
GGAAAACAUUCAGUUU	chr12:133779120-133779341(+)$1	221	164	180	14.0397
AAAUAAUGAAGUCUGU	chr11:27389786-27390008(-)$1	222	77	93	13.0804
UUUAAUUUUUUUUUUA	chr2:171853112-171853342(-)$1	230	54	70	12.6488
CUUCUCCUGAUAUAGA	chr7:104742399-104742619(+)$1	220	84	100	14.0397
GACUUGGUCCCUGGAG	chr17:72862564-72862786(-)$1	222	36	52	13.4745
CAGAUUCCACAUCAUC	chr7:77407904-77408129(+)$1	225	174	190	14.0397
ACUUGCACUAAUUCAA	chr8:131130685-131130906(-)$1	221	105	121	12.6488
AUUCUGUAAUAAAAGC	chr17:41246548-41246781(-)$1	233	142	158	12.3794
CAUUAUCAGAAAUUAA	chr5:138661798-138662017(+)$1	219	157	173	13.7753
GUGUGUAGCAGUUCAU	chr19:9721429-9721655(-)$1	226	44	60	14.0397
CAGGUAUUUAUCCAUC	chr17:65927972-65928196(+)$1	224	160	176	13.7753
CUAGUUAUAUUCUACU	chr7:128632026-128632244(-)$1	218	96	112	13.2923
CUAAAUAAAUCAUUUU	chr1:193060686-193060917(+)$1	231	111	127	14.0397
AGAACCAGGAGAAGUU	chr1:35656862-35657081(-)$1	219	85	101	12.6947
GGUCAGAUCCAGAUGA	chr5:133535959-133536185(-)$1	226	20	36	13.4029
AGAUCCAGAAAGUGAU	chr14:75537547-75537766(+)$1	219	10	26	13.4765
CAAGUUCUGCAUUACU	chr12:69158457-69158683(+)$1	226	47	63	13.0189
CCAUCCGCAAGAAGAU	chr9:35060924-35061144(-)$1	220	38	54	14.0397
CGGGGCCCAUCUAUCC	chr15:55488937-55489155(-)$1	218	95	111	13.1708
UAACAAUAAAUAAUGU	chr15:52893202-52893422(-)$1	220	199	215	12.6947
GUCCUCUUCUGCAAGG	chr9:130742265-130742491(-)$1	226	162	178	13.2923
UGAACAUAAGAGAGUU	chr7:64388954-64389184(+)$1	230	173	189	14.0397
CAUAGAACAUCCACUU	chr18:48702867-48703085(-)$1	218	37	53	12.9072
AAGGUAUGAAUGAACU	chr3:160149418-160149655(+)$1	237	192	208	12.3304
UAACUUAAAUUCUGGU	chr5:65309289-65309514(+)$1	225	60	76	13.5576
CAGACAAACAGCAGGC	chr3:129389823-129390047(-)$1	224	169	185	13.1013
UGUUGAGAUAUUCCAA	chr2:86831810-86832040(-)$1	230	194	210	14.0397
GAUCUGAAUGAAGAGC	chr3:182576951-182577174(+)$1	223	172	188	12.6994
UAAUUUUAAUAAUAAU	chr6:82933079-82933302(-)$1	223	172	188	13.6796
ACGGCAACCCCAAGCU	chr8:145011047-145011267(-)$1	220	65	81	12.6488
UUCUCCCUAUGUCGAG	chrX:41027311-41027532(+)$1	221	144	160	13.6796
AAGUACUUGAAAAUAU	chr8:103850876-103851100(-)$1	224	143	159	13.7343
AUUAUUUCAUUUUAUG	chr3:196650242-196650467(+)$1	225	129	145	13.2367
CAAAGAUUCUAAACUG	chr3:131181551-131181781(-)$1	230	64	80	12.6710
AGGGUAUAGAAAAGCC	chr5:145616871-145617092(+)$1	221	155	171	13.7136
GGCACAGAUCAAGGAG	chr9:32542003-32542234(-)$1	231	8	24	13.1013
UCCUGGAAGAUAACAG	chr10:123727069-123727291(-)$1	222	57	73	13.4505
GUCAGAAGAACCCCUG	chr6:33287407-33287632(-)$1	225	134	150	14.0397
AUGAACCUUUAGAUUU	chr8:117868350-117868580(-)$1	230	184	200	12.6947
CCCAGUUACAAUUCUG	chr15:56993011-56993240(-)$1	229	179	195	13.7343
AAUAUGAUGUUUAAUG	chr3:142747114-142747330(+)$1	216	33	49	12.6947
ACUGCCUAUCCUAGCU	chr20:44511534-44511753(+)$1	219	155	171	12.2531
GUAUAAUUCCUCCUGU	chr11:32953989-32954201(+)$1	212	97	113	14.0397
UAGACACUCAUACGUC	chr13:60240826-60241051(-)$1	225	170	186	14.0397
GCUACAGCUGUGAGUG	chr6:33255115-33255336(-)$1	221	196	212	13.2367
GGUCCAAUCACGCGGA	chr1:151372061-151372280(+)$1	219	122	138	14.0397
AGGAUGUGAAGUGAUC	chr9:19286747-19286974(+)$1	227	52	68	14.0397
CAGUUAACACAUCAGC	chr2:73961564-73961789(-)$1	225	96	112	14.0397
CAUUGAUCCAAUACAU	chr7:92764628-92764849(-)$1	221	140	156	13.7221
CAUUCCAACAAUAGAA	chr3:112251460-112251692(-)$1	232	101	117	12.5831
CACCUCUUAGAUCAGG	chr2:219411567-219411785(-)$1	218	113	129	13.4745
UUUAAUGAAGUAUUUA	chr1:53676304-53676534(+)$1	230	191	207	13.2367
AGAUGAAUUACUACAC	chr3:121527717-121527940(-)$1	223	95	111	12.5457
CAUUUACAGGUAAGAA	chr14:103363539-103363759(+)$1	220	190	206	13.7343
UUUGAAAAACAGAUCA	chr6:24657971-24658197(-)$1	226	190	206	13.6796
CUGUCUUUCAGAUGGC	chr8:144902736-144902958(-)$1	222	61	77	14.0397
UUGUGGAGAUUAUCAC	chr18:54285149-54285369(-)$1	220	158	174	13.5984
CUGGGCCUCUACUUCC	chr17:26646210-26646440(+)$1	230	94	110	13.7753
UUAGACUAUAUAUUCU	chr13:29246384-29246617(+)$1	233	21	37	13.6630

#DB
..(((........)))	chr19:53453768-53453987(-)$1	1	42	58	13.5984
(((((........)))	chr13:31713051-31713274(-)$1	1	176	192	13.1708
(((((........)))	chr8:21832151-21832381(+)$1	1	147	163	14.0397
(((((........)))	chr14:60616715-60616940(-)$1	1	34	50	12.6947
(((((........)))	chr12:46245708-46245934(+)$1	1	74	90	14.0397
(((((........)))	chr18:72589165-72589383(+)$1	1	6	22	14.0397
(((((........)))	chr6:42985780-42986012(+)$1	1	210	226	12.6947
(((((........)))	chr12:133779120-133779341(+)$1	1	164	180	14.0397
.((((........)))	chr11:27389786-27390008(-)$1	1	77	93	13.0804
.((((........)))	chr2:171853112-171853342(-)$1	1	54	70	12.6488
(((((........)))	chr7:104742399-104742619(+)$1	1	84	100	14.0397
(.(((........)))	chr17:72862564-72862786(-)$1	1	36	52	13.4745
(((((........)))	chr7:77407904-77408129(+)$1	1	174	190	14.0397
.((((........)))	chr8:131130685-131130906(-)$1	1	105	121	12.6488
...((........)).	chr17:41246548-41246781(-)$1	1	142	158	12.3794
..(((........)))	chr5:138661798-138662017(+)$1	1	157	173	13.7753
(((((........)))	chr19:9721429-9721655(-)$1	1	44	60	14.0397
..(((........)))	chr17:65927972-65928196(+)$1	1	160	176	13.7753
(.(((........)))	chr7:128632026-128632244(-)$1	1	96	112	13.2923
(((((........)))	chr1:193060686-193060917(+)$1	1	111	127	14.0397
(((((........)))	chr1:35656862-35657081(-)$1	1	85	101	12.6947
(((((........)))	chr5:133535959-133536185(-)$1	1	20	36	13.4029
.((((........)))	chr14:75537547-75537766(+)$1	1	10	26	13.4765
.((((........)))	chr12:69158457-69158683(+)$1	1	47	63	13.0189
(((((........)))	chr9:35060924-35061144(-)$1	1	38	54	14.0397
(((((........)))	chr15:55488937-55489155(-)$1	1	95	111	13.1708
(((((........)))	chr15:52893202-52893422(-)$1	1	199	215	12.6947
(.(((........)))	chr9:130742265-130742491(-)$1	1	162	178	13.2923
(((((........)))	chr7:64388954-64389184(+)$1	1	173	189	14.0397
((.((........)))	chr18:48702867-48703085(-)$1	1	37	53	12.9072
..(((........)))	chr3:160149418-160149655(+)$1	1	192	208	12.3304
..(((........)))	chr5:65309289-65309514(+)$1	1	60	76	13.5576
(((.(........).)	chr3:129389823-129390047(-)$1	1	169	185	13.1013
(((((........)))	chr2:86831810-86832040(-)$1	1	194	210	14.0397
((.((........)).	chr3:182576951-182577174(+)$1	1	172	188	12.6994
.((((........)))	chr6:82933079-82933302(-)$1	1	172	188	13.6796
.((((........)))	chr8:145011047-145011267(-)$1	1	65	81	12.6488
.((((........)))	chrX:41027311-41027532(+)$1	1	144	160	13.6796
.((((........)))	chr8:103850876-103851100(-)$1	1	143	159	13.7343
(((((........)))	chr3:196650242-196650467(+)$1	1	129	145	13.2367
...((........)))	chr3:131181551-131181781(-)$1	1	64	80	12.6710
(((((........)))	chr5:145616871-145617092(+)$1	1	155	171	13.7136
(((.(........).)	chr9:32542003-32542234(-)$1	1	8	24	13.1013
)((((........)))	chr10:123727069-123727291(-)$1	1	57	73	13.4505
(((((........)))	chr6:33287407-33287632(-)$1	1	134	150	14.0397
(((((........)))	chr8:117868350-117868580(-)$1	1	184	200	12.6947
.((((........)))	chr15:56993011-56993240(-)$1	1	179	195	13.7343
(((((........)))	chr3:142747114-142747330(+)$1	1	33	49	12.6947
(..((........)).	chr20:44511534-44511753(+)$1	1	155	171	12.2531
(((((........)))	chr11:32953989-32954201(+)$1	1	97	113	14.0397
(((((........)))	chr13:60240826-60241051(-)$1	1	170	186	14.0397
(((((........)))	chr6:33255115-33255336(-)$1	1	196	212	13.2367
(((((........)))	chr1:151372061-151372280(+)$1	1	122	138	14.0397
(((((........)))	chr9:19286747-19286974(+)$1	1	52	68	14.0397
(((((........)))	chr2:73961564-73961789(-)$1	1	96	112	14.0397
(((.(........)))	chr7:92764628-92764849(-)$1	1	140	156	13.7221
(((((........)).	chr3:112251460-112251692(-)$1	1	101	117	12.5831
(.(((........)))	chr2:219411567-219411785(-)$1	1	113	129	13.4745
(((((........)))	chr1:53676304-53676534(+)$1	1	191	207	13.2367
((.((........)))	chr3:121527717-121527940(-)$1	1	95	111	12.5457
.((((........)))	chr14:103363539-103363759(+)$1	1	190	206	13.7343
.((((........)))	chr6:24657971-24658197(-)$1	1	190	206	13.6796
(((((........)))	chr8:144902736-144902958(-)$1	1	61	77	14.0397
..(((........)))	chr18:54285149-54285369(-)$1	1	158	174	13.5984
..(((........)))	chr17:26646210-26646440(+)$1	1	94	110	13.7753
.((((........)))	chr13:29246384-29246617(+)$1	1	21	37	13.6630

#PSSM
e : 0.34	f : 0.09	d : 0.09	! : 0.09	" : 0.06	g : 0.06	: : 0.04	[ : 0.04	i : 0.03	# : 0.03	b : 0.03	% : 0.01	= : 0.01	$ : 0.01	( : 0.01	& : 0.01	
e : 0.34	d : 0.24	f : 0.09	[ : 0.06	! : 0.06	g : 0.06	" : 0.04	i : 0.03	# : 0.03	= : 0.01	& : 0.01	
e : 0.30	d : 0.24	c : 0.18	f : 0.09	[ : 0.04	g : 0.04	i : 0.03	# : 0.01	= : 0.01	" : 0.01	! : 0.01	
e : 0.27	d : 0.21	c : 0.18	b : 0.10	f : 0.09	[ : 0.04	g : 0.04	i : 0.03	= : 0.01	
e : 0.27	d : 0.21	c : 0.18	b : 0.10	f : 0.09	a : 0.04	g : 0.04	i : 0.03	= : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.27	d : 0.21	c : 0.18	b : 0.10	f : 0.09	a : 0.04	g : 0.04	i : 0.03	= : 0.01	
e : 0.28	d : 0.21	c : 0.18	b : 0.10	f : 0.09	g : 0.04	i : 0.03	] : 0.03	= : 0.01	
e : 0.31	d : 0.24	c : 0.18	f : 0.09	g : 0.06	i : 0.03	2 : 0.03	4 : 0.01	= : 0.01	] : 0.01	

#score	884.8385730801344
#seq	66
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_UTR_m2_run1.txt

#BEAR
dddd[cccqqqqqqqqccc]ddd	chr5:151184133-151184367(+)$1	234	137	160	14.9874
gggg!!bbqqqqqqqqbb22ggg	chr7:133975458-133975675(-)$1	217	184	207	15.2085
:gggggggqqqqqqqqggggggg	chr20:33128630-33128857(+)$1	227	96	119	15.1422
!!ffffffqqqqqqqqffffff]	chr14:64484271-64484500(+)$1	229	55	78	15.2649
e!!eeeeeqqqqqqqqeeeee]e	chr3:15112127-15112351(-)$1	224	50	73	15.5245
%gggggggqqqqqqqqggggggg	chr7:44866710-44866938(-)$1	228	188	211	15.5567
====ddddqqqqqqqqdddd666	chr14:60762460-60762682(+)$1	222	146	169	13.8164
eeeee[bbqqqqqqqqbb22eee	chr10:62553745-62553983(+)$1	238	121	144	14.3679
[ccc[cccqqqqqqqqccc]ccc	chr11:125525279-125525506(+)$1	227	160	183	15.9885
dddd[cccqqqqqqqqccc]ddd	chr2:204296700-204296933(+)$1	233	132	155	14.9874
%gggggggqqqqqqqqggggggg	chr8:29964727-29964961(+)$1	234	55	78	15.5567
e[ffffffqqqqqqqqffffff]	chr7:94296687-94296908(+)$1	221	108	131	15.0037
ccc[ddddqqqqqqqqdddd]cc	chrX:103437160-103437382(+)$1	222	61	84	14.9303
ddd!!cccqqqqqqqqccc22dd	chr1:225590186-225590408(-)$1	222	16	39	15.1617
"""eeeeeqqqqqqqqeeeee44	chr1:193060686-193060915(+)$1	229	108	131	15.7858
iiiiiiiiqqqqqqqqiiiiiii	chr7:70256365-70256594(+)$1	229	159	182	16.1920
ii!!ddddqqqqqqqqdddd]ii	chr2:174089695-174089935(+)$1	240	55	78	15.3642
[gggggggqqqqqqqqggggggg	chr2:136664412-136664648(-)$1	236	160	183	16.0996
ffffffffqqqqqqqqffffff:	chr8:17078107-17078333(+)$1	226	90	113	13.5408
fffeeeeeqqqqqqqqeeeee]f	chr5:79774324-79774549(+)$1	225	3	26	14.9176
iiiiiiiiqqqqqqqqiiiiiii	chr19:22849525-22849756(+)$1	231	26	49	16.1920
eee"""bbqqqqqqqqbb333ee	chr5:167975555-167975776(-)$1	221	123	146	14.7805
""ccc[bbqqqqqqqqbb]ccc]	chr12:92537443-92537677(-)$1	234	76	99	15.0845
iiiiiiiiqqqqqqqqiiiiiii	chr15:83515421-83515648(-)$1	227	140	163	16.1920
""ffffffqqqqqqqqffffff2	chr16:50833419-50833643(+)$1	224	149	172	14.9987
(eeeeebbqqqqqqqqbb22eee	chr5:83238201-83238432(-)$1	231	182	205	13.7910
dgggggggqqqqqqqqggggggg	chr2:128059488-128059718(-)$1	230	138	161	15.8828
g####cccqqqqqqqqccc4444	chr2:203429351-203429585(+)$1	234	45	68	15.9731
eee!!cccqqqqqqqqccc333e	chr1:23634473-23634700(-)$1	227	78	101	16.0386
========qqqqqqqq=======	chr5:52393810-52394038(-)$1	228	142	165	16.6369
b!!eeeeeqqqqqqqqeeeee44	chr20:23352239-23352464(+)$1	225	193	216	15.4911
:gggggggqqqqqqqqggggggg	chr16:75205294-75205529(+)$1	235	23	46	15.1422
dddeeeeeqqqqqqqqeeeee:g	chr4:39123342-39123565(+)$1	223	143	166	13.9154
eeeee!!aqqqqqqqqa22eeee	chr1:65696571-65696798(+)$1	227	139	162	14.3758
iiiiiiiiqqqqqqqqiiiiiii	chr4:6884442-6884665(+)$1	223	121	144	16.1920
ccc!!cccqqqqqqqqccc333c	chr1:111489930-111490162(-)$1	232	0	23	16.3579
d"""ddddqqqqqqqqdddd333	chr12:1895303-1895530(+)$1	227	157	180	15.3663
gggg[cccqqqqqqqqccc]ggg	chr1:150447060-150447286(+)$1	226	36	59	16.3101
iiiiiiiiqqqqqqqqiiiiiii	chr1:78030684-78030909(-)$1	225	186	209	16.1920
%%ffffffqqqqqqqqffffff7	chr1:162495024-162495245(+)$1	221	186	209	13.3084
ee[eeeeeqqqqqqqqeeeee22	chr9:19375828-19376050(-)$1	222	110	133	15.0197
fff!!cccqqqqqqqqccc22ff	chr3:57545794-57546017(+)$1	223	29	52	15.3519
ggg!!cccqqqqqqqqccc22gg	chr3:65340720-65340951(-)$1	231	193	216	16.0569
ggggg[bbqqqqqqqqbb22ggg	chr15:50792174-50792397(+)$1	223	42	65	15.1157
[ccc!!bbqqqqqqqqbbccca]	chr5:171289472-171289706(-)$1	234	136	159	15.0870
"""eeeeeqqqqqqqqeeeee==	chr14:81940805-81941046(-)$1	241	199	222	15.8840
:ccc[cccqqqqqqqqccc]ccc	chr18:56997389-56997616(-)$1	227	154	177	15.0311
iiiiiiiiqqqqqqqqiiiiiii	chr1:75231837-75232059(+)$1	222	90	113	16.1920
ccbbddddqqqqqqqqdddd]bb	chr20:30920237-30920459(+)$1	222	48	71	13.5880
c[dddd[aqqqqqqqqa]dddd]	chr1:78414182-78414403(-)$1	221	34	57	14.5077
####ddddqqqqqqqqddddiii	chr16:74339813-74340042(+)$1	229	134	157	15.2439
lcccddddqqqqqqqqddddeee	chr2:174090624-174090855(+)$1	231	38	61	14.1540
%%%eeeeeqqqqqqqqeeeee44	chr14:57756019-57756243(+)$1	224	159	182	13.8157
========qqqqqqqq=======	chr1:54232662-54232894(-)$1	232	12	35	16.6369
iiiiiiiiqqqqqqqqiiiiiii	chr19:34960416-34960642(+)$1	226	71	94	16.1920
==ffffffqqqqqqqqffffff4	chr1:113454882-113455107(-)$1	225	127	150	15.0783
ccceeeeeqqqqqqqqeeeee22	chr17:45196501-45196728(-)$1	227	64	87	15.0807
eee"""bbqqqqqqqqbb22eee	chr17:28793494-28793717(+)$1	223	39	62	14.3514
::ccccccqqqqqqqqccc]ccc	chr12:79984187-79984419(-)$1	232	94	117	13.8040
c[ffffffqqqqqqqqffffff]	chr1:231487443-231487671(+)$1	228	20	43	15.0879
cc[eeeeeqqqqqqqqeeeeecc	chr16:46731917-46732137(+)$1	220	45	68	15.3988
cc[eeeeeqqqqqqqqeeeee33	chr14:63839682-63839903(-)$1	221	123	146	15.7486
ddd!!cccqqqqqqqqccc]ddd	chr12:27955186-27955410(+)$1	224	15	38	15.2892
d"""ddddqqqqqqqqdddd]dd	chr2:145142483-145142710(-)$1	227	104	127	14.7515
##ffffffqqqqqqqqffffffd	chr14:51722630-51722863(+)$1	233	136	159	14.9009

#otherMatches

#Seq PSSM
UUACCAUUGAAAUUUAAAUUGUG	chr5:151184133-151184367(+)$1	234	137	160	14.9874
GUUCACUCUUAAGGUUGAAAGAA	chr7:133975458-133975675(-)$1	217	184	207	15.2085
CUGUUUUUCUUUAACUAAAAAUA	chr20:33128630-33128857(+)$1	227	96	119	15.1422
AGAAGAUUACUAUGAAAAUCUUG	chr14:64484271-64484500(+)$1	229	55	78	15.2649
UAAAAUCAUAUUCUUUUGAUUAA	chr3:15112127-15112351(-)$1	224	50	73	15.5245
AUGUAUAAUAGCCAUUUUAUGCA	chr7:44866710-44866938(-)$1	228	188	211	15.5567
UUCUCUCUAAAGUUAAAGAGUAA	chr14:60762460-60762682(+)$1	222	146	169	13.8164
aauauaacuuaaaaauguaaaua	chr10:62553745-62553983(+)$1	238	121	144	14.3679
UCAUUUGAUUAUUUCUUCAUGUG	chr11:125525279-125525506(+)$1	227	160	183	15.9885
GUAUUUGGAAUUGUUGCCGUGUA	chr2:204296700-204296933(+)$1	233	132	155	14.9874
CAUGAUCAAUUUAUAGUGGUCGU	chr8:29964727-29964961(+)$1	234	55	78	15.5567
UUAAAAUUUUUAGUAUAAUUUUU	chr7:94296687-94296908(+)$1	221	108	131	15.0037
CAGCUUUCUAAAGGAUGAGACUU	chrX:103437160-103437382(+)$1	222	61	84	14.9303
AUAGCUUAGUUUUUUGUAAUAUA	chr1:225590186-225590408(-)$1	222	16	39	15.1617
CUACUAAAUAAAUCAUUUUAGAC	chr1:193060686-193060915(+)$1	229	108	131	15.7858
AACACAGUCGGCUAAAGCUGUGU	chr7:70256365-70256594(+)$1	229	159	182	16.1920
UGAAUCUCUCAGUUGUGGGAAUA	chr2:174089695-174089935(+)$1	240	55	78	15.3642
UAUUUGAACUUAUUUUUUUAAAU	chr2:136664412-136664648(-)$1	236	160	183	16.0996
UGGAAGUGGCAAACCAUACUUCU	chr8:17078107-17078333(+)$1	226	90	113	13.5408
UGGGGGGCAUAUUGUAGUCCUGU	chr5:79774324-79774549(+)$1	225	3	26	14.9176
aauuaguauauuauuuuacuaau	chr19:22849525-22849756(+)$1	231	26	49	16.1920
UUGUUUGUAUUGGAUAACCAUUA	chr5:167975555-167975776(-)$1	221	123	146	14.7805
UAGGGUGGUUUCAGUUUCUCCCA	chr12:92537443-92537677(-)$1	234	76	99	15.0845
CACACAAGACCUCGAACUUGUGU	chr15:83515421-83515648(-)$1	227	140	163	16.1920
GUAUGGAAGAUUAAGAUUCCAUU	chr16:50833419-50833643(+)$1	224	149	172	14.9987
AGUGCUGCAUAGUUUGGCCAAGC	chr5:83238201-83238432(-)$1	231	182	205	13.7910
GCAGCUAUUCCUACUUAUAGUUG	chr2:128059488-128059718(-)$1	230	138	161	15.8828
UACAAGUUUCCAGAUUAACAUAA	chr2:203429351-203429585(+)$1	234	45	68	15.9731
GUGGCUAUUUUAAAUUGUAAAGC	chr1:23634473-23634700(-)$1	227	78	101	16.0386
AAAAAGAGUAUUUUCUUUUUUUU	chr5:52393810-52394038(-)$1	228	142	165	16.6369
UGUGAAAACACUUUGAUUUUCUA	chr20:23352239-23352464(+)$1	225	193	216	15.4911
AAAGGAGGCAUUUCUACUUCCUU	chr16:75205294-75205529(+)$1	235	23	46	15.1422
GGAUUUGUUUUAUAUUAUAAAAG	chr4:39123342-39123565(+)$1	223	143	166	13.9154
UAUUUGGUGUCUUUAAAAAAAAU	chr1:65696571-65696798(+)$1	227	139	162	14.3758
UGACGAUUAUUCUAGAAAUCGUU	chr4:6884442-6884665(+)$1	223	121	144	16.1920
GAUUUGUAUAUGUACUUGCUUUA	chr1:111489930-111490162(-)$1	232	0	23	16.3579
ACAUAGCCCAAACCCUGGCUUAU	chr12:1895303-1895530(+)$1	227	157	180	15.3663
GACAAUCACUGUACUUUGAGUGU	chr1:150447060-150447286(+)$1	226	36	59	16.3101
GGAGGCAACUGUGGCAUUGCUUC	chr1:78030684-78030909(-)$1	225	186	209	16.1920
CUUCCCAGUUACUUCUUUGGGGU	chr1:162495024-162495245(+)$1	221	186	209	13.3084
AAUUUAAUACAUGAAAAUUGACC	chr9:19375828-19376050(-)$1	222	110	133	15.0197
AGGAAUGGUAAAAUGUUCAGCCC	chr3:57545794-57546017(+)$1	223	29	52	15.3519
UUAAGUGGAUUACUGCCUAGCUG	chr3:65340720-65340951(-)$1	231	193	216	16.0569
UUAAAGGAGCUUAUAAUUUAUUU	chr15:50792174-50792397(+)$1	223	42	65	15.1157
AGGUUUGAUUUGCCCUUCGCCAU	chr5:171289472-171289706(-)$1	234	136	159	15.0870
CUAACUCCAGGAUUCAGGAGUUU	chr14:81940805-81941046(-)$1	241	199	222	15.8840
GAGGAUUUAAAUUCACAAAACCU	chr18:56997389-56997616(-)$1	227	154	177	15.0311
auuuuaggguauacuacuuaaaa	chr1:75231837-75232059(+)$1	222	90	113	16.1920
AUGCUGGUGAAGAAUAGCUGUGU	chr20:30920237-30920459(+)$1	222	48	71	13.5880
UGAAGAUCUUAAUUUUGUUUUUG	chr1:78414182-78414403(-)$1	221	34	57	14.5077
GAAUUUUCCUCAUCUUGAAAGAC	chr16:74339813-74340042(+)$1	229	134	157	15.2439
UGAGAUAGCUACAGUUCUAUAGG	chr2:174090624-174090855(+)$1	231	38	61	14.1540
GCUGUUCUUCUUAAUCAGAACUA	chr14:57756019-57756243(+)$1	224	159	182	13.8157
UUUGCUUUCUUUUUCUGGAGCAA	chr1:54232662-54232894(-)$1	232	12	35	16.6369
GCUAGAAGAAGAAUUAUUUUUAG	chr19:34960416-34960642(+)$1	226	71	94	16.1920
AAACAUUUCUUCUCCCAAAUGUC	chr1:113454882-113455107(-)$1	225	127	150	15.0783
ACAGAUUUCCCUACCUAAAUUUA	chr17:45196501-45196728(-)$1	227	64	87	15.0807
CUGCCACCUCAUACAUGGAACAG	chr17:28793494-28793717(+)$1	223	39	62	14.3514
UAAAGGAACAUUUCAUUUCACUU	chr12:79984187-79984419(-)$1	232	94	117	13.8040
CCACUGUCCAUGAAAUGAUGGUA	chr1:231487443-231487671(+)$1	228	20	43	15.0879
guugcagugagccgagauugcac	chr16:46731917-46732137(+)$1	220	45	68	15.3988
AUCAAGCAUGCAUUCCUGUUUCU	chr14:63839682-63839903(-)$1	221	123	146	15.7486
CUUGUUCCAGUGAAAAGGAGGAG	chr12:27955186-27955410(+)$1	224	15	38	15.2892
UUCUAUAUAUUAAUAAAUAUUAU	chr2:145142483-145142710(-)$1	227	104	127	14.7515
AAGACCAGUAUGAUUUCUGGUUG	chr14:51722630-51722863(+)$1	233	136	159	14.9009

#DB
((((.(((........))).)))	chr5:151184133-151184367(+)$1	1	137	160	14.9874
((((..((........))..)))	chr7:133975458-133975675(-)$1	1	184	207	15.2085
.(((((((........)))))))	chr20:33128630-33128857(+)$1	1	96	119	15.1422
..((((((........)))))).	chr14:64484271-64484500(+)$1	1	55	78	15.2649
(..(((((........))))).)	chr3:15112127-15112351(-)$1	1	50	73	15.5245
.(((((((........)))))))	chr7:44866710-44866938(-)$1	1	188	211	15.5567
((((((((........))))...	chr14:60762460-60762682(+)$1	1	146	169	13.8164
(((((.((........))..)))	chr10:62553745-62553983(+)$1	1	121	144	14.3679
.(((.(((........))).)))	chr11:125525279-125525506(+)$1	1	160	183	15.9885
((((.(((........))).)))	chr2:204296700-204296933(+)$1	1	132	155	14.9874
.(((((((........)))))))	chr8:29964727-29964961(+)$1	1	55	78	15.5567
(.((((((........)))))).	chr7:94296687-94296908(+)$1	1	108	131	15.0037
(((.((((........)))).))	chrX:103437160-103437382(+)$1	1	61	84	14.9303
(((..(((........)))..))	chr1:225590186-225590408(-)$1	1	16	39	15.1617
...(((((........)))))..	chr1:193060686-193060915(+)$1	1	108	131	15.7858
((((((((........)))))))	chr7:70256365-70256594(+)$1	1	159	182	16.1920
((..((((........)))).))	chr2:174089695-174089935(+)$1	1	55	78	15.3642
.(((((((........)))))))	chr2:136664412-136664648(-)$1	1	160	183	16.0996
))((((((........)))))).	chr8:17078107-17078333(+)$1	1	90	113	13.5408
((((((((........))))).)	chr5:79774324-79774549(+)$1	1	3	26	14.9176
((((((((........)))))))	chr19:22849525-22849756(+)$1	1	26	49	16.1920
(((...((........))...))	chr5:167975555-167975776(-)$1	1	123	146	14.7805
..(((.((........)).))).	chr12:92537443-92537677(-)$1	1	76	99	15.0845
((((((((........)))))))	chr15:83515421-83515648(-)$1	1	140	163	16.1920
..((((((........)))))).	chr16:50833419-50833643(+)$1	1	149	172	14.9987
.(((((((........))..)))	chr5:83238201-83238432(-)$1	1	182	205	13.7910
((((((((........)))))))	chr2:128059488-128059718(-)$1	1	138	161	15.8828
(....(((........)))....	chr2:203429351-203429585(+)$1	1	45	68	15.9731
(((..(((........)))...)	chr1:23634473-23634700(-)$1	1	78	101	16.0386
((((((((........)))))))	chr5:52393810-52394038(-)$1	1	142	165	16.6369
(..(((((........)))))..	chr20:23352239-23352464(+)$1	1	193	216	15.4911
.(((((((........)))))))	chr16:75205294-75205529(+)$1	1	23	46	15.1422
)))(((((........))))).(	chr4:39123342-39123565(+)$1	1	143	166	13.9154
(((((..(........)..))))	chr1:65696571-65696798(+)$1	1	139	162	14.3758
((((((((........)))))))	chr4:6884442-6884665(+)$1	1	121	144	16.1920
(((..(((........)))...)	chr1:111489930-111490162(-)$1	1	0	23	16.3579
(...((((........))))...	chr12:1895303-1895530(+)$1	1	157	180	15.3663
((((.(((........))).)))	chr1:150447060-150447286(+)$1	1	36	59	16.3101
((((((((........)))))))	chr1:78030684-78030909(-)$1	1	186	209	16.1920
..((((((........)))))).	chr1:162495024-162495245(+)$1	1	186	209	13.3084
((.(((((........)))))..	chr9:19375828-19376050(-)$1	1	110	133	15.0197
(((..(((........)))..))	chr3:57545794-57546017(+)$1	1	29	52	15.3519
(((..(((........)))..))	chr3:65340720-65340951(-)$1	1	193	216	16.0569
(((((.((........))..)))	chr15:50792174-50792397(+)$1	1	42	65	15.1157
.(((..((........)))))).	chr5:171289472-171289706(-)$1	1	136	159	15.0870
...(((((........)))))))	chr14:81940805-81941046(-)$1	1	199	222	15.8840
.(((.(((........))).)))	chr18:56997389-56997616(-)$1	1	154	177	15.0311
((((((((........)))))))	chr1:75231837-75232059(+)$1	1	90	113	16.1920
((((((((........)))).))	chr20:30920237-30920459(+)$1	1	48	71	13.5880
(.((((.(........).)))).	chr1:78414182-78414403(-)$1	1	34	57	14.5077
....((((........)))))))	chr16:74339813-74340042(+)$1	1	134	157	15.2439
.)))((((........))))(((	chr2:174090624-174090855(+)$1	1	38	61	14.1540
...(((((........)))))..	chr14:57756019-57756243(+)$1	1	159	182	13.8157
((((((((........)))))))	chr1:54232662-54232894(-)$1	1	12	35	16.6369
((((((((........)))))))	chr19:34960416-34960642(+)$1	1	71	94	16.1920
((((((((........)))))).	chr1:113454882-113455107(-)$1	1	127	150	15.0783
((((((((........)))))..	chr17:45196501-45196728(-)$1	1	64	87	15.0807
(((...((........))..)))	chr17:28793494-28793717(+)$1	1	39	62	14.3514
..((((((........))).)))	chr12:79984187-79984419(-)$1	1	94	117	13.8040
(.((((((........)))))).	chr1:231487443-231487671(+)$1	1	20	43	15.0879
((.(((((........)))))))	chr16:46731917-46732137(+)$1	1	45	68	15.3988
((.(((((........)))))..	chr14:63839682-63839903(-)$1	1	123	146	15.7486
(((..(((........))).)))	chr12:27955186-27955410(+)$1	1	15	38	15.2892
(...((((........)))).))	chr2:145142483-145142710(-)$1	1	104	127	14.7515
..((((((........)))))))	chr14:51722630-51722863(+)$1	1	136	159	14.9009

#PSSM
d : 0.12	e : 0.12	c : 0.12	i : 0.12	g : 0.07	: : 0.06	% : 0.06	= : 0.06	" : 0.06	[ : 0.04	f : 0.04	# : 0.03	! : 0.01	( : 0.01	b : 0.01	l : 0.01	
g : 0.15	c : 0.15	i : 0.12	e : 0.10	" : 0.09	d : 0.07	= : 0.06	! : 0.04	[ : 0.04	f : 0.04	# : 0.04	% : 0.03	: : 0.01	
g : 0.15	f : 0.15	c : 0.13	i : 0.10	d : 0.09	e : 0.09	" : 0.06	! : 0.04	= : 0.04	[ : 0.04	# : 0.03	b : 0.01	% : 0.01	
e : 0.21	g : 0.13	f : 0.12	! : 0.10	i : 0.10	c : 0.09	" : 0.06	d : 0.04	= : 0.04	# : 0.03	[ : 0.01	b : 0.01	
e : 0.21	d : 0.13	! : 0.12	f : 0.12	g : 0.10	i : 0.10	[ : 0.07	" : 0.03	c : 0.03	= : 0.03	# : 0.01	
c : 0.20	e : 0.18	d : 0.13	f : 0.12	i : 0.10	g : 0.09	! : 0.04	[ : 0.04	" : 0.03	= : 0.03	
c : 0.20	e : 0.16	b : 0.12	f : 0.12	d : 0.12	i : 0.10	g : 0.09	= : 0.03	! : 0.01	[ : 0.01	
c : 0.20	e : 0.16	b : 0.12	f : 0.12	d : 0.12	i : 0.10	g : 0.09	= : 0.03	a : 0.03	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.20	e : 0.16	b : 0.12	f : 0.12	d : 0.12	i : 0.10	g : 0.09	= : 0.03	a : 0.03	
c : 0.20	e : 0.16	b : 0.12	f : 0.12	d : 0.12	i : 0.10	g : 0.09	= : 0.03	2 : 0.01	] : 0.01	
c : 0.21	e : 0.16	d : 0.13	f : 0.12	i : 0.10	2 : 0.09	g : 0.09	= : 0.03	3 : 0.01	] : 0.01	
e : 0.18	d : 0.13	2 : 0.12	f : 0.12	] : 0.10	i : 0.10	g : 0.09	3 : 0.04	c : 0.03	= : 0.03	4 : 0.01	
e : 0.24	g : 0.13	f : 0.12	i : 0.12	c : 0.07	d : 0.06	] : 0.06	3 : 0.06	2 : 0.04	= : 0.03	6 : 0.01	4 : 0.01	
g : 0.15	f : 0.13	i : 0.13	d : 0.09	e : 0.09	c : 0.09	4 : 0.06	3 : 0.06	= : 0.04	] : 0.03	2 : 0.03	6 : 0.01	: : 0.01	a : 0.01	b : 0.01	
g : 0.16	i : 0.13	e : 0.12	d : 0.09	] : 0.09	c : 0.09	4 : 0.07	2 : 0.04	= : 0.04	f : 0.03	3 : 0.03	6 : 0.01	: : 0.01	7 : 0.01	b : 0.01	

#score	988.9893547313177
#seq	65
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_CDS_m3_run1.txt

#BEAR
fffffqqqqqqqqffffff	chr12:133683094-133683326(+)$1	232	191	210	14.0746
eeeeeqqqqqqqqeeeee2	chrX:47102773-47103015(+)$1	242	90	109	15.1564
eeeeeqqqqqqqqeeeee2	chr2:63215030-63215252(+)$1	222	97	116	15.1564
eeeeeqqqqqqqqeeeee]	chr5:37000991-37001215(+)$1	224	109	128	15.2628
gggggqqqqqqqqgggggg	chr3:196650271-196650496(+)$1	225	100	119	13.9149
cc[bbqqqqqqqqbbccc:	chr13:23908794-23909014(-)$1	220	95	114	12.1268
fffffqqqqqqqqffffff	chr22:32111595-32111817(-)$1	222	9	28	14.0746
dddddqqqqqqqqdddd]d	chr14:32624013-32624247(+)$1	234	125	144	12.7251
eeeerrrrrrrrreeeee2	chr21:34929413-34929647(+)$1	234	107	126	8.7344
eeeeeqqqqqqqqeeeee:	chr5:36975970-36976200(+)$1	230	135	154	14.4910
[a[bbqqqqqqqqbb]a]c	chr17:26680654-26680875(-)$1	221	121	140	12.7015
eeeeeqqqqqqqqeeeee:	chr4:16164980-16165200(-)$1	220	106	125	14.4910
eeeeeqqqqqqqqeeeee:	chr21:30698964-30699191(+)$1	227	120	139	14.4910
eeeeeqqqqqqqqeeeeeD	chr17:27024824-27025053(+)$1	229	195	214	14.1156
eeeeeqqqqqqqqeeeeec	chr4:140438951-140439175(-)$1	224	24	43	15.0806
eeeeeqqqqqqqqeeeee:	chr15:91347400-91347631(+)$1	231	6	25	14.4910
##cccqqqqqqqqccc444	chr13:49772130-49772357(+)$1	227	42	61	13.5622
ddcccqqqqqqqqccc333	chr2:86360370-86360595(+)$1	225	170	189	13.8525
eeeeeqqqqqqqqeeeee4	chr19:44739207-44739438(+)$1	231	146	165	15.1872
ff[bbqqqqqqqqbbffff	chr16:58592323-58592549(-)$1	226	151	170	13.0960
fffffqqqqqqqqffffff	chr3:169504343-169504565(+)$1	222	196	215	14.0746
eee[aqqqqqqqqa]eeee	chr2:44547467-44547690(-)$1	223	181	200	14.4841
c[cccqqqqqqqqccc333	chr12:53776940-53777209(+)$1	269	60	79	14.0561
eeeerrrrrrrrreeeeed	chr6:160199675-160199904(-)$1	229	24	43	8.4863
fffffqqqqqqqqffffff	chr7:27832685-27832923(+)$1	238	147	166	14.0746
eeeeeqqqqqqqqeeeee:	chr5:31484923-31485147(-)$1	224	0	19	14.4910
fffffqqqqqqqqffffff	chr10:5768778-5769014(+)$1	236	22	41	14.0746
!!cccqqqqqqqqccc22b	chr12:123813261-123813481(-)$1	220	13	32	13.2529
fffffqqqqqqqqffffff	chr2:198324589-198324816(+)$1	227	33	52	14.0746
eeeeeqqqqqqqqeeeee:	chr2:61719089-61719310(-)$1	221	193	212	14.4910
!!cccqqqqqqqqccc22e	chr2:198256919-198257144(-)$1	225	72	91	13.2676
gggggqqqqqqqqgggggg	chr19:44418937-44419172(-)$1	235	15	34	13.9149
ccc[aqqqqqqqqa]ccc4	chr3:107799056-107799274(-)$1	218	173	192	13.6484
##cccqqqqqqqqccc]ii	chr17:47119512-47119732(+)$1	220	116	135	13.4863
:ddddqqqqqqqqddddcc	chr19:21299741-21299968(+)$1	227	28	47	11.8628
fff[aqqqqqqqqa]ffff	chr4:77979635-77979860(-)$1	225	204	223	13.9746
gggggqqqqqqqqgggggg	chr13:73334597-73334823(-)$1	226	56	75	13.9149
eeeeeqqqqqqqqeeeee:	chr1:16174481-16174705(+)$1	224	201	220	14.4910
fffffqqqqqqqqffffff	chr19:35741225-35741451(+)$1	226	180	199	14.0746
fff[aqqqqqqqqa]ffff	chr20:52198613-52198836(-)$1	223	84	103	13.9746
cc[bbqqqqqqqqbbccc]	chr21:40587062-40587284(-)$1	222	151	170	12.8986
fffffqqqqqqqqffffff	chr1:109338865-109339086(+)$1	221	182	201	14.0746
ddd[aqqqqqqqqa]dddd	chr9:124522499-124522723(+)$1	224	187	206	12.9596
gggggqqqqqqqqgggggg	chrX:71425807-71426038(-)$1	231	79	98	13.9149
##cccqqqqqqqqcccbb]	chr1:226549571-226549791(-)$1	220	162	181	13.0558
eeeeeqqqqqqqqeeeee2	chr5:32406854-32407076(-)$1	222	148	167	15.1564
eeeeeqqqqqqqqeeeee2	chr22:46712167-46712399(+)$1	232	72	91	15.1564
eeeeeqqqqqqqqeeeee:	chr8:12943847-12944072(-)$1	225	194	213	14.4910
fffffqqqqqqqqffffff	chrX:24006430-24006668(-)$1	238	136	155	14.0746
eeeeeqqqqqqqqeeeee4	chrX:40993920-40994155(+)$1	235	172	191	15.1872
"""bbqqqqqqqqbb333f	chr13:42876069-42876301(+)$1	232	185	204	12.4895
fffffqqqqqqqqffffff	chr17:65971872-65972115(+)$1	243	109	128	14.0746
eeeeeqqqqqqqqeeeee:	chr13:110435081-110435307(-)$1	226	155	174	14.4910
iiiiiqqqqqqqqiiiiii	chr1:182827625-182827848(+)$1	223	201	220	13.5115
b[cccqqqqqqqqccc]bb	chr5:79285890-79286123(-)$1	233	182	201	13.0180
eeeeeqqqqqqqqeeeee2	chr2:191760295-191760517(+)$1	222	145	164	15.1564
dddddqqqqqqqqdddd22	chr1:16255779-16256028(+)$1	249	118	137	12.7717

#otherMatches

#Seq PSSM
AAGUAUAAUGCCUUACUUC	chr12:133683094-133683326(+)$1	232	191	210	14.0746
GCGGGAGCGCACCCCUGCC	chrX:47102773-47103015(+)$1	242	90	109	15.1564
GGUGGAGAUGAACUUACUA	chr2:63215030-63215252(+)$1	222	97	116	15.1564
CUCUUCAACUUUUAAGAGA	chr5:37000991-37001215(+)$1	224	109	128	15.2628
AUUAUUUCAUUUUAUGAUU	chr3:196650271-196650496(+)$1	225	100	119	13.9149
GGAUGAAUUACAACACCUU	chr13:23908794-23909014(-)$1	220	95	114	12.1268
CAUUUAAACAAAGAGAUGC	chr22:32111595-32111817(-)$1	222	9	28	14.0746
UCUUGGUAUUAUAUGAGUA	chr14:32624013-32624247(+)$1	234	125	144	12.7251
GGUGUCCCUUUACCACCAA	chr21:34929413-34929647(+)$1	234	107	126	8.7344
GGUCUUCAGACAUGGACCA	chr5:36975970-36976200(+)$1	230	135	154	14.4910
GGUGCUGAUUGAUGCUCGU	chr17:26680654-26680875(-)$1	221	121	140	12.7015
UCAUACCAUUACUUGUGAC	chr4:16164980-16165200(-)$1	220	106	125	14.4910
UCCAUAGACCCUCAUGGAC	chr21:30698964-30699191(+)$1	227	120	139	14.4910
CUGGGAUACCAGCCCCGGG	chr17:27024824-27025053(+)$1	229	195	214	14.1156
GAUGAAGAAACGGUCAUUG	chr4:140438951-140439175(-)$1	224	24	43	15.0806
UGGAAACAGAAAAUUCCAG	chr15:91347400-91347631(+)$1	231	6	25	14.4910
CACCAUCAGUUCCUGGCAU	chr13:49772130-49772357(+)$1	227	42	61	13.5622
AUUCCUAAAAUUUGGAAAG	chr2:86360370-86360595(+)$1	225	170	189	13.8525
GGGCUUCAGUUAUAGCCCA	chr19:44739207-44739438(+)$1	231	146	165	15.1872
GGACUUUCAUCACAGCUUC	chr16:58592323-58592549(-)$1	226	151	170	13.0960
UAAAUUCCCAUUCAUUUGA	chr3:169504343-169504565(+)$1	222	196	215	14.0746
GAACCACGAUAAAGAUUCU	chr2:44547467-44547690(-)$1	223	181	200	14.4841
ACCUUUACAACUCAAGCCA	chr12:53776940-53777209(+)$1	269	60	79	14.0561
UGUUCAAAGUUUAAGCAAU	chr6:160199675-160199904(-)$1	229	24	43	8.4863
UAAGUAUCAUUAAAUUUAC	chr7:27832685-27832923(+)$1	238	147	166	14.0746
UUGACAAGAACAAGUUGAA	chr5:31484923-31485147(-)$1	224	0	19	14.4910
GGGAUUGCAGAAUAUUCCU	chr10:5768778-5769014(+)$1	236	22	41	14.0746
CUAAAUUCUUUUCUUUUCU	chr12:123813261-123813481(-)$1	220	13	32	13.2529
UCACUCUAAAUCAGGUGAU	chr2:198324589-198324816(+)$1	227	33	52	14.0746
UCUGUAUGUAUCAAUGGAA	chr2:61719089-61719310(-)$1	221	193	212	14.4910
UGAUAAGAACACCUAUAUU	chr2:198256919-198257144(-)$1	225	72	91	13.2676
GAUUCAGUAAUCAGAGUUC	chr19:44418937-44419172(-)$1	235	15	34	13.9149
UGGAGGCACAAAACACUAC	chr3:107799056-107799274(-)$1	218	173	192	13.6484
CCUGAGAGGACCAUCACUG	chr17:47119512-47119732(+)$1	220	116	135	13.4863
AGGUUAUGAACUAAACCAG	chr19:21299741-21299968(+)$1	227	28	47	11.8628
AGUGUUUUAAGAUAGACUU	chr4:77979635-77979860(-)$1	225	204	223	13.9746
AUACAGUGUUCCAUGUAUU	chr13:73334597-73334823(-)$1	226	56	75	13.9149
GGGCGCCGCUUCCCGCCCC	chr1:16174481-16174705(+)$1	224	201	220	14.4910
CAGCUCAAUGCCCAGCUGG	chr19:35741225-35741451(+)$1	226	180	199	14.0746
UGCACGCGGCCGAGAGCAU	chr20:52198613-52198836(-)$1	223	84	103	13.9746
GUGACUGCAUAUUGUGCUA	chr21:40587062-40587284(-)$1	222	151	170	12.8986
UCUUUGAAAACUGAAAGAU	chr1:109338865-109339086(+)$1	221	182	201	14.0746
UGCACAUCCUGCAGAGCAC	chr9:124522499-124522723(+)$1	224	187	206	12.9596
UGAUGAGAUUUUACGUCAU	chrX:71425807-71426038(-)$1	231	79	98	13.9149
UUCUCGAGCUACAGAGUCA	chr1:226549571-226549791(-)$1	220	162	181	13.0558
CACAGAUUCACUAUUGUGA	chr5:32406854-32407076(-)$1	222	148	167	15.1564
UGUCUAAAUUCCAAGACAA	chr22:46712167-46712399(+)$1	232	72	91	15.1564
GUGCUCUUGUCCAGGUAUU	chr8:12943847-12944072(-)$1	225	194	213	14.4910
AAGCAAGUGUGCGUGUUUG	chrX:24006430-24006668(-)$1	238	136	155	14.0746
GAGUCUUGCAUUUGACUUU	chrX:40993920-40994155(+)$1	235	172	191	15.1872
AAGGGAGAAUUAGCCAAAG	chr13:42876069-42876301(+)$1	232	185	204	12.4895
UUACUACAAUCCAAGUGAC	chr17:65971872-65972115(+)$1	243	109	128	14.0746
GCCGCAACCUAUCGCGGCC	chr13:110435081-110435307(-)$1	226	155	174	14.4910
GCAAAUCAUAUUUUUUGUU	chr1:182827625-182827848(+)$1	223	201	220	13.5115
AUCCCUGCAUGUUGGGCuu	chr5:79285890-79286123(-)$1	233	182	201	13.0180
CUUUUUAAAAAGUAAAAGU	chr2:191760295-191760517(+)$1	222	145	164	15.1564
GACAGACUUAAUACUGUUG	chr1:16255779-16256028(+)$1	249	118	137	12.7717

#DB
(((((........))))))	chr12:133683094-133683326(+)$1	1	191	210	14.0746
(((((........))))).	chrX:47102773-47103015(+)$1	1	90	109	15.1564
(((((........))))).	chr2:63215030-63215252(+)$1	1	97	116	15.1564
(((((........))))).	chr5:37000991-37001215(+)$1	1	109	128	15.2628
(((((........))))))	chr3:196650271-196650496(+)$1	1	100	119	13.9149
((.((........))))).	chr13:23908794-23909014(-)$1	1	95	114	12.1268
(((((........))))))	chr22:32111595-32111817(-)$1	1	9	28	14.0746
(((((........)))).)	chr14:32624013-32624247(+)$1	1	125	144	12.7251
((((.........))))).	chr21:34929413-34929647(+)$1	1	107	126	8.7344
(((((........))))).	chr5:36975970-36976200(+)$1	1	135	154	14.4910
.(.((........)).).)	chr17:26680654-26680875(-)$1	1	121	140	12.7015
(((((........))))).	chr4:16164980-16165200(-)$1	1	106	125	14.4910
(((((........))))).	chr21:30698964-30699191(+)$1	1	120	139	14.4910
(((((........))))))	chr17:27024824-27025053(+)$1	1	195	214	14.1156
(((((........)))))(	chr4:140438951-140439175(-)$1	1	24	43	15.0806
(((((........))))).	chr15:91347400-91347631(+)$1	1	6	25	14.4910
..(((........)))...	chr13:49772130-49772357(+)$1	1	42	61	13.5622
(((((........)))...	chr2:86360370-86360595(+)$1	1	170	189	13.8525
(((((........))))).	chr19:44739207-44739438(+)$1	1	146	165	15.1872
((.((........))))))	chr16:58592323-58592549(-)$1	1	151	170	13.0960
(((((........))))))	chr3:169504343-169504565(+)$1	1	196	215	14.0746
(((.(........).))))	chr2:44547467-44547690(-)$1	1	181	200	14.4841
(.(((........)))...	chr12:53776940-53777209(+)$1	1	60	79	14.0561
((((.........))))))	chr6:160199675-160199904(-)$1	1	24	43	8.4863
(((((........))))))	chr7:27832685-27832923(+)$1	1	147	166	14.0746
(((((........))))).	chr5:31484923-31485147(-)$1	1	0	19	14.4910
(((((........))))))	chr10:5768778-5769014(+)$1	1	22	41	14.0746
..(((........)))..)	chr12:123813261-123813481(-)$1	1	13	32	13.2529
(((((........))))))	chr2:198324589-198324816(+)$1	1	33	52	14.0746
(((((........))))).	chr2:61719089-61719310(-)$1	1	193	212	14.4910
..(((........)))..)	chr2:198256919-198257144(-)$1	1	72	91	13.2676
(((((........))))))	chr19:44418937-44419172(-)$1	1	15	34	13.9149
(((.(........).))).	chr3:107799056-107799274(-)$1	1	173	192	13.6484
..(((........))).))	chr17:47119512-47119732(+)$1	1	116	135	13.4863
.((((........))))((	chr19:21299741-21299968(+)$1	1	28	47	11.8628
(((.(........).))))	chr4:77979635-77979860(-)$1	1	204	223	13.9746
(((((........))))))	chr13:73334597-73334823(-)$1	1	56	75	13.9149
(((((........))))).	chr1:16174481-16174705(+)$1	1	201	220	14.4910
(((((........))))))	chr19:35741225-35741451(+)$1	1	180	199	14.0746
(((.(........).))))	chr20:52198613-52198836(-)$1	1	84	103	13.9746
((.((........))))).	chr21:40587062-40587284(-)$1	1	151	170	12.8986
(((((........))))))	chr1:109338865-109339086(+)$1	1	182	201	14.0746
(((.(........).))))	chr9:124522499-124522723(+)$1	1	187	206	12.9596
(((((........))))))	chrX:71425807-71426038(-)$1	1	79	98	13.9149
..(((........))))).	chr1:226549571-226549791(-)$1	1	162	181	13.0558
(((((........))))).	chr5:32406854-32407076(-)$1	1	148	167	15.1564
(((((........))))).	chr22:46712167-46712399(+)$1	1	72	91	15.1564
(((((........))))).	chr8:12943847-12944072(-)$1	1	194	213	14.4910
(((((........))))))	chrX:24006430-24006668(-)$1	1	136	155	14.0746
(((((........))))).	chrX:40993920-40994155(+)$1	1	172	191	15.1872
...((........))...)	chr13:42876069-42876301(+)$1	1	185	204	12.4895
(((((........))))))	chr17:65971872-65972115(+)$1	1	109	128	14.0746
(((((........))))).	chr13:110435081-110435307(-)$1	1	155	174	14.4910
(((((........))))))	chr1:182827625-182827848(+)$1	1	201	220	13.5115
(.(((........))).))	chr5:79285890-79286123(-)$1	1	182	201	13.0180
(((((........))))).	chr2:191760295-191760517(+)$1	1	145	164	15.1564
(((((........))))..	chr1:16255779-16256028(+)$1	1	118	137	12.7717

#PSSM
e : 0.38	f : 0.22	g : 0.07	c : 0.07	d : 0.07	# : 0.05	! : 0.03	[ : 0.01	: : 0.01	" : 0.01	i : 0.01	b : 0.01	
e : 0.38	f : 0.22	d : 0.08	g : 0.07	c : 0.05	# : 0.05	[ : 0.03	! : 0.03	a : 0.01	" : 0.01	i : 0.01	
e : 0.38	f : 0.21	c : 0.15	g : 0.07	[ : 0.07	d : 0.07	" : 0.01	i : 0.01	
e : 0.36	f : 0.17	c : 0.14	b : 0.08	[ : 0.08	g : 0.07	d : 0.05	i : 0.01	
e : 0.33	f : 0.17	c : 0.14	b : 0.08	a : 0.08	g : 0.07	d : 0.05	r : 0.03	i : 0.01	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
e : 0.36	f : 0.17	c : 0.14	b : 0.08	a : 0.08	g : 0.07	d : 0.05	i : 0.01	
e : 0.36	f : 0.17	c : 0.14	b : 0.08	] : 0.08	g : 0.07	d : 0.05	i : 0.01	
e : 0.38	f : 0.22	c : 0.19	g : 0.07	d : 0.07	] : 0.01	3 : 0.01	i : 0.01	
e : 0.38	f : 0.22	g : 0.07	d : 0.07	c : 0.05	3 : 0.05	2 : 0.03	] : 0.03	a : 0.01	4 : 0.01	b : 0.01	i : 0.01	
e : 0.38	f : 0.22	g : 0.07	c : 0.07	3 : 0.05	2 : 0.05	] : 0.03	i : 0.03	b : 0.03	4 : 0.01	d : 0.01	
f : 0.24	: : 0.17	2 : 0.12	g : 0.07	4 : 0.07	] : 0.05	d : 0.05	c : 0.05	3 : 0.03	e : 0.03	b : 0.03	i : 0.03	D : 0.01	

#score	785.4396418610991
#seq	57
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_UTR_m2_run1.txt

#BEAR
fffvvvvvvvvvvvvvfffffff	chr3:132387609-132387831(+)$1	222	15	38	21.6150
[dddduuuuuuuuuuuudddd]c	chr21:30716185-30716438(+)$1	253	150	173	22.2388
eeeeevvvvvvvvvvvvveeeee	chr7:128142285-128142513(+)$1	228	98	121	23.0751
eeeeevvvvvvvvvvvvveeeee	chrX:17772103-17772339(+)$1	236	90	113	23.0751
iiiiitttttttttttiiiiiii	chrX:123236132-123236353(+)$1	221	60	83	23.0250
h[ccctttttttttttccc333h	chr19:32875775-32875998(+)$1	223	69	92	22.9042
f[ccctttttttttttccc]fff	chr12:104378491-104378721(+)$1	230	101	124	23.0273
gggggvvvvvvvvvvvvvggggg	chr2:74382888-74383113(-)$1	225	192	215	23.5221
ffffftttttttttttffffff:	chr10:96361359-96361585(+)$1	226	31	54	21.7777
[ddddtttttttttttdddd22d	chr13:31710773-31711008(-)$1	235	129	152	21.6221
hhhhhwwwwwwwwwwwwwwhhhh	chr3:155660381-155660623(+)$1	242	60	83	20.0626
eeeeevvvvvvvvvvvvveeeee	chr8:37716636-37716882(-)$1	246	140	163	23.0751
fffbbwwwwwwwwwwwwwwbb]f	chr3:160152161-160152386(+)$1	225	105	128	20.0547
gggggwwwwwwwwwwwwwwgggg	chr1:229458035-229458256(-)$1	221	128	151	21.7231
fffffuuuuuuuuuuuuffffff	chr1:150237713-150237931(-)$1	218	100	123	22.6668
eeeeevvvvvvvvvvvvveeeee	chr18:33572091-33572329(-)$1	238	144	167	23.0751
cccvvvvvvvvvvvvvccc22gg	chr5:149364982-149365207(+)$1	225	167	190	21.8388
ddddvvvvvvvvvvvvvdddd33	chr9:91091201-91091435(+)$1	234	167	190	22.0656
iiiiitttttttttttiiiiiii	chr4:47849301-47849526(-)$1	225	191	214	23.0250
[dddduuuuuuuuuuuuddddgg	chr7:131179295-131179528(+)$1	233	44	67	22.3144
ggggguuuuuuuuuuuugggggg	chrX:123511822-123512058(-)$1	236	141	164	23.4105
eeeeettttttttttteeeeeCC	chr6:105528862-105529098(+)$1	236	24	47	20.3148
eeeeyyyyyyyyyyyyyyyyeee	chr10:75557562-75557793(+)$1	231	36	59	19.3656
gggggtttttttttttggggggg	chr2:203633705-203633933(+)$1	228	191	214	23.2328
ffffftttttttttttffffff6	chr18:33755922-33756153(+)$1	231	165	188	22.2466
!cccuuuuuuuuuuuuccc22bb	chrX:131339303-131339528(-)$1	225	127	150	21.6699
eeeeewwwwwwwwwwwwwweeee	chr4:139089958-139090180(-)$1	222	21	44	21.3152
cddddtttttttttttdddd333	chr2:87004270-87004504(+)$1	234	62	85	22.1170
!cccuuuuuuuuuuuuccc22cc	chr3:188605930-188606164(+)$1	234	28	51	22.0957
cccwwwwwwwwwwwwwwccc]bb	chr1:210024995-210025220(+)$1	225	57	80	20.6269
gggggtttttttttttggggggg	chr7:28863740-28863967(+)$1	227	125	148	23.2328
eeeeeuuuuuuuuuuuueeeeed	chr11:119175214-119175448(+)$1	234	121	144	22.8014
hhhhvvvvvvvvvvvvvhhhhhh	chr1:109178143-109178369(+)$1	226	121	144	21.4351
eeeeeuuuuuuuuuuuueeeee2	chr1:38268637-38268906(-)$1	269	199	222	22.8024
ffffftttttttttttffffff:	chr7:99128843-99129085(+)$1	242	151	174	21.7777
=====uuuuuuuuuuuu======	chr12:120899732-120899958(-)$1	226	52	75	23.3639
iiiivvvvvvvvvvvvviiiiii	chr5:32601494-32601716(+)$1	222	97	120	23.2533
"""bbtttttttttttbb333==	chr1:243666320-243666542(-)$1	222	83	106	21.5284
eeeeeuuuuuuuuuuuueeeee:	chr5:145667987-145668215(+)$1	228	155	178	22.1069
fffffuuuuuuuuuuuuffffff	chr13:113919292-113919514(+)$1	222	67	90	22.6668
hhhhhttttttttttthhhhhhh	chr11:27517171-27517417(-)$1	246	218	241	20.8952
ffffftttttttttttffffff:	chr9:21862394-21862617(+)$1	223	79	102	21.7777
gggggtttttttttttggggggg	chr4:174244842-174245066(+)$1	224	129	152	23.2328
ffffwwwwwwwwwwwwwwfffff	chr12:57909719-57909942(+)$1	223	71	94	21.2092
gggggvvvvvvvvvvvvvggggg	chr5:135516196-135516423(+)$1	227	172	195	23.5221
ddddattttttttttta]dddd]	chr1:205683120-205683343(-)$1	223	13	36	22.1898
e[ccctttttttttttccc]eee	chr20:34536197-34536422(+)$1	225	62	85	23.1035
gggggtttttttttttggggggg	chr5:176722480-176722717(+)$1	237	36	59	23.2328
ddwwwwwwwwwwwwwwdddd]a]	chr2:215592079-215592302(-)$1	223	129	152	19.2335
fffffuuuuuuuuuuuuffffff	chr3:196666125-196666347(-)$1	222	153	176	22.6668
ffffftttttttttttffffff]	chr8:81432205-81432431(+)$1	226	9	32	22.7233
=====ttttttttttt=======	chr10:112658014-112658235(+)$1	221	16	39	23.2372
gggggwwwwwwwwwwwwwwgggg	chr4:88059675-88059910(+)$1	235	19	42	21.7231
eeeeettttttttttteeeee]b	chr2:87003825-87004067(+)$1	242	79	102	22.6421
eeeeuuuuuuuuuuuueeeee66	chr21:35472703-35472933(+)$1	230	110	133	21.2214
cccvvvvvvvvvvvvvccc4444	chrX:123046113-123046342(+)$1	229	82	105	21.7684
ffffftttttttttttffffff5	chr4:40817722-40817949(-)$1	227	97	120	21.9333
hhhhhuuuuuuuuuuuuhhhhhh	chr17:39985042-39985291(-)$1	249	70	93	21.2973
eeeeevvvvvvvvvvvvveeeee	chr9:123525789-123526017(-)$1	228	88	111	23.0751
:ddddwwwwwwwwwwwwwwdddd	chr3:178736136-178736372(-)$1	236	115	138	19.1174
$cccuuuuuuuuuuuuccc4444	chr5:36183567-36183800(+)$1	233	23	46	21.7910
hhhbbvvvvvvvvvvvvvbb]hh	chr7:65423096-65423320(+)$1	224	53	76	21.4541
[ddddtttttttttttddddbb8	chr1:229459406-229459635(-)$1	229	80	103	21.1733
=====ttttttttttt=======	chr8:26228038-26228273(+)$1	235	6	29	23.2372
ffffftttttttttttffffff:	chr20:11906699-11906930(+)$1	231	145	168	21.7777
hhhhhwwwwwwwwwwwwwwhhhh	chr11:9429987-9430219(+)$1	232	48	71	20.0626
eeeeewwwwwwwwwwwwwweeee	chr1:224346960-224347195(+)$1	235	91	114	21.3152

#otherMatches

#Seq PSSM
UAUGUUUUUCAUCAGAAUACCAC	chr3:132387609-132387831(+)$1	222	15	38	21.6150
UGGACAUUUAAAGAUCAGUCUUA	chr21:30716185-30716438(+)$1	253	150	173	22.2388
GUAAACCUUAAACCACCAUUUAU	chr7:128142285-128142513(+)$1	228	98	121	23.0751
UGAAGUCUGACUACUUUUUUUCA	chrX:17772103-17772339(+)$1	236	90	113	23.0751
AGCAGUUCUUACAGCUUUGUUUU	chrX:123236132-123236353(+)$1	221	60	83	23.0250
AUUUCAAAUUCAAAUAGAACAUU	chr19:32875775-32875998(+)$1	223	69	92	22.9042
CAUUACUACAUAAAACUGAAGGA	chr12:104378491-104378721(+)$1	230	101	124	23.0273
AAGCUUAAUUCAGAUAGUAGCUU	chr2:74382888-74383113(-)$1	225	192	215	23.5221
AGAAUAGCUUUUAAAAGUUCUUA	chr10:96361359-96361585(+)$1	226	31	54	21.7777
AUACAGUAUAUUGUCAUGUGAAA	chr13:31710773-31711008(-)$1	235	129	152	21.6221
UUGCUAAUUUUGAGAUCUGGGCA	chr3:155660381-155660623(+)$1	242	60	83	20.0626
AAGGCUGAAAAAUUAAUUGCCUU	chr8:37716636-37716882(-)$1	246	140	163	23.0751
uuacaaauuuucaacuuuaugau	chr3:160152161-160152386(+)$1	225	105	128	20.0547
CUUUGUCAUUGUGUUUCAUCGAA	chr1:229458035-229458256(-)$1	221	128	151	21.7231
AUUUUGACUAAUAAAAAAGAAUU	chr1:150237713-150237931(-)$1	218	100	123	22.6668
GAACACAAUAUUCGUUAAUGUUC	chr18:33572091-33572329(-)$1	238	144	167	23.0751
UCUGAAUAUAAAAGUGAGAAAAG	chr5:149364982-149365207(+)$1	225	167	190	21.8388
AGACAAACAGCAGCUUAGUCUCC	chr9:91091201-91091435(+)$1	234	167	190	22.0656
UUGAAUUAUAAUUCCUUUCAAAU	chr4:47849301-47849526(-)$1	225	191	214	23.0250
UGGGAUUUUUUUUCCUUUCCCAG	chr7:131179295-131179528(+)$1	233	44	67	22.3144
GGUUUUAAUACUGCCUUGAACUA	chrX:123511822-123512058(-)$1	236	141	164	23.4105
UCUUACCAGACUAAACUAAGAGC	chr6:105528862-105529098(+)$1	236	24	47	20.3148
AGCUGCACACUUCUACUUCGAGC	chr10:75557562-75557793(+)$1	231	36	59	19.3656
AAAGUCCUUUUUCUUUGCUUUCA	chr2:203633705-203633933(+)$1	228	191	214	23.2328
caguauaaaaaccuguuacugaa	chr18:33755922-33756153(+)$1	231	165	188	22.2466
CCUUUUAUAGCUUUCUAAGUUCU	chrX:131339303-131339528(-)$1	225	127	150	21.6699
UUUUAAAAGAUUCUAAAGCUAAA	chr4:139089958-139090180(-)$1	222	21	44	21.3152
AGCUGGAAUUGGCUUACAGCACA	chr2:87004270-87004504(+)$1	234	62	85	22.1170
UAUCAUUACUCUAACAGAUUUAG	chr3:188605930-188606164(+)$1	234	28	51	22.0957
CACUUGUGAAUAUUUUUGUGAGA	chr1:210024995-210025220(+)$1	225	57	80	20.6269
AGCAUGUUUUUUAAAAAUGUUAU	chr7:28863740-28863967(+)$1	227	125	148	23.2328
CUUAAuuuuuuuuuuuuuugaga	chr11:119175214-119175448(+)$1	234	121	144	22.8014
UACAGCAUUGUAUAAAGUGUGGG	chr1:109178143-109178369(+)$1	226	121	144	21.4351
UGUGUACCAAGUGUUAAACAUAA	chr1:38268637-38268906(-)$1	269	199	222	22.8024
CACAUAAAUGUAACGAGUGUGGG	chr7:99128843-99129085(+)$1	242	151	174	21.7777
GUCUCGGUCUGGGUCAAGGGGCC	chr12:120899732-120899958(-)$1	226	52	75	23.3639
UGAUCUUUUCUCUUCCAAUCAAA	chr5:32601494-32601716(+)$1	222	97	120	23.2533
GUUACAGUAAAUGGUAGUUCAUU	chr1:243666320-243666542(-)$1	222	83	106	21.5284
UGCCAUACAUGUUUUCUUGGCAU	chr5:145667987-145668215(+)$1	228	155	178	22.1069
UUACAUUAAUAAAACUUUGUGAU	chr13:113919292-113919514(+)$1	222	67	90	22.6668
UGUUUGUUAUUUGAGAAAGCAUG	chr11:27517171-27517417(-)$1	246	218	241	20.8952
gcugggaacucuacaucuagcaa	chr9:21862394-21862617(+)$1	223	79	102	21.7777
UGCAGAUUUUGAUACACUGUAUG	chr4:174244842-174245066(+)$1	224	129	152	23.2328
CUGUGCCCUCGCUCCACAACAGC	chr12:57909719-57909942(+)$1	223	71	94	21.2092
UAUAAAUAAUUUUUCACAUUGUA	chr5:135516196-135516423(+)$1	227	172	195	23.5221
ACCCCUGAAGUAUUGUGUGGGUG	chr1:205683120-205683343(-)$1	223	13	36	22.1898
AAACCGAAGCAGGCAGGGUCUGG	chr20:34536197-34536422(+)$1	225	62	85	23.1035
GGAAAUCUUUUCUUUCUUUCCCC	chr5:176722480-176722717(+)$1	237	36	59	23.2328
GAAUAUACUUAUAAAAUUAAAGA	chr2:215592079-215592302(-)$1	223	129	152	19.2335
GUGGUGACAUAAAGAAAAUCAUU	chr3:196666125-196666347(-)$1	222	153	176	22.6668
auuaauuuuauuuuuUUUAAUAC	chr8:81432205-81432431(+)$1	226	9	32	22.7233
UUUUCGAGGGGGCAAGGAGGGAC	chr10:112658014-112658235(+)$1	221	16	39	23.2372
ACACUGUUUUAUUUUUUAAAGUG	chr4:88059675-88059910(+)$1	235	19	42	21.7231
UCACUAGGAUGUAUAAGGUGACG	chr2:87003825-87004067(+)$1	242	79	102	22.6421
UAGGGCUUCCUUUUCACUUGGCU	chr21:35472703-35472933(+)$1	230	110	133	21.2214
UGCAAAAAAAAAAAAAGCAAUUA	chrX:123046113-123046342(+)$1	229	82	105	21.7684
GUGAACAUUACUUAACUUCACAC	chr4:40817722-40817949(-)$1	227	97	120	21.9333
CCUCCAUCUCUUUUCAGGGAGGG	chr17:39985042-39985291(-)$1	249	70	93	21.2973
CCUGAUUCAUGGUUUCUUUCAGG	chr9:123525789-123526017(-)$1	228	88	111	23.0751
ACUAAUUACACUUUUUUUUUUAG	chr3:178736136-178736372(-)$1	236	115	138	19.1174
aaucuccugaccucaugauccgc	chr5:36183567-36183800(+)$1	233	23	46	21.7910
CUUCCAUCAAACAAAAAGGGCAA	chr7:65423096-65423320(+)$1	224	53	76	21.4541
UCAAUUUUUAGAACAUAUUGCUU	chr1:229459406-229459635(-)$1	229	80	103	21.1733
GUGUGCCAUUCGACAACACAUUG	chr8:26228038-26228273(+)$1	235	6	29	23.2372
GAUGCUUUUCCCCAACGUAUCUG	chr20:11906699-11906930(+)$1	231	145	168	21.7777
UUAUCUAUCUGAAAAAUAUGAUA	chr11:9429987-9430219(+)$1	232	48	71	20.0626
AAAUGAAGCUUUUUCUAUCCAUU	chr1:224346960-224347195(+)$1	235	91	114	21.3152

#DB
(((.............))))))(	chr3:132387609-132387831(+)$1	1	15	38	21.6150
.((((............)))).)	chr21:30716185-30716438(+)$1	1	150	173	22.2388
(((((.............)))))	chr7:128142285-128142513(+)$1	1	98	121	23.0751
(((((.............)))))	chrX:17772103-17772339(+)$1	1	90	113	23.0751
(((((...........)))))))	chrX:123236132-123236353(+)$1	1	60	83	23.0250
(.(((...........)))...)	chr19:32875775-32875998(+)$1	1	69	92	22.9042
(.(((...........))).)))	chr12:104378491-104378721(+)$1	1	101	124	23.0273
(((((.............)))))	chr2:74382888-74383113(-)$1	1	192	215	23.5221
(((((...........)))))).	chr10:96361359-96361585(+)$1	1	31	54	21.7777
.((((...........))))..)	chr13:31710773-31711008(-)$1	1	129	152	21.6221
(((((..............))))	chr3:155660381-155660623(+)$1	1	60	83	20.0626
(((((.............)))))	chr8:37716636-37716882(-)$1	1	140	163	23.0751
(((((..............)).)	chr3:160152161-160152386(+)$1	1	105	128	20.0547
(((((..............))))	chr1:229458035-229458256(-)$1	1	128	151	21.7231
(((((............))))))	chr1:150237713-150237931(-)$1	1	100	123	22.6668
(((((.............)))))	chr18:33572091-33572329(-)$1	1	144	167	23.0751
(((.............)))..))	chr5:149364982-149365207(+)$1	1	167	190	21.8388
((((.............))))..	chr9:91091201-91091435(+)$1	1	167	190	22.0656
(((((...........)))))))	chr4:47849301-47849526(-)$1	1	191	214	23.0250
.((((............))))))	chr7:131179295-131179528(+)$1	1	44	67	22.3144
(((((............))))))	chrX:123511822-123512058(-)$1	1	141	164	23.4105
(((((...........)))))))	chr6:105528862-105529098(+)$1	1	24	47	20.3148
((((................)))	chr10:75557562-75557793(+)$1	1	36	59	19.3656
(((((...........)))))))	chr2:203633705-203633933(+)$1	1	191	214	23.2328
(((((...........)))))).	chr18:33755922-33756153(+)$1	1	165	188	22.2466
.(((............)))..))	chrX:131339303-131339528(-)$1	1	127	150	21.6699
(((((..............))))	chr4:139089958-139090180(-)$1	1	21	44	21.3152
(((((...........))))...	chr2:87004270-87004504(+)$1	1	62	85	22.1170
.(((............)))..))	chr3:188605930-188606164(+)$1	1	28	51	22.0957
(((..............))).))	chr1:210024995-210025220(+)$1	1	57	80	20.6269
(((((...........)))))))	chr7:28863740-28863967(+)$1	1	125	148	23.2328
(((((............))))))	chr11:119175214-119175448(+)$1	1	121	144	22.8014
((((.............))))))	chr1:109178143-109178369(+)$1	1	121	144	21.4351
(((((............))))).	chr1:38268637-38268906(-)$1	1	199	222	22.8024
(((((...........)))))).	chr7:99128843-99129085(+)$1	1	151	174	21.7777
(((((............))))))	chr12:120899732-120899958(-)$1	1	52	75	23.3639
((((.............))))))	chr5:32601494-32601716(+)$1	1	97	120	23.2533
...((...........))...))	chr1:243666320-243666542(-)$1	1	83	106	21.5284
(((((............))))).	chr5:145667987-145668215(+)$1	1	155	178	22.1069
(((((............))))))	chr13:113919292-113919514(+)$1	1	67	90	22.6668
(((((...........)))))))	chr11:27517171-27517417(-)$1	1	218	241	20.8952
(((((...........)))))).	chr9:21862394-21862617(+)$1	1	79	102	21.7777
(((((...........)))))))	chr4:174244842-174245066(+)$1	1	129	152	23.2328
((((..............)))))	chr12:57909719-57909942(+)$1	1	71	94	21.2092
(((((.............)))))	chr5:135516196-135516423(+)$1	1	172	195	23.5221
(((((...........).)))).	chr1:205683120-205683343(-)$1	1	13	36	22.1898
(.(((...........))).)))	chr20:34536197-34536422(+)$1	1	62	85	23.1035
(((((...........)))))))	chr5:176722480-176722717(+)$1	1	36	59	23.2328
((..............)))).).	chr2:215592079-215592302(-)$1	1	129	152	19.2335
(((((............))))))	chr3:196666125-196666347(-)$1	1	153	176	22.6668
(((((...........)))))).	chr8:81432205-81432431(+)$1	1	9	32	22.7233
(((((...........)))))))	chr10:112658014-112658235(+)$1	1	16	39	23.2372
(((((..............))))	chr4:88059675-88059910(+)$1	1	19	42	21.7231
(((((...........))))).)	chr2:87003825-87004067(+)$1	1	79	102	22.6421
((((............)))))..	chr21:35472703-35472933(+)$1	1	110	133	21.2214
(((.............)))....	chrX:123046113-123046342(+)$1	1	82	105	21.7684
(((((...........)))))).	chr4:40817722-40817949(-)$1	1	97	120	21.9333
(((((............))))))	chr17:39985042-39985291(-)$1	1	70	93	21.2973
(((((.............)))))	chr9:123525789-123526017(-)$1	1	88	111	23.0751
.((((..............))))	chr3:178736136-178736372(-)$1	1	115	138	19.1174
.(((............)))....	chr5:36183567-36183800(+)$1	1	23	46	21.7910
(((((.............)).))	chr7:65423096-65423320(+)$1	1	53	76	21.4541
.((((...........)))))).	chr1:229459406-229459635(-)$1	1	80	103	21.1733
(((((...........)))))))	chr8:26228038-26228273(+)$1	1	6	29	23.2372
(((((...........)))))).	chr20:11906699-11906930(+)$1	1	145	168	21.7777
(((((..............))))	chr11:9429987-9430219(+)$1	1	48	71	20.0626
(((((..............))))	chr1:224346960-224347195(+)$1	1	91	114	21.3152

#PSSM
e : 0.22	f : 0.20	g : 0.13	h : 0.10	[ : 0.05	c : 0.05	i : 0.04	d : 0.04	= : 0.04	! : 0.02	" : 0.01	: : 0.01	$ : 0.01	
e : 0.20	f : 0.19	d : 0.13	g : 0.13	h : 0.08	c : 0.08	i : 0.04	[ : 0.04	= : 0.04	" : 0.01	
e : 0.20	f : 0.19	c : 0.13	g : 0.13	d : 0.11	h : 0.08	i : 0.04	= : 0.04	" : 0.01	w : 0.01	
e : 0.20	f : 0.16	g : 0.13	d : 0.11	c : 0.08	h : 0.07	v : 0.04	i : 0.04	b : 0.04	= : 0.04	w : 0.02	
e : 0.17	f : 0.14	g : 0.13	v : 0.08	d : 0.08	h : 0.05	u : 0.05	c : 0.04	b : 0.04	w : 0.04	= : 0.04	i : 0.02	y : 0.01	a : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
t : 0.38	u : 0.22	v : 0.20	w : 0.16	y : 0.01	
u : 0.16	v : 0.16	w : 0.14	f : 0.11	c : 0.11	d : 0.05	g : 0.05	e : 0.04	i : 0.02	= : 0.02	y : 0.01	b : 0.01	h : 0.01	a : 0.01	
f : 0.16	c : 0.13	w : 0.13	v : 0.11	d : 0.10	e : 0.08	g : 0.07	i : 0.04	h : 0.04	= : 0.04	y : 0.01	b : 0.01	] : 0.01	
f : 0.17	e : 0.16	c : 0.13	d : 0.11	w : 0.11	g : 0.10	i : 0.04	h : 0.04	= : 0.04	y : 0.01	3 : 0.01	b : 0.01	
e : 0.19	f : 0.17	d : 0.13	g : 0.13	h : 0.07	i : 0.04	2 : 0.04	= : 0.04	3 : 0.02	] : 0.02	b : 0.02	4 : 0.02	y : 0.01	c : 0.01	
e : 0.22	f : 0.19	g : 0.13	d : 0.07	h : 0.07	2 : 0.05	i : 0.04	3 : 0.04	] : 0.04	= : 0.04	b : 0.02	4 : 0.02	
f : 0.19	e : 0.17	g : 0.16	h : 0.08	= : 0.05	] : 0.04	i : 0.04	3 : 0.04	b : 0.04	d : 0.02	4 : 0.02	2 : 0.01	C : 0.01	c : 0.01	a : 0.01	6 : 0.01	
g : 0.16	e : 0.13	f : 0.10	h : 0.10	: : 0.07	= : 0.05	i : 0.04	d : 0.04	b : 0.04	] : 0.04	c : 0.02	3 : 0.02	6 : 0.02	4 : 0.02	C : 0.01	2 : 0.01	5 : 0.01	8 : 0.01	

#score	1477.7634369504992
#seq	67
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_UTR_m2_run1.txt

#BEAR
[gggggggtttttttttttggggg	chr17:65335408-65335731(-)$1	323	193	217	23.3679
ba[dddduuuuuuuuuuuudddd]	chr11:73114979-73115329(-)$1	350	279	303	22.9705
fff[cccuuuuuuuuuuuuccc33	chr6:82456879-82457166(-)$1	287	93	117	23.2469
ffffffyyyyyyyyyyyyyyyyff	chr12:16516806-16517058(+)$1	252	61	85	20.2448
hhhhhhhhuuuuuuuuuuuuhhhh	chrX:53611086-53611382(-)$1	296	22	46	22.0120
hhhhhhhvvvvvvvvvvvvvhhhh	chr18:33290470-33290924(+)$1	454	392	416	21.6913
ggggg[bbvvvvvvvvvvvvvbb]	chr15:85348520-85348879(+)$1	359	229	253	21.8842
=="""cccuuuuuuuuuuuuccc5	chr18:47309871-47310251(-)$1	380	221	245	23.0018
###eeeeettttttttttteeeee	chr5:78622661-78622927(+)$1	266	212	236	22.7672
"ffffffuuuuuuuuuuuufffff	chr7:135611406-135611876(-)$1	470	151	175	21.3497
[a[eeeeeuuuuuuuuuuuueeee	chr2:175939244-175939651(-)$1	407	127	151	23.2220
dddd[bbwwwwwwwwwwwwwwbb]	chr15:83807049-83807475(-)$1	426	115	139	20.1158
hhhhhhhhttttttttttthhhhh	chr6:100836344-100836623(-)$1	279	73	97	21.7063
hhhhhhhyyyyyyyyyyyyyyyyh	chr1:114308594-114308854(-)$1	260	66	90	20.5519
=======yyyyyyyyyyyyyyyy=	chr12:27182420-27182715(+)$1	295	121	145	21.4667
fff[cccuuuuuuuuuuuucccff	chr5:110835496-110835817(-)$1	321	184	208	22.9152
eeeee[bbuuuuuuuuuuuubb]e	chr1:107601218-107601564(+)$1	346	104	128	22.1251
ccc!!cccuuuuuuuuuuuuccc]	chr2:30381611-30381921(+)$1	310	174	198	24.2153
dd!!cccvvvvvvvvvvvvvccc2	chr19:47113651-47114138(+)$1	487	333	357	23.2420
ccc[ccctttttttttttcccccc	chr22:42302439-42302858(+)$1	419	0	24	22.0873
[a!!dddduuuuuuuuuuuudddd	chr5:150070954-150071265(-)$1	311	99	123	23.9581
iii:ddddtttttttttttdddd:	chr22:42334672-42334969(-)$1	297	267	291	21.6081
!a!!ddddtttttttttttdddd2	chr2:64859676-64859955(-)$1	279	131	155	23.9633
ccc!!ccctttttttttttccc22	chr7:134653400-134653663(+)$1	263	5	29	23.8112
ffffdddduuuuuuuuuuuudddd	chr17:7490643-7490939(+)$1	296	234	258	23.0006
hhhhhhhhttttttttttthhhhh	chr2:9725032-9725431(-)$1	399	253	277	21.7063
eeeee[bbuuuuuuuuuuuubb]e	chr1:111983146-111983500(-)$1	354	185	209	22.1251
%dddd[bbtttttttttttbb]dd	chr3:167401992-167402275(-)$1	283	154	178	21.2212
eee:dddduuuuuuuuuuuudddd	chr1:218507791-218508155(+)$1	364	276	300	22.0830
ffffffwwwwwwwwwwwwwwffff	chr1:193220208-193220456(+)$1	248	50	74	20.1010
gggggggvvvvvvvvvvvvvgggg	chr6:52366955-52367262(-)$1	307	252	276	23.0260
:gggggggtttttttttttggggg	chrX:133904222-133904657(-)$1	435	6	30	22.3194
[bb[cccvvvvvvvvvvvvvccc]	chr2:97259347-97259640(-)$1	293	205	229	23.1115
b[a[ddddtttttttttttdddd]	chr19:50191322-50191604(+)$1	282	5	29	23.7388
ggggggguuuuuuuuuuuuggggg	chr10:127524698-127524970(+)$1	272	137	161	22.9508
ee[dddduuuuuuuuuuuudddd]	chr8:74705111-74705361(-)$1	250	31	55	23.0060
:gggggggtttttttttttggggg	chr3:148749527-148749876(-)$1	349	193	217	22.3194
eeeee[bbtttttttttttbbeee	chr3:124948567-124948895(-)$1	328	261	285	22.0873
iiiiiiiiuuuuuuuuuuuuiiii	chr10:105785591-105786056(+)$1	465	22	46	23.5345
eeeeewwwwwwwwwwwwwweeeee	chr19:54697144-54697427(+)$1	283	202	226	19.6675
ccc[ddddtttttttttttddddc	chr2:172821852-172822139(+)$1	287	251	275	23.7139
F:eeeeeuuuuuuuuuuuueeeee	chr2:204293881-204294203(+)$1	322	29	53	20.8052
:gggggggtttttttttttggggg	chr1:25687071-25687474(+)$1	403	90	114	22.3194
:gggggggtttttttttttggggg	chr3:23632017-23632297(+)$1	280	114	138	22.3194
dddd[ccctttttttttttccc33	chr4:52729502-52729773(+)$1	271	104	128	23.1281
$$$$$ccctttttttttttccc44	chr15:72533426-72533736(-)$1	310	51	75	22.4181
e"""ddddtttttttttttdddd2	chr10:89512405-89512761(-)$1	356	315	339	23.5202
c!!eeeeeuuuuuuuuuuuueeee	chr4:52888154-52888434(-)$1	280	80	104	23.2618
ccc[dddduuuuuuuuuuuudddd	chrX:119390109-119390372(+)$1	263	144	168	23.7651
####dddduuuuuuuuuuuudddd	chr1:114448079-114448497(+)$1	418	295	319	23.4300
ccc[ddddtttttttttttdddd]	chr20:37581186-37581525(+)$1	339	95	119	23.9591
h"""ddddwwwwwwwwwwwwwwdd	chr10:32557188-32557465(-)$1	277	35	59	21.1335
iiieeeeeyyyyyyyyyyyyyyyy	chr10:73995332-73995617(+)$1	285	103	127	20.5379
fff[cccvvvvvvvvvvvvvccc]	chr1:225674518-225674799(-)$1	281	239	263	23.2792
f[a!!ccctttttttttttccc22	chrX:119391437-119391832(+)$1	395	323	347	23.7120
cc!!cccvvvvvvvvvvvvvccc2	chr10:16554374-16554753(+)$1	379	330	354	23.6211
hhh[cccwwwwwwwwwwwwwwccc	chr7:90017451-90017871(+)$1	420	171	195	21.7748
cc!!dddduuuuuuuuuuuudddd	chr12:50871266-50871542(+)$1	276	209	233	23.9306
hhhhhhhhttttttttttthhhhh	chr13:21729738-21730050(-)$1	312	27	51	21.7063
hhddddvvvvvvvvvvvvvdddd]	chr6:486056-486348(-)$1	292	180	204	21.5468
dddddddduuuuuuuuuuuudddd	chr12:110784002-110784394(+)$1	392	328	352	22.8023
ccc[ddddvvvvvvvvvvvvvddd	chr18:319312-319585(-)$1	273	95	119	22.7581
"""eeeeeuuuuuuuuuuuueeee	chr10:5807627-5807963(-)$1	336	212	236	23.0004
ii[eeeeeuuuuuuuuuuuueeee	chr15:49935493-49935749(+)$1	256	174	198	23.2459
cgggggggyyyyyyyyyyyyyyyy	chr8:101165660-101165999(+)$1	339	236	260	20.7198
ffffff[attttttttttta]fff	chr15:89739887-89740335(+)$1	448	349	373	22.3290

#otherMatches

#Seq PSSM
AUCUUUUUAAAACUAACCAAAAAA	chr17:65335408-65335731(-)$1	323	193	217	23.3679
cagagccacucgaaucccaggcug	chr11:73114979-73115329(-)$1	350	279	303	22.9705
GGGUUUGAAAAAUUAAUUGCAACU	chr6:82456879-82457166(-)$1	287	93	117	23.2469
UAUUUGACACCCCUUCCCCAGCCA	chr12:16516806-16517058(+)$1	252	61	85	20.2448
ACCUUUAUAAUUCAUUUUUGGUAG	chrX:53611086-53611382(-)$1	296	22	46	22.0120
GAUAUGCUUCAUUGUCAAAUGCAU	chr18:33290470-33290924(+)$1	454	392	416	21.6913
AUUUUCCAACUGCUUUAUCUCUGU	chr15:85348520-85348879(+)$1	359	229	253	21.8842
UUCUCUCAGAUUUGAACCAGUGAA	chr18:47309871-47310251(-)$1	380	221	245	23.0018
AUUUCAUGUUUUUUACACUCAUGA	chr5:78622661-78622927(+)$1	266	212	236	22.7672
AUGGAGAAACAAUCAUAUCUUUCU	chr7:135611406-135611876(-)$1	470	151	175	21.3497
CGAGUAGUCCACAUACAGAAGCUA	chr2:175939244-175939651(-)$1	407	127	151	23.2220
GGCAAUGAUUUAUUUUUUUCCCAG	chr15:83807049-83807475(-)$1	426	115	139	20.1158
CAAUUUUGGAAACAGAACAUGAAA	chr6:100836344-100836623(-)$1	279	73	97	21.7063
UGAAUCUGAAGAAGCAUGCACAGA	chr1:114308594-114308854(-)$1	260	66	90	20.5519
CUUGAAAAGUACUAUGUUUCAAAU	chr12:27182420-27182715(+)$1	295	121	145	21.4667
UGGCAAGCACUUUAACCAACUUCU	chr5:110835496-110835817(-)$1	321	184	208	22.9152
GCCCAAGGGCUUAUUCAUCACCAU	chr1:107601218-107601564(+)$1	346	104	128	22.1251
UAGCAUCAGAGUCGGAUUAAUGAA	chr2:30381611-30381921(+)$1	310	174	198	24.2153
GCUGUGAAGAAAAAUAUAUAUCAA	chr19:47113651-47114138(+)$1	487	333	357	23.2420
GGGCUGGGAGAAAUGAAGCCACCC	chr22:42302439-42302858(+)$1	419	0	24	22.0873
GCUUUCCUAUACUUGUUCAAAGGA	chr5:150070954-150071265(-)$1	311	99	123	23.9581
ACUGACUCAGAACAAUUAAGAGUA	chr22:42334672-42334969(-)$1	297	267	291	21.6081
UUUUACUCUUCUCUAAUAUGGGUC	chr2:64859676-64859955(-)$1	279	131	155	23.9633
CAGAAGAUCCAAGUUUAAAAUUGC	chr7:134653400-134653663(+)$1	263	5	29	23.8112
ACUGGAGUCAUUCCGUUUCCACUC	chr17:7490643-7490939(+)$1	296	234	258	23.0006
ACAUAAGUAACUCCCAAACACUUA	chr2:9725032-9725431(-)$1	399	253	277	21.7063
UGGUACGGUUUUACACAACUCCUU	chr1:111983146-111983500(-)$1	354	185	209	22.1251
UUCAGACCUUCAAAACUGUGGCCU	chr3:167401992-167402275(-)$1	283	154	178	21.2212
AUAAGCCCUGUAGAUAUUAUGGGU	chr1:218507791-218508155(+)$1	364	276	300	22.0830
ACAUCCAAAACCAAGCAAAGGGAU	chr1:193220208-193220456(+)$1	248	50	74	20.1010
GUCAGGGGCCAAACUUACUACCUU	chr6:52366955-52367262(-)$1	307	252	276	23.0260
CCAUUUUUAAGUGAAUGUAAGAAA	chrX:133904222-133904657(-)$1	435	6	30	22.3194
AUGCUGGGGACAAAGAAAAACUAA	chr2:97259347-97259640(-)$1	293	205	229	23.1115
GCCCGGCUCAUCGUCGCAUAGCCU	chr19:50191322-50191604(+)$1	282	5	29	23.7388
CUGUCUAACCCAUUUCCAAUGGAC	chr10:127524698-127524970(+)$1	272	137	161	22.9508
UUGAAUGUUACAAUACUUUUAUUG	chr8:74705111-74705361(-)$1	250	31	55	23.0060
AGGUCAGACCUUUUAUACUUUUGA	chr3:148749527-148749876(-)$1	349	193	217	22.3194
UUUCUAUCUGGGCAUUAAUGGAGA	chr3:124948567-124948895(-)$1	328	261	285	22.0873
uuuuguuuuguuuuguuuuuAAGC	chr10:105785591-105786056(+)$1	465	22	46	23.5345
GAACACUACAUCUUUUUUAUGUUC	chr19:54697144-54697427(+)$1	283	202	226	19.6675
UUGUCAGUGAUUUAUUCUAACUGC	chr2:172821852-172822139(+)$1	287	251	275	23.7139
CCAGUAUACAUUCCACUUCGUGCU	chr2:204293881-204294203(+)$1	322	29	53	20.8052
UUAAGUUUGGCCGCACUGAAGACU	chr1:25687071-25687474(+)$1	403	90	114	22.3194
AGGCUUGUCUAAUUCAAUUACAGG	chr3:23632017-23632297(+)$1	280	114	138	22.3194
UCAGCUGAACUCUCAUCUCUCAAC	chr4:52729502-52729773(+)$1	271	104	128	23.1281
AAGGGGCAGGAAAAGGAUAUGUAA	chr15:72533426-72533736(-)$1	310	51	75	22.4181
AACAUCUAUCCUUCUGUUUUAGAC	chr10:89512405-89512761(-)$1	356	315	339	23.5202
UUUUAAAUGAAAAGAAUGAGAUUU	chr4:52888154-52888434(-)$1	280	80	104	23.2618
GCAUAUAUUUUUAAAUGUUCAUAU	chrX:119390109-119390372(+)$1	263	144	168	23.7651
ACCUCUUGCAUCGUCACCUACAGG	chr1:114448079-114448497(+)$1	418	295	319	23.4300
UGUUGUCUUUGAAUUCUUUAGGCU	chr20:37581186-37581525(+)$1	339	95	119	23.9591
UAUCAUGUGAAAAAAAAUGGUGAC	chr10:32557188-32557465(-)$1	277	35	59	21.1335
UUAGAAGCAAUCACUACCUUUCUC	chr10:73995332-73995617(+)$1	285	103	127	20.5379
GAAAUAAAAACAUGAAAUACUUAA	chr1:225674518-225674799(-)$1	281	239	263	23.2792
UGCUAAAUUACCUGUAAAUAUUCU	chrX:119391437-119391832(+)$1	395	323	347	23.7120
UUCCuuuaaauaaauaaaaaaaaa	chr10:16554374-16554753(+)$1	379	330	354	23.6211
AAAUGCAAUUUUCAAAAUAUAUGC	chr7:90017451-90017871(+)$1	420	171	195	21.7748
ACAUGGUAUACUACUAUAUUUACU	chr12:50871266-50871542(+)$1	276	209	233	23.9306
UGUAACUUCUUCCAAAUUUAGGUU	chr13:21729738-21730050(-)$1	312	27	51	21.7063
UUCUAAUUCAAGCGGGUUUUUGGA	chr6:486056-486348(-)$1	292	180	204	21.5468
UUAAAGCAACUGUCUAUUUCUGCU	chr12:110784002-110784394(+)$1	392	328	352	22.8023
UGGAGCCAAAGAAAACAAUAAUGG	chr18:319312-319585(-)$1	273	95	119	22.7581
CAAACUGGCUUUUUUUUUUUCUAG	chr10:5807627-5807963(-)$1	336	212	236	23.0004
UACAGAGGGCAAUAUGACAAUCUU	chr15:49935493-49935749(+)$1	256	174	198	23.2459
augugguugacuacagguaaccaa	chr8:101165660-101165999(+)$1	339	236	260	20.7198
CAGACUGGAAUAUAAGUAGUGGGU	chr15:89739887-89740335(+)$1	448	349	373	22.3290

#DB
.(((((((...........)))))	chr17:65335408-65335731(-)$1	1	193	217	23.3679
)(.((((............)))).	chr11:73114979-73115329(-)$1	1	279	303	22.9705
(((.(((............)))..	chr6:82456879-82457166(-)$1	1	93	117	23.2469
((((((................))	chr12:16516806-16517058(+)$1	1	61	85	20.2448
((((((((............))))	chrX:53611086-53611382(-)$1	1	22	46	22.0120
(((((((.............))))	chr18:33290470-33290924(+)$1	1	392	416	21.6913
(((((.((.............)).	chr15:85348520-85348879(+)$1	1	229	253	21.8842
((...(((............))).	chr18:47309871-47310251(-)$1	1	221	245	23.0018
...(((((...........)))))	chr5:78622661-78622927(+)$1	1	212	236	22.7672
.((((((............)))))	chr7:135611406-135611876(-)$1	1	151	175	21.3497
.(.(((((............))))	chr2:175939244-175939651(-)$1	1	127	151	23.2220
((((.((..............)).	chr15:83807049-83807475(-)$1	1	115	139	20.1158
((((((((...........)))))	chr6:100836344-100836623(-)$1	1	73	97	21.7063
(((((((................)	chr1:114308594-114308854(-)$1	1	66	90	20.5519
(((((((................)	chr12:27182420-27182715(+)$1	1	121	145	21.4667
(((.(((............)))))	chr5:110835496-110835817(-)$1	1	184	208	22.9152
(((((.((............)).)	chr1:107601218-107601564(+)$1	1	104	128	22.1251
(((..(((............))).	chr2:30381611-30381921(+)$1	1	174	198	24.2153
((..(((.............))).	chr19:47113651-47114138(+)$1	1	333	357	23.2420
(((.(((...........))))))	chr22:42302439-42302858(+)$1	1	0	24	22.0873
.(..((((............))))	chr5:150070954-150071265(-)$1	1	99	123	23.9581
))).((((...........)))).	chr22:42334672-42334969(-)$1	1	267	291	21.6081
.(..((((...........)))).	chr2:64859676-64859955(-)$1	1	131	155	23.9633
(((..(((...........)))..	chr7:134653400-134653663(+)$1	1	5	29	23.8112
))))((((............))))	chr17:7490643-7490939(+)$1	1	234	258	23.0006
((((((((...........)))))	chr2:9725032-9725431(-)$1	1	253	277	21.7063
(((((.((............)).)	chr1:111983146-111983500(-)$1	1	185	209	22.1251
.((((.((...........)).))	chr3:167401992-167402275(-)$1	1	154	178	21.2212
))).((((............))))	chr1:218507791-218508155(+)$1	1	276	300	22.0830
((((((..............))))	chr1:193220208-193220456(+)$1	1	50	74	20.1010
(((((((.............))))	chr6:52366955-52367262(-)$1	1	252	276	23.0260
.(((((((...........)))))	chrX:133904222-133904657(-)$1	1	6	30	22.3194
.((.(((.............))).	chr2:97259347-97259640(-)$1	1	205	229	23.1115
(.(.((((...........)))).	chr19:50191322-50191604(+)$1	1	5	29	23.7388
(((((((............)))))	chr10:127524698-127524970(+)$1	1	137	161	22.9508
((.((((............)))).	chr8:74705111-74705361(-)$1	1	31	55	23.0060
.(((((((...........)))))	chr3:148749527-148749876(-)$1	1	193	217	22.3194
(((((.((...........)))))	chr3:124948567-124948895(-)$1	1	261	285	22.0873
((((((((............))))	chr10:105785591-105786056(+)$1	1	22	46	23.5345
(((((..............)))))	chr19:54697144-54697427(+)$1	1	202	226	19.6675
(((.((((...........)))))	chr2:172821852-172822139(+)$1	1	251	275	23.7139
(.(((((............)))))	chr2:204293881-204294203(+)$1	1	29	53	20.8052
.(((((((...........)))))	chr1:25687071-25687474(+)$1	1	90	114	22.3194
.(((((((...........)))))	chr3:23632017-23632297(+)$1	1	114	138	22.3194
((((.(((...........)))..	chr4:52729502-52729773(+)$1	1	104	128	23.1281
.....(((...........)))..	chr15:72533426-72533736(-)$1	1	51	75	22.4181
(...((((...........)))).	chr10:89512405-89512761(-)$1	1	315	339	23.5202
(..(((((............))))	chr4:52888154-52888434(-)$1	1	80	104	23.2618
(((.((((............))))	chrX:119390109-119390372(+)$1	1	144	168	23.7651
....((((............))))	chr1:114448079-114448497(+)$1	1	295	319	23.4300
(((.((((...........)))).	chr20:37581186-37581525(+)$1	1	95	119	23.9591
(...((((..............))	chr10:32557188-32557465(-)$1	1	35	59	21.1335
)))(((((................	chr10:73995332-73995617(+)$1	1	103	127	20.5379
(((.(((.............))).	chr1:225674518-225674799(-)$1	1	239	263	23.2792
(.(..(((...........)))..	chrX:119391437-119391832(+)$1	1	323	347	23.7120
((..(((.............))).	chr10:16554374-16554753(+)$1	1	330	354	23.6211
(((.(((..............)))	chr7:90017451-90017871(+)$1	1	171	195	21.7748
((..((((............))))	chr12:50871266-50871542(+)$1	1	209	233	23.9306
((((((((...........)))))	chr13:21729738-21730050(-)$1	1	27	51	21.7063
((((((.............)))).	chr6:486056-486348(-)$1	1	180	204	21.5468
))))((((............))))	chr12:110784002-110784394(+)$1	1	328	352	22.8023
(((.((((.............)))	chr18:319312-319585(-)$1	1	95	119	22.7581
...(((((............))))	chr10:5807627-5807963(-)$1	1	212	236	23.0004
((.(((((............))))	chr15:49935493-49935749(+)$1	1	174	198	23.2459
)(((((((................	chr8:101165660-101165999(+)$1	1	236	260	20.7198
((((((.(...........).)))	chr15:89739887-89740335(+)$1	1	349	373	22.3290

#PSSM
c : 0.16	h : 0.13	f : 0.12	e : 0.10	[ : 0.06	d : 0.06	i : 0.06	: : 0.06	g : 0.04	b : 0.03	= : 0.03	# : 0.03	" : 0.03	! : 0.01	% : 0.01	F : 0.01	$ : 0.01	
g : 0.13	c : 0.13	f : 0.12	h : 0.12	e : 0.09	d : 0.07	a : 0.06	i : 0.06	" : 0.04	= : 0.03	# : 0.03	[ : 0.03	b : 0.01	: : 0.01	$ : 0.01	! : 0.01	
g : 0.13	f : 0.12	h : 0.10	c : 0.10	e : 0.09	! : 0.09	d : 0.07	[ : 0.06	" : 0.06	i : 0.04	# : 0.03	a : 0.03	= : 0.01	b : 0.01	$ : 0.01	
[ : 0.16	e : 0.16	g : 0.13	! : 0.12	d : 0.10	h : 0.09	f : 0.07	" : 0.04	: : 0.03	= : 0.01	i : 0.01	$ : 0.01	# : 0.01	
d : 0.28	e : 0.16	g : 0.13	c : 0.12	h : 0.09	f : 0.06	! : 0.04	[ : 0.03	" : 0.01	= : 0.01	i : 0.01	$ : 0.01	
d : 0.27	c : 0.21	g : 0.12	e : 0.10	h : 0.09	[ : 0.07	f : 0.06	b : 0.01	= : 0.01	i : 0.01	w : 0.01	
d : 0.25	c : 0.21	g : 0.12	e : 0.10	h : 0.09	b : 0.09	w : 0.03	y : 0.01	f : 0.01	= : 0.01	i : 0.01	v : 0.01	[ : 0.01	
d : 0.22	u : 0.10	v : 0.10	g : 0.09	c : 0.09	e : 0.09	b : 0.07	h : 0.06	w : 0.06	y : 0.04	t : 0.01	i : 0.01	a : 0.01	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.34	v : 0.13	y : 0.07	w : 0.07	
u : 0.36	t : 0.33	v : 0.13	y : 0.07	w : 0.07	c : 0.01	
u : 0.25	d : 0.13	v : 0.12	c : 0.10	g : 0.09	y : 0.07	w : 0.06	e : 0.04	h : 0.04	b : 0.03	f : 0.01	a : 0.01	
d : 0.24	c : 0.19	g : 0.10	e : 0.10	y : 0.07	h : 0.07	b : 0.06	w : 0.04	v : 0.03	f : 0.03	i : 0.01	] : 0.01	
d : 0.25	c : 0.21	e : 0.12	g : 0.10	y : 0.07	h : 0.07	b : 0.06	f : 0.04	] : 0.01	i : 0.01	w : 0.01	
d : 0.28	c : 0.12	e : 0.12	g : 0.10	f : 0.07	h : 0.07	y : 0.06	3 : 0.03	b : 0.03	] : 0.03	2 : 0.03	i : 0.01	4 : 0.01	
] : 0.15	e : 0.15	d : 0.15	g : 0.10	h : 0.09	2 : 0.09	f : 0.07	c : 0.04	3 : 0.03	y : 0.03	5 : 0.01	= : 0.01	: : 0.01	i : 0.01	4 : 0.01	

#score	1482.2644416384123
#seq	66
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_CDS_m1_run1.txt

#BEAR
e!!ccc^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:10752-10997(+)$1	245	100	131	38.8248
::ccc^^^^^^^^^^^^^^^^^^^^ccc:::	chrM:13982-14258(+)$1	276	32	63	31.3768
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:9959-10231(+)$1	272	139	170	39.8618
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr2:65300059-65300291(+)$1	232	182	213	39.8618
::dddd^^^^^^^^^^^^^^^^^^^dddd::	chrM:3130-3416(+)$1	286	117	148	29.7526
e!!ccc^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:10815-11094(+)$1	279	37	68	38.8248
::ccc^^^^^^^^^^^^^^^^^^^^ccc:::	chrM:13941-14177(+)$1	236	73	104	31.3768
iiiiii^^^^^^^^^^^^^^^^^^iiiiiii	chr7:63981671-63981906(-)$1	235	105	136	31.1161
ffffff^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:3680-3913(+)$1	233	64	95	37.8569
======^^^^^^^^^^^^^^^^^^^^^^^^^	chr2:204354380-204354606(-)$1	226	160	191	38.3597
eeeee^^^^^^^^^^^^^^^^^^^^^^^eee	chrM:12237-12543(+)$1	306	79	110	37.1506
gggggg^^^^^^^^^^^^^^^^^^^^^^^^^	chr10:64973484-64973717(-)$1	233	97	128	38.1946
gggggg^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:4779-5011(+)$1	232	71	102	38.1946
eee^^^^^^^^^^^^^^^^^^^^^^^^^eee	chrM:9201-9430(+)$1	229	105	136	37.9786
cc[ccc^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:10500-10730(+)$1	230	25	56	38.6733
b^^^^^^^^^^^^^^^^^^^^^^^^^^^^bb	chr4:83763430-83763662(-)$1	232	118	149	37.9309
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr12:116428896-116429128(-)$1	232	104	135	39.8618
dd[bb^^^^^^^^^^^^^^^^^^^^^bb]dd	chr19:6415577-6415800(-)$1	223	96	127	34.8401
hhhhhh^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:11910-12144(+)$1	234	60	91	36.6043
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr15:66030049-66030275(-)$1	226	96	127	39.8618
ffffff^^^^^^^^^^^^^^^^^^ffffff5	chr7:64168344-64168576(+)$1	232	194	225	31.0007
dd^^^^^^^^^^^^^^^^^^^^^^^^dddd]	chrM:7760-7997(+)$1	237	174	205	35.6402
c!!ccc^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:4610-4868(+)$1	258	62	93	38.7340
fff^^^^^^^^^^^^^^^^^^^^^^^^^fff	chrM:3536-3769(+)$1	233	71	102	37.3351
eee[bb^^^^^^^^^^^^^^^^^^^bb]eee	chr6:53135290-53135516(-)$1	226	94	125	33.2957
dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr19:21300580-21300812(+)$1	232	26	57	39.0730
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:6381-6605(+)$1	224	2	33	39.8618
^^^^^^^^^^^^^^^^^^^^^^^^^^^ccc:	chrM:11146-11408(+)$1	262	133	164	36.4050
g[bbbb^^^^^^^^^^^^^^^^^^^^bb]bb	chr10:35857954-35858184(+)$1	230	122	153	33.7152
eeeee^^^^^^^^^^^^^^^^^^^^^^eeee	chr4:77700199-77700456(+)$1	257	95	126	36.3177
eeeee^^^^^^^^^^^^^^^^^^^^^^^eee	chrM:11753-12065(+)$1	312	165	196	37.1506
fffff^^^^^^^^^^^^^^^^^^^^^fffff	chrM:13319-13551(+)$1	232	180	211	34.6209
$$$ccc^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:8965-9207(+)$1	242	102	133	37.8619
ggggggg^^^^^^^^^^^^^^^^^^gggggg	chr19:58452293-58452515(-)$1	222	106	137	31.4609
[ccc^^^^^^^^^^^^^^^^^^^^^ccc]bb	chr1:36068776-36068999(-)$1	223	179	210	35.2047
cc[ccc^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:7594-7837(+)$1	243	107	138	38.6733
::eeeee^^^^^^^^^^^^^^^^^^eeeee:	chrM:8529-8801(+)$1	272	61	92	29.3939
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:214791882-214792123(+)$1	241	107	138	39.8618
c^^^^^^^^^^^^^^^^^^^^^^^^ccc777	chr16:24573240-24573466(+)$1	226	73	104	35.4302
"""ccc^^^^^^^^^^^^^^^^^^^^^ccc5	chr10:24834786-24835018(+)$1	232	95	126	35.9032
bb[ccc^^^^^^^^^^^^^^^^^^^cccbb:	chrM:11085-11323(+)$1	238	161	192	33.2339
dd^^^^^^^^^^^^^^^^^^^^^^^^^^^dd	chr17:5336526-5336750(-)$1	224	96	127	38.1330
ffffff^^^^^^^^^^^^^^^^^^^^^^^^^	chr17:7417184-7417439(+)$1	255	121	152	37.8569
eee^^^^^^^^^^^^^^^^^^^^^^^^^eee	chr4:77979634-77979860(-)$1	226	124	155	37.9786
gggggg^^^^^^^^^^^^^^^^^^^^^^^^^	chr13:42874296-42874529(+)$1	233	184	215	38.1946
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:9702-10036(+)$1	334	135	166	39.8618
eeeee^^^^^^^^^^^^^^^^^^^^^eeeee	chr1:54704657-54704889(-)$1	232	4	35	35.3126
ee[ccc^^^^^^^^^^^^^^^^^^^ccc]ee	chr5:139908405-139908637(+)$1	232	85	116	34.5738
ddeeeee^^^^^^^^^^^^^^^^^^eeeee2	chr6:111694185-111694417(-)$1	232	21	52	31.4932
hhhhhh^^^^^^^^^^^^^^^^^^^^^^^^^	chr13:73636646-73636878(+)$1	232	96	127	36.6043
dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:5256-5501(+)$1	245	15	46	39.0730
dd^^^^^^^^^^^^^^^^^^^^^^^^^^ddd	chr12:46758155-46758381(-)$1	226	89	120	37.4067
[ccc^^^^^^^^^^^^^^^^^^^^^ccc]cc	chrM:5217-5454(+)$1	237	47	78	35.4020
dd^^^^^^^^^^^^^^^^^^^^^^^^^dddd	chrM:15524-15783(+)$1	259	99	130	36.5317
bb[ccc^^^^^^^^^^^^^^^^^^ccc]bb6	chr2:71576915-71577139(+)$1	224	99	130	32.3031
[ccc^^^^^^^^^^^^^^^^^^^^^ccc333	chrM:13631-13905(+)$1	274	97	128	35.9510
fffff^^^^^^^^^^^^^^^^^^^^^^ffff	chr4:123813305-123813530(+)$1	225	95	126	35.6568
ffffff^^^^^^^^^^^^^^^^^^^^^^^^^	chr13:115089647-115089882(+)$1	235	94	125	37.8569
[ccc^^^^^^^^^^^^^^^^^^^^^ccc]gg	chr19:10870331-10870561(+)$1	230	131	162	35.2053

#otherMatches

#Seq PSSM
CCUAAUUAUUAGCAUCAUCCCCCUACUAUUU	chrM:10752-10997(+)$1	245	100	131	38.8248
AAGCUAUUACCUAAAACAAUUUCACAGCACC	chrM:13982-14258(+)$1	276	32	63	31.3768
GCCUUACUACUAAUAAUUAUUACAUUUUGAC	chrM:9959-10231(+)$1	272	139	170	39.8618
ccuuaucuuauucaguccucacaacuuuuac	chr2:65300059-65300291(+)$1	232	182	213	39.8618
cgguaaucgcauaaaacuuaaaacuuuacag	chrM:3130-3416(+)$1	286	117	148	29.7526
CCUAAUUAUUAGCAUCAUCCCCCUACUAUUU	chrM:10815-11094(+)$1	279	37	68	38.8248
AAGCUAUUACCUAAAACAAUUUCACAGCACC	chrM:13941-14177(+)$1	236	73	104	31.3768
CUUUAUUUUCAACCCUUACUAACCAUAAAGU	chr7:63981671-63981906(-)$1	235	105	136	31.1161
AGCCAUCAUUCUACUAUCAACAUUACUAAUA	chrM:3680-3913(+)$1	233	64	95	37.8569
AUGCUGAAGUACACUCUAUUAGUAAUUCCUC	chr2:204354380-204354606(-)$1	226	160	191	38.3597
GUGCAACUCCAAAUAAAAGUAAUAACCAUGC	chrM:12237-12543(+)$1	306	79	110	37.1506
UAGUCAAACUCCAUUACCUACCAUUAACACU	chr10:64973484-64973717(-)$1	233	97	128	38.1946
CCUGCUUCUUCUCACAUGACAAAAACUAGCC	chrM:4779-5011(+)$1	232	71	102	38.1946
UGAUUUCACUUCCACUCCAUAACGCUCCUCA	chrM:9201-9430(+)$1	229	105	136	37.9786
UACUAGUAUAUCGCUCACACCUCAUAUCCUC	chrM:10500-10730(+)$1	230	25	56	38.6733
CUUACCCUAACACCCCUUACAUAUCUUCUGC	chr4:83763430-83763662(-)$1	232	118	149	37.9309
CAUUUCCUCUAACAAUCGCCAAACUCUUCCC	chr12:116428896-116429128(-)$1	232	104	135	39.8618
GCCGCCUACUACUCACACUACUACCAGCAgc	chr19:6415577-6415800(-)$1	223	96	127	34.8401
CCCUAUACUCCCUCUACAUAUUUACCACAAC	chrM:11910-12144(+)$1	234	60	91	36.6043
UAGUUCCAAAACAAUUCAUACUAACAAAUGC	chr15:66030049-66030275(-)$1	226	96	127	39.8618
AUUCUCAAACCUAACUAUACAUAAGAGAAUU	chr7:64168344-64168576(+)$1	232	194	225	31.0007
AUCUUCAACUCCUACAUACUUCCCCCAUUAU	chrM:7760-7997(+)$1	237	174	205	35.6402
UAAUCCUUCUAAUAGCUAUCCUCUUCAACAA	chrM:4610-4868(+)$1	258	62	93	38.7340
GGCCUCCUAUUUAUUCUAGCCACCUCUAGCC	chrM:3536-3769(+)$1	233	71	102	37.3351
UGAUUGCUCUCUUCACAAACUUCUACAUUCA	chr6:53135290-53135516(-)$1	226	94	125	33.2957
CUCCUCAAAACUUACUAUACAUAAGAUAAUU	chr19:21300580-21300812(+)$1	232	26	57	39.0730
GGCCAUCAAUUUCAUCACAACAAUUAUCAAU	chrM:6381-6605(+)$1	224	2	33	39.8618
CUAAACAUUCUACUACUCACUCUCACUGCCC	chrM:11146-11408(+)$1	262	133	164	36.4050
GUCCCCAGCCAUCAUCUCUUAACUACGGAGG	chr10:35857954-35858184(+)$1	230	122	153	33.7152
AGUGGUAUUUUCCCAACAUUAACCUCUCCAC	chr4:77700199-77700456(+)$1	257	95	126	36.3177
UCCUGAUCAAAUAUCACUCUCCUACUUACAG	chrM:11753-12065(+)$1	312	165	196	37.1506
GUUUCUACUCCAAAGACCACAUCAUCGAAAC	chrM:13319-13551(+)$1	232	180	211	34.6209
AUAUCAACCAUUAACCUUCCCUCUACACUUA	chrM:8965-9207(+)$1	242	102	133	37.8619
CCUCACUAAUCACCAGCGAAUUCACAGUGGG	chr19:58452293-58452515(-)$1	222	106	137	31.4609
UCCUUUAUUUUUUUCUACUCUUUUCAGGCGC	chr1:36068776-36068999(-)$1	223	179	210	35.2047
UGUAUGCCCUUUUCCUAACACUCACAACAAA	chrM:7594-7837(+)$1	243	107	138	38.6733
CUGAUCAUUCUAUUUCCCCCUCUAUUGAUCC	chrM:8529-8801(+)$1	272	61	92	29.3939
CACAAAAAAUUUUUACAACUCCACUAACACC	chr1:214791882-214792123(+)$1	241	107	138	39.8618
CAUCUUCAUCAACUCACCCAGCUCCGUCUAU	chr16:24573240-24573466(+)$1	226	73	104	35.4302
GACAGCUCUAACCUCCCUAAUCCACCUGCUA	chr10:24834786-24835018(+)$1	232	95	126	35.9032
GCACUAAUUUACACUCACAACACCCUAGGCU	chrM:11085-11323(+)$1	238	161	192	33.2339
AAGGAUACUAAUUAUACACUCAACACAGAUU	chr17:5336526-5336750(-)$1	224	96	127	38.1330
aguacucaccuacuagccccacuuacucgcc	chr17:7417184-7417439(+)$1	255	121	152	37.8569
AGUACCAAUUCAACCUUUACCCAGAAACAUU	chr4:77979634-77979860(-)$1	226	124	155	37.9786
UGAUCAAAAAAAUAAAUCUAAAAAUAAAUCC	chr13:42874296-42874529(+)$1	233	184	215	38.1946
GGCUCAACUUUCCUCACUAUCUGCUUCAUCC	chrM:9702-10036(+)$1	334	135	166	39.8618
CACUGUUCUACAGAUUCAACAAAUUCCAGUG	chr1:54704657-54704889(-)$1	232	4	35	35.3126
CUUCUGUCUCCUCUGCACCUAUCACUAGCGG	chr5:139908405-139908637(+)$1	232	85	116	34.5738
GUACUUUAAGUCCUGAAAUUUUUGAGAAGUC	chr6:111694185-111694417(-)$1	232	21	52	31.4932
CUGGCAAUUCACAAUCCAAAUUUACCCACCA	chr13:73636646-73636878(+)$1	232	96	127	36.6043
GAAGAAUUCACAAAAAACAAUAGCCUCAUCA	chrM:5256-5501(+)$1	245	15	46	39.0730
GAUAAUUAACGAAACAAUAAACACCACCUUA	chr12:46758155-46758381(-)$1	226	89	120	37.4067
CAUUAUCGAAGAAUUCACAAAAAACAAUAGC	chrM:5217-5454(+)$1	237	47	78	35.4020
GCCCUAUUACUAUCCAUCCUCAUCCUAGCAA	chrM:15524-15783(+)$1	259	99	130	36.5317
GUCAACCAAUCCAUUAACCAAACAGUUAGCC	chr2:71576915-71577139(+)$1	224	99	130	32.3031
AGGAUUUCUCAUUACUAACAACAUUUCCCCC	chrM:13631-13905(+)$1	274	97	128	35.9510
AUUGGAAUCUAAUAACUACAAUACUUACCGG	chr4:123813305-123813530(+)$1	225	95	126	35.6568
CUCCAGAAUCGCCAAAACCUACUCCUCUUAC	chr13:115089647-115089882(+)$1	235	94	125	37.8569
CUGCAGCUCAUCUUCUCAAAAACAGGUAAAA	chr19:10870331-10870561(+)$1	230	131	162	35.2053

#DB
(..(((.........................	chrM:10752-10997(+)$1	1	100	131	38.8248
..(((....................)))...	chrM:13982-14258(+)$1	1	32	63	31.3768
(((............................	chrM:9959-10231(+)$1	1	139	170	39.8618
(((............................	chr2:65300059-65300291(+)$1	1	182	213	39.8618
..((((...................))))..	chrM:3130-3416(+)$1	1	117	148	29.7526
(..(((.........................	chrM:10815-11094(+)$1	1	37	68	38.8248
..(((....................)))...	chrM:13941-14177(+)$1	1	73	104	31.3768
((((((..................)))))))	chr7:63981671-63981906(-)$1	1	105	136	31.1161
((((((.........................	chrM:3680-3913(+)$1	1	64	95	37.8569
((((((.........................	chr2:204354380-204354606(-)$1	1	160	191	38.3597
(((((.......................)))	chrM:12237-12543(+)$1	1	79	110	37.1506
((((((.........................	chr10:64973484-64973717(-)$1	1	97	128	38.1946
((((((.........................	chrM:4779-5011(+)$1	1	71	102	38.1946
(((.........................)))	chrM:9201-9430(+)$1	1	105	136	37.9786
((.(((.........................	chrM:10500-10730(+)$1	1	25	56	38.6733
(............................))	chr4:83763430-83763662(-)$1	1	118	149	37.9309
(((............................	chr12:116428896-116429128(-)$1	1	104	135	39.8618
((.((.....................)).))	chr19:6415577-6415800(-)$1	1	96	127	34.8401
((((((.........................	chrM:11910-12144(+)$1	1	60	91	36.6043
(((............................	chr15:66030049-66030275(-)$1	1	96	127	39.8618
((((((..................)))))).	chr7:64168344-64168576(+)$1	1	194	225	31.0007
((........................)))).	chrM:7760-7997(+)$1	1	174	205	35.6402
(..(((.........................	chrM:4610-4868(+)$1	1	62	93	38.7340
(((.........................)))	chrM:3536-3769(+)$1	1	71	102	37.3351
(((.((...................)).)))	chr6:53135290-53135516(-)$1	1	94	125	33.2957
((((...........................	chr19:21300580-21300812(+)$1	1	26	57	39.0730
(((............................	chrM:6381-6605(+)$1	1	2	33	39.8618
...........................))).	chrM:11146-11408(+)$1	1	133	164	36.4050
(.((((....................)).))	chr10:35857954-35858184(+)$1	1	122	153	33.7152
(((((......................))))	chr4:77700199-77700456(+)$1	1	95	126	36.3177
(((((.......................)))	chrM:11753-12065(+)$1	1	165	196	37.1506
(((((.....................)))))	chrM:13319-13551(+)$1	1	180	211	34.6209
...(((.........................	chrM:8965-9207(+)$1	1	102	133	37.8619
(((((((..................))))))	chr19:58452293-58452515(-)$1	1	106	137	31.4609
.(((.....................))).))	chr1:36068776-36068999(-)$1	1	179	210	35.2047
((.(((.........................	chrM:7594-7837(+)$1	1	107	138	38.6733
..(((((..................))))).	chrM:8529-8801(+)$1	1	61	92	29.3939
(((............................	chr1:214791882-214792123(+)$1	1	107	138	39.8618
(........................)))...	chr16:24573240-24573466(+)$1	1	73	104	35.4302
...(((.....................))).	chr10:24834786-24835018(+)$1	1	95	126	35.9032
((.(((...................))))).	chrM:11085-11323(+)$1	1	161	192	33.2339
((...........................))	chr17:5336526-5336750(-)$1	1	96	127	38.1330
((((((.........................	chr17:7417184-7417439(+)$1	1	121	152	37.8569
(((.........................)))	chr4:77979634-77979860(-)$1	1	124	155	37.9786
((((((.........................	chr13:42874296-42874529(+)$1	1	184	215	38.1946
(((............................	chrM:9702-10036(+)$1	1	135	166	39.8618
(((((.....................)))))	chr1:54704657-54704889(-)$1	1	4	35	35.3126
((.(((...................))).))	chr5:139908405-139908637(+)$1	1	85	116	34.5738
(((((((..................))))).	chr6:111694185-111694417(-)$1	1	21	52	31.4932
((((((.........................	chr13:73636646-73636878(+)$1	1	96	127	36.6043
((((...........................	chrM:5256-5501(+)$1	1	15	46	39.0730
((..........................)))	chr12:46758155-46758381(-)$1	1	89	120	37.4067
.(((.....................))).))	chrM:5217-5454(+)$1	1	47	78	35.4020
((.........................))))	chrM:15524-15783(+)$1	1	99	130	36.5317
((.(((..................))).)).	chr2:71576915-71577139(+)$1	1	99	130	32.3031
.(((.....................)))...	chrM:13631-13905(+)$1	1	97	128	35.9510
(((((......................))))	chr4:123813305-123813530(+)$1	1	95	126	35.6568
((((((.........................	chr13:115089647-115089882(+)$1	1	94	125	37.8569
.(((.....................))).))	chr19:10870331-10870561(+)$1	1	131	162	35.2053

#PSSM
e : 0.28	d : 0.13	f : 0.11	g : 0.08	: : 0.06	c : 0.06	[ : 0.06	b : 0.05	h : 0.03	i : 0.01	= : 0.01	^ : 0.01	$ : 0.01	" : 0.01	
e : 0.25	d : 0.13	f : 0.11	c : 0.10	: : 0.06	g : 0.06	! : 0.05	^ : 0.05	h : 0.03	b : 0.03	i : 0.01	= : 0.01	[ : 0.01	$ : 0.01	" : 0.01	
e : 0.27	f : 0.11	^ : 0.11	c : 0.10	[ : 0.10	g : 0.06	! : 0.05	d : 0.05	h : 0.03	i : 0.01	= : 0.01	b : 0.01	$ : 0.01	" : 0.01	
^ : 0.28	c : 0.27	f : 0.10	e : 0.10	g : 0.06	d : 0.05	b : 0.03	h : 0.03	i : 0.01	= : 0.01	[ : 0.01	
^ : 0.38	c : 0.20	f : 0.10	e : 0.10	g : 0.06	b : 0.05	h : 0.03	d : 0.01	i : 0.01	= : 0.01	
^ : 0.54	c : 0.16	f : 0.06	g : 0.06	h : 0.03	b : 0.03	e : 0.03	d : 0.01	i : 0.01	= : 0.01	
^ : 0.94	e : 0.03	g : 0.01	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.94	i : 0.01	f : 0.01	c : 0.01	
^ : 0.71	c : 0.16	e : 0.03	d : 0.01	i : 0.01	f : 0.01	b : 0.01	g : 0.01	
^ : 0.62	c : 0.16	b : 0.05	e : 0.05	d : 0.03	f : 0.03	i : 0.01	g : 0.01	
^ : 0.54	c : 0.18	e : 0.06	d : 0.05	f : 0.05	b : 0.03	] : 0.03	i : 0.01	g : 0.01	
^ : 0.44	e : 0.15	] : 0.10	d : 0.06	f : 0.06	: : 0.03	c : 0.03	b : 0.03	i : 0.01	g : 0.01	7 : 0.01	3 : 0.01	
^ : 0.40	e : 0.16	b : 0.08	d : 0.08	f : 0.06	: : 0.05	c : 0.05	g : 0.03	i : 0.01	7 : 0.01	3 : 0.01	
^ : 0.40	e : 0.13	: : 0.10	d : 0.06	b : 0.05	f : 0.05	5 : 0.03	g : 0.03	i : 0.01	] : 0.01	7 : 0.01	2 : 0.01	c : 0.01	6 : 0.01	3 : 0.01	

#score	2142.0745077340875
#seq	59
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_UTR_m3_run1.txt

#BEAR
iiiiiiiooooooiiiiiii	chr12:70738898-70739133(+)$1	235	137	157	13.3159
iiiiiiiiillliiiiiiii	chr17:53241320-53241551(+)$1	231	200	220	8.7727
cc[ddddoooooodddd]cc	chr4:53462702-53462929(-)$1	227	140	160	11.2657
ccc[cccooooooccc]ccc	chr13:38935372-38935612(+)$1	240	6	26	12.3036
gggggggooooooggggggg	chr4:89647339-89647577(-)$1	238	57	77	12.8723
gggggbboooooobb]gggg	chr1:39329227-39329454(-)$1	227	147	167	11.5968
gg[ddddoooooodddd333	chr17:45195034-45195276(-)$1	242	169	189	11.5505
hhhhhhhoooooohhhhhhh	chr1:213166035-213166267(-)$1	232	168	188	11.0841
hhhhhhhoooooohhhhhhh	chr21:28208611-28208843(-)$1	232	10	30	11.0841
gggggggooooooggggggg	chr7:23235393-23235615(+)$1	222	127	147	12.8723
gggggggooooooggggggg	chr10:35468458-35468692(+)$1	234	119	139	12.8723
fff!!bboooooobb22fff	chr1:225590305-225590533(-)$1	228	195	215	10.0633
!!eeeeeooooooeeeee]g	chr5:124080847-124081079(-)$1	232	161	181	11.9739
gggggggooooooggggggg	chr6:76625024-76625259(+)$1	235	11	31	12.8723
=========mmmm=======	chr14:92530123-92530357(-)$1	234	132	152	8.3344
ccc[cccooooooccc]ccc	chr9:123363231-123363463(-)$1	232	3	23	12.3036
=======oooooo=======	chr14:70238473-70238705(+)$1	232	64	84	13.2619
!!eeeeeooooooeeeee22	chr8:37556309-37556558(+)$1	249	176	196	11.4630
==========lll=======	chr6:36568158-36568388(+)$1	230	190	210	9.1857
ee!!cccooooooccc22ee	chr5:36170375-36170605(+)$1	230	78	98	11.5932
eee[cccooooooccc]eee	chrX:37312779-37313019(+)$1	240	176	196	11.8413
[a[ddddoooooodddd]a]	chr6:36567679-36567911(+)$1	232	17	37	11.3524
hhhhhhhoooooohhhhhhh	chr2:135816342-135816574(+)$1	232	119	139	11.0841
!!a[cccoooooocccaggg	chr15:83685836-83686064(-)$1	228	41	61	12.6318
hhhhhhhoooooohhhhhhh	chr21:46226468-46226700(-)$1	232	74	94	11.0841
iiiiiiiiillliiiiiiii	chr2:241517978-241518210(+)$1	232	115	135	8.7727
fff"""aooooooa333fff	chr2:105474412-105474644(+)$1	232	76	96	10.7982
==========lll=======	chr22:39257987-39258216(-)$1	229	142	162	9.1857
[ffffffooooooffffff]	chr1:47843597-47843825(+)$1	228	205	225	10.6390
b!!ddddoooooodddd22b	chr10:18965777-18966016(+)$1	239	155	175	10.5492
c[eeeeeooooooeeeee]c	chr3:156423842-156424070(+)$1	228	148	168	11.7710
=======oooooo=======	chr9:100847885-100848110(-)$1	225	132	152	13.2619
a[eeeeeooooooeeeee]a	chr16:21666738-21666970(+)$1	232	79	99	11.6529
gggggggooooooggggggg	chr19:55790891-55791123(-)$1	232	11	31	12.8723
fffddddoooooodddd333	chr4:177250918-177251150(+)$1	232	98	118	10.9090
""eeeeeooooooeeeee22	chr7:102952520-102952753(+)$1	233	44	64	11.2740
cc[acccooooooccc]a]c	chr19:24312011-24312245(+)$1	234	44	64	12.3666
ddeeeeeooooooeeeee]d	chr5:167981439-167981704(-)$1	265	209	229	11.0025
gg[bb[aooooooa]bb]gg	chr17:28444045-28444273(+)$1	228	177	197	10.9992
ccc[cccooooooccccccd	chr2:37324036-37324264(+)$1	228	78	98	11.9074
cceeeeeooooooeeeeeee	chr9:101911969-101912204(+)$1	235	147	167	11.2687
##eeeeeooooooeeeee44	chr19:36728103-36728331(+)$1	228	62	82	11.2944
gggggggooooooggggggg	chr15:65441182-65441414(-)$1	232	95	115	12.8723
"ffffffooooooffffffg	chr5:114461348-114461579(-)$1	231	180	200	10.5799
gggggggooooooggggggg	chr3:183399334-183399591(+)$1	257	234	254	12.8723
##eeeeeooooooeeeeeee	chr5:133307525-133307750(-)$1	225	58	78	11.2567
b!!ddddoooooodddd]bb	chr14:21678027-21678252(-)$1	225	18	38	10.6104
ffffcccooooooccc]fff	chr5:82876925-82877163(+)$1	238	23	43	11.5510
iiiiiiiooooooiiiiiii	chr10:35297647-35297879(-)$1	232	17	37	13.3159
iiiicccooooooccc22ii	chr19:14640312-14640537(+)$1	225	30	50	12.6252
=======oooooo=======	chr2:37334179-37334414(-)$1	235	131	151	13.2619
b####bboooooobb333bb	chr3:53529091-53529321(+)$1	230	40	60	9.8816
hhhhhhhoooooohhhhhhh	chr15:83686243-83686475(-)$1	232	181	201	11.0841
gbb[cccooooooccc]bb]	chr12:50870195-50870421(+)$1	226	142	162	11.3457
ddddcccooooooccc]ddd	chr1:161009666-161009898(-)$1	232	104	124	10.9040

#otherMatches

#Seq PSSM
UUUGGAUCAAAUAGUUUAAA	chr12:70738898-70739133(+)$1	235	137	157	13.3159
UGAAAUACCCAAGGUGUUUU	chr17:53241320-53241551(+)$1	231	200	220	8.7727
GCACUGGCGAGUCCCAGGGC	chr4:53462702-53462929(-)$1	227	140	160	11.2657
UGAAGUGAAUAGACAUAUCA	chr13:38935372-38935612(+)$1	240	6	26	12.3036
UAUAUAAAAUAAAUUGUGUA	chr4:89647339-89647577(-)$1	238	57	77	12.8723
gugaacuacucugagauuua	chr1:39329227-39329454(-)$1	227	147	167	11.5968
UUAUUUGGAAUAUCAAAAUA	chr17:45195034-45195276(-)$1	242	169	189	11.5505
GUGAAAAUUUAAUUUUUUAU	chr1:213166035-213166267(-)$1	232	168	188	11.0841
AUAGUAAAAUAUGUUACUAU	chr21:28208611-28208843(-)$1	232	10	30	11.0841
ACUUACAGAGUUAUGUAAGU	chr7:23235393-23235615(+)$1	222	127	147	12.8723
AUUCUUACUAAUCUGAGAGU	chr10:35468458-35468692(+)$1	234	119	139	12.8723
UGAAUGUGAGAUGAUUGUCA	chr1:225590305-225590533(-)$1	228	195	215	10.0633
AUUCUGGUAACACCCAGACA	chr5:124080847-124081079(-)$1	232	161	181	11.9739
GUUCUCUAGGAAAAGAGAAC	chr6:76625024-76625259(+)$1	235	11	31	12.8723
AGGAAAGUAUCUCUACUUUC	chr14:92530123-92530357(-)$1	234	132	152	8.3344
GUCAAGUUGUAAUGCUAGGC	chr9:123363231-123363463(-)$1	232	3	23	12.3036
GUUUAAUGCCUUAAUUAAAC	chr14:70238473-70238705(+)$1	232	64	84	13.2619
GUUAUUUUUUCUUAGAUAUA	chr8:37556309-37556558(+)$1	249	176	196	11.4630
UUUCAAAAUUUAAAAUUUUG	chr6:36568158-36568388(+)$1	230	190	210	9.1857
CAAAAAACUCAAAUUUAGUG	chr5:36170375-36170605(+)$1	230	78	98	11.5932
UCAUUGACUUAUUUUAUUGG	chrX:37312779-37313019(+)$1	240	176	196	11.8413
CUGGUGUCGUUUCACAUGAC	chr6:36567679-36567911(+)$1	232	17	37	11.3524
auuauuaauucaauaguaau	chr2:135816342-135816574(+)$1	232	119	139	11.0841
ACGACUGGGUGAACAGCCAU	chr15:83685836-83686064(-)$1	228	41	61	12.6318
UGGGUACUUUUGUGUGCUCA	chr21:46226468-46226700(-)$1	232	74	94	11.0841
GCUGUGAUGGGGUAUCACGG	chr2:241517978-241518210(+)$1	232	115	135	8.7727
GGACGAUGCCUAAAGAUUCC	chr2:105474412-105474644(+)$1	232	76	96	10.7982
AGCUGGAGCGAAGCGUUCCG	chr22:39257987-39258216(-)$1	229	142	162	9.1857
UUUUUAUAUUUUAAUAGAAU	chr1:47843597-47843825(+)$1	228	205	225	10.6390
AGACAUAAAUCGAUAUGGAU	chr10:18965777-18966016(+)$1	239	155	175	10.5492
UGCCAGUGGUCCAGCUGGAG	chr3:156423842-156424070(+)$1	228	148	168	11.7710
AACUCUGGCUGGACAGAGUU	chr9:100847885-100848110(-)$1	225	132	152	13.2619
UGUUCACAAUUACGUGAAGG	chr16:21666738-21666970(+)$1	232	79	99	11.6529
GGGGGGUCGCCGAGCUCCCC	chr19:55790891-55791123(-)$1	232	11	31	12.8723
UGAAAUACAUCACUAUUUAA	chr4:177250918-177251150(+)$1	232	98	118	10.9090
UAUUGCUGCUGUUGGUAAGC	chr7:102952520-102952753(+)$1	233	44	64	11.2740
CUUCUAUGAAAUAAUAUGCA	chr19:24312011-24312245(+)$1	234	44	64	12.3666
GCUGGGUGCAGUGGCUCAUG	chr5:167981439-167981704(-)$1	265	209	229	11.0025
GCAGUGUGAAGAGAGACAGU	chr17:28444045-28444273(+)$1	228	177	197	10.9992
GUCAGAGGCAAUGUUCGACC	chr2:37324036-37324264(+)$1	228	78	98	11.9074
ACCUCAUAUAGUAGUGAGGA	chr9:101911969-101912204(+)$1	235	147	167	11.2687
AAGCUUUCAGCCAGAAGUCA	chr19:36728103-36728331(+)$1	228	62	82	11.2944
AUGUGUUCACACUAACAUAU	chr15:65441182-65441414(-)$1	232	95	115	12.8723
UGUUCUUAUGUCAAAGAAUU	chr5:114461348-114461579(-)$1	231	180	200	10.5799
AUAUAUCAAAAGGGGUAUAU	chr3:183399334-183399591(+)$1	257	234	254	12.8723
UCUUCCAUUUUGUUGGAAUU	chr5:133307525-133307750(-)$1	225	58	78	11.2567
CCAUGUUCCUGAAAACAAGA	chr14:21678027-21678252(-)$1	225	18	38	10.6104
AAGGCCUGAAUGGAGGACUU	chr5:82876925-82877163(+)$1	238	23	43	11.5510
UUAAAAUCggaauauuuuaa	chr10:35297647-35297879(-)$1	232	17	37	13.3159
UCGUGCCCUGAUUGGCCGAC	chr19:14640312-14640537(+)$1	225	30	50	12.6252
CUUUCUGCAGAAACAGAAAG	chr2:37334179-37334414(-)$1	235	131	151	13.2619
cccccgccucaacgcccagc	chr3:53529091-53529321(+)$1	230	40	60	9.8816
UAGCAUUUGUAAUAAUGCUA	chr15:83686243-83686475(-)$1	232	181	201	11.0841
GUACUUAGAGAUGUGACUAC	chr12:50870195-50870421(+)$1	226	142	162	11.3457
AGAUCUUAAAAACAAGAAUC	chr1:161009666-161009898(-)$1	232	104	124	10.9040

#DB
(((((((......)))))))	chr12:70738898-70739133(+)$1	1	137	157	13.3159
(((((((((...))))))))	chr17:53241320-53241551(+)$1	1	200	220	8.7727
((.((((......)))).))	chr4:53462702-53462929(-)$1	1	140	160	11.2657
(((.(((......))).)))	chr13:38935372-38935612(+)$1	1	6	26	12.3036
(((((((......)))))))	chr4:89647339-89647577(-)$1	1	57	77	12.8723
(((((((......)).))))	chr1:39329227-39329454(-)$1	1	147	167	11.5968
((.((((......))))...	chr17:45195034-45195276(-)$1	1	169	189	11.5505
(((((((......)))))))	chr1:213166035-213166267(-)$1	1	168	188	11.0841
(((((((......)))))))	chr21:28208611-28208843(-)$1	1	10	30	11.0841
(((((((......)))))))	chr7:23235393-23235615(+)$1	1	127	147	12.8723
(((((((......)))))))	chr10:35468458-35468692(+)$1	1	119	139	12.8723
(((..((......))..)))	chr1:225590305-225590533(-)$1	1	195	215	10.0633
..(((((......))))).)	chr5:124080847-124081079(-)$1	1	161	181	11.9739
(((((((......)))))))	chr6:76625024-76625259(+)$1	1	11	31	12.8723
(((((((((....)))))))	chr14:92530123-92530357(-)$1	1	132	152	8.3344
(((.(((......))).)))	chr9:123363231-123363463(-)$1	1	3	23	12.3036
(((((((......)))))))	chr14:70238473-70238705(+)$1	1	64	84	13.2619
..(((((......)))))..	chr8:37556309-37556558(+)$1	1	176	196	11.4630
((((((((((...)))))))	chr6:36568158-36568388(+)$1	1	190	210	9.1857
((..(((......)))..))	chr5:36170375-36170605(+)$1	1	78	98	11.5932
(((.(((......))).)))	chrX:37312779-37313019(+)$1	1	176	196	11.8413
.(.((((......)))).).	chr6:36567679-36567911(+)$1	1	17	37	11.3524
(((((((......)))))))	chr2:135816342-135816574(+)$1	1	119	139	11.0841
..(.(((......)))))))	chr15:83685836-83686064(-)$1	1	41	61	12.6318
(((((((......)))))))	chr21:46226468-46226700(-)$1	1	74	94	11.0841
(((((((((...))))))))	chr2:241517978-241518210(+)$1	1	115	135	8.7727
(((...(......)...)))	chr2:105474412-105474644(+)$1	1	76	96	10.7982
((((((((((...)))))))	chr22:39257987-39258216(-)$1	1	142	162	9.1857
.((((((......)))))).	chr1:47843597-47843825(+)$1	1	205	225	10.6390
(..((((......))))..)	chr10:18965777-18966016(+)$1	1	155	175	10.5492
(.(((((......))))).)	chr3:156423842-156424070(+)$1	1	148	168	11.7710
(((((((......)))))))	chr9:100847885-100848110(-)$1	1	132	152	13.2619
(.(((((......))))).)	chr16:21666738-21666970(+)$1	1	79	99	11.6529
(((((((......)))))))	chr19:55790891-55791123(-)$1	1	11	31	12.8723
(((((((......))))...	chr4:177250918-177251150(+)$1	1	98	118	10.9090
..(((((......)))))..	chr7:102952520-102952753(+)$1	1	44	64	11.2740
((.((((......))).).)	chr19:24312011-24312245(+)$1	1	44	64	12.3666
(((((((......))))).)	chr5:167981439-167981704(-)$1	1	209	229	11.0025
((.((.(......).)).))	chr17:28444045-28444273(+)$1	1	177	197	10.9992
(((.(((......)))))))	chr2:37324036-37324264(+)$1	1	78	98	11.9074
))(((((......)))))((	chr9:101911969-101912204(+)$1	1	147	167	11.2687
..(((((......)))))..	chr19:36728103-36728331(+)$1	1	62	82	11.2944
(((((((......)))))))	chr15:65441182-65441414(-)$1	1	95	115	12.8723
.((((((......)))))))	chr5:114461348-114461579(-)$1	1	180	200	10.5799
(((((((......)))))))	chr3:183399334-183399591(+)$1	1	234	254	12.8723
..(((((......)))))))	chr5:133307525-133307750(-)$1	1	58	78	11.2567
(..((((......)))).))	chr14:21678027-21678252(-)$1	1	18	38	10.6104
(((((((......))).)))	chr5:82876925-82877163(+)$1	1	23	43	11.5510
(((((((......)))))))	chr10:35297647-35297879(-)$1	1	17	37	13.3159
(((((((......)))..))	chr19:14640312-14640537(+)$1	1	30	50	12.6252
(((((((......)))))))	chr2:37334179-37334414(-)$1	1	131	151	13.2619
(....((......))...))	chr3:53529091-53529321(+)$1	1	40	60	9.8816
(((((((......)))))))	chr15:83686243-83686475(-)$1	1	181	201	11.0841
(((.(((......))).)).	chr12:50870195-50870421(+)$1	1	142	162	11.3457
(((((((......))).)))	chr1:161009666-161009898(-)$1	1	104	124	10.9040

#PSSM
g : 0.20	c : 0.12	= : 0.10	i : 0.09	h : 0.09	f : 0.07	! : 0.05	b : 0.05	e : 0.03	[ : 0.03	" : 0.03	d : 0.03	# : 0.03	a : 0.01	
g : 0.18	c : 0.10	f : 0.10	= : 0.10	i : 0.09	h : 0.09	! : 0.09	# : 0.05	e : 0.03	[ : 0.03	d : 0.03	a : 0.01	" : 0.01	b : 0.01	
e : 0.18	g : 0.14	f : 0.10	= : 0.10	i : 0.09	[ : 0.09	h : 0.09	c : 0.05	! : 0.05	a : 0.01	# : 0.01	b : 0.01	d : 0.01	
e : 0.16	g : 0.14	d : 0.12	[ : 0.10	= : 0.10	i : 0.09	h : 0.09	f : 0.05	! : 0.03	" : 0.01	a : 0.01	b : 0.01	# : 0.01	
c : 0.20	e : 0.16	g : 0.14	d : 0.10	= : 0.10	h : 0.09	i : 0.07	f : 0.03	! : 0.01	" : 0.01	b : 0.01	# : 0.01	
c : 0.20	e : 0.16	g : 0.12	d : 0.10	= : 0.10	h : 0.09	i : 0.07	b : 0.05	f : 0.03	" : 0.01	[ : 0.01	
c : 0.20	e : 0.16	g : 0.12	d : 0.10	= : 0.10	h : 0.09	i : 0.07	b : 0.05	a : 0.03	f : 0.03	
o : 0.90	= : 0.05	i : 0.03	
o : 0.90	= : 0.05	i : 0.03	
o : 0.90	l : 0.03	= : 0.03	m : 0.01	
o : 0.90	l : 0.07	m : 0.01	
o : 0.90	l : 0.07	m : 0.01	
o : 0.90	i : 0.03	l : 0.03	m : 0.01	
c : 0.20	e : 0.16	g : 0.12	d : 0.10	= : 0.10	h : 0.09	i : 0.07	b : 0.05	a : 0.03	f : 0.03	
c : 0.20	e : 0.16	g : 0.12	d : 0.10	= : 0.10	h : 0.09	i : 0.07	b : 0.05	f : 0.03	3 : 0.01	] : 0.01	
c : 0.20	e : 0.16	g : 0.12	d : 0.10	= : 0.10	h : 0.09	i : 0.07	3 : 0.03	f : 0.03	] : 0.01	2 : 0.01	b : 0.01	
e : 0.16	g : 0.14	] : 0.12	d : 0.10	= : 0.10	h : 0.09	i : 0.07	2 : 0.05	3 : 0.03	f : 0.03	a : 0.01	b : 0.01	c : 0.01	
e : 0.18	g : 0.16	= : 0.10	h : 0.09	f : 0.09	i : 0.07	] : 0.07	c : 0.05	3 : 0.05	2 : 0.05	a : 0.01	b : 0.01	d : 0.01	
g : 0.18	= : 0.10	i : 0.09	h : 0.09	f : 0.09	] : 0.09	c : 0.07	e : 0.07	2 : 0.05	b : 0.05	3 : 0.03	a : 0.01	4 : 0.01	d : 0.01	
g : 0.21	= : 0.10	i : 0.09	c : 0.09	h : 0.09	e : 0.07	f : 0.05	] : 0.05	b : 0.05	d : 0.05	3 : 0.03	2 : 0.03	a : 0.01	4 : 0.01	

#score	631.3233612887348
#seq	55
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_CDS_m3_run1.txt

#BEAR
ffddddnnnnndddd]fff	chr8:48769709-48769928(-)$1	219	95	114	10.2357
d[ddddnnnnndddd]ddd	chr13:111531997-111532222(-)$1	225	65	84	10.7046
ggggbbnnnnnbb22gggg	chr15:41657646-41657865(+)$1	219	84	103	10.9843
a[ddddnnnnndddd]a22	chr4:10447814-10448031(-)$1	217	160	179	10.6529
ggggggnnnnnggggggg]	chr1:242048517-242048743(+)$1	226	103	122	11.8305
======nnnnn========	chr13:23911819-23912040(-)$1	221	182	201	11.8943
ggggggnnnnnggggggg]	chr16:88786410-88786632(-)$1	222	170	189	11.8305
ccc[bbnnnnnbbccc]cc	chr12:110779983-110780199(+)$1	216	156	175	10.8771
dd!!bbnnnnnbb22dddd	chr19:56179814-56180040(+)$1	226	195	214	10.2434
ggggggnnnnnggggggg:	chr1:151204144-151204362(+)$1	218	149	168	11.1000
dd[cccnnnnnccc]dddd	chr3:17051954-17052168(+)$1	214	167	186	11.6334
ddd[bbnnnnnbb333ddd	chr2:241682262-241682480(-)$1	218	118	137	10.7285
ggggggnnnnnggggggg:	chr6:36463527-36463743(-)$1	216	145	164	11.1000
cc[cccnnnnnccc]ccc:	chr1:224377448-224377670(+)$1	222	6	25	11.7233
dd[cccnnnnnccc]dddd	chr4:39918597-39918817(-)$1	220	191	210	11.6334
======nnnnn========	chrX:123185117-123185337(+)$1	220	132	151	11.8943
"""cccnnnnnccc22ddd	chr12:57038912-57039131(-)$1	219	53	72	12.3111
##ddddnnnnndddd22ee	chr4:187542491-187542708(-)$1	217	105	124	10.5640
ffffffnnnnnffffff33	chr1:2237362-2237585(+)$1	223	170	189	10.3174
[a[cccnnnnnccc]a]gg	chr1:16263985-16264209(+)$1	224	198	217	12.4151
ggggggooooooggggggg	chr8:48883895-48884128(+)$1	233	118	137	7.1119
!!acccnnnnnccc]a22c	chr6:31604935-31605147(+)$1	212	133	152	12.1290
ggggggnnnnnggggggg3	chr17:76798392-76798613(-)$1	221	102	121	11.8883
ggggggooooooggggggg	chr17:4575805-4576023(-)$1	218	30	49	7.1119
"""cccnnnnnccc]ccc]	chr3:194174891-194175108(-)$1	217	106	125	12.6425
ccc[bbnnnnnbb]cccbb	chr12:12630156-12630373(-)$1	217	4	23	10.2849
ffffffnnnnnffffffbb	chr19:44351562-44351782(+)$1	220	168	187	9.7523
ggggggnnnnnggggggg:	chr6:7226662-7226880(+)$1	218	40	59	11.1000
ggggggnnnnnggggggg:	chr3:184041572-184041799(+)$1	227	7	26	11.1000
d!!cccnnnnnccc22ddd	chr12:48465350-48465571(-)$1	221	144	163	12.2391
cc[cccnnnnnccc]ccc]	chr8:90921828-90922047(+)$1	219	176	195	12.4538
e!!cccnnnnnccc22eee	chr10:121339347-121339566(-)$1	219	103	122	12.0376
[eeeeennnnneeeee]cc	chr11:71716258-71716505(-)$1	247	181	200	10.1458
!!ddddnnnnndddd22bb	chr20:34241104-34241353(-)$1	249	90	109	10.6523
b!!cccnnnnnccc22bb3	chr22:51043376-51043590(+)$1	214	157	176	11.8817
c[ddddnnnnndddd]ccc	chrX:74295127-74295348(-)$1	221	152	171	11.1063
cc[cccnnnnncccccc::	chr2:111398550-111398775(-)$1	225	150	169	10.4386
ggggggnnnnnggggggga	chr1:11298449-11298673(-)$1	224	139	158	11.7897
ffffffnnnnnffffff33	chr10:5789120-5789362(+)$1	242	89	108	10.3174
!eeeeennnnneeeee22a	chr13:23908523-23908745(-)$1	222	180	199	9.8553
d"""bbnnnnnbb4444dd	chr19:44500320-44500539(+)$1	219	93	112	10.8446
!!ddddnnnnndddd4444	chr6:52133835-52134060(-)$1	225	143	162	11.0919
###cccnnnnnccc22ddd	chr5:32380159-32380375(-)$1	216	110	129	12.1628
cc[cccnnnnnccc]ccc6	chr5:5460483-5460703(+)$1	220	137	156	12.0711
c[ddddnnnnndddd]ccc	chr19:59057143-59057363(+)$1	220	143	162	11.1063
ffffbbnnnnnbb]fffff	chr12:57033814-57034057(-)$1	243	52	71	9.8038
"""cccnnnnnccc333dd	chr7:23358659-23358878(-)$1	219	150	169	12.7672

#otherMatches

#Seq PSSM
CUUAGCCCCUUGCUGCAGC	chr8:48769709-48769928(-)$1	219	95	114	10.2357
UGGGUGGAAGACAUUGGGG	chr13:111531997-111532222(-)$1	225	65	84	10.7046
GGGUCUGAAGGGGUCACUC	chr15:41657646-41657865(+)$1	219	84	103	10.9843
GAUGCUAAUGGAGCACCUC	chr4:10447814-10448031(-)$1	217	160	179	10.6529
UGGGCUAUAUAAGUCCAGU	chr1:242048517-242048743(+)$1	226	103	122	11.8305
GAGAAACAGUUUUUUUCUG	chr13:23911819-23912040(-)$1	221	182	201	11.8943
GGGGGCGCUCGGUCUCCAG	chr16:88786410-88786632(-)$1	222	170	189	11.8305
GGAUGACAACUUCUCCACC	chr12:110779983-110780199(+)$1	216	156	175	10.8771
CCCUGAUGGACUCUCGGCU	chr19:56179814-56180040(+)$1	226	195	214	10.2434
UCAGGAGCAUGUCCUGGAA	chr1:151204144-151204362(+)$1	218	149	168	11.1000
GAAGCAACCUCUGUCUCAU	chr3:17051954-17052168(+)$1	214	167	186	11.6334
GCCACUGUCCAAGCCAGGU	chr2:241682262-241682480(-)$1	218	118	137	10.7285
GGGGGGCAAUACCUUCCUA	chr6:36463527-36463743(-)$1	216	145	164	11.1000
GCUAUUCAUGAGAUUGCCC	chr1:224377448-224377670(+)$1	222	6	25	11.7233
GUUUCUAGAGCAGGCACAA	chr4:39918597-39918817(-)$1	220	191	210	11.6334
UAUGUAUUUGUUGCAUAUU	chrX:123185117-123185337(+)$1	220	132	151	11.8943
AUCGUGGCGGUCAUUGGCG	chr12:57038912-57039131(-)$1	219	53	72	12.3111
AAUCCACAUUCUGGAACUA	chr4:187542491-187542708(-)$1	217	105	124	10.5640
GGAGAUCGAGCGUCUCCGC	chr1:2237362-2237585(+)$1	223	170	189	10.3174
UGCCAUGUCAAAUGUCCUA	chr1:16263985-16264209(+)$1	224	198	217	12.4151
UACUUUAUUAUCAAGGUAU	chr8:48883895-48884128(+)$1	233	118	137	7.1119
UUCCGCACCCAGCGCGUCG	chr6:31604935-31605147(+)$1	212	133	152	12.1290
GGGCAUCUCAAAUGCCCAA	chr17:76798392-76798613(-)$1	221	102	121	11.8883
UUUGUCCACUAUGACAAGG	chr17:4575805-4576023(-)$1	218	30	49	7.1119
AUAUUCCAUUAGAAAGGUA	chr3:194174891-194175108(-)$1	217	106	125	12.6425
AGCAUCCCCAAGAAGCUGC	chr12:12630156-12630373(-)$1	217	4	23	10.2849
GGCCUUUUUUUGGGGCUCA	chr19:44351562-44351782(+)$1	220	168	187	9.7523
UGACAUUUGUUGUGUCACC	chr6:7226662-7226880(+)$1	218	40	59	11.1000
AGGGUGCGCUCCAUCCUGA	chr3:184041572-184041799(+)$1	227	7	26	11.1000
UCuuuauuaauuaauuaau	chr12:48465350-48465571(-)$1	221	144	163	12.2391
AUAAAUCUACAGUUAGUAC	chr8:90921828-90922047(+)$1	219	176	195	12.4538
CUUUUUAUAACAAACUGGU	chr10:121339347-121339566(-)$1	219	103	122	12.0376
AGUGUGCCCCCCACAUCUG	chr11:71716258-71716505(-)$1	247	181	200	10.1458
GACUGCCCAGUGCAGGACU	chr20:34241104-34241353(-)$1	249	90	109	10.6523
GUGCAGACUCCCUGGCCCC	chr22:51043376-51043590(+)$1	214	157	176	11.8817
GUAAGUUAAACAUUUUUCA	chrX:74295127-74295348(-)$1	221	152	171	11.1063
CCAUGGAACUACCAGGUAU	chr2:111398550-111398775(-)$1	225	150	169	10.4386
GUGGUUAGCCAGACCGCAG	chr1:11298449-11298673(-)$1	224	139	158	11.7897
UCAGAGGAAGAUUCUGACA	chr10:5789120-5789362(+)$1	242	89	108	10.3174
UGAGGGAUUGCCCCUUCUC	chr13:23908523-23908745(-)$1	222	180	199	9.8553
AGCAGGACUACCCACAAUU	chr19:44500320-44500539(+)$1	219	93	112	10.8446
UGUGGAGUUGGUCCAGUAU	chr6:52133835-52134060(-)$1	225	143	162	11.0919
UAUGGUGAAAGACCCACCG	chr5:32380159-32380375(-)$1	216	110	129	12.1628
GUUUCAGAAGAUGAUACAA	chr5:5460483-5460703(+)$1	220	137	156	12.0711
UUGGAGUUGUUCUCCCAUG	chr19:59057143-59057363(+)$1	220	143	162	11.1063
UUCCUGUUCUUCAUGGGAU	chr12:57033814-57034057(-)$1	243	52	71	9.8038
GUUCUUUAAGUAAGUUACA	chr7:23358659-23358878(-)$1	219	150	169	12.7672

#DB
((((((.....)))).)))	chr8:48769709-48769928(-)$1	1	95	114	10.2357
(.((((.....)))).)))	chr13:111531997-111532222(-)$1	1	65	84	10.7046
((((((.....))..))))	chr15:41657646-41657865(+)$1	1	84	103	10.9843
(.((((.....)))).)..	chr4:10447814-10448031(-)$1	1	160	179	10.6529
((((((.....))))))).	chr1:242048517-242048743(+)$1	1	103	122	11.8305
((((((.....))))))))	chr13:23911819-23912040(-)$1	1	182	201	11.8943
((((((.....))))))).	chr16:88786410-88786632(-)$1	1	170	189	11.8305
(((.((.....))))).))	chr12:110779983-110780199(+)$1	1	156	175	10.8771
((..((.....))..))))	chr19:56179814-56180040(+)$1	1	195	214	10.2434
((((((.....))))))).	chr1:151204144-151204362(+)$1	1	149	168	11.1000
((.(((.....))).))))	chr3:17051954-17052168(+)$1	1	167	186	11.6334
(((.((.....))...)))	chr2:241682262-241682480(-)$1	1	118	137	10.7285
((((((.....))))))).	chr6:36463527-36463743(-)$1	1	145	164	11.1000
((.(((.....))).))).	chr1:224377448-224377670(+)$1	1	6	25	11.7233
((.(((.....))).))))	chr4:39918597-39918817(-)$1	1	191	210	11.6334
((((((.....))))))))	chrX:123185117-123185337(+)$1	1	132	151	11.8943
...(((.....)))..)))	chr12:57038912-57039131(-)$1	1	53	72	12.3111
..((((.....))))..))	chr4:187542491-187542708(-)$1	1	105	124	10.5640
((((((.....))))))..	chr1:2237362-2237585(+)$1	1	170	189	10.3174
.(.(((.....))).).))	chr1:16263985-16264209(+)$1	1	198	217	12.4151
((((((......)))))))	chr8:48883895-48884128(+)$1	1	118	137	7.1119
..((((.....))).)..)	chr6:31604935-31605147(+)$1	1	133	152	12.1290
((((((.....))))))).	chr17:76798392-76798613(-)$1	1	102	121	11.8883
((((((......)))))))	chr17:4575805-4576023(-)$1	1	30	49	7.1119
...(((.....))).))).	chr3:194174891-194175108(-)$1	1	106	125	12.6425
(((.((.....)).)))))	chr12:12630156-12630373(-)$1	1	4	23	10.2849
((((((.....))))))))	chr19:44351562-44351782(+)$1	1	168	187	9.7523
((((((.....))))))).	chr6:7226662-7226880(+)$1	1	40	59	11.1000
((((((.....))))))).	chr3:184041572-184041799(+)$1	1	7	26	11.1000
(..(((.....)))..)))	chr12:48465350-48465571(-)$1	1	144	163	12.2391
((.(((.....))).))).	chr8:90921828-90922047(+)$1	1	176	195	12.4538
(..(((.....)))..)))	chr10:121339347-121339566(-)$1	1	103	122	12.0376
.(((((.....))))).))	chr11:71716258-71716505(-)$1	1	181	200	10.1458
..((((.....))))..))	chr20:34241104-34241353(-)$1	1	90	109	10.6523
(..(((.....)))..)).	chr22:51043376-51043590(+)$1	1	157	176	11.8817
(.((((.....)))).)))	chrX:74295127-74295348(-)$1	1	152	171	11.1063
((.(((.....))))))..	chr2:111398550-111398775(-)$1	1	150	169	10.4386
((((((.....))))))))	chr1:11298449-11298673(-)$1	1	139	158	11.7897
((((((.....))))))..	chr10:5789120-5789362(+)$1	1	89	108	10.3174
.(((((.....)))))..)	chr13:23908523-23908745(-)$1	1	180	199	9.8553
(...((.....))....))	chr19:44500320-44500539(+)$1	1	93	112	10.8446
..((((.....))))....	chr6:52133835-52134060(-)$1	1	143	162	11.0919
...(((.....)))..)))	chr5:32380159-32380375(-)$1	1	110	129	12.1628
((.(((.....))).))).	chr5:5460483-5460703(+)$1	1	137	156	12.0711
(.((((.....)))).)))	chr19:59057143-59057363(+)$1	1	143	162	11.1063
((((((.....)).)))))	chr12:57033814-57034057(-)$1	1	52	71	9.8038
...(((.....)))...))	chr7:23358659-23358878(-)$1	1	150	169	12.7672

#PSSM
g : 0.23	c : 0.17	d : 0.14	f : 0.10	! : 0.08	" : 0.06	= : 0.04	# : 0.04	[ : 0.04	a : 0.02	e : 0.02	b : 0.02	
g : 0.23	c : 0.12	! : 0.12	f : 0.10	[ : 0.08	d : 0.08	" : 0.08	= : 0.04	# : 0.04	e : 0.04	a : 0.02	
g : 0.23	d : 0.19	[ : 0.14	! : 0.08	" : 0.08	f : 0.08	= : 0.04	c : 0.04	e : 0.04	a : 0.02	# : 0.02	
c : 0.31	g : 0.23	d : 0.17	f : 0.08	[ : 0.06	= : 0.04	e : 0.04	! : 0.02	" : 0.02	
c : 0.31	g : 0.21	d : 0.17	b : 0.14	f : 0.06	= : 0.04	e : 0.04	
c : 0.31	g : 0.21	d : 0.17	b : 0.14	f : 0.06	= : 0.04	e : 0.04	
n : 0.95	o : 0.04	
n : 0.95	o : 0.04	
n : 0.95	o : 0.04	
n : 0.95	o : 0.04	
n : 0.95	o : 0.04	
c : 0.31	d : 0.17	g : 0.17	b : 0.14	f : 0.06	= : 0.04	o : 0.04	e : 0.04	
c : 0.31	g : 0.21	d : 0.17	b : 0.14	f : 0.06	= : 0.04	e : 0.04	
c : 0.34	g : 0.21	d : 0.17	f : 0.06	2 : 0.04	= : 0.04	] : 0.04	e : 0.04	3 : 0.02	4 : 0.02	
g : 0.21	d : 0.17	] : 0.17	2 : 0.14	f : 0.08	c : 0.06	= : 0.04	3 : 0.04	e : 0.04	4 : 0.02	
g : 0.23	c : 0.14	2 : 0.14	] : 0.10	f : 0.08	d : 0.06	= : 0.04	3 : 0.04	a : 0.04	e : 0.04	4 : 0.04	
g : 0.23	d : 0.17	c : 0.17	f : 0.10	2 : 0.08	] : 0.06	= : 0.04	4 : 0.04	a : 0.02	e : 0.02	b : 0.02	3 : 0.02	
g : 0.25	d : 0.21	c : 0.17	b : 0.08	2 : 0.06	f : 0.04	= : 0.04	e : 0.04	3 : 0.04	: : 0.02	4 : 0.02	
d : 0.21	: : 0.12	c : 0.10	g : 0.08	] : 0.08	3 : 0.08	b : 0.06	f : 0.04	= : 0.04	e : 0.04	a : 0.04	2 : 0.02	4 : 0.02	6 : 0.02	

#score	520.561958856398
#seq	47
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_CDS_m3_run2.txt

#BEAR
eee!!cccooooooccc22eee	chr2:54101433-54101673(-)$1	240	204	226	12.6312
eee!!cccooooooccceeeee	chr11:19191975-19192215(+)$1	240	125	147	12.6114
ggggg[bboooooobbgggggg	chr1:214816452-214816692(+)$1	240	140	162	12.6265
hhhhhhhhoooooohhhhhhhh	chr13:67800731-67800971(-)$1	240	165	187	12.1782
eeeeecccooooooccc22eee	chr11:94917483-94917723(-)$1	240	211	233	12.1746
"gggggggooooooggggggg3	chr20:47768143-47768383(-)$1	240	24	46	12.8129
!!ccc[cccnnnnnccc]ccc3	chr1:64038061-64038301(+)$1	240	58	80	8.7397
dddd[cccooooooccc]dddd	chr7:152346068-152346309(-)$1	241	135	157	12.2320
hhhhhhhhoooooohhhhhhhh	chr1:62907803-62908043(+)$1	240	207	229	12.1782
d[ffffffooooooffffff]d	chr12:102154933-102155173(-)$1	240	5	27	10.0182
e"""ddddoooooodddd22ee	chr5:43502387-43502627(-)$1	240	71	93	10.2865
iiiiiiooooooiiiiiiiiic	chr3:194140543-194140783(-)$1	240	3	25	10.2511
iiiiiiiiooooooiiiiiiii	chr2:242276784-242277024(+)$1	240	214	236	13.5202
========oooooo========	chr11:9812011-9812251(-)$1	240	193	215	13.0332
[eeeee[aooooooa]eeeeec	chr8:141561299-141561539(-)$1	240	149	171	11.5869
%gggggggooooooggggggg2	chr2:27263486-27263726(+)$1	240	22	44	11.9260
hhhhhhhhoooooohhhhhhhh	chr1:197112086-197112326(-)$1	240	21	43	12.1782
hhhhhhhhoooooohhhhhhhh	chr15:60747161-60747401(-)$1	240	114	136	12.1782
dddd[cccooooooccc]dddd	chr15:99251073-99251313(+)$1	240	44	66	12.2320
fffffcccooooooccc22fff	chr4:164049948-164050188(-)$1	240	119	141	11.3914
d####cccooooooccc]dddd	chr11:82959025-82959265(+)$1	240	185	207	12.0356
cc!!ddddoooooodddd]ccc	chr3:73006363-73006603(+)$1	240	210	232	11.2015
eeeee[bboooooobb]eeeee	chr11:10821615-10821865(-)$1	250	226	248	11.2012
eeeeecccooooooccc]eeee	chr11:46680895-46681135(+)$1	240	125	147	12.5203
ggggggg[aooooooagggggg	chr6:44219449-44219689(+)$1	240	208	230	12.0174
iiiiiiiiinnnnniiiiiiii	chr6:107361017-107361258(+)$1	241	107	129	9.3451
a[dddd[aooooooa]dddda3	chr2:102490032-102490272(+)$1	240	156	178	11.2067
===========lll========	chr14:73464796-73465036(-)$1	240	66	88	9.0079
ee!!cccbboooooobb]ccc2	chr1:165697120-165697363(-)$1	243	37	59	10.6613
hhhhhhhhoooooohhhhhhhh	chr6:7585949-7586189(+)$1	240	37	59	12.1782
gggggggannnnna]ggggggg	chr7:73096986-73097226(-)$1	240	18	40	8.9548
gccc[cccooooooccc]ccc]	chr21:26957895-26958135(-)$1	240	135	157	13.2101
gggg[cccooooooccc]gggg	chr12:46758071-46758311(-)$1	240	160	182	13.7868
gg!!ddddoooooodddd22gg	chr8:119122593-119122833(-)$1	240	11	33	11.1763
c!!ccc[bboooooobb]cccc	chr10:124921783-124922023(+)$1	240	2	24	10.7342
ffff!!bboooooobb]fffff	chr5:72798690-72798930(+)$1	240	207	229	10.5652
[dddd!!aooooooa22ddddg	chr19:38055997-38056237(-)$1	240	170	192	10.9270
gggggg[aooooooa]gggggg	chr14:102550943-102551191(-)$1	248	159	181	13.1526
[eeeee[aooooooaeeeeeee	chr11:9307995-9308235(-)$1	240	87	109	11.4439
iiiiiiiiooooooiiiiiiii	chr1:47716692-47716932(-)$1	240	189	211	13.5202
gg"""cccoooooocccggggg	chrX:13754635-13754875(+)$1	240	13	35	13.1504
bgggggggooooooggggggg]	chr5:110097337-110097577(+)$1	240	55	77	12.6851
eeee!!bboooooobbeeeee6	chr19:3976160-3976400(-)$1	240	45	67	10.7649
hhhhhhhhoooooohhhhhhhh	chr11:62348918-62349278(-)$1	360	273	295	12.1782
hhhhhhhhoooooohhhhhhhh	chr11:62348778-62349110(-)$1	332	105	127	12.1782
==========lll=========	chr12:12976113-12976353(+)$1	240	135	157	9.0558
fff!!cccooooooccc22fff	chr2:48033313-48033553(+)$1	240	195	217	12.0260
d[ddddbboooooobb]dddd]	chr11:62348556-62348975(-)$1	419	78	100	10.7974
hhhhhcccooooooccc]hhhh	chr8:125498221-125498461(+)$1	240	46	68	13.0079
dddd[cccooooooccc]dddd	chr11:18330416-18330656(-)$1	240	133	155	12.2320
ggggg[bboooooobbgggggg	chr3:41267075-41267315(+)$1	240	146	168	12.6265
ddddddddoooooodddd]ddd	chr12:57180929-57181171(+)$1	242	143	165	10.2306
cc[ccc[bboooooobb]ccc]	chr1:7724827-7725067(+)$1	240	18	40	10.7302
hhh[a[cccnnnnnccc]a]hh	chr6:99991312-99991552(-)$1	240	168	190	8.6354

#otherMatches

#Seq PSSM
UUUAAGUUAUAGAAAACGGAAA	chr2:54101433-54101673(-)$1	240	204	226	12.6312
AAUCAACUCUUUCAGGUAUUUA	chr11:19191975-19192215(+)$1	240	125	147	12.6114
CUGGAAGUAGCACGACUCCAGC	chr1:214816452-214816692(+)$1	240	140	162	12.6265
UACUGUGGGGGUAAUCACAGUG	chr13:67800731-67800971(-)$1	240	165	187	12.1782
GUGGAUAUGUAAAAAUGAUUCU	chr11:94917483-94917723(-)$1	240	211	233	12.1746
UUGCAUUUGCCAGAGAGUGUAU	chr20:47768143-47768383(-)$1	240	24	46	12.8129
AACAUGUAAUGCCUUUGAAUGA	chr1:64038061-64038301(+)$1	240	58	80	8.7397
ACUAGAAAGUAUGUUUUGUAGU	chr7:152346068-152346309(-)$1	241	135	157	12.2320
AGUAAAUUAAUGGAAAUUUACU	chr1:62907803-62908043(+)$1	240	207	229	12.1782
AUACUUUGAAUAUCCAGAGUUU	chr12:102154933-102155173(-)$1	240	5	27	10.0182
GGGAUGGAUCUGUUUUCAAAUC	chr5:43502387-43502627(-)$1	240	71	93	10.2865
GACAGUAUACCAGCUGUUAUUG	chr3:194140543-194140783(-)$1	240	3	25	10.2511
AUUUUAAUAUAAGAAUUAAGAU	chr2:242276784-242277024(+)$1	240	214	236	13.5202
UUAAGGUUUUCCUUAGUUUUAA	chr11:9812011-9812251(-)$1	240	193	215	13.0332
ACAGGCAGAGGCUCCGGCCUGG	chr8:141561299-141561539(-)$1	240	149	171	11.5869
AAGCUUUCAUCCCCGAAAGUUG	chr2:27263486-27263726(+)$1	240	22	44	11.9260
UGAAAUUUAUCAGAAAAUUUUA	chr1:197112086-197112326(-)$1	240	21	43	12.1782
AUUAUUUACCUUAUUAAAUAAU	chr15:60747161-60747401(-)$1	240	114	136	12.1782
UCAGGAUUGAGAAAAAUGCUGA	chr15:99251073-99251313(+)$1	240	44	66	12.2320
CAUUUUGGACCUUACUAUUAGG	chr4:164049948-164050188(-)$1	240	119	141	11.3914
ucuuuggacuugaauccuggcu	chr11:82959025-82959265(+)$1	240	185	207	12.0356
CCCGGGUUGCUAUUGACUAGGC	chr3:73006363-73006603(+)$1	240	210	232	11.2015
CAGGUAAGAGAAUGCUGACUUG	chr11:10821615-10821865(-)$1	250	226	248	11.2012
UCCCCACCAUCCCAGGUAGGGG	chr11:46680895-46681135(+)$1	240	125	147	12.5203
GGGGAGCACAAUUAGGGCUUCC	chr6:44219449-44219689(+)$1	240	208	230	12.0174
AUUAUAAAACACUUUUUUAUAA	chr6:107361017-107361258(+)$1	241	107	129	9.3451
GAUUUCUCCAUCUAGCGGAACA	chr2:102490032-102490272(+)$1	240	156	178	11.2067
UCUGAAAGUGGUUUCCAUUUUU	chr14:73464796-73465036(-)$1	240	66	88	9.0079
ACGAGCCGCCACCAAGCAGGCA	chr1:165697120-165697363(-)$1	243	37	59	10.6613
cgggaucucgcuccggaucucg	chr6:7585949-7586189(+)$1	240	37	59	12.1782
GAGGGCCCGGCGGGAGGCCCUU	chr7:73096986-73097226(-)$1	240	18	40	8.9548
auauguauaauaaaauaaaugu	chr21:26957895-26958135(-)$1	240	135	157	13.2101
UCUCAAAAGAAGAGUUUAGGGA	chr12:46758071-46758311(-)$1	240	160	182	13.7868
UCCUGAGUCUGGAUACUUUAGA	chr8:119122593-119122833(-)$1	240	11	33	11.1763
CAGUUGAGUAUUUGGACCCAAG	chr10:124921783-124922023(+)$1	240	2	24	10.7342
GUCUGACUAGUUUAAGGAGACU	chr5:72798690-72798930(+)$1	240	207	229	10.5652
UAAGGAAUGUGGAAAGGCCUUU	chr19:38055997-38056237(-)$1	240	170	192	10.9270
CACUUGGCAGUGAAGGUGAGUG	chr14:102550943-102551191(-)$1	248	159	181	13.1526
UAUGACAGGUUGAACGUCAUAG	chr11:9307995-9308235(-)$1	240	87	109	11.4439
AGGAGCCUACCACAAGGCUCCU	chr1:47716692-47716932(-)$1	240	189	211	13.5202
GAGAACUGCAGCCUCGGUCCAU	chrX:13754635-13754875(+)$1	240	13	35	13.1504
GGUGCUGUUAUAAUACAGUACA	chr5:110097337-110097577(+)$1	240	55	77	12.6851
GAGGCAGCAGACACGCCCUCUU	chr19:3976160-3976400(-)$1	240	45	67	10.7649
CAGCUGGCCAAAGCGCUAGCUG	chr11:62348918-62349278(-)$1	360	273	295	12.1782
CAGCUGGCCAAAGCGCUAGCUG	chr11:62348778-62349110(-)$1	332	105	127	12.1782
UCAAGGUAAAAUGUUUACUUUG	chr12:12976113-12976353(+)$1	240	135	157	9.0558
UUGUUUUUUUCCACAAAUUCGG	chr2:48033313-48033553(+)$1	240	195	217	12.0260
GUGGCCCUGAUGCAGGAGGUCU	chr11:62348556-62348975(-)$1	419	78	100	10.7974
GUGGAUGGCACUUAUCGUUCUA	chr8:125498221-125498461(+)$1	240	46	68	13.0079
UUACUCGAUCCUUCUUGUGUGA	chr11:18330416-18330656(-)$1	240	133	155	12.2320
CUAAAAUGGCAGUGCGUUUAGC	chr3:41267075-41267315(+)$1	240	146	168	12.6265
CUGGCAGACUACAUUUUGACUA	chr12:57180929-57181171(+)$1	242	143	165	10.2306
GUGGCCCAGCCCAGCCUCGGCA	chr1:7724827-7725067(+)$1	240	18	40	10.7302
GGACAGAUUUCAGUAAUGUCUU	chr6:99991312-99991552(-)$1	240	168	190	8.6354

#DB
(((..(((......)))..)))	chr2:54101433-54101673(-)$1	1	204	226	12.6312
(((..(((......))))))))	chr11:19191975-19192215(+)$1	1	125	147	12.6114
(((((.((......))))))))	chr1:214816452-214816692(+)$1	1	140	162	12.6265
((((((((......))))))))	chr13:67800731-67800971(-)$1	1	165	187	12.1782
((((((((......)))..)))	chr11:94917483-94917723(-)$1	1	211	233	12.1746
.(((((((......))))))).	chr20:47768143-47768383(-)$1	1	24	46	12.8129
..(((.(((.....))).))).	chr1:64038061-64038301(+)$1	1	58	80	8.7397
((((.(((......))).))))	chr7:152346068-152346309(-)$1	1	135	157	12.2320
((((((((......))))))))	chr1:62907803-62908043(+)$1	1	207	229	12.1782
(.((((((......)))))).)	chr12:102154933-102155173(-)$1	1	5	27	10.0182
(...((((......))))..))	chr5:43502387-43502627(-)$1	1	71	93	10.2865
((((((......)))))))))(	chr3:194140543-194140783(-)$1	1	3	25	10.2511
((((((((......))))))))	chr2:242276784-242277024(+)$1	1	214	236	13.5202
((((((((......))))))))	chr11:9812011-9812251(-)$1	1	193	215	13.0332
.(((((.(......).))))))	chr8:141561299-141561539(-)$1	1	149	171	11.5869
.(((((((......))))))).	chr2:27263486-27263726(+)$1	1	22	44	11.9260
((((((((......))))))))	chr1:197112086-197112326(-)$1	1	21	43	12.1782
((((((((......))))))))	chr15:60747161-60747401(-)$1	1	114	136	12.1782
((((.(((......))).))))	chr15:99251073-99251313(+)$1	1	44	66	12.2320
((((((((......)))..)))	chr4:164049948-164050188(-)$1	1	119	141	11.3914
(....(((......))).))))	chr11:82959025-82959265(+)$1	1	185	207	12.0356
((..((((......)))).)))	chr3:73006363-73006603(+)$1	1	210	232	11.2015
(((((.((......)).)))))	chr11:10821615-10821865(-)$1	1	226	248	11.2012
((((((((......))).))))	chr11:46680895-46681135(+)$1	1	125	147	12.5203
(((((((.(......)))))))	chr6:44219449-44219689(+)$1	1	208	230	12.0174
(((((((((.....))))))))	chr6:107361017-107361258(+)$1	1	107	129	9.3451
(.((((.(......).))))).	chr2:102490032-102490272(+)$1	1	156	178	11.2067
(((((((((((...))))))))	chr14:73464796-73465036(-)$1	1	66	88	9.0079
((..(((((......)).))).	chr1:165697120-165697363(-)$1	1	37	59	10.6613
((((((((......))))))))	chr6:7585949-7586189(+)$1	1	37	59	12.1782
((((((((.....).)))))))	chr7:73096986-73097226(-)$1	1	18	40	8.9548
((((.(((......))).))).	chr21:26957895-26958135(-)$1	1	135	157	13.2101
((((.(((......))).))))	chr12:46758071-46758311(-)$1	1	160	182	13.7868
((..((((......))))..))	chr8:119122593-119122833(-)$1	1	11	33	11.1763
(..(((.((......)).))))	chr10:124921783-124922023(+)$1	1	2	24	10.7342
((((..((......)).)))))	chr5:72798690-72798930(+)$1	1	207	229	10.5652
.((((..(......)..)))))	chr19:38055997-38056237(-)$1	1	170	192	10.9270
((((((.(......).))))))	chr14:102550943-102551191(-)$1	1	159	181	13.1526
.(((((.(......))))))))	chr11:9307995-9308235(-)$1	1	87	109	11.4439
((((((((......))))))))	chr1:47716692-47716932(-)$1	1	189	211	13.5202
((...(((......))))))))	chrX:13754635-13754875(+)$1	1	13	35	13.1504
((((((((......))))))).	chr5:110097337-110097577(+)$1	1	55	77	12.6851
((((..((......))))))).	chr19:3976160-3976400(-)$1	1	45	67	10.7649
((((((((......))))))))	chr11:62348918-62349278(-)$1	1	273	295	12.1782
((((((((......))))))))	chr11:62348778-62349110(-)$1	1	105	127	12.1782
((((((((((...)))))))))	chr12:12976113-12976353(+)$1	1	135	157	9.0558
(((..(((......)))..)))	chr2:48033313-48033553(+)$1	1	195	217	12.0260
(.((((((......)).)))).	chr11:62348556-62348975(-)$1	1	78	100	10.7974
((((((((......))).))))	chr8:125498221-125498461(+)$1	1	46	68	13.0079
((((.(((......))).))))	chr11:18330416-18330656(-)$1	1	133	155	12.2320
(((((.((......))))))))	chr3:41267075-41267315(+)$1	1	146	168	12.6265
((((((((......)))).)))	chr12:57180929-57181171(+)$1	1	143	165	10.2306
((.(((.((......)).))).	chr1:7724827-7725067(+)$1	1	18	40	10.7302
(((.(.(((.....))).).))	chr6:99991312-99991552(-)$1	1	168	190	8.6354

#PSSM
g : 0.16	h : 0.16	e : 0.14	d : 0.12	i : 0.07	= : 0.05	[ : 0.05	f : 0.05	c : 0.05	" : 0.01	! : 0.01	% : 0.01	a : 0.01	b : 0.01	
g : 0.20	e : 0.16	h : 0.16	d : 0.09	i : 0.07	[ : 0.05	= : 0.05	f : 0.05	c : 0.05	! : 0.03	" : 0.01	# : 0.01	
g : 0.16	h : 0.16	e : 0.14	d : 0.12	f : 0.07	i : 0.07	! : 0.07	= : 0.05	c : 0.03	" : 0.03	# : 0.01	[ : 0.01	
g : 0.16	h : 0.14	d : 0.12	! : 0.11	e : 0.11	c : 0.07	i : 0.07	f : 0.05	= : 0.05	" : 0.03	# : 0.01	[ : 0.01	
g : 0.14	h : 0.14	d : 0.12	! : 0.09	e : 0.09	[ : 0.09	c : 0.07	i : 0.07	= : 0.05	f : 0.03	# : 0.01	" : 0.01	a : 0.01	
c : 0.31	h : 0.12	g : 0.11	d : 0.11	[ : 0.09	i : 0.07	= : 0.05	! : 0.05	e : 0.03	f : 0.01	
c : 0.31	h : 0.12	b : 0.11	[ : 0.11	g : 0.09	d : 0.07	i : 0.05	= : 0.05	f : 0.01	o : 0.01	! : 0.01	
c : 0.29	b : 0.16	h : 0.12	a : 0.11	d : 0.07	g : 0.05	i : 0.05	= : 0.05	f : 0.01	o : 0.01	[ : 0.01	
o : 0.81	b : 0.05	c : 0.03	= : 0.03	a : 0.01	i : 0.01	n : 0.01	
o : 0.88	n : 0.07	= : 0.03	
o : 0.88	n : 0.07	= : 0.01	l : 0.01	
o : 0.88	n : 0.07	l : 0.03	
o : 0.87	n : 0.07	l : 0.03	i : 0.01	
o : 0.87	n : 0.05	i : 0.01	l : 0.01	a : 0.01	= : 0.01	
c : 0.29	h : 0.12	b : 0.11	a : 0.09	d : 0.07	i : 0.07	o : 0.07	g : 0.05	= : 0.05	f : 0.01	] : 0.01	
c : 0.29	b : 0.16	h : 0.12	g : 0.07	d : 0.07	i : 0.07	= : 0.05	] : 0.05	f : 0.01	a : 0.01	2 : 0.01	e : 0.01	
c : 0.29	g : 0.14	h : 0.12	d : 0.09	i : 0.07	= : 0.05	e : 0.05	] : 0.05	b : 0.05	f : 0.01	2 : 0.01	
] : 0.24	g : 0.16	h : 0.12	d : 0.12	e : 0.09	2 : 0.07	i : 0.07	= : 0.05	f : 0.03	
g : 0.18	h : 0.14	d : 0.12	2 : 0.11	e : 0.11	c : 0.09	i : 0.07	= : 0.05	f : 0.03	] : 0.03	a : 0.01	
g : 0.18	e : 0.14	h : 0.14	d : 0.14	c : 0.11	f : 0.07	i : 0.07	= : 0.05	2 : 0.03	] : 0.01	
g : 0.20	e : 0.16	h : 0.16	d : 0.12	c : 0.11	i : 0.07	= : 0.05	f : 0.05	] : 0.01	a : 0.01	
g : 0.16	h : 0.16	e : 0.12	d : 0.11	c : 0.07	] : 0.07	3 : 0.05	i : 0.05	= : 0.05	f : 0.05	2 : 0.03	6 : 0.01	

#score	625.934263987148
#seq	54
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_UTR_m2_run2.txt

#BEAR
[ggggggg[ccc!!ddddllldddd]ccc]ggggggg]bb	chr16:743277-743657(-)$1	380	333	373	14.9369
dddd[eeeee####cccnnnnnccc4444eeeee]dddd3	chr4:103717659-103718070(-)$1	411	286	326	12.9143
"ccc[dddd%%%%%%ddddllldddd]ddddccc333ggg	chr19:19617055-19617514(+)$1	459	182	222	11.9693
ccc!!dddd!!bb!!cccmmmmccc]bb22dddd22ccc]	chr11:66394309-66394765(+)$1	456	123	163	12.2439
dddd!!bb####ddddoooooodddd22bb22dddd333c	chr5:137087882-137088342(-)$1	460	183	223	13.1331
a[a"""ggggggg[ddddmmmmdddd]gggggggaa]===	chr1:162498062-162498321(+)$1	259	162	202	16.3256
ggggggg[bb!!a!!ddddllldddd22a22bbggggggg	chr22:29184175-29184600(+)$1	425	69	109	15.3842
ggggggg"""ccc!!cccmmmmccc22ccc]ggggggg]d	chr3:120048421-120048764(-)$1	343	4	44	14.7942
eeeegggggggcccddddnnnnndddd22ccc]ggggggg	chr14:104164750-104165039(-)$1	289	112	152	13.6935
c[bb[============aooooooa]============]b	chr6:121770014-121770274(+)$1	260	73	113	13.6771
""iiiiiiiii"""ddddooooooddddiiiiiiiii666	chr7:107401655-107402063(+)$1	408	80	120	14.4143
:bb####===========mmmm===========333bb:g	chr15:65738218-65738501(-)$1	283	73	113	11.3244
ggggggbb[a$$$$$ddddllldddda]bb]gggggggee	chr5:172742739-172743112(-)$1	373	144	184	14.2074
ggg[a[eeeee"""ddddnnnnndddd22eeeee]a]ggg	chr6:31500524-31500788(-)$1	264	176	216	15.7308
cccccc[ccc####cccnnnnnccc4444ccc]ccc]ccc	chr2:171822808-171823186(+)$1	378	202	242	14.5799
#a[ffffff[ccc[ddddmmmmdddd]cccffffffa444	chr12:69053907-69054374(+)$1	467	192	232	13.8686
hhhh"""eeeee!!ddddmmmmdddd22eeeeehhhhhhh	chr19:7084666-7085067(+)$1	401	43	83	14.6571
$$$$$ffffff####cccmmmmccc333ffffff4444dd	chr13:107144127-107144401(-)$1	274	202	242	13.3453
eeee[eeeee[bba[cccmmmmccc]a]bb]eeeee]eee	chr10:72181720-72182161(+)$1	441	21	61	11.9821
!!ccceeeee"""eeeeennnnneeeee333eeeee]ccc	chr12:56668685-56668935(-)$1	250	101	141	12.8513
ggggg####ccc!!cccmmmmccc22ccc4444ggggggg	chr20:2128676-2128965(+)$1	289	27	67	13.2854
eee[dddddddd[ddddoooooodddddddd]dddd]eee	chr5:176730818-176731138(+)$1	320	154	194	11.6884
cc####dddd[eeeee[ammmma]eeeee]dddd333ccc	chr16:89627885-89628259(+)$1	374	170	210	12.0143
b[==========!!ddddoooooodddd22==========	chr3:196662863-196663158(-)$1	295	231	271	16.1435
ebbccc[gggggggddddmmmmdddd4444gggggggccc	chr14:93406807-93407074(-)$1	267	119	159	15.3447
c[ccc[ffffff!!ddddmmmmdddd22ffffffccc]cc	chr10:70742911-70743208(+)$1	297	226	266	15.1892
=======ccc!!ccc!!aooooooa22ccc]ccc333===	chr12:53806265-53806586(+)$1	321	114	154	14.4984
[ggggggg[bb####cccmmmmccc333bbggggggg22c	chr5:148732844-148733151(+)$1	307	245	285	15.2092
ggggggg[bb####eeeeellleeeee4444bbggggggg	chr1:153634056-153634343(+)$1	287	63	103	13.8977
hhhhh"""a!!bb[ddddmmmmdddd22bb22a4444hhh	chr16:18805820-18806104(-)$1	284	63	103	14.0085
=====[a[dddd!!ddddmmmmdddddddd]a]=======	chrX:24003753-24004174(-)$1	421	342	382	15.9527
eee$$$$$eeeee[ddddooooooddddeeeee22eeeee	chrX:100646642-100646910(+)$1	268	120	160	11.7466
ggg!!ddddddddddddnnnnndddd]dddd]dddd22gg	chr6:32944479-32944795(+)$1	316	228	268	12.0327
========[ccc"""cccmmmmccc4444ccc]=======	chr2:206862521-206862786(-)$1	265	110	150	16.6356
$$$ffffff$$$$$ddddmmmmdddd4444ffffff333=	chr6:122765759-122765991(-)$1	232	181	221	15.1039
eeebbdddd####eeeeennnnneeeee333dddd333bb	chr19:1439917-1440352(+)$1	435	154	194	11.1957
gg$$$$$dddd[ddddoooooodddd]dddd4444ggggg	chr13:114295221-114295623(+)$1	402	272	312	13.0011
eee"""ffffff[eeeeemmmmeeeee22ffffff4444e	chr12:54062831-54063223(-)$1	392	185	225	12.1522
ggg%%%%%%ccc!!ddddlllddddccc333ggggggg]e	chr6:7288458-7288729(-)$1	271	205	245	12.6814
ccceeeee%%%%%%cccooooooccc4444eeeee]cccg	chr6:34213616-34213937(+)$1	321	243	283	11.4970
ggg"""dddd####ddddmmmmdddd4444ddddgggggg	chr10:60155135-60155423(+)$1	288	196	236	17.6368
""a!!ggggggg!!a[bbmmmmbb]a22ggggggg22a22	chr5:149823704-149823970(-)$1	266	65	105	13.1034
"ccc"""ffffff[ddddlllddddffffff333ccc333	chr10:124924462-124924762(+)$1	300	24	64	13.1652
ffffffeeeee"""cccooooooccc333eeeee22ffff	chr3:38531428-38531781(+)$1	353	30	70	13.9507
ggg[bb"""ccc!!cccnnnnnccc22cccbb]ggggggg	chr6:27099996-27100468(-)$1	472	215	255	13.3673
eee[ccc[dddd!!cccooooooccc22dddd]ccc]eee	chr12:24968649-24968927(-)$1	278	94	134	13.4942
[hhhhhhhh!!cccddddmmmmdddd22ccc333hhhhhh	chr17:41154589-41154861(+)$1	272	108	148	13.3474
fff[a[eeeee!!a[ddddllldddd]a]eeeeeafffff	chr11:46699847-46700182(-)$1	335	163	203	13.9195
hhhh::eeeee"""ddddmmmmdddd333eeeee:=====	chr16:30078454-30078705(+)$1	251	47	87	14.0013
:iiiiiiiii[a!!ddddmmmmdddd22a22iiiiiiiii	chr22:29190954-29191260(-)$1	306	17	57	16.4814
ggg[eeeee[ccc[ddddmmmmdddd]ccceeeee333gg	chr4:6643386-6643733(+)$1	347	253	293	15.8463
"""bb[gggggggbb!!ccclllccc333bb]ggggggg3	chr10:62554043-62554391(+)$1	348	234	274	11.6395
dd[ggggggg[bbeeeeellleeeee4444bbggggggg]	chr9:137024826-137025091(+)$1	265	43	83	12.3774
gggg$$$$$bb[ddddoooooodddd]bb]gggggggccc	chr1:214526181-214526410(-)$1	229	187	227	13.1610

#otherMatches

#Seq PSSM
GUGGGUCUCCUCAGGUGGAGUCUGCAGAGUGGACCCAGCC	chr16:743277-743657(-)$1	380	333	373	14.9369
AUUGAUUUAUUUUUCUUCAAUAAAGUUGCAUAAACCAAUG	chr4:103717659-103718070(-)$1	411	286	326	12.9143
UGGACGCAAUCUUAAGCCACCCUGGCCUUGCUCCUGGGAG	chr19:19617055-19617514(+)$1	459	182	222	11.9693
GGCUCCCUUUUAUUUUUGUGCGCGAUAUUUAAGGUCGUCU	chr11:66394309-66394765(+)$1	456	123	163	12.2439
CCUGCUAGUUGCGUGUUGAAUUAUAUCCCUUACAGGCAAA	chr5:137087882-137088342(-)$1	460	183	223	13.1331
GUGAAACCAGAUUAAAUAUCUAUAUUCAGUUUGGCCuaau	chr1:162498062-162498321(+)$1	259	162	202	16.3256
UGUUUGAUGGGACCAACUUGUAAAGUAUGAGCCUUAAAUA	chr22:29184175-29184600(+)$1	425	69	109	15.3842
UAUUAGAAAUUACCAAAUUUUUAUUAAGUACuuuaauaug	chr3:120048421-120048764(-)$1	343	4	44	14.7942
GGUCUGGGGACAGGCCCGCUUGCUGGGUACCUGGUCCCCA	chr14:104164750-104165039(-)$1	289	112	152	13.6935
AUUUUUGUGGUGUGGGCCAAUAUGGUGUUUACAUUAUAUA	chr6:121770014-121770274(+)$1	260	73	113	13.6771
AUAAAAUUUUGAAUUAAGAGAACCCUUGUAGAGUUUUUAA	chr7:107401655-107402063(+)$1	408	80	120	14.4143
AGUUUUUUUUUUUCCUUUAAGAAAAGGAAAAAGUACACAU	chr15:65738218-65738501(-)$1	283	73	113	11.3244
CCAAUCCCAGUCUUUCAUGAUCCAUGCCGGCGGUUGGGUG	chr5:172742739-172743112(-)$1	373	144	184	14.2074
ACAACGAGAAGAACCGGAAGCUCUUUGACCUUCUGGAUGU	chr6:31500524-31500788(-)$1	264	176	216	15.7308
AAUACUCACACGCAACAUUUCUUGUACUUUGUAAGUCGUU	chr2:171822808-171823186(+)$1	378	202	242	14.5799
UGUAUGCAUUAAUGUUUGGAUGUAAAGAUUGUGUGUCUAU	chr12:69053907-69054374(+)$1	467	192	232	13.8686
GUUAACUCACUCUAGAGAGAAAUCUUGUGAGUGUAAUCUG	chr19:7084666-7085067(+)$1	401	43	83	14.6571
AAAUCUGACCUAAAAGUUGAAAAGCCAAAGGUCAAACAGG	chr13:107144127-107144401(-)$1	274	202	242	13.3453
CUGUAUUUCUGUAGAGCUAAGCAGCCCUUAGAGGAAAACA	chr10:72181720-72182161(+)$1	441	21	61	11.9821
AGCAGCCAUGAACGGGCUGGCAGGGCCUCUCCAUGGACUG	chr12:56668685-56668935(-)$1	250	101	141	12.8513
CCGUUGCCUGCCCGAGGGCCCCCUAAGGUUAUAGACGGUA	chr20:2128676-2128965(+)$1	289	27	67	13.2854
CUUCGGCCGGGACGAUGGUGAAGUAUUUCCUGGGCCAGAG	chr5:176730818-176731138(+)$1	320	154	194	11.6884
CCACGGAGUCCCUGCAGGCCAACGUGCAGCGGCUGAAGGA	chr16:89627885-89628259(+)$1	374	170	210	12.0143
AAGUUUAUUCUUUUCAUUUUCAGUGAUGUUGGGAAUGGAC	chr3:196662863-196663158(-)$1	295	231	271	16.1435
CGCGGGAGCCUCGGCAUGACACCAUGGAGAUCGGGGCCCU	chr14:93406807-93407074(-)$1	267	119	159	15.3447
AGAUGUAGUAUGUUUGAUGUGGAUUACCUAUACUUAUGUU	chr10:70742911-70743208(+)$1	297	226	266	15.1892
UCCCUUAACUUUUCCUUGUAUGUUCUUGGGUGGUUCCUAA	chr12:53806265-53806586(+)$1	321	114	154	14.4984
caggcaagugcaccaccaugacuggcuaguuuuguuuuuu	chr5:148732844-148733151(+)$1	307	245	285	15.2092
GGUUACAUGGGCCUGGACAGCAUGUCCUCUACCUGUGACU	chr1:153634056-153634343(+)$1	287	63	103	13.8977
gaaguuuugauauUAAAUUCUUGUUUUCAUUGCUAGUACU	chr16:18805820-18806104(-)$1	284	63	103	14.0085
UAGAUAUGACUUCAUGACCCUAGUCAGGGUGACAUCUGGG	chrX:24003753-24004174(-)$1	421	342	382	15.9527
AAGCAGAGUGGCUAUGGUGGGCAAACUAAGCCGAUUUUCC	chrX:100646642-100646910(+)$1	268	120	160	11.7466
GUCAAGGUACCCACUGCAUGGGGCAGAUGGGAUGCUCAGG	chr6:32944479-32944795(+)$1	316	228	268	12.0327
UUACACACAUGCAAAAAUAUACAUUGGGGGCACGUGUGUG	chr2:206862521-206862786(-)$1	265	110	150	16.6356
UGAUGUGUUGCCUGGCAGGAUACUGCAAAGAACAUGGUUU	chr6:122765759-122765991(-)$1	232	181	221	15.1039
CCUGCGGCGGAAGCAGCACUCCCUGCUGAAGCGCCUGCGC	chr19:1439917-1440352(+)$1	435	154	194	11.1957
UGUUUUAACAAUUUUUUAACUCAAAAUUUGUCAAUCAUUU	chr13:114295221-114295623(+)$1	402	272	312	13.0011
GACACAGCAGCCAAGUUCAUUGGAGCUGGGGCUGCCACAG	chr12:54062831-54063223(-)$1	392	185	225	12.1522
UUGAUUUUGAGAAAGCUCUAUGAGCUCUAAGUAACUGCAU	chr6:7288458-7288729(-)$1	271	205	245	12.6814
GGGGGCCCAAAUCGACCAUAAAGGGUGUAGGGGCCACCUC	chr6:34213616-34213937(+)$1	321	243	283	11.4970
ACAUAUAAGUGAUUGCUGGUUUUAGUUGCAACUUUGUAUA	chr10:60155135-60155423(+)$1	288	196	236	17.6368
CCCAUCCCCUCUGACAGCACUCGCAGGAAGGGGGGUCGCC	chr5:149823704-149823970(-)$1	266	65	105	13.1034
UUUUUUUUUAAGUAUUUCAGUGAAAACUUGGUGUAAGUCU	chr10:124924462-124924762(+)$1	300	24	64	13.1652
CUCGCUGCUUCAAUCUGUGGAAUCAGCCAGGAGCCCAGUG	chr3:38531428-38531781(+)$1	353	30	70	13.9507
AGGGAGAUCCAGACGGCCGUGCGCCUGCUGCUGCCUGGGG	chr6:27099996-27100468(-)$1	472	215	255	13.3673
UAACUAAAUUUCUAUUCCUAUGAGAAAUGAGAAUUAUUUA	chr12:24968649-24968927(-)$1	278	94	134	13.4942
UGGAUAUCCCCUUGGACAAAACUGUCGUCAAUAAGGAUGU	chr17:41154589-41154861(+)$1	272	108	148	13.3474
GAGUGACAGGGCUGGAGACUGUGUCUGCUUUCUGCCUCCU	chr11:46699847-46700182(-)$1	335	163	203	13.9195
GAUGAUGGGAAACCCUAGCUAACUAGUCCUUCCCCUCUGU	chr16:30078454-30078705(+)$1	251	47	87	14.0013
AUGUCCUCUCUGCUUGGUGUAAACCAUUCUUGGGAGGACA	chr22:29190954-29191260(-)$1	306	17	57	16.4814
UGUUUGGGAAGUAAUUUUGUUUGAAAAUGCUCUCACAUAC	chr4:6643386-6643733(+)$1	347	253	293	15.8463
AUAGGAGUUUUCAGUAACUUAAAAAGCUAACAUGAGAGCA	chr10:62554043-62554391(+)$1	348	234	274	11.6395
GAGCUCCGCGUGCCAGCCUGUGGCUGCCCUGCUGUGGGGG	chr9:137024826-137025091(+)$1	265	43	83	12.3774
UAUUCUGCUGCUGUGUUUUAUUAUAUUGCCAAUGGUUUUG	chr1:214526181-214526410(-)$1	229	187	227	13.1610

#DB
.(((((((.(((..((((...)))).))).))))))).))	chr16:743277-743657(-)$1	1	333	373	14.9369
((((.(((((....(((.....)))....))))).)))).	chr4:103717659-103718070(-)$1	1	286	326	12.9143
.(((.((((......((((...)))).)))))))...)))	chr19:19617055-19617514(+)$1	1	182	222	11.9693
(((..((((..((..(((....))).))..))))..))).	chr11:66394309-66394765(+)$1	1	123	163	12.2439
((((..((....((((......))))..))..))))...)	chr5:137087882-137088342(-)$1	1	183	223	13.1331
(.(...(((((((.((((....)))).))))))))).)))	chr1:162498062-162498321(+)$1	1	162	202	16.3256
(((((((.((..(..((((...))))..)..)))))))))	chr22:29184175-29184600(+)$1	1	69	109	15.3842
(((((((...(((..(((....)))..))).))))))).)	chr3:120048421-120048764(-)$1	1	4	44	14.7942
((((((((((((((((((.....))))..))).)))))))	chr14:104164750-104165039(-)$1	1	112	152	13.6935
(.((.(((((((((((((......).)))))))))))).)	chr6:121770014-121770274(+)$1	1	73	113	13.6771
..(((((((((...((((......)))))))))))))...	chr7:107401655-107402063(+)$1	1	80	120	14.4143
.((....(((((((((((....)))))))))))...)).(	chr15:65738218-65738501(-)$1	1	73	113	11.3244
((((((((.(.....((((...))))).)).)))))))))	chr5:172742739-172743112(-)$1	1	144	184	14.2074
(((.(.(((((...((((.....))))..))))).).)))	chr6:31500524-31500788(-)$1	1	176	216	15.7308
((((((.(((....(((.....)))....))).))).)))	chr2:171822808-171823186(+)$1	1	202	242	14.5799
.(.((((((.(((.((((....)))).))))))))))...	chr12:69053907-69054374(+)$1	1	192	232	13.8686
((((...(((((..((((....))))..))))))))))))	chr19:7084666-7085067(+)$1	1	43	83	14.6571
.....((((((....(((....)))...))))))....))	chr13:107144127-107144401(-)$1	1	202	242	13.3453
((((.(((((.(((.(((....))).).)).))))).)))	chr10:72181720-72182161(+)$1	1	21	61	11.9821
..((((((((...(((((.....)))))...))))).)))	chr12:56668685-56668935(-)$1	1	101	141	12.8513
(((((....(((..(((....)))..)))....)))))))	chr20:2128676-2128965(+)$1	1	27	67	13.2854
(((.((((((((.((((......)))))))).)))).)))	chr5:176730818-176731138(+)$1	1	154	194	11.6884
((....((((.(((((.(....).))))).))))...)))	chr16:89627885-89628259(+)$1	1	170	210	12.0143
(.((((((((((..((((......))))..))))))))))	chr3:196662863-196663158(-)$1	1	231	271	16.1435
)))(((.(((((((((((....))))....))))))))))	chr14:93406807-93407074(-)$1	1	119	159	15.3447
(.(((.((((((..((((....))))..))))))))).))	chr10:70742911-70743208(+)$1	1	226	266	15.1892
((((((((((..(((..(......)..))).)))...)))	chr12:53806265-53806586(+)$1	1	114	154	14.4984
.(((((((.((....(((....)))...)))))))))..)	chr5:148732844-148733151(+)$1	1	245	285	15.2092
(((((((.((....(((((...)))))....)))))))))	chr1:153634056-153634343(+)$1	1	63	103	13.8977
(((((...(..((.((((....))))..))..)....)))	chr16:18805820-18806104(-)$1	1	63	103	14.0085
(((((.(.((((..((((....)))))))).).)))))))	chrX:24003753-24004174(-)$1	1	342	382	15.9527
(((.....(((((.((((......)))))))))..)))))	chrX:100646642-100646910(+)$1	1	120	160	11.7466
(((..((((((((((((.....)))).)))).))))..))	chr6:32944479-32944795(+)$1	1	228	268	12.0327
((((((((.(((...(((....)))....))).)))))))	chr2:206862521-206862786(-)$1	1	110	150	16.6356
...((((((.....((((....))))....))))))...)	chr6:122765759-122765991(-)$1	1	181	221	15.1039
(((((((((....(((((.....)))))...))))...))	chr19:1439917-1440352(+)$1	1	154	194	11.1957
((.....((((.((((......)))).))))....)))))	chr13:114295221-114295623(+)$1	1	272	312	13.0011
(((...((((((.(((((....)))))..))))))....)	chr12:54062831-54063223(-)$1	1	185	225	12.1522
(((......(((..((((...)))))))...))))))).)	chr6:7288458-7288729(-)$1	1	205	245	12.6814
((((((((......(((......)))....))))).)))(	chr6:34213616-34213937(+)$1	1	243	283	11.4970
(((...((((....((((....))))....))))))))))	chr10:60155135-60155423(+)$1	1	196	236	17.6368
..(..(((((((..(.((....)).)..)))))))..)..	chr5:149823704-149823970(-)$1	1	65	105	13.1034
.(((...((((((.((((...))))))))))...)))...	chr10:124924462-124924762(+)$1	1	24	64	13.1652
(((((((((((...(((......)))...)))))..))))	chr3:38531428-38531781(+)$1	1	30	70	13.9507
(((.((...(((..(((.....)))..))))).)))))))	chr6:27099996-27100468(-)$1	1	215	255	13.3673
(((.(((.((((..(((......)))..)))).))).)))	chr12:24968649-24968927(-)$1	1	94	134	13.4942
.((((((((..(((((((....))))..)))...))))))	chr17:41154589-41154861(+)$1	1	108	148	13.3474
(((.(.(((((..(.((((...)))).).)))))))))))	chr11:46699847-46700182(-)$1	1	163	203	13.9195
))))..(((((...((((....))))...))))).(((((	chr16:30078454-30078705(+)$1	1	47	87	14.0013
.(((((((((.(..((((....))))..)..)))))))))	chr22:29190954-29191260(-)$1	1	17	57	16.4814
(((.(((((.(((.((((....)))).))))))))...))	chr4:6643386-6643733(+)$1	1	253	293	15.8463
...((.(((((((((..(((...)))...)).))))))).	chr10:62554043-62554391(+)$1	1	234	274	11.6395
((.(((((((.(((((((...)))))....))))))))).	chr9:137024826-137025091(+)$1	1	43	83	12.3774
((((.....((.((((......)))).)).))))))))))	chr1:214526181-214526410(-)$1	1	187	227	13.1610

#PSSM
g : 0.24	e : 0.14	c : 0.11	" : 0.09	[ : 0.05	d : 0.05	h : 0.05	= : 0.05	: : 0.03	$ : 0.03	f : 0.03	a : 0.01	# : 0.01	! : 0.01	b : 0.01	
g : 0.27	e : 0.12	c : 0.11	[ : 0.07	h : 0.07	d : 0.05	" : 0.05	= : 0.05	b : 0.03	$ : 0.03	f : 0.03	a : 0.01	! : 0.01	i : 0.01	
g : 0.25	c : 0.12	e : 0.12	h : 0.07	= : 0.07	b : 0.05	$ : 0.05	d : 0.03	a : 0.03	i : 0.03	[ : 0.03	f : 0.03	# : 0.01	" : 0.01	
g : 0.16	c : 0.11	[ : 0.11	h : 0.07	= : 0.07	! : 0.05	" : 0.05	e : 0.05	b : 0.05	f : 0.05	$ : 0.05	d : 0.03	i : 0.03	# : 0.03	% : 0.01	
g : 0.16	" : 0.09	c : 0.09	[ : 0.07	! : 0.07	$ : 0.07	= : 0.07	f : 0.05	b : 0.05	i : 0.03	# : 0.03	a : 0.03	h : 0.03	e : 0.03	d : 0.01	% : 0.01	: : 0.01	
g : 0.16	" : 0.11	e : 0.09	d : 0.09	[ : 0.09	= : 0.07	f : 0.07	# : 0.05	c : 0.05	$ : 0.05	i : 0.03	! : 0.01	% : 0.01	b : 0.01	h : 0.01	: : 0.01	
g : 0.18	e : 0.16	d : 0.12	f : 0.09	= : 0.07	" : 0.07	$ : 0.05	b : 0.03	i : 0.03	# : 0.03	[ : 0.03	a : 0.01	% : 0.01	c : 0.01	h : 0.01	
e : 0.18	g : 0.14	d : 0.14	f : 0.11	[ : 0.07	= : 0.07	" : 0.05	b : 0.03	i : 0.03	c : 0.03	$ : 0.03	# : 0.01	% : 0.01	h : 0.01	
e : 0.18	d : 0.18	g : 0.11	f : 0.11	[ : 0.07	= : 0.05	# : 0.03	b : 0.03	" : 0.03	i : 0.03	c : 0.03	% : 0.03	a : 0.01	h : 0.01	$ : 0.01	
e : 0.16	c : 0.12	d : 0.12	g : 0.11	b : 0.07	f : 0.07	! : 0.05	= : 0.05	% : 0.03	# : 0.03	i : 0.03	[ : 0.03	" : 0.01	a : 0.01	$ : 0.01	
c : 0.14	# : 0.11	e : 0.11	! : 0.09	g : 0.09	d : 0.09	f : 0.07	[ : 0.07	= : 0.05	% : 0.03	$ : 0.03	b : 0.03	i : 0.01	" : 0.01	
c : 0.18	# : 0.14	" : 0.09	b : 0.07	g : 0.07	d : 0.07	! : 0.05	= : 0.05	e : 0.05	f : 0.05	% : 0.03	$ : 0.03	[ : 0.03	a : 0.01	
! : 0.22	# : 0.12	c : 0.11	" : 0.11	b : 0.07	d : 0.07	g : 0.05	% : 0.03	= : 0.03	$ : 0.03	[ : 0.03	e : 0.03	a : 0.01	f : 0.01	
! : 0.25	# : 0.11	[ : 0.11	d : 0.09	" : 0.09	e : 0.09	c : 0.05	% : 0.03	= : 0.03	$ : 0.03	a : 0.03	g : 0.01	b : 0.01	
d : 0.48	c : 0.14	e : 0.11	! : 0.05	= : 0.03	# : 0.03	[ : 0.03	% : 0.01	$ : 0.01	" : 0.01	a : 0.01	b : 0.01	
d : 0.55	c : 0.24	e : 0.11	= : 0.03	! : 0.03	[ : 0.01	
d : 0.49	c : 0.24	e : 0.09	o : 0.05	= : 0.03	! : 0.03	[ : 0.01	b : 0.01	
d : 0.46	c : 0.12	o : 0.12	e : 0.09	n : 0.07	a : 0.05	= : 0.01	m : 0.01	b : 0.01	
m : 0.44	o : 0.22	n : 0.14	l : 0.07	d : 0.07	e : 0.01	c : 0.01	
m : 0.44	o : 0.22	l : 0.16	n : 0.14	c : 0.01	
m : 0.44	o : 0.22	l : 0.18	n : 0.14	
m : 0.42	o : 0.22	n : 0.14	l : 0.11	d : 0.05	c : 0.01	e : 0.01	
d : 0.44	c : 0.18	o : 0.16	n : 0.07	e : 0.05	= : 0.01	a : 0.01	b : 0.01	l : 0.01	
d : 0.49	c : 0.25	o : 0.09	e : 0.09	= : 0.01	] : 0.01	b : 0.01	
d : 0.55	c : 0.24	e : 0.11	a : 0.03	= : 0.01	2 : 0.01	] : 0.01	
d : 0.49	e : 0.11	c : 0.09	] : 0.07	2 : 0.07	4 : 0.05	3 : 0.03	= : 0.01	a : 0.01	f : 0.01	
2 : 0.22	4 : 0.14	] : 0.14	d : 0.12	3 : 0.09	e : 0.09	c : 0.05	= : 0.03	a : 0.03	b : 0.01	f : 0.01	
2 : 0.22	4 : 0.16	c : 0.14	d : 0.14	3 : 0.09	e : 0.05	b : 0.03	= : 0.03	] : 0.03	g : 0.01	f : 0.01	a : 0.01	
4 : 0.16	c : 0.14	d : 0.11	b : 0.11	3 : 0.11	2 : 0.09	e : 0.05	f : 0.05	g : 0.03	a : 0.03	= : 0.03	i : 0.01	] : 0.01	
c : 0.16	e : 0.12	4 : 0.12	d : 0.11	b : 0.11	2 : 0.07	f : 0.07	] : 0.05	3 : 0.05	g : 0.03	= : 0.03	i : 0.01	
e : 0.16	d : 0.14	g : 0.11	f : 0.11	] : 0.09	2 : 0.07	c : 0.07	= : 0.05	3 : 0.05	b : 0.05	4 : 0.03	i : 0.01	
e : 0.20	g : 0.16	c : 0.09	d : 0.09	f : 0.09	b : 0.07	= : 0.05	] : 0.05	2 : 0.03	i : 0.03	4 : 0.03	3 : 0.03	a : 0.01	
g : 0.20	e : 0.20	d : 0.12	] : 0.11	f : 0.09	= : 0.05	c : 0.03	b : 0.03	i : 0.03	4 : 0.03	3 : 0.03	a : 0.01	
g : 0.29	e : 0.16	d : 0.12	f : 0.09	c : 0.07	= : 0.07	3 : 0.05	i : 0.03	4 : 0.03	h : 0.01	2 : 0.01	
g : 0.29	3 : 0.07	d : 0.07	= : 0.07	c : 0.07	e : 0.07	2 : 0.05	f : 0.05	4 : 0.05	] : 0.03	a : 0.03	i : 0.03	h : 0.03	: : 0.01	
g : 0.29	3 : 0.11	= : 0.09	d : 0.07	c : 0.07	2 : 0.05	f : 0.05	4 : 0.05	e : 0.05	a : 0.03	i : 0.03	h : 0.03	] : 0.01	
g : 0.29	3 : 0.12	] : 0.12	= : 0.09	c : 0.07	4 : 0.05	i : 0.03	h : 0.03	2 : 0.03	f : 0.03	d : 0.01	b : 0.01	a : 0.01	e : 0.01	
g : 0.25	c : 0.12	= : 0.12	3 : 0.09	e : 0.07	4 : 0.05	h : 0.05	] : 0.03	2 : 0.03	f : 0.03	d : 0.01	6 : 0.01	b : 0.01	a : 0.01	i : 0.01	
g : 0.24	c : 0.14	= : 0.11	e : 0.09	3 : 0.05	] : 0.05	h : 0.05	b : 0.03	d : 0.03	4 : 0.03	2 : 0.03	f : 0.03	6 : 0.01	: : 0.01	i : 0.01	
g : 0.24	c : 0.14	= : 0.12	e : 0.12	b : 0.05	3 : 0.05	h : 0.05	] : 0.03	d : 0.03	f : 0.03	6 : 0.01	4 : 0.01	2 : 0.01	i : 0.01	

#score	744.8055387948091
#seq	54
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_UTR_m2_run2.txt

#BEAR
c[cccqqqqqqqqccc22	chr10:115489116-115489337(+)$1	221	180	198	13.7218
eeeeeqqqqqqqqeeeee	chr15:90375691-90375946(-)$1	255	92	110	14.9642
!!cccqqqqqqqqccc22	chr17:2497045-2497267(+)$1	222	27	45	13.8603
eeeeeqqqqqqqqeeeee	chr5:141532066-141532293(+)$1	227	166	184	14.9642
fff[aqqqqqqqqa]fff	chr14:21969770-21970145(-)$1	375	91	109	13.4587
eee[aqqqqqqqqa]eee	chr16:89353880-89354103(-)$1	223	189	207	14.4979
dddddqqqqqqqqdddd]	chrX:153580459-153580699(-)$1	240	75	93	14.0886
eeeeeqqqqqqqqeeeee	chr1:114519217-114519444(+)$1	227	186	204	14.9642
f[cccqqqqqqqqccc]f	chr1:67874719-67874957(-)$1	238	9	27	14.1103
eeeeeqqqqqqqqeeeee	chr8:144519826-144520054(-)$1	228	194	212	14.9642
cddddqqqqqqqqdddd:	chr17:40931156-40931386(+)$1	230	12	30	13.0501
[ddddqqqqqqqqddddd	chr11:10530350-10530617(-)$1	267	161	179	14.1582
""cccqqqqqqqqccc33	chr3:169711532-169711770(+)$1	238	125	143	13.9866
gggggqqqqqqqqggggg	chr15:64447954-64448186(-)$1	232	6	24	13.8666
$ddddqqqqqqqqdddd4	chr18:31599417-31599646(-)$1	229	159	177	13.8902
fffffqqqqqqqqfffff	chr7:99689325-99689545(+)$1	220	138	156	13.3779
eeeeeqqqqqqqqeeeee	chr15:75191251-75191480(+)$1	229	114	132	14.9642
iiiiiqqqqqqqqiiiii	chr1:1477318-1477553(-)$1	235	172	190	13.7088
eeeeeqqqqqqqqeeeee	chr22:21243870-21244090(+)$1	220	172	190	14.9642
$ddddqqqqqqqqdddd4	chr14:94847040-94847267(+)$1	227	172	190	13.8902
eeeeeqqqqqqqqeeeee	chr11:77779910-77780153(-)$1	243	85	103	14.9642
fffffqqqqqqqqfffff	chr19:19115104-19115335(-)$1	231	133	151	13.3779
gggggqqqqqqqqggggg	chr20:34288623-34288869(+)$1	246	79	97	13.8666
eeeeeqqqqqqqqeeeee	chr19:7991991-7992224(-)$1	233	205	223	14.9642
fffffqqqqqqqqfffff	chr22:38687040-38687267(-)$1	227	1	19	13.3779
eeeeeqqqqqqqqeeeee	chr16:2498757-2498985(+)$1	228	12	30	14.9642
eeeeeqqqqqqqqeeeee	chr17:21094535-21094756(+)$1	221	117	135	14.9642
fffffqqqqqqqqfffff	chr2:32538870-32539110(+)$1	240	104	122	13.3779
d[cccqqqqqqqqccc]d	chr19:15359571-15359790(-)$1	219	176	194	13.9770
b[cccqqqqqqqqccc]b	chr15:65447980-65448209(-)$1	229	37	55	13.4710
eeeeeqqqqqqqqeeeee	chr7:41724982-41725201(-)$1	219	67	85	14.9642
[ddddqqqqqqqqdddde	chr8:99053902-99054143(-)$1	241	161	179	14.3994
$ddddqqqqqqqqdddd4	chr1:204524213-204524471(+)$1	258	189	207	13.8902
eeeeeqqqqqqqqeeeee	chr4:102020732-102020955(-)$1	223	41	59	14.9642
!ddddqqqqqqqqdddd2	chr2:85547528-85547753(-)$1	225	10	28	14.0892
b[cccqqqqqqqqccc33	chr20:43383039-43383261(-)$1	222	192	210	13.8385
eeeeeqqqqqqqqeeeee	chr18:211465-211685(+)$1	220	106	124	14.9642
iiiiiqqqqqqqqiiiii	chr17:33463937-33464178(-)$1	241	83	101	13.7088
eeebbqqqqqqqqbb]ee	chr22:19710478-19710700(-)$1	222	119	137	13.6207
e[cccqqqqqqqqccc]e	chr19:10506632-10506873(-)$1	241	163	181	14.4480
ffffaqqqqqqqqa]fff	chr19:16989932-16990164(+)$1	232	3	21	13.4607
f!!bbqqqqqqqqbbfff	chr9:140772372-140772594(+)$1	222	56	74	12.9130
dd[bbqqqqqqqqbb]dd	chr5:140998495-140998715(-)$1	220	103	121	12.8123
[ddddqqqqqqqqdddde	chr2:73466768-73467000(+)$1	232	14	32	14.3994
iiiiiqqqqqqqqiiiii	chr19:4268689-4268915(+)$1	226	158	176	13.7088
[ddddqqqqqqqqdddd]	chr1:116234052-116234275(+)$1	223	194	212	14.3054
fffffqqqqqqqqfffff	chr4:159644392-159644630(-)$1	238	175	193	13.3779
eeeeeqqqqqqqqeeeee	chr1:19655548-19655788(+)$1	240	141	159	14.9642
eeeeeqqqqqqqqeeeee	chr4:39979076-39979302(-)$1	226	31	49	14.9642
d[cccqqqqqqqqcccdd	chr19:24097608-24097833(+)$1	225	56	74	13.9984
dd[bbqqqqqqqqbbddd	chr10:17271222-17271453(+)$1	231	132	150	12.9278
eecccqqqqqqqqccc]e	chr3:20217996-20218228(-)$1	232	89	107	14.4894
fffffqqqqqqqqfffff	chr3:195112733-195112955(-)$1	222	13	31	13.3779
fffffqqqqqqqqfffff	chr17:73124814-73125039(+)$1	225	182	200	13.3779
[ddddqqqqqqqqddddd	chr5:79946498-79946748(-)$1	250	161	179	14.1582
##cccqqqqqqqqccc22	chr5:89813207-89813430(-)$1	223	72	90	13.5440
eeeeeqqqqqqqqeeeee	chr17:1303323-1303550(-)$1	227	10	28	14.9642
a[cccqqqqqqqqcccae	chr7:73610973-73611226(+)$1	253	226	244	14.1001
eddddqqqqqqqqdddd]	chr7:65423553-65423772(+)$1	219	87	105	14.3184
ddddaqqqqqqqqa]ddd	chr9:88642625-88642846(-)$1	221	155	173	13.7562
ee[bbqqqqqqqqbbeee	chr7:127947091-127947312(-)$1	221	81	99	13.6821
!ddddqqqqqqqqdddd3	chr16:3740731-3740983(-)$1	252	204	222	14.2854
eeeeeqqqqqqqqeeeee	chr5:180665983-180666217(-)$1	234	129	147	14.9642
[ddddqqqqqqqqdddd]	chr3:32611575-32611802(-)$1	227	149	167	14.3054
eeeeeqqqqqqqqeeeee	chr11:118916056-118916280(-)$1	224	159	177	14.9642
gg!!aqqqqqqqqa22gg	chr5:34906185-34906414(-)$1	229	126	144	13.1060
eeeeeqqqqqqqqeeeee	chr11:65421432-65421679(-)$1	247	116	134	14.9642
gggbbqqqqqqqqbb]gg	chr5:172116539-172116772(+)$1	233	67	85	12.9836
gggggqqqqqqqqggggg	chr7:65618589-65618816(+)$1	227	181	199	13.8666
eeeeeqqqqqqqqeeeee	chr19:541421-541640(+)$1	219	74	92	14.9642
eddddqqqqqqqqdddd:	chr16:87743057-87743280(-)$1	223	197	215	13.2513
!!cccqqqqqqqqcccee	chr12:31478892-31479128(-)$1	236	98	116	14.5105

#otherMatches

#Seq PSSM
UAGCCAUAUCAGGGGUAC	chr10:115489116-115489337(+)$1	221	180	198	13.7218
cagcuacucaggaggcug	chr15:90375691-90375946(-)$1	255	92	110	14.9642
GAGCGAGAGAAACCGCGA	chr17:2497045-2497267(+)$1	222	27	45	13.8603
GUUAUAAUGUAGAAUGAU	chr5:141532066-141532293(+)$1	227	166	184	14.9642
CUGUCACAGGUCAGUCAG	chr14:21969770-21970145(-)$1	375	91	109	13.4587
CUGGGGCAUCCGAUGCAG	chr16:89353880-89354103(-)$1	223	189	207	14.4979
CCCCUAGGGGAAGGGGGA	chrX:153580459-153580699(-)$1	240	75	93	14.0886
GGUCACAGUGACCUGACC	chr1:114519217-114519444(+)$1	227	186	204	14.9642
CCGGAACUGUCACUCUCG	chr1:67874719-67874957(-)$1	238	9	27	14.1103
UUUAUGUUCAGCAAUAAA	chr8:144519826-144520054(-)$1	228	194	212	14.9642
CUGGAUCUGUGACUCCAC	chr17:40931156-40931386(+)$1	230	12	30	13.0501
UCUAUGUAGCAAAAUAGU	chr11:10530350-10530617(-)$1	267	161	179	14.1582
AAUUAAGACCAUGUAAGG	chr3:169711532-169711770(+)$1	238	125	143	13.9866
CCUGUAGUCCGCCACAGG	chr15:64447954-64448186(-)$1	232	6	24	13.8666
GGGAGAUGGGAGACUCCA	chr18:31599417-31599646(-)$1	229	159	177	13.8902
GGAGGGCACUACACUUCC	chr7:99689325-99689545(+)$1	220	138	156	13.3779
CAACAUACUCAACUGUUG	chr15:75191251-75191480(+)$1	229	114	132	14.9642
UUUGUUUUUACUUACAGG	chr1:1477318-1477553(-)$1	235	172	190	13.7088
UAGCUCAGACCUAAGCUA	chr22:21243870-21244090(+)$1	220	172	190	14.9642
GUCUUCAUUUUCCAGGAA	chr14:94847040-94847267(+)$1	227	172	190	13.8902
cagcuacucauaaggcug	chr11:77779910-77780153(-)$1	243	85	103	14.9642
gggggagaggaggCCCCC	chr19:19115104-19115335(-)$1	231	133	151	13.3779
CUUGGUUUCCUCCUCAGG	chr20:34288623-34288869(+)$1	246	79	97	13.8666
CCGCAACACCACCUGCGG	chr19:7991991-7992224(-)$1	233	205	223	14.9642
UGUCUACUAACAAGGACA	chr22:38687040-38687267(-)$1	227	1	19	13.3779
GAGGCCUCCUAAAGCCUU	chr16:2498757-2498985(+)$1	228	12	30	14.9642
GGGUGAGGGGAAACACUU	chr17:21094535-21094756(+)$1	221	117	135	14.9642
uuggucucgaacugcuaa	chr2:32538870-32539110(+)$1	240	104	122	13.3779
gugugcggaagaacacuc	chr19:15359571-15359790(-)$1	219	176	194	13.9770
GCACAAUAGUCAAUGUUC	chr15:65447980-65448209(-)$1	229	37	55	13.4710
AUGUUCUGUGGUUGAUGU	chr7:41724982-41725201(-)$1	219	67	85	14.9642
AUUUUCCUUUAAUAAAAU	chr8:99053902-99054143(-)$1	241	161	179	14.3994
cucccuaguagcugggac	chr1:204524213-204524471(+)$1	258	189	207	13.8902
aauauuuauuuuuauauu	chr4:102020732-102020955(-)$1	223	41	59	14.9642
UGCUGGUAUCGAAUAGUU	chr2:85547528-85547753(-)$1	225	10	28	14.0892
CCACCCUGUUCCUGGUCC	chr20:43383039-43383261(-)$1	222	192	210	13.8385
ACCAUUUCCUUCUGUGGU	chr18:211465-211685(+)$1	220	106	124	14.9642
UCUCCGGUGGGGAGGGGA	chr17:33463937-33464178(-)$1	241	83	101	13.7088
GGUGUAAGCGGUCACGAC	chr22:19710478-19710700(-)$1	222	119	137	13.6207
UGCGCAAGGAGGAGCGGA	chr19:10506632-10506873(-)$1	241	163	181	14.4480
GGUCCAUGUCCAAGAGAC	chr19:16989932-16990164(+)$1	232	3	21	13.4607
ccggcggcggagagcggg	chr9:140772372-140772594(+)$1	222	56	74	12.9130
CGCGCGCAGCCCGGCAUG	chr5:140998495-140998715(-)$1	220	103	121	12.8123
AUCCUAUUGAAAGAGGGG	chr2:73466768-73467000(+)$1	232	14	32	14.3994
GCCUCAGCCCCAGGAGGU	chr19:4268689-4268915(+)$1	226	158	176	13.7088
GAGCUUCUGUUACAGCUG	chr1:116234052-116234275(+)$1	223	194	212	14.3054
CGUCUGCAAGUCAAGAUG	chr4:159644392-159644630(-)$1	238	175	193	13.3779
gcggugaaccgagaucgu	chr1:19655548-19655788(+)$1	240	141	159	14.9642
CCGCGUCUCCCCCCGCGG	chr4:39979076-39979302(-)$1	226	31	49	14.9642
UUCCGGGAUUUGGCGGGG	chr19:24097608-24097833(+)$1	225	56	74	13.9984
UCGCCUCUUCUCCGGGAG	chr10:17271222-17271453(+)$1	231	132	150	12.9278
UGAAGAAACUGAACUUCC	chr3:20217996-20218228(-)$1	232	89	107	14.4894
ACUUUUCAAGAGUAAAGU	chr3:195112733-195112955(-)$1	222	13	31	13.3779
CCAGGCUCCGGAACCUGG	chr17:73124814-73125039(+)$1	225	182	200	13.3779
UCUAUGUAGCAAAAUAGU	chr5:79946498-79946748(-)$1	250	161	179	14.1582
UGGCUAAGUAAGAAGCAU	chr5:89813207-89813430(-)$1	223	72	90	13.5440
UCCGCGUGCGCAGGCGGA	chr17:1303323-1303550(-)$1	227	10	28	14.9642
GUGGUGUAAUCAAACCCG	chr7:73610973-73611226(+)$1	253	226	244	14.1001
AACCUCAUUUCUAAGGUA	chr7:65423553-65423772(+)$1	219	87	105	14.3184
AUGACUAUAAAAUGUUCA	chr9:88642625-88642846(-)$1	221	155	173	13.7562
AUAGACUGCUCCUUCAUG	chr7:127947091-127947312(-)$1	221	81	99	13.6821
UGUGCGUAAAGGGGCAUU	chr16:3740731-3740983(-)$1	252	204	222	14.2854
CCUCUGUGCUUCUGGAGG	chr5:180665983-180666217(-)$1	234	129	147	14.9642
CGGGGACCCGCCCUCCCU	chr3:32611575-32611802(-)$1	227	149	167	14.3054
UCUGUGGUUAAAAAUGGA	chr11:118916056-118916280(-)$1	224	159	177	14.9642
ggaaguucgagaucagcc	chr5:34906185-34906414(-)$1	229	126	144	13.1060
UGGGGUCCCCCAUCCCCA	chr11:65421432-65421679(-)$1	247	116	134	14.9642
guccugugagugaaguga	chr5:172116539-172116772(+)$1	233	67	85	12.9836
gguguagcggcccacacc	chr7:65618589-65618816(+)$1	227	181	199	13.8666
GAGGCCGACAGCUGCUUC	chr19:541421-541640(+)$1	219	74	92	14.9642
GGUCUGAGGACGAAGACA	chr16:87743057-87743280(-)$1	223	197	215	13.2513
UGAGGGGGACUGGCCUGG	chr12:31478892-31479128(-)$1	236	98	116	14.5105

#DB
(.(((........)))..	chr10:115489116-115489337(+)$1	1	180	198	13.7218
(((((........)))))	chr15:90375691-90375946(-)$1	1	92	110	14.9642
..(((........)))..	chr17:2497045-2497267(+)$1	1	27	45	13.8603
(((((........)))))	chr5:141532066-141532293(+)$1	1	166	184	14.9642
(((.(........).)))	chr14:21969770-21970145(-)$1	1	91	109	13.4587
(((.(........).)))	chr16:89353880-89354103(-)$1	1	189	207	14.4979
(((((........)))).	chrX:153580459-153580699(-)$1	1	75	93	14.0886
(((((........)))))	chr1:114519217-114519444(+)$1	1	186	204	14.9642
(.(((........))).)	chr1:67874719-67874957(-)$1	1	9	27	14.1103
(((((........)))))	chr8:144519826-144520054(-)$1	1	194	212	14.9642
)((((........)))).	chr17:40931156-40931386(+)$1	1	12	30	13.0501
.((((........)))))	chr11:10530350-10530617(-)$1	1	161	179	14.1582
..(((........)))..	chr3:169711532-169711770(+)$1	1	125	143	13.9866
(((((........)))))	chr15:64447954-64448186(-)$1	1	6	24	13.8666
.((((........)))).	chr18:31599417-31599646(-)$1	1	159	177	13.8902
(((((........)))))	chr7:99689325-99689545(+)$1	1	138	156	13.3779
(((((........)))))	chr15:75191251-75191480(+)$1	1	114	132	14.9642
(((((........)))))	chr1:1477318-1477553(-)$1	1	172	190	13.7088
(((((........)))))	chr22:21243870-21244090(+)$1	1	172	190	14.9642
.((((........)))).	chr14:94847040-94847267(+)$1	1	172	190	13.8902
(((((........)))))	chr11:77779910-77780153(-)$1	1	85	103	14.9642
(((((........)))))	chr19:19115104-19115335(-)$1	1	133	151	13.3779
(((((........)))))	chr20:34288623-34288869(+)$1	1	79	97	13.8666
(((((........)))))	chr19:7991991-7992224(-)$1	1	205	223	14.9642
(((((........)))))	chr22:38687040-38687267(-)$1	1	1	19	13.3779
(((((........)))))	chr16:2498757-2498985(+)$1	1	12	30	14.9642
(((((........)))))	chr17:21094535-21094756(+)$1	1	117	135	14.9642
(((((........)))))	chr2:32538870-32539110(+)$1	1	104	122	13.3779
(.(((........))).)	chr19:15359571-15359790(-)$1	1	176	194	13.9770
(.(((........))).)	chr15:65447980-65448209(-)$1	1	37	55	13.4710
(((((........)))))	chr7:41724982-41725201(-)$1	1	67	85	14.9642
.((((........)))))	chr8:99053902-99054143(-)$1	1	161	179	14.3994
.((((........)))).	chr1:204524213-204524471(+)$1	1	189	207	13.8902
(((((........)))))	chr4:102020732-102020955(-)$1	1	41	59	14.9642
.((((........)))).	chr2:85547528-85547753(-)$1	1	10	28	14.0892
(.(((........)))..	chr20:43383039-43383261(-)$1	1	192	210	13.8385
(((((........)))))	chr18:211465-211685(+)$1	1	106	124	14.9642
(((((........)))))	chr17:33463937-33464178(-)$1	1	83	101	13.7088
(((((........)).))	chr22:19710478-19710700(-)$1	1	119	137	13.6207
(.(((........))).)	chr19:10506632-10506873(-)$1	1	163	181	14.4480
(((((........).)))	chr19:16989932-16990164(+)$1	1	3	21	13.4607
(..((........)))))	chr9:140772372-140772594(+)$1	1	56	74	12.9130
((.((........)).))	chr5:140998495-140998715(-)$1	1	103	121	12.8123
.((((........)))))	chr2:73466768-73467000(+)$1	1	14	32	14.3994
(((((........)))))	chr19:4268689-4268915(+)$1	1	158	176	13.7088
.((((........)))).	chr1:116234052-116234275(+)$1	1	194	212	14.3054
(((((........)))))	chr4:159644392-159644630(-)$1	1	175	193	13.3779
(((((........)))))	chr1:19655548-19655788(+)$1	1	141	159	14.9642
(((((........)))))	chr4:39979076-39979302(-)$1	1	31	49	14.9642
(.(((........)))))	chr19:24097608-24097833(+)$1	1	56	74	13.9984
((.((........)))))	chr10:17271222-17271453(+)$1	1	132	150	12.9278
(((((........))).)	chr3:20217996-20218228(-)$1	1	89	107	14.4894
(((((........)))))	chr3:195112733-195112955(-)$1	1	13	31	13.3779
(((((........)))))	chr17:73124814-73125039(+)$1	1	182	200	13.3779
.((((........)))))	chr5:79946498-79946748(-)$1	1	161	179	14.1582
..(((........)))..	chr5:89813207-89813430(-)$1	1	72	90	13.5440
(((((........)))))	chr17:1303323-1303550(-)$1	1	10	28	14.9642
(.(((........)))))	chr7:73610973-73611226(+)$1	1	226	244	14.1001
(((((........)))).	chr7:65423553-65423772(+)$1	1	87	105	14.3184
(((((........).)))	chr9:88642625-88642846(-)$1	1	155	173	13.7562
((.((........)))))	chr7:127947091-127947312(-)$1	1	81	99	13.6821
.((((........)))).	chr16:3740731-3740983(-)$1	1	204	222	14.2854
(((((........)))))	chr5:180665983-180666217(-)$1	1	129	147	14.9642
.((((........)))).	chr3:32611575-32611802(-)$1	1	149	167	14.3054
(((((........)))))	chr11:118916056-118916280(-)$1	1	159	177	14.9642
((..(........)..))	chr5:34906185-34906414(-)$1	1	126	144	13.1060
(((((........)))))	chr11:65421432-65421679(-)$1	1	116	134	14.9642
(((((........)).))	chr5:172116539-172116772(+)$1	1	67	85	12.9836
(((((........)))))	chr7:65618589-65618816(+)$1	1	181	199	13.8666
(((((........)))))	chr19:541421-541640(+)$1	1	74	92	14.9642
)((((........)))).	chr16:87743057-87743280(-)$1	1	197	215	13.2513
..(((........)))))	chr12:31478892-31479128(-)$1	1	98	116	14.5105

#PSSM
e : 0.37	f : 0.15	d : 0.08	[ : 0.08	g : 0.06	! : 0.05	$ : 0.04	i : 0.04	c : 0.02	b : 0.02	" : 0.01	# : 0.01	a : 0.01	
e : 0.33	d : 0.25	f : 0.12	[ : 0.11	g : 0.06	! : 0.04	i : 0.04	" : 0.01	# : 0.01	
e : 0.30	d : 0.22	c : 0.18	f : 0.12	g : 0.05	i : 0.04	[ : 0.04	! : 0.02	
e : 0.27	d : 0.22	c : 0.18	f : 0.11	b : 0.08	g : 0.04	i : 0.04	[ : 0.02	! : 0.01	
e : 0.27	d : 0.20	c : 0.18	f : 0.09	b : 0.08	a : 0.06	g : 0.04	i : 0.04	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.27	d : 0.20	c : 0.18	f : 0.09	b : 0.08	a : 0.06	g : 0.04	i : 0.04	
e : 0.27	d : 0.20	c : 0.18	f : 0.09	b : 0.08	] : 0.05	g : 0.04	i : 0.04	2 : 0.01	
e : 0.30	d : 0.23	c : 0.18	f : 0.13	g : 0.04	i : 0.04	] : 0.04	2 : 0.01	
e : 0.33	d : 0.26	f : 0.13	] : 0.06	g : 0.06	2 : 0.04	i : 0.04	3 : 0.02	a : 0.01	
e : 0.40	f : 0.15	d : 0.09	g : 0.06	2 : 0.05	] : 0.05	3 : 0.04	4 : 0.04	i : 0.04	: : 0.02	b : 0.01	

#score	1015.4148869818689
#seq	72
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_UTR_m2_run1.txt

#BEAR
===!!bboooooobb22==	chr1:47143960-47144190(-)$1	230	196	215	10.8971
:ffffffooooooffffff	chr2:135926251-135926469(+)$1	218	36	55	10.5993
eeeeebboooooobb4444	chr17:34417353-34417583(-)$1	230	120	139	10.3229
ff"""bboooooobb333f	chr1:160248803-160249027(-)$1	224	57	76	10.7203
ccc[cccoooooocccccc	chr1:193054922-193055146(+)$1	224	124	143	12.0710
#ffffffooooooffffff	chr1:168216296-168216526(+)$1	230	178	197	11.3575
gggggggoooooogggggg	chr2:8953275-8953505(-)$1	230	201	220	12.2901
gggddddoooooodddd22	chr1:234739924-234740170(-)$1	246	187	206	10.7371
iiiiiiiooooooiiiiii	chr9:4586050-4586272(+)$1	222	87	106	12.0947
ddeeeeeooooooeeeeeE	chr8:71022188-71022412(-)$1	224	178	197	9.9043
dd!!cccooooooccc]dd	chr2:114697609-114697839(+)$1	230	114	133	11.6352
dd[ddddoooooodddd33	chr14:99977674-99977895(+)$1	221	50	69	10.7990
ccc[cccooooooccc]cc	chr15:52605076-52605298(-)$1	222	76	95	12.2629
ee[bb[aooooooa]bb]e	chr7:95750035-95750261(-)$1	226	118	137	9.9636
ggggg[aooooooa]gggg	chr1:28822981-28823211(+)$1	230	128	147	11.9307
gggggggoooooogggggg	chr7:100277301-100277531(-)$1	230	86	105	12.2901
:ffffffooooooffffff	chr8:6615493-6615723(+)$1	230	206	225	10.5993
=======oooooo======	chr16:71962601-71962823(+)$1	222	148	167	12.1664
bb!!cccooooooccc22b	chr12:122277463-122277679(-)$1	216	33	52	11.4216
fff[cccooooooccc22f	chr6:31321671-31321901(-)$1	230	115	134	11.7464
c[eeeeeooooooeeeeec	chr5:151183832-151184062(+)$1	230	14	33	11.4298
))eeeeeooooooeeeeeg	chr2:96916478-96916708(-)$1	230	139	158	10.4607
ddeeeeeooooooeeeee:	chr14:93706884-93707108(-)$1	224	71	90	9.9598
=======oooooo======	chr15:65255260-65255478(+)$1	218	183	202	12.1664
hhhhhhhoooooohhhhhh	chr15:70341408-70341631(-)$1	223	1	20	9.9734
gggggggoooooogggggg	chrX:154467096-154467319(+)$1	223	139	158	12.2901
cc!!cccooooooccc]cc	chr18:9860538-9860763(+)$1	225	144	163	12.4005
accc[bboooooobb]ccc	chr4:6644304-6644528(+)$1	224	37	56	10.7933
!!eeeeeooooooeeeee]	chrX:117583601-117583824(+)$1	223	124	143	11.4819
dffffffooooooffffff	chr17:56051110-56051334(-)$1	224	146	165	11.2464
eeeddddoooooodddd]e	chr1:172580093-172580323(+)$1	230	150	169	10.4767
bb!!cccooooooccc]bb	chr18:47808825-47809048(-)$1	223	183	202	11.4198
hhhhhhhoooooohhhhhh	chr15:45654000-45654237(-)$1	237	168	187	9.9734
:ffffffooooooffffff	chr19:50412814-50413041(-)$1	227	13	32	10.5993
:ffffffooooooffffff	chr11:32877238-32877468(+)$1	230	123	142	10.5993
ccc[cccoooooocccccc	chr4:73940948-73941175(-)$1	227	13	32	12.0710
d"""cccooooooccc333	chr14:95555504-95555734(-)$1	230	135	154	11.9907
gggggggoooooogggggg	chr16:24836648-24836878(+)$1	230	160	179	12.2901
hhhhhhhoooooohhhhhh	chr8:130854281-130854511(-)$1	230	175	194	9.9734
ee!!cccooooooccc]ee	chr6:32546458-32546694(-)$1	236	109	128	11.9555
:ffffffooooooffffff	chr15:72877560-72877816(+)$1	256	133	152	10.5993
hhh!!bboooooobb]hhh	chr2:172411983-172412213(+)$1	230	34	53	10.2218
gggggggoooooogggggg	chr1:12204127-12204357(+)$1	230	2	21	12.2901
!!eeeeeooooooeeeee8	chr15:45009756-45010004(+)$1	248	158	177	10.9750
ccc[cccooooooccc]cc	chrX:123045805-123046060(+)$1	255	223	242	12.2629
cc[ddddoooooodddd]c	chr3:178736544-178736764(-)$1	220	25	44	11.0993
gggggbboooooobb]ggg	chr1:154556536-154556759(-)$1	223	113	132	11.3915
:ffffffooooooffffff	chr15:44706940-44707165(+)$1	225	34	53	10.5993
gggggggoooooogggggg	chr10:74647047-74647277(+)$1	230	189	208	12.2901
$$eeeeeooooooeeeeed	chr7:123324309-123324544(-)$1	235	177	196	10.6661
bb[ddddoooooodddd22	chr4:57325811-57326041(+)$1	230	165	184	10.3679
=======oooooo======	chr11:33375274-33375499(+)$1	225	75	94	12.1664
+ffffffooooooffffff	chr9:108311015-108311237(+)$1	222	173	192	10.8735
fff[cccooooooccc]ff	chr9:36123726-36123956(+)$1	230	164	183	12.0635
b!!ddddoooooodddd22	chr7:5271640-5271870(+)$1	230	114	133	10.6473
gggggggoooooogggggg	chr11:77033764-77033985(-)$1	221	9	28	12.2901
cffffffooooooffffff	chr1:204374123-204374353(-)$1	230	43	62	11.4118
"""ddddoooooodddd33	chr1:160968508-160968735(-)$1	227	28	47	10.9024
$$eeeeeooooooeeeee6	chr15:78792945-78793165(+)$1	220	93	112	10.4139
hhhhcccooooooccc]hh	chr13:79886414-79886644(-)$1	230	205	224	11.2701
b[eeeeeooooooeeeee]	chr2:73956931-73957161(-)$1	230	127	146	11.3198

#otherMatches

#Seq PSSM
AAGCUAUAUAAAAGUUAUU	chr1:47143960-47144190(-)$1	230	196	215	10.8971
UGUUCUCACCAAAGAGGAC	chr2:135926251-135926469(+)$1	218	36	55	10.5993
UCAGUCCUUUCUUGGCUCU	chr17:34417353-34417583(-)$1	230	120	139	10.3229
UACUCCCUCUCUUGGAUCU	chr1:160248803-160249027(-)$1	224	57	76	10.7203
UGCAUUAUUUUAUUGAGCA	chr1:193054922-193055146(+)$1	224	124	143	12.0710
uuuuaaauuauacuuuaag	chr1:168216296-168216526(+)$1	230	178	197	11.3575
AGGUUGAUUAUAUUUGGCU	chr2:8953275-8953505(-)$1	230	201	220	12.2901
GCAAGCUUAGAAUGGCUAU	chr1:234739924-234740170(-)$1	246	187	206	10.7371
AAAGGGAGAAGGAUUCUUU	chr9:4586050-4586272(+)$1	222	87	106	12.0947
CUGAACAUCACUUUGUUCA	chr8:71022188-71022412(-)$1	224	178	197	9.9043
ACAUUUAUAACAUUAACGU	chr2:114697609-114697839(+)$1	230	114	133	11.6352
CUUUGCAAAUUCCUGUACA	chr14:99977674-99977895(+)$1	221	50	69	10.7990
AGGCACUACAAUAAGUUUC	chr15:52605076-52605298(-)$1	222	76	95	12.2629
GGUGCUCAGAGCAGUGUUU	chr7:95750035-95750261(-)$1	226	118	137	9.9636
CUCCAAAGUGACAUAUGGA	chr1:28822981-28823211(+)$1	230	128	147	11.9307
CCCUGUGAGGAAGUAUAGG	chr7:100277301-100277531(-)$1	230	86	105	12.2901
UGAAAACGUUAAGGUUUUC	chr8:6615493-6615723(+)$1	230	206	225	10.5993
CAUCCUUCCCCACAGGGGU	chr16:71962601-71962823(+)$1	222	148	167	12.1664
GCCCGGCAUGUAAGCCCCG	chr12:122277463-122277679(-)$1	216	33	52	11.4216
UUACUUCCCUACUGAAAAU	chr6:31321671-31321901(-)$1	230	115	134	11.7464
ACUUCCAAUUUUGUGGAAU	chr5:151183832-151184062(+)$1	230	14	33	11.4298
UAGGUAAUGAAUCUUACUA	chr2:96916478-96916708(-)$1	230	139	158	10.4607
ACUUCAACAUUAUUUGAGC	chr14:93706884-93707108(-)$1	224	71	90	9.9598
AAAUUAAAAGCAGUUGAUU	chr15:65255260-65255478(+)$1	218	183	202	12.1664
GCAGAAAUGGAGCUUUCUG	chr15:70341408-70341631(-)$1	223	1	20	9.9734
AGAUAAACACCauuuuauu	chrX:154467096-154467319(+)$1	223	139	158	12.2901
AGAAAUGGUUAAUCAUGCU	chr18:9860538-9860763(+)$1	225	144	163	12.4005
CCAGCUGUAAGUUCAUUUG	chr4:6644304-6644528(+)$1	224	37	56	10.7933
UUAAAGCAUUGUAGUUUUU	chrX:117583601-117583824(+)$1	223	124	143	11.4819
AUAUUUGGAGAUGUAAAUA	chr17:56051110-56051334(-)$1	224	146	165	11.2464
UUUUAUUAGUAUGAAUAUA	chr1:172580093-172580323(+)$1	230	150	169	10.4767
CCCUGUGCCCAUCCACCGG	chr18:47808825-47809048(-)$1	223	183	202	11.4198
UUUGGUGAAUGUGUACCAA	chr15:45654000-45654237(-)$1	237	168	187	9.9734
ACAGGCGGGUUCACGUUUG	chr19:50412814-50413041(-)$1	227	13	32	10.5993
AUUUUAAUCCUCUUUAAAG	chr11:32877238-32877468(+)$1	230	123	142	10.5993
CAGUAAAAUUAUCUUUCUG	chr4:73940948-73941175(-)$1	227	13	32	12.0710
GGUCAUUAAUUUAGAUAAA	chr14:95555504-95555734(-)$1	230	135	154	11.9907
UUGUAGGCUCUUUUUUAUA	chr16:24836648-24836878(+)$1	230	160	179	12.2901
CUGAGAAUGCAGUUUUUUA	chr8:130854281-130854511(-)$1	230	175	194	9.9734
CACAUUACAUUAUUAAAUG	chr6:32546458-32546694(-)$1	236	109	128	11.9555
AUUAUUUUACUUCAAAUGA	chr15:72877560-72877816(+)$1	256	133	152	10.5993
CCCCAAGACUUCCCUAGGG	chr2:172411983-172412213(+)$1	230	34	53	10.2218
GCCAGGCAGGGCAGUCUGG	chr1:12204127-12204357(+)$1	230	2	21	12.2901
UAAUGUUAACAUGGACAUG	chr15:45009756-45010004(+)$1	248	158	177	10.9750
uccauggauucaaccaagg	chrX:123045805-123046060(+)$1	255	223	242	12.2629
UAAAGGGUCAAACCCCUAU	chr3:178736544-178736764(-)$1	220	25	44	11.0993
CUGCACUUUAGCCAGCUGC	chr1:154556536-154556759(-)$1	223	113	132	11.3915
ACUUAAUAUGUUAGUUAAG	chr15:44706940-44707165(+)$1	225	34	53	10.5993
AUCCUGUUUGUGCAUAGGG	chr10:74647047-74647277(+)$1	230	189	208	12.2901
UUGUGUGCAAGUUUACACC	chr7:123324309-123324544(-)$1	235	177	196	10.6661
UCCUUAACACUGAUUAAAU	chr4:57325811-57326041(+)$1	230	165	184	10.3679
AGCAGAAGUCCAGUUUUGC	chr11:33375274-33375499(+)$1	225	75	94	12.1664
UUAAACUGGAGAAAGUUUG	chr9:108311015-108311237(+)$1	222	173	192	10.8735
UGUAGUUCAUGUAAAUAAU	chr9:36123726-36123956(+)$1	230	164	183	12.0635
CAUUUAAGUGGCAUUAAUG	chr7:5271640-5271870(+)$1	230	114	133	10.6473
GACUAUAUAAAUUUAUGGU	chr11:77033764-77033985(-)$1	221	9	28	12.2901
UCAGAGCAAUUUGGUUUUG	chr1:204374123-204374353(-)$1	230	43	62	11.4118
UAUUUCUGCAGGGAGAAUU	chr1:160968508-160968735(-)$1	227	28	47	10.9024
UUGGGGUUUUGCUACUCUU	chr15:78792945-78793165(+)$1	220	93	112	10.4139
UUGGGUAUGAUGCUACUUC	chr13:79886414-79886644(-)$1	230	205	224	11.2701
AAGAAAACAUUGAUUUUCC	chr2:73956931-73957161(-)$1	230	127	146	11.3198

#DB
(((..((......))..))	chr1:47143960-47144190(-)$1	1	196	215	10.8971
.((((((......))))))	chr2:135926251-135926469(+)$1	1	36	55	10.5993
(((((((......))....	chr17:34417353-34417583(-)$1	1	120	139	10.3229
((...((......))...)	chr1:160248803-160249027(-)$1	1	57	76	10.7203
(((.(((......))))))	chr1:193054922-193055146(+)$1	1	124	143	12.0710
.((((((......))))))	chr1:168216296-168216526(+)$1	1	178	197	11.3575
(((((((......))))))	chr2:8953275-8953505(-)$1	1	201	220	12.2901
(((((((......))))..	chr1:234739924-234740170(-)$1	1	187	206	10.7371
(((((((......))))))	chr9:4586050-4586272(+)$1	1	87	106	12.0947
))(((((......))))))	chr8:71022188-71022412(-)$1	1	178	197	9.9043
((..(((......))).))	chr2:114697609-114697839(+)$1	1	114	133	11.6352
((.((((......))))..	chr14:99977674-99977895(+)$1	1	50	69	10.7990
(((.(((......))).))	chr15:52605076-52605298(-)$1	1	76	95	12.2629
((.((.(......).)).)	chr7:95750035-95750261(-)$1	1	118	137	9.9636
(((((.(......).))))	chr1:28822981-28823211(+)$1	1	128	147	11.9307
(((((((......))))))	chr7:100277301-100277531(-)$1	1	86	105	12.2901
.((((((......))))))	chr8:6615493-6615723(+)$1	1	206	225	10.5993
(((((((......))))))	chr16:71962601-71962823(+)$1	1	148	167	12.1664
((..(((......)))..)	chr12:122277463-122277679(-)$1	1	33	52	11.4216
(((.(((......)))..)	chr6:31321671-31321901(-)$1	1	115	134	11.7464
(.(((((......))))))	chr5:151183832-151184062(+)$1	1	14	33	11.4298
..(((((......))))))	chr2:96916478-96916708(-)$1	1	139	158	10.4607
))(((((......))))).	chr14:93706884-93707108(-)$1	1	71	90	9.9598
(((((((......))))))	chr15:65255260-65255478(+)$1	1	183	202	12.1664
(((((((......))))))	chr15:70341408-70341631(-)$1	1	1	20	9.9734
(((((((......))))))	chrX:154467096-154467319(+)$1	1	139	158	12.2901
((..(((......))).))	chr18:9860538-9860763(+)$1	1	144	163	12.4005
((((.((......)).)))	chr4:6644304-6644528(+)$1	1	37	56	10.7933
..(((((......))))).	chrX:117583601-117583824(+)$1	1	124	143	11.4819
(((((((......))))))	chr17:56051110-56051334(-)$1	1	146	165	11.2464
(((((((......)))).)	chr1:172580093-172580323(+)$1	1	150	169	10.4767
((..(((......))).))	chr18:47808825-47809048(-)$1	1	183	202	11.4198
(((((((......))))))	chr15:45654000-45654237(-)$1	1	168	187	9.9734
.((((((......))))))	chr19:50412814-50413041(-)$1	1	13	32	10.5993
.((((((......))))))	chr11:32877238-32877468(+)$1	1	123	142	10.5993
(((.(((......))))))	chr4:73940948-73941175(-)$1	1	13	32	12.0710
(...(((......)))...	chr14:95555504-95555734(-)$1	1	135	154	11.9907
(((((((......))))))	chr16:24836648-24836878(+)$1	1	160	179	12.2901
(((((((......))))))	chr8:130854281-130854511(-)$1	1	175	194	9.9734
((..(((......))).))	chr6:32546458-32546694(-)$1	1	109	128	11.9555
.((((((......))))))	chr15:72877560-72877816(+)$1	1	133	152	10.5993
(((..((......)).)))	chr2:172411983-172412213(+)$1	1	34	53	10.2218
(((((((......))))))	chr1:12204127-12204357(+)$1	1	2	21	12.2901
..(((((......))))).	chr15:45009756-45010004(+)$1	1	158	177	10.9750
(((.(((......))).))	chrX:123045805-123046060(+)$1	1	223	242	12.2629
((.((((......)))).)	chr3:178736544-178736764(-)$1	1	25	44	11.0993
(((((((......)).)))	chr1:154556536-154556759(-)$1	1	113	132	11.3915
.((((((......))))))	chr15:44706940-44707165(+)$1	1	34	53	10.5993
(((((((......))))))	chr10:74647047-74647277(+)$1	1	189	208	12.2901
..(((((......))))))	chr7:123324309-123324544(-)$1	1	177	196	10.6661
((.((((......))))..	chr4:57325811-57326041(+)$1	1	165	184	10.3679
(((((((......))))))	chr11:33375274-33375499(+)$1	1	75	94	12.1664
.((((((......))))))	chr9:108311015-108311237(+)$1	1	173	192	10.8735
(((.(((......))).))	chr9:36123726-36123956(+)$1	1	164	183	12.0635
(..((((......))))..	chr7:5271640-5271870(+)$1	1	114	133	10.6473
(((((((......))))))	chr11:77033764-77033985(-)$1	1	9	28	12.2901
)((((((......))))))	chr1:204374123-204374353(-)$1	1	43	62	11.4118
...((((......))))..	chr1:160968508-160968735(-)$1	1	28	47	10.9024
..(((((......))))).	chr15:78792945-78793165(+)$1	1	93	112	10.4139
(((((((......))).))	chr13:79886414-79886644(-)$1	1	205	224	11.2701
(.(((((......))))).	chr2:73956931-73957161(-)$1	1	127	146	11.3198

#PSSM
g : 0.16	c : 0.13	: : 0.09	d : 0.09	b : 0.08	h : 0.08	= : 0.06	e : 0.06	f : 0.04	! : 0.03	$ : 0.03	# : 0.01	i : 0.01	) : 0.01	a : 0.01	+ : 0.01	" : 0.01	
f : 0.21	g : 0.16	c : 0.11	h : 0.08	= : 0.06	e : 0.06	d : 0.06	b : 0.04	! : 0.04	[ : 0.03	" : 0.03	$ : 0.03	i : 0.01	) : 0.01	
f : 0.19	e : 0.18	g : 0.16	! : 0.09	c : 0.08	h : 0.08	= : 0.06	[ : 0.06	" : 0.04	i : 0.01	
f : 0.16	e : 0.16	g : 0.14	! : 0.11	d : 0.11	[ : 0.09	h : 0.06	= : 0.04	" : 0.03	i : 0.01	b : 0.01	c : 0.01	
c : 0.21	f : 0.16	e : 0.16	g : 0.14	d : 0.11	= : 0.04	h : 0.04	! : 0.03	" : 0.01	i : 0.01	b : 0.01	[ : 0.01	
c : 0.21	f : 0.16	e : 0.14	g : 0.11	d : 0.11	b : 0.09	= : 0.04	h : 0.04	[ : 0.03	i : 0.01	
c : 0.21	f : 0.16	e : 0.14	g : 0.11	d : 0.11	b : 0.09	= : 0.04	h : 0.04	a : 0.03	i : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
c : 0.21	f : 0.16	e : 0.14	g : 0.11	d : 0.11	b : 0.09	= : 0.04	h : 0.04	a : 0.03	i : 0.01	
c : 0.21	f : 0.16	e : 0.14	g : 0.11	d : 0.11	b : 0.09	= : 0.04	h : 0.04	] : 0.03	i : 0.01	
c : 0.21	f : 0.16	e : 0.14	g : 0.13	d : 0.11	= : 0.04	h : 0.04	] : 0.04	2 : 0.01	4 : 0.01	3 : 0.01	i : 0.01	b : 0.01	
f : 0.16	g : 0.14	e : 0.14	] : 0.13	d : 0.11	h : 0.06	2 : 0.04	c : 0.04	= : 0.04	3 : 0.03	4 : 0.01	i : 0.01	b : 0.01	
f : 0.18	e : 0.16	g : 0.14	c : 0.09	2 : 0.08	h : 0.08	= : 0.06	3 : 0.06	] : 0.04	4 : 0.01	i : 0.01	d : 0.01	b : 0.01	
f : 0.21	g : 0.16	c : 0.13	h : 0.08	= : 0.06	2 : 0.04	3 : 0.04	e : 0.04	d : 0.03	b : 0.03	] : 0.03	4 : 0.01	i : 0.01	E : 0.01	: : 0.01	8 : 0.01	6 : 0.01	

#score	685.4865935985134
#seq	61
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_CDS_m2_run1.txt

#BEAR
gggggg!!eeeeennnnneeeee22ggggggg	chr12:56721071-56721294(-)$1	223	139	171	11.8783
dddd"""eeeeeooooooeeeee22ddddddd	chr2:179481216-179481441(+)$1	225	88	120	14.1420
!!ccc[dddd[aooooooa]ddddccceeeee	chr10:98714821-98715049(+)$1	228	190	222	13.3575
bb!!ccceeeeeooooooeeeee22ccc22bb	chrX:24197752-24197980(+)$1	228	70	102	13.1190
i[ccc"""eeeeemmmmeeeee]ccciiiiii	chr3:132387609-132387831(+)$1	222	185	217	11.1393
"""ccc"""ddddnnnnndddd333ccc333g	chr2:198363394-198363623(-)$1	229	125	157	13.2110
cc!!ccc!!cccooooooccc333ccc22ccc	chr11:32949519-32949749(+)$1	230	34	66	16.3141
ggggggg[eeeeeooooooeeeee]ggggggg	chr16:14041708-14041943(+)$1	235	158	190	13.8504
ggggggg"""bboooooobb]ggggggg]ccc	chr17:16021145-16021370(-)$1	225	29	61	15.0652
=======####cccmmmmccc==========]	chr3:15269262-15269498(+)$1	236	20	52	11.1585
====ccc[ddddoooooodddd22ccc]====	chr11:108384522-108384751(-)$1	229	13	45	15.9245
hh####a[cccooooooccc]a4444hhhhhh	chr17:60140328-60140559(-)$1	231	10	42	13.0164
dddd[gggggggoooooogggggggddddddd	chr16:75664249-75664477(-)$1	228	111	143	13.2216
$$$$$gggggggooooooggggggg333gggg	chr1:200376947-200377190(-)$1	243	77	109	13.8968
eeee[gggggggooooooggggggg333eeee	chr22:18138465-18138698(+)$1	233	72	104	13.9224
eeee$$$$$cccooooooccc666666eeeee	chr12:53776663-53776888(+)$1	225	160	192	12.0042
gdddd"""ddddoooooodddd333dddd:::	chr10:27437812-27438052(-)$1	240	63	95	13.3119
eee"""ddddcccooooooccc]dddd]eeee	chr4:185550324-185550545(-)$1	221	106	138	12.4581
ccggggggg[bboooooobb]ggggggg]ccc	chr15:52188516-52188740(+)$1	224	25	57	14.3371
gggggg####bboooooobb4444ggggggg:	chrX:153197423-153197647(-)$1	224	4	36	14.7892
e[abb[bb[cccooooooccc22bb]bb]a]e	chr17:65908531-65908754(+)$1	223	32	64	12.6144
"""ccc"""ddddnnnnnddddccc333ccc]	chr16:58572584-58572804(-)$1	220	44	76	12.1472
!!eeeee[ddddoooooodddd333eeeee]=	chrM:12401-12831(+)$1	430	368	400	15.2461
fffff[ccc[bboooooobb]ccc]ffffff4	chr2:232324872-232325098(-)$1	226	177	209	12.3627
ggggggg[bbbboooooobb]bb]ggggggg:	chr4:53476607-53476832(-)$1	225	116	148	12.6836
fff####eeeeeooooooeeeee4444fffff	chr20:5096019-5096248(-)$1	229	67	99	14.4414
d[ggggggg[bboooooobb]ggggggg]ddd	chr21:34120790-34121015(-)$1	225	183	215	14.0575
ggggggg[ddddoooooodddd]gggggggcc	chr2:152271299-152271524(+)$1	225	16	48	15.8792
cc[bb[ffffffooooooffffff]bb]ccc]	chr16:58570840-58571079(-)$1	239	186	218	12.1423
ccc[gggggggaooooooa]ggggggg333cc	chr19:30104740-30104964(+)$1	224	45	77	14.7494
&&&bb"""ddddoooooodddd333bb4444f	chr1:16242616-16242836(+)$1	220	25	57	13.9525
gggggg"""cccooooooccc22gggggggff	chr15:49420064-49420297(-)$1	233	40	72	16.2438
ebbdddd[ddddoooooodddd]dddd22bb8	chr8:8875791-8876012(+)$1	221	41	73	12.2869
cccbb"""eeeeemmmmeeeee333bb]ccc3	chr11:110007905-110008125(+)$1	220	153	185	11.0014
ccc[bb"""cccoooooocccbbccc]fffff	chr22:32110432-32110653(-)$1	221	136	168	14.2636
!!dddd!!ddddoooooodddd]dddd333dd	chr17:27805235-27805457(+)$1	222	5	37	15.0407
ggggg####ddddnnnnnddddgggggggFFF	chr19:44611689-44611922(+)$1	233	5	37	11.1165
""dddd[eeeeeooooooeeeeeddddfffff	chr17:78109945-78110181(-)$1	236	157	189	13.0285
ccc!!a[eeeeeooooooeeeee]a22ccc44	chr19:36036579-36036807(+)$1	228	63	95	14.3350
d[dddd"""cccooooooccc333dddd]ddd	chr17:35608835-35609058(-)$1	223	184	216	15.5977
eeee####ddddnnnnndddd4444eeeee22	chr14:32562153-32562376(+)$1	223	120	152	10.9905
cc[iiiiiiiiiooooooiiiiiiiii22ccc	chr14:39648514-39648741(+)$1	227	60	92	14.6901
ddd!!eeeeebboooooobb]eeeee]dddd2	chr10:102684069-102684291(+)$1	222	87	119	12.1928
[dddd"""ddddoooooodddd333dddd]dd	chr10:30630305-30630530(-)$1	225	107	139	16.0514
gggggg"""cccooooooccc22ggggggg==	chr22:29692140-29692376(+)$1	236	46	78	16.5065
=======!!cccmmmmccc4444=========	chr3:169504343-169504565(+)$1	222	68	100	11.4388
"ggggggg[cccoooooocccgggggggdddd	chr9:34250556-34250784(+)$1	228	12	44	14.8983
ddd[bb"""cccooooooccc333bbdddddd	chr4:39457937-39458172(-)$1	235	29	61	14.9226
ggg####eeeeeooooooeeeee4444ggggg	chr19:36728104-36728331(+)$1	227	56	88	15.6383
iiiiiiiiddddoooooodddd333iiiiiii	chr9:106894230-106894456(+)$1	226	45	77	16.5126

#otherMatches

#Seq PSSM
UCAGUCAGGUAUGAAGGGCAUAUGGGAUUGGG	chr12:56721071-56721294(-)$1	223	139	171	11.8783
UGAGUCCUUGGUUAUAUCACCAAAUUUCAAUU	chr2:179481216-179481441(+)$1	225	88	120	14.1420
AUGGUGCACUCAGCAACAUCAGUGACCUUCCU	chr10:98714821-98715049(+)$1	228	190	222	13.3575
UGGGAUCCCUGUGGACCAGCAGGAUGAUGACA	chrX:24197752-24197980(+)$1	228	70	102	13.1190
CCAUAUUCAGUGAAAUCUUACUUUAUGUAUUU	chr3:132387609-132387831(+)$1	222	185	217	11.1393
UUAUGCCAAAGAUGUAAAAUUUGGUGCAGAUG	chr2:198363394-198363623(-)$1	229	125	157	13.2110
CACUAAAGAGUCUUCAGUGAUGAAUUUUCUGU	chr11:32949519-32949749(+)$1	230	34	66	16.3141
CUCCUCAUGCAACGGCGGAGUUGUUUGAGGAG	chr16:14041708-14041943(+)$1	235	158	190	13.8504
GUCUAGUAGAACAUGGUCGUAACUGGGCAGCA	chr17:16021145-16021370(-)$1	225	29	61	15.0652
AUUUUGGCUUUGAGUCAUCUUUUAAGauuaau	chr3:15269262-15269498(+)$1	236	20	52	11.1585
CAUUCAGUUCUUCUGACAGAGACUUUGAAAUG	chr11:108384522-108384751(-)$1	229	13	45	15.9245
CCUUAAGGCAGAUGUACUUGGUGUUUGGCGGC	chr17:60140328-60140559(-)$1	231	10	42	13.0164
CAUUCAUCUGUGAUCACCCACAGAUAAUGAGC	chr16:75664249-75664477(-)$1	228	111	143	13.2216
UUUUGGACAAUGAGGCACCAUUGUCACUUAUU	chr1:200376947-200377190(-)$1	243	77	109	13.8968
AGCUACUUGGGACUCCUCUCUCAAGAGAAGCU	chr22:18138465-18138698(+)$1	233	72	104	13.9224
UCUGAUGCUCUGAACAUCCAGCAAAACCAGAC	chr12:53776663-53776888(+)$1	225	160	192	12.0042
UAACUUUUAUCUUUUUCUAGGUUACAGUUCCU	chr10:27437812-27438052(-)$1	240	63	95	13.3119
AUUUUUAUCACUAAAGAAAUGGUUGGUUGGUG	chr4:185550324-185550545(-)$1	221	106	138	12.4581
AUAUAUUUGAUUAAUGGAAACUAAAUAUAAUG	chr15:52188516-52188740(+)$1	224	25	57	14.3371
GAGGGGCAAGACCUGGACGUGCUACCCCUCCC	chrX:153197423-153197647(-)$1	224	4	36	14.7892
UGUCCAGAAAGCAAUUCAGUUAAUCAGGUAGA	chr17:65908531-65908754(+)$1	223	32	64	12.6144
ACAGGGAAUGCCACCUCUUGGUCCUAAAAGCU	chr16:58572584-58572804(-)$1	220	44	76	12.1472
GAGGGCGUAGGAAUUAUAUCCUUCUUGCUCAU	chrM:12401-12831(+)$1	430	368	400	15.2461
AGCGAUGUUUUUGCUAAAAAUGAUCUUGCUGU	chr2:232324872-232325098(-)$1	226	177	209	12.3627
ACUGUCUAAGGUAUAUGAACUCUGAGGCAGUU	chr4:53476607-53476832(-)$1	225	116	148	12.6836
UUGCACUGAGGUACCUGAACUUCUUUACAAAA	chr20:5096019-5096248(-)$1	229	67	99	14.4414
UCCUCACUUGGACUCCUCUUGAGGUGAGUGGC	chr21:34120790-34121015(-)$1	225	183	215	14.0575
AAUGUGAUUUUGUUUUUGUAGACUCACAUUUC	chr2:152271299-152271524(+)$1	225	16	48	15.8792
GGUAGAGCUUUUGGAAAGAAAGGUGCUUUUUA	chr16:58570840-58571079(-)$1	239	186	218	12.1423
UCCAAAUGCCCCUCUUAUGUGGGUAUUACAGG	chr19:30104740-30104964(+)$1	224	45	77	14.7494
AUUUCGCCCCUUGGAUGAAAGGAUAGAUGAAU	chr1:16242616-16242836(+)$1	220	25	57	13.9525
CUCCUUGAACUGGAUCAUCAGAAGAGGGGUGG	chr15:49420064-49420297(-)$1	233	40	72	16.2438
CCCUCAGGUACUAAAAAAAGUAAUUGACUGGA	chr8:8875791-8876012(+)$1	221	41	73	12.2869
AUCUCCAAUGCAAGAGAUUGUAACAGAUGAUG	chr11:110007905-110008125(+)$1	220	153	185	11.0014
CUGCACAUACAGGAACAACUGGUCAGGAUUCA	chr22:32110432-32110653(-)$1	221	136	168	14.2636
UAUUAAUUAUUUUGAAAUAAAUUUUAAGUUCA	chr17:27805235-27805457(+)$1	222	5	37	15.0407
GUGGGAAGAGCUUUAGUCGGGCCCCAUGUCUU	chr19:44611689-44611922(+)$1	233	5	37	11.1165
AAGGUGCAAGCUCUCAUUGGCUUCACUUCUGU	chr17:78109945-78110181(-)$1	236	157	189	13.0285
UGACCCUGUUUCACUUCGGGAACUGCUUCGCU	chr19:36036579-36036807(+)$1	228	63	95	14.3350
CUGAAGCUCAAAGACCCAUUUAUUCUUCUGUC	chr17:35608835-35609058(-)$1	223	184	216	15.5977
UUGAUUCUCAUUCUUGCAGUGCUGCUCAAGCU	chr14:32562153-32562376(+)$1	223	120	152	10.9905
AACUAAGACAAAGCCCCAUUUGUUUUAUAUUC	chr14:39648514-39648741(+)$1	227	60	92	14.6901
AAGGAGAAGGAGACAAAACUACCUUUACUUUC	chr10:102684069-102684291(+)$1	222	87	119	12.1928
AAUAAUCAUUUCUUCUAUGAAAGCUUUGUAAG	chr10:30630305-30630530(-)$1	225	107	139	16.0514
AGUAUAUUCUAGUCAUGCCUAACUAUGCUAUU	chr22:29692140-29692376(+)$1	236	46	78	16.5065
AACUGUGAAUGGGUAUUCAGAACCACAGUUGA	chr3:169504343-169504565(+)$1	222	68	100	11.4388
GGACUUCACACACUAGUUUGUUGAGGUCUCUU	chr9:34250556-34250784(+)$1	228	12	44	14.8983
AUGAGGUCUGUGUAUGCUCACUUCCCCAUCAA	chr4:39457937-39458172(-)$1	235	29	61	14.9226
UGGGAAAGCUUUCAGCCAGAAGUCACACCACA	chr19:36728104-36728331(+)$1	227	56	88	15.6383
UUUUUAUCUCAUAGUACAAUGACUUGAUGAAG	chr9:106894230-106894456(+)$1	226	45	77	16.5126

#DB
((((((..(((((.....)))))..)))))))	chr12:56721071-56721294(-)$1	1	139	171	11.8783
((((...(((((......)))))..))))(((	chr2:179481216-179481441(+)$1	1	88	120	14.1420
..(((.((((.(......).))))))))))))	chr10:98714821-98715049(+)$1	1	190	222	13.3575
((..((((((((......)))))..)))..))	chrX:24197752-24197980(+)$1	1	70	102	13.1190
(.(((...(((((....))))).)))))))))	chr3:132387609-132387831(+)$1	1	185	217	11.1393
...(((...((((.....))))...)))...)	chr2:198363394-198363623(-)$1	1	125	157	13.2110
((..(((..(((......)))...)))..)))	chr11:32949519-32949749(+)$1	1	34	66	16.3141
(((((((.(((((......))))).)))))))	chr16:14041708-14041943(+)$1	1	158	190	13.8504
(((((((...((......)).))))))).)))	chr17:16021145-16021370(-)$1	1	29	61	15.0652
(((((((....(((....))))))))))))).	chr3:15269262-15269498(+)$1	1	20	52	11.1585
(((((((.((((......))))..))).))))	chr11:108384522-108384751(-)$1	1	13	45	15.9245
((....(.(((......))).)....))))))	chr17:60140328-60140559(-)$1	1	10	42	13.0164
((((.(((((((......)))))))))))(((	chr16:75664249-75664477(-)$1	1	111	143	13.2216
.....(((((((......)))))))...))))	chr1:200376947-200377190(-)$1	1	77	109	13.8968
((((.(((((((......)))))))...))))	chr22:18138465-18138698(+)$1	1	72	104	13.9224
((((.....(((......)))......)))))	chr12:53776663-53776888(+)$1	1	160	192	12.0042
)((((...((((......))))...))))...	chr10:27437812-27438052(-)$1	1	63	95	13.3119
(((...(((((((......))).)))).))))	chr4:185550324-185550545(-)$1	1	106	138	12.4581
(((((((((.((......)).))))))).)))	chr15:52188516-52188740(+)$1	1	25	57	14.3371
((((((....((......))....))))))).	chrX:153197423-153197647(-)$1	1	4	36	14.7892
(.(((.((.(((......)))..)).)).).)	chr17:65908531-65908754(+)$1	1	32	64	12.6144
...(((...((((.....)))))))...))).	chr16:58572584-58572804(-)$1	1	44	76	12.1472
..(((((.((((......))))...))))).)	chrM:12401-12831(+)$1	1	368	400	15.2461
(((((.(((.((......)).))).)))))).	chr2:232324872-232325098(-)$1	1	177	209	12.3627
(((((((.((((......)).)).))))))).	chr4:53476607-53476832(-)$1	1	116	148	12.6836
(((....(((((......)))))....)))))	chr20:5096019-5096248(-)$1	1	67	99	14.4414
(.(((((((.((......)).))))))).)))	chr21:34120790-34121015(-)$1	1	183	215	14.0575
(((((((.((((......)))).)))))))((	chr2:152271299-152271524(+)$1	1	16	48	15.8792
((.((.((((((......)))))).)).))).	chr16:58570840-58571079(-)$1	1	186	218	12.1423
(((.((((((((......).)))))))...))	chr19:30104740-30104964(+)$1	1	45	77	14.7494
...((...((((......))))...))....)	chr1:16242616-16242836(+)$1	1	25	57	13.9525
((((((...(((......)))..)))))))((	chr15:49420064-49420297(-)$1	1	40	72	16.2438
(((((((.((((......)))).))))..)).	chr8:8875791-8876012(+)$1	1	41	73	12.2869
(((((...(((((....)))))...)).))).	chr11:110007905-110008125(+)$1	1	153	185	11.0014
(((.((...(((......)))))))).)))))	chr22:32110432-32110653(-)$1	1	136	168	14.2636
..((((..((((......)))).))))...))	chr17:27805235-27805457(+)$1	1	5	37	15.0407
(((((....((((.....)))))))))))(((	chr19:44611689-44611922(+)$1	1	5	37	11.1165
..((((.(((((......))))))))))))))	chr17:78109945-78110181(-)$1	1	157	189	13.0285
(((..(.(((((......))))).)..)))..	chr19:36036579-36036807(+)$1	1	63	95	14.3350
(.((((...(((......)))...)))).)))	chr17:35608835-35609058(-)$1	1	184	216	15.5977
((((....((((.....))))....)))))..	chr14:32562153-32562376(+)$1	1	120	152	10.9905
((.(((((((((......)))))))))..)))	chr14:39648514-39648741(+)$1	1	60	92	14.6901
(((..(((((((......)).))))).)))).	chr10:102684069-102684291(+)$1	1	87	119	12.1928
.((((...((((......))))...)))).))	chr10:30630305-30630530(-)$1	1	107	139	16.0514
((((((...(((......)))..)))))))((	chr22:29692140-29692376(+)$1	1	46	78	16.5065
(((((((..(((....)))....)))))))))	chr3:169504343-169504565(+)$1	1	68	100	11.4388
.(((((((.(((......))))))))))))))	chr9:34250556-34250784(+)$1	1	12	44	14.8983
(((.((...(((......)))...))))))))	chr4:39457937-39458172(-)$1	1	29	61	14.9226
(((....(((((......)))))....)))))	chr19:36728104-36728331(+)$1	1	56	88	15.6383
((((((((((((......))))...)))))))	chr9:106894230-106894456(+)$1	1	45	77	16.5126

#PSSM
g : 0.21	c : 0.16	d : 0.12	e : 0.12	" : 0.08	! : 0.06	= : 0.06	i : 0.04	f : 0.04	b : 0.02	h : 0.02	$ : 0.02	& : 0.02	[ : 0.02	
g : 0.21	c : 0.16	d : 0.12	[ : 0.08	e : 0.08	! : 0.06	" : 0.06	= : 0.06	b : 0.04	f : 0.04	h : 0.02	$ : 0.02	& : 0.02	i : 0.02	
g : 0.25	d : 0.18	c : 0.12	e : 0.10	= : 0.06	! : 0.04	" : 0.04	f : 0.04	[ : 0.04	# : 0.02	$ : 0.02	a : 0.02	& : 0.02	b : 0.02	i : 0.02	
g : 0.23	d : 0.16	c : 0.08	! : 0.08	e : 0.08	b : 0.08	= : 0.06	# : 0.06	[ : 0.06	i : 0.04	$ : 0.02	" : 0.02	f : 0.02	
g : 0.25	c : 0.14	d : 0.12	b : 0.12	# : 0.08	" : 0.04	= : 0.04	[ : 0.04	$ : 0.04	! : 0.04	i : 0.04	e : 0.02	f : 0.02	
g : 0.30	" : 0.14	c : 0.10	# : 0.10	[ : 0.08	d : 0.08	= : 0.04	e : 0.04	b : 0.04	i : 0.04	$ : 0.02	a : 0.02	
" : 0.25	g : 0.21	# : 0.10	c : 0.08	d : 0.06	! : 0.04	= : 0.04	e : 0.04	[ : 0.04	i : 0.04	a : 0.02	$ : 0.02	b : 0.02	f : 0.02	
" : 0.25	e : 0.14	[ : 0.14	g : 0.14	! : 0.08	# : 0.08	d : 0.04	i : 0.04	$ : 0.02	b : 0.02	c : 0.02	f : 0.02	
d : 0.23	e : 0.21	" : 0.16	g : 0.12	# : 0.06	! : 0.04	c : 0.04	[ : 0.04	$ : 0.02	b : 0.02	f : 0.02	i : 0.02	
d : 0.30	e : 0.21	c : 0.21	g : 0.08	[ : 0.06	# : 0.04	" : 0.02	b : 0.02	f : 0.02	i : 0.02	
d : 0.25	c : 0.23	e : 0.19	b : 0.14	g : 0.08	[ : 0.02	# : 0.02	f : 0.02	i : 0.02	
d : 0.25	c : 0.23	e : 0.19	b : 0.14	g : 0.06	a : 0.04	o : 0.02	f : 0.02	i : 0.02	
o : 0.78	e : 0.08	d : 0.06	c : 0.04	n : 0.02	m : 0.02	
o : 0.82	n : 0.10	m : 0.06	c : 0.02	
o : 0.82	n : 0.10	m : 0.08	
o : 0.82	n : 0.10	m : 0.08	
o : 0.82	n : 0.10	m : 0.06	c : 0.02	
o : 0.80	n : 0.08	e : 0.04	c : 0.04	m : 0.02	d : 0.02	
d : 0.25	c : 0.23	e : 0.18	b : 0.14	g : 0.06	a : 0.04	o : 0.04	f : 0.02	i : 0.02	
d : 0.25	c : 0.23	e : 0.19	b : 0.14	g : 0.06	] : 0.04	f : 0.02	i : 0.02	4 : 0.02	
d : 0.27	c : 0.21	e : 0.19	] : 0.14	g : 0.08	4 : 0.04	f : 0.02	i : 0.02	
d : 0.25	e : 0.21	g : 0.16	3 : 0.06	4 : 0.06	2 : 0.06	c : 0.04	b : 0.04	= : 0.02	a : 0.02	6 : 0.02	f : 0.02	i : 0.02	
3 : 0.19	e : 0.18	g : 0.18	] : 0.10	2 : 0.08	4 : 0.08	c : 0.04	b : 0.04	d : 0.02	= : 0.02	6 : 0.02	f : 0.02	i : 0.02	
g : 0.23	3 : 0.19	d : 0.10	4 : 0.10	2 : 0.08	c : 0.08	e : 0.04	= : 0.04	] : 0.04	6 : 0.02	b : 0.02	f : 0.02	i : 0.02	
g : 0.27	3 : 0.14	c : 0.12	d : 0.10	4 : 0.08	2 : 0.06	] : 0.06	= : 0.04	b : 0.04	6 : 0.02	a : 0.02	i : 0.02	e : 0.02	
g : 0.25	d : 0.18	c : 0.14	b : 0.08	4 : 0.06	3 : 0.06	e : 0.06	= : 0.04	i : 0.04	6 : 0.02	] : 0.02	f : 0.02	2 : 0.02	
g : 0.25	d : 0.19	c : 0.10	b : 0.08	i : 0.06	3 : 0.06	= : 0.04	e : 0.04	4 : 0.04	] : 0.04	h : 0.02	6 : 0.02	f : 0.02	2 : 0.02	
g : 0.25	d : 0.14	3 : 0.10	e : 0.08	] : 0.08	f : 0.08	c : 0.06	2 : 0.06	i : 0.04	= : 0.04	h : 0.02	b : 0.02	4 : 0.02	
g : 0.19	d : 0.14	e : 0.12	] : 0.10	2 : 0.08	c : 0.08	f : 0.08	3 : 0.06	= : 0.06	i : 0.04	h : 0.02	4 : 0.02	
g : 0.18	c : 0.16	d : 0.14	e : 0.12	f : 0.08	3 : 0.06	= : 0.06	i : 0.04	2 : 0.02	h : 0.02	: : 0.02	a : 0.02	4 : 0.02	b : 0.02	F : 0.02	] : 0.02	
d : 0.18	c : 0.18	g : 0.12	f : 0.10	e : 0.08	= : 0.08	b : 0.04	i : 0.04	] : 0.04	4 : 0.04	3 : 0.02	h : 0.02	: : 0.02	F : 0.02	2 : 0.02	
d : 0.16	c : 0.12	g : 0.10	e : 0.10	f : 0.10	= : 0.08	] : 0.06	: : 0.06	i : 0.04	4 : 0.04	2 : 0.04	b : 0.02	h : 0.02	8 : 0.02	3 : 0.02	F : 0.02	

#score	687.1524237819441
#seq	50
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_CDS_m1_run1.txt

#BEAR
$$$$bb[ddddnnnnnddddbbhhhh	chr4:140261975-140262189(+)$1	214	10	36	11.1728
DDiiiiiiiiinnnnniiiiiiiii:	chr12:39703325-39703571(-)$1	246	208	234	10.9647
$$$ccc!!cccnnnnnccc4444ccc	chr20:5095874-5096100(-)$1	226	73	99	13.5931
ccc[a[eeeeennnnneeeee]accc	chr3:13461600-13461813(-)$1	213	55	81	12.6494
"""bb!!ddddnnnnndddd333bb4	chr9:139726626-139726856(+)$1	230	182	208	12.9127
dddd[bb[cccnnnnnccc]bbdddd	chr19:49636986-49637209(+)$1	223	161	187	11.7019
[eeeee[ddddnnnnnddddeeeee]	chr17:26669299-26669521(+)$1	222	166	192	12.1045
iiiii"""cccnnnnnccc333iiii	chr16:27518228-27518481(-)$1	253	185	211	14.6249
"""bb"""cccnnnnnccc333bb33	chr16:30990851-30991076(+)$1	225	173	199	13.6736
F:iiiiiiiiinnnnniiiiiiiii:	chr2:48026961-48027247(+)$1	286	35	61	11.2112
ggggggg[a[annnnna]a]gggggg	chr3:47451145-47451365(+)$1	220	58	84	12.8502
c####ccc[bbnnnnnbbcccccc]c	chr11:77377897-77378115(-)$1	218	100	126	12.9709
dddeeeee[bbnnnnnbb]eeeee33	chr4:493068-493290(+)$1	222	150	176	11.5954
cc!!ccc[cccnnnnnccc]ccc22c	chr10:119134183-119134478(-)$1	295	145	171	13.4971
dddd!!eeeeennnnneeeee]dddd	chr8:41834602-41834830(-)$1	228	201	227	11.6380
ccccc####bbnnnnnbb22ccc]cc	chr9:35711611-35711867(-)$1	256	203	229	12.8516
dd"""ccc!!annnnna]ccc333dd	chr2:219134051-219134263(-)$1	212	57	83	13.1396
[iiiiiiiiiooooooiiiiiiiiic	chr4:113153153-113153364(+)$1	211	126	152	9.2223
!dddd####bbnnnnnbbdddd22ee	chr5:156809504-156809739(+)$1	235	107	133	12.0072
c!!ccc[cccannnnna]ccc]ccc2	chr1:153914469-153914686(-)$1	217	33	59	13.4404
===========lll===========c	chr1:35652714-35652935(-)$1	221	69	95	9.5102
ffff[ffffffnnnnnffffff]fff	chr15:44038698-44038916(+)$1	218	166	192	10.8384
:eeeee[ddddnnnnndddd]eeeee	chr1:244587159-244587376(-)$1	217	115	141	11.2642
ccc[dddd[bbnnnnnbb]dddd]cc	chr1:166827305-166827538(-)$1	233	195	221	12.0481
===========oooooo=========	chr10:135098895-135099124(-)$1	229	188	214	9.6938
dd[bb####bbnnnnnbb333bb]dd	chr16:70302074-70302293(-)$1	219	53	79	12.2245
!bb####ddddnnnnnddddbbhhhh	chr1:226549582-226549881(-)$1	299	222	248	11.9860
dddd####cccnnnnncccdddd]ee	chr16:28124233-28124459(-)$1	226	187	213	12.9324
d:dddd!!cccnnnnnccc22dddd:	chr16:31072469-31072693(-)$1	224	190	216	10.5192
!ccc[ffffffnnnnnffffffccce	chr3:45677591-45677824(+)$1	233	141	167	12.0554
c[cccffffffnnnnnffffff]ccc	chr17:38320184-38320421(+)$1	237	23	49	11.9779
ccc[bb!!cccnnnnnccc]bb]ccc	chr19:33182925-33183224(+)$1	299	92	118	13.3733
cc$$$$$ddddnnnnndddd333ccc	chr7:128694682-128694912(-)$1	230	103	129	13.1367
eee!!ffffffnnnnnffffffeeee	chr17:7794237-7794456(+)$1	219	167	193	11.3697
####bb[ddddnnnnndddd]bb333	chr1:55560890-55561110(-)$1	220	162	188	12.6544
[ccc[a!!cccnnnnnccc22acccb	chrX:129203278-129203506(-)$1	228	105	131	13.5944
gggg$$$$$bbnnnnnbb4444gggg	chr16:3831108-3831332(-)$1	224	185	211	12.3515
ooeeeee:cccnnnnnccccccdddd	chr1:154245837-154246059(+)$1	222	140	166	10.5965
dd[ccc[ddddnnnnndddd]ccc]d	chr17:78301570-78301786(+)$1	216	99	125	12.9125
gggg!!eeeeennnnneeeeeggggg	chr1:46752050-46752267(-)$1	217	47	73	12.4589
hh!!bbeeeeennnnneeeee]bb22	chr18:48573316-48573530(+)$1	214	46	72	10.8098
cc!!gggggggnnnnnggggggg22c	chr5:36177226-36177445(+)$1	219	8	34	12.9203
beeeee!!cccnnnnnccc]eeeee2	chr3:101370383-101370601(-)$1	218	149	175	12.4250
:ffffff[cccnnnnnccc]ffffff	chr11:10800285-10800503(+)$1	218	2	28	11.0254
:ccc[ccc[bbnnnnnbb]ccc]ccc	chr9:86586885-86587123(-)$1	238	146	172	12.1367
:ggggggg[bbnnnnnbbggggggg:	chr4:30725640-30725862(+)$1	222	148	174	11.1053
hhhh"""ddddnnnnndddd22hhhh	chr3:25646189-25646415(-)$1	226	96	122	12.0115
"==========nnnnn==========	chr13:42871085-42871346(+)$1	261	173	199	14.1601
bbiiiiiiiiinnnnniiiiiiiii:	chr1:156504249-156504465(-)$1	216	56	82	12.1448
eeee[ffffffnnnnnffffff]eee	chr1:150551896-150552113(-)$1	217	37	63	11.3262
$$ccc!!ddddoooooodddd]ccc3	chr2:198274544-198274805(-)$1	261	85	111	8.7445
ccc[dddd[bbnnnnnbb]dddd]cc	chr11:134086832-134087051(-)$1	219	37	63	12.0481
eeeee!!ddddnnnnndddd333eee	chr2:30785007-30785229(+)$1	222	1	27	12.9520
da!!a!!ddddnnnnndddd22a22a	chr15:83735557-83735824(-)$1	267	99	125	13.0502
iiiii[eeeeennnnneeeee333ii	chr12:53699606-53699843(+)$1	237	45	71	12.8312
[ccc[ffffffnnnnnffffff]ccc	chr20:33369903-33370136(-)$1	233	42	68	12.2505
eeeee[ddddannnnna]dddd]eee	chr19:47883003-47883231(+)$1	228	82	108	11.7583

#otherMatches

#Seq PSSM
UGGUUCUCCAAGUUUUUUGGGAGGUC	chr4:140261975-140262189(+)$1	214	10	36	11.1728
AUAAAGGAGGAAUAGCUCUUCUUUUU	chr12:39703325-39703571(-)$1	246	208	234	10.9647
CCAUCUUCCUGUCUUUCAGUUGUAGA	chr20:5095874-5096100(-)$1	226	73	99	13.5931
cgcagggucgcgggaggugacgcgcg	chr3:13461600-13461813(-)$1	213	55	81	12.6494
UUUUGCAGCUUCAGGUAAGCACUCAC	chr9:139726626-139726856(+)$1	230	182	208	12.9127
GAAGACUGCACAGAGGGUGGGGCUUC	chr19:49636986-49637209(+)$1	223	161	187	11.7019
AAGGUGUGGGGGAUUGCCCCUGCCUG	chr17:26669299-26669521(+)$1	222	166	192	12.1045
UCUCUGAGUCGGACAGUGAGGAGGAG	chr16:27518228-27518481(-)$1	253	185	211	14.6249
CAAGCCCACGCCCCCUGCGCCAGCCC	chr16:30990851-30991076(+)$1	225	173	199	13.6736
CCAGUUUUGGGAUGCAUCCAAAACUU	chr2:48026961-48027247(+)$1	286	35	61	11.2112
AGAAGUCGCAGGAGGGCAGGGACUUC	chr3:47451145-47451365(+)$1	220	58	84	12.8502
CUUUUGAGAGUGACUGACCUUGUUGA	chr11:77377897-77378115(-)$1	218	100	126	12.9709
UUCGUUCCUCUGCCAGAGCGGAACAC	chr4:493068-493290(+)$1	222	150	176	11.5954
GCCGGGCGCCUGCUGGAGGGGCUGAG	chr10:119134183-119134478(-)$1	295	145	171	13.4971
CCCUGAUGGGCGGAAAGCUCGGGGGG	chr8:41834602-41834830(-)$1	228	201	227	11.6380
AGCCUCAGGCCGAUUUGGACAGGACU	chr9:35711611-35711867(-)$1	256	203	229	12.8516
AAGAGGGCAACGAAGAGGGCUGGGUU	chr2:219134051-219134263(-)$1	212	57	83	13.1396
ACUGCUUCGCAAGGAAGCGGGGCGGC	chr4:113153153-113153364(+)$1	211	126	152	9.2223
CUGCGAUUUGCUCCAUGCCGCACCCU	chr5:156809504-156809739(+)$1	235	107	133	12.0072
UGGAGUGUGGCAAGGGGUCCAGGCUA	chr1:153914469-153914686(-)$1	217	33	59	13.4404
UUUUUUUCUUGCAGCGGGAAAGAGAC	chr1:35652714-35652935(-)$1	221	69	95	9.5102
GCUCUGCGGGCCUCAUGCUCGUCGAG	chr15:44038698-44038916(+)$1	218	166	192	10.8384
CUGAGAGGUAACUAACUUGUGUUUCA	chr1:244587159-244587376(-)$1	217	115	141	11.2642
UCCUUAAAGUUUACCUAGGUUUAUGG	chr1:166827305-166827538(-)$1	233	195	221	12.0481
CUGCCAGAUCUUCACUCAGGUUUGGC	chr10:135098895-135099124(-)$1	229	188	214	9.6938
CCAUGAAAAGCUCAAUGCCAGCAGGG	chr16:70302074-70302293(-)$1	219	53	79	12.2245
UUGAGUAUGCUGUGUGAGCACAAAGG	chr1:226549582-226549881(-)$1	299	222	248	11.9860
GUAUUCAACAGAAUCACUGAUGCCUC	chr16:28124233-28124459(-)$1	226	187	213	12.9324
GAGUGCCAGCGACUUGCGCAAGCAUG	chr16:31072469-31072693(-)$1	224	190	216	10.5192
UGCAGCUUGCAGUAAGUGUGGGUGUG	chr3:45677591-45677824(+)$1	233	141	167	12.0554
UGCAGAGGAGGUGCCCCCUCCUCCUG	chr17:38320184-38320421(+)$1	237	23	49	11.9779
CGCACCAAGGCUUCAUGCCGGGCGCG	chr19:33182925-33183224(+)$1	299	92	118	13.3733
CCGACAUUGCAGCUCGUGUACCAGGC	chr7:128694682-128694912(-)$1	230	103	129	13.1367
UCGCUAAUUGACACUUUUAAUUUGAG	chr17:7794237-7794456(+)$1	219	167	193	11.3697
GGAAGCUGAGGAUCUCUCUCUGUAAG	chr1:55560890-55561110(-)$1	220	162	188	12.6544
AGCAUGUCGGUCUCCAGCCAUCUGCG	chrX:129203278-129203506(-)$1	228	105	131	13.5944
CACAAAACUGAUUCUUUCUAAAUGUG	chr16:3831108-3831332(-)$1	224	185	211	12.3515
CGUUUCCACGAUAACUUCGGCUUUGA	chr1:154245837-154246059(+)$1	222	140	166	10.5965
CUGUUGCCGACUCUGUGUUGACGAAA	chr17:78301570-78301786(+)$1	216	99	125	12.9125
CAGUUUCAUGGAUAUAUCAUGGCUGU	chr1:46752050-46752267(-)$1	217	47	73	12.4589
AAAUUGCUUCAGAAAUUGGAGACAUA	chr18:48573316-48573530(+)$1	214	46	72	10.8098
AUCUAGGAUCAAUGUGUGAUUUUCAA	chr5:36177226-36177445(+)$1	219	8	34	12.9203
CACAUACUGGUGAACGGCCCUAUGUC	chr3:101370383-101370601(-)$1	218	149	175	12.4250
CCUCAUCAGAGAGUGAUUCCGAUGAG	chr11:10800285-10800503(+)$1	218	2	28	11.0254
GAGGUGGUUUUGACAGAAUGCCUCCU	chr9:86586885-86587123(-)$1	238	146	172	12.1367
CAAAAAAGAUCACGAAGACUUUUUUA	chr4:30725640-30725862(+)$1	222	148	174	11.1053
UUUUUUCACCAUCAUUUGGUCUGAAA	chr3:25646189-25646415(-)$1	226	96	122	12.0115
AUUAUUUGUAUGAAGAAUAUAAAUAA	chr13:42871085-42871346(+)$1	261	173	199	14.1601
CCUGGGGGCUGUGGCUCAGCUCCUAC	chr1:156504249-156504465(-)$1	216	56	82	12.1448
UCCGCUUCCUUCCAGUAAGGAGUCGG	chr1:150551896-150552113(-)$1	217	37	63	11.3262
UACUCCUUCCUUAAGAUGGGAUGAGA	chr2:198274544-198274805(-)$1	261	85	111	8.7445
GUGAUUUGCGGUCUCCCCACAGAGUA	chr11:134086832-134087051(-)$1	219	37	63	12.0481
UAGGUUGGGCCAUGCAGGCUGCUGCC	chr2:30785007-30785229(+)$1	222	1	27	12.9520
CCUUCCUCUUCAACUCGGAGCUGCUG	chr15:83735557-83735824(-)$1	267	99	125	13.0502
GCAGGUAGCCUCAAGAAGGUUUCCCC	chr12:53699606-53699843(+)$1	237	45	71	12.8312
AAGACUCAGAGAUGGAUUUUGACUCU	chr20:33369903-33370136(-)$1	233	42	68	12.2505
UUCCCUGCGGCUCCGUGCCCGCUGGG	chr19:47883003-47883231(+)$1	228	82	108	11.7583

#DB
....((.((((.....))))))))))	chr4:140261975-140262189(+)$1	1	10	36	11.1728
))(((((((((.....))))))))).	chr12:39703325-39703571(-)$1	1	208	234	10.9647
...(((..(((.....)))....)))	chr20:5095874-5096100(-)$1	1	73	99	13.5931
(((.(.(((((.....))))).))))	chr3:13461600-13461813(-)$1	1	55	81	12.6494
...((..((((.....))))...)).	chr9:139726626-139726856(+)$1	1	182	208	12.9127
((((.((.(((.....))).))))))	chr19:49636986-49637209(+)$1	1	161	187	11.7019
.(((((.((((.....))))))))).	chr17:26669299-26669521(+)$1	1	166	192	12.1045
(((((...(((.....)))...))))	chr16:27518228-27518481(-)$1	1	185	211	14.6249
...((...(((.....)))...))..	chr16:30990851-30991076(+)$1	1	173	199	13.6736
(.(((((((((.....))))))))).	chr2:48026961-48027247(+)$1	1	35	61	11.2112
(((((((.(.(.....).).))))))	chr3:47451145-47451365(+)$1	1	58	84	12.8502
(....(((.((.....)))))))).)	chr11:77377897-77378115(-)$1	1	100	126	12.9709
((((((((.((.....)).)))))..	chr4:493068-493290(+)$1	1	150	176	11.5954
((..(((.(((.....))).)))..)	chr10:119134183-119134478(-)$1	1	145	171	13.4971
((((..(((((.....))))).))))	chr8:41834602-41834830(-)$1	1	201	227	11.6380
(((((....((.....))..))).))	chr9:35711611-35711867(-)$1	1	203	229	12.8516
((...(((..(.....).)))...))	chr2:219134051-219134263(-)$1	1	57	83	13.1396
.(((((((((......))))))))))	chr4:113153153-113153364(+)$1	1	126	152	9.2223
.((((....((.....))))))..))	chr5:156809504-156809739(+)$1	1	107	133	12.0072
(..(((.((((.....).))).))).	chr1:153914469-153914686(-)$1	1	33	59	13.4404
(((((((((((...)))))))))))(	chr1:35652714-35652935(-)$1	1	69	95	9.5102
((((.((((((.....)))))).)))	chr15:44038698-44038916(+)$1	1	166	192	10.8384
.(((((.((((.....)))).)))))	chr1:244587159-244587376(-)$1	1	115	141	11.2642
(((.((((.((.....)).)))).))	chr1:166827305-166827538(-)$1	1	195	221	12.0481
(((((((((((......)))))))))	chr10:135098895-135099124(-)$1	1	188	214	9.6938
((.((....((.....))...)).))	chr16:70302074-70302293(-)$1	1	53	79	12.2245
.((....((((.....))))))))))	chr1:226549582-226549881(-)$1	1	222	248	11.9860
((((....(((.....))))))).))	chr16:28124233-28124459(-)$1	1	187	213	12.9324
).((((..(((.....)))..)))).	chr16:31072469-31072693(-)$1	1	190	216	10.5192
.(((.((((((.....))))))))))	chr3:45677591-45677824(+)$1	1	141	167	12.0554
(.(((((((((.....)))))).)))	chr17:38320184-38320421(+)$1	1	23	49	11.9779
(((.((..(((.....))).)).)))	chr19:33182925-33183224(+)$1	1	92	118	13.3733
((.....((((.....))))...)))	chr7:128694682-128694912(-)$1	1	103	129	13.1367
(((..((((((.....))))))))))	chr17:7794237-7794456(+)$1	1	167	193	11.3697
....((.((((.....)))).))...	chr1:55560890-55561110(-)$1	1	162	188	12.6544
.(((.(..(((.....)))..)))))	chrX:129203278-129203506(-)$1	1	105	131	13.5944
((((.....((.....))....))))	chr16:3831108-3831332(-)$1	1	185	211	12.3515
..))))).(((.....)))(((((((	chr1:154245837-154246059(+)$1	1	140	166	10.5965
((.(((.((((.....)))).))).)	chr17:78301570-78301786(+)$1	1	99	125	12.9125
((((..(((((.....))))))))))	chr1:46752050-46752267(-)$1	1	47	73	12.4589
((..(((((((.....))))).))..	chr18:48573316-48573530(+)$1	1	46	72	10.8098
((..(((((((.....)))))))..)	chr5:36177226-36177445(+)$1	1	8	34	12.9203
((((((..(((.....))).))))).	chr3:101370383-101370601(-)$1	1	149	175	12.4250
.((((((.(((.....))).))))))	chr11:10800285-10800503(+)$1	1	2	28	11.0254
.(((.(((.((.....)).))).)))	chr9:86586885-86587123(-)$1	1	146	172	12.1367
.(((((((.((.....))))))))).	chr4:30725640-30725862(+)$1	1	148	174	11.1053
((((...((((.....))))..))))	chr3:25646189-25646415(-)$1	1	96	122	12.0115
.((((((((((.....))))))))))	chr13:42871085-42871346(+)$1	1	173	199	14.1601
))(((((((((.....))))))))).	chr1:156504249-156504465(-)$1	1	56	82	12.1448
((((.((((((.....)))))).)))	chr1:150551896-150552113(-)$1	1	37	63	11.3262
..(((..((((......)))).))).	chr2:198274544-198274805(-)$1	1	85	111	8.7445
(((.((((.((.....)).)))).))	chr11:134086832-134087051(-)$1	1	37	63	12.0481
(((((..((((.....))))...)))	chr2:30785007-30785229(+)$1	1	1	27	12.9520
((..(..((((.....))))..)..)	chr15:83735557-83735824(-)$1	1	99	125	13.0502
(((((.(((((.....)))))...))	chr12:53699606-53699843(+)$1	1	45	71	12.8312
.(((.((((((.....)))))).)))	chr20:33369903-33370136(-)$1	1	42	68	12.2505
(((((.(((((.....).)))).)))	chr19:47883003-47883231(+)$1	1	82	108	11.7583

#PSSM
c : 0.19	d : 0.15	[ : 0.07	: : 0.07	e : 0.07	$ : 0.05	" : 0.05	g : 0.05	! : 0.05	i : 0.03	= : 0.03	h : 0.03	b : 0.03	D : 0.01	F : 0.01	f : 0.01	# : 0.01	o : 0.01	
c : 0.21	d : 0.14	e : 0.12	g : 0.07	$ : 0.05	i : 0.05	= : 0.05	" : 0.03	: : 0.03	# : 0.03	f : 0.03	b : 0.03	h : 0.03	D : 0.01	! : 0.01	[ : 0.01	o : 0.01	a : 0.01	
c : 0.19	e : 0.14	i : 0.10	d : 0.10	! : 0.08	g : 0.07	$ : 0.05	" : 0.05	= : 0.05	# : 0.03	f : 0.03	[ : 0.03	b : 0.01	h : 0.01	
c : 0.17	e : 0.14	i : 0.10	d : 0.08	! : 0.08	[ : 0.07	g : 0.07	b : 0.05	# : 0.05	= : 0.05	$ : 0.03	f : 0.03	" : 0.01	h : 0.01	
b : 0.12	c : 0.12	[ : 0.12	e : 0.12	i : 0.10	d : 0.07	g : 0.05	# : 0.05	! : 0.05	= : 0.05	a : 0.03	" : 0.03	$ : 0.03	f : 0.01	
c : 0.12	f : 0.12	! : 0.10	b : 0.08	e : 0.08	# : 0.08	i : 0.07	[ : 0.05	" : 0.05	g : 0.05	= : 0.05	d : 0.05	$ : 0.03	a : 0.01	
! : 0.15	e : 0.12	f : 0.12	[ : 0.10	# : 0.08	i : 0.07	c : 0.07	" : 0.05	g : 0.05	= : 0.05	d : 0.05	$ : 0.03	b : 0.01	
d : 0.26	e : 0.10	f : 0.10	! : 0.08	i : 0.07	[ : 0.07	c : 0.07	# : 0.07	= : 0.05	" : 0.03	g : 0.03	$ : 0.01	: : 0.01	
d : 0.22	c : 0.22	[ : 0.10	f : 0.10	e : 0.08	i : 0.07	# : 0.05	= : 0.05	a : 0.01	! : 0.01	$ : 0.01	g : 0.01	
d : 0.22	c : 0.22	b : 0.17	f : 0.10	e : 0.08	i : 0.07	= : 0.05	[ : 0.01	! : 0.01	g : 0.01	
d : 0.21	c : 0.21	b : 0.17	f : 0.10	e : 0.08	a : 0.07	i : 0.05	= : 0.05	o : 0.01	g : 0.01	
n : 0.92	o : 0.05	l : 0.01	
n : 0.92	o : 0.05	l : 0.01	
n : 0.92	o : 0.05	l : 0.01	
n : 0.92	o : 0.05	= : 0.01	
n : 0.92	o : 0.05	= : 0.01	
c : 0.21	d : 0.19	b : 0.17	f : 0.10	e : 0.08	i : 0.07	a : 0.07	= : 0.03	o : 0.03	g : 0.01	
d : 0.21	c : 0.21	b : 0.17	f : 0.10	e : 0.08	i : 0.07	] : 0.07	= : 0.05	g : 0.01	
c : 0.26	d : 0.24	f : 0.10	e : 0.08	i : 0.07	] : 0.07	= : 0.05	g : 0.03	a : 0.01	2 : 0.01	3 : 0.01	4 : 0.01	
d : 0.29	e : 0.10	] : 0.10	f : 0.10	c : 0.08	i : 0.07	3 : 0.05	2 : 0.05	= : 0.05	4 : 0.03	g : 0.03	
e : 0.14	c : 0.12	f : 0.12	3 : 0.10	d : 0.10	b : 0.07	i : 0.07	2 : 0.07	g : 0.05	= : 0.05	] : 0.05	4 : 0.03	
3 : 0.12	f : 0.12	b : 0.10	c : 0.10	d : 0.10	] : 0.08	i : 0.07	e : 0.07	g : 0.07	= : 0.05	4 : 0.03	2 : 0.03	a : 0.01	
c : 0.14	d : 0.12	] : 0.12	i : 0.08	3 : 0.08	e : 0.08	g : 0.08	b : 0.07	h : 0.05	= : 0.05	a : 0.03	4 : 0.01	2 : 0.01	f : 0.01	
c : 0.22	e : 0.14	i : 0.08	] : 0.08	d : 0.07	g : 0.07	2 : 0.07	h : 0.05	b : 0.05	3 : 0.05	= : 0.05	f : 0.03	
c : 0.24	e : 0.15	i : 0.10	d : 0.10	g : 0.07	2 : 0.07	h : 0.05	3 : 0.05	= : 0.05	] : 0.03	f : 0.03	b : 0.01	
c : 0.26	e : 0.14	d : 0.10	: : 0.08	3 : 0.07	h : 0.05	g : 0.05	2 : 0.05	i : 0.03	f : 0.03	= : 0.03	4 : 0.01	] : 0.01	b : 0.01	a : 0.01	

#score	689.0221211139776
#seq	57
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_CDS_m1_run2.txt

#BEAR
gggguuuuuuuuuuuuggggggg::	chr8:117658609-117658875(-)$1	266	98	123	19.3020
eeevvvvvvvvvvvvveeeee22a]	chr21:33073988-33074334(-)$1	346	61	86	22.0755
[a^^^^^^^^^^^^^^^^^^^^^^^	chr1:42664669-42665002(-)$1	333	58	83	18.1160
ccuuuuuuuuuuuuccc::eeeee$	chr22:24237122-24237496(+)$1	374	113	138	17.7374
iivvvvvvvvvvvvviiiiiiiii:	chr5:102433193-102433506(-)$1	313	274	299	19.8929
[cccuuuuuuuuuuuuccc]bbbb[	chr16:89346827-89347198(-)$1	371	145	170	20.1463
gg^^^^^^^^^^^^^^^^^^^^ggg	chr19:33078074-33078421(+)$1	347	210	235	18.2189
cc^^^^^^^^^^^^^^^^^^^^^^^	chr16:50259002-50259297(+)$1	295	114	139	18.2154
cc^^^^^^^^^^^^^^^^^^^^ccc	chr1:214803774-214804106(+)$1	332	241	266	18.3611
eeevvvvvvvvvvvvveeeee::DD	chr17:61890544-61890830(+)$1	286	5	30	19.1287
cc^^^^^^^^^^^^^^^^^^^^^cc	chr12:106641154-106641476(-)$1	322	76	101	18.3531
ffxxxxxxxxxxxxxxxffffffee	chr11:118239342-118239622(+)$1	280	119	144	18.1001
ggyyyyyyyyyyyyyyyyggggggg	chr1:70700283-70700568(+)$1	285	125	150	20.5885
ii^^^^^^^^^^^^^^^^^^^^^^i	chr19:35741162-35741490(+)$1	328	147	172	18.1674
h[bbuuuuuuuuuuuubbhhhhhhh	chr16:23080594-23080947(-)$1	353	203	228	18.0567
eeeeuuuuuuuuuuuueeeee4444	chr14:55510695-55511037(+)$1	342	113	138	21.4228
ddduuuuuuuuuuuuddddddddcc	chr1:183497927-183498277(+)$1	350	103	128	20.0380
eeyyyyyyyyyyyyyyyyeeeee]e	chr14:52174731-52175051(+)$1	320	128	153	20.7217
eeevvvvvvvvvvvvveeeee::::	chr8:95538574-95538876(-)$1	302	252	277	19.5369
eewwwwwwwwwwwwwweeeee333f	chr13:49030289-49030584(+)$1	295	176	201	22.8178
eewwwwwwwwwwwwwweeeee::::	chr14:51107371-51107709(-)$1	338	178	203	19.9359
eeuuuuuuuuuuuueeeee]ccc]b	chr19:9059381-9059761(-)$1	380	227	252	19.8774
ffffuuuuuuuuuuuuffffff]==	chr11:18530986-18531302(-)$1	316	101	126	19.6782
ddddtttttttttttdddd]bb22d	chr16:89629192-89629448(+)$1	256	140	165	17.3472
!!ccctttttttttttccc22ccc:	chr12:85695123-85695437(+)$1	314	104	129	17.5508
ccwwwwwwwwwwwwwwccc::eeee	chr14:31122623-31122873(+)$1	250	123	148	20.0788
eeeeettttttttttteeeee22cc	chr18:33289598-33289922(+)$1	324	96	121	18.2843
cc^^^^^^^^^^^^^^^^^^^^^^^	chr10:64973827-64974187(-)$1	360	155	180	18.2154
dddtttttttttttdddd]ccc333	chr16:2809470-2809765(+)$1	295	182	207	17.8344
gg^^^^^^^^^^^^^^^^^^ggggg	chr3:194168483-194168730(-)$1	247	187	212	18.1248
ffxxxxxxxxxxxxxxxffffff22	chr7:135080435-135080724(-)$1	289	69	94	17.9990
eewwwwwwwwwwwwwweeeeeEEEE	chr5:173036255-173036540(-)$1	285	149	174	19.3277
dd^^^^^^^^^^^^^^^^^^^^^dd	chr19:55899514-55899799(+)$1	285	6	31	18.0025
eeevvvvvvvvvvvvveeeee22dd	chr10:28970996-28971277(+)$1	281	77	102	21.8156
dddvvvvvvvvvvvvvdddd22ccc	chr10:64967674-64968055(-)$1	381	71	96	21.3604
ccwwwwwwwwwwwwwwccc]dddd9	chr7:82582625-82582938(-)$1	313	138	163	21.3598
ggwwwwwwwwwwwwwwggggggg55	chrX:122754662-122754916(-)$1	254	63	88	20.8103
ccwwwwwwwwwwwwwwcccdddddd	chr7:100174216-100174460(-)$1	244	195	220	21.5443
ffffuuuuuuuuuuuuffffff]dd	chr16:70560398-70560729(+)$1	331	283	308	19.5234
ccxxxxxxxxxxxxxxxccc]bb]f	chr2:223497816-223498126(-)$1	310	140	165	18.7252
eewwwwwwwwwwwwwweeeee:::c	chr12:121755978-121756296(-)$1	318	102	127	20.5537
ccvvvvvvvvvvvvvccc333ffff	chr9:98734967-98735313(+)$1	346	88	113	20.9005
[bbvvvvvvvvvvvvvbb]bb]a]g	chr3:124951625-124951973(-)$1	348	116	141	20.4660
ggwwwwwwwwwwwwwwggggggg::	chrX:76763812-76764172(-)$1	360	146	171	20.9213
dd^^^^^^^^^^^^^^^^^^^^^^d	chr7:40027330-40027586(+)$1	256	202	227	18.0921
!!auuuuuuuuuuuua22eeeee]c	chr2:73479879-73480223(+)$1	344	208	233	21.1878
gggguuuuuuuuuuuugggggggCC	chr5:123983360-123983634(-)$1	274	236	261	18.9384
ggxxxxxxxxxxxxxxxggggggg:	chr17:65145893-65146150(-)$1	257	223	248	18.5753
e[bbuuuuuuuuuuuubb]eeeee2	chr19:9047086-9047364(-)$1	278	138	163	19.8559
ddvvvvvvvvvvvvvdddd:eeeee	chr2:71220726-71221005(-)$1	279	127	152	19.7120
eeevvvvvvvvvvvvveeeee4444	chr18:56998620-56998861(-)$1	241	18	43	22.4031
dddduuuuuuuuuuuudddd333cc	chr7:97822696-97822955(+)$1	259	145	170	20.9077
eeevvvvvvvvvvvvveeeee22ee	chr3:10018561-10018821(-)$1	260	62	87	21.8137
iaxxxxxxxxxxxxxxxa]iiiiii	chr2:85866285-85866609(+)$1	324	26	51	18.9284
$$ccctttttttttttccc4444cc	chr12:27067340-27067610(-)$1	270	124	149	18.0397
ddxxxxxxxxxxxxxxxdddd]fff	chr19:48894423-48894824(-)$1	401	62	87	18.5380
eeevvvvvvvvvvvvveeeee:EEE	chr21:44328887-44329214(+)$1	327	294	319	19.1100
eeevvvvvvvvvvvvveeeeeeeee	chr10:8006423-8006694(+)$1	271	35	60	21.7398
ggwwwwwwwwwwwwwwggggggg44	chr11:9456380-9456657(+)$1	277	105	130	22.1974
cc^^^^^^^^^^^^^^^^^^^^ccc	chr2:201768271-201768724(+)$1	453	308	333	18.3611
ddduuuuuuuuuuuudddd]eeeee	chr17:65925363-65925682(+)$1	319	138	163	20.2174
ccctttttttttttccc333dddd]	chr4:52729502-52729773(+)$1	271	109	134	17.9009
hhwwwwwwwwwwwwwwhhhhhhhh]	chr15:49170832-49171122(+)$1	290	149	174	19.6642
gg^^^^^^^^^^^^^^^^^^^gggg	chr9:82339948-82340444(+)$1	496	98	123	18.1414
ddyyyyyyyyyyyyyyyydddd:::	chr11:122931733-122932066(-)$1	333	245	270	18.3583
gg^^^^^^^^^^^^^^^^^^ggggg	chr18:13008373-13008730(+)$1	357	70	95	18.1248
[cccuuuuuuuuuuuuccc]ccc]g	chr16:71961508-71961744(+)$1	236	189	214	21.2368
dddduuuuuuuuuuuudddd22fff	chr19:9045685-9046075(-)$1	390	153	178	19.8198
eewwwwwwwwwwwwwweeeee:::g	chr5:176721223-176721565(+)$1	342	293	318	20.4720
ddvvvvvvvvvvvvvdddd]ccc::	chr1:21546347-21546711(-)$1	364	46	71	19.7871
gggvvvvvvvvvvvvvggggggg]b	chr7:36455267-36455541(+)$1	274	159	184	21.4995
ddwwwwwwwwwwwwwwddddHHHHH	chr4:26432480-26432765(+)$1	285	241	266	19.1111

#otherMatches

#Seq PSSM
GGAGGACCUGUCCAAACUCUUCAAA	chr8:117658609-117658875(-)$1	266	98	123	19.3020
GUUAACUUUUUUUUUAGGCCUUAAU	chr21:33073988-33074334(-)$1	346	61	86	22.0755
AGUACCCUUAUAUUCAAUUGUCAUU	chr1:42664669-42665002(-)$1	333	58	83	18.1160
CAACUAUUACGACAUGAACGCGGCC	chr22:24237122-24237496(+)$1	374	113	138	17.7374
UUUUAUUACAAAAUUGACGUUUAUU	chr5:102433193-102433506(-)$1	313	274	299	19.8929
CCUCUGAAAACCCUGUGAGCUGGCC	chr16:89346827-89347198(-)$1	371	145	170	20.1463
UUGUCUAUAUGCCUUUUAAAAAAAU	chr19:33078074-33078421(+)$1	347	210	235	18.2189
CUCUUAGUAAACACUCUUCAAACUC	chr16:50259002-50259297(+)$1	295	114	139	18.2154
UGUCUCUCUCUCUCUCCUUAAUCAU	chr1:214803774-214804106(+)$1	332	241	266	18.3611
GAUGAAGAAUAAAAGAAUUUGGUUG	chr17:61890544-61890830(+)$1	286	5	30	19.1287
gcAAGUCCUCCUCCUCCUCCUccgc	chr12:106641154-106641476(-)$1	322	76	101	18.3531
GAGCAACUCAACAUCAAUCACAUGA	chr11:118239342-118239622(+)$1	280	119	144	18.1001
GCUCCUACUCUUGAUCCUGCCCUUG	chr1:70700283-70700568(+)$1	285	125	150	20.5885
ACCUCGACCCCCACGCAACCCAUCG	chr19:35741162-35741490(+)$1	328	147	172	18.1674
CACCUUGGAGAAGAUUGGGGAGGCA	chr16:23080594-23080947(-)$1	353	203	228	18.0567
UGUCUUCCAUUCUCCUGACAUUACU	chr14:55510695-55511037(+)$1	342	113	138	21.4228
GCCUUAUAAUCAGUUGGCUAUCUUA	chr1:183497927-183498277(+)$1	350	103	128	20.0380
UUGCACUAACAGCUUCCGAAGCUCA	chr14:52174731-52175051(+)$1	320	128	153	20.7217
CUCAAAUAUAAGUGAAGGGGAAAUA	chr8:95538574-95538876(-)$1	302	252	277	19.5369
UUCACUGUUUUAUAAAAAAGGUUAG	chr13:49030289-49030584(+)$1	295	176	201	22.8178
CAAAUCCAUAUCAUACUGCAGAAAU	chr14:51107371-51107709(-)$1	338	178	203	19.9359
AAAAAGCACUGUCCUUUCUAGUGUG	chr19:9059381-9059761(-)$1	380	227	252	19.8774
CUUGUUGGGGCUUAUUCAGGUCAUG	chr11:18530986-18531302(-)$1	316	101	126	19.6782
GAAGAAUUUCAAAGCCUUCGCUAGU	chr16:89629192-89629448(+)$1	256	140	165	17.3472
CCGCCAAUAUUUCAUGGGCCAUGUA	chr12:85695123-85695437(+)$1	314	104	129	17.5508
CCUUUACAUCAUACUUGGACAUAUC	chr14:31122623-31122873(+)$1	250	123	148	20.0788
GUGGCUUCUUCGAAACGUCACCCUG	chr18:33289598-33289922(+)$1	324	96	121	18.2843
AUACUCACAAGAUAAAAUCCAGCCC	chr10:64973827-64974187(-)$1	360	155	180	18.2154
CCCGCAGUCGGUAAGGGGUAGUCCA	chr16:2809470-2809765(+)$1	295	182	207	17.8344
AUUAUUUAUcauaugcagcuauuga	chr3:194168483-194168730(-)$1	247	187	212	18.1248
UGUUUUCCUUUUUUAUUCAGAUAUC	chr7:135080435-135080724(-)$1	289	69	94	17.9990
GUGGAUCCAAAACUUAACCACAUCU	chr5:173036255-173036540(-)$1	285	149	174	19.3277
CUUUCAGCCUACUCCCCACACCCAG	chr19:55899514-55899799(+)$1	285	6	31	18.0025
UUCGAAGUGAAAAUAAGAGGCUGCA	chr10:28970996-28971277(+)$1	281	77	102	21.8156
UUGAUUAAACACCAACCAGAAAGUG	chr10:64967674-64968055(-)$1	381	71	96	21.3604
CAUCUUCAAUUCCAUCUGGACUUGU	chr7:82582625-82582938(-)$1	313	138	163	21.3598
UGUACCUUAUUCUGACUAUUUCUUU	chrX:122754662-122754916(-)$1	254	63	88	20.8103
GCUACAUCACCCUUCUGCCCUGGGA	chr7:100174216-100174460(-)$1	244	195	220	21.5443
UUGCUUAGUCUCUUGUGCAGGAAAU	chr16:70560398-70560729(+)$1	331	283	308	19.5234
ACAAACCCCUGUAUCCAGUUAUCUA	chr2:223497816-223498126(-)$1	310	140	165	18.7252
AUCUUCCUCCCCUACCAUCGCGCUG	chr12:121755978-121756296(-)$1	318	102	127	20.5537
AAACCAAAAAAGAACUUCACAAUUC	chr9:98734967-98735313(+)$1	346	88	113	20.9005
AUCAAUAAAUUCUUCAGAAGUACCA	chr3:124951625-124951973(-)$1	348	116	141	20.4660
UAUCAACAAGCAACACUGGGUCACC	chrX:76763812-76764172(-)$1	360	146	171	20.9213
AGAAAAUUAAAAUUGAACAUGCACC	chr7:40027330-40027586(+)$1	256	202	227	18.0921
CACUCUCUUCUUACUGGAGGCUAUU	chr2:73479879-73480223(+)$1	344	208	233	21.1878
UCCCAGCCCUUCCAUAGGGAGCGCC	chr5:123983360-123983634(-)$1	274	236	261	18.9384
UUAAUAUUCUAUUUCUAAAACAUCC	chr17:65145893-65146150(-)$1	257	223	248	18.5753
ACAGACAGCACUACAACUUUCCCAA	chr19:9047086-9047364(-)$1	278	138	163	19.8559
UGAUAGAAGAAUACACAGUGGCCAC	chr2:71220726-71221005(-)$1	279	127	152	19.7120
AGAUUUCACAUUUAUUUCUUUUUCC	chr18:56998620-56998861(-)$1	241	18	43	22.4031
UGCCCCCCGAUAAGCCGGCAGACAG	chr7:97822696-97822955(+)$1	259	145	170	20.9077
AAACACUUUUUUUUUUUUUUACUAG	chr3:10018561-10018821(-)$1	260	62	87	21.8137
UCAUUCAUUUCUAGCCAGCAGAAGA	chr2:85866285-85866609(+)$1	324	26	51	18.9284
ACAGAUUAACUCCUUUUCUAGACCC	chr12:27067340-27067610(-)$1	270	124	149	18.0397
CCCAAAGUCCCCUCCCCGGAGCGGA	chr19:48894423-48894824(-)$1	401	62	87	18.5380
GUGCAAAAAUAAAAUCCACUCAAGA	chr21:44328887-44329214(+)$1	327	294	319	19.1100
ACAUUCCCCAAACACCUGUGAGACC	chr10:8006423-8006694(+)$1	271	35	60	21.7398
AUGCCCCUCCUUCAUAAUUAUGUAA	chr11:9456380-9456657(+)$1	277	105	130	22.1974
ACUACCAUAUUAAAUAACAAAUGUU	chr2:201768271-201768724(+)$1	453	308	333	18.3611
GGUACCAGUCAGCAAACCUUUACUU	chr17:65925363-65925682(+)$1	319	138	163	20.2174
UGAACUCUCAUCUCUCAACACUGGC	chr4:52729502-52729773(+)$1	271	109	134	17.9009
AACUUUCCGCUAUCUUUUGGGUUCA	chr15:49170832-49171122(+)$1	290	149	174	19.6642
AGUUAUUUAUUAAAGACAAAUCUUC	chr9:82339948-82340444(+)$1	496	98	123	18.1414
UCCUAAUUUUAAAUGACAGAACAAA	chr11:122931733-122932066(-)$1	333	245	270	18.3583
UAAUAAAAAAGUUCUAUCUCUAGGA	chr18:13008373-13008730(+)$1	357	70	95	18.1248
GCUGAAAAAGAAAACAUAGGUCUCU	chr16:71961508-71961744(+)$1	236	189	214	21.2368
CAGUGCCUCUAUAACAACUGAUAAG	chr19:9045685-9046075(-)$1	390	153	178	19.8198
GCCUGAGACUUCCGCCGCCAGACAG	chr5:176721223-176721565(+)$1	342	293	318	20.4720
CCCCACAGUGACCCUGGCCUCUCCC	chr1:21546347-21546711(-)$1	364	46	71	19.7871
CUUCCAGUAACAGAAAAGGUGACCG	chr7:36455267-36455541(+)$1	274	159	184	21.4995
GGGAAAACUUUUCAUACCAGGUGAU	chr4:26432480-26432765(+)$1	285	241	266	19.1111

#DB
((((............)))))))..	chr8:117658609-117658875(-)$1	1	98	123	19.3020
(((.............)))))..).	chr21:33073988-33074334(-)$1	1	61	86	22.0755
.(.......................	chr1:42664669-42665002(-)$1	1	58	83	18.1160
((............)))..(((((.	chr22:24237122-24237496(+)$1	1	113	138	17.7374
((.............))))))))).	chr5:102433193-102433506(-)$1	1	274	299	19.8929
.(((............))).))((.	chr16:89346827-89347198(-)$1	1	145	170	20.1463
((....................)))	chr19:33078074-33078421(+)$1	1	210	235	18.2189
((.......................	chr16:50259002-50259297(+)$1	1	114	139	18.2154
((....................)))	chr1:214803774-214804106(+)$1	1	241	266	18.3611
(((.............)))))..((	chr17:61890544-61890830(+)$1	1	5	30	19.1287
((.....................))	chr12:106641154-106641476(-)$1	1	76	101	18.3531
((...............))))))((	chr11:118239342-118239622(+)$1	1	119	144	18.1001
((................)))))))	chr1:70700283-70700568(+)$1	1	125	150	20.5885
((......................)	chr19:35741162-35741490(+)$1	1	147	172	18.1674
(.((............)))))))))	chr16:23080594-23080947(-)$1	1	203	228	18.0567
((((............)))))....	chr14:55510695-55511037(+)$1	1	113	138	21.4228
(((............))))))))))	chr1:183497927-183498277(+)$1	1	103	128	20.0380
((................))))).)	chr14:52174731-52175051(+)$1	1	128	153	20.7217
(((.............)))))....	chr8:95538574-95538876(-)$1	1	252	277	19.5369
((..............)))))...)	chr13:49030289-49030584(+)$1	1	176	201	22.8178
((..............)))))....	chr14:51107371-51107709(-)$1	1	178	203	19.9359
((............))))).))).)	chr19:9059381-9059761(-)$1	1	227	252	19.8774
((((............)))))).))	chr11:18530986-18531302(-)$1	1	101	126	19.6782
((((...........)))).))..)	chr16:89629192-89629448(+)$1	1	140	165	17.3472
..(((...........)))..))).	chr12:85695123-85695437(+)$1	1	104	129	17.5508
((..............)))..((((	chr14:31122623-31122873(+)$1	1	123	148	20.0788
(((((...........)))))..))	chr18:33289598-33289922(+)$1	1	96	121	18.2843
((.......................	chr10:64973827-64974187(-)$1	1	155	180	18.2154
(((...........)))).)))...	chr16:2809470-2809765(+)$1	1	182	207	17.8344
((..................)))))	chr3:194168483-194168730(-)$1	1	187	212	18.1248
((...............))))))..	chr7:135080435-135080724(-)$1	1	69	94	17.9990
((..............)))))))))	chr5:173036255-173036540(-)$1	1	149	174	19.3277
((.....................))	chr19:55899514-55899799(+)$1	1	6	31	18.0025
(((.............)))))..))	chr10:28970996-28971277(+)$1	1	77	102	21.8156
(((.............))))..)))	chr10:64967674-64968055(-)$1	1	71	96	21.3604
((..............))).)))).	chr7:82582625-82582938(-)$1	1	138	163	21.3598
((..............)))))))..	chrX:122754662-122754916(-)$1	1	63	88	20.8103
((..............)))))))))	chr7:100174216-100174460(-)$1	1	195	220	21.5443
((((............)))))).))	chr16:70560398-70560729(+)$1	1	283	308	19.5234
((...............))).)).)	chr2:223497816-223498126(-)$1	1	140	165	18.7252
((..............)))))...(	chr12:121755978-121756296(-)$1	1	102	127	20.5537
((.............)))...))))	chr9:98734967-98735313(+)$1	1	88	113	20.9005
.((.............)).)).).)	chr3:124951625-124951973(-)$1	1	116	141	20.4660
((..............)))))))..	chrX:76763812-76764172(-)$1	1	146	171	20.9213
((......................)	chr7:40027330-40027586(+)$1	1	202	227	18.0921
..(............)..))))).)	chr2:73479879-73480223(+)$1	1	208	233	21.1878
((((............)))))))))	chr5:123983360-123983634(-)$1	1	236	261	18.9384
((...............))))))).	chr17:65145893-65146150(-)$1	1	223	248	18.5753
(.((............)).))))).	chr19:9047086-9047364(-)$1	1	138	163	19.8559
((.............)))).(((((	chr2:71220726-71221005(-)$1	1	127	152	19.7120
(((.............)))))....	chr18:56998620-56998861(-)$1	1	18	43	22.4031
((((............))))...))	chr7:97822696-97822955(+)$1	1	145	170	20.9077
(((.............)))))..))	chr3:10018561-10018821(-)$1	1	62	87	21.8137
((...............).))))))	chr2:85866285-85866609(+)$1	1	26	51	18.9284
..(((...........)))....))	chr12:27067340-27067610(-)$1	1	124	149	18.0397
((...............)))).)))	chr19:48894423-48894824(-)$1	1	62	87	18.5380
(((.............))))).)))	chr21:44328887-44329214(+)$1	1	294	319	19.1100
(((.............)))))))))	chr10:8006423-8006694(+)$1	1	35	60	21.7398
((..............)))))))..	chr11:9456380-9456657(+)$1	1	105	130	22.1974
((....................)))	chr2:201768271-201768724(+)$1	1	308	333	18.3611
(((............)))).)))))	chr17:65925363-65925682(+)$1	1	138	163	20.2174
(((...........)))...)))).	chr4:52729502-52729773(+)$1	1	109	134	17.9009
((..............)))))))).	chr15:49170832-49171122(+)$1	1	149	174	19.6642
((...................))))	chr9:82339948-82340444(+)$1	1	98	123	18.1414
((................))))...	chr11:122931733-122932066(-)$1	1	245	270	18.3583
((..................)))))	chr18:13008373-13008730(+)$1	1	70	95	18.1248
.(((............))).))).)	chr16:71961508-71961744(+)$1	1	189	214	21.2368
((((............))))..)))	chr19:9045685-9046075(-)$1	1	153	178	19.8198
((..............)))))...(	chr5:176721223-176721565(+)$1	1	293	318	20.4720
((.............)))).)))..	chr1:21546347-21546711(-)$1	1	46	71	19.7871
(((.............))))))).)	chr7:36455267-36455541(+)$1	1	159	184	21.4995
((..............)))))))))	chr4:26432480-26432765(+)$1	1	241	266	19.1111

#PSSM
e : 0.25	d : 0.19	g : 0.16	c : 0.16	[ : 0.05	f : 0.05	i : 0.04	h : 0.02	! : 0.02	$ : 0.01	
e : 0.23	c : 0.19	d : 0.19	g : 0.16	f : 0.05	a : 0.02	i : 0.02	[ : 0.02	! : 0.02	b : 0.01	$ : 0.01	h : 0.01	
^ : 0.18	w : 0.18	e : 0.13	d : 0.09	x : 0.08	c : 0.06	v : 0.05	g : 0.04	y : 0.04	b : 0.04	u : 0.02	f : 0.02	a : 0.01	
v : 0.20	^ : 0.18	w : 0.18	x : 0.08	u : 0.06	c : 0.05	y : 0.04	d : 0.04	g : 0.02	b : 0.02	e : 0.02	f : 0.02	t : 0.02	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	y : 0.04	t : 0.04	c : 0.02	e : 0.01	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	t : 0.08	y : 0.04	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	t : 0.08	y : 0.04	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	t : 0.08	y : 0.04	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	t : 0.08	y : 0.04	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	t : 0.08	y : 0.04	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	t : 0.08	y : 0.04	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	t : 0.08	y : 0.04	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	t : 0.08	y : 0.04	
u : 0.22	v : 0.20	^ : 0.18	w : 0.18	x : 0.08	t : 0.08	y : 0.04	
v : 0.20	u : 0.19	^ : 0.18	w : 0.18	x : 0.08	t : 0.05	y : 0.04	c : 0.02	e : 0.01	d : 0.01	
^ : 0.18	w : 0.18	u : 0.15	v : 0.15	x : 0.08	d : 0.08	c : 0.04	y : 0.04	t : 0.04	i : 0.01	e : 0.01	a : 0.01	
e : 0.22	^ : 0.18	c : 0.13	d : 0.13	g : 0.08	x : 0.08	y : 0.04	b : 0.04	f : 0.02	i : 0.01	2 : 0.01	h : 0.01	
e : 0.22	^ : 0.18	d : 0.15	c : 0.12	g : 0.09	f : 0.05	y : 0.04	b : 0.04	: : 0.01	i : 0.01	2 : 0.01	a : 0.01	3 : 0.01	h : 0.01	
e : 0.25	^ : 0.18	d : 0.15	g : 0.11	c : 0.11	f : 0.05	] : 0.05	h : 0.02	3 : 0.02	: : 0.01	i : 0.01	
e : 0.26	^ : 0.18	g : 0.11	d : 0.11	] : 0.09	f : 0.05	i : 0.02	h : 0.02	: : 0.02	c : 0.02	3 : 0.02	2 : 0.01	b : 0.01	4 : 0.01	
e : 0.29	^ : 0.15	g : 0.13	d : 0.08	f : 0.05	c : 0.05	b : 0.04	2 : 0.04	i : 0.02	h : 0.02	3 : 0.02	: : 0.01	] : 0.01	4 : 0.01	H : 0.01	
g : 0.15	^ : 0.13	e : 0.11	2 : 0.08	: : 0.08	f : 0.06	d : 0.06	c : 0.06	b : 0.04	4 : 0.04	i : 0.02	h : 0.02	3 : 0.02	] : 0.02	E : 0.01	H : 0.01	
g : 0.16	e : 0.11	^ : 0.09	c : 0.09	: : 0.08	2 : 0.06	f : 0.06	d : 0.05	4 : 0.04	3 : 0.04	i : 0.02	b : 0.02	h : 0.02	] : 0.02	E : 0.02	a : 0.01	H : 0.01	
c : 0.12	: : 0.11	e : 0.11	] : 0.09	g : 0.08	d : 0.08	^ : 0.06	4 : 0.04	f : 0.04	i : 0.02	h : 0.02	3 : 0.02	2 : 0.02	E : 0.02	a : 0.01	b : 0.01	D : 0.01	= : 0.01	5 : 0.01	C : 0.01	H : 0.01	
c : 0.13	: : 0.12	g : 0.11	e : 0.09	d : 0.08	f : 0.06	] : 0.04	^ : 0.04	4 : 0.04	i : 0.02	b : 0.02	2 : 0.02	E : 0.02	$ : 0.01	[ : 0.01	D : 0.01	h : 0.01	= : 0.01	3 : 0.01	9 : 0.01	5 : 0.01	C : 0.01	H : 0.01	

#score	1411.9712472519705
#seq	72
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_CDS_m3_run2.txt

#BEAR
b[ddddqqqqqqqqdddd2	chr20:44437694-44437912(+)$1	218	70	89	14.4029
ddddddqqqqqqqqdddd:	chr1:90058331-90058559(+)$1	228	148	167	13.3589
eeee[aqqqqqqqqa]eee	chr3:141671698-141671945(-)$1	247	168	187	14.1848
======qqqqqqqq=====	chr17:4458150-4458376(-)$1	226	174	193	14.3120
eeddddqqqqqqqqdddd]	chr1:28601390-28601625(+)$1	235	10	29	14.4838
GGddddqqqqqqqqdddd:	chr1:16259828-16260068(+)$1	240	92	111	12.6766
[bbcccqqqqqqqqccc]b	chr11:58892779-58893005(+)$1	226	101	120	13.9545
!!bb[aqqqqqqqqa]bb2	chrX:47040562-47040785(+)$1	223	93	112	13.4592
ffffffqqqqqqqqfffff	chr1:200377072-200377308(-)$1	236	82	101	12.8867
""ddddqqqqqqqqdddd4	chr11:62291173-62291405(-)$1	232	167	186	14.9019
F:ddddqqqqqqqqdddd:	chr5:71490468-71490712(+)$1	244	153	172	12.3612
!eeeeeqqqqqqqqeeeee	chr13:73336048-73336272(-)$1	224	140	159	14.0400
d!!cccqqqqqqqqccc22	chr13:46563022-46563245(-)$1	223	106	125	14.5300
:eeeeeqqqqqqqqeeeee	chr5:102894886-102895110(-)$1	224	38	57	12.9875
[ccc[aqqqqqqqqa]ccc	chr5:32390388-32390611(-)$1	223	130	149	14.5534
ccc[bbqqqqqqqqbb]cc	chr19:16629976-16630215(-)$1	239	172	191	13.1641
ffffffqqqqqqqqfffff	chr13:113914941-113915166(+)$1	225	186	205	12.8867
!!ddddqqqqqqqqdddd]	chr6:159205625-159205854(-)$1	229	82	101	15.0065
"ccc[aqqqqqqqqa]ccc	chr4:159631865-159632093(-)$1	228	164	183	14.5703
ccccccqqqqqqqqccc]c	chr8:146033334-146033561(+)$1	227	186	205	14.5718
e!!cccqqqqqqqqccc55	chr7:6731020-6731260(-)$1	240	57	76	13.3276
eeeeeeqqqqqqqqeeeee	chr10:43882791-43883045(-)$1	254	44	63	13.7780
e!!cccqqqqqqqqccc44	chr19:37853152-37853397(+)$1	245	123	142	14.9180
::ddddqqqqqqqqdddde	chr10:75527642-75527865(+)$1	223	169	188	12.6986
b[ddddqqqqqqqqdddd]	chr11:77825264-77825504(-)$1	240	81	100	14.5511
eee[bbqqqqqqqqbb]ee	chr17:57032974-57033200(+)$1	226	7	26	13.1821
:eeeeeqqqqqqqqeeeee	chr10:64973487-64973745(-)$1	258	56	75	12.9875
[a[cccqqqqqqqqccc22	chr16:2009620-2009851(+)$1	231	21	40	14.5709
!!ddddqqqqqqqqdddd]	chr6:150004271-150004497(-)$1	226	145	164	15.0065
ccc[bbqqqqqqqqbb]cc	chr11:118454521-118454748(+)$1	227	121	140	13.1641
======qqqqqqqq=====	chr7:92354948-92355177(-)$1	229	18	37	14.3120
f!!a[aqqqqqqqqa]a]f	chr22:50716923-50717147(-)$1	224	141	160	14.4429
[eeeeeqqqqqqqqeeeee	chr2:128036796-128037029(-)$1	233	94	113	13.9988
"""cccqqqqqqqqccc]e	chr7:6730514-6730756(-)$1	242	64	83	14.9724
fccc[aqqqqqqqqa]ccc	chr6:87965487-87965715(+)$1	228	136	155	14.3206
ggggggqqqqqqqqggggg	chr15:60741443-60741668(-)$1	225	87	106	13.9025
iiddddqqqqqqqqdddd:	chr1:54675634-54675898(+)$1	264	151	170	13.6795
#eeeeeqqqqqqqqeeeee	chr13:45826921-45827145(+)$1	224	161	180	13.9802
dddd[aqqqqqqqqa]ddd	chr6:136582405-136582635(-)$1	230	37	56	14.0754
##ddddqqqqqqqqddddc	chr10:5782214-5782439(+)$1	225	150	169	14.7349
ddbb[aqqqqqqqqa]bb]	chr10:104572259-104572484(+)$1	225	39	58	12.8766
eee!!aqqqqqqqqa22ee	chr6:136554449-136554678(-)$1	229	117	136	13.6131
bb[cccqqqqqqqqccc]b	chr19:35757490-35757741(+)$1	251	134	153	13.9578
f[ddddqqqqqqqqdddd3	chr15:68438884-68439105(+)$1	221	16	35	14.7423
ggggggqqqqqqqqggggg	chrM:12400-12663(+)$1	263	235	254	13.9025
#eeeeeqqqqqqqqeeeee	chr2:128482626-128482858(-)$1	232	180	199	13.9802
eeecccqqqqqqqqccc]e	chr8:71071649-71071886(-)$1	237	58	77	14.5414
eeeebbqqqqqqqqbb444	chr13:50296024-50296262(-)$1	238	195	214	13.3063
%%%cccqqqqqqqqccc33	chr10:63700009-63700240(+)$1	231	91	110	13.1304
!eeeeeqqqqqqqqeeeee	chr6:36449271-36449498(+)$1	227	110	129	14.0400
""ddddqqqqqqqqddddd	chr10:103869257-103869483(-)$1	226	177	196	14.6728
!!ddddqqqqqqqqddddc	chr17:4908084-4908321(+)$1	237	125	144	14.8948
ccccccqqqqqqqqccc]c	chr17:38546190-38546432(-)$1	242	39	58	14.5718
ffffffqqqqqqqqfffff	chr12:76740326-76740565(-)$1	239	15	34	12.8867
!!ddddqqqqqqqqdddd2	chr4:79847688-79847909(-)$1	221	179	198	14.8583
ccc[bbqqqqqqqqbb]cc	chr20:8665576-8665812(+)$1	236	76	95	13.1641
=[ddddqqqqqqqqdddd2	chr11:28110008-28110234(-)$1	226	187	206	14.6661
bb[cccqqqqqqqqccc]b	chr1:154186832-154187064(-)$1	232	80	99	13.9578
c!!cccqqqqqqqqccc]c	chr2:164466581-164466808(-)$1	227	28	47	14.9404
dd[cccqqqqqqqqcccdd	chr19:58805795-58806041(+)$1	246	24	43	14.2049
ff[cccqqqqqqqqccc]f	chr1:151373917-151374163(+)$1	246	175	194	14.4283
gggg[aqqqqqqqqa]ggg	chr7:70255153-70255377(+)$1	224	34	53	14.2365
c"""bbqqqqqqqqbb22c	chr1:150620971-150621199(-)$1	228	200	219	12.9480
"""cccqqqqqqqqcccee	chr19:6364480-6364730(+)$1	250	26	45	14.8870
ggggggqqqqqqqqggggg	chr2:170591504-170591745(+)$1	241	72	91	13.9025
ffffffqqqqqqqqfffff	chr11:65049044-65049281(+)$1	237	125	144	12.8867
e[ddddqqqqqqqqdddd]	chr1:36605267-36605488(-)$1	221	137	156	14.6952

#otherMatches

#Seq PSSM
CCCCAGGAUAAGCACUGGC	chr20:44437694-44437912(+)$1	218	70	89	14.4029
CCUCCUGAACUAGAAGGAU	chr1:90058331-90058559(+)$1	228	148	167	13.3589
CUGGUGCCACCUUACCCCA	chr3:141671698-141671945(-)$1	247	168	187	14.1848
UCGGGCGAGAAACAGCCCG	chr17:4458150-4458376(-)$1	226	174	193	14.3120
GCUGGAUGAGAAGUUCCAG	chr1:28601390-28601625(+)$1	235	10	29	14.4838
CAGUCAUGUACUUCUGACC	chr1:16259828-16260068(+)$1	240	92	111	12.6766
CUUCGGAAAAAUGACUGCA	chr11:58892779-58893005(+)$1	226	101	120	13.9545
CCGCCGGUCGACUACAGCU	chrX:47040562-47040785(+)$1	223	93	112	13.4592
GUUUUCAAAGAAAAGAAGA	chr1:200377072-200377308(-)$1	236	82	101	12.8867
AACUUGAAAGGCCCCAAGG	chr11:62291173-62291405(-)$1	232	167	186	14.9019
UGCGGAGAAAAUCAUCCGA	chr5:71490468-71490712(+)$1	244	153	172	12.3612
AAUGGAUAAUGAUUUUCAU	chr13:73336048-73336272(-)$1	224	140	159	14.0400
UCCUUCUCCUCGUCGAAAA	chr13:46563022-46563245(-)$1	223	106	125	14.5300
AAAGGUGGGAAGAAGCCUU	chr5:102894886-102895110(-)$1	224	38	57	12.9875
GCCGCCGAAUGCCAGAUGG	chr5:32390388-32390611(-)$1	223	130	149	14.5534
CCUAUGAGAACUACCGCAG	chr19:16629976-16630215(-)$1	239	172	191	13.1641
AGCAUGUUUAAUUCUAUGU	chr13:113914941-113915166(+)$1	225	186	205	12.8867
UUUUGCAUUCCAGAGUGAU	chr6:159205625-159205854(-)$1	229	82	101	15.0065
AUAUGAUCAAGCAUUGGUA	chr4:159631865-159632093(-)$1	228	164	183	14.5703
GCAAGUCCAACCUCACUCU	chr8:146033334-146033561(+)$1	227	186	205	14.5718
GAACUCAUUCAGGAGAGAA	chr7:6731020-6731260(-)$1	240	57	76	13.3276
GCUUCGUGCGGCUUCGAGG	chr10:43882791-43883045(-)$1	254	44	63	13.7780
AAAGGCACUUUCCAGCCCA	chr19:37853152-37853397(+)$1	245	123	142	14.9180
AUCUGCUUAUAUAUGCAGU	chr10:75527642-75527865(+)$1	223	169	188	12.6986
GGAGCAUUUCUCUUUGCUG	chr11:77825264-77825504(-)$1	240	81	100	14.5511
AAAUGGCCUUUUAUCUUUU	chr17:57032974-57033200(+)$1	226	7	26	13.1821
AACCUGUUUAAAUCCAGGU	chr10:64973487-64973745(-)$1	258	56	75	12.9875
ACAAGGAUGUGUACCCUGA	chr16:2009620-2009851(+)$1	231	21	40	14.5709
GAGCGAAGGGAAUCUCGUA	chr6:150004271-150004497(-)$1	226	145	164	15.0065
UGCAGUAUCUGGAGGCAGC	chr11:118454521-118454748(+)$1	227	121	140	13.1641
GCUCAACUUCCGUUUUGAG	chr7:92354948-92355177(-)$1	229	18	37	14.3120
GCGGGCGAGAACUGGGCAC	chr22:50716923-50717147(-)$1	224	141	160	14.4429
CUCCUGAAUUUUACCGGGA	chr2:128036796-128037029(-)$1	233	94	113	13.9988
UUCAGGAGAGAAACCCUUU	chr7:6730514-6730756(-)$1	242	64	83	14.9724
UGGUUUUAAUAGUUACGCC	chr6:87965487-87965715(+)$1	228	136	155	14.3206
GAUAUGACUAUAGAUAUAU	chr15:60741443-60741668(-)$1	225	87	106	13.9025
GAUGUGAAAAAUGACACAG	chr1:54675634-54675898(+)$1	264	151	170	13.6795
CUGUUGCUAAUCAUCAAUA	chr13:45826921-45827145(+)$1	224	161	180	13.9802
UGGUGUGGAUUAUUGGGCC	chr6:136582405-136582635(-)$1	230	37	56	14.0754
GAUCACUUUCAAAUGUGAA	chr10:5782214-5782439(+)$1	225	150	169	14.7349
GCCUAGAACAAUGACCAGU	chr10:104572259-104572484(+)$1	225	39	58	12.8766
GCACUUAAACAGAAAUUUG	chr6:136554449-136554678(-)$1	229	117	136	13.6131
CAGCAGUGUGGCCUCUGGU	chr19:35757490-35757741(+)$1	251	134	153	13.9578
UAGGGUUACCUUCCACCUA	chr15:68438884-68439105(+)$1	221	16	35	14.7423
UCAUAGAAUUCUCACUGUG	chrM:12400-12663(+)$1	263	235	254	13.9025
AGAAGAGCUUCAAGUCUUC	chr2:128482626-128482858(-)$1	232	180	199	13.9802
CUUGUUGCUGCACAAACGA	chr8:71071649-71071886(-)$1	237	58	77	14.5414
AGAUGGUAUAUUUUCCCUA	chr13:50296024-50296262(-)$1	238	195	214	13.3063
UACAGGCAGUCAACCCUAA	chr10:63700009-63700240(+)$1	231	91	110	13.1304
GUUUGAUCACUACCUCGAA	chr6:36449271-36449498(+)$1	227	110	129	14.0400
CAUGUCUGUCCCCUGACAA	chr10:103869257-103869483(-)$1	226	177	196	14.6728
CCGGCUGAUUAGAGAGCUG	chr17:4908084-4908321(+)$1	237	125	144	14.8948
GGUGCCAAAAAAAGGGCUG	chr17:38546190-38546432(-)$1	242	39	58	14.5718
UCUCAUUGAACAACAUGAG	chr12:76740326-76740565(-)$1	239	15	34	12.8867
UUCCUACUCUUCACUGGGU	chr4:79847688-79847909(-)$1	221	179	198	14.8583
GAUUUGAAUGAAGACAUGU	chr20:8665576-8665812(+)$1	236	76	95	13.1641
UAAAUAGUUUGAAAUAUUG	chr11:28110008-28110234(-)$1	226	187	206	14.6661
CUUGCAGAUGAUGAUGCUA	chr1:154186832-154187064(-)$1	232	80	99	13.9578
GCAUCCUUUUAUUUGGACC	chr2:164466581-164466808(-)$1	227	28	47	14.9404
UUAGUCAGUCAGCAGACAG	chr19:58805795-58806041(+)$1	246	24	43	14.2049
GCCCACAUGAUCAGGUGAG	chr1:151373917-151374163(+)$1	246	175	194	14.4283
GCCCCGCAGACCCACCGGG	chr7:70255153-70255377(+)$1	224	34	53	14.2365
ACAAGCGAACACUAGCACU	chr1:150620971-150621199(-)$1	228	200	219	12.9480
UACAUCCUCAACCCGAUCU	chr19:6364480-6364730(+)$1	250	26	45	14.8870
AUCCAGUGGAUUUUCUGGA	chr2:170591504-170591745(+)$1	241	72	91	13.9025
UGGUAGGAAACUUGUUGCC	chr11:65049044-65049281(+)$1	237	125	144	12.8867
CUUUCGGGAAACUGCGGAU	chr1:36605267-36605488(-)$1	221	137	156	14.6952

#DB
(.((((........)))).	chr20:44437694-44437912(+)$1	1	70	89	14.4029
))((((........)))).	chr1:90058331-90058559(+)$1	1	148	167	13.3589
((((.(........).)))	chr3:141671698-141671945(-)$1	1	168	187	14.1848
((((((........)))))	chr17:4458150-4458376(-)$1	1	174	193	14.3120
((((((........)))).	chr1:28601390-28601625(+)$1	1	10	29	14.4838
))((((........)))).	chr1:16259828-16260068(+)$1	1	92	111	12.6766
.(((((........))).)	chr11:58892779-58893005(+)$1	1	101	120	13.9545
..((.(........).)).	chrX:47040562-47040785(+)$1	1	93	112	13.4592
((((((........)))))	chr1:200377072-200377308(-)$1	1	82	101	12.8867
..((((........)))).	chr11:62291173-62291405(-)$1	1	167	186	14.9019
(.((((........)))).	chr5:71490468-71490712(+)$1	1	153	172	12.3612
.(((((........)))))	chr13:73336048-73336272(-)$1	1	140	159	14.0400
(..(((........)))..	chr13:46563022-46563245(-)$1	1	106	125	14.5300
.(((((........)))))	chr5:102894886-102895110(-)$1	1	38	57	12.9875
.(((.(........).)))	chr5:32390388-32390611(-)$1	1	130	149	14.5534
(((.((........)).))	chr19:16629976-16630215(-)$1	1	172	191	13.1641
((((((........)))))	chr13:113914941-113915166(+)$1	1	186	205	12.8867
..((((........)))).	chr6:159205625-159205854(-)$1	1	82	101	15.0065
.(((.(........).)))	chr4:159631865-159632093(-)$1	1	164	183	14.5703
((((((........))).)	chr8:146033334-146033561(+)$1	1	186	205	14.5718
(..(((........)))..	chr7:6731020-6731260(-)$1	1	57	76	13.3276
((((((........)))))	chr10:43882791-43883045(-)$1	1	44	63	13.7780
(..(((........)))..	chr19:37853152-37853397(+)$1	1	123	142	14.9180
..((((........))))(	chr10:75527642-75527865(+)$1	1	169	188	12.6986
(.((((........)))).	chr11:77825264-77825504(-)$1	1	81	100	14.5511
(((.((........)).))	chr17:57032974-57033200(+)$1	1	7	26	13.1821
.(((((........)))))	chr10:64973487-64973745(-)$1	1	56	75	12.9875
.(.(((........)))..	chr16:2009620-2009851(+)$1	1	21	40	14.5709
..((((........)))).	chr6:150004271-150004497(-)$1	1	145	164	15.0065
(((.((........)).))	chr11:118454521-118454748(+)$1	1	121	140	13.1641
((((((........)))))	chr7:92354948-92355177(-)$1	1	18	37	14.3120
(..(.(........).).)	chr22:50716923-50717147(-)$1	1	141	160	14.4429
.(((((........)))))	chr2:128036796-128037029(-)$1	1	94	113	13.9988
...(((........))).)	chr7:6730514-6730756(-)$1	1	64	83	14.9724
((((.(........).)))	chr6:87965487-87965715(+)$1	1	136	155	14.3206
((((((........)))))	chr15:60741443-60741668(-)$1	1	87	106	13.9025
))((((........)))).	chr1:54675634-54675898(+)$1	1	151	170	13.6795
.(((((........)))))	chr13:45826921-45827145(+)$1	1	161	180	13.9802
((((.(........).)))	chr6:136582405-136582635(-)$1	1	37	56	14.0754
..((((........)))))	chr10:5782214-5782439(+)$1	1	150	169	14.7349
((((.(........).)).	chr10:104572259-104572484(+)$1	1	39	58	12.8766
(((..(........)..))	chr6:136554449-136554678(-)$1	1	117	136	13.6131
((.(((........))).)	chr19:35757490-35757741(+)$1	1	134	153	13.9578
(.((((........)))).	chr15:68438884-68439105(+)$1	1	16	35	14.7423
((((((........)))))	chrM:12400-12663(+)$1	1	235	254	13.9025
.(((((........)))))	chr2:128482626-128482858(-)$1	1	180	199	13.9802
((((((........))).)	chr8:71071649-71071886(-)$1	1	58	77	14.5414
((((((........))...	chr13:50296024-50296262(-)$1	1	195	214	13.3063
...(((........)))..	chr10:63700009-63700240(+)$1	1	91	110	13.1304
.(((((........)))))	chr6:36449271-36449498(+)$1	1	110	129	14.0400
..((((........)))))	chr10:103869257-103869483(-)$1	1	177	196	14.6728
..((((........)))))	chr17:4908084-4908321(+)$1	1	125	144	14.8948
((((((........))).)	chr17:38546190-38546432(-)$1	1	39	58	14.5718
((((((........)))))	chr12:76740326-76740565(-)$1	1	15	34	12.8867
..((((........)))).	chr4:79847688-79847909(-)$1	1	179	198	14.8583
(((.((........)).))	chr20:8665576-8665812(+)$1	1	76	95	13.1641
(.((((........)))).	chr11:28110008-28110234(-)$1	1	187	206	14.6661
((.(((........))).)	chr1:154186832-154187064(-)$1	1	80	99	13.9578
(..(((........))).)	chr2:164466581-164466808(-)$1	1	28	47	14.9404
((.(((........)))))	chr19:58805795-58806041(+)$1	1	24	43	14.2049
((.(((........))).)	chr1:151373917-151374163(+)$1	1	175	194	14.4283
((((.(........).)))	chr7:70255153-70255377(+)$1	1	34	53	14.2365
(...((........))..)	chr1:150620971-150621199(-)$1	1	200	219	12.9480
...(((........)))))	chr19:6364480-6364730(+)$1	1	26	45	14.8870
((((((........)))))	chr2:170591504-170591745(+)$1	1	72	91	13.9025
((((((........)))))	chr11:65049044-65049281(+)$1	1	125	144	12.8867
(.((((........)))).	chr1:36605267-36605488(-)$1	1	137	156	14.6952

#PSSM
e : 0.14	f : 0.11	! : 0.10	c : 0.10	d : 0.07	" : 0.07	b : 0.05	[ : 0.05	g : 0.05	= : 0.04	: : 0.04	# : 0.04	G : 0.01	F : 0.01	i : 0.01	% : 0.01	
e : 0.20	! : 0.14	c : 0.11	[ : 0.07	f : 0.07	" : 0.07	d : 0.05	g : 0.05	b : 0.04	= : 0.02	: : 0.02	G : 0.01	a : 0.01	i : 0.01	# : 0.01	% : 0.01	
d : 0.28	e : 0.19	c : 0.11	! : 0.07	[ : 0.07	f : 0.05	g : 0.05	b : 0.04	" : 0.04	= : 0.02	% : 0.01	
d : 0.28	c : 0.28	e : 0.14	f : 0.05	[ : 0.05	g : 0.05	= : 0.02	b : 0.02	a : 0.01	! : 0.01	" : 0.01	
d : 0.26	c : 0.23	[ : 0.13	e : 0.11	b : 0.08	f : 0.05	g : 0.04	= : 0.02	! : 0.01	
d : 0.26	c : 0.23	a : 0.14	e : 0.11	b : 0.08	f : 0.05	g : 0.04	= : 0.02	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
d : 0.26	c : 0.23	a : 0.14	e : 0.11	b : 0.08	f : 0.05	g : 0.04	= : 0.02	
d : 0.26	c : 0.23	] : 0.13	e : 0.11	b : 0.08	f : 0.05	g : 0.04	= : 0.02	2 : 0.01	
d : 0.28	c : 0.28	e : 0.13	f : 0.05	] : 0.05	g : 0.05	= : 0.02	b : 0.02	2 : 0.02	a : 0.01	4 : 0.01	
d : 0.29	e : 0.17	] : 0.14	c : 0.08	f : 0.05	g : 0.05	2 : 0.04	= : 0.02	b : 0.02	4 : 0.02	5 : 0.01	3 : 0.01	
e : 0.22	c : 0.17	2 : 0.08	] : 0.08	f : 0.08	: : 0.05	g : 0.05	b : 0.04	4 : 0.04	d : 0.04	= : 0.02	3 : 0.02	5 : 0.01	

#score	936.7925577526246
#seq	67
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_CDS_m1_run1.txt

#BEAR
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^fffff	chrM:11068-11407(+)$1	339	229	264	38.1828
ggg!!a^^^^^^^^^^^^^^^^^^^^a22gggggg	chr20:47679744-47679968(+)$1	224	97	132	35.2379
^^^^^^^^^^^^^^^^^^^^^^^^^^^^eeeeedd	chr1:154226278-154226506(+)$1	228	168	203	38.0893
!bb^^^^^^^^^^^^^^^^^^^^^^^^^bb22ccc	chr1:54262329-54262562(-)$1	233	98	133	36.2535
:::ccc^^^^^^^^^^^^^^^^^^^cccbb!!ddd	chr7:112124851-112125077(+)$1	226	95	130	30.3828
:eeeeecccyyyyyyyyyyyyyyyyccc22eeeee	chr3:152553793-152554017(+)$1	224	97	132	23.5044
eee[eeeeeyyyyyyyyyyyyyyyyeeeee]eeee	chr7:5239134-5239359(+)$1	225	167	202	23.9126
cc!!ccc^^^^^^^^^^^^^^^^^^ccc22cccgg	chr19:44680608-44680842(+)$1	234	24	59	33.3245
f^^^^^^^^^^^^^^^^^^^^^^^^ffffff:fff	chr2:198256919-198257140(-)$1	221	96	131	34.6097
^^^^^^^^^^^^^^^^^^^^^^^^^dddd]eeeee	chr14:23239348-23239577(+)$1	229	24	59	36.3513
^^^^^^^^^^^^^^^^^^^^^^^^^^^hhhhhhhh	chr8:77895678-77895902(-)$1	224	100	135	36.5162
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr19:37734448-37734676(+)$1	228	100	135	38.1171
b^^^^^^^^^^^^^^^^^^^^^^^^bb]hhhhhhh	chr17:57917082-57917309(+)$1	227	97	132	34.8565
cc^^^^^^^^^^^^^^^^^^^^^^^ccc22eeeee	chr8:120843832-120844053(-)$1	221	97	132	36.0901
[bb[ccc^^^^^^^^^^^^^^^^^^^^^^ccc]bb	chr1:227843173-227843397(+)$1	224	172	207	33.8001
[ffffff^^^^^^^^^^^^^^^^^^ffffff]ddd	chr10:98287069-98287301(-)$1	232	106	141	31.0316
:ffffff^^^^^^^^^^^^^^^^^^^^^^^fffff	chr1:197111637-197111863(-)$1	226	10	45	32.7987
dffffff^^^^^^^^^^^^^^^^^^^^^ffffff8	chr14:55529286-55529514(+)$1	228	49	84	32.7087
bcccccc^^^^^^^^^^^^^^^^^^^^^ccc]ccc	chr5:145890093-145890325(+)$1	232	56	91	34.2998
fff^^^^^^^^^^^^^^^^^^^^^^^^^^^fffff	chrM:7017-7262(+)$1	245	114	149	36.9702
^^^^^^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chrM:10000-10253(+)$1	253	86	121	38.7470
^^^^^^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chr11:16769575-16769799(+)$1	224	127	162	38.7470
b^^^^^^^^^^^^^^^^^^^^^^^^^bb22dddd2	chr3:142741643-142741874(+)$1	231	112	147	35.7114
^^^^^^^^^^^^^^^^^^^^^^^^^ddddgggggg	chr2:227729342-227729573(+)$1	231	100	135	36.6981
!bb[ccc^^^^^^^^^^^^^^^^^^cccbb22ggg	chr13:33017486-33017708(-)$1	222	93	128	32.2052
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr5:138643283-138643509(+)$1	226	58	93	37.2131
ggggg^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chr19:44739410-44739641(+)$1	231	102	137	36.1709
eee^^^^^^^^^^^^^^^^^^^^^^^eeeeedddd	chr12:27156099-27156328(-)$1	229	98	133	35.5989
="""ccc^^^^^^^^^^^^^^^^^^^^ccc=====	chr12:98927401-98927636(+)$1	235	91	126	35.0129
c[bbeeeeeyyyyyyyyyyyyyyyyeeeee]bb]c	chr3:128356671-128356900(-)$1	229	92	127	23.0180
ccc:eeeeeyyyyyyyyyyyyyyyyeeeeeeeeee	chr2:18736776-18736999(-)$1	223	98	133	23.2923
^^^^^^^^^^^^^^^^^^^^^^^^^ccc]ccc]hh	chrM:10439-10665(+)$1	226	93	128	36.4671
[dddd^^^^^^^^^^^^^^^^^^^^^ddddfffff	chr2:103340238-103340467(-)$1	229	96	131	34.1600
e^^^^^^^^^^^^^^^^^^^^^^^^eeeeebbfff	chr2:176972113-176972336(+)$1	223	95	130	35.5557
^^^^^^^^^^^^^^^^^^^^^^^^^eeeee]gggg	chr19:35174922-35175155(+)$1	233	186	221	36.7830
e[bb^^^^^^^^^^^^^^^^^^^^^^^bbeeeee2	chr12:50481063-50481290(+)$1	227	96	131	35.3596
ddd^^^^^^^^^^^^^^^^^^^^^^^^dddd]ccc	chrM:7755-8020(+)$1	265	178	213	36.1260
g^^^^^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chr14:91947844-91948072(-)$1	228	7	42	38.5371
ffff^^^^^^^^^^^^^^^^^^^^^^^^^ffffff	chr3:180327551-180327774(+)$1	223	93	128	36.1531
^^^^^^^^^^^^^^^^^^^^^^^^^eeeeeggggg	chrM:9209-9430(+)$1	221	100	135	36.8298
b^^^^^^^^^^^^^^^^^^^^^^^^bbccc::===	chr16:11940577-11940799(-)$1	222	5	40	34.1006
ee"""cccyyyyyyyyyyyyyyyyccc4444eeee	chr9:127912069-127912295(-)$1	226	93	128	25.3913
ccc^^^^^^^^^^^^^^^^^^^^^^ccc22iiiii	chr12:57458397-57458619(-)$1	222	99	134	35.8575
iiiiiii^^^^^^^^^^^^^^^^^^^^iiiiiiii	chr12:46758072-46758299(-)$1	227	84	119	33.3395
ggg^^^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chrX:107977027-107977250(-)$1	223	94	129	37.6907
eeedddd^^^^^^^^^^^^^^^^^^dddd:ccc!!	chr2:225370631-225370853(-)$1	222	60	95	30.3753
!ffffff^^^^^^^^^^^^^^^^^^^^^ffffff2	chr7:135635298-135635523(-)$1	225	96	131	33.3571
&&&&ccc^^^^^^^^^^^^^^^^^^^^^^^^^ccc	chr10:112655698-112655927(+)$1	229	144	179	32.9383
gggggg^^^^^^^^^^^^^^^^^^^^^^ggggggg	chr19:9676517-9676752(-)$1	235	119	154	35.2589
[dddd^^^^^^^^^^^^^^^^^^^^dddd]eeeee	chr2:170487207-170487441(+)$1	234	175	210	33.6320
####ccc^^^^^^^^^^^^^^^^^^cccggggggg	chr12:95645616-95645842(+)$1	226	100	135	34.1449
eee^^^^^^^^^^^^^^^^^^^^^^eeeeeeeeee	chr8:26218454-26218690(+)$1	236	110	145	35.3651
bdddd^^^^^^^^^^^^^^^^^^^^^^^dddd]bb	chr19:30500111-30500346(+)$1	235	95	130	34.3349
==========yyyyyyyyyyyyyyyy=========	chr6:24781629-24781866(+)$1	237	25	60	24.0261
dd[dddd^^^^^^^^^^^^^^^^^^dddddddd88	chr14:55510114-55510334(+)$1	220	72	107	29.7292

#otherMatches

#Seq PSSM
ACUCUCACUGCCCAAGAACUAUCAAACUCCUGAGC	chrM:11068-11407(+)$1	339	229	264	38.1828
AGUAACAUUCAAAAACUAUAUUAAAAGGAACUGGA	chr20:47679744-47679968(+)$1	224	97	132	35.2379
CAACCUAUACCUCCCAAAAUAAUGCUCAGGGCCCU	chr1:154226278-154226506(+)$1	228	168	203	38.0893
UGAAUUUUCUAAUCCUUCUCCAUCUACCUCUAUUA	chr1:54262329-54262562(-)$1	233	98	133	36.2535
AAUGACUUAAACAAACUAAACCUCUGUCCAGCCGG	chr7:112124851-112125077(+)$1	226	95	130	30.3828
UGAUCUUCUACUACUUCAAUAAAACAGACUGGAUC	chr3:152553793-152554017(+)$1	224	97	132	23.5044
UUUAUUUUUCCCCUUCUUAAAAAAAAAAAAAAAAG	chr7:5239134-5239359(+)$1	225	167	202	23.9126
UCAAUCCCAUCAAAGAGUUCAUACAGGAGAGAAAC	chr19:44680608-44680842(+)$1	234	24	59	33.3245
CUUGACUAUAUCUUAUAAUUUUAUUGUUUAUUUUG	chr2:198256919-198257140(-)$1	221	96	131	34.6097
CCAACCAUUAAUUUCCCCUCACCUCACAGAUUACA	chr14:23239348-23239577(+)$1	229	24	59	36.3513
AUUUUUCUCUUACCACUUAUCAAUGUCCAGAAGUU	chr8:77895678-77895902(-)$1	224	100	135	36.5162
AUUCAUACuaauaaauaauaaaaauuaaaGCCCCU	chr19:37734448-37734676(+)$1	228	100	135	38.1171
UGUUACUUCAUCCUAUCUAUCAUUAACUCCAUGGC	chr17:57917082-57917309(+)$1	227	97	132	34.8565
CUGCAUCAACAACAUAAAUUUCCAGAGAAAAUCUG	chr8:120843832-120844053(-)$1	221	97	132	36.0901
AUGUGGCAAAGCCUUUAACCAGUUCUCAAGCCUUA	chr1:227843173-227843397(+)$1	224	172	207	33.8001
UUUUACUACUAUUUUUUCAAAACAAAGUAAGUGGA	chr10:98287069-98287301(-)$1	232	106	141	31.0316
CUGAGAUUAAUAAACCAAAAGCAAAAAGAUGUCUC	chr1:197111637-197111863(-)$1	226	10	45	32.7987
UUGGCAGAUGCACUACCUGAACACUCCCCUGCCAA	chr14:55529286-55529514(+)$1	228	49	84	32.7087
GGGGUCCACCCCCACCUCCCACAGCAUCGGAGCCC	chr5:145890093-145890325(+)$1	232	56	91	34.2998
GCCAAAAUCCAUUUCACUAUCAUAUUCAUCGGCGU	chrM:7017-7262(+)$1	245	114	149	36.9702
AACACCCUCCUAGCCUUACUACUAAUAAUUAUUAC	chrM:10000-10253(+)$1	253	86	121	38.7470
CGGUAAGAAAGUAAAGUGUAAUUAAAAUGGAAGUG	chr11:16769575-16769799(+)$1	224	127	162	38.7470
ACAUCCAAUAUACAUUCCGCCUUCUAUGAUGGAAC	chr3:142741643-142741874(+)$1	231	112	147	35.7114
CUUAUUCUACUCCUUUCUCAAAUCUUCCAUGUUGG	chr2:227729342-227729573(+)$1	231	100	135	36.6981
ACAAGUGUAUACAACUAAAAUCAAUCACUGGGCUU	chr13:33017486-33017708(-)$1	222	93	128	32.2052
UCCCAUAAUUUGCAGUCUAUAUUUAACAUUGGAAG	chr5:138643283-138643509(+)$1	226	58	93	37.2131
UUUUCAUUCUUAUCAAUCUAAUCAUACAGGAGAGA	chr19:44739410-44739641(+)$1	231	102	137	36.1709
UGACUUUUCUUAUUUUCCAAAUACACUCACAGUAU	chr12:27156099-27156328(-)$1	229	98	133	35.5989
UGCCUCAGAACUAUCUUUUCCCUUCCAUGAAUCUA	chr12:98927401-98927636(+)$1	235	91	126	35.0129
UUGAGGGGAACCAUUAUUUCUACUCUCCCUAUCCA	chr3:128356671-128356900(-)$1	229	92	127	23.0180
AGUUUCUUCCAAACUUUAUAAAUACGGAGACAUCA	chr2:18736776-18736999(-)$1	223	98	133	23.2923
AUAUCGCUCACACCUCAUAUCCUCCCUACUAUGCC	chrM:10439-10665(+)$1	226	93	128	36.4671
CAGGUAUUUUUAAACACACUCUCUCCAUCUCAAGG	chr2:103340238-103340467(-)$1	229	96	131	34.1600
GAUGACUUUCCCCUACUCUUCCAACCUGGCUCCGC	chr2:176972113-176972336(+)$1	223	95	130	35.5557
aaaaaaaaaaaaaaaaaGGCAGUGCUUUGCUUUCU	chr19:35174922-35175155(+)$1	233	186	221	36.7830
GCGAAUUUUCAUUUCUAACACUUUCAAUCCGGCUA	chr12:50481063-50481290(+)$1	227	96	131	35.3596
AAUCUUCAACUCCUACAUACUUCCCCCAUUAUUCC	chrM:7755-8020(+)$1	265	178	213	36.1260
UGAAACAAAAAAUUCAUCAGACAUACAGAGUUCAG	chr14:91947844-91948072(-)$1	228	7	42	38.5371
CUUCAGCAUCUUUUCUUAACCAUAAACAAGAAGUG	chr3:180327551-180327774(+)$1	223	93	128	36.1531
UUUCACUUCCACUCCAUAACGCUCCUCAUACUAGG	chrM:9209-9430(+)$1	221	100	135	36.8298
AUUUUUAAAUCCAAAUCCAAAUUGUUGCCUAAGUA	chr16:11940577-11940799(-)$1	222	5	40	34.1006
AGUUUGUUCAUAUCAACAACUUAAAACUCAUCUGC	chr9:127912069-127912295(-)$1	226	93	128	25.3913
GUCAAAUUUUCUACUACUCUACUGGGAUGACUGUG	chr12:57458397-57458619(-)$1	222	99	134	35.8575
AAAAUGACUCUUGCAGACCUCACUAUUUUAUUUUC	chr12:46758072-46758299(-)$1	227	84	119	33.3395
UCCUACUUCUCUCUACCAAACCCUUUUCGGAGCUC	chrX:107977027-107977250(-)$1	223	94	129	37.6907
UGACCGUCUCUUUAAACAAACUAUUGCGGGUGACU	chr2:225370631-225370853(-)$1	222	60	95	30.3753
CCAGAUAAACAUCAUAUUACUCCUCUUCUGUCUGC	chr7:135635298-135635523(-)$1	225	96	131	33.3571
AAGGUACUUUAUUUAAAUACUACUUUCUCAAUGUA	chr10:112655698-112655927(+)$1	229	144	179	32.9383
CAUUUAAAAACACACUGAAGAAAAACUCUGAAUGU	chr19:9676517-9676752(-)$1	235	119	154	35.2589
CCUCUGAUUCCGAAAGUGCUACUGAAGAGAAAUCA	chr2:170487207-170487441(+)$1	234	175	210	33.6320
AUUCUCCACUUUACCAAUACUUACAGGAUCUGGGA	chr12:95645616-95645842(+)$1	226	100	135	34.1449
CACAUCAACUCAAUUUCUAUUAAUAGUGAUUAUGA	chr8:26218454-26218690(+)$1	236	110	145	35.3651
GGAGAUAAUUCUAUACCAACAAUAUAUUUUUCACA	chr19:30500111-30500346(+)$1	235	95	130	34.3349
CUUGUUAAUUAAAUCAAAGUAAAUACAGUUGAUAA	chr6:24781629-24781866(+)$1	237	25	60	24.0261
GGUGGCAUUUUAUUAAACGACACACUGCUCCUAUA	chr14:55510114-55510334(+)$1	220	72	107	29.7292

#DB
..............................)))))	chrM:11068-11407(+)$1	1	229	264	38.1828
(((..(....................)..))))))	chr20:47679744-47679968(+)$1	1	97	132	35.2379
............................)))))))	chr1:154226278-154226506(+)$1	1	168	203	38.0893
.((.........................))..)))	chr1:54262329-54262562(-)$1	1	98	133	36.2535
...(((...................)))((..(((	chr7:112124851-112125077(+)$1	1	95	130	30.3828
.((((((((................)))..)))))	chr3:152553793-152554017(+)$1	1	97	132	23.5044
(((.(((((................))))).))))	chr7:5239134-5239359(+)$1	1	167	202	23.9126
((..(((..................)))..)))((	chr19:44680608-44680842(+)$1	1	24	59	33.3245
(........................)))))).(((	chr2:198256919-198257140(-)$1	1	96	131	34.6097
.........................)))).)))))	chr14:23239348-23239577(+)$1	1	24	59	36.3513
...........................))))))))	chr8:77895678-77895902(-)$1	1	100	135	36.5162
...............................))))	chr19:37734448-37734676(+)$1	1	100	135	38.1171
(........................)).)))))))	chr17:57917082-57917309(+)$1	1	97	132	34.8565
((.......................)))..)))))	chr8:120843832-120844053(-)$1	1	97	132	36.0901
.((.(((......................))).))	chr1:227843173-227843397(+)$1	1	172	207	33.8001
.((((((..................)))))).)))	chr10:98287069-98287301(-)$1	1	106	141	31.0316
.((((((.......................)))))	chr1:197111637-197111863(-)$1	1	10	45	32.7987
(((((((.....................)))))).	chr14:55529286-55529514(+)$1	1	49	84	32.7087
(((((((.....................))).)))	chr5:145890093-145890325(+)$1	1	56	91	34.2998
(((...........................)))))	chrM:7017-7262(+)$1	1	114	149	36.9702
............................)))))))	chrM:10000-10253(+)$1	1	86	121	38.7470
............................)))))))	chr11:16769575-16769799(+)$1	1	127	162	38.7470
(.........................))..)))).	chr3:142741643-142741874(+)$1	1	112	147	35.7114
.........................))))((((((	chr2:227729342-227729573(+)$1	1	100	135	36.6981
.((.(((..................)))))..)))	chr13:33017486-33017708(-)$1	1	93	128	32.2052
(((...........................)))))	chr5:138643283-138643509(+)$1	1	58	93	37.2131
(((((.......................)))))))	chr19:44739410-44739641(+)$1	1	102	137	36.1709
(((.......................)))))((((	chr12:27156099-27156328(-)$1	1	98	133	35.5989
(...(((....................))))))))	chr12:98927401-98927636(+)$1	1	91	126	35.0129
(.(((((((................))))).)).)	chr3:128356671-128356900(-)$1	1	92	127	23.0180
))).(((((................)))))(((((	chr2:18736776-18736999(-)$1	1	98	133	23.2923
.........................))).))).))	chrM:10439-10665(+)$1	1	93	128	36.4671
.((((.....................)))))))))	chr2:103340238-103340467(-)$1	1	96	131	34.1600
(........................)))))(((((	chr2:176972113-176972336(+)$1	1	95	130	35.5557
.........................))))).))))	chr19:35174922-35175155(+)$1	1	186	221	36.7830
(.((.......................))))))).	chr12:50481063-50481290(+)$1	1	96	131	35.3596
(((........................)))).)))	chrM:7755-8020(+)$1	1	178	213	36.1260
(...........................)))))))	chr14:91947844-91948072(-)$1	1	7	42	38.5371
((((.........................))))))	chr3:180327551-180327774(+)$1	1	93	128	36.1531
.........................))))))))))	chrM:9209-9430(+)$1	1	100	135	36.8298
(........................)))))..(((	chr16:11940577-11940799(-)$1	1	5	40	34.1006
((...(((................)))....))))	chr9:127912069-127912295(-)$1	1	93	128	25.3913
(((......................)))..)))))	chr12:57458397-57458619(-)$1	1	99	134	35.8575
(((((((....................))))))))	chr12:46758072-46758299(-)$1	1	84	119	33.3395
(((.........................)))))))	chrX:107977027-107977250(-)$1	1	94	129	37.6907
)))((((..................)))).(((..	chr2:225370631-225370853(-)$1	1	60	95	30.3753
.((((((.....................)))))).	chr7:135635298-135635523(-)$1	1	96	131	33.3571
....(((.........................)))	chr10:112655698-112655927(+)$1	1	144	179	32.9383
((((((......................)))))))	chr19:9676517-9676752(-)$1	1	119	154	35.2589
.((((....................)))).)))))	chr2:170487207-170487441(+)$1	1	175	210	33.6320
....(((..................))))))))))	chr12:95645616-95645842(+)$1	1	100	135	34.1449
(((......................))))))))))	chr8:26218454-26218690(+)$1	1	110	145	35.3651
(((((.......................)))).))	chr19:30500111-30500346(+)$1	1	95	130	34.3349
((((((((((................)))))))))	chr6:24781629-24781866(+)$1	1	25	60	24.0261
((.((((..................))))))))..	chr14:55510114-55510334(+)$1	1	72	107	29.7292

#PSSM
^ : 0.20	e : 0.14	g : 0.09	c : 0.09	b : 0.09	[ : 0.07	! : 0.05	: : 0.05	f : 0.05	d : 0.05	= : 0.03	i : 0.01	& : 0.01	# : 0.01	
^ : 0.30	e : 0.12	f : 0.10	c : 0.09	d : 0.09	g : 0.07	b : 0.05	[ : 0.03	: : 0.01	" : 0.01	i : 0.01	& : 0.01	# : 0.01	= : 0.01	
^ : 0.32	e : 0.10	f : 0.10	b : 0.09	g : 0.07	d : 0.07	c : 0.05	" : 0.03	: : 0.01	! : 0.01	i : 0.01	& : 0.01	# : 0.01	= : 0.01	[ : 0.01	
^ : 0.47	f : 0.09	d : 0.09	[ : 0.05	! : 0.03	c : 0.03	g : 0.03	" : 0.03	b : 0.03	e : 0.01	: : 0.01	i : 0.01	& : 0.01	# : 0.01	= : 0.01	
^ : 0.50	c : 0.14	d : 0.09	e : 0.07	f : 0.07	g : 0.03	! : 0.01	" : 0.01	i : 0.01	= : 0.01	
^ : 0.58	c : 0.16	e : 0.07	f : 0.07	d : 0.03	a : 0.01	i : 0.01	g : 0.01	= : 0.01	
^ : 0.63	c : 0.16	f : 0.07	e : 0.05	d : 0.03	i : 0.01	= : 0.01	
^ : 0.89	e : 0.05	c : 0.03	= : 0.01	
^ : 0.89	e : 0.05	c : 0.01	y : 0.01	= : 0.01	
^ : 0.89	y : 0.09	= : 0.01	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.10	
^ : 0.89	y : 0.09	c : 0.01	
^ : 0.52	c : 0.16	e : 0.12	d : 0.09	f : 0.03	b : 0.03	y : 0.01	
^ : 0.45	c : 0.16	e : 0.14	d : 0.10	b : 0.05	f : 0.03	a : 0.01	= : 0.01	
^ : 0.36	c : 0.18	e : 0.14	d : 0.12	f : 0.03	b : 0.03	2 : 0.01	h : 0.01	] : 0.01	4 : 0.01	i : 0.01	= : 0.01	
e : 0.16	^ : 0.14	d : 0.14	g : 0.12	2 : 0.10	b : 0.07	f : 0.07	c : 0.05	h : 0.03	] : 0.01	4 : 0.01	i : 0.01	= : 0.01	
e : 0.18	g : 0.16	^ : 0.10	2 : 0.09	f : 0.09	c : 0.09	d : 0.07	b : 0.05	] : 0.03	h : 0.03	4 : 0.01	i : 0.01	: : 0.01	= : 0.01	
g : 0.18	e : 0.18	f : 0.16	c : 0.09	d : 0.07	] : 0.05	2 : 0.03	h : 0.03	^ : 0.03	= : 0.03	i : 0.03	! : 0.01	b : 0.01	: : 0.01	4 : 0.01	
e : 0.21	g : 0.20	f : 0.12	c : 0.07	d : 0.07	] : 0.05	2 : 0.03	: : 0.03	h : 0.03	= : 0.03	b : 0.03	i : 0.03	! : 0.01	^ : 0.01	
g : 0.21	e : 0.21	f : 0.16	c : 0.10	d : 0.09	] : 0.05	= : 0.05	h : 0.03	i : 0.03	b : 0.01	
g : 0.23	e : 0.20	f : 0.16	d : 0.09	c : 0.07	h : 0.05	= : 0.05	b : 0.03	i : 0.03	] : 0.01	! : 0.01	8 : 0.01	
g : 0.23	e : 0.18	f : 0.12	c : 0.09	d : 0.07	h : 0.05	2 : 0.05	= : 0.05	b : 0.03	8 : 0.03	i : 0.03	! : 0.01	

#score	1864.9680350561819
#seq	55
#width	35
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_UTR_m2_run2.txt

#BEAR
f[ccceeeeeooooooeeeee]ccc]f	chr19:44585122-44585323(+)$1	201	71	98	12.6461
[eeeee!!bboooooobbeeeee]a]d	chr12:109967636-109967837(+)$1	201	142	169	12.4204
===[bbddddoooooodddd]bb]===	chr22:32875114-32875315(+)$1	201	104	131	12.5826
!ggggggg[aooooooa]ggggggg]c	chr16:697401-697602(+)$1	201	111	138	13.9845
c####eeeeeooooooeeeee22ccc]	chr17:47010549-47010750(-)$1	201	145	172	12.6617
dddd[ccc[aooooooa]ccc]dddd4	chr12:56537741-56537942(+)$1	201	62	89	12.7175
!ddddeeeeeooooooeeeee333ddd	chr10:121347590-121347791(-)$1	201	57	84	12.3732
eeeee!!cccooooooccc]eeeee22	chr12:56507413-56507614(+)$1	201	109	136	13.2618
==========mmmm==========22e	chr12:3907807-3908008(-)$1	201	168	195	9.7912
eeeee!!cccooooooccc22eeeeef	chr16:30094687-30094888(+)$1	201	116	143	12.9592
dd[cccddddoooooodddd]cccddd	chr22:21977621-21977822(+)$1	201	88	115	12.6547
cc####ddddoooooodddd4444ccc	chr16:30771338-30771539(-)$1	201	28	55	13.3911
iiiii"""bboooooobb4444iiiii	chr15:34520479-34520680(+)$1	201	72	99	13.8768
dddd"""cccooooooccc333dddd3	chr10:58117488-58117689(-)$1	201	73	100	14.0202
e!!ccc!!bboooooobb22ccc]eee	chrX:153592605-153592806(-)$1	201	135	162	13.1182
eeeee[cccaooooooa]ccceeeee:	chr16:75665550-75665751(-)$1	201	111	138	11.7306
ddd####cccooooooccc22dddd22	chr5:157214639-157214840(-)$1	201	63	90	13.1092
ee[gggggggoooooogggggggeeee	chr19:37042735-37042936(-)$1	201	116	143	13.2765
=="""eeeeeooooooeeeee333===	chr17:30190366-30190567(-)$1	201	26	53	13.7231
============lll============	chr17:8160146-8160347(+)$1	201	86	113	11.0192
e!!bb[ddddoooooodddd]bb333e	chr6:111697433-111697634(-)$1	201	37	64	12.8407
cc!!ffffffooooooffffff22ccc	chr1:198190039-198190240(+)$1	201	134	161	12.2402
ggggggg!!aooooooa22gggggggE	chr5:31551406-31551607(+)$1	201	163	190	12.2699
ccc[ffffffooooooffffff22ccc	chr20:44053067-44053268(+)$1	201	122	149	12.0025
"iiiiiiiiiooooooiiiiiiiiidd	chr3:49763623-49763824(-)$1	201	106	133	14.3276
iiiiiiiiirrrrrrrrriiiiiiiii	chr11:61732892-61733093(-)$1	201	156	183	9.3840
h!!cccbbbboooooobb]bb]ccc]h	chr14:103800613-103800814(+)$1	201	109	136	11.9163
iiiiiiiiccclllccc4444iiiiii	chr22:42301429-42301630(+)$1	201	112	139	9.5573
fffffffcccooooooccc]ffffff2	chr3:169854119-169854320(-)$1	201	132	159	12.0469
ccc"""ddddoooooodddd22ccc66	chr1:183521278-183521479(+)$1	201	84	111	12.2545
$iiiiiiiiinnnnniiiiiiiii444	chr10:30306348-30306549(-)$1	201	25	52	10.0507
bb[a"""cccooooooccc]a]bb22c	chr17:61904949-61905150(+)$1	201	22	49	13.5169
c[a!!eeeeeooooooeeeee22accc	chr12:12274034-12274235(-)$1	201	6	33	12.7371
==========oooooo===========	chr11:130747548-130747749(-)$1	201	37	64	15.0386
d!!ccc[cccooooooccc]ccc22dd	chr12:50493584-50493785(+)$1	201	55	82	14.1992
ccc[ffffffooooooffffff333cc	chr18:13762082-13762283(+)$1	201	14	41	12.5904
d[iiiiiiiiinnnnniiiiiiiii]d	chr6:111214715-111214916(+)$1	201	142	169	10.1515
cc####ddddooooooddddccc333e	chr19:44236323-44236524(-)$1	201	88	115	13.6131
ddd[a[ddddoooooodddd]addddF	chr15:42140005-42140206(+)$1	201	90	117	12.0512
:gggggggbboooooobb]ggggggg:	chrX:154002810-154003011(+)$1	201	20	47	11.3268
!!eeeeecccooooooccc]eeeee]f	chr21:40568964-40569165(-)$1	201	44	71	13.3421
!!hhhhhhhhoooooohhhhhhhh]dd	chr1:46079704-46079905(+)$1	201	61	88	11.3458
"""gggggggooooooggggggg6666	chr10:14965023-14965224(-)$1	201	54	81	12.3776
[dddda!!bboooooobb22a]ddddc	chr15:40330407-40330608(-)$1	201	99	126	12.1501
hhhhhbbcccooooooccc]bb]hhhh	chr2:85545389-85545590(-)$1	201	16	43	11.4687
e[ccc"""cccnnnnnccc]ccc]eee	chr1:153614846-153615047(+)$1	201	123	150	9.7382
[bb[a"""bboooooobb333a]bb22	chr17:80209241-80209442(-)$1	201	139	166	12.5947
bb[ccc[cccooooooccccccbb]dd	chr11:125875791-125875992(-)$1	201	76	103	12.9525
"""ccc[cccoooooocccccc66666	chr17:62486950-62487151(-)$1	201	156	183	12.1881
###gggggggoooooogggggggffff	chr6:64421751-64421952(+)$1	201	159	186	13.2947
dddbb[ddddooooooddddbb]dddd	chr8:144731870-144732071(+)$1	201	83	110	11.3773
c[ccc!!cccooooooccc333ccc]c	chr12:133161599-133161800(+)$1	201	55	82	15.1351

#otherMatches

#Seq PSSM
UGUGGUCUUCACCGAGGAGGAGCUGGG	chr19:44585122-44585323(+)$1	201	71	98	12.6461
UUCCAUUAUCAAACCCGAGUGGAUCCG	chr12:109967636-109967837(+)$1	201	142	169	12.4204
AAGGACAGGCAGCCCAGUCUGGUGUUU	chr22:32875114-32875315(+)$1	201	104	131	12.5826
CCACGAGGAGAAUGUCCGCUUUGUGUC	chr16:697401-697602(+)$1	201	111	138	13.9845
CUCAAUAUGGAUCACACCGUGGUGCUG	chr17:47010549-47010750(-)$1	201	145	172	12.6617
AAAGAGAAGAACCGUAUGUUCCCUUUA	chr12:56537741-56537942(+)$1	201	62	89	12.7175
UGACAGAAGUCCUUAUACUUCAGUUGU	chr10:121347590-121347791(-)$1	201	57	84	12.3732
UCUGAAGCUAUGGACUUGGAUUGGAUU	chr12:56507413-56507614(+)$1	201	109	136	13.2618
AUAUUUGCAUAACAAUGUAAGUAUUGU	chr12:3907807-3908008(-)$1	201	168	195	9.7912
GCGCAAGUACGGCUCGGUGACUGUGUG	chr16:30094687-30094888(+)$1	201	116	143	12.9592
UGAUGAUGGAUUUUAUUUCACUCACAC	chr22:21977621-21977822(+)$1	201	88	115	12.6547
GCCUGGAAUAugucauuauuaguagca	chr16:30771338-30771539(-)$1	201	28	55	13.3911
GAAUUUAAUAUACAGUUGGCUUGAUUC	chr15:34520479-34520680(+)$1	201	72	99	13.8768
UAUGUGGGAAGAUAAUUUUAUUCAUGG	chr10:58117488-58117689(-)$1	201	73	100	14.0202
GAUGCCAAGCACGGUGGCAAGGCCCCA	chrX:153592605-153592806(-)$1	201	135	162	13.1182
CUAUGCAGACUAUCACGAUCUCAUGGA	chr16:75665550-75665751(-)$1	201	111	138	11.7306
GUCCGCUGCUGGGAUGGGCUUGACAGG	chr5:157214639-157214840(-)$1	201	63	90	13.1092
cauggaauugacauacuaguucuugag	chr19:37042735-37042936(-)$1	201	116	143	13.2765
UAAAAGAUCUUUGGAUGGAUUAUAUGA	chr17:30190366-30190567(-)$1	201	26	53	13.7231
GUGGUGGCUGGCACUGCCGGCUAUUGC	chr17:8160146-8160347(+)$1	201	86	113	11.0192
CCUGUGAAAGUAGUAUUUUUGAUUAUG	chr6:111697433-111697634(-)$1	201	37	64	12.8407
AGAAUUCUGAAAAAAAUCAGAAAACUA	chr1:198190039-198190240(+)$1	201	134	161	12.2402
cagagaugugcacauccuaaucucugg	chr5:31551406-31551607(+)$1	201	163	190	12.2699
CUGGGAAGAGAGUCCCCUCUUCAACAG	chr20:44053067-44053268(+)$1	201	122	149	12.0025
UUUCGGCAGCUGUGCUGCUGCUGGAUG	chr3:49763623-49763824(-)$1	201	106	133	14.3276
CUUUCUUCACCAAUCUCAUGAGGAGAG	chr11:61732892-61733093(-)$1	201	156	183	9.3840
CAGGUCGCCCAGCUCCGGCGCUGACGG	chr14:103800613-103800814(+)$1	201	109	136	11.9163
CGGGCAGUGCUGCUGGCCGAAGCUGCC	chr22:42301429-42301630(+)$1	201	112	139	9.5573
UGAAAAUAGUUGUAUUAUUCAUUUUCU	chr3:169854119-169854320(-)$1	201	132	159	12.0469
CAUGUCCCCAGCCACAUGGGAAGUGAA	chr1:183521278-183521479(+)$1	201	84	111	12.2545
GACUAAGCUGGUAAAUAGUUUGGUGUU	chr10:30306348-30306549(-)$1	201	25	52	10.0507
GGUCGGAGGUGCCUGGACCAGUCCAUG	chr17:61904949-61905150(+)$1	201	22	49	13.5169
GUGACUUGAACUAUGAUUCAGAACCUG	chr12:12274034-12274235(-)$1	201	6	33	12.7371
AGCCUUAUGGAAGAUGUCAUGAGGCUG	chr11:130747548-130747749(-)$1	201	37	64	15.0386
GCCUCUGCAUCCCUUAAUGGAGAAACG	chr12:50493584-50493785(+)$1	201	55	82	14.1992
CCUGUUGCUGCAAGCUCAGUGAAGUGG	chr18:13762082-13762283(+)$1	201	14	41	12.5904
UGUAGAAGGUGGUGGAUGCUUUCUAGA	chr6:111214715-111214916(+)$1	201	142	169	10.1515
UCCUCAUCUUACUUCAAAGAGAAAAAU	chr19:44236323-44236524(-)$1	201	88	115	13.6131
CCCUGGCUGCUGAGUUGCAGGUGGGAA	chr15:42140005-42140206(+)$1	201	90	117	12.0512
CCAGCAUUGACACCAUUCUAAUGUUGA	chrX:154002810-154003011(+)$1	201	20	47	11.3268
AAAUGGAAGGAAAAAACCUCUCCAUCU	chr21:40568964-40569165(-)$1	201	44	71	13.3421
AGUCUCUUCAAGAAAAUGAGGAGGAGG	chr1:46079704-46079905(+)$1	201	61	88	11.3458
CAUAAGAGAGUUCUGCUUCUCUUUCCC	chr10:14965023-14965224(-)$1	201	54	81	12.3776
GAUGGGAAGAAGAAGAUCAGCACUGUG	chr15:40330407-40330608(-)$1	201	99	126	12.1501
AGCUAACAGUGACUCAACUCGUCUAGU	chr2:85545389-85545590(-)$1	201	16	43	11.4687
AUGGACACGUUUGUUUAACAUCUUUAA	chr1:153614846-153615047(+)$1	201	123	150	9.7382
CCAGGGCUUCUCCUAUGACUACGUGUU	chr17:80209241-80209442(-)$1	201	139	166	12.5947
CACUUCCUGAUGCUGCUCAGAAUGAUG	chr11:125875791-125875992(-)$1	201	76	103	12.9525
GAAAGGAGUUAAUAGAAACCCUGUGGA	chr17:62486950-62487151(-)$1	201	156	183	12.1881
CCACUGGUCAAGUAUAUGACCAGGCCC	chr6:64421751-64421952(+)$1	201	159	186	13.2947
AGGGGCAGAGGAAACACUUUCCACCUC	chr8:144731870-144732071(+)$1	201	83	110	11.3773
GCCACUUGCUUUGCUCAGUUCUGUGUU	chr12:133161599-133161800(+)$1	201	55	82	15.1351

#DB
(.((((((((......))))).))).)	chr19:44585122-44585323(+)$1	1	71	98	12.6461
.(((((..((......))))))).).)	chr12:109967636-109967837(+)$1	1	142	169	12.4204
(((.((((((......)))).)).)))	chr22:32875114-32875315(+)$1	1	104	131	12.5826
.(((((((.(......).))))))).)	chr16:697401-697602(+)$1	1	111	138	13.9845
(....(((((......)))))..))).	chr17:47010549-47010750(-)$1	1	145	172	12.6617
((((.(((.(......).))).)))).	chr12:56537741-56537942(+)$1	1	62	89	12.7175
.(((((((((......)))))...)))	chr10:121347590-121347791(-)$1	1	57	84	12.3732
(((((..(((......))).)))))..	chr12:56507413-56507614(+)$1	1	109	136	13.2618
((((((((((....))))))))))..)	chr12:3907807-3908008(-)$1	1	168	195	9.7912
(((((..(((......)))..))))))	chr16:30094687-30094888(+)$1	1	116	143	12.9592
((.(((((((......)))).))))))	chr22:21977621-21977822(+)$1	1	88	115	12.6547
((....((((......))))....)))	chr16:30771338-30771539(-)$1	1	28	55	13.3911
(((((...((......))....)))))	chr15:34520479-34520680(+)$1	1	72	99	13.8768
((((...(((......)))...)))).	chr10:58117488-58117689(-)$1	1	73	100	14.0202
(..(((..((......))..))).)))	chrX:153592605-153592806(-)$1	1	135	162	13.1182
(((((.((((......).)))))))).	chr16:75665550-75665751(-)$1	1	111	138	11.7306
(((....(((......)))..))))..	chr5:157214639-157214840(-)$1	1	63	90	13.1092
((.(((((((......)))))))))))	chr19:37042735-37042936(-)$1	1	116	143	13.2765
((...(((((......)))))...)))	chr17:30190366-30190567(-)$1	1	26	53	13.7231
((((((((((((...))))))))))))	chr17:8160146-8160347(+)$1	1	86	113	11.0192
(..((.((((......)))).))...)	chr6:111697433-111697634(-)$1	1	37	64	12.8407
((..((((((......))))))..)))	chr1:198190039-198190240(+)$1	1	134	161	12.2402
(((((((..(......)..))))))))	chr5:31551406-31551607(+)$1	1	163	190	12.2699
(((.((((((......))))))..)))	chr20:44053067-44053268(+)$1	1	122	149	12.0025
.(((((((((......)))))))))))	chr3:49763623-49763824(-)$1	1	106	133	14.3276
(((((((((.........)))))))))	chr11:61732892-61733093(-)$1	1	156	183	9.3840
(..(((((((......)).)).))).)	chr14:103800613-103800814(+)$1	1	109	136	11.9163
(((((((((((...)))....))))))	chr22:42301429-42301630(+)$1	1	112	139	9.5573
((((((((((......))).)))))).	chr3:169854119-169854320(-)$1	1	132	159	12.0469
(((...((((......))))..)))..	chr1:183521278-183521479(+)$1	1	84	111	12.2545
.(((((((((.....)))))))))...	chr10:30306348-30306549(-)$1	1	25	52	10.0507
((.(...(((......))).).))..)	chr17:61904949-61905150(+)$1	1	22	49	13.5169
(.(..(((((......)))))..))))	chr12:12274034-12274235(-)$1	1	6	33	12.7371
((((((((((......)))))))))))	chr11:130747548-130747749(-)$1	1	37	64	15.0386
(..(((.(((......))).)))..))	chr12:50493584-50493785(+)$1	1	55	82	14.1992
(((.((((((......))))))...))	chr18:13762082-13762283(+)$1	1	14	41	12.5904
(.(((((((((.....))))))))).)	chr6:111214715-111214916(+)$1	1	142	169	10.1515
((....((((......)))))))...)	chr19:44236323-44236524(-)$1	1	88	115	13.6131
(((.(.((((......)))).))))))	chr15:42140005-42140206(+)$1	1	90	117	12.0512
.(((((((((......)).))))))).	chrX:154002810-154003011(+)$1	1	20	47	11.3268
..((((((((......))).))))).)	chr21:40568964-40569165(-)$1	1	44	71	13.3421
..((((((((......)))))))).))	chr1:46079704-46079905(+)$1	1	61	88	11.3458
...(((((((......)))))))....	chr10:14965023-14965224(-)$1	1	54	81	12.3776
.(((((..((......))..).)))))	chr15:40330407-40330608(-)$1	1	99	126	12.1501
((((((((((......))).)).))))	chr2:85545389-85545590(-)$1	1	16	43	11.4687
(.(((...(((.....))).))).)))	chr1:153614846-153615047(+)$1	1	123	150	9.7382
.((.(...((......))...).))..	chr17:80209241-80209442(-)$1	1	139	166	12.5947
((.(((.(((......)))))))).))	chr11:125875791-125875992(-)$1	1	76	103	12.9525
...(((.(((......)))))).....	chr17:62486950-62487151(-)$1	1	156	183	12.1881
...(((((((......)))))))))))	chr6:64421751-64421952(+)$1	1	159	186	13.2947
(((((.((((......)))))).))))	chr8:144731870-144732071(+)$1	1	83	110	11.3773
(.(((..(((......)))...))).)	chr12:133161599-133161800(+)$1	1	55	82	15.1351

#PSSM
c : 0.17	d : 0.15	e : 0.13	= : 0.09	! : 0.07	[ : 0.05	i : 0.05	" : 0.05	f : 0.03	h : 0.03	b : 0.03	g : 0.01	$ : 0.01	: : 0.01	# : 0.01	
d : 0.15	c : 0.11	! : 0.11	[ : 0.09	e : 0.09	= : 0.09	i : 0.09	g : 0.05	b : 0.05	# : 0.03	" : 0.03	f : 0.01	h : 0.01	
d : 0.13	c : 0.11	i : 0.11	e : 0.09	! : 0.09	= : 0.07	# : 0.07	[ : 0.07	g : 0.05	" : 0.05	h : 0.03	f : 0.01	a : 0.01	b : 0.01	
c : 0.17	g : 0.11	i : 0.11	e : 0.09	[ : 0.09	# : 0.07	d : 0.07	= : 0.05	" : 0.03	b : 0.03	! : 0.03	h : 0.03	f : 0.01	a : 0.01	
c : 0.17	g : 0.11	i : 0.11	e : 0.09	# : 0.07	" : 0.07	f : 0.07	b : 0.05	= : 0.05	d : 0.03	a : 0.03	h : 0.03	[ : 0.01	! : 0.01	
e : 0.13	c : 0.13	g : 0.11	" : 0.11	i : 0.09	[ : 0.07	f : 0.07	! : 0.05	= : 0.05	# : 0.05	b : 0.03	h : 0.01	a : 0.01	
d : 0.15	e : 0.11	! : 0.11	g : 0.11	" : 0.09	i : 0.09	f : 0.07	= : 0.05	[ : 0.05	c : 0.03	b : 0.03	# : 0.01	h : 0.01	
c : 0.26	d : 0.15	e : 0.09	g : 0.09	i : 0.09	! : 0.07	= : 0.05	" : 0.05	f : 0.05	b : 0.01	h : 0.01	
c : 0.28	d : 0.15	b : 0.13	e : 0.09	i : 0.07	= : 0.05	g : 0.05	f : 0.05	[ : 0.03	! : 0.01	h : 0.01	
c : 0.26	d : 0.15	b : 0.13	e : 0.09	a : 0.07	= : 0.05	g : 0.05	f : 0.05	i : 0.05	r : 0.01	h : 0.01	
o : 0.86	c : 0.03	m : 0.01	= : 0.01	r : 0.01	n : 0.01	i : 0.01	
o : 0.86	n : 0.05	m : 0.01	= : 0.01	r : 0.01	l : 0.01	
o : 0.86	n : 0.05	l : 0.03	m : 0.01	r : 0.01	
o : 0.86	n : 0.05	l : 0.03	m : 0.01	r : 0.01	
o : 0.86	n : 0.05	= : 0.01	l : 0.01	r : 0.01	c : 0.01	
o : 0.86	= : 0.03	n : 0.03	r : 0.01	c : 0.01	i : 0.01	
c : 0.26	d : 0.15	b : 0.13	e : 0.09	a : 0.07	= : 0.05	g : 0.05	f : 0.05	i : 0.05	r : 0.01	h : 0.01	
c : 0.24	d : 0.15	b : 0.13	e : 0.09	] : 0.05	= : 0.05	g : 0.05	f : 0.05	i : 0.05	2 : 0.01	r : 0.01	4 : 0.01	h : 0.01	
c : 0.28	d : 0.15	e : 0.11	g : 0.07	i : 0.07	= : 0.05	2 : 0.05	f : 0.05	4 : 0.03	] : 0.03	h : 0.01	3 : 0.01	
d : 0.15	] : 0.13	e : 0.11	g : 0.11	c : 0.07	2 : 0.07	i : 0.07	= : 0.05	3 : 0.05	f : 0.05	4 : 0.03	b : 0.01	h : 0.01	
e : 0.15	c : 0.15	g : 0.11	] : 0.07	f : 0.07	i : 0.07	= : 0.05	2 : 0.05	4 : 0.05	3 : 0.05	b : 0.05	a : 0.03	h : 0.01	
c : 0.13	g : 0.11	] : 0.09	e : 0.09	i : 0.09	b : 0.07	3 : 0.07	f : 0.07	2 : 0.05	= : 0.05	4 : 0.03	a : 0.03	d : 0.01	h : 0.01	
c : 0.17	g : 0.11	i : 0.11	e : 0.09	d : 0.09	b : 0.07	2 : 0.07	3 : 0.05	= : 0.05	] : 0.05	4 : 0.01	f : 0.01	h : 0.01	6 : 0.01	
c : 0.11	d : 0.11	i : 0.11	3 : 0.09	e : 0.09	] : 0.07	g : 0.05	= : 0.05	2 : 0.05	b : 0.05	f : 0.03	h : 0.03	6 : 0.03	4 : 0.01	a : 0.01	
c : 0.17	d : 0.15	e : 0.13	i : 0.09	= : 0.07	g : 0.05	2 : 0.05	3 : 0.05	f : 0.03	] : 0.03	6 : 0.03	a : 0.01	4 : 0.01	h : 0.01	b : 0.01	
d : 0.21	] : 0.13	c : 0.11	2 : 0.09	e : 0.09	= : 0.07	i : 0.05	6 : 0.05	3 : 0.03	g : 0.03	f : 0.03	4 : 0.01	h : 0.01	
d : 0.17	c : 0.17	e : 0.11	f : 0.07	= : 0.07	2 : 0.07	i : 0.05	6 : 0.05	4 : 0.03	: : 0.03	h : 0.03	] : 0.01	3 : 0.01	E : 0.01	F : 0.01	

#score	647.400203559691
#seq	52
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_UTR_m1_run2.txt

#BEAR
####ccc[bb!!ffffffooooooffffff22bb]ccc3	chr22:24236606-24236855(+)$1	249	94	133	11.5275
[ffffffggggggg!!bb[bblllbb]bb4444gggggg	chr17:6916926-6917157(+)$1	231	72	111	11.7374
===!!dddd"""gggggggmmmmggggggg333dddd22	chr8:42259397-42259628(+)$1	231	15	54	14.0967
gggggggccczzzzzzzzzzzzzzzzzccc4444ggggg	chr8:127564631-127564850(-)$1	219	178	217	11.6381
ggg"""ccc"""ddddllldddd4444ccc333gggggg	chr17:36918580-36918810(+)$1	230	134	173	12.3089
hhhhhhh"""ccc!!cccbbmmmmbb]ccc22ccc333h	chr5:72206170-72206399(+)$1	229	77	116	13.0879
ddd[dddd"""dddd[cccmmmmcccdddd22ddddddd	chr9:74969525-74969758(-)$1	233	28	67	12.2774
ddddeeeee"""ccc[cccnnnnnccc]ccc]eeeee]d	chr17:1248275-1248506(-)$1	231	113	152	12.1882
ccc===========!!bbmmmmbb22===========]c	chr9:133761619-133761845(+)$1	226	1	40	13.2857
iiiiiiiiibb[dddd[aooooooa]dddd333bb]iii	chr19:2428606-2428841(-)$1	235	20	59	14.5433
dffffff####ddddddddmmmmdddd]dddd4444fff	chrX:153667299-153667539(+)$1	240	157	196	12.4371
hhhhh[ccc"""gggggggmmmmggggggg333ccc]hh	chr10:112771582-112771809(+)$1	227	159	198	14.8319
hhhhh"""ccc!!cccbboooooobb]ccc22ccc22hh	chr9:6506767-6507014(+)$1	247	133	172	13.6308
e[bb[a####dddd[ddddmmmmdddddddd22a]bb]e	chr17:61769043-61769268(+)$1	225	145	184	12.0914
d[ccc!!dddd[a[eeeeeooooooeeeee]a]dddd44	chr1:70727558-70727779(-)$1	221	158	197	10.3090
ffffff[ccc[ccc[cccnnnnnccc]cccccc]fffff	chr17:47131140-47131367(+)$1	227	106	145	12.5349
g:ffffff"""dddd[bboooooobb]dddd333fffff	chr1:154192750-154192985(-)$1	235	156	195	14.0138
===========ddddddddmmmmdddd]dddd]======	chr1:11072622-11072853(+)$1	231	4	43	13.2149
eeeeffffff!!ccc!!bbmmmmbb22ccc333ffffff	chr20:2639033-2639271(-)$1	238	48	87	14.0312
hhhhhhhh[dddd[ccc[aooooooa]ccc22ddddhhh	chr6:170892610-170892865(-)$1	255	156	195	11.3785
$gggggggggggggg[ccclllcccggggggg4444ggg	chr16:4659086-4659315(-)$1	229	94	133	13.6597
!!ffffff!!ccc"""cccmmmmccc333ccc]ffffff	chr2:61711067-61711330(-)$1	263	103	142	14.2272
e[dddd[ccc"""a[bb[ammmmabb]a22ccc]dddde	chr1:44435628-44435881(+)$1	253	139	178	11.6730
gggg[a[============mmmm============]a44	chr17:39847452-39847701(+)$1	249	42	81	14.7448
gggggggg####ccc!!bbnnnnnbb22ccc4444gggg	chr12:104341337-104341559(+)$1	222	166	205	15.6699
eee!!ccc####dddd[bblllbb]dddd4444ccc]ee	chr16:30094875-30095147(+)$1	272	17	56	13.7743
bccc####bb!!bb[ddddmmmmdddd]bb4444bb333	chr2:217365986-217366224(+)$1	238	94	133	12.7225
e:eeeeebb!!ccc"""bbmmmmbb333ccc4444bb]e	chr5:157186778-157187027(+)$1	249	157	196	12.9344
b[ggggggg"""ccc!!bbnnnnnbb22ccc22gggggg	chr1:28300387-28300616(-)$1	229	136	175	15.0975
iiiiiiiii"""ccc[cccmmmmccc]ccc333iiiiii	chr17:47131623-47131859(+)$1	236	175	214	18.5418
d"""bbccc"""ccc[bbmmmmbbccc22ccc]bb333d	chr4:83372126-83372347(+)$1	221	178	217	12.5354
=======!!ccc####cccmmmmccc333ccc22=====	chr14:104208187-104208412(-)$1	225	129	168	15.5507
ggggggg!!cccgggggggmmmmggggggg333ccc]gg	chr5:71403228-71403447(+)$1	219	128	167	14.9314
c[a"""eeeee[eeeeebbmmmmbb]eeeee333eeeee	chr15:34633951-34634175(-)$1	224	109	148	11.2760
!a[a[cccbb"""bb[cccmmmmccc]bb]bb]ccca]a	chr5:180669158-180669407(-)$1	249	92	131	13.2998
eeeee####ccc!!a[bbmmmmbb]a]ccc4444eeeee	chr17:42766922-42767146(-)$1	224	46	85	13.0507
[ccc!!ccc[ccc[aooooooa]ccc]ccc22ccc]fff	chr14:104152310-104152533(+)$1	223	126	165	13.0479
ggggggg!!dddd"""ccclllccc22dddd22gggggg	chr1:28150239-28150466(+)$1	227	118	157	14.0216
##ggggggg####cccrrrrrrrrrccc4444ggggggg	chr19:33873130-33873370(+)$1	240	133	172	12.8950
cceeeee$$$$$ccc[cccnnnnnccc]ccceeeee]cc	chr7:120989413-120989634(-)$1	221	112	151	11.8974
""ffffff"""ccc!!cccrrrrrrrrrccc22ccc333	chr17:76210270-76210491(+)$1	221	166	205	13.1556
[===========abbddddllldddd333bb]a]=====	chr1:115260655-115260875(-)$1	220	15	54	13.1098
:ggggggg####ccc[ddddlllddddccc22ggggggg	chr12:110973186-110973417(-)$1	231	69	108	13.8827
ffff[a[ccc!!gggggggmmmmggggggg666666ccc	chr16:87866280-87866506(-)$1	226	131	170	11.4444
fff!!cccbb[dddd[ccclllccc]ddddbb]ccc444	chr11:69466755-69466984(+)$1	229	74	113	11.9903
fff"""ccc!!ccc!!cccmmmmccc22ccc333ccc44	chr20:57480375-57480612(+)$1	237	116	155	16.2360
ffffff!!bb####bbbboooooobb]bb333bb]ffff	chr3:47889692-47889932(+)$1	240	150	189	12.7459
========="""bboooooobb==========4444fff	chr10:81851798-81852027(+)$1	229	85	124	12.1465
iiiiiiii"""dddd[bboooooobb]dddd]iiiiiii	chr16:2312644-2312873(-)$1	229	154	193	15.5409
============[a[cccnnnnnccc]a]==========	chr12:49523205-49523436(-)$1	231	50	89	14.5057
===========!!eeeeellleeeee]===========d	chr3:184086068-184086290(+)$1	222	43	82	12.5335
hhhhh!!bb!!ccc!!ddddlllddddccc333bb22hh	chr17:28792726-28792950(+)$1	224	6	45	13.2382
:ccc!!bb"""gggggggooooooggggggg22bb22cc	chr1:165865373-165865603(+)$1	230	100	139	12.7688
bb[ffffffdddd[cccooooooccc]dddd333fffff	chr19:11663845-11664091(-)$1	246	68	107	12.7068

#otherMatches

#Seq PSSM
UCCGUGCCGGACGGGUUCCUCUCCGAGCUCACCCAGCAG	chr22:24236606-24236855(+)$1	249	94	133	11.5275
AUUUUUCAAUGUCCAUUCCGCUGUGUUGAUUGAGGACGU	chr17:6916926-6917157(+)$1	231	72	111	11.7374
UGGCCUUCGAAGGGUGGCUUGCUGGCUAUCAGAUGAGUU	chr8:42259397-42259628(+)$1	231	15	54	14.0967
CUUGAAUACCUUUUUUCUGACAUUUUUGGUCCAAAUUCA	chr8:127564631-127564850(-)$1	219	178	217	11.6381
GACCGGGAUGCAGUGUCAGGCAUGGGAGUCAUUGUCCAC	chr17:36918580-36918810(+)$1	230	134	173	12.3089
UUUAUUAAUUUGGAUUGCCUGAACAGUGUAUCCCAUGAU	chr5:72206170-72206399(+)$1	229	77	116	13.0879
CUUGUCUGGUAAUAAUCACUUCUGUGUUAUAAUGGAAGG	chr9:74969525-74969758(-)$1	233	28	67	12.2774
AUAGGUGAUGCAAGCAUCUAAGAGAGAGGUUAAUCACAC	chr17:1248275-1248506(-)$1	231	113	152	12.1882
GGUCACUCUGCCCUCUGCUGCUGCCCGGGGUGGGGUGCA	chr9:133761619-133761845(+)$1	226	1	40	13.2857
UUGAGAAUUGAGUCUUUGGAAACACUAAGAAAAUCAAAU	chr19:2428606-2428841(-)$1	235	20	59	14.5433
CGUCCACUGAGACUGAGGCCUUGGCUUCCAGUGAGUGUG	chrX:153667299-153667539(+)$1	240	157	196	12.4371
AAUUCUGUACAAAAGGCUUAUAUAAGUUUUCUUUGCUGA	chr10:112771582-112771809(+)$1	227	159	198	14.8319
UUUAGUGUCUCACCAGUGGUUUUACAUCUGCAGAGUUUU	chr9:6506767-6507014(+)$1	247	133	172	13.6308
CACAGCAACAUGAUUGUUCACCGGGACAUUAAgggugag	chr17:61769043-61769268(+)$1	225	145	184	12.0914
UCCUUGUUAUGGUCAUCAUAAGGUAAUGGUUAGCAUGUU	chr1:70727558-70727779(-)$1	221	158	197	10.3090
CUGUUUGCCUGUUUCUUGAAAACCAGUAGAAGGGAAACA	chr17:47131140-47131367(+)$1	227	106	145	12.5349
UACGGGAGCCUGGUGAGGAGAUUACCCCACCCCAUUCCU	chr1:154192750-154192985(-)$1	235	156	195	14.0138
CUCUCGUCGGUGCCUUCCACCUCUGGACAGGCAACCGGU	chr1:11072622-11072853(+)$1	231	4	43	13.2149
GGGAUUGUUAGGAUGGAGCCCAGGCCACAUGGAUGAUGA	chr20:2639033-2639271(-)$1	238	48	87	14.0312
UUUGUGGCUGUUUAGGCCCCAAAACGUGCUCCAGAUGCC	chr6:170892610-170892865(-)$1	255	156	195	11.3785
CCGCAUGUGUGCGCGUGGCCGUGUCUGUGUAUUUCUACG	chr16:4659086-4659315(-)$1	229	94	133	13.6597
AUCCUGAACAUAGAACGAACUUUUUCUUACUACUUCAGG	chr2:61711067-61711330(-)$1	263	103	142	14.2272
GAGGGCUGCUCUAGAGGACUCAGGCCCCGAAGCUGUCCC	chr1:44435628-44435881(+)$1	253	139	178	11.6730
CCAGCUGUACUACUAGAAGGGAGCUUUUGGUGGUAGAUC	chr17:39847452-39847701(+)$1	249	42	81	14.7448
UGGGAGAGACUUGUUUUGGAUGCCCCCUAAUCCCCUUCU	chr12:104341337-104341559(+)$1	222	166	205	15.6699
GCCAGCCCAGGGCUCCAUGGGACAGGGAGAGGAGGGGGG	chr16:30094875-30095147(+)$1	272	17	56	13.7743
CGGUAAAGUCCGCCAUCAGAAGACUGAAGGAGUUGAAAG	chr2:217365986-217366224(+)$1	238	94	133	12.7225
UAUCUUGCACUGCUCUAAUAAAAAUGAAAGCUCUCUGAC	chr5:157186778-157187027(+)$1	249	157	196	12.9344
GCAGACUUUUAUGAUAACAUCUCUUGCAGUCUUAGAGUC	chr1:28300387-28300616(-)$1	229	136	175	15.0975
AGGACAAGUGAGUUGAGGCUUGUGCCACAAAAGGUUUGU	chr17:47131623-47131859(+)$1	236	175	214	18.5418
GGCAGAUGUCCCUGGAUCGAAAGACCACUGCACUCAAAC	chr4:83372126-83372347(+)$1	221	178	217	12.5354
UUCCUGGCUGAUAAAGGGUCAAGGCCACAGUCUCCCAGG	chr14:104208187-104208412(-)$1	225	129	168	15.5507
GGAUGGCGACCGUGGUGGUGGAAGCCACCGAGCCGGAGC	chr5:71403228-71403447(+)$1	219	128	167	14.9314
CUCUUUGGCAUCCAGUCUCUCGUGGCGAUUGAUUAUGCU	chr15:34633951-34634175(-)$1	224	109	148	11.2760
GGGAUGAGACCAACUAUGGAAUUCCACAGCGUGCUCUGC	chr5:180669158-180669407(-)$1	249	92	131	13.2998
GCCGCGAUAGCCCCUGGCGAAGGCGAUGGCGGAGGCGGC	chr17:42766922-42767146(-)$1	224	46	85	13.0507
CAGUAGCAUUUGCUGUGUAGUCUGUGUGUGAAAUUUGGG	chr14:104152310-104152533(+)$1	223	126	165	13.0479
UUCCAAGAAAACUGGACACCAGGUGAGGGUUGGUUUGGA	chr1:28150239-28150466(+)$1	227	118	157	14.0216
AGACAGUUUAACAUUUGGUAUUAAAGGAGAGGAAAUUGU	chr19:33873130-33873370(+)$1	240	133	172	12.8950
GGCGGACUGAUAACAUUUAAAAAAUAAUUGUGUUUGACC	chr7:120989413-120989634(-)$1	221	112	151	11.8974
CUCAAGGACCACCGCAUCUCUACAUUCAAGAACUGGCCC	chr17:76210270-76210491(+)$1	221	166	205	13.1556
UUUUUUUUUUCUCCCCCCCACAGGGGUUUGGUGCAGAAA	chr1:115260655-115260875(-)$1	220	15	54	13.1098
AUUAAAAUUUAUGUUUGAGGUUACCUCAACUUGUUUUAA	chr12:110973186-110973417(-)$1	231	69	108	13.8827
CAGGUGUGCCUGUGCUCCUGCCCAGGAGCAGCUUUUGGU	chr16:87866280-87866506(-)$1	226	131	170	11.4444
GUAGCAGGGUCGGGAAAGGCCACCUGUCCCACUCCUACG	chr11:69466755-69466984(+)$1	229	74	113	11.9903
UACGAACGCUCCAACGAGUACCAGCUGAUUGACUGUGCC	chr20:57480375-57480612(+)$1	237	116	155	16.2360
GCUGCAAGCGAAAAUCCACAUGCCUGAGAAGACGGUGCG	chr3:47889692-47889932(+)$1	240	150	189	12.7459
CCCUGGAGGACUGCCUGCUUGCUUUCUGGGGACACUAGC	chr10:81851798-81852027(+)$1	229	85	124	12.1465
UGUGGGCAGUGGGGUGUGGACAAGCAGGCCUGUGCCUGC	chr16:2312644-2312873(-)$1	229	154	193	15.5409
CAUUGGGGGAGGAGAUGACUCCUUCAACACCUUCUUCAG	chr12:49523205-49523436(-)$1	231	50	89	14.5057
GUCACUCAGGUCAUGGGCAUUGUUCAAGCCUGAGUGGCA	chr3:184086068-184086290(+)$1	222	43	82	12.5335
UUCAGAUGACCCAGCCAUCUACAAGAUCUGAAUUCUACU	chr17:28792726-28792950(+)$1	224	6	45	13.2382
AAGGGAUCCUGGCCUUCUACUCCCAGGAGGUACGAGACC	chr1:165865373-165865603(+)$1	230	100	139	12.7688
GCCGUUCCCCAGGUCCCUGGGCUGGGCCCUGACAGGGAG	chr19:11663845-11664091(-)$1	246	68	107	12.7068

#DB
....(((.((..((((((......))))))..)).))).	chr22:24236606-24236855(+)$1	1	94	133	11.5275
.(((((((((((((..((.((...)).))....))))))	chr17:6916926-6917157(+)$1	1	72	111	11.7374
(((..((((...(((((((....)))))))...))))..	chr8:42259397-42259628(+)$1	1	15	54	14.0967
((((((((((.................)))....)))))	chr8:127564631-127564850(-)$1	1	178	217	11.6381
(((...(((...((((...))))....)))...))))))	chr17:36918580-36918810(+)$1	1	134	173	12.3089
(((((((...(((..(((((....)).)))..)))...)	chr5:72206170-72206399(+)$1	1	77	116	13.0879
(((.((((...((((.(((....)))))))..)))))))	chr9:74969525-74969758(-)$1	1	28	67	12.2774
(((((((((...(((.(((.....))).))).))))).)	chr17:1248275-1248506(-)$1	1	113	152	12.1882
((((((((((((((..((....))..))))))))))).)	chr9:133761619-133761845(+)$1	1	1	40	13.2857
(((((((((((.((((.(......).))))...)).)))	chr19:2428606-2428841(-)$1	1	20	59	14.5433
)((((((....((((((((....)))).))))....)))	chrX:153667299-153667539(+)$1	1	157	196	12.4371
(((((.(((...(((((((....)))))))...))).))	chr10:112771582-112771809(+)$1	1	159	198	14.8319
(((((...(((..(((((......)).)))..)))..))	chr9:6506767-6507014(+)$1	1	133	172	13.6308
(.((.(....((((.((((....))))))))..).)).)	chr17:61769043-61769268(+)$1	1	145	184	12.0914
(.(((..((((.(.(((((......))))).).))))..	chr1:70727558-70727779(-)$1	1	158	197	10.3090
((((((.(((.(((.(((.....))).)))))).)))))	chr17:47131140-47131367(+)$1	1	106	145	12.5349
).((((((...((((.((......)).))))...)))))	chr1:154192750-154192985(-)$1	1	156	195	14.0138
(((((((((((((((((((....)))).)))).))))))	chr1:11072622-11072853(+)$1	1	4	43	13.2149
((((((((((..(((..((....))..)))...))))))	chr20:2639033-2639271(-)$1	1	48	87	14.0312
((((((((.((((.(((.(......).)))..)))))))	chr6:170892610-170892865(-)$1	1	156	195	11.3785
.((((((((((((((.(((...))))))))))....)))	chr16:4659086-4659315(-)$1	1	94	133	13.6597
..((((((..(((...(((....)))...))).))))))	chr2:61711067-61711330(-)$1	1	103	142	14.2272
(.((((.(((...(.((.(....))).)..))).)))))	chr1:44435628-44435881(+)$1	1	139	178	11.6730
((((.(.((((((((((((....)))))))))))).)..	chr17:39847452-39847701(+)$1	1	42	81	14.7448
)(((((((....(((..((.....))..)))....))))	chr12:104341337-104341559(+)$1	1	166	205	15.6699
(((..(((....((((.((...)).))))....))).))	chr16:30094875-30095147(+)$1	1	17	56	13.7743
((((....((..((.((((....)))).))....))...	chr2:217365986-217366224(+)$1	1	94	133	12.7225
).(((((((..(((...((....))...)))....)).)	chr5:157186778-157187027(+)$1	1	157	196	12.9344
(.(((((((...(((..((.....))..)))..))))))	chr1:28300387-28300616(-)$1	1	136	175	15.0975
(((((((((...(((.(((....))).)))...))))))	chr17:47131623-47131859(+)$1	1	175	214	18.5418
(...(((((...(((.((....)))))..))).))...)	chr4:83372126-83372347(+)$1	1	178	217	12.5354
(((((((..(((....(((....)))...)))..)))))	chr14:104208187-104208412(-)$1	1	129	168	15.5507
(((((((..((((((((((....)))))))...))).))	chr5:71403228-71403447(+)$1	1	128	167	14.9314
(.(...(((((.(((((((....)).)))))...)))))	chr15:34633951-34634175(-)$1	1	109	148	11.2760
.(.(.(((((...((.(((....))).)).)).)))).)	chr5:180669158-180669407(-)$1	1	92	131	13.2998
(((((....(((..(.((....)).).)))....)))))	chr17:42766922-42767146(-)$1	1	46	85	13.0507
.(((..(((.(((.(......).))).)))..))).)))	chr14:104152310-104152533(+)$1	1	126	165	13.0479
(((((((..((((...(((...)))..))))..))))))	chr1:28150239-28150466(+)$1	1	118	157	14.0216
..(((((((....(((.........)))....)))))))	chr19:33873130-33873370(+)$1	1	133	172	12.8950
(((((((.....(((.(((.....))).)))))))).))	chr7:120989413-120989634(-)$1	1	112	151	11.8974
..((((((...(((..(((.........)))..)))...	chr17:76210270-76210491(+)$1	1	166	205	13.1556
.((((((((((((((((((...))))...)).).)))))	chr1:115260655-115260875(-)$1	1	15	54	13.1098
.(((((((....(((.((((...)))))))..)))))))	chr12:110973186-110973417(-)$1	1	69	108	13.8827
((((.(.(((..(((((((....)))))))......)))	chr16:87866280-87866506(-)$1	1	131	170	11.4444
(((..(((((.((((.(((...))).)))))).)))...	chr11:69466755-69466984(+)$1	1	74	113	11.9903
(((...(((..(((..(((....)))..)))...)))..	chr20:57480375-57480612(+)$1	1	116	155	16.2360
((((((..((....((((......)).))...)).))))	chr3:47889692-47889932(+)$1	1	150	189	12.7459
(((((((((...((......))))))))))))....)))	chr10:81851798-81852027(+)$1	1	85	124	12.1465
((((((((...((((.((......)).)))).)))))))	chr16:2312644-2312873(-)$1	1	154	193	15.5409
((((((((((((.(.(((.....))).).))))))))))	chr12:49523205-49523436(-)$1	1	50	89	14.5057
(((((((((((..(((((...))))).)))))))))))(	chr3:184086068-184086290(+)$1	1	43	82	12.5335
(((((..((..(((..((((...)))))))...))..))	chr17:28792726-28792950(+)$1	1	6	45	13.2382
.(((..((...(((((((......)))))))..))..))	chr1:165865373-165865603(+)$1	1	100	139	12.7688
((.((((((((((.(((......))).))))...)))))	chr19:11663845-11664091(-)$1	1	68	107	12.7068

#PSSM
g : 0.12	= : 0.11	e : 0.11	h : 0.09	d : 0.09	f : 0.09	[ : 0.05	c : 0.05	i : 0.05	b : 0.05	# : 0.03	! : 0.03	: : 0.03	$ : 0.01	" : 0.01	
g : 0.14	f : 0.12	= : 0.12	h : 0.09	c : 0.09	[ : 0.09	i : 0.05	e : 0.05	# : 0.03	d : 0.03	: : 0.03	" : 0.03	! : 0.01	a : 0.01	b : 0.01	
f : 0.18	g : 0.18	= : 0.12	h : 0.09	c : 0.09	e : 0.09	d : 0.05	i : 0.05	[ : 0.03	# : 0.01	b : 0.01	" : 0.01	a : 0.01	
f : 0.16	g : 0.16	= : 0.12	h : 0.09	" : 0.07	c : 0.07	e : 0.07	! : 0.05	i : 0.05	d : 0.03	# : 0.01	[ : 0.01	b : 0.01	a : 0.01	
f : 0.16	g : 0.14	= : 0.12	! : 0.09	h : 0.09	e : 0.07	[ : 0.07	" : 0.05	i : 0.05	c : 0.03	d : 0.03	# : 0.01	b : 0.01	
f : 0.16	g : 0.14	= : 0.12	c : 0.07	" : 0.07	! : 0.07	d : 0.05	e : 0.05	i : 0.05	a : 0.05	h : 0.03	# : 0.03	[ : 0.01	b : 0.01	
c : 0.16	g : 0.14	f : 0.12	= : 0.12	e : 0.07	[ : 0.07	i : 0.05	# : 0.05	! : 0.05	d : 0.03	h : 0.03	" : 0.01	b : 0.01	
c : 0.22	= : 0.12	g : 0.11	f : 0.09	# : 0.07	! : 0.07	d : 0.05	i : 0.05	b : 0.05	" : 0.03	e : 0.03	[ : 0.01	h : 0.01	$ : 0.01	
c : 0.18	b : 0.12	= : 0.12	" : 0.11	# : 0.11	g : 0.07	! : 0.07	d : 0.03	e : 0.03	i : 0.03	f : 0.03	[ : 0.01	$ : 0.01	
" : 0.25	c : 0.14	b : 0.11	= : 0.11	# : 0.11	d : 0.07	! : 0.07	g : 0.03	f : 0.01	e : 0.01	[ : 0.01	$ : 0.01	
" : 0.27	! : 0.12	c : 0.12	= : 0.11	# : 0.11	d : 0.09	g : 0.03	[ : 0.03	z : 0.01	b : 0.01	e : 0.01	$ : 0.01	
c : 0.20	" : 0.18	d : 0.18	! : 0.11	# : 0.09	= : 0.07	g : 0.05	[ : 0.05	z : 0.01	$ : 0.01	
c : 0.29	d : 0.24	g : 0.12	! : 0.05	# : 0.05	= : 0.03	a : 0.03	" : 0.03	b : 0.03	f : 0.01	z : 0.01	e : 0.01	[ : 0.01	
c : 0.27	d : 0.18	g : 0.12	[ : 0.07	b : 0.07	! : 0.03	= : 0.03	" : 0.03	a : 0.03	# : 0.03	e : 0.03	f : 0.01	z : 0.01	
c : 0.22	d : 0.16	! : 0.11	g : 0.11	[ : 0.09	e : 0.05	" : 0.05	b : 0.05	a : 0.03	f : 0.01	z : 0.01	= : 0.01	# : 0.01	o : 0.01	
[ : 0.22	! : 0.14	d : 0.14	c : 0.12	g : 0.09	e : 0.05	" : 0.05	b : 0.03	o : 0.03	f : 0.01	z : 0.01	= : 0.01	# : 0.01	
c : 0.31	b : 0.16	d : 0.12	g : 0.09	e : 0.05	! : 0.05	[ : 0.03	o : 0.03	f : 0.01	z : 0.01	l : 0.01	= : 0.01	" : 0.01	r : 0.01	
c : 0.27	b : 0.25	d : 0.12	g : 0.09	o : 0.05	e : 0.03	[ : 0.03	f : 0.01	z : 0.01	l : 0.01	a : 0.01	= : 0.01	r : 0.01	
c : 0.22	o : 0.18	b : 0.12	d : 0.12	g : 0.07	m : 0.05	l : 0.03	n : 0.03	a : 0.03	[ : 0.01	z : 0.01	e : 0.01	= : 0.01	r : 0.01	
m : 0.40	o : 0.22	n : 0.11	l : 0.11	d : 0.05	b : 0.03	r : 0.03	z : 0.01	
m : 0.42	o : 0.20	l : 0.14	n : 0.11	b : 0.03	r : 0.03	z : 0.01	d : 0.01	
m : 0.42	o : 0.18	l : 0.14	n : 0.11	r : 0.03	z : 0.01	d : 0.01	a : 0.01	b : 0.01	e : 0.01	
m : 0.37	o : 0.18	n : 0.11	b : 0.07	l : 0.05	c : 0.05	d : 0.03	r : 0.03	z : 0.01	] : 0.01	= : 0.01	e : 0.01	
c : 0.24	o : 0.16	b : 0.12	d : 0.12	g : 0.07	n : 0.07	= : 0.03	r : 0.03	l : 0.01	z : 0.01	4 : 0.01	m : 0.01	a : 0.01	e : 0.01	
c : 0.29	b : 0.22	d : 0.12	g : 0.09	o : 0.03	= : 0.03	] : 0.03	r : 0.03	f : 0.01	z : 0.01	4 : 0.01	2 : 0.01	a : 0.01	e : 0.01	
c : 0.25	b : 0.16	d : 0.14	g : 0.11	2 : 0.05	] : 0.05	e : 0.03	a : 0.03	= : 0.03	f : 0.01	z : 0.01	4 : 0.01	3 : 0.01	r : 0.01	
] : 0.29	d : 0.18	g : 0.11	2 : 0.09	c : 0.07	3 : 0.07	= : 0.05	e : 0.03	f : 0.01	z : 0.01	4 : 0.01	r : 0.01	
c : 0.24	d : 0.16	g : 0.11	] : 0.09	= : 0.07	3 : 0.07	2 : 0.07	b : 0.05	e : 0.03	a : 0.03	f : 0.01	r : 0.01	
c : 0.35	d : 0.20	g : 0.11	b : 0.07	= : 0.07	3 : 0.05	e : 0.03	2 : 0.03	f : 0.01	4 : 0.01	] : 0.01	
c : 0.40	d : 0.18	g : 0.11	= : 0.09	4 : 0.05	e : 0.03	b : 0.03	f : 0.01	2 : 0.01	] : 0.01	3 : 0.01	
c : 0.22	3 : 0.16	2 : 0.12	d : 0.12	4 : 0.11	= : 0.09	b : 0.05	g : 0.03	] : 0.01	e : 0.01	6 : 0.01	
3 : 0.24	2 : 0.22	4 : 0.14	= : 0.09	c : 0.09	] : 0.05	d : 0.03	b : 0.03	a : 0.01	g : 0.01	e : 0.01	6 : 0.01	
3 : 0.22	4 : 0.18	2 : 0.11	] : 0.11	c : 0.09	= : 0.07	b : 0.03	d : 0.03	e : 0.03	g : 0.03	a : 0.01	6 : 0.01	i : 0.01	
c : 0.16	4 : 0.14	b : 0.11	g : 0.11	= : 0.09	d : 0.07	3 : 0.07	] : 0.05	e : 0.03	f : 0.03	i : 0.03	a : 0.01	2 : 0.01	6 : 0.01	
c : 0.18	g : 0.12	= : 0.12	d : 0.09	b : 0.09	4 : 0.09	f : 0.09	e : 0.07	] : 0.05	i : 0.03	6 : 0.01	
c : 0.14	g : 0.14	= : 0.11	f : 0.11	d : 0.09	e : 0.07	] : 0.05	4 : 0.05	2 : 0.05	b : 0.05	3 : 0.03	i : 0.03	6 : 0.01	
g : 0.16	f : 0.16	= : 0.11	d : 0.07	3 : 0.07	] : 0.07	c : 0.05	e : 0.05	i : 0.05	2 : 0.05	b : 0.03	a : 0.03	h : 0.01	4 : 0.01	
g : 0.18	f : 0.16	] : 0.09	= : 0.09	c : 0.07	3 : 0.07	h : 0.07	4 : 0.07	i : 0.05	e : 0.05	d : 0.03	2 : 0.01	
g : 0.18	f : 0.16	e : 0.11	h : 0.09	d : 0.07	c : 0.07	4 : 0.07	= : 0.07	3 : 0.05	i : 0.05	2 : 0.01	a : 0.01	

#score	716.723590609359
#seq	54
#width	39
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_UTR_m3_run2.txt

#BEAR
hhhhhqqqqqqqqhhhhh	chr19:55741233-55741480(-)$1	247	191	209	12.6431
fffffqqqqqqqqfffff	chr3:72427424-72427664(-)$1	240	2	20	13.3656
&ddddqqqqqqqqdddd2	chr4:38699716-38699956(+)$1	240	90	108	12.6840
h[cccqqqqqqqqccc]h	chr8:91637471-91637711(-)$1	240	81	99	14.3176
hhhhhqqqqqqqqhhhhh	chr18:73001144-73001384(+)$1	240	142	160	12.6431
hhhhhqqqqqqqqhhhhh	chr22:22051346-22051586(+)$1	240	97	115	12.6431
fffffqqqqqqqqfffff	chr1:182568446-182568686(-)$1	240	196	214	13.3656
a!!bbqqqqqqqqbb22a	chr21:15753579-15753819(-)$1	240	12	30	13.0161
::cccqqqqqqqqcccff	chr13:73329348-73329588(+)$1	240	165	183	12.2076
gggggqqqqqqqqggggg	chr15:64657708-64658028(-)$1	320	208	226	14.0975
fffffqqqqqqqqfffff	chr1:204372566-204372806(-)$1	240	57	75	13.3656
fffffqqqqqqqqfffff	chr5:133956590-133956830(-)$1	240	19	37	13.3656
d[cccqqqqqqqqccc22	chr6:11134972-11135212(+)$1	240	37	55	14.2730
!!cccqqqqqqqqccc33	chr19:7087631-7087871(+)$1	240	176	194	14.9842
fffffqqqqqqqqfffff	chr5:171290653-171290893(-)$1	240	212	230	13.3656
gggggqqqqqqqqggggg	chr19:34922675-34922915(+)$1	240	56	74	14.0975
eeeeeqqqqqqqqeeeee	chr10:103919925-103920165(+)$1	240	155	173	13.3996
cc[bbqqqqqqqqbb]cc	chr14:23299096-23299336(+)$1	240	91	109	13.1219
fff[aqqqqqqqqaffff	chr9:108537173-108537413(+)$1	240	136	154	13.3550
$ddddqqqqqqqqdddd]	chr11:126133105-126133476(-)$1	371	95	113	13.2370
##cccqqqqqqqqccc22	chr8:131065593-131065837(-)$1	244	91	109	14.4192
[a[bbqqqqqqqqbbacc	chr6:31698405-31698645(-)$1	240	104	122	13.2604
gg[bbqqqqqqqqbb]gg	chr7:1199536-1199776(-)$1	240	157	175	13.3660
"ddddqqqqqqqqddddd	chr16:23075998-23076238(-)$1	240	217	235	13.1406
bb[bbqqqqqqqqbb333	chr11:73638578-73638818(+)$1	240	146	164	12.9054
[ddddqqqqqqqqdddd]	chr11:60658346-60658586(-)$1	240	80	98	13.5004
c[cccqqqqqqqqccc]c	chr20:418072-418312(-)$1	240	153	171	14.5950
gggggqqqqqqqqggggg	chr19:15234103-15234343(-)$1	240	44	62	14.0975
eeeeeqqqqqqqqeeeee	chr7:120427621-120427901(-)$1	280	163	181	13.3996
d[cccqqqqqqqqccc]d	chr22:39911151-39911391(+)$1	240	64	82	14.2729
==cccqqqqqqqqccc::	chr11:47593016-47593256(+)$1	240	145	163	12.5234
fffffqqqqqqqqfffff	chr2:135711167-135711416(+)$1	249	161	179	13.3656
eeeeeqqqqqqqqeeeee	chr1:181059474-181059722(+)$1	248	57	75	13.3996
$$cccqqqqqqqqccc44	chr15:58925391-58925631(-)$1	240	125	143	14.1612
gggggqqqqqqqqggggg	chr3:45959783-45960049(-)$1	266	13	31	14.0975
hddddqqqqqqqqdddd]	chr22:24811175-24811415(+)$1	240	92	110	13.1815
gggggqqqqqqqqggggg	chrX:150575720-150575965(+)$1	245	215	233	14.0975
eeeeeqqqqqqqqeeeee	chr19:44981147-44981387(-)$1	240	109	127	13.3996
eeeeeqqqqqqqqeeeee	chr2:201845197-201845438(-)$1	241	132	150	13.3996
cc[bbqqqqqqqqbb]cc	chr12:104498482-104498722(+)$1	240	195	213	13.1219
eeeeeqqqqqqqqeeeee	chr9:128729482-128729722(+)$1	240	3	21	13.3996
##cccqqqqqqqqccc44	chr22:32078425-32078665(-)$1	240	57	75	14.5267
eddddqqqqqqqqdddd:	chr8:38068113-38068361(+)$1	248	190	208	12.2357
eeeeeqqqqqqqqeeeee	chr20:34817335-34817579(+)$1	244	20	38	13.3996
e[cccqqqqqqqqccc]e	chr20:61826957-61827197(-)$1	240	33	51	14.5727
fffffqqqqqqqqfffff	chr2:32842840-32843080(+)$1	240	199	217	13.3656
cc[bbqqqqqqqqbb22c	chr21:40566023-40566263(-)$1	240	145	163	12.8788
##cccqqqqqqqqccc]e	chr1:154961011-154961281(+)$1	270	74	92	14.5708
fffffqqqqqqqqfffff	chr1:43829425-43829670(-)$1	245	101	119	13.3656
eeeeeqqqqqqqqeeeee	chr7:32907726-32907966(-)$1	240	21	39	13.3996
eeeeeqqqqqqqqeeeee	chr1:227178011-227178251(-)$1	240	137	155	13.3996
e!!bbqqqqqqqqbb22e	chr1:161093877-161094117(-)$1	240	174	192	13.0091
##cccqqqqqqqqccc44	chr22:45591804-45592044(-)$1	240	38	56	14.5267
!ddddqqqqqqqqdddd2	chr5:72205758-72205998(+)$1	240	95	113	13.3894
!ddddqqqqqqqqdddd2	chr15:40512957-40513197(+)$1	240	208	226	13.3894
$$cccqqqqqqqqccc55	chr11:611874-612114(+)$1	240	203	221	12.6499
[ddddqqqqqqqqddddf	chr17:27076522-27076762(+)$1	240	16	34	13.3523
ggg[aqqqqqqqqa]ggg	chr15:43668633-43668873(+)$1	240	136	154	13.7543
gggggqqqqqqqqggggg	chr14:50361221-50361515(+)$1	294	213	231	14.0975
eeeeeqqqqqqqqeeeee	chr1:11346145-11346385(+)$1	240	43	61	13.3996
fffffqqqqqqqqfffff	chr17:27952904-27953144(-)$1	240	183	201	13.3656
ggcccqqqqqqqqccc::	chr12:2966984-2967224(-)$1	240	175	193	12.5386
fffffqqqqqqqqfffff	chr12:46581600-46581840(-)$1	240	61	79	13.3656
iiiiiqqqqqqqqiiiii	chrX:48436512-48436752(+)$1	240	68	86	13.9161
!ddddqqqqqqqqdddd2	chr5:125828736-125828976(+)$1	240	105	123	13.3894
$$cccqqqqqqqqccccc	chr1:37958116-37958369(-)$1	253	114	132	14.0721
!!cccqqqqqqqqccc22	chr1:32846723-32846963(-)$1	240	130	148	14.6442
""cccqqqqqqqqccc33	chr6:41756865-41757124(+)$1	259	202	220	14.7947
hhhhhqqqqqqqqhhhhh	chr9:21331737-21331979(-)$1	242	142	160	12.6431
c[cccqqqqqqqqccccc	chr12:123350664-123350905(-)$1	241	90	108	14.4513
hhhhhqqqqqqqqhhhhh	chr22:38880691-38880931(-)$1	240	179	197	12.6431
&&cccqqqqqqqqccc77	chr5:134061989-134062229(+)$1	240	103	121	12.2290

#otherMatches

#Seq PSSM
GCCUUGAGGGUCUGAGGU	chr19:55741233-55741480(-)$1	247	191	209	12.6431
GACCUCCAGUGCAGGGUC	chr3:72427424-72427664(-)$1	240	2	20	13.3656
GAUCAUCAAACAUUGAUA	chr4:38699716-38699956(+)$1	240	90	108	12.6840
UGUGUAUUUACGAACAGA	chr8:91637471-91637711(-)$1	240	81	99	14.3176
UGAAAAAUGCCACUUUCG	chr18:73001144-73001384(+)$1	240	142	160	12.6431
CUCAGACACCAAGCUGGG	chr22:22051346-22051586(+)$1	240	97	115	12.6431
UAGGAAAUAAGUCUCUUG	chr1:182568446-182568686(-)$1	240	196	214	13.3656
UGCCUACUCCUAAAGUGA	chr21:15753579-15753819(-)$1	240	12	30	13.0161
AACAGAAAUGCUCCUGGA	chr13:73329348-73329588(+)$1	240	165	183	12.2076
UUUUUGCACAUUAAAAAA	chr15:64657708-64658028(-)$1	320	208	226	14.0975
AUUUCUGAGUGAUGAAAU	chr1:204372566-204372806(-)$1	240	57	75	13.3656
CAAAUUUAAAUUCAUUUG	chr5:133956590-133956830(-)$1	240	19	37	13.3656
UAUAAAUUUCAUCUUAAA	chr6:11134972-11135212(+)$1	240	37	55	14.2730
UAAGUGCUCCAUGAUUCU	chr19:7087631-7087871(+)$1	240	176	194	14.9842
GCUUUCAUUUUCAAAAGU	chr5:171290653-171290893(-)$1	240	212	230	13.3656
UAUUGUAGUAAUUCAGUG	chr19:34922675-34922915(+)$1	240	56	74	14.0975
GAGCUCUUCAGACAGCUC	chr10:103919925-103920165(+)$1	240	155	173	13.3996
CUUUGGGGACGGGCACAG	chr14:23299096-23299336(+)$1	240	91	109	13.1219
CUAUGUCUUUUUUCUAGU	chr9:108537173-108537413(+)$1	240	136	154	13.3550
CUAGGAUACACAGCCUGC	chr11:126133105-126133476(-)$1	371	95	113	13.2370
CAAGUUUUUGAACGCUGC	chr8:131065593-131065837(-)$1	244	91	109	14.4192
ACACACUCCAAAAUGGCC	chr6:31698405-31698645(-)$1	240	104	122	13.2604
GGGUCCCCGACGAGAGCC	chr7:1199536-1199776(-)$1	240	157	175	13.3660
UGGAGUGACAGUUCUCCU	chr16:23075998-23076238(-)$1	240	217	235	13.1406
AGUACUAAAGCCUGUUCU	chr11:73638578-73638818(+)$1	240	146	164	12.9054
UGGUCUGAGUGGUGGCCU	chr11:60658346-60658586(-)$1	240	80	98	13.5004
CGUUGGAAACUUGCAAAG	chr20:418072-418312(-)$1	240	153	171	14.5950
GUGGGCACAUUUCCCCGC	chr19:15234103-15234343(-)$1	240	44	62	14.0975
UUUUCUCCCAAAUGAAGA	chr7:120427621-120427901(-)$1	280	163	181	13.3996
UUAUUUUAUUGCCAAUCA	chr22:39911151-39911391(+)$1	240	64	82	14.2729
UUGUCAUUUCAAAGACAU	chr11:47593016-47593256(+)$1	240	145	163	12.5234
CUUUAGAUAAAUAUAGAG	chr2:135711167-135711416(+)$1	249	161	179	13.3656
CCAAGAGCACAGACUUGG	chr1:181059474-181059722(+)$1	248	57	75	13.3996
GAAGUCCUUAAACACUGG	chr15:58925391-58925631(-)$1	240	125	143	14.1612
CCAAGAAACUGUCCUUGG	chr3:45959783-45960049(-)$1	266	13	31	14.0975
CUGGCGGGAAGCAGUUAC	chr22:24811175-24811415(+)$1	240	92	110	13.1815
UAUAUACUUCAAGAUGUA	chrX:150575720-150575965(+)$1	245	215	233	14.0975
UUUAUCCAGAGCUAUAAA	chr19:44981147-44981387(-)$1	240	109	127	13.3996
GUGUAAUUGAUAAUGCAC	chr2:201845197-201845438(-)$1	241	132	150	13.3996
UGUACUUUACAAUGUUUA	chr12:104498482-104498722(+)$1	240	195	213	13.1219
CGAUUCUGAAACUGAUUG	chr9:128729482-128729722(+)$1	240	3	21	13.3996
UCAACUGUGUUUUGUUUU	chr22:32078425-32078665(-)$1	240	57	75	14.5267
GGAGGGAAACACACUUCA	chr8:38068113-38068361(+)$1	248	190	208	12.2357
ACGUCCCAGCUGCGACGU	chr20:34817335-34817579(+)$1	244	20	38	13.3996
UUUCCUGUUGAAUGGGUA	chr20:61826957-61827197(-)$1	240	33	51	14.5727
UGUAAGAAACUAAUUAUG	chr2:32842840-32843080(+)$1	240	199	217	13.3656
AGGCUUCAUUAAUAGAAC	chr21:40566023-40566263(-)$1	240	145	163	12.8788
UCGCCCCCAUUCUGGCUG	chr1:154961011-154961281(+)$1	270	74	92	14.5708
GGCGCCCACCUAAGUGCC	chr1:43829425-43829670(-)$1	245	101	119	13.3656
UCUGGCAUUAAUCCCAGG	chr7:32907726-32907966(-)$1	240	21	39	13.3996
GACUUUGUUACUCAAGUC	chr1:227178011-227178251(-)$1	240	137	155	13.3996
AAGAGGAGACGGGCUGGU	chr1:161093877-161094117(-)$1	240	174	192	13.0091
AGGCGUUUCCAUCUGCAA	chr22:45591804-45592044(-)$1	240	38	56	14.5267
GAUUGCUAUAUUUCAAUG	chr5:72205758-72205998(+)$1	240	95	113	13.3894
AAGAACUAUUUUAUUCUA	chr15:40512957-40513197(+)$1	240	208	226	13.3894
UACUUGGAAGAUAAAGCA	chr11:611874-612114(+)$1	240	203	221	12.6499
GAUGAUGCAGUCUUCAUC	chr17:27076522-27076762(+)$1	240	16	34	13.3523
CUGGAUUCUGUUUUGCAG	chr15:43668633-43668873(+)$1	240	136	154	13.7543
AGACUAUGUUGCAAGUCU	chr14:50361221-50361515(+)$1	294	213	231	14.0975
GGGGACAAGUAGCUCCCC	chr1:11346145-11346385(+)$1	240	43	61	13.3996
AUGAAACGUGUACUUCAU	chr17:27952904-27953144(-)$1	240	183	201	13.3656
UAAUGUCCCCAAUCAUAC	chr12:2966984-2967224(-)$1	240	175	193	12.5386
GCACAGAGAAUCAUGUGU	chr12:46581600-46581840(-)$1	240	61	79	13.3656
UUUUUUUAAUACUGGAAG	chrX:48436512-48436752(+)$1	240	68	86	13.9161
ACCUUGACUCUCUGAGGA	chr5:125828736-125828976(+)$1	240	105	123	13.3894
CUACUGUAAAACAAGUCU	chr1:37958116-37958369(-)$1	253	114	132	14.0721
UACUGUAAUGAACCAGAU	chr1:32846723-32846963(-)$1	240	130	148	14.6442
CAAGUAGGUAAGCACUGA	chr6:41756865-41757124(+)$1	259	202	220	14.7947
GGAGAUAACAUUUUCUUC	chr9:21331737-21331979(-)$1	242	142	160	12.6431
GAGCAGAUCGAAAUGCCG	chr12:123350664-123350905(-)$1	241	90	108	14.4513
GGACUAAAGCCUAAGUCC	chr22:38880691-38880931(-)$1	240	179	197	12.6431
UUUUGUUUUGUUUUAAUG	chr5:134061989-134062229(+)$1	240	103	121	12.2290

#DB
(((((........)))))	chr19:55741233-55741480(-)$1	1	191	209	12.6431
(((((........)))))	chr3:72427424-72427664(-)$1	1	2	20	13.3656
.((((........)))).	chr4:38699716-38699956(+)$1	1	90	108	12.6840
(.(((........))).)	chr8:91637471-91637711(-)$1	1	81	99	14.3176
(((((........)))))	chr18:73001144-73001384(+)$1	1	142	160	12.6431
(((((........)))))	chr22:22051346-22051586(+)$1	1	97	115	12.6431
(((((........)))))	chr1:182568446-182568686(-)$1	1	196	214	13.3656
(..((........))..)	chr21:15753579-15753819(-)$1	1	12	30	13.0161
..(((........)))((	chr13:73329348-73329588(+)$1	1	165	183	12.2076
(((((........)))))	chr15:64657708-64658028(-)$1	1	208	226	14.0975
(((((........)))))	chr1:204372566-204372806(-)$1	1	57	75	13.3656
(((((........)))))	chr5:133956590-133956830(-)$1	1	19	37	13.3656
(.(((........)))..	chr6:11134972-11135212(+)$1	1	37	55	14.2730
..(((........)))..	chr19:7087631-7087871(+)$1	1	176	194	14.9842
(((((........)))))	chr5:171290653-171290893(-)$1	1	212	230	13.3656
(((((........)))))	chr19:34922675-34922915(+)$1	1	56	74	14.0975
(((((........)))))	chr10:103919925-103920165(+)$1	1	155	173	13.3996
((.((........)).))	chr14:23299096-23299336(+)$1	1	91	109	13.1219
(((.(........)))))	chr9:108537173-108537413(+)$1	1	136	154	13.3550
.((((........)))).	chr11:126133105-126133476(-)$1	1	95	113	13.2370
..(((........)))..	chr8:131065593-131065837(-)$1	1	91	109	14.4192
.(.((........)))))	chr6:31698405-31698645(-)$1	1	104	122	13.2604
((.((........)).))	chr7:1199536-1199776(-)$1	1	157	175	13.3660
.((((........)))))	chr16:23075998-23076238(-)$1	1	217	235	13.1406
((.((........))...	chr11:73638578-73638818(+)$1	1	146	164	12.9054
.((((........)))).	chr11:60658346-60658586(-)$1	1	80	98	13.5004
(.(((........))).)	chr20:418072-418312(-)$1	1	153	171	14.5950
(((((........)))))	chr19:15234103-15234343(-)$1	1	44	62	14.0975
(((((........)))))	chr7:120427621-120427901(-)$1	1	163	181	13.3996
(.(((........))).)	chr22:39911151-39911391(+)$1	1	64	82	14.2729
))(((........)))..	chr11:47593016-47593256(+)$1	1	145	163	12.5234
(((((........)))))	chr2:135711167-135711416(+)$1	1	161	179	13.3656
(((((........)))))	chr1:181059474-181059722(+)$1	1	57	75	13.3996
..(((........)))..	chr15:58925391-58925631(-)$1	1	125	143	14.1612
(((((........)))))	chr3:45959783-45960049(-)$1	1	13	31	14.0975
(((((........)))).	chr22:24811175-24811415(+)$1	1	92	110	13.1815
(((((........)))))	chrX:150575720-150575965(+)$1	1	215	233	14.0975
(((((........)))))	chr19:44981147-44981387(-)$1	1	109	127	13.3996
(((((........)))))	chr2:201845197-201845438(-)$1	1	132	150	13.3996
((.((........)).))	chr12:104498482-104498722(+)$1	1	195	213	13.1219
(((((........)))))	chr9:128729482-128729722(+)$1	1	3	21	13.3996
..(((........)))..	chr22:32078425-32078665(-)$1	1	57	75	14.5267
)((((........)))).	chr8:38068113-38068361(+)$1	1	190	208	12.2357
(((((........)))))	chr20:34817335-34817579(+)$1	1	20	38	13.3996
(.(((........))).)	chr20:61826957-61827197(-)$1	1	33	51	14.5727
(((((........)))))	chr2:32842840-32843080(+)$1	1	199	217	13.3656
((.((........))..)	chr21:40566023-40566263(-)$1	1	145	163	12.8788
..(((........))).)	chr1:154961011-154961281(+)$1	1	74	92	14.5708
(((((........)))))	chr1:43829425-43829670(-)$1	1	101	119	13.3656
(((((........)))))	chr7:32907726-32907966(-)$1	1	21	39	13.3996
(((((........)))))	chr1:227178011-227178251(-)$1	1	137	155	13.3996
(..((........))..)	chr1:161093877-161094117(-)$1	1	174	192	13.0091
..(((........)))..	chr22:45591804-45592044(-)$1	1	38	56	14.5267
.((((........)))).	chr5:72205758-72205998(+)$1	1	95	113	13.3894
.((((........)))).	chr15:40512957-40513197(+)$1	1	208	226	13.3894
..(((........)))..	chr11:611874-612114(+)$1	1	203	221	12.6499
.((((........)))))	chr17:27076522-27076762(+)$1	1	16	34	13.3523
(((.(........).)))	chr15:43668633-43668873(+)$1	1	136	154	13.7543
(((((........)))))	chr14:50361221-50361515(+)$1	1	213	231	14.0975
(((((........)))))	chr1:11346145-11346385(+)$1	1	43	61	13.3996
(((((........)))))	chr17:27952904-27953144(-)$1	1	183	201	13.3656
))(((........)))..	chr12:2966984-2967224(-)$1	1	175	193	12.5386
(((((........)))))	chr12:46581600-46581840(-)$1	1	61	79	13.3656
(((((........)))))	chrX:48436512-48436752(+)$1	1	68	86	13.9161
.((((........)))).	chr5:125828736-125828976(+)$1	1	105	123	13.3894
..(((........)))))	chr1:37958116-37958369(-)$1	1	114	132	14.0721
..(((........)))..	chr1:32846723-32846963(-)$1	1	130	148	14.6442
..(((........)))..	chr6:41756865-41757124(+)$1	1	202	220	14.7947
(((((........)))))	chr9:21331737-21331979(-)$1	1	142	160	12.6431
(.(((........)))))	chr12:123350664-123350905(-)$1	1	90	108	14.4513
(((((........)))))	chr22:38880691-38880931(-)$1	1	179	197	12.6431
..(((........)))..	chr5:134061989-134062229(+)$1	1	103	121	12.2290

#PSSM
e : 0.18	f : 0.15	g : 0.12	h : 0.09	! : 0.06	c : 0.06	$ : 0.05	# : 0.05	[ : 0.04	& : 0.02	d : 0.02	" : 0.02	a : 0.01	: : 0.01	b : 0.01	= : 0.01	i : 0.01	
f : 0.15	d : 0.13	e : 0.13	g : 0.12	[ : 0.08	h : 0.06	! : 0.05	# : 0.05	c : 0.04	$ : 0.04	: : 0.01	a : 0.01	b : 0.01	= : 0.01	i : 0.01	" : 0.01	& : 0.01	
c : 0.27	f : 0.15	d : 0.13	e : 0.13	g : 0.09	[ : 0.08	h : 0.06	! : 0.02	i : 0.01	
c : 0.27	f : 0.13	d : 0.13	e : 0.13	b : 0.11	g : 0.08	h : 0.06	[ : 0.02	i : 0.01	
c : 0.27	f : 0.13	d : 0.13	e : 0.13	b : 0.11	g : 0.08	h : 0.06	a : 0.02	i : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.27	f : 0.13	d : 0.13	e : 0.13	b : 0.11	g : 0.08	h : 0.06	a : 0.02	i : 0.01	
c : 0.27	f : 0.15	d : 0.13	e : 0.13	b : 0.11	g : 0.08	h : 0.06	] : 0.01	i : 0.01	
c : 0.27	f : 0.15	d : 0.13	e : 0.13	g : 0.09	h : 0.06	2 : 0.04	] : 0.04	a : 0.01	3 : 0.01	i : 0.01	
f : 0.16	d : 0.13	e : 0.13	g : 0.11	2 : 0.08	h : 0.06	] : 0.06	c : 0.06	3 : 0.04	4 : 0.04	: : 0.02	5 : 0.01	i : 0.01	7 : 0.01	
f : 0.18	e : 0.18	g : 0.11	2 : 0.09	c : 0.09	h : 0.08	3 : 0.04	] : 0.04	: : 0.04	4 : 0.04	d : 0.02	a : 0.01	5 : 0.01	i : 0.01	7 : 0.01	

#score	971.9912919720097
#seq	72
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_UTR_m1_run2.txt

#BEAR
f!!ffffff[bb!!cccmmmmccc]bb]fffffffff	chr19:51600936-51601161(-)$1	225	124	161	11.8759
ccc[eeeee####cccooooooccc333eeeee]ccc	chr1:154550734-154550958(-)$1	224	54	91	13.3447
hh[a!!dddd[bbaddddllldddd]a]bb22dddd2	chr12:6982318-6982549(+)$1	231	145	182	10.4199
ccceeeeeccc[cccooooooccc333ccc22eeeee	chr19:2271681-2271900(+)$1	219	11	48	13.4366
[ccc[eeeee####cccnnnnnccc4444eeeee]cc	chr16:53967816-53968083(+)$1	267	154	191	12.5987
#dddd!!bb####eeeeemmmmeeeee]bb22ddddd	chr19:52467591-52467811(+)$1	220	125	162	10.3210
ddddbbggggggg[cccmmmmccc]ggggggg22bb]	chr12:120972109-120972334(+)$1	225	111	148	11.9631
[eeeee####ddddccclllccc]dddd4444eeeee	chr6:34557226-34557456(-)$1	230	110	147	11.4503
!!eeeee[ccc[eeeeennnnneeeee]ccc]eeeee	chr19:50302914-50303145(+)$1	231	85	122	10.6723
!eeeee[dddd"""cccmmmmccc55555dddd]eee	chr15:41021602-41021892(-)$1	290	73	110	10.7761
dddd[ccc[ccc!!ccclllccc]ccc]ccc]dddd3	chr5:10264896-10265122(+)$1	226	137	174	12.8724
ffffffccc!!eeeeemmmmeeeee333ccc]fffff	chr7:150759744-150759969(+)$1	225	149	186	9.9115
dd[ccc!!ffffff[ccclllccc]ffffff]ccc]d	chr6:31804789-31805018(+)$1	229	73	110	11.2437
"""bb"""eeeeebb[aooooooa]bb333eeeee22	chr19:38865652-38865893(+)$1	241	137	174	10.4736
eeeee!!ccc!!a[ddddllldddd]a22ccceeeee	chr15:41021956-41022225(+)$1	269	28	65	12.4906
:gggggggccc"""cccmmmmccc22ccc]ggggggg	chr4:184367370-184367590(-)$1	220	131	168	13.7919
####ffffff####cccmmmmccc]ffffff4444dd	chr14:21969771-21970147(-)$1	376	132	169	13.0692
c[eeeee[ccc[ccc[aooooooa]cccccc]eeeee	chrX:129139083-129139310(+)$1	227	12	49	12.6856
cc]===========cccmmmmccceeeeemmmmeeee	chr4:184426073-184426299(+)$1	226	89	126	10.8609
"""dddd####ffffffmmmmffffff4444dddd]b	chr17:8159477-8159702(+)$1	225	45	82	10.7214
:ggggggg[aa[ddddllldddd]a]a333ggggggg	chr13:41885485-41885704(+)$1	219	102	139	9.9336
$$$iiiiiiiii!!cccmmmmccciiiiiiiii4444	chr11:8705775-8705999(+)$1	224	76	113	13.5719
dddd$$$$$ccc[bbccclllccc]bbccc333dddd	chr2:43798857-43799082(-)$1	225	181	218	11.2934
#bb[eeeee####a[bbmmmmbb]a4444eeeeebb5	chr19:36119898-36120126(+)$1	228	52	89	10.8499
cc[dddd$$$$$eeeeemmmmeeeee333dddd]ccc	chr1:28218423-28218643(-)$1	220	126	163	10.4968
[gggggggabb"""cccmmmmccc4444bb]a]gggg	chr5:137610150-137610375(-)$1	225	114	151	14.9248
""ggggggg[a[eeeeemmmmeeeee]a]ggggggg3	chr1:228364043-228364269(+)$1	226	88	125	12.0958
g"""a[==========aooooooa]==========]a	chr19:7978305-7978531(+)$1	226	103	140	13.2226
ggggggbb!!ddddcccmmmmccc22dddd22bb]gg	chrX:48761886-48762106(-)$1	220	168	205	11.3119
ddd[bba[bb[a[ddddmmmmdddd]a]bb22a]bb]	chr1:156692588-156692808(-)$1	220	160	197	11.2649
ccc!!a[dddd!!ddddmmmmdddd22dddd]a22cc	chr1:151665820-151666047(+)$1	227	91	128	11.5129
iiiiiidddd"""cccnnnnnccc333dddd]iiiii	chr10:111985742-111985974(+)$1	232	166	203	12.6149
eeee####bb!!ddddoooooodddd22bb333eeee	chr19:10671789-10672015(-)$1	226	161	198	11.7982
eee[bb[ccc!!fffffflllffffff]ccc]bb]ee	chr2:71558835-71559055(+)$1	220	111	148	10.1780
dddd[ggggggg"""bbmmmmbb333ggggggg]ddd	chr1:28845051-28845283(+)$1	232	48	85	12.4542
eeee!!cccffffffooooooffffff]ccc]eeeee	chr1:247151334-247151563(-)$1	229	153	190	10.9311
"""bb[dddd[a!!bboooooobb4444a]dddd]bb	chr10:24497764-24497991(-)$1	227	99	136	11.0071
[ccc[ccc[ccc!!cccmmmmccc]cccccc22ccc]	chr3:48732681-48732937(-)$1	256	9	46	14.2123
[ggggggg[bb"""bboooooobb]bb]ggggggg44	chrX:69723829-69724058(+)$1	229	58	95	12.2033
ggggggg[bb!!a[cccmmmmccc]a22bb22ggggg	chr15:100268101-100268321(+)$1	220	11	48	14.4478
iiiii!!dddd[a[cccmmmmccc]adddd333iiii	chr9:139256148-139256380(-)$1	232	168	205	14.2010
ff[a[eeeee####cccmmmmccceeeee22a]ffff	chr9:34399424-34399648(-)$1	224	29	66	12.4430
iiiii"""bb[ffffffmmmmffffff]bb22iiiii	chr4:114682578-114682803(-)$1	225	23	60	11.5143
eeeee!!ccc####cccmmmmccc4444ccc]eeeee	chr6:62283948-62284192(+)$1	244	190	227	16.1316
gggg"""gggggggooooooggggggg22ggggggg]	chr14:21979166-21979466(-)$1	300	56	93	10.4527
ceeeeeggggggg!!bbmmmmbb333ggggggg22ee	chr1:203783929-203784176(+)$1	247	75	112	11.9077
dd[ggggggg[bbddddmmmmdddd]bbgggggggdd	chr2:128615341-128615579(-)$1	238	49	86	11.4487
hhhhhh==========4444eeeee333=========	chr3:119886218-119886438(+)$1	220	136	173	10.4450
eeeee!!ffffff[cccmmmmcccffffffeeeee:F	chr22:42455781-42456010(-)$1	229	128	165	10.6868
!!ggggggg[bb!!ddddllldddd22bbgggggggd	chr7:26241396-26241620(+)$1	224	146	183	11.5572
"ggggggg[ccc[ddddooooooddddcccggggggg	chr12:110781022-110781252(+)$1	230	79	116	11.6484
dd!!bb[dddd!!cccnnnnncccdddd]bb]dddd2	chr1:3805961-3806191(-)$1	230	117	154	9.9540
"""dddd!!dddd[cccmmmmccc]dddd22ddddii	chr4:109088935-109089155(-)$1	220	38	75	11.8156
!ccc####bb[bb[cccmmmmcccbbbb4444ccc22	chr20:30946447-30946673(+)$1	226	99	136	12.1550
dddeeeee!!bb!!cccmmmmccc22bb22eeeee]d	chr14:21971816-21972039(+)$1	223	118	155	12.5866
iiii[eeeee####cccooooooccc4444eeeee55	chr1:156209272-156209497(+)$1	225	67	104	11.9854
dddd"""cccbb!!ccclllccc333bb]ccc22ddd	chr13:100633922-100634154(+)$1	232	176	213	12.2649
ddddd[a[ccc!!ddddmmmmdddd333ccc]a333d	chr17:48827813-48828068(+)$1	255	154	191	13.7697
ccc[a[dddd!!bb[ccclllccc]bb4444dddd]a	chr19:13029956-13030180(-)$1	224	34	71	12.0109
dd####ggggggg[cccmmmmccc4444gggggggdd	chr14:21971532-21971810(-)$1	278	172	209	14.4163
eeeee[bbccc[ccc[bblllbb]ccc]ccc22bb]e	chr17:7297784-7298017(-)$1	233	178	215	10.1462
"a[eeeeebb[ccc!!bbmmmmbb22cccbb]eeeee	chr7:75597066-75597287(+)$1	221	87	124	10.1215

#otherMatches

#Seq PSSM
GCAGGGUUGUGUGAGCCUGUCGGUGACUUAGCCUCUU	chr19:51600936-51601161(-)$1	225	124	161	11.8759
AAAGAGGUCAAACAGCAGACAAGCUCUAGGCCUGUUU	chr1:154550734-154550958(-)$1	224	54	91	13.3447
AAAGAAGCCGAGGCGCGCAGGGCGCAGACCGCCGGCC	chr12:6982318-6982549(+)$1	231	145	182	10.4199
GGCCUAGGCCCAAGCUUUAGCGCUGCCGGGUUCUUGG	chr19:2271681-2271900(+)$1	219	11	48	13.4366
CCUUGCCUCGCUCACUGCACGCCAGAACCUGAGGAGA	chr16:53967816-53968083(+)$1	267	154	191	12.5987
AGGAAACUGAAUUGACACAUAUGUGUCCCACAUUCCA	chr19:52467591-52467811(+)$1	220	125	162	10.3210
GUUGCUGUGUCGGAGACACUAGUCCCCGACACCGAGA	chr12:120972109-120972334(+)$1	225	111	148	11.9631
AGGCAAGCUUGAAGGUGGCCCAUGCUUCUCUGUUGUC	chr6:34557226-34557456(-)$1	230	110	147	11.4503
GACUACGCCAUCCGCGAGGAGAUCGUGAGUGCUGUgg	chr19:50302914-50303145(+)$1	231	85	122	10.6723
CGCAGAAGCAUCCGCAGAAACCUGGCCAAGUGCAUCU	chr15:41021602-41021892(-)$1	290	73	110	10.7761
CCAUAGUUUCACUUGUUCAAAGCUGUGUAAUCGUGGG	chr5:10264896-10265122(+)$1	226	137	174	12.8724
AGAGGGGAGAAGCCAGCCCCCUGGCCCGCUCACCUUC	chr7:150759744-150759969(+)$1	225	149	186	9.9115
AUUUCACAGACUAGAGUCUCCGAUGCUGGUCAUGAUG	chr6:31804789-31805018(+)$1	229	73	110	11.2437
AGAGAGGGACAGGGAGCGUUgauggucacgccuguaa	chr19:38865652-38865893(+)$1	241	137	174	10.4736
GUGGCAGCAUUAAGGCUUUUGGAGUGUCUAUGGCCAC	chr15:41021956-41022225(+)$1	269	28	65	12.4906
GAUCUCCAUCACUUGUAGAGCUAUUCUGACUGGAGAU	chr4:184367370-184367590(-)$1	220	131	168	13.7919
ACUACAACAGCCAAGGAACAAUCCAUUGUUGAAAAAU	chr14:21969771-21970147(-)$1	376	132	169	13.0692
UGUGUAAAAGGUGAUUGAAGCAGCUGUCCCUGUUACG	chrX:129139083-129139310(+)$1	227	12	49	12.6856
CUGCGGGGGCGGGGAGUGAGGGCUGCUCUGGGGGGAG	chr4:184426073-184426299(+)$1	226	89	126	10.8609
CAUGGCAUUAAGAAAUGACCCCGUUUCCACCUGCCUU	chr17:8159477-8159702(+)$1	225	45	82	10.7214
CGGUGCCCACCCCCGCGAAGCGGAGCGCCCGGGCACC	chr13:41885485-41885704(+)$1	219	102	139	9.9336
UUCACUGGCUGUGGGCCUUAUGGCACAGUCAGUCACC	chr11:8705775-8705999(+)$1	224	76	113	13.5719
AUCUUAACAGCCAGUCUCCAGGAGUGCGGCAACAGAU	chr2:43798857-43799082(-)$1	225	181	218	11.2934
GUCAUCCUCGGGAGCCCACCCGGACGAAGGGGGAGAG	chr19:36119898-36120126(+)$1	228	52	89	10.8499
CUGUUUUAUUUUGUUUUGUUUGAAGCUCAGAGGGAGA	chr1:28218423-28218643(-)$1	220	126	163	10.4968
GGCGGCGCCCAGGACCCUGGUGGGAGAGUGUGUGCGU	chr5:137610150-137610375(-)$1	225	114	151	14.9248
UAGUUUUUGUGAUCUGGCUGACUGGACCCCGGGAACA	chr1:228364043-228364269(+)$1	226	88	125	12.0958
gcugagggugggggugcgagguggUCACUCCCAUCGU	chr19:7978305-7978531(+)$1	226	103	140	13.2226
GACCCAAGUCGCCACCCUCCGGGGCCUGGCUCCUCUG	chrX:48761886-48762106(-)$1	220	168	205	11.3119
ggcgggcggaucaccugagaucaggaguucaagacca	chr1:156692588-156692808(-)$1	220	160	197	11.2649
CAUGAGUGCUUCGAGAGGGUGUUCUGCGAGCUCAAGU	chr1:151665820-151666047(+)$1	227	91	128	11.5129
CGCCUCCUGUCGGCCCGAGAAGGGAGUGCGGAGAGGC	chr10:111985742-111985974(+)$1	232	166	203	12.6149
GCAGGAGAAGGUGGGUACUGGGGCCUGACUGGACUGC	chr19:10671789-10672015(-)$1	226	161	198	11.7982
CUGAGUGCUAAACUGUGUGGGGCGCGGAUGGGAUCCA	chr2:71558835-71559055(+)$1	220	111	148	10.1780
GCGCCCGCGCAGGCGGGAGAUUCAAACUGCGCGAgcg	chr1:28845051-28845283(+)$1	232	48	85	12.4542
GGCAGAAGGCAAGUUAUAAUGGACUUGACCUAUGCUC	chr1:247151334-247151563(-)$1	229	153	190	10.9311
ucuguccguccguccguccguccguccUCAGGCGCGC	chr10:24497764-24497991(-)$1	227	99	136	11.0071
GAGCAGGGUGAGCAGCUCUAAGGCACUUCCCACGCUA	chr3:48732681-48732937(-)$1	256	9	46	14.2123
AACAGUUGUCCAACCAGCAGAAUGAGGCUAACUGUAU	chrX:69723829-69724058(+)$1	229	58	95	12.2033
ACAGGGCAGCACCAACUCCCAAGUAGUAGCAGGCUCU	chr15:100268101-100268321(+)$1	220	11	48	14.4478
CUCUUGCCCACAGAGGCCACAGUCGCguggaaagggg	chr9:139256148-139256380(-)$1	232	168	205	14.2010
GUGUGUCUCAGUAUACCUAAAGGUUGGGGUGGGGCGG	chr9:34399424-34399648(-)$1	224	29	66	12.4430
GCGCGCACGCUCGUCGGAGCCCCGGCGCGCCCCGCGC	chr4:114682578-114682803(-)$1	225	23	60	11.5143
ACCGCCUGCCCAGUGACAUAUGUUUAACGGCCGUGGU	chr6:62283948-62284192(+)$1	244	190	227	16.1316
GUCCGCCGCGCCUUAUUCGAGAGGUGUCAGGGCUGGG	chr14:21979166-21979466(-)$1	300	56	93	10.4527
auggagugcagugcaugaucucggcucacugcaaccu	chr1:203783929-203784176(+)$1	247	75	112	11.9077
UUCGCCCAAGGCCCUGCCUCAGCGGCGGCUUGGGCAA	chr2:128615341-128615579(-)$1	238	49	86	11.4487
GUCUUCGUACUCUGGAAUCAGUAGUUUGUGGGGCCAG	chr3:119886218-119886438(+)$1	220	136	173	10.4450
UGUGAUUGGCUUUUCUACCCAUAGAGGGCCUUGCAGC	chr22:42455781-42456010(-)$1	229	128	165	10.6868
CCUUCUCGCCGGACCCCGCGCCGGGAGCUGCGGGAAG	chr7:26241396-26241620(+)$1	224	146	183	11.5572
AUCUGGUGACAGAUGGCCUGCCUGCCACUGCACUGGG	chr12:110781022-110781252(+)$1	230	79	116	11.6484
cguuggccaggcuggucucaaacuccugaccucguga	chr1:3805961-3806191(-)$1	230	117	154	9.9540
GAUUCGGGCGCCGCGGCAGCUGCUCCGGCUgccggcc	chr4:109088935-109089155(-)$1	220	38	75	11.8156
GCGUGGAGCUGCCGCCGCCGCCGGGGAGAAGGAUGAA	chr20:30946447-30946673(+)$1	226	99	136	12.1550
UGGGCUUAGGGCCACCAGAGGUGGGUGCAGUAGGCAC	chr14:21971816-21972039(+)$1	223	118	155	12.5866
CUCUACACAGAGAACAGAGGGAGCUGGUUGCUGUGCU	chr1:156209272-156209497(+)$1	225	67	104	11.9854
ccucUCCGCGCCUUCGCUACGCGCCCGGCCGCCCGAG	chr13:100633922-100634154(+)$1	232	176	213	12.2649
GGUCAAUGGGACCAGUGAAGACAUUAAAUCUGAAGGU	chr17:48827813-48828068(+)$1	255	154	191	13.7697
GCGGGAGCGCAGCUGGCCAGGGGCGGGGUCGGCGCAU	chr19:13029956-13030180(-)$1	224	34	71	12.0109
GUCUCCUACAAGAUGAUGCACAUCCUACUCUUGUAAC	chr14:21971532-21971810(-)$1	278	172	209	14.4163
GAGCUGCCGAGUGCUAGGCACCCGGGCUCUUCUGGGG	chr17:7297784-7298017(-)$1	233	178	215	10.1462
GGGCUCCAGAUGUUGCAGAGUUCUUGGGCUCAUGGGG	chr7:75597066-75597287(+)$1	221	87	124	10.1215

#DB
(..((((((.((..(((....))).)).)))))))))	chr19:51600936-51601161(-)$1	1	124	161	11.8759
(((.(((((....(((......)))...))))).)))	chr1:154550734-154550958(-)$1	1	54	91	13.3447
((.(..((((.(((((((...)))).).))..)))).	chr12:6982318-6982549(+)$1	1	145	182	10.4199
(((((((((((.(((......)))...)))..)))))	chr19:2271681-2271900(+)$1	1	11	48	13.4366
.(((.(((((....(((.....)))....))))).))	chr16:53967816-53968083(+)$1	1	154	191	12.5987
.((((..((....(((((....))))).))..)))))	chr19:52467591-52467811(+)$1	1	125	162	10.3210
(((((((((((((.(((....))).)))))))..)).	chr12:120972109-120972334(+)$1	1	111	148	11.9631
.(((((....(((((((...))).))))....)))))	chr6:34557226-34557456(-)$1	1	110	147	11.4503
..(((((.(((.(((((.....))))).))).)))))	chr19:50302914-50303145(+)$1	1	85	122	10.6723
.(((((.((((...(((....))).....)))).)))	chr15:41021602-41021892(-)$1	1	73	110	10.7761
((((.(((.(((..(((...))).))).))).)))).	chr5:10264896-10265122(+)$1	1	137	174	12.8724
(((((((((..(((((....)))))...))).)))))	chr7:150759744-150759969(+)$1	1	149	186	9.9115
((.(((..((((((.(((...))).)))))).))).)	chr6:31804789-31805018(+)$1	1	73	110	11.2437
...((...(((((((.(......).))...)))))..	chr19:38865652-38865893(+)$1	1	137	174	10.4736
(((((..(((..(.((((...)))).)..))))))))	chr15:41021956-41022225(+)$1	1	28	65	12.4906
.((((((((((...(((....)))..))).)))))))	chr4:184367370-184367590(-)$1	1	131	168	13.7919
....((((((....(((....))).))))))....))	chr14:21969771-21970147(-)$1	1	132	169	13.0692
(.(((((.(((.(((.(......).)))))).)))))	chrX:129139083-129139310(+)$1	1	12	49	12.6856
)).)))))))))))(((....)))(((((....))))	chr4:184426073-184426299(+)$1	1	89	126	10.8609
...((((....((((((....))))))....)))).)	chr17:8159477-8159702(+)$1	1	45	82	10.7214
.(((((((.((.((((...)))).).)...)))))))	chr13:41885485-41885704(+)$1	1	102	139	9.9336
...(((((((((..(((....))))))))))))....	chr11:8705775-8705999(+)$1	1	76	113	13.5719
((((.....(((.(((((...))).)))))...))))	chr2:43798857-43799082(-)$1	1	181	218	11.2934
.((.(((((....(.((....)).)....))))))).	chr19:36119898-36120126(+)$1	1	52	89	10.8499
((.((((.....(((((....)))))...)))).)))	chr1:28218423-28218643(-)$1	1	126	163	10.4968
.((((((((((...(((....)))....)).).))))	chr5:137610150-137610375(-)$1	1	114	151	14.9248
..(((((((.(.(((((....))))).).))))))).	chr1:228364043-228364269(+)$1	1	88	125	12.0958
(...(.(((((((((((......).)))))))))).)	chr19:7978305-7978531(+)$1	1	103	140	13.2226
((((((((..(((((((....)))..))))..)).))	chrX:48761886-48762106(-)$1	1	168	205	11.3119
(((.(((.((.(.((((....)))).).))..).)).	chr1:156692588-156692808(-)$1	1	160	197	11.2649
(((..(.((((..((((....))))..)))).)..))	chr1:151665820-151666047(+)$1	1	91	128	11.5129
((((((((((...(((.....)))...)))).)))))	chr10:111985742-111985974(+)$1	1	166	203	12.6149
((((....((..((((......))))..))...))))	chr19:10671789-10672015(-)$1	1	161	198	11.7982
(((.((.(((..((((((...)))))).))).)).))	chr2:71558835-71559055(+)$1	1	111	148	10.1780
((((.(((((((...((....))...))))))).)))	chr1:28845051-28845283(+)$1	1	48	85	12.4542
((((..(((((((((......)))))).))).)))))	chr1:247151334-247151563(-)$1	1	153	190	10.9311
...((.((((.(..((......))....).)))).))	chr10:24497764-24497991(-)$1	1	99	136	11.0071
.(((.(((.(((..(((....))).))))))..))).	chr3:48732681-48732937(-)$1	1	9	46	14.2123
.(((((((.((...((......)).)).)))))))..	chrX:69723829-69724058(+)$1	1	58	95	12.2033
(((((((.((..(.(((....))).)..))..)))))	chr15:100268101-100268321(+)$1	1	11	48	14.4478
(((((..((((.(.(((....))).)))))...))))	chr9:139256148-139256380(-)$1	1	168	205	14.2010
((.(.(((((....(((....))))))))..).))))	chr9:34399424-34399648(-)$1	1	29	66	12.4430
(((((...((.((((((....)))))).))..)))))	chr4:114682578-114682803(-)$1	1	23	60	11.5143
(((((..(((....(((....)))....))).)))))	chr6:62283948-62284192(+)$1	1	190	227	16.1316
((((...(((((((......)))))))..))))))).	chr14:21979166-21979466(-)$1	1	56	93	10.4527
(((((((((((((..((....))...)))))))..))	chr1:203783929-203784176(+)$1	1	75	112	11.9077
((.(((((((.((((((....)))).)))))))))))	chr2:128615341-128615579(-)$1	1	49	86	11.4487
))))))))))))))))....)))))...)))))))))	chr3:119886218-119886438(+)$1	1	136	173	10.4450
(((((..((((((.(((....)))))))))))))).)	chr22:42455781-42456010(-)$1	1	128	165	10.6868
..(((((((.((..((((...))))..))))))))))	chr7:26241396-26241620(+)$1	1	146	183	11.5572
.(((((((.(((.((((......))))))))))))))	chr12:110781022-110781252(+)$1	1	79	116	11.6484
((..((.((((..(((.....))))))).)).)))).	chr1:3805961-3806191(-)$1	1	117	154	9.9540
...((((..((((.(((....))).))))..))))))	chr4:109088935-109089155(-)$1	1	38	75	11.8156
.(((....((.((.(((....)))))))....)))..	chr20:30946447-30946673(+)$1	1	99	136	12.1550
((((((((..((..(((....)))..))..))))).)	chr14:21971816-21972039(+)$1	1	118	155	12.5866
((((.(((((....(((......)))....)))))..	chr1:156209272-156209497(+)$1	1	67	104	11.9854
((((...(((((..(((...)))...)).)))..)))	chr13:100633922-100634154(+)$1	1	176	213	12.2649
(((((.(.(((..((((....))))...))).)...)	chr17:48827813-48828068(+)$1	1	154	191	13.7697
(((.(.((((..((.(((...))).))....)))).)	chr19:13029956-13030180(-)$1	1	34	71	12.0109
((....(((((((.(((....)))....)))))))))	chr14:21971532-21971810(-)$1	1	172	209	14.4163
(((((.(((((.(((.((...)).))).)))..)).)	chr17:7297784-7298017(-)$1	1	178	215	10.1462
.(.(((((((.(((..((....))..))))).)))))	chr7:75597066-75597287(+)$1	1	87	124	10.1215

#PSSM
d : 0.19	c : 0.12	" : 0.11	e : 0.11	[ : 0.08	! : 0.06	g : 0.06	i : 0.06	f : 0.04	# : 0.04	h : 0.03	: : 0.03	$ : 0.01	
d : 0.20	e : 0.16	c : 0.14	g : 0.12	" : 0.09	i : 0.06	! : 0.04	h : 0.03	f : 0.03	# : 0.01	[ : 0.01	$ : 0.01	b : 0.01	a : 0.01	
e : 0.19	g : 0.16	d : 0.14	c : 0.11	[ : 0.09	" : 0.08	i : 0.06	! : 0.03	# : 0.03	f : 0.01	] : 0.01	$ : 0.01	b : 0.01	h : 0.01	
e : 0.22	g : 0.17	d : 0.16	[ : 0.08	i : 0.08	c : 0.06	f : 0.03	a : 0.03	b : 0.03	# : 0.03	! : 0.03	= : 0.01	" : 0.01	h : 0.01	
e : 0.22	g : 0.16	[ : 0.09	b : 0.09	d : 0.08	i : 0.06	f : 0.04	! : 0.04	# : 0.04	a : 0.03	" : 0.03	c : 0.01	= : 0.01	$ : 0.01	h : 0.01	
e : 0.20	g : 0.17	! : 0.11	[ : 0.08	b : 0.06	" : 0.06	f : 0.04	c : 0.04	d : 0.04	# : 0.04	i : 0.03	= : 0.01	$ : 0.01	a : 0.01	h : 0.01	
g : 0.20	e : 0.16	d : 0.11	! : 0.09	[ : 0.06	c : 0.06	" : 0.06	# : 0.04	= : 0.04	f : 0.03	b : 0.03	a : 0.03	i : 0.01	$ : 0.01	
g : 0.20	e : 0.12	d : 0.12	c : 0.12	[ : 0.08	# : 0.06	f : 0.04	b : 0.04	= : 0.04	! : 0.03	" : 0.03	$ : 0.03	i : 0.01	
c : 0.19	d : 0.12	g : 0.12	b : 0.11	e : 0.09	[ : 0.08	f : 0.06	= : 0.04	! : 0.04	# : 0.03	$ : 0.03	i : 0.01	a : 0.01	
c : 0.22	d : 0.14	b : 0.12	g : 0.09	# : 0.08	e : 0.06	f : 0.06	[ : 0.04	! : 0.04	= : 0.04	a : 0.01	i : 0.01	$ : 0.01	
c : 0.16	# : 0.14	[ : 0.11	d : 0.11	b : 0.09	! : 0.09	g : 0.08	f : 0.04	= : 0.04	a : 0.03	e : 0.01	i : 0.01	$ : 0.01	" : 0.01	
# : 0.12	! : 0.12	b : 0.11	[ : 0.11	g : 0.08	" : 0.08	c : 0.08	f : 0.08	d : 0.04	= : 0.04	e : 0.03	a : 0.03	i : 0.01	$ : 0.01	
! : 0.17	# : 0.12	" : 0.09	f : 0.09	d : 0.08	e : 0.08	b : 0.06	c : 0.06	g : 0.06	a : 0.04	= : 0.04	[ : 0.04	
! : 0.14	d : 0.14	[ : 0.12	c : 0.11	# : 0.08	e : 0.08	" : 0.08	f : 0.08	b : 0.04	= : 0.04	a : 0.03	g : 0.01	
c : 0.48	d : 0.16	e : 0.08	b : 0.06	f : 0.06	[ : 0.04	= : 0.03	! : 0.03	" : 0.01	o : 0.01	
c : 0.48	d : 0.16	e : 0.08	b : 0.08	o : 0.04	[ : 0.04	f : 0.04	= : 0.03	! : 0.01	
c : 0.43	d : 0.12	o : 0.11	b : 0.08	e : 0.06	a : 0.04	f : 0.04	n : 0.03	m : 0.01	l : 0.01	4 : 0.01	
m : 0.49	o : 0.19	n : 0.06	l : 0.06	d : 0.04	c : 0.04	b : 0.03	e : 0.01	f : 0.01	4 : 0.01	
m : 0.53	o : 0.19	l : 0.19	n : 0.06	4 : 0.01	
m : 0.53	o : 0.19	l : 0.17	n : 0.06	d : 0.01	4 : 0.01	
m : 0.51	o : 0.17	l : 0.12	n : 0.06	c : 0.04	e : 0.03	d : 0.01	g : 0.01	
c : 0.45	o : 0.14	d : 0.12	e : 0.06	f : 0.06	b : 0.06	n : 0.03	m : 0.03	g : 0.01	
c : 0.48	d : 0.14	b : 0.11	e : 0.09	o : 0.08	f : 0.06	g : 0.01	
c : 0.45	d : 0.14	e : 0.09	] : 0.08	f : 0.06	a : 0.04	3 : 0.04	b : 0.04	g : 0.01	
] : 0.22	d : 0.17	e : 0.12	c : 0.08	3 : 0.08	f : 0.08	2 : 0.06	4 : 0.06	a : 0.03	5 : 0.01	i : 0.01	g : 0.01	b : 0.01	
3 : 0.14	f : 0.11	b : 0.09	4 : 0.09	e : 0.09	2 : 0.09	] : 0.08	d : 0.08	c : 0.08	g : 0.03	a : 0.03	5 : 0.01	i : 0.01	= : 0.01	
b : 0.14	3 : 0.11	4 : 0.11	f : 0.11	d : 0.09	c : 0.09	a : 0.06	e : 0.06	g : 0.06	2 : 0.06	5 : 0.01	i : 0.01	] : 0.01	= : 0.01	
] : 0.17	4 : 0.14	3 : 0.11	c : 0.11	d : 0.11	b : 0.08	2 : 0.06	g : 0.04	f : 0.04	e : 0.03	5 : 0.01	i : 0.01	a : 0.01	= : 0.01	
c : 0.24	b : 0.12	4 : 0.11	g : 0.09	d : 0.08	f : 0.06	e : 0.04	3 : 0.04	2 : 0.04	] : 0.04	= : 0.03	5 : 0.01	i : 0.01	a : 0.01	
c : 0.24	b : 0.14	g : 0.14	d : 0.09	4 : 0.08	f : 0.06	e : 0.04	2 : 0.04	3 : 0.03	] : 0.03	= : 0.03	m : 0.01	i : 0.01	
g : 0.19	c : 0.19	2 : 0.14	e : 0.11	d : 0.08	4 : 0.06	f : 0.04	3 : 0.04	= : 0.03	b : 0.03	m : 0.01	i : 0.01	] : 0.01	
] : 0.20	g : 0.19	2 : 0.14	e : 0.11	d : 0.09	4 : 0.04	3 : 0.04	c : 0.03	a : 0.03	= : 0.03	f : 0.01	m : 0.01	i : 0.01	
e : 0.24	g : 0.19	d : 0.16	2 : 0.06	i : 0.04	3 : 0.04	a : 0.04	f : 0.03	c : 0.03	] : 0.03	= : 0.03	b : 0.03	4 : 0.01	m : 0.01	
e : 0.25	g : 0.17	d : 0.14	] : 0.08	2 : 0.06	f : 0.04	c : 0.04	b : 0.04	i : 0.04	4 : 0.03	= : 0.03	3 : 0.01	
e : 0.24	g : 0.17	d : 0.16	c : 0.08	] : 0.06	b : 0.06	f : 0.04	i : 0.04	4 : 0.03	= : 0.03	2 : 0.03	3 : 0.01	
e : 0.20	d : 0.16	g : 0.14	] : 0.09	c : 0.08	b : 0.06	i : 0.06	f : 0.04	2 : 0.03	4 : 0.03	= : 0.01	: : 0.01	5 : 0.01	3 : 0.01	
e : 0.22	d : 0.17	g : 0.09	c : 0.06	2 : 0.06	] : 0.06	i : 0.06	f : 0.04	3 : 0.03	b : 0.03	4 : 0.03	5 : 0.03	a : 0.03	= : 0.01	F : 0.01	

#score	738.9701413371713
#seq	62
#width	37
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_CDS_m1_run2.txt

#BEAR
gggggg^^^^^^^^^^^^^^^^^^^^^	chr2:48692653-48692869(+)$1	216	88	115	24.4728
eeee^^^^^^^^^^^^^^^^^^^^^^^	chr7:64864262-64864487(+)$1	225	158	185	24.5457
ccdddduuuuuuuuuuuudddd]cccH	chr3:142743253-142743474(+)$1	221	176	203	17.9093
ddd[bbyyyyyyyyyyyyyyyybb]dd	chr18:45422807-45423037(-)$1	230	50	77	21.6036
:eeeeeyyyyyyyyyyyyyyyyeeeee	chr6:138198267-138198494(+)$1	227	192	219	21.8558
deeeeevvvvvvvvvvvvveeeee22d	chr7:138968241-138968471(+)$1	230	36	63	20.0165
iiiiiiyyyyyyyyyyyyyyyyiiiii	chr3:52964313-52964535(-)$1	222	50	77	22.4069
iiiiiiiiuuuuuuuuuuuuiiiiiii	chr8:48877092-48877311(+)$1	219	2	29	18.4803
ffffffvvvvvvvvvvvvvffffff::	chr12:71147863-71148081(+)$1	218	135	162	18.3552
[eeeeeuuuuuuuuuuuueeeee22ff	chr1:41236963-41237181(+)$1	218	144	171	19.0351
eeeee[cccuuuuuuuuuuuuccc22e	chr11:763658-763885(+)$1	227	103	130	18.8548
#ccc^^^^^^^^^^^^^^^^^^^^^^^	chr12:112884074-112884299(+)$1	225	125	152	24.5913
bb!!bbyyyyyyyyyyyyyyyybb22b	chr12:8192543-8192773(+)$1	230	112	139	21.2395
[ccc[bbwwwwwwwwwwwwwwbb]ccc	chr7:99042319-99042543(+)$1	224	102	129	20.1452
gggggyyyyyyyyyyyyyyyygggggg	chr5:68492786-68493013(+)$1	227	124	151	22.3872
cc^^^^^^^^^^^^^^^^^^^^ccccc	chr10:51027341-51027571(-)$1	230	107	134	22.0552
!ffffffvvvvvvvvvvvvvffffff2	chr1:44201847-44202063(+)$1	216	43	70	19.6311
[ffffffvvvvvvvvvvvvvffffff]	chr1:29040674-29040900(+)$1	226	105	132	19.7697
[addddwwwwwwwwwwwwwwdddd22a	chr12:39701323-39701549(-)$1	226	131	158	20.9116
fffff^^^^^^^^^^^^^^^^^^^^^^	chr8:96057743-96057966(+)$1	223	50	77	24.4119
!!ccc^^^^^^^^^^^^^^^^^^^^^^	chr18:33744361-33744587(+)$1	226	10	37	24.8049
:eeeeevvvvvvvvvvvvveeeeefff	chr19:36884073-36884292(-)$1	219	92	119	19.0304
[dddd^^^^^^^^^^^^^^^^^^^ddd	chr3:23930609-23930841(+)$1	232	51	78	23.3312
!!ffffffuuuuuuuuuuuuffffff2	chr19:48887387-48887613(-)$1	226	105	132	18.6918
deeeee^^^^^^^^^^^^^^^^^^^^^	chr17:43181065-43181298(+)$1	233	42	69	24.3363
ggggggwwwwwwwwwwwwwwggggggg	chr8:90994861-90995072(-)$1	211	159	186	20.8373
eeeeeexxxxxxxxxxxxxxxeeeee]	chr8:17092224-17092455(-)$1	231	169	196	20.2355
ffffffvvvvvvvvvvvvvffffff00	chr6:44220940-44221157(+)$1	217	71	98	19.3167
bb[cccvvvvvvvvvvvvvccc]bb::	chr6:87968199-87968421(+)$1	222	46	73	18.0675
fffff^^^^^^^^^^^^^^^^^^^^^^	chr1:111673954-111674175(-)$1	221	59	86	24.4119
ggggggvvvvvvvvvvvvvggggggg:	chr11:62361708-62361933(-)$1	225	138	165	19.3302
gggggg^^^^^^^^^^^^^^^^^^^^^	chr3:25635934-25636155(+)$1	221	127	154	24.4728
gggggg^^^^^^^^^^^^^^^^^^^^^	chr2:210887606-210887836(+)$1	230	4	31	24.4728
!!ddddwwwwwwwwwwwwwwdddd22a	chr7:72892690-72892920(-)$1	230	26	53	21.0115
#dddd^^^^^^^^^^^^^^^^^^^^^^	chr4:147430987-147431201(-)$1	214	93	120	24.6123
ffffffvvvvvvvvvvvvvffffff:c	chr9:134064343-134064563(+)$1	220	93	120	18.9479
!!cccyyyyyyyyyyyyyyyyccc22a	chr16:24831403-24831625(+)$1	222	29	56	22.9991
ddd!!cccuuuuuuuuuuuucccdddd	chr16:30081414-30081634(+)$1	220	133	160	18.9945
ffffffuuuuuuuuuuuuffffff]bb	chr17:4585699-4585912(-)$1	213	127	154	18.2206
gggggg^^^^^^^^^^^^^^^^^^^^^	chr6:151687871-151688101(-)$1	230	43	70	24.4728
$ddddyyyyyyyyyyyyyyyyddddee	chr14:106174068-106174285(-)$1	217	141	168	21.9507
ddd^^^^^^^^^^^^^^^^^^^dddd:	chr8:74893340-74893564(+)$1	224	146	173	21.2589
iiiiii^^^^^^^^^^^^^^^^^^^^^	chr5:59894932-59895147(-)$1	215	13	40	24.3177
eeeeddddvvvvvvvvvvvvvdddd]e	chr3:63825248-63825470(-)$1	222	63	90	18.8985
eee[bb^^^^^^^^^^^^^^^^^^bbe	chr19:37238995-37239225(-)$1	230	19	46	22.3124
[eeeeexxxxxxxxxxxxxxxeeeee]	chr11:14515088-14515312(-)$1	224	75	102	20.6244
:eeeeeyyyyyyyyyyyyyyyyeeeee	chr7:104753397-104753616(+)$1	219	148	175	21.8558
======^^^^^^^^^^^^^^^^^^^^^	chr14:68117950-68118172(-)$1	222	54	81	24.5187
#dddd^^^^^^^^^^^^^^^^^^^^dd	chr19:52469033-52469263(-)$1	230	151	178	23.6773
"eeeeewwwwwwwwwwwwwweeeee44	chr2:75929357-75929580(-)$1	223	13	40	21.7777
beeeeevvvvvvvvvvvvveeeee:::	chr11:118404708-118404935(+)$1	227	114	141	18.0267
!!dddd^^^^^^^^^^^^^^^^^^^^^	chr1:183599622-183599842(-)$1	220	3	30	24.3948
[dddd[bbuuuuuuuuuuuubb]dddd	chr12:46320876-46321096(-)$1	220	100	127	18.7239
cddddyyyyyyyyyyyyyyyydddd]c	chr3:141161387-141161618(+)$1	231	199	226	22.1719
!!bb^^^^^^^^^^^^^^^^^^^^^^b	chr6:116987956-116988186(-)$1	230	114	141	23.6726
ddd^^^^^^^^^^^^^^^^^^^dddd2	chr20:20006219-20006449(+)$1	230	21	48	21.7562
[bb^^^^^^^^^^^^^^^^^^^^^^^^	chr12:109495781-109496010(+)$1	229	81	108	23.9827
[ccc^^^^^^^^^^^^^^^^^^^^^^^	chr19:20727577-20727801(-)$1	224	164	191	24.7121
!eeeee^^^^^^^^^^^^^^^^^^^^e	chr2:118586876-118587092(+)$1	216	83	110	24.3859
gggggg^^^^^^^^^^^^^^^^^^^gg	chr19:20003245-20003486(+)$1	241	42	69	23.6485
ggggggwwwwwwwwwwwwwwggggggg	chr9:98002888-98003118(-)$1	230	18	45	20.8373
[ddddyyyyyyyyyyyyyyyydddd]d	chr4:175223113-175223355(+)$1	242	125	152	22.3940
gggggg^^^^^^^^^^^^^^^^^^^^g	chr9:128109052-128109277(+)$1	225	9	36	24.0846
ffffffvvvvvvvvvvvvvffffff::	chr18:47908451-47908677(+)$1	226	195	222	18.3552
[ddddyyyyyyyyyyyyyyyydddd]e	chr17:674544-674768(-)$1	224	69	96	22.4356
fffff^^^^^^^^^^^^^^^^^^^^^^	chr12:106500092-106500322(-)$1	230	166	193	24.4119
!eeeee^^^^^^^^^^^^^^^^^^^^^	chr10:1038432-1038649(+)$1	217	152	179	24.7788
$ffffffvvvvvvvvvvvvvfffffff	chr10:69648541-69648759(+)$1	218	21	48	19.2859

#otherMatches

#Seq PSSM
UGAUUCUGCCAUUGACACUAUAUCUCC	chr2:48692653-48692869(+)$1	216	88	115	24.4728
UCUCAACCCUUACUAAACAUAAAAUAA	chr7:64864262-64864487(+)$1	225	158	185	24.5457
CUCUUUCAACACACUAUUAAAGCAGAA	chr3:142743253-142743474(+)$1	221	176	203	17.9093
UCUGGUGAAGAAGCUAAAGAAAACAGG	chr18:45422807-45423037(-)$1	230	50	77	21.6036
UUGCUGCCACCCUGAAGCUCAACAGUA	chr6:138198267-138198494(+)$1	227	192	219	21.8558
UACUUCAACAAGGACUUCAGAGGUCAA	chr7:138968241-138968471(+)$1	230	36	63	20.0165
AUACUAUGUUUUCAUCCCCUUUUGGUG	chr3:52964313-52964535(-)$1	222	50	77	22.4069
GAUAUGAAUACAAAUACAUCUUCAUAU	chr8:48877092-48877311(+)$1	219	2	29	18.4803
AUGCUGAGAAAAAUGACAACAGCAUAA	chr12:71147863-71148081(+)$1	218	135	162	18.3552
UGGGUGGAUUCAUUGCCACACUCUUUU	chr1:41236963-41237181(+)$1	218	144	171	19.0351
CUAAAAUCUACAACUACUACAAGAAGU	chr11:763658-763885(+)$1	227	103	130	18.8548
UAGGUAAGUUGGAAUGAAAAGAGAGGA	chr12:112884074-112884299(+)$1	225	125	152	24.5913
CUAUGCCAUCAACUCCUCUCCAGCCAA	chr12:8192543-8192773(+)$1	230	112	139	21.2395
UGCUGUCUGUGAAUUCUUUUUGAAAGC	chr7:99042319-99042543(+)$1	224	102	129	20.1452
CUGGAGAAAAUUAGCAGACAGUCUAGG	chr5:68492786-68493013(+)$1	227	124	151	22.3872
GCUUUAUCCAUUCAUAUACCAUGCUGU	chr10:51027341-51027571(-)$1	230	107	134	22.0552
UUUUCUUUUCUAGGUCAUUUAGGAAAU	chr1:44201847-44202063(+)$1	216	43	70	19.6311
CACCCAUCACCAUCACCCCAGUGGGUC	chr1:29040674-29040900(+)$1	226	105	132	19.7697
CCUUCCUCUAUGCUGCUUCUGGAAAUG	chr12:39701323-39701549(-)$1	226	131	158	20.9116
GCAUAUCGUAAUAUCAAGGAACUGGAA	chr8:96057743-96057966(+)$1	223	50	77	24.4119
UUUAAAAUGUUUUCUCUUCAGUUUAUU	chr18:33744361-33744587(+)$1	226	10	37	24.8049
AGAGUGCGACAACAACUAACACUCCAU	chr19:36884073-36884292(-)$1	219	92	119	19.0304
UGGACAUAUUGAAAGAUAAUUGGAGUC	chr3:23930609-23930841(+)$1	232	51	78	23.3312
UUCUACCUCUAUAUCACCAAAGGUAGC	chr19:48887387-48887613(-)$1	226	105	132	18.6918
GCUUUUAUACGCUGCCCUCCACCAUCA	chr17:43181065-43181298(+)$1	233	42	69	24.3363
GGGGGUUGAAAUCACAAAAUAUUCUCU	chr8:90994861-90995072(-)$1	211	159	186	20.8373
GAUUGUUUUUUCCUGUCAUUUAUGAUG	chr8:17092224-17092455(-)$1	231	169	196	20.2355
GGUGGUGCUGCUGUUUGAAACCGCCCU	chr6:44220940-44221157(+)$1	217	71	98	19.3167
AGUUGCUCCUCCACUAAUUGCACCUAA	chr6:87968199-87968421(+)$1	222	46	73	18.0675
GCUGCUUUCAUAUUUUCAUACAUUACU	chr1:111673954-111674175(-)$1	221	59	86	24.4119
CGUCAGAAACUAAACCCAGCUGAUGCC	chr11:62361708-62361933(-)$1	225	138	165	19.3302
UGCUGGAAGCACUAAAAAUUUAUAUCA	chr3:25635934-25636155(+)$1	221	127	154	24.4728
AACAGGGCUUUAUUUCCUCCCAUCUUU	chr2:210887606-210887836(+)$1	230	4	31	24.4728
GACUCUCAACCCUUCUACUAAGAGGAA	chr7:72892690-72892920(-)$1	230	26	53	21.0115
CAGCUUUUAUCAAUCACACCCAUCAAC	chr4:147430987-147431201(-)$1	214	93	120	24.6123
UAGGGGUCUCUAAUAAAUUCCCUUAAG	chr9:134064343-134064563(+)$1	220	93	120	18.9479
CUCUCCAUUUUUUCCCCCUUUGAGUAG	chr16:24831403-24831625(+)$1	222	29	56	22.9991
AGGCUGCCCCCAACACUCCAGGCCCUG	chr16:30081414-30081634(+)$1	220	133	160	18.9945
UGCACUCUUCUCCCCACCAGUGUAAGC	chr17:4585699-4585912(-)$1	213	127	154	18.2206
ACUCACGUAUUUUUUUACUUGUUUCUU	chr6:151687871-151688101(-)$1	230	43	70	24.4728
AACCGCCACCCUCUCAAAAUCCGGUGG	chr14:106174068-106174285(-)$1	217	141	168	21.9507
GCCUAUUCAAAUCAUAUUCUAUGGCAU	chr8:74893340-74893564(+)$1	224	146	173	21.2589
AUUUGAAAAUAUGCUAUAUUCUUUCAC	chr5:59894932-59895147(-)$1	215	13	40	24.3177
CUGGAGAUGAUCGGAGAAUUAAUCUGC	chr3:63825248-63825470(-)$1	222	63	90	18.8985
UACUCAACAUCAACGAAUCCAUACUGG	chr19:37238995-37239225(-)$1	230	19	46	22.3124
CACAGCUAUGUUAGAAGAAAUGCUGUU	chr11:14515088-14515312(-)$1	224	75	102	20.6244
AACAGGGCCACAUUGUCCAUUACCUGU	chr7:104753397-104753616(+)$1	219	148	175	21.8558
UCUUUCGCAGCCAUUGAACUUCUAUAG	chr14:68117950-68118172(-)$1	222	54	81	24.5187
AACACGAAAAUUAGAGAAGCAUCAUGU	chr19:52469033-52469263(-)$1	230	151	178	23.6773
CGUCUUUGUUUCCUUCAGUUAAGAUCC	chr2:75929357-75929580(-)$1	223	13	40	21.7777
GACCUCACUCCAGAUUCCAGAGGUAUA	chr11:118404708-118404935(+)$1	227	114	141	18.0267
uuucUGAAAUUCUAAACCCUCCUCAUA	chr1:183599622-183599842(-)$1	220	3	30	24.3948
UCUCAAUCACCAUCUCCUAAGAAUGAG	chr12:46320876-46321096(-)$1	220	100	127	18.7239
GGAAGACCUUACUGAUCGCAACUUCUC	chr3:141161387-141161618(+)$1	231	199	226	22.1719
GUGCAUCUAAUCAUCCAAAAAAUUCAG	chr6:116987956-116988186(-)$1	230	114	141	23.6726
AGGAAACUUUUUUUACAAUAUCCCUUA	chr20:20006219-20006449(+)$1	230	21	48	21.7562
AGCCCCCCUCACACCAGUAUUUAUCCU	chr12:109495781-109496010(+)$1	229	81	108	23.9827
UGUGGCAAAGCCUUCAACUCGUCCUCA	chr19:20727577-20727801(-)$1	224	164	191	24.7121
ACAGAUCUUUAAUGUUAAUAACCUAAA	chr2:118586876-118587092(+)$1	216	83	110	24.3859
UCUCCAAACAUAAAAGAACUCAUACUG	chr19:20003245-20003486(+)$1	241	42	69	23.6485
AUAUAAUGUUUACAGUGUUUUUAUAUU	chr9:98002888-98003118(-)$1	230	18	45	20.8373
UUUACCUCAUACUCACCUUAUGUAACA	chr4:175223113-175223355(+)$1	242	125	152	22.3940
AAGGGGCUAAUUCUCUCACUCUCCUUU	chr9:128109052-128109277(+)$1	225	9	36	24.0846
AACAAGUUCUUCAAAGCCUUUUGUUCU	chr18:47908451-47908677(+)$1	226	195	222	18.3552
ccuguauuaaaaguaacucuagcAGUG	chr17:674544-674768(-)$1	224	69	96	22.4356
CCCAUAUCAGUUACCAUUUCUCAUACC	chr12:106500092-106500322(-)$1	230	166	193	24.4119
UUCCCCAAAUUGGAUGUAAGUGACUUA	chr10:1038432-1038649(+)$1	217	152	179	24.7788
ACUCAUUACUUCAGAAAAUAAAUGAGA	chr10:69648541-69648759(+)$1	218	21	48	19.2859

#DB
((((((.....................	chr2:48692653-48692869(+)$1	1	88	115	24.4728
((((.......................	chr7:64864262-64864487(+)$1	1	158	185	24.5457
((((((............)))).))))	chr3:142743253-142743474(+)$1	1	176	203	17.9093
(((.((................)).))	chr18:45422807-45423037(-)$1	1	50	77	21.6036
.(((((................)))))	chr6:138198267-138198494(+)$1	1	192	219	21.8558
((((((.............)))))..)	chr7:138968241-138968471(+)$1	1	36	63	20.0165
((((((................)))))	chr3:52964313-52964535(-)$1	1	50	77	22.4069
((((((((............)))))))	chr8:48877092-48877311(+)$1	1	2	29	18.4803
((((((.............))))))..	chr12:71147863-71148081(+)$1	1	135	162	18.3552
.(((((............)))))..))	chr1:41236963-41237181(+)$1	1	144	171	19.0351
(((((.(((............)))..)	chr11:763658-763885(+)$1	1	103	130	18.8548
.(((.......................	chr12:112884074-112884299(+)$1	1	125	152	24.5913
((..((................))..)	chr12:8192543-8192773(+)$1	1	112	139	21.2395
.(((.((..............)).)))	chr7:99042319-99042543(+)$1	1	102	129	20.1452
(((((................))))))	chr5:68492786-68493013(+)$1	1	124	151	22.3872
((....................)))((	chr10:51027341-51027571(-)$1	1	107	134	22.0552
.((((((.............)))))).	chr1:44201847-44202063(+)$1	1	43	70	19.6311
.((((((.............)))))).	chr1:29040674-29040900(+)$1	1	105	132	19.7697
.(((((..............))))..)	chr12:39701323-39701549(-)$1	1	131	158	20.9116
(((((......................	chr8:96057743-96057966(+)$1	1	50	77	24.4119
..(((......................	chr18:33744361-33744587(+)$1	1	10	37	24.8049
.(((((.............)))))(((	chr19:36884073-36884292(-)$1	1	92	119	19.0304
.((((...................)))	chr3:23930609-23930841(+)$1	1	51	78	23.3312
..((((((............)))))).	chr19:48887387-48887613(-)$1	1	105	132	18.6918
((((((.....................	chr17:43181065-43181298(+)$1	1	42	69	24.3363
((((((..............)))))))	chr8:90994861-90995072(-)$1	1	159	186	20.8373
((((((...............))))).	chr8:17092224-17092455(-)$1	1	169	196	20.2355
((((((.............))))))..	chr6:44220940-44221157(+)$1	1	71	98	19.3167
((.(((.............))).))..	chr6:87968199-87968421(+)$1	1	46	73	18.0675
(((((......................	chr1:111673954-111674175(-)$1	1	59	86	24.4119
((((((.............))))))).	chr11:62361708-62361933(-)$1	1	138	165	19.3302
((((((.....................	chr3:25635934-25636155(+)$1	1	127	154	24.4728
((((((.....................	chr2:210887606-210887836(+)$1	1	4	31	24.4728
..((((..............))))..)	chr7:72892690-72892920(-)$1	1	26	53	21.0115
.((((......................	chr4:147430987-147431201(-)$1	1	93	120	24.6123
((((((.............)))))).(	chr9:134064343-134064563(+)$1	1	93	120	18.9479
..(((................)))..)	chr16:24831403-24831625(+)$1	1	29	56	22.9991
(((..(((............)))))))	chr16:30081414-30081634(+)$1	1	133	160	18.9945
((((((............)))))).))	chr17:4585699-4585912(-)$1	1	127	154	18.2206
((((((.....................	chr6:151687871-151688101(-)$1	1	43	70	24.4728
.((((................))))))	chr14:106174068-106174285(-)$1	1	141	168	21.9507
(((...................)))).	chr8:74893340-74893564(+)$1	1	146	173	21.2589
((((((.....................	chr5:59894932-59895147(-)$1	1	13	40	24.3177
((((((((.............)))).)	chr3:63825248-63825470(-)$1	1	63	90	18.8985
(((.((..................)))	chr19:37238995-37239225(-)$1	1	19	46	22.3124
.(((((...............))))).	chr11:14515088-14515312(-)$1	1	75	102	20.6244
.(((((................)))))	chr7:104753397-104753616(+)$1	1	148	175	21.8558
((((((.....................	chr14:68117950-68118172(-)$1	1	54	81	24.5187
.((((....................))	chr19:52469033-52469263(-)$1	1	151	178	23.6773
.(((((..............)))))..	chr2:75929357-75929580(-)$1	1	13	40	21.7777
)(((((.............)))))...	chr11:118404708-118404935(+)$1	1	114	141	18.0267
..((((.....................	chr1:183599622-183599842(-)$1	1	3	30	24.3948
.((((.((............)).))))	chr12:46320876-46321096(-)$1	1	100	127	18.7239
(((((................)))).)	chr3:141161387-141161618(+)$1	1	199	226	22.1719
..((......................)	chr6:116987956-116988186(-)$1	1	114	141	23.6726
(((...................)))).	chr20:20006219-20006449(+)$1	1	21	48	21.7562
.((........................	chr12:109495781-109496010(+)$1	1	81	108	23.9827
.(((.......................	chr19:20727577-20727801(-)$1	1	164	191	24.7121
.(((((....................)	chr2:118586876-118587092(+)$1	1	83	110	24.3859
((((((...................))	chr19:20003245-20003486(+)$1	1	42	69	23.6485
((((((..............)))))))	chr9:98002888-98003118(-)$1	1	18	45	20.8373
.((((................)))).)	chr4:175223113-175223355(+)$1	1	125	152	22.3940
((((((....................)	chr9:128109052-128109277(+)$1	1	9	36	24.0846
((((((.............))))))..	chr18:47908451-47908677(+)$1	1	195	222	18.3552
.((((................)))).)	chr17:674544-674768(-)$1	1	69	96	22.4356
(((((......................	chr12:106500092-106500322(-)$1	1	166	193	24.4119
.(((((.....................	chr10:1038432-1038649(+)$1	1	152	179	24.7788
.((((((.............)))))))	chr10:69648541-69648759(+)$1	1	21	48	19.2859

#PSSM
[ : 0.16	g : 0.14	! : 0.13	f : 0.11	d : 0.08	e : 0.07	c : 0.04	: : 0.04	i : 0.04	# : 0.04	b : 0.04	$ : 0.02	= : 0.01	" : 0.01	
e : 0.23	d : 0.17	f : 0.16	g : 0.14	! : 0.08	c : 0.07	i : 0.04	b : 0.04	a : 0.01	= : 0.01	
e : 0.23	d : 0.23	f : 0.17	g : 0.14	c : 0.07	i : 0.04	b : 0.02	! : 0.01	^ : 0.01	[ : 0.01	= : 0.01	
e : 0.22	d : 0.17	f : 0.17	g : 0.14	c : 0.08	^ : 0.05	i : 0.04	[ : 0.02	! : 0.02	= : 0.01	b : 0.01	
d : 0.19	e : 0.19	f : 0.17	g : 0.14	^ : 0.11	b : 0.04	i : 0.04	c : 0.04	[ : 0.01	! : 0.01	= : 0.01	
^ : 0.22	e : 0.17	g : 0.13	f : 0.13	y : 0.08	d : 0.07	b : 0.05	i : 0.04	[ : 0.02	c : 0.02	= : 0.01	
^ : 0.41	y : 0.16	v : 0.13	w : 0.07	f : 0.05	u : 0.04	c : 0.02	b : 0.02	x : 0.02	i : 0.01	d : 0.01	
^ : 0.41	v : 0.17	y : 0.16	w : 0.08	u : 0.04	c : 0.02	x : 0.02	i : 0.01	f : 0.01	d : 0.01	b : 0.01	
^ : 0.41	v : 0.19	y : 0.16	u : 0.10	w : 0.08	x : 0.02	c : 0.01	
^ : 0.41	v : 0.19	y : 0.16	u : 0.11	w : 0.08	x : 0.02	
^ : 0.41	v : 0.19	y : 0.16	u : 0.11	w : 0.08	x : 0.02	
^ : 0.41	v : 0.19	y : 0.16	u : 0.11	w : 0.08	x : 0.02	
^ : 0.41	v : 0.19	y : 0.16	u : 0.11	w : 0.08	x : 0.02	
^ : 0.41	v : 0.19	y : 0.16	u : 0.11	w : 0.08	x : 0.02	
^ : 0.41	v : 0.19	y : 0.16	u : 0.11	w : 0.08	x : 0.02	
^ : 0.41	v : 0.19	y : 0.16	u : 0.11	w : 0.08	x : 0.02	
^ : 0.41	v : 0.19	y : 0.16	u : 0.11	w : 0.08	x : 0.02	
^ : 0.41	v : 0.19	y : 0.16	u : 0.11	w : 0.08	x : 0.02	
^ : 0.41	v : 0.19	y : 0.16	w : 0.08	u : 0.07	x : 0.02	d : 0.01	e : 0.01	f : 0.01	
^ : 0.41	y : 0.16	w : 0.08	u : 0.07	f : 0.07	e : 0.05	v : 0.05	x : 0.02	d : 0.01	c : 0.01	g : 0.01	
^ : 0.41	y : 0.16	f : 0.13	e : 0.07	d : 0.04	g : 0.04	x : 0.02	c : 0.02	i : 0.01	u : 0.01	w : 0.01	v : 0.01	b : 0.01	
^ : 0.41	f : 0.13	d : 0.11	e : 0.10	y : 0.07	c : 0.05	g : 0.05	b : 0.02	i : 0.01	
^ : 0.36	e : 0.13	f : 0.13	d : 0.13	c : 0.05	g : 0.05	] : 0.04	b : 0.04	i : 0.02	
^ : 0.36	d : 0.16	f : 0.13	e : 0.11	c : 0.05	g : 0.05	b : 0.04	i : 0.02	2 : 0.01	] : 0.01	
^ : 0.33	d : 0.14	f : 0.13	2 : 0.10	e : 0.07	g : 0.05	c : 0.04	] : 0.02	i : 0.02	b : 0.02	: : 0.01	
^ : 0.30	d : 0.10	2 : 0.08	f : 0.08	e : 0.07	: : 0.07	g : 0.07	] : 0.05	c : 0.04	i : 0.02	b : 0.02	0 : 0.01	4 : 0.01	
^ : 0.26	e : 0.11	d : 0.10	: : 0.08	g : 0.07	c : 0.05	f : 0.04	b : 0.04	2 : 0.04	] : 0.04	a : 0.04	i : 0.02	H : 0.01	0 : 0.01	4 : 0.01	

#score	1476.5308677596192
#seq	68
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_UTR_m3_run2.txt

#BEAR
ff]ccc7777777iiiiiii	chr13:98674964-98675194(+)$1	230	62	82	13.7977
oodddd7777777dddd22b	chr15:44816622-44816852(+)$1	230	31	51	13.0574
oodddd7777777bb]====	chr8:80950139-80950369(-)$1	230	94	114	13.5385
d22dddd666666eeeee22	chr1:85112362-85112592(-)$1	230	146	166	11.4568
eeee999999999eeeee33	chr6:135539893-135540118(+)$1	225	84	104	13.8402
iiii999999999iiiiiii	chr19:39899913-39900139(+)$1	226	72	92	13.0320
333dddd666666dddd333	chr6:26031733-26031963(-)$1	230	184	204	11.7375
eee0000000000eeeee]d	chr2:128061138-128061368(-)$1	230	62	82	15.0995
cc>>>>>>>>>>>eeeee22	chr17:61788057-61788283(-)$1	226	173	193	14.6039
>>>>>>>>>>>>>ffffff3	chr10:60156342-60156569(+)$1	227	132	152	14.2407
gggggg7777777eeeee:g	chr2:128062109-128062332(-)$1	223	61	81	13.0417
qqqccc7777777dddd22f	chr15:65255260-65255478(+)$1	218	40	60	12.1064
>>>>>>>>>>>>>>>fffff	chr5:149779524-149779754(+)$1	230	39	59	13.7414
ffffff7777777eeeee77	chr1:167388160-167388390(+)$1	230	118	138	12.3985
0000bb7777777ggggggg	chr10:94660431-94660661(+)$1	230	194	214	13.7969
lleeeee666666eeeee33	chr9:72325627-72325850(-)$1	223	70	90	10.9995
>>>>bb666666ccc]ccc]	chr14:23494957-23495200(-)$1	243	126	146	11.6135
d>>>>>>>>>>>>iiiiiii	chr15:59147370-59147600(+)$1	230	136	156	14.4127
gggggg7777777bb]hhhh	chrX:106308638-106308868(-)$1	230	178	198	12.4986
>>>>>>>>>>>>>>gggggg	chr5:134166452-134166675(+)$1	223	52	72	14.5440
ccc0000000000eeeee33	chr1:47142318-47142542(-)$1	224	97	117	15.6224
ccc]bb666666ffffff44	chrX:154563759-154563986(-)$1	227	114	134	10.7914
gggggg7777777eeeee]i	chr14:58839803-58840033(+)$1	230	84	104	14.2449
ggggg88888888ccc]bb2	chr8:124825004-124825226(+)$1	222	107	127	14.0289
eeeee88888888dddd22d	chr13:52986925-52987149(-)$1	224	126	146	14.1845
>>>>>>>>>>>>>=======	chr11:33000875-33001105(+)$1	230	109	129	14.6995
ggg>>>>>>>>>>>>fffff	chr18:61654429-61654659(+)$1	230	111	131	13.2266
iiiiii7777777ccc333=	chr10:91343817-91344040(-)$1	223	159	179	13.5267
>>>>>>>>>>>>>>dddd]b	chr3:119348466-119348688(+)$1	222	96	116	13.8811
mmccc88888888eeeeehh	chr2:232026080-232026310(+)$1	230	167	187	14.0779
cc>>>>>>>>>>>>dddd]c	chr5:111066224-111066454(-)$1	230	118	138	13.9373
eee0000000000ffffff]	chr1:24291415-24291645(-)$1	230	133	153	14.5842
lldddd666666bb]=====	chr4:129191532-129191756(-)$1	224	188	208	10.8387
>>>>>>>>>>>>>ffffff2	chr14:77935647-77935877(+)$1	230	186	206	14.0680
cc22bb7777777eeeee]g	chrX:38664687-38664917(+)$1	230	163	183	14.2695
555ccc88888888gggggg	chr3:40575439-40575665(+)$1	226	161	181	13.0250
nnnccc7777777ccc4444	chr17:28614832-28615054(-)$1	222	109	129	12.2628
]eeeee7777777ggggggg	chr14:55512635-55512869(+)$1	234	179	199	13.7366
]dddd88888888ddddddd	chr9:139745328-139745558(+)$1	230	139	159	13.9214
22dddd7777777eeeee]g	chr3:197767966-197768189(+)$1	223	176	196	14.3347
d]dddd88888888bb333d	chr21:30717202-30717428(+)$1	226	137	157	13.6515
qqqccc7777777=======	chrX:77305428-77305658(+)$1	230	59	79	12.9177
c]dddd7777777eeeee]f	chr6:160526319-160526544(+)$1	225	98	118	14.2795
nnnnbb88888888gggggg	chr6:144147010-144147240(+)$1	230	49	69	12.1106
ee]ccc7777777iiiiiii	chr11:113668508-113668730(-)$1	222	137	157	13.9650
dddd999999999ggggggg	chr6:149980639-149980869(-)$1	230	95	115	13.1968
neeeee7777777ddddbb]	chr12:104498488-104498718(+)$1	230	62	82	12.3355
oeeeee7777777ccc22dd	chr12:111886204-111886424(+)$1	220	65	85	12.4752
e>>>>>>>>>>>>eeeee22	chr16:24953292-24953515(-)$1	223	59	79	14.7731
eeeee88888888ffffff2	chr7:64292979-64293202(+)$1	223	107	127	14.4372
e>>>>>>>>>>>>hhhhhhh	chr17:27873281-27873511(+)$1	230	54	74	13.0340
d>>>>>>>>>>>>>>fffff	chr1:168222085-168222315(+)$1	230	106	126	13.6635
mmmccc88888888gggggg	chr6:24719540-24719765(-)$1	225	101	121	13.1563
44dddd7777777eeeeecc	chr9:95042978-95043208(-)$1	230	166	186	14.5221
eedddd7777777eeeeecc	chr8:81887495-81887725(-)$1	230	193	213	14.0039
dddd]a666666ffffff22	chr6:32151674-32151904(-)$1	230	128	148	10.8326
bb]bb88888888bb]cccE	chr3:196674765-196674983(-)$1	218	166	186	12.3718

#otherMatches

#Seq PSSM
CUUAGUGUUUUCAUUGCAAA	chr13:98674964-98675194(+)$1	230	62	82	13.7977
GUUUCUGCCACCAGCAGUUU	chr15:44816622-44816852(+)$1	230	31	51	13.0574
GCCAUGAAUUUCUACCAGAU	chr8:80950139-80950369(-)$1	230	94	114	13.5385
GAAAGGUAUUCCAUGAAGCU	chr1:85112362-85112592(-)$1	230	146	166	11.4568
UUUUGUUAUUGUUGGUUUAU	chr6:135539893-135540118(+)$1	225	84	104	13.8402
uuauuaCCUUAAAAGUCUAU	chr19:39899913-39900139(+)$1	226	72	92	13.0320
UUAACAGAACAAAUUUCUAA	chr6:26031733-26031963(-)$1	230	184	204	11.7375
AGAAUGAAUCUUCUUUGUUU	chr2:128061138-128061368(-)$1	230	62	82	15.0995
UGUCACAUCAUUCAUGGCAU	chr17:61788057-61788283(-)$1	226	173	193	14.6039
GCAAAAUAUUUAGAAAUUGU	chr10:60156342-60156569(+)$1	227	132	152	14.2407
UUCUUUCUAAUAAUGAUAUG	chr2:128062109-128062332(-)$1	223	61	81	13.0417
UUCUCAGAAAGUCCUAGGCC	chr15:65255260-65255478(+)$1	218	40	60	12.1064
CAUGACCUCACCCCACUCCC	chr5:149779524-149779754(+)$1	230	39	59	13.7414
CCAUCAUCCCUAGAUAUUCU	chr1:167388160-167388390(+)$1	230	118	138	12.3985
UUUUCUCAACUAUCCCCAAA	chr10:94660431-94660661(+)$1	230	194	214	13.7969
UUUCUUAUAGUUUAUGUUUA	chr9:72325627-72325850(-)$1	223	70	90	10.9995
CACUACUCAAUCUCAGCCUG	chr14:23494957-23495200(-)$1	243	126	146	11.6135
AUUAAUGACUUUGUAGUGUU	chr15:59147370-59147600(+)$1	230	136	156	14.4127
uaguguuuaucugaagccua	chrX:106308638-106308868(-)$1	230	178	198	12.4986
AGUUUGUUUUCUUUGGUAGA	chr5:134166452-134166675(+)$1	223	52	72	14.5440
GUGUCCCCUUAUCUCAUUAU	chr1:47142318-47142542(-)$1	224	97	117	15.6224
CAGUCCACUACAAGCUAGAC	chrX:154563759-154563986(-)$1	227	114	134	10.7914
CAGUUUUUAUGUUUGCUAUA	chr14:58839803-58840033(+)$1	230	84	104	14.2449
UGCACAUCUUAUUGCGACAA	chr8:124825004-124825226(+)$1	222	107	127	14.0289
AUGUGUCUUUUUCCAGUAGG	chr13:52986925-52987149(-)$1	224	126	146	14.1845
UAUAACCCAAUUUCCACUUA	chr11:33000875-33001105(+)$1	230	109	129	14.6995
UUUCCUUCUACCUAUCUUGC	chr18:61654429-61654659(+)$1	230	111	131	13.2266
GAAAAGUUGUUUGAUGUUUA	chr10:91343817-91344040(-)$1	223	159	179	13.5267
UUGCUUUAUCUCCUUGGGCA	chr3:119348466-119348688(+)$1	222	96	116	13.8811
GUAGUAUUUCCUGUUCACCG	chr2:232026080-232026310(+)$1	230	167	187	14.0779
CAACUCAAACUCCCACCGCG	chr5:111066224-111066454(-)$1	230	118	138	13.9373
GGUUAUCUUUAUUAUGUUUC	chr1:24291415-24291645(-)$1	230	133	153	14.5842
UAUACACAAACUCAAUUAGC	chr4:129191532-129191756(-)$1	224	188	208	10.8387
GUUGAUUGAGUGGCUGGUAU	chr14:77935647-77935877(+)$1	230	186	206	14.0680
GGCAGACUGCAAACUGGGGG	chrX:38664687-38664917(+)$1	230	163	183	14.2695
UUCUGUUUUUUUUUCUUUGU	chr3:40575439-40575665(+)$1	226	161	181	13.0250
CUUGAGUGCUUUUGUGGACA	chr17:28614832-28615054(-)$1	222	109	129	12.2628
CUCUUAGCAGUGAUGAGGCU	chr14:55512635-55512869(+)$1	234	179	199	13.7366
UGCCACACCUGCCGGCUUCU	chr9:139745328-139745558(+)$1	230	139	159	13.9214
AAGCUAAUAcagguugagca	chr3:197767966-197768189(+)$1	223	176	196	14.3347
GGGUUUCUAUUAAUGACACA	chr21:30717202-30717428(+)$1	226	137	157	13.6515
UAAGUAUUAUUUUACAAAAU	chrX:77305428-77305658(+)$1	230	59	79	12.9177
CAUUCGAAGAAACCCUUGCU	chr6:160526319-160526544(+)$1	225	98	118	14.2795
AAAAUGAAAAUCUGGUAUUU	chr6:144147010-144147240(+)$1	230	49	69	12.1106
UUGGUGUGCAGUAUGGUCUU	chr11:113668508-113668730(-)$1	222	137	157	13.9650
AGUUGUUUUACUUUUGGACU	chr6:149980639-149980869(-)$1	230	95	115	13.1968
AAGAAAAUAUGCAAAUUGUU	chr12:104498488-104498718(+)$1	230	62	82	12.3355
AGGGCCCUCCUGUAGGUUUC	chr12:111886204-111886424(+)$1	220	65	85	12.4752
UUUAAUGUAUCAGAAGCAUU	chr16:24953292-24953515(-)$1	223	59	79	14.7731
UCUUACUGCACAUAAGAUCA	chr7:64292979-64293202(+)$1	223	107	127	14.4372
AAACAUUCAGUACACUAAAG	chr17:27873281-27873511(+)$1	230	54	74	13.0340
UCCCCCAUCACAAUUGUUAG	chr1:168222085-168222315(+)$1	230	106	126	13.6635
CCCCGGUAUACACUGUAGUU	chr6:24719540-24719765(-)$1	225	101	121	13.1563
AUGUGAAAAUUAAAGGUAAG	chr9:95042978-95043208(-)$1	230	166	186	14.5221
ACUGAUGGUUUUUAAAGACU	chr8:81887495-81887725(-)$1	230	193	213	14.0039
GCUAUCUCCCAGGGGCAGUA	chr6:32151674-32151904(-)$1	230	128	148	10.8326
CCUGGCAGUCAACGGCUUCC	chr3:196674765-196674983(-)$1	218	166	186	12.3718

#DB
)).))).......)))))))	chr13:98674964-98675194(+)$1	1	62	82	13.7977
..)))).......))))..)	chr15:44816622-44816852(+)$1	1	31	51	13.0574
..)))).......)).))))	chr8:80950139-80950369(-)$1	1	94	114	13.5385
)..))))......)))))..	chr1:85112362-85112592(-)$1	1	146	166	11.4568
)))).........)))))..	chr6:135539893-135540118(+)$1	1	84	104	13.8402
)))).........)))))))	chr19:39899913-39900139(+)$1	1	72	92	13.0320
...))))......))))...	chr6:26031733-26031963(-)$1	1	184	204	11.7375
)))..........))))).)	chr2:128061138-128061368(-)$1	1	62	82	15.0995
))...........)))))..	chr17:61788057-61788283(-)$1	1	173	193	14.6039
.............)))))).	chr10:60156342-60156569(+)$1	1	132	152	14.2407
)))))).......))))).(	chr2:128062109-128062332(-)$1	1	61	81	13.0417
...))).......))))..)	chr15:65255260-65255478(+)$1	1	40	60	12.1064
...............)))))	chr5:149779524-149779754(+)$1	1	39	59	13.7414
)))))).......)))))..	chr1:167388160-167388390(+)$1	1	118	138	12.3985
....)).......)))))))	chr10:94660431-94660661(+)$1	1	194	214	13.7969
..)))))......)))))..	chr9:72325627-72325850(-)$1	1	70	90	10.9995
....))......))).))).	chr14:23494957-23495200(-)$1	1	126	146	11.6135
)............)))))))	chr15:59147370-59147600(+)$1	1	136	156	14.4127
)))))).......)).))))	chrX:106308638-106308868(-)$1	1	178	198	12.4986
..............))))))	chr5:134166452-134166675(+)$1	1	52	72	14.5440
)))..........)))))..	chr1:47142318-47142542(-)$1	1	97	117	15.6224
))).))......))))))..	chrX:154563759-154563986(-)$1	1	114	134	10.7914
)))))).......))))).)	chr14:58839803-58840033(+)$1	1	84	104	14.2449
)))))........))).)).	chr8:124825004-124825226(+)$1	1	107	127	14.0289
)))))........))))..)	chr13:52986925-52987149(-)$1	1	126	146	14.1845
.............)))))))	chr11:33000875-33001105(+)$1	1	109	129	14.6995
)))............)))))	chr18:61654429-61654659(+)$1	1	111	131	13.2266
)))))).......)))...)	chr10:91343817-91344040(-)$1	1	159	179	13.5267
..............)))).)	chr3:119348466-119348688(+)$1	1	96	116	13.8811
..)))........)))))))	chr2:232026080-232026310(+)$1	1	167	187	14.0779
))............)))).)	chr5:111066224-111066454(-)$1	1	118	138	13.9373
)))..........)))))).	chr1:24291415-24291645(-)$1	1	133	153	14.5842
..))))......)).)))))	chr4:129191532-129191756(-)$1	1	188	208	10.8387
.............)))))).	chr14:77935647-77935877(+)$1	1	186	206	14.0680
))..)).......))))).)	chrX:38664687-38664917(+)$1	1	163	183	14.2695
...)))........))))))	chr3:40575439-40575665(+)$1	1	161	181	13.0250
...))).......)))....	chr17:28614832-28615054(-)$1	1	109	129	12.2628
.))))).......)))))))	chr14:55512635-55512869(+)$1	1	179	199	13.7366
.))))........)))))))	chr9:139745328-139745558(+)$1	1	139	159	13.9214
..)))).......))))).)	chr3:197767966-197768189(+)$1	1	176	196	14.3347
).))))........))...)	chr21:30717202-30717428(+)$1	1	137	157	13.6515
...))).......)))))))	chrX:77305428-77305658(+)$1	1	59	79	12.9177
).)))).......))))).)	chr6:160526319-160526544(+)$1	1	98	118	14.2795
....))........))))))	chr6:144147010-144147240(+)$1	1	49	69	12.1106
)).))).......)))))))	chr11:113668508-113668730(-)$1	1	137	157	13.9650
)))).........)))))))	chr6:149980639-149980869(-)$1	1	95	115	13.1968
.))))).......)))))).	chr12:104498488-104498718(+)$1	1	62	82	12.3355
.))))).......)))..))	chr12:111886204-111886424(+)$1	1	65	85	12.4752
)............)))))..	chr16:24953292-24953515(-)$1	1	59	79	14.7731
)))))........)))))).	chr7:64292979-64293202(+)$1	1	107	127	14.4372
)............)))))))	chr17:27873281-27873511(+)$1	1	54	74	13.0340
)..............)))))	chr1:168222085-168222315(+)$1	1	106	126	13.6635
...)))........))))))	chr6:24719540-24719765(-)$1	1	101	121	13.1563
..)))).......)))))))	chr9:95042978-95043208(-)$1	1	166	186	14.5221
)))))).......)))))))	chr8:81887495-81887725(-)$1	1	193	213	14.0039
)))).)......))))))..	chr6:32151674-32151904(-)$1	1	128	148	10.8326
)).))........)).))))	chr3:196674765-196674983(-)$1	1	166	186	12.3718

#PSSM
e : 0.15	> : 0.12	d : 0.10	c : 0.10	g : 0.08	o : 0.05	n : 0.05	f : 0.03	i : 0.03	q : 0.03	l : 0.03	m : 0.03	] : 0.03	3 : 0.01	0 : 0.01	5 : 0.01	2 : 0.01	4 : 0.01	b : 0.01	
> : 0.19	e : 0.17	c : 0.08	g : 0.08	d : 0.05	f : 0.03	o : 0.03	2 : 0.03	i : 0.03	q : 0.03	l : 0.03	m : 0.03	n : 0.03	] : 0.03	3 : 0.01	0 : 0.01	5 : 0.01	4 : 0.01	b : 0.01	
> : 0.22	d : 0.19	e : 0.15	g : 0.08	] : 0.05	c : 0.05	2 : 0.03	i : 0.03	q : 0.03	n : 0.03	3 : 0.01	f : 0.01	0 : 0.01	5 : 0.01	m : 0.01	
> : 0.24	d : 0.22	c : 0.14	e : 0.12	0 : 0.07	g : 0.07	i : 0.03	f : 0.01	] : 0.01	2 : 0.01	n : 0.01	b : 0.01	
> : 0.22	d : 0.19	c : 0.14	b : 0.10	e : 0.10	g : 0.07	9 : 0.05	0 : 0.05	f : 0.01	i : 0.01	] : 0.01	
> : 0.22	d : 0.17	c : 0.12	8 : 0.10	b : 0.08	e : 0.07	9 : 0.05	0 : 0.05	g : 0.05	f : 0.01	i : 0.01	a : 0.01	
7 : 0.36	> : 0.22	8 : 0.17	6 : 0.07	9 : 0.05	0 : 0.05	d : 0.03	e : 0.01	
7 : 0.36	> : 0.22	8 : 0.17	6 : 0.12	9 : 0.05	0 : 0.05	
7 : 0.36	> : 0.22	8 : 0.17	6 : 0.12	9 : 0.05	0 : 0.05	
7 : 0.36	> : 0.22	8 : 0.17	6 : 0.12	9 : 0.05	0 : 0.05	
7 : 0.36	> : 0.22	8 : 0.17	6 : 0.12	9 : 0.05	0 : 0.05	
7 : 0.36	> : 0.22	8 : 0.17	6 : 0.12	9 : 0.05	0 : 0.05	
7 : 0.36	> : 0.22	8 : 0.17	6 : 0.05	9 : 0.05	0 : 0.05	f : 0.03	c : 0.01	b : 0.01	
e : 0.28	d : 0.10	f : 0.10	> : 0.10	c : 0.08	i : 0.07	b : 0.07	8 : 0.07	g : 0.05	= : 0.03	h : 0.01	
e : 0.28	d : 0.14	g : 0.12	f : 0.10	c : 0.08	i : 0.07	b : 0.07	> : 0.05	= : 0.03	] : 0.01	h : 0.01	
e : 0.28	f : 0.15	d : 0.14	g : 0.12	i : 0.07	] : 0.07	c : 0.07	= : 0.05	b : 0.01	h : 0.01	
e : 0.28	f : 0.15	d : 0.14	g : 0.12	i : 0.07	= : 0.07	c : 0.03	h : 0.03	3 : 0.03	] : 0.01	4 : 0.01	2 : 0.01	
e : 0.28	f : 0.15	g : 0.12	i : 0.07	2 : 0.07	= : 0.07	3 : 0.05	d : 0.05	c : 0.03	h : 0.03	b : 0.03	4 : 0.01	
2 : 0.12	] : 0.12	f : 0.12	g : 0.12	3 : 0.10	i : 0.07	= : 0.07	c : 0.07	h : 0.05	4 : 0.03	b : 0.03	d : 0.03	: : 0.01	7 : 0.01	
g : 0.17	2 : 0.12	i : 0.08	= : 0.08	3 : 0.08	d : 0.08	f : 0.08	] : 0.05	h : 0.05	c : 0.05	b : 0.03	4 : 0.03	7 : 0.01	E : 0.01	

#score	762.5486973428334
#seq	57
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_CDS_m3_run2.txt

#BEAR
==========ddddqqqqqqqqdddd333=====	chr21:34948062-34948298(+)$1	236	136	170	16.9519
iiiiiii"""cccapppppppa]ccc4444iiii	chr12:104742039-104742292(+)$1	253	66	100	12.0245
ccc####bb!!bbssssssssssbb22bb4444c	chr2:191862484-191862706(-)$1	222	14	48	10.1936
ee[bbeeeee[arrrrrrrrraeeeee]bb]eee	chr9:139743783-139744006(+)$1	223	144	178	10.2387
###===========qqqqqqqq===========2	chr6:119345629-119345844(-)$1	215	102	136	17.0333
dccc"""gggggggqqqqqqqqgggggggccc]d	chr17:8273287-8273511(-)$1	224	144	178	14.8741
dd!!iiiiiiiiirrrrrrrrriiiiiiiii22d	chr3:124456899-124457128(+)$1	229	8	42	13.0215
cc[bb[ccc[ddddqqqqqqqqdddd]cccbb]c	chr20:55982621-55982841(+)$1	220	48	82	14.3907
e[bb!!ccc[ddddqqqqqqqqdddd4444ccc2	chr1:151496692-151496915(+)$1	223	70	104	14.7235
#bb####ccc[cccqqqqqqqqccc]ccc22bb4	chr11:61914111-61914337(+)$1	226	139	173	14.5535
eee[dddd[eeeeerrrrrrrrreeeee]dddd]	chr16:71317640-71317858(-)$1	218	73	107	11.0887
d!!ccc$$$$$cccqqqqqqqqccc4444ccc]d	chr3:47957513-47957741(-)$1	228	74	108	15.0084
cc!!==========ppppppp==========]cc	chr19:1438745-1438987(+)$1	242	13	47	12.2854
:ccc[eeeee!!bbrrrrrrrrrbb22eeeee]c	chr12:49420709-49420934(-)$1	225	107	141	11.2871
ccccc[eeeee[bbqqqqqqqqbb]eeeee]ccc	chr3:47129559-47129769(-)$1	210	44	78	13.9851
c::===========qqqqqqqq===========E	chr22:17629255-17629487(-)$1	232	150	184	13.9940
$ffffff!!bb[aqqqqqqqqa]bb22ffffff]	chr17:45742358-45742618(+)$1	260	58	92	11.8786
eeeeeee[bb!!bbqqqqqqqqbb]bb]eeeee2	chr19:9270805-9271022(+)$1	217	10	44	12.7073
==========ddddqqqqqqqqdddd]=======	chr14:100069739-100069963(-)$1	224	105	139	16.6158
ccc"""ccc[ddddqqqqqqqqdddd]ccc333c	chr10:103898349-103898615(+)$1	266	189	223	15.4963
ee!!bb[ccc!!bbqqqqqqqqbb22cccbb22e	chr11:46430044-46430263(-)$1	219	124	158	13.2310
cceeeeegggggggqqqqqqqqggggggg]eeee	chr15:40500753-40501002(+)$1	249	214	248	14.4464
#ccc!!eeeeecccqqqqqqqqccc]eeeeeccc	chr17:55187292-55187532(+)$1	240	189	223	15.0277
ddd[ccc"""ddddqqqqqqqqddddccc22ddd	chr19:46294155-46294372(-)$1	217	27	61	14.0814
iiiiiiiibb!!bbqqqqqqqqbb4444bb]iii	chr19:33697423-33697670(+)$1	247	76	110	14.8084
Deeeee####cccrrrrrrrrrccc333eeeee:	chr1:113460080-113460307(-)$1	227	10	44	11.7139
""a[ffffff[cccoooooocccffffffa]ccc	chr3:15262274-15262492(+)$1	218	85	119	9.7809
c[dddd!!ffffffrrrrrrrrrffffffddddc	chr1:236748328-236748556(-)$1	228	175	209	10.7483
eeee[bbcccddddqqqqqqqqdddd4444ccc]	chr5:145551387-145551618(-)$1	231	164	198	14.2652
#ggggggg[ddddrrrrrrrrrdddd333ggggg	chr19:46122268-46122492(-)$1	224	116	150	13.5950
c"""eeeeeeeeeeooooooeeeee22eeeeecc	chr15:43075589-43075804(-)$1	215	97	131	9.6252
:iiiiiiiii[cccqqqqqqqqccc22iiiiiii	chr2:96852865-96853119(-)$1	254	22	56	15.9871
:gggggggffffffqqqqqqqqffffff]ggggg	chr7:150768772-150769016(+)$1	244	132	166	13.4226
!cccbb!!ffffffqqqqqqqqffffff22bb]c	chr5:88100449-88100678(-)$1	229	142	176	13.0824
:dddd!!ccc[cccqqqqqqqqccc]ccc22ddd	chr12:121154675-121154904(+)$1	229	185	219	13.9194
#=============qqqqqqqq============	chr16:30537169-30537401(-)$1	232	185	219	17.2768
hhhhhhhh[ccc[aqqqqqqqqa]ccc]hhhhhh	chr7:98556907-98557152(+)$1	245	172	206	12.3549
##eeeee!!eeeeerrrrrrrrreeeee]eeeee	chr3:47162174-47162398(-)$1	224	26	60	12.0370
""eeeee!!eeeeeooooooeeeee22eeeee22	chr7:780381-780661(+)$1	280	162	196	9.6831
gggggg"""eeeeeooooooeeeee333gggggg	chr3:51708200-51708433(+)$1	233	198	232	11.1754
ggggg[bb[eeeeerrrrrrrrreeeee]bb]gg	chr1:36359238-36359457(+)$1	219	102	136	11.4551
::==========rrrrrrrrr==========ddd	chr20:34063231-34063448(+)$1	217	10	44	11.4762
cc[ggggggg[ddddoooooodddd]ggggggg]	chr7:32623458-32623684(+)$1	226	170	204	10.8832
cc####gggggggssssssssssggggggg]ccc	chr10:5781922-5782144(+)$1	222	108	142	11.5551
ccc[bb[dddd[bbqqqqqqqqbbdddd]bb333	chr19:2216918-2217134(+)$1	216	61	95	13.1613
iiieeeee"""cccqqqqqqqqccc333eeeee:	chr17:40048462-40048729(-)$1	267	147	181	15.0331
gggggg####ccc[aooooooaccc22ggggggg	chr14:55510702-55510941(+)$1	239	140	174	11.9214
eee####ffffffrrrrrrrrrffffff22eeee	chr17:27861090-27861316(+)$1	226	92	126	11.0231
=========$$$$$bboooooobb==========	chr7:43906286-43906508(-)$1	222	25	59	10.3659
ffffff[ccc[cccqqqqqqqqcccccc]fffff	chrX:44922672-44922891(+)$1	219	80	114	14.1103
"eeeeeccc!!bb[aooooooa]bb22ccc]eee	chr17:19559657-19559886(+)$1	229	89	123	10.3341
b[dddd"""eeeeeqqqqqqqqeeeee4444ddd	chr1:145439978-145440214(+)$1	236	174	208	14.0276
####gggggggcccqqqqqqqqccc]ggggggg3	chr2:47703434-47703661(+)$1	227	20	54	16.0768
=========[bbddddoooooodddd]bb]====	chr22:32875089-32875309(+)$1	220	123	157	10.2959
ff!!dddd!!ddddqqqqqqqqdddd333dddd3	chr2:37520255-37520479(-)$1	224	101	135	14.7882
GGGeeeee!!ddddqqqqqqqqdddd333eeeee	chr2:170857735-170857959(+)$1	224	84	118	13.5293
:dddd[ccc[ccc[aooooooa]ccc]cccdddd	chr19:5918430-5918664(-)$1	234	107	141	9.5178
cc!!bb[ccc[ccc[aooooooa]cccccc]bb2	chr1:85724160-85724378(-)$1	218	79	113	10.0293
fff[a[eeeee[bbqqqqqqqqbb]eeeee]aff	chr15:75093263-75093534(+)$1	271	87	121	13.4092

#otherMatches

#Seq PSSM
GGUAAAUAUGAAUUUCUGCauuaauuauauauau	chr21:34948062-34948298(+)$1	236	136	170	16.9519
UGUUGUGCUUUCUCUUCCCCUGCAGGUAUUCACA	chr12:104742039-104742292(+)$1	253	66	100	12.0245
ACUUACCCAGAAUGCCCUGAUUAAUGAUGAACUA	chr2:191862484-191862706(-)$1	222	14	48	10.1936
UCCGACGGCGUCUUCAAGUAUGUGCUGAUCCGAG	chr9:139743783-139744006(+)$1	223	144	178	10.2387
UAAGCACAGAGUUGAGGACAUGCAACUUUGUGCA	chr6:119345629-119345844(-)$1	215	102	136	17.0333
ACAUAAGGAAGAGUUGUUUGAUAUUCUUCAUGAU	chr17:8273287-8273511(-)$1	224	144	178	14.8741
GCUAGCAGAUGCUUUAGGACCUAGUAUCUGCAUG	chr3:124456899-124457128(+)$1	229	8	42	13.0215
CGUCGCUGUCCUCGCCCUACAUUGAGUACACGCC	chr20:55982621-55982841(+)$1	220	48	82	14.3907
CAGGUGAUGGAGCUGCAGAACAAGCUGAAACAUG	chr1:151496692-151496915(+)$1	223	70	104	14.7235
agcaggagcggcgcgagcaggagcggcgcgagca	chr11:61914111-61914337(+)$1	226	139	173	14.5535
UGAGGACCUGCGCAGUCCUGCUAUGUGUUGGUUA	chr16:71317640-71317858(-)$1	218	73	107	11.0887
AGCCCUCAAAACAGAAGCACCCCUGGCUAAGGAU	chr3:47957513-47957741(-)$1	228	74	108	15.0084
GAGAUGGGUGUCGGGAUCCCGCUGACGCCCGAUC	chr19:1438745-1438987(+)$1	242	13	47	12.2854
CCGUCCUCCUCGCCUCAAGAAAUGGAAAGGAGUG	chr12:49420709-49420934(-)$1	225	107	141	11.2871
CUAGAAGCUCUGAUGGAAAAUGGUGAGGGUCUCU	chr3:47129559-47129769(-)$1	210	44	78	13.9851
GUAUCCUUUUGGUCUUAACUCUGGCUGAAGGGAA	chr22:17629255-17629487(-)$1	232	150	184	13.9940
CCUCAGGCAGCAGAACAAGGACGGCCCCCUGAGC	chr17:45742358-45742618(+)$1	260	58	92	11.8786
CACUGAAUACGCUCACUUGUUCGAAGUCUUUGGC	chr19:9270805-9271022(+)$1	217	10	44	12.7073
CUGGUGCUGCUGCUGGACGAGGAGCGCGCGGCAC	chr14:100069739-100069963(-)$1	224	105	139	16.6158
GGGAAGGGGAUUAGUACAAAGUUUAGACCCAUGC	chr10:103898349-103898615(+)$1	266	189	223	15.4963
UCAGCUGCAGAAUGCCGAAACACAGACUGAGAGG	chr11:46430044-46430263(-)$1	219	124	158	13.2310
UCAGGUAGGAUAUACAUACCACUAUAUCCAUGCC	chr15:40500753-40501002(+)$1	249	214	248	14.4464
AGGUCGACCUCAUCAUCUGGGAGAUCGAGGUGCC	chr17:55187292-55187532(+)$1	240	189	223	15.0277
UCCAUUGACCUCAACAAGCCAAUUGACAAGCGGA	chr19:46294155-46294372(-)$1	217	27	61	14.0814
CUUCUAGGGCCUUCGAGACCCAGAUGACGCGCCU	chr19:33697423-33697670(+)$1	247	76	110	14.8084
CAGUCUUCCAAACAAUUAAUCAGUUCCUGGACUU	chr1:113460080-113460307(-)$1	227	10	44	11.7139
ACCUCCAGUGAGAGCACAUUUUCCACUGGGCGCU	chr3:15262274-15262492(+)$1	218	85	119	9.7809
GUCUUCAGUUUGUUGCAGAAAAAAAUAAAGAAGC	chr1:236748328-236748556(-)$1	228	175	209	10.7483
UUGGUUUCUACUCUUUUUAGUUGGAGCAAAUAGU	chr5:145551387-145551618(-)$1	231	164	198	14.2652
AGCUGGUGCAUCUAUGGAGCUCAGAUUCCCACCA	chr19:46122268-46122492(-)$1	224	116	150	13.5950
UGGAUCUCUGGGACACCCCCGUCCCCAGGAGAAG	chr15:43075589-43075804(-)$1	215	97	131	9.6252
UAUGGAGGUUGUGGUUGGUGAUUCAGGGAUCUUC	chr2:96852865-96853119(-)$1	254	22	56	15.9871
UUGAGGAGGCCUUCUUCUCGGUGAGGGCUCUUCU	chr7:150768772-150769016(+)$1	244	132	166	13.4226
UCAUCUUCAACAGCACCAACAAGCUGUUCCAGUA	chr5:88100449-88100678(-)$1	229	142	176	13.0824
CCCUUACAGCACUCUAGAUUCUGAGGGCUACAAG	chr12:121154675-121154904(+)$1	229	185	219	13.9194
AAAGCCCGGGGUUUGAGUCCCGAAGCCCUGGGCU	chr16:30537169-30537401(-)$1	232	185	219	17.2768
GCUGCAGUGGUUCGACAAGCUGCUGAUGACUGUG	chr7:98556907-98557152(+)$1	245	172	206	12.3549
UCAGAAGAGCUCAGAAACUUAGGUUGGGACUUCU	chr3:47162174-47162398(-)$1	224	26	60	12.0370
UGCUCAGUAGCCUCAACGACGAGGUGCCUGAGGU	chr7:780381-780661(+)$1	280	162	196	9.6831
UACUCAGGGCUACUGGCUGGGGUGGAAGUGAGUG	chr3:51708200-51708433(+)$1	233	198	232	11.1754
GCGCGAGGUCUGGUUCGGCUUUCACCAGUCUGUG	chr1:36359238-36359457(+)$1	219	102	136	11.4551
agcAAAGGUGAUUAUAUUCCUGUUACCUUUGGGG	chr20:34063231-34063448(+)$1	217	10	44	11.4762
AACUGUUUACAUGGAUGUUGCUCUAAGUGAAUGU	chr7:32623458-32623684(+)$1	226	170	204	10.8832
CACUUACUGAGGAAAUGCUAGAAUCUUCAGAUGC	chr10:5781922-5782144(+)$1	222	108	142	11.5551
UUCCCUACCAGAGCCCCAGCGUGCCUGGCAGCAU	chr19:2216918-2217134(+)$1	216	61	95	13.1613
UCUCUCCGCUCUGCCUAUGACAGCACCAUGGAGA	chr17:40048462-40048729(-)$1	267	147	181	15.0331
GAACAUUAUAAGGACCCAAGCGCCUGUAUGUUCU	chr14:55510702-55510941(+)$1	239	140	174	11.9214
GCAGCUGCAGCAGGAACUGGAGCUGUUGAAUGCG	chr17:27861090-27861316(+)$1	226	92	126	11.0231
CAGCUGGUUUUAAAGCGCCGGGGUAACCAGUUGG	chr7:43906286-43906508(-)$1	222	25	59	10.3659
CUCUGGCCAGCAGCCACAGCUUGCUCUGACCAGA	chrX:44922672-44922891(+)$1	219	80	114	14.1103
CAUUUUCUAUACGGGAAACACUGCGGUUGGCAAA	chr17:19559657-19559886(+)$1	229	89	123	10.3341
UGCUUAUGGCAGUUAAAACAGGAACUGGGUUUAG	chr1:145439978-145440214(+)$1	236	174	208	14.0276
GUAGCAGAAAGAAGUUUAAAAUCUUGCUUUCUGA	chr2:47703434-47703661(+)$1	227	20	54	16.0768
CAUUCCAAGGACAGGCAGCCCAGUCUGGUGUUUG	chr22:32875089-32875309(+)$1	220	123	157	10.2959
AUUCUUCUCUUUCGCCAUGACAUGAACUCAGAAA	chr2:37520255-37520479(-)$1	224	101	135	14.7882
UGUCUCUUGGCAGUAUCAAUUGGCUGGGAAGGAG	chr2:170857735-170857959(+)$1	224	84	118	13.5293
AUCACAGCCAUGGACACCGAGGACCAGGGCGUGA	chr19:5918430-5918664(-)$1	234	107	141	9.5178
GGUCUAACAUAUAUGAGGACAAUGGUGAUGAUGC	chr1:85724160-85724378(-)$1	218	79	113	10.0293
AGGCAACUGCGGCAUAGCAACCUGGUGCAGCUCC	chr15:75093263-75093534(+)$1	271	87	121	13.4092

#DB
((((((((((((((........))))...)))))	chr21:34948062-34948298(+)$1	1	136	170	16.9519
(((((((...((((.......).)))....))))	chr12:104742039-104742292(+)$1	1	66	100	12.0245
(((....((..((..........))..))....)	chr2:191862484-191862706(-)$1	1	14	48	10.1936
((.(((((((.(.........)))))).)).)))	chr9:139743783-139744006(+)$1	1	144	178	10.2387
...(((((((((((........))))))))))).	chr6:119345629-119345844(-)$1	1	102	136	17.0333
((((...(((((((........)))))))))).)	chr17:8273287-8273511(-)$1	1	144	178	14.8741
((..(((((((((.........)))))))))..)	chr3:124456899-124457128(+)$1	1	8	42	13.0215
((.((.(((.((((........)))).))))).)	chr20:55982621-55982841(+)$1	1	48	82	14.3907
(.((..(((.((((........))))....))).	chr1:151496692-151496915(+)$1	1	70	104	14.7235
.((....(((.(((........))).)))..)).	chr11:61914111-61914337(+)$1	1	139	173	14.5535
(((.((((.(((((.........))))).)))).	chr16:71317640-71317858(-)$1	1	73	107	11.0887
(..(((.....(((........)))....))).)	chr3:47957513-47957741(-)$1	1	74	108	15.0084
((..((((((((((.......)))))))))).))	chr19:1438745-1438987(+)$1	1	13	47	12.2854
.(((.(((((..((.........))..))))).)	chr12:49420709-49420934(-)$1	1	107	141	11.2871
))(((.(((((.((........)).))))).)))	chr3:47129559-47129769(-)$1	1	44	78	13.9851
)..(((((((((((........))))))))))))	chr22:17629255-17629487(-)$1	1	150	184	13.9940
.((((((..((.(........).))..)))))).	chr17:45742358-45742618(+)$1	1	58	92	11.8786
(((((((.((..((........)).)).))))).	chr19:9270805-9271022(+)$1	1	10	44	12.7073
((((((((((((((........)))).)))))))	chr14:100069739-100069963(-)$1	1	105	139	16.6158
(((...(((.((((........)))).)))...)	chr10:103898349-103898615(+)$1	1	189	223	15.4963
((..((.(((..((........))..)))))..)	chr11:46430044-46430263(-)$1	1	124	158	13.2310
))((((((((((((........))))))).))))	chr15:40500753-40501002(+)$1	1	214	248	14.4464
.(((..((((((((........))).))))))))	chr17:55187292-55187532(+)$1	1	189	223	15.0277
(((.(((...((((........)))))))..)))	chr19:46294155-46294372(-)$1	1	27	61	14.0814
((((((((((..((........))....)).)))	chr19:33697423-33697670(+)$1	1	76	110	14.8084
((((((....(((.........)))...))))).	chr1:113460080-113460307(-)$1	1	10	44	11.7139
..(.((((((.(((......)))))))))).)))	chr3:15262274-15262492(+)$1	1	85	119	9.7809
(.((((..((((((.........)))))))))))	chr1:236748328-236748556(-)$1	1	175	209	10.7483
((((.(((((((((........))))....))).	chr5:145551387-145551618(-)$1	1	164	198	14.2652
.(((((((.((((.........))))...)))))	chr19:46122268-46122492(-)$1	1	116	150	13.5950
(...((((((((((......)))))..)))))))	chr15:43075589-43075804(-)$1	1	97	131	9.6252
.(((((((((.(((........)))..)))))))	chr2:96852865-96853119(-)$1	1	22	56	15.9871
.(((((((((((((........)))))).)))))	chr7:150768772-150769016(+)$1	1	132	166	13.4226
.(((((..((((((........))))))..)).)	chr5:88100449-88100678(-)$1	1	142	176	13.0824
.((((..(((.(((........))).)))..)))	chr12:121154675-121154904(+)$1	1	185	219	13.9194
.(((((((((((((........))))))))))))	chr16:30537169-30537401(-)$1	1	185	219	17.2768
((((((((.(((.(........).))).))))))	chr7:98556907-98557152(+)$1	1	172	206	12.3549
..(((((..(((((.........))))).)))))	chr3:47162174-47162398(-)$1	1	26	60	12.0370
..(((((..(((((......)))))..)))))..	chr7:780381-780661(+)$1	1	162	196	9.6831
((((((...(((((......)))))...))))))	chr3:51708200-51708433(+)$1	1	198	232	11.1754
(((((.((.(((((.........))))).)).))	chr1:36359238-36359457(+)$1	1	102	136	11.4551
..((((((((((.........))))))))))(((	chr20:34063231-34063448(+)$1	1	10	44	11.4762
((.(((((((.((((......)))).))))))).	chr7:32623458-32623684(+)$1	1	170	204	10.8832
((....(((((((..........))))))).)))	chr10:5781922-5782144(+)$1	1	108	142	11.5551
(((.((.((((.((........)))))).))...	chr19:2216918-2217134(+)$1	1	61	95	13.1613
)))(((((...(((........)))...))))).	chr17:40048462-40048729(-)$1	1	147	181	15.0331
((((((....(((.(......))))..)))))))	chr14:55510702-55510941(+)$1	1	140	174	11.9214
(((....((((((.........))))))..))))	chr17:27861090-27861316(+)$1	1	92	126	11.0231
(((((((((.....((......))))))))))))	chr7:43906286-43906508(-)$1	1	25	59	10.3659
((((((.(((.(((........)))))).)))))	chrX:44922672-44922891(+)$1	1	80	114	14.1103
.((((((((..((.(......).))..))).)))	chr17:19559657-19559886(+)$1	1	89	123	10.3341
(.((((...(((((........)))))....)))	chr1:145439978-145440214(+)$1	1	174	208	14.0276
....((((((((((........))).))))))).	chr2:47703434-47703661(+)$1	1	20	54	16.0768
(((((((((.((((((......)))).)).))))	chr22:32875089-32875309(+)$1	1	123	157	10.2959
((..((((..((((........))))...)))).	chr2:37520255-37520479(-)$1	1	101	135	14.7882
((((((((..((((........))))...)))))	chr2:170857735-170857959(+)$1	1	84	118	13.5293
.((((.(((.(((.(......).))).)))))))	chr19:5918430-5918664(-)$1	1	107	141	9.5178
((..((.(((.(((.(......).)))))).)).	chr1:85724160-85724378(-)$1	1	79	113	10.0293
(((.(.(((((.((........)).))))).)))	chr15:75093263-75093534(+)$1	1	87	121	13.4092

#PSSM
c : 0.22	e : 0.11	# : 0.11	: : 0.10	= : 0.06	d : 0.06	i : 0.05	" : 0.05	g : 0.05	f : 0.05	$ : 0.01	D : 0.01	! : 0.01	h : 0.01	b : 0.01	G : 0.01	
c : 0.23	e : 0.13	= : 0.08	g : 0.08	i : 0.06	d : 0.06	f : 0.06	# : 0.05	[ : 0.05	" : 0.05	: : 0.03	b : 0.01	! : 0.01	h : 0.01	G : 0.01	
e : 0.15	c : 0.13	= : 0.10	! : 0.10	d : 0.08	g : 0.08	i : 0.06	[ : 0.05	# : 0.05	f : 0.05	b : 0.03	: : 0.01	a : 0.01	" : 0.01	h : 0.01	G : 0.01	
e : 0.15	= : 0.13	c : 0.10	g : 0.10	# : 0.08	! : 0.08	[ : 0.08	d : 0.06	i : 0.05	b : 0.05	f : 0.03	" : 0.03	h : 0.01	
= : 0.15	e : 0.15	g : 0.11	b : 0.10	d : 0.10	i : 0.06	# : 0.06	c : 0.05	f : 0.05	" : 0.03	! : 0.03	[ : 0.03	h : 0.01	a : 0.01	
e : 0.18	= : 0.15	g : 0.10	[ : 0.08	b : 0.08	i : 0.06	# : 0.06	d : 0.06	! : 0.05	f : 0.05	" : 0.03	c : 0.03	h : 0.01	
e : 0.20	= : 0.15	c : 0.10	# : 0.08	g : 0.08	i : 0.06	[ : 0.06	" : 0.05	! : 0.05	d : 0.03	f : 0.03	b : 0.03	$ : 0.01	h : 0.01	
c : 0.18	= : 0.15	e : 0.13	g : 0.11	! : 0.08	" : 0.06	i : 0.05	d : 0.05	b : 0.03	# : 0.03	f : 0.03	$ : 0.01	[ : 0.01	h : 0.01	
c : 0.18	= : 0.15	e : 0.10	" : 0.08	g : 0.08	! : 0.08	f : 0.08	[ : 0.06	b : 0.05	i : 0.03	# : 0.03	$ : 0.01	d : 0.01	
e : 0.20	= : 0.11	c : 0.11	g : 0.08	[ : 0.08	f : 0.08	! : 0.06	" : 0.05	b : 0.05	i : 0.03	$ : 0.03	# : 0.03	d : 0.03	
d : 0.18	e : 0.16	[ : 0.13	! : 0.10	c : 0.08	= : 0.08	g : 0.06	f : 0.06	$ : 0.03	b : 0.03	i : 0.01	" : 0.01	
c : 0.25	d : 0.18	e : 0.11	= : 0.08	! : 0.06	[ : 0.06	f : 0.06	b : 0.05	g : 0.05	a : 0.01	i : 0.01	$ : 0.01	
c : 0.23	d : 0.20	b : 0.15	e : 0.11	= : 0.06	f : 0.06	g : 0.05	r : 0.03	i : 0.01	a : 0.01	[ : 0.01	$ : 0.01	
d : 0.18	c : 0.16	e : 0.11	b : 0.11	r : 0.10	= : 0.06	f : 0.05	[ : 0.05	a : 0.03	s : 0.03	g : 0.03	q : 0.01	$ : 0.01	
q : 0.55	r : 0.18	o : 0.06	a : 0.05	p : 0.03	s : 0.03	d : 0.03	b : 0.01	[ : 0.01	
q : 0.55	r : 0.18	o : 0.13	p : 0.03	s : 0.03	b : 0.01	d : 0.01	a : 0.01	
q : 0.55	r : 0.18	o : 0.18	p : 0.03	s : 0.03	
q : 0.55	r : 0.18	o : 0.18	p : 0.03	s : 0.03	
q : 0.55	r : 0.18	o : 0.18	p : 0.03	s : 0.03	
q : 0.55	r : 0.18	o : 0.18	p : 0.03	s : 0.03	
q : 0.55	r : 0.18	o : 0.11	e : 0.05	p : 0.03	s : 0.03	c : 0.01	
q : 0.54	r : 0.15	a : 0.10	e : 0.05	o : 0.05	s : 0.03	= : 0.03	c : 0.01	d : 0.01	
d : 0.20	c : 0.18	b : 0.11	e : 0.08	= : 0.08	r : 0.08	] : 0.06	f : 0.05	s : 0.03	g : 0.03	a : 0.03	i : 0.01	
d : 0.20	c : 0.20	b : 0.18	e : 0.13	= : 0.08	f : 0.08	g : 0.05	] : 0.03	i : 0.01	
c : 0.23	d : 0.22	e : 0.13	= : 0.10	f : 0.08	b : 0.06	g : 0.05	] : 0.05	i : 0.01	2 : 0.01	4 : 0.01	
d : 0.20	2 : 0.15	e : 0.11	= : 0.10	c : 0.08	] : 0.08	f : 0.08	g : 0.05	3 : 0.05	4 : 0.03	i : 0.01	b : 0.01	
2 : 0.13	e : 0.13	3 : 0.11	c : 0.11	= : 0.10	4 : 0.08	g : 0.08	] : 0.08	f : 0.08	i : 0.01	b : 0.01	d : 0.01	
c : 0.16	e : 0.15	3 : 0.11	= : 0.11	4 : 0.10	g : 0.10	f : 0.10	] : 0.05	b : 0.03	i : 0.03	d : 0.01	
c : 0.15	e : 0.15	= : 0.11	g : 0.11	] : 0.10	4 : 0.08	3 : 0.06	b : 0.06	f : 0.05	i : 0.03	2 : 0.03	h : 0.01	
e : 0.18	= : 0.13	c : 0.11	g : 0.11	4 : 0.08	b : 0.08	2 : 0.08	d : 0.05	i : 0.03	f : 0.03	] : 0.03	a : 0.01	h : 0.01	
e : 0.18	= : 0.15	] : 0.13	g : 0.10	b : 0.08	c : 0.06	d : 0.06	i : 0.05	2 : 0.05	4 : 0.03	f : 0.03	3 : 0.01	h : 0.01	
e : 0.20	c : 0.13	d : 0.13	= : 0.11	g : 0.10	b : 0.06	i : 0.05	2 : 0.03	] : 0.03	f : 0.03	3 : 0.03	4 : 0.01	h : 0.01	a : 0.01	
e : 0.15	c : 0.13	d : 0.13	= : 0.11	g : 0.11	] : 0.08	i : 0.05	2 : 0.05	f : 0.05	b : 0.03	3 : 0.03	4 : 0.01	h : 0.01	
c : 0.20	d : 0.13	e : 0.11	= : 0.08	2 : 0.08	g : 0.08	] : 0.06	i : 0.05	3 : 0.05	: : 0.03	f : 0.03	4 : 0.01	E : 0.01	h : 0.01	

#score	765.610020293978
#seq	59
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_CDS_m2_run1.txt

#BEAR
gggggggcccnnnnnccc]gggg	chr1:95368619-95368820(-)$1	201	25	48	9.2451
Cccc!!cccooooooccc22ccc	chr20:61915110-61915311(+)$1	201	114	137	12.9927
d[gggggggooooooggggggg]	chr2:111406745-111406946(-)$1	201	165	188	13.1933
##gggggggooooooggggggg3	chr18:12691311-12691512(-)$1	201	159	182	13.3925
ggggggg[aooooooa]gggggg	chr19:36224451-36224652(+)$1	201	0	23	13.0609
fff[eeeeeooooooeeeee22f	chr17:15935631-15935832(-)$1	201	6	29	11.7842
cc"""ddddoooooodddd4444	chr15:91026586-91026787(+)$1	201	21	44	12.5235
ccc[eeeeeooooooeeeeeccc	chr5:98193903-98194104(-)$1	201	50	73	12.5688
gg!!eeeeeooooooeeeee444	chr17:18156776-18156977(-)$1	201	152	175	12.7629
d[dddd[bboooooobbdddd22	chr5:112312525-112312726(+)$1	201	93	116	11.0432
ccgggggggooooooggggggg2	chr3:44692498-44692699(+)$1	201	85	108	13.0567
eeeee[cccooooooccceeeee	chr4:140299816-140300017(+)$1	201	76	99	13.2166
dd####cccooooooccc]dddd	chr5:70819902-70820103(+)$1	201	27	50	13.0739
eeee!!cccooooooccceeeee	chr6:27419885-27420086(-)$1	201	66	89	13.3804
gggg!!cccoooooocccggggg	chr4:185621885-185622086(-)$1	201	90	113	14.2453
ffffff[bboooooobb333fff	chr5:177656984-177657185(-)$1	201	160	183	11.5907
d!!bb[cccoooooocccbb22d	chr12:53699698-53699899(+)$1	201	152	175	12.2932
feeeeecccooooooccc22eee	chr9:86585100-86585301(-)$1	201	50	73	13.1368
gggg!!cccooooooccc22ggg	chr16:85015413-85015614(-)$1	201	123	146	14.3933
ccc!!ddddoooooodddd22cc	chr12:49441735-49441936(-)$1	201	49	72	12.4889
eeeee[cccooooooccceeeee	chr5:122718479-122718680(-)$1	201	0	23	13.2166
[bb[eeeeeooooooeeeeebb]	chr17:57289704-57289905(+)$1	201	27	50	11.5092
g####a[cccnnnnnccc]aggg	chr16:838986-839187(+)$1	201	168	191	9.2007
"eeeee[bboooooobbeeeee3	chr1:234562998-234563199(-)$1	201	157	180	12.0984
"""ccccccooooooccc]ccc5	chr1:52520597-52520798(-)$1	201	87	110	13.2120
##a[ccc[bboooooobb]ccc]	chr11:110108240-110108441(-)$1	201	85	108	11.0615
cc[a!!cccooooooccc]a]cc	chr14:102471074-102471275(+)$1	201	107	130	14.4091
dd[ffffffooooooffffff22	chr2:29001665-29001866(+)$1	201	56	79	11.2014
ggggg[cccooooooccc22ggg	chr10:70153996-70154197(-)$1	201	54	77	14.2716
iiiiiicccooooooccc22iii	chr7:23552505-23552706(-)$1	201	96	119	14.1476
ggggggcccooooooccc]gggg	chr13:99171452-99171653(-)$1	201	120	143	14.2044
ggggggcccooooooccceeeee	chr18:29454483-29454684(-)$1	201	115	138	13.6702
=========oooooo========	chr11:800264-800465(-)$1	201	31	54	13.7499
c!!ffffffooooooffffffcc	chr1:235940323-235940524(-)$1	201	86	109	11.9643
ccc####bboooooobb4444cc	chr2:98418866-98419067(-)$1	201	136	159	12.2713
e[adddd[aooooooa]dddd]a	chr17:38416780-38416981(+)$1	201	120	143	11.7246
ccc[eeeeeooooooeeeee]cc	chr14:67147775-67147976(+)$1	201	6	29	12.6177
iiiiiiiiiooooooiiiiiiii	chr3:142238495-142238696(-)$1	201	138	161	13.2254
ffff[ddddoooooodddd]fff	chr14:96991586-96991787(+)$1	201	85	108	11.6137
ccceeeeeooooooeeeee]ccc	chr5:151176776-151176977(+)$1	201	0	23	10.7894
###eeeeeaooooooa]eeeeed	chr16:66977106-66977307(+)$1	201	14	37	12.4436
b!!bb[cccooooooccc]bb]b	chr14:105239606-105239807(-)$1	201	154	177	12.6860
!!ddddcccooooooccc4444d	chr20:33029944-33030145(+)$1	201	19	42	13.2043
%ccc!!cccooooooccc22ccc	chr1:36219328-36219529(-)$1	201	155	178	13.5108
==[a[ddddoooooodddda]==	chr18:47812367-47812568(-)$1	201	63	86	12.7489
!bb!!ddddoooooodddd22bb	chrX:108906407-108906608(-)$1	201	104	127	11.3521
eeccccccbboooooobb]ccc2	chr10:118713519-118713720(-)$1	201	40	63	10.5658
=========oooooo========	chr4:152571519-152571720(+)$1	201	114	137	13.7499
b[gggggggooooooggggggg]	chr10:124697313-124697514(-)$1	201	37	60	13.0910
""ccc[cccooooooccc22ccc	chr3:169814935-169815136(-)$1	201	58	81	14.0907
a!!bb[cccooooooccc]bb22	chr5:150075132-150075333(-)$1	201	41	64	13.0279
hh!!eeeeeooooooeeeeehhh	chr11:63662977-63663178(+)$1	201	29	52	11.9235
#eeeee[bboooooobb]eeeee	chr21:33039493-33039694(+)$1	201	142	165	11.7286

#otherMatches

#Seq PSSM
CUUGUUUUUGUGUGCCAGUAAAU	chr1:95368619-95368820(-)$1	201	25	48	9.2451
CGGAGCCGGUAAAGCCCGUGUCU	chr20:61915110-61915311(+)$1	201	114	137	12.9927
AAUUCUUGUUUCUCUAUGAGAAG	chr2:111406745-111406946(-)$1	201	165	188	13.1933
GUAAAUUAUAUUAGAAUAAUUUU	chr18:12691311-12691512(-)$1	201	159	182	13.3925
GAUGGGCGGGAGAUGCGGCUCAU	chr19:36224451-36224652(+)$1	201	0	23	13.0609
CAAUGAAAACCUAAUUUUUCUUU	chr17:15935631-15935832(-)$1	201	6	29	11.7842
CUUUAUUAUCGAUACAUGAAUCC	chr15:91026586-91026787(+)$1	201	21	44	12.5235
CAGCAGGGACAGUUAUUCCUCUG	chr5:98193903-98194104(-)$1	201	50	73	12.5688
GGAAGGCCGUGAGCCUGGCCCUG	chr17:18156776-18156977(-)$1	201	152	175	12.7629
UGGGUCCUCAUCAUGGAGACCAA	chr5:112312525-112312726(+)$1	201	93	116	11.0432
AUGGCCCUAGCCCCAUGGGGCCC	chr3:44692498-44692699(+)$1	201	85	108	13.0567
ACUUUCUCUUUUUAUAGAAAAGU	chr4:140299816-140300017(+)$1	201	76	99	13.2166
GUAAGACCUCUAAGAAGGAACCU	chr5:70819902-70820103(+)$1	201	27	50	13.0739
CAUACUGGGGAGAAACCCUAUGA	chr6:27419885-27420086(-)$1	201	66	89	13.3804
GAAGUCCAGGAUGAACUGCUUCG	chr4:185621885-185622086(-)$1	201	90	113	14.2453
UGCAUGACAACAUCGUGGACUAU	chr5:177656984-177657185(-)$1	201	160	183	11.5907
UGGCCUGGGAGGAGACCCGGAGA	chr12:53699698-53699899(+)$1	201	152	175	12.2932
UUCAGUUGGCUGGAUCUAUUAUU	chr9:86585100-86585301(-)$1	201	50	73	13.1368
GCGCCCACCACUGCAGGUACGUG	chr16:85015413-85015614(-)$1	201	123	146	14.3933
UAGUUGGACAUUUGGGUUUCUCU	chr12:49441735-49441936(-)$1	201	49	72	12.4889
GGUAAAUAUAAUUGAAUGUUAUC	chr5:122718479-122718680(-)$1	201	0	23	13.2166
CUGUGCUAUAUCACAAUAGCCGA	chr17:57289704-57289905(+)$1	201	27	50	11.5092
CGGAGUGGGCGCGAGGCUGAGGA	chr16:838986-839187(+)$1	201	168	191	9.2007
CUGUCUUCACAUAAAUGAGAUAC	chr1:234562998-234563199(-)$1	201	157	180	12.0984
CUCGUCAUCUCUUCUGAUGGACA	chr1:52520597-52520798(-)$1	201	87	110	13.2120
AAGCUCUAGAACUGGAUCAAGAA	chr11:110108240-110108441(-)$1	201	85	108	11.0615
CACCCUGGCCAAACUGCUUGCUG	chr14:102471074-102471275(+)$1	201	107	130	14.4091
GGAGGUUUCCCACCAGAAGCCAA	chr2:29001665-29001866(+)$1	201	56	79	11.2014
UUGGCCUGAAUGUGAUCGAUGCU	chr10:70153996-70154197(-)$1	201	54	77	14.2716
GACCAUUGAGUGGUGUCAAUGUG	chr7:23552505-23552706(-)$1	201	96	119	14.1476
UCCAUAUGUAACCAAAUAUUAUG	chr13:99171452-99171653(-)$1	201	120	143	14.2044
CCAGUCCUAUACUCUUAGACAGC	chr18:29454483-29454684(-)$1	201	115	138	13.6702
GAGGGCAGAAUCUGCUUUGUCUU	chr11:800264-800465(-)$1	201	31	54	13.7499
UACUGAAUAUAAAACUAUUCAAG	chr1:235940323-235940524(-)$1	201	86	109	11.9643
UAUUCCAACCCUUCAGUGUUUGU	chr2:98418866-98419067(-)$1	201	136	159	12.2713
AGUGCUCCCAUCCUCGAGAGUGA	chr17:38416780-38416981(+)$1	201	120	143	11.7246
AGACAAAAAUUAAUUUUUUUUUC	chr14:67147775-67147976(+)$1	201	6	29	12.6177
AUUUCCUGAGCAUGUUCGGGAAA	chr3:142238495-142238696(-)$1	201	138	161	13.2254
AUGUUGGAGGAAAAAUUUUUACA	chr14:96991586-96991787(+)$1	201	85	108	11.6137
UCCUGUCAAAGUAAUGACAUGGA	chr5:151176776-151176977(+)$1	201	0	23	10.7894
UCGGGGGCCAAGGACGAGCUCCA	chr16:66977106-66977307(+)$1	201	14	37	12.4436
GAGGGGAUCAAGGACGGUGCCAC	chr14:105239606-105239807(-)$1	201	154	177	12.6860
CAGGUAACUCAUGCAAGUAUUUU	chr20:33029944-33030145(+)$1	201	19	42	13.2043
GUUGGAUGGAGCAAGCCACACAA	chr1:36219328-36219529(-)$1	201	155	178	13.5108
CCAGACCUGCAGCGCCGGGCAGG	chr18:47812367-47812568(-)$1	201	63	86	12.7489
ACAAAGGUGGUUUUGCACUGGUG	chrX:108906407-108906608(-)$1	201	104	127	11.3521
GUACAUGGCCAAGCUGGGACCAG	chr10:118713519-118713720(-)$1	201	40	63	10.5658
UUAUAGCGGAGAUGCCUGCUGUA	chr4:152571519-152571720(+)$1	201	114	137	13.7499
CCUGGUGGAGAGAAUUCUACCAA	chr10:124697313-124697514(-)$1	201	37	60	13.0910
UAUCAAGCUAGGCCCAGCCCUGA	chr3:169814935-169815136(-)$1	201	58	81	14.0907
CCUUGUUUUUUUCUUGAAUCAUA	chr5:150075132-150075333(-)$1	201	41	64	13.0279
CGCUGGUCAGAGAAGUGAUUUGG	chr11:63662977-63663178(+)$1	201	29	52	11.9235
AUUCUGUGAUCUCACUCUCAGGA	chr21:33039493-33039694(+)$1	201	142	165	11.7286

#DB
((((((((((.....))).))))	chr1:95368619-95368820(-)$1	1	25	48	9.2451
)(((..(((......)))..)))	chr20:61915110-61915311(+)$1	1	114	137	12.9927
(.(((((((......))))))).	chr2:111406745-111406946(-)$1	1	165	188	13.1933
..(((((((......))))))).	chr18:12691311-12691512(-)$1	1	159	182	13.3925
(((((((.(......).))))))	chr19:36224451-36224652(+)$1	1	0	23	13.0609
(((.(((((......)))))..)	chr17:15935631-15935832(-)$1	1	6	29	11.7842
((...((((......))))....	chr15:91026586-91026787(+)$1	1	21	44	12.5235
(((.(((((......))))))))	chr5:98193903-98194104(-)$1	1	50	73	12.5688
((..(((((......)))))...	chr17:18156776-18156977(-)$1	1	152	175	12.7629
(.((((.((......))))))..	chr5:112312525-112312726(+)$1	1	93	116	11.0432
(((((((((......))))))).	chr3:44692498-44692699(+)$1	1	85	108	13.0567
(((((.(((......))))))))	chr4:140299816-140300017(+)$1	1	76	99	13.2166
((....(((......))).))))	chr5:70819902-70820103(+)$1	1	27	50	13.0739
((((..(((......))))))))	chr6:27419885-27420086(-)$1	1	66	89	13.3804
((((..(((......))))))))	chr4:185621885-185622086(-)$1	1	90	113	14.2453
((((((.((......))...)))	chr5:177656984-177657185(-)$1	1	160	183	11.5907
(..((.(((......)))))..)	chr12:53699698-53699899(+)$1	1	152	175	12.2932
(((((((((......)))..)))	chr9:86585100-86585301(-)$1	1	50	73	13.1368
((((..(((......)))..)))	chr16:85015413-85015614(-)$1	1	123	146	14.3933
(((..((((......))))..))	chr12:49441735-49441936(-)$1	1	49	72	12.4889
(((((.(((......))))))))	chr5:122718479-122718680(-)$1	1	0	23	13.2166
.((.(((((......))))))).	chr17:57289704-57289905(+)$1	1	27	50	11.5092
(....(.(((.....))).))))	chr16:838986-839187(+)$1	1	168	191	9.2007
.(((((.((......))))))).	chr1:234562998-234563199(-)$1	1	157	180	12.0984
...((((((......))).))).	chr1:52520597-52520798(-)$1	1	87	110	13.2120
..(.(((.((......)).))).	chr11:110108240-110108441(-)$1	1	85	108	11.0615
((.(..(((......))).).))	chr14:102471074-102471275(+)$1	1	107	130	14.4091
((.((((((......))))))..	chr2:29001665-29001866(+)$1	1	56	79	11.2014
(((((.(((......)))..)))	chr10:70153996-70154197(-)$1	1	54	77	14.2716
(((((((((......)))..)))	chr7:23552505-23552706(-)$1	1	96	119	14.1476
(((((((((......))).))))	chr13:99171452-99171653(-)$1	1	120	143	14.2044
))))))(((......)))(((((	chr18:29454483-29454684(-)$1	1	115	138	13.6702
(((((((((......))))))))	chr11:800264-800465(-)$1	1	31	54	13.7499
(..((((((......))))))))	chr1:235940323-235940524(-)$1	1	86	109	11.9643
(((....((......))....))	chr2:98418866-98419067(-)$1	1	136	159	12.2713
(.(((((.(......).)))).)	chr17:38416780-38416981(+)$1	1	120	143	11.7246
(((.(((((......))))).))	chr14:67147775-67147976(+)$1	1	6	29	12.6177
(((((((((......))))))))	chr3:142238495-142238696(-)$1	1	138	161	13.2254
((((.((((......)))).)))	chr14:96991586-96991787(+)$1	1	85	108	11.6137
((((((((......))))).)))	chr5:151176776-151176977(+)$1	1	0	23	10.7894
...((((((......).))))))	chr16:66977106-66977307(+)$1	1	14	37	12.4436
(..((.(((......))).)).)	chr14:105239606-105239807(-)$1	1	154	177	12.6860
..(((((((......)))....)	chr20:33029944-33030145(+)$1	1	19	42	13.2043
.(((..(((......)))..)))	chr1:36219328-36219529(-)$1	1	155	178	13.5108
((.(.((((......))))).))	chr18:47812367-47812568(-)$1	1	63	86	12.7489
.((..((((......))))..))	chrX:108906407-108906608(-)$1	1	104	127	11.3521
((((((((((......)).))).	chr10:118713519-118713720(-)$1	1	40	63	10.5658
(((((((((......))))))))	chr4:152571519-152571720(+)$1	1	114	137	13.7499
(.(((((((......))))))).	chr10:124697313-124697514(-)$1	1	37	60	13.0910
..(((.(((......)))..)))	chr3:169814935-169815136(-)$1	1	58	81	14.0907
(..((.(((......))).))..	chr5:150075132-150075333(-)$1	1	41	64	13.0279
((..(((((......))))))))	chr11:63662977-63663178(+)$1	1	29	52	11.9235
.(((((.((......)).)))))	chr21:33039493-33039694(+)$1	1	142	165	11.7286

#PSSM
g : 0.16	c : 0.16	d : 0.09	e : 0.09	# : 0.07	f : 0.07	" : 0.05	= : 0.05	i : 0.03	b : 0.03	! : 0.03	C : 0.01	[ : 0.01	% : 0.01	a : 0.01	h : 0.01	
c : 0.18	g : 0.15	e : 0.13	! : 0.09	[ : 0.07	# : 0.07	f : 0.05	= : 0.05	d : 0.03	b : 0.03	" : 0.03	i : 0.03	h : 0.01	
g : 0.20	c : 0.16	! : 0.11	e : 0.11	f : 0.05	# : 0.05	[ : 0.05	" : 0.03	d : 0.03	b : 0.03	a : 0.03	i : 0.03	= : 0.03	
g : 0.20	e : 0.15	c : 0.09	[ : 0.09	! : 0.07	f : 0.07	d : 0.05	# : 0.05	b : 0.05	a : 0.03	i : 0.03	= : 0.03	" : 0.01	
e : 0.24	g : 0.16	! : 0.15	c : 0.07	d : 0.05	# : 0.05	f : 0.05	b : 0.05	i : 0.03	= : 0.03	[ : 0.03	" : 0.01	
e : 0.20	g : 0.15	d : 0.15	[ : 0.13	! : 0.11	f : 0.05	c : 0.05	# : 0.03	i : 0.03	= : 0.03	a : 0.01	
c : 0.41	e : 0.15	g : 0.11	d : 0.11	[ : 0.09	f : 0.03	= : 0.03	# : 0.01	i : 0.01	
c : 0.43	e : 0.15	d : 0.09	b : 0.09	g : 0.07	[ : 0.05	f : 0.03	= : 0.03	i : 0.01	
c : 0.41	b : 0.13	e : 0.11	d : 0.09	g : 0.07	a : 0.05	f : 0.03	= : 0.03	i : 0.01	o : 0.01	
o : 0.92	c : 0.03	b : 0.03	
o : 0.96	n : 0.03	
o : 0.96	n : 0.03	
o : 0.96	n : 0.03	
o : 0.96	n : 0.03	
o : 0.94	n : 0.03	e : 0.01	
c : 0.41	e : 0.13	d : 0.09	b : 0.09	g : 0.07	a : 0.05	o : 0.03	f : 0.03	= : 0.03	i : 0.01	
c : 0.41	e : 0.13	b : 0.13	d : 0.09	g : 0.07	] : 0.05	f : 0.03	= : 0.03	i : 0.01	
c : 0.41	e : 0.16	d : 0.13	g : 0.09	b : 0.03	f : 0.03	= : 0.03	3 : 0.01	4 : 0.01	i : 0.01	] : 0.01	
e : 0.26	] : 0.18	2 : 0.13	d : 0.13	g : 0.11	f : 0.03	= : 0.03	4 : 0.03	3 : 0.01	b : 0.01	i : 0.01	
e : 0.24	2 : 0.16	g : 0.15	4 : 0.05	d : 0.05	b : 0.05	a : 0.05	c : 0.05	f : 0.03	= : 0.03	] : 0.03	3 : 0.01	i : 0.01	
g : 0.20	c : 0.15	e : 0.15	2 : 0.07	4 : 0.07	f : 0.07	d : 0.05	b : 0.05	] : 0.05	i : 0.03	= : 0.03	h : 0.01	
c : 0.24	g : 0.20	e : 0.15	2 : 0.09	4 : 0.05	= : 0.05	f : 0.03	b : 0.03	i : 0.03	] : 0.03	d : 0.01	h : 0.01	
c : 0.18	g : 0.13	e : 0.11	2 : 0.09	] : 0.07	d : 0.07	f : 0.05	= : 0.05	3 : 0.03	4 : 0.03	i : 0.03	b : 0.03	5 : 0.01	a : 0.01	h : 0.01	

#score	667.7274049651033
#seq	53
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_CDS_m2_run1.txt

#BEAR
!!ffffffcccvvvvvvvvvvvvvccc22f	chr14:105716612-105716852(+)$1	240	155	185	24.7220
""bb"""ddddtttttttttttddddbb33	chr1:95363380-95363630(-)$1	250	195	225	22.3072
e[bb####ccctttttttttttccc4444b	chr1:93620135-93620439(-)$1	304	186	216	23.1778
a[a[ffffffxxxxxxxxxxxxxxxfffff	chr6:31498455-31498742(-)$1	287	13	43	19.6715
:cccffffffvvvvvvvvvvvvvffffff]	chr5:118451852-118452092(+)$1	240	147	177	23.4960
a!!dddd[cccuuuuuuuuuuuuccc]ddd	chr3:9490148-9490388(+)$1	240	10	40	24.5072
b[ccceeeeewwwwwwwwwwwwwweeeee2	chr2:27607812-27608054(-)$1	242	19	49	23.0800
fff!!fffffftttttttttttffffff]f	chr16:53488558-53488798(+)$1	240	149	179	22.9491
eeeegggggggwwwwwwwwwwwwwwggggg	chr5:112312533-112312773(+)$1	240	156	186	23.2092
I:gggggggwwwwwwwwwwwwwwggggggg	chr13:99114005-99114245(-)$1	240	136	166	21.8960
eeee[ddddccctttttttttttccc]ddd	chr17:38319884-38320125(+)$1	241	199	229	22.0355
ggdddd!!cccwwwwwwwwwwwwwwcccdd	chr17:55028134-55028379(-)$1	245	144	174	22.6818
ffffggggggguuuuuuuuuuuuggggggg	chr2:24290569-24290812(-)$1	243	192	222	24.5036
hhhhh[ddddwwwwwwwwwwwwwwdddd]h	chr16:28854960-28855200(-)$1	240	170	200	22.0510
:::ccc[dddduuuuuuuuuuuuddddccc	chr17:37648982-37649222(+)$1	240	119	149	21.5266
b[iiiiiiiiivvvvvvvvvvvvviiiiii	chr19:8528380-8528660(+)$1	280	7	37	24.6215
$$$$a[ddddwwwwwwwwwwwwwwdddd]a	chrX:48767051-48767296(-)$1	245	65	95	23.3268
"ccc[ffffffuuuuuuuuuuuuffffff]	chr19:14521719-14521959(-)$1	240	88	118	24.9066
eee####dddduuuuuuuuuuuudddd22e	chr3:112727003-112727243(-)$1	240	129	159	23.5875
fffff!!ddddtttttttttttdddd333f	chr3:52440193-52440433(-)$1	240	49	79	22.3856
ggggg:fffffftttttttttttffffffF	chr1:84955906-84956146(+)$1	240	68	98	20.9156
!!==========ttttttttttt=======	chr7:150768729-150768969(+)$1	240	81	111	23.4311
ccchhhhhhhhuuuuuuuuuuuuhhhhhhh	chr14:61445881-61446201(-)$1	320	152	182	21.5560
e[ccc[eeeeeuuuuuuuuuuuueeeee]c	chr13:41704716-41705007(-)$1	291	205	235	24.5322
&ccc[ffffffuuuuuuuuuuuuffffff]	chr9:20789455-20789695(+)$1	240	74	104	24.4293
$$$gggggggxxxxxxxxxxxxxxxggggg	chr10:69804077-69804317(-)$1	240	181	211	19.7458
dd"""ddddbbuuuuuuuuuuuubb22ddd	chr3:9495355-9495595(+)$1	240	129	159	22.7521
!dddd[cccxxxxxxxxxxxxxxxccc333	chr10:71144460-71144700(+)$1	240	31	61	19.8377
a[ffffffccctttttttttttccc4444f	chr11:4104432-4104672(+)$1	240	28	58	23.5903
dddd[ffffffuuuuuuuuuuuuffffff]	chr1:24021088-24021331(+)$1	243	116	146	24.1812
##hhhhhhhhwwwwwwwwwwwwwwhhhhhh	chr20:25204629-25204870(+)$1	241	93	123	21.5752
"""hhhhhhhhuuuuuuuuuuuuhhhhhhh	chr12:110975929-110976169(-)$1	240	20	50	22.0674
:::gggggggwwwwwwwwwwwwwwgggggg	chr13:20221223-20221463(+)$1	240	19	49	22.0309
))))))eeeeeuuuuuuuuuuuueeeee]h	chr6:33288995-33289235(-)$1	240	188	218	22.0019
fffff[cccwwwwwwwwwwwwwwcccffff	chr3:52570692-52570933(+)$1	241	151	181	23.4831
ii"""fffffftttttttttttffffff]i	chr3:53275047-53275287(-)$1	240	177	207	23.3631
eee"""cccyyyyyyyyyyyyyyyyccc22	chr17:74401189-74401429(-)$1	240	99	129	22.2222
###gggggggvvvvvvvvvvvvvggggggg	chr22:20909170-20909410(+)$1	240	36	66	25.0893
&&&&&&&cccauuuuuuuuuuuua]ccc77	chr3:47059078-47059318(-)$1	240	62	92	20.8389
c[bb!!cccwwwwwwwwwwwwwwccc333b	chr5:145878067-145878347(+)$1	280	81	111	24.4105
c[gggggggwwwwwwwwwwwwwwggggggg	chr20:62292558-62292798(+)$1	240	5	35	24.0628
ddd::ffffffvvvvvvvvvvvvvffffff	chr8:146066957-146067199(+)$1	242	144	174	21.7137
ddd$$$$$ccctttttttttttccc4444d	chr3:136059244-136059484(-)$1	240	96	126	22.1475
===========uuuuuuuuuuuu=======	chr18:48702741-48702981(-)$1	240	141	171	25.2532
b"""cccdddduuuuuuuuuuuudddd]cc	chr13:25068623-25068863(-)$1	240	39	69	24.1369
bccc[ddddxxxxxxxxxxxxxxxdddd]c	chr15:91290538-91290778(+)$1	240	86	116	18.8588
Effffffcccvvvvvvvvvvvvvccc]fff	chr17:21217391-21217636(+)$1	245	207	237	23.6120
=!!bb!!cccvvvvvvvvvvvvvccc]bb2	chr5:149429856-149430096(+)$1	240	14	44	24.2601
d####fffffftttttttttttffffff33	chr16:1837851-1838091(+)$1	240	157	187	23.4783
E{BBffffffwwwwwwwwwwwwwwffffff	chr3:39135399-39135639(+)$1	240	61	91	20.5004
======eeeeeuuuuuuuuuuuueeeee::	chr8:11695952-11696267(+)$1	315	104	134	22.2927
ddd"""cccyyyyyyyyyyyyyyyyccc]d	chr20:52192453-52192693(-)$1	240	29	59	22.3312
eeeeeccc!!bbtttttttttttbb22ccc	chr17:61498683-61498923(+)$1	240	158	188	21.0408
===========vvvvvvvvvvvvv======	chr17:40993442-40993722(+)$1	280	243	273	24.8621
fffff[eeeeettttttttttteeeee22f	chr1:236371328-236371568(+)$1	240	93	123	21.9074
:ffffff!!bbvvvvvvvvvvvvvbb22ff	chr6:150016129-150016372(-)$1	243	160	190	22.1532
$$bb"""cccwwwwwwwwwwwwwwccc444	chr12:56814720-56814960(-)$1	240	116	146	24.3876
:::a[fffffftttttttttttffffff]a	chr19:9453471-9453711(+)$1	240	40	70	20.8607
ffadddd"""bbtttttttttttbb333dd	chr15:82520489-82520729(-)$1	240	192	222	20.8013

#otherMatches

#Seq PSSM
UGUCAGACGGAUCCAGUAACACCUUCCCGG	chr14:105716612-105716852(+)$1	240	155	185	24.7220
AGCCAAGGAACAGGAACAAAUGGUUCGGAA	chr1:95363380-95363630(-)$1	250	195	225	22.3072
GAAGAUAAGAGGAAAAGUAGAACUUAAAAC	chr1:93620135-93620439(-)$1	304	186	216	23.1778
CAGUGCUACCCUCUGUCUCCCUCCAGGUGG	chr6:31498455-31498742(-)$1	287	13	43	19.6715
UCCUGGCGUAAAACAAGCAAAUAUAUGCCU	chr5:118451852-118452092(+)$1	240	147	177	23.4960
GUACUGGCAACGACCCUAAACAUGUUACCA	chr3:9490148-9490388(+)$1	240	10	40	24.5072
AAGGGCUGUUGAGGUAGUGAGAGGGACGGA	chr2:27607812-27608054(-)$1	242	19	49	23.0800
CUGAAAGGGUGCAGAUGAAAAACAUCUUAC	chr16:53488558-53488798(+)$1	240	149	179	22.9491
CGCUACCCGACCCCCUUUCGCCCCCGUCGG	chr5:112312533-112312773(+)$1	240	156	186	23.2092
CUGGAUCUUCACAAUCCGAGAAAAAGAUCC	chr13:99114005-99114245(-)$1	240	136	166	21.8960
CAGCCUCAGAGCCACCAGCUGCUGCUCCUG	chr17:38319884-38320125(+)$1	241	199	229	22.0355
AACCAGAUUGCAAAUAUUCAAAGAAGCAUU	chr17:55028134-55028379(-)$1	245	144	174	22.6818
AUUUUCAUUUGGACUAAAUCCCACGAAUGA	chr2:24290569-24290812(-)$1	243	192	222	24.5036
UGGAGGGGGGACUUUUUAUAUUACCUUUGC	chr16:28854960-28855200(-)$1	240	170	200	22.0510
GAACCUAUGGCCAAGUAUAUAAAGCCAAGG	chr17:37648982-37649222(+)$1	240	119	149	21.5266
CGUAAGUAUCGUCUAGUUACUUAUUGGUAU	chr19:8528380-8528660(+)$1	280	7	37	24.6215
UCCAGAAUGCCUCCCUCAUCCUCAGCAUCC	chrX:48767051-48767296(-)$1	245	65	95	23.3268
UAGGAGCUUCAGCCUAAAGAAUGUGAAGCA	chr19:14521719-14521959(-)$1	240	88	118	24.9066
GGUGCAGGAGCAAAAAACUCAAGGCUCAGG	chr3:112727003-112727243(-)$1	240	129	159	23.5875
ACCACGACAUCCGCUUCAACCUGAUGGCAG	chr3:52440193-52440433(-)$1	240	49	79	22.3856
CAAAAUUUUUGUUAUUUUGUUUUGCAGAGA	chr1:84955906-84956146(+)$1	240	68	98	20.9156
CUGAUUAUGUCCACAGCGCUCCAGGGCGUG	chr7:150768729-150768969(+)$1	240	81	111	23.4311
GCUUCCUGAAGGUCAAGAUGUAACUUCAGG	chr14:61445881-61446201(-)$1	320	152	182	21.5560
GCUCGUGUUUAUCCUUCCUGCCUUGAACCU	chr13:41704716-41705007(-)$1	291	205	235	24.5322
CUUGUUGAAGACAAAGGACAAAAUCUUCAC	chr9:20789455-20789695(+)$1	240	74	104	24.4293
UCCUUAACAAUCUUUUAAAAUAAAUUUGUU	chr10:69804077-69804317(-)$1	240	181	211	19.7458
UAGAACUCAGCACCUAUACCAAAGCAAUGA	chr3:9495355-9495595(+)$1	240	129	159	22.7521
UGUGCACUGAUAAAAUUAAAACCACAGAGA	chr10:71144460-71144700(+)$1	240	31	61	19.8377
CAUGCCUGCAGUUCUCUUUCCUCUGUCUUC	chr11:4104432-4104672(+)$1	240	28	58	23.5903
UUGGGAUCCAGGAACACAUCGAUCUGGGUA	chr1:24021088-24021331(+)$1	243	116	146	24.1812
UGUGUCUCCCACAGAUGCGGAGAAGGGAGG	chr20:25204629-25204870(+)$1	241	93	123	21.5752
GAAAAGGUGGUUAGAUAAAUGUUACUGUCU	chr12:110975929-110976169(-)$1	240	20	50	22.0674
AACAGGAAGCUAGAGAACAAGAACGCUUUC	chr13:20221223-20221463(+)$1	240	19	49	22.0309
ACAAAUGCUGAAAACACUGCCUCUCAGUCU	chr6:33288995-33289235(-)$1	240	188	218	22.0019
UUCCUGCCCUUCUUUUUUGUCCUGGGAGGA	chr3:52570692-52570933(+)$1	241	151	181	23.4831
CCACUUCCUAUUUCCCAGACAUGUGGGACG	chr3:53275047-53275287(-)$1	240	177	207	23.3631
GCAUCAUCUAUCCCGUCAACAGCAAGGACC	chr17:74401189-74401429(-)$1	240	99	129	22.2222
CCUUGUGUUCCCACAGAUCCUAUGAAUGCA	chr22:20909170-20909410(+)$1	240	36	66	25.0893
AACGUGUUCUCUUUUCUCUGCCUGCAGAUG	chr3:47059078-47059318(-)$1	240	62	92	20.8389
AAGCAAUUGAAAAGAUGAAAGACCGAGAAG	chr5:145878067-145878347(+)$1	280	81	111	24.4105
CUGGCUGCCGAAGCUUGUCUCAGGGCAGCU	chr20:62292558-62292798(+)$1	240	5	35	24.0628
GGCAUCAGAGCCACUUCAGAUAUCGCUCUG	chr8:146066957-146067199(+)$1	242	144	174	21.7137
GAAGCCAGUUAGAAGAUAUGAAUGAAGAAU	chr3:136059244-136059484(-)$1	240	96	126	22.1475
GUUCCAUGUGGCCACAACCUCUUCUGCAUG	chr18:48702741-48702981(-)$1	240	141	171	25.2532
GAUGCAAGUGAAUACUUUGAAAAUUACAUU	chr13:25068623-25068863(-)$1	240	39	69	24.1369
GGCUGCUGUUCCUCAAAAUAAUCUACAGGA	chr15:91290538-91290778(+)$1	240	86	116	18.8588
GGGCAGUGCUCACCCACACCAUAAGCUACU	chr17:21217391-21217636(+)$1	245	207	237	23.6120
CCUGCUUGCCUCUUCCCGCCACUGGCCGCC	chr5:149429856-149430096(+)$1	240	14	44	24.2601
GAAUCGUGGAGAAUAUGAGCGGCUUCACCU	chr16:1837851-1838091(+)$1	240	157	187	23.4783
UAGCUCUUCUAAUAAUGAAAAACCAGGAGA	chr3:39135399-39135639(+)$1	240	61	91	20.5004
GGCAGUACCUGACCACUCUCUCCCAGGUAA	chr8:11695952-11696267(+)$1	315	104	134	22.2927
GUUCCAUCGACUACCCCGCCAAGAACGACA	chr20:52192453-52192693(-)$1	240	29	59	22.3312
CCCCAGUGAGCCCACCCGAUCCAGGACCAC	chr17:61498683-61498923(+)$1	240	158	188	21.0408
GCUGGAAAUAGUAAUCACACCUCUCUGUUU	chr17:40993442-40993722(+)$1	280	243	273	24.8621
CUCAACUUUGGAUCCUGACAAACCAAGCCU	chr1:236371328-236371568(+)$1	240	93	123	21.9074
CAGGUGAUUAAUCAAAUAUUUUAUUUUCUC	chr6:150016129-150016372(-)$1	243	160	190	22.1532
CAGCGAAGAGGAAGAAGAAGGGGGCUCAGA	chr12:56814720-56814960(-)$1	240	116	146	24.3876
AGAGGCCAUAUAAAUGUCAAAAGUGUGGGC	chr19:9453471-9453711(+)$1	240	40	70	20.8607
UUCUUGGUAUCCUUUAUUCUAAUGGUUUUU	chr15:82520489-82520729(-)$1	240	192	222	20.8013

#DB
..(((((((((.............)))..)	chr14:105716612-105716852(+)$1	1	155	185	24.7220
..((...((((...........))))))..	chr1:95363380-95363630(-)$1	1	195	225	22.3072
(.((....(((...........)))....)	chr1:93620135-93620439(-)$1	1	186	216	23.1778
(.(.((((((...............)))))	chr6:31498455-31498742(-)$1	1	13	43	19.6715
.(((((((((.............)))))).	chr5:118451852-118452092(+)$1	1	147	177	23.4960
(..((((.(((............))).)))	chr3:9490148-9490388(+)$1	1	10	40	24.5072
(.((((((((..............))))).	chr2:27607812-27608054(-)$1	1	19	49	23.0800
(((..((((((...........)))))).)	chr16:53488558-53488798(+)$1	1	149	179	22.9491
))))(((((((..............)))))	chr5:112312533-112312773(+)$1	1	156	186	23.2092
).(((((((..............)))))))	chr13:99114005-99114245(-)$1	1	136	166	21.8960
((((.(((((((...........))).)))	chr17:38319884-38320125(+)$1	1	199	229	22.0355
))((((..(((..............)))))	chr17:55028134-55028379(-)$1	1	144	174	22.6818
))))(((((((............)))))))	chr2:24290569-24290812(-)$1	1	192	222	24.5036
(((((.((((..............)))).)	chr16:28854960-28855200(-)$1	1	170	200	22.0510
...(((.((((............)))))))	chr17:37648982-37649222(+)$1	1	119	149	21.5266
(.(((((((((.............))))))	chr19:8528380-8528660(+)$1	1	7	37	24.6215
....(.((((..............)))).)	chrX:48767051-48767296(-)$1	1	65	95	23.3268
.(((.((((((............)))))).	chr19:14521719-14521959(-)$1	1	88	118	24.9066
(((....((((............))))..)	chr3:112727003-112727243(-)$1	1	129	159	23.5875
(((((..((((...........))))...)	chr3:52440193-52440433(-)$1	1	49	79	22.3856
))))).((((((...........))))))(	chr1:84955906-84956146(+)$1	1	68	98	20.9156
..((((((((((...........)))))))	chr7:150768729-150768969(+)$1	1	81	111	23.4311
(((((((((((............)))))))	chr14:61445881-61446201(-)$1	1	152	182	21.5560
(.(((.(((((............))))).)	chr13:41704716-41705007(-)$1	1	205	235	24.5322
.(((.((((((............)))))).	chr9:20789455-20789695(+)$1	1	74	104	24.4293
...(((((((...............)))))	chr10:69804077-69804317(-)$1	1	181	211	19.7458
((...((((((............))..)))	chr3:9495355-9495595(+)$1	1	129	159	22.7521
.((((.(((...............)))...	chr10:71144460-71144700(+)$1	1	31	61	19.8377
(.(((((((((...........)))....)	chr11:4104432-4104672(+)$1	1	28	58	23.5903
((((.((((((............)))))).	chr1:24021088-24021331(+)$1	1	116	146	24.1812
..((((((((..............))))))	chr20:25204629-25204870(+)$1	1	93	123	21.5752
...((((((((............)))))))	chr12:110975929-110976169(-)$1	1	20	50	22.0674
...(((((((..............))))))	chr13:20221223-20221463(+)$1	1	19	49	22.0309
......(((((............))))).)	chr6:33288995-33289235(-)$1	1	188	218	22.0019
(((((.(((..............)))))))	chr3:52570692-52570933(+)$1	1	151	181	23.4831
((...((((((...........)))))).)	chr3:53275047-53275287(-)$1	1	177	207	23.3631
(((...(((................)))..	chr17:74401189-74401429(-)$1	1	99	129	22.2222
...(((((((.............)))))))	chr22:20909170-20909410(+)$1	1	36	66	25.0893
.......((((............).)))..	chr3:47059078-47059318(-)$1	1	62	92	20.8389
(.((..(((..............)))...)	chr5:145878067-145878347(+)$1	1	81	111	24.4105
(.(((((((..............)))))))	chr20:62292558-62292798(+)$1	1	5	35	24.0628
)))..((((((.............))))))	chr8:146066957-146067199(+)$1	1	144	174	21.7137
(((.....(((...........)))....)	chr3:136059244-136059484(-)$1	1	96	126	22.1475
(((((((((((............)))))))	chr18:48702741-48702981(-)$1	1	141	171	25.2532
(...(((((((............)))).))	chr13:25068623-25068863(-)$1	1	39	69	24.1369
)(((.((((...............)))).)	chr15:91290538-91290778(+)$1	1	86	116	18.8588
)(((((((((.............))).)))	chr17:21217391-21217636(+)$1	1	207	237	23.6120
(..((..(((.............))).)).	chr5:149429856-149430096(+)$1	1	14	44	24.2601
(....((((((...........))))))..	chr16:1837851-1838091(+)$1	1	157	187	23.4783
(.((((((((..............))))))	chr3:39135399-39135639(+)$1	1	61	91	20.5004
))))))(((((............)))))..	chr8:11695952-11696267(+)$1	1	104	134	22.2927
(((...(((................))).)	chr20:52192453-52192693(-)$1	1	29	59	22.3312
((((((((..((...........))..)))	chr17:61498683-61498923(+)$1	1	158	188	21.0408
(((((((((((.............))))))	chr17:40993442-40993722(+)$1	1	243	273	24.8621
(((((.(((((...........)))))..)	chr1:236371328-236371568(+)$1	1	93	123	21.9074
.((((((..((.............))..))	chr6:150016129-150016372(-)$1	1	160	190	22.1532
..((...(((..............)))...	chr12:56814720-56814960(-)$1	1	116	146	24.3876
...(.((((((...........)))))).)	chr19:9453471-9453711(+)$1	1	40	70	20.8607
(((((((...((...........))...))	chr15:82520489-82520729(-)$1	1	192	222	20.8013

#PSSM
e : 0.11	f : 0.10	d : 0.10	: : 0.08	b : 0.06	= : 0.06	! : 0.05	" : 0.05	a : 0.05	$ : 0.05	c : 0.05	g : 0.03	& : 0.03	# : 0.03	E : 0.03	I : 0.01	h : 0.01	) : 0.01	i : 0.01	
[ : 0.13	f : 0.13	d : 0.10	c : 0.08	e : 0.08	! : 0.06	: : 0.06	" : 0.05	$ : 0.05	# : 0.05	= : 0.05	g : 0.03	h : 0.01	) : 0.01	i : 0.01	& : 0.01	{ : 0.01	
f : 0.15	c : 0.11	d : 0.10	e : 0.08	b : 0.06	= : 0.06	" : 0.06	g : 0.05	: : 0.05	a : 0.03	! : 0.03	h : 0.03	$ : 0.03	# : 0.03	i : 0.01	) : 0.01	& : 0.01	B : 0.01	
f : 0.13	c : 0.11	g : 0.10	b : 0.08	d : 0.08	" : 0.08	h : 0.06	= : 0.06	e : 0.05	$ : 0.03	# : 0.03	[ : 0.01	! : 0.01	i : 0.01	) : 0.01	& : 0.01	: : 0.01	B : 0.01	a : 0.01	
f : 0.16	g : 0.13	" : 0.10	[ : 0.10	d : 0.06	c : 0.06	h : 0.06	= : 0.06	# : 0.05	! : 0.03	i : 0.01	a : 0.01	) : 0.01	& : 0.01	: : 0.01	$ : 0.01	b : 0.01	e : 0.01	
f : 0.25	g : 0.11	d : 0.10	[ : 0.10	" : 0.06	= : 0.06	c : 0.05	! : 0.05	h : 0.05	# : 0.03	e : 0.01	i : 0.01	: : 0.01	) : 0.01	& : 0.01	$ : 0.01	
f : 0.27	d : 0.11	g : 0.11	c : 0.11	e : 0.08	! : 0.05	= : 0.05	h : 0.05	" : 0.03	# : 0.03	[ : 0.01	i : 0.01	& : 0.01	$ : 0.01	
f : 0.23	d : 0.16	c : 0.16	g : 0.11	e : 0.08	= : 0.05	h : 0.05	! : 0.03	# : 0.01	[ : 0.01	i : 0.01	$ : 0.01	" : 0.01	
c : 0.25	f : 0.20	d : 0.16	g : 0.11	e : 0.08	= : 0.05	h : 0.05	! : 0.03	i : 0.01	" : 0.01	
f : 0.20	c : 0.18	d : 0.11	e : 0.08	g : 0.08	w : 0.06	= : 0.05	h : 0.05	b : 0.03	x : 0.03	y : 0.03	i : 0.01	! : 0.01	" : 0.01	
w : 0.18	f : 0.15	c : 0.11	d : 0.08	x : 0.06	v : 0.06	e : 0.06	b : 0.06	= : 0.05	g : 0.03	h : 0.03	y : 0.03	i : 0.01	a : 0.01	
u : 0.27	w : 0.22	t : 0.16	v : 0.15	x : 0.06	y : 0.03	b : 0.03	c : 0.01	f : 0.01	= : 0.01	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	t : 0.25	w : 0.22	v : 0.15	x : 0.06	y : 0.03	
u : 0.27	w : 0.22	v : 0.15	t : 0.08	x : 0.06	f : 0.06	c : 0.05	d : 0.03	y : 0.03	e : 0.01	
c : 0.15	f : 0.15	w : 0.15	v : 0.08	d : 0.08	x : 0.06	g : 0.06	e : 0.06	b : 0.05	= : 0.03	h : 0.03	y : 0.03	a : 0.01	
c : 0.20	f : 0.18	d : 0.13	e : 0.08	g : 0.08	b : 0.06	= : 0.05	h : 0.05	x : 0.03	w : 0.03	y : 0.03	i : 0.01	] : 0.01	
c : 0.22	f : 0.20	d : 0.13	g : 0.11	e : 0.08	4 : 0.05	= : 0.05	h : 0.05	2 : 0.03	i : 0.01	b : 0.01	3 : 0.01	
f : 0.22	c : 0.11	g : 0.11	d : 0.10	e : 0.08	] : 0.06	4 : 0.05	3 : 0.05	= : 0.05	h : 0.05	2 : 0.05	b : 0.01	i : 0.01	
f : 0.23	g : 0.11	d : 0.10	c : 0.10	2 : 0.06	4 : 0.06	e : 0.06	3 : 0.06	= : 0.05	h : 0.05	b : 0.03	i : 0.01	] : 0.01	
f : 0.18	] : 0.15	g : 0.11	3 : 0.08	d : 0.08	2 : 0.06	4 : 0.06	c : 0.05	= : 0.05	h : 0.05	e : 0.01	i : 0.01	7 : 0.01	b : 0.01	: : 0.01	
f : 0.18	d : 0.11	g : 0.11	h : 0.08	c : 0.08	] : 0.06	3 : 0.05	2 : 0.05	= : 0.05	b : 0.03	i : 0.03	a : 0.03	e : 0.01	F : 0.01	7 : 0.01	: : 0.01	4 : 0.01	

#score	1341.360141963884
#seq	59
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_CDS_m1_run1.txt

#BEAR
eee[cccwwwwwwwwwwwwwwccc]eeee	chr2:55825477-55825717(-)$1	240	49	78	22.3927
ee[eeeeevvvvvvvvvvvvveeeeeeee	chr4:122737863-122738113(-)$1	250	148	177	21.0548
dddd[bbwwwwwwwwwwwwwwbbdddd]f	chr8:64099251-64099491(+)$1	240	9	38	21.0942
dd[ddddyyyyyyyyyyyyyyyydddddd	chr11:47774427-47774667(-)$1	240	9	38	21.7788
ffffffyyyyyyyyyyyyyyyyffffff3	chr18:214495-214735(-)$1	240	193	222	22.0574
ggggggg^^^^^^^^^^^^^^^^^^^^^^	chr19:44739401-44739641(+)$1	240	109	138	25.3914
ffff[cccvvvvvvvvvvvvvccc]ffff	chr12:70206507-70206747(+)$1	240	78	107	21.2264
!!eeeeeyyyyyyyyyyyyyyyyeeeee>	chr1:84961548-84961788(+)$1	240	33	62	23.3888
=======yyyyyyyyyyyyyyyy======	chr3:194140543-194140783(-)$1	240	206	235	23.5946
iiiiiiiivvvvvvvvvvvvviiiiiiii	chr1:245019722-245019962(-)$1	240	103	132	20.8318
ddeeeee^^^^^^^^^^^^^^^^^^^^^^	chr14:95590482-95590722(-)$1	240	79	108	24.9903
d!!dddd^^^^^^^^^^^^^^^^^^^^^^	chr11:10800136-10800376(+)$1	240	79	108	24.8353
#ffffffxxxxxxxxxxxxxxxffffff2	chr3:57647129-57647369(-)$1	240	138	167	21.4150
""eeeeevvvvvvvvvvvvveeeee]bb]	chr16:29822345-29822585(+)$1	240	50	79	20.9605
##eeeee^^^^^^^^^^^^^^^^^^^^^^	chr5:112178191-112178431(+)$1	240	107	136	25.3319
ffff!!bbvvvvvvvvvvvvvbb22ffff	chrX:41055464-41055704(+)$1	240	118	147	20.2973
eeee[bbwwwwwwwwwwwwwwbb]eeeee	chr22:39917913-39918153(+)$1	240	157	186	21.9151
iiii[bbwwwwwwwwwwwwwwbb22iiii	chr8:11687740-11687980(+)$1	240	80	109	21.9127
eeedddd^^^^^^^^^^^^^^^^^^^^^^	chr18:61067712-61067953(-)$1	241	95	124	24.7341
iiiiiii^^^^^^^^^^^^^^^^^^^^^^	chr1:116935464-116935704(+)$1	240	198	227	25.3117
gg[dddd^^^^^^^^^^^^^^^^^^^^^^	chr6:111628590-111628830(-)$1	240	100	129	25.0256
gggggggvvvvvvvvvvvvvggggggghh	chr2:203071820-203072101(-)$1	281	45	74	20.2430
d[ffffffvvvvvvvvvvvvvffffff]d	chr12:12814039-12814279(-)$1	240	182	211	20.4951
eee[ccc^^^^^^^^^^^^^^^^^^^^^^	chr16:69725942-69726182(+)$1	240	94	123	25.0679
g!!ddddxxxxxxxxxxxxxxxdddd22g	chr20:47686670-47686910(+)$1	240	69	98	21.2778
bbeeeeevvvvvvvvvvvvveeeee]bb]	chr19:57803351-57803591(+)$1	240	63	92	20.3109
iiiiiii^^^^^^^^^^^^^^^^^^^^ii	chr12:46758071-46758311(-)$1	240	96	125	24.5517
effffff^^^^^^^^^^^^^^^^^^^^^^	chr8:77776365-77776605(+)$1	240	157	186	24.9251
:dddd^^^^^^^^^^^^^^^^^^^^^ddd	chr9:36356247-36356487(-)$1	240	83	112	21.6758
""eeeee^^^^^^^^^^^^^^^^^^^^^^	chr9:19096605-19096845(-)$1	240	40	69	25.4042
+++ddddwwwwwwwwwwwwwwdddd>>>>	chrX:40456415-40456655(+)$1	240	103	132	19.6735
:ffffff^^^^^^^^^^^^^^^^^^^^ff	chr3:156262052-156262292(-)$1	240	182	211	23.2221
gggggggwwwwwwwwwwwwwwggggggg5	chr1:197112086-197112326(-)$1	240	151	180	22.1890
:ffffffwwwwwwwwwwwwwwffffff::	chr5:133295131-133295371(-)$1	240	152	181	19.5418
!!eeeeexxxxxxxxxxxxxxxeeeee22	chr22:46712159-46712399(+)$1	240	34	63	22.1823
ggggg!!avvvvvvvvvvvvva22ggggg	chr1:55557613-55557853(-)$1	240	132	161	21.8585
c[eeeee^^^^^^^^^^^^^^^^^^^^^^	chr20:47587730-47587973(+)$1	243	105	134	25.3854
hhhh[bbwwwwwwwwwwwwwwbb]hhhhh	chr9:110091831-110092080(+)$1	249	73	102	19.7261
%ffffffxxxxxxxxxxxxxxxfffffff	chr5:145522356-145522596(-)$1	240	47	76	20.7447
ccc!!cccvvvvvvvvvvvvvccc22ccc	chr1:100174500-100174740(-)$1	240	42	71	21.2007
gggggggwwwwwwwwwwwwwwggggggg3	chr12:112568218-112568458(+)$1	240	30	59	22.8140
hhhhhhh^^^^^^^^^^^^^^^^^^^^^^	chr8:66651693-66651933(-)$1	240	65	94	23.9869
gg!!ccc^^^^^^^^^^^^^^^^^^^^^c	chr19:32930585-32930825(+)$1	240	114	143	24.9133
e!!ffffffuuuuuuuuuuuuffffff22	chr19:48887386-48887626(-)$1	240	117	146	19.6558
cc[eeeeevvvvvvvvvvvvveeeee22c	chr10:119043318-119043558(-)$1	240	93	122	21.2645
!ffffff^^^^^^^^^^^^^^^^^^^^^^	chr5:71494446-71494686(+)$1	240	65	94	25.1439
gggggggwwwwwwwwwwwwwwgggggggc	chr10:1038365-1038605(+)$1	240	33	62	22.5808
!!eeeee^^^^^^^^^^^^^^^^^^^^^^	chr7:73096986-73097226(-)$1	240	123	152	25.5495
eeee[bb^^^^^^^^^^^^^^^^^^^^^^	chr12:50481050-50481290(+)$1	240	106	135	24.8494
####cccwwwwwwwwwwwwwwccc55555	chr8:77764084-77764324(+)$1	240	116	145	20.1850
iiiiiii^^^^^^^^^^^^^^^^^^^^^^	chr7:94167019-94167261(+)$1	242	93	122	25.3117
"ccc[bbwwwwwwwwwwwwwwbb]ccc33	chr5:41904416-41904656(+)$1	240	136	165	22.5179
ff[cccyyyyyyyyyyyyyyyyccc]fff	chr6:96034241-96034481(+)$1	240	30	59	22.2072
c[eeeee^^^^^^^^^^^^^^^^^^^^^^	chr5:88018284-88018524(-)$1	240	193	222	25.3854
"eeeeexxxxxxxxxxxxxxxeeeee22g	chrX:138901401-138901641(-)$1	240	184	213	21.1457
beeeeeyyyyyyyyyyyyyyyyeeeee]b	chr3:128356670-128356910(-)$1	240	105	134	22.0354
eeeddddxxxxxxxxxxxxxxxdddd22e	chr7:152346068-152346309(-)$1	241	25	54	20.9306
iffffffwwwwwwwwwwwwwwffffff:G	chr8:95780589-95780829(+)$1	240	147	176	20.8261
!ffffff^^^^^^^^^^^^^^^^^^^^^^	chr8:146016686-146016926(-)$1	240	152	181	25.1439
fff[cccwwwwwwwwwwwwwwccc]ffff	chr2:48033313-48033553(+)$1	240	117	146	22.3041
gggggggxxxxxxxxxxxxxxxggggggg	chr13:21721358-21721608(+)$1	250	120	149	22.0290
iiiiiii^^^^^^^^^^^^^^^^^^iiii	chr7:63981671-63981911(-)$1	240	109	138	23.6965
gggggggyyyyyyyyyyyyyyyygggggg	chr8:141561299-141561539(-)$1	240	59	88	23.2813
gggggggyyyyyyyyyyyyyyyygggggg	chr11:62346261-62346597(-)$1	336	59	88	23.2813
bb[ddddwwwwwwwwwwwwwwdddd]bbf	chr16:58584953-58585193(-)$1	240	78	107	21.0364
[ffffff^^^^^^^^^^^^^^^^^^^^^^	chr13:39587141-39587381(-)$1	240	185	214	25.0966
ccc!!dddduuuuuuuuuuuudddd22cc	chr17:10595126-10595366(-)$1	240	77	106	19.3865
dd[eeeeeuuuuuuuuuuuueeeee]ddd	chr2:55252584-55252824(-)$1	240	10	39	19.8951
dddd[bb^^^^^^^^^^^^^^^^^^^^^^	chr17:79535989-79536229(-)$1	240	119	148	24.3019
""eeeee^^^^^^^^^^^^^^^^^^^^^^	chr8:26218450-26218690(+)$1	240	110	139	25.4042
eee[dddduuuuuuuuuuuuddddeeeee	chr11:9307995-9308235(-)$1	240	144	173	19.5270

#otherMatches

#Seq PSSM
GUACAGUACAUUCAGGACAUCAUUUUGCC	chr2:55825477-55825717(-)$1	240	49	78	22.3927
CUUGGUGCUUUUUCUUGUUUUGCACUGGU	chr4:122737863-122738113(-)$1	250	148	177	21.0548
CAGCACCUAAACCAACCUCCUGGGCUGCC	chr8:64099251-64099491(+)$1	240	9	38	21.0942
GAAGGAGAUCGAUGCCAUAACAGCUCCUC	chr11:47774427-47774667(-)$1	240	9	38	21.7788
AACAAUAAACAUUUUUAUAACAAUUGUUG	chr18:214495-214735(-)$1	240	193	222	22.0574
UCUUUUCAUUCUUAUCAAUCUAAUCAUAC	chr19:44739401-44739641(+)$1	240	109	138	25.3914
UCCUGUAAACACAGAAUUAAAUUAGGGGA	chr12:70206507-70206747(+)$1	240	78	107	21.2264
CACAGAACACAUACCUGAAAUAAUUCUGA	chr1:84961548-84961788(+)$1	240	33	62	23.3888
AAAAAGACUAACCUGUAUACAUUUCUUUU	chr3:194140543-194140783(-)$1	240	206	235	23.5946
UGUAGUUUGCCCAAAAGAUGAAGACUAUA	chr1:245019722-245019962(-)$1	240	103	132	20.8318
AGAAAUUGAAGAAAAAGAGAAGCCAGAGA	chr14:95590482-95590722(-)$1	240	79	108	24.9903
UCUUUGCCAGACAUCCCAGGAACAGCAAC	chr11:10800136-10800376(+)$1	240	79	108	24.8353
UGUGCUCAAACAGAUAGCACCAGAGUAUU	chr3:57647129-57647369(-)$1	240	138	167	21.4150
AUCGUGUUCCUGUGUCCCCUGCAUGUACC	chr16:29822345-29822585(+)$1	240	50	79	20.9605
AAGUCCUCCUAACAAAUUAUCUCAACUUC	chr5:112178191-112178431(+)$1	240	107	136	25.3319
UUCAUUACUCUACUCUUUACUGUUUUGGG	chrX:41055464-41055704(+)$1	240	118	147	20.2973
CCAGAUCAUUCCUUUAGUUUAGAGCUGGG	chr22:39917913-39918153(+)$1	240	157	186	21.9151
GUGCCUGAAUGAACUUAUAACCAAUGCAC	chr8:11687740-11687980(+)$1	240	80	109	21.9127
CAACAGAAGCCAACAACUCAACAUUUUUU	chr18:61067712-61067953(-)$1	241	95	124	24.7341
GGGGAGGUACAUGAGCAGGAAGAGGAAAU	chr1:116935464-116935704(+)$1	240	198	227	25.3117
GGAAAGGCACUAUUUCACAAUAUUUUACU	chr6:111628590-111628830(-)$1	240	100	129	25.0256
UUCCUCUUACAGCUGGGAAUGGAGGAAGA	chr2:203071820-203072101(-)$1	281	45	74	20.2430
AAAGCUUUAACUAUAAAAACAGAAGCUAU	chr12:12814039-12814279(-)$1	240	182	211	20.4951
CUUUACAGCAGCAGAUUUCAUCAAAUAUU	chr16:69725942-69726182(+)$1	240	94	123	25.0679
AGGAUCUCCCUGAAUUUUUUGAAGAUAAU	chr20:47686670-47686910(+)$1	240	69	98	21.2778
GUCCCACGAACCCAUCCAGAGUGGGAACG	chr19:57803351-57803591(+)$1	240	63	92	20.3109
AAAAUGACUCUUGCAGACCUCACUAUUUU	chr12:46758071-46758311(-)$1	240	96	125	24.5517
UCCUGGCCUAAUAUCCUUUUCCAAGCGUC	chr8:77776365-77776605(+)$1	240	157	186	24.9251
AGUGAUCCAUUUCUUAUACAUCCUCCUCA	chr9:36356247-36356487(-)$1	240	83	112	21.6758
UUUUCUUUUUCUAUUUCUAUUUCAUUUUU	chr9:19096605-19096845(-)$1	240	40	69	25.4042
GACAGUGUUGCAAAUUCCAUUCACUCCUU	chrX:40456415-40456655(+)$1	240	103	132	19.6735
UUCAACCCCACAGUGUAUCCUUUUCAAGG	chr3:156262052-156262292(-)$1	240	182	211	23.2221
UAUAUGUGUACAUCUCAGCAAACAUGUAA	chr1:197112086-197112326(-)$1	240	151	180	22.1890
CUGUUGUUUACAUUACAUAUCACAACAAA	chr5:133295131-133295371(-)$1	240	152	181	19.5418
AUCUUCUCAAUUGAAUAAGACUAGAAGUA	chr22:46712159-46712399(+)$1	240	34	63	22.1823
UAUCUACGGACAAAGAAGAAACUCAGGUG	chr1:55557613-55557853(-)$1	240	132	161	21.8585
CCAUUUUUCUUACUCUUCUUUCAAACUUU	chr20:47587730-47587973(+)$1	243	105	134	25.3854
UUUCUUCUACAGCAGAACUUUGAUGAAGA	chr9:110091831-110092080(+)$1	249	73	102	19.7261
AGCAGGAGUUUGAAUUCUGGUAUCCUGUU	chr5:145522356-145522596(-)$1	240	47	76	20.7447
CAUAUCUCAAUUUUUCUUUCAGGGUCAUG	chr1:100174500-100174740(-)$1	240	42	71	21.2007
UUUUUGCAUGUCAUCUUUAAAGCAGAAAU	chr12:112568218-112568458(+)$1	240	30	59	22.8140
UUUCCUACUAAUGUAAUGUCUCUUCUUUC	chr8:66651693-66651933(-)$1	240	65	94	23.9869
AUUUUCAUAUCAACUUUUCUCUUUAGUCU	chr19:32930585-32930825(+)$1	240	114	143	24.9133
CUUCUACCUCUAUAUCACCAAAGGUAGCU	chr19:48887386-48887626(-)$1	240	117	146	19.6558
UCAGUCAAUAAAACAACAGGUUUGACAAG	chr10:119043318-119043558(-)$1	240	93	122	21.2645
AGCUCUCUCCAAAAUCUGAUAUCUCUCCA	chr5:71494446-71494686(+)$1	240	65	94	25.1439
GUAAUUAUGUUUUAUUUUCUUUAAUUGCA	chr10:1038365-1038605(+)$1	240	33	62	22.5808
AAUCUUCAUCAUCAUCGGCUUUUAUAUUU	chr7:73096986-73097226(-)$1	240	123	152	25.5495
GCUGCGAAUUUUCAUUUCUAACACUUUCA	chr12:50481050-50481290(+)$1	240	106	135	24.8494
CAACCUGCACAUCACCCACCACAGUCACC	chr8:77764084-77764324(+)$1	240	116	145	20.1850
GAAGGAAAACAAAUUUUAUACACAUUCAU	chr7:94167019-94167261(+)$1	242	93	122	25.3117
AGCUGCCGGUGAAGAUGGUGAGGGAGCGG	chr5:41904416-41904656(+)$1	240	136	165	22.5179
UUGCAGCAAAACACUUACUAUUUUGGAGU	chr6:96034241-96034481(+)$1	240	30	59	22.2072
AUGUGCCGUGUGUGGAAAAAAAAAAAGUC	chr5:88018284-88018524(-)$1	240	193	222	25.3854
UGAUUGCUUUAAACGAAUUUUCAAUCUAU	chrX:138901401-138901641(-)$1	240	184	213	21.1457
AGGGGAACCAUUAUUUCUACUCUCCCUAU	chr3:128356670-128356910(-)$1	240	105	134	22.0354
CUUGAGCACAGACUAUCCCAAAGCUCUGA	chr7:152346068-152346309(-)$1	241	25	54	20.9306
UAUUUGUUUUCUUUCUAUGUUGCAAGUUA	chr8:95780589-95780829(+)$1	240	147	176	20.8261
AUCAGGGAACUAUGCCACCGUUAUCUCCC	chr8:146016686-146016926(-)$1	240	152	181	25.1439
UUCAACUCACUACCAUUCAUUAGUAGAAG	chr2:48033313-48033553(+)$1	240	117	146	22.3041
UAAAUUCUAUUUACUAUUUGUUGAAUUUA	chr13:21721358-21721608(+)$1	250	120	149	22.0290
ACUUUAUUUUCAACCCUUACUAACCAUAA	chr7:63981671-63981911(-)$1	240	109	138	23.6965
UCCACACGGGCAUCGAGAUCAAGGUGUGG	chr8:141561299-141561539(-)$1	240	59	88	23.2813
GCAGAAACAUUUCACUCAGUUCAUUUCUG	chr11:62346261-62346597(-)$1	336	59	88	23.2813
UUGUGGAGCCCCCAGAAAAUAUCCAGGAG	chr16:58584953-58585193(-)$1	240	78	107	21.0364
CGCUGCCACCUCCACAUCUCUCCCUCAUC	chr13:39587141-39587381(-)$1	240	185	214	25.0966
UCUUUCAGAUAGCAUUACAACUCUGCCAG	chr17:10595126-10595366(-)$1	240	77	106	19.3865
AGAUAACACAAAAGAUACCCUGUUACCUG	chr2:55252584-55252824(-)$1	240	10	39	19.8951
GUUUACACUUUUUCUAUUUCGCAAAAUCC	chr17:79535989-79536229(-)$1	240	119	148	24.3019
AUAUCACAUCAACUCAAUUUCUAUUAAUA	chr8:26218450-26218690(+)$1	240	110	139	25.4042
UAACACCAUUUCUGCCUAAUUGGUUUAUU	chr11:9307995-9308235(-)$1	240	144	173	19.5270

#DB
(((.(((..............))).))))	chr2:55825477-55825717(-)$1	1	49	78	22.3927
((.(((((.............))))))))	chr4:122737863-122738113(-)$1	1	148	177	21.0548
((((.((..............)))))).)	chr8:64099251-64099491(+)$1	1	9	38	21.0942
((.((((................))))))	chr11:47774427-47774667(-)$1	1	9	38	21.7788
((((((................)))))).	chr18:214495-214735(-)$1	1	193	222	22.0574
(((((((......................	chr19:44739401-44739641(+)$1	1	109	138	25.3914
((((.(((.............))).))))	chr12:70206507-70206747(+)$1	1	78	107	21.2264
..(((((................))))).	chr1:84961548-84961788(+)$1	1	33	62	23.3888
(((((((................))))))	chr3:194140543-194140783(-)$1	1	206	235	23.5946
((((((((.............))))))))	chr1:245019722-245019962(-)$1	1	103	132	20.8318
(((((((......................	chr14:95590482-95590722(-)$1	1	79	108	24.9903
(..((((......................	chr11:10800136-10800376(+)$1	1	79	108	24.8353
.((((((...............)))))).	chr3:57647129-57647369(-)$1	1	138	167	21.4150
..(((((.............))))).)).	chr16:29822345-29822585(+)$1	1	50	79	20.9605
..(((((......................	chr5:112178191-112178431(+)$1	1	107	136	25.3319
((((..((.............))..))))	chrX:41055464-41055704(+)$1	1	118	147	20.2973
((((.((..............)).)))))	chr22:39917913-39918153(+)$1	1	157	186	21.9151
((((.((..............))..))))	chr8:11687740-11687980(+)$1	1	80	109	21.9127
(((((((......................	chr18:61067712-61067953(-)$1	1	95	124	24.7341
(((((((......................	chr1:116935464-116935704(+)$1	1	198	227	25.3117
((.((((......................	chr6:111628590-111628830(-)$1	1	100	129	25.0256
(((((((.............)))))))))	chr2:203071820-203072101(-)$1	1	45	74	20.2430
(.((((((.............)))))).)	chr12:12814039-12814279(-)$1	1	182	211	20.4951
(((.(((......................	chr16:69725942-69726182(+)$1	1	94	123	25.0679
(..((((...............))))..)	chr20:47686670-47686910(+)$1	1	69	98	21.2778
(((((((.............))))).)).	chr19:57803351-57803591(+)$1	1	63	92	20.3109
(((((((....................))	chr12:46758071-46758311(-)$1	1	96	125	24.5517
)((((((......................	chr8:77776365-77776605(+)$1	1	157	186	24.9251
.((((.....................)))	chr9:36356247-36356487(-)$1	1	83	112	21.6758
..(((((......................	chr9:19096605-19096845(-)$1	1	40	69	25.4042
...((((..............))))....	chrX:40456415-40456655(+)$1	1	103	132	19.6735
.((((((....................))	chr3:156262052-156262292(-)$1	1	182	211	23.2221
(((((((..............))))))).	chr1:197112086-197112326(-)$1	1	151	180	22.1890
.((((((..............))))))..	chr5:133295131-133295371(-)$1	1	152	181	19.5418
..(((((...............)))))..	chr22:46712159-46712399(+)$1	1	34	63	22.1823
(((((..(.............)..)))))	chr1:55557613-55557853(-)$1	1	132	161	21.8585
(.(((((......................	chr20:47587730-47587973(+)$1	1	105	134	25.3854
((((.((..............)).)))))	chr9:110091831-110092080(+)$1	1	73	102	19.7261
.((((((...............)))))))	chr5:145522356-145522596(-)$1	1	47	76	20.7447
(((..(((.............)))..)))	chr1:100174500-100174740(-)$1	1	42	71	21.2007
(((((((..............))))))).	chr12:112568218-112568458(+)$1	1	30	59	22.8140
(((((((......................	chr8:66651693-66651933(-)$1	1	65	94	23.9869
((..(((.....................)	chr19:32930585-32930825(+)$1	1	114	143	24.9133
(..((((((............))))))..	chr19:48887386-48887626(-)$1	1	117	146	19.6558
((.(((((.............)))))..)	chr10:119043318-119043558(-)$1	1	93	122	21.2645
.((((((......................	chr5:71494446-71494686(+)$1	1	65	94	25.1439
(((((((..............)))))))(	chr10:1038365-1038605(+)$1	1	33	62	22.5808
..(((((......................	chr7:73096986-73097226(-)$1	1	123	152	25.5495
((((.((......................	chr12:50481050-50481290(+)$1	1	106	135	24.8494
....(((..............))).....	chr8:77764084-77764324(+)$1	1	116	145	20.1850
(((((((......................	chr7:94167019-94167261(+)$1	1	93	122	25.3117
.(((.((..............)).)))..	chr5:41904416-41904656(+)$1	1	136	165	22.5179
((.(((................))).)))	chr6:96034241-96034481(+)$1	1	30	59	22.2072
(.(((((......................	chr5:88018284-88018524(-)$1	1	193	222	25.3854
.(((((...............)))))..)	chrX:138901401-138901641(-)$1	1	184	213	21.1457
((((((................))))).)	chr3:128356670-128356910(-)$1	1	105	134	22.0354
(((((((...............))))..)	chr7:152346068-152346309(-)$1	1	25	54	20.9306
)((((((..............)))))).)	chr8:95780589-95780829(+)$1	1	147	176	20.8261
.((((((......................	chr8:146016686-146016926(-)$1	1	152	181	25.1439
(((.(((..............))).))))	chr2:48033313-48033553(+)$1	1	117	146	22.3041
(((((((...............)))))))	chr13:21721358-21721608(+)$1	1	120	149	22.0290
(((((((..................))))	chr7:63981671-63981911(-)$1	1	109	138	23.6965
(((((((................))))))	chr8:141561299-141561539(-)$1	1	59	88	23.2813
(((((((................))))))	chr11:62346261-62346597(-)$1	1	59	88	23.2813
((.((((..............)))).))(	chr16:58584953-58585193(-)$1	1	78	107	21.0364
.((((((......................	chr13:39587141-39587381(-)$1	1	185	214	25.0966
(((..((((............))))..))	chr17:10595126-10595366(-)$1	1	77	106	19.3865
((.(((((............))))).)))	chr2:55252584-55252824(-)$1	1	10	39	19.8951
((((.((......................	chr17:79535989-79536229(-)$1	1	119	148	24.3019
..(((((......................	chr8:26218450-26218690(+)$1	1	110	139	25.4042
(((.((((............)))))))))	chr11:9307995-9308235(-)$1	1	144	173	19.5270

#PSSM
g : 0.16	e : 0.14	d : 0.09	i : 0.09	f : 0.07	! : 0.07	" : 0.07	c : 0.07	# : 0.04	b : 0.04	: : 0.04	h : 0.02	= : 0.01	+ : 0.01	% : 0.01	[ : 0.01	
f : 0.19	g : 0.15	e : 0.14	d : 0.08	! : 0.08	i : 0.08	c : 0.05	" : 0.04	[ : 0.04	# : 0.02	b : 0.02	h : 0.02	= : 0.01	+ : 0.01	
e : 0.28	f : 0.19	g : 0.12	[ : 0.09	i : 0.08	! : 0.05	d : 0.04	c : 0.04	h : 0.02	= : 0.01	+ : 0.01	# : 0.01	
e : 0.25	f : 0.19	d : 0.15	g : 0.12	i : 0.08	[ : 0.05	! : 0.04	h : 0.02	c : 0.02	= : 0.01	# : 0.01	
e : 0.22	f : 0.16	d : 0.14	g : 0.12	[ : 0.11	c : 0.08	i : 0.07	! : 0.04	= : 0.01	h : 0.01	
e : 0.22	f : 0.16	d : 0.14	c : 0.11	g : 0.11	b : 0.09	i : 0.07	! : 0.02	= : 0.01	^ : 0.01	h : 0.01	
e : 0.19	f : 0.15	d : 0.14	b : 0.11	g : 0.11	c : 0.09	i : 0.07	y : 0.04	= : 0.01	^ : 0.01	! : 0.01	h : 0.01	x : 0.01	
^ : 0.36	w : 0.21	y : 0.11	x : 0.09	e : 0.04	v : 0.04	c : 0.02	f : 0.02	d : 0.02	i : 0.01	b : 0.01	a : 0.01	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.02	f : 0.01	d : 0.01	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.15	y : 0.11	x : 0.09	u : 0.05	
^ : 0.36	w : 0.21	v : 0.11	y : 0.11	x : 0.09	e : 0.04	u : 0.02	g : 0.01	d : 0.01	
^ : 0.36	y : 0.11	e : 0.08	b : 0.08	x : 0.08	c : 0.07	g : 0.05	f : 0.05	d : 0.05	i : 0.01	a : 0.01	
^ : 0.36	e : 0.11	f : 0.09	c : 0.08	b : 0.08	d : 0.08	y : 0.07	g : 0.07	i : 0.01	2 : 0.01	
^ : 0.36	e : 0.12	d : 0.11	f : 0.09	g : 0.09	c : 0.08	2 : 0.04	] : 0.04	= : 0.01	i : 0.01	
^ : 0.36	e : 0.15	g : 0.11	d : 0.09	f : 0.09	] : 0.04	2 : 0.04	c : 0.02	= : 0.01	i : 0.01	h : 0.01	5 : 0.01	
^ : 0.35	f : 0.14	e : 0.12	g : 0.11	] : 0.07	d : 0.05	i : 0.04	2 : 0.02	= : 0.01	> : 0.01	h : 0.01	5 : 0.01	c : 0.01	
^ : 0.33	f : 0.15	g : 0.11	e : 0.09	2 : 0.07	d : 0.05	i : 0.04	b : 0.04	c : 0.02	= : 0.01	> : 0.01	h : 0.01	5 : 0.01	
^ : 0.30	f : 0.11	g : 0.09	2 : 0.08	e : 0.07	i : 0.05	] : 0.04	d : 0.04	b : 0.04	h : 0.02	: : 0.02	c : 0.02	= : 0.01	> : 0.01	5 : 0.01	3 : 0.01	
^ : 0.29	f : 0.11	g : 0.08	e : 0.07	c : 0.07	d : 0.05	i : 0.05	3 : 0.04	2 : 0.04	> : 0.02	] : 0.02	h : 0.02	5 : 0.02	= : 0.01	: : 0.01	b : 0.01	G : 0.01	

#score	1604.9061874511933
#seq	71
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_CDS_m1_run1.txt

#BEAR
f!!cccwwwwwwwwwwwwwwccc]ffff	chr11:47073914-47074154(+)$1	240	17	45	23.9441
hhhhhhhvvvvvvvvvvvvvhhhhhhhh	chr9:100777594-100777881(+)$1	287	183	211	22.4088
========ttttttttttt=========	chr16:19559190-19559430(+)$1	240	191	219	23.7807
cgggggggtttttttttttggggggg::	chr20:3804454-3804694(+)$1	240	43	71	21.4118
ffffff[attttttttttta]ffffff]	chr20:21349069-21349309(+)$1	240	157	185	23.3096
ggggggvvvvvvvvvvvvvggggggg]d	chr13:77595820-77596100(-)$1	280	175	203	24.9231
ii"""bbvvvvvvvvvvvvvbb333iii	chr10:93619162-93619402(+)$1	240	160	188	24.0473
"ffffffuuuuuuuuuuuuffffffccc	chr11:72553655-72553895(-)$1	240	88	116	23.7759
eee[cccuuuuuuuuuuuuccc]eeeee	chr4:122739868-122740108(-)$1	240	153	181	24.3824
!eeeeevvvvvvvvvvvvveeeee333b	chr4:113570675-113570915(+)$1	240	125	153	24.4419
'eeeeevvvvvvvvvvvvveeeee====	chr3:184049448-184049689(+)$1	241	100	128	23.8614
[eeeeexxxxxxxxxxxxxxxeeeee]b	chr17:3919610-3919850(-)$1	240	74	102	19.6362
bb[cccwwwwwwwwwwwwwwccc]bb::	chr14:64518551-64518831(+)$1	280	183	211	21.3504
fff[ccctttttttttttccc]ffffff	chr3:133327639-133327879(-)$1	240	163	191	22.4859
c!!bbyyyyyyyyyyyyyyyybb22ccc	chrX:107331940-107332183(-)$1	243	3	31	21.7022
ffffffwwwwwwwwwwwwwwffffff::	chr13:21956998-21957238(-)$1	240	198	226	21.8498
eeeeeeeettttttttttteeeee4444	chr1:31418144-31418384(-)$1	240	81	109	22.4814
gggggyyyyyyyyyyyyyyyyggggggg	chr3:130449144-130449384(-)$1	240	70	98	23.7494
gggggyyyyyyyyyyyyyyyyggggggg	chr5:68396568-68396808(+)$1	240	93	121	23.7494
hhhhhyyyyyyyyyyyyyyyyhhhhhhh	chr20:43108803-43109043(+)$1	240	124	152	21.6496
iiiiiyyyyyyyyyyyyyyyyiiiiiii	chr14:21969034-21969274(-)$1	240	83	111	23.7460
gg!!cccuuuuuuuuuuuuccc]ggggg	chr3:20156326-20156566(+)$1	240	99	127	25.2827
eeeeeyyyyyyyyyyyyyyyyeeeee66	chr1:231410881-231411121(+)$1	240	81	109	22.1688
dddd[bbvvvvvvvvvvvvvbbdddd]c	chr12:100453090-100453330(-)$1	240	12	40	22.7077
!eeeeewwwwwwwwwwwwwweeeeeccc	chr12:1372112-1372392(+)$1	280	198	226	24.1781
ggg!!bbwwwwwwwwwwwwwwbb]gggg	chr22:41922184-41922436(-)$1	252	171	199	23.4098
#eeeeexxxxxxxxxxxxxxxeeeee44	chr8:87439880-87440120(+)$1	240	189	217	19.6813
ggggg[auuuuuuuuuuuua]ggggggg	chr13:76179772-76180012(+)$1	240	184	212	25.7176
deeeeewwwwwwwwwwwwwweeeee]dd	chr5:176618847-176619087(+)$1	240	90	118	23.5905
f[fffffftttttttttttffffff333	chr19:2130337-2130581(-)$1	244	172	200	22.7205
hhhhhhhvvvvvvvvvvvvvhhhhhhhh	chr10:5777164-5777404(+)$1	240	146	174	22.4088
:eeeeevvvvvvvvvvvvveeeeebb[b	chr19:14574806-14575046(+)$1	240	35	63	22.1299
ffffffvvvvvvvvvvvvvffffff]gg	chr17:38290513-38290758(+)$1	245	13	41	23.9513
"""dddduuuuuuuuuuuudddd4444d	chr17:16062015-16062255(-)$1	240	205	233	22.7583
a[eeeeevvvvvvvvvvvvveeeee]a:	chr1:46826338-46826578(+)$1	240	161	189	23.6679
iiiiiyyyyyyyyyyyyyyyyiiiiiii	chr2:170753025-170753265(+)$1	240	196	224	23.7460
ggggggwwwwwwwwwwwwwwggggggg2	chr19:49463996-49464283(+)$1	287	174	202	24.7043
e!!ddddvvvvvvvvvvvvvdddd22ee	chr1:200635028-200635279(-)$1	251	45	73	22.8345
fffffyyyyyyyyyyyyyyyyffffff]	chr17:21102015-21102255(-)$1	240	77	105	22.6684
ffff[avvvvvvvvvvvvva]ffffff8	chr2:17851609-17851849(-)$1	240	82	110	24.0782
ffffffvvvvvvvvvvvvvffffffccc	chr5:37048631-37048871(+)$1	240	150	178	23.7996
hhhh!!auuuuuuuuuuuua22hhhhhh	chr3:39125603-39125843(+)$1	240	77	105	23.4159
gg"""bbuuuuuuuuuuuubbggggggg	chr8:117866554-117866794(-)$1	240	145	173	24.3215
eeee[bbvvvvvvvvvvvvvbb]eeeee	chr2:10188300-10188540(+)$1	240	197	225	23.6369
hhh!!bbtttttttttttbb]hhhhhhh	chr11:122928440-122928727(-)$1	287	54	82	21.1565
ccc[cccuuuuuuuuuuuuccc]ccc]c	chr12:995030-995270(+)$1	240	4	32	24.7169
agggggggtttttttttttggggggg]a	chr19:11141302-11141542(+)$1	240	159	187	23.3424
eee[cccuuuuuuuuuuuuccc]eeeee	chrX:99885722-99885962(-)$1	240	82	110	24.3824
c!!bbccctttttttttttccc]bb666	chr14:23528250-23528491(-)$1	241	183	211	21.1111
fff!!avvvvvvvvvvvvva22ffffff	chr2:169417693-169417933(+)$1	240	81	109	23.9136
!!eeeeevvvvvvvvvvvvveeeee22c	chr5:43295863-43296103(-)$1	240	205	233	24.4555
ggggggguuuuuuuuuuuuggggggg33	chr7:124475278-124475518(-)$1	240	65	93	25.2112
ffffffvvvvvvvvvvvvvffffff22h	chr15:56385572-56385812(-)$1	240	72	100	23.5311
dddbbyyyyyyyyyyyyyyyybb]dddd	chr3:46009979-46010219(-)$1	240	59	87	20.6620
!!eeeeevvvvvvvvvvvvveeeee22a	chr21:40571248-40571488(-)$1	240	48	76	24.4629
======wwwwwwwwwwwwww========	chr5:60786601-60786841(+)$1	240	35	63	24.9050
iiiiiiwwwwwwwwwwwwwwiiiiiiii	chr4:125590250-125590490(-)$1	240	71	99	24.8795
"""ddddvvvvvvvvvvvvvdddd4444	chrX:18341895-18342135(-)$1	240	28	56	23.2239
cc"""ccctttttttttttccc333ccc	chr19:9271188-9271428(+)$1	240	88	116	23.0215
#eeeeewwwwwwwwwwwwwweeeee333	chr14:70839687-70839936(-)$1	249	214	242	24.4949
========ttttttttttt=========	chr5:145872388-145872669(+)$1	281	58	86	23.7807
[ffffffvvvvvvvvvvvvvffffff22	chr10:27821368-27821608(+)$1	240	9	37	23.9123
bbbcccwwwwwwwwwwwwwwccc22bb]	chr6:35257975-35258215(+)$1	240	163	191	22.2956
hhhhhhhuuuuuuuuuuuuhhhhhhhh7	chr17:35557284-35557524(-)$1	240	52	80	21.6708

#otherMatches

#Seq PSSM
UUUGCAGUUUUAACAGUGUAUGCCAGGG	chr11:47073914-47074154(+)$1	240	17	45	23.9441
GCUGUUUAAAAAAAAAAAAAAGGUAGCU	chr9:100777594-100777881(+)$1	287	183	211	22.4088
UAGAUUUGAGAGGGAAAAAUAAAUCUAG	chr16:19559190-19559430(+)$1	240	191	219	23.7807
GACCUGCCCACUCUCCCCAGGCAGGUAG	chr20:3804454-3804694(+)$1	240	43	71	21.4118
AAGUAAGCUUUUACAAAUCGGUUAUUUU	chr20:21349069-21349309(+)$1	240	157	185	23.3096
UGAGGACUACAAAUGAGCAUUCUCAGAC	chr13:77595820-77596100(-)$1	280	175	203	24.9231
AAAAGCAAUCAAUAUGUAUAUGGAAUUG	chr10:93619162-93619402(+)$1	240	160	188	24.0473
UAUCUUGAACAAAGAAAACCAAGAUGAU	chr11:72553655-72553895(-)$1	240	88	116	23.7759
GGUAUGUAUUACGGUCUUCACACACCUA	chr4:122739868-122740108(-)$1	240	153	181	24.3824
ACAGUGGAGUACCUCAAAACACUGGAAU	chr4:113570675-113570915(+)$1	240	125	153	24.4419
ACGUUAGUUCGAGCCCUCAUGACGGCUG	chr3:184049448-184049689(+)$1	241	100	128	23.8614
GUCUGCUUCCCACCAGAUCCUGCAGAAA	chr17:3919610-3919850(-)$1	240	74	102	19.6362
UUGGAGGAUGGAAUAAAUAACUUGAAGA	chr14:64518551-64518831(+)$1	280	183	211	21.3504
GUUUGUAUCAAAUUAAUUUACUGACCUU	chr3:133327639-133327879(-)$1	240	163	191	22.4859
AUUUCGUAUUUUCAAACUAUAGAUUUGC	chrX:107331940-107332183(-)$1	243	3	31	21.7022
UGCUUUUCUAUAUUCAUCAUAAAGCAAA	chr13:21956998-21957238(-)$1	240	198	226	21.8498
CAUGUCUUGAAGUGUGUGAAAGAUCAGA	chr1:31418144-31418384(-)$1	240	81	109	22.4814
AUAAAUUUUCUUCCUUUUUAUUUUAUAG	chr3:130449144-130449384(-)$1	240	70	98	23.7494
UUCACUAAAUUUUUGAAGGCUGUGGGAC	chr5:68396568-68396808(+)$1	240	93	121	23.7494
CAGCUCCUCGUCAACUACCACAGCUGUA	chr20:43108803-43109043(+)$1	240	124	152	21.6496
AGUAUGUUCACUAUGAAAUUGAUGCUUG	chr14:21969034-21969274(-)$1	240	83	111	23.7460
GAUCAGGAUUUUCUCUCAGCCUCUUCCA	chr3:20156326-20156566(+)$1	240	99	127	25.2827
UCAGAUAAUUUGCAAGUACCUUUUGAGU	chr1:231410881-231411121(+)$1	240	81	109	22.1688
CUUCUAGUUUGUCAUUCCUUCUGAAGUG	chr12:100453090-100453330(-)$1	240	12	40	22.7077
AGGACCAAUGCUGAAAAACAGGUCUGCU	chr12:1372112-1372392(+)$1	280	198	226	24.1781
CUUGGGUGGUAAGUAGAGAGGACAGAGG	chr22:41922184-41922436(-)$1	252	171	199	23.4098
UAACAUAACUUCCUCCCUCAGGUGUUUC	chr8:87439880-87440120(+)$1	240	189	217	19.6813
UAAUGGAAACACCAAAAACUGUAUUAUU	chr13:76179772-76180012(+)$1	240	184	212	25.7176
CUGGGCAAAAUUCAAGAGACGCCCAUGG	chr5:176618847-176619087(+)$1	240	90	118	23.5905
CCGGUUUGUGGAUUUGAGUUAAGCCUCA	chr19:2130337-2130581(-)$1	244	172	200	22.7205
GAUAGGAAAAACCAAGAAGCUCCUAUUU	chr10:5777164-5777404(+)$1	240	146	174	22.4088
CCAGACACACCCUCCUCUCGUCUGCUGC	chr19:14574806-14575046(+)$1	240	35	63	22.1299
GCCAGGAAUUUUGAGCUACCCUGGUUGG	chr17:38290513-38290758(+)$1	245	13	41	23.9513
GCACAGGCCUUUAACCCCACUUGACGAU	chr17:16062015-16062255(-)$1	240	205	233	22.7583
CGUGAGUGACAGAUUUUUAAACUCAGGA	chr1:46826338-46826578(+)$1	240	161	189	23.6679
GCCUUAUUAAAAGUGAGCUACAAGGUAA	chr2:170753025-170753265(+)$1	240	196	224	23.7460
GGUGAGACUCCUCAAGCCUccucacccc	chr19:49463996-49464283(+)$1	287	174	202	24.7043
AGGUCUUAAAUCACAACUUGAAGAAAUC	chr1:200635028-200635279(-)$1	251	45	73	22.8345
CCUUUCCUGCCCCCUCCAUCAAAAGGGU	chr17:21102015-21102255(-)$1	240	77	105	22.6684
ACAGUGUGUUUUAUUCUUUCCCUGUGGU	chr2:17851609-17851849(-)$1	240	82	110	24.0782
GUGAAAAUAUAUUUUUAAAUUUCAUAGC	chr5:37048631-37048871(+)$1	240	150	178	23.7996
UGAAGAUGAAAUUAAGAAAAGAUUUAAA	chr3:39125603-39125843(+)$1	240	77	105	23.4159
GGAUAGCAAGACAAUUAGAGCCCAACUU	chr8:117866554-117866794(-)$1	240	145	173	24.3215
AGGGAGCCCUCCCUCCGCCUGCCCCCUG	chr2:10188300-10188540(+)$1	240	197	225	23.6369
AUUAACAUUAAAAGAACUUGCAGUAAUU	chr11:122928440-122928727(-)$1	287	54	82	21.1565
ACACCAGGCAUCCCAACUACUGCUGUUG	chr12:995030-995270(+)$1	240	4	32	24.7169
UCUGAGUACUUCAUCUUCCUGCUCAGCA	chr19:11141302-11141542(+)$1	240	159	187	23.3424
UCCUAUUUUAUUUCUAGCUGAUUGGAAU	chrX:99885722-99885962(-)$1	240	82	110	24.3824
UUAUGGCCACAGAGGGAUAGGCACAGUC	chr14:23528250-23528491(-)$1	241	183	211	21.1111
UUCGACAAAGACGCAAUCAGGAGAAGCC	chr2:169417693-169417933(+)$1	240	81	109	23.9136
GAAUAGAGAUAAAAAUAGUAUCUAUAGU	chr5:43295863-43296103(-)$1	240	205	233	24.4555
AAAUUUGCAAACUCUCGAACAAGUUUAA	chr7:124475278-124475518(-)$1	240	65	93	25.2112
GAUUUGAACACUUUAGACCCAAAUCUAC	chr15:56385572-56385812(-)$1	240	72	100	23.5311
CCCCCUAAACAACGAGGCAUUGGAGGGC	chr3:46009979-46010219(-)$1	240	59	87	20.6620
UGUGGCUGCCAAUAAAAUAAAGCUAAUG	chr21:40571248-40571488(-)$1	240	48	76	24.4629
CUAGUAUAGAUGAUGAAAACUGCUGGCA	chr5:60786601-60786841(+)$1	240	35	63	24.9050
AAAUUGGUCGAUCUCAACAGCAGUUUCU	chr4:125590250-125590490(-)$1	240	71	99	24.8795
GGGCCAGGUUACGGUUACGACUGGAUGG	chrX:18341895-18342135(-)$1	240	28	56	23.2239
GCCACCUCAUCGCACACAAGAGAACGCA	chr19:9271188-9271428(+)$1	240	88	116	23.0215
CGGCAACAACUUUGAAAAACUUGCUCUC	chr14:70839687-70839936(-)$1	249	214	242	24.4949
AGAUUGACUUGUCAAAUUUGUUGAUUUU	chr5:145872388-145872669(+)$1	281	58	86	23.7807
UAGUAUAUUGAAGGUCUAUUUAUACUUU	chr10:27821368-27821608(+)$1	240	9	37	23.9123
ACCACCGCUCAUCACUUAAAGGUAAGGU	chr6:35257975-35258215(+)$1	240	163	191	22.2956
AAUGGAAAUCUCAUCUAUCUUCUGUUUU	chr17:35557284-35557524(-)$1	240	52	80	21.6708

#DB
(..(((..............))).))))	chr11:47073914-47074154(+)$1	1	17	45	23.9441
(((((((.............))))))))	chr9:100777594-100777881(+)$1	1	183	211	22.4088
((((((((...........)))))))))	chr16:19559190-19559430(+)$1	1	191	219	23.7807
)(((((((...........)))))))..	chr20:3804454-3804694(+)$1	1	43	71	21.4118
((((((.(...........).)))))).	chr20:21349069-21349309(+)$1	1	157	185	23.3096
((((((.............))))))).)	chr13:77595820-77596100(-)$1	1	175	203	24.9231
((...((.............))...)))	chr10:93619162-93619402(+)$1	1	160	188	24.0473
.((((((............)))))))))	chr11:72553655-72553895(-)$1	1	88	116	23.7759
(((.(((............))).)))))	chr4:122739868-122740108(-)$1	1	153	181	24.3824
.(((((.............)))))...)	chr4:113570675-113570915(+)$1	1	125	153	24.4419
.(((((.............)))))))))	chr3:184049448-184049689(+)$1	1	100	128	23.8614
.(((((...............))))).)	chr17:3919610-3919850(-)$1	1	74	102	19.6362
((.(((..............))).))..	chr14:64518551-64518831(+)$1	1	183	211	21.3504
(((.(((...........))).))))))	chr3:133327639-133327879(-)$1	1	163	191	22.4859
(..((................))..)))	chrX:107331940-107332183(-)$1	1	3	31	21.7022
((((((..............))))))..	chr13:21956998-21957238(-)$1	1	198	226	21.8498
((((((((...........)))))....	chr1:31418144-31418384(-)$1	1	81	109	22.4814
(((((................)))))))	chr3:130449144-130449384(-)$1	1	70	98	23.7494
(((((................)))))))	chr5:68396568-68396808(+)$1	1	93	121	23.7494
(((((................)))))))	chr20:43108803-43109043(+)$1	1	124	152	21.6496
(((((................)))))))	chr14:21969034-21969274(-)$1	1	83	111	23.7460
((..(((............))).)))))	chr3:20156326-20156566(+)$1	1	99	127	25.2827
(((((................)))))..	chr1:231410881-231411121(+)$1	1	81	109	22.1688
((((.((.............)))))).)	chr12:100453090-100453330(-)$1	1	12	40	22.7077
.(((((..............))))))))	chr12:1372112-1372392(+)$1	1	198	226	24.1781
(((..((..............)).))))	chr22:41922184-41922436(-)$1	1	171	199	23.4098
.(((((...............)))))..	chr8:87439880-87440120(+)$1	1	189	217	19.6813
(((((.(............).)))))))	chr13:76179772-76180012(+)$1	1	184	212	25.7176
((((((..............))))).))	chr5:176618847-176619087(+)$1	1	90	118	23.5905
(.((((((...........))))))...	chr19:2130337-2130581(-)$1	1	172	200	22.7205
(((((((.............))))))))	chr10:5777164-5777404(+)$1	1	146	174	22.4088
.(((((.............)))))((.(	chr19:14574806-14575046(+)$1	1	35	63	22.1299
((((((.............)))))).))	chr17:38290513-38290758(+)$1	1	13	41	23.9513
...((((............))))....)	chr17:16062015-16062255(-)$1	1	205	233	22.7583
(.(((((.............))))).).	chr1:46826338-46826578(+)$1	1	161	189	23.6679
(((((................)))))))	chr2:170753025-170753265(+)$1	1	196	224	23.7460
((((((..............))))))).	chr19:49463996-49464283(+)$1	1	174	202	24.7043
(..((((.............))))..))	chr1:200635028-200635279(-)$1	1	45	73	22.8345
(((((................)))))).	chr17:21102015-21102255(-)$1	1	77	105	22.6684
((((.(.............).)))))).	chr2:17851609-17851849(-)$1	1	82	110	24.0782
((((((.............))))))(((	chr5:37048631-37048871(+)$1	1	150	178	23.7996
((((..(............)..))))))	chr3:39125603-39125843(+)$1	1	77	105	23.4159
((...((............)))))))))	chr8:117866554-117866794(-)$1	1	145	173	24.3215
((((.((.............)).)))))	chr2:10188300-10188540(+)$1	1	197	225	23.6369
(((..((...........)).)))))))	chr11:122928440-122928727(-)$1	1	54	82	21.1565
(((.(((............))).))).)	chr12:995030-995270(+)$1	1	4	32	24.7169
((((((((...........))))))).)	chr19:11141302-11141542(+)$1	1	159	187	23.3424
(((.(((............))).)))))	chrX:99885722-99885962(-)$1	1	82	110	24.3824
(..(((((...........))).))...	chr14:23528250-23528491(-)$1	1	183	211	21.1111
(((..(.............)..))))))	chr2:169417693-169417933(+)$1	1	81	109	23.9136
..(((((.............)))))..)	chr5:43295863-43296103(-)$1	1	205	233	24.4555
(((((((............)))))))..	chr7:124475278-124475518(-)$1	1	65	93	25.2112
((((((.............))))))..)	chr15:56385572-56385812(-)$1	1	72	100	23.5311
(((((................)).))))	chr3:46009979-46010219(-)$1	1	59	87	20.6620
..(((((.............)))))..)	chr21:40571248-40571488(-)$1	1	48	76	24.4629
((((((..............))))))))	chr5:60786601-60786841(+)$1	1	35	63	24.9050
((((((..............))))))))	chr4:125590250-125590490(-)$1	1	71	99	24.8795
...((((.............))))....	chrX:18341895-18342135(-)$1	1	28	56	23.2239
((...(((...........)))...)))	chr19:9271188-9271428(+)$1	1	88	116	23.0215
.(((((..............)))))...	chr14:70839687-70839936(-)$1	1	214	242	24.4949
((((((((...........)))))))))	chr5:145872388-145872669(+)$1	1	58	86	23.7807
.((((((.............))))))..	chr10:27821368-27821608(+)$1	1	9	37	23.9123
((((((..............)))..)).	chr6:35257975-35258215(+)$1	1	163	191	22.2956
(((((((............)))))))).	chr17:35557284-35557524(-)$1	1	52	80	21.6708

#PSSM
f : 0.17	g : 0.14	h : 0.09	e : 0.09	c : 0.07	i : 0.06	! : 0.06	= : 0.04	" : 0.04	d : 0.04	[ : 0.03	b : 0.03	# : 0.03	a : 0.03	' : 0.01	: : 0.01	
e : 0.20	g : 0.17	f : 0.17	! : 0.09	h : 0.09	i : 0.06	= : 0.04	b : 0.03	d : 0.03	[ : 0.03	" : 0.03	c : 0.03	
e : 0.25	f : 0.18	g : 0.14	h : 0.09	! : 0.07	" : 0.07	= : 0.04	i : 0.04	d : 0.03	[ : 0.01	c : 0.01	b : 0.01	
e : 0.21	f : 0.15	g : 0.12	h : 0.07	[ : 0.06	! : 0.06	d : 0.06	c : 0.04	= : 0.04	" : 0.04	b : 0.04	i : 0.04	
e : 0.20	f : 0.14	c : 0.12	g : 0.12	h : 0.06	! : 0.06	= : 0.04	" : 0.04	b : 0.04	i : 0.04	[ : 0.04	d : 0.04	
e : 0.18	c : 0.15	y : 0.14	f : 0.12	b : 0.09	g : 0.07	h : 0.04	= : 0.04	d : 0.04	a : 0.03	[ : 0.01	! : 0.01	i : 0.01	
w : 0.15	v : 0.14	y : 0.14	c : 0.10	b : 0.09	e : 0.06	h : 0.04	g : 0.04	f : 0.04	d : 0.04	= : 0.03	x : 0.03	a : 0.03	[ : 0.01	
v : 0.31	w : 0.17	u : 0.17	y : 0.14	= : 0.03	g : 0.03	x : 0.03	t : 0.03	c : 0.03	a : 0.01	e : 0.01	f : 0.01	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	t : 0.17	u : 0.17	y : 0.14	x : 0.03	
v : 0.31	w : 0.17	u : 0.17	t : 0.14	y : 0.14	x : 0.03	c : 0.01	b : 0.01	
w : 0.17	v : 0.17	y : 0.14	c : 0.10	a : 0.07	f : 0.07	g : 0.06	e : 0.06	= : 0.03	x : 0.03	b : 0.03	d : 0.01	h : 0.01	
c : 0.15	e : 0.15	y : 0.14	f : 0.10	g : 0.07	] : 0.06	b : 0.06	h : 0.04	= : 0.04	d : 0.04	x : 0.03	2 : 0.03	w : 0.01	i : 0.01	
e : 0.20	f : 0.15	c : 0.14	g : 0.14	b : 0.09	h : 0.07	= : 0.04	i : 0.04	d : 0.04	2 : 0.03	] : 0.01	
e : 0.20	f : 0.18	g : 0.14	h : 0.09	] : 0.09	d : 0.06	c : 0.04	= : 0.04	b : 0.04	i : 0.04	3 : 0.03	
e : 0.25	f : 0.18	g : 0.15	h : 0.09	] : 0.06	= : 0.04	i : 0.04	d : 0.04	3 : 0.03	2 : 0.03	4 : 0.01	c : 0.01	b : 0.01	
f : 0.20	e : 0.18	g : 0.17	h : 0.09	= : 0.06	3 : 0.04	b : 0.04	2 : 0.04	4 : 0.04	i : 0.04	d : 0.03	c : 0.01	
g : 0.17	f : 0.12	h : 0.09	c : 0.09	e : 0.09	= : 0.06	i : 0.06	2 : 0.06	3 : 0.04	b : 0.04	4 : 0.04	] : 0.04	d : 0.03	6 : 0.01	
g : 0.12	f : 0.09	h : 0.09	] : 0.07	c : 0.07	= : 0.06	i : 0.06	e : 0.06	3 : 0.06	4 : 0.06	2 : 0.06	: : 0.04	6 : 0.03	d : 0.03	[ : 0.01	a : 0.01	b : 0.01	
c : 0.12	g : 0.10	h : 0.09	= : 0.06	: : 0.06	d : 0.06	i : 0.06	e : 0.06	f : 0.04	] : 0.04	b : 0.04	4 : 0.04	3 : 0.04	6 : 0.03	2 : 0.03	a : 0.03	8 : 0.01	7 : 0.01	

#score	1489.398707768412
#seq	64
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_UTR_m3_run1.txt

#BEAR
ddddqqqqqqqqdddd:::	chr2:30862921-30863145(+)$1	224	40	59	12.7139
[cccqqqqqqqqccc]bb:	chr17:53038484-53038710(-)$1	226	138	157	13.1454
gg[aqqqqqqqqa]ggggg	chr4:76567882-76568104(-)$1	222	64	83	13.2784
"cccqqqqqqqqccc22==	chr5:143538113-143538339(-)$1	226	173	192	13.6482
ddddqqqqqqqqdddd22i	chr7:17831479-17831700(-)$1	221	154	173	14.5022
eeeeqqqqqqqqeeeee::	chr13:20397776-20397998(-)$1	222	58	77	13.2223
ee[aqqqqqqqqa]eeeee	chr2:44547467-44547690(-)$1	223	182	201	13.4725
ddddqqqqqqqqdddd777	chr1:6284590-6284813(-)$1	223	111	130	13.5243
eeeeqqqqqqqqeeeee::	chr3:120113809-120114045(-)$1	236	9	28	13.2223
"cccqqqqqqqqccc333d	chr3:169711532-169711764(+)$1	232	126	145	14.2157
eeeeqqqqqqqqeeeee::	chr15:44096950-44097172(-)$1	222	155	174	13.2223
ddddqqqqqqqqdddd:ff	chr1:220197639-220197858(-)$1	219	6	25	13.5348
ggggqqqqqqqqggggggg	chr2:153616664-153616888(+)$1	224	180	199	13.5604
ddddqqqqqqqqdddd:::	chr1:115260173-115260428(-)$1	255	32	51	12.7139
ddddqqqqqqqqdddd::d	chr6:149980073-149980303(-)$1	230	122	141	13.1357
!!bbqqqqqqqqbb333a]	chr10:119037299-119037526(-)$1	227	23	42	12.7611
ggggqqqqqqqqggggggg	chr21:18966144-18966368(-)$1	224	181	200	13.5604
ddddqqqqqqqqdddd333	chr16:89353755-89353973(-)$1	218	10	29	15.0739
ddddqqqqqqqqddddbb[	chr15:35272488-35272713(-)$1	225	73	92	13.9311
ddddqqqqqqqqddddccc	chrX:102471873-102472101(+)$1	228	140	159	14.4483
"cccqqqqqqqqccc]hhh	chr4:120980717-120980939(-)$1	222	63	82	12.9980
eeeeqqqqqqqqeeeee::	chr19:44680608-44680842(+)$1	234	85	104	13.2223
ddddqqqqqqqqdddd22b	chr1:235274456-235274679(-)$1	223	30	49	14.4036
"cccqqqqqqqqccc333d	chr7:99488451-99488682(-)$1	231	92	111	14.2157
eeeeqqqqqqqqeeeee33	chr12:54680487-54680708(+)$1	221	121	140	14.6740
eeeeqqqqqqqqeeeee33	chr1:159997759-159997993(-)$1	234	53	72	14.6740
ddddqqqqqqqqdddd::E	chr12:111158714-111158938(-)$1	224	182	201	12.5004
[cccqqqqqqqqccceeee	chr8:11667167-11667400(+)$1	233	79	98	13.8663
ffffqqqqqqqqffffff]	chr20:25427448-25427705(+)$1	257	43	62	12.8541
eeeeqqqqqqqqeeeee::	chr6:43581737-43581960(+)$1	223	109	128	13.2223
ddddqqqqqqqqdddd333	chr17:27587419-27587656(-)$1	237	25	44	15.0739
ggggqqqqqqqqggggggg	chr5:179156646-179156870(+)$1	224	80	99	13.5604
ddddqqqqqqqqdddd:bb	chrX:24004530-24004764(-)$1	234	146	165	13.5221
ddddqqqqqqqqdddd:::	chr12:72180226-72180452(+)$1	226	26	45	12.7139
ggggqqqqqqqqggggggg	chrX:68380857-68381081(-)$1	224	95	114	13.5604
[cccqqqqqqqqccc]ddd	chr18:72909611-72909843(-)$1	232	8	27	13.5681
====qqqqqqqq=======	chr4:52781616-52781842(+)$1	226	8	27	13.5769
iiiiqqqqqqqqiiiiiii	chr12:93862920-93863142(+)$1	222	197	216	13.3524
ffffqqqqqqqqffffffb	chr2:85547698-85547921(-)$1	223	111	130	12.6273
ccccqqqqqqqqccc]ccc	chr12:79984187-79984409(-)$1	222	88	107	13.8714
eeeeqqqqqqqqeeeee]c	chr5:175953662-175953885(-)$1	223	56	75	14.4270
ecccqqqqqqqqccc22ee	chrX:24002875-24003097(-)$1	222	71	90	13.6187
ffffqqqqqqqqffffff]	chr12:54680199-54680419(+)$1	220	196	215	12.8541
ddddqqqqqqqqdddd]ee	chr11:33001533-33001753(+)$1	220	113	132	14.3744
ddddqqqqqqqqdddd333	chr1:93308519-93308740(+)$1	221	126	145	15.0739
eeeeqqqqqqqqeeeee99	chr19:44679880-44680105(+)$1	225	108	127	13.6497
eeeeqqqqqqqqeeeeegg	chr1:227505053-227505283(-)$1	230	140	159	14.2690
ffffqqqqqqqqffffff:	chr3:142169627-142169850(-)$1	223	93	112	12.2414
eeeeqqqqqqqqeeeee66	chr9:133513171-133513393(+)$1	222	87	106	13.8780
:cccqqqqqqqqcccccc!	chr19:5916044-5916274(-)$1	230	9	28	12.5841
e[bbqqqqqqqqbb]eeee	chr1:198289382-198289612(+)$1	230	133	152	12.4085
ddddqqqqqqqqdddd:::	chr6:168370735-168370958(+)$1	223	86	105	12.7139
[cccqqqqqqqqccc]ccc	chr10:59952985-59953211(-)$1	226	169	188	13.9514
ggggqqqqqqqqggggggg	chr5:10264889-10265122(+)$1	233	58	77	13.5604
ddddqqqqqqqqdddd333	chr3:179045279-179045501(+)$1	222	156	175	15.0739
eeeeqqqqqqqqeeeee]e	chr19:33077004-33077227(+)$1	223	154	173	14.3354
eeeeqqqqqqqqeeeee>>	chrX:49031260-49031495(+)$1	235	165	184	14.3176
fcccqqqqqqqqccc]fff	chr6:19839745-19839967(+)$1	222	54	73	13.5517
eeeeqqqqqqqqeeeee]e	chr7:19737549-19737771(-)$1	222	147	166	14.3354
"cccqqqqqqqqccc333d	chr22:19956377-19956604(+)$1	227	9	28	14.2157
ddddqqqqqqqqddddbb]	chr11:85372547-85372775(-)$1	228	168	187	14.2550
eeeeqqqqqqqqeeeee::	chr4:30732450-30732671(+)$1	221	14	33	13.2223
ddddqqqqqqqqdddd:FF	chr1:115249041-115249265(-)$1	224	146	165	13.2228
ddddqqqqqqqqdddd22a	chr15:25583977-25584223(-)$1	246	48	67	14.5907
Fcccqqqqqqqqcccffff	chr22:40731632-40731859(+)$1	227	18	37	13.0989
d[bbqqqqqqqqbb]dddd	chr1:23636308-23636528(-)$1	220	84	103	12.1559
ddddqqqqqqqqddddddd	chr16:24801366-24801586(+)$1	220	186	205	14.0649
eeeeqqqqqqqqeeeee22	chr5:78982295-78982518(+)$1	223	134	153	14.2278
ffffqqqqqqqqffffff]	chr5:134193829-134194059(+)$1	230	18	37	12.8541
ddddqqqqqqqqdddd]dd	chr5:60455144-60455370(-)$1	226	127	146	14.3176
ffffqqqqqqqqffffffd	chr22:38363654-38363879(+)$1	225	178	197	12.6632

#otherMatches

#Seq PSSM
UUUCAUCUUUUCGAAACCC	chr2:30862921-30863145(+)$1	224	40	59	12.7139
CCAGUAUUCAUCCUGUCCU	chr17:53038484-53038710(-)$1	226	138	157	13.1454
AAGUAUUCUUUGAGUUUCC	chr4:76567882-76568104(-)$1	222	64	83	13.2784
UCAGUAUAGUUUUUGUUAA	chr5:143538113-143538339(-)$1	226	173	192	13.6482
GAAGAGUUUAUAUUUCAGA	chr7:17831479-17831700(-)$1	221	154	173	14.5022
AUUGAUCAAUACCAGUUUG	chr13:20397776-20397998(-)$1	222	58	77	13.2223
AACCACGAUAAAGAUUCUG	chr2:44547467-44547690(-)$1	223	182	201	13.4725
UUUCAUUUAACCGAAAAAC	chr1:6284590-6284813(-)$1	223	111	130	13.5243
UGUUGUGCCAAAAAUAGAA	chr3:120113809-120114045(-)$1	236	9	28	13.2223
AUUAAGACCAUGUAAGGGU	chr3:169711532-169711764(+)$1	232	126	145	14.2157
CCCAUAUUUACUUGGGACU	chr15:44096950-44097172(-)$1	222	155	174	13.2223
UGCACGAAAAAAUGCAAAA	chr1:220197639-220197858(-)$1	219	6	25	13.5348
UAUUUAAUUUUUGAUAUUC	chr2:153616664-153616888(+)$1	224	180	199	13.5604
GGCAAGAUGUUCUGCCUUA	chr1:115260173-115260428(-)$1	255	32	51	12.7139
UUCUUCCAGUAUAGAAUCU	chr6:149980073-149980303(-)$1	230	122	141	13.1357
UUGCUUUUCUCUGCUUUCG	chr10:119037299-119037526(-)$1	227	23	42	12.7611
GUUUUUAAUAUUGGACUUG	chr21:18966144-18966368(-)$1	224	181	200	13.5604
CUGCAGGGGAGGGCAGGUG	chr16:89353755-89353973(-)$1	218	10	29	15.0739
AGGAUUUUUUUUUUCUCCC	chr15:35272488-35272713(-)$1	225	73	92	13.9311
guaccaaaaucagugccau	chrX:102471873-102472101(+)$1	228	140	159	14.4483
GUCUAAAUAUUCAGAAUCU	chr4:120980717-120980939(-)$1	222	63	82	12.9980
GGCUUCAUUUGUAGCUCAA	chr19:44680608-44680842(+)$1	234	85	104	13.2223
ACGUGAGAGAAUGCGUCUG	chr1:235274456-235274679(-)$1	223	30	49	14.4036
aagUUAUGCACUACUAACA	chr7:99488451-99488682(-)$1	231	92	111	14.2157
UAAUCUCAUCCAAUUGCAA	chr12:54680487-54680708(+)$1	221	121	140	14.6740
GUGGCUUACUCUUCAUACU	chr1:159997759-159997993(-)$1	234	53	72	14.6740
CAUUUUUGAUUUAGUGAAU	chr12:111158714-111158938(-)$1	224	182	201	12.5004
UGGAAAAGAAGGUCCCGCU	chr8:11667167-11667400(+)$1	233	79	98	13.8663
uuuaaauuuugaugaaauc	chr20:25427448-25427705(+)$1	257	43	62	12.8541
CUCUUUACCAACAGAGUAU	chr6:43581737-43581960(+)$1	223	109	128	13.2223
AUGAUUUAUCUUUUGUAAU	chr17:27587419-27587656(-)$1	237	25	44	15.0739
AGUACAGAAAAAUACUUUG	chr5:179156646-179156870(+)$1	224	80	99	13.5604
GUUAAGCAAGAAUAACCUG	chrX:24004530-24004764(-)$1	234	146	165	13.5221
ACAGGCCCGUAACUGUCUA	chr12:72180226-72180452(+)$1	226	26	45	12.7139
GAUUGCAUUAAAAAUCAUA	chrX:68380857-68381081(-)$1	224	95	114	13.5604
UGGACAGUAAUUUCCUAGG	chr18:72909611-72909843(-)$1	232	8	27	13.5681
UGGCAAGCAACAGCUAUUA	chr4:52781616-52781842(+)$1	226	8	27	13.5769
AUUUCCAGUCCAAAGUAAG	chr12:93862920-93863142(+)$1	222	197	216	13.3524
UUCUUCAUCCUCGGAGUGA	chr2:85547698-85547921(-)$1	223	111	130	12.6273
GGAACAUUUCAUUUCACUU	chr12:79984187-79984409(-)$1	222	88	107	13.8714
UUUUUUUAAAAUGAAAGUU	chr5:175953662-175953885(-)$1	223	56	75	14.4270
UUACUAGAAUUUGUGAAAU	chrX:24002875-24003097(-)$1	222	71	90	13.6187
AGAUGGGACUUGGUCUUAG	chr12:54680199-54680419(+)$1	220	196	215	12.8541
UUAUAAGUGACAAUAAUUG	chr11:33001533-33001753(+)$1	220	113	132	14.3744
GUUUAUGGAAUGAAGCUUU	chr1:93308519-93308740(+)$1	221	126	145	15.0739
AUAAAAAAUAAAUUAUGUC	chr19:44679880-44680105(+)$1	225	108	127	13.6497
UAUUCUUUUAAAAAUGCAU	chr1:227505053-227505283(-)$1	230	140	159	14.2690
UGAGCUGCUAUUUUCACCA	chr3:142169627-142169850(-)$1	223	93	112	12.2414
AUAAAAAUGUAGUUAUAAC	chr9:133513171-133513393(+)$1	222	87	106	13.8780
AAGCCUUAGCCAGCUAGUG	chr19:5916044-5916274(-)$1	230	9	28	12.5841
AUUUUAACUCAUAAUUGUA	chr1:198289382-198289612(+)$1	230	133	152	12.4085
AAACACUGUCUAGUUUCUU	chr6:168370735-168370958(+)$1	223	86	105	12.7139
CGUCUGUAUUUUGAUUGAG	chr10:59952985-59953211(-)$1	226	169	188	13.9514
AUGUCUCGUGAUGCAUCUA	chr5:10264889-10265122(+)$1	233	58	77	13.5604
GAAACUAAUUAAUUUUGUA	chr3:179045279-179045501(+)$1	222	156	175	15.0739
AGGUGCUAAGAUGCCUUGC	chr19:33077004-33077227(+)$1	223	154	173	14.3354
UUGUUAAAAUAUACGAUAA	chrX:49031260-49031495(+)$1	235	165	184	14.3176
UCAAUUUUUGUUUUGAAGC	chr6:19839745-19839967(+)$1	222	54	73	13.5517
AAUACAAUAUUAUAUUACU	chr7:19737549-19737771(-)$1	222	147	166	14.3354
UGCGCCCUGACAUGCUAAC	chr22:19956377-19956604(+)$1	227	9	28	14.2157
UUAUUUGAAAUUGUGGGCU	chr11:85372547-85372775(-)$1	228	168	187	14.2550
UCCGAAACCUGCUGGAGCC	chr4:30732450-30732671(+)$1	221	14	33	13.2223
AGAUGUUGAUAAAUCUAAG	chr1:115249041-115249265(-)$1	224	146	165	13.2228
CAGUACAAAAAGGCUGUAA	chr15:25583977-25584223(-)$1	246	48	67	14.5907
CAGCUUAUuuuuguuuuug	chr22:40731632-40731859(+)$1	227	18	37	13.0989
CUGUGUUUUUAAAUUGUUA	chr1:23636308-23636528(-)$1	220	84	103	12.1559
UGGAGACAAAUGUUCAGGC	chr16:24801366-24801586(+)$1	220	186	205	14.0649
GUAUGAUGUCAAAUGCAAU	chr5:78982295-78982518(+)$1	223	134	153	14.2278
AAUGGAUAACAUCAUUUAG	chr5:134193829-134194059(+)$1	230	18	37	12.8541
AGUACUUCUAUUUGCUGCA	chr5:60455144-60455370(-)$1	226	127	146	14.3176
AAUGUCACCACCUGUUGCU	chr22:38363654-38363879(+)$1	225	178	197	12.6632

#DB
((((........))))...	chr2:30862921-30863145(+)$1	1	40	59	12.7139
.(((........))).)).	chr17:53038484-53038710(-)$1	1	138	157	13.1454
((.(........).)))))	chr4:76567882-76568104(-)$1	1	64	83	13.2784
.(((........)))..))	chr5:143538113-143538339(-)$1	1	173	192	13.6482
((((........))))..)	chr7:17831479-17831700(-)$1	1	154	173	14.5022
((((........)))))..	chr13:20397776-20397998(-)$1	1	58	77	13.2223
((.(........).)))))	chr2:44547467-44547690(-)$1	1	182	201	13.4725
((((........))))...	chr1:6284590-6284813(-)$1	1	111	130	13.5243
((((........)))))..	chr3:120113809-120114045(-)$1	1	9	28	13.2223
.(((........)))...)	chr3:169711532-169711764(+)$1	1	126	145	14.2157
((((........)))))..	chr15:44096950-44097172(-)$1	1	155	174	13.2223
((((........)))).((	chr1:220197639-220197858(-)$1	1	6	25	13.5348
((((........)))))))	chr2:153616664-153616888(+)$1	1	180	199	13.5604
((((........))))...	chr1:115260173-115260428(-)$1	1	32	51	12.7139
((((........))))..(	chr6:149980073-149980303(-)$1	1	122	141	13.1357
..((........))...).	chr10:119037299-119037526(-)$1	1	23	42	12.7611
((((........)))))))	chr21:18966144-18966368(-)$1	1	181	200	13.5604
((((........))))...	chr16:89353755-89353973(-)$1	1	10	29	15.0739
((((........))))((.	chr15:35272488-35272713(-)$1	1	73	92	13.9311
((((........)))))))	chrX:102471873-102472101(+)$1	1	140	159	14.4483
.(((........))).)))	chr4:120980717-120980939(-)$1	1	63	82	12.9980
((((........)))))..	chr19:44680608-44680842(+)$1	1	85	104	13.2223
((((........))))..)	chr1:235274456-235274679(-)$1	1	30	49	14.4036
.(((........)))...)	chr7:99488451-99488682(-)$1	1	92	111	14.2157
((((........)))))..	chr12:54680487-54680708(+)$1	1	121	140	14.6740
((((........)))))..	chr1:159997759-159997993(-)$1	1	53	72	14.6740
((((........))))..)	chr12:111158714-111158938(-)$1	1	182	201	12.5004
.(((........)))))))	chr8:11667167-11667400(+)$1	1	79	98	13.8663
((((........)))))).	chr20:25427448-25427705(+)$1	1	43	62	12.8541
((((........)))))..	chr6:43581737-43581960(+)$1	1	109	128	13.2223
((((........))))...	chr17:27587419-27587656(-)$1	1	25	44	15.0739
((((........)))))))	chr5:179156646-179156870(+)$1	1	80	99	13.5604
((((........)))).((	chrX:24004530-24004764(-)$1	1	146	165	13.5221
((((........))))...	chr12:72180226-72180452(+)$1	1	26	45	12.7139
((((........)))))))	chrX:68380857-68381081(-)$1	1	95	114	13.5604
.(((........))).)))	chr18:72909611-72909843(-)$1	1	8	27	13.5681
((((........)))))))	chr4:52781616-52781842(+)$1	1	8	27	13.5769
((((........)))))))	chr12:93862920-93863142(+)$1	1	197	216	13.3524
((((........))))))(	chr2:85547698-85547921(-)$1	1	111	130	12.6273
((((........))).)))	chr12:79984187-79984409(-)$1	1	88	107	13.8714
((((........))))).)	chr5:175953662-175953885(-)$1	1	56	75	14.4270
((((........)))..))	chrX:24002875-24003097(-)$1	1	71	90	13.6187
((((........)))))).	chr12:54680199-54680419(+)$1	1	196	215	12.8541
((((........)))).))	chr11:33001533-33001753(+)$1	1	113	132	14.3744
((((........))))...	chr1:93308519-93308740(+)$1	1	126	145	15.0739
((((........)))))..	chr19:44679880-44680105(+)$1	1	108	127	13.6497
((((........)))))))	chr1:227505053-227505283(-)$1	1	140	159	14.2690
((((........)))))).	chr3:142169627-142169850(-)$1	1	93	112	12.2414
((((........)))))..	chr9:133513171-133513393(+)$1	1	87	106	13.8780
.(((........)))(((.	chr19:5916044-5916274(-)$1	1	9	28	12.5841
(.((........)).))))	chr1:198289382-198289612(+)$1	1	133	152	12.4085
((((........))))...	chr6:168370735-168370958(+)$1	1	86	105	12.7139
.(((........))).)))	chr10:59952985-59953211(-)$1	1	169	188	13.9514
((((........)))))))	chr5:10264889-10265122(+)$1	1	58	77	13.5604
((((........))))...	chr3:179045279-179045501(+)$1	1	156	175	15.0739
((((........))))).)	chr19:33077004-33077227(+)$1	1	154	173	14.3354
((((........)))))..	chrX:49031260-49031495(+)$1	1	165	184	14.3176
((((........))).)))	chr6:19839745-19839967(+)$1	1	54	73	13.5517
((((........))))).)	chr7:19737549-19737771(-)$1	1	147	166	14.3354
.(((........)))...)	chr22:19956377-19956604(+)$1	1	9	28	14.2157
((((........)))))).	chr11:85372547-85372775(-)$1	1	168	187	14.2550
((((........)))))..	chr4:30732450-30732671(+)$1	1	14	33	13.2223
((((........)))).))	chr1:115249041-115249265(-)$1	1	146	165	13.2228
((((........))))..)	chr15:25583977-25584223(-)$1	1	48	67	14.5907
((((........)))((((	chr22:40731632-40731859(+)$1	1	18	37	13.0989
(.((........)).))))	chr1:23636308-23636528(-)$1	1	84	103	12.1559
((((........))))(((	chr16:24801366-24801586(+)$1	1	186	205	14.0649
((((........)))))..	chr5:78982295-78982518(+)$1	1	134	153	14.2278
((((........)))))).	chr5:134193829-134194059(+)$1	1	18	37	12.8541
((((........)))).))	chr5:60455144-60455370(-)$1	1	127	146	14.3176
((((........))))))(	chr22:38363654-38363879(+)$1	1	178	197	12.6632

#PSSM
d : 0.33	e : 0.26	f : 0.09	g : 0.08	" : 0.07	[ : 0.05	! : 0.01	= : 0.01	i : 0.01	c : 0.01	: : 0.01	F : 0.01	
d : 0.32	e : 0.23	c : 0.19	g : 0.08	f : 0.08	[ : 0.02	! : 0.01	= : 0.01	i : 0.01	
d : 0.32	e : 0.22	c : 0.19	f : 0.08	g : 0.07	b : 0.04	[ : 0.02	= : 0.01	i : 0.01	
d : 0.32	e : 0.22	c : 0.19	f : 0.08	g : 0.07	b : 0.04	a : 0.02	= : 0.01	i : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
d : 0.32	e : 0.22	c : 0.19	f : 0.08	g : 0.07	b : 0.04	a : 0.02	= : 0.01	i : 0.01	
d : 0.32	e : 0.22	c : 0.19	f : 0.08	g : 0.07	b : 0.04	] : 0.02	= : 0.01	i : 0.01	
d : 0.32	e : 0.23	c : 0.19	g : 0.08	f : 0.08	] : 0.02	3 : 0.01	= : 0.01	i : 0.01	
d : 0.33	e : 0.26	f : 0.09	] : 0.08	g : 0.08	3 : 0.05	2 : 0.02	= : 0.01	i : 0.01	c : 0.01	
e : 0.26	: : 0.12	3 : 0.11	f : 0.11	g : 0.08	2 : 0.07	c : 0.05	b : 0.04	d : 0.04	] : 0.02	7 : 0.01	h : 0.01	= : 0.01	i : 0.01	
: : 0.16	3 : 0.12	f : 0.12	g : 0.09	e : 0.07	b : 0.05	2 : 0.05	c : 0.05	d : 0.05	] : 0.04	= : 0.02	7 : 0.01	a : 0.01	h : 0.01	i : 0.01	9 : 0.01	6 : 0.01	> : 0.01	F : 0.01	
: : 0.16	d : 0.12	g : 0.09	e : 0.09	3 : 0.08	] : 0.07	c : 0.05	f : 0.04	b : 0.04	= : 0.02	i : 0.02	7 : 0.01	[ : 0.01	h : 0.01	E : 0.01	9 : 0.01	6 : 0.01	! : 0.01	> : 0.01	F : 0.01	a : 0.01	2 : 0.01	

#score	967.0555971453723
#seq	71
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_UTR_m3_run2.txt

#BEAR
eeedddd[bb[bb!!ddddoooooodddd22bbbb]dddd	chr17:73261800-73262030(+)$1	230	13	53	12.4108
FFFF:===========[bboooooobb]===========:	chr16:87743057-87743280(-)$1	223	118	158	14.1577
ff####bb[ccc[ffffffooooooffffff]ccc]bb33	chr19:10801333-10801575(+)$1	242	59	99	14.3435
gggggggbbccc!!bbrrrrrrrrrbb22ccc333bb]gg	chr12:53873137-53873377(+)$1	240	16	56	11.6923
ee####ggggggg[bb[cccnnnnnccc]bb]ggggggg5	chr10:12212708-12212936(-)$1	228	19	59	12.1488
cc!!gggggggccc[ddddoooooodddd333ccc]gggg	chr15:41021611-41021875(+)$1	264	142	182	16.3838
=========="""bb"""ccclllccc333bb22======	chr2:47129944-47130170(-)$1	226	124	164	14.2600
"""dddd!!ffffff[cccoooooocccffffff22dddd	chr17:78185191-78185446(-)$1	255	161	201	14.0364
"eeeee[ffffff"""cccooooooccc333ffffff333	chr11:66203202-66203426(-)$1	224	157	197	15.9509
""ccc####===========nnnnn===========ccc2	chr17:41154633-41154872(+)$1	239	177	217	15.3863
a[==========[ffffffnnnnnffffff333=======	chr3:129612240-129612464(-)$1	224	170	210	14.7483
faggggggg"""bb[ddddoooooodddd]bb22gggggg	chr11:117185143-117185381(-)$1	238	129	169	14.8898
hhh[dddd$$$$$ddddbboooooobb]dddd4444dddd	chr7:148844670-148844896(-)$1	226	42	82	12.3128
!a!!ccc!!ggggggg[bbrrrrrrrrrbbgggggggccc	chr9:33042825-33043059(-)$1	234	137	177	13.0597
===a[a[============ppppppp============22	chr1:900773-901001(+)$1	228	172	212	14.0208
hhhh!!a####ccc[ccc[ammmma]ccc]ccc4444a22	chr17:21433870-21434093(-)$1	223	107	147	13.0043
eeeee####eeeee[cccrrrrrrrrrccc333eeeeeee	chr11:117157344-117157570(-)$1	226	29	69	11.9766
=============!!ddddmmmmdddd]============	chr22:19024877-19025100(-)$1	223	94	134	14.6181
eeeeggggggg[bb!!ccclllccc22bb]ggggggg444	chr19:52517609-52517834(-)$1	225	123	163	12.2674
!ffffff[dddd"""a[ccclllccc]adddd]ffffff]	chr5:149829168-149829393(-)$1	225	127	167	10.5608
[============"""ccclllccc666666=========	chr1:150241019-150241241(-)$1	222	100	140	13.4761
eeegggggggeeeee[cccooooooccceeeee333gggg	chr1:156288583-156288802(-)$1	219	26	66	15.5057
h[eeeee[bbccc[cccbboooooobb]ccc]ccc22bb2	chr16:3584222-3584444(+)$1	222	44	84	13.7392
ee"""cccdddd"""ddddoooooodddd4444dddd]cc	chr4:7061752-7061982(-)$1	230	164	204	14.6424
ooa]==========eeeeeooooooeeeeedddd"""ccc	chr5:179224913-179225140(-)$1	227	160	200	13.6110
dddd[dddd[==========nnnnn==========333dd	chrX:20025687-20025920(-)$1	233	113	153	13.9726
ffffff[a[bb[ccc[cccoooooocccccc]bb]a333f	chr4:83346672-83346902(-)$1	230	174	214	15.1593
==========!!ccc[ccclllccc]ccc333========	chr11:62334789-62335013(-)$1	224	92	132	16.0769
c[hhhhhhhh[a[bb!!bboooooobb4444bb]a]hhhh	chr17:80200895-80201115(-)$1	220	77	117	13.1971
e"""ddddeeeee[ccc[aooooooa]ccc]eeeee7777	chr14:96829774-96830001(+)$1	227	136	176	12.2950
===================oooooo===============	chr19:16989932-16990164(+)$1	232	110	150	19.5237
=[bb"""bb"""gggggggooooooggggggg333bb]bb	chr21:46067190-46067413(+)$1	223	168	208	15.3299
cc:dddd!!ggggggg[bboooooobb]ggggggg333dd	chr1:151118957-151119190(-)$1	233	111	151	14.4187
hhhhh!!===========[bbmmmmbb22===========	chr12:121138215-121138438(+)$1	223	67	107	12.8354
ii$$$$$ggggggg[ddddooooooddddggggggg6666	chr8:124026637-124026858(-)$1	221	14	54	13.6774
========"""gggggggpppppppggggggg========	chr19:6413902-6414148(-)$1	246	165	205	12.8767
a[dddd[ccc[ccceeeeeooooooeeeee4444ccc]cc	chr9:139007124-139007346(-)$1	222	140	180	15.1985
eeeee[ccc"""ggggggglllggggggg4444ccc]eee	chr1:151104532-151104751(-)$1	219	161	201	12.0995
[dddd[cccccc[ccc[bbmmmmbb]ccc4444ccc4444	chr3:52265073-52265296(-)$1	223	168	208	12.0821
ddd!!eeeee"""ffffffooooooffffff333eeeee]	chr7:4803405-4803627(+)$1	222	170	210	14.1536
ggggg!!ccc[dddd[cccrrrrrrrrrcccddddccc33	chr20:43383039-43383261(-)$1	222	134	174	12.9668
gggggggccc[a[ccc[ddddllldddd22ccc]accc77	chr16:87732706-87732937(-)$1	231	72	112	11.4926
gggg!!dddd"""eeeeeaooooooa]eeeee4444dddd	chr5:140998495-140998715(-)$1	220	166	206	14.6062
hhhhhh!!bbccc[eeeeeooooooeeeee]ccc]bb000	chr14:75201723-75201949(+)$1	226	115	155	12.5137
!!bb[ffffff[bb[ddddooooooddddbb]ffffffbb	chr19:42373032-42373272(+)$1	240	69	109	12.4143
a[ccc[iiiiiiiii[cccooooooccc]iiiiiiiii]c	chr2:219270140-219270373(+)$1	233	8	48	18.1791
b[dddd!!ccc[cccacccooooooccc]a]cccccc]dd	chr19:7991991-7992224(-)$1	233	122	162	15.8437
[ggggggg[ccc"""ddddrrrrrrrrrdddd4444ccc]	chr19:2072937-2073166(-)$1	229	104	144	13.5716
[ccc[ccc[==========rrrrrrrrr==========cc	chr22:39117660-39117891(+)$1	231	46	86	15.6323
a!!ccc[ggggggg!!cccooooooccc22ggggggg333	chr17:77912338-77912597(-)$1	259	125	165	17.7644
####iiiiiiiiibb[cccoooooocccbb]iiiiiiiii	chr6:43970400-43970626(+)$1	226	56	96	17.0555
ggggggcccdddd!!ccc[ammmma]ccc]dddd]ccc]g	chr10:100027798-100028024(-)$1	226	59	99	11.8715
#dddd!!eeeee[ffffffooooooffffff]eeeee22d	chr5:177576555-177576776(-)$1	221	103	143	13.1186

#otherMatches

#Seq PSSM
GCUUCCUAGCCAUGAAGUGGAUGAUCACUGAGUGCCGGGA	chr17:73261800-73262030(+)$1	230	13	53	12.4108
AAGGAGGUGGUGGCCGAGGAUGGCACCGUGGUCACCAUUA	chr16:87743057-87743280(-)$1	223	118	158	14.1577
GGACCACACGUCUGCAGAGAUCCUGCUCUGCUGGCCUGAG	chr19:10801333-10801575(+)$1	242	59	99	14.3435
GGGGAAACUAACUGAGUUCUUGUUUCUGUGUUACAGGCUU	chr12:53873137-53873377(+)$1	240	16	56	11.6923
UUAUUUCCAGGGGAUGGAGGUAUGUUCUGCAACUCCUGGU	chr10:12212708-12212936(-)$1	228	19	59	12.1488
CUCGGGUCGAGGUGAGCUUUCAGCCAGGCAGAUGCACUUG	chr15:41021611-41021875(+)$1	264	142	182	16.3838
CUGAAAAGUAAAACAACAGGCUUUGCCAAGUGGAUGCUUU	chr2:47129944-47130170(-)$1	226	124	164	14.2600
UUCGGCACAGGGCAGAGGCUCGUGUGUCCUGCCCACUGCC	chr17:78185191-78185446(-)$1	255	161	201	14.0364
ACCAGUACUGGUGGUAGCCAAUAUGGGCAGACAUUAGGAA	chr11:66203202-66203426(-)$1	224	157	197	15.9509
UUUGGUAGUGAAUGGUGGAGUAUGGUUUCACUAUUUCCAU	chr17:41154633-41154872(+)$1	239	177	217	15.3863
CCCCCUCACGGCCCUCCGCGGUGGGUGGGGACAGUCGUGA	chr3:129612240-129612464(-)$1	224	170	210	14.7483
UCCGGAUCUGUGUCUGGGAAGUCUGUCCUUGGGAGGGUCU	chr11:117185143-117185381(-)$1	238	129	169	14.8898
GCCGGGGCCGCCUCAGCCAUGGCCCUGCGCUGUCUAGCCC	chr7:148844670-148844896(-)$1	226	42	82	12.3128
ggcagagguugcagugagcugagacugugccacugcacuc	chr9:33042825-33043059(-)$1	234	137	177	13.0597
GGGGUCCCGGGAAGGGUGGGGAGCAGUUGUCCUUCCUGUC	chr1:900773-901001(+)$1	228	172	212	14.0208
GCAUGGGGAGUUGGAUGUGCCUGUGGACACCCAUGGACAA	chr17:21433870-21434093(-)$1	223	107	147	13.0043
AGUGGGUCACCUGACCUCUGAAGAGCUGAGUACUCAGGCC	chr11:117157344-117157570(-)$1	226	29	69	11.9766
GUGCUGUCUCGCUCAGUCUUUCCAGACCAGCGGGGCAGCA	chr22:19024877-19025100(-)$1	223	94	134	14.6181
aucaccauucagaacugcagguuguccuugugaguggcau	chr19:52517609-52517834(-)$1	225	123	163	12.2674
GGUAGGAGGCCCGGGCGCGACAAUCGGGGGGCAUCCUGCG	chr5:149829168-149829393(-)$1	225	127	167	10.5608
ACUGUGGCUGGGGACCCGCUUCGCGUUAUCAUCCUGGUCG	chr1:150241019-150241241(-)$1	222	100	140	13.4761
CUUGCGUGGAGUCAUGAUUAACAAGGAUGUGACCCAUCCA	chr1:156288583-156288802(-)$1	219	26	66	15.5057
cgaggucagugaaggccccugacguggugguguuugagca	chr16:3584222-3584444(+)$1	222	44	84	13.7392
uauuuaaGAGGAUUAAAGCCCUAAUGUUUAUUUUCCUACU	chr4:7061752-7061982(-)$1	230	164	204	14.6424
CUGCCGUCCCCGGAGGGCCAGAUACGGCCCCGCCCAAAGG	chr5:179224913-179225140(-)$1	227	160	200	13.6110
UUCAUGCUGUAGUCACUCCAGACCAUGGAGUGGCUUUCCA	chrX:20025687-20025920(-)$1	233	113	153	13.9726
ACGCUGUCCUGUGGUAUGGUCUCUUCCAACUUCAUGUACC	chr4:83346672-83346902(-)$1	230	174	214	15.1593
GGGCUGUCUUGGGCGAAGUGAAACUGUGUGAGAAGAUGGC	chr11:62334789-62335013(-)$1	224	92	132	16.0769
AUGGAUGCUUUCUCAAUCCUAGGCUGGUUACUGUGUAAGC	chr17:80200895-80201115(-)$1	220	77	117	13.1971
CGGCAGCCGGGGUGGCUGCGGGCGAGGGGCGGCCCCCGAG	chr14:96829774-96830001(+)$1	227	136	176	12.2950
GAGGGUUUGGGCAUCAGCUCUGCCUGGCUGGUGUUCAGGC	chr19:16989932-16990164(+)$1	232	110	150	19.5237
CACCAGCUCCAUCAGUAGCCACAGAGCUGCUGCCUGAAGG	chr21:46067190-46067413(+)$1	223	168	208	15.3299
GACUUGGACCCAGGGCUCUCCCGACAGCGCCCUGGAACCC	chr1:151118957-151119190(-)$1	233	111	151	14.4187
UUUGGGCUUUCUCCUUCUGUGGCCCCGGAGGAAGGAGAGA	chr12:121138215-121138438(+)$1	223	67	107	12.8354
GGAGUAGUUGGGUUGCUUUGUGUUAGGAGGAUCCAGAUCA	chr8:124026637-124026858(-)$1	221	14	54	13.6774
UGGGGGGGACUUGGGGGCAUGCCGGGCCCUCACUCUCUCG	chr19:6413902-6414148(-)$1	246	165	205	12.8767
GUGUUCAGGGAGGGUGGCCACCAUGGGCCGAGGUCUCACC	chr9:139007124-139007346(-)$1	222	140	180	15.1985
UGGGACGUGCCUCUCCUACUGUGUAGGAGCCUCCGCUUCC	chr1:151104532-151104751(-)$1	219	161	201	12.0995
GAGGCCCCAGCCUUGAGCCCUCAGGGUCAUAUCGGCCCAG	chr3:52265073-52265296(-)$1	223	168	208	12.0821
UGCCUGAGGAGCAGUGGUUCUUGGAAAUCGCCCGUCCUCC	chr7:4803405-4803627(+)$1	222	170	210	14.1536
CCUGGUCUCCAUUAGAGGGUGUUGUUUUCUCCUGAGGACA	chr20:43383039-43383261(-)$1	222	134	174	12.9668
GCACAUUCUGUGCGCUACUGAACUUCAGAAAGCACCAGUC	chr16:87732706-87732937(-)$1	231	72	112	11.4926
CGGCGGGCGCGGAGCUGCCAGGCGGGAGCGGCGUAGGCGC	chr5:140998495-140998715(-)$1	220	166	206	14.6062
uuguggggccgcggggguuggggggaaucugugcaggggg	chr14:75201723-75201949(+)$1	226	115	155	12.5137
UUCCACAGCGCGGCACCUGUACCUCCGGGGUGGCGCUGGG	chr19:42373032-42373272(+)$1	240	69	109	12.4143
ugcccagcauaugcuaggcCCACCAGCUAAGUGUGUGUGG	chr2:219270140-219270373(+)$1	233	8	48	18.1791
CUCGGCCUCCAGCACCGAGCAGAUUCUCUGAGUGUGGUGC	chr19:7991991-7992224(-)$1	233	122	162	15.8437
UGGCUCCCAGGCUCCUGGAACUUCUGCCUCCACCUCGCUG	chr19:2072937-2073166(-)$1	229	104	144	13.5716
UUCUCUCUCGUCCUGACACUUCCUUUCUGUGUUGGGGCAG	chr22:39117660-39117891(+)$1	231	46	86	15.6323
cugagaauuuggagggcuaaacaacugggacUCUGGAGAG	chr17:77912338-77912597(-)$1	259	125	165	17.7644
AGACGCUGGCCCGGAUGUCGCGGAGGACUCGCGGGCCGGU	chr6:43970400-43970626(+)$1	226	56	96	17.0555
GGCGCCCGGGGAGGGAGCCCGUUAGCGCUGCUCCGCCGCG	chr10:100027798-100028024(-)$1	226	59	99	11.8715
UUGGGCUGGCAGCAGGACGACUGGCUGUCCUCCUGCCCAC	chr5:177576555-177576776(-)$1	221	103	143	13.1186

#DB
(((((((.((.((..((((......))))..)))).))))	chr17:73261800-73262030(+)$1	1	13	53	12.4108
((((.(((((((((((.((......)).))))))))))).	chr16:87743057-87743280(-)$1	1	118	158	14.1577
((....((.(((.((((((......)))))).))).))..	chr19:10801333-10801575(+)$1	1	59	99	14.3435
((((((((((((..((.........))..)))...)).))	chr12:53873137-53873377(+)$1	1	16	56	11.6923
((....(((((((.((.(((.....))).)).))))))).	chr10:12212708-12212936(-)$1	1	19	59	12.1488
((..((((((((((.((((......))))...))).))))	chr15:41021611-41021875(+)$1	1	142	182	16.3838
((((((((((...((...(((...)))...))..))))))	chr2:47129944-47130170(-)$1	1	124	164	14.2600
...((((..((((((.(((......)))))))))..))))	chr17:78185191-78185446(-)$1	1	161	201	14.0364
.(((((.((((((...(((......)))...))))))...	chr11:66203202-66203426(-)$1	1	157	197	15.9509
..(((....(((((((((((.....)))))))))))))).	chr17:41154633-41154872(+)$1	1	177	217	15.3863
(.((((((((((.((((((.....))))))...)))))))	chr3:129612240-129612464(-)$1	1	170	210	14.7483
(((((((((...((.((((......)))).))..))))))	chr11:117185143-117185381(-)$1	1	129	169	14.8898
(((.((((.....((((((......)).))))....))))	chr7:148844670-148844896(-)$1	1	42	82	12.3128
.(..(((..(((((((.((.........))))))))))))	chr9:33042825-33043059(-)$1	1	137	177	13.0597
((((.(.((((((((((((.......))))))))))))..	chr1:900773-901001(+)$1	1	172	212	14.0208
((((..(....(((.(((.(....).))).)))....)..	chr17:21433870-21434093(-)$1	1	107	147	13.0043
(((((....(((((.(((.........)))...)))))))	chr11:117157344-117157570(-)$1	1	29	69	11.9766
(((((((((((((..((((....)))).))))))))))))	chr22:19024877-19025100(-)$1	1	94	134	14.6181
(((((((((((.((..(((...)))..)).)))))))...	chr19:52517609-52517834(-)$1	1	123	163	12.2674
.((((((.((((...(.(((...))).))))).)))))).	chr5:149829168-149829393(-)$1	1	127	167	10.5608
.((((((((((((...(((...)))......)))))))))	chr1:150241019-150241241(-)$1	1	100	140	13.4761
)))((((((((((((.(((......))))))))...))))	chr1:156288583-156288802(-)$1	1	26	66	15.5057
(.(((((.(((((.(((((......)).))).)))..)).	chr16:3584222-3584444(+)$1	1	44	84	13.7392
((...(((((((...((((......))))....)))).))	chr4:7061752-7061982(-)$1	1	164	204	14.6424
..).))))))))))(((((......)))))((((...(((	chr5:179224913-179225140(-)$1	1	160	200	13.6110
((((.((((.((((((((((.....))))))))))...))	chrX:20025687-20025920(-)$1	1	113	153	13.9726
((((((.(.((.(((.(((......)))))).)).)...)	chr4:83346672-83346902(-)$1	1	174	214	15.1593
((((((((((..(((.(((...))).)))...))))))))	chr11:62334789-62335013(-)$1	1	92	132	16.0769
(.((((((((.(.((..((......))....)).).))))	chr17:80200895-80201115(-)$1	1	77	117	13.1971
(...(((((((((.(((.(......).))).)))))....	chr14:96829774-96830001(+)$1	1	136	176	12.2950
(((((((((((((((((((......)))))))))))))))	chr19:16989932-16990164(+)$1	1	110	150	19.5237
(.((...((...(((((((......)))))))...)).))	chr21:46067190-46067413(+)$1	1	168	208	15.3299
)).((((..(((((((.((......)).)))))))...))	chr1:151118957-151119190(-)$1	1	111	151	14.4187
(((((..(((((((((((.((....))..)))))))))))	chr12:121138215-121138438(+)$1	1	67	107	12.8354
((.....(((((((.((((......)))))))))))....	chr8:124026637-124026858(-)$1	1	14	54	13.6774
((((((((...(((((((.......)))))))))))))))	chr19:6413902-6414148(-)$1	1	165	205	12.8767
(.((((.(((.((((((((......)))))....))).))	chr9:139007124-139007346(-)$1	1	140	180	15.1985
(((((.(((...(((((((...)))))))....))).)))	chr1:151104532-151104751(-)$1	1	161	201	12.0995
.((((.((((((.(((.((....)).)))....)))....	chr3:52265073-52265296(-)$1	1	168	208	12.0821
(((..(((((...((((((......))))))...))))).	chr7:4803405-4803627(+)$1	1	170	210	14.1536
(((((..(((.((((.(((.........))))))))))..	chr20:43383039-43383261(-)$1	1	134	174	12.9668
((((((((((.(.(((.((((...))))..))).))))..	chr16:87732706-87732937(-)$1	1	72	112	11.4926
((((..((((...((((((......).)))))....))))	chr5:140998495-140998715(-)$1	1	166	206	14.6062
((((((..(((((.(((((......))))).))).))...	chr14:75201723-75201949(+)$1	1	115	155	12.5137
..((.((((((.((.((((......)))))).))))))))	chr19:42373032-42373272(+)$1	1	69	109	12.4143
(.(((.(((((((((.(((......))).))))))))).)	chr2:219270140-219270373(+)$1	1	8	48	18.1791
(.((((..(((.(((((((......))).).)))))).))	chr19:7991991-7992224(-)$1	1	122	162	15.8437
.(((((((.(((...((((.........))))....))).	chr19:2072937-2073166(-)$1	1	104	144	13.5716
.(((.(((.((((((((((.........))))))))))))	chr22:39117660-39117891(+)$1	1	46	86	15.6323
(..(((.(((((((..(((......)))..)))))))...	chr17:77912338-77912597(-)$1	1	125	165	17.7644
....(((((((((((.(((......))))).)))))))))	chr6:43970400-43970626(+)$1	1	56	96	17.0555
(((((((((((((..(((.(....).))).)))).))).)	chr10:100027798-100028024(-)$1	1	59	99	11.8715
.((((..(((((.((((((......)))))).)))))..)	chr5:177576555-177576776(-)$1	1	103	143	13.1186

#PSSM
e : 0.15	= : 0.13	g : 0.09	h : 0.09	a : 0.07	[ : 0.07	f : 0.05	c : 0.05	" : 0.05	! : 0.05	d : 0.03	# : 0.03	F : 0.01	o : 0.01	i : 0.01	b : 0.01	
e : 0.15	= : 0.13	[ : 0.13	g : 0.11	h : 0.07	d : 0.07	f : 0.05	c : 0.05	" : 0.05	a : 0.03	! : 0.03	F : 0.01	o : 0.01	i : 0.01	# : 0.01	
= : 0.15	e : 0.13	g : 0.13	d : 0.11	h : 0.09	# : 0.05	! : 0.05	" : 0.05	c : 0.05	f : 0.03	b : 0.03	F : 0.01	a : 0.01	: : 0.01	$ : 0.01	
d : 0.15	g : 0.15	= : 0.13	e : 0.09	c : 0.07	h : 0.07	# : 0.05	! : 0.05	f : 0.03	" : 0.03	b : 0.03	F : 0.01	[ : 0.01	a : 0.01	] : 0.01	$ : 0.01	
d : 0.16	g : 0.16	= : 0.15	e : 0.07	c : 0.07	[ : 0.07	! : 0.05	h : 0.05	# : 0.03	f : 0.03	" : 0.03	: : 0.01	$ : 0.01	i : 0.01	
= : 0.16	d : 0.15	g : 0.15	! : 0.09	# : 0.07	c : 0.07	e : 0.05	f : 0.05	[ : 0.05	h : 0.03	a : 0.01	" : 0.01	$ : 0.01	i : 0.01	
= : 0.16	g : 0.15	d : 0.13	c : 0.11	[ : 0.09	! : 0.09	# : 0.03	f : 0.03	e : 0.03	i : 0.03	b : 0.01	a : 0.01	h : 0.01	" : 0.01	$ : 0.01	
= : 0.20	g : 0.15	c : 0.15	! : 0.09	d : 0.07	[ : 0.05	b : 0.05	# : 0.05	f : 0.03	e : 0.03	i : 0.03	a : 0.01	h : 0.01	
= : 0.18	g : 0.13	c : 0.13	b : 0.09	[ : 0.07	d : 0.07	! : 0.05	# : 0.05	e : 0.05	f : 0.03	i : 0.03	$ : 0.01	h : 0.01	" : 0.01	
= : 0.22	c : 0.15	g : 0.15	b : 0.07	" : 0.07	e : 0.07	d : 0.07	f : 0.05	i : 0.03	$ : 0.01	# : 0.01	[ : 0.01	h : 0.01	
= : 0.20	c : 0.13	g : 0.13	" : 0.13	[ : 0.09	e : 0.07	f : 0.05	d : 0.05	i : 0.03	$ : 0.01	# : 0.01	b : 0.01	! : 0.01	
= : 0.20	c : 0.16	g : 0.11	" : 0.11	e : 0.07	[ : 0.07	d : 0.07	f : 0.03	a : 0.03	i : 0.03	b : 0.01	$ : 0.01	! : 0.01	
= : 0.18	g : 0.15	c : 0.15	[ : 0.11	" : 0.11	b : 0.07	e : 0.05	f : 0.03	d : 0.03	i : 0.03	! : 0.01	$ : 0.01	
= : 0.15	c : 0.15	g : 0.13	b : 0.11	f : 0.09	" : 0.09	! : 0.07	[ : 0.07	e : 0.05	d : 0.03	i : 0.01	
= : 0.13	c : 0.13	[ : 0.11	! : 0.09	f : 0.09	b : 0.09	" : 0.09	g : 0.09	e : 0.09	d : 0.03	i : 0.01	
d : 0.16	= : 0.13	[ : 0.13	c : 0.13	g : 0.09	f : 0.07	e : 0.07	" : 0.05	! : 0.05	b : 0.03	a : 0.03	
c : 0.32	d : 0.16	[ : 0.13	= : 0.11	f : 0.07	e : 0.07	g : 0.05	r : 0.01	" : 0.01	! : 0.01	
c : 0.32	d : 0.16	b : 0.13	= : 0.11	f : 0.07	e : 0.07	g : 0.05	r : 0.01	" : 0.01	[ : 0.01	
c : 0.28	d : 0.16	b : 0.13	= : 0.09	f : 0.07	[ : 0.05	e : 0.05	r : 0.03	a : 0.03	g : 0.03	p : 0.01	
o : 0.54	r : 0.11	l : 0.07	c : 0.05	= : 0.03	p : 0.03	a : 0.03	m : 0.03	n : 0.01	b : 0.01	d : 0.01	
o : 0.54	r : 0.11	l : 0.09	n : 0.07	m : 0.07	p : 0.03	c : 0.01	b : 0.01	d : 0.01	
o : 0.54	l : 0.13	r : 0.11	m : 0.09	n : 0.07	p : 0.03	
o : 0.54	r : 0.11	m : 0.09	n : 0.07	l : 0.05	c : 0.05	p : 0.03	g : 0.01	
o : 0.54	r : 0.11	n : 0.07	c : 0.07	m : 0.05	l : 0.03	p : 0.03	d : 0.01	g : 0.01	b : 0.01	
o : 0.54	r : 0.11	c : 0.09	n : 0.05	p : 0.03	a : 0.03	d : 0.03	f : 0.01	m : 0.01	g : 0.01	b : 0.01	
c : 0.20	d : 0.15	b : 0.13	r : 0.09	f : 0.07	] : 0.07	= : 0.05	e : 0.05	g : 0.05	a : 0.03	p : 0.01	2 : 0.01	6 : 0.01	
c : 0.26	d : 0.15	b : 0.13	r : 0.09	f : 0.07	= : 0.07	] : 0.05	e : 0.05	g : 0.05	2 : 0.01	6 : 0.01	
c : 0.28	d : 0.13	] : 0.09	f : 0.07	= : 0.07	r : 0.07	e : 0.07	g : 0.05	2 : 0.03	3 : 0.01	b : 0.01	a : 0.01	6 : 0.01	4 : 0.01	
d : 0.16	c : 0.16	= : 0.13	f : 0.09	e : 0.09	2 : 0.07	g : 0.07	] : 0.05	b : 0.05	3 : 0.03	6 : 0.01	4 : 0.01	
= : 0.15	c : 0.11	f : 0.09	e : 0.09	b : 0.07	3 : 0.07	] : 0.07	4 : 0.07	g : 0.07	2 : 0.05	d : 0.05	6 : 0.01	i : 0.01	a : 0.01	
= : 0.15	g : 0.13	c : 0.11	3 : 0.09	d : 0.09	4 : 0.09	f : 0.07	b : 0.07	] : 0.07	e : 0.03	2 : 0.01	6 : 0.01	i : 0.01	
= : 0.16	g : 0.13	] : 0.11	d : 0.11	c : 0.09	3 : 0.09	b : 0.07	4 : 0.07	e : 0.05	f : 0.03	i : 0.03	
= : 0.20	c : 0.13	4 : 0.13	g : 0.11	3 : 0.09	b : 0.05	f : 0.05	e : 0.05	d : 0.05	2 : 0.03	i : 0.03	] : 0.01	
= : 0.22	c : 0.13	g : 0.11	4 : 0.09	3 : 0.07	f : 0.07	d : 0.07	e : 0.05	b : 0.03	2 : 0.03	] : 0.03	i : 0.03	
= : 0.24	c : 0.13	g : 0.13	4 : 0.07	e : 0.07	3 : 0.05	f : 0.05	] : 0.05	d : 0.03	a : 0.03	i : 0.03	b : 0.01	2 : 0.01	" : 0.01	
= : 0.22	c : 0.13	g : 0.11	] : 0.07	4 : 0.07	e : 0.07	b : 0.05	f : 0.05	3 : 0.05	2 : 0.03	i : 0.03	d : 0.01	" : 0.01	a : 0.01	
= : 0.20	g : 0.13	c : 0.13	d : 0.09	b : 0.07	f : 0.05	e : 0.05	3 : 0.05	4 : 0.03	i : 0.03	2 : 0.01	" : 0.01	h : 0.01	7 : 0.01	6 : 0.01	] : 0.01	
= : 0.20	c : 0.13	] : 0.09	3 : 0.09	d : 0.07	g : 0.07	e : 0.05	b : 0.03	4 : 0.03	f : 0.03	i : 0.03	a : 0.01	h : 0.01	7 : 0.01	6 : 0.01	0 : 0.01	2 : 0.01	
= : 0.16	d : 0.13	c : 0.13	3 : 0.09	g : 0.09	2 : 0.05	e : 0.05	b : 0.05	4 : 0.03	7 : 0.03	] : 0.03	f : 0.01	h : 0.01	6 : 0.01	0 : 0.01	i : 0.01	
d : 0.15	= : 0.15	c : 0.11	g : 0.09	3 : 0.07	2 : 0.07	] : 0.05	e : 0.03	4 : 0.03	7 : 0.03	b : 0.03	: : 0.01	5 : 0.01	f : 0.01	h : 0.01	6 : 0.01	0 : 0.01	i : 0.01	

#score	743.132632184608
#seq	53
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_CDS_m2_run1.txt

#BEAR
!!a[ccc[cccooooooccc]ccc22a22	chr12:110600643-110600883(+)$1	240	173	202	14.5697
b[ffffff[bboooooobb]ffffff]bb	chr2:54001355-54001635(+)$1	280	220	249	12.0912
eeeee[eeeeeooooooeeeee]eeeeeb	chr15:75664266-75664506(-)$1	240	146	175	12.9767
eeeee[bb[bboooooobbbb22eeeee4	chr7:99057634-99057874(-)$1	240	51	80	13.4602
gggggg!!cccoooooocccggggggg::	chr19:35435295-35435544(+)$1	249	172	201	13.5197
ffccc!!ddddoooooodddd333ccc44	chr20:464505-464747(-)$1	242	135	164	16.1115
eeea"""ddddoooooodddd333a]eee	chr7:44524588-44524828(-)$1	240	77	106	15.9675
c[dddd!!cccoooooocccdddd]ccc4	chr19:2115261-2115501(-)$1	240	63	92	14.5257
[dddd[a[cccooooooccc]adddd333	chr1:220804285-220804525(+)$1	240	40	69	14.9848
ddccc!!ddddoooooodddd22ccc22d	chr11:20409484-20409744(+)$1	260	12	41	15.2560
[ffffff[cccoooooocccffffff]bb	chr3:182662762-182663042(-)$1	280	208	237	13.6882
ffff!!bb[bboooooobbbb22ffffff	chr12:133354150-133354390(-)$1	240	14	43	13.1617
eeeee!!ddddoooooodddd]eeeeebb	chr7:17378903-17379143(+)$1	240	22	51	15.0934
ddeeeee!!bboooooobb22eeeee]dd	chr3:38518848-38519088(+)$1	240	29	58	12.6191
eeee"""ddddoooooodddd333eeeee	chr17:74733045-74733297(-)$1	252	39	68	16.0152
"""eeeee[bboooooobbeeeeebb]cc	chr2:86302131-86302372(-)$1	241	129	158	12.6989
ff[bb!!ddddoooooodddd4444bb]f	chr11:134064476-134064716(-)$1	240	71	100	14.3940
ffff[ddddbboooooobb]dddd]ffff	chr22:43286953-43287193(-)$1	240	141	170	12.7260
!==========oooooo==========22	chr9:2807743-2807983(-)$1	240	80	109	14.7832
eeee[dddd[aooooooaddddeeeeebb	chr1:14106623-14106863(+)$1	240	166	195	13.4070
$$$$gggggggooooooggggggg22a]d	chr3:112719647-112719887(+)$1	240	194	223	12.4642
!!ccc!!ddddoooooodddd]ccc]bb]	chr19:41781976-41782275(+)$1	299	246	275	15.6352
!!ccc[bbcccooooooccc333bb]ccc	chr1:24981349-24981600(+)$1	251	106	135	15.0778
!!ccc!!ddddoooooodddd]ccc]eee	chr3:38519318-38519559(+)$1	241	170	199	15.7925
hhhhhhh[cccooooooccc333hhhhhh	chr1:118477164-118477406(+)$1	242	162	191	13.0996
iiiii####cccnnnnnccciiiiiiiii	chr2:27282097-27282337(+)$1	240	134	163	10.3511
iiiiiii[cccooooooccc22iiiiiii	chr12:76740897-76741137(-)$1	240	183	212	15.2014
%eeeee[ddddoooooodddd]eeeee33	chr21:30426294-30426539(+)$1	245	68	97	14.6621
eeeee!!ddddoooooodddd22eeeee4	chr11:10823119-10823420(-)$1	301	208	237	15.7227
fffff"""cccooooooccc333ffffff	chr1:29040993-29041313(+)$1	320	36	65	15.7660
!bb[gggggggoooooogggggggbb22a	chr14:103371513-103371796(+)$1	283	102	131	12.7900
ccc[eeeeebboooooobb]eeeeeccc]	chr3:141164062-141164302(+)$1	240	200	229	12.9838
Ecccgggggggooooooggggggg333cc	chr2:170747569-170747809(+)$1	240	6	35	12.8057
d####ffffffooooooffffff333ddd	chr19:36592019-36592259(+)$1	240	78	107	11.7779
fffff"""cccooooooccc333ffffff	chr12:80199919-80200159(-)$1	240	129	158	15.7660
eee"""a[ddddoooooodddda333eee	chr9:88636767-88637007(+)$1	240	133	162	13.3553
fffff!!bb[aooooooa]bb22ffffff	chr18:19348549-19348791(+)$1	242	95	124	13.3050
gggg"""ddddooooooddddggggggg]	chr3:134201607-134201847(-)$1	240	114	143	15.5812
ddd[gggggggooooooggggggg]dddd	chr1:120468211-120468531(-)$1	320	230	259	13.0155
!dddd[a[cccooooooccc]adddd333	chr12:77236599-77236843(+)$1	244	201	230	15.0229
hhh[a!!a[bboooooobb]a22a]hhhh	chr1:120461030-120461270(-)$1	240	132	161	13.4864
####ccc[cccooooooccccccgggggg	chr17:41000999-41001239(+)$1	240	126	155	14.5945
fffff[a[cccooooooccca]ffffff]	chr6:1611348-1611588(+)$1	240	131	160	15.0163
dffffffcccooooooccc333ffffff]	chr12:105536848-105537088(+)$1	240	108	137	12.3780
eeee$$$$$bboooooobbeeeeecccbb	chrX:68381542-68381782(-)$1	240	25	54	12.7036
i"""bb[ddddoooooodddd333bb22i	chr3:101371292-101371532(-)$1	240	169	198	14.4561
ddddcccddddoooooodddd22cccggg	chr12:57011147-57011387(-)$1	240	8	37	14.4857
##dddd[ddddoooooodddd]ddddbb2	chr19:10225270-10225510(+)$1	240	129	158	13.7825
!!ccc"""ddddnnnnndddd]ccc333g	chrX:12736491-12736731(+)$1	240	165	194	11.3789
###dddd[cccooooooccc]ddddeeee	chr16:68260267-68260547(+)$1	280	103	132	13.5724
dddd"""bb[aooooooabb4444dddd2	chr18:32681894-32682174(+)$1	280	125	154	13.3912
eeee"""ddddooooooddddeeeee444	chr2:203748820-203749060(-)$1	240	84	113	15.3625

#otherMatches

#Seq PSSM
AAGAGAAAUCAGACCCGUGAAUUUGAUGG	chr12:110600643-110600883(+)$1	240	173	202	14.5697
CCAGAAGAAGCAGAUGAGCAUCUUUUCGC	chr2:54001355-54001635(+)$1	280	220	249	12.0912
AGUAUCGUGUCAAAUACGGCACAGUAUUC	chr15:75664266-75664506(-)$1	240	146	175	12.9767
GUUUCAGUACCAGUGAAGGACAAGAAACU	chr7:99057634-99057874(-)$1	240	51	80	13.4602
UUCAUACUGGGGAGAAACCCUAUGAAUGU	chr19:35435295-35435544(+)$1	249	172	201	13.5197
AGCAGUAACGGCCCUAUCUGUCUCCUGAU	chr20:464505-464747(-)$1	242	135	164	16.1115
GUCCCAGUUCCAGUCCAGGAAAUAGAGAU	chr7:44524588-44524828(-)$1	240	77	106	15.9675
CUGCCCGCUGCCGGCCCGCAGGGCUGCCU	chr19:2115261-2115501(-)$1	240	63	92	14.5257
AGUGGCUGAAUGUUCUGAUUGACCACACA	chr1:220804285-220804525(+)$1	240	40	69	14.9848
CCUGCUCCUCGAGCCCCCGGGCCGCACCG	chr11:20409484-20409744(+)$1	260	12	41	15.2560
ACAGAAAAUUGCACAGUCAAUUUCUGCUG	chr3:182662762-182663042(-)$1	280	208	237	13.6882
GUGGAAGCCGGGCAUAACCGCCGCCACUU	chr12:133354150-133354390(-)$1	240	14	43	13.1617
UGCAGAAAUUGGCAAGAUAAUACUGCACC	chr7:17378903-17379143(+)$1	240	22	51	15.0934
CGAGCAGGACAAGCGGCUGCACUGCUACG	chr3:38518848-38519088(+)$1	240	29	58	12.6191
GCCGCCACUCAGAGCUAUGAGCUACGGCC	chr17:74733045-74733297(-)$1	252	39	68	16.0152
GAGCGCUGUGGACAUGACCCAGCGAGAGG	chr2:86302131-86302372(-)$1	241	129	158	12.6989
UUCCCUCUACAGAAAGAUGUGUCAUGGCA	chr11:134064476-134064716(-)$1	240	71	100	14.3940
AGCCUUUCACAAGCAGAUGAUGGGCGGCU	chr22:43286953-43287193(-)$1	240	141	170	12.7260
UUGUUUUGCAAAAACACUUGUAGAGCAUG	chr9:2807743-2807983(-)$1	240	80	109	14.7832
GCUGAGGGUACAGGCAAGACUCCAGUCCA	chr1:14106623-14106863(+)$1	240	166	195	13.4070
AUUUCAACAUUGUUUUAAAUGUUGUGCAU	chr3:112719647-112719887(+)$1	240	194	223	12.4642
GGGGAAGGGACAGAGAAGUCCAUCCAUUG	chr19:41781976-41782275(+)$1	299	246	275	15.6352
AAACUCGUAGGUUAUCUCCUUCAGCAAGU	chr1:24981349-24981600(+)$1	251	106	135	15.0778
UUGAGUCAGCCGACCUGGGCUUCUUUGGC	chr3:38519318-38519559(+)$1	241	170	199	15.7925
GGCUUUGAUCUAUUAAAGGAAUGUAAGGC	chr1:118477164-118477406(+)$1	242	162	191	13.0996
UACCCAAAAGGUCACCCACCGGGUGCUGG	chr2:27282097-27282337(+)$1	240	134	163	10.3511
UCUGGAUCAGAGUUUAUUCUAAAUUCAGA	chr12:76740897-76741137(-)$1	240	183	212	15.2014
UGAUUUUUCAUUUUCUCAUGACAGAUUUU	chr21:30426294-30426539(+)$1	245	68	97	14.6621
AUGAGGUACAUUUGCCUAUGUUACUUAUA	chr11:10823119-10823420(-)$1	301	208	237	15.7227
CACCAUGGUUAGCCCUGUGGAAUUGGUGG	chr1:29040993-29041313(+)$1	320	36	65	15.7660
ACAUGGACCUGCGCUUCCAGGUCCUGGAG	chr14:103371513-103371796(+)$1	283	102	131	12.7900
CUGCGAGCUCUGCGCCAAGCAGUUCCAGA	chr3:141164062-141164302(+)$1	240	200	229	12.9838
UGCAUAUAUUAUGUGUUUAAUGUAAUUUG	chr2:170747569-170747809(+)$1	240	6	35	12.8057
CCCCCACUGGCACUGCAGCCAGUAUUGCA	chr19:36592019-36592259(+)$1	240	78	107	11.7779
CUGGGCUUCAGAAAAGCCUGCUUUCCAGC	chr12:80199919-80200159(-)$1	240	129	158	15.7660
GGGGCAGAGUCUUCUUUCAGACCCAACUC	chr9:88636767-88637007(+)$1	240	133	162	13.3553
GCCAGAGUGGUGCGAGGAGUGGACUGGCA	chr18:19348549-19348791(+)$1	242	95	124	13.3050
UUCAGAGAGAUGGAAGGAUCUUGGAUUUG	chr3:134201607-134201847(-)$1	240	114	143	15.5812
AGUAGCCCCUGCCAGCACGGGGGCAGCUG	chr1:120468211-120468531(-)$1	320	230	259	13.0155
UCCUGACAGUGGCAUAGCAUAGCGGGUAU	chr12:77236599-77236843(+)$1	244	201	230	15.0229
GAUGAAUGAUGGUACUACACCCCUGAUCC	chr1:120461030-120461270(-)$1	240	132	161	13.4864
GAAGACGUGGUGUUUAAACCUGUGGCUGC	chr17:41000999-41001239(+)$1	240	126	155	14.5945
UGUCCAGCGGGAGCAGCCCCCCGGGCAGC	chr6:1611348-1611588(+)$1	240	131	160	15.0163
AUUUAGAGUCCUAUGAGAUACUUCUGGAU	chr12:105536848-105537088(+)$1	240	108	137	12.3780
AAGAAGUUCGAGAACCAUCUCUUCAGGAA	chrX:68381542-68381782(-)$1	240	25	54	12.7036
GGAGACACAUGAACAACCAUGAAGGUAAC	chr3:101371292-101371532(-)$1	240	169	198	14.4561
UCCAGGUGACAUAACCUUGUUUAACCGCC	chr12:57011147-57011387(-)$1	240	8	37	14.4857
GAGCUGAGCCAAUGAUGUGGCCUAGCGGA	chr19:10225270-10225510(+)$1	240	129	158	13.7825
CCGCUCUGCCCCUCCCUGGGGAAGCACUU	chrX:12736491-12736731(+)$1	240	165	194	11.3789
CUAACAGUGCUUACUGCAGCCUUGUGUCC	chr16:68260267-68260547(+)$1	280	103	132	13.5724
UGUAGAGGCACGACAAGGGCAAGAUGCAA	chr18:32681894-32682174(+)$1	280	125	154	13.3912
UUUAGCAUCUGGAAGCACAGAUAGGCAUA	chr2:203748820-203749060(-)$1	240	84	113	15.3625

#DB
..(.(((.(((......))).)))..)..	chr12:110600643-110600883(+)$1	1	173	202	14.5697
(.((((((.((......)).)))))).))	chr2:54001355-54001635(+)$1	1	220	249	12.0912
(((((.(((((......))))).)))))(	chr15:75664266-75664506(-)$1	1	146	175	12.9767
(((((.((.((......))))..))))).	chr7:99057634-99057874(-)$1	1	51	80	13.4602
((((((..(((......))))))))))..	chr19:35435295-35435544(+)$1	1	172	201	13.5197
(((((..((((......))))...)))..	chr20:464505-464747(-)$1	1	135	164	16.1115
((((...((((......))))...).)))	chr7:44524588-44524828(-)$1	1	77	106	15.9675
(.((((..(((......))))))).))).	chr19:2115261-2115501(-)$1	1	63	92	14.5257
.((((.(.(((......))).)))))...	chr1:220804285-220804525(+)$1	1	40	69	14.9848
(((((..((((......))))..)))..)	chr11:20409484-20409744(+)$1	1	12	41	15.2560
.((((((.(((......))))))))).))	chr3:182662762-182663042(-)$1	1	208	237	13.6882
((((..((.((......))))..))))))	chr12:133354150-133354390(-)$1	1	14	43	13.1617
(((((..((((......)))).)))))((	chr7:17378903-17379143(+)$1	1	22	51	15.0934
(((((((..((......))..))))).))	chr3:38518848-38519088(+)$1	1	29	58	12.6191
((((...((((......))))...)))))	chr17:74733045-74733297(-)$1	1	39	68	16.0152
...(((((.((......))))))))).))	chr2:86302131-86302372(-)$1	1	129	158	12.6989
((.((..((((......))))....)).)	chr11:134064476-134064716(-)$1	1	71	100	14.3940
((((.((((((......)).)))).))))	chr22:43286953-43287193(-)$1	1	141	170	12.7260
.((((((((((......))))))))))..	chr9:2807743-2807983(-)$1	1	80	109	14.7832
((((.((((.(......))))))))))((	chr1:14106623-14106863(+)$1	1	166	195	13.4070
....(((((((......)))))))..).)	chr3:112719647-112719887(+)$1	1	194	223	12.4642
..(((..((((......)))).))).)).	chr19:41781976-41782275(+)$1	1	246	275	15.6352
..(((.(((((......)))...)).)))	chr1:24981349-24981600(+)$1	1	106	135	15.0778
..(((..((((......)))).))).)))	chr3:38519318-38519559(+)$1	1	170	199	15.7925
(((((((.(((......)))...))))))	chr1:118477164-118477406(+)$1	1	162	191	13.0996
(((((....(((.....))))))))))))	chr2:27282097-27282337(+)$1	1	134	163	10.3511
(((((((.(((......)))..)))))))	chr12:76740897-76741137(-)$1	1	183	212	15.2014
.(((((.((((......)))).)))))..	chr21:30426294-30426539(+)$1	1	68	97	14.6621
(((((..((((......))))..))))).	chr11:10823119-10823420(-)$1	1	208	237	15.7227
(((((...(((......)))...))))))	chr1:29040993-29041313(+)$1	1	36	65	15.7660
.((.(((((((......)))))))))..)	chr14:103371513-103371796(+)$1	1	102	131	12.7900
(((.(((((((......)).)))))))).	chr3:141164062-141164302(+)$1	1	200	229	12.9838
(((((((((((......)))))))...))	chr2:170747569-170747809(+)$1	1	6	35	12.8057
(....((((((......))))))...)))	chr19:36592019-36592259(+)$1	1	78	107	11.7779
(((((...(((......)))...))))))	chr12:80199919-80200159(-)$1	1	129	158	15.7660
(((...(.((((......)))))...)))	chr9:88636767-88637007(+)$1	1	133	162	13.3553
(((((..((.(......).))..))))))	chr18:19348549-19348791(+)$1	1	95	124	13.3050
((((...((((......))))))))))).	chr3:134201607-134201847(-)$1	1	114	143	15.5812
(((.(((((((......))))))).))))	chr1:120468211-120468531(-)$1	1	230	259	13.0155
.((((.(.(((......))).)))))...	chr12:77236599-77236843(+)$1	1	201	230	15.0229
(((.(..(.((......)).)..).))))	chr1:120461030-120461270(-)$1	1	132	161	13.4864
....(((.(((......))))))))))))	chr17:41000999-41001239(+)$1	1	126	155	14.5945
(((((.(.(((......)))).)))))).	chr6:1611348-1611588(+)$1	1	131	160	15.0163
((((((((((......)))...)))))).	chr12:105536848-105537088(+)$1	1	108	137	12.3780
((((.....((......))))))))))))	chrX:68381542-68381782(-)$1	1	25	54	12.7036
(...((.((((......))))...))..)	chr3:101371292-101371532(-)$1	1	169	198	14.4561
))))(((((((......))))..)))(((	chr12:57011147-57011387(-)$1	1	8	37	14.4857
..((((.((((......)))).)))))).	chr19:10225270-10225510(+)$1	1	129	158	13.7825
..(((...((((.....)))).)))...)	chrX:12736491-12736731(+)$1	1	165	194	11.3789
...((((.(((......))).))))))))	chr16:68260267-68260547(+)$1	1	103	132	13.5724
((((...((.(......)))....)))).	chr18:32681894-32682174(+)$1	1	125	154	13.3912
((((...((((......)))))))))...	chr2:203748820-203749060(-)$1	1	84	113	15.3625

#PSSM
e : 0.19	! : 0.15	f : 0.15	d : 0.13	i : 0.05	# : 0.05	g : 0.03	c : 0.03	[ : 0.03	h : 0.03	b : 0.01	" : 0.01	$ : 0.01	% : 0.01	E : 0.01	
e : 0.21	f : 0.19	d : 0.13	! : 0.09	# : 0.07	[ : 0.03	g : 0.03	" : 0.03	h : 0.03	i : 0.03	c : 0.03	= : 0.01	$ : 0.01	b : 0.01	
e : 0.23	f : 0.17	c : 0.15	d : 0.13	# : 0.05	g : 0.03	" : 0.03	h : 0.03	i : 0.03	a : 0.01	[ : 0.01	= : 0.01	$ : 0.01	b : 0.01	
e : 0.21	f : 0.17	c : 0.13	d : 0.13	[ : 0.09	g : 0.03	i : 0.03	# : 0.03	" : 0.03	a : 0.01	b : 0.01	= : 0.01	$ : 0.01	h : 0.01	
c : 0.17	e : 0.15	f : 0.13	" : 0.11	g : 0.09	d : 0.09	b : 0.03	[ : 0.03	i : 0.03	! : 0.01	= : 0.01	h : 0.01	# : 0.01	a : 0.01	$ : 0.01	
! : 0.19	" : 0.17	[ : 0.11	g : 0.09	d : 0.09	f : 0.07	e : 0.07	c : 0.05	= : 0.01	h : 0.01	# : 0.01	i : 0.01	$ : 0.01	b : 0.01	
! : 0.21	" : 0.15	f : 0.07	e : 0.07	a : 0.07	g : 0.07	c : 0.05	b : 0.05	d : 0.05	[ : 0.05	= : 0.01	h : 0.01	# : 0.01	i : 0.01	$ : 0.01	
d : 0.32	[ : 0.19	b : 0.09	g : 0.07	e : 0.05	! : 0.05	" : 0.05	f : 0.03	= : 0.01	# : 0.01	a : 0.01	c : 0.01	$ : 0.01	
d : 0.36	c : 0.28	[ : 0.09	g : 0.07	e : 0.03	b : 0.03	! : 0.01	= : 0.01	# : 0.01	f : 0.01	$ : 0.01	
d : 0.32	c : 0.30	b : 0.17	g : 0.07	[ : 0.05	e : 0.01	= : 0.01	f : 0.01	
d : 0.32	c : 0.28	b : 0.17	g : 0.07	a : 0.05	e : 0.01	= : 0.01	f : 0.01	o : 0.01	
o : 0.94	d : 0.03	c : 0.01	
o : 0.96	n : 0.03	
o : 0.96	n : 0.03	
o : 0.96	n : 0.03	
o : 0.96	n : 0.03	
o : 0.94	n : 0.03	c : 0.01	
c : 0.30	d : 0.30	b : 0.17	g : 0.07	a : 0.05	e : 0.01	= : 0.01	f : 0.01	o : 0.01	
d : 0.34	c : 0.30	b : 0.19	g : 0.07	e : 0.01	= : 0.01	f : 0.01	] : 0.01	
d : 0.34	c : 0.28	] : 0.07	b : 0.07	g : 0.07	e : 0.05	2 : 0.01	= : 0.01	f : 0.01	3 : 0.01	
d : 0.38	g : 0.09	3 : 0.09	] : 0.07	e : 0.07	f : 0.05	b : 0.05	2 : 0.03	a : 0.03	= : 0.01	i : 0.01	c : 0.01	4 : 0.01	
3 : 0.17	2 : 0.15	] : 0.13	e : 0.11	g : 0.11	d : 0.09	f : 0.05	c : 0.03	a : 0.03	4 : 0.03	= : 0.01	i : 0.01	
3 : 0.15	e : 0.15	2 : 0.13	g : 0.11	d : 0.11	c : 0.09	f : 0.09	4 : 0.03	i : 0.03	] : 0.01	= : 0.01	a : 0.01	
e : 0.21	f : 0.15	g : 0.13	c : 0.11	3 : 0.11	d : 0.11	4 : 0.03	i : 0.03	= : 0.01	b : 0.01	h : 0.01	a : 0.01	
e : 0.19	f : 0.15	c : 0.13	d : 0.09	] : 0.07	b : 0.07	g : 0.05	3 : 0.05	2 : 0.03	i : 0.03	a : 0.01	4 : 0.01	= : 0.01	h : 0.01	
e : 0.19	f : 0.17	c : 0.11	d : 0.09	] : 0.07	b : 0.07	3 : 0.07	g : 0.05	2 : 0.03	h : 0.03	i : 0.03	= : 0.01	
e : 0.21	f : 0.13	c : 0.09	] : 0.07	g : 0.07	3 : 0.07	2 : 0.05	b : 0.05	d : 0.05	a : 0.03	h : 0.03	i : 0.03	= : 0.01	4 : 0.01	
e : 0.15	b : 0.13	f : 0.13	2 : 0.09	c : 0.09	3 : 0.07	d : 0.07	g : 0.05	4 : 0.03	] : 0.03	h : 0.03	i : 0.03	: : 0.01	
b : 0.11	f : 0.11	4 : 0.09	e : 0.09	d : 0.09	] : 0.09	2 : 0.07	3 : 0.05	c : 0.05	i : 0.05	g : 0.05	h : 0.03	: : 0.01	a : 0.01	

#score	726.8360624374703
#seq	52
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_CDS_m1_run1.txt

#BEAR
[eeeee[ccc"""ddddqqqqqqqqdddd333ccc]eeee	chr1:155899018-155899258(-)$1	240	174	214	12.9820
[ggggggg[ccc!!ddddooooooddddccc]ggggggg]	chr16:30718551-30718789(+)$1	238	77	117	12.7891
$$ccc[dddd^^^^^^^^^^^^^^^^^^^^^dddd]ccc3	chr17:44248134-44248375(-)$1	241	189	229	10.5154
ddd!!bb!!dddd[eeeeennnnneeeee22dddd]bb]d	chr1:1248091-1248334(-)$1	243	179	219	11.0428
ggggggg[dddd^^^^^^^^^^^^^^^^^^ddddgggggg	chr19:10220769-10221020(+)$1	251	58	98	10.9404
cccffffffccc####bbqqqqqqqqbb4444ccc]ffff	chr12:1025822-1026045(-)$1	223	169	209	11.2357
:::ccc[dddd"""ddddoooooodddd333dddd]ccc:	chr17:36002176-36002398(-)$1	222	41	81	11.4901
d[ccc!!ggggggg[ddddoooooodddd22ggggggg33	chr5:179049995-179050239(-)$1	244	68	108	14.1065
cccccc!!gggggggwwwwwwwwwwwwwwggggggg22cc	chr1:115263199-115263425(-)$1	226	181	221	11.0790
eeee!!ccc[bb!!ccc[annnnna]ccc22bb]ccc]ee	chr5:134010779-134011006(+)$1	227	101	141	11.8821
iiiiiiiii[bb!!cccooooooccc]bb]iiiiiiiii]	chr15:75198930-75199153(-)$1	223	112	152	11.4008
iiiiiiiiddddccctttttttttttccc]dddd4444ii	chr5:71493077-71493306(+)$1	229	159	199	11.0624
[bbccc[a!!a!!ddddqqqqqqqqdddd22a22a]ccc]	chr19:40748342-40748572(-)$1	230	67	107	13.0307
"ccc!!ccc####ddddqqqqqqqqdddd333ccc]ccc]	chr19:2438281-2438506(-)$1	225	161	201	13.9357
ffff$$$$$ccc!!ddddqqqqqqqqdddd333cccffff	chr5:176562894-176563119(+)$1	225	60	100	11.8989
hhhhhhhdddd[ccc!!cccooooooccc333ccc]dddd	chr5:145849168-145849392(+)$1	224	159	199	12.8123
eeee"""bbccc!!eeeeennnnneeeee22ccc4444bb	chr5:145547639-145547876(-)$1	237	87	127	12.1055
g[ccc!!bb[ccc!!bblllbb4444ccc]bbcccggggg	chr5:137910904-137911135(-)$1	231	53	93	9.8458
gggggg!!bb"""ccc[bbmmmmbb]ccc22bb333gggg	chr22:24236528-24236764(+)$1	236	60	100	10.7047
gggg[ccc[eeeee[aooooooa]eeeee22cccgggggg	chr2:24149336-24149565(-)$1	229	74	114	11.9554
===========!!bb[cccpppppppccc]bb]=======	chr19:36223663-36223883(+)$1	220	68	108	10.3942
dd[ccc####ccc[cccrrrrrrrrrccc]ccc4444ccc	chr19:42794904-42795127(+)$1	223	28	68	14.6318
ffff####dddd"""cccpppppppccc333dddd77777	chr5:134032727-134032950(+)$1	223	30	70	11.7020
eeee[iiiiiiiii[cccqqqqqqqqccc]iiiiiiiii]	chr5:179247910-179248136(+)$1	226	91	131	11.7287
cc[ccc[ccc[bb[ccc!!cccmmmmccc22ccc]bb]cc	chr2:198285066-198285288(-)$1	222	85	125	10.4146
cc]bbcccccc!!eeeeeooooooeeeee333ccc]cccE	chr17:62502102-62502351(-)$1	249	139	179	12.6580
ffffff!!dddd!!cccrrrrrrrrrccc22dddd]ffff	chr13:35692296-35692517(+)$1	221	91	131	16.3102
!cccccc[eeeee[bbrrrrrrrrrbbeeeee]ccc]ccc	chr19:50906252-50906474(+)$1	222	116	156	11.1454
::ffffffdddd!!ddddoooooodddd22dddd333fff	chr2:96949590-96949816(-)$1	226	96	136	11.6224
ccc:ccc!!ccc[cccabboooooobb]a]ccc]ccc333	chr7:98586462-98586684(+)$1	222	117	157	11.9937
###bb"""gggggggdddd!!aooooooa22dddd333gg	chr7:107599696-107599921(-)$1	225	100	140	12.7505
=ccc[bb!!dddd!!ddddoooooodddd22dddd]bb]c	chr5:137495672-137495903(-)$1	231	141	181	14.6840
fffffdddd[cccddddrrrrrrrrrdddd22ccc]dddd	chr22:50666235-50666465(-)$1	230	21	61	12.6608
=====!!ccc[ccc[ddddpppppppdddd]ccc]ccc]=	chr13:96705345-96705567(-)$1	222	17	57	10.6103
!!ccc"""dddd[bb[cccmmmmcccbb333dddd333cc	chr1:54666117-54666357(+)$1	240	66	106	12.6612
a####ggggggg!!ddddcccnnnnnccc22dddd22ggg	chr2:39090427-39090648(-)$1	221	114	154	12.0840
ff[dddd[dddd####ddddoooooodddddddddddd44	chr8:22102922-22103158(+)$1	236	159	199	11.7528
[eeeee[bb!!dddd[eeeeellleeeee22dddd22bb3	chr17:43112111-43112335(-)$1	224	94	134	10.9461
cceeeee####dddd!!cccooooooccc22dddd22eee	chr17:1583919-1584152(-)$1	233	51	91	13.4904
!dddd[dddd[eeeee[allla]eeeee333dddd333dd	chr17:3527282-3527515(-)$1	233	118	158	11.4324
ffffff[dddd"""ddddpppppppdddd333dddd]fff	chr16:2139734-2139960(-)$1	226	62	102	11.8880
ffffff"""ccc!!ccczzzzzzzzzzzzzzzzzccc22c	chr12:116446708-116446936(-)$1	228	152	192	11.7627
eee[ccc[dddd[a!!cccooooooccc]a]ddddccc]e	chr10:70101299-70101525(+)$1	226	72	112	14.0571
ggggg"""dddd[bb[a[cccmmmmccc]a22bb333ddd	chr15:64423932-64424160(+)$1	228	58	98	10.8889
ffff[ddddddddbb!!assssssssssa22bb]dddd22	chr1:154246308-154246535(+)$1	227	97	137	10.5546
=======[ccc!!ccc[a[bblllbbaccc4444ccc22=	chr19:36595434-36595663(+)$1	229	128	168	11.2915
ee[dddd[dddd!!cccqqqqqqqqccc333dddd]dddd	chr12:46633374-46633604(-)$1	230	22	62	13.6273
iiiiii!!ccceeeeerrrrrrrrreeeee22ccc88888	chr15:44794089-44794320(+)$1	231	148	188	12.4613
eeee[cccdddd!!bb[cccooooooccc]bb4444dddd	chr20:5165433-5165654(+)$1	221	68	108	12.3201
ff[bb[bbeeeee####cccooooooccc22eeeee7777	chr12:53856194-53856423(+)$1	229	102	142	10.6768
eeeee[eeeeebb[ccc"""ccclllccc22ccc]bb444	chr7:92869118-92869342(+)$1	224	85	125	10.0208
fff[bb!!a!!ggggggg^^^^^^^^^^^^^^^^^^gggg	chr3:49737016-49737258(+)$1	242	117	157	9.6512
:ffffff[ccceeeeerrrrrrrrreeeee]ccc22ffff	chr11:62655880-62656113(+)$1	233	115	155	10.8325
bbb####ccc[eeeeeqqqqqqqqeeeee22ccc333bb]	chr3:37090372-37090590(+)$1	218	128	168	11.5397
[a[dddd[a[a[ddddqqqqqqqqdddda22a]dddd]a]	chr9:95050043-95050274(-)$1	231	138	178	11.3605
dddd[a!!cccdddd!!cccooooooccc22dddd>>>>>	chr17:3717585-3717811(-)$1	226	145	185	14.1187
ddd$$$$$dddd"""eeeeemmmmeeeee22dddd4444d	chr5:179044716-179044984(-)$1	268	53	93	11.4545

#otherMatches

#Seq PSSM
GCGUAUUCUCUUAUCUUGUUUAUGGAAGGGUUGGGUGUAU	chr1:155899018-155899258(-)$1	240	174	214	12.9820
GCAGUGGCUCUCUGCUGACUUUGCUCAGGAGCGCCGUUGG	chr16:30718551-30718789(+)$1	238	77	117	12.7891
AAAUGUUGGCACAAGGAAGAAUGAAUGAAUCGCCAUUAUG	chr17:44248134-44248375(-)$1	241	189	229	10.5154
GGCGGGCGGCGUGGGGCCCACCUCGGGUCAGCACGGGCAG	chr1:1248091-1248334(-)$1	243	179	219	11.0428
AGCCUGACGGCGACCACAACAUCACAGAGCUGCCUCAGGC	chr19:10220769-10221020(+)$1	251	58	98	10.9404
GCUGCAGCAGGUGACCUCCCCUUCCAGACCCAGCCAUGCU	chr12:1025822-1026045(-)$1	223	169	209	11.2357
UUACAUUUUUUGGGUUUUAGAUAGGAAAAAGGAAAUAUGA	chr17:36002176-36002398(-)$1	222	41	81	11.4901
UUGCAGUUUGUUUCGACGCCGGACCGCGUAAGAGACGAUG	chr5:179049995-179050239(-)$1	244	68	108	14.1065
GUGUGUCCUGGGCCAAAAUGCACAAACUAUGGCUUACAAC	chr1:115263199-115263425(-)$1	226	181	221	11.0790
CAUCCAGAAACUCAACUGUAACCCAGAGUAAGGCUUCAGA	chr5:134010779-134011006(+)$1	227	101	141	11.8821
CCUCCGGGCAGAUCGGUAAUAGAGCCCUCCGUCUGGGGGA	chr15:75198930-75199153(-)$1	223	112	152	11.4008
UCAUUGAAAAACCACCAGCAGUUCCAGUGAGUUUUGAAUU	chr5:71493077-71493306(+)$1	229	159	199	11.0624
CCCCCAGUGACUCCUCCACGACUGAGGAGAUGGAAGUGGC	chr19:40748342-40748572(-)$1	230	67	107	13.0307
CAGCAGGGUAUAUGCAACAGACAGAUUGUCACACCAGCUC	chr19:2438281-2438506(-)$1	225	161	201	13.9357
CCAGUACCAGUACAUUAGGAAACAUGCUAGAAUUACCUGG	chr5:176562894-176563119(+)$1	225	60	100	11.8989
CUUGGAAAGUAGUAUAAACUGUAAUAAGUAGAAUGGUAUU	chr5:145849168-145849392(+)$1	224	159	199	12.8123
GGUUGCCCCCCUGAUUUUCCAGAUGAAGAAGAGGAAGAGG	chr5:145547639-145547876(-)$1	237	87	127	12.1055
UGCCGCCACCGCAUCGCGCAGCUCUUUGCCGUCGGAGCGC	chr5:137910904-137911135(-)$1	231	53	93	9.8458
GGCACGUAGCUCAGCGGCGGCCGCGGCGCGUGCGUCUGUG	chr22:24236528-24236764(+)$1	236	60	100	10.7047
CGCCAGCUGCCCCGCCGCCAAAGCCGGGGGAAGCGGUGGC	chr2:24149336-24149565(-)$1	229	74	114	11.9554
GGUCCUUGGGGCUGCAGGGGACAGGGCCCGGCCUCCUGAG	chr19:36223663-36223883(+)$1	220	68	108	10.3942
GGUCACCAAUGUGGUGCGGCCUGUCAGCAGCACUCCUGUG	chr19:42794904-42795127(+)$1	223	28	68	14.6318
GAUUUUAUGACAAUGUAAUGAUUUUUUAAAAUGUCUCUUU	chr5:134032727-134032950(+)$1	223	30	70	11.7020
CUUCAGCUUCUGCUGCAGCCCCGAGCCUGAGGCGGAAGCC	chr5:179247910-179248136(+)$1	226	91	131	11.7287
CAUAGGCGGACCAUGAUAAUUUCCCCAGAGCGUCUUGAUC	chr2:198285066-198285288(-)$1	222	85	125	10.4146
ACCGCGGCCGGGACCGAGGGUGAGUUUGGGAGCCGAGCUG	chr17:62502102-62502351(-)$1	249	139	179	12.6580
ACUUCAGAGUAUAUUAAAUUACCUACUUACGAUGCAUGAG	chr13:35692296-35692517(+)$1	221	91	131	16.3102
UGGGGGGAGCCGGAGCCCUUCCUACGCCUGGCGCUCACCC	chr19:50906252-50906474(+)$1	222	116	156	11.1454
CCCGAAUGCGCUACAUCUCCUCCCAGAUUGAGCGGCCCAU	chr2:96949590-96949816(-)$1	226	96	136	11.6224
CUUAGCCAAGGUGAGACCGAAAAAACGAGCUUUGACCAGA	chr7:98586462-98586684(+)$1	222	117	157	11.9937
UUACCUGGGCACUGGGGCUUUCCAAGUUGCCAGCCCUGCC	chr7:107599696-107599921(-)$1	225	100	140	12.7505
AGAAGGUGAGGCGAUCAGGAAGGAACCUGUGUGCCAGUGU	chr5:137495672-137495903(-)$1	231	141	181	14.6840
GCCUGAGGAGGUACCUGCAGUAUUACCGGGCCUGCGUCCU	chr22:50666235-50666465(-)$1	230	21	61	12.6608
CCACGAACGUGGUGCGGCUGCUACUAGGCUCCACAGCGCU	chr13:96705345-96705567(-)$1	222	17	57	10.6103
UCGCCCCCUCUUCACGAGCAUCCGCUGUACAAAGACCAGG	chr1:54666117-54666357(+)$1	240	66	106	12.6612
CUGCAAGAACAAGAUGCUGAUGCUGGAUCUGAGUAAAUUG	chr2:39090427-39090648(-)$1	221	114	154	12.0840
UCCCUCCAUCCGUUCCAGGGACCUCACCCUCGGGGGAGUC	chr8:22102922-22103158(+)$1	236	159	199	11.7528
GGCCUGACAGGGGGCAUUGCCUCAGGCAAGAGCUCAGUGA	chr17:43112111-43112335(-)$1	224	94	134	10.9461
CAUCAAAACUGAGGAUCCUGACUUGCCAGCUUUCUACUUU	chr17:1583919-1584152(-)$1	233	51	91	13.4904
CUCAGUGUGGCCACGGGCUUCGGCUGUGCAACCAUCUUCU	chr17:3527282-3527515(-)$1	233	118	158	11.4324
GGCCGCAGGAGCAGCCGGGCGCCCGCCGGAUCUUCCCGUG	chr16:2139734-2139960(-)$1	226	62	102	11.8880
GCUGCAAAAGAGACCCUUAAUACCAUUUCACCAUAGGCCC	chr12:116446708-116446936(-)$1	228	152	192	11.7627
CUACUCCUGGAGGCGGCUCUGGCAUGGGAGGUUCUGGAAU	chr10:70101299-70101525(+)$1	226	72	112	14.0571
AAGAAAAAAUUGAGCAGCUCCACCAGGAACAGGCCAACAA	chr15:64423932-64424160(+)$1	228	58	98	10.8889
CAGACUGGGGCUCCCAGAGGCCAUUUCAUAGGGUGAGUAU	chr1:154246308-154246535(+)$1	227	97	137	10.5546
GACCUUUACCGUGUGGUGAGCUAAGCCCCAGAGUUGGGAA	chr19:36595434-36595663(+)$1	229	128	168	11.2915
UGAUGCAUUUCAAAAGUGGACUCGAAUUAACUGAGUUGCA	chr12:46633374-46633604(-)$1	230	22	62	13.6273
CAUUAUUAGGUAAGAUGUAACUUAAAUCUUUAACCACUGU	chr15:44794089-44794320(+)$1	231	148	188	12.4613
AGGUUCAUUGUCCCCAUAUCUUGUGUGAUCUGUAAUGACA	chr20:5165433-5165654(+)$1	221	68	108	12.3201
CAUCCCGUACCGGCCCAAGCCGUCCAGCUCUCCGGUCAUC	chr12:53856194-53856423(+)$1	229	102	142	10.6768
UCAGUGAUCUUGGUGCCAUAGAGAGUCUCCGGGUCCCUGG	chr7:92869118-92869342(+)$1	224	85	125	10.0208
UGGCGGUUGCGGGGCCAGCCCACCGUCCUCCUCACACUGG	chr3:49737016-49737258(+)$1	242	117	157	9.6512
CGGCUGGACUGCAGGCCUCCGACCUGCCUGCCAGCGCCAG	chr11:62655880-62656113(+)$1	233	115	155	10.8325
GCCAGCAGGUACAGUGGUGAUGCACACUGGCACCCCAGGA	chr3:37090372-37090590(+)$1	218	128	168	11.5397
GGGGAUUACAGAGUAUAACAAUCAGUGCCGAGCAAUUGUG	chr9:95050043-95050274(-)$1	231	138	178	11.3605
CCAGGCAGGAUAGUAAAGGCCUCUACGCCGAUACUCGGGA	chr17:3717585-3717811(-)$1	226	145	185	14.1187
CUCAAUUACUGUUUUUCAGGAAUGUCUGAUCACAGAUACG	chr5:179044716-179044984(-)$1	268	53	93	11.4545

#DB
.(((((.(((...((((........))))...))).))))	chr1:155899018-155899258(-)$1	1	174	214	12.9820
.(((((((.(((..((((......))))))).))))))).	chr16:30718551-30718789(+)$1	1	77	117	12.7891
..(((.((((.....................)))).))).	chr17:44248134-44248375(-)$1	1	189	229	10.5154
(((..((..((((.(((((.....)))))..)))).)).)	chr1:1248091-1248334(-)$1	1	179	219	11.0428
(((((((.((((..................))))))))))	chr19:10220769-10221020(+)$1	1	58	98	10.9404
)))(((((((((....((........))....))).))))	chr12:1025822-1026045(-)$1	1	169	209	11.2357
...(((.((((...((((......))))...)))).))).	chr17:36002176-36002398(-)$1	1	41	81	11.4901
(.(((..(((((((.((((......))))..)))))))..	chr5:179049995-179050239(-)$1	1	68	108	14.1065
((((((..(((((((..............)))))))..))	chr1:115263199-115263425(-)$1	1	181	221	11.0790
((((..(((.((..(((.(.....).)))..)).))).))	chr5:134010779-134011006(+)$1	1	101	141	11.8821
(((((((((.((..(((......))).)).))))))))).	chr15:75198930-75199153(-)$1	1	112	152	11.4008
(((((((((((((((...........))).))))....))	chr5:71493077-71493306(+)$1	1	159	199	11.0624
.(((((.(..(..((((........))))..)..).))).	chr19:40748342-40748572(-)$1	1	67	107	13.0307
.(((..(((....((((........))))...))).))).	chr19:2438281-2438506(-)$1	1	161	201	13.9357
((((.....(((..((((........))))...)))))))	chr5:176562894-176563119(+)$1	1	60	100	11.8989
(((((((((((.(((..(((......)))...))).))))	chr5:145849168-145849392(+)$1	1	159	199	12.8123
((((...(((((..(((((.....)))))..)))....))	chr5:145547639-145547876(-)$1	1	87	127	12.1055
(.(((..((.(((..((...))....))).))))))))))	chr5:137910904-137911135(-)$1	1	53	93	9.8458
((((((..((...(((.((....)).)))..))...))))	chr22:24236528-24236764(+)$1	1	60	100	10.7047
((((.(((.(((((.(......).)))))..)))))))))	chr2:24149336-24149565(-)$1	1	74	114	11.9554
(((((((((((..((.(((.......))).)).)))))))	chr19:36223663-36223883(+)$1	1	68	108	10.3942
((.(((....(((.(((.........))).)))....)))	chr19:42794904-42795127(+)$1	1	28	68	14.6318
((((....((((...(((.......)))...)))).....	chr5:134032727-134032950(+)$1	1	30	70	11.7020
((((.(((((((((.(((........))).))))))))).	chr5:179247910-179248136(+)$1	1	91	131	11.7287
((.(((.(((.((.(((..(((....)))..))).)).))	chr2:198285066-198285288(-)$1	1	85	125	10.4146
)).))((((((..(((((......)))))...))).))))	chr17:62502102-62502351(-)$1	1	139	179	12.6580
((((((..((((..(((.........)))..)))).))))	chr13:35692296-35692517(+)$1	1	91	131	16.3102
.((((((.(((((.((.........))))))).))).)))	chr19:50906252-50906474(+)$1	1	116	156	11.1454
..((((((((((..((((......))))..))))...)))	chr2:96949590-96949816(-)$1	1	96	136	11.6224
))).(((..(((.((((((......)).).))).)))...	chr7:98586462-98586684(+)$1	1	117	157	11.9937
...((...(((((((((((..(......)..))))...))	chr7:107599696-107599921(-)$1	1	100	140	12.7505
((((.((..((((..((((......))))..)))).)).)	chr5:137495672-137495903(-)$1	1	141	181	14.6840
)))))((((.(((((((.........))))..))).))))	chr22:50666235-50666465(-)$1	1	21	61	12.6608
(((((..(((.(((.((((.......)))).))).))).)	chr13:96705345-96705567(-)$1	1	17	57	10.6103
..(((...((((.((.(((....)))))...))))...))	chr1:54666117-54666357(+)$1	1	66	106	12.6612
(....(((((((..(((((((.....)))..))))..)))	chr2:39090427-39090648(-)$1	1	114	154	12.0840
((.((((.((((....((((......))))))))))))..	chr8:22102922-22103158(+)$1	1	159	199	11.7528
.(((((.((..((((.(((((...)))))..))))..)).	chr17:43112111-43112335(-)$1	1	94	134	10.9461
(((((((....((((..(((......)))..))))..)))	chr17:1583919-1584152(-)$1	1	51	91	13.4904
.((((.((((.(((((.(...).)))))...))))...))	chr17:3527282-3527515(-)$1	1	118	158	11.4324
((((((.((((...((((.......))))...)))).)))	chr16:2139734-2139960(-)$1	1	62	102	11.8880
((((((...(((..(((.................)))..)	chr12:116446708-116446936(-)$1	1	152	192	11.7627
(((.(((.((((.(..(((......))).).))))))).)	chr10:70101299-70101525(+)$1	1	72	112	14.0571
(((((...((((.((.(.(((....))).)..))...)))	chr15:64423932-64424160(+)$1	1	58	98	10.8889
((((.((((((((((..(..........)..)).))))..	chr1:154246308-154246535(+)$1	1	97	137	10.5546
(((((((.(((..(((.(.((...))))))....)))..)	chr19:36595434-36595663(+)$1	1	128	168	11.2915
((.((((.((((..(((........)))...)))).))))	chr12:46633374-46633604(-)$1	1	22	62	13.6273
((((((..((((((((.........)))))..))).....	chr15:44794089-44794320(+)$1	1	148	188	12.4613
((((.(((((((..((.(((......))).))....))))	chr20:5165433-5165654(+)$1	1	68	108	12.3201
((.((.(((((((....(((......)))..)))))....	chr12:53856194-53856423(+)$1	1	102	142	10.6768
(((((.(((((((.(((...(((...)))..))).))...	chr7:92869118-92869342(+)$1	1	85	125	10.0208
(((.((..(..(((((((..................))))	chr3:49737016-49737258(+)$1	1	117	157	9.6512
.((((((.((((((((.........))))).)))..))))	chr11:62655880-62656113(+)$1	1	115	155	10.8325
(((....(((.(((((........)))))..)))...)).	chr3:37090372-37090590(+)$1	1	128	168	11.5397
.(.((((.(.(.((((........)))))..).)))).).	chr9:95050043-95050274(-)$1	1	138	178	11.3605
((((.(..(((((((..(((......)))..)))).....	chr17:3717585-3717811(-)$1	1	145	185	14.1187
(((.....((((...(((((....)))))..))))....)	chr5:179044716-179044984(-)$1	1	53	93	11.4545

#PSSM
f : 0.17	e : 0.12	c : 0.10	[ : 0.08	d : 0.08	g : 0.08	= : 0.07	: : 0.05	i : 0.05	! : 0.05	$ : 0.01	" : 0.01	h : 0.01	# : 0.01	a : 0.01	b : 0.01	
f : 0.19	e : 0.15	c : 0.15	g : 0.08	d : 0.08	i : 0.05	= : 0.05	: : 0.03	[ : 0.03	b : 0.03	# : 0.03	$ : 0.01	h : 0.01	! : 0.01	a : 0.01	
c : 0.17	f : 0.17	e : 0.15	[ : 0.10	g : 0.08	d : 0.07	i : 0.05	= : 0.05	b : 0.03	# : 0.03	: : 0.01	h : 0.01	] : 0.01	
c : 0.21	f : 0.17	e : 0.14	g : 0.08	d : 0.08	i : 0.05	= : 0.05	b : 0.05	# : 0.03	[ : 0.03	! : 0.01	h : 0.01	: : 0.01	$ : 0.01	
c : 0.21	f : 0.12	[ : 0.10	e : 0.07	g : 0.07	b : 0.07	d : 0.07	! : 0.05	i : 0.05	= : 0.05	# : 0.05	$ : 0.03	h : 0.01	" : 0.01	
c : 0.19	f : 0.10	! : 0.08	d : 0.08	g : 0.07	[ : 0.07	i : 0.07	" : 0.07	e : 0.05	b : 0.05	$ : 0.03	= : 0.03	# : 0.03	h : 0.01	a : 0.01	
! : 0.15	c : 0.14	d : 0.12	[ : 0.10	" : 0.08	g : 0.05	b : 0.05	f : 0.05	i : 0.05	# : 0.05	$ : 0.03	= : 0.03	e : 0.03	h : 0.01	
c : 0.15	! : 0.15	[ : 0.14	d : 0.12	b : 0.07	" : 0.07	g : 0.05	i : 0.05	# : 0.05	f : 0.03	$ : 0.03	a : 0.01	= : 0.01	e : 0.01	
d : 0.33	c : 0.19	! : 0.07	g : 0.07	b : 0.07	e : 0.05	[ : 0.03	i : 0.03	# : 0.03	a : 0.03	f : 0.01	$ : 0.01	= : 0.01	" : 0.01	
d : 0.35	c : 0.26	[ : 0.08	g : 0.07	e : 0.07	! : 0.05	# : 0.05	b : 0.01	= : 0.01	i : 0.01	
d : 0.31	c : 0.24	g : 0.07	e : 0.07	[ : 0.07	" : 0.03	b : 0.03	a : 0.03	# : 0.03	! : 0.03	^ : 0.01	= : 0.01	i : 0.01	
d : 0.31	c : 0.17	e : 0.12	g : 0.08	" : 0.07	b : 0.07	! : 0.07	[ : 0.03	^ : 0.01	# : 0.01	i : 0.01	
! : 0.26	d : 0.12	e : 0.12	" : 0.10	c : 0.10	g : 0.07	[ : 0.07	# : 0.05	^ : 0.03	b : 0.03	i : 0.01	
! : 0.22	d : 0.14	c : 0.10	e : 0.10	[ : 0.08	" : 0.07	g : 0.07	b : 0.07	# : 0.05	^ : 0.03	i : 0.01	a : 0.01	
d : 0.24	c : 0.22	e : 0.12	b : 0.10	[ : 0.07	# : 0.05	g : 0.05	! : 0.05	^ : 0.03	" : 0.03	
d : 0.26	c : 0.22	e : 0.14	! : 0.08	[ : 0.07	# : 0.05	b : 0.05	^ : 0.03	w : 0.01	t : 0.01	a : 0.01	g : 0.01	
d : 0.26	c : 0.22	e : 0.08	! : 0.07	[ : 0.07	r : 0.05	^ : 0.03	b : 0.03	a : 0.03	q : 0.03	w : 0.01	t : 0.01	o : 0.01	# : 0.01	g : 0.01	
d : 0.19	c : 0.17	q : 0.10	r : 0.10	e : 0.08	b : 0.05	a : 0.05	^ : 0.03	[ : 0.03	o : 0.03	w : 0.01	t : 0.01	l : 0.01	! : 0.01	z : 0.01	" : 0.01	g : 0.01	
c : 0.17	q : 0.15	o : 0.10	r : 0.10	d : 0.08	e : 0.07	^ : 0.05	l : 0.03	b : 0.03	p : 0.03	w : 0.01	a : 0.01	t : 0.01	! : 0.01	z : 0.01	s : 0.01	[ : 0.01	" : 0.01	
o : 0.17	q : 0.15	c : 0.14	r : 0.10	p : 0.07	^ : 0.05	n : 0.05	l : 0.03	m : 0.03	e : 0.03	w : 0.01	t : 0.01	! : 0.01	d : 0.01	z : 0.01	s : 0.01	b : 0.01	" : 0.01	
o : 0.28	q : 0.15	r : 0.10	p : 0.07	c : 0.07	^ : 0.05	n : 0.05	m : 0.05	b : 0.03	w : 0.01	t : 0.01	! : 0.01	e : 0.01	l : 0.01	z : 0.01	s : 0.01	
o : 0.28	q : 0.15	r : 0.10	n : 0.07	m : 0.07	p : 0.07	^ : 0.05	c : 0.03	a : 0.03	l : 0.03	w : 0.01	t : 0.01	b : 0.01	z : 0.01	s : 0.01	
o : 0.28	q : 0.15	r : 0.10	m : 0.08	n : 0.07	p : 0.07	^ : 0.05	l : 0.03	w : 0.01	t : 0.01	4 : 0.01	a : 0.01	] : 0.01	z : 0.01	s : 0.01	c : 0.01	
o : 0.26	q : 0.15	r : 0.10	n : 0.07	p : 0.07	^ : 0.05	m : 0.05	l : 0.05	c : 0.03	w : 0.01	t : 0.01	4 : 0.01	b : 0.01	] : 0.01	e : 0.01	z : 0.01	s : 0.01	
o : 0.19	e : 0.14	q : 0.12	r : 0.10	d : 0.07	p : 0.07	^ : 0.05	c : 0.03	b : 0.03	m : 0.03	w : 0.01	a : 0.01	t : 0.01	4 : 0.01	n : 0.01	z : 0.01	s : 0.01	l : 0.01	
d : 0.17	e : 0.17	o : 0.12	c : 0.10	^ : 0.05	q : 0.05	r : 0.05	b : 0.05	] : 0.03	p : 0.03	w : 0.01	t : 0.01	4 : 0.01	m : 0.01	n : 0.01	z : 0.01	s : 0.01	l : 0.01	
c : 0.35	d : 0.24	e : 0.17	b : 0.07	^ : 0.05	w : 0.01	] : 0.01	o : 0.01	z : 0.01	s : 0.01	a : 0.01	
c : 0.36	d : 0.24	e : 0.19	^ : 0.05	b : 0.05	w : 0.01	] : 0.01	o : 0.01	z : 0.01	s : 0.01	
c : 0.31	d : 0.17	e : 0.17	3 : 0.08	a : 0.07	^ : 0.05	] : 0.03	4 : 0.01	w : 0.01	b : 0.01	2 : 0.01	z : 0.01	
2 : 0.38	3 : 0.17	] : 0.14	d : 0.07	^ : 0.05	e : 0.05	c : 0.03	a : 0.03	4 : 0.01	g : 0.01	z : 0.01	
2 : 0.42	3 : 0.19	d : 0.07	c : 0.05	b : 0.05	] : 0.05	^ : 0.03	4 : 0.03	i : 0.03	g : 0.01	e : 0.01	z : 0.01	
d : 0.35	c : 0.15	3 : 0.10	b : 0.10	2 : 0.05	4 : 0.03	g : 0.03	i : 0.03	a : 0.03	e : 0.03	] : 0.01	z : 0.01	^ : 0.01	
d : 0.36	c : 0.29	b : 0.07	g : 0.05	] : 0.05	i : 0.03	4 : 0.03	2 : 0.01	3 : 0.01	z : 0.01	e : 0.01	^ : 0.01	
d : 0.38	c : 0.29	g : 0.05	] : 0.05	4 : 0.05	i : 0.03	2 : 0.01	3 : 0.01	= : 0.01	z : 0.01	b : 0.01	e : 0.01	^ : 0.01	
d : 0.35	c : 0.24	g : 0.08	4 : 0.07	3 : 0.07	] : 0.05	i : 0.03	a : 0.01	= : 0.01	e : 0.01	^ : 0.01	2 : 0.01	
] : 0.22	c : 0.14	3 : 0.12	g : 0.10	4 : 0.08	2 : 0.07	d : 0.07	i : 0.03	b : 0.03	= : 0.01	7 : 0.01	8 : 0.01	e : 0.01	^ : 0.01	> : 0.01	
c : 0.19	g : 0.12	d : 0.12	3 : 0.10	b : 0.07	f : 0.07	2 : 0.07	4 : 0.07	i : 0.03	7 : 0.03	] : 0.03	e : 0.01	= : 0.01	8 : 0.01	> : 0.01	
c : 0.15	g : 0.14	d : 0.12	f : 0.10	b : 0.07	4 : 0.07	3 : 0.07	2 : 0.05	] : 0.05	e : 0.03	i : 0.03	7 : 0.03	= : 0.01	8 : 0.01	> : 0.01	
c : 0.17	g : 0.14	f : 0.10	d : 0.10	] : 0.07	e : 0.05	i : 0.05	b : 0.05	4 : 0.05	2 : 0.05	3 : 0.03	7 : 0.03	= : 0.01	8 : 0.01	a : 0.01	> : 0.01	
d : 0.14	] : 0.12	g : 0.12	c : 0.12	f : 0.10	e : 0.07	3 : 0.07	= : 0.05	7 : 0.03	4 : 0.03	: : 0.01	i : 0.01	b : 0.01	E : 0.01	2 : 0.01	8 : 0.01	> : 0.01	

#score	680.9980953461135
#seq	57
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_CDS_m2_run2.txt

#BEAR
bddddpppppppdddd]bb	chr1:6294869-6295134(-)$1	265	44	63	14.1124
[ddddpppppppdddd22c	chr16:4861076-4861368(-)$1	292	200	219	14.7162
f"""apppppppa333fff	chr16:28844303-28844774(+)$1	471	336	355	12.7590
eeeeepppppppeeeee>>	chr2:100055084-100055410(-)$1	326	52	71	15.2123
d[cccpppppppccc]ddd	chrM:6909-7160(+)$1	251	92	111	14.4244
iiiiipppppppiiiiiii	chr16:3534575-3534954(+)$1	379	73	92	13.6918
ddd[apppppppa]dddd3	chr1:27267847-27268089(+)$1	242	120	139	13.8134
eeeeepppppppeeeee33	chr12:64819498-64819783(+)$1	285	207	226	15.5536
!!cccpppppppccc333d	chr2:61710086-61710325(-)$1	239	68	87	15.0376
eeeeepppppppeeeee33	chr1:46827135-46827586(+)$1	451	357	376	15.5536
eeeeepppppppeeeee::	chr7:97821834-97822143(+)$1	309	53	72	14.1056
b[cccpppppppccc]bb:	chr3:123667712-123667986(-)$1	274	53	72	13.4695
[ddddpppppppdddd]a:	chr20:50768793-50769062(-)$1	269	186	205	14.2539
##cccpppppppcccdddd	chr7:77256646-77256915(+)$1	269	99	118	14.2070
""cccpppppppccc22dd	chr2:175673548-175673831(-)$1	283	218	237	14.2134
h[cccpppppppccc]hhh	chr15:69714231-69714544(+)$1	313	236	255	13.9022
eeeeepppppppeeeee22	chr17:729148-729418(-)$1	270	58	77	15.2530
e[cccpppppppccc22ee	chr5:142779120-142779496(-)$1	376	281	300	14.3106
c[cccpppppppccc]ccc	chr11:102272546-102273037(-)$1	491	18	37	14.6257
c[cccpppppppccc]ccc	chr15:41570858-41571182(+)$1	324	123	142	14.6257
eeeeepppppppeeeee22	chr1:152005120-152005365(-)$1	245	10	29	15.2530
[ddddpppppppdddd]a:	chr12:76444276-76444523(-)$1	247	133	152	14.2539
eeebbpppppppbb]eeee	chr13:30091609-30091902(-)$1	293	273	292	13.0851
ddcccpppppppccc]ddd	chr13:30091180-30091547(-)$1	367	220	239	14.3207
eeeeepppppppeeeee::	chr18:60241304-60241647(+)$1	343	151	170	14.1056
:ddddpppppppddddggg	chr9:125627688-125628023(-)$1	335	147	166	13.4760
eddddpppppppdddd>>>	chr16:23647189-23647532(-)$1	343	214	233	14.4294
:ddddpppppppddddddd	chr1:47110732-47111003(-)$1	271	69	88	13.3579
gggggpppppppggggggg	chr16:67904692-67904964(+)$1	272	119	138	13.7960
:ddddpppppppddddccc	chr4:144446525-144446765(+)$1	240	94	113	13.5228
eeeeepppppppeeeee]d	chr17:53036441-53036773(-)$1	332	16	35	15.2713
eeeeepppppppeeeee]e	chr21:34924635-34925105(+)$1	470	398	417	15.1823
!ddddpppppppdddd22d	chr10:22015070-22015361(+)$1	291	98	117	14.6634
a[cccpppppppccc]a::	chrX:53586221-53586595(-)$1	374	58	77	13.5553
eeeeepppppppeeeee::	chr1:115252093-115252432(-)$1	339	70	89	14.1056
fffffpppppppffffff]	chr22:24176225-24176540(+)$1	315	205	224	12.7481
dddbbpppppppbb]dddd	chr1:169390675-169390943(-)$1	268	136	155	12.6114
gggggpppppppggggggg	chr1:31441100-31441426(-)$1	326	208	227	13.7960
eeeeepppppppeeeee]b	chr12:122958586-122958927(-)$1	341	129	148	15.2445
[ddddpppppppdddd]bb	chr2:242174433-242174772(-)$1	339	202	221	14.5132
fffffpppppppffffff2	chrX:153197668-153197978(-)$1	310	286	305	12.6985
!ddddpppppppdddd22a	chr5:55265391-55265663(-)$1	272	95	114	14.7965
eeeeepppppppeeeee22	chr1:153789817-153790116(-)$1	299	39	58	15.2530
c[cccpppppppccc]ccc	chr19:6733754-6734022(-)$1	268	153	172	14.6257
eeeeepppppppeeeee33	chr8:125498203-125498461(+)$1	258	179	198	15.5536
[ddddpppppppdddd]dd	chr4:1834400-1834672(-)$1	272	118	137	14.5562
bbcccpppppppccc]bb4	chr4:39929480-39929838(-)$1	358	107	126	13.5211
!!cccpppppppccc22bb	chrX:71492330-71492643(-)$1	313	53	72	14.4280
!!cccpppppppccc]ddd	chr19:9058106-9058570(-)$1	464	149	168	14.6578
eeeeepppppppeeeee]a	chr16:23641085-23641403(-)$1	318	219	238	15.4044
eeeeepppppppeeeee:E	chr1:220141949-220142288(-)$1	339	12	31	13.9150
h[cccpppppppccc]hhh	chr19:40330790-40331054(-)$1	264	94	113	13.9022
eeeeepppppppeeeee]c	chr16:2569171-2569504(+)$1	333	289	308	15.3484
!!cccpppppppccc22dd	chr22:50893562-50893860(-)$1	298	129	148	14.4710
eeeeepppppppeeeeebb	chrX:107977911-107978401(-)$1	490	390	409	15.0022
eeeeepppppppeeeee::	chr16:2303774-2304092(-)$1	318	96	115	14.1056
eeeeepppppppeeeee::	chr22:36893943-36894306(-)$1	363	30	49	14.1056
gggggpppppppggggggg	chr3:64004174-64004450(-)$1	276	28	47	13.7960
!ddddpppppppdddd333	chr5:169031041-169031302(+)$1	261	198	217	15.1082
eeeeepppppppeeeee::	chr17:15878443-15878694(+)$1	251	90	109	14.1056

#otherMatches

#Seq PSSM
CCAGAUCUGUACUCUGAGG	chr1:6294869-6295134(-)$1	265	44	63	14.1124
AGGGUAGAUGUGGCCCAAG	chr16:4861076-4861368(-)$1	292	200	219	14.7162
CAAGGGAGAAGACAAAGAU	chr16:28844303-28844774(+)$1	471	336	355	12.7590
CACUAAAAUCAAUGGUGCU	chr2:100055084-100055410(-)$1	326	52	71	15.2123
ACUACACGACACGUACUAC	chrM:6909-7160(+)$1	251	92	111	14.4244
CUGGCGAGCGUGGUCAGGG	chr16:3534575-3534954(+)$1	379	73	92	13.6918
CCACCACAAUCAGCUGGCA	chr1:27267847-27268089(+)$1	242	120	139	13.8134
AGCUAUUAUGUUUAGUUAU	chr12:64819498-64819783(+)$1	285	207	226	15.5536
UAACUUUCCAUUGGUAUUC	chr2:61710086-61710325(-)$1	239	68	87	15.0376
UCUGCAAAAUGCGUAGGCU	chr1:46827135-46827586(+)$1	451	357	376	15.5536
AUCUUAUGCACCAAGAUAA	chr7:97821834-97822143(+)$1	309	53	72	14.1056
AAGUGAAAGAGACACAUCA	chr3:123667712-123667986(-)$1	274	53	72	13.4695
GCCUUGAUUCAGGAGGGGA	chr20:50768793-50769062(-)$1	269	186	205	14.2539
CAUGAUAACACUUCACCAC	chr7:77256646-77256915(+)$1	269	99	118	14.2070
UUUCAAAUAACCUGACAAC	chr2:175673548-175673831(-)$1	283	218	237	14.2134
GUAAGUAUGAUUCUUUUGU	chr15:69714231-69714544(+)$1	313	236	255	13.9022
UGGUUUGGACUUAACCACC	chr17:729148-729418(-)$1	270	58	77	15.2530
AUCAGUGUUUUUCUGUUUC	chr5:142779120-142779496(-)$1	376	281	300	14.3106
GUGACCAUGAAAGUCUCAG	chr11:102272546-102273037(-)$1	491	18	37	14.6257
CGGAGUAAAUAUCUCAGAU	chr15:41570858-41571182(+)$1	324	123	142	14.6257
uuugaaagcacauuagaag	chr1:152005120-152005365(-)$1	245	10	29	15.2530
GUCACUUUUUACGUGAGCG	chr12:76444276-76444523(-)$1	247	133	152	14.2539
UGCCAGAGAAGAUGAGCAU	chr13:30091609-30091902(-)$1	293	273	292	13.0851
GCGUCAUCUGGAGGCAGCC	chr13:30091180-30091547(-)$1	367	220	239	14.3207
GCAUAUUUCUUUUAUGCCA	chr18:60241304-60241647(+)$1	343	151	170	14.1056
AGUUGGUGUAAACAACACU	chr9:125627688-125628023(-)$1	335	147	166	13.4760
UAGCAAAAAUCCUGCUAGA	chr16:23647189-23647532(-)$1	343	214	233	14.4294
UCACAGUUUCUAUGUGCUC	chr1:47110732-47111003(-)$1	271	69	88	13.3579
GCUGACCUCCUCUCAGCUA	chr16:67904692-67904964(+)$1	272	119	138	13.7960
ACUGAGAGAUUAUCAGGUC	chr4:144446525-144446765(+)$1	240	94	113	13.5228
aagugauccuuccacuuca	chr17:53036441-53036773(-)$1	332	16	35	15.2713
CAAUGACACCACCAUUGCC	chr21:34924635-34925105(+)$1	470	398	417	15.1823
UUAGGCAAAUACUCUAUCU	chr10:22015070-22015361(+)$1	291	98	117	14.6634
CUCUGGACUUAACAGUGAU	chrX:53586221-53586595(-)$1	374	58	77	13.5553
UUCCCGUUUUUAGGGAGCA	chr1:115252093-115252432(-)$1	339	70	89	14.1056
UUCUGGCAAGGACAGAGGC	chr22:24176225-24176540(+)$1	315	205	224	12.7481
CUGGCUUAUAUCGCUCAGC	chr1:169390675-169390943(-)$1	268	136	155	12.6114
UGGCAGCAGGCAUGCCAGG	chr1:31441100-31441426(-)$1	326	208	227	13.7960
AGAGCAGCGAAAGUUUUCA	chr12:122958586-122958927(-)$1	341	129	148	15.2445
GUGUGAAGGAGCUACAGGC	chr2:242174433-242174772(-)$1	339	202	221	14.5132
UUUGGUGAAGAUCCAGGAA	chrX:153197668-153197978(-)$1	310	286	305	12.6985
AAAUGCUAAUUACAUUGUC	chr5:55265391-55265663(-)$1	272	95	114	14.7965
GCUGUAUUAUACACAGCGU	chr1:153789817-153790116(-)$1	299	39	58	15.2530
CCUACAACUUCAGUGUGAG	chr19:6733754-6734022(-)$1	268	153	172	14.6257
GGCUUAAUCACAGAGCUAC	chr8:125498203-125498461(+)$1	258	179	198	15.5536
CUGGAGCUACAGUCCAUCG	chr4:1834400-1834672(-)$1	272	118	137	14.5562
GCAGUAUCUCCCACUAGCC	chr4:39929480-39929838(-)$1	358	107	126	13.5211
AAAGGGUAUCCGCCUCACC	chrX:71492330-71492643(-)$1	313	53	72	14.4280
UACCCUUCCCUUGGGCACC	chr19:9058106-9058570(-)$1	464	149	168	14.6578
AAGACUCAGUCUGUCUUGC	chr16:23641085-23641403(-)$1	318	219	238	15.4044
GCUCCAUCCAUGGGAGCUA	chr1:220141949-220142288(-)$1	339	12	31	13.9150
CAUUUGUCGAGGAAAGGAA	chr19:40330790-40331054(-)$1	264	94	113	13.9022
UCACCUGUGGGUGGUGACC	chr16:2569171-2569504(+)$1	333	289	308	15.3484
CCGUGGAGCUCACACCCUG	chr22:50893562-50893860(-)$1	298	129	148	14.4710
UGUUCAGGCGAGGGACAGG	chrX:107977911-107978401(-)$1	490	390	409	15.0022
GGAGCCGCUCCAGCUCCAA	chr16:2303774-2304092(-)$1	318	96	115	14.1056
CUGGGCAUCCCUCCCAGUG	chr22:36893943-36894306(-)$1	363	30	49	14.1056
GUACAUUUUUUUUGUAUAU	chr3:64004174-64004450(-)$1	276	28	47	13.7960
CACUUGCCUCAAAAGUUAC	chr5:169031041-169031302(+)$1	261	198	217	15.1082
CGGAACCGAGACUUCCGCU	chr17:15878443-15878694(+)$1	251	90	109	14.1056

#DB
(((((.......)))).))	chr1:6294869-6295134(-)$1	1	44	63	14.1124
.((((.......))))..)	chr16:4861076-4861368(-)$1	1	200	219	14.7162
(...(.......)...)))	chr16:28844303-28844774(+)$1	1	336	355	12.7590
(((((.......)))))..	chr2:100055084-100055410(-)$1	1	52	71	15.2123
(.(((.......))).)))	chrM:6909-7160(+)$1	1	92	111	14.4244
(((((.......)))))))	chr16:3534575-3534954(+)$1	1	73	92	13.6918
(((.(.......).)))).	chr1:27267847-27268089(+)$1	1	120	139	13.8134
(((((.......)))))..	chr12:64819498-64819783(+)$1	1	207	226	15.5536
..(((.......)))...)	chr2:61710086-61710325(-)$1	1	68	87	15.0376
(((((.......)))))..	chr1:46827135-46827586(+)$1	1	357	376	15.5536
(((((.......)))))..	chr7:97821834-97822143(+)$1	1	53	72	14.1056
(.(((.......))).)).	chr3:123667712-123667986(-)$1	1	53	72	13.4695
.((((.......)))).).	chr20:50768793-50769062(-)$1	1	186	205	14.2539
..(((.......)))))))	chr7:77256646-77256915(+)$1	1	99	118	14.2070
..(((.......)))..))	chr2:175673548-175673831(-)$1	1	218	237	14.2134
(.(((.......))).)))	chr15:69714231-69714544(+)$1	1	236	255	13.9022
(((((.......)))))..	chr17:729148-729418(-)$1	1	58	77	15.2530
(.(((.......)))..))	chr5:142779120-142779496(-)$1	1	281	300	14.3106
(.(((.......))).)))	chr11:102272546-102273037(-)$1	1	18	37	14.6257
(.(((.......))).)))	chr15:41570858-41571182(+)$1	1	123	142	14.6257
(((((.......)))))..	chr1:152005120-152005365(-)$1	1	10	29	15.2530
.((((.......)))).).	chr12:76444276-76444523(-)$1	1	133	152	14.2539
(((((.......)).))))	chr13:30091609-30091902(-)$1	1	273	292	13.0851
(((((.......))).)))	chr13:30091180-30091547(-)$1	1	220	239	14.3207
(((((.......)))))..	chr18:60241304-60241647(+)$1	1	151	170	14.1056
.((((.......))))(((	chr9:125627688-125628023(-)$1	1	147	166	13.4760
(((((.......))))...	chr16:23647189-23647532(-)$1	1	214	233	14.4294
.((((.......))))(((	chr1:47110732-47111003(-)$1	1	69	88	13.3579
(((((.......)))))))	chr16:67904692-67904964(+)$1	1	119	138	13.7960
.((((.......))))(((	chr4:144446525-144446765(+)$1	1	94	113	13.5228
(((((.......))))).)	chr17:53036441-53036773(-)$1	1	16	35	15.2713
(((((.......))))).)	chr21:34924635-34925105(+)$1	1	398	417	15.1823
.((((.......))))..)	chr10:22015070-22015361(+)$1	1	98	117	14.6634
(.(((.......))).)..	chrX:53586221-53586595(-)$1	1	58	77	13.5553
(((((.......)))))..	chr1:115252093-115252432(-)$1	1	70	89	14.1056
(((((.......)))))).	chr22:24176225-24176540(+)$1	1	205	224	12.7481
(((((.......)).))))	chr1:169390675-169390943(-)$1	1	136	155	12.6114
(((((.......)))))))	chr1:31441100-31441426(-)$1	1	208	227	13.7960
(((((.......))))).)	chr12:122958586-122958927(-)$1	1	129	148	15.2445
.((((.......)))).))	chr2:242174433-242174772(-)$1	1	202	221	14.5132
(((((.......)))))).	chrX:153197668-153197978(-)$1	1	286	305	12.6985
.((((.......))))..)	chr5:55265391-55265663(-)$1	1	95	114	14.7965
(((((.......)))))..	chr1:153789817-153790116(-)$1	1	39	58	15.2530
(.(((.......))).)))	chr19:6733754-6734022(-)$1	1	153	172	14.6257
(((((.......)))))..	chr8:125498203-125498461(+)$1	1	179	198	15.5536
.((((.......)))).))	chr4:1834400-1834672(-)$1	1	118	137	14.5562
(((((.......))).)).	chr4:39929480-39929838(-)$1	1	107	126	13.5211
..(((.......)))..))	chrX:71492330-71492643(-)$1	1	53	72	14.4280
..(((.......))).)))	chr19:9058106-9058570(-)$1	1	149	168	14.6578
(((((.......))))).)	chr16:23641085-23641403(-)$1	1	219	238	15.4044
(((((.......))))).(	chr1:220141949-220142288(-)$1	1	12	31	13.9150
(.(((.......))).)))	chr19:40330790-40331054(-)$1	1	94	113	13.9022
(((((.......))))).)	chr16:2569171-2569504(+)$1	1	289	308	15.3484
..(((.......)))..))	chr22:50893562-50893860(-)$1	1	129	148	14.4710
(((((.......)))))))	chrX:107977911-107978401(-)$1	1	390	409	15.0022
(((((.......)))))..	chr16:2303774-2304092(-)$1	1	96	115	14.1056
(((((.......)))))..	chr22:36893943-36894306(-)$1	1	30	49	14.1056
(((((.......)))))))	chr3:64004174-64004450(-)$1	1	28	47	13.7960
.((((.......))))...	chr5:169031041-169031302(+)$1	1	198	217	15.1082
(((((.......)))))..	chr17:15878443-15878694(+)$1	1	90	109	14.1056

#PSSM
e : 0.38	! : 0.11	[ : 0.08	d : 0.06	b : 0.05	f : 0.05	c : 0.05	: : 0.05	g : 0.05	h : 0.03	i : 0.01	# : 0.01	" : 0.01	a : 0.01	
e : 0.35	d : 0.26	[ : 0.15	! : 0.06	g : 0.05	" : 0.03	f : 0.03	i : 0.01	# : 0.01	b : 0.01	
e : 0.35	c : 0.28	d : 0.24	g : 0.05	f : 0.03	" : 0.01	i : 0.01	
e : 0.33	c : 0.28	d : 0.21	g : 0.05	b : 0.03	f : 0.03	" : 0.01	i : 0.01	[ : 0.01	
e : 0.33	c : 0.28	d : 0.21	g : 0.05	a : 0.03	b : 0.03	f : 0.03	i : 0.01	
p : 1.00	
p : 1.00	
p : 1.00	
p : 1.00	
p : 1.00	
p : 1.00	
p : 1.00	
e : 0.33	c : 0.28	d : 0.21	g : 0.05	a : 0.03	b : 0.03	f : 0.03	i : 0.01	
e : 0.33	c : 0.28	d : 0.21	g : 0.05	b : 0.03	f : 0.03	3 : 0.01	i : 0.01	] : 0.01	
e : 0.33	c : 0.28	d : 0.23	g : 0.05	] : 0.03	f : 0.03	3 : 0.01	i : 0.01	
e : 0.35	d : 0.26	] : 0.18	2 : 0.06	g : 0.05	3 : 0.03	f : 0.03	i : 0.01	
e : 0.35	2 : 0.11	d : 0.11	] : 0.08	c : 0.06	g : 0.06	f : 0.05	3 : 0.03	b : 0.03	h : 0.03	i : 0.01	> : 0.01	a : 0.01	
d : 0.16	: : 0.13	b : 0.09	2 : 0.09	3 : 0.08	] : 0.08	c : 0.06	g : 0.06	f : 0.05	> : 0.03	a : 0.03	h : 0.03	e : 0.03	i : 0.01	
d : 0.19	: : 0.16	c : 0.09	b : 0.08	3 : 0.08	2 : 0.06	g : 0.06	e : 0.05	> : 0.03	h : 0.03	a : 0.03	f : 0.01	i : 0.01	] : 0.01	4 : 0.01	E : 0.01	

#score	858.4902742032259
#seq	60
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_UTR_m1_run1.txt

#BEAR
eeeeeuuuuuuuuuuuueeeee2	chr9:5921661-5921884(-)$1	223	106	129	23.1292
eeeeevvvvvvvvvvvvveeeee	chr8:104344449-104344715(+)$1	266	117	140	22.6063
ii[bbuuuuuuuuuuuubbiiii	chrX:67755054-67755276(+)$1	222	14	37	22.6857
fffffftttttttttttffffff	chr5:137502242-137502472(-)$1	230	37	60	20.6841
ggggggtttttttttttgggggg	chr12:25357034-25357259(+)$1	225	52	75	20.9939
dcccvvvvvvvvvvvvvccc]dd	chr3:182637234-182637446(+)$1	212	72	95	21.8408
====wwwwwwwwwwwwww=====	chr20:47862371-47862604(-)$1	233	56	79	22.3493
c[cccuuuuuuuuuuuucccccc	chr7:23017722-23017952(-)$1	230	192	215	23.2256
:cccwwwwwwwwwwwwwwcccGG	chr1:193053737-193053968(+)$1	231	199	222	20.1886
eeeeewwwwwwwwwwwwwweeee	chr16:69732638-69732873(+)$1	235	134	157	22.4422
ggggguuuuuuuuuuuugggggg	chr1:145498961-145499181(+)$1	220	111	134	23.0593
%eeeeettttttttttteeeee6	chr1:227845208-227845438(+)$1	230	188	211	20.2636
fbbwwwwwwwwwwwwwwbb]fff	chr9:127642451-127642677(-)$1	226	114	137	20.8103
fffbbuuuuuuuuuuuubb]fff	chr8:71510343-71510567(-)$1	224	133	156	22.5774
!cccxxxxxxxxxxxxxxxcccd	chr15:41773531-41773745(+)$1	214	133	156	19.0524
dddyyyyyyyyyyyyyyyydddd	chr2:179974281-179974507(-)$1	226	79	102	20.8274
eecccuuuuuuuuuuuuccc]ee	chr3:45720737-45720957(+)$1	220	138	161	23.4074
f[cccuuuuuuuuuuuuccc22f	chr10:70513621-70513848(+)$1	227	85	108	22.8129
ggggwwwwwwwwwwwwwwggggg	chr5:115628195-115628421(+)$1	226	164	187	22.4208
d[ccctttttttttttccc]ddd	chr5:917624-917834(+)$1	210	140	163	20.8929
eeeeevvvvvvvvvvvvveeeee	chr5:171304920-171305142(-)$1	222	33	56	22.6063
geeeeettttttttttteeeee>	chr22:40721080-40721302(+)$1	222	168	191	21.2782
fffffvvvvvvvvvvvvvfffff	chr6:83878748-83878972(-)$1	224	149	172	21.9899
ffffxxxxxxxxxxxxxxxffff	chr2:169628419-169628647(+)$1	228	200	223	19.0105
bbbwwwwwwwwwwwwwwbb]bb]	chr3:69220704-69220923(-)$1	219	77	100	19.9933
eeeexxxxxxxxxxxxxxxeeee	chr19:52919694-52919924(+)$1	230	189	212	19.3917
iiiiiwwwwwwwwwwwwwwiiii	chr5:96370590-96370813(+)$1	223	42	65	22.2003
cc[bbuuuuuuuuuuuubb]ccc	chr1:113213641-113213864(+)$1	223	187	210	22.4642
eeeeeuuuuuuuuuuuueeeee4	chr19:44980916-44981133(-)$1	217	95	118	23.2518
cccyyyyyyyyyyyyyyyyccc]	chr19:57982016-57982240(-)$1	224	112	135	21.4602
eeeeeuuuuuuuuuuuueeeee]	chr8:126445461-126445708(+)$1	247	46	69	23.3865
hhhhwwwwwwwwwwwwwwhhhhh	chr1:118406026-118406259(-)$1	233	27	50	20.7434
[eeeeettttttttttteeeeee	chr17:79858005-79858231(+)$1	226	73	96	21.5146
fffyyyyyyyyyyyyyyyyffff	chr3:33134022-33134245(-)$1	223	43	66	21.4218
====xxxxxxxxxxxxxxx====	chr5:89812453-89812677(-)$1	224	153	176	19.3150
===yyyyyyyyyyyyyyyy====	chr1:183521451-183521681(+)$1	230	189	212	21.6640
edddduuuuuuuuuuuudddd22	chr21:45526074-45526302(+)$1	228	94	117	21.8512
hhhhwwwwwwwwwwwwwwhhhhh	chr3:120500377-120500594(+)$1	217	81	104	20.7434
ggggguuuuuuuuuuuugggggg	chr5:56190908-56191140(+)$1	232	114	137	23.0593
&eeeeettttttttttteeeee]	chr18:60646758-60646984(+)$1	226	123	146	20.8320
[eeeeettttttttttteeeeeg	chr15:93570220-93570442(+)$1	222	144	167	21.5811
fffbbuuuuuuuuuuuubb]fff	chr8:71025447-71025685(-)$1	238	103	126	22.5774
fffffuuuuuuuuuuuuffffff	chr4:141302467-141302726(+)$1	259	30	53	22.6197
ddcccuuuuuuuuuuuuccc]dd	chr12:12941587-12941818(+)$1	231	50	73	22.8900
dddyyyyyyyyyyyyyyyydddd	chr1:21133407-21133631(-)$1	224	96	119	20.8274
fffffftttttttttttffffff	chr6:32948933-32949163(+)$1	230	71	94	20.6841
fffffwwwwwwwwwwwwwwffff	chr10:93809334-93809553(-)$1	219	37	60	21.9300
hhhhhuuuuuuuuuuuuhhhhhh	chr15:49419356-49419580(-)$1	224	108	131	20.8963
""ccctttttttttttccc333i	chrX:102007170-102007397(+)$1	227	134	157	20.8286
gg[bbuuuuuuuuuuuubb]ggg	chr1:205578995-205579214(-)$1	219	161	184	22.8151
dddawwwwwwwwwwwwwwa]ddd	chr1:90401386-90401616(+)$1	230	72	95	21.8021
fffffuuuuuuuuuuuuffffff	chr3:52444934-52445148(+)$1	214	133	156	22.6197
""cccuuuuuuuuuuuuccc333	chr3:107527812-107528042(+)$1	230	176	199	22.9932
b[ddddtttttttttttdddd]b	chr14:57877204-57877424(+)$1	220	172	195	19.9183
eeeeewwwwwwwwwwwwwweeee	chr1:184042901-184043131(+)$1	230	32	55	22.4422
hhhhhvvvvvvvvvvvvvhhhhh	chr22:32353240-32353466(+)$1	226	147	170	20.5272
eeeeeuuuuuuuuuuuueeeee:	chr12:102467919-102468150(-)$1	231	93	116	22.3498
ffffxxxxxxxxxxxxxxxffff	chr6:75963224-75963450(-)$1	226	111	134	19.0105
ggcccuuuuuuuuuuuuccc:::	chr1:28148839-28149058(+)$1	219	138	161	20.2428
eeeeewwwwwwwwwwwwwweeee	chr12:57906604-57906847(+)$1	243	121	144	22.4422
!ddddwwwwwwwwwwwwwwdddd	chr1:233394779-233394992(+)$1	213	80	103	21.4746
:ddddvvvvvvvvvvvvvdddd:	chr13:42816753-42816969(+)$1	216	2	25	19.5676
eeeeevvvvvvvvvvvvveeeee	chr1:112255065-112255286(+)$1	221	38	61	22.6063
[dddduuuuuuuuuuuudddd]d	chr22:29183640-29183861(+)$1	221	127	150	22.2583
fffffftttttttttttffffff	chrX:131510617-131510839(-)$1	222	126	149	20.6841

#otherMatches

#Seq PSSM
ACUACCAUCAACAACAAGUAGUU	chr9:5921661-5921884(-)$1	223	106	129	23.1292
UAAUGUUUCAUGACCACCCAUUG	chr8:104344449-104344715(+)$1	266	117	140	22.6063
UACUAUAUUUGUCUUUUUAUAAA	chrX:67755054-67755276(+)$1	222	14	37	22.6857
GUACCUCUUUAUAUGUUAGGUGC	chr5:137502242-137502472(-)$1	230	37	60	20.6841
CAUUUUCCUUAAAAACAAAGAUG	chr12:25357034-25357259(+)$1	225	52	75	20.9939
UGAGAACUAUUACCCAGCUCUAA	chr3:182637234-182637446(+)$1	212	72	95	21.8408
UAGGUAUCUCAGGUCCUUUCUAA	chr20:47862371-47862604(-)$1	233	56	79	22.3493
UUCCAAAUAUAACUUUCUGGGGA	chr7:23017722-23017952(-)$1	230	192	215	23.2256
AAUCUCCACCCAAUGAAUGAUGA	chr1:193053737-193053968(+)$1	231	199	222	20.1886
CAGAGCUACUUUAUAAAUUCUCU	chr16:69732638-69732873(+)$1	235	134	157	22.4422
CACUAAAAGAUUAACUCUAGUGU	chr1:145498961-145499181(+)$1	220	111	134	23.0593
AGCUUUAAGAGAAUUACAGAGCA	chr1:227845208-227845438(+)$1	230	188	211	20.2636
GCUAAUAUCCCAGCUCCAGCCAG	chr9:127642451-127642677(-)$1	226	114	137	20.8103
ACUGUUUUCUUCUACAUGCUAGU	chr8:71510343-71510567(-)$1	224	133	156	22.5774
UGUGUAACUUCCCCAUUCCCACC	chr15:41773531-41773745(+)$1	214	133	156	19.0524
UCCAAGUAUCUUAAAAGAAGGAA	chr2:179974281-179974507(-)$1	226	79	102	20.8274
CAGGCCCUUACACAAAAGCCAUG	chr3:45720737-45720957(+)$1	220	138	161	23.4074
CUUUGUCAAGACCAUUUCAGCUG	chr10:70513621-70513848(+)$1	227	85	108	22.8129
GAGGUUCUAAUAUACUUUCUUUA	chr5:115628195-115628421(+)$1	226	164	187	22.4208
CAACUGAGAAAAAAAUGGUCGGU	chr5:917624-917834(+)$1	210	140	163	20.8929
UGUUUGAAAGUGUUAACAGGACA	chr5:171304920-171305142(-)$1	222	33	56	22.6063
AAUACAACAAUGCCUAAUGUAUU	chr22:40721080-40721302(+)$1	222	168	191	21.2782
CUGUUUUUCUUAAACACUAACAG	chr6:83878748-83878972(-)$1	224	149	172	21.9899
GCAGUAUCUCAUCCUCCCCCUGU	chr2:169628419-169628647(+)$1	228	200	223	19.0105
CCCACAAAGCCCCUAAAGGAGGA	chr3:69220704-69220923(-)$1	219	77	100	19.9933
CAAUCACCAUAGAAUUCACAUUG	chr19:52919694-52919924(+)$1	230	189	212	19.3917
uguguauauacacacaagaacac	chr5:96370590-96370813(+)$1	223	42	65	22.2003
UGUGAUAAAAUAACCUUUCCCAG	chr1:113213641-113213864(+)$1	223	187	210	22.4642
UGUGGAAAAUCUUUUAACCGCAG	chr19:44980916-44981133(-)$1	217	95	118	23.2518
caaaauauuauuuucauacuugu	chr19:57982016-57982240(-)$1	224	112	135	21.4602
GGCUGCCUUUGCUUUUCUAGCCC	chr8:126445461-126445708(+)$1	247	46	69	23.3865
GGGGUAAAUAGCUAAAUUUCCUU	chr1:118406026-118406259(-)$1	233	27	50	20.7434
AUGUUGACACUUUUAUCCAAUAA	chr17:79858005-79858231(+)$1	226	73	96	21.5146
CACAAGCCUGACUCAAACAGUGA	chr3:33134022-33134245(-)$1	223	43	66	21.4218
auauauuugaauuaauugaauau	chr5:89812453-89812677(-)$1	224	153	176	19.3150
GGUGGUGACAGGAUGGGGAACCG	chr1:183521451-183521681(+)$1	230	189	212	21.6640
AAAUGCUCCUUUCUCUACAUUUA	chr21:45526074-45526302(+)$1	228	94	117	21.8512
GUUUGACUUUUAUGCCAGAAACU	chr3:120500377-120500594(+)$1	217	81	104	20.7434
UGCUUACAAUUUUUAAAAGGCAG	chr5:56190908-56191140(+)$1	232	114	137	23.0593
UUGUUAACUUCUCCCCCUAACAU	chr18:60646758-60646984(+)$1	226	123	146	20.8320
UGUGCUGGGAAAAAGGAAGCAUU	chr15:93570220-93570442(+)$1	222	144	167	21.5811
ACAGGCAAAUUUCAUACCCAUGU	chr8:71025447-71025685(-)$1	238	103	126	22.5774
GAAACUUAAAGAUGAAUGUUUUA	chr4:141302467-141302726(+)$1	259	30	53	22.6197
cugaguuuaaacaauuucucugg	chr12:12941587-12941818(+)$1	231	50	73	22.8900
GACUCAUACUUAAAAAAAUGUUU	chr1:21133407-21133631(-)$1	224	96	119	20.8274
UGGGGGUUUCAGUCAUCUCCCCA	chr6:32948933-32949163(+)$1	230	71	94	20.6841
UAAAAUAACACUGAGAUUUUUUU	chr10:93809334-93809553(-)$1	219	37	60	21.9300
UUAUUUUAUCUUCAGUUAAUGAU	chr15:49419356-49419580(-)$1	224	108	131	20.8963
cuugcuuccccccacuguauacu	chrX:102007170-102007397(+)$1	227	134	157	20.8286
UGGAAUUUAUAGGGUGUUUGUAG	chr1:205578995-205579214(-)$1	219	161	184	22.8151
GUUCUUUUUAAAUUGUUUGUAAC	chr1:90401386-90401616(+)$1	230	72	95	21.8021
GAAACAACUUGAUAAUCGUUUCG	chr3:52444934-52445148(+)$1	214	133	156	22.6197
CAAGCUAAUUACAAAUUGCUACA	chr3:107527812-107528042(+)$1	230	176	199	22.9932
GGGGAGCUUUGCUUUUCUUCUGC	chr14:57877204-57877424(+)$1	220	172	195	19.9183
cugcuguaugaagcacaaaagca	chr1:184042901-184043131(+)$1	230	32	55	22.4422
UAACUUUUUUUUUUUUUUGGUUG	chr22:32353240-32353466(+)$1	226	147	170	20.5272
UUUGAAGAAUUUUUAUAUCAAAU	chr12:102467919-102468150(-)$1	231	93	116	22.3498
AACAAAAUUAAUUUUGCUAUGUU	chr6:75963224-75963450(-)$1	226	111	134	19.0105
uagucuuuggaauucgugaccua	chr1:28148839-28149058(+)$1	219	138	161	20.2428
ACCUGGGCAACUUCAUCAACAGG	chr12:57906604-57906847(+)$1	243	121	144	22.4422
UAUCCACUAAGCCACCCUCGGAU	chr1:233394779-233394992(+)$1	213	80	103	21.4746
UGGAAUAUAUUGUUACAUUUCCU	chr13:42816753-42816969(+)$1	216	2	25	19.5676
CUUCAAAAAUAAAAAAUCUGAAG	chr1:112255065-112255286(+)$1	221	38	61	22.6063
AAUGGUAUAAUGCCCUUCCAUCA	chr22:29183640-29183861(+)$1	221	127	150	22.2583
AGUCACAAAACUAAUCAGUGACU	chrX:131510617-131510839(-)$1	222	126	149	20.6841

#DB
(((((............))))).	chr9:5921661-5921884(-)$1	1	106	129	23.1292
(((((.............)))))	chr8:104344449-104344715(+)$1	1	117	140	22.6063
((.((............))))))	chrX:67755054-67755276(+)$1	1	14	37	22.6857
((((((...........))))))	chr5:137502242-137502472(-)$1	1	37	60	20.6841
((((((...........))))))	chr12:25357034-25357259(+)$1	1	52	75	20.9939
((((.............))).))	chr3:182637234-182637446(+)$1	1	72	95	21.8408
((((..............)))))	chr20:47862371-47862604(-)$1	1	56	79	22.3493
(.(((............))))))	chr7:23017722-23017952(-)$1	1	192	215	23.2256
.(((..............)))))	chr1:193053737-193053968(+)$1	1	199	222	20.1886
(((((..............))))	chr16:69732638-69732873(+)$1	1	134	157	22.4422
(((((............))))))	chr1:145498961-145499181(+)$1	1	111	134	23.0593
.(((((...........))))).	chr1:227845208-227845438(+)$1	1	188	211	20.2636
(((..............)).)))	chr9:127642451-127642677(-)$1	1	114	137	20.8103
(((((............)).)))	chr8:71510343-71510567(-)$1	1	133	156	22.5774
.(((...............))))	chr15:41773531-41773745(+)$1	1	133	156	19.0524
(((................))))	chr2:179974281-179974507(-)$1	1	79	102	20.8274
(((((............))).))	chr3:45720737-45720957(+)$1	1	138	161	23.4074
(.(((............)))..)	chr10:70513621-70513848(+)$1	1	85	108	22.8129
((((..............)))))	chr5:115628195-115628421(+)$1	1	164	187	22.4208
(.(((...........))).)))	chr5:917624-917834(+)$1	1	140	163	20.8929
(((((.............)))))	chr5:171304920-171305142(-)$1	1	33	56	22.6063
((((((...........))))).	chr22:40721080-40721302(+)$1	1	168	191	21.2782
(((((.............)))))	chr6:83878748-83878972(-)$1	1	149	172	21.9899
((((...............))))	chr2:169628419-169628647(+)$1	1	200	223	19.0105
(((..............)).)).	chr3:69220704-69220923(-)$1	1	77	100	19.9933
((((...............))))	chr19:52919694-52919924(+)$1	1	189	212	19.3917
(((((..............))))	chr5:96370590-96370813(+)$1	1	42	65	22.2003
((.((............)).)))	chr1:113213641-113213864(+)$1	1	187	210	22.4642
(((((............))))).	chr19:44980916-44981133(-)$1	1	95	118	23.2518
(((................))).	chr19:57982016-57982240(-)$1	1	112	135	21.4602
(((((............))))).	chr8:126445461-126445708(+)$1	1	46	69	23.3865
((((..............)))))	chr1:118406026-118406259(-)$1	1	27	50	20.7434
.(((((...........))))))	chr17:79858005-79858231(+)$1	1	73	96	21.5146
(((................))))	chr3:33134022-33134245(-)$1	1	43	66	21.4218
((((...............))))	chr5:89812453-89812677(-)$1	1	153	176	19.3150
(((................))))	chr1:183521451-183521681(+)$1	1	189	212	21.6640
(((((............))))..	chr21:45526074-45526302(+)$1	1	94	117	21.8512
((((..............)))))	chr3:120500377-120500594(+)$1	1	81	104	20.7434
(((((............))))))	chr5:56190908-56191140(+)$1	1	114	137	23.0593
.(((((...........))))).	chr18:60646758-60646984(+)$1	1	123	146	20.8320
.(((((...........))))))	chr15:93570220-93570442(+)$1	1	144	167	21.5811
(((((............)).)))	chr8:71025447-71025685(-)$1	1	103	126	22.5774
(((((............))))))	chr4:141302467-141302726(+)$1	1	30	53	22.6197
(((((............))).))	chr12:12941587-12941818(+)$1	1	50	73	22.8900
(((................))))	chr1:21133407-21133631(-)$1	1	96	119	20.8274
((((((...........))))))	chr6:32948933-32949163(+)$1	1	71	94	20.6841
(((((..............))))	chr10:93809334-93809553(-)$1	1	37	60	21.9300
(((((............))))))	chr15:49419356-49419580(-)$1	1	108	131	20.8963
..(((...........)))...)	chrX:102007170-102007397(+)$1	1	134	157	20.8286
((.((............)).)))	chr1:205578995-205579214(-)$1	1	161	184	22.8151
((((..............).)))	chr1:90401386-90401616(+)$1	1	72	95	21.8021
(((((............))))))	chr3:52444934-52445148(+)$1	1	133	156	22.6197
..(((............)))...	chr3:107527812-107528042(+)$1	1	176	199	22.9932
(.((((...........)))).)	chr14:57877204-57877424(+)$1	1	172	195	19.9183
(((((..............))))	chr1:184042901-184043131(+)$1	1	32	55	22.4422
(((((.............)))))	chr22:32353240-32353466(+)$1	1	147	170	20.5272
(((((............))))).	chr12:102467919-102468150(-)$1	1	93	116	22.3498
((((...............))))	chr6:75963224-75963450(-)$1	1	111	134	19.0105
))(((............)))...	chr1:28148839-28149058(+)$1	1	138	161	20.2428
(((((..............))))	chr12:57906604-57906847(+)$1	1	121	144	22.4422
.((((..............))))	chr1:233394779-233394992(+)$1	1	80	103	21.4746
.((((.............)))).	chr13:42816753-42816969(+)$1	1	2	25	19.5676
(((((.............)))))	chr1:112255065-112255286(+)$1	1	38	61	22.6063
.((((............)))).)	chr22:29183640-29183861(+)$1	1	127	150	22.2583
((((((...........))))))	chrX:131510617-131510839(-)$1	1	126	149	20.6841

#PSSM
f : 0.21	e : 0.20	g : 0.10	d : 0.09	h : 0.06	= : 0.04	c : 0.04	[ : 0.04	i : 0.03	: : 0.03	! : 0.03	b : 0.03	" : 0.03	% : 0.01	& : 0.01	
e : 0.26	f : 0.18	d : 0.12	g : 0.09	c : 0.07	[ : 0.06	h : 0.06	= : 0.04	i : 0.03	b : 0.03	" : 0.03	
e : 0.24	f : 0.18	c : 0.18	d : 0.12	g : 0.06	h : 0.06	[ : 0.04	= : 0.04	b : 0.03	i : 0.01	
e : 0.24	c : 0.16	f : 0.13	b : 0.07	y : 0.07	d : 0.07	g : 0.06	h : 0.06	= : 0.03	w : 0.03	i : 0.01	a : 0.01	
e : 0.23	w : 0.12	c : 0.12	f : 0.10	b : 0.07	x : 0.07	y : 0.07	d : 0.07	g : 0.04	h : 0.03	v : 0.01	i : 0.01	
u : 0.33	w : 0.21	v : 0.10	e : 0.07	x : 0.07	y : 0.07	f : 0.04	t : 0.03	g : 0.01	d : 0.01	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.18	v : 0.10	x : 0.07	y : 0.07	
u : 0.33	w : 0.21	t : 0.15	v : 0.10	x : 0.07	y : 0.07	c : 0.03	
w : 0.18	e : 0.13	c : 0.13	b : 0.10	v : 0.09	f : 0.07	x : 0.07	y : 0.07	g : 0.04	d : 0.04	h : 0.01	
e : 0.18	c : 0.15	b : 0.10	f : 0.09	w : 0.09	x : 0.07	y : 0.07	g : 0.06	h : 0.06	d : 0.06	= : 0.01	a : 0.01	
e : 0.24	f : 0.15	c : 0.15	] : 0.12	d : 0.10	g : 0.06	h : 0.06	= : 0.04	i : 0.03	3 : 0.01	
e : 0.24	f : 0.20	d : 0.13	g : 0.07	c : 0.07	h : 0.06	] : 0.04	= : 0.04	i : 0.03	3 : 0.03	2 : 0.01	b : 0.01	: : 0.01	
e : 0.26	f : 0.20	d : 0.12	g : 0.07	c : 0.06	h : 0.06	= : 0.04	i : 0.03	2 : 0.03	3 : 0.03	] : 0.03	G : 0.01	b : 0.01	: : 0.01	
f : 0.21	e : 0.13	d : 0.13	g : 0.09	] : 0.06	h : 0.06	i : 0.04	= : 0.04	: : 0.04	2 : 0.03	c : 0.03	G : 0.01	6 : 0.01	> : 0.01	4 : 0.01	3 : 0.01	b : 0.01	

#score	1403.0396439125896
#seq	65
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_CDS_m1_run1.txt

#BEAR
gggggguuuuuuuuuuuuggggggg	chr21:47656642-47656869(-)$1	227	105	130	21.7577
:eeeeeuuuuuuuuuuuueeeee::	chr7:6730514-6730751(-)$1	237	173	198	19.6298
^^^^^^^^^^^^^^^^^^cccccc]	chr4:26422085-26422317(+)$1	232	76	101	17.4354
:eeeeeuuuuuuuuuuuueeeeehh	chr1:109952484-109952709(-)$1	225	112	137	21.0040
=!!ccctttttttttttccc22===	chr9:74489520-74489745(-)$1	225	64	89	20.0848
gggggwwwwwwwwwwwwwwgggggg	chr10:129909910-129910137(-)$1	227	90	115	21.5157
[eeeeevvvvvvvvvvvvveeeee]	chr11:70229074-70229306(+)$1	232	75	100	22.5949
$fffffftttttttttttffffff5	chr21:26957879-26958135(-)$1	256	223	248	18.7817
###ccctttttttttttccc333cc	chr7:77408381-77408622(+)$1	241	21	46	20.3577
iiiiiiitttttttttttiiiiiii	chr7:35006411-35006643(-)$1	232	105	130	19.2633
"""cccuuuuuuuuuuuuccc]iii	chr9:98229448-98229680(-)$1	232	184	209	22.5557
^^^^^^^^^^^^^^^^^^^^^eeee	chr14:24408825-24409062(-)$1	237	55	80	17.7199
^^^^^^^^^^^^^^^^^^^ffffff	chr15:42175558-42175777(-)$1	219	66	91	17.6558
ff!!bbuuuuuuuuuuuubb22fff	chr3:194150333-194150553(-)$1	220	54	79	20.6237
ccc[ccctttttttttttccc]ccc	chr2:201756735-201756974(+)$1	239	47	72	19.9883
a!!bbwwwwwwwwwwwwwwbb22a2	chr1:93312662-93312885(-)$1	223	107	132	20.4424
ffffffuuuuuuuuuuuuffffffE	chr5:36183943-36184165(+)$1	222	189	214	20.2179
=====xxxxxxxxxxxxxxx=====	chr3:139071465-139071696(+)$1	231	88	113	18.0449
%cccccctttttttttttccc]ccc	chr1:54678086-54678318(+)$1	232	93	118	19.7471
ddyyyyyyyyyyyyyyyydddd]hh	chrM:10374-10631(+)$1	257	130	155	19.0494
$$eeeeettttttttttteeeee55	chr1:227843172-227843397(+)$1	225	72	97	18.7868
^^^^^^^^^^^^^^^^^^^gggggg	chr5:114859941-114860173(-)$1	232	27	52	17.8857
^^^^^^^^^^^^^^^^^^^^fffff	chrM:11097-11374(+)$1	277	210	235	17.7327
^^^^^^^^^^^^^^^^^^ccc]a]d	chr12:111158717-111158963(-)$1	246	128	153	17.2724
cc[ccctttttttttttcccccccc	chr9:32541458-32541690(-)$1	232	53	78	19.9941
"ddddvvvvvvvvvvvvvdddd333	chr2:101885499-101885728(+)$1	229	158	183	21.2457
deeeeeuuuuuuuuuuuueeeee22	chr3:100467037-100467263(+)$1	226	30	55	21.8282
[eeeeeuuuuuuuuuuuueeeeedd	chr3:179051939-179052173(+)$1	234	144	169	21.9500
^^^^^^^^^^^^^^^^^^^^^eeee	chr4:83977982-83978203(+)$1	221	16	41	17.7199
:eeeeevvvvvvvvvvvvveeeee:	chr8:21857037-21857269(+)$1	232	25	50	20.7549
e"""bbvvvvvvvvvvvvvbb333e	chrX:17768263-17768486(+)$1	223	102	127	21.3042
hhhhhhvvvvvvvvvvvvvhhhhhh	chr19:12127125-12127364(-)$1	239	33	58	18.8345
ffffffvvvvvvvvvvvvvffffff	chr16:24583031-24583270(+)$1	239	127	152	21.4231
!!dddduuuuuuuuuuuudddd22e	chr16:48395931-48396159(-)$1	228	130	155	20.8533
"""cccxxxxxxxxxxxxxxxccc4	chrM:6267-6518(+)$1	251	215	240	17.7527
^^^^^^^^^^^^^^^^^^^^fffff	chr12:57652632-57652858(-)$1	226	78	103	17.7327
gggggyyyyyyyyyyyyyyyygggg	chr15:83686713-83686938(-)$1	225	121	146	20.5058
[eeeeevvvvvvvvvvvvveeeee]	chr2:20113182-20113422(-)$1	240	206	231	22.5949
!eeeeeuuuuuuuuuuuueeeee22	chr9:5921578-5921807(-)$1	229	28	53	22.2380
ffffffuuuuuuuuuuuuffffffc	chr5:114860230-114860454(-)$1	224	126	151	21.2449
:eeeeeuuuuuuuuuuuueeeee:e	chr7:8260881-8261113(-)$1	232	108	133	20.4128
gggggwwwwwwwwwwwwwwgggggg	chr17:1584133-1584371(-)$1	238	91	116	21.5157
eeddddtttttttttttdddd]eee	chr5:126171845-126172068(+)$1	223	122	147	18.8705
ceeeeeuuuuuuuuuuuueeeee66	chr1:224605910-224606133(-)$1	223	103	128	21.5201
ffffffuuuuuuuuuuuuffffff:	chr13:108882448-108882693(+)$1	245	23	48	20.4321
^^^^^^^^^^^^^^^^^^^^^eeee	chr1:165712315-165712549(-)$1	234	33	58	17.7199
iiiiiwwwwwwwwwwwwwwiiiiii	chr8:48752496-48752719(-)$1	223	64	89	21.3409
^^^^^^^^^^^^^^^^^^^eeeee]	chr19:11241993-11242227(+)$1	234	103	128	18.1162
eeeeeyyyyyyyyyyyyyyyyeeee	chr8:96070011-96070244(+)$1	233	101	126	20.5222
ffffffwwwwwwwwwwwwwwfffff	chr20:47705691-47705916(+)$1	225	70	95	20.6574
^^^^^^^^^^^^^^^^^^^^fffff	chr13:31232110-31232361(+)$1	251	210	235	17.7327
^^^^^^^^^^^^^^^^^^^gggggg	chr5:118280172-118280404(-)$1	232	126	151	17.8857
gggggguuuuuuuuuuuuggggggg	chr18:33689475-33689704(-)$1	229	144	169	21.7577
f!!cccvvvvvvvvvvvvvccc333	chr3:122133611-122133838(-)$1	227	124	149	22.5537
[eeeeeuuuuuuuuuuuueeeee44	chr3:41280725-41280946(+)$1	221	99	124	22.4525
:eeeeeuuuuuuuuuuuueeeeeGG	chr10:70513541-70513765(+)$1	224	191	216	20.4477
!!eeeeettttttttttteeeee66	chr15:32929903-32930156(+)$1	253	160	185	19.8142
:ddddvvvvvvvvvvvvvddddeee	chr9:34017043-34017289(-)$1	246	135	160	20.0175
^^^^^^^^^^^^^^^^^^^^fffff	chr1:175956103-175956333(-)$1	230	196	221	17.7327
====bbvvvvvvvvvvvvvbb]===	chrM:3526-3771(+)$1	245	139	164	21.4933
hhhhhhvvvvvvvvvvvvvhhhhhh	chr13:76432032-76432254(+)$1	222	133	158	18.8345
ee[ccctttttttttttccceeeee	chr15:55474225-55474457(-)$1	232	93	118	20.2513
eeee[bbtttttttttttbbeeeee	chrX:38128765-38129003(-)$1	238	89	114	19.2664
ffyyyyyyyyyyyyyyyyffffff:	chr11:9459297-9459536(+)$1	239	30	55	19.1729
cc[ccctttttttttttcccccc44	chr7:64292463-64292695(+)$1	232	157	182	20.1695
deeeeevvvvvvvvvvvvveeeee7	chr1:231509639-231509864(-)$1	225	156	181	21.7496
^^^^^^^^^^^^^^^^^^ccc4444	chr5:118582808-118583052(+)$1	244	160	185	17.3976
======uuuuuuuuuuuu=======	chr18:48702584-48702840(-)$1	256	5	30	22.1458
:ffffffvvvvvvvvvvvvvfffff	chr16:24582958-24583184(+)$1	226	199	224	19.1664
fffffftttttttttttffffff22	chr20:52185586-52185806(-)$1	220	168	193	18.9604

#otherMatches

#Seq PSSM
AUCUGUAACUACUAGCCCACAGGUG	chr21:47656642-47656869(-)$1	227	105	130	21.7577
AUGUGGAAAAAAAUUCUACCACAAA	chr7:6730514-6730751(-)$1	237	173	198	19.6298
UUCUUUCACAGAACUAUUGCACAGC	chr4:26422085-26422317(+)$1	232	76	101	17.4354
AUCCUCAAACAAGUAAUGGAGGAGA	chr1:109952484-109952709(-)$1	225	112	137	21.0040
CAAAUGAGCAGCUUUUACAUAGGAC	chr9:74489520-74489745(-)$1	225	64	89	20.0848
ACAGGCCACGCAAACUCUCCUUGUA	chr10:129909910-129910137(-)$1	227	90	115	21.5157
AUCCAACAAAGACUACAUUUUGGAA	chr11:70229074-70229306(+)$1	232	75	100	22.5949
UUACUUUUUCUUUUCUCUAAAGUAU	chr21:26957879-26958135(-)$1	256	223	248	18.7817
GAAAUCUAAGUCUAGUUGAUACAAG	chr7:77408381-77408622(+)$1	241	21	46	20.3577
UGUAAAUUACGGAAGAUCAUUUAUA	chr7:35006411-35006643(-)$1	232	105	130	19.2633
ACCUACACAGGAGUUUCAGUAACGU	chr9:98229448-98229680(-)$1	232	184	209	22.5557
ucuccccaccauguaccuugugacc	chr14:24408825-24409062(-)$1	237	55	80	17.7199
GAUCUCCCUUAUUCUCAUAUCCUCU	chr15:42175558-42175777(-)$1	219	66	91	17.6558
GGCCGUGCUGCUUUAAUAACUUCCU	chr3:194150333-194150553(-)$1	220	54	79	20.6237
CUUUGCAUCCCUCUCGUUUGCUGAG	chr2:201756735-201756974(+)$1	239	47	72	19.9883
GUACAAAAAUUUAAAGAAAUGGUCU	chr1:93312662-93312885(-)$1	223	107	132	20.4424
GAGUGCUUAAACUAAGUUGUAUUCC	chr5:36183943-36184165(+)$1	222	189	214	20.2179
AUACUUUGGUGGAAUGGUGUGGUAU	chr3:139071465-139071696(+)$1	231	88	113	18.0449
AGGAAGGCUAUCCUUACCCCUAUCC	chr1:54678086-54678318(+)$1	232	93	118	19.7471
UUACCAUCUCACUUCUAGGAAUACU	chrM:10374-10631(+)$1	257	130	155	19.0494
CCCUACAAAUGUAAAGAAUGUGGCA	chr1:227843172-227843397(+)$1	225	72	97	18.7868
GGAAAUAGCUAAAAAUUUAAUCCAG	chr5:114859941-114860173(-)$1	232	27	52	17.8857
CCCAAGAACUAUCAAACUCCUGAGC	chrM:11097-11374(+)$1	277	210	235	17.7327
AUAACCUUCAUUUUUAAGACUGUAA	chr12:111158717-111158963(-)$1	246	128	153	17.2724
GGACAAGGAAUGUGAUAUUGCCACA	chr9:32541458-32541690(-)$1	232	53	78	19.9941
UUUUUUUUUUCCUUUUUCAGAAUCG	chr2:101885499-101885728(+)$1	229	158	183	21.2457
CACCAGCUCCUGCCUUUUCUGGUCA	chr3:100467037-100467263(+)$1	226	30	55	21.8282
AGAUCUUAAAAUUCAUCUAGAUUUC	chr3:179051939-179052173(+)$1	234	144	169	21.9500
AAAACAACAUAUCUUCUAUUAUUCC	chr4:83977982-83978203(+)$1	221	16	41	17.7199
GCCAGUCUUAUUAUUCACUACUGGA	chr8:21857037-21857269(+)$1	232	25	50	20.7549
UCCACAACACUUACUCAACUGACCA	chrX:17768263-17768486(+)$1	223	102	127	21.3042
AUCUCUUAAUAGGCACAUCAGAGAU	chr19:12127125-12127364(-)$1	239	33	58	18.8345
UUAACCCACCAGAGACACAGGUUGA	chr16:24583031-24583270(+)$1	239	127	152	21.4231
GAUGUGAAAUAACUCUGCCACACAC	chr16:48395931-48396159(-)$1	228	130	155	20.8533
CCUACUUCUCCUAUCUCUCCCAGUC	chrM:6267-6518(+)$1	251	215	240	17.7527
CCCCCUCAGAACCCAUCCAUGGUCC	chr12:57652632-57652858(-)$1	226	78	103	17.7327
UUAGCAUUAUAAUACAUCUUGGCUA	chr15:83686713-83686938(-)$1	225	121	146	20.5058
AUCAGCCUCAUUAUUUAUAGUUGAA	chr2:20113182-20113422(-)$1	240	206	231	22.5949
UACUACCAUCAACAACAAGUAGUUC	chr9:5921578-5921807(-)$1	229	28	53	22.2380
ACUGCAAUACUGAUAGAAUGUGGUG	chr5:114860230-114860454(-)$1	224	126	151	21.2449
CUGGGAAAAUUUCUUCGAUCCCAAG	chr7:8260881-8261113(-)$1	232	108	133	20.4128
ACAAGAUUGCUUUUCCUUACUUGUA	chr17:1584133-1584371(-)$1	238	91	116	21.5157
GUCUUCCUCAAAAUAAAGAAGUAUG	chr5:126171845-126172068(+)$1	223	122	147	18.8705
AUAUCACAAUACCAAACUUGAUAAU	chr1:224605910-224606133(-)$1	223	103	128	21.5201
GCAGUGCCAAGGCUAUUUCACUGCA	chr13:108882448-108882693(+)$1	245	23	48	20.4321
UUACCCCUCUUUCUUACAUCCAAGG	chr1:165712315-165712549(-)$1	234	33	58	17.7199
UGGAAUUCGUUUCCCAUCCUUCUAC	chr8:48752496-48752719(-)$1	223	64	89	21.3409
UGUUUUAUAUAUUUAUUCAUCUGGG	chr19:11241993-11242227(+)$1	234	103	128	18.1162
AUACAUUACUUCCAUUAUAUUUGUA	chr8:96070011-96070244(+)$1	233	101	126	20.5222
GGUUUUUUUUUUUUAAUUUCAGAAC	chr20:47705691-47705916(+)$1	225	70	95	20.6574
AAACAAUUCCUUACACCAAAAACUG	chr13:31232110-31232361(+)$1	251	210	235	17.7327
GUACAUAAUUCAGCAUCCAGCAGAG	chr5:118280172-118280404(-)$1	232	126	151	17.8857
UCUAGUUAAGGUUUAAAUGCUAGAG	chr18:33689475-33689704(-)$1	229	144	169	21.7577
AUGGUAAAUACAUUCUCACUGCAAC	chr3:122133611-122133838(-)$1	227	124	149	22.5537
GACCUGUAAAUCAUCCUUUAGGUAA	chr3:41280725-41280946(+)$1	221	99	124	22.4525
AAUUACUGCAAUUUUUAUGUAAUGC	chr10:70513541-70513765(+)$1	224	191	216	20.4477
UGUCAUUAAUGUAAAUAAAGUGAGU	chr15:32929903-32930156(+)$1	253	160	185	19.8142
UACUGUAUAUGAUGACUUCAGUGAG	chr9:34017043-34017289(-)$1	246	135	160	20.0175
AAGAAGAUGAUACAAAUGAAUUUGU	chr1:175956103-175956333(-)$1	230	196	221	17.7327
GGUGAGCAUCAAACUCAAACUACGC	chrM:3526-3771(+)$1	245	139	164	21.4933
UUUUUUGCUUUUUUUUUAAAAAAAA	chr13:76432032-76432254(+)$1	222	133	158	18.8345
GAAGAUGCUCCUUAAAAAUCUCUGU	chr15:55474225-55474457(-)$1	232	93	118	20.2513
ACAGAGAGAAGAUCAAAAUCCUGUA	chrX:38128765-38129003(-)$1	238	89	114	19.2664
UUAGAAAGACUGACAAGAGAGGUUA	chr11:9459297-9459536(+)$1	239	30	55	19.1729
CCUACAAAUGUGAAGAAUGUGGCAA	chr7:64292463-64292695(+)$1	232	157	182	20.1695
GCAUUUAUUUUUUUCUUACAGGUGU	chr1:231509639-231509864(-)$1	225	156	181	21.7496
AUAAUAUACAGUGAUCAUUCUCUAU	chr5:118582808-118583052(+)$1	244	160	185	17.3976
AUGUGGCCACAACCUCUUCUGCAUG	chr18:48702584-48702840(-)$1	256	5	30	22.1458
CUUAACCCACCAGAGACACAGGUUG	chr16:24582958-24583184(+)$1	226	199	224	19.1664
UUUGUACCAAAUAGCAAUACAAACU	chr20:52185586-52185806(-)$1	220	168	193	18.9604

#DB
((((((............)))))))	chr21:47656642-47656869(-)$1	1	105	130	21.7577
.(((((............)))))..	chr7:6730514-6730751(-)$1	1	173	198	19.6298
..................)))))).	chr4:26422085-26422317(+)$1	1	76	101	17.4354
.(((((............)))))((	chr1:109952484-109952709(-)$1	1	112	137	21.0040
(..(((...........)))..)))	chr9:74489520-74489745(-)$1	1	64	89	20.0848
(((((..............))))))	chr10:129909910-129910137(-)$1	1	90	115	21.5157
.(((((.............))))).	chr11:70229074-70229306(+)$1	1	75	100	22.5949
.((((((...........)))))).	chr21:26957879-26958135(-)$1	1	223	248	18.7817
...(((...........)))...))	chr7:77408381-77408622(+)$1	1	21	46	20.3577
(((((((...........)))))))	chr7:35006411-35006643(-)$1	1	105	130	19.2633
...(((............))).)))	chr9:98229448-98229680(-)$1	1	184	209	22.5557
.....................))))	chr14:24408825-24409062(-)$1	1	55	80	17.7199
...................))))))	chr15:42175558-42175777(-)$1	1	66	91	17.6558
((..((............))..)))	chr3:194150333-194150553(-)$1	1	54	79	20.6237
(((.(((...........))).)))	chr2:201756735-201756974(+)$1	1	47	72	19.9883
(..((..............))..).	chr1:93312662-93312885(-)$1	1	107	132	20.4424
((((((............)))))))	chr5:36183943-36184165(+)$1	1	189	214	20.2179
(((((...............)))))	chr3:139071465-139071696(+)$1	1	88	113	18.0449
.((((((...........))).)))	chr1:54678086-54678318(+)$1	1	93	118	19.7471
((................)))).))	chrM:10374-10631(+)$1	1	130	155	19.0494
..(((((...........)))))..	chr1:227843172-227843397(+)$1	1	72	97	18.7868
...................))))))	chr5:114859941-114860173(-)$1	1	27	52	17.8857
....................)))))	chrM:11097-11374(+)$1	1	210	235	17.7327
..................))).).)	chr12:111158717-111158963(-)$1	1	128	153	17.2724
((.(((...........))))))))	chr9:32541458-32541690(-)$1	1	53	78	19.9941
.((((.............))))...	chr2:101885499-101885728(+)$1	1	158	183	21.2457
((((((............)))))..	chr3:100467037-100467263(+)$1	1	30	55	21.8282
.(((((............)))))))	chr3:179051939-179052173(+)$1	1	144	169	21.9500
.....................))))	chr4:83977982-83978203(+)$1	1	16	41	17.7199
.(((((.............))))).	chr8:21857037-21857269(+)$1	1	25	50	20.7549
(...((.............))...)	chrX:17768263-17768486(+)$1	1	102	127	21.3042
((((((.............))))))	chr19:12127125-12127364(-)$1	1	33	58	18.8345
((((((.............))))))	chr16:24583031-24583270(+)$1	1	127	152	21.4231
..((((............))))..)	chr16:48395931-48396159(-)$1	1	130	155	20.8533
...(((...............))).	chrM:6267-6518(+)$1	1	215	240	17.7527
....................)))))	chr12:57652632-57652858(-)$1	1	78	103	17.7327
(((((................))))	chr15:83686713-83686938(-)$1	1	121	146	20.5058
.(((((.............))))).	chr2:20113182-20113422(-)$1	1	206	231	22.5949
.(((((............)))))..	chr9:5921578-5921807(-)$1	1	28	53	22.2380
((((((............)))))))	chr5:114860230-114860454(-)$1	1	126	151	21.2449
.(((((............))))).(	chr7:8260881-8261113(-)$1	1	108	133	20.4128
(((((..............))))))	chr17:1584133-1584371(-)$1	1	91	116	21.5157
((((((...........)))).)))	chr5:126171845-126172068(+)$1	1	122	147	18.8705
((((((............)))))..	chr1:224605910-224606133(-)$1	1	103	128	21.5201
((((((............)))))).	chr13:108882448-108882693(+)$1	1	23	48	20.4321
.....................))))	chr1:165712315-165712549(-)$1	1	33	58	17.7199
(((((..............))))))	chr8:48752496-48752719(-)$1	1	64	89	21.3409
...................))))).	chr19:11241993-11242227(+)$1	1	103	128	18.1162
(((((................))))	chr8:96070011-96070244(+)$1	1	101	126	20.5222
((((((..............)))))	chr20:47705691-47705916(+)$1	1	70	95	20.6574
....................)))))	chr13:31232110-31232361(+)$1	1	210	235	17.7327
...................))))))	chr5:118280172-118280404(-)$1	1	126	151	17.8857
((((((............)))))))	chr18:33689475-33689704(-)$1	1	144	169	21.7577
(..(((.............)))...	chr3:122133611-122133838(-)$1	1	124	149	22.5537
.(((((............)))))..	chr3:41280725-41280946(+)$1	1	99	124	22.4525
.(((((............)))))))	chr10:70513541-70513765(+)$1	1	191	216	20.4477
..(((((...........)))))..	chr15:32929903-32930156(+)$1	1	160	185	19.8142
.((((.............))))(((	chr9:34017043-34017289(-)$1	1	135	160	20.0175
....................)))))	chr1:175956103-175956333(-)$1	1	196	221	17.7327
((((((.............)).)))	chrM:3526-3771(+)$1	1	139	164	21.4933
((((((.............))))))	chr13:76432032-76432254(+)$1	1	133	158	18.8345
((.(((...........))))))))	chr15:55474225-55474457(-)$1	1	93	118	20.2513
((((.((...........)))))))	chrX:38128765-38129003(-)$1	1	89	114	19.2664
((................)))))).	chr11:9459297-9459536(+)$1	1	30	55	19.1729
((.(((...........))))))..	chr7:64292463-64292695(+)$1	1	157	182	20.1695
((((((.............))))).	chr1:231509639-231509864(-)$1	1	156	181	21.7496
..................)))....	chr5:118582808-118583052(+)$1	1	160	185	17.3976
((((((............)))))))	chr18:48702584-48702840(-)$1	1	5	30	22.1458
.((((((.............)))))	chr16:24582958-24583184(+)$1	1	199	224	19.1664
((((((...........))))))..	chr20:52185586-52185806(-)$1	1	168	193	18.9604

#PSSM
^ : 0.20	f : 0.12	: : 0.10	g : 0.07	e : 0.07	= : 0.05	[ : 0.05	c : 0.05	" : 0.04	d : 0.04	! : 0.04	$ : 0.02	i : 0.02	h : 0.02	# : 0.01	a : 0.01	% : 0.01	
e : 0.24	^ : 0.20	f : 0.14	g : 0.07	! : 0.07	c : 0.05	" : 0.04	= : 0.04	d : 0.04	i : 0.02	h : 0.02	# : 0.01	$ : 0.01	
e : 0.24	^ : 0.20	f : 0.11	g : 0.07	! : 0.05	d : 0.05	" : 0.04	= : 0.04	[ : 0.04	i : 0.02	c : 0.02	y : 0.02	h : 0.02	# : 0.01	
e : 0.24	^ : 0.20	c : 0.12	f : 0.11	g : 0.07	d : 0.05	= : 0.04	i : 0.02	y : 0.02	h : 0.02	! : 0.01	[ : 0.01	b : 0.01	" : 0.01	
e : 0.22	^ : 0.20	c : 0.14	f : 0.11	g : 0.07	b : 0.05	d : 0.05	i : 0.02	= : 0.02	y : 0.02	h : 0.02	[ : 0.01	
e : 0.21	^ : 0.20	c : 0.14	f : 0.11	w : 0.05	b : 0.05	y : 0.05	g : 0.02	v : 0.02	h : 0.02	d : 0.02	i : 0.01	x : 0.01	= : 0.01	
u : 0.25	^ : 0.20	v : 0.17	t : 0.10	w : 0.07	y : 0.05	f : 0.02	c : 0.02	x : 0.02	e : 0.02	i : 0.01	b : 0.01	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	t : 0.20	v : 0.18	w : 0.07	y : 0.05	x : 0.02	
u : 0.25	^ : 0.20	v : 0.18	t : 0.10	c : 0.07	w : 0.07	y : 0.05	x : 0.02	d : 0.01	f : 0.01	
e : 0.15	c : 0.15	v : 0.15	^ : 0.15	f : 0.08	w : 0.07	d : 0.07	g : 0.02	b : 0.02	x : 0.02	y : 0.02	i : 0.01	= : 0.01	
e : 0.22	c : 0.17	f : 0.11	^ : 0.10	g : 0.08	b : 0.07	d : 0.07	i : 0.02	x : 0.02	h : 0.02	y : 0.02	w : 0.01	= : 0.01	v : 0.01	
e : 0.25	f : 0.20	c : 0.12	g : 0.08	d : 0.07	^ : 0.04	b : 0.04	2 : 0.02	i : 0.02	= : 0.02	h : 0.02	y : 0.02	3 : 0.01	x : 0.01	
e : 0.31	f : 0.20	g : 0.10	] : 0.08	c : 0.07	d : 0.05	2 : 0.04	3 : 0.02	i : 0.02	= : 0.02	h : 0.02	4 : 0.01	
e : 0.34	f : 0.21	g : 0.10	c : 0.08	= : 0.05	3 : 0.05	i : 0.04	2 : 0.02	h : 0.02	] : 0.01	a : 0.01	4 : 0.01	
f : 0.20	e : 0.18	g : 0.10	c : 0.08	h : 0.05	= : 0.05	2 : 0.05	i : 0.04	3 : 0.04	4 : 0.04	: : 0.02	6 : 0.02	a : 0.01	5 : 0.01	] : 0.01	d : 0.01	G : 0.01	
e : 0.15	f : 0.12	g : 0.10	c : 0.07	: : 0.05	] : 0.05	h : 0.05	= : 0.05	2 : 0.05	4 : 0.05	i : 0.04	5 : 0.02	d : 0.02	3 : 0.02	6 : 0.02	E : 0.01	G : 0.01	7 : 0.01	

#score	1398.2376756743622
#seq	70
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_UTR_m1_run1.txt

#BEAR
c[bbwwwwwwwwwwwwwwbb]ccc]	chr5:134364067-134364310(-)$1	243	95	120	21.9739
iiiiiiuuuuuuuuuuuuiiiiiii	chr18:60994975-60995207(-)$1	232	52	77	24.0495
[eeeeeuuuuuuuuuuuueeeee]e	chr17:62496703-62496990(-)$1	287	213	238	24.2444
fffffvvvvvvvvvvvvvffffff]	chr16:66755223-66755455(-)$1	232	65	90	24.0621
!bb[bbuuuuuuuuuuuubb]bb22	chr1:225590674-225590953(-)$1	279	24	49	22.2785
ccccccuuuuuuuuuuuuccc]ccc	chr13:50274981-50275213(-)$1	232	9	34	23.7399
ffffffuuuuuuuuuuuuffffff5	chr9:137024881-137025104(+)$1	223	134	159	23.8797
e[bbwwwwwwwwwwwwwwbb]eeee	chr10:81852173-81852406(+)$1	233	88	113	21.5631
#eeeeeuuuuuuuuuuuueeeee44	chr13:79886422-79886644(-)$1	222	131	156	24.5625
ggggggwwwwwwwwwwwwwwggggg	chr3:20025868-20026096(+)$1	228	53	78	22.5667
hhhhwwwwwwwwwwwwwwhhhhhhh	chr6:75963034-75963293(-)$1	259	58	83	20.2086
$eeeeeuuuuuuuuuuuueeeee55	chr2:60686555-60686814(-)$1	259	89	114	23.0025
aeeeeettttttttttteeeee]a]	chr12:22843051-22843278(+)$1	227	106	131	22.6010
!!dddduuuuuuuuuuuudddd22a	chr5:150070998-150071231(-)$1	233	67	92	23.1944
##dddduuuuuuuuuuuuddddbb]	chr14:94514629-94514862(+)$1	233	166	191	23.1282
iiiyyyyyyyyyyyyyyyyiiiiii	chr6:137518887-137519127(-)$1	240	183	208	21.4371
gggggguuuuuuuuuuuuggggggg	chr22:29182378-29182604(+)$1	226	34	59	24.3150
ffffwwwwwwwwwwwwwwffffff3	chr19:33871214-33871464(+)$1	250	20	45	23.3022
iiiiiiuuuuuuuuuuuuiiiiiii	chr15:77338276-77338506(-)$1	230	184	209	24.0495
eeeeavvvvvvvvvvvvva]eeeee	chr8:42251634-42251860(+)$1	226	5	30	23.4058
##cccwwwwwwwwwwwwwwccc333	chrX:23801365-23801588(+)$1	223	87	112	23.2364
ffff[auuuuuuuuuuuua]fffff	chr14:61179597-61179832(-)$1	235	111	136	24.3149
fffffwwwwwwwwwwwwwwffffff	chr12:122957393-122957625(-)$1	232	170	195	22.9618
!!ddddwwwwwwwwwwwwwwdddd2	chr1:65890923-65891143(+)$1	220	139	164	21.9231
======uuuuuuuuuuuu=======	chr3:45763427-45763651(+)$1	224	42	67	24.4588
$$ddddvvvvvvvvvvvvvdddd55	chr9:36338037-36338263(-)$1	226	77	102	21.2704
fffffftttttttttttffffff22	chr14:102552328-102552560(-)$1	232	134	159	22.5283
ddd[ccctttttttttttccc]ddd	chr2:97499009-97499249(+)$1	240	105	130	21.4189
gggggguuuuuuuuuuuuggggggg	chr2:24290491-24290728(-)$1	237	113	138	24.3150
'eeeeeuuuuuuuuuuuueeeee00	chr15:41248142-41248402(+)$1	260	211	236	23.1271
:eeeeeuuuuuuuuuuuueeeee::	chr7:44916152-44916413(-)$1	261	166	191	21.3679
fffyyyyyyyyyyyyyyyyffffff	chr12:27573837-27574072(+)$1	235	76	101	21.4866
fffffftttttttttttffffff66	chr5:72210007-72210226(+)$1	219	23	48	22.0560
[bb[bbuuuuuuuuuuuubb]bb]e	chr3:5221617-5221837(+)$1	220	62	87	22.1655
eeeeevvvvvvvvvvvvveeeee66	chr8:117670992-117671251(-)$1	259	214	239	23.1581
ddddccctttttttttttccccccn	chr1:150938442-150938679(-)$1	237	48	73	21.1802
"eeeeeuuuuuuuuuuuueeeee33	chr7:92905386-92905610(+)$1	224	132	157	24.7906
eeeexxxxxxxxxxxxxxxeeeee]	chr10:70100830-70101095(+)$1	265	211	236	19.1801
ffffffvvvvvvvvvvvvvffffff	chr16:24836036-24836283(+)$1	247	149	174	23.4987
eeeeewwwwwwwwwwwwwweeeee4	chr12:54424201-54424450(+)$1	249	9	34	23.1082
ffffffvvvvvvvvvvvvvffffff	chr19:1257967-1258191(+)$1	224	102	127	23.4987
ggggggtttttttttttggggggg]	chr18:60245534-60245757(+)$1	223	191	216	22.7133
[fffffftttttttttttffffff]	chr12:6643571-6643798(+)$1	227	38	63	22.9072
ffffffuuuuuuuuuuuuffffff]	chr5:71502511-71502747(+)$1	236	35	60	24.5570
!!ddddwwwwwwwwwwwwwwdddd2	chr14:61909743-61909972(+)$1	229	105	130	21.9231
b[ddddtttttttttttdddd]bb4	chr5:73924474-73924704(-)$1	230	70	95	21.1596
e!!cccvvvvvvvvvvvvvccc22e	chr1:211746682-211746910(-)$1	228	51	76	22.8094
ffffffuuuuuuuuuuuuffffff:	chr6:7882453-7882676(-)$1	223	16	41	23.4593
gggggvvvvvvvvvvvvvggggggg	chr12:49389278-49389499(-)$1	221	47	72	23.8069
======uuuuuuuuuuuu=======	chr3:122146296-122146522(-)$1	226	164	189	24.4588
ddddyyyyyyyyyyyyyyyydddd2	chr1:179310203-179310447(+)$1	244	57	82	20.4671
"""ddddtttttttttttdddd333	chr4:88998783-88999015(+)$1	232	96	121	22.0038
c[dddduuuuuuuuuuuudddd]cc	chr12:53808627-53808865(+)$1	238	40	65	23.3344
ffffffuuuuuuuuuuuuffffff]	chr2:198416104-198416324(+)$1	220	104	129	24.5570
ffffwwwwwwwwwwwwwwffffff]	chr17:27940847-27941092(+)$1	245	80	105	23.2140
==:cccvvvvvvvvvvvvvcccccc	chr2:232327900-232328122(-)$1	222	95	120	22.3001
[eeeeeuuuuuuuuuuuueeeeecc	chr17:66247162-66247392(+)$1	230	111	136	24.2378
gggggguuuuuuuuuuuuggggggg	chr19:36128461-36128693(+)$1	232	3	28	24.3150
eeeeewwwwwwwwwwwwwweeeee3	chr5:41918437-41918667(+)$1	230	152	177	23.2287
ffffwwwwwwwwwwwwwwffffff2	chr15:78782730-78782960(+)$1	230	170	195	23.0718
eeee[attttttttttta]eeeee]	chr3:15613135-15613360(-)$1	225	35	60	23.2431
ffffffuuuuuuuuuuuuffffff3	chr2:10567397-10567622(+)$1	225	186	211	24.6452
ggyyyyyyyyyyyyyyyyggggggg	chr12:53806752-53806989(+)$1	237	211	236	21.1105
gggggggtttttttttttggggggg	chr6:44416628-44416860(+)$1	232	177	202	22.3613
""dddduuuuuuuuuuuudddd]dd	chr6:21598120-21598341(+)$1	221	5	30	23.0396

#otherMatches

#Seq PSSM
CCGCGAAAAAAUGGAUGAGUUGCAA	chr5:134364067-134364310(-)$1	243	95	120	21.9739
UAUAUUUUACACUUGCUUGAUGUGA	chr18:60994975-60995207(-)$1	232	52	77	24.0495
UCUUUACACCUAAUAACAUAAAGCA	chr17:62496703-62496990(-)$1	287	213	238	24.2444
AAGGCCAAAUAAUAAACAGCCUUUA	chr16:66755223-66755455(-)$1	232	65	90	24.0621
ACUUUCUUUUGUUGCACUGACAGGG	chr1:225590674-225590953(-)$1	279	24	49	22.2785
GACCACUCUCUUCAGCCUGUGUGUU	chr13:50274981-50275213(-)$1	232	9	34	23.7399
UCUACAUUUGAAUUCUGUUGUAGAU	chr9:137024881-137025104(+)$1	223	134	159	23.8797
UGAAUGAAAUUGAUUAACUUGAAUA	chr10:81852173-81852406(+)$1	233	88	113	21.5631
AUGAUAGAAUGUUUUAAGUAUCAGC	chr13:79886422-79886644(-)$1	222	131	156	24.5625
UGGGGUAAAAAUCAAAUGCAACCCC	chr3:20025868-20026096(+)$1	228	53	78	22.5667
AGGUUUUAACUUCUUCAUGCCUGGA	chr6:75963034-75963293(-)$1	259	58	83	20.2086
UUAGGAACUAGCAUAUAAUUCUAUA	chr2:60686555-60686814(-)$1	259	89	114	23.0025
CUUAAAUGAAUGCAACUUUUGAUGU	chr12:22843051-22843278(+)$1	227	106	131	22.6010
UUUCCUAUACUUGUUCAAAGGAUCG	chr5:150070998-150071231(-)$1	233	67	92	23.1944
uucagcauucacuuacuagcuguau	chr14:94514629-94514862(+)$1	233	166	191	23.1282
UAUGAACCUUUACAUCCAGAUAGGU	chr6:137518887-137519127(-)$1	240	183	208	21.4371
CGGGUGUAAUAAUAUCUCCACCUGU	chr22:29182378-29182604(+)$1	226	34	59	24.3150
UAAAAAAUACAAAUAACAUUUAGGA	chr19:33871214-33871464(+)$1	250	20	45	23.3022
GUAUCAUGUUUUCUUUGUUGGUGCU	chr15:77338276-77338506(-)$1	230	184	209	24.0495
UUCUCACAGGAUUAAACAGCAGAAG	chr8:42251634-42251860(+)$1	226	5	30	23.4058
AAAGCAAAAGACGAAAAUGGCUAAA	chrX:23801365-23801588(+)$1	223	87	112	23.2364
UUUUACUCCAUGGGCAUUGAAAAGG	chr14:61179597-61179832(-)$1	235	111	136	24.3149
GUUUUCAUAUACAUAAUCUAAGACU	chr12:122957393-122957625(-)$1	232	170	195	22.9618
UAAGUUAUCAUUUCAAAAAGAACUA	chr1:65890923-65891143(+)$1	220	139	164	21.9231
UCUUAAUUUUUUUUCUAUUUAGGAA	chr3:45763427-45763651(+)$1	224	42	67	24.4588
AUUACUUUCUCAUUCUUUUAGUGUA	chr9:36338037-36338263(-)$1	226	77	102	21.2704
UCCCAGUAAAUUAGACUCUGGGAAA	chr14:102552328-102552560(-)$1	232	134	159	22.5283
GGGAUCGUCAUGCUGCAUCGAAUCC	chr2:97499009-97499249(+)$1	240	105	130	21.4189
CAUUUGGACUAAAUCCCACGAAUGA	chr2:24290491-24290728(-)$1	237	113	138	24.3150
GCCCAGCCAUCCAUAGCCCUGGGAA	chr15:41248142-41248402(+)$1	260	211	236	23.1271
AUUCAGAAAUCACACUUCCUGAAAA	chr7:44916152-44916413(-)$1	261	166	191	21.3679
UACACACUUUAAGAAAACAGUGAGU	chr12:27573837-27574072(+)$1	235	76	101	21.4866
CGGUUUUAAUUUUUGAUAAGCUGCU	chr5:72210007-72210226(+)$1	219	23	48	22.0560
CAUUUGUAAAUUAUUAUUCAUAUAG	chr3:5221617-5221837(+)$1	220	62	87	22.1655
UAUUAUUCUUUUUUCCCUUAAUAUU	chr8:117670992-117671251(-)$1	259	214	239	23.1581
AUGACUGAACCAUUACUCCAGCUGC	chr1:150938442-150938679(-)$1	237	48	73	21.1802
CACAACACCGUGUUUCAAGUUGUUC	chr7:92905386-92905610(+)$1	224	132	157	24.7906
AUGUCUAAAGAUAAAAAUAACAUGC	chr10:70100830-70101095(+)$1	265	211	236	19.1801
UUUUCUCUGCCAAAAAAAAAGAAAA	chr16:24836036-24836283(+)$1	247	149	174	23.4987
GGCCCCACACCAACCCCCAGGGCCU	chr12:54424201-54424450(+)$1	249	9	34	23.1082
GGCGGACUGUGCUGUUUCCUCCGCC	chr19:1257967-1258191(+)$1	224	102	127	23.4987
UGGAAAGGCCACUUAUAUUUCUAGA	chr18:60245534-60245757(+)$1	223	191	216	22.7133
GAGGCGGGGUCCGAGUCACCGCCUG	chr12:6643571-6643798(+)$1	227	38	63	22.9072
AAGACAAAAAUUGAAUAAUGUUUUU	chr5:71502511-71502747(+)$1	236	35	60	24.5570
AUCUUCAAACAUUUUACCAGGAAGC	chr14:61909743-61909972(+)$1	229	105	130	21.9231
UGCCAUAACCACAUUUAAUGGGAAA	chr5:73924474-73924704(-)$1	230	70	95	21.1596
UUACAUAAACAUUUCAGCAAUGAUA	chr1:211746682-211746910(-)$1	228	51	76	22.8094
AACAUGUCUUUAGUUCCUCAUGUUA	chr6:7882453-7882676(-)$1	223	16	41	23.4593
CGGCCAGGCAAGGAAAGAGGCCGGU	chr12:49389278-49389499(-)$1	221	47	72	23.8069
AUGGCCAAGAAUGAAUUGGGUCAUA	chr3:122146296-122146522(-)$1	226	164	189	24.4588
CCUAUUUUCUGUUUCAACAUUGGGC	chr1:179310203-179310447(+)$1	244	57	82	20.4671
UGUGUAAUACUGAGCACUUUACUUC	chr4:88998783-88999015(+)$1	232	96	121	22.0038
CAGAUCAAGAGUUUUGGAGAUCAGG	chr12:53808627-53808865(+)$1	238	40	65	23.3344
UACAUUACACUACAAGAAAAUGUAU	chr2:198416104-198416324(+)$1	220	104	129	24.5570
AGCGCUGUCCCUAUCCCUUGCUCCU	chr17:27940847-27941092(+)$1	245	80	105	23.2140
GCAGGUAAAAAUCAAGGUGACCCCA	chr2:232327900-232328122(-)$1	222	95	120	22.3001
AGAGACUCGUGGAAUUUUGUCUUUG	chr17:66247162-66247392(+)$1	230	111	136	24.2378
GCCAGGCACCCGCUCCCACCUGGCC	chr19:36128461-36128693(+)$1	232	3	28	24.3150
ACCAGUUAUUCUUCUUUCCCUGGUC	chr5:41918437-41918667(+)$1	230	152	177	23.2287
GAUUGUUAUAAACUAAGAAGUCUUG	chr15:78782730-78782960(+)$1	230	170	195	23.0718
CAAAGAAAAAGUUUAUGUGUUUGUG	chr3:15613135-15613360(-)$1	225	35	60	23.2431
UCUUUGUCUGCCUGUUUCUAAGGAA	chr2:10567397-10567622(+)$1	225	186	211	24.6452
AGAAAUCUAUCUUAAAACCUGGGUA	chr12:53806752-53806989(+)$1	237	211	236	21.1105
AGUUUAUUUGCACUUUUUGUAGACU	chr6:44416628-44416860(+)$1	232	177	202	22.3613
GCCCCCGUCUUGUAAAAAGGGGAGG	chr6:21598120-21598341(+)$1	221	5	30	23.0396

#DB
(.((..............)).))).	chr5:134364067-134364310(-)$1	1	95	120	21.9739
((((((............)))))))	chr18:60994975-60995207(-)$1	1	52	77	24.0495
.(((((............))))).)	chr17:62496703-62496990(-)$1	1	213	238	24.2444
(((((.............)))))).	chr16:66755223-66755455(-)$1	1	65	90	24.0621
.((.((............)).))..	chr1:225590674-225590953(-)$1	1	24	49	22.2785
((((((............))).)))	chr13:50274981-50275213(-)$1	1	9	34	23.7399
((((((............)))))).	chr9:137024881-137025104(+)$1	1	134	159	23.8797
(.((..............)).))))	chr10:81852173-81852406(+)$1	1	88	113	21.5631
.(((((............)))))..	chr13:79886422-79886644(-)$1	1	131	156	24.5625
((((((..............)))))	chr3:20025868-20026096(+)$1	1	53	78	22.5667
((((..............)))))))	chr6:75963034-75963293(-)$1	1	58	83	20.2086
.(((((............)))))..	chr2:60686555-60686814(-)$1	1	89	114	23.0025
((((((...........))))).).	chr12:22843051-22843278(+)$1	1	106	131	22.6010
..((((............))))..)	chr5:150070998-150071231(-)$1	1	67	92	23.1944
..((((............)))))).	chr14:94514629-94514862(+)$1	1	166	191	23.1282
(((................))))))	chr6:137518887-137519127(-)$1	1	183	208	21.4371
((((((............)))))))	chr22:29182378-29182604(+)$1	1	34	59	24.3150
((((..............)))))).	chr19:33871214-33871464(+)$1	1	20	45	23.3022
((((((............)))))))	chr15:77338276-77338506(-)$1	1	184	209	24.0495
(((((.............).)))))	chr8:42251634-42251860(+)$1	1	5	30	23.4058
..(((..............)))...	chrX:23801365-23801588(+)$1	1	87	112	23.2364
((((.(............).)))))	chr14:61179597-61179832(-)$1	1	111	136	24.3149
(((((..............))))))	chr12:122957393-122957625(-)$1	1	170	195	22.9618
..((((..............)))).	chr1:65890923-65891143(+)$1	1	139	164	21.9231
((((((............)))))))	chr3:45763427-45763651(+)$1	1	42	67	24.4588
..((((.............))))..	chr9:36338037-36338263(-)$1	1	77	102	21.2704
((((((...........))))))..	chr14:102552328-102552560(-)$1	1	134	159	22.5283
(((.(((...........))).)))	chr2:97499009-97499249(+)$1	1	105	130	21.4189
((((((............)))))))	chr2:24290491-24290728(-)$1	1	113	138	24.3150
.(((((............)))))..	chr15:41248142-41248402(+)$1	1	211	236	23.1271
.(((((............)))))..	chr7:44916152-44916413(-)$1	1	166	191	21.3679
(((................))))))	chr12:27573837-27574072(+)$1	1	76	101	21.4866
((((((...........))))))..	chr5:72210007-72210226(+)$1	1	23	48	22.0560
.((.((............)).)).)	chr3:5221617-5221837(+)$1	1	62	87	22.1655
(((((.............)))))..	chr8:117670992-117671251(-)$1	1	214	239	23.1581
))))(((...........)))(((.	chr1:150938442-150938679(-)$1	1	48	73	21.1802
.(((((............)))))..	chr7:92905386-92905610(+)$1	1	132	157	24.7906
((((...............))))).	chr10:70100830-70101095(+)$1	1	211	236	19.1801
((((((.............))))))	chr16:24836036-24836283(+)$1	1	149	174	23.4987
(((((..............))))).	chr12:54424201-54424450(+)$1	1	9	34	23.1082
((((((.............))))))	chr19:1257967-1258191(+)$1	1	102	127	23.4987
((((((...........))))))).	chr18:60245534-60245757(+)$1	1	191	216	22.7133
.((((((...........)))))).	chr12:6643571-6643798(+)$1	1	38	63	22.9072
((((((............)))))).	chr5:71502511-71502747(+)$1	1	35	60	24.5570
..((((..............)))).	chr14:61909743-61909972(+)$1	1	105	130	21.9231
(.((((...........)))).)).	chr5:73924474-73924704(-)$1	1	70	95	21.1596
(..(((.............)))..)	chr1:211746682-211746910(-)$1	1	51	76	22.8094
((((((............)))))).	chr6:7882453-7882676(-)$1	1	16	41	23.4593
(((((.............)))))))	chr12:49389278-49389499(-)$1	1	47	72	23.8069
((((((............)))))))	chr3:122146296-122146522(-)$1	1	164	189	24.4588
((((................)))).	chr1:179310203-179310447(+)$1	1	57	82	20.4671
...((((...........))))...	chr4:88998783-88999015(+)$1	1	96	121	22.0038
(.((((............)))).))	chr12:53808627-53808865(+)$1	1	40	65	23.3344
((((((............)))))).	chr2:198416104-198416324(+)$1	1	104	129	24.5570
((((..............)))))).	chr17:27940847-27941092(+)$1	1	80	105	23.2140
)).(((.............)))(((	chr2:232327900-232328122(-)$1	1	95	120	22.3001
.(((((............)))))))	chr17:66247162-66247392(+)$1	1	111	136	24.2378
((((((............)))))))	chr19:36128461-36128693(+)$1	1	3	28	24.3150
(((((..............))))).	chr5:41918437-41918667(+)$1	1	152	177	23.2287
((((..............)))))).	chr15:78782730-78782960(+)$1	1	170	195	23.0718
((((.(...........).))))).	chr3:15613135-15613360(-)$1	1	35	60	23.2431
((((((............)))))).	chr2:10567397-10567622(+)$1	1	186	211	24.6452
((................)))))))	chr12:53806752-53806989(+)$1	1	211	236	21.1105
(((((((...........)))))))	chr6:44416628-44416860(+)$1	1	177	202	22.3613
..((((............)))).))	chr6:21598120-21598341(+)$1	1	5	30	23.0396

#PSSM
f : 0.24	e : 0.12	g : 0.12	[ : 0.06	! : 0.06	c : 0.04	i : 0.04	# : 0.04	= : 0.04	d : 0.04	" : 0.04	$ : 0.03	h : 0.01	a : 0.01	' : 0.01	: : 0.01	b : 0.01	
f : 0.26	e : 0.21	g : 0.12	[ : 0.06	! : 0.06	i : 0.04	= : 0.04	d : 0.04	b : 0.03	# : 0.03	" : 0.03	c : 0.01	h : 0.01	$ : 0.01	
f : 0.26	e : 0.21	d : 0.16	g : 0.10	b : 0.06	i : 0.04	c : 0.03	= : 0.03	h : 0.01	! : 0.01	" : 0.01	: : 0.01	y : 0.01	
f : 0.24	e : 0.21	d : 0.16	g : 0.10	c : 0.06	[ : 0.04	y : 0.04	b : 0.03	i : 0.03	= : 0.03	h : 0.01	
f : 0.18	e : 0.16	d : 0.13	g : 0.10	w : 0.09	c : 0.09	y : 0.06	i : 0.03	b : 0.03	[ : 0.03	= : 0.03	a : 0.01	x : 0.01	
w : 0.15	f : 0.15	d : 0.13	e : 0.12	g : 0.09	c : 0.07	v : 0.06	y : 0.06	i : 0.03	b : 0.03	a : 0.03	= : 0.03	x : 0.01	
u : 0.41	w : 0.20	v : 0.13	t : 0.09	y : 0.06	c : 0.03	x : 0.01	f : 0.01	d : 0.01	g : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	t : 0.16	v : 0.13	y : 0.06	x : 0.01	
u : 0.41	w : 0.20	v : 0.13	t : 0.07	y : 0.06	f : 0.03	e : 0.01	x : 0.01	g : 0.01	d : 0.01	a : 0.01	
f : 0.18	e : 0.13	w : 0.10	g : 0.10	d : 0.09	v : 0.07	b : 0.06	c : 0.04	y : 0.04	i : 0.03	a : 0.03	= : 0.03	h : 0.01	x : 0.01	] : 0.01	
f : 0.24	e : 0.20	d : 0.10	g : 0.10	c : 0.09	b : 0.06	i : 0.04	w : 0.04	] : 0.03	= : 0.03	h : 0.01	y : 0.01	
f : 0.26	e : 0.21	d : 0.15	g : 0.12	c : 0.09	] : 0.06	i : 0.04	= : 0.03	h : 0.01	
f : 0.26	e : 0.23	d : 0.13	g : 0.12	c : 0.07	i : 0.04	] : 0.04	b : 0.03	= : 0.03	h : 0.01	
f : 0.26	e : 0.21	g : 0.12	d : 0.07	c : 0.06	b : 0.06	i : 0.04	] : 0.04	2 : 0.03	3 : 0.03	= : 0.03	h : 0.01	
f : 0.23	g : 0.12	c : 0.09	e : 0.09	d : 0.07	2 : 0.06	i : 0.04	3 : 0.04	] : 0.03	5 : 0.03	b : 0.03	= : 0.03	6 : 0.03	4 : 0.01	h : 0.01	a : 0.01	0 : 0.01	: : 0.01	
] : 0.16	g : 0.10	2 : 0.09	3 : 0.09	e : 0.07	f : 0.07	c : 0.06	i : 0.04	5 : 0.04	4 : 0.04	= : 0.03	d : 0.03	: : 0.03	6 : 0.03	h : 0.01	a : 0.01	0 : 0.01	n : 0.01	

#score	1489.5373714203445
#seq	65
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_UTR_m1_run2.txt

#BEAR
a[ffffffvvvvvvvvvvvvvffffff]	chr13:97874550-97874790(+)$1	240	187	215	24.8418
gggggggvvvvvvvvvvvvvggggggg:	chr1:27106566-27106806(+)$1	240	117	145	24.1568
cc[ccc[bbuuuuuuuuuuuubb]ccc]	chr10:98281236-98281530(-)$1	294	233	261	23.5712
ddd[eeeeeuuuuuuuuuuuueeeee]d	chr3:129599084-129599324(-)$1	240	176	204	23.4709
####ddddvvvvvvvvvvvvvdddd444	chr17:4069216-4069456(-)$1	240	89	117	23.4426
gggggggvvvvvvvvvvvvvggggggg]	chr8:23538009-23538249(-)$1	240	45	73	25.2435
!!eeeeexxxxxxxxxxxxxxxeeeee3	chrX:73809980-73810221(-)$1	241	162	190	20.2067
[ffffffwwwwwwwwwwwwwwffffff]	chr8:17427750-17427990(+)$1	240	100	128	24.5678
fff[cccwwwwwwwwwwwwwwccc]fff	chr18:66341234-66341474(-)$1	240	51	79	24.2886
e!!ddddwwwwwwwwwwwwwwdddd22e	chr1:228294308-228294548(-)$1	240	101	129	23.0619
iiiiiiiivvvvvvvvvvvvviiiiiii	chr3:120045515-120045795(-)$1	280	97	125	25.8763
ccbb[eeeeettttttttttteeeee]b	chr4:187630849-187631089(-)$1	240	65	93	21.4380
"eeeeexxxxxxxxxxxxxxxeeeee]i	chr21:18966135-18966419(-)$1	284	169	197	19.8830
fffffbbwwwwwwwwwwwwwwbb]ffff	chr11:92917506-92917746(-)$1	240	122	150	22.9861
d!!eeeeeuuuuuuuuuuuueeeee333	chr1:78482190-78482430(+)$1	240	179	207	24.2701
"ffffffwwwwwwwwwwwwwwffffff4	chr11:67924191-67924431(-)$1	240	100	128	24.3862
ccc!!bbvvvvvvvvvvvvvbb22ccc3	chr8:109252148-109252388(-)$1	240	178	206	22.9960
ggggg[cccuuuuuuuuuuuucccgggg	chr17:4068650-4068890(-)$1	240	174	202	25.1038
"ffffffwwwwwwwwwwwwwwffffff3	chr9:134371538-134371778(+)$1	240	201	229	24.5693
ca!!fffffftttttttttttffffff2	chr1:117118559-117118799(-)$1	240	193	221	22.1091
gggggggyyyyyyyyyyyyyyyyggggg	chr1:78030102-78030342(-)$1	240	48	76	23.0032
========vvvvvvvvvvvvv=======	chr14:102394112-102394392(+)$1	280	28	56	26.0526
g[aa[cccvvvvvvvvvvvvvccc]a]a	chr15:40759188-40759428(+)$1	240	37	65	25.2926
========vvvvvvvvvvvvv=======	chr8:33405189-33405429(-)$1	240	43	71	26.0526
gggggggvvvvvvvvvvvvvggggggg:	chr1:89225796-89226036(+)$1	240	78	106	24.1568
gg[dddduuuuuuuuuuuudddd333gg	chr17:2287993-2288233(-)$1	240	193	221	21.8968
ddddfffffftttttttttttffffff2	chr11:115045697-115045954(-)$1	257	32	60	21.3287
g:ccc[cccuuuuuuuuuuuuccc]ccc	chr17:5393255-5393535(+)$1	280	138	166	23.2773
""eeeeewwwwwwwwwwwwwweeeee]i	chr5:31554300-31554580(+)$1	280	94	122	24.7871
h[bb[cccvvvvvvvvvvvvvccc]bbh	chr10:93038132-93038372(+)$1	240	127	155	23.8646
dddd"""ccctttttttttttccc333d	chr13:100617274-100617514(-)$1	240	156	184	21.5982
hhhhhh[auuuuuuuuuuuua]hhhhhh	chr13:98116892-98117182(+)$1	290	252	280	23.1600
hhhhhhhwwwwwwwwwwwwwwhhhhhhh	chr11:9610755-9611009(+)$1	254	159	187	22.8010
f[gggggggtttttttttttggggggg]	chr18:74073003-74073283(-)$1	280	214	242	23.3006
=======yyyyyyyyyyyyyyyy=====	chr13:113977410-113977650(+)$1	240	79	107	23.1532
eeeeeyyyyyyyyyyyyyyyyeeeeeHH	chr12:8207357-8207597(+)$1	240	204	232	20.2289
=======yyyyyyyyyyyyyyyy=====	chr10:38119921-38120181(-)$1	260	125	153	23.1532
[eeeeeyyyyyyyyyyyyyyyyeeeee]	chr17:65066749-65066989(-)$1	240	168	196	22.0496
bbggggggguuuuuuuuuuuuggggggg	chrX:24004885-24005214(-)$1	329	201	229	24.3015
hhhheeeeeuuuuuuuuuuuueeeeeFF	chr15:100254412-100254652(+)$1	240	30	58	22.6913
::eeeeewwwwwwwwwwwwwweeeee:E	chr11:124502869-124503153(+)$1	284	210	238	20.1250
ccc[cccuuuuuuuuuuuuccc]ccc>>	chr11:94603997-94604237(+)$1	240	151	179	22.4379
hhhhhhhhvvvvvvvvvvvvvhhhhhhh	chr18:12725523-12725803(+)$1	280	193	221	22.7127
cccfffffftttttttttttffffff]c	chr2:184024144-184024384(+)$1	240	140	168	22.1880
========vvvvvvvvvvvvv=======	chr5:180005015-180005255(+)$1	240	113	141	26.0526
hhhh[cccvvvvvvvvvvvvvccc]hhh	chr13:77457491-77457773(-)$1	282	138	166	24.3123
!!ffffffvvvvvvvvvvvvvffffff2	chr2:27016917-27017170(+)$1	253	77	105	24.8784
ddddeeeeettttttttttteeeee333	chr3:13358917-13359157(-)$1	240	145	173	22.1959
ff[gggggggtttttttttttggggggg	chr17:48460140-48460380(-)$1	240	91	119	22.6026
gggggggwwwwwwwwwwwwwwggggggg	chr3:152182800-152183086(+)$1	286	48	76	25.6324
dd!!eeeeeuuuuuuuuuuuueeeee22	chr13:73282642-73282882(-)$1	240	48	76	23.8347
"""ddddwwwwwwwwwwwwwwdddd333	chr16:68225078-68225318(+)$1	240	108	136	23.9326
hhhhhh[attttttttttta]hhhhhhh	chr18:9861825-9862105(+)$1	280	27	55	21.0022
cffffffwwwwwwwwwwwwwwffffff]	chr21:36161427-36161667(-)$1	240	169	197	24.4650
cccgggggggtttttttttttggggggg	chr3:8922568-8922808(-)$1	240	108	136	22.7401
gggggggvvvvvvvvvvvvvggggggg:	chrX:24005380-24005660(-)$1	280	45	73	24.1568
=======xxxxxxxxxxxxxxx======	chr17:56050317-56050557(-)$1	240	169	197	21.0882
=======wwwwwwwwwwwwww=======	chr4:154702256-154702496(-)$1	240	126	154	25.7767
""eeeeevvvvvvvvvvvvveeeee333	chr5:172195065-172195305(-)$1	240	4	32	24.5876
=======wwwwwwwwwwwwww=======	chr9:116169484-116169724(-)$1	240	56	84	25.7767
eee!!a[ccctttttttttttccc]a22	chr19:4046488-4046808(-)$1	320	131	159	22.5077
ccggggggguuuuuuuuuuuuggggggg	chr1:52250080-52250320(+)$1	240	32	60	24.8615
"ffffffwwwwwwwwwwwwwwffffff3	chr22:41755891-41756131(+)$1	240	115	143	24.5693

#otherMatches

#Seq PSSM
UGUUCCUGGGGUUACUGUAAAUGGGAAG	chr13:97874550-97874790(+)$1	240	187	215	24.8418
GCCCAGGACCCCUUUUCCACCCUGGGCC	chr1:27106566-27106806(+)$1	240	117	145	24.1568
CAAUUUACUGUACAGUUAGAAAGCAAAG	chr10:98281236-98281530(-)$1	294	233	261	23.5712
UGUCGUUUUUUCUUCUACUGCAAAAUCA	chr3:129599084-129599324(-)$1	240	176	204	23.4709
GAAGAGAUCCCCCGUCCCCCAGUCUGAC	chr17:4069216-4069456(-)$1	240	89	117	23.4426
CUCAUGCUCAGCACAUAUUUGCAUGGGA	chr8:23538009-23538249(-)$1	240	45	73	25.2435
GCUCCUCAAAAAUGAAAAAAUGGAGGAA	chrX:73809980-73810221(-)$1	241	162	190	20.2067
UAUGUCUGUAAAAACCAACAAAGGCAUU	chr8:17427750-17427990(+)$1	240	100	128	24.5678
UAUCUGAUUUAGAAAUAACAUUUAAAUG	chr18:66341234-66341474(-)$1	240	51	79	24.2886
CACCCCGGGACAUUGCUAAGAUGGGAGG	chr1:228294308-228294548(-)$1	240	101	129	23.0619
GUAGCUAUGUAAAAAAAGUUAAUGGUUA	chr3:120045515-120045795(-)$1	280	97	125	25.8763
ACGAUUCUGAUUUCUUCUGUUUCAGAUU	chr4:187630849-187631089(-)$1	240	65	93	21.4380
AUAUAUGCACUUUAGAUAUUGAUAUAGU	chr21:18966135-18966419(-)$1	284	169	197	19.8830
CAUUGGCAAUAAAAAAUGCAGGCAUAGU	chr11:92917506-92917746(-)$1	240	122	150	22.9861
UUAUUAGAUUUAAAUCACCUUCUGAAAU	chr1:78482190-78482430(+)$1	240	179	207	24.2701
UGAACUACAGCUAUCUUAAUUUGGUUCU	chr11:67924191-67924431(-)$1	240	100	128	24.3862
UACAAGGCAAAUGCAGUCAACCAGGUAA	chr8:109252148-109252388(-)$1	240	178	206	22.9960
UUGCGUACAAACCUGCCUAGCUGUUGUA	chr17:4068650-4068890(-)$1	240	174	202	25.1038
CCAUGUGUAUAGCUGAACUUUUAUAUGU	chr9:134371538-134371778(+)$1	240	201	229	24.5693
CCUUUCUGUUUGCCUAGUCUCAGCAGAC	chr1:117118559-117118799(-)$1	240	193	221	22.1091
UUGUAUGUUUCUUCUUAUCUGUGUAUAC	chr1:78030102-78030342(-)$1	240	48	76	23.0032
AUGUUAAGUACCGACAUAUUUUUUAACA	chr14:102394112-102394392(+)$1	280	28	56	26.0526
ACCCACCUGAAAUCAAACCAAAGGAGUG	chr15:40759188-40759428(+)$1	240	37	65	25.2926
AAUCUCCAGAAUGGAAGGGGGUGGGGAU	chr8:33405189-33405429(-)$1	240	43	71	26.0526
UAAGUAAUUUUAACAAUAUUUUAUUUAC	chr1:89225796-89226036(+)$1	240	78	106	24.1568
AGUGGGCAGUCACCACCCAGCCCUUCCU	chr17:2287993-2288233(-)$1	240	193	221	21.8968
UCUGCUGUCGCUCUCAGUUCUCGAUAGG	chr11:115045697-115045954(-)$1	257	32	60	21.3287
gcugAGUGGCUCUUUUAUUAACCAGUCA	chr17:5393255-5393535(+)$1	280	138	166	23.2773
AUGUAGCUAAAAUUAUAGUGUGCUGCCU	chr5:31554300-31554580(+)$1	280	94	122	24.7871
CAUUCUGCUACUGAACCAUCUGCAUAAG	chr10:93038132-93038372(+)$1	240	127	155	23.8646
AAUUGUACCAAGGAAAAUGAAUGGAGAG	chr13:100617274-100617514(-)$1	240	156	184	21.5982
GGGAUAGAGCUUCUAACCAAUGUAUUCC	chr13:98116892-98117182(+)$1	290	252	280	23.1600
UUACUGGUUUUGUAACUUGUUCUGGUAA	chr11:9610755-9611009(+)$1	254	159	187	22.8010
CUAGGUUUUUUUUUAAUUGUGAAAUUUU	chr18:74073003-74073283(-)$1	280	214	242	23.3006
CUUGGGCGUCUCUAAUGUCUGCAGCUCA	chr13:113977410-113977650(+)$1	240	79	107	23.1532
UCUUCUGCAAACUAGUCUCAUGAAGAAU	chr12:8207357-8207597(+)$1	240	204	232	20.2289
GUAUUUGUUAAUAUUUUCUACACUAAAU	chr10:38119921-38120181(-)$1	260	125	153	23.1532
ACUUUGUACCAUAAAAUAACCCCAAAGC	chr17:65066749-65066989(-)$1	240	168	196	22.0496
GCAUUUAGGUAAUACCAGACUCCUAAAU	chrX:24004885-24005214(-)$1	329	201	229	24.3015
UGUAAGGCAUUAUUUAAAACUUGCCUUU	chr15:100254412-100254652(+)$1	240	30	58	22.6913
CCAUAUGAUAACACAAAUUCACAUAUAA	chr11:124502869-124503153(+)$1	284	210	238	20.1250
UGCGAUGGAUUUUAUUACACAUGGUGGA	chr11:94603997-94604237(+)$1	240	151	179	22.4379
AUAAAAUUUUAUUUCCUAAGUAAUUUUG	chr18:12725523-12725803(+)$1	280	193	221	22.7127
ACUCUAGGUACACCAACACAACCUGGAA	chr2:184024144-184024384(+)$1	240	140	168	22.1880
GGGAAAUGGUGUAAACUAAUGUAUUUCU	chr5:180005015-180005255(+)$1	240	113	141	26.0526
AUGGAAUAAAUUCCCAAUGCAUAUCCUA	chr13:77457491-77457773(-)$1	282	138	166	24.3123
CUUAUUAUUUUAGCUCUUUCUGUAAUAU	chr2:27016917-27017170(+)$1	253	77	105	24.8784
CAUUAGCUCAUUUUAUGUAGGAGUUUUA	chr3:13358917-13359157(-)$1	240	145	173	22.1959
UUCUGCUGGACACAACCUCUUUUUAGCA	chr17:48460140-48460380(-)$1	240	91	119	22.6026
CCUCAUGACUGACAAAAACUCCAUGGGG	chr3:152182800-152183086(+)$1	286	48	76	25.6324
AAUCAACACUACAAAUACUAUGUGUUAU	chr13:73282642-73282882(-)$1	240	48	76	23.8347
CUGUGCAUACCCUGCCUCAUCUGCAAUC	chr16:68225078-68225318(+)$1	240	108	136	23.9326
CCAUGUGUUAAUAUAAAGUAGGCAUGGC	chr18:9861825-9862105(+)$1	280	27	55	21.0022
AGUUCUUCCCCCUUCACAUAAAGGAACA	chr21:36161427-36161667(-)$1	240	169	197	24.4650
GCCAUUCUCCUUCUCUUCCAUGGAGAAU	chr3:8922568-8922808(-)$1	240	108	136	22.7401
AGUUUUAUUAUUUAAAAGUUUAAAACUC	chrX:24005380-24005660(-)$1	280	45	73	24.1568
AUUUUUUAAUCAUUGCAGUUAAGAGAAA	chr17:56050317-56050557(-)$1	240	169	197	21.0882
AUAUUCAAACUAAUAAAAUCAUGAAUAU	chr4:154702256-154702496(-)$1	240	126	154	25.7767
AUCCUGUAAAUAUAUCUUAAGCAGGUUU	chr5:172195065-172195305(-)$1	240	4	32	24.5876
AGCGCUUUUUGUUUCUAAGUUGAGUGCU	chr9:116169484-116169724(-)$1	240	56	84	25.7767
GAUGGGGGGAGAGAGAGAAAAUCCACAA	chr19:4046488-4046808(-)$1	320	131	159	22.5077
GGUCUAUCCUCACAGUGCCCUGGGUGGA	chr1:52250080-52250320(+)$1	240	32	60	24.8615
CACUUUAAUAUUAAAUAUUCAUAAGGUC	chr22:41755891-41756131(+)$1	240	115	143	24.5693

#DB
(.((((((.............)))))).	chr13:97874550-97874790(+)$1	1	187	215	24.8418
(((((((.............))))))).	chr1:27106566-27106806(+)$1	1	117	145	24.1568
((.(((.((............)).))).	chr10:98281236-98281530(-)$1	1	233	261	23.5712
(((.(((((............))))).)	chr3:129599084-129599324(-)$1	1	176	204	23.4709
....((((.............))))...	chr17:4069216-4069456(-)$1	1	89	117	23.4426
(((((((.............))))))).	chr8:23538009-23538249(-)$1	1	45	73	25.2435
..(((((...............))))).	chrX:73809980-73810221(-)$1	1	162	190	20.2067
.((((((..............)))))).	chr8:17427750-17427990(+)$1	1	100	128	24.5678
(((.(((..............))).)))	chr18:66341234-66341474(-)$1	1	51	79	24.2886
(..((((..............))))..)	chr1:228294308-228294548(-)$1	1	101	129	23.0619
((((((((.............)))))))	chr3:120045515-120045795(-)$1	1	97	125	25.8763
((((.(((((...........))))).)	chr4:187630849-187631089(-)$1	1	65	93	21.4380
.(((((...............))))).)	chr21:18966135-18966419(-)$1	1	169	197	19.8830
(((((((..............)).))))	chr11:92917506-92917746(-)$1	1	122	150	22.9861
(..(((((............)))))...	chr1:78482190-78482430(+)$1	1	179	207	24.2701
.((((((..............)))))).	chr11:67924191-67924431(-)$1	1	100	128	24.3862
(((..((.............))..))).	chr8:109252148-109252388(-)$1	1	178	206	22.9960
(((((.(((............)))))))	chr17:4068650-4068890(-)$1	1	174	202	25.1038
.((((((..............)))))).	chr9:134371538-134371778(+)$1	1	201	229	24.5693
((..((((((...........)))))).	chr1:117118559-117118799(-)$1	1	193	221	22.1091
(((((((................)))))	chr1:78030102-78030342(-)$1	1	48	76	23.0032
((((((((.............)))))))	chr14:102394112-102394392(+)$1	1	28	56	26.0526
(.((.(((.............))).).)	chr15:40759188-40759428(+)$1	1	37	65	25.2926
((((((((.............)))))))	chr8:33405189-33405429(-)$1	1	43	71	26.0526
(((((((.............))))))).	chr1:89225796-89226036(+)$1	1	78	106	24.1568
((.((((............))))...))	chr17:2287993-2288233(-)$1	1	193	221	21.8968
((((((((((...........)))))).	chr11:115045697-115045954(-)$1	1	32	60	21.3287
).(((.(((............))).)))	chr17:5393255-5393535(+)$1	1	138	166	23.2773
..(((((..............))))).)	chr5:31554300-31554580(+)$1	1	94	122	24.7871
(.((.(((.............))).)))	chr10:93038132-93038372(+)$1	1	127	155	23.8646
((((...(((...........)))...)	chr13:100617274-100617514(-)$1	1	156	184	21.5982
((((((.(............).))))))	chr13:98116892-98117182(+)$1	1	252	280	23.1600
(((((((..............)))))))	chr11:9610755-9611009(+)$1	1	159	187	22.8010
(.(((((((...........))))))).	chr18:74073003-74073283(-)$1	1	214	242	23.3006
(((((((................)))))	chr13:113977410-113977650(+)$1	1	79	107	23.1532
(((((................)))))))	chr12:8207357-8207597(+)$1	1	204	232	20.2289
(((((((................)))))	chr10:38119921-38120181(-)$1	1	125	153	23.1532
.(((((................))))).	chr17:65066749-65066989(-)$1	1	168	196	22.0496
(((((((((............)))))))	chrX:24004885-24005214(-)$1	1	201	229	24.3015
))))(((((............)))))))	chr15:100254412-100254652(+)$1	1	30	58	22.6913
..(((((..............))))).)	chr11:124502869-124503153(+)$1	1	210	238	20.1250
(((.(((............))).)))..	chr11:94603997-94604237(+)$1	1	151	179	22.4379
((((((((.............)))))))	chr18:12725523-12725803(+)$1	1	193	221	22.7127
(((((((((...........)))))).)	chr2:184024144-184024384(+)$1	1	140	168	22.1880
((((((((.............)))))))	chr5:180005015-180005255(+)$1	1	113	141	26.0526
((((.(((.............))).)))	chr13:77457491-77457773(-)$1	1	138	166	24.3123
..((((((.............)))))).	chr2:27016917-27017170(+)$1	1	77	105	24.8784
(((((((((...........)))))...	chr3:13358917-13359157(-)$1	1	145	173	22.1959
((.(((((((...........)))))))	chr17:48460140-48460380(-)$1	1	91	119	22.6026
(((((((..............)))))))	chr3:152182800-152183086(+)$1	1	48	76	25.6324
((..(((((............)))))..	chr13:73282642-73282882(-)$1	1	48	76	23.8347
...((((..............))))...	chr16:68225078-68225318(+)$1	1	108	136	23.9326
((((((.(...........).)))))))	chr18:9861825-9862105(+)$1	1	27	55	21.0022
(((((((..............)))))).	chr21:36161427-36161667(-)$1	1	169	197	24.4650
)))(((((((...........)))))))	chr3:8922568-8922808(-)$1	1	108	136	22.7401
(((((((.............))))))).	chrX:24005380-24005660(-)$1	1	45	73	24.1568
(((((((...............))))))	chr17:56050317-56050557(-)$1	1	169	197	21.0882
(((((((..............)))))))	chr4:154702256-154702496(-)$1	1	126	154	25.7767
..(((((.............)))))...	chr5:172195065-172195305(-)$1	1	4	32	24.5876
(((((((..............)))))))	chr9:116169484-116169724(-)$1	1	56	84	25.7767
(((..(.(((...........))).)..	chr19:4046488-4046808(-)$1	1	131	159	22.5077
))(((((((............)))))))	chr1:52250080-52250320(+)$1	1	32	60	24.8615
.((((((..............)))))).	chr22:41755891-41756131(+)$1	1	115	143	24.5693

#PSSM
g : 0.15	c : 0.14	= : 0.12	" : 0.11	h : 0.11	d : 0.09	f : 0.06	e : 0.04	! : 0.03	[ : 0.03	a : 0.01	# : 0.01	i : 0.01	b : 0.01	: : 0.01	
g : 0.12	f : 0.12	= : 0.12	c : 0.11	h : 0.09	d : 0.07	[ : 0.06	! : 0.06	e : 0.06	" : 0.04	: : 0.03	# : 0.01	i : 0.01	a : 0.01	b : 0.01	
g : 0.15	f : 0.14	e : 0.12	= : 0.12	h : 0.09	c : 0.07	d : 0.06	! : 0.06	[ : 0.04	b : 0.03	# : 0.01	i : 0.01	a : 0.01	" : 0.01	
g : 0.19	f : 0.14	e : 0.12	= : 0.12	d : 0.09	h : 0.09	! : 0.06	[ : 0.04	c : 0.03	b : 0.03	# : 0.01	i : 0.01	a : 0.01	
g : 0.19	e : 0.19	f : 0.17	= : 0.12	c : 0.06	d : 0.06	[ : 0.06	h : 0.06	! : 0.03	i : 0.01	" : 0.01	
e : 0.19	g : 0.17	f : 0.15	= : 0.12	c : 0.09	d : 0.06	h : 0.06	b : 0.03	[ : 0.03	i : 0.01	" : 0.01	y : 0.01	a : 0.01	
g : 0.17	f : 0.15	e : 0.15	= : 0.12	c : 0.11	[ : 0.06	d : 0.06	b : 0.03	h : 0.03	y : 0.03	i : 0.01	x : 0.01	" : 0.01	
w : 0.23	c : 0.11	v : 0.09	e : 0.09	f : 0.07	y : 0.07	g : 0.07	x : 0.04	= : 0.04	u : 0.03	a : 0.03	b : 0.01	d : 0.01	i : 0.01	h : 0.01	
v : 0.26	w : 0.23	e : 0.07	y : 0.07	g : 0.07	u : 0.06	c : 0.06	x : 0.04	f : 0.04	b : 0.01	t : 0.01	
v : 0.26	w : 0.23	u : 0.19	y : 0.07	t : 0.06	x : 0.04	f : 0.03	c : 0.03	g : 0.03	e : 0.01	
v : 0.26	w : 0.23	u : 0.19	t : 0.17	y : 0.07	x : 0.04	
v : 0.26	w : 0.23	u : 0.19	t : 0.17	y : 0.07	x : 0.04	
v : 0.26	w : 0.23	u : 0.19	t : 0.17	y : 0.07	x : 0.04	
v : 0.26	w : 0.23	u : 0.19	t : 0.17	y : 0.07	x : 0.04	
v : 0.26	w : 0.23	u : 0.19	t : 0.17	y : 0.07	x : 0.04	
v : 0.26	w : 0.23	u : 0.19	t : 0.17	y : 0.07	x : 0.04	
v : 0.26	w : 0.23	u : 0.19	t : 0.17	y : 0.07	x : 0.04	
v : 0.26	w : 0.23	u : 0.19	t : 0.17	y : 0.07	x : 0.04	
v : 0.26	w : 0.23	u : 0.19	t : 0.17	y : 0.07	x : 0.04	
v : 0.26	w : 0.23	u : 0.15	t : 0.15	y : 0.07	x : 0.04	d : 0.01	c : 0.01	a : 0.01	
w : 0.23	v : 0.17	u : 0.12	t : 0.11	g : 0.07	y : 0.07	x : 0.04	e : 0.04	b : 0.01	d : 0.01	a : 0.01	c : 0.01	f : 0.01	] : 0.01	
e : 0.17	f : 0.15	g : 0.15	c : 0.14	= : 0.07	d : 0.06	y : 0.06	b : 0.04	h : 0.04	x : 0.03	i : 0.01	] : 0.01	
e : 0.20	f : 0.15	g : 0.15	c : 0.12	= : 0.09	d : 0.06	h : 0.06	y : 0.04	b : 0.03	i : 0.01	2 : 0.01	] : 0.01	
e : 0.20	g : 0.17	f : 0.15	c : 0.14	= : 0.12	h : 0.06	d : 0.04	] : 0.03	i : 0.01	2 : 0.01	3 : 0.01	
e : 0.20	g : 0.19	f : 0.17	= : 0.12	] : 0.09	h : 0.06	c : 0.04	d : 0.04	3 : 0.03	i : 0.01	
f : 0.19	g : 0.19	e : 0.15	= : 0.12	3 : 0.09	h : 0.07	c : 0.06	a : 0.03	4 : 0.01	2 : 0.01	i : 0.01	b : 0.01	
g : 0.20	f : 0.17	= : 0.12	] : 0.09	3 : 0.07	h : 0.07	c : 0.04	2 : 0.04	e : 0.03	4 : 0.01	i : 0.01	b : 0.01	H : 0.01	F : 0.01	: : 0.01	> : 0.01	
3 : 0.12	g : 0.12	= : 0.12	] : 0.11	h : 0.09	2 : 0.07	: : 0.04	i : 0.04	d : 0.03	4 : 0.03	f : 0.03	c : 0.03	e : 0.01	b : 0.01	a : 0.01	H : 0.01	F : 0.01	E : 0.01	> : 0.01	

#score	1479.0595369636303
#seq	63
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_UTR_m1_run2.txt

#BEAR
""dddduuuuuuuuuuuudddd22c	chr3:12626527-12626828(-)$1	301	182	207	21.5739
hhhhhhhuuuuuuuuuuuuhhhhhh	chr2:98272448-98272795(-)$1	347	211	236	21.6393
:fffffftttttttttttffffff:	chr14:93704173-93704439(-)$1	266	226	251	21.2662
hhhhhhhuuuuuuuuuuuuhhhhhh	chrX:40465505-40465841(+)$1	336	235	260	21.6393
iiiiiiitttttttttttiiiiiii	chr3:178740370-178740674(-)$1	304	30	55	23.8820
[eeeeeyyyyyyyyyyyyyyyyeee	chr11:4112929-4113311(+)$1	382	58	83	22.1263
[ffffffyyyyyyyyyyyyyyyyff	chr6:150131875-150132139(+)$1	264	83	108	22.6416
[a[ddddtttttttttttdddd]aa	chr16:1750781-1751280(+)$1	499	90	115	22.8814
!bb!!bbwwwwwwwwwwwwwwbb22	chr11:58388062-58388327(+)$1	265	37	62	19.8843
hhhhcccyyyyyyyyyyyyyyyycc	chr14:93695181-93695409(+)$1	228	103	128	21.9873
fff[cccvvvvvvvvvvvvvccc]f	chr11:9468438-9468681(+)$1	243	120	145	22.7597
ggggggguuuuuuuuuuuugggggg	chrX:150575675-150576060(+)$1	385	349	374	24.2442
"""ddddtttttttttttdddd22d	chr12:6647190-6647627(+)$1	437	177	202	22.2986
#ffffffuuuuuuuuuuuuffffff	chrX:24002167-24002483(-)$1	316	215	240	23.4341
ffffffvvvvvvvvvvvvvffffff	chr10:71899396-71899748(-)$1	352	225	250	22.0185
ee[cccwwwwwwwwwwwwwwccc]e	chr1:62917140-62917509(+)$1	369	111	136	21.3691
fff[bbuuuuuuuuuuuubb]ffff	chr1:46782302-46782539(+)$1	237	173	198	22.1269
hhhhhhhuuuuuuuuuuuuhhhhhh	chr10:27827750-27828053(+)$1	303	31	56	21.6393
$$$$ccctttttttttttccc4444	chr17:33678625-33679002(-)$1	377	96	121	22.3099
ee[ddddtttttttttttdddd]ee	chr2:204294938-204295207(+)$1	269	22	47	22.5147
###ddddtttttttttttdddd22d	chr9:127620076-127620446(-)$1	370	96	121	22.2126
:eeeeeuuuuuuuuuuuueeeeeff	chr12:111157704-111158166(-)$1	462	284	309	20.9842
ddd[cccwwwwwwwwwwwwwwcccd	chr19:18418098-18418465(-)$1	367	187	212	20.7669
ggg:cccyyyyyyyyyyyyyyyycc	chr9:139099384-139099671(-)$1	287	55	80	21.6038
gggggggwwwwwwwwwwwwwwgggg	chr12:53862460-53862716(+)$1	256	77	102	22.0369
[ffffffyyyyyyyyyyyyyyyyff	chr1:45244151-45244492(+)$1	341	235	260	22.6416
:ffffffuuuuuuuuuuuuffffff	chr10:7838909-7839204(+)$1	295	138	163	22.4327
bbeeeeevvvvvvvvvvvvveeeee	chr5:137906548-137906838(-)$1	290	21	46	21.2339
iiiiiiuuuuuuuuuuuuiiiiiii	chr1:222841944-222842303(-)$1	359	37	62	23.0299
ggggggguuuuuuuuuuuugggggg	chr1:225590818-225591134(-)$1	316	188	213	24.2442
:ffffffuuuuuuuuuuuuffffff	chr7:44921828-44922237(-)$1	409	209	234	22.4327
gggggggtttttttttttggggggg	chr10:27475413-27475682(+)$1	269	187	212	24.0576
!ffffffyyyyyyyyyyyyyyyyff	chr2:131805418-131805717(-)$1	299	166	191	22.6393
cccdddduuuuuuuuuuuudddd]c	chr19:8536109-8536403(+)$1	294	198	223	22.7486
ffffffyyyyyyyyyyyyyyyyfff	chr3:119544222-119544469(-)$1	247	129	154	22.5521
iiiiiiitttttttttttiiiiiii	chr6:149731678-149732013(+)$1	335	20	45	23.8820
gggggggtttttttttttggggggg	chr8:37917626-37917960(+)$1	334	129	154	24.0576
[ccccccyyyyyyyyyyyyyyyycc	chr22:42059856-42060125(+)$1	269	23	48	22.6215
dfffffftttttttttttffffff:	chr17:42113378-42113684(-)$1	306	106	131	21.9959
hhhhhhhyyyyyyyyyyyyyyyyhh	chr12:76441259-76441571(-)$1	312	172	197	21.2855
[bbddddtttttttttttdddd]bb	chr9:133579347-133579601(+)$1	254	88	113	21.9736
####cccuuuuuuuuuuuuccc333	chr9:131852166-131852555(+)$1	389	29	54	23.6430
b[eeeeettttttttttteeeee]b	chr2:87003730-87004067(+)$1	337	172	197	22.5062
e[eeeeettttttttttteeeeeee	chr17:79857970-79858277(+)$1	307	107	132	22.5441
ccc[bbuuuuuuuuuuuubb]ccc]	chr17:73315131-73315457(-)$1	326	291	316	22.1422
dfffffftttttttttttffffff:	chr19:58772283-58772516(+)$1	233	106	131	21.9959
ggggggguuuuuuuuuuuugggggg	chrX:24024484-24024917(-)$1	433	43	68	24.2442
dddd[bbtttttttttttbb]dddd	chr11:32126620-32126941(+)$1	321	167	192	21.6858
gggggggtttttttttttggggggg	chr22:36912688-36912937(-)$1	249	99	124	24.0576
gggggggvvvvvvvvvvvvvggggg	chr5:137902633-137902878(-)$1	245	197	222	23.1499
f####bbtttttttttttbb4444f	chr14:74178634-74178940(-)$1	306	148	173	22.2137
ggggggguuuuuuuuuuuugggggg	chr17:5346925-5347164(-)$1	239	187	212	24.2442
!!eeeeettttttttttteeeeeii	chr19:39423371-39423738(+)$1	367	163	188	23.1208
====[bbuuuuuuuuuuuubb]===	chr11:62327440-62327764(-)$1	324	261	286	23.2981
ffffffvvvvvvvvvvvvvffffff	chr22:42980548-42981039(-)$1	491	375	400	22.0185
iiiiiiivvvvvvvvvvvvviiiii	chr14:96852976-96853241(+)$1	265	211	236	23.0233
bb[dddduuuuuuuuuuuudddd]b	chr17:26888461-26888713(-)$1	252	125	150	22.2644
ggg!!bbtttttttttttbb22ggg	chr3:14154104-14154387(-)$1	283	166	191	23.1009
iiiiiiivvvvvvvvvvvvviiiii	chr10:85911928-85912274(+)$1	346	294	319	23.0233
fff[a[auuuuuuuuuuuua]a]ff	chr9:133761778-133762088(+)$1	310	46	71	23.8724
:fffffftttttttttttffffff:	chr17:8107970-8108249(-)$1	279	120	145	21.2662
fffff[auuuuuuuuuuuua]ffff	chr10:74035571-74035882(+)$1	311	122	147	23.6774
!!ddddwwwwwwwwwwwwwwdddd]	chr1:212792912-212793174(+)$1	262	78	103	20.6923
gggggggtttttttttttggggggg	chr6:43147632-43148066(+)$1	434	38	63	24.0576
gggggggtttttttttttggggggg	chr11:111965677-111965968(+)$1	291	147	172	24.0576
$$cccvvvvvvvvvvvvvcccffff	chr6:24777349-24777589(+)$1	240	117	142	20.7752
eee[bbyyyyyyyyyyyyyyyybb]	chr20:34292497-34292768(-)$1	271	229	254	21.4757
ff[ddddtttttttttttdddd]ff	chr3:196313689-196313991(+)$1	302	224	249	22.9369
!!cccbbtttttttttttbb]ccc2	chr19:50000350-50000682(+)$1	332	295	320	23.0736

#otherMatches

#Seq PSSM
AUUCUCACAUCAACAACCGAGAUCA	chr3:12626527-12626828(-)$1	301	182	207	21.5739
GGUGGGGGACAUUUUCUUACCUCAC	chr2:98272448-98272795(-)$1	347	211	236	21.6393
AGAAAUUUUUCUUAAACUGAUUUCA	chr14:93704173-93704439(-)$1	266	226	251	21.2662
GUAACUUUUCCCCCUGUGUAAGUUA	chrX:40465505-40465841(+)$1	336	235	260	21.6393
UUAAACAACUCAGACCCAUGUUUAA	chr3:178740370-178740674(-)$1	304	30	55	23.8820
AGUUUCCCCUCAAAAUCUUUAAGAA	chr11:4112929-4113311(+)$1	382	58	83	22.1263
CAAAGUAUAAAUUUGUGUAAUAUUA	chr6:150131875-150132139(+)$1	264	83	108	22.6416
AGAGGAAAAGCUCUUUACUUCCGCC	chr16:1750781-1751280(+)$1	499	90	115	22.8814
UAGCAUCCACAUAGAGCACUUGAAC	chr11:58388062-58388327(+)$1	265	37	62	19.8843
CUAUUCCUUCUUUCACAUUAACUGG	chr14:93695181-93695409(+)$1	228	103	128	21.9873
AUUAUAUAAAGUCAAUAAAAAUGAA	chr11:9468438-9468681(+)$1	243	120	145	22.7597
CUGAUUGUAAGAAUAACCUCAGUUA	chrX:150575675-150576060(+)$1	385	349	374	24.2442
CAAGAGGAAGAGAGAGACCCUCACU	chr12:6647190-6647627(+)$1	437	177	202	22.2986
GGUUUUCUUUUUACAUUUUGGGAAC	chrX:24002167-24002483(-)$1	316	215	240	23.4341
UGGGGCAAACUUCUCUUCAGCCCCA	chr10:71899396-71899748(-)$1	352	225	250	22.0185
GUACCCUAGUAUAUCUUUUUGGGCA	chr1:62917140-62917509(+)$1	369	111	136	21.3691
aauuuuuuuuuuuaauuugauauuu	chr1:46782302-46782539(+)$1	237	173	198	22.1269
CCAACAUCUUUUUUCAUAAAUGUUG	chr10:27827750-27828053(+)$1	303	31	56	21.6393
CUUGACAUUUAUCUUUGCUGUAUUC	chr17:33678625-33679002(-)$1	377	96	121	22.3099
GAAUUUCAAAUGAAUGCAGAAAAUC	chr2:204294938-204295207(+)$1	269	22	47	22.5147
CCAGGGCAAGAAGUACAAGCCCCUG	chr9:127620076-127620446(-)$1	370	96	121	22.2126
AAGUUAAAACAAAGGAACUAACUUA	chr12:111157704-111158166(-)$1	462	284	309	20.9842
AGUGAGCGCCCACCCAGACCGGCUG	chr19:18418098-18418465(-)$1	367	187	212	20.7669
GGGAGACUUCUAAAGCCCCCCCUGU	chr9:139099384-139099671(-)$1	287	55	80	21.6038
GCUUGCUCUCUUCUGUCUUUUAGCA	chr12:53862460-53862716(+)$1	256	77	102	22.0369
AAGGUGUUUAUUGUUUUGUUCCCAC	chr1:45244151-45244492(+)$1	341	235	260	22.6416
AUUACCAAGUCUAUGAAAAUGGUAG	chr10:7838909-7839204(+)$1	295	138	163	22.4327
CCGAAGGUGCCAGAACCACCCCUUC	chr5:137906548-137906838(-)$1	290	21	46	21.2339
AUAGGAUCGCCAUUUAUUUCCUAUU	chr1:222841944-222842303(-)$1	359	37	62	23.0299
AAGGAAAAAAAUCCGAAACUUUCUU	chr1:225590818-225591134(-)$1	316	188	213	24.2442
CUCUACUCUCAUCAUCCACAGUAGA	chr7:44921828-44922237(-)$1	409	209	234	22.4327
CAGCUUUCACAGAGUUAAAAGGCUG	chr10:27475413-27475682(+)$1	269	187	212	24.0576
AUGAGAUGAGCUCAGAUUUAAAAAU	chr2:131805418-131805717(-)$1	299	166	191	22.6393
GCAGGUGAGAAUGACAGUGCACCUU	chr19:8536109-8536403(+)$1	294	198	223	22.7486
AUACUGCCUUUUUUUUUGUCUACAG	chr3:119544222-119544469(-)$1	247	129	154	22.5521
AGAAUAACUUUCCUCUACUUAUUCU	chr6:149731678-149732013(+)$1	335	20	45	23.8820
CAGCAGUUCCAGCCCCUCGCUGCUG	chr8:37917626-37917960(+)$1	334	129	154	24.0576
CAGCCAGUUAAAAUGUGUUUCUCCU	chr22:42059856-42060125(+)$1	269	23	48	22.6215
UGAGUCCGUACACAUGGAGGACUCU	chr17:42113378-42113684(-)$1	306	106	131	21.9959
CUAAAAUAAAAAUUUCAAAUACAAU	chr12:76441259-76441571(-)$1	312	172	197	21.2855
CUCCCAUCCUGGAAUAAUAUGGAGA	chr9:133579347-133579601(+)$1	254	88	113	21.9736
AUAUGUCCUUGUCCUUCCUGACCCA	chr9:131852166-131852555(+)$1	389	29	54	23.6430
CAUCACUAGGAUGUAUAAGGUGACG	chr2:87003730-87004067(+)$1	337	172	197	22.5062
UAUGUUGACACUUUUAUCCAAUAAG	chr17:79857970-79858277(+)$1	307	107	132	22.5441
GGUGCAGUGUGAGUGUGAUGGGCCA	chr17:73315131-73315457(-)$1	326	291	316	22.1422
UUGAGGUUCAUGGUACUCACCUCAG	chr19:58772283-58772516(+)$1	233	106	131	21.9959
UAUUUUCUUCUGAAUGCAUGGAAGU	chrX:24024484-24024917(-)$1	433	43	68	24.2442
CCUGAUCUUUGAAAUAGUGAAUAGG	chr11:32126620-32126941(+)$1	321	167	192	21.6858
GGGGAAGGAAAGAUACAACUUCCCC	chr22:36912688-36912937(-)$1	249	99	124	24.0576
CCAAUGUGGUUAAUAUGUAGACGUU	chr5:137902633-137902878(-)$1	245	197	222	23.1499
UUAUUAGCUAUUACUCAACUUUACA	chr14:74178634-74178940(-)$1	306	148	173	22.2137
CAGUUUUAAAAUAGAAAACAAAACU	chr17:5346925-5347164(-)$1	239	187	212	24.2442
UCAACACCCUUGGCUCCUGUGUUUA	chr19:39423371-39423738(+)$1	367	163	188	23.1208
GGCAGGGAUAUAAGAAGCACUGUGU	chr11:62327440-62327764(-)$1	324	261	286	23.2981
CCCAGCAUAGGCGCAGACAGUUGGG	chr22:42980548-42981039(-)$1	491	375	400	22.0185
UUGUUUUUUAAUGGUCACCUAAAGC	chr14:96852976-96853241(+)$1	265	211	236	23.0233
GGAGGCCUUUAACAUCAUUGGCCGC	chr17:26888461-26888713(-)$1	252	125	150	22.2644
AUACACUGAAAAAAAUGGGGGUUGU	chr3:14154104-14154387(-)$1	283	166	191	23.1009
UCAUAUUUAAAUGUUCCGGUAAUGU	chr10:85911928-85912274(+)$1	346	294	319	23.0233
UGUGACGUGCACUGUGAAUCCUGGC	chr9:133761778-133762088(+)$1	310	46	71	23.8724
GAAGGGAUCCCUAACUGUUCCCUUA	chr17:8107970-8108249(-)$1	279	120	145	21.2662
AUGAAGAUAAGAUACUCACUGUUCA	chr10:74035571-74035882(+)$1	311	122	147	23.6774
ACCUCUAGAAUCCCAGCAGCAGAGA	chr1:212792912-212793174(+)$1	262	78	103	20.6923
uaaauauauauuuuuaaaauauuua	chr6:43147632-43148066(+)$1	434	38	63	24.0576
AAGAUUAUUUUCAGAAUUUAAUCUU	chr11:111965677-111965968(+)$1	291	147	172	24.0576
UCUACAUAAUGAAUCCCAGUAUGAA	chr6:24777349-24777589(+)$1	240	117	142	20.7752
AGAUGCUAAACCCAACAUGUCUGUU	chr20:34292497-34292768(-)$1	271	229	254	21.4757
UGAUCAGGGAAAGUGUAACUGAGUA	chr3:196313689-196313991(+)$1	302	224	249	22.9369
UUGCCCUGCCUGCAUCUAAGUGGCU	chr19:50000350-50000682(+)$1	332	295	320	23.0736

#DB
..((((............))))..)	chr3:12626527-12626828(-)$1	1	182	207	21.5739
(((((((............))))))	chr2:98272448-98272795(-)$1	1	211	236	21.6393
.((((((...........)))))).	chr14:93704173-93704439(-)$1	1	226	251	21.2662
(((((((............))))))	chrX:40465505-40465841(+)$1	1	235	260	21.6393
(((((((...........)))))))	chr3:178740370-178740674(-)$1	1	30	55	23.8820
.(((((................)))	chr11:4112929-4113311(+)$1	1	58	83	22.1263
.((((((................))	chr6:150131875-150132139(+)$1	1	83	108	22.6416
.(.((((...........)))).))	chr16:1750781-1751280(+)$1	1	90	115	22.8814
.((..((..............))..	chr11:58388062-58388327(+)$1	1	37	62	19.8843
))))(((................))	chr14:93695181-93695409(+)$1	1	103	128	21.9873
(((.(((.............))).)	chr11:9468438-9468681(+)$1	1	120	145	22.7597
(((((((............))))))	chrX:150575675-150576060(+)$1	1	349	374	24.2442
...((((...........))))..)	chr12:6647190-6647627(+)$1	1	177	202	22.2986
.((((((............))))))	chrX:24002167-24002483(-)$1	1	215	240	23.4341
((((((.............))))))	chr10:71899396-71899748(-)$1	1	225	250	22.0185
((.(((..............))).)	chr1:62917140-62917509(+)$1	1	111	136	21.3691
(((.((............)).))))	chr1:46782302-46782539(+)$1	1	173	198	22.1269
(((((((............))))))	chr10:27827750-27828053(+)$1	1	31	56	21.6393
....(((...........)))....	chr17:33678625-33679002(-)$1	1	96	121	22.3099
((.((((...........)))).))	chr2:204294938-204295207(+)$1	1	22	47	22.5147
...((((...........))))..)	chr9:127620076-127620446(-)$1	1	96	121	22.2126
.(((((............)))))((	chr12:111157704-111158166(-)$1	1	284	309	20.9842
(((.(((..............))))	chr19:18418098-18418465(-)$1	1	187	212	20.7669
))).(((................))	chr9:139099384-139099671(-)$1	1	55	80	21.6038
(((((((..............))))	chr12:53862460-53862716(+)$1	1	77	102	22.0369
.((((((................))	chr1:45244151-45244492(+)$1	1	235	260	22.6416
.((((((............))))))	chr10:7838909-7839204(+)$1	1	138	163	22.4327
))(((((.............)))))	chr5:137906548-137906838(-)$1	1	21	46	21.2339
((((((............)))))))	chr1:222841944-222842303(-)$1	1	37	62	23.0299
(((((((............))))))	chr1:225590818-225591134(-)$1	1	188	213	24.2442
.((((((............))))))	chr7:44921828-44922237(-)$1	1	209	234	22.4327
(((((((...........)))))))	chr10:27475413-27475682(+)$1	1	187	212	24.0576
.((((((................))	chr2:131805418-131805717(-)$1	1	166	191	22.6393
(((((((............)))).)	chr19:8536109-8536403(+)$1	1	198	223	22.7486
((((((................)))	chr3:119544222-119544469(-)$1	1	129	154	22.5521
(((((((...........)))))))	chr6:149731678-149732013(+)$1	1	20	45	23.8820
(((((((...........)))))))	chr8:37917626-37917960(+)$1	1	129	154	24.0576
.((((((................))	chr22:42059856-42060125(+)$1	1	23	48	22.6215
)((((((...........)))))).	chr17:42113378-42113684(-)$1	1	106	131	21.9959
(((((((................))	chr12:76441259-76441571(-)$1	1	172	197	21.2855
.((((((...........)))).))	chr9:133579347-133579601(+)$1	1	88	113	21.9736
....(((............)))...	chr9:131852166-131852555(+)$1	1	29	54	23.6430
(.(((((...........))))).)	chr2:87003730-87004067(+)$1	1	172	197	22.5062
(.(((((...........)))))))	chr17:79857970-79858277(+)$1	1	107	132	22.5441
(((.((............)).))).	chr17:73315131-73315457(-)$1	1	291	316	22.1422
)((((((...........)))))).	chr19:58772283-58772516(+)$1	1	106	131	21.9959
(((((((............))))))	chrX:24024484-24024917(-)$1	1	43	68	24.2442
((((.((...........)).))))	chr11:32126620-32126941(+)$1	1	167	192	21.6858
(((((((...........)))))))	chr22:36912688-36912937(-)$1	1	99	124	24.0576
(((((((.............)))))	chr5:137902633-137902878(-)$1	1	197	222	23.1499
(....((...........))....)	chr14:74178634-74178940(-)$1	1	148	173	22.2137
(((((((............))))))	chr17:5346925-5347164(-)$1	1	187	212	24.2442
..(((((...........)))))))	chr19:39423371-39423738(+)$1	1	163	188	23.1208
((((.((............)).)))	chr11:62327440-62327764(-)$1	1	261	286	23.2981
((((((.............))))))	chr22:42980548-42981039(-)$1	1	375	400	22.0185
(((((((.............)))))	chr14:96852976-96853241(+)$1	1	211	236	23.0233
((.((((............)))).)	chr17:26888461-26888713(-)$1	1	125	150	22.2644
(((..((...........))..)))	chr3:14154104-14154387(-)$1	1	166	191	23.1009
(((((((.............)))))	chr10:85911928-85912274(+)$1	1	294	319	23.0233
(((.(.(............).).))	chr9:133761778-133762088(+)$1	1	46	71	23.8724
.((((((...........)))))).	chr17:8107970-8108249(-)$1	1	120	145	21.2662
(((((.(............).))))	chr10:74035571-74035882(+)$1	1	122	147	23.6774
..((((..............)))).	chr1:212792912-212793174(+)$1	1	78	103	20.6923
(((((((...........)))))))	chr6:43147632-43148066(+)$1	1	38	63	24.0576
(((((((...........)))))))	chr11:111965677-111965968(+)$1	1	147	172	24.0576
..(((.............)))))))	chr6:24777349-24777589(+)$1	1	117	142	20.7752
(((.((................)).	chr20:34292497-34292768(-)$1	1	229	254	21.4757
((.((((...........)))).))	chr3:196313689-196313991(+)$1	1	224	249	22.9369
..(((((...........)).))).	chr19:50000350-50000682(+)$1	1	295	320	23.0736

#PSSM
g : 0.18	f : 0.13	[ : 0.08	h : 0.07	: : 0.07	i : 0.07	! : 0.07	e : 0.05	d : 0.05	# : 0.04	b : 0.04	" : 0.02	$ : 0.02	c : 0.02	= : 0.01	
f : 0.26	g : 0.18	h : 0.07	i : 0.07	e : 0.07	b : 0.05	# : 0.04	c : 0.04	! : 0.04	" : 0.02	$ : 0.02	d : 0.02	[ : 0.02	a : 0.01	= : 0.01	
f : 0.24	g : 0.18	e : 0.10	h : 0.07	i : 0.07	[ : 0.07	c : 0.07	d : 0.05	# : 0.04	b : 0.02	" : 0.01	$ : 0.01	= : 0.01	
f : 0.20	d : 0.15	g : 0.15	e : 0.08	[ : 0.08	h : 0.07	i : 0.07	c : 0.05	! : 0.02	# : 0.02	$ : 0.01	: : 0.01	= : 0.01	
f : 0.20	g : 0.15	d : 0.14	c : 0.14	e : 0.08	i : 0.07	h : 0.05	b : 0.04	! : 0.02	[ : 0.02	# : 0.01	a : 0.01	
f : 0.18	g : 0.15	d : 0.14	b : 0.13	c : 0.11	e : 0.08	i : 0.07	h : 0.05	[ : 0.02	v : 0.01	
g : 0.15	f : 0.14	d : 0.11	c : 0.10	b : 0.08	u : 0.07	h : 0.05	i : 0.05	e : 0.05	y : 0.04	v : 0.04	w : 0.02	a : 0.02	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
t : 0.36	u : 0.30	y : 0.14	v : 0.11	w : 0.07	
u : 0.23	y : 0.14	d : 0.10	v : 0.10	b : 0.08	w : 0.07	g : 0.07	f : 0.05	e : 0.05	i : 0.04	c : 0.02	
y : 0.14	d : 0.13	f : 0.13	g : 0.13	b : 0.10	w : 0.07	v : 0.07	e : 0.05	h : 0.04	i : 0.04	c : 0.04	a : 0.02	
d : 0.14	y : 0.14	g : 0.14	f : 0.13	] : 0.08	i : 0.07	c : 0.07	e : 0.07	h : 0.04	w : 0.04	4 : 0.01	b : 0.01	2 : 0.01	
f : 0.17	d : 0.15	g : 0.15	y : 0.14	c : 0.08	i : 0.07	e : 0.07	h : 0.04	4 : 0.02	b : 0.01	] : 0.01	2 : 0.01	a : 0.01	
f : 0.18	g : 0.17	y : 0.10	e : 0.08	i : 0.07	] : 0.07	c : 0.07	d : 0.05	2 : 0.04	h : 0.04	b : 0.02	4 : 0.02	3 : 0.01	= : 0.01	
f : 0.27	g : 0.17	i : 0.08	c : 0.08	] : 0.07	2 : 0.05	h : 0.05	e : 0.05	4 : 0.02	b : 0.02	d : 0.02	a : 0.01	3 : 0.01	= : 0.01	
f : 0.24	g : 0.17	i : 0.08	c : 0.07	e : 0.07	h : 0.05	: : 0.05	d : 0.05	b : 0.04	] : 0.04	2 : 0.02	a : 0.01	4 : 0.01	3 : 0.01	= : 0.01	

#score	1553.8335234776052
#seq	69
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_UTR_m1_run2.txt

#BEAR
hhhhhhhhuuuuuuuuuuuuhhhhh	chr1:39304017-39304247(-)$1	230	72	97	21.7474
ggggggwwwwwwwwwwwwwwggggg	chr20:43121044-43121266(+)$1	222	93	118	22.9531
bb[eeeeeuuuuuuuuuuuueeeee	chr2:11965846-11966092(+)$1	246	36	61	23.0689
e!!dddduuuuuuuuuuuudddd22	chr10:112772333-112772559(+)$1	226	57	82	22.7566
gggggggtttttttttttggggggg	chr6:45869372-45869602(-)$1	230	142	167	21.2671
h!!eeeeeuuuuuuuuuuuueeeee	chr3:44701742-44701954(+)$1	212	21	46	23.5195
[a[dddduuuuuuuuuuuudddd]a	chr7:105732001-105732234(-)$1	233	153	178	23.1296
ddd[ddddtttttttttttdddd]d	chr5:31400672-31400895(-)$1	223	91	116	21.9220
========uuuuuuuuuuuu=====	chr2:46988710-46988938(+)$1	228	112	137	23.4955
iiiiiiixxxxxxxxxxxxxxxiii	chr2:201354143-201354361(-)$1	218	86	111	19.1268
d[eeeeevvvvvvvvvvvvveeeee	chr10:115675163-115675390(+)$1	227	160	185	23.5674
c"""ddddtttttttttttdddd33	chrX:70794442-70794665(+)$1	223	153	178	21.8198
gggggggyyyyyyyyyyyyyyyygg	chr7:92166244-92166467(+)$1	223	32	57	22.4613
b:eeeeewwwwwwwwwwwwwweeee	chr22:37523408-37523635(-)$1	227	93	118	21.6617
!!ffffffuuuuuuuuuuuufffff	chr21:40565505-40565724(-)$1	219	75	100	22.0517
:ddddyyyyyyyyyyyyyyyydddd	chr2:64139651-64139872(-)$1	221	45	70	20.5626
iiiiiiwwwwwwwwwwwwwwiiiii	chr21:34932742-34932951(+)$1	209	148	173	23.0173
dd!!ddddtttttttttttdddd44	chr1:25688308-25688529(+)$1	221	132	157	21.8533
hhhhhhhhuuuuuuuuuuuuhhhhh	chr12:113448526-113448745(+)$1	219	36	61	21.7474
#bb[ddddtttttttttttdddd]b	chr22:32081187-32081417(-)$1	230	43	68	21.4401
ccceeeeeuuuuuuuuuuuueeeee	chr1:38268568-38268793(-)$1	225	83	108	23.3034
eee[eeeeettttttttttteeeee	chr17:79857971-79858202(+)$1	231	104	129	21.6572
ee"""bbvvvvvvvvvvvvvbb]ee	chr5:134121169-134121389(+)$1	220	102	127	22.1576
e[ddddyyyyyyyyyyyyyyyyddd	chr16:87443667-87443897(-)$1	230	20	45	21.8364
b:eeeeewwwwwwwwwwwwwweeee	chr22:37523456-37523683(-)$1	227	141	166	21.6617
hhhh!!avvvvvvvvvvvvva22hh	chr6:49460628-49460861(+)$1	233	72	97	22.7860
eeeee[bbtttttttttttbb]eee	chr12:45823412-45823642(+)$1	230	57	82	21.3936
gggggggvvvvvvvvvvvvvggggg	chr1:31404442-31404665(-)$1	223	191	216	23.7764
hhhhh[avvvvvvvvvvvvva]hhh	chr2:169627225-169627455(+)$1	230	42	67	22.9655
e[eeeeeuuuuuuuuuuuueeeee]	chr6:45869866-45870096(-)$1	230	100	125	23.2363
dd!!cccuuuuuuuuuuuuccc444	chr4:166000398-166000631(-)$1	233	19	44	23.0479
eee[cccvvvvvvvvvvvvvccc]e	chr7:32623798-32624028(+)$1	230	86	111	23.7303
ddd[cccyyyyyyyyyyyyyyyycc	chr5:157216323-157216542(-)$1	219	114	139	21.8988
gggggggvvvvvvvvvvvvvggggg	chr6:57054648-57054864(-)$1	216	175	200	23.7764
!!eeeeexxxxxxxxxxxxxxxeee	chr4:148556218-148556451(+)$1	233	94	119	19.0418
gggggggvvvvvvvvvvvvvggggg	chr1:52882425-52882650(+)$1	225	25	50	23.7764
[bb[dddduuuuuuuuuuuudddd]	chr1:111490467-111490692(-)$1	225	49	74	22.7705
ddddyyyyyyyyyyyyyyyydddd3	chr16:22358147-22358373(-)$1	226	51	76	20.9946
(ffffffuuuuuuuuuuuuffffff	chr17:4585699-4585912(-)$1	213	126	151	20.8724
"bb[eeeeettttttttttteeeee	chr8:57875324-57875544(-)$1	220	114	139	21.2668
ggggggguuuuuuuuuuuugggggg	chr1:180083332-180083561(+)$1	229	120	145	23.3116
:ddddyyyyyyyyyyyyyyyydddd	chr6:36078495-36078714(+)$1	219	50	75	20.5626
#ffffffvvvvvvvvvvvvvfffff	chr11:93545424-93545644(+)$1	220	140	165	21.9332
dddd[ayyyyyyyyyyyyyyyya]d	chr20:1147837-1148062(+)$1	225	158	183	21.9410
hhhhhhhyyyyyyyyyyyyyyyyhh	chr12:46299127-46299353(+)$1	226	89	114	21.4162
::eeeeeyyyyyyyyyyyyyyyyee	chr10:73995241-73995464(+)$1	223	195	220	20.2531
gggggggvvvvvvvvvvvvvggggg	chr1:185089431-185089675(-)$1	244	3	28	23.7764
hhhhhhhhuuuuuuuuuuuuhhhhh	chr16:74657465-74657687(-)$1	222	64	89	21.7474
eee!!aavvvvvvvvvvvvva]a22	chr2:171849168-171849388(-)$1	220	129	154	23.2265
a[eeeeevvvvvvvvvvvvveeeee	chr14:74667371-74667597(+)$1	226	43	68	23.6335
ggg[cccvvvvvvvvvvvvvccc]g	chr12:48438005-48438235(-)$1	230	9	34	24.0348
hhhhhhhvvvvvvvvvvvvvhhhhh	chr5:78980993-78981223(+)$1	230	112	137	22.2665
gggdddduuuuuuuuuuuudddd]g	chr13:100638677-100638903(+)$1	226	132	157	23.2760
ffffffwwwwwwwwwwwwwwfffff	chr5:130977670-130977900(-)$1	230	22	47	21.1470
ff[dddduuuuuuuuuuuudddd]f	chr4:68483927-68484146(-)$1	219	120	145	22.7634
!bb!!bbvvvvvvvvvvvvvbb22b	chr12:22208331-22208546(+)$1	215	75	100	21.6922
dd[cccwwwwwwwwwwwwwwccc]d	chr15:41601425-41601655(-)$1	230	96	121	22.5481
ddd!!cccuuuuuuuuuuuuccc55	chr14:74182950-74183172(-)$1	222	25	50	21.5615

#otherMatches

#Seq PSSM
GUUGAUGGUUGAUACCCUUUCCAUU	chr1:39304017-39304247(-)$1	230	72	97	21.7474
AUAGAGAUCUAUACUCCAAACUUUA	chr20:43121044-43121266(+)$1	222	93	118	22.9531
UCAAGAAGUUCAACUAUAUUCUUUU	chr2:11965846-11966092(+)$1	246	36	61	23.0689
GAAAGUUGCAGAUCCACAAAACUAA	chr10:112772333-112772559(+)$1	226	57	82	22.7566
UAAGUUUCAUCUCCUAAAAAGCUUA	chr6:45869372-45869602(-)$1	230	142	167	21.2671
AUUUUGUUUUUUAAAACUCUGAUGA	chr3:44701742-44701954(+)$1	212	21	46	23.5195
AAGAUGUAAAUGUAUUCUCACAUGU	chr7:105732001-105732234(-)$1	233	153	178	23.1296
CAAUUUUCUGUGUGUGUUUGAGAUU	chr5:31400672-31400895(-)$1	223	91	116	21.9220
AUUAACUAACAACCUUUCUAUAGUU	chr2:46988710-46988938(+)$1	228	112	137	23.4955
GAAUUAGCACUUUGACUCUCACUUA	chr2:201354143-201354361(-)$1	218	86	111	19.1268
AUGCUGAGAAGUAGACAAAAUCAGC	chr10:115675163-115675390(+)$1	227	160	185	23.5674
UUCUAAAGUUUUUUUUUUUUUUUUU	chrX:70794442-70794665(+)$1	223	153	178	21.8198
CUAAAAAGAACAUUUAUUAUUUAUU	chr7:92166244-92166467(+)$1	223	32	57	22.4613
cucagagcucccucacacccccucu	chr22:37523408-37523635(-)$1	227	93	118	21.6617
GUAUUCUUGAGAAAAAGAUAAAGGG	chr21:40565505-40565724(-)$1	219	75	100	22.0517
CUCCAUUAUAUAUCUACUCCCUGGA	chr2:64139651-64139872(-)$1	221	45	70	20.5626
uauauauauauCUGUAUCUUUGUAU	chr21:34932742-34932951(+)$1	209	148	173	23.0173
ccauggaaauuuaaacgacuuccuc	chr1:25688308-25688529(+)$1	221	132	157	21.8533
UCCUUUUUCCUUCCAGUCUAAAAAA	chr12:113448526-113448745(+)$1	219	36	61	21.7474
UCCAUGAAUUUUUACCUAUUUCAAG	chr22:32081187-32081417(-)$1	230	43	68	21.4401
AUAUGUGUACCAAGUGUUAAACAUA	chr1:38268568-38268793(-)$1	225	83	108	23.3034
ACUAUGUUGACACUUUUAUCCAAUA	chr17:79857971-79858202(+)$1	231	104	129	21.6572
AGCAGGUAGUUAUAUAAGAAACAUU	chr5:134121169-134121389(+)$1	220	102	127	22.1576
UCUGGCAACAGAACGUUAUUAAGCC	chr16:87443667-87443897(-)$1	230	20	45	21.8364
cucagagcucccucacacccccucu	chr22:37523456-37523683(-)$1	227	141	166	21.6617
AUAUGUGAAUAAGUUAUAACCUAGU	chr6:49460628-49460861(+)$1	233	72	97	22.7860
AGCCAUGUUUCAUUUCUUCACUUGG	chr12:45823412-45823642(+)$1	230	57	82	21.3936
GUGUAUAAUUAACAAACCUGUGUAU	chr1:31404442-31404665(-)$1	223	191	216	23.7764
GAAAGACUAUUUUACCCUUUGCUUU	chr2:169627225-169627455(+)$1	230	42	67	22.9655
AUUACAGGCCUGGGUUUGACUGUGC	chr6:45869866-45870096(-)$1	230	100	125	23.2363
GAAGCCCGGAUAACUUGAGGGGAAU	chr4:166000398-166000631(-)$1	233	19	44	23.0479
UAAUUUAUACUUGCUAAAAUUAAUU	chr7:32623798-32624028(+)$1	230	86	111	23.7303
GGUAUGCAGCCUUCCAAACCCCAGC	chr5:157216323-157216542(-)$1	219	114	139	21.8988
AUGUGCAGUAUUUAAGAAAAUGUAC	chr6:57054648-57054864(-)$1	216	175	200	23.7764
AACAGUUAUAUCCCUAUUCCUCAAC	chr4:148556218-148556451(+)$1	233	94	119	19.0418
AUAAGAAUAUUUUAGUUUUUUUCUU	chr1:52882425-52882650(+)$1	225	25	50	23.7764
CAGGUGCUGAGAGAGAAAGAAGCAG	chr1:111490467-111490692(-)$1	225	49	74	22.7705
GAGAACAAAAUACCGAUCACUCUCC	chr16:22358147-22358373(-)$1	226	51	76	20.9946
AUGCACUCUUCUCCCCACCAGUGUA	chr17:4585699-4585912(-)$1	213	126	151	20.8724
UUACAUGAAUUGAACUGCCUUUCAU	chr8:57875324-57875544(-)$1	220	114	139	21.2668
UUUACUACCUUAAGAAUACUAGUGA	chr1:180083332-180083561(+)$1	229	120	145	23.3116
UCAAGUUUAUUAUAUUUUUCUCUUG	chr6:36078495-36078714(+)$1	219	50	75	20.5626
AAAAAAAUCUCCAAAUACCUUUUUU	chr11:93545424-93545644(+)$1	220	140	165	21.9332
auugagauauaauuuacauacccau	chr20:1147837-1148062(+)$1	225	158	183	21.9410
GAUGAAAUAGAAGCAUUAAAUAUUU	chr12:46299127-46299353(+)$1	226	89	114	21.4162
UAGAAGCAAUCACUACCUUUCUCGU	chr10:73995241-73995464(+)$1	223	195	220	20.2531
AGCAUGCUAACUUUGUAUGUGUAUG	chr1:185089431-185089675(-)$1	244	3	28	23.7764
GAUGGGUACUUUAUCUACAUUAUCC	chr16:74657465-74657687(-)$1	222	64	89	21.7474
UCUUUGCUAAAAAAUUAAAUGACCU	chr2:171849168-171849388(-)$1	220	129	154	23.2265
UGCUACAUAGAAGGUUAGGUUGUAG	chr14:74667371-74667597(+)$1	226	43	68	23.6335
UGGCUAGUUUAAAUAUGUUUCUAAC	chr12:48438005-48438235(-)$1	230	9	34	24.0348
AUUUCUUAAUAAAUUCUUCCAAGAA	chr5:78980993-78981223(+)$1	230	112	137	22.2665
AUAUUUAUCCAUUUGUAAUUAAAUU	chr13:100638677-100638903(+)$1	226	132	157	23.2760
GCUUGUUCUAAAUAAUUUUUACAAG	chr5:130977670-130977900(-)$1	230	22	47	21.1470
GACUCUCACAACGCUCUUAGAGAAU	chr4:68483927-68484146(-)$1	219	120	145	22.7634
AUAUUCAAGCUACUUCUCCAUGUUU	chr12:22208331-22208546(+)$1	215	75	100	21.6922
UAUGAAUACUAAUACAUCACUUUUU	chr15:41601425-41601655(-)$1	230	96	121	22.5481
ccucggccucccaaagugcuggcau	chr14:74182950-74183172(-)$1	222	25	50	21.5615

#DB
((((((((............)))))	chr1:39304017-39304247(-)$1	1	72	97	21.7474
((((((..............)))))	chr20:43121044-43121266(+)$1	1	93	118	22.9531
((.(((((............)))))	chr2:11965846-11966092(+)$1	1	36	61	23.0689
(..((((............))))..	chr10:112772333-112772559(+)$1	1	57	82	22.7566
(((((((...........)))))))	chr6:45869372-45869602(-)$1	1	142	167	21.2671
(..(((((............)))))	chr3:44701742-44701954(+)$1	1	21	46	23.5195
.(.((((............)))).)	chr7:105732001-105732234(-)$1	1	153	178	23.1296
(((.((((...........)))).)	chr5:31400672-31400895(-)$1	1	91	116	21.9220
((((((((............)))))	chr2:46988710-46988938(+)$1	1	112	137	23.4955
(((((((...............)))	chr2:201354143-201354361(-)$1	1	86	111	19.1268
(.(((((.............)))))	chr10:115675163-115675390(+)$1	1	160	185	23.5674
(...((((...........))))..	chrX:70794442-70794665(+)$1	1	153	178	21.8198
(((((((................))	chr7:92166244-92166467(+)$1	1	32	57	22.4613
).(((((..............))))	chr22:37523408-37523635(-)$1	1	93	118	21.6617
..((((((............)))))	chr21:40565505-40565724(-)$1	1	75	100	22.0517
.((((................))))	chr2:64139651-64139872(-)$1	1	45	70	20.5626
((((((..............)))))	chr21:34932742-34932951(+)$1	1	148	173	23.0173
((..((((...........))))..	chr1:25688308-25688529(+)$1	1	132	157	21.8533
((((((((............)))))	chr12:113448526-113448745(+)$1	1	36	61	21.7474
.((.((((...........)))).)	chr22:32081187-32081417(-)$1	1	43	68	21.4401
((((((((............)))))	chr1:38268568-38268793(-)$1	1	83	108	23.3034
(((.(((((...........)))))	chr17:79857971-79858202(+)$1	1	104	129	21.6572
((...((.............)).))	chr5:134121169-134121389(+)$1	1	102	127	22.1576
(.((((................)))	chr16:87443667-87443897(-)$1	1	20	45	21.8364
).(((((..............))))	chr22:37523456-37523683(-)$1	1	141	166	21.6617
((((..(.............)..))	chr6:49460628-49460861(+)$1	1	72	97	22.7860
(((((.((...........)).)))	chr12:45823412-45823642(+)$1	1	57	82	21.3936
(((((((.............)))))	chr1:31404442-31404665(-)$1	1	191	216	23.7764
(((((.(.............).)))	chr2:169627225-169627455(+)$1	1	42	67	22.9655
(.(((((............))))).	chr6:45869866-45870096(-)$1	1	100	125	23.2363
((..(((............)))...	chr4:166000398-166000631(-)$1	1	19	44	23.0479
(((.(((.............))).)	chr7:32623798-32624028(+)$1	1	86	111	23.7303
(((.(((................))	chr5:157216323-157216542(-)$1	1	114	139	21.8988
(((((((.............)))))	chr6:57054648-57054864(-)$1	1	175	200	23.7764
..(((((...............)))	chr4:148556218-148556451(+)$1	1	94	119	19.0418
(((((((.............)))))	chr1:52882425-52882650(+)$1	1	25	50	23.7764
.((.((((............)))).	chr1:111490467-111490692(-)$1	1	49	74	22.7705
((((................)))).	chr16:22358147-22358373(-)$1	1	51	76	20.9946
.((((((............))))))	chr17:4585699-4585912(-)$1	1	126	151	20.8724
.((.(((((...........)))))	chr8:57875324-57875544(-)$1	1	114	139	21.2668
(((((((............))))))	chr1:180083332-180083561(+)$1	1	120	145	23.3116
.((((................))))	chr6:36078495-36078714(+)$1	1	50	75	20.5626
.((((((.............)))))	chr11:93545424-93545644(+)$1	1	140	165	21.9332
((((.(................).)	chr20:1147837-1148062(+)$1	1	158	183	21.9410
(((((((................))	chr12:46299127-46299353(+)$1	1	89	114	21.4162
..(((((................))	chr10:73995241-73995464(+)$1	1	195	220	20.2531
(((((((.............)))))	chr1:185089431-185089675(-)$1	1	3	28	23.7764
((((((((............)))))	chr16:74657465-74657687(-)$1	1	64	89	21.7474
(((..((.............).)..	chr2:171849168-171849388(-)$1	1	129	154	23.2265
(.(((((.............)))))	chr14:74667371-74667597(+)$1	1	43	68	23.6335
(((.(((.............))).)	chr12:48438005-48438235(-)$1	1	9	34	24.0348
(((((((.............)))))	chr5:78980993-78981223(+)$1	1	112	137	22.2665
(((((((............)))).)	chr13:100638677-100638903(+)$1	1	132	157	23.2760
((((((..............)))))	chr5:130977670-130977900(-)$1	1	22	47	21.1470
((.((((............)))).)	chr4:68483927-68484146(-)$1	1	120	145	22.7634
.((..((.............))..)	chr12:22208331-22208546(+)$1	1	75	100	21.6922
((.(((..............))).)	chr15:41601425-41601655(-)$1	1	96	121	22.5481
(((..(((............)))..	chr14:74182950-74183172(-)$1	1	25	50	21.5615

#PSSM
g : 0.17	d : 0.15	h : 0.13	e : 0.13	b : 0.05	! : 0.05	: : 0.05	[ : 0.03	i : 0.03	c : 0.03	# : 0.03	f : 0.03	= : 0.01	( : 0.01	" : 0.01	a : 0.01	
g : 0.17	d : 0.17	h : 0.12	b : 0.08	e : 0.08	! : 0.06	[ : 0.06	f : 0.06	: : 0.05	i : 0.03	a : 0.01	= : 0.01	" : 0.01	c : 0.01	
e : 0.18	g : 0.17	d : 0.13	h : 0.12	[ : 0.06	! : 0.06	f : 0.06	b : 0.06	i : 0.03	" : 0.03	= : 0.01	c : 0.01	
e : 0.18	d : 0.15	g : 0.13	[ : 0.13	h : 0.12	! : 0.08	f : 0.06	i : 0.03	" : 0.03	= : 0.01	c : 0.01	
e : 0.22	d : 0.20	g : 0.13	h : 0.10	c : 0.08	f : 0.06	! : 0.06	i : 0.03	= : 0.01	" : 0.01	y : 0.01	[ : 0.01	
e : 0.20	d : 0.17	g : 0.13	c : 0.10	h : 0.08	f : 0.06	y : 0.05	i : 0.03	b : 0.03	[ : 0.03	a : 0.03	= : 0.01	! : 0.01	
e : 0.20	d : 0.15	g : 0.12	h : 0.08	y : 0.08	c : 0.08	w : 0.06	f : 0.05	b : 0.05	a : 0.05	= : 0.01	i : 0.01	
v : 0.25	y : 0.15	u : 0.13	w : 0.10	e : 0.08	d : 0.08	h : 0.05	x : 0.03	t : 0.01	= : 0.01	f : 0.01	b : 0.01	c : 0.01	
u : 0.31	v : 0.25	y : 0.15	w : 0.10	t : 0.10	x : 0.03	e : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.13	w : 0.10	x : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.13	w : 0.10	x : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.13	w : 0.10	x : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.13	w : 0.10	x : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.13	w : 0.10	x : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.13	w : 0.10	x : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.13	w : 0.10	x : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.13	w : 0.10	x : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.13	w : 0.10	x : 0.03	
u : 0.31	v : 0.25	y : 0.15	t : 0.12	w : 0.10	x : 0.03	g : 0.01	
v : 0.25	u : 0.17	y : 0.15	d : 0.13	w : 0.10	g : 0.03	x : 0.03	t : 0.03	b : 0.01	e : 0.01	c : 0.01	f : 0.01	
d : 0.17	e : 0.13	y : 0.13	g : 0.12	c : 0.08	h : 0.06	f : 0.06	b : 0.05	a : 0.05	x : 0.03	w : 0.03	= : 0.01	i : 0.01	
d : 0.20	e : 0.17	g : 0.12	y : 0.10	c : 0.08	h : 0.06	f : 0.06	] : 0.05	x : 0.03	b : 0.03	= : 0.01	i : 0.01	2 : 0.01	
d : 0.22	e : 0.20	g : 0.12	h : 0.08	y : 0.06	f : 0.06	c : 0.06	i : 0.03	2 : 0.03	a : 0.03	= : 0.01	] : 0.01	4 : 0.01	
e : 0.24	] : 0.15	g : 0.13	h : 0.12	d : 0.08	f : 0.06	2 : 0.05	i : 0.03	4 : 0.03	= : 0.01	3 : 0.01	c : 0.01	5 : 0.01	
e : 0.24	g : 0.17	h : 0.12	d : 0.10	f : 0.08	2 : 0.03	i : 0.03	3 : 0.03	4 : 0.03	b : 0.03	] : 0.03	a : 0.01	= : 0.01	c : 0.01	5 : 0.01	

#score	1290.2130132852642
#seq	58
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_CDS_m2_run1.txt

#BEAR
fffffuuuuuuuuuuuufffff	chr11:18536257-18536487(-)$1	230	76	98	22.0580
[dddduuuuuuuuuuuudddd]	chr1:156756811-156757066(+)$1	255	91	113	22.5109
###bbuuuuuuuuuuuubb444	chr1:233802378-233802609(+)$1	231	4	26	21.8066
ggggguuuuuuuuuuuuggggg	chr3:127778849-127779080(+)$1	231	185	207	22.6996
d[cccvvvvvvvvvvvvvcccd	chr20:3128944-3129166(-)$1	222	128	150	22.4309
eeeeevvvvvvvvvvvvveeee	chrX:123197617-123197849(+)$1	232	149	171	22.9288
[ddddvvvvvvvvvvvvvdddd	chr16:2812452-2812692(+)$1	240	121	143	22.2001
ggggguuuuuuuuuuuuggggg	chr19:36128352-36128610(+)$1	258	113	135	22.6996
fffffvvvvvvvvvvvvvffff	chr17:58023929-58024167(+)$1	238	106	128	22.0032
gggggwwwwwwwwwwwwwwggg	chr10:12214676-12214929(-)$1	253	28	50	22.5229
c!!bbvvvvvvvvvvvvvbb22	chr5:130498181-130498467(-)$1	286	46	68	21.7684
cc[bbtttttttttttbbccc]	chr7:92163802-92164022(+)$1	220	71	93	20.4060
ggggguuuuuuuuuuuuggggg	chr12:124496759-124496989(+)$1	230	122	144	22.6996
[ddddxxxxxxxxxxxxxxxdd	chr8:37914640-37914883(+)$1	243	113	135	18.1248
ggggguuuuuuuuuuuuggggg	chr3:52722048-52722281(+)$1	233	85	107	22.6996
ggddddtttttttttttdddd:	chrX:71493679-71493913(-)$1	234	27	49	19.5031
eeeeeuuuuuuuuuuuueeeee	chr20:35384032-35384258(-)$1	226	182	204	23.0509
eeeeexxxxxxxxxxxxxxxee	chr16:69776370-69776598(-)$1	228	115	137	18.6919
gggggyyyyyyyyyyyyyyyyg	chr11:18636992-18637214(-)$1	222	173	195	21.1600
======ttttttttttt=====	chr17:16285792-16286046(+)$1	254	51	73	20.9092
bb[bbvvvvvvvvvvvvvbb]b	chr1:45213000-45213239(+)$1	239	203	225	21.1134
FFcccvvvvvvvvvvvvvcccB	chr1:20978854-20979112(-)$1	258	139	161	20.7186
fffffvvvvvvvvvvvvvffff	chr12:4771626-4771867(+)$1	241	46	68	22.0032
eeeeettttttttttteeeee]	chr1:156280639-156280895(-)$1	256	15	37	21.0093
[dddduuuuuuuuuuuudddd]	chrX:70518556-70518812(+)$1	256	105	127	22.5109
eeeeevvvvvvvvvvvvveeee	chr17:7411505-7411757(+)$1	252	226	248	22.9288
eeeeewwwwwwwwwwwwwweee	chr6:37349004-37349225(+)$1	221	175	197	22.7618
iiiiiitttttttttttiiiii	chr12:111158795-111159070(-)$1	275	53	75	20.4509
ceeeeettttttttttteeeee	chr17:40011104-40011327(-)$1	223	84	106	21.0601
eeeeevvvvvvvvvvvvveeee	chr1:204379861-204380137(-)$1	276	171	193	22.9288
hh[awwwwwwwwwwwwwwa]hh	chr7:5567543-5567776(-)$1	233	123	145	21.2811
c[cccuuuuuuuuuuuuccc22	chr17:76166823-76167086(+)$1	263	122	144	22.5763
eeeeewwwwwwwwwwwwwweee	chr19:40328286-40328580(-)$1	294	136	158	22.7618
fffffvvvvvvvvvvvvvffff	chr19:39123004-39123235(+)$1	231	41	63	22.0032
ddcccwwwwwwwwwwwwwwccc	chr16:53476513-53476741(+)$1	228	194	216	22.1529
fffffftttttttttttfffff	chr17:78113718-78113951(-)$1	233	183	205	20.0662
$dddduuuuuuuuuuuudddd2	chr15:89169775-89170103(+)$1	328	192	214	21.9014
eeeeevvvvvvvvvvvvveeee	chr3:127775459-127775725(+)$1	266	176	198	22.9288
"""bbvvvvvvvvvvvvvbb22	chr10:70098270-70098500(+)$1	230	83	105	21.5078
ee[bbuuuuuuuuuuuubbeee	chr17:6917576-6917858(+)$1	282	150	172	22.6118
c[cccuuuuuuuuuuuuccc]c	chr1:156564923-156565149(-)$1	226	30	52	22.8223
fffffwwwwwwwwwwwwwwfff	chr12:98927488-98927759(+)$1	271	138	160	21.9272
cc[bbyyyyyyyyyyyyyyyyb	chr1:161721375-161721628(+)$1	253	103	125	20.4407
fffffuuuuuuuuuuuufffff	chr16:72829845-72830072(-)$1	227	131	153	22.0580
hhhhhuuuuuuuuuuuuhhhhh	chr9:35664651-35664887(-)$1	236	45	67	20.6690
ddddyyyyyyyyyyyyyyyydd	chr5:125939594-125939861(+)$1	267	199	221	20.5598
=====uuuuuuuuuuuu=====	chr12:120899759-120899994(-)$1	235	88	110	22.9571
iiiiixxxxxxxxxxxxxxxii	chr5:138643831-138644093(+)$1	262	164	186	18.4828
eeeeexxxxxxxxxxxxxxxee	chr2:27604464-27604698(-)$1	234	3	25	18.6919
eeeeewwwwwwwwwwwwwweee	chr12:42858154-42858387(-)$1	233	81	103	22.7618
eeeeeuuuuuuuuuuuueeeee	chr1:3547520-3547767(-)$1	247	24	46	23.0509
[dddduuuuuuuuuuuudddd2	chr4:56283162-56283389(+)$1	227	56	78	22.3052
eeeeexxxxxxxxxxxxxxxee	chr5:72865250-72865519(+)$1	269	209	231	18.6919
ddddddtttttttttttdddd]	chr13:41515363-41515602(-)$1	239	95	117	20.2871
d!!bbtttttttttttbb]ddd	chr1:43826345-43826570(+)$1	225	4	26	19.9350
eeeeeyyyyyyyyyyyyyyyye	chr1:145439969-145440210(+)$1	241	15	37	21.2540
[cccyyyyyyyyyyyyyyyycc	chr16:19548690-19548925(+)$1	235	79	101	20.9985
[bbbbwwwwwwwwwwwwwwbb]	chr1:150202843-150203108(-)$1	265	162	184	21.2134
!!cccwwwwwwwwwwwwwwccc	chr4:57796596-57796849(+)$1	253	76	98	22.4602

#otherMatches

#Seq PSSM
UGAAGUUUCUAUUUCUUUUUCA	chr11:18536257-18536487(-)$1	230	76	98	22.0580
CGACUACAGCUACAAUCAGUUU	chr1:156756811-156757066(+)$1	255	91	113	22.5109
UCUGCAUCAUCUACUCCGUCAU	chr1:233802378-233802609(+)$1	231	4	26	21.8066
GCCUGCUAAUCACCAUUCAGGU	chr3:127778849-127779080(+)$1	231	185	207	22.6996
GUGUAUGAGACCAAGUGUUGCC	chr20:3128944-3129166(-)$1	222	128	150	22.4309
GCAUGUUCUAAAACUUACCAUG	chrX:123197617-123197849(+)$1	232	149	171	22.9288
GCUCCAGAACACCAGCCAGGAG	chr16:2812452-2812692(+)$1	240	121	143	22.2001
CCAGGCACCCGCUCCCACCUGG	chr19:36128352-36128610(+)$1	258	113	135	22.6996
AGUGGGGAAGCAUCGGCACCAC	chr17:58023929-58024167(+)$1	238	106	128	22.0032
GGGACUGACGCAUCUGACUGUC	chr10:12214676-12214929(-)$1	253	28	50	22.5229
CCUACCAAUAUACUAAAAGUUU	chr5:130498181-130498467(-)$1	286	46	68	21.7684
UUAUGUUAUUUCUCCUCAAAAU	chr7:92163802-92164022(+)$1	220	71	93	20.4060
GUGGUAAGGAUUUUAGCACUAC	chr12:124496759-124496989(+)$1	230	122	144	22.6996
AGCCCAGAAGAUAAGCGGGCGG	chr8:37914640-37914883(+)$1	243	113	135	18.1248
CUUUGCAAAACUGAGAACAAAG	chr3:52722048-52722281(+)$1	233	85	107	22.6996
CUGUAUAGGGUUAAAAAGUACA	chrX:71493679-71493913(-)$1	234	27	49	19.5031
GCUCAUGUUUAUUUAGUUGAGU	chr20:35384032-35384258(-)$1	226	182	204	23.0509
GGGGGCAAAUACGCCAUCAACC	chr16:69776370-69776598(-)$1	228	115	137	18.6919
UGCUGAGAAGAAAUCAAGACCC	chr11:18636992-18637214(-)$1	222	173	195	21.1600
UUUCUGACUACAACAUCCAGAA	chr17:16285792-16286046(+)$1	254	51	73	20.9092
UUUGCUUAUUGACUCUUUGCUG	chr1:45213000-45213239(+)$1	239	203	225	21.1134
UCGGCCUACCCCUACUACGCCA	chr1:20978854-20979112(-)$1	258	139	161	20.7186
AACAGGUUUGUUUGGUUAUUGU	chr12:4771626-4771867(+)$1	241	46	68	22.0032
CCUUGACAGAAAAAUCCAAGGC	chr1:156280639-156280895(-)$1	256	15	37	21.0093
GAUUGGUAAUAAAACUGCAGUG	chrX:70518556-70518812(+)$1	256	105	127	22.5109
AAGACUCCUUCGCUUACUGUCU	chr17:7411505-7411757(+)$1	252	226	248	22.9288
CCAAACUUCAACAAAUAUUUUU	chr6:37349004-37349225(+)$1	221	175	197	22.7618
UUGGGGUUGAGUAUAUUUCCUA	chr12:111158795-111159070(-)$1	275	53	75	20.4509
CAGGUUGUCCCAGAUGAAACCU	chr17:40011104-40011327(-)$1	223	84	106	21.0601
UCCCGUCUGUACUCUAACCGGG	chr1:204379861-204380137(-)$1	276	171	193	22.9288
CAGCACAAUGAAGAUCAAGGUG	chr7:5567543-5567776(-)$1	233	123	145	21.2811
AAUGCCCACGAGUCUAAGCAGA	chr17:76166823-76167086(+)$1	263	122	144	22.5763
GGCCGUGACCUCAUUAACUUGG	chr19:40328286-40328580(-)$1	294	136	158	22.7618
UGUGAACAUCAAUUCCCAUCAC	chr19:39123004-39123235(+)$1	231	41	63	22.0032
UCAGGACAUCUUUAAAUACCCU	chr16:53476513-53476741(+)$1	228	194	216	22.1529
UAUUUGUAAGAAGUGCUUAAAU	chr17:78113718-78113951(-)$1	233	183	205	20.0662
GGCCCAGAAAGAGGUAAGGGCA	chr15:89169775-89170103(+)$1	328	192	214	21.9014
UUGGUGACACCCCAAAAGACCG	chr3:127775459-127775725(+)$1	266	176	198	22.9288
AGACCAAUAGGAGGAAGAGGGG	chr10:70098270-70098500(+)$1	230	83	105	21.5078
GACUGAAUCCCUUCUCCCAUCU	chr17:6917576-6917858(+)$1	282	150	172	22.6118
CAGCCGAAGAAAGAAGAGGCAG	chr1:156564923-156565149(-)$1	226	30	52	22.8223
UAUCAGUUCCAAAAGUAGAUGA	chr12:98927488-98927759(+)$1	271	138	160	21.9272
UGUGGCCAUAAUAACUGCUUUU	chr1:161721375-161721628(+)$1	253	103	125	20.4407
CCUCCUAUCACCAGCCUGGAGG	chr16:72829845-72830072(-)$1	227	131	153	22.0580
UUUGGGGAUCCUGAAAGCCAAG	chr9:35664651-35664887(-)$1	236	45	67	20.6690
GACCAGAAAUGAACUAUAAAGG	chr5:125939594-125939861(+)$1	267	199	221	20.5598
GUCUCGGUCUGGGUCAAGGGGC	chr12:120899759-120899994(-)$1	235	88	110	22.9571
UUGCCAGUUCAUUCUAAUAAGG	chr5:138643831-138644093(+)$1	262	164	186	18.4828
AGCUACCCCCAUCCCUUUCUUA	chr2:27604464-27604698(-)$1	234	3	25	18.6919
UCAUGAUGAAACACAGUGGUAU	chr12:42858154-42858387(-)$1	233	81	103	22.7618
GCCCAUCCCCCAGAAUCUGGGC	chr1:3547520-3547767(-)$1	247	24	46	23.0509
UACUGUUGUAUUUUUUCCAGUU	chr4:56283162-56283389(+)$1	227	56	78	22.3052
UGGAUGUGCUAGCAAACUUAAU	chr5:72865250-72865519(+)$1	269	209	231	18.6919
GGUACUAUUACCAAAGGGGUAU	chr13:41515363-41515602(-)$1	239	95	117	20.2871
CUUGCUUGCAUUUGGUGCUGCC	chr1:43826345-43826570(+)$1	225	4	26	19.9350
UUGGGCAUUAGAUUGAAGCAUC	chr1:145439969-145440210(+)$1	241	15	37	21.2540
UGGUUUGCAAAAAGAAAACUGC	chr16:19548690-19548925(+)$1	235	79	101	20.9985
GUGGAAACAAAAUAAAAGAUCU	chr1:150202843-150203108(-)$1	265	162	184	21.2134
AAUCCAAAAAUAAUAGUCAGGA	chr4:57796596-57796849(+)$1	253	76	98	22.4602

#DB
(((((............)))))	chr11:18536257-18536487(-)$1	1	76	98	22.0580
.((((............)))).	chr1:156756811-156757066(+)$1	1	91	113	22.5109
...((............))...	chr1:233802378-233802609(+)$1	1	4	26	21.8066
(((((............)))))	chr3:127778849-127779080(+)$1	1	185	207	22.6996
(.(((.............))))	chr20:3128944-3129166(-)$1	1	128	150	22.4309
(((((.............))))	chrX:123197617-123197849(+)$1	1	149	171	22.9288
.((((.............))))	chr16:2812452-2812692(+)$1	1	121	143	22.2001
(((((............)))))	chr19:36128352-36128610(+)$1	1	113	135	22.6996
(((((.............))))	chr17:58023929-58024167(+)$1	1	106	128	22.0032
(((((..............)))	chr10:12214676-12214929(-)$1	1	28	50	22.5229
(..((.............))..	chr5:130498181-130498467(-)$1	1	46	68	21.7684
((.((...........))))).	chr7:92163802-92164022(+)$1	1	71	93	20.4060
(((((............)))))	chr12:124496759-124496989(+)$1	1	122	144	22.6996
.((((...............))	chr8:37914640-37914883(+)$1	1	113	135	18.1248
(((((............)))))	chr3:52722048-52722281(+)$1	1	85	107	22.6996
))((((...........)))).	chrX:71493679-71493913(-)$1	1	27	49	19.5031
(((((............)))))	chr20:35384032-35384258(-)$1	1	182	204	23.0509
(((((...............))	chr16:69776370-69776598(-)$1	1	115	137	18.6919
(((((................)	chr11:18636992-18637214(-)$1	1	173	195	21.1600
((((((...........)))))	chr17:16285792-16286046(+)$1	1	51	73	20.9092
((.((.............)).)	chr1:45213000-45213239(+)$1	1	203	225	21.1134
(((((.............)))(	chr1:20978854-20979112(-)$1	1	139	161	20.7186
(((((.............))))	chr12:4771626-4771867(+)$1	1	46	68	22.0032
(((((...........))))).	chr1:156280639-156280895(-)$1	1	15	37	21.0093
.((((............)))).	chrX:70518556-70518812(+)$1	1	105	127	22.5109
(((((.............))))	chr17:7411505-7411757(+)$1	1	226	248	22.9288
(((((..............)))	chr6:37349004-37349225(+)$1	1	175	197	22.7618
((((((...........)))))	chr12:111158795-111159070(-)$1	1	53	75	20.4509
)(((((...........)))))	chr17:40011104-40011327(-)$1	1	84	106	21.0601
(((((.............))))	chr1:204379861-204380137(-)$1	1	171	193	22.9288
((.(..............).))	chr7:5567543-5567776(-)$1	1	123	145	21.2811
(.(((............)))..	chr17:76166823-76167086(+)$1	1	122	144	22.5763
(((((..............)))	chr19:40328286-40328580(-)$1	1	136	158	22.7618
(((((.............))))	chr19:39123004-39123235(+)$1	1	41	63	22.0032
))(((..............)))	chr16:53476513-53476741(+)$1	1	194	216	22.1529
((((((...........)))))	chr17:78113718-78113951(-)$1	1	183	205	20.0662
.((((............)))).	chr15:89169775-89170103(+)$1	1	192	214	21.9014
(((((.............))))	chr3:127775459-127775725(+)$1	1	176	198	22.9288
...((.............))..	chr10:70098270-70098500(+)$1	1	83	105	21.5078
((.((............)))))	chr17:6917576-6917858(+)$1	1	150	172	22.6118
(.(((............))).)	chr1:156564923-156565149(-)$1	1	30	52	22.8223
(((((..............)))	chr12:98927488-98927759(+)$1	1	138	160	21.9272
((.((................)	chr1:161721375-161721628(+)$1	1	103	125	20.4407
(((((............)))))	chr16:72829845-72830072(-)$1	1	131	153	22.0580
(((((............)))))	chr9:35664651-35664887(-)$1	1	45	67	20.6690
((((................))	chr5:125939594-125939861(+)$1	1	199	221	20.5598
(((((............)))))	chr12:120899759-120899994(-)$1	1	88	110	22.9571
(((((...............))	chr5:138643831-138644093(+)$1	1	164	186	18.4828
(((((...............))	chr2:27604464-27604698(-)$1	1	3	25	18.6919
(((((..............)))	chr12:42858154-42858387(-)$1	1	81	103	22.7618
(((((............)))))	chr1:3547520-3547767(-)$1	1	24	46	23.0509
.((((............)))).	chr4:56283162-56283389(+)$1	1	56	78	22.3052
(((((...............))	chr5:72865250-72865519(+)$1	1	209	231	18.6919
((((((...........)))).	chr13:41515363-41515602(-)$1	1	95	117	20.2871
(..((...........)).)))	chr1:43826345-43826570(+)$1	1	4	26	19.9350
(((((................)	chr1:145439969-145440210(+)$1	1	15	37	21.2540
.(((................))	chr16:19548690-19548925(+)$1	1	79	101	20.9985
.((((..............)).	chr1:150202843-150203108(-)$1	1	162	184	21.2134
..(((..............)))	chr4:57796596-57796849(+)$1	1	76	98	22.4602

#PSSM
e : 0.25	f : 0.11	[ : 0.11	g : 0.11	c : 0.10	d : 0.08	= : 0.03	i : 0.03	h : 0.03	# : 0.01	b : 0.01	F : 0.01	$ : 0.01	" : 0.01	! : 0.01	
e : 0.27	d : 0.15	f : 0.11	g : 0.11	[ : 0.05	! : 0.05	c : 0.05	= : 0.03	b : 0.03	i : 0.03	h : 0.03	# : 0.01	F : 0.01	" : 0.01	
e : 0.25	d : 0.15	f : 0.11	c : 0.11	g : 0.10	[ : 0.08	! : 0.03	= : 0.03	i : 0.03	# : 0.01	" : 0.01	h : 0.01	b : 0.01	
e : 0.25	d : 0.15	b : 0.15	f : 0.11	c : 0.11	g : 0.10	= : 0.03	i : 0.03	a : 0.01	h : 0.01	
e : 0.25	b : 0.15	d : 0.13	f : 0.11	g : 0.10	c : 0.10	= : 0.03	i : 0.03	y : 0.03	w : 0.01	h : 0.01	
u : 0.30	v : 0.22	w : 0.15	x : 0.08	y : 0.08	t : 0.05	d : 0.03	= : 0.01	i : 0.01	e : 0.01	f : 0.01	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.15	x : 0.08	y : 0.08	
u : 0.30	v : 0.22	w : 0.15	t : 0.10	x : 0.08	y : 0.08	b : 0.03	e : 0.01	
v : 0.22	w : 0.15	d : 0.10	x : 0.08	y : 0.08	b : 0.06	g : 0.06	e : 0.06	f : 0.05	= : 0.03	c : 0.03	i : 0.01	h : 0.01	
e : 0.13	w : 0.13	d : 0.11	f : 0.10	b : 0.08	c : 0.08	x : 0.08	y : 0.08	g : 0.06	= : 0.03	i : 0.01	a : 0.01	h : 0.01	] : 0.01	
e : 0.20	d : 0.13	f : 0.11	c : 0.11	g : 0.08	x : 0.08	y : 0.08	b : 0.06	= : 0.03	4 : 0.01	i : 0.01	] : 0.01	h : 0.01	
e : 0.25	d : 0.16	f : 0.11	c : 0.10	g : 0.08	2 : 0.05	y : 0.05	= : 0.03	] : 0.03	i : 0.03	h : 0.03	4 : 0.01	b : 0.01	
e : 0.25	f : 0.11	] : 0.10	g : 0.10	d : 0.08	2 : 0.08	c : 0.06	= : 0.03	b : 0.03	i : 0.03	h : 0.03	4 : 0.01	: : 0.01	B : 0.01	

#score	1271.7210891401135
#seq	59
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_UTR_m2_run1.txt

#BEAR
$$eeeee[eeeeeooooooeeeee]eeeee555	chr12:75891172-75891393(-)$1	221	73	106	11.9225
ggggggg"""cccooooooccc333ggggggg:	chr8:87572453-87572670(+)$1	217	48	81	15.1787
ccc[ccc[eeeeeooooooeeeee22ccc]ccc	chr12:22837357-22837574(+)$1	217	77	110	14.0488
=========[bbnnnnnbb==========333d	chr2:87001821-87002042(+)$1	221	109	142	12.3956
=========[bb[ccclllccc]bb]=======	chr16:11966295-11966526(-)$1	231	161	194	11.8680
gggga[eeeee[aooooooa]eeeee]a66666	chr8:141541754-141541973(-)$1	219	16	49	12.4027
eeee"""ffffffooooooffffffeeeeeddd	chr16:71681900-71682118(-)$1	218	54	87	11.2065
b[eeeee!!ddddoooooodddd]eeeee22bb	chr22:45582923-45583142(+)$1	219	40	73	13.6845
dddd"""ccceeeeellleeeee333ccc333d	chr8:64100001-64100219(+)$1	218	74	107	11.3238
ff[==========mmmm==========]fffff	chr12:53805304-53805526(+)$1	222	130	163	11.6691
dddddddd[ddddoooooodddd]dddd]dddd	chrX:24231244-24231467(+)$1	223	113	146	11.8400
iiiiiiii[ddddoooooodddd]iiiiiiiii	chr6:139499977-139500204(+)$1	227	57	90	15.9378
ee!!ccc[eeeeeooooooeeeee]ccc22eee	chr3:5222172-5222391(+)$1	219	166	199	13.5354
a[===========oooooo===========]a2	chrX:24230551-24230774(+)$1	223	28	61	17.6021
[ccc[cccccccccooooooccc22ccc22ccc	chr6:56380206-56380427(-)$1	221	26	59	13.5518
ggggg!!bb[cccooooooccc333bb22gggg	chr6:11136518-11136740(+)$1	222	122	155	14.2697
:::==========oooooo==========iiii	chr1:101445923-101446145(+)$1	222	113	146	14.3231
ccc[iiiiiiiiiooooooiiiiiiiii]cccf	chr7:5108720-5108946(+)$1	226	17	50	15.6584
!!ccc[eeeeerrrrrrrrreeeee]ccc333g	chr6:75965706-75965931(-)$1	225	82	115	11.7236
:ffffffccccccooooooccc4444ccc333f	chr17:33678680-33678901(-)$1	221	121	154	14.8429
=============oooooo==============	chr13:53049771-53049989(+)$1	218	84	117	17.7645
!!eeeee!!ddddoooooodddd333eeeee22	chr15:93569100-93569320(+)$1	220	68	101	14.7883
b$$$$$ccc[cccooooooccc]cccbb]eeee	chr3:143708723-143708940(+)$1	217	72	105	12.7283
eeeee!!bb[cccooooooccc]bb22eeeee4	chr5:31535881-31536099(+)$1	218	107	140	12.6969
+++dddd!!ddddoooooodddd22dddd4444	chr1:70727834-70728054(-)$1	220	25	58	12.9321
bb[gggggggcccooooooccc]ggggggg22b	chr5:114950219-114950442(-)$1	223	83	116	15.4500
ccgggggggddddmmmmdddd]ggggggg333c	chrX:16860559-16860781(+)$1	222	6	39	11.3379
!==========qqqqqqqq==========333b	chr5:112176713-112176932(+)$1	219	74	107	12.7550
$$$ggggggg[ccclllccc]ggggggg4444b	chr2:180809744-180809969(-)$1	225	128	161	11.8455
c!!dddd"""cccooooooccc]dddd]cccgg	chr1:211745749-211745966(-)$1	217	22	55	14.1240
ffffff####cccooooooccc22ffffff22h	chr5:55247196-55247418(-)$1	222	129	162	13.4413
gggggggccc[ddddoooooodddd]ccc333g	chr11:10825617-10825839(-)$1	222	15	48	13.4896
"""bb[gggggggooooooggggggg]bb4444	chr6:75964717-75964934(-)$1	217	48	81	15.2452
"ffffff[ccc!!cccooooooccc]ccc333f	chr3:107524232-107524449(+)$1	217	174	207	11.7260
a!!ccc"""ddddoooooodddd333ccc5555	chr10:22617508-22617727(+)$1	219	41	74	14.1846
==============lll==============::	chr1:87573284-87573506(+)$1	222	15	48	12.7004
b!!cccgggggggooooooggggggg]ccc22b	chr7:38269751-38269974(+)$1	223	118	151	15.1304
##ggggggg[cccooooooccc22ggggggg44	chr12:57450117-57450338(-)$1	221	54	87	16.0873
==========[ddddmmmmdddd]=========	chr8:81436061-81436282(+)$1	221	47	80	12.3574
"""==========oooooo==========333d	chr6:11136288-11136514(+)$1	226	88	121	18.9055
iiiiiii[ccc!!cccnnnnnccc22ccc333i	chr2:46809601-46809825(+)$1	224	135	168	10.7441
=============oooooo==============	chr13:53049690-53049908(+)$1	218	165	198	17.7645
gggg[ccc[ddddrrrrrrrrrddddccc333g	chr6:136580745-136580965(-)$1	220	55	88	11.6675
cc[dddd[bb[bboooooobbbb]dddd]ccc]	chr13:30778911-30779130(-)$1	219	58	91	11.4644
!ccc!!bb[ddddoooooodddd]bb22ccc22	chr18:67995557-67995775(+)$1	218	165	198	13.4370
dddeeeeeeeeeeooooooeeeee4444eeeee	chr1:47184081-47184301(-)$1	220	7	40	12.1568

#otherMatches

#Seq PSSM
ACUUUCAAGUAAGCCUAAACUUACAUGAAAACA	chr12:75891172-75891393(-)$1	221	73	106	11.9225
Ugugguuuucagaauuuucucuuuuaaucacaa	chr8:87572453-87572670(+)$1	217	48	81	15.1787
GGAUUGUGGGCUUUGAUUCAAGCCAAAUACUCC	chr12:22837357-22837574(+)$1	217	77	110	14.0488
UUUAAACUACAGAUGGACUUGGUUUGAGGGAGG	chr2:87001821-87002042(+)$1	221	109	142	12.3956
UUAAAGGAAAGGAUUAGUUUGACCCCUUCUUUU	chr16:11966295-11966526(-)$1	231	161	194	11.8680
GACCUGUAUGAGAACCCAAUGUCAUAGGAAAUA	chr8:141541754-141541973(-)$1	219	16	49	12.4027
UCACCUUAUCUCAGACUAAUGGGGUGUGAUGUG	chr16:71681900-71682118(-)$1	218	54	87	11.2065
AUAUACGUGGCCUAAAGCAAGGUGUGUAUUUUG	chr22:45582923-45583142(+)$1	219	40	73	13.6845
GUUAAAUGGAUCUUUGUCAAAGAUGUUCCCAAU	chr8:64100001-64100219(+)$1	218	74	107	11.3238
UUAUuauauauauauauauauauauaaagauau	chr12:53805304-53805526(+)$1	222	130	163	11.6691
AACAAACUCGGUUAAUUAGAACUUGGUUAUGUU	chrX:24231244-24231467(+)$1	223	113	146	11.8400
UUGAUGUUUUGUUUGAAACAAUACAGCAUUAAA	chr6:139499977-139500204(+)$1	227	57	90	15.9378
UAAAUAUGUGAAUUUUUUUAUUUAGGUGGAUGC	chr3:5222172-5222391(+)$1	219	166	199	13.5354
AGUAAAGAUAUUUUCUUUUAAAUAUCUUUGGUA	chrX:24230551-24230774(+)$1	223	28	61	17.6021
GCAGCUGGAACGGGCACAGUCCCUGGUUAACCA	chr6:56380206-56380427(-)$1	221	26	59	13.5518
UUCUUUUUAUGUUUUUCUUAACCUUUAUUAAGG	chr6:11136518-11136740(+)$1	222	122	155	14.2697
caaacuuagcauggauucacaugcugaguaaau	chr1:101445923-101446145(+)$1	222	113	146	14.3231
uaagauauguguauuuuucugcauguguguuaa	chr7:5108720-5108946(+)$1	226	17	50	15.6584
ACAGUAGUAAUACAGCUGACAUUACCAUUUAAU	chr6:75965706-75965931(-)$1	225	82	115	11.7236
GUGGUCUCCAGAGCUUGUUCUCAGAAUGGCCCA	chr17:33678680-33678901(-)$1	221	121	154	14.8429
GAUGGAAAGUGUCUGCACUGACACUUUUCGUCA	chr13:53049771-53049989(+)$1	218	84	117	17.7645
CUCUUAGAAUAUAAUCAGGUAUAAACCUAAGUU	chr15:93569100-93569320(+)$1	220	68	101	14.7883
AAACUUGCACUGAUAGAUCUUAAUGUUAACAUC	chr3:143708723-143708940(+)$1	217	72	105	12.7283
CACAACAAUCAGGUAAUUUCCUCAUAUUUGUGA	chr5:31535881-31536099(+)$1	218	107	140	12.6969
CCUGGACCAUUAACGUAAAUUAAAUGUCUUAAG	chr1:70727834-70728054(-)$1	220	25	58	12.9321
AGCAAAGGGUGAACAUGUUUUCAACCCUUUAAC	chr5:114950219-114950442(-)$1	223	83	116	15.4500
UCAUCCUGCUUUGGUUUCAGGUGUGGGAUUUGG	chrX:16860559-16860781(+)$1	222	6	39	11.3379
AGAGUCAGAGGAAGUUUUGCUUUUGAUUCACCU	chr5:112176713-112176932(+)$1	219	74	107	12.7550
AUAAACUGGACAUGCCUUAUAUUCAGUUGAAAC	chr2:180809744-180809969(-)$1	225	128	161	11.8455
AACUUGAAUAGGAAAAAUGUCCAUCAAAUGCAC	chr1:211745749-211745966(-)$1	217	22	55	14.1240
AAGAAAUAAUGAAGUUUGGUUUUUUUUCUUUCU	chr5:55247196-55247418(-)$1	222	129	162	13.4413
AGUUUUUGUUUGCUUGUUUUAAAGUUGACUUGA	chr11:10825617-10825839(-)$1	222	15	48	13.4896
CAGGUAAGUGUUUUGACUUAAGUACUAAUAUUC	chr6:75964717-75964934(-)$1	217	48	81	15.2452
ACAAGUGCUUGUUGCCCCACACGGCCCAGAUUC	chr3:107524232-107524449(+)$1	217	174	207	11.7260
CGAUGCCCAGCAGCAAUGACUGUGAUGCACUUA	chr10:22617508-22617727(+)$1	219	41	74	14.1846
UAUGUGUGUAUGUGAAauauauauacauauaua	chr1:87573284-87573506(+)$1	222	15	48	12.7004
CACAGAAUGGAAUUUUUUUGUUUCAUGUCUCAG	chr7:38269751-38269974(+)$1	223	118	151	15.1304
AAGAAUUGUAUCUGAAACAAGAGAACAGUUUGA	chr12:57450117-57450338(-)$1	221	54	87	16.0873
UUUGUAAAAGCUCUUUGGGAAGAUCUUUUACGA	chr8:81436061-81436282(+)$1	221	47	80	12.3574
GUGUUGUGGAGAAAAACACUUCUUCACAAACAA	chr6:11136288-11136514(+)$1	226	88	121	18.9055
AUUUAAACUUGCUGUUGCCCAAAUUAUAAUUUU	chr2:46809601-46809825(+)$1	224	135	168	10.7441
GAUGGAAAGUGUCUGCACUGACACUUUUCGUCA	chr13:53049690-53049908(+)$1	218	165	198	17.7645
CUUAUUCUGUUAAUGUAAACUUUUGAAGAUCUU	chr6:136580745-136580965(-)$1	220	55	88	11.6675
CCUUCUAGUGAUCCAAGUAGACAAUAGAUGGUG	chr13:30778911-30779130(-)$1	219	58	91	11.4644
AUUAUUGAGAUUUUCAUCUAAAUGUUUUUAAAA	chr18:67995557-67995775(+)$1	218	165	198	13.4370
GCAAGGAAGGGACUGACGCGUUCCCACUUUCUU	chr1:47184081-47184301(-)$1	220	7	40	12.1568

#DB
..(((((.(((((......))))).)))))...	chr12:75891172-75891393(-)$1	1	73	106	11.9225
(((((((...(((......)))...))))))).	chr8:87572453-87572670(+)$1	1	48	81	15.1787
(((.(((.(((((......)))))..))).)))	chr12:22837357-22837574(+)$1	1	77	110	14.0488
(((((((((.((.....))))))))))))...)	chr2:87001821-87002042(+)$1	1	109	142	12.3956
(((((((((.((.(((...))).)).)))))))	chr16:11966295-11966526(-)$1	1	161	194	11.8680
(((((.(((((.(......).))))).).....	chr8:141541754-141541973(-)$1	1	16	49	12.4027
((((...((((((......)))))))))))(((	chr16:71681900-71682118(-)$1	1	54	87	11.2065
(.(((((..((((......)))).)))))..))	chr22:45582923-45583142(+)$1	1	40	73	13.6845
((((...((((((((...)))))...)))...)	chr8:64100001-64100219(+)$1	1	74	107	11.3238
((.((((((((((....)))))))))).)))))	chr12:53805304-53805526(+)$1	1	130	163	11.6691
((((((((.((((......)))).)))).))))	chrX:24231244-24231467(+)$1	1	113	146	11.8400
((((((((.((((......)))).)))))))))	chr6:139499977-139500204(+)$1	1	57	90	15.9378
((..(((.(((((......))))).)))..)))	chr3:5222172-5222391(+)$1	1	166	199	13.5354
(.(((((((((((......))))))))))).).	chrX:24230551-24230774(+)$1	1	28	61	17.6021
.(((.(((((((((......)))..)))..)))	chr6:56380206-56380427(-)$1	1	26	59	13.5518
(((((..((.(((......)))...))..))))	chr6:11136518-11136740(+)$1	1	122	155	14.2697
...((((((((((......))))))))))((((	chr1:101445923-101446145(+)$1	1	113	146	14.3231
(((.(((((((((......))))))))).)))(	chr7:5108720-5108946(+)$1	1	17	50	15.6584
..(((.(((((.........))))).)))...)	chr6:75965706-75965931(-)$1	1	82	115	11.7236
.((((((((((((......)))....)))...)	chr17:33678680-33678901(-)$1	1	121	154	14.8429
(((((((((((((......))))))))))))))	chr13:53049771-53049989(+)$1	1	84	117	17.7645
..(((((..((((......))))...)))))..	chr15:93569100-93569320(+)$1	1	68	101	14.7883
(.....(((.(((......))).))))).))))	chr3:143708723-143708940(+)$1	1	72	105	12.7283
(((((..((.(((......))).))..))))).	chr5:31535881-31536099(+)$1	1	107	140	12.6969
...((((..((((......))))..))))....	chr1:70727834-70728054(-)$1	1	25	58	12.9321
((.((((((((((......))).)))))))..)	chr5:114950219-114950442(-)$1	1	83	116	15.4500
(((((((((((((....)))).)))))))...)	chrX:16860559-16860781(+)$1	1	6	39	11.3379
.((((((((((........))))))))))...)	chr5:112176713-112176932(+)$1	1	74	107	12.7550
...(((((((.(((...))).)))))))....)	chr2:180809744-180809969(-)$1	1	128	161	11.8455
(..((((...(((......))).)))).)))))	chr1:211745749-211745966(-)$1	1	22	55	14.1240
((((((....(((......)))..))))))..)	chr5:55247196-55247418(-)$1	1	129	162	13.4413
((((((((((.((((......)))).)))...)	chr11:10825617-10825839(-)$1	1	15	48	13.4896
...((.(((((((......))))))).))....	chr6:75964717-75964934(-)$1	1	48	81	15.2452
.((((((.(((..(((......))).)))...)	chr3:107524232-107524449(+)$1	1	174	207	11.7260
(..(((...((((......))))...)))....	chr10:22617508-22617727(+)$1	1	41	74	14.1846
((((((((((((((...))))))))))))))..	chr1:87573284-87573506(+)$1	1	15	48	12.7004
(..((((((((((......))))))).)))..)	chr7:38269751-38269974(+)$1	1	118	151	15.1304
..(((((((.(((......)))..)))))))..	chr12:57450117-57450338(-)$1	1	54	87	16.0873
((((((((((.((((....)))).)))))))))	chr8:81436061-81436282(+)$1	1	47	80	12.3574
...((((((((((......))))))))))...)	chr6:11136288-11136514(+)$1	1	88	121	18.9055
(((((((.(((..(((.....)))..)))...)	chr2:46809601-46809825(+)$1	1	135	168	10.7441
(((((((((((((......))))))))))))))	chr13:53049690-53049908(+)$1	1	165	198	17.7645
((((.(((.((((.........)))))))...)	chr6:136580745-136580965(-)$1	1	55	88	11.6675
((.((((.((.((......)))).)))).))).	chr13:30778911-30779130(-)$1	1	58	91	11.4644
.(((..((.((((......)))).))..)))..	chr18:67995557-67995775(+)$1	1	165	198	13.4370
(((((((((((((......)))))....)))))	chr1:47184081-47184301(-)$1	1	7	40	12.1568

#PSSM
= : 0.13	g : 0.10	c : 0.10	b : 0.08	! : 0.08	e : 0.06	d : 0.06	" : 0.06	$ : 0.04	f : 0.04	i : 0.04	a : 0.04	: : 0.04	[ : 0.02	+ : 0.02	# : 0.02	
= : 0.15	c : 0.13	g : 0.10	! : 0.10	f : 0.08	$ : 0.06	e : 0.06	d : 0.06	[ : 0.04	i : 0.04	" : 0.04	: : 0.02	+ : 0.02	b : 0.02	# : 0.02	
= : 0.17	g : 0.15	e : 0.10	c : 0.10	! : 0.08	d : 0.06	[ : 0.06	f : 0.06	i : 0.04	$ : 0.04	" : 0.04	: : 0.02	+ : 0.02	
= : 0.23	g : 0.19	e : 0.13	d : 0.10	c : 0.10	f : 0.06	[ : 0.04	i : 0.04	! : 0.02	$ : 0.02	b : 0.02	
= : 0.23	g : 0.15	e : 0.10	c : 0.10	d : 0.08	i : 0.06	f : 0.06	" : 0.04	[ : 0.04	a : 0.02	$ : 0.02	b : 0.02	! : 0.02	
= : 0.23	g : 0.13	c : 0.13	e : 0.08	d : 0.08	[ : 0.06	i : 0.06	! : 0.06	f : 0.06	" : 0.04	$ : 0.02	
= : 0.23	g : 0.17	e : 0.13	c : 0.10	d : 0.08	" : 0.06	i : 0.06	! : 0.04	f : 0.04	# : 0.02	b : 0.02	
= : 0.23	[ : 0.13	c : 0.13	g : 0.13	" : 0.06	e : 0.06	! : 0.06	b : 0.06	i : 0.04	f : 0.02	d : 0.02	# : 0.02	
= : 0.23	c : 0.15	e : 0.13	g : 0.13	[ : 0.08	" : 0.06	! : 0.06	b : 0.06	f : 0.02	i : 0.02	# : 0.02	
d : 0.19	= : 0.19	e : 0.13	[ : 0.13	c : 0.13	g : 0.08	" : 0.04	f : 0.02	i : 0.02	# : 0.02	b : 0.02	
c : 0.26	d : 0.19	= : 0.17	e : 0.15	[ : 0.08	b : 0.04	g : 0.04	f : 0.02	i : 0.02	
c : 0.23	d : 0.23	= : 0.15	e : 0.10	b : 0.06	g : 0.04	! : 0.04	[ : 0.02	f : 0.02	i : 0.02	r : 0.02	q : 0.02	
c : 0.23	d : 0.23	= : 0.15	e : 0.10	g : 0.04	! : 0.04	n : 0.02	[ : 0.02	a : 0.02	f : 0.02	i : 0.02	r : 0.02	q : 0.02	b : 0.02	
o : 0.67	c : 0.10	m : 0.04	r : 0.04	d : 0.04	n : 0.02	e : 0.02	q : 0.02	= : 0.02	
o : 0.69	c : 0.06	m : 0.04	r : 0.04	l : 0.04	d : 0.04	n : 0.02	e : 0.02	q : 0.02	
o : 0.71	c : 0.06	l : 0.06	m : 0.06	r : 0.04	n : 0.02	q : 0.02	
o : 0.73	l : 0.08	m : 0.06	n : 0.04	r : 0.04	q : 0.02	
o : 0.73	l : 0.04	= : 0.04	r : 0.04	b : 0.02	d : 0.02	q : 0.02	c : 0.02	m : 0.02	n : 0.02	
o : 0.73	= : 0.04	r : 0.04	b : 0.02	l : 0.02	e : 0.02	d : 0.02	q : 0.02	c : 0.02	m : 0.02	n : 0.02	
c : 0.23	= : 0.19	d : 0.19	e : 0.10	o : 0.06	r : 0.04	g : 0.04	a : 0.02	f : 0.02	i : 0.02	n : 0.02	b : 0.02	
c : 0.23	= : 0.19	d : 0.19	e : 0.13	] : 0.04	o : 0.04	g : 0.04	f : 0.02	i : 0.02	n : 0.02	r : 0.02	b : 0.02	
c : 0.26	= : 0.19	d : 0.19	e : 0.15	g : 0.06	f : 0.02	i : 0.02	] : 0.02	o : 0.02	r : 0.02	b : 0.02	
d : 0.21	= : 0.19	e : 0.15	] : 0.10	g : 0.08	c : 0.06	3 : 0.04	2 : 0.04	f : 0.02	i : 0.02	4 : 0.02	b : 0.02	
= : 0.19	e : 0.13	] : 0.13	3 : 0.10	g : 0.10	2 : 0.08	c : 0.06	d : 0.06	b : 0.04	f : 0.02	i : 0.02	4 : 0.02	
= : 0.21	g : 0.13	3 : 0.10	d : 0.10	2 : 0.08	b : 0.06	e : 0.06	] : 0.04	f : 0.04	i : 0.04	4 : 0.04	c : 0.04	
= : 0.21	g : 0.15	d : 0.10	e : 0.08	] : 0.08	2 : 0.06	3 : 0.06	c : 0.06	i : 0.04	b : 0.04	4 : 0.04	f : 0.02	
c : 0.23	= : 0.23	g : 0.10	e : 0.08	d : 0.08	] : 0.06	i : 0.04	b : 0.04	2 : 0.04	f : 0.02	4 : 0.02	
c : 0.26	= : 0.21	e : 0.10	g : 0.10	d : 0.06	] : 0.04	i : 0.04	2 : 0.04	b : 0.04	a : 0.02	f : 0.02	4 : 0.02	
c : 0.26	= : 0.21	e : 0.13	g : 0.08	] : 0.08	2 : 0.06	f : 0.04	6 : 0.02	i : 0.02	d : 0.02	4 : 0.02	b : 0.02	
3 : 0.23	e : 0.13	= : 0.13	c : 0.10	g : 0.08	2 : 0.06	4 : 0.06	f : 0.04	i : 0.04	] : 0.02	6 : 0.02	d : 0.02	5 : 0.02	
3 : 0.23	c : 0.13	= : 0.10	e : 0.10	2 : 0.08	g : 0.06	4 : 0.06	5 : 0.04	d : 0.04	i : 0.04	6 : 0.02	f : 0.02	] : 0.02	
3 : 0.23	2 : 0.10	c : 0.08	= : 0.08	e : 0.08	4 : 0.08	g : 0.06	5 : 0.04	d : 0.04	i : 0.04	6 : 0.02	b : 0.02	f : 0.02	a : 0.02	: : 0.02	
d : 0.10	b : 0.10	g : 0.10	= : 0.08	f : 0.08	4 : 0.08	c : 0.06	i : 0.06	e : 0.06	2 : 0.06	5 : 0.04	: : 0.04	6 : 0.02	h : 0.02	] : 0.02	

#score	625.911720728539
#seq	46
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_CDS_m1_run2.txt

#BEAR
##ddddwwwwwwwwwwwwwwdddd2	chr10:30611293-30611516(-)$1	223	170	195	19.1067
b!!bbyyyyyyyyyyyyyyyybb22	chr15:84286891-84287110(+)$1	219	26	51	22.0214
eeeeexxxxxxxxxxxxxxxeeeee	chr19:44611689-44611922(+)$1	233	96	121	21.2568
g[ccc^^^^^^^^^^^^^^^^^^^^	chr17:49239037-49239262(+)$1	225	176	201	25.5879
eee^^^^^^^^^^^^^^^^^^eeee	chr19:1599401-1599626(-)$1	225	177	202	24.7941
ddddyyyyyyyyyyyyyyyydddd:	chr20:52188256-52188478(-)$1	222	155	180	21.0158
fffff^^^^^^^^^^^^^^^^^^^^	chr17:76219783-76220007(+)$1	224	97	122	25.3386
ccc^^^^^^^^^^^^^^^^^^^^cc	chr13:48934116-48934344(+)$1	228	163	188	25.6437
c^^^^^^^^^^^^^^^^^^^ccc]f	chr10:81923190-81923422(-)$1	232	78	103	24.3303
[dddd^^^^^^^^^^^^^^^^^^^^	chrM:14558-14796(+)$1	238	50	75	24.9467
ff[bb^^^^^^^^^^^^^^^^^^^^	chr16:31200973-31201201(-)$1	228	35	60	25.3674
gggggxxxxxxxxxxxxxxxggggg	chr1:84412778-84413003(-)$1	225	109	134	21.2746
dddd^^^^^^^^^^^^^^^^^^ddd	chr2:37501662-37501897(-)$1	235	191	216	24.2566
iibb^^^^^^^^^^^^^^^^^^bb]	chr17:1556775-1557018(-)$1	243	40	65	24.4505
fffff^^^^^^^^^^^^^^^^^^^^	chr17:7417294-7417519(+)$1	225	12	37	25.3386
^^^^^^^^^^^^^^^^^^^^eeeee	chr5:43292499-43292718(-)$1	219	87	112	24.3444
^^^^^^^^^^^^^^^^^^^^ccc]d	chr7:51096832-51097052(-)$1	220	178	203	24.2328
fffff^^^^^^^^^^^^^^^^^^ff	chr10:98287068-98287301(-)$1	233	108	133	24.9670
^^^^^^^^^^^^^^^^^^^^ddddg	chr19:39873818-39874053(+)$1	235	120	145	23.9537
eee^^^^^^^^^^^^^^^^^^eeee	chr1:200377570-200377790(-)$1	220	58	83	24.7941
ffffyyyyyyyyyyyyyyyyfffff	chr10:114710383-114710618(-)$1	235	184	209	22.5231
ff[bbxxxxxxxxxxxxxxxbb]ff	chrX:17767990-17768217(+)$1	227	74	99	21.1223
ee[bb^^^^^^^^^^^^^^^^^^bb	chr4:56225413-56225641(+)$1	228	10	35	24.5552
ggggg^^^^^^^^^^^^^^^^^^gg	chr13:100189939-100190159(+)$1	220	184	209	24.9631
##bbyyyyyyyyyyyyyyyybb333	chr1:156237204-156237435(-)$1	231	190	215	22.5093
!!ccc^^^^^^^^^^^^^^^^^^^^	chr12:14631261-14631481(+)$1	220	108	133	25.6968
ffffyyyyyyyyyyyyyyyyfffff	chrM:8329-8609(-)$1	280	196	221	22.5231
ccc^^^^^^^^^^^^^^^^^^ccc:	chr9:131512881-131513104(-)$1	223	102	127	24.1386
eeeeexxxxxxxxxxxxxxxeeeee	chr7:99144187-99144425(-)$1	238	117	142	21.2568
cc[bbwwwwwwwwwwwwwwbbccc]	chr10:60549340-60549789(+)$1	449	112	137	19.7672
=====^^^^^^^^^^^^^^^^^^^^	chr4:41951235-41951457(+)$1	222	94	119	25.5174
a[ccc^^^^^^^^^^^^^^^^^^^^	chr1:230795188-230795412(+)$1	224	96	121	25.5933
eeeeexxxxxxxxxxxxxxxeeeee	chr9:94171851-94172072(-)$1	221	90	115	21.2568
^^^^^^^^^^^^^^^^^^^^cccee	chr1:22021566-22021787(-)$1	221	101	126	24.4515
^^^^^^^^^^^^^^^^^^^^eeeee	chr3:169801872-169802091(+)$1	219	167	192	24.3444
^^^^^^^^^^^^^^^^^^^^^^^^^	chrX:114874630-114874856(+)$1	226	115	140	26.0635
gggggwwwwwwwwwwwwwwgggggg	chr1:70618057-70618284(-)$1	227	167	192	19.3448
^^^^^^^^^^^^^^^^^^^^eeeee	chr8:21849278-21849505(-)$1	227	159	184	24.3444
d!!bb^^^^^^^^^^^^^^^^^^bb	chr20:25288533-25288754(-)$1	221	75	100	24.6106
iiiii^^^^^^^^^^^^^^^^^^^^	chr11:3740557-3740778(-)$1	221	158	183	25.2108
ggggg^^^^^^^^^^^^^^^^^^^^	chr10:70959948-70960172(+)$1	224	113	138	25.3221
ffffffwwwwwwwwwwwwwwfffff	chr5:133295089-133295313(-)$1	224	95	120	19.5376
!ddddxxxxxxxxxxxxxxxdddd2	chr3:182990713-182990937(+)$1	224	15	40	20.6898
hhh^^^^^^^^^^^^^^^^^^^^hh	chr10:60553144-60553442(-)$1	298	163	188	24.1978
=====yyyyyyyyyyyyyyyy====	chr3:150281225-150281446(+)$1	221	174	199	23.0397
gggggyyyyyyyyyyyyyyyygggg	chr15:83686714-83686938(-)$1	224	121	146	22.6646
ffffyyyyyyyyyyyyyyyyfffff	chr19:1010708-1010935(-)$1	227	159	184	22.5231
cc^^^^^^^^^^^^^^^^^^^ccc]	chr15:59009741-59009963(-)$1	222	98	123	25.0417
fffffxxxxxxxxxxxxxxxfffff	chr3:47618599-47618825(-)$1	226	11	36	21.2840
###bbwwwwwwwwwwwwwwbb4444	chr19:44635158-44635377(+)$1	219	16	41	20.2882
ee[cccauuuuuuuuuuuua]ccce	chr1:62910801-62911021(+)$1	220	97	122	19.0137
eee^^^^^^^^^^^^^^^^^^eeee	chr7:100485299-100485520(+)$1	221	2	27	24.7941
ddddyyyyyyyyyyyyyyyydddd]	chr3:182988407-182988627(+)$1	220	95	120	21.8976
[eeeeewwwwwwwwwwwwwweeeee	chr12:133780297-133780517(+)$1	220	192	217	19.7621
!!ddddwwwwwwwwwwwwwwdddd2	chr20:30345223-30345445(+)$1	222	95	120	19.2590
"""bb^^^^^^^^^^^^^^^^^^bb	chr14:53525103-53525327(-)$1	224	95	120	24.7023
[dddd^^^^^^^^^^^^^^^^^^^d	chr2:86344123-86344355(+)$1	232	85	110	24.6416
fffff^^^^^^^^^^^^^^^^^^^^	chr21:43413735-43413962(-)$1	227	117	142	25.3386
fffff^^^^^^^^^^^^^^^^^^^^	chr3:156262055-156262290(-)$1	235	182	207	25.3386
e[cccawwwwwwwwwwwwwwa]ccc	chr17:80014099-80014331(+)$1	232	129	154	20.8239
ffffffwwwwwwwwwwwwwwfffff	chr19:3976160-3976393(-)$1	233	156	181	19.5376
:ccc^^^^^^^^^^^^^^^^^^ccc	chrM:14286-14532(+)$1	246	76	101	24.2121
ffffffwwwwwwwwwwwwwwfffff	chr1:31782886-31783106(+)$1	220	99	124	19.5376
fffff^^^^^^^^^^^^^^^^^^^^	chr3:33442384-33442608(-)$1	224	92	117	25.3386
b[cccxxxxxxxxxxxxxxxcccbb	chr3:15345579-15345805(-)$1	226	184	209	21.2197
^^^^^^^^^^^^^^^^^^^^eeeee	chr1:229794879-229795108(+)$1	229	138	163	24.3444
^^^^^^^^^^^^^^^^^^^^eeeee	chr16:3071756-3071984(+)$1	228	107	132	24.3444
ffffffwwwwwwwwwwwwwwfffff	chr18:33607033-33607252(-)$1	219	157	182	19.5376

#otherMatches

#Seq PSSM
CACUAGAUUCCUUAAAAACCCUAGC	chr10:30611293-30611516(-)$1	223	170	195	19.1067
AAGGGGACAUCAUUACAUUAACCAA	chr15:84286891-84287110(+)$1	219	26	51	22.0214
GAGAUUUACUCAAAAUUCACAUCUU	chr19:44611689-44611922(+)$1	233	96	121	21.2568
GCAGACCACAUUGCUUUUCACAUCC	chr17:49239037-49239262(+)$1	225	176	201	25.5879
AGGAUAAUUAAUUACACAAACCCUU	chr19:1599401-1599626(-)$1	225	177	202	24.7941
UUGGGAAUGCACAUUAUCGACCAAA	chr20:52188256-52188478(-)$1	222	155	180	21.0158
GGCUCAUUUUUGCUGUUUUGAUUCC	chr17:76219783-76220007(+)$1	224	97	122	25.3386
UGCCCCUUUUACUUUCucauucagc	chr13:48934116-48934344(+)$1	228	163	188	25.6437
CAUUCGAAGCGACACAUCAGGGCAC	chr10:81923190-81923422(-)$1	232	78	103	24.3303
CUUAGAAGAAAACCCCACAAACCCC	chrM:14558-14796(+)$1	238	50	75	24.9467
CUUGCUGCCCUAUAUCCCCAGCCCC	chr16:31200973-31201201(-)$1	228	35	60	25.3674
AAUUCCAAAAUUAUGUGAAAGAAUU	chr1:84412778-84413003(-)$1	225	109	134	21.2746
CAGCUCUCAUAAUCCUGUUCUUGCU	chr2:37501662-37501897(-)$1	235	191	216	24.2566
GGGCCAUCUCUGCUGCCAACCUGCA	chr17:1556775-1557018(-)$1	243	40	65	24.4505
guacucaccuacuagccccacuuac	chr17:7417294-7417519(+)$1	225	12	37	25.3386
AUGAUGACACUUUGGAUGAAGGAGU	chr5:43292499-43292718(-)$1	219	87	112	24.3444
CAGACAACCUAAAUGCAAAAGUGAA	chr7:51096832-51097052(-)$1	220	178	203	24.2328
UUACUACUAUUUUUUCAAAACAAAG	chr10:98287068-98287301(-)$1	233	108	133	24.9670
UUUCCUCUUUCCCUGACCCAGCUCC	chr19:39873818-39874053(+)$1	235	120	145	23.9537
GGUGAAGUCAUAGUUAAAGGAGCCA	chr1:200377570-200377790(-)$1	220	58	83	24.7941
UUGCCCCCCCAAAAAAUAUUGCAAG	chr10:114710383-114710618(-)$1	235	184	209	22.5231
CUCCAGAAAAUGAAGAAAAAUGAGG	chrX:17767990-17768217(+)$1	227	74	99	21.1223
AAAGACAGAGAAACUAAAAAUAAUC	chr4:56225413-56225641(+)$1	228	10	35	24.5552
AUAUUAAUGAUAAAAAGUAAACAAG	chr13:100189939-100190159(+)$1	220	184	209	24.9631
UUCCUCUUUUCUCUUCCACUGGCUU	chr1:156237204-156237435(-)$1	231	190	215	22.5093
GGACCAUCUCAGACCACCAUACACU	chr12:14631261-14631481(+)$1	220	108	133	25.6968
AUGGGGGUAAUUAUGGUGGGCCAUA	chrM:8329-8609(-)$1	280	196	221	22.5231
CUCUUCUACCUAACAAAUUCCGAGU	chr9:131512881-131513104(-)$1	223	102	127	24.1386
auacaaacuuuacaaaauucugugu	chr7:99144187-99144425(-)$1	238	117	142	21.2568
CAUGCUGUUAGAACAUCUUGCUGGG	chr10:60549340-60549789(+)$1	449	112	137	19.7672
GUUUGCUCCAACCUUUUAUAUACUA	chr4:41951235-41951457(+)$1	222	94	119	25.5174
GAGCUCUACUAUAAACUUCUUAAAA	chr1:230795188-230795412(+)$1	224	96	121	25.5933
UGAGGCCACGCAAAAACUUUCCUCA	chr9:94171851-94172072(-)$1	221	90	115	21.2568
UAUCCCAUCAAAAUUAUAUAGCCUA	chr1:22021566-22021787(-)$1	221	101	126	24.4515
AUCUGCCUAUUUACUCAAAUUAUUU	chr3:169801872-169802091(+)$1	219	167	192	24.3444
CAAUCAAAUCGCACCAAAAGGACAA	chrX:114874630-114874856(+)$1	226	115	140	26.0635
AGGUAUUUAUUGAUACUAUUGCUUG	chr1:70618057-70618284(-)$1	227	167	192	19.3448
AUACCAAGAAUUCAAAGCUGUGCAU	chr8:21849278-21849505(-)$1	227	159	184	24.3444
ACGCCUCCAGAUGCCCUUAUAUUGG	chr20:25288533-25288754(-)$1	221	75	100	24.6106
GAAAAUUAUCAGCUAAAUCACAAUU	chr11:3740557-3740778(-)$1	221	158	183	25.2108
CCCUUAUAAAGCCCAGUAUCAAUGA	chr10:70959948-70960172(+)$1	224	113	138	25.3221
UGUUGUUUACAUUACAUAUCACAAC	chr5:133295089-133295313(-)$1	224	95	120	19.5376
UGCUUAGAAUAGAAUGGAACAAGUU	chr3:182990713-182990937(+)$1	224	15	40	20.6898
CUUCAUAUCAAACAUCAACACAAGA	chr10:60553144-60553442(-)$1	298	163	188	24.1978
UGGUAAAUAAAUGGCUUAAAAUACU	chr3:150281225-150281446(+)$1	221	174	199	23.0397
UUAGCAUUAUAAUACAUCUUGGCUA	chr15:83686714-83686938(-)$1	224	121	146	22.6646
CCGAUGACAUGAACAACAACUCGGG	chr19:1010708-1010935(-)$1	227	159	184	22.5231
GGAUUCAUUACACCAAAAACACCAG	chr15:59009741-59009963(-)$1	222	98	123	25.0417
CUCAGAGAACCACCCUGAUACUGAG	chr3:47618599-47618825(-)$1	226	11	36	21.2840
AGGACUAUCUAUAAUUCACGUAAGA	chr19:44635158-44635377(+)$1	219	16	41	20.2882
AGCAUUCUUUCUAAAUUUUGUAGUC	chr1:62910801-62911021(+)$1	220	97	122	19.0137
CCCCUCUCCUCUCUCCACCCAGGGU	chr7:100485299-100485520(+)$1	221	2	27	24.7941
AGGGUAAAACUCCUUAUCAUCCCUG	chr3:182988407-182988627(+)$1	220	95	120	21.8976
AUUGUGCAUCAGAGAAUUCACACAG	chr12:133780297-133780517(+)$1	220	192	217	19.7621
UCGGAUUUCAUCAAUUUUUCAUCCU	chr20:30345223-30345445(+)$1	222	95	120	19.2590
ACCGGUUACUAAAUAUUUUUCAUCC	chr14:53525103-53525327(-)$1	224	95	120	24.7023
AGAAUGUGGCCAAGUUUAUUAUUAA	chr2:86344123-86344355(+)$1	232	85	110	24.6416
AACACCUCAAGCCCCCUUUCCAACG	chr21:43413735-43413962(-)$1	227	117	142	25.3386
CAACCCCACAGUGUAUCCUUUUCAA	chr3:156262055-156262290(-)$1	235	182	207	25.3386
AAGUACGCCUCAUGUCUCAAGAUGC	chr17:80014099-80014331(+)$1	232	129	154	20.8239
AAUUUUAACAAACGCAUUAAGAGGU	chr19:3976160-3976393(-)$1	233	156	181	19.5376
CAGCACCAAUCCUACCUCCAUCGCU	chrM:14286-14532(+)$1	246	76	101	24.2121
CUCUCUACACUAUUUUCCAAGGAGA	chr1:31782886-31783106(+)$1	220	99	124	19.5376
CUCCCCAGCAAUUCUUCUUCCCCAA	chr3:33442384-33442608(-)$1	224	92	117	25.3386
GUGGCGAGGCAGGUAAGAUAGCCCC	chr3:15345579-15345805(-)$1	226	184	209	21.2197
GAAGGAGAGAAAAGAUAUACGGCCU	chr1:229794879-229795108(+)$1	229	138	163	24.3444
UCAUUCAUUCAUCCAUUCUAGAGCC	chr16:3071756-3071984(+)$1	228	107	132	24.3444
ACAGCAUAUGUCAUUGUUUUUGUUG	chr18:33607033-33607252(-)$1	219	157	182	19.5376

#DB
..((((..............)))).	chr10:30611293-30611516(-)$1	1	170	195	19.1067
(..((................))..	chr15:84286891-84287110(+)$1	1	26	51	22.0214
(((((...............)))))	chr19:44611689-44611922(+)$1	1	96	121	21.2568
(.(((....................	chr17:49239037-49239262(+)$1	1	176	201	25.5879
(((..................))))	chr19:1599401-1599626(-)$1	1	177	202	24.7941
((((................)))).	chr20:52188256-52188478(-)$1	1	155	180	21.0158
(((((....................	chr17:76219783-76220007(+)$1	1	97	122	25.3386
(((....................))	chr13:48934116-48934344(+)$1	1	163	188	25.6437
(...................))).)	chr10:81923190-81923422(-)$1	1	78	103	24.3303
.((((....................	chrM:14558-14796(+)$1	1	50	75	24.9467
((.((....................	chr16:31200973-31201201(-)$1	1	35	60	25.3674
(((((...............)))))	chr1:84412778-84413003(-)$1	1	109	134	21.2746
((((..................)))	chr2:37501662-37501897(-)$1	1	191	216	24.2566
((((..................)).	chr17:1556775-1557018(-)$1	1	40	65	24.4505
(((((....................	chr17:7417294-7417519(+)$1	1	12	37	25.3386
....................)))))	chr5:43292499-43292718(-)$1	1	87	112	24.3444
....................))).)	chr7:51096832-51097052(-)$1	1	178	203	24.2328
(((((..................))	chr10:98287068-98287301(-)$1	1	108	133	24.9670
....................)))))	chr19:39873818-39874053(+)$1	1	120	145	23.9537
(((..................))))	chr1:200377570-200377790(-)$1	1	58	83	24.7941
((((................)))))	chr10:114710383-114710618(-)$1	1	184	209	22.5231
((.((...............)).))	chrX:17767990-17768217(+)$1	1	74	99	21.1223
((.((..................))	chr4:56225413-56225641(+)$1	1	10	35	24.5552
(((((..................))	chr13:100189939-100190159(+)$1	1	184	209	24.9631
..((................))...	chr1:156237204-156237435(-)$1	1	190	215	22.5093
..(((....................	chr12:14631261-14631481(+)$1	1	108	133	25.6968
((((................)))))	chrM:8329-8609(-)$1	1	196	221	22.5231
(((..................))).	chr9:131512881-131513104(-)$1	1	102	127	24.1386
(((((...............)))))	chr7:99144187-99144425(-)$1	1	117	142	21.2568
((.((..............))))).	chr10:60549340-60549789(+)$1	1	112	137	19.7672
(((((....................	chr4:41951235-41951457(+)$1	1	94	119	25.5174
(.(((....................	chr1:230795188-230795412(+)$1	1	96	121	25.5933
(((((...............)))))	chr9:94171851-94172072(-)$1	1	90	115	21.2568
....................)))((	chr1:22021566-22021787(-)$1	1	101	126	24.4515
....................)))))	chr3:169801872-169802091(+)$1	1	167	192	24.3444
.........................	chrX:114874630-114874856(+)$1	1	115	140	26.0635
(((((..............))))))	chr1:70618057-70618284(-)$1	1	167	192	19.3448
....................)))))	chr8:21849278-21849505(-)$1	1	159	184	24.3444
(..((..................))	chr20:25288533-25288754(-)$1	1	75	100	24.6106
(((((....................	chr11:3740557-3740778(-)$1	1	158	183	25.2108
(((((....................	chr10:70959948-70960172(+)$1	1	113	138	25.3221
((((((..............)))))	chr5:133295089-133295313(-)$1	1	95	120	19.5376
.((((...............)))).	chr3:182990713-182990937(+)$1	1	15	40	20.6898
(((....................))	chr10:60553144-60553442(-)$1	1	163	188	24.1978
(((((................))))	chr3:150281225-150281446(+)$1	1	174	199	23.0397
(((((................))))	chr15:83686714-83686938(-)$1	1	121	146	22.6646
((((................)))))	chr19:1010708-1010935(-)$1	1	159	184	22.5231
((...................))).	chr15:59009741-59009963(-)$1	1	98	123	25.0417
(((((...............)))))	chr3:47618599-47618825(-)$1	1	11	36	21.2840
...((..............))....	chr19:44635158-44635377(+)$1	1	16	41	20.2882
((.((((............).))))	chr1:62910801-62911021(+)$1	1	97	122	19.0137
(((..................))))	chr7:100485299-100485520(+)$1	1	2	27	24.7941
((((................)))).	chr3:182988407-182988627(+)$1	1	95	120	21.8976
.(((((..............)))))	chr12:133780297-133780517(+)$1	1	192	217	19.7621
..((((..............)))).	chr20:30345223-30345445(+)$1	1	95	120	19.2590
...((..................))	chr14:53525103-53525327(-)$1	1	95	120	24.7023
.((((...................)	chr2:86344123-86344355(+)$1	1	85	110	24.6416
(((((....................	chr21:43413735-43413962(-)$1	1	117	142	25.3386
(((((....................	chr3:156262055-156262290(-)$1	1	182	207	25.3386
(.((((..............).)))	chr17:80014099-80014331(+)$1	1	129	154	20.8239
((((((..............)))))	chr19:3976160-3976393(-)$1	1	156	181	19.5376
.(((..................)))	chrM:14286-14532(+)$1	1	76	101	24.2121
((((((..............)))))	chr1:31782886-31783106(+)$1	1	99	124	19.5376
(((((....................	chr3:33442384-33442608(-)$1	1	92	117	25.3386
(.(((...............)))))	chr3:15345579-15345805(-)$1	1	184	209	21.2197
....................)))))	chr1:229794879-229795108(+)$1	1	138	163	24.3444
....................)))))	chr16:3071756-3071984(+)$1	1	107	132	24.3444
((((((..............)))))	chr18:33607033-33607252(-)$1	1	157	182	19.5376

#PSSM
f : 0.23	e : 0.13	^ : 0.13	g : 0.08	c : 0.07	d : 0.05	# : 0.04	[ : 0.04	! : 0.04	b : 0.02	i : 0.02	= : 0.02	a : 0.01	h : 0.01	" : 0.01	: : 0.01	
f : 0.23	^ : 0.14	e : 0.13	d : 0.08	c : 0.07	g : 0.07	! : 0.05	[ : 0.05	# : 0.04	i : 0.02	= : 0.02	h : 0.01	" : 0.01	
f : 0.20	^ : 0.16	d : 0.11	c : 0.11	e : 0.10	[ : 0.07	g : 0.07	! : 0.02	b : 0.02	= : 0.02	i : 0.01	h : 0.01	# : 0.01	" : 0.01	
^ : 0.25	f : 0.20	b : 0.14	d : 0.11	c : 0.10	g : 0.07	e : 0.05	= : 0.02	i : 0.01	
^ : 0.29	f : 0.16	b : 0.11	c : 0.08	y : 0.08	d : 0.07	g : 0.07	e : 0.05	= : 0.02	i : 0.01	
^ : 0.57	y : 0.13	x : 0.11	f : 0.05	w : 0.04	d : 0.02	c : 0.01	e : 0.01	a : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	a : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	w : 0.16	y : 0.13	x : 0.11	u : 0.01	
^ : 0.57	y : 0.13	w : 0.11	x : 0.11	b : 0.02	g : 0.01	a : 0.01	
^ : 0.44	e : 0.13	f : 0.11	d : 0.08	c : 0.05	b : 0.05	y : 0.04	g : 0.02	] : 0.01	a : 0.01	
^ : 0.36	e : 0.17	c : 0.11	f : 0.11	d : 0.08	b : 0.04	g : 0.04	= : 0.01	4 : 0.01	] : 0.01	
^ : 0.32	e : 0.17	c : 0.14	f : 0.11	d : 0.10	g : 0.04	b : 0.02	] : 0.01	3 : 0.01	= : 0.01	4 : 0.01	
^ : 0.22	e : 0.19	f : 0.14	d : 0.10	c : 0.10	b : 0.07	g : 0.05	] : 0.02	2 : 0.01	3 : 0.01	h : 0.01	= : 0.01	4 : 0.01	
e : 0.20	^ : 0.20	f : 0.16	g : 0.07	2 : 0.05	] : 0.05	b : 0.05	c : 0.04	d : 0.04	: : 0.02	3 : 0.01	h : 0.01	= : 0.01	4 : 0.01	

#score	1575.0502539557929
#seq	68
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_CDS_m2_run2.txt

#BEAR
======ccc"""ddddlllddddccc22===========	chr16:19126393-19126633(+)$1	240	172	211	15.1240
$$$$$dddd####cccooooooccc22ddddeeeee:::	chr1:29040653-29040933(+)$1	280	227	266	14.2616
ffffff[bb####cccooooooccc333bb]ffffff]d	chr22:38247251-38247491(+)$1	240	149	188	16.8958
ddd"""bb[ccc[cccooooooccc]cccbbdddd4444	chr19:42792955-42793195(+)$1	240	100	139	15.9957
:iiiiiiiii!!ddddoooooodddd333iiiiiiiii:	chr17:48776879-48777119(-)$1	240	76	115	17.0022
f####bb"""bb[cccoooooocccbb333bb333ffff	chr4:2946804-2947050(-)$1	246	173	212	16.5345
dd####bb####ddddnnnnndddd333bbdddd4444b	chr11:34153571-34153811(+)$1	240	101	140	14.8973
ee####ccc[ccccccooooooccc]cccccc333eeee	chr19:19033408-19033648(+)$1	240	117	156	17.2029
ggg"""ccc"""cccnnnnncccccc333ggggggg]cc	chr16:84779009-84779249(+)$1	240	52	91	15.0848
========="""ddddnnnnndddd22==========:D	chr10:428558-428798(-)$1	240	6	45	14.5524
ccccccddddddddrrrrrrrrrdddd4444dddd22cc	chr11:3723978-3724218(-)$1	240	145	184	10.6339
dd[a!!ccc!!eeeeeooooooeeeee4444ccc22add	chr8:101270722-101270962(-)$1	240	162	201	16.1217
gggiiiiiiiii[cccooooooccc]iiiiiiiii5555	chr3:132400720-132400960(-)$1	240	7	46	14.4733
ccc[ccc$$$$$ddddoooooodddd4444ccc]ccc:e	chr3:124951531-124951771(-)$1	240	181	220	16.5457
dddd!!a[ccc[bb[aooooooa]bb]ccc]a22ddddb	chr12:116408382-116408622(-)$1	240	177	216	13.7544
$$$ccc[ccc[ccc!!aooooooa22ccc]ccc]cccee	chr18:34191920-34192160(+)$1	240	7	46	14.2428
iii$$$$$ccc"""bboooooobb4444ccc22iiiiii	chr20:52192750-52192990(-)$1	240	105	144	16.6781
####a!!ccc!!ddddooooooddddccc22a4444bb]	chr19:37211181-37211421(+)$1	240	16	55	17.1914
ee!!ccc[dddd[cccooooooccc]ddddccceeeeeb	chr7:86848669-86848909(-)$1	240	190	229	14.8895
[cccdddd[ccc!!bboooooobb22ccc333dddd]cc	chr20:62642608-62642848(+)$1	240	182	221	14.6405
[ccca!!ccc[eeeeeooooooeeeee]ccc22a]cccd	chr1:161721561-161721845(+)$1	284	161	200	15.3749
fff!!dddd!!ddddddddllldddd333dddd333ddd	chr19:39860377-39860617(+)$1	240	47	86	12.6657
ffeeeee%%%%%%cccooooooccc4444eeeee]ffff	chr10:104679663-104679906(+)$1	243	193	232	14.0624
e[dddddddd[eeeeeooooooeeeee22dddd333ddd	chr15:41191468-41191708(+)$1	240	32	71	14.0160
cc:ggggggg####bboooooobb666666gggggggbb	chr2:43813934-43814174(-)$1	240	38	77	13.2885
d"""eeeee####bboooooobb4444eeeeeddddbbo	chr4:141543398-141543638(-)$1	240	111	150	14.0354
iiiiiiiii####cccqqqqqqqqccc4444iiiiiiii	chr19:9452412-9452652(+)$1	240	36	75	13.4637
$$$$$eeeee[eeeeeooooooeeeeeeeeee333ffff	chr12:50847211-50847451(+)$1	240	72	111	13.6124
eee####ccc"""cccoooooocccccceeeee]dddd:	chr14:23299306-23299548(+)$1	242	140	179	16.3235
bbffffffbb!!a!!aooooooa22a22bb333ffffff	chrX:24006429-24006710(-)$1	281	211	250	13.3288
b[a[bb[eeeee[cccooooooccc]eeeee]bb]a]bb	chr17:26961440-26961680(-)$1	240	20	59	14.0125
!ccc!!bb[bb!!cccoooooocccbb]bbcccdddd22	chr1:51436012-51436252(+)$1	240	34	73	14.8443
========####eeeeennnnneeeee]===========	chr1:15987695-15987975(+)$1	280	202	241	14.4001
f[eeeee[dddd!!bboooooobb4444dddd22eeeee	chr12:123687760-123688000(-)$1	240	9	48	14.2566
[eeeee"""ccc[ccclllcccccc333eeeeeeeeeed	chr13:72440068-72440308(-)$1	240	154	193	12.7243
==========!!cccqqqqqqqqccc============:	chr7:157000432-157000672(+)$1	240	112	151	12.3750
""ggggggg####cccooooooccc333ggggggg22dd	chr12:116399000-116399240(-)$1	240	197	236	19.4737
=============[bbnnnnnbb================	chr2:223793514-223793754(+)$1	240	165	204	13.5309
[ggggggg!!a[ddddnnnnndddd]a22gggggggccc	chr1:213037065-213037305(+)$1	240	3	42	13.9514
=======bb####ddddnnnnndddd4444bb333====	chr10:91492561-91492801(+)$1	240	31	70	15.7871
c[dddd!!ccc[ddddooooooddddccc22dddd333c	chr22:41660612-41660852(-)$1	240	175	214	15.7588
ccccc"""ccc!!cccooooooccc4444ccc22ccc]c	chr1:24020263-24020503(+)$1	240	55	94	18.6491
!!ccc[bb[a!!ddddoooooodddd333a]bbccc]cc	chr1:160276051-160276291(-)$1	240	75	114	17.7047
e####eeeee"""cccooooooccc55555eeeee22ee	chr5:134364557-134364797(-)$1	240	176	215	14.9991
[bbggggggg"""cccooooooccc22ggggggg]bb]c	chr2:86067297-86067537(-)$1	240	89	128	17.2098
ggggggg####eeeeeooooooeeeee22ggggggg333	chr2:32353392-32353632(+)$1	240	72	111	16.0799
eeeee!!bbccc[cccooooooccc22ccc22bb22eee	chr5:126154593-126154833(+)$1	240	157	196	15.0511
"""dddd[ccc!!ddddmmmmdddd22ccc]dddd22cc	chr9:32541312-32541552(-)$1	240	38	77	12.1319
dddd[gggggggddddoooooodddd]ggggggg]dddd	chr16:84778827-84779067(+)$1	240	6	45	14.9225
c####dddd####ddddllldddd4444dddd4444ccc	chr5:102611999-102612240(+)$1	241	188	227	14.9396

#otherMatches

#Seq PSSM
CUCCUUGGCCACUGUGCGUUACAGCCUGGAGGGGCGCUG	chr16:19126393-19126633(+)$1	240	172	211	15.1240
CCUUCUGGCCCUCAGCUCUUCCGCUAUGCCACAGUGGUC	chr1:29040653-29040933(+)$1	280	227	266	14.2616
UGAUUGACCAGAAAGUGUAUGAGCUACAGGCCAGUCGUG	chr22:38247251-38247491(+)$1	240	149	188	16.8958
GUCCGUUGCAGCCCAGACACUCCUGAGCUCAGACACCAA	chr19:42792955-42793195(+)$1	240	100	139	15.9957
CCCUGGGGAACCUCCCCUGUUAGGGACCUUUCCCCGGGA	chr17:48776879-48777119(-)$1	240	76	115	17.0022
GCCUCAGUCAGCUGCUCACCAAGGUGCGUUCUCUCCACA	chr4:2946804-2947050(-)$1	246	173	212	16.5345
UACUAUGUUAAUAGAGAUACCCUCUUUUGCUACCACAAG	chr11:34153571-34153811(+)$1	240	101	140	14.8973
CCAUUAUCAUCUUCACCAACACGUGCAAGUGAGCGGGGC	chr19:19033408-19033648(+)$1	240	117	156	17.2029
CGGCACGGGCUCUGCAUCAGGCACCCUUCCUGUCAGCCA	chr16:84779009-84779249(+)$1	240	52	91	15.0848
AAUCCCACCUUCGGAACUAUUUUCUAUGGUGGGAUUUUG	chr10:428558-428798(-)$1	240	6	45	14.5524
AAGUGUCUCUGUGCAAGAAUGUCGUACUCCCAGAGCAGC	chr11:3723978-3724218(-)$1	240	145	184	10.6339
UUCAGACUGAAAUUUAGGCCCAUAAAUGCUGCAGAAUAA	chr8:101270722-101270962(-)$1	240	162	201	16.1217
UUUGUUUUCUCUCUCAAAGCUAUGAAGGAGGAGAUUUUG	chr3:132400720-132400960(-)$1	240	7	46	14.4733
AUCAGGAAUGAAUUCUCCACUAAGAACAACUCCAGAUAA	chr3:124951531-124951771(-)$1	240	181	220	16.5457
GGCUCCAGCCAACUACCCCAAUGAAGAUGGGUUUAGCCC	chr12:116408382-116408622(-)$1	240	177	216	13.7544
UACCAGACCAAGACACCUUCUACGACGUCGUGGACUGCC	chr18:34191920-34192160(+)$1	240	7	46	14.2428
AGGGAUAGACUCUAGCACUUUAGCCCCAAGUAACCUGAA	chr20:52192750-52192990(-)$1	240	105	144	16.6781
GAGAAUUCAUACAGGGGAGAAACCCUAUGUUUGUAAUGA	chr19:37211181-37211421(+)$1	240	16	55	17.1914
GACUGGGAUGGGGGGUGUGUCUGCUGCCUGCCCUCUGGC	chr7:86848669-86848909(-)$1	240	190	229	14.8895
AUCGACCGAGCCAUCACCUCGCUGCGGGCCAACGGUGUG	chr20:62642608-62642848(+)$1	240	182	221	14.6405
AGUGCAAUUUAUAAGCAAUAUCGUUUACAAAAGGUUACA	chr1:161721561-161721845(+)$1	284	161	200	15.3749
GGCCUACUCAAUCGAGAGCAAUGCUUUCAUCGAGGAGAG	chr19:39860377-39860617(+)$1	240	47	86	12.6657
AGGUGGGAAAUUUUGGUCUCUUUCAUUGGCUUGCUCUUU	chr10:104679663-104679906(+)$1	243	193	232	14.0624
UCGGGACUGCCCAAGGCCACAUCUUUGAAGCAGAGCUCU	chr15:41191468-41191708(+)$1	240	32	71	14.0160
UAAAUAGCCUGCCUGAUUUUUUUCUACCUGAGGCUAUGC	chr2:43813934-43814174(-)$1	240	38	77	13.2885
ACUGGGCCAUCACCUUCGAGCAGUUCCUGGCCUCCCUCU	chr4:141543398-141543638(-)$1	240	111	150	14.0354
ACUCACAGGAGAACUUACUUUAGAAAGAAAACCUGUGAG	chr19:9452412-9452652(+)$1	240	36	75	13.4637
UUAUCGAUUAAUGGAUUCUAGUAUCUAUAGUCACCCCAU	chr12:50847211-50847451(+)$1	240	72	111	13.6124
AGACUGGUCAUAUGCGGGUAAGCGCUGAUCUGGCAGUUA	chr14:23299306-23299548(+)$1	242	140	179	16.3235
GGGACCAUAGAACAACGGACCAGGAGAACUCAAGUGGUU	chrX:24006429-24006710(-)$1	281	211	250	13.3288
AUGGUCCUGAGCAUGUGGUAGAACAGGUUCAAGAGCUUG	chr17:26961440-26961680(-)$1	240	20	59	14.0125
GAGCCUUGGGGGAACGAGUUGGCGUCCGCAGCUGCCAGG	chr1:51436012-51436252(+)$1	240	34	73	14.8443
AGUCUUUGUCAUCCAAUUUCAUAUUGGUUAAAGACUUAG	chr1:15987695-15987975(+)$1	280	202	241	14.4001
GCUUAUUUUGAUAUCAUUAAUUUGUUUCAUUAUUGAUAA	chr12:123687760-123688000(-)$1	240	9	48	14.2566
AUCCUGAGGGGACUGGGCGCCAUCCAGCCAGGAGUGAAC	chr13:72440068-72440308(-)$1	240	154	193	12.7243
AUUUCAGAGUAUUGGAGUUACUACUAGCUCUGAAAUGCA	chr7:157000432-157000672(+)$1	240	112	151	12.3750
CAGUUCCUUCUCCCUGCAACCUCAGUCCAAGGAACCUGC	chr12:116399000-116399240(-)$1	240	197	236	19.4737
CAUUAAUUUUUAAAGUAUUAAACUUGAAAAUUAGUGCUU	chr2:223793514-223793754(+)$1	240	165	204	13.5309
UGGAACUGCAGUUGGCUUUUUGCUACCACCAGUUUUAGU	chr1:213037065-213037305(+)$1	240	3	42	13.9514
UUUAUGUGAUUUGUACAUUUUUUGUAGCUUUCUAUAUGU	chr10:91492561-91492801(+)$1	240	31	70	15.7871
CGGCGGCAAGGUGGGUGUGGCAGCCCCCUCCCCGCAGAG	chr22:41660612-41660852(-)$1	240	175	214	15.7588
UGGCAUCCGGAGAAAUGAAAAGAUUGCUGUCCACUGCAC	chr1:24020263-24020503(+)$1	240	55	94	18.6491
UCUAUGCUGGCACAGGCAAUCUCCUGCUUCGAGAUGCGG	chr1:160276051-160276291(-)$1	240	75	114	17.7047
GGCACUCCCGCCUCGCCCUACAGCGUCUACCGGGACACG	chr5:134364557-134364797(-)$1	240	176	215	14.9991
CGGGUUUUGGAUAUGACCUCAAUCAACCCAGAACACCUU	chr2:86067297-86067537(-)$1	240	89	128	17.2098
UGAUUUUUAAAGGCUAAAGCAGUAGCUGCAGAAUCGAAU	chr2:32353392-32353632(+)$1	240	72	111	16.0799
CUAUGAACAGCUUCUUGAUGUAAAGUUAGCCCUGGACAU	chr5:126154593-126154833(+)$1	240	157	196	15.0511
CUUUGUUUCUGAUUUGGAGAACCAGCCCAGUAACAUUGU	chr9:32541312-32541552(-)$1	240	38	77	12.1319
UUUUGGUCAGUCCUGCUUCCCUGCAGAGGCUGGCAGAGA	chr16:84778827-84779067(+)$1	240	6	45	14.9225
CUUCAACACCUAACCCUCCGAGGGGACCGUGUGUUUGCU	chr5:102611999-102612240(+)$1	241	188	227	14.9396

#DB
(((((((((...((((...)))))))..)))))))))))	chr16:19126393-19126633(+)$1	1	172	211	15.1240
.....((((....(((......)))..)))))))))...	chr1:29040653-29040933(+)$1	1	227	266	14.2616
((((((.((....(((......)))...)).)))))).)	chr22:38247251-38247491(+)$1	1	149	188	16.8958
(((...((.(((.(((......))).)))))))))....	chr19:42792955-42793195(+)$1	1	100	139	15.9957
.(((((((((..((((......))))...))))))))).	chr17:48776879-48777119(-)$1	1	76	115	17.0022
(....((...((.(((......)))))...))...))))	chr4:2946804-2947050(-)$1	1	173	212	16.5345
((....((....((((.....))))...))))))....)	chr11:34153571-34153811(+)$1	1	101	140	14.8973
((....(((.((((((......))).))))))...))))	chr19:19033408-19033648(+)$1	1	117	156	17.2029
(((...(((...(((.....))))))...))))))).))	chr16:84779009-84779249(+)$1	1	52	91	15.0848
(((((((((...((((.....))))..)))))))))).(	chr10:428558-428798(-)$1	1	6	45	14.5524
((((((((((((((.........))))....))))..))	chr11:3723978-3724218(-)$1	1	145	184	10.6339
((.(..(((..(((((......)))))....)))..)))	chr8:101270722-101270962(-)$1	1	162	201	16.1217
((((((((((((.(((......))).)))))))))....	chr3:132400720-132400960(-)$1	1	7	46	14.4733
(((.(((.....((((......))))....))).))).(	chr3:124951531-124951771(-)$1	1	181	220	16.5457
((((..(.(((.((.(......).)).))).)..)))))	chr12:116408382-116408622(-)$1	1	177	216	13.7544
...(((.(((.(((..(......)..))).))).)))))	chr18:34191920-34192160(+)$1	1	7	46	14.2428
(((.....(((...((......))....)))..))))))	chr20:52192750-52192990(-)$1	1	105	144	16.6781
....(..(((..((((......)))))))..)....)).	chr19:37211181-37211421(+)$1	1	16	55	17.1914
((..(((.((((.(((......))).)))))))))))))	chr7:86848669-86848909(-)$1	1	190	229	14.8895
.(((((((.(((..((......))..)))...)))).))	chr20:62642608-62642848(+)$1	1	182	221	14.6405
.((((..(((.(((((......))))).)))..).))))	chr1:161721561-161721845(+)$1	1	161	200	15.3749
(((..((((..((((((((...))))...))))...)))	chr19:39860377-39860617(+)$1	1	47	86	12.6657
(((((((......(((......)))....))))).))))	chr10:104679663-104679906(+)$1	1	193	232	14.0624
(.((((((((.(((((......)))))..))))...)))	chr15:41191468-41191708(+)$1	1	32	71	14.0160
)).(((((((....((......))......)))))))((	chr2:43813934-43814174(-)$1	1	38	77	13.2885
(...(((((....((......))....)))))))))((.	chr4:141543398-141543638(-)$1	1	111	150	14.0354
(((((((((....(((........)))....))))))))	chr19:9452412-9452652(+)$1	1	36	75	13.4637
.....(((((.(((((......))))))))))...))))	chr12:50847211-50847451(+)$1	1	72	111	13.6124
(((....(((...(((......))))))))))).)))).	chr14:23299306-23299548(+)$1	1	140	179	16.3235
((((((((((..(..(......)..)..))...))))))	chrX:24006429-24006710(-)$1	1	211	250	13.3288
(.(.((.(((((.(((......))).))))).)).).))	chr17:26961440-26961680(-)$1	1	20	59	14.0125
.(((..((.((..(((......))))).)))))))))..	chr1:51436012-51436252(+)$1	1	34	73	14.8443
((((((((....(((((.....))))).)))))))))))	chr1:15987695-15987975(+)$1	1	202	241	14.4001
(.(((((.((((..((......))....))))..)))))	chr12:123687760-123688000(-)$1	1	9	48	14.2566
.(((((...(((.(((...))))))...)))))))))))	chr13:72440068-72440308(-)$1	1	154	193	12.7243
((((((((((..(((........))))))))))))))).	chr7:157000432-157000672(+)$1	1	112	151	12.3750
..(((((((....(((......)))...)))))))..))	chr12:116399000-116399240(-)$1	1	197	236	19.4737
(((((((((((((.((.....))))))))))))))))))	chr2:223793514-223793754(+)$1	1	165	204	13.5309
.(((((((..(.((((.....)))).)..))))))))))	chr1:213037065-213037305(+)$1	1	3	42	13.9514
(((((((((....((((.....))))....))...))))	chr10:91492561-91492801(+)$1	1	31	70	15.7871
(.((((..(((.((((......)))))))..))))...)	chr22:41660612-41660852(-)$1	1	175	214	15.7588
(((((...(((..(((......)))....)))..))).)	chr1:24020263-24020503(+)$1	1	55	94	18.6491
..(((.((.(..((((......))))...).))))).))	chr1:160276051-160276291(-)$1	1	75	114	17.7047
(....(((((...(((......))).....)))))..))	chr5:134364557-134364797(-)$1	1	176	215	14.9991
.(((((((((...(((......)))..))))))).)).)	chr2:86067297-86067537(-)$1	1	89	128	17.2098
(((((((....(((((......)))))..)))))))...	chr2:32353392-32353632(+)$1	1	72	111	16.0799
(((((..(((((.(((......)))..)))..))..)))	chr5:126154593-126154833(+)$1	1	157	196	15.0511
...((((.(((..((((....))))..))).))))..))	chr9:32541312-32541552(-)$1	1	38	77	12.1319
((((.(((((((((((......)))).))))))).))))	chr16:84778827-84779067(+)$1	1	6	45	14.9225
(....((((....((((...))))....))))....)))	chr5:102611999-102612240(+)$1	1	188	227	14.9396

#PSSM
= : 0.12	d : 0.12	e : 0.12	c : 0.12	f : 0.10	[ : 0.10	$ : 0.06	g : 0.06	i : 0.04	b : 0.04	! : 0.04	" : 0.04	: : 0.02	# : 0.02	
c : 0.14	= : 0.12	d : 0.10	e : 0.10	# : 0.08	g : 0.08	[ : 0.08	$ : 0.06	f : 0.06	i : 0.06	" : 0.06	b : 0.04	! : 0.02	
c : 0.14	= : 0.12	# : 0.12	d : 0.10	g : 0.10	e : 0.10	$ : 0.06	f : 0.06	i : 0.06	" : 0.04	[ : 0.02	! : 0.02	: : 0.02	a : 0.02	b : 0.02	
# : 0.14	c : 0.14	= : 0.12	d : 0.10	g : 0.10	e : 0.08	$ : 0.06	" : 0.06	i : 0.06	f : 0.04	[ : 0.04	! : 0.04	a : 0.02	
= : 0.12	# : 0.12	c : 0.12	e : 0.10	g : 0.10	! : 0.08	d : 0.08	$ : 0.06	i : 0.06	f : 0.04	" : 0.04	a : 0.04	b : 0.02	[ : 0.02	
d : 0.14	= : 0.12	! : 0.12	e : 0.12	g : 0.12	c : 0.08	" : 0.06	i : 0.06	# : 0.06	f : 0.04	b : 0.04	$ : 0.02	[ : 0.02	
d : 0.14	c : 0.12	g : 0.12	b : 0.10	= : 0.10	e : 0.10	! : 0.08	[ : 0.06	i : 0.06	" : 0.04	a : 0.02	$ : 0.02	# : 0.02	f : 0.02	
c : 0.16	b : 0.14	d : 0.12	g : 0.10	= : 0.08	[ : 0.08	e : 0.08	i : 0.06	" : 0.06	$ : 0.04	% : 0.02	f : 0.02	! : 0.02	# : 0.02	
c : 0.25	d : 0.14	b : 0.08	[ : 0.08	g : 0.08	e : 0.08	i : 0.06	# : 0.06	= : 0.06	" : 0.04	$ : 0.02	% : 0.02	! : 0.02	
c : 0.25	# : 0.19	" : 0.08	d : 0.08	! : 0.06	g : 0.06	e : 0.06	i : 0.04	b : 0.04	= : 0.04	[ : 0.02	$ : 0.02	% : 0.02	a : 0.02	
# : 0.21	c : 0.19	! : 0.14	" : 0.12	[ : 0.08	d : 0.06	b : 0.04	i : 0.02	$ : 0.02	% : 0.02	e : 0.02	= : 0.02	a : 0.02	g : 0.02	
# : 0.19	! : 0.16	" : 0.14	c : 0.12	e : 0.12	d : 0.08	[ : 0.06	b : 0.02	i : 0.02	$ : 0.02	% : 0.02	= : 0.02	g : 0.02	
d : 0.23	# : 0.16	[ : 0.14	e : 0.12	! : 0.10	c : 0.08	" : 0.08	b : 0.02	% : 0.02	a : 0.02	= : 0.02	
c : 0.42	d : 0.30	e : 0.12	! : 0.06	b : 0.04	" : 0.02	# : 0.02	[ : 0.02	
c : 0.40	d : 0.27	e : 0.12	b : 0.12	! : 0.04	r : 0.02	[ : 0.02	
c : 0.36	d : 0.27	e : 0.12	b : 0.10	a : 0.04	n : 0.02	r : 0.02	! : 0.02	o : 0.02	q : 0.02	
o : 0.68	n : 0.10	d : 0.08	l : 0.04	q : 0.04	r : 0.02	a : 0.02	e : 0.02	
o : 0.70	n : 0.14	l : 0.06	q : 0.04	r : 0.02	d : 0.02	m : 0.02	
o : 0.70	n : 0.14	l : 0.06	q : 0.04	r : 0.02	d : 0.02	m : 0.02	
o : 0.70	n : 0.14	l : 0.04	q : 0.04	d : 0.02	r : 0.02	c : 0.02	m : 0.02	
o : 0.70	n : 0.12	d : 0.04	c : 0.04	q : 0.04	r : 0.02	l : 0.02	m : 0.02	
o : 0.68	d : 0.12	c : 0.04	b : 0.04	q : 0.04	n : 0.04	r : 0.02	l : 0.02	
c : 0.36	d : 0.27	e : 0.12	b : 0.12	a : 0.04	q : 0.04	r : 0.02	o : 0.02	
c : 0.40	d : 0.27	e : 0.12	b : 0.08	] : 0.02	a : 0.02	4 : 0.02	q : 0.02	2 : 0.02	= : 0.02	
c : 0.42	d : 0.25	e : 0.12	4 : 0.08	2 : 0.06	b : 0.02	6 : 0.02	= : 0.02	
d : 0.18	2 : 0.14	] : 0.12	e : 0.12	4 : 0.12	c : 0.10	3 : 0.08	b : 0.06	6 : 0.02	a : 0.02	= : 0.02	5 : 0.02	
3 : 0.16	c : 0.16	4 : 0.16	2 : 0.14	e : 0.14	b : 0.04	d : 0.04	] : 0.04	= : 0.04	i : 0.02	6 : 0.02	a : 0.02	5 : 0.02	
c : 0.19	4 : 0.19	3 : 0.18	2 : 0.10	= : 0.06	] : 0.06	e : 0.06	d : 0.04	g : 0.04	i : 0.02	6 : 0.02	5 : 0.02	
c : 0.21	4 : 0.14	= : 0.10	3 : 0.10	e : 0.10	d : 0.08	b : 0.08	2 : 0.06	g : 0.06	i : 0.02	6 : 0.02	5 : 0.02	
c : 0.14	d : 0.12	g : 0.12	e : 0.12	= : 0.10	b : 0.10	4 : 0.10	i : 0.04	3 : 0.04	2 : 0.04	] : 0.02	6 : 0.02	a : 0.02	5 : 0.02	
c : 0.16	g : 0.14	e : 0.14	d : 0.12	= : 0.10	] : 0.08	b : 0.06	4 : 0.06	2 : 0.06	i : 0.04	3 : 0.04	
d : 0.18	e : 0.14	c : 0.14	g : 0.14	= : 0.10	i : 0.06	b : 0.06	2 : 0.06	a : 0.04	3 : 0.04	f : 0.02	] : 0.02	
d : 0.18	g : 0.14	= : 0.10	e : 0.10	3 : 0.10	c : 0.10	2 : 0.10	i : 0.06	b : 0.06	4 : 0.04	f : 0.02	
d : 0.16	g : 0.14	3 : 0.12	= : 0.10	e : 0.10	i : 0.08	] : 0.06	2 : 0.06	f : 0.04	c : 0.04	4 : 0.04	b : 0.04	a : 0.02	
d : 0.18	3 : 0.12	= : 0.10	e : 0.10	g : 0.10	] : 0.10	i : 0.08	c : 0.08	4 : 0.06	f : 0.04	2 : 0.04	
= : 0.12	2 : 0.12	d : 0.12	e : 0.10	f : 0.10	c : 0.10	4 : 0.08	g : 0.08	i : 0.06	3 : 0.06	5 : 0.02	a : 0.02	b : 0.02	
= : 0.12	c : 0.12	d : 0.12	f : 0.10	e : 0.10	] : 0.08	2 : 0.08	i : 0.06	b : 0.06	4 : 0.04	3 : 0.04	: : 0.02	a : 0.02	5 : 0.02	g : 0.02	
c : 0.16	e : 0.14	d : 0.14	= : 0.10	f : 0.08	b : 0.08	: : 0.06	] : 0.06	i : 0.06	4 : 0.04	3 : 0.04	5 : 0.02	2 : 0.02	
c : 0.19	d : 0.16	e : 0.12	b : 0.10	= : 0.08	: : 0.08	f : 0.08	i : 0.04	4 : 0.02	D : 0.02	5 : 0.02	] : 0.02	o : 0.02	2 : 0.02	3 : 0.02	

#score	749.6990329926799
#seq	50
#width	39
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_UTR_m1_run2.txt

#BEAR
iiiiiiiiwwwwwwwwwwwwwwiiiiii	chr9:114696712-114696937(+)$1	225	109	137	23.2520
gggggggcccvvvvvvvvvvvvvccc::	chr1:214510011-214510234(+)$1	223	180	208	19.7711
"""eeeeeyyyyyyyyyyyyyyyyeeee	chr10:27486075-27486321(-)$1	246	160	188	22.5984
ccc!!cccvvvvvvvvvvvvvccc22cc	chr15:52675228-52675455(-)$1	227	2	30	22.2600
eee[ddddwwwwwwwwwwwwwwdddd]e	chr16:71764873-71765094(-)$1	221	11	39	22.4696
iiiiiiii^^^^^^^^^^^^^^^^^^^^	chr8:133024910-133025140(+)$1	230	81	109	21.1334
bb!!eeeeevvvvvvvvvvvvveeeeeb	chr2:133430387-133430612(-)$1	225	89	117	21.7532
=========vvvvvvvvvvvvv======	chr11:108344774-108345004(-)$1	230	157	185	22.9786
ffff[eeeeeuuuuuuuuuuuueeeee2	chr5:86687060-86687284(+)$1	224	93	121	20.7719
$$$$bb[ayyyyyyyyyyyyyyyya]bb	chr11:57585554-57585784(+)$1	230	74	102	21.2962
b[eeeeexxxxxxxxxxxxxxxeeeee]	chr6:30568718-30568948(-)$1	230	30	58	20.1605
bb####cccvvvvvvvvvvvvvccc22b	chr4:77956266-77956496(+)$1	230	29	57	21.9660
========xxxxxxxxxxxxxxx=====	chr2:105964213-105964440(+)$1	227	122	150	21.6668
ffffffyyyyyyyyyyyyyyyyffffff	chr2:61749698-61749921(-)$1	223	118	146	20.9816
ffffff[bbvvvvvvvvvvvvvbb]fff	chr16:69735961-69736186(+)$1	225	24	52	20.7531
##acccbb^^^^^^^^^^^^^^^^^^^^	chr5:110465158-110465393(+)$1	235	134	162	20.3821
!!eeeee^^^^^^^^^^^^^^^^^^^^e	chr15:38782561-38782791(-)$1	230	127	155	20.4499
gggggggxxxxxxxxxxxxxxxgggggg	chr3:122133197-122133419(-)$1	222	186	214	20.6083
eeee[ccc^^^^^^^^^^^^^^^^^^^^	chr19:15533693-15533919(-)$1	226	97	125	20.7086
::ffffffwwwwwwwwwwwwwwffffff	chr17:17748075-17748296(-)$1	221	162	190	20.4036
"""eeeeeuuuuuuuuuuuueeeee333	chr6:139225990-139226213(-)$1	223	154	182	21.7893
iiii[ccc^^^^^^^^^^^^^^^^^^^^	chr1:231700792-231701022(+)$1	230	139	167	21.3296
!!ccc[dddduuuuuuuuuuuudddd]c	chr1:12571859-12572089(+)$1	230	92	120	21.1653
e####cccyyyyyyyyyyyyyyyyccc5	chr16:24815986-24816216(+)$1	230	46	74	22.5289
e"""ffffffuuuuuuuuuuuuffffff	chr10:112723900-112724122(+)$1	222	171	199	20.7938
=========vvvvvvvvvvvvv======	chr1:21069374-21069604(-)$1	230	48	76	22.9786
dddd"""cccuuuuuuuuuuuuccc333	chr4:100819617-100819841(-)$1	224	107	135	21.6051
dd"""cccxxxxxxxxxxxxxxxcccdd	chr14:69256025-69256255(-)$1	230	115	143	20.8892
ccc[eeeeettttttttttteeeeeccc	chr20:279837-280069(+)$1	232	161	189	18.7637
!ccc[ccc^^^^^^^^^^^^^^^^^^^^	chr9:36337483-36337708(-)$1	225	119	147	21.1680
eeeeeeeexxxxxxxxxxxxxxxeeeee	chr9:4706070-4706291(+)$1	221	167	195	20.0620
:ccc!!bbuuuuuuuuuuuubb22cccb	chr7:40134487-40134714(+)$1	227	33	61	19.2657
$$$$ddddvvvvvvvvvvvvvdddd]dd	chr7:38725527-38725749(+)$1	222	110	138	20.8752
ccc!!dddduuuuuuuuuuuudddd333	chr1:33323489-33323709(+)$1	220	187	215	22.1726
ccffffffxxxxxxxxxxxxxxxfffff	chr16:15960258-15960478(-)$1	220	34	62	20.0676
hhhhhhhhwwwwwwwwwwwwwwhhhhhh	chr17:26935127-26935357(-)$1	230	159	187	19.5443
dddd!!awwwwwwwwwwwwwwa22dddd	chr20:5095760-5095983(-)$1	223	0	28	20.8589
dddd[cccwwwwwwwwwwwwwwccc333	chr13:42896539-42896769(+)$1	230	197	225	23.4413
GGG:ddddwwwwwwwwwwwwwwddddgg	chr4:83344460-83344690(-)$1	230	48	76	19.9943
fff[dddd^^^^^^^^^^^^^^^^^^^^	chr6:82455786-82456011(-)$1	225	70	98	20.4841
ffffffyyyyyyyyyyyyyyyyffffff	chr11:77780194-77780424(-)$1	230	115	143	20.9816
ggggggg^^^^^^^^^^^^^^^^^^^^^	chr12:58142008-58142238(-)$1	230	62	90	20.8963
cc!!dddd^^^^^^^^^^^^^^^^^^dd	chr7:12393826-12394049(+)$1	223	102	130	20.4323
==[a[ccc^^^^^^^^^^^^^^^^^^^^	chr3:182839935-182840158(-)$1	223	164	192	21.4144
e!!bb[dddduuuuuuuuuuuuddddbb	chr6:136878559-136878784(-)$1	225	9	37	20.1756
:gggggggwwwwwwwwwwwwwwgggggg	chr4:119644410-119644637(-)$1	227	51	79	22.2562
]cccffffffuuuuuuuuuuuuffffff	chr1:36395036-36395266(+)$1	230	57	85	20.1152
b!!eeeee^^^^^^^^^^^^^^^^^^^^	chr8:55060151-55060381(+)$1	230	175	203	20.7954
!a!!ddddwwwwwwwwwwwwwwdddd22	chr5:65375198-65375420(+)$1	222	57	85	22.9404
ffff[cccwwwwwwwwwwwwwwccc]ff	chr8:61778449-61778679(+)$1	230	110	138	22.9966
"eeeee[bbvvvvvvvvvvvvvbbeeee	chr11:32617424-32617644(+)$1	220	21	49	21.0468
iiiiiiii^^^^^^^^^^^^^^^^^^ii	chr5:132212487-132212717(-)$1	230	58	86	20.8229
""ffffffuuuuuuuuuuuuffffff33	chr2:131907245-131907475(+)$1	230	152	180	20.7708
c####ddddvvvvvvvvvvvvvdddd44	chr1:33475198-33475425(-)$1	227	28	56	22.6013
c"""dddd^^^^^^^^^^^^^^^^^^^^	chrX:103347036-103347266(-)$1	230	76	104	21.1483
cc"""ccc^^^^^^^^^^^^^^^^^^^^	chr2:223436366-223436587(-)$1	221	24	52	21.4277
=====ccc^^^^^^^^^^^^^^^^^^^^	chr5:67593641-67593868(+)$1	227	24	52	21.4135
ddd[dddduuuuuuuuuuuudddddddd	chr3:170610692-170610918(-)$1	226	71	99	19.9390
iiiiiiiiitttttttttttiiiiiiii	chr12:12629555-12629782(-)$1	227	45	73	18.5136
DeeeeeyyyyyyyyyyyyyyyyeeeeeF	chr10:75557562-75557792(+)$1	230	34	62	20.1249
ccc!!cccwwwwwwwwwwwwwwccc22c	chr1:157091523-157091747(-)$1	224	102	130	23.5225
cc"""eeeeeuuuuuuuuuuuueeeee6	chr11:9746130-9746354(+)$1	224	135	163	21.3936
eeddddyyyyyyyyyyyyyyyydddd33	chr3:40351227-40351452(+)$1	225	93	121	21.3939
"ddddddddvvvvvvvvvvvvvdddd]d	chr13:41764757-41764987(-)$1	230	32	60	21.1968
:ggggggguuuuuuuuuuuugggggggb	chr21:45643003-45643228(-)$1	225	156	184	19.8644
bbffffffvvvvvvvvvvvvvffffff]	chr5:67522304-67522534(+)$1	230	96	124	20.6568
e"""dddd^^^^^^^^^^^^^^^^^^^^	chr19:11032455-11032685(+)$1	230	132	160	21.0128
CCffffffwwwwwwwwwwwwwwffffff	chr4:41270015-41270245(+)$1	230	82	110	20.1269
iiiiiiiiuuuuuuuuuuuuiiiiiiii	chr1:224348923-224349153(+)$1	230	8	36	20.9597
==========ttttttttttt=======	chr18:9400973-9401203(+)$1	230	63	91	19.5959
g[gggggggvvvvvvvvvvvvvgggggg	chr14:35871068-35871288(-)$1	220	124	152	22.1732

#otherMatches

#Seq PSSM
AUGUGUAGCAUAUCAGCAAUAACUACAU	chr9:114696712-114696937(+)$1	225	109	137	23.2520
UUCAAAUUGCACACGUCACUCCAGCAUC	chr1:214510011-214510234(+)$1	223	180	208	19.7711
GAUACUUGAAUAAUCAAUCUCUACUAGG	chr10:27486075-27486321(-)$1	246	160	188	22.5984
CCAUUGUUUUACCUCACCUUUGACUUUG	chr15:52675228-52675455(-)$1	227	2	30	22.2600
GGACUAGUGCAUAUUUCAGACAACUGCU	chr16:71764873-71765094(-)$1	221	11	39	22.4696
auauauauaauuuaauaguauaaaaaau	chr8:133024910-133025140(+)$1	230	81	109	21.1334
GCUUGAUAGAGAUAACAAUAAACUAUUG	chr2:133430387-133430612(-)$1	225	89	117	21.7532
UUUCUCUUCCACUUCCAAUUAUGAAGAG	chr11:108344774-108345004(-)$1	230	157	185	22.9786
AUUAGGAAUAUGACCAUUUGACUGUUCA	chr5:86687060-86687284(+)$1	224	93	121	20.7719
UCUUGAUCUCUCUUGUCCUCUUCUGCUC	chr11:57585554-57585784(+)$1	230	74	102	21.2962
GCACUUAAGAAAUCAUCCCAGCUAAGUU	chr6:30568718-30568948(-)$1	230	30	58	20.1605
CUGAAUGCCUGCCUUCAAUCCUGGCCAA	chr4:77956266-77956496(+)$1	230	29	57	21.9660
UCCAGUAAAGCCAGCUUUUCUUAUUAUU	chr2:105964213-105964440(+)$1	227	122	150	21.6668
AUUUUGGAAAAUGUGAUAAAAACAAGGU	chr2:61749698-61749921(-)$1	223	118	146	20.9816
GUGCUAGUAUUUCUGUGACUGUUAGUGG	chr16:69735961-69736186(+)$1	225	24	52	20.7531
cucuuguauuuucuguauuuuaugucug	chr5:110465158-110465393(+)$1	235	134	162	20.3821
CAGCUUUAAAACAGUACUUUAAAAGGAA	chr15:38782561-38782791(-)$1	230	127	155	20.4499
AGUUGAAAAAGCACAUCUAGAAUUCAGC	chr3:122133197-122133419(-)$1	222	186	214	20.6083
uugucccucuuccucuuucuuuccguuu	chr19:15533693-15533919(-)$1	226	97	125	20.7086
GGGAAUGUGUUUAACCCUUUCUGCGUUC	chr17:17748075-17748296(-)$1	221	162	190	20.4036
UAUUUAAGUAUCUUUUAUUUUUUAAUUU	chr6:139225990-139226213(-)$1	223	154	182	21.7893
AGAGUGUACCUUUUGCCAUAACCUAUUU	chr1:231700792-231701022(+)$1	230	139	167	21.3296
CUGCUUGAUAAAAUUCUAAAAAUAUCUG	chr1:12571859-12572089(+)$1	230	92	120	21.1653
UUGUAGCAGAUGAAUCCCAAAACAUGCA	chr16:24815986-24816216(+)$1	230	46	74	22.5289
AAAAUAAAAGGAGUUCAUGUAGUUUUUG	chr10:112723900-112724122(+)$1	222	171	199	20.7938
UAGUAUUGUGAAGUUGUGUUAAAUAGUA	chr1:21069374-21069604(-)$1	230	48	76	22.9786
UGCAUAUACACACAAACAUUAUUGUCCU	chr4:100819617-100819841(-)$1	224	107	135	21.6051
GUUAAGCUCAACCCCUUUCCCCCAGCAC	chr14:69256025-69256255(-)$1	230	115	143	20.8892
caguguuguuagaaguguauauaaucug	chr20:279837-280069(+)$1	232	161	189	18.7637
UAUAUCUGUACAGAUCUAACACUACGAC	chr9:36337483-36337708(-)$1	225	119	147	21.1680
UACUGAAAUGUUUUGUAAAUUUUUUUUA	chr9:4706070-4706291(+)$1	221	167	195	20.0620
ACAGGGGACAUAUUAGCACAUCAACUGG	chr7:40134487-40134714(+)$1	227	33	61	19.2657
UCUCGGCGUCCUCUUACCACUCGCUUGG	chr7:38725527-38725749(+)$1	222	110	138	20.8752
CCAUAGCAUAGUUAAAAUUAAAUGUAGU	chr1:33323489-33323709(+)$1	220	187	215	22.1726
UUGUUUGGGCUCCGAAACUCUUACCAAA	chr16:15960258-15960478(-)$1	220	34	62	20.0676
uagaccauuuagagcccaauuugugguc	chr17:26935127-26935357(-)$1	230	159	187	19.5443
GGGACACUUAAAAUACUACUUGGCUCCC	chr20:5095760-5095983(-)$1	223	0	28	20.8589
UCACCAGCACAAGAGAAUUAGAGCUUCA	chr13:42896539-42896769(+)$1	230	197	225	23.4413
UCCUGGGCUAUCACAUUAUAAUGCUCUU	chr4:83344460-83344690(-)$1	230	48	76	19.9943
UGUUAGGUGAAACCAAAAAGCCAAAAAA	chr6:82455786-82456011(-)$1	225	70	98	20.4841
GGUGCAAUUAGAAGCAAAAGACUGUACC	chr11:77780194-77780424(-)$1	230	115	143	20.9816
GCCUUAAUGACAUUCCCCUCCCACCUCU	chr12:58142008-58142238(-)$1	230	62	90	20.8963
UUAACUGCAGCAAAAAAAAUCUCAUAGC	chr7:12393826-12394049(+)$1	223	102	130	20.4323
CAUGUCAUUUAUUUUUUAUGAUUCAUUU	chr3:182839935-182840158(-)$1	223	164	192	21.4144
UACUCAUGUUAAAAAAAAAAAAAACAGA	chr6:136878559-136878784(-)$1	225	9	37	20.1756
AGUUUUGAUUUCUUGCUCAUUUUCAGAA	chr4:119644410-119644637(-)$1	227	51	79	22.2562
CAGAGGGGUUGAGGAUAUAAAAGACCCU	chr1:36395036-36395266(+)$1	230	57	85	20.1152
CUGAAGGAUCUAUAUUCCCUUAUUGCAU	chr8:55060151-55060381(+)$1	230	175	203	20.7954
Cauuuaaaucuaauuuauaauuuuuauu	chr5:65375198-65375420(+)$1	222	57	85	22.9404
AGUUAAUGUUCAUACCUAGUUUUAUAAG	chr8:61778449-61778679(+)$1	230	110	138	22.9966
uagaauaucuuacaauaAAUCUGAAUUC	chr11:32617424-32617644(+)$1	220	21	49	21.0468
UUCAGUAAAACUAAUAGAAGAGAUAAUU	chr5:132212487-132212717(-)$1	230	58	86	20.8229
UAAAGCAUUAACCUUAAAGCAUGUUUCA	chr2:131907245-131907475(+)$1	230	152	180	20.7708
GUAUGUGCAUAUGAGAUAAGCCUGCAAC	chr1:33475198-33475425(-)$1	227	28	56	22.6013
auaaugaugcugcuacugauaauaauaa	chrX:103347036-103347266(-)$1	230	76	104	21.1483
UUCCCAGGUGUCCCUUUCUCCUCCCCUA	chr2:223436366-223436587(-)$1	221	24	52	21.4277
CUUUGGUUUAAUUUAAAGCCACAACCAC	chr5:67593641-67593868(+)$1	227	24	52	21.4135
CUGUGUUUUAGUUAGAUGAUAAACCAGG	chr3:170610692-170610918(-)$1	226	71	99	19.9390
AAUUUUUUUUUCUUGUUCACAAAAAAAU	chr12:12629555-12629782(-)$1	227	45	73	18.5136
GCAGCUGCACACUUCUACUUCGAGCUGG	chr10:75557562-75557792(+)$1	230	34	62	20.1249
UUAAACCCAACUCACUAACACAGGGAAU	chr1:157091523-157091747(-)$1	224	102	130	23.5225
UUGAACAUUAUAAAAUCAACUUUGAUGA	chr11:9746130-9746354(+)$1	224	135	163	21.3936
GAAGCGUUUUCUUAUUUAUUUCCGUUUU	chr3:40351227-40351452(+)$1	225	93	121	21.3939
UAUAUGUUCUGUGUUUCUCUGUGAACAA	chr13:41764757-41764987(-)$1	230	32	60	21.1968
AUGAGGGCCCUUCCCAACCCGCCCUCAG	chr21:45643003-45643228(-)$1	225	156	184	19.8644
AGGAAUUCUAACACAUUCUCUGAAUUCA	chr5:67522304-67522534(+)$1	230	96	124	20.6568
UGCCGCCGUCCCCACCCUAACCCCCACC	chr19:11032455-11032685(+)$1	230	132	160	21.0128
UGGGAGGGACUUUGCUGAUUUCCCCUCU	chr4:41270015-41270245(+)$1	230	82	110	20.1269
CauuauauaauuuuaauuuaauGUAAUG	chr1:224348923-224349153(+)$1	230	8	36	20.9597
AUUUGUAAUAUUAUGAUCAACUGUUAUA	chr18:9400973-9401203(+)$1	230	63	91	19.5959
UAUUUUUCUAAAAAAAGAAAAAAGAAGA	chr14:35871068-35871288(-)$1	220	124	152	22.1732

#DB
((((((((..............))))))	chr9:114696712-114696937(+)$1	1	109	137	23.2520
)))))))(((.............)))..	chr1:214510011-214510234(+)$1	1	180	208	19.7711
...(((((................))))	chr10:27486075-27486321(-)$1	1	160	188	22.5984
(((..(((.............)))..))	chr15:52675228-52675455(-)$1	1	2	30	22.2600
(((.((((..............)))).)	chr16:71764873-71765094(-)$1	1	11	39	22.4696
((((((((....................	chr8:133024910-133025140(+)$1	1	81	109	21.1334
((..(((((.............))))))	chr2:133430387-133430612(-)$1	1	89	117	21.7532
(((((((((.............))))))	chr11:108344774-108345004(-)$1	1	157	185	22.9786
((((.(((((............))))).	chr5:86687060-86687284(+)$1	1	93	121	20.7719
....((.(................).))	chr11:57585554-57585784(+)$1	1	74	102	21.2962
(.(((((...............))))).	chr6:30568718-30568948(-)$1	1	30	58	20.1605
((....(((.............)))..)	chr4:77956266-77956496(+)$1	1	29	57	21.9660
((((((((...............)))))	chr2:105964213-105964440(+)$1	1	122	150	21.6668
((((((................))))))	chr2:61749698-61749921(-)$1	1	118	146	20.9816
((((((.((.............)).)))	chr16:69735961-69736186(+)$1	1	24	52	20.7531
..((((((....................	chr5:110465158-110465393(+)$1	1	134	162	20.3821
..(((((....................)	chr15:38782561-38782791(-)$1	1	127	155	20.4499
(((((((...............))))))	chr3:122133197-122133419(-)$1	1	186	214	20.6083
((((.(((....................	chr19:15533693-15533919(-)$1	1	97	125	20.7086
..((((((..............))))))	chr17:17748075-17748296(-)$1	1	162	190	20.4036
...(((((............)))))...	chr6:139225990-139226213(-)$1	1	154	182	21.7893
((((.(((....................	chr1:231700792-231701022(+)$1	1	139	167	21.3296
..(((.((((............)))).)	chr1:12571859-12572089(+)$1	1	92	120	21.1653
(....(((................))).	chr16:24815986-24816216(+)$1	1	46	74	22.5289
(...((((((............))))))	chr10:112723900-112724122(+)$1	1	171	199	20.7938
(((((((((.............))))))	chr1:21069374-21069604(-)$1	1	48	76	22.9786
((((...(((............)))...	chr4:100819617-100819841(-)$1	1	107	135	21.6051
((...(((...............)))))	chr14:69256025-69256255(-)$1	1	115	143	20.8892
(((.(((((...........))))))))	chr20:279837-280069(+)$1	1	161	189	18.7637
.(((.(((....................	chr9:36337483-36337708(-)$1	1	119	147	21.1680
((((((((...............)))))	chr9:4706070-4706291(+)$1	1	167	195	20.0620
.(((..((............))..)))(	chr7:40134487-40134714(+)$1	1	33	61	19.2657
....((((.............)))).))	chr7:38725527-38725749(+)$1	1	110	138	20.8752
(((..((((............))))...	chr1:33323489-33323709(+)$1	1	187	215	22.1726
))((((((...............)))))	chr16:15960258-15960478(-)$1	1	34	62	20.0676
((((((((..............))))))	chr17:26935127-26935357(-)$1	1	159	187	19.5443
((((..(..............)..))))	chr20:5095760-5095983(-)$1	1	0	28	20.8589
((((.(((..............)))...	chr13:42896539-42896769(+)$1	1	197	225	23.4413
(((.((((..............))))((	chr4:83344460-83344690(-)$1	1	48	76	19.9943
(((.((((....................	chr6:82455786-82456011(-)$1	1	70	98	20.4841
((((((................))))))	chr11:77780194-77780424(-)$1	1	115	143	20.9816
(((((((.....................	chr12:58142008-58142238(-)$1	1	62	90	20.8963
((..((((..................))	chr7:12393826-12394049(+)$1	1	102	130	20.4323
((.(.(((....................	chr3:182839935-182840158(-)$1	1	164	192	21.4144
(..((.((((............))))))	chr6:136878559-136878784(-)$1	1	9	37	20.1756
.(((((((..............))))))	chr4:119644410-119644637(-)$1	1	51	79	22.2562
.)))((((((............))))))	chr1:36395036-36395266(+)$1	1	57	85	20.1152
(..(((((....................	chr8:55060151-55060381(+)$1	1	175	203	20.7954
.(..((((..............))))..	chr5:65375198-65375420(+)$1	1	57	85	22.9404
((((.(((..............))).))	chr8:61778449-61778679(+)$1	1	110	138	22.9966
.(((((.((.............))))))	chr11:32617424-32617644(+)$1	1	21	49	21.0468
((((((((..................))	chr5:132212487-132212717(-)$1	1	58	86	20.8229
..((((((............))))))..	chr2:131907245-131907475(+)$1	1	152	180	20.7708
(....((((.............))))..	chr1:33475198-33475425(-)$1	1	28	56	22.6013
(...((((....................	chrX:103347036-103347266(-)$1	1	76	104	21.1483
((...(((....................	chr2:223436366-223436587(-)$1	1	24	52	21.4277
((((((((....................	chr5:67593641-67593868(+)$1	1	24	52	21.4135
(((.((((............))))))))	chr3:170610692-170610918(-)$1	1	71	99	19.9390
(((((((((...........))))))))	chr12:12629555-12629782(-)$1	1	45	73	18.5136
((((((................)))))(	chr10:75557562-75557792(+)$1	1	34	62	20.1249
(((..(((..............)))..)	chr1:157091523-157091747(-)$1	1	102	130	23.5225
((...(((((............))))).	chr11:9746130-9746354(+)$1	1	135	163	21.3936
((((((................))))..	chr3:40351227-40351452(+)$1	1	93	121	21.3939
.((((((((.............)))).)	chr13:41764757-41764987(-)$1	1	32	60	21.1968
.(((((((............)))))))(	chr21:45643003-45643228(-)$1	1	156	184	19.8644
((((((((.............)))))).	chr5:67522304-67522534(+)$1	1	96	124	20.6568
(...((((....................	chr19:11032455-11032685(+)$1	1	132	160	21.0128
))((((((..............))))))	chr4:41270015-41270245(+)$1	1	82	110	20.1269
((((((((............))))))))	chr1:224348923-224349153(+)$1	1	8	36	20.9597
((((((((((...........)))))))	chr18:9400973-9401203(+)$1	1	63	91	19.5959
(.(((((((.............))))))	chr14:35871068-35871288(-)$1	1	124	152	22.1732

#PSSM
c : 0.14	e : 0.11	i : 0.08	= : 0.08	f : 0.08	" : 0.07	b : 0.07	d : 0.07	g : 0.05	! : 0.05	: : 0.05	$ : 0.02	# : 0.01	h : 0.01	G : 0.01	] : 0.01	D : 0.01	C : 0.01	
c : 0.15	i : 0.08	" : 0.08	e : 0.08	= : 0.08	f : 0.08	d : 0.08	g : 0.07	! : 0.05	b : 0.04	# : 0.04	$ : 0.02	[ : 0.02	: : 0.01	h : 0.01	G : 0.01	a : 0.01	C : 0.01	
f : 0.15	" : 0.11	c : 0.11	e : 0.09	i : 0.08	g : 0.08	d : 0.08	! : 0.07	= : 0.07	# : 0.04	$ : 0.02	a : 0.01	h : 0.01	G : 0.01	[ : 0.01	
f : 0.14	e : 0.12	i : 0.08	g : 0.08	! : 0.08	" : 0.08	= : 0.07	c : 0.07	d : 0.07	[ : 0.05	# : 0.04	$ : 0.02	h : 0.01	: : 0.01	a : 0.01	b : 0.01	
d : 0.15	e : 0.14	f : 0.14	[ : 0.09	g : 0.08	i : 0.07	! : 0.07	= : 0.07	" : 0.05	# : 0.04	b : 0.02	c : 0.02	h : 0.01	
c : 0.18	d : 0.18	e : 0.16	f : 0.14	g : 0.08	i : 0.07	= : 0.05	[ : 0.02	! : 0.02	b : 0.01	# : 0.01	" : 0.01	h : 0.01	
d : 0.19	c : 0.18	e : 0.14	f : 0.09	g : 0.08	i : 0.07	= : 0.05	y : 0.05	[ : 0.04	b : 0.02	" : 0.01	h : 0.01	a : 0.01	
c : 0.21	d : 0.19	e : 0.11	f : 0.09	i : 0.07	= : 0.05	y : 0.05	b : 0.05	g : 0.04	x : 0.02	^ : 0.02	a : 0.01	h : 0.01	w : 0.01	
^ : 0.22	w : 0.16	y : 0.09	x : 0.08	u : 0.08	d : 0.07	e : 0.05	c : 0.04	v : 0.04	= : 0.04	b : 0.02	f : 0.02	i : 0.01	g : 0.01	
^ : 0.22	w : 0.16	v : 0.16	y : 0.09	u : 0.09	x : 0.08	c : 0.02	e : 0.02	d : 0.02	f : 0.02	t : 0.02	= : 0.01	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	u : 0.19	v : 0.18	w : 0.16	y : 0.09	x : 0.08	t : 0.04	
^ : 0.22	v : 0.18	w : 0.16	u : 0.11	y : 0.09	x : 0.08	e : 0.02	i : 0.02	b : 0.01	f : 0.01	d : 0.01	g : 0.01	t : 0.01	
^ : 0.22	w : 0.15	v : 0.14	y : 0.09	u : 0.09	x : 0.08	d : 0.04	e : 0.02	f : 0.02	i : 0.02	c : 0.01	b : 0.01	a : 0.01	g : 0.01	= : 0.01	
^ : 0.22	d : 0.15	f : 0.11	e : 0.09	c : 0.08	x : 0.05	g : 0.05	i : 0.04	y : 0.04	= : 0.04	b : 0.02	2 : 0.02	v : 0.01	h : 0.01	
^ : 0.22	d : 0.15	f : 0.12	c : 0.11	e : 0.11	= : 0.05	g : 0.05	i : 0.04	y : 0.04	b : 0.02	2 : 0.02	h : 0.01	
^ : 0.22	d : 0.16	e : 0.14	c : 0.12	f : 0.12	= : 0.05	g : 0.05	i : 0.04	2 : 0.01	a : 0.01	] : 0.01	h : 0.01	
^ : 0.22	d : 0.14	f : 0.14	e : 0.11	c : 0.07	= : 0.05	g : 0.05	3 : 0.05	i : 0.04	2 : 0.04	] : 0.04	h : 0.01	
^ : 0.19	f : 0.14	e : 0.11	3 : 0.08	g : 0.07	d : 0.07	i : 0.05	c : 0.05	= : 0.05	] : 0.04	2 : 0.04	b : 0.02	: : 0.01	h : 0.01	4 : 0.01	
^ : 0.18	f : 0.12	b : 0.08	3 : 0.08	d : 0.08	e : 0.07	i : 0.05	c : 0.05	= : 0.05	g : 0.05	2 : 0.02	] : 0.02	: : 0.01	5 : 0.01	h : 0.01	4 : 0.01	F : 0.01	6 : 0.01	

#score	1498.85544626821
#seq	71
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_CDS_m2_run2.txt

#BEAR
gggggg[cccooooooccc]ggggggg	chr16:2011411-2011636(+)$1	225	168	195	12.6062
eeeee"""cccnnnnnccc]eeeeeee	chr2:43453323-43453548(-)$1	225	87	114	13.6531
gggggg!!cccnnnnnccc]ggggggg	chr19:38229649-38229874(-)$1	225	39	66	14.3644
gggg####cccnnnnnccc4444gggg	chr14:102552054-102552281(-)$1	227	149	176	15.9498
$$eeeee[cccooooooccc]eeeee4	chr12:29524434-29524666(-)$1	232	124	151	10.4459
ggg[ccc[bboooooobb]ccc]gggg	chr16:30006823-30007046(-)$1	223	135	162	10.6718
ffccc"""cccmmmmccc]ccc]ffff	chr5:137522768-137523004(+)$1	236	197	224	10.7202
eee[bb"""cccmmmmccc333bb]ee	chr3:58303327-58303549(+)$1	222	128	155	10.8338
iiiii!!ddddllldddd4444iiiii	chr10:6157338-6157563(+)$1	225	71	98	9.8822
ff[bb"""cccmmmmccc4444bb]ff	chr16:75338928-75339162(-)$1	234	101	128	11.2889
ccc$$$$$cccmmmmccc4444ccccc	chr1:151664904-151665143(+)$1	239	32	59	11.0526
!!ccc"""bboooooobb4444ccc22	chr19:50285184-50285405(+)$1	221	49	76	12.9827
ccc####cccooooooccc333ccc]d	chr3:196612253-196612478(+)$1	225	136	163	13.9132
Eccc[bb[cccnnnnncccbb]cccdd	chrX:30873086-30873309(-)$1	223	15	42	10.8139
a!!ddddcccooooooccc333dddd2	chr17:38567332-38567558(-)$1	226	90	117	11.1766
ee"""bb[cccnnnnnccc]bb]eeee	chr2:101883117-101883341(+)$1	224	154	181	12.2094
dddd####cccnnnnncccdddd22cc	chr17:15928238-15928468(+)$1	230	77	104	12.3925
eeee"""bbbboooooobb]bb4444e	chr19:12790915-12791155(-)$1	240	28	55	10.4056
gggggg[a[bbnnnnnbbaggggggg:	chr19:40827715-40827956(-)$1	241	103	130	10.6778
ggggg"""cccmmmmccc333gggggg	chr20:2442275-2442531(-)$1	256	219	246	12.9082
"""bb####bboooooobb4444bb44	chr2:178095798-178096043(-)$1	245	13	40	11.8643
eeee####bboooooobb4444eeeee	chrX:44928883-44929115(+)$1	232	68	95	12.4393
fffccc!!ccc[aooooooa]cccccc	chr6:27860470-27860700(-)$1	230	27	54	9.9594
ffffff[cccoooooocccffffffcc	chr2:160615672-160615916(+)$1	244	180	207	10.5733
iiii####cccnnnnnccc22iiiiii	chr15:91419387-91419610(+)$1	223	53	80	15.3068
fffff!!ddddnnnnndddd22fffff	chr7:99697104-99697342(-)$1	238	39	66	10.5229
gggg"""ddddnnnnnddddggggggg	chr21:33043650-33043882(-)$1	232	203	230	11.8548
!!gggggggcccmmmmccc]ggggggg	chr5:33455041-33455276(+)$1	235	162	189	9.8849
========[aooooooa==========	chr21:34931483-34931708(+)$1	225	121	148	11.7887
:ffffffacccnnnnnccc]a]fffff	chr11:65623351-65623611(-)$1	260	3	30	11.1729
!!bb[bb[cccnnnnnccc]bb]bb]d	chr11:64889724-64889944(+)$1	220	176	203	11.7822
gggggg"""bbnnnnnbb333gggggg	chr21:34907481-34907711(-)$1	230	123	150	13.9907
fffff"""cccooooooccc333ffff	chrX:135055697-135055917(-)$1	220	111	138	13.7734
[dddd"""cccnnnnnccc333dddde	chr3:101474266-101474486(+)$1	220	188	215	14.5097
gggg####cccooooooccc>>>>>>>	chr1:36751977-36752202(+)$1	225	15	42	12.5923
e"""ccc[cccnnnnnccc]ccc6666	chr17:57247083-57247336(+)$1	253	141	168	11.2176
ggggg"""cccnnnnnccc333ggggg	chr3:196528794-196529012(+)$1	218	105	132	16.3562
gccc####cccooooooccc4444ccc	chr1:231501988-231502264(-)$1	276	79	106	13.9418
iiiiiiiii[annnnna]iiiiiiiii	chr3:47868826-47869061(+)$1	235	180	207	11.4024
::ccc"""cccnnnnnccc333ccc:h	chr15:89169381-89169613(+)$1	232	104	131	12.6264
[ffffff!!bboooooobb22ffffff	chrX:17767420-17767645(+)$1	225	70	97	10.1120
dd[ccc!!cccnnnnnccc22ccc]dd	chr1:36521142-36521448(+)$1	306	239	266	13.5235
ii!!ccc!!bbnnnnnbb22ccciiii	chr21:34924424-34924685(+)$1	261	116	143	11.7164
!dddd!!ccc[aooooooa]ccc>>>>	chr10:101715380-101715606(-)$1	226	62	89	9.7989
eeeee####bbnnnnnbb333eeeee3	chr6:83963262-83963482(-)$1	220	77	104	13.0135
##bb"""cccooooooccc4444bb]g	chr19:41811565-41811786(+)$1	221	180	207	13.0537
eeee[bb[cccnnnnncccbb22eeee	chr12:49443628-49443865(-)$1	237	30	57	11.3429
gggggg!!cccnnnnnccc]ggggggg	chr19:37130011-37130245(-)$1	234	131	158	14.3644
)))ccc!!cccnnnnnccc22ccc333	chr15:66169699-66169931(+)$1	232	57	84	12.7990
ggggg"""ddddooooooddddggggg	chr20:4766837-4767065(-)$1	228	175	202	10.3493
cccbb"""cccmmmmccc333bb]ccc	chr11:60665512-60665749(-)$1	237	67	94	11.2785
##eeeee[cccnnnnnccceeeee]ee	chr12:68052262-68052504(+)$1	242	201	228	11.3918
========cccnnnnnccc]=======	chr17:61684581-61684805(+)$1	224	67	94	14.1356

#otherMatches

#Seq PSSM
AACUGUAUCAAGGAAGUGGAGCAGUUC	chr16:2011411-2011636(+)$1	225	168	195	12.6062
CAGAAACAUGUCGACCACACUUCUGUC	chr2:43453323-43453548(-)$1	225	87	114	13.6531
UUCAUACUGGUAUGAAACCCUAUGAAU	chr19:38229649-38229874(-)$1	225	39	66	14.3644
CUCAGCAGGGGGAUCAUUCACAGUGAG	chr14:102552054-102552281(-)$1	227	149	176	15.9498
ACUUUAAGUUUGGUAAAAGAGUUGGAU	chr12:29524434-29524666(-)$1	232	124	151	10.4459
GAGAUGCAGGAGUUCACCCGUAGCUUC	chr16:30006823-30007046(-)$1	223	135	162	10.6718
AGAAACCAUUCCUUCGAAAUUUACUUC	chr5:137522768-137523004(+)$1	236	197	224	10.7202
GAGACCGCGCUGAACUUAGGAGGGCCU	chr3:58303327-58303549(+)$1	222	128	155	10.8338
UUUCAGCGGUUGUUGACUUGAAUGGGA	chr10:6157338-6157563(+)$1	225	71	98	9.8822
AUGAGCAGCCUUUUGGGGAAAAUUGGU	chr16:75338928-75339162(-)$1	234	101	128	11.2889
GGGCUACAAUGAAAUCAUCUUUCCCCA	chr1:151664904-151665143(+)$1	239	32	59	11.0526
AAAAAUAUGUGUGUAAACUGCUUUUCA	chr19:50285184-50285405(+)$1	221	49	76	12.9827
GACUCCAAGCAGAGAAGCUGUUGUCAU	chr3:196612253-196612478(+)$1	225	136	163	13.9132
UGCAAACAGGAAUGAAUCCGUCUGCUA	chrX:30873086-30873309(-)$1	223	15	42	10.8139
GCCUUAAUUGAAAACCCAACCUUUGAC	chr17:38567332-38567558(-)$1	226	90	117	11.1766
AGAUCACUGAGUAUUUCUCUGUCCUGG	chr2:101883117-101883341(+)$1	224	154	181	12.2094
CUCUUUUCUCCUUAGUGGAAGAGAAAG	chr17:15928238-15928468(+)$1	230	77	104	12.3925
CUGGAACCACUGUCACAGGAUGAAGAC	chr19:12790915-12791155(-)$1	240	28	55	10.4056
GUGCCCAGAUGGACCACGCGGGCACUG	chr19:40827715-40827956(-)$1	241	103	130	10.6778
AUAAUAAACUCUUAAGAGAACAUUAUA	chr20:2442275-2442531(-)$1	256	219	246	12.9082
CUGGUCAUCGGAAAACCCCAUUCACAA	chr2:178095798-178096043(-)$1	245	13	40	11.8643
CCUGCCUAGCAAUUCAGUAACACAGGG	chrX:44928883-44929115(+)$1	232	68	95	12.4393
GCUGGCCAUCCGCAACGACGAGGAGCU	chr6:27860470-27860700(-)$1	230	27	54	9.9594
AUAUUUUGCCUAAUUUGGUAAGUGUCU	chr2:160615672-160615916(+)$1	244	180	207	10.5733
CUGACAGAUGGAAAGCCCAGCUCAGUC	chr15:91419387-91419610(+)$1	223	53	80	15.3068
UGGUGGACUCAAUUUGUGAGAAUGCCA	chr7:99697104-99697342(-)$1	238	39	66	10.5229
CUUCCUGGAGUGUAGAGCUUGAGGUGU	chr21:33043650-33043882(-)$1	232	203	230	11.8548
UCAAUGACUAUGGAUCCAUAAGUUAUU	chr5:33455041-33455276(+)$1	235	162	189	9.8849
GAAGAGGAAGAAGAACCUCCUUUUUAU	chr21:34931483-34931708(+)$1	225	121	148	11.7887
CUCUUCUGCCUGAGUGAGGACAAGAAG	chr11:65623351-65623611(-)$1	260	3	30	11.1729
GAGCGCUGAGCGAGGAGCUGAGGGCAU	chr11:64889724-64889944(+)$1	220	176	203	11.7822
UGCAAAGAGAAGAAAAUUGAAUUUGUA	chr21:34907481-34907711(-)$1	230	123	150	13.9907
UGGGCAUCGGUCUCUUUGCCCUAGCCC	chrX:135055697-135055917(-)$1	220	111	138	13.7734
CUAACAACUGAUGAAUUCACAAGUUAA	chr3:101474266-101474486(+)$1	220	188	215	14.5097
UUCUCCAGCUCAUAACAGAGAAAGAAA	chr1:36751977-36752202(+)$1	225	15	42	12.5923
CCACCCUCACCAGAAAGGUAAGGCUUA	chr17:57247083-57247336(+)$1	253	141	168	11.2176
UAAGUUAACCUAGUUCGGGCCCAUUUA	chr3:196528794-196529012(+)$1	218	105	132	16.3562
CAGAUUCGGUCGGUAAAGACGUCUUCU	chr1:231501988-231502264(-)$1	276	79	106	13.9418
CAGAAAGGAGGCUGUUUGUCCUUUCUG	chr3:47868826-47869061(+)$1	235	180	207	11.4024
UCCCUCACCAUCCCAAAUGCCAAGGAU	chr15:89169381-89169613(+)$1	232	104	131	12.6264
AAUUAUAUGACUACAUUGUAUUAUAAU	chrX:17767420-17767645(+)$1	225	70	97	10.1120
AAGAUGAAUUGACAUACAACGUAUGUU	chr1:36521142-36521448(+)$1	306	239	266	13.5235
UCCUAUGCUGCAGAACGUUCCAUGAUG	chr21:34924424-34924685(+)$1	261	116	143	11.7164
UUGGCAGGGCCCGGCACAGAGCCAGAU	chr10:101715380-101715606(-)$1	226	62	89	9.7989
UUUCGUCUCCUGAACAAGUAUCGAAAC	chr6:83963262-83963482(-)$1	220	77	104	13.0135
CAGCCCAGCUAUAACCAGUAUCAGCAG	chr19:41811565-41811786(+)$1	221	180	207	13.0537
GCUCACCAUGUGAAGAACAGGAAGAGC	chr12:49443628-49443865(-)$1	237	30	57	11.3429
UUCAUACUGGUGAGAAACCCUAUGAAU	chr19:37130011-37130245(-)$1	234	131	158	14.3644
CCAUUGGAGUAGAGUUUGCAACAAGAA	chr15:66169699-66169931(+)$1	232	57	84	12.7990
AAGCUGAUGCGCAAGUAAGUGUGGCUU	chr20:4766837-4767065(-)$1	228	175	202	10.3493
CUGAGAAUGGUUACUACCUGGCUACAG	chr11:60665512-60665749(-)$1	237	67	94	11.2785
AGGACAGUGUUGCCAAAACUUGUUAGC	chr12:68052262-68052504(+)$1	242	201	228	11.3918
GAGUGAUGGCUGUAGGAGCUCGUCACU	chr17:61684581-61684805(+)$1	224	67	94	14.1356

#DB
((((((.(((......))).)))))))	chr16:2011411-2011636(+)$1	1	168	195	12.6062
(((((...(((.....))).)))))))	chr2:43453323-43453548(-)$1	1	87	114	13.6531
((((((..(((.....))).)))))))	chr19:38229649-38229874(-)$1	1	39	66	14.3644
((((....(((.....)))....))))	chr14:102552054-102552281(-)$1	1	149	176	15.9498
..(((((.(((......))).))))).	chr12:29524434-29524666(-)$1	1	124	151	10.4459
(((.(((.((......)).))).))))	chr16:30006823-30007046(-)$1	1	135	162	10.6718
(((((...(((....))).))).))))	chr5:137522768-137523004(+)$1	1	197	224	10.7202
(((.((...(((....)))...)).))	chr3:58303327-58303549(+)$1	1	128	155	10.8338
(((((..((((...))))....)))))	chr10:6157338-6157563(+)$1	1	71	98	9.8822
((.((...(((....)))....)).))	chr16:75338928-75339162(-)$1	1	101	128	11.2889
(((.....(((....)))....)))))	chr1:151664904-151665143(+)$1	1	32	59	11.0526
..(((...((......))....)))..	chr19:50285184-50285405(+)$1	1	49	76	12.9827
(((....(((......)))...))).)	chr3:196612253-196612478(+)$1	1	136	163	13.9132
((((.((.(((.....))))).)))((	chrX:30873086-30873309(-)$1	1	15	42	10.8139
(..(((((((......)))...)))).	chr17:38567332-38567558(-)$1	1	90	117	11.1766
((...((.(((.....))).)).))))	chr2:101883117-101883341(+)$1	1	154	181	12.2094
((((....(((.....)))))))..))	chr17:15928238-15928468(+)$1	1	77	104	12.3925
((((...((((......)).))....)	chr19:12790915-12791155(-)$1	1	28	55	10.4056
((((((.(.((.....)))))))))).	chr19:40827715-40827956(-)$1	1	103	130	10.6778
(((((...(((....)))...))))))	chr20:2442275-2442531(-)$1	1	219	246	12.9082
...((....((......))....))..	chr2:178095798-178096043(-)$1	1	13	40	11.8643
((((....((......))....)))))	chrX:44928883-44929115(+)$1	1	68	95	12.4393
((((((..(((.(......).))))))	chr6:27860470-27860700(-)$1	1	27	54	9.9594
((((((.(((......)))))))))))	chr2:160615672-160615916(+)$1	1	180	207	10.5733
((((....(((.....)))..))))))	chr15:91419387-91419610(+)$1	1	53	80	15.3068
(((((..((((.....))))..)))))	chr7:99697104-99697342(-)$1	1	39	66	10.5229
((((...((((.....)))))))))))	chr21:33043650-33043882(-)$1	1	203	230	11.8548
..((((((((((....))).)))))))	chr5:33455041-33455276(+)$1	1	162	189	9.8849
((((((((.(......)))))))))))	chr21:34931483-34931708(+)$1	1	121	148	11.7887
.((((((((((.....))).).)))))	chr11:65623351-65623611(-)$1	1	3	30	11.1729
..((.((.(((.....))).)).)).)	chr11:64889724-64889944(+)$1	1	176	203	11.7822
((((((...((.....))...))))))	chr21:34907481-34907711(-)$1	1	123	150	13.9907
(((((...(((......)))...))))	chrX:135055697-135055917(-)$1	1	111	138	13.7734
.((((...(((.....)))...)))))	chr3:101474266-101474486(+)$1	1	188	215	14.5097
((((....(((......))).......	chr1:36751977-36752202(+)$1	1	15	42	12.5923
(...(((.(((.....))).)))....	chr17:57247083-57247336(+)$1	1	141	168	11.2176
(((((...(((.....)))...)))))	chr3:196528794-196529012(+)$1	1	105	132	16.3562
)(((....(((......)))....)))	chr1:231501988-231502264(-)$1	1	79	106	13.9418
(((((((((.(.....).)))))))))	chr3:47868826-47869061(+)$1	1	180	207	11.4024
..(((...(((.....)))...))).(	chr15:89169381-89169613(+)$1	1	104	131	12.6264
.((((((..((......))..))))))	chrX:17767420-17767645(+)$1	1	70	97	10.1120
((.(((..(((.....)))..))).))	chr1:36521142-36521448(+)$1	1	239	266	13.5235
((..(((..((.....))..)))))))	chr21:34924424-34924685(+)$1	1	116	143	11.7164
.((((..(((.(......).)))....	chr10:101715380-101715606(-)$1	1	62	89	9.7989
(((((....((.....))...))))).	chr6:83963262-83963482(-)$1	1	77	104	13.0135
..((...(((......)))....)).)	chr19:41811565-41811786(+)$1	1	180	207	13.0537
((((.((.(((.....)))))..))))	chr12:49443628-49443865(-)$1	1	30	57	11.3429
((((((..(((.....))).)))))))	chr19:37130011-37130245(-)$1	1	131	158	14.3644
...(((..(((.....)))..)))...	chr15:66169699-66169931(+)$1	1	57	84	12.7990
(((((...((((......)))))))))	chr20:4766837-4767065(-)$1	1	175	202	10.3493
(((((...(((....)))...)).)))	chr11:60665512-60665749(-)$1	1	67	94	11.2785
..(((((.(((.....)))))))).))	chr12:68052262-68052504(+)$1	1	201	228	11.3918
(((((((((((.....))).)))))))	chr17:61684581-61684805(+)$1	1	67	94	14.1356

#PSSM
g : 0.24	e : 0.15	f : 0.11	i : 0.07	! : 0.07	c : 0.05	d : 0.03	= : 0.03	: : 0.03	[ : 0.03	# : 0.03	$ : 0.01	E : 0.01	a : 0.01	" : 0.01	) : 0.01	
g : 0.22	f : 0.15	e : 0.13	c : 0.09	i : 0.07	! : 0.07	d : 0.07	" : 0.03	= : 0.03	# : 0.03	$ : 0.01	: : 0.01	) : 0.01	
g : 0.24	e : 0.15	c : 0.15	f : 0.11	i : 0.05	" : 0.05	d : 0.05	[ : 0.03	! : 0.03	= : 0.03	b : 0.03	) : 0.01	
g : 0.22	c : 0.15	e : 0.13	b : 0.09	f : 0.09	d : 0.07	i : 0.05	[ : 0.03	" : 0.03	= : 0.03	$ : 0.01	# : 0.01	! : 0.01	
g : 0.16	c : 0.16	# : 0.13	f : 0.09	e : 0.07	b : 0.07	" : 0.07	[ : 0.05	d : 0.05	i : 0.03	= : 0.03	$ : 0.01	
" : 0.26	# : 0.16	g : 0.11	c : 0.11	b : 0.09	! : 0.05	f : 0.05	e : 0.03	= : 0.03	$ : 0.01	d : 0.01	i : 0.01	
" : 0.30	# : 0.16	! : 0.15	b : 0.07	[ : 0.05	c : 0.05	e : 0.03	= : 0.03	f : 0.03	$ : 0.01	d : 0.01	g : 0.01	i : 0.01	
" : 0.24	# : 0.15	[ : 0.15	! : 0.13	c : 0.11	d : 0.05	a : 0.03	= : 0.03	$ : 0.01	b : 0.01	g : 0.01	i : 0.01	
c : 0.66	b : 0.07	d : 0.07	" : 0.03	[ : 0.03	# : 0.03	! : 0.03	g : 0.01	i : 0.01	
c : 0.69	b : 0.18	d : 0.07	a : 0.01	[ : 0.01	
c : 0.58	o : 0.16	b : 0.13	d : 0.07	a : 0.01	[ : 0.01	
n : 0.49	o : 0.30	m : 0.09	c : 0.03	l : 0.01	[ : 0.01	a : 0.01	d : 0.01	
n : 0.49	o : 0.33	m : 0.13	l : 0.01	a : 0.01	
n : 0.49	o : 0.35	m : 0.13	l : 0.01	
n : 0.49	o : 0.35	m : 0.13	d : 0.01	
n : 0.49	o : 0.35	c : 0.09	m : 0.03	d : 0.01	
c : 0.58	o : 0.18	b : 0.13	d : 0.05	a : 0.03	
c : 0.66	b : 0.18	d : 0.05	o : 0.05	= : 0.01	] : 0.01	
c : 0.56	4 : 0.09	3 : 0.07	b : 0.05	d : 0.05	] : 0.03	a : 0.03	o : 0.01	= : 0.01	i : 0.01	2 : 0.01	
] : 0.22	3 : 0.18	4 : 0.15	c : 0.11	2 : 0.09	d : 0.07	b : 0.03	g : 0.01	a : 0.01	f : 0.01	= : 0.01	i : 0.01	e : 0.01	
3 : 0.20	4 : 0.16	g : 0.11	c : 0.09	b : 0.09	2 : 0.09	e : 0.03	] : 0.03	d : 0.03	= : 0.03	f : 0.01	a : 0.01	> : 0.01	i : 0.01	
4 : 0.16	g : 0.15	c : 0.15	3 : 0.13	e : 0.07	b : 0.07	] : 0.03	d : 0.03	f : 0.03	i : 0.03	2 : 0.03	= : 0.03	> : 0.01	
c : 0.20	g : 0.18	e : 0.09	4 : 0.09	] : 0.07	f : 0.07	b : 0.05	i : 0.05	d : 0.05	= : 0.03	3 : 0.01	> : 0.01	2 : 0.01	
g : 0.22	c : 0.15	e : 0.13	f : 0.11	b : 0.09	i : 0.07	d : 0.03	4 : 0.03	= : 0.03	> : 0.03	2 : 0.01	6 : 0.01	] : 0.01	
g : 0.22	c : 0.15	e : 0.11	f : 0.11	] : 0.07	i : 0.07	b : 0.05	d : 0.03	= : 0.03	> : 0.03	2 : 0.01	4 : 0.01	6 : 0.01	3 : 0.01	
g : 0.22	e : 0.15	f : 0.11	c : 0.11	i : 0.07	d : 0.07	] : 0.05	4 : 0.03	= : 0.03	> : 0.03	2 : 0.01	6 : 0.01	: : 0.01	3 : 0.01	
g : 0.22	e : 0.15	f : 0.11	c : 0.11	i : 0.07	d : 0.07	4 : 0.03	2 : 0.03	= : 0.03	> : 0.03	3 : 0.03	: : 0.01	6 : 0.01	h : 0.01	

#score	643.3911965894547
#seq	53
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_UTR_m3_run1.txt

#BEAR
b[ggggggg####cccqqqqqqqqcccggggggg]bb	chr6:111347107-111347331(+)$1	224	124	161	16.7422
GGGG::ffffffddddqqqqqqqqdddd333ffffff	chr2:103431440-103431676(+)$1	236	19	56	12.4724
ggg!!dddd!!eeeeebbqqqqqqqqbb]eeeee333	chr19:33871993-33872236(+)$1	243	65	102	11.5393
""bb[eeeee[a[cccrrrrrrrrrcccaeeeee333	chr16:20809281-20809521(-)$1	240	152	189	12.4065
ffffiiiiiiiiicccqqqqqqqqccc:fffffflll	chr17:42884695-42884918(-)$1	223	167	204	13.8565
[bb$$$$$ddddddddqqqqqqqqdddd]dddd22bb	chr2:153511744-153511979(-)$1	235	135	172	13.6558
!eeeee[iiiiiiiiiqqqqqqqqiiiiiiiiieeee	chr1:179814372-179814610(-)$1	238	190	227	15.3025
""ffffff####ddddpppppppdddd22ffffff22	chr6:89873446-89873673(+)$1	227	145	182	11.6918
iii[ccc$$$$$ddddqqqqqqqqdddd55555ccc]	chr8:28425494-28425717(+)$1	223	48	85	14.0455
ddddccc!!bb[ddddqqqqqqqqdddd]bb22cccB	chr10:63855628-63855859(+)$1	231	41	78	15.2570
ffffffdddda[cccrrrrrrrrrccc]a]dddd]ff	chr17:35875113-35875339(-)$1	226	104	141	12.3901
[ccc[a####ddddssssssssssdddd22acccccc	chr1:93811887-93812129(+)$1	242	142	179	13.0207
fff:eeeee"""ddddssssssssssdddd333eeee	chr9:72331682-72331910(-)$1	228	147	184	11.4739
fffff[eeeee[ddddqqqqqqqqdddd]eeeee444	chr14:96751459-96751683(-)$1	224	27	64	16.3842
fff[ffffff####ddddoooooodddd]ffffff]f	chr12:27951673-27951896(+)$1	223	53	90	9.9535
eeeee[ccc!!eeeeeqqqqqqqqeeeee22ccc]ee	chr16:66756033-66756273(-)$1	240	28	65	15.8355
ffffff[dddd[cccrrrrrrrrrccc]ddddfffff	chr11:85374699-85374940(-)$1	241	78	115	12.3437
fffff[eeeee"""cccooooooccc333eeeeefff	chr1:21071077-21071304(-)$1	227	72	109	9.6375
ee[ccc[bb"""cccrrrrrrrrrccc333bb]ccc8	chr7:64169347-64169578(+)$1	231	116	153	13.6495
###ggggggg"""bbrrrrrrrrrbb4444ggggggg	chr8:71040962-71041186(-)$1	224	90	127	13.0936
ddd[a[ccc[eeeeeqqqqqqqqeeeee]ccc]a]dd	chr5:79275615-79275842(-)$1	227	62	99	14.0105
'''ccc####ddddssssssssssdddd333ccc22g	chr5:167979463-167979699(-)$1	236	86	123	11.7589
ee[ffffff"""ddddqqqqqqqqdddd333ffffff	chr3:179045279-179045501(+)$1	222	144	181	17.8223
bb[dddd"""ffffffqqqqqqqqffffff4444ddd	chr2:230900055-230900292(-)$1	237	36	73	14.4543
eeeeeeee!!eeeeeaqqqqqqqqa]eeeee22eeee	chr12:46753711-46753938(-)$1	227	141	178	14.8992
[dddd[a####eeeeeqqqqqqqqeeeee4444addd	chr2:204292891-204293124(+)$1	233	119	156	16.6383
:ggggggg!!bb[ddddpppppppdddd]bb4444gg	chr16:15959506-15959734(-)$1	228	159	196	10.7866
hhhhhhh"""ffffffqqqqqqqqffffff4444hhh	chr18:723913-724140(-)$1	227	125	162	13.9363
:dddd[bb[gggggggqqqqqqqqggggggg22bb]d	chr10:72183963-72184184(+)$1	221	68	105	13.2339
""adddd$$$$$ddddqqqqqqqqdddddddd]a333	chr12:25360488-25360719(-)$1	231	79	116	16.2696
!!ffffff[a[bbcccqqqqqqqqccc]bb]afffff	chr17:27873655-27873908(+)$1	253	201	238	15.7221
ddddffffff!!ddddqqqqqqqqdddd4444fffff	chr6:105528954-105529206(+)$1	252	180	217	16.7677
bb]cccffffff[cccqqqqqqqqccc]ffffffeee	chr8:105502429-105502658(-)$1	229	146	183	14.5829
d[ccc####gggggggqqqqqqqqggggggg333ccc	chr10:70931786-70932023(+)$1	237	135	172	16.5053
!!ccc####gggggggqqqqqqqqgggggggccc22a	chr4:128754152-128754384(+)$1	232	67	104	16.1890
ee"""dddd!!eeeeeqqqqqqqqeeeee333dddd2	chr12:69235226-69235456(+)$1	230	7	44	15.2028
=========="""ddddpppppppdddd=========	chr10:5805114-5805352(+)$1	238	53	90	12.6731
ffffff[bb"""ddddqqqqqqqqddddbb22fffff	chr1:150938026-150938261(-)$1	235	79	116	16.5954
ggggggg!!a!!cccrrrrrrrrrccc22a]gggggg	chr9:129645805-129646066(+)$1	261	218	255	14.9603
ccceeeee[bb!!cccqqqqqqqqccc]bb]eeeee]	chr2:43449808-43450031(-)$1	223	21	58	15.3690
ccc[ccc!!bb!!bbqqqqqqqqbb]bb22cccccc3	chr17:42879309-42879537(-)$1	228	168	205	13.4275
g[a####dddd[eeeeeqqqqqqqqeeeeedddd22a	chr19:12739401-12739635(+)$1	234	39	76	12.6593
ggggg####dddd[bbqqqqqqqqbb]ddddgggggg	chr10:69676733-69676962(+)$1	229	157	194	14.9125
ggggggg"""ffffffqqqqqqqqffffff4444ggg	chr2:152299688-152299925(+)$1	237	146	183	16.1847
hhhhhh!!bb[ddddrrrrrrrrrdddd]bb22hhhh	chr18:67995339-67995569(+)$1	230	112	149	11.5503
dddd[ggggggg!!bbqqqqqqqqbb22gggggggdd	chr2:110376044-110376291(+)$1	247	153	190	14.0071
fffff####eeeeerrrrrrrrreeeee]ffffff]e	chr7:156763770-156763998(+)$1	228	117	154	11.9651
[gggggggccc!!cccqqqqqqqqcccccc]gggggg	chr5:138661781-138662017(+)$1	236	163	200	16.9297
:dddd[ccc!!ddddrrrrrrrrrdddd22ccc]ddd	chr1:225682862-225683102(-)$1	240	70	107	12.4966

#otherMatches

#Seq PSSM
CCUGAAAUCCUACUCGUUGACAUUUGAGAUUUUAAGC	chr6:111347107-111347331(+)$1	224	124	161	16.7422
AUUUUAAAACAAGGAAUACUUUUUUUCCAUUUUGUUU	chr2:103431440-103431676(+)$1	236	19	56	12.4724
AGAGACUGAGUCAUAACUGAUUUAAAAGUUUGUGUUA	chr19:33871993-33872236(+)$1	243	65	102	11.5393
GAGCCAUGGAAGAGUGGGAAAAUGACACCUCCAUUAU	chr16:20809281-20809521(-)$1	240	152	189	12.4065
UUUAAACUUUGGUGGUGCUGACAAAUCAUCUGUAAUC	chr17:42884695-42884918(-)$1	223	167	204	13.8565
UGUGUACUAGUAUUUAUUUCUACUUAAACUGCUCAGC	chr2:153511744-153511979(-)$1	235	135	172	13.6558
uuguaucagagcaguucugcuuuuaacuguuuuauau	chr1:179814372-179814610(-)$1	238	190	227	15.3025
ACUUUAAAAGAUGUUAUCUAAAUUAAUGGUUUAAAUA	chr6:89873446-89873673(+)$1	227	145	182	11.6918
CAUUGUGGCAAAACUUUAAAUUUUAAGUCAUCACACU	chr8:28425494-28425717(+)$1	223	48	85	14.0455
UCCAAGAAAUGUUGCAAUUCAAAAUGCACUAAGUCUG	chr10:63855628-63855859(+)$1	231	41	78	15.2570
UACUUAAUUCCAUUAUUUAUAUGUUGACGUGAAUGUA	chr17:35875113-35875339(-)$1	226	104	141	12.3901
CGAGUGUUCCCAGCCCUCAAGCCAGCUGCUCCUCCGU	chr1:93811887-93812129(+)$1	242	142	179	13.0207
CCCCUAUUUGCAAUGAAUUUCAUACCUCAUCUAAAAU	chr9:72331682-72331910(-)$1	228	147	184	11.4739
AUAGGAUUUUCAAUAUAAAUAUCAGUGUGGAAAAAUA	chr14:96751459-96751683(-)$1	224	27	64	16.3842
UUUUUCCAGCCUUUUUUGCAGUUACAAAUGCUGGAUA	chr12:27951673-27951896(+)$1	223	53	90	9.9535
AAGGGAAAAAACCACAGUUCACCAUGUGGAGUUUACU	chr16:66756033-66756273(-)$1	240	28	65	15.8355
AAAUGUAGGGUCAAGUAAUCUGCUCUUUAUCCGCGUU	chr11:85374699-85374940(-)$1	241	78	115	12.3437
GUGUGCAUUUGUUUAGUUUUGAUGCUUUUCAAAUUAC	chr1:21071077-21071304(-)$1	227	72	109	9.6375
UACCUUACUAUACAGAAAUUCAUACUGGAGAGAAAGC	chr7:64169347-64169578(+)$1	231	116	153	13.6495
UUCUCCCAUGCAAGAUCCAAACUUUCACACCAUGGGA	chr8:71040962-71041186(-)$1	224	90	127	13.0936
CAUAGAUUAAAUGUAUCAUUAUCUAUAUAUAAACCAU	chr5:79275615-79275842(-)$1	227	62	99	14.0105
UGAAGUUGGACCAGACUCCGUUCCCUGGAAUACUGUG	chr5:167979463-167979699(-)$1	236	86	123	11.7589
GUGGACUGUAUUGAAACUAAUUAAUUUUGUAACAGUU	chr3:179045279-179045501(+)$1	222	144	181	17.8223
UCUAUCUCUCUCUGUGUAAUUUACCAUAGAAUUAGGA	chr2:230900055-230900292(-)$1	237	36	73	14.4543
CUUGACAAUGUAUGGCUUAGUUGUGUUCAUGUUUUGU	chr12:46753711-46753938(-)$1	227	141	178	14.8992
CCUUCACUAUCUAGAAAAACGCUAUUCUACUUUGGAA	chr2:204292891-204293124(+)$1	233	119	156	16.6383
CUUUGGUGCAAAGGGUGUUCAUAUCACUGUUCUCUCA	chr16:15959506-15959734(-)$1	228	159	196	10.7866
AAGGAAUAUCAUGGGACCAAAUAAUUCCAUUCCAGUU	chr18:723913-724140(-)$1	227	125	162	13.9363
UGGGAGUGUCAGCUGUAUAAUGCAGCAGCUGUUCAAU	chr10:72183963-72184184(+)$1	221	68	105	13.2339
AACCUGGUAUGAAUAGACAGAACCCUAUCCAGUGGAA	chr12:25360488-25360719(-)$1	231	79	116	16.2696
AGAAUGCAUGUGUUUCUUAAGAAUGAGUACUCUGCGU	chr17:27873655-27873908(+)$1	253	201	238	15.7221
CUGAGUUUGACACAGAUCAAAAUUUUUGAAUAUCAGA	chr6:105528954-105529206(+)$1	252	180	217	16.7677
GCCAACACAUCUUGUAACUUAAUAUACUAGAUGUUAA	chr8:105502429-105502658(-)$1	229	146	183	14.5829
AGGGGAAAAUUUUGGGAUGGGGGACUCAGGAGGACCU	chr10:70931786-70932023(+)$1	237	135	172	16.5053
UUAGCCGAAUUAGAUUUACAAGACAAUCUAAGCUUUC	chr4:128754152-128754384(+)$1	232	67	104	16.1890
GGAGUAAUGAUGUUAUCUGUGAAAAUAGCCACCAUUU	chr12:69235226-69235456(+)$1	230	7	44	15.2028
GGCAUUGCAGUUGUCUGUUAGCUUUGGGUUGCAGUGC	chr10:5805114-5805352(+)$1	238	53	90	12.6731
AAGCUCCCUAACUUGGGCCAGAAACCAAAGCUGAGCU	chr1:150938026-150938261(-)$1	235	79	116	16.5954
GGCUUCGAGGGAGGCAGCGCCUAGGCCAGCACGGAGC	chr9:129645805-129646066(+)$1	261	218	255	14.9603
UUCCUCAACCAAAUAAGUAUUUUAUUAGUGCUUGAGA	chr2:43449808-43450031(-)$1	223	21	58	15.3690
UGCCUUCUUAGUACAUGUCUUUCUGCCUUUGAAGCAU	chr17:42879309-42879537(-)$1	228	168	205	13.4275
UAGAAUCAGUUACUUUCGAAUACAUGAAAGGACUCAC	chr19:12739401-12739635(+)$1	234	39	76	12.6593
UUUUAAAAUCUCAAAUGACAUGCAGUGUGAGUAGAAG	chr10:69676733-69676962(+)$1	229	157	194	14.9125
AGAUGAAAGGUAAGUUUGUACUUUAACUUGAAACUUU	chr2:152299688-152299925(+)$1	237	146	183	16.1847
UUUUAAAACAACUUAAAGUAUAUCUAGGGUGAGUUAA	chr18:67995339-67995569(+)$1	230	112	149	11.5503
GUCAAGAUUAUAAAAAGCAAAUGAUUGAUAUAAUUUG	chr2:110376044-110376291(+)$1	247	153	190	14.0071
UCUUACCUUUGAUUGUUGAAAAAAGUCACUAAGAUGU	chr7:156763770-156763998(+)$1	228	117	154	11.9651
GCAGCCUUCCUCAUUAUCAGAAAUUAAAGGUAAGGUU	chr5:138661781-138662017(+)$1	236	163	200	16.9297
AGUAAUUAAAAUGGGAAACAGAAGCCUAAGUUAUUUA	chr1:225682862-225683102(-)$1	240	70	107	12.4966

#DB
(.(((((((....(((........)))))))))).))	chr6:111347107-111347331(+)$1	1	124	161	16.7422
((((..((((((((((........))))...))))))	chr2:103431440-103431676(+)$1	1	19	56	12.4724
(((..((((..(((((((........)).)))))...	chr19:33871993-33872236(+)$1	1	65	102	11.5393
..((.(((((.(.(((.........)))))))))...	chr16:20809281-20809521(-)$1	1	152	189	12.4065
)))))))))))))(((........))).((((((...	chr17:42884695-42884918(-)$1	1	167	204	13.8565
.((.....((((((((........)))).))))..))	chr2:153511744-153511979(-)$1	1	135	172	13.6558
.(((((.(((((((((........)))))))))))))	chr1:179814372-179814610(-)$1	1	190	227	15.3025
..((((((....((((.......))))..))))))..	chr6:89873446-89873673(+)$1	1	145	182	11.6918
(((.(((.....((((........)))).....))).	chr8:28425494-28425717(+)$1	1	48	85	14.0455
))))(((..((.((((........)))).))..)))(	chr10:63855628-63855859(+)$1	1	41	78	15.2570
(((((((((((.(((.........))).).)))).))	chr17:35875113-35875339(-)$1	1	104	141	12.3901
.(((.(....((((..........))))..)))))))	chr1:93811887-93812129(+)$1	1	142	179	13.0207
))).(((((...((((..........))))...))))	chr9:72331682-72331910(-)$1	1	147	184	11.4739
(((((.(((((.((((........)))).)))))...	chr14:96751459-96751683(-)$1	1	27	64	16.3842
(((.((((((....((((......)))).)))))).)	chr12:27951673-27951896(+)$1	1	53	90	9.9535
(((((.(((..(((((........)))))..))).))	chr16:66756033-66756273(-)$1	1	28	65	15.8355
((((((.((((.(((.........))).)))))))))	chr11:85374699-85374940(-)$1	1	78	115	12.3437
(((((.(((((...(((......)))...))))))))	chr1:21071077-21071304(-)$1	1	72	109	9.6375
((.(((.((...(((.........)))...)).))).	chr7:64169347-64169578(+)$1	1	116	153	13.6495
...(((((((...((.........))....)))))))	chr8:71040962-71041186(-)$1	1	90	127	13.0936
(((.(.(((.(((((........))))).))).).))	chr5:79275615-79275842(-)$1	1	62	99	14.0105
...(((....((((..........))))...)))..)	chr5:167979463-167979699(-)$1	1	86	123	11.7589
((.((((((...((((........))))...))))))	chr3:179045279-179045501(+)$1	1	144	181	17.8223
((.((((...((((((........))))))....)))	chr2:230900055-230900292(-)$1	1	36	73	14.4543
)))(((((..((((((........).)))))..))))	chr12:46753711-46753938(-)$1	1	141	178	14.8992
.((((.(....(((((........)))))....))))	chr2:204292891-204293124(+)$1	1	119	156	16.6383
.(((((((..((.((((.......)))).))....))	chr16:15959506-15959734(-)$1	1	159	196	10.7866
(((((((...((((((........))))))....)))	chr18:723913-724140(-)$1	1	125	162	13.9363
.((((.((.(((((((........)))))))..)).)	chr10:72183963-72184184(+)$1	1	68	105	13.2339
..(((((.....((((........)))))))).)...	chr12:25360488-25360719(-)$1	1	79	116	16.2696
..((((((.(.(((((........))).)).))))))	chr17:27873655-27873908(+)$1	1	201	238	15.7221
((((((((((..((((........))))....)))))	chr6:105528954-105529206(+)$1	1	180	217	16.7677
)).)))((((((.(((........))).))))))(((	chr8:105502429-105502658(-)$1	1	146	183	14.5829
(.(((....(((((((........)))))))...)))	chr10:70931786-70932023(+)$1	1	135	172	16.5053
..(((....(((((((........))))))))))..)	chr4:128754152-128754384(+)$1	1	67	104	16.1890
((...((((..(((((........)))))...)))).	chr12:69235226-69235456(+)$1	1	7	44	15.2028
((((((((((...((((.......)))))))))))))	chr10:5805114-5805352(+)$1	1	53	90	12.6731
((((((.((...((((........))))))..)))))	chr1:150938026-150938261(-)$1	1	79	116	16.5954
(((((((..(..(((.........)))..).))))))	chr9:129645805-129646066(+)$1	1	218	255	14.9603
((((((((.((..(((........))).)).))))).	chr2:43449808-43450031(-)$1	1	21	58	15.3690
(((.(((..((..((........)).))..)))))).	chr17:42879309-42879537(-)$1	1	168	205	13.4275
(.(....((((.(((((........)))))))))..)	chr19:12739401-12739635(+)$1	1	39	76	12.6593
(((((....((((.((........)).))))))))))	chr10:69676733-69676962(+)$1	1	157	194	14.9125
(((((((...((((((........))))))....)))	chr2:152299688-152299925(+)$1	1	146	183	16.1847
((((((..((.((((.........)))).))..))))	chr18:67995339-67995569(+)$1	1	112	149	11.5503
((((.(((((((..((........))..)))))))))	chr2:110376044-110376291(+)$1	1	153	190	14.0071
(((((....(((((.........))))).)))))).)	chr7:156763770-156763998(+)$1	1	117	154	11.9651
.((((((((((..(((........)))))).))))))	chr5:138661781-138662017(+)$1	1	163	200	16.9297
.((((.(((..((((.........))))..))).)))	chr1:225682862-225683102(-)$1	1	70	107	12.4966

#PSSM
f : 0.18	g : 0.10	d : 0.10	e : 0.10	[ : 0.08	b : 0.06	" : 0.06	! : 0.06	: : 0.06	h : 0.04	c : 0.04	G : 0.02	i : 0.02	# : 0.02	' : 0.02	= : 0.02	
f : 0.18	d : 0.14	g : 0.12	e : 0.12	[ : 0.06	" : 0.06	b : 0.06	c : 0.06	h : 0.04	! : 0.04	G : 0.02	i : 0.02	# : 0.02	' : 0.02	= : 0.02	
f : 0.22	g : 0.14	d : 0.14	c : 0.10	e : 0.06	[ : 0.06	b : 0.04	h : 0.04	a : 0.04	G : 0.02	i : 0.02	# : 0.02	' : 0.02	] : 0.02	" : 0.02	= : 0.02	
f : 0.20	d : 0.16	g : 0.14	c : 0.12	e : 0.08	[ : 0.08	h : 0.04	G : 0.02	! : 0.02	b : 0.02	$ : 0.02	: : 0.02	" : 0.02	= : 0.02	# : 0.02	
f : 0.22	c : 0.16	g : 0.14	e : 0.10	d : 0.10	[ : 0.06	h : 0.04	: : 0.02	! : 0.02	i : 0.02	$ : 0.02	a : 0.02	" : 0.02	= : 0.02	# : 0.02	
f : 0.16	g : 0.14	[ : 0.14	c : 0.12	e : 0.10	# : 0.10	d : 0.08	h : 0.04	: : 0.02	i : 0.02	$ : 0.02	a : 0.02	= : 0.02	
g : 0.14	f : 0.14	# : 0.14	e : 0.12	c : 0.12	d : 0.10	[ : 0.08	i : 0.02	$ : 0.02	a : 0.02	h : 0.02	b : 0.02	= : 0.02	! : 0.02	
f : 0.14	# : 0.14	e : 0.12	g : 0.10	d : 0.10	! : 0.08	$ : 0.06	c : 0.06	b : 0.06	" : 0.06	i : 0.04	= : 0.02	
# : 0.16	d : 0.12	f : 0.10	! : 0.10	e : 0.08	c : 0.08	g : 0.06	b : 0.06	" : 0.06	[ : 0.06	i : 0.04	$ : 0.04	= : 0.02	
" : 0.14	! : 0.12	# : 0.10	d : 0.10	g : 0.10	f : 0.08	e : 0.08	b : 0.08	i : 0.04	$ : 0.04	a : 0.04	[ : 0.02	= : 0.02	c : 0.02	
! : 0.12	d : 0.12	" : 0.12	f : 0.10	e : 0.10	# : 0.08	b : 0.08	g : 0.08	[ : 0.06	i : 0.04	$ : 0.04	a : 0.02	c : 0.02	
e : 0.14	" : 0.14	d : 0.12	f : 0.10	[ : 0.10	! : 0.10	g : 0.08	# : 0.06	i : 0.04	$ : 0.04	b : 0.04	a : 0.02	
d : 0.32	e : 0.16	c : 0.08	! : 0.08	[ : 0.06	" : 0.06	f : 0.06	g : 0.06	# : 0.04	i : 0.04	b : 0.02	
d : 0.34	c : 0.22	e : 0.16	f : 0.06	g : 0.06	b : 0.04	i : 0.02	# : 0.02	" : 0.02	[ : 0.02	! : 0.02	
d : 0.32	c : 0.24	e : 0.14	b : 0.08	f : 0.06	g : 0.06	s : 0.04	i : 0.02	r : 0.02	
d : 0.28	c : 0.16	r : 0.16	e : 0.10	f : 0.06	g : 0.06	s : 0.04	q : 0.04	b : 0.04	i : 0.02	a : 0.02	
q : 0.61	r : 0.18	s : 0.06	d : 0.06	b : 0.02	p : 0.02	c : 0.02	e : 0.02	
q : 0.63	r : 0.18	p : 0.06	s : 0.06	b : 0.02	d : 0.02	o : 0.02	
q : 0.65	r : 0.18	p : 0.06	s : 0.06	o : 0.04	
q : 0.65	r : 0.18	p : 0.06	s : 0.06	o : 0.04	
q : 0.65	r : 0.18	p : 0.06	s : 0.06	o : 0.04	
q : 0.65	r : 0.18	p : 0.06	s : 0.06	o : 0.04	
q : 0.65	r : 0.18	p : 0.06	s : 0.06	o : 0.04	
q : 0.61	r : 0.16	s : 0.06	e : 0.04	p : 0.04	d : 0.02	o : 0.02	c : 0.02	b : 0.02	
d : 0.34	c : 0.22	e : 0.10	b : 0.08	f : 0.06	g : 0.06	q : 0.04	r : 0.02	i : 0.02	s : 0.02	a : 0.02	
d : 0.34	c : 0.24	e : 0.12	b : 0.06	f : 0.06	g : 0.06	] : 0.04	q : 0.02	i : 0.02	s : 0.02	
d : 0.36	c : 0.22	e : 0.14	f : 0.06	g : 0.06	b : 0.04	i : 0.02	3 : 0.02	4 : 0.02	] : 0.02	2 : 0.02	
d : 0.36	e : 0.14	] : 0.10	g : 0.08	2 : 0.06	f : 0.06	b : 0.04	c : 0.04	3 : 0.04	: : 0.02	i : 0.02	4 : 0.02	
] : 0.18	g : 0.10	3 : 0.10	f : 0.10	2 : 0.10	e : 0.10	d : 0.08	b : 0.06	a : 0.04	4 : 0.04	i : 0.02	5 : 0.02	= : 0.02	c : 0.02	
f : 0.16	e : 0.12	b : 0.12	g : 0.10	3 : 0.10	d : 0.10	2 : 0.08	4 : 0.06	c : 0.04	i : 0.02	5 : 0.02	] : 0.02	= : 0.02	a : 0.02	
g : 0.12	d : 0.12	3 : 0.10	e : 0.10	f : 0.10	4 : 0.10	b : 0.08	] : 0.08	c : 0.06	2 : 0.04	i : 0.02	5 : 0.02	a : 0.02	= : 0.02	
f : 0.14	c : 0.14	g : 0.12	4 : 0.12	e : 0.10	d : 0.10	2 : 0.10	3 : 0.06	i : 0.02	5 : 0.02	b : 0.02	a : 0.02	= : 0.02	
f : 0.22	g : 0.12	c : 0.12	e : 0.10	4 : 0.10	d : 0.08	2 : 0.08	] : 0.06	3 : 0.04	i : 0.02	5 : 0.02	= : 0.02	
f : 0.22	e : 0.16	c : 0.16	g : 0.12	4 : 0.08	d : 0.06	a : 0.06	2 : 0.02	b : 0.02	3 : 0.02	= : 0.02	h : 0.02	] : 0.02	
f : 0.20	c : 0.12	g : 0.12	e : 0.10	] : 0.08	2 : 0.08	d : 0.08	3 : 0.06	4 : 0.04	h : 0.04	l : 0.02	b : 0.02	= : 0.02	
f : 0.16	e : 0.12	c : 0.12	g : 0.12	d : 0.12	2 : 0.08	3 : 0.06	] : 0.06	b : 0.04	h : 0.04	l : 0.02	4 : 0.02	= : 0.02	
f : 0.18	g : 0.14	e : 0.12	d : 0.12	3 : 0.08	b : 0.04	2 : 0.04	] : 0.04	c : 0.04	h : 0.04	a : 0.04	l : 0.02	B : 0.02	4 : 0.02	8 : 0.02	= : 0.02	

#score	687.2647633680491
#seq	49
#width	37
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_CDS_m1_run1.txt

#BEAR
ddddqqqqqqqqdddd	chr3:148875187-148875409(+)$1	222	167	183	13.5026
ddddqqqqqqqqdddd	chr10:5799422-5799658(+)$1	236	70	86	13.5026
eeeeqqqqqqqqeeee	chr4:42122052-42122270(-)$1	218	90	106	13.2925
eeeeqqqqqqqqeeee	chr17:80049041-80049281(-)$1	240	28	44	13.2925
acccqqqqqqqqccc]	chr6:4037621-4037861(+)$1	240	19	35	13.8043
[a[aqqqqqqqqa]a]	chr14:104195146-104195364(+)$1	218	47	63	12.9850
ffffqqqqqqqqffff	chr3:5244696-5244924(+)$1	228	8	24	12.4096
[cccqqqqqqqqcccb	chr15:91304191-91304411(+)$1	220	46	62	13.5286
ffffqqqqqqqqffff	chr22:51043363-51043593(+)$1	230	181	197	12.4096
:cccqqqqqqqqccc:	chr18:55273794-55274031(-)$1	237	16	32	12.1692
[cccqqqqqqqqccc]	chr10:71148860-71149100(+)$1	240	7	23	13.8754
ddddqqqqqqqqdddd	chr19:34710258-34710468(+)$1	210	54	70	13.5026
ddddqqqqqqqqdddd	chr16:67662271-67662493(+)$1	222	119	135	13.5026
eeeeqqqqqqqqeeee	chr19:7685369-7685588(-)$1	219	34	50	13.2925
[cccqqqqqqqqccc3	chr1:114454647-114454859(+)$1	212	40	56	13.8360
eeeeqqqqqqqqeeee	chr7:151845615-151845851(-)$1	236	90	106	13.2925
ddddqqqqqqqqdddd	chr20:39728683-39728924(+)$1	241	80	96	13.5026
"cccqqqqqqqqccc]	chr12:123687420-123687639(-)$1	219	103	119	13.7972
eeeeqqqqqqqqeeee	chr19:32844531-32844767(+)$1	236	20	36	13.2925
[cccqqqqqqqqccc]	chr22:47107984-47108198(-)$1	214	29	45	13.8754
eeeeqqqqqqqqeeee	chr11:47788667-47788895(-)$1	228	39	55	13.2925
"cccqqqqqqqqccc4	chr16:71701048-71701270(-)$1	222	162	178	13.7699
cabbqqqqqqqqbb]a	chr12:6966717-6966945(+)$1	228	62	78	12.2875
%cccqqqqqqqqccc8	chr7:148451053-148451277(+)$1	224	85	101	12.7660
ddddqqqqqqqqdddd	chr11:65546345-65546565(-)$1	220	137	153	13.5026
ddddqqqqqqqqdddd	chr17:2577286-2577507(+)$1	221	118	134	13.5026
ddddqqqqqqqqdddd	chr1:16044964-16045191(+)$1	227	2	18	13.5026
ffffqqqqqqqqffff	chr6:111708976-111709193(-)$1	217	63	79	12.4096
eebbqqqqqqqqbb22	chr10:129905054-129905275(-)$1	221	107	123	12.1220
ddddqqqqqqqqdddd	chr7:77397888-77398098(+)$1	210	167	183	13.5026
acccqqqqqqqqccc7	chr19:36273423-36273639(+)$1	216	145	161	13.2625
ee[aqqqqqqqqa]ee	chr9:134385219-134385433(+)$1	214	144	160	13.1025
ddddqqqqqqqqdddd	chr3:194147805-194148025(-)$1	220	73	89	13.5026
iiiiqqqqqqqqiiii	chr20:40120337-40120556(-)$1	219	7	23	12.8390
eeeeqqqqqqqqeeee	chr3:11600053-11600274(-)$1	221	50	66	13.2925
ddddqqqqqqqqdddd	chr10:44053038-44053260(-)$1	222	35	51	13.5026
[cccqqqqqqqqccc]	chr6:90405580-90405806(-)$1	226	184	200	13.8754
eeeeqqqqqqqqeeee	chr6:7584296-7584540(+)$1	244	169	185	13.2925
ffffqqqqqqqqffff	chrX:147022013-147022249(+)$1	236	203	219	12.4096
:cccqqqqqqqqccc=	chrM:13722-13987(-)$1	265	44	60	12.9002
eeeeqqqqqqqqeeee	chr14:23373998-23374213(-)$1	215	105	121	13.2925
ccccqqqqqqqqccc]	chr20:30803037-30803249(+)$1	212	140	156	13.7811
ddddqqqqqqqqdddd	chr1:155282047-155282273(+)$1	226	32	48	13.5026
Ecccqqqqqqqqccc:	chr12:53776484-53776718(+)$1	234	187	203	12.1448
ddddqqqqqqqqdddd	chrX:53586221-53586447(-)$1	226	88	104	13.5026
:cccqqqqqqqqccc:	chr20:40033625-40033843(-)$1	218	193	209	12.1692
eeeeqqqqqqqqeeee	chr1:232596780-232597005(-)$1	225	6	22	13.2925
ddddqqqqqqqqdddd	chr12:49425255-49425488(-)$1	233	29	45	13.5026
eeeeqqqqqqqqeeee	chr12:49431579-49431797(-)$1	218	112	128	13.2925
ddddqqqqqqqqdddd	chr16:89613030-89613247(+)$1	217	76	92	13.5026
dddaqqqqqqqqa]dd	chr6:30570158-30570375(-)$1	217	150	166	13.2546
eeeeqqqqqqqqeeee	chr17:76993172-76993392(-)$1	220	92	108	13.2925
##bbqqqqqqqqbb44	chr1:214551260-214551479(-)$1	219	43	59	12.2820
ddddqqqqqqqqdddd	chr2:234201829-234202047(+)$1	218	113	129	13.5026
gcccqqqqqqqqcccd	chr14:23392162-23392383(-)$1	221	106	122	13.7272
ffffqqqqqqqqffff	chr6:30571289-30571530(-)$1	241	164	180	12.4096
:cccqqqqqqqqccc:	chr1:27106272-27106489(+)$1	217	107	123	12.1692
:cccqqqqqqqqcccE	chr14:39650710-39650931(+)$1	221	101	117	12.0630
bb[aqqqqqqqqa]bb	chr11:65393296-65393511(+)$1	215	85	101	11.8397
iiiiqqqqqqqqiiii	chr17:40009931-40010148(-)$1	217	66	82	12.8390
eeeeqqqqqqqqeeee	chr20:42320795-42321018(+)$1	223	37	53	13.2925
!!bbqqqqqqqqbb22	chr11:74547199-74547419(+)$1	220	149	165	12.0966
[cccqqqqqqqqcccd	chr3:57542347-57542564(+)$1	217	55	71	13.8393
e[bbqqqqqqqqbb]e	chr15:91448463-91448674(+)$1	211	15	31	12.4622
e[bbqqqqqqqqbb]e	chr1:120483192-120483411(-)$1	219	186	202	12.4622
ffffqqqqqqqqffff	chr2:60688152-60688375(-)$1	223	92	108	12.4096
:cccqqqqqqqqccc:	chr10:88232349-88232575(-)$1	226	114	130	12.1692
c[bbqqqqqqqqbb22	chr1:245019292-245019509(-)$1	217	96	112	11.9848
:cccqqqqqqqqcccE	chr3:49052543-49052772(+)$1	229	11	27	12.0630

#otherMatches

#Seq PSSM
AUCUUGAACUUUGGGU	chr3:148875187-148875409(+)$1	222	167	183	13.5026
UGCUGAAGCUGAAGCA	chr10:5799422-5799658(+)$1	236	70	86	13.5026
UGAGCUUAAGUACUCA	chr4:42122052-42122270(-)$1	218	90	106	13.2925
AGGACCUGGCUUUCCU	chr17:80049041-80049281(-)$1	240	28	44	13.2925
CGAGAUGAUAUCCUCA	chr6:4037621-4037861(+)$1	240	19	35	13.8043
AGGUGGAAAAGAAGCA	chr14:104195146-104195364(+)$1	218	47	63	12.9850
GGAGCCGGUUCCCUCC	chr3:5244696-5244924(+)$1	228	8	24	12.4096
AGAAACCCAACCUUCC	chr15:91304191-91304411(+)$1	220	46	62	13.5286
CUGGCCCCAGUCCCAG	chr22:51043363-51043593(+)$1	230	181	197	12.4096
AAGCAGUGCUGAGCUA	chr18:55273794-55274031(-)$1	237	16	32	12.1692
ACUGCAGUGCAACAGA	chr10:71148860-71149100(+)$1	240	7	23	13.8754
GCUCCAAGGAGAGGGC	chr19:34710258-34710468(+)$1	210	54	70	13.5026
ACGACCCCAACUUCGU	chr16:67662271-67662493(+)$1	222	119	135	13.5026
UGCUGUCGGACGAGCA	chr19:7685369-7685588(-)$1	219	34	50	13.2925
CUUCUAGCUACUGAAU	chr1:114454647-114454859(+)$1	212	40	56	13.8360
AAGGCUACUCAACCUU	chr7:151845615-151845851(-)$1	236	90	106	13.2925
GAGGAUUGCUAACUUC	chr20:39728683-39728924(+)$1	241	80	96	13.5026
AUCCUUUUCCCCGGAC	chr12:123687420-123687639(-)$1	219	103	119	13.7972
GGAGGUUGAUUGCUCC	chr19:32844531-32844767(+)$1	236	20	36	13.2925
UGGUAUUUAUCAACCC	chr22:47107984-47108198(-)$1	214	29	45	13.8754
CGCGCUUGGGCUCGCG	chr11:47788667-47788895(-)$1	228	39	55	13.2925
CAGACACCCUCUUCUC	chr16:71701048-71701270(-)$1	222	162	178	13.7699
CCUCCUGCUCUAGACG	chr12:6966717-6966945(+)$1	228	62	78	12.2875
AGUCGAAAAAGGGGCA	chr7:148451053-148451277(+)$1	224	85	101	12.7660
CUCUGAGCUGAGGGAG	chr11:65546345-65546565(-)$1	220	137	153	13.5026
GCCAAAUCAAGAUGGC	chr17:2577286-2577507(+)$1	221	118	134	13.5026
UGGUAAGGUUAGGCCA	chr1:16044964-16045191(+)$1	227	2	18	13.5026
UUUUAAUUAAGCAGAA	chr6:111708976-111709193(-)$1	217	63	79	12.4096
CUCCUAGCAGUUGGCA	chr10:129905054-129905275(-)$1	221	107	123	12.1220
GUUCGUCCAGGAGAAC	chr7:77397888-77398098(+)$1	210	167	183	13.5026
CACCACAUUACAGGUA	chr19:36273423-36273639(+)$1	216	145	161	13.2625
GAGACCAGACUUUGUC	chr9:134385219-134385433(+)$1	214	144	160	13.1025
GUGGCACAAAGACCAC	chr3:194147805-194148025(-)$1	220	73	89	13.5026
AGUGAGAUUUACCACU	chr20:40120337-40120556(-)$1	219	7	23	12.8390
GCACCCAACUCCGUGU	chr3:11600053-11600274(-)$1	221	50	66	13.2925
CACUGAGAGAAAAGUG	chr10:44053038-44053260(-)$1	222	35	51	13.5026
ACAUGCAGAACUGUGA	chr6:90405580-90405806(-)$1	226	184	200	13.8754
AGUUCAAAGAGAAGCU	chr6:7584296-7584540(+)$1	244	169	185	13.2925
UGUACUAAAAUAUACA	chrX:147022013-147022249(+)$1	236	203	219	12.4096
UGCGGUGUGUGAUGCU	chrM:13722-13987(-)$1	265	44	60	12.9002
GGGCAUCUUUGAGCCC	chr14:23373998-23374213(-)$1	215	105	121	13.2925
CCCCUGAGAAGCGGGU	chr20:30803037-30803249(+)$1	212	140	156	13.7811
ACCGGGGUUUGACGGU	chr1:155282047-155282273(+)$1	226	32	48	13.5026
AAGCCAGUUCCAGCUC	chr12:53776484-53776718(+)$1	234	187	203	12.1448
UGGAUGACUUUUUCCA	chrX:53586221-53586447(-)$1	226	88	104	13.5026
UGUGAAAACAGACACU	chr20:40033625-40033843(-)$1	218	193	209	12.1692
GGCUGGCAUGGAGGCC	chr1:232596780-232597005(-)$1	225	6	22	13.2925
CCCCAAACCUCAGGGG	chr12:49425255-49425488(-)$1	233	29	45	13.5026
CUGGGGCUAAAGCCAG	chr12:49431579-49431797(-)$1	218	112	128	13.2925
GCUGACCCAGUCCAGC	chr16:89613030-89613247(+)$1	217	76	92	13.5026
CCCCAAAUGGACGAGG	chr6:30570158-30570375(-)$1	217	150	166	13.2546
CCUGUCAGACAGUGGG	chr17:76993172-76993392(-)$1	220	92	108	13.2925
AAGCAGAAGAUGGCAG	chr1:214551260-214551479(-)$1	219	43	59	12.2820
CUCUGUAUAUCUGGAG	chr2:234201829-234202047(+)$1	218	113	129	13.5026
AAGGACCGUGACCCUG	chr14:23392162-23392383(-)$1	221	106	122	13.7272
AGGCUCCAAGUUGCCU	chr6:30571289-30571530(-)$1	241	164	180	12.4096
UGACUUUGAGAUGUCC	chr1:27106272-27106489(+)$1	217	107	123	12.1692
UCGGAGUAGGGGCCGG	chr14:39650710-39650931(+)$1	221	101	117	12.0630
UGGGUUUCGUGUUGUA	chr11:65393296-65393511(+)$1	215	85	101	11.8397
GUGGCAGAAGGACCGC	chr17:40009931-40010148(-)$1	217	66	82	12.8390
CAUCAAAAGGAAGGUG	chr20:42320795-42321018(+)$1	223	37	53	13.2925
CAUGAAAAUCACCACA	chr11:74547199-74547419(+)$1	220	149	165	12.0966
GCCGAAUGCUAGCGGC	chr3:57542347-57542564(+)$1	217	55	71	13.8393
AGAGCCAAAUUUCUGU	chr15:91448463-91448674(+)$1	211	15	31	12.4622
ACCUACCGCUGCAGCU	chr1:120483192-120483411(-)$1	219	186	202	12.4622
CUCGGUGGCCGGCGAG	chr2:60688152-60688375(-)$1	223	92	108	12.4096
CCACCAUCCAAAGUGA	chr10:88232349-88232575(-)$1	226	114	130	12.1692
UAUGUUGAACUUCAGA	chr1:245019292-245019509(-)$1	217	96	112	11.9848
GGCUGACCUUCUGGCG	chr3:49052543-49052772(+)$1	229	11	27	12.0630

#DB
((((........))))	chr3:148875187-148875409(+)$1	1	167	183	13.5026
((((........))))	chr10:5799422-5799658(+)$1	1	70	86	13.5026
((((........))))	chr4:42122052-42122270(-)$1	1	90	106	13.2925
((((........))))	chr17:80049041-80049281(-)$1	1	28	44	13.2925
((((........))).	chr6:4037621-4037861(+)$1	1	19	35	13.8043
.(.(........).).	chr14:104195146-104195364(+)$1	1	47	63	12.9850
((((........))))	chr3:5244696-5244924(+)$1	1	8	24	12.4096
.(((........))))	chr15:91304191-91304411(+)$1	1	46	62	13.5286
((((........))))	chr22:51043363-51043593(+)$1	1	181	197	12.4096
.(((........))).	chr18:55273794-55274031(-)$1	1	16	32	12.1692
.(((........))).	chr10:71148860-71149100(+)$1	1	7	23	13.8754
((((........))))	chr19:34710258-34710468(+)$1	1	54	70	13.5026
((((........))))	chr16:67662271-67662493(+)$1	1	119	135	13.5026
((((........))))	chr19:7685369-7685588(-)$1	1	34	50	13.2925
.(((........))).	chr1:114454647-114454859(+)$1	1	40	56	13.8360
((((........))))	chr7:151845615-151845851(-)$1	1	90	106	13.2925
((((........))))	chr20:39728683-39728924(+)$1	1	80	96	13.5026
.(((........))).	chr12:123687420-123687639(-)$1	1	103	119	13.7972
((((........))))	chr19:32844531-32844767(+)$1	1	20	36	13.2925
.(((........))).	chr22:47107984-47108198(-)$1	1	29	45	13.8754
((((........))))	chr11:47788667-47788895(-)$1	1	39	55	13.2925
.(((........))).	chr16:71701048-71701270(-)$1	1	162	178	13.7699
((((........)).)	chr12:6966717-6966945(+)$1	1	62	78	12.2875
.(((........))).	chr7:148451053-148451277(+)$1	1	85	101	12.7660
((((........))))	chr11:65546345-65546565(-)$1	1	137	153	13.5026
((((........))))	chr17:2577286-2577507(+)$1	1	118	134	13.5026
((((........))))	chr1:16044964-16045191(+)$1	1	2	18	13.5026
((((........))))	chr6:111708976-111709193(-)$1	1	63	79	12.4096
((((........))..	chr10:129905054-129905275(-)$1	1	107	123	12.1220
((((........))))	chr7:77397888-77398098(+)$1	1	167	183	13.5026
((((........))).	chr19:36273423-36273639(+)$1	1	145	161	13.2625
((.(........).))	chr9:134385219-134385433(+)$1	1	144	160	13.1025
((((........))))	chr3:194147805-194148025(-)$1	1	73	89	13.5026
((((........))))	chr20:40120337-40120556(-)$1	1	7	23	12.8390
((((........))))	chr3:11600053-11600274(-)$1	1	50	66	13.2925
((((........))))	chr10:44053038-44053260(-)$1	1	35	51	13.5026
.(((........))).	chr6:90405580-90405806(-)$1	1	184	200	13.8754
((((........))))	chr6:7584296-7584540(+)$1	1	169	185	13.2925
((((........))))	chrX:147022013-147022249(+)$1	1	203	219	12.4096
.(((........)))(	chrM:13722-13987(-)$1	1	44	60	12.9002
((((........))))	chr14:23373998-23374213(-)$1	1	105	121	13.2925
((((........))).	chr20:30803037-30803249(+)$1	1	140	156	13.7811
((((........))))	chr1:155282047-155282273(+)$1	1	32	48	13.5026
)(((........))).	chr12:53776484-53776718(+)$1	1	187	203	12.1448
((((........))))	chrX:53586221-53586447(-)$1	1	88	104	13.5026
.(((........))).	chr20:40033625-40033843(-)$1	1	193	209	12.1692
((((........))))	chr1:232596780-232597005(-)$1	1	6	22	13.2925
((((........))))	chr12:49425255-49425488(-)$1	1	29	45	13.5026
((((........))))	chr12:49431579-49431797(-)$1	1	112	128	13.2925
((((........))))	chr16:89613030-89613247(+)$1	1	76	92	13.5026
((((........).))	chr6:30570158-30570375(-)$1	1	150	166	13.2546
((((........))))	chr17:76993172-76993392(-)$1	1	92	108	13.2925
..((........))..	chr1:214551260-214551479(-)$1	1	43	59	12.2820
((((........))))	chr2:234201829-234202047(+)$1	1	113	129	13.5026
)(((........)))(	chr14:23392162-23392383(-)$1	1	106	122	13.7272
((((........))))	chr6:30571289-30571530(-)$1	1	164	180	12.4096
.(((........))).	chr1:27106272-27106489(+)$1	1	107	123	12.1692
.(((........))))	chr14:39650710-39650931(+)$1	1	101	117	12.0630
((.(........).))	chr11:65393296-65393511(+)$1	1	85	101	11.8397
((((........))))	chr17:40009931-40010148(-)$1	1	66	82	12.8390
((((........))))	chr20:42320795-42321018(+)$1	1	37	53	13.2925
..((........))..	chr11:74547199-74547419(+)$1	1	149	165	12.0966
.(((........))))	chr3:57542347-57542564(+)$1	1	55	71	13.8393
(.((........)).)	chr15:91448463-91448674(+)$1	1	15	31	12.4622
(.((........)).)	chr1:120483192-120483411(-)$1	1	186	202	12.4622
((((........))))	chr2:60688152-60688375(-)$1	1	92	108	12.4096
.(((........))).	chr10:88232349-88232575(-)$1	1	114	130	12.1692
(.((........))..	chr1:245019292-245019509(-)$1	1	96	112	11.9848
.(((........)))(	chr3:49052543-49052772(+)$1	1	11	27	12.0630

#PSSM
d : 0.24	e : 0.24	[ : 0.10	: : 0.10	f : 0.08	c : 0.04	a : 0.02	" : 0.02	i : 0.02	% : 0.01	E : 0.01	# : 0.01	g : 0.01	b : 0.01	! : 0.01	
c : 0.30	d : 0.24	e : 0.21	f : 0.08	[ : 0.04	a : 0.02	i : 0.02	# : 0.01	b : 0.01	! : 0.01	
c : 0.30	d : 0.24	e : 0.18	b : 0.10	f : 0.08	[ : 0.04	i : 0.02	
c : 0.30	d : 0.23	e : 0.18	b : 0.10	f : 0.08	a : 0.05	i : 0.02	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.30	d : 0.23	e : 0.18	b : 0.10	f : 0.08	a : 0.05	i : 0.02	
c : 0.30	d : 0.23	e : 0.18	b : 0.10	f : 0.08	] : 0.05	i : 0.02	
c : 0.30	d : 0.24	e : 0.20	f : 0.08	] : 0.04	2 : 0.04	i : 0.02	a : 0.01	4 : 0.01	b : 0.01	
d : 0.27	e : 0.23	] : 0.10	f : 0.08	: : 0.07	2 : 0.04	b : 0.02	4 : 0.02	i : 0.02	E : 0.02	3 : 0.01	a : 0.01	8 : 0.01	7 : 0.01	= : 0.01	

#score	901.446952537734
#seq	69
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_UTR_m1_run1.txt

#BEAR
=============ssssssssss===========	chr19:39923787-39924067(-)$1	280	189	223	13.1813
d[iiiiiiiiivvvvvvvvvvvvviiiiiiiii]	chrX:38664835-38665316(+)$1	481	275	309	11.8392
ee"""ccc!!ddddoooooodddd22ccc4444e	chr2:54091457-54091697(-)$1	240	167	201	11.8846
==========oooooo==========333ggggg	chr20:23351070-23351310(+)$1	240	87	121	15.0220
ffffffgggggggooooooggggggg333fffff	chr2:187373515-187373756(+)$1	241	162	196	11.9232
d"""ddddccccccnnnnnccc]ccc333dddd3	chr6:30867616-30867856(+)$1	240	54	88	11.2145
##ccc"""bb[cccmmmmcccbb]ccc]ccc]==	chr12:6623605-6623845(+)$1	240	37	71	12.2756
$$$$ccc[ccccccooooooccc]ccc]ccc22c	chr2:242168573-242168813(-)$1	240	79	113	12.2505
==="""cccrrrrrrrrrccc22===========	chr1:207533384-207533626(+)$1	242	139	173	13.6035
ccc[dddd"""cccmmmmccc]dddd]ccc]ddd	chr18:51692387-51692630(-)$1	243	157	191	10.7985
####ggggggg[ccclllccc333ggggggg]hh	chr17:33331749-33332004(+)$1	255	22	56	12.8874
==============mmmm================	chr17:7093243-7093523(-)$1	280	120	154	17.0791
d[eeeee"""ddddoooooodddd333eeeee]d	chr7:131188312-131188552(-)$1	240	143	177	11.0756
==========!!bbnnnnnbb22==========>	chrX:16780349-16780589(+)$1	240	105	139	14.1381
dddd!!a[ccccccooooooccc]ccc]a22ddd	chr6:148869729-148869969(+)$1	240	72	106	11.9891
:::===========mmmm===========bb[dd	chr2:27016778-27017018(+)$1	240	4	38	11.4544
"dddd!!cccddddmmmmdddd]ccc22dddd33	chr6:30593464-30593704(+)$1	240	85	119	10.9147
dda[==========mmmm==========]a:ddd	chr3:12705379-12705628(-)$1	249	123	157	13.4291
===========[bboooooobb]===========	chr16:84212327-84212567(-)$1	240	186	220	16.7412
=========[accclllccc]a]===========	chr2:74330685-74330931(+)$1	246	94	128	16.3781
==========ddddmmmmdddd22==========	chr12:53806646-53806886(+)$1	240	203	237	15.7187
ddd####ccc[cccoooooocccccc333dddd2	chr7:128850716-128850956(+)$1	240	82	116	13.1559
iiiiia!!a[ddddmmmmdddd]a22a]iiiiii	chr18:71930520-71930760(-)$1	240	40	74	13.6181
ii"""ffffffcccmmmmccc22ffffff333ii	chr1:113667028-113667273(+)$1	245	202	236	11.6231
g[bb"""bb[ddddmmmmdddd]bb333bb]ggg	chr3:9489329-9489583(+)$1	254	187	221	11.7323
iii!!iiiiiiiiimmmmiiiiiiiii]iiiiii	chr14:24780495-24780735(+)$1	240	44	78	15.3228
ccc[a[bb[aooooooa]bb]a]ccc22iiiiii	chr15:34634061-34634301(-)$1	240	143	177	11.3017
ggggggg[bb[cccmmmmccc]bb333ggggggg	chr2:32530753-32530993(+)$1	240	197	231	12.7334
iiiii[dddd[cccmmmmcccdddd]iiiiiiii	chr9:21837828-21838068(+)$1	240	40	74	13.1423
ggggiiiiiiiiinnnnniiiiiiiii22ggggg	chr7:102982149-102982389(-)$1	240	173	207	12.8225
!!ccc!!ccc[cccmmmmccc]ccc22ccc]ccc	chr15:70347290-70347611(-)$1	321	38	72	12.6730
:============rrrrrrrrr============	chr14:39502329-39502576(-)$1	247	159	193	14.3132
fffffccc!!ddddllldddd333ccc333ffff	chrX:109438317-109438557(-)$1	240	114	148	11.0323
eee!!ccc[ddddooooooddddccc4444eeee	chr9:131493067-131493307(-)$1	240	145	179	12.0642
ccc[bb[gggggggooooooggggggg22bb]cc	chr10:82279679-82279959(+)$1	280	62	96	12.0839
b]ffffffddddoooooodddd:===========	chr16:30751195-30751515(+)$1	320	171	205	11.9974
!ccc[a[ccc[cccmmmmccc]ccc]accc333c	chr15:42059407-42059661(+)$1	254	160	194	12.9904
ccc[ccc"""bboooooobb333cccccc]gggg	chr2:43450351-43450591(-)$1	240	146	180	12.4019
c==========[ccclllccc22==========:	chr6:139693497-139693740(-)$1	243	118	152	15.0644
=========[cccrrrrrrrrrccc]========	chr17:15878649-15878889(+)$1	240	203	237	14.6394
iiiiiiiii[ddddmmmmdddd]iiiiiiiii::	chr5:72208852-72209092(+)$1	240	199	233	12.6289
============apppppppa]============	chr15:75663703-75663944(-)$1	241	92	126	12.5905
iiiii!!cccddddmmmmdddd]ccc333iiiii	chr1:205056797-205057063(-)$1	266	204	238	14.5885
============oooooo============>>>>	chr18:45362924-45363164(-)$1	240	156	190	15.6559
===========[bboooooobb]===========	chr8:53535101-53535341(-)$1	240	188	222	16.7412
ccc!!bb[ddddoooooodddd]bb4444ccc]d	chr17:38420971-38421211(+)$1	240	84	118	12.0181
!!ggggggg[ddddmmmmdddd]ggggggg22dd	chr6:36839470-36839750(-)$1	280	155	189	12.3190
d####a!!ccc[bboooooobb]ccc22adddd]	chr1:155451594-155451852(-)$1	258	92	126	12.2646
iiiiiiiii!!ccclllccc22iiiiiiiiiFFF	chr8:134266693-134266933(-)$1	240	185	219	12.7700
===$$$$$ddddoooooodddd22==========	chr3:53319299-53319550(-)$1	251	182	216	14.0419
::iiiiiiiiicccmmmmccc]iiiiiiiiiddd	chr15:45899181-45899421(+)$1	240	30	64	12.5606
==========[cccmmmmccc]==========44	chr17:79686770-79687010(+)$1	240	17	51	16.7767
ffff[ggggggg[aooooooaggggggg]fffff	chr17:7147134-7147377(-)$1	243	208	242	12.0295
============wwwwwwwwwwwwww========	chr9:97177385-97177625(+)$1	240	202	236	11.8621
d####============nnnnn============	chrX:119660358-119660598(-)$1	240	187	221	12.5893
$ggggggg!!bboooooobbggggggg22=====	chr21:45565313-45565553(+)$1	240	85	119	13.0765

#otherMatches

#Seq PSSM
ACAGUUUUUGAGGGAUUUUAAAGUUUCAAGAACU	chr19:39923787-39924067(-)$1	280	189	223	13.1813
CGCUGGGUUGCCACACUUGGGAAAGCAGCCCGGA	chrX:38664835-38665316(+)$1	481	275	309	11.8392
AUUUUUGUGUGCAUCUCUCAAUGCUAACACCACA	chr2:54091457-54091697(-)$1	240	167	201	11.8846
UUGUCCAUGUGCAAAGAUGUGGGCAAGAAUGGCC	chr20:23351070-23351310(+)$1	240	87	121	15.0220
UAUAAUGGUCAUUGCAGAAAAUGAUUGAUGUUGU	chr2:187373515-187373756(+)$1	241	162	196	11.9232
GUCUUGUAGCUAGAACUUCUCUAAGCCUAUACGU	chr6:30867616-30867856(+)$1	240	54	88	11.2145
GAUCAUCCAGAUGCUGCAGCACUUUGAACACCUG	chr12:6623605-6623845(+)$1	240	37	71	12.2756
AGUCAGCACUCUGGCCUUCAUCACGAGAGCUCCG	chr2:242168573-242168813(-)$1	240	79	113	12.2505
GGAAUAUAGAAUGAAAGACUGAAUCUUCCUUUGU	chr1:207533384-207533626(+)$1	242	139	173	13.6035
ACCAUGGAACUACCCAAAGGUCUUCAAGGUAUUA	chr18:51692387-51692630(-)$1	243	157	191	10.7985
UCUUUGAAAAGCAGCUUAGUUACCCUUUUUAUAA	chr17:33331749-33332004(+)$1	255	22	56	12.8874
UUUUUUUCCUGGGAAUUUUUUUGGGGAAAAGGGA	chr17:7093243-7093523(-)$1	280	120	154	17.0791
GCACAGGUUAUUCAUAACCUUGAACCCCUUGUUC	chr7:131188312-131188552(-)$1	240	143	177	11.0756
AUGGCAAUAGAGGUGUGUGACAGUUAUUGCUAUC	chrX:16780349-16780589(+)$1	240	105	139	14.1381
AAGGCCUGGCGUGUGGCCAAACAGCGUGAAACCU	chr6:148869729-148869969(+)$1	240	72	106	11.9891
UAUUUUUCUUUUUUUUGAGAAGGAGAAGACUGCA	chr2:27016778-27017018(+)$1	240	4	38	11.4544
GACAGGCCCUCAGAGUGCUCUGUAGGAGCUGUAG	chr6:30593464-30593704(+)$1	240	85	119	10.9147
CCGGGCUUUGGGGCGCGUGCCCUGAGGCGCGGAG	chr3:12705379-12705628(-)$1	249	123	157	13.4291
ACAAAAUACAGUAGUAGUUUCUUUUGUAUUUUGU	chr16:84212327-84212567(-)$1	240	186	220	16.7412
UUAAUUUUUGUGACGUUGUCGAGAGAGGUUGGGC	chr2:74330685-74330931(+)$1	246	94	128	16.3781
AUGUGUGGGUGAAUGUGUGUUCAUGCCCGUAUAU	chr12:53806646-53806886(+)$1	240	203	237	15.7187
CUCUCAGGUUGACUGGGCAGAGUGACGAUGAGCC	chr7:128850716-128850956(+)$1	240	82	116	13.1559
UUGAACAGCAUCCUGGUGGGGAAGAAGUUUUAAG	chr18:71930520-71930760(-)$1	240	40	74	13.6181
UCCCAGGCUUGACCAACUGGUACCAGGUCAAAGA	chr1:113667028-113667273(+)$1	245	202	236	11.6231
UCACAAGCUGCCUUGGAAGAGGGAGGAAGUAACA	chr3:9489329-9489583(+)$1	254	187	221	11.7323
cggcUGGUGAGCGCCAUCGUGCUUGCCUUCGGCU	chr14:24780495-24780735(+)$1	240	44	78	15.3228
AACUGAUGUCUUUUCUGCCACCUGUUACCCCUCG	chr15:34634061-34634301(-)$1	240	143	177	11.3017
GUUUUUAAGAUUGUGUCGAUAUUCACCUAAAAAC	chr2:32530753-32530993(+)$1	240	197	231	12.7334
AUAAAACAAACAAAAACCUUUUUUGCUUUAUUUU	chr9:21837828-21838068(+)$1	240	40	74	13.1423
UGGAAGGUAUUUAAUAUCUGAAUAUUUUGUUCAG	chr7:102982149-102982389(-)$1	240	173	207	12.8225
CUGGCAGGCCCCGGCAUCCCGAGGCACGCCCGGC	chr15:70347290-70347611(-)$1	321	38	72	12.6730
AAGAAGAUGAAAUAAUAUUCAAAUUUCAUUUUUU	chr14:39502329-39502576(-)$1	247	159	193	14.3132
UACAGUCCCAGUGCCCAGCACACCGGAAGUUUGU	chrX:109438317-109438557(-)$1	240	114	148	11.0323
CCCCUGCCUGAGAACGCCAUCUCGGCUCCCGGGC	chr9:131493067-131493307(-)$1	240	145	179	12.0642
UUAUUGAUCCAAGCAGAAGAGCUUGGGGACACUG	chr10:82279679-82279959(+)$1	280	62	96	12.0839
GAGGGGCUUCUCUACAAUGAGGuuuuuuucuuuu	chr16:30751195-30751515(+)$1	320	171	205	11.9974
AACUUGGAUCCUUGACUUCAAUGAUGCAGUGGAU	chr15:42059407-42059661(+)$1	254	160	194	12.9904
AUAUGCCUUUUGUAACUUCACUUGGUUAUUUUAU	chr2:43450351-43450591(-)$1	240	146	180	12.4019
GUGUGGAAUGUCGUCAGUGGCAAACAUUUCACAG	chr6:139693497-139693740(-)$1	243	118	152	15.0644
AUGAUCUAUUCAGCUGCUUUUACUGUGUGGAUUA	chr17:15878649-15878889(+)$1	240	203	237	14.6394
UAAAAUUAAAUUUUACAUAAAAGUUAGUUUUAUU	chr5:72208852-72209092(+)$1	240	199	233	12.6289
AGGAAAAAAAAGCUGGAUUUGAUUUUUUUUUUCU	chr15:75663703-75663944(-)$1	241	92	126	12.5905
UUGUUGUUCUUUAUAAAAAUAACAGAUUGGAUAG	chr1:205056797-205057063(-)$1	266	204	238	14.5885
UAUAUGUGUAUGAAUUUAUAUAUACAUAUACACU	chr18:45362924-45363164(-)$1	240	156	190	15.6559
auauuuaauuucuucauaaaaauaaguuaaauau	chr8:53535101-53535341(-)$1	240	188	222	16.7412
CCACCGACGCCUGGACAAAGGCUUCACCCUGGUC	chr17:38420971-38421211(+)$1	240	84	118	12.0181
AGAACUUUGCUGAGUUGGCUCGUCGAGGUUACUA	chr6:36839470-36839750(-)$1	280	155	189	12.3190
AAUAAGGACUCUGUGAAAAAACUGGGAACUGGCA	chr1:155451594-155451852(-)$1	258	92	126	12.2646
UGCUGAGCAAGGCAUUGUGUGGUGCUCAGCACAG	chr8:134266693-134266933(-)$1	240	185	219	12.7700
GAUGACCCUGGCCCGAAAGUCACAGUUCAGUUGC	chr3:53319299-53319550(-)$1	251	182	216	14.0419
UUUCAUCAGAAGCUCUAUAGCUUUUUGGUGAGAG	chr15:45899181-45899421(+)$1	240	30	64	12.5606
GCCUGGGAGGGGAUUUUCGUUGCCUUUUGGGUGA	chr17:79686770-79687010(+)$1	240	17	51	16.7767
GAAGCCAAGUCAGCUUUGUUGUGAUUUGAUUUUU	chr17:7147134-7147377(-)$1	243	208	242	12.0295
UAGGCACGUAUCACUGUGUAUGUCUAGAUACGUG	chr9:97177385-97177625(+)$1	240	202	236	11.8621
AACUCUUUGCAUGUUAUUUAGUAUGAUGUGCAGA	chrX:119660358-119660598(-)$1	240	187	221	12.5893
GUGAGGAAUGGCAGUGAGGUUUCUUCAAUUAGUC	chr21:45565313-45565553(+)$1	240	85	119	13.0765

#DB
(((((((((((((..........)))))))))))	chr19:39923787-39924067(-)$1	1	189	223	13.1813
(.(((((((((.............))))))))).	chrX:38664835-38665316(+)$1	1	275	309	11.8392
((...(((..((((......))))..)))....)	chr2:54091457-54091697(-)$1	1	167	201	11.8846
((((((((((......))))))))))...)))))	chr20:23351070-23351310(+)$1	1	87	121	15.0220
(((((((((((((......)))))))...)))))	chr2:187373515-187373756(+)$1	1	162	196	11.9232
(...((((((((((.....))).)))...)))).	chr6:30867616-30867856(+)$1	1	54	88	11.2145
..(((...((.(((....))))).))).))).))	chr12:6623605-6623845(+)$1	1	37	71	12.2756
....(((.((((((......))).))).)))..)	chr2:242168573-242168813(-)$1	1	79	113	12.2505
(((...(((.........)))..)))))))))))	chr1:207533384-207533626(+)$1	1	139	173	13.6035
(((.((((...(((....))).)))).))).)))	chr18:51692387-51692630(-)$1	1	157	191	10.7985
....(((((((.(((...)))...))))))).))	chr17:33331749-33332004(+)$1	1	22	56	12.8874
((((((((((((((....))))))))))))))))	chr17:7093243-7093523(-)$1	1	120	154	17.0791
(.(((((...((((......))))...))))).)	chr7:131188312-131188552(-)$1	1	143	177	11.0756
((((((((((..((.....))..)))))))))).	chrX:16780349-16780589(+)$1	1	105	139	14.1381
((((..(.((((((......))).))).)..)))	chr6:148869729-148869969(+)$1	1	72	106	11.9891
...(((((((((((....)))))))))))((.((	chr2:27016778-27017018(+)$1	1	4	38	11.4544
.((((..(((((((....)))).)))..))))..	chr6:30593464-30593704(+)$1	1	85	119	10.9147
))(.((((((((((....)))))))))).).(((	chr3:12705379-12705628(-)$1	1	123	157	13.4291
(((((((((((.((......)).)))))))))))	chr16:84212327-84212567(-)$1	1	186	220	16.7412
(((((((((.((((...))).).)))))))))))	chr2:74330685-74330931(+)$1	1	94	128	16.3781
((((((((((((((....))))..))))))))))	chr12:53806646-53806886(+)$1	1	203	237	15.7187
(((....(((.(((......))))))...)))).	chr7:128850716-128850956(+)$1	1	82	116	13.1559
((((((..(.((((....)))).)..).))))))	chr18:71930520-71930760(-)$1	1	40	74	13.6181
((...(((((((((....)))..))))))...))	chr1:113667028-113667273(+)$1	1	202	236	11.6231
(.((...((.((((....)))).))...)).)))	chr3:9489329-9489583(+)$1	1	187	221	11.7323
(((..(((((((((....))))))))).))))))	chr14:24780495-24780735(+)$1	1	44	78	15.3228
(((.(.((.(......).)).).)))..))))))	chr15:34634061-34634301(-)$1	1	143	177	11.3017
(((((((.((.(((....))).))...)))))))	chr2:32530753-32530993(+)$1	1	197	231	12.7334
(((((.((((.(((....))))))).))))))))	chr9:21837828-21838068(+)$1	1	40	74	13.1423
(((((((((((((.....)))))))))..)))))	chr7:102982149-102982389(-)$1	1	173	207	12.8225
..(((..(((.(((....))).)))..))).)))	chr15:70347290-70347611(-)$1	1	38	72	12.6730
.((((((((((((.........))))))))))))	chr14:39502329-39502576(-)$1	1	159	193	14.3132
((((((((..((((...))))...)))...))))	chrX:109438317-109438557(-)$1	1	114	148	11.0323
(((..(((.((((......)))))))....))))	chr9:131493067-131493307(-)$1	1	145	179	12.0642
(((.((.(((((((......)))))))..)).))	chr10:82279679-82279959(+)$1	1	62	96	12.0839
).))))))((((......)))).(((((((((((	chr16:30751195-30751515(+)$1	1	171	205	11.9974
.(((.(.(((.(((....))).))).))))...)	chr15:42059407-42059661(+)$1	1	160	194	12.9904
(((.(((...((......))...)))))).))))	chr2:43450351-43450591(-)$1	1	146	180	12.4019
)((((((((((.(((...)))..)))))))))).	chr6:139693497-139693740(-)$1	1	118	152	15.0644
(((((((((.(((.........))).))))))))	chr17:15878649-15878889(+)$1	1	203	237	14.6394
(((((((((.((((....)))).)))))))))..	chr5:72208852-72209092(+)$1	1	199	233	12.6289
(((((((((((((.......).))))))))))))	chr15:75663703-75663944(-)$1	1	92	126	12.5905
(((((..(((((((....)))).)))...)))))	chr1:205056797-205057063(-)$1	1	204	238	14.5885
((((((((((((......))))))))))))....	chr18:45362924-45363164(-)$1	1	156	190	15.6559
(((((((((((.((......)).)))))))))))	chr8:53535101-53535341(-)$1	1	188	222	16.7412
(((..((.((((......)))).))....))).)	chr17:38420971-38421211(+)$1	1	84	118	12.0181
..(((((((.((((....)))).)))))))..))	chr6:36839470-36839750(-)$1	1	155	189	12.3190
(....(..(((.((......)).)))..))))).	chr1:155451594-155451852(-)$1	1	92	126	12.2646
(((((((((..(((...)))..))))))))))))	chr8:134266693-134266933(-)$1	1	185	219	12.7700
(((.....((((......))))..))))))))))	chr3:53319299-53319550(-)$1	1	182	216	14.0419
..((((((((((((....))).)))))))))(((	chr15:45899181-45899421(+)$1	1	30	64	12.5606
((((((((((.(((....))).))))))))))..	chr17:79686770-79687010(+)$1	1	17	51	16.7767
((((.(((((((.(......)))))))).)))))	chr17:7147134-7147377(-)$1	1	208	242	12.0295
((((((((((((..............))))))))	chr9:97177385-97177625(+)$1	1	202	236	11.8621
(....((((((((((((.....))))))))))))	chrX:119660358-119660598(-)$1	1	187	221	12.5893
.(((((((..((......)))))))))..)))))	chr21:45565313-45565553(+)$1	1	85	119	13.0765

#PSSM
= : 0.26	d : 0.14	i : 0.12	c : 0.10	f : 0.05	: : 0.05	g : 0.05	! : 0.05	e : 0.03	# : 0.03	$ : 0.03	" : 0.01	b : 0.01	
= : 0.30	i : 0.12	c : 0.10	# : 0.07	d : 0.07	[ : 0.05	f : 0.05	g : 0.05	e : 0.03	: : 0.03	! : 0.03	" : 0.01	$ : 0.01	] : 0.01	
= : 0.30	i : 0.14	c : 0.14	f : 0.07	g : 0.07	" : 0.05	# : 0.05	d : 0.05	e : 0.03	$ : 0.01	: : 0.01	a : 0.01	b : 0.01	
= : 0.28	i : 0.12	[ : 0.08	" : 0.07	f : 0.07	# : 0.07	g : 0.07	c : 0.05	! : 0.05	$ : 0.03	d : 0.03	e : 0.01	b : 0.01	
= : 0.30	i : 0.14	" : 0.07	c : 0.07	g : 0.07	! : 0.07	f : 0.05	d : 0.05	# : 0.05	[ : 0.03	e : 0.01	a : 0.01	b : 0.01	$ : 0.01	
= : 0.32	i : 0.10	c : 0.08	g : 0.08	! : 0.07	f : 0.05	" : 0.05	a : 0.05	d : 0.03	[ : 0.03	b : 0.03	e : 0.01	# : 0.01	$ : 0.01	
= : 0.32	i : 0.10	c : 0.10	g : 0.10	! : 0.08	d : 0.05	" : 0.03	f : 0.03	b : 0.03	[ : 0.03	e : 0.01	a : 0.01	# : 0.01	$ : 0.01	
= : 0.32	c : 0.16	i : 0.10	g : 0.10	[ : 0.07	d : 0.05	" : 0.05	! : 0.03	f : 0.03	b : 0.03	$ : 0.01	
= : 0.32	c : 0.17	i : 0.10	g : 0.08	d : 0.07	! : 0.05	b : 0.05	" : 0.05	[ : 0.03	a : 0.01	f : 0.01	
= : 0.28	c : 0.16	[ : 0.10	d : 0.08	i : 0.07	! : 0.07	g : 0.07	" : 0.05	b : 0.03	r : 0.01	f : 0.01	a : 0.01	
d : 0.24	= : 0.21	[ : 0.12	c : 0.08	i : 0.07	g : 0.07	o : 0.03	! : 0.03	b : 0.03	r : 0.01	" : 0.01	a : 0.01	f : 0.01	
c : 0.28	d : 0.24	= : 0.16	[ : 0.08	g : 0.05	o : 0.03	i : 0.03	b : 0.03	v : 0.01	r : 0.01	! : 0.01	
c : 0.32	d : 0.19	o : 0.14	= : 0.10	b : 0.07	g : 0.03	i : 0.03	v : 0.01	r : 0.01	a : 0.01	[ : 0.01	w : 0.01	
c : 0.30	d : 0.17	o : 0.17	= : 0.07	b : 0.07	r : 0.05	s : 0.01	v : 0.01	i : 0.01	n : 0.01	g : 0.01	p : 0.01	a : 0.01	w : 0.01	
o : 0.35	m : 0.35	n : 0.05	r : 0.05	l : 0.05	c : 0.03	s : 0.01	v : 0.01	p : 0.01	w : 0.01	= : 0.01	
o : 0.35	m : 0.35	l : 0.08	n : 0.05	r : 0.05	s : 0.01	v : 0.01	p : 0.01	w : 0.01	= : 0.01	
m : 0.35	o : 0.32	l : 0.08	n : 0.05	r : 0.05	= : 0.03	s : 0.01	v : 0.01	a : 0.01	p : 0.01	w : 0.01	
m : 0.35	o : 0.32	n : 0.07	r : 0.05	l : 0.03	c : 0.03	s : 0.01	v : 0.01	= : 0.01	] : 0.01	d : 0.01	p : 0.01	w : 0.01	
c : 0.24	o : 0.21	d : 0.19	= : 0.08	n : 0.05	b : 0.05	i : 0.03	r : 0.03	s : 0.01	v : 0.01	p : 0.01	w : 0.01	
c : 0.26	d : 0.21	o : 0.17	= : 0.08	b : 0.07	i : 0.03	r : 0.03	s : 0.01	v : 0.01	g : 0.01	p : 0.01	w : 0.01	n : 0.01	
c : 0.28	d : 0.24	= : 0.08	b : 0.07	g : 0.05	] : 0.03	i : 0.03	r : 0.03	a : 0.03	s : 0.01	v : 0.01	3 : 0.01	2 : 0.01	w : 0.01	n : 0.01	
d : 0.24	] : 0.12	= : 0.08	2 : 0.08	g : 0.07	c : 0.07	b : 0.07	3 : 0.05	a : 0.03	i : 0.03	r : 0.03	s : 0.01	v : 0.01	w : 0.01	n : 0.01	
] : 0.23	= : 0.16	c : 0.10	2 : 0.10	d : 0.08	g : 0.07	i : 0.07	3 : 0.05	b : 0.03	s : 0.01	v : 0.01	: : 0.01	w : 0.01	
= : 0.30	c : 0.19	g : 0.08	i : 0.08	d : 0.07	] : 0.05	b : 0.05	3 : 0.03	2 : 0.03	v : 0.01	a : 0.01	f : 0.01	w : 0.01	
= : 0.33	c : 0.26	i : 0.10	g : 0.10	2 : 0.03	d : 0.03	3 : 0.03	b : 0.03	f : 0.01	w : 0.01	
= : 0.33	c : 0.21	i : 0.10	g : 0.10	2 : 0.05	3 : 0.05	] : 0.05	d : 0.01	f : 0.01	4 : 0.01	w : 0.01	
= : 0.35	3 : 0.14	i : 0.12	c : 0.10	g : 0.08	2 : 0.07	a : 0.03	4 : 0.03	] : 0.01	f : 0.01	
= : 0.35	3 : 0.12	2 : 0.10	i : 0.08	c : 0.08	] : 0.08	g : 0.07	4 : 0.03	e : 0.01	f : 0.01	
= : 0.33	i : 0.14	c : 0.12	3 : 0.10	g : 0.05	2 : 0.05	a : 0.03	] : 0.03	4 : 0.03	e : 0.01	d : 0.01	f : 0.01	b : 0.01	
= : 0.33	i : 0.16	c : 0.10	g : 0.08	d : 0.07	b : 0.05	4 : 0.03	f : 0.03	3 : 0.03	e : 0.01	2 : 0.01	a : 0.01	] : 0.01	
= : 0.32	i : 0.16	g : 0.08	d : 0.07	f : 0.05	c : 0.05	] : 0.05	e : 0.03	2 : 0.03	b : 0.03	3 : 0.03	4 : 0.01	: : 0.01	> : 0.01	
= : 0.32	d : 0.14	i : 0.12	g : 0.08	f : 0.05	] : 0.05	2 : 0.03	e : 0.03	3 : 0.03	c : 0.03	4 : 0.01	[ : 0.01	> : 0.01	F : 0.01	
= : 0.32	d : 0.16	i : 0.12	g : 0.08	f : 0.05	4 : 0.03	] : 0.03	3 : 0.03	c : 0.03	2 : 0.01	h : 0.01	e : 0.01	: : 0.01	> : 0.01	F : 0.01	
= : 0.28	d : 0.14	i : 0.10	g : 0.08	c : 0.07	f : 0.05	] : 0.03	e : 0.03	3 : 0.03	> : 0.03	: : 0.03	h : 0.01	2 : 0.01	F : 0.01	4 : 0.01	

#score	735.0267798289478
#seq	56
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_CDS_m3_run1.txt

#BEAR
b"""ccc!!gggggggnnnnnggggggg]ccc333	chr7:102760206-102760446(-)$1	240	61	96	10.3587
ggggggg####eeeeemmmmeeeee22ggggggg:	chr1:171763459-171763699(+)$1	240	10	45	11.0404
###ccc$$$$$bb[bbmmmmbb]bb4444cccfff	chr5:133944056-133944296(-)$1	240	147	182	10.4541
ggggg!!a[bb!!cccmmmmccc4444bb]a22gg	chr14:24613090-24613330(-)$1	240	106	141	14.8383
========$$$$$cccmmmmccc333=========	chr10:105780220-105780460(+)$1	240	9	44	15.2874
$$$dddd[dddd[cccmmmmccc]dddd]dddd66	chr10:33481118-33481398(-)$1	280	80	115	11.1096
[dddd"""a[bb[ddddmmmmdddd]bb]adddd=	chrX:47086390-47086721(+)$1	331	189	224	10.5977
ffff!!ccc!!a[cccnnnnnccc]a22ccc333f	chr2:113007696-113007936(-)$1	240	173	208	11.5276
!eeeee[ccc[eeeeellleeeee]ccc4444eee	chr8:26510663-26510943(+)$1	280	19	54	10.1290
f!!bb[bb$$$$$cccmmmmccc4444bb]bb22f	chr19:55743076-55743325(-)$1	249	138	173	12.7661
::ccc[ccc"""ccc!!ammmma22ccc]ccc]cc	chr19:41183124-41183364(-)$1	240	112	147	9.0466
[a[ccc[a"""eeeeemmmmeeeeeaccc]adddd	chr17:953276-953516(-)$1	240	96	131	12.1577
bb"""ffffff!!cccmmmmccc22ffffff333b	chr7:99022531-99022771(-)$1	240	175	210	13.2683
c####eeeee[a[ccclllccca]eeeee333ccc	chr18:72345845-72346088(+)$1	243	134	169	11.7605
!eeeee"""bb!!cccnnnnnccc22bbeeeee]b	chr17:26961787-26962027(-)$1	240	156	191	11.0688
FF:ccc!!==========lll==========22cc	chr5:151176829-151177075(+)$1	246	147	182	9.4217
eeeee"""ccc[ddddmmmmddddccc4444eeee	chr1:183522018-183522298(+)$1	280	165	200	12.5997
eeeeee[bbeeeee[ammmma]eeeee]bb]eeee	chr8:136657211-136657451(+)$1	240	119	154	9.9751
dddd!!bb####ddddmmmmdddd333bbdddd::	chr8:77767361-77767601(+)$1	240	2	37	10.7479
d[a####ffffff[ccclllccc]ffffff4444a	chr5:174940386-174940674(+)$1	288	178	213	10.8495
[a####eeeee!!cccmmmmccc22eeeeea]eee	chr2:64321906-64322181(-)$1	275	133	168	13.8125
ffffffddddccccccmmmmccc333ccc333ddd	chr1:155899404-155899650(-)$1	246	202	237	12.7966
!eeeee!!bb"""cccmmmmccc]bb22eeeee22	chr4:139981452-139981692(-)$1	240	35	70	13.3653
!bb[a!!dddd!!ddddmmmmdddd]dddd22a]b	chr12:49953997-49954237(-)$1	240	141	176	10.7839
c[dddd[ccc####bbmmmmbbccc]dddd22ccc	chr2:86258395-86258635(-)$1	240	150	185	11.8331
eeeee[a$$$$$ddddmmmmdddda]eeeeeeeee	chr19:44661770-44662014(+)$1	244	30	65	11.7436
ggggggg!!bb!!cccmmmmccc22bb22gggggg	chr4:185631169-185631409(-)$1	240	145	180	13.4547
d!!ccc[bb"""ddddmmmmdddd333bb]ccc22	chr13:75863015-75863255(-)$1	240	188	223	13.5806
ee"""eeeee!!ddddmmmmdddd22eeeee]eee	chr4:69179895-69180135(-)$1	240	123	158	12.2997
###ccc[bb####cccmmmmccc333bb]ccc333	chr13:20346524-20346764(-)$1	240	16	51	16.2242
fffffa[eeeee[ccclllccc]eeeee]a333ff	chr20:62223341-62223582(-)$1	241	43	78	10.8262
fff####bbccc[cccmmmmccc22ccc]bbffff	chr7:94293335-94293575(+)$1	240	167	202	13.0033
"cccggggggga[cccmmmmccc]a]ggggggg]c	chr16:30016576-30016826(+)$1	250	87	122	13.7955
ggggg!!eeeee[cccmmmmccc]eeeee333ggg	chr1:145586543-145586783(-)$1	240	49	84	13.8174
:eeeee!!a[gggggggmmmmggggggg]a]eeee	chr12:50385735-50386015(-)$1	280	59	94	9.9663
f"""bb$$$$$eeeeemmmmeeeee333bb]ffff	chr12:120636253-120636493(-)$1	240	94	129	10.9392
dddd[ccc[bb!!cccmmmmcccbb]cccdddd99	chr22:29736699-29736939(-)$1	240	157	192	11.3183
!!dddd"""gggggggmmmmggggggg333dddd2	chr8:42259384-42259629(+)$1	245	31	66	12.0568
gg!!bb!!dddd[cccmmmmccc]dddd22bb22g	chr1:100533933-100534227(+)$1	294	244	279	12.3002
a[ccc"""dddd!!ccclllccc]dddd333ccc]	chr12:1192556-1192796(+)$1	240	17	52	11.8913
ccccdddd[bb!!cccmmmmccc22bb]dddd555	chr6:107096919-107097161(+)$1	242	66	101	10.5526
ffdddd[ccc[ccc[ammmmaccc]ccc]dddd]f	chr16:2141738-2141981(-)$1	243	32	67	12.4207
gggg[a!!ccc!!bbmmmmbb]ccc22a]gggggg	chr10:6146798-6147038(+)$1	240	34	69	10.8958
aeeeee[ffffffcccmmmmccc]ffffffeeeee	chr4:89442640-89442888(-)$1	248	14	49	11.4213
====[a[bb$$$$$ccclllccc4444bba]====	chr16:30748885-30749125(+)$1	240	90	125	12.3458
[eeeee[ccc[addddmmmmdddd]a]ccc333ee	chr17:74046420-74046700(-)$1	280	223	258	13.3073
bb!!ccc[bb####bbmmmmbb4444bb]ccc22b	chr2:122120657-122120897(-)$1	240	204	239	12.3811
bb####eeeee[ddddmmmmdddd22eeeee4444	chrX:154292157-154292397(-)$1	240	156	191	12.2556
cchhhhhhhh"""cccmmmmccchhhhhhhh]ccc	chr13:98667889-98668129(+)$1	240	142	177	10.6554
[bb[ccc[ccc[eeeeemmmmeeeeecccccc]bb	chr19:2042375-2042616(-)$1	241	170	205	9.6191
#bb"""dddd!!ddddmmmmdddd22dddd>>>>>	chr3:107492104-107492344(+)$1	240	70	105	11.6933

#otherMatches

#Seq PSSM
AAUUCUGUCAUUGCUUUGAAUGAGCGAUUUGGUAA	chr7:102760206-102760446(-)$1	240	61	96	10.3587
UGUUGGAAUGUAAAUGGUAUUAUUUUAUCCAGCAA	chr1:171763459-171763699(+)$1	240	10	45	11.0404
UCUUGGGAAUAAGAUCGACAGACCUGAAGCCAUCA	chr5:133944056-133944296(-)$1	240	147	182	10.4541
GUGGGGAUGCUGUGGCCAAGGCCUCCAAGGAGACU	chr14:24613090-24613330(-)$1	240	106	141	14.8383
UUUUUCUUAUUUAUAGUUUGCUGCACAAGAAGAAA	chr10:105780220-105780460(+)$1	240	9	44	15.2874
AUUUGGCUGGGGCUCUCACAAGACCUUCUGCCACU	chr10:33481118-33481398(-)$1	280	80	115	11.1096
ACUUGAUAGCGACGGGGCCGACCUCCUCACCAAGC	chrX:47086390-47086721(+)$1	331	189	224	10.5977
GAUUAAGUUGACCACUGUUUAAGUUGAAAACGCAG	chr2:113007696-113007936(-)$1	240	173	208	11.5276
AGGGUUUCUAGAGAGGUAUCCUCUGUGGCUGUGGC	chr8:26510663-26510943(+)$1	280	19	54	10.1290
UGACGCCCUGCAGCUCAGGUGAGAACCGGAUGGAA	chr19:55743076-55743325(-)$1	249	138	173	12.7661
AUGUGGGGUCACGGCCGCCUUCGAUGCCAGCCGCA	chr19:41183124-41183364(-)$1	240	112	147	9.0466
AGUUUGAGAUCGAGCUGGAGGGCUCCCAGUCCCUG	chr17:953276-953516(-)$1	240	96	131	12.1577
UGACAUUCUUUAACACGCUGGUGAGAAAGAAGAGC	chr7:99022531-99022771(-)$1	240	175	210	13.2683
CGGGGGAUGUGUACUCCCAGAGAGAUGUUACAGGC	chr18:72345845-72346088(+)$1	243	134	169	11.7605
GAUGCUAAAGUGGCCGCCCUUCGGAAGCAGCAUGG	chr17:26961787-26962027(-)$1	240	156	191	11.0688
GGAAGACUUGAGGGUAUGAAACGUGUCUUCAUUUU	chr5:151176829-151177075(+)$1	246	147	182	9.4217
GUAGCCCACAGAGGGCCCAGGCCCCUGCCCAGCUG	chr1:183522018-183522298(+)$1	280	165	200	12.5997
GACUCAGUGAGGAGACUUAUGAUUCCUACGGUGAG	chr8:136657211-136657451(+)$1	240	119	154	9.9751
CAUUAACUAAAAUUGAUCUAUCAAGUGAGAAUGAA	chr8:77767361-77767601(+)$1	240	2	37	10.7479
CAGGAUUCUCAUGGCAGCCCCUGGCAUGGGUUAGC	chr5:174940386-174940674(+)$1	288	178	213	10.8495
UGUGAAGCUGGAUUUUAUGUGGACGCCGGCCCUCC	chr2:64321906-64322181(-)$1	275	133	168	13.8125
AGACCUCUAAAUAGACAGGCGUCAGAUAUUUAUUA	chr1:155899404-155899650(-)$1	246	202	237	12.7966
UGCAGAAAGUCUCCUGAAAGCAGCAUCCUCUGUUC	chr4:139981452-139981692(-)$1	240	35	70	13.3653
UUGAUGACAGUAAGCUCAAGUGAGUGGCUGGAGAC	chr12:49953997-49954237(-)$1	240	141	176	10.7839
CAGUACGACACCGAGGAGAGCCUGUGGUGCCAGGU	chr2:86258395-86258635(-)$1	240	150	185	11.8331
GUGUGGGAAGAGCUUCAGUCGGAGUGCACACCUUC	chr19:44661770-44662014(+)$1	244	30	65	11.7436
UGUUUUGCCUGAAUUUGAGAAAACCCACCUAGAGC	chr4:185631169-185631409(-)$1	240	145	180	13.4547
AAAGAAAUAAAGAUUUGAGCAAAUAAGUACUUCAA	chr13:75863015-75863255(-)$1	240	188	223	13.5806
CCUUCGUCGCACACAAGCUGUUGUCAGUGGCCGGA	chr4:69179895-69180135(-)$1	240	123	158	12.2997
CAAACACUGUUUUGAAUUUUUUCUGUUACUGUCAU	chr13:20346524-20346764(-)$1	240	16	51	16.2242
AAGGGCUUGGGCUCUCACUGAGUGUCCGCGUUACC	chr20:62223341-62223582(-)$1	241	43	78	10.8262
ACCACAUUCAGGAGGAGCUCUCCCACCUCGAGGUC	chr7:94293335-94293575(+)$1	240	167	202	13.0033
GAUCCUGAGCACGGUCCCUCGGCAGAUGUUCAGCG	chr16:30016576-30016826(+)$1	250	87	122	13.7955
GGGAAAGCAGGAAAGGACAACCUCUCUUGGAAUUC	chr1:145586543-145586783(-)$1	240	49	84	13.8174
UGAGCUUUGGAAGUUUGCUAACAGAUUUGCUGGCU	chr12:50385735-50386015(-)$1	280	59	94	9.9663
GCUUGAUAUCACAGAGGAAACUCUGCAUUCUCGCU	chr12:120636253-120636493(-)$1	240	94	129	10.9392
GUCAUCCCCGCCCAGGGCGACCUGCUGGGUGACCU	chr22:29736699-29736939(-)$1	240	157	192	11.3183
CCUUCGAAGGGUGGCUUGCUGGCUAUCAGAUGAGU	chr8:42259384-42259629(+)$1	245	31	66	12.0568
CAUUGUCUAGUGCUUUAAUAAAAAUAUUUAAUCUU	chr1:100533933-100534227(+)$1	294	244	279	12.3002
GGGAUGAAUCCAUUAAGAAGCUUCUGGAAAUGUUG	chr12:1192556-1192796(+)$1	240	17	52	11.8913
CCCACAGCGAGAAUGAAGAUUCAGACUGGCUGAUA	chr6:107096919-107097161(+)$1	242	66	101	10.5526
GAAGGGCUGGGGUGCGGCACCCACGCCACCCCUCU	chr16:2141738-2141981(-)$1	243	32	67	12.4207
UCCUGUGAGUAAACUGGUAAGAUAUAAAGAGGAUU	chr10:6146798-6147038(+)$1	240	34	69	10.8958
UCAGCCUCUGUGGAAGAAAACUUCCCACAGGGCUG	chr4:89442640-89442888(-)$1	248	14	49	11.4213
UCAGUCACUAAUCUCCCCUUGGGCUUGAGGCCUGA	chr16:30748885-30749125(+)$1	240	90	125	12.3458
UCUGGGCGGGUCCAGGUCAGCCUGUGUCCCCUUCU	chr17:74046420-74046700(-)$1	280	223	258	13.3073
UGGACAUGGAGAUAGAGGAAUCAGAAUCAGUGCAC	chr2:122120657-122120897(-)$1	240	204	239	12.3811
GGUAGUAUAUUGUAAAAUGCUUUAAAAAUAUUUUU	chrX:154292157-154292397(-)$1	240	156	191	12.2556
UGAGGUAAGUUAUUCCCUUUGGAACUUACUUACGU	chr13:98667889-98668129(+)$1	240	142	177	10.6554
ACCCCGGAGCUGCUCACUCCGGUGAGGGCCCGCGG	chr19:2042375-2042616(-)$1	241	170	205	9.6191
AGAAAAUGUCAAAGGAGAAAUCCUCAGACACCACC	chr3:107492104-107492344(+)$1	240	70	105	11.6933

#DB
(...(((..(((((((.....))))))).)))...	chr7:102760206-102760446(-)$1	1	61	96	10.3587
(((((((....(((((....)))))..))))))).	chr1:171763459-171763699(+)$1	1	10	45	11.0404
...(((.....((.((....)).))....))))))	chr5:133944056-133944296(-)$1	1	147	182	10.4541
(((((..(.((..(((....)))....)).)..))	chr14:24613090-24613330(-)$1	1	106	141	14.8383
((((((((.....(((....)))...)))))))))	chr10:105780220-105780460(+)$1	1	9	44	15.2874
...((((.((((.(((....))).)))).))))..	chr10:33481118-33481398(-)$1	1	80	115	11.1096
.((((...(.((.((((....)))).)).))))))	chrX:47086390-47086721(+)$1	1	189	224	10.5977
((((..(((..(.(((.....))).)..)))...)	chr2:113007696-113007936(-)$1	1	173	208	11.5276
.(((((.(((.(((((...))))).)))....)))	chr8:26510663-26510943(+)$1	1	19	54	10.1290
(..((.((.....(((....)))....)).))..)	chr19:55743076-55743325(-)$1	1	138	173	12.7661
..(((.(((...(((..(....)..))).))).))	chr19:41183124-41183364(-)$1	1	112	147	9.0466
.(.(((.(...(((((....))))))))).)))))	chr17:953276-953516(-)$1	1	96	131	12.1577
((...((((((..(((....)))..))))))...)	chr7:99022531-99022771(-)$1	1	175	210	13.2683
(....(((((.(.(((...)))).)))))...)))	chr18:72345845-72346088(+)$1	1	134	169	11.7605
.(((((...((..(((.....)))..))))))).)	chr17:26961787-26962027(-)$1	1	156	191	11.0688
)).(((..((((((((((...))))))))))..))	chr5:151176829-151177075(+)$1	1	147	182	9.4217
(((((...(((.((((....)))))))....))))	chr1:183522018-183522298(+)$1	1	165	200	12.5997
)(((((.(((((((.(....).))))).)).))))	chr8:136657211-136657451(+)$1	1	119	154	9.9751
((((..((....((((....))))...))))))..	chr8:77767361-77767601(+)$1	1	2	37	10.7479
(.(....((((((.(((...))).))))))....)	chr5:174940386-174940674(+)$1	1	178	213	10.8495
.(....(((((..(((....)))..)))))).)))	chr2:64321906-64322181(-)$1	1	133	168	13.8125
((((((((((((((((....)))...)))...)))	chr1:155899404-155899650(-)$1	1	202	237	12.7966
.(((((..((...(((....))).))..)))))..	chr4:139981452-139981692(-)$1	1	35	70	13.3653
.((.(..((((..((((....)))).))))..).)	chr12:49953997-49954237(-)$1	1	141	176	10.7839
(.((((.(((....((....))))).))))..)))	chr2:86258395-86258635(-)$1	1	150	185	11.8331
(((((.(.....((((....))))).)))))))))	chr19:44661770-44662014(+)$1	1	30	65	11.7436
(((((((..((..(((....)))..))..))))))	chr4:185631169-185631409(-)$1	1	145	180	13.4547
(..(((.((...((((....))))...)).)))..	chr13:75863015-75863255(-)$1	1	188	223	13.5806
((...(((((..((((....))))..))))).)))	chr4:69179895-69180135(-)$1	1	123	158	12.2997
...(((.((....(((....)))...)).)))...	chr13:20346524-20346764(-)$1	1	16	51	16.2242
((((((.(((((.(((...))).))))).)...))	chr20:62223341-62223582(-)$1	1	43	78	10.8262
(((....(((((.(((....)))..))).))))))	chr7:94293335-94293575(+)$1	1	167	202	13.0033
.(((((((((((.(((....))).).))))))).)	chr16:30016576-30016826(+)$1	1	87	122	13.7955
(((((..(((((.(((....))).)))))...)))	chr1:145586543-145586783(-)$1	1	49	84	13.8174
.(((((..(.(((((((....))))))).).))))	chr12:50385735-50386015(-)$1	1	59	94	9.9663
(...((.....(((((....)))))...)).))))	chr12:120636253-120636493(-)$1	1	94	129	10.9392
((((.(((.((..(((....))))).)))))))..	chr22:29736699-29736939(-)$1	1	157	192	11.3183
..((((...(((((((....)))))))...)))).	chr8:42259384-42259629(+)$1	1	31	66	12.0568
((..((..((((.(((....))).))))..))..)	chr1:100533933-100534227(+)$1	1	244	279	12.3002
(.(((...((((..(((...))).))))...))).	chr12:1192556-1192796(+)$1	1	17	52	11.8913
((((((((.((..(((....)))..)).))))...	chr6:107096919-107097161(+)$1	1	66	101	10.5526
((((((.(((.(((.(....)))).))).)))).)	chr16:2141738-2141981(-)$1	1	32	67	12.4207
((((.(..(((..((....)).)))..).))))))	chr10:6146798-6147038(+)$1	1	34	69	10.8958
((((((.(((((((((....))).)))))))))))	chr4:89442640-89442888(-)$1	1	14	49	11.4213
((((.(.((.....(((...)))....))).))))	chr16:30748885-30749125(+)$1	1	90	125	12.3458
.(((((.(((.(((((....)))).).)))...))	chr17:74046420-74046700(-)$1	1	223	258	13.3073
((..(((.((....((....))....)).)))..)	chr2:122120657-122120897(-)$1	1	204	239	12.3811
((....(((((.((((....))))..)))))....	chrX:154292157-154292397(-)$1	1	156	191	12.2556
((((((((((...(((....))))))))))).)))	chr13:98667889-98668129(+)$1	1	142	177	10.6554
.((.(((.(((.(((((....))))))))))).))	chr19:2042375-2042616(-)$1	1	170	205	9.6191
.((...((((..((((....))))..)))).....	chr3:107492104-107492344(+)$1	1	70	105	11.6933

#PSSM
f : 0.13	g : 0.11	[ : 0.09	! : 0.09	b : 0.07	c : 0.07	e : 0.07	d : 0.07	# : 0.05	= : 0.03	: : 0.03	a : 0.03	$ : 0.01	F : 0.01	" : 0.01	
e : 0.19	g : 0.11	b : 0.11	f : 0.09	# : 0.05	d : 0.05	! : 0.05	[ : 0.05	c : 0.05	" : 0.03	= : 0.03	a : 0.03	$ : 0.01	: : 0.01	F : 0.01	
e : 0.17	d : 0.11	g : 0.09	# : 0.09	" : 0.07	f : 0.07	! : 0.07	c : 0.07	b : 0.05	= : 0.03	$ : 0.01	[ : 0.01	: : 0.01	a : 0.01	h : 0.01	
c : 0.17	e : 0.17	d : 0.13	" : 0.09	g : 0.09	# : 0.09	f : 0.05	= : 0.03	[ : 0.03	! : 0.03	b : 0.01	h : 0.01	
c : 0.19	e : 0.17	d : 0.11	g : 0.09	# : 0.09	b : 0.05	" : 0.05	[ : 0.05	! : 0.03	f : 0.03	= : 0.01	a : 0.01	h : 0.01	
c : 0.17	e : 0.17	! : 0.09	d : 0.09	" : 0.07	# : 0.07	g : 0.05	[ : 0.05	a : 0.05	f : 0.03	b : 0.03	= : 0.01	h : 0.01	
[ : 0.21	! : 0.15	c : 0.11	" : 0.09	d : 0.07	e : 0.07	g : 0.05	$ : 0.03	b : 0.03	# : 0.03	= : 0.01	f : 0.01	a : 0.01	h : 0.01	
! : 0.13	c : 0.13	b : 0.13	e : 0.11	" : 0.09	d : 0.07	$ : 0.05	[ : 0.05	f : 0.05	a : 0.03	# : 0.01	= : 0.01	g : 0.01	h : 0.01	
c : 0.17	b : 0.13	d : 0.11	e : 0.11	$ : 0.09	[ : 0.05	" : 0.05	f : 0.05	! : 0.03	# : 0.03	a : 0.03	= : 0.01	g : 0.01	h : 0.01	
c : 0.15	b : 0.13	e : 0.13	$ : 0.11	d : 0.11	g : 0.05	# : 0.05	" : 0.05	f : 0.05	[ : 0.03	! : 0.01	= : 0.01	h : 0.01	
$ : 0.11	b : 0.11	# : 0.09	" : 0.09	c : 0.09	e : 0.09	g : 0.07	d : 0.07	[ : 0.07	! : 0.05	f : 0.05	= : 0.01	
! : 0.21	e : 0.13	$ : 0.07	a : 0.07	" : 0.07	# : 0.07	g : 0.05	d : 0.05	[ : 0.05	c : 0.05	b : 0.03	f : 0.03	= : 0.01	
! : 0.19	[ : 0.17	d : 0.15	e : 0.11	g : 0.05	$ : 0.05	c : 0.05	# : 0.05	f : 0.03	" : 0.03	b : 0.01	= : 0.01	
c : 0.47	d : 0.19	e : 0.11	g : 0.05	[ : 0.03	# : 0.03	= : 0.01	! : 0.01	b : 0.01	$ : 0.01	
c : 0.50	d : 0.19	e : 0.09	b : 0.07	g : 0.05	[ : 0.03	= : 0.01	
c : 0.49	d : 0.19	e : 0.09	g : 0.05	b : 0.05	a : 0.03	! : 0.01	= : 0.01	m : 0.01	
m : 0.70	n : 0.05	l : 0.05	c : 0.05	d : 0.03	! : 0.01	= : 0.01	g : 0.01	e : 0.01	
m : 0.78	l : 0.11	n : 0.05	a : 0.01	= : 0.01	
m : 0.80	l : 0.13	n : 0.05	
m : 0.78	l : 0.07	n : 0.05	c : 0.03	e : 0.01	b : 0.01	
c : 0.45	d : 0.15	m : 0.09	e : 0.07	b : 0.07	n : 0.05	a : 0.03	l : 0.01	g : 0.01	
c : 0.50	d : 0.19	e : 0.09	g : 0.05	b : 0.05	] : 0.03	m : 0.01	= : 0.01	
c : 0.50	d : 0.19	e : 0.11	g : 0.05	] : 0.03	a : 0.03	= : 0.01	4 : 0.01	
d : 0.19	] : 0.17	e : 0.13	2 : 0.11	c : 0.09	4 : 0.07	g : 0.05	3 : 0.05	b : 0.03	= : 0.01	h : 0.01	
2 : 0.19	e : 0.15	3 : 0.09	d : 0.09	4 : 0.07	] : 0.07	g : 0.05	b : 0.05	c : 0.05	f : 0.03	a : 0.03	= : 0.01	h : 0.01	
2 : 0.11	3 : 0.11	] : 0.11	e : 0.11	4 : 0.09	c : 0.09	g : 0.05	d : 0.05	a : 0.05	f : 0.05	b : 0.05	= : 0.01	h : 0.01	
c : 0.17	e : 0.15	d : 0.11	b : 0.11	g : 0.07	2 : 0.07	4 : 0.07	f : 0.05	3 : 0.05	= : 0.03	] : 0.01	h : 0.01	
b : 0.17	c : 0.17	e : 0.13	d : 0.11	g : 0.07	2 : 0.05	f : 0.05	4 : 0.03	= : 0.03	] : 0.03	3 : 0.03	a : 0.01	h : 0.01	
] : 0.21	e : 0.15	b : 0.13	c : 0.11	d : 0.07	4 : 0.05	f : 0.05	g : 0.03	= : 0.03	2 : 0.03	3 : 0.03	h : 0.01	
c : 0.15	d : 0.15	e : 0.11	3 : 0.09	g : 0.07	] : 0.07	a : 0.07	f : 0.05	b : 0.05	= : 0.03	4 : 0.03	2 : 0.01	h : 0.01	
c : 0.15	d : 0.13	3 : 0.11	e : 0.11	g : 0.07	] : 0.07	a : 0.05	4 : 0.05	b : 0.05	= : 0.03	2 : 0.03	f : 0.01	h : 0.01	> : 0.01	
c : 0.15	d : 0.15	3 : 0.13	e : 0.13	g : 0.07	2 : 0.07	4 : 0.05	] : 0.05	= : 0.03	b : 0.03	f : 0.03	> : 0.01	
e : 0.19	d : 0.15	3 : 0.11	g : 0.09	2 : 0.09	c : 0.09	f : 0.05	= : 0.03	] : 0.03	4 : 0.03	a : 0.01	5 : 0.01	> : 0.01	
e : 0.17	c : 0.11	g : 0.09	2 : 0.09	3 : 0.07	f : 0.07	d : 0.07	] : 0.07	= : 0.03	4 : 0.03	6 : 0.01	: : 0.01	9 : 0.01	5 : 0.01	b : 0.01	> : 0.01	
e : 0.17	f : 0.13	c : 0.11	g : 0.09	b : 0.09	= : 0.05	2 : 0.05	3 : 0.03	: : 0.03	d : 0.03	6 : 0.01	a : 0.01	9 : 0.01	] : 0.01	5 : 0.01	4 : 0.01	> : 0.01	

#score	606.3641858496552
#seq	51
#width	35
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_UTR_m2_run1.txt

#BEAR
ccc[ddddnnnnndddd]ccc	chr4:184210579-184210823(+)$1	244	148	169	13.1584
[gggggggnnnnnggggggg]	chr16:53967816-53968083(+)$1	267	233	254	11.5899
b[bbddddnnnnndddd]bb]	chr15:75940264-75940489(-)$1	225	194	215	11.5911
ccc[ddddnnnnnddddccc4	chr7:65422378-65422602(+)$1	224	165	186	12.8901
cc[eeeeennnnneeeee22c	chr10:111985742-111985974(+)$1	232	136	157	12.1883
ccc"""bbnnnnnbb333ccc	chr14:21967348-21967599(-)$1	251	90	111	10.2871
ddd[ddddnnnnndddd]ddd	chr1:100315733-100315955(+)$1	222	1	22	12.5850
ddd!!cccnnnnncccdddd2	chr2:85825834-85826056(+)$1	222	181	202	11.7213
b"""ddddnnnnndddd22bb	chr11:8985664-8985897(-)$1	233	137	158	12.6036
""aeeeeennnnneeeee]a4	chr22:24808522-24808749(+)$1	227	188	209	12.1759
fffeeeeennnnneeeee]ff	chr10:103912050-103912277(+)$1	227	10	31	11.6517
eee[ddddnnnnndddd]eee	chr7:72951105-72951325(-)$1	220	51	72	12.4738
ccc[ddddnnnnndddd]ccc	chr20:44441240-44441459(+)$1	219	157	178	13.1584
gggggg[annnnnaggggggg	chr2:242665229-242665448(+)$1	219	6	27	11.3926
ddddddddnnnnndddd4444	chr19:49510229-49510466(+)$1	237	191	212	12.3895
bb[eeeeennnnneeeee]bb	chr16:2164294-2164521(-)$1	227	35	56	11.7892
ddd!!cccnnnnnccc22ddd	chr14:60749596-60749817(+)$1	221	7	28	11.6299
cc[eeeeennnnneeeee]cc	chr19:50302914-50303145(+)$1	231	94	115	12.4349
ccceeeeennnnneeeee]cc	chr12:125431896-125432137(-)$1	241	14	35	12.2906
gggg[cccnnnnncccggggg	chr1:85725193-85725418(-)$1	225	15	36	12.0027
b"""ddddnnnnndddd22bb	chr19:2271681-2271900(+)$1	219	189	210	12.6036
ebb[ddddnnnnndddd22bb	chr3:12458207-12458441(+)$1	234	151	172	12.4025
bb[eeeeennnnneeeee]bb	chr12:112460354-112460579(+)$1	225	61	82	11.7892
cgggggggnnnnnggggggg:	chr2:231931676-231931899(+)$1	223	109	130	10.7886
ddd[ddddnnnnndddddddd	chr19:19617404-19617633(+)$1	229	156	177	12.2674
fff!!cccnnnnnccc22fff	chr4:119606601-119606855(-)$1	254	135	156	11.5088
hh[eeeeennnnneeeee22h	chr19:36633512-36633732(+)$1	220	87	108	11.5133
!gggggggnnnnnggggggg3	chrX:23748849-23749068(-)$1	219	78	99	11.6886
[bb[ddddnnnnndddd]bbe	chr17:8076671-8076971(-)$1	300	137	158	12.1762
cccddddannnnna]dddd::	chr19:42373010-42373234(+)$1	224	129	150	10.0066
iiiiiiiinnnnniiiiiiii	chr7:100876089-100876310(-)$1	221	89	110	11.4623
gggggg[annnnnaggggggg	chr14:21967534-21967808(-)$1	274	165	186	11.3926
b!!a[cccnnnnnccc]a22b	chr5:79946505-79946748(-)$1	243	3	24	11.6980
========nnnnn========	chr19:12811816-12812039(-)$1	223	131	152	11.8927
a####cccnnnnnccc22a44	chr9:35757446-35757668(+)$1	222	22	43	11.7975
[cccddddoooooodddd]cc	chr11:506515-506755(-)$1	240	76	97	8.0289
$$$eeeeennnnneeeee22f	chr19:37180270-37180498(+)$1	228	112	133	11.1521
eeee[cccnnnnnccceeeee	chr8:56986856-56987082(-)$1	226	89	110	11.4106
eeee[cccnnnnnccc]eeee	chr11:64619989-64620223(-)$1	234	126	147	11.3152
ddd[ddddnnnnndddddddd	chr11:64845933-64846157(-)$1	224	149	170	12.2674
dda!!cccnnnnnccc22a]d	chr20:3804881-3805100(-)$1	219	27	48	11.8656
ee[eeeeennnnneeeee333	chr7:26241396-26241620(+)$1	224	95	116	12.4330
fff[ddddnnnnndddd]fff	chr9:36162776-36162999(+)$1	223	114	135	12.4639
ggg[ddddnnnnndddd]ggg	chr1:154550734-154550958(-)$1	224	116	137	13.1305
[gggggggnnnnnggggggg3	chr17:7245259-7245484(+)$1	225	87	108	11.6935
Jbb[ddddnnnnndddd]bb:	chr2:220403279-220403515(+)$1	236	15	36	10.1138
ddd[eeeeennnnneeeee33	chr12:124457031-124457253(-)$1	222	77	98	9.7900
ddd[ddddnnnnndddd22dd	chr22:51051907-51052131(+)$1	224	122	143	12.7222
ffff[cccnnnnncccfffff	chr3:127790086-127790310(+)$1	224	169	190	10.8538
ddd[ddddoooooodddd]dd	chr16:53922645-53922882(+)$1	237	212	233	7.9853
[gggggggnnnnnggggggg]	chr19:6424207-6424435(-)$1	228	157	178	11.5899
ee[a[cccnnnnnccc]a333	chr1:16785320-16785556(+)$1	236	141	162	12.2861
bb[eeeeennnnneeeee]bb	chr12:48138482-48138701(-)$1	219	135	156	11.7892
dddd[cccnnnnncccdddd:	chr7:2701902-2702121(+)$1	219	192	213	10.6237

#otherMatches

#Seq PSSM
UCCACCAGGCGUGCUGGAGGA	chr4:184210579-184210823(+)$1	244	148	169	13.1584
UGUUCUUGACAAACAAGAACU	chr16:53967816-53968083(+)$1	267	233	254	11.5899
CCUCCGCUCCGCCAGCGAGAA	chr15:75940264-75940489(-)$1	225	194	215	11.5911
gcaugguggcucacaccugua	chr7:65422378-65422602(+)$1	224	165	186	12.8901
GGAACGGCGCCCGGCCGUAGC	chr10:111985742-111985974(+)$1	232	136	157	12.1883
GUCAAAGGAAAUCCCCAAGGC	chr14:21967348-21967599(-)$1	251	90	111	10.2871
GCGAAGUCGCUGAGACUCUGC	chr1:100315733-100315955(+)$1	222	1	22	12.5850
UGGCAGCUGGCAGGGCCCACU	chr2:85825834-85826056(+)$1	222	181	202	11.7213
CCAAGGUGAGUCCCGCCCAGC	chr11:8985664-8985897(-)$1	233	137	158	12.6036
CUCCUUCUGGUUAAGAAGAGU	chr22:24808522-24808749(+)$1	227	188	209	12.1759
UAUGCGCCCGCGCGGCGCAAU	chr10:103912050-103912277(+)$1	227	10	31	11.6517
CACCUUCUAGAAGAGAGCGUG	chr7:72951105-72951325(-)$1	220	51	72	12.4738
CCGAGCGGGGGCGCCGCCCGG	chr20:44441240-44441459(+)$1	219	157	178	13.1584
CGUGGGUCUGUGUGUCCGUGA	chr2:242665229-242665448(+)$1	219	6	27	11.3926
AGGCGGGUGCCAGACCCCAGA	chr19:49510229-49510466(+)$1	237	191	212	12.3895
GCUCCAGGUGGACUCUGGUGC	chr16:2164294-2164521(-)$1	227	35	56	11.7892
GCAUGCUGGUUCUCAGGUUGC	chr14:60749596-60749817(+)$1	221	7	28	11.6299
AUCCGCGAGGAGAUCGUGAGU	chr19:50302914-50303145(+)$1	231	94	115	12.4349
GUGGAUGAUGAUUUCAUCUCA	chr12:125431896-125432137(-)$1	241	14	35	12.2906
GGCCACGCGAGGGGCGGGCCC	chr1:85725193-85725418(-)$1	225	15	36	12.0027
AUUAACUGGCGAACAGUGCUG	chr19:2271681-2271900(+)$1	219	189	210	12.6036
GAGUAUGCCAAAAGCAUUCCU	chr3:12458207-12458441(+)$1	234	151	172	12.4025
CUGCCUUCCAGAAGAAGGGGG	chr12:112460354-112460579(+)$1	225	61	82	11.7892
ACGAAGACUGGACGUCUUUGA	chr2:231931676-231931899(+)$1	223	109	130	10.7886
CCGUGUCUCUUGCAGGCUGGG	chr19:19617404-19617633(+)$1	229	156	177	12.2674
GCUCCCGGAUCUCCUGCAAGC	chr4:119606601-119606855(-)$1	254	135	156	11.5088
AGGUCCGGCAGUUCCGGAGAC	chr19:36633512-36633732(+)$1	220	87	108	11.5133
CUUUGGGCAGUGAGCCUGAAU	chrX:23748849-23749068(-)$1	219	78	99	11.6886
ugaaacgugauuaacgucucu	chr17:8076671-8076971(-)$1	300	137	158	12.1762
GGGUUGGCUCCAUGACCAAGA	chr19:42373010-42373234(+)$1	224	129	150	10.0066
GACUGGGGUCGUCCUCCGGUC	chr7:100876089-100876310(-)$1	221	89	110	11.4623
ACUGCUUGGUGAGCAGCAGUG	chr14:21967534-21967808(-)$1	274	165	186	11.3926
GGAAAGAUGAAAAAUUAUAAC	chr5:79946505-79946748(-)$1	243	3	24	11.6980
cACUUGCCCUCCUGGCAGGUG	chr19:12811816-12812039(-)$1	223	131	152	11.8927
CGUAACCCAGAAAGGGAAGGA	chr9:35757446-35757668(+)$1	222	22	43	11.7975
CGGCCUCCCGGGAAGGAGCGC	chr11:506515-506755(-)$1	240	76	97	8.0289
UACCACUAUAAUUUAGUGUAA	chr19:37180270-37180498(+)$1	228	112	133	11.1521
GUUCGCUCUCGCCGAGGAACA	chr8:56986856-56987082(-)$1	226	89	110	11.4106
GGCAAGGUGACCAACCCUGCC	chr11:64619989-64620223(-)$1	234	126	147	11.3152
GACAUUCAGCCUGUGGAGUCU	chr11:64845933-64846157(-)$1	224	149	170	12.2674
GGCUUGUGUCACCCACUUGUC	chr20:3804881-3805100(-)$1	219	27	48	11.8656
UCAGAUGCCACACGCGUCCCG	chr7:26241396-26241620(+)$1	224	95	116	12.4330
AAGUUCAUUUUAUGUGAUCUU	chr9:36162776-36162999(+)$1	223	114	135	12.4639
GAGGAGCUGGACAAGCUGCUC	chr1:154550734-154550958(-)$1	224	116	137	13.1305
UGACCUGGCCCGCCUGGGUCC	chr17:7245259-7245484(+)$1	225	87	108	11.6935
UGGCCCAGCAGGCCUGGCCCA	chr2:220403279-220403515(+)$1	236	15	36	10.1138
ccccgcccagcccaugggcca	chr12:124457031-124457253(-)$1	222	77	98	9.7900
UGGCCAGCUCCCUGUUGAACC	chr22:51051907-51052131(+)$1	224	122	143	12.7222
CUUGGCCUCUGGCAGGCAGGC	chr3:127790086-127790310(+)$1	224	169	190	10.8538
GGUGUGGUAAGUCCAUCAGAC	chr16:53922645-53922882(+)$1	237	212	233	7.9853
CCCCCUGCAGGGAGUAGGGGC	chr19:6424207-6424435(-)$1	228	157	178	11.5899
CUCCUCAGCUGGCCUGUGUUU	chr1:16785320-16785556(+)$1	236	141	162	12.2861
GGAUCUGCUAUACGCAGAGCU	chr12:48138482-48138701(-)$1	219	135	156	11.7892
UGGCCGCCUUCUUGGUGCCAA	chr7:2701902-2702121(+)$1	219	192	213	10.6237

#DB
(((.((((.....)))).)))	chr4:184210579-184210823(+)$1	1	148	169	13.1584
.(((((((.....))))))).	chr16:53967816-53968083(+)$1	1	233	254	11.5899
(.((((((.....)))).)).	chr15:75940264-75940489(-)$1	1	194	215	11.5911
(((.((((.....))))))).	chr7:65422378-65422602(+)$1	1	165	186	12.8901
((.(((((.....)))))..)	chr10:111985742-111985974(+)$1	1	136	157	12.1883
(((...((.....))...)))	chr14:21967348-21967599(-)$1	1	90	111	10.2871
(((.((((.....)))).)))	chr1:100315733-100315955(+)$1	1	1	22	12.5850
(((..(((.....))))))).	chr2:85825834-85826056(+)$1	1	181	202	11.7213
(...((((.....))))..))	chr11:8985664-8985897(-)$1	1	137	158	12.6036
..((((((.....))))).).	chr22:24808522-24808749(+)$1	1	188	209	12.1759
((((((((.....))))).))	chr10:103912050-103912277(+)$1	1	10	31	11.6517
(((.((((.....)))).)))	chr7:72951105-72951325(-)$1	1	51	72	12.4738
(((.((((.....)))).)))	chr20:44441240-44441459(+)$1	1	157	178	13.1584
((((((.(.....))))))))	chr2:242665229-242665448(+)$1	1	6	27	11.3926
((((((((.....))))....	chr19:49510229-49510466(+)$1	1	191	212	12.3895
((.(((((.....))))).))	chr16:2164294-2164521(-)$1	1	35	56	11.7892
(((..(((.....)))..)))	chr14:60749596-60749817(+)$1	1	7	28	11.6299
((.(((((.....))))).))	chr19:50302914-50303145(+)$1	1	94	115	12.4349
((((((((.....))))).))	chr12:125431896-125432137(-)$1	1	14	35	12.2906
((((.(((.....))))))))	chr1:85725193-85725418(-)$1	1	15	36	12.0027
(...((((.....))))..))	chr19:2271681-2271900(+)$1	1	189	210	12.6036
)((.((((.....))))..))	chr3:12458207-12458441(+)$1	1	151	172	12.4025
((.(((((.....))))).))	chr12:112460354-112460579(+)$1	1	61	82	11.7892
)(((((((.....))))))).	chr2:231931676-231931899(+)$1	1	109	130	10.7886
(((.((((.....))))))))	chr19:19617404-19617633(+)$1	1	156	177	12.2674
(((..(((.....)))..)))	chr4:119606601-119606855(-)$1	1	135	156	11.5088
((.(((((.....)))))..)	chr19:36633512-36633732(+)$1	1	87	108	11.5133
.(((((((.....))))))).	chrX:23748849-23749068(-)$1	1	78	99	11.6886
.((.((((.....)))).)))	chr17:8076671-8076971(-)$1	1	137	158	12.1762
)))(((((.....).))))..	chr19:42373010-42373234(+)$1	1	129	150	10.0066
((((((((.....))))))))	chr7:100876089-100876310(-)$1	1	89	110	11.4623
((((((.(.....))))))))	chr14:21967534-21967808(-)$1	1	165	186	11.3926
(..(.(((.....))).)..)	chr5:79946505-79946748(-)$1	1	3	24	11.6980
((((((((.....))))))))	chr19:12811816-12812039(-)$1	1	131	152	11.8927
(....(((.....)))..)..	chr9:35757446-35757668(+)$1	1	22	43	11.7975
.(((((((......)))).))	chr11:506515-506755(-)$1	1	76	97	8.0289
...(((((.....)))))..)	chr19:37180270-37180498(+)$1	1	112	133	11.1521
((((.(((.....))))))))	chr8:56986856-56987082(-)$1	1	89	110	11.4106
((((.(((.....))).))))	chr11:64619989-64620223(-)$1	1	126	147	11.3152
(((.((((.....))))))))	chr11:64845933-64846157(-)$1	1	149	170	12.2674
(((..(((.....)))..).)	chr20:3804881-3805100(-)$1	1	27	48	11.8656
((.(((((.....)))))...	chr7:26241396-26241620(+)$1	1	95	116	12.4330
(((.((((.....)))).)))	chr9:36162776-36162999(+)$1	1	114	135	12.4639
(((.((((.....)))).)))	chr1:154550734-154550958(-)$1	1	116	137	13.1305
.(((((((.....))))))).	chr17:7245259-7245484(+)$1	1	87	108	11.6935
(((.((((.....)))).)).	chr2:220403279-220403515(+)$1	1	15	36	10.1138
(((.(((((.....)))))..	chr12:124457031-124457253(-)$1	1	77	98	9.7900
(((.((((.....))))..))	chr22:51051907-51052131(+)$1	1	122	143	12.7222
((((.(((.....))))))))	chr3:127790086-127790310(+)$1	1	169	190	10.8538
(((.((((......)))).))	chr16:53922645-53922882(+)$1	1	212	233	7.9853
.(((((((.....))))))).	chr19:6424207-6424435(-)$1	1	157	178	11.5899
((.(.(((.....))).)...	chr1:16785320-16785556(+)$1	1	141	162	12.2861
((.(((((.....))))).))	chr12:48138482-48138701(-)$1	1	135	156	11.7892
((((.(((.....))))))).	chr7:2701902-2702121(+)$1	1	192	213	10.6237

#PSSM
d : 0.20	c : 0.16	b : 0.12	e : 0.11	[ : 0.09	f : 0.07	g : 0.07	" : 0.01	h : 0.01	! : 0.01	i : 0.01	= : 0.01	a : 0.01	$ : 0.01	J : 0.01	
d : 0.20	c : 0.16	g : 0.16	b : 0.11	e : 0.09	f : 0.07	" : 0.05	[ : 0.01	h : 0.01	i : 0.01	! : 0.01	= : 0.01	# : 0.01	$ : 0.01	
d : 0.18	g : 0.16	[ : 0.14	c : 0.12	b : 0.07	f : 0.07	e : 0.05	" : 0.03	a : 0.03	i : 0.01	! : 0.01	= : 0.01	# : 0.01	$ : 0.01	
[ : 0.27	e : 0.24	g : 0.14	! : 0.07	" : 0.05	d : 0.05	a : 0.03	b : 0.01	i : 0.01	= : 0.01	# : 0.01	c : 0.01	f : 0.01	
d : 0.37	e : 0.22	g : 0.12	[ : 0.12	! : 0.07	" : 0.01	i : 0.01	= : 0.01	# : 0.01	
d : 0.37	e : 0.22	c : 0.22	g : 0.12	" : 0.01	i : 0.01	= : 0.01	
d : 0.37	e : 0.22	c : 0.22	g : 0.09	[ : 0.03	b : 0.01	i : 0.01	= : 0.01	
d : 0.35	e : 0.22	c : 0.22	g : 0.09	a : 0.05	b : 0.01	i : 0.01	= : 0.01	
n : 0.94	o : 0.03	e : 0.01	
n : 0.96	o : 0.03	
n : 0.96	o : 0.03	
n : 0.96	o : 0.03	
n : 0.96	o : 0.03	
d : 0.31	c : 0.22	e : 0.20	g : 0.09	a : 0.05	o : 0.03	b : 0.01	i : 0.01	= : 0.01	n : 0.01	
d : 0.35	e : 0.22	c : 0.22	g : 0.12	b : 0.01	] : 0.01	i : 0.01	= : 0.01	
d : 0.37	e : 0.22	c : 0.22	g : 0.12	3 : 0.01	i : 0.01	= : 0.01	
d : 0.40	e : 0.24	g : 0.14	2 : 0.07	] : 0.05	3 : 0.01	i : 0.01	= : 0.01	f : 0.01	
e : 0.25	] : 0.16	g : 0.14	2 : 0.14	d : 0.12	a : 0.03	c : 0.01	3 : 0.01	4 : 0.01	i : 0.01	= : 0.01	f : 0.01	
g : 0.16	] : 0.16	2 : 0.14	d : 0.12	c : 0.07	e : 0.07	b : 0.05	f : 0.05	a : 0.03	3 : 0.03	4 : 0.01	i : 0.01	= : 0.01	
g : 0.16	b : 0.16	d : 0.14	c : 0.12	2 : 0.07	f : 0.07	e : 0.05	3 : 0.05	4 : 0.03	a : 0.01	: : 0.01	i : 0.01	= : 0.01	] : 0.01	
c : 0.12	d : 0.12	b : 0.12	f : 0.09	3 : 0.09	4 : 0.07	e : 0.07	g : 0.07	: : 0.07	] : 0.05	2 : 0.01	h : 0.01	i : 0.01	= : 0.01	

#score	630.5091825629197
#seq	54
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_UTR_m3_run1.txt

#BEAR
f[ddddqqqqqqqqdddd]f	chr14:61177822-61178049(-)$1	227	124	144	13.3290
ffffffqqqqqqqqffffff	chr22:38879632-38879860(-)$1	228	192	212	14.4143
ffffffqqqqqqqqffffff	chr11:71707943-71708165(+)$1	222	101	121	14.4143
"""cccqqqqqqqqccc333	chr1:231499567-231499789(-)$1	222	82	102	15.1015
ffffffqqqqqqqqffffff	chr7:75957301-75957525(-)$1	224	61	81	14.4143
:eeeeeqqqqqqqqeeeeeC	chr21:36162663-36162884(-)$1	221	0	20	13.1413
"""cccqqqqqqqqccc333	chr19:541961-542184(+)$1	223	161	181	15.1015
"eeeeeqqqqqqqqeeeee3	chr17:58741703-58741925(+)$1	222	94	114	15.1809
:eeeeeqqqqqqqqeeeee:	chr1:205686184-205686406(-)$1	222	6	26	13.3513
:eeeeeqqqqqqqqeeeee:	chr2:122155840-122156059(-)$1	219	165	185	13.3513
ccc[bbqqqqqqqqbb]ccc	chr4:140394905-140395133(+)$1	228	80	100	13.5581
ee[cccqqqqqqqqccc22e	chrX:99884601-99884825(-)$1	224	118	138	14.3305
[eeeeeqqqqqqqqeeeeed	chr19:12739414-12739635(+)$1	221	37	57	14.8431
ggggggqqqqqqqqgggggg	chrX:153289535-153289759(-)$1	224	129	149	14.9609
:eeeeeqqqqqqqqeeeee:	chr2:179369676-179369902(+)$1	226	64	84	13.3513
gggggaqqqqqqqqa]gggg	chr1:26797353-26797578(+)$1	225	140	160	14.6639
cc[cccqqqqqqqqccc]cc	chr5:179263350-179263573(-)$1	223	183	203	14.8451
ggg[bbqqqqqqqqbb]ggg	chr6:109786225-109786452(-)$1	227	99	119	14.0665
dd[cccqqqqqqqqccc]dd	chr3:9483728-9483949(+)$1	221	44	64	14.2518
""ddddqqqqqqqqdddd44	chr13:100615894-100616134(-)$1	240	33	53	13.4137
g!!cccqqqqqqqqccc444	chr2:10044980-10045201(+)$1	221	135	155	14.8935
ccc[bbqqqqqqqqbb]ccc	chr1:10518290-10518512(-)$1	222	11	31	13.5581
dddcccqqqqqqqqccc]dd	chr1:203770316-203770541(+)$1	225	178	198	13.9793
ggggggqqqqqqqqgggggg	chr10:72183963-72184184(+)$1	221	78	98	14.9609
ffffffqqqqqqqqffffff	chr22:50283172-50283402(+)$1	230	77	97	14.4143
======qqqqqqqq======	chrX:70504784-70505005(+)$1	221	187	207	14.7301
ffffffqqqqqqqqffffff	chr8:33229769-33229989(-)$1	220	195	215	14.4143
###cccqqqqqqqqccc333	chr1:93603604-93603826(+)$1	222	135	155	15.0244
"eeeeeqqqqqqqqeeeee3	chr12:120649245-120649467(-)$1	222	137	157	15.1809
!eeeeeqqqqqqqqeeeee2	chr6:29913409-29913636(+)$1	227	138	158	14.9518
ggggggqqqqqqqqgggggg	chr20:61569400-61569621(+)$1	221	131	151	14.9609
ggggggqqqqqqqqgggggg	chr13:108860690-108860918(-)$1	228	80	100	14.9609
dddcccqqqqqqqqccc333	chr1:91990724-91990946(+)$1	222	52	72	14.5499
:eeeeeqqqqqqqqeeeeea	chrX:24233285-24233515(+)$1	230	133	153	14.1152
b!!cccqqqqqqqqccc]bb	chr1:112255398-112255624(+)$1	226	189	209	14.2419
&&&cccqqqqqqqqccc444	chr4:95585308-95585529(+)$1	221	106	126	12.8684
ee!!bbqqqqqqqqbb22ee	chr7:99668592-99668814(-)$1	222	4	24	13.3824
cc!!bbqqqqqqqqbb22cc	chr4:38700040-38700269(+)$1	229	138	158	13.4280
ggggggqqqqqqqqgggggg	chrX:77084491-77084722(-)$1	231	65	85	14.9609
fffffaqqqqqqqqa]ffff	chrX:12842089-12842316(+)$1	227	12	32	14.1989
:eeeeeqqqqqqqqeeeee:	chr3:10321663-10321889(+)$1	226	126	146	13.3513
ffffffqqqqqqqqffffff	chr16:23478528-23478751(-)$1	223	172	192	14.4143
e::cccqqqqqqqqcccfff	chrX:53405090-53405310(-)$1	220	148	168	12.4088
ggggggqqqqqqqqgggggg	chr17:58026766-58026986(+)$1	220	8	28	14.9609
ggggggqqqqqqqqgggggg	chr12:67707967-67708187(+)$1	220	131	151	14.9609
!eeeeeqqqqqqqqeeeee3	chr9:135568586-135568814(+)$1	228	193	213	15.2174
ffffffqqqqqqqqffffff	chr2:32534536-32534764(+)$1	228	142	162	14.4143
gg[cccqqqqqqqqccc]gg	chr6:64286630-64286863(+)$1	233	189	209	15.0988
ggg[bbqqqqqqqqbb]ggg	chr12:54628635-54628858(-)$1	223	109	129	14.0665
ggggggqqqqqqqqgggggg	chr1:225678280-225678504(-)$1	224	109	129	14.9609
[eeeeeqqqqqqqqeeeeed	chr17:43228237-43228466(+)$1	229	10	30	14.8431
ffffffqqqqqqqqffffff	chr20:11906875-11907096(+)$1	221	31	51	14.4143
:eeeeeqqqqqqqqeeeee:	chr15:25583930-25584165(-)$1	235	43	63	13.3513
[eeeeeqqqqqqqqeeeeec	chr21:30378429-30378652(-)$1	223	129	149	15.0419
:eeeeeqqqqqqqqeeeeeG	chr5:64964833-64965058(-)$1	225	1	21	13.8038

#otherMatches

#Seq PSSM
AUAGAGCUUGUUUUUUCUUU	chr14:61177822-61178049(-)$1	227	124	144	13.3290
UAAAAGGUUAGUGGCUUUUG	chr22:38879632-38879860(-)$1	228	192	212	14.4143
CCAUGGAUACUCGCCCGUGG	chr11:71707943-71708165(+)$1	222	101	121	14.4143
UAAAGCUUCAUAAUGCUGUU	chr1:231499567-231499789(-)$1	222	82	102	15.1015
CGGGUGAAUCUGUCUAUCUG	chr7:75957301-75957525(-)$1	224	61	81	14.4143
UGUCACUACUGUCCGUGGCU	chr21:36162663-36162884(-)$1	221	0	20	13.1413
CUCCACGUCCAUGAGUGACU	chr19:541961-542184(+)$1	223	161	181	15.1015
AUGGGUAUAUAUUCAUCUAA	chr17:58741703-58741925(+)$1	222	94	114	15.1809
GAUUUUUCCUUUAUGAAAUA	chr1:205686184-205686406(-)$1	222	6	26	13.3513
AGUAAUUAUUUGUCAUUACA	chr2:122155840-122156059(-)$1	219	165	185	13.3513
UCUAAUUAAUACUUAUCAGA	chr4:140394905-140395133(+)$1	228	80	100	13.5581
UAAAUUGUAAAUGAAGUAAU	chrX:99884601-99884825(-)$1	224	118	138	14.3305
ACUUUCGAAUACAUGAAAGG	chr19:12739414-12739635(+)$1	221	37	57	14.8431
AUUGCAUUUGCUUUUGUAAU	chrX:153289535-153289759(-)$1	224	129	149	14.9609
AGUUAAUCAUAUGUUUAAUA	chr2:179369676-179369902(+)$1	226	64	84	13.3513
UUCUGGGAAAGGUACACAGG	chr1:26797353-26797578(+)$1	225	140	160	14.6639
UGAGUGACCCGAAACACAUA	chr5:179263350-179263573(-)$1	223	183	203	14.8451
AAACAUAAAUUUACAUAUUU	chr6:109786225-109786452(-)$1	227	99	119	14.0665
UUGUGUUGAGAAUUACAGGA	chr3:9483728-9483949(+)$1	221	44	64	14.2518
UCUUGUCAUUGUUAAUAACU	chr13:100615894-100616134(-)$1	240	33	53	13.4137
GAUGGAAGUCAACCUCCCUG	chr2:10044980-10045201(+)$1	221	135	155	14.8935
GCUUAGAUCUUCUACUCAGC	chr1:10518290-10518512(-)$1	222	11	31	13.5581
AAAACUAAGCAGUCGGUAUU	chr1:203770316-203770541(+)$1	225	178	198	13.9793
AGCUGUAUAAUGCAGCAGCU	chr10:72183963-72184184(+)$1	221	78	98	14.9609
UUCCUGAAUGACACUAGGAG	chr22:50283172-50283402(+)$1	230	77	97	14.4143
UUAUAGGUGCUUUAUUAUGA	chrX:70504784-70505005(+)$1	221	187	207	14.7301
UUCCUUGUGCAAUGGAGGGA	chr8:33229769-33229989(-)$1	220	195	215	14.4143
UACCAAGAUUUAAAUUGAUA	chr1:93603604-93603826(+)$1	222	135	155	15.0244
UUAAAGACGUUCCCUUUUGU	chr12:120649245-120649467(-)$1	222	137	157	15.1809
AAAUUUACUUUCUCAAAUUC	chr6:29913409-29913636(+)$1	227	138	158	14.9518
CUCUCCCCAGCCCAGGAGAG	chr20:61569400-61569621(+)$1	221	131	151	14.9609
CAUUGCAGCAGGUGGUAAUG	chr13:108860690-108860918(-)$1	228	80	100	14.9609
GACCAAGGUGAAGAUUGAUA	chr1:91990724-91990946(+)$1	222	52	72	14.5499
UCAUGUAAGGAAAAACAUGG	chrX:24233285-24233515(+)$1	230	133	153	14.1152
UUAUAGGAAAAAAACUGGGA	chr1:112255398-112255624(+)$1	226	189	209	14.2419
UAUUACUUUUUCCUGUAUUU	chr4:95585308-95585529(+)$1	221	106	126	12.8684
UCCCUCAGAGUUACGACCGA	chr7:99668592-99668814(-)$1	222	4	24	13.3824
AAAACCACAGAUCAGGGAUU	chr4:38700040-38700269(+)$1	229	138	158	13.4280
GUGUUUGAAAAGAAGAAUGC	chrX:77084491-77084722(-)$1	231	65	85	14.9609
CUGGCCAAAAACAGGAGCCA	chrX:12842089-12842316(+)$1	227	12	32	14.1989
UGUACAGUCCUUUGUGUACC	chr3:10321663-10321889(+)$1	226	126	146	13.3513
GGUUGGAGGUUUUAUCAGCC	chr16:23478528-23478751(-)$1	223	172	192	14.4143
uauguaugaaaguuuaccua	chrX:53405090-53405310(-)$1	220	148	168	12.4088
AAAGAGAUUAAGUGCUUUUU	chr17:58026766-58026986(+)$1	220	8	28	14.9609
GAUAACAUACUGUGGUUAUU	chr12:67707967-67708187(+)$1	220	131	151	14.9609
AUCUGGGGUCCUAACCAGAG	chr9:135568586-135568814(+)$1	228	193	213	15.2174
UGAAUACUUCUAAAUAUUCA	chr2:32534536-32534764(+)$1	228	142	162	14.4143
UCACAUACAAGAACAUGAGA	chr6:64286630-64286863(+)$1	233	189	209	15.0988
AGUUACUUCAACUUGUCACU	chr12:54628635-54628858(-)$1	223	109	129	14.0665
UCUUCUUUAUUACUAGAGGG	chr1:225678280-225678504(-)$1	224	109	129	14.9609
UGUGCUUGCUUUCUAGUGCC	chr17:43228237-43228466(+)$1	229	10	30	14.8431
GGAACUAGGCUAGCAGUUCU	chr20:11906875-11907096(+)$1	221	31	51	14.4143
CUCCCUUCUUUAUUGGGGAC	chr15:25583930-25584165(-)$1	235	43	63	13.3513
AGAUAUUUCUUCACAUAUCA	chr21:30378429-30378652(-)$1	223	129	149	15.0419
CAUUGCUUGUUCAUGUAAUC	chr5:64964833-64965058(-)$1	225	1	21	13.8038

#DB
(.((((........)))).)	chr14:61177822-61178049(-)$1	1	124	144	13.3290
((((((........))))))	chr22:38879632-38879860(-)$1	1	192	212	14.4143
((((((........))))))	chr11:71707943-71708165(+)$1	1	101	121	14.4143
...(((........)))...	chr1:231499567-231499789(-)$1	1	82	102	15.1015
((((((........))))))	chr7:75957301-75957525(-)$1	1	61	81	14.4143
.(((((........)))))(	chr21:36162663-36162884(-)$1	1	0	20	13.1413
...(((........)))...	chr19:541961-542184(+)$1	1	161	181	15.1015
.(((((........))))).	chr17:58741703-58741925(+)$1	1	94	114	15.1809
.(((((........))))).	chr1:205686184-205686406(-)$1	1	6	26	13.3513
.(((((........))))).	chr2:122155840-122156059(-)$1	1	165	185	13.3513
(((.((........)).)))	chr4:140394905-140395133(+)$1	1	80	100	13.5581
((.(((........)))..)	chrX:99884601-99884825(-)$1	1	118	138	14.3305
.(((((........))))))	chr19:12739414-12739635(+)$1	1	37	57	14.8431
((((((........))))))	chrX:153289535-153289759(-)$1	1	129	149	14.9609
.(((((........))))).	chr2:179369676-179369902(+)$1	1	64	84	13.3513
((((((........).))))	chr1:26797353-26797578(+)$1	1	140	160	14.6639
((.(((........))).))	chr5:179263350-179263573(-)$1	1	183	203	14.8451
(((.((........)).)))	chr6:109786225-109786452(-)$1	1	99	119	14.0665
((.(((........))).))	chr3:9483728-9483949(+)$1	1	44	64	14.2518
..((((........))))..	chr13:100615894-100616134(-)$1	1	33	53	13.4137
(..(((........)))...	chr2:10044980-10045201(+)$1	1	135	155	14.8935
(((.((........)).)))	chr1:10518290-10518512(-)$1	1	11	31	13.5581
((((((........))).))	chr1:203770316-203770541(+)$1	1	178	198	13.9793
((((((........))))))	chr10:72183963-72184184(+)$1	1	78	98	14.9609
((((((........))))))	chr22:50283172-50283402(+)$1	1	77	97	14.4143
((((((........))))))	chrX:70504784-70505005(+)$1	1	187	207	14.7301
((((((........))))))	chr8:33229769-33229989(-)$1	1	195	215	14.4143
...(((........)))...	chr1:93603604-93603826(+)$1	1	135	155	15.0244
.(((((........))))).	chr12:120649245-120649467(-)$1	1	137	157	15.1809
.(((((........))))).	chr6:29913409-29913636(+)$1	1	138	158	14.9518
((((((........))))))	chr20:61569400-61569621(+)$1	1	131	151	14.9609
((((((........))))))	chr13:108860690-108860918(-)$1	1	80	100	14.9609
((((((........)))...	chr1:91990724-91990946(+)$1	1	52	72	14.5499
.(((((........)))))(	chrX:24233285-24233515(+)$1	1	133	153	14.1152
(..(((........))).))	chr1:112255398-112255624(+)$1	1	189	209	14.2419
...(((........)))...	chr4:95585308-95585529(+)$1	1	106	126	12.8684
((..((........))..))	chr7:99668592-99668814(-)$1	1	4	24	13.3824
((..((........))..))	chr4:38700040-38700269(+)$1	1	138	158	13.4280
((((((........))))))	chrX:77084491-77084722(-)$1	1	65	85	14.9609
((((((........).))))	chrX:12842089-12842316(+)$1	1	12	32	14.1989
.(((((........))))).	chr3:10321663-10321889(+)$1	1	126	146	13.3513
((((((........))))))	chr16:23478528-23478751(-)$1	1	172	192	14.4143
)..(((........)))(((	chrX:53405090-53405310(-)$1	1	148	168	12.4088
((((((........))))))	chr17:58026766-58026986(+)$1	1	8	28	14.9609
((((((........))))))	chr12:67707967-67708187(+)$1	1	131	151	14.9609
.(((((........))))).	chr9:135568586-135568814(+)$1	1	193	213	15.2174
((((((........))))))	chr2:32534536-32534764(+)$1	1	142	162	14.4143
((.(((........))).))	chr6:64286630-64286863(+)$1	1	189	209	15.0988
(((.((........)).)))	chr12:54628635-54628858(-)$1	1	109	129	14.0665
((((((........))))))	chr1:225678280-225678504(-)$1	1	109	129	14.9609
.(((((........))))))	chr17:43228237-43228466(+)$1	1	10	30	14.8431
((((((........))))))	chr20:11906875-11907096(+)$1	1	31	51	14.4143
.(((((........))))).	chr15:25583930-25584165(-)$1	1	43	63	13.3513
.(((((........))))))	chr21:30378429-30378652(-)$1	1	129	149	15.0419
.(((((........)))))(	chr5:64964833-64965058(-)$1	1	1	21	13.8038

#PSSM
g : 0.23	f : 0.18	: : 0.14	" : 0.09	c : 0.07	e : 0.05	[ : 0.05	d : 0.05	! : 0.03	= : 0.01	# : 0.01	b : 0.01	& : 0.01	
e : 0.30	g : 0.21	f : 0.16	c : 0.07	" : 0.05	d : 0.05	! : 0.03	[ : 0.01	= : 0.01	# : 0.01	& : 0.01	: : 0.01	
e : 0.27	g : 0.20	f : 0.16	d : 0.07	[ : 0.07	! : 0.07	" : 0.03	c : 0.03	= : 0.01	# : 0.01	& : 0.01	: : 0.01	
e : 0.27	c : 0.23	f : 0.16	g : 0.16	[ : 0.07	d : 0.03	! : 0.03	= : 0.01	
e : 0.27	c : 0.23	f : 0.16	g : 0.16	b : 0.10	d : 0.03	= : 0.01	
e : 0.27	c : 0.23	f : 0.14	g : 0.14	b : 0.10	d : 0.03	a : 0.03	= : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
e : 0.27	c : 0.23	f : 0.14	g : 0.14	b : 0.10	d : 0.03	a : 0.03	= : 0.01	
e : 0.27	c : 0.23	f : 0.14	g : 0.14	b : 0.10	d : 0.03	] : 0.03	= : 0.01	
e : 0.27	c : 0.23	f : 0.16	g : 0.16	] : 0.07	d : 0.03	2 : 0.03	= : 0.01	
e : 0.27	g : 0.20	f : 0.18	] : 0.09	3 : 0.07	2 : 0.05	d : 0.03	c : 0.03	4 : 0.03	= : 0.01	
e : 0.29	g : 0.21	f : 0.18	3 : 0.07	c : 0.07	4 : 0.05	d : 0.03	] : 0.01	2 : 0.01	= : 0.01	b : 0.01	
g : 0.21	f : 0.20	3 : 0.12	: : 0.09	c : 0.09	d : 0.07	4 : 0.05	e : 0.03	C : 0.01	= : 0.01	2 : 0.01	a : 0.01	b : 0.01	G : 0.01	

#score	787.1711499620816
#seq	55
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_CDS_m3_run2.txt

#BEAR
eeee[aqqqqqqqqa]eeee	chrM:10831-11073(-)$1	242	82	102	14.2407
ggggggqqqqqqqqgggggg	chr5:10264737-10264967(+)$1	230	208	228	14.4779
bbddddqqqqqqqqdddd]b	chr12:46764249-46764468(-)$1	219	83	103	14.2768
[a[cccqqqqqqqqccc]a2	chr20:30748999-30749219(+)$1	220	7	27	15.0298
b[ddddqqqqqqqqdddd]b	chr12:6687918-6688156(-)$1	238	125	145	14.7094
[ccc[aqqqqqqqqa]cccb	chr12:88568324-88568555(+)$1	231	175	195	14.2727
[cccbbqqqqqqqqbb]ccc	chr7:39990601-39990824(+)$1	223	191	211	13.5033
deeeeeqqqqqqqqeeeee]	chr18:77733711-77733936(-)$1	225	162	182	14.3848
###cccqqqqqqqqccc22f	chr1:91405709-91405935(-)$1	226	55	75	14.7950
ffffffqqqqqqqqffffff	chr16:8889796-8890020(-)$1	224	114	134	13.4184
hhhhhaqqqqqqqqa]hhhh	chr1:212002356-212002577(-)$1	221	83	103	12.9552
$$ddddqqqqqqqqdddd33	chr1:70639081-70639307(-)$1	226	137	157	14.7939
[eeeeeqqqqqqqqeeeeed	chr19:36727941-36728163(+)$1	222	134	154	14.5304
b[ddddqqqqqqqqdddd]b	chrM:13821-14163(-)$1	342	177	197	14.7094
!eeeeeqqqqqqqqeeeee2	chr19:7998966-7999187(-)$1	221	133	153	14.7147
%%ddddqqqqqqqqdddd22	chr12:125466958-125467186(-)$1	228	116	136	13.6119
c[ddddqqqqqqqqdddd]c	chr6:26388372-26388596(+)$1	224	154	174	14.9068
##ddddqqqqqqqqdddd22	chr14:69588875-69589094(-)$1	219	48	68	14.8902
eeecccqqqqqqqqccc22e	chrX:71495442-71495673(-)$1	231	62	82	14.4854
iiiiiiqqqqqqqqiiiiii	chr3:196304457-196304680(+)$1	223	90	110	14.4593
!!ddddqqqqqqqqdddd22	chr5:151174987-151175229(+)$1	242	166	186	15.0281
cc!!bbqqqqqqqqbb22cc	chr20:5096029-5096264(-)$1	235	170	190	13.1856
=!!cccqqqqqqqqccc===	chr7:157000460-157000689(+)$1	229	93	113	15.2419
b[ddddqqqqqqqqdddd]b	chr6:85473572-85473797(-)$1	225	147	167	14.7094
b[ddddqqqqqqqqddddbb	chr7:39990465-39990688(+)$1	223	147	167	14.2708
ffffffqqqqqqqqffffff	chrM:12486-12714(-)$1	228	184	204	13.4184
ccccccqqqqqqqqccc]cc	chr19:10790462-10790692(-)$1	230	0	20	14.6037
ee[cccqqqqqqqqccc]ee	chr6:105406021-105406259(+)$1	238	165	185	14.7001
gg[cccqqqqqqqqccc]gg	chr6:155113900-155114122(+)$1	222	140	160	15.0455
c!!cccqqqqqqqqccc22c	chr14:92600513-92600733(+)$1	220	135	155	14.9155
!!ddddqqqqqqqqdddd22	chr12:39763587-39763812(-)$1	225	126	146	15.0281
:eeeeeqqqqqqqqeeeeee	chrM:15714-15962(+)$1	248	200	220	13.5741
ff[cccqqqqqqqqccc]ff	chr22:20229741-20229964(-)$1	223	191	211	14.6727
!!ddddqqqqqqqqdddd22	chr17:53007407-53007629(+)$1	222	143	163	15.0281
[eeeeeqqqqqqqqeeeee]	chr19:50000458-50000698(+)$1	240	22	42	14.7975
!eeeeeqqqqqqqqeeeee2	chr7:157000432-157000658(+)$1	226	188	208	14.7147
ggggggqqqqqqqqgggggg	chr20:46311768-46311994(-)$1	226	72	92	14.4779
ddddddqqqqqqqqdddd:e	chrM:7882-8135(+)$1	253	101	121	13.2167
eeee[aqqqqqqqqa]eeee	chr8:11058582-11058808(-)$1	226	179	199	14.2407
b!!cccqqqqqqqqcccbb2	chr16:30456205-30456430(-)$1	225	182	202	14.1858
:eeeeeqqqqqqqqeeeee:	chr17:79428459-79428695(+)$1	236	70	90	12.8178
ffffffqqqqqqqqffffff	chr3:184910717-184910942(-)$1	225	22	42	13.4184
ffffffqqqqqqqqffffff	chr5:145836650-145836872(+)$1	222	14	34	13.4184
ceeeeeqqqqqqqqeeeee:	chr3:8609097-8609322(+)$1	225	188	208	13.6706
======qqqqqqqq======	chr12:6691961-6692182(-)$1	221	88	108	14.7642
cc[cccqqqqqqqqccc]cc	chrM:11911-12171(+)$1	260	140	160	14.7749
iii!!aqqqqqqqqa22iii	chr3:66433323-66433552(+)$1	229	123	143	13.9721
bbddddqqqqqqqqdddd]b	chr10:112557205-112557464(-)$1	259	175	195	14.2768
bb!!bbqqqqqqqqbb22bb	chr2:61721056-61721283(-)$1	227	59	79	12.5399
iiiibbqqqqqqqqbb]iii	chr19:33878789-33879015(-)$1	226	186	206	13.6694
bb[cccqqqqqqqqccc]bb	chr9:123952749-123952989(-)$1	240	82	102	14.1292
ee!!bbqqqqqqqqbb22ee	chr8:30332205-30332460(+)$1	255	117	137	13.1108
ffffffqqqqqqqqffffff	chr5:127597457-127597678(-)$1	221	45	65	13.4184
###cccqqqqqqqqccc22f	chr17:4926981-4927227(+)$1	246	101	121	14.7950
[eeeeeqqqqqqqqeeeeee	chr6:44360360-44360582(+)$1	222	17	37	14.6457
ggggggqqqqqqqqgggggg	chr3:50616201-50616425(+)$1	224	36	56	14.4779
[eeeeeqqqqqqqqeeeeeb	chr3:120067827-120068057(-)$1	230	4	24	14.6126
iiii[aqqqqqqqqaiiiii	chr3:9986072-9986291(+)$1	219	122	142	14.5472
##ddddqqqqqqqqdddd33	chr11:118343072-118343295(+)$1	223	93	113	15.1863
""ddddqqqqqqqqddddgg	chr19:39899051-39899280(+)$1	229	76	96	14.9757
ggggggqqqqqqqqgggggg	chr1:67423674-67423896(+)$1	222	16	36	14.4779
ffffffqqqqqqqqffffff	chr11:62558151-62558378(-)$1	227	89	109	13.4184
[eeeeeqqqqqqqqeeeee]	chr12:115109739-115109962(-)$1	223	23	43	14.7975

#otherMatches

#Seq PSSM
GAUUGUGAGGGGUAGGAGUC	chrM:10831-11073(-)$1	242	82	102	14.2407
GGAUGUCUCGUGAUGCAUCU	chr5:10264737-10264967(+)$1	230	208	228	14.4779
UGUCAGUAUUUAAUCUGAGC	chr12:46764249-46764468(-)$1	219	83	103	14.2768
AAGCAACUGUGAAAUUGGUA	chr20:30748999-30749219(+)$1	220	7	27	15.0298
UAUUGUGGUAGAAGACAAAG	chr12:6687918-6688156(-)$1	238	125	145	14.7094
UGAAGGUAAAGUGUUGUUCA	chr12:88568324-88568555(+)$1	231	175	195	14.2727
UCCGGCACCCAGCGGCGCGG	chr7:39990601-39990824(+)$1	223	191	211	13.5033
GACAUCAUCGAGACGGUGUA	chr18:77733711-77733936(-)$1	225	162	182	14.3848
AAGUGAAGCCUGAAUCAACU	chr1:91405709-91405935(-)$1	226	55	75	14.7950
GUGGGAAACAGACCUUCUAC	chr16:8889796-8890020(-)$1	224	114	134	13.4184
CUGGACAGUAAGCGGUUCUG	chr1:212002356-212002577(-)$1	221	83	103	12.9552
AUAUCUACGAAGCAAGAUCA	chr1:70639081-70639307(-)$1	226	137	157	14.7939
GUGGGAAAGCUUUCUCUCAG	chr19:36727941-36728163(+)$1	222	134	154	14.5304
AGGGGCAGGUUUUGGCUCGU	chrM:13821-14163(-)$1	342	177	197	14.7094
ACGGCCAAGCAGUCGGCCGA	chr19:7998966-7999187(-)$1	221	133	153	14.7147
UAUCACACCAAAGAGUGAGU	chr12:125466958-125467186(-)$1	228	116	136	13.6119
GUUCUCUGCCCUCUGAGACC	chr6:26388372-26388596(+)$1	224	154	174	14.9068
CAUGGAACAAGCCAUCCACU	chr14:69588875-69589094(-)$1	219	48	68	14.8902
UGAAUCCCAACAGUGAUUAU	chrX:71495442-71495673(-)$1	231	62	82	14.4854
GUGCCAAGGUUAUGUGGCAU	chr3:196304457-196304680(+)$1	223	90	110	14.4593
ACAUGUCCGGGGCUGCAUAA	chr5:151174987-151175229(+)$1	242	166	186	15.0281
GUAAGAUAAUAAAUUUGAAC	chr20:5096029-5096264(-)$1	235	170	190	13.1856
UAUUGGAGUUACUACUAGCU	chr7:157000460-157000689(+)$1	229	93	113	15.2419
GGGCCGGCUCGGAGUGGCGC	chr6:85473572-85473797(-)$1	225	147	167	14.7094
CAGCCGCAGCAGGACGGCGG	chr7:39990465-39990688(+)$1	223	147	167	14.2708
UCGAGAUAAUAACUUCUUGG	chrM:12486-12714(-)$1	228	184	204	13.4184
CUGCUGUCCUAACCCAGUCA	chr19:10790462-10790692(-)$1	230	0	20	14.6037
CUUCAUCUUUUUCCAUGUGG	chr6:105406021-105406259(+)$1	238	165	185	14.7001
GCCGGGAUUCCGCCUCCAGU	chr6:155113900-155114122(+)$1	222	140	160	15.0455
CCUUUGAUAAAAUACAGCAG	chr14:92600513-92600733(+)$1	220	135	155	14.9155
GGAACAGGAUUUGAUGUUAA	chr12:39763587-39763812(-)$1	225	126	146	15.0281
AGUCUUGUAAACCGGAGACG	chrM:15714-15962(+)$1	248	200	220	13.5741
GGCCGUGACCUCAAACGCCU	chr22:20229741-20229964(-)$1	223	191	211	14.6727
AUCCUUGGAUAUGAGAGGUG	chr17:53007407-53007629(+)$1	222	143	163	15.0281
AUCUUUCAAAACAAGAAGAG	chr19:50000458-50000698(+)$1	240	22	42	14.7975
UUAUUUAAGGUAUAGAGUAU	chr7:157000432-157000658(+)$1	226	188	208	14.7147
GUGUUGCAGAUUUACAACAU	chr20:46311768-46311994(-)$1	226	72	92	14.4779
UGCGACUCCUUGACGUUGAC	chrM:7882-8135(+)$1	253	101	121	13.2167
CUGCGCUCCCUCCUGGGCAG	chr8:11058582-11058808(-)$1	226	179	199	14.2407
UAAUCCUGAAAGAUGGAAUA	chr16:30456205-30456430(-)$1	225	182	202	14.1858
CCGCUGCCCUACGACAGCGA	chr17:79428459-79428695(+)$1	236	70	90	12.8178
UGAUCGUCCUCACUUGGUCA	chr3:184910717-184910942(-)$1	225	22	42	13.4184
GUUUUACUUUUGAAUAGAAU	chr5:145836650-145836872(+)$1	222	14	34	13.4184
GGGCUGCCCACCCACAGCCA	chr3:8609097-8609322(+)$1	225	188	208	13.6706
AGGCCCAGUCGUAAGGGCCU	chr12:6691961-6692182(-)$1	221	88	108	14.7642
CACGAGAAAACACCCUCAUG	chrM:11911-12171(+)$1	260	140	160	14.7749
UGGUAGAUGAUGCACACCCA	chr3:66433323-66433552(+)$1	229	123	143	13.9721
GCCAGCCCCUUUCCGCUGUG	chr10:112557205-112557464(-)$1	259	175	195	14.2768
CCUUCAUUAUAUGUUGUUGG	chr2:61721056-61721283(-)$1	227	59	79	12.5399
CGAGGUCCUGCAGCGCUUUC	chr19:33878789-33879015(-)$1	226	186	206	13.6694
AGGAGCGAUUUAGGGCUGUU	chr9:123952749-123952989(-)$1	240	82	102	14.1292
CUCUGGAUAUCAAACCUCGG	chr8:30332205-30332460(+)$1	255	117	137	13.1108
UAAAGUCUAACAAUACUUUG	chr5:127597457-127597678(-)$1	221	45	65	13.4184
CAACCCCCAGCACCGGGAGU	chr17:4926981-4927227(+)$1	246	101	121	14.7950
UAUAUAAAAUGAUCUAUGUU	chr6:44360360-44360582(+)$1	222	17	37	14.6457
UUCUUUGACGACAGAAAGGA	chr3:50616201-50616425(+)$1	224	36	56	14.4779
AGGCCGAACUGAACUGGUCC	chr3:120067827-120068057(-)$1	230	4	24	14.6126
GCCAUGACUGGCUACUGGUU	chr3:9986072-9986291(+)$1	219	122	142	14.5472
AUGAGGAUUAUGACCCUCCA	chr11:118343072-118343295(+)$1	223	93	113	15.1863
CUCCUAUCAGCGUCUGGGGG	chr19:39899051-39899280(+)$1	229	76	96	14.9757
AAUCAGAAAUAUCACUGAUU	chr1:67423674-67423896(+)$1	222	16	36	14.4779
GCCCCCUUUGGCUUGGGGGC	chr11:62558151-62558378(-)$1	227	89	109	13.4184
GUGCCGGUCCCGGACGGCAG	chr12:115109739-115109962(-)$1	223	23	43	14.7975

#DB
((((.(........).))))	chrM:10831-11073(-)$1	1	82	102	14.2407
((((((........))))))	chr5:10264737-10264967(+)$1	1	208	228	14.4779
((((((........)))).)	chr12:46764249-46764468(-)$1	1	83	103	14.2768
.(.(((........))).).	chr20:30748999-30749219(+)$1	1	7	27	15.0298
(.((((........)))).)	chr12:6687918-6688156(-)$1	1	125	145	14.7094
.(((.(........).))))	chr12:88568324-88568555(+)$1	1	175	195	14.2727
.(((((........)).)))	chr7:39990601-39990824(+)$1	1	191	211	13.5033
((((((........))))).	chr18:77733711-77733936(-)$1	1	162	182	14.3848
...(((........)))..)	chr1:91405709-91405935(-)$1	1	55	75	14.7950
((((((........))))))	chr16:8889796-8890020(-)$1	1	114	134	13.4184
((((((........).))))	chr1:212002356-212002577(-)$1	1	83	103	12.9552
..((((........))))..	chr1:70639081-70639307(-)$1	1	137	157	14.7939
.(((((........))))))	chr19:36727941-36728163(+)$1	1	134	154	14.5304
(.((((........)))).)	chrM:13821-14163(-)$1	1	177	197	14.7094
.(((((........))))).	chr19:7998966-7999187(-)$1	1	133	153	14.7147
..((((........))))..	chr12:125466958-125467186(-)$1	1	116	136	13.6119
(.((((........)))).)	chr6:26388372-26388596(+)$1	1	154	174	14.9068
..((((........))))..	chr14:69588875-69589094(-)$1	1	48	68	14.8902
((((((........)))..)	chrX:71495442-71495673(-)$1	1	62	82	14.4854
((((((........))))))	chr3:196304457-196304680(+)$1	1	90	110	14.4593
..((((........))))..	chr5:151174987-151175229(+)$1	1	166	186	15.0281
((..((........))..))	chr20:5096029-5096264(-)$1	1	170	190	13.1856
(..(((........))))))	chr7:157000460-157000689(+)$1	1	93	113	15.2419
(.((((........)))).)	chr6:85473572-85473797(-)$1	1	147	167	14.7094
(.((((........))))))	chr7:39990465-39990688(+)$1	1	147	167	14.2708
((((((........))))))	chrM:12486-12714(-)$1	1	184	204	13.4184
((((((........))).))	chr19:10790462-10790692(-)$1	1	0	20	14.6037
((.(((........))).))	chr6:105406021-105406259(+)$1	1	165	185	14.7001
((.(((........))).))	chr6:155113900-155114122(+)$1	1	140	160	15.0455
(..(((........)))..)	chr14:92600513-92600733(+)$1	1	135	155	14.9155
..((((........))))..	chr12:39763587-39763812(-)$1	1	126	146	15.0281
.(((((........)))))(	chrM:15714-15962(+)$1	1	200	220	13.5741
((.(((........))).))	chr22:20229741-20229964(-)$1	1	191	211	14.6727
..((((........))))..	chr17:53007407-53007629(+)$1	1	143	163	15.0281
.(((((........))))).	chr19:50000458-50000698(+)$1	1	22	42	14.7975
.(((((........))))).	chr7:157000432-157000658(+)$1	1	188	208	14.7147
((((((........))))))	chr20:46311768-46311994(-)$1	1	72	92	14.4779
))((((........)))).(	chrM:7882-8135(+)$1	1	101	121	13.2167
((((.(........).))))	chr8:11058582-11058808(-)$1	1	179	199	14.2407
(..(((........))))).	chr16:30456205-30456430(-)$1	1	182	202	14.1858
.(((((........))))).	chr17:79428459-79428695(+)$1	1	70	90	12.8178
((((((........))))))	chr3:184910717-184910942(-)$1	1	22	42	13.4184
((((((........))))))	chr5:145836650-145836872(+)$1	1	14	34	13.4184
)(((((........))))).	chr3:8609097-8609322(+)$1	1	188	208	13.6706
((((((........))))))	chr12:6691961-6692182(-)$1	1	88	108	14.7642
((.(((........))).))	chrM:11911-12171(+)$1	1	140	160	14.7749
(((..(........)..)))	chr3:66433323-66433552(+)$1	1	123	143	13.9721
((((((........)))).)	chr10:112557205-112557464(-)$1	1	175	195	14.2768
((..((........))..))	chr2:61721056-61721283(-)$1	1	59	79	12.5399
((((((........)).)))	chr19:33878789-33879015(-)$1	1	186	206	13.6694
((.(((........))).))	chr9:123952749-123952989(-)$1	1	82	102	14.1292
((..((........))..))	chr8:30332205-30332460(+)$1	1	117	137	13.1108
((((((........))))))	chr5:127597457-127597678(-)$1	1	45	65	13.4184
...(((........)))..)	chr17:4926981-4927227(+)$1	1	101	121	14.7950
.(((((........))))))	chr6:44360360-44360582(+)$1	1	17	37	14.6457
((((((........))))))	chr3:50616201-50616425(+)$1	1	36	56	14.4779
.(((((........))))))	chr3:120067827-120068057(-)$1	1	4	24	14.6126
((((.(........))))))	chr3:9986072-9986291(+)$1	1	122	142	14.5472
..((((........))))..	chr11:118343072-118343295(+)$1	1	93	113	15.1863
..((((........))))))	chr19:39899051-39899280(+)$1	1	76	96	14.9757
((((((........))))))	chr1:67423674-67423896(+)$1	1	16	36	14.4779
((((((........))))))	chr11:62558151-62558378(-)$1	1	89	109	13.4184
.(((((........))))).	chr12:115109739-115109962(-)$1	1	23	43	14.7975

#PSSM
b : 0.14	[ : 0.12	f : 0.11	c : 0.09	e : 0.07	g : 0.07	! : 0.07	# : 0.06	i : 0.06	d : 0.03	= : 0.03	: : 0.03	h : 0.01	$ : 0.01	% : 0.01	" : 0.01	
e : 0.25	f : 0.11	! : 0.09	g : 0.07	[ : 0.07	c : 0.07	b : 0.06	# : 0.06	i : 0.06	a : 0.01	h : 0.01	$ : 0.01	% : 0.01	d : 0.01	= : 0.01	" : 0.01	
d : 0.25	e : 0.22	[ : 0.09	f : 0.09	! : 0.09	g : 0.06	i : 0.06	c : 0.04	# : 0.03	h : 0.01	= : 0.01	
d : 0.25	c : 0.23	e : 0.20	f : 0.09	g : 0.06	! : 0.06	i : 0.04	h : 0.01	= : 0.01	
d : 0.25	c : 0.20	e : 0.17	f : 0.09	b : 0.07	[ : 0.06	g : 0.06	h : 0.01	i : 0.01	= : 0.01	! : 0.01	
d : 0.25	c : 0.20	e : 0.17	a : 0.09	f : 0.09	b : 0.07	g : 0.06	i : 0.01	= : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
d : 0.25	c : 0.20	e : 0.17	a : 0.09	f : 0.09	b : 0.07	g : 0.06	i : 0.01	= : 0.01	
d : 0.25	c : 0.20	e : 0.17	f : 0.09	b : 0.07	] : 0.06	g : 0.06	i : 0.03	= : 0.01	2 : 0.01	
d : 0.25	c : 0.22	e : 0.20	f : 0.09	g : 0.06	2 : 0.06	] : 0.03	i : 0.03	h : 0.01	= : 0.01	
d : 0.25	e : 0.20	] : 0.11	2 : 0.11	f : 0.09	g : 0.06	i : 0.06	c : 0.03	= : 0.03	h : 0.01	b : 0.01	
e : 0.23	2 : 0.14	f : 0.11	g : 0.09	] : 0.09	c : 0.07	i : 0.06	b : 0.06	3 : 0.03	= : 0.03	a : 0.01	h : 0.01	: : 0.01	
b : 0.15	2 : 0.14	f : 0.14	e : 0.12	g : 0.09	c : 0.09	i : 0.06	] : 0.04	3 : 0.03	= : 0.03	: : 0.03	h : 0.01	d : 0.01	

#score	900.1390011301603
#seq	63
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_CDS_m3_run2.txt

#BEAR
iddddqqqqqqqqdddd2	chrM:14386-14619(-)$1	233	89	107	13.7810
eeeeeqqqqqqqqeeeee	chr10:32115149-32115377(-)$1	228	96	114	15.1503
[ddddqqqqqqqqdddde	chr6:101163200-101163419(-)$1	219	111	129	14.1481
fffffqqqqqqqqfffff	chr2:73957757-73957989(-)$1	232	62	80	13.6827
eeeeeqqqqqqqqeeeee	chr1:193060686-193060915(+)$1	229	111	129	15.1503
fffffqqqqqqqqfffff	chr19:38055999-38056234(-)$1	235	93	111	13.6827
d[cccqqqqqqqqcccdd	chr9:34398209-34398427(-)$1	218	146	164	13.8673
ffcccqqqqqqqqccc44	chr7:23650928-23651145(+)$1	217	50	68	14.0616
h[cccqqqqqqqqccc]h	chr11:32953513-32953740(+)$1	227	14	32	13.6524
[ddddqqqqqqqqdddd2	chrM:6286-6511(+)$1	225	172	190	13.9210
fffffqqqqqqqqfffff	chr2:150426549-150426774(-)$1	225	14	32	13.6827
$$cccqqqqqqqqccc22	chr13:100206571-100206798(+)$1	227	113	131	13.3083
eeeeeqqqqqqqqeeeee	chrM:15178-15401(+)$1	223	196	214	15.1503
ee[bbqqqqqqqqbb]ee	chr13:79189904-79190122(-)$1	218	95	113	13.3976
eeeeeqqqqqqqqeeeee	chr19:11256948-11257167(-)$1	219	197	215	15.1503
eeeeeqqqqqqqqeeeee	chr2:149449229-149449447(+)$1	218	16	34	15.1503
!ddddqqqqqqqqdddd3	chr5:176562812-176563041(+)$1	229	155	173	14.1321
gggggqqqqqqqqggggg	chr12:76741089-76741312(-)$1	223	100	118	13.9905
eeeeeqqqqqqqqeeeee	chr4:48036800-48037025(+)$1	225	118	136	15.1503
fffffqqqqqqqqfffff	chr15:66624964-66625190(-)$1	226	119	137	13.6827
eeeeeqqqqqqqqeeeee	chr6:96034253-96034481(+)$1	228	114	132	15.1503
gggggqqqqqqqqggggg	chr6:119150120-119150341(-)$1	221	112	130	13.9905
eeeeeqqqqqqqqeeeee	chr12:4627180-4627396(-)$1	216	56	74	15.1503
fffffqqqqqqqqfffff	chr15:66624999-66625220(-)$1	221	149	167	13.6827
eeeeeqqqqqqqqeeeee	chr15:48591305-48591524(-)$1	219	80	98	15.1503
""cccqqqqqqqqccc44	chr3:101378573-101378797(-)$1	224	8	26	14.1497
##cccqqqqqqqqccc44	chr6:32948334-32948556(+)$1	222	129	147	14.0689
fffffqqqqqqqqfffff	chr2:54150411-54150640(-)$1	229	95	113	13.6827
eeeeeqqqqqqqqeeeee	chrM:15340-15563(+)$1	223	34	52	15.1503
addddqqqqqqqqdddd]	chr1:62907805-62908027(+)$1	222	75	93	13.8627
$ddddqqqqqqqqdddd3	chrX:76814189-76814411(-)$1	222	130	148	13.7992
gggggqqqqqqqqggggg	chr5:32594578-32594801(+)$1	223	81	99	13.9905
[ddddqqqqqqqqdddd]	chr3:101284048-101284267(+)$1	219	151	169	14.0775
eee[aqqqqqqqqa]eee	chr22:19470115-19470338(+)$1	223	63	81	14.5428
[ddddqqqqqqqqddddc	chr4:99982358-99982579(+)$1	221	76	94	13.9227
=====qqqqqqqq=====	chr7:120610670-120610905(+)$1	235	12	30	14.0162
eeeeeqqqqqqqqeeeee	chr14:35044881-35045102(-)$1	221	19	37	15.1503
!!cccqqqqqqqqccc33	chr1:63884953-63885180(+)$1	227	189	207	14.4307
fffffqqqqqqqqfffff	chr3:160151366-160151585(+)$1	219	171	189	13.6827
[ddddqqqqqqqqdddde	chr3:135871130-135871357(-)$1	227	166	184	14.1481
ebb[aqqqqqqqqa]bb3	chr5:87501635-87501862(-)$1	227	166	184	12.6222
eeeeeqqqqqqqqeeeee	chr1:203786122-203786345(+)$1	223	165	183	15.1503
eeeeeqqqqqqqqeeeee	chr1:90399033-90399258(+)$1	225	165	183	15.1503
fffffqqqqqqqqfffff	chr5:43619000-43619235(+)$1	235	198	216	13.6827
"""bbqqqqqqqqbb444	chr12:133660661-133660886(+)$1	225	82	100	12.7159
dddbbqqqqqqqqbb]dd	chr8:17921911-17922135(-)$1	224	192	210	12.6087
eeeeeqqqqqqqqeeeee	chr4:44449608-44449828(+)$1	220	83	101	15.1503
eeeeeqqqqqqqqeeeee	chr14:99959775-99959992(+)$1	217	96	114	15.1503
!!cccqqqqqqqqccca]	chr13:33110189-33110408(-)$1	219	52	70	14.2707
""cccqqqqqqqqccc33	chrX:53654597-53654816(-)$1	219	105	123	14.2418
eee[aqqqqqqqqa]eee	chr2:44547467-44547689(-)$1	222	180	198	14.5428
""cccqqqqqqqqccc33	chr1:203768156-203768374(+)$1	218	30	48	14.2418
gggggqqqqqqqqggggg	chr12:96263148-96263368(+)$1	220	35	53	13.9905
gggggqqqqqqqqggggg	chrM:12586-12833(+)$1	247	50	68	13.9905
eecccqqqqqqqqccc]e	chr17:34893439-34893659(+)$1	220	163	181	14.4946
dddbbqqqqqqqqbb]dd	chr12:49445821-49446042(-)$1	221	44	62	12.6087
bddddqqqqqqqqddddH	chr6:5260864-5261088(-)$1	224	193	211	12.7736
fffffqqqqqqqqfffff	chr10:124749725-124749945(+)$1	220	181	199	13.6827
eeeeeqqqqqqqqeeeee	chr5:39315795-39316014(-)$1	219	160	178	15.1503
eeeeeqqqqqqqqeeeee	chr14:57698234-57698463(-)$1	229	26	44	15.1503
eeeeeqqqqqqqqeeeee	chr6:87966408-87966638(+)$1	230	175	193	15.1503
!!cccqqqqqqqqccccc	chr1:173772063-173772283(-)$1	220	130	148	14.1459
eeeeeqqqqqqqqeeeee	chr3:128356671-128356893(-)$1	222	152	170	15.1503
eeeeeqqqqqqqqeeeee	chrM:15727-15962(+)$1	235	188	206	15.1503

#otherMatches

#Seq PSSM
GGUUAUAUGGGUUUAAUA	chrM:14386-14619(-)$1	233	89	107	13.7810
AGGGUUCAUCUUUACUUU	chr10:32115149-32115377(-)$1	228	96	114	15.1503
AUUUAUCUGCUUUUAGAG	chr6:101163200-101163419(-)$1	219	111	129	14.1481
GUUUCAGACGUAGGAAAC	chr2:73957757-73957989(-)$1	232	62	80	13.6827
CUAAAUAAAUCAUUUUAG	chr1:193060686-193060915(+)$1	229	111	129	15.1503
GGGAAAGCCUUUAUUUCU	chr19:38055999-38056234(-)$1	235	93	111	13.6827
UAUAAUAUUUUUUUUAAC	chr9:34398209-34398427(-)$1	218	146	164	13.8673
UUUACUGUUGCUUGUAUU	chr7:23650928-23651145(+)$1	217	50	68	14.0616
UUGGCAUUUGAGCGCCUG	chr11:32953513-32953740(+)$1	227	14	32	13.6524
CUGAUCCGUCCUAAUCAC	chrM:6286-6511(+)$1	225	172	190	13.9210
AGGUGUUCAUGUUUACCU	chr2:150426549-150426774(-)$1	225	14	32	13.6827
UUUUCUUCAUUCUGAAUA	chr13:100206571-100206798(+)$1	227	113	131	13.3083
GGAAUCACCUCCCAUUCC	chrM:15178-15401(+)$1	223	196	214	15.1503
UGAAGAUUUUUCACUCCA	chr13:79189904-79190122(-)$1	218	95	113	13.3976
CCCuuacucauucagggg	chr19:11256948-11257167(-)$1	219	197	215	15.1503
GUUCAUUUGUUUUUGGAC	chr2:149449229-149449447(+)$1	218	16	34	15.1503
AUUAGGAAACAUGCUAGA	chr5:176562812-176563041(+)$1	229	155	173	14.1321
AAUAAUCAUAAAUUUAUU	chr12:76741089-76741312(-)$1	223	100	118	13.9905
UUUAAACGAGCACUUGAA	chr4:48036800-48037025(+)$1	225	118	136	15.1503
AUAUUAUGACCAGAAUAU	chr15:66624964-66625190(-)$1	226	119	137	13.6827
UUAUUUUCUCUCUGAUGA	chr6:96034253-96034481(+)$1	228	114	132	15.1503
UUUAUCUUAGAAAAUAAA	chr6:119150120-119150341(-)$1	221	112	130	13.9905
GAAGUGGUGUGAAACUUC	chr12:4627180-4627396(-)$1	216	56	74	15.1503
AUAUUAUGACCAGAAUAU	chr15:66624999-66625220(-)$1	221	149	167	13.6827
UCUGUAAUUUUCCACGGA	chr15:48591305-48591524(-)$1	219	80	98	15.1503
CUCGUCCAAUUCCACGUC	chr3:101378573-101378797(-)$1	224	8	26	14.1497
CUUCAGACACCAGUGAUU	chr6:32948334-32948556(+)$1	222	129	147	14.0689
GAAGGUUUUUAAUUUUUC	chr2:54150411-54150640(-)$1	229	95	113	13.6827
GGAAUCACCUCCCAUUCC	chrM:15340-15563(+)$1	223	34	52	15.1503
CCCGGUUUUAAAUCUGGA	chr1:62907805-62908027(+)$1	222	75	93	13.8627
UCUAGGAAUUAAUCUGGU	chrX:76814189-76814411(-)$1	222	130	148	13.7992
CUUUUUUGUGUUUGAAGG	chr5:32594578-32594801(+)$1	223	81	99	13.9905
GCUGGAAGGGUGCCCAGG	chr3:101284048-101284267(+)$1	219	151	169	14.0775
UAUAGCUACUUUACAAUA	chr22:19470115-19470338(+)$1	223	63	81	14.5428
CAGUGCACGGCCUCACUU	chr4:99982358-99982579(+)$1	221	76	94	13.9227
AGUUAUUCUCAGUUAACU	chr7:120610670-120610905(+)$1	235	12	30	14.0162
GUUGAUUAAAUAUUCAAU	chr14:35044881-35045102(-)$1	221	19	37	15.1503
UUGUUUAUAAUAUAACUU	chr1:63884953-63885180(+)$1	227	189	207	14.4307
AACAUAACAAAAAGUGUU	chr3:160151366-160151585(+)$1	219	171	189	13.6827
UCUGAAAGCACCCUCAGC	chr3:135871130-135871357(-)$1	227	166	184	14.1481
UCCUGGAUUACGACUGGC	chr5:87501635-87501862(-)$1	227	166	184	12.6222
AAUUUGCUUAAUAGAAUU	chr1:203786122-203786345(+)$1	223	165	183	15.1503
CAAAAGUAGAACAUUUUG	chr1:90399033-90399258(+)$1	225	165	183	15.1503
CUGGAAAAGUUCCUCCAG	chr5:43619000-43619235(+)$1	235	198	216	13.6827
UUUCAUUUCUUUUUGUUU	chr12:133660661-133660886(+)$1	225	82	100	12.7159
UGGGCAGCAUGAAGCACU	chr8:17921911-17922135(-)$1	224	192	210	12.6087
CAGGCGAUCAAAGGCCUG	chr4:44449608-44449828(+)$1	220	83	101	15.1503
UGGAAUAAUUUAUUUUCA	chr14:99959775-99959992(+)$1	217	96	114	15.1503
CAGUAUAUCCUUUUAUAG	chr13:33110189-33110408(-)$1	219	52	70	14.2707
UAUCUUCAUUUAUAGACU	chrX:53654597-53654816(-)$1	219	105	123	14.2418
GAACCACGAUAAAGAUUC	chr2:44547467-44547689(-)$1	222	180	198	14.5428
AAUGGCAGGAUCCCCGAU	chr1:203768156-203768374(+)$1	218	30	48	14.2418
ACGAAUAAAGUAUUUUGU	chr12:96263148-96263368(+)$1	220	35	53	13.9905
CAUAGAAUUCUCACUGUG	chrM:12586-12833(+)$1	247	50	68	13.9905
CCAUUAUAAAAUCAAUAG	chr17:34893439-34893659(+)$1	220	163	181	14.4946
GAGGAAUCGCCCCUCUCU	chr12:49445821-49446042(-)$1	221	44	62	12.6087
CGCCUACAAUUACAGGUG	chr6:5260864-5261088(-)$1	224	193	211	12.7736
UCAAAUGUCUCAUUUUGG	chr10:124749725-124749945(+)$1	220	181	199	13.6827
GGAAUAUAGAAAGGUUCC	chr5:39315795-39316014(-)$1	219	160	178	15.1503
AAAGAACCACCAAUCUUU	chr14:57698234-57698463(-)$1	229	26	44	15.1503
CCUAAGUAAUUCAUUAGG	chr6:87966408-87966638(+)$1	230	175	193	15.1503
UAGUUCGUGUUUCAACAU	chr1:173772063-173772283(-)$1	220	130	148	14.1459
CUCUCGAAAUGUGGAGAG	chr3:128356671-128356893(-)$1	222	152	170	15.1503
GUCUUGUAAACCGGAGAC	chrM:15727-15962(+)$1	235	188	206	15.1503

#DB
(((((........)))).	chrM:14386-14619(-)$1	1	89	107	13.7810
(((((........)))))	chr10:32115149-32115377(-)$1	1	96	114	15.1503
.((((........)))))	chr6:101163200-101163419(-)$1	1	111	129	14.1481
(((((........)))))	chr2:73957757-73957989(-)$1	1	62	80	13.6827
(((((........)))))	chr1:193060686-193060915(+)$1	1	111	129	15.1503
(((((........)))))	chr19:38055999-38056234(-)$1	1	93	111	13.6827
(.(((........)))))	chr9:34398209-34398427(-)$1	1	146	164	13.8673
(((((........)))..	chr7:23650928-23651145(+)$1	1	50	68	14.0616
(.(((........))).)	chr11:32953513-32953740(+)$1	1	14	32	13.6524
.((((........)))).	chrM:6286-6511(+)$1	1	172	190	13.9210
(((((........)))))	chr2:150426549-150426774(-)$1	1	14	32	13.6827
..(((........)))..	chr13:100206571-100206798(+)$1	1	113	131	13.3083
(((((........)))))	chrM:15178-15401(+)$1	1	196	214	15.1503
((.((........)).))	chr13:79189904-79190122(-)$1	1	95	113	13.3976
(((((........)))))	chr19:11256948-11257167(-)$1	1	197	215	15.1503
(((((........)))))	chr2:149449229-149449447(+)$1	1	16	34	15.1503
.((((........)))).	chr5:176562812-176563041(+)$1	1	155	173	14.1321
(((((........)))))	chr12:76741089-76741312(-)$1	1	100	118	13.9905
(((((........)))))	chr4:48036800-48037025(+)$1	1	118	136	15.1503
(((((........)))))	chr15:66624964-66625190(-)$1	1	119	137	13.6827
(((((........)))))	chr6:96034253-96034481(+)$1	1	114	132	15.1503
(((((........)))))	chr6:119150120-119150341(-)$1	1	112	130	13.9905
(((((........)))))	chr12:4627180-4627396(-)$1	1	56	74	15.1503
(((((........)))))	chr15:66624999-66625220(-)$1	1	149	167	13.6827
(((((........)))))	chr15:48591305-48591524(-)$1	1	80	98	15.1503
..(((........)))..	chr3:101378573-101378797(-)$1	1	8	26	14.1497
..(((........)))..	chr6:32948334-32948556(+)$1	1	129	147	14.0689
(((((........)))))	chr2:54150411-54150640(-)$1	1	95	113	13.6827
(((((........)))))	chrM:15340-15563(+)$1	1	34	52	15.1503
(((((........)))).	chr1:62907805-62908027(+)$1	1	75	93	13.8627
.((((........)))).	chrX:76814189-76814411(-)$1	1	130	148	13.7992
(((((........)))))	chr5:32594578-32594801(+)$1	1	81	99	13.9905
.((((........)))).	chr3:101284048-101284267(+)$1	1	151	169	14.0775
(((.(........).)))	chr22:19470115-19470338(+)$1	1	63	81	14.5428
.((((........)))))	chr4:99982358-99982579(+)$1	1	76	94	13.9227
(((((........)))))	chr7:120610670-120610905(+)$1	1	12	30	14.0162
(((((........)))))	chr14:35044881-35045102(-)$1	1	19	37	15.1503
..(((........)))..	chr1:63884953-63885180(+)$1	1	189	207	14.4307
(((((........)))))	chr3:160151366-160151585(+)$1	1	171	189	13.6827
.((((........)))))	chr3:135871130-135871357(-)$1	1	166	184	14.1481
(((.(........).)).	chr5:87501635-87501862(-)$1	1	166	184	12.6222
(((((........)))))	chr1:203786122-203786345(+)$1	1	165	183	15.1503
(((((........)))))	chr1:90399033-90399258(+)$1	1	165	183	15.1503
(((((........)))))	chr5:43619000-43619235(+)$1	1	198	216	13.6827
...((........))...	chr12:133660661-133660886(+)$1	1	82	100	12.7159
(((((........)).))	chr8:17921911-17922135(-)$1	1	192	210	12.6087
(((((........)))))	chr4:44449608-44449828(+)$1	1	83	101	15.1503
(((((........)))))	chr14:99959775-99959992(+)$1	1	96	114	15.1503
..(((........)))).	chr13:33110189-33110408(-)$1	1	52	70	14.2707
..(((........)))..	chrX:53654597-53654816(-)$1	1	105	123	14.2418
(((.(........).)))	chr2:44547467-44547689(-)$1	1	180	198	14.5428
..(((........)))..	chr1:203768156-203768374(+)$1	1	30	48	14.2418
(((((........)))))	chr12:96263148-96263368(+)$1	1	35	53	13.9905
(((((........)))))	chrM:12586-12833(+)$1	1	50	68	13.9905
(((((........))).)	chr17:34893439-34893659(+)$1	1	163	181	14.4946
(((((........)).))	chr12:49445821-49446042(-)$1	1	44	62	12.6087
)((((........)))))	chr6:5260864-5261088(-)$1	1	193	211	12.7736
(((((........)))))	chr10:124749725-124749945(+)$1	1	181	199	13.6827
(((((........)))))	chr5:39315795-39316014(-)$1	1	160	178	15.1503
(((((........)))))	chr14:57698234-57698463(-)$1	1	26	44	15.1503
(((((........)))))	chr6:87966408-87966638(+)$1	1	175	193	15.1503
..(((........)))))	chr1:173772063-173772283(-)$1	1	130	148	14.1459
(((((........)))))	chr3:128356671-128356893(-)$1	1	152	170	15.1503
(((((........)))))	chrM:15727-15962(+)$1	1	188	206	15.1503

#PSSM
e : 0.39	f : 0.15	[ : 0.07	g : 0.07	! : 0.06	" : 0.06	d : 0.04	$ : 0.03	i : 0.01	h : 0.01	# : 0.01	a : 0.01	= : 0.01	b : 0.01	
e : 0.37	d : 0.18	f : 0.15	g : 0.07	" : 0.06	! : 0.04	[ : 0.03	$ : 0.01	# : 0.01	= : 0.01	b : 0.01	
e : 0.34	d : 0.18	c : 0.18	f : 0.14	g : 0.07	[ : 0.01	= : 0.01	b : 0.01	" : 0.01	
e : 0.31	c : 0.18	d : 0.15	f : 0.14	g : 0.07	b : 0.06	[ : 0.04	= : 0.01	
e : 0.31	c : 0.18	d : 0.15	f : 0.14	g : 0.07	b : 0.06	a : 0.04	= : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
e : 0.31	c : 0.18	d : 0.15	f : 0.14	g : 0.07	b : 0.06	a : 0.04	= : 0.01	
e : 0.31	c : 0.18	d : 0.15	f : 0.14	g : 0.07	b : 0.06	] : 0.04	= : 0.01	
e : 0.34	c : 0.18	d : 0.15	f : 0.14	g : 0.07	] : 0.04	= : 0.01	b : 0.01	4 : 0.01	
e : 0.35	d : 0.20	f : 0.14	g : 0.07	4 : 0.06	3 : 0.04	] : 0.03	2 : 0.01	= : 0.01	b : 0.01	a : 0.01	c : 0.01	
e : 0.40	f : 0.14	3 : 0.09	g : 0.07	4 : 0.06	2 : 0.04	d : 0.04	] : 0.04	c : 0.03	h : 0.01	= : 0.01	H : 0.01	

#score	910.6606650206701
#seq	64
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_CDS_m3_run1.txt

#BEAR
==========!!ccclllccc==========:	chr4:85656155-85656356(-)$1	201	70	102	10.4885
!!ccca!!ddddnnnnndddd22a]ccc22a]	chr7:91722469-91722670(+)$1	201	130	162	12.4909
eeee!!gggggggooooooggggggg333eee	chr12:88487509-88487710(-)$1	201	102	134	11.2104
""dddd"""ddddmmmmdddd22ddddggggg	chr11:134054723-134054924(-)$1	201	47	79	10.9224
bb!!dddd[cccooooooccc22ddddbbddd	chr11:32955133-32955334(+)$1	201	134	166	11.5495
$$$$eeeee[cccnnnnnccc]eeeee22ccc	chr17:59967081-59967282(-)$1	201	126	158	12.0961
$$dddd!!ddddnnnnndddd22dddd4444d	chr1:52260096-52260297(-)$1	201	142	174	11.7083
ggggggg!!cccooooooccc22gggggggff	chr11:108180806-108181007(+)$1	201	87	119	13.4727
ffffff####a[ccclllccc]a333ffffff	chr1:227307480-227307681(-)$1	201	165	197	10.8643
fff[iiiiiiiiiooooooiiiiiiiiiffff	chr10:121336916-121337117(-)$1	201	57	89	11.1068
gggggg[bb[cccooooooccc]bb22ggggg	chr8:117861123-117861324(-)$1	201	139	171	10.8910
ff"""dddd!!bbnnnnnbb22dddd4444ff	chr22:39710087-39710288(-)$1	201	164	196	11.5992
cc!!ccc[cccbboooooobb]ccc4444ccc	chr7:97936981-97937182(-)$1	201	66	98	12.3704
ccc!!ccc[ddddnnnnndddd]ccc22ccc2	chr1:11896087-11896288(+)$1	201	77	109	13.5436
dd!!ccc[ddddnnnnndddd22ccc22dddd	chr14:105222974-105223175(+)$1	201	41	73	12.8105
ccc[ccc"""cccnnnnnccc22ccc333ccc	chr12:105557953-105558154(+)$1	201	102	134	16.8410
ffffffccccccooooooccc22ccc]fffff	chr6:10935198-10935399(+)$1	201	152	184	12.4192
[a!!eeeee!!bbnnnnnbb22eeeee22a]c	chr12:120172928-120173129(-)$1	201	143	175	11.0689
ffffff"""ddddnnnnndddd333ffffffd	chr16:2127583-2127784(+)$1	201	107	139	12.4686
fff####bb[cccnnnnnccc]bb333fffff	chr10:43882706-43882907(-)$1	201	22	54	12.6675
====$$$$$ddddnnnnndddd4444======	chr5:38953019-38953220(-)$1	201	163	195	12.7828
ii"""bb"""ddddllldddd333bb333iii	chr7:38908710-38908911(-)$1	201	92	124	13.4463
ee####gggggggnnnnnggggggg4444eee	chrX:70777358-70777559(+)$1	201	105	137	12.2730
"ggggggg[cccooooooccc]ggggggg]dd	chr10:64945951-64946152(-)$1	201	21	53	12.3233
%%%%ccc####cccmmmmccc333ccc22bbd	chr6:64286323-64286524(+)$1	201	85	117	10.3184
eee"""a####ccclllccc333a]eeeee]d	chr22:50869612-50869813(+)$1	201	121	153	12.2415
ccc[ffffffcccmmmmccc333ffffff333	chr11:108123463-108123664(+)$1	201	33	65	10.3031
ccc!!ccc!!ccclllccc4444ccc22ccc3	chr7:151845865-151846066(-)$1	201	16	48	12.9619
ddccc[ccccccooooooccc22ccc]ccc22	chrX:53615351-53615552(-)$1	201	64	96	12.5732
ddffffff!!cccmmmmccc333ffffff]dd	chr7:112112746-112112947(+)$1	201	73	105	10.2792
ccc$$$$$ggggggglllggggggg4444ccc	chr19:34916906-34917107(+)$1	201	66	98	10.3278
!!dddd"""cccooooooccc22dddd22ccc	chr3:100057839-100058040(+)$1	201	41	73	13.9039
ddd[bb####ddddllldddd4444bbddddf	chr8:95894326-95894527(-)$1	201	138	170	10.2711
dd"""ccc[ddddmmmmdddd22ccc333ddd	chr12:56384393-56384594(+)$1	201	130	162	12.7862
!!dddd"""ddddnnnnndddd]dddd22ccc	chr15:51780690-51780891(-)$1	201	13	45	12.9508
d[ffffff!!cccnnnnnccc333ffffff]d	chr11:47587388-47587589(+)$1	201	157	189	13.0994
:ccc!!a!!cccnnnnnccc333a22ccceee	chr19:5667775-5667976(+)$1	201	0	32	12.0423
ccc####a!!eeeeellleeeee22a333ccc	chr17:46673769-46673970(-)$1	201	122	154	10.9842
iiiiiiii!!cccnnnnnccc4444iiiiiii	chr1:1463054-1463255(+)$1	201	64	96	14.0841
ii[bbccc[ddddmmmmdddd22ccc]bb]ii	chr17:79205705-79205906(-)$1	201	81	113	10.4994
%bb[iiiiiiiiinnnnniiiiiiiiibb]ff	chrX:47861858-47862059(-)$1	201	21	53	10.7744
ddd[ccc"""cccnnnnnccc22ccc]dddd2	chr3:38404343-38404544(+)$1	201	30	62	14.4220
ff!!ccc!!ddddmmmmdddd22ccc22ffff	chr21:30412878-30413079(+)$1	201	82	114	12.4963
c[a[iiiiiiiiinnnnniiiiiiiiia]ccc	chr5:138643849-138644050(+)$1	201	40	72	12.7373
$$$$$ccc!!cccoooooocccccc22dddd:	chr17:79638699-79638900(+)$1	201	79	111	10.6018
[bb"""gggggggnnnnngggggggbb]dddd	chr10:112653805-112654006(+)$1	201	107	139	10.8990
ccc[ccc[eeeeennnnneeeee22ccc]ccc	chr14:105174230-105174431(+)$1	201	132	164	11.3587
ff!!ccc[eeeeemmmmeeeee]ccc4444ff	chr17:20919104-20919305(-)$1	201	136	168	10.2227
:a[ccc[bb[cccnnnnnccc]bb]ccc]acc	chr16:2143547-2143748(-)$1	201	67	99	11.5957
ccdddd!!ddddoooooodddd]dddd333cc	chr7:138263967-138264168(+)$1	201	104	136	11.9340
"""dddd"""bboooooobb333dddd22fff	chr13:111298230-111298431(-)$1	201	108	140	12.3172

#otherMatches

#Seq PSSM
CAUCCAUUGUUAGGAGAUUUCGCAGUGGAUGU	chr4:85656155-85656356(-)$1	201	70	102	10.4885
AUAAACACCUAAAAGAAUUGGAGGCUUUCAGG	chr7:91722469-91722670(+)$1	201	130	162	12.4909
UACGGACUUCGUUAAAGCAAAUGGAGGAACGU	chr12:88487509-88487710(-)$1	201	102	134	11.2104
AAACACCUUAGGACAUAUUCUCUGUGUGAUUG	chr11:134054723-134054924(-)$1	201	47	79	10.9224
GAACAGCACGAUCAAAUAAUUAAUGCUUCAUC	chr11:32955133-32955334(+)$1	201	134	166	11.5495
AAGACUUUAGGUAAGUUGUACGUAGAGGAGUG	chr17:59967081-59967282(-)$1	201	126	158	12.0961
GUGUACUACCAGGUCAGUUGGGUGUACUAAAG	chr1:52260096-52260297(-)$1	201	142	174	11.7083
UCAGGAACAAUUUUUAAUGAUGCUUUCUGGCU	chr11:108180806-108181007(+)$1	201	87	119	13.4727
GAUCUAAAUAAGGUAAAAUAUGUGACUAGAUC	chr1:227307480-227307681(-)$1	201	165	197	10.8643
UUUUGUUUUAUAGAUCAGCUUAUGAGACAGAC	chr10:121336916-121337117(-)$1	201	57	89	11.1068
GGUAUUGCCGCUGUUGUCUCAGAGGAAAAUGC	chr8:117861123-117861324(-)$1	201	139	171	10.8910
CAUCAACCCUCUGGUAAGUAAUGGGUGUUCUG	chr22:39710087-39710288(-)$1	201	164	196	11.5992
CACACUGCGGGCUCCAACAAGACCUUACUCAG	chr7:97936981-97937182(-)$1	201	66	98	12.3704
GUUCAUGAAGGGCAACCAGCUCAUCAGCAACA	chr1:11896087-11896288(+)$1	201	77	109	13.5436
GUGAGCGAGCCCUGUGCGGGCAGUGUGUGCGC	chr14:105222974-105223175(+)$1	201	41	73	12.8105
ACUCAGAAGCGACUGGAUGUCUAUCUACAGGU	chr12:105557953-105558154(+)$1	201	102	134	16.8410
AAGACUUCUGAACAAAAAUUCCAAGAUAGUUU	chr6:10935198-10935399(+)$1	201	152	184	12.4192
GCAGCUUACCAGCCAGAAGCAAGUAAGGAGGG	chr12:120172928-120173129(-)$1	201	143	175	11.0689
GCCGCAGCAUCAGUGUGUCUGAACAUGUGGUC	chr16:2127583-2127784(+)$1	201	107	139	12.4686
AAGAUUACAGGGGAAGCGUUCGUGCAGUUUGC	chr10:43882706-43882907(-)$1	201	22	54	12.6675
AUGUAGACGUUGUUAUUCACAAAUGGAUGUUA	chr5:38953019-38953220(-)$1	201	163	195	12.7828
AUGAAAGGCUUUCCAAUGGGGUAACUGAAAUA	chr7:38908710-38908911(-)$1	201	92	124	13.4463
UUUCUCAUGGCUUCAGGAAGGCUAUUGCUGAG	chrX:70777358-70777559(+)$1	201	105	137	12.2730
UCUGGUGUGCAUAAGAAAAUGAACAUUAGCCU	chr10:64945951-64946152(-)$1	201	21	53	12.3233
ACAGCACGACCUCUAUGCAGACAAGUGAACUG	chr6:64286323-64286524(+)$1	201	85	117	10.3184
CCGCAUGAGAACGGGAACCGGAGCCUGGAGAC	chr22:50869612-50869813(+)$1	201	121	153	12.2415
ACAUGGCUUUUGGUCUUCUAAGUGAAGCUUUU	chr11:108123463-108123664(+)$1	201	33	65	10.3031
AGCCAGAUGAGCUGAAGGUGACAGUCAAGCUG	chr7:151845865-151846066(-)$1	201	16	48	12.9619
GAAGCUGCUGAUGUAUUGAUCAAAGCUGCUCU	chrX:53615351-53615552(-)$1	201	64	96	12.5732
GUCAAAUGAAUUCCUUCGAAAUGUAUUUGAAC	chr7:112112746-112112947(+)$1	201	73	105	10.2792
UGGAAGAAUUUUGUAUUAUACAAGAAGACCCA	chr19:34916906-34917107(+)$1	201	66	98	10.3278
UCCAGCAGUUCGAUCUUCUGAUAGCUGUUUUC	chr3:100057839-100058040(+)$1	201	41	73	13.9039
CAGACACAUACAAACUAUUUGGCUAUGCUGGU	chr8:95894326-95894527(-)$1	201	138	170	10.2711
GCAUCGUUAUUGCCCUGGCAGGGAACAAAGCU	chr12:56384393-56384594(+)$1	201	130	162	12.7862
UCAAAUUGUGAAUUUAAUAUUUUAUUUAUCAU	chr15:51780690-51780891(-)$1	201	13	45	12.9508
ACCGGGCCGAGGGGCAGGCUCGGGGGCCCGCU	chr11:47587388-47587589(+)$1	201	157	189	13.0994
UGGGUUCCACGCCGUGUGCGCAAGUUCCCUGU	chr19:5667775-5667976(+)$1	201	0	32	12.0423
GGAAAAAGGAGAGCAAACUGCUCAGCGCGUCU	chr17:46673769-46673970(-)$1	201	122	154	10.9842
GGGCCAUCAAUGACCGCAUCAAUGAGAUGGUC	chr1:1463054-1463255(+)$1	201	64	96	14.0841
CCAGCUGUGAGGCAUCAGCCUGGGCAGGCCGG	chr17:79205705-79205906(-)$1	201	81	113	10.4994
AUCUCUGCUUUUUCCCAAGAAGAGCAGGAAAU	chrX:47861858-47862059(-)$1	201	21	53	10.7744
GUGUCUGAUUCAGUGGUUCUGUACAGUCAUGG	chr3:38404343-38404544(+)$1	201	30	62	14.4220
GUAAUUCUACUGAAAAGUUGGAUGAAGAACUA	chr21:30412878-30413079(+)$1	201	82	114	12.4963
GAGAUCUCUCUUUGAGAAAAAGAGAGGCGCUC	chr5:138643849-138644050(+)$1	201	40	72	12.7373
AGAAGCGGCGACUAGAUAAAGUCCGACGGAAA	chr17:79638699-79638900(+)$1	201	79	111	10.6018
AGGAACUGGAAGUACCUCAUUUUCACCAUGAG	chr10:112653805-112654006(+)$1	201	107	139	10.8990
GGAAGCUUCCCCUAGGACGGGGGCUGGUCUCU	chr14:105174230-105174431(+)$1	201	132	164	11.3587
UGCACCUGGUGUGGACCCACGCGAGGCACCUA	chr17:20919104-20919305(-)$1	201	136	168	10.2227
AUGACACCCUGGUAGAGAGCCCGGCUGUGACG	chr16:2143547-2143748(-)$1	201	67	99	11.5957
CAGGACAAUUCCUCAAAUGGAAAGUCUGAAUG	chr7:138263967-138264168(+)$1	201	104	136	11.9340
GUCCCUGAAGGUAGCUCAACGAACAGGUGGCC	chr13:111298230-111298431(-)$1	201	108	140	12.3172

#DB
((((((((((..(((...))))))))))))).	chr4:85656155-85656356(-)$1	1	70	102	10.4885
..((((..((((.....))))..).)))..).	chr7:91722469-91722670(+)$1	1	130	162	12.4909
((((..(((((((......)))))))...)))	chr12:88487509-88487710(-)$1	1	102	134	11.2104
..((((...((((....))))..)))))))))	chr11:134054723-134054924(-)$1	1	47	79	10.9224
((..((((.(((......)))..)))))))))	chr11:32955133-32955334(+)$1	1	134	166	11.5495
....(((((.(((.....))).)))))..)))	chr17:59967081-59967282(-)$1	1	126	158	12.0961
..((((..((((.....))))..))))....)	chr1:52260096-52260297(-)$1	1	142	174	11.7083
(((((((..(((......)))..)))))))((	chr11:108180806-108181007(+)$1	1	87	119	13.4727
((((((....(.(((...))).)...))))))	chr1:227307480-227307681(-)$1	1	165	197	10.8643
(((.(((((((((......)))))))))))))	chr10:121336916-121337117(-)$1	1	57	89	11.1068
((((((.((.(((......))).))..)))))	chr8:117861123-117861324(-)$1	1	139	171	10.8910
((...((((..((.....))..))))....))	chr22:39710087-39710288(-)$1	1	164	196	11.5992
((..(((.(((((......)).)))....)))	chr7:97936981-97937182(-)$1	1	66	98	12.3704
(((..(((.((((.....)))).)))..))).	chr1:11896087-11896288(+)$1	1	77	109	13.5436
((..(((.((((.....))))..)))..))))	chr14:105222974-105223175(+)$1	1	41	73	12.8105
(((.(((...(((.....)))..)))...)))	chr12:105557953-105558154(+)$1	1	102	134	16.8410
((((((((((((......)))..))).)))))	chr6:10935198-10935399(+)$1	1	152	184	12.4192
.(..(((((..((.....))..)))))..).)	chr12:120172928-120173129(-)$1	1	143	175	11.0689
((((((...((((.....))))...))))))(	chr16:2127583-2127784(+)$1	1	107	139	12.4686
(((....((.(((.....))).))...)))))	chr10:43882706-43882907(-)$1	1	22	54	12.6675
((((.....((((.....))))....))))))	chr5:38953019-38953220(-)$1	1	163	195	12.7828
((...((...((((...))))...))...)))	chr7:38908710-38908911(-)$1	1	92	124	13.4463
((....(((((((.....)))))))....)))	chrX:70777358-70777559(+)$1	1	105	137	12.2730
.(((((((.(((......))).))))))).))	chr10:64945951-64946152(-)$1	1	21	53	12.3233
....(((....(((....)))...)))..)))	chr6:64286323-64286524(+)$1	1	85	117	10.3184
(((...(....(((...)))...).))))).)	chr22:50869612-50869813(+)$1	1	121	153	12.2415
(((.(((((((((....)))...))))))...	chr11:108123463-108123664(+)$1	1	33	65	10.3031
(((..(((..(((...)))....)))..))).	chr7:151845865-151846066(-)$1	1	16	48	12.9619
(((((.((((((......)))..))).)))..	chrX:53615351-53615552(-)$1	1	64	96	12.5732
((((((((..(((....)))...)))))).))	chr7:112112746-112112947(+)$1	1	73	105	10.2792
(((.....(((((((...)))))))....)))	chr19:34916906-34917107(+)$1	1	66	98	10.3278
..((((...(((......)))..))))..)))	chr3:100057839-100058040(+)$1	1	41	73	13.9039
(((.((....((((...))))....)))))))	chr8:95894326-95894527(-)$1	1	138	170	10.2711
((...(((.((((....))))..)))...)))	chr12:56384393-56384594(+)$1	1	130	162	12.7862
..((((...((((.....)))).))))..)))	chr15:51780690-51780891(-)$1	1	13	45	12.9508
(.((((((..(((.....)))...)))))).)	chr11:47587388-47587589(+)$1	1	157	189	13.0994
.(((..(..(((.....)))...)..)))(((	chr19:5667775-5667976(+)$1	1	0	32	12.0423
(((....(..(((((...)))))..)...)))	chr17:46673769-46673970(-)$1	1	122	154	10.9842
((((((((..(((.....)))....)))))))	chr1:1463054-1463255(+)$1	1	64	96	14.0841
((.(((((.((((....))))..))).)).))	chr17:79205705-79205906(-)$1	1	81	113	10.4994
.((.(((((((((.....))))))))))).))	chrX:47861858-47862059(-)$1	1	21	53	10.7744
(((.(((...(((.....)))..))).)))).	chr3:38404343-38404544(+)$1	1	30	62	14.4220
((..(((..((((....))))..)))..))))	chr21:30412878-30413079(+)$1	1	82	114	12.4963
(.(.(((((((((.....)))))))))).)))	chr5:138643849-138644050(+)$1	1	40	72	12.7373
.....(((..(((......))))))..)))).	chr17:79638699-79638900(+)$1	1	79	111	10.6018
.((...(((((((.....))))))))).))))	chr10:112653805-112654006(+)$1	1	107	139	10.8990
(((.(((.(((((.....)))))..))).)))	chr14:105174230-105174431(+)$1	1	132	164	11.3587
((..(((.(((((....))))).)))....))	chr17:20919104-20919305(-)$1	1	136	168	10.2227
.(.(((.((.(((.....))).)).))).)((	chr16:2143547-2143748(-)$1	1	67	99	11.5957
((((((..((((......)))).))))...))	chr7:138263967-138264168(+)$1	1	104	136	11.9340
...((((...((......))...))))..)))	chr13:111298230-111298431(-)$1	1	108	140	12.3172

#PSSM
c : 0.19	f : 0.15	d : 0.13	! : 0.05	e : 0.05	" : 0.05	$ : 0.05	i : 0.05	= : 0.03	g : 0.03	[ : 0.03	% : 0.03	: : 0.03	b : 0.01	
c : 0.19	f : 0.15	d : 0.11	! : 0.05	e : 0.05	b : 0.05	$ : 0.05	g : 0.05	i : 0.05	= : 0.03	" : 0.03	a : 0.03	[ : 0.03	% : 0.01	
c : 0.19	d : 0.13	f : 0.13	! : 0.11	" : 0.07	g : 0.05	= : 0.03	e : 0.03	$ : 0.03	[ : 0.03	b : 0.03	# : 0.01	% : 0.01	i : 0.01	a : 0.01	
! : 0.15	[ : 0.15	d : 0.11	f : 0.09	" : 0.09	c : 0.07	$ : 0.05	g : 0.05	# : 0.05	= : 0.03	e : 0.01	% : 0.01	i : 0.01	b : 0.01	
c : 0.21	d : 0.13	f : 0.11	" : 0.09	! : 0.07	i : 0.07	g : 0.05	# : 0.05	$ : 0.05	e : 0.03	b : 0.03	= : 0.01	
c : 0.27	d : 0.15	f : 0.11	i : 0.07	g : 0.05	# : 0.05	! : 0.03	e : 0.03	$ : 0.03	b : 0.03	" : 0.03	= : 0.01	a : 0.01	[ : 0.01	
c : 0.29	g : 0.09	" : 0.07	# : 0.07	i : 0.07	! : 0.05	d : 0.05	f : 0.05	e : 0.03	[ : 0.03	$ : 0.03	a : 0.03	= : 0.01	b : 0.01	
" : 0.15	c : 0.13	! : 0.11	g : 0.07	# : 0.07	i : 0.07	[ : 0.07	b : 0.05	f : 0.05	d : 0.03	e : 0.03	$ : 0.03	= : 0.01	a : 0.01	
! : 0.17	" : 0.15	d : 0.09	[ : 0.09	g : 0.07	e : 0.07	# : 0.07	i : 0.05	b : 0.05	c : 0.05	= : 0.01	$ : 0.01	f : 0.01	
d : 0.23	c : 0.15	! : 0.15	g : 0.07	[ : 0.07	# : 0.07	" : 0.07	i : 0.05	e : 0.03	= : 0.01	f : 0.01	
c : 0.39	d : 0.27	g : 0.07	! : 0.05	i : 0.05	e : 0.05	# : 0.03	a : 0.01	b : 0.01	
c : 0.41	d : 0.27	g : 0.07	b : 0.07	i : 0.05	e : 0.05	! : 0.01	[ : 0.01	
c : 0.31	d : 0.19	o : 0.15	n : 0.07	g : 0.07	i : 0.05	b : 0.05	e : 0.05	
n : 0.43	o : 0.25	m : 0.13	c : 0.07	d : 0.03	l : 0.01	g : 0.01	e : 0.01	
n : 0.43	o : 0.25	m : 0.15	l : 0.07	c : 0.03	g : 0.01	e : 0.01	
n : 0.43	o : 0.25	l : 0.15	m : 0.15	
n : 0.43	o : 0.25	m : 0.15	l : 0.13	c : 0.01	
n : 0.35	o : 0.25	d : 0.17	c : 0.09	l : 0.07	m : 0.01	e : 0.01	
c : 0.41	d : 0.27	o : 0.09	b : 0.05	g : 0.05	e : 0.05	i : 0.03	
c : 0.43	d : 0.27	g : 0.07	b : 0.07	i : 0.05	e : 0.05	4 : 0.01	
c : 0.35	d : 0.27	3 : 0.09	g : 0.07	i : 0.05	e : 0.05	2 : 0.03	b : 0.01	4 : 0.01	
2 : 0.31	3 : 0.15	] : 0.11	d : 0.09	g : 0.07	i : 0.05	4 : 0.05	e : 0.05	c : 0.03	= : 0.01	
2 : 0.27	3 : 0.17	g : 0.09	] : 0.09	e : 0.07	4 : 0.07	i : 0.05	c : 0.03	b : 0.03	= : 0.01	a : 0.01	d : 0.01	
c : 0.25	d : 0.15	g : 0.11	3 : 0.09	a : 0.05	i : 0.05	b : 0.05	4 : 0.05	e : 0.03	f : 0.03	2 : 0.03	= : 0.01	
c : 0.27	d : 0.15	g : 0.11	] : 0.05	3 : 0.05	i : 0.05	4 : 0.05	f : 0.05	2 : 0.05	e : 0.03	b : 0.03	= : 0.01	
c : 0.29	d : 0.15	i : 0.07	4 : 0.07	f : 0.07	g : 0.05	e : 0.05	2 : 0.05	b : 0.05	3 : 0.03	= : 0.01	a : 0.01	
d : 0.13	3 : 0.11	2 : 0.11	c : 0.09	f : 0.09	4 : 0.09	i : 0.07	] : 0.07	e : 0.05	= : 0.03	g : 0.03	b : 0.03	
2 : 0.19	f : 0.13	3 : 0.11	4 : 0.11	c : 0.09	g : 0.07	b : 0.05	d : 0.05	= : 0.03	i : 0.03	e : 0.01	a : 0.01	] : 0.01	
f : 0.17	2 : 0.13	3 : 0.11	4 : 0.11	d : 0.09	g : 0.07	c : 0.07	b : 0.05	] : 0.05	= : 0.03	e : 0.01	i : 0.01	
c : 0.23	f : 0.15	d : 0.13	e : 0.07	] : 0.07	g : 0.05	4 : 0.05	= : 0.03	a : 0.03	i : 0.03	3 : 0.03	2 : 0.01	b : 0.01	
c : 0.25	f : 0.21	d : 0.17	e : 0.05	] : 0.05	i : 0.05	= : 0.03	g : 0.03	a : 0.01	4 : 0.01	b : 0.01	3 : 0.01	2 : 0.01	
c : 0.23	d : 0.21	f : 0.21	e : 0.05	2 : 0.05	i : 0.05	: : 0.03	g : 0.03	3 : 0.03	] : 0.01	= : 0.01	

#score	612.4031588176962
#seq	51
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_CDS_m3_run2.txt

#BEAR
gggggg[a[ccclllccc]aggggg	chrX:70513984-70514207(+)$1	223	20	45	9.7341
:ccc"""cccnnnnnccc4444ccc	chr2:38978270-38978503(-)$1	233	125	150	12.1577
[eeeee[cccnnnnnccc]eeeee]	chr13:107220058-107220278(-)$1	220	23	48	11.9907
==========nnnnn==========	chr16:2159748-2159975(-)$1	227	59	84	12.9608
e####a[cccnnnnncccaeeeeec	chr17:2236751-2236981(-)$1	230	11	36	11.7067
ee[ccc[cccnnnnnccc]ccceee	chr17:62499840-62500073(-)$1	233	119	144	12.3202
!ffffff[accclllccc]a]ffff	chr19:46289078-46289297(-)$1	219	67	92	8.4194
ggggggcccooooooccc]gggggg	chr6:90403696-90403917(-)$1	221	123	148	10.1427
==========oooooo=========	chr20:33442247-33442470(-)$1	223	2	27	10.6860
gggggg[cccmmmmccc22gggggg	chr17:35981143-35981369(-)$1	226	70	95	8.4995
[a!!ccc[cccmmmmcccccca]dd	chr17:80019424-80019644(-)$1	220	29	54	8.3030
iiiiii[cccnnnnnccciiiiiii	chr17:7212842-7213083(+)$1	241	183	208	13.1688
========bbnnnnnbb]=======	chr1:205696774-205697016(-)$1	242	181	206	11.9018
$$$cccddddnnnnndddd]ccc66	chr7:148526735-148526961(-)$1	226	44	69	9.6273
e[ccc"""cccmmmmcccccc]eee	chr19:3980413-3980643(-)$1	230	155	180	8.6825
eeee!!ddddnnnnndddd333eee	chr9:135919154-135919400(+)$1	246	9	34	11.3091
!!eeeee[bbnnnnnbbeeeee22d	chr1:27618657-27618878(+)$1	221	148	173	9.1510
!bb[bb[cccnnnnnccc]bb]bb2	chr4:1732527-1732753(+)$1	226	102	127	10.5597
dd[bb[ddddnnnnndddd333bbd	chr1:31465136-31465364(-)$1	228	22	47	10.2367
::dddd[cccnnnnnccc333dddd	chr1:19432966-19433197(-)$1	231	89	114	9.9739
!!iiiiiiiiimmmmiiiiiiiii]	chr10:6157338-6157563(+)$1	225	142	167	8.9247
##ccc"""cccmmmmccc333ccc5	chr5:76326191-76326414(+)$1	223	78	103	9.1355
==========nnnnn==========	chr13:30091217-30091436(-)$1	219	54	79	12.9608
beeeee[cccnnnnnccc]eeeee7	chr14:70237954-70238184(+)$1	230	68	93	11.0642
ffffff[cccnnnnncccffffff:	chr12:57145973-57146193(-)$1	220	188	213	10.0079
ggggggg[ccclllccc]ggggggg	chr13:111862198-111862437(+)$1	239	155	180	9.1714
cccgggggggnnnnnggggggg888	chr1:41514390-41514617(-)$1	227	161	186	9.6450
###bb[ddddnnnnndddd]bb333	chr19:50100342-50100567(+)$1	225	171	196	10.4133
dddd!!ddddnnnnndddd4444dd	chr6:52133797-52134060(-)$1	263	139	164	10.7314
#dddd!!cccnnnnncccdddd444	chr1:20981884-20982114(-)$1	230	92	117	11.4358
ggggggg[bboooooobbggggggg	chr10:96334320-96334562(+)$1	242	84	109	8.3348
eeee"""bboooooobb333eeeee	chr9:33948356-33948580(-)$1	224	130	155	8.4891
iiiiiiiiiooooooiiiiiiiiid	chr12:56827280-56827510(-)$1	230	153	178	9.8187
iiiiiiicccnnnnnccc]iiiiii	chr1:220960286-220960517(+)$1	231	49	74	13.1671
iiii[ddddccclllccc]ddddii	chr8:87520622-87520863(-)$1	241	106	131	8.6649
fffffccc[ccclllccc]ccc]ff	chr16:2149768-2149998(-)$1	230	94	119	8.4533
eeeee"""cccmmmmccc22eeeee	chr1:224586500-224586723(-)$1	223	52	77	8.1070
%%ccc[ddddnnnnndddd]ccc44	chr8:22102922-22103158(+)$1	236	119	144	10.2016
:ccc"""cccmmmmccc333cccdd	chr19:42736555-42736782(-)$1	227	116	141	8.2084
gggg"""cccmmmmccc333ggggg	chr4:77926809-77927032(+)$1	223	72	97	9.4733
##ccc[ddddnnnnndddd]ccca]	chr20:44441238-44441459(+)$1	221	157	182	11.3467
=========annnnna]========	chr3:122283279-122283507(-)$1	228	77	102	12.6951
"ccc[eeeeennnnneeeee]ccc3	chr20:47585669-47585907(+)$1	238	63	88	10.4443
ffff!!ddddnnnnndddd]fffff	chr5:137909657-137909882(-)$1	225	50	75	10.4124
gg[ccc[bbccclllccc333bbcc	chr21:34926704-34926955(+)$1	251	37	62	9.0959
:ccc[bbcccnnnnnccc]bb]ccc	chr10:120802079-120802328(-)$1	249	211	236	10.3948
:iiiiiiiiiooooooiiiiiiiii	chr14:75283619-75283841(+)$1	222	144	169	8.9957
cccccc[cccnnnnnccc4444ccc	chr12:57892179-57892413(+)$1	234	125	150	12.6882
eddddeeeeennnnneeeee333dd	chr13:60582588-60582814(-)$1	226	192	217	9.4683
ffffff[cccnnnnnccc]ffffff	chr9:95050307-95050529(-)$1	222	151	176	11.2909
[bb"""ddddnnnnndddd4444bb	chr14:69369104-69369331(-)$1	227	83	108	10.5521
eee!!ddddoooooodddd4444ee	chr6:126211739-126211961(+)$1	222	84	109	8.7033
"==========mmmm==========	chr10:1046818-1047048(+)$1	230	31	56	9.7598
dd[eeeee[annnnnaeeeee]ddd	chrX:107978916-107979146(-)$1	230	204	229	9.5124
eee[aeeeeennnnneeeee]a]ee	chr17:27067865-27068091(+)$1	226	36	61	9.7329

#otherMatches

#Seq PSSM
CUUUAGACUGUUGAUGGCUGCUAAG	chrX:70513984-70514207(+)$1	223	20	45	9.7341
CGGAGGAGGUAAGAAGCUGGAGUCC	chr2:38978270-38978503(-)$1	233	125	150	12.1577
CGGAGCCGGAGCUCGUCCCGCUCCA	chr13:107220058-107220278(-)$1	220	23	48	11.9907
CUUGGUCCUUGGAGGAGGGGCUGAG	chr16:2159748-2159975(-)$1	227	59	84	12.9608
UUAAAGUCCUAAUGAAGGCAGACCC	chr17:2236751-2236981(-)$1	230	11	36	11.7067
UCAGCCAUUCCUAGAGAGAGGCGAU	chr17:62499840-62500073(-)$1	233	119	144	12.3202
GGGUGUGGCGGCAGAGCCUGGCACA	chr19:46289078-46289297(-)$1	219	67	92	8.4194
AGGUAACACAGCAGAGUGAUUAUUU	chr6:90403696-90403917(-)$1	221	123	148	10.1427
UGGGAGGGGCCUGGCAGCCUCUUCC	chr20:33442247-33442470(-)$1	223	2	27	10.6860
CAGAGCAGGAAAAAUCUGGGUUCUG	chr17:35981143-35981369(-)$1	226	70	95	8.4995
GCAUUUCUCUGCCAACAGGAAGGCU	chr17:80019424-80019644(-)$1	220	29	54	8.3030
AUUACGUAAGAAUGGCUUUGUGGUG	chr17:7212842-7213083(+)$1	241	183	208	13.1688
GAAGAUAGGUAAGAGGCAUUGUUUU	chr1:205696774-205697016(-)$1	242	181	206	11.9018
UAACAUUCCUUAUAUGGGAGAUGAA	chr7:148526735-148526961(-)$1	226	44	69	9.6273
GCCCCUUGGCACUGUUGCGGGCCCU	chr19:3980413-3980643(-)$1	230	155	180	8.6825
GCAUACGUCAAUGUAUGACAAGGUG	chr9:135919154-135919400(+)$1	246	9	34	11.3091
CCCCAGGACAACAACUGCCUGGCAG	chr1:27618657-27618878(+)$1	221	148	173	9.1510
UCAGCGGAGGACACGCCUGUGGUGC	chr4:1732527-1732753(+)$1	226	102	127	10.5597
ACAUGUGGGCAUGGAGCCUCUUCAG	chr1:31465136-31465364(-)$1	228	22	47	10.2367
CUCCCCCUUGGAUCUCAAACUGGGG	chr1:19432966-19433197(-)$1	231	89	114	9.9739
GACAAAUUCAGGGUCUUGGAUUUGG	chr10:6157338-6157563(+)$1	225	142	167	8.9247
CUGGCCUCUGGUUUUCCGACUGCUU	chr5:76326191-76326414(+)$1	223	78	103	9.1355
CUGUGGGCAGUCUUUCUGCUCGCAG	chr13:30091217-30091436(-)$1	219	54	79	12.9608
CGGAGCCGGAGCAAGUCCCGUUCUG	chr14:70237954-70238184(+)$1	230	68	93	11.0642
CUAUCGCUGGCUCAACUACGGUGGA	chr12:57145973-57146193(-)$1	220	188	213	10.0079
GUUUGAGAGAUUUUGUUACUUAAAU	chr13:111862198-111862437(+)$1	239	155	180	9.1714
GCAGCAGGCUGUCCAGGCCUGUAUC	chr1:41514390-41514617(-)$1	227	161	186	9.6450
CAAGGCUGGCGCUGGGCCACCCCCC	chr19:50100342-50100567(+)$1	225	171	196	10.4133
AAGCUGUGGAGUUGGUCCAGUAUGC	chr6:52133797-52134060(-)$1	263	139	164	10.7314
GCUCAUCGUGGCUGACACUGAGAAC	chr1:20981884-20982114(-)$1	230	92	117	11.4358
AGAGAGGAGUACCAGGACCUUUUCU	chr10:96334320-96334562(+)$1	242	84	109	8.3348
AGUACAAGUCACCCUACAACUACUA	chr9:33948356-33948580(-)$1	224	130	155	8.4891
UUGCAGGUGCUAACUUAUUUGCAGG	chr12:56827280-56827510(-)$1	230	153	178	9.8187
AAUCCCGGCCCGGGUGGCUCGGGGU	chr1:220960286-220960517(+)$1	231	49	74	13.1671
CGGGCAUUGCGGCCCCUGUCGAUUC	chr8:87520622-87520863(-)$1	241	106	131	8.6649
CCAACGCCGUGUGGUACGGGGCUGU	chr16:2149768-2149998(-)$1	230	94	119	8.4533
UGAUGGAAAGACUGUUCUGGCAUCA	chr1:224586500-224586723(-)$1	223	52	77	8.1070
UCGGGCGGCGGCCGGCGCCUCCCCU	chr8:22102922-22103158(+)$1	236	119	144	10.2016
UUCAACUUCAGUGCUGGUGGUGAGG	chr19:42736555-42736782(-)$1	227	116	141	8.2084
AAUGUACGGCUGAAGUUAACCAUUG	chr4:77926809-77927032(+)$1	223	72	97	9.4733
AGCCGAGCGGGGGCGCCGCCCGGGG	chr20:44441238-44441459(+)$1	221	157	182	11.3467
UGCCCGGGGCUUCGUGUUCCUGGGU	chr3:122283279-122283507(-)$1	228	77	102	12.6951
UGCAGAAGGAUGCCUUCCUUGUGUU	chr20:47585669-47585907(+)$1	238	63	88	10.4443
AGUUUUUUCUUUUUUAGGAUAGCUG	chr5:137909657-137909882(-)$1	225	50	75	10.4124
ACCGUUACUUCCUAAGGACAUGGAA	chr21:34926704-34926955(+)$1	251	37	62	9.0959
CUGAGGAAGAUAGGUUCUCUCGUCG	chr10:120802079-120802328(-)$1	249	211	236	10.3948
GGCAUUUUGACCAGUUUUGGAGUGC	chr14:75283619-75283841(+)$1	222	144	169	8.9957
GGAGAUCUGCGACAAGUACCACAUC	chr12:57892179-57892413(+)$1	234	125	150	12.6882
GGUUUUAUGAUUGGUUUAUAUGAAA	chr13:60582588-60582814(-)$1	226	192	217	9.4683
UCUGAUUUUUUUUAUAAGCAUUAGA	chr9:95050307-95050529(-)$1	222	151	176	11.2909
AGCCAUCAUGACUUACGUGUCUAGC	chr14:69369104-69369331(-)$1	227	83	108	10.5521
CACCCAUGUUCCUGUGCAUCAAAGU	chr6:126211739-126211961(+)$1	222	84	109	8.7033
CGAGAAUAAUGAUUUCAUUAUUUUU	chr10:1046818-1047048(+)$1	230	31	56	9.7598
GCAGCCGGACGGAGAGCCGGCCGCG	chrX:107978916-107979146(-)$1	230	204	229	9.5124
UGGAGGAGGCCCUGAGCUUCACACU	chr17:27067865-27068091(+)$1	226	36	61	9.7329

#DB
((((((.(.(((...))).))))))	chrX:70513984-70514207(+)$1	1	20	45	9.7341
.(((...(((.....)))....)))	chr2:38978270-38978503(-)$1	1	125	150	12.1577
.(((((.(((.....))).))))).	chr13:107220058-107220278(-)$1	1	23	48	11.9907
((((((((((.....))))))))))	chr16:2159748-2159975(-)$1	1	59	84	12.9608
(....(.(((.....)))))))))(	chr17:2236751-2236981(-)$1	1	11	36	11.7067
((.(((.(((.....))).))))))	chr17:62499840-62500073(-)$1	1	119	144	12.3202
.((((((.((((...))).).))))	chr19:46289078-46289297(-)$1	1	67	92	8.4194
(((((((((......))).))))))	chr6:90403696-90403917(-)$1	1	123	148	10.1427
((((((((((......)))))))))	chr20:33442247-33442470(-)$1	1	2	27	10.6860
((((((.(((....)))..))))))	chr17:35981143-35981369(-)$1	1	70	95	8.4995
.(..(((.(((....))))))).))	chr17:80019424-80019644(-)$1	1	29	54	8.3030
((((((.(((.....))))))))))	chr17:7212842-7213083(+)$1	1	183	208	13.1688
((((((((((.....)).)))))))	chr1:205696774-205697016(-)$1	1	181	206	11.9018
...(((((((.....)))).)))..	chr7:148526735-148526961(-)$1	1	44	69	9.6273
(.(((...(((....)))))).)))	chr19:3980413-3980643(-)$1	1	155	180	8.6825
((((..((((.....))))...)))	chr9:135919154-135919400(+)$1	1	9	34	11.3091
..(((((.((.....)))))))..)	chr1:27618657-27618878(+)$1	1	148	173	9.1510
.((.((.(((.....))).)).)).	chr4:1732527-1732753(+)$1	1	102	127	10.5597
((.((.((((.....))))...)))	chr1:31465136-31465364(-)$1	1	22	47	10.2367
..((((.(((.....)))...))))	chr1:19432966-19433197(-)$1	1	89	114	9.9739
..(((((((((....))))))))).	chr10:6157338-6157563(+)$1	1	142	167	8.9247
..(((...(((....)))...))).	chr5:76326191-76326414(+)$1	1	78	103	9.1355
((((((((((.....))))))))))	chr13:30091217-30091436(-)$1	1	54	79	12.9608
((((((.(((.....))).))))).	chr14:70237954-70238184(+)$1	1	68	93	11.0642
((((((.(((.....))))))))).	chr12:57145973-57146193(-)$1	1	188	213	10.0079
(((((((.(((...))).)))))))	chr13:111862198-111862437(+)$1	1	155	180	9.1714
((((((((((.....)))))))...	chr1:41514390-41514617(-)$1	1	161	186	9.6450
...((.((((.....)))).))...	chr19:50100342-50100567(+)$1	1	171	196	10.4133
((((..((((.....))))....))	chr6:52133797-52134060(-)$1	1	139	164	10.7314
.((((..(((.....)))))))...	chr1:20981884-20982114(-)$1	1	92	117	11.4358
(((((((.((......)))))))))	chr10:96334320-96334562(+)$1	1	84	109	8.3348
((((...((......))...)))))	chr9:33948356-33948580(-)$1	1	130	155	8.4891
(((((((((......)))))))))(	chr12:56827280-56827510(-)$1	1	153	178	9.8187
((((((((((.....))).))))))	chr1:220960286-220960517(+)$1	1	49	74	13.1671
((((.(((((((...))).))))))	chr8:87520622-87520863(-)$1	1	106	131	8.6649
((((((((.(((...))).))).))	chr16:2149768-2149998(-)$1	1	94	119	8.4533
(((((...(((....)))..)))))	chr1:224586500-224586723(-)$1	1	52	77	8.1070
..(((.((((.....)))).)))..	chr8:22102922-22103158(+)$1	1	119	144	10.2016
.(((...(((....)))...)))((	chr19:42736555-42736782(-)$1	1	116	141	8.2084
((((...(((....)))...)))))	chr4:77926809-77927032(+)$1	1	72	97	9.4733
..(((.((((.....)))).)))).	chr20:44441238-44441459(+)$1	1	157	182	11.3467
((((((((((.....).))))))))	chr3:122283279-122283507(-)$1	1	77	102	12.6951
.(((.(((((.....))))).))).	chr20:47585669-47585907(+)$1	1	63	88	10.4443
((((..((((.....)))).)))))	chr5:137909657-137909882(-)$1	1	50	75	10.4124
((.(((.(((((...)))...))))	chr21:34926704-34926955(+)$1	1	37	62	9.0959
.(((.(((((.....))).)).)))	chr10:120802079-120802328(-)$1	1	211	236	10.3948
.(((((((((......)))))))))	chr14:75283619-75283841(+)$1	1	144	169	8.9957
((((((.(((.....)))....)))	chr12:57892179-57892413(+)$1	1	125	150	12.6882
((((((((((.....)))))...))	chr13:60582588-60582814(-)$1	1	192	217	9.4683
((((((.(((.....))).))))))	chr9:95050307-95050529(-)$1	1	151	176	11.2909
.((...((((.....))))....))	chr14:69369104-69369331(-)$1	1	83	108	10.5521
(((..((((......))))....))	chr6:126211739-126211961(+)$1	1	84	109	8.7033
.((((((((((....))))))))))	chr10:1046818-1047048(+)$1	1	31	56	9.7598
((.(((((.(.....)))))).)))	chrX:107978916-107979146(-)$1	1	204	229	9.5124
(((.((((((.....))))).).))	chr17:27067865-27068091(+)$1	1	36	61	9.7329

#PSSM
e : 0.16	g : 0.12	: : 0.09	= : 0.09	! : 0.07	i : 0.07	# : 0.07	f : 0.07	[ : 0.05	d : 0.05	c : 0.03	" : 0.03	$ : 0.01	b : 0.01	% : 0.01	
e : 0.14	g : 0.12	c : 0.10	= : 0.10	f : 0.09	i : 0.09	d : 0.09	# : 0.07	! : 0.03	b : 0.03	a : 0.01	$ : 0.01	[ : 0.01	: : 0.01	% : 0.01	
c : 0.18	e : 0.14	g : 0.10	= : 0.10	i : 0.10	f : 0.09	[ : 0.07	d : 0.07	# : 0.03	b : 0.03	! : 0.01	$ : 0.01	
c : 0.21	g : 0.12	e : 0.12	= : 0.10	i : 0.10	f : 0.09	d : 0.07	! : 0.03	[ : 0.03	b : 0.03	# : 0.01	" : 0.01	
c : 0.16	g : 0.10	= : 0.10	" : 0.09	e : 0.09	i : 0.09	f : 0.07	! : 0.07	b : 0.05	d : 0.05	[ : 0.05	# : 0.01	a : 0.01	
" : 0.14	e : 0.12	g : 0.10	= : 0.10	c : 0.10	i : 0.09	! : 0.07	[ : 0.07	f : 0.05	d : 0.05	b : 0.03	a : 0.01	
[ : 0.23	d : 0.20	" : 0.12	= : 0.10	e : 0.09	i : 0.07	c : 0.05	g : 0.05	f : 0.01	! : 0.01	b : 0.01	
c : 0.34	d : 0.20	= : 0.10	[ : 0.09	e : 0.07	" : 0.05	i : 0.05	b : 0.03	a : 0.01	g : 0.01	
c : 0.41	d : 0.20	= : 0.09	b : 0.09	[ : 0.05	i : 0.05	e : 0.05	a : 0.01	g : 0.01	
c : 0.49	d : 0.16	= : 0.07	o : 0.07	b : 0.05	e : 0.05	i : 0.03	a : 0.03	g : 0.01	
n : 0.60	c : 0.18	o : 0.12	m : 0.05	i : 0.01	= : 0.01	
n : 0.60	m : 0.16	o : 0.12	c : 0.09	l : 0.01	
n : 0.60	m : 0.16	o : 0.12	l : 0.10	
n : 0.60	m : 0.16	o : 0.12	l : 0.10	
n : 0.60	o : 0.12	m : 0.10	l : 0.09	c : 0.07	
c : 0.50	d : 0.18	= : 0.05	o : 0.05	b : 0.05	e : 0.05	i : 0.03	a : 0.03	g : 0.01	
c : 0.50	d : 0.18	= : 0.07	b : 0.07	e : 0.07	i : 0.05	g : 0.01	] : 0.01	
c : 0.43	d : 0.18	= : 0.09	e : 0.09	i : 0.05	3 : 0.05	] : 0.03	2 : 0.01	g : 0.01	b : 0.01	
] : 0.21	d : 0.20	= : 0.10	3 : 0.10	e : 0.09	i : 0.07	g : 0.05	4 : 0.03	2 : 0.03	c : 0.03	a : 0.01	f : 0.01	
e : 0.14	3 : 0.14	= : 0.10	4 : 0.09	g : 0.09	i : 0.09	] : 0.09	c : 0.07	a : 0.03	b : 0.03	f : 0.03	d : 0.03	2 : 0.01	
c : 0.14	g : 0.12	e : 0.12	= : 0.10	3 : 0.10	4 : 0.09	i : 0.09	] : 0.05	b : 0.05	f : 0.05	d : 0.03	
c : 0.14	g : 0.12	e : 0.10	= : 0.10	4 : 0.09	i : 0.09	f : 0.07	] : 0.07	3 : 0.05	d : 0.05	a : 0.03	b : 0.03	
c : 0.16	e : 0.14	g : 0.10	= : 0.10	i : 0.09	f : 0.07	4 : 0.07	] : 0.05	b : 0.05	d : 0.05	3 : 0.03	2 : 0.01	8 : 0.01	
e : 0.18	g : 0.10	c : 0.10	= : 0.10	d : 0.10	i : 0.10	f : 0.09	b : 0.05	4 : 0.03	6 : 0.01	2 : 0.01	8 : 0.01	3 : 0.01	a : 0.01	
d : 0.16	e : 0.12	g : 0.10	= : 0.10	c : 0.09	f : 0.07	i : 0.07	] : 0.05	3 : 0.03	4 : 0.03	6 : 0.01	2 : 0.01	5 : 0.01	7 : 0.01	: : 0.01	8 : 0.01	b : 0.01	

#score	563.0348200895472
#seq	55
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_CDS_m1_run2.txt

#BEAR
!eeeeeyyyyyyyyyyyyyyyyee	chr11:17158010-17158211(-)$1	201	50	74	21.0475
bb!!cccuuuuuuuuuuuuccc44	chr4:156714981-156715182(+)$1	201	150	174	23.3121
ccccccwwwwwwwwwwwwwwccc]	chr7:121985604-121985805(-)$1	201	57	81	22.6452
ccc[ccctttttttttttccc22c	chr5:140913881-140914082(-)$1	201	117	141	22.0146
:ddddwwwwwwwwwwwwwwddddF	chr10:64974241-64974442(-)$1	201	172	196	20.7413
dddyyyyyyyyyyyyyyyydddd]	chr2:98427527-98427728(-)$1	201	13	37	20.4732
bb[cccvvvvvvvvvvvvvccc]b	chr10:94267802-94268003(-)$1	201	10	34	23.2088
ccc[bbuuuuuuuuuuuubb]ccc	chr3:44882557-44882758(+)$1	201	50	74	21.7780
!!ddddvvvvvvvvvvvvvdddd4	chr1:202933663-202933864(-)$1	201	38	62	23.8533
[eeeeeuuuuuuuuuuuueeeee]	chr11:62648414-62648615(+)$1	201	65	89	22.5707
!eeeeevvvvvvvvvvvvveeeee	chr6:56482079-56482280(-)$1	201	37	61	23.5345
!dddd[bbtttttttttttbb22d	chr5:140059295-140059496(-)$1	201	146	170	20.6269
c:ddddvvvvvvvvvvvvvddddH	chr7:44620696-44620897(-)$1	201	35	59	21.9721
###cccvvvvvvvvvvvvvccc44	chr12:939177-939378(+)$1	201	22	46	23.7128
ff!!ddddtttttttttttdddd2	chr12:57038920-57039121(-)$1	201	69	93	21.6004
dd!!ddddtttttttttttdddd2	chr19:36550785-36550986(+)$1	201	126	150	21.6307
hhh[cccuuuuuuuuuuuuccc22	chr8:25280686-25280887(-)$1	201	145	169	23.1021
ddddyyyyyyyyyyyyyyyydddd	chr18:20573412-20573613(+)$1	201	98	122	20.5659
[ccc!!auuuuuuuuuuuua22cc	chr6:44360368-44360569(+)$1	201	50	74	22.9758
iiiiiwwwwwwwwwwwwwwiiiii	chr10:114192052-114192253(-)$1	201	162	186	22.2025
a!!eeeeettttttttttteeeee	chr1:110882431-110882632(+)$1	201	102	126	21.7531
d!!cccwwwwwwwwwwwwwwccc2	chr18:9563349-9563550(-)$1	201	98	122	22.5317
hhhhhhhuuuuuuuuuuuuhhhhh	chr14:64537279-64537480(+)$1	201	57	81	21.2243
ggggggguuuuuuuuuuuuggggg	chr17:65907722-65907923(+)$1	201	152	176	23.0740
::eeeeeuuuuuuuuuuuueeeee	chr21:40578069-40578270(-)$1	201	47	71	21.2248
!!fffffftttttttttttfffff	chr7:135304078-135304279(+)$1	201	78	102	20.8158
hhhhhhwwwwwwwwwwwwwwhhhh	chr3:132179014-132179215(+)$1	201	147	171	20.9074
gggggggtttttttttttgggggg	chr17:34937727-34937928(+)$1	201	34	58	21.7377
b[cccyyyyyyyyyyyyyyyyccc	chr1:154562213-154562414(-)$1	201	126	150	21.0449
b[eeeeettttttttttteeeee]	chr6:133789714-133789915(+)$1	201	66	90	21.8771
####cccuuuuuuuuuuuuccc66	chr14:57749737-57749938(+)$1	201	15	39	22.3417
::ddddvvvvvvvvvvvvvdddd:	chr7:27203249-27203450(-)$1	201	36	60	20.9867
(eeeeevvvvvvvvvvvvveeeee	chr1:180067976-180068177(+)$1	201	67	91	22.8061
eecccwwwwwwwwwwwwwwccc33	chr17:41852045-41852246(-)$1	201	128	152	22.2972
iiiiiiiuuuuuuuuuuuuiiiii	chr15:89803925-89804126(+)$1	201	164	188	23.1923
ffffffwwwwwwwwwwwwwwffff	chr12:101759176-101759377(+)$1	201	155	179	21.1066
ddd[bbvvvvvvvvvvvvvbbddd	chr15:28459812-28460013(-)$1	201	167	191	22.5524
======yyyyyyyyyyyyyyyy==	chr22:41565490-41565691(+)$1	201	112	136	21.1703
ffffffwwwwwwwwwwwwwwffff	chr19:4409629-4409830(+)$1	201	26	50	21.1066
hhhhhhvvvvvvvvvvvvvhhhhh	chr22:31884603-31884804(-)$1	201	53	77	22.0022
dddd[ccctttttttttttccc]d	chr17:80041810-80042011(-)$1	201	20	44	21.9097
ccc:cccuuuuuuuuuuuuccc::	chr17:40061701-40061902(-)$1	201	62	86	20.6004
ggeeeeeuuuuuuuuuuuueeeee	chr6:161527523-161527724(+)$1	201	96	120	22.9653
:a[cccvvvvvvvvvvvvvccc]a	chr10:99139324-99139525(-)$1	201	114	138	22.9915
fff!!ccctttttttttttccc22	chr11:65484092-65484293(+)$1	201	108	132	21.8985
iiiiiiyyyyyyyyyyyyyyyyii	chr5:137654831-137655032(-)$1	201	122	146	21.1346
:dddd[attttttttttta]dddd	chr1:151146836-151147037(-)$1	201	29	53	21.6788
ccc[ddddtttttttttttdddd]	chr17:17124691-17124892(-)$1	201	62	86	21.9891
gggggggtttttttttttgggggg	chr14:70490016-70490217(+)$1	201	79	103	21.7377
ffffffyyyyyyyyyyyyyyyyff	chr22:21153375-21153576(-)$1	201	27	51	20.1203
[bb[bbvvvvvvvvvvvvvbb]bb	chr1:224621367-224621568(-)$1	201	15	39	21.7544
!!ddddvvvvvvvvvvvvvdddd2	chr2:216211556-216211757(+)$1	201	10	34	23.8510
gggggggtttttttttttgggggg	chr10:98292774-98292975(-)$1	201	24	48	21.7377
""ddddvvvvvvvvvvvvvdddd]	chr22:38273889-38274090(+)$1	201	78	102	23.7909
bbb[bbuuuuuuuuuuuubb]bb]	chr1:109466594-109466795(+)$1	201	145	169	20.7696
ggggggvvvvvvvvvvvvvggggg	chr11:9199770-9199971(-)$1	201	7	31	23.6112
ggggggvvvvvvvvvvvvvggggg	chr5:137525252-137525453(-)$1	201	7	31	23.6112
d[ddddvvvvvvvvvvvvvdddd2	chr19:2215438-2215639(+)$1	201	104	128	23.5616
eeeeewwwwwwwwwwwwwweeeee	chr17:41228473-41228674(-)$1	201	133	157	21.8338
=bb[bbvvvvvvvvvvvvvbbbb]	chr13:33222838-33223039(+)$1	201	72	96	22.0025
!!dddduuuuuuuuuuuudddd22	chr19:17322616-17322817(+)$1	201	55	79	22.4876
ffffffyyyyyyyyyyyyyyyyff	chr4:144469001-144469202(+)$1	201	121	145	20.1203
eeeee[attttttttttta]eeee	chr20:47589665-47589866(+)$1	201	111	135	22.4790
##ddddvvvvvvvvvvvvvdddd2	chr18:47918460-47918661(+)$1	201	73	97	23.6150
::ddddvvvvvvvvvvvvvdddd:	chr9:86586807-86587008(-)$1	201	80	104	20.9867
ddd[cccuuuuuuuuuuuucccdd	chr1:109472385-109472586(+)$1	201	76	100	23.2963
[eeeeevvvvvvvvvvvvveeeee	chr10:35320391-35320592(-)$1	201	21	45	23.4977
dddd[ccctttttttttttcccdd	chr11:63756002-63756203(+)$1	201	68	92	21.9148
ffffffwwwwwwwwwwwwwwffff	chr10:22209653-22209854(-)$1	201	134	158	21.1066
eeeeeyyyyyyyyyyyyyyyyeee	chr3:9517402-9517603(+)$1	201	102	126	20.8821
E:eeeeeuuuuuuuuuuuueeeee	chr2:45800337-45800538(-)$1	201	4	28	21.1580
hhhhhhvvvvvvvvvvvvvhhhhh	chr9:6013986-6014187(-)$1	201	47	71	22.0022
b[eeeeettttttttttteeeee]	chr13:21370264-21370465(-)$1	201	167	191	21.8771

#otherMatches

#Seq PSSM
AGCAGUAGAUCAAGUAAUUAAAGC	chr11:17158010-17158211(-)$1	201	50	74	21.0475
GCAUCAGCCCAUAUACAUUCUGCA	chr4:156714981-156715182(+)$1	201	150	174	23.3121
UCCUUCACAACAGAAACCAGGAAU	chr7:121985604-121985805(-)$1	201	57	81	22.6452
UCUGUGCAAAAGAAAAAAGUAAAA	chr5:140913881-140914082(-)$1	201	117	141	22.0146
UUCUUGGAAACAGCAAAAAAAGAU	chr10:64974241-64974442(-)$1	201	172	196	20.7413
ACCAUUUCUACUAUCUACAGGUAA	chr2:98427527-98427728(-)$1	201	13	37	20.4732
CAAUCGUAUUGAUUUCCUUUGAAU	chr10:94267802-94268003(-)$1	201	10	34	23.2088
CUCCUGGAAACACAAGAACAAGAG	chr3:44882557-44882758(+)$1	201	50	74	21.7780
CAGGGCAUUUUAACAUUCAGCCCA	chr1:202933663-202933864(-)$1	201	38	62	23.8533
CGGUUCUGCAGGCACCAUGAGCCA	chr11:62648414-62648615(+)$1	201	65	89	22.5707
UUAACAUUUUAUAAAUUCCUGUUA	chr6:56482079-56482280(-)$1	201	37	61	23.5345
UUGAGACUUUGGAUGGAUUGGCAC	chr5:140059295-140059496(-)$1	201	146	170	20.6269
CAUACAUUCCAUGUUUCCUUGUAG	chr7:44620696-44620897(-)$1	201	35	59	21.9721
UGAGGAGAAAUAUGAUGAAUCCGU	chr12:939177-939378(+)$1	201	22	46	23.7128
GGACGUCCAGUUUGAUGAGGGACU	chr12:57038920-57039121(-)$1	201	69	93	21.6004
GCACAUCUUUAACACCGCCAGGUA	chr19:36550785-36550986(+)$1	201	126	150	21.6307
GAGAGAUGCCGAAAAUUUGAUUGA	chr8:25280686-25280887(-)$1	201	145	169	23.1021
CAUUACAAAUAAAAGAAGAAAAUG	chr18:20573412-20573613(+)$1	201	98	122	20.5659
UCCAAGCAUUAAGAAGACAGAAUG	chr6:44360368-44360569(+)$1	201	50	74	22.9758
UUAAUAUCUAGCCUAAAAAAUUAA	chr10:114192052-114192253(-)$1	201	162	186	22.2025
CAAGACUCUGAAGAUAAGCGAGUU	chr1:110882431-110882632(+)$1	201	102	126	21.7531
AACUGGAUAUAAAUGAGCUACCAA	chr18:9563349-9563550(-)$1	201	98	122	22.5317
UUAGUUCUUUUUGUUUUUUGAAUU	chr14:64537279-64537480(+)$1	201	57	81	21.2243
GUUCUGAUACCGUGUCUAUUCAGG	chr17:65907722-65907923(+)$1	201	152	176	23.0740
ACUUUGUUUUUAUAUCCUUGCAGA	chr21:40578069-40578270(-)$1	201	47	71	21.2248
CCUUGUCCUUUAAGAUACUGGAUG	chr7:135304078-135304279(+)$1	201	78	102	20.8158
GUUUCUGGAAAACUUACUGGAGAA	chr3:132179014-132179215(+)$1	201	147	171	20.9074
UUUUUAUAAUAGAUGACCGUGGAA	chr17:34937727-34937928(+)$1	201	34	58	21.7377
CAUCAUUAUGAAAAAAGACUCUGA	chr1:154562213-154562414(-)$1	201	126	150	21.0449
GACAUCGAAUAACACAGCCGAUGG	chr6:133789714-133789915(+)$1	201	66	90	21.8771
UUAUUGAUUUUUUUUCUUUUCAUU	chr14:57749737-57749938(+)$1	201	15	39	22.3417
GCGGUGCCCCUAUACAAAACACCA	chr7:27203249-27203450(-)$1	201	36	60	20.9867
AGCCAAACCACAAAACAGAUUGGC	chr1:180067976-180068177(+)$1	201	67	91	22.8061
CUGCCGACUUCAUUGACCAGGCUU	chr17:41852045-41852246(-)$1	201	128	152	22.2972
AAAACUUUUAUUUGGGGGUAGGUU	chr15:89803925-89804126(+)$1	201	164	188	23.1923
AGCUGAAUCCAUUCUAUUACUCAG	chr12:101759176-101759377(+)$1	201	155	179	21.1066
GGAAGCUUGCUCACUACCUGCUCC	chr15:28459812-28460013(-)$1	201	167	191	22.5524
AUAUGUCAAGAAAUUAGGGUAAGC	chr22:41565490-41565691(+)$1	201	112	136	21.1703
UGAGCUCUCCCUCUUCCACCAGCU	chr19:4409629-4409830(+)$1	201	26	50	21.1066
UGUGCCGAUUUAUCUUCCAGGUGC	chr22:31884603-31884804(-)$1	201	53	77	22.0022
GCACGGCCUACUACGCGCUGGUGG	chr17:80041810-80042011(-)$1	201	20	44	21.9097
AGCAGCAGACCUAUGACUAUGCCA	chr17:40061701-40061902(-)$1	201	62	86	20.6004
GAAAUGAGGAGAAAGAAUAUCAUU	chr6:161527523-161527724(+)$1	201	96	120	22.9653
UGUGCCUUUGGAAAUUGAUGGCUC	chr10:99139324-99139525(-)$1	201	114	138	22.9915
GACACAGACCCUUUCCUCUUCUAC	chr11:65484092-65484293(+)$1	201	108	132	21.8985
AAGGUAAAGUGUUCUGUGGUAGUA	chr5:137654831-137655032(-)$1	201	122	146	21.1346
GCUGGACUAAGACAACGUGACCAG	chr1:151146836-151147037(-)$1	201	29	53	21.6788
CCGGGGCCUUGGCCCGGAUGGCCG	chr17:17124691-17124892(-)$1	201	62	86	21.9891
GUGACCUGAACAAAGACAAGGUCA	chr14:70490016-70490217(+)$1	201	79	103	21.7377
UCCCGACCACACAAUCCGAGCCUU	chr22:21153375-21153576(-)$1	201	27	51	20.1203
cgccgcauccucagccaccgucgc	chr1:224621367-224621568(-)$1	201	15	39	21.7544
ACCAUCCACAAGUGCUUUCGAUGA	chr2:216211556-216211757(+)$1	201	10	34	23.8510
ACAGGUGGCCGUUUGUUGCAUCUG	chr10:98292774-98292975(-)$1	201	24	48	21.7377
CCAGCUUUCAACCAUCCGCAGCUU	chr22:38273889-38274090(+)$1	201	78	102	23.7909
UCUAACACAAAACAGCCAGUCGGU	chr1:109466594-109466795(+)$1	201	145	169	20.7696
UUGACAUUACCCUUUUCCCUGUCA	chr11:9199770-9199971(-)$1	201	7	31	23.6112
UCUAGGAAAUAGUAGAACACUUGG	chr5:137525252-137525453(-)$1	201	7	31	23.6112
GCUGGACCUCUGCUGCCUUUUCAA	chr19:2215438-2215639(+)$1	201	104	128	23.5616
GUUCUACCAGUAAAAAUAAAGAAC	chr17:41228473-41228674(-)$1	201	133	157	21.8338
UGGCUCAUUCAAAGACUAGGACCA	chr13:33222838-33223039(+)$1	201	72	96	22.0025
CUGCAGUAACCCUGCCAUCUGUCU	chr19:17322616-17322817(+)$1	201	55	79	22.4876
UAUGGUACUAACAAAGGAAAAAAC	chr4:144469001-144469202(+)$1	201	121	145	20.1203
GCUCAGGGAAGAAGUGGACAUGAG	chr20:47589665-47589866(+)$1	201	111	135	22.4790
CACGUGUUACUGAAUAUUUUACGA	chr18:47918460-47918661(+)$1	201	73	97	23.6150
UCCAUCUAGAAGAGAUUAUGAUGA	chr9:86586807-86587008(-)$1	201	80	104	20.9867
GAGAUCAAAACAGAGACACUGACU	chr1:109472385-109472586(+)$1	201	76	100	23.2963
AUUUAUUAUCAAUUUCUACAUGAG	chr10:35320391-35320592(-)$1	201	21	45	23.4977
GGCAUGGGUCACUCCAUCUCCCUG	chr11:63756002-63756203(+)$1	201	68	92	21.9148
GUUAGUAAUAAAUCAAAUGAACUA	chr10:22209653-22209854(-)$1	201	134	158	21.1066
AGACUCGCCAACCUCAGAUUCAGU	chr3:9517402-9517603(+)$1	201	102	126	20.8821
UAAAGCACAAAUUAAUAACUGCUU	chr2:45800337-45800538(-)$1	201	4	28	21.1580
GUGGAUAGUAUGGUGAAAAAUCUA	chr9:6013986-6014187(-)$1	201	47	71	22.0022
AAGAGCAAUACCAAGACCUGCUUC	chr13:21370264-21370465(-)$1	201	167	191	21.8771

#DB
.(((((................))	chr11:17158010-17158211(-)$1	1	50	74	21.0475
((..(((............)))..	chr4:156714981-156715182(+)$1	1	150	174	23.3121
((((((..............))).	chr7:121985604-121985805(-)$1	1	57	81	22.6452
(((.(((...........)))..)	chr5:140913881-140914082(-)$1	1	117	141	22.0146
.((((..............)))))	chr10:64974241-64974442(-)$1	1	172	196	20.7413
(((................)))).	chr2:98427527-98427728(-)$1	1	13	37	20.4732
((.(((.............))).)	chr10:94267802-94268003(-)$1	1	10	34	23.2088
(((.((............)).)))	chr3:44882557-44882758(+)$1	1	50	74	21.7780
..((((.............)))).	chr1:202933663-202933864(-)$1	1	38	62	23.8533
.(((((............))))).	chr11:62648414-62648615(+)$1	1	65	89	22.5707
.(((((.............)))))	chr6:56482079-56482280(-)$1	1	37	61	23.5345
.((((.((...........))..)	chr5:140059295-140059496(-)$1	1	146	170	20.6269
).((((.............))))(	chr7:44620696-44620897(-)$1	1	35	59	21.9721
...(((.............)))..	chr12:939177-939378(+)$1	1	22	46	23.7128
((..((((...........)))).	chr12:57038920-57039121(-)$1	1	69	93	21.6004
((..((((...........)))).	chr19:36550785-36550986(+)$1	1	126	150	21.6307
(((.(((............)))..	chr8:25280686-25280887(-)$1	1	145	169	23.1021
((((................))))	chr18:20573412-20573613(+)$1	1	98	122	20.5659
.(((..(............)..))	chr6:44360368-44360569(+)$1	1	50	74	22.9758
(((((..............)))))	chr10:114192052-114192253(-)$1	1	162	186	22.2025
(..(((((...........)))))	chr1:110882431-110882632(+)$1	1	102	126	21.7531
(..(((..............))).	chr18:9563349-9563550(-)$1	1	98	122	22.5317
(((((((............)))))	chr14:64537279-64537480(+)$1	1	57	81	21.2243
(((((((............)))))	chr17:65907722-65907923(+)$1	1	152	176	23.0740
..(((((............)))))	chr21:40578069-40578270(-)$1	1	47	71	21.2248
..((((((...........)))))	chr7:135304078-135304279(+)$1	1	78	102	20.8158
((((((..............))))	chr3:132179014-132179215(+)$1	1	147	171	20.9074
(((((((...........))))))	chr17:34937727-34937928(+)$1	1	34	58	21.7377
(.(((................)))	chr1:154562213-154562414(-)$1	1	126	150	21.0449
(.(((((...........))))).	chr6:133789714-133789915(+)$1	1	66	90	21.8771
....(((............)))..	chr14:57749737-57749938(+)$1	1	15	39	22.3417
..((((.............)))).	chr7:27203249-27203450(-)$1	1	36	60	20.9867
.(((((.............)))))	chr1:180067976-180068177(+)$1	1	67	91	22.8061
(((((..............)))..	chr17:41852045-41852246(-)$1	1	128	152	22.2972
(((((((............)))))	chr15:89803925-89804126(+)$1	1	164	188	23.1923
((((((..............))))	chr12:101759176-101759377(+)$1	1	155	179	21.1066
(((.((.............)))))	chr15:28459812-28460013(-)$1	1	167	191	22.5524
((((((................))	chr22:41565490-41565691(+)$1	1	112	136	21.1703
((((((..............))))	chr19:4409629-4409830(+)$1	1	26	50	21.1066
((((((.............)))))	chr22:31884603-31884804(-)$1	1	53	77	22.0022
((((.(((...........))).)	chr17:80041810-80042011(-)$1	1	20	44	21.9097
))).(((............)))..	chr17:40061701-40061902(-)$1	1	62	86	20.6004
))(((((............)))))	chr6:161527523-161527724(+)$1	1	96	120	22.9653
.(.(((.............))).)	chr10:99139324-99139525(-)$1	1	114	138	22.9915
(((..(((...........)))..	chr11:65484092-65484293(+)$1	1	108	132	21.8985
((((((................))	chr5:137654831-137655032(-)$1	1	122	146	21.1346
.((((.(...........).))))	chr1:151146836-151147037(-)$1	1	29	53	21.6788
(((.((((...........)))).	chr17:17124691-17124892(-)$1	1	62	86	21.9891
(((((((...........))))))	chr14:70490016-70490217(+)$1	1	79	103	21.7377
((((((................))	chr22:21153375-21153576(-)$1	1	27	51	20.1203
.((.((.............)).))	chr1:224621367-224621568(-)$1	1	15	39	21.7544
..((((.............)))).	chr2:216211556-216211757(+)$1	1	10	34	23.8510
(((((((...........))))))	chr10:98292774-98292975(-)$1	1	24	48	21.7377
..((((.............)))).	chr22:38273889-38274090(+)$1	1	78	102	23.7909
(((.((............)).)).	chr1:109466594-109466795(+)$1	1	145	169	20.7696
((((((.............)))))	chr11:9199770-9199971(-)$1	1	7	31	23.6112
((((((.............)))))	chr5:137525252-137525453(-)$1	1	7	31	23.6112
(.((((.............)))).	chr19:2215438-2215639(+)$1	1	104	128	23.5616
(((((..............)))))	chr17:41228473-41228674(-)$1	1	133	157	21.8338
(((.((.............)))).	chr13:33222838-33223039(+)$1	1	72	96	22.0025
..((((............))))..	chr19:17322616-17322817(+)$1	1	55	79	22.4876
((((((................))	chr4:144469001-144469202(+)$1	1	121	145	20.1203
(((((.(...........).))))	chr20:47589665-47589866(+)$1	1	111	135	22.4790
..((((.............)))).	chr18:47918460-47918661(+)$1	1	73	97	23.6150
..((((.............)))).	chr9:86586807-86587008(-)$1	1	80	104	20.9867
(((.(((............)))))	chr1:109472385-109472586(+)$1	1	76	100	23.2963
.(((((.............)))))	chr10:35320391-35320592(-)$1	1	21	45	23.4977
((((.(((...........)))))	chr11:63756002-63756203(+)$1	1	68	92	21.9148
((((((..............))))	chr10:22209653-22209854(-)$1	1	134	158	21.1066
(((((................)))	chr3:9517402-9517603(+)$1	1	102	126	20.8821
(.(((((............)))))	chr2:45800337-45800538(-)$1	1	4	28	21.1580
((((((.............)))))	chr9:6013986-6014187(-)$1	1	47	71	22.0022
(.(((((...........))))).	chr13:21370264-21370465(-)$1	1	167	191	21.8771

#PSSM
d : 0.12	! : 0.09	f : 0.09	g : 0.09	b : 0.08	c : 0.08	: : 0.08	h : 0.06	[ : 0.05	e : 0.05	# : 0.04	i : 0.04	= : 0.02	a : 0.01	( : 0.01	" : 0.01	E : 0.01	
d : 0.13	e : 0.12	f : 0.09	g : 0.09	c : 0.08	! : 0.08	b : 0.06	: : 0.06	h : 0.06	[ : 0.05	# : 0.04	i : 0.04	= : 0.01	a : 0.01	" : 0.01	
d : 0.24	e : 0.17	c : 0.10	f : 0.09	g : 0.08	! : 0.06	h : 0.06	i : 0.04	b : 0.04	[ : 0.02	# : 0.02	= : 0.01	
d : 0.20	e : 0.19	[ : 0.12	c : 0.10	g : 0.08	f : 0.08	! : 0.05	h : 0.05	i : 0.04	y : 0.01	# : 0.01	= : 0.01	: : 0.01	
d : 0.20	e : 0.19	c : 0.17	g : 0.08	f : 0.08	b : 0.06	h : 0.05	i : 0.04	y : 0.02	! : 0.02	[ : 0.02	= : 0.01	
c : 0.19	d : 0.16	e : 0.15	g : 0.08	f : 0.08	b : 0.06	w : 0.05	y : 0.05	h : 0.05	[ : 0.04	i : 0.02	! : 0.01	= : 0.01	
v : 0.28	w : 0.13	y : 0.12	c : 0.12	e : 0.08	u : 0.05	g : 0.05	d : 0.04	a : 0.04	b : 0.01	h : 0.01	f : 0.01	i : 0.01	
v : 0.28	u : 0.21	w : 0.13	y : 0.12	t : 0.10	d : 0.04	c : 0.04	b : 0.01	e : 0.01	f : 0.01	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	t : 0.23	u : 0.21	w : 0.13	y : 0.12	
v : 0.28	u : 0.16	w : 0.13	y : 0.12	t : 0.12	e : 0.04	g : 0.04	b : 0.02	a : 0.02	c : 0.01	d : 0.01	
d : 0.19	c : 0.17	e : 0.15	y : 0.10	w : 0.08	b : 0.08	g : 0.08	h : 0.04	i : 0.02	] : 0.02	a : 0.01	f : 0.01	
d : 0.21	c : 0.20	e : 0.16	y : 0.09	g : 0.08	b : 0.05	h : 0.05	f : 0.05	] : 0.02	i : 0.02	2 : 0.01	
d : 0.23	c : 0.21	e : 0.17	g : 0.08	y : 0.06	h : 0.05	f : 0.05	2 : 0.04	i : 0.02	b : 0.02	] : 0.01	
d : 0.24	e : 0.19	g : 0.08	f : 0.08	c : 0.06	2 : 0.06	h : 0.05	] : 0.04	i : 0.04	b : 0.04	4 : 0.02	6 : 0.01	3 : 0.01	= : 0.01	: : 0.01	
e : 0.15	] : 0.12	2 : 0.12	d : 0.09	g : 0.08	f : 0.08	c : 0.05	h : 0.05	4 : 0.04	i : 0.04	: : 0.04	b : 0.02	F : 0.01	H : 0.01	6 : 0.01	3 : 0.01	= : 0.01	a : 0.01	

#score	1608.298224915517
#seq	73
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_CDS_m3_run2.txt

#BEAR
ffffffnnnnnfffff	chr3:56673965-56674194(-)$1	229	88	104	10.6825
ffffffnnnnnfffff	chr17:27614235-27614466(-)$1	231	149	165	10.6825
fffffflllfffffff	chr7:97821931-97822165(+)$1	234	172	188	11.0894
ffffffmmmmffffff	chr19:37239037-37239275(-)$1	238	94	110	12.2585
ffffffmmmmffffff	chrX:84526258-84526497(+)$1	239	141	157	12.2585
ffffffmmmmffffff	chr1:23637307-23637543(-)$1	236	168	184	12.2585
fffffflllffffffg	chr17:76219646-76219877(+)$1	231	172	188	10.6127
ffffffmmmmffffff	chr5:36183943-36184196(+)$1	253	174	190	12.2585
ffffffmmmmffffff	chr2:48027236-48027467(+)$1	231	206	222	12.2585
[fffffflllffffff	chr19:10795586-10795818(+)$1	232	179	195	10.9066
ffffffooooooffff	chr13:77834461-77834691(-)$1	230	149	165	10.9555
ffffffmmmmffffff	chr1:243800826-243801068(-)$1	242	161	177	12.2585
ffffffmmmmffffff	chrX:135954347-135954603(-)$1	256	7	23	12.2585
ffffffmmmmffffff	chr17:17712607-17712835(+)$1	228	37	53	12.2585
ffffffmmmmffffff	chr5:61686703-61686936(+)$1	233	202	218	12.2585
ffffffmmmmffffff	chr1:16258270-16258505(+)$1	235	32	48	12.2585
ffffffnnnnnfffff	chr1:40035452-40035691(-)$1	239	36	52	10.6825
ffffffooooooffff	chr8:126034019-126034264(+)$1	245	197	213	10.9555
ffffffnnnnnfffff	chr5:126889376-126889605(+)$1	229	154	170	10.6825
ffffffooooooffff	chr2:70315790-70316023(+)$1	233	72	88	10.9555
ffffffnnnnnfffff	chr8:101718870-101719133(-)$1	263	42	58	10.6825
ffffffmmmmffffff	chr1:62905381-62905641(+)$1	260	221	237	12.2585
ffffffmmmmffffff	chr7:44869631-44869886(-)$1	255	171	187	12.2585
!fffffflllffffff	chr6:153292262-153292515(-)$1	253	202	218	10.7081
dfffffflllffffff	chr17:41151984-41152219(+)$1	235	80	96	10.5156
ffffffmmmmffffff	chr3:47162894-47163125(-)$1	231	86	102	12.2585
ffffffmmmmffffff	chr1:115263202-115263430(-)$1	228	38	54	12.2585
fff[bbmmmmbb]fff	chr7:135612194-135612417(-)$1	223	73	89	8.6614
ffffffmmmmffffff	chr17:44159743-44159972(-)$1	229	79	95	12.2585
ffffffmmmmffffff	chr10:129902295-129902522(-)$1	227	140	156	12.2585
ffffffooooooffff	chr2:176042863-176043127(-)$1	264	148	164	10.9555
ffffffooooooffff	chr1:243827980-243828220(-)$1	240	73	89	10.9555
[fffffflllffffff	chr6:26104205-26104434(+)$1	229	149	165	10.9066
ffffffmmmmffffff	chr12:98927741-98927961(+)$1	220	57	73	12.2585
ffffffooooooffff	chr1:16262184-16262406(+)$1	222	195	211	10.9555
ffffffooooooffff	chr13:45007958-45008207(-)$1	249	160	176	10.9555
ffffffmmmmffffff	chr22:50637408-50637656(+)$1	248	92	108	12.2585
fffffflllffffffc	chr15:32929673-32929902(+)$1	229	78	94	10.5230
ffffffmmmmffffff	chr17:37006535-37006746(-)$1	211	155	171	12.2585
!fffffflllffffff	chr12:53776648-53776893(+)$1	245	102	118	10.7081
ffffffmmmmffffff	chr1:16256114-16256333(+)$1	219	73	89	12.2585
[fffffflllffffff	chr10:97816618-97816841(+)$1	223	113	129	10.9066
ffffffmmmmffffff	chrX:71493679-71493922(-)$1	243	206	222	12.2585
fffff[allla]ffff	chr19:40478309-40478534(+)$1	225	152	168	10.5019
ffffffnnnnnfffff	chr17:76220614-76220825(+)$1	211	11	27	10.6825
ffffffmmmmffffff	chr12:110787996-110788230(+)$1	234	25	41	12.2585
ffffffmmmmffffff	chrX:107976387-107976619(-)$1	232	94	110	12.2585
ffffffmmmmffffff	chr3:48594089-48594309(+)$1	220	27	43	12.2585
ff[cccmmmmccc]ff	chr7:6502517-6502785(-)$1	268	221	237	8.2168
ffffffmmmmffffff	chr12:46756755-46757008(-)$1	253	205	221	12.2585
ffffffnnnnnfffff	chr13:25670763-25671001(+)$1	238	95	111	10.6825
ffffffooooooffff	chr15:45713222-45713461(+)$1	239	2	18	10.9555
ffffffooooooffff	chr19:42364744-42364983(+)$1	239	48	64	10.9555
ffffffmmmmffffff	chr20:17930869-17931115(-)$1	246	0	16	12.2585
fff[bbmmmmbb]fff	chr12:111157843-111158123(-)$1	280	53	69	8.6614

#otherMatches

#Seq PSSM
GUGUUCCCAUUGAACA	chr3:56673965-56674194(-)$1	229	88	104	10.6825
AGGGUUGUGAAAACCU	chr17:27614235-27614466(-)$1	231	149	165	10.6825
AUAAGCCAGGCUUGUC	chr7:97821931-97822165(+)$1	234	172	188	11.0894
GGUGAGAAACCUUAUC	chr19:37239037-37239275(-)$1	238	94	110	12.2585
CCUCACAAAUGUGAGG	chrX:84526258-84526497(+)$1	239	141	157	12.2585
GGCUAUGAUGAUGGCU	chr1:23637307-23637543(-)$1	236	168	184	12.2585
GCCUGUGCAGCGGGUG	chr17:76219646-76219877(+)$1	231	172	188	10.6127
CAUUUUUAUAAAAAUG	chr5:36183943-36184196(+)$1	253	174	190	12.2585
UAAAGCAAUGGCUUUG	chr2:48027236-48027467(+)$1	231	206	222	12.2585
GUGGCUGGUUUAGCUA	chr19:10795586-10795818(+)$1	232	179	195	10.9066
ACUUUUAUGCAAAGAA	chr13:77834461-77834691(-)$1	230	149	165	10.9555
UGAUUUAUUAAAGUUG	chr1:243800826-243801068(-)$1	242	161	177	12.2585
UUUUCUUUCUGGAAAA	chrX:135954347-135954603(-)$1	256	7	23	12.2585
CCCCACAGCUGUGGGG	chr17:17712607-17712835(+)$1	228	37	53	12.2585
UUAAUAUAUCUGUUAA	chr5:61686703-61686936(+)$1	233	202	218	12.2585
UUCUCCUCGGGGAGAA	chr1:16258270-16258505(+)$1	235	32	48	12.2585
UCUCGCAAAGAGCGGG	chr1:40035452-40035691(-)$1	239	36	52	10.6825
AUUUGGAACUUACCAA	chr8:126034019-126034264(+)$1	245	197	213	10.9555
UGGCUUGGUUGAAGCU	chr5:126889376-126889605(+)$1	229	154	170	10.6825
ACUGGCUCUGCUGCCA	chr2:70315790-70316023(+)$1	233	72	88	10.9555
AAAUUGAUCACCAAUU	chr8:101718870-101719133(-)$1	263	42	58	10.6825
GACUUUCCUUAAAGUU	chr1:62905381-62905641(+)$1	260	221	237	12.2585
CGGCAAGGUUUUGCUG	chr7:44869631-44869886(-)$1	255	171	187	12.2585
UUUACGAAGAUUGUGA	chr6:153292262-153292515(-)$1	253	202	218	10.7081
CAAAGAUAAAAUCUUU	chr17:41151984-41152219(+)$1	235	80	96	10.5156
AAUUGUGUCUACAGUU	chr3:47162894-47163125(-)$1	231	86	102	12.2585
CAGCAGAGGACUGUUG	chr1:115263202-115263430(-)$1	228	38	54	12.2585
UAAUGUUCAUAUUUUG	chr7:135612194-135612417(-)$1	223	73	89	8.6614
GGGGAGGUACCUCCCC	chr17:44159743-44159972(-)$1	229	79	95	12.2585
GUCAAUGACUAUUGAC	chr10:129902295-129902522(-)$1	227	140	156	12.2585
UACGGAUGUAAUUCUG	chr2:176042863-176043127(-)$1	264	148	164	10.9555
ACAUUUAUAAUCAGAU	chr1:243827980-243828220(-)$1	240	73	89	10.9555
GGUUUUCUUAGAGAAC	chr6:26104205-26104434(+)$1	229	149	165	10.9066
UGUAGCUAAGGCUAUG	chr12:98927741-98927961(+)$1	220	57	73	12.2585
GGUGGUGAAGGUGCCA	chr1:16262184-16262406(+)$1	222	195	211	10.9555
UGAAAUUUAGUUGUUU	chr13:45007958-45008207(-)$1	249	160	176	10.9555
UUUUAAUGUCUUAAAA	chr22:50637408-50637656(+)$1	248	92	108	12.2585
AUCUUUCUUAAAGAUG	chr15:32929673-32929902(+)$1	229	78	94	10.5230
CCUUAGGUCUCUGAGG	chr17:37006535-37006746(-)$1	211	155	171	12.2585
CUUUACUACCAGUGGA	chr12:53776648-53776893(+)$1	245	102	118	10.7081
UUCAGUAAAUACUGAA	chr1:16256114-16256333(+)$1	219	73	89	12.2585
UUACUUCCUGGAAGUA	chr10:97816618-97816841(+)$1	223	113	129	10.9066
UGAAUGAUACCAUUCA	chrX:71493679-71493922(-)$1	243	206	222	12.2585
GGUGUGCUAAGGACAC	chr19:40478309-40478534(+)$1	225	152	168	10.5019
CAGCUCCCGCAGGGCU	chr17:76220614-76220825(+)$1	211	11	27	10.6825
AUCUAUUUAAAUAGGU	chr12:110787996-110788230(+)$1	234	25	41	12.2585
UUGAAGUAAUUUUCAA	chrX:107976387-107976619(-)$1	232	94	110	12.2585
CGCGCUGGCAAGCGUG	chr3:48594089-48594309(+)$1	220	27	43	12.2585
UACAAAGAUUUUUUUA	chr7:6502517-6502785(-)$1	268	221	237	8.2168
GUAAGUAAUCACUUGC	chr12:46756755-46757008(-)$1	253	205	221	12.2585
UCUCGUAAAGAACGAG	chr13:25670763-25671001(+)$1	238	95	111	10.6825
GCUUGUCUCUUAAUAG	chr15:45713222-45713461(+)$1	239	2	18	10.9555
UGGCAGUCGUCUCUGC	chr19:42364744-42364983(+)$1	239	48	64	10.9555
UAUAUUGAUAAAUGUA	chr20:17930869-17931115(-)$1	246	0	16	12.2585
AAAGGUAAUAACAUUU	chr12:111157843-111158123(-)$1	280	53	69	8.6614

#DB
((((((.....)))))	chr3:56673965-56674194(-)$1	1	88	104	10.6825
((((((.....)))))	chr17:27614235-27614466(-)$1	1	149	165	10.6825
((((((...))))))(	chr7:97821931-97822165(+)$1	1	172	188	11.0894
((((((....))))))	chr19:37239037-37239275(-)$1	1	94	110	12.2585
((((((....))))))	chrX:84526258-84526497(+)$1	1	141	157	12.2585
((((((....))))))	chr1:23637307-23637543(-)$1	1	168	184	12.2585
((((((...))))))(	chr17:76219646-76219877(+)$1	1	172	188	10.6127
((((((....))))))	chr5:36183943-36184196(+)$1	1	174	190	12.2585
((((((....))))))	chr2:48027236-48027467(+)$1	1	206	222	12.2585
.((((((...))))))	chr19:10795586-10795818(+)$1	1	179	195	10.9066
((((((......))))	chr13:77834461-77834691(-)$1	1	149	165	10.9555
((((((....))))))	chr1:243800826-243801068(-)$1	1	161	177	12.2585
((((((....))))))	chrX:135954347-135954603(-)$1	1	7	23	12.2585
((((((....))))))	chr17:17712607-17712835(+)$1	1	37	53	12.2585
((((((....))))))	chr5:61686703-61686936(+)$1	1	202	218	12.2585
((((((....))))))	chr1:16258270-16258505(+)$1	1	32	48	12.2585
((((((.....)))))	chr1:40035452-40035691(-)$1	1	36	52	10.6825
((((((......))))	chr8:126034019-126034264(+)$1	1	197	213	10.9555
((((((.....)))))	chr5:126889376-126889605(+)$1	1	154	170	10.6825
((((((......))))	chr2:70315790-70316023(+)$1	1	72	88	10.9555
((((((.....)))))	chr8:101718870-101719133(-)$1	1	42	58	10.6825
((((((....))))))	chr1:62905381-62905641(+)$1	1	221	237	12.2585
((((((....))))))	chr7:44869631-44869886(-)$1	1	171	187	12.2585
.((((((...))))))	chr6:153292262-153292515(-)$1	1	202	218	10.7081
)((((((...))))))	chr17:41151984-41152219(+)$1	1	80	96	10.5156
((((((....))))))	chr3:47162894-47163125(-)$1	1	86	102	12.2585
((((((....))))))	chr1:115263202-115263430(-)$1	1	38	54	12.2585
(((.((....)).)))	chr7:135612194-135612417(-)$1	1	73	89	8.6614
((((((....))))))	chr17:44159743-44159972(-)$1	1	79	95	12.2585
((((((....))))))	chr10:129902295-129902522(-)$1	1	140	156	12.2585
((((((......))))	chr2:176042863-176043127(-)$1	1	148	164	10.9555
((((((......))))	chr1:243827980-243828220(-)$1	1	73	89	10.9555
.((((((...))))))	chr6:26104205-26104434(+)$1	1	149	165	10.9066
((((((....))))))	chr12:98927741-98927961(+)$1	1	57	73	12.2585
((((((......))))	chr1:16262184-16262406(+)$1	1	195	211	10.9555
((((((......))))	chr13:45007958-45008207(-)$1	1	160	176	10.9555
((((((....))))))	chr22:50637408-50637656(+)$1	1	92	108	12.2585
((((((...))))))(	chr15:32929673-32929902(+)$1	1	78	94	10.5230
((((((....))))))	chr17:37006535-37006746(-)$1	1	155	171	12.2585
.((((((...))))))	chr12:53776648-53776893(+)$1	1	102	118	10.7081
((((((....))))))	chr1:16256114-16256333(+)$1	1	73	89	12.2585
.((((((...))))))	chr10:97816618-97816841(+)$1	1	113	129	10.9066
((((((....))))))	chrX:71493679-71493922(-)$1	1	206	222	12.2585
(((((.(...).))))	chr19:40478309-40478534(+)$1	1	152	168	10.5019
((((((.....)))))	chr17:76220614-76220825(+)$1	1	11	27	10.6825
((((((....))))))	chr12:110787996-110788230(+)$1	1	25	41	12.2585
((((((....))))))	chrX:107976387-107976619(-)$1	1	94	110	12.2585
((((((....))))))	chr3:48594089-48594309(+)$1	1	27	43	12.2585
((.(((....))).))	chr7:6502517-6502785(-)$1	1	221	237	8.2168
((((((....))))))	chr12:46756755-46757008(-)$1	1	205	221	12.2585
((((((.....)))))	chr13:25670763-25671001(+)$1	1	95	111	10.6825
((((((......))))	chr15:45713222-45713461(+)$1	1	2	18	10.9555
((((((......))))	chr19:42364744-42364983(+)$1	1	48	64	10.9555
((((((....))))))	chr20:17930869-17931115(-)$1	1	0	16	12.2585
(((.((....)).)))	chr12:111157843-111158123(-)$1	1	53	69	8.6614

#PSSM
f : 0.89	[ : 0.05	! : 0.03	d : 0.01	
f : 1.00	
f : 0.98	[ : 0.01	
f : 0.94	[ : 0.03	c : 0.01	
f : 0.94	b : 0.03	c : 0.01	
f : 0.92	b : 0.03	[ : 0.01	c : 0.01	
m : 0.52	o : 0.16	n : 0.12	f : 0.10	l : 0.05	a : 0.01	
m : 0.52	l : 0.18	o : 0.16	n : 0.12	
m : 0.52	l : 0.18	o : 0.16	n : 0.12	
m : 0.52	o : 0.16	n : 0.12	l : 0.12	f : 0.05	
f : 0.63	o : 0.16	n : 0.12	b : 0.03	a : 0.01	c : 0.01	
f : 0.76	o : 0.16	b : 0.03	] : 0.01	c : 0.01	
f : 0.94	] : 0.03	c : 0.01	
f : 0.98	] : 0.01	
f : 1.00	
f : 0.96	g : 0.01	c : 0.01	

#score	625.019286250811
#seq	55
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_UTR_m2_run1.txt

#BEAR
c[ggggggguuuuuuuuuuuuggggggg2	chr5:139781361-139781584(+)$1	223	51	80	25.7791
eee[fffffftttttttttttffffff]e	chr6:126299189-126299407(+)$1	218	32	61	22.8918
hh!!ddddvvvvvvvvvvvvvddddhhhh	chr10:14561353-14561570(-)$1	217	91	120	24.6391
dddd[ddddtttttttttttdddd]dddd	chr1:231501437-231501656(-)$1	219	187	216	22.4399
ffff[ddddtttttttttttdddd]ffff	chr15:56132559-56132783(-)$1	224	135	164	22.7550
iiiii!!bbwwwwwwwwwwwwwwbb333i	chr20:61827319-61827540(-)$1	221	7	36	23.4591
"ccc[ddddvvvvvvvvvvvvvdddd]cc	chr9:117360382-117360601(+)$1	219	119	148	24.6984
iiiiii[bbuuuuuuuuuuuubb]iiiii	chr10:120793157-120793375(-)$1	218	47	76	25.1071
eeee[eeeeettttttttttteeeeeeee	chr7:24729996-24730217(+)$1	221	52	81	22.8638
ggggg!!bbwwwwwwwwwwwwwwbb22gg	chr22:35660625-35660844(+)$1	219	90	119	23.0488
dd[aeeeeevvvvvvvvvvvvveeeee]a	chr13:50107227-50107449(-)$1	222	139	168	24.6999
ddddeeeeevvvvvvvvvvvvveeeee]d	chr7:139060760-139060985(+)$1	225	16	45	24.2317
h[ggggggguuuuuuuuuuuuggggggg]	chr19:9272253-9272479(+)$1	226	139	168	25.7714
:dddd[ddddtttttttttttdddddddd	chr5:112176976-112177196(+)$1	220	26	55	21.3673
+++eeeeevvvvvvvvvvvvveeeee333	chr5:6611745-6611967(-)$1	222	88	117	23.4803
!a[ffffffuuuuuuuuuuuuffffff]a	chr21:37758310-37758533(+)$1	223	76	105	24.7527
========vvvvvvvvvvvvv========	chr11:47492287-47492507(-)$1	220	112	141	26.4199
gggg!!ddddtttttttttttdddd22gg	chr10:119037459-119037681(-)$1	222	61	90	23.8078
gggggggwwwwwwwwwwwwwwggggggg2	chr1:229458035-229458258(-)$1	223	128	157	24.5611
eedddd!!bbtttttttttttbb22dddd	chr13:34411111-34411328(+)$1	217	84	113	21.4647
fffff[cccuuuuuuuuuuuucccfffff	chr14:77977053-77977273(-)$1	220	80	109	24.5045
fff[cccwwwwwwwwwwwwwwccc]ffff	chr21:45113312-45113540(+)$1	228	24	53	23.4514
)hhhhhhhhuuuuuuuuuuuuhhhhhhhh	chr1:114516410-114516629(+)$1	219	173	202	22.2049
ggggggg[avvvvvvvvvvvvva]ggggg	chr19:50411263-50411494(-)$1	231	140	169	25.7077
=========uuuuuuuuuuuu========	chr1:150446809-150447032(+)$1	223	80	109	26.1740
dd!!cccwwwwwwwwwwwwwwcccdddd2	chr1:23634474-23634700(-)$1	226	145	174	23.5483
HHffffffvvvvvvvvvvvvvffffff::	chr10:73857052-73857272(-)$1	220	7	36	21.1957
=======wwwwwwwwwwwwww========	chrX:24003657-24003880(-)$1	223	106	135	24.8977
dd!!ddddvvvvvvvvvvvvvdddd22dd	chr1:20234823-20235042(+)$1	219	20	49	24.9981
ccffffffvvvvvvvvvvvvvffffff]c	chrX:46918740-46918962(+)$1	222	56	85	24.7071
"""ddddwwwwwwwwwwwwwwdddd333b	chr14:93706076-93706297(-)$1	221	170	199	23.9116
ff!!cccwwwwwwwwwwwwwwccc22fff	chr5:64017133-64017355(-)$1	222	167	196	23.6191
cc[ffffffuuuuuuuuuuuuffffff22	chr2:29169933-29170151(+)$1	218	95	124	24.4315
ee[ffffffuuuuuuuuuuuuffffffee	chr19:47503952-47504173(+)$1	221	43	72	24.2632
eeeee[cccuuuuuuuuuuuuccc333ee	chr7:99637167-99637386(+)$1	219	39	68	25.1996
eeeee[ddddtttttttttttdddd22ee	chr8:124332667-124332890(-)$1	223	61	90	23.0120
###fffffftttttttttttffffffccc	chr18:212918-213136(+)$1	218	178	207	22.8346
hhh[bb[bbuuuuuuuuuuuubbbbhhhh	chr19:47231111-47231352(-)$1	241	29	58	22.4535
cc[ddddwwwwwwwwwwwwwwdddd4444	chrX:76761770-76761995(-)$1	225	55	84	23.7093
e[a[ddddvvvvvvvvvvvvvdddd]a]e	chrX:153714052-153714266(-)$1	214	54	83	25.5174
f"""eeeeeuuuuuuuuuuuueeeee333	chrX:12842056-12842277(+)$1	221	151	180	25.2876
dddd[ddddwwwwwwwwwwwwwwdddd]d	chr6:28348131-28348348(-)$1	217	175	204	22.5589
h!!dddd[attttttttttta]dddd22h	chr10:6157494-6157714(+)$1	220	160	189	23.9306
f[ggggggguuuuuuuuuuuuggggggg]	chr2:183790209-183790429(-)$1	220	175	204	25.8257
hhhhhhhwwwwwwwwwwwwwwhhhhhhhh	chr7:5520741-5520963(-)$1	222	28	57	21.8572
eeeeeeeeeuuuuuuuuuuuueeeee:::	chr20:56938226-56938446(+)$1	220	189	218	21.5402
g[ggggggguuuuuuuuuuuuggggggg4	chr12:99019424-99019643(-)$1	219	132	161	25.8583
==========ttttttttttt========	chr6:89320102-89320322(-)$1	220	126	155	24.5434
ddddeeeeettttttttttteeeee]ddd	chr1:156280678-156280905(-)$1	227	21	50	22.5337
##ggggggguuuuuuuuuuuugggggggd	chr6:32945171-32945419(+)$1	248	148	177	25.5390
iiiiiiiiitttttttttttiiiiiiiii	chr13:77457147-77457371(-)$1	224	164	193	24.0365
c!!ddddbbtttttttttttbb]dddd22	chr10:100004293-100004505(+)$1	212	96	125	22.8526
ea[eeeeevvvvvvvvvvvvveeeee]a]	chr7:44920968-44921189(-)$1	221	139	168	25.4322
gggggg[bbtttttttttttbb]gggggg	chr12:50870458-50870682(+)$1	224	145	174	23.7790
!!a!!dddduuuuuuuuuuuudddd22a2	chr14:62214784-62215005(+)$1	221	96	125	25.2002
iiiiiiiivvvvvvvvvvvvviiiiiiii	chr10:85912208-85912430(+)$1	222	13	42	26.1500
ffff!!cccuuuuuuuuuuuuccc22fff	chr16:23614535-23614754(-)$1	219	31	60	24.5594
$$$$cccwwwwwwwwwwwwwwccc22ccc	chr12:69233412-69233644(+)$1	232	137	166	22.9341
!!gggggggwwwwwwwwwwwwwwgggggg	chr5:176731648-176731876(+)$1	228	81	110	24.1646

#otherMatches

#Seq PSSM
UAGGCAGUGAGAAGUUAGUGGCGCUGCUG	chr5:139781361-139781584(+)$1	223	51	80	25.7791
UGUGAAGGAGAAAAAUAGCUAUUUCUUGA	chr6:126299189-126299407(+)$1	218	32	61	22.8918
UGGAAUGGUAACUAUUUUUUCCCAUCGUU	chr10:14561353-14561570(-)$1	217	91	120	24.6391
CAUUUACUACCAAUAACUUUUAGUUAAUG	chr1:231501437-231501656(-)$1	219	187	216	22.4399
UGUGGUAUGUCUUUUUCACUUAUAGUAUA	chr15:56132559-56132783(-)$1	224	135	164	22.7550
CUAGACAGAUAACUUUUAAUUUUUCAAAU	chr20:61827319-61827540(-)$1	221	7	36	23.4591
GCUAAUGGUUAGAACAGUGAAUACUAGUG	chr9:117360382-117360601(+)$1	219	119	148	24.6984
UUGGGGUACUAUGAAAGGACUGUUCCUUG	chr10:120793157-120793375(-)$1	218	47	76	25.1071
ACAUGCAUGUGCUUUUGGGAAACAUGAUG	chr7:24729996-24730217(+)$1	221	52	81	22.8638
UGUUGAAAGCUAUCACUUCCCCACUGGCA	chr22:35660625-35660844(+)$1	219	90	119	23.0488
CUUCAAGUCAACCCUCUUACAAGACUUAG	chr13:50107227-50107449(-)$1	222	139	168	24.6999
CUUGAAUGUUAUUAACUCUUCUAUAUUAC	chr7:139060760-139060985(+)$1	225	16	45	24.2317
UUAAUGUCAAAAUCCAAGCCGUGGCAUUU	chr19:9272253-9272479(+)$1	226	139	168	25.7714
ACAAUCAGCUAAUAAGACACAAGCUAUUG	chr5:112176976-112177196(+)$1	220	26	55	21.3673
CUGCCAGGGCUGAAGUGGAUGCCUGGAAU	chr5:6611745-6611967(-)$1	222	88	117	23.4803
AGUAGAACGGUGCCCGAGAAACGUUUUUC	chr21:37758310-37758533(+)$1	223	76	105	24.7527
GCCUCUGCUCUAAGAAGUGCUGUGGGGGU	chr11:47492287-47492507(-)$1	220	112	141	26.4199
UUAUCAUGUUUAAACAACCUUGACAGUAU	chr10:119037459-119037681(-)$1	222	61	90	23.8078
AUCUUUGUCAUUGUGUUUCAUCGAAGAUC	chr1:229458035-229458258(-)$1	223	128	157	24.5611
GUGUGACAGACUCCGAACAAUUCCUUUAC	chr13:34411111-34411328(+)$1	217	84	113	21.4647
CUUUUUGUAUCCAUCAAGUAUUACAGGAG	chr14:77977053-77977273(-)$1	220	80	109	24.5045
GGGCCUUUUUUAUGAUUUUGUAAGUUCCC	chr21:45113312-45113540(+)$1	228	24	53	23.4514
UGACAAAAAAAGAAAAAUUACUUUUUGUU	chr1:114516410-114516629(+)$1	219	173	202	22.2049
GUGCUUUGCGUUUUUCCAUUUAGGAGGGU	chr19:50411263-50411494(-)$1	231	140	169	25.7077
AAAGGAGGAGAUUCAGUAGCAUUUUCCUU	chr1:150446809-150447032(+)$1	223	80	109	26.1740
GUCUUGUAAAUUAACACUGUAGCAGCAUU	chr1:23634474-23634700(-)$1	226	145	174	23.5483
UAAUAUUUUCAUCUAUACUUUAAAUAUUC	chr10:73857052-73857272(-)$1	220	7	36	21.1957
UGGUCUUCCAUUUUAAAGACAGAGGCCAA	chrX:24003657-24003880(-)$1	223	106	135	24.8977
CUUCCUGAUUCUGAUGUUAUUUCAGAUGG	chr1:20234823-20235042(+)$1	219	20	49	24.9981
UCCUUGCAUUGUUAACUGAUUUGCAAGAG	chrX:46918740-46918962(+)$1	222	56	85	24.7071
GCCACUAUUCCUAAGAUUAUUUAGUUUAU	chr14:93706076-93706297(-)$1	221	170	199	23.9116
GAUAAAAAUGCCAUUGAAuccuuucuuca	chr5:64017133-64017355(-)$1	222	167	196	23.6191
UUGGUAUCUUUCAUCAAAUCCAGAUGCAA	chr2:29169933-29170151(+)$1	218	95	124	24.4315
GGCAUUUGGCCUUGAACAAAACCAAGUCC	chr19:47503952-47504173(+)$1	221	43	72	24.2632
UCAGUCACUUUUAUUCCAGGUAGUCAUGC	chr7:99637167-99637386(+)$1	219	39	68	25.1996
ACAAUUCUGUACUUGAGUAUCACAGUCAU	chr8:124332667-124332890(-)$1	223	61	90	23.0120
GACCAUGAAaauuauaaugauucauguau	chr18:212918-213136(+)$1	218	178	207	22.8346
CUAUGCCAGACUGGGUUGGAACUGCUGGG	chr19:47231111-47231352(-)$1	241	29	58	22.4535
AUGGUCUAAUUAUUUACUCAAAGACAUAG	chrX:76761770-76761995(-)$1	225	55	84	23.7093
GGCCGACUCCCCACCCCCGCAGGUCUGGC	chrX:153714052-153714266(-)$1	214	54	83	25.5174
UCUUUUUAGAUACUACAUCAACUAGAUUC	chrX:12842056-12842277(+)$1	221	151	180	25.2876
AUCUGCACAAUAAACAUGAUGAAUGUGGA	chr6:28348131-28348348(-)$1	217	175	204	22.5589
AUUGAUCCCUUUUUUAUUUUGUGGUUUUU	chr10:6157494-6157714(+)$1	220	160	189	23.9306
UUGAUUUAGGUUGCACAUUCACUGAAUUC	chr2:183790209-183790429(-)$1	220	175	204	25.8257
CCGUGUAUCUGAGUGUCCCCUUGCAUGGU	chr7:5520741-5520963(-)$1	222	28	57	21.8572
UAACGGAUGAGCCCCCCUAAACAUCCACG	chr20:56938226-56938446(+)$1	220	189	218	21.5402
auagaaauaguucuuuaaaaauauuucuc	chr12:99019424-99019643(-)$1	219	132	161	25.8583
GAAGUUUUUUAGACAAGAAUAAGAAAACU	chr6:89320102-89320322(-)$1	220	126	155	24.5434
CAUGCCUUGACAGAAAAAUCCAAGGCCAU	chr1:156280678-156280905(-)$1	227	21	50	22.5337
UGUUGUGGCAAUGGCACGAAAGCUACAGG	chr6:32945171-32945419(+)$1	248	148	177	25.5390
UUUGAUGAGUUUCUUACAUCCUUAUCGAG	chr13:77457147-77457371(-)$1	224	164	193	24.0365
GUGUCUGGUUUACUUGGCAUACACAGAAU	chr10:100004293-100004505(+)$1	212	96	125	22.8526
GCUGUGGAUUAAUUGUAGCAUUUCACUGA	chr7:44920968-44921189(-)$1	221	139	168	25.4322
AGCAGUCUAGUCAAAUCAUAUAAAUUGUU	chr12:50870458-50870682(+)$1	224	145	174	23.7790
UUGUACAAAUUUUUCAUUCCUUUUGCUCU	chr14:62214784-62215005(+)$1	221	96	125	25.2002
AUCAUAUUUAAAUGUUCCGGUAAUGUGAU	chr10:85912208-85912430(+)$1	222	13	42	26.1500
UGGAGUUUUAAAUAUAAAGGAGAAUAUCU	chr16:23614535-23614754(-)$1	219	31	60	24.5594
AGAAGCUAAAGAAAAGGAAUAAGCCCUGC	chr12:69233412-69233644(+)$1	232	137	166	22.9341
CCGAGCGACUAUUUCCUGCCAAUGUUGCU	chr5:176731648-176731876(+)$1	228	81	110	24.1646

#DB
(.(((((((............))))))).	chr5:139781361-139781584(+)$1	1	51	80	25.7791
(((.((((((...........)))))).)	chr6:126299189-126299407(+)$1	1	32	61	22.8918
((..((((.............))))))))	chr10:14561353-14561570(-)$1	1	91	120	24.6391
((((.((((...........)))).))))	chr1:231501437-231501656(-)$1	1	187	216	22.4399
((((.((((...........)))).))))	chr15:56132559-56132783(-)$1	1	135	164	22.7550
(((((..((..............))...)	chr20:61827319-61827540(-)$1	1	7	36	23.4591
.(((.((((.............)))).))	chr9:117360382-117360601(+)$1	1	119	148	24.6984
((((((.((............)).)))))	chr10:120793157-120793375(-)$1	1	47	76	25.1071
((((.(((((...........))))))))	chr7:24729996-24730217(+)$1	1	52	81	22.8638
(((((..((..............))..))	chr22:35660625-35660844(+)$1	1	90	119	23.0488
((.((((((.............))))).)	chr13:50107227-50107449(-)$1	1	139	168	24.6999
(((((((((.............))))).)	chr7:139060760-139060985(+)$1	1	16	45	24.2317
(.(((((((............))))))).	chr19:9272253-9272479(+)$1	1	139	168	25.7714
.((((.((((...........))))))))	chr5:112176976-112177196(+)$1	1	26	55	21.3673
...(((((.............)))))...	chr5:6611745-6611967(-)$1	1	88	117	23.4803
.(.((((((............)))))).)	chr21:37758310-37758533(+)$1	1	76	105	24.7527
((((((((.............))))))))	chr11:47492287-47492507(-)$1	1	112	141	26.4199
((((..((((...........))))..))	chr10:119037459-119037681(-)$1	1	61	90	23.8078
(((((((..............))))))).	chr1:229458035-229458258(-)$1	1	128	157	24.5611
((((((..((...........))..))))	chr13:34411111-34411328(+)$1	1	84	113	21.4647
(((((.(((............))))))))	chr14:77977053-77977273(-)$1	1	80	109	24.5045
(((.(((..............))).))))	chr21:45113312-45113540(+)$1	1	24	53	23.4514
.((((((((............))))))))	chr1:114516410-114516629(+)$1	1	173	202	22.2049
(((((((.(.............).)))))	chr19:50411263-50411494(-)$1	1	140	169	25.7077
(((((((((............))))))))	chr1:150446809-150447032(+)$1	1	80	109	26.1740
((..(((..............))))))).	chr1:23634474-23634700(-)$1	1	145	174	23.5483
((((((((.............))))))..	chr10:73857052-73857272(-)$1	1	7	36	21.1957
(((((((..............))))))))	chrX:24003657-24003880(-)$1	1	106	135	24.8977
((..((((.............))))..))	chr1:20234823-20235042(+)$1	1	20	49	24.9981
((((((((.............)))))).)	chrX:46918740-46918962(+)$1	1	56	85	24.7071
...((((..............))))...)	chr14:93706076-93706297(-)$1	1	170	199	23.9116
((..(((..............)))..)))	chr5:64017133-64017355(-)$1	1	167	196	23.6191
((.((((((............))))))..	chr2:29169933-29170151(+)$1	1	95	124	24.4315
((.((((((............))))))))	chr19:47503952-47504173(+)$1	1	43	72	24.2632
(((((.(((............)))...))	chr7:99637167-99637386(+)$1	1	39	68	25.1996
(((((.((((...........))))..))	chr8:124332667-124332890(-)$1	1	61	90	23.0120
...((((((...........)))))))))	chr18:212918-213136(+)$1	1	178	207	22.8346
(((.((.((............))))))))	chr19:47231111-47231352(-)$1	1	29	58	22.4535
((.((((..............))))....	chrX:76761770-76761995(-)$1	1	55	84	23.7093
(.(.((((.............)))).).)	chrX:153714052-153714266(-)$1	1	54	83	25.5174
(...(((((............)))))...	chrX:12842056-12842277(+)$1	1	151	180	25.2876
((((.((((..............)))).)	chr6:28348131-28348348(-)$1	1	175	204	22.5589
(..((((.(...........).))))..)	chr10:6157494-6157714(+)$1	1	160	189	23.9306
(.(((((((............))))))).	chr2:183790209-183790429(-)$1	1	175	204	25.8257
(((((((..............))))))))	chr7:5520741-5520963(-)$1	1	28	57	21.8572
))))(((((............)))))...	chr20:56938226-56938446(+)$1	1	189	218	21.5402
(.(((((((............))))))).	chr12:99019424-99019643(-)$1	1	132	161	25.8583
((((((((((...........))))))))	chr6:89320102-89320322(-)$1	1	126	155	24.5434
(((((((((...........))))).)))	chr1:156280678-156280905(-)$1	1	21	50	22.5337
..(((((((............))))))))	chr6:32945171-32945419(+)$1	1	148	177	25.5390
(((((((((...........)))))))))	chr13:77457147-77457371(-)$1	1	164	193	24.0365
(..((((((...........)).))))..	chr10:100004293-100004505(+)$1	1	96	125	22.8526
((.(((((.............))))).).	chr7:44920968-44921189(-)$1	1	139	168	25.4322
((((((.((...........)).))))))	chr12:50870458-50870682(+)$1	1	145	174	23.7790
..(..((((............))))..).	chr14:62214784-62215005(+)$1	1	96	125	25.2002
((((((((.............))))))))	chr10:85912208-85912430(+)$1	1	13	42	26.1500
((((..(((............)))..)))	chr16:23614535-23614754(-)$1	1	31	60	24.5594
....(((..............)))..)))	chr12:69233412-69233644(+)$1	1	137	166	22.9341
..(((((((..............))))))	chr5:176731648-176731876(+)$1	1	81	110	24.1646

#PSSM
e : 0.15	d : 0.11	f : 0.11	g : 0.10	c : 0.08	h : 0.08	i : 0.06	= : 0.06	! : 0.05	" : 0.03	# : 0.03	: : 0.01	+ : 0.01	) : 0.01	H : 0.01	$ : 0.01	
d : 0.13	e : 0.11	[ : 0.08	f : 0.08	g : 0.08	h : 0.06	i : 0.06	c : 0.06	= : 0.06	! : 0.06	a : 0.03	" : 0.03	# : 0.03	+ : 0.01	H : 0.01	$ : 0.01	
g : 0.18	! : 0.10	d : 0.10	f : 0.10	[ : 0.10	e : 0.08	i : 0.06	= : 0.06	h : 0.05	" : 0.03	a : 0.03	c : 0.01	+ : 0.01	# : 0.01	$ : 0.01	
g : 0.18	d : 0.16	f : 0.15	e : 0.10	! : 0.08	[ : 0.06	i : 0.06	= : 0.06	h : 0.03	c : 0.01	a : 0.01	" : 0.01	$ : 0.01	
g : 0.16	d : 0.15	e : 0.15	f : 0.13	[ : 0.08	i : 0.06	= : 0.06	c : 0.06	! : 0.05	h : 0.03	b : 0.01	
d : 0.22	g : 0.15	e : 0.13	f : 0.11	! : 0.06	[ : 0.06	= : 0.06	c : 0.06	i : 0.05	h : 0.03	b : 0.01	
d : 0.25	g : 0.13	e : 0.13	f : 0.11	c : 0.11	= : 0.06	! : 0.05	[ : 0.05	h : 0.03	i : 0.03	
d : 0.18	w : 0.15	e : 0.13	f : 0.11	g : 0.10	b : 0.10	= : 0.05	c : 0.05	[ : 0.03	i : 0.03	! : 0.01	h : 0.01	
v : 0.15	w : 0.15	d : 0.13	b : 0.11	g : 0.10	e : 0.10	f : 0.08	c : 0.05	a : 0.03	= : 0.03	h : 0.01	i : 0.01	
u : 0.30	v : 0.22	w : 0.22	t : 0.13	d : 0.05	f : 0.01	e : 0.01	b : 0.01	= : 0.01	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	t : 0.25	v : 0.22	w : 0.22	
u : 0.30	v : 0.22	w : 0.22	t : 0.11	d : 0.03	b : 0.03	f : 0.01	a : 0.01	e : 0.01	i : 0.01	
d : 0.18	f : 0.11	c : 0.11	g : 0.10	e : 0.10	b : 0.08	w : 0.06	v : 0.06	= : 0.06	h : 0.03	i : 0.03	] : 0.01	
d : 0.22	e : 0.13	f : 0.11	c : 0.11	g : 0.10	w : 0.06	= : 0.06	b : 0.05	h : 0.03	i : 0.03	] : 0.03	a : 0.01	
d : 0.25	g : 0.13	e : 0.13	f : 0.11	c : 0.11	= : 0.06	b : 0.05	] : 0.03	h : 0.03	i : 0.03	2 : 0.01	
d : 0.23	g : 0.15	f : 0.13	e : 0.13	= : 0.06	2 : 0.06	] : 0.05	b : 0.05	i : 0.05	h : 0.03	3 : 0.01	
f : 0.16	g : 0.15	d : 0.13	2 : 0.13	e : 0.11	h : 0.06	= : 0.06	3 : 0.05	i : 0.05	] : 0.03	4 : 0.01	
f : 0.18	g : 0.15	d : 0.11	2 : 0.10	3 : 0.08	h : 0.06	= : 0.06	i : 0.05	e : 0.05	] : 0.03	c : 0.03	4 : 0.01	a : 0.01	: : 0.01	
g : 0.18	] : 0.11	d : 0.10	f : 0.08	h : 0.06	3 : 0.06	e : 0.06	= : 0.06	c : 0.05	i : 0.05	2 : 0.05	: : 0.03	a : 0.03	4 : 0.01	
d : 0.13	2 : 0.10	e : 0.10	h : 0.08	f : 0.08	g : 0.08	i : 0.06	c : 0.06	= : 0.06	] : 0.05	a : 0.03	3 : 0.03	: : 0.03	4 : 0.03	b : 0.01	

#score	1417.1663174248918
#seq	59
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_CDS_m2_run2.txt

#BEAR
oooddddcccoooooocccffffffp	chr20:46275854-46276069(+)$1	215	47	73	10.7376
dd!!ffffffooooooffffff22dd	chr19:34891400-34891621(+)$1	221	137	163	12.5710
a[dddd[cccooooooccc22dddd]	chr6:159208072-159208294(-)$1	222	83	109	11.8471
ffff!!ddddoooooodddd4444ff	chr5:154179394-154179619(+)$1	225	6	32	11.3285
Fiiiiiiiiiooooooiiiiiiiii:	chr20:61477145-61477369(-)$1	224	31	57	12.4154
#ccc[ffffffooooooffffff22c	chr4:151771799-151772029(-)$1	230	107	133	11.8949
e####cccbboooooobb]ccc7777	chr3:194168486-194168716(-)$1	230	91	117	10.8155
#cccddddbboooooobb]dddd]cc	chr15:101853596-101853818(+)$1	222	144	170	11.7154
dd!!gggggggnnnnnggggggg22d	chr10:75523220-75523442(+)$1	222	149	175	9.2802
======[cccooooooccc]======	chr18:12697229-12697459(-)$1	230	19	45	14.2294
cffffff[bboooooobbffffff::	chr6:97246696-97246926(-)$1	230	191	217	10.3519
[a[iiiiiiiiillliiiiiiiiiad	chr7:127229528-127229748(+)$1	220	124	150	9.4034
ggggggggggooooooggggggg:::	chr9:79972573-79972795(+)$1	222	193	219	11.1926
bb[gggggggooooooggggggg]bb	chr3:182607116-182607346(+)$1	230	200	226	13.3294
f"""ffffffooooooffffffffff	chr3:33438447-33438666(-)$1	219	87	113	12.5501
""eeeeeccc[aooooooa]ccc22e	chr11:122930301-122930522(-)$1	221	25	51	10.8361
cccgggggggnnnnnggggggg]ccc	chr5:171295625-171295855(-)$1	230	31	57	8.9340
:eeeee[cccooooooccceeeee::	chr8:104340436-104340659(+)$1	223	67	93	10.1677
dd"""eeeeeooooooeeeee333dd	chr7:86820170-86820409(+)$1	239	89	115	12.4944
"""gggggggooooooggggggg333	chr9:72349030-72349260(-)$1	230	168	194	14.9922
+iiiiiiiiiooooooiiiiiiiiif	chr15:38643500-38643726(+)$1	226	131	157	13.0349
!!a[ffffffooooooffffff]a44	chr20:18506373-18506603(+)$1	230	136	162	13.4166
#ccc[bb[bboooooobbbbccc22c	chr11:64814899-64815119(+)$1	220	165	191	12.1373
"""eeeeebboooooobb]eeeee]c	chr16:68225427-68225650(+)$1	223	90	116	12.7394
c!!cccbb[aooooooa]bb]ccc22	chr17:62290678-62290902(-)$1	224	16	42	12.1380
ffffa[ddddoooooodddd]a]fff	chr10:70722958-70723179(+)$1	221	51	77	11.0733
bb[eeeeebboooooobb]eeeee]b	chr3:58303068-58303294(+)$1	226	21	47	11.7593
%%%%%ccc[aooooooa]cccggggg	chr3:196281284-196281504(-)$1	220	56	82	10.6395
ccc[bb[cccooooooccc]bb]ccc	chr9:114986085-114986307(-)$1	222	44	70	12.5856
iii!!eeeeeooooooeeeee]iiii	chr7:111517087-111517317(-)$1	230	57	83	12.4045
ggggggg!!aooooooa22ggggggg	chr21:44845186-44845416(-)$1	230	78	104	12.8205
cca!!a[cccooooooccc]a22a]c	chr8:145065791-145066015(+)$1	224	71	97	13.5422
dddgggggggooooooggggggg]dd	chr2:198288443-198288661(-)$1	218	160	186	13.2192
[affffff[aooooooa]ffffff44	chr4:16510139-16510358(+)$1	219	20	46	12.9431
$bbgggggggooooooggggggg]bb	chr3:57846354-57846571(+)$1	217	151	177	13.0977
ff[bb!!cccooooooccc22bb]ff	chr6:88385491-88385714(+)$1	223	171	197	11.7325
"cccccccccooooooccc22ccc]c	chr7:44685000-44685222(+)$1	222	74	100	13.1801
ba[eeeee[aooooooaeeeee]a]b	chr19:18576562-18576783(-)$1	221	194	220	12.7859
!ccc[bb[bboooooobbbbccc]cc	chr5:149826351-149826574(-)$1	223	154	180	12.0335
b[dddd[cccooooooccc]dddd]b	chr22:50716924-50717154(-)$1	230	12	38	12.1985
$$$$$ggggggglllggggggg333=	chr17:5336528-5336750(-)$1	222	42	68	9.0194
"""a[bb[bboooooobb]bba333f	chr5:96111723-96111942(-)$1	219	138	164	12.9296
EEEgggggggoooooogggggggccc	chr6:150057592-150057822(-)$1	230	9	35	10.7107
c!!bb[ddddoooooodddd]bb22c	chr10:38407470-38407688(+)$1	218	156	182	11.4591
g[eeeeecccooooooccc]eeeee]	chr15:48802226-48802446(-)$1	220	123	149	12.5397
dd!!ffffffooooooffffff333d	chrX:148564496-148564721(-)$1	225	86	112	13.4383
###gggggggoooooogggggggggg	chr5:133292436-133292663(-)$1	227	21	47	14.1498
"bb!!ffffffooooooffffff22b	chr14:55618343-55618563(-)$1	220	122	148	11.5160
!!ffffff[aooooooa]ffffff]b	chr19:37240256-37240486(-)$1	230	25	51	13.0946
[dddd"""cccooooooccc4444dd	chr16:71949496-71949717(+)$1	221	82	108	10.9744
eeee[eeeeeooooooeeeeeeeeee	chr1:109441224-109441454(+)$1	230	73	99	11.0681
===========lll===========:	chr9:139371478-139371702(-)$1	224	142	168	9.4694
ff!!dddd[aooooooa]dddd22ff	chr16:47549332-47549554(+)$1	222	20	46	11.9911
dddd!!ddddoooooodddd333ddd	chr6:43170795-43171025(+)$1	230	187	213	11.2551
dddccc[cccoooooocccccc]ddd	chr10:93257787-93258009(+)$1	222	87	113	12.5478
[iiiiiiiiiooooooiiiiiiiii]	chr3:43743675-43743898(+)$1	223	133	159	13.7382

#otherMatches

#Seq PSSM
AGACAUACCCAGCACAGGGGCCUCCA	chr20:46275854-46276069(+)$1	215	47	73	10.7376
UUGUUUCGGGUGAAUUCCUGGACAAG	chr19:34891400-34891621(+)$1	221	137	163	12.5710
GAAGUGUGGUACUUUGGCCUCCACUA	chr6:159208072-159208294(-)$1	222	83	109	11.8471
AGGGAUGAGGACUUCCCCUUUCCACC	chr5:154179394-154179619(+)$1	225	6	32	11.3285
CAGGAGCUUUGCAUUUGAAGUUUCUA	chr20:61477145-61477369(-)$1	224	31	57	12.4154
ACUGAUCUAUUAUUUUCAAUAGAAAC	chr4:151771799-151772029(-)$1	230	107	133	11.8949
GGCAUUGGGUUUAUCUACACUAUUAU	chr3:194168486-194168716(-)$1	230	91	117	10.8155
AGGGAUGGCUGGCAGAAGACCAUGCC	chr15:101853596-101853818(+)$1	222	144	170	11.7154
AAUUAGCUCCUCCCACAGGGGCUUUU	chr10:75523220-75523442(+)$1	222	149	175	9.2802
UGUGGUAUAAUUUCGUUUGGAUUAUA	chr18:12697229-12697459(-)$1	230	19	45	14.2294
GGGUCUCAUGAGUCUGCAGAGACCUU	chr6:97246696-97246926(-)$1	230	191	217	10.3519
AGUGUUGGGAGGGGACUUUCUAACCC	chr7:127229528-127229748(+)$1	220	124	150	9.4034
GAAAAUAUAGGCAAAAUUGUAUUCUA	chr9:79972573-79972795(+)$1	222	193	219	11.1926
CUCUGCUUGGAAAUGGCCAGGUAAAG	chr3:182607116-182607346(+)$1	230	200	226	13.3294
GUGCAGCCGAUGGAAUUCGGCUCUAU	chr3:33438447-33438666(-)$1	219	87	113	12.5501
ACGUGCUAAGCGUACCCUCUCUUCCA	chr11:122930301-122930522(-)$1	221	25	51	10.8361
UUCAUGAAGUUUUGUAUUUCAUAGGA	chr5:171295625-171295855(-)$1	230	31	57	8.9340
AAAAGCUCGACCAGAAUUGGCUUUAU	chr8:104340436-104340659(+)$1	223	67	93	10.1677
GCUUCAGCAGACUCUCCUGCUACCGU	chr7:86820170-86820409(+)$1	239	89	115	12.4944
AAAGAGUCCAGAAACAUGGAUUCACA	chr9:72349030-72349260(-)$1	230	168	194	14.9922
UGCAUGCUCUGUGCAGAGAGCAUGUU	chr15:38643500-38643726(+)$1	226	131	157	13.0349
AACUCAGGGGAAGAGACCUUUGCGAU	chr20:18506373-18506603(+)$1	230	136	162	13.4166
AGAGCGCUGGGCCGGACCGCCUCGCU	chr11:64814899-64815119(+)$1	220	165	191	12.1373
CCAGGGGGGUCUUUCUGCACCUUCAU	chr16:68225427-68225650(+)$1	223	90	116	12.7394
AUACAGUGUCCUAUAAGCCACCUGAU	chr17:62290678-62290902(-)$1	224	16	42	12.1380
AUUGCAGUGUGAGAUAACACAGUUAA	chr10:70722958-70723179(+)$1	221	51	77	11.0733
ACUGGGCAUGUUUCCCCAUUGCCCUG	chr3:58303068-58303294(+)$1	226	21	47	11.7593
UAAGGGCCACACUUCAGGGGUAUCCC	chr3:196281284-196281504(-)$1	220	56	82	10.6395
GAAAGAUCGCAAAAUGGCGCUCAUUC	chr9:114986085-114986307(-)$1	222	44	70	12.5856
UUUAAAUAUUUUUAACAGUGUGAAGA	chr7:111517087-111517317(-)$1	230	57	83	12.4045
GGUUCAGCUGAUGAAGCUUCUGAACC	chr21:44845186-44845416(-)$1	230	78	104	12.8205
CCCAGCAUGGAAACUACCAGGAGGAG	chr8:145065791-145066015(+)$1	224	71	97	13.5422
UAUUUUUUUGAGAGAGCAAGAAAUAU	chr2:198288443-198288661(-)$1	218	160	186	13.2192
GUACCUGACUGGACAGACUCAGGUUU	chr4:16510139-16510358(+)$1	219	20	46	12.9431
GUCCCUGAGGCGGGUUCUUCAGGAGA	chr3:57846354-57846571(+)$1	217	151	177	13.0977
UACUUGUCAAUUACAUUUGUAAAAUG	chr6:88385491-88385714(+)$1	223	171	197	11.7325
GGAGGACCACCUGGCAGUGCAGUCGC	chr7:44685000-44685222(+)$1	222	74	100	13.1801
CCCAGAGCACCCCGCCGGCUCUUGAG	chr19:18576562-18576783(-)$1	221	194	220	12.7859
AAGGAGCUGGGUAUCACCGCCCUACA	chr5:149826351-149826574(-)$1	223	154	180	12.0335
GCUGUCUCUUCCCACAGAGUGGCGUC	chr22:50716924-50717154(-)$1	230	12	38	12.1985
GACAUCUUCUCUAUCAGGGAAGUUAG	chr17:5336528-5336750(-)$1	222	42	68	9.0194
CCCGUGUCCAAAACCCUGUACCCCAU	chr5:96111723-96111942(-)$1	219	138	164	12.9296
CAAAGAUAAAUUAUACUUUAUUUGAU	chr6:150057592-150057822(-)$1	230	9	35	10.7107
ACACACAGGGGAGAAACCCUAUGAAU	chr10:38407470-38407688(+)$1	218	156	182	11.4591
ACGCUGCAUCAACACAGAUGGCAGUU	chr15:48802226-48802446(-)$1	220	123	149	12.5397
GCAGAGAAGGCAAGAACCUUCUGAAG	chrX:148564496-148564721(-)$1	225	86	112	13.4383
CUUUGUUCCAAAACAGUGGAAUACCA	chr5:133292436-133292663(-)$1	227	21	47	14.1498
AGAAGGGGAAACUAAAAUUUCUCAGU	chr14:55618343-55618563(-)$1	220	122	148	11.5160
GACACCAGCGAAUCCACACUGGUGAG	chr19:37240256-37240486(-)$1	230	25	51	13.0946
AGUGAAUUUGAGAUUAGUCAUAAAUC	chr16:71949496-71949717(+)$1	221	82	108	10.9744
CGAGCGGCACAAGGACGUGCCUUUGG	chr1:109441224-109441454(+)$1	230	73	99	11.0681
UCUCAUGGGGGCCACCCUCAUGGGAA	chr9:139371478-139371702(-)$1	224	142	168	9.4694
AAUUUUAGCCUUAAUUGAUUAAUUUU	chr16:47549332-47549554(+)$1	222	20	46	11.9911
GGCACACAAGUUUCUCCUUGAUCUGC	chr6:43170795-43171025(+)$1	230	187	213	11.2551
AUGGAUUAAGUGAACUCUUAUCACAU	chr10:93257787-93258009(+)$1	222	87	113	12.5478
UCCUUCUCCAUGGUUUUGGAGGAGGU	chr3:43743675-43743898(+)$1	223	133	159	13.7382

#DB
...))))(((......)))((((((.	chr20:46275854-46276069(+)$1	1	47	73	10.7376
((..((((((......))))))..))	chr19:34891400-34891621(+)$1	1	137	163	12.5710
(.((((.(((......)))..)))).	chr6:159208072-159208294(-)$1	1	83	109	11.8471
((((..((((......))))....))	chr5:154179394-154179619(+)$1	1	6	32	11.3285
((((((((((......))))))))).	chr20:61477145-61477369(-)$1	1	31	57	12.4154
.(((.((((((......))))))..)	chr4:151771799-151772029(-)$1	1	107	133	11.8949
(....(((((......)).)))....	chr3:194168486-194168716(-)$1	1	91	117	10.8155
.(((((((((......)).)))).))	chr15:101853596-101853818(+)$1	1	144	170	11.7154
((..(((((((.....)))))))..)	chr10:75523220-75523442(+)$1	1	149	175	9.2802
((((((.(((......))).))))))	chr18:12697229-12697459(-)$1	1	19	45	14.2294
)((((((.((......))))))))..	chr6:97246696-97246926(-)$1	1	191	217	10.3519
.(.(((((((((...)))))))))))	chr7:127229528-127229748(+)$1	1	124	150	9.4034
)))(((((((......)))))))...	chr9:79972573-79972795(+)$1	1	193	219	11.1926
((.(((((((......))))))).))	chr3:182607116-182607346(+)$1	1	200	226	13.3294
(...((((((......))))))))))	chr3:33438447-33438666(-)$1	1	87	113	12.5501
..((((((((.(......).)))..)	chr11:122930301-122930522(-)$1	1	25	51	10.8361
((((((((((.....))))))).)))	chr5:171295625-171295855(-)$1	1	31	57	8.9340
.(((((.(((......))))))))..	chr8:104340436-104340659(+)$1	1	67	93	10.1677
((...(((((......)))))...))	chr7:86820170-86820409(+)$1	1	89	115	12.4944
...(((((((......)))))))...	chr9:72349030-72349260(-)$1	1	168	194	14.9922
.(((((((((......))))))))))	chr15:38643500-38643726(+)$1	1	131	157	13.0349
..(.((((((......)))))).)..	chr20:18506373-18506603(+)$1	1	136	162	13.4166
.(((.((.((......)))))))..)	chr11:64814899-64815119(+)$1	1	165	191	12.1373
...(((((((......)).))))).)	chr16:68225427-68225650(+)$1	1	90	116	12.7394
(..(((((.(......).)).)))..	chr17:62290678-62290902(-)$1	1	16	42	12.1380
(((((.((((......)))).).)))	chr10:70722958-70723179(+)$1	1	51	77	11.0733
((.(((((((......)).))))).)	chr3:58303068-58303294(+)$1	1	21	47	11.7593
.....(((.(......).))))))))	chr3:196281284-196281504(-)$1	1	56	82	10.6395
(((.((.(((......))).)).)))	chr9:114986085-114986307(-)$1	1	44	70	12.5856
(((..(((((......))))).))))	chr7:111517087-111517317(-)$1	1	57	83	12.4045
(((((((..(......)..)))))))	chr21:44845186-44845416(-)$1	1	78	104	12.8205
(((..(.(((......))).)..).)	chr8:145065791-145066015(+)$1	1	71	97	13.5422
((((((((((......))))))).))	chr2:198288443-198288661(-)$1	1	160	186	13.2192
.(((((((.(......).))))))..	chr4:16510139-16510358(+)$1	1	20	46	12.9431
.(((((((((......))))))).))	chr3:57846354-57846571(+)$1	1	151	177	13.0977
((.((..(((......)))..)).))	chr6:88385491-88385714(+)$1	1	171	197	11.7325
.(((((((((......)))..))).)	chr7:44685000-44685222(+)$1	1	74	100	13.1801
((.(((((.(......)))))).).)	chr19:18576562-18576783(-)$1	1	194	220	12.7859
.(((.((.((......))))))).))	chr5:149826351-149826574(-)$1	1	154	180	12.0335
(.((((.(((......))).)))).)	chr22:50716924-50717154(-)$1	1	12	38	12.1985
.....(((((((...)))))))...)	chr17:5336528-5336750(-)$1	1	42	68	9.0194
...(.((.((......)).)))...)	chr5:96111723-96111942(-)$1	1	138	164	12.9296
((((((((((......)))))))(((	chr6:150057592-150057822(-)$1	1	9	35	10.7107
(..((.((((......)))).))..)	chr10:38407470-38407688(+)$1	1	156	182	11.4591
(.((((((((......))).))))).	chr15:48802226-48802446(-)$1	1	123	149	12.5397
((..((((((......))))))...)	chrX:148564496-148564721(-)$1	1	86	112	13.4383
...(((((((......))))))))))	chr5:133292436-133292663(-)$1	1	21	47	14.1498
.((..((((((......))))))..)	chr14:55618343-55618563(-)$1	1	122	148	11.5160
..((((((.(......).)))))).)	chr19:37240256-37240486(-)$1	1	25	51	13.0946
.((((...(((......)))....))	chr16:71949496-71949717(+)$1	1	82	108	10.9744
((((.(((((......))))))))))	chr1:109441224-109441454(+)$1	1	73	99	11.0681
(((((((((((...))))))))))).	chr9:139371478-139371702(-)$1	1	142	168	9.4694
((..((((.(......).))))..))	chr16:47549332-47549554(+)$1	1	20	46	11.9911
((((..((((......))))...)))	chr6:43170795-43171025(+)$1	1	187	213	11.2551
((((((.(((......)))))).)))	chr10:93257787-93258009(+)$1	1	87	113	12.5478
.(((((((((......))))))))).	chr3:43743675-43743898(+)$1	1	133	159	13.7382

#PSSM
d : 0.12	c : 0.10	" : 0.10	f : 0.08	# : 0.07	[ : 0.07	b : 0.07	g : 0.05	! : 0.05	e : 0.03	= : 0.03	$ : 0.03	o : 0.01	a : 0.01	F : 0.01	: : 0.01	+ : 0.01	% : 0.01	i : 0.01	E : 0.01	
d : 0.14	c : 0.14	f : 0.08	" : 0.08	i : 0.07	b : 0.07	! : 0.07	[ : 0.05	a : 0.05	# : 0.03	= : 0.03	g : 0.03	e : 0.03	o : 0.01	% : 0.01	$ : 0.01	E : 0.01	
c : 0.12	! : 0.10	d : 0.10	f : 0.08	[ : 0.08	" : 0.08	i : 0.07	e : 0.07	# : 0.03	= : 0.03	g : 0.03	a : 0.03	b : 0.03	o : 0.01	% : 0.01	$ : 0.01	E : 0.01	
g : 0.16	! : 0.12	c : 0.12	e : 0.12	d : 0.08	f : 0.08	i : 0.07	= : 0.03	" : 0.03	[ : 0.03	b : 0.03	# : 0.01	% : 0.01	$ : 0.01	a : 0.01	
g : 0.17	f : 0.12	d : 0.10	e : 0.10	! : 0.08	[ : 0.08	i : 0.07	c : 0.05	b : 0.05	= : 0.03	# : 0.01	" : 0.01	a : 0.01	% : 0.01	$ : 0.01	
g : 0.19	f : 0.16	e : 0.16	d : 0.08	c : 0.08	i : 0.07	b : 0.07	! : 0.05	= : 0.03	[ : 0.03	a : 0.01	" : 0.01	
g : 0.19	f : 0.16	e : 0.14	d : 0.12	[ : 0.12	i : 0.07	b : 0.07	c : 0.05	! : 0.01	" : 0.01	= : 0.01	
c : 0.24	g : 0.17	f : 0.14	d : 0.10	e : 0.10	i : 0.07	[ : 0.07	b : 0.01	! : 0.01	" : 0.01	= : 0.01	
c : 0.23	g : 0.17	b : 0.14	f : 0.10	[ : 0.10	d : 0.07	i : 0.07	e : 0.05	! : 0.01	= : 0.01	
c : 0.23	g : 0.17	b : 0.14	a : 0.12	f : 0.10	d : 0.07	i : 0.07	e : 0.05	= : 0.01	
o : 0.83	f : 0.03	g : 0.03	i : 0.01	[ : 0.01	n : 0.01	c : 0.01	= : 0.01	
o : 0.89	n : 0.03	i : 0.01	a : 0.01	g : 0.01	l : 0.01	
o : 0.91	l : 0.05	n : 0.03	
o : 0.91	l : 0.05	n : 0.03	
o : 0.91	n : 0.03	l : 0.03	= : 0.01	
o : 0.91	g : 0.03	n : 0.01	i : 0.01	= : 0.01	
c : 0.19	g : 0.17	b : 0.14	a : 0.12	f : 0.07	d : 0.07	i : 0.07	o : 0.07	e : 0.05	= : 0.01	
c : 0.21	g : 0.17	b : 0.14	f : 0.10	] : 0.08	d : 0.07	i : 0.07	e : 0.07	o : 0.01	2 : 0.01	= : 0.01	
c : 0.23	g : 0.17	f : 0.16	d : 0.08	] : 0.08	i : 0.07	e : 0.07	b : 0.05	a : 0.01	2 : 0.01	= : 0.01	
g : 0.19	f : 0.17	e : 0.12	d : 0.10	] : 0.10	i : 0.07	c : 0.07	b : 0.07	2 : 0.05	= : 0.01	
g : 0.19	f : 0.17	e : 0.14	c : 0.10	i : 0.07	2 : 0.05	d : 0.05	] : 0.05	4 : 0.03	= : 0.03	b : 0.03	a : 0.01	3 : 0.01	
g : 0.21	f : 0.17	c : 0.12	e : 0.10	d : 0.07	i : 0.07	b : 0.05	4 : 0.03	= : 0.03	3 : 0.03	a : 0.03	] : 0.01	2 : 0.01	
g : 0.17	f : 0.12	] : 0.10	i : 0.08	c : 0.08	e : 0.08	3 : 0.08	2 : 0.05	d : 0.05	4 : 0.03	= : 0.03	b : 0.03	7 : 0.01	
2 : 0.14	f : 0.10	] : 0.10	i : 0.08	c : 0.08	e : 0.08	3 : 0.08	d : 0.07	a : 0.05	g : 0.05	4 : 0.03	= : 0.03	7 : 0.01	: : 0.01	
d : 0.12	2 : 0.12	] : 0.12	f : 0.10	c : 0.08	i : 0.07	3 : 0.07	: : 0.05	g : 0.05	= : 0.03	b : 0.03	4 : 0.03	e : 0.03	7 : 0.01	a : 0.01	
c : 0.19	d : 0.16	f : 0.12	b : 0.12	: : 0.08	] : 0.05	g : 0.05	= : 0.03	e : 0.03	4 : 0.03	p : 0.01	7 : 0.01	3 : 0.01	2 : 0.01	i : 0.01	

#score	670.4727254996305
#seq	56
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_UTR_m3_run2.txt

#BEAR
#ffffffqqqqqqqqffff	chr12:32943881-32944121(-)$1	240	188	207	13.9629
dddd[bbqqqqqqqqbb]d	chr1:93621878-93622118(-)$1	240	41	60	13.0028
[bb[cccqqqqqqqqccc]	chr19:8483551-8483791(+)$1	240	172	191	13.9171
gggggggqqqqqqqqgggg	chr1:153779177-153779417(-)$1	240	27	46	14.1461
cceeeeeqqqqqqqqeeee	chr5:175953716-175953956(-)$1	240	124	143	14.9238
hh[a[bbqqqqqqqqbb]a	chr14:75549501-75549741(-)$1	240	43	62	12.8739
gffffffqqqqqqqqffff	chr11:118402948-118403188(+)$1	240	108	127	13.8649
!ffffffqqqqqqqqffff	chr19:58199657-58199897(+)$1	240	25	44	14.0723
::eeeeeqqqqqqqqeeee	chrX:154005650-154005890(+)$1	240	219	238	13.4272
gbb[cccqqqqqqqqccc3	chr2:101886046-101886286(+)$1	240	28	47	13.7247
hhhh[bbqqqqqqqqbb]h	chr20:48520212-48520452(-)$1	240	13	32	12.4933
!!eeeeeqqqqqqqqeeee	chr7:140159542-140159782(-)$1	240	27	46	15.3143
J:eeeeeqqqqqqqqeeee	chr12:89916379-89916619(-)$1	240	99	118	12.8501
::eeeeeqqqqqqqqeeee	chr8:77777689-77777942(+)$1	253	152	171	13.4272
ee[ddddqqqqqqqqdddd	chr6:24650244-24650484(-)$1	240	32	51	13.4373
!!eeeeeqqqqqqqqeeee	chr10:88195283-88195523(-)$1	240	99	118	15.3143
iiiiiiiqqqqqqqqiiii	chr7:29960954-29961194(-)$1	240	188	207	13.8676
$$$$cccqqqqqqqqccci	chr4:7058635-7058875(+)$1	240	144	163	13.3670
a[eeeeeqqqqqqqqeeee	chr10:91180607-91180847(+)$1	240	50	69	15.0733
fff[cccqqqqqqqqccc2	chr1:107601629-107601869(+)$1	240	156	175	13.7032
gggddddqqqqqqqqdddd	chr19:57804602-57804842(+)$1	240	83	102	13.6222
[ffffffqqqqqqqqffff	chr17:46626470-46626767(-)$1	297	67	86	13.9977
hhhhcccqqqqqqqqccc]	chr6:82950171-82950411(-)$1	240	204	223	13.3771
"ffffffqqqqqqqqffff	chr15:101717142-101717382(-)$1	240	173	192	13.9911
[ffffffqqqqqqqqffff	chr1:57177214-57177494(+)$1	280	237	256	13.9977
bbeeeeeqqqqqqqqeeee	chr13:25914320-25914560(+)$1	240	96	115	14.5619
ddd[cccqqqqqqqqcccd	chr16:22295326-22295566(+)$1	240	11	30	13.8915
ccc[cccqqqqqqqqcccc	chr18:72913236-72913516(-)$1	280	232	251	14.1520
ddd[cccqqqqqqqqccc]	chr7:102743748-102743988(-)$1	240	114	133	13.9108
!ccc[bbqqqqqqqqbb]c	chr7:1192537-1192777(-)$1	240	144	163	13.4942
dd[ddddqqqqqqqqdddd	chr3:152883378-152883658(+)$1	280	225	244	13.4016
dd[ddddqqqqqqqqdddd	chr15:49171657-49171897(+)$1	240	198	217	13.4016
d:eeeeeqqqqqqqqeeee	chr14:77581832-77582107(+)$1	275	77	96	14.0528
ggggg[aqqqqqqqqa]gg	chr17:65979442-65979682(+)$1	240	50	69	13.7885
gggggggqqqqqqqqgggg	chr12:1896609-1896849(+)$1	240	203	222	14.1461
gggggggqqqqqqqqgggg	chrX:118377621-118377861(+)$1	240	29	48	14.1461
::eeeeeqqqqqqqqeeee	chr1:54387156-54387451(-)$1	295	153	172	13.4272
::eeeeeqqqqqqqqeeee	chr1:16723439-16723679(+)$1	240	111	130	13.4272
ee!!cccqqqqqqqqccce	chr19:32973523-32973803(+)$1	280	205	224	14.2195
!!eeeeeqqqqqqqqeeee	chr1:120457242-120457488(-)$1	246	157	176	15.3143
f"""cccqqqqqqqqccc3	chr16:66968874-66969154(+)$1	280	59	78	13.8548
!!eeeeeqqqqqqqqeeee	chr16:66756028-66756268(-)$1	240	32	51	15.3143
dddd[bbqqqqqqqqbb]d	chr17:19678213-19678453(-)$1	240	73	92	13.0028
!ffffffqqqqqqqqffff	chr2:239359361-239359601(+)$1	240	186	205	14.0723
b!!ddddqqqqqqqqdddd	chr5:180028485-180028765(-)$1	280	214	233	13.5800
eeee[bbqqqqqqqqbb]e	chr5:157182190-157182436(+)$1	246	221	240	13.6231
gggggggqqqqqqqqgggg	chr14:24908875-24909115(+)$1	240	98	117	14.1461
ddd[cccqqqqqqqqcccd	chr5:176562031-176562271(+)$1	240	59	78	13.8915
e!!ddddqqqqqqqqdddd	chr10:90774183-90774423(+)$1	240	65	84	13.6814
ggeeeeeqqqqqqqqeeee	chr11:118394120-118394360(+)$1	240	42	61	14.9615
:ffffffqqqqqqqqffff	chr3:52083302-52083542(-)$1	240	209	228	13.1192
::eeeeeqqqqqqqqeeee	chr15:73044271-73044511(-)$1	240	43	62	13.4272
a[eeeeeqqqqqqqqeeee	chr6:21597893-21598133(+)$1	240	71	90	15.0733
::eeeeeqqqqqqqqeeee	chr20:61827456-61827696(-)$1	240	79	98	13.4272
$$eeeeeqqqqqqqqeeee	chr2:240899657-240899897(-)$1	240	191	210	14.7726
c"""cccqqqqqqqqccc]	chr21:16333904-16334144(-)$1	240	15	34	14.0890
dccc[bbqqqqqqqqbb]c	chr8:92097549-92097789(+)$1	240	146	165	13.1668
!!eeeeeqqqqqqqqeeee	chr10:70102557-70102797(+)$1	240	173	192	15.3143
eeeeeeeqqqqqqqqeeee	chr3:40353590-40353830(+)$1	240	211	230	14.7268
[ffffffqqqqqqqqffff	chr13:98045163-98045403(+)$1	240	124	143	13.9977
##eeeeeqqqqqqqqeeee	chr2:32842964-32843204(+)$1	240	36	55	15.1042
"""ddddqqqqqqqqdddd	chr15:70341951-70342191(-)$1	240	37	56	13.7333
ccc[cccqqqqqqqqcccc	chr1:93618154-93618434(-)$1	280	37	56	14.1520
Gffffffqqqqqqqqffff	chr1:154557141-154557381(-)$1	240	181	200	13.4219
eeee[bbqqqqqqqqbb]e	chr9:36338906-36339146(-)$1	240	19	38	13.6231

#otherMatches

#Seq PSSM
UUUGAAGCAAUUUUUUUUC	chr12:32943881-32944121(-)$1	240	188	207	13.9629
UACAGGUAACUUAAAACAU	chr1:93621878-93622118(-)$1	240	41	60	13.0028
AUUUUGAUUGGCAGUUUAC	chr19:8483551-8483791(+)$1	240	172	191	13.9171
UUCCUUUCCCCUUUAAAAG	chr1:153779177-153779417(-)$1	240	27	46	14.1461
UACUUUUUUUAAAAUGAAA	chr5:175953716-175953956(-)$1	240	124	143	14.9238
GAUCUUCUUUGGUUUGAUG	chr14:75549501-75549741(-)$1	240	43	62	12.8739
CUGGAGGCACCAGCACCUU	chr11:118402948-118403188(+)$1	240	108	127	13.8649
AUUCAGUAUAAUAGCACUG	chr19:58199657-58199897(+)$1	240	25	44	14.0723
UUGGGUUUUCUUGUUGAUC	chrX:154005650-154005890(+)$1	240	219	238	13.4272
AGGUGUCUUGCUGAUGACU	chr2:101886046-101886286(+)$1	240	28	47	13.7247
cuauCUGGUAGAUCACAUG	chr20:48520212-48520452(-)$1	240	13	32	12.4933
CUUUUGAAUUUUUUCUUAG	chr7:140159542-140159782(-)$1	240	27	46	15.3143
UGAAGAUUGUAUUUUAUUU	chr12:89916379-89916619(-)$1	240	99	118	12.8501
GAAAGUAGUACUGUAUACU	chr8:77777689-77777942(+)$1	253	152	171	13.4272
AUUCAUGUUUGUAGUCAUG	chr6:24650244-24650484(-)$1	240	32	51	13.4373
UUUGUUUUGUUUUUUAAAU	chr10:88195283-88195523(-)$1	240	99	118	15.3143
GAAUGUUCAUUUUUAAAUG	chr7:29960954-29961194(-)$1	240	188	207	13.8676
CUCCCUGAUUUUCUACAGC	chr4:7058635-7058875(+)$1	240	144	163	13.3670
CCAGGAAAUCCUAAGUUCC	chr10:91180607-91180847(+)$1	240	50	69	15.0733
UUCGAGCUUCUGUAUGCUA	chr1:107601629-107601869(+)$1	240	156	175	13.7032
UCUUACAGAAGAUUGUGUG	chr19:57804602-57804842(+)$1	240	83	102	13.6222
UCUGGGCCUGCAGAAGUCC	chr17:46626470-46626767(-)$1	297	67	86	13.9977
UAGGAUGAGUUCACCCAUG	chr6:82950171-82950411(-)$1	240	204	223	13.3771
CCACAGAUUCUACCUUUUG	chr15:101717142-101717382(-)$1	240	173	192	13.9911
cuaagguaccuuugagcuu	chr1:57177214-57177494(+)$1	280	237	256	13.9977
CAUGUUUGCCAUACUGAAC	chr13:25914320-25914560(+)$1	240	96	115	14.5619
UAGUCCCAAGCAAACGGGC	chr16:22295326-22295566(+)$1	240	11	30	13.8915
UAAUGGAUAUAAUAUUUCU	chr18:72913236-72913516(-)$1	280	232	251	14.1520
AAAUGUGAGCACAGGCACU	chr7:102743748-102743988(-)$1	240	114	133	13.9108
GUGGAGCCCCAUUGAGCAC	chr7:1192537-1192777(-)$1	240	144	163	13.4942
UUCGUUCUUGUAUUUGAAU	chr3:152883378-152883658(+)$1	280	225	244	13.4016
AACAGUUAUUcuaucaacu	chr15:49171657-49171897(+)$1	240	198	217	13.4016
CAACUAUGUUUCUAAAUAG	chr14:77581832-77582107(+)$1	275	77	96	14.0528
UAAUGCGACAAGAUACACA	chr17:65979442-65979682(+)$1	240	50	69	13.7885
GACUCCAUUAUAUCCUGGG	chr12:1896609-1896849(+)$1	240	203	222	14.1461
UGUUUUAUCUACCUCUAAA	chrX:118377621-118377861(+)$1	240	29	48	14.1461
UUUUUAACAAUAUAUUUAA	chr1:54387156-54387451(-)$1	295	153	172	13.4272
ACUUUCCUUUUAAUUGGAG	chr1:16723439-16723679(+)$1	240	111	130	13.4272
AAAUGUAAUGUGGAGUACU	chr19:32973523-32973803(+)$1	280	205	224	14.2195
UCCCUUGGAGUCUCACAAG	chr1:120457242-120457488(-)$1	246	157	176	15.3143
AGACCCUGGACUGUAAGGA	chr16:66968874-66969154(+)$1	280	59	78	13.8548
AACCACAGUUCACCAUGUG	chr16:66756028-66756268(-)$1	240	32	51	15.3143
CUCUUUGACAAAUUGCACA	chr17:19678213-19678453(-)$1	240	73	92	13.0028
GGAUCCCUACCGGCUGGGA	chr2:239359361-239359601(+)$1	240	186	205	14.0723
AAGAGAUAAUAAUAAAUCU	chr5:180028485-180028765(-)$1	280	214	233	13.5800
CCCUGGAAGAUGAGCUCAA	chr5:157182190-157182436(+)$1	246	221	240	13.6231
AGUGAGACAAUUUAUUUUU	chr14:24908875-24909115(+)$1	240	98	117	14.1461
GAUGCCGGCCCAGGAUGGA	chr5:176562031-176562271(+)$1	240	59	78	13.8915
UGUUUGAAAAGAUUCUUAA	chr10:90774183-90774423(+)$1	240	65	84	13.6814
CAAAACAGCAUCAAAUGUU	chr11:118394120-118394360(+)$1	240	42	61	14.9615
AGUCAGGCCAGGGUCCCUG	chr3:52083302-52083542(-)$1	240	209	228	13.1192
CAGAGCUAAAAACUCAGUU	chr15:73044271-73044511(-)$1	240	43	62	13.4272
GUAAAUCGCUGUUUGGAUU	chr6:21597893-21598133(+)$1	240	71	90	15.0733
UUAAUGAUUUUUUGUUCAU	chr20:61827456-61827696(-)$1	240	79	98	13.4272
AAAACCAAAACAAGCUGGU	chr2:240899657-240899897(-)$1	240	191	210	14.7726
UAUACAGUUGCAAGUCUGG	chr21:16333904-16334144(-)$1	240	15	34	14.0890
UUCAGUUGUUUAAAGAAGU	chr8:92097549-92097789(+)$1	240	146	165	13.1668
UUGGGUUUUGUAUCUGAUC	chr10:70102557-70102797(+)$1	240	173	192	15.3143
GUUGUAUUAAACCAUGUAC	chr3:40353590-40353830(+)$1	240	211	230	14.7268
UAUUUAUCUUAUAUCGUAG	chr13:98045163-98045403(+)$1	240	124	143	13.9977
AAGGCUUCGAAGCACAAGC	chr2:32842964-32843204(+)$1	240	36	55	15.1042
UCCGGUUCCCCCACAGACC	chr15:70341951-70342191(-)$1	240	37	56	13.7333
AGGUCAAUAAGAUCCUUGC	chr1:93618154-93618434(-)$1	280	37	56	14.1520
CAGGGGAUUUUUUUUUCUC	chr1:154557141-154557381(-)$1	240	181	200	13.4219
GCACACUGAUUGCUGAGGG	chr9:36338906-36339146(-)$1	240	19	38	13.6231

#DB
.((((((........))))	chr12:32943881-32944121(-)$1	1	188	207	13.9629
((((.((........)).)	chr1:93621878-93622118(-)$1	1	41	60	13.0028
.((.(((........))).	chr19:8483551-8483791(+)$1	1	172	191	13.9171
(((((((........))))	chr1:153779177-153779417(-)$1	1	27	46	14.1461
(((((((........))))	chr5:175953716-175953956(-)$1	1	124	143	14.9238
((.(.((........)).)	chr14:75549501-75549741(-)$1	1	43	62	12.8739
)((((((........))))	chr11:118402948-118403188(+)$1	1	108	127	13.8649
.((((((........))))	chr19:58199657-58199897(+)$1	1	25	44	14.0723
..(((((........))))	chrX:154005650-154005890(+)$1	1	219	238	13.4272
(((.(((........))).	chr2:101886046-101886286(+)$1	1	28	47	13.7247
((((.((........)).)	chr20:48520212-48520452(-)$1	1	13	32	12.4933
..(((((........))))	chr7:140159542-140159782(-)$1	1	27	46	15.3143
(.(((((........))))	chr12:89916379-89916619(-)$1	1	99	118	12.8501
..(((((........))))	chr8:77777689-77777942(+)$1	1	152	171	13.4272
((.((((........))))	chr6:24650244-24650484(-)$1	1	32	51	13.4373
..(((((........))))	chr10:88195283-88195523(-)$1	1	99	118	15.3143
(((((((........))))	chr7:29960954-29961194(-)$1	1	188	207	13.8676
....(((........))))	chr4:7058635-7058875(+)$1	1	144	163	13.3670
(.(((((........))))	chr10:91180607-91180847(+)$1	1	50	69	15.0733
(((.(((........))).	chr1:107601629-107601869(+)$1	1	156	175	13.7032
(((((((........))))	chr19:57804602-57804842(+)$1	1	83	102	13.6222
.((((((........))))	chr17:46626470-46626767(-)$1	1	67	86	13.9977
(((((((........))).	chr6:82950171-82950411(-)$1	1	204	223	13.3771
.((((((........))))	chr15:101717142-101717382(-)$1	1	173	192	13.9911
.((((((........))))	chr1:57177214-57177494(+)$1	1	237	256	13.9977
(((((((........))))	chr13:25914320-25914560(+)$1	1	96	115	14.5619
(((.(((........))))	chr16:22295326-22295566(+)$1	1	11	30	13.8915
(((.(((........))))	chr18:72913236-72913516(-)$1	1	232	251	14.1520
(((.(((........))).	chr7:102743748-102743988(-)$1	1	114	133	13.9108
.(((.((........)).)	chr7:1192537-1192777(-)$1	1	144	163	13.4942
((.((((........))))	chr3:152883378-152883658(+)$1	1	225	244	13.4016
((.((((........))))	chr15:49171657-49171897(+)$1	1	198	217	13.4016
).(((((........))))	chr14:77581832-77582107(+)$1	1	77	96	14.0528
(((((.(........).))	chr17:65979442-65979682(+)$1	1	50	69	13.7885
(((((((........))))	chr12:1896609-1896849(+)$1	1	203	222	14.1461
(((((((........))))	chrX:118377621-118377861(+)$1	1	29	48	14.1461
..(((((........))))	chr1:54387156-54387451(-)$1	1	153	172	13.4272
..(((((........))))	chr1:16723439-16723679(+)$1	1	111	130	13.4272
((..(((........))))	chr19:32973523-32973803(+)$1	1	205	224	14.2195
..(((((........))))	chr1:120457242-120457488(-)$1	1	157	176	15.3143
(...(((........))).	chr16:66968874-66969154(+)$1	1	59	78	13.8548
..(((((........))))	chr16:66756028-66756268(-)$1	1	32	51	15.3143
((((.((........)).)	chr17:19678213-19678453(-)$1	1	73	92	13.0028
.((((((........))))	chr2:239359361-239359601(+)$1	1	186	205	14.0723
(..((((........))))	chr5:180028485-180028765(-)$1	1	214	233	13.5800
((((.((........)).)	chr5:157182190-157182436(+)$1	1	221	240	13.6231
(((((((........))))	chr14:24908875-24909115(+)$1	1	98	117	14.1461
(((.(((........))))	chr5:176562031-176562271(+)$1	1	59	78	13.8915
(..((((........))))	chr10:90774183-90774423(+)$1	1	65	84	13.6814
))(((((........))))	chr11:118394120-118394360(+)$1	1	42	61	14.9615
.((((((........))))	chr3:52083302-52083542(-)$1	1	209	228	13.1192
..(((((........))))	chr15:73044271-73044511(-)$1	1	43	62	13.4272
(.(((((........))))	chr6:21597893-21598133(+)$1	1	71	90	15.0733
..(((((........))))	chr20:61827456-61827696(-)$1	1	79	98	13.4272
..(((((........))))	chr2:240899657-240899897(-)$1	1	191	210	14.7726
(...(((........))).	chr21:16333904-16334144(-)$1	1	15	34	14.0890
((((.((........)).)	chr8:92097549-92097789(+)$1	1	146	165	13.1668
..(((((........))))	chr10:70102557-70102797(+)$1	1	173	192	15.3143
(((((((........))))	chr3:40353590-40353830(+)$1	1	211	230	14.7268
.((((((........))))	chr13:98045163-98045403(+)$1	1	124	143	13.9977
..(((((........))))	chr2:32842964-32843204(+)$1	1	36	55	15.1042
...((((........))))	chr15:70341951-70342191(-)$1	1	37	56	13.7333
(((.(((........))))	chr1:93618154-93618434(-)$1	1	37	56	14.1520
)((((((........))))	chr1:154557141-154557381(-)$1	1	181	200	13.4219
((((.((........)).)	chr9:36338906-36339146(-)$1	1	19	38	13.6231

#PSSM
d : 0.13	g : 0.13	! : 0.12	: : 0.10	e : 0.09	[ : 0.06	c : 0.06	h : 0.04	# : 0.03	$ : 0.03	a : 0.03	f : 0.03	" : 0.03	b : 0.03	J : 0.01	i : 0.01	G : 0.01	
f : 0.16	: : 0.12	d : 0.10	g : 0.10	! : 0.10	c : 0.07	e : 0.07	b : 0.04	h : 0.04	" : 0.04	$ : 0.03	[ : 0.03	i : 0.01	# : 0.01	
e : 0.35	f : 0.16	g : 0.09	d : 0.07	[ : 0.06	c : 0.06	! : 0.04	" : 0.04	b : 0.03	h : 0.03	i : 0.01	$ : 0.01	
e : 0.35	f : 0.15	d : 0.13	[ : 0.12	g : 0.07	h : 0.03	c : 0.03	" : 0.03	a : 0.01	i : 0.01	$ : 0.01	! : 0.01	
e : 0.32	c : 0.20	f : 0.15	[ : 0.12	d : 0.10	g : 0.07	i : 0.01	
e : 0.32	c : 0.20	f : 0.15	b : 0.12	d : 0.10	g : 0.06	i : 0.01	[ : 0.01	
e : 0.32	c : 0.20	f : 0.15	b : 0.12	d : 0.10	g : 0.06	i : 0.01	a : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.32	c : 0.20	f : 0.15	b : 0.12	d : 0.10	g : 0.06	i : 0.01	a : 0.01	
e : 0.32	c : 0.20	f : 0.15	b : 0.12	d : 0.10	g : 0.06	i : 0.01	] : 0.01	
e : 0.32	c : 0.20	f : 0.15	] : 0.12	d : 0.10	g : 0.07	i : 0.01	
e : 0.36	d : 0.16	f : 0.15	g : 0.07	] : 0.06	c : 0.06	3 : 0.03	i : 0.03	a : 0.01	h : 0.01	2 : 0.01	

#score	906.3636635356021
#seq	65
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_CDS_m1_run1.txt

#BEAR
ccc^^^^^^^^^^^^^^^^^^^^^^^^ccc22	chr3:20189373-20189599(-)$1	226	127	159	37.8933
===^^^^^^^^^^^^^^^^^^^^^^=======	chr12:64879100-64879335(+)$1	235	83	115	36.6085
f^^^^^^^^^^^^^^^^^^^^^^^^^^^ffff	chrM:7033-7262(+)$1	229	100	132	38.5558
c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^c	chr4:84383542-84383777(+)$1	235	115	147	39.2601
g^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^g	chr8:71499066-71499287(-)$1	221	101	133	39.4081
ggggg^^^^^^^^^^^^^^^^^^^^^^ggggg	chr19:9676517-9676752(-)$1	235	120	152	36.8485
c!!dddd^^^^^^^^^^^^^^^^^^^^^^^^d	chr13:103443207-103443436(-)$1	229	65	97	35.2021
ddddd^^^^^^^^^^^^^^^^^^^^^^dddd]	chrX:23412090-23412316(-)$1	226	94	126	35.6129
eeeee^^^^^^^^^^^^^^^^^^^^eeeee22	chr2:74392249-74392468(-)$1	219	101	133	34.5122
^^^^^^^^^^^^^^^^^^^^^^^^^^^ccc22	chrM:4622-4840(+)$1	218	64	96	38.4675
d^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr8:81412405-81412633(+)$1	228	80	112	39.2610
d^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr17:48941237-48941455(-)$1	218	3	35	39.2610
g!!ccc^^^^^^^^^^^^^^^^^^^^^ccc]g	chr19:32930598-32930825(+)$1	227	102	134	36.7089
f^^^^^^^^^^^^^^^^^^^^^^^^^ffffff	chr2:190323381-190323599(+)$1	218	26	58	37.1882
g[eeeee^^^^^^^^^^^^^^^^^^^eeeee]	chr1:87188198-87188422(+)$1	224	185	217	33.7133
^^^^^^^^^^^^^^^^^^^^^^^^^dddd333	chr1:171553521-171553739(+)$1	218	180	212	36.3723
ee[bb^^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:10963-11187(+)$1	224	132	164	37.4946
:ffffff^^^^^^^^^^^^^^^^^^^^fffff	chr3:156262055-156262289(-)$1	234	179	211	32.8294
ddd^^^^^^^^^^^^^^^^^^^^^^^dddd22	chr1:24112725-24112957(+)$1	232	108	140	36.0402
ffffff^^^^^^^^^^^^^^^^^^^^ffffff	chr16:11933547-11933771(-)$1	224	173	205	34.0774
$$$ccc^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:8966-9206(+)$1	240	101	133	36.7591
g^^^^^^^^^^^^^^^^^^^^^^^^^^ggggg	chr3:101284241-101284462(+)$1	221	184	216	38.6568
ffffff^^^^^^^^^^^^^^^^^^^^^fffff	chr14:61180503-61180729(-)$1	226	122	154	35.0306
=[ccc^^^^^^^^^^^^^^^^^^^^^^^ccc]	chr6:170103987-170104211(+)$1	224	54	86	37.5776
h^^^^^^^^^^^^^^^^^^^^^^^^^^hhhhh	chr8:66651696-66651916(-)$1	220	54	86	36.9839
eeeee^^^^^^^^^^^^^^^^^^^eeeeeccc	chr16:66836849-66837075(-)$1	226	97	129	32.8797
eeeee^^^^^^^^^^^^^^^^^^^^^^^eeee	chr16:15138090-15138317(-)$1	227	131	163	36.7774
hhhhhhh^^^^^^^^^^^^^^^^^^^hhhhhh	chr12:104333281-104333503(+)$1	222	84	116	29.3157
""eeeee^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:9209-9430(+)$1	221	93	125	35.5717
^^^^^^^^^^^^^^^^^^^^^^^^ffffff22	chr10:116623275-116623511(+)$1	236	102	134	34.4892
=======^^^^^^^^^^^^^^^^^^^^=====	chr4:41951235-41951457(+)$1	222	92	124	35.4832
ggggggg^^^^^^^^^^^^^^^^^^ggggggg	chr1:213037082-213037305(+)$1	223	92	124	32.5500
c^^^^^^^^^^^^^^^^^^^^^^^ccc]bb]g	chr12:122701288-122701512(-)$1	224	104	136	35.1113
"ffffff^^^^^^^^^^^^^^^^^^ffffff3	chr16:46726195-46726415(+)$1	220	94	126	32.0379
e^^^^^^^^^^^^^^^^^^^^^^^^^^^^eee	chrM:9770-10007(+)$1	237	69	101	38.8755
##eeeee^^^^^^^^^^^^^^^^^^eeeeedd	chr3:38739832-38740051(-)$1	219	141	173	32.1781
e"""bb^^^^^^^^^^^^^^^^^^^^^^^^^^	chr7:64864573-64864794(+)$1	221	102	134	37.1324
e^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr9:14658656-14658879(-)$1	223	74	106	39.3650
"ccc[bb^^^^^^^^^^^^^^^^^^bb]cccf	chr5:102440195-102440420(-)$1	225	123	155	32.6245
a[bb^^^^^^^^^^^^^^^^^^^^^^^^bb]a	chr10:38406535-38406755(+)$1	220	118	150	37.3300
[bbbb^^^^^^^^^^^^^^^^^^^^bb]bb]g	chr10:35857985-35858203(+)$1	218	92	124	34.0349
d^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:6382-6605(+)$1	223	3	35	39.2610
=======^^^^^^^^^^^^^^^^^^^^=====	chr14:74363103-74363332(+)$1	229	13	45	35.4832
iiiiiii^^^^^^^^^^^^^^^^^^^iiiiii	chr16:54317462-54317682(-)$1	220	91	123	33.5513
$$$$$bb^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:64951332-64951563(+)$1	231	150	182	35.5105
ee^^^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr7:99144614-99144839(-)$1	225	13	45	38.3225
eeeee^^^^^^^^^^^^^^^^^^^^^^^^eee	chr6:111697234-111697455(-)$1	221	20	52	36.9901
ggggg^^^^^^^^^^^^^^^^^^^^^^ggggg	chr10:98286912-98287137(-)$1	225	179	211	36.8485
e!!bbbb^^^^^^^^^^^^^^^^^^bb]bb22	chr8:42711327-42711553(-)$1	226	92	124	32.5633
eeeee^^^^^^^^^^^^^^^^^^^^eeeee66	chr2:20234628-20234847(-)$1	219	164	196	33.9398
f^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:6286-6511(+)$1	225	99	131	39.2738
gggggg^^^^^^^^^^^^^^^^^^^^^ggggg	chr10:70959948-70960172(+)$1	224	112	144	35.8542
gggg^^^^^^^^^^^^^^^^^^^^^^^ggggg	chr19:44739410-44739641(+)$1	231	103	135	37.4530
^^^^^^^^^^^^^^^^^^^^^^^^^iiiiiii	chr7:82543847-82544075(-)$1	228	109	141	36.3363
ee[bb^^^^^^^^^^^^^^^^^^^^bb]eeee	chr8:53536163-53536385(-)$1	222	94	126	34.4623
ii^^^^^^^^^^^^^^^^^^^^^^^iiiiiii	chr7:94167020-94167253(+)$1	233	97	129	36.2102
iiiiiii^^^^^^^^^^^^^^^^^^iiiiiii	chr1:78414438-78414676(-)$1	238	185	217	32.3843
ddd^^^^^^^^^^^^^^^^^^^^^^^^^dddd	chr13:39587158-39587379(-)$1	221	185	217	37.1658
d[a^^^^^^^^^^^^^^^^^^^^^^^^^^^a]	chr21:26959969-26960189(-)$1	220	90	122	38.9346
fff^^^^^^^^^^^^^^^^^^^^^^^^fffff	chr1:201824118-201824354(+)$1	236	193	225	37.2980
ii[ccc^^^^^^^^^^^^^^^^^^^ccc]iii	chr11:107375508-107375726(-)$1	218	14	46	34.3340

#otherMatches

#Seq PSSM
GUUUCCAGCCUGUCUCUCCUAUACGUCAACAA	chr3:20189373-20189599(-)$1	226	127	159	37.8933
UGAUUUUUUCAAAAAGUUUUCUUUCUCAUUUU	chr12:64879100-64879335(+)$1	235	83	115	36.6085
CAAAAUCCAUUUCACUAUCAUAUUCAUCGGCG	chrM:7033-7262(+)$1	229	100	132	38.5558
CUUCAUCUUUUCAAUUUCUUCAUCUGUUUCUG	chr4:84383542-84383777(+)$1	235	115	147	39.2601
AUUUCUUUUCCACAUUUCCCGCCUGUUUUAUU	chr8:71499066-71499287(-)$1	221	101	133	39.4081
AUUUAAAAACACACUGAAGAAAAACUCUGAAU	chr19:9676517-9676752(-)$1	235	120	152	36.8485
ACUCAGUAGAAAACACCCAGAACUCAUAGACG	chr13:103443207-103443436(-)$1	229	65	97	35.2021
CAGGAUUUUUCUUCUCUUUCCUUUUUUUCUUA	chrX:23412090-23412316(-)$1	226	94	126	35.6129
AACUCUUUUUCCUUCUAAGAUUGGUGAGUUAA	chr2:74392249-74392468(-)$1	219	101	133	34.5122
GCUAUCCUCUUCAACAAUAUACUCUCCGGACA	chrM:4622-4840(+)$1	218	64	96	38.4675
AAAACCAAACUACAAAAAGAUUUAUUUAUAAU	chr8:81412405-81412633(+)$1	228	80	112	39.2610
CAAACUGAACAUCuuuuuuuuuuuuuuuuuuu	chr17:48941237-48941455(-)$1	218	3	35	39.2610
UUUUCAUAUCAACUUUUCUCUUUAGUCUGACA	chr19:32930598-32930825(+)$1	227	102	134	36.7089
UUUACUUAACUACAUCACCACUUAUCAAGAGA	chr2:190323381-190323599(+)$1	218	26	58	37.1882
AGUAAAAUCAUUUAGAUAUAUAUACUUUUUAA	chr1:87188198-87188422(+)$1	224	185	217	33.7133
UAUUAUUAUUUUUAUUGCUUUUGUUAUUGUUU	chr1:171553521-171553739(+)$1	218	180	212	36.3723
CACAGAACUAAUCAUAUUUUAUAUCUUCUUCG	chrM:10963-11187(+)$1	224	132	164	37.4946
UUCAACCCCACAGUGUAUCCUUUUCAAGGUUG	chr3:156262055-156262289(-)$1	234	179	211	32.8294
UCUCAAUUCAUAUUUCAAAAAACUUCGGAGCA	chr1:24112725-24112957(+)$1	232	108	140	36.0402
AGCUGGUACCAAUAGGAAAGAAGACUCCAGCU	chr16:11933547-11933771(-)$1	224	173	205	34.0774
AUAUCAACCAUUAACCUUCCCUCUACACUUAU	chrM:8966-9206(+)$1	240	101	133	36.7591
CAAAUUGCUUUUAACAUCAACAGAAAAGUCUC	chr3:101284241-101284462(+)$1	221	184	216	38.6568
CUCAGUCCCUCUACACUACUAAAUCCCACUGA	chr14:61180503-61180729(-)$1	226	122	154	35.0306
AAAUGGCACCAAAUAUUCCACUUAAAUGCAUA	chr6:170103987-170104211(+)$1	224	54	86	37.5776
ACUAAUGUAAUGUCUCUUCUUUCUUUUUAGGA	chr8:66651696-66651916(-)$1	220	54	86	36.9839
UGUAAUUUUUAAUAAUACUUACAUUUACAGUG	chr16:66836849-66837075(-)$1	226	97	129	32.8797
GUUCAUUUUUUUUUUCUUUCCCCCAAAUUGGA	chr16:15138090-15138317(-)$1	227	131	163	36.7774
AAGAUGAAUACAAAGCUUUCUACAAAUCAUUU	chr12:104333281-104333503(+)$1	222	84	116	29.3157
CAUGUGAUUUCACUUCCACUCCAUAACGCUCC	chrM:9209-9430(+)$1	221	93	125	35.5717
UUCAUCCCUUCUUUUUUCUUUUAUAUUUAGUU	chr10:116623275-116623511(+)$1	236	102	134	34.4892
AAGUUUGCUCCAACCUUUUAUAUACUAUAGAU	chr4:41951235-41951457(+)$1	222	92	124	35.4832
GCUGUUGCCACACUUUUAUUUAUUUUAACAGC	chr1:213037082-213037305(+)$1	223	92	124	32.5500
UACCUUAACUUCUCUUUACCGACAAUAUACAA	chr12:122701288-122701512(-)$1	224	104	136	35.1113
ACAGGCUUAUUUAAUUAAACUUUCUGGUUUGA	chr16:46726195-46726415(+)$1	220	94	126	32.0379
CUCAACUUUCCUCACUAUCUGCUUCAUCCGCC	chrM:9770-10007(+)$1	237	69	101	38.8755
AUGAUGUCCCUGCCUGCCCUCUUCAACAUCGG	chr3:38739832-38740051(-)$1	219	141	173	32.1781
CAACCCUUAUUACACAUCAGAUAAUUUAUACU	chr7:64864573-64864794(+)$1	221	102	134	37.1324
CACUGAUGUUUUCUUUCUGCCACUAUUACUAU	chr9:14658656-14658879(-)$1	223	74	106	39.3650
AUGGACCUCCUCAGAAAAUAAUAAUGGACCAA	chr5:102440195-102440420(-)$1	225	123	155	32.6245
AGCAAACACAUCCAAGAGAAAACCACUAUGGU	chr10:38406535-38406755(+)$1	220	118	150	37.3300
UCCCCAGCCAUCAUCUCUUAACUACGGAGGCC	chr10:35857985-35858203(+)$1	218	92	124	34.0349
CCAUCAAUUUCAUCACAACAAUUAUCAAUAUA	chrM:6382-6605(+)$1	223	3	35	39.2610
AGAGCUCAGACUGUACAGAAAUCCCCGGAGUU	chr14:74363103-74363332(+)$1	229	13	45	35.4832
AAAAAAAACAAAAAAACAAAAAAAACUUUUUU	chr16:54317462-54317682(-)$1	220	91	123	33.5513
AAUUUGauuuuuuauuauaaauuuuuauaCUU	chr5:64951332-64951563(+)$1	231	150	182	35.5105
uauugcaacacaucgaagagaacauuauuaau	chr7:99144614-99144839(-)$1	225	13	45	38.3225
ACUUUUCUGACUUAAAUCAUUCAAAAAAUAAA	chr6:111697234-111697455(-)$1	221	20	52	36.9901
AAUUCUUUGAACAUCAUGAGUAAAUCUGAGUU	chr10:98286912-98287137(-)$1	225	179	211	36.8485
AAUGGGAGCUUUUUUCUAUCUUAUAUCACCUC	chr8:42711327-42711553(-)$1	226	92	124	32.5633
GUGAAUCUAAACCUUUUUGCUGCCUUUCACCU	chr2:20234628-20234847(-)$1	219	164	196	33.9398
CCAUCAAUUUCAUCACAACAAUUAUCAAUAUA	chrM:6286-6511(+)$1	225	99	131	39.2738
UCCCUUAUAAAGCCCAGUAUCAAUGAAAAGGG	chr10:70959948-70960172(+)$1	224	112	144	35.8542
UUUCAUUCUUAUCAAUCUAAUCAUACAGGAGA	chr19:44739410-44739641(+)$1	231	103	135	37.4530
AACUCAAACUCUUAUUUUUCUGCAUGUUUAAU	chr7:82543847-82544075(-)$1	228	109	141	36.3363
GCAGUGCUCAUUCAUCACUCCAAAAACAGCAG	chr8:53536163-53536385(-)$1	222	94	126	34.4623
AAAACAAAUUUUAUACACAUUCAUCUUUCUUU	chr7:94167020-94167253(+)$1	233	97	129	36.2102
UUGUGUAUUUCUUAUGUAUCUCUUCUGCACAG	chr1:78414438-78414676(-)$1	238	185	217	32.3843
CUGCCACCUCCACAUCUCUCCCUCAUCCUAGC	chr13:39587158-39587379(-)$1	221	185	217	37.1658
UCCAUUUCCCAUUCUCCUUCUAUUUACUACGC	chr21:26959969-26960189(-)$1	220	90	122	38.9346
UAUGUAGUUUAUUUGAUCUUUAUAGAAAUACC	chr1:201824118-201824354(+)$1	236	193	225	37.2980
CUGUCCCCCGCAUUAAUGACUCUCAGGAAGGA	chr11:107375508-107375726(-)$1	218	14	46	34.3340

#DB
(((........................)))..	chr3:20189373-20189599(-)$1	1	127	159	37.8933
(((......................)))))))	chr12:64879100-64879335(+)$1	1	83	115	36.6085
(...........................))))	chrM:7033-7262(+)$1	1	100	132	38.5558
(..............................)	chr4:84383542-84383777(+)$1	1	115	147	39.2601
(..............................)	chr8:71499066-71499287(-)$1	1	101	133	39.4081
(((((......................)))))	chr19:9676517-9676752(-)$1	1	120	152	36.8485
(..((((........................)	chr13:103443207-103443436(-)$1	1	65	97	35.2021
(((((......................)))).	chrX:23412090-23412316(-)$1	1	94	126	35.6129
(((((....................)))))..	chr2:74392249-74392468(-)$1	1	101	133	34.5122
...........................)))..	chrM:4622-4840(+)$1	1	64	96	38.4675
(...............................	chr8:81412405-81412633(+)$1	1	80	112	39.2610
(...............................	chr17:48941237-48941455(-)$1	1	3	35	39.2610
(..(((.....................))).)	chr19:32930598-32930825(+)$1	1	102	134	36.7089
(.........................))))))	chr2:190323381-190323599(+)$1	1	26	58	37.1882
(.(((((...................))))).	chr1:87188198-87188422(+)$1	1	185	217	33.7133
.........................))))...	chr1:171553521-171553739(+)$1	1	180	212	36.3723
((.((...........................	chrM:10963-11187(+)$1	1	132	164	37.4946
.((((((....................)))))	chr3:156262055-156262289(-)$1	1	179	211	32.8294
(((.......................))))..	chr1:24112725-24112957(+)$1	1	108	140	36.0402
((((((....................))))))	chr16:11933547-11933771(-)$1	1	173	205	34.0774
...(((..........................	chrM:8966-9206(+)$1	1	101	133	36.7591
(..........................)))))	chr3:101284241-101284462(+)$1	1	184	216	38.6568
((((((.....................)))))	chr14:61180503-61180729(-)$1	1	122	154	35.0306
(.(((.......................))).	chr6:170103987-170104211(+)$1	1	54	86	37.5776
(..........................)))))	chr8:66651696-66651916(-)$1	1	54	86	36.9839
(((((...................)))))(((	chr16:66836849-66837075(-)$1	1	97	129	32.8797
(((((.......................))))	chr16:15138090-15138317(-)$1	1	131	163	36.7774
(((((((...................))))))	chr12:104333281-104333503(+)$1	1	84	116	29.3157
..(((((.........................	chrM:9209-9430(+)$1	1	93	125	35.5717
........................))))))..	chr10:116623275-116623511(+)$1	1	102	134	34.4892
(((((((....................)))))	chr4:41951235-41951457(+)$1	1	92	124	35.4832
(((((((..................)))))))	chr1:213037082-213037305(+)$1	1	92	124	32.5500
(.......................))).)).)	chr12:122701288-122701512(-)$1	1	104	136	35.1113
.((((((..................)))))).	chr16:46726195-46726415(+)$1	1	94	126	32.0379
(............................)))	chrM:9770-10007(+)$1	1	69	101	38.8755
..(((((..................)))))))	chr3:38739832-38740051(-)$1	1	141	173	32.1781
(...((..........................	chr7:64864573-64864794(+)$1	1	102	134	37.1324
(...............................	chr9:14658656-14658879(-)$1	1	74	106	39.3650
.(((.((..................)).))))	chr5:102440195-102440420(-)$1	1	123	155	32.6245
(.((........................)).)	chr10:38406535-38406755(+)$1	1	118	150	37.3300
.((((....................)).)).)	chr10:35857985-35858203(+)$1	1	92	124	34.0349
(...............................	chrM:6382-6605(+)$1	1	3	35	39.2610
(((((((....................)))))	chr14:74363103-74363332(+)$1	1	13	45	35.4832
(((((((...................))))))	chr16:54317462-54317682(-)$1	1	91	123	33.5513
.....((.........................	chr5:64951332-64951563(+)$1	1	150	182	35.5105
((..........................))))	chr7:99144614-99144839(-)$1	1	13	45	38.3225
(((((........................)))	chr6:111697234-111697455(-)$1	1	20	52	36.9901
(((((......................)))))	chr10:98286912-98287137(-)$1	1	179	211	36.8485
(..((((..................)).))..	chr8:42711327-42711553(-)$1	1	92	124	32.5633
(((((....................)))))..	chr2:20234628-20234847(-)$1	1	164	196	33.9398
(...............................	chrM:6286-6511(+)$1	1	99	131	39.2738
((((((.....................)))))	chr10:70959948-70960172(+)$1	1	112	144	35.8542
((((.......................)))))	chr19:44739410-44739641(+)$1	1	103	135	37.4530
.........................)))))))	chr7:82543847-82544075(-)$1	1	109	141	36.3363
((.((....................)).))))	chr8:53536163-53536385(-)$1	1	94	126	34.4623
((.......................)))))))	chr7:94167020-94167253(+)$1	1	97	129	36.2102
(((((((..................)))))))	chr1:78414438-78414676(-)$1	1	185	217	32.3843
(((.........................))))	chr13:39587158-39587379(-)$1	1	185	217	37.1658
(.(...........................).	chr21:26959969-26960189(-)$1	1	90	122	38.9346
(((........................)))))	chr1:201824118-201824354(+)$1	1	193	225	37.2980
((.(((...................))).)))	chr11:107375508-107375726(-)$1	1	14	46	34.3340

#PSSM
e : 0.19	g : 0.14	d : 0.11	f : 0.09	c : 0.06	= : 0.06	^ : 0.06	i : 0.06	" : 0.04	$ : 0.03	h : 0.03	: : 0.01	# : 0.01	a : 0.01	[ : 0.01	
^ : 0.27	e : 0.13	g : 0.08	f : 0.08	[ : 0.06	i : 0.06	= : 0.04	! : 0.04	d : 0.04	c : 0.03	$ : 0.03	" : 0.03	h : 0.01	# : 0.01	b : 0.01	
^ : 0.31	e : 0.13	g : 0.08	f : 0.08	c : 0.04	= : 0.04	! : 0.04	d : 0.04	[ : 0.04	$ : 0.03	b : 0.03	i : 0.03	h : 0.01	" : 0.01	a : 0.01	
^ : 0.40	e : 0.13	g : 0.08	c : 0.08	b : 0.08	f : 0.06	d : 0.03	= : 0.03	i : 0.03	h : 0.01	" : 0.01	$ : 0.01	
^ : 0.44	e : 0.13	b : 0.08	g : 0.06	c : 0.06	f : 0.06	d : 0.03	= : 0.03	i : 0.03	h : 0.01	[ : 0.01	$ : 0.01	
^ : 0.63	f : 0.06	b : 0.06	c : 0.04	e : 0.04	= : 0.03	g : 0.03	i : 0.03	d : 0.01	h : 0.01	
^ : 0.75	e : 0.04	b : 0.04	f : 0.03	= : 0.03	i : 0.03	d : 0.01	h : 0.01	g : 0.01	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 0.95	e : 0.01	f : 0.01	c : 0.01	
^ : 0.70	e : 0.06	b : 0.06	i : 0.04	f : 0.03	c : 0.03	= : 0.01	d : 0.01	g : 0.01	
^ : 0.60	e : 0.08	f : 0.06	b : 0.06	i : 0.06	d : 0.03	c : 0.03	= : 0.01	h : 0.01	g : 0.01	
^ : 0.36	f : 0.11	g : 0.09	e : 0.08	] : 0.08	c : 0.06	i : 0.06	= : 0.04	d : 0.04	h : 0.03	
^ : 0.26	f : 0.13	e : 0.13	g : 0.09	c : 0.08	d : 0.06	b : 0.06	i : 0.06	= : 0.04	h : 0.03	] : 0.01	
^ : 0.22	e : 0.14	f : 0.13	c : 0.09	g : 0.09	i : 0.08	b : 0.06	= : 0.04	d : 0.04	h : 0.03	3 : 0.01	
^ : 0.21	f : 0.11	2 : 0.09	g : 0.09	e : 0.09	i : 0.08	] : 0.06	= : 0.04	d : 0.04	c : 0.04	h : 0.03	3 : 0.01	6 : 0.01	a : 0.01	
g : 0.16	^ : 0.16	f : 0.11	2 : 0.09	e : 0.08	i : 0.08	] : 0.06	= : 0.04	d : 0.04	c : 0.03	3 : 0.03	h : 0.03	a : 0.01	6 : 0.01	

#score	2198.259486786613
#seq	61
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_CDS_m1_run1.txt

#BEAR
gggggg^^^^^^^^^^^^^^^^^^^^^	chr17:40986690-40986910(+)$1	220	153	180	26.8797
""eeeeevvvvvvvvvvvvveeeee]b	chr16:29822244-29822466(+)$1	222	151	178	18.5190
c!!ccc^^^^^^^^^^^^^^^^^^ccc	chr19:44680608-44680829(+)$1	221	25	52	25.8663
ggggggxxxxxxxxxxxxxxxgggggg	chr6:26189178-26189425(-)$1	247	47	74	21.7755
ffffff^^^^^^^^^^^^^^^^^^^^^	chr4:123813306-123813530(+)$1	224	93	120	26.5475
!!ddddyyyyyyyyyyyyyyyydddd2	chr6:80626367-80626599(-)$1	232	120	147	22.9967
d[bb"""avvvvvvvvvvvvva333bb	chr1:217793392-217793613(-)$1	221	190	217	19.6313
^^^^^^^^^^^^^^^^^^^^^bb333g	chr3:107938171-107938394(-)$1	223	104	131	22.8686
eeeee^^^^^^^^^^^^^^^^^^^^^^	chr5:71489705-71489929(+)$1	224	0	27	26.3992
d[ccc^^^^^^^^^^^^^^^^^^ccc]	chr1:235599631-235599852(+)$1	221	149	176	25.0900
[bb[cccwwwwwwwwwwwwwwccc]bb	chr10:112341704-112341923(+)$1	219	63	90	20.4734
======^^^^^^^^^^^^^^^^^^^^^	chr14:68118056-68118276(-)$1	220	158	185	26.8925
ggg!!ayyyyyyyyyyyyyyyya22gg	chr9:100760787-100761020(+)$1	233	176	203	24.0282
!a[eeeeevvvvvvvvvvvvveeeee2	chr6:64286739-64286988(+)$1	249	127	154	18.5309
hhh[bb^^^^^^^^^^^^^^^^^^^^^	chr17:57917082-57917312(+)$1	230	92	119	25.8273
####bbwwwwwwwwwwwwwwbb333gg	chr1:29068822-29069055(+)$1	233	62	89	20.8653
!ffffffwwwwwwwwwwwwwwffffff	chr12:57009232-57009452(-)$1	220	9	36	20.5240
""dddd^^^^^^^^^^^^^^^^^^^^^	chr14:92471910-92472133(-)$1	223	92	119	26.4308
dd!!bb^^^^^^^^^^^^^^^^^^^^b	chr11:118971695-118971916(-)$1	221	95	122	25.6018
ggggggxxxxxxxxxxxxxxxgggggg	chr8:91643806-91644028(-)$1	222	150	177	21.7755
"ccc^^^^^^^^^^^^^^^^^^^ccc3	chr19:48260173-48260411(+)$1	238	116	143	25.1440
d[dddd^^^^^^^^^^^^^^^^^^^dd	chr2:86344123-86344355(+)$1	232	84	111	25.3560
:eeeeexxxxxxxxxxxxxxxeeeeed	chr2:71582761-71582985(+)$1	224	89	116	20.3405
"eeeeewwwwwwwwwwwwwweeeeegg	chr1:6295684-6295949(-)$1	265	23	50	20.5496
Deeeeeyyyyyyyyyyyyyyyyeeeee	chr2:112767502-112767728(+)$1	226	195	222	22.2876
ffffff^^^^^^^^^^^^^^^^^^^^^	chr12:50529681-50529904(-)$1	223	5	32	26.5475
GGddddwwwwwwwwwwwwwwddddccc	chr1:19948518-19948742(+)$1	224	40	67	18.8618
&ccc^^^^^^^^^^^^^^^^^^^^^^^	chr10:112655707-112655927(+)$1	220	138	165	25.8670
d[dddd^^^^^^^^^^^^^^^^^^^^^	chr14:62207632-62207861(+)$1	229	96	123	26.2335
:ffffffwwwwwwwwwwwwwwffffff	chr5:162869432-162869657(+)$1	225	145	172	19.3641
hhhhha^^^^^^^^^^^^^^^^^^^^^	chr5:10407180-10407401(+)$1	221	91	118	25.7821
$eeeeexxxxxxxxxxxxxxxeeeee6	chr12:50571680-50571909(-)$1	229	182	209	21.2710
##ccc^^^^^^^^^^^^^^^^^^ccc6	chr19:35175898-35176124(+)$1	226	184	211	25.0786
ddddcccwwwwwwwwwwwwwwccc]dd	chr1:55562533-55562754(-)$1	221	143	170	20.3021
eeee[axxxxxxxxxxxxxxxaeeeee	chrM:15423-15654(+)$1	231	72	99	21.7560
ffffffyyyyyyyyyyyyyyyyfffff	chr9:14120421-14120643(-)$1	222	124	151	23.4550
ffffffyyyyyyyyyyyyyyyyfffff	chr22:36745122-36745344(-)$1	222	96	123	23.4550
i!!ccc^^^^^^^^^^^^^^^^^^^^^	chr12:57458395-57458619(-)$1	224	96	123	26.9182
hhhhhh^^^^^^^^^^^^^^^^^^^hh	chr12:67698382-67698614(+)$1	232	24	51	24.2688
geeeee^^^^^^^^^^^^^^^^^^^^^	chr19:35174922-35175155(+)$1	233	151	178	26.6116
"""cccyyyyyyyyyyyyyyyyccc22	chrX:13790897-13791119(-)$1	222	48	75	23.7153
iiiiiiiivvvvvvvvvvvvviiiiii	chr15:83698918-83699141(-)$1	223	92	119	18.1321
eee[bb^^^^^^^^^^^^^^^^^^^^^	chr2:196545054-196545278(+)$1	224	70	97	26.2261
hhhhhh^^^^^^^^^^^^^^^^^^^^^	chr5:110462405-110462641(+)$1	236	133	160	25.5337
gggggg^^^^^^^^^^^^^^^^^^^^g	chr6:97730162-97730382(-)$1	220	12	39	26.6075
=====[bbuuuuuuuuuuuubb]====	chr10:27415543-27415770(-)$1	227	25	52	18.7997
fffffbbwwwwwwwwwwwwwwbb]fff	chr18:46858226-46858448(-)$1	222	72	99	20.3413
ffffffxxxxxxxxxxxxxxxffffff	chr11:77814973-77815197(-)$1	224	24	51	21.3558
ffffffxxxxxxxxxxxxxxxffffff	chr6:110429631-110429862(-)$1	231	195	222	21.3558
"eeeeeyyyyyyyyyyyyyyyyeeeee	chr5:34933853-34934073(+)$1	220	178	205	23.5874
[eeeee^^^^^^^^^^^^^^^^^^^^^	chr5:162910245-162910472(+)$1	227	97	124	26.7383
ccc[bbxxxxxxxxxxxxxxxbb]ccc	chr19:37240942-37241163(-)$1	221	14	41	21.3488
ff[ccc^^^^^^^^^^^^^^^^^^^^^	chr19:47712332-47712561(+)$1	229	11	38	26.6930
[a!!bb^^^^^^^^^^^^^^^^^^^bb	chr2:42556976-42557201(+)$1	225	49	76	25.6088
g[ccccccvvvvvvvvvvvvvccc]cc	chr3:88104531-88104752(-)$1	221	156	183	19.4402
$$ddddyyyyyyyyyyyyyyyydddd6	chr6:71571259-71571485(+)$1	226	41	68	22.4093
gggggg^^^^^^^^^^^^^^^^^^^^^	chrX:107977028-107977251(-)$1	223	92	119	26.8797
ffffffxxxxxxxxxxxxxxxffffff	chr1:227842919-227843149(+)$1	230	163	190	21.3558
^^^^^^^^^^^^^^^^^^^^^ccc]gg	chr19:32930598-32930825(+)$1	227	108	135	22.6457
ffffff^^^^^^^^^^^^^^^^^^^ff	chr5:134235172-134235396(+)$1	224	170	197	25.9042
[eeeee^^^^^^^^^^^^^^^^^^^ee	chr19:53057793-53058020(+)$1	227	88	115	26.0117
c[dddd^^^^^^^^^^^^^^^^^^ddd	chr1:183085909-183086134(+)$1	225	124	151	24.8731
gggggg^^^^^^^^^^^^^^^^^^ggg	chr13:100189939-100190159(+)$1	220	183	210	25.7807
gggggg^^^^^^^^^^^^^^^^^^^^g	chr15:78786264-78786490(+)$1	226	89	116	26.6075
ffffff^^^^^^^^^^^^^^^^^^^^^	chrM:11028-11448(+)$1	420	245	272	26.5475
ffffffyyyyyyyyyyyyyyyyfffff	chr1:197072802-197073023(-)$1	221	97	124	23.4550
======xxxxxxxxxxxxxxx======	chrX:106959858-106960090(-)$1	232	115	142	22.2123

#otherMatches

#Seq PSSM
CAGUCCCUGACCCCAUUCUUCUCACCA	chr17:40986690-40986910(+)$1	220	153	180	26.8797
AUCGUGUUCCUGUGUCCCCUGCAUGUA	chr16:29822244-29822466(+)$1	222	151	178	18.5190
CAAUCCCAUCAAAGAGUUCAUACAGGA	chr19:44680608-44680829(+)$1	221	25	52	25.8663
UCAUGCUAUUAUAAAAGUGCUGCGUGG	chr6:26189178-26189425(-)$1	247	47	74	21.7755
GAUUGGAAUCUAAUAACUACAAUACUU	chr4:123813306-123813530(+)$1	224	93	120	26.5475
ACUUCUACAUUCGGACAUACAAAGAGC	chr6:80626367-80626599(-)$1	232	120	147	22.9967
CGCAGGAGGAGAAAGGUAAAACGCAUG	chr1:217793392-217793613(-)$1	221	190	217	19.6313
AAUAUCUAACAUACUAUCCGAGCUUCG	chr3:107938171-107938394(-)$1	223	104	131	22.8686
UAAGCACCACCCAUCCUGCCAACAAAG	chr5:71489705-71489929(+)$1	224	0	27	26.3992
AAAGUUCCCCACUGCCCCCCCACACUA	chr1:235599631-235599852(+)$1	221	149	176	25.0900
AGUAUCAGAAGUGGGAUAAAAUGAGAC	chr10:112341704-112341923(+)$1	219	63	90	20.4734
UCUUUCGCAGCCAUUGAACUUCUAUAG	chr14:68118056-68118276(-)$1	220	158	185	26.8925
AGUAACUGAGAAUUUGGAAACUGGAAC	chr9:100760787-100761020(+)$1	233	176	203	24.0282
GCGACCUUAAACAAAUUUAUAGAGGUA	chr6:64286739-64286988(+)$1	249	127	154	18.5309
UGGUGUGUUACUUCAUCCUAUCUAUCA	chr17:57917082-57917312(+)$1	230	92	119	25.8273
UUUUGAUUUGCCUUUUUUUUUCUUCCA	chr1:29068822-29069055(+)$1	233	62	89	20.8653
AAGUUGCUUGCCUACAUAUCUGUAACU	chr12:57009232-57009452(-)$1	220	9	36	20.5240
AACAUGAGCAUUUAAUUAAACUCAAUC	chr14:92471910-92472133(-)$1	223	92	119	26.4308
UGCUGUUUUCCUUAUCAUCCUCUUCUG	chr11:118971695-118971916(-)$1	221	95	122	25.6018
ACCCAGCUUCUGAAUUCUUACUUGGGU	chr8:91643806-91644028(-)$1	222	150	177	21.7755
UUCAAUAAAAAAUCUCUUCUAGCUGAU	chr19:48260173-48260411(+)$1	238	116	143	25.1440
GAGAAUGUGGCCAAGUUUAUUAUUAAU	chr2:86344123-86344355(+)$1	232	84	111	25.3560
UUGGAUUCAGCAUCAAAAUACAUCUAC	chr2:71582761-71582985(+)$1	224	89	116	20.3405
CUCAGCCUCGCCACCUUCCUGCUGGGC	chr1:6295684-6295949(-)$1	265	23	50	20.5496
CCAGGACAACCAAAUCAUCUAAUCUUG	chr2:112767502-112767728(+)$1	226	195	222	22.2876
CUAGGGCCCAGCUUUUACCUCCCUCUU	chr12:50529681-50529904(-)$1	223	5	32	26.5475
AUGAGAUUUAGCAUGUUUUUUCUCCCU	chr1:19948518-19948742(+)$1	224	40	67	18.8618
GUACUUUAUUUAAAUACUACUUUCUCA	chr10:112655707-112655927(+)$1	220	138	165	25.8670
UUGCAUCUCCAUCUCCUACCCACAUAC	chr14:62207632-62207861(+)$1	229	96	123	26.2335
AAUUUGGUCCGUUAUUAUUCUCCAGAU	chr5:162869432-162869657(+)$1	225	145	172	19.3641
GUGUGCUGCCUAAUUUUCUUCCAUACA	chr5:10407180-10407401(+)$1	221	91	118	25.7821
GCAAAAAUGAAAACGAAGAGAUUUUGG	chr12:50571680-50571909(-)$1	229	182	209	21.2710
UUCUCAUUUCUUGUUCAACAUCAGAGU	chr19:35175898-35176124(+)$1	226	184	211	25.0786
GAGGCAGCACUUACUCACUUUCUGCCC	chr1:55562533-55562754(-)$1	221	143	170	20.3021
UAGGCGACCCAGACAAUUAUACCCUAG	chrM:15423-15654(+)$1	231	72	99	21.7560
UAUCCUCCCCACCUGAAUCCUCAGGAU	chr9:14120421-14120643(-)$1	222	124	151	23.4550
GUGGAUAAAAACUUCAUCAACAAUCCG	chr22:36745122-36745344(-)$1	222	96	123	23.4550
GAAGUCAAAUUUUCUACUACUCUACUG	chr12:57458395-57458619(-)$1	224	96	123	26.9182
UUCACAAACAGAUGAAAGAAAAAAGUG	chr12:67698382-67698614(+)$1	232	24	51	24.2688
AGUaaaaaaaaaaaaaaaaaaaaaaaa	chr19:35174922-35175155(+)$1	233	151	178	26.6116
AAAGCAAAGGAAGAACAGGAACUGCAA	chrX:13790897-13791119(-)$1	222	48	75	23.7153
UGAAGUGGUAAACCUCUUUCUUCAUUU	chr15:83698918-83699141(-)$1	223	92	119	18.1321
GAAAGCAUUUUCACUCACAUAACCACC	chr2:196545054-196545278(+)$1	224	70	97	26.2261
AAGCAUGUGUAUUUUAAAUUAUCUCAA	chr5:110462405-110462641(+)$1	236	133	160	25.5337
AGAACAUGAAGUAAACAAUGGAGAACU	chr6:97730162-97730382(-)$1	220	12	39	26.6075
AAAGUUAUUUGGAAAAUUGUGUCACUU	chr10:27415543-27415770(-)$1	227	25	52	18.7997
UCUUCCAUACACCAGCAAACUUGUGAA	chr18:46858226-46858448(-)$1	222	72	99	20.3413
GCUUAUAUUACUUUCAGCAUCAUAAGU	chr11:77814973-77815197(-)$1	224	24	51	21.3558
CCCCAAACAUUCUUUAUUUCAUUGGGG	chr6:110429631-110429862(-)$1	231	195	222	21.3558
UUCCCAUCCUAGUUUAUGAUGUUGGGA	chr5:34933853-34934073(+)$1	220	178	205	23.5874
AGAACUAUAUAAUAAAACAAAACCUUU	chr5:162910245-162910472(+)$1	227	97	124	26.7383
UCUGCACAUCUUAUUCAACAUUGGAGA	chr19:37240942-37241163(-)$1	221	14	41	21.3488
UUUAGAAUUUUUUUUUCCCUCUAUUCC	chr19:47712332-47712561(+)$1	229	11	38	26.6930
UGUAGCGGAUACUACUCUAACCAAAGC	chr2:42556976-42557201(+)$1	225	49	76	25.6088
AGAUAAAUGUGGAGUAUUAAAGUUAUG	chr3:88104531-88104752(-)$1	221	156	183	19.4402
ACUCCAAACAUCCUCUUCCAUAUGGAU	chr6:71571259-71571485(+)$1	226	41	68	22.4093
AGCUCCUACUUCUCUCUACCAAACCCU	chrX:107977028-107977251(-)$1	223	92	119	26.8797
AAAUGCAAAGAAUGUGGCAAAGCGUUU	chr1:227842919-227843149(+)$1	230	163	190	21.3558
UAUCAACUUUUCUCUUUAGUCUGACAU	chr19:32930598-32930825(+)$1	227	108	135	22.6457
AUUCCAGGACAAGAGCAGGAACAUGUG	chr5:134235172-134235396(+)$1	224	170	197	25.9042
AUGUGGGAAAGCUUUUAAUCAACAAUC	chr19:53057793-53058020(+)$1	227	88	115	26.0117
GAUUGGUAAUUUAGACCUCAUCCCCCA	chr1:183085909-183086134(+)$1	225	124	151	24.8731
UAUAUUAAUGAUAAAAAGUAAACAAGU	chr13:100189939-100190159(+)$1	220	183	210	25.7807
GGAAAACCAGCUCCUAAAACAAUUCAU	chr15:78786264-78786490(+)$1	226	89	116	26.6075
GGCUCACUAAACAUUCUACUACUCACU	chrM:11028-11448(+)$1	420	245	272	26.5475
CAGCUAAUCAAACAACAAUCUAUAGCU	chr1:197072802-197073023(-)$1	221	97	124	23.4550
UCCUUCUUCUCUUCUCUGCUUGGAGGG	chrX:106959858-106960090(-)$1	232	115	142	22.2123

#DB
((((((.....................	chr17:40986690-40986910(+)$1	1	153	180	26.8797
..(((((.............))))).)	chr16:29822244-29822466(+)$1	1	151	178	18.5190
(..(((..................)))	chr19:44680608-44680829(+)$1	1	25	52	25.8663
((((((...............))))))	chr6:26189178-26189425(-)$1	1	47	74	21.7755
((((((.....................	chr4:123813306-123813530(+)$1	1	93	120	26.5475
..((((................)))).	chr6:80626367-80626599(-)$1	1	120	147	22.9967
(.((...(.............)...))	chr1:217793392-217793613(-)$1	1	190	217	19.6313
.....................))...)	chr3:107938171-107938394(-)$1	1	104	131	22.8686
(((((......................	chr5:71489705-71489929(+)$1	1	0	27	26.3992
(.(((..................))).	chr1:235599631-235599852(+)$1	1	149	176	25.0900
.((.(((..............))).))	chr10:112341704-112341923(+)$1	1	63	90	20.4734
((((((.....................	chr14:68118056-68118276(-)$1	1	158	185	26.8925
(((..(................)..))	chr9:100760787-100761020(+)$1	1	176	203	24.0282
.(.(((((.............))))).	chr6:64286739-64286988(+)$1	1	127	154	18.5309
(((.((.....................	chr17:57917082-57917312(+)$1	1	92	119	25.8273
....((..............))...))	chr1:29068822-29069055(+)$1	1	62	89	20.8653
.((((((..............))))))	chr12:57009232-57009452(-)$1	1	9	36	20.5240
..((((.....................	chr14:92471910-92472133(-)$1	1	92	119	26.4308
((..((....................)	chr11:118971695-118971916(-)$1	1	95	122	25.6018
((((((...............))))))	chr8:91643806-91644028(-)$1	1	150	177	21.7755
.(((...................))).	chr19:48260173-48260411(+)$1	1	116	143	25.1440
(.((((...................))	chr2:86344123-86344355(+)$1	1	84	111	25.3560
.(((((...............)))))(	chr2:71582761-71582985(+)$1	1	89	116	20.3405
.(((((..............)))))))	chr1:6295684-6295949(-)$1	1	23	50	20.5496
)(((((................)))))	chr2:112767502-112767728(+)$1	1	195	222	22.2876
((((((.....................	chr12:50529681-50529904(-)$1	1	5	32	26.5475
((((((..............))))(((	chr1:19948518-19948742(+)$1	1	40	67	18.8618
.(((.......................	chr10:112655707-112655927(+)$1	1	138	165	25.8670
(.((((.....................	chr14:62207632-62207861(+)$1	1	96	123	26.2335
.((((((..............))))))	chr5:162869432-162869657(+)$1	1	145	172	19.3641
((((((.....................	chr5:10407180-10407401(+)$1	1	91	118	25.7821
.(((((...............))))).	chr12:50571680-50571909(-)$1	1	182	209	21.2710
..(((..................))).	chr19:35175898-35176124(+)$1	1	184	211	25.0786
(((((((..............))).))	chr1:55562533-55562754(-)$1	1	143	170	20.3021
((((.(...............))))))	chrM:15423-15654(+)$1	1	72	99	21.7560
((((((................)))))	chr9:14120421-14120643(-)$1	1	124	151	23.4550
((((((................)))))	chr22:36745122-36745344(-)$1	1	96	123	23.4550
(..(((.....................	chr12:57458395-57458619(-)$1	1	96	123	26.9182
((((((...................))	chr12:67698382-67698614(+)$1	1	24	51	24.2688
((((((.....................	chr19:35174922-35175155(+)$1	1	151	178	26.6116
...(((................)))..	chrX:13790897-13791119(-)$1	1	48	75	23.7153
((((((((.............))))))	chr15:83698918-83699141(-)$1	1	92	119	18.1321
(((.((.....................	chr2:196545054-196545278(+)$1	1	70	97	26.2261
((((((.....................	chr5:110462405-110462641(+)$1	1	133	160	25.5337
((((((....................)	chr6:97730162-97730382(-)$1	1	12	39	26.6075
(((((.((............)).))))	chr10:27415543-27415770(-)$1	1	25	52	18.7997
(((((((..............)).)))	chr18:46858226-46858448(-)$1	1	72	99	20.3413
((((((...............))))))	chr11:77814973-77815197(-)$1	1	24	51	21.3558
((((((...............))))))	chr6:110429631-110429862(-)$1	1	195	222	21.3558
.(((((................)))))	chr5:34933853-34934073(+)$1	1	178	205	23.5874
.(((((.....................	chr5:162910245-162910472(+)$1	1	97	124	26.7383
(((.((...............)).)))	chr19:37240942-37241163(-)$1	1	14	41	21.3488
((.(((.....................	chr19:47712332-47712561(+)$1	1	11	38	26.6930
.(..((...................))	chr2:42556976-42557201(+)$1	1	49	76	25.6088
(.((((((.............))).))	chr3:88104531-88104752(-)$1	1	156	183	19.4402
..((((................)))).	chr6:71571259-71571485(+)$1	1	41	68	22.4093
((((((.....................	chrX:107977028-107977251(-)$1	1	92	119	26.8797
((((((...............))))))	chr1:227842919-227843149(+)$1	1	163	190	21.3558
.....................))).))	chr19:32930598-32930825(+)$1	1	108	135	22.6457
((((((...................))	chr5:134235172-134235396(+)$1	1	170	197	25.9042
.(((((...................))	chr19:53057793-53058020(+)$1	1	88	115	26.0117
(.((((..................)))	chr1:183085909-183086134(+)$1	1	124	151	24.8731
((((((..................)))	chr13:100189939-100190159(+)$1	1	183	210	25.7807
((((((....................)	chr15:78786264-78786490(+)$1	1	89	116	26.6075
((((((.....................	chrM:11028-11448(+)$1	1	245	272	26.5475
((((((................)))))	chr1:197072802-197073023(-)$1	1	97	124	23.4550
((((((...............))))))	chrX:106959858-106960090(-)$1	1	115	142	22.2123

#PSSM
f : 0.17	g : 0.14	" : 0.08	d : 0.08	[ : 0.05	h : 0.05	c : 0.04	! : 0.04	e : 0.04	= : 0.04	^ : 0.02	# : 0.02	: : 0.02	$ : 0.02	i : 0.02	D : 0.01	G : 0.01	& : 0.01	
f : 0.20	e : 0.16	g : 0.11	[ : 0.08	h : 0.05	" : 0.04	! : 0.04	= : 0.04	c : 0.04	^ : 0.02	a : 0.02	# : 0.02	d : 0.02	b : 0.01	G : 0.01	i : 0.01	$ : 0.01	
f : 0.19	e : 0.17	g : 0.11	d : 0.11	c : 0.08	! : 0.05	h : 0.05	= : 0.04	b : 0.02	^ : 0.02	[ : 0.02	# : 0.01	" : 0.01	i : 0.01	
f : 0.19	e : 0.17	c : 0.13	d : 0.11	g : 0.10	[ : 0.05	= : 0.04	! : 0.04	h : 0.04	^ : 0.02	b : 0.01	# : 0.01	i : 0.01	
f : 0.19	e : 0.16	c : 0.13	g : 0.10	d : 0.10	b : 0.08	^ : 0.05	= : 0.04	h : 0.04	" : 0.01	! : 0.01	[ : 0.01	i : 0.01	
f : 0.17	e : 0.14	g : 0.10	c : 0.10	d : 0.10	^ : 0.10	b : 0.10	a : 0.04	= : 0.02	h : 0.02	" : 0.01	i : 0.01	[ : 0.01	
^ : 0.50	x : 0.14	y : 0.13	c : 0.04	w : 0.04	e : 0.02	f : 0.02	b : 0.02	" : 0.01	i : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.01	a : 0.01	e : 0.01	i : 0.01	b : 0.01	c : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.11	v : 0.07	u : 0.01	
^ : 0.50	x : 0.14	y : 0.13	w : 0.07	v : 0.05	e : 0.02	b : 0.02	d : 0.01	
^ : 0.47	y : 0.13	e : 0.07	b : 0.07	f : 0.07	c : 0.05	g : 0.02	a : 0.02	d : 0.01	i : 0.01	= : 0.01	
^ : 0.47	e : 0.11	f : 0.11	c : 0.07	d : 0.04	b : 0.04	g : 0.02	3 : 0.02	a : 0.01	i : 0.01	] : 0.01	= : 0.01	
^ : 0.43	e : 0.11	c : 0.11	f : 0.11	d : 0.04	3 : 0.04	g : 0.02	= : 0.02	] : 0.02	2 : 0.01	i : 0.01	
^ : 0.38	f : 0.13	e : 0.11	c : 0.10	] : 0.05	g : 0.04	d : 0.04	3 : 0.04	= : 0.02	2 : 0.01	i : 0.01	
^ : 0.31	f : 0.14	c : 0.10	g : 0.10	e : 0.10	d : 0.07	b : 0.04	= : 0.02	] : 0.01	3 : 0.01	h : 0.01	2 : 0.01	i : 0.01	
^ : 0.26	g : 0.14	f : 0.14	b : 0.07	c : 0.05	d : 0.05	e : 0.05	2 : 0.04	6 : 0.04	= : 0.02	] : 0.01	3 : 0.01	h : 0.01	i : 0.01	

#score	1577.1434668245006
#seq	67
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_UTR_m3_run2.txt

#BEAR
fffffqqqqqqqqffffff:	chr12:56666530-56666754(-)$1	224	168	188	12.9588
[ddddqqqqqqqqdddd333	chr18:67755252-67755478(-)$1	226	115	135	14.2756
'ddddqqqqqqqqdddd]ff	chr17:78369479-78369708(-)$1	229	163	183	13.2192
c[cccqqqqqqqqccc]ccc	chr7:155530669-155530891(+)$1	222	104	124	14.8721
cc[bbqqqqqqqqbb]ccc:	chr13:75936601-75936826(-)$1	225	123	143	13.5312
eeeeeqqqqqqqqeeeee33	chr14:97263650-97263869(+)$1	219	63	83	14.1267
eee[aqqqqqqqqa]eeeee	chr16:4666447-4666677(+)$1	230	206	226	13.8525
d[a[aqqqqqqqqaa]dddd	chr16:23678315-23678539(+)$1	224	162	182	13.8367
gggggqqqqqqqqggggggg	chr17:48814249-48814487(+)$1	238	89	109	14.3082
[ddddqqqqqqqqdddda]d	chr3:119813160-119813386(-)$1	226	203	223	13.7952
cccccqqqqqqqqccc4444	chr17:78518938-78519158(+)$1	220	191	211	14.6948
!!cccqqqqqqqqccc22bb	chr1:193028301-193028523(-)$1	222	111	131	14.5199
eeeeeqqqqqqqqeeeeeFF	chr9:115633496-115633720(+)$1	224	198	218	13.1046
[ddddqqqqqqqqddddbbb	chr12:112525398-112525634(-)$1	236	56	76	13.1993
fffffqqqqqqqqffffff2	chr4:37687801-37688064(-)$1	263	123	143	13.6892
gggggqqqqqqqqggggggg	chr3:50127748-50127970(+)$1	222	140	160	14.3082
cc[bbqqqqqqqqbb22ccc	chr2:47388852-47389077(-)$1	225	116	136	14.1626
"""bbqqqqqqqqbbeeeee	chr21:27107583-27107806(-)$1	223	117	137	14.4109
cccccqqqqqqqqccc]ccc	chr5:56531720-56531944(+)$1	224	74	94	14.6689
ee[bbqqqqqqqqbb]eeee	chr14:100259750-100259975(+)$1	225	4	24	14.2995
eeeeeqqqqqqqqeeeee:F	chr19:50185186-50185411(+)$1	225	70	90	12.5696
fffffqqqqqqqqffffff4	chr9:95042979-95043211(-)$1	232	148	168	13.8448
gg[bbqqqqqqqqbb]gggg	chr17:36002176-36002398(-)$1	222	147	167	14.5655
bbcccqqqqqqqqccc]bb]	chr19:1581104-1581333(-)$1	229	81	101	13.8216
eeeeeqqqqqqqqeeeee44	chr3:122283279-122283507(-)$1	228	141	161	13.9793
$$cccqqqqqqqqccc22cc	chr17:3721470-3721698(-)$1	228	18	38	14.4480
[ddddqqqqqqqqdddd]ff	chr11:118972411-118972644(-)$1	233	151	171	13.8732
eee[aqqqqqqqqa]eeeee	chr4:1723207-1723436(+)$1	229	141	161	13.8525
eeeeeqqqqqqqqeeeee]c	chr1:115280549-115280778(-)$1	229	24	44	13.8942
gggggqqqqqqqqggggggg	chr1:145441530-145441762(+)$1	232	51	71	14.3082
fffffqqqqqqqqffffff:	chrX:41205501-41205729(+)$1	228	208	228	12.9588
"ddddqqqqqqqqdddd]ee	chr4:17841613-17841844(+)$1	231	108	128	13.8144
ffcccqqqqqqqqccc]fff	chr17:62499461-62499697(-)$1	236	159	179	14.5100
!!cccqqqqqqqqccc]ddd	chr19:46119961-46120189(-)$1	228	17	37	14.8104
ii[bbqqqqqqqqbbiiiii	chr22:42987922-42988158(-)$1	236	137	157	14.3561
"""bbqqqqqqqqbb]ccce	chr22:38901932-38902175(-)$1	243	160	180	14.5237
fffffqqqqqqqqffffff6	chr8:37636586-37636829(+)$1	243	68	88	13.4537
""cccqqqqqqqqccc333e	chr14:55615047-55615274(-)$1	227	12	32	15.2233
b[cccqqqqqqqqcccbb22	chr22:22020211-22020441(+)$1	230	165	185	13.7761
###bbqqqqqqqqbb4444c	chr12:1025822-1026045(-)$1	223	182	202	14.5015
gggggqqqqqqqqggggggg	chr1:235491198-235491437(-)$1	239	128	148	14.3082
eeeeeqqqqqqqqeeeee22	chr3:194362528-194362757(-)$1	229	137	157	13.6442
bb[bbqqqqqqqqbb]bbdd	chr7:98030184-98030408(-)$1	224	29	49	13.1591
d!!bbqqqqqqqqbb22ddd	chr17:80037252-80037480(-)$1	228	53	73	13.8724
##cccqqqqqqqqccc]hhh	chr15:68583961-68584189(+)$1	228	50	70	14.3480
!ddddqqqqqqqqdddd]cc	chr1:40041937-40042177(-)$1	240	209	229	14.0294
[bbbbqqqqqqqqbb]bb22	chr19:36595434-36595663(+)$1	229	8	28	13.1801
eeeeeqqqqqqqqeeeeeee	chr5:134193494-134193722(+)$1	228	30	50	13.7199
fffffqqqqqqqqffffff2	chr2:176974165-176974387(+)$1	222	9	29	13.6892
!ddddqqqqqqqqdddd]bb	chr19:10250317-10250537(-)$1	220	89	109	13.5287
###bbqqqqqqqqbb22fff	chrX:119763735-119763958(-)$1	223	126	146	14.2112
!!a[aqqqqqqqqa]a22dd	chr20:36662096-36662338(+)$1	242	139	159	14.0972
eeeeeqqqqqqqqeeeee66	chrX:20252774-20253027(-)$1	253	152	172	13.1602
eeeeeqqqqqqqqeeeee44	chr22:30983177-30983457(-)$1	280	133	153	13.9793
gggggqqqqqqqqggggggg	chr3:45763442-45763663(+)$1	221	133	153	14.3082
gggggqqqqqqqqggggggg	chr10:96354453-96354675(+)$1	222	41	61	14.3082
b!!bbqqqqqqqqbb22bb6	chr1:27106998-27107225(+)$1	227	45	65	13.4044
fffffqqqqqqqqffffffd	chr6:99936043-99936271(-)$1	228	127	147	13.6617
dd[bbqqqqqqqqbb]dddd	chr9:95036612-95036833(-)$1	221	145	165	13.7998
!!cccqqqqqqqqccc22a]	chr17:35687092-35687321(-)$1	229	154	174	15.0240
fffffqqqqqqqqffffff]	chr1:41457381-41457603(+)$1	222	64	84	13.8203
c[cccqqqqqqqqcccccc:	chr7:26240094-26240352(-)$1	258	49	69	13.8890
f[cccqqqqqqqqccc]fff	chr2:200322010-200322240(-)$1	230	15	35	14.7464
ee[bbqqqqqqqqbb]eeee	chr17:33679764-33679989(-)$1	225	129	149	14.2995
!!cccqqqqqqqqccc22cc	chr11:62396570-62396797(-)$1	227	71	91	15.0206
:ddddqqqqqqqqddddddd	chr1:204522763-204522987(+)$1	224	109	129	12.4116
"a[bbqqqqqqqqbb]a333	chr17:79634729-79634953(+)$1	224	55	75	14.9365
!!cccqqqqqqqqccc22cc	chr11:62396637-62396867(-)$1	230	141	161	15.0206
)ddddqqqqqqqqddddhhh	chr5:167944865-167945087(+)$1	222	134	154	12.7139
!!cccqqqqqqqqcccbb]f	chr17:40270262-40270496(-)$1	234	131	151	14.4435

#otherMatches

#Seq PSSM
UCACUAUCUCUAGAGUGAGA	chr12:56666530-56666754(-)$1	224	168	188	12.9588
AUUAGGAUCAGCACUGACCA	chr18:67755252-67755478(-)$1	226	115	135	14.2756
GCACUCCAACGUCAGUGGGC	chr17:78369479-78369708(-)$1	229	163	183	13.2192
CCGAGCCAUCUUUUUCUGGA	chr7:155530669-155530891(+)$1	222	104	124	14.8721
CGGCCAUGAAAGAGGAUGCC	chr13:75936601-75936826(-)$1	225	123	143	13.5312
GCCGAGUUACGAGUCGGCGA	chr14:97263650-97263869(+)$1	219	63	83	14.1267
GACACUAUUUGUUGAGUCUU	chr16:4666447-4666677(+)$1	230	206	226	13.8525
AUGUCUUGAAUCUGCUUGAG	chr16:23678315-23678539(+)$1	224	162	182	13.8367
UGUGGUUUUUGUCCUGCGGA	chr17:48814249-48814487(+)$1	238	89	109	14.3082
CAGCCGCUGACAGGGCUCUG	chr3:119813160-119813386(-)$1	226	203	223	13.7952
CUCUGGAAACGUACAGCCUC	chr17:78518938-78519158(+)$1	220	191	211	14.6948
GGGGCGGUGUGUGGCCAGGG	chr1:193028301-193028523(-)$1	222	111	131	14.5199
UUUUGACCAAGCACAAAAGA	chr9:115633496-115633720(+)$1	224	198	218	13.1046
CAGCUGUGAAGAAAGUUCCC	chr12:112525398-112525634(-)$1	236	56	76	13.1993
GCCCUGGGGGAGGAGGGCGA	chr4:37687801-37688064(-)$1	263	123	143	13.6892
GUUACUACAGUACGUGGCUU	chr3:50127748-50127970(+)$1	222	140	160	14.3082
CAUGUGAUGACAAACCUUGG	chr2:47388852-47389077(-)$1	225	116	136	14.1626
UCCAGGACUACAACUCCCGG	chr21:27107583-27107806(-)$1	223	117	137	14.4109
GUCUUUAAAUCCUGAGUAUG	chr5:56531720-56531944(+)$1	224	74	94	14.6689
guggugagcggcggcggcgc	chr14:100259750-100259975(+)$1	225	4	24	14.2995
GUCGGCUCGGGCACCGGCAU	chr19:50185186-50185411(+)$1	225	70	90	12.5696
GUGUUAAUCCAGAAAUGCAA	chr9:95042979-95043211(-)$1	232	148	168	13.8448
GUGUGGAGCAUCACAAACAC	chr17:36002176-36002398(-)$1	222	147	167	14.5655
CACGGAUGAGACGCUGCUGU	chr19:1581104-1581333(-)$1	229	81	101	13.8216
CUGGAAGUAGCUCUCCAGCU	chr3:122283279-122283507(-)$1	228	141	161	13.9793
GCUCAGACUCAGAUGAAAUG	chr17:3721470-3721698(-)$1	228	18	38	14.4480
GCUCAGAUUGGUGUGGGAAG	chr11:118972411-118972644(-)$1	233	151	171	13.8732
CCGGCAACGGGCGGGCGGGC	chr4:1723207-1723436(+)$1	229	141	161	13.8525
GAAGCAAUAUAUCGUUUCGC	chr1:115280549-115280778(-)$1	229	24	44	13.8942
UUUGUAAAUUGUGAUAGGAA	chr1:145441530-145441762(+)$1	232	51	71	14.3082
AUUUGUUUUCUUUUAAGUGG	chrX:41205501-41205729(+)$1	228	208	228	12.9588
CUUUGGAGAAAAUCAAGAUU	chr4:17841613-17841844(+)$1	231	108	128	13.8144
GAAAAGGGUUUUAUUUGUCA	chr17:62499461-62499697(-)$1	236	159	179	14.5100
GCGGCCUCUCUCUGUCAGAU	chr19:46119961-46120189(-)$1	228	17	37	14.8104
UUUGUGAAAAAGGACGAUGC	chr22:42987922-42988158(-)$1	236	137	157	14.3561
UUUUGGGACCAUGCGCGGAG	chr22:38901932-38902175(-)$1	243	160	180	14.5237
GGAGGACUUGGGCCUUUCUG	chr8:37636586-37636829(+)$1	243	68	88	13.4537
AGAAUGUUGAAGAAUUAAUU	chr14:55615047-55615274(-)$1	227	12	32	15.2233
CGCCGCUCCGCCAUGGGGAA	chr22:22020211-22020441(+)$1	230	165	185	13.7761
ACCUCCCCUUCCAGACCCAG	chr12:1025822-1026045(-)$1	223	182	202	14.5015
GGGAUUUUUCGUCGUCCCCC	chr1:235491198-235491437(-)$1	239	128	148	14.3082
ACUCUGACAAAAAGGAGUCA	chr3:194362528-194362757(-)$1	229	137	157	13.6442
UCCUCUGCUCCUCGAAGAAG	chr7:98030184-98030408(-)$1	224	29	49	13.1591
GACCUGAUCAUCAAGAGCCA	chr17:80037252-80037480(-)$1	228	53	73	13.8724
GAGGAAUGGGAUAUCCAGGU	chr15:68583961-68584189(+)$1	228	50	70	14.3480
AAAGGAUUUUUACCCUUCGG	chr1:40041937-40042177(-)$1	240	209	229	14.0294
AGCCCUGCCCGCUGGAGUGA	chr19:36595434-36595663(+)$1	229	8	28	13.1801
AUUAUUGUGUUUUAUAGUAA	chr5:134193494-134193722(+)$1	228	30	50	13.7199
GUCUGUAGGAAGUUGGGCCG	chr2:176974165-176974387(+)$1	222	9	29	13.6892
CAGGAACUUUGUCUCCUUCA	chr19:10250317-10250537(-)$1	220	89	109	13.5287
AACGUGAGAGGAAACCCGUG	chrX:119763735-119763958(-)$1	223	126	146	14.2112
CAGUCGGUAAAAAGUCCCGC	chr20:36662096-36662338(+)$1	242	139	159	14.0972
GUAAGUAAAAUAUUUUAUCA	chrX:20252774-20253027(-)$1	253	152	172	13.1602
GUUUAAAGGACAAUAAGCCC	chr22:30983177-30983457(-)$1	280	133	153	13.9793
AGGCAAGUUGUUAUGUCUGU	chr3:45763442-45763663(+)$1	221	133	153	14.3082
UUGGUCAGACAAAGCCAGUU	chr10:96354453-96354675(+)$1	222	41	61	14.3082
CAGAACCCACCCUUUGAGCC	chr1:27106998-27107225(+)$1	227	45	65	13.4044
GAUCUGAUGAAUGAGAUCAA	chr6:99936043-99936271(-)$1	228	127	147	13.6617
CAAAUGUAUUUGAGUAUGUC	chr9:95036612-95036833(-)$1	221	145	165	13.7998
CACUCUCUGAUUUGGGGAUC	chr17:35687092-35687321(-)$1	229	154	174	15.0240
AGGUGCUCAAAUCCACUUGA	chr1:41457381-41457603(+)$1	222	64	84	13.8203
CAGUUCUCACUACAGCGCCA	chr7:26240094-26240352(-)$1	258	49	69	13.8890
GACCUUAAACAUUAGGACCU	chr2:200322010-200322240(-)$1	230	15	35	14.7464
UUACAAAAAGAAAUGCAAGU	chr17:33679764-33679989(-)$1	225	129	149	14.2995
UUGAAGAUCUCUAUUCCUAU	chr11:62396570-62396797(-)$1	227	71	91	15.0206
UCACUCUCCUUCCAGUGUAC	chr1:204522763-204522987(+)$1	224	109	129	12.4116
AGCCCAAGAACCAGGACGAA	chr17:79634729-79634953(+)$1	224	55	75	14.9365
UUGAAGAUCUCUAUUCCUAU	chr11:62396637-62396867(-)$1	230	141	161	15.0206
UGAGCUGGCAACUGCUUUCA	chr5:167944865-167945087(+)$1	222	134	154	12.7139
CAGGCUUCACCAUGCCACCC	chr17:40270262-40270496(-)$1	234	131	151	14.4435

#DB
(((((........)))))).	chr12:56666530-56666754(-)$1	1	168	188	12.9588
.((((........))))...	chr18:67755252-67755478(-)$1	1	115	135	14.2756
.((((........)))).))	chr17:78369479-78369708(-)$1	1	163	183	13.2192
(.(((........))).)))	chr7:155530669-155530891(+)$1	1	104	124	14.8721
((.((........)).))).	chr13:75936601-75936826(-)$1	1	123	143	13.5312
(((((........)))))..	chr14:97263650-97263869(+)$1	1	63	83	14.1267
(((.(........).)))))	chr16:4666447-4666677(+)$1	1	206	226	13.8525
(.(.(........)).))))	chr16:23678315-23678539(+)$1	1	162	182	13.8367
(((((........)))))))	chr17:48814249-48814487(+)$1	1	89	109	14.3082
.((((........))))).)	chr3:119813160-119813386(-)$1	1	203	223	13.7952
(((((........)))....	chr17:78518938-78519158(+)$1	1	191	211	14.6948
..(((........)))..))	chr1:193028301-193028523(-)$1	1	111	131	14.5199
(((((........)))))))	chr9:115633496-115633720(+)$1	1	198	218	13.1046
.((((........)))))))	chr12:112525398-112525634(-)$1	1	56	76	13.1993
(((((........)))))).	chr4:37687801-37688064(-)$1	1	123	143	13.6892
(((((........)))))))	chr3:50127748-50127970(+)$1	1	140	160	14.3082
((.((........))..)))	chr2:47388852-47389077(-)$1	1	116	136	14.1626
...((........)))))))	chr21:27107583-27107806(-)$1	1	117	137	14.4109
(((((........))).)))	chr5:56531720-56531944(+)$1	1	74	94	14.6689
((.((........)).))))	chr14:100259750-100259975(+)$1	1	4	24	14.2995
(((((........))))).(	chr19:50185186-50185411(+)$1	1	70	90	12.5696
(((((........)))))).	chr9:95042979-95043211(-)$1	1	148	168	13.8448
((.((........)).))))	chr17:36002176-36002398(-)$1	1	147	167	14.5655
(((((........))).)).	chr19:1581104-1581333(-)$1	1	81	101	13.8216
(((((........)))))..	chr3:122283279-122283507(-)$1	1	141	161	13.9793
..(((........)))..))	chr17:3721470-3721698(-)$1	1	18	38	14.4480
.((((........)))).))	chr11:118972411-118972644(-)$1	1	151	171	13.8732
(((.(........).)))))	chr4:1723207-1723436(+)$1	1	141	161	13.8525
(((((........))))).)	chr1:115280549-115280778(-)$1	1	24	44	13.8942
(((((........)))))))	chr1:145441530-145441762(+)$1	1	51	71	14.3082
(((((........)))))).	chrX:41205501-41205729(+)$1	1	208	228	12.9588
.((((........)))).))	chr4:17841613-17841844(+)$1	1	108	128	13.8144
(((((........))).)))	chr17:62499461-62499697(-)$1	1	159	179	14.5100
..(((........))).)))	chr19:46119961-46120189(-)$1	1	17	37	14.8104
((.((........)))))))	chr22:42987922-42988158(-)$1	1	137	157	14.3561
...((........)).))))	chr22:38901932-38902175(-)$1	1	160	180	14.5237
(((((........)))))).	chr8:37636586-37636829(+)$1	1	68	88	13.4537
..(((........)))...)	chr14:55615047-55615274(-)$1	1	12	32	15.2233
(.(((........)))))..	chr22:22020211-22020441(+)$1	1	165	185	13.7761
...((........))....)	chr12:1025822-1026045(-)$1	1	182	202	14.5015
(((((........)))))))	chr1:235491198-235491437(-)$1	1	128	148	14.3082
(((((........)))))..	chr3:194362528-194362757(-)$1	1	137	157	13.6442
((.((........)).))))	chr7:98030184-98030408(-)$1	1	29	49	13.1591
(..((........))..)))	chr17:80037252-80037480(-)$1	1	53	73	13.8724
..(((........))).)))	chr15:68583961-68584189(+)$1	1	50	70	14.3480
.((((........)))).))	chr1:40041937-40042177(-)$1	1	209	229	14.0294
.((((........)).))..	chr19:36595434-36595663(+)$1	1	8	28	13.1801
(((((........)))))))	chr5:134193494-134193722(+)$1	1	30	50	13.7199
(((((........)))))).	chr2:176974165-176974387(+)$1	1	9	29	13.6892
.((((........)))).))	chr19:10250317-10250537(-)$1	1	89	109	13.5287
...((........))..)))	chrX:119763735-119763958(-)$1	1	126	146	14.2112
..(.(........).)..))	chr20:36662096-36662338(+)$1	1	139	159	14.0972
(((((........)))))..	chrX:20252774-20253027(-)$1	1	152	172	13.1602
(((((........)))))..	chr22:30983177-30983457(-)$1	1	133	153	13.9793
(((((........)))))))	chr3:45763442-45763663(+)$1	1	133	153	14.3082
(((((........)))))))	chr10:96354453-96354675(+)$1	1	41	61	14.3082
(..((........))..)).	chr1:27106998-27107225(+)$1	1	45	65	13.4044
(((((........)))))))	chr6:99936043-99936271(-)$1	1	127	147	13.6617
((.((........)).))))	chr9:95036612-95036833(-)$1	1	145	165	13.7998
..(((........)))..).	chr17:35687092-35687321(-)$1	1	154	174	15.0240
(((((........)))))).	chr1:41457381-41457603(+)$1	1	64	84	13.8203
(.(((........)))))).	chr7:26240094-26240352(-)$1	1	49	69	13.8890
(.(((........))).)))	chr2:200322010-200322240(-)$1	1	15	35	14.7464
((.((........)).))))	chr17:33679764-33679989(-)$1	1	129	149	14.2995
..(((........)))..))	chr11:62396570-62396797(-)$1	1	71	91	15.0206
.((((........))))(((	chr1:204522763-204522987(+)$1	1	109	129	12.4116
.(.((........)).)...	chr17:79634729-79634953(+)$1	1	55	75	14.9365
..(((........)))..))	chr11:62396637-62396867(-)$1	1	141	161	15.0206
.((((........)))))))	chr5:167944865-167945087(+)$1	1	134	154	12.7139
..(((........))))).)	chr17:40270262-40270496(-)$1	1	131	151	14.4435

#PSSM
e : 0.18	f : 0.14	! : 0.12	g : 0.10	c : 0.08	[ : 0.07	" : 0.07	b : 0.05	d : 0.04	# : 0.04	' : 0.01	$ : 0.01	i : 0.01	: : 0.01	) : 0.01	
e : 0.18	d : 0.15	f : 0.12	! : 0.12	g : 0.10	[ : 0.07	c : 0.05	" : 0.04	b : 0.04	# : 0.04	$ : 0.01	i : 0.01	a : 0.01	
c : 0.24	e : 0.15	d : 0.14	[ : 0.12	f : 0.11	g : 0.08	a : 0.02	" : 0.02	# : 0.02	! : 0.02	b : 0.01	
c : 0.24	b : 0.22	d : 0.14	e : 0.12	f : 0.11	g : 0.08	[ : 0.05	
c : 0.24	b : 0.22	d : 0.14	e : 0.12	f : 0.11	g : 0.08	a : 0.05	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.24	b : 0.22	d : 0.14	e : 0.12	f : 0.11	g : 0.08	a : 0.05	
c : 0.24	b : 0.22	d : 0.14	e : 0.12	f : 0.11	g : 0.08	] : 0.04	a : 0.01	
c : 0.24	e : 0.17	d : 0.14	] : 0.14	f : 0.11	g : 0.08	2 : 0.05	i : 0.01	4 : 0.01	a : 0.01	
e : 0.20	d : 0.17	2 : 0.14	f : 0.11	] : 0.10	g : 0.10	b : 0.05	c : 0.04	4 : 0.02	i : 0.01	3 : 0.01	a : 0.01	
e : 0.20	f : 0.15	g : 0.10	b : 0.10	c : 0.08	2 : 0.08	] : 0.07	d : 0.07	3 : 0.04	4 : 0.02	h : 0.02	a : 0.01	i : 0.01	
f : 0.18	c : 0.14	e : 0.10	d : 0.10	g : 0.10	b : 0.07	3 : 0.05	4 : 0.05	] : 0.04	2 : 0.04	h : 0.02	F : 0.01	: : 0.01	i : 0.01	6 : 0.01	a : 0.01	
c : 0.12	e : 0.12	d : 0.12	g : 0.10	f : 0.08	2 : 0.07	: : 0.05	4 : 0.05	3 : 0.04	b : 0.04	] : 0.04	6 : 0.04	F : 0.02	h : 0.02	i : 0.01	

#score	979.6579730120244
#seq	70
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_UTR_m3_run1.txt

#BEAR
============oooooo==========	chr10:22619674-22619898(+)$1	224	193	221	17.0501
c!!ccc"""cccoooooocccccc]ccc	chr13:46110446-46110668(+)$1	222	9	37	14.0202
cc!!==========mmmm==========	chr5:173316217-173316447(+)$1	230	84	112	12.8276
cc!!eeeee!!bboooooobb22eeeee	chrX:40465619-40465841(+)$1	222	37	65	10.3320
============oooooo==========	chr8:57874841-57875061(-)$1	220	168	196	17.0501
g"""ccc!!cccooooooccc22ccc]g	chr4:83840443-83840658(-)$1	215	102	130	14.0797
ciiiiiiiiirrrrrrrrriiiiiiiii	chr10:60156970-60157191(+)$1	221	178	206	11.4489
!ccc[bb[ddddoooooodddd]bb]cc	chr3:179305806-179306037(+)$1	231	121	149	12.2765
ee"""gggggggoooooogggggggeee	chr13:52606501-52606723(+)$1	222	61	89	14.0753
[dddd####cccooooooccc4444ddd	chr12:13233652-13233871(+)$1	219	122	150	12.8883
"bb[ccc[ddddoooooodddd]cccbb	chr6:138411891-138412126(-)$1	235	118	146	12.4854
D:==========oooooo==========	chr17:60021163-60021382(-)$1	219	78	106	15.3940
gggg!!bb[cccooooooccc333bb22	chr6:11136518-11136740(+)$1	222	123	151	12.9942
dd!!ccc[ddddoooooodddd333ccc	chr17:29859924-29860155(+)$1	231	44	72	13.7826
ddd[dddd[cccoooooocccdddd]dd	chr13:30780389-30780608(-)$1	219	11	39	12.0602
c[dddd[eeeeeooooooeeeeeddddc	chr8:124265235-124265457(-)$1	222	61	89	11.7615
B===========nnnnn===========	chr3:185635109-185635328(-)$1	219	35	63	12.6339
dd"""gggggggrrrrrrrrrggggggg	chr3:156259612-156259844(-)$1	232	65	93	10.5797
"""iiiiiiiiiooooooiiiiiiiiif	chr4:135119771-135119992(-)$1	221	181	209	15.9671
d!!iiiiiiiiiooooooiiiiiiiiid	chr4:77035729-77035954(-)$1	225	76	104	15.7792
ffff!!ccc[bboooooobbccc4444f	chr19:22850064-22850298(+)$1	234	14	42	12.1456
"==========ppppppp==========	chr2:26358518-26358736(+)$1	218	63	91	10.7893
dd!!==========lll==========]	chr13:98045541-98045767(+)$1	226	119	147	13.4043
:===========oooooo==========	chr3:40558281-40558516(+)$1	235	8	36	16.2646
:===========mmmm===========b	chr2:27016676-27016899(+)$1	223	108	136	11.4916
bb"""===========[===========	chr14:21928658-21928882(-)$1	224	32	60	11.5711
"""ddddeeeeeooooooeeeee333dd	chr1:204518744-204518963(+)$1	219	72	100	13.0714
c:ccc[ffffffooooooffffff]ccc	chr2:32248863-32249083(-)$1	220	120	148	11.0619
iii[dddd[cccoooooocccdddd]ii	chr7:92239816-92240053(-)$1	237	71	99	12.9937
=========!!annnnna22========	chr12:12628903-12629123(-)$1	220	110	138	12.0761
$$$ccc[ccc[bboooooobb]ccc]cc	chr1:228285998-228286213(+)$1	215	57	85	11.2598
[bb!!gggggggoooooogggggggbba	chr2:60679418-60679646(-)$1	228	188	216	13.6641
::==========oooooo==========	chr10:71910290-71910516(-)$1	226	101	129	15.3247
ddd$$$$$ddddoooooodddd22dddd	chr11:125761257-125761487(-)$1	230	118	146	11.2335
dd[ccc[eeeeeooooooeeeee]cccd	chr19:16628749-16628976(-)$1	227	4	32	13.0533
cc####ccc[cccnnnnnccc]ccc444	chr7:130146117-130146341(-)$1	224	102	130	10.4602
hhh!!gggggggooooooggggggg]hh	chr2:32534536-32534764(+)$1	228	58	86	13.4695
e:bb"""eeeeeooooooeeeee333bb	chr17:7215154-7215394(+)$1	240	53	81	12.2076
ddd[bb[eeeeeooooooeeeee]bbdd	chr6:17615283-17615508(-)$1	225	47	75	11.8959
ffffff[eeeeeooooooeeeee4444f	chr8:10582449-10582669(-)$1	220	40	68	12.2849
======iiiiiiiiillliiiiiiiii>	chr12:65091177-65091396(+)$1	219	41	69	11.8035
:iiiiiiiii[aooooooa]iiiiiiii	chr13:79888337-79888561(-)$1	224	112	140	14.5904
iiiii[bbddddoooooodddd4444bb	chrX:30849242-30849470(-)$1	228	36	64	12.8767
bb####bb[cccooooooccc]bb4444	chr1:151040018-151040256(+)$1	238	88	116	13.5176
bb"""gggggggrrrrrrrrrggggggg	chr5:40831533-40831757(-)$1	224	63	91	10.5049
!!ffffffddddoooooodddd22ffff	chr5:108529294-108529520(+)$1	226	176	204	11.2305
c[a####eeeeeooooooeeeee333a]	chr2:113090128-113090356(+)$1	228	174	202	14.2950

#otherMatches

#Seq PSSM
CUAUAUGAAUAUUGUUUCAUGUUUGUAU	chr10:22619674-22619898(+)$1	224	193	221	17.0501
UGACUGAUUUAAUUUGAUUUACAGAGCG	chr13:46110446-46110668(+)$1	222	9	37	14.0202
AACCAUAUGUGAUUGUUAAAUUAUAUAU	chr5:173316217-173316447(+)$1	230	84	112	12.8276
UGGAGUAUAUAGAUGCUUUUCAUUAUAC	chrX:40465619-40465841(+)$1	222	37	65	10.3320
AUGUACGUUCUAGCCUGGUGGAAUGUGC	chr8:57874841-57875061(-)$1	220	168	196	17.0501
UCAAACUAUAAUUUUCAUAUUUAAGUAA	chr4:83840443-83840658(-)$1	215	102	130	14.0797
UGUUAAGUACGUUUCUCAAGUACUUAAC	chr10:60156970-60157191(+)$1	221	178	206	11.4489
UUUUUUAAAGCUUUAACUGGCUCUAUAA	chr3:179305806-179306037(+)$1	231	121	149	12.2765
GAUAUGGCUAUAAAGACCUAUAGCUUUU	chr13:52606501-52606723(+)$1	222	61	89	14.0753
CUGCAUUAAUCCCCUCUAGGAACUCUGC	chr12:13233652-13233871(+)$1	219	122	150	12.8883
AUAUCAGAUUAUUAUUUUGUAAGUUGUG	chr6:138411891-138412126(-)$1	235	118	146	12.4854
UAGUUUUGUUUAAAUAGGUAAGCAAAAU	chr17:60021163-60021382(-)$1	219	78	106	15.3940
UCUUUUUAUGUUUUUCUUAACCUUUAUU	chr6:11136518-11136740(+)$1	222	123	151	12.9942
GACAUGGUACUUACCUUAGAGUUUUCCA	chr17:29859924-29860155(+)$1	231	44	72	13.7826
CCUAACUUUACUAUGUUAAGUGAGUCAG	chr13:30780389-30780608(-)$1	219	11	39	12.0602
AUCAUGUGUAGUUUUAUUAUUAUUAUGU	chr8:124265235-124265457(-)$1	222	61	89	11.7615
AGAAAAGUAUGUUUUGCAUGUAUUUUUU	chr3:185635109-185635328(-)$1	219	35	63	12.6339
AAAUUUAAUGUGAAUUUCAUACAUGUUA	chr3:156259612-156259844(-)$1	232	65	93	10.5797
agaGUUAUUUAAUUACAUUUAAAUAAUU	chr4:135119771-135119992(-)$1	221	181	209	15.9671
GCCUUUUUAUUUCUAAAAAGAUGAAAAC	chr4:77035729-77035954(-)$1	225	76	104	15.7792
GGUAAAAGAAUGCACUAACAUCUGUAGU	chr19:22850064-22850298(+)$1	234	14	42	12.1456
UGUUUUAAGUGGCCUUGAUAUUUAAAAC	chr2:26358518-26358736(+)$1	218	63	91	10.7893
UUUCAUGAUUUUGAUUUUUAAAAUUAUU	chr13:98045541-98045767(+)$1	226	119	147	13.4043
GCUGGUGUGGAAGAUUCAUUCUGCAUCA	chr3:40558281-40558516(+)$1	235	8	36	16.2646
UUUUUCUUUUUUUUGAGAAGGAGAAGAC	chr2:27016676-27016899(+)$1	223	108	136	11.4916
cgcuaagccaagaucacgccauugcacu	chr14:21928658-21928882(-)$1	224	32	60	11.5711
UACGAACAUAAAAAUGCAUUUAUUCCGU	chr1:204518744-204518963(+)$1	219	72	100	13.0714
GUAGUUUUUGUUCUGUAUGACAAAUAUU	chr2:32248863-32249083(-)$1	220	120	148	11.0619
CUGUUUUCCUCAAAAGCAUGAGAAACUA	chr7:92239816-92240053(-)$1	237	71	99	12.9937
UUUCUUCUCAGCUUUAUGAAGAGAAGGG	chr12:12628903-12629123(-)$1	220	110	138	12.0761
CCUUGGCUUUAGAGCUGUGUUGAAAUCC	chr1:228285998-228286213(+)$1	215	57	85	11.2598
UGGACCAUCGCUGUCAUGAGUGAUGCCC	chr2:60679418-60679646(-)$1	228	188	216	13.6641
AUAUUUUUAAUUUCCUUUGGUUAAAGGU	chr10:71910290-71910516(-)$1	226	101	129	15.3247
ACCUUAUUUCAAUGUAUCUUGAUUGGUA	chr11:125761257-125761487(-)$1	230	118	146	11.2335
GUUGGGAAUCGGCCACACCUGGUGUCCA	chr19:16628749-16628976(-)$1	227	4	32	13.0533
UAACUUCAUUUUAUUCUUUAAUGUGUAC	chr7:130146117-130146341(-)$1	224	102	130	10.4602
uaaaaauuuuGUGAUGUAACAAAAUGUU	chr2:32534536-32534764(+)$1	228	58	86	13.4695
CUGGCCCGGUCCUAAGCUGGACUCCUCC	chr17:7215154-7215394(+)$1	240	53	81	12.2076
UUUCUGAUCCAGUUUUGUUUGGACCAAA	chr6:17615283-17615508(-)$1	225	47	75	11.8959
UUAAAACUAUUUUAUUUUAAAUAUACAU	chr8:10582449-10582669(-)$1	220	40	68	12.2849
AGUAAAAAGUUAUAAUAUUUAUAAUUUU	chr12:65091177-65091396(+)$1	219	41	69	11.8035
uaaaaauuauauGUCUUAACAUAAUUUU	chr13:79888337-79888561(-)$1	224	112	140	14.5904
AGCGGGGAGGAGGAAUGGCUUUGUGGUC	chrX:30849242-30849470(-)$1	228	36	64	12.8767
GAGUUCUAUGUAUUUAUUUAUCUAUCUG	chr1:151040018-151040256(+)$1	238	88	116	13.5176
GAACAGCUACAUAAAAUAGUGAUGUAGC	chr5:40831533-40831757(-)$1	224	63	91	10.5049
AUAUUGAAUAAUGUUGUAAUUGGUUUCA	chr5:108529294-108529520(+)$1	226	176	204	11.2305
UACUUUUAUUGUAAAUAAACAAUCAUGA	chr2:113090128-113090356(+)$1	228	174	202	14.2950

#DB
((((((((((((......))))))))))	chr10:22619674-22619898(+)$1	1	193	221	17.0501
(..(((...(((......)))))).)))	chr13:46110446-46110668(+)$1	1	9	37	14.0202
((..((((((((((....))))))))))	chr5:173316217-173316447(+)$1	1	84	112	12.8276
((..(((((..((......))..)))))	chrX:40465619-40465841(+)$1	1	37	65	10.3320
((((((((((((......))))))))))	chr8:57874841-57875061(-)$1	1	168	196	17.0501
(...(((..(((......)))..))).)	chr4:83840443-83840658(-)$1	1	102	130	14.0797
((((((((((.........)))))))))	chr10:60156970-60157191(+)$1	1	178	206	11.4489
.(((.((.((((......)))).)).))	chr3:179305806-179306037(+)$1	1	121	149	12.2765
((...(((((((......))))))))))	chr13:52606501-52606723(+)$1	1	61	89	14.0753
.((((....(((......)))....)))	chr12:13233652-13233871(+)$1	1	122	150	12.8883
.((.(((.((((......)))).)))))	chr6:138411891-138412126(-)$1	1	118	146	12.4854
(.((((((((((......))))))))))	chr17:60021163-60021382(-)$1	1	78	106	15.3940
((((..((.(((......)))...))..	chr6:11136518-11136740(+)$1	1	123	151	12.9942
((..(((.((((......))))...)))	chr17:29859924-29860155(+)$1	1	44	72	13.7826
(((.((((.(((......))))))).))	chr13:30780389-30780608(-)$1	1	11	39	12.0602
(.((((.(((((......))))))))))	chr8:124265235-124265457(-)$1	1	61	89	11.7615
((((((((((((.....)))))))))))	chr3:185635109-185635328(-)$1	1	35	63	12.6339
((...(((((((.........)))))))	chr3:156259612-156259844(-)$1	1	65	93	10.5797
...(((((((((......))))))))))	chr4:135119771-135119992(-)$1	1	181	209	15.9671
(..(((((((((......))))))))))	chr4:77035729-77035954(-)$1	1	76	104	15.7792
((((..(((.((......)))))....)	chr19:22850064-22850298(+)$1	1	14	42	12.1456
.((((((((((.......))))))))))	chr2:26358518-26358736(+)$1	1	63	91	10.7893
((..((((((((((...)))))))))).	chr13:98045541-98045767(+)$1	1	119	147	13.4043
.(((((((((((......))))))))))	chr3:40558281-40558516(+)$1	1	8	36	16.2646
.(((((((((((....)))))))))))(	chr2:27016676-27016899(+)$1	1	108	136	11.4916
((...(((((((((((.(((((((((((	chr14:21928658-21928882(-)$1	1	32	60	11.5711
...(((((((((......)))))...))	chr1:204518744-204518963(+)$1	1	72	100	13.0714
).(((.((((((......)))))).)))	chr2:32248863-32249083(-)$1	1	120	148	11.0619
(((.((((.(((......))))))).))	chr7:92239816-92240053(-)$1	1	71	99	12.9937
(((((((((..(.....)..))))))))	chr12:12628903-12629123(-)$1	1	110	138	12.0761
...(((.(((.((......)).))).))	chr1:228285998-228286213(+)$1	1	57	85	11.2598
.((..(((((((......))))))))))	chr2:60679418-60679646(-)$1	1	188	216	13.6641
..((((((((((......))))))))))	chr10:71910290-71910516(-)$1	1	101	129	15.3247
(((.....((((......))))..))))	chr11:125761257-125761487(-)$1	1	118	146	11.2335
((.(((.(((((......))))).))))	chr19:16628749-16628976(-)$1	1	4	32	13.0533
((....(((.(((.....))).)))...	chr7:130146117-130146341(-)$1	1	102	130	10.4602
(((..(((((((......))))))).))	chr2:32534536-32534764(+)$1	1	58	86	13.4695
).((...(((((......)))))...))	chr17:7215154-7215394(+)$1	1	53	81	12.2076
(((.((.(((((......))))).))))	chr6:17615283-17615508(-)$1	1	47	75	11.8959
((((((.(((((......)))))....)	chr8:10582449-10582669(-)$1	1	40	68	12.2849
(((((((((((((((...))))))))).	chr12:65091177-65091396(+)$1	1	41	69	11.8035
.(((((((((.(......).))))))))	chr13:79888337-79888561(-)$1	1	112	140	14.5904
(((((.((((((......))))....))	chrX:30849242-30849470(-)$1	1	36	64	12.8767
((....((.(((......))).))....	chr1:151040018-151040256(+)$1	1	88	116	13.5176
((...(((((((.........)))))))	chr5:40831533-40831757(-)$1	1	63	91	10.5049
..((((((((((......))))..))))	chr5:108529294-108529520(+)$1	1	176	204	11.2305
(.(....(((((......)))))...).	chr2:113090128-113090356(+)$1	1	174	202	14.2950

#PSSM
c : 0.17	d : 0.17	= : 0.08	" : 0.08	: : 0.08	b : 0.06	g : 0.04	! : 0.04	e : 0.04	[ : 0.04	f : 0.04	i : 0.04	D : 0.02	B : 0.02	$ : 0.02	h : 0.02	
= : 0.17	d : 0.17	b : 0.10	c : 0.08	i : 0.08	: : 0.08	! : 0.06	" : 0.06	[ : 0.04	f : 0.04	e : 0.02	g : 0.02	$ : 0.02	h : 0.02	
= : 0.21	" : 0.14	! : 0.12	d : 0.10	i : 0.08	b : 0.06	f : 0.06	c : 0.04	# : 0.04	g : 0.02	$ : 0.02	[ : 0.02	h : 0.02	a : 0.02	
= : 0.21	! : 0.12	c : 0.10	" : 0.10	i : 0.10	[ : 0.08	d : 0.06	f : 0.06	# : 0.06	g : 0.02	$ : 0.02	b : 0.02	
= : 0.25	c : 0.14	i : 0.10	" : 0.10	d : 0.10	! : 0.08	# : 0.06	f : 0.04	e : 0.02	[ : 0.02	$ : 0.02	b : 0.02	
= : 0.27	c : 0.12	g : 0.10	i : 0.08	# : 0.08	d : 0.08	b : 0.04	! : 0.04	[ : 0.04	f : 0.04	e : 0.02	$ : 0.02	" : 0.02	
= : 0.25	c : 0.10	i : 0.10	g : 0.10	[ : 0.10	b : 0.08	d : 0.06	" : 0.04	# : 0.04	f : 0.04	e : 0.02	$ : 0.02	
= : 0.25	e : 0.17	i : 0.10	g : 0.10	[ : 0.06	b : 0.06	c : 0.06	d : 0.04	f : 0.04	" : 0.02	! : 0.02	# : 0.02	$ : 0.02	
= : 0.25	e : 0.17	d : 0.12	i : 0.10	g : 0.10	[ : 0.08	c : 0.06	" : 0.02	! : 0.02	# : 0.02	f : 0.02	
= : 0.23	c : 0.17	e : 0.14	d : 0.12	i : 0.10	g : 0.10	! : 0.04	[ : 0.04	f : 0.02	
= : 0.23	c : 0.17	e : 0.14	d : 0.12	g : 0.10	i : 0.06	! : 0.04	[ : 0.04	r : 0.02	b : 0.02	f : 0.02	
= : 0.21	c : 0.17	e : 0.14	d : 0.12	g : 0.10	b : 0.06	i : 0.06	a : 0.04	r : 0.02	p : 0.02	f : 0.02	
o : 0.70	= : 0.06	r : 0.06	b : 0.04	n : 0.04	p : 0.02	m : 0.02	c : 0.02	i : 0.02	
o : 0.74	= : 0.06	r : 0.06	n : 0.06	p : 0.02	m : 0.02	i : 0.02	
o : 0.74	r : 0.06	n : 0.06	m : 0.04	p : 0.02	l : 0.02	= : 0.02	i : 0.02	
o : 0.74	r : 0.06	n : 0.06	m : 0.04	l : 0.04	p : 0.02	= : 0.02	
o : 0.74	r : 0.06	n : 0.06	l : 0.04	m : 0.02	p : 0.02	= : 0.02	[ : 0.02	
o : 0.74	= : 0.08	r : 0.06	m : 0.02	p : 0.02	a : 0.02	n : 0.02	l : 0.02	
= : 0.23	c : 0.17	e : 0.14	d : 0.12	r : 0.06	g : 0.06	i : 0.06	o : 0.04	b : 0.02	f : 0.02	2 : 0.02	a : 0.02	
= : 0.23	c : 0.17	e : 0.14	d : 0.12	i : 0.08	b : 0.06	g : 0.06	r : 0.04	f : 0.02	2 : 0.02	] : 0.02	
= : 0.25	c : 0.19	e : 0.14	d : 0.12	i : 0.10	g : 0.06	b : 0.04	r : 0.04	f : 0.02	
= : 0.25	d : 0.17	e : 0.14	i : 0.10	g : 0.10	] : 0.06	c : 0.04	2 : 0.04	4 : 0.02	3 : 0.02	f : 0.02	
= : 0.25	e : 0.14	i : 0.10	g : 0.10	c : 0.08	2 : 0.08	] : 0.04	4 : 0.04	3 : 0.04	d : 0.04	f : 0.02	b : 0.02	
= : 0.25	c : 0.10	i : 0.10	g : 0.10	3 : 0.10	4 : 0.08	d : 0.06	b : 0.04	2 : 0.04	] : 0.04	e : 0.02	f : 0.02	
= : 0.25	c : 0.10	i : 0.10	g : 0.10	4 : 0.10	3 : 0.08	d : 0.08	b : 0.06	] : 0.04	e : 0.02	f : 0.02	
= : 0.25	c : 0.12	i : 0.10	] : 0.10	4 : 0.10	d : 0.06	b : 0.06	3 : 0.06	e : 0.04	g : 0.04	f : 0.02	
= : 0.25	c : 0.12	i : 0.12	d : 0.12	b : 0.08	4 : 0.08	e : 0.04	g : 0.04	] : 0.02	2 : 0.02	h : 0.02	f : 0.02	a : 0.02	
= : 0.21	d : 0.14	c : 0.12	b : 0.08	f : 0.08	g : 0.06	i : 0.06	e : 0.04	] : 0.04	4 : 0.04	2 : 0.02	a : 0.02	h : 0.02	> : 0.02	

#score	608.030329810834
#seq	47
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_UTR_m3_run1.txt

#BEAR
eee!!eeeeeooooooeeeee22eeee	chr14:53238156-53238396(+)$1	240	54	81	11.1575
:iiiiiiiiiooooooiiiiiiiii::	chr9:73000568-73000808(-)$1	240	178	205	12.7584
[ccc####cccnnnnnccc4444ccc]	chr4:69179381-69179621(-)$1	240	123	150	10.3491
!!ccc[ddddoooooodddd]ccc22b	chr12:93895064-93895306(+)$1	242	31	58	12.1460
a[ccc[ddddoooooodddd]ccc]a]	chr13:103331363-103331603(+)$1	240	140	167	12.7137
======[cccooooooccc]=======	chr10:30305723-30305963(-)$1	240	10	37	16.4823
eeeee!!cccooooooccc22eeeeeg	chr3:32524928-32525179(-)$1	251	174	201	12.8105
[iiiiiiiiiooooooiiiiiiiii22	chr5:112213402-112213642(-)$1	240	196	223	15.8789
======[cccooooooccc]=======	chr5:74075130-74075370(-)$1	240	107	134	16.4823
eeegggggggooooooggggggg4444	chr4:68482630-68482870(-)$1	240	165	192	14.0204
iiiiiiiiirrrrrrrrriiiiiiiii	chr18:57571079-57571359(+)$1	280	168	195	12.2208
0eeeee:cccoooooocccgggggggl	chr3:158323308-158323548(+)$1	240	191	218	11.3041
"ffffff[bboooooobb22ffffff]	chr1:32374216-32374456(-)$1	240	80	107	10.9680
==========ppppppp==========	chr5:114950665-114950905(-)$1	240	82	109	11.7552
============lll============	chr3:40575515-40575755(+)$1	240	128	155	13.6528
dddd!!ddddoooooodddd22dddd3	chr10:99434295-99434535(+)$1	240	38	65	11.2679
==========ppppppp==========	chr1:182352088-182352368(-)$1	280	136	163	11.7552
gggg"""cccooooooccc]ggggggg	chrX:24229990-24230230(+)$1	240	208	235	14.7233
iiiiiibbbboooooobb]bb]iiiii	chr1:65692940-65693180(+)$1	240	65	92	12.9551
===="""cccooooooccc]=======	chr2:62451439-62451686(+)$1	247	148	175	16.3745
ee!!iiiiiiiiillliiiiiiiii22	chr12:69234503-69234745(+)$1	242	86	113	11.3802
ccc"""ddddoooooodddd4444ccc	chr13:39585374-39585614(-)$1	240	141	168	12.6254
[bb"""ddddoooooodddd4444bb]	chr8:28608578-28608818(+)$1	240	119	146	12.0836
ccc!!cccrrrrrrrrrccc333ccc]	chr5:125829041-125829281(+)$1	240	106	133	10.4216
f!!gggggggooooooggggggg]fff	chr1:215794801-215795041(+)$1	240	31	58	13.5702
!!dddd[cccooooooccc]dddd22d	chr3:47893617-47893859(-)$1	242	37	64	12.0878
#eeeee!!bboooooobb22eeeee44	chr3:176742613-176742853(-)$1	240	43	70	11.9232
eeee!!ddddoooooodddd22eeeee	chr12:72317619-72317859(+)$1	240	54	81	11.6603
==========ppppppp==========	chr10:72637452-72637692(+)$1	240	32	59	11.7552
==========oooooo==========]	chr5:34907878-34908118(-)$1	240	111	138	17.1100
:iiiiiiiiiooooooiiiiiiiii::	chr6:13978878-13979118(+)$1	240	147	174	12.7584
feeeee[cccooooooccc]eeeee33	chr1:21070664-21070927(-)$1	263	50	77	13.2925
cc[gggggggooooooggggggg]ccc	chr4:40815198-40815438(-)$1	240	145	172	13.8469
cggggggg[aooooooa]ggggggg33	chr21:15745095-15745335(-)$1	240	131	158	14.4734
==========rrrrrrrrr========	chr1:53289075-53289318(+)$1	243	58	85	13.0577
==========oooooo===========	chr1:150620482-150620727(-)$1	245	36	63	17.0276
##ccc"""bboooooobb333ccc333	chr2:29023745-29023985(+)$1	240	75	102	13.8853
!!bb[eeeeeooooooeeeee]bb333	chr7:112461109-112461349(-)$1	240	101	128	11.9882
iiiiiiiiirrrrrrrrriiiiiiiii	chr7:107560096-107560342(+)$1	246	117	144	12.2208
!!==========mmmm==========c	chr6:7417823-7418063(+)$1	240	189	216	12.4210
eee####cccooooooccc333eeeee	chr1:32373901-32374141(-)$1	240	41	68	13.7184
ffffffcccaooooooa]ccc]fffff	chr1:236713991-236714231(-)$1	240	1	28	11.6265
===========lll============2	chr11:113148560-113148800(+)$1	240	179	206	13.4848
iiiiiii[bboooooobb333iiiiii	chr11:65180347-65180589(+)$1	242	43	70	14.9420
!!iiiiiiiiinnnnniiiiiiiii]d	chr12:77415061-77415301(-)$1	240	204	231	12.1098
cc[gggggggooooooggggggg]ccc	chr1:230416050-230416290(+)$1	240	121	148	13.8469
c"""gggggggnnnnnggggggg4444	chr9:133513196-133513439(+)$1	243	115	142	10.5022

#otherMatches

#Seq PSSM
UGGGUAAUUUAUAACAAAAUUUGCUAA	chr14:53238156-53238396(+)$1	240	54	81	11.1575
CGAAAUAGGUUAGGCUGCCUAUUUCUC	chr9:73000568-73000808(-)$1	240	178	205	12.7584
UGUUUUUUUCCUUUUUGGAUCUUGAUU	chr4:69179381-69179621(-)$1	240	123	150	10.3491
GAUAAAAUAUCUUUUCAUAUAUUAGAA	chr12:93895064-93895306(+)$1	242	31	58	12.1460
UGAAUAUUGAAGCUUCUUAAAGUUGGU	chr13:103331363-103331603(+)$1	240	140	167	12.7137
UUUAAGGAAGUAUUAUUUUAUUUAAGA	chr10:30305723-30305963(-)$1	240	10	37	16.4823
AUGUUCUGUUAAUGGGAAUUUAACAUA	chr3:32524928-32525179(-)$1	251	174	201	12.8105
AUCAUUAGCAACAACAUGCUAAUGACG	chr5:112213402-112213642(-)$1	240	196	223	15.8789
AAAAUACUUUCUUUUCAAAUUAUUUUa	chr5:74075130-74075370(-)$1	240	107	134	16.4823
CUGUUUGGUUCUACUAAGCUAGAAAGC	chr4:68482630-68482870(-)$1	240	165	192	14.0204
GAAAAUGUGUAUUAAAGUUACAUUUUU	chr18:57571079-57571359(+)$1	280	168	195	12.2208
ACUAGUACUCUUUUAUGAGAAAAUAGU	chr3:158323308-158323548(+)$1	240	191	218	11.3041
AUAUUACCUGUGUCAUCAAAGUAGUGA	chr1:32374216-32374456(-)$1	240	80	107	10.9680
UUCAUUGACUUUUCUUUAGUUAAUGAG	chr5:114950665-114950905(-)$1	240	82	109	11.7552
uucauauuuaugaauuauaaauaugaa	chr3:40575515-40575755(+)$1	240	128	155	13.6528
GUGGUCUAUGGGUGAACAUAUCCCACC	chr10:99434295-99434535(+)$1	240	38	65	11.2679
AAGGAAUAAACCCCACCUUUAUUCCUU	chr1:182352088-182352368(-)$1	280	136	163	11.7552
GUAUUUUGAUUAUUCUGUCUGUGCGGC	chrX:24229990-24230230(+)$1	240	208	235	14.7233
UGUACUAGCUGUGCCUGGACUGAGUAU	chr1:65692940-65693180(+)$1	240	65	92	12.9551
uauuuGUAUACAGUGUUGUUGAUGAAA	chr2:62451439-62451686(+)$1	247	148	175	16.3745
AAUUAGUAUUUAAAUUUUAGAUACUCu	chr12:69234503-69234745(+)$1	242	86	113	11.3802
GCAACAUCAGAAUUGCCUGAGAACUGC	chr13:39585374-39585614(-)$1	240	141	168	12.6254
CAUUCAAUAACAACUAUUAUGAUUAUU	chr8:28608578-28608818(+)$1	240	119	146	12.0836
AAGUAACAUCUACAUUUUGUCUUUUUU	chr5:125829041-125829281(+)$1	240	106	133	10.4216
UCUGAAUUUUGGGUUAAAGGUUUUGGC	chr1:215794801-215795041(+)$1	240	31	58	13.5702
UGGGGGUCAGUGCUGCCUGUCCCCAUG	chr3:47893617-47893859(-)$1	242	37	64	12.0878
UUUCGUUUUUGGUUUAGAUUAUGGAUG	chr3:176742613-176742853(-)$1	240	43	70	11.9232
AUUUAUAUAACCUGGUUUAUCAAAAUU	chr12:72317619-72317859(+)$1	240	54	81	11.6603
GGAGGCGUUUACAUAACAGAUGUUUCC	chr10:72637452-72637692(+)$1	240	32	59	11.7552
UUAAAGGAAACUUUUUUUUUCUUUAAU	chr5:34907878-34908118(-)$1	240	111	138	17.1100
UUAGGAUUUACUUAACUGAAUCUUAUA	chr6:13978878-13979118(+)$1	240	147	174	12.7584
CACAAUAUAGCACUGACUGAGUUGUAA	chr1:21070664-21070927(-)$1	263	50	77	13.2925
UACUGCAUUAUUGUGUUAAUGUAUUAU	chr4:40815198-40815438(-)$1	240	145	172	13.8469
AUUAUUCUGUUUGGUUAGAGAAUAAAA	chr21:15745095-15745335(-)$1	240	131	158	14.4734
AGAUAAAUUUUCACAGACUAAGUUUAU	chr1:53289075-53289318(+)$1	243	58	85	13.0577
UCUUGAAUCAGACUUGUGAUUUGGGGA	chr1:150620482-150620727(-)$1	245	36	63	17.0276
AUAUGUCUUUUUUUCUAAUUCCGUUUU	chr2:29023745-29023985(+)$1	240	75	102	13.8853
UUGGUGAUAAUUCUUUUUAUUUCUUCC	chr7:112461109-112461349(-)$1	240	101	128	11.9882
ACCUCUAAAUUCUUUCAUUUUAGGGGU	chr7:107560096-107560342(+)$1	246	117	144	12.2208
UACAUGAGUGUCCAGAGGCACUCAUGG	chr6:7417823-7418063(+)$1	240	189	216	12.4210
UGCAAAACCAUCUGUUUGGGGAGCACA	chr1:32373901-32374141(-)$1	240	41	68	13.7184
UGGGAGAGCCACUCCAGAGCUAUUUCU	chr1:236713991-236714231(-)$1	240	1	28	11.6265
AUGUGUGUAUGUGCCAUACAUAUGUAU	chr11:113148560-113148800(+)$1	240	179	206	13.4848
AGCUGCCCGCCUGCCUGUUCUGGCGGC	chr11:65180347-65180589(+)$1	242	43	70	14.9420
UUUUUUUCUAAUAUUUUUAGGAAAAUA	chr12:77415061-77415301(-)$1	240	204	231	12.1098
UAAAUUUCUUUUCUCUAAGGAAUAUAA	chr1:230416050-230416290(+)$1	240	121	148	13.8469
UUUUAAAUAUUUUCUUAAUAUUUUGUC	chr9:133513196-133513439(+)$1	243	115	142	10.5022

#DB
(((..(((((......)))))..))))	chr14:53238156-53238396(+)$1	1	54	81	11.1575
.(((((((((......)))))))))..	chr9:73000568-73000808(-)$1	1	178	205	12.7584
.(((....(((.....)))....))).	chr4:69179381-69179621(-)$1	1	123	150	10.3491
..(((.((((......)))).)))..)	chr12:93895064-93895306(+)$1	1	31	58	12.1460
(.(((.((((......)))).))).).	chr13:103331363-103331603(+)$1	1	140	167	12.7137
((((((.(((......))).)))))))	chr10:30305723-30305963(-)$1	1	10	37	16.4823
(((((..(((......)))..))))))	chr3:32524928-32525179(-)$1	1	174	201	12.8105
.(((((((((......)))))))))..	chr5:112213402-112213642(-)$1	1	196	223	15.8789
((((((.(((......))).)))))))	chr5:74075130-74075370(-)$1	1	107	134	16.4823
((((((((((......)))))))....	chr4:68482630-68482870(-)$1	1	165	192	14.0204
(((((((((.........)))))))))	chr18:57571079-57571359(+)$1	1	168	195	12.2208
.))))).(((......)))(((((((.	chr3:158323308-158323548(+)$1	1	191	218	11.3041
.((((((.((......))..)))))).	chr1:32374216-32374456(-)$1	1	80	107	10.9680
((((((((((.......))))))))))	chr5:114950665-114950905(-)$1	1	82	109	11.7552
((((((((((((...))))))))))))	chr3:40575515-40575755(+)$1	1	128	155	13.6528
((((..((((......))))..)))).	chr10:99434295-99434535(+)$1	1	38	65	11.2679
((((((((((.......))))))))))	chr1:182352088-182352368(-)$1	1	136	163	11.7552
((((...(((......))).)))))))	chrX:24229990-24230230(+)$1	1	208	235	14.7233
((((((((((......)).)).)))))	chr1:65692940-65693180(+)$1	1	65	92	12.9551
((((...(((......))).)))))))	chr2:62451439-62451686(+)$1	1	148	175	16.3745
((..(((((((((...)))))))))..	chr12:69234503-69234745(+)$1	1	86	113	11.3802
(((...((((......))))....)))	chr13:39585374-39585614(-)$1	1	141	168	12.6254
.((...((((......))))....)).	chr8:28608578-28608818(+)$1	1	119	146	12.0836
(((..(((.........)))...))).	chr5:125829041-125829281(+)$1	1	106	133	10.4216
(..(((((((......))))))).)))	chr1:215794801-215795041(+)$1	1	31	58	13.5702
..((((.(((......))).))))..)	chr3:47893617-47893859(-)$1	1	37	64	12.0878
.(((((..((......))..)))))..	chr3:176742613-176742853(-)$1	1	43	70	11.9232
((((..((((......))))..)))))	chr12:72317619-72317859(+)$1	1	54	81	11.6603
((((((((((.......))))))))))	chr10:72637452-72637692(+)$1	1	32	59	11.7552
((((((((((......)))))))))).	chr5:34907878-34908118(-)$1	1	111	138	17.1100
.(((((((((......)))))))))..	chr6:13978878-13979118(+)$1	1	147	174	12.7584
((((((.(((......))).)))))..	chr1:21070664-21070927(-)$1	1	50	77	13.2925
((.(((((((......))))))).)))	chr4:40815198-40815438(-)$1	1	145	172	13.8469
((((((((.(......).)))))))..	chr21:15745095-15745335(-)$1	1	131	158	14.4734
((((((((((.........))))))))	chr1:53289075-53289318(+)$1	1	58	85	13.0577
((((((((((......)))))))))))	chr1:150620482-150620727(-)$1	1	36	63	17.0276
..(((...((......))...)))...	chr2:29023745-29023985(+)$1	1	75	102	13.8853
..((.(((((......))))).))...	chr7:112461109-112461349(-)$1	1	101	128	11.9882
(((((((((.........)))))))))	chr7:107560096-107560342(+)$1	1	117	144	12.2208
..((((((((((....)))))))))))	chr6:7417823-7418063(+)$1	1	189	216	12.4210
(((....(((......)))...)))))	chr1:32373901-32374141(-)$1	1	41	68	13.7184
((((((((((......).))).)))))	chr1:236713991-236714231(-)$1	1	1	28	11.6265
(((((((((((...)))))))))))).	chr11:113148560-113148800(+)$1	1	179	206	13.4848
(((((((.((......))...))))))	chr11:65180347-65180589(+)$1	1	43	70	14.9420
..(((((((((.....))))))))).)	chr12:77415061-77415301(-)$1	1	204	231	12.1098
((.(((((((......))))))).)))	chr1:230416050-230416290(+)$1	1	121	148	13.8469
(...(((((((.....)))))))....	chr9:133513196-133513439(+)$1	1	115	142	10.5022

#PSSM
= : 0.23	e : 0.12	c : 0.12	! : 0.10	i : 0.08	[ : 0.06	f : 0.06	: : 0.04	# : 0.04	a : 0.02	0 : 0.02	" : 0.02	d : 0.02	g : 0.02	
= : 0.23	e : 0.19	i : 0.14	! : 0.12	c : 0.10	f : 0.04	g : 0.04	[ : 0.02	d : 0.02	b : 0.02	# : 0.02	" : 0.02	
= : 0.25	e : 0.17	i : 0.17	c : 0.12	f : 0.04	d : 0.04	g : 0.04	! : 0.04	b : 0.04	[ : 0.04	" : 0.02	
= : 0.25	i : 0.17	g : 0.12	e : 0.10	c : 0.08	! : 0.06	" : 0.06	f : 0.04	d : 0.04	b : 0.02	# : 0.02	
= : 0.23	i : 0.19	g : 0.12	! : 0.08	e : 0.08	" : 0.08	c : 0.06	# : 0.04	f : 0.04	d : 0.02	[ : 0.02	
= : 0.23	i : 0.19	g : 0.12	e : 0.10	" : 0.10	! : 0.06	# : 0.04	[ : 0.04	f : 0.04	c : 0.02	d : 0.02	
= : 0.19	i : 0.17	d : 0.12	g : 0.12	[ : 0.08	" : 0.06	e : 0.04	# : 0.04	! : 0.04	c : 0.04	: : 0.02	f : 0.02	b : 0.02	
c : 0.23	= : 0.19	i : 0.14	d : 0.12	g : 0.12	e : 0.04	[ : 0.04	# : 0.02	b : 0.02	! : 0.02	" : 0.02	
c : 0.23	= : 0.19	i : 0.14	d : 0.12	g : 0.10	b : 0.10	e : 0.04	r : 0.02	[ : 0.02	
c : 0.21	= : 0.19	d : 0.12	i : 0.10	g : 0.10	b : 0.10	r : 0.06	e : 0.04	a : 0.04	
o : 0.70	r : 0.08	p : 0.06	= : 0.06	i : 0.04	c : 0.02	g : 0.02	
o : 0.70	r : 0.08	n : 0.06	p : 0.06	= : 0.04	i : 0.02	l : 0.02	
o : 0.70	r : 0.08	n : 0.06	p : 0.06	l : 0.04	i : 0.02	m : 0.02	
o : 0.70	r : 0.08	n : 0.06	p : 0.06	l : 0.06	m : 0.02	
o : 0.70	r : 0.08	n : 0.06	p : 0.06	l : 0.04	m : 0.02	= : 0.02	
o : 0.70	r : 0.08	n : 0.06	p : 0.06	= : 0.04	l : 0.02	m : 0.02	
c : 0.21	d : 0.12	i : 0.10	g : 0.10	b : 0.10	= : 0.10	r : 0.08	p : 0.06	e : 0.04	a : 0.04	
c : 0.23	= : 0.17	d : 0.12	i : 0.10	g : 0.10	b : 0.10	r : 0.06	e : 0.04	] : 0.04	
c : 0.25	= : 0.17	i : 0.14	d : 0.12	g : 0.12	e : 0.04	2 : 0.04	3 : 0.04	] : 0.02	r : 0.02	
= : 0.19	i : 0.14	g : 0.14	d : 0.12	] : 0.12	2 : 0.06	3 : 0.06	e : 0.04	c : 0.04	4 : 0.02	b : 0.02	
= : 0.25	g : 0.17	i : 0.14	e : 0.08	3 : 0.08	4 : 0.06	2 : 0.06	] : 0.04	f : 0.02	b : 0.02	d : 0.02	c : 0.02	
= : 0.25	i : 0.17	g : 0.17	2 : 0.06	4 : 0.06	c : 0.06	e : 0.06	] : 0.06	3 : 0.04	f : 0.02	d : 0.02	
= : 0.25	i : 0.19	g : 0.17	e : 0.10	4 : 0.06	c : 0.06	f : 0.04	d : 0.04	2 : 0.02	3 : 0.02	b : 0.02	
= : 0.25	i : 0.19	e : 0.12	c : 0.10	4 : 0.08	g : 0.06	] : 0.06	f : 0.04	d : 0.04	b : 0.02	
= : 0.25	i : 0.19	e : 0.12	c : 0.10	g : 0.06	f : 0.06	2 : 0.04	4 : 0.04	3 : 0.04	] : 0.02	d : 0.02	b : 0.02	
= : 0.25	c : 0.10	e : 0.08	2 : 0.08	i : 0.08	3 : 0.08	4 : 0.06	f : 0.06	: : 0.04	g : 0.04	a : 0.02	d : 0.02	b : 0.02	] : 0.02	
= : 0.19	] : 0.12	3 : 0.10	i : 0.08	c : 0.08	e : 0.06	2 : 0.06	4 : 0.06	: : 0.04	g : 0.04	f : 0.04	d : 0.04	b : 0.02	l : 0.02	

#score	611.598134940206
#seq	47
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_CDS_m2_run2.txt

#BEAR
dd[cccqqqqqqqqccc]ddd	chr5:137910904-137911139(-)$1	235	172	193	15.0362
ffffffqqqqqqqqffffff:	chr15:68582871-68583117(+)$1	246	120	141	13.9098
eeeebbqqqqqqqqbb]eeee	chr17:8108506-8108762(-)$1	256	88	109	13.7473
[eeeeeqqqqqqqqeeeee]c	chr17:56166511-56166762(+)$1	251	77	98	14.2967
c!!cccqqqqqqqqccc4444	chr6:64421867-64422147(+)$1	280	239	260	16.0156
ffffffqqqqqqqqffffff:	chr2:44152160-44152392(-)$1	232	42	63	13.9098
[eeeeeqqqqqqqqeeeee55	chr3:160149979-160150314(+)$1	335	101	122	12.9429
iiiiiiqqqqqqqqiiiiiii	chr1:23637640-23637905(-)$1	265	35	56	14.5321
!!ddddqqqqqqqqdddd]cc	chr19:33535131-33535365(-)$1	234	199	220	14.5495
ee[cccqqqqqqqqccceeee	chr7:151843580-151843846(-)$1	266	71	92	15.2845
ffffffqqqqqqqqffffffe	chr6:111208609-111208869(+)$1	260	171	192	14.4611
bb[cccqqqqqqqqcccbb44	chr7:32914645-32914871(-)$1	226	164	185	14.5374
a[ddddqqqqqqqqdddd]a:	chr21:26978666-26978897(-)$1	231	94	115	13.6587
ffffffqqqqqqqqffffffJ	chr6:44217332-44217608(+)$1	276	229	250	13.3107
ccc[bbqqqqqqqqbb]ccc:	chr9:96285480-96285705(+)$1	225	133	154	13.4013
!!ddddqqqqqqqqdddd]cc	chr9:88292290-88292525(-)$1	235	109	130	14.5495
ffffffqqqqqqqqffffff:	chr15:23021104-23021411(-)$1	307	88	109	13.9098
iiiiiiqqqqqqqqiiiiiii	chr1:54273228-54273544(-)$1	316	93	114	14.5321
ee[cccqqqqqqqqccc]eee	chr3:56700278-56700512(-)$1	234	94	115	15.4699
!!ddddqqqqqqqqdddd22a	chr10:116734894-116735155(+)$1	261	47	68	14.2516
fff[bbqqqqqqqqbbfffff	chr5:140966514-140966762(-)$1	248	175	196	13.9981
ccccccqqqqqqqqccc]ccc	chrX:131762555-131762818(-)$1	263	119	140	15.4592
dddcccqqqqqqqqccc::dd	chr7:107559575-107559803(+)$1	228	95	116	12.8340
f!!cccqqqqqqqqccc22ff	chr16:31201251-31201547(+)$1	296	104	125	15.5800
ccddddqqqqqqqqdddd]cc	chr13:48807390-48807617(+)$1	227	133	154	14.3374
ffffffqqqqqqqqffffff:	chrM:15364-15658(+)$1	294	192	213	13.9098
ggggggqqqqqqqqggggggg	chr1:53692583-53692861(-)$1	278	6	27	14.7515
!!ddddqqqqqqqqdddd22b	chr16:2305489-2305720(-)$1	231	57	78	14.0443
bb[cccqqqqqqqqccc]bb:	chr8:124042809-124043050(-)$1	241	98	119	13.9504
c[ddddqqqqqqqqdddd]cc	chr8:104432527-104432774(+)$1	247	224	245	14.4958
ffffffqqqqqqqqffffffd	chr19:3975996-3976389(-)$1	393	154	175	14.4614
[eeeeeqqqqqqqqeeeee]d	chr3:185638791-185639075(-)$1	284	225	246	14.1652
[ccc[aqqqqqqqqa]ccc]i	chr5:32390366-32390610(-)$1	244	129	150	14.4790
deeeeeqqqqqqqqeeeee::	chr15:70343653-70343879(-)$1	226	92	113	12.3702
ggggggqqqqqqqqggggggg	chr1:205696744-205696987(-)$1	243	35	56	14.7515
ggggggqqqqqqqqggggggg	chr10:85910398-85910737(+)$1	339	101	122	14.7515
dd!!bbqqqqqqqqbb333dd	chr12:110813750-110814008(-)$1	258	208	229	14.2569
ffffffqqqqqqqqffffff4	chr12:123795501-123795731(-)$1	230	105	126	14.6279
ee[cccqqqqqqqqccc333e	chr12:93969276-93969535(+)$1	259	84	105	15.9845
cc[cccqqqqqqqqccc]ccc	chr17:34893434-34893659(+)$1	225	144	165	15.7766
c[ddddqqqqqqqqdddd]cc	chr17:10600642-10600874(-)$1	232	60	81	14.4958
=!!cccqqqqqqqqccc333=	chr10:76729696-76729959(+)$1	263	82	103	16.2602
ceeeeeqqqqqqqqeeeee]c	chr3:197677918-197678185(+)$1	267	176	197	14.2180
ff!!bbqqqqqqqqbb22fff	chr5:162883807-162884061(-)$1	254	146	167	13.9595
cc[cccqqqqqqqqccc]ccc	chr1:29069072-29069363(+)$1	291	126	147	15.7766
gg!!bbqqqqqqqqbb]gggg	chr12:120903391-120903639(-)$1	248	181	202	14.4316
fffcccqqqqqqqqccc0000	chr1:200377053-200377431(-)$1	378	205	226	13.8945
d!!cccqqqqqqqqccc]ddd	chr1:151314457-151314716(-)$1	259	195	216	15.2977
!eeeeeqqqqqqqqeeeee22	chr5:33461678-33461949(+)$1	271	77	98	13.8431
ffffffqqqqqqqqffffff]	chr8:27632928-27633151(+)$1	223	152	173	14.5648
bbddddqqqqqqqqdddd333	chr15:65868541-65868831(+)$1	290	41	62	14.0409
ee[cccqqqqqqqqccc22ee	chr7:158468106-158468355(-)$1	249	55	76	15.3926
d!!cccqqqqqqqqccc22dd	chr21:30433543-30433817(-)$1	274	29	50	15.3658
ffffffqqqqqqqqffffff:	chr2:24262123-24262361(-)$1	238	115	136	13.9098
###abbqqqqqqqqbb]a444	chr10:106019233-106019485(+)$1	252	155	176	14.2667
ee!!bbqqqqqqqqbbeeeee	chr12:56500673-56500969(+)$1	296	77	98	14.0563
###cccqqqqqqqqccc22cc	chr15:90170140-90170441(+)$1	301	127	148	15.4379
e!!cccqqqqqqqqccc22ee	chr2:114512666-114512911(-)$1	245	160	181	15.5011
ggggggqqqqqqqqggggggg	chr22:46711840-46712078(+)$1	238	102	123	14.7515
cc[cccqqqqqqqqcccccc4	chr15:65450063-65450347(-)$1	284	148	169	15.5982

#otherMatches

#Seq PSSM
GCGCCGCAGCCUCCCGGGGCC	chr5:137910904-137911139(-)$1	235	172	193	15.0362
UGUCCACAAUGCUAUGGACAA	chr15:68582871-68583117(+)$1	246	120	141	13.9098
CCCCCAGAGAUGAUUGAGGGG	chr17:8108506-8108762(-)$1	256	88	109	13.7473
CAUCUAUUUUUACUUGGGUCA	chr17:56166511-56166762(+)$1	251	77	98	14.2967
AACAUCAGUAGUAGGGUCCUC	chr6:64421867-64422147(+)$1	280	239	260	16.0156
UGUAAAAUACAUCCUUUACAC	chr2:44152160-44152392(-)$1	232	42	63	13.9098
AUUUGCAACGGGUAGCAGAAU	chr3:160149979-160150314(+)$1	335	101	122	12.9429
UAAAACAAAAUACAGUUUUAU	chr1:23637640-23637905(-)$1	265	35	56	14.5321
AAACCUUCUGAAGUAGGUGUC	chr19:33535131-33535365(-)$1	234	199	220	14.5495
AGUCUGAAAUGCUCCAGCUUU	chr7:151843580-151843846(-)$1	266	71	92	15.2845
GCUUAUGUACUCAGGUAAGUC	chr6:111208609-111208869(+)$1	260	171	192	14.4611
AUGCUGCCACCUUACAGAUAA	chr7:32914645-32914871(-)$1	226	164	185	14.5374
GUGAUGAAUAAAAACAUUUCA	chr21:26978666-26978897(-)$1	231	94	115	13.6587
GCUGACCAUGGUAAGUUAGCU	chr6:44217332-44217608(+)$1	276	229	250	13.3107
AUCGUGCUCUGCUCCAGGAUC	chr9:96285480-96285705(+)$1	225	133	154	13.4013
AAUCUCCCCCACAUGAGGACU	chr9:88292290-88292525(-)$1	235	109	130	14.5495
GUGGAAAAUAUGACUUCUAUA	chr15:23021104-23021411(-)$1	307	88	109	13.9098
CCACUUGACACAGUGAGUGGC	chr1:54273228-54273544(-)$1	316	93	114	14.5321
UUUUAGUAUUAUUUUUAUGAG	chr3:56700278-56700512(-)$1	234	94	115	15.4699
UAGAAGAACAUGCCCUUCCUG	chr10:116734894-116735155(+)$1	261	47	68	14.2516
UGUUGCUUCUUCCUGUGCAUU	chr5:140966514-140966762(-)$1	248	175	196	13.9981
CCCAGUAUAAUACCACUAGGG	chrX:131762555-131762818(-)$1	263	119	140	15.4592
UGCUGCGUCAUUUGGCAAAUC	chr7:107559575-107559803(+)$1	228	95	116	12.8340
UCUAGGUAAAGAAUUCUCCGG	chr16:31201251-31201547(+)$1	296	104	125	15.5800
CUGGCCCAGAAGGAGGCCAAG	chr13:48807390-48807617(+)$1	227	133	154	14.3374
CGAAUGAUAUUUCCUAUUCGC	chrM:15364-15658(+)$1	294	192	213	13.9098
AAGUUUUAAUGCCUAAACUUU	chr1:53692583-53692861(-)$1	278	6	27	14.7515
CAGGAGAUUCAGCCCUCCCAG	chr16:2305489-2305720(-)$1	231	57	78	14.0443
GGAGGCCAAUCACUGCCACCU	chr8:124042809-124043050(-)$1	241	98	119	13.9504
UUUAGUUUUUAGUUACUGUAG	chr8:104432527-104432774(+)$1	247	224	245	14.4958
UUUUAACAAACGCAUUAAGAG	chr19:3975996-3976389(-)$1	393	154	175	14.4614
CAGUGUACAGAGCAGCACUAU	chr3:185638791-185639075(-)$1	284	225	246	14.1652
GCCGCCGAAUGCCAGAUGGAG	chr5:32390366-32390610(-)$1	244	129	150	14.4790
UGGGAAAGAUAACCUUCUCAA	chr15:70343653-70343879(-)$1	226	92	113	12.3702
UUUGAAAAACACUGUUUAGAU	chr1:205696744-205696987(-)$1	243	35	56	14.7515
GCCACUCUUUACUCAGUGGCA	chr10:85910398-85910737(+)$1	339	101	122	14.7515
GUUAUGGAAACACACACACAC	chr12:110813750-110814008(-)$1	258	208	229	14.2569
UCGGGAAUUCUUACUCUCGAU	chr12:123795501-123795731(-)$1	230	105	126	14.6279
GCCUCACUGCAAUUUGAUAUG	chr12:93969276-93969535(+)$1	259	84	105	15.9845
UCUUCCUAGGAAUCGGACGAU	chr17:34893434-34893659(+)$1	225	144	165	15.7766
UGGUCCUAGUACCCGGACGAG	chr17:10600642-10600874(-)$1	232	60	81	14.4958
AUAAUAUGCUUUUUUGUGAUU	chr10:76729696-76729959(+)$1	263	82	103	16.2602
CUCUUCUUAAAAUUGAAGGUG	chr3:197677918-197678185(+)$1	267	176	197	14.2180
UGAGUAUGUGuaauuaaauau	chr5:162883807-162884061(-)$1	254	146	167	13.9595
UCAGGGACAGUCUACUCAGAG	chr1:29069072-29069363(+)$1	291	126	147	15.7766
AAGAUCUGAUUUCCGAGUUCU	chr12:120903391-120903639(-)$1	248	181	202	14.4316
GUUUUCAAAGAAAAGAAGAUA	chr1:200377053-200377431(-)$1	378	205	226	13.8945
UCUACUUAGUACCUGGUUGCU	chr1:151314457-151314716(-)$1	259	195	216	15.2977
UUUGCUUUAUCCUCAGCAACU	chr5:33461678-33461949(+)$1	271	77	98	13.8431
ACAGGUGAAUCUCAGCCUGUG	chr8:27632928-27633151(+)$1	223	152	173	14.5648
CUUCUGGUUAUAAAUAGACAA	chr15:65868541-65868831(+)$1	290	41	62	14.0409
GGUGUUUGUAAAAUAACUUCU	chr7:158468106-158468355(-)$1	249	55	76	15.3926
UCUUUCCAUUGCUUGAAUAAA	chr21:30433543-30433817(-)$1	274	29	50	15.3658
GGCUUCACAGUGGAGAGGUCA	chr2:24262123-24262361(-)$1	238	115	136	13.9098
AAUCCCUUUGGUCUGGUGCCA	chr10:106019233-106019485(+)$1	252	155	176	14.2667
GGCUGAUGAUUCUUUCUUUAC	chr12:56500673-56500969(+)$1	296	77	98	14.0563
GAACUUAUACACGGAAGAAGC	chr15:90170140-90170441(+)$1	301	127	148	15.4379
ACUUACUUCGGUAUGUACCUU	chr2:114512666-114512911(-)$1	245	160	181	15.5011
UUUGCAAGUAUUCCUGCAAAU	chr22:46711840-46712078(+)$1	238	102	123	14.7515
UGCUAUCUGUGACUGUACAAC	chr15:65450063-65450347(-)$1	284	148	169	15.5982

#DB
((.(((........))).)))	chr5:137910904-137911139(-)$1	1	172	193	15.0362
((((((........)))))).	chr15:68582871-68583117(+)$1	1	120	141	13.9098
((((((........)).))))	chr17:8108506-8108762(-)$1	1	88	109	13.7473
.(((((........))))).)	chr17:56166511-56166762(+)$1	1	77	98	14.2967
(..(((........)))....	chr6:64421867-64422147(+)$1	1	239	260	16.0156
((((((........)))))).	chr2:44152160-44152392(-)$1	1	42	63	13.9098
.(((((........)))))..	chr3:160149979-160150314(+)$1	1	101	122	12.9429
((((((........)))))))	chr1:23637640-23637905(-)$1	1	35	56	14.5321
..((((........)))).))	chr19:33535131-33535365(-)$1	1	199	220	14.5495
((.(((........)))))))	chr7:151843580-151843846(-)$1	1	71	92	15.2845
((((((........)))))))	chr6:111208609-111208869(+)$1	1	171	192	14.4611
((.(((........)))))..	chr7:32914645-32914871(-)$1	1	164	185	14.5374
(.((((........)))).).	chr21:26978666-26978897(-)$1	1	94	115	13.6587
((((((........)))))))	chr6:44217332-44217608(+)$1	1	229	250	13.3107
(((.((........)).))).	chr9:96285480-96285705(+)$1	1	133	154	13.4013
..((((........)))).))	chr9:88292290-88292525(-)$1	1	109	130	14.5495
((((((........)))))).	chr15:23021104-23021411(-)$1	1	88	109	13.9098
((((((........)))))))	chr1:54273228-54273544(-)$1	1	93	114	14.5321
((.(((........))).)))	chr3:56700278-56700512(-)$1	1	94	115	15.4699
..((((........))))..)	chr10:116734894-116735155(+)$1	1	47	68	14.2516
(((.((........)))))))	chr5:140966514-140966762(-)$1	1	175	196	13.9981
((((((........))).)))	chrX:131762555-131762818(-)$1	1	119	140	15.4592
)))(((........)))..((	chr7:107559575-107559803(+)$1	1	95	116	12.8340
(..(((........)))..))	chr16:31201251-31201547(+)$1	1	104	125	15.5800
((((((........)))).))	chr13:48807390-48807617(+)$1	1	133	154	14.3374
((((((........)))))).	chrM:15364-15658(+)$1	1	192	213	13.9098
((((((........)))))))	chr1:53692583-53692861(-)$1	1	6	27	14.7515
..((((........))))..)	chr16:2305489-2305720(-)$1	1	57	78	14.0443
((.(((........))).)).	chr8:124042809-124043050(-)$1	1	98	119	13.9504
(.((((........)))).))	chr8:104432527-104432774(+)$1	1	224	245	14.4958
((((((........)))))))	chr19:3975996-3976389(-)$1	1	154	175	14.4614
.(((((........))))).)	chr3:185638791-185639075(-)$1	1	225	246	14.1652
.(((.(........).))).)	chr5:32390366-32390610(-)$1	1	129	150	14.4790
)(((((........)))))..	chr15:70343653-70343879(-)$1	1	92	113	12.3702
((((((........)))))))	chr1:205696744-205696987(-)$1	1	35	56	14.7515
((((((........)))))))	chr10:85910398-85910737(+)$1	1	101	122	14.7515
((..((........))...))	chr12:110813750-110814008(-)$1	1	208	229	14.2569
((((((........)))))).	chr12:123795501-123795731(-)$1	1	105	126	14.6279
((.(((........)))...)	chr12:93969276-93969535(+)$1	1	84	105	15.9845
((.(((........))).)))	chr17:34893434-34893659(+)$1	1	144	165	15.7766
(.((((........)))).))	chr17:10600642-10600874(-)$1	1	60	81	14.4958
(..(((........)))...)	chr10:76729696-76729959(+)$1	1	82	103	16.2602
((((((........))))).)	chr3:197677918-197678185(+)$1	1	176	197	14.2180
((..((........))..)))	chr5:162883807-162884061(-)$1	1	146	167	13.9595
((.(((........))).)))	chr1:29069072-29069363(+)$1	1	126	147	15.7766
((..((........)).))))	chr12:120903391-120903639(-)$1	1	181	202	14.4316
((((((........)))....	chr1:200377053-200377431(-)$1	1	205	226	13.8945
(..(((........))).)))	chr1:151314457-151314716(-)$1	1	195	216	15.2977
.(((((........)))))..	chr5:33461678-33461949(+)$1	1	77	98	13.8431
((((((........)))))).	chr8:27632928-27633151(+)$1	1	152	173	14.5648
((((((........))))...	chr15:65868541-65868831(+)$1	1	41	62	14.0409
((.(((........)))..))	chr7:158468106-158468355(-)$1	1	55	76	15.3926
(..(((........)))..))	chr21:30433543-30433817(-)$1	1	29	50	15.3658
((((((........)))))).	chr2:24262123-24262361(-)$1	1	115	136	13.9098
...(((........)).)...	chr10:106019233-106019485(+)$1	1	155	176	14.2667
((..((........)))))))	chr12:56500673-56500969(+)$1	1	77	98	14.0563
...(((........)))..))	chr15:90170140-90170441(+)$1	1	127	148	15.4379
(..(((........)))..))	chr2:114512666-114512911(-)$1	1	160	181	15.5011
((((((........)))))))	chr22:46711840-46712078(+)$1	1	102	123	14.7515
((.(((........)))))).	chr15:65450063-65450347(-)$1	1	148	169	15.5982

#PSSM
f : 0.23	c : 0.16	e : 0.11	d : 0.09	! : 0.08	g : 0.08	[ : 0.06	b : 0.05	i : 0.03	# : 0.03	a : 0.01	= : 0.01	
f : 0.21	e : 0.19	! : 0.16	c : 0.11	g : 0.08	d : 0.05	b : 0.05	[ : 0.05	i : 0.03	# : 0.03	
f : 0.19	[ : 0.16	! : 0.16	d : 0.16	e : 0.11	g : 0.06	c : 0.05	i : 0.03	# : 0.03	
c : 0.35	f : 0.16	d : 0.15	e : 0.11	g : 0.06	! : 0.06	i : 0.03	[ : 0.03	a : 0.01	
c : 0.33	f : 0.16	d : 0.15	b : 0.13	e : 0.09	g : 0.06	i : 0.03	[ : 0.01	
c : 0.33	f : 0.16	d : 0.15	b : 0.13	e : 0.09	g : 0.06	i : 0.03	a : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.33	f : 0.16	d : 0.15	b : 0.13	e : 0.09	g : 0.06	i : 0.03	a : 0.01	
c : 0.33	f : 0.16	d : 0.15	b : 0.13	e : 0.09	g : 0.06	i : 0.03	] : 0.01	
c : 0.35	f : 0.18	d : 0.15	e : 0.11	] : 0.06	g : 0.06	i : 0.03	3 : 0.01	2 : 0.01	
f : 0.18	e : 0.15	d : 0.15	] : 0.11	2 : 0.09	g : 0.08	c : 0.05	3 : 0.05	i : 0.03	4 : 0.01	b : 0.01	: : 0.01	0 : 0.01	a : 0.01	
f : 0.19	e : 0.16	2 : 0.11	] : 0.09	c : 0.09	g : 0.08	3 : 0.06	d : 0.03	4 : 0.03	i : 0.03	b : 0.03	: : 0.01	0 : 0.01	
f : 0.21	c : 0.18	e : 0.09	d : 0.08	g : 0.08	] : 0.06	4 : 0.05	2 : 0.05	3 : 0.05	i : 0.03	5 : 0.01	a : 0.01	b : 0.01	: : 0.01	0 : 0.01	
c : 0.18	: : 0.15	e : 0.13	d : 0.11	4 : 0.08	g : 0.08	i : 0.05	f : 0.05	5 : 0.01	J : 0.01	a : 0.01	b : 0.01	= : 0.01	0 : 0.01	2 : 0.01	] : 0.01	3 : 0.01	

#score	870.3579667832444
#seq	60
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_CDS_m1_run1.txt

#BEAR
dddddddd"""bboooooobb333dddd]ddd	chr14:31077051-31077269(+)$1	218	125	157	13.4454
eeeedddd!!cccoooooocccdddd4444ee	chr2:27446363-27446586(+)$1	223	46	78	14.6140
d####bb!!cccaooooooa]ccc22bb22dd	chr6:151669803-151670022(+)$1	219	58	90	12.6256
"""dddd[a!!cccnnnnnccc22a]dddd33	chr19:37238906-37239121(-)$1	215	48	80	12.9604
'''eeeee[ddddoooooodddd]eeeeeeee	chr12:109540609-109540829(+)$1	220	50	82	12.2050
=============oooooo=============	chr17:30678796-30679020(+)$1	224	184	216	13.9271
"bb"""gggggggooooooggggggg333bb4	chr6:151266509-151266727(+)$1	218	27	59	12.7316
fffffbb!!a!!aooooooa22a22bb333ff	chrX:24006340-24006585(-)$1	245	89	121	12.1610
eeeee[ccc[ccclllcccccc333eeeee:h	chr19:11136877-11137115(+)$1	238	137	169	11.1900
c[bbeeeee!!cccnnnnnccc]eeeee22bb	chr3:101370386-101370602(-)$1	216	147	179	11.3346
e$$$$$ccc[cccooooooccc]ccc4444ee	chr1:203768666-203768888(+)$1	222	171	203	14.6557
dd!!ddddccc[annnnnaccc22dddddddd	chr19:6415480-6415707(-)$1	227	110	142	12.1840
eeeeeeeeee!!cccmmmmccc22eeeee:cc	chr1:153642572-153642783(-)$1	211	124	156	10.3931
d[a"""a[eeeeeooooooeeeeea]a]dddd	chr10:43883045-43883433(-)$1	388	89	121	12.1396
dddd$$$$$ddddoooooodddddddd]dddd	chr19:9677400-9677623(-)$1	223	54	86	11.5936
ffff[dddd[cccooooooccc]ddddfffff	chr2:64780142-64780360(+)$1	218	111	143	13.9359
ccc!!iiiiiiiiiooooooiiiiiiiii22c	chr14:102446620-102446841(+)$1	221	174	206	12.4227
!ggggggg[ddddoooooodddd]gggggggc	chr1:155932659-155932883(-)$1	224	132	164	13.2813
"""eeeee!!cccooooooccc333eeeeeee	chr1:151006339-151006564(+)$1	225	116	148	17.2797
ddd####eeeeeooooooeeeee333dddd]e	chr1:231003828-231004049(-)$1	221	122	154	11.8887
b[ggggggg[cccooooooccc]ggggggg]b	chr12:12318093-12318316(-)$1	223	17	49	14.7486
ccdddd"""ddddoooooodddd22ddddddd	chr11:35641375-35641598(+)$1	223	83	115	13.4666
eeee[dddd!!cccnnnnnccc22ddddeeee	chr19:3381841-3382075(+)$1	234	39	71	12.7187
ddd[a!!eeeeeooooooeeeee22a]dddd2	chr9:35717532-35717771(-)$1	239	40	72	11.4163
ccc!!eeeeecccooooooccc22eeeee22c	chr7:72987563-72987774(-)$1	211	160	192	16.1307
ccggggggg!!bboooooobb]ggggggg]cc	chr2:86269047-86269262(-)$1	215	19	51	12.7346
!bb[aeeeeecccnnnnnccc]eeeee]a22b	chr8:145666117-145666346(-)$1	229	181	213	10.2141
ccceeeee!!cccooooooccc22eeeee]cc	chr4:2941204-2941427(-)$1	223	152	184	16.8491
:ggggggg!!cccooooooccc]ggggggg::	chr13:42875219-42875441(+)$1	222	100	132	12.8296
dddd[cccddddoooooodddd333ccc]ddd	chr2:97427768-97427986(+)$1	218	18	50	12.6923
[eeeee####cccooooooccc333eeeee]d	chr1:28661284-28661494(+)$1	210	29	61	16.6614
bb[ccc!!a[cccooooooccc]a22cccbb:	chr1:11983349-11983571(-)$1	222	24	56	13.2930
"""bb!!eeeeecccmmmmccc22eeeee]bb	chr17:80011746-80011966(+)$1	220	43	75	10.4519
c:eeeee[ccc!!ccclllccc22ccceeeee	chr2:97474267-97474486(+)$1	219	120	152	11.2521
ff[eeeee!!cccooooooccc333eeeeeff	chr16:24801514-24801726(+)$1	212	131	163	16.8309
ee[eeeee####cccmmmmccc333eeeee]e	chr7:6189618-6189845(+)$1	227	83	115	12.1194
Fbb[eeeeeddddoooooodddd]eeeee]bb	chr1:28601240-28601626(+)$1	386	289	321	12.6418
::eeeee"""cccnnnnnccc333eeeeeiii	chr19:33696837-33697095(+)$1	258	86	118	11.2828
fff[dddd!!cccooooooccc22dddd]fff	chr14:21461210-21461441(+)$1	231	25	57	15.6974
cc!!ccc[cccrrrrrrrrrccc333ccc22c	chr3:9799401-9799620(-)$1	219	81	113	10.6356
[a"""dddd[cccooooooccc333dddd]a]	chr17:79892783-79893014(-)$1	231	74	106	16.5258
cc####ccc!!cccnnnnnccc]ccc333ccc	chr17:40963679-40963904(-)$1	225	122	154	12.6511
eeee!!cccddddoooooodddd]ccc4444e	chr14:90755110-90755343(-)$1	233	90	122	13.5671
::dddd[ccccccooooooccc]ccc]ddddG	chr21:40186764-40186994(+)$1	230	162	194	12.3339
abb[eeeeeccc[ccclllccc22ccc22eee	chr10:75757898-75758114(+)$1	216	153	185	11.5065
dcccddddccc[aooooooa]ccc]dddd]cc	chr17:42882968-42883197(-)$1	229	19	51	13.3573
[a[eeeee[ccc[ccclllccc22ccc]eeee	chr18:74090819-74091038(-)$1	219	36	68	12.5570
eeeee!!ccc[cccnnnnnccc]ccc]eeeee	chr3:47866517-47866739(+)$1	222	160	192	12.0511
gccc!!gggggggccclllccc22ggggggg2	chr3:196304483-196304712(+)$1	229	139	171	11.2841
$$ffffff!!cccooooooccc]ffffffccc	chr14:21859581-21859818(-)$1	237	155	187	13.5748
ffffffccc[cccooooooccc]ccc333fff	chr9:32541621-32541839(-)$1	218	129	161	14.3967
ddd!!ccc!!cccooooooccc22cccdddd2	chr17:4577764-4577998(-)$1	234	154	186	16.1019
fdddd####ddddoooooodddddddd]ffff	chr22:30403029-30403270(+)$1	241	183	215	12.0912

#otherMatches

#Seq PSSM
UCUAAAACCUUGUUUAACUGCCUUGUUUAUGG	chr14:31077051-31077269(+)$1	218	125	157	13.4454
UCGGCAUGCUUCUACCUCCAGAUAUGGGAACC	chr2:27446363-27446586(+)$1	223	46	78	14.6140
UGAAGAUGUGAGCAAAAGAGACUCCGAUAAAG	chr6:151669803-151670022(+)$1	219	58	90	12.6256
ACAUGUGGGAAGUCCUUCAGACAGCGUACACA	chr19:37238906-37239121(-)$1	215	48	80	12.9604
AAAGAGUUGUCUACAGACAUAGAGGAUUUUGU	chr12:109540609-109540829(+)$1	220	50	82	12.2050
CUUGAAAGAAUAAUCuuuuuuauuuuuuugag	chr17:30678796-30679020(+)$1	224	184	216	13.9271
UGUGAAUUGUCCAAGUUCAUGGACAACUAACU	chr6:151266509-151266727(+)$1	218	27	59	12.7316
ACCAUAGAACAACGGACCAGGAGAACUCAAGU	chrX:24006340-24006585(-)$1	245	89	121	12.1610
GUCCAAGGGUGAGAAGCUUCCCAACUGGAUGG	chr19:11136877-11137115(+)$1	238	137	169	11.1900
GAACACAUACUGGUGAACGGCCCUAUGUCUGU	chr3:101370386-101370602(-)$1	216	147	179	11.3346
UUUCAAGUCAGAGGUAUUACUCAGGCCCUCAA	chr1:203768666-203768888(+)$1	222	171	203	14.6557
CACCGGCCAGUCGGACUACACUAAGGCCUGGG	chr19:6415480-6415707(-)$1	227	110	142	12.1840
GCCCAGGAGGAGGGUGAGUACCAGCUUUUAGC	chr1:153642572-153642783(-)$1	211	124	156	10.3931
UGACAAGUGUCCAUGAUGCUGGGCCCUGAGGG	chr10:43883045-43883433(-)$1	388	89	121	12.1396
CCACCAAAUGUUCACCAGAGAACGUGGAUAGG	chr19:9677400-9677623(-)$1	223	54	86	11.5936
GCAAUGGUUUUCAAGACUCUGAUGAUUUUGCA	chr2:64780142-64780360(+)$1	218	111	143	13.9359
AGAAACGGGAGAGCCCGGAAGUUCUCCUGACU	chr14:102446620-102446841(+)$1	221	174	206	12.4227
UCGCUUGGGUGAUCUGCUCAUCAGCCAGGUGG	chr1:155932659-155932883(-)$1	224	132	164	13.2813
UCAGGACAGCCUGAGACAGCAGAUGUGUCCAG	chr1:151006339-151006564(+)$1	225	116	148	17.2797
AGGUAGGUGCGGGCCUGGCCGCGGACCCUCUU	chr1:231003828-231004049(-)$1	221	122	154	11.8887
GGAUUUGUUAUUUUUAGCUGAAGAAUAAAUGC	chr12:12318093-12318316(-)$1	223	17	49	14.7486
GCACUGUAAGGCCAAGUACGGCCGCCGGUCUG	chr11:35641375-35641598(+)$1	223	83	115	13.4666
GUCAAGCAGAAGUGGGCGUCGCGGCUGCUGGC	chr19:3381841-3382075(+)$1	234	39	71	12.7187
UCCUCAAGGCCAAGAGUGUGGCCCAGCGGACA	chr9:35717532-35717771(-)$1	239	40	72	11.4163
CAUGAAGGAAAGAUCCAGUUCUAUUUCCUCAA	chr7:72987563-72987774(-)$1	211	160	192	16.1307
CCCAUCCUUCUGUUCAGAUGCUGAGGAUGUGG	chr2:86269047-86269262(-)$1	215	19	51	12.7346
ACCACCAUGGGGCCGUGCGCCACUAUGAGGAG	chr8:145666117-145666346(-)$1	229	181	213	10.2141
UCACACCCCGGCUGGUCAAAGUGUGGGUGCUG	chr4:2941204-2941427(-)$1	223	152	184	16.8491
AUGGUGAUUCUGCCCAAGUGCAUAUUGCCACA	chr13:42875219-42875441(+)$1	222	100	132	12.8296
UAUAAUGACCUCGUGAAAGAGGAGCUCAAUAU	chr2:97427768-97427986(+)$1	218	18	50	12.6923
CCAGGGAACACAGACAGCACUGAGGCCUUGUC	chr1:28661284-28661494(+)$1	210	29	61	16.6614
GGAGUGGAAAUGAAGAAGAUCACUGACACCCA	chr1:11983349-11983571(-)$1	222	24	56	13.2930
AACGGCUGCAGUUCAUUGCUGAUCACUGCCCC	chr17:80011746-80011966(+)$1	220	43	75	10.4519
CAGGCAGCAGCAACCAGUUUGGCAGCUCUGUC	chr2:97474267-97474486(+)$1	219	120	152	11.2521
UAACUUUCAAGUUAACACAAACAAAGGAGGUG	chr16:24801514-24801726(+)$1	212	131	163	16.8309
GAAUGGGAUUGGUACGAUUGUGAGCUCCCACU	chr7:6189618-6189845(+)$1	227	83	115	12.1194
AGCUCAUAUCCCUUCAUUUGGGGCAUGUGUGC	chr1:28601240-28601626(+)$1	386	289	321	12.6418
CCCGCCCGACCAGUACCCCUGCGAGGGUGGCA	chr19:33696837-33697095(+)$1	258	86	118	11.2828
UAUCUAAUUACCCUACUGUGGGAUGUUGUAUA	chr14:21461210-21461441(+)$1	231	25	57	15.6974
CAAUGCCAGCAAGCCUUCAAUGCCACGGCUGU	chr3:9799401-9799620(-)$1	219	81	113	10.6356
GUAUGCCACAGGCACGCACGCCCAGGUGGAGG	chr17:79892783-79893014(-)$1	231	74	106	16.5258
UUUUUCUGGGACAACAAGUUUGACCAUGCAAU	chr17:40963679-40963904(-)$1	225	122	154	12.6511
GCUCAGUCUGCUCUAUGCUGAGCUGGAGGUGG	chr14:90755110-90755343(-)$1	233	90	122	13.5671
UCUCCUUGUCCAGGAUGAGCUGUGGCCGGGAA	chr21:40186764-40186994(+)$1	230	162	194	12.3339
GGGCGAGGUGGACGGCAAAGCCAUUCCUGACC	chr10:75757898-75758114(+)$1	216	153	185	11.5065
GGAGCUUCCUGACUCGCCUGCUAGAGGAGAUU	chr17:42882968-42883197(-)$1	229	19	51	13.3573
ACGCGGCCUUGCAGGCCCAGCCCGGCGUGGCU	chr18:74090819-74091038(-)$1	219	36	68	12.5570
AGGCCGAGUCAGGGAUGGCCCCCGGCGGGCCU	chr3:47866517-47866739(+)$1	222	160	192	12.0511
ACAUAAUGGAGAAGUCAAUGGCAGUUUUCCAC	chr3:196304483-196304712(+)$1	229	139	171	11.2841
CAGGGUCAUCCAGAGUUUGCUGUUGAUCCCCG	chr14:21859581-21859818(-)$1	237	155	187	13.5748
AGUUUUUGGCUCCUUCCUUGGAACCAUUUGAA	chr9:32541621-32541839(-)$1	218	129	161	14.3967
AGCAAUGCCAACAGCGACGUGUGUGCGGCUGC	chr17:4577764-4577998(-)$1	234	154	186	16.1019
GUGCCUCUGACUCCCGAUCGAGUGGCAGCAAG	chr22:30403029-30403270(+)$1	241	183	215	12.0912

#DB
((((((((...((......))...)))).)))	chr14:31077051-31077269(+)$1	1	125	157	13.4454
((((((((..(((......)))))))....))	chr2:27446363-27446586(+)$1	1	46	78	14.6140
(....((..((((......).)))..))..))	chr6:151669803-151670022(+)$1	1	58	90	12.6256
...((((.(..(((.....)))..).))))..	chr19:37238906-37239121(-)$1	1	48	80	12.9604
...(((((.((((......)))).))))))))	chr12:109540609-109540829(+)$1	1	50	82	12.2050
(((((((((((((......)))))))))))))	chr17:30678796-30679020(+)$1	1	184	216	13.9271
.((...(((((((......)))))))...)).	chr6:151266509-151266727(+)$1	1	27	59	12.7316
(((((((..(..(......)..)..))...))	chrX:24006340-24006585(-)$1	1	89	121	12.1610
(((((.(((.(((...))))))...))))).(	chr19:11136877-11137115(+)$1	1	137	169	11.1900
(.(((((((..(((.....))).)))))..))	chr3:101370386-101370602(-)$1	1	147	179	11.3346
(.....(((.(((......))).)))....))	chr1:203768666-203768888(+)$1	1	171	203	14.6557
((..(((((((.(.....))))..))))))))	chr19:6415480-6415707(-)$1	1	110	142	12.1840
)))))(((((..(((....)))..))))).((	chr1:153642572-153642783(-)$1	1	124	156	10.3931
(.(...(.(((((......)))))).).))))	chr10:43883045-43883433(-)$1	1	89	121	12.1396
((((.....((((......)))))))).))))	chr19:9677400-9677623(-)$1	1	54	86	11.5936
((((.((((.(((......))).)))))))))	chr2:64780142-64780360(+)$1	1	111	143	13.9359
(((..(((((((((......)))))))))..)	chr14:102446620-102446841(+)$1	1	174	206	12.4227
.(((((((.((((......)))).))))))))	chr1:155932659-155932883(-)$1	1	132	164	13.2813
...(((((..(((......)))...)))))))	chr1:151006339-151006564(+)$1	1	116	148	17.2797
(((....(((((......)))))...)))).)	chr1:231003828-231004049(-)$1	1	122	154	11.8887
(.(((((((.(((......))).))))))).)	chr12:12318093-12318316(-)$1	1	17	49	14.7486
))((((...((((......))))..))))(((	chr11:35641375-35641598(+)$1	1	83	115	13.4666
((((.((((..(((.....)))..))))))))	chr19:3381841-3382075(+)$1	1	39	71	12.7187
(((.(..(((((......)))))..).)))).	chr9:35717532-35717771(-)$1	1	40	72	11.4163
(((..((((((((......)))..)))))..)	chr7:72987563-72987774(-)$1	1	160	192	16.1307
(((((((((..((......)).))))))).))	chr2:86269047-86269262(-)$1	1	19	51	12.7346
.((.(((((((((.....))).))))).)..)	chr8:145666117-145666346(-)$1	1	181	213	10.2141
((((((((..(((......)))..))))).))	chr4:2941204-2941427(-)$1	1	152	184	16.8491
.(((((((..(((......))).)))))))..	chr13:42875219-42875441(+)$1	1	100	132	12.8296
((((.(((((((......))))...))).)))	chr2:97427768-97427986(+)$1	1	18	50	12.6923
.(((((....(((......)))...))))).)	chr1:28661284-28661494(+)$1	1	29	61	16.6614
((.(((..(.(((......))).)..))))).	chr1:11983349-11983571(-)$1	1	24	56	13.2930
...((..((((((((....)))..))))).))	chr17:80011746-80011966(+)$1	1	43	75	10.4519
).(((((.(((..(((...)))..))))))))	chr2:97474267-97474486(+)$1	1	120	152	11.2521
((.(((((..(((......)))...)))))))	chr16:24801514-24801726(+)$1	1	131	163	16.8309
((.(((((....(((....)))...))))).)	chr7:6189618-6189845(+)$1	1	83	115	12.1194
)((.(((((((((......)))).))))).))	chr1:28601240-28601626(+)$1	1	289	321	12.6418
..(((((...(((.....)))...)))))(((	chr19:33696837-33697095(+)$1	1	86	118	11.2828
(((.((((..(((......)))..)))).)))	chr14:21461210-21461441(+)$1	1	25	57	15.6974
((..(((.(((.........)))...)))..)	chr3:9799401-9799620(-)$1	1	81	113	10.6356
.(...((((.(((......)))...)))).).	chr17:79892783-79893014(-)$1	1	74	106	16.5258
((....(((..(((.....))).)))...)))	chr17:40963679-40963904(-)$1	1	122	154	12.6511
((((..(((((((......)))).)))....)	chr14:90755110-90755343(-)$1	1	90	122	13.5671
..((((.((((((......))).))).)))))	chr21:40186764-40186994(+)$1	1	162	194	12.3339
(((.((((((((.(((...)))..)))..)))	chr10:75757898-75758114(+)$1	1	153	185	11.5065
(((((((((((.(......).))).)))).))	chr17:42882968-42883197(-)$1	1	19	51	13.3573
.(.(((((.(((.(((...)))..))).))))	chr18:74090819-74091038(-)$1	1	36	68	12.5570
(((((..(((.(((.....))).))).)))))	chr3:47866517-47866739(+)$1	1	160	192	12.0511
)(((..((((((((((...)))..))))))).	chr3:196304483-196304712(+)$1	1	139	171	11.2841
..((((((..(((......))).)))))))))	chr14:21859581-21859818(-)$1	1	155	187	13.5748
(((((((((.(((......))).)))...)))	chr9:32541621-32541839(-)$1	1	129	161	14.3967
(((..(((..(((......)))..))))))).	chr17:4577764-4577998(-)$1	1	154	186	16.1019
(((((....((((......)))))))).))))	chr22:30403029-30403270(+)$1	1	183	215	12.0912

#PSSM
d : 0.18	c : 0.16	e : 0.15	f : 0.11	" : 0.07	: : 0.05	[ : 0.05	! : 0.03	b : 0.03	' : 0.01	= : 0.01	F : 0.01	a : 0.01	g : 0.01	$ : 0.01	
c : 0.16	d : 0.15	e : 0.15	b : 0.09	f : 0.09	" : 0.05	[ : 0.05	: : 0.05	$ : 0.03	g : 0.03	a : 0.03	# : 0.01	' : 0.01	= : 0.01	
d : 0.16	e : 0.16	b : 0.09	f : 0.09	c : 0.09	" : 0.07	g : 0.07	[ : 0.07	# : 0.03	! : 0.03	' : 0.01	= : 0.01	$ : 0.01	a : 0.01	
e : 0.28	d : 0.13	! : 0.09	[ : 0.09	f : 0.07	g : 0.07	# : 0.05	" : 0.05	c : 0.05	b : 0.03	= : 0.01	$ : 0.01	
e : 0.28	d : 0.16	! : 0.09	g : 0.07	# : 0.05	" : 0.05	f : 0.05	[ : 0.05	$ : 0.03	a : 0.03	c : 0.03	= : 0.01	b : 0.01	
e : 0.28	d : 0.20	! : 0.09	g : 0.07	c : 0.07	# : 0.05	b : 0.03	" : 0.03	$ : 0.03	f : 0.03	= : 0.01	[ : 0.01	i : 0.01	
e : 0.26	d : 0.16	c : 0.15	g : 0.11	! : 0.07	# : 0.05	b : 0.03	= : 0.01	a : 0.01	$ : 0.01	i : 0.01	" : 0.01	[ : 0.01	f : 0.01	
e : 0.28	c : 0.16	d : 0.15	g : 0.11	[ : 0.07	! : 0.05	" : 0.03	# : 0.03	= : 0.01	$ : 0.01	i : 0.01	f : 0.01	
c : 0.20	! : 0.18	e : 0.18	g : 0.07	d : 0.07	" : 0.05	[ : 0.05	# : 0.05	a : 0.03	= : 0.01	$ : 0.01	i : 0.01	
! : 0.24	c : 0.16	d : 0.15	[ : 0.13	e : 0.13	" : 0.03	g : 0.03	# : 0.03	= : 0.01	a : 0.01	i : 0.01	
c : 0.50	d : 0.15	! : 0.13	e : 0.07	g : 0.03	" : 0.01	= : 0.01	i : 0.01	# : 0.01	[ : 0.01	
c : 0.52	d : 0.15	e : 0.07	! : 0.05	b : 0.03	g : 0.03	[ : 0.03	= : 0.01	i : 0.01	# : 0.01	r : 0.01	
c : 0.52	d : 0.13	a : 0.07	o : 0.05	b : 0.03	g : 0.03	[ : 0.03	= : 0.01	e : 0.01	i : 0.01	! : 0.01	r : 0.01	
o : 0.66	c : 0.22	n : 0.05	l : 0.01	i : 0.01	r : 0.01	
o : 0.67	n : 0.15	c : 0.13	l : 0.01	r : 0.01	
o : 0.67	n : 0.15	c : 0.07	m : 0.05	l : 0.01	r : 0.01	
o : 0.67	n : 0.15	l : 0.07	m : 0.05	c : 0.01	r : 0.01	
o : 0.67	n : 0.15	l : 0.07	m : 0.05	c : 0.01	r : 0.01	
o : 0.62	n : 0.09	l : 0.07	c : 0.05	m : 0.05	e : 0.03	a : 0.01	d : 0.01	r : 0.01	
c : 0.62	d : 0.15	a : 0.05	e : 0.05	b : 0.03	= : 0.01	g : 0.01	o : 0.01	r : 0.01	
c : 0.64	d : 0.15	e : 0.05	b : 0.03	] : 0.03	= : 0.01	g : 0.01	2 : 0.01	i : 0.01	
c : 0.64	d : 0.15	e : 0.05	3 : 0.03	] : 0.03	= : 0.01	g : 0.01	2 : 0.01	i : 0.01	
2 : 0.24	] : 0.20	3 : 0.16	d : 0.15	e : 0.07	c : 0.05	g : 0.03	= : 0.01	a : 0.01	i : 0.01	
2 : 0.30	3 : 0.20	c : 0.13	d : 0.07	] : 0.07	g : 0.07	e : 0.05	= : 0.01	i : 0.01	a : 0.01	f : 0.01	
c : 0.18	e : 0.16	3 : 0.16	d : 0.15	g : 0.11	2 : 0.09	a : 0.03	= : 0.01	i : 0.01	] : 0.01	f : 0.01	
e : 0.26	d : 0.20	c : 0.20	g : 0.11	2 : 0.03	] : 0.03	3 : 0.03	= : 0.01	b : 0.01	i : 0.01	a : 0.01	f : 0.01	
e : 0.26	d : 0.22	c : 0.15	g : 0.09	3 : 0.05	] : 0.05	4 : 0.03	b : 0.03	= : 0.01	a : 0.01	i : 0.01	f : 0.01	
e : 0.28	d : 0.22	] : 0.09	g : 0.09	3 : 0.07	4 : 0.05	c : 0.05	f : 0.03	b : 0.01	= : 0.01	i : 0.01	2 : 0.01	
e : 0.30	d : 0.20	g : 0.09	3 : 0.07	] : 0.05	4 : 0.05	2 : 0.05	f : 0.05	c : 0.03	= : 0.01	i : 0.01	a : 0.01	
d : 0.20	e : 0.20	2 : 0.11	] : 0.11	f : 0.07	g : 0.07	4 : 0.05	b : 0.03	c : 0.03	= : 0.01	3 : 0.01	: : 0.01	i : 0.01	
d : 0.18	e : 0.16	f : 0.11	c : 0.11	b : 0.09	2 : 0.07	] : 0.07	: : 0.03	g : 0.03	3 : 0.01	= : 0.01	i : 0.01	a : 0.01	4 : 0.01	
e : 0.22	c : 0.18	d : 0.15	f : 0.11	b : 0.09	2 : 0.05	: : 0.03	3 : 0.01	= : 0.01	4 : 0.01	h : 0.01	i : 0.01	] : 0.01	G : 0.01	

#score	693.6371557880603
#seq	53
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_UTR_m3_run2.txt

#BEAR
ffffffqqqqqqqqfffff	chrX:48888913-48889153(-)$1	240	208	227	14.0436
ggggggqqqqqqqqggggg	chr19:21304510-21304830(+)$1	320	296	315	14.8248
dddcccqqqqqqqqccc77	chr16:89616808-89617048(+)$1	240	94	113	13.4294
[eeeeeqqqqqqqqeeeee	chr16:29985645-29985885(+)$1	240	185	204	14.5894
c[ddddqqqqqqqqdddd3	chr14:95555838-95556118(-)$1	280	18	37	13.8669
$$$cccqqqqqqqqccc44	chr8:26149161-26149407(+)$1	246	184	203	14.6557
======qqqqqqqq=====	chr17:42878186-42878432(-)$1	246	149	168	14.8647
ee[cccqqqqqqqqcccee	chr10:22619687-22619927(+)$1	240	152	171	15.2197
"""cccqqqqqqqqccc44	chr5:60840057-60840299(+)$1	242	127	146	15.3633
!!ddddqqqqqqqqdddd2	chr10:81113859-81114099(+)$1	240	22	41	13.8556
ffffffqqqqqqqqfffff	chr1:119618938-119619178(-)$1	240	175	194	14.0436
ggggggqqqqqqqqggggg	chr8:74705945-74706193(-)$1	248	57	76	14.8248
!eeeeeqqqqqqqqeeeee	chr12:116714790-116715071(-)$1	281	174	193	14.6062
dd[cccqqqqqqqqccc22	chrX:150157599-150157885(+)$1	286	247	266	15.0820
cc[cccqqqqqqqqccc]c	chr11:43877576-43877816(+)$1	240	44	63	15.2866
ggggggqqqqqqqqggggg	chr10:75289361-75289601(-)$1	240	189	208	14.8248
ggggggqqqqqqqqggggg	chr1:227968382-227968625(+)$1	243	87	106	14.8248
Geeeeeqqqqqqqqeeeee	chr11:111954382-111954622(+)$1	240	95	114	13.9738
ccc[bbqqqqqqqqbb]cc	chr6:108190079-108190319(-)$1	240	209	228	13.1298
"""cccqqqqqqqqcccee	chr1:214837634-214837956(+)$1	322	285	304	15.2988
ggggggqqqqqqqqggggg	chr16:23649082-23649322(-)$1	240	79	98	14.8248
e!!cccqqqqqqqqccc]e	chr22:46757692-46757932(-)$1	240	25	44	15.3996
ggggggqqqqqqqqggggg	chr3:120501738-120501990(+)$1	252	137	156	14.8248
eeee[aqqqqqqqqa]eee	chr11:35684557-35684802(+)$1	245	98	117	14.2915
[eeeeeqqqqqqqqeeeee	chr8:146155908-146156148(-)$1	240	44	63	14.5894
#eeeeeqqqqqqqqeeeee	chr22:29449478-29449723(+)$1	245	201	220	14.5375
fffcccqqqqqqqqccc33	chr8:37612232-37612476(+)$1	244	177	196	15.2601
dd[cccqqqqqqqqcccdd	chr19:21305803-21306043(+)$1	240	51	70	14.6709
gg[cccqqqqqqqqccc22	chr19:10427400-10427640(-)$1	240	69	88	15.4143
cc[cccqqqqqqqqccc]c	chr1:33323498-33323823(+)$1	325	122	141	15.2866
cc[cccqqqqqqqqccc]c	chr11:82643225-82643466(+)$1	241	120	139	15.2866
d"""bbqqqqqqqqbb444	chr13:30085920-30086169(-)$1	249	159	178	13.4158
iiiiiiqqqqqqqqiiiii	chr21:40566514-40566758(-)$1	244	205	224	14.5508
ggggggqqqqqqqqggggg	chr7:6502561-6502859(-)$1	298	107	126	14.8248
ggggggqqqqqqqqggggg	chr6:24785925-24786190(+)$1	265	66	85	14.8248
c[ddddqqqqqqqqdddd]	chr1:31413910-31414150(-)$1	240	110	129	13.7672
e[ddddqqqqqqqqdddd]	chr22:20941580-20941820(+)$1	240	199	218	13.6800
dd[cccqqqqqqqqccc]d	chr14:104220366-104220606(-)$1	240	185	204	14.9731
d"""bbqqqqqqqqbb333	chr2:113304607-113304847(+)$1	240	205	224	13.7409
ff[cccqqqqqqqqccc22	chr1:107601631-107601871(+)$1	240	155	174	15.2491
ffffffqqqqqqqqfffff	chr5:157183509-157183752(+)$1	243	125	144	14.0436
$eeeeeqqqqqqqqeeeee	chr6:159186862-159187266(-)$1	404	208	227	14.3595
b[cccaqqqqqqqqa]ccc	chr1:28087030-28087271(+)$1	241	179	198	14.2063
ccddddqqqqqqqqdddd]	chr3:129023575-129023828(+)$1	253	194	213	13.6084
ggggggqqqqqqqqggggg	chr22:39080202-39080562(+)$1	360	236	255	14.8248
ffffffqqqqqqqqfffff	chr1:8044949-8045248(+)$1	299	149	168	14.0436
"eeeeeqqqqqqqqeeeee	chr19:36909288-36909528(-)$1	240	86	105	14.5753
:eeeeeqqqqqqqqeeeee	chr5:176739034-176739274(-)$1	240	99	118	13.4938
ffffffqqqqqqqqfffff	chr16:70697837-70698157(-)$1	320	265	284	14.0436
a!!cccqqqqqqqqccc22	chr15:77775851-77776091(+)$1	240	76	95	15.3640
[eeeeeqqqqqqqqeeeee	chr4:71894980-71895231(+)$1	251	92	111	14.5894
#a[cccqqqqqqqqccc]a	chr17:29112903-29113143(-)$1	240	137	156	15.3477
[eeeeeqqqqqqqqeeeee	chr6:17608939-17609259(+)$1	320	256	275	14.5894
"a!!bbqqqqqqqqbb22a	chr5:135514220-135514464(+)$1	244	123	142	13.3945
ffff[aqqqqqqqqa]fff	chr12:109994124-109994364(-)$1	240	167	186	14.0000
deeeeeqqqqqqqqeeeee	chr17:2593370-2593616(-)$1	246	218	237	14.3451
beeeeeqqqqqqqqeeeee	chr1:149895239-149895479(-)$1	240	131	150	14.2085
ffffffqqqqqqqqfffff	chr7:99689311-99689552(+)$1	241	151	170	14.0436
###cccqqqqqqqqccc22	chr1:45976868-45977111(-)$1	243	149	168	15.2147
ffffffqqqqqqqqfffff	chr17:43227482-43227779(+)$1	297	198	217	14.0436
======qqqqqqqq=====	chr1:198290263-198290590(+)$1	327	294	313	14.8647
eeeeeeqqqqqqqqeeeee	chr9:5786430-5786672(-)$1	242	165	184	14.3730
$eeeeeqqqqqqqqeeeee	chr3:14239527-14239769(+)$1	242	178	197	14.3595
eeee[aqqqqqqqqa]eee	chr14:24909915-24910156(+)$1	241	89	108	14.2915
"""cccqqqqqqqqccc22	chr13:21950421-21950661(-)$1	240	121	140	15.3434
dd[cccqqqqqqqqccc22	chr21:44453323-44453565(+)$1	242	205	224	15.0820
ffffffqqqqqqqqfffff	chrX:73807106-73807426(-)$1	320	112	131	14.0436
ggggggqqqqqqqqggggg	chr16:67229648-67229888(+)$1	240	77	96	14.8248
d!!cccqqqqqqqqccc22	chr7:156432436-156432680(-)$1	244	94	113	15.2836
dd[cccqqqqqqqqccc22	chr1:67451396-67451643(+)$1	247	43	62	15.0820
ccccccqqqqqqqqccc]c	chr16:30937042-30937296(+)$1	254	122	141	14.9724

#otherMatches

#Seq PSSM
GCAGGCCAACCGCAGCCUG	chrX:48888913-48889153(-)$1	240	208	227	14.0436
AGAGCACUCCAUUUUGUUC	chr19:21304510-21304830(+)$1	320	296	315	14.8248
GACUGCCAAAAAGAGCAAG	chr16:89616808-89617048(+)$1	240	94	113	13.4294
CCGCCCCUCAGGAAGGGCG	chr16:29985645-29985885(+)$1	240	185	204	14.5894
AUUUUAUUAUGCAUUAGAC	chr14:95555838-95556118(-)$1	280	18	37	13.8669
AAGGAGAAAUCCCCCUCGC	chr8:26149161-26149407(+)$1	246	184	203	14.6557
GAAAAUUAGAUAGCAUUUU	chr17:42878186-42878432(-)$1	246	149	168	14.8647
CCAUCAGUUAUUUGUGAGG	chr10:22619687-22619927(+)$1	240	152	171	15.2197
GAUGGUUUGUUUUUACUUG	chr5:60840057-60840299(+)$1	242	127	146	15.3633
UGUGCCUUGGACAUGGUGA	chr10:81113859-81114099(+)$1	240	22	41	13.8556
GGAAAAAAGCAUCCUUUUC	chr1:119618938-119619178(-)$1	240	175	194	14.0436
AUUAGUCAUACAGUAUUAA	chr8:74705945-74706193(-)$1	248	57	76	14.8248
CUGGAGGAUUGUCACUCCA	chr12:116714790-116715071(-)$1	281	174	193	14.6062
CCACCUGAGCUAUAGGGCA	chrX:150157599-150157885(+)$1	286	247	266	15.0820
UAUGACACAGGCUAGUCCU	chr11:43877576-43877816(+)$1	240	44	63	15.2866
CAUUGUCUCUUGCAGCAAU	chr10:75289361-75289601(-)$1	240	189	208	14.8248
CCGGAGUGGUCUUCCUCUG	chr1:227968382-227968625(+)$1	243	87	106	14.8248
AAUCAUGUUGUCUAAUGGU	chr11:111954382-111954622(+)$1	240	95	114	13.9738
ACAAUUCUUAUUUCAAAUG	chr6:108190079-108190319(-)$1	240	209	228	13.1298
AUUCCUAAGUGUAAAGGCA	chr1:214837634-214837956(+)$1	322	285	304	15.2988
UCUAUUAAGAAAACAGUAG	chr16:23649082-23649322(-)$1	240	79	98	14.8248
CUUCAAAUGGCCAAUUGUG	chr22:46757692-46757932(-)$1	240	25	44	15.3996
GUUAAUGACUGAAUGUUGA	chr3:120501738-120501990(+)$1	252	137	156	14.8248
CCACAUGGCCUCUGGAGUG	chr11:35684557-35684802(+)$1	245	98	117	14.2915
UGAAACCGAGCAUAGUUUC	chr8:146155908-146156148(-)$1	240	44	63	14.5894
CAAAAACAAAAAAUUUUUU	chr22:29449478-29449723(+)$1	245	201	220	14.5375
ACAGGGACAAACAACUCAA	chr8:37612232-37612476(+)$1	244	177	196	15.2601
gcugaugcaggagaaucgc	chr19:21305803-21306043(+)$1	240	51	70	14.6709
CAUGGCUGUCUCCUGCCCC	chr19:10427400-10427640(-)$1	240	69	88	15.4143
AGGCUGCCCUAAAUUAGGU	chr1:33323498-33323823(+)$1	325	122	141	15.2866
GAGUGCAGUUCACAGCAGU	chr11:82643225-82643466(+)$1	241	120	139	15.2866
UAGAGGCACACCCACCAAG	chr13:30085920-30086169(-)$1	249	159	178	13.4158
AGAAGGUACAUUUUCUUUC	chr21:40566514-40566758(-)$1	244	205	224	14.5508
GCAUCUGUCCUUCAGGGUG	chr7:6502561-6502859(-)$1	298	107	126	14.8248
GUAUCUUCCUCUACGGAUG	chr6:24785925-24786190(+)$1	265	66	85	14.8248
UCCGAGGCAAUGUACUUGU	chr1:31413910-31414150(-)$1	240	110	129	13.7672
GGAGCGCCUCCCUAUGUUG	chr22:20941580-20941820(+)$1	240	199	218	13.6800
UGAACGGCAAUCUGUGUAC	chr14:104220366-104220606(-)$1	240	185	204	14.9731
GGGUGCCUAAUAAAGUUUA	chr2:113304607-113304847(+)$1	240	205	224	13.7409
UCGAGCUUCUGUAUGCUAA	chr1:107601631-107601871(+)$1	240	155	174	15.2491
UGGUCCUGCUAGCUGGACC	chr5:157183509-157183752(+)$1	243	125	144	14.0436
UGCAUGUAAUGGACUAUGC	chr6:159186862-159187266(-)$1	404	208	227	14.3595
UUAUCCUUCUUUGUGCGAU	chr1:28087030-28087271(+)$1	241	179	198	14.2063
CACUGUGUUAGUUGACAGU	chr3:129023575-129023828(+)$1	253	194	213	13.6084
AGAAGUCAGUGCUCACUUU	chr22:39080202-39080562(+)$1	360	236	255	14.8248
UGUUCUUAAAGACUAGAGC	chr1:8044949-8045248(+)$1	299	149	168	14.0436
GUCCUGGUAAUCUGUAGGA	chr19:36909288-36909528(-)$1	240	86	105	14.5753
GACGCCAAUGAGCCGGCGU	chr5:176739034-176739274(-)$1	240	99	118	13.4938
CUGGGGCAGCCCAUCCCCA	chr16:70697837-70698157(-)$1	320	265	284	14.0436
GCAAGGCUGUGUUUCCUAC	chr15:77775851-77776091(+)$1	240	76	95	15.3640
AAGAGUUUUUGAGUACUUU	chr4:71894980-71895231(+)$1	251	92	111	14.5894
GUGUGUGCAGAAAAACAGG	chr17:29112903-29113143(-)$1	240	137	156	15.3477
UAAUGCUUGAACAUGUAUU	chr6:17608939-17609259(+)$1	320	256	275	14.5894
AGGACCUAUGCACUGGAGC	chr5:135514220-135514464(+)$1	244	123	142	13.3945
GGGUGCAGCUUAGAGGACC	chr12:109994124-109994364(-)$1	240	167	186	14.0000
GGGUUUAGGCCGAAAAACC	chr17:2593370-2593616(-)$1	246	218	237	14.3451
CAAAGGUACUAAUCCCUUU	chr1:149895239-149895479(-)$1	240	131	150	14.2085
GGGAGGGCACUACACUUCC	chr7:99689311-99689552(+)$1	241	151	170	14.0436
CAUGAGAACAAAACCUCUU	chr1:45976868-45977111(-)$1	243	149	168	15.2147
GUGAUGGAAUGUAACAUUA	chr17:43227482-43227779(+)$1	297	198	217	14.0436
UUUAAUGUAAUAUAAUUGA	chr1:198290263-198290590(+)$1	327	294	313	14.8647
ACACAGAUGCACUGCUGUG	chr9:5786430-5786672(-)$1	242	165	184	14.3730
CAUUUUGAUAUUAAGAAAU	chr3:14239527-14239769(+)$1	242	178	197	14.3595
CUGGCGUGUAGAAUCUCCA	chr14:24909915-24910156(+)$1	241	89	108	14.2915
GUUGCUAUAAUAUGAGCUG	chr13:21950421-21950661(-)$1	240	121	140	15.3434
CUCAGCAAUCUUUCGUUCU	chr21:44453323-44453565(+)$1	242	205	224	15.0820
AUUUGAUUUUUUUUUUAAG	chrX:73807106-73807426(-)$1	320	112	131	14.0436
CUCAGUUCACUCCCACUGG	chr16:67229648-67229888(+)$1	240	77	96	14.8248
CGACGCCACAAAUAGUGCA	chr7:156432436-156432680(-)$1	244	94	113	15.2836
AGUAAUUAAGUCAUAUUUC	chr1:67451396-67451643(+)$1	247	43	62	15.0820
CGGGGAUUGCCACUUCUGC	chr16:30937042-30937296(+)$1	254	122	141	14.9724

#DB
((((((........)))))	chrX:48888913-48889153(-)$1	1	208	227	14.0436
((((((........)))))	chr19:21304510-21304830(+)$1	1	296	315	14.8248
((((((........)))..	chr16:89616808-89617048(+)$1	1	94	113	13.4294
.(((((........)))))	chr16:29985645-29985885(+)$1	1	185	204	14.5894
(.((((........)))).	chr14:95555838-95556118(-)$1	1	18	37	13.8669
...(((........)))..	chr8:26149161-26149407(+)$1	1	184	203	14.6557
((((((........)))))	chr17:42878186-42878432(-)$1	1	149	168	14.8647
((.(((........)))))	chr10:22619687-22619927(+)$1	1	152	171	15.2197
...(((........)))..	chr5:60840057-60840299(+)$1	1	127	146	15.3633
..((((........)))).	chr10:81113859-81114099(+)$1	1	22	41	13.8556
((((((........)))))	chr1:119618938-119619178(-)$1	1	175	194	14.0436
((((((........)))))	chr8:74705945-74706193(-)$1	1	57	76	14.8248
.(((((........)))))	chr12:116714790-116715071(-)$1	1	174	193	14.6062
((.(((........)))..	chrX:150157599-150157885(+)$1	1	247	266	15.0820
((.(((........))).)	chr11:43877576-43877816(+)$1	1	44	63	15.2866
((((((........)))))	chr10:75289361-75289601(-)$1	1	189	208	14.8248
((((((........)))))	chr1:227968382-227968625(+)$1	1	87	106	14.8248
((((((........)))))	chr11:111954382-111954622(+)$1	1	95	114	13.9738
(((.((........)).))	chr6:108190079-108190319(-)$1	1	209	228	13.1298
...(((........)))))	chr1:214837634-214837956(+)$1	1	285	304	15.2988
((((((........)))))	chr16:23649082-23649322(-)$1	1	79	98	14.8248
(..(((........))).)	chr22:46757692-46757932(-)$1	1	25	44	15.3996
((((((........)))))	chr3:120501738-120501990(+)$1	1	137	156	14.8248
((((.(........).)))	chr11:35684557-35684802(+)$1	1	98	117	14.2915
.(((((........)))))	chr8:146155908-146156148(-)$1	1	44	63	14.5894
.(((((........)))))	chr22:29449478-29449723(+)$1	1	201	220	14.5375
((((((........)))..	chr8:37612232-37612476(+)$1	1	177	196	15.2601
((.(((........)))))	chr19:21305803-21306043(+)$1	1	51	70	14.6709
((.(((........)))..	chr19:10427400-10427640(-)$1	1	69	88	15.4143
((.(((........))).)	chr1:33323498-33323823(+)$1	1	122	141	15.2866
((.(((........))).)	chr11:82643225-82643466(+)$1	1	120	139	15.2866
(...((........))...	chr13:30085920-30086169(-)$1	1	159	178	13.4158
((((((........)))))	chr21:40566514-40566758(-)$1	1	205	224	14.5508
((((((........)))))	chr7:6502561-6502859(-)$1	1	107	126	14.8248
((((((........)))))	chr6:24785925-24786190(+)$1	1	66	85	14.8248
(.((((........)))).	chr1:31413910-31414150(-)$1	1	110	129	13.7672
(.((((........)))).	chr22:20941580-20941820(+)$1	1	199	218	13.6800
((.(((........))).)	chr14:104220366-104220606(-)$1	1	185	204	14.9731
(...((........))...	chr2:113304607-113304847(+)$1	1	205	224	13.7409
((.(((........)))..	chr1:107601631-107601871(+)$1	1	155	174	15.2491
((((((........)))))	chr5:157183509-157183752(+)$1	1	125	144	14.0436
.(((((........)))))	chr6:159186862-159187266(-)$1	1	208	227	14.3595
(.((((........).)))	chr1:28087030-28087271(+)$1	1	179	198	14.2063
((((((........)))).	chr3:129023575-129023828(+)$1	1	194	213	13.6084
((((((........)))))	chr22:39080202-39080562(+)$1	1	236	255	14.8248
((((((........)))))	chr1:8044949-8045248(+)$1	1	149	168	14.0436
.(((((........)))))	chr19:36909288-36909528(-)$1	1	86	105	14.5753
.(((((........)))))	chr5:176739034-176739274(-)$1	1	99	118	13.4938
((((((........)))))	chr16:70697837-70698157(-)$1	1	265	284	14.0436
(..(((........)))..	chr15:77775851-77776091(+)$1	1	76	95	15.3640
.(((((........)))))	chr4:71894980-71895231(+)$1	1	92	111	14.5894
.(.(((........))).)	chr17:29112903-29113143(-)$1	1	137	156	15.3477
.(((((........)))))	chr6:17608939-17609259(+)$1	1	256	275	14.5894
.(..((........))..)	chr5:135514220-135514464(+)$1	1	123	142	13.3945
((((.(........).)))	chr12:109994124-109994364(-)$1	1	167	186	14.0000
)(((((........)))))	chr17:2593370-2593616(-)$1	1	218	237	14.3451
((((((........)))))	chr1:149895239-149895479(-)$1	1	131	150	14.2085
((((((........)))))	chr7:99689311-99689552(+)$1	1	151	170	14.0436
...(((........)))..	chr1:45976868-45977111(-)$1	1	149	168	15.2147
((((((........)))))	chr17:43227482-43227779(+)$1	1	198	217	14.0436
((((((........)))))	chr1:198290263-198290590(+)$1	1	294	313	14.8647
)(((((........)))))	chr9:5786430-5786672(-)$1	1	165	184	14.3730
.(((((........)))))	chr3:14239527-14239769(+)$1	1	178	197	14.3595
((((.(........).)))	chr14:24909915-24910156(+)$1	1	89	108	14.2915
...(((........)))..	chr13:21950421-21950661(-)$1	1	121	140	15.3434
((.(((........)))..	chr21:44453323-44453565(+)$1	1	205	224	15.0820
((((((........)))))	chrX:73807106-73807426(-)$1	1	112	131	14.0436
((((((........)))))	chr16:67229648-67229888(+)$1	1	77	96	14.8248
(..(((........)))..	chr7:156432436-156432680(-)$1	1	94	113	15.2836
((.(((........)))..	chr1:67451396-67451643(+)$1	1	43	62	15.0820
((((((........))).)	chr16:30937042-30937296(+)$1	1	122	141	14.9724

#PSSM
f : 0.15	g : 0.15	d : 0.14	c : 0.11	e : 0.08	" : 0.07	[ : 0.05	$ : 0.04	# : 0.04	= : 0.02	! : 0.02	b : 0.02	G : 0.01	i : 0.01	: : 0.01	a : 0.01	
e : 0.23	f : 0.15	g : 0.15	d : 0.08	c : 0.08	" : 0.07	[ : 0.05	! : 0.05	= : 0.02	a : 0.02	$ : 0.01	i : 0.01	# : 0.01	
e : 0.22	[ : 0.16	f : 0.14	g : 0.14	d : 0.08	" : 0.07	! : 0.05	c : 0.04	= : 0.02	$ : 0.01	i : 0.01	# : 0.01	
c : 0.33	e : 0.22	g : 0.14	f : 0.12	d : 0.07	= : 0.02	" : 0.02	[ : 0.01	i : 0.01	! : 0.01	
c : 0.33	e : 0.19	g : 0.14	f : 0.11	d : 0.07	b : 0.05	[ : 0.04	= : 0.02	i : 0.01	
c : 0.32	e : 0.19	g : 0.14	f : 0.11	d : 0.07	b : 0.05	a : 0.05	= : 0.02	i : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.32	e : 0.19	g : 0.14	f : 0.11	d : 0.07	b : 0.05	a : 0.05	= : 0.02	i : 0.01	
c : 0.32	e : 0.19	g : 0.14	f : 0.11	d : 0.07	b : 0.05	] : 0.05	= : 0.02	i : 0.01	
c : 0.33	e : 0.22	g : 0.14	f : 0.12	d : 0.07	= : 0.02	] : 0.01	4 : 0.01	i : 0.01	3 : 0.01	2 : 0.01	
e : 0.25	g : 0.14	2 : 0.14	f : 0.12	] : 0.09	d : 0.08	4 : 0.04	= : 0.02	c : 0.02	3 : 0.02	7 : 0.01	i : 0.01	
e : 0.26	g : 0.14	2 : 0.14	f : 0.12	c : 0.08	3 : 0.04	4 : 0.04	] : 0.04	= : 0.02	d : 0.02	a : 0.02	7 : 0.01	i : 0.01	

#score	1032.883997141132
#seq	71
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_CDS_m1_run2.txt

#BEAR
==========vvvvvvvvvvvvv======	chr5:154317471-154317687(-)$1	216	85	114	22.3539
^^^^^^^^^^^^^^^^^^^^^^^eeeee]	chr22:19344342-19344557(-)$1	215	52	81	18.5126
eccc[ddddtttttttttttdddd333cc	chr2:207653449-207653665(+)$1	216	107	136	18.6425
c==========ttttttttttt=======	chr16:29818665-29818881(+)$1	216	105	134	19.2630
'''eeeeeyyyyyyyyyyyyyyyyeeeee	chr13:73293029-73293253(-)$1	224	100	129	20.6832
d!!bb[eeeeettttttttttteeeee]b	chr3:178921380-178921601(+)$1	221	164	193	18.8139
ccc[ddddxxxxxxxxxxxxxxxddddcc	chr13:78272079-78272301(+)$1	222	78	107	20.0371
ee[ffffff^^^^^^^^^^^^^^^^^^ff	chr16:69196886-69197118(+)$1	232	194	223	18.9957
fffff[cccxxxxxxxxxxxxxxxcccff	chr16:2052564-2052780(-)$1	216	1	30	19.7463
b[gggggggbbuuuuuuuuuuuubb]ggg	chr19:59059413-59059632(+)$1	219	53	82	20.6182
eeeee[cccuuuuuuuuuuuuccc]eeee	chr10:14938785-14939000(+)$1	215	109	138	21.3274
"""ffffff^^^^^^^^^^^^^^^^^^^^	chr2:216861063-216861286(-)$1	223	52	81	19.6877
f!!dddd[cccuuuuuuuuuuuuccc]dd	chrX:24006020-24006232(-)$1	212	114	143	21.7191
cc####ccctttttttttttccc333ccc	chr9:134362478-134362698(+)$1	220	47	76	19.7212
c$$$$$eeeeeuuuuuuuuuuuueeeee7	chrX:53672249-53672466(-)$1	217	33	62	20.1626
dddd!!cccvvvvvvvvvvvvvccc22dd	chr12:57009001-57009223(-)$1	222	161	190	21.9491
dddd"""bbuuuuuuuuuuuubb333ddd	chr18:73000312-73000531(+)$1	219	56	85	20.6461
b[ccc[dddduuuuuuuuuuuudddd]cc	chr9:131765081-131765306(+)$1	225	85	114	21.5143
"""ffffff^^^^^^^^^^^^^^^^^^^f	chr17:29667442-29667664(+)$1	222	152	181	19.6709
dddd^^^^^^^^^^^^^^^^^^^^^dddd	chr4:57797560-57797779(+)$1	219	63	92	18.8153
:::ffffffwwwwwwwwwwwwwwffffff	chr11:92539529-92539755(+)$1	226	42	71	18.8491
:ddddddddwwwwwwwwwwwwwwdddd]d	chr16:19548309-19548529(+)$1	220	150	179	21.3753
e[gggggggvvvvvvvvvvvvvggggggg	chr11:71733333-71733553(-)$1	220	7	36	21.8403
!!ddddcccwwwwwwwwwwwwwwccc22d	chr12:432747-432967(-)$1	220	141	170	22.9354
g"""ddddxxxxxxxxxxxxxxxdddd44	chr1:179816637-179816861(-)$1	224	157	186	20.8298
d!!ffffffwwwwwwwwwwwwwwffffff	chr7:138943153-138943373(+)$1	220	60	89	22.1657
iiii[dddd[attttttttttta]dddd2	chr16:20808165-20808386(-)$1	221	6	35	19.4664
###ffffff^^^^^^^^^^^^^^^^^^^f	chr10:5790930-5791151(+)$1	221	151	180	19.5708
c^^^^^^^^^^^^^^^^^^^^^^cccccc	chr7:101840027-101840246(+)$1	219	91	120	18.9789
g!!bb[cccuuuuuuuuuuuuccc]bb]g	chrX:133927788-133928009(-)$1	221	40	69	21.7292
d!!ddddccc^^^^^^^^^^^^^^^^^^^	chr11:92565017-92565239(+)$1	222	113	142	19.3146
dd"""ddddwwwwwwwwwwwwwwdddd55	chr17:63010364-63010588(-)$1	224	91	120	21.6243
dd"""ddddtttttttttttdddd333dd	chr6:170892611-170892831(-)$1	220	52	81	18.8591
""gggggggxxxxxxxxxxxxxxxggggg	chr20:32264506-32264723(-)$1	217	87	116	20.5707
cc[a[ddddtttttttttttdddd]a]cc	chr10:5781662-5781884(+)$1	222	100	129	18.6949
hhhheeeeewwwwwwwwwwwwwweeeee>	chr22:31738799-31739016(-)$1	217	27	56	21.4001
dddd[cccxxxxxxxxxxxxxxxccc]dd	chr14:59826031-59826249(+)$1	218	94	123	19.9571
###ccc[bbyyyyyyyyyyyyyyyybb]c	chr22:20073997-20074220(+)$1	223	20	49	22.1503
ii"""ddddwwwwwwwwwwwwwwddddii	chr1:11298449-11298673(-)$1	224	36	65	23.2217
=========xxxxxxxxxxxxxxx=====	chr21:27263945-27264163(-)$1	218	2	31	21.0495
c[ggggggg^^^^^^^^^^^^^^^^^^^^	chr2:48692590-48692813(+)$1	223	148	177	19.8377
c[ccc!!bbwwwwwwwwwwwwwwbb]ccc	chr8:71126095-71126315(-)$1	220	126	155	22.5368
e"""ccc^^^^^^^^^^^^^^^^^^^^^c	chr7:5104311-5104533(+)$1	222	158	187	20.4215
cc[bb####bbuuuuuuuuuuuubb4444	chrX:53223672-53223889(-)$1	217	61	90	20.7363
g!!bb^^^^^^^^^^^^^^^^^^^bb]gg	chr1:24077930-24078153(+)$1	223	49	78	19.2470
$$$ddddccctttttttttttccc]dddd	chr22:29192015-29192237(-)$1	222	20	49	19.1125
c!!fffffftttttttttttffffff22c	chr10:105779412-105779631(+)$1	219	55	84	17.7389
FFccc!!ccctttttttttttccc22ccc	chr16:2809277-2809497(+)$1	220	82	111	18.3878
ddd!!dddduuuuuuuuuuuudddd22dd	chr5:71482380-71482604(+)$1	224	41	70	20.8152
eeeeeddddwwwwwwwwwwwwwwdddd::	chr16:48329839-48330059(+)$1	220	110	139	20.4442
iiiiiiiiyyyyyyyyyyyyyyyyiiiii	chr1:33244985-33245201(-)$1	216	51	80	22.5373
===:eeeeexxxxxxxxxxxxxxxeeeee	chr10:75853999-75854226(+)$1	227	120	149	19.2787
d"""bbeeeeettttttttttteeeee]b	chr22:50356248-50356464(+)$1	216	106	135	18.6210
=======^^^^^^^^^^^^^^^^^^^^==	chr22:36701015-36701241(-)$1	226	98	127	20.2857
::ccc[cccvvvvvvvvvvvvvccc]ccc	chr12:493103-493316(-)$1	213	79	108	20.6996
gggggddddyyyyyyyyyyyyyyyydddd	chr1:40703155-40703371(+)$1	216	71	100	22.3761
cceeeeedddduuuuuuuuuuuudddd22	chrX:53441630-53441843(-)$1	213	90	119	20.1292
d[eeeee^^^^^^^^^^^^^^^^^^^^ee	chr1:8073364-8073586(-)$1	222	94	123	19.5384
e####ddddvvvvvvvvvvvvvdddd22e	chr19:50411498-50411724(-)$1	226	91	120	22.2361
a!!bb^^^^^^^^^^^^^^^^^^^bb22a	chr2:42556976-42557199(+)$1	223	50	79	19.0393
e:gggggggvvvvvvvvvvvvvggggggg	chr2:201758008-201758227(+)$1	219	179	208	20.7176
eeeee[eeeeettttttttttteeeee]e	chr4:120214248-120214466(+)$1	218	151	180	18.3226
cc[dddd[bbvvvvvvvvvvvvvbb]ddd	chr7:5567263-5567485(-)$1	222	83	112	21.1436
eee[eeeeewwwwwwwwwwwwwweeeee]	chr17:17721530-17721744(-)$1	214	76	105	22.2359
gggggggggwwwwwwwwwwwwwwgggggg	chr3:120499891-120500109(+)$1	218	159	188	22.6215
c[dddd[cccvvvvvvvvvvvvvcccddd	chr20:3128945-3129166(-)$1	221	123	152	21.9317
ggggg[ccc^^^^^^^^^^^^^^^^^^^^	chr13:23913838-23914059(-)$1	221	143	172	19.9001
g^^^^^^^^^^^^^^^^^^^^^^gggggg	chr3:50142915-50143139(+)$1	224	120	149	18.6782

#otherMatches

#Seq PSSM
CCGCGCGGACCUCCGUCUUCCUUGUCCGC	chr5:154317471-154317687(-)$1	216	85	114	22.3539
CUCUCCCAUCCUCCUGCCAUCCCCGAUCU	chr22:19344342-19344557(-)$1	215	52	81	18.5126
AUGGACACUAACAGGAAUCAAGUGCUACC	chr2:207653449-207653665(+)$1	216	107	136	18.6425
CGGGUGCUAUGAAGAUGCCGACCAUGGUG	chr16:29818665-29818881(+)$1	216	105	134	19.2630
AAUUAACCCAGAAGCUUUAUCAUCGGUUA	chr13:73293029-73293253(-)$1	224	100	129	20.6832
UACGUGAAUGUAAAUAUUCGAGACAUUGA	chr3:178921380-178921601(+)$1	221	164	193	18.8139
GCAAGCUGGAGAAGCAGAACGAGCAGCUG	chr13:78272079-78272301(+)$1	222	78	107	20.0371
GGUAAGGGAGAUUCCAGUGCUUUCUAUUC	chr16:69196886-69197118(+)$1	232	194	223	18.9957
AGGCUUGGGGUCCCCCAGCCUGUGCCCAG	chr16:2052564-2052780(-)$1	216	1	30	19.7463
CACCAGGAGCACAUUCUGCGCUUUGCCUC	chr19:59059413-59059632(+)$1	219	53	82	20.6182
UACUUGGGAACCUUUGCAAAAUCUGAAGU	chr10:14938785-14939000(+)$1	215	109	138	21.3274
UUAUGUAUAUUAUAAAACCCCAAUCUUUC	chr2:216861063-216861286(-)$1	223	52	81	19.6877
CCCUGCAAGCUGGAUGGUUUACAAGUAUG	chrX:24006020-24006232(-)$1	212	114	143	21.7191
CUCCCCGACCCCGUUUUCCCGUUCACAGG	chr9:134362478-134362698(+)$1	220	47	76	19.7212
CCUUUUUUGUCCCUUUAGCAUUUGACAAC	chrX:53672249-53672466(-)$1	217	33	62	20.1626
AUGGGGCUUAACUUUGAUUCACAAGAACU	chr12:57009001-57009223(-)$1	222	161	190	21.9491
CUGCCACUCAAUCAGAUUCAAGAACAGCA	chr18:73000312-73000531(+)$1	219	56	85	20.6461
GAUGGAGCAGCUGCUCAAAACUCUGCGCU	chr9:131765081-131765306(+)$1	225	85	114	21.5143
UCAGCAGGUACCGCACUUCUUGAACAAAA	chr17:29667442-29667664(+)$1	222	152	181	19.6709
UGCCAAAGGAAAAUUUAAGAGAAGAGGCA	chr4:57797560-57797779(+)$1	219	63	92	18.8153
AAUCAUCCUGAAAGUCAGUGCAAAGGAUG	chr11:92539529-92539755(+)$1	226	42	71	18.8491
GCGCACACAUAAUGAACAGUACCUGUGCU	chr16:19548309-19548529(+)$1	220	150	179	21.3753
GAGUCCCCAGAACAGCCCAGAAUGGGGGC	chr11:71733333-71733553(-)$1	220	7	36	21.8403
UUGUAUGUCUCUACCAUCCAACUGAUCUG	chr12:432747-432967(-)$1	220	141	170	22.9354
GAGACAGAUUAAUAAAAAGGGUUUUUGGA	chr1:179816637-179816861(-)$1	224	157	186	20.8298
UUUUUUGUUUUUUAAUCUAGUAUGAUGAA	chr7:138943153-138943373(+)$1	220	60	89	22.1657
UUUAUGACCUCUCCAUCAUCUUGUGGUUU	chr16:20808165-20808386(-)$1	221	6	35	19.4664
GCUGCGGUAAAGAAAGAAGAGAAGUGUGU	chr10:5790930-5791151(+)$1	221	151	180	19.5708
AAAAUUUGCACUAAACUCUCUUCUCCAGC	chr7:101840027-101840246(+)$1	219	91	120	18.9789
AUUACUAAUUUUGUUUUUUUUGUUUGUUU	chrX:133927788-133928009(-)$1	221	40	69	21.7292
CCGGUCUGGGAACGAACAAGGGAAAUUUA	chr11:92565017-92565239(+)$1	222	113	142	19.3146
CAACAGAAGCCCUUAUACCACCACUUCAC	chr17:63010364-63010588(-)$1	224	91	120	21.6243
GAGAAUCCUCCCCCAGAAACAGGAGAAUC	chr6:170892611-170892831(-)$1	220	52	81	18.8591
CACGAGGCCCUCGACUACCACUUCGGCCU	chr20:32264506-32264723(-)$1	217	87	116	20.5707
UCUGCUACUUCUUCCACACCAGUAUCUGA	chr10:5781662-5781884(+)$1	222	100	129	18.6949
CUGGCCAAGUUUCUAAAGUCCCUCUUGGU	chr22:31738799-31739016(-)$1	217	27	56	21.4001
UUUUGCACUAUCUCAUCACUAUUGUGGAA	chr14:59826031-59826249(+)$1	218	94	123	19.9571
AGUGCUGAUAAGAAGGAUGAGGAGAAUGA	chr22:20073997-20074220(+)$1	223	20	49	22.1503
UCAUUUCCUGAACAGUGAGCACAAGGAGA	chr1:11298449-11298673(-)$1	224	36	65	23.2217
UGGGUUCAAACAAAGGUGCAAUCAUUGGA	chr21:27263945-27264163(-)$1	218	2	31	21.0495
UGUUGAUUCUGCCAUUGACACUAUAUCUC	chr2:48692590-48692813(+)$1	223	148	177	19.8377
UGUGCAAUCUUAAAAGAAACUGUGAAGCA	chr8:71126095-71126315(-)$1	220	126	155	22.5368
AUGUGGCAAAACCUUCAAUUUAAAUUCAG	chr7:5104311-5104533(+)$1	222	158	187	20.4215
AUCGAGCACGGCCUCCUCUACAACCUCUA	chrX:53223672-53223889(-)$1	217	61	90	20.7363
UAGUGGCGUAAAGAAAGAGAAGGACAGAG	chr1:24077930-24078153(+)$1	223	49	78	19.2470
CUUGAAGCUGUUUAUUCACUUUGGUCUUU	chr22:29192015-29192237(-)$1	222	20	49	19.1125
GGAUUCUAUUUAAAACUUUCAUAGGAAAC	chr10:105779412-105779631(+)$1	219	55	84	17.7389
ACUCCAAAGAGCAAACGUAAAUCUAAGGA	chr16:2809277-2809497(+)$1	220	82	111	18.3878
GUUCUGUGCUUUAUUUCAGGUGCGCUUAA	chr5:71482380-71482604(+)$1	224	41	70	20.8152
AACUUCACAGAUCAUUAUCUAAAUGUGGC	chr16:48329839-48330059(+)$1	220	110	139	20.4442
UCUUCUCUUGUCCUGUGUCUUCCCAGAGA	chr1:33244985-33245201(-)$1	216	51	80	22.5373
GCCAACAGCAGACCGGCCAAAGCAGCUGU	chr10:75853999-75854226(+)$1	227	120	149	19.2787
CCCCGGAGUGGAUCCGCUACCACCGCUAC	chr22:50356248-50356464(+)$1	216	106	135	18.6210
AGAUCCUGACUCCAAACUCCAUUCCCAAG	chr22:36701015-36701241(-)$1	226	98	127	20.2857
UGGUAGAGAGAAAAAUCCUGGAUCUGUAU	chr12:493103-493316(-)$1	213	79	108	20.6996
GACUAAGUUUACCUGUGGUUUUGAUGGCU	chr1:40703155-40703371(+)$1	216	71	100	22.3761
AGAAGUUGGGCAUUCUCAUCAAAGCUCGU	chrX:53441630-53441843(-)$1	213	90	119	20.1292
UAGUUCAACACAUUAUUACCUACUACCUG	chr1:8073364-8073586(-)$1	222	94	123	19.5384
CUCAAUGCGCACAUGGACUCACUGCAGUG	chr19:50411498-50411724(-)$1	226	91	120	22.2361
GUAGCGGAUACUACUCUAACCAAAGCCCC	chr2:42556976-42557199(+)$1	223	50	79	19.0393
CAAAGUCUAUAACCCUGGUAUUUAGGCUU	chr2:201758008-201758227(+)$1	219	179	208	20.7176
AUCUUGGUUCAAGCUGCCCUUCUGAACAA	chr4:120214248-120214466(+)$1	218	151	180	18.3226
AUCGUCCACCGCAAAUGCUUCUAGGCGGA	chr7:5567263-5567485(-)$1	222	83	112	21.1436
GCGCAAGGCCAUCGACUACAUUCGCUUUC	chr17:17721530-17721744(-)$1	214	76	105	22.2359
AGUGACUCAGAAAGCGAGACCAGUGAGUC	chr3:120499891-120500109(+)$1	218	159	188	22.6215
UAGAUGUGUAUGAGACCAAGUGUUGCCAU	chr20:3128945-3129166(-)$1	221	123	152	21.9317
UAUAGCAAUCAGAUUCCAGCAAGCCCCAA	chr13:23913838-23914059(-)$1	221	143	172	19.9001
CACUGUCUCCUUACGCGUCUUUAGCUGUC	chr3:50142915-50143139(+)$1	224	120	149	18.6782

#DB
((((((((((.............))))))	chr5:154317471-154317687(-)$1	1	85	114	22.3539
.......................))))).	chr22:19344342-19344557(-)$1	1	52	81	18.5126
((((.((((...........))))...))	chr2:207653449-207653665(+)$1	1	107	136	18.6425
(((((((((((...........)))))))	chr16:29818665-29818881(+)$1	1	105	134	19.2630
...(((((................)))))	chr13:73293029-73293253(-)$1	1	100	129	20.6832
(..((.(((((...........))))).)	chr3:178921380-178921601(+)$1	1	164	193	18.8139
(((.((((...............))))))	chr13:78272079-78272301(+)$1	1	78	107	20.0371
((.((((((..................))	chr16:69196886-69197118(+)$1	1	194	223	18.9957
(((((.(((...............)))))	chr16:2052564-2052780(-)$1	1	1	30	19.7463
(.(((((((((............)).)))	chr19:59059413-59059632(+)$1	1	53	82	20.6182
(((((.(((............))).))))	chr10:14938785-14939000(+)$1	1	109	138	21.3274
...((((((....................	chr2:216861063-216861286(-)$1	1	52	81	19.6877
(..((((.(((............))).))	chrX:24006020-24006232(-)$1	1	114	143	21.7191
((....(((...........)))...)))	chr9:134362478-134362698(+)$1	1	47	76	19.7212
(.....(((((............))))).	chrX:53672249-53672466(-)$1	1	33	62	20.1626
((((..(((.............)))..))	chr12:57009001-57009223(-)$1	1	161	190	21.9491
((((...((............))...)))	chr18:73000312-73000531(+)$1	1	56	85	20.6461
(.(((.((((............)))).))	chr9:131765081-131765306(+)$1	1	85	114	21.5143
...((((((...................)	chr17:29667442-29667664(+)$1	1	152	181	19.6709
((((.....................))))	chr4:57797560-57797779(+)$1	1	63	92	18.8153
...((((((..............))))))	chr11:92539529-92539755(+)$1	1	42	71	18.8491
.((((((((..............)))).)	chr16:19548309-19548529(+)$1	1	150	179	21.3753
(.(((((((.............)))))))	chr11:71733333-71733553(-)$1	1	7	36	21.8403
..(((((((..............)))..)	chr12:432747-432967(-)$1	1	141	170	22.9354
(...((((...............))))..	chr1:179816637-179816861(-)$1	1	157	186	20.8298
(..((((((..............))))))	chr7:138943153-138943373(+)$1	1	60	89	22.1657
((((.((((.(...........).)))).	chr16:20808165-20808386(-)$1	1	6	35	19.4664
...((((((...................)	chr10:5790930-5791151(+)$1	1	151	180	19.5708
(......................)))(((	chr7:101840027-101840246(+)$1	1	91	120	18.9789
(..((.(((............))).)).)	chrX:133927788-133928009(-)$1	1	40	69	21.7292
(..(((((((...................	chr11:92565017-92565239(+)$1	1	113	142	19.3146
((...((((..............))))..	chr17:63010364-63010588(-)$1	1	91	120	21.6243
((...((((...........))))...))	chr6:170892611-170892831(-)$1	1	52	81	18.8591
..(((((((...............)))))	chr20:32264506-32264723(-)$1	1	87	116	20.5707
((.(.((((...........)))).).))	chr10:5781662-5781884(+)$1	1	100	129	18.6949
(((((((((..............))))).	chr22:31738799-31739016(-)$1	1	27	56	21.4001
((((.(((...............))).))	chr14:59826031-59826249(+)$1	1	94	123	19.9571
...(((.((................)).)	chr22:20073997-20074220(+)$1	1	20	49	22.1503
((...((((..............))))))	chr1:11298449-11298673(-)$1	1	36	65	23.2217
(((((((((...............)))))	chr21:27263945-27264163(-)$1	1	2	31	21.0495
(.(((((((....................	chr2:48692590-48692813(+)$1	1	148	177	19.8377
(.(((..((..............)).)))	chr8:71126095-71126315(-)$1	1	126	155	22.5368
(...(((.....................)	chr7:5104311-5104533(+)$1	1	158	187	20.4215
((.((....((............))....	chrX:53223672-53223889(-)$1	1	61	90	20.7363
(..((...................)).))	chr1:24077930-24078153(+)$1	1	49	78	19.2470
...(((((((...........))).))))	chr22:29192015-29192237(-)$1	1	20	49	19.1125
(..((((((...........))))))..)	chr10:105779412-105779631(+)$1	1	55	84	17.7389
(((((..(((...........)))..)))	chr16:2809277-2809497(+)$1	1	82	111	18.3878
(((..((((............))))..))	chr5:71482380-71482604(+)$1	1	41	70	20.8152
)))))((((..............))))..	chr16:48329839-48330059(+)$1	1	110	139	20.4442
((((((((................)))))	chr1:33244985-33245201(-)$1	1	51	80	22.5373
))).(((((...............)))))	chr10:75853999-75854226(+)$1	1	120	149	19.2787
(...(((((((...........))))).)	chr22:50356248-50356464(+)$1	1	106	135	18.6210
(((((((....................))	chr22:36701015-36701241(-)$1	1	98	127	20.2857
..(((.(((.............))).)))	chr12:493103-493316(-)$1	1	79	108	20.6996
(((((((((................))))	chr1:40703155-40703371(+)$1	1	71	100	22.3761
(((((((((((............))))..	chrX:53441630-53441843(-)$1	1	90	119	20.1292
(.(((((....................))	chr1:8073364-8073586(-)$1	1	94	123	19.5384
(....((((.............))))..)	chr19:50411498-50411724(-)$1	1	91	120	22.2361
(..((...................))..)	chr2:42556976-42557199(+)$1	1	50	79	19.0393
).(((((((.............)))))))	chr2:201758008-201758227(+)$1	1	179	208	20.7176
(((((.(((((...........))))).)	chr4:120214248-120214466(+)$1	1	151	180	18.3226
((.((((.((.............)).)))	chr7:5567263-5567485(-)$1	1	83	112	21.1436
(((.(((((..............))))).	chr17:17721530-17721744(-)$1	1	76	105	22.2359
))(((((((..............))))))	chr3:120499891-120500109(+)$1	1	159	188	22.6215
(.((((.(((.............))))))	chr20:3128945-3129166(-)$1	1	123	152	21.9317
(((((.(((....................	chr13:23913838-23914059(-)$1	1	143	172	19.9001
(......................))))))	chr3:50142915-50143139(+)$1	1	120	149	18.6782

#PSSM
c : 0.19	d : 0.17	e : 0.14	g : 0.10	= : 0.05	" : 0.04	: : 0.04	i : 0.04	f : 0.02	b : 0.02	# : 0.02	^ : 0.01	' : 0.01	! : 0.01	h : 0.01	$ : 0.01	F : 0.01	a : 0.01	
! : 0.13	d : 0.11	c : 0.10	[ : 0.10	" : 0.08	= : 0.07	e : 0.07	^ : 0.04	: : 0.04	i : 0.04	# : 0.04	g : 0.04	$ : 0.02	' : 0.01	f : 0.01	h : 0.01	F : 0.01	
! : 0.11	g : 0.11	" : 0.11	d : 0.11	c : 0.08	e : 0.08	= : 0.07	[ : 0.05	# : 0.05	^ : 0.04	$ : 0.02	i : 0.02	' : 0.01	f : 0.01	: : 0.01	h : 0.01	
d : 0.16	f : 0.11	g : 0.11	c : 0.08	e : 0.08	" : 0.08	b : 0.07	= : 0.05	^ : 0.04	[ : 0.02	# : 0.02	i : 0.02	$ : 0.01	a : 0.01	h : 0.01	! : 0.01	: : 0.01	
e : 0.13	d : 0.13	f : 0.11	g : 0.11	b : 0.08	c : 0.08	= : 0.05	^ : 0.05	[ : 0.05	" : 0.05	# : 0.02	! : 0.02	$ : 0.01	i : 0.01	
d : 0.27	[ : 0.11	f : 0.10	^ : 0.08	e : 0.08	g : 0.08	= : 0.05	! : 0.04	c : 0.04	# : 0.02	$ : 0.01	" : 0.01	i : 0.01	b : 0.01	
d : 0.26	e : 0.14	c : 0.14	f : 0.10	^ : 0.08	g : 0.08	= : 0.05	[ : 0.02	! : 0.02	" : 0.01	# : 0.01	i : 0.01	
d : 0.22	c : 0.19	^ : 0.13	e : 0.11	f : 0.10	g : 0.08	= : 0.04	b : 0.04	[ : 0.02	# : 0.01	i : 0.01	
d : 0.19	c : 0.19	^ : 0.13	e : 0.10	f : 0.10	g : 0.08	b : 0.05	= : 0.04	x : 0.04	y : 0.02	# : 0.01	
^ : 0.22	w : 0.16	x : 0.10	t : 0.07	c : 0.07	v : 0.07	y : 0.05	e : 0.05	u : 0.05	b : 0.04	= : 0.02	d : 0.02	[ : 0.01	
^ : 0.23	w : 0.16	v : 0.11	t : 0.10	x : 0.10	u : 0.07	y : 0.05	e : 0.05	b : 0.02	= : 0.01	c : 0.01	a : 0.01	d : 0.01	
^ : 0.23	t : 0.17	w : 0.16	u : 0.14	v : 0.11	x : 0.10	y : 0.05	
^ : 0.23	t : 0.17	w : 0.16	u : 0.14	v : 0.11	x : 0.10	y : 0.05	
^ : 0.23	t : 0.17	w : 0.16	u : 0.14	v : 0.11	x : 0.10	y : 0.05	
^ : 0.23	t : 0.17	w : 0.16	u : 0.14	v : 0.11	x : 0.10	y : 0.05	
^ : 0.23	t : 0.17	w : 0.16	u : 0.14	v : 0.11	x : 0.10	y : 0.05	
^ : 0.23	t : 0.17	w : 0.16	u : 0.14	v : 0.11	x : 0.10	y : 0.05	
^ : 0.23	t : 0.17	w : 0.16	u : 0.14	v : 0.11	x : 0.10	y : 0.05	
^ : 0.23	t : 0.17	w : 0.16	u : 0.14	v : 0.11	x : 0.10	y : 0.05	
^ : 0.23	t : 0.17	w : 0.16	u : 0.14	v : 0.11	x : 0.10	y : 0.05	
^ : 0.23	w : 0.16	u : 0.14	v : 0.11	t : 0.10	x : 0.10	y : 0.05	d : 0.04	c : 0.01	f : 0.01	
^ : 0.23	w : 0.16	v : 0.11	x : 0.10	u : 0.08	t : 0.07	c : 0.07	d : 0.05	y : 0.05	b : 0.01	f : 0.01	
^ : 0.23	w : 0.16	x : 0.10	c : 0.10	d : 0.08	u : 0.07	y : 0.05	v : 0.04	e : 0.04	g : 0.02	= : 0.01	b : 0.01	a : 0.01	f : 0.01	
d : 0.19	^ : 0.19	c : 0.16	e : 0.10	y : 0.05	x : 0.05	b : 0.05	g : 0.05	f : 0.04	= : 0.02	3 : 0.02	] : 0.01	
d : 0.16	^ : 0.16	e : 0.13	c : 0.11	b : 0.08	g : 0.07	3 : 0.05	] : 0.05	= : 0.04	f : 0.04	y : 0.02	2 : 0.01	i : 0.01	
d : 0.19	e : 0.14	^ : 0.14	c : 0.08	g : 0.07	3 : 0.05	] : 0.05	b : 0.05	= : 0.04	2 : 0.04	f : 0.04	a : 0.01	4 : 0.01	i : 0.01	
d : 0.20	e : 0.14	^ : 0.14	c : 0.08	g : 0.08	2 : 0.08	] : 0.07	= : 0.04	3 : 0.02	f : 0.02	b : 0.02	4 : 0.01	i : 0.01	
d : 0.17	c : 0.13	e : 0.11	g : 0.10	^ : 0.10	] : 0.08	2 : 0.07	= : 0.05	f : 0.05	4 : 0.02	i : 0.02	5 : 0.01	: : 0.01	
d : 0.19	c : 0.17	g : 0.11	e : 0.08	f : 0.08	= : 0.05	^ : 0.05	] : 0.02	b : 0.02	4 : 0.02	2 : 0.02	i : 0.02	7 : 0.01	5 : 0.01	> : 0.01	: : 0.01	a : 0.01	

#score	1387.0375853496091
#seq	68
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011c_hg19_CDS_m3_run1.txt

#BEAR
ddddqqqqqqqqdddd	chr2:232320124-232320357(-)$1	233	37	53	14.5870
ffffqqqqqqqqffff	chr1:231696798-231697025(+)$1	227	34	50	12.4888
ddddqqqqqqqqdddd	chr2:128087957-128088177(-)$1	220	19	35	14.5870
eeeeqqqqqqqqeeee	chr2:38527333-38527569(-)$1	236	197	213	13.5417
ddbbqqqqqqqqbb]d	chr21:34926305-34926543(+)$1	238	29	45	12.6398
gcccqqqqqqqqccc:	chr1:173915801-173916038(-)$1	237	193	209	12.5761
ddddqqqqqqqqdddd	chr11:85366534-85366755(-)$1	221	118	134	14.5870
ddddqqqqqqqqdddd	chr20:43567730-43567960(+)$1	230	40	56	14.5870
ddddqqqqqqqqdddd	chr2:190647048-190647274(-)$1	226	148	164	14.5870
[cccqqqqqqqqcccb	chr19:36219801-36220023(+)$1	222	183	199	13.2154
ddddqqqqqqqqdddd	chr1:100524132-100524356(+)$1	224	126	142	14.5870
cc[aqqqqqqqqa]cc	chr2:109381283-109381504(+)$1	221	195	211	12.9238
eeeeqqqqqqqqeeee	chr1:82409296-82409515(+)$1	219	96	112	13.5417
ffffqqqqqqqqffff	chr2:150426549-150426774(-)$1	225	15	31	12.4888
&cccqqqqqqqqccc5	chr17:1582906-1583127(-)$1	221	169	185	12.1040
ddddqqqqqqqqdddd	chr20:2464725-2464949(-)$1	224	84	100	14.5870
eeeeqqqqqqqqeeee	chr1:227838639-227838874(+)$1	235	31	47	13.5417
ddddqqqqqqqqdddd	chrX:123034279-123034502(+)$1	223	112	128	14.5870
eeeeqqqqqqqqeeee	chrX:55170136-55170358(-)$1	222	157	173	13.5417
eeeeqqqqqqqqeeee	chr17:27050564-27050788(+)$1	224	185	201	13.5417
ffffqqqqqqqqffff	chr7:35674687-35674908(-)$1	221	188	204	12.4888
$cccqqqqqqqqccc6	chr19:54969721-54969946(+)$1	225	61	77	12.7868
ffffqqqqqqqqffff	chrM:15423-15654(+)$1	231	135	151	12.4888
eeeeqqqqqqqqeeee	chr1:12443026-12443251(+)$1	225	27	43	13.5417
eeeeqqqqqqqqeeee	chr12:100603988-100604212(+)$1	224	192	208	13.5417
ddddqqqqqqqqdddd	chr2:225346526-225346750(-)$1	224	148	164	14.5870
eeeeqqqqqqqqeeee	chr2:197710587-197710810(-)$1	223	158	174	13.5417
eeeeqqqqqqqqeeee	chr2:61726886-61727116(-)$1	230	103	119	13.5417
ddddqqqqqqqqdddd	chr2:30862921-30863145(+)$1	224	40	56	14.5870
ddddqqqqqqqqdddd	chr5:64925870-64926092(+)$1	222	5	21	14.5870
ggggqqqqqqqqgggg	chr16:53262870-53263093(+)$1	223	171	187	12.9213
ddddqqqqqqqqdddd	chr17:42264988-42265209(+)$1	221	113	129	14.5870
eeeeqqqqqqqqeeee	chr3:136573275-136573498(+)$1	223	17	33	13.5417
ddddqqqqqqqqdddd	chr19:38230746-38230969(-)$1	223	170	186	14.5870
ddddqqqqqqqqdddd	chr19:6391858-6392084(-)$1	226	126	142	14.5870
ffffqqqqqqqqffff	chr1:63329633-63329856(+)$1	223	80	96	12.4888
[cccqqqqqqqqccc]	chr15:42470349-42470574(-)$1	225	78	94	13.4848
ddddqqqqqqqqdddd	chr19:38229675-38229895(-)$1	220	161	177	14.5870
[cccqqqqqqqqccc]	chr5:178140151-178140384(-)$1	233	131	147	13.4848
ddddqqqqqqqqdddd	chr10:124921791-124922019(+)$1	228	31	47	14.5870
#cccqqqqqqqqccc2	chr21:34901112-34901333(-)$1	221	187	203	13.1350
ffffqqqqqqqqffff	chr12:56221961-56222185(-)$1	224	98	114	12.4888
dcccqqqqqqqqccc:	chr1:67889861-67890083(-)$1	222	97	113	12.7866
ddddqqqqqqqqdddd	chr19:40541702-40541921(-)$1	219	65	81	14.5870
ddddqqqqqqqqdddd	chr17:73520297-73520519(+)$1	222	69	85	14.5870
ddddqqqqqqqqdddd	chr16:19553251-19553481(+)$1	230	19	35	14.5870
ddddqqqqqqqqdddd	chr16:24802342-24802565(+)$1	223	140	156	14.5870
eeeeqqqqqqqqeeee	chr5:36976095-36976334(+)$1	239	11	27	13.5417
ggbbqqqqqqqqbb]g	chr16:68055730-68055950(-)$1	220	124	140	11.9988
dd[aqqqqqqqqa]dd	chr2:202141501-202141722(+)$1	221	118	134	13.5698
c[bbqqqqqqqqbbcc	chr14:55529286-55529514(+)$1	228	201	217	12.1672
ffffqqqqqqqqffff	chr17:3623533-3623759(-)$1	226	63	79	12.4888
ddddqqqqqqqqdddd	chr6:7568674-7568894(+)$1	220	1	17	14.5870
ddddqqqqqqqqdddd	chr12:112478208-112478429(-)$1	221	74	90	14.5870
(cccqqqqqqqqccc8	chr1:155450637-155450855(-)$1	218	87	103	12.4448
ddddqqqqqqqqdddd	chr2:174086015-174086238(+)$1	223	73	89	14.5870
ggggqqqqqqqqgggg	chr15:49935584-49935812(+)$1	228	177	193	12.9213
acccqqqqqqqqccc]	chr6:126176131-126176357(+)$1	226	141	157	13.4156
ddddqqqqqqqqdddd	chr3:107881299-107881521(-)$1	222	140	156	14.5870
!cccqqqqqqqqcccc	chr2:100181878-100182097(-)$1	219	120	136	13.5410
ddddqqqqqqqqdddd	chr7:17373536-17373765(+)$1	229	58	74	14.5870
ffffqqqqqqqqffff	chr7:141423687-141423908(-)$1	221	115	131	12.4888
ddddqqqqqqqqdddd	chr1:235498520-235498742(+)$1	222	67	83	14.5870
ddddqqqqqqqqdddd	chr7:98545763-98545985(+)$1	222	205	221	14.5870
e[bbqqqqqqqqbbee	chr7:888006-888229(+)$1	223	82	98	12.3100
%cccqqqqqqqqccc6	chr21:45152365-45152586(+)$1	221	26	42	12.3837
iiiiqqqqqqqqiiii	chr1:29069768-29069990(+)$1	222	147	163	12.8001
ddddqqqqqqqqdddd	chr18:8085677-8085908(+)$1	231	104	120	14.5870

#otherMatches

#Seq PSSM
CUUCAACAGUGAGGAG	chr2:232320124-232320357(-)$1	233	37	53	14.5870
UAAGUGCUUAUUCUUA	chr1:231696798-231697025(+)$1	227	34	50	12.4888
UUCCUUAGUAGUGGAG	chr2:128087957-128088177(-)$1	220	19	35	14.5870
UUAUGAGGGAGAAUAA	chr2:38527333-38527569(-)$1	236	197	213	13.5417
GCUCUGGAACCUGAUG	chr21:34926305-34926543(+)$1	238	29	45	12.6398
ACCUUUAAAAUUAGGC	chr1:173915801-173916038(-)$1	237	193	209	12.5761
CUAGGAAAUAAAUUAG	chr11:85366534-85366755(-)$1	221	118	134	14.5870
GGAAAUCCUCGCUUCC	chr20:43567730-43567960(+)$1	230	40	56	14.5870
AAACACUUAAAAGUUU	chr2:190647048-190647274(-)$1	226	148	164	14.5870
CUGCUCUGUGACGCAC	chr19:36219801-36220023(+)$1	222	183	199	13.2154
UGAACGGCUUAAUUCA	chr1:100524132-100524356(+)$1	224	126	142	14.5870
GCUCUACAAAAUGUGC	chr2:109381283-109381504(+)$1	221	195	211	12.9238
UGGAACAAUAACUUCA	chr1:82409296-82409515(+)$1	219	96	112	13.5417
GGUGUUCAUGUUUACC	chr2:150426549-150426774(-)$1	225	15	31	12.4888
AACCUACGCUCUGGUC	chr17:1582906-1583127(-)$1	221	169	185	12.1040
CCGGACCAUAACCUGG	chr20:2464725-2464949(-)$1	224	84	100	14.5870
uguuaaaauagaagca	chr1:227838639-227838874(+)$1	235	31	47	13.5417
GUUCAGUUUCAAGGAC	chrX:123034279-123034502(+)$1	223	112	128	14.5870
CUCCGCUAUGAAGGAG	chrX:55170136-55170358(-)$1	222	157	173	13.5417
GUCAUAAUUAACUGAC	chr17:27050564-27050788(+)$1	224	185	201	13.5417
GUGGUUUAAUUUCUGC	chr7:35674687-35674908(-)$1	221	188	204	12.4888
AGGCCUCCCCCAGCCC	chr19:54969721-54969946(+)$1	225	61	77	12.7868
AAUGAUAUUUCCUAUU	chrM:15423-15654(+)$1	231	135	151	12.4888
GUUUGUUUGAUGGAGC	chr1:12443026-12443251(+)$1	225	27	43	13.5417
UUUACAGUAAUUUAAG	chr12:100603988-100604212(+)$1	224	192	208	13.5417
GGAAUUAUAUUUUUCC	chr2:225346526-225346750(-)$1	224	148	164	14.5870
GUGGAGCACUAGCCAU	chr2:197710587-197710810(-)$1	223	158	174	13.5417
GGCCCAAACAUUGGCC	chr2:61726886-61727116(-)$1	230	103	119	13.5417
UUUCAUCUUUUCGAAA	chr2:30862921-30863145(+)$1	224	40	56	14.5870
UAGUUUAAAGGCACUA	chr5:64925870-64926092(+)$1	222	5	21	14.5870
UGUUGGUCUCUGAAUA	chr16:53262870-53263093(+)$1	223	171	187	12.9213
accucaugagguaggu	chr17:42264988-42265209(+)$1	221	113	129	14.5870
AUCUGAAGAAAUGGAU	chr3:136573275-136573498(+)$1	223	17	33	13.5417
AACUUUAGAAGUGGUU	chr19:38230746-38230969(-)$1	223	170	186	14.5870
GGCUUUUAAUGCAGCC	chr19:6391858-6392084(-)$1	226	126	142	14.5870
GGUCAUUCCAGAGACU	chr1:63329633-63329856(+)$1	223	80	96	12.4888
AGACUCAUCCCUGUCC	chr15:42470349-42470574(-)$1	225	78	94	13.4848
CCUUUUGAAUGUAAGG	chr19:38229675-38229895(-)$1	220	161	177	14.5870
CAGCAGAUAAACGCUA	chr5:178140151-178140384(-)$1	233	131	147	13.4848
GAAGAAGUAUGCCUUC	chr10:124921791-124922019(+)$1	228	31	47	14.5870
CCCACAUUACUAUGGA	chr21:34901112-34901333(-)$1	221	187	203	13.1350
GGAACUCUUUUCUUUC	chr12:56221961-56222185(-)$1	224	98	114	12.4888
CAGAAACAAAUAUCUU	chr1:67889861-67890083(-)$1	222	97	113	12.7866
CCCUUUGUAUGUAGGG	chr19:40541702-40541921(-)$1	219	65	81	14.5870
CUGCAGCCUCAAGCGG	chr17:73520297-73520519(+)$1	222	69	85	14.5870
GUUGGACAUUAACAAU	chr16:19553251-19553481(+)$1	230	19	35	14.5870
UGAUGGACAAAAAUCA	chr16:24802342-24802565(+)$1	223	140	156	14.5870
GUCUUCAGACAUGGAC	chr5:36976095-36976334(+)$1	239	11	27	13.5417
UGCAGGGGCAAAUGCC	chr16:68055730-68055950(-)$1	220	124	140	11.9988
UUGCAAAAGCACGGGA	chr2:202141501-202141722(+)$1	221	118	134	13.5698
AACACCCUCCACUGUG	chr14:55529286-55529514(+)$1	228	201	217	12.1672
UUACUAAAAGAUGUAA	chr17:3623533-3623759(-)$1	226	63	79	12.4888
CGAGAGAAAAUCCUUG	chr6:7568674-7568894(+)$1	220	1	17	14.5870
UCUUAGAAGUUAAAGA	chr12:112478208-112478429(-)$1	221	74	90	14.5870
AGAGGUAAAUGAUUCA	chr1:155450637-155450855(-)$1	218	87	103	12.4448
UGCAGAUAAACAUGCA	chr2:174086015-174086238(+)$1	223	73	89	14.5870
AACUUACACAUUAGUU	chr15:49935584-49935812(+)$1	228	177	193	12.9213
ACAAGUGCAACAUUGC	chr6:126176131-126176357(+)$1	226	141	157	13.4156
CAUGACUAGGAACAUG	chr3:107881299-107881521(-)$1	222	140	156	14.5870
AUGUAUUCAGAAACAG	chr2:100181878-100182097(-)$1	219	120	136	13.5410
UGGAUCAAUACUUCCA	chr7:17373536-17373765(+)$1	229	58	74	14.5870
UUCUAUGACUCCAGAG	chr7:141423687-141423908(-)$1	221	115	131	12.4888
GACUCAAGAAACAGUC	chr1:235498520-235498742(+)$1	222	67	83	14.5870
GGCCAUACUGAAGGCU	chr7:98545763-98545985(+)$1	222	205	221	14.5870
GCUGGCCAGAUACACU	chr7:888006-888229(+)$1	223	82	98	12.3100
GCGACUUCAUUCUCGG	chr21:45152365-45152586(+)$1	221	26	42	12.3837
UGGAUCUACUCCUUCA	chr1:29069768-29069990(+)$1	222	147	163	12.8001
GGGGACCACAUACUCC	chr18:8085677-8085908(+)$1	231	104	120	14.5870

#DB
((((........))))	chr2:232320124-232320357(-)$1	1	37	53	14.5870
((((........))))	chr1:231696798-231697025(+)$1	1	34	50	12.4888
((((........))))	chr2:128087957-128088177(-)$1	1	19	35	14.5870
((((........))))	chr2:38527333-38527569(-)$1	1	197	213	13.5417
((((........)).)	chr21:34926305-34926543(+)$1	1	29	45	12.6398
)(((........))).	chr1:173915801-173916038(-)$1	1	193	209	12.5761
((((........))))	chr11:85366534-85366755(-)$1	1	118	134	14.5870
((((........))))	chr20:43567730-43567960(+)$1	1	40	56	14.5870
((((........))))	chr2:190647048-190647274(-)$1	1	148	164	14.5870
.(((........))))	chr19:36219801-36220023(+)$1	1	183	199	13.2154
((((........))))	chr1:100524132-100524356(+)$1	1	126	142	14.5870
((.(........).))	chr2:109381283-109381504(+)$1	1	195	211	12.9238
((((........))))	chr1:82409296-82409515(+)$1	1	96	112	13.5417
((((........))))	chr2:150426549-150426774(-)$1	1	15	31	12.4888
.(((........))).	chr17:1582906-1583127(-)$1	1	169	185	12.1040
((((........))))	chr20:2464725-2464949(-)$1	1	84	100	14.5870
((((........))))	chr1:227838639-227838874(+)$1	1	31	47	13.5417
((((........))))	chrX:123034279-123034502(+)$1	1	112	128	14.5870
((((........))))	chrX:55170136-55170358(-)$1	1	157	173	13.5417
((((........))))	chr17:27050564-27050788(+)$1	1	185	201	13.5417
((((........))))	chr7:35674687-35674908(-)$1	1	188	204	12.4888
.(((........))).	chr19:54969721-54969946(+)$1	1	61	77	12.7868
((((........))))	chrM:15423-15654(+)$1	1	135	151	12.4888
((((........))))	chr1:12443026-12443251(+)$1	1	27	43	13.5417
((((........))))	chr12:100603988-100604212(+)$1	1	192	208	13.5417
((((........))))	chr2:225346526-225346750(-)$1	1	148	164	14.5870
((((........))))	chr2:197710587-197710810(-)$1	1	158	174	13.5417
((((........))))	chr2:61726886-61727116(-)$1	1	103	119	13.5417
((((........))))	chr2:30862921-30863145(+)$1	1	40	56	14.5870
((((........))))	chr5:64925870-64926092(+)$1	1	5	21	14.5870
((((........))))	chr16:53262870-53263093(+)$1	1	171	187	12.9213
((((........))))	chr17:42264988-42265209(+)$1	1	113	129	14.5870
((((........))))	chr3:136573275-136573498(+)$1	1	17	33	13.5417
((((........))))	chr19:38230746-38230969(-)$1	1	170	186	14.5870
((((........))))	chr19:6391858-6392084(-)$1	1	126	142	14.5870
((((........))))	chr1:63329633-63329856(+)$1	1	80	96	12.4888
.(((........))).	chr15:42470349-42470574(-)$1	1	78	94	13.4848
((((........))))	chr19:38229675-38229895(-)$1	1	161	177	14.5870
.(((........))).	chr5:178140151-178140384(-)$1	1	131	147	13.4848
((((........))))	chr10:124921791-124922019(+)$1	1	31	47	14.5870
.(((........))).	chr21:34901112-34901333(-)$1	1	187	203	13.1350
((((........))))	chr12:56221961-56222185(-)$1	1	98	114	12.4888
)(((........))).	chr1:67889861-67890083(-)$1	1	97	113	12.7866
((((........))))	chr19:40541702-40541921(-)$1	1	65	81	14.5870
((((........))))	chr17:73520297-73520519(+)$1	1	69	85	14.5870
((((........))))	chr16:19553251-19553481(+)$1	1	19	35	14.5870
((((........))))	chr16:24802342-24802565(+)$1	1	140	156	14.5870
((((........))))	chr5:36976095-36976334(+)$1	1	11	27	13.5417
((((........)).)	chr16:68055730-68055950(-)$1	1	124	140	11.9988
((.(........).))	chr2:202141501-202141722(+)$1	1	118	134	13.5698
(.((........))))	chr14:55529286-55529514(+)$1	1	201	217	12.1672
((((........))))	chr17:3623533-3623759(-)$1	1	63	79	12.4888
((((........))))	chr6:7568674-7568894(+)$1	1	1	17	14.5870
((((........))))	chr12:112478208-112478429(-)$1	1	74	90	14.5870
.(((........))).	chr1:155450637-155450855(-)$1	1	87	103	12.4448
((((........))))	chr2:174086015-174086238(+)$1	1	73	89	14.5870
((((........))))	chr15:49935584-49935812(+)$1	1	177	193	12.9213
((((........))).	chr6:126176131-126176357(+)$1	1	141	157	13.4156
((((........))))	chr3:107881299-107881521(-)$1	1	140	156	14.5870
.(((........))))	chr2:100181878-100182097(-)$1	1	120	136	13.5410
((((........))))	chr7:17373536-17373765(+)$1	1	58	74	14.5870
((((........))))	chr7:141423687-141423908(-)$1	1	115	131	12.4888
((((........))))	chr1:235498520-235498742(+)$1	1	67	83	14.5870
((((........))))	chr7:98545763-98545985(+)$1	1	205	221	14.5870
(.((........))))	chr7:888006-888229(+)$1	1	82	98	12.3100
.(((........))).	chr21:45152365-45152586(+)$1	1	26	42	12.3837
((((........))))	chr1:29069768-29069990(+)$1	1	147	163	12.8001
((((........))))	chr18:8085677-8085908(+)$1	1	104	120	14.5870

#PSSM
d : 0.45	e : 0.17	f : 0.11	g : 0.05	[ : 0.04	c : 0.02	& : 0.01	$ : 0.01	# : 0.01	( : 0.01	a : 0.01	! : 0.01	% : 0.01	i : 0.01	
d : 0.44	c : 0.19	e : 0.16	f : 0.11	g : 0.04	[ : 0.02	i : 0.01	
d : 0.41	c : 0.17	e : 0.16	f : 0.11	b : 0.05	[ : 0.02	g : 0.02	i : 0.01	
d : 0.41	c : 0.17	e : 0.16	f : 0.11	b : 0.05	a : 0.02	g : 0.02	i : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
d : 0.41	c : 0.17	e : 0.16	f : 0.11	b : 0.05	a : 0.02	g : 0.02	i : 0.01	
d : 0.41	c : 0.17	e : 0.16	f : 0.11	b : 0.05	] : 0.02	g : 0.02	i : 0.01	
d : 0.42	c : 0.20	e : 0.17	f : 0.11	] : 0.02	g : 0.02	i : 0.01	
d : 0.44	e : 0.17	f : 0.11	c : 0.04	g : 0.04	] : 0.04	: : 0.02	6 : 0.02	b : 0.01	5 : 0.01	2 : 0.01	8 : 0.01	i : 0.01	

#score	926.9182488162813
#seq	68
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_UTR_m3_run2.txt

#BEAR
hhhhhh!!a[bboooooobb]a4444hhh	chr19:56179814-56180040(+)$1	226	77	106	12.9809
ddd!!ddddcccooooooccc]dddd333	chr1:75231536-75231776(+)$1	240	11	40	13.0198
ffff[gggggggooooooggggggg]fff	chr1:90498894-90499120(+)$1	226	172	201	14.2878
dddd####ddddoooooodddd333dddd	chr2:208465544-208465778(+)$1	234	9	38	13.1686
eeeee[ccccccooooooccc333ccc]e	chr10:96361359-96361585(+)$1	226	62	91	14.5537
======[eeeeeooooooeeeee333===	chr7:32627626-32627857(+)$1	231	52	81	16.3347
=======[arrrrrrrrra==========	chr16:50833010-50833230(+)$1	220	187	216	13.1483
f!!bb!!eeeeeooooooeeeee22bb33	chr4:128754152-128754384(+)$1	232	186	215	13.1627
E============mmmm============	chr11:12966004-12966228(+)$1	224	4	33	12.8940
f[ccc[bb[cccooooooccc]bbccc]f	chr7:135298897-135299121(+)$1	224	153	182	13.9376
dddd"""eeeeeooooooeeeee333ddd	chrX:24005327-24005549(-)$1	222	72	101	13.3901
c===========oooooo===========	chr1:32371925-32372147(-)$1	222	19	48	18.1689
ffffff[eeeeeooooooeeeee]fffff	chr12:1895518-1895740(+)$1	222	125	154	13.0280
[============mmmm============	chr5:137841805-137842035(-)$1	230	63	92	13.8273
###===========mmmm===========	chr6:36893230-36893462(+)$1	232	158	187	13.4043
ccc[ccc[ddddoooooodddd]cccccc	chr16:19563340-19563566(+)$1	226	60	89	14.0336
:ffffff!!cccooooooccc22ffffff	chr17:65074247-65074489(-)$1	242	33	62	12.4028
==============mmmm===========	chr3:196660186-196660406(+)$1	220	5	34	13.9000
Hgggggggddddoooooodddd333gggg	chr1:162493772-162494006(+)$1	234	192	221	14.9247
ggggg!!eeeeeooooooeeeee333ggg	chr1:62916788-62917029(+)$1	241	133	162	15.4241
iiiiiii[ddddoooooodddd]iiiiii	chr2:25960480-25960707(-)$1	227	156	185	15.9567
gggggggbb[bboooooobb]bb]ggggg	chr17:27875057-27875286(+)$1	229	134	163	13.5694
iiiiiiii"""cccmmmmccc]iiiiiii	chr1:173857452-173857683(+)$1	231	74	103	11.7633
==========rrrrrrrrr==========	chr17:27954589-27954813(-)$1	224	68	97	13.4482
eee[ccc!!cccoooooocccccceeeee	chr1:93307305-93307550(+)$1	245	15	44	13.5636
BBiiiiiiiiiaooooooa]iiiiiiiii	chr12:54633363-54633595(-)$1	232	29	58	14.9210
iiiiiiiiddddoooooodddd4444iii	chr8:124332429-124332650(-)$1	221	124	153	16.0343
========ddddoooooodddd=======	chr1:235331624-235331867(-)$1	243	53	82	16.7309
============oooooo===========	chr12:46753261-46753491(-)$1	230	28	57	18.2301
bb[iiiiiiiiiooooooiiiiiiiii]b	chr6:13361157-13361390(-)$1	233	27	56	16.0092
qqgggggggcccooooooccceeeeeggg	chr5:153435053-153435279(+)$1	226	138	167	13.4482
cc[ccc[eeeeeooooooeeeeecccccc	chr17:17095193-17095429(+)$1	236	146	175	13.9521
ff[ffffff[bboooooobb]ffffff]f	chr6:105526649-105526910(+)$1	261	183	212	12.1800
d!!ccc[eeeeeooooooeeeee]ccc]d	chr11:32999231-32999456(+)$1	225	14	43	14.1209
b[gggggggcccooooooccc]ggggggg	chr5:114950174-114950403(-)$1	229	45	74	15.6167
!!ggggggg[a[annnnna]a]ggggggg	chr10:6157592-6157823(+)$1	231	120	149	11.4761
ccc[dddd"""aooooooa333ddddccc	chr1:205685096-205685320(-)$1	224	184	213	12.8702
ff"""gggggggooooooggggggg]fff	chr11:118268956-118269185(+)$1	229	178	207	14.4536
ccc!!gggggggooooooggggggg333c	chr14:81643765-81644001(-)$1	236	168	197	15.1735
gggggggbbcccooooooccc333bbddd	chr17:18112670-18112904(+)$1	234	115	144	14.1954
""eeeee!!cccooooooccc4444eeee	chr3:196314121-196314352(+)$1	231	38	67	14.1520
ggggg[ddddbboooooobb333dddd]g	chr12:110973015-110973239(-)$1	224	106	135	13.4653
::==========oooooo==========i	chr1:101445923-101446145(+)$1	222	114	143	16.0333
cc[===========lll===========]	chr1:67877466-67877692(-)$1	226	193	222	14.1323
d[ccc!!bbcccooooooccc]bb333cc	chr5:135514704-135514929(+)$1	225	69	98	14.3334
!!ffffffddddoooooodddd4444fff	chr4:186083585-186083812(-)$1	227	117	146	13.7572
============oooooo===========	chr11:43364533-43364763(+)$1	230	191	220	18.2301
c[==========oooooo==========c	chr5:135517986-135518207(+)$1	221	91	120	18.0164
=======[arrrrrrrrra]=========	chr10:112772232-112772455(+)$1	223	16	45	12.9798
ggggg!!addddoooooodddd4444a22	chr2:178087737-178087962(+)$1	225	175	204	14.6184

#otherMatches

#Seq PSSM
CCCCGACUCUGCCCACAAGCUGUUCAUCG	chr19:56179814-56180040(+)$1	226	77	106	12.9809
AUAUAAGGUAUAGUAUAGUAUAAUCUGUU	chr1:75231536-75231776(+)$1	240	11	40	13.0198
UUUUAGAGGUUAUUGUACUAAUUUUAAAA	chr1:90498894-90499120(+)$1	226	172	201	14.2878
GGGUGACAUGUGGAAUCAUACAAAGGCUU	chr2:208465544-208465778(+)$1	234	9	38	13.1686
UAGUGAUUUCCCUGUAUUGGGUUUGAAAU	chr10:96361359-96361585(+)$1	226	62	91	14.5537
AUAUGAAAGAUAACUAUAUAUUUAAAUCA	chr7:32627626-32627857(+)$1	231	52	81	16.3347
gugugugucuguguguguguauauaugua	chr16:50833010-50833230(+)$1	220	187	216	13.1483
ACCUCAAUUCCUUUAUUCAGGAAAGGAUA	chr4:128754152-128754384(+)$1	232	186	215	13.1627
AUUUUUUUAUAAAGUGCUUUGUAAAAAAA	chr11:12966004-12966228(+)$1	224	4	33	12.8940
AACACAUUUAUAAUUCCAUGUUAAGUGAU	chr7:135298897-135299121(+)$1	224	153	182	13.9376
UGUGUUAGUGAAAGCAUAUUCAUACUCGC	chrX:24005327-24005549(-)$1	222	72	101	13.3901
CCAGUUUGACAUAGAGAGAUGUCAGAUUG	chr1:32371925-32372147(-)$1	222	19	48	18.1689
ACAUUUAUAUCCGAUAAGGGGUGGGAGUG	chr12:1895518-1895740(+)$1	222	125	154	13.0280
UUAUAUAUUGAUGUGUGUAUCAAUAUAUA	chr5:137841805-137842035(-)$1	230	63	92	13.8273
AGGGGAAAAUUCUCCAAAGAGGGUUUUCU	chr6:36893230-36893462(+)$1	232	158	187	13.4043
UCAUAGUCUGUUUUUUCUAGCAUGCUUGA	chr16:19563340-19563566(+)$1	226	60	89	14.0336
AGAAGAGUAGCGACCCUCUGUCUCUCUUC	chr17:65074247-65074489(-)$1	242	33	62	12.4028
UAAGUAUUUUAAAAGUCAUUUUAAAAUAU	chr3:196660186-196660406(+)$1	220	5	34	13.9000
UGCAGGUUGCUGAGAGUCCAGUUAGAAUU	chr1:162493772-162494006(+)$1	234	192	221	14.9247
AACACUUGGAUUUACACCAGUCUUUUGUG	chr1:62916788-62917029(+)$1	241	133	162	15.4241
ACCUUGGAGUUUUUUGGUGAAUCUUGAGG	chr2:25960480-25960707(-)$1	227	156	185	15.9567
AGAGACUCCAUUUAGCUUAACGGUAGUCU	chr17:27875057-27875286(+)$1	229	134	163	13.5694
AGAAAUAGUAUGCUAGAAAGUUCUGUuuu	chr1:173857452-173857683(+)$1	231	74	103	11.7633
UACUGUAGUAGACAUGUAGUACUAUAGUA	chr17:27954589-27954813(-)$1	224	68	97	13.4482
AGGUGGAACCGUCCCAAAAUGUCCCUUGC	chr1:93307305-93307550(+)$1	245	15	44	13.5636
ACAGACUGGAACAAUGAAGCUUUUGGUUU	chr12:54633363-54633595(-)$1	232	29	58	14.9210
UAAAAGCAUGCACUUCCAUGCAUACUUGC	chr8:124332429-124332650(-)$1	221	124	153	16.0343
CACUUAAUGGCUGUUGAGGGCCACUUUUU	chr1:235331624-235331867(-)$1	243	53	82	16.7309
AUUUAUCGUACGUCACAGUGUAUGGUGAA	chr12:46753261-46753491(-)$1	230	28	57	18.2301
GGGUAGUCUUGGCCAACUCCAAGACUGGC	chr6:13361157-13361390(-)$1	233	27	56	16.0092
UUUUUUucuguccacugagacuggagugc	chr5:153435053-153435279(+)$1	226	138	167	13.4482
CAGCUGUGCCCUUCUGUCAGGGUCAGUGU	chr17:17095193-17095429(+)$1	236	146	175	13.9521
UCAUGUUUUAUGUUAAUUCAGAGAAUAAG	chr6:105526649-105526910(+)$1	261	183	212	12.1800
AUGUAUUAGGUUCAACAUGACCUUGUGUU	chr11:32999231-32999456(+)$1	225	14	43	14.1209
GCAAAGGGUGAACAUGUUUUCAACCCUUU	chr5:114950174-114950403(-)$1	229	45	74	15.6167
ACAACAAUCUGUGUGCCUCUCUGGUUGUU	chr10:6157592-6157823(+)$1	231	120	149	11.4761
AGACAGGCUCUGAAUAACCUUUGUUUUCU	chr1:205685096-205685320(-)$1	224	184	213	12.8702
AAACUCUGCACAAGCAAGUGUGUAGCUUA	chr11:118268956-118269185(+)$1	229	178	207	14.4536
GGAAAUGUGUGCCUUUCAGUAUACAAACU	chr14:81643765-81644001(-)$1	236	168	197	15.1735
GGUGCCUCCUCCGCUUCAGGGUAUGGGAG	chr17:18112670-18112904(+)$1	234	115	144	14.1954
UUGUGGUUAAUGUCAUUUCAUAGUUGCCA	chr3:196314121-196314352(+)$1	231	38	67	14.1520
AUCUACUAUUCCUAAAUUGGCAUAAUGUU	chr12:110973015-110973239(-)$1	224	106	135	13.4653
aaacuuagcauggauucacaugcugagua	chr1:101445923-101446145(+)$1	222	114	143	16.0333
AGGAAUUUUUAAAAAAUUUUUAAGAAUUG	chr1:67877466-67877692(-)$1	226	193	222	14.1323
AACGAAUAUAGACUCUUCUCUCAUUUAUC	chr5:135514704-135514929(+)$1	225	69	98	14.3334
UAAUUAUUCAGUUGUCAUGCUGUCAAAAU	chr4:186083585-186083812(-)$1	227	117	146	13.7572
cauacauacauaagcauauaugugugugu	chr11:43364533-43364763(+)$1	230	191	220	18.2301
GUAUUUUGAAAUUCACUUAUUUUAAAAUC	chr5:135517986-135518207(+)$1	221	91	120	18.0164
UUGCUUCUCUGACGAGUUGUGAAGCAAAA	chr10:112772232-112772455(+)$1	223	16	45	12.9798
UUUAAAUCAGAACCCAAUUUCUACGCGUG	chr2:178087737-178087962(+)$1	225	175	204	14.6184

#DB
((((((..(.((......)).)....)))	chr19:56179814-56180040(+)$1	1	77	106	12.9809
(((..(((((((......))).))))...	chr1:75231536-75231776(+)$1	1	11	40	13.0198
((((.(((((((......))))))).)))	chr1:90498894-90499120(+)$1	1	172	201	14.2878
((((....((((......))))...))))	chr2:208465544-208465778(+)$1	1	9	38	13.1686
(((((.((((((......)))...))).)	chr10:96361359-96361585(+)$1	1	62	91	14.5537
((((((.(((((......)))))...)))	chr7:32627626-32627857(+)$1	1	52	81	16.3347
(((((((.(.........)))))))))))	chr16:50833010-50833230(+)$1	1	187	216	13.1483
(..((..(((((......)))))..))..	chr4:128754152-128754384(+)$1	1	186	215	13.1627
(((((((((((((....))))))))))))	chr11:12966004-12966228(+)$1	1	4	33	12.8940
(.(((.((.(((......))).))))).)	chr7:135298897-135299121(+)$1	1	153	182	13.9376
((((...(((((......)))))...)))	chrX:24005327-24005549(-)$1	1	72	101	13.3901
)(((((((((((......)))))))))))	chr1:32371925-32372147(-)$1	1	19	48	18.1689
((((((.(((((......))))).)))))	chr12:1895518-1895740(+)$1	1	125	154	13.0280
.((((((((((((....))))))))))))	chr5:137841805-137842035(-)$1	1	63	92	13.8273
...(((((((((((....)))))))))))	chr6:36893230-36893462(+)$1	1	158	187	13.4043
(((.(((.((((......)))).))))))	chr16:19563340-19563566(+)$1	1	60	89	14.0336
.((((((..(((......)))..))))))	chr17:65074247-65074489(-)$1	1	33	62	12.4028
((((((((((((((....)))))))))))	chr3:196660186-196660406(+)$1	1	5	34	13.9000
)(((((((((((......))))...))))	chr1:162493772-162494006(+)$1	1	192	221	14.9247
(((((..(((((......)))))...)))	chr1:62916788-62917029(+)$1	1	133	162	15.4241
(((((((.((((......)))).))))))	chr2:25960480-25960707(-)$1	1	156	185	15.9567
(((((((((.((......)).)).)))))	chr17:27875057-27875286(+)$1	1	134	163	13.5694
((((((((...(((....))).)))))))	chr1:173857452-173857683(+)$1	1	74	103	11.7633
((((((((((.........))))))))))	chr17:27954589-27954813(-)$1	1	68	97	13.4482
(((.(((..(((......)))))))))))	chr1:93307305-93307550(+)$1	1	15	44	13.5636
((((((((((((......).)))))))))	chr12:54633363-54633595(-)$1	1	29	58	14.9210
((((((((((((......))))....)))	chr8:124332429-124332650(-)$1	1	124	153	16.0343
))))))))((((......))))(((((((	chr1:235331624-235331867(-)$1	1	53	82	16.7309
((((((((((((......)))))))))))	chr12:46753261-46753491(-)$1	1	28	57	18.2301
((.(((((((((......))))))))).)	chr6:13361157-13361390(-)$1	1	27	56	16.0092
..)))))))(((......)))((((((((	chr5:153435053-153435279(+)$1	1	138	167	13.4482
((.(((.(((((......)))))))))))	chr17:17095193-17095429(+)$1	1	146	175	13.9521
((.((((((.((......)).)))))).)	chr6:105526649-105526910(+)$1	1	183	212	12.1800
(..(((.(((((......))))).))).)	chr11:32999231-32999456(+)$1	1	14	43	14.1209
(.((((((((((......))).)))))))	chr5:114950174-114950403(-)$1	1	45	74	15.6167
..(((((((.(.(.....).).)))))))	chr10:6157592-6157823(+)$1	1	120	149	11.4761
(((.((((...(......)...)))))))	chr1:205685096-205685320(-)$1	1	184	213	12.8702
((...(((((((......))))))).)))	chr11:118268956-118269185(+)$1	1	178	207	14.4536
(((..(((((((......)))))))...)	chr14:81643765-81644001(-)$1	1	168	197	15.1735
)))))))(((((......)))...))(((	chr17:18112670-18112904(+)$1	1	115	144	14.1954
..(((((..(((......)))....))))	chr3:196314121-196314352(+)$1	1	38	67	14.1520
(((((.((((((......))...)))).)	chr12:110973015-110973239(-)$1	1	106	135	13.4653
..((((((((((......))))))))))(	chr1:101445923-101446145(+)$1	1	114	143	16.0333
((.(((((((((((...))))))))))).	chr1:67877466-67877692(-)$1	1	193	222	14.1323
(.(((..(((((......))).))...))	chr5:135514704-135514929(+)$1	1	69	98	14.3334
..((((((((((......))))....)))	chr4:186083585-186083812(-)$1	1	117	146	13.7572
((((((((((((......)))))))))))	chr11:43364533-43364763(+)$1	1	191	220	18.2301
(.((((((((((......)))))))))))	chr5:135517986-135518207(+)$1	1	91	120	18.0164
(((((((.(.........).)))))))))	chr10:112772232-112772455(+)$1	1	16	45	12.9798
(((((..(((((......))))....)..	chr2:178087737-178087962(+)$1	1	175	204	14.6184

#PSSM
= : 0.16	c : 0.14	f : 0.12	d : 0.10	g : 0.10	i : 0.06	e : 0.04	: : 0.04	b : 0.04	! : 0.04	h : 0.02	E : 0.02	[ : 0.02	# : 0.02	H : 0.02	B : 0.02	q : 0.02	" : 0.02	
= : 0.21	g : 0.12	f : 0.10	c : 0.10	! : 0.08	[ : 0.08	d : 0.06	i : 0.06	e : 0.04	h : 0.02	# : 0.02	B : 0.02	b : 0.02	q : 0.02	" : 0.02	: : 0.02	
= : 0.25	g : 0.18	c : 0.10	f : 0.08	i : 0.08	[ : 0.08	d : 0.06	e : 0.06	! : 0.04	h : 0.02	# : 0.02	" : 0.02	
= : 0.30	g : 0.18	f : 0.10	i : 0.10	c : 0.08	[ : 0.06	! : 0.04	d : 0.04	e : 0.04	h : 0.02	b : 0.02	" : 0.02	
= : 0.30	g : 0.18	c : 0.12	i : 0.10	f : 0.08	! : 0.04	e : 0.04	" : 0.04	h : 0.02	[ : 0.02	# : 0.02	b : 0.02	d : 0.02	
= : 0.30	g : 0.18	i : 0.10	! : 0.08	f : 0.08	c : 0.08	[ : 0.06	d : 0.04	h : 0.02	# : 0.02	" : 0.02	e : 0.02	
= : 0.27	g : 0.18	! : 0.10	i : 0.10	[ : 0.08	d : 0.06	c : 0.06	f : 0.06	# : 0.02	b : 0.02	" : 0.02	e : 0.02	
= : 0.23	g : 0.14	e : 0.14	! : 0.08	[ : 0.08	b : 0.08	i : 0.08	d : 0.06	f : 0.04	# : 0.02	c : 0.02	a : 0.02	
= : 0.21	d : 0.19	e : 0.14	g : 0.12	a : 0.06	! : 0.06	b : 0.06	" : 0.04	i : 0.04	c : 0.02	[ : 0.02	f : 0.02	
= : 0.21	c : 0.19	d : 0.18	e : 0.14	[ : 0.08	g : 0.06	r : 0.04	" : 0.04	i : 0.04	
c : 0.19	= : 0.19	d : 0.16	e : 0.14	b : 0.08	g : 0.06	r : 0.06	" : 0.04	i : 0.04	a : 0.02	
c : 0.21	= : 0.19	d : 0.16	e : 0.14	b : 0.08	g : 0.06	r : 0.06	a : 0.04	i : 0.02	[ : 0.02	
o : 0.80	= : 0.10	r : 0.06	c : 0.02	a : 0.02	
o : 0.80	r : 0.06	= : 0.06	m : 0.04	c : 0.02	n : 0.02	
o : 0.80	m : 0.10	r : 0.06	n : 0.02	l : 0.02	
o : 0.80	m : 0.10	r : 0.06	n : 0.02	l : 0.02	
o : 0.80	m : 0.10	r : 0.06	n : 0.02	l : 0.02	
o : 0.80	r : 0.06	= : 0.06	m : 0.06	n : 0.02	
c : 0.21	= : 0.19	d : 0.16	e : 0.14	a : 0.10	b : 0.08	g : 0.06	r : 0.02	i : 0.02	
= : 0.23	c : 0.21	d : 0.16	e : 0.14	b : 0.08	g : 0.06	] : 0.06	i : 0.02	3 : 0.02	
= : 0.25	c : 0.21	d : 0.16	e : 0.14	] : 0.06	g : 0.06	i : 0.04	3 : 0.04	a : 0.02	
= : 0.25	d : 0.16	e : 0.16	] : 0.12	3 : 0.08	g : 0.06	i : 0.04	a : 0.02	2 : 0.02	b : 0.02	c : 0.02	f : 0.02	4 : 0.02	
= : 0.27	e : 0.16	4 : 0.10	g : 0.10	3 : 0.10	b : 0.06	i : 0.06	d : 0.04	] : 0.04	2 : 0.02	c : 0.02	f : 0.02	
= : 0.27	3 : 0.14	4 : 0.10	g : 0.10	i : 0.08	d : 0.06	] : 0.06	c : 0.06	b : 0.04	f : 0.04	2 : 0.02	e : 0.02	
= : 0.27	g : 0.12	3 : 0.12	4 : 0.10	c : 0.10	i : 0.08	d : 0.06	f : 0.06	e : 0.04	2 : 0.02	b : 0.02	
= : 0.27	c : 0.10	3 : 0.10	4 : 0.08	d : 0.08	g : 0.08	i : 0.08	f : 0.06	e : 0.06	] : 0.04	b : 0.04	
= : 0.30	f : 0.12	c : 0.12	g : 0.12	i : 0.10	d : 0.08	3 : 0.06	e : 0.04	h : 0.02	b : 0.02	a : 0.02	
= : 0.30	] : 0.12	g : 0.12	f : 0.10	c : 0.08	i : 0.08	3 : 0.06	d : 0.06	e : 0.04	h : 0.02	2 : 0.02	
= : 0.23	f : 0.14	g : 0.14	c : 0.12	i : 0.10	d : 0.08	e : 0.06	3 : 0.04	h : 0.02	b : 0.02	] : 0.02	2 : 0.02	

#score	717.4262319966601
#seq	50
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_UTR_m3_run1.txt

#BEAR
gggggggnnnnnggggggg:	chr17:38290674-38290897(+)$1	223	41	61	11.5222
eee[cccnnnnnccc]eeee	chr10:5805161-5805383(+)$1	222	25	45	10.5199
b[ggggggglllggggggg]	chr2:113496000-113496221(-)$1	221	195	215	8.4076
iiiiiiinnnnniiiiiiii	chr13:73333650-73333866(-)$1	216	128	148	12.5515
gggggggnnnnngggggggd	chr18:43844940-43845159(+)$1	219	183	203	12.3462
b[ggggggglllggggggg]	chr7:102950722-102950943(+)$1	221	71	91	8.4076
gggggggnnnnnggggggg:	chr5:71504684-71504904(+)$1	220	167	187	11.5222
gggggggnnnnnggggggg:	chr14:60759932-60760152(+)$1	220	18	38	11.5222
ggeeeeennnnneeeee]gg	chr19:2428070-2428293(-)$1	223	27	47	10.2502
gg!!cccnnnnnccc]gggg	chr19:38230244-38230465(-)$1	221	130	150	11.9613
hhhhhhhnnnnnhhhhhhhh	chr3:196312443-196312664(+)$1	221	133	153	9.9639
gggggggnnnnnggggggg3	chr1:242052717-242052937(+)$1	220	16	36	12.5935
hhh[cccnnnnnccchhhhh	chr15:49281318-49281544(-)$1	226	88	108	10.6649
[gggggggmmmmggggggg3	chr4:177249968-177250186(+)$1	218	34	54	7.9039
[a[ddddnnnnndddd]a]a	chr4:159825580-159825797(+)$1	217	192	212	9.4409
gggggggooooooggggggg	chrX:20142819-20143039(-)$1	220	133	153	9.5726
gggggggnnnnnggggggge	chr16:14043699-14043918(+)$1	219	139	159	12.4156
=======nnnnn========	chr8:37719850-37720070(-)$1	220	8	28	12.5049
ffffcccnnnnnccc333ff	chr8:9636324-9636541(+)$1	217	118	138	10.1808
gggggggooooooggggggg	chr6:28334953-28335172(+)$1	219	62	82	9.5726
=======nnnnn========	chr3:185635109-185635328(-)$1	219	40	60	12.5049
hhh!!bbnnnnnbbhhhhhh	chr20:61576498-61576716(+)$1	218	14	34	9.6929
iiiiiiinnnnniiiiiiii	chr5:121363496-121363719(+)$1	223	25	45	12.5515
eccc[bbnnnnnbbccc]ee	chr5:10437204-10437423(+)$1	219	136	156	9.5528
ggggg[annnnna]gggggg	chr6:163987150-163987370(+)$1	220	190	210	12.0226
hh[ddddnnnnndddd22hh	chr1:78030281-78030504(-)$1	223	71	91	8.9131
gggggggooooooggggggg	chr2:74442364-74442585(+)$1	221	117	137	9.5726
gggggggnnnnnggggggg]	chr11:9753976-9754198(+)$1	222	20	40	12.6226
iiiiiiillliiiiiiiii2	chr1:23634839-23635057(-)$1	218	68	88	8.4159
dd!!cccnnnnnccc22ddd	chr8:64100001-64100219(+)$1	218	166	186	9.7098
gggggggooooooggggggg	chr19:41812321-41812548(+)$1	227	171	191	9.5726
[ffffffnnnnnffffff33	chr18:43674923-43675145(-)$1	222	50	70	9.7349
!!ggggggglllggggggg3	chr17:42884699-42884918(-)$1	219	68	88	8.7671
####cccnnnnnccc4444d	chr15:38646810-38647031(+)$1	221	76	96	9.7368
eeee!!annnnna22eeeee	chr12:69238992-69239210(+)$1	218	135	155	9.3185
gggggggooooooggggggg	chr14:57672002-57672219(-)$1	217	64	84	9.5726
ccc[cccnnnnnccc]ccc5	chr19:36883392-36883611(-)$1	219	57	77	10.0965
=====bbnnnnnbb]=====	chr12:111158042-111158262(-)$1	220	91	111	11.1550
=========lll========	chr17:58525018-58525243(-)$1	225	33	53	9.3618
iiiiiiiiillliiiiiiii	chr14:104025463-104025680(-)$1	217	136	156	9.0661
gggggggnnnnngggggggd	chr1:82456645-82456867(+)$1	222	43	63	12.3462
!ffffffnnnnnffffff33	chr11:10819062-10819281(-)$1	219	10	30	9.7087
gggggggooooooggggggg	chr17:10596104-10596323(-)$1	219	88	108	9.5726
"""ddddnnnnndddd]hhh	chr5:132215253-132215475(-)$1	222	93	113	9.2083
iiiiiiinnnnniiiiiiii	chr13:79894397-79894617(-)$1	220	84	104	12.5515
d[eeeeennnnneeeee22d	chr16:89347484-89347704(-)$1	220	50	70	9.0861
ccc[cccnnnnnccc]cccc	chr11:17394127-17394350(+)$1	223	158	178	10.8325
eeee[bbnnnnnbb]eeeee	chr2:181927508-181927728(+)$1	220	131	151	9.2099
ddd[cccnnnnnccc]dddd	chrX:133561040-133561264(+)$1	224	176	196	9.7046
[gggggggmmmmggggggg]	chr19:21366742-21366959(+)$1	217	156	176	7.9330
g[eeeeennnnneeeee]gg	chr1:70727559-70727778(-)$1	219	52	72	10.2628
###ddddnnnnnddddffff	chr17:27585286-27585512(-)$1	226	150	170	8.7357
iiiiiiiimmmmiiiiiiii	chr1:231470361-231470580(-)$1	219	157	177	7.9857
eeeeebbnnnnnbb22eeee	chr7:94298219-94298436(+)$1	217	52	72	8.6999

#otherMatches

#Seq PSSM
GUUAUCACUCGCUGAUAAUA	chr17:38290674-38290897(+)$1	223	41	61	11.5222
AGCUUUGGGUUGCAGUGCUA	chr10:5805161-5805383(+)$1	222	25	45	10.5199
GUUCUUUCAUCGUGGAAGAU	chr2:113496000-113496221(-)$1	221	195	215	8.4076
AUUAUUUAUGCAGAAUAAUU	chr13:73333650-73333866(-)$1	216	128	148	12.5515
CAGAAAUGUACAAUUUCUGG	chr18:43844940-43845159(+)$1	219	183	203	12.3462
UCAUGGCAAUCUUUGCCAUA	chr7:102950722-102950943(+)$1	221	71	91	8.4076
AUUAGGUUAUUCACCUGGUA	chr5:71504684-71504904(+)$1	220	167	187	11.5222
UUCCUACAUAUAGUAGGAAA	chr14:60759932-60760152(+)$1	220	18	38	11.5222
GAUGCAUGCCUAAUGUGUUC	chr19:2428070-2428293(-)$1	223	27	47	10.2502
UAAAGGUGGAAAACCCUAUG	chr19:38230244-38230465(-)$1	221	130	150	11.9613
UUCUUUUGUUAGAAAAGAAA	chr3:196312443-196312664(+)$1	221	133	153	9.9639
AAAAUACCAAAUGUAUUUUA	chr1:242052717-242052937(+)$1	220	16	36	12.5935
AGUAGUGAAUGCUACACUCA	chr15:49281318-49281544(-)$1	226	88	108	10.6649
UGAUGGAAUUUAUUCCAUUU	chr4:177249968-177250186(+)$1	218	34	54	7.9039
GUGAUGUCAAAAGCAUGAGA	chr4:159825580-159825797(+)$1	217	192	212	9.4409
CAGAUGAAGUCUCUCAUUUG	chrX:20142819-20143039(-)$1	220	133	153	9.5726
gacagagucucccucuguug	chr16:14043699-14043918(+)$1	219	139	159	12.4156
ACUGAGAUUUUUUUUCAGUA	chr8:37719850-37720070(-)$1	220	8	28	12.5049
UGAAUGGAUGCGCCAGUUUU	chr8:9636324-9636541(+)$1	217	118	138	10.1808
ACUAGGAAUUCUAUUCUAGU	chr6:28334953-28335172(+)$1	219	62	82	9.5726
AGUAUGUUUUGCAUGUAUUU	chr3:185635109-185635328(-)$1	219	40	60	12.5049
AGGUUGCGGUUUGCUCUUCC	chr20:61576498-61576716(+)$1	218	14	34	9.6929
UUAAUUAUAUUUUAGUUAAG	chr5:121363496-121363719(+)$1	223	25	45	12.5515
UCUCUACUUACUGUGAGAAG	chr5:10437204-10437423(+)$1	219	136	156	9.5528
UUAAGUGAUAAACUCUUGAA	chr6:163987150-163987370(+)$1	220	190	210	12.0226
GUAGUCUGCACAAGAUCCAU	chr1:78030281-78030504(-)$1	223	71	91	8.9131
AAUGUAGCUAUUCCUAUAUU	chr2:74442364-74442585(+)$1	221	117	137	9.5726
acugugccauuugcAUAGUA	chr11:9753976-9754198(+)$1	222	20	40	12.6226
CUUUUAAACUUUGAAAGUAC	chr1:23634839-23635057(-)$1	218	68	88	8.4159
GGACACUCAAGAGGUACCCC	chr8:64100001-64100219(+)$1	218	166	186	9.7098
GGAGGCCCCUGCCGGCUUCC	chr19:41812321-41812548(+)$1	227	171	191	9.5726
CUCCAGAAAUGCUUUGGGUU	chr18:43674923-43675145(-)$1	222	50	70	9.7349
UUUUCCCUUCCAGAGGGAAU	chr17:42884699-42884918(-)$1	219	68	88	8.7671
UUGGCUUGCUGAAAGAUUUU	chr15:38646810-38647031(+)$1	221	76	96	9.7368
CACCAGCACUUGGAAGGUGU	chr12:69238992-69239210(+)$1	218	135	155	9.3185
UGGGAGAUUAACUUUUUUUA	chr14:57672002-57672219(-)$1	217	64	84	9.5726
UAGAGGUUUUAUACCAUUAA	chr19:36883392-36883611(-)$1	219	57	77	10.0965
GUAUGGUUGUAUACACAUGC	chr12:111158042-111158262(-)$1	220	91	111	11.1550
UCUUUUUUGUUACAGGGAAG	chr17:58525018-58525243(-)$1	225	33	53	9.3618
UUUUUGUGUGCAACAUAAGA	chr14:104025463-104025680(-)$1	217	136	156	9.0661
ggagcuggccaucagcuuca	chr1:82456645-82456867(+)$1	222	43	63	12.3462
UAAUGUUUUCACAAUAUUUA	chr11:10819062-10819281(-)$1	219	10	30	9.7087
UGGGGGACCGUUUUCCCUCA	chr17:10596104-10596323(-)$1	219	88	108	9.5726
AAAUGUACCCUCUAUACUUU	chr5:132215253-132215475(-)$1	222	93	113	9.2083
GAAACAUAUGCAAUGUUUUU	chr13:79894397-79894617(-)$1	220	84	104	12.5515
GUGGCUUCAAGUGGGCUUUC	chr16:89347484-89347704(-)$1	220	50	70	9.0861
agagaugaacaacaugucuu	chr11:17394127-17394350(+)$1	223	158	178	10.8325
AAGGAGCAGAAGGCAUCUUC	chr2:181927508-181927728(+)$1	220	131	151	9.2099
ACUAGCUUUAGUAGUGGGUU	chrX:133561040-133561264(+)$1	224	176	196	9.7046
gcucccagcauuuugggagg	chr19:21366742-21366959(+)$1	217	156	176	7.9330
CUUAGUGCAAUUCAUUGUGG	chr1:70727559-70727778(-)$1	219	52	72	10.2628
AGCAAAGGAAAACUUUAGUG	chr17:27585286-27585512(-)$1	226	150	170	8.7357
GUUGCUAAUUAAUUAGCAGC	chr1:231470361-231470580(-)$1	219	157	177	7.9857
CUGCUGGAAAGACCUGGGCA	chr7:94298219-94298436(+)$1	217	52	72	8.6999

#DB
(((((((.....))))))).	chr17:38290674-38290897(+)$1	1	41	61	11.5222
(((.(((.....))).))))	chr10:5805161-5805383(+)$1	1	25	45	10.5199
(.(((((((...))))))).	chr2:113496000-113496221(-)$1	1	195	215	8.4076
(((((((.....))))))))	chr13:73333650-73333866(-)$1	1	128	148	12.5515
(((((((.....))))))))	chr18:43844940-43845159(+)$1	1	183	203	12.3462
(.(((((((...))))))).	chr7:102950722-102950943(+)$1	1	71	91	8.4076
(((((((.....))))))).	chr5:71504684-71504904(+)$1	1	167	187	11.5222
(((((((.....))))))).	chr14:60759932-60760152(+)$1	1	18	38	11.5222
(((((((.....))))).))	chr19:2428070-2428293(-)$1	1	27	47	10.2502
((..(((.....))).))))	chr19:38230244-38230465(-)$1	1	130	150	11.9613
(((((((.....))))))))	chr3:196312443-196312664(+)$1	1	133	153	9.9639
(((((((.....))))))).	chr1:242052717-242052937(+)$1	1	16	36	12.5935
(((.(((.....))))))))	chr15:49281318-49281544(-)$1	1	88	108	10.6649
.(((((((....))))))).	chr4:177249968-177250186(+)$1	1	34	54	7.9039
.(.((((.....)))).).)	chr4:159825580-159825797(+)$1	1	192	212	9.4409
(((((((......)))))))	chrX:20142819-20143039(-)$1	1	133	153	9.5726
(((((((.....)))))))(	chr16:14043699-14043918(+)$1	1	139	159	12.4156
(((((((.....))))))))	chr8:37719850-37720070(-)$1	1	8	28	12.5049
(((((((.....)))...))	chr8:9636324-9636541(+)$1	1	118	138	10.1808
(((((((......)))))))	chr6:28334953-28335172(+)$1	1	62	82	9.5726
(((((((.....))))))))	chr3:185635109-185635328(-)$1	1	40	60	12.5049
(((..((.....))))))))	chr20:61576498-61576716(+)$1	1	14	34	9.6929
(((((((.....))))))))	chr5:121363496-121363719(+)$1	1	25	45	12.5515
((((.((.....))))).))	chr5:10437204-10437423(+)$1	1	136	156	9.5528
(((((.(.....).))))))	chr6:163987150-163987370(+)$1	1	190	210	12.0226
((.((((.....))))..))	chr1:78030281-78030504(-)$1	1	71	91	8.9131
(((((((......)))))))	chr2:74442364-74442585(+)$1	1	117	137	9.5726
(((((((.....))))))).	chr11:9753976-9754198(+)$1	1	20	40	12.6226
(((((((...))))))))).	chr1:23634839-23635057(-)$1	1	68	88	8.4159
((..(((.....)))..)))	chr8:64100001-64100219(+)$1	1	166	186	9.7098
(((((((......)))))))	chr19:41812321-41812548(+)$1	1	171	191	9.5726
.((((((.....))))))..	chr18:43674923-43675145(-)$1	1	50	70	9.7349
..(((((((...))))))).	chr17:42884699-42884918(-)$1	1	68	88	8.7671
....(((.....)))....)	chr15:38646810-38647031(+)$1	1	76	96	9.7368
((((..(.....)..)))))	chr12:69238992-69239210(+)$1	1	135	155	9.3185
(((((((......)))))))	chr14:57672002-57672219(-)$1	1	64	84	9.5726
(((.(((.....))).))).	chr19:36883392-36883611(-)$1	1	57	77	10.0965
(((((((.....)).)))))	chr12:111158042-111158262(-)$1	1	91	111	11.1550
(((((((((...))))))))	chr17:58525018-58525243(-)$1	1	33	53	9.3618
(((((((((...))))))))	chr14:104025463-104025680(-)$1	1	136	156	9.0661
(((((((.....))))))))	chr1:82456645-82456867(+)$1	1	43	63	12.3462
.((((((.....))))))..	chr11:10819062-10819281(-)$1	1	10	30	9.7087
(((((((......)))))))	chr17:10596104-10596323(-)$1	1	88	108	9.5726
...((((.....)))).)))	chr5:132215253-132215475(-)$1	1	93	113	9.2083
(((((((.....))))))))	chr13:79894397-79894617(-)$1	1	84	104	12.5515
(.(((((.....)))))..)	chr16:89347484-89347704(-)$1	1	50	70	9.0861
(((.(((.....))).))))	chr11:17394127-17394350(+)$1	1	158	178	10.8325
((((.((.....)).)))))	chr2:181927508-181927728(+)$1	1	131	151	9.2099
(((.(((.....))).))))	chrX:133561040-133561264(+)$1	1	176	196	9.7046
.(((((((....))))))).	chr19:21366742-21366959(+)$1	1	156	176	7.9330
(.(((((.....))))).))	chr1:70727559-70727778(-)$1	1	52	72	10.2628
...((((.....))))))))	chr17:27585286-27585512(-)$1	1	150	170	8.7357
((((((((....))))))))	chr1:231470361-231470580(-)$1	1	157	177	7.9857
(((((((.....))..))))	chr7:94298219-94298436(+)$1	1	52	72	8.6999

#PSSM
g : 0.33	i : 0.11	e : 0.09	h : 0.07	[ : 0.07	= : 0.07	d : 0.05	b : 0.03	! : 0.03	# : 0.03	c : 0.03	f : 0.01	" : 0.01	
g : 0.35	i : 0.11	e : 0.07	[ : 0.07	h : 0.07	= : 0.07	f : 0.05	c : 0.05	d : 0.03	# : 0.03	a : 0.01	! : 0.01	" : 0.01	
g : 0.37	e : 0.12	i : 0.11	= : 0.07	h : 0.05	f : 0.05	c : 0.05	! : 0.03	[ : 0.03	# : 0.03	" : 0.01	d : 0.01	
g : 0.37	i : 0.11	e : 0.11	[ : 0.09	d : 0.07	= : 0.07	! : 0.05	f : 0.05	h : 0.01	c : 0.01	# : 0.01	
g : 0.37	c : 0.16	i : 0.11	e : 0.07	d : 0.07	= : 0.07	! : 0.03	[ : 0.03	f : 0.03	h : 0.01	
g : 0.35	c : 0.16	i : 0.11	b : 0.09	d : 0.07	e : 0.05	= : 0.05	f : 0.03	h : 0.01	[ : 0.01	! : 0.01	
g : 0.35	c : 0.16	i : 0.11	b : 0.09	d : 0.07	e : 0.05	= : 0.05	a : 0.03	f : 0.03	h : 0.01	
n : 0.72	o : 0.11	g : 0.09	i : 0.03	l : 0.01	= : 0.01	
n : 0.72	o : 0.11	g : 0.05	m : 0.05	l : 0.01	= : 0.01	i : 0.01	
n : 0.72	l : 0.11	o : 0.11	m : 0.05	
n : 0.72	o : 0.11	l : 0.09	m : 0.05	i : 0.01	
n : 0.72	o : 0.11	l : 0.09	m : 0.05	i : 0.01	
g : 0.24	c : 0.16	i : 0.11	o : 0.11	b : 0.09	d : 0.07	e : 0.05	= : 0.05	a : 0.03	f : 0.03	h : 0.01	
g : 0.35	c : 0.16	i : 0.11	b : 0.09	d : 0.07	e : 0.05	= : 0.05	f : 0.03	h : 0.01	] : 0.01	2 : 0.01	
g : 0.37	c : 0.18	i : 0.11	d : 0.07	e : 0.05	= : 0.05	h : 0.03	f : 0.03	2 : 0.03	] : 0.03	
g : 0.37	i : 0.11	] : 0.09	e : 0.09	d : 0.07	= : 0.07	h : 0.05	2 : 0.03	f : 0.03	3 : 0.01	c : 0.01	4 : 0.01	
g : 0.38	e : 0.12	i : 0.11	= : 0.07	h : 0.05	c : 0.05	f : 0.05	] : 0.03	2 : 0.03	3 : 0.01	4 : 0.01	d : 0.01	
g : 0.38	i : 0.11	e : 0.07	h : 0.07	= : 0.07	] : 0.05	f : 0.05	2 : 0.03	d : 0.03	c : 0.03	a : 0.01	3 : 0.01	4 : 0.01	
g : 0.42	i : 0.11	e : 0.09	h : 0.09	= : 0.07	f : 0.03	d : 0.03	3 : 0.03	c : 0.03	] : 0.01	4 : 0.01	2 : 0.01	
g : 0.18	e : 0.11	d : 0.11	i : 0.09	h : 0.09	3 : 0.09	] : 0.07	= : 0.07	: : 0.05	f : 0.03	a : 0.01	2 : 0.01	5 : 0.01	c : 0.01	

#score	551.6050827137813
#seq	54
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_UTR_m3_run1.txt

#BEAR
eeeee!!bbqqqqqqqqbb22eeee	chr15:89743647-89743863(+)$1	216	139	164	15.4474
ddd[eeeeeqqqqqqqqeeeee]dd	chr1:243663156-243663377(-)$1	221	11	36	15.2410
gggg!!cccqqqqqqqqccc]gggg	chrX:46920078-46920290(+)$1	212	22	47	16.8734
ccc!!ddddqqqqqqqqdddd]ccc	chr1:23411632-23411871(-)$1	239	11	36	15.1329
fffff!!bbqqqqqqqqbb22ffff	chr8:81436147-81436389(+)$1	242	158	183	15.6758
c"""eeeeeqqqqqqqqeeeee]cc	chrX:118722296-118722520(-)$1	224	126	151	16.1844
ffffff[bbqqqqqqqqbbffffff	chr8:12942797-12943029(-)$1	232	112	137	15.4614
:ccc!!cccqqqqqqqqccc22ccc	chr6:138660094-138660321(+)$1	227	156	181	15.5010
dddffffffqqqqqqqqffffff33	chr16:23074101-23074332(-)$1	231	79	104	15.1778
eeeee[cccqqqqqqqqccceeeee	chr19:58805784-58806025(+)$1	241	32	57	16.1431
###ffffffqqqqqqqqffffff44	chr3:37032428-37032647(-)$1	219	89	114	15.5609
ff!!eeeeeqqqqqqqqeeeee333	chr4:77700544-77700756(+)$1	212	89	114	16.2834
iiiiiiiiiqqqqqqqqiiiiiiii	chr5:148892569-148892796(-)$1	227	18	43	15.8180
ccc[eeeeeqqqqqqqqeeeee]cc	chr1:6245616-6245857(-)$1	241	3	28	15.9696
eeeee[cccqqqqqqqqccceeeee	chr16:56464290-56464517(-)$1	227	89	114	16.1431
c[ccc[cccqqqqqqqqccc]cccc	chr10:73577032-73577251(-)$1	219	86	111	16.6256
:eeeeecccqqqqqqqqccc]eeee	chr14:93704289-93704553(-)$1	264	21	46	15.1490
ffff!!cccqqqqqqqqccc333ff	chr13:42806751-42806971(+)$1	220	15	40	16.7964
c!!ffffffqqqqqqqqffffff22	chr20:31436892-31437191(+)$1	299	193	218	15.5450
ff"""ddddqqqqqqqqdddd]fff	chr12:16050784-16051006(+)$1	222	75	100	15.2145
c"""eeeeeqqqqqqqqeeeee]cc	chr5:176724342-176724608(+)$1	266	197	222	16.1844
bb[ffffffqqqqqqqqffffff]b	chr3:152884451-152884674(+)$1	223	0	25	14.9626
b!!ccc[bbqqqqqqqqbb22ccc2	chr17:43183133-43183344(+)$1	211	119	144	15.3727
hhhhh"""aqqqqqqqqa333hhhh	chr2:70315883-70316093(+)$1	210	3	28	14.2578
ee!!eeeeeqqqqqqqqeeeee]ee	chr22:42906856-42907079(-)$1	223	84	109	15.8944
ffffff[bbqqqqqqqqbbffffff	chr8:12942683-12942933(-)$1	250	16	41	15.4614
bb[ffffffqqqqqqqqffffff]b	chr2:183790243-183790490(-)$1	247	135	160	14.9626
:dddd[cccqqqqqqqqcccdddd:	chr14:104025135-104025354(-)$1	219	24	49	13.4089
fff[bb[bbqqqqqqqqbb]bbfff	chr12:6626868-6627095(+)$1	227	115	140	14.4989
d$$$$$cccqqqqqqqqccc333dd	chr12:29655470-29655697(-)$1	227	79	104	15.4973
ff####cccqqqqqqqqccc]ffff	chr12:123774293-123774504(-)$1	211	19	44	16.7586
$$$ffffffqqqqqqqqffffffaf	chr3:160151468-160151836(+)$1	368	65	90	14.9120
=[dddd!!aqqqqqqqqa22dddd7	chr6:150046781-150047001(-)$1	220	103	128	13.9353
]eeeeecccqqqqqqqqccc::ddd	chr3:73115781-73116034(+)$1	253	165	190	13.4599
!!dddd[bbqqqqqqqqbb]ddddb	chr9:99149766-99149986(-)$1	220	159	184	14.5563
cc####cccqqqqqqqqcccccc]c	chr8:81549982-81550195(-)$1	213	152	177	16.5230
ff####cccqqqqqqqqcccfffff	chr1:150446929-150447155(+)$1	226	189	214	16.5793
d[bb!!cccqqqqqqqqccc22bbd	chr19:3613010-3613222(-)$1	212	3	28	15.2565
iiiiiiiiiqqqqqqqqiiiiiiii	chr5:151191823-151192049(+)$1	226	118	143	15.8180
f[gggggggqqqqqqqqgggggggf	chr14:31067652-31067872(+)$1	220	14	39	16.0741
eeeee[cccqqqqqqqqccc]eeee	chr1:244870700-244870960(+)$1	260	165	190	16.2597
e[bb"""bbqqqqqqqqbb4444bb	chr1:229729011-229729222(-)$1	211	24	49	14.8724
ffff!!cccqqqqqqqqccc22fff	chr3:53319489-53319746(-)$1	257	52	77	16.4601
ddddeeeeeqqqqqqqqeeeee444	chr12:24968556-24968777(-)$1	221	111	136	15.1083
eeeee[cccqqqqqqqqccc22eee	chr15:69740043-69740311(+)$1	268	32	57	15.9592
bbgggggggqqqqqqqqggggggg]	chr7:158443505-158443721(-)$1	216	119	144	15.4664
f####ddddqqqqqqqqddddffff	chr3:152554928-152555153(+)$1	225	88	113	15.1727
ffa[eeeeeqqqqqqqqeeeee]a]	chr12:59267827-59268046(-)$1	219	77	102	15.9456
e!!ffffffqqqqqqqqffffff22	chr1:168215235-168215484(+)$1	249	43	68	15.4792
fffff!!bbqqqqqqqqbbffffff	chr3:138409762-138409975(-)$1	213	169	194	15.7644
ffff"""bbqqqqqqqqbb333fff	chr21:34882067-34882286(-)$1	219	59	84	16.0720
ccc[eeeeeqqqqqqqqeeeee]cc	chr7:2273855-2274079(-)$1	224	52	77	15.9696
gggdddd[aqqqqqqqqa]dddd22	chr4:1949412-1949625(+)$1	213	88	113	14.4657
ccc[eeeeeqqqqqqqqeeeeeccc	chr7:133975108-133975341(-)$1	233	36	61	15.8607
!!eeeee[aqqqqqqqqa]eeeee2	chr21:40627515-40627744(-)$1	229	169	194	15.6147
ffffeeeeeqqqqqqqqeeeee22f	chr12:393745-393980(-)$1	235	184	209	15.2778
ee[dddd[aqqqqqqqqa]dddd]e	chr1:244871686-244871926(+)$1	240	84	109	14.7383
[ccc!!cccqqqqqqqqccc22ccc	chr1:218507277-218507507(+)$1	230	155	180	16.4714
!!gggggggqqqqqqqqggggggg]	chr1:24087402-24087619(+)$1	217	113	138	16.1063
dd[ccc[bbqqqqqqqqbb]ccc]d	chr3:47890177-47890401(+)$1	224	24	49	15.2110
####eeeeeqqqqqqqqeeeee666	chr5:139495336-139495607(+)$1	271	105	130	14.4857
hhhhhhcccqqqqqqqqccc]hhhh	chr6:143745046-143745268(-)$1	222	110	135	14.3079
=========qqqqqqqq========	chr12:49082796-49083027(-)$1	231	131	156	16.3148
!!bb"""bbqqqqqqqqbb]bbiii	chr19:47506806-47507023(+)$1	217	123	148	14.8470

#otherMatches

#Seq PSSM
GAUGAUCUGGUAAUAUACAAUUUGU	chr15:89743647-89743863(+)$1	216	139	164	15.4474
CAUAUGUAUAACCUAGCAUACGAAU	chr1:243663156-243663377(-)$1	221	11	36	15.2410
UUUGUUUGGGAAAAAAACUAUCAAA	chrX:46920078-46920290(+)$1	212	22	47	16.8734
CCAGCUCAGAACAUAUACUGAAUGG	chr1:23411632-23411871(-)$1	239	11	36	15.1329
GAAUUUUAUUGACUGACAUUUAAUU	chr8:81436147-81436389(+)$1	242	158	183	15.6758
CUAUUUUCGCUUAUUUCUGGAAUGU	chrX:118722296-118722520(-)$1	224	126	151	16.1844
UCUUGGAUGUGUUUUCUCACCAAGA	chr8:12942797-12943029(-)$1	232	112	137	15.4614
UUCAACCAGAACCAUCACUGAGUGA	chr6:138660094-138660321(+)$1	227	156	181	15.5010
AUUAUGGCGAGAAUCACUGCCAUUU	chr16:23074101-23074332(-)$1	231	79	104	15.1778
AGCUUAGUCAGUCAGCAGACAGGCU	chr19:58805784-58806025(+)$1	241	32	57	16.1431
ACAUGAGAAUGCCACCUUUUUUAAA	chr3:37032428-37032647(-)$1	219	89	114	15.5609
GGCAACAUGGAUCAGUGUGUGUCCC	chr4:77700544-77700756(+)$1	212	89	114	16.2834
UUAAAGUUAUUCCUUAUUGAUUUUG	chr5:148892569-148892796(-)$1	227	18	43	15.8180
CAUGACUGGAUUUAAUGUCAGUGGU	chr1:6245616-6245857(-)$1	241	3	28	15.9696
AUGGGCUCUUGAUUAAUAGACCCAU	chr16:56464290-56464517(-)$1	227	89	114	16.1431
AGCAUUGGUUUUUUUCUACUUGUGU	chr10:73577032-73577251(-)$1	219	86	111	16.6256
AAAGAUUACUUGCAAGUGUGUGUCU	chr14:93704289-93704553(-)$1	264	21	46	15.1490
UGUUAGGAAGAAAACAAUUUAAAGA	chr13:42806751-42806971(+)$1	220	15	40	16.7964
UCAUAGGCCUAGGCUUUGGUCUAAA	chr20:31436892-31437191(+)$1	299	193	218	15.5450
CUGCAUCUCUUCAUCCUGAGAAAGA	chr12:16050784-16051006(+)$1	222	75	100	15.2145
UCCAGUCAUCUGUAGUUGUGAUCAG	chr5:176724342-176724608(+)$1	266	197	222	16.1844
CUUUGAGAGUUACGGUUCUUUCGUA	chr3:152884451-152884674(+)$1	223	0	25	14.9626
UGAUCAAGGGAAUGUAACUGCUGAA	chr17:43183133-43183344(+)$1	211	119	144	15.3727
CUGGCCCAGUAUCUAAUCAAUGCCA	chr2:70315883-70316093(+)$1	210	3	28	14.2578
CCUGGCCCCAAGAAGGAGGGGUGGG	chr22:42906856-42907079(-)$1	223	84	109	15.8944
UCUUGGAUGUGUUUUCUCACCAAGA	chr8:12942683-12942933(-)$1	250	16	41	15.4614
CCUUAAGACCUGAAAAAGUUUUGUG	chr2:183790243-183790490(-)$1	247	135	160	14.9626
CUCAUACCUGUAGUUGGAGGAUGAA	chr14:104025135-104025354(-)$1	219	24	49	13.4089
UGCCAGAGUUGAAGUCUACCCUGCA	chr12:6626868-6627095(+)$1	227	115	140	14.4989
AAAGAAGUCUUAACAAUGAUGUAUG	chr12:29655470-29655697(-)$1	227	79	104	15.4973
CCUUGUGGCCCAUUUGUGCCUGGGC	chr12:123774293-123774504(-)$1	211	19	44	16.7586
AUACAACAUAACAAAAAGUGUUGCU	chr3:160151468-160151836(+)$1	368	65	90	14.9120
CUAUCUUUCCAAACUUUGUUAGAUU	chr6:150046781-150047001(-)$1	220	103	128	13.9353
UUUAGGGGUGCAUAGAAACCACCAU	chr3:73115781-73116034(+)$1	253	165	190	13.4599
CAUCCCUAGCAUGUUAACUUGGGAA	chr9:99149766-99149986(-)$1	220	159	184	14.5563
CAGUGUCAGGAAAAAAGCUGUGGGU	chr8:81549982-81550195(-)$1	213	152	177	16.5230
UUUAUAUCUUUAUAUCUAGGGACAC	chr1:150446929-150447155(+)$1	226	189	214	16.5793
CAUGGAGGAGGACCUGAUCCAGCAG	chr19:3613010-3613222(-)$1	212	3	28	15.2565
UACAUUUUUGGAAUAAAGGAAAUGU	chr5:151191823-151192049(+)$1	226	118	143	15.8180
UAUUUUAUAUCUUCUUUUAUAGAGA	chr14:31067652-31067872(+)$1	220	14	39	16.0741
GACUUGUUCACUAAAAAGAGAGAGU	chr1:244870700-244870960(+)$1	260	165	190	16.2597
UCUCCCCUCAAAAGAAAGAUUAUGA	chr1:229729011-229729222(-)$1	211	24	49	14.8724
UUUUGAGUAUGUAAUAUUAUGAGAG	chr3:53319489-53319746(-)$1	257	52	77	16.4601
CCUUUUCAUCAGACCCAGUGAAAAC	chr12:24968556-24968777(-)$1	221	111	136	15.1083
UGAAUGUGUUACUAAUUGCAAAGUU	chr15:69740043-69740311(+)$1	268	32	57	15.9592
AGACACCCCUGUGCACCGGGGUGUA	chr7:158443505-158443721(-)$1	216	119	144	15.4664
UGAUAUUAGUAAUUUCUCUAAGAAA	chr3:152554928-152555153(+)$1	225	88	113	15.1727
AGGAAGCUACUUAACACUAGUUACU	chr12:59267827-59268046(-)$1	219	77	102	15.9456
AUCCAGCAAAGCUUUUGUUGUUGAU	chr1:168215235-168215484(+)$1	249	43	68	15.4792
UGCUUUAGUAACUAUAAACAAGCAU	chr3:138409762-138409975(-)$1	213	169	194	15.7644
GUUCCCCACGUGUGAAAGUCAAGAA	chr21:34882067-34882286(-)$1	219	59	84	16.0720
UAUGGUCUGAAUUUAUCCAGGCAGU	chr7:2273855-2274079(-)$1	224	52	77	15.9696
UAUUUAUUGUUCAAGGUCUGUAAUU	chr4:1949412-1949625(+)$1	213	88	113	14.4657
AGCAUGUUGUCUUUUUCUAGCAGCU	chr7:133975108-133975341(-)$1	233	36	61	15.8607
UUUAGGUUUGUUUUAGGAUAUCUAU	chr21:40627515-40627744(-)$1	229	169	194	15.6147
GAUGACGAUGAUGACCAGUCGUACU	chr12:393745-393980(-)$1	235	184	209	15.2778
AGCAUUUGUACAGAGCAGGGAAUUC	chr1:244871686-244871926(+)$1	240	84	109	14.7383
GUUAUUUUUAAGCAUCAGAAUUUGA	chr1:218507277-218507507(+)$1	230	155	180	16.4714
GAUACAGAGCCAGUGUUUUCUGUAA	chr1:24087402-24087619(+)$1	217	113	138	16.1063
GUUGGCUGCCAUCUUCCGUUGCCUG	chr3:47890177-47890401(+)$1	224	24	49	15.2110
AACAAUAAGUGCUCUCUUUUAUACA	chr5:139495336-139495607(+)$1	271	105	130	14.4857
GGAUAUUGGGUUGAACACCACAUAU	chr6:143745046-143745268(-)$1	222	110	135	14.3079
GUUAAGCAUGGAGAGGGAUGCUUGA	chr12:49082796-49083027(-)$1	231	131	156	16.3148
CCGCCUUGGUUUUGCUUCCUGCUGG	chr19:47506806-47507023(+)$1	217	123	148	14.8470

#DB
(((((..((........))..))))	chr15:89743647-89743863(+)$1	1	139	164	15.4474
(((.(((((........))))).))	chr1:243663156-243663377(-)$1	1	11	36	15.2410
((((..(((........))).))))	chrX:46920078-46920290(+)$1	1	22	47	16.8734
(((..((((........)))).)))	chr1:23411632-23411871(-)$1	1	11	36	15.1329
(((((..((........))..))))	chr8:81436147-81436389(+)$1	1	158	183	15.6758
(...(((((........))))).))	chrX:118722296-118722520(-)$1	1	126	151	16.1844
((((((.((........))))))))	chr8:12942797-12943029(-)$1	1	112	137	15.4614
.(((..(((........)))..)))	chr6:138660094-138660321(+)$1	1	156	181	15.5010
(((((((((........))))))..	chr16:23074101-23074332(-)$1	1	79	104	15.1778
(((((.(((........))))))))	chr19:58805784-58806025(+)$1	1	32	57	16.1431
...((((((........))))))..	chr3:37032428-37032647(-)$1	1	89	114	15.5609
((..(((((........)))))...	chr4:77700544-77700756(+)$1	1	89	114	16.2834
(((((((((........))))))))	chr5:148892569-148892796(-)$1	1	18	43	15.8180
(((.(((((........))))).))	chr1:6245616-6245857(-)$1	1	3	28	15.9696
(((((.(((........))))))))	chr16:56464290-56464517(-)$1	1	89	114	16.1431
(.(((.(((........))).))))	chr10:73577032-73577251(-)$1	1	86	111	16.6256
.((((((((........))).))))	chr14:93704289-93704553(-)$1	1	21	46	15.1490
((((..(((........)))...))	chr13:42806751-42806971(+)$1	1	15	40	16.7964
(..((((((........))))))..	chr20:31436892-31437191(+)$1	1	193	218	15.5450
((...((((........)))).)))	chr12:16050784-16051006(+)$1	1	75	100	15.2145
(...(((((........))))).))	chr5:176724342-176724608(+)$1	1	197	222	16.1844
((.((((((........)))))).)	chr3:152884451-152884674(+)$1	1	0	25	14.9626
(..(((.((........))..))).	chr17:43183133-43183344(+)$1	1	119	144	15.3727
(((((...(........)...))))	chr2:70315883-70316093(+)$1	1	3	28	14.2578
((..(((((........))))).))	chr22:42906856-42907079(-)$1	1	84	109	15.8944
((((((.((........))))))))	chr8:12942683-12942933(-)$1	1	16	41	15.4614
((.((((((........)))))).)	chr2:183790243-183790490(-)$1	1	135	160	14.9626
.((((.(((........))))))).	chr14:104025135-104025354(-)$1	1	24	49	13.4089
(((.((.((........)).)))))	chr12:6626868-6627095(+)$1	1	115	140	14.4989
(.....(((........)))...))	chr12:29655470-29655697(-)$1	1	79	104	15.4973
((....(((........))).))))	chr12:123774293-123774504(-)$1	1	19	44	16.7586
...((((((........))))))))	chr3:160151468-160151836(+)$1	1	65	90	14.9120
(.((((..(........)..)))).	chr6:150046781-150047001(-)$1	1	103	128	13.9353
.)))))(((........)))..(((	chr3:73115781-73116034(+)$1	1	165	190	13.4599
..((((.((........)).)))))	chr9:99149766-99149986(-)$1	1	159	184	14.5563
((....(((........)))))).)	chr8:81549982-81550195(-)$1	1	152	177	16.5230
((....(((........))))))))	chr1:150446929-150447155(+)$1	1	189	214	16.5793
(.((..(((........)))..)))	chr19:3613010-3613222(-)$1	1	3	28	15.2565
(((((((((........))))))))	chr5:151191823-151192049(+)$1	1	118	143	15.8180
(.(((((((........))))))))	chr14:31067652-31067872(+)$1	1	14	39	16.0741
(((((.(((........))).))))	chr1:244870700-244870960(+)$1	1	165	190	16.2597
(.((...((........))....))	chr1:229729011-229729222(-)$1	1	24	49	14.8724
((((..(((........)))..)))	chr3:53319489-53319746(-)$1	1	52	77	16.4601
(((((((((........)))))...	chr12:24968556-24968777(-)$1	1	111	136	15.1083
(((((.(((........)))..)))	chr15:69740043-69740311(+)$1	1	32	57	15.9592
(((((((((........))))))).	chr7:158443505-158443721(-)$1	1	119	144	15.4664
(....((((........))))))))	chr3:152554928-152555153(+)$1	1	88	113	15.1727
(((.(((((........))))).).	chr12:59267827-59268046(-)$1	1	77	102	15.9456
(..((((((........))))))..	chr1:168215235-168215484(+)$1	1	43	68	15.4792
(((((..((........))))))))	chr3:138409762-138409975(-)$1	1	169	194	15.7644
((((...((........))...)))	chr21:34882067-34882286(-)$1	1	59	84	16.0720
(((.(((((........))))).))	chr7:2273855-2274079(-)$1	1	52	77	15.9696
(((((((.(........).))))..	chr4:1949412-1949625(+)$1	1	88	113	14.4657
(((.(((((........))))))))	chr7:133975108-133975341(-)$1	1	36	61	15.8607
..(((((.(........).))))).	chr21:40627515-40627744(-)$1	1	169	194	15.6147
(((((((((........)))))..)	chr12:393745-393980(-)$1	1	184	209	15.2778
((.((((.(........).)))).)	chr1:244871686-244871926(+)$1	1	84	109	14.7383
.(((..(((........)))..)))	chr1:218507277-218507507(+)$1	1	155	180	16.4714
..(((((((........))))))).	chr1:24087402-24087619(+)$1	1	113	138	16.1063
((.(((.((........)).))).)	chr3:47890177-47890401(+)$1	1	24	49	15.2110
....(((((........)))))...	chr5:139495336-139495607(+)$1	1	105	130	14.4857
(((((((((........))).))))	chr6:143745046-143745268(-)$1	1	110	135	14.3079
(((((((((........))))))))	chr12:49082796-49083027(-)$1	1	131	156	16.3148
..((...((........)).)))))	chr19:47506806-47507023(+)$1	1	123	148	14.8470

#PSSM
f : 0.25	e : 0.14	c : 0.14	d : 0.09	b : 0.06	! : 0.06	: : 0.04	g : 0.03	# : 0.03	i : 0.03	h : 0.03	= : 0.03	$ : 0.01	] : 0.01	[ : 0.01	
f : 0.21	e : 0.14	c : 0.10	! : 0.10	d : 0.07	[ : 0.07	# : 0.04	b : 0.04	g : 0.03	" : 0.03	i : 0.03	h : 0.03	$ : 0.03	= : 0.01	
f : 0.14	e : 0.12	c : 0.10	d : 0.09	# : 0.09	g : 0.07	! : 0.07	[ : 0.06	" : 0.04	b : 0.04	i : 0.03	h : 0.03	$ : 0.03	a : 0.01	= : 0.01	
f : 0.23	e : 0.12	[ : 0.09	d : 0.09	c : 0.07	# : 0.07	g : 0.06	! : 0.04	" : 0.04	b : 0.04	i : 0.03	h : 0.03	$ : 0.01	= : 0.01	
e : 0.31	f : 0.17	! : 0.10	d : 0.07	" : 0.06	# : 0.06	c : 0.04	g : 0.04	i : 0.03	h : 0.03	b : 0.01	$ : 0.01	= : 0.01	
e : 0.23	! : 0.14	f : 0.14	d : 0.10	[ : 0.09	" : 0.06	# : 0.04	g : 0.04	i : 0.03	c : 0.03	b : 0.01	$ : 0.01	h : 0.01	= : 0.01	
c : 0.29	e : 0.20	f : 0.10	[ : 0.09	d : 0.07	! : 0.06	" : 0.06	g : 0.04	i : 0.03	= : 0.01	
c : 0.29	b : 0.18	e : 0.18	f : 0.10	d : 0.04	g : 0.04	[ : 0.04	i : 0.03	" : 0.01	! : 0.01	= : 0.01	
c : 0.29	b : 0.18	e : 0.18	f : 0.10	a : 0.07	d : 0.04	g : 0.04	i : 0.03	= : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.29	b : 0.18	e : 0.18	f : 0.10	a : 0.07	d : 0.04	g : 0.04	i : 0.03	= : 0.01	
c : 0.29	b : 0.18	e : 0.18	f : 0.10	d : 0.04	g : 0.04	] : 0.04	i : 0.03	3 : 0.01	2 : 0.01	= : 0.01	
c : 0.29	e : 0.20	f : 0.15	d : 0.07	2 : 0.06	] : 0.06	g : 0.04	i : 0.03	3 : 0.03	4 : 0.01	= : 0.01	
e : 0.23	f : 0.17	2 : 0.12	d : 0.12	] : 0.09	3 : 0.06	g : 0.04	i : 0.03	b : 0.03	c : 0.03	: : 0.01	4 : 0.01	= : 0.01	
e : 0.28	f : 0.21	2 : 0.07	d : 0.07	g : 0.06	c : 0.06	3 : 0.04	] : 0.03	i : 0.03	h : 0.03	b : 0.03	: : 0.01	4 : 0.01	= : 0.01	
f : 0.28	c : 0.12	e : 0.10	] : 0.10	d : 0.09	g : 0.06	3 : 0.04	i : 0.04	h : 0.03	4 : 0.03	b : 0.01	2 : 0.01	6 : 0.01	= : 0.01	
f : 0.18	c : 0.15	e : 0.12	d : 0.09	] : 0.07	g : 0.06	2 : 0.06	i : 0.04	3 : 0.03	4 : 0.03	h : 0.03	a : 0.03	b : 0.03	6 : 0.01	= : 0.01	
f : 0.23	c : 0.15	e : 0.12	d : 0.07	2 : 0.07	b : 0.06	i : 0.04	] : 0.04	3 : 0.03	4 : 0.03	h : 0.03	g : 0.01	: : 0.01	7 : 0.01	6 : 0.01	= : 0.01	

#score	992.5514485415689
#seq	64
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_UTR_m2_run2.txt

#BEAR
ggggg####ccc!!cccmmmmccc22ccc4444ggggggg	chr20:2128586-2128831(+)$1	245	117	157	14.6725
gg"""cccccc[cccddddllldddd]ccc]ccc4444cc	chr12:105561596-105561836(+)$1	240	71	111	13.4398
c[ccc[a[bb[a!!cccooooooccc]a]bb]a]ccc]cc	chr21:35747688-35747928(+)$1	240	95	135	16.7338
ee[bb####ccc!!cccnnnnnccc22ccc22bbeeeeec	chr17:26904622-26904862(-)$1	240	37	77	13.2929
!!eeeee[ccc"""ddddmmmmdddd333ccc22eeeee2	chr12:56635607-56635919(-)$1	312	74	114	12.0674
b[ggggggg"""ccc[bboooooobb]ccc22ggggggg]	chr4:88057122-88057362(+)$1	240	134	174	14.6352
==!!ccc"""ccc[cccooooooccc]ccc333ccc4444	chr5:108670423-108670751(-)$1	328	43	83	18.5335
===========!!cccpppppppccc22============	chrX:131348073-131348313(-)$1	240	2	42	14.4741
============!!bb[bbnnnnnbb]bb22=========	chr12:46753289-46753529(-)$1	240	155	195	13.7700
iiiiiii[dddda[ccclllccc]a]dddd333iiiiiii	chr19:11258396-11258640(-)$1	244	165	205	14.2030
GGG:============cccmmmmccc333===========	chr15:89744851-89745131(+)$1	280	238	278	13.5387
===========[a[cccrrrrrrrrrccc]a=========	chr11:8126714-8126954(+)$1	240	152	192	16.2944
ffffdddd!!gggggggoooooogggggggdddd333fff	chr12:32892897-32893177(+)$1	280	17	57	13.4719
cc[bb!!dddd"""cccnnnnnccc333dddd]bbccc22	chr10:1038386-1038626(+)$1	240	37	77	13.2480
fffccc"""==========mmmm==========ccc]fff	chr6:158734009-158734249(+)$1	240	3	43	13.4995
ggggggg[a[a[a[cccqqqqqqqqccc]a]aa]gggggg	chr12:49222243-49222483(+)$1	240	179	219	12.4912
===============[cccmmmmccc]=============	chr6:105527984-105528231(+)$1	247	175	215	16.6666
=======!!ccc[bbrrrrrrrrrbb]ccc]=========	chr6:109689016-109689312(-)$1	296	164	204	15.2646
fffff[a####bb[cccooooooccc]bb4444a]fffff	chr1:26797593-26797833(+)$1	240	47	87	15.5941
[a[ccc!!ccc"""bboooooobb]ccc4444ccc]a]bb	chr14:31843932-31844172(-)$1	240	150	190	15.1675
gggg"""ccc[ffffffooooooffffffccc]ggggggg	chr17:76671517-76671809(-)$1	292	188	228	14.7936
ddd####dddd!!ddddoooooodddd]dddd4444dddd	chr2:37479130-37479375(-)$1	245	147	187	13.9212
iiiiii!!iiiiiiiiimmmmiiiiiiiii]iiiiiiiii	chr14:24780495-24780735(+)$1	240	41	81	14.8850
dddd[bb[ccc"""cccmmmmccc333ccc]bbdddd]bb	chr19:1577884-1578284(-)$1	400	26	66	12.9002
b[ccc[bb####eeeeeooooooeeeeebb]ccc]bb]dd	chr6:101095094-101095334(-)$1	240	77	117	13.0448
[iiiiiiiii####ccclllccciiiiiiiii22ccc444	chr12:69235289-69235579(+)$1	290	136	176	14.5520
ddd[dddd[bb"""cccooooooccc333bb]dddd]ddd	chr22:39127667-39127907(+)$1	240	42	82	15.6186
gggggggggg[eeeeecccmmmmccc]eeeee4444gggg	chr5:135515207-135515449(+)$1	242	69	109	12.3803
dd[ffffff[ccc[cccoooooocccccc]ffffffdddd	chr6:14135331-14135571(+)$1	240	120	160	14.2518
===!!dddd$$$$$cccooooooccc333dddd=======	chr2:197001324-197001564(-)$1	240	42	82	17.9389
ddd[dddd[ccc[acccooooooccc]accc]dddddddd	chr20:5171538-5171897(+)$1	359	92	132	15.2262
====="""dddd!!cccooooooccc22dddd55555===	chr16:90110489-90110729(+)$1	240	89	129	14.3651
=========[bb!!cccooooooccc22bb==========	chr1:41478060-41478300(+)$1	240	185	225	19.2901
dd####dddd[ffffffooooooffffff]dddddddd]d	chr17:61668063-61668307(+)$1	244	65	105	12.5050
bb"""ffffff"""cccammmma]ccc333ffffff]bb]	chr15:77403097-77403337(-)$1	240	90	130	12.8582
iiiiiiiiiccceeeeeooooooeeeee333ccc]iiiii	chr14:58730319-58730564(+)$1	245	39	79	16.2590
dd!!ggggggg####cccmmmmcccgggggggdddd]ddd	chr5:77775795-77776035(+)$1	240	7	47	13.3390
::iiiiiiiii####cccnnnnnccc4444iiiiiiiii:	chr2:114697500-114697740(+)$1	240	44	84	13.2784
ccc####ddddffffffooooooffffff22dddd333cc	chr9:136271292-136271573(-)$1	281	89	129	13.5132
cccdddd[ccc!!cccooooooccc22ccc]ddddeeeee	chr11:57468467-57468707(+)$1	240	70	110	14.7043
cc!!iiiiiiiii!!bboooooobb55555iiiiiiiiic	chr17:75211412-75211692(+)$1	280	196	236	13.2793
======!!ccc[ddddoooooodddd]ccc==========	chr20:23352168-23352408(+)$1	240	195	235	17.2232
=======[gggggggssssssssssggggggg22======	chr3:111710615-111710908(+)$1	293	167	207	12.3313
hhhhh####dddd[cccooooooccc22dddd4444hhhh	chr4:5822956-5823196(-)$1	240	180	220	15.0238
=========[ccc[ddddmmmmdddd]ccc]=========	chr5:137087029-137087276(-)$1	247	89	129	15.7064
ddd####dddd"""cccmmmmccc333dddddddddddd[	chr12:109888795-109889035(-)$1	240	172	212	12.5259
bba[ffffff!!eeeeeooooooeeeee333ffffff]a]	chr19:1853060-1853324(-)$1	264	71	111	12.8100
bb[a[a[bb[gggggggooooooggggggg]bba]a]bbb	chr3:57303477-57303724(+)$1	247	142	182	13.7357
iiiiiiiii"""eeeee[annnnna]eeeeeiiiiiiiii	chr10:131634148-131634388(-)$1	240	69	109	12.8719
a!!dddd[cccbb[a[ccclllccc]a]bb]ccc]dddd4	chr19:35512509-35512749(+)$1	240	122	162	12.1622

#otherMatches

#Seq PSSM
CCGUUGCCUGCCCGAGGGCCCCCUAAGGUUAUAGACGGUA	chr20:2128586-2128831(+)$1	245	117	157	14.6725
AUACAUCACUUACUGAUUUUAAAAAUACAGAAAGAUUUUG	chr12:105561596-105561836(+)$1	240	71	111	13.4398
GGGACCUGUAGUUUUCCCCGGCAGGACGGUAGAAGUCGUG	chr21:35747688-35747928(+)$1	240	95	135	16.7338
UGUGGUCCUGAGCUGCGUUUUCUGCCUCUCUUCCCAGACC	chr17:26904622-26904862(-)$1	240	37	77	13.2929
ACUCCUGAUCUGAAGCCAAAGAUGGUAGGAGGGGCAGGGC	chr12:56635607-56635919(-)$1	312	74	114	12.0674
UCCCAGAAGGAAAUUUUUUUUUUUAACAAUGACUUUUGGU	chr4:88057122-88057362(+)$1	240	134	174	14.6352
GACUUAACCUAAUUUUAUUUUUUUAACAUUUUCUUAUUUC	chr5:108670423-108670751(-)$1	328	43	83	18.5335
CGGCAAAAAGUAAAUCAAUGGUGGAUGAACUUUUUGCUGA	chrX:131348073-131348313(-)$1	240	2	42	14.4741
AUAAUUCCAUUAAGUGGUUGAAGGAAGCAAAUAAUGGAAU	chr12:46753289-46753529(-)$1	240	155	195	13.7700
cauuuuaacccuugugcacuguagguagggacauaaaaug	chr19:11258396-11258640(-)$1	244	165	205	14.2030
CGAGAGGGGAGGGGGAGCGAGUUCGCAUCUCUCCUUUUCC	chr15:89744851-89745131(+)$1	280	238	278	13.5387
UCAGGGCCCAGAGUUGGGACUCUAUACUACCCUGGGCUCU	chr11:8126714-8126954(+)$1	240	152	192	16.2944
GACUACUGUCAAAUAAAAUGAACUUUGUUUUAGUUAAGGU	chr12:32892897-32893177(+)$1	280	17	57	13.4719
UGCAGGACUUCAUAGACCUCACGUUGUCGAAGACUCAACG	chr10:1038386-1038626(+)$1	240	37	77	13.2480
UAAGAUUAGCUUUUUUCAUCAAGAUGGAAAAAGAUCUUUA	chr6:158734009-158734249(+)$1	240	3	43	13.4995
AAGGAGGGCAUGUGUAGCAGAGAACUUAGGGGGGCCUCCU	chr12:49222243-49222483(+)$1	240	179	219	12.4912
AUUAUAGUGCUUAAUAUUGGGAAUAAGAUUAAGCAUUAUA	chr6:105527984-105528231(+)$1	247	175	215	16.6666
UAUAGAGCUAAAUUGAUUUAAUUACACUUUCCUUUGUACU	chr6:109689016-109689312(-)$1	296	164	204	15.2646
GAUUUGUGCAAGCCAGGUUCAACCCUUGCCUCAAGAAAUC	chr1:26797593-26797833(+)$1	240	47	87	15.5941
GGUAGGUUGGAUUUAGUCUUUUCUCUCCCUUUCCUUUGGC	chr14:31843932-31844172(-)$1	240	150	190	15.1675
GGCAUCAGCCUGGGCCCGCGGCAGGGCCUGGCCUGCCUCU	chr17:76671517-76671809(-)$1	292	188	228	14.7936
UUAUAAGGCUGGGGCUGUAUUAUCAGCACAGCAAAUUAAA	chr2:37479130-37479375(-)$1	245	147	187	13.9212
ggccggcUGGUGAGCGCCAUCGUGCUUGCCUUCGGCUUGC	chr14:24780495-24780735(+)$1	240	41	81	14.8850
GGGAUGACGGGUGCCUCCCAAGAGCUUCCCAUCUCCCUAG	chr19:1577884-1578284(-)$1	400	26	66	12.9002
GGCUCCUGAAUCUUAGUAAAGUCAUUGACAAGAGGCUUUG	chr6:101095094-101095334(-)$1	240	77	117	13.0448
UGGCCUGGGUUACAUGGUUCCCAGCCUAGGUUUCAGACUU	chr12:69235289-69235579(+)$1	290	136	176	14.5520
GCCAGGCUGAGACUAGAACCCCAUCUUCCCUGAGCCAGGC	chr22:39127667-39127907(+)$1	240	42	82	15.6186
UUUGUGUUUCAGCUCACAGUUCUUUGCUGGGUAAAAGAAA	chr5:135515207-135515449(+)$1	242	69	109	12.3803
GACAGAACUGGUAUGAGCAGGAUUUCUGCAGGUUCUUCUU	chr6:14135331-14135571(+)$1	240	120	160	14.2518
gaguagcaugccuucguauuuuaacgcaaaugucuuuuuc	chr2:197001324-197001564(-)$1	240	42	82	17.9389
GUCUCCUGUAGGUCCACCUAACUGUGUGUUUUCAGGGACA	chr20:5171538-5171897(+)$1	359	92	132	15.2262
CCAGUGUGGGGUGAGGCAGUGAGGUUAGGCCCAGAGAGCU	chr16:90110489-90110729(+)$1	240	89	129	14.3651
GCUUCUCAUUCUCUUUAUGUCAUUGGCCAGAUGGGAAGCG	chr1:41478060-41478300(+)$1	240	185	225	19.2901
GUCCUCUUUGGUUCUCACCUGCUUGAGAAGUAAAACAGUA	chr17:61668063-61668307(+)$1	244	65	105	12.5050
CUAGAACUUCAAGAAGCCUCCUGUGCUGGCUGAGGUGAGC	chr15:77403097-77403337(-)$1	240	90	130	12.8582
GUAGUCAUUAAUUACAUAUGAUAGUGUACUAAUUCAGUGA	chr14:58730319-58730564(+)$1	245	39	79	16.2590
agcuugcagugagccgagaucucuccacugcacuccagcc	chr5:77775795-77776035(+)$1	240	7	47	13.3390
UAUGUGAUUGGCAGCUGUAUUAAACACAUUCCAAUCGCAG	chr2:114697500-114697740(+)$1	240	44	84	13.2784
GCUUCUCCCCAUAGCACGAGGAUGUGUUGCCUGGGCACGG	chr9:136271292-136271573(-)$1	281	89	129	13.5132
ACCUGGGUUCUAACCUCUAAAUAGGGGAGAUCCCAGCCUC	chr11:57468467-57468707(+)$1	240	70	110	14.7043
GGAUCAGGAGGGCGGGGGAGGGACCGAGCAGCCCUCUUGC	chr17:75211412-75211692(+)$1	280	196	236	13.2793
GGGAACCUUGGAGAAUUCUUUUGUUCACUAGUUCCUUUUU	chr20:23352168-23352408(+)$1	240	195	235	17.2232
UUUUUUUCAUUAAAGUAUUUCCUUUUUUUAAUUCAAGAAA	chr3:111710615-111710908(+)$1	293	167	207	12.3313
GCAGUCCCAAAACCCUUACAGUGAAGAUGUUUACUCAUUG	chr4:5822956-5823196(-)$1	240	180	220	15.0238
UGUUAAUAUUUAACUUAAAUAUUUGACUUACAUGUUGACG	chr5:137087029-137087276(-)$1	247	89	129	15.7064
UAGACGUGCUUUCUGCCAUGUGGCUUUGGGCCUAGAGCUU	chr12:109888795-109889035(-)$1	240	172	212	12.5259
CUGGGCCCCCAUGGGUGGUCCGGCAUCCUCAGGGGGUGUG	chr19:1853060-1853324(-)$1	264	71	111	12.8100
GCCAGUAGUGAGGGGCAGUUUGUUGUCCUUAGCAGUAGCC	chr3:57303477-57303724(+)$1	247	142	182	13.7357
CCUCCUGGGCCCACCUCCGAUUCACAGAGGUUUCAGGGGG	chr10:131634148-131634388(-)$1	240	69	109	12.8719
GGAAGGCGGGAAGGAUGCCCGGGGCUUGCUAUCCGGCCUG	chr19:35512509-35512749(+)$1	240	122	162	12.1622

#DB
(((((....(((..(((....)))..)))....)))))))	chr20:2128586-2128831(+)$1	1	117	157	14.6725
((...((((((.(((((((...)))).))).)))....))	chr12:105561596-105561836(+)$1	1	71	111	13.4398
(.(((.(.((.(..(((......))).).)).).))).))	chr21:35747688-35747928(+)$1	1	95	135	16.7338
((.((....(((..(((.....)))..)))..))))))))	chr17:26904622-26904862(-)$1	1	37	77	13.2929
..(((((.(((...((((....))))...)))..))))).	chr12:56635607-56635919(-)$1	1	74	114	12.0674
(.(((((((...(((.((......)).)))..))))))).	chr4:88057122-88057362(+)$1	1	134	174	14.6352
((..(((...(((.(((......))).)))...)))....	chr5:108670423-108670751(-)$1	1	43	83	18.5335
(((((((((((..(((.......)))..))))))))))))	chrX:131348073-131348313(-)$1	1	2	42	14.4741
((((((((((((..((.((.....)).))..)))))))))	chr12:46753289-46753529(-)$1	1	155	195	13.7700
(((((((.(((((.(((...))).).))))...)))))))	chr19:11258396-11258640(-)$1	1	165	205	14.2030
))).(((((((((((((((....)))...)))))))))))	chr15:89744851-89745131(+)$1	1	238	278	13.5387
(((((((((((.(.(((.........))).))))))))))	chr11:8126714-8126954(+)$1	1	152	192	16.2944
((((((((..(((((((......)))))))))))...)))	chr12:32892897-32893177(+)$1	1	17	57	13.4719
((.((..((((...(((.....)))...)))).)))))..	chr10:1038386-1038626(+)$1	1	37	77	13.2480
((((((...((((((((((....))))))))))))).)))	chr6:158734009-158734249(+)$1	1	3	43	13.4995
(((((((.(.(.(.(((........))).).)).))))))	chr12:49222243-49222483(+)$1	1	179	219	12.4912
(((((((((((((((.(((....))).)))))))))))))	chr6:105527984-105528231(+)$1	1	175	215	16.6666
(((((((..(((.((.........)).))).)))))))))	chr6:109689016-109689312(-)$1	1	164	204	15.2646
(((((.(....((.(((......))).))....).)))))	chr1:26797593-26797833(+)$1	1	47	87	15.5941
.(.(((..(((...((......)).)))....))).).))	chr14:31843932-31844172(-)$1	1	150	190	15.1675
((((...(((.((((((......))))))))).)))))))	chr17:76671517-76671809(-)$1	1	188	228	14.7936
(((....((((..((((......)))).))))....))))	chr2:37479130-37479375(-)$1	1	147	187	13.9212
((((((..(((((((((....))))))))).)))))))))	chr14:24780495-24780735(+)$1	1	41	81	14.8850
((((.((.(((...(((....)))...))).)))))).))	chr19:1577884-1578284(-)$1	1	26	66	12.9002
(.(((.((....(((((......))))))).))).)).))	chr6:101095094-101095334(-)$1	1	77	117	13.0448
.(((((((((....(((...))))))))))))..)))...	chr12:69235289-69235579(+)$1	1	136	176	14.5520
(((.((((.((...(((......)))...)).)))).)))	chr22:39127667-39127907(+)$1	1	42	82	15.6186
)))(((((((.((((((((....))).)))))....))))	chr5:135515207-135515449(+)$1	1	69	109	12.3803
((.((((((.(((.(((......)))))).))))))))))	chr6:14135331-14135571(+)$1	1	120	160	14.2518
(((..((((.....(((......)))...)))))))))))	chr2:197001324-197001564(-)$1	1	42	82	17.9389
(((.((((.(((.((((......))).)))).))))))))	chr20:5171538-5171897(+)$1	1	92	132	15.2262
(((((...((((..(((......)))..)))).....)))	chr16:90110489-90110729(+)$1	1	89	129	14.3651
(((((((((.((..(((......)))..))))))))))))	chr1:41478060-41478300(+)$1	1	185	225	19.2901
((....((((.((((((......)))))).)))))))).)	chr17:61668063-61668307(+)$1	1	65	105	12.5050
((...((((((...((((....).)))...)))))).)).	chr15:77403097-77403337(-)$1	1	90	130	12.8582
(((((((((((((((((......)))))...))).)))))	chr14:58730319-58730564(+)$1	1	39	79	16.2590
((..(((((((....(((....)))))))))))))).)))	chr5:77775795-77776035(+)$1	1	7	47	13.3390
..(((((((((....(((.....)))....))))))))).	chr2:114697500-114697740(+)$1	1	44	84	13.2784
(((....((((((((((......))))))..))))...))	chr9:136271292-136271573(-)$1	1	89	129	13.5132
)))((((.(((..(((......)))..))).))))(((((	chr11:57468467-57468707(+)$1	1	70	110	14.7043
((..(((((((((..((......)).....))))))))))	chr17:75211412-75211692(+)$1	1	196	236	13.2793
((((((..(((.((((......)))).)))))))))))))	chr20:23352168-23352408(+)$1	1	195	235	17.2232
(((((((.(((((((..........)))))))..))))))	chr3:111710615-111710908(+)$1	1	167	207	12.3313
(((((....((((.(((......)))..))))....))))	chr4:5822956-5823196(-)$1	1	180	220	15.0238
(((((((((.(((.((((....)))).))).)))))))))	chr5:137087029-137087276(-)$1	1	89	129	15.7064
(((....((((...(((....)))...))))))))((((.	chr12:109888795-109889035(-)$1	1	172	212	12.5259
(((.((((((..(((((......)))))...)))))).).	chr19:1853060-1853324(-)$1	1	71	111	12.8100
((.(.(.((.(((((((......))))))).))).).))(	chr3:57303477-57303724(+)$1	1	142	182	13.7357
(((((((((...(((((.(.....).))))))))))))))	chr10:131634148-131634388(-)$1	1	69	109	12.8719
(..((((.(((((.(.(((...))).).)).))).)))).	chr19:35512509-35512749(+)$1	1	122	162	12.1622

#PSSM
= : 0.23	d : 0.16	g : 0.10	c : 0.10	b : 0.10	i : 0.08	f : 0.06	[ : 0.04	e : 0.02	! : 0.02	G : 0.02	: : 0.02	h : 0.02	a : 0.02	
= : 0.23	d : 0.16	g : 0.10	i : 0.10	c : 0.08	[ : 0.06	f : 0.06	b : 0.06	! : 0.04	e : 0.02	G : 0.02	a : 0.02	: : 0.02	h : 0.02	
= : 0.21	i : 0.12	g : 0.10	[ : 0.10	d : 0.10	c : 0.08	! : 0.08	f : 0.06	" : 0.04	e : 0.02	G : 0.02	# : 0.02	h : 0.02	a : 0.02	
= : 0.19	i : 0.12	g : 0.10	c : 0.08	! : 0.08	# : 0.08	f : 0.06	d : 0.06	[ : 0.06	" : 0.04	b : 0.04	e : 0.02	: : 0.02	h : 0.02	a : 0.02	
= : 0.21	i : 0.14	g : 0.10	c : 0.10	d : 0.10	# : 0.08	" : 0.06	f : 0.06	b : 0.04	[ : 0.04	e : 0.02	! : 0.02	h : 0.02	
= : 0.19	# : 0.14	i : 0.14	d : 0.12	c : 0.08	g : 0.08	[ : 0.06	f : 0.06	" : 0.04	e : 0.02	! : 0.02	b : 0.02	a : 0.02	
= : 0.18	d : 0.14	# : 0.12	i : 0.12	g : 0.08	! : 0.08	" : 0.06	f : 0.06	c : 0.04	a : 0.04	b : 0.04	e : 0.02	[ : 0.02	
d : 0.18	[ : 0.16	= : 0.14	i : 0.10	# : 0.08	! : 0.08	g : 0.06	" : 0.06	f : 0.06	c : 0.04	b : 0.04	
c : 0.16	d : 0.16	= : 0.14	i : 0.12	# : 0.10	g : 0.08	f : 0.06	b : 0.04	" : 0.04	! : 0.04	[ : 0.04	a : 0.02	
c : 0.25	d : 0.16	= : 0.12	[ : 0.10	i : 0.08	" : 0.06	g : 0.06	b : 0.04	# : 0.04	f : 0.04	! : 0.02	$ : 0.02	
c : 0.30	d : 0.14	= : 0.12	[ : 0.08	g : 0.08	# : 0.06	i : 0.06	" : 0.04	b : 0.04	a : 0.02	$ : 0.02	f : 0.02	! : 0.02	
" : 0.18	c : 0.16	[ : 0.08	! : 0.08	= : 0.08	# : 0.08	d : 0.06	g : 0.06	b : 0.06	f : 0.06	i : 0.04	a : 0.02	e : 0.02	$ : 0.02	
! : 0.18	" : 0.14	c : 0.10	e : 0.10	a : 0.06	= : 0.06	g : 0.06	f : 0.06	# : 0.06	[ : 0.04	b : 0.04	i : 0.04	d : 0.04	$ : 0.02	
[ : 0.18	! : 0.14	" : 0.14	e : 0.10	c : 0.08	= : 0.06	g : 0.06	f : 0.06	# : 0.06	d : 0.04	b : 0.02	i : 0.02	$ : 0.02	a : 0.02	
c : 0.48	e : 0.10	d : 0.08	b : 0.06	= : 0.06	g : 0.06	f : 0.06	# : 0.04	i : 0.02	! : 0.02	a : 0.02	
c : 0.48	d : 0.10	e : 0.10	[ : 0.06	b : 0.06	f : 0.06	= : 0.04	g : 0.04	r : 0.02	i : 0.02	s : 0.02	
c : 0.52	d : 0.08	e : 0.08	o : 0.06	f : 0.06	b : 0.04	g : 0.04	p : 0.02	[ : 0.02	= : 0.02	r : 0.02	i : 0.02	s : 0.02	
o : 0.46	c : 0.12	m : 0.08	d : 0.06	n : 0.04	b : 0.04	l : 0.04	r : 0.04	p : 0.02	= : 0.02	q : 0.02	a : 0.02	s : 0.02	[ : 0.02	
o : 0.48	m : 0.16	c : 0.08	n : 0.06	l : 0.04	r : 0.04	d : 0.02	p : 0.02	b : 0.02	= : 0.02	q : 0.02	s : 0.02	a : 0.02	
o : 0.48	m : 0.23	n : 0.10	l : 0.08	r : 0.04	p : 0.02	q : 0.02	s : 0.02	
o : 0.48	m : 0.23	n : 0.10	l : 0.04	c : 0.04	r : 0.04	p : 0.02	q : 0.02	s : 0.02	
o : 0.48	m : 0.16	c : 0.10	n : 0.10	l : 0.04	r : 0.04	p : 0.02	q : 0.02	i : 0.02	s : 0.02	
o : 0.42	c : 0.19	d : 0.08	m : 0.08	n : 0.06	r : 0.04	p : 0.02	q : 0.02	b : 0.02	i : 0.02	a : 0.02	s : 0.02	
c : 0.46	d : 0.10	f : 0.06	e : 0.06	n : 0.04	] : 0.04	r : 0.04	g : 0.04	b : 0.04	i : 0.04	o : 0.02	= : 0.02	q : 0.02	s : 0.02	
c : 0.42	d : 0.10	b : 0.08	f : 0.06	e : 0.06	a : 0.04	g : 0.04	i : 0.04	3 : 0.04	2 : 0.02	r : 0.02	= : 0.02	q : 0.02	] : 0.02	s : 0.02	
c : 0.36	d : 0.10	g : 0.08	2 : 0.06	b : 0.06	] : 0.06	3 : 0.06	f : 0.06	e : 0.06	i : 0.04	r : 0.02	= : 0.02	5 : 0.02	
] : 0.23	3 : 0.14	c : 0.12	2 : 0.12	g : 0.08	e : 0.08	f : 0.06	d : 0.04	i : 0.04	= : 0.02	4 : 0.02	5 : 0.02	a : 0.02	
c : 0.27	3 : 0.12	e : 0.10	2 : 0.08	g : 0.08	f : 0.06	a : 0.04	b : 0.04	d : 0.04	= : 0.04	] : 0.04	i : 0.04	4 : 0.02	5 : 0.02	
c : 0.25	3 : 0.14	d : 0.12	b : 0.10	g : 0.08	= : 0.06	f : 0.06	] : 0.04	4 : 0.04	i : 0.04	e : 0.04	5 : 0.02	
c : 0.23	d : 0.14	b : 0.10	4 : 0.08	= : 0.08	g : 0.08	] : 0.06	3 : 0.06	2 : 0.04	i : 0.04	e : 0.04	a : 0.02	5 : 0.02	
] : 0.19	d : 0.16	= : 0.12	2 : 0.08	3 : 0.08	4 : 0.06	c : 0.06	i : 0.06	b : 0.04	e : 0.04	f : 0.04	g : 0.04	a : 0.02	
= : 0.19	d : 0.19	c : 0.12	i : 0.10	4 : 0.06	] : 0.06	f : 0.06	2 : 0.04	3 : 0.04	b : 0.04	g : 0.04	a : 0.02	e : 0.02	
= : 0.19	d : 0.18	4 : 0.10	c : 0.10	i : 0.08	b : 0.06	2 : 0.06	f : 0.06	a : 0.04	3 : 0.04	] : 0.04	g : 0.02	5 : 0.02	
= : 0.19	d : 0.18	c : 0.14	i : 0.10	g : 0.06	2 : 0.06	4 : 0.06	f : 0.06	] : 0.04	b : 0.04	a : 0.04	5 : 0.02	
= : 0.21	d : 0.16	c : 0.10	i : 0.10	] : 0.10	g : 0.08	4 : 0.08	f : 0.06	e : 0.04	3 : 0.02	b : 0.02	5 : 0.02	
= : 0.21	d : 0.14	i : 0.12	c : 0.10	g : 0.08	4 : 0.08	f : 0.08	e : 0.06	3 : 0.04	] : 0.02	b : 0.02	5 : 0.02	a : 0.02	
= : 0.21	d : 0.14	i : 0.12	g : 0.10	] : 0.10	c : 0.06	e : 0.06	4 : 0.04	3 : 0.04	f : 0.04	a : 0.02	b : 0.02	5 : 0.02	h : 0.02	
= : 0.23	d : 0.16	i : 0.12	g : 0.10	] : 0.10	4 : 0.06	e : 0.06	f : 0.06	b : 0.04	c : 0.02	3 : 0.02	h : 0.02	
= : 0.23	d : 0.16	i : 0.12	g : 0.10	b : 0.08	c : 0.06	e : 0.06	f : 0.06	4 : 0.04	2 : 0.02	] : 0.02	h : 0.02	a : 0.02	
= : 0.23	d : 0.14	c : 0.10	g : 0.08	i : 0.08	] : 0.06	4 : 0.06	f : 0.06	b : 0.06	2 : 0.04	: : 0.02	e : 0.02	h : 0.02	[ : 0.02	

#score	718.3559188932779
#seq	50
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_UTR_m2_run2.txt

#BEAR
hhhhhhhhnnnnnhhhhhhh	chr1:180080337-180080557(+)$1	220	106	126	9.4972
cc[ggggggglllggggggg	chr9:123523416-123523653(-)$1	237	40	60	7.1198
gg"""cccnnnnncccgggg	chr3:126753260-126753502(+)$1	242	131	151	11.5209
ccc[ddddnnnnnddddccc	chr19:39220539-39220759(+)$1	220	63	83	10.5724
dd!!ddddnnnnndddd444	chr15:90814884-90815113(+)$1	229	2	22	10.2133
hhhhhhhhnnnnnhhhhhhh	chrX:153585519-153585740(-)$1	221	184	204	9.4972
:gggggggnnnnnggggggg	chr3:49050994-49051219(+)$1	225	127	147	10.8459
!!ffffffnnnnnffffff2	chr1:54231588-54231806(-)$1	218	56	76	10.6884
bb[eeeeennnnneeeee]b	chr6:30684931-30685152(-)$1	221	14	34	10.1814
[a[ggggggglllggggggg	chr1:229761880-229762099(+)$1	219	49	69	7.1843
gg[eeeeennnnneeeee]g	chr1:153778597-153778821(-)$1	224	162	182	11.1629
gggggggooooooggggggg	chr3:111835402-111835630(+)$1	228	176	196	7.8474
gggggggooooooggggggg	chr19:37002127-37002341(-)$1	214	46	66	7.8474
==========lll=======	chr4:140431752-140431970(-)$1	218	153	173	7.4666
effffffannnnna]fffff	chr2:27549302-27549529(-)$1	227	38	58	10.4315
###eeeeennnnneeeee66	chr8:22109296-22109517(+)$1	221	139	159	9.8282
!!ffffffnnnnnffffff2	chr17:61911971-61912223(-)$1	252	144	164	10.6884
ee[eeeeennnnneeeee22	chr17:47130806-47131039(+)$1	233	154	174	10.5777
""cccbbannnnna]bb]cc	chr5:65474594-65474821(+)$1	227	98	118	9.8772
!!bb[cccnnnnnccc]bb2	chr17:26968885-26969144(-)$1	259	178	198	10.2954
ffffff[annnnna]fffff	chr1:16266377-16266617(+)$1	240	116	136	10.4549
[bb[ddddnnnnndddd]bb	chr10:1177408-1177638(+)$1	230	88	108	9.6243
hhhhhhhhnnnnnhhhhhhh	chr14:96010452-96010671(+)$1	219	157	177	9.4972
cc[eeeeennnnneeeee]c	chrX:153735669-153735900(-)$1	231	79	99	11.0283
"""eeeeennnnneeeee22	chr22:26888240-26888468(+)$1	228	161	181	10.7376
edddd!!annnnna22dddd	chr12:123350375-123350602(-)$1	227	118	138	9.1303
eeee[cccnnnnnccc22ee	chr17:649730-649974(-)$1	244	40	60	10.1385
cc!!ddddnnnnndddd22c	chr1:27733026-27733256(-)$1	230	183	203	10.3834
d"""ddddnnnnndddd]dd	chr1:59249395-59249616(-)$1	221	88	108	10.1981
gggggggooooooggggggg	chr5:176726576-176726823(+)$1	247	55	75	7.8474
:gggggggnnnnnggggggg	chr3:49050660-49050880(+)$1	220	84	104	10.8459
c[ffffffnnnnnffffff]	chr7:99489546-99489765(-)$1	219	121	141	10.6197
ddd!!cccnnnnncccdddd	chr20:32667752-32668008(+)$1	256	6	26	10.3062
!!ccc[bbnnnnnbb]ccc2	chr3:128211846-128212063(+)$1	217	105	125	10.0345
:gggggggnnnnnggggggg	chr1:27733549-27733789(-)$1	240	8	28	10.8459
gggggg[annnnna]ggggg	chr2:26614330-26614551(+)$1	221	179	199	11.7541
eeeeeeeennnnneeeee44	chr2:97260745-97260972(-)$1	227	104	124	10.2779
##ffffffnnnnnffffff4	chr19:16661995-16662223(-)$1	228	159	179	10.3957
!ccc[cccnnnnncccccc2	chr1:54683814-54684037(+)$1	223	182	202	11.2959
ccc[ddddnnnnnddddccc	chr19:11030484-11030715(+)$1	231	27	47	10.5724
c[ffffffnnnnnffffff]	chr1:146630761-146630982(-)$1	221	87	107	10.6197
dgggggggnnnnnggggggg	chr1:228881603-228881842(+)$1	239	30	50	11.6804
hhhh[cccnnnnnccchhhh	chr4:42116858-42117079(-)$1	221	33	53	10.4202
ee!!ddddnnnnndddd]ee	chr7:104749405-104749632(+)$1	227	29	49	10.3548
ffff[cccnnnnnccc]fff	chr2:97499127-97499337(+)$1	210	39	59	10.7953
ff"""cccnnnnncccffff	chr6:28871437-28871653(-)$1	216	177	197	10.7531
[dddd[bbnnnnnbb]dddd	chr16:89711354-89711585(-)$1	231	191	211	8.8396
ffffff[annnnna]fffff	chr17:21437662-21437878(-)$1	216	114	134	10.4549
dd[eeeeennnnneeeeedd	chr12:125514882-125515099(+)$1	217	134	154	10.3648
d!!bbcccnnnnnccc333b	chr17:17090574-17090798(+)$1	224	192	212	10.3802
ccc[ddddnnnnnddddccc	chr9:134372133-134372401(+)$1	268	160	180	10.5724
iiiiiiiinnnnniiiiiii	chr22:38693971-38694204(-)$1	233	200	220	11.6017
iiiiiiiiillliiiiiiii	chrX:153275881-153276188(-)$1	307	29	49	7.0260

#otherMatches

#Seq PSSM
UGUGGUACACCUGGUAUUAC	chr1:180080337-180080557(+)$1	220	106	126	9.4972
GGUGGAAGCCAGCGGCUUCU	chr9:123523416-123523653(-)$1	237	40	60	7.1198
GUCUGGGCCCGUUGCCACCG	chr3:126753260-126753502(+)$1	242	131	151	11.5209
CAACAAGCACCCCGCUUUUG	chr19:39220539-39220759(+)$1	220	63	83	10.5724
GCAGUGGUGCGUUGCCAAGU	chr15:90814884-90815113(+)$1	229	2	22	10.2133
UCUUGGGGCCGAUUCCCAGG	chrX:153585519-153585740(-)$1	221	184	204	9.4972
UAUGGAGUGCCCAGCUUCAU	chr3:49050994-49051219(+)$1	225	127	147	10.8459
UGCUGUGUACUAAAUACAGG	chr1:54231588-54231806(-)$1	218	56	76	10.6884
GCGGUUGUGAAAGACAGCGG	chr6:30684931-30685152(-)$1	221	14	34	10.1814
GCGCCGCCGGCGUCCGGCGG	chr1:229761880-229762099(+)$1	219	49	69	7.1843
AUUAUUAUGAAUUGUAAUUG	chr1:153778597-153778821(-)$1	224	162	182	11.1629
UUCUGUGGAUUAAUACAGAA	chr3:111835402-111835630(+)$1	228	176	196	7.8474
aggugugagccaccacgccu	chr19:37002127-37002341(-)$1	214	46	66	7.8474
UUUGAAUUCUAACAGAAUUC	chr4:140431752-140431970(-)$1	218	153	173	7.4666
CCCUAUGCACAGAGCCAUAG	chr2:27549302-27549529(-)$1	227	38	58	10.4315
UCAGGAAGAACCGCUUCCCC	chr8:22109296-22109517(+)$1	221	139	159	9.8282
AAUCACCUGGUGGAGGUGAG	chr17:61911971-61912223(-)$1	252	144	164	10.6884
CAGGCCUGGCAGACGGGCAG	chr17:47130806-47131039(+)$1	233	154	174	10.5777
AUAGGACCGACAAGUGUACC	chr5:65474594-65474821(+)$1	227	98	118	9.8772
UCCAGAGCCAACUGCUGUGC	chr17:26968885-26969144(-)$1	259	178	198	10.2954
CGUCUUUGAUUCACCGGGAU	chr1:16266377-16266617(+)$1	240	116	136	10.4549
UGGUGCUCAGGCAGAGCUCU	chr10:1177408-1177638(+)$1	230	88	108	9.6243
UUGGUCUGGUGUUCGGGCUA	chr14:96010452-96010671(+)$1	219	157	177	9.4972
AUGUCAACGACCUGUUGAAG	chrX:153735669-153735900(-)$1	231	79	99	11.0283
UUGGCCCAGGUCUUGGGUGU	chr22:26888240-26888468(+)$1	228	161	181	10.7376
CUGCACUCCAACCGUCUGCA	chr12:123350375-123350602(-)$1	227	118	138	9.1303
AGCCAGACUUGGUGUUGAGG	chr17:649730-649974(-)$1	244	40	60	10.1385
UGCUGGCUUCUCCGGCUUUC	chr1:27733026-27733256(-)$1	230	183	203	10.3834
GUGUCCAGAGAGCCUGGUCU	chr1:59249395-59249616(-)$1	221	88	108	10.1981
CUCGGAAGAAGUGUUUCGAG	chr5:176726576-176726823(+)$1	247	55	75	7.8474
AGCUGUUUGUACGAGACGGC	chr3:49050660-49050880(+)$1	220	84	104	10.8459
CCUUUGUGUGCUUCACAAGA	chr7:99489546-99489765(-)$1	219	121	141	10.6197
CCCCAGGCCUCAAGCCGGGC	chr20:32667752-32668008(+)$1	256	6	26	10.3062
GAUGUGGCGGCAGGCAAUAG	chr3:128211846-128212063(+)$1	217	105	125	10.0345
agugacuugcucaaggucac	chr1:27733549-27733789(-)$1	240	8	28	10.8459
AGAGGCUCGUAUUGUGUUUC	chr2:26614330-26614551(+)$1	221	179	199	11.7541
UCAGAGCCGGACGGGCUUGU	chr2:97260745-97260972(-)$1	227	104	124	10.2779
ACUUUGGUCCCAAGCUGAGA	chr19:16661995-16662223(-)$1	228	159	179	10.3957
UCAGUGCCCGUUUGGCCUGC	chr1:54683814-54684037(+)$1	223	182	202	11.2959
CUGUCUGGCUUCCCCAGCAG	chr19:11030484-11030715(+)$1	231	27	47	10.5724
GCUAGAAGUAUUGUUUCUGC	chr1:146630761-146630982(-)$1	221	87	107	10.6197
caaaacuugaaagaaguuuu	chr1:228881603-228881842(+)$1	239	30	50	11.6804
GAAAUGUUCCUACGACUUUU	chr4:42116858-42117079(-)$1	221	33	53	10.4202
GUGGCUCUAAGACAGAGAAC	chr7:104749405-104749632(+)$1	227	29	49	10.3548
GUAGCUGCCUGUUGCACCUG	chr2:97499127-97499337(+)$1	210	39	59	10.7953
AUUAUGGCUAUUUGCUGUCA	chr6:28871437-28871653(-)$1	216	177	197	10.7531
GGGAGGCUGAGAGAGGCUUU	chr16:89711354-89711585(-)$1	231	191	211	8.8396
GCAGCUGAUUUUCUGGGCUG	chr17:21437662-21437878(-)$1	216	114	134	10.4549
GGUGUAAACAAAUUUUAUUC	chr12:125514882-125515099(+)$1	217	134	154	10.3648
CAGCCACCAUCUGGGUCAAG	chr17:17090574-17090798(+)$1	224	192	212	10.3802
GUGCUGUGUUUUUCACACAU	chr9:134372133-134372401(+)$1	268	160	180	10.5724
GUGCCCGGCUCCCCUGGGCA	chr22:38693971-38694204(-)$1	233	200	220	11.6017
AAGACAUGUAUCACAUGUCU	chrX:153275881-153276188(-)$1	307	29	49	7.0260

#DB
((((((((.....)))))))	chr1:180080337-180080557(+)$1	1	106	126	9.4972
((.(((((((...)))))))	chr9:123523416-123523653(-)$1	1	40	60	7.1198
((...(((.....)))))))	chr3:126753260-126753502(+)$1	1	131	151	11.5209
(((.((((.....)))))))	chr19:39220539-39220759(+)$1	1	63	83	10.5724
((..((((.....))))...	chr15:90814884-90815113(+)$1	1	2	22	10.2133
((((((((.....)))))))	chrX:153585519-153585740(-)$1	1	184	204	9.4972
.(((((((.....)))))))	chr3:49050994-49051219(+)$1	1	127	147	10.8459
..((((((.....)))))).	chr1:54231588-54231806(-)$1	1	56	76	10.6884
((.(((((.....))))).)	chr6:30684931-30685152(-)$1	1	14	34	10.1814
.(.(((((((...)))))))	chr1:229761880-229762099(+)$1	1	49	69	7.1843
((.(((((.....))))).)	chr1:153778597-153778821(-)$1	1	162	182	11.1629
(((((((......)))))))	chr3:111835402-111835630(+)$1	1	176	196	7.8474
(((((((......)))))))	chr19:37002127-37002341(-)$1	1	46	66	7.8474
((((((((((...)))))))	chr4:140431752-140431970(-)$1	1	153	173	7.4666
)(((((((.....).)))))	chr2:27549302-27549529(-)$1	1	38	58	10.4315
...(((((.....)))))..	chr8:22109296-22109517(+)$1	1	139	159	9.8282
..((((((.....)))))).	chr17:61911971-61912223(-)$1	1	144	164	10.6884
((.(((((.....)))))..	chr17:47130806-47131039(+)$1	1	154	174	10.5777
..((((((.....).)).))	chr5:65474594-65474821(+)$1	1	98	118	9.8772
..((.(((.....))).)).	chr17:26968885-26969144(-)$1	1	178	198	10.2954
((((((.(.....).)))))	chr1:16266377-16266617(+)$1	1	116	136	10.4549
.((.((((.....)))).))	chr10:1177408-1177638(+)$1	1	88	108	9.6243
((((((((.....)))))))	chr14:96010452-96010671(+)$1	1	157	177	9.4972
((.(((((.....))))).)	chrX:153735669-153735900(-)$1	1	79	99	11.0283
...(((((.....)))))..	chr22:26888240-26888468(+)$1	1	161	181	10.7376
(((((..(.....)..))))	chr12:123350375-123350602(-)$1	1	118	138	9.1303
((((.(((.....)))..))	chr17:649730-649974(-)$1	1	40	60	10.1385
((..((((.....))))..)	chr1:27733026-27733256(-)$1	1	183	203	10.3834
(...((((.....)))).))	chr1:59249395-59249616(-)$1	1	88	108	10.1981
(((((((......)))))))	chr5:176726576-176726823(+)$1	1	55	75	7.8474
.(((((((.....)))))))	chr3:49050660-49050880(+)$1	1	84	104	10.8459
(.((((((.....)))))).	chr7:99489546-99489765(-)$1	1	121	141	10.6197
(((..(((.....)))))))	chr20:32667752-32668008(+)$1	1	6	26	10.3062
..(((.((.....)).))).	chr3:128211846-128212063(+)$1	1	105	125	10.0345
.(((((((.....)))))))	chr1:27733549-27733789(-)$1	1	8	28	10.8459
((((((.(.....).)))))	chr2:26614330-26614551(+)$1	1	179	199	11.7541
((((((((.....)))))..	chr2:97260745-97260972(-)$1	1	104	124	10.2779
..((((((.....)))))).	chr19:16661995-16662223(-)$1	1	159	179	10.3957
.(((.(((.....)))))).	chr1:54683814-54684037(+)$1	1	182	202	11.2959
(((.((((.....)))))))	chr19:11030484-11030715(+)$1	1	27	47	10.5724
(.((((((.....)))))).	chr1:146630761-146630982(-)$1	1	87	107	10.6197
((((((((.....)))))))	chr1:228881603-228881842(+)$1	1	30	50	11.6804
((((.(((.....)))))))	chr4:42116858-42117079(-)$1	1	33	53	10.4202
((..((((.....)))).))	chr7:104749405-104749632(+)$1	1	29	49	10.3548
((((.(((.....))).)))	chr2:97499127-97499337(+)$1	1	39	59	10.7953
((...(((.....)))))))	chr6:28871437-28871653(-)$1	1	177	197	10.7531
.((((.((.....)).))))	chr16:89711354-89711585(-)$1	1	191	211	8.8396
((((((.(.....).)))))	chr17:21437662-21437878(-)$1	1	114	134	10.4549
((.(((((.....)))))))	chr12:125514882-125515099(+)$1	1	134	154	10.3648
(..(((((.....)))...)	chr17:17090574-17090798(+)$1	1	192	212	10.3802
(((.((((.....)))))))	chr9:134372133-134372401(+)$1	1	160	180	10.5724
((((((((.....)))))))	chr22:38693971-38694204(-)$1	1	200	220	11.6017
(((((((((...))))))))	chrX:153275881-153276188(-)$1	1	29	49	7.0260

#PSSM
c : 0.15	g : 0.11	d : 0.11	e : 0.11	! : 0.09	h : 0.07	f : 0.07	: : 0.05	[ : 0.05	# : 0.03	" : 0.03	i : 0.03	b : 0.01	= : 0.01	
g : 0.18	c : 0.13	d : 0.09	! : 0.09	f : 0.09	h : 0.07	e : 0.07	" : 0.05	b : 0.03	# : 0.03	[ : 0.03	i : 0.03	a : 0.01	= : 0.01	
f : 0.16	g : 0.15	[ : 0.13	c : 0.11	h : 0.07	" : 0.07	! : 0.07	d : 0.05	b : 0.03	e : 0.03	i : 0.03	= : 0.01	# : 0.01	
g : 0.18	f : 0.16	e : 0.16	h : 0.07	[ : 0.07	! : 0.07	" : 0.05	c : 0.05	b : 0.03	d : 0.03	i : 0.03	= : 0.01	
g : 0.18	d : 0.18	f : 0.15	e : 0.15	[ : 0.09	h : 0.05	" : 0.03	c : 0.03	i : 0.03	= : 0.01	! : 0.01	b : 0.01	
g : 0.18	c : 0.16	d : 0.15	f : 0.15	e : 0.15	h : 0.05	[ : 0.03	i : 0.03	= : 0.01	b : 0.01	! : 0.01	
g : 0.16	c : 0.16	d : 0.15	e : 0.15	f : 0.11	h : 0.05	b : 0.05	[ : 0.05	i : 0.03	= : 0.01	! : 0.01	
c : 0.16	d : 0.15	e : 0.15	g : 0.11	a : 0.11	f : 0.09	h : 0.05	o : 0.05	b : 0.03	i : 0.03	= : 0.01	
n : 0.86	o : 0.05	g : 0.03	= : 0.01	i : 0.01	
n : 0.86	o : 0.05	g : 0.03	= : 0.01	l : 0.01	
n : 0.86	l : 0.07	o : 0.05	
n : 0.86	l : 0.07	o : 0.05	
n : 0.86	l : 0.05	o : 0.05	i : 0.01	
g : 0.16	c : 0.16	d : 0.15	e : 0.15	a : 0.11	f : 0.09	h : 0.05	b : 0.03	i : 0.03	= : 0.01	
g : 0.16	c : 0.16	d : 0.15	e : 0.15	f : 0.09	] : 0.09	h : 0.05	b : 0.03	i : 0.03	= : 0.01	2 : 0.01	
g : 0.18	c : 0.16	d : 0.15	f : 0.15	e : 0.15	h : 0.05	] : 0.03	i : 0.03	= : 0.01	b : 0.01	2 : 0.01	
g : 0.20	d : 0.20	f : 0.16	e : 0.15	h : 0.07	] : 0.03	c : 0.03	i : 0.03	= : 0.01	b : 0.01	2 : 0.01	3 : 0.01	
g : 0.20	f : 0.18	e : 0.15	c : 0.09	h : 0.07	] : 0.07	d : 0.05	2 : 0.03	i : 0.03	4 : 0.01	= : 0.01	b : 0.01	3 : 0.01	
g : 0.20	f : 0.18	c : 0.11	d : 0.09	h : 0.07	] : 0.05	2 : 0.05	4 : 0.03	b : 0.03	e : 0.03	i : 0.03	= : 0.01	6 : 0.01	3 : 0.01	
g : 0.22	2 : 0.13	c : 0.11	f : 0.09	d : 0.09	h : 0.07	4 : 0.05	b : 0.05	e : 0.03	] : 0.03	i : 0.03	= : 0.01	6 : 0.01	

#score	533.1973042723412
#seq	53
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_CDS_m3_run1.txt

#BEAR
eeeeeooooooeeeee	chr2:207173083-207173308(+)$1	225	81	97	10.6587
eeeeeooooooeeeee	chr7:150763547-150763775(+)$1	228	179	195	10.6587
eeeebbnnnnnbb]ee	chr16:27523085-27523310(-)$1	225	105	121	9.7531
eeeeeooooooeeeee	chr3:141896294-141896513(-)$1	219	22	38	10.6587
!eeeeennnnneeeee	chr19:44056144-44056396(-)$1	252	80	96	13.3606
geeeeennnnneeeee	chr10:103901251-103901516(+)$1	265	34	50	13.1248
eee[bbnnnnnbbeee	chr14:21868521-21868734(-)$1	213	106	122	9.7858
eeeeeooooooeeeee	chr3:139094336-139094555(-)$1	219	123	139	10.6587
eeeeeooooooeeeee	chr16:3715900-3716127(-)$1	227	175	191	10.6587
:eeeeennnnneeeee	chr2:160604718-160604941(+)$1	223	8	24	12.6318
ddddddnnnnndddd]	chr17:3629459-3629711(+)$1	252	136	152	8.7530
eeeeeannnnna]eee	chr17:60140412-60140631(-)$1	219	105	121	12.1053
:eeeeennnnneeeee	chr3:9483296-9483516(+)$1	220	72	88	12.6318
deeeeennnnneeeee	chr14:21896044-21896274(-)$1	230	91	107	13.0996
dddd[annnnna]ddd	chr3:196613016-196613243(+)$1	227	1	17	8.6645
:eeeeennnnneeeee	chr19:11132485-11132710(+)$1	225	1	17	12.6318
eeeeeooooooeeeee	chr16:89348854-89349152(-)$1	298	265	281	10.6587
eeeeeooooooeeeee	chr21:43413868-43414111(-)$1	243	201	217	10.6587
ggggggnnnnnggggg	chr2:207174875-207175088(+)$1	213	92	108	8.3747
:eeeeennnnneeeee	chr7:98608984-98609204(+)$1	220	40	56	12.6318
eeeeeennnnneeeee	chr6:151257884-151258122(+)$1	238	144	160	13.2574
:eeeeennnnneeeee	chr6:32939490-32939712(+)$1	222	205	221	12.6318
ceeeeeooooooeeee	chr7:140159445-140159674(-)$1	229	154	170	10.1514
:eeeeennnnneeeee	chr21:30701727-30701951(+)$1	224	162	178	12.6318
:eeeeennnnneeeee	chr12:2906879-2907104(+)$1	225	47	63	12.6318
[eeeeeooooooeeee	chr12:51203248-51203466(+)$1	218	171	187	10.3094
!eeeeennnnneeeee	chr11:47189608-47189835(-)$1	227	165	181	13.3606
:eeeeennnnneeeee	chr7:19748380-19748639(-)$1	259	211	227	12.6318
"eeeeennnnneeeee	chr1:24077930-24078159(+)$1	229	105	121	13.2639
eeeeeennnnneeeee	chr1:203767425-203767635(+)$1	210	117	133	13.2574
[eeeeennnnneeeee	chr19:47111641-47111872(+)$1	231	210	226	13.2748
#eeeeennnnneeeee	chr1:19445975-19446185(-)$1	210	149	165	13.2511
!!ddddnnnnndddd2	chr3:49065612-49065842(-)$1	230	146	162	8.6792
:eeeeennnnneeeee	chr12:56814515-56814746(-)$1	231	167	183	12.6318
:eeeeennnnneeeee	chr8:23148859-23149082(+)$1	223	1	17	12.6318
!eeeeennnnneeeee	chr1:61554068-61554287(+)$1	219	190	206	13.3606
eeeeeooooooeeeee	chr7:100481994-100482232(+)$1	238	62	78	10.6587
eeee[aooooooaeee	chr10:75529028-75529299(+)$1	271	177	193	9.0602
!eeeeennnnneeeee	chr9:131387961-131388180(+)$1	219	45	61	13.3606
ddddddnnnnndddd]	chr16:81078379-81078610(+)$1	231	103	119	8.7530
[eeeeennnnneeeee	chr19:42848591-42848812(+)$1	221	49	65	13.2748
eeeeennnnneeeee:	chr5:14462793-14463004(+)$1	211	0	16	9.5249

#otherMatches

#Seq PSSM
AAAGAAAUAAAUCUUU	chr2:207173083-207173308(+)$1	225	81	97	10.6587
CCUUCAGGAGAGGAGG	chr7:150763547-150763775(+)$1	228	179	195	10.6587
CGGUGCCUCAAGCUGC	chr16:27523085-27523310(-)$1	225	105	121	9.7531
CAUAAUUCUGUUUGUG	chr3:141896294-141896513(-)$1	219	22	38	10.6587
GCCCAGAGGAGCUGGG	chr19:44056144-44056396(-)$1	252	80	96	13.3606
UGGGAGAGCUGUUCCC	chr10:103901251-103901516(+)$1	265	34	50	13.1248
GGGACUUGAUUAGCCC	chr14:21868521-21868734(-)$1	213	106	122	9.7858
CCAAACUUCACUUUGG	chr3:139094336-139094555(-)$1	219	123	139	10.6587
GGCCUUUUUCUGGGCC	chr16:3715900-3716127(-)$1	227	175	191	10.6587
UGAAUUCUGAAAAUUC	chr2:160604718-160604941(+)$1	223	8	24	12.6318
CUUGCUCUGCCAGCAC	chr17:3629459-3629711(+)$1	252	136	152	8.7530
UUUGGCGGCGAGAUCA	chr17:60140412-60140631(-)$1	219	105	121	12.1053
UCGUGGGAAAGUCAUG	chr3:9483296-9483516(+)$1	220	72	88	12.6318
AGUCUUAAAUGAGGAC	chr14:21896044-21896274(-)$1	230	91	107	13.0996
UGUGCCUGAUUGCCAC	chr3:196613016-196613243(+)$1	227	1	17	8.6645
UGUGGCACCCCGCCGC	chr19:11132485-11132710(+)$1	225	1	17	12.6318
UCUUCAUCCAAGAAGA	chr16:89348854-89349152(-)$1	298	265	281	10.6587
CUUGCUGCUGUGCAAG	chr21:43413868-43414111(-)$1	243	201	217	10.6587
AUUGAUGACUUGUCAG	chr2:207174875-207175088(+)$1	213	92	108	8.3747
UGGAUGCCAACCGUCC	chr7:98608984-98609204(+)$1	220	40	56	12.6318
UUGCCUGCUUGAGGCA	chr6:151257884-151258122(+)$1	238	144	160	13.2574
UGUGGCGGGUUGCCAC	chr6:32939490-32939712(+)$1	222	205	221	12.6318
CUACUGUGGCCGUAGU	chr7:140159445-140159674(-)$1	229	154	170	10.1514
CUCCAGAACAGCUGGA	chr21:30701727-30701951(+)$1	224	162	178	12.6318
GCCACCAUGAAGGUGG	chr12:2906879-2907104(+)$1	225	47	63	12.6318
UUUUCUGUAGAAAGAA	chr12:51203248-51203466(+)$1	218	171	187	10.3094
AGGCUGUUUUCUAGCU	chr11:47189608-47189835(-)$1	227	165	181	13.3606
UUCGAGAACAGCUUGA	chr7:19748380-19748639(-)$1	259	211	227	12.6318
UGCCUCCCUCAGAGGC	chr1:24077930-24078159(+)$1	229	105	121	13.2639
GGUCCCACUUAGGGAC	chr1:203767425-203767635(+)$1	210	117	133	13.2574
AGCCCUCUCCAGGGGC	chr19:47111641-47111872(+)$1	231	210	226	13.2748
AUGGUCAGAGGGGCCA	chr1:19445975-19446185(-)$1	210	149	165	13.2511
AGUUCGGAAAGUGAAG	chr3:49065612-49065842(-)$1	230	146	162	8.6792
ACUUUUAGGAGAAGAG	chr12:56814515-56814746(-)$1	231	167	183	12.6318
CGAUCUCUCCUAGAUC	chr8:23148859-23149082(+)$1	223	1	17	12.6318
UGCUCUAAUCCAGGGC	chr1:61554068-61554287(+)$1	219	190	206	13.3606
CAGGCAGGAAAGCCUG	chr7:100481994-100482232(+)$1	238	62	78	10.6587
UGAGACUGACACGCUC	chr10:75529028-75529299(+)$1	271	177	193	9.0602
CUGUGGAGUCACCACA	chr9:131387961-131388180(+)$1	219	45	61	13.3606
CUGGCUGAUCUGGCCU	chr16:81078379-81078610(+)$1	231	103	119	8.7530
CAGGCCUGCCUGGCCU	chr19:42848591-42848812(+)$1	221	49	65	13.2748
CCAAGUAACCCUUGGU	chr5:14462793-14463004(+)$1	211	0	16	9.5249

#DB
(((((......)))))	chr2:207173083-207173308(+)$1	1	81	97	10.6587
(((((......)))))	chr7:150763547-150763775(+)$1	1	179	195	10.6587
((((((.....)).))	chr16:27523085-27523310(-)$1	1	105	121	9.7531
(((((......)))))	chr3:141896294-141896513(-)$1	1	22	38	10.6587
.(((((.....)))))	chr19:44056144-44056396(-)$1	1	80	96	13.3606
((((((.....)))))	chr10:103901251-103901516(+)$1	1	34	50	13.1248
(((.((.....)))))	chr14:21868521-21868734(-)$1	1	106	122	9.7858
(((((......)))))	chr3:139094336-139094555(-)$1	1	123	139	10.6587
(((((......)))))	chr16:3715900-3716127(-)$1	1	175	191	10.6587
.(((((.....)))))	chr2:160604718-160604941(+)$1	1	8	24	12.6318
((((((.....)))).	chr17:3629459-3629711(+)$1	1	136	152	8.7530
((((((.....).)))	chr17:60140412-60140631(-)$1	1	105	121	12.1053
.(((((.....)))))	chr3:9483296-9483516(+)$1	1	72	88	12.6318
)(((((.....)))))	chr14:21896044-21896274(-)$1	1	91	107	13.0996
((((.(.....).)))	chr3:196613016-196613243(+)$1	1	1	17	8.6645
.(((((.....)))))	chr19:11132485-11132710(+)$1	1	1	17	12.6318
(((((......)))))	chr16:89348854-89349152(-)$1	1	265	281	10.6587
(((((......)))))	chr21:43413868-43414111(-)$1	1	201	217	10.6587
((((((.....)))))	chr2:207174875-207175088(+)$1	1	92	108	8.3747
.(((((.....)))))	chr7:98608984-98609204(+)$1	1	40	56	12.6318
((((((.....)))))	chr6:151257884-151258122(+)$1	1	144	160	13.2574
.(((((.....)))))	chr6:32939490-32939712(+)$1	1	205	221	12.6318
)(((((......))))	chr7:140159445-140159674(-)$1	1	154	170	10.1514
.(((((.....)))))	chr21:30701727-30701951(+)$1	1	162	178	12.6318
.(((((.....)))))	chr12:2906879-2907104(+)$1	1	47	63	12.6318
.(((((......))))	chr12:51203248-51203466(+)$1	1	171	187	10.3094
.(((((.....)))))	chr11:47189608-47189835(-)$1	1	165	181	13.3606
.(((((.....)))))	chr7:19748380-19748639(-)$1	1	211	227	12.6318
.(((((.....)))))	chr1:24077930-24078159(+)$1	1	105	121	13.2639
)(((((.....)))))	chr1:203767425-203767635(+)$1	1	117	133	13.2574
.(((((.....)))))	chr19:47111641-47111872(+)$1	1	210	226	13.2748
.(((((.....)))))	chr1:19445975-19446185(-)$1	1	149	165	13.2511
..((((.....)))).	chr3:49065612-49065842(-)$1	1	146	162	8.6792
.(((((.....)))))	chr12:56814515-56814746(-)$1	1	167	183	12.6318
.(((((.....)))))	chr8:23148859-23149082(+)$1	1	1	17	12.6318
.(((((.....)))))	chr1:61554068-61554287(+)$1	1	190	206	13.3606
(((((......)))))	chr7:100481994-100482232(+)$1	1	62	78	10.6587
((((.(......))))	chr10:75529028-75529299(+)$1	1	177	193	9.0602
.(((((.....)))))	chr9:131387961-131388180(+)$1	1	45	61	13.3606
((((((.....)))).	chr16:81078379-81078610(+)$1	1	103	119	8.7530
.(((((.....)))))	chr19:42848591-42848812(+)$1	1	49	65	13.2748
(((((.....))))).	chr5:14462793-14463004(+)$1	1	0	16	9.5249

#PSSM
e : 0.35	: : 0.23	! : 0.11	d : 0.09	[ : 0.07	g : 0.04	c : 0.02	" : 0.02	# : 0.02	
e : 0.88	d : 0.07	g : 0.02	! : 0.02	
e : 0.88	d : 0.09	g : 0.02	
e : 0.85	d : 0.09	[ : 0.02	g : 0.02	
e : 0.80	d : 0.07	b : 0.04	[ : 0.04	g : 0.02	
e : 0.57	o : 0.19	d : 0.07	a : 0.07	b : 0.04	g : 0.02	n : 0.02	
n : 0.73	o : 0.26	
n : 0.73	o : 0.26	
n : 0.73	o : 0.26	
n : 0.73	o : 0.26	
n : 0.71	o : 0.26	e : 0.02	
e : 0.73	d : 0.07	o : 0.07	b : 0.04	a : 0.04	g : 0.02	
e : 0.78	d : 0.07	b : 0.04	] : 0.04	g : 0.02	a : 0.02	
e : 0.85	d : 0.09	] : 0.02	g : 0.02	
e : 0.88	d : 0.09	g : 0.02	
e : 0.85	] : 0.04	d : 0.02	g : 0.02	2 : 0.02	: : 0.02	

#score	484.750555200931
#seq	42
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_UTR_m2_run2.txt

#BEAR
g[cccvvvvvvvvvvvvvccc]gg	chr5:149420235-149420452(+)$1	217	14	38	23.7323
eee[bbtttttttttttbbeeeee	chr3:15111511-15111772(-)$1	261	31	55	21.7643
f"""bbvvvvvvvvvvvvvbb333	chr2:242206192-242206418(-)$1	226	190	214	21.4733
ddddvvvvvvvvvvvvvdddd]dd	chr1:156697450-156697672(-)$1	222	112	136	21.4737
hhhhhhuuuuuuuuuuuuhhhhhh	chrX:99549347-99549570(-)$1	223	64	88	20.5908
$$ddddtttttttttttdddd777	chr11:117038808-117039020(+)$1	212	68	92	19.7082
ffffffuuuuuuuuuuuuffffff	chr22:29184143-29184358(+)$1	215	54	78	22.1913
gg[bbwwwwwwwwwwwwwwbb]gg	chr7:26230612-26230835(-)$1	223	168	192	21.5833
[cccwwwwwwwwwwwwwwccc]cc	chr17:27246126-27246338(-)$1	212	75	99	22.3578
eeeeewwwwwwwwwwwwwweeeee	chr2:179379720-179379952(+)$1	232	7	31	21.1693
dddwwwwwwwwwwwwwwdddd444	chr9:123525625-123525844(-)$1	219	156	180	20.4420
eeddddtttttttttttdddd]ee	chr17:5991220-5991442(+)$1	222	16	40	22.2276
g!!ccctttttttttttccc22gg	chr4:128638929-128639157(+)$1	228	87	111	23.1291
=======ssssssssss=======	chr1:6282672-6282893(-)$1	221	68	92	15.5888
cccccctttttttttttccc]ccc	chr12:133303301-133303525(-)$1	224	139	163	23.0051
ggggggwwwwwwwwwwwwwwgggg	chr1:166820095-166820314(+)$1	219	23	47	21.0530
ffffffuuuuuuuuuuuuffffff	chr1:166819681-166819913(+)$1	232	183	207	22.1913
hhddddtttttttttttdddd22h	chr18:25531848-25532076(-)$1	228	181	205	21.4476
======vvvvvvvvvvvvv=====	chr5:180004959-180005175(+)$1	216	171	195	22.4579
!eeeeeuuuuuuuuuuuueeeee2	chr3:119545064-119545283(-)$1	219	90	114	21.8756
fffffuuuuuuuuuuuuffffff]	chr16:30670497-30670717(+)$1	220	85	109	22.5056
c[cccuuuuuuuuuuuucccccc2	chr8:109260790-109261013(-)$1	223	107	131	23.2747
=======ssssssssss=======	chr11:9773740-9773962(+)$1	222	82	106	15.5888
ggg[bbtttttttttttbb]gggg	chrX:73807402-73807629(-)$1	227	27	51	22.4423
gggggguuuuuuuuuuuugggggg	chr1:214837221-214837455(+)$1	234	115	139	22.9416
e[cccvvvvvvvvvvvvvccc]ee	chr15:66618332-66618552(+)$1	220	189	213	23.4409
fffffuuuuuuuuuuuuffffffd	chr22:19837964-19838189(-)$1	225	57	81	22.2528
d[ddddtttttttttttddddddd	chr11:94609614-94609835(+)$1	221	143	167	21.5907
eeeeewwwwwwwwwwwwwweeeee	chr20:34329911-34330137(-)$1	226	79	103	21.1693
eeyyyyyyyyyyyyyyyyeeeee=	chr10:102753196-102753418(+)$1	222	120	144	19.8618
ggggguuuuuuuuuuuuggggggg	chr17:33678827-33679048(-)$1	221	31	55	23.0767
eeeee[assssssssssaeeeee]	chr6:64345771-64345992(+)$1	221	167	191	15.5600
ffffvvvvvvvvvvvvvffffffe	chr9:33025190-33025411(+)$1	221	79	103	21.8176
cc[ccctttttttttttcccccc2	chr11:94604645-94604866(+)$1	221	30	54	23.1253
!!cccuuuuuuuuuuuuccc22bb	chr19:10427471-10427682(-)$1	211	179	203	22.4013
fffffuuuuuuuuuuuuffffff]	chr15:83698794-83699014(-)$1	220	157	181	22.5056
ccccccuuuuuuuuuuuuccc]cc	chr20:34214472-34214698(-)$1	226	192	216	23.3382
fff[bbvvvvvvvvvvvvvbb]ff	chr3:47098575-47098793(-)$1	218	110	134	21.5915
dd[bbuuuuuuuuuuuubb]dddd	chr6:155054571-155054792(+)$1	221	153	177	21.2255
a[cccvvvvvvvvvvvvvccc]ae	chr11:71707618-71707836(+)$1	218	139	163	23.3428
ccyyyyyyyyyyyyyyyyccc333	chr11:60673909-60674138(-)$1	229	113	137	20.7393
ccyyyyyyyyyyyyyyyyccc333	chr1:243666870-243667094(-)$1	224	123	147	20.7393
ffffffuuuuuuuuuuuuffffff	chr12:54625789-54626011(-)$1	222	161	185	22.1913
hhhhhuuuuuuuuuuuuhhhhhhh	chr16:29869867-29870110(-)$1	243	45	69	20.7167
:dddduuuuuuuuuuuudddd===	chr14:23540404-23540623(-)$1	219	58	82	21.3061
e[ddddtttttttttttdddd]ee	chr1:27733789-27734005(-)$1	216	119	143	22.4172
ffffvvvvvvvvvvvvvffffff:	chr1:193055184-193055413(+)$1	229	172	196	20.8557
bb[ccctttttttttttccc]bb2	chr1:162467681-162467911(+)$1	230	87	111	21.8487
cdddduuuuuuuuuuuuddddccc	chr12:6623347-6623572(+)$1	225	156	180	22.1129
ggggvvvvvvvvvvvvvggggggg	chr16:66921464-66921683(+)$1	219	180	204	22.4835
ggggggtttttttttttggggggg	chr13:30085309-30085528(-)$1	219	19	43	22.8567
fff[bbvvvvvvvvvvvvvbb]ff	chr6:56417573-56417798(-)$1	225	49	73	21.5915
ggggggtttttttttttggggggg	chr1:109178358-109178581(+)$1	223	188	212	22.8567

#otherMatches

#Seq PSSM
UCUAUUUUUUGCCAUUGUGUAUGA	chr5:149420235-149420452(+)$1	217	14	38	23.7323
GACUCAAAAUGAAAAGGUGGUCUC	chr3:15111511-15111772(-)$1	261	31	55	21.7643
GGUUCCGCAACAAAUCAAAGGUGA	chr2:242206192-242206418(-)$1	226	190	214	21.4733
GUGUACUACAGACCUCCACAUGUU	chr1:156697450-156697672(-)$1	222	112	136	21.4737
UCCUAGCUUUACGCAUUACUAGGA	chrX:99549347-99549570(-)$1	223	64	88	20.5908
AGAUUCUUAUGUAUACUGAAUAUU	chr11:117038808-117039020(+)$1	212	68	92	19.7082
CAAGUGUUUGAUUCAUGCCAUUUG	chr22:29184143-29184358(+)$1	215	54	78	22.1913
AGUGAUCAUUAAUAAAGCUUUUCU	chr7:26230612-26230835(-)$1	223	168	192	21.5833
UGACUAUUGCCCUCUCCUGUUUCA	chr17:27246126-27246338(-)$1	212	75	99	22.3578
ACCGAUGACUUACCAAUUUUUGGU	chr2:179379720-179379952(+)$1	232	7	31	21.1693
ugccucuaacuuaaucugcagccu	chr9:123525625-123525844(-)$1	219	156	180	20.4420
UCCCCUGGCUUUUCCUAAGGGUGG	chr17:5991220-5991442(+)$1	222	16	40	22.2276
aguuccuuguagauccuggauauc	chr4:128638929-128639157(+)$1	228	87	111	23.1291
UGUCUUGUUGAUAGGUCUAGGGCA	chr1:6282672-6282893(-)$1	221	68	92	15.5888
CCGCCCUGUCUUUUCCUGGGUUGG	chr12:133303301-133303525(-)$1	224	139	163	23.0051
gcugGUAUAGAUAACAGACCAUUA	chr1:166820095-166820314(+)$1	219	23	47	21.0530
caggugagcaagcauuaccaccug	chr1:166819681-166819913(+)$1	232	183	207	22.1913
AAGCACUGGGAUUUUAUGUGCCUU	chr18:25531848-25532076(-)$1	228	181	205	21.4476
GAAAUGGUGUAAACUAAUGUAUUU	chr5:180004959-180005175(+)$1	216	171	195	22.4579
CAGCUUGAAAUUGGUUGGGAGCUU	chr3:119545064-119545283(-)$1	219	90	114	21.8756
ACGGCCGCCCCGUUUUCGCCGUCG	chr16:30670497-30670717(+)$1	220	85	109	22.5056
GCAUCGCGCACUUUUUGGAUCGGC	chr8:109260790-109261013(-)$1	223	107	131	23.2747
UGGGGCUUAGCUGCUCUAGCCCUG	chr11:9773740-9773962(+)$1	222	82	106	15.5888
AAGGGUUAUCACAUAAUAUGCUUU	chrX:73807402-73807629(-)$1	227	27	51	22.4423
CAUUGCCAUUCCUCUACUGCAAUG	chr1:214837221-214837455(+)$1	234	115	139	22.9416
CCCUGGAAGUCCACGAGACAGUGG	chr15:66618332-66618552(+)$1	220	189	213	23.4409
GCAUCUUGGCAAAGAAUGAUGUUU	chr22:19837964-19838189(-)$1	225	57	81	22.2528
CCAAAGAUUUUCCUCUCCUUUGCU	chr11:94609614-94609835(+)$1	221	143	167	21.5907
UCUAAUUCCAUUGUUUUUUUUAGA	chr20:34329911-34330137(-)$1	226	79	103	21.1693
GCAUAAAACUCUGCAAGGGCUCCU	chr10:102753196-102753418(+)$1	222	120	144	19.8618
gugacuucaugcaguuuguugcuu	chr17:33678827-33679048(-)$1	221	31	55	23.0767
CUGCGCGUACCCCCUCUCCGCGGC	chr6:64345771-64345992(+)$1	221	167	191	15.5600
GGCGGAACUUUCCAGAACGCUCGG	chr9:33025190-33025411(+)$1	221	79	103	21.8176
UUCAUUUUUUUCUUUUUAAUAAGA	chr11:94604645-94604866(+)$1	221	30	54	23.1253
CGCAGCCCCCUCCCCUUCUGAUGC	chr19:10427471-10427682(-)$1	211	179	203	22.4013
AGUGGGGGUAGCAGUUACCAUUUG	chr15:83698794-83699014(-)$1	220	157	181	22.5056
UACCGCCGGUUCCAGAAUGUGAGU	chr20:34214472-34214698(-)$1	226	192	216	23.3382
GUGUUCUCCUGCUCCUUAUGAUCA	chr3:47098575-47098793(-)$1	218	110	134	21.5915
ggggcagagAAGAGAAggcgccgc	chr6:155054571-155054792(+)$1	221	153	177	21.2255
CCCACUCCCUUCUUCCCUGUGUGG	chr11:71707618-71707836(+)$1	218	139	163	23.3428
CGGCUGUCCCCAUUCCCACGUGAA	chr11:60673909-60674138(-)$1	229	113	137	20.7393
AGAUUCCAACAUUUCUCACUGAAA	chr1:243666870-243667094(-)$1	224	123	147	20.7393
UGGGGAUUAAAGUUCCUUUCCCCA	chr12:54625789-54626011(-)$1	222	161	185	22.1913
CUGCCUACCCUGGUCCUGGCGGGA	chr16:29869867-29870110(-)$1	243	45	69	20.7167
UUCCAUUUACCAUUUUUUGGAUCC	chr14:23540404-23540623(-)$1	219	58	82	21.3061
CUGGCUGUCAGGAGCAAAGCCUGA	chr1:27733789-27734005(-)$1	216	119	143	22.4172
CAUAUUUUCUUCUGUUUUAUGUGA	chr1:193055184-193055413(+)$1	229	172	196	20.8557
UCCGUGCCCUUAACCCACACCGAU	chr1:162467681-162467911(+)$1	230	87	111	21.8487
GAAGCCAUAACACACCUGCUUGGU	chr12:6623347-6623572(+)$1	225	156	180	22.1129
cgggaauucgagaccagccugacc	chr16:66921464-66921683(+)$1	219	180	204	22.4835
CUGAGAUCUCCCCCCACUUUUGGU	chr13:30085309-30085528(-)$1	219	19	43	22.8567
GUUUCCAAAGAAUCUAAAAGGCAG	chr6:56417573-56417798(-)$1	225	49	73	21.5915
UCUUAACUCAUUGAAUAUUAAGAU	chr1:109178358-109178581(+)$1	223	188	212	22.8567

#DB
(.(((.............))).))	chr5:149420235-149420452(+)$1	1	14	38	23.7323
(((.((...........)))))))	chr3:15111511-15111772(-)$1	1	31	55	21.7643
(...((.............))...	chr2:242206192-242206418(-)$1	1	190	214	21.4733
((((.............)))).))	chr1:156697450-156697672(-)$1	1	112	136	21.4737
((((((............))))))	chrX:99549347-99549570(-)$1	1	64	88	20.5908
..((((...........))))...	chr11:117038808-117039020(+)$1	1	68	92	19.7082
((((((............))))))	chr22:29184143-29184358(+)$1	1	54	78	22.1913
((.((..............)).))	chr7:26230612-26230835(-)$1	1	168	192	21.5833
.(((..............))).))	chr17:27246126-27246338(-)$1	1	75	99	22.3578
(((((..............)))))	chr2:179379720-179379952(+)$1	1	7	31	21.1693
(((..............))))...	chr9:123525625-123525844(-)$1	1	156	180	20.4420
((((((...........)))).))	chr17:5991220-5991442(+)$1	1	16	40	22.2276
(..(((...........)))..))	chr4:128638929-128639157(+)$1	1	87	111	23.1291
(((((((..........)))))))	chr1:6282672-6282893(-)$1	1	68	92	15.5888
((((((...........))).)))	chr12:133303301-133303525(-)$1	1	139	163	23.0051
((((((..............))))	chr1:166820095-166820314(+)$1	1	23	47	21.0530
((((((............))))))	chr1:166819681-166819913(+)$1	1	183	207	22.1913
((((((...........))))..)	chr18:25531848-25532076(-)$1	1	181	205	21.4476
((((((.............)))))	chr5:180004959-180005175(+)$1	1	171	195	22.4579
.(((((............))))).	chr3:119545064-119545283(-)$1	1	90	114	21.8756
(((((............)))))).	chr16:30670497-30670717(+)$1	1	85	109	22.5056
(.(((............)))))).	chr8:109260790-109261013(-)$1	1	107	131	23.2747
(((((((..........)))))))	chr11:9773740-9773962(+)$1	1	82	106	15.5888
(((.((...........)).))))	chrX:73807402-73807629(-)$1	1	27	51	22.4423
((((((............))))))	chr1:214837221-214837455(+)$1	1	115	139	22.9416
(.(((.............))).))	chr15:66618332-66618552(+)$1	1	189	213	23.4409
(((((............)))))))	chr22:19837964-19838189(-)$1	1	57	81	22.2528
(.((((...........)))))))	chr11:94609614-94609835(+)$1	1	143	167	21.5907
(((((..............)))))	chr20:34329911-34330137(-)$1	1	79	103	21.1693
((................))))))	chr10:102753196-102753418(+)$1	1	120	144	19.8618
(((((............)))))))	chr17:33678827-33679048(-)$1	1	31	55	23.0767
(((((.(..........)))))).	chr6:64345771-64345992(+)$1	1	167	191	15.5600
((((.............))))))(	chr9:33025190-33025411(+)$1	1	79	103	21.8176
((.(((...........)))))).	chr11:94604645-94604866(+)$1	1	30	54	23.1253
..(((............)))..))	chr19:10427471-10427682(-)$1	1	179	203	22.4013
(((((............)))))).	chr15:83698794-83699014(-)$1	1	157	181	22.5056
((((((............))).))	chr20:34214472-34214698(-)$1	1	192	216	23.3382
(((.((.............)).))	chr3:47098575-47098793(-)$1	1	110	134	21.5915
((.((............)).))))	chr6:155054571-155054792(+)$1	1	153	177	21.2255
(.(((.............))).))	chr11:71707618-71707836(+)$1	1	139	163	23.3428
((................)))...	chr11:60673909-60674138(-)$1	1	113	137	20.7393
((................)))...	chr1:243666870-243667094(-)$1	1	123	147	20.7393
((((((............))))))	chr12:54625789-54626011(-)$1	1	161	185	22.1913
(((((............)))))))	chr16:29869867-29870110(-)$1	1	45	69	20.7167
.((((............))))(((	chr14:23540404-23540623(-)$1	1	58	82	21.3061
(.((((...........)))).))	chr1:27733789-27734005(-)$1	1	119	143	22.4172
((((.............)))))).	chr1:193055184-193055413(+)$1	1	172	196	20.8557
((.(((...........))).)).	chr1:162467681-162467911(+)$1	1	87	111	21.8487
)((((............))))(((	chr12:6623347-6623572(+)$1	1	156	180	22.1129
((((.............)))))))	chr16:66921464-66921683(+)$1	1	180	204	22.4835
((((((...........)))))))	chr13:30085309-30085528(-)$1	1	19	43	22.8567
(((.((.............)).))	chr6:56417573-56417798(-)$1	1	49	73	21.5915
((((((...........)))))))	chr1:109178358-109178581(+)$1	1	188	212	22.8567

#PSSM
f : 0.20	g : 0.18	e : 0.15	c : 0.13	d : 0.07	h : 0.05	= : 0.05	! : 0.03	$ : 0.01	[ : 0.01	a : 0.01	: : 0.01	b : 0.01	
f : 0.18	g : 0.15	e : 0.13	[ : 0.11	c : 0.11	d : 0.09	h : 0.05	= : 0.05	! : 0.03	" : 0.01	$ : 0.01	b : 0.01	
f : 0.18	d : 0.16	c : 0.15	g : 0.13	e : 0.09	[ : 0.07	= : 0.05	y : 0.05	h : 0.03	" : 0.01	! : 0.01	
c : 0.20	d : 0.15	f : 0.15	g : 0.11	[ : 0.07	e : 0.07	= : 0.05	y : 0.05	h : 0.03	b : 0.03	" : 0.01	w : 0.01	
c : 0.18	b : 0.13	d : 0.13	f : 0.11	g : 0.09	v : 0.07	e : 0.07	= : 0.05	y : 0.05	h : 0.03	w : 0.03	
u : 0.18	v : 0.13	b : 0.09	d : 0.09	w : 0.09	c : 0.09	g : 0.07	f : 0.05	= : 0.05	y : 0.05	h : 0.01	e : 0.01	[ : 0.01	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	y : 0.05	= : 0.03	a : 0.01	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
u : 0.32	t : 0.24	v : 0.20	w : 0.11	s : 0.05	y : 0.05	
d : 0.16	v : 0.13	u : 0.13	c : 0.11	w : 0.09	f : 0.09	g : 0.07	b : 0.05	y : 0.05	= : 0.03	a : 0.01	h : 0.01	
c : 0.24	d : 0.16	f : 0.15	g : 0.09	v : 0.07	w : 0.07	b : 0.05	e : 0.05	h : 0.03	= : 0.03	
c : 0.24	d : 0.16	f : 0.15	e : 0.11	g : 0.09	b : 0.07	= : 0.05	h : 0.03	] : 0.03	w : 0.01	
d : 0.18	c : 0.16	f : 0.15	g : 0.13	e : 0.11	b : 0.07	= : 0.05	h : 0.03	2 : 0.03	] : 0.03	
] : 0.20	f : 0.15	g : 0.13	e : 0.11	= : 0.07	c : 0.07	3 : 0.05	2 : 0.05	h : 0.03	d : 0.03	7 : 0.01	4 : 0.01	b : 0.01	
g : 0.18	f : 0.18	e : 0.16	c : 0.11	= : 0.07	3 : 0.05	d : 0.05	h : 0.03	b : 0.03	7 : 0.01	4 : 0.01	2 : 0.01	a : 0.01	
g : 0.18	e : 0.15	f : 0.09	= : 0.09	d : 0.07	c : 0.07	2 : 0.07	3 : 0.05	h : 0.05	] : 0.05	7 : 0.01	4 : 0.01	b : 0.01	: : 0.01	

#score	1145.2335136728925
#seq	53
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_UTR_m2_run1.txt

#BEAR
cc[a[ccc"""bbnnnnnbb333ccc]acc	chr15:86291808-86292038(+)$1	230	181	211	10.8985
!==========bbmmmmbb]==========	chr3:169713071-169713293(+)$1	222	48	78	13.4824
ggggg[ccc[bbmmmmbb333ccc22gggg	chr8:70580004-70580223(-)$1	219	178	208	10.8264
iiiiii[bb[cccmmmmccc22bb]iiiii	chr11:67131642-67131864(-)$1	222	119	149	13.9344
ggggg$$$$$cccnnnnnccc4444ggggg	chr3:156424038-156424262(+)$1	224	22	52	12.4065
hhhhhhh!!acccmmmmccc]a4444hhhh	chr10:112657961-112658181(+)$1	220	125	155	12.7078
gggggg####cccooooooccc333ggggg	chr3:178738316-178738542(-)$1	226	118	148	13.8683
##eeeee"""cccnnnnnccc4444eeeee	chr20:49200863-49201086(+)$1	223	103	133	11.6146
iiiiii$$$$$bbmmmmbb4444iiiiiii	chr19:11172586-11172805(+)$1	219	17	47	13.7633
ggggggg[bbccclllccc333bb]ggggg	chr14:51188887-51189104(-)$1	217	115	145	12.6159
b[ccc####ddddmmmmdddd22ccc]bb]	chr16:67970565-67970795(-)$1	230	136	166	11.3273
iiiiiiiiicccnnnnnccc]iiiiiiiii	chr22:50810357-50810577(+)$1	220	50	80	11.8856
iiiii[gggggggmmmmggggggg]iiiii	chr3:24019126-24019346(+)$1	220	157	187	12.4211
ggggggccc[cccmmmmccc]ccc]ggggg	chr10:96369520-96369750(+)$1	230	75	105	14.1029
hhh[eeeee[ccclllccc333eeeee]hh	chr14:74183867-74184091(-)$1	224	32	62	10.8160
!!ggggggg"""bblllbb4444ggggggg	chr20:43704023-43704246(+)$1	223	31	61	12.1482
ggggggggeeeeemmmmeeeee]ggggggg	chr7:36492210-36492429(+)$1	219	168	198	10.8817
fffff####ddddmmmmdddd4444fffff	chr11:9495391-9495616(+)$1	225	128	158	11.2461
cc[ccc$$$$$bbmmmmbb4444ccc]ccc	chr11:32623731-32623951(+)$1	220	110	140	12.3406
ggggggga!!cccmmmmccc333a]ggggg	chr12:12630801-12631031(-)$1	230	63	93	15.9452
b####ccc[cccnnnnnccc]ccc333bb4	chr10:11372319-11372537(+)$1	218	180	210	9.8876
=============mmmm===========::	chr15:60782291-60782511(-)$1	220	126	156	11.8165
cc!!dddd!!cccmmmmcccdddd22ccc3	chr7:99228469-99228693(+)$1	224	155	185	11.4467
a[a[ffffffcccmmmmccc]ffffff]a]	chr6:150047004-150047234(-)$1	230	180	210	11.1386
!!ccc[bb[cccammmma]ccc]bb]ccc2	chr3:111710404-111710629(+)$1	225	13	43	11.4032
eee[bb####cccmmmmccc22bb]eeeee	chr11:65659837-65660062(-)$1	225	127	157	13.1333
b:ggggggg[cccmmmmccc]ggggggg::	chr19:32877441-32877671(+)$1	230	134	164	10.4904
gggggg"""eeeeellleeeee22gggggg	chr16:75690990-75691208(+)$1	218	53	83	10.4379
ffffff####cccmmmmccc22ffffff::	chr11:75116606-75116829(+)$1	223	131	161	10.9880
gggggg[ddddoooooodddd333gggggg	chr3:23961307-23961532(+)$1	225	32	62	10.8888
[ggggggg"""bbmmmmbb333ggggggg2	chr18:29127552-29127788(+)$1	236	24	54	14.1162
!!ccc####ddddllldddd22ccc22ccc	chr2:111924473-111924692(+)$1	219	103	133	10.7030
##eeeee"""cccooooooccc333eeeee	chrX:46741263-46741500(+)$1	237	169	199	11.9693
ggggggg####bbmmmmbb4444ggggggg	chr5:89814761-89814981(-)$1	220	46	76	14.4493
gg[==========mmmm==========]gg	chr4:106199165-106199388(+)$1	223	160	190	13.8293
eeee!!gggggggmmmmggggggg]eeeee	chrX:41091984-41092214(+)$1	230	62	92	10.7758
:eeeee####cccmmmmccc4444eeeeee	chr11:111611451-111611668(-)$1	217	140	170	13.0090
!eeeee[a!!ccclllccc22a]eeeee33	chr17:37054589-37054810(+)$1	221	65	95	11.6734
ddd[ccc!!ddddmmmmdddd22ccc]ddd	chr4:79835584-79835814(+)$1	230	132	162	10.3997
"ggggggg!!ccclllcccggggggg4444	chr8:29920883-29921105(-)$1	222	20	50	11.9585
ggggga!!a[bboooooobb]a22a]gggg	chr7:66421153-66421380(+)$1	227	117	147	11.5605
!!a[iiiiiiiiimmmmiiiiiiiii]ahh	chr17:27585597-27585817(-)$1	220	114	144	12.5024
=========[bbnnnnnbb==========3	chr2:87001821-87002042(+)$1	221	109	139	11.5382
eeee!!gggggggmmmmggggggg22eeee	chr16:48643939-48644157(-)$1	218	89	119	10.5473
!iiiiiiiii[ccclllccc]iiiiiiiii	chr6:71567538-71567763(+)$1	225	84	114	12.8134
ggggg####ddddmmmmdddd4444ggggg	chr14:55531308-55531530(+)$1	222	17	47	13.4189
eeeeee!!a[cccmmmmccca]eeeeeccc	chr1:9787177-9787398(+)$1	221	87	117	12.4970
dddd[bb[a[cccmmmmccca]bbddddee	chr19:57135615-57135845(+)$1	230	124	154	10.6747
####eeeee[cccooooooccceeeeeggg	chr16:8948686-8948916(-)$1	230	15	45	9.9309
$$$$$bb"""cccmmmmccc333bb333gg	chr22:29191135-29191365(-)$1	230	40	70	13.5139
========!!cccmmmmccc22========	chr8:79514696-79514923(+)$1	227	57	87	15.6255
gggggg[bb[cccmmmmccc]bb]gggggg	chr17:36922335-36922555(-)$1	220	39	69	13.3648
[bb!!bb"""cccmmmmccc333bb22bb]	chr6:16305837-16306064(-)$1	227	82	112	13.3353

#otherMatches

#Seq PSSM
GGCGUGCAACCCCCCACUGGCUGUGUCCCC	chr15:86291808-86292038(+)$1	230	181	211	10.8985
GUAAGAAUAAUGCAUAUGUGAUUGUUCUUA	chr3:169713071-169713293(+)$1	222	48	78	13.4824
AUUUUAGCAAGAAUAAUCAGAUGCCAAAAA	chr8:70580004-70580223(-)$1	219	178	208	10.8264
UAAGUGUGUUGUAUUAAUAUUUAUUUAUUU	chr11:67131642-67131864(-)$1	222	119	149	13.9344
AGGUAAACUCCUUAUAAAAAGCAAAUACCU	chr3:156424038-156424262(+)$1	224	22	52	12.4065
AAUAAGCUACCUUUUGUAAGUGCCAUGUUU	chr10:112657961-112658181(+)$1	220	125	155	12.7078
GAGGCAUAUGCUAGGACAAUAGAGCUGCUU	chr3:178738316-178738542(-)$1	226	118	148	13.8683
CCACCUUGUUACACAUUAUGUUAGAGAGGU	chr20:49200863-49201086(+)$1	223	103	133	11.6146
UAUAAACAAAAGAAUCUUCCAUAUUUAUAC	chr19:11172586-11172805(+)$1	219	17	47	13.7633
UUGGCAUGCCACCUGAGGUCAAGGAGUGCC	chr14:51188887-51189104(-)$1	217	115	145	12.6159
CCCCAAGAUGCUGAAGCCAGCCCUGGAGCC	chr16:67970565-67970795(-)$1	230	136	166	11.3273
GAGGAAGAACUUAAAGCAAGAUUUUUCCUC	chr22:50810357-50810577(+)$1	220	50	80	11.8856
UAGGAGUUCUGUUGAAUGAUGGAAAUCUUA	chr3:24019126-24019346(+)$1	220	157	187	12.4211
UCUCUUCGUACUAGCACUAGGGCGCAAGAG	chr10:96369520-96369750(+)$1	230	75	105	14.1029
GAAAGGGCCAGGAGGUUCUGGAGGCCCCUU	chr14:74183867-74184091(-)$1	224	32	62	10.8160
CAGAGUUUUAAACCCCAGGAACAGAGACUC	chr20:43704023-43704246(+)$1	223	31	61	12.1482
GAUUUCUGUCAUUCAUCAAUGAGUAGAAGU	chr7:36492210-36492429(+)$1	219	168	198	10.8817
UUGGAAGAUGGUUCUGCGGCCUAUGUUCAA	chr11:9495391-9495616(+)$1	225	128	158	11.2461
CAUUUGGAAAACAGCAGUGGCAACAACUGU	chr11:32623731-32623951(+)$1	220	110	140	12.3406
UUUUUUCCUCUCUCUGCAGAUUUGUGAAAG	chr12:12630801-12631031(-)$1	230	63	93	15.9452
GUUUCUGAUGUCUUUCUGACCUCACAUCAU	chr10:11372319-11372537(+)$1	218	180	210	9.8876
uuuguauauauauacauauauauauauauC	chr15:60782291-60782511(-)$1	220	126	156	11.8165
aggcccuguaacaaacaugucaggaacucu	chr7:99228469-99228693(+)$1	224	155	185	11.4467
AGUGUGAUUAAUCAAAUGAUAUGAUCAGAG	chr6:150047004-150047234(-)$1	230	180	210	11.1386
AAUGCAGGUUGCCGAUCGAGUACUCAGCAC	chr3:111710404-111710629(+)$1	225	13	43	11.4032
ACCAGCCCCACUGCCAGCAGCAGCAGGUGA	chr11:65659837-65660062(-)$1	225	127	157	13.1333
UAGGACUGUGUUCAUGGGAGAGCAGUUCAU	chr19:32877441-32877671(+)$1	230	134	164	10.4904
UAUUCAUUUUGCUAACUUAGUAUUUGGGUA	chr16:75690990-75691208(+)$1	218	53	83	10.4379
GUCUGACUAGACUGUUCAGUAUUCAGACUG	chr11:75116606-75116829(+)$1	223	131	161	10.9880
GAGUGAUGGCAAUGCUCUGCUGGUUUAUUU	chr3:23961307-23961532(+)$1	225	32	62	10.8888
uugcagugagccgagaucgcaccauugcac	chr18:29127552-29127788(+)$1	236	24	54	14.1162
CUUUUUCAAAAUCAAGGAUUGUAAAUAUUG	chr2:111924473-111924692(+)$1	219	103	133	10.7030
AUAAGACCUUUUACCCAUUUAAUUUGUCUU	chrX:46741263-46741500(+)$1	237	169	199	11.9693
CCCUAUUAUGGAGCAGACUGGGGAAUAGGG	chr5:89814761-89814981(-)$1	220	46	76	14.4493
uacauauauauauauauauauauauauaua	chr4:106199165-106199388(+)$1	223	160	190	13.8293
CUUAAGCAAGAAACUUUUUUCUUGAUGAGA	chrX:41091984-41092214(+)$1	230	62	92	10.7758
AGUUCUGUAUUUCGAAUGAGUCUAAGAACC	chr11:111611451-111611668(-)$1	217	140	170	13.0090
CCUCCUGCAGGUGCGCUACAAGGAGGAGUU	chr17:37054589-37054810(+)$1	221	65	95	11.6734
uugugagaauuaugagaauaaagcucccaa	chr4:79835584-79835814(+)$1	230	132	162	10.3997
GUUGUACUAAUAGAAACUAAGUACAGAAAA	chr8:29920883-29921105(-)$1	222	20	50	11.9585
AGGAGGUUCUACUGUCUUGUCGUCCACUCU	chr7:66421153-66421380(+)$1	227	117	147	11.5605
CUGAUAUUGUCCUAUGAAGGACAAUAACUU	chr17:27585597-27585817(-)$1	220	114	144	12.5024
UUUAAACUACAGAUGGACUUGGUUUGAGGG	chr2:87001821-87002042(+)$1	221	109	139	11.5382
GCCAAGCUGCUGCGGUCGUGGCGGGAUGGU	chr16:48643939-48644157(-)$1	218	89	119	10.5473
AGGUGUAUUUAUGGGACCCACAAAUAUACC	chr6:71567538-71567763(+)$1	225	84	114	12.8134
UAUUGCAGUCUUACCAUUAAGUUAACAAUG	chr14:55531308-55531530(+)$1	222	17	47	13.4189
AGUUUAAGGAGCUAAACAGCCAUAAACGGA	chr1:9787177-9787398(+)$1	221	87	117	12.4970
AUCCUCAGGCUGGCUUCCCACGUGGGAUUG	chr19:57135615-57135845(+)$1	230	124	154	10.6747
UCAAGUAUCUCCUGGAGGAAGGGGUAUGGG	chr16:8948686-8948916(-)$1	230	15	45	9.9309
CCACUGCCCAAAGCCAUCUUCCUGCCUACU	chr22:29191135-29191365(-)$1	230	40	70	13.5139
GAUGAGUUGAUUAAGUCUAACAGAUUCAUC	chr8:79514696-79514923(+)$1	227	57	87	15.6255
UCUCUUCCUGGCAGUCAUGCGGGCAGGAGG	chr17:36922335-36922555(-)$1	220	39	69	13.3648
AAGUUAACCAUUUAAAAGAACAUUUUUCUC	chr6:16305837-16306064(-)$1	227	82	112	13.3353

#DB
((.(.(((...((.....))...))).)))	chr15:86291808-86292038(+)$1	1	181	211	10.8985
.((((((((((((....)).))))))))))	chr3:169713071-169713293(+)$1	1	48	78	13.4824
(((((.(((.((....))...)))..))))	chr8:70580004-70580223(-)$1	1	178	208	10.8264
((((((.((.(((....)))..)).)))))	chr11:67131642-67131864(-)$1	1	119	149	13.9344
(((((.....(((.....)))....)))))	chr3:156424038-156424262(+)$1	1	22	52	12.4065
(((((((..((((....))).)....))))	chr10:112657961-112658181(+)$1	1	125	155	12.7078
((((((....(((......)))...)))))	chr3:178738316-178738542(-)$1	1	118	148	13.8683
..(((((...(((.....)))....)))))	chr20:49200863-49201086(+)$1	1	103	133	11.6146
((((((.....((....))....)))))))	chr19:11172586-11172805(+)$1	1	17	47	13.7633
(((((((.(((((...)))...)).)))))	chr14:51188887-51189104(-)$1	1	115	145	12.6159
(.(((....((((....))))..))).)).	chr16:67970565-67970795(-)$1	1	136	166	11.3273
((((((((((((.....))).)))))))))	chr22:50810357-50810577(+)$1	1	50	80	11.8856
(((((.(((((((....))))))).)))))	chr3:24019126-24019346(+)$1	1	157	187	12.4211
(((((((((.(((....))).))).)))))	chr10:96369520-96369750(+)$1	1	75	105	14.1029
(((.(((((.(((...)))...))))).))	chr14:74183867-74184091(-)$1	1	32	62	10.8160
..(((((((...((...))....)))))))	chr20:43704023-43704246(+)$1	1	31	61	12.1482
(((((((((((((....))))).)))))))	chr7:36492210-36492429(+)$1	1	168	198	10.8817
(((((....((((....))))....)))))	chr11:9495391-9495616(+)$1	1	128	158	11.2461
((.(((.....((....))....))).)))	chr11:32623731-32623951(+)$1	1	110	140	12.3406
((((((((..(((....)))...).)))))	chr12:12630801-12631031(-)$1	1	63	93	15.9452
(....(((.(((.....))).)))...)).	chr10:11372319-11372537(+)$1	1	180	210	9.8876
))(((((((((((....)))))))))))..	chr15:60782291-60782511(-)$1	1	126	156	11.8165
((..((((..(((....)))))))..))).	chr7:99228469-99228693(+)$1	1	155	185	11.4467
(.(.(((((((((....))).)))))).).	chr6:150047004-150047234(-)$1	1	180	210	11.1386
..(((.((.((((....).))).)).))).	chr3:111710404-111710629(+)$1	1	13	43	11.4032
(((.((....(((....)))..)).)))))	chr11:65659837-65660062(-)$1	1	127	157	13.1333
).(((((((.(((....))).)))))))..	chr19:32877441-32877671(+)$1	1	134	164	10.4904
((((((...(((((...)))))..))))))	chr16:75690990-75691208(+)$1	1	53	83	10.4379
((((((....(((....)))..))))))..	chr11:75116606-75116829(+)$1	1	131	161	10.9880
((((((.((((......))))...))))))	chr3:23961307-23961532(+)$1	1	32	62	10.8888
.(((((((...((....))...))))))).	chr18:29127552-29127788(+)$1	1	24	54	14.1162
..(((....((((...))))..)))..)))	chr2:111924473-111924692(+)$1	1	103	133	10.7030
..(((((...(((......)))...)))))	chrX:46741263-46741500(+)$1	1	169	199	11.9693
(((((((....((....))....)))))))	chr5:89814761-89814981(-)$1	1	46	76	14.4493
((.((((((((((....)))))))))).))	chr4:106199165-106199388(+)$1	1	160	190	13.8293
((((..(((((((....))))))).)))))	chrX:41091984-41092214(+)$1	1	62	92	10.7758
.(((((....(((....)))....)))))(	chr11:111611451-111611668(-)$1	1	140	170	13.0090
.(((((.(..(((...)))..).)))))..	chr17:37054589-37054810(+)$1	1	65	95	11.6734
(((.(((..((((....))))..))).)))	chr4:79835584-79835814(+)$1	1	132	162	10.3997
.(((((((..(((...))))))))))....	chr8:29920883-29921105(-)$1	1	20	50	11.9585
((((((..(.((......)).)..).))))	chr7:66421153-66421380(+)$1	1	117	147	11.5605
..(.(((((((((....))))))))).)))	chr17:27585597-27585817(-)$1	1	114	144	12.5024
(((((((((.((.....)))))))))))).	chr2:87001821-87002042(+)$1	1	109	139	11.5382
((((..(((((((....)))))))..))))	chr16:48643939-48644157(-)$1	1	89	119	10.5473
.(((((((((.(((...))).)))))))))	chr6:71567538-71567763(+)$1	1	84	114	12.8134
(((((....((((....))))....)))))	chr14:55531308-55531530(+)$1	1	17	47	13.4189
)(((((..(.(((....)))).)))))(((	chr1:9787177-9787398(+)$1	1	87	117	12.4970
((((.((.(.(((....)))).))))))))	chr19:57135615-57135845(+)$1	1	124	154	10.6747
....(((((.(((......)))))))))))	chr16:8948686-8948916(-)$1	1	15	45	9.9309
.....((...(((....)))...))...))	chr22:29191135-29191365(-)$1	1	40	70	13.5139
((((((((..(((....)))..))))))))	chr8:79514696-79514923(+)$1	1	57	87	15.6255
((((((.((.(((....))).)).))))))	chr17:36922335-36922555(-)$1	1	39	69	13.3648
.((..((...(((....)))...))..)).	chr6:16305837-16306064(-)$1	1	82	112	13.3353

#PSSM
g : 0.26	! : 0.13	i : 0.07	e : 0.07	c : 0.05	# : 0.05	b : 0.05	= : 0.05	h : 0.03	f : 0.03	[ : 0.03	d : 0.03	a : 0.01	: : 0.01	" : 0.01	$ : 0.01	
g : 0.30	e : 0.11	i : 0.09	= : 0.07	# : 0.07	! : 0.07	c : 0.05	h : 0.03	[ : 0.03	f : 0.03	d : 0.03	: : 0.01	$ : 0.01	b : 0.01	
g : 0.32	e : 0.15	i : 0.09	= : 0.07	[ : 0.05	c : 0.05	h : 0.03	f : 0.03	# : 0.03	a : 0.03	d : 0.03	! : 0.01	$ : 0.01	b : 0.01	
g : 0.32	e : 0.13	= : 0.09	i : 0.09	[ : 0.09	c : 0.07	f : 0.03	# : 0.03	! : 0.03	a : 0.01	h : 0.01	d : 0.01	$ : 0.01	
g : 0.32	e : 0.13	i : 0.11	= : 0.09	c : 0.09	f : 0.05	! : 0.05	[ : 0.03	h : 0.01	# : 0.01	d : 0.01	b : 0.01	$ : 0.01	
g : 0.24	e : 0.13	= : 0.09	i : 0.09	c : 0.07	# : 0.07	b : 0.07	[ : 0.05	f : 0.03	! : 0.03	$ : 0.01	h : 0.01	d : 0.01	a : 0.01	
g : 0.20	# : 0.15	c : 0.09	= : 0.09	[ : 0.07	e : 0.07	b : 0.07	$ : 0.05	i : 0.05	! : 0.03	h : 0.01	d : 0.01	f : 0.01	" : 0.01	
# : 0.16	g : 0.15	= : 0.09	" : 0.09	c : 0.07	! : 0.07	b : 0.05	$ : 0.05	i : 0.05	[ : 0.03	e : 0.03	a : 0.03	d : 0.03	f : 0.01	
# : 0.16	" : 0.13	! : 0.13	g : 0.09	= : 0.07	b : 0.05	$ : 0.05	i : 0.05	e : 0.05	a : 0.05	c : 0.03	[ : 0.03	f : 0.01	d : 0.01	
[ : 0.20	" : 0.13	d : 0.11	# : 0.09	! : 0.09	= : 0.05	$ : 0.05	c : 0.05	g : 0.05	e : 0.03	i : 0.03	a : 0.01	b : 0.01	f : 0.01	
c : 0.52	d : 0.11	" : 0.05	= : 0.05	b : 0.05	g : 0.05	$ : 0.03	e : 0.03	# : 0.01	i : 0.01	[ : 0.01	
c : 0.54	b : 0.16	d : 0.09	g : 0.05	e : 0.03	= : 0.03	" : 0.01	o : 0.01	i : 0.01	
c : 0.49	b : 0.13	d : 0.09	n : 0.05	g : 0.05	e : 0.03	= : 0.03	o : 0.03	m : 0.01	a : 0.01	i : 0.01	
m : 0.64	n : 0.11	o : 0.09	l : 0.09	b : 0.01	e : 0.01	c : 0.01	
m : 0.64	l : 0.15	n : 0.11	o : 0.09	
m : 0.64	l : 0.15	n : 0.11	o : 0.09	
m : 0.62	n : 0.11	o : 0.09	c : 0.07	l : 0.05	b : 0.01	d : 0.01	
c : 0.43	b : 0.15	d : 0.11	o : 0.07	n : 0.05	g : 0.05	e : 0.03	= : 0.03	a : 0.01	i : 0.01	
c : 0.47	b : 0.16	d : 0.11	o : 0.05	g : 0.05	e : 0.03	= : 0.03	3 : 0.01	] : 0.01	i : 0.01	
c : 0.47	d : 0.11	3 : 0.07	4 : 0.07	g : 0.07	= : 0.05	b : 0.03	e : 0.03	] : 0.01	2 : 0.01	i : 0.01	
] : 0.16	3 : 0.15	2 : 0.11	c : 0.11	d : 0.11	4 : 0.09	= : 0.07	g : 0.07	e : 0.03	a : 0.03	i : 0.01	
4 : 0.16	3 : 0.15	c : 0.13	2 : 0.13	g : 0.09	= : 0.07	a : 0.05	i : 0.05	e : 0.03	] : 0.03	d : 0.01	f : 0.01	b : 0.01	
4 : 0.18	3 : 0.13	g : 0.11	= : 0.09	b : 0.09	c : 0.07	2 : 0.07	i : 0.05	e : 0.05	] : 0.05	f : 0.03	d : 0.01	
g : 0.16	c : 0.15	b : 0.13	4 : 0.11	= : 0.09	i : 0.07	e : 0.07	3 : 0.05	f : 0.03	2 : 0.03	a : 0.01	d : 0.01	] : 0.01	
g : 0.16	] : 0.13	c : 0.09	= : 0.09	4 : 0.09	e : 0.09	i : 0.07	2 : 0.05	3 : 0.05	b : 0.05	f : 0.03	a : 0.01	d : 0.01	
g : 0.28	e : 0.16	i : 0.11	= : 0.09	2 : 0.09	c : 0.07	f : 0.05	3 : 0.03	] : 0.03	4 : 0.01	d : 0.01	
g : 0.30	e : 0.18	] : 0.09	= : 0.09	i : 0.09	f : 0.05	3 : 0.03	c : 0.03	2 : 0.03	h : 0.01	4 : 0.01	d : 0.01	
g : 0.32	e : 0.13	i : 0.09	c : 0.09	= : 0.07	b : 0.05	] : 0.05	a : 0.03	f : 0.03	d : 0.03	h : 0.01	4 : 0.01	3 : 0.01	
g : 0.33	e : 0.13	c : 0.11	i : 0.09	= : 0.05	h : 0.05	b : 0.05	: : 0.05	f : 0.01	a : 0.01	3 : 0.01	d : 0.01	4 : 0.01	
g : 0.32	e : 0.13	i : 0.09	c : 0.07	h : 0.05	] : 0.05	: : 0.05	3 : 0.05	= : 0.03	4 : 0.03	2 : 0.03	f : 0.01	d : 0.01	

#score	645.0730652677657
#seq	53
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_transcript_m3_run1.txt

#BEAR
=====ppppppp======	chr19:48287537-48287757(+)$1	220	124	142	14.4316
gggggpppppppgggggg	chr1:8419911-8420145(-)$1	234	166	184	14.2965
fffffpppppppffffff	chr19:12811816-12812039(-)$1	223	184	202	13.6080
e[cccpppppppccc]ee	chr8:8688863-8689095(+)$1	232	28	46	14.5101
fffffpppppppffffff	chr12:94169879-94170110(+)$1	231	95	113	13.6080
gggggpppppppgggggg	chr7:38939511-38939761(-)$1	250	226	244	14.2965
!!cccpppppppccc444	chr2:27273609-27273851(+)$1	242	204	222	14.2823
fffffpppppppffffff	chr1:155895649-155895943(-)$1	294	24	42	13.6080
eee[apppppppa]eeee	chr16:579432-579659(+)$1	227	152	170	14.1724
c!!bbpppppppbb22cc	chr15:41022040-41022270(+)$1	230	98	116	13.0330
eeeeepppppppeeeee2	chr10:118362048-118362268(-)$1	220	174	192	14.4415
=====ppppppp======	chr7:48672265-48672505(+)$1	240	19	37	14.4316
eeeeepppppppeeeee:	chrX:108297249-108297599(+)$1	350	196	214	13.7617
fffbbpppppppbb]fff	chr11:66418405-66418624(+)$1	219	30	48	13.1780
[ddddpppppppdddd]c	chr1:196306844-196307065(+)$1	221	177	195	14.0053
eeeeepppppppeeeee]	chr2:220088777-220088997(-)$1	220	89	107	14.6796
[ddddpppppppdddddd	chr7:139025383-139025631(+)$1	248	74	92	13.6887
d[cccpppppppccc]dd	chr7:92007498-92007718(-)$1	220	142	160	14.0680
[ddddpppppppddddee	chr5:139740409-139740641(+)$1	232	33	51	13.9250
f[cccpppppppccc22f	chr4:48399571-48399790(+)$1	219	168	186	14.0079
eeeeepppppppeeeee:	chr9:28450493-28450713(+)$1	220	91	109	13.7617
hh[bbpppppppbbhhhh	chr9:115207147-115207378(-)$1	231	147	165	12.4840
ccc[apppppppa]ccc3	chr17:33478038-33478328(-)$1	290	134	152	13.8969
iii[apppppppa]iiii	chr12:85562628-85562859(-)$1	231	79	97	14.0156
!ddddpppppppdddd33	chr1:154232103-154232329(+)$1	226	36	54	14.0206
gddddpppppppddddee	chr5:141001086-141001312(-)$1	226	87	105	13.8962
gggggpppppppgggggg	chr12:69112961-69113185(+)$1	224	35	53	14.2965
eeeeepppppppeeeee:	chr1:94313029-94313312(+)$1	283	159	177	13.7617
fffffpppppppffffff	chr2:173789680-173789909(+)$1	229	69	87	13.6080
gggggpppppppgggggg	chr5:126793063-126793289(+)$1	226	61	79	14.2965
ff[bbpppppppbbffff	chr10:134373581-134373807(+)$1	226	119	137	13.2410
eeeeepppppppeeeee]	chr9:35724785-35725008(-)$1	223	92	110	14.6796
cc[bbpppppppbb]ccc	chr6:53133040-53133261(-)$1	221	105	123	13.2953
fffffpppppppffffff	chr11:109283508-109283730(+)$1	222	111	129	13.6080
g!!bbpppppppbb22gg	chr16:53860041-53860337(+)$1	296	199	217	13.1661
eddddpppppppdddd:f	chr14:20791366-20791587(-)$1	221	85	103	12.8708
bbcccpppppppccc]bb	chr7:137590441-137590669(-)$1	228	163	181	13.2031
b[cccpppppppcccbbb	chr1:29475586-29475811(-)$1	225	39	57	13.2433
eeeeepppppppeeeeed	chr2:69869948-69870174(-)$1	226	52	70	14.4397
eeeeepppppppeeeee4	chr1:566181-566452(-)$1	271	221	239	14.5957
eeeeepppppppeeeee4	chr1:566106-566379(-)$1	273	148	166	14.5957
gggggpppppppgggggg	chr13:79891584-79891816(-)$1	232	38	56	14.2965
g[cccpppppppccc]gg	chr4:119626673-119626925(-)$1	252	99	117	14.5892
eeeeepppppppeeeee]	chr14:100069677-100069903(-)$1	226	81	99	14.6796
b[cccpppppppccc22b	chr22:26854196-26854433(-)$1	237	18	36	13.5620
cccccpppppppccc]cc	chrX:45605509-45605730(-)$1	221	177	195	14.2788
c[cccpppppppcccccc	chr17:42284588-42284826(-)$1	238	161	179	14.3231
dd[bbpppppppbb]ddd	chr14:103988440-103988659(-)$1	219	10	28	12.9352
[ddddpppppppdddd]a	chr9:36162776-36162999(+)$1	223	197	215	13.9563
eeeeepppppppeeeee]	chr17:4837148-4837368(-)$1	220	20	38	14.6796
!ddddpppppppdddd22	chr12:131357537-131357771(+)$1	234	56	74	13.5746
c[cccpppppppccc]cc	chr4:848267-848501(-)$1	234	27	45	14.4561
eeeeepppppppeeeee:	chr1:149680128-149680380(-)$1	252	146	164	13.7617
fffffpppppppffffff	chr7:72062456-72062680(+)$1	224	75	93	13.6080
cddddpppppppdddd]c	chr10:70091794-70092049(+)$1	255	156	174	13.8957
eeeeepppppppeeeeed	chr11:66115489-66115781(+)$1	292	158	176	14.4397
[ddddpppppppdddda]	chr9:130210680-130210914(-)$1	234	21	39	13.9770
eeeeepppppppeeeeeC	chr17:19764075-19764311(+)$1	236	145	163	13.5897
iiiiipppppppiiiiii	chr15:75940264-75940489(-)$1	225	87	105	14.1663

#otherMatches

#Seq PSSM
GAUUGACGCCCCCGGUCU	chr19:48287537-48287757(+)$1	220	124	142	14.4316
GCCGGGUCCAAGCUGGCC	chr1:8419911-8420145(-)$1	234	166	184	14.2965
GAGGUGGGGGGGACUUCU	chr19:12811816-12812039(-)$1	223	184	202	13.6080
UUGAUCGAAUAAAUCCAA	chr8:8688863-8689095(+)$1	232	28	46	14.5101
gugguccacuguacugcu	chr12:94169879-94170110(+)$1	231	95	113	13.6080
AUGGGGUAUUCACCCAUU	chr7:38939511-38939761(-)$1	250	226	244	14.2965
UAGCAUUCGUACUGCCGU	chr2:27273609-27273851(+)$1	242	204	222	14.2823
UGAAGUUAGUGGUUUUAA	chr1:155895649-155895943(-)$1	294	24	42	13.6080
GGUGUUGUUCAUGGGCCU	chr16:579432-579659(+)$1	227	152	170	14.1724
GAGGAAAUAUCAUCGCCC	chr15:41022040-41022270(+)$1	230	98	116	13.0330
caagcccaacacgcuugu	chr10:118362048-118362268(-)$1	220	174	192	14.4415
ccaggaguaaacccuggg	chr7:48672265-48672505(+)$1	240	19	37	14.4316
ggaguaacuaugacucuc	chrX:108297249-108297599(+)$1	350	196	214	13.7617
ugagcagagauggcauca	chr11:66418405-66418624(+)$1	219	30	48	13.1780
cuucuccauaauagaaug	chr1:196306844-196307065(+)$1	221	177	195	14.0053
CAUUUAUGACGAAGAUGU	chr2:220088777-220088997(-)$1	220	89	107	14.6796
uaauggauaaggcauugg	chr7:139025383-139025631(+)$1	248	74	92	13.6887
guauacugcaaauauucc	chr7:92007498-92007718(-)$1	220	142	160	14.0680
AGUGCCCCCCACGUGCCC	chr5:139740409-139740641(+)$1	232	33	51	13.9250
cuguucagcucuaacuug	chr4:48399571-48399790(+)$1	219	168	186	14.0079
ACUGAAGUAUGAUCAGUC	chr9:28450493-28450713(+)$1	220	91	109	13.7617
gggcuaugaucgagccac	chr9:115207147-115207378(-)$1	231	147	165	12.4840
ucaguaauggcgagugaa	chr17:33478038-33478328(-)$1	290	134	152	13.8969
AUUGAAACAUAGUGAGUG	chr12:85562628-85562859(-)$1	231	79	97	14.0156
AUAGGGAUGACACCUAGA	chr1:154232103-154232329(+)$1	226	36	54	14.0206
UCUCUACCAACAAGAGGA	chr5:141001086-141001312(-)$1	226	87	105	13.8962
AUCCCUUGUAAUGGGAUG	chr12:69112961-69113185(+)$1	224	35	53	14.2965
ccggguucgagucccggc	chr1:94313029-94313312(+)$1	283	159	177	13.7617
acugcaagcuccgcagug	chr2:173789680-173789909(+)$1	229	69	87	13.6080
UUUGGACAUGAACCAGAA	chr5:126793063-126793289(+)$1	226	61	79	14.2965
ugugaaccugugucugca	chr10:134373581-134373807(+)$1	226	119	137	13.2410
UCCGUAUGCUGGAUGGAA	chr9:35724785-35725008(-)$1	223	92	110	14.6796
GUGUAGGGUGAGUAGGCC	chr6:53133040-53133261(-)$1	221	105	123	13.2953
UAGUGGUUAUCACACUAC	chr11:109283508-109283730(+)$1	222	111	129	13.6080
GCAGCAUACAACGUAACU	chr16:53860041-53860337(+)$1	296	199	217	13.1661
UGGUUGGAGUUAAACUUU	chr14:20791366-20791587(-)$1	221	85	103	12.8708
CCCUGUCAAAAUCAGAGG	chr7:137590441-137590669(-)$1	228	163	181	13.2031
CAUGUGACACAAACAGUA	chr1:29475586-29475811(-)$1	225	39	57	13.2433
CUCCGGCUCCAGCGGAGG	chr2:69869948-69870174(-)$1	226	52	70	14.4397
GUGGGUUUAAGUCCCAUU	chr1:566181-566452(-)$1	271	221	239	14.5957
GUGGGUUUAAGUCCCAUU	chr1:566106-566379(-)$1	273	148	166	14.5957
GAGGUAAAAUACACUUUU	chr13:79891584-79891816(-)$1	232	38	56	14.2965
GAAUGAAGUCCCCGUCUG	chr4:119626673-119626925(-)$1	252	99	117	14.5892
gcggcgacgggggccgca	chr14:100069677-100069903(-)$1	226	81	99	14.6796
GAUGGGUAAGAACCAGCC	chr22:26854196-26854433(-)$1	237	18	36	13.5620
AUGUUUCUGAAUAACUGU	chrX:45605509-45605730(-)$1	221	177	195	14.2788
GCAGCAGCUCCAGCUCCU	chr17:42284588-42284826(-)$1	238	161	179	14.3231
UGGACAACCCGGGUACGC	chr14:103988440-103988659(-)$1	219	10	28	12.9352
AUAAAAUACAGCUUUAAG	chr9:36162776-36162999(+)$1	223	197	215	13.9563
UUUUGUGGUAGUUAAAAA	chr17:4837148-4837368(-)$1	220	20	38	14.6796
AGGACCUAUUAAGUUCAA	chr12:131357537-131357771(+)$1	234	56	74	13.5746
cacaaaucaacauugcgg	chr4:848267-848501(-)$1	234	27	45	14.4561
ccggguuuaauucccggu	chr1:149680128-149680380(-)$1	252	146	164	13.7617
uagacacaccucgucuau	chr7:72062456-72062680(+)$1	224	75	93	13.6080
CGGCGUAACUAUCGCCUG	chr10:70091794-70092049(+)$1	255	156	174	13.8957
guggguucgaaucccauc	chr11:66115489-66115781(+)$1	292	158	176	14.4397
ACCAGGUCUCUGUUGGCU	chr9:130210680-130210914(-)$1	234	21	39	13.9770
ccagguucgauuccuggc	chr17:19764075-19764311(+)$1	236	145	163	13.5897
AUGGCGCGGCCAGCCGUC	chr15:75940264-75940489(-)$1	225	87	105	14.1663

#DB
(((((.......))))))	chr19:48287537-48287757(+)$1	1	124	142	14.4316
(((((.......))))))	chr1:8419911-8420145(-)$1	1	166	184	14.2965
(((((.......))))))	chr19:12811816-12812039(-)$1	1	184	202	13.6080
(.(((.......))).))	chr8:8688863-8689095(+)$1	1	28	46	14.5101
(((((.......))))))	chr12:94169879-94170110(+)$1	1	95	113	13.6080
(((((.......))))))	chr7:38939511-38939761(-)$1	1	226	244	14.2965
..(((.......)))...	chr2:27273609-27273851(+)$1	1	204	222	14.2823
(((((.......))))))	chr1:155895649-155895943(-)$1	1	24	42	13.6080
(((.(.......).))))	chr16:579432-579659(+)$1	1	152	170	14.1724
(..((.......))..))	chr15:41022040-41022270(+)$1	1	98	116	13.0330
(((((.......))))).	chr10:118362048-118362268(-)$1	1	174	192	14.4415
(((((.......))))))	chr7:48672265-48672505(+)$1	1	19	37	14.4316
(((((.......))))).	chrX:108297249-108297599(+)$1	1	196	214	13.7617
(((((.......)).)))	chr11:66418405-66418624(+)$1	1	30	48	13.1780
.((((.......)))).)	chr1:196306844-196307065(+)$1	1	177	195	14.0053
(((((.......))))).	chr2:220088777-220088997(-)$1	1	89	107	14.6796
.((((.......))))))	chr7:139025383-139025631(+)$1	1	74	92	13.6887
(.(((.......))).))	chr7:92007498-92007718(-)$1	1	142	160	14.0680
.((((.......))))))	chr5:139740409-139740641(+)$1	1	33	51	13.9250
(.(((.......)))..)	chr4:48399571-48399790(+)$1	1	168	186	14.0079
(((((.......))))).	chr9:28450493-28450713(+)$1	1	91	109	13.7617
((.((.......))))))	chr9:115207147-115207378(-)$1	1	147	165	12.4840
(((.(.......).))).	chr17:33478038-33478328(-)$1	1	134	152	13.8969
(((.(.......).))))	chr12:85562628-85562859(-)$1	1	79	97	14.0156
.((((.......))))..	chr1:154232103-154232329(+)$1	1	36	54	14.0206
)((((.......))))((	chr5:141001086-141001312(-)$1	1	87	105	13.8962
(((((.......))))))	chr12:69112961-69113185(+)$1	1	35	53	14.2965
(((((.......))))).	chr1:94313029-94313312(+)$1	1	159	177	13.7617
(((((.......))))))	chr2:173789680-173789909(+)$1	1	69	87	13.6080
(((((.......))))))	chr5:126793063-126793289(+)$1	1	61	79	14.2965
((.((.......))))))	chr10:134373581-134373807(+)$1	1	119	137	13.2410
(((((.......))))).	chr9:35724785-35725008(-)$1	1	92	110	14.6796
((.((.......)).)))	chr6:53133040-53133261(-)$1	1	105	123	13.2953
(((((.......))))))	chr11:109283508-109283730(+)$1	1	111	129	13.6080
(..((.......))..))	chr16:53860041-53860337(+)$1	1	199	217	13.1661
)((((.......)))).(	chr14:20791366-20791587(-)$1	1	85	103	12.8708
(((((.......))).))	chr7:137590441-137590669(-)$1	1	163	181	13.2031
(.(((.......))))))	chr1:29475586-29475811(-)$1	1	39	57	13.2433
(((((.......)))))(	chr2:69869948-69870174(-)$1	1	52	70	14.4397
(((((.......))))).	chr1:566181-566452(-)$1	1	221	239	14.5957
(((((.......))))).	chr1:566106-566379(-)$1	1	148	166	14.5957
(((((.......))))))	chr13:79891584-79891816(-)$1	1	38	56	14.2965
(.(((.......))).))	chr4:119626673-119626925(-)$1	1	99	117	14.5892
(((((.......))))).	chr14:100069677-100069903(-)$1	1	81	99	14.6796
(.(((.......)))..)	chr22:26854196-26854433(-)$1	1	18	36	13.5620
(((((.......))).))	chrX:45605509-45605730(-)$1	1	177	195	14.2788
(.(((.......))))))	chr17:42284588-42284826(-)$1	1	161	179	14.3231
((.((.......)).)))	chr14:103988440-103988659(-)$1	1	10	28	12.9352
.((((.......)))).)	chr9:36162776-36162999(+)$1	1	197	215	13.9563
(((((.......))))).	chr17:4837148-4837368(-)$1	1	20	38	14.6796
.((((.......))))..	chr12:131357537-131357771(+)$1	1	56	74	13.5746
(.(((.......))).))	chr4:848267-848501(-)$1	1	27	45	14.4561
(((((.......))))).	chr1:149680128-149680380(-)$1	1	146	164	13.7617
(((((.......))))))	chr7:72062456-72062680(+)$1	1	75	93	13.6080
(((((.......)))).)	chr10:70091794-70092049(+)$1	1	156	174	13.8957
(((((.......)))))(	chr11:66115489-66115781(+)$1	1	158	176	14.4397
.((((.......))))).	chr9:130210680-130210914(-)$1	1	21	39	13.9770
(((((.......))))))	chr17:19764075-19764311(+)$1	1	145	163	13.5897
(((((.......))))))	chr15:75940264-75940489(-)$1	1	87	105	14.1663

#PSSM
e : 0.28	f : 0.15	g : 0.13	c : 0.11	[ : 0.08	! : 0.05	b : 0.05	= : 0.03	d : 0.03	i : 0.03	h : 0.01	
e : 0.25	d : 0.18	f : 0.13	[ : 0.13	g : 0.08	! : 0.05	c : 0.05	= : 0.03	i : 0.03	h : 0.01	b : 0.01	
e : 0.25	c : 0.20	d : 0.16	f : 0.11	g : 0.08	[ : 0.06	= : 0.03	! : 0.03	i : 0.03	
e : 0.23	c : 0.18	d : 0.16	b : 0.11	f : 0.10	g : 0.08	[ : 0.05	= : 0.03	i : 0.01	
e : 0.23	c : 0.18	d : 0.16	b : 0.11	f : 0.10	g : 0.08	a : 0.05	= : 0.03	i : 0.01	
p : 0.99	
p : 0.99	
p : 0.99	
p : 0.99	
p : 0.99	
p : 0.99	
p : 0.99	
e : 0.23	c : 0.18	d : 0.16	b : 0.11	f : 0.10	g : 0.08	a : 0.05	= : 0.03	i : 0.01	
e : 0.23	c : 0.18	d : 0.16	b : 0.11	f : 0.10	g : 0.08	] : 0.05	= : 0.03	i : 0.01	
e : 0.25	c : 0.20	d : 0.16	f : 0.11	g : 0.08	] : 0.05	= : 0.03	2 : 0.03	i : 0.03	h : 0.01	
e : 0.25	d : 0.18	f : 0.13	] : 0.10	g : 0.08	2 : 0.06	c : 0.05	= : 0.03	i : 0.03	4 : 0.01	h : 0.01	b : 0.01	
e : 0.30	f : 0.13	g : 0.11	c : 0.10	] : 0.05	d : 0.05	2 : 0.05	= : 0.03	i : 0.03	b : 0.03	4 : 0.01	h : 0.01	3 : 0.01	: : 0.01	a : 0.01	
f : 0.16	g : 0.11	c : 0.11	] : 0.08	d : 0.08	e : 0.06	: : 0.06	4 : 0.05	b : 0.05	= : 0.03	2 : 0.03	3 : 0.03	i : 0.03	h : 0.01	a : 0.01	C : 0.01	

#score	821.7816612990347
#seq	59
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_CDS_m3_run2.txt

#BEAR
eeeeyyyyyyyyyyyyyyyyeeeeef	chr17:3436046-3436272(-)$1	226	68	94	19.6832
ccc[cccvvvvvvvvvvvvvccc]cc	chr7:75695505-75695736(+)$1	231	54	80	22.8497
eeeeeyyyyyyyyyyyyyyyyeeeee	chr17:38554768-38554992(-)$1	224	109	135	20.5758
"ggggggguuuuuuuuuuuugggggg	chr3:121500534-121500767(-)$1	233	44	70	23.5160
b[bbcccxxxxxxxxxxxxxxxccc]	chr14:21979243-21979462(+)$1	219	132	158	17.0750
!ddddbbbbtttttttttttbb]bb]	chr18:33557380-33557606(+)$1	226	118	144	20.9844
!bb[eeeeettttttttttteeeee]	chr10:75832457-75832686(+)$1	229	88	114	22.5253
ccc!!ddddtttttttttttdddd]c	chr9:35062172-35062391(-)$1	219	140	166	22.5550
dd"""ddddvvvvvvvvvvvvvdddd	chr4:1820976-1821205(-)$1	229	103	129	21.3871
b[ffffffuuuuuuuuuuuuffffff	chr4:119626667-119626931(+)$1	264	106	132	22.2057
d[gggggggtttttttttttgggggg	chr15:40998302-40998551(-)$1	249	190	216	23.1129
##ffffffattttttttttta]ffff	chr19:3984099-3984352(-)$1	253	193	219	22.6199
c!!cccyyyyyyyyyyyyyyyyccc2	chr4:119625032-119625307(-)$1	275	193	219	21.5864
!!gggggggvvvvvvvvvvvvvgggg	chr2:217364575-217364834(+)$1	259	82	108	23.1308
ppcccddddtttttttttttdddd:F	chrX:53432088-53432326(-)$1	238	80	106	19.2897
eeee[ddddtttttttttttddddee	chr12:7044651-7044873(+)$1	222	85	111	22.1476
eeeee[cccvvvvvvvvvvvvvccc]	chr15:41022040-41022270(+)$1	230	157	183	22.7108
ggggg[cccvvvvvvvvvvvvvccc]	chr6:31630195-31630419(-)$1	224	141	167	23.2706
c[bb[cccwwwwwwwwwwwwwwccc]	chr5:180687234-180687468(-)$1	234	92	118	22.4165
ffffff[bbtttttttttttbb333f	chr14:21968957-21969221(-)$1	264	74	100	21.7611
[ddddddddtttttttttttdddd22	chr17:7476752-7476976(+)$1	224	101	127	21.6804
CCgggggggtttttttttttgggggg	chr16:15703423-15703642(-)$1	219	19	45	21.0659
##cccyyyyyyyyyyyyyyyyccc22	chr14:99976950-99977172(+)$1	222	95	121	21.0292
gggggggvvvvvvvvvvvvvgggggg	chr6:43591613-43591838(-)$1	225	29	55	23.0613
hhhhhhh[awwwwwwwwwwwwwwa]h	chr5:180670670-180670898(-)$1	228	28	54	20.1116
b!!ccc[bbtttttttttttbb]ccc	chr6:22570244-22570465(+)$1	221	22	48	22.3549
ffffff[bbtttttttttttbb333f	chr14:21969023-21969364(-)$1	341	217	243	21.7611
ccc!!cccuuuuuuuuuuuucccccc	chr3:183273314-183273536(-)$1	222	4	30	23.5104
$$$ddddvvvvvvvvvvvvvddddee	chr4:119615517-119615749(-)$1	232	86	112	21.4801
hhhhhhhhvvvvvvvvvvvvvhhhhh	chr14:21966350-21966595(-)$1	245	3	29	20.9565
gggggggwwwwwwwwwwwwwwggggg	chr4:119624998-119625243(+)$1	245	14	40	22.7396
::::eeeeettttttttttteeeeeF	chr1:165667589-165667811(-)$1	222	190	216	18.7451
dd::eeeeevvvvvvvvvvvvveeee	chr19:50311852-50312075(+)$1	223	103	129	20.1026
!!gggggggvvvvvvvvvvvvvgggg	chr2:100938421-100938642(+)$1	221	39	65	23.1308
::gggggggtttttttttttgggggg	chr4:119610423-119610712(+)$1	289	207	233	21.4932
ccc!!dddduuuuuuuuuuuudddd2	chr7:98507819-98508046(+)$1	227	108	134	22.6599
:ffffffvvvvvvvvvvvvvffffff	chr4:119613036-119613325(+)$1	289	0	26	21.0444
b[bb[bbvvvvvvvvvvvvvbb]bb]	chr2:232326262-232326527(-)$1	265	95	121	21.2196
::::eeeeettttttttttteeeeei	chr16:53843950-53844207(+)$1	257	115	141	19.1792
gggg[ddddtttttttttttddddgg	chr11:6703432-6703659(-)$1	227	63	89	22.8339
eeeee[aauuuuuuuuuuuua]a]ee	chr1:35653509-35653790(-)$1	281	93	119	22.9571
ddddeeeeettttttttttteeeee]	chr1:156280660-156280912(-)$1	252	28	54	22.2437
eeeee!!avvvvvvvvvvvvva22ee	chr5:180670212-180670478(-)$1	266	27	53	22.4052
a[ddddxxxxxxxxxxxxxxxdddd]	chr1:19557250-19557489(+)$1	239	123	149	16.6201
ggggeeeeeuuuuuuuuuuuueeeee	chr6:135787057-135787284(-)$1	227	160	186	22.8633
ggggggxxxxxxxxxxxxxxxggggg	chr3:12458207-12458441(+)$1	234	88	114	17.4705
ccc"""cccuuuuuuuuuuuuccc33	chr16:2139853-2140072(-)$1	219	111	137	23.2826
!a[bb[ccctttttttttttccc]bb	chr2:105471944-105472164(+)$1	220	146	172	22.1747
:ggggggguuuuuuuuuuuugggggg	chr1:183520115-183520345(+)$1	230	89	115	22.7245
gggggggwwwwwwwwwwwwwwggggg	chr1:155234410-155234634(-)$1	224	35	61	22.7396
!!ccc[cccvvvvvvvvvvvvvccc]	chr1:1413986-1414216(+)$1	230	86	112	23.3895
ffffffwwwwwwwwwwwwwwffffff	chr4:119613034-119613323(-)$1	289	165	191	20.6276

#otherMatches

#Seq PSSM
GCACCAACCAGCCCGAGAUUGUGCAG	chr17:3436046-3436272(-)$1	226	68	94	19.6832
UGGAAACUUCAUUUUAACAUGUUCCC	chr7:75695505-75695736(+)$1	231	54	80	22.8497
UGGACACAUUAAAAAGAAAGAGUCCA	chr17:38554768-38554992(-)$1	224	109	135	20.5758
AGGCGCUUAAAUUCCUAGCGAAGUGC	chr3:121500534-121500767(-)$1	233	44	70	23.5160
CAGCCCUGACACCUCUCGAAUAAGGC	chr14:21979243-21979462(+)$1	219	132	158	17.0750
AGGACUGCAAACCCAAAUCAUGACAU	chr18:33557380-33557606(+)$1	226	118	144	20.9844
GCACCGAGUGAUGUUGGUGAACUCGA	chr10:75832457-75832686(+)$1	229	88	114	22.5253
UUGAUGAGCUAGAUGCCAUCGCUCCC	chr9:35062172-35062391(-)$1	219	140	166	22.5550
UGGAGCUGCUGAAGGAGGAUGUGCAG	chr4:1820976-1821205(-)$1	229	103	129	21.3871
CCUCAUGGGGAUCAAAGGAACUGUGA	chr4:119626667-119626931(+)$1	264	106	132	22.2057
GAAAUAUUAAAUCAACAAAAUAAUAU	chr15:40998302-40998551(-)$1	249	190	216	23.1129
GAGCGUUGCAUCACCAUCAAGUCAAC	chr19:3984099-3984352(-)$1	253	193	219	22.6199
UUCUGUAACCCCAUUUUCGUAAACAC	chr4:119625032-119625307(-)$1	275	193	219	21.5864
GUUCUCUUUUAUAGACCAAGAUGAAG	chr2:217364575-217364834(+)$1	259	82	108	23.1308
ACGGCGCUGGGAUGAGAAAGCAGUAG	chrX:53432088-53432326(-)$1	238	80	106	19.2897
UCCGAUCUGGAUAGCUUGGACGGGCG	chr12:7044651-7044873(+)$1	222	85	111	22.1476
UCUUUUCGGAAUGUCAUAUUAACUGU	chr15:41022040-41022270(+)$1	230	157	183	22.7108
AGGGCCGUGCCAAUCCCAUCCCCACU	chr6:31630195-31630419(-)$1	224	141	167	23.2706
GUCUACCGAGAAGAAGAAAUACUGGA	chr5:180687234-180687468(-)$1	234	92	118	22.4165
CCUGGCAGCAAAGACCACACGCCAAG	chr14:21968957-21969221(-)$1	264	74	100	21.7611
GAGCGGCCUGAGGUAUGGGAGGGCGA	chr17:7476752-7476976(+)$1	224	101	127	21.6804
GAAAAAAACUGUGAUUUUAUGUUUUU	chr16:15703423-15703642(-)$1	219	19	45	21.0659
CUGUGCCCCCGCCCAUUCCCCCACCC	chr14:99976950-99977172(+)$1	222	95	121	21.0292
ACAGUGUCACCCCCAUCUUCACAUUG	chr6:43591613-43591838(-)$1	225	29	55	23.0613
UGGUGCUAGUUUCUCUAAGCCAUCCA	chr5:180670670-180670898(-)$1	228	28	54	20.1116
GACGCCCCCAAACGACCCAAGGAGGC	chr6:22570244-22570465(+)$1	221	22	48	22.3549
CCUGGCAGCAAAGACCACACGCCAAG	chr14:21969023-21969364(-)$1	341	217	243	21.7611
CAGCUGGUGAUAAGUGGAGGGCCCUG	chr3:183273314-183273536(-)$1	222	4	30	23.5104
UUAGCUAUUAACUCAUCCUUUAGCCU	chr4:119615517-119615749(-)$1	232	86	112	21.4801
UUUGGUAUGCAUUUUUUAACAAUAUU	chr14:21966350-21966595(-)$1	245	3	29	20.9565
UAAUGCUGGUUGUUAUUGUUAAGUAU	chr4:119624998-119625243(+)$1	245	14	40	22.7396
GCAACCGGUAACUGCAACGAGCCGGG	chr1:165667589-165667811(-)$1	222	190	216	18.7451
CCUCCAUCCGAGCCCUACCCGAGGAU	chr19:50311852-50312075(+)$1	223	103	129	20.1026
UCGUCGCCCUCCUCUAAGCGCUGGGC	chr2:100938421-100938642(+)$1	221	39	65	23.1308
AAGUUUAUGGUCAAAGAAAACAUAAA	chr4:119610423-119610712(+)$1	289	207	233	21.4932
GACAAGGAAGACAAGCAGACAUUCCA	chr7:98507819-98508046(+)$1	227	108	134	22.6599
GAUUGCAUUUUAUAUCACCUUGUAAU	chr4:119613036-119613325(+)$1	289	0	26	21.0444
CAGugaugaagaggaggaugaugaca	chr2:232326262-232326527(-)$1	265	95	121	21.2196
UGAAGAGCUUGAAGACACUUGGCUCC	chr16:53843950-53844207(+)$1	257	115	141	19.1792
CCCCUCGGUACAAAGAUCAAACUGGG	chr11:6703432-6703659(-)$1	227	63	89	22.8339
UUCUAGGCAAGAGGAGGAACGACGUA	chr1:35653509-35653790(-)$1	281	93	119	22.9571
CAUGCCUUGACAGAAAAAUCCAAGGC	chr1:156280660-156280912(-)$1	252	28	54	22.2437
GGAGAGUUGGAAACUUUUAAAAUAUC	chr5:180670212-180670478(-)$1	266	27	53	22.4052
UGCAUCCACCAAAUAGAAGAAGAUGG	chr1:19557250-19557489(+)$1	239	123	149	16.6201
CAGUGCCAUGUAACUGAAGAAAUGGC	chr6:135787057-135787284(-)$1	227	160	186	22.8633
GUGGCCAUCCGCAUCUUUCAGGGCUG	chr3:12458207-12458441(+)$1	234	88	114	17.4705
GACCGACUCAACCAGGCCACAGAGGA	chr16:2139853-2140072(-)$1	219	111	137	23.2826
gggcggcgcagggggcgggggcggcg	chr2:105471944-105472164(+)$1	220	146	172	22.1747
UCUCUCAGCAACGUCAUCCUCUGAGA	chr1:183520115-183520345(+)$1	230	89	115	22.7245
GCAGAGGUUCAUCCUCUUUCUCCUCU	chr1:155234410-155234634(-)$1	224	35	61	22.7396
AGGCUGAGGAGAGGAGGAAGACCCUG	chr1:1413986-1414216(+)$1	230	86	112	23.3895
UGGGGAUUUAAGCUCUGUGUUCCCUA	chr4:119613034-119613323(-)$1	289	165	191	20.6276

#DB
((((................))))))	chr17:3436046-3436272(-)$1	1	68	94	19.6832
(((.(((.............))).))	chr7:75695505-75695736(+)$1	1	54	80	22.8497
(((((................)))))	chr17:38554768-38554992(-)$1	1	109	135	20.5758
.(((((((............))))))	chr3:121500534-121500767(-)$1	1	44	70	23.5160
(.(((((...............))).	chr14:21979243-21979462(+)$1	1	132	158	17.0750
.((((((((...........)).)).	chr18:33557380-33557606(+)$1	1	118	144	20.9844
.((.(((((...........))))).	chr10:75832457-75832686(+)$1	1	88	114	22.5253
(((..((((...........)))).)	chr9:35062172-35062391(-)$1	1	140	166	22.5550
((...((((.............))))	chr4:1820976-1821205(-)$1	1	103	129	21.3871
(.((((((............))))))	chr4:119626667-119626931(+)$1	1	106	132	22.2057
(.(((((((...........))))))	chr15:40998302-40998551(-)$1	1	190	216	23.1129
..(((((((...........).))))	chr19:3984099-3984352(-)$1	1	193	219	22.6199
(..(((................))).	chr4:119625032-119625307(-)$1	1	193	219	21.5864
..(((((((.............))))	chr2:217364575-217364834(+)$1	1	82	108	23.1308
..)))((((...........)))).(	chrX:53432088-53432326(-)$1	1	80	106	19.2897
((((.((((...........))))))	chr12:7044651-7044873(+)$1	1	85	111	22.1476
(((((.(((.............))).	chr15:41022040-41022270(+)$1	1	157	183	22.7108
(((((.(((.............))).	chr6:31630195-31630419(-)$1	1	141	167	23.2706
(.((.(((..............))).	chr5:180687234-180687468(-)$1	1	92	118	22.4165
((((((.((...........))...)	chr14:21968957-21969221(-)$1	1	74	100	21.7611
.((((((((...........))))..	chr17:7476752-7476976(+)$1	1	101	127	21.6804
(((((((((...........))))))	chr16:15703423-15703642(-)$1	1	19	45	21.0659
..(((................)))..	chr14:99976950-99977172(+)$1	1	95	121	21.0292
(((((((.............))))))	chr6:43591613-43591838(-)$1	1	29	55	23.0613
(((((((.(..............).)	chr5:180670670-180670898(-)$1	1	28	54	20.1116
(..(((.((...........)).)))	chr6:22570244-22570465(+)$1	1	22	48	22.3549
((((((.((...........))...)	chr14:21969023-21969364(-)$1	1	217	243	21.7611
(((..(((............))))))	chr3:183273314-183273536(-)$1	1	4	30	23.5104
...((((.............))))))	chr4:119615517-119615749(-)$1	1	86	112	21.4801
((((((((.............)))))	chr14:21966350-21966595(-)$1	1	3	29	20.9565
(((((((..............)))))	chr4:119624998-119625243(+)$1	1	14	40	22.7396
....(((((...........))))))	chr1:165667589-165667811(-)$1	1	190	216	18.7451
))..(((((.............))))	chr19:50311852-50312075(+)$1	1	103	129	20.1026
..(((((((.............))))	chr2:100938421-100938642(+)$1	1	39	65	23.1308
..(((((((...........))))))	chr4:119610423-119610712(+)$1	1	207	233	21.4932
(((..((((............)))).	chr7:98507819-98508046(+)$1	1	108	134	22.6599
.((((((.............))))))	chr4:119613036-119613325(+)$1	1	0	26	21.0444
(.((.((.............)).)).	chr2:232326262-232326527(-)$1	1	95	121	21.2196
....(((((...........)))))(	chr16:53843950-53844207(+)$1	1	115	141	19.1792
((((.((((...........))))))	chr11:6703432-6703659(-)$1	1	63	89	22.8339
(((((.((............).).))	chr1:35653509-35653790(-)$1	1	93	119	22.9571
(((((((((...........))))).	chr1:156280660-156280912(-)$1	1	28	54	22.2437
(((((..(.............)..))	chr5:180670212-180670478(-)$1	1	27	53	22.4052
(.((((...............)))).	chr1:19557250-19557489(+)$1	1	123	149	16.6201
))))(((((............)))))	chr6:135787057-135787284(-)$1	1	160	186	22.8633
((((((...............)))))	chr3:12458207-12458441(+)$1	1	88	114	17.4705
(((...(((............)))..	chr16:2139853-2140072(-)$1	1	111	137	23.2826
.(.((.(((...........))).))	chr2:105471944-105472164(+)$1	1	146	172	22.1747
.(((((((............))))))	chr1:183520115-183520345(+)$1	1	89	115	22.7245
(((((((..............)))))	chr1:155234410-155234634(-)$1	1	35	61	22.7396
..(((.(((.............))).	chr1:1413986-1414216(+)$1	1	86	112	23.3895
((((((..............))))))	chr4:119613034-119613323(-)$1	1	165	191	20.6276

#PSSM
c : 0.13	g : 0.13	e : 0.11	! : 0.11	: : 0.09	b : 0.07	d : 0.07	f : 0.05	# : 0.03	h : 0.03	" : 0.01	p : 0.01	[ : 0.01	C : 0.01	$ : 0.01	a : 0.01	
g : 0.17	e : 0.11	[ : 0.11	c : 0.09	d : 0.09	! : 0.09	f : 0.07	: : 0.05	# : 0.03	h : 0.03	b : 0.01	p : 0.01	C : 0.01	$ : 0.01	a : 0.01	
g : 0.26	c : 0.15	e : 0.11	f : 0.11	b : 0.07	d : 0.07	: : 0.05	! : 0.03	h : 0.03	" : 0.01	$ : 0.01	[ : 0.01	
g : 0.26	e : 0.11	f : 0.11	d : 0.09	c : 0.09	b : 0.07	! : 0.05	: : 0.05	[ : 0.03	" : 0.03	h : 0.03	
g : 0.23	e : 0.19	c : 0.13	f : 0.11	d : 0.07	[ : 0.07	! : 0.05	" : 0.03	h : 0.03	y : 0.01	b : 0.01	
g : 0.21	d : 0.17	c : 0.11	e : 0.11	f : 0.11	[ : 0.09	y : 0.05	b : 0.03	h : 0.03	! : 0.01	" : 0.01	
g : 0.19	c : 0.17	d : 0.15	e : 0.11	y : 0.07	f : 0.05	[ : 0.05	b : 0.03	h : 0.03	x : 0.03	a : 0.01	! : 0.01	w : 0.01	
g : 0.13	d : 0.13	c : 0.13	e : 0.11	v : 0.09	y : 0.07	b : 0.07	x : 0.05	w : 0.05	f : 0.03	a : 0.03	[ : 0.01	h : 0.01	
v : 0.13	d : 0.13	e : 0.11	u : 0.09	g : 0.09	c : 0.09	y : 0.07	b : 0.07	w : 0.07	x : 0.05	a : 0.03	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
t : 0.34	v : 0.26	u : 0.15	w : 0.09	y : 0.07	x : 0.05	
v : 0.17	g : 0.11	d : 0.11	e : 0.09	b : 0.09	w : 0.07	c : 0.05	y : 0.05	x : 0.05	f : 0.05	u : 0.05	a : 0.03	
g : 0.17	d : 0.15	e : 0.13	v : 0.13	c : 0.09	b : 0.09	f : 0.05	] : 0.03	w : 0.03	x : 0.01	y : 0.01	h : 0.01	a : 0.01	
c : 0.21	g : 0.21	d : 0.17	e : 0.15	f : 0.07	] : 0.05	3 : 0.03	w : 0.01	h : 0.01	a : 0.01	2 : 0.01	
g : 0.21	c : 0.19	d : 0.17	e : 0.15	f : 0.07	] : 0.05	b : 0.03	3 : 0.03	a : 0.01	h : 0.01	2 : 0.01	
e : 0.23	g : 0.23	c : 0.17	f : 0.07	b : 0.05	d : 0.05	3 : 0.05	] : 0.03	2 : 0.03	: : 0.01	h : 0.01	
g : 0.23	] : 0.19	f : 0.13	e : 0.13	c : 0.07	2 : 0.07	F : 0.03	h : 0.03	d : 0.01	i : 0.01	3 : 0.01	b : 0.01	

#score	1125.0644021438848
#seq	52
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_UTR_m3_run1.txt

#BEAR
eeeeennnnneeee	chr7:63985200-63985401(-)$1	201	70	84	9.2767
eeeeemmmmeeeee	chr17:80407035-80407236(-)$1	201	56	70	10.4854
!eeeeellleeeee	chr3:20012032-20012233(+)$1	201	118	132	10.1545
eeeeemmmmeeeee	chr1:91966347-91966548(+)$1	201	115	129	10.4854
:eeeeellleeeee	chr17:37564162-37564363(-)$1	201	8	22	9.1303
eeeeellleeeee4	chr3:9876276-9876477(+)$1	201	154	168	9.1118
eeeeennnnneeee	chrX:131208108-131208309(+)$1	201	150	164	9.2767
eeeeennnnneeee	chr7:112090592-112090793(+)$1	201	92	106	9.2767
:eeeeellleeeee	chr10:51026531-51026732(-)$1	201	164	178	9.1303
eeeeennnnneeee	chr1:171454705-171454906(+)$1	201	107	121	9.2767
[eeeeellleeeee	chr3:47870434-47870635(+)$1	201	29	43	10.1625
eeeeemmmmeeeee	chr17:7489244-7489445(+)$1	201	155	169	10.4854
eeeeemmmmeeeee	chr16:142619-142820(-)$1	201	85	99	10.4854
eeeeemmmmeeeee	chr7:132470162-132470363(-)$1	201	2	16	10.4854
#eeeeellleeeee	chr10:102721592-102721793(+)$1	201	56	70	9.9978
eeeeemmmmeeeee	chr16:66852386-66852587(-)$1	201	168	182	10.4854
eeeeennnnneeee	chr19:37441990-37442191(+)$1	201	94	108	9.2767
eeeeemmmmeeeee	chr1:242012368-242012569(+)$1	201	148	162	10.4854
eeeeemmmmeeeee	chr1:19444277-19444478(-)$1	201	84	98	10.4854
eeeeemmmmeeeee	chr6:41066535-41066736(+)$1	201	48	62	10.4854
eeeeellleeeee]	chr2:242033389-242033590(-)$1	201	74	88	9.1456
eeeeellleeeee]	chr1:86851125-86851326(-)$1	201	111	125	9.1456
:eeeeellleeeee	chr17:35444215-35444416(-)$1	201	40	54	9.1303
eeeeemmmmeeeee	chr18:25727602-25727803(-)$1	201	171	185	10.4854
[eeeeellleeeee	chr8:42935049-42935250(+)$1	201	178	192	10.1625
eeeeeooooooeee	chr2:27820880-27821081(+)$1	201	42	56	8.9531
[eeeeellleeeee	chr7:26230579-26230780(-)$1	201	80	94	10.1625
eeeeemmmmeeeee	chr17:35804708-35804909(+)$1	201	161	175	10.4854
eeeeeellleeeee	chr20:62367468-62367669(+)$1	201	110	124	10.4486
eeeeemmmmeeeee	chr17:16046829-16047030(-)$1	201	36	50	10.4854
:eeeeellleeeee	chr4:113567702-113567903(+)$1	201	149	163	9.1303
eeeeennnnneeee	chr5:112337232-112337433(+)$1	201	99	113	9.2767
eeeeeooooooeee	chr19:7978835-7979036(+)$1	201	171	185	8.9531
'eeeeellleeeee	chr17:78184588-78184789(-)$1	201	155	169	9.4356
eeeeennnnneeee	chr19:14674915-14675116(+)$1	201	27	41	9.2767
[eeeeellleeeee	chr11:134126347-134126548(+)$1	201	33	47	10.1625
eeeeemmmmeeeee	chr14:73637514-73637715(+)$1	201	47	61	10.4854
eeeeemmmmeeeee	chr3:160117751-160117952(+)$1	201	124	138	10.4854
eeeeemmmmeeeee	chr10:120442140-120442341(-)$1	201	63	77	10.4854
eeeeeooooooeee	chr12:57627748-57627949(+)$1	201	25	39	8.9531
eeeeemmmmeeeee	chr11:93534936-93535137(+)$1	201	99	113	10.4854
eeeeemmmmeeeee	chr15:75137060-75137261(-)$1	201	7	21	10.4854
eee[ammmma]eee	chr16:2285984-2286185(-)$1	201	107	121	8.1654
eeeeemmmmeeeee	chr3:196202035-196202236(-)$1	201	134	148	10.4854
eeeeemmmmeeeee	chr19:52496296-52496497(-)$1	201	109	123	10.4854
eeeeennnnneeee	chr10:75531627-75531828(+)$1	201	21	35	9.2767
"eeeeellleeeee	chr19:16515381-16515582(-)$1	201	63	77	10.0097
eeeeemmmmeeeee	chr3:52598030-52598231(-)$1	201	101	115	10.4854
[eeeeellleeeee	chr1:20235854-20236055(+)$1	201	132	146	10.1625
eeeeeooooooeee	chr16:30768760-30768961(+)$1	201	91	105	8.9531
eeeeennnnneeee	chr11:66411612-66411813(+)$1	201	178	192	9.2767
eeeeeooooooeee	chr12:76749528-76749729(-)$1	201	21	35	8.9531
[eeeeellleeeee	chr2:109429205-109429406(+)$1	201	121	135	10.1625
eeeeemmmmeeeee	chr7:151052894-151053095(+)$1	201	145	159	10.4854
eeeeemmmmeeeee	chr17:45759757-45759958(+)$1	201	0	14	10.4854
[eeeeellleeeee	chr19:4501807-4502008(+)$1	201	121	135	10.1625
eeeeemmmmeeeee	chr19:15469697-15469898(-)$1	201	125	139	10.4854
eeeeemmmmeeeee	chr19:19467213-19467414(+)$1	201	33	47	10.4854
eeeeemmmmeeeee	chr1:6681784-6681985(+)$1	201	12	26	10.4854

#otherMatches

#Seq PSSM
aagauuaauuauuu	chr7:63985200-63985401(-)$1	201	70	84	9.2767
GUCUGUUCCCAGAC	chr17:80407035-80407236(-)$1	201	56	70	10.4854
augguucuuagcca	chr3:20012032-20012233(+)$1	201	118	132	10.1545
CCCAGGCAUCUGGG	chr1:91966347-91966548(+)$1	201	115	129	10.4854
UUCUUCUAAGAAGA	chr17:37564162-37564363(-)$1	201	8	22	9.1303
AGGGCCAGGUCCUC	chr3:9876276-9876477(+)$1	201	154	168	9.1118
GCUUAACCCAUGAG	chrX:131208108-131208309(+)$1	201	150	164	9.2767
CAGCUCCAUCGGCU	chr7:112090592-112090793(+)$1	201	92	106	9.2767
GGUGCUUGAGGCAU	chr10:51026531-51026732(-)$1	201	164	178	9.1303
UCUUUCGAUCAGAG	chr1:171454705-171454906(+)$1	201	107	121	9.2767
ACUCUAGUCUGGAG	chr3:47870434-47870635(+)$1	201	29	43	10.1625
AGGGGCCCACCCUU	chr17:7489244-7489445(+)$1	201	155	169	10.4854
ACCUGCCUGCAGGU	chr16:142619-142820(-)$1	201	85	99	10.4854
UUCCAGAGAUGGAA	chr7:132470162-132470363(-)$1	201	2	16	10.4854
UUCUGGGUACCAGA	chr10:102721592-102721793(+)$1	201	56	70	9.9978
GUGUGACCUUACAU	chr16:66852386-66852587(-)$1	201	168	182	10.4854
acuuuguuaaaagg	chr19:37441990-37442191(+)$1	201	94	108	9.2767
GGGUAAAGCUGCCU	chr1:242012368-242012569(+)$1	201	148	162	10.4854
GGCUUAGUGGAGUU	chr1:19444277-19444478(-)$1	201	84	98	10.4854
AGAAAUCUAUUUCU	chr6:41066535-41066736(+)$1	201	48	62	10.4854
CACUGUGCCAGUGU	chr2:242033389-242033590(-)$1	201	74	88	9.1456
GAGUUGGUAACUCA	chr1:86851125-86851326(-)$1	201	111	125	9.1456
AGCUUGGUCCAGGC	chr17:35444215-35444416(-)$1	201	40	54	9.1303
UAUCUCAAAAGAUA	chr18:25727602-25727803(-)$1	201	171	185	10.4854
cguugugaaaugac	chr8:42935049-42935250(+)$1	201	178	192	10.1625
UGUUGUAUUAGUAG	chr2:27820880-27821081(+)$1	201	42	56	8.9531
AAAGUGCUUCAUUU	chr7:26230579-26230780(-)$1	201	80	94	10.1625
GGUAACAGUUUAUU	chr17:35804708-35804909(+)$1	201	161	175	10.4854
GGGCCUAGGAGGCC	chr20:62367468-62367669(+)$1	201	110	124	10.4486
GCUGGUCUUUCAGC	chr17:16046829-16047030(-)$1	201	36	50	10.4854
AGUCAGAAACUGGC	chr4:113567702-113567903(+)$1	201	149	163	9.1303
CUGGUAGCACGCCG	chr5:112337232-112337433(+)$1	201	99	113	9.2767
GGGCCAGCACAGGC	chr19:7978835-7979036(+)$1	201	171	185	8.9531
AUGCGCUCCGUGCA	chr17:78184588-78184789(-)$1	201	155	169	9.4356
GGCAGAAGACCUGC	chr19:14674915-14675116(+)$1	201	27	41	9.2767
GCAACACCUUGUUG	chr11:134126347-134126548(+)$1	201	33	47	10.1625
CCAUUAUCUAAUGG	chr14:73637514-73637715(+)$1	201	47	61	10.4854
UCAGCCUUCGCUGG	chr3:160117751-160117952(+)$1	201	124	138	10.4854
CAGUGCUCACACUG	chr10:120442140-120442341(-)$1	201	63	77	10.4854
GCCUCGUUCCAGGG	chr12:57627748-57627949(+)$1	201	25	39	8.9531
UUGAGGAUCCUCAG	chr11:93534936-93535137(+)$1	201	99	113	10.4854
GGGAAUUUUUUCCC	chr15:75137060-75137261(-)$1	201	7	21	10.4854
GCAUCUCCUGCUGC	chr16:2285984-2286185(-)$1	201	107	121	8.1654
GGUAUGUUGAUACU	chr3:196202035-196202236(-)$1	201	134	148	10.4854
AGGAAAGACUUCCU	chr19:52496296-52496497(-)$1	201	109	123	10.4854
CCCGGGGUUGUUGG	chr10:75531627-75531828(+)$1	201	21	35	9.2767
GGAGCUCGAGGCUC	chr19:16515381-16515582(-)$1	201	63	77	10.0097
UUCAAAGGAUUGAA	chr3:52598030-52598231(-)$1	201	101	115	10.4854
GCCUUACUCUAAGG	chr1:20235854-20236055(+)$1	201	132	146	10.1625
GCAGUCAACUUGCU	chr16:30768760-30768961(+)$1	201	91	105	8.9531
UGGCCCUCAUGGCU	chr11:66411612-66411813(+)$1	201	178	192	9.2767
GAUUUUGCUUCAAG	chr12:76749528-76749729(-)$1	201	21	35	8.9531
GUUCAUGAAAUGAA	chr2:109429205-109429406(+)$1	201	121	135	10.1625
CCCAGAGCUCUGGG	chr7:151052894-151053095(+)$1	201	145	159	10.4854
AUCUGUUUUCAGAU	chr17:45759757-45759958(+)$1	201	0	14	10.4854
ACGGGAGGGUCCCG	chr19:4501807-4502008(+)$1	201	121	135	10.1625
GUGCUUGCAAGUAC	chr19:15469697-15469898(-)$1	201	125	139	10.4854
UGCAGGUGAUUGUA	chr19:19467213-19467414(+)$1	201	33	47	10.4854
GGCAGAUCCCUGCC	chr1:6681784-6681985(+)$1	201	12	26	10.4854

#DB
(((((.....))))	chr7:63985200-63985401(-)$1	1	70	84	9.2767
(((((....)))))	chr17:80407035-80407236(-)$1	1	56	70	10.4854
.(((((...)))))	chr3:20012032-20012233(+)$1	1	118	132	10.1545
(((((....)))))	chr1:91966347-91966548(+)$1	1	115	129	10.4854
.(((((...)))))	chr17:37564162-37564363(-)$1	1	8	22	9.1303
(((((...))))).	chr3:9876276-9876477(+)$1	1	154	168	9.1118
(((((.....))))	chrX:131208108-131208309(+)$1	1	150	164	9.2767
(((((.....))))	chr7:112090592-112090793(+)$1	1	92	106	9.2767
.(((((...)))))	chr10:51026531-51026732(-)$1	1	164	178	9.1303
(((((.....))))	chr1:171454705-171454906(+)$1	1	107	121	9.2767
.(((((...)))))	chr3:47870434-47870635(+)$1	1	29	43	10.1625
(((((....)))))	chr17:7489244-7489445(+)$1	1	155	169	10.4854
(((((....)))))	chr16:142619-142820(-)$1	1	85	99	10.4854
(((((....)))))	chr7:132470162-132470363(-)$1	1	2	16	10.4854
.(((((...)))))	chr10:102721592-102721793(+)$1	1	56	70	9.9978
(((((....)))))	chr16:66852386-66852587(-)$1	1	168	182	10.4854
(((((.....))))	chr19:37441990-37442191(+)$1	1	94	108	9.2767
(((((....)))))	chr1:242012368-242012569(+)$1	1	148	162	10.4854
(((((....)))))	chr1:19444277-19444478(-)$1	1	84	98	10.4854
(((((....)))))	chr6:41066535-41066736(+)$1	1	48	62	10.4854
(((((...))))).	chr2:242033389-242033590(-)$1	1	74	88	9.1456
(((((...))))).	chr1:86851125-86851326(-)$1	1	111	125	9.1456
.(((((...)))))	chr17:35444215-35444416(-)$1	1	40	54	9.1303
(((((....)))))	chr18:25727602-25727803(-)$1	1	171	185	10.4854
.(((((...)))))	chr8:42935049-42935250(+)$1	1	178	192	10.1625
(((((......)))	chr2:27820880-27821081(+)$1	1	42	56	8.9531
.(((((...)))))	chr7:26230579-26230780(-)$1	1	80	94	10.1625
(((((....)))))	chr17:35804708-35804909(+)$1	1	161	175	10.4854
((((((...)))))	chr20:62367468-62367669(+)$1	1	110	124	10.4486
(((((....)))))	chr17:16046829-16047030(-)$1	1	36	50	10.4854
.(((((...)))))	chr4:113567702-113567903(+)$1	1	149	163	9.1303
(((((.....))))	chr5:112337232-112337433(+)$1	1	99	113	9.2767
(((((......)))	chr19:7978835-7979036(+)$1	1	171	185	8.9531
.(((((...)))))	chr17:78184588-78184789(-)$1	1	155	169	9.4356
(((((.....))))	chr19:14674915-14675116(+)$1	1	27	41	9.2767
.(((((...)))))	chr11:134126347-134126548(+)$1	1	33	47	10.1625
(((((....)))))	chr14:73637514-73637715(+)$1	1	47	61	10.4854
(((((....)))))	chr3:160117751-160117952(+)$1	1	124	138	10.4854
(((((....)))))	chr10:120442140-120442341(-)$1	1	63	77	10.4854
(((((......)))	chr12:57627748-57627949(+)$1	1	25	39	8.9531
(((((....)))))	chr11:93534936-93535137(+)$1	1	99	113	10.4854
(((((....)))))	chr15:75137060-75137261(-)$1	1	7	21	10.4854
(((.(....).)))	chr16:2285984-2286185(-)$1	1	107	121	8.1654
(((((....)))))	chr3:196202035-196202236(-)$1	1	134	148	10.4854
(((((....)))))	chr19:52496296-52496497(-)$1	1	109	123	10.4854
(((((.....))))	chr10:75531627-75531828(+)$1	1	21	35	9.2767
.(((((...)))))	chr19:16515381-16515582(-)$1	1	63	77	10.0097
(((((....)))))	chr3:52598030-52598231(-)$1	1	101	115	10.4854
.(((((...)))))	chr1:20235854-20236055(+)$1	1	132	146	10.1625
(((((......)))	chr16:30768760-30768961(+)$1	1	91	105	8.9531
(((((.....))))	chr11:66411612-66411813(+)$1	1	178	192	9.2767
(((((......)))	chr12:76749528-76749729(-)$1	1	21	35	8.9531
.(((((...)))))	chr2:109429205-109429406(+)$1	1	121	135	10.1625
(((((....)))))	chr7:151052894-151053095(+)$1	1	145	159	10.4854
(((((....)))))	chr17:45759757-45759958(+)$1	1	0	14	10.4854
.(((((...)))))	chr19:4501807-4502008(+)$1	1	121	135	10.1625
(((((....)))))	chr19:15469697-15469898(-)$1	1	125	139	10.4854
(((((....)))))	chr19:19467213-19467414(+)$1	1	33	47	10.4854
(((((....)))))	chr1:6681784-6681985(+)$1	1	12	26	10.4854

#PSSM
e : 0.74	[ : 0.11	: : 0.06	! : 0.01	# : 0.01	' : 0.01	" : 0.01	
e : 0.99	
e : 0.99	
e : 0.98	[ : 0.01	
e : 0.98	a : 0.01	
m : 0.44	e : 0.27	n : 0.15	o : 0.08	l : 0.05	
m : 0.44	l : 0.32	n : 0.15	o : 0.08	
m : 0.44	l : 0.32	n : 0.15	o : 0.08	
m : 0.44	l : 0.27	n : 0.15	o : 0.08	e : 0.05	
e : 0.74	n : 0.15	o : 0.08	a : 0.01	
e : 0.89	o : 0.08	] : 0.01	
e : 0.99	
e : 0.99	
e : 0.94	] : 0.03	4 : 0.01	

#score	583.666152532942
#seq	59
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_UTR_m2_run1.txt

#BEAR
eeee!!ccc!!ddddnnnnndddd22ccc]ee	chr16:1414248-1414466(-)$1	218	121	153	12.4936
#ggggggg####eeeeellleeeeeggggggg	chr4:129793416-129793643(+)$1	227	9	41	11.6215
ggggg!!bbeeeeeooooooeeeee]bbgggg	chr13:42808788-42809008(+)$1	220	170	202	10.8693
eee[dddd$$$$$bboooooobb333dddd]e	chr1:200828519-200828740(+)$1	221	49	81	10.7200
eeee####ccc[cccnnnnnccc]ccc]eeee	chr4:129029632-129029854(+)$1	222	104	136	11.2663
b[a!!==========mmmm==========22a	chr6:31698299-31698519(-)$1	220	3	35	12.3609
fff!!ccc!!ddddoooooodddd22ccc22f	chr4:119644236-119644459(-)$1	223	176	208	12.4826
===!!dddd"""ccclllccc]dddd======	chr6:20492380-20492601(+)$1	221	154	186	11.8312
bb!!=============lll============	chr1:181059783-181060007(+)$1	224	54	86	12.8673
dccc"""dddd[cccnnnnnccc22dddd333	chr5:108672022-108672252(-)$1	230	126	158	11.4783
iiiiiiiii####ccc####============	chr14:64152657-64152877(-)$1	220	13	45	11.3930
a!!ccc####eeeeennnnneeeee22ccc22	chr13:21353165-21353395(-)$1	230	131	163	11.7747
iiiiiiiii"""cccnnnnnccc333iiiiii	chr7:127231517-127231743(+)$1	226	57	89	15.7493
ccc####eeeeecccooooooccc]eeeee>>	chr3:141167472-141167702(+)$1	230	62	94	10.6131
=:iiiiiiiii[ddddllldddd]iiiiiiii	chr5:96370590-96370812(+)$1	222	109	141	11.5570
cc[dddd"""ccccccmmmmccc22ccc333d	chr6:44228113-44228330(-)$1	217	82	114	11.3838
d==========!!bbmmmmbb4444=======	chr9:95474147-95474377(-)$1	230	12	44	12.2907
eeeee[ccc[eeeeennnnneeeee]ccc333	chr2:234204132-234204354(+)$1	222	131	163	11.6375
!!eeeee####ddddoooooodddd]eeeee3	chr3:113524238-113524463(+)$1	225	32	64	12.5741
ffff[ggggggg[bbnnnnnbb]ggggggg44	chr1:67876850-67877072(-)$1	222	143	175	10.4233
ccc[eeeee!!ddddmmmmdddd4444eeeee	chr21:35473522-35473752(+)$1	230	136	168	10.8617
=====[ccc####bbnnnnnbb4444ccc]==	chr14:91737779-91737999(-)$1	220	67	99	13.4766
ggggggg####ddddmmmmdddd333gggggg	chr1:40537180-40537410(+)$1	230	70	102	13.4771
biiiiiiiii[ddddmmmmddddiiiiiiiii	chr21:19164929-19165172(-)$1	243	43	75	12.1238
dd!!cccdddd[cccooooooccc]dddd]cc	chr6:147885885-147886112(+)$1	227	135	167	11.0221
bb"""ccc!!eeeeennnnneeeee22ccc33	chr14:77491360-77491583(-)$1	223	153	185	11.5263
"ddddccc####cccnnnnnccc4444ccc33	chr1:107601772-107601993(+)$1	221	60	92	13.9248
!!ccc!!eeeeeooooooeeeee333ccc333	chr7:6501793-6502037(-)$1	244	53	85	10.6021
eeeee[==========mmmm==========ee	chr5:88014675-88014896(-)$1	221	22	54	11.5812
iiiiiii!!bb[cccooooooccc]bb22iii	chr6:46113646-46113871(+)$1	225	48	80	12.6299
dhhhhhhhh[ddddoooooodddd22hhhhhh	chr7:26252174-26252404(+)$1	230	42	74	10.2648
=ggggggg[bb!!cccmmmmccc22bb]gggg	chr5:77773372-77773602(+)$1	230	178	210	11.2375
gggggggccc[cccooooooccc]ccc4444g	chr1:234740344-234740568(-)$1	224	9	41	12.7736
[bbggggggg[ddddooooooddddggggggg	chr5:132215185-132215441(-)$1	256	167	199	12.1958
ccc[ccc"""ddddoooooodddd333ccc22	chr3:152183232-152183453(+)$1	221	156	188	13.7581
==========="""ammmma333=========	chr22:39887934-39888173(+)$1	239	1	33	13.0664
d::ggggggg!!cccooooooccc22gggggg	chr5:112203322-112203545(+)$1	223	188	220	11.7171
d!!ccc$$$$$a[bbmmmmbb]a4444ccc33	chr12:16703941-16704163(-)$1	222	96	128	10.7222
========####cccooooooccc666666==	chr11:58973989-58974213(+)$1	224	39	71	12.2311
ccc[ccc!!ccc[cccmmmmccc]ccc22ccc	chr13:113540596-113540818(+)$1	222	12	44	10.4545
ccc[eeeee####cccmmmmccc]eeeee]cc	chr14:74666068-74666288(+)$1	220	94	126	10.8193
!!ffffff"""ddddnnnnnddddffffff33	chr15:43281041-43281264(-)$1	223	87	119	11.8167
ddddeeeee"""cccnnnnnccc333eeeee2	chr2:219103446-219103669(+)$1	223	170	202	12.4117
eeeee!!bb[eeeeennnnneeeee]bb4444	chr6:13613896-13614126(+)$1	230	83	115	10.2772
dddd[iiiiiiiiiooooooiiiiiiiii22d	chr3:127410190-127410416(-)$1	226	44	76	11.9589
"hhhhhhhh!!ddddnnnnnddddhhhhhhhh	chr6:79910969-79911189(-)$1	220	50	82	9.9137
b::============nnnnn============	chr11:118621565-118621787(-)$1	222	136	168	11.6480
!!ggggggg$$$$$ccclllcccggggggg22	chr11:94905653-94905880(-)$1	227	49	81	11.4641
c!!ggggggg"""cccmmmmccc333gggggg	chr18:51681454-51681675(-)$1	221	134	166	13.4090
========bb!!cccmmmmcccbb]=======	chr19:11893101-11893331(+)$1	230	35	67	12.3812
!ggggggg"""ddddoooooodddd4444ggg	chr13:41764770-41764991(-)$1	221	5	37	13.9702
iii[ccc####ddddooooooddddccc]iii	chr2:100016943-100017160(+)$1	217	13	45	13.7105
:gggggggccc[cccmmmmcccccc]gggggg	chr3:119348402-119348621(+)$1	219	16	48	10.7177
:iiiiiiiiiddddoooooodddd]iiiiiii	chr15:91509289-91509516(-)$1	227	182	214	12.5579
ffffff####eeeeennnnneeeee4444fff	chr6:4061778-4062008(+)$1	230	82	114	10.4994
!!eeeee[bb"""ccclllccc333bb]eeee	chr19:1597950-1598169(-)$1	219	28	60	10.8336
""ggggggg!!eeeeellleeeee]ggggggg	chr5:114951569-114951818(-)$1	249	27	59	11.6278
hh"""bb####ddddmmmmdddd333bb333h	chrX:70279138-70279368(-)$1	230	157	189	11.9228

#otherMatches

#Seq PSSM
ACCAAAUUAGAAUGUAUUUAAUAUAGUAGGUG	chr16:1414248-1414466(-)$1	218	121	153	12.4936
AGAUGAUGCGGAAGCCCUUUGGGCUCGUCAUU	chr4:129793416-129793643(+)$1	227	9	41	11.6215
UGACUUUUGUAUAGCAACCUCUGUGUCAAGUC	chr13:42808788-42809008(+)$1	220	170	202	10.8693
AAGAAUAGGAAUGAGAUGUCCCUGAGCUGUAC	chr1:200828519-200828740(+)$1	221	49	81	10.7200
GCUUCUAAUCCCAGUAAGCAACUUGGACAGGC	chr4:129029632-129029854(+)$1	222	104	136	11.2663
AGGGAAUCCUGGAGCACUUGUUCCGGGAUGGU	chr6:31698299-31698519(-)$1	220	3	35	12.3609
AAAAAAAGCUUAAUUUUUACAUUAUACUUAAU	chr4:119644236-119644459(-)$1	223	176	208	12.4826
AAACAAAGGUGCAGACUAUCUUCCUUUUUUUC	chr6:20492380-20492601(+)$1	221	154	186	11.8312
GUGACUCCAGUCUUUGUUGUAUAAAGGUUGGG	chr1:181059783-181060007(+)$1	224	54	86	12.8673
CACUCAUGGCACAUUUGUUUAAUAUUGCUUAU	chr5:108672022-108672252(-)$1	230	126	158	11.4783
UUUUUUGUUCCUUACAUAUUUUUCUUUAUUGG	chr14:64152657-64152877(-)$1	220	13	45	11.3930
AGACUUUUCAGUUUUAUUUAAAGACCCAGGGA	chr13:21353165-21353395(-)$1	230	131	163	11.7747
UGGAAGGGGCUUCCUGGCCAAGGCCCCCUCUU	chr7:127231517-127231743(+)$1	226	57	89	15.7493
UAUUCCUACAUUAAGUCUCUUUUUAAAUGUUU	chr3:141167472-141167702(+)$1	230	62	94	10.6131
uUUGCUACAUUCUGUGUGUUAUAUAAUGUGGU	chr5:96370590-96370812(+)$1	222	109	141	11.5570
UCAGAAGAACCAACCACUCAUGGAAUUGCUGC	chr6:44228113-44228330(-)$1	217	82	114	11.3838
AGUAGGGGAUGAGGGUUAGCCAUAGUAUUCUU	chr9:95474147-95474377(-)$1	230	12	44	12.2907
ACAGAACUUGAUUGUAAAUAAUAAUAAAGAAA	chr2:234204132-234204354(+)$1	222	131	163	11.6375
GCUGUUGAAACCACUGCCCAGAGUGACAAUAA	chr3:113524238-113524463(+)$1	225	32	64	12.5741
AGAGACAACAUAGCAAUAUCUGGUAUGUUGCA	chr1:67876850-67877072(-)$1	222	143	175	10.4233
UACGAAGUUUGUUACCACAGUAGAGAUAAUUU	chr21:35473522-35473752(+)$1	230	136	168	10.8617
AAUCUUAUCUGCUGCUUUGUGUCUUUGGUCAG	chr14:91737779-91737999(-)$1	220	67	99	13.4766
AAAUCUGUAUCAAGACGGUUCUUUUCUAGAUU	chr1:40537180-40537410(+)$1	230	70	102	13.4771
GAUUAGAAAUCUGAGUUGUUUUAAUUUCUAAU	chr21:19164929-19165172(-)$1	243	43	75	12.1238
AACAGUAGCUUUAAUUUUUAUAUUCAAGCAUA	chr6:147885885-147886112(+)$1	227	135	167	11.0221
UAAUAGCCCUUAGCAACGACUGCUGCUGGUGU	chr14:77491360-77491583(-)$1	223	153	185	11.5263
UGAAAUAGCCUAACAUUUAUUGUAAUUCUGAA	chr1:107601772-107601993(+)$1	221	60	92	13.9248
GAUCAUUUGGAUAUAGCAAUCUACUCUGAGAA	chr7:6501793-6502037(-)$1	244	53	85	10.6021
UUCUUUCUUUAAAAAACAUUUUUUUUAAAGAA	chr5:88014675-88014896(-)$1	221	22	54	11.5812
AAUCUUAUAGUAAAACUAGCCUUUCACAUUAA	chr6:46113646-46113871(+)$1	225	48	80	12.6299
uguguguguguguguguAUCCAUAAAAUGCAU	chr7:26252174-26252404(+)$1	230	42	74	10.2648
GUUUUAAAAUCCAGUUAUUUAAUAUGAGUUUG	chr5:77773372-77773602(+)$1	230	178	210	11.2375
CAUCGGGACAUGGGUUUGAUCUUUUGUUGUAC	chr1:234740344-234740568(-)$1	224	9	41	12.7736
CUAGGACCAGAUCGUCCAUACAUGAUUGGUCU	chr5:132215185-132215441(-)$1	256	167	199	12.1958
GUGCUUGGUUUUACUAUUAUGUAAUCACAACU	chr3:152183232-152183453(+)$1	221	156	188	13.7581
GUUCCCAGGGGCAGCAUGGGAGAUCUUUGGGG	chr22:39887934-39888173(+)$1	239	1	33	13.0664
UACUUGAAAUAAGUUGUUUCAGAUAAAUUUCA	chr5:112203322-112203545(+)$1	223	188	220	11.7171
CUACUGAAUAGCGUAGAUAUAGGAAGGCAGGA	chr12:16703941-16704163(-)$1	222	96	128	10.7222
AGGUUUUUGAUGCUAGAAAAAUGGAAACAAGA	chr11:58973989-58974213(+)$1	224	39	71	12.2311
GGCCAGGGGUCCGGUGCUGUCGCGGGAAACCU	chr13:113540596-113540818(+)$1	222	12	44	10.4545
CUGUGAACUCUCCAGUAUAUACUAAGUUCCCA	chr14:74666068-74666288(+)$1	220	94	126	10.8193
UUUUAUUUAUAGGAUUAAAUAUUCAAAUAGCA	chr15:43281041-43281264(-)$1	223	87	119	11.8167
ACCACCAUGGCACUUACUGAAAGAAAUAUGGC	chr2:219103446-219103669(+)$1	223	170	202	12.4117
UGUAAUAGUCUUAUAGUACUUAUAAAGCAGUU	chr6:13613896-13614126(+)$1	230	83	115	10.2772
CCUGCCCUUCCCCUCCUGCCAGGGGGAGGCUC	chr3:127410190-127410416(-)$1	226	44	76	11.9589
CUGUGCAUACUGUGGUGUUUUUACUGUGCAUA	chr6:79910969-79911189(-)$1	220	50	82	9.9137
CUCGUGCUGUAGAGAGCAGAUUUCUAUGGUAC	chr11:118621565-118621787(-)$1	222	136	168	11.6480
AUUGUUGUUUUACUGCUAUUGGCGAUAACAUG	chr11:94905653-94905880(-)$1	227	49	81	11.4641
GUAUUUUUGAUGUAUAUAUCUAUUAUUCAAAA	chr18:51681454-51681675(-)$1	221	134	166	13.4090
uucugaggugaauugauuccagcacccucagg	chr19:11893101-11893331(+)$1	230	35	67	12.3812
GGUAUACAUGGUUAUUUUAUUAUGAGAUUUGU	chr13:41764770-41764991(-)$1	221	5	37	13.9702
UAUUUUAAAGUUAUGGCAUAACAUAUAACAUA	chr2:100016943-100017160(+)$1	217	13	45	13.7105
AAGGAGAAAAGCAAAGCUCUUUCUUAUUUUCC	chr3:119348402-119348621(+)$1	219	16	48	10.7177
CUGuuuuuaaaauauacaauuauucuuaaaaa	chr15:91509289-91509516(-)$1	227	182	214	12.5579
UUUGUGAUCAUGUUGUCUUUCAAUACAGGCAU	chr6:4061778-4062008(+)$1	230	82	114	10.4994
AGAGGAAACCCACAGCUCAGCUUCAGGCUUCU	chr19:1597950-1598169(-)$1	219	28	60	10.8336
UGUUGGGAGGGAUGUACAAUGCAUAUUCCCAA	chr5:114951569-114951818(-)$1	249	27	59	11.6278
CCAUUUCUGCUGUGUAUAUAUAUCCUGACUCG	chrX:70279138-70279368(-)$1	230	157	189	11.9228

#DB
((((..(((..((((.....))))..))).))	chr16:1414248-1414466(-)$1	1	121	153	12.4936
.(((((((....(((((...))))))))))))	chr4:129793416-129793643(+)$1	1	9	41	11.6215
(((((..(((((((......))))).))))))	chr13:42808788-42809008(+)$1	1	170	202	10.8693
(((.((((.....((......))...)))).)	chr1:200828519-200828740(+)$1	1	49	81	10.7200
((((....(((.(((.....))).))).))))	chr4:129029632-129029854(+)$1	1	104	136	11.2663
(.(..((((((((((....))))))))))..)	chr6:31698299-31698519(-)$1	1	3	35	12.3609
(((..(((..((((......))))..)))..)	chr4:119644236-119644459(-)$1	1	176	208	12.4826
(((..((((...(((...))).))))))))))	chr6:20492380-20492601(+)$1	1	154	186	11.8312
((..(((((((((((((...))))))))))))	chr1:181059783-181060007(+)$1	1	54	86	12.8673
((((...((((.(((.....)))..))))...	chr5:108672022-108672252(-)$1	1	126	158	11.4783
(((((((((....(((....((((((((((((	chr14:64152657-64152877(-)$1	1	13	45	11.3930
(..(((....(((((.....)))))..)))..	chr13:21353165-21353395(-)$1	1	131	163	11.7747
(((((((((...(((.....)))...))))))	chr7:127231517-127231743(+)$1	1	57	89	15.7493
(((....((((((((......))).)))))..	chr3:141167472-141167702(+)$1	1	62	94	10.6131
).(((((((((.((((...)))).))))))))	chr5:96370590-96370812(+)$1	1	109	141	11.5570
((.((((...((((((....)))..)))...)	chr6:44228113-44228330(-)$1	1	82	114	11.3838
(((((((((((..((....))....)))))))	chr9:95474147-95474377(-)$1	1	12	44	12.2907
(((((.(((.(((((.....))))).)))...	chr2:234204132-234204354(+)$1	1	131	163	11.6375
..(((((....((((......)))).))))).	chr3:113524238-113524463(+)$1	1	32	64	12.5741
((((.(((((((.((.....)).)))))))..	chr1:67876850-67877072(-)$1	1	143	175	10.4233
(((.(((((..((((....))))....)))))	chr21:35473522-35473752(+)$1	1	136	168	10.8617
(((((.(((....((.....))....))).))	chr14:91737779-91737999(-)$1	1	67	99	13.4766
(((((((....((((....))))...))))))	chr1:40537180-40537410(+)$1	1	70	102	13.4771
((((((((((.((((....)))))))))))))	chr21:19164929-19165172(-)$1	1	43	75	12.1238
((..(((((((.(((......))).)))).))	chr6:147885885-147886112(+)$1	1	135	167	11.0221
((...(((..(((((.....)))))..)))..	chr14:77491360-77491583(-)$1	1	153	185	11.5263
.(((((((....(((.....)))....)))..	chr1:107601772-107601993(+)$1	1	60	92	13.9248
..(((..(((((......)))))...)))...	chr7:6501793-6502037(-)$1	1	53	85	10.6021
(((((.((((((((((....))))))))))))	chr5:88014675-88014896(-)$1	1	22	54	11.5812
(((((((..((.(((......))).))..)))	chr6:46113646-46113871(+)$1	1	48	80	12.6299
(((((((((.((((......))))..))))))	chr7:26252174-26252404(+)$1	1	42	74	10.2648
)(((((((.((..(((....)))..)).))))	chr5:77773372-77773602(+)$1	1	178	210	11.2375
((((((((((.(((......))).)))....)	chr1:234740344-234740568(-)$1	1	9	41	12.7736
.(((((((((.((((......)))))))))))	chr5:132215185-132215441(-)$1	1	167	199	12.1958
(((.(((...((((......))))...)))..	chr3:152183232-152183453(+)$1	1	156	188	13.7581
(((((((((((...(....)...)))))))))	chr22:39887934-39888173(+)$1	1	1	33	13.0664
)..(((((((..(((......)))..))))))	chr5:112203322-112203545(+)$1	1	188	220	11.7171
(..(((.....(.((....)).)....)))..	chr12:16703941-16704163(-)$1	1	96	128	10.7222
((((((((....(((......)))......))	chr11:58973989-58974213(+)$1	1	39	71	12.2311
(((.(((..(((.(((....))).)))..)))	chr13:113540596-113540818(+)$1	1	12	44	10.4545
(((.(((((....(((....))).))))).))	chr14:74666068-74666288(+)$1	1	94	126	10.8193
..((((((...((((.....))))))))))..	chr15:43281041-43281264(-)$1	1	87	119	11.8167
(((((((((...(((.....)))...))))).	chr2:219103446-219103669(+)$1	1	170	202	12.4117
(((((..((.(((((.....))))).))....	chr6:13613896-13614126(+)$1	1	83	115	10.2772
((((.(((((((((......)))))))))..)	chr3:127410190-127410416(-)$1	1	44	76	11.9589
.((((((((..((((.....))))))))))))	chr6:79910969-79911189(-)$1	1	50	82	9.9137
)..((((((((((((.....))))))))))))	chr11:118621565-118621787(-)$1	1	136	168	11.6480
..(((((((.....(((...))))))))))..	chr11:94905653-94905880(-)$1	1	49	81	11.4641
(..(((((((...(((....)))...))))))	chr18:51681454-51681675(-)$1	1	134	166	13.4090
((((((((((..(((....))))).)))))))	chr19:11893101-11893331(+)$1	1	35	67	12.3812
.(((((((...((((......))))....)))	chr13:41764770-41764991(-)$1	1	5	37	13.9702
(((.(((....((((......))))))).)))	chr2:100016943-100017160(+)$1	1	13	45	13.7105
.((((((((((.(((....)))))).))))))	chr3:119348402-119348621(+)$1	1	16	48	10.7177
.(((((((((((((......)))).)))))))	chr15:91509289-91509516(-)$1	1	182	214	12.5579
((((((....(((((.....)))))....)))	chr6:4061778-4062008(+)$1	1	82	114	10.4994
..(((((.((...(((...)))...)).))))	chr19:1597950-1598169(-)$1	1	28	60	10.8336
..(((((((..(((((...))))).)))))))	chr5:114951569-114951818(-)$1	1	27	59	11.6278
((...((....((((....))))...))...)	chrX:70279138-70279368(-)$1	1	157	189	11.9228

#PSSM
d : 0.13	= : 0.12	c : 0.12	e : 0.10	! : 0.10	b : 0.08	i : 0.06	g : 0.05	f : 0.05	" : 0.05	: : 0.03	# : 0.01	a : 0.01	[ : 0.01	h : 0.01	
! : 0.13	g : 0.12	c : 0.12	e : 0.10	= : 0.10	i : 0.10	d : 0.06	f : 0.05	b : 0.05	: : 0.05	h : 0.05	[ : 0.01	" : 0.01	
g : 0.15	e : 0.13	c : 0.12	i : 0.12	= : 0.10	! : 0.08	f : 0.06	d : 0.05	" : 0.03	h : 0.03	: : 0.03	a : 0.01	[ : 0.01	b : 0.01	
g : 0.20	e : 0.12	[ : 0.10	i : 0.10	= : 0.10	! : 0.08	c : 0.06	d : 0.06	f : 0.05	" : 0.03	h : 0.03	# : 0.01	
g : 0.20	e : 0.13	= : 0.12	c : 0.12	i : 0.10	! : 0.06	d : 0.05	" : 0.05	# : 0.03	[ : 0.03	h : 0.03	f : 0.03	
g : 0.20	c : 0.15	= : 0.12	i : 0.12	e : 0.08	! : 0.06	d : 0.05	[ : 0.05	# : 0.03	h : 0.03	f : 0.03	" : 0.01	b : 0.01	
g : 0.20	c : 0.17	= : 0.13	i : 0.12	e : 0.08	# : 0.06	! : 0.05	d : 0.05	h : 0.03	" : 0.01	$ : 0.01	f : 0.01	b : 0.01	
g : 0.17	= : 0.13	c : 0.12	# : 0.12	i : 0.10	e : 0.08	d : 0.06	b : 0.03	" : 0.03	! : 0.03	h : 0.03	$ : 0.01	f : 0.01	[ : 0.01	
# : 0.15	c : 0.10	= : 0.10	i : 0.10	g : 0.10	e : 0.08	b : 0.06	! : 0.06	" : 0.06	d : 0.05	$ : 0.03	h : 0.03	[ : 0.01	
# : 0.20	" : 0.12	! : 0.10	= : 0.10	c : 0.06	i : 0.06	g : 0.06	b : 0.06	e : 0.05	$ : 0.05	[ : 0.05	d : 0.03	
# : 0.17	e : 0.13	" : 0.12	! : 0.10	= : 0.10	d : 0.10	c : 0.06	$ : 0.05	[ : 0.05	i : 0.03	b : 0.03	g : 0.01	
d : 0.25	e : 0.15	# : 0.10	[ : 0.10	" : 0.10	= : 0.06	! : 0.06	c : 0.05	$ : 0.03	g : 0.01	a : 0.01	i : 0.01	
d : 0.27	c : 0.25	e : 0.13	= : 0.06	# : 0.05	[ : 0.05	" : 0.05	$ : 0.03	! : 0.03	o : 0.01	i : 0.01	
c : 0.36	d : 0.27	e : 0.13	b : 0.08	= : 0.06	o : 0.01	" : 0.01	i : 0.01	$ : 0.01	
c : 0.36	d : 0.20	o : 0.13	e : 0.12	b : 0.08	= : 0.06	a : 0.01	
o : 0.31	n : 0.27	m : 0.17	c : 0.13	e : 0.03	= : 0.03	l : 0.01	d : 0.01	
o : 0.31	n : 0.27	m : 0.27	l : 0.06	e : 0.01	= : 0.01	# : 0.01	c : 0.01	
o : 0.31	n : 0.27	m : 0.27	l : 0.12	# : 0.01	
o : 0.29	n : 0.27	m : 0.27	l : 0.10	c : 0.01	# : 0.01	e : 0.01	
o : 0.29	n : 0.27	m : 0.10	d : 0.08	c : 0.06	l : 0.05	b : 0.03	e : 0.03	= : 0.01	# : 0.01	a : 0.01	
c : 0.27	d : 0.20	o : 0.17	e : 0.15	= : 0.08	b : 0.06	3 : 0.01	i : 0.01	
c : 0.34	d : 0.27	e : 0.15	= : 0.08	b : 0.05	] : 0.03	4 : 0.01	3 : 0.01	i : 0.01	
c : 0.31	d : 0.29	e : 0.15	= : 0.08	b : 0.03	4 : 0.03	3 : 0.03	] : 0.01	a : 0.01	i : 0.01	
d : 0.20	e : 0.13	3 : 0.13	= : 0.10	c : 0.10	] : 0.08	4 : 0.08	2 : 0.05	g : 0.03	i : 0.03	b : 0.01	
3 : 0.15	e : 0.13	2 : 0.12	= : 0.10	] : 0.10	d : 0.08	4 : 0.08	c : 0.06	i : 0.05	g : 0.03	6 : 0.01	f : 0.01	h : 0.01	
3 : 0.13	= : 0.13	2 : 0.10	4 : 0.10	g : 0.08	] : 0.08	c : 0.08	i : 0.06	d : 0.05	b : 0.05	e : 0.03	6 : 0.01	f : 0.01	h : 0.01	
c : 0.17	g : 0.15	= : 0.15	b : 0.10	i : 0.08	4 : 0.08	e : 0.06	d : 0.05	2 : 0.03	h : 0.03	3 : 0.01	6 : 0.01	f : 0.01	
c : 0.20	g : 0.15	= : 0.15	i : 0.08	e : 0.08	b : 0.05	d : 0.05	] : 0.05	4 : 0.05	2 : 0.03	h : 0.03	6 : 0.01	f : 0.01	
g : 0.18	c : 0.17	= : 0.15	e : 0.12	i : 0.08	4 : 0.06	d : 0.05	3 : 0.03	2 : 0.03	h : 0.03	6 : 0.01	f : 0.01	] : 0.01	
g : 0.20	= : 0.13	e : 0.10	c : 0.10	i : 0.10	3 : 0.08	] : 0.06	2 : 0.05	h : 0.03	4 : 0.03	f : 0.03	d : 0.01	6 : 0.01	
g : 0.17	= : 0.15	3 : 0.15	e : 0.12	2 : 0.10	i : 0.10	4 : 0.05	c : 0.05	h : 0.03	] : 0.01	> : 0.01	f : 0.01	
g : 0.18	= : 0.15	3 : 0.13	e : 0.10	i : 0.10	2 : 0.06	c : 0.05	h : 0.05	f : 0.03	d : 0.03	4 : 0.03	a : 0.01	> : 0.01	

#score	688.9761811943897
#seq	58
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_UTR_m1_run1.txt

#BEAR
hhhhhh^^^^^^^^^^^^^^^^^^^^hhhh	chr19:40029277-40029505(-)$1	228	102	132	27.5245
=======^^^^^^^^^^^^^^^^^^=====	chrX:12841538-12841763(+)$1	225	7	37	29.4579
ccc^^^^^^^^^^^^^^^^^^^^^^^^ccc	chr3:119150378-119150604(-)$1	226	98	128	30.0132
[ffffff^^^^^^^^^^^^^^^^^^^^fff	chr5:134191563-134191783(+)$1	220	143	173	28.4865
^^^^^^^^^^^^^^^^^^^^^^^^bb]===	chr1:67450821-67451046(+)$1	225	168	198	28.4156
gggg^^^^^^^^^^^^^^^^^^^^^^^ggg	chr2:191365587-191365814(+)$1	227	76	106	30.6395
=======bbwwwwwwwwwwwwwwbb]====	chrX:73809185-73809409(-)$1	224	80	110	20.7754
ccc[bb^^^^^^^^^^^^^^^^^^^^^^^^	chr7:131180205-131180437(+)$1	232	31	61	29.0852
gggggg^^^^^^^^^^^^^^^^^^^^gggg	chr6:1614002-1614225(+)$1	223	85	115	30.0709
c[eeeee^^^^^^^^^^^^^^^^^^^^eee	chr3:193413276-193413513(+)$1	237	109	139	29.1626
ggggggg^^^^^^^^^^^^^^^^^^^^^^^	chr1:150280627-150280856(+)$1	229	56	86	29.3739
eeee^^^^^^^^^^^^^^^^^^^^^^eeee	chr22:35690557-35690782(+)$1	225	28	58	29.9693
^^^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr10:12206661-12206888(+)$1	227	109	139	29.6830
iiiiiiiixxxxxxxxxxxxxxxiiiiiii	chr8:67955364-67955591(-)$1	227	97	127	22.6021
^^^^^^^^^^^^^^^^^^^^^^^ccc]iii	chr6:75964203-75964439(-)$1	236	52	82	28.1118
dd[dddd^^^^^^^^^^^^^^^^^^^^^^^	chr6:89872112-89872335(+)$1	223	89	119	28.2381
^^^^^^^^^^^^^^^^^^^^^^^^^a]iii	chr15:83673248-83673482(-)$1	234	109	139	29.6633
ee[ddddyyyyyyyyyyyyyyyydddd]ee	chr10:12207269-12207494(-)$1	225	181	211	25.1106
gggggggyyyyyyyyyyyyyyyyggggggg	chr8:9634518-9634740(+)$1	222	50	80	26.5530
ggggggg^^^^^^^^^^^^^^^^^^^^^^^	chr1:155224944-155225163(-)$1	219	60	90	29.3739
ee!!ccc^^^^^^^^^^^^^^^^^^^ccc2	chr1:171562427-171562666(+)$1	239	111	141	29.2444
gggggggyyyyyyyyyyyyyyyyggggggg	chr17:48829387-48829609(+)$1	222	96	126	26.5530
fff[cccxxxxxxxxxxxxxxxcccfffff	chr6:151422854-151423073(+)$1	219	84	114	22.4819
b[eeeeeyyyyyyyyyyyyyyyyeeeee]b	chr16:54148224-54148461(+)$1	237	113	143	25.2893
ee[ccccccwwwwwwwwwwwwwwccc]ccc	chr1:25568818-25569050(-)$1	232	135	165	20.8523
!!eeeee^^^^^^^^^^^^^^^^^^eeeee	chr2:183789840-183790070(-)$1	230	113	143	28.5348
eee^^^^^^^^^^^^^^^^^^^^^^^^eee	chr13:78337606-78337827(+)$1	221	63	93	30.2214
^^^^^^^^^^^^^^^^^^^^^^^ccc====	chr3:10193307-10193528(+)$1	221	97	127	28.1159
:ccc^^^^^^^^^^^^^^^^^^^cccffff	chr6:21598288-21598515(+)$1	227	103	133	26.6722
bbeeeeeyyyyyyyyyyyyyyyyeeeee33	chr20:48252147-48252373(-)$1	226	153	183	25.2626
f:eeeeeyyyyyyyyyyyyyyyyeeeee::	chr1:32637942-32638180(+)$1	238	150	180	22.6623
ggeeeee^^^^^^^^^^^^^^^^^^eeeee	chr4:109732875-109733105(-)$1	230	175	205	28.5381
ggg[cccyyyyyyyyyyyyyyyyccc]ggg	chr8:37611664-37611887(+)$1	223	153	183	27.3043
gggggggyyyyyyyyyyyyyyyyggggggg	chr12:116396432-116396654(-)$1	222	52	82	26.5530
gggggg^^^^^^^^^^^^^^^^^^^^gggg	chr11:82924461-82924685(+)$1	224	164	194	30.0709
gggg!!axxxxxxxxxxxxxxxa22ggggg	chr19:32874439-32874660(+)$1	221	36	66	23.8490
eee^^^^^^^^^^^^^^^^^^^^^^^eeee	chr6:75965591-75965812(-)$1	221	104	134	30.0371
hhhh^^^^^^^^^^^^^^^^^^^^^^^hhh	chr1:226333317-226333552(-)$1	235	101	131	28.9498
ggggggg^^^^^^^^^^^^^^^^^^^^^^^	chr9:101911970-101912204(+)$1	234	94	124	29.3739
h!!dddd^^^^^^^^^^^^^^^^^^dddd2	chr12:88590323-88590547(+)$1	224	98	128	27.2979
g"""cccyyyyyyyyyyyyyyyycccgggg	chr19:46325956-46326182(-)$1	226	36	66	26.9452
^^^^^^^^^^^^^^^^^^^^^^dddd]hhh	chr7:129474596-129474821(-)$1	225	128	158	25.2838
ggggggg^^^^^^^^^^^^^^^^^^ggggg	chr5:148874830-148875056(-)$1	226	6	36	29.1181
ggg!!a^^^^^^^^^^^^^^^^^^^a22gg	chrX:119570593-119570815(-)$1	222	45	75	29.7752
eeee[a^^^^^^^^^^^^^^^^^^a]eeee	chr5:72201133-72201352(+)$1	219	1	31	28.7582
ggggggg^^^^^^^^^^^^^^^^^^ggggg	chr9:96208734-96208959(-)$1	225	86	116	29.1181
eee^^^^^^^^^^^^^^^^^^^^^^^^^^e	chr5:133492258-133492487(-)$1	229	43	73	30.0482
eee"""bbwwwwwwwwwwwwwwbb333eee	chr6:56969175-56969407(+)$1	232	186	216	20.9182
iiiiiiiyyyyyyyyyyyyyyyyiiiiiii	chr17:38145959-38146190(+)$1	231	3	33	26.2896
fff[cccyyyyyyyyyyyyyyyyccc]fff	chr1:52553559-52553783(+)$1	224	179	209	26.3966
=======^^^^^^^^^^^^^^^^^^^^^^^	chr2:73989247-73989474(-)$1	227	87	117	29.5681
eeee^^^^^^^^^^^^^^^^^^^^^^eeee	chr7:26252696-26252922(+)$1	226	96	126	29.9693
===[ccc^^^^^^^^^^^^^^^^^^^^^^^	chr11:96085865-96086087(-)$1	222	99	129	29.6108
ebb[cccyyyyyyyyyyyyyyyycccbb::	chr11:27519540-27519762(-)$1	222	99	129	23.5574
[ffffffyyyyyyyyyyyyyyyyffffff]	chr6:80626160-80626379(-)$1	219	147	177	25.0508
ddd!!cccwwwwwwwwwwwwwwccc22ddd	chr12:107366779-107367003(+)$1	224	122	152	19.9216

#otherMatches

#Seq PSSM
UUUGGUAUUAAAAAAUCUAUUCACAAGCCA	chr19:40029277-40029505(-)$1	228	102	132	27.5245
GGUAUACAUUAGACAUAUCAGAGCAGUGUA	chrX:12841538-12841763(+)$1	225	7	37	29.4579
GCUUUUCUUUCAAUCCUCAUUAUCUUUAGC	chr3:119150378-119150604(-)$1	226	98	128	30.0132
UUAGGUUUAAGCAGCUUGUAAUUUAUUGAU	chr5:134191563-134191783(+)$1	220	143	173	28.4865
CAAAUUUCUGCUUAAUACCAAUUUCUCUGA	chr1:67450821-67451046(+)$1	225	168	198	28.4156
GAGAAAAAAAACAGAAACAAGCGAUUAUUU	chr2:191365587-191365814(+)$1	227	76	106	30.6395
GAAAUAAUGUCCAAACAAAGCUUCACUUAU	chrX:73809185-73809409(-)$1	224	80	110	20.7754
ACUAGGAAAUUACUAAGUAUAAAGAAGAAA	chr7:131180205-131180437(+)$1	232	31	61	29.0852
UUAAAGGAUUGCUGCAAAUAAAUACACUUU	chr6:1614002-1614225(+)$1	223	85	115	30.0709
ACAAUACUACCUUCACAACAUUUUCAUGUG	chr3:193413276-193413513(+)$1	237	109	139	29.1626
GUGCGAAACCCUCAUCCAGUUUUCUCUCCA	chr1:150280627-150280856(+)$1	229	56	86	29.3739
GCAAAAACAAAACAAAACUCACUCUCUUGU	chr22:35690557-35690782(+)$1	225	28	58	29.9693
UCAAAACACUUCAUAUUGCCCCCACUUGUU	chr10:12206661-12206888(+)$1	227	109	139	29.6830
CUGUUUAAUCAAAUUAACAUCUCUUAAACA	chr8:67955364-67955591(-)$1	227	97	127	22.6021
CCUUCAGUUAUAUUUUAAAUCAAAAGGUCU	chr6:75964203-75964439(-)$1	236	52	82	28.1118
GUAUGUGAUGCCAUUCUUUCUUUUUUUUUA	chr6:89872112-89872335(+)$1	223	89	119	28.2381
CUUCCUCUAAUAACUUAAAUAAUCAGCAAA	chr15:83673248-83673482(-)$1	234	109	139	29.6633
UGUGAGUACAACAACAGACACAAAUUCCUA	chr10:12207269-12207494(-)$1	225	181	211	25.1106
CAAAUGUUCACAAUUCACACACUACAUUUG	chr8:9634518-9634740(+)$1	222	50	80	26.5530
UCUAGAGUCACCCCACGCCGACCCCUCCCC	chr1:155224944-155225163(-)$1	219	60	90	29.3739
UAAACUUAAUUUUUUUCCAUUUGUACAGGG	chr1:171562427-171562666(+)$1	239	111	141	29.2444
GGGCCAACACUUUCUCAUAAAAAUUGGCCU	chr17:48829387-48829609(+)$1	222	96	126	26.5530
GUGUGAACUAAAAGGUAACAUUUUCCACUC	chr6:151422854-151423073(+)$1	219	84	114	22.4819
cauauccaauaaacauauuaaaaggaugag	chr16:54148224-54148461(+)$1	237	113	143	25.2893
UUCUCUUGCAGAUAUGAGAGAUAGCACAGA	chr1:25568818-25569050(-)$1	232	135	165	20.8523
UUUAUUUUGAAACAUUUGCCAAACUAAAUA	chr2:183789840-183790070(-)$1	230	113	143	28.5348
AGUUUUUUAAAGUAACUUGUUCAAUUUACU	chr13:78337606-78337827(+)$1	221	63	93	30.2214
UGCAUCUUUAAUUCCUUAUCCUAGCCUUUG	chr3:10193307-10193528(+)$1	221	97	127	28.1159
UGACUAUUUAAUCCUUUCUACUUGUCGCUA	chr6:21598288-21598515(+)$1	227	103	133	26.6722
GUAAAAUGCCUUUUUAAAAUUUAAUUUUCU	chr20:48252147-48252373(-)$1	226	153	183	25.2626
CUGCUUUUUUUUUUUUUUUUUUUAGAGCUA	chr1:32637942-32638180(+)$1	238	150	180	22.6623
UUCUGGUAACAUUCCACACCCCUAAGCCAG	chr4:109732875-109733105(-)$1	230	175	205	28.5381
GUUUUAUUUCAGGUAAGCAGUUUAUAUGAC	chr8:37611664-37611887(+)$1	223	153	183	27.3043
UCUUUUAUAUAUAGCAAACAAUUUGAAAGA	chr12:116396432-116396654(-)$1	222	52	82	26.5530
gauguaucucauugcaguuucaaauuuaca	chr11:82924461-82924685(+)$1	224	164	194	30.0709
AGUCAACAAGGAAACAUAAUUAGAGGGCUU	chr19:32874439-32874660(+)$1	221	36	66	23.8490
AACUUUUCUAAAAAAAAGCAGUCUUUGUUG	chr6:75965591-75965812(-)$1	221	104	134	30.0371
AUUAAAAUACAUAAAAUCAUUUAAAUAUAA	chr1:226333317-226333552(-)$1	235	101	131	28.9498
UCAGGAUCUUAAAACUAACACUUAUAAAAC	chr9:101911970-101912204(+)$1	234	94	124	29.3739
GUUUAUUUUCAAACACUAACUUCUUGAUAU	chr12:88590323-88590547(+)$1	224	98	128	27.2979
GUAUGUGACUCAACUCCCACCCCCACCACC	chr19:46325956-46326182(-)$1	226	36	66	26.9452
AUUUUUUUUAUUACUAAACAAGGUUUUUAU	chr7:129474596-129474821(-)$1	225	128	158	25.2838
GCGUGCGCUUCCUCUCAAUCUUCUUUGCAC	chr5:148874830-148875056(-)$1	226	6	36	29.1181
AUGCUGUUAAUAUUUCUAAAAGUUUCUACA	chrX:119570593-119570815(-)$1	222	45	75	29.7752
UCAUGGAUUUAAAAAUCAAGUUGGCGAUGA	chr5:72201133-72201352(+)$1	219	1	31	28.7582
UUAAGGGCUAAAAGUUUAUAAUCAUCCCUU	chr9:96208734-96208959(-)$1	225	86	116	29.1181
ACAUAACCAUAACUUCUGUCCCUUCUAAUU	chr5:133492258-133492487(-)$1	229	43	73	30.0482
UAAUAUGCUUCCCCUUCCCUUUGCCUUUUA	chr6:56969175-56969407(+)$1	232	186	216	20.9182
GCUUUGACAUCUUUCUUUCCUUCUUGAAGC	chr17:38145959-38146190(+)$1	231	3	33	26.2896
AGAAGCUUACUUUUUGCUAUAUCAGCAUUU	chr1:52553559-52553783(+)$1	224	179	209	26.3966
UUUUCUAUAACUGUUCAAAAUUUAUAUUAA	chr2:73989247-73989474(-)$1	227	87	117	29.5681
AUGUUUUUUCUUUACCCCAAUUCAUUACAU	chr7:26252696-26252922(+)$1	226	96	126	29.9693
GCAUAUCUAAAUUUUCCCAUAAAGUAAUAA	chr11:96085865-96086087(-)$1	222	99	129	29.6108
CACACACAUAAUAUAUAUAACCAGUGGUAA	chr11:27519540-27519762(-)$1	222	99	129	23.5574
GGUGGGGAGAAAAGACAAAUGUGCUCUAUG	chr6:80626160-80626379(-)$1	219	147	177	25.0508
UGAAAAGUCAUUAAGGAGUUCAACUAAUCA	chr12:107366779-107367003(+)$1	224	122	152	19.9216

#DB
((((((....................))))	chr19:40029277-40029505(-)$1	1	102	132	27.5245
(((((((..................)))))	chrX:12841538-12841763(+)$1	1	7	37	29.4579
(((........................)))	chr3:119150378-119150604(-)$1	1	98	128	30.0132
.((((((....................)))	chr5:134191563-134191783(+)$1	1	143	173	28.4865
........................)).)))	chr1:67450821-67451046(+)$1	1	168	198	28.4156
((((.......................)))	chr2:191365587-191365814(+)$1	1	76	106	30.6395
(((((((((..............)).))))	chrX:73809185-73809409(-)$1	1	80	110	20.7754
(((.((........................	chr7:131180205-131180437(+)$1	1	31	61	29.0852
((((((....................))))	chr6:1614002-1614225(+)$1	1	85	115	30.0709
(.(((((....................)))	chr3:193413276-193413513(+)$1	1	109	139	29.1626
(((((((.......................	chr1:150280627-150280856(+)$1	1	56	86	29.3739
((((......................))))	chr22:35690557-35690782(+)$1	1	28	58	29.9693
..........................))))	chr10:12206661-12206888(+)$1	1	109	139	29.6830
((((((((...............)))))))	chr8:67955364-67955591(-)$1	1	97	127	22.6021
.......................))).)))	chr6:75964203-75964439(-)$1	1	52	82	28.1118
((.((((.......................	chr6:89872112-89872335(+)$1	1	89	119	28.2381
.........................).)))	chr15:83673248-83673482(-)$1	1	109	139	29.6633
((.((((................)))).))	chr10:12207269-12207494(-)$1	1	181	211	25.1106
(((((((................)))))))	chr8:9634518-9634740(+)$1	1	50	80	26.5530
(((((((.......................	chr1:155224944-155225163(-)$1	1	60	90	29.3739
((..(((...................))).	chr1:171562427-171562666(+)$1	1	111	141	29.2444
(((((((................)))))))	chr17:48829387-48829609(+)$1	1	96	126	26.5530
(((.(((...............))))))))	chr6:151422854-151423073(+)$1	1	84	114	22.4819
(.(((((................))))).)	chr16:54148224-54148461(+)$1	1	113	143	25.2893
((.((((((..............))).)))	chr1:25568818-25569050(-)$1	1	135	165	20.8523
..(((((..................)))))	chr2:183789840-183790070(-)$1	1	113	143	28.5348
(((........................)))	chr13:78337606-78337827(+)$1	1	63	93	30.2214
.......................)))((((	chr3:10193307-10193528(+)$1	1	97	127	28.1159
.(((...................)))((((	chr6:21598288-21598515(+)$1	1	103	133	26.6722
(((((((................)))))..	chr20:48252147-48252373(-)$1	1	153	183	25.2626
).(((((................)))))..	chr1:32637942-32638180(+)$1	1	150	180	22.6623
))(((((..................)))))	chr4:109732875-109733105(-)$1	1	175	205	28.5381
(((.(((................))).)))	chr8:37611664-37611887(+)$1	1	153	183	27.3043
(((((((................)))))))	chr12:116396432-116396654(-)$1	1	52	82	26.5530
((((((....................))))	chr11:82924461-82924685(+)$1	1	164	194	30.0709
((((..(...............)..)))))	chr19:32874439-32874660(+)$1	1	36	66	23.8490
(((.......................))))	chr6:75965591-75965812(-)$1	1	104	134	30.0371
((((.......................)))	chr1:226333317-226333552(-)$1	1	101	131	28.9498
(((((((.......................	chr9:101911970-101912204(+)$1	1	94	124	29.3739
(..((((..................)))).	chr12:88590323-88590547(+)$1	1	98	128	27.2979
(...(((................)))))))	chr19:46325956-46326182(-)$1	1	36	66	26.9452
......................)))).)))	chr7:129474596-129474821(-)$1	1	128	158	25.2838
(((((((..................)))))	chr5:148874830-148875056(-)$1	1	6	36	29.1181
(((..(...................)..))	chrX:119570593-119570815(-)$1	1	45	75	29.7752
((((.(..................).))))	chr5:72201133-72201352(+)$1	1	1	31	28.7582
(((((((..................)))))	chr9:96208734-96208959(-)$1	1	86	116	29.1181
(((..........................)	chr5:133492258-133492487(-)$1	1	43	73	30.0482
(((...((..............))...)))	chr6:56969175-56969407(+)$1	1	186	216	20.9182
(((((((................)))))))	chr17:38145959-38146190(+)$1	1	3	33	26.2896
(((.(((................))).)))	chr1:52553559-52553783(+)$1	1	179	209	26.3966
(((((((.......................	chr2:73989247-73989474(-)$1	1	87	117	29.5681
((((......................))))	chr7:26252696-26252922(+)$1	1	96	126	29.9693
(((.(((.......................	chr11:96085865-96086087(-)$1	1	99	129	29.6108
)((.(((................)))))..	chr11:27519540-27519762(-)$1	1	99	129	23.5574
.((((((................)))))).	chr6:80626160-80626379(-)$1	1	147	177	25.0508
(((..(((..............)))..)))	chr12:107366779-107367003(+)$1	1	122	152	19.9216

#PSSM
g : 0.28	e : 0.19	^ : 0.10	= : 0.07	h : 0.05	c : 0.05	f : 0.05	[ : 0.03	i : 0.03	d : 0.03	b : 0.03	! : 0.01	: : 0.01	
g : 0.26	e : 0.17	^ : 0.10	= : 0.07	f : 0.07	c : 0.05	h : 0.03	[ : 0.03	i : 0.03	d : 0.03	! : 0.03	b : 0.03	: : 0.01	" : 0.01	
g : 0.24	e : 0.23	^ : 0.10	= : 0.07	f : 0.07	c : 0.05	[ : 0.05	h : 0.03	i : 0.03	! : 0.03	" : 0.01	b : 0.01	d : 0.01	
g : 0.21	^ : 0.17	e : 0.16	[ : 0.10	= : 0.05	d : 0.05	! : 0.05	h : 0.03	f : 0.03	i : 0.03	c : 0.03	" : 0.03	
^ : 0.26	g : 0.17	c : 0.14	e : 0.10	= : 0.05	d : 0.05	! : 0.05	f : 0.03	i : 0.03	h : 0.01	b : 0.01	[ : 0.01	" : 0.01	
^ : 0.26	g : 0.17	c : 0.16	e : 0.10	= : 0.05	d : 0.05	f : 0.03	i : 0.03	a : 0.03	h : 0.01	b : 0.01	! : 0.01	" : 0.01	
^ : 0.37	c : 0.16	g : 0.14	e : 0.10	= : 0.05	d : 0.05	f : 0.03	i : 0.03	a : 0.01	b : 0.01	
^ : 0.64	y : 0.23	b : 0.03	x : 0.03	c : 0.03	i : 0.01	
^ : 0.64	y : 0.23	x : 0.05	w : 0.03	b : 0.01	c : 0.01	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.64	y : 0.23	w : 0.07	x : 0.05	
^ : 0.62	y : 0.23	w : 0.03	c : 0.03	x : 0.01	a : 0.01	d : 0.01	b : 0.01	
^ : 0.57	c : 0.17	g : 0.05	e : 0.05	b : 0.03	i : 0.03	d : 0.03	2 : 0.01	f : 0.01	
^ : 0.53	c : 0.17	g : 0.05	e : 0.05	b : 0.03	i : 0.03	d : 0.03	2 : 0.01	a : 0.01	3 : 0.01	f : 0.01	
^ : 0.39	c : 0.14	g : 0.10	e : 0.08	d : 0.05	] : 0.03	i : 0.03	a : 0.03	f : 0.03	= : 0.01	b : 0.01	3 : 0.01	2 : 0.01	
^ : 0.24	e : 0.17	g : 0.16	] : 0.12	= : 0.05	f : 0.05	i : 0.03	d : 0.03	2 : 0.03	h : 0.01	c : 0.01	3 : 0.01	b : 0.01	
e : 0.23	g : 0.19	^ : 0.14	f : 0.08	= : 0.07	i : 0.07	h : 0.05	c : 0.05	d : 0.03	] : 0.01	2 : 0.01	b : 0.01	
g : 0.21	e : 0.19	^ : 0.14	f : 0.08	= : 0.07	i : 0.07	h : 0.05	c : 0.05	: : 0.03	d : 0.03	] : 0.01	3 : 0.01	
g : 0.21	e : 0.21	^ : 0.12	= : 0.07	f : 0.07	i : 0.07	h : 0.05	c : 0.03	2 : 0.03	: : 0.03	b : 0.01	3 : 0.01	] : 0.01	d : 0.01	

#score	1530.5062450101657
#seq	56
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_UTR_m2_run2.txt

#BEAR
iiiiiiii$$$$$ddddnnnnndddd22iiiiiiii	chr14:24679770-24680010(-)$1	240	19	55	14.7279
gggggg============mmmm============44	chr1:85731832-85732058(-)$1	226	112	148	15.6367
d[ccc[============mmmm============]c	chr17:38438679-38438928(+)$1	249	15	51	15.6270
b"""ccc[dddd[cccooooooccc]dddd]ccc33	chr1:235301132-235301355(-)$1	223	166	202	14.2688
============[cccooooooccc===========	chr1:153618228-153618450(+)$1	222	107	143	19.8790
!eeeee"""ccc[cccnnnnnccc22ccc333eeee	chr10:101474025-101474274(-)$1	249	190	226	12.7482
========$$$$$cccooooooccc333========	chr11:33743878-33744107(-)$1	229	5	41	19.0389
iiiiii[bb[ccccccooooooccc]cccbbiiiii	chr4:174254559-174254921(-)$1	362	19	55	16.2487
#ccc[iiiiiiiiiddddllldddd22iiiiiiiii	chr7:148700698-148700938(-)$1	240	81	117	14.7271
DDiiiiiiiii[bbbboooooobb]bb]iiiiiiii	chr6:27778121-27778418(+)$1	297	173	209	13.3101
!!ccc"""dddd[cccooooooccc22dddd333cc	chr2:128520558-128520797(-)$1	239	80	116	15.0041
:eeeee[bb!!eeeeeooooooeeeee22bb]eeee	chr20:280670-280923(+)$1	253	201	237	12.6455
dggggggg"""eeeeeooooooeeeeeggggggg]d	chr5:176733642-176733883(+)$1	241	157	193	15.5753
ffffeeeee[ccccccooooooccc333ccc]eeee	chr15:70342015-70342270(-)$1	255	4	40	14.8247
ddd[ccc[a[aeeeeeooooooeeeee]a]a]cccd	chr22:39913867-39914122(+)$1	255	42	78	14.4255
ccc[ffffff!!ddddoooooodddd22ffffff33	chr1:228285651-228285884(+)$1	233	119	155	13.7869
gggggg$$$$$eeeeeooooooeeeee22ggggggg	chr7:151163544-151163789(-)$1	245	174	210	14.5449
ddddiiiiiiiii[cccnnnnnccc22iiiiiiiii	chr1:33240935-33241246(-)$1	311	190	226	15.4624
&bb"""==========oooooo==========]bbd	chr13:108882850-108883084(+)$1	234	160	196	16.8196
eeecccggggggg[ddddllldddd]ggggggg444	chr1:157091617-157091894(-)$1	277	185	221	12.6227
eeeee"""ggggggg[annnnna]ggggggg]eeee	chr7:40172279-40172507(-)$1	228	160	196	13.2406
=====####ggggggglllggggggg22========	chr17:3715494-3715730(-)$1	236	146	182	14.5598
ddd"""==========oooooo==========333d	chr6:11136149-11136429(+)$1	280	224	260	18.5517
==========[a[cccooooooccc]a]========	chr12:69970412-69970635(+)$1	223	61	97	19.7240
eee[ccc[bb[cccddddllldddd333ccc]bb]c	chr11:62327131-62327357(-)$1	226	55	91	12.3332
eeee####ccceeeeeooooooeeeee]ccc333ee	chr1:28607316-28607651(+)$1	335	247	283	14.7935
$$$bb[bb[ccc[cccoooooocccccc]bbbbggg	chr12:110778506-110778743(+)$1	237	19	55	12.9872
hhhh"""ccc!!a[ddddllldddd]a333ccc333	chr2:38976702-38976943(-)$1	241	183	219	12.9720
""ccc[ccc####cccnnnnncccccc]ccc]eeee	chr22:38062437-38062719(+)$1	282	187	223	13.8825
::==============nnnnn==============F	chr4:108831933-108832169(+)$1	236	194	230	14.9156
=========!!cccrrrrrrrrrccc22========	chr3:149236273-149236502(-)$1	229	189	225	15.7243
:=============cccmmmmccc]===========	chrX:70793638-70793885(+)$1	247	83	119	15.2911
d[eeeeeeeeee[cccooooooccc]eeeee]eeee	chr7:131191252-131191475(-)$1	223	76	112	13.4368
ddd[a[ccc"""ddddoooooodddd333ccc]a]d	chr3:133307466-133307752(+)$1	286	21	57	16.0736
hh==============!!bb!!dddd==========	chr12:4410619-4410842(+)$1	223	21	57	12.6301
iiiiiiiii[bb[cccmmmmcccbb]iiiiiiiii]	chr5:137902616-137902876(-)$1	260	58	94	13.4201
==========!!ddddoooooodddd==========	chr7:99637166-99637396(+)$1	230	187	223	18.8004
:eeeee[iiiiiiiiirrrrrrrrriiiiiiiii]e	chr2:60686294-60686521(-)$1	227	71	107	12.5334
ff[a!!ccc####ddddmmmmdddd333ccc22a]f	chr12:54628261-54628640(-)$1	379	329	365	12.3402
c"""eeeeegggggggooooooggggggg]eeeee3	chr1:224346022-224346260(+)$1	238	39	75	14.0148
"""a[ccc[gggggggoooooogggggggccca333	chr20:34257032-34257271(-)$1	239	5	41	15.7595
[ccc[iiiiiiiii[bbnnnnnbbiiiiiiiii]cc	chr1:155305547-155305798(-)$1	251	80	116	14.1641
ff:a[===========oooooo===========]a:	chr1:46035529-46035826(+)$1	297	16	52	16.1964
ddd[bb[==========nnnnn==========]bb]	chr8:127565110-127565336(-)$1	226	168	204	15.0439
dddd!!ccc!!eeeeeooooooeeeeeccc22dddd	chr13:28519447-28519668(+)$1	221	160	196	13.3736
=========[ffffffnnnnnffffff]========	chr1:179813810-179814063(-)$1	253	57	93	14.7469
=========!!cccrrrrrrrrrccc22========	chr18:56997989-56998212(-)$1	223	107	143	15.7243
cca[a[ccc"""ddddoooooodddd333ccc]a]a	chr5:151183574-151183798(+)$1	224	13	49	16.3036
gggggg"""dddd[cccnnnnnccc]dddd]ggggg	chr17:41844361-41844604(-)$1	243	192	228	12.7488
========[bb[eeeeennnnneeeee]bb]=====	chr12:27908200-27908457(+)$1	257	185	221	14.1221

#otherMatches

#Seq PSSM
AUCUAUCUCAUUCUCAGGGACAUUGACAAGGUAGAU	chr14:24679770-24680010(-)$1	240	19	55	14.7279
AAAUUUUUUUAAAGUAGUGAGUGCUAUUUUGGAGUU	chr1:85731832-85732058(-)$1	226	112	148	15.6367
ACGUGUGCGUGCGCACGCGUGUGCGUGUGUGUGUUC	chr17:38438679-38438928(+)$1	249	15	51	15.6270
AAGUAGUACUUGAUUUGUUUAAAGAACGAGAGCUUU	chr1:235301132-235301355(-)$1	223	166	202	14.2688
GUGGUAGCAGCUCUGGUUUGAUUCAAGUUGCUACCA	chr1:153618228-153618450(+)$1	222	107	143	19.8790
UUGCUGCUUAACAGGCUUUGUGUCAGGUUUUUCAGU	chr10:101474025-101474274(-)$1	249	190	226	12.7482
CAGAAGCCUUCUUGGCCUUCCAGCCCUUGGUUUUUG	chr11:33743878-33744107(-)$1	229	5	41	19.0389
GAGCCCCGCCAGCGCCCGCCCUGGCAGCUGCGGGCU	chr4:174254559-174254921(-)$1	362	19	55	16.2487
AGGCAGACGCCCUGCGUGGCCCAUGGUCGGGGCGUC	chr7:148700698-148700938(-)$1	240	81	117	14.7271
GCUCUUUUCAGAGCCACCCACAUGCGCGCUGAAAAG	chr6:27778121-27778418(+)$1	297	173	209	13.3101
AAUAAAUUUGCUACAUGCUCUGAUGACGGCACUGUU	chr2:128520558-128520797(-)$1	239	80	116	15.0041
CUAUAUGUUUUGCUAUUUCCUUGUGGCUUAGAAUGU	chr20:280670-280923(+)$1	253	201	237	12.6455
ugacuugcccggggCUCCAGGUAGCCUGCAGGUUAA	chr5:176733642-176733883(+)$1	241	157	193	15.5753
ACUCCUGGGCCUGGAUUGAUGUGUCUCACAGACUCG	chr15:70342015-70342270(-)$1	255	4	40	14.8247
UAGUCACUUGCCUGCCCGCAGUGGUGGUGGAUGUGU	chr22:39913867-39914122(+)$1	255	42	78	14.4255
ACGUGCGGCUCGUGGUGUGAGUGCCAGAAGCUGCCU	chr1:228285651-228285884(+)$1	233	119	155	13.7869
GGGCUGGGUUACAGCUGAUUGAAGCUGAGUGGCCCU	chr7:151163544-151163789(-)$1	245	174	210	14.5449
GGCACUGGGGGCCAGGGCCUGCCCCAGGGCUCCUGG	chr1:33240935-33241246(-)$1	311	190	226	15.4624
AAGUUAAAUGAAAUGCAUGAUGGUAUUUUAUUCCUU	chr13:108882850-108883084(+)$1	234	160	196	16.8196
GUAGGAGUGAAAUAUUUAAUGUAAACAUUUCACCAA	chr1:157091617-157091894(-)$1	277	185	221	12.6227
CUUCUAGCUAUUGUGGUUUUGUGGUAUGAUAAAGAA	chr7:40172279-40172507(-)$1	228	160	196	13.2406
AAGUCUGUAUUAUGUUUAAAACAUGAAUGAUUUGAA	chr17:3715494-3715730(-)$1	236	146	182	14.5598
AAUGUGUUGUGGAGAAAAACACUUCUUCACAAACAA	chr6:11136149-11136429(+)$1	280	224	260	18.5517
AUUAAAGGUGUCUUUAUCGUUUUAGUGCCAUUUUUA	chr12:69970412-69970635(+)$1	223	61	97	19.7240
CAGAUUGGCAGGUGGACUACGAGUCAUACACAUGGC	chr11:62327131-62327357(-)$1	226	55	91	12.3332
UCCUCCUUCCCCUGCCCACAGAGGCAGAGGGCACAG	chr1:28607316-28607651(+)$1	335	247	283	14.7935
CUCCGUGAAGCUGUGCCGGCAAGCAGGCAUCCGGGU	chr12:110778506-110778743(+)$1	237	19	55	12.9872
CUUUGAUCCAAAUGAUAGAUGCUAUGAGUGUGGCGA	chr2:38976702-38976943(-)$1	241	183	219	12.9720
AAGAGUGGUCCACGUCCUAAAGACACCUCUCCUUUA	chr22:38062437-38062719(+)$1	282	187	223	13.8825
CUGCCUAAUGUUGAGAGUGGUUUUUAGCAUUAGGUU	chr4:108831933-108832169(+)$1	236	194	230	14.9156
UCUUUUUGUCUUUUGUUAGCAAAAAAUUGCAAAAAG	chr3:149236273-149236502(-)$1	229	189	225	15.7243
CUUACUUGUCUGUACAGUACCUUGUUGCAGAUGGGU	chrX:70793638-70793885(+)$1	247	83	119	15.2911
CAUACGGCUGGCAUCUGUUCCAGGAAGUCAGACCGU	chr7:131191252-131191475(-)$1	223	76	112	13.4368
CACUGCUGAAAAGAACUGAUGUGUUCAGAUCAUCUG	chr3:133307466-133307752(+)$1	286	21	57	16.0736
UUUUUUUUUUUUUUGCACAAUUGUAAUUGACAGGUA	chr12:4410619-4410842(+)$1	223	21	57	12.6301
GAUAUUUCUAUCCUGGAAAUUCAGAAAGGAGUAUUU	chr5:137902616-137902876(-)$1	260	58	94	13.4201
CAGGGUGGGGGCCAUAUUUCUCUGUGUCCUACUCUG	chr7:99637166-99637396(+)$1	230	187	223	18.8004
AUUUUAUGAAGAUAUUUGCUUUAAUAAUGUCUUUUU	chr2:60686294-60686521(-)$1	227	71	107	12.5334
GAAAUUAGGCCAAAUUGAAUGCAGUGAACUUUUUAU	chr12:54628261-54628640(-)$1	379	329	365	12.3402
UUAUACAUGUUUUCAGUUCUCUUUGGGGGCCAUGUC	chr1:224346022-224346260(+)$1	238	39	75	14.0148
GCACAUCUGUGCUCUUGGUGAGGAGAGCAAGAGGAA	chr20:34257032-34257271(-)$1	239	5	41	15.7595
UUUUGUUUUUCAUUGCAGGGAGUGGGUGGGAGGGAG	chr1:155305547-155305798(-)$1	251	80	116	14.1641
UCUGUCUCUCUUUCCAGGUGGAUGGGAAGAGAGUCC	chr1:46035529-46035826(+)$1	297	16	52	16.1964
AACCAUUUUUUGUUUUAUAAAUUAGAAUAAAAUAUA	chr8:127565110-127565336(-)$1	226	168	204	15.0439
CAUGUUAUGGCAGAUUGAAAAGGAUCUCAUUUCAUG	chr13:28519447-28519668(+)$1	221	160	196	13.3736
aaauuuauuuuugaauaaccaauuuaauaguaaauu	chr1:179813810-179814063(-)$1	253	57	93	14.7469
GGUCAGUAUGAUGCAGCCUCUGAGCAGAAUAUUGAC	chr18:56997989-56998212(-)$1	223	107	143	15.7243
CCCGUGGAGGCAUGGUGCAGAAACCAGGAUUUGGAG	chr5:151183574-151183798(+)$1	224	13	49	16.3036
UUACUUAACAAGAUUUAGCUCUUAGUUCUUCAAGUA	chr17:41844361-41844604(-)$1	243	192	228	12.7488
UAUGGAGUAGAAAAAUCUGCUUGAUUUAUUAAUUUU	chr12:27908200-27908457(+)$1	257	185	221	14.1221

#DB
((((((((.....((((.....))))..))))))))	chr14:24679770-24680010(-)$1	1	19	55	14.7279
((((((((((((((((((....))))))))))))..	chr1:85731832-85732058(-)$1	1	112	148	15.6367
(.(((.((((((((((((....)))))))))))).)	chr17:38438679-38438928(+)$1	1	15	51	15.6270
(...(((.((((.(((......))).)))).)))..	chr1:235301132-235301355(-)$1	1	166	202	14.2688
((((((((((((.(((......))))))))))))))	chr1:153618228-153618450(+)$1	1	107	143	19.8790
.(((((...(((.(((.....)))..)))...))))	chr10:101474025-101474274(-)$1	1	190	226	12.7482
((((((((.....(((......)))...))))))))	chr11:33743878-33744107(-)$1	1	5	41	19.0389
((((((.((.((((((......))).))))))))))	chr4:174254559-174254921(-)$1	1	19	55	16.2487
.(((.(((((((((((((...))))..)))))))))	chr7:148700698-148700938(-)$1	1	81	117	14.7271
))(((((((((.((((......)).)).))))))))	chr6:27778121-27778418(+)$1	1	173	209	13.3101
..(((...((((.(((......)))..))))...))	chr2:128520558-128520797(-)$1	1	80	116	15.0041
.(((((.((..(((((......)))))..)).))))	chr20:280670-280923(+)$1	1	201	237	12.6455
((((((((...(((((......)))))))))))).)	chr5:176733642-176733883(+)$1	1	157	193	15.5753
(((((((((.((((((......)))...))).))))	chr15:70342015-70342270(-)$1	1	4	40	14.8247
(((.(((.(.((((((......))))).).).))))	chr22:39913867-39914122(+)$1	1	42	78	14.4255
(((.((((((..((((......))))..))))))..	chr1:228285651-228285884(+)$1	1	119	155	13.7869
((((((.....(((((......)))))..)))))))	chr7:151163544-151163789(-)$1	1	174	210	14.5449
))))(((((((((.(((.....)))..)))))))))	chr1:33240935-33241246(-)$1	1	190	226	15.4624
.((...((((((((((......)))))))))).)))	chr13:108882850-108883084(+)$1	1	160	196	16.8196
(((((((((((((.((((...)))).)))))))...	chr1:157091617-157091894(-)$1	1	185	221	12.6227
(((((...(((((((.(.....).))))))).))))	chr7:40172279-40172507(-)$1	1	160	196	13.2406
(((((....(((((((...)))))))..))))))))	chr17:3715494-3715730(-)$1	1	146	182	14.5598
(((...((((((((((......))))))))))...)	chr6:11136149-11136429(+)$1	1	224	260	18.5517
((((((((((.(.(((......))).).))))))))	chr12:69970412-69970635(+)$1	1	61	97	19.7240
(((.(((.((.(((((((...))))...))).)).)	chr11:62327131-62327357(-)$1	1	55	91	12.3332
((((....((((((((......))))).)))...))	chr1:28607316-28607651(+)$1	1	247	283	14.7935
...((.((.(((.(((......)))))).)))))))	chr12:110778506-110778743(+)$1	1	19	55	12.9872
((((...(((..(.((((...)))).)...)))...	chr2:38976702-38976943(-)$1	1	183	219	12.9720
..(((.(((....(((.....)))))).))).))))	chr22:38062437-38062719(+)$1	1	187	223	13.8825
..((((((((((((((.....)))))))))))))))	chr4:108831933-108832169(+)$1	1	194	230	14.9156
(((((((((..(((.........)))..))))))))	chr3:149236273-149236502(-)$1	1	189	225	15.7243
.((((((((((((((((....))).)))))))))))	chrX:70793638-70793885(+)$1	1	83	119	15.2911
(.((((((((((.(((......))).))))).))))	chr7:131191252-131191475(-)$1	1	76	112	13.4368
(((.(.(((...((((......))))...))).).)	chr3:133307466-133307752(+)$1	1	21	57	16.0736
))((((((((((((((..((..((((((((((((((	chr12:4410619-4410842(+)$1	1	21	57	12.6301
(((((((((.((.(((....))))).))))))))).	chr5:137902616-137902876(-)$1	1	58	94	13.4201
((((((((((..((((......))))))))))))))	chr7:99637166-99637396(+)$1	1	187	223	18.8004
.(((((.(((((((((.........))))))))).)	chr2:60686294-60686521(-)$1	1	71	107	12.5334
((.(..(((....((((....))))...)))..).)	chr12:54628261-54628640(-)$1	1	329	365	12.3402
(...((((((((((((......))))))).))))).	chr1:224346022-224346260(+)$1	1	39	75	14.0148
...(.(((.(((((((......)))))))))))...	chr20:34257032-34257271(-)$1	1	5	41	15.7595
.(((.(((((((((.((.....))))))))))).))	chr1:155305547-155305798(-)$1	1	80	116	14.1641
)).(.(((((((((((......))))))))))).).	chr1:46035529-46035826(+)$1	1	16	52	16.1964
(((.((.((((((((((.....)))))))))).)).	chr8:127565110-127565336(-)$1	1	168	204	15.0439
((((..(((..(((((......))))))))..))))	chr13:28519447-28519668(+)$1	1	160	196	13.3736
(((((((((.((((((.....)))))).))))))))	chr1:179813810-179814063(-)$1	1	57	93	14.7469
(((((((((..(((.........)))..))))))))	chr18:56997989-56998212(-)$1	1	107	143	15.7243
(((.(.(((...((((......))))...))).).)	chr5:151183574-151183798(+)$1	1	13	49	16.3036
((((((...((((.(((.....))).)))).)))))	chr17:41844361-41844604(-)$1	1	192	228	12.7488
((((((((.((.(((((.....))))).)).)))))	chr12:27908200-27908457(+)$1	1	185	221	14.1221

#PSSM
d : 0.18	= : 0.18	: : 0.08	e : 0.08	i : 0.06	g : 0.06	f : 0.06	c : 0.06	! : 0.04	h : 0.04	" : 0.04	b : 0.02	# : 0.02	D : 0.02	& : 0.02	$ : 0.02	[ : 0.02	
= : 0.19	e : 0.14	d : 0.12	g : 0.08	" : 0.08	c : 0.08	i : 0.06	f : 0.06	[ : 0.04	h : 0.04	D : 0.02	! : 0.02	b : 0.02	$ : 0.02	: : 0.02	
= : 0.23	e : 0.16	c : 0.12	d : 0.12	i : 0.08	g : 0.08	" : 0.06	f : 0.02	b : 0.02	$ : 0.02	h : 0.02	[ : 0.02	: : 0.02	a : 0.02	
= : 0.23	c : 0.12	e : 0.12	[ : 0.12	i : 0.08	g : 0.08	" : 0.08	a : 0.06	d : 0.04	f : 0.02	b : 0.02	h : 0.02	
= : 0.23	c : 0.14	e : 0.14	i : 0.10	g : 0.08	[ : 0.08	" : 0.06	b : 0.04	a : 0.04	! : 0.04	f : 0.02	# : 0.02	
= : 0.23	i : 0.14	e : 0.12	[ : 0.10	c : 0.10	" : 0.10	g : 0.08	# : 0.04	! : 0.04	f : 0.02	b : 0.02	
= : 0.32	c : 0.18	i : 0.12	" : 0.10	[ : 0.08	e : 0.06	g : 0.04	# : 0.04	f : 0.02	$ : 0.02	b : 0.02	
= : 0.34	i : 0.14	c : 0.14	" : 0.08	[ : 0.06	b : 0.06	e : 0.06	g : 0.04	# : 0.04	f : 0.02	$ : 0.02	
= : 0.30	c : 0.14	i : 0.12	$ : 0.06	" : 0.06	b : 0.06	e : 0.06	[ : 0.06	d : 0.04	g : 0.04	a : 0.02	f : 0.02	# : 0.02	
= : 0.23	[ : 0.10	i : 0.10	g : 0.10	c : 0.08	! : 0.08	$ : 0.06	d : 0.06	" : 0.06	b : 0.04	# : 0.04	f : 0.02	e : 0.02	
= : 0.19	! : 0.14	c : 0.10	i : 0.10	g : 0.10	$ : 0.06	d : 0.06	" : 0.06	[ : 0.04	# : 0.04	b : 0.04	a : 0.02	e : 0.02	f : 0.02	
= : 0.19	c : 0.14	e : 0.14	g : 0.10	i : 0.08	d : 0.06	! : 0.06	$ : 0.04	[ : 0.04	# : 0.04	" : 0.04	a : 0.02	b : 0.02	f : 0.02	
= : 0.18	[ : 0.16	e : 0.14	c : 0.10	d : 0.10	g : 0.10	i : 0.08	$ : 0.04	# : 0.04	b : 0.02	a : 0.02	f : 0.02	
c : 0.30	= : 0.18	e : 0.14	d : 0.12	[ : 0.08	g : 0.08	i : 0.06	b : 0.02	f : 0.02	
c : 0.30	d : 0.19	= : 0.16	e : 0.14	g : 0.08	r : 0.04	b : 0.02	i : 0.02	[ : 0.02	f : 0.02	
c : 0.30	d : 0.19	= : 0.16	e : 0.14	g : 0.06	b : 0.04	r : 0.04	[ : 0.02	i : 0.02	f : 0.02	
o : 0.50	d : 0.12	n : 0.08	= : 0.06	c : 0.06	r : 0.06	a : 0.02	l : 0.02	! : 0.02	m : 0.02	b : 0.02	e : 0.02	
o : 0.50	n : 0.21	d : 0.08	r : 0.06	m : 0.06	= : 0.04	l : 0.02	! : 0.02	
o : 0.50	n : 0.21	m : 0.10	l : 0.10	r : 0.06	b : 0.02	
o : 0.50	n : 0.21	m : 0.10	l : 0.08	r : 0.06	g : 0.02	b : 0.02	
o : 0.50	n : 0.21	m : 0.08	l : 0.08	r : 0.06	g : 0.02	! : 0.02	c : 0.02	
o : 0.50	n : 0.14	d : 0.10	c : 0.08	r : 0.06	m : 0.04	g : 0.02	= : 0.02	! : 0.02	f : 0.02	
c : 0.30	d : 0.21	= : 0.14	e : 0.14	g : 0.06	r : 0.06	b : 0.04	a : 0.02	f : 0.02	
c : 0.32	d : 0.21	= : 0.14	e : 0.14	b : 0.06	g : 0.06	] : 0.02	r : 0.02	f : 0.02	
c : 0.27	d : 0.21	= : 0.14	e : 0.14	g : 0.08	] : 0.04	2 : 0.02	b : 0.02	r : 0.02	i : 0.02	f : 0.02	
= : 0.18	] : 0.16	e : 0.14	d : 0.12	2 : 0.08	3 : 0.08	g : 0.08	c : 0.08	i : 0.04	b : 0.02	f : 0.02	
= : 0.21	2 : 0.16	e : 0.16	3 : 0.12	c : 0.08	g : 0.08	i : 0.06	d : 0.04	a : 0.04	b : 0.02	f : 0.02	
= : 0.21	2 : 0.14	3 : 0.14	] : 0.14	i : 0.10	g : 0.10	c : 0.08	d : 0.06	e : 0.02	
= : 0.34	c : 0.16	i : 0.14	g : 0.10	d : 0.06	3 : 0.06	2 : 0.04	a : 0.02	f : 0.02	] : 0.02	e : 0.02	b : 0.02	
= : 0.34	c : 0.18	i : 0.14	b : 0.08	g : 0.08	d : 0.06	3 : 0.04	] : 0.04	f : 0.02	e : 0.02	
= : 0.34	c : 0.18	i : 0.14	g : 0.08	] : 0.06	b : 0.06	e : 0.04	3 : 0.02	d : 0.02	a : 0.02	f : 0.02	2 : 0.02	
= : 0.36	i : 0.16	] : 0.14	c : 0.10	g : 0.08	3 : 0.06	2 : 0.04	f : 0.02	b : 0.02	e : 0.02	
= : 0.30	i : 0.16	e : 0.14	g : 0.08	] : 0.08	c : 0.06	3 : 0.06	b : 0.04	f : 0.02	2 : 0.02	a : 0.02	d : 0.02	
= : 0.27	i : 0.14	e : 0.14	3 : 0.10	g : 0.08	b : 0.06	a : 0.06	c : 0.04	] : 0.04	f : 0.02	4 : 0.02	d : 0.02	
= : 0.23	e : 0.16	] : 0.14	i : 0.12	3 : 0.10	c : 0.06	g : 0.06	4 : 0.04	b : 0.04	a : 0.02	d : 0.02	
= : 0.21	e : 0.16	d : 0.12	i : 0.10	3 : 0.10	c : 0.08	g : 0.06	4 : 0.04	] : 0.04	F : 0.02	f : 0.02	: : 0.02	a : 0.02	

#score	742.3346125355903
#seq	50
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_CDS_m3_run1.txt

#BEAR
[ccccccnnnnnccc]ccc]d	chr5:149826283-149826501(-)$1	218	161	182	11.9593
hhh[cccnnnnnccc]hhhhh	chr15:45968218-45968444(+)$1	226	66	87	10.7710
"""ddddnnnnndddd333bb	chr2:70315020-70315245(+)$1	225	182	203	10.3333
ffffcccnnnnnccc4444ff	chr14:35871639-35871869(-)$1	230	72	93	11.6653
eeeee[annnnna]eeeee]a	chr12:111169493-111169718(-)$1	225	179	200	10.0973
eeeeebbnnnnnbb333eeee	chr12:56718034-56718252(-)$1	218	134	155	10.5638
!ffffffnnnnnffffff22d	chr10:91477312-91477532(+)$1	220	40	61	9.7218
cc!!cccnnnnnccc333ccc	chr4:13605829-13606056(-)$1	227	51	72	13.0338
eeee[bbnnnnnbb]eeeeec	chr2:99261841-99262068(-)$1	227	49	70	10.0343
[ffffffnnnnnffffff22c	chr19:19790702-19790926(+)$1	224	8	29	9.8232
ddd[cccnnnnncccdddd44	chr5:179048281-179048494(-)$1	213	131	152	11.2266
ccc[cccooooooccc]ccc2	chr10:124753312-124753532(-)$1	220	184	205	9.2903
gggggggooooooggggggg:	chr15:52902264-52902483(-)$1	219	53	74	7.7556
eeee[bbnnnnnbbeeeee]e	chr5:180276323-180276552(-)$1	229	87	108	9.9858
eee[cccooooooccc]eeee	chr12:48177507-48177732(-)$1	225	17	38	9.0373
gggggggooooooggggggg2	chr13:30805458-30805676(-)$1	218	33	54	8.4470
eeeecccnnnnnccc]eeeee	chr17:38325557-38325784(+)$1	227	35	56	11.3662
gggggggooooooggggggg]	chr20:30914562-30914781(+)$1	219	71	92	8.6226
dddddddnnnnndddd333dd	chr21:30316781-30317006(-)$1	225	146	167	10.0929
#ffffffnnnnnffffff22d	chr12:97328854-97329077(+)$1	223	192	213	9.6167
mccccccnnnnnccccccccc	chr9:71679814-71680045(+)$1	231	79	100	11.1505
c!!ddddnnnnndddd333cc	chr2:73678240-73678470(+)$1	230	143	164	11.0028
####cccnnnnncccbb333d	chr16:23491958-23492188(-)$1	230	112	133	11.8080
gggggggnnnnnggggggg:c	chr11:117034447-117034680(+)$1	233	194	215	10.4846
d"""cccnnnnncccdddddd	chr6:109689950-109690172(-)$1	222	153	174	11.2181
fff[cccnnnnnccc]fffff	chr14:102551629-102551849(-)$1	220	17	38	11.4302
iiiiiiinnnnniiiiiiiii	chr1:78187676-78187898(-)$1	222	52	73	11.4049
iiiiiiiooooooiiiiiiii	chr5:37314252-37314475(-)$1	223	173	194	8.6801
=====bbnnnnnbb333====	chr17:73625375-73625592(-)$1	217	56	77	11.7392
b####bbnnnnnbb333bb44	chr11:111953388-111953608(+)$1	220	123	144	10.4133
ddd!!bbnnnnnbb22dddd]	chr19:33353323-33353540(+)$1	217	71	92	9.6146
gggggggooooooggggggg3	chr3:33853490-33853717(+)$1	227	13	34	8.7080
eeeeebbnnnnnbb]eeeee3	chr10:97453048-97453273(-)$1	225	35	56	9.9243
gggggggnnnnngggggggdd	chr1:70736491-70736713(-)$1	222	143	164	11.1330
ccc!!bbnnnnnbb22ccc:f	chr14:72201903-72202121(+)$1	218	97	118	9.6306
ddd[cccooooooccc]dddd	chr17:18219207-18219444(+)$1	237	123	144	8.5798
ccc[cccnnnnncccccc000	chr19:58058759-58058983(-)$1	224	122	143	11.0737
:bb[cccnnnnnccc]bbggg	chr7:43917708-43917930(-)$1	222	109	130	10.1193
gggggggnnnnnggggggg]c	chr13:32698639-32698860(+)$1	221	12	33	11.4388
iiiiiiinnnnniiiiiiiii	chr1:160061534-160061755(-)$1	221	145	166	11.4049
ggggcccnnnnnccc>>>>>>	chr19:12222958-12223178(+)$1	220	58	79	11.0987
cc!!cccnnnnncccccc]cc	chr3:127779310-127779552(+)$1	242	155	176	12.3495
c"""cccnnnnnccc333ccc	chr19:41257192-41257417(+)$1	225	170	191	12.9237
gggggggnnnnnggggggg::	chr20:55048290-55048506(+)$1	216	34	55	9.5605
cc!!cccooooooccc4444c	chr16:3274126-3274350(-)$1	224	106	127	9.8904
"""ddddnnnnndddd4444b	chr1:223940460-223940685(+)$1	225	115	136	10.3358
g[eeeeeooooooeeeee]gg	chr16:14041708-14041943(+)$1	235	164	185	7.3126
ggg[cccnnnnnccc22gggg	chr15:56985205-56985436(-)$1	231	62	83	12.3558
fff[cccnnnnnccc4444ff	chr2:233074945-233075168(+)$1	223	151	172	12.0835
eee[cccooooooccc22eee	chr16:58199402-58199632(-)$1	230	108	129	8.9293
c"""cccnnnnnccc333ccc	chr16:68225311-68225536(+)$1	225	23	44	12.9237
cccddddnnnnndddd]cccb	chr19:6380200-6380420(-)$1	220	110	131	9.9211
ggggg[annnnna]ggggggg	chr1:90058443-90058670(+)$1	227	85	106	11.1520
"ccc[bbnnnnnbbccc22cc	chr16:70605499-70605736(+)$1	237	202	223	10.6820
[bb[cccnnnnnccc]bbddd	chr11:11374195-11374419(-)$1	224	9	30	10.9141
c[eeeeennnnneeeee4444	chr10:17278205-17278435(+)$1	230	26	47	10.1388
###cccooooooccc333iii	chr16:2580913-2581143(-)$1	230	171	192	9.3648
eee[cccooooooccc]eeee	chr9:104170273-104170490(+)$1	217	118	139	9.0373

#otherMatches

#Seq PSSM
GGGUGGUAGAAAACCUGCUGG	chr5:149826283-149826501(-)$1	218	161	182	11.9593
CUUAUUUUUCUCAGACAGGGA	chr15:45968218-45968444(+)$1	226	66	87	10.7710
GGCUCCCUGAUUGGGAAAGGC	chr2:70315020-70315245(+)$1	225	182	203	10.3333
UUGAAGUGUGGGGCUGAUGUC	chr14:35871639-35871869(-)$1	230	72	93	11.6653
UGAUUGAUUAACUGAGUCAAG	chr12:111169493-111169718(-)$1	225	179	200	10.0973
GAGCUGGAAAUACCACAGGCU	chr12:56718034-56718252(-)$1	218	134	155	10.5638
CUGGUUCAGAACGAACUAUGA	chr10:91477312-91477532(+)$1	220	40	61	9.7218
ACAAAUCAAGAAGGUCAAGUG	chr4:13605829-13606056(-)$1	227	51	72	13.0338
UCAAUUUUCUCUAGCUUGAAG	chr2:99261841-99262068(-)$1	227	49	70	10.0343
AGUGGAGGAAAACUCUACGAA	chr19:19790702-19790926(+)$1	224	8	29	9.8232
UUCAUCUACACCAGAGAAGGC	chr5:179048281-179048494(-)$1	213	131	152	11.2266
ACAAGUAUGAUUUUGCCUGUC	chr10:124753312-124753532(-)$1	220	184	205	9.2903
CAGUAUUCACACUAAUAUUGG	chr15:52902264-52902483(-)$1	219	53	74	7.7556
UGUGUGGAAAAGCCUACAUCU	chr5:180276323-180276552(-)$1	229	87	108	9.9858
CUGCAGCCCUGGUGCUCCAGC	chr12:48177507-48177732(-)$1	225	17	38	9.0373
GAUAAAUCAUUUAAUUUGUCU	chr13:30805458-30805676(-)$1	218	33	54	8.4470
AUGGAGGAGUGACCUACUAUA	chr17:38325557-38325784(+)$1	227	35	56	11.3662
CUUCUUUGAUGAAGAGGAAGA	chr20:30914562-30914781(+)$1	219	71	92	8.6226
UCAGCUGUGAUUUGGCCUGUG	chr21:30316781-30317006(-)$1	225	146	167	10.0929
AUUUGUGAUUUAUAUAGACCU	chr12:97328854-97329077(+)$1	223	192	213	9.6167
CCUAUGUGAUCAACAAGCAGA	chr9:71679814-71680045(+)$1	231	79	100	11.1505
CGAUUGUUAACUACAAACAGG	chr2:73678240-73678470(+)$1	230	143	164	11.0028
CAAAUGACCUCCUCACCCAAG	chr16:23491958-23492188(-)$1	230	112	133	11.8080
UCUUUAGGUCAGCUGAGGAAU	chr11:117034447-117034680(+)$1	233	194	215	10.4846
AUUUGUGUAACUCACUGAAGC	chr6:109689950-109690172(-)$1	222	153	174	11.2181
GUUAGGCAUGGCGUUGAGCAC	chr14:102551629-102551849(-)$1	220	17	38	11.4302
CUUGCCAAUUCCUGGCAAGGA	chr1:78187676-78187898(-)$1	222	52	73	11.4049
AAGGuaauuuuuuuuauuuuu	chr5:37314252-37314475(-)$1	223	173	194	8.6801
GAGCUGGUUUCCCCAAAGGCU	chr17:73625375-73625592(-)$1	217	56	77	11.7392
AUUCAGCAUCCAGCAGUUCUG	chr11:111953388-111953608(+)$1	220	123	144	10.4133
GAUGAUGAUGGCCACGAUCAC	chr19:33353323-33353540(+)$1	217	71	92	9.6146
AUUACAUAAAUGCAUGUAAUA	chr3:33853490-33853717(+)$1	227	13	34	8.7080
CAUAGUCUUACCGAUCUGUGU	chr10:97453048-97453273(-)$1	225	35	56	9.9243
GAAGCUUCCUCCAGGCUUUCC	chr1:70736491-70736713(-)$1	222	143	164	11.1330
AGCCUCAUUUUUUGCUGCUAG	chr14:72201903-72202121(+)$1	218	97	118	9.6306
CAAUGACACCAAAGUUUUUGG	chr17:18219207-18219444(+)$1	237	123	144	8.5798
CUCAUCCACACCGGGGAGAAA	chr19:58058759-58058983(-)$1	224	122	143	11.0737
AUGUCCUGGUAAAGGUCAGCA	chr7:43917708-43917930(-)$1	222	109	130	10.1193
UGAUUGUCAUAUAUAGUUAUU	chr13:32698639-32698860(+)$1	221	12	33	11.4388
CCUUACUCCCCAGGUGAGGGA	chr1:160061534-160061755(-)$1	221	145	166	11.4049
ACUGGGGAGAAACCCUAUGAA	chr19:12222958-12223178(+)$1	220	58	79	11.0987
GGAAGGCAUUCAGCCCCACUA	chr3:127779310-127779552(+)$1	242	155	176	12.3495
UCAAUGAGAAGAUCAAGAAGG	chr19:41257192-41257417(+)$1	225	170	191	12.9237
GAAAAUUAAUUGAAUUUUUUG	chr20:55048290-55048506(+)$1	216	34	55	9.5605
CCUAUGACUGUAAUCACUGUG	chr16:3274126-3274350(-)$1	224	106	127	9.8904
UACCUACAAGAAGUGGAAACU	chr1:223940460-223940685(+)$1	225	115	136	10.3358
AUGCAACGGCGGAGUUGUUUG	chr16:14041708-14041943(+)$1	235	164	185	7.3126
UCAUCAGAGUUACUGUUUGAC	chr15:56985205-56985436(-)$1	231	62	83	12.3558
UGCAAGCCACUCGCUGACGGU	chr2:233074945-233075168(+)$1	223	151	172	12.0835
CUGCGAUACGACCAUCAACAG	chr16:58199402-58199632(-)$1	230	108	129	8.9293
GUCUGCUACAACAGCUUCCCC	chr16:68225311-68225536(+)$1	225	23	44	12.9237
CUUCUCCCUCAAGGAGUGAGG	chr19:6380200-6380420(-)$1	220	110	131	9.9211
UUGAGGAGAACUUGCUCAAUA	chr1:90058443-90058670(+)$1	227	85	106	11.1520
CGCUACGCCUUCUGAGCCCUC	chr16:70605499-70605736(+)$1	237	202	223	10.6820
AGAAUUUGAGAGGAGGUCCCA	chr11:11374195-11374419(-)$1	224	9	30	10.9141
UACUUGGUUUUUCCAAGAAAA	chr10:17278205-17278435(+)$1	230	26	47	10.1388
CCUGGCAAGACAGCUCCUCUC	chr16:2580913-2581143(-)$1	230	171	192	9.3648
CCUAUGGGAAAUACCAAGGGA	chr9:104170273-104170490(+)$1	217	118	139	9.0373

#DB
.((((((.....))).))).)	chr5:149826283-149826501(-)$1	1	161	182	11.9593
(((.(((.....))).)))))	chr15:45968218-45968444(+)$1	1	66	87	10.7710
...((((.....))))...))	chr2:70315020-70315245(+)$1	1	182	203	10.3333
(((((((.....)))....))	chr14:35871639-35871869(-)$1	1	72	93	11.6653
(((((.(.....).))))).)	chr12:111169493-111169718(-)$1	1	179	200	10.0973
(((((((.....))...))))	chr12:56718034-56718252(-)$1	1	134	155	10.5638
.((((((.....))))))..)	chr10:91477312-91477532(+)$1	1	40	61	9.7218
((..(((.....)))...)))	chr4:13605829-13606056(-)$1	1	51	72	13.0338
((((.((.....)).))))))	chr2:99261841-99262068(-)$1	1	49	70	10.0343
.((((((.....))))))..)	chr19:19790702-19790926(+)$1	1	8	29	9.8232
(((.(((.....)))))))..	chr5:179048281-179048494(-)$1	1	131	152	11.2266
(((.(((......))).))).	chr10:124753312-124753532(-)$1	1	184	205	9.2903
(((((((......))))))).	chr15:52902264-52902483(-)$1	1	53	74	7.7556
((((.((.....))))))).)	chr5:180276323-180276552(-)$1	1	87	108	9.9858
(((.(((......))).))))	chr12:48177507-48177732(-)$1	1	17	38	9.0373
(((((((......))))))).	chr13:30805458-30805676(-)$1	1	33	54	8.4470
(((((((.....))).)))))	chr17:38325557-38325784(+)$1	1	35	56	11.3662
(((((((......))))))).	chr20:30914562-30914781(+)$1	1	71	92	8.6226
(((((((.....))))...))	chr21:30316781-30317006(-)$1	1	146	167	10.0929
.((((((.....))))))..)	chr12:97328854-97329077(+)$1	1	192	213	9.6167
.)))(((.....)))((((((	chr9:71679814-71680045(+)$1	1	79	100	11.1505
(..((((.....))))...))	chr2:73678240-73678470(+)$1	1	143	164	11.0028
....(((.....)))))...)	chr16:23491958-23492188(-)$1	1	112	133	11.8080
(((((((.....))))))).(	chr11:117034447-117034680(+)$1	1	194	215	10.4846
(...(((.....)))))))))	chr6:109689950-109690172(-)$1	1	153	174	11.2181
(((.(((.....))).)))))	chr14:102551629-102551849(-)$1	1	17	38	11.4302
(((((((.....)))))))))	chr1:78187676-78187898(-)$1	1	52	73	11.4049
(((((((......))))))))	chr5:37314252-37314475(-)$1	1	173	194	8.6801
(((((((.....))...))))	chr17:73625375-73625592(-)$1	1	56	77	11.7392
(....((.....))...))..	chr11:111953388-111953608(+)$1	1	123	144	10.4133
(((..((.....))..)))).	chr19:33353323-33353540(+)$1	1	71	92	9.6146
(((((((......))))))).	chr3:33853490-33853717(+)$1	1	13	34	8.7080
(((((((.....)).))))).	chr10:97453048-97453273(-)$1	1	35	56	9.9243
(((((((.....)))))))((	chr1:70736491-70736713(-)$1	1	143	164	11.1330
(((..((.....))..))).(	chr14:72201903-72202121(+)$1	1	97	118	9.6306
(((.(((......))).))))	chr17:18219207-18219444(+)$1	1	123	144	8.5798
(((.(((.....))))))...	chr19:58058759-58058983(-)$1	1	122	143	11.0737
.((.(((.....))).))(((	chr7:43917708-43917930(-)$1	1	109	130	10.1193
(((((((.....))))))).)	chr13:32698639-32698860(+)$1	1	12	33	11.4388
(((((((.....)))))))))	chr1:160061534-160061755(-)$1	1	145	166	11.4049
(((((((.....)))......	chr19:12222958-12223178(+)$1	1	58	79	11.0987
((..(((.....)))))).))	chr3:127779310-127779552(+)$1	1	155	176	12.3495
(...(((.....)))...)))	chr19:41257192-41257417(+)$1	1	170	191	12.9237
(((((((.....)))))))..	chr20:55048290-55048506(+)$1	1	34	55	9.5605
((..(((......)))....)	chr16:3274126-3274350(-)$1	1	106	127	9.8904
...((((.....))))....)	chr1:223940460-223940685(+)$1	1	115	136	10.3358
(.(((((......))))).))	chr16:14041708-14041943(+)$1	1	164	185	7.3126
(((.(((.....)))..))))	chr15:56985205-56985436(-)$1	1	62	83	12.3558
(((.(((.....)))....))	chr2:233074945-233075168(+)$1	1	151	172	12.0835
(((.(((......)))..)))	chr16:58199402-58199632(-)$1	1	108	129	8.9293
(...(((.....)))...)))	chr16:68225311-68225536(+)$1	1	23	44	12.9237
(((((((.....)))).))))	chr19:6380200-6380420(-)$1	1	110	131	9.9211
(((((.(.....).)))))))	chr1:90058443-90058670(+)$1	1	85	106	11.1520
.(((.((.....)))))..))	chr16:70605499-70605736(+)$1	1	202	223	10.6820
.((.(((.....))).)))))	chr11:11374195-11374419(-)$1	1	9	30	10.9141
(.(((((.....)))))....	chr10:17278205-17278435(+)$1	1	26	47	10.1388
...(((......)))...)))	chr16:2580913-2581143(-)$1	1	171	192	9.3648
(((.(((......))).))))	chr9:104170273-104170490(+)$1	1	118	139	9.0373

#PSSM
g : 0.20	c : 0.18	e : 0.15	d : 0.08	[ : 0.05	" : 0.05	f : 0.05	# : 0.05	i : 0.05	h : 0.01	! : 0.01	m : 0.01	= : 0.01	b : 0.01	: : 0.01	
g : 0.18	c : 0.17	e : 0.15	f : 0.10	" : 0.08	d : 0.06	# : 0.05	i : 0.05	b : 0.03	[ : 0.03	h : 0.01	! : 0.01	= : 0.01	
e : 0.18	g : 0.18	c : 0.12	f : 0.10	" : 0.08	! : 0.06	d : 0.06	# : 0.05	i : 0.05	b : 0.03	h : 0.01	= : 0.01	
[ : 0.22	g : 0.17	e : 0.13	d : 0.08	! : 0.08	c : 0.06	f : 0.06	" : 0.05	i : 0.05	# : 0.03	= : 0.01	
c : 0.44	g : 0.15	d : 0.08	e : 0.08	f : 0.05	[ : 0.05	i : 0.05	! : 0.03	= : 0.01	# : 0.01	
c : 0.44	b : 0.15	g : 0.13	d : 0.08	f : 0.05	i : 0.05	[ : 0.03	e : 0.03	
c : 0.43	b : 0.15	g : 0.13	d : 0.08	f : 0.05	i : 0.05	a : 0.03	e : 0.03	o : 0.01	
n : 0.77	o : 0.22	
n : 0.77	o : 0.22	
n : 0.77	o : 0.22	
n : 0.77	o : 0.22	
n : 0.77	o : 0.22	
c : 0.34	o : 0.20	b : 0.15	d : 0.08	g : 0.06	f : 0.05	a : 0.03	i : 0.03	e : 0.01	
c : 0.44	b : 0.15	g : 0.13	d : 0.08	f : 0.05	i : 0.05	] : 0.03	e : 0.03	
c : 0.46	g : 0.15	d : 0.08	e : 0.06	3 : 0.05	f : 0.05	i : 0.05	] : 0.03	2 : 0.03	
c : 0.17	g : 0.15	d : 0.12	3 : 0.12	] : 0.10	e : 0.10	f : 0.05	i : 0.05	2 : 0.05	4 : 0.03	b : 0.01	> : 0.01	
3 : 0.17	g : 0.15	e : 0.12	c : 0.10	] : 0.08	4 : 0.06	f : 0.06	d : 0.05	b : 0.05	i : 0.05	2 : 0.03	h : 0.01	> : 0.01	
g : 0.17	e : 0.15	3 : 0.13	c : 0.12	4 : 0.08	f : 0.06	d : 0.06	i : 0.05	b : 0.05	2 : 0.03	h : 0.01	= : 0.01	> : 0.01	
g : 0.18	e : 0.15	c : 0.13	4 : 0.08	d : 0.08	3 : 0.06	2 : 0.06	i : 0.06	] : 0.03	h : 0.01	f : 0.01	= : 0.01	b : 0.01	0 : 0.01	> : 0.01	
c : 0.15	g : 0.13	e : 0.12	d : 0.10	4 : 0.08	] : 0.06	i : 0.06	f : 0.05	2 : 0.05	: : 0.05	h : 0.01	b : 0.01	3 : 0.01	= : 0.01	0 : 0.01	> : 0.01	
c : 0.20	d : 0.15	e : 0.10	f : 0.06	i : 0.06	g : 0.06	b : 0.05	4 : 0.05	2 : 0.03	: : 0.03	] : 0.03	3 : 0.03	h : 0.01	a : 0.01	= : 0.01	0 : 0.01	> : 0.01	

#score	605.3791659441055
#seq	58
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_CDS_m1_run1.txt

#BEAR
========vvvvvvvvvvvvv=====	chr2:198267206-198267454(-)$1	248	194	220	23.7714
[dddd[bbtttttttttttbb]dddd	chr2:181925384-181925637(+)$1	253	119	145	22.4229
ggfffffftttttttttttffffff2	chrX:53440123-53440347(-)$1	224	78	104	22.9908
[gggggggtttttttttttggggggg	chr10:79795009-79795235(+)$1	226	27	53	23.7660
hhh[ddddtttttttttttdddd333	chr7:50514713-50514955(-)$1	242	69	95	23.1771
!!fffffftttttttttttffffffb	chr17:55026652-55026886(-)$1	234	10	36	23.0452
bb[dddduuuuuuuuuuuudddd]bb	chr11:61897371-61897594(+)$1	223	64	90	22.0783
dd[ddddavvvvvvvvvvvvva]ddd	chr3:122990327-122990549(+)$1	222	145	171	22.9767
eee!!ccctttttttttttccc22ee	chr2:9580552-9580780(+)$1	228	189	215	23.2225
ff:eeeeettttttttttteeeee::	chr12:12630356-12630585(-)$1	229	97	123	20.8678
dddd[cccuuuuuuuuuuuuccc444	chr12:29493979-29494226(-)$1	247	84	110	23.2346
$eeeeevvvvvvvvvvvvveeeee22	chr10:28971005-28971237(+)$1	232	65	91	22.5848
d!!eeeeeuuuuuuuuuuuueeeee2	chr10:129909822-129910060(-)$1	238	163	189	23.9541
)))))ccctttttttttttccc0000	chr8:94747460-94747732(-)$1	272	176	202	20.3037
==a[ddddvvvvvvvvvvvvvdddd5	chr6:142525056-142525301(+)$1	245	69	95	22.6865
ggggggvvvvvvvvvvvvvggggggg	chr1:197070194-197070430(-)$1	236	32	58	22.7964
c[ddddbbvvvvvvvvvvvvvbb]dd	chr1:150432581-150432811(+)$1	230	33	59	22.2140
ffff[ccctttttttttttcccffff	chr11:34118691-34118942(+)$1	251	208	234	23.2365
$$fffffftttttttttttffffff6	chr19:44636497-44636724(+)$1	227	134	160	22.6429
d!!eeeeettttttttttteeeee22	chr3:128889280-128889505(-)$1	225	65	91	23.9898
ddd[bbvvvvvvvvvvvvvbb]dddd	chr19:58805634-58805859(+)$1	225	165	191	21.1791
fffffyyyyyyyyyyyyyyyyfffff	chr14:24658820-24659045(-)$1	225	5	31	19.6380
###eeeeeuuuuuuuuuuuueeeeeb	chrX:153667085-153667318(+)$1	233	20	46	23.6593
"""dddduuuuuuuuuuuudddd]ee	chr7:98961070-98961306(+)$1	236	8	34	23.1838
fffeeeeevvvvvvvvvvvvveeeee	chr2:176981789-176982015(+)$1	226	72	98	23.1486
:::eeeeevvvvvvvvvvvvveeeee	chr5:134010634-134010866(+)$1	232	195	221	20.6618
bffffffvvvvvvvvvvvvvffffff	chr5:98224717-98224946(-)$1	229	113	139	22.4410
[eeeeewwwwwwwwwwwwwweeeee]	chr9:97563126-97563350(+)$1	224	46	72	22.2559
gdddd[bbtttttttttttbb]dddd	chrX:119387881-119388108(+)$1	227	33	59	22.2978
e[a[ddddtttttttttttdddd]a]	chr1:82455975-82456224(+)$1	249	4	30	23.8045
eeeeeeevvvvvvvvvvvvveeeee]	chr1:45480932-45481168(+)$1	236	145	171	23.6768
%gggggggtttttttttttggggggg	chr6:36566615-36566854(+)$1	239	171	197	23.2111
cgggggggtttttttttttggggggg	chr5:68661067-68661294(-)$1	227	18	44	23.6640
========uuuuuuuuuuuu======	chr3:169700887-169701120(+)$1	233	174	200	23.9075
ddd[ddddtttttttttttdddd]dd	chr22:38897051-38897279(-)$1	228	56	82	23.1372
d[ddddvvvvvvvvvvvvvdddd333	chr15:68570841-68571077(+)$1	236	162	188	22.8510
dd[eeeeeuuuuuuuuuuuueeeee]	chr1:112304812-112305034(+)$1	222	121	147	23.8208
c!!eeeeeuuuuuuuuuuuueeeee]	chr1:36766495-36766731(+)$1	236	128	154	24.2093
cc[ddddyyyyyyyyyyyyyyyyddd	chr2:27870606-27870829(+)$1	223	128	154	20.0793
""fffffftttttttttttffffff3	chr11:34135247-34135477(+)$1	230	79	105	23.4597
D:eeeeeuuuuuuuuuuuueeeee::	chr19:3121299-3121525(+)$1	226	52	78	19.5523
$$$$$ccctttttttttttccc5555	chr17:7473659-7473911(+)$1	252	148	174	20.1247
hhhhhhhhwwwwwwwwwwwwwwhhhh	chr3:52741714-52741938(+)$1	224	179	205	18.9098
eefffffftttttttttttffffff]	chr17:34149552-34149793(+)$1	241	75	101	22.9345
D:eeeeeuuuuuuuuuuuueeeeeff	chr19:44980979-44981199(-)$1	220	159	185	21.1649
cc[cccvvvvvvvvvvvvvccc]ccc	chr16:69317894-69318126(+)$1	232	101	127	22.7524
fffff[bbtttttttttttbb22fff	chr1:23645045-23645266(-)$1	221	174	200	21.8234
eeeeecccwwwwwwwwwwwwwwccc]	chr3:47543039-47543264(-)$1	225	179	205	21.4363
iiiiiiiiuuuuuuuuuuuuiiiiii	chr7:100486008-100486233(+)$1	225	62	88	23.3722
####cccuuuuuuuuuuuuccc22ee	chr1:109235275-109235533(+)$1	258	90	116	22.8776
=====[bbvvvvvvvvvvvvvbb]==	chr1:186321012-186321243(-)$1	231	163	189	22.7849
cc[eeeeevvvvvvvvvvvvveeeee	chr3:9807433-9807659(+)$1	226	16	42	23.6414
ii!!dddduuuuuuuuuuuudddd44	chr10:121336906-121337130(-)$1	224	33	59	23.5993
[gggggggtttttttttttggggggg	chr15:101120370-101120594(-)$1	224	133	159	23.7660
$$$$dddduuuuuuuuuuuudddd55	chr1:153784167-153784392(-)$1	225	44	70	21.4178
ddd!!ccctttttttttttccc]ddd	chr2:3200594-3200826(-)$1	232	130	156	23.3401
b[bba!!attttttttttta22a]bb	chr9:128099687-128099913(+)$1	226	65	91	22.0899
ggggggguuuuuuuuuuuuggggggg	chr19:4028705-4028930(+)$1	225	17	43	23.0445
$$$dddduuuuuuuuuuuuddddggg	chr19:19136650-19136878(-)$1	228	58	84	22.6151
========vvvvvvvvvvvvv=====	chr6:159026204-159026431(+)$1	227	154	180	23.7714

#otherMatches

#Seq PSSM
ugucuuuuuuuuuuuuucuuuaggag	chr2:198267206-198267454(-)$1	248	194	220	23.7714
UGUCUAUUUGUUCCCUUUUGACAGAC	chr2:181925384-181925637(+)$1	253	119	145	22.4229
GAAGGCUGAAGAGGACACACAGUUUA	chrX:53440123-53440347(-)$1	224	78	104	22.9908
AGGUCUUGGAAAAUCACAGCAAGGCC	chr10:79795009-79795235(+)$1	226	27	53	23.7660
UACCGUGCACAGAUAUUACGCAUUCA	chr7:50514713-50514955(-)$1	242	69	95	23.1771
AACAUGGCAUGAUGGAGGAGCUGUGG	chr17:55026652-55026886(-)$1	234	10	36	23.0452
CUGAGUCUCCCACGAUGCUGACUAAG	chr11:61897371-61897594(+)$1	223	64	90	22.0783
CUGGCAGCUUUUCUUUCAUGUGACUG	chr3:122990327-122990549(+)$1	222	145	171	22.9767
AAACAGAUCAACAUCAAUAAUCCCUU	chr2:9580552-9580780(+)$1	228	189	215	23.2225
CUUUGGAAUACUACAAACCUUCCACU	chr12:12630356-12630585(-)$1	229	97	123	20.8678
GAGGAUGGCCACACAGACAACCACUU	chr12:29493979-29494226(-)$1	247	84	110	23.2346
UGCUUCGAAGUGAAAAUAAGAGGCUG	chr10:28971005-28971237(+)$1	232	65	91	22.5848
GUCUUAGAUCUUAUAAAUCUUUUGAC	chr10:129909822-129910060(-)$1	238	163	189	23.9541
ACAAAUGCUGAAGUUCAUUGCACGUU	chr8:94747460-94747732(-)$1	272	176	202	20.3037
AGCAAGUAAUACUAUCCAACCUACUC	chr6:142525056-142525301(+)$1	245	69	95	22.6865
AACUGCAGUGCGUACCCAAGCAGUUA	chr1:197070194-197070430(-)$1	236	32	58	22.7964
AAAGGCCUCUUCAUGUACCCCAGUGC	chr1:150432581-150432811(+)$1	230	33	59	22.2140
UUAGUGUUGUUGCUUAAUGAACCUAA	chr11:34118691-34118942(+)$1	251	208	234	23.2365
AGCCAUACAAAUGUGAGAAGUGUGGA	chr19:44636497-44636724(+)$1	227	134	160	22.6429
UGUGAAAACUUUUAAUUUCUUUUUUA	chr3:128889280-128889505(-)$1	225	65	91	23.9898
ACUCAGAACAUAACUCCAGCUUAGUC	chr19:58805634-58805859(+)$1	225	165	191	21.1791
CUGUGUAUCAUCUCUUUUCUUCACAG	chr14:24658820-24659045(-)$1	225	5	31	19.6380
UACAGCUGUAUAAGCGUUUUCAGUUG	chrX:153667085-153667318(+)$1	233	20	46	23.6593
UAAGCUGCCCUUACACUAUUAGUCAG	chr7:98961070-98961306(+)$1	236	8	34	23.1838
UGCUCCUUCACCACCAACAUUAAGGA	chr2:176981789-176982015(+)$1	226	72	98	23.1486
CAUGCUUCCGUCAACACCUUUGAAGC	chr5:134010634-134010866(+)$1	232	195	221	20.6618
CUCAUUAAACCACCAGAUAAUAAUGA	chr5:98224717-98224946(-)$1	229	113	139	22.4410
GGCUGAUCCCUCCUUGCCUCUCAGCA	chr9:97563126-97563350(+)$1	224	46	72	22.2559
ACAGGUCCAAUCUAACCCAGGCCCUG	chrX:119387881-119388108(+)$1	227	33	59	22.2978
UCCUGAACGACAUUAAAAAGUUUUGU	chr1:82455975-82456224(+)$1	249	4	30	23.8045
GGCCAUGGGCUUUAUCCUGACAUGGA	chr1:45480932-45481168(+)$1	236	145	171	23.6768
GUAUUGGUGUAAUGGAGUAGCUAGUA	chr6:36566615-36566854(+)$1	239	171	197	23.2111
AGGCAAAGAAAUCAAACCCCUUUGCC	chr5:68661067-68661294(-)$1	227	18	44	23.6640
AGAAGUUCAGUUUUCUAUAGGAGUUU	chr3:169700887-169701120(+)$1	233	174	200	23.9075
UGCGUAAAAAAAAGUGGGAUUUGAGU	chr22:38897051-38897279(-)$1	228	56	82	23.1372
GUAGGUACAUCCCAAGCCAGCCUCUC	chr15:68570841-68571077(+)$1	236	162	188	22.8510
GCAGAGUCCUCAUUUCCACAGAUUUG	chr1:112304812-112305034(+)$1	222	121	147	23.8208
UGGGGACCAAAGACUUUGUGGGUCCA	chr1:36766495-36766731(+)$1	236	128	154	24.2093
UUGAUCCUGACUCGAGGAACCUUGGA	chr2:27870606-27870829(+)$1	223	128	154	20.0793
UAGUGGUCAUCCUCCUACGGACCAUG	chr11:34135247-34135477(+)$1	230	79	105	23.4597
GAUGUACAUCUCUCCCUCCGUACACU	chr19:3121299-3121525(+)$1	226	52	78	19.5523
UAAGGUUUGAGGGGGUAGGAGAGAGA	chr17:7473659-7473911(+)$1	252	148	174	20.1247
AUAAGAGCUAAAACCACCUAAUGCUC	chr3:52741714-52741938(+)$1	224	179	205	18.9098
CUCCAUUUCUAUUUAGCCAAGGUGGA	chr17:34149552-34149793(+)$1	241	75	101	22.9345
AAUGUGGAAAAUCUUUUAACCGCAGU	chr19:44980979-44981199(-)$1	220	159	185	21.1649
UGACCUUACAUUUGCUACCAGGACAG	chr16:69317894-69318126(+)$1	232	101	127	22.7524
UCAGCAGCACAAGCCAGACGCCGGCU	chr1:23645045-23645266(-)$1	221	174	200	21.8234
AGGUCCAGACCUCACUUGCUUGCUGU	chr3:47543039-47543264(-)$1	225	179	205	21.4363
CAUCCUGUACCUCUCACCUCACAGGA	chr7:100486008-100486233(+)$1	225	62	88	23.3722
CAACGAGAAGACCAUGAACCUCAACC	chr1:109235275-109235533(+)$1	258	90	116	22.8776
AAAAUGUAUAAAAGUUAAAUUUAGAU	chr1:186321012-186321243(-)$1	231	163	189	22.7849
GGACAGCAAUCUCAUUCUCCAUGCUG	chr3:9807433-9807659(+)$1	226	16	42	23.6414
AUUUCAUGAUACACAUCAGCCAUGUU	chr10:121336906-121337130(-)$1	224	33	59	23.5993
UAAGUAAUCAAAGUAUGUUAUUAUUU	chr15:101120370-101120594(-)$1	224	133	159	23.7660
UCCACUGUCUCCUCAUCAUUGCAGGC	chr1:153784167-153784392(-)$1	225	44	70	21.4178
AGCGAACGACACCACCCUCCGUGGCU	chr2:3200594-3200826(-)$1	232	130	156	23.3401
GCGUCCAGGAAAUGAAGAGCGAGAAC	chr9:128099687-128099913(+)$1	226	65	91	22.0899
CUACCCCUCCAAUAAGCCCGGGGUGG	chr19:4028705-4028930(+)$1	225	17	43	23.0445
UUUUCUCACUCUGAUUCUCGGGACCA	chr19:19136650-19136878(-)$1	228	58	84	22.6151
GUGCUCACCUUCAUCGUCACUGUGAG	chr6:159026204-159026431(+)$1	227	154	180	23.7714

#DB
((((((((.............)))))	chr2:198267206-198267454(-)$1	1	194	220	23.7714
.((((.((...........)).))))	chr2:181925384-181925637(+)$1	1	119	145	22.4229
((((((((...........)))))).	chrX:53440123-53440347(-)$1	1	78	104	22.9908
.(((((((...........)))))))	chr10:79795009-79795235(+)$1	1	27	53	23.7660
(((.((((...........))))...	chr7:50514713-50514955(-)$1	1	69	95	23.1771
..((((((...........)))))))	chr17:55026652-55026886(-)$1	1	10	36	23.0452
((.((((............)))).))	chr11:61897371-61897594(+)$1	1	64	90	22.0783
((.(((((.............).)))	chr3:122990327-122990549(+)$1	1	145	171	22.9767
(((..(((...........)))..))	chr2:9580552-9580780(+)$1	1	189	215	23.2225
)).(((((...........)))))..	chr12:12630356-12630585(-)$1	1	97	123	20.8678
((((.(((............)))...	chr12:29493979-29494226(-)$1	1	84	110	23.2346
.(((((.............)))))..	chr10:28971005-28971237(+)$1	1	65	91	22.5848
(..(((((............))))).	chr10:129909822-129910060(-)$1	1	163	189	23.9541
.....(((...........)))....	chr8:94747460-94747732(-)$1	1	176	202	20.3037
(((.((((.............)))).	chr6:142525056-142525301(+)$1	1	69	95	22.6865
((((((.............)))))))	chr1:197070194-197070430(-)$1	1	32	58	22.7964
(.((((((.............)).))	chr1:150432581-150432811(+)$1	1	33	59	22.2140
((((.(((...........)))))))	chr11:34118691-34118942(+)$1	1	208	234	23.2365
..((((((...........)))))).	chr19:44636497-44636724(+)$1	1	134	160	22.6429
(..(((((...........)))))..	chr3:128889280-128889505(-)$1	1	65	91	23.9898
(((.((.............)).))))	chr19:58805634-58805859(+)$1	1	165	191	21.1791
(((((................)))))	chr14:24658820-24659045(-)$1	1	5	31	19.6380
...(((((............))))))	chrX:153667085-153667318(+)$1	1	20	46	23.6593
...((((............)))).))	chr7:98961070-98961306(+)$1	1	8	34	23.1838
)))(((((.............)))))	chr2:176981789-176982015(+)$1	1	72	98	23.1486
...(((((.............)))))	chr5:134010634-134010866(+)$1	1	195	221	20.6618
)((((((.............))))))	chr5:98224717-98224946(-)$1	1	113	139	22.4410
.(((((..............))))).	chr9:97563126-97563350(+)$1	1	46	72	22.2559
(((((.((...........)).))))	chrX:119387881-119388108(+)$1	1	33	59	22.2978
(.(.((((...........)))).).	chr1:82455975-82456224(+)$1	1	4	30	23.8045
(((((((.............))))).	chr1:45480932-45481168(+)$1	1	145	171	23.6768
.(((((((...........)))))))	chr6:36566615-36566854(+)$1	1	171	197	23.2111
((((((((...........)))))))	chr5:68661067-68661294(-)$1	1	18	44	23.6640
((((((((............))))))	chr3:169700887-169701120(+)$1	1	174	200	23.9075
(((.((((...........)))).))	chr22:38897051-38897279(-)$1	1	56	82	23.1372
(.((((.............))))...	chr15:68570841-68571077(+)$1	1	162	188	22.8510
((.(((((............))))).	chr1:112304812-112305034(+)$1	1	121	147	23.8208
(..(((((............))))).	chr1:36766495-36766731(+)$1	1	128	154	24.2093
((.((((................)))	chr2:27870606-27870829(+)$1	1	128	154	20.0793
..((((((...........)))))).	chr11:34135247-34135477(+)$1	1	79	105	23.4597
(.(((((............)))))..	chr19:3121299-3121525(+)$1	1	52	78	19.5523
.....(((...........)))....	chr17:7473659-7473911(+)$1	1	148	174	20.1247
((((((((..............))))	chr3:52741714-52741938(+)$1	1	179	205	18.9098
((((((((...........)))))).	chr17:34149552-34149793(+)$1	1	75	101	22.9345
(.(((((............)))))((	chr19:44980979-44981199(-)$1	1	159	185	21.1649
((.(((.............))).)))	chr16:69317894-69318126(+)$1	1	101	127	22.7524
(((((.((...........))..)))	chr1:23645045-23645266(-)$1	1	174	200	21.8234
((((((((..............))).	chr3:47543039-47543264(-)$1	1	179	205	21.4363
((((((((............))))))	chr7:100486008-100486233(+)$1	1	62	88	23.3722
....(((............)))..))	chr1:109235275-109235533(+)$1	1	90	116	22.8776
(((((.((.............)).))	chr1:186321012-186321243(-)$1	1	163	189	22.7849
((.(((((.............)))))	chr3:9807433-9807659(+)$1	1	16	42	23.6414
((..((((............))))..	chr10:121336906-121337130(-)$1	1	33	59	23.5993
.(((((((...........)))))))	chr15:101120370-101120594(-)$1	1	133	159	23.7660
....((((............))))..	chr1:153784167-153784392(-)$1	1	44	70	21.4178
(((..(((...........))).)))	chr2:3200594-3200826(-)$1	1	130	156	23.3401
(.(((..(...........)..).))	chr9:128099687-128099913(+)$1	1	65	91	22.0899
(((((((............)))))))	chr19:4028705-4028930(+)$1	1	17	43	23.0445
...((((............)))))))	chr19:19136650-19136878(-)$1	1	58	84	22.6151
((((((((.............)))))	chr6:159026204-159026431(+)$1	1	154	180	23.7714

#PSSM
d : 0.15	c : 0.09	= : 0.08	e : 0.08	f : 0.08	$ : 0.08	[ : 0.06	g : 0.06	b : 0.05	h : 0.03	# : 0.03	" : 0.03	D : 0.03	i : 0.03	! : 0.01	) : 0.01	: : 0.01	% : 0.01	
d : 0.13	g : 0.11	e : 0.09	f : 0.09	= : 0.08	! : 0.06	[ : 0.06	$ : 0.06	: : 0.05	c : 0.05	h : 0.03	# : 0.03	" : 0.03	i : 0.03	b : 0.01	) : 0.01	
f : 0.16	d : 0.13	e : 0.11	g : 0.09	[ : 0.09	= : 0.06	! : 0.06	$ : 0.05	h : 0.03	: : 0.03	a : 0.03	# : 0.03	) : 0.01	" : 0.01	i : 0.01	b : 0.01	
e : 0.24	d : 0.16	f : 0.15	g : 0.09	[ : 0.08	= : 0.06	! : 0.05	$ : 0.03	) : 0.01	h : 0.01	c : 0.01	i : 0.01	# : 0.01	b : 0.01	
d : 0.24	e : 0.24	f : 0.13	g : 0.09	= : 0.06	! : 0.03	[ : 0.03	c : 0.03	) : 0.01	b : 0.01	$ : 0.01	h : 0.01	i : 0.01	a : 0.01	
e : 0.23	d : 0.21	c : 0.15	f : 0.09	g : 0.09	[ : 0.06	= : 0.05	b : 0.01	y : 0.01	h : 0.01	i : 0.01	! : 0.01	
e : 0.19	d : 0.18	c : 0.13	f : 0.09	b : 0.08	g : 0.08	v : 0.08	= : 0.05	y : 0.01	w : 0.01	h : 0.01	i : 0.01	! : 0.01	
e : 0.15	u : 0.11	c : 0.11	v : 0.11	d : 0.09	b : 0.08	f : 0.08	g : 0.06	= : 0.05	a : 0.03	y : 0.03	w : 0.01	h : 0.01	i : 0.01	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
t : 0.38	v : 0.26	u : 0.26	w : 0.05	y : 0.03	
v : 0.18	u : 0.15	d : 0.11	c : 0.11	g : 0.09	f : 0.08	e : 0.08	b : 0.06	w : 0.05	y : 0.03	a : 0.01	
e : 0.18	v : 0.15	d : 0.15	c : 0.13	f : 0.09	g : 0.09	b : 0.06	y : 0.03	w : 0.03	= : 0.01	i : 0.01	2 : 0.01	
e : 0.23	d : 0.16	c : 0.13	f : 0.11	g : 0.09	= : 0.05	] : 0.05	b : 0.03	w : 0.03	2 : 0.03	a : 0.01	y : 0.01	i : 0.01	
e : 0.23	d : 0.21	f : 0.13	g : 0.09	= : 0.05	] : 0.05	2 : 0.05	c : 0.03	b : 0.03	0 : 0.01	y : 0.01	5 : 0.01	h : 0.01	i : 0.01	a : 0.01	
e : 0.23	d : 0.15	f : 0.15	g : 0.11	] : 0.11	= : 0.05	3 : 0.03	2 : 0.03	c : 0.03	4 : 0.01	0 : 0.01	5 : 0.01	h : 0.01	i : 0.01	
e : 0.19	f : 0.16	d : 0.15	g : 0.11	= : 0.06	3 : 0.03	b : 0.03	: : 0.03	4 : 0.03	2 : 0.03	5 : 0.03	c : 0.03	0 : 0.01	a : 0.01	h : 0.01	i : 0.01	
d : 0.13	g : 0.11	] : 0.11	e : 0.09	f : 0.08	= : 0.06	2 : 0.06	b : 0.06	3 : 0.05	5 : 0.05	: : 0.03	4 : 0.03	0 : 0.01	6 : 0.01	h : 0.01	c : 0.01	i : 0.01	

#score	1355.269961570395
#seq	60
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_UTR_m3_run2.txt

#BEAR
ffffff####cccooooooccc4444ffffff	chr12:69665505-69665726(+)$1	221	109	141	15.8685
%dddd"""eeeeeooooooeeeeedddd6666	chr11:77376525-77376748(-)$1	223	12	44	11.1602
gg[bbccceeeeeooooooeeeee]ccc]bb2	chr16:87442521-87442741(-)$1	220	136	168	12.5318
gggg$$$$$ddddoooooodddd333gggggg	chr1:213167948-213168171(-)$1	223	181	213	15.6967
fffff"""eeeeeooooooeeeee>>>>>>>>	chr2:128058214-128058432(-)$1	218	156	188	13.0603
cc[bb[ccc!!bboooooobb22cccbb]ccc	chr1:233518383-233518605(+)$1	222	148	180	12.5264
========[bbrrrrrrrrrbb]=========	chr20:30825527-30825753(+)$1	226	159	191	10.7899
!ffffff####bboooooobb4444ffffff2	chr2:128238485-128238703(-)$1	218	61	93	13.9671
=========[ddddmmmmdddd==========	chr16:4740279-4740499(+)$1	220	82	114	11.6412
fffff[gggggggooooooggggggg333fff	chrX:21902025-21902247(+)$1	222	178	210	13.6381
c]bbeeeeeacccooooooccc]a]eeeee:c	chr13:53049241-53049462(+)$1	221	109	141	11.8965
ffffff"""ddddoooooodddd333ffffff	chr15:59955899-59956117(-)$1	218	139	171	15.5939
#eeeee"""ddddoooooodddd666666eee	chr15:89173668-89173888(+)$1	220	170	202	13.0351
ffffff"""ddddnnnnndddd333ffffff]	chr3:192514937-192515154(-)$1	217	130	162	11.8478
ee####cccddddoooooodddd]ccceeeee	chr12:12974150-12974372(+)$1	222	14	46	13.8825
#ggggggg[ddddooooooddddggggggg44	chr14:61176289-61176507(-)$1	218	70	102	14.8289
ggggg!!ffffffooooooffffff]gggggg	chr14:69519038-69519258(-)$1	220	14	46	12.9440
e####dddd!!bboooooobb22dddd4444e	chr9:133579465-133579687(+)$1	222	139	171	12.1257
!!ccc"""cccrrrrrrrrrccc333ccc22c	chr17:60021865-60022083(-)$1	218	91	123	11.6680
:eeeee!!eeeeeooooooeeeee22eeeee:	chr19:23404705-23404926(-)$1	221	125	157	11.6316
======####cccooooooccc333=======	chr1:36646175-36646396(+)$1	221	102	134	18.2472
gggg!!a####ddddllldddd333a22gggg	chr9:123522114-123522334(-)$1	220	60	92	12.3717
$$$$ccc!!ddddoooooodddd]ccc4444e	chr13:28869049-28869269(+)$1	220	112	144	14.6447
eeee$$$$$ddddoooooodddd333eeeeeG	chr15:83685758-83685979(-)$1	221	150	182	14.2954
ffffff!!ccc[bboooooobb]ccc4444ff	chr16:74657351-74657568(-)$1	217	147	179	12.3331
ffffff!!eeeeeooooooeeeee333fffff	chr14:57878878-57879105(+)$1	227	64	96	14.0345
"""eeeee!!cccooooooccc22eeeee333	chr7:148497928-148498143(+)$1	215	152	184	14.9146
ddd!!bb[eeeeeooooooeeeee]bb22ddd	chr16:29810925-29811142(+)$1	217	22	54	12.3319
dd!!iiiiiiiiiooooooiiiiiiiii22dd	chr15:83685121-83685341(-)$1	220	102	134	13.9223
eee[ccc[a[cccnnnnnccc]a]ccc]eeee	chr6:7250057-7250269(+)$1	212	142	174	10.6021
ddd!!a[ffffffooooooffffff]a22ddd	chr1:227847360-227847581(+)$1	221	167	199	11.6447
eeeee!!bb!!cccnnnnnccc333bb333ee	chr17:29652833-29653049(+)$1	216	94	126	11.7354
====[cccdddd!!aooooooa22dddd]ccc	chr19:57841491-57841719(+)$1	228	168	200	11.5128
####bb####ddddmmmmdddd]bbiiiiiii	chr10:15254608-15254824(-)$1	216	158	190	10.3670
gggg!!gggggggooooooggggggg22gggg	chr6:36078260-36078482(+)$1	222	19	51	13.7377
ddd"""cccddddoooooodddd333ccc333	chr3:176739564-176739785(-)$1	221	67	99	15.2341
===========[aooooooa]===========	chr22:24810699-24810922(+)$1	223	86	118	15.5731
[eeeee"""eeeeellleeeee333eeeee]d	chr5:141359722-141359944(+)$1	222	70	102	11.2256
a[ggggggg!!bboooooobb22ggggggg]a	chr9:138702014-138702238(-)$1	224	15	47	13.7836
ggg[bb[bb[cccoooooocccbb22bb]ggg	chr5:1462057-1462274(-)$1	217	123	155	13.3524
ccc[ccc"""ddddllldddd4444ccc]ccc	chr2:74383159-74383378(-)$1	219	76	108	11.8120
iiiiiiii"""bbammmma]bb22iiiiiiii	chr8:66516080-66516302(-)$1	222	176	208	10.6713
$$dddd####cccooooooccc22dddd5555	chr14:81643013-81643234(-)$1	221	20	52	11.8517
eeee!!bb!!cccooooooccc4444bb22ee	chr3:196662467-196662685(-)$1	218	131	163	15.1414
=========ddddoooooodddd]========	chr15:68585158-68585381(+)$1	223	182	214	16.0349
"""ccc!!cccddddllldddd333ccc22cc	chr3:191110045-191110265(+)$1	220	63	95	12.0245
::===========oooooo===========::	chr4:77700439-77700661(+)$1	222	102	134	11.7543
:eeeee####cccooooooccc]eeeeedddd	chr13:53049199-53049418(+)$1	219	25	57	13.4601
d[a!!bb"""cccooooooccc4444bb22ad	chr5:74668658-74668878(-)$1	220	67	99	15.7238
[eeeee!!eeeeeooooooeeeee]eeeee]e	chr4:108832182-108832401(+)$1	219	133	165	13.7545
fffffbb"""cccooooooccc333bb]ffff	chr2:182778539-182778760(+)$1	221	38	70	15.4734
!!ggggggg[cccooooooccc]ggggggg22	chr13:110406320-110406538(-)$1	218	146	178	15.1188
"""gggggggcccooooooccc]ggggggg]d	chr2:201846225-201846445(-)$1	220	91	123	15.0644
=========[cccrrrrrrrrrccc=======	chr7:99488717-99488942(-)$1	225	53	85	11.5562

#otherMatches

#Seq PSSM
CUUUUUUUAAUGUGUAAAAACAAUCCAAAGAG	chr12:69665505-69665726(+)$1	221	109	141	15.8685
AGACUUCUAUUAAAAUUCAUUAAUAGUCAUAC	chr11:77376525-77376748(-)$1	223	12	44	11.1602
UGUCUGAAAUUUACGGACUUAAAUCUUCAAGG	chr16:87442521-87442741(-)$1	220	136	168	12.5318
UCCUUUCCAGAAGGCUUGAUUUCAUUAGGAGA	chr1:213167948-213168171(-)$1	223	181	213	15.6967
GACCAACAAUUGUUUUAAUGCAAUCUUAAUUA	chr2:128058214-128058432(-)$1	218	156	188	13.0603
UUUCAUGCUGCUGUGUUUUCAAAAGCUGUGGC	chr1:233518383-233518605(+)$1	222	148	180	12.5264
aaugauuagauucugaacauauGUAauuauuu	chr20:30825527-30825753(+)$1	226	159	191	10.7899
AGGGCAACAAAAUGCCAUUGUGACCUUGCCUG	chr2:128238485-128238703(-)$1	218	61	93	13.9671
UGCAGCUGGGCCUGGGGACAGGUCGGCUGUGG	chr16:4740279-4740499(+)$1	220	82	114	11.6412
uaaaacuuuuuaaucauuuuuaagaaacuuuu	chrX:21902025-21902247(+)$1	222	178	210	13.6381
CUCUUAGGUCUGGAGUUGGCCAUGUACCUAUG	chr13:53049241-53049462(+)$1	221	109	141	11.8965
UGAAUGAUGCAUCUUCUUCGGUGAAAUAUUUA	chr15:59955899-59956117(-)$1	218	139	171	15.5939
CAGGUUGCCGUGGCCUUCCCCACCCCCCAGAU	chr15:89173668-89173888(+)$1	220	170	202	13.0351
CUGUUCAAAAGCAGGUAUUGCUAUAGAGCAGC	chr3:192514937-192515154(-)$1	217	130	162	11.8478
GAAACUGGCUCUGGAAAGACAGGCGCCUUUGC	chr12:12974150-12974372(+)$1	222	14	46	13.8825
ACACAGAGCAUGUCCCAGAACAUUUCUGUGCU	chr14:61176289-61176507(-)$1	218	70	102	14.8289
CAGGAAGGUCUGGGAAUGACCAGAUAUCUUGU	chr14:69519038-69519258(-)$1	220	14	46	12.9440
UAAAGUUGGAAGAAUAAAGUUAACCAAGCAgg	chr9:133579465-133579687(+)$1	222	139	171	12.1257
UUUCUUAUGAACAACAUAACUUCUUCAGAUUG	chr17:60021865-60022083(-)$1	218	91	123	11.6680
GUUCAUACUUAAUAGAAGCAUUAAAGAUGAAA	chr19:23404705-23404926(-)$1	221	125	157	11.6316
UUCCUCUCUCUAUUUAACUGUAACUGAGGGGG	chr1:36646175-36646396(+)$1	221	102	134	18.2472
GGUUCCCCAUGCCUGCUCUAGGAAAGUAAACU	chr9:123522114-123522334(-)$1	220	60	92	12.3717
ACACCUUCCUGUCGUGACAGAUAAAAGCACAG	chr13:28869049-28869269(+)$1	220	112	144	14.6447
CCCAUUAGUCAGUGUUACAGCUGUGUUGGGGA	chr15:83685758-83685979(-)$1	221	150	182	14.2954
AGUAUCCUUGAAGGGACUAACCAUCGUCUUGG	chr16:74657351-74657568(-)$1	217	147	179	12.3331
AGAAAAAAUAAAAAAUCGAUUUUAAUAUUUUC	chr14:57878878-57879105(+)$1	227	64	96	14.0345
CAUUUUUUAAUGUGUGAAAAUAAAGAAAAUUA	chr7:148497928-148498143(+)$1	215	152	184	14.9146
GGACUCUCUGGGUGGCUCAGCCCACAGUAUCC	chr16:29810925-29811142(+)$1	217	22	54	12.3319
UACUAACUUUGGGACAUCCCCUGGAGuuuuua	chr15:83685121-83685341(-)$1	220	102	134	13.9223
GUAAUGAGACAAGCCUUUCUUCUGUCACUGCA	chr6:7250057-7250269(+)$1	212	142	174	10.6021
uuuaccucaauaguuauuuuuauugugagaaa	chr1:227847360-227847581(+)$1	221	167	199	11.6447
AGUGGACCUUACCCAUACCGGGCCUAGCAAUC	chr17:29652833-29653049(+)$1	216	94	126	11.7354
GGAUAGGGAUGAUAGUGUAAUUGUUCAUGCCC	chr19:57841491-57841719(+)$1	228	168	200	11.5128
CCGAGGACUCGGCGUAUCCGCCACCAGGGACA	chr10:15254608-15254824(-)$1	216	158	190	10.3670
CUUUGCACAUGUGACCACAUACGUGUUAGGAG	chr6:36078260-36078482(+)$1	222	19	51	13.7377
AGCUAAGUAGAGAAAUAAAUCUCAAAUGCAGC	chr3:176739564-176739785(-)$1	221	67	99	15.2341
CCCACAUGACCCGUCCAUUCAGGUCAUGUGGG	chr22:24810699-24810922(+)$1	223	86	118	15.5731
UGCCAGCUGCCUGUGAUGCAGGAACCUGGCUG	chr5:141359722-141359944(+)$1	222	70	102	11.2256
AGCUGACAGUCCCUUCAGUGGUUUUGUUAGGU	chr9:138702014-138702238(-)$1	224	15	47	13.7836
UUUUUUAGCAUGGACACUGCCAGCAGGACAGA	chr5:1462057-1462274(-)$1	217	123	155	13.3524
UUAUGAAUAAGUUUCCAGAACAAAUUUCCUAA	chr2:74383159-74383378(-)$1	219	76	108	11.8120
CUUUUUAUUUUGCCAACCGUGUUUAUAGAAAG	chr8:66516080-66516302(-)$1	222	176	208	10.6713
CUGUUUUUCCGAUUAUUUCAUCUUGAACUUUC	chr14:81643013-81643234(-)$1	221	20	52	11.8517
GGGGCUGAAGUACCUAAGUGUGAAUGUCUCUC	chr3:196662467-196662685(-)$1	218	131	163	15.1414
AACCUGAGAUUUUACAAGGAAGGUUUUUAGGU	chr15:68585158-68585381(+)$1	223	182	214	16.0349
AUUUCUCAGCCCUCCUGGGGAGAUUGGCCUAG	chr3:191110045-191110265(+)$1	220	63	95	12.0245
CCCUUUCUAUUAUUACUUUGUAGUAGAAAGAA	chr4:77700439-77700661(+)$1	222	102	134	11.7543
CCGCCCUAAUGCAGCACUGUGCCGGGUGUACU	chr13:53049199-53049418(+)$1	219	25	57	13.4601
AAGGAAUAGUACUCACUGAAGUUGAAAUGACU	chr5:74668658-74668878(-)$1	220	67	99	15.7238
guuuuUAAAAGAUCAUUUUAUCUUAAAAAGGA	chr4:108832182-108832401(+)$1	219	133	165	13.7545
UGUUACGUACUGCAAGUCAGCAUUCCGAUAGC	chr2:182778539-182778760(+)$1	221	38	70	15.4734
UAUUUCUUGCUAUUGUGAUAUGACAAGAGACU	chr13:110406320-110406538(-)$1	218	146	178	15.1188
AACCAACUGAUCUUAGUGUAGAUUCAGUUGAG	chr2:201846225-201846445(-)$1	220	91	123	15.0644
ucaguauuggccagcugguaaauggcaguguu	chr7:99488717-99488942(-)$1	225	53	85	11.5562

#DB
((((((....(((......)))....))))))	chr12:69665505-69665726(+)$1	1	109	141	15.8685
.((((...(((((......)))))))))....	chr11:77376525-77376748(-)$1	1	12	44	11.1602
((.((((((((((......))))).))).)).	chr16:87442521-87442741(-)$1	1	136	168	12.5318
((((.....((((......))))...))))))	chr1:213167948-213168171(-)$1	1	181	213	15.6967
(((((...(((((......)))))........	chr2:128058214-128058432(-)$1	1	156	188	13.0603
((.((.(((..((......))..))))).)))	chr1:233518383-233518605(+)$1	1	148	180	12.5264
((((((((.((.........)).)))))))))	chr20:30825527-30825753(+)$1	1	159	191	10.7899
.((((((....((......))....)))))).	chr2:128238485-128238703(-)$1	1	61	93	13.9671
(((((((((.((((....))))))))))))))	chr16:4740279-4740499(+)$1	1	82	114	11.6412
(((((.(((((((......)))))))...)))	chrX:21902025-21902247(+)$1	1	178	210	13.6381
).))(((((((((......))).).))))).(	chr13:53049241-53049462(+)$1	1	109	141	11.8965
((((((...((((......))))...))))))	chr15:59955899-59956117(-)$1	1	139	171	15.5939
.(((((...((((......))))......)))	chr15:89173668-89173888(+)$1	1	170	202	13.0351
((((((...((((.....))))...)))))).	chr3:192514937-192515154(-)$1	1	130	162	11.8478
((....(((((((......)))).))))))))	chr12:12974150-12974372(+)$1	1	14	46	13.8825
.(((((((.((((......)))))))))))..	chr14:61176289-61176507(-)$1	1	70	102	14.8289
(((((..((((((......)))))).))))))	chr14:69519038-69519258(-)$1	1	14	46	12.9440
(....((((..((......))..))))....)	chr9:133579465-133579687(+)$1	1	139	171	12.1257
..(((...(((.........)))...)))..)	chr17:60021865-60022083(-)$1	1	91	123	11.6680
.(((((..(((((......)))))..))))).	chr19:23404705-23404926(-)$1	1	125	157	11.6316
((((((....(((......)))...)))))))	chr1:36646175-36646396(+)$1	1	102	134	18.2472
((((..(....((((...))))...)..))))	chr9:123522114-123522334(-)$1	1	60	92	12.3717
....(((..((((......)))).)))....)	chr13:28869049-28869269(+)$1	1	112	144	14.6447
((((.....((((......))))...))))))	chr15:83685758-83685979(-)$1	1	150	182	14.2954
((((((..(((.((......)).)))....))	chr16:74657351-74657568(-)$1	1	147	179	12.3331
((((((..(((((......)))))...)))))	chr14:57878878-57879105(+)$1	1	64	96	14.0345
...(((((..(((......)))..)))))...	chr7:148497928-148498143(+)$1	1	152	184	14.9146
(((..((.(((((......))))).))..)))	chr16:29810925-29811142(+)$1	1	22	54	12.3319
((..(((((((((......)))))))))..))	chr15:83685121-83685341(-)$1	1	102	134	13.9223
(((.(((.(.(((.....))).).))).))))	chr6:7250057-7250269(+)$1	1	142	174	10.6021
(((..(.((((((......)))))).)..)))	chr1:227847360-227847581(+)$1	1	167	199	11.6447
(((((..((..(((.....)))...))...))	chr17:29652833-29653049(+)$1	1	94	126	11.7354
((((.(((((((..(......)..)))).)))	chr19:57841491-57841719(+)$1	1	168	200	11.5128
....((....((((....)))).)))))))))	chr10:15254608-15254824(-)$1	1	158	190	10.3670
((((..(((((((......)))))))..))))	chr6:36078260-36078482(+)$1	1	19	51	13.7377
(((...(((((((......))))...)))...	chr3:176739564-176739785(-)$1	1	67	99	15.2341
(((((((((((.(......).)))))))))))	chr22:24810699-24810922(+)$1	1	86	118	15.5731
.(((((...(((((...)))))...))))).)	chr5:141359722-141359944(+)$1	1	70	102	11.2256
(.(((((((..((......))..))))))).)	chr9:138702014-138702238(-)$1	1	15	47	13.7836
(((.((.((.(((......)))))..)).)))	chr5:1462057-1462274(-)$1	1	123	155	13.3524
(((.(((...((((...))))....))).)))	chr2:74383159-74383378(-)$1	1	76	108	11.8120
((((((((...(((....).))..))))))))	chr8:66516080-66516302(-)$1	1	176	208	10.6713
..((((....(((......)))..))))....	chr14:81643013-81643234(-)$1	1	20	52	11.8517
((((..((..(((......)))....))..))	chr3:196662467-196662685(-)$1	1	131	163	15.1414
(((((((((((((......)))).))))))))	chr15:68585158-68585381(+)$1	1	182	214	16.0349
...(((..(((((((...))))...)))..))	chr3:191110045-191110265(+)$1	1	63	95	12.0245
..(((((((((((......)))))))))))..	chr4:77700439-77700661(+)$1	1	102	134	11.7543
.(((((....(((......))).)))))((((	chr13:53049199-53049418(+)$1	1	25	57	13.4601
(.(..((...(((......)))....))..))	chr5:74668658-74668878(-)$1	1	67	99	15.7238
.(((((..(((((......))))).))))).)	chr4:108832182-108832401(+)$1	1	133	165	13.7545
(((((((...(((......)))...)).))))	chr2:182778539-182778760(+)$1	1	38	70	15.4734
..(((((((.(((......))).)))))))..	chr13:110406320-110406538(-)$1	1	146	178	15.1188
...((((((((((......))).))))))).)	chr2:201846225-201846445(-)$1	1	91	123	15.0644
(((((((((.(((.........))))))))))	chr7:99488717-99488942(-)$1	1	53	85	11.5562

#PSSM
f : 0.14	= : 0.12	g : 0.11	e : 0.11	d : 0.09	c : 0.05	! : 0.05	# : 0.05	: : 0.05	" : 0.05	$ : 0.03	[ : 0.03	% : 0.01	a : 0.01	i : 0.01	
e : 0.18	f : 0.16	g : 0.12	= : 0.12	d : 0.09	" : 0.05	c : 0.03	# : 0.03	! : 0.03	$ : 0.03	[ : 0.03	] : 0.01	i : 0.01	: : 0.01	
f : 0.16	e : 0.16	g : 0.14	= : 0.14	d : 0.09	# : 0.05	" : 0.05	[ : 0.03	c : 0.03	b : 0.01	$ : 0.01	! : 0.01	i : 0.01	a : 0.01	
f : 0.16	e : 0.16	g : 0.14	= : 0.14	! : 0.07	b : 0.05	# : 0.05	[ : 0.05	d : 0.03	c : 0.03	$ : 0.01	" : 0.01	i : 0.01	
f : 0.16	e : 0.14	= : 0.12	! : 0.11	g : 0.09	c : 0.09	b : 0.07	d : 0.03	$ : 0.03	# : 0.03	i : 0.03	[ : 0.01	" : 0.01	
= : 0.12	e : 0.12	f : 0.11	c : 0.11	! : 0.09	b : 0.09	" : 0.07	g : 0.07	$ : 0.03	[ : 0.03	d : 0.03	i : 0.03	# : 0.01	a : 0.01	
c : 0.14	" : 0.12	! : 0.12	= : 0.11	g : 0.11	# : 0.09	b : 0.07	$ : 0.03	e : 0.03	i : 0.03	[ : 0.03	f : 0.01	d : 0.01	a : 0.01	
" : 0.18	# : 0.12	= : 0.11	g : 0.11	! : 0.11	c : 0.09	b : 0.05	$ : 0.03	e : 0.03	f : 0.03	[ : 0.03	i : 0.03	d : 0.01	
e : 0.14	" : 0.14	# : 0.12	c : 0.11	= : 0.09	g : 0.09	! : 0.05	$ : 0.03	[ : 0.03	f : 0.03	d : 0.03	b : 0.03	i : 0.01	a : 0.01	
d : 0.20	e : 0.14	# : 0.12	! : 0.11	[ : 0.09	" : 0.07	g : 0.05	c : 0.05	f : 0.03	= : 0.03	b : 0.01	a : 0.01	i : 0.01	
c : 0.31	d : 0.25	e : 0.14	! : 0.07	# : 0.03	g : 0.03	f : 0.03	= : 0.03	b : 0.01	i : 0.01	" : 0.01	
d : 0.29	c : 0.27	e : 0.14	b : 0.09	r : 0.03	g : 0.03	f : 0.03	[ : 0.03	i : 0.01	= : 0.01	
c : 0.27	d : 0.27	e : 0.14	b : 0.11	r : 0.03	g : 0.03	f : 0.03	i : 0.01	! : 0.01	a : 0.01	= : 0.01	
o : 0.72	d : 0.09	r : 0.05	n : 0.03	b : 0.01	c : 0.01	! : 0.01	e : 0.01	a : 0.01	
o : 0.74	r : 0.05	m : 0.05	n : 0.05	d : 0.03	l : 0.03	a : 0.01	
o : 0.75	l : 0.07	r : 0.05	m : 0.05	n : 0.05	
o : 0.75	l : 0.07	r : 0.05	m : 0.05	n : 0.05	
o : 0.75	r : 0.05	m : 0.05	n : 0.05	l : 0.03	e : 0.01	d : 0.01	
o : 0.75	d : 0.11	r : 0.05	c : 0.01	n : 0.01	e : 0.01	a : 0.01	
d : 0.27	c : 0.25	e : 0.14	b : 0.07	r : 0.05	g : 0.03	f : 0.03	o : 0.03	i : 0.01	a : 0.01	] : 0.01	= : 0.01	
c : 0.27	d : 0.27	e : 0.14	b : 0.12	g : 0.03	f : 0.03	i : 0.01	o : 0.01	] : 0.01	= : 0.01	r : 0.01	
c : 0.25	d : 0.25	e : 0.14	2 : 0.05	b : 0.05	4 : 0.03	g : 0.03	f : 0.03	= : 0.03	i : 0.01	] : 0.01	a : 0.01	r : 0.01	
d : 0.16	e : 0.12	2 : 0.12	] : 0.12	3 : 0.12	4 : 0.09	= : 0.05	g : 0.03	f : 0.03	c : 0.03	i : 0.01	a : 0.01	b : 0.01	
3 : 0.22	e : 0.14	g : 0.11	4 : 0.09	= : 0.07	] : 0.07	2 : 0.07	c : 0.05	f : 0.03	b : 0.03	a : 0.01	6 : 0.01	d : 0.01	i : 0.01	
3 : 0.24	c : 0.11	g : 0.11	4 : 0.09	= : 0.09	d : 0.07	] : 0.07	f : 0.03	2 : 0.03	e : 0.03	i : 0.03	> : 0.01	6 : 0.01	b : 0.01	
c : 0.14	= : 0.12	3 : 0.11	g : 0.11	e : 0.09	d : 0.07	4 : 0.05	b : 0.05	i : 0.05	f : 0.03	] : 0.03	2 : 0.03	> : 0.01	6 : 0.01	a : 0.01	
c : 0.14	b : 0.12	= : 0.12	e : 0.12	g : 0.11	f : 0.07	d : 0.07	i : 0.05	3 : 0.03	2 : 0.03	> : 0.01	6 : 0.01	4 : 0.01	a : 0.01	
e : 0.14	= : 0.12	g : 0.11	f : 0.09	c : 0.09	b : 0.07	2 : 0.07	d : 0.05	4 : 0.05	i : 0.05	3 : 0.03	] : 0.03	> : 0.01	6 : 0.01	
g : 0.14	e : 0.14	= : 0.12	f : 0.11	2 : 0.11	] : 0.09	4 : 0.05	6 : 0.03	3 : 0.03	c : 0.03	i : 0.03	> : 0.01	5 : 0.01	d : 0.01	
g : 0.16	e : 0.14	f : 0.12	= : 0.12	2 : 0.09	c : 0.05	4 : 0.05	3 : 0.05	d : 0.05	i : 0.03	6 : 0.01	b : 0.01	> : 0.01	5 : 0.01	
f : 0.14	e : 0.12	= : 0.11	g : 0.09	c : 0.07	d : 0.07	] : 0.07	4 : 0.05	: : 0.03	2 : 0.03	3 : 0.03	i : 0.03	6 : 0.01	b : 0.01	> : 0.01	5 : 0.01	a : 0.01	
e : 0.14	d : 0.12	f : 0.11	c : 0.11	= : 0.11	g : 0.09	2 : 0.05	: : 0.03	3 : 0.03	i : 0.03	6 : 0.01	> : 0.01	] : 0.01	4 : 0.01	G : 0.01	a : 0.01	5 : 0.01	

#score	715.641946896481
#seq	54
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_CDS_m1_run2.txt

#BEAR
dddd!!cccqqqqqqqqccc]dddd	chr14:90429413-90429664(+)$1	251	32	57	16.2950
ddd[eeeeeqqqqqqqqeeeee]dd	chr6:47501284-47501546(+)$1	262	35	60	15.1354
eeee[ddddqqqqqqqqdddd4444	chr3:184025639-184025879(+)$1	240	52	77	16.1394
eeee!!cccqqqqqqqqccc]eeee	chr16:85011434-85011674(-)$1	240	105	130	16.5199
cccccddddqqqqqqqqdddd:eee	chr14:24737516-24737849(-)$1	333	103	128	14.4975
=======[aqqqqqqqqa=======	chr11:47599086-47599326(-)$1	240	135	160	16.6063
bb!!a[cccqqqqqqqqccca22bb	chr11:840282-840574(-)$1	292	168	193	16.2934
bb[ffffffqqqqqqqqffffffbb	chr5:154242706-154242946(+)$1	240	58	83	13.7506
a[eeeee[aqqqqqqqqa]eeeeea	chr14:21854093-21854333(-)$1	240	180	205	15.2479
ddd[bb[bbqqqqqqqqbb]bbddd	chr1:204094991-204095231(+)$1	240	182	207	13.8790
:ccc!!cccqqqqqqqqccc22ccc	chr19:3611994-3612234(-)$1	240	36	61	16.2162
h[bb"""bbqqqqqqqqbb333bb]	chr10:121607061-121607301(-)$1	240	160	185	15.0606
::gggggggqqqqqqqqgggggggf	chr11:65046215-65046455(+)$1	240	15	40	13.8667
bbdddd[bbqqqqqqqqbbdddd]b	chr11:60689460-60689700(+)$1	240	196	221	14.1147
$$gggggggqqqqqqqqgggggggd	chr5:133534689-133534929(-)$1	240	176	201	15.4038
ccc"""cccqqqqqqqqccc55555	chr17:37671909-37672149(+)$1	240	207	232	13.9151
a!!ffffffqqqqqqqqffffff22	chr1:155491029-155491269(-)$1	240	179	204	14.6190
gg"""ddddqqqqqqqqdddd22gg	chr11:608295-608535(+)$1	240	118	143	16.3535
ccc"""cccqqqqqqqqccc]cccc	chr10:32326134-32326374(-)$1	240	131	156	17.2257
!!gggggggqqqqqqqqggggggg4	chr3:139071449-139071689(+)$1	240	33	58	16.0914
dddd!!cccqqqqqqqqccc333dd	chr13:53035854-53036094(+)$1	240	207	232	17.2656
ee[ffffffqqqqqqqqffffff33	chrX:53431854-53432094(-)$1	240	3	28	14.7715
cccbb[cccqqqqqqqqccc]bb]c	chr17:56581701-56581941(-)$1	240	154	179	15.5654
""gggggggqqqqqqqqggggggg5	chr19:44980501-44980741(-)$1	240	53	78	15.2426
ddccc[cccqqqqqqqqccc]cccH	chr19:39860300-39860540(+)$1	240	208	233	15.7069
gggg[a[bbqqqqqqqqbb]a]ggg	chr22:32112787-32113027(-)$1	240	122	147	15.7616
eeeee[cccqqqqqqqqccceeeee	chr2:10188042-10188282(+)$1	240	180	205	15.9033
ddd[eeeeeqqqqqqqqeeeeeddd	chrX:47098708-47098948(+)$1	240	131	156	14.9409
ddd!!ddddqqqqqqqqdddd22dd	chr12:69136077-69136317(+)$1	240	43	68	16.1498
a[a[eeeeeqqqqqqqqeeeeea]a	chr7:72985503-72985743(-)$1	240	156	181	15.5227
d!!ccc[bbqqqqqqqqbb]ccc22	chr12:122720253-122720493(-)$1	240	4	29	15.1852
bb!!eeeeeqqqqqqqqeeeee22b	chr19:15379635-15379890(-)$1	255	152	177	14.9561
iiiiiiiiiqqqqqqqqiiiiiiii	chr5:148892560-148892800(-)$1	240	22	47	15.9022
ddd"""cccqqqqqqqqccc333dd	chr2:38973738-38973978(-)$1	240	89	114	17.6012
eee"""cccqqqqqqqqccc22eee	chr2:86830965-86831205(-)$1	240	172	197	16.8924
bb[ffffffqqqqqqqqffffffbb	chr1:197073585-197073825(-)$1	240	103	128	13.7506
eee!!ddddqqqqqqqqdddd]eee	chr16:67262176-67262416(+)$1	240	133	158	16.0501
"""ccc[bbqqqqqqqqbbcccccc	chr12:56531907-56532147(+)$1	240	83	108	15.4363
fbb!!ddddqqqqqqqqdddd4444	chr10:103291953-103292193(+)$1	240	94	119	16.1140
ddd"""cccqqqqqqqqccc333dd	chr5:179268890-179269130(-)$1	240	165	190	17.6012
ddd!!ddddqqqqqqqqdddd333d	chr16:47536801-47537041(+)$1	240	74	99	16.8271
ggggggg[aqqqqqqqqaggggggg	chr4:6925393-6925633(+)$1	240	88	113	15.9035
eee[eeeeeqqqqqqqqeeeee22e	chr1:151062874-151063114(+)$1	240	196	221	15.1168
=========qqqqqqqq========	chr11:43400723-43400970(+)$1	247	169	194	16.5462
h[bb!!cccqqqqqqqqccc22bb]	chr14:103806670-103806910(+)$1	240	30	55	15.8968
c[dddd!!aqqqqqqqqa]dddd]c	chr1:164790716-164790956(+)$1	240	58	83	15.2078
fccc[ddddqqqqqqqqddddccc2	chr2:215617110-215617350(-)$1	240	166	191	15.5511
eeeee!!bbqqqqqqqqbb]eeeee	chr7:99631297-99631537(+)$1	240	178	203	14.9487
"ccc[bb[aqqqqqqqqa]bb]ccc	chr6:170866026-170866266(+)$1	240	70	95	15.0037
a"""eeeeeqqqqqqqqeeeee333	chr16:733979-734219(-)$1	240	142	167	16.1186
ccc####bbqqqqqqqqbb22cccC	chr12:27156147-27156387(-)$1	240	201	226	14.5851
gggg[ddddqqqqqqqqdddd333g	chr2:96861039-96861279(-)$1	240	9	34	16.6469
"""a[ddddqqqqqqqqdddd]a]e	chr8:144903940-144904180(-)$1	240	186	211	16.2615
cc!!ccc[aqqqqqqqqaccc]ccc	chrX:99662166-99662406(-)$1	240	126	151	16.6610
=$$$$$cccqqqqqqqqccc66666	chr11:47594405-47594645(-)$1	240	12	37	14.3167
eeee!!cccqqqqqqqqccc22eee	chr2:38525580-38525820(-)$1	240	111	136	16.6199
gggg!!cccqqqqqqqqcccggggg	chr22:31328486-31328726(-)$1	240	74	99	16.9344
ccc!!ddddqqqqqqqqdddd22cc	chr1:200376111-200376360(-)$1	249	139	164	16.4742

#otherMatches

#Seq PSSM
UUCCAGGAGUAUAAUGUCUCAGGAA	chr14:90429413-90429664(+)$1	251	32	57	16.2950
UUAUUUUCCCUUUUGUAGGAAAUUA	chr6:47501284-47501546(+)$1	262	35	60	15.1354
AGGGAAGGGCACCCUUACCCUCUGC	chr3:184025639-184025879(+)$1	240	52	77	16.1394
GGAUUUCAGUUCAUCUCCUGUGUCC	chr16:85011434-85011674(-)$1	240	105	130	16.5199
UCCAGAAAGAAUGCGUGCUUUUAAA	chr14:24737516-24737849(-)$1	333	103	128	14.4975
GUGUCAGACAUGUAUCAGCUGACAU	chr11:47599086-47599326(-)$1	240	135	160	16.6063
AGAAGCUGCUCAAUUAUGCACCCCU	chr11:840282-840574(-)$1	292	168	193	16.2934
AGAUCAGACCAAACAUUGUCUGGCU	chr5:154242706-154242946(+)$1	240	58	83	13.7506
GUCUGUGUCAUCUUUGGGUCACAGC	chr14:21854093-21854333(-)$1	240	180	205	15.2479
CUGAUGGCGAGAUGUACCGGUACAG	chr1:204094991-204095231(+)$1	240	182	207	13.8790
ACCCACCGCCCAAGAUCGUGCAGGG	chr19:3611994-3612234(-)$1	240	36	61	16.2162
CUGAAUAAUGAUGAAAGGUGAGUCU	chr10:121607061-121607301(-)$1	240	160	185	15.0606
AAGUAACCGAGGAGAAGUGGUUACC	chr11:65046215-65046455(+)$1	240	15	40	13.8667
GCCAGUGUCAUACCAAAGAGCUGAG	chr11:60689460-60689700(+)$1	240	196	221	14.1147
UUCUUGCAUUACUGAAUAUGUAGGG	chr5:133534689-133534929(-)$1	240	176	201	15.4038
CAGUUUCUAACACUUUCUAGUCAUU	chr17:37671909-37672149(+)$1	240	207	232	13.9151
CAGUGAAAGAAACAAACUUUUCAGA	chr1:155491029-155491269(-)$1	240	179	204	14.6190
GCUCAGGCCCCCUUCCCGGUCCCGC	chr11:608295-608535(+)$1	240	118	143	16.3535
CACAAACGGAACAAAAGCUGAGUGG	chr10:32326134-32326374(-)$1	240	131	156	17.2257
GGAUAGGUUCAUCACAAGACCUAUG	chr3:139071449-139071689(+)$1	240	33	58	16.0914
GUAAGUAGAUAUAAUUUUCUUUAUU	chr13:53035854-53036094(+)$1	240	207	232	17.2656
UUCCCUUCAGGAGCAGAUGAAGGCA	chrX:53431854-53432094(-)$1	240	3	28	14.7715
UGGCCACCAAGAGAAUGUGGAGGAC	chr17:56581701-56581941(-)$1	240	154	179	15.5654
CAUUAAUAGCUAUAAACUUAUUAGG	chr19:44980501-44980741(-)$1	240	53	78	15.2426
GGAGGACCGCAACGCACUGGCCCUC	chr19:39860300-39860540(+)$1	240	208	233	15.7069
AAGCAGAUGACAAUCACCAACAGCU	chr22:32112787-32113027(-)$1	240	122	147	15.7616
UGGUGCAGUUCAGACUUGCUCACCA	chr2:10188042-10188282(+)$1	240	180	205	15.9033
GGUAUGGUCUAGAGCAUGGCCAGCC	chrX:47098708-47098948(+)$1	240	131	156	14.9409
UUUUUAAAAAUCAGGUAUUUUCUAA	chr12:69136077-69136317(+)$1	240	43	68	16.1498
GCGAGCCUUCGAACUAAAGGGCCAC	chr7:72985503-72985743(-)$1	240	156	181	15.5227
CAAAUGACUUCCCUUGCAGACAUAC	chr12:122720253-122720493(-)$1	240	4	29	15.1852
CAAAUUGUUACAUCUACAACAAGGU	chr19:15379635-15379890(-)$1	255	152	177	14.9561
UUAAAGUUAUUCCUUAUUGAUUUUG	chr5:148892560-148892800(-)$1	240	22	47	15.9022
AUCCCCGUCGAGGUCAAGAUCAAGA	chr2:38973738-38973978(-)$1	240	89	114	17.6012
GGCCUUCUUAUAAAAAAAAGCAGCC	chr2:86830965-86831205(-)$1	240	172	197	16.8924
UCAUAAUUUAUGUAGACAAAUUAGA	chr1:197073585-197073825(-)$1	240	103	128	13.7506
GGGCCUGGGUAAGUAUCUCCAUCCU	chr16:67262176-67262416(+)$1	240	133	158	16.0501
UCUGGCCGCCUGCACUUGCGCCUGG	chr12:56531907-56532147(+)$1	240	83	108	15.4363
UCAGACAAUAGAAUCUAAUUGGAGA	chr10:103291953-103292193(+)$1	240	94	119	16.1140
CCUUCAUCCAAAAUGGAGGAGCCAG	chr5:179268890-179269130(-)$1	240	165	190	17.6012
UUUCAUGAGUUAUCUCUCUCACCCA	chr16:47536801-47537041(+)$1	240	74	99	16.8271
GAGCGUGCGCAAAUCCUCCACGUUU	chr4:6925393-6925633(+)$1	240	88	113	15.9035
GGUUAUGUUGUUAAAAAGGCAUCCA	chr1:151062874-151063114(+)$1	240	196	221	15.1168
AGAUGCAGCUGAUGCUUGUUGCAUU	chr11:43400723-43400970(+)$1	247	169	194	16.5462
UGUAUAAAUAAUCAAAAGUUGUUAA	chr14:103806670-103806910(+)$1	240	30	55	15.8968
UGGAUACCCUUCGCCAUGUUAUCAG	chr1:164790716-164790956(+)$1	240	58	83	15.2078
GCCACUGCUCAGUAGUAAGUAUGGA	chr2:215617110-215617350(-)$1	240	166	191	15.5511
CUCCAUCAGCGCAUCCACUCUGGAG	chr7:99631297-99631537(+)$1	240	178	203	14.9487
GCCAAGAAGAAAGUGAACAUCAUGG	chr6:170866026-170866266(+)$1	240	70	95	15.0037
GUUCGUGCAGCAGUACGUGCGCCCC	chr16:733979-734219(-)$1	240	142	167	16.1186
ACUGUUUCCUUUUCUCCGGUAAGUG	chr12:27156147-27156387(-)$1	240	201	226	14.5851
AGCGGUUGGAAGAAAUGUCAAAUAU	chr2:96861039-96861279(-)$1	240	9	34	16.6469
UCAGAAGGUGAGCAUGGACCUCCCA	chr8:144903940-144904180(-)$1	240	186	211	16.2615
UUACCGUGCUCAUCACUGACGAAAA	chrX:99662166-99662406(-)$1	240	126	151	16.6610
UUGCCAGCUGUAACGGGAGCAUCUA	chr11:47594405-47594645(-)$1	240	12	37	14.3167
AGGGGACAAGCCUUACAUUGCACCU	chr2:38525580-38525820(-)$1	240	111	136	16.6199
UGGCCCAGCAGGCCAUAGCUGUCGC	chr22:31328486-31328726(-)$1	240	74	99	16.9344
UACAAAUAUGAUGUCUGAUGUAAGU	chr1:200376111-200376360(-)$1	249	139	164	16.4742

#DB
((((..(((........))).))))	chr14:90429413-90429664(+)$1	1	32	57	16.2950
(((.(((((........))))).))	chr6:47501284-47501546(+)$1	1	35	60	15.1354
((((.((((........))))....	chr3:184025639-184025879(+)$1	1	52	77	16.1394
((((..(((........))).))))	chr16:85011434-85011674(-)$1	1	105	130	16.5199
)))))((((........)))).(((	chr14:24737516-24737849(-)$1	1	103	128	14.4975
(((((((.(........))))))))	chr11:47599086-47599326(-)$1	1	135	160	16.6063
((..(.(((........))))..))	chr11:840282-840574(-)$1	1	168	193	16.2934
((.((((((........))))))))	chr5:154242706-154242946(+)$1	1	58	83	13.7506
(.(((((.(........).))))))	chr14:21854093-21854333(-)$1	1	180	205	15.2479
(((.((.((........)).)))))	chr1:204094991-204095231(+)$1	1	182	207	13.8790
.(((..(((........)))..)))	chr19:3611994-3612234(-)$1	1	36	61	16.2162
(.((...((........))...)).	chr10:121607061-121607301(-)$1	1	160	185	15.0606
..(((((((........)))))))(	chr11:65046215-65046455(+)$1	1	15	40	13.8667
((((((.((........)))))).)	chr11:60689460-60689700(+)$1	1	196	221	14.1147
..(((((((........))))))))	chr5:133534689-133534929(-)$1	1	176	201	15.4038
(((...(((........))).....	chr17:37671909-37672149(+)$1	1	207	232	13.9151
(..((((((........))))))..	chr1:155491029-155491269(-)$1	1	179	204	14.6190
((...((((........))))..))	chr11:608295-608535(+)$1	1	118	143	16.3535
(((...(((........))).)))(	chr10:32326134-32326374(-)$1	1	131	156	17.2257
..(((((((........))))))).	chr3:139071449-139071689(+)$1	1	33	58	16.0914
((((..(((........)))...))	chr13:53035854-53036094(+)$1	1	207	232	17.2656
((.((((((........))))))..	chrX:53431854-53432094(-)$1	1	3	28	14.7715
(((((.(((........))).)).)	chr17:56581701-56581941(-)$1	1	154	179	15.5654
..(((((((........))))))).	chr19:44980501-44980741(-)$1	1	53	78	15.2426
))(((.(((........))).))))	chr19:39860300-39860540(+)$1	1	208	233	15.7069
((((.(.((........)).).)))	chr22:32112787-32113027(-)$1	1	122	147	15.7616
(((((.(((........))))))))	chr2:10188042-10188282(+)$1	1	180	205	15.9033
(((.(((((........))))))))	chrX:47098708-47098948(+)$1	1	131	156	14.9409
(((..((((........))))..))	chr12:69136077-69136317(+)$1	1	43	68	16.1498
(.(.(((((........)))))).)	chr7:72985503-72985743(-)$1	1	156	181	15.5227
(..(((.((........)).)))..	chr12:122720253-122720493(-)$1	1	4	29	15.1852
((..(((((........)))))..)	chr19:15379635-15379890(-)$1	1	152	177	14.9561
(((((((((........))))))))	chr5:148892560-148892800(-)$1	1	22	47	15.9022
(((...(((........)))...))	chr2:38973738-38973978(-)$1	1	89	114	17.6012
(((...(((........)))..)))	chr2:86830965-86831205(-)$1	1	172	197	16.8924
((.((((((........))))))))	chr1:197073585-197073825(-)$1	1	103	128	13.7506
(((..((((........)))).)))	chr16:67262176-67262416(+)$1	1	133	158	16.0501
...(((.((........))))))))	chr12:56531907-56532147(+)$1	1	83	108	15.4363
(((..((((........))))....	chr10:103291953-103292193(+)$1	1	94	119	16.1140
(((...(((........)))...))	chr5:179268890-179269130(-)$1	1	165	190	17.6012
(((..((((........))))...)	chr16:47536801-47537041(+)$1	1	74	99	16.8271
(((((((.(........))))))))	chr4:6925393-6925633(+)$1	1	88	113	15.9035
(((.(((((........)))))..)	chr1:151062874-151063114(+)$1	1	196	221	15.1168
(((((((((........))))))))	chr11:43400723-43400970(+)$1	1	169	194	16.5462
(.((..(((........)))..)).	chr14:103806670-103806910(+)$1	1	30	55	15.8968
(.((((..(........).)))).)	chr1:164790716-164790956(+)$1	1	58	83	15.2078
((((.((((........))))))).	chr2:215617110-215617350(-)$1	1	166	191	15.5511
(((((..((........)).)))))	chr7:99631297-99631537(+)$1	1	178	203	14.9487
.(((.((.(........).)).)))	chr6:170866026-170866266(+)$1	1	70	95	15.0037
(...(((((........)))))...	chr16:733979-734219(-)$1	1	142	167	16.1186
(((....((........))..))))	chr12:27156147-27156387(-)$1	1	201	226	14.5851
((((.((((........))))...)	chr2:96861039-96861279(-)$1	1	9	34	16.6469
...(.((((........)))).).)	chr8:144903940-144904180(-)$1	1	186	211	16.2615
((..(((.(........)))).)))	chrX:99662166-99662406(-)$1	1	126	151	16.6610
(.....(((........))).....	chr11:47594405-47594645(-)$1	1	12	37	14.3167
((((..(((........)))..)))	chr2:38525580-38525820(-)$1	1	111	136	16.6199
((((..(((........))))))))	chr22:31328486-31328726(-)$1	1	74	99	16.9344
(((..((((........))))..))	chr1:200376111-200376360(-)$1	1	139	164	16.4742

#PSSM
d : 0.18	e : 0.15	c : 0.13	b : 0.08	g : 0.08	a : 0.06	" : 0.06	= : 0.05	: : 0.03	h : 0.03	f : 0.03	$ : 0.01	! : 0.01	i : 0.01	
d : 0.17	c : 0.17	e : 0.15	b : 0.10	[ : 0.08	g : 0.08	" : 0.06	! : 0.05	= : 0.03	$ : 0.03	: : 0.01	i : 0.01	
d : 0.18	c : 0.17	e : 0.15	g : 0.13	! : 0.08	" : 0.06	[ : 0.05	b : 0.05	= : 0.03	a : 0.01	i : 0.01	$ : 0.01	
! : 0.13	g : 0.13	c : 0.12	" : 0.12	e : 0.10	[ : 0.08	d : 0.06	f : 0.06	b : 0.05	= : 0.03	i : 0.01	# : 0.01	a : 0.01	$ : 0.01	
! : 0.20	e : 0.15	" : 0.12	[ : 0.10	c : 0.08	g : 0.08	f : 0.06	= : 0.03	b : 0.03	d : 0.03	a : 0.01	i : 0.01	# : 0.01	$ : 0.01	
d : 0.22	! : 0.13	e : 0.12	" : 0.10	g : 0.08	[ : 0.06	f : 0.06	c : 0.05	= : 0.03	b : 0.03	a : 0.01	i : 0.01	# : 0.01	$ : 0.01	
c : 0.31	d : 0.18	e : 0.12	[ : 0.08	g : 0.08	f : 0.06	= : 0.03	! : 0.03	" : 0.01	i : 0.01	b : 0.01	# : 0.01	
c : 0.29	d : 0.18	b : 0.13	e : 0.10	[ : 0.08	f : 0.06	g : 0.06	i : 0.01	= : 0.01	! : 0.01	
c : 0.29	d : 0.18	b : 0.13	e : 0.10	a : 0.10	f : 0.06	g : 0.06	i : 0.01	= : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.29	d : 0.18	b : 0.13	e : 0.10	a : 0.10	f : 0.06	g : 0.06	i : 0.01	= : 0.01	
c : 0.31	d : 0.18	b : 0.13	e : 0.10	g : 0.08	f : 0.06	] : 0.05	= : 0.03	i : 0.01	
c : 0.32	d : 0.22	e : 0.12	g : 0.08	f : 0.06	] : 0.06	= : 0.03	3 : 0.01	i : 0.01	b : 0.01	2 : 0.01	
d : 0.22	e : 0.15	g : 0.10	] : 0.08	2 : 0.08	f : 0.06	3 : 0.06	c : 0.05	= : 0.03	a : 0.03	b : 0.03	5 : 0.01	i : 0.01	6 : 0.01	
e : 0.17	2 : 0.13	3 : 0.10	g : 0.10	c : 0.10	] : 0.08	f : 0.06	d : 0.05	4 : 0.03	= : 0.03	b : 0.03	: : 0.01	5 : 0.01	i : 0.01	6 : 0.01	
c : 0.15	e : 0.13	g : 0.12	2 : 0.10	3 : 0.10	d : 0.08	f : 0.06	b : 0.05	4 : 0.03	= : 0.03	a : 0.03	] : 0.01	5 : 0.01	i : 0.01	6 : 0.01	
c : 0.15	d : 0.13	e : 0.13	g : 0.13	b : 0.08	] : 0.08	2 : 0.06	3 : 0.06	4 : 0.03	= : 0.03	5 : 0.01	i : 0.01	6 : 0.01	
d : 0.17	e : 0.15	c : 0.13	b : 0.08	g : 0.08	4 : 0.05	2 : 0.05	= : 0.03	a : 0.03	] : 0.03	5 : 0.03	3 : 0.03	f : 0.01	H : 0.01	i : 0.01	C : 0.01	6 : 0.01	

#score	909.1741900270056
#seq	58
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_UTR_m1_run2.txt

#BEAR
^^^^^^^^^^^^^^^^^^^^^^^^^ccc2	chr16:69737625-69737857(+)$1	232	179	208	22.9464
e####ddddvvvvvvvvvvvvvdddd444	chr4:48041376-48041621(+)$1	245	114	143	20.6739
ggg^^^^^^^^^^^^^^^^^^^^gggggg	chr19:33078167-33078395(+)$1	228	116	145	22.6016
d!!gggggggvvvvvvvvvvvvvgggggg	chr16:46732153-46732404(+)$1	251	20	49	21.8454
ga^^^^^^^^^^^^^^^^^^^^^a]gggg	chr12:104341500-104341723(+)$1	223	36	65	23.0256
cc[a[ddddwwwwwwwwwwwwwwdddd]a	chr8:30040743-30040992(+)$1	249	124	153	21.6074
hhh[eeeeewwwwwwwwwwwwwweeeee2	chr4:57897174-57897422(+)$1	248	57	86	22.2080
gg[ffffff^^^^^^^^^^^^^^^^^^^^	chr1:154197459-154197702(+)$1	243	43	72	21.5985
""gggggggyyyyyyyyyyyyyyyygggg	chr2:160624775-160625007(+)$1	232	135	164	23.2587
ff^^^^^^^^^^^^^^^^^^^^^ffffff	chr13:23903365-23903586(-)$1	221	173	202	21.9864
=========xxxxxxxxxxxxxxx=====	chr3:139071465-139071696(+)$1	231	84	113	22.4456
e^^^^^^^^^^^^^^^^^^^^^^eeeee3	chr22:50713323-50713579(-)$1	256	107	136	22.9158
^^^^^^^^^^^^^^^^^^^^^^^eeeeee	chr2:74335086-74335318(+)$1	232	16	45	22.6687
eeeeffffffvvvvvvvvvvvvvffffff	chr14:90874056-90874294(+)$1	238	74	103	20.3202
ccc[eeeeewwwwwwwwwwwwwweeeee]	chr17:74730324-74730570(-)$1	246	164	193	23.1403
gggggggyyyyyyyyyyyyyyyygggggg	chr14:50089323-50089553(+)$1	230	125	154	23.1611
=========^^^^^^^^^^^^^^^^^^^^	chr12:14651027-14651253(+)$1	226	39	68	22.2163
d[a[eeeeewwwwwwwwwwwwwweeeee]	chr18:60997348-60997595(-)$1	247	161	190	23.2695
####eeeee^^^^^^^^^^^^^^^^^^^^	chr20:62521890-62522123(+)$1	233	92	121	22.3969
^^^^^^^^^^^^^^^^^^^^^^^eeeee:	chrX:24005397-24005654(-)$1	257	155	184	21.7346
c[ffffff[bbuuuuuuuuuuuubb]fff	chr6:142767001-142767228(+)$1	227	108	137	19.9388
ee!!eeeeeuuuuuuuuuuuueeeee333	chr1:209961617-209961855(-)$1	238	35	64	21.1514
b"""eeeeeyyyyyyyyyyyyyyyyeeee	chr14:93649187-93649424(-)$1	237	38	67	23.5336
!!ggggggg^^^^^^^^^^^^^^^^^^gg	chr8:124332593-124332835(-)$1	242	140	169	22.3270
===========uuuuuuuuuuuu======	chr18:48702584-48702840(-)$1	256	0	29	21.5984
cc!!eeeee^^^^^^^^^^^^^^^^^^^^	chr5:149361418-149361648(+)$1	230	62	91	22.3814
#hhhhhhhhwwwwwwwwwwwwwwhhhhhh	chr15:92707204-92707438(+)$1	234	141	170	18.5372
gggggg!!cccuuuuuuuuuuuuccc]gg	chr17:1324432-1324658(-)$1	226	175	204	21.3601
:::ffffffwwwwwwwwwwwwwwffffff	chr14:91337286-91337538(-)$1	252	200	229	19.4271
:::eeeeeyyyyyyyyyyyyyyyyeeeee	chr17:56082502-56082747(-)$1	245	195	224	20.7201
ggggggg^^^^^^^^^^^^^^^^^^gggg	chr6:119228910-119229142(+)$1	232	106	135	22.8289
:eeeee!!cccuuuuuuuuuuuuccc333	chr12:14939455-14939707(-)$1	252	53	82	20.2834
bb^^^^^^^^^^^^^^^^^^^^^bbhhhh	chr13:100215034-100215275(+)$1	241	74	103	21.0082
ccc[ccc[bbuuuuuuuuuuuubb]ccc]	chr2:198415295-198415526(+)$1	231	79	108	20.5795
iii^^^^^^^^^^^^^^^^^^^^iiiiii	chr3:5259310-5259552(+)$1	242	37	66	22.5967
ff!!eeeeevvvvvvvvvvvvveeeeeff	chr9:128125838-128126070(+)$1	232	144	173	21.7198
eee[eeeeeuuuuuuuuuuuueeeee]ee	chr19:12299545-12299777(+)$1	232	146	175	20.4299
dddffffffwwwwwwwwwwwwwwffffff	chr10:65383213-65383441(+)$1	228	76	105	21.3522
d"""ffffff^^^^^^^^^^^^^^^^^^f	chr1:109351948-109352170(+)$1	222	136	165	20.8441
====ggggggguuuuuuuuuuuugggggg	chr17:49042997-49043235(-)$1	238	186	215	20.9343
:ffffffyyyyyyyyyyyyyyyyffffff	chr1:113000975-113001195(+)$1	220	130	159	21.3447
g^^^^^^^^^^^^^^^^^^^^^^^ggggg	chr12:111889934-111890175(-)$1	241	118	147	23.1855
bb[bb[cccwwwwwwwwwwwwwwccc]bb	chr12:59265889-59266111(-)$1	222	75	104	21.1145
h^^^^^^^^^^^^^^^^^^^^^^^^hhhh	chr20:5095713-5095946(-)$1	233	28	57	22.0596
b[dddd^^^^^^^^^^^^^^^^^^dddd]	chr17:77768078-77768308(-)$1	230	21	50	21.3797
[bb[dddd^^^^^^^^^^^^^^^^^^^^^	chr18:29709308-29709537(+)$1	229	159	188	21.2256
ggggg[cccwwwwwwwwwwwwwwccc]gg	chr7:102952711-102952939(+)$1	228	120	149	22.6012
::gggggggwwwwwwwwwwwwwwgggggg	chr1:41492776-41493007(-)$1	231	179	208	21.0091
ffffeeeeexxxxxxxxxxxxxxxeeeee	chr1:87210912-87211135(+)$1	223	186	215	21.2865
J:gggggggwwwwwwwwwwwwwwgggggg	chr3:4887909-4888162(+)$1	253	209	238	20.5156
hhhhhh[bbyyyyyyyyyyyyyyyybb]h	chr5:149366605-149366831(+)$1	226	3	32	19.9976
ccc[eeeee^^^^^^^^^^^^^^^^^^^e	chr2:169628439-169628686(+)$1	247	158	187	22.0777
cc[ffffffyyyyyyyyyyyyyyyyffff	chr12:53806944-53807170(+)$1	226	12	41	22.6247
===========uuuuuuuuuuuu======	chr15:76640723-76640944(-)$1	221	62	91	21.5984
h[eeeeeyyyyyyyyyyyyyyyyeeeee]	chr13:73329617-73329853(+)$1	236	94	123	23.0880
^^^^^^^^^^^^^^^^^^^^^^^eeeeef	chr1:29474257-29474482(-)$1	225	185	214	22.7204
g"""eeeeevvvvvvvvvvvvveeeee22	chr6:25620607-25620842(+)$1	235	158	187	22.0148
cccffffff^^^^^^^^^^^^^^^^^^ff	chr2:176792745-176792989(-)$1	244	171	200	21.5638
==========vvvvvvvvvvvvv======	chr1:110597063-110597289(+)$1	226	152	181	22.2768
d!!cccayyyyyyyyyyyyyyyya]ccc3	chr16:69342709-69342939(+)$1	230	8	37	23.4553
g"""eeeeewwwwwwwwwwwwwweeeee3	chr8:29964260-29964501(+)$1	241	99	128	23.6260
d!!ffffff^^^^^^^^^^^^^^^^^^^^	chr2:87002289-87002515(+)$1	226	81	110	21.7699
^^^^^^^^^^^^^^^^^^^^^^^ffffff	chr1:226170669-226170919(-)$1	250	16	45	22.2876
dd!!bbyyyyyyyyyyyyyyyybbdddd]	chr19:34960287-34960508(+)$1	221	19	48	20.5108
==:eeeeecccvvvvvvvvvvvvvccc22	chr11:82896680-82896913(+)$1	233	63	92	19.5957
e^^^^^^^^^^^^^^^^^^^^^^eeeee2	chr1:155232694-155232926(-)$1	232	81	110	22.7226
=========xxxxxxxxxxxxxxx=====	chr13:77579335-77579568(-)$1	233	83	112	22.4456
+++eeeee[avvvvvvvvvvvvva]eeee	chr17:27877172-27877407(+)$1	235	133	162	21.0353
:::ffffffwwwwwwwwwwwwwwffffff	chr1:170522444-170522686(+)$1	242	74	103	19.4271
iiiiiiiiiuuuuuuuuuuuuiiiiiiii	chr8:48890579-48890809(+)$1	230	178	207	20.1932
ee!!cccwwwwwwwwwwwwwwccceeeee	chr17:2940767-2941013(+)$1	246	211	240	20.5126

#otherMatches

#Seq PSSM
CUCUCCCCUUCCUUUCUCUCUCUUCCAGA	chr16:69737625-69737857(+)$1	232	179	208	22.9464
UCUUAAGAUUUAUUAUGUGAAUAUCUGCA	chr4:48041376-48041621(+)$1	245	114	143	20.6739
AUUGUCUAUAUGCCUUUUAAAAAAAUAAA	chr19:33078167-33078395(+)$1	228	116	145	22.6016
CUUAUUCAGAAUAUAAAAUUCAGUCUGAA	chr16:46732153-46732404(+)$1	251	20	49	21.8454
CCUUCUCCCCUGCACUGUAAAAUGUGGGA	chr12:104341500-104341723(+)$1	223	36	65	23.0256
AAUGUAUUAUUUUCCUAUAUCCUUGGUUC	chr8:30040743-30040992(+)$1	249	124	153	21.6074
AUAUGUACUGUGUUGUGAUAAAAAGUAUU	chr4:57897174-57897422(+)$1	248	57	86	22.2080
GAGUUAAAAACAUAUUUUGCCCACAUUUA	chr1:154197459-154197702(+)$1	243	43	72	21.5985
ACCCUUAGGAUACACUUUAAAACACCUUA	chr2:160624775-160625007(+)$1	232	135	164	23.2587
GUGCUGCAGUUAAAAAAAAAACAACCUUU	chr13:23903365-23903586(-)$1	221	173	202	21.9864
CAAGAUACUUUGGUGGAAUGGUGUGGUAU	chr3:139071465-139071696(+)$1	231	84	113	22.4456
ACCACCCCACCCCUUUUUGUAAAUCUUGU	chr22:50713323-50713579(-)$1	256	107	136	22.9158
CCCCUCCUUACCCUCCCUUCUCCCUCAGU	chr2:74335086-74335318(+)$1	232	16	45	22.6687
GUUCAUUCAAUUAUUUUAAGCAUUUGAAU	chr14:90874056-90874294(+)$1	238	74	103	20.3202
ACCUUUUUUUCCCUCUUCCCCCUAAAAAU	chr17:74730324-74730570(-)$1	246	164	193	23.1403
AAAAGGUGUCCAAAUACAUAGUAAUCUUU	chr14:50089323-50089553(+)$1	230	125	154	23.1611
UCUUGUGCAUGAUACCCCAUGUAAAAUCC	chr12:14651027-14651253(+)$1	226	39	68	22.2163
ACCUAAAAAUUAUAGCAUACCUUUUUUUU	chr18:60997348-60997595(-)$1	247	161	190	23.2695
GCCUUAUGCUUUAUUUCUUUCUAAUUUUU	chr20:62521890-62522123(+)$1	233	92	121	22.3969
AGCUGCCUUCUCUUAUCCGCAUUGUGUUA	chrX:24005397-24005654(-)$1	257	155	184	21.7346
GUACAUAUUUAUUUAUUUGUGUUUAUAUA	chr6:142767001-142767228(+)$1	227	108	137	19.9388
AGCCCAUGCAGCCCACCCCCAGCAUGCAA	chr1:209961617-209961855(-)$1	238	35	64	21.1514
UCUGUGCCUAUUUAAAGUCUCCUAAAGGU	chr14:93649187-93649424(-)$1	237	38	67	23.5336
CUACCUUGUUAAACACCUUUUAAUAGCAC	chr8:124332593-124332835(-)$1	242	140	169	22.3270
GUUCCAUGUGGCCACAACCUCUUCUGCAU	chr18:48702584-48702840(-)$1	256	0	29	21.5984
CAAGUGGCUAGAUAUUAUUCCUCCUUUGA	chr5:149361418-149361648(+)$1	230	62	91	22.3814
UCUGUGUUAACCCUUCAAGUCACUAACAC	chr15:92707204-92707438(+)$1	234	141	170	18.5372
AUCCAGGGCCGUUCAUGAACCACUGGGCU	chr17:1324432-1324658(-)$1	226	175	204	21.3601
AUUUUUCUGUUAAAUUUUAAAUCCAGAAA	chr14:91337286-91337538(-)$1	252	200	229	19.4271
AUUUAGUUAACUCCAUACUCUUCAGACUG	chr17:56082502-56082747(-)$1	245	195	224	20.7201
GCAUAUAUAUUAUUUUCUUCUCCUUUAUA	chr6:119228910-119229142(+)$1	232	106	135	22.8289
AGAGAUUUCUGGAGAAAAAAAAACAGUUU	chr12:14939455-14939707(-)$1	252	53	82	20.2834
GGCCUAGUAAUCCUUCAGAAACACCGUAA	chr13:100215034-100215275(+)$1	241	74	103	21.0082
AAUCAUAGGAAAAAUGUACUGAUCAUAUA	chr2:198415295-198415526(+)$1	231	79	108	20.5795
UCUAUUUUACCUUUUUUCAUUUCAGAAGC	chr3:5259310-5259552(+)$1	242	37	66	22.5967
ACAUUGAAUGCACAGACCAAGAAUUCAGU	chr9:128125838-128126070(+)$1	232	144	173	21.7198
GGUCAUGUAGUCUCUAGAAAAUACAUAAC	chr19:12299545-12299777(+)$1	232	146	175	20.4299
AAUUGCAGCUGGUAUUUUAUUUUGCUGUA	chr10:65383213-65383441(+)$1	228	76	105	21.3522
UAAAUUAGAAAACCAAAAAUCAUGAACAU	chr1:109351948-109352170(+)$1	222	136	165	20.8441
GGGGGGUUUUAUAUUAAAGAAAUUAAGAC	chr17:49042997-49043235(-)$1	238	186	215	20.9343
ACACACUUAAACACAUAAAUACUAGUGUG	chr1:113000975-113001195(+)$1	220	130	159	21.3447
uaaaaaaaauuuaaaaaauaaaaaaaguu	chr12:111889934-111890175(-)$1	241	118	147	23.1855
ACUAAAGCAUUUUAAAUAAUACCUGCCUU	chr12:59265889-59266111(-)$1	222	75	104	21.1145
AAUUCAAGAAAAUAAAACUAAGCUCUUUG	chr20:5095713-5095946(-)$1	233	28	57	22.0596
CCUUCCUCCCCCUCAGUUUUUGUUGGAAA	chr17:77768078-77768308(-)$1	230	21	50	21.3797
UUGAUGCAUUCCUCCCAUUUACUUUAUUA	chr18:29709308-29709537(+)$1	229	159	188	21.2256
UUUCAAAGGAUAAAAAGACUACCCCUCUG	chr7:102952711-102952939(+)$1	228	120	149	22.6012
uuggaccagucauuccccuucucuugguc	chr1:41492776-41493007(-)$1	231	179	208	21.0091
UGCACCAGAGAUACCUCUUUUACAUCUGG	chr1:87210912-87211135(+)$1	223	186	215	21.2865
UGCCAAAAAUAUUAAAAAUGCCUUUUUUG	chr3:4887909-4888162(+)$1	253	209	238	20.5156
UGAAUGAACUUAAAUUCUCAGUCUUGUCU	chr5:149366605-149366831(+)$1	226	3	32	19.9976
AGGCUGAGAGAGAAAAAUAUGUGCAGUAU	chr2:169628439-169628686(+)$1	247	158	187	22.0777
AUUACCUAGAAAUCUAUCUUAAAACCUGG	chr12:53806944-53807170(+)$1	226	12	41	22.6247
CCAUGUUUAUACUCUUCCCACACUGUAGA	chr15:76640723-76640944(-)$1	221	62	91	21.5984
ACUAUGUUAAAACUGAAGGCACUAUAUAU	chr13:73329617-73329853(+)$1	236	94	123	23.0880
GUUUCCAUUAAAUUUGAAUAAAGACUAUU	chr1:29474257-29474482(-)$1	225	185	214	22.7204
CUUCUCCAGUUACAUUUUUAGUUUGGACU	chr6:25620607-25620842(+)$1	235	158	187	22.0148
CUGUGGAAUAUAAACUUUUUAAAAAUAAU	chr2:176792745-176792989(-)$1	244	171	200	21.5638
UUUAAUGUGAUUGUGUAUUCUGUUUACAU	chr1:110597063-110597289(+)$1	226	152	181	22.2768
GGAUACCAAAUCAAAAACCCAACGCGUAA	chr16:69342709-69342939(+)$1	230	8	37	23.4553
GUAUGUUGUAUAUAUUACAUAAAAUAACU	chr8:29964260-29964501(+)$1	241	99	128	23.6260
GACCAAGGGUGUAAACCAGUUUAUUAUAU	chr2:87002289-87002515(+)$1	226	81	110	21.7699
uucuauuaauuuacuuugugcuucugugc	chr1:226170669-226170919(-)$1	250	16	45	22.2876
AGUAGGAAUAUAGUUUUAAAAACCCUUUG	chr19:34960287-34960508(+)$1	221	19	48	20.5108
UAUGGUUAACUUUUUUCUUUUGUUGGUUU	chr11:82896680-82896913(+)$1	233	63	92	19.5957
CCUAUCACUUCAACCCCUGCCUUGUACAU	chr1:155232694-155232926(-)$1	232	81	110	22.7226
AUAAGCAAAAUGCAUAGUACUUAAUUUGU	chr13:77579335-77579568(-)$1	233	83	112	22.4456
AGUAUAGUGCACAUAACUUCCCCGGACUG	chr17:27877172-27877407(+)$1	235	133	162	21.0353
UACUAGUACUUGACCAAUACAUUGUGCUA	chr1:170522444-170522686(+)$1	242	74	103	19.4271
CAUUUUUUAAUAAAGUAUCCAUAGAAAAU	chr8:48890579-48890809(+)$1	230	178	207	20.1932
UUGUUGCUUAAAUGUGUCUUUGCAGAAAU	chr17:2940767-2941013(+)$1	246	211	240	20.5126

#DB
.........................))).	chr16:69737625-69737857(+)$1	1	179	208	22.9464
(....((((.............))))...	chr4:48041376-48041621(+)$1	1	114	143	20.6739
(((....................))))))	chr19:33078167-33078395(+)$1	1	116	145	22.6016
(..(((((((.............))))))	chr16:46732153-46732404(+)$1	1	20	49	21.8454
((.....................).))))	chr12:104341500-104341723(+)$1	1	36	65	23.0256
((.(.((((..............)))).)	chr8:30040743-30040992(+)$1	1	124	153	21.6074
(((.(((((..............))))).	chr4:57897174-57897422(+)$1	1	57	86	22.2080
((.((((((....................	chr1:154197459-154197702(+)$1	1	43	72	21.5985
..(((((((................))))	chr2:160624775-160625007(+)$1	1	135	164	23.2587
((.....................))))))	chr13:23903365-23903586(-)$1	1	173	202	21.9864
(((((((((...............)))))	chr3:139071465-139071696(+)$1	1	84	113	22.4456
(......................))))).	chr22:50713323-50713579(-)$1	1	107	136	22.9158
.......................)))))(	chr2:74335086-74335318(+)$1	1	16	45	22.6687
))))((((((.............))))))	chr14:90874056-90874294(+)$1	1	74	103	20.3202
(((.(((((..............))))).	chr17:74730324-74730570(-)$1	1	164	193	23.1403
(((((((................))))))	chr14:50089323-50089553(+)$1	1	125	154	23.1611
(((((((((....................	chr12:14651027-14651253(+)$1	1	39	68	22.2163
(.(.(((((..............))))).	chr18:60997348-60997595(-)$1	1	161	190	23.2695
....(((((....................	chr20:62521890-62522123(+)$1	1	92	121	22.3969
.......................))))).	chrX:24005397-24005654(-)$1	1	155	184	21.7346
(.((((((.((............)).)))	chr6:142767001-142767228(+)$1	1	108	137	19.9388
((..(((((............)))))...	chr1:209961617-209961855(-)$1	1	35	64	21.1514
(...(((((................))))	chr14:93649187-93649424(-)$1	1	38	67	23.5336
..(((((((..................))	chr8:124332593-124332835(-)$1	1	140	169	22.3270
(((((((((((............))))))	chr18:48702584-48702840(-)$1	1	0	29	21.5984
((..(((((....................	chr5:149361418-149361648(+)$1	1	62	91	22.3814
.((((((((..............))))))	chr15:92707204-92707438(+)$1	1	141	170	18.5372
((((((..(((............))).))	chr17:1324432-1324658(-)$1	1	175	204	21.3601
...((((((..............))))))	chr14:91337286-91337538(-)$1	1	200	229	19.4271
...(((((................)))))	chr17:56082502-56082747(-)$1	1	195	224	20.7201
(((((((..................))))	chr6:119228910-119229142(+)$1	1	106	135	22.8289
.(((((..(((............)))...	chr12:14939455-14939707(-)$1	1	53	82	20.2834
((.....................))))))	chr13:100215034-100215275(+)$1	1	74	103	21.0082
(((.(((.((............)).))).	chr2:198415295-198415526(+)$1	1	79	108	20.5795
(((....................))))))	chr3:5259310-5259552(+)$1	1	37	66	22.5967
((..(((((.............)))))))	chr9:128125838-128126070(+)$1	1	144	173	21.7198
(((.(((((............))))).))	chr19:12299545-12299777(+)$1	1	146	175	20.4299
(((((((((..............))))))	chr10:65383213-65383441(+)$1	1	76	105	21.3522
(...((((((..................)	chr1:109351948-109352170(+)$1	1	136	165	20.8441
))))(((((((............))))))	chr17:49042997-49043235(-)$1	1	186	215	20.9343
.((((((................))))))	chr1:113000975-113001195(+)$1	1	130	159	21.3447
(.......................)))))	chr12:111889934-111890175(-)$1	1	118	147	23.1855
((.((.(((..............))).))	chr12:59265889-59266111(-)$1	1	75	104	21.1145
(........................))))	chr20:5095713-5095946(-)$1	1	28	57	22.0596
(.((((..................)))).	chr17:77768078-77768308(-)$1	1	21	50	21.3797
.((.((((.....................	chr18:29709308-29709537(+)$1	1	159	188	21.2256
(((((.(((..............))).))	chr7:102952711-102952939(+)$1	1	120	149	22.6012
..(((((((..............))))))	chr1:41492776-41493007(-)$1	1	179	208	21.0091
))))(((((...............)))))	chr1:87210912-87211135(+)$1	1	186	215	21.2865
).(((((((..............))))))	chr3:4887909-4888162(+)$1	1	209	238	20.5156
((((((.((................)).)	chr5:149366605-149366831(+)$1	1	3	32	19.9976
(((.(((((...................)	chr2:169628439-169628686(+)$1	1	158	187	22.0777
((.((((((................))))	chr12:53806944-53807170(+)$1	1	12	41	22.6247
(((((((((((............))))))	chr15:76640723-76640944(-)$1	1	62	91	21.5984
(.(((((................))))).	chr13:73329617-73329853(+)$1	1	94	123	23.0880
.......................))))))	chr1:29474257-29474482(-)$1	1	185	214	22.7204
(...(((((.............)))))..	chr6:25620607-25620842(+)$1	1	158	187	22.0148
(((((((((..................))	chr2:176792745-176792989(-)$1	1	171	200	21.5638
((((((((((.............))))))	chr1:110597063-110597289(+)$1	1	152	181	22.2768
(..((((................).))).	chr16:69342709-69342939(+)$1	1	8	37	23.4553
(...(((((..............))))).	chr8:29964260-29964501(+)$1	1	99	128	23.6260
(..((((((....................	chr2:87002289-87002515(+)$1	1	81	110	21.7699
.......................))))))	chr1:226170669-226170919(-)$1	1	16	45	22.2876
((..((................)))))).	chr19:34960287-34960508(+)$1	1	19	48	20.5108
)).((((((((.............)))..	chr11:82896680-82896913(+)$1	1	63	92	19.5957
(......................))))).	chr1:155232694-155232926(-)$1	1	81	110	22.7226
(((((((((...............)))))	chr13:77579335-77579568(-)$1	1	83	112	22.4456
...(((((.(.............).))))	chr17:27877172-27877407(+)$1	1	133	162	21.0353
...((((((..............))))))	chr1:170522444-170522686(+)$1	1	74	103	19.4271
(((((((((............))))))))	chr8:48890579-48890809(+)$1	1	178	207	20.1932
((..(((..............))))))))	chr17:2940767-2941013(+)$1	1	211	240	20.5126

#PSSM
g : 0.14	c : 0.11	= : 0.11	e : 0.09	d : 0.09	: : 0.08	^ : 0.07	h : 0.05	b : 0.05	f : 0.04	# : 0.02	i : 0.02	" : 0.01	! : 0.01	[ : 0.01	J : 0.01	+ : 0.01	
^ : 0.12	= : 0.11	c : 0.09	g : 0.08	" : 0.07	e : 0.07	: : 0.07	! : 0.05	f : 0.05	[ : 0.05	h : 0.04	b : 0.04	# : 0.02	i : 0.02	d : 0.02	a : 0.01	+ : 0.01	
^ : 0.16	g : 0.12	! : 0.11	= : 0.09	[ : 0.05	e : 0.05	c : 0.05	" : 0.05	: : 0.05	h : 0.04	f : 0.04	# : 0.02	i : 0.02	d : 0.02	a : 0.01	b : 0.01	+ : 0.01	
^ : 0.19	f : 0.14	g : 0.12	[ : 0.09	= : 0.09	e : 0.08	! : 0.07	" : 0.05	# : 0.02	h : 0.02	a : 0.01	b : 0.01	d : 0.01	c : 0.01	i : 0.01	
e : 0.25	^ : 0.19	f : 0.15	g : 0.14	= : 0.08	c : 0.04	h : 0.02	b : 0.02	d : 0.02	# : 0.01	[ : 0.01	i : 0.01	
e : 0.25	^ : 0.19	f : 0.15	g : 0.12	= : 0.08	d : 0.05	c : 0.04	h : 0.02	[ : 0.02	b : 0.01	i : 0.01	
e : 0.23	^ : 0.21	f : 0.15	g : 0.11	= : 0.08	c : 0.05	d : 0.04	! : 0.02	h : 0.01	[ : 0.01	a : 0.01	y : 0.01	i : 0.01	
^ : 0.22	e : 0.22	f : 0.14	g : 0.08	= : 0.08	y : 0.07	d : 0.04	! : 0.02	c : 0.02	h : 0.01	[ : 0.01	b : 0.01	i : 0.01	w : 0.01	
^ : 0.23	e : 0.18	f : 0.12	g : 0.08	= : 0.08	y : 0.08	c : 0.07	d : 0.02	[ : 0.02	b : 0.02	h : 0.01	i : 0.01	w : 0.01	
^ : 0.35	w : 0.19	y : 0.14	v : 0.04	x : 0.04	u : 0.04	= : 0.04	c : 0.04	g : 0.02	f : 0.02	b : 0.02	a : 0.01	
^ : 0.36	w : 0.19	y : 0.14	v : 0.09	u : 0.05	x : 0.04	c : 0.04	= : 0.02	b : 0.01	g : 0.01	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.19	y : 0.14	u : 0.14	v : 0.11	x : 0.04	
^ : 0.36	w : 0.18	y : 0.14	v : 0.11	u : 0.09	x : 0.04	e : 0.02	i : 0.01	c : 0.01	
^ : 0.36	w : 0.18	y : 0.12	u : 0.08	v : 0.07	e : 0.05	x : 0.04	b : 0.02	d : 0.01	i : 0.01	c : 0.01	
^ : 0.21	e : 0.19	f : 0.09	g : 0.08	y : 0.07	c : 0.07	b : 0.05	a : 0.04	x : 0.04	= : 0.04	d : 0.02	i : 0.02	h : 0.01	v : 0.01	
e : 0.23	^ : 0.18	g : 0.09	f : 0.09	= : 0.07	c : 0.07	d : 0.05	] : 0.05	y : 0.05	b : 0.02	i : 0.02	h : 0.01	
e : 0.26	g : 0.14	^ : 0.14	c : 0.11	f : 0.11	= : 0.07	d : 0.05	h : 0.04	i : 0.02	] : 0.01	b : 0.01	
e : 0.23	g : 0.14	^ : 0.14	f : 0.12	= : 0.07	c : 0.05	] : 0.05	d : 0.04	h : 0.04	3 : 0.02	i : 0.02	4 : 0.01	b : 0.01	
e : 0.22	g : 0.18	f : 0.15	^ : 0.11	= : 0.07	c : 0.04	h : 0.04	] : 0.02	3 : 0.02	i : 0.02	d : 0.02	2 : 0.02	4 : 0.01	b : 0.01	
g : 0.18	f : 0.18	e : 0.11	^ : 0.08	] : 0.08	2 : 0.07	= : 0.07	3 : 0.07	h : 0.05	i : 0.02	4 : 0.01	a : 0.01	: : 0.01	b : 0.01	

#score	1540.8419216445373
#seq	71
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_UTR_m3_run2.txt

#BEAR
]ccceeeeecccnnnnnccc>>>>>>>	chr2:46810017-46810259(+)$1	242	178	205	10.7688
!ccc"""eeeeennnnneeeee333cc	chr14:97032505-97032751(+)$1	246	47	74	13.7732
ggg"""eeeeeooooooeeeee]gggg	chr2:32249125-32249380(-)$1	255	177	204	10.1907
::==========nnnnn==========	chr11:86520112-86520352(+)$1	240	136	163	12.5578
fffffgggggggnnnnnggggggg555	chr5:142657500-142657741(-)$1	241	169	196	11.4566
"ggggggg!!ccclllccc]ggggggg	chr1:47843083-47843446(+)$1	363	141	168	9.8937
Jffffffeeeeennnnneeeee333ff	chr1:32640544-32640944(+)$1	400	14	41	11.9358
fffff!!eeeeennnnneeeee22fff	chr6:123047320-123047568(+)$1	248	62	89	13.0333
ccc!!gggggggmmmmggggggg]ccc	chr14:78198786-78199026(-)$1	240	182	209	8.8304
"dddd!!eeeeennnnneeeeeddddg	chr12:53873463-53873704(+)$1	241	207	234	11.5453
[a[bb!!eeeeennnnneeeee]bb]a	chr10:104240296-104240536(-)$1	240	85	112	12.2658
a[dddd!!ddddnnnnndddd]dddd]	chr12:53434439-53434722(+)$1	283	36	63	10.3905
b!!ffffffcccnnnnnccc333ffff	chr11:44266066-44266315(+)$1	249	9	36	12.7629
(ccc[gggggggnnnnnggggggg]cc	chr4:38700375-38700623(+)$1	248	90	117	13.4093
:ffffff!!cccnnnnnccc22fffff	chr17:4172872-4173137(-)$1	265	234	261	11.6925
gggg####ddddnnnnndddd4444gg	chr1:222905880-222906188(+)$1	308	260	287	12.0639
###bb!!eeeeennnnneeeee22bb4	chr19:13205560-13205807(+)$1	247	163	190	12.0929
:::iiiiiiiiinnnnniiiiiiiiid	chr12:113596550-113596798(-)$1	248	56	83	10.6984
c[==========nnnnn==========	chr4:39825884-39826124(-)$1	240	115	142	14.4027
d[ccc[aeeeeennnnneeeee]a]cc	chr18:32917284-32917532(-)$1	248	212	239	13.0322
gggggg[eeeeennnnneeeee]gggg	chr15:76191767-76192007(+)$1	240	205	232	13.7473
[eeeee"""cccnnnnnccc333eeee	chr3:139076364-139076606(-)$1	242	45	72	12.1701
[ffffff[acccnnnnnccc]a]ffff	chr2:136482573-136482813(+)$1	240	35	62	12.7094
b!!iiiiiiiiillliiiiiiiii333	chr5:134193099-134193339(+)$1	240	35	62	10.3478
dd"""gggggggnnnnnggggggg333	chr7:96810552-96810792(+)$1	240	72	99	13.9899
eeeeegggggggnnnnngggggggggg	chr20:25594869-25595109(-)$1	240	79	106	13.3161
eeeeegggggggooooooggggggg33	chr19:47567650-47567896(-)$1	246	69	96	10.2262
:ggggggg!!bbnnnnnbb]ggggggg	chr2:120934786-120935066(+)$1	280	171	198	11.8207
f"""a!!eeeeennnnneeeee22aff	chr7:105182885-105183125(+)$1	240	182	209	13.0869
fffff####cccnnnnnccc>>>>>>>	chr20:37581084-37581324(+)$1	240	122	149	11.3739
""ffffff[cccnnnnncccffffff]	chr12:22839788-22840108(+)$1	320	282	309	12.4672
ggggggg[ddddnnnnndddd22gggg	chr2:131906731-131906971(+)$1	240	141	168	12.3849
ggggg!!eeeeellleeeee22ggggg	chr16:23584859-23585099(+)$1	240	22	49	9.3577
e!!cccffffffnnnnnffffff333c	chr19:52826162-52826402(+)$1	240	18	45	12.3326
ffffffffffffnnnnnffffff]fff	chr3:169812957-169813197(-)$1	240	24	51	11.6343
ffffffdddd[annnnna]dddd333f	chr17:8339142-8339382(+)$1	240	109	136	11.4262
dddd[gggggggnnnnnggggggg22d	chr10:124923999-124924239(+)$1	240	89	116	12.7691
eeee[a[eeeeeooooooeeeeeaeee	chr2:163217635-163217881(+)$1	246	132	159	8.7958
ffffff:eeeeennnnneeeeecccff	chr10:98745142-98745384(+)$1	242	59	86	11.3860
g####gggggggnnnnngggggggggg	chr2:223806608-223806889(+)$1	281	201	228	13.9254
============lll============	chr20:32868126-32868368(-)$1	242	50	77	10.8866
ffffff"""cccnnnnncccffffff:	chr12:56295965-56296205(-)$1	240	157	184	11.5001
EEEiiiiiiiiinnnnniiiiiiiiif	chr6:90038860-90039106(-)$1	246	69	96	10.9282
cc"""gggggggnnnnnggggggg]cc	chr17:80209170-80209464(-)$1	294	177	204	13.9888
ggggggg!!bboooooobb333ggggg	chr5:31400751-31400991(-)$1	240	52	79	9.4285
:ccc[gggggggnnnnnggggggg]cc	chr19:45683229-45683509(+)$1	280	52	79	13.2344
ggggggg!!cccmmmmccc]ggggggg	chr6:160211491-160211731(+)$1	240	97	124	9.0936
$$$$dddd[cccnnnnnccc]ddddcc	chr9:116170200-116170449(-)$1	249	216	243	10.4903
dd[iiiiiiiiiooooooiiiiiiiii	chr18:74681457-74681699(+)$1	242	111	138	10.2896
ffff!!gggggggmmmmggggggg333	chr9:140509724-140510004(-)$1	280	191	218	9.2044
ggggggg[cccooooooccc]gggggg	chr5:99922047-99922288(+)$1	241	56	83	10.5832
d!!cccffffffnnnnnffffff22cc	chr1:10441339-10441585(+)$1	246	161	188	11.7317

#otherMatches

#Seq PSSM
CUGAGUUGUCCAACACAUGGUAUAAAC	chr2:46810017-46810259(+)$1	242	178	205	10.7688
UUGUCAGUACAUUUUACGUGUAGAAGC	chr14:97032505-97032751(+)$1	246	47	74	13.7732
UUAAGAGGCAGCUUUAAUUGCCAUGAU	chr2:32249125-32249380(-)$1	255	177	204	10.1907
CUGAGAUUCAUCUUGGUGGUGGGUUUU	chr11:86520112-86520352(+)$1	240	136	163	12.5578
UGGCAGUAAAUGUUAGCCAUUUACAGC	chr5:142657500-142657741(-)$1	241	169	196	11.4566
UAUGCUAAAAUGAUUCUCAGUUAGCAU	chr1:47843083-47843446(+)$1	363	141	168	9.8937
CAUUCUUUUGUUAAGCCAACAAGUUGA	chr1:32640544-32640944(+)$1	400	14	41	11.9358
AAAUGUCAGUAAUUAAUUUAUUUUCAU	chr6:123047320-123047568(+)$1	248	62	89	13.0333
ACAUUGCUGAUCGGAAGGUUGGUUUGU	chr14:78198786-78199026(-)$1	240	182	209	8.8304
CUCAAAGGACCCUUCUUGGGUUUUGAA	chr12:53873463-53873704(+)$1	241	207	234	11.5453
ACGAUGAACUACCUGCAGUGGUGAUGG	chr10:104240296-104240536(-)$1	240	85	112	12.2658
GGUAGAUUUAGCCUCAAGUUGUUCUAG	chr12:53434439-53434722(+)$1	283	36	63	10.3905
AAAAUGCCAAGUGGAAGACUUUGUGGC	chr11:44266066-44266315(+)$1	249	9	36	12.7629
AUUCCCCUUCAUCAAGAAUGGAGGAGA	chr4:38700375-38700623(+)$1	248	90	117	13.4093
AGUACUGUGAUCACGUGGGUGUCAGUA	chr17:4172872-4173137(-)$1	265	234	261	11.6925
UGAAGCUUGUAGAAUAACUAUUAUAUU	chr1:222905880-222906188(+)$1	308	260	287	12.0639
ACAUGGACUCUGUCAAGUAGAGGACAG	chr19:13205560-13205807(+)$1	247	163	190	12.0929
GCAGGGCGCCUUCGGCCGGGGUGCCCG	chr12:113596550-113596798(-)$1	248	56	83	10.6984
UAAUGUGUGCACUUUAUGUGUACACAU	chr4:39825884-39826124(-)$1	240	115	142	14.4027
UCCAUACUGGGGAGAAACCUUAUGAAU	chr18:32917284-32917532(-)$1	248	212	239	13.0322
UGCUCAUUUUAGAUAUCUUGGACUGAG	chr15:76191767-76192007(+)$1	240	205	232	13.7473
CCACAUCAUCUUAAGAAGAGUUUAUGU	chr3:139076364-139076606(-)$1	242	45	72	12.1701
CUCCUUGUGGAUUUUUUGUCACCUAAG	chr2:136482573-136482813(+)$1	240	35	62	12.7094
CAUUGUAUGUGGGGACUAUGUGCACUG	chr5:134193099-134193339(+)$1	240	35	62	10.3478
UUAUUAAUGAAAUACUCUUUUAUUUUG	chr7:96810552-96810792(+)$1	240	72	99	13.9899
GGGGCUUAUUAAAGUGGUUAAUAAAUA	chr20:25594869-25595109(-)$1	240	79	106	13.3161
UUUUGUAAAAGAAAAAUAUUUUUUAAA	chr19:47567650-47567896(-)$1	246	69	96	10.2262
ACGCCUCGGACGGAGCACGGUGGGGUG	chr2:120934786-120935066(+)$1	280	171	198	11.8207
AAAUGGAUUUCACAAAUUGAAGAACUA	chr7:105182885-105183125(+)$1	240	182	209	13.0869
GACAUCAUCAGCUUCCUGCUUUAAAAA	chr20:37581084-37581324(+)$1	240	122	149	11.3739
ACAAAAUAAGAUAUCUAAUCUAUUUUC	chr12:22839788-22840108(+)$1	320	282	309	12.4672
AAGAAGUGCUUGAGUUACAAGAAACUU	chr2:131906731-131906971(+)$1	240	141	168	12.3849
AGCUCUUUUUAAAUGUUGAACUGAGCU	chr16:23584859-23585099(+)$1	240	22	49	9.3577
CCAUACUGCAAAGAAAUUUUGCAAAUG	chr19:52826162-52826402(+)$1	240	18	45	12.3326
UAGUAAUGUUUUAAAAAAAGAUGUUUA	chr3:169812957-169813197(-)$1	240	24	51	11.6343
GCUCGGGGCUGCGUAGGGGAGCUGAGC	chr17:8339142-8339382(+)$1	240	109	136	11.4262
AAAUAAUUGUAACGUAAUUGCAGUGCA	chr10:124923999-124924239(+)$1	240	89	116	12.7691
UUUCUGCGUGGUACUAAAACUGCCGAA	chr2:163217635-163217881(+)$1	246	132	159	8.7958
AAAAAGCUGAUCUAUGUGAUUAAAGGC	chr10:98745142-98745384(+)$1	242	59	86	11.3860
UGAUAUGAAAUUAUGUAAAUUUCAAAU	chr2:223806608-223806889(+)$1	281	201	228	13.9254
UUUAGUCCCUGUUUUACAGGGGUUAGA	chr20:32868126-32868368(-)$1	242	50	77	10.8866
AGGCCUGAAGGUGGUGAACCAGGCCUC	chr12:56295965-56296205(-)$1	240	157	184	11.5001
AGUUACUCAAUACCACUUAUUGAGUAC	chr6:90038860-90039106(-)$1	246	69	96	10.9282
GACUACGUGUUCGACUGGAACAUGCUC	chr17:80209170-80209464(-)$1	294	177	204	13.9888
UUAGAAUAGGAGAGAAAUCAUGAUUCU	chr5:31400751-31400991(-)$1	240	52	79	9.4285
CCCAUGGGGGCUAAUCCGGUCCCCUUG	chr19:45683229-45683509(+)$1	280	52	79	13.2344
GAGGCGAGGCUUUUCCGAGAUCGUCUC	chr6:160211491-160211731(+)$1	240	97	124	9.0936
UUUCAUUCUUCAAUUCAUGACGAGUGC	chr9:116170200-116170449(-)$1	249	216	243	10.4903
GUUUUAUUUUUUUUUCCUGAAAAAUAA	chr18:74681457-74681699(+)$1	242	111	138	10.2896
CUCUACAAAUAAAGUGUUUUAUUUACA	chr9:140509724-140510004(-)$1	280	191	218	9.2044
GGAUAAAGUAUACUGUAAUAAUUUAUC	chr5:99922047-99922288(+)$1	241	56	83	10.5832
ACUGUAAAUAUAGUUCUUGUAUUUGUA	chr1:10441339-10441585(+)$1	246	161	188	11.7317

#DB
.)))((((((((.....))).......	chr2:46810017-46810259(+)$1	1	178	205	10.7688
.(((...(((((.....)))))...))	chr14:97032505-97032751(+)$1	1	47	74	13.7732
(((...(((((......))))).))))	chr2:32249125-32249380(-)$1	1	177	204	10.1907
..((((((((((.....))))))))))	chr11:86520112-86520352(+)$1	1	136	163	12.5578
((((((((((((.....)))))))...	chr5:142657500-142657741(-)$1	1	169	196	11.4566
.(((((((..(((...))).)))))))	chr1:47843083-47843446(+)$1	1	141	168	9.8937
((((((((((((.....)))))...))	chr1:32640544-32640944(+)$1	1	14	41	11.9358
(((((..(((((.....)))))..)))	chr6:123047320-123047568(+)$1	1	62	89	13.0333
(((..(((((((....))))))).)))	chr14:78198786-78199026(-)$1	1	182	209	8.8304
.((((..(((((.....))))))))))	chr12:53873463-53873704(+)$1	1	207	234	11.5453
.(.((..(((((.....))))).)).)	chr10:104240296-104240536(-)$1	1	85	112	12.2658
(.((((..((((.....)))).)))).	chr12:53434439-53434722(+)$1	1	36	63	10.3905
(..(((((((((.....)))...))))	chr11:44266066-44266315(+)$1	1	9	36	12.7629
.(((.(((((((.....))))))).))	chr4:38700375-38700623(+)$1	1	90	117	13.4093
.((((((..(((.....)))..)))))	chr17:4172872-4173137(-)$1	1	234	261	11.6925
((((....((((.....))))....))	chr1:222905880-222906188(+)$1	1	260	287	12.0639
...((..(((((.....)))))..)).	chr19:13205560-13205807(+)$1	1	163	190	12.0929
...(((((((((.....)))))))))(	chr12:113596550-113596798(-)$1	1	56	83	10.6984
(.((((((((((.....))))))))))	chr4:39825884-39826124(-)$1	1	115	142	14.4027
(.(((.((((((.....))))).).))	chr18:32917284-32917532(-)$1	1	212	239	13.0322
((((((.(((((.....))))).))))	chr15:76191767-76192007(+)$1	1	205	232	13.7473
.(((((...(((.....)))...))))	chr3:139076364-139076606(-)$1	1	45	72	12.1701
.((((((.((((.....))).).))))	chr2:136482573-136482813(+)$1	1	35	62	12.7094
(..(((((((((...)))))))))...	chr5:134193099-134193339(+)$1	1	35	62	10.3478
((...(((((((.....)))))))...	chr7:96810552-96810792(+)$1	1	72	99	13.9899
)))))(((((((.....)))))))(((	chr20:25594869-25595109(-)$1	1	79	106	13.3161
((((((((((((......)))))))..	chr19:47567650-47567896(-)$1	1	69	96	10.2262
.(((((((..((.....)).)))))))	chr2:120934786-120935066(+)$1	1	171	198	11.8207
(...(..(((((.....)))))..)))	chr7:105182885-105183125(+)$1	1	182	209	13.0869
(((((....(((.....))).......	chr20:37581084-37581324(+)$1	1	122	149	11.3739
..((((((.(((.....))))))))).	chr12:22839788-22840108(+)$1	1	282	309	12.4672
(((((((.((((.....))))..))))	chr2:131906731-131906971(+)$1	1	141	168	12.3849
(((((..(((((...)))))..)))))	chr16:23584859-23585099(+)$1	1	22	49	9.3577
(..(((((((((.....))))))...)	chr19:52826162-52826402(+)$1	1	18	45	12.3326
((((((((((((.....)))))).)))	chr3:169812957-169813197(-)$1	1	24	51	11.6343
((((((((((.(.....).))))...)	chr17:8339142-8339382(+)$1	1	109	136	11.4262
((((.(((((((.....)))))))..)	chr10:124923999-124924239(+)$1	1	89	116	12.7691
((((.(.(((((......)))))))))	chr2:163217635-163217881(+)$1	1	132	159	8.7958
)))))).(((((.....)))))(((((	chr10:98745142-98745384(+)$1	1	59	86	11.3860
(....(((((((.....))))))))))	chr2:223806608-223806889(+)$1	1	201	228	13.9254
((((((((((((...))))))))))))	chr20:32868126-32868368(-)$1	1	50	77	10.8866
((((((...(((.....))))))))).	chr12:56295965-56296205(-)$1	1	157	184	11.5001
((((((((((((.....)))))))))(	chr6:90038860-90039106(-)$1	1	69	96	10.9282
((...(((((((.....))))))).))	chr17:80209170-80209464(-)$1	1	177	204	13.9888
(((((((..((......))...)))))	chr5:31400751-31400991(-)$1	1	52	79	9.4285
.(((.(((((((.....))))))).))	chr19:45683229-45683509(+)$1	1	52	79	13.2344
(((((((..(((....))).)))))))	chr6:160211491-160211731(+)$1	1	97	124	9.0936
....((((.(((.....))).))))))	chr9:116170200-116170449(-)$1	1	216	243	10.4903
((.(((((((((......)))))))))	chr18:74681457-74681699(+)$1	1	111	138	10.2896
((((..(((((((....)))))))...	chr9:140509724-140510004(-)$1	1	191	218	9.2044
(((((((.(((......))).))))))	chr5:99922047-99922288(+)$1	1	56	83	10.5832
(..(((((((((.....))))))..))	chr1:10441339-10441585(+)$1	1	161	188	11.7317

#PSSM
g : 0.17	f : 0.17	: : 0.09	d : 0.09	e : 0.07	" : 0.05	c : 0.05	[ : 0.05	b : 0.03	] : 0.01	! : 0.01	J : 0.01	a : 0.01	( : 0.01	# : 0.01	= : 0.01	E : 0.01	$ : 0.01	
f : 0.21	g : 0.19	c : 0.11	d : 0.07	! : 0.07	e : 0.07	[ : 0.05	: : 0.03	# : 0.03	" : 0.03	a : 0.01	= : 0.01	E : 0.01	$ : 0.01	
f : 0.23	g : 0.19	c : 0.11	! : 0.07	e : 0.07	= : 0.05	d : 0.05	" : 0.05	[ : 0.03	# : 0.03	: : 0.01	E : 0.01	$ : 0.01	
f : 0.24	g : 0.17	c : 0.13	" : 0.07	i : 0.07	e : 0.07	= : 0.05	d : 0.05	b : 0.03	! : 0.01	# : 0.01	$ : 0.01	
f : 0.23	g : 0.15	e : 0.07	" : 0.07	[ : 0.07	i : 0.07	= : 0.05	d : 0.05	c : 0.05	! : 0.03	b : 0.03	# : 0.03	a : 0.01	
g : 0.32	f : 0.17	! : 0.13	i : 0.07	= : 0.05	e : 0.03	" : 0.03	d : 0.03	# : 0.03	c : 0.03	[ : 0.01	a : 0.01	
g : 0.32	f : 0.15	! : 0.13	i : 0.07	" : 0.05	= : 0.05	e : 0.03	# : 0.03	[ : 0.03	d : 0.03	a : 0.01	: : 0.01	
e : 0.26	g : 0.24	f : 0.09	! : 0.07	i : 0.07	= : 0.05	[ : 0.05	# : 0.03	" : 0.03	d : 0.03	
e : 0.26	g : 0.21	! : 0.09	d : 0.07	f : 0.07	i : 0.07	= : 0.05	" : 0.03	[ : 0.03	a : 0.01	# : 0.01	c : 0.01	
e : 0.24	c : 0.21	g : 0.21	d : 0.07	i : 0.07	= : 0.05	f : 0.05	! : 0.03	b : 0.01	
e : 0.24	c : 0.23	g : 0.21	i : 0.07	= : 0.05	d : 0.05	f : 0.05	b : 0.03	[ : 0.01	
e : 0.23	c : 0.21	g : 0.21	i : 0.07	o : 0.05	= : 0.05	d : 0.05	f : 0.05	b : 0.01	a : 0.01	
n : 0.75	o : 0.11	l : 0.05	m : 0.03	c : 0.01	g : 0.01	
n : 0.75	o : 0.11	l : 0.07	m : 0.05	
n : 0.75	o : 0.11	l : 0.07	m : 0.05	
n : 0.75	o : 0.11	m : 0.05	l : 0.01	i : 0.01	e : 0.01	= : 0.01	
n : 0.75	o : 0.11	c : 0.03	g : 0.01	i : 0.01	e : 0.01	= : 0.01	m : 0.01	
c : 0.23	e : 0.23	g : 0.19	= : 0.05	d : 0.05	i : 0.05	o : 0.05	f : 0.05	b : 0.03	a : 0.01	
e : 0.24	c : 0.23	g : 0.21	i : 0.07	= : 0.05	d : 0.05	f : 0.05	b : 0.03	] : 0.01	
e : 0.24	g : 0.21	c : 0.19	d : 0.07	i : 0.07	= : 0.05	] : 0.05	f : 0.05	3 : 0.01	
g : 0.26	e : 0.23	f : 0.09	d : 0.07	i : 0.07	= : 0.05	3 : 0.05	] : 0.05	> : 0.03	2 : 0.03	
g : 0.28	e : 0.23	f : 0.09	i : 0.07	= : 0.05	3 : 0.05	2 : 0.05	> : 0.03	d : 0.03	] : 0.01	4 : 0.01	a : 0.01	
g : 0.32	f : 0.11	] : 0.09	3 : 0.07	2 : 0.07	d : 0.07	i : 0.07	= : 0.05	> : 0.03	4 : 0.01	e : 0.01	c : 0.01	
g : 0.36	f : 0.09	3 : 0.07	2 : 0.07	i : 0.07	= : 0.05	d : 0.05	> : 0.03	] : 0.03	a : 0.03	b : 0.01	4 : 0.01	e : 0.01	c : 0.01	
g : 0.23	3 : 0.13	f : 0.13	] : 0.07	= : 0.05	d : 0.05	i : 0.05	> : 0.03	c : 0.03	b : 0.03	e : 0.03	2 : 0.03	5 : 0.01	4 : 0.01	a : 0.01	
g : 0.23	f : 0.19	c : 0.15	3 : 0.11	= : 0.05	i : 0.05	> : 0.03	d : 0.03	e : 0.03	5 : 0.01	] : 0.01	b : 0.01	2 : 0.01	
g : 0.24	f : 0.19	c : 0.17	3 : 0.07	= : 0.05	> : 0.03	] : 0.03	d : 0.03	e : 0.03	5 : 0.01	a : 0.01	4 : 0.01	: : 0.01	i : 0.01	

#score	607.4263466610076
#seq	52
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_CDS_m3_run2.txt

#BEAR
ffwwwwwwwwwwwwwwfff	chr19:3976116-3976348(-)$1	232	115	134	20.1587
fffvvvvvvvvvvvvvfff	chr11:22257680-22257905(+)$1	225	84	103	21.1643
ddduuuuuuuuuuuudddd	chr13:108861547-108861780(-)$1	233	123	142	22.2881
davvvvvvvvvvvvva]dd	chr19:56953048-56953272(-)$1	224	129	148	21.6831
bbwwwwwwwwwwwwwwbb]	chr2:172821868-172822098(+)$1	230	14	33	19.9752
ccctttttttttttccc]a	chr2:204354380-204354606(-)$1	226	30	49	20.7796
dddvvvvvvvvvvvvvddd	chrM:9201-9430(+)$1	229	185	204	22.0849
ddduuuuuuuuuuuudddd	chr2:111395503-111395729(-)$1	226	137	156	22.2881
eeeettttttttttteeee	chr7:64864056-64864288(+)$1	232	75	94	20.8200
eewwwwwwwwwwwwwweee	chr16:24573240-24573466(+)$1	226	151	170	20.4507
ffyyyyyyyyyyyyyyyyf	chrM:8330-8586(+)$1	256	61	80	19.9335
hhbbtttttttttttbb]h	chr1:46532550-46532772(-)$1	222	96	115	20.1502
==yyyyyyyyyyyyyyyy=	chr21:37415924-37416163(-)$1	239	160	179	20.1969
ddddtttttttttttdddd	chr2:70676620-70676845(-)$1	225	27	46	21.5047
hhhhttttttttttthhhh	chr16:58581368-58581595(-)$1	227	81	100	19.4091
ggggtttttttttttgggg	chr6:44390311-44390542(+)$1	231	11	30	20.8404
ccwwwwwwwwwwwwwwccc	chr7:102952520-102952753(+)$1	233	133	152	20.9176
ccwwwwwwwwwwwwwwccc	chr14:103958226-103958468(+)$1	242	117	136	20.9176
eeeettttttttttteeee	chr9:125797133-125797365(+)$1	232	116	135	20.8200
ggguuuuuuuuuuuugggg	chr19:37382561-37382786(-)$1	225	5	24	21.7536
fffftttttttttttffff	chr1:241797965-241798198(-)$1	233	176	195	20.3701
cccvvvvvvvvvvvvvccc	chr2:183866834-183867073(-)$1	239	148	167	22.1421
dddvvvvvvvvvvvvvddd	chrM:10161-10421(+)$1	260	82	101	22.0849
ggguuuuuuuuuuuugggg	chr3:148788994-148789227(-)$1	233	130	149	21.7536
eeeettttttttttteeee	chr19:21719463-21719697(+)$1	234	160	179	20.8200
ccctttttttttttccccc	chr7:64292463-64292690(+)$1	227	160	179	21.0711
ddddtttttttttttdddd	chr11:130108359-130108591(-)$1	232	171	190	21.5047
ddddtttttttttttdddd	chrM:14063-14299(+)$1	236	14	33	21.5047
cccuuuuuuuuuuuuccc]	chrX:107976466-107976689(-)$1	223	68	87	22.4165
""bbtttttttttttbb33	chr2:20508141-20508367(-)$1	226	82	101	20.2466
fffvvvvvvvvvvvvvfff	chr5:140789513-140789745(+)$1	232	12	31	21.1643
ggguuuuuuuuuuuugggg	chr1:214791882-214792123(+)$1	241	210	229	21.7536
awwwwwwwwwwwwwwa]bb	chr7:64864317-64864557(+)$1	240	170	189	19.4692
fffuuuuuuuuuuuuffff	chr5:54591985-54592217(-)$1	232	194	213	21.2311
=bbvvvvvvvvvvvvvbb]	chrM:3571-3817(+)$1	246	97	116	21.3131
cccuuuuuuuuuuuuccc>	chr6:26031909-26032148(-)$1	239	192	211	22.0981
cccvvvvvvvvvvvvvccc	chrM:11753-12065(+)$1	312	45	64	22.1421
ddwwwwwwwwwwwwwwddd	chr13:99098260-99098492(+)$1	232	113	132	20.9428
ddduuuuuuuuuuuudddd	chr10:121341977-121342205(-)$1	228	163	182	22.2881
cyyyyyyyyyyyyyyyycc	chr1:38287784-38288041(-)$1	257	109	128	20.4438
ddduuuuuuuuuuuudddd	chr19:21476274-21476506(-)$1	232	97	116	22.2881
ffyyyyyyyyyyyyyyyyf	chrM:8288-8520(+)$1	232	103	122	19.9335
ccctttttttttttccc::	chr10:71977550-71977774(-)$1	224	97	116	19.1173
fffftttttttttttffff	chr4:104057269-104057501(-)$1	232	90	109	20.3701
ddddtttttttttttdddd	chr12:7044800-7045032(+)$1	232	7	26	21.5047
cccvvvvvvvvvvvvvccc	chr10:124746304-124746530(+)$1	226	48	67	22.1421
ddduuuuuuuuuuuudddd	chrM:14647-14894(+)$1	247	225	244	22.2881
eewwwwwwwwwwwwwweee	chr1:55349269-55349496(-)$1	227	129	148	20.4507
ddwwwwwwwwwwwwwwddd	chr16:24801218-24801443(+)$1	225	200	219	20.9428
dyyyyyyyyyyyyyyyydd	chr10:27422867-27423093(-)$1	226	57	76	20.5165
=bbvvvvvvvvvvvvvbb]	chrM:3637-3878(+)$1	241	31	50	21.3131
[bbvvvvvvvvvvvvvbb]	chr4:123813305-123813530(+)$1	225	145	164	21.2526
d[auuuuuuuuuuuuaddd	chr12:88560046-88560274(+)$1	228	112	131	22.6130
bbbvvvvvvvvvvvvvbb]	chr19:13035192-13035424(-)$1	232	111	130	21.0401
hhhuuuuuuuuuuuuhhhh	chr12:11174233-11174459(-)$1	226	58	77	20.5609
cccvvvvvvvvvvvvvccc	chr17:7416738-7416980(+)$1	242	194	213	22.1421
ddddtttttttttttdddd	chr3:23930590-23930820(+)$1	230	130	149	21.5047
eeeettttttttttteeee	chr6:56505096-56505323(-)$1	227	60	79	20.8200
ddddtttttttttttdddd	chr15:32928891-32929123(+)$1	232	60	79	21.5047
dyyyyyyyyyyyyyyyydd	chr17:29170922-29171151(+)$1	229	138	157	20.5165
eyyyyyyyyyyyyyyyyee	chr8:61136995-61137221(-)$1	226	78	97	20.2136
ddddtttttttttttdddd	chrM:13941-14177(+)$1	236	52	71	21.5047
=bbvvvvvvvvvvvvvbb]	chrM:3536-3769(+)$1	233	132	151	21.3131
cyyyyyyyyyyyyyyyycc	chr15:70350480-70350706(-)$1	226	108	127	20.4438
ddddtttttttttttdddd	chr1:29069376-29069598(+)$1	222	98	117	21.5047

#otherMatches

#Seq PSSM
UUAACAAACGCAUUAAGAG	chr19:3976116-3976348(-)$1	232	115	134	20.1587
UGGGAUUGAAAGACUGCUA	chr11:22257680-22257905(+)$1	225	84	103	21.1643
AAAAUUUCUAAUAUAUUUG	chr13:108861547-108861780(-)$1	233	123	142	22.2881
UCAUACAAAGAAAAAGAAA	chr19:56953048-56953272(-)$1	224	129	148	21.6831
AGACAAAUCAUUCCACCUG	chr2:172821868-172822098(+)$1	230	14	33	19.9752
GACGUCACUGCACAGUUAG	chr2:204354380-204354606(-)$1	226	30	49	20.7796
UGUAACACGAGAAAGCACA	chrM:9201-9430(+)$1	229	185	204	22.0849
ACGUAAUAGGCUAAUUGUA	chr2:111395503-111395729(-)$1	226	137	156	22.2881
UACAAAUGUGAUGAAUGUG	chr7:64864056-64864288(+)$1	232	75	94	20.8200
GAAAUCCGUCUUCUGCUCC	chr16:24573240-24573466(+)$1	226	151	170	20.4507
GGCCCACCAUAAUUACCCC	chrM:8330-8586(+)$1	256	61	80	19.9335
GGAGCUCAUUAACCACUAU	chr1:46532550-46532772(-)$1	222	96	115	20.1502
AAUAAAAAUAUCAAAACCU	chr21:37415924-37416163(-)$1	239	160	179	20.1969
UGCUAUUUAUUUUCGAGCA	chr2:70676620-70676845(-)$1	225	27	46	21.5047
CUAGGAAUGAUCACAUUAG	chr16:58581368-58581595(-)$1	227	81	100	19.4091
UUUGAAAGCACAAUCCAAA	chr6:44390311-44390542(+)$1	231	11	30	20.8404
GUCCCAUUAAGCAACUACC	chr7:102952520-102952753(+)$1	233	133	152	20.9176
GUAAAUUAACUUCAAAACU	chr14:103958226-103958468(+)$1	242	117	136	20.9176
AACCUAUAAUACUCUGGUU	chr9:125797133-125797365(+)$1	232	116	135	20.8200
CUUUACUCAACACUCAAGG	chr19:37382561-37382786(-)$1	225	5	24	21.7536
AUCUUGCACUACAAUAGAU	chr1:241797965-241798198(-)$1	233	176	195	20.3701
UCUCGAAUUGAAGAAAGGA	chr2:183866834-183867073(-)$1	239	148	167	22.1421
UCUUAUUAUUUGAUCUAGA	chrM:10161-10421(+)$1	260	82	101	22.0849
CUGAGAAGGACCGACCAGA	chr3:148788994-148789227(-)$1	233	130	149	21.7536
UACAAAUGUAAAGAAUGUG	chr19:21719463-21719697(+)$1	234	160	179	20.8200
ACAAAUGUGAAGAAUGUGG	chr7:64292463-64292690(+)$1	227	160	179	21.0711
GACAGACCUUUUCAGUGUC	chr11:130108359-130108591(-)$1	232	171	190	21.5047
AAAGGCAUAAUUAAACUUU	chrM:14063-14299(+)$1	236	14	33	21.5047
CCAACCCCUUAUCUCUGGA	chrX:107976466-107976689(-)$1	223	68	87	22.4165
UACUAAUCCCUCAGAAGGA	chr2:20508141-20508367(-)$1	226	82	101	20.2466
ACCUAGUGACUAAGGUGGU	chr5:140789513-140789745(+)$1	232	12	31	21.1643
UUCUGCAAAAUAAAUGAAU	chr1:214791882-214792123(+)$1	241	210	229	21.7536
CAAAGCCUUUAACCAGUCC	chr7:64864317-64864557(+)$1	240	170	189	19.4692
CAGUUUCUAAACCUUUUGA	chr5:54591985-54592217(-)$1	232	194	213	21.2311
GAGCAUCAAACUCAAACUA	chrM:3571-3817(+)$1	246	97	116	21.3131
CGCCAUCCAUGCUAAGCGA	chr6:26031909-26032148(-)$1	239	192	211	22.0981
GGACUUCAAACUCUACUCC	chrM:11753-12065(+)$1	312	45	64	22.1421
UGAGGAAAUUCAAAAACAG	chr13:99098260-99098492(+)$1	232	113	132	20.9428
GUGGAAUUUUAUGAACACA	chr10:121341977-121342205(-)$1	228	163	182	22.2881
UCCUAACUAAUAAUCCCAC	chr1:38287784-38288041(-)$1	257	109	128	20.4438
UGGCAAAACUUUUAACUAC	chr19:21476274-21476506(-)$1	232	97	116	22.2881
GGCCCACCAUAAUUACCCC	chrM:8288-8520(+)$1	232	103	122	19.9335
AGGACCCUUUAAACCCUAU	chr10:71977550-71977774(-)$1	224	97	116	19.1173
AGAGUUAAAGCAAACCUCU	chr4:104057269-104057501(-)$1	232	90	109	20.3701
GGACAACCGAAGCACGUCC	chr12:7044800-7045032(+)$1	232	7	26	21.5047
GACUUCUAAUAACAAUGUC	chr10:124746304-124746530(+)$1	226	48	67	22.1421
CCUCCAAAUCACCACAGGA	chrM:14647-14894(+)$1	247	225	244	22.2881
UCGGGAAGUACAAGAAGAC	chr1:55349269-55349496(-)$1	227	129	148	20.4507
AGCACAAUGAAUCAUCCUC	chr16:24801218-24801443(+)$1	225	200	219	20.9428
CCCGUCUGAUUCUCUUCGU	chr10:27422867-27423093(-)$1	226	57	76	20.5165
GAGCAUCAAACUCAAACUA	chrM:3637-3878(+)$1	241	31	50	21.3131
GGUAUGUGGCACUGAAACG	chr4:123813305-123813530(+)$1	225	145	164	21.2526
AACUACCUCCUUCCUGUGA	chr12:88560046-88560274(+)$1	228	112	131	22.6130
CCUACAACCCAUACACAGA	chr19:13035192-13035424(-)$1	232	111	130	21.0401
GCAAACUUGUACUCCUGCU	chr12:11174233-11174459(-)$1	226	58	77	20.5609
AGCCCAACCUCUCCAAGCU	chr17:7416738-7416980(+)$1	242	194	213	22.1421
UCUGCUCACUUCUUACAGA	chr3:23930590-23930820(+)$1	230	130	149	21.5047
AGACCUUACACCCUAGUCU	chr6:56505096-56505323(-)$1	227	60	79	20.8200
CACCACACUGGUAAAGGUG	chr15:32928891-32929123(+)$1	232	60	79	21.5047
AUCAGAGUUAAUAAUAUUU	chr17:29170922-29171151(+)$1	229	138	157	20.5165
GGAAGUCCAAAACAAUACC	chr8:61136995-61137221(-)$1	226	78	97	20.2136
CUAGACCUAACCUGACUAG	chrM:13941-14177(+)$1	236	52	71	21.5047
GAGCAUCAAACUCAAACUA	chrM:3536-3769(+)$1	233	132	151	21.3131
CAACACACCAACCCCAAGG	chr15:70350480-70350706(-)$1	226	108	127	20.4438
UGCUCCUCCAAAACCAGCA	chr1:29069376-29069598(+)$1	222	98	117	21.5047

#DB
((..............)))	chr19:3976116-3976348(-)$1	1	115	134	20.1587
(((.............)))	chr11:22257680-22257905(+)$1	1	84	103	21.1643
(((............))))	chr13:108861547-108861780(-)$1	1	123	142	22.2881
((.............).))	chr19:56953048-56953272(-)$1	1	129	148	21.6831
((..............)).	chr2:172821868-172822098(+)$1	1	14	33	19.9752
(((...........))).)	chr2:204354380-204354606(-)$1	1	30	49	20.7796
(((.............)))	chrM:9201-9430(+)$1	1	185	204	22.0849
(((............))))	chr2:111395503-111395729(-)$1	1	137	156	22.2881
((((...........))))	chr7:64864056-64864288(+)$1	1	75	94	20.8200
((..............)))	chr16:24573240-24573466(+)$1	1	151	170	20.4507
((................)	chrM:8330-8586(+)$1	1	61	80	19.9335
((((...........)).)	chr1:46532550-46532772(-)$1	1	96	115	20.1502
((................)	chr21:37415924-37416163(-)$1	1	160	179	20.1969
((((...........))))	chr2:70676620-70676845(-)$1	1	27	46	21.5047
((((...........))))	chr16:58581368-58581595(-)$1	1	81	100	19.4091
((((...........))))	chr6:44390311-44390542(+)$1	1	11	30	20.8404
((..............)))	chr7:102952520-102952753(+)$1	1	133	152	20.9176
((..............)))	chr14:103958226-103958468(+)$1	1	117	136	20.9176
((((...........))))	chr9:125797133-125797365(+)$1	1	116	135	20.8200
(((............))))	chr19:37382561-37382786(-)$1	1	5	24	21.7536
((((...........))))	chr1:241797965-241798198(-)$1	1	176	195	20.3701
(((.............)))	chr2:183866834-183867073(-)$1	1	148	167	22.1421
(((.............)))	chrM:10161-10421(+)$1	1	82	101	22.0849
(((............))))	chr3:148788994-148789227(-)$1	1	130	149	21.7536
((((...........))))	chr19:21719463-21719697(+)$1	1	160	179	20.8200
(((...........)))))	chr7:64292463-64292690(+)$1	1	160	179	21.0711
((((...........))))	chr11:130108359-130108591(-)$1	1	171	190	21.5047
((((...........))))	chrM:14063-14299(+)$1	1	14	33	21.5047
(((............))).	chrX:107976466-107976689(-)$1	1	68	87	22.4165
..((...........))..	chr2:20508141-20508367(-)$1	1	82	101	20.2466
(((.............)))	chr5:140789513-140789745(+)$1	1	12	31	21.1643
(((............))))	chr1:214791882-214792123(+)$1	1	210	229	21.7536
(..............).))	chr7:64864317-64864557(+)$1	1	170	189	19.4692
(((............))))	chr5:54591985-54592217(-)$1	1	194	213	21.2311
(((.............)).	chrM:3571-3817(+)$1	1	97	116	21.3131
(((............))).	chr6:26031909-26032148(-)$1	1	192	211	22.0981
(((.............)))	chrM:11753-12065(+)$1	1	45	64	22.1421
((..............)))	chr13:99098260-99098492(+)$1	1	113	132	20.9428
(((............))))	chr10:121341977-121342205(-)$1	1	163	182	22.2881
(................))	chr1:38287784-38288041(-)$1	1	109	128	20.4438
(((............))))	chr19:21476274-21476506(-)$1	1	97	116	22.2881
((................)	chrM:8288-8520(+)$1	1	103	122	19.9335
(((...........)))..	chr10:71977550-71977774(-)$1	1	97	116	19.1173
((((...........))))	chr4:104057269-104057501(-)$1	1	90	109	20.3701
((((...........))))	chr12:7044800-7045032(+)$1	1	7	26	21.5047
(((.............)))	chr10:124746304-124746530(+)$1	1	48	67	22.1421
(((............))))	chrM:14647-14894(+)$1	1	225	244	22.2881
((..............)))	chr1:55349269-55349496(-)$1	1	129	148	20.4507
((..............)))	chr16:24801218-24801443(+)$1	1	200	219	20.9428
(................))	chr10:27422867-27423093(-)$1	1	57	76	20.5165
(((.............)).	chrM:3637-3878(+)$1	1	31	50	21.3131
.((.............)).	chr4:123813305-123813530(+)$1	1	145	164	21.2526
(.(............))))	chr12:88560046-88560274(+)$1	1	112	131	22.6130
(((.............)).	chr19:13035192-13035424(-)$1	1	111	130	21.0401
(((............))))	chr12:11174233-11174459(-)$1	1	58	77	20.5609
(((.............)))	chr17:7416738-7416980(+)$1	1	194	213	22.1421
((((...........))))	chr3:23930590-23930820(+)$1	1	130	149	21.5047
((((...........))))	chr6:56505096-56505323(-)$1	1	60	79	20.8200
((((...........))))	chr15:32928891-32929123(+)$1	1	60	79	21.5047
(................))	chr17:29170922-29171151(+)$1	1	138	157	20.5165
(................))	chr8:61136995-61137221(-)$1	1	78	97	20.2136
((((...........))))	chrM:13941-14177(+)$1	1	52	71	21.5047
(((.............)).	chrM:3536-3769(+)$1	1	132	151	21.3131
(................))	chr15:70350480-70350706(-)$1	1	108	127	20.4438
((((...........))))	chr1:29069376-29069598(+)$1	1	98	117	21.5047

#PSSM
d : 0.32	c : 0.20	f : 0.12	e : 0.10	= : 0.06	g : 0.06	h : 0.04	b : 0.03	" : 0.01	a : 0.01	[ : 0.01	
d : 0.26	c : 0.16	f : 0.12	b : 0.09	e : 0.09	y : 0.07	g : 0.06	h : 0.04	a : 0.01	= : 0.01	" : 0.01	w : 0.01	[ : 0.01	
d : 0.23	w : 0.13	c : 0.13	y : 0.12	b : 0.10	f : 0.07	e : 0.06	g : 0.06	h : 0.03	v : 0.01	a : 0.01	
v : 0.21	u : 0.20	w : 0.13	y : 0.12	d : 0.12	e : 0.06	t : 0.04	b : 0.03	f : 0.03	h : 0.01	g : 0.01	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.32	v : 0.21	u : 0.20	w : 0.13	y : 0.12	
t : 0.27	v : 0.21	u : 0.20	w : 0.13	y : 0.12	c : 0.04	
v : 0.20	d : 0.20	w : 0.12	y : 0.12	c : 0.07	e : 0.06	g : 0.06	a : 0.04	f : 0.04	b : 0.03	h : 0.03	
d : 0.27	c : 0.16	b : 0.12	y : 0.12	f : 0.09	e : 0.09	g : 0.06	] : 0.03	h : 0.03	
d : 0.32	c : 0.16	b : 0.10	e : 0.10	f : 0.09	g : 0.06	y : 0.04	] : 0.03	h : 0.03	3 : 0.01	: : 0.01	
d : 0.32	c : 0.13	f : 0.12	] : 0.10	e : 0.10	g : 0.06	h : 0.04	a : 0.01	= : 0.01	3 : 0.01	b : 0.01	> : 0.01	: : 0.01	

#score	1372.7009349382852
#seq	65
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_CDS_m3_run2.txt

#BEAR
eeeeennnnneeee	chr1:26878065-26878283(+)$1	218	192	206	10.9796
gggggnnnnngggg	chr4:57190309-57190528(+)$1	219	129	143	9.3570
fffffnnnnnffff	chr19:34935880-34936103(+)$1	223	133	147	9.2803
eeeeeooooooeee	chr3:49049157-49049403(+)$1	246	124	138	7.1166
eeeeennnnneeee	chr2:61715710-61715940(-)$1	230	159	173	10.9796
eeeeeooooooeee	chr7:92131213-92131429(-)$1	216	194	208	7.1166
fffffnnnnnffff	chr17:78319761-78319983(+)$1	222	177	191	9.2803
cccccnnnnnccc]	chr5:141359628-141359839(+)$1	211	114	128	9.3304
eeeeennnnneeee	chr1:115273115-115273325(-)$1	210	68	82	10.9796
eeeeennnnneeee	chr6:1390504-1390726(+)$1	222	177	191	10.9796
eeeeennnnneeee	chr22:46929502-46929726(-)$1	224	31	45	10.9796
eeeeennnnneeee	chr3:47918871-47919091(-)$1	220	37	51	10.9796
eeeeeooooooeee	chr3:53260745-53260985(-)$1	240	184	198	7.1166
eeeeennnnneeee	chr11:10820674-10820920(-)$1	246	197	211	10.9796
gggggnnnnngggg	chr13:23909182-23909446(-)$1	264	70	84	9.3570
!!cccnnnnnccc]	chr3:160248569-160248786(-)$1	217	120	134	9.5545
[ddddnnnnndddd	chr2:203420234-203420457(+)$1	223	15	29	9.1405
fffffnnnnnffff	chr19:37854515-37854731(+)$1	216	89	103	9.2803
eeeeennnnneeee	chr9:138713655-138713870(-)$1	215	32	46	10.9796
fffffnnnnnffff	chr11:607209-607431(+)$1	222	191	205	9.2803
eee[annnnna]ee	chr17:8381573-8381790(-)$1	217	95	109	10.1670
fffffnnnnnffff	chr2:231947517-231947751(+)$1	234	27	41	9.2803
fffffnnnnnffff	chr22:41573352-41573571(+)$1	219	44	58	9.2803
eeeeeooooooeee	chr19:3977995-3978240(-)$1	245	168	182	7.1166
dddddnnnnndddd	chr15:41999924-42000141(+)$1	217	90	104	8.9452
[ddddnnnnndddd	chr17:29509447-29509664(+)$1	217	72	86	9.1405
eeeeennnnneeee	chr1:46744565-46744788(-)$1	223	3	17	10.9796
fffffnnnnnffff	chr16:30748837-30749083(+)$1	246	203	217	9.2803
$ddddnnnnndddd	chr22:28394694-28394928(-)$1	234	209	223	8.7572
eeeeennnnneeee	chr3:185766405-185766628(-)$1	223	9	23	10.9796
eecccnnnnnccc]	chr9:139368571-139368817(-)$1	246	9	23	9.9046
"ddddnnnnndddd	chr16:72992053-72992277(-)$1	224	186	200	8.9884
cccccnnnnnccc]	chr19:10252634-10252847(-)$1	213	151	165	9.3304
eeeeennnnneeee	chr16:28109855-28110079(-)$1	224	129	143	10.9796
eeeeeooooooeee	chr6:79726231-79726450(-)$1	219	146	160	7.1166
e[cccnnnnnccc]	chr19:50882214-50882433(+)$1	219	13	27	9.7322
!ddddnnnnndddd	chr11:62287347-62287572(-)$1	225	90	104	9.1185
eeeeennnnneeee	chr18:19752041-19752260(+)$1	219	138	152	10.9796
eeeeennnnneeee	chr12:21624356-21624575(-)$1	219	29	43	10.9796
d[a[annnnna]a]	chr15:22955150-22955374(+)$1	224	8	22	8.9842
a[cccnnnnnccc]	chr10:30316330-30316552(-)$1	222	202	216	9.4361
!!cccnnnnnccc2	chr5:74018145-74018365(-)$1	220	133	147	9.2029
fffffnnnnnffff	chr6:56350108-56350329(-)$1	221	14	28	9.2803
eeeeeooooooeee	chr12:6976703-6976921(+)$1	218	147	161	7.1166
[cccannnnna]cc	chr2:160035447-160035663(+)$1	216	22	36	9.1246
b[cccnnnnnccc]	chr5:77458553-77458776(-)$1	223	93	107	9.1657
eeeeennnnneeee	chr8:71069335-71069556(-)$1	221	196	210	10.9796
eeeeennnnneeee	chr17:62290043-62290290(-)$1	247	188	202	10.9796
eeeeennnnneeee	chr5:78532780-78532995(+)$1	215	145	159	10.9796
gggggnnnnngggg	chr1:214819950-214820170(+)$1	220	18	32	9.3570
[acccnnnnnccc]	chr13:114294379-114294619(+)$1	240	174	188	9.4560

#otherMatches

#Seq PSSM
GGGACGACAAGUCC	chr1:26878065-26878283(+)$1	218	192	206	10.9796
AGCAGGUCCAUUGC	chr4:57190309-57190528(+)$1	219	129	143	9.3570
ACUUUUUACCAAGG	chr19:34935880-34936103(+)$1	223	133	147	9.2803
GGAGCUUUGGCGCU	chr3:49049157-49049403(+)$1	246	124	138	7.1166
UAUGCUUAAUGUAU	chr2:61715710-61715940(-)$1	230	159	173	10.9796
ACUCUCUCGUCAGA	chr7:92131213-92131429(-)$1	216	194	208	7.1166
GUUGAGUCCAUCAG	chr17:78319761-78319983(+)$1	222	177	191	9.2803
AGUCCUCCUUGGAC	chr5:141359628-141359839(+)$1	211	114	128	9.3304
GCCAUGAGAGAUGG	chr1:115273115-115273325(-)$1	210	68	82	10.9796
GGCCCGGCAAGGGC	chr6:1390504-1390726(+)$1	222	177	191	10.9796
GGCUGCAUCCCGGC	chr22:46929502-46929726(-)$1	224	31	45	10.9796
AUGUUUGCUUAGCA	chr3:47918871-47919091(-)$1	220	37	51	10.9796
UCCUCACCGUGGAG	chr3:53260745-53260985(-)$1	240	184	198	7.1166
GUUCUUAAACAGAA	chr11:10820674-10820920(-)$1	246	197	211	10.9796
CAUUUCAUGUGAAU	chr13:23909182-23909446(-)$1	264	70	84	9.3570
AAACUCAAGCAGUA	chr3:160248569-160248786(-)$1	217	120	134	9.5545
CGCCAAGUACUGGC	chr2:203420234-203420457(+)$1	223	15	29	9.1405
UUGCAGAAAGUGUG	chr19:37854515-37854731(+)$1	216	89	103	9.2803
GGGCCAUCGAGGCC	chr9:138713655-138713870(-)$1	215	32	46	10.9796
AUCUCAAGCAGAGA	chr11:607209-607431(+)$1	222	191	205	9.2803
UGAGGAUGAGCGUC	chr17:8381573-8381790(-)$1	217	95	109	10.1670
UGUAUGUUAAGUAC	chr2:231947517-231947751(+)$1	234	27	41	9.2803
CCCUGUGUCCCAGG	chr22:41573352-41573571(+)$1	219	44	58	9.2803
GAAGGCGCGGCCCU	chr19:3977995-3978240(-)$1	245	168	182	7.1166
UUUCCUUUUUGGAA	chr15:41999924-42000141(+)$1	217	90	104	8.9452
AUGCAGAAUGUGCA	chr17:29509447-29509664(+)$1	217	72	86	9.1405
UGGAUAUCUAAUCC	chr1:46744565-46744788(-)$1	223	3	17	10.9796
UCCAGAGUCCCUGG	chr16:30748837-30749083(+)$1	246	203	217	9.2803
GGGCCUUCCUGGCU	chr22:28394694-28394928(-)$1	234	209	223	8.7572
GUCUGUGACCCAGA	chr3:185766405-185766628(-)$1	223	9	23	10.9796
UGCCCGCACAGGGA	chr9:139368571-139368817(-)$1	246	9	23	9.9046
UCCCGCUCGCUGGG	chr16:72992053-72992277(-)$1	224	186	200	8.9884
CCCUGCUUGCUAGA	chr19:10252634-10252847(-)$1	213	151	165	9.3304
CAUUCACCCAGAAU	chr16:28109855-28110079(-)$1	224	129	143	10.9796
GAGUGGAAGAGCAU	chr6:79726231-79726450(-)$1	219	146	160	7.1166
CUGGGAGUGACCCU	chr19:50882214-50882433(+)$1	219	13	27	9.7322
AGCCUGCCCAAGGC	chr11:62287347-62287572(-)$1	225	90	104	9.1185
CUGCACAGCCUGCA	chr18:19752041-19752260(+)$1	219	138	152	10.9796
GAUCUAAUCAAGAU	chr12:21624356-21624575(-)$1	219	29	43	10.9796
UGUGUGACUGGGAG	chr15:22955150-22955374(+)$1	224	8	22	8.9842
UGAGAGUAAGUCUG	chr10:30316330-30316552(-)$1	222	202	216	9.4361
UUGGAUUUGUUCCC	chr5:74018145-74018365(-)$1	220	133	147	9.2029
UGACGUUUUUUGUU	chr6:56350108-56350329(-)$1	221	14	28	9.2803
CCCUCGCCGAGGAG	chr12:6976703-6976921(+)$1	218	147	161	7.1166
CAGACGAGCAGAUC	chr2:160035447-160035663(+)$1	216	22	36	9.1246
GUGCCUCAAUGGCU	chr5:77458553-77458776(-)$1	223	93	107	9.1657
GGUCAGGACAUGAC	chr8:71069335-71069556(-)$1	221	196	210	10.9796
CCACUAUGUGAGUG	chr17:62290043-62290290(-)$1	247	188	202	10.9796
UCAGAAAACAUCUG	chr5:78532780-78532995(+)$1	215	145	159	10.9796
AGAGCAUGCAGCUC	chr1:214819950-214820170(+)$1	220	18	32	9.3570
acuucaacgagaau	chr13:114294379-114294619(+)$1	240	174	188	9.4560

#DB
(((((.....))))	chr1:26878065-26878283(+)$1	1	192	206	10.9796
(((((.....))))	chr4:57190309-57190528(+)$1	1	129	143	9.3570
(((((.....))))	chr19:34935880-34936103(+)$1	1	133	147	9.2803
(((((......)))	chr3:49049157-49049403(+)$1	1	124	138	7.1166
(((((.....))))	chr2:61715710-61715940(-)$1	1	159	173	10.9796
(((((......)))	chr7:92131213-92131429(-)$1	1	194	208	7.1166
(((((.....))))	chr17:78319761-78319983(+)$1	1	177	191	9.2803
(((((.....))).	chr5:141359628-141359839(+)$1	1	114	128	9.3304
(((((.....))))	chr1:115273115-115273325(-)$1	1	68	82	10.9796
(((((.....))))	chr6:1390504-1390726(+)$1	1	177	191	10.9796
(((((.....))))	chr22:46929502-46929726(-)$1	1	31	45	10.9796
(((((.....))))	chr3:47918871-47919091(-)$1	1	37	51	10.9796
(((((......)))	chr3:53260745-53260985(-)$1	1	184	198	7.1166
(((((.....))))	chr11:10820674-10820920(-)$1	1	197	211	10.9796
(((((.....))))	chr13:23909182-23909446(-)$1	1	70	84	9.3570
..(((.....))).	chr3:160248569-160248786(-)$1	1	120	134	9.5545
.((((.....))))	chr2:203420234-203420457(+)$1	1	15	29	9.1405
(((((.....))))	chr19:37854515-37854731(+)$1	1	89	103	9.2803
(((((.....))))	chr9:138713655-138713870(-)$1	1	32	46	10.9796
(((((.....))))	chr11:607209-607431(+)$1	1	191	205	9.2803
(((.(.....).))	chr17:8381573-8381790(-)$1	1	95	109	10.1670
(((((.....))))	chr2:231947517-231947751(+)$1	1	27	41	9.2803
(((((.....))))	chr22:41573352-41573571(+)$1	1	44	58	9.2803
(((((......)))	chr19:3977995-3978240(-)$1	1	168	182	7.1166
)((((.....))))	chr15:41999924-42000141(+)$1	1	90	104	8.9452
.((((.....))))	chr17:29509447-29509664(+)$1	1	72	86	9.1405
(((((.....))))	chr1:46744565-46744788(-)$1	1	3	17	10.9796
(((((.....))))	chr16:30748837-30749083(+)$1	1	203	217	9.2803
.((((.....))))	chr22:28394694-28394928(-)$1	1	209	223	8.7572
(((((.....))))	chr3:185766405-185766628(-)$1	1	9	23	10.9796
(((((.....))).	chr9:139368571-139368817(-)$1	1	9	23	9.9046
.((((.....))))	chr16:72992053-72992277(-)$1	1	186	200	8.9884
(((((.....))).	chr19:10252634-10252847(-)$1	1	151	165	9.3304
(((((.....))))	chr16:28109855-28110079(-)$1	1	129	143	10.9796
(((((......)))	chr6:79726231-79726450(-)$1	1	146	160	7.1166
(.(((.....))).	chr19:50882214-50882433(+)$1	1	13	27	9.7322
.((((.....))))	chr11:62287347-62287572(-)$1	1	90	104	9.1185
(((((.....))))	chr18:19752041-19752260(+)$1	1	138	152	10.9796
(((((.....))))	chr12:21624356-21624575(-)$1	1	29	43	10.9796
(.(.(.....).).	chr15:22955150-22955374(+)$1	1	8	22	8.9842
(.(((.....))).	chr10:30316330-30316552(-)$1	1	202	216	9.4361
..(((.....))).	chr5:74018145-74018365(-)$1	1	133	147	9.2029
(((((.....))))	chr6:56350108-56350329(-)$1	1	14	28	9.2803
(((((......)))	chr12:6976703-6976921(+)$1	1	147	161	7.1166
.((((.....).))	chr2:160035447-160035663(+)$1	1	22	36	9.1246
(.(((.....))).	chr5:77458553-77458776(-)$1	1	93	107	9.1657
(((((.....))))	chr8:71069335-71069556(-)$1	1	196	210	10.9796
(((((.....))))	chr17:62290043-62290290(-)$1	1	188	202	10.9796
(((((.....))))	chr5:78532780-78532995(+)$1	1	145	159	10.9796
(((((.....))))	chr1:214819950-214820170(+)$1	1	18	32	9.3570
.((((.....))).	chr13:114294379-114294619(+)$1	1	174	188	9.4560

#PSSM
e : 0.49	f : 0.15	[ : 0.07	g : 0.05	! : 0.05	c : 0.03	d : 0.03	$ : 0.01	" : 0.01	a : 0.01	b : 0.01	
e : 0.47	f : 0.15	d : 0.11	[ : 0.07	g : 0.05	c : 0.05	! : 0.03	a : 0.01	
e : 0.45	c : 0.19	f : 0.15	d : 0.11	g : 0.05	a : 0.01	
e : 0.43	c : 0.19	f : 0.15	d : 0.11	g : 0.05	[ : 0.03	
e : 0.43	c : 0.17	f : 0.15	d : 0.11	g : 0.05	a : 0.05	
n : 0.88	o : 0.11	
n : 0.88	o : 0.11	
n : 0.88	o : 0.11	
n : 0.88	o : 0.11	
n : 0.88	o : 0.11	
e : 0.31	c : 0.17	f : 0.15	o : 0.11	d : 0.11	g : 0.05	a : 0.05	
e : 0.43	c : 0.17	f : 0.15	d : 0.11	g : 0.05	] : 0.05	
e : 0.45	c : 0.19	f : 0.15	d : 0.11	g : 0.05	a : 0.01	
e : 0.45	] : 0.17	f : 0.15	d : 0.11	g : 0.05	2 : 0.01	c : 0.01	

#score	488.1667131271415
#seq	51
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_UTR_m1_run1.txt

#BEAR
:ddddvvvvvvvvvvvvvddddg	chr7:135359121-135359344(+)$1	223	1	24	21.8003
[ddddvvvvvvvvvvvvvddddi	chr10:5805411-5805640(+)$1	229	79	102	22.7840
Jeeeeeuuuuuuuuuuuueeeee	chr7:158424076-158424300(-)$1	224	95	118	21.4987
hhhhhhvvvvvvvvvvvvvhhhh	chr20:61509139-61509367(-)$1	228	136	159	21.6648
"bbccctttttttttttccc]bb	chr10:75882139-75882374(-)$1	235	80	103	21.2826
======vvvvvvvvvvvvv====	chr11:89935251-89935475(-)$1	224	191	214	23.5675
:fffffftttttttttttfffff	chr11:116618806-116619030(-)$1	224	177	200	21.3897
bb[ddddtttttttttttdddd]	chr7:115897780-115898015(+)$1	235	18	41	21.3746
++dddduuuuuuuuuuuudddd2	chr10:17757160-17757382(+)$1	222	93	116	21.4182
gggggguuuuuuuuuuuuggggg	chr13:25906000-25906223(+)$1	223	44	67	23.6681
ff[ddddtttttttttttddddf	chr6:18225189-18225415(-)$1	226	71	94	21.8486
hhhccctttttttttttccc22h	chr12:120899095-120899324(+)$1	229	147	170	21.2132
ggggggvvvvvvvvvvvvvgggg	chr7:135612240-135612460(-)$1	220	138	161	23.7541
e!!ccctttttttttttccc22e	chr21:15745505-15745734(-)$1	229	54	77	21.8607
ffffffuuuuuuuuuuuufffff	chr1:234741411-234741644(-)$1	233	2	25	23.3808
hhhhhwwwwwwwwwwwwwwhhhh	chr3:52741847-52742069(+)$1	222	49	72	20.6968
!!dddduuuuuuuuuuuuddddc	chr13:47351405-47351627(-)$1	222	145	168	23.1535
eeeeyyyyyyyyyyyyyyyyeee	chr1:1717904-1718127(-)$1	223	100	123	20.0898
ffffffvvvvvvvvvvvvvffff	chr5:135516775-135517010(+)$1	235	144	167	23.4561
c!!cccwwwwwwwwwwwwwwccc	chr2:8823741-8823967(+)$1	226	93	116	22.1563
dd[ccctttttttttttccc]dd	chr15:49032621-49032849(-)$1	228	178	201	21.9236
:ddddvvvvvvvvvvvvvdddd:	chr1:70717130-70717356(+)$1	226	167	190	20.6796
ceeeeevvvvvvvvvvvvveeee	chr1:241794094-241794318(-)$1	224	132	155	23.0230
!!cccvvvvvvvvvvvvvccc]e	chr14:45394978-45395205(-)$1	227	196	219	23.5703
[fffffftttttttttttfffff	chr2:225338780-225339004(-)$1	224	102	125	22.4143
ddddyyyyyyyyyyyyyyyyddd	chr13:111372454-111372686(+)$1	232	33	56	19.6676
gggggguuuuuuuuuuuuggggg	chrX:102005667-102005890(+)$1	223	36	59	23.6681
ggggggvvvvvvvvvvvvvgggg	chr7:124555566-124555796(-)$1	230	9	32	23.7541
!!ddddvvvvvvvvvvvvvdddd	chr7:44920537-44920759(-)$1	222	139	162	23.0884
ggggggvvvvvvvvvvvvvgggg	chr2:85548370-85548593(-)$1	223	13	36	23.7541
g"""ccctttttttttttccc44	chr1:229458901-229459122(-)$1	221	48	71	22.0880
ggggyyyyyyyyyyyyyyyyggg	chr1:29474221-29474444(-)$1	223	13	36	20.7248
:eeeeeuuuuuuuuuuuueeeee	chr6:43474157-43474389(+)$1	232	92	115	22.0347
b!!cccvvvvvvvvvvvvvccc2	chrX:70794482-70794703(+)$1	221	85	108	23.2804
ffffyyyyyyyyyyyyyyyyfff	chr17:30703041-30703262(+)$1	221	98	121	20.4816
ffffffvvvvvvvvvvvvvffff	chr6:91224892-91225117(-)$1	225	42	65	23.4561
e[cccvvvvvvvvvvvvvccc]e	chr19:44662911-44663132(+)$1	221	149	172	23.3464
!!dddduuuuuuuuuuuudddde	chr1:42643988-42644217(-)$1	229	111	134	23.1874
ccc[bbuuuuuuuuuuuubb]cc	chr1:113213668-113213900(+)$1	232	159	182	22.5700
##dddduuuuuuuuuuuudddd5	chr19:13063845-13064066(-)$1	221	126	149	22.0261
eeeeeeettttttttttteeeee	chr6:111216663-111216882(+)$1	219	162	185	21.6097
ffffffuuuuuuuuuuuufffff	chr20:57253215-57253448(+)$1	233	138	161	23.3808
ffffffvvvvvvvvvvvvvffff	chr12:53873127-53873358(+)$1	231	28	51	23.4561
#eeeeettttttttttteeeeee	chr15:64364690-64364913(-)$1	223	119	142	21.4965
hhhhhhuuuuuuuuuuuuhhhhh	chr20:44039117-44039343(+)$1	226	158	181	21.3455
!eeeeevvvvvvvvvvvvveeee	chr17:60021964-60022182(-)$1	218	10	33	23.1628
==bbwwwwwwwwwwwwwwbb]==	chrX:73809185-73809409(-)$1	224	85	108	20.8158
e[cccvvvvvvvvvvvvvccc]e	chr12:49521485-49521715(-)$1	230	26	49	23.3464
[ddddvvvvvvvvvvvvvdddde	chr13:41702586-41702807(-)$1	221	158	181	22.7728
ffffffwwwwwwwwwwwwwwfff	chr8:90938365-90938594(+)$1	229	152	175	22.0466
ffffffuuuuuuuuuuuufffff	chr1:234741747-234741966(-)$1	219	190	213	23.3808
:fffffftttttttttttfffff	chr7:135614305-135614544(-)$1	239	20	43	21.3897
ccccccvvvvvvvvvvvvvccc5	chr5:132440540-132440770(+)$1	230	155	178	22.6991
ccc[bbuuuuuuuuuuuubb]cc	chr17:17158135-17158359(-)$1	224	116	139	22.5700
iiiiiiuuuuuuuuuuuuiiiii	chr6:139364121-139364350(+)$1	229	183	206	23.4497
:fffffftttttttttttfffff	chr1:22054772-22054993(-)$1	221	175	198	21.3897
ffffffwwwwwwwwwwwwwwfff	chr7:112130964-112131187(+)$1	223	34	57	22.0466
ffffffuuuuuuuuuuuufffff	chr8:130853715-130853935(-)$1	220	182	205	23.3808
[fffffftttttttttttfffff	chr2:176794165-176794385(-)$1	220	30	53	22.4143
[bb[ccctttttttttttccc22	chr22:38880894-38881123(-)$1	229	159	182	21.7495
ddd[bbuuuuuuuuuuuubb]dd	chr20:42090902-42091122(+)$1	220	94	117	22.0284
ffffyyyyyyyyyyyyyyyyfff	chr4:113198194-113198418(-)$1	224	165	188	20.4816
g[dddduuuuuuuuuuuudddd6	chr15:83686244-83686474(-)$1	230	125	148	22.6290
gggggguuuuuuuuuuuuggggg	chr10:60155284-60155508(+)$1	224	96	119	23.6681
ffffffuuuuuuuuuuuufffff	chr12:79982765-79982987(-)$1	222	76	99	23.3808
gggggwwwwwwwwwwwwwwgggg	chrX:150574435-150574657(+)$1	222	107	130	22.5470
!!dddduuuuuuuuuuuudddd2	chr19:10243994-10244219(-)$1	225	73	96	22.9837
gggggguuuuuuuuuuuuggggg	chr19:37002973-37003201(-)$1	228	45	68	23.6681

#otherMatches

#Seq PSSM
AUCCCUUUCCAACUGCAUGGGAG	chr7:135359121-135359344(+)$1	223	1	24	21.8003
CUAUCAUUUUUCACUUACGGUAU	chr10:5805411-5805640(+)$1	229	79	102	22.7840
AGGAGAUAACUCAAAACUUCUUC	chr7:158424076-158424300(-)$1	224	95	118	21.4987
CAAGUGUGUUUCUUUAGUUUACU	chr20:61509139-61509367(-)$1	228	136	159	21.6648
UUGCACUCAAUUUCAUUGUGACA	chr10:75882139-75882374(-)$1	235	80	103	21.2826
CUUUGUAUUUCUCUGUUAAGCAA	chr11:89935251-89935475(-)$1	224	191	214	23.5675
AUACAGGCUAAUAUUGAACCUGU	chr11:116618806-116619030(-)$1	224	177	200	21.3897
GCUUGGAUCUCAUUAAACUUCAU	chr7:115897780-115898015(+)$1	235	18	41	21.3746
UUAAGGUAAUUAUACUAUCCUUU	chr10:17757160-17757382(+)$1	222	93	116	21.4182
CAGAGAUCAUCCAUCCAUUCUUU	chr13:25906000-25906223(+)$1	223	44	67	23.6681
UAUAAAGUUUUUUUAUUUCUUUU	chr6:18225189-18225415(-)$1	226	71	94	21.8486
GGCAGCCUAAUUUACAAGCUUGG	chr12:120899095-120899324(+)$1	229	147	170	21.2132
GGAAGCUAAAACCAUGUUUGCUU	chr7:135612240-135612460(-)$1	220	138	161	23.7541
UAUGGAUAACUAUAUUUUCUGGA	chr21:15745505-15745734(-)$1	229	54	77	21.8607
GGGUUUUAUAUAAUAGACAGGCC	chr1:234741411-234741644(-)$1	233	2	25	23.3808
AGAGCUAAAACCACCUAAUGCUC	chr3:52741847-52742069(+)$1	222	49	72	20.6968
AAGUUUUUAAUUAUAUUCAGACA	chr13:47351405-47351627(-)$1	222	145	168	23.1535
CAUUCAUAUUUCCUUUUUAAAAU	chr1:1717904-1718127(-)$1	223	100	123	20.0898
GAAUUUUUUGAUAAUUACUGAGU	chr5:135516775-135517010(+)$1	235	144	167	23.4561
UCUUUGCACAACAACAACAACAA	chr2:8823741-8823967(+)$1	226	93	116	22.1563
GUUUGAAacaucaacaaucacac	chr15:49032621-49032849(-)$1	228	178	201	21.9236
AAAGAAAAAAACCUUAUCUCUUG	chr1:70717130-70717356(+)$1	226	167	190	20.6796
AGGCUGGUGUUAAGCAGAACAGC	chr1:241794094-241794318(-)$1	224	132	155	23.0230
UCCAAGGAUAUUUAUAAAUUGUG	chr14:45394978-45395205(-)$1	227	196	219	23.5703
CUUUUAAAUCAUUAAAUAUUAAG	chr2:225338780-225339004(-)$1	224	102	125	22.4143
AUUUUAGAAACUACAAAUAUAGG	chr13:111372454-111372686(+)$1	232	33	56	19.6676
GGGUAUCAAAUGAAUAUUAUACC	chrX:102005667-102005890(+)$1	223	36	59	23.6681
UAGAAAAUUCUAAUUUUUAUUUC	chr7:124555566-124555796(-)$1	230	9	32	23.7541
UAUUGUCCCUAUCAUUUCAGCAA	chr7:44920537-44920759(-)$1	222	139	162	23.0884
CUCAGGGAAAUACAAAUAACUUG	chr2:85548370-85548593(-)$1	223	13	36	23.7541
CUUUGAACCGCCAGACUUUUCUC	chr1:229458901-229459122(-)$1	221	48	71	22.0880
CAGUAACCCAUAGGAAAUAAACU	chr1:29474221-29474444(-)$1	223	13	36	20.7248
AUUGAUGACUAUUUUAAAAUCAA	chr6:43474157-43474389(+)$1	232	92	115	22.0347
AUAGUGUGUGUAAGAUUUUUACC	chrX:70794482-70794703(+)$1	221	85	108	23.2804
GUUUUCUAAACUACUAUCUUAAG	chr17:30703041-30703262(+)$1	221	98	121	20.4816
AUUUUGCUACCAAAACCUUCAGA	chr6:91224892-91225117(-)$1	225	42	65	23.4561
uguuuguuaacugaaucaaAAGG	chr19:44662911-44663132(+)$1	221	149	172	23.3464
CAUCACUCCUUUUACCAUGUGAA	chr1:42643988-42644217(-)$1	229	111	134	23.1874
CUGUGAUAAAAUAACCUUUCCCA	chr1:113213668-113213900(+)$1	232	159	182	22.5700
uauauauauuuuuucuuuuauaa	chr19:13063845-13064066(-)$1	221	126	149	22.0261
CACUGGUGUUGGACUUAAAUCAG	chr6:111216663-111216882(+)$1	219	162	185	21.6097
UGAGGGUUGGUUUUUGUUCCCUC	chr20:57253215-57253448(+)$1	233	138	161	23.3808
GGAAACUAACUGAGUUCUUGUUU	chr12:53873127-53873358(+)$1	231	28	51	23.4561
CUCUGUAAAAUAAAUAAGCAGAU	chr15:64364690-64364913(-)$1	223	119	142	21.4965
AGAUAUCAAACCCACUACAUGUC	chr20:44039117-44039343(+)$1	226	158	181	21.3455
GCCGAGUCUACCUAGCUUUCUUG	chr17:60021964-60022182(-)$1	218	10	33	23.1628
AAUGUCCAAACAAAGCUUCACUU	chrX:73809185-73809409(-)$1	224	85	108	20.8158
UCAGCUUAACUGACAGACGUUAA	chr12:49521485-49521715(-)$1	230	26	49	23.3464
UGUUUUGUAUUUCUCUGUAAACC	chr13:41702586-41702807(-)$1	221	158	181	22.7728
GACAUCCAAGAACUCACCAAGAU	chr8:90938365-90938594(+)$1	229	152	175	22.0466
UUGGGCAUAUCAGUGACAGCCCA	chr1:234741747-234741966(-)$1	219	190	213	23.3808
ACCAGAAAAAAAAAAUUGUUUUG	chr7:135614305-135614544(-)$1	239	20	43	21.3897
AAGGGCUCCCAUUAUAAAUGCCA	chr5:132440540-132440770(+)$1	230	155	178	22.6991
CAUUACAAGAUAUGGCAAGUCGU	chr17:17158135-17158359(-)$1	224	116	139	22.5700
UGUUUGUUCAUAAAUAAUUAGAC	chr6:139364121-139364350(+)$1	229	183	206	23.4497
CUCUGCAUCCAUGAGUAUUGUAG	chr1:22054772-22054993(-)$1	221	175	198	21.3897
AGAAUGUAUUAUGAUUCUAUCAU	chr7:112130964-112131187(+)$1	223	34	57	22.0466
GUUGAUGAUAAAAUAAAAAUCAG	chr8:130853715-130853935(-)$1	220	182	205	23.3808
AGAACUUUGGUUAAGAGUAAGUU	chr2:176794165-176794385(-)$1	220	30	53	22.4143
AGCUAGAUUAAAAGCAACUCUUU	chr22:38880894-38881123(-)$1	229	159	182	21.7495
AAGUGAAUUAACCUUACAUCCCU	chr20:42090902-42091122(+)$1	220	94	117	22.0284
AAAGUUUAAUUAGCCAUUUUCUU	chr4:113198194-113198418(-)$1	224	165	188	20.4816
UUUCAGAAAAUUAAGAAGCUGAC	chr15:83686244-83686474(-)$1	230	125	148	22.6290
GAGAAAUUUAUAAACUUUUUUCU	chr10:60155284-60155508(+)$1	224	96	119	23.6681
CCAGUAAGUUGCAUGUAGUGCUG	chr12:79982765-79982987(-)$1	222	76	99	23.3808
AAACACUCCCACAAGUAuuuguu	chrX:150574435-150574657(+)$1	222	107	130	22.5470
UCUGGAUUUUAAAAGUUUUUUAU	chr19:10243994-10244219(-)$1	225	73	96	22.9837
AAGAUAUUUCUAAAAUCUUAUCU	chr19:37002973-37003201(-)$1	228	45	68	23.6681

#DB
.((((.............))))(	chr7:135359121-135359344(+)$1	1	1	24	21.8003
.((((.............)))))	chr10:5805411-5805640(+)$1	1	79	102	22.7840
((((((............)))))	chr7:158424076-158424300(-)$1	1	95	118	21.4987
((((((.............))))	chr20:61509139-61509367(-)$1	1	136	159	21.6648
.(((((...........))).))	chr10:75882139-75882374(-)$1	1	80	103	21.2826
((((((.............))))	chr11:89935251-89935475(-)$1	1	191	214	23.5675
.((((((...........)))))	chr11:116618806-116619030(-)$1	1	177	200	21.3897
((.((((...........)))).	chr7:115897780-115898015(+)$1	1	18	41	21.3746
..((((............)))).	chr10:17757160-17757382(+)$1	1	93	116	21.4182
((((((............)))))	chr13:25906000-25906223(+)$1	1	44	67	23.6681
((.((((...........)))))	chr6:18225189-18225415(-)$1	1	71	94	21.8486
((((((...........)))..)	chr12:120899095-120899324(+)$1	1	147	170	21.2132
((((((.............))))	chr7:135612240-135612460(-)$1	1	138	161	23.7541
(..(((...........)))..)	chr21:15745505-15745734(-)$1	1	54	77	21.8607
((((((............)))))	chr1:234741411-234741644(-)$1	1	2	25	23.3808
(((((..............))))	chr3:52741847-52742069(+)$1	1	49	72	20.6968
..((((............)))))	chr13:47351405-47351627(-)$1	1	145	168	23.1535
((((................)))	chr1:1717904-1718127(-)$1	1	100	123	20.0898
((((((.............))))	chr5:135516775-135517010(+)$1	1	144	167	23.4561
(..(((..............)))	chr2:8823741-8823967(+)$1	1	93	116	22.1563
((.(((...........))).))	chr15:49032621-49032849(-)$1	1	178	201	21.9236
.((((.............)))).	chr1:70717130-70717356(+)$1	1	167	190	20.6796
((((((.............))))	chr1:241794094-241794318(-)$1	1	132	155	23.0230
..(((.............))).)	chr14:45394978-45395205(-)$1	1	196	219	23.5703
.((((((...........)))))	chr2:225338780-225339004(-)$1	1	102	125	22.4143
((((................)))	chr13:111372454-111372686(+)$1	1	33	56	19.6676
((((((............)))))	chrX:102005667-102005890(+)$1	1	36	59	23.6681
((((((.............))))	chr7:124555566-124555796(-)$1	1	9	32	23.7541
..((((.............))))	chr7:44920537-44920759(-)$1	1	139	162	23.0884
((((((.............))))	chr2:85548370-85548593(-)$1	1	13	36	23.7541
(...(((...........)))..	chr1:229458901-229459122(-)$1	1	48	71	22.0880
((((................)))	chr1:29474221-29474444(-)$1	1	13	36	20.7248
.(((((............)))))	chr6:43474157-43474389(+)$1	1	92	115	22.0347
(..(((.............))).	chrX:70794482-70794703(+)$1	1	85	108	23.2804
((((................)))	chr17:30703041-30703262(+)$1	1	98	121	20.4816
((((((.............))))	chr6:91224892-91225117(-)$1	1	42	65	23.4561
(.(((.............))).)	chr19:44662911-44663132(+)$1	1	149	172	23.3464
..((((............)))))	chr1:42643988-42644217(-)$1	1	111	134	23.1874
(((.((............)).))	chr1:113213668-113213900(+)$1	1	159	182	22.5700
..((((............)))).	chr19:13063845-13064066(-)$1	1	126	149	22.0261
(((((((...........)))))	chr6:111216663-111216882(+)$1	1	162	185	21.6097
((((((............)))))	chr20:57253215-57253448(+)$1	1	138	161	23.3808
((((((.............))))	chr12:53873127-53873358(+)$1	1	28	51	23.4561
.(((((...........))))))	chr15:64364690-64364913(-)$1	1	119	142	21.4965
((((((............)))))	chr20:44039117-44039343(+)$1	1	158	181	21.3455
.(((((.............))))	chr17:60021964-60022182(-)$1	1	10	33	23.1628
((((..............)).))	chrX:73809185-73809409(-)$1	1	85	108	20.8158
(.(((.............))).)	chr12:49521485-49521715(-)$1	1	26	49	23.3464
.((((.............)))))	chr13:41702586-41702807(-)$1	1	158	181	22.7728
((((((..............)))	chr8:90938365-90938594(+)$1	1	152	175	22.0466
((((((............)))))	chr1:234741747-234741966(-)$1	1	190	213	23.3808
.((((((...........)))))	chr7:135614305-135614544(-)$1	1	20	43	21.3897
((((((.............))).	chr5:132440540-132440770(+)$1	1	155	178	22.6991
(((.((............)).))	chr17:17158135-17158359(-)$1	1	116	139	22.5700
((((((............)))))	chr6:139364121-139364350(+)$1	1	183	206	23.4497
.((((((...........)))))	chr1:22054772-22054993(-)$1	1	175	198	21.3897
((((((..............)))	chr7:112130964-112131187(+)$1	1	34	57	22.0466
((((((............)))))	chr8:130853715-130853935(-)$1	1	182	205	23.3808
.((((((...........)))))	chr2:176794165-176794385(-)$1	1	30	53	22.4143
.((.(((...........)))..	chr22:38880894-38881123(-)$1	1	159	182	21.7495
(((.((............)).))	chr20:42090902-42091122(+)$1	1	94	117	22.0284
((((................)))	chr4:113198194-113198418(-)$1	1	165	188	20.4816
(.((((............)))).	chr15:83686244-83686474(-)$1	1	125	148	22.6290
((((((............)))))	chr10:60155284-60155508(+)$1	1	96	119	23.6681
((((((............)))))	chr12:79982765-79982987(-)$1	1	76	99	23.3808
(((((..............))))	chrX:150574435-150574657(+)$1	1	107	130	22.5470
..((((............)))).	chr19:10243994-10244219(-)$1	1	73	96	22.9837
((((((............)))))	chr19:37002973-37003201(-)$1	1	45	68	23.6681

#PSSM
f : 0.19	g : 0.16	: : 0.08	! : 0.08	[ : 0.07	e : 0.07	c : 0.07	h : 0.05	d : 0.04	= : 0.02	b : 0.02	# : 0.02	J : 0.01	" : 0.01	+ : 0.01	i : 0.01	
f : 0.26	g : 0.13	! : 0.11	d : 0.10	e : 0.10	h : 0.05	b : 0.04	[ : 0.04	c : 0.04	= : 0.02	+ : 0.01	" : 0.01	# : 0.01	i : 0.01	
f : 0.25	d : 0.19	g : 0.13	e : 0.10	c : 0.08	h : 0.05	b : 0.04	[ : 0.04	! : 0.04	= : 0.01	" : 0.01	i : 0.01	
f : 0.25	d : 0.20	c : 0.14	g : 0.13	e : 0.10	[ : 0.05	h : 0.04	= : 0.01	" : 0.01	b : 0.01	i : 0.01	
f : 0.22	d : 0.19	c : 0.17	g : 0.11	e : 0.08	y : 0.07	h : 0.04	b : 0.04	= : 0.01	w : 0.01	i : 0.01	
f : 0.22	c : 0.13	d : 0.13	v : 0.10	g : 0.10	e : 0.08	y : 0.07	w : 0.04	b : 0.04	h : 0.02	= : 0.01	i : 0.01	
u : 0.32	v : 0.29	w : 0.08	t : 0.07	f : 0.07	y : 0.07	d : 0.02	c : 0.02	e : 0.01	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.22	w : 0.08	y : 0.07	
u : 0.32	v : 0.29	t : 0.14	w : 0.08	y : 0.07	c : 0.05	e : 0.01	
v : 0.19	d : 0.17	f : 0.14	c : 0.13	w : 0.07	y : 0.07	e : 0.05	g : 0.05	b : 0.05	h : 0.01	i : 0.01	
d : 0.19	f : 0.19	c : 0.16	g : 0.11	e : 0.08	y : 0.07	b : 0.05	h : 0.04	w : 0.04	= : 0.01	i : 0.01	
f : 0.25	d : 0.20	g : 0.13	c : 0.11	e : 0.10	] : 0.08	h : 0.04	2 : 0.02	= : 0.01	i : 0.01	
f : 0.25	d : 0.23	g : 0.13	e : 0.10	c : 0.07	h : 0.04	2 : 0.04	] : 0.04	= : 0.02	b : 0.01	4 : 0.01	i : 0.01	
f : 0.26	e : 0.19	g : 0.14	h : 0.05	2 : 0.05	c : 0.05	d : 0.05	i : 0.02	= : 0.02	5 : 0.02	b : 0.01	] : 0.01	: : 0.01	4 : 0.01	6 : 0.01	

#score	1520.090739460011
#seq	68
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_UTR_m1_run1.txt

#BEAR
==========wwwwwwwwwwwwww==========	chr21:34730650-34730878(+)$1	228	35	69	21.1947
ggg!!ddddyyyyyyyyyyyyyyyyddddggggg	chr1:226171937-226172168(-)$1	231	195	229	23.7514
ccc[eeeeeyyyyyyyyyyyyyyyyeeeeeccc:	chr8:26229492-26229715(+)$1	223	92	126	22.6170
e!!ddddyyyyyyyyyyyyyyyydddd22eeeee	chr4:41956687-41956908(+)$1	221	152	186	22.2351
eeeeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr16:3071756-3071984(+)$1	228	91	125	32.8403
ffff[ccc^^^^^^^^^^^^^^^^^^cccfffff	chr10:72182027-72182265(+)$1	238	153	187	31.0018
bb[bb^^^^^^^^^^^^^^^^^^^^^bb]bbFFF	chr1:6284783-6285012(-)$1	229	103	137	29.9595
cccccc[cccwwwwwwwwwwwwwwccc]ccc]cc	chr1:78107194-78107423(-)$1	229	129	163	20.8052
iiiiiii^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr3:182638180-182638405(+)$1	225	81	115	33.4062
ff^^^^^^^^^^^^^^^^^^^^^^^^^ffffff]	chr8:81432510-81432737(+)$1	227	116	150	32.9070
==[dddd^^^^^^^^^^^^^^^^^^^^dddd333	chr5:172195544-172195767(-)$1	223	88	122	32.5998
fffffccc^^^^^^^^^^^^^^^^^^ccc]ffff	chr6:34841805-34842033(+)$1	228	135	169	30.8950
ffff^^^^^^^^^^^^^^^^^^^^^^^ffffff]	chr5:112176034-112176255(+)$1	221	94	128	33.0336
hhhhhhh^^^^^^^^^^^^^^^^^^^hhhhhhhh	chr2:120740506-120740734(+)$1	228	193	227	29.7676
hhhhhhh^^^^^^^^^^^^^^^^^^^^^^hhhhh	chrX:16778933-16779154(+)$1	221	85	119	31.6182
gggg^^^^^^^^^^^^^^^^^^^^^^gggggggc	chr19:9676447-9676674(-)$1	227	43	77	33.3703
eeee[bb^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr6:35801347-35801577(-)$1	230	94	128	32.6228
^^^^^^^^^^^^^^^^^^^^^^^^^^ddddiiii	chr8:28420623-28420848(+)$1	225	98	132	32.1017
e[eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr11:111611484-111611720(-)$1	236	105	139	33.0027
fffff^^^^^^^^^^^^^^^^^^^^^^ffffff]	chr9:104152481-104152711(-)$1	230	153	187	32.8603
ee!!ccc^^^^^^^^^^^^^^^^^^^ccc22eee	chr5:159829423-159829648(-)$1	225	97	131	32.2041
eee^^^^^^^^^^^^^^^^^^^^^^^eeeeeccc	chr12:1604934-1605172(+)$1	238	60	94	32.5644
dddd^^^^^^^^^^^^^^^^^^^^^^^dddd666	chr8:87571478-87571708(+)$1	230	62	96	31.3235
+++ccc^^^^^^^^^^^^^^^^^^^^cccdddde	chr8:38131040-38131265(-)$1	225	20	54	30.2938
hhhhhhh^^^^^^^^^^^^^^^^^^^^^hhhhhh	chr15:83425171-83425402(+)$1	231	169	203	31.2705
=======^^^^^^^^^^^^^^^^^^^^^^^^^==	chr13:42893810-42894036(+)$1	226	9	43	33.7024
ffffff^^^^^^^^^^^^^^^^^^^^ffffff::	chr16:66650107-66650331(-)$1	224	169	203	29.8894
hhhhhhh^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr6:64292033-64292263(+)$1	230	125	159	32.1330
ggggggg^^^^^^^^^^^^^^^^^^^^^^^^ggg	chr1:203768481-203768720(+)$1	239	104	138	33.6771
hh[dddd^^^^^^^^^^^^^^^^^^^^^^^^^dd	chr1:179069505-179069733(-)$1	228	101	135	32.4174
^^^^^^^^^^^^^^^^^^^^^^^^^^dddd====	chr20:56941545-56941769(+)$1	224	151	185	32.1508
!gggggggyyyyyyyyyyyyyyyygggggggbb2	chr5:37289707-37289932(-)$1	225	93	127	23.4206
d[dddd^^^^^^^^^^^^^^^^^^^^^^^ddddd	chr8:9635514-9635736(+)$1	222	3	37	32.4835
"bb[dddd^^^^^^^^^^^^^^^^^^dddd]bb]	chr17:27587990-27588225(-)$1	235	177	211	29.7677
gggggg[bbyyyyyyyyyyyyyyyybb]gggggg	chr12:133347540-133347778(-)$1	238	12	46	24.1960
eeeee^^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr2:8871796-8872024(-)$1	228	2	36	33.6452
eeee^^^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr6:127610095-127610330(-)$1	235	99	133	33.7365
hhhhhhh^^^^^^^^^^^^^^^^^^hhhhhhhh3	chrX:37316301-37316529(+)$1	228	99	133	28.3527
c"""ccc^^^^^^^^^^^^^^^^^^^^^ccc333	chr19:57981896-57982117(-)$1	221	47	81	33.4869
##ccc!!cccwwwwwwwwwwwwwwccc333ccc8	chr3:121410388-121410615(-)$1	227	103	137	20.7198
eeeee^^^^^^^^^^^^^^^^^^^^^^^eeeee:	chrX:70520372-70520595(+)$1	223	100	134	32.7309
gggg^^^^^^^^^^^^^^^^^^^^^^ggggggg]	chr1:224563954-224564179(+)$1	225	92	126	33.5769
[iiiiiiiiiwwwwwwwwwwwwwwiiiiiiiii]	chr4:139090063-139090286(-)$1	223	56	90	20.2515
=====[bb^^^^^^^^^^^^^^^^^^bb22====	chr1:115314409-115314637(-)$1	228	30	64	30.8763
^^^^^^^^^^^^^^^^^^^^^^^^^^dddd]bb]	chr15:52842764-52842989(-)$1	225	150	184	31.7363
c[eeeee^^^^^^^^^^^^^^^^^^^^^eeeeec	chr12:25361727-25361953(-)$1	226	154	188	33.0881
f^^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff	chr5:54460230-54460452(+)$1	222	82	116	32.9013
hhhhhhh^^^^^^^^^^^^^^^^^^^hhhhhhhh	chr2:128058047-128058270(-)$1	223	156	190	29.7676
[ffffff^^^^^^^^^^^^^^^^^^^^ffffffb	chr4:85593415-85593643(-)$1	228	111	145	31.7456
hheeeee^^^^^^^^^^^^^^^^^^^^eeeee:f	chr1:225589517-225589750(-)$1	233	96	130	31.4525
ggggggg^^^^^^^^^^^^^^^^^^^ggggggg3	chr5:71503255-71503491(+)$1	236	97	131	33.0139
eeee^^^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr18:51904637-51904864(+)$1	227	94	128	33.7365
==========xxxxxxxxxxxxxxx=========	chr2:166540534-166540766(+)$1	232	152	186	22.7544
hhhhhhh^^^^^^^^^^^^^^^^^^^hhhhhhhh	chr14:60753689-60753911(+)$1	222	77	111	29.7676

#otherMatches

#Seq PSSM
AGUUCUUAGAGAGACCAGAUAUAAUCUAAGAAUU	chr21:34730650-34730878(+)$1	228	35	69	21.1947
cuaauuuucuuuuuuuuuucuuuuugagauggaa	chr1:226171937-226172168(-)$1	231	195	229	23.7514
GACCGUGAUUCCCUCUACUACAAAUAUUAUGUCU	chr8:26229492-26229715(+)$1	223	92	126	22.6170
AAAGGCUCAACUGUAAGCCUCUUAGCCAGUUGGA	chr4:41956687-41956908(+)$1	221	152	186	22.2351
GGGGCUCGCCCACUCAUCAUUCAUUCAUCCAUUC	chr16:3071756-3071984(+)$1	228	91	125	32.8403
AUUAUAGUUCAUCUUCCCAUUCUUUUACUUAGUG	chr10:72182027-72182265(+)$1	238	153	187	31.0018
GGGGCAAAUCACAGCAAUAUUCCACAGCGCCCUC	chr1:6284783-6285012(-)$1	229	103	137	29.9595
GUCUCAGUGUAACAUGGACAAUUAACAGUGAUGA	chr1:78107194-78107423(-)$1	229	129	163	20.8052
AGGAAAGUGUCCCCUUUGCAUAUUUCUUUAAAAU	chr3:182638180-182638405(+)$1	225	81	115	33.4062
CACUAUUCUUGUUUGCCUCUUUAUUUUUGCCAGU	chr8:81432510-81432737(+)$1	227	116	150	32.9070
CGAGAGGGCUGGUCCUUAUUUAUUUAACUUCACC	chr5:172195544-172195767(-)$1	223	88	122	32.5998
aguaggauuuuacagugaaaucaaaugucacuac	chr6:34841805-34842033(+)$1	228	135	169	30.8950
CUGUGUACAAACUUCUACCAUCACAAAACAGGUU	chr5:112176034-112176255(+)$1	221	94	128	33.0336
UCUUUCAUGAACUUUGCUAUAACUGUUGAAAGGA	chr2:120740506-120740734(+)$1	228	193	227	29.7676
UUUAAUGAUAUAAGCAUCACACAAUUUUACAUUA	chrX:16778933-16779154(+)$1	221	85	119	31.6182
UUUAAAAACACACUGAAGAAAAACUCUGAAUGUA	chr19:9676447-9676674(-)$1	227	43	77	33.3703
UUAUGCAAUCCAUUUAACUCAUAAACAUAUUACU	chr6:35801347-35801577(-)$1	230	94	128	32.6228
GAAUUCUAUCAUCACAAAAAUAAUUCGUCUUUCU	chr8:28420623-28420848(+)$1	225	98	132	32.1017
AUUUAAAAAUACUUCUCUCUCUUUUCUAAAAAGC	chr11:111611484-111611720(-)$1	236	105	139	33.0027
UUCAUAUUUGCUGAAACCAUUUUUUAAAUGAAAU	chr9:104152481-104152711(-)$1	230	153	187	32.8603
GUGACUACAuuuauuuuuauuuuuuuuagagaca	chr5:159829423-159829648(-)$1	225	97	131	32.2041
AUAUUCAACUUUGCCUUGAUAAUUAUUGUAAACA	chr12:1604934-1605172(+)$1	238	60	94	32.5644
UUCAGAAUUCCGUUUCCUUCUAACUAAUGAAAAA	chr8:87571478-87571708(+)$1	230	62	96	31.3235
UACAGCUCACCAAAACACUAAACUUUGCUCUUGA	chr8:38131040-38131265(-)$1	225	20	54	30.2938
GCAAGUCUCAAACCAACUUUCCAAUUCUGACUUG	chr15:83425171-83425402(+)$1	231	169	203	31.2705
UAAAAAUUUCUAGUAGAUUUUUGGCCUUUCCUGU	chr13:42893810-42894036(+)$1	226	9	43	33.7024
AAGGCAAAUAAUCACUUCACCUCUGGUGCCUUCC	chr16:66650107-66650331(-)$1	224	169	203	29.8894
AAAUGUUAAACUAUUACCACACAGCCCAUAAAAC	chr6:64292033-64292263(+)$1	230	125	159	32.1330
GGCCAUUGGAUUUCUACUUUUUAUAUGUUAAAAU	chr1:203768481-203768720(+)$1	239	104	138	33.6771
GAAUGGGACUUAAAUUUUCACAUAUAUGUAUACU	chr1:179069505-179069733(-)$1	228	101	135	32.4174
AAAACAAAUAAAAUAAGAAACACAGAGGCCAGUG	chr20:56941545-56941769(+)$1	224	151	185	32.1508
UAUGUUGUUAUAUAUACUCAGCUCACAACAUUGA	chr5:37289707-37289932(-)$1	225	93	127	23.4206
ACAAGGAGAACAAAAAUUGAAACCAAAGCCCUUU	chr8:9635514-9635736(+)$1	222	3	37	32.4835
UGAAGUUAAUUACAUAGCCUUUCUUCUAACCUCC	chr17:27587990-27588225(-)$1	235	177	211	29.7677
UGUUUGGUAUUUAAAAAAUAUUCUCUAGCAAAUA	chr12:133347540-133347778(-)$1	238	12	46	24.1960
GAGUAUAGAGAUGCCUAUAGAGAAUACAUUGCUC	chr2:8871796-8872024(-)$1	228	2	36	33.6452
GAAAAACAACUAACCUUCUAACAACUAUCUUUCA	chr6:127610095-127610330(-)$1	235	99	133	33.7365
UAUUUUAUUAUAAUAUUUCUCAUUUUAAGAUGCU	chrX:37316301-37316529(+)$1	228	99	133	28.3527
uacugguaaugucuauauuuuucuuuuaaccuug	chr19:57981896-57982117(-)$1	221	47	81	33.4869
AAUAAGGAGCUGGAAAAUAAAUAUGCUAAAUUAG	chr3:121410388-121410615(-)$1	227	103	137	20.7198
UUCUUAUCCUUACACUCCCCCAGCCCCAGAGAAA	chrX:70520372-70520595(+)$1	223	100	134	32.7309
AGAAUGGCAUCUCAAAAUAUAUAUAUUUCUUUGC	chr1:224563954-224564179(+)$1	225	92	126	33.5769
UGAAUACUGUUUAAAAUAACUAAUAUAGUAUUUU	chr4:139090063-139090286(-)$1	223	56	90	20.2515
UAGUGUUCUUCAAAAUGUGCUUcccugaccuacu	chr1:115314409-115314637(-)$1	228	30	64	30.8763
UGUUAACuucuuucucuuuuuuuuuuaggauagg	chr15:52842764-52842989(-)$1	225	150	184	31.7363
UUGUGACAUUAAAAGAUUAUUUGGGCCAGUUAUA	chr12:25361727-25361953(-)$1	226	154	188	33.0881
GCCAAAGAAUCAACAUGAAAUAUAUUAACUACUU	chr5:54460230-54460452(+)$1	222	82	116	32.9013
UUAUUCAUUGUAAAUAAAAGUAAACUUGGAUAAA	chr2:128058047-128058270(-)$1	223	156	190	29.7676
UAAACCACUAACUCAAUGAACUACUUAUGGUUUG	chr4:85593415-85593643(-)$1	228	111	145	31.7456
UGGGUUUUAAUUACACAUUUUAUAUAUGAGCCAU	chr1:225589517-225589750(-)$1	233	96	130	31.4525
AGAAAUGCAGCUUUUAUUUAUUACCCCAUUUCUU	chr5:71503255-71503491(+)$1	236	97	131	33.0139
CAAGGAUUAUAUAUUUCUAAAACACUAAACUUGA	chr18:51904637-51904864(+)$1	227	94	128	33.7365
CUGUUGCAAAUUCCAAAGACAUCACUUUGCAGCA	chr2:166540534-166540766(+)$1	232	152	186	22.7544
AAGUUGAUAUUUAAUGUAUUGGCACUUUAACUUG	chr14:60753689-60753911(+)$1	222	77	111	29.7676

#DB
((((((((((..............))))))))))	chr21:34730650-34730878(+)$1	1	35	69	21.1947
(((..((((................)))))))))	chr1:226171937-226172168(-)$1	1	195	229	23.7514
(((.(((((................)))))))).	chr8:26229492-26229715(+)$1	1	92	126	22.6170
(..((((................))))..)))))	chr4:41956687-41956908(+)$1	1	152	186	22.2351
))(((((...........................	chr16:3071756-3071984(+)$1	1	91	125	32.8403
((((.(((..................))))))))	chr10:72182027-72182265(+)$1	1	153	187	31.0018
((.((.....................)).)))))	chr1:6284783-6285012(-)$1	1	103	137	29.9595
((((((.(((..............))).))).))	chr1:78107194-78107423(-)$1	1	129	163	20.8052
(((((((...........................	chr3:182638180-182638405(+)$1	1	81	115	33.4062
((.........................)))))).	chr8:81432510-81432737(+)$1	1	116	150	32.9070
((.((((....................))))...	chr5:172195544-172195767(-)$1	1	88	122	32.5998
((((((((..................))).))))	chr6:34841805-34842033(+)$1	1	135	169	30.8950
((((.......................)))))).	chr5:112176034-112176255(+)$1	1	94	128	33.0336
(((((((...................))))))))	chr2:120740506-120740734(+)$1	1	193	227	29.7676
(((((((......................)))))	chrX:16778933-16779154(+)$1	1	85	119	31.6182
((((......................)))))))(	chr19:9676447-9676674(-)$1	1	43	77	33.3703
((((.((...........................	chr6:35801347-35801577(-)$1	1	94	128	32.6228
..........................))))))))	chr8:28420623-28420848(+)$1	1	98	132	32.1017
(.(((((...........................	chr11:111611484-111611720(-)$1	1	105	139	33.0027
(((((......................)))))).	chr9:104152481-104152711(-)$1	1	153	187	32.8603
((..(((...................)))..)))	chr5:159829423-159829648(-)$1	1	97	131	32.2041
(((.......................))))))))	chr12:1604934-1605172(+)$1	1	60	94	32.5644
((((.......................))))...	chr8:87571478-87571708(+)$1	1	62	96	31.3235
...(((....................))))))))	chr8:38131040-38131265(-)$1	1	20	54	30.2938
(((((((.....................))))))	chr15:83425171-83425402(+)$1	1	169	203	31.2705
(((((((.........................))	chr13:42893810-42894036(+)$1	1	9	43	33.7024
((((((....................))))))..	chr16:66650107-66650331(-)$1	1	169	203	29.8894
(((((((...........................	chr6:64292033-64292263(+)$1	1	125	159	32.1330
(((((((........................)))	chr1:203768481-203768720(+)$1	1	104	138	33.6771
((.((((.........................))	chr1:179069505-179069733(-)$1	1	101	135	32.4174
..........................))))))))	chr20:56941545-56941769(+)$1	1	151	185	32.1508
.(((((((................))))))))).	chr5:37289707-37289932(-)$1	1	93	127	23.4206
(.((((.......................)))))	chr8:9635514-9635736(+)$1	1	3	37	32.4835
.((.((((..................)))).)).	chr17:27587990-27588225(-)$1	1	177	211	29.7677
((((((.((................)).))))))	chr12:133347540-133347778(-)$1	1	12	46	24.1960
(((((........................)))))	chr2:8871796-8872024(-)$1	1	2	36	33.6452
((((.........................)))))	chr6:127610095-127610330(-)$1	1	99	133	33.7365
(((((((..................)))))))).	chrX:37316301-37316529(+)$1	1	99	133	28.3527
(...(((.....................)))...	chr19:57981896-57982117(-)$1	1	47	81	33.4869
..(((..(((..............)))...))).	chr3:121410388-121410615(-)$1	1	103	137	20.7198
(((((.......................))))).	chrX:70520372-70520595(+)$1	1	100	134	32.7309
((((......................))))))).	chr1:224563954-224564179(+)$1	1	92	126	33.5769
.(((((((((..............))))))))).	chr4:139090063-139090286(-)$1	1	56	90	20.2515
(((((.((..................))..))))	chr1:115314409-115314637(-)$1	1	30	64	30.8763
..........................)))).)).	chr15:52842764-52842989(-)$1	1	150	184	31.7363
(.(((((.....................))))))	chr12:25361727-25361953(-)$1	1	154	188	33.0881
(...........................))))))	chr5:54460230-54460452(+)$1	1	82	116	32.9013
(((((((...................))))))))	chr2:128058047-128058270(-)$1	1	156	190	29.7676
.((((((....................)))))))	chr4:85593415-85593643(-)$1	1	111	145	31.7456
))(((((....................))))).(	chr1:225589517-225589750(-)$1	1	96	130	31.4525
(((((((...................))))))).	chr5:71503255-71503491(+)$1	1	97	131	33.0139
((((.........................)))))	chr18:51904637-51904864(+)$1	1	94	128	33.7365
((((((((((...............)))))))))	chr2:166540534-166540766(+)$1	1	152	186	22.7544
(((((((...................))))))))	chr14:60753689-60753911(+)$1	1	77	111	29.7676

#PSSM
e : 0.18	h : 0.16	f : 0.12	g : 0.11	= : 0.09	c : 0.07	^ : 0.05	d : 0.03	[ : 0.03	b : 0.01	i : 0.01	+ : 0.01	! : 0.01	" : 0.01	# : 0.01	
h : 0.16	e : 0.14	g : 0.12	f : 0.12	= : 0.09	^ : 0.07	[ : 0.05	c : 0.03	b : 0.03	i : 0.03	! : 0.01	d : 0.01	+ : 0.01	" : 0.01	# : 0.01	
e : 0.18	g : 0.12	h : 0.12	f : 0.11	^ : 0.09	= : 0.07	c : 0.05	[ : 0.05	! : 0.03	i : 0.03	d : 0.03	+ : 0.01	b : 0.01	" : 0.01	
e : 0.16	h : 0.12	f : 0.11	^ : 0.11	g : 0.11	d : 0.09	= : 0.07	c : 0.05	! : 0.03	[ : 0.03	i : 0.03	b : 0.01	" : 0.01	
^ : 0.22	e : 0.12	h : 0.12	d : 0.09	c : 0.09	= : 0.07	f : 0.07	g : 0.07	[ : 0.03	i : 0.03	! : 0.01	b : 0.01	
^ : 0.29	h : 0.12	d : 0.11	c : 0.11	e : 0.09	g : 0.07	= : 0.05	i : 0.03	f : 0.03	b : 0.01	! : 0.01	[ : 0.01	
^ : 0.35	h : 0.12	d : 0.09	e : 0.09	c : 0.07	= : 0.05	g : 0.05	[ : 0.03	i : 0.03	b : 0.03	! : 0.01	f : 0.01	
^ : 0.74	c : 0.07	= : 0.03	d : 0.03	b : 0.03	e : 0.01	y : 0.01	g : 0.01	i : 0.01	
^ : 0.81	= : 0.03	y : 0.03	c : 0.03	d : 0.01	e : 0.01	b : 0.01	i : 0.01	
^ : 0.81	y : 0.09	= : 0.03	c : 0.03	i : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	y : 0.09	w : 0.07	x : 0.01	
^ : 0.81	w : 0.07	y : 0.07	d : 0.01	x : 0.01	
^ : 0.81	y : 0.05	c : 0.03	= : 0.01	d : 0.01	g : 0.01	i : 0.01	x : 0.01	
^ : 0.79	= : 0.03	d : 0.03	c : 0.03	e : 0.01	g : 0.01	b : 0.01	h : 0.01	i : 0.01	
^ : 0.46	d : 0.11	c : 0.11	h : 0.07	g : 0.07	b : 0.05	= : 0.03	e : 0.03	f : 0.01	i : 0.01	
^ : 0.33	d : 0.12	f : 0.09	c : 0.07	h : 0.07	g : 0.07	e : 0.05	= : 0.03	b : 0.03	] : 0.03	2 : 0.01	3 : 0.01	i : 0.01	
^ : 0.24	d : 0.12	c : 0.11	f : 0.11	e : 0.09	h : 0.09	g : 0.09	= : 0.03	2 : 0.03	] : 0.01	3 : 0.01	i : 0.01	
e : 0.16	^ : 0.14	d : 0.14	f : 0.12	g : 0.11	h : 0.11	= : 0.03	c : 0.03	2 : 0.03	b : 0.01	] : 0.01	3 : 0.01	i : 0.01	
e : 0.14	^ : 0.14	f : 0.14	g : 0.11	h : 0.11	= : 0.07	c : 0.07	d : 0.07	i : 0.03	] : 0.03	b : 0.01	2 : 0.01	
e : 0.14	f : 0.14	^ : 0.12	g : 0.11	h : 0.11	= : 0.07	c : 0.05	b : 0.05	3 : 0.03	i : 0.03	d : 0.03	F : 0.01	] : 0.01	6 : 0.01	
e : 0.12	f : 0.12	g : 0.11	h : 0.11	= : 0.09	^ : 0.09	c : 0.07	d : 0.05	b : 0.05	3 : 0.03	i : 0.03	: : 0.03	F : 0.01	6 : 0.01	
] : 0.12	e : 0.11	= : 0.09	^ : 0.09	h : 0.09	f : 0.07	c : 0.07	3 : 0.07	g : 0.05	: : 0.05	d : 0.03	F : 0.01	i : 0.01	6 : 0.01	2 : 0.01	8 : 0.01	b : 0.01	

#score	1631.4277390062127
#seq	54
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_CDS_m1_run2.txt

#BEAR
e!!ddddyyyyyyyyyyyyyyyydddd	chr21:34953625-34953843(-)$1	218	170	197	21.3523
ggggggguuuuuuuuuuuuggggggg:	chr12:56504263-56504480(+)$1	217	151	178	20.4510
!ffffff^^^^^^^^^^^^^^^^^^^^	chr21:30338975-30339201(-)$1	226	18	45	20.0240
gggg[cccvvvvvvvvvvvvvccc]gg	chr19:38126307-38126524(-)$1	217	146	173	22.7724
c!!dddduuuuuuuuuuuudddd22cc	chr17:10595139-10595360(-)$1	221	73	100	20.9988
ddddcccyyyyyyyyyyyyyyyyccc2	chr17:65346282-65346500(-)$1	218	112	139	20.9729
ddddcccwwwwwwwwwwwwwwccc]dd	chr1:55562533-55562754(-)$1	221	143	170	22.6086
c!!ddddvvvvvvvvvvvvvdddd22c	chr12:49087609-49087827(-)$1	218	65	92	22.5782
ggggggg^^^^^^^^^^^^^^^^^^^^	chr12:49426356-49426574(-)$1	218	156	183	20.7277
ggggggg^^^^^^^^^^^^^^^^^^gg	chr21:33060573-33060799(-)$1	226	72	99	20.5354
"ccceeeeeuuuuuuuuuuuueeeee6	chr1:224605911-224606131(-)$1	220	98	125	21.1255
::eeeeewwwwwwwwwwwwwweeeeee	chr1:14108081-14108302(+)$1	221	39	66	21.8281
####cccwwwwwwwwwwwwwwccc444	chr9:125641959-125642177(-)$1	218	96	123	23.6798
dd[ddddwwwwwwwwwwwwwwdddddd	chr4:141545170-141545389(-)$1	219	57	84	22.4482
###eeeeevvvvvvvvvvvvveeeee6	chr1:236306106-236306326(+)$1	220	44	71	22.9827
gggg[bbwwwwwwwwwwwwwwbb]ggg	chr11:10785241-10785458(+)$1	217	91	118	22.5072
b####bbuuuuuuuuuuuubb4444bb	chrX:53223696-53223914(-)$1	218	90	117	20.2003
g!!ddddwwwwwwwwwwwwwwdddd22	chr2:136615426-136615640(-)$1	214	167	194	23.3915
ggggggcccuuuuuuuuuuuuccc999	chr6:17675682-17675899(-)$1	217	4	31	20.0626
d[dddd^^^^^^^^^^^^^^^^^^^^^	chr6:87968651-87968869(+)$1	218	148	175	20.2962
!!eeeeewwwwwwwwwwwwwweeeee2	chr5:56546688-56546909(+)$1	221	62	89	24.3180
ggggggg^^^^^^^^^^^^^^^^^^^g	chr19:20003260-20003485(+)$1	225	26	53	20.5810
!!eeeeevvvvvvvvvvvvveeeee22	chr4:104074252-104074472(-)$1	220	89	116	23.6984
!!ddddyyyyyyyyyyyyyyyydddd2	chr10:98312684-98312906(-)$1	222	141	168	21.2753
3bb:eeeeeuuuuuuuuuuuueeeeeC	chr21:34926437-34926660(+)$1	223	129	156	18.5466
ggggggg^^^^^^^^^^^^^^^^^^^^	chr17:29528344-29528568(+)$1	224	47	74	20.7277
ffeeeeewwwwwwwwwwwwwweeeee2	chr16:2812940-2813159(+)$1	219	97	124	23.7128
"bb!!cccvvvvvvvvvvvvvccc22b	chr1:203768075-203768302(+)$1	227	45	72	21.7344
iiiiiiiivvvvvvvvvvvvviiiiii	chr1:52703907-52704128(+)$1	221	184	211	21.9987
e[eeeeewwwwwwwwwwwwwweeeee2	chr12:62949751-62949974(+)$1	223	66	93	24.1694
c!!eeeeevvvvvvvvvvvvveeeee2	chr5:132424702-132424921(+)$1	219	89	116	23.4996
!ccc[bbxxxxxxxxxxxxxxxbb]cc	chr12:67703698-67703918(+)$1	220	145	172	19.3576
gggggggvvvvvvvvvvvvvggggggg	chr16:30744864-30745081(+)$1	217	96	123	22.5505
eeeeeyyyyyyyyyyyyyyyyeeeee2	chr12:67706470-67706689(+)$1	219	98	125	21.0102
=======^^^^^^^^^^^^^^^^^^^^	chr1:63284696-63284915(+)$1	219	82	109	20.7664
bffffffvvvvvvvvvvvvvffffffE	chr11:33768695-33768917(-)$1	222	183	210	20.2584
ggggggguuuuuuuuuuuuggggggg:	chr5:176637953-176638177(+)$1	224	146	173	20.4510
f:eeeeevvvvvvvvvvvvveeeeedd	chrX:84519216-84519434(+)$1	218	68	95	21.9553
c[eeeee^^^^^^^^^^^^^^^^^^^e	chr10:35318363-35318587(-)$1	224	107	134	20.8478
ggggggg^^^^^^^^^^^^^^^^^^gg	chr7:64168439-64168662(+)$1	223	98	125	20.5354
e[eeeeewwwwwwwwwwwwwweeeee]	chr10:120828897-120829114(-)$1	217	177	204	24.1176
gggggggxxxxxxxxxxxxxxxggggg	chr10:38344060-38344282(+)$1	222	34	61	20.4257
e[eeeeeuuuuuuuuuuuueeeee]ee	chr17:62496631-62496854(-)$1	223	76	103	21.9432
Dffffffvvvvvvvvvvvvvffffffh	chr17:73945284-73945503(-)$1	219	40	67	20.0947
c[eeeeettttttttttteeeee22cc	chr6:89871442-89871663(+)$1	221	102	129	18.7795
ggggggguuuuuuuuuuuuggggggg:	chr19:37382562-37382786(-)$1	224	1	28	20.4510
e"""cccvvvvvvvvvvvvvccc333e	chr7:127014464-127014684(-)$1	220	36	63	23.0433
ggggggg^^^^^^^^^^^^^^^^^^gg	chr1:227842596-227842819(+)$1	223	97	124	20.5354
c[cccdddduuuuuuuuuuuudddd22	chr22:42609891-42610109(-)$1	218	70	97	20.7513
=======xxxxxxxxxxxxxxx=====	chr1:235894076-235894307(-)$1	231	40	67	20.6736
b[a!!dddduuuuuuuuuuuudddd22	chr5:138654543-138654763(+)$1	220	90	117	20.6744
ddddddduuuuuuuuuuuudddd]ddd	chr10:5773010-5773229(+)$1	219	134	161	20.2069
dddd!!bbvvvvvvvvvvvvvbb]ddd	chr4:24541767-24541987(-)$1	220	84	111	20.9891
"""eeeeevvvvvvvvvvvvveeeee5	chr7:64388846-64389069(+)$1	223	141	168	22.8161
"""eeeeevvvvvvvvvvvvveeeee5	chr19:23542649-23542868(-)$1	219	145	172	22.8161
:ffffffvvvvvvvvvvvvvffffff:	chr12:71147863-71148081(+)$1	218	134	161	19.8818
c[cccyyyyyyyyyyyyyyyycccccc	chr5:41917261-41917488(+)$1	227	98	125	20.7362
fffffcccvvvvvvvvvvvvvccc333	chr12:27066836-27067055(-)$1	219	102	129	22.6383
ee[ddddvvvvvvvvvvvvvddddeee	chr4:266066-266282(+)$1	216	53	80	22.0973
ggggggg^^^^^^^^^^^^^^^^^^^^	chr10:102684069-102684290(+)$1	221	44	71	20.7277
b[eeeeevvvvvvvvvvvvveeeee]b	chr6:30681771-30681997(-)$1	226	109	136	23.1014
e[dddd^^^^^^^^^^^^^^^^^^ddd	chr1:40980773-40980992(+)$1	219	22	49	19.8072
c[dddd^^^^^^^^^^^^^^^^^^^dd	chr6:149700164-149700389(+)$1	225	166	193	20.1122
ccc!!bbxxxxxxxxxxxxxxxbb22c	chr10:120830369-120830589(-)$1	220	98	125	19.2547
::eeeeevvvvvvvvvvvvveeeeedd	chr12:105538422-105538643(+)$1	221	66	93	21.1797
""eeeee^^^^^^^^^^^^^^^^^^^^	chr8:26218454-26218685(+)$1	231	106	133	21.0064
eee!!bbwwwwwwwwwwwwwwbb]eee	chr19:47422881-47423098(+)$1	217	133	160	22.1898
effffff^^^^^^^^^^^^^^^^^^^^	chr12:89992954-89993176(-)$1	222	117	144	19.8501
f[eeeeevvvvvvvvvvvvveeeee22	chr1:85116008-85116224(-)$1	216	43	70	23.4987
iiiiiiixxxxxxxxxxxxxxxiiiii	chr6:57012497-57012717(+)$1	220	43	70	20.1834

#otherMatches

#Seq PSSM
GCAGGACUUCCUCCAACCCUCUUGUCC	chr21:34953625-34953843(-)$1	218	170	197	21.3523
ACUUCACGUGCCUUCUUCAGUGAGGUG	chr12:56504263-56504480(+)$1	217	151	178	20.4510
GAGAUACUUGAAAGCAAUAAAGAGAAU	chr21:30338975-30339201(-)$1	226	18	45	20.0240
AUUGUAAGGAAUGUGGGAAGACUUUCA	chr19:38126307-38126524(-)$1	217	146	173	22.7724
UUUCAGAUAGCAUUACAACUCUGCCAG	chr17:10595139-10595360(-)$1	221	73	100	20.9988
AACUUCGAUUAAUUGAUACUCUACGAA	chr17:65346282-65346500(-)$1	218	112	139	20.9729
GAGGCAGCACUUACUCACUUUCUGCCC	chr1:55562533-55562754(-)$1	221	143	170	22.6086
CCAAUGUGAAGUCACAAUAUGCAUAUG	chr12:49087609-49087827(-)$1	218	65	92	22.5782
AAGGAACAAAACACCGUAGACCCAGCC	chr12:49426356-49426574(-)$1	218	156	183	20.7277
GGUGCUGAAACCUCACACACAGAACCA	chr21:33060573-33060799(-)$1	226	72	99	20.5354
CCUAUAUCACAAUACCAAACUUGAUAA	chr1:224605911-224606131(-)$1	220	98	125	21.1255
UUCUGGAAUAAAGACAAAAGAUCCAGA	chr1:14108081-14108302(+)$1	221	39	66	21.8281
GUGGACUUCAUACAAAAUUAUAGUAGA	chr9:125641959-125642177(-)$1	218	96	123	23.6798
CUGUGGACUCCAGAAAAUAAAUCUAAG	chr4:141545170-141545389(-)$1	219	57	84	22.4482
UACCAGAGCGUCUUCCUCUUUCUCUGC	chr1:236306106-236306326(+)$1	220	44	71	22.9827
UUUGAAAGCUUAUCCUAAUAAUUACGA	chr11:10785241-10785458(+)$1	217	91	118	22.5072
AGCACGGCCUCCUCUACAACCUCUAUC	chrX:53223696-53223914(-)$1	218	90	117	20.2003
AGUGAAGGUAUGUGUUAUCUACUUCUG	chr2:136615426-136615640(-)$1	214	167	194	23.3915
CUGUCAGCCAUCUACAUCCUCGGCAUU	chr6:17675682-17675899(-)$1	217	4	31	20.0626
UCAUGCCAACAAAAAGUAACAUUCCUC	chr6:87968651-87968869(+)$1	218	148	175	20.2962
UUUUUUUUUUUUUAACUCUCUAAAAAU	chr5:56546688-56546909(+)$1	221	62	89	24.3180
CUCUCCAAACAUAAAAGAACUCAUACU	chr19:20003260-20003485(+)$1	225	26	53	20.5810
GAUUUGGAAGCUAAAAAUACCCAAACA	chr4:104074252-104074472(-)$1	220	89	116	23.6984
GGCUUAGUUUCAAUGAUUUUAAUGAGA	chr10:98312684-98312906(-)$1	222	141	168	21.2753
AGGAUACAGAAGAACCAUUACCUGUAA	chr21:34926437-34926660(+)$1	223	129	156	18.5466
AUAGAAAUAAUCUGCUUUUUUUUUUCU	chr17:29528344-29528568(+)$1	224	47	74	20.7277
AGUUCAUCUCCUCAUCCUAAAGUGAAA	chr16:2812940-2813159(+)$1	219	97	124	23.7128
CCAUCCACUGACUAUUUUAUUGUGACU	chr1:203768075-203768302(+)$1	227	45	72	21.7344
UCUGGUUUACCUUUGCUUCUCAAACCA	chr1:52703907-52704128(+)$1	221	184	211	21.9987
UGCAGACAAAGAAAAGAUUGAGUCUGG	chr12:62949751-62949974(+)$1	223	66	93	24.1694
ACUGAUGUAGUACCAUAUCCAAUAUCU	chr5:132424702-132424921(+)$1	219	89	116	23.4996
AAGAGAGGUAAGUUAGAUCACACUGUU	chr12:67703698-67703918(+)$1	220	145	172	19.3576
CUGCUUCAUCCUUUCAACUCGGAGUGG	chr16:30744864-30745081(+)$1	217	96	123	22.5505
GAUUCAUCAUCUACUAACUUGGAAUCA	chr12:67706470-67706689(+)$1	219	98	125	21.0102
AGGGGAAAGAGAAUUCAAAACCCCAAC	chr1:63284696-63284915(+)$1	219	82	109	20.7664
UUGCCAUUCCCCGAUUCCAUAUGGCAU	chr11:33768695-33768917(-)$1	222	183	210	20.2584
UAUUGAACCAGACUACAAAUUCAGUAC	chr5:176637953-176638177(+)$1	224	146	173	20.4510
UGAUGUUGGAGAAAAAUUAGAGCAUAU	chrX:84519216-84519434(+)$1	218	68	95	21.9553
AUUUUAUCAAAAACCAAGACACAGUAA	chr10:35318363-35318587(-)$1	224	107	134	20.8478
GAUUCUCAAACCUAACUAUACAUAAGA	chr7:64168439-64168662(+)$1	223	98	125	20.5354
UAAUGUUGAAAUUCUGUAACAAAUAUC	chr10:120828897-120829114(-)$1	217	177	204	24.1176
AGAGGGUGCACACAGGACAGAAACCCU	chr10:38344060-38344282(+)$1	222	34	61	20.4257
UUCUUUACACCUAAUAACAUAAAGCAA	chr17:62496631-62496854(-)$1	223	76	103	21.9432
GGUGUUUUCUUUUUAAUCUUAGGCACA	chr17:73945284-73945503(-)$1	219	40	67	20.0947
UCAUCCAUAUUUUCACAUUGGAUCUAA	chr6:89871442-89871663(+)$1	221	102	129	18.7795
AAGCCUUUACUCAACACUCAAGGCUUA	chr19:37382562-37382786(-)$1	224	1	28	20.4510
CACAUUCGAAAAGUACACAAGAAAAAG	chr7:127014464-127014684(-)$1	220	36	63	23.0433
AGUUCUCAAACCUUACUCAACAUAAGA	chr1:227842596-227842819(+)$1	223	97	124	20.5354
AUGCCCAGUCCUAAUUCUCAUGCUGCA	chr22:42609891-42610109(-)$1	218	70	97	20.7513
AAUAUUUACUUUUCUCCUCAACAGAUG	chr1:235894076-235894307(-)$1	231	40	67	20.6736
CCGCAGUGGAUUAUUACACAACCACAC	chr5:138654543-138654763(+)$1	220	90	117	20.6744
UUUCCUCAGAAAAGAAAAAGAGGUAAG	chr10:5773010-5773229(+)$1	219	134	161	20.2069
AGCCCUGGAACUUUUGAAUUACCUGGC	chr4:24541767-24541987(-)$1	220	84	111	20.9891
AAACCAUACAAAUGUGAAGAAUGUGGA	chr7:64388846-64389069(+)$1	223	141	168	22.8161
AAACCAUACAAAUGUGAAGAAUGUGGC	chr19:23542649-23542868(-)$1	219	145	172	22.8161
GAUGCUGAGAAAAAUGACAACAGCAUA	chr12:71147863-71148081(+)$1	218	134	161	19.8818
GCAAAACAAAUUUUAAACUUCUUUCAU	chr5:41917261-41917488(+)$1	227	98	125	20.7362
CCUCUACCUAUUUCCACAGUUGGUACA	chr12:27066836-27067055(-)$1	219	102	129	22.6383
AUGACUUGCCACAUUCUUUAAAGUGUU	chr4:266066-266282(+)$1	216	53	80	22.0973
AGCUAGCAACCUUCAGAAAAAUAAAAC	chr10:102684069-102684290(+)$1	221	44	71	20.7277
CUAUCUCCAAACAACAUGCAGAGAUUG	chr6:30681771-30681997(-)$1	226	109	136	23.1014
CUGGCGGAACUCAAGACACGCAGGCGC	chr1:40980773-40980992(+)$1	219	22	49	19.8072
GCAUGGGUCCUGCCUUUAUUCAUCACC	chr6:149700164-149700389(+)$1	225	166	193	20.1122
GGCAAUCAAUCUUAAUAAUCCAGAGAG	chr10:120830369-120830589(-)$1	220	98	125	19.2547
UUGGUAGCUUACGUAACUCACUACCUA	chr12:105538422-105538643(+)$1	221	66	93	21.1797
AUAUCACAUCAACUCAAUUUCUAUUAA	chr8:26218454-26218685(+)$1	231	106	133	21.0064
AAGCUGCAUAAAAGCCAAAAAGCUCUU	chr19:47422881-47423098(+)$1	217	133	160	22.1898
AACUAGCCGUUUAAAAUUCCUCAAAGA	chr12:89992954-89993176(-)$1	222	117	144	19.8501
UCGAGGCAGCCGCAAAAGAAGCCUCAC	chr1:85116008-85116224(-)$1	216	43	70	23.4987
UUCAUAAUGGACACAGAUAUUUUUAUG	chr6:57012497-57012717(+)$1	220	43	70	20.1834

#DB
(..((((................))))	chr21:34953625-34953843(-)$1	1	170	197	21.3523
(((((((............))))))).	chr12:56504263-56504480(+)$1	1	151	178	20.4510
.((((((....................	chr21:30338975-30339201(-)$1	1	18	45	20.0240
((((.(((.............))).))	chr19:38126307-38126524(-)$1	1	146	173	22.7724
(..((((............))))..))	chr17:10595139-10595360(-)$1	1	73	100	20.9988
(((((((................))).	chr17:65346282-65346500(-)$1	1	112	139	20.9729
(((((((..............))).))	chr1:55562533-55562754(-)$1	1	143	170	22.6086
(..((((.............))))..)	chr12:49087609-49087827(-)$1	1	65	92	22.5782
(((((((....................	chr12:49426356-49426574(-)$1	1	156	183	20.7277
(((((((..................))	chr21:33060573-33060799(-)$1	1	72	99	20.5354
.((((((((............))))).	chr1:224605911-224606131(-)$1	1	98	125	21.1255
..(((((..............)))))(	chr1:14108081-14108302(+)$1	1	39	66	21.8281
....(((..............)))...	chr9:125641959-125642177(-)$1	1	96	123	23.6798
((.((((..............))))))	chr4:141545170-141545389(-)$1	1	57	84	22.4482
...(((((.............))))).	chr1:236306106-236306326(+)$1	1	44	71	22.9827
((((.((..............)).)))	chr11:10785241-10785458(+)$1	1	91	118	22.5072
(....((............))....))	chrX:53223696-53223914(-)$1	1	90	117	20.2003
(..((((..............))))..	chr2:136615426-136615640(-)$1	1	167	194	23.3915
(((((((((............)))...	chr6:17675682-17675899(-)$1	1	4	31	20.0626
(.((((.....................	chr6:87968651-87968869(+)$1	1	148	175	20.2962
..(((((..............))))).	chr5:56546688-56546909(+)$1	1	62	89	24.3180
(((((((...................)	chr19:20003260-20003485(+)$1	1	26	53	20.5810
..(((((.............)))))..	chr4:104074252-104074472(-)$1	1	89	116	23.6984
..((((................)))).	chr10:98312684-98312906(-)$1	1	141	168	21.2753
.)).(((((............))))))	chr21:34926437-34926660(+)$1	1	129	156	18.5466
(((((((....................	chr17:29528344-29528568(+)$1	1	47	74	20.7277
(((((((..............))))).	chr16:2812940-2813159(+)$1	1	97	124	23.7128
.((..(((.............)))..)	chr1:203768075-203768302(+)$1	1	45	72	21.7344
((((((((.............))))))	chr1:52703907-52704128(+)$1	1	184	211	21.9987
(.(((((..............))))).	chr12:62949751-62949974(+)$1	1	66	93	24.1694
(..(((((.............))))).	chr5:132424702-132424921(+)$1	1	89	116	23.4996
.(((.((...............)).))	chr12:67703698-67703918(+)$1	1	145	172	19.3576
(((((((.............)))))))	chr16:30744864-30745081(+)$1	1	96	123	22.5505
(((((................))))).	chr12:67706470-67706689(+)$1	1	98	125	21.0102
(((((((....................	chr1:63284696-63284915(+)$1	1	82	109	20.7664
)((((((.............)))))))	chr11:33768695-33768917(-)$1	1	183	210	20.2584
(((((((............))))))).	chr5:176637953-176638177(+)$1	1	146	173	20.4510
).(((((.............)))))((	chrX:84519216-84519434(+)$1	1	68	95	21.9553
(.(((((...................)	chr10:35318363-35318587(-)$1	1	107	134	20.8478
(((((((..................))	chr7:64168439-64168662(+)$1	1	98	125	20.5354
(.(((((..............))))).	chr10:120828897-120829114(-)$1	1	177	204	24.1176
(((((((...............)))))	chr10:38344060-38344282(+)$1	1	34	61	20.4257
(.(((((............))))).))	chr17:62496631-62496854(-)$1	1	76	103	21.9432
(((((((.............))))))(	chr17:73945284-73945503(-)$1	1	40	67	20.0947
(.(((((...........)))))..))	chr6:89871442-89871663(+)$1	1	102	129	18.7795
(((((((............))))))).	chr19:37382562-37382786(-)$1	1	1	28	20.4510
(...(((.............)))...)	chr7:127014464-127014684(-)$1	1	36	63	23.0433
(((((((..................))	chr1:227842596-227842819(+)$1	1	97	124	20.5354
(.(((((((............))))..	chr22:42609891-42610109(-)$1	1	70	97	20.7513
(((((((...............)))))	chr1:235894076-235894307(-)$1	1	40	67	20.6736
(.(..((((............))))..	chr5:138654543-138654763(+)$1	1	90	117	20.6744
(((((((............)))).)))	chr10:5773010-5773229(+)$1	1	134	161	20.2069
((((..((.............)).)))	chr4:24541767-24541987(-)$1	1	84	111	20.9891
...(((((.............))))).	chr7:64388846-64389069(+)$1	1	141	168	22.8161
...(((((.............))))).	chr19:23542649-23542868(-)$1	1	145	172	22.8161
.((((((.............)))))).	chr12:71147863-71148081(+)$1	1	134	161	19.8818
(.(((................))))))	chr5:41917261-41917488(+)$1	1	98	125	20.7362
((((((((.............)))...	chr12:27066836-27067055(-)$1	1	102	129	22.6383
((.((((.............)))))))	chr4:266066-266282(+)$1	1	53	80	22.0973
(((((((....................	chr10:102684069-102684290(+)$1	1	44	71	20.7277
(.(((((.............))))).)	chr6:30681771-30681997(-)$1	1	109	136	23.1014
(.((((..................)))	chr1:40980773-40980992(+)$1	1	22	49	19.8072
(.((((...................))	chr6:149700164-149700389(+)$1	1	166	193	20.1122
(((..((...............))..)	chr10:120830369-120830589(-)$1	1	98	125	19.2547
..(((((.............)))))((	chr12:105538422-105538643(+)$1	1	66	93	21.1797
..(((((....................	chr8:26218454-26218685(+)$1	1	106	133	21.0064
(((..((..............)).)))	chr19:47422881-47423098(+)$1	1	133	160	22.1898
(((((((....................	chr12:89992954-89993176(-)$1	1	117	144	19.8501
(.(((((.............)))))..	chr1:85116008-85116224(-)$1	1	43	70	23.4987
(((((((...............)))))	chr6:57012497-57012717(+)$1	1	43	70	20.1834

#PSSM
g : 0.22	e : 0.14	c : 0.12	d : 0.08	! : 0.07	" : 0.07	b : 0.05	f : 0.05	: : 0.04	# : 0.02	i : 0.02	= : 0.02	3 : 0.01	D : 0.01	
g : 0.21	[ : 0.18	! : 0.11	f : 0.10	d : 0.07	" : 0.05	c : 0.04	: : 0.04	# : 0.04	e : 0.04	b : 0.02	i : 0.02	= : 0.02	
e : 0.22	g : 0.21	d : 0.11	f : 0.08	! : 0.07	c : 0.07	# : 0.04	" : 0.04	[ : 0.02	b : 0.02	i : 0.02	= : 0.02	a : 0.01	
e : 0.27	g : 0.21	d : 0.20	f : 0.08	c : 0.05	! : 0.05	# : 0.02	i : 0.02	= : 0.02	: : 0.01	" : 0.01	
e : 0.30	g : 0.18	d : 0.15	f : 0.08	c : 0.08	! : 0.07	[ : 0.04	i : 0.02	= : 0.02	# : 0.01	
e : 0.28	d : 0.18	g : 0.18	c : 0.10	f : 0.07	b : 0.07	i : 0.02	y : 0.02	= : 0.02	! : 0.01	
e : 0.28	g : 0.17	d : 0.12	c : 0.11	b : 0.08	f : 0.07	^ : 0.04	y : 0.04	i : 0.02	= : 0.02	
^ : 0.21	v : 0.17	w : 0.15	u : 0.10	e : 0.08	y : 0.07	x : 0.07	c : 0.05	d : 0.02	i : 0.01	t : 0.01	b : 0.01	
v : 0.30	^ : 0.21	w : 0.15	u : 0.10	y : 0.07	x : 0.07	e : 0.02	d : 0.02	c : 0.01	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	t : 0.01	
v : 0.30	^ : 0.21	u : 0.17	w : 0.15	y : 0.07	x : 0.07	e : 0.01	
v : 0.30	^ : 0.21	w : 0.15	y : 0.07	u : 0.07	x : 0.07	g : 0.04	d : 0.02	e : 0.02	b : 0.01	
^ : 0.21	w : 0.15	v : 0.12	e : 0.10	y : 0.07	u : 0.07	x : 0.07	g : 0.05	d : 0.05	f : 0.04	b : 0.01	c : 0.01	
e : 0.27	^ : 0.21	c : 0.11	d : 0.11	x : 0.07	g : 0.05	y : 0.04	b : 0.04	f : 0.04	4 : 0.01	i : 0.01	
e : 0.27	^ : 0.21	d : 0.12	c : 0.11	g : 0.07	b : 0.07	f : 0.04	y : 0.02	i : 0.02	4 : 0.01	= : 0.01	
e : 0.25	^ : 0.21	d : 0.11	c : 0.11	g : 0.07	] : 0.05	f : 0.04	2 : 0.02	i : 0.02	b : 0.02	4 : 0.01	3 : 0.01	= : 0.01	
e : 0.27	^ : 0.20	d : 0.12	g : 0.08	2 : 0.07	] : 0.05	f : 0.04	c : 0.02	4 : 0.02	i : 0.02	3 : 0.02	9 : 0.01	= : 0.01	
e : 0.21	d : 0.14	g : 0.14	^ : 0.14	2 : 0.11	c : 0.07	f : 0.04	i : 0.02	3 : 0.02	4 : 0.01	b : 0.01	9 : 0.01	= : 0.01	] : 0.01	
2 : 0.17	d : 0.12	^ : 0.11	g : 0.11	c : 0.08	e : 0.08	: : 0.05	b : 0.04	6 : 0.02	i : 0.02	5 : 0.02	4 : 0.01	9 : 0.01	C : 0.01	E : 0.01	] : 0.01	h : 0.01	= : 0.01	3 : 0.01	

#score	1498.1241295494096
#seq	70
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_CDS_m2_run2.txt

#BEAR
cc[ccc============mmmm============22c	chr1:1463035-1463262(+)$1	227	150	187	13.9293
eeee$$$$$dddd!!cccmmmmccc333dddd333ee	chr8:20068593-20068812(+)$1	219	117	154	14.2485
eeee####dddda[ddddmmmmdddd]a]dddd333e	chrX:118723239-118723471(-)$1	232	2	39	12.6773
ccc[ccc"""bb[eeeeellleeeee22bb333cccc	chr3:16419183-16419408(-)$1	225	160	197	10.6866
ccdddd$$$$$ccc[cccmmmmccc]ccc4444dddd	chr17:4701487-4701706(+)$1	219	70	107	11.7695
a[a[a[ggggggg!!bboooooobb22ggggggg22a	chr19:17690272-17690494(+)$1	222	59	96	12.8419
dddd[a[ggggggg[cccmmmmccc333ggggggg33	chr19:1278960-1279182(+)$1	222	52	89	15.7838
dd!!bb[a"""ddddddddllldddd333dddd333a	chr12:50528304-50528524(-)$1	220	154	191	12.0706
bb[==========xxxxxxxxxxxxxxx=========	chrX:106959858-106960090(-)$1	232	108	145	9.5930
ee:ccc!!eeeee!!cccnnnnnccc]eeeee22ccc	chr9:6504530-6504752(+)$1	222	132	169	10.3110
a!!eeeee[a[bb[cccoooooocccbb]a]eeeee2	chr22:43564769-43565008(-)$1	239	186	223	10.7275
ffffff"""ffffff[ccclllccc333ffffff22f	chr5:68523972-68524192(+)$1	220	57	94	11.9433
ddd"""ccc[ccc[ddddllldddd]ccc]ccc333d	chr11:4128565-4128806(+)$1	241	145	182	12.7735
ccc$$$$$cccgggggggmmmmggggggg333ccc33	chr12:12974856-12975082(+)$1	226	38	75	12.8088
eee%%%%%%eeeee[cccmmmmccc4444eeeee444	chr16:74506362-74506592(-)$1	230	139	176	11.4369
ddggggggg[bb!!ddddmmmmdddd]bb]ggggggg	chr6:170878738-170878964(+)$1	226	142	179	11.9169
ffff"""bb[dddd!!bbmmmmbb333ddddbb]fff	chr8:68105631-68105854(+)$1	223	106	143	11.2121
cc[ccc[bb[bb!!ddddmmmmdddd22bb]bbccc]	chr18:21761045-21761265(-)$1	220	32	69	11.8026
hhhhhbbdddd####ccclllccc4444dddd]bb]h	chr19:49993404-49993624(+)$1	220	87	124	10.8724
dd"""eeeee"""ggggggglllgggggggeeeee33	chr6:32125580-32125801(+)$1	221	75	112	10.4075
:ccc"""ccc"""ddddmmmmdddd333ccc333ccc	chr19:5691333-5691558(+)$1	225	76	113	12.5810
#ccc[eeeee"""eeeeemmmmeeeee]eeeee]ccc	chr3:120053675-120053897(-)$1	222	17	54	10.9551
a[ggggggg!!bb[bb[ammmmabb]bb]ggggggga	chr6:37616935-37617162(-)$1	227	134	171	11.2772
fff"""eeeee!!bb!!ammmma22bb]eeeeeffff	chr13:99092859-99093084(+)$1	225	16	53	10.5035
ggggg[ddddbb[a[cccmmmmccc]a]bb]ddddgg	chr16:30456205-30456430(-)$1	225	26	63	12.5753
eeee[dddd[ccccccooooooccc]ccc333dddde	chr8:22107514-22107750(+)$1	236	175	212	10.8063
!ggggggg[ccc####bbmmmmbb333cccggggggg	chr10:14909661-14909885(+)$1	224	149	186	13.5249
!eeeee[dddd####cccmmmmcccddddeeeee22d	chr5:179498359-179498580(-)$1	221	153	190	12.1074
cc####ggggggg!!cccmmmmccc333ggggggg33	chr7:107822199-107822419(-)$1	220	25	62	17.2397
c[abb[ffffff!!cccooooooccc22ffffff]bb	chr11:65744419-65744641(+)$1	222	67	104	11.6584
edddd!!bb!!bb"""bbmmmmbb4444bb]bb22dd	chr17:27869929-27870151(+)$1	222	30	67	11.5180
ccc"""bbeeeee[a[bbmmmmbb]a]eeeee]bb33	chr6:1391027-1391259(+)$1	232	73	110	12.0624
ee####eeeeeffffffooooooffffff]eeeee33	chrM:8087-8309(-)$1	222	98	135	10.8151
ccc[eeeee!!ddddcccmmmmccc333dddd]eeee	chr11:65652306-65652525(-)$1	219	97	134	13.2008
$============"""bbmmmmbb333==========	chr5:33461222-33461451(+)$1	229	178	215	14.6047
ccc"""ccc[a[fffffflllffffff333a]ccc33	chr11:77531540-77531765(-)$1	225	31	68	11.9762
::::==========[cccmmmmccc]==========:	chrM:14354-14611(-)$1	257	107	144	10.5524
dddiiiiiiiii####aooooooa4444iiiiiiiii	chr12:133383749-133383977(-)$1	228	116	153	13.6353
d$$$$$eeeee####cccmmmmccc333eeeee6666	chr16:85712110-85712334(-)$1	224	30	67	13.4436
gg####dddd$$$$$cccmmmmccc666666dddd44	chr18:72997443-72997676(+)$1	233	31	68	11.3271
[ggggggg[bb!!eeeeemmmmeeeee]bb]gggggg	chr2:61721029-61721254(-)$1	225	160	197	10.8455
eeeee[cccccc[aooooooa]ccc333ccceeeeed	chr9:71395190-71395412(+)$1	222	101	138	10.8576
gggg[bb"""ccc!!cccnnnnnccc22cccbb]ggg	chr6:27100204-27100424(-)$1	220	170	207	12.2607
ee"""cccccc!!addddoooooodddd]a22ccc]c	chr15:52353481-52353705(+)$1	224	18	55	11.4009
dd[ffffff[dddd[cccooooooccc]dddd]ffff	chr2:233431548-233431776(+)$1	228	21	58	10.4845
[dddd[bb[ccc[a[cccmmmmccc333a]ccc22bb	chr17:36718020-36718243(-)$1	223	23	60	14.0904
idddd"""ffffff[cccnnnnnccc]ffffff333d	chr15:101591837-101592062(+)$1	225	124	161	11.5435
fff!!ffffff[a!!ccc[aooooooa]ccc]a]fff	chr17:53007334-53007560(+)$1	226	107	144	10.1869
ccc[bba[ffffffddddmmmmdddd22ffffff]a]	chr12:49420629-49420857(-)$1	228	157	194	11.3288
iiiiiiiieeeee[ddddmmmmdddd]eeeee4444i	chr7:154777723-154777946(-)$1	223	177	214	12.1220
f"""ggggggg[ccc[ccclllccc]ccc]ggggggg	chr11:102319457-102319682(-)$1	225	64	101	12.6995
iiiiibb!!bb[a!!cccmmmmccc22abb22bb666	chr20:279178-279419(+)$1	241	23	60	12.0335
ccca"""bb"""ccccccnnnnnccc]ccc333bb33	chr19:42855283-42855513(+)$1	230	116	153	12.9572
^^^a]ggggggg333ccc4444ccc333ggggggg]a	chr7:27285589-27285814(+)$1	225	76	113	10.9053
###bb[bbccc[ccccccmmmmccc]ccc]ccc22bb	chr1:149898204-149898433(-)$1	229	18	55	12.3197
cc[ccc!!ccc[bbcccooooooccc333bb]ccc22	chr1:24981406-24981640(+)$1	234	43	80	13.1821
cc####ccc!!ccc[ccclllcccccc22ccc4444c	chr14:96993718-96993943(+)$1	225	54	91	14.1820

#otherMatches

#Seq PSSM
CCUGGUGAGAAUGUAUUUUGACAAGUAUGUUCUUAAG	chr1:1463035-1463262(+)$1	227	150	187	13.9293
CGAAUCUACCCAGAGGAAAUGAUUCAGACUGGCAUUU	chr8:20068593-20068812(+)$1	219	117	154	14.2485
CCCAGAAGUAUGGUCUUAAGAGUAAGUCUCAUGGGGU	chrX:118723239-118723471(-)$1	232	2	39	12.6773
UGCAUGAAGAGCCACUCUCAGGGAGUAAGUAUGUCAG	chr3:16419183-16419408(-)$1	225	160	197	10.6866
UCUUCUUUUAUCCACAGCUCUCGCUUUGGCCAUGGAG	chr17:4701487-4701706(+)$1	219	70	107	11.7695
UGACCUGCGUUUUGAGAUCUUCUUCAAGAGACGUCUG	chr19:17690272-17690494(+)$1	222	59	96	12.8419
UGGCCGAGGGUCCCAGGUGAAGACUGGAGGGACCCCA	chr19:1278960-1279182(+)$1	222	52	89	15.7838
CUAAUUGCACGGAUUGCUUUGAAAGCCUUGAUCAGGG	chr12:50528304-50528524(-)$1	220	154	191	12.0706
CUCCAUCUCCUUCUUCUCUUCUCUGCUUGGAGGGGAU	chrX:106959858-106960090(-)$1	232	108	145	9.5930
CAACUGAGUGCUUCCACAAUGUCUGUAAAGUAAGUAG	chr9:6504530-6504752(+)$1	222	132	169	10.3110
UAUGCCGUCGACCUCAUGCUGAAGUGGGACAACGGCC	chr22:43564769-43565008(-)$1	239	186	223	10.7275
CAGAAGCUUUGAGAUCAGCAGGGCUACCAUCUCACUC	chr5:68523972-68524192(+)$1	220	57	94	11.9433
ACACUCUCCCAUGGUGGCCAAGUCAACAUUGGAUAUU	chr11:4128565-4128806(+)$1	241	145	182	12.7735
GUAGCAACUCCUGGUCGACUGAUUGACCACUUGGAAA	chr12:12974856-12975082(+)$1	226	38	75	12.8088
CUACUUCAAAUACUAGAAUCGUUUCCAAAAGUAUGUA	chr16:74506362-74506592(-)$1	230	139	176	11.4369
GUAUUAUGAUUGUUAUUGGCAACAGUUCAUUUAUAAU	chr6:170878738-170878964(+)$1	226	142	179	11.9169
CUAAAAUCUAUAUCCAGUGUAAAUGUUGAUGAGCUUA	chr8:68105631-68105854(+)$1	223	106	143	11.2121
AGAUCACGAUGCCAGUUAUAUUUAAUGAGCCUCUGAG	chr18:21761045-21761265(-)$1	220	32	69	11.8026
GGAAGGUGGUGGUCGUACGCUGUGAAGGCAUCAACAU	chr19:49993404-49993624(+)$1	220	87	124	10.8724
UGAUUGGGGGCCCUGAUGAUGGUGUUAUUACUCCCUG	chr6:32125580-32125801(+)$1	221	75	112	10.4075
GGAGUUACUGAAGGUCUCCAAGGACAAACGGGCCCUC	chr19:5691333-5691558(+)$1	225	76	113	12.5810
CCAUUGGUUGUUCGUUUUGUUAGAGAUUUAACCUAUG	chr3:120053675-120053897(-)$1	222	17	54	10.9551
GAGCCCAGUUCCCAGGACGUGCGCCAGGCGCUGGGCC	chr6:37616935-37617162(-)$1	227	134	171	11.2772
GCGCUGGGAGGAAAGAUCAGAAGUGCUGCCUUUUGCC	chr13:99092859-99093084(+)$1	225	16	53	10.5035
GGUGGUCAACCCUUGGAUUAUAAUCGGUGGAGUUGCC	chr16:30456205-30456430(-)$1	225	26	63	12.5753
GGCAAGGUGACUCUGGACGUGACCAUGGGAACUGCCU	chr8:22107514-22107750(+)$1	236	175	212	10.8063
ACACAUUGCAAGCCCCUGGAAGCAUAUCUUCAGUGUG	chr10:14909661-14909885(+)$1	224	149	186	13.5249
gUGGUCGCUGCAUCCCGCGUAGGCGGCGGGACUAGGG	chr5:179498359-179498580(-)$1	221	153	190	12.1074
GUCCUUUUCCUAGUCCCAAUGGUGGCUCCUGGGAACG	chr7:107822199-107822419(-)$1	220	25	62	17.2397
CUCUGCUUCCUCCACCACCAUCCUGGACGAGGAACCG	chr11:65744419-65744641(+)$1	222	67	104	11.6584
GGACGGACGGAGCAGGGCAUGAGCAGAAGCACGAGUG	chr17:27869929-27870151(+)$1	222	30	67	11.5180
gACUACGGGCCGGACAGCAGCAGCAGCCCGGUACCCU	chr6:1391027-1391259(+)$1	232	73	110	12.0624
UGGGCAUGAAACUGUGGUUUGCUCCACAGAUUUCAGA	chrM:8087-8309(-)$1	222	98	135	10.8151
CUGAGAUGGAAGCCAACUUCAAGGUCUGUGGUCCCAU	chr11:65652306-65652525(-)$1	219	97	134	13.2008
GUAAGUGGUGUUUUUCAGCGUGCUUUUGAAUACUGUU	chr5:33461222-33461451(+)$1	229	178	215	14.6047
ggUGAUGGCUCCUCCGGGCUGCCCGGGUUCGUGCCCC	chr11:77531540-77531765(-)$1	225	31	68	11.9762
AAUUUAUUUAGGGGGAAUGAUGGUUGUCUUUGGAUAU	chrM:14354-14611(-)$1	257	107	144	10.5524
AGCUCUGCAGCAGAAACACAGGAGGAGAUGCUGCAGG	chr12:133383749-133383977(-)$1	228	116	153	13.6353
UCCCCGACUGACUUUAGCCCUUGCUCCUUUAGUGCUU	chr16:85712110-85712334(-)$1	224	30	67	13.4436
UGGACAUUCAGGAAAGUGAGUACAUGUGCAAUGAAGA	chr18:72997443-72997676(+)$1	233	31	68	11.3271
CUUUCUGGAAGUCAACAUUUUGAUGUUCCUCCCAGGA	chr2:61721029-61721254(-)$1	225	160	197	10.8455
UGCUGCUGCCGGCCUCCCCUGUCCGCAUGCACAGCAG	chr9:71395190-71395412(+)$1	222	101	138	10.8576
CAGGGAGAUCCAGACGGCCGUGCGCCUGCUGCUGCCU	chr6:27100204-27100424(-)$1	220	170	207	12.2607
GGAUUUCCUGGAACAAAUUUUGACAUUUAGCCCCAUG	chr15:52353481-52353705(+)$1	224	18	55	11.4009
UUAUUCGGCUGCGGAAGGGCUUGGCCUCCCGUUGCUG	chr2:233431548-233431776(+)$1	228	21	58	10.4845
GGGCCUCUAUGCUGACCCCUACGGGCUGCUGCACGAG	chr17:36718020-36718243(-)$1	223	23	60	14.0904
CGUGCCCUGCCCGGUCUGCGAGACAGCCUGGGCCCAG	chr15:101591837-101592062(+)$1	225	124	161	11.5435
UAAAACAGGUCGGGAGAUGCAGGAGAGGAUCAUGGAC	chr17:53007334-53007560(+)$1	226	107	144	10.1869
GGCACAGCCUUGCGACCUGACAAGGUACCGCGAGACA	chr12:49420629-49420857(-)$1	228	157	194	11.3288
CCCGGUAUUGAUGCAGGCUGAGGCCUCUGUUGUAAUG	chr7:154777723-154777946(-)$1	223	177	214	12.1220
UAUUUCUUUAUUUUUACAGCAUCUGCAAACAUAGAGA	chr11:102319457-102319682(-)$1	225	64	101	12.6995
CUACAGCUGGUACAAGGGGCAGCCCAAGACAUGCUUU	chr20:279178-279419(+)$1	241	23	60	12.0335
CCGCAAAGGGGACGCGGCAUGCAGCCGGCGGGGCCGG	chr19:42855283-42855513(+)$1	230	116	153	12.9572
CUCGCCGGUGGGCCUGGGCGCCGCAUCCGCCGCCUCC	chr7:27285589-27285814(+)$1	225	76	113	10.9053
CAUGGCUCAGCAGCCGAACGACUUCUGGCAGCUCAGA	chr1:149898204-149898433(-)$1	229	18	55	12.3197
CUCGGAAAACUCGUAGGUUAUCUCCUUCAGCAAGUCC	chr1:24981406-24981640(+)$1	234	43	80	13.1821
AUAUUGAUGCGUUGUGUGUUGCACCAAGACAUGUUGA	chr14:96993718-96993943(+)$1	225	54	91	14.1820

#DB
((.(((((((((((((((....))))))))))))..)	chr1:1463035-1463262(+)$1	1	150	187	13.9293
((((.....((((..(((....)))...))))...))	chr8:20068593-20068812(+)$1	1	117	154	14.2485
((((....(((((.((((....)))).).))))...)	chrX:118723239-118723471(-)$1	1	2	39	12.6773
(((.(((...((.(((((...)))))..))...))))	chr3:16419183-16419408(-)$1	1	160	197	10.6866
))((((.....(((.(((....))).)))....))))	chr17:4701487-4701706(+)$1	1	70	107	11.7695
(.(.(.(((((((..((......))..)))))))..)	chr19:17690272-17690494(+)$1	1	59	96	12.8419
((((.(.(((((((.(((....)))...)))))))..	chr19:1278960-1279182(+)$1	1	52	89	15.7838
((..((.(...((((((((...))))...))))...)	chr12:50528304-50528524(-)$1	1	154	191	12.0706
((.((((((((((...............)))))))))	chrX:106959858-106960090(-)$1	1	108	145	9.5930
)).(((..(((((..(((.....))).)))))..)))	chr9:6504530-6504752(+)$1	1	132	169	10.3110
(..(((((.(.((.(((......))))).).))))).	chr22:43564769-43565008(-)$1	1	186	223	10.7275
((((((...((((((.(((...)))...))))))..)	chr5:68523972-68524192(+)$1	1	57	94	11.9433
(((...(((.(((.((((...)))).))).)))...)	chr11:4128565-4128806(+)$1	1	145	182	12.7735
(((.....((((((((((....)))))))...)))..	chr12:12974856-12975082(+)$1	1	38	75	12.8088
(((......(((((.(((....)))....)))))...	chr16:74506362-74506592(-)$1	1	139	176	11.4369
(((((((((.((..((((....)))).)).)))))))	chr6:170878738-170878964(+)$1	1	142	179	11.9169
((((...((.((((..((....))...)))))).)))	chr8:68105631-68105854(+)$1	1	106	143	11.2121
((.(((.((.((..((((....))))..)).))))).	chr18:21761045-21761265(-)$1	1	32	69	11.8026
(((((((((((....(((...)))....)))).)).)	chr19:49993404-49993624(+)$1	1	87	124	10.8724
((...(((((...(((((((...))))))))))))..	chr6:32125580-32125801(+)$1	1	75	112	10.4075
.(((...(((...((((....))))...)))...)))	chr19:5691333-5691558(+)$1	1	76	113	12.5810
.(((.(((((...(((((....))))).))))).)))	chr3:120053675-120053897(-)$1	1	17	54	10.9551
(.(((((((..((.((.(....))).)).))))))))	chr6:37616935-37617162(-)$1	1	134	171	11.2772
(((...(((((..((..(....)..)).)))))))))	chr13:99092859-99093084(+)$1	1	16	53	10.5035
(((((.((((((.(.(((....))).).)).))))))	chr16:30456205-30456430(-)$1	1	26	63	12.5753
((((.((((.((((((......))).)))...)))))	chr8:22107514-22107750(+)$1	1	175	212	10.8063
.(((((((.(((....((....))...))))))))))	chr10:14909661-14909885(+)$1	1	149	186	13.5249
.(((((.((((....(((....))))))))))))..)	chr5:179498359-179498580(-)$1	1	153	190	12.1074
((....(((((((..(((....)))...)))))))..	chr7:107822199-107822419(-)$1	1	25	62	17.2397
(.(((.((((((..(((......)))..)))))).))	chr11:65744419-65744641(+)$1	1	67	104	11.6584
(((((..((..((...((....))....)).))..))	chr17:27869929-27870151(+)$1	1	30	67	11.5180
(((...(((((((.(.((....)).).))))).))..	chr6:1391027-1391259(+)$1	1	73	110	12.0624
((....(((((((((((......)))))).)))))..	chrM:8087-8309(-)$1	1	98	135	10.8151
(((.(((((..(((((((....)))...)))).))))	chr11:65652306-65652525(-)$1	1	97	134	13.2008
.((((((((((((...((....))...))))))))))	chr5:33461222-33461451(+)$1	1	178	215	14.6047
(((...(((.(.((((((...))))))...).)))..	chr11:77531540-77531765(-)$1	1	31	68	11.9762
....((((((((((.(((....))).)))))))))).	chrM:14354-14611(-)$1	1	107	144	10.5524
((((((((((((....(......)....)))))))))	chr12:133383749-133383977(-)$1	1	116	153	13.6353
(.....(((((....(((....)))...)))))....	chr16:85712110-85712334(-)$1	1	30	67	13.4436
((....((((.....(((....)))......))))..	chr18:72997443-72997676(+)$1	1	31	68	11.3271
.(((((((.((..(((((....))))).)).))))))	chr2:61721029-61721254(-)$1	1	160	197	10.8455
(((((.((((((.(......).)))...)))))))))	chr9:71395190-71395412(+)$1	1	101	138	10.8576
((((.((...(((..(((.....)))..))))).)))	chr6:27100204-27100424(-)$1	1	170	207	12.2607
((...((((((..(((((......)))).)..))).)	chr15:52353481-52353705(+)$1	1	18	55	11.4009
((.((((((.((((.(((......))).)))).))))	chr2:233431548-233431776(+)$1	1	21	58	10.4845
.((((.((.(((.(.(((....)))...).)))..))	chr17:36718020-36718243(-)$1	1	23	60	14.0904
)((((...((((((.(((.....))).))))))...)	chr15:101591837-101592062(+)$1	1	124	161	11.5435
(((..((((((.(..(((.(......).))).).)))	chr17:53007334-53007560(+)$1	1	107	144	10.1869
(((.(((.((((((((((....))))..)))))).).	chr12:49420629-49420857(-)$1	1	157	194	11.3288
(((((((((((((.((((....)))).)))))....)	chr7:154777723-154777946(-)$1	1	177	214	12.1220
(...(((((((.(((.(((...))).))).)))))))	chr11:102319457-102319682(-)$1	1	64	101	12.6995
(((((((..((.(..(((....)))..)))..))...	chr20:279178-279419(+)$1	1	23	60	12.0335
((((...((...((((((.....))).)))...))..	chr19:42855283-42855513(+)$1	1	116	153	12.9572
...).)))))))...)))....)))...))))))).)	chr7:27285589-27285814(+)$1	1	76	113	10.9053
...((.(((((.((((((....))).))).)))..))	chr1:149898204-149898433(-)$1	1	18	55	12.3197
((.(((..(((.(((((......)))...)).)))..	chr1:24981406-24981640(+)$1	1	43	80	13.1821
((....(((..(((.(((...))))))..)))....)	chr14:96993718-96993943(+)$1	1	54	91	14.1820

#PSSM
c : 0.24	e : 0.15	d : 0.14	f : 0.08	a : 0.05	g : 0.05	i : 0.05	: : 0.03	# : 0.03	! : 0.03	[ : 0.03	b : 0.01	h : 0.01	$ : 0.01	^ : 0.01	
c : 0.26	d : 0.17	e : 0.15	g : 0.08	f : 0.07	[ : 0.05	i : 0.03	b : 0.01	! : 0.01	h : 0.01	= : 0.01	: : 0.01	$ : 0.01	" : 0.01	^ : 0.01	# : 0.01	
c : 0.15	d : 0.12	e : 0.10	g : 0.10	[ : 0.08	# : 0.08	f : 0.07	" : 0.05	a : 0.03	! : 0.03	: : 0.03	i : 0.03	h : 0.01	= : 0.01	$ : 0.01	^ : 0.01	
" : 0.12	c : 0.10	e : 0.10	g : 0.10	d : 0.08	[ : 0.07	# : 0.07	f : 0.05	i : 0.05	! : 0.03	= : 0.03	$ : 0.03	b : 0.03	a : 0.03	% : 0.01	h : 0.01	: : 0.01	
" : 0.15	g : 0.10	c : 0.08	# : 0.08	d : 0.07	[ : 0.07	b : 0.07	e : 0.07	$ : 0.05	= : 0.05	i : 0.05	f : 0.03	a : 0.01	% : 0.01	h : 0.01	! : 0.01	] : 0.01	
" : 0.14	c : 0.10	[ : 0.10	g : 0.10	# : 0.08	b : 0.08	e : 0.08	$ : 0.05	= : 0.05	f : 0.05	d : 0.03	i : 0.03	a : 0.01	% : 0.01	! : 0.01	
g : 0.14	e : 0.12	c : 0.10	b : 0.10	" : 0.08	= : 0.07	[ : 0.07	$ : 0.05	! : 0.05	d : 0.05	f : 0.05	i : 0.03	# : 0.01	% : 0.01	a : 0.01	
g : 0.15	e : 0.12	b : 0.12	c : 0.10	d : 0.08	= : 0.07	" : 0.07	$ : 0.05	! : 0.05	f : 0.05	i : 0.03	# : 0.01	a : 0.01	% : 0.01	[ : 0.01	
e : 0.15	c : 0.15	g : 0.12	d : 0.10	f : 0.08	= : 0.07	" : 0.07	[ : 0.07	b : 0.07	$ : 0.03	% : 0.01	i : 0.01	! : 0.01	
e : 0.15	c : 0.14	[ : 0.12	d : 0.10	g : 0.08	f : 0.08	= : 0.07	" : 0.07	! : 0.07	b : 0.03	$ : 0.01	a : 0.01	i : 0.01	
c : 0.17	e : 0.12	d : 0.10	b : 0.10	g : 0.08	" : 0.08	f : 0.08	= : 0.07	! : 0.07	$ : 0.03	[ : 0.01	a : 0.01	i : 0.01	
c : 0.14	b : 0.12	d : 0.10	[ : 0.10	g : 0.08	f : 0.08	= : 0.07	e : 0.07	" : 0.07	# : 0.05	! : 0.05	i : 0.01	$ : 0.01	
c : 0.14	! : 0.10	d : 0.08	f : 0.08	# : 0.08	= : 0.07	[ : 0.07	g : 0.07	e : 0.07	b : 0.07	a : 0.05	" : 0.05	$ : 0.01	3 : 0.01	
! : 0.17	[ : 0.10	c : 0.10	d : 0.08	f : 0.08	# : 0.08	e : 0.07	a : 0.07	g : 0.05	= : 0.03	b : 0.03	" : 0.03	x : 0.01	$ : 0.01	3 : 0.01	
d : 0.17	[ : 0.15	! : 0.14	c : 0.12	# : 0.08	e : 0.05	f : 0.05	g : 0.03	b : 0.03	" : 0.03	= : 0.01	x : 0.01	a : 0.01	$ : 0.01	o : 0.01	3 : 0.01	
c : 0.47	d : 0.15	e : 0.05	[ : 0.05	b : 0.03	g : 0.03	! : 0.03	# : 0.03	" : 0.03	f : 0.03	= : 0.01	x : 0.01	o : 0.01	
c : 0.49	d : 0.15	b : 0.10	e : 0.05	g : 0.03	o : 0.03	f : 0.03	= : 0.01	x : 0.01	[ : 0.01	! : 0.01	a : 0.01	
c : 0.43	d : 0.14	o : 0.14	b : 0.08	e : 0.05	g : 0.03	a : 0.03	= : 0.01	x : 0.01	m : 0.01	f : 0.01	
m : 0.54	o : 0.17	l : 0.08	n : 0.07	c : 0.03	d : 0.01	x : 0.01	g : 0.01	[ : 0.01	4 : 0.01	
m : 0.54	o : 0.17	l : 0.14	n : 0.07	x : 0.01	g : 0.01	a : 0.01	4 : 0.01	
m : 0.54	o : 0.17	l : 0.15	n : 0.07	x : 0.01	a : 0.01	4 : 0.01	
m : 0.52	o : 0.17	l : 0.07	n : 0.07	d : 0.03	c : 0.03	e : 0.01	x : 0.01	f : 0.01	] : 0.01	4 : 0.01	
c : 0.36	o : 0.15	d : 0.14	b : 0.08	n : 0.07	e : 0.05	a : 0.03	= : 0.01	x : 0.01	g : 0.01	l : 0.01	f : 0.01	
c : 0.49	d : 0.14	b : 0.12	e : 0.05	o : 0.05	g : 0.03	f : 0.03	= : 0.01	x : 0.01	2 : 0.01	a : 0.01	
c : 0.49	d : 0.15	e : 0.05	3 : 0.05	4 : 0.05	b : 0.03	g : 0.03	f : 0.03	= : 0.01	x : 0.01	2 : 0.01	] : 0.01	o : 0.01	
3 : 0.22	c : 0.15	d : 0.14	] : 0.14	4 : 0.07	e : 0.05	2 : 0.03	g : 0.03	f : 0.03	= : 0.01	x : 0.01	b : 0.01	a : 0.01	6 : 0.01	o : 0.01	
3 : 0.26	] : 0.12	2 : 0.12	c : 0.12	4 : 0.07	b : 0.05	= : 0.03	g : 0.03	e : 0.03	a : 0.03	d : 0.03	f : 0.03	x : 0.01	6 : 0.01	
3 : 0.22	c : 0.12	2 : 0.10	] : 0.10	4 : 0.07	= : 0.05	g : 0.05	e : 0.05	b : 0.05	d : 0.05	a : 0.03	f : 0.03	x : 0.01	6 : 0.01	
c : 0.19	b : 0.12	d : 0.10	g : 0.10	e : 0.10	f : 0.08	= : 0.07	] : 0.07	3 : 0.05	4 : 0.01	i : 0.01	6 : 0.01	a : 0.01	2 : 0.01	
e : 0.14	d : 0.12	b : 0.12	c : 0.12	g : 0.10	] : 0.10	= : 0.07	f : 0.07	3 : 0.05	a : 0.03	4 : 0.01	i : 0.01	6 : 0.01	
e : 0.17	g : 0.14	c : 0.14	d : 0.12	] : 0.08	= : 0.07	3 : 0.07	f : 0.07	2 : 0.03	4 : 0.01	a : 0.01	i : 0.01	6 : 0.01	b : 0.01	
e : 0.21	g : 0.15	d : 0.14	3 : 0.08	= : 0.07	f : 0.07	c : 0.07	b : 0.07	] : 0.05	2 : 0.03	4 : 0.01	i : 0.01	
g : 0.15	e : 0.15	c : 0.12	d : 0.08	b : 0.08	= : 0.07	3 : 0.07	f : 0.07	] : 0.07	4 : 0.05	2 : 0.01	i : 0.01	a : 0.01	
g : 0.15	e : 0.12	3 : 0.10	c : 0.10	f : 0.08	= : 0.07	d : 0.07	2 : 0.07	] : 0.07	b : 0.07	4 : 0.03	i : 0.01	6 : 0.01	
c : 0.15	g : 0.15	2 : 0.12	3 : 0.08	e : 0.08	d : 0.07	f : 0.07	= : 0.05	4 : 0.05	b : 0.05	] : 0.03	6 : 0.03	i : 0.01	
3 : 0.21	g : 0.12	2 : 0.08	c : 0.08	e : 0.07	4 : 0.07	f : 0.07	d : 0.05	= : 0.05	] : 0.05	b : 0.05	6 : 0.03	i : 0.01	a : 0.01	
3 : 0.14	c : 0.12	d : 0.10	g : 0.10	f : 0.08	e : 0.07	a : 0.07	b : 0.05	= : 0.03	2 : 0.03	4 : 0.03	] : 0.03	i : 0.03	6 : 0.03	h : 0.01	: : 0.01	

#score	689.5804018348433
#seq	57
#width	37
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_CDS_m3_run1.txt

#BEAR
iiiiiqqqqqqqqiiii	chr16:21987388-21987664(+)$1	276	217	234	13.1521
dddddqqqqqqqqdddd	chr1:227842579-227842828(+)$1	249	207	224	15.6339
[ddddqqqqqqqqdddd	chr1:231410878-231411169(+)$1	291	193	210	16.0345
bddddqqqqqqqqdddd	chr11:82645071-82645370(+)$1	299	138	155	15.5760
ccc[aqqqqqqqqaccc	chr1:24978901-24979219(+)$1	318	195	212	13.4383
[ddddqqqqqqqqdddd	chr13:23929727-23930089(-)$1	362	244	261	16.0345
!!cccqqqqqqqqccc2	chr7:138255480-138255848(+)$1	368	160	177	13.6749
eeeeeqqqqqqqqeeee	chrX:70783175-70783449(+)$1	274	182	199	13.5908
#ddddqqqqqqqqdddd	chr22:43026792-43027089(-)$1	297	187	204	15.9647
"ddddqqqqqqqqdddd	chr18:56998107-56998447(-)$1	340	89	106	15.9857
!!cccqqqqqqqqccc2	chr12:123813249-123813481(-)$1	232	13	30	13.6749
cddddqqqqqqqqdddd	chr2:85874971-85875239(+)$1	268	124	141	15.7921
eeeeeqqqqqqqqeeee	chr19:989642-989973(+)$1	331	280	297	13.5908
c[cccqqqqqqqqccc]	chr12:123687690-123688004(-)$1	314	221	238	13.5561
cddddqqqqqqqqdddd	chr1:162487800-162488071(+)$1	271	70	87	15.7921
ddcccqqqqqqqqccc]	chr17:40965873-40966126(-)$1	253	59	76	13.7593
cccbbqqqqqqqqbb]c	chr15:43653715-43653983(-)$1	268	65	82	12.4091
cccbbqqqqqqqqbb]c	chr8:74893444-74893729(+)$1	285	81	98	12.4091
:ddddqqqqqqqqdddd	chr17:29226395-29226752(-)$1	357	14	31	15.1090
:ddddqqqqqqqqdddd	chr17:60064268-60064589(-)$1	321	183	200	15.1090
eeeeeqqqqqqqqeeee	chr1:90049202-90049471(+)$1	269	178	195	13.5908
:ddddqqqqqqqqdddd	chr5:60839406-60839821(+)$1	415	275	292	15.1090
eeeeeqqqqqqqqeeee	chr7:116339799-116340077(+)$1	278	234	251	13.5908
=====qqqqqqqq====	chr15:66029948-66030276(-)$1	328	241	258	13.3501
!ddddqqqqqqqqdddd	chr6:64423079-64423383(+)$1	304	176	193	16.0470
[ddddqqqqqqqqdddd	chr10:3207554-3207819(-)$1	265	8	25	16.0345
"ddddqqqqqqqqdddd	chr17:46620812-46621075(-)$1	263	50	67	15.9857
ccc[aqqqqqqqqa]cc	chr7:4798586-4798885(+)$1	299	78	95	13.2516
cddddqqqqqqqqdddd	chr11:18501763-18502219(-)$1	456	139	156	15.7921
cccbbqqqqqqqqbb]c	chr17:60062000-60062246(-)$1	246	221	238	12.4091
[ddddqqqqqqqqdddd	chr15:59376267-59376535(+)$1	268	61	78	16.0345
c[cccqqqqqqqqcccc	chr2:152293241-152293541(+)$1	300	163	180	13.6484
[ddddqqqqqqqqdddd	chr1:116931242-116931496(+)$1	254	99	116	16.0345
[ddddqqqqqqqqdddd	chr11:32979319-32979609(+)$1	290	133	150	16.0345
=====qqqqqqqq====	chrX:53577850-53578226(-)$1	376	230	247	13.3501
[ddddqqqqqqqqdddd	chr14:75276223-75276600(+)$1	377	136	153	16.0345
:ddddqqqqqqqqdddd	chr7:104746849-104747310(+)$1	461	295	312	15.1090
:ddddqqqqqqqqdddd	chr1:36921783-36922034(-)$1	251	120	137	15.1090
dd[bbqqqqqqqqbbdd	chrX:13790981-13791455(-)$1	474	115	132	13.0862
gggggqqqqqqqqgggg	chr12:46245125-46245559(+)$1	434	131	148	13.0138
:ddddqqqqqqqqdddd	chr5:89815006-89815391(-)$1	385	103	120	15.1090
""cccqqqqqqqqccc3	chr19:36255865-36256176(+)$1	311	261	278	13.6531
Bddddqqqqqqqqdddd	chr16:31926873-31927146(+)$1	273	35	52	15.1216
:ddddqqqqqqqqdddd	chr12:936220-936532(+)$1	312	95	112	15.1090
gggggqqqqqqqqgggg	chr19:38655020-38655283(+)$1	263	84	101	13.0138
[ddddqqqqqqqqdddd	chr5:72798692-72798938(+)$1	246	143	160	16.0345
[ddddqqqqqqqqdddd	chr1:51822103-51822476(-)$1	373	223	240	16.0345
!!cccqqqqqqqqccc]	chr5:82835232-82835523(+)$1	291	140	157	13.8709
[ddddqqqqqqqqdddd	chr17:76396671-76396966(+)$1	295	96	113	16.0345
[ddddqqqqqqqqdddd	chr17:1559585-1559961(-)$1	376	82	99	16.0345
'ddddqqqqqqqqdddd	chr15:65856454-65856696(+)$1	242	105	122	15.3320
!ddddqqqqqqqqdddd	chr19:44681707-44682055(+)$1	348	306	323	16.0470
gggggqqqqqqqqgggg	chr22:35688861-35689223(+)$1	362	260	277	13.0138
eeeeeqqqqqqqqeeee	chr22:32097549-32097830(-)$1	281	96	113	13.5908
ddd[aqqqqqqqqa]dd	chr17:79826763-79827051(-)$1	288	238	255	14.1891
eeeeeqqqqqqqqeeee	chr9:135554630-135554976(+)$1	346	223	240	13.5908
eeeeeqqqqqqqqeeee	chr20:47731315-47731715(-)$1	400	243	260	13.5908
:ddddqqqqqqqqdddd	chr15:64968070-64968318(+)$1	248	52	69	15.1090
[ddddqqqqqqqqdddd	chr5:68503988-68504280(+)$1	292	19	36	16.0345
#ddddqqqqqqqqdddd	chr2:152293656-152293937(+)$1	281	15	32	15.9647
gddddqqqqqqqqdddd	chr19:17678127-17678440(+)$1	313	9	26	15.7770
hddddqqqqqqqqdddd	chr15:65257588-65257894(-)$1	306	53	70	15.5640
eeeeeqqqqqqqqeeee	chr16:69727297-69727632(+)$1	335	89	106	13.5908
:ddddqqqqqqqqdddd	chr5:98115409-98115713(+)$1	304	78	95	15.1090

#otherMatches

#Seq PSSM
GAAAGUUGUAuucuuuu	chr16:21987388-21987664(+)$1	276	217	234	13.1521
ACCUAACUAGACAUAGG	chr1:227842579-227842828(+)$1	249	207	224	15.6339
UCACUGCUCUGUGGGUG	chr1:231410878-231411169(+)$1	291	193	210	16.0345
UGGAUUUCCAAAUGUCC	chr11:82645071-82645370(+)$1	299	138	155	15.5760
CGGCGCCAUAGAUCCCG	chr1:24978901-24979219(+)$1	318	195	212	13.4383
UGCAGACACAGUGCUGC	chr13:23929727-23930089(-)$1	362	244	261	16.0345
CCCACGAUUACUAGUGC	chr7:138255480-138255848(+)$1	368	160	177	13.6749
AUAAUAAUACACCAUUA	chrX:70783175-70783449(+)$1	274	182	199	13.5908
GACCUGGUCAUCAAGGU	chr22:43026792-43027089(-)$1	297	187	204	15.9647
UCAGCAAGAAGCAGCUG	chr18:56998107-56998447(-)$1	340	89	106	15.9857
CUAAAUUCUUUUCUUUU	chr12:123813249-123813481(-)$1	232	13	30	13.6749
ACAUCCUUCCCCAGAUG	chr2:85874971-85875239(+)$1	268	124	141	15.7921
CCUGGAACUGCACCCGG	chr19:989642-989973(+)$1	331	280	297	13.5908
CAUUCUGCCGAGUGAAC	chr12:123687690-123688004(-)$1	314	221	238	13.5561
GUUAUGUGUUUUAAUAA	chr1:162487800-162488071(+)$1	271	70	87	15.7921
GAGGAGUCCUGUAUCCA	chr17:40965873-40966126(-)$1	253	59	76	13.7593
GUCCUAAGUCAACAGAG	chr15:43653715-43653983(-)$1	268	65	82	12.4091
UACGGUGAUCACCCCAG	chr8:74893444-74893729(+)$1	285	81	98	12.4091
AUAGuauaaauuaacua	chr17:29226395-29226752(-)$1	357	14	31	15.1090
CUUGAUAAUCUCUUCAA	chr17:60064268-60064589(-)$1	321	183	200	15.1090
UCAGUGAGAACAAACUG	chr1:90049202-90049471(+)$1	269	178	195	13.5908
UCAGGACACACACCCUG	chr5:60839406-60839821(+)$1	415	275	292	15.1090
UUCUCACAGAAAAGAGA	chr7:116339799-116340077(+)$1	278	234	251	13.5908
GUGUUCUUGGUUCAACA	chr15:66029948-66030276(-)$1	328	241	258	13.3501
UAGUGAUUCACACCAUU	chr6:64423079-64423383(+)$1	304	176	193	16.0470
GUCCUAGGACAAAGGGG	chr10:3207554-3207819(-)$1	265	8	25	16.0345
AGAAGGAAUUCCACUUU	chr17:46620812-46621075(-)$1	263	50	67	15.9857
CCUUGCCUGUCUUCCAG	chr7:4798586-4798885(+)$1	299	78	95	13.2516
CAGCUGGAGGUUGAGCU	chr11:18501763-18502219(-)$1	456	139	156	15.7921
CUUCUGAAAUUAAAGUA	chr17:60062000-60062246(-)$1	246	221	238	12.4091
CGGGCACAUGAACGCCC	chr15:59376267-59376535(+)$1	268	61	78	16.0345
AAUGGCCACAAUCCCAU	chr2:152293241-152293541(+)$1	300	163	180	13.6484
GAGGAGACCGAAUUCCU	chr1:116931242-116931496(+)$1	254	99	116	16.0345
CUGAUCCUCUAGCAUCA	chr11:32979319-32979609(+)$1	290	133	150	16.0345
UGAUGCCACCUGACAUU	chrX:53577850-53578226(-)$1	376	230	247	13.3501
CAGCAAUUCCAUCUGCU	chr14:75276223-75276600(+)$1	377	136	153	16.0345
AAUGGUUAUAAACCCAU	chr7:104746849-104747310(+)$1	461	295	312	15.1090
CCGUAACACCAACUAUG	chr1:36921783-36922034(-)$1	251	120	137	15.1090
UCAGCCUUUUAAUGCGA	chrX:13790981-13791455(-)$1	474	115	132	13.0862
UCAGCAGCUAUUGGUUG	chr12:46245125-46245559(+)$1	434	131	148	13.0138
AGAGAGUUAACAAUCUC	chr5:89815006-89815391(-)$1	385	103	120	15.1090
cucugccacugaccagc	chr19:36255865-36256176(+)$1	311	261	278	13.6531
CGUAGUUCAUGCCUUAC	chr16:31926873-31927146(+)$1	273	35	52	15.1216
CCGCGAUCUUAAAUGUG	chr12:936220-936532(+)$1	312	95	112	15.1090
CUCUUGCCUCUCAGGGA	chr19:38655020-38655283(+)$1	263	84	101	13.0138
UGCUGAGACAAAGCAGC	chr5:72798692-72798938(+)$1	246	143	160	16.0345
UAAAUGUGACAAAAUUU	chr1:51822103-51822476(-)$1	373	223	240	16.0345
AUCCAGAUGCAAAUGGC	chr5:82835232-82835523(+)$1	291	140	157	13.8709
AGUGACUCCUACUUCAC	chr17:76396671-76396966(+)$1	295	96	113	16.0345
UGGACUUGAUCUUGUCU	chr17:1559585-1559961(-)$1	376	82	99	16.0345
UUAUGACACAUUCCAUA	chr15:65856454-65856696(+)$1	242	105	122	15.3320
AAGAGUGAAAUUUUUCU	chr19:44681707-44682055(+)$1	348	306	323	16.0470
GAUUUUUAGAGUCAGAU	chr22:35688861-35689223(+)$1	362	260	277	13.0138
GAGGCCAAAGAAAGUCU	chr22:32097549-32097830(-)$1	281	96	113	13.5908
ACAAGACCGACCACCUG	chr17:79826763-79827051(-)$1	288	238	255	14.1891
UGCUGACGAUGAACAGC	chr9:135554630-135554976(+)$1	346	223	240	13.5908
ACAUUUCAAAACUAGUG	chr20:47731315-47731715(-)$1	400	243	260	13.5908
AAGGCAGAGAUGGGCCU	chr15:64968070-64968318(+)$1	248	52	69	15.1090
UUUUUAACCUAACAGAA	chr5:68503988-68504280(+)$1	292	19	36	16.0345
UAGACAUUUUAAAGUUU	chr2:152293656-152293937(+)$1	281	15	32	15.9647
ACUGGCCUUUGCCCCAG	chr19:17678127-17678440(+)$1	313	9	26	15.7770
UUACCUUUCCUAUGGUG	chr15:65257588-65257894(-)$1	306	53	70	15.5640
AACCCCCGCAGCAGGGU	chr16:69727297-69727632(+)$1	335	89	106	13.5908
ACCUCAUGAGCCAGAGG	chr5:98115409-98115713(+)$1	304	78	95	15.1090

#DB
(((((........))))	chr16:21987388-21987664(+)$1	1	217	234	13.1521
)((((........))))	chr1:227842579-227842828(+)$1	1	207	224	15.6339
.((((........))))	chr1:231410878-231411169(+)$1	1	193	210	16.0345
)((((........))))	chr11:82645071-82645370(+)$1	1	138	155	15.5760
(((.(........))))	chr1:24978901-24979219(+)$1	1	195	212	13.4383
.((((........))))	chr13:23929727-23930089(-)$1	1	244	261	16.0345
..(((........))).	chr7:138255480-138255848(+)$1	1	160	177	13.6749
(((((........))))	chrX:70783175-70783449(+)$1	1	182	199	13.5908
.((((........))))	chr22:43026792-43027089(-)$1	1	187	204	15.9647
.((((........))))	chr18:56998107-56998447(-)$1	1	89	106	15.9857
..(((........))).	chr12:123813249-123813481(-)$1	1	13	30	13.6749
(((((........))))	chr2:85874971-85875239(+)$1	1	124	141	15.7921
(((((........))))	chr19:989642-989973(+)$1	1	280	297	13.5908
(.(((........))).	chr12:123687690-123688004(-)$1	1	221	238	13.5561
(((((........))))	chr1:162487800-162488071(+)$1	1	70	87	15.7921
(((((........))).	chr17:40965873-40966126(-)$1	1	59	76	13.7593
(((((........)).)	chr15:43653715-43653983(-)$1	1	65	82	12.4091
(((((........)).)	chr8:74893444-74893729(+)$1	1	81	98	12.4091
.((((........))))	chr17:29226395-29226752(-)$1	1	14	31	15.1090
.((((........))))	chr17:60064268-60064589(-)$1	1	183	200	15.1090
(((((........))))	chr1:90049202-90049471(+)$1	1	178	195	13.5908
.((((........))))	chr5:60839406-60839821(+)$1	1	275	292	15.1090
(((((........))))	chr7:116339799-116340077(+)$1	1	234	251	13.5908
(((((........))))	chr15:66029948-66030276(-)$1	1	241	258	13.3501
.((((........))))	chr6:64423079-64423383(+)$1	1	176	193	16.0470
.((((........))))	chr10:3207554-3207819(-)$1	1	8	25	16.0345
.((((........))))	chr17:46620812-46621075(-)$1	1	50	67	15.9857
(((.(........).))	chr7:4798586-4798885(+)$1	1	78	95	13.2516
)((((........))))	chr11:18501763-18502219(-)$1	1	139	156	15.7921
(((((........)).)	chr17:60062000-60062246(-)$1	1	221	238	12.4091
.((((........))))	chr15:59376267-59376535(+)$1	1	61	78	16.0345
(.(((........))))	chr2:152293241-152293541(+)$1	1	163	180	13.6484
.((((........))))	chr1:116931242-116931496(+)$1	1	99	116	16.0345
.((((........))))	chr11:32979319-32979609(+)$1	1	133	150	16.0345
(((((........))))	chrX:53577850-53578226(-)$1	1	230	247	13.3501
.((((........))))	chr14:75276223-75276600(+)$1	1	136	153	16.0345
.((((........))))	chr7:104746849-104747310(+)$1	1	295	312	15.1090
.((((........))))	chr1:36921783-36922034(-)$1	1	120	137	15.1090
((.((........))))	chrX:13790981-13791455(-)$1	1	115	132	13.0862
(((((........))))	chr12:46245125-46245559(+)$1	1	131	148	13.0138
.((((........))))	chr5:89815006-89815391(-)$1	1	103	120	15.1090
..(((........))).	chr19:36255865-36256176(+)$1	1	261	278	13.6531
(((((........))))	chr16:31926873-31927146(+)$1	1	35	52	15.1216
.((((........))))	chr12:936220-936532(+)$1	1	95	112	15.1090
(((((........))))	chr19:38655020-38655283(+)$1	1	84	101	13.0138
.((((........))))	chr5:72798692-72798938(+)$1	1	143	160	16.0345
.((((........))))	chr1:51822103-51822476(-)$1	1	223	240	16.0345
..(((........))).	chr5:82835232-82835523(+)$1	1	140	157	13.8709
.((((........))))	chr17:76396671-76396966(+)$1	1	96	113	16.0345
.((((........))))	chr17:1559585-1559961(-)$1	1	82	99	16.0345
.((((........))))	chr15:65856454-65856696(+)$1	1	105	122	15.3320
.((((........))))	chr19:44681707-44682055(+)$1	1	306	323	16.0470
(((((........))))	chr22:35688861-35689223(+)$1	1	260	277	13.0138
(((((........))))	chr22:32097549-32097830(-)$1	1	96	113	13.5908
(((.(........).))	chr17:79826763-79827051(-)$1	1	238	255	14.1891
(((((........))))	chr9:135554630-135554976(+)$1	1	223	240	13.5908
(((((........))))	chr20:47731315-47731715(-)$1	1	243	260	13.5908
.((((........))))	chr15:64968070-64968318(+)$1	1	52	69	15.1090
.((((........))))	chr5:68503988-68504280(+)$1	1	19	36	16.0345
.((((........))))	chr2:152293656-152293937(+)$1	1	15	32	15.9647
(((((........))))	chr19:17678127-17678440(+)$1	1	9	26	15.7770
)((((........))))	chr15:65257588-65257894(-)$1	1	53	70	15.5640
(((((........))))	chr16:69727297-69727632(+)$1	1	89	106	13.5908
.((((........))))	chr5:98115409-98115713(+)$1	1	78	95	15.1090

#PSSM
[ : 0.18	c : 0.15	: : 0.14	e : 0.12	! : 0.07	d : 0.06	g : 0.06	" : 0.04	# : 0.03	= : 0.03	i : 0.01	b : 0.01	B : 0.01	' : 0.01	h : 0.01	
d : 0.60	e : 0.12	c : 0.07	! : 0.04	g : 0.04	[ : 0.03	= : 0.03	i : 0.01	" : 0.01	
d : 0.57	c : 0.18	e : 0.12	g : 0.04	= : 0.03	i : 0.01	[ : 0.01	
d : 0.56	e : 0.12	c : 0.10	b : 0.06	[ : 0.04	g : 0.04	= : 0.03	i : 0.01	
d : 0.56	e : 0.12	c : 0.10	b : 0.06	a : 0.04	g : 0.04	= : 0.03	i : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
d : 0.56	e : 0.12	c : 0.10	b : 0.06	a : 0.04	g : 0.04	= : 0.03	i : 0.01	
d : 0.56	c : 0.12	e : 0.12	b : 0.06	g : 0.04	= : 0.03	] : 0.03	i : 0.01	
d : 0.59	c : 0.14	e : 0.12	] : 0.04	g : 0.04	= : 0.03	i : 0.01	
d : 0.59	e : 0.12	c : 0.09	] : 0.04	g : 0.04	2 : 0.03	= : 0.03	i : 0.01	3 : 0.01	

#score	939.4234734765151
#seq	64
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_UTR_m3_run1.txt

#BEAR
ffffffqqqqqqqqffffff	chr12:21669957-21670261(+)$1	304	63	83	14.3829
ggggggqqqqqqqqgggggg	chr17:60020730-60020963(-)$1	233	79	99	15.4777
ceeeeeqqqqqqqqeeeee]	chr7:116200676-116200932(+)$1	256	120	140	14.3255
d!!cccqqqqqqqqcccddd	chr17:38436236-38436506(+)$1	270	188	208	14.9608
ggggggqqqqqqqqgggggg	chr2:42670537-42670764(-)$1	227	81	101	15.4777
####bbqqqqqqqqbb333b	chr10:73995340-73995560(+)$1	220	64	84	13.7610
[eeeeeqqqqqqqqeeeeef	chr5:72877201-72877431(+)$1	230	181	201	14.3922
[a[cccqqqqqqqqccca]c	chr1:36067374-36067612(-)$1	238	90	110	15.5623
ggggggqqqqqqqqgggggg	chr17:20904651-20904879(-)$1	228	69	89	15.4777
ggggggqqqqqqqqgggggg	chr9:14082628-14082863(-)$1	235	21	41	15.4777
d[ddddqqqqqqqqdddddd	chr2:99935934-99936242(-)$1	308	193	213	13.7848
ggggggqqqqqqqqgggggg	chr11:65421568-65421817(-)$1	249	196	216	15.4777
$$$cccqqqqqqqqccc444	chr22:38879966-38880193(-)$1	227	30	50	14.8290
ggggggqqqqqqqqgggggg	chr15:64447934-64448193(-)$1	259	12	32	15.4777
dddd[aqqqqqqqqa]dddd	chr1:245016920-245017151(-)$1	231	179	199	13.6910
ffffffqqqqqqqqffffff	chr11:88026776-88027022(-)$1	246	216	236	14.3829
ggggggqqqqqqqqgggggg	chr12:54630044-54630332(-)$1	288	256	276	15.4777
deeeeeqqqqqqqqeeeee]	chr6:72013739-72013993(+)$1	254	17	37	14.1554
ee[cccqqqqqqqqccc]ee	chr16:21666837-21667084(+)$1	247	105	125	15.2036
ffffffqqqqqqqqffffff	chr1:193059118-193059352(+)$1	234	114	134	14.3829
fffcccqqqqqqqqccc777	chr12:79985483-79985726(-)$1	243	151	171	13.4233
ggggggqqqqqqqqgggggg	chr6:7287074-7287319(-)$1	245	66	86	15.4777
deeeeeqqqqqqqqeeeee:	chr9:131851302-131851536(+)$1	234	114	134	13.0833
hh[cccqqqqqqqqccc22h	chr2:36777276-36777540(+)$1	264	184	204	14.7381
ggggggqqqqqqqqgggggg	chr8:98740562-98740804(+)$1	242	175	195	15.4777
dd[cccqqqqqqqqccc]dd	chr4:123819177-123819409(+)$1	232	95	115	14.8329
eee!!aqqqqqqqqa22eee	chr12:27181923-27182198(+)$1	275	237	257	13.7021
ffffffqqqqqqqqffffff	chr1:207967179-207967489(+)$1	310	226	246	14.3829
iiiiiiqqqqqqqqiiiiii	chr7:26230747-26231000(-)$1	253	74	94	15.2740
======qqqqqqqq======	chr7:129805038-129805274(-)$1	236	134	154	15.6005
[eeeeeqqqqqqqqeeeee]	chr1:162494288-162494530(+)$1	242	32	52	14.4843
cc[cccqqqqqqqqccc]cc	chr8:38961084-38961386(+)$1	302	138	158	15.4285
!eeeeeqqqqqqqqeeeeec	chr6:7288925-7289183(-)$1	258	224	244	14.4116
!!ddddqqqqqqqqdddd]d	chr2:145146400-145146653(-)$1	253	47	67	14.4033
$$$cccqqqqqqqqccc22b	chr2:70107435-70107675(+)$1	240	171	191	14.3725
!ccc[aqqqqqqqqaccc22	chr3:133876513-133876748(-)$1	235	198	218	14.9063
ff[cccqqqqqqqqccc]ff	chr6:64286617-64286893(+)$1	276	202	222	15.4303
======qqqqqqqq======	chr7:128409735-128409995(+)$1	260	26	46	15.6005
ggggggqqqqqqqqgggggg	chr22:39910594-39910827(+)$1	233	186	206	15.4777
""ddddqqqqqqqqdddd44	chr4:169848031-169848291(+)$1	260	216	236	14.3475
ggggggqqqqqqqqgggggg	chr4:177251237-177251510(+)$1	273	36	56	15.4777
======qqqqqqqq======	chr7:139249803-139250042(-)$1	239	81	101	15.6005
!eeeeeqqqqqqqqeeeee2	chr4:57327136-57327366(+)$1	230	121	141	14.3062
c[ddddqqqqqqqqdddd22	chr1:25168768-25169053(+)$1	285	29	49	14.1792
"""cccqqqqqqqqccc333	chr12:54632845-54633101(-)$1	256	58	78	15.8930
c[ddddqqqqqqqqdddd]c	chr14:35180746-35180979(-)$1	233	118	138	14.4194
ggggggqqqqqqqqgggggg	chr9:33112954-33113230(-)$1	276	143	163	15.4777
"ccc[aqqqqqqqqa]ccc3	chr17:48939742-48940015(-)$1	273	156	176	14.9024
cc!!bbqqqqqqqqbb333c	chr4:1205459-1205728(-)$1	269	23	43	14.2132
ffffffqqqqqqqqffffff	chr17:56168249-56168473(+)$1	224	123	143	14.3829
cc[cccqqqqqqqqcccccc	chr4:100869462-100869699(-)$1	237	35	55	15.2908
c[ddddqqqqqqqqdddd]c	chr5:40714944-40715178(-)$1	234	3	23	14.4194
f!!cccqqqqqqqqcccfff	chr10:103544924-103545169(-)$1	245	7	27	15.4546
ffffffqqqqqqqqffffff	chr12:98928425-98928728(+)$1	303	114	134	14.3829
ffffffqqqqqqqqffffff	chr1:168044619-168044848(+)$1	229	93	113	14.3829
""ddddqqqqqqqqdddd33	chr22:43266467-43266748(-)$1	281	160	180	14.6185
###cccqqqqqqqqccc333	chr10:119766519-119766767(-)$1	248	76	96	15.7650
c!!cccqqqqqqqqccc22c	chr21:34930753-34931008(+)$1	255	220	240	15.4334
fddddaqqqqqqqqa]dddd	chrX:46920408-46920660(+)$1	252	225	245	13.7467
!!ddddqqqqqqqqdddd22	chr5:41918716-41918944(+)$1	228	82	102	14.3288
======qqqqqqqq======	chr5:1317870-1318120(-)$1	250	6	26	15.6005
fff[bbqqqqqqqqbb]fff	chr15:67494801-67495034(-)$1	233	149	169	13.6070
ee[cccqqqqqqqqccc]ee	chr16:9211195-9211427(+)$1	232	73	93	15.2036
iiiiiiqqqqqqqqiiiiii	chr7:75957963-75958243(-)$1	280	43	63	15.2740
ffffffqqqqqqqqffffff	chr2:110374872-110375107(+)$1	235	58	78	14.3829

#otherMatches

#Seq PSSM
GCUUUUUAAUGCAUAAAAGU	chr12:21669957-21670261(+)$1	304	63	83	14.3829
CGUACUCAAUUGUCAGUAUG	chr17:60020730-60020963(-)$1	233	79	99	15.4777
UUAUGAUUUUUUUUUCAUAC	chr7:116200676-116200932(+)$1	256	120	140	14.3255
GAAGCAAACAGAACUgccgg	chr17:38436236-38436506(+)$1	270	188	208	14.9608
ACAUUUUCAUUUCUAAAUGU	chr2:42670537-42670764(-)$1	227	81	101	15.4777
UAAACCUUUAAAUUGGAUUU	chr10:73995340-73995560(+)$1	220	64	84	13.7610
AGAUUUUGUAAUGCGAAUCU	chr5:72877201-72877431(+)$1	230	181	201	14.3922
ucaugggcaguuaaccaguU	chr1:36067374-36067612(-)$1	238	90	110	15.5623
gacauauauuguucuguguc	chr17:20904651-20904879(-)$1	228	69	89	15.4777
GCUACAGGGACUGAUGUGGC	chr9:14082628-14082863(-)$1	235	21	41	15.4777
AUACUCAUAUUCUCGAGUUU	chr2:99935934-99936242(-)$1	308	193	213	13.7848
GGGAAACUCAAACUUUUCCC	chr11:65421568-65421817(-)$1	249	196	216	15.4777
CCCCAACCCCAAAUUUGUCU	chr22:38879966-38880193(-)$1	227	30	50	14.8290
CCCUGUAGUCCGCCACAGGG	chr15:64447934-64448193(-)$1	259	12	32	15.4777
AACUUGUUGUAAAUCCAGUU	chr1:245016920-245017151(-)$1	231	179	199	13.6910
AAAAUAGAUGCUCauauuuu	chr11:88026776-88027022(-)$1	246	216	236	14.3829
GAACUGACCAUUAAUAGUUU	chr12:54630044-54630332(-)$1	288	256	276	15.4777
GGAUUUCUUGAAAAGAAUCA	chr6:72013739-72013993(+)$1	254	17	37	14.1554
AACCCAACUCUUUGUGGAUU	chr16:21666837-21667084(+)$1	247	105	125	15.2036
cAACUUUUCAUCUUAAGUUG	chr1:193059118-193059352(+)$1	234	114	134	14.3829
GUAGGAGAAAAAAAUCCAUA	chr12:79985483-79985726(-)$1	243	151	171	13.4233
ACUAGACCCUGUAUUUUAGU	chr6:7287074-7287319(-)$1	245	66	86	15.4777
CUUAUUUUAAUUUUAAUGAA	chr9:131851302-131851536(+)$1	234	114	134	13.0833
GCCUCAAAUAUAACUGACUG	chr2:36777276-36777540(+)$1	264	184	204	14.7381
GUGCAAUAUGUCAUUUGCAU	chr8:98740562-98740804(+)$1	242	175	195	15.4777
AUCAGAUGUAUUACUCUUAU	chr4:123819177-123819409(+)$1	232	95	115	14.8329
GUUCUUUUGCCCUUAUUAAC	chr12:27181923-27182198(+)$1	275	237	257	13.7021
UCUUGUGCAUAAAAACAAGA	chr1:207967179-207967489(+)$1	310	226	246	14.3829
AGUUUAACAAUUUAUAAACU	chr7:26230747-26231000(-)$1	253	74	94	15.2740
UGUAGUAGCUGGCAAUUGCA	chr7:129805038-129805274(-)$1	236	134	154	15.6005
GUGGUGAUUAGAAACAUCAG	chr1:162494288-162494530(+)$1	242	32	52	14.4843
UUUUAACCUUCUUUUUGCAA	chr8:38961084-38961386(+)$1	302	138	158	15.4285
UAGAUUGUAAAUUAAGUUUG	chr6:7288925-7289183(-)$1	258	224	244	14.4116
UUGUUAUUCCUUUUUAAUUU	chr2:145146400-145146653(-)$1	253	47	67	14.4033
ACCCUUGACCCUCAGAGCUG	chr2:70107435-70107675(+)$1	240	171	191	14.3725
UUUGUCUUCAAGAUGCAAUA	chr3:133876513-133876748(-)$1	235	198	218	14.9063
UCACAUACAAGAACAUGAGA	chr6:64286617-64286893(+)$1	276	202	222	15.4303
GUUGCUAUAGGUCCAGCAAC	chr7:128409735-128409995(+)$1	260	26	46	15.6005
UUUAGUUGAAUGCCACUGAA	chr22:39910594-39910827(+)$1	233	186	206	15.4777
aGUGCUCUGAAUAAAGCAGA	chr4:169848031-169848291(+)$1	260	216	236	14.3475
GUUCAGCAAAGAGAUUGAAC	chr4:177251237-177251510(+)$1	273	36	56	15.4777
UUUUUUUUUUUUUUAGAAGG	chr7:139249803-139250042(-)$1	239	81	101	15.6005
CCUAUUUGUUAGCUAGUAGA	chr4:57327136-57327366(+)$1	230	121	141	14.3062
UAUUUACUCUUUUUUAAAAG	chr1:25168768-25169053(+)$1	285	29	49	14.1792
CAUUCAUAAAAAUCUGAUAU	chr12:54632845-54633101(-)$1	256	58	78	15.8930
AUUUACAUUUCUAAGUAGUU	chr14:35180746-35180979(-)$1	233	118	138	14.4194
GUUUUCUUAUUCGUGAAAAU	chr9:33112954-33113230(-)$1	276	143	163	15.4777
CUAUUCUAAAAAUUGUGUAC	chr17:48939742-48940015(-)$1	273	156	176	14.9024
AGGAGCAUUUGGAAGUCAAU	chr4:1205459-1205728(-)$1	269	23	43	14.2132
GGGCACAAAAUUGAGUGCUU	chr17:56168249-56168473(+)$1	224	123	143	14.3829
CCACAAAUCUCUGAUUGGGA	chr4:100869462-100869699(-)$1	237	35	55	15.2908
GUGAUUUAUAGUACAAUCUC	chr5:40714944-40715178(-)$1	234	3	23	14.4194
CAGUUGUUUAAUCUCAAGAC	chr10:103544924-103545169(-)$1	245	7	27	15.4546
GAUACUUUUAUCUCAGUAUC	chr12:98928425-98928728(+)$1	303	114	134	14.3829
GUAUAAGACAUUUAUUAUAU	chr1:168044619-168044848(+)$1	229	93	113	14.3829
ACAAUUUUAUCACUGAUUCA	chr22:43266467-43266748(-)$1	281	160	180	14.6185
UUUUUUUUUUUUUUAAACAU	chr10:119766519-119766767(-)$1	248	76	96	15.7650
uuuuuaccaccaccugacua	chr21:34930753-34931008(+)$1	255	220	240	15.4334
AACUGCUACCUACUGUCAGU	chrX:46920408-46920660(+)$1	252	225	245	13.7467
UCCCAUUUCCCGCUGUGGCU	chr5:41918716-41918944(+)$1	228	82	102	14.3288
AUUUCAAACACGUAUGGAAU	chr5:1317870-1318120(-)$1	250	6	26	15.6005
AUCUCAGAGGUCUGUGUGAU	chr15:67494801-67495034(-)$1	233	149	169	13.6070
CAAUUCUAAUUAUUGGACUG	chr16:9211195-9211427(+)$1	232	73	93	15.2036
UUGGUUUUGCUGUUGAUCGG	chr7:75957963-75958243(-)$1	280	43	63	15.2740
AAUGAAAAAUACCAUUCAUU	chr2:110374872-110375107(+)$1	235	58	78	14.3829

#DB
((((((........))))))	chr12:21669957-21670261(+)$1	1	63	83	14.3829
((((((........))))))	chr17:60020730-60020963(-)$1	1	79	99	15.4777
((((((........))))).	chr7:116200676-116200932(+)$1	1	120	140	14.3255
(..(((........))))))	chr17:38436236-38436506(+)$1	1	188	208	14.9608
((((((........))))))	chr2:42670537-42670764(-)$1	1	81	101	15.4777
....((........))...)	chr10:73995340-73995560(+)$1	1	64	84	13.7610
.(((((........))))))	chr5:72877201-72877431(+)$1	1	181	201	14.3922
.(.(((........)))).)	chr1:36067374-36067612(-)$1	1	90	110	15.5623
((((((........))))))	chr17:20904651-20904879(-)$1	1	69	89	15.4777
((((((........))))))	chr9:14082628-14082863(-)$1	1	21	41	15.4777
(.((((........))))))	chr2:99935934-99936242(-)$1	1	193	213	13.7848
((((((........))))))	chr11:65421568-65421817(-)$1	1	196	216	15.4777
...(((........)))...	chr22:38879966-38880193(-)$1	1	30	50	14.8290
((((((........))))))	chr15:64447934-64448193(-)$1	1	12	32	15.4777
((((.(........).))))	chr1:245016920-245017151(-)$1	1	179	199	13.6910
((((((........))))))	chr11:88026776-88027022(-)$1	1	216	236	14.3829
((((((........))))))	chr12:54630044-54630332(-)$1	1	256	276	15.4777
((((((........))))).	chr6:72013739-72013993(+)$1	1	17	37	14.1554
((.(((........))).))	chr16:21666837-21667084(+)$1	1	105	125	15.2036
((((((........))))))	chr1:193059118-193059352(+)$1	1	114	134	14.3829
((((((........)))...	chr12:79985483-79985726(-)$1	1	151	171	13.4233
((((((........))))))	chr6:7287074-7287319(-)$1	1	66	86	15.4777
)(((((........))))).	chr9:131851302-131851536(+)$1	1	114	134	13.0833
((.(((........)))..)	chr2:36777276-36777540(+)$1	1	184	204	14.7381
((((((........))))))	chr8:98740562-98740804(+)$1	1	175	195	15.4777
((.(((........))).))	chr4:123819177-123819409(+)$1	1	95	115	14.8329
(((..(........)..)))	chr12:27181923-27182198(+)$1	1	237	257	13.7021
((((((........))))))	chr1:207967179-207967489(+)$1	1	226	246	14.3829
((((((........))))))	chr7:26230747-26231000(-)$1	1	74	94	15.2740
((((((........))))))	chr7:129805038-129805274(-)$1	1	134	154	15.6005
.(((((........))))).	chr1:162494288-162494530(+)$1	1	32	52	14.4843
((.(((........))).))	chr8:38961084-38961386(+)$1	1	138	158	15.4285
.(((((........))))))	chr6:7288925-7289183(-)$1	1	224	244	14.4116
..((((........)))).)	chr2:145146400-145146653(-)$1	1	47	67	14.4033
...(((........)))..)	chr2:70107435-70107675(+)$1	1	171	191	14.3725
.(((.(........))))..	chr3:133876513-133876748(-)$1	1	198	218	14.9063
((.(((........))).))	chr6:64286617-64286893(+)$1	1	202	222	15.4303
((((((........))))))	chr7:128409735-128409995(+)$1	1	26	46	15.6005
((((((........))))))	chr22:39910594-39910827(+)$1	1	186	206	15.4777
..((((........))))..	chr4:169848031-169848291(+)$1	1	216	236	14.3475
((((((........))))))	chr4:177251237-177251510(+)$1	1	36	56	15.4777
((((((........))))))	chr7:139249803-139250042(-)$1	1	81	101	15.6005
.(((((........))))).	chr4:57327136-57327366(+)$1	1	121	141	14.3062
(.((((........))))..	chr1:25168768-25169053(+)$1	1	29	49	14.1792
...(((........)))...	chr12:54632845-54633101(-)$1	1	58	78	15.8930
(.((((........)))).)	chr14:35180746-35180979(-)$1	1	118	138	14.4194
((((((........))))))	chr9:33112954-33113230(-)$1	1	143	163	15.4777
.(((.(........).))).	chr17:48939742-48940015(-)$1	1	156	176	14.9024
((..((........))...)	chr4:1205459-1205728(-)$1	1	23	43	14.2132
((((((........))))))	chr17:56168249-56168473(+)$1	1	123	143	14.3829
((.(((........))))))	chr4:100869462-100869699(-)$1	1	35	55	15.2908
(.((((........)))).)	chr5:40714944-40715178(-)$1	1	3	23	14.4194
(..(((........))))))	chr10:103544924-103545169(-)$1	1	7	27	15.4546
((((((........))))))	chr12:98928425-98928728(+)$1	1	114	134	14.3829
((((((........))))))	chr1:168044619-168044848(+)$1	1	93	113	14.3829
..((((........))))..	chr22:43266467-43266748(-)$1	1	160	180	14.6185
...(((........)))...	chr10:119766519-119766767(-)$1	1	76	96	15.7650
(..(((........)))..)	chr21:34930753-34931008(+)$1	1	220	240	15.4334
)(((((........).))))	chrX:46920408-46920660(+)$1	1	225	245	13.7467
..((((........))))..	chr5:41918716-41918944(+)$1	1	82	102	14.3288
((((((........))))))	chr5:1317870-1318120(-)$1	1	6	26	15.6005
(((.((........)).)))	chr15:67494801-67495034(-)$1	1	149	169	13.6070
((.(((........))).))	chr16:9211195-9211427(+)$1	1	73	93	15.2036
((((((........))))))	chr7:75957963-75958243(-)$1	1	43	63	15.2740
((((((........))))))	chr2:110374872-110375107(+)$1	1	58	78	14.3829

#PSSM
f : 0.20	g : 0.18	c : 0.12	d : 0.09	! : 0.07	= : 0.06	" : 0.06	[ : 0.04	e : 0.04	# : 0.03	$ : 0.03	i : 0.03	h : 0.01	
g : 0.18	f : 0.16	e : 0.15	! : 0.07	c : 0.07	[ : 0.06	= : 0.06	d : 0.04	" : 0.04	# : 0.03	$ : 0.03	i : 0.03	a : 0.01	h : 0.01	
g : 0.18	f : 0.15	d : 0.15	e : 0.12	[ : 0.12	! : 0.06	= : 0.06	# : 0.03	$ : 0.03	i : 0.03	c : 0.03	" : 0.01	
c : 0.27	g : 0.18	d : 0.15	f : 0.12	e : 0.10	= : 0.06	! : 0.03	i : 0.03	# : 0.01	[ : 0.01	
c : 0.24	g : 0.18	d : 0.13	f : 0.12	e : 0.10	= : 0.06	b : 0.04	[ : 0.04	i : 0.03	! : 0.01	
c : 0.24	g : 0.18	f : 0.12	d : 0.12	e : 0.10	a : 0.07	= : 0.06	b : 0.04	i : 0.03	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.24	g : 0.18	f : 0.12	d : 0.12	e : 0.10	a : 0.07	= : 0.06	b : 0.04	i : 0.03	
c : 0.26	g : 0.18	f : 0.12	d : 0.12	e : 0.10	= : 0.06	b : 0.04	] : 0.04	i : 0.03	2 : 0.01	
c : 0.27	g : 0.18	d : 0.15	f : 0.12	e : 0.10	= : 0.06	3 : 0.03	i : 0.03	2 : 0.01	] : 0.01	
g : 0.18	d : 0.16	f : 0.15	e : 0.12	] : 0.07	3 : 0.06	= : 0.06	2 : 0.04	c : 0.04	i : 0.03	a : 0.01	4 : 0.01	7 : 0.01	
g : 0.18	f : 0.16	e : 0.15	2 : 0.09	d : 0.07	3 : 0.07	] : 0.06	= : 0.06	c : 0.04	4 : 0.03	i : 0.03	7 : 0.01	
f : 0.18	g : 0.18	c : 0.12	d : 0.09	= : 0.06	2 : 0.06	3 : 0.06	] : 0.04	e : 0.04	b : 0.03	4 : 0.03	i : 0.03	7 : 0.01	: : 0.01	h : 0.01	

#score	961.7593916426998
#seq	65
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_UTR_m3_run1.txt

#BEAR
ff[bbqqqqqqqqbb]ff	chr2:26612520-26612758(+)$1	238	184	202	12.9679
cccccqqqqqqqqccc33	chr16:30792839-30793139(-)$1	300	91	109	13.6167
eeeeeqqqqqqqqeeeee	chr10:7838909-7839204(+)$1	295	225	243	15.7749
cc[bbqqqqqqqqbb]cc	chr5:133307777-133308125(-)$1	348	233	251	12.6705
eecccqqqqqqqqccc33	chr3:185634892-185635222(-)$1	330	268	286	14.2118
ddd[aqqqqqqqqa]ddd	chr1:10520803-10521063(-)$1	260	238	256	13.6533
d"""aqqqqqqqqa333d	chrX:38665137-38665406(+)$1	269	150	168	13.0671
gddddqqqqqqqqdddd]	chr1:43166404-43166817(+)$1	413	248	266	13.6078
fffffqqqqqqqqfffff	chr22:21305084-21305414(+)$1	330	218	236	13.8799
eeeeaqqqqqqqqa]eee	chr13:111291452-111291741(+)$1	289	96	114	15.4259
fffffqqqqqqqqfffff	chr12:58215383-58215655(-)$1	272	192	210	13.8799
gggggqqqqqqqqggggg	chr10:61551692-61551950(-)$1	258	70	88	14.0770
eeeeeqqqqqqqqeeeee	chr6:34558113-34558404(-)$1	291	244	262	15.7749
eeeeeqqqqqqqqeeeee	chr16:67671700-67672023(+)$1	323	250	268	15.7749
eeeeeqqqqqqqqeeeee	chr10:53457032-53457261(-)$1	229	15	33	15.7749
eeeeeqqqqqqqqeeeee	chr3:113438394-113438662(-)$1	268	20	38	15.7749
gggggqqqqqqqqggggg	chr18:19208977-19209476(+)$1	499	378	396	14.0770
eeeeeqqqqqqqqeeeee	chr12:53873357-53873777(+)$1	420	303	321	15.7749
fffffqqqqqqqqfffff	chr12:51566677-51566923(-)$1	246	122	140	13.8799
eeeeeqqqqqqqqeeeee	chr2:131807522-131807969(-)$1	447	250	268	15.7749
ee[bbqqqqqqqqbbeee	chr8:30643558-30643923(-)$1	365	250	268	14.0966
eeeeeqqqqqqqqeeeee	chr19:33203729-33204110(+)$1	381	288	306	15.7749
eeebbqqqqqqqqbb]ee	chr17:8108506-8108790(-)$1	284	117	135	14.0540
eeeeeqqqqqqqqeeeee	chr22:29190954-29191260(-)$1	306	153	171	15.7749
eeeeeqqqqqqqqeeeee	chr20:55093524-55093982(+)$1	458	303	321	15.7749
eeeeeqqqqqqqqeeeee	chr4:146048858-146049099(+)$1	241	163	181	15.7749
eeeeeqqqqqqqqeeeee	chr14:93704173-93704439(-)$1	266	206	224	15.7749
ccc[aqqqqqqqqa]ccc	chr6:26158438-26158929(+)$1	491	466	484	13.6885
eeeeeqqqqqqqqeeeee	chr6:116599220-116599645(-)$1	425	273	291	15.7749
eeeeeqqqqqqqqeeeee	chrX:77381217-77381636(+)$1	419	303	321	15.7749
eee[aqqqqqqqqa]eee	chr1:2240919-2241146(+)$1	227	155	173	15.2952
!!cccqqqqqqqqcccee	chr1:28607341-28607739(+)$1	398	361	379	14.2915
eeeeeqqqqqqqqeeeee	chr3:196080876-196081195(-)$1	319	198	216	15.7749
eeeeeqqqqqqqqeeeee	chr12:124499697-124500061(+)$1	364	212	230	15.7749
eeeeeqqqqqqqqeeeee	chr9:91931187-91931617(+)$1	430	397	415	15.7749
b[cccqqqqqqqqccc]b	chr1:67876597-67876932(-)$1	335	34	52	13.0992
!!cccqqqqqqqqccc33	chr10:18964896-18965189(+)$1	293	241	259	13.7247
[ddddqqqqqqqqddddc	chr12:56622871-56623265(+)$1	394	317	335	13.5264
eeeeeqqqqqqqqeeeee	chr20:33890518-33890872(-)$1	354	76	94	15.7749
gggggqqqqqqqqggggg	chr10:62554043-62554391(+)$1	348	142	160	14.0770
fffffqqqqqqqqfffff	chr19:42799550-42799968(+)$1	418	346	364	13.8799
ee[bbqqqqqqqqbb]ee	chr17:33678625-33679002(-)$1	377	273	291	13.8725
fddddqqqqqqqqdddd6	chr19:47278632-47279104(-)$1	472	155	173	12.9966
eee[aqqqqqqqqa]eee	chr16:31202640-31203058(+)$1	418	255	273	15.2952
fffffqqqqqqqqfffff	chr12:122498525-122498830(+)$1	305	65	83	13.8799
eeeeeqqqqqqqqeeeee	chr7:100274215-100274522(+)$1	307	167	185	15.7749
[ddddqqqqqqqqdddd]	chr17:27049640-27049964(+)$1	324	164	182	13.5881
ccc[aqqqqqqqqa]ccc	chr22:41626907-41627150(+)$1	243	92	110	13.6885
[ddddqqqqqqqqddddf	chr5:56218081-56218378(-)$1	297	203	221	13.6215
gggggqqqqqqqqggggg	chr8:22880254-22880576(-)$1	322	142	160	14.0770
fffffqqqqqqqqfffff	chr7:99054349-99054846(+)$1	497	158	176	13.8799
eeeeeqqqqqqqqeeeee	chr3:185635080-185635529(-)$1	449	266	284	15.7749
gggggqqqqqqqqggggg	chrX:24004014-24004504(-)$1	490	448	466	14.0770
fffffqqqqqqqqfffff	chr1:113455831-113456241(-)$1	410	279	297	13.8799
gddddqqqqqqqqdddd]	chr11:27516563-27516839(-)$1	276	230	248	13.6078
eeeeeqqqqqqqqeeeee	chr11:27519929-27520208(-)$1	279	56	74	15.7749
eecccqqqqqqqqccc]e	chr2:201687826-201688223(+)$1	397	296	314	14.5080
fffffqqqqqqqqfffff	chr17:26888461-26888713(-)$1	252	16	34	13.8799
ggggaqqqqqqqqa]ggg	chr5:14694650-14694919(+)$1	269	224	242	14.1196
fffffqqqqqqqqfffff	chr12:54633466-54633937(-)$1	471	115	133	13.8799
a[cccqqqqqqqqccca4	chr12:49663510-49663859(+)$1	349	31	49	13.5634
eeeeeqqqqqqqqeeeee	chr10:38408293-38408555(+)$1	262	232	250	15.7749
:ddddqqqqqqqqdddde	chr19:1980507-1980811(+)$1	304	222	240	12.7277
eeeeeqqqqqqqqeeeee	chr13:113831980-113832234(-)$1	254	150	168	15.7749
e[cccqqqqqqqqcccee	chr19:7989288-7989551(-)$1	263	168	186	14.5546
eeeeeqqqqqqqqeeeee	chr3:23959245-23959622(+)$1	377	278	296	15.7749
eeeeeqqqqqqqqeeeee	chr17:16285703-16286138(+)$1	435	288	306	15.7749

#otherMatches

#Seq PSSM
GUUCCUGAGAUUUGGUGC	chr2:26612520-26612758(+)$1	238	184	202	12.9679
CUCCCUGUGAAAUGGGUC	chr16:30792839-30793139(-)$1	300	91	109	13.6167
UCUUUAGGUAAGGGAAGA	chr10:7838909-7839204(+)$1	295	225	243	15.7749
ACUUAUUCCUUCUUGUGU	chr5:133307777-133308125(-)$1	348	233	251	12.6705
UUAGAACUAAAAAUCUUA	chr3:185634892-185635222(-)$1	330	268	286	14.2118
aucacgaggucaggagau	chr1:10520803-10521063(-)$1	260	238	256	13.6533
GAAUCUCCUCCUUGCUCU	chrX:38665137-38665406(+)$1	269	150	168	13.0671
CGCUCCCGAGGCUGAGCA	chr1:43166404-43166817(+)$1	413	248	266	13.6078
UUGUUUUGCCAGUGAUAA	chr22:21305084-21305414(+)$1	330	218	236	13.8799
GGAGCUCUGAGACGCCUC	chr13:111291452-111291741(+)$1	289	96	114	15.4259
UCUUGAAGGAAAGCAGGA	chr12:58215383-58215655(-)$1	272	192	210	13.8799
UUAGAAUGUGUUAUUUGA	chr10:61551692-61551950(-)$1	258	70	88	14.0770
UGUGAAUGCUGAAUCACA	chr6:34558113-34558404(-)$1	291	244	262	15.7749
UGCUGUCUGAUGUUAGCA	chr16:67671700-67672023(+)$1	323	250	268	15.7749
AGUUACUUUAAAAUAACU	chr10:53457032-53457261(-)$1	229	15	33	15.7749
GGACUAUCUAAUCAGUCC	chr3:113438394-113438662(-)$1	268	20	38	15.7749
AGguuaaaauaaaagccu	chr18:19208977-19209476(+)$1	499	378	396	14.0770
CCUUUUAUCCCUCAAAGG	chr12:53873357-53873777(+)$1	420	303	321	15.7749
UUUCCAGGCCGUGGGGGG	chr12:51566677-51566923(-)$1	246	122	140	13.8799
GUGGGCUGCACCCCCCAC	chr2:131807522-131807969(-)$1	447	250	268	15.7749
CAACAGUAAUCUAUGUGU	chr8:30643558-30643923(-)$1	365	250	268	14.0966
GUUUCCCAAAUUAGAAAU	chr19:33203729-33204110(+)$1	381	288	306	15.7749
CCCCAGAGAUGAUUGAGG	chr17:8108506-8108790(-)$1	284	117	135	14.0540
GCAGAGAAGCCUGUCUGU	chr22:29190954-29191260(-)$1	306	153	171	15.7749
CUAGCUAAAUACUGUUAG	chr20:55093524-55093982(+)$1	458	303	321	15.7749
GUAUUAUAUUCACGGUAC	chr4:146048858-146049099(+)$1	241	163	181	15.7749
GCCUUCAAUGCUAAAGGC	chr14:93704173-93704439(-)$1	266	206	224	15.7749
AAUCUUUAAUGUUACGUU	chr6:26158438-26158929(+)$1	491	466	484	13.6885
CCCUGUUUAUUCCCAGGG	chr6:116599220-116599645(-)$1	425	273	291	15.7749
UUCAAGAUCCCAUUUGAA	chrX:77381217-77381636(+)$1	419	303	321	15.7749
CCCCCUCCUCCCUGUGGG	chr1:2240919-2241146(+)$1	227	155	173	15.2952
CCGGGACUGACACUCCAG	chr1:28607341-28607739(+)$1	398	361	379	14.2915
GGGUUGAUAUAAAGGCCC	chr3:196080876-196081195(-)$1	319	198	216	15.7749
UCAGAAAAUAUUAUUUGA	chr12:124499697-124500061(+)$1	364	212	230	15.7749
ACUUUUGUUCAAUAAAGU	chr9:91931187-91931617(+)$1	430	397	415	15.7749
AAGCUUUCAAGAUAGCCU	chr1:67876597-67876932(-)$1	335	34	52	13.0992
CAUAGCAUUUUUACUACC	chr10:18964896-18965189(+)$1	293	241	259	13.7247
UCAGGACCCUCUGCCUGC	chr12:56622871-56623265(+)$1	394	317	335	13.5264
GAGGACCAGCCCCUCCUC	chr20:33890518-33890872(-)$1	354	76	94	15.7749
AUAUUUUUCUACUGGUAU	chr10:62554043-62554391(+)$1	348	142	160	14.0770
UUCUUACUGUGCCGAGAA	chr19:42799550-42799968(+)$1	418	346	364	13.8799
AUAGUGAAUAUUAAUGGU	chr17:33678625-33679002(-)$1	377	273	291	13.8725
CUCCAAAAUUACGUGGAC	chr19:47278632-47279104(-)$1	472	155	173	12.9966
GUUCCCAUUAAAAGUGAC	chr16:31202640-31203058(+)$1	418	255	273	15.2952
GGUGCAUAUUCAGGUACC	chr12:122498525-122498830(+)$1	305	65	83	13.8799
UGGCAAAGAUCUAUGCCA	chr7:100274215-100274522(+)$1	307	167	185	15.7749
GACAACAACACACUUGUG	chr17:27049640-27049964(+)$1	324	164	182	13.5881
GCUACCUGCUCCUGAAGC	chr22:41626907-41627150(+)$1	243	92	110	13.6885
GUUUUGGCAUUUGAAGAU	chr5:56218081-56218378(-)$1	297	203	221	13.6215
UGAGGAAGUUGGGCCUCA	chr8:22880254-22880576(-)$1	322	142	160	14.0770
GUCAUUCAAAGCUGUGGC	chr7:99054349-99054846(+)$1	497	158	176	13.8799
CAGUCUAAAUUUUGACUG	chr3:185635080-185635529(-)$1	449	266	284	15.7749
AAAUACAUUAUUUUAUUU	chrX:24004014-24004504(-)$1	490	448	466	14.0770
UGGCAUAUGUUUCUGCUA	chr1:113455831-113456241(-)$1	410	279	297	13.8799
CAUUUAAUAGAAGAAAUG	chr11:27516563-27516839(-)$1	276	230	248	13.6078
AAGUUUUCCUUGUGACUU	chr11:27519929-27520208(-)$1	279	56	74	15.7749
GCUACCCAUCUAUGUAUG	chr2:201687826-201688223(+)$1	397	296	314	14.5080
GGCUUUCUUUUCUGAGCC	chr17:26888461-26888713(-)$1	252	16	34	13.8799
UGUUCUUCACUGUGAAAU	chr5:14694650-14694919(+)$1	269	224	242	14.1196
GUUUUUGAUUUUUAAAAC	chr12:54633466-54633937(-)$1	471	115	133	13.8799
GCUGGUCACUCACCCACU	chr12:49663510-49663859(+)$1	349	31	49	13.5634
UAGCAUUUUACUUUGUUA	chr10:38408293-38408555(+)$1	262	232	250	15.7749
AGGCCGUGCCCCAGGCCU	chr19:1980507-1980811(+)$1	304	222	240	12.7277
UUUGAAUGUGUUAUCAAA	chr13:113831980-113832234(-)$1	254	150	168	15.7749
uuacugcaugccaaguag	chr19:7989288-7989551(-)$1	263	168	186	14.5546
UACGUGAUCGACUGCGUG	chr3:23959245-23959622(+)$1	377	278	296	15.7749
AUUACAAGUUUCAGUAAU	chr17:16285703-16286138(+)$1	435	288	306	15.7749

#DB
((.((........)).))	chr2:26612520-26612758(+)$1	1	184	202	12.9679
(((((........)))..	chr16:30792839-30793139(-)$1	1	91	109	13.6167
(((((........)))))	chr10:7838909-7839204(+)$1	1	225	243	15.7749
((.((........)).))	chr5:133307777-133308125(-)$1	1	233	251	12.6705
(((((........)))..	chr3:185634892-185635222(-)$1	1	268	286	14.2118
(((.(........).)))	chr1:10520803-10521063(-)$1	1	238	256	13.6533
(...(........)...)	chrX:38665137-38665406(+)$1	1	150	168	13.0671
(((((........)))).	chr1:43166404-43166817(+)$1	1	248	266	13.6078
(((((........)))))	chr22:21305084-21305414(+)$1	1	218	236	13.8799
(((((........).)))	chr13:111291452-111291741(+)$1	1	96	114	15.4259
(((((........)))))	chr12:58215383-58215655(-)$1	1	192	210	13.8799
(((((........)))))	chr10:61551692-61551950(-)$1	1	70	88	14.0770
(((((........)))))	chr6:34558113-34558404(-)$1	1	244	262	15.7749
(((((........)))))	chr16:67671700-67672023(+)$1	1	250	268	15.7749
(((((........)))))	chr10:53457032-53457261(-)$1	1	15	33	15.7749
(((((........)))))	chr3:113438394-113438662(-)$1	1	20	38	15.7749
(((((........)))))	chr18:19208977-19209476(+)$1	1	378	396	14.0770
(((((........)))))	chr12:53873357-53873777(+)$1	1	303	321	15.7749
(((((........)))))	chr12:51566677-51566923(-)$1	1	122	140	13.8799
(((((........)))))	chr2:131807522-131807969(-)$1	1	250	268	15.7749
((.((........)))))	chr8:30643558-30643923(-)$1	1	250	268	14.0966
(((((........)))))	chr19:33203729-33204110(+)$1	1	288	306	15.7749
(((((........)).))	chr17:8108506-8108790(-)$1	1	117	135	14.0540
(((((........)))))	chr22:29190954-29191260(-)$1	1	153	171	15.7749
(((((........)))))	chr20:55093524-55093982(+)$1	1	303	321	15.7749
(((((........)))))	chr4:146048858-146049099(+)$1	1	163	181	15.7749
(((((........)))))	chr14:93704173-93704439(-)$1	1	206	224	15.7749
(((.(........).)))	chr6:26158438-26158929(+)$1	1	466	484	13.6885
(((((........)))))	chr6:116599220-116599645(-)$1	1	273	291	15.7749
(((((........)))))	chrX:77381217-77381636(+)$1	1	303	321	15.7749
(((.(........).)))	chr1:2240919-2241146(+)$1	1	155	173	15.2952
..(((........)))))	chr1:28607341-28607739(+)$1	1	361	379	14.2915
(((((........)))))	chr3:196080876-196081195(-)$1	1	198	216	15.7749
(((((........)))))	chr12:124499697-124500061(+)$1	1	212	230	15.7749
(((((........)))))	chr9:91931187-91931617(+)$1	1	397	415	15.7749
(.(((........))).)	chr1:67876597-67876932(-)$1	1	34	52	13.0992
..(((........)))..	chr10:18964896-18965189(+)$1	1	241	259	13.7247
.((((........)))))	chr12:56622871-56623265(+)$1	1	317	335	13.5264
(((((........)))))	chr20:33890518-33890872(-)$1	1	76	94	15.7749
(((((........)))))	chr10:62554043-62554391(+)$1	1	142	160	14.0770
(((((........)))))	chr19:42799550-42799968(+)$1	1	346	364	13.8799
((.((........)).))	chr17:33678625-33679002(-)$1	1	273	291	13.8725
(((((........)))).	chr19:47278632-47279104(-)$1	1	155	173	12.9966
(((.(........).)))	chr16:31202640-31203058(+)$1	1	255	273	15.2952
(((((........)))))	chr12:122498525-122498830(+)$1	1	65	83	13.8799
(((((........)))))	chr7:100274215-100274522(+)$1	1	167	185	15.7749
.((((........)))).	chr17:27049640-27049964(+)$1	1	164	182	13.5881
(((.(........).)))	chr22:41626907-41627150(+)$1	1	92	110	13.6885
.((((........)))))	chr5:56218081-56218378(-)$1	1	203	221	13.6215
(((((........)))))	chr8:22880254-22880576(-)$1	1	142	160	14.0770
(((((........)))))	chr7:99054349-99054846(+)$1	1	158	176	13.8799
(((((........)))))	chr3:185635080-185635529(-)$1	1	266	284	15.7749
(((((........)))))	chrX:24004014-24004504(-)$1	1	448	466	14.0770
(((((........)))))	chr1:113455831-113456241(-)$1	1	279	297	13.8799
(((((........)))).	chr11:27516563-27516839(-)$1	1	230	248	13.6078
(((((........)))))	chr11:27519929-27520208(-)$1	1	56	74	15.7749
(((((........))).)	chr2:201687826-201688223(+)$1	1	296	314	14.5080
(((((........)))))	chr17:26888461-26888713(-)$1	1	16	34	13.8799
(((((........).)))	chr5:14694650-14694919(+)$1	1	224	242	14.1196
(((((........)))))	chr12:54633466-54633937(-)$1	1	115	133	13.8799
(.(((........)))).	chr12:49663510-49663859(+)$1	1	31	49	13.5634
(((((........)))))	chr10:38408293-38408555(+)$1	1	232	250	15.7749
.((((........))))(	chr19:1980507-1980811(+)$1	1	222	240	12.7277
(((((........)))))	chr13:113831980-113832234(-)$1	1	150	168	15.7749
(.(((........)))))	chr19:7989288-7989551(-)$1	1	168	186	14.5546
(((((........)))))	chr3:23959245-23959622(+)$1	1	278	296	15.7749
(((((........)))))	chr17:16285703-16286138(+)$1	1	288	306	15.7749

#PSSM
e : 0.50	f : 0.16	g : 0.11	c : 0.05	[ : 0.04	d : 0.02	! : 0.02	b : 0.01	a : 0.01	: : 0.01	
e : 0.49	f : 0.14	d : 0.11	g : 0.08	c : 0.05	[ : 0.04	! : 0.02	" : 0.01	
e : 0.43	c : 0.14	f : 0.13	d : 0.11	g : 0.08	[ : 0.05	" : 0.01	
e : 0.38	f : 0.13	c : 0.11	d : 0.10	g : 0.08	b : 0.07	[ : 0.07	" : 0.01	
e : 0.37	f : 0.13	c : 0.11	a : 0.11	d : 0.10	b : 0.07	g : 0.07	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
e : 0.37	f : 0.13	c : 0.11	a : 0.11	d : 0.10	b : 0.07	g : 0.07	
e : 0.37	f : 0.13	c : 0.11	] : 0.10	d : 0.10	b : 0.07	g : 0.07	3 : 0.01	
e : 0.43	c : 0.14	f : 0.13	d : 0.11	g : 0.08	] : 0.05	3 : 0.01	
e : 0.49	f : 0.14	d : 0.11	g : 0.08	3 : 0.05	c : 0.04	] : 0.02	a : 0.01	
e : 0.52	f : 0.16	g : 0.08	c : 0.05	3 : 0.04	] : 0.04	d : 0.02	b : 0.01	6 : 0.01	4 : 0.01	

#score	976.8214782176269
#seq	67
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_UTR_m3_run1.txt

#BEAR
eeeeemmmmeeeee	chr22:43015572-43015823(-)$1	251	9	23	10.4803
eeeeemmmmeeeee	chr1:228879957-228880259(+)$1	302	167	181	10.4803
eeeeemmmmeeeee	chr11:129996534-129996781(+)$1	247	187	201	10.4803
eeeeeooooooeee	chr19:41313687-41313935(+)$1	248	39	53	9.8783
eeeeemmmmeeeee	chr19:4039142-4039366(+)$1	224	15	29	10.4803
eeeeeooooooeee	chr22:42556642-42556870(-)$1	228	197	211	9.8783
eeeeennnnneeee	chr11:102269138-102269383(-)$1	245	121	135	9.1040
eeeeemmmmeeeee	chr8:116424556-116424785(-)$1	229	28	42	10.4803
eeeeennnnneeee	chr11:111956696-111956971(-)$1	275	235	249	9.1040
[eeeeellleeeee	chr18:57567134-57567384(+)$1	250	216	230	9.5278
eeeeemmmmeeeee	chr5:137891268-137891542(-)$1	274	221	235	10.4803
eeeeemmmmeeeee	chr6:34253595-34253844(-)$1	249	19	33	10.4803
eeeeeooooooeee	chr6:110931839-110932063(-)$1	224	198	212	9.8783
eeeeemmmmeeeee	chrX:73805296-73805553(-)$1	257	93	107	10.4803
eeeeeooooooeee	chr1:90184760-90184988(+)$1	228	110	124	9.8783
eeeeeooooooeee	chr2:224623066-224623295(-)$1	229	189	203	9.8783
eeeeennnnneeee	chr17:33679750-33680045(-)$1	295	229	243	9.1040
eeeeemmmmeeeee	chr11:65622516-65622745(-)$1	229	202	216	10.4803
ceeeeellleeeee	chr9:125620908-125621151(-)$1	243	194	208	9.4210
eeeeemmmmeeeee	chr12:72181237-72181462(+)$1	225	21	35	10.4803
eeeeemmmmeeeee	chr19:46190634-46190971(-)$1	337	168	182	10.4803
eeeeeooooooeee	chr7:75957563-75957804(-)$1	241	85	99	9.8783
eeeee4444eeeee	chr16:58741512-58741741(-)$1	229	122	136	8.8211
eeeeemmmmeeeee	chr8:64124438-64124677(+)$1	239	76	90	10.4803
eeeeennnnneeee	chr22:44369038-44369267(+)$1	229	210	224	9.1040
eeeeemmmmeeeee	chr3:121382917-121383139(-)$1	222	158	172	10.4803
eeeeeooooooeee	chr8:37917471-37917825(+)$1	354	58	72	9.8783
eeeeemmmmeeeee	chr1:40033362-40033618(-)$1	256	226	240	10.4803
eeeeemmmmeeeee	chr17:7144023-7144264(-)$1	241	55	69	10.4803
eeeeennnnneeee	chrX:123234514-123234747(+)$1	233	115	129	9.1040
eeeeemmmmeeeee	chrX:102471687-102471914(+)$1	227	31	45	10.4803
eeeeennnnneeee	chr17:18639251-18639488(+)$1	237	199	213	9.1040
[eeeeellleeeee	chrX:84527671-84527932(+)$1	261	42	56	9.5278
eeeeennnnneeee	chr22:35820229-35820481(+)$1	252	169	183	9.1040
eeeeemmmmeeeee	chrX:153213574-153213840(-)$1	266	61	75	10.4803
eeeee4444eeeee	chr13:53049816-53050040(+)$1	224	190	204	8.8211
Feeeeellleeeee	chr10:98280695-98280966(-)$1	271	45	59	9.2152
eeeeemmmmeeeee	chrX:107328033-107328269(-)$1	236	17	31	10.4803
eeeeemmmmeeeee	chrX:106894057-106894301(+)$1	244	43	57	10.4803
eeeeeooooooeee	chr9:73002163-73002431(-)$1	268	165	179	9.8783
eeeeemmmmeeeee	chr3:107526602-107526825(+)$1	223	110	124	10.4803
:eeeeellleeeee	chr20:34257032-34257271(-)$1	239	56	70	8.5347
eeeeeooooooeee	chrX:48770443-48770667(-)$1	224	15	29	9.8783
[eeeeellleeeee	chr2:191799578-191799804(+)$1	226	175	189	9.5278
[eeeeellleeeee	chr5:33461714-33461949(+)$1	235	94	108	9.5278
Feeeeellleeeee	chr7:100470838-100471075(+)$1	237	13	27	9.2152
eeeeeooooooeee	chr4:7062148-7062404(-)$1	256	123	137	9.8783
eeeeemmmmeeeee	chr12:68043536-68043765(+)$1	229	30	44	10.4803
eeeeeooooooeee	chr16:24979956-24980180(-)$1	224	152	166	9.8783
eeeeemmmmeeeee	chr2:208627545-208627778(-)$1	233	183	197	10.4803
eeeee4444eeeee	chr4:53462369-53462627(-)$1	258	231	245	8.8211
eeeeemmmmeeeee	chr1:228581919-228582198(-)$1	279	250	264	10.4803
eeeeemmmmeeeee	chr22:39911981-39912239(+)$1	258	6	20	10.4803
eeeeemmmmeeeee	chrX:149931698-149931929(+)$1	231	193	207	10.4803
eeeeellleeeee3	chr19:12739932-12740156(+)$1	224	138	152	8.9043
eeeeeooooooeee	chr17:663058-663301(-)$1	243	43	57	9.8783
Feeeeellleeeee	chr13:27261460-27261754(+)$1	294	266	280	9.2152
eeeeeooooooeee	chr19:8028104-8028333(-)$1	229	123	137	9.8783
eeeeemmmmeeeee	chr3:197680814-197681044(+)$1	230	94	108	10.4803
eeeeeooooooeee	chr12:22837914-22838140(+)$1	226	111	125	9.8783
eeeeemmmmeeeee	chrX:84526988-84527219(+)$1	231	170	184	10.4803
:eeeeellleeeee	chr14:102547690-102547942(-)$1	252	151	165	8.5347
eeeeemmmmeeeee	chr10:105049528-105049773(+)$1	245	13	27	10.4803
eeeeellleeeeed	chr20:33866655-33866998(-)$1	343	21	35	9.0770
eeeeeooooooeee	chr21:37445093-37445316(+)$1	223	203	217	9.8783

#otherMatches

#Seq PSSM
GUGGGCCACCCCAC	chr22:43015572-43015823(-)$1	251	9	23	10.4803
AAGGAAACUUCCUU	chr1:228879957-228880259(+)$1	302	167	181	10.4803
CAGGGUAAACCUUG	chr11:129996534-129996781(+)$1	247	187	201	10.4803
AGGUGUCCAAGUAC	chr19:41313687-41313935(+)$1	248	39	53	9.8783
UUUGUAUAAACAGA	chr19:4039142-4039366(+)$1	224	15	29	10.4803
ACUAUUUAUUUAUG	chr22:42556642-42556870(-)$1	228	197	211	9.8783
AUGCCAUCUGGGCA	chr11:102269138-102269383(-)$1	245	121	135	9.1040
AAUAUUAAUGUAUU	chr8:116424556-116424785(-)$1	229	28	42	10.4803
GAGAACUGAUUUCU	chr11:111956696-111956971(-)$1	275	235	249	9.1040
CCAGUUGGAGGCUG	chr18:57567134-57567384(+)$1	250	216	230	9.5278
AGUACUGCUGUACU	chr5:137891268-137891542(-)$1	274	221	235	10.4803
ACAUUUUUAAAUGU	chr6:34253595-34253844(-)$1	249	19	33	10.4803
ACAAGUAAUAUUUU	chr6:110931839-110932063(-)$1	224	198	212	9.8783
GACCUUGAAAGGUC	chrX:73805296-73805553(-)$1	257	93	107	10.4803
UGGAGCUCAAACUC	chr1:90184760-90184988(+)$1	228	110	124	9.8783
UGCAAUUUUUUUUG	chr2:224623066-224623295(-)$1	229	189	203	9.8783
CAUCCCCACUGGGU	chr17:33679750-33680045(-)$1	295	229	243	9.1040
CCCCAGUUGUGGGG	chr11:65622516-65622745(-)$1	229	202	216	10.4803
UUUACCAAGGGUAA	chr9:125620908-125621151(-)$1	243	194	208	9.4210
UAAUAAAGCUAUUA	chr12:72181237-72181462(+)$1	225	21	35	10.4803
CUGUCUGUUGACAG	chr19:46190634-46190971(-)$1	337	168	182	10.4803
UUUUCCUCCCCGAA	chr7:75957563-75957804(-)$1	241	85	99	9.8783
ACUGCAGAAAUGAU	chr16:58741512-58741741(-)$1	229	122	136	8.8211
AUAUUGCAAAAUAU	chr8:64124438-64124677(+)$1	239	76	90	10.4803
GGUGGCUUUUUCAC	chr22:44369038-44369267(+)$1	229	210	224	9.1040
GGUUUCAAUAAACC	chr3:121382917-121383139(-)$1	222	158	172	10.4803
UAUGAAAGUGAUCA	chr8:37917471-37917825(+)$1	354	58	72	9.8783
AGUGGUAUUCCAUU	chr1:40033362-40033618(-)$1	256	226	240	10.4803
CAUUGCCUACAGUG	chr17:7144023-7144264(-)$1	241	55	69	10.4803
CAAGUAAACAAUUU	chrX:123234514-123234747(+)$1	233	115	129	9.1040
CUUAUUUUUGUAAG	chrX:102471687-102471914(+)$1	227	31	45	10.4803
ugugcuuccugcac	chr17:18639251-18639488(+)$1	237	199	213	9.1040
UGAUUGUUCUAGUC	chrX:84527671-84527932(+)$1	261	42	56	9.5278
GUAGUGUCCUGCUG	chr22:35820229-35820481(+)$1	252	169	183	9.1040
GCCUGUCCUCAGGC	chrX:153213574-153213840(-)$1	266	61	75	10.4803
GUGGUUUAACUUUU	chr13:53049816-53050040(+)$1	224	190	204	8.8211
UGUGUGUGUCAUAC	chr10:98280695-98280966(-)$1	271	45	59	9.2152
GGCCAAAGGUGGCC	chrX:107328033-107328269(-)$1	236	17	31	10.4803
GGUAUCGUAGUGCC	chrX:106894057-106894301(+)$1	244	43	57	10.4803
CUGUGGCCUCGCAC	chr9:73002163-73002431(-)$1	268	165	179	9.8783
ACAAACCUUUUUGU	chr3:107526602-107526825(+)$1	223	110	124	10.4803
UUGGUCAGGGACCA	chr20:34257032-34257271(-)$1	239	56	70	8.5347
UGGGGCGCUCCCUC	chrX:48770443-48770667(-)$1	224	15	29	9.8783
UCUUGAUAUUCAAG	chr2:191799578-191799804(+)$1	226	175	189	9.5278
GGGAGUUAAACUCU	chr5:33461714-33461949(+)$1	235	94	108	9.5278
GGCACAUCUUGUGC	chr7:100470838-100471075(+)$1	237	13	27	9.2152
UUUUAAACAAAUAA	chr4:7062148-7062404(-)$1	256	123	137	9.8783
UGGCUUCCAGGCCG	chr12:68043536-68043765(+)$1	229	30	44	10.4803
UCUUUGUUGAGAAG	chr16:24979956-24980180(-)$1	224	152	166	9.8783
GAUGAGUUUUUGUU	chr2:208627545-208627778(-)$1	233	183	197	10.4803
AUGCAAACUUUGGG	chr4:53462369-53462627(-)$1	258	231	245	8.8211
CUGUGACCCCACAG	chr1:228581919-228582198(-)$1	279	250	264	10.4803
UAGGGUUAACCUUG	chr22:39911981-39912239(+)$1	258	6	20	10.4803
CGCCUCUUGGGGCG	chrX:149931698-149931929(+)$1	231	193	207	10.4803
AUAGAAACUCUAUA	chr19:12739932-12740156(+)$1	224	138	152	8.9043
UCUGAUGUAAUUUA	chr17:663058-663301(-)$1	243	43	57	9.8783
UCCCAGGUGCUGGG	chr13:27261460-27261754(+)$1	294	266	280	9.2152
GACAUGUUCAAAUG	chr19:8028104-8028333(-)$1	229	123	137	9.8783
CCAGAGUCAUCUGG	chr3:197680814-197681044(+)$1	230	94	108	10.4803
UCAAAUCUAUUUUU	chr12:22837914-22838140(+)$1	226	111	125	9.8783
UUUCUGAGAAGAGA	chrX:84526988-84527219(+)$1	231	170	184	10.4803
GUAACAUGAUGUUA	chr14:102547690-102547942(-)$1	252	151	165	8.5347
UUUUGUCACCAGAA	chr10:105049528-105049773(+)$1	245	13	27	10.4803
GGGCUCCUGGCUCU	chr20:33866655-33866998(-)$1	343	21	35	9.0770
AUUAGCACUCACUA	chr21:37445093-37445316(+)$1	223	203	217	9.8783

#DB
(((((....)))))	chr22:43015572-43015823(-)$1	1	9	23	10.4803
(((((....)))))	chr1:228879957-228880259(+)$1	1	167	181	10.4803
(((((....)))))	chr11:129996534-129996781(+)$1	1	187	201	10.4803
(((((......)))	chr19:41313687-41313935(+)$1	1	39	53	9.8783
(((((....)))))	chr19:4039142-4039366(+)$1	1	15	29	10.4803
(((((......)))	chr22:42556642-42556870(-)$1	1	197	211	9.8783
(((((.....))))	chr11:102269138-102269383(-)$1	1	121	135	9.1040
(((((....)))))	chr8:116424556-116424785(-)$1	1	28	42	10.4803
(((((.....))))	chr11:111956696-111956971(-)$1	1	235	249	9.1040
.(((((...)))))	chr18:57567134-57567384(+)$1	1	216	230	9.5278
(((((....)))))	chr5:137891268-137891542(-)$1	1	221	235	10.4803
(((((....)))))	chr6:34253595-34253844(-)$1	1	19	33	10.4803
(((((......)))	chr6:110931839-110932063(-)$1	1	198	212	9.8783
(((((....)))))	chrX:73805296-73805553(-)$1	1	93	107	10.4803
(((((......)))	chr1:90184760-90184988(+)$1	1	110	124	9.8783
(((((......)))	chr2:224623066-224623295(-)$1	1	189	203	9.8783
(((((.....))))	chr17:33679750-33680045(-)$1	1	229	243	9.1040
(((((....)))))	chr11:65622516-65622745(-)$1	1	202	216	10.4803
)(((((...)))))	chr9:125620908-125621151(-)$1	1	194	208	9.4210
(((((....)))))	chr12:72181237-72181462(+)$1	1	21	35	10.4803
(((((....)))))	chr19:46190634-46190971(-)$1	1	168	182	10.4803
(((((......)))	chr7:75957563-75957804(-)$1	1	85	99	9.8783
)))))....)))))	chr16:58741512-58741741(-)$1	1	122	136	8.8211
(((((....)))))	chr8:64124438-64124677(+)$1	1	76	90	10.4803
(((((.....))))	chr22:44369038-44369267(+)$1	1	210	224	9.1040
(((((....)))))	chr3:121382917-121383139(-)$1	1	158	172	10.4803
(((((......)))	chr8:37917471-37917825(+)$1	1	58	72	9.8783
(((((....)))))	chr1:40033362-40033618(-)$1	1	226	240	10.4803
(((((....)))))	chr17:7144023-7144264(-)$1	1	55	69	10.4803
(((((.....))))	chrX:123234514-123234747(+)$1	1	115	129	9.1040
(((((....)))))	chrX:102471687-102471914(+)$1	1	31	45	10.4803
(((((.....))))	chr17:18639251-18639488(+)$1	1	199	213	9.1040
.(((((...)))))	chrX:84527671-84527932(+)$1	1	42	56	9.5278
(((((.....))))	chr22:35820229-35820481(+)$1	1	169	183	9.1040
(((((....)))))	chrX:153213574-153213840(-)$1	1	61	75	10.4803
)))))....)))))	chr13:53049816-53050040(+)$1	1	190	204	8.8211
((((((...)))))	chr10:98280695-98280966(-)$1	1	45	59	9.2152
(((((....)))))	chrX:107328033-107328269(-)$1	1	17	31	10.4803
(((((....)))))	chrX:106894057-106894301(+)$1	1	43	57	10.4803
(((((......)))	chr9:73002163-73002431(-)$1	1	165	179	9.8783
(((((....)))))	chr3:107526602-107526825(+)$1	1	110	124	10.4803
.(((((...)))))	chr20:34257032-34257271(-)$1	1	56	70	8.5347
(((((......)))	chrX:48770443-48770667(-)$1	1	15	29	9.8783
.(((((...)))))	chr2:191799578-191799804(+)$1	1	175	189	9.5278
.(((((...)))))	chr5:33461714-33461949(+)$1	1	94	108	9.5278
((((((...)))))	chr7:100470838-100471075(+)$1	1	13	27	9.2152
(((((......)))	chr4:7062148-7062404(-)$1	1	123	137	9.8783
(((((....)))))	chr12:68043536-68043765(+)$1	1	30	44	10.4803
(((((......)))	chr16:24979956-24980180(-)$1	1	152	166	9.8783
(((((....)))))	chr2:208627545-208627778(-)$1	1	183	197	10.4803
)))))....)))))	chr4:53462369-53462627(-)$1	1	231	245	8.8211
(((((....)))))	chr1:228581919-228582198(-)$1	1	250	264	10.4803
(((((....)))))	chr22:39911981-39912239(+)$1	1	6	20	10.4803
(((((....)))))	chrX:149931698-149931929(+)$1	1	193	207	10.4803
(((((...))))).	chr19:12739932-12740156(+)$1	1	138	152	8.9043
(((((......)))	chr17:663058-663301(-)$1	1	43	57	9.8783
)(((((...)))))	chr13:27261460-27261754(+)$1	1	266	280	9.2152
(((((......)))	chr19:8028104-8028333(-)$1	1	123	137	9.8783
(((((....)))))	chr3:197680814-197681044(+)$1	1	94	108	10.4803
(((((......)))	chr12:22837914-22838140(+)$1	1	111	125	9.8783
(((((....)))))	chrX:84526988-84527219(+)$1	1	170	184	10.4803
.(((((...)))))	chr14:102547690-102547942(-)$1	1	151	165	8.5347
(((((....)))))	chr10:105049528-105049773(+)$1	1	13	27	10.4803
(((((...))))))	chr20:33866655-33866998(-)$1	1	21	35	9.0770
(((((......)))	chr21:37445093-37445316(+)$1	1	203	217	9.8783

#PSSM
e : 0.84	[ : 0.06	F : 0.04	: : 0.03	c : 0.01	
e : 0.99	
e : 0.99	
e : 0.99	
e : 0.99	
m : 0.43	o : 0.23	e : 0.15	n : 0.10	4 : 0.04	l : 0.03	
m : 0.43	o : 0.23	l : 0.18	n : 0.10	4 : 0.04	
m : 0.43	o : 0.23	l : 0.18	n : 0.10	4 : 0.04	
m : 0.43	o : 0.23	l : 0.15	n : 0.10	4 : 0.04	e : 0.03	
e : 0.66	o : 0.23	n : 0.10	
e : 0.76	o : 0.23	
e : 0.99	
e : 0.99	
e : 0.96	3 : 0.01	d : 0.01	

#score	642.0451884595301
#seq	65
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_CDS_m3_run2.txt

#BEAR
"bb[ccc[ccc[aooooooa]ccc]ccc]bb	chr8:27685584-27685808(-)$1	224	120	151	13.5516
gg[eeeee[ddddooooooddddeeeeeggg	chr1:203768201-203768426(+)$1	225	18	49	11.9562
:dddd[ccc"""aooooooa333ccc]dddd	chr7:883095-883315(+)$1	220	185	216	12.3417
hhhh[ccceeeeeooooooeeeee22ccc33	chr19:37383068-37383290(-)$1	222	173	204	12.1216
aeeeee[ffffffooooooffffffeeeee]	chrM:8007-8242(+)$1	235	168	199	11.2764
ddd[ccc"""cccooooooccc333ccc22d	chr1:26440960-26441184(+)$1	224	110	141	15.2210
=========[cccmmmmccc==========d	chr4:128904046-128904272(+)$1	226	50	81	12.2215
"ccc!!a"""cccooooooccca22ccc]ff	chr3:23848777-23849010(+)$1	233	86	117	15.0872
"eeeee####ccclllccc4444eeeee333	chr1:54433435-54433658(+)$1	223	73	104	10.5920
gg####ccc[cccmmmmccccccggggggg:	chr2:183790311-183790534(-)$1	223	122	153	10.1484
iiiiii$$$$$bbnnnnnbb333iiiiiiii	chr12:21661270-21661494(+)$1	224	130	161	10.6802
###==========oooooo==========33	chr6:56918710-56918931(+)$1	221	126	157	16.4183
dd[eeeee!!cccooooooccc>>>>>>>>>	chr16:2813851-2814071(+)$1	220	102	133	12.2976
cc:eeeee!!cccooooooccc22eeeee:E	chr21:34926437-34926660(+)$1	223	37	68	10.9346
bb[a[iiiiiiiiimmmmiiiiiiiii]a]b	chr2:170675975-170676200(-)$1	225	56	87	10.4126
::ggggggg[cccooooooccc]ggggggg:	chr1:155449498-155449718(-)$1	220	36	67	13.1369
####iiiiiiiiiooooooiiiiiiiii22d	chr6:53135291-53135516(-)$1	225	155	186	15.0360
[ggggggg"""ddddlllddddggggggg]b	chr7:44161434-44161671(-)$1	237	134	165	10.4562
::===========oooooo===========:	chr6:44216342-44216574(+)$1	232	201	232	13.5517
ggggggg!!eeeeennnnneeeee333gggg	chrM:10374-10635(+)$1	261	85	116	10.1483
=========[cccnnnnnccc==========	chr10:72298795-72299012(+)$1	217	13	44	13.3508
hhhhhhhh####aooooooa333hhhhhhhh	chr16:47733158-47733378(+)$1	220	144	175	12.0449
cc!!ccc"""cccmmmmccc333ccc]ccc]	chr19:44513138-44513369(+)$1	231	185	216	11.6796
fff!!==========mmmm==========22	chr10:95266662-95266890(+)$1	228	44	75	11.4831
ggggggg!!ccc[ccclllccc]ccc]gggg	chr19:9949020-9949244(+)$1	224	173	204	11.0574
$ggggggg!!cccnnnnnccc]ggggggg55	chr19:37239767-37239987(-)$1	220	124	155	11.1539
======[ccc[bbnnnnnbb]ccc]======	chr8:28385188-28385419(+)$1	231	48	79	11.0630
a[ccc[bb[ddddoooooodddd]bb]ccc]	chr20:57015873-57016099(+)$1	226	92	123	12.0494
!!ccc!!ccccccrrrrrrrrrccc]ccc33	chr14:91948268-91948492(-)$1	224	117	148	10.4812
ccc!!hhhhhhhhoooooohhhhhhhh]ccc	chr10:75542819-75543041(+)$1	222	118	149	11.4706
=####ccc[bb[aooooooa]bbccc=====	chr6:17661883-17662107(-)$1	224	170	201	13.6226
ccc[ffffff[aaooooooa]a]ffffff22	chr5:114956106-114956326(-)$1	220	162	193	12.7171
!ggggggg!!cccooooooccc22ggggggg	chr15:23012307-23012530(-)$1	223	9	40	15.7721
ccc[iiiiiiiiiooooooiiiiiiiii]cc	chr17:34169277-34169500(+)$1	223	174	205	15.1499
cc[dddd!!bbbboooooobb]bb22dddd]	chr1:54509051-54509274(-)$1	223	125	156	10.8623
h!!ccc[ffffffooooooffffff]ccc]h	chr7:40172584-40172803(-)$1	219	181	212	12.1148
dddd[bb!!ddddoooooodddd22bb333d	chr2:44549870-44550093(-)$1	223	108	139	11.5190
$ggggggg!!cccoooooocccggggggg55	chr19:36940130-36940351(-)$1	221	124	155	14.4543
f$$$$$gggggggooooooggggggg22fff	chr1:116932072-116932294(+)$1	222	103	134	11.8680
$==========ddddllldddd]========	chr11:31392272-31392506(+)$1	234	140	171	11.2032
ggg!!cccbb[bboooooobb]bb]ccc22g	chr1:19948518-19948742(+)$1	224	86	117	12.4306
:ccc[ccceeeeeooooooeeeee333ccc]	chr19:38230746-38230969(-)$1	223	33	64	12.2300
eeeeeffffff[aooooooa]ffffffhhhh	chr5:138643283-138643509(+)$1	226	106	137	11.0671
[eeeee####cccooooooccc4444eeeee	chr12:54423534-54423759(+)$1	225	87	118	14.0842
"aggggggg[cccnnnnnccc4444gggggg	chr14:102552278-102552495(-)$1	217	164	195	12.4236
ee"""eeeeecccooooooccc]eeeee22e	chr17:5302778-5303002(-)$1	224	53	84	13.1814
========!!cccmmmmccc4444=======	chr3:169504343-169504565(+)$1	222	67	98	12.5294
:ccc[ccc!!cccooooooccc]cccccc::	chr21:34110480-34110701(-)$1	221	66	97	13.0078
:::==========oooooo==========:C	chr15:45713302-45713527(+)$1	225	125	156	11.3028
ffffff!!eeeeeooooooeeeee22fffff	chr7:79841993-79842221(+)$1	228	188	219	10.9070
eeeeebbbb[cccooooooccc]bb22bb]e	chr5:37351251-37351475(-)$1	224	117	148	11.7778
FFccc[ccc[cccooooooccc333ccc]cc	chr2:232322956-232323176(-)$1	220	110	141	14.4770

#otherMatches

#Seq PSSM
UCCCGGCCUCUCCGUUUAUGCAGAAGCUUGG	chr8:27685584-27685808(-)$1	224	120	151	13.5516
GUGCUUUGUGUUACAGGUUUGGCUAAAGACU	chr1:203768201-203768426(+)$1	225	18	49	11.9562
AGAAGUACACCCCAAACCAGCUUUGUCCUUC	chr7:883095-883315(+)$1	220	185	216	12.3417
CUUUAGUCGUGGCUCACUCGUUACUCGACAU	chr19:37383068-37383290(-)$1	222	173	204	12.1216
CUGAAAUCUGUGGAGCAAACCACAGUUUCAU	chrM:8007-8242(+)$1	235	168	199	11.2764
CCCUUUAUUUACAGGUAUGUGUUGUUGAUUG	chr1:26440960-26441184(+)$1	224	110	141	15.2210
CUUGUUUGCUACUGAUGGGUGUGAGCAAGUU	chr4:128904046-128904272(+)$1	226	50	81	12.2215
AAGUCAGCAUGAGCAAAAACUCCAAACUCCU	chr3:23848777-23849010(+)$1	233	86	117	15.0872
CUUUUGAGGAGUCAGAGACAGAACAGAAUAA	chr1:54433435-54433658(+)$1	223	73	104	10.5920
AGAUAAGCACGCAUUUUUGUUGCCUUGGUUU	chr2:183790311-183790534(-)$1	223	122	153	10.1484
ACAGGUUUUUUUCUGGGUGGUGUAUUUGUAG	chr12:21661270-21661494(+)$1	224	130	161	10.6802
GCGAAGAGAUUAGCUAACAUUAAUUUCUUAC	chr6:56918710-56918931(+)$1	221	126	157	16.4183
CUUCUUCAUAUCCUACAGUGGACUCGAAUUC	chr16:2813851-2814071(+)$1	220	102	133	12.2976
UCCUAGUGGUGGUAGUGAAGCUGACAUUGAA	chr21:34926437-34926660(+)$1	223	37	68	10.9346
UGGCUUUUCUAAAGACUGCUUUGGAAAUGGC	chr2:170675975-170676200(-)$1	225	56	87	10.4126
GAGAAAGAAACUGUUGAAUCAGAUUCUUUCA	chr1:155449498-155449718(-)$1	220	36	67	13.1369
AUCUGGGGCCUUUACCAACAAAGGCCCUCau	chr6:53135291-53135516(-)$1	225	155	186	15.0360
UCCGGCUAGGAGAGCGCAGCUUUAGCCGGCA	chr7:44161434-44161671(-)$1	237	134	165	10.4562
GUUUUUUUUUUUGAUACUCUAGAAGGAGGGG	chr6:44216342-44216574(+)$1	232	201	232	13.5517
AUAUUUACCAAAUGCCCCUCAUUUACAUAAA	chrM:10374-10635(+)$1	261	85	116	10.1483
GGAGGGCUGAGCACUCACUGCCGGCCCUCCU	chr10:72298795-72299012(+)$1	217	13	44	13.3508
GAGACACAUGUUCUGAAGUGUGUUGUGUUUC	chr16:47733158-47733378(+)$1	220	144	175	12.0449
UAAGAAGCAAGCAACUGUGUGUCCUUGUACA	chr19:44513138-44513369(+)$1	231	185	216	11.6796
GGAAUGUCUGAUGUUAACUAAUGUUGGAUUA	chr10:95266662-95266890(+)$1	228	44	75	11.4831
CGGGCAGGGGGAGCCUGCCAGGGUCCGCUGC	chr19:9949020-9949244(+)$1	224	173	204	11.0574
AAUUCAUACUGGUGAGAAACCUUAUGAAUGU	chr19:37239767-37239987(-)$1	220	124	155	11.1539
UAGUGAAGCUAUUGAGAAGAAAGCAUUGCUG	chr8:28385188-28385419(+)$1	231	48	79	11.0630
GAUGUAGAAAUAAAUAAAAUUAUAUCCACAA	chr20:57015873-57016099(+)$1	226	92	123	12.0494
CCUCUUCGUCGUGAAAAACUUGCACUGGCAC	chr14:91948268-91948492(-)$1	224	117	148	10.4812
UCAGCUGAAAAUGGACAAGUAUUUUCAAUGA	chr10:75542819-75543041(+)$1	222	118	149	11.4706
AAGAUGAGACGAGAAAGAACACGCUUUGUUG	chr6:17661883-17662107(-)$1	224	170	201	13.6226
CCUAGUGAGAACCGAGUCAGUGCUCUUACCC	chr5:114956106-114956326(-)$1	220	162	193	12.7171
AUUUAAAUUACGAGUUUUAUUGAUAUUUGAA	chr15:23012307-23012530(-)$1	223	9	40	15.7721
GUGGGCGGCGAGGUAAGAUCCUUGCUGCGUA	chr17:34169277-34169500(+)$1	223	174	205	15.1499
UGAGGUCAUUCUGGAGUGACAUGAUGGACUC	chr1:54509051-54509274(-)$1	223	125	156	10.8623
GGAACAUCUUGGACAAAACUUUAAGUUGUGU	chr7:40172584-40172803(-)$1	219	181	212	12.1148
UUCAAUUCACAUAACGGCAUAUGAAAACGAU	chr2:44549870-44550093(-)$1	223	108	139	11.5190
AAUUCAUACUGGGGAAAAACCCUAUGAAUGU	chr19:36940130-36940351(-)$1	221	124	155	14.4543
UUUUAUCCACAUCAUCACGGGUGUGGCUGUG	chr1:116932072-116932294(+)$1	222	103	134	11.8680
CUUUUCUUUCAGAUUUUAAAUCAUGAGGGGA	chr11:31392272-31392506(+)$1	234	140	171	11.2032
GGAUUAGGAAUUGUUUUCUCACUUACCUUCU	chr1:19948518-19948742(+)$1	224	86	117	12.4306
AUCACAGGUUUCAUGUCAUUGAGAGACCCUA	chr19:38230746-38230969(-)$1	223	33	64	12.2300
CCUUUAUCUUCUCAACACCGUGGAGAUGCAG	chr5:138643283-138643509(+)$1	226	106	137	11.0671
AGUGGAAAAAAGAAUCUAAUCUCACAUCCAC	chr12:54423534-54423759(+)$1	225	87	118	14.0842
UGACCAAGGCUGACUUGAUCAAUAACCUUGG	chr14:102552278-102552495(-)$1	217	164	195	12.4236
AUCACUGUACUCAUGAAGCUGGUGUACAUAG	chr17:5302778-5303002(-)$1	224	53	84	13.1814
CAACUGUGAAUGGGUAUUCAGAACCACAGUU	chr3:169504343-169504565(+)$1	222	67	98	12.5294
UCCAGCUGUUAGGCAAUUUUCUUCAGUGGUA	chr21:34110480-34110701(-)$1	221	66	97	13.0078
UUCAGUUCACAUUAAUUGAAAUGUGAACUUG	chr15:45713302-45713527(+)$1	225	125	156	11.3028
GCAGGUAUUUUCCUUUUCUGGGAAUAACUUG	chr7:79841993-79842221(+)$1	228	188	219	10.9070
UUCCACUGAUAAUGGCAGAAUUUUCUUGGCU	chr5:37351251-37351475(-)$1	224	117	148	11.7778
CCCUUACAAAGUCACUCAGGAUGAAUUGAAA	chr2:232322956-232323176(-)$1	220	110	141	14.4770

#DB
.((.(((.(((.(......).))).))).))	chr8:27685584-27685808(-)$1	1	120	151	13.5516
((.(((((.((((......))))))))))))	chr1:203768201-203768426(+)$1	1	18	49	11.9562
.((((.(((...(......)...))).))))	chr7:883095-883315(+)$1	1	185	216	12.3417
((((.((((((((......)))))..)))..	chr19:37383068-37383290(-)$1	1	173	204	12.1216
((((((.((((((......))))))))))).	chrM:8007-8242(+)$1	1	168	199	11.2764
(((.(((...(((......)))...)))..)	chr1:26440960-26441184(+)$1	1	110	141	15.2210
(((((((((.(((....)))))))))))))(	chr4:128904046-128904272(+)$1	1	50	81	12.2215
.(((..(...(((......))))..))).))	chr3:23848777-23849010(+)$1	1	86	117	15.0872
.(((((....(((...)))....)))))...	chr1:54433435-54433658(+)$1	1	73	104	10.5920
((....(((.(((....))))))))))))).	chr2:183790311-183790534(-)$1	1	122	153	10.1484
((((((.....((.....))...))))))))	chr12:21661270-21661494(+)$1	1	130	161	10.6802
...((((((((((......))))))))))..	chr6:56918710-56918931(+)$1	1	126	157	16.4183
((.(((((..(((......))).........	chr16:2813851-2814071(+)$1	1	102	133	12.2976
)).(((((..(((......)))..))))).(	chr21:34926437-34926660(+)$1	1	37	68	10.9346
((.(.(((((((((....))))))))).).)	chr2:170675975-170676200(-)$1	1	56	87	10.4126
..(((((((.(((......))).))))))).	chr1:155449498-155449718(-)$1	1	36	67	13.1369
....(((((((((......)))))))))..)	chr6:53135291-53135516(-)$1	1	155	186	15.0360
.(((((((...((((...))))))))))).)	chr7:44161434-44161671(-)$1	1	134	165	10.4562
..(((((((((((......))))))))))).	chr6:44216342-44216574(+)$1	1	201	232	13.5517
(((((((..(((((.....)))))...))))	chrM:10374-10635(+)$1	1	85	116	10.1483
(((((((((.(((.....)))))))))))))	chr10:72298795-72299012(+)$1	1	13	44	13.3508
((((((((....(......)...))))))))	chr16:47733158-47733378(+)$1	1	144	175	12.0449
((..(((...(((....)))...))).))).	chr19:44513138-44513369(+)$1	1	185	216	11.6796
(((..((((((((((....))))))))))..	chr10:95266662-95266890(+)$1	1	44	75	11.4831
(((((((..(((.(((...))).))).))))	chr19:9949020-9949244(+)$1	1	173	204	11.0574
.(((((((..(((.....))).)))))))..	chr19:37239767-37239987(-)$1	1	124	155	11.1539
((((((.(((.((.....)).))).))))))	chr8:28385188-28385419(+)$1	1	48	79	11.0630
(.(((.((.((((......)))).)).))).	chr20:57015873-57016099(+)$1	1	92	123	12.0494
..(((..((((((.........))).)))..	chr14:91948268-91948492(-)$1	1	117	148	10.4812
(((..((((((((......)))))))).)))	chr10:75542819-75543041(+)$1	1	118	149	11.4706
(....(((.((.(......).))))))))))	chr6:17661883-17662107(-)$1	1	170	201	13.6226
(((.((((((.((......).).))))))..	chr5:114956106-114956326(-)$1	1	162	193	12.7171
.(((((((..(((......)))..)))))))	chr15:23012307-23012530(-)$1	1	9	40	15.7721
(((.(((((((((......))))))))).))	chr17:34169277-34169500(+)$1	1	174	205	15.1499
((.((((..((((......)).))..)))).	chr1:54509051-54509274(-)$1	1	125	156	10.8623
(..(((.((((((......)))))).))).)	chr7:40172584-40172803(-)$1	1	181	212	12.1148
((((.((..((((......))))..))...)	chr2:44549870-44550093(-)$1	1	108	139	11.5190
.(((((((..(((......))))))))))..	chr19:36940130-36940351(-)$1	1	124	155	14.4543
(.....(((((((......)))))))..)))	chr1:116932072-116932294(+)$1	1	103	134	11.8680
.((((((((((((((...)))).))))))))	chr11:31392272-31392506(+)$1	1	140	171	11.2032
(((..(((((.((......)).)).)))..)	chr1:19948518-19948742(+)$1	1	86	117	12.4306
.(((.((((((((......)))))...))).	chr19:38230746-38230969(-)$1	1	33	64	12.2300
)))))((((((.(......).))))))((((	chr5:138643283-138643509(+)$1	1	106	137	11.0671
.(((((....(((......)))....)))))	chr12:54423534-54423759(+)$1	1	87	118	14.0842
.((((((((.(((.....)))....))))))	chr14:102552278-102552495(-)$1	1	164	195	12.4236
((...((((((((......))).)))))..)	chr17:5302778-5303002(-)$1	1	53	84	13.1814
((((((((..(((....)))....)))))))	chr3:169504343-169504565(+)$1	1	67	98	12.5294
.(((.(((..(((......))).))))))..	chr21:34110480-34110701(-)$1	1	66	97	13.0078
...((((((((((......)))))))))).)	chr15:45713302-45713527(+)$1	1	125	156	11.3028
((((((..(((((......)))))..)))))	chr7:79841993-79842221(+)$1	1	188	219	10.9070
(((((((((.(((......))).))..)).)	chr5:37351251-37351475(-)$1	1	117	148	11.7778
(((((.(((.(((......)))...))).))	chr2:232322956-232323176(-)$1	1	110	141	14.4770

#PSSM
: : 0.11	c : 0.11	g : 0.09	= : 0.09	" : 0.07	h : 0.05	d : 0.05	f : 0.05	$ : 0.05	e : 0.05	a : 0.03	# : 0.03	[ : 0.03	! : 0.03	i : 0.01	b : 0.01	F : 0.01	
g : 0.17	c : 0.17	e : 0.11	= : 0.09	d : 0.07	# : 0.05	: : 0.05	b : 0.03	h : 0.03	f : 0.03	! : 0.03	i : 0.01	[ : 0.01	$ : 0.01	a : 0.01	F : 0.01	
c : 0.17	g : 0.17	= : 0.11	e : 0.09	[ : 0.07	# : 0.07	d : 0.05	h : 0.03	: : 0.03	! : 0.03	f : 0.03	b : 0.01	i : 0.01	$ : 0.01	" : 0.01	
e : 0.15	= : 0.15	g : 0.15	c : 0.13	[ : 0.07	! : 0.07	d : 0.05	# : 0.05	h : 0.03	i : 0.01	a : 0.01	$ : 0.01	" : 0.01	f : 0.01	
e : 0.15	= : 0.15	g : 0.15	c : 0.13	[ : 0.09	! : 0.07	i : 0.05	d : 0.03	# : 0.03	f : 0.03	h : 0.01	$ : 0.01	" : 0.01	
c : 0.17	= : 0.17	g : 0.15	e : 0.13	i : 0.07	[ : 0.05	f : 0.05	! : 0.03	h : 0.03	b : 0.03	# : 0.01	d : 0.01	$ : 0.01	
c : 0.21	g : 0.17	= : 0.15	e : 0.07	[ : 0.05	i : 0.05	b : 0.05	# : 0.03	h : 0.03	! : 0.03	f : 0.03	a : 0.01	$ : 0.01	d : 0.01	
c : 0.19	= : 0.15	g : 0.13	! : 0.09	e : 0.07	f : 0.07	" : 0.05	i : 0.05	# : 0.03	h : 0.03	b : 0.03	[ : 0.01	$ : 0.01	
! : 0.21	= : 0.13	c : 0.11	e : 0.07	f : 0.07	" : 0.07	[ : 0.05	# : 0.05	i : 0.05	g : 0.05	b : 0.03	$ : 0.01	h : 0.01	
[ : 0.13	! : 0.13	" : 0.09	e : 0.09	= : 0.09	c : 0.07	f : 0.07	d : 0.05	# : 0.05	i : 0.05	b : 0.05	$ : 0.01	h : 0.01	g : 0.01	
c : 0.44	= : 0.09	e : 0.07	d : 0.05	f : 0.05	i : 0.05	[ : 0.05	" : 0.03	b : 0.03	$ : 0.01	# : 0.01	h : 0.01	g : 0.01	
c : 0.42	d : 0.09	e : 0.07	b : 0.07	= : 0.07	[ : 0.05	i : 0.05	f : 0.03	" : 0.01	# : 0.01	h : 0.01	a : 0.01	g : 0.01	
c : 0.40	a : 0.11	d : 0.09	e : 0.07	b : 0.07	= : 0.07	i : 0.05	f : 0.03	[ : 0.01	h : 0.01	g : 0.01	
o : 0.67	n : 0.09	m : 0.07	d : 0.03	l : 0.01	i : 0.01	e : 0.01	= : 0.01	c : 0.01	r : 0.01	
o : 0.67	n : 0.11	m : 0.09	d : 0.03	l : 0.01	= : 0.01	c : 0.01	r : 0.01	
o : 0.67	m : 0.11	n : 0.11	l : 0.05	c : 0.01	r : 0.01	
o : 0.67	m : 0.11	n : 0.11	l : 0.05	c : 0.01	r : 0.01	
o : 0.67	n : 0.11	c : 0.09	l : 0.05	m : 0.03	r : 0.01	
o : 0.67	c : 0.15	b : 0.03	d : 0.03	i : 0.01	n : 0.01	m : 0.01	l : 0.01	r : 0.01	
c : 0.38	a : 0.11	d : 0.09	e : 0.07	b : 0.07	= : 0.07	i : 0.05	f : 0.03	4 : 0.01	r : 0.01	h : 0.01	g : 0.01	
c : 0.32	] : 0.09	d : 0.09	= : 0.09	3 : 0.07	e : 0.07	i : 0.05	f : 0.03	4 : 0.03	b : 0.03	r : 0.01	h : 0.01	g : 0.01	
c : 0.30	= : 0.11	d : 0.09	3 : 0.07	e : 0.07	f : 0.05	4 : 0.05	i : 0.05	] : 0.05	r : 0.01	h : 0.01	b : 0.01	a : 0.01	g : 0.01	
] : 0.13	3 : 0.11	= : 0.11	c : 0.07	e : 0.07	4 : 0.07	g : 0.07	d : 0.05	f : 0.05	i : 0.05	b : 0.05	2 : 0.03	a : 0.01	> : 0.01	h : 0.01	
c : 0.15	e : 0.13	= : 0.13	g : 0.11	f : 0.07	2 : 0.07	i : 0.07	b : 0.05	4 : 0.05	3 : 0.03	h : 0.03	> : 0.01	] : 0.01	
= : 0.15	g : 0.13	c : 0.11	2 : 0.09	e : 0.07	f : 0.07	3 : 0.07	i : 0.07	] : 0.05	h : 0.03	b : 0.03	4 : 0.03	> : 0.01	
c : 0.19	= : 0.17	g : 0.15	e : 0.09	2 : 0.07	i : 0.07	3 : 0.03	h : 0.03	b : 0.03	] : 0.03	f : 0.03	> : 0.01	4 : 0.01	
= : 0.19	c : 0.17	g : 0.13	e : 0.11	] : 0.07	i : 0.07	f : 0.05	3 : 0.03	h : 0.03	2 : 0.03	> : 0.01	d : 0.01	b : 0.01	
c : 0.23	= : 0.19	g : 0.17	e : 0.11	i : 0.05	d : 0.03	] : 0.03	h : 0.03	f : 0.03	> : 0.01	3 : 0.01	2 : 0.01	b : 0.01	
g : 0.19	= : 0.19	c : 0.15	] : 0.07	2 : 0.07	e : 0.05	f : 0.05	d : 0.03	3 : 0.03	h : 0.03	i : 0.01	> : 0.01	a : 0.01	b : 0.01	
g : 0.13	= : 0.13	2 : 0.11	c : 0.11	3 : 0.09	] : 0.07	f : 0.05	: : 0.05	d : 0.03	e : 0.03	h : 0.03	5 : 0.03	b : 0.01	i : 0.01	> : 0.01	
g : 0.11	d : 0.09	] : 0.09	= : 0.09	3 : 0.07	: : 0.07	b : 0.05	f : 0.05	h : 0.05	c : 0.05	e : 0.05	2 : 0.03	5 : 0.03	i : 0.01	> : 0.01	E : 0.01	C : 0.01	

#score	642.1286287503771
#seq	52
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_UTR_m1_run1.txt

#BEAR
ccc!!cccyyyyyyyyyyyyyyyyccc22ccc	chr16:1416050-1416290(-)$1	240	164	196	24.1481
eeeee[cccuuuuuuuuuuuuccceeeee333	chr4:183811204-183811444(-)$1	240	85	117	25.8272
iiiiiii[attttttttttta]iiiiiiiii:	chr7:32907876-32908116(-)$1	240	73	105	24.6645
cddddyyyyyyyyyyyyyyyydddd]ccc22f	chr6:126249987-126250227(+)$1	240	163	195	22.6420
hhhhhhhhwwwwwwwwwwwwwwhhhhhhhh]c	chr14:54893562-54893802(-)$1	240	170	202	21.8465
hhhheeeeeuuuuuuuuuuuueeeeeffffff	chr15:100254414-100254654(+)$1	240	28	60	24.0077
=========ttttttttttt==========gg	chr12:70704594-70704834(+)$1	240	43	75	24.7309
[ccceeeeeuuuuuuuuuuuueeeee22ccc]	chr12:110973274-110973567(-)$1	293	162	194	25.2779
dddd!!ccctttttttttttcccdddd]bb44	chr11:59405537-59405777(-)$1	240	83	115	24.3325
ccc!!ddddtttttttttttdddd]ccc::EE	chr7:157061293-157061570(+)$1	277	35	67	21.0692
fffffyyyyyyyyyyyyyyyyffffff]eeee	chr18:12817217-12817457(-)$1	240	38	70	21.6186
eeee[ddddtttttttttttddddeeeee:::	chr15:80430266-80430506(+)$1	240	8	40	21.8112
ee!!ddddvvvvvvvvvvvvvdddd22eeeee	chr6:36199329-36199569(+)$1	240	89	121	24.5244
ee!!eeeeeuuuuuuuuuuuueeeeeeeeee:	chr7:80434910-80435153(-)$1	243	209	241	24.7197
ddd[ddddvvvvvvvvvvvvvdddd22ddddd	chr8:144520092-144520332(-)$1	240	188	220	23.9089
gggggggwwwwwwwwwwwwwwggggggg::dd	chr9:139334774-139335014(-)$1	240	36	68	21.5896
ccc:eeeeeuuuuuuuuuuuueeeee::dddd	chr15:41641246-41641486(+)$1	240	94	126	22.0956
dd[bb!!bbtttttttttttbb]bb]dddd]e	chr12:50185025-50185306(-)$1	281	127	159	22.2902
dddddddduuuuuuuuuuuudddd]ddddccc	chr3:98516933-98517173(-)$1	240	159	191	23.8157
hh####ccctttttttttttccc4444hhhhh	chr1:227844090-227844330(+)$1	240	59	91	24.0634
cc!!eeeeeuuuuuuuuuuuueeeee55555c	chr5:150112886-150113126(-)$1	240	197	229	22.6439
c!!eeeeevvvvvvvvvvvvveeeee22ccc:	chr7:87835181-87835421(-)$1	240	122	154	24.3374
ii!!eeeeeuuuuuuuuuuuueeeee666666	chr17:4621116-4621356(+)$1	240	17	49	23.6156
i####dddduuuuuuuuuuuudddd333iiii	chr2:128062459-128062699(-)$1	240	61	93	25.7713
hhhhh[cccuuuuuuuuuuuuccc]hhhhhhh	chr3:184049664-184049904(+)$1	240	157	189	24.0369
eeefffffftttttttttttffffff>>>>>>	chr5:52978974-52979214(+)$1	240	37	69	21.9246
ddd!!cccvvvvvvvvvvvvvccc22dddd]c	chr16:28977555-28977795(+)$1	240	91	123	24.6371
dccc!!ccctttttttttttccc333ccc555	chr19:57724571-57724811(+)$1	240	169	201	23.3151
bbccc[ccctttttttttttccc]ccc]bb22	chr12:124081484-124081724(+)$1	240	23	55	23.6002
ee[ddddyyyyyyyyyyyyyyyydddd22eee	chr19:58773578-58773818(+)$1	240	70	102	23.1566
h####cccyyyyyyyyyyyyyyyyccc4444h	chr1:879691-879931(-)$1	240	157	189	23.8852
!gggggggwwwwwwwwwwwwwwggggggg22c	chrX:150574410-150574650(+)$1	240	129	161	23.7514
c$$$$$cccuuuuuuuuuuuuccc55555ccc	chr10:70743302-70743542(+)$1	240	201	233	21.2562
"cccddddwwwwwwwwwwwwwwdddd]ccc33	chr5:56215336-56215576(-)$1	240	30	62	23.9604
ddddeeeeettttttttttteeeee]dddd::	chr1:156280730-156280970(-)$1	240	86	118	22.1136
cc!!ddddwwwwwwwwwwwwwwddddccc::i	chr19:44741127-44741367(+)$1	240	71	103	22.6639
gg[eeeeewwwwwwwwwwwwwweeeee]gggg	chr15:67485857-67486097(+)$1	240	192	224	24.2220
=========ttttttttttt============	chr5:74073854-74074094(-)$1	240	55	87	24.7763
gggggyyyyyyyyyyyyyyyyggggggg]ccc	chr1:185266743-185266983(-)$1	240	7	39	23.3953
fffff[bbwwwwwwwwwwwwwwbbffffff]c	chr16:46864934-46865174(-)$1	240	48	80	21.5419
hhhffffffuuuuuuuuuuuuffffffeeeee	chr1:203276918-203277158(+)$1	240	78	110	23.1791
e"""cccyyyyyyyyyyyyyyyyccceeeee2	chr1:150238465-150238705(-)$1	240	81	113	23.6581
h!!fffffftttttttttttffffff4444hh	chr5:173386637-173386917(+)$1	280	103	135	22.8727
gg"""ddddtttttttttttdddd333ggggg	chr4:88998762-88999002(+)$1	240	115	147	24.8545
ddd[a[cccuuuuuuuuuuuucccaddddddd	chr6:160210466-160210744(-)$1	278	107	139	24.8906
iiiiiiiivvvvvvvvvvvvviiiiiiiii]f	chr5:109202628-109202875(+)$1	247	206	238	25.0172
hhhhhhhhwwwwwwwwwwwwwwhhhhhhhh22	chr17:27240020-27240267(-)$1	247	169	201	21.5484
cc!!ddddwwwwwwwwwwwwwwdddd]cccdd	chr7:102742134-102742389(-)$1	255	126	158	24.1935
ccca[dddduuuuuuuuuuuudddd]a]ccc]	chr2:64321650-64321942(-)$1	292	95	127	25.7010
========wwwwwwwwwwwwww==========	chr16:24834875-24835119(+)$1	244	124	156	24.4187
dd[bbcccwwwwwwwwwwwwwwccc]bbdddd	chr2:228222284-228222524(+)$1	240	190	222	22.6685
eee"""ccctttttttttttccc333eeeee:	chr1:230979285-230979525(-)$1	240	141	173	24.0236
eeeeeeebbvvvvvvvvvvvvvbb]eeeee44	chr1:164790716-164790956(+)$1	240	152	184	23.3006
!!eeeee[attttttttttta]eeeee22fff	chr9:119462677-119462917(+)$1	240	153	185	24.3757
c!!eeeeeyyyyyyyyyyyyyyyyeeeee]cc	chr1:205686555-205686835(-)$1	280	234	266	24.0857
b!!eeeeewwwwwwwwwwwwwweeeee22bb:	chr18:19110088-19110328(-)$1	240	8	40	22.6381
ccc!!cccuuuuuuuuuuuuccc4444ccc]d	chr7:98626732-98626972(-)$1	240	16	48	25.5811
[hhhhhhhhuuuuuuuuuuuuhhhhhhhh]dd	chr5:138665674-138665954(+)$1	280	207	239	22.4088
eeee[dddduuuuuuuuuuuudddd]eeeee:	chr4:120218135-120218375(-)$1	240	1	33	24.2780

#otherMatches

#Seq PSSM
CCCUUCCUGUUACACGUUAUCAUGAGGCUGGG	chr16:1416050-1416290(-)$1	240	164	196	24.1481
UUUCAUGAGUUUUUAUUUUGUCUCUGAGAUUU	chr4:183811204-183811444(-)$1	240	85	117	25.8272
UUAACCUGUUGUGUGCGUGUGGGGGUUAGGAU	chr7:32907876-32908116(-)$1	240	73	105	24.6645
CCACUUCCUCCAAAUCCAUACAGUGAGGAAUC	chr6:126249987-126250227(+)$1	240	163	195	22.6420
GUUUGAGAUUAAAAAUAGUAUUUCUUAAACUU	chr14:54893562-54893802(-)$1	240	170	202	21.8465
UGUAAGGCAUUAUUUAAAACUUGCCUUUUGUG	chr15:100254414-100254654(+)$1	240	28	60	24.0077
AAGUAUUACCCCUGAUAAAAGUAAUAUUUUUG	chr12:70704594-70704834(+)$1	240	43	75	24.7309
ACUUGAGAAUAUAGAAAGUCUUUCUCUAAAGG	chr12:110973274-110973567(-)$1	293	162	194	25.2779
CCCACUGCUCUAUGAAAUUUGGCUGGGUGAUA	chr11:59405537-59405777(-)$1	240	83	115	24.3325
CGCUCGCCCUCCUUUCCCCUGGGCUGCGCCCA	chr7:157061293-157061570(+)$1	277	35	67	21.0692
GUUUUUUAAAAGAAAAAAGUUAGAACUAACUU	chr18:12817217-12817457(-)$1	240	38	70	21.6186
AAACAUGCAUGCAUUAAUCUUGCAGUUUAUUU	chr15:80430266-80430506(+)$1	240	8	40	21.8112
GCCUGCCACCAAACAUCUUCCUGGCCUGCGCU	chr6:36199329-36199569(+)$1	240	89	121	24.5244
AUUUGAUGCAUUUAUUUUUUAGUAUCGUGUUA	chr7:80434910-80435153(-)$1	243	209	241	24.7197
AGGAGGGCCGCCCGCCACCAAGCCUCACCUGG	chr8:144520092-144520332(-)$1	240	188	220	23.9089
CAGUAGAUAAUUUCUGUAGGUUCUGCUGGAGG	chr9:139334774-139335014(-)$1	240	36	68	21.5896
CAGAUCAGCAACCAGGAAGAAGCUGAGAGACA	chr15:41641246-41641486(+)$1	240	94	126	22.0956
ACAAGUUGCCUUCUCUCUCUGCCCUGGUCCUC	chr12:50185025-50185306(-)$1	281	127	159	22.2902
UAUAUGUCACCUAGGGAACAGACAUUAUAGCU	chr3:98516933-98517173(-)$1	240	159	191	23.8157
auucauaucucaaauaacuugauuuuuauuau	chr1:227844090-227844330(+)$1	240	59	91	24.0634
GUGAGAAUUUGGUACUAAAAUGAUUUGCAAGA	chr5:150112886-150113126(-)$1	240	197	229	22.6439
CCUUCAAAACCUGUUGAAUAAUUUGAUUGGCA	chr7:87835181-87835421(-)$1	240	122	154	24.3374
GGUUGGGGUGUGUGAGGAAUGACCCCUCCUGC	chr17:4621116-4621356(+)$1	240	17	49	23.6156
CUAAAUGCUAUAGAAAAUAAAGGCACCUGAAA	chr2:128062459-128062699(-)$1	240	61	93	25.7713
ACAGGCGCUCUACGCCCUCCAGGCCCUUGUAG	chr3:184049664-184049904(+)$1	240	157	189	24.0369
CUUUUCUUGGAACAAAAGAACAAGAGUAUCCA	chr5:52978974-52979214(+)$1	240	37	69	21.9246
GCACAUCAUUUUAAAACUAUUUGAGAUGCACU	chr16:28977555-28977795(+)$1	240	91	123	24.6371
AAAGUAUGCAAACUUUAAUCGCACAUCUUCUG	chr19:57724571-57724811(+)$1	240	169	201	23.3151
UCCUUCCAGGAACUCAAACACUGUAAGUGAAA	chr12:124081484-124081724(+)$1	240	23	55	23.6002
GAACUCUAACCUCGUCAUACAUCAGAGAAUUC	chr19:58773578-58773818(+)$1	240	70	102	23.1566
CCCCUGGCCCCUUCCACCACCUCUGCCCUCCG	chr1:879691-879931(-)$1	240	157	189	23.8852
UAAAAACACUCCCACAAGUAuuuguuuuuuaa	chrX:150574410-150574650(+)$1	240	129	161	23.7514
CAAAAAGGUAACAAAUUCAUAACUGGAAAGCA	chr10:70743302-70743542(+)$1	240	201	233	21.2562
CUAUUGCAUUGAUUUUAAUAUUUGUACAUAAA	chr5:56215336-56215576(-)$1	240	30	62	23.9604
CAUGCCUUGACAGAAAAAUCCAAGGCCAUGAC	chr1:156280730-156280970(-)$1	240	86	118	22.1136
GUAAGAUCUAGUUAAUAUAAAUGAUCACCUUU	chr19:44741127-44741367(+)$1	240	71	103	22.6639
ACCAUGGUGAUUAUUUUUUUAAACCAUCGUUA	chr15:67485857-67486097(+)$1	240	192	224	24.2220
GGGUGUGAUUAGUUACAAAUGUUAUGCUUAUG	chr5:74073854-74074094(-)$1	240	55	87	24.7763
GGUCUGUUUUGUGUACUUUUAAGACUUUGGUU	chr1:185266743-185266983(-)$1	240	7	39	23.3953
GGGCUGCCGAAGUGUGAGGGGAGGAGCCCGAG	chr16:46864934-46865174(-)$1	240	48	80	21.5419
CCCAGCCAGACACCUGCAUCCCUGGCUCCUCU	chr1:203276918-203277158(+)$1	240	78	110	23.1791
CCCAAGACUCACCUCCCUUCCCCUCUGCAGGC	chr1:150238465-150238705(-)$1	240	81	113	23.6581
UUUGCUUUAUUUUAUUAUUUUAAAGCUACUGU	chr5:173386637-173386917(+)$1	280	103	135	22.8727
AAUGUGUAAUACUGAGCACUUUACUUCUUAAU	chr4:88998762-88999002(+)$1	240	115	147	24.8545
CCCAGUAGCUCCUGGGACAUCGCUCGGGUACG	chr6:160210466-160210744(-)$1	278	107	139	24.8906
UUUUUCUUUUACCAGUACAGUaagaaaaaaaa	chr5:109202628-109202875(+)$1	247	206	238	25.0172
CUCAGGGAUUAGCACCCAGAAUUCCCUGAGCU	chr17:27240020-27240267(-)$1	247	169	201	21.5484
GGCAGUGCUCUAUAAUUUAUUUGCACACCUGU	chr7:102742134-102742389(-)$1	255	126	158	24.1935
CCUCUAGACUAACAGACCAUUGUCUUGCAGGA	chr2:64321650-64321942(-)$1	292	95	127	25.7010
ACCCCGCAUUAUUCCACAAGCCUGUGGGGUCC	chr16:24834875-24835119(+)$1	244	124	156	24.4187
UCAUGCGUGAACAAUUUAAAAAACGACAGAAU	chr2:228222284-228222524(+)$1	240	190	222	22.6685
AUCAAGUCCAUGGAGAAGGGGGAAAAGGUCUU	chr1:230979285-230979525(-)$1	240	141	173	24.0236
AAAACAAGCCCCCCCACCCCCUGCUUUGUUUU	chr1:164790716-164790956(+)$1	240	152	184	23.3006
GUGUCUAAGGAAUUGUACAACAUAGGCCAGGG	chr9:119462677-119462917(+)$1	240	153	185	24.3757
UUUCAUAUUUCCUUCUCUAAAUAUAUAUGUAU	chr1:205686555-205686835(-)$1	280	234	266	24.0857
GACAGAAUAGCACGUAAAACAAAUUCUUGCCU	chr18:19110088-19110328(-)$1	240	8	40	22.6381
AUUUUAUCUUAAAGUGGCUUGAUUUCCAAUAG	chr7:98626732-98626972(-)$1	240	16	48	25.5811
CAAGAUGUAAUUUUACAUUUCUGCAUUUUUAA	chr5:138665674-138665954(+)$1	280	207	239	22.4088
uuuuaagguguugucacaucaaccuaaagaga	chr4:120218135-120218375(-)$1	240	1	33	24.2780

#DB
(((..(((................)))..)))	chr16:1416050-1416290(-)$1	1	164	196	24.1481
(((((.(((............))))))))...	chr4:183811204-183811444(-)$1	1	85	117	25.8272
(((((((.(...........).))))))))).	chr7:32907876-32908116(-)$1	1	73	105	24.6645
(((((................)))).)))..)	chr6:126249987-126250227(+)$1	1	163	195	22.6420
((((((((..............)))))))).)	chr14:54893562-54893802(-)$1	1	170	202	21.8465
))))(((((............)))))((((((	chr15:100254414-100254654(+)$1	1	28	60	24.0077
(((((((((...........))))))))))))	chr12:70704594-70704834(+)$1	1	43	75	24.7309
.((((((((............)))))..))).	chr12:110973274-110973567(-)$1	1	162	194	25.2779
((((..(((...........))))))).))..	chr11:59405537-59405777(-)$1	1	83	115	24.3325
(((..((((...........)))).)))..((	chr7:157061293-157061570(+)$1	1	35	67	21.0692
(((((................)))))).))))	chr18:12817217-12817457(-)$1	1	38	70	21.6186
((((.((((...........)))))))))...	chr15:80430266-80430506(+)$1	1	8	40	21.8112
((..((((.............))))..)))))	chr6:36199329-36199569(+)$1	1	89	121	24.5244
((..(((((............)))))))))).	chr7:80434910-80435153(-)$1	1	209	241	24.7197
(((.((((.............))))..)))))	chr8:144520092-144520332(-)$1	1	188	220	23.9089
(((((((..............)))))))..((	chr9:139334774-139335014(-)$1	1	36	68	21.5896
))).(((((............)))))..((((	chr15:41641246-41641486(+)$1	1	94	126	22.0956
((.((..((...........)).)).)))).)	chr12:50185025-50185306(-)$1	1	127	159	22.2902
((((((((............)))).))))(((	chr3:98516933-98517173(-)$1	1	159	191	23.8157
((....(((...........)))....)))))	chr1:227844090-227844330(+)$1	1	59	91	24.0634
((..(((((............))))).....)	chr5:150112886-150113126(-)$1	1	197	229	22.6439
(..(((((.............)))))..))).	chr7:87835181-87835421(-)$1	1	122	154	24.3374
((..(((((............)))))......	chr17:4621116-4621356(+)$1	1	17	49	23.6156
(....((((............))))...))))	chr2:128062459-128062699(-)$1	1	61	93	25.7713
(((((.(((............))).)))))))	chr3:184049664-184049904(+)$1	1	157	189	24.0369
(((((((((...........))))))......	chr5:52978974-52979214(+)$1	1	37	69	21.9246
(((..(((.............)))..)))).)	chr16:28977555-28977795(+)$1	1	91	123	24.6371
((((..(((...........)))...)))...	chr19:57724571-57724811(+)$1	1	169	201	23.3151
(((((.(((...........))).))).))..	chr12:124081484-124081724(+)$1	1	23	55	23.6002
((.((((................))))..)))	chr19:58773578-58773818(+)$1	1	70	102	23.1566
(....(((................)))....)	chr1:879691-879931(-)$1	1	157	189	23.8852
.(((((((..............)))))))..)	chrX:150574410-150574650(+)$1	1	129	161	23.7514
(.....(((............))).....)))	chr10:70743302-70743542(+)$1	1	201	233	21.2562
.(((((((..............)))).)))..	chr5:56215336-56215576(-)$1	1	30	62	23.9604
(((((((((...........))))).))))..	chr1:156280730-156280970(-)$1	1	86	118	22.1136
((..((((..............)))))))..(	chr19:44741127-44741367(+)$1	1	71	103	22.6639
((.(((((..............))))).))))	chr15:67485857-67486097(+)$1	1	192	224	24.2220
(((((((((...........))))))))))))	chr5:74073854-74074094(-)$1	1	55	87	24.7763
(((((................))))))).)))	chr1:185266743-185266983(-)$1	1	7	39	23.3953
(((((.((..............)))))))).)	chr16:46864934-46865174(-)$1	1	48	80	21.5419
)))((((((............))))))(((((	chr1:203276918-203277158(+)$1	1	78	110	23.1791
(...(((................)))))))).	chr1:150238465-150238705(-)$1	1	81	113	23.6581
(..((((((...........))))))....))	chr5:173386637-173386917(+)$1	1	103	135	22.8727
((...((((...........))))...)))))	chr4:88998762-88999002(+)$1	1	115	147	24.8545
(((.(.(((............)))))))))))	chr6:160210466-160210744(-)$1	1	107	139	24.8906
((((((((.............))))))))).)	chr5:109202628-109202875(+)$1	1	206	238	25.0172
((((((((..............))))))))..	chr17:27240020-27240267(-)$1	1	169	201	21.5484
((..((((..............)))).)))))	chr7:102742134-102742389(-)$1	1	126	158	24.1935
((((.((((............)))).).))).	chr2:64321650-64321942(-)$1	1	95	127	25.7010
((((((((..............))))))))))	chr16:24834875-24835119(+)$1	1	124	156	24.4187
((.(((((..............))).))))))	chr2:228222284-228222524(+)$1	1	190	222	22.6685
(((...(((...........)))...))))).	chr1:230979285-230979525(-)$1	1	141	173	24.0236
(((((((((.............)).)))))..	chr1:164790716-164790956(+)$1	1	152	184	23.3006
..(((((.(...........).)))))..)))	chr9:119462677-119462917(+)$1	1	153	185	24.3757
(..(((((................))))).))	chr1:205686555-205686835(-)$1	1	234	266	24.0857
(..(((((..............)))))..)).	chr18:19110088-19110328(-)$1	1	8	40	22.6381
(((..(((............)))....))).)	chr7:98626732-98626972(-)$1	1	16	48	25.5811
.((((((((............)))))))).))	chr5:138665674-138665954(+)$1	1	207	239	22.4088
((((.((((............)))).))))).	chr4:120218135-120218375(-)$1	1	1	33	24.2780

#PSSM
c : 0.20	e : 0.16	d : 0.15	h : 0.13	i : 0.06	g : 0.06	= : 0.05	[ : 0.03	f : 0.03	b : 0.03	! : 0.03	" : 0.01	
c : 0.18	e : 0.15	d : 0.15	h : 0.11	g : 0.08	! : 0.08	i : 0.05	= : 0.05	f : 0.03	# : 0.03	b : 0.01	$ : 0.01	" : 0.01	
! : 0.16	c : 0.15	e : 0.11	d : 0.11	h : 0.10	[ : 0.06	= : 0.05	g : 0.05	# : 0.05	i : 0.03	f : 0.03	" : 0.03	$ : 0.01	
! : 0.16	e : 0.15	d : 0.08	h : 0.08	f : 0.08	c : 0.06	= : 0.05	g : 0.05	# : 0.05	" : 0.05	i : 0.03	[ : 0.03	b : 0.03	: : 0.01	$ : 0.01	a : 0.01	
e : 0.23	d : 0.13	! : 0.10	f : 0.08	h : 0.06	= : 0.05	[ : 0.05	g : 0.05	# : 0.05	i : 0.03	b : 0.03	c : 0.03	" : 0.03	$ : 0.01	a : 0.01	
e : 0.22	d : 0.22	c : 0.10	[ : 0.08	y : 0.05	h : 0.05	= : 0.05	! : 0.05	f : 0.05	i : 0.03	g : 0.03	# : 0.01	$ : 0.01	" : 0.01	
c : 0.25	e : 0.22	d : 0.22	y : 0.05	h : 0.05	= : 0.05	f : 0.05	i : 0.03	g : 0.03	! : 0.01	b : 0.01	
c : 0.23	d : 0.20	e : 0.18	y : 0.08	h : 0.05	= : 0.05	b : 0.05	f : 0.05	[ : 0.03	w : 0.01	g : 0.01	i : 0.01	
w : 0.20	c : 0.15	y : 0.13	e : 0.11	d : 0.10	v : 0.08	f : 0.05	a : 0.03	= : 0.03	b : 0.03	u : 0.03	h : 0.01	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.28	t : 0.27	w : 0.20	y : 0.13	v : 0.10	
u : 0.25	w : 0.20	y : 0.13	c : 0.10	v : 0.10	d : 0.06	a : 0.03	= : 0.03	f : 0.03	b : 0.01	e : 0.01	
c : 0.18	w : 0.18	d : 0.16	e : 0.13	y : 0.08	f : 0.06	] : 0.03	= : 0.03	g : 0.03	b : 0.01	i : 0.01	v : 0.01	h : 0.01	
d : 0.22	c : 0.20	e : 0.18	y : 0.08	f : 0.06	h : 0.05	= : 0.05	g : 0.05	i : 0.03	b : 0.03	] : 0.01	
d : 0.25	e : 0.18	c : 0.11	f : 0.06	y : 0.05	h : 0.05	= : 0.05	g : 0.05	b : 0.05	i : 0.03	4 : 0.03	3 : 0.03	] : 0.01	
e : 0.23	d : 0.18	c : 0.08	f : 0.08	] : 0.06	h : 0.05	= : 0.05	g : 0.05	3 : 0.05	i : 0.03	4 : 0.03	b : 0.01	2 : 0.01	5 : 0.01	a : 0.01	
e : 0.23	d : 0.11	] : 0.10	c : 0.08	f : 0.08	h : 0.06	3 : 0.06	= : 0.05	2 : 0.05	g : 0.05	i : 0.03	4 : 0.03	5 : 0.01	
e : 0.18	c : 0.11	d : 0.11	h : 0.06	f : 0.06	2 : 0.06	= : 0.05	g : 0.05	4 : 0.05	i : 0.03	5 : 0.03	3 : 0.03	] : 0.03	: : 0.01	6 : 0.01	> : 0.01	a : 0.01	b : 0.01	
e : 0.16	c : 0.11	2 : 0.10	d : 0.10	h : 0.08	] : 0.08	g : 0.06	= : 0.05	i : 0.03	f : 0.03	5 : 0.03	4 : 0.03	: : 0.01	6 : 0.01	3 : 0.01	> : 0.01	b : 0.01	
e : 0.18	c : 0.15	d : 0.13	h : 0.08	2 : 0.06	i : 0.05	= : 0.05	g : 0.05	f : 0.03	b : 0.03	: : 0.03	5 : 0.03	4 : 0.03	6 : 0.01	> : 0.01	] : 0.01	
c : 0.16	e : 0.15	d : 0.11	h : 0.06	: : 0.06	i : 0.05	f : 0.05	= : 0.05	b : 0.05	2 : 0.03	5 : 0.03	4 : 0.03	g : 0.03	] : 0.03	3 : 0.01	6 : 0.01	> : 0.01	
c : 0.13	e : 0.13	d : 0.11	] : 0.10	2 : 0.06	g : 0.05	4 : 0.05	: : 0.05	h : 0.05	3 : 0.03	i : 0.03	f : 0.03	5 : 0.03	= : 0.03	E : 0.01	6 : 0.01	> : 0.01	b : 0.01	
c : 0.16	: : 0.13	d : 0.13	e : 0.08	f : 0.06	h : 0.06	g : 0.05	2 : 0.05	3 : 0.03	] : 0.03	4 : 0.03	i : 0.03	= : 0.03	E : 0.01	6 : 0.01	> : 0.01	5 : 0.01	

#score	1391.2854318952357
#seq	59
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_UTR_m3_run2.txt

#BEAR
hhhhhhhh[bbtttttttttttbb]hhh	chr17:80861200-80861427(+)$1	227	12	40	19.5543
"hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr1:16785320-16785556(+)$1	236	74	102	20.9129
ddddd[ddddwwwwwwwwwwwwwwdddd	chr1:116612436-116612661(+)$1	225	33	61	21.0968
dd!!ccc[ccctttttttttttcccccc	chr20:3804881-3805100(-)$1	219	167	195	22.2848
""ffffffwwwwwwwwwwwwwwffffff	chr13:41885485-41885704(+)$1	219	147	175	21.0211
ggggg[dddduuuuuuuuuuuuddddgg	chr17:22023638-22023881(+)$1	243	44	72	23.3914
=======^^^^^^^^^^^^^^^^^^===	chr1:44431691-44431915(+)$1	224	37	65	16.1375
fbb!!eeeeeuuuuuuuuuuuueeeee]	chr6:168364582-168364803(+)$1	221	179	207	22.7022
gggg[ccc[bbtttttttttttbb]ccc	chr6:31802940-31803169(+)$1	229	15	43	21.3495
eeeee[cccvvvvvvvvvvvvvccc]ee	chr15:41022040-41022270(+)$1	230	157	185	23.2647
mmddddeeeeettttttttttteeeeeB	chr10:102265662-102265891(-)$1	229	194	222	18.7421
ccc!!eeeeeuuuuuuuuuuuueeeee2	chr19:1434834-1435069(+)$1	235	32	60	23.1611
::ccceeeeettttttttttteeeee]c	chr11:66372897-66373117(+)$1	220	58	86	20.0542
gggggeeeeeuuuuuuuuuuuueeeee5	chr7:6156431-6156659(+)$1	228	138	166	22.4903
:iiiiiiiiiyyyyyyyyyyyyyyyyii	chr14:21968957-21969221(-)$1	264	25	53	20.8347
eeegggggggtttttttttttggggggg	chr17:8076671-8076971(-)$1	300	159	187	21.4669
c!!ffffffxxxxxxxxxxxxxxxffff	chr16:4745099-4745334(+)$1	235	187	215	18.2154
bb!!bb[cccuuuuuuuuuuuuccc]bb	chr1:19638886-19639129(+)$1	243	152	180	22.6453
$$$$bb[ccctttttttttttccc]bb3	chr3:129033570-129033791(-)$1	221	175	203	20.2203
:::gggggggtttttttttttggggggg	chr2:85133539-85133765(+)$1	226	165	193	19.2122
FFFFeeeeewwwwwwwwwwwwwweeeee	chr3:50685587-50685816(+)$1	229	32	60	20.4342
gg[dddd[ccctttttttttttccc]dd	chr7:102065741-102065961(+)$1	220	68	96	21.5897
!!hhhhhhhhwwwwwwwwwwwwwwhhhh	chr2:242695143-242695375(+)$1	232	26	54	20.5342
b!!affffffxxxxxxxxxxxxxxxfff	chr14:94847044-94847267(+)$1	223	8	36	17.7914
ccc$$$$$ccctttttttttttccc333	chr7:103629706-103629934(-)$1	228	55	83	20.7235
qqqbbfffffftttttttttttffffff	chr1:55207904-55208125(-)$1	221	182	210	18.6542
d!!bb[ccc^^^^^^^^^^^^^^^^^^c	chr4:119606601-119606855(-)$1	254	211	239	16.1873
=====[ddddtttttttttttdddd]==	chr7:54819938-54820158(-)$1	220	37	65	21.7408
"gggggggwwwwwwwwwwwwwwgggggg	chr6:117996611-117996835(+)$1	224	36	64	22.2253
==========yyyyyyyyyyyyyyyy==	chr17:46657162-46657388(-)$1	226	113	141	21.6287
ee[bb[cccyyyyyyyyyyyyyyyyccc	chr12:5024027-5024248(-)$1	221	39	67	21.9341
[iiiiiiiii^^^^^^^^^^^^^^^^^^	chr1:934311-934539(-)$1	228	171	199	15.6358
ee[ffffffvvvvvvvvvvvvvffffff	chr1:23696647-23696874(+)$1	227	151	179	22.2702
e[ccc[ddddtttttttttttdddd22c	chr19:3985341-3985561(-)$1	220	4	32	21.2375
::::eeeeewwwwwwwwwwwwwweeeee	chr17:72765291-72765515(+)$1	224	182	210	18.7425
bccc:fffffftttttttttttffffff	chr19:50001103-50001340(+)$1	237	175	203	19.7293
ee"""eeeeeuuuuuuuuuuuueeeeee	chr7:129771443-129771697(+)$1	254	85	113	23.0544
leeeeedddduuuuuuuuuuuuddddEE	chr19:1383456-1383687(+)$1	231	7	35	20.0377
d[ccc[cccwwwwwwwwwwwwwwccccc	chr5:176884029-176884280(-)$1	251	128	156	23.0402
dd[gggggggtttttttttttggggggg	chr15:40998302-40998551(-)$1	249	189	217	21.6433
dddd!!cccwwwwwwwwwwwwwwccc]d	chr16:18937410-18937632(-)$1	222	84	112	22.3706
fffff[dddduuuuuuuuuuuudddd]f	chrX:64741166-64741391(-)$1	225	106	134	22.5646
c[eeeee!!avvvvvvvvvvvvva22ee	chr5:180670212-180670478(-)$1	266	25	53	22.5823
eggggggg^^^^^^^^^^^^^^^^^^^^	chr1:28563840-28564063(+)$1	223	133	161	15.7727
&&ccc[cccvvvvvvvvvvvvvccc]cc	chr12:12340199-12340418(-)$1	219	62	90	22.6563
:::cccdddduuuuuuuuuuuudddd]c	chr1:209955621-209955848(-)$1	227	83	111	20.5545
cccffffffvvvvvvvvvvvvvffffff	chr17:1613444-1613675(-)$1	231	166	194	22.2116
eeee!!bbwwwwwwwwwwwwwwbb22ee	chr15:100268101-100268321(+)$1	220	170	198	20.4794
:hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr14:21966350-21966595(-)$1	245	2	30	20.2113
:dddd[cccwwwwwwwwwwwwwwccc]d	chr9:35757446-35757668(+)$1	222	54	82	21.6482
fffff[cccyyyyyyyyyyyyyyyyccc	chr15:41001160-41001400(+)$1	240	180	208	21.6445
ddd::eeeeevvvvvvvvvvvvveeeee	chr19:50311852-50312075(+)$1	223	102	130	20.5052
ee[ddddddddtttttttttttdddd22	chr17:7476752-7476976(+)$1	224	99	127	20.3273
d!!ggggggguuuuuuuuuuuugggggg	chr9:138396111-138396342(+)$1	231	151	179	23.8453

#otherMatches

#Seq PSSM
UUUUAUGAAUUGAAUAAAGCUAGAAUCA	chr17:80861200-80861427(+)$1	227	12	40	19.5543
GGUUUUUCCUCAUGUGACUUCUGGGAAG	chr1:16785320-16785556(+)$1	236	74	102	20.9129
UUUAUAUUCAUAACAAAUACAUAUUGAA	chr1:116612436-116612661(+)$1	225	33	61	21.0968
AAGCGGCACUGAAUUCCUUCUCCAGGCC	chr20:3804881-3805100(-)$1	219	167	195	22.2848
CUGCCGGCCACCUAGCCUCCCUGCCGGC	chr13:41885485-41885704(+)$1	219	147	175	21.0211
CCUAGUGAUAACAGUACAAUCCUAUUCU	chr17:22023638-22023881(+)$1	243	44	72	23.3914
UCCUGCUGUACUUUUCUUCUUUUUGAGC	chr1:44431691-44431915(+)$1	224	37	65	16.1375
AACUCUUGGGUUAUUUAAUUUUUCCAAU	chr6:168364582-168364803(+)$1	221	179	207	22.7022
CCCCUGCUGACUCAAAACAACUGUGAGU	chr6:31802940-31803169(+)$1	229	15	43	21.3495
UCUUUUCGGAAUGUCAUAUUAACUGUGA	chr15:41022040-41022270(+)$1	230	157	185	23.2647
GACCAGGGCCCGGGGUUUGGGAGGGCUG	chr10:102265662-102265891(-)$1	229	194	222	18.7421
GGGCAGAACCACAACGUGCAAGGGUUCC	chr19:1434834-1435069(+)$1	235	32	60	23.1611
AAAGGUGUGGGAUGUGAUUGGCCGCAGC	chr11:66372897-66373117(+)$1	220	58	86	20.0542
GGUGCCUAUCUUUUAUGCUACUGGUAGU	chr7:6156431-6156659(+)$1	228	138	166	22.4903
CUGCAAGUAUGUUCACUAUGAAAUUGAU	chr14:21968957-21969221(-)$1	264	25	53	20.8347
cguaaucaggacuugcaacacccugauu	chr17:8076671-8076971(-)$1	300	159	187	21.4669
GCGAGUGGGCAUCCUGUCAUCAUCUCCA	chr16:4745099-4745334(+)$1	235	187	215	18.2154
GCCAGUGGCCCCCCACCUCAAAGGCGAC	chr1:19638886-19639129(+)$1	243	152	180	22.6453
UCAGCCUCUCUCGUUUAAUCUGAGUGGA	chr3:129033570-129033791(-)$1	221	175	203	20.2203
CCCAAUCGGACUGCCAAAUUCUCCGGUU	chr2:85133539-85133765(+)$1	226	165	193	19.2122
GGAUGGAGGACCCUGACCCUAAACCUCC	chr3:50685587-50685816(+)$1	229	32	60	20.4342
CACCUUGCCACAUAUUUGAACAGUGAUG	chr7:102065741-102065961(+)$1	220	68	96	21.5897
AACAUGCUGCUGCCCUAACCCCGUGUGG	chr2:242695143-242695375(+)$1	232	26	54	20.5342
CCUCAUUCUGGAAGCCAAGUUUAUACAG	chr14:94847044-94847267(+)$1	223	8	36	17.7914
CUCCGUCCCGGCGUCUCCAAAACUGAAU	chr7:103629706-103629934(-)$1	228	55	83	20.7235
ACAGCUGCAGACAAAAAUAUACUCUGUA	chr1:55207904-55208125(-)$1	221	182	210	18.6542
AGUGAACUCUUAUCCAACCUUUCUUCCG	chr4:119606601-119606855(-)$1	254	211	239	16.1873
UUUUACAGUGGUGGCUGAAUACAUUUUG	chr7:54819938-54820158(-)$1	220	37	65	21.7408
GGCUGCCAAGGGAGGAGGAAGAUGGCGG	chr6:117996611-117996835(+)$1	224	36	64	22.2253
CGAAUUUGUGUAAGGAAUUUUGUGGUCA	chr17:46657162-46657388(-)$1	226	113	141	21.6287
AAGGCCUAGGAAAGGUUAUUAUGAACUG	chr12:5024027-5024248(-)$1	221	39	67	21.9341
CAGAGAAAACGUAUUUAUUAUUCCAGAG	chr1:934311-934539(-)$1	228	171	199	15.6358
aaguuaguauacaaccccccacugcuaa	chr1:23696647-23696874(+)$1	227	151	179	22.2702
UUGCGCGGCGUCCCUUCGCCCCGCCUUC	chr19:3985341-3985561(-)$1	220	4	32	21.2375
UUCAGCUGGUUCCUCCAAACCCUUCAGC	chr17:72765291-72765515(+)$1	224	182	210	18.7425
CUGUACACCUGUCCCCCUGCUUCAGGUG	chr19:50001103-50001340(+)$1	237	175	203	19.7293
CCAGGCAGAGAAAACCUGCAUCCUCUGG	chr7:129771443-129771697(+)$1	254	85	113	23.0544
CGUCCCGCGCUGCGCCUUCCCUGCGCAG	chr19:1383456-1383687(+)$1	231	7	35	20.0377
GAUUGUAGCUCUUAGUCCUCCCUGCUCA	chr5:176884029-176884280(-)$1	251	128	156	23.0402
AGAAAUAUUAAAUCAACAAAAUAAUAUU	chr15:40998302-40998551(-)$1	249	189	217	21.6433
CGGAACGGCCGuccucuucccccgcccu	chr16:18937410-18937632(-)$1	222	84	112	22.3706
gggcaaggacucuacaucagcuguccgu	chrX:64741166-64741391(-)$1	225	106	134	22.5646
UUGGAGAGUUGGAAACUUUUAAAAUAUC	chr5:180670212-180670478(-)$1	266	25	53	22.5823
AAUGGAUAUUUGCCUUUUAGCUACACCC	chr1:28563840-28564063(+)$1	223	133	161	15.7727
CAGCAGUGCAAACAAUGAAAAAGCAGUG	chr12:12340199-12340418(-)$1	219	62	90	22.6563
AUAUGCCUCCAACUGAAUUUGAGGAGAG	chr1:209955621-209955848(-)$1	227	83	111	20.5545
GGCGCCUCCUUCCUCGCGUUCCGGGGGC	chr17:1613444-1613675(-)$1	231	166	194	22.2116
CUAGCCCCUCCAUCAAGUCUUUGGUCCU	chr15:100268101-100268321(+)$1	220	170	198	20.4794
AUUUGGUAUGCAUUUUUUAACAAUAUUA	chr14:21966350-21966595(-)$1	245	2	30	20.2113
AUUGGGGUGAGAGAGGAAGGAAGCACGC	chr9:35757446-35757668(+)$1	222	54	82	21.6482
AAAUAAGCAAGCAUUACUUCAUUCCUGC	chr15:41001160-41001400(+)$1	240	180	208	21.6445
CCCUCCAUCCGAGCCCUACCCGAGGAUG	chr19:50311852-50312075(+)$1	223	102	130	20.5052
GUGAGCGGCCUGAGGUAUGGGAGGGCGA	chr17:7476752-7476976(+)$1	224	99	127	20.3273
GAUGCUGCUGUCCCUGUGAUCCCAGCAG	chr9:138396111-138396342(+)$1	231	151	179	23.8453

#DB
((((((((.((...........)).)))	chr17:80861200-80861427(+)$1	1	12	40	19.5543
.((((((((.............))))))	chr1:16785320-16785556(+)$1	1	74	102	20.9129
(((((.((((..............))))	chr1:116612436-116612661(+)$1	1	33	61	21.0968
((..(((.(((...........))))))	chr20:3804881-3805100(-)$1	1	167	195	22.2848
..((((((..............))))))	chr13:41885485-41885704(+)$1	1	147	175	21.0211
(((((.((((............))))))	chr17:22023638-22023881(+)$1	1	44	72	23.3914
(((((((..................)))	chr1:44431691-44431915(+)$1	1	37	65	16.1375
(((..(((((............))))).	chr6:168364582-168364803(+)$1	1	179	207	22.7022
((((.(((.((...........)).)))	chr6:31802940-31803169(+)$1	1	15	43	21.3495
(((((.(((.............))).))	chr15:41022040-41022270(+)$1	1	157	185	23.2647
..))))(((((...........))))))	chr10:102265662-102265891(-)$1	1	194	222	18.7421
(((..(((((............))))).	chr19:1434834-1435069(+)$1	1	32	60	23.1611
..((((((((...........))))).)	chr11:66372897-66373117(+)$1	1	58	86	20.0542
((((((((((............))))).	chr7:6156431-6156659(+)$1	1	138	166	22.4903
.(((((((((................))	chr14:21968957-21969221(-)$1	1	25	53	20.8347
)))(((((((...........)))))))	chr17:8076671-8076971(-)$1	1	159	187	21.4669
(..((((((...............))))	chr16:4745099-4745334(+)$1	1	187	215	18.2154
((..((.(((............))).))	chr1:19638886-19639129(+)$1	1	152	180	22.6453
....((.(((...........))).)).	chr3:129033570-129033791(-)$1	1	175	203	20.2203
...(((((((...........)))))))	chr2:85133539-85133765(+)$1	1	165	193	19.2122
(((((((((..............)))))	chr3:50685587-50685816(+)$1	1	32	60	20.4342
((.((((.(((...........))).))	chr7:102065741-102065961(+)$1	1	68	96	21.5897
..((((((((..............))))	chr2:242695143-242695375(+)$1	1	26	54	20.5342
(..(((((((...............)))	chr14:94847044-94847267(+)$1	1	8	36	17.7914
(((.....(((...........)))...	chr7:103629706-103629934(-)$1	1	55	83	20.7235
...))((((((...........))))))	chr1:55207904-55208125(-)$1	1	182	210	18.6542
(..((.(((..................)	chr4:119606601-119606855(-)$1	1	211	239	16.1873
(((((.((((...........)))).))	chr7:54819938-54820158(-)$1	1	37	65	21.7408
.(((((((..............))))))	chr6:117996611-117996835(+)$1	1	36	64	22.2253
((((((((((................))	chr17:46657162-46657388(-)$1	1	113	141	21.6287
((.((.(((................)))	chr12:5024027-5024248(-)$1	1	39	67	21.9341
.(((((((((..................	chr1:934311-934539(-)$1	1	171	199	15.6358
((.((((((.............))))))	chr1:23696647-23696874(+)$1	1	151	179	22.2702
(.(((.((((...........))))..)	chr19:3985341-3985561(-)$1	1	4	32	21.2375
....(((((..............)))))	chr17:72765291-72765515(+)$1	1	182	210	18.7425
)))).((((((...........))))))	chr19:50001103-50001340(+)$1	1	175	203	19.7293
((...(((((............))))))	chr7:129771443-129771697(+)$1	1	85	113	23.0544
.)))))((((............))))((	chr19:1383456-1383687(+)$1	1	7	35	20.0377
(.(((.(((..............)))))	chr5:176884029-176884280(-)$1	1	128	156	23.0402
((.(((((((...........)))))))	chr15:40998302-40998551(-)$1	1	189	217	21.6433
((((..(((..............))).)	chr16:18937410-18937632(-)$1	1	84	112	22.3706
(((((.((((............)))).)	chrX:64741166-64741391(-)$1	1	106	134	22.5646
(.(((((..(.............)..))	chr5:180670212-180670478(-)$1	1	25	53	22.5823
((((((((....................	chr1:28563840-28564063(+)$1	1	133	161	15.7727
..(((.(((.............))).))	chr12:12340199-12340418(-)$1	1	62	90	22.6563
...(((((((............)))).)	chr1:209955621-209955848(-)$1	1	83	111	20.5545
)))((((((.............))))))	chr17:1613444-1613675(-)$1	1	166	194	22.2116
((((..((..............))..))	chr15:100268101-100268321(+)$1	1	170	198	20.4794
.((((((((.............))))))	chr14:21966350-21966595(-)$1	1	2	30	20.2113
.((((.(((..............))).)	chr9:35757446-35757668(+)$1	1	54	82	21.6482
(((((.(((................)))	chr15:41001160-41001400(+)$1	1	180	208	21.6445
)))..(((((.............)))))	chr19:50311852-50312075(+)$1	1	102	130	20.5052
((.((((((((...........))))..	chr17:7476752-7476976(+)$1	1	99	127	20.3273
(..(((((((............))))))	chr9:138396111-138396342(+)$1	1	151	179	23.8453

#PSSM
e : 0.16	d : 0.14	: : 0.12	c : 0.09	g : 0.07	" : 0.05	= : 0.05	f : 0.05	b : 0.05	h : 0.01	m : 0.01	$ : 0.01	F : 0.01	! : 0.01	q : 0.01	[ : 0.01	l : 0.01	& : 0.01	
e : 0.14	d : 0.11	g : 0.11	! : 0.09	c : 0.07	: : 0.07	h : 0.05	= : 0.05	[ : 0.05	b : 0.03	i : 0.03	f : 0.03	" : 0.01	m : 0.01	$ : 0.01	F : 0.01	q : 0.01	& : 0.01	
c : 0.14	! : 0.11	d : 0.09	g : 0.09	e : 0.09	[ : 0.09	h : 0.07	f : 0.05	= : 0.05	: : 0.05	i : 0.03	b : 0.01	$ : 0.01	F : 0.01	q : 0.01	" : 0.01	
g : 0.16	d : 0.11	f : 0.11	c : 0.11	h : 0.07	! : 0.07	e : 0.07	= : 0.05	b : 0.05	i : 0.03	$ : 0.03	: : 0.03	F : 0.01	a : 0.01	" : 0.01	
g : 0.14	f : 0.12	c : 0.11	d : 0.09	e : 0.09	b : 0.09	h : 0.07	! : 0.07	= : 0.05	i : 0.03	: : 0.03	[ : 0.01	$ : 0.01	" : 0.01	
[ : 0.22	e : 0.18	f : 0.12	g : 0.11	h : 0.07	c : 0.05	d : 0.05	= : 0.03	i : 0.03	b : 0.03	! : 0.03	$ : 0.01	
c : 0.18	e : 0.18	d : 0.16	f : 0.12	g : 0.11	h : 0.07	= : 0.03	i : 0.03	[ : 0.03	$ : 0.01	b : 0.01	
c : 0.20	e : 0.16	d : 0.14	f : 0.12	g : 0.11	h : 0.07	[ : 0.03	i : 0.03	^ : 0.01	$ : 0.01	= : 0.01	! : 0.01	b : 0.01	
c : 0.24	e : 0.16	d : 0.14	f : 0.11	g : 0.07	h : 0.05	w : 0.05	[ : 0.03	^ : 0.03	i : 0.03	= : 0.01	! : 0.01	
d : 0.14	w : 0.14	e : 0.12	v : 0.11	c : 0.09	g : 0.07	^ : 0.05	f : 0.05	b : 0.03	i : 0.03	y : 0.03	x : 0.01	h : 0.01	= : 0.01	a : 0.01	
w : 0.18	u : 0.18	v : 0.14	t : 0.12	^ : 0.07	y : 0.07	c : 0.05	b : 0.03	x : 0.03	f : 0.03	e : 0.01	d : 0.01	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
t : 0.29	w : 0.18	u : 0.18	v : 0.14	^ : 0.07	y : 0.07	x : 0.03	
w : 0.18	u : 0.18	t : 0.16	v : 0.14	^ : 0.07	y : 0.07	g : 0.05	x : 0.03	d : 0.03	e : 0.01	c : 0.01	
w : 0.12	c : 0.12	d : 0.12	e : 0.11	f : 0.09	g : 0.09	^ : 0.07	y : 0.07	b : 0.05	h : 0.03	x : 0.03	v : 0.03	
c : 0.18	e : 0.16	d : 0.12	f : 0.09	g : 0.09	^ : 0.07	y : 0.07	b : 0.05	h : 0.03	w : 0.03	x : 0.03	a : 0.01	
c : 0.16	e : 0.16	d : 0.14	f : 0.11	g : 0.09	^ : 0.07	y : 0.07	] : 0.05	h : 0.05	2 : 0.03	x : 0.01	
e : 0.16	c : 0.12	f : 0.12	d : 0.11	] : 0.09	g : 0.09	h : 0.07	^ : 0.05	2 : 0.05	y : 0.03	= : 0.01	b : 0.01	3 : 0.01	
e : 0.20	f : 0.12	c : 0.11	g : 0.11	] : 0.09	h : 0.07	= : 0.05	^ : 0.05	d : 0.03	b : 0.03	2 : 0.03	i : 0.01	3 : 0.01	E : 0.01	
c : 0.18	f : 0.14	e : 0.12	g : 0.11	h : 0.07	d : 0.07	= : 0.05	2 : 0.03	3 : 0.03	^ : 0.03	] : 0.01	B : 0.01	5 : 0.01	i : 0.01	b : 0.01	E : 0.01	

#score	1124.9688580861773
#seq	54
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_CDS_m3_run1.txt

#BEAR
eeeeennnnneeeee	chr3:16310641-16310867(+)$1	226	210	225	12.9411
gggggnnnnnggggg	chr6:138198170-138198390(+)$1	220	94	109	9.9810
eeeeennnnneeeee	chr9:36665281-36665501(+)$1	220	125	140	12.9411
eeeeennnnneeeee	chr15:43621647-43621877(-)$1	230	202	217	12.9411
eeeeennnnneeeee	chr15:52681409-52681632(-)$1	223	187	202	12.9411
gggggnnnnnggggg	chr17:62499011-62499234(-)$1	223	118	133	9.9810
eeeeennnnneeeee	chr13:23927843-23928068(-)$1	225	146	161	12.9411
$ddddnnnnndddd3	chr6:31378222-31378446(+)$1	224	85	100	10.1366
Gddddnnnnnddddd	chr9:123533541-123533763(-)$1	222	72	87	9.8374
!!cccnnnnnccc]a	chr11:73789580-73789799(-)$1	219	146	161	9.5675
eeeeennnnneeeee	chr3:172046718-172046940(+)$1	222	16	31	12.9411
ffcccnnnnnccc]f	chr17:62496159-62496385(-)$1	226	183	198	9.3752
eeeeennnnneeeee	chr8:56864513-56864743(+)$1	230	20	35	12.9411
eeeeennnnneeeee	chr3:121190876-121191106(-)$1	230	13	28	12.9411
eddddnnnnnddddc	chr6:111697416-111697640(-)$1	224	73	88	10.6905
eeeeennnnneeeee	chr4:184605859-184606079(+)$1	220	48	63	12.9411
cddddnnnnndddd]	chr17:76694278-76694503(-)$1	225	13	28	10.3970
!ddddnnnnndddd5	chr14:64954607-64954837(-)$1	230	106	121	9.6642
eeeeennnnneeeee	chr20:52192199-52192420(-)$1	221	197	212	12.9411
!!cccnnnnnccc22	chr14:77935329-77935552(+)$1	223	128	143	9.2253
fddddnnnnndddd]	chr8:48769672-48769902(-)$1	230	70	85	10.4376
d[cccnnnnncccdd	chr5:179048268-179048488(-)$1	220	127	142	9.6135
eeebbnnnnnbb]ee	chr2:220116686-220116916(-)$1	230	131	146	10.4425
iiiiinnnnniiiii	chr3:127429367-127429590(-)$1	223	199	214	9.7305
eeeeennnnneeeee	chr12:70149215-70149436(+)$1	221	164	179	12.9411
eeeeennnnneeeee	chr10:22207611-22207841(-)$1	230	132	147	12.9411
eeeeennnnneeeee	chr2:70503797-70504024(+)$1	227	110	125	12.9411
gggggnnnnnggggg	chr5:102526468-102526698(+)$1	230	210	225	9.9810
eeeeennnnneeeee	chr8:71069218-71069448(-)$1	230	193	208	12.9411
!ddddnnnnndddd2	chr14:95590716-95590935(-)$1	219	183	198	10.3392
cddddnnnnnddddd	chr16:14340417-14340637(+)$1	220	173	188	10.3324
ee[bbnnnnnbb]ee	chr13:33306191-33306409(+)$1	218	63	78	10.0963
eeeeennnnneeeee	chr16:67331366-67331586(+)$1	220	56	71	12.9411
eeeeennnnneeeee	chrX:149901021-149901240(+)$1	219	170	185	12.9411
eeeeennnnneeeee	chr20:5539319-5539537(-)$1	218	7	22	12.9411
eeeeennnnneeeee	chr4:2966922-2967152(+)$1	230	197	212	12.9411
eeebbnnnnnbb]ee	chr1:2321299-2321520(-)$1	221	155	170	10.4425
eeeeennnnneeeee	chr16:27460462-27460680(+)$1	218	135	150	12.9411
gggggnnnnnggggg	chr19:48630439-48630656(-)$1	217	62	77	9.9810
eeeeennnnneeeee	chr2:70441446-70441668(-)$1	222	188	203	12.9411
eeeeennnnneeeee	chr6:160105818-160106038(-)$1	220	81	96	12.9411
[ddddnnnnndddd]	chr4:164061296-164061526(-)$1	230	151	166	10.5292
eeeeennnnneeeee	chr8:68139373-68139597(-)$1	224	166	181	12.9411
ee[bbnnnnnbbeee	chr15:52902192-52902422(-)$1	230	89	104	10.4391
eeeeennnnneeeee	chr8:134050739-134050959(-)$1	220	117	132	12.9411
eeeeennnnneeeee	chr22:18567813-18568037(+)$1	224	11	26	12.9411
eeeeennnnneeeee	chr6:71235551-71235771(+)$1	220	158	173	12.9411
eeeeennnnneeeee	chr17:4800439-4800660(+)$1	221	57	72	12.9411

#otherMatches

#Seq PSSM
ACUACGUUUAGUGGU	chr3:16310641-16310867(+)$1	226	210	225	12.9411
AAAAGUUCACUUUUU	chr6:138198170-138198390(+)$1	220	94	109	9.9810
UGCAGAACACCUGCA	chr9:36665281-36665501(+)$1	220	125	140	12.9411
CAGGGGUAUUCCCUG	chr15:43621647-43621877(-)$1	230	202	217	12.9411
UUGCUGACAAAGUAA	chr15:52681409-52681632(-)$1	223	187	202	12.9411
CACUUGAACUGAGUG	chr17:62499011-62499234(-)$1	223	118	133	9.9810
UAUUAUAGUUUAGUA	chr13:23927843-23928068(-)$1	225	146	161	12.9411
CCUCUUCCCCAGAGC	chr6:31378222-31378446(+)$1	224	85	100	10.1366
AUACAUUGUCUGUAG	chr9:123533541-123533763(-)$1	222	72	87	9.8374
GCAUCGUGGAGAUAG	chr11:73789580-73789799(-)$1	219	146	161	9.5675
CUUUUAGGGAAAAAG	chr3:172046718-172046940(+)$1	222	16	31	12.9411
AAUCCAACAGGGACU	chr17:62496159-62496385(-)$1	226	183	198	9.3752
CUCUGUCUGUCAGAG	chr8:56864513-56864743(+)$1	230	20	35	12.9411
CUGUAUUAUUUACAG	chr3:121190876-121191106(-)$1	230	13	28	12.9411
AAGAUAUUCCAUCUG	chr6:111697416-111697640(-)$1	224	73	88	10.6905
CUGUAUUAACUACAG	chr4:184605859-184606079(+)$1	220	48	63	12.9411
AGACAUAAAUUGUCA	chr17:76694278-76694503(-)$1	225	13	28	10.3970
UCAGCUAUUUGUUGC	chr14:64954607-64954837(-)$1	230	106	121	9.6642
GAUUAAUAGCUAAUC	chr20:52192199-52192420(-)$1	221	197	212	12.9411
AACGGAGAGACUGAG	chr14:77935329-77935552(+)$1	223	128	143	9.2253
UUAGCCCCUUGCUGC	chr8:48769672-48769902(-)$1	230	70	85	10.4376
CAUCUACACCAGAGA	chr5:179048268-179048488(-)$1	220	127	142	9.6135
UGCUGGAAAACACGU	chr2:220116686-220116916(-)$1	230	131	146	10.4425
UAGCUUGGGUGGCUG	chr3:127429367-127429590(-)$1	223	199	214	9.7305
UACACAACCCGUGUA	chr12:70149215-70149436(+)$1	221	164	179	12.9411
AGGUAAAAUGUACCU	chr10:22207611-22207841(-)$1	230	132	147	12.9411
CUGAGACUCGUUCAG	chr2:70503797-70504024(+)$1	227	110	125	12.9411
AAUUUGUAGGAAAUU	chr5:102526468-102526698(+)$1	230	210	225	9.9810
CAUGUGUCAGGCAUG	chr8:71069218-71069448(-)$1	230	193	208	12.9411
AAUAUAAACCAUAUG	chr14:95590716-95590935(-)$1	219	183	198	10.3392
AACGCAACCCGUGUG	chr16:14340417-14340637(+)$1	220	173	188	10.3324
UACAUCACAAAUCUA	chr13:33306191-33306409(+)$1	218	63	78	10.0963
GCCAAAGUCCUUGGC	chr16:67331366-67331586(+)$1	220	56	71	12.9411
AUACCAACAAGGUAU	chrX:149901021-149901240(+)$1	219	170	185	12.9411
AUUCCAAAAAGGAAU	chr20:5539319-5539537(-)$1	218	7	22	12.9411
CUGUGCUAGCCACGG	chr4:2966922-2967152(+)$1	230	197	212	12.9411
CGGUGAGAAGCAUCU	chr1:2321299-2321520(-)$1	221	155	170	10.4425
CAGCUAAUGAGGCUG	chr16:27460462-27460680(+)$1	218	135	150	12.9411
GUCUGAGAUCCAGGU	chr19:48630439-48630656(-)$1	217	62	77	9.9810
GUAAGCAUAUCUUAU	chr2:70441446-70441668(-)$1	222	188	203	12.9411
GUUUCAAUAAGGAAC	chr6:160105818-160106038(-)$1	220	81	96	12.9411
AGUAAGUACUUUACC	chr4:164061296-164061526(-)$1	230	151	166	10.5292
CAUCUGAUCAAGAUG	chr8:68139373-68139597(-)$1	224	166	181	12.9411
GGUACAAACAGUUCA	chr15:52902192-52902422(-)$1	230	89	104	10.4391
GCAUCUCCCUGAUGU	chr8:134050739-134050959(-)$1	220	117	132	12.9411
GGGAAGCUGAUUCCC	chr22:18567813-18568037(+)$1	224	11	26	12.9411
GGCACUCCUUGUGUC	chr6:71235551-71235771(+)$1	220	158	173	12.9411
AGGUGUUUUUUGCCU	chr17:4800439-4800660(+)$1	221	57	72	12.9411

#DB
(((((.....)))))	chr3:16310641-16310867(+)$1	1	210	225	12.9411
(((((.....)))))	chr6:138198170-138198390(+)$1	1	94	109	9.9810
(((((.....)))))	chr9:36665281-36665501(+)$1	1	125	140	12.9411
(((((.....)))))	chr15:43621647-43621877(-)$1	1	202	217	12.9411
(((((.....)))))	chr15:52681409-52681632(-)$1	1	187	202	12.9411
(((((.....)))))	chr17:62499011-62499234(-)$1	1	118	133	9.9810
(((((.....)))))	chr13:23927843-23928068(-)$1	1	146	161	12.9411
.((((.....)))).	chr6:31378222-31378446(+)$1	1	85	100	10.1366
(((((.....))))(	chr9:123533541-123533763(-)$1	1	72	87	9.8374
..(((.....))).)	chr11:73789580-73789799(-)$1	1	146	161	9.5675
(((((.....)))))	chr3:172046718-172046940(+)$1	1	16	31	12.9411
(((((.....))).)	chr17:62496159-62496385(-)$1	1	183	198	9.3752
(((((.....)))))	chr8:56864513-56864743(+)$1	1	20	35	12.9411
(((((.....)))))	chr3:121190876-121191106(-)$1	1	13	28	12.9411
)((((.....))))(	chr6:111697416-111697640(-)$1	1	73	88	10.6905
(((((.....)))))	chr4:184605859-184606079(+)$1	1	48	63	12.9411
(((((.....)))).	chr17:76694278-76694503(-)$1	1	13	28	10.3970
.((((.....)))).	chr14:64954607-64954837(-)$1	1	106	121	9.6642
(((((.....)))))	chr20:52192199-52192420(-)$1	1	197	212	12.9411
..(((.....)))..	chr14:77935329-77935552(+)$1	1	128	143	9.2253
(((((.....)))).	chr8:48769672-48769902(-)$1	1	70	85	10.4376
(.(((.....)))))	chr5:179048268-179048488(-)$1	1	127	142	9.6135
(((((.....)).))	chr2:220116686-220116916(-)$1	1	131	146	10.4425
(((((.....)))))	chr3:127429367-127429590(-)$1	1	199	214	9.7305
(((((.....)))))	chr12:70149215-70149436(+)$1	1	164	179	12.9411
(((((.....)))))	chr10:22207611-22207841(-)$1	1	132	147	12.9411
(((((.....)))))	chr2:70503797-70504024(+)$1	1	110	125	12.9411
(((((.....)))))	chr5:102526468-102526698(+)$1	1	210	225	9.9810
(((((.....)))))	chr8:71069218-71069448(-)$1	1	193	208	12.9411
.((((.....)))).	chr14:95590716-95590935(-)$1	1	183	198	10.3392
)((((.....))))(	chr16:14340417-14340637(+)$1	1	173	188	10.3324
((.((.....)).))	chr13:33306191-33306409(+)$1	1	63	78	10.0963
(((((.....)))))	chr16:67331366-67331586(+)$1	1	56	71	12.9411
(((((.....)))))	chrX:149901021-149901240(+)$1	1	170	185	12.9411
(((((.....)))))	chr20:5539319-5539537(-)$1	1	7	22	12.9411
(((((.....)))))	chr4:2966922-2967152(+)$1	1	197	212	12.9411
(((((.....)).))	chr1:2321299-2321520(-)$1	1	155	170	10.4425
(((((.....)))))	chr16:27460462-27460680(+)$1	1	135	150	12.9411
(((((.....)))))	chr19:48630439-48630656(-)$1	1	62	77	9.9810
(((((.....)))))	chr2:70441446-70441668(-)$1	1	188	203	12.9411
(((((.....)))))	chr6:160105818-160106038(-)$1	1	81	96	12.9411
.((((.....)))).	chr4:164061296-164061526(-)$1	1	151	166	10.5292
(((((.....)))))	chr8:68139373-68139597(-)$1	1	166	181	12.9411
((.((.....)))))	chr15:52902192-52902422(-)$1	1	89	104	10.4391
(((((.....)))))	chr8:134050739-134050959(-)$1	1	117	132	12.9411
(((((.....)))))	chr22:18567813-18568037(+)$1	1	11	26	12.9411
(((((.....)))))	chr6:71235551-71235771(+)$1	1	158	173	12.9411
(((((.....)))))	chr17:4800439-4800660(+)$1	1	57	72	12.9411

#PSSM
e : 0.64	g : 0.08	! : 0.08	f : 0.04	c : 0.04	$ : 0.02	G : 0.02	d : 0.02	i : 0.02	[ : 0.02	
e : 0.62	d : 0.18	g : 0.08	! : 0.04	f : 0.02	[ : 0.02	i : 0.02	
e : 0.58	d : 0.18	g : 0.08	c : 0.08	[ : 0.04	i : 0.02	
e : 0.54	d : 0.18	g : 0.08	c : 0.08	b : 0.08	i : 0.02	
e : 0.54	d : 0.18	g : 0.08	c : 0.08	b : 0.08	i : 0.02	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
e : 0.54	d : 0.18	g : 0.08	c : 0.08	b : 0.08	i : 0.02	
e : 0.54	d : 0.18	g : 0.08	c : 0.08	b : 0.08	i : 0.02	
e : 0.56	d : 0.18	g : 0.08	c : 0.08	] : 0.06	i : 0.02	
e : 0.62	d : 0.20	g : 0.08	] : 0.04	2 : 0.02	i : 0.02	
e : 0.62	g : 0.08	d : 0.06	] : 0.06	2 : 0.04	3 : 0.02	a : 0.02	f : 0.02	c : 0.02	5 : 0.02	i : 0.02	

#score	557.6904894191752
#seq	48
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_CDS_m3_run2.txt

#BEAR
ggggccc[cccoooooocccccc22gg	chr12:57107220-57107481(-)$1	261	170	197	14.9454
[addddeeeeeooooooeeeee333dd	chr17:40010858-40011223(-)$1	365	240	267	13.0732
!!bb!!eeeeeooooooeeeeebb22b	chr14:54894419-54894655(-)$1	236	56	83	11.9228
===hhhhhhhhoooooohhhhhhhh22	chrX:153998940-153999183(+)$1	243	21	48	11.7305
ggggg!!ddddoooooodddd22gggg	chr2:239186344-239186586(-)$1	242	147	174	13.0287
ff[dddd[cccooooooccc]dddd33	chr2:44457644-44457880(+)$1	236	191	218	13.3510
iiiiiiiiibboooooobb22iiiiii	chr4:24541694-24542016(-)$1	322	264	291	14.1712
d[ccc####bboooooobb]ccc]ddd	chr19:57802538-57802795(+)$1	257	75	102	13.9081
hhhccc[ddddoooooodddd]ccc]h	chr17:40141350-40141593(-)$1	243	87	114	12.3693
ggggggg[cccooooooccc]gggggg	chr19:3977963-3978230(-)$1	267	30	57	14.9214
dd[dddd[cccoooooocccddddddd	chr3:50144158-50144381(+)$1	223	137	164	13.0520
[eeeee!!cccooooooccc333eeee	chr2:170003196-170003442(-)$1	246	22	49	14.3581
[eeeee"""bboooooobb]eeeeecc	chr13:42876892-42877163(+)$1	271	9	36	13.5786
ggggggg!!bboooooobb22gggggg	chr2:25965426-25965658(-)$1	232	127	154	14.2062
g!!ccc[ddddoooooodddd]cccgg	chr4:24529339-24529763(-)$1	424	80	107	13.3216
eeeeccc!!cccoooooocccccc]ee	chr14:102467771-102468034(+)$1	263	233	260	12.6582
eeeee[a[cccooooooccca]eeeee	chr3:135870195-135870437(-)$1	242	27	54	13.8833
==ccc[eeeeeooooooeeeee]ccc:	chr18:47906385-47906649(+)$1	264	152	179	12.3446
#eeeee####aooooooa4444eeeee	chr6:36442495-36442797(+)$1	302	46	73	12.8922
eeeegggggggoooooogggggggccc	chr12:64853887-64854140(+)$1	253	141	168	14.1050
c[iiiiiiiiiooooooiiiiiiiii2	chr14:39648513-39648753(+)$1	240	62	89	14.3787
d!!hhhhhhhhoooooohhhhhhhhdd	chr14:39782444-39782684(+)$1	240	50	77	11.9457
gggggg[ddddooooooddddgggggg	chr1:242021837-242022120(+)$1	283	248	275	13.3482
bb"""bb[cccoooooocccbb333bb	chr19:30505835-30506116(+)$1	281	38	65	12.9064
ccc!!ffffffooooooffffff22cc	chr20:49508006-49508278(-)$1	272	135	162	13.6928
##a!!ccc[bboooooobb]ccc22ad	chr1:155451556-155451845(-)$1	289	88	115	14.6862
::iiiiiiiiiooooooiiiiiiiii:	chr11:92887181-92887411(-)$1	230	135	162	11.7412
eeee!!ddddaooooooa]dddd22ee	chr16:19548048-19548499(+)$1	451	58	85	13.0325
ddddgggggggooooooggggggg]dd	chr1:46080610-46080840(+)$1	230	15	42	13.7420
iiiiiiiiibboooooobb]iiiiiii	chr1:234603238-234603462(-)$1	224	140	167	14.6248
Dffffff[cccooooooccc]ffffff	chr1:91967243-91967480(+)$1	237	144	171	12.1833
e[ddddeeeeeooooooeeeee22ddd	chr10:94366864-94367092(+)$1	228	111	138	12.3577
cc[eeeee[bboooooobb]eeeee]c	chr1:113456615-113456901(-)$1	286	186	213	13.5342
FFggggggg[aooooooaggggggg::	chr6:64356450-64356674(+)$1	224	133	160	11.6453
gggggffffffooooooffffff22gg	chr10:70726793-70727055(+)$1	262	3	30	13.5653
"ccc[ccc[bboooooobb]ccc]ccc	chr17:30678470-30678744(+)$1	274	73	100	14.5739
ccc!!ccc[bboooooobb]ccc4444	chr19:36883818-36884065(-)$1	247	94	121	14.5801
eeee:ccccccooooooccc333cccE	chrM:3762-4035(+)$1	273	167	194	12.6875
dddd[ffffffooooooffffff]ddd	chr19:44777544-44777806(+)$1	262	226	253	12.8086
!!cccffffffooooooffffff22cc	chr15:78837111-78837396(+)$1	285	137	164	13.6778
eeeeaccc[bboooooobb]ccc]a]e	chr1:8923886-8924114(-)$1	228	179	206	14.2165
=====ffffffooooooffffff4444	chr4:71889215-71889521(+)$1	306	236	263	13.5878
eeffffffcccooooooccc22fffff	chr10:70515148-70515382(+)$1	234	26	53	12.7044
eee!!ffffffooooooffffff333e	chr6:34825457-34825713(+)$1	256	65	92	13.9216
c####ccccccooooooccc4444ccc	chr10:91479158-91479459(+)$1	301	200	227	14.4670
dddd####cccooooooccc333dddd	chr22:22153209-22153463(-)$1	254	167	194	13.8035
c:iiiiiiiiiooooooiiiiiiiiiB	chr1:156696626-156696871(-)$1	245	49	76	12.7230
cc$$$$$cccaooooooa]ccc22ccc	chr14:32562037-32562280(+)$1	243	104	131	13.0295
""a[a[eeeeeooooooeeeee]a]a4	chr5:138704329-138704576(+)$1	247	134	161	13.2328
####dddd[bboooooobb]dddd22c	chr9:74300062-74300316(-)$1	254	85	112	13.0326

#otherMatches

#Seq PSSM
CUUUUCUUGGGCAUUGUUCCAGACcag	chr12:57107220-57107481(-)$1	261	170	197	14.9454
GAUACUUUGUUGAUGAGGACAGAUGGG	chr17:40010858-40011223(-)$1	365	240	267	13.0732
UUAGUAAUGUUCAAAUUAACAUCUUUU	chr14:54894419-54894655(-)$1	236	56	83	11.9228
UCCUUUACUCUGGUGUGGGAGUGGGGU	chrX:153998940-153999183(+)$1	243	21	48	11.7305
UGCUCCACGGGGCGGGACUCGCAGGGC	chr2:239186344-239186586(-)$1	242	147	174	13.0287
GAUGAGUGGUGAAAAAAUAUGACUUUC	chr2:44457644-44457880(+)$1	236	191	218	13.3510
UCUAUUACUGCUAUGUUGUCAGGUAAU	chr4:24541694-24542016(-)$1	322	264	291	14.1712
CAGGUCACACCUCACACGGCACCAGCG	chr19:57802538-57802795(+)$1	257	75	102	13.9081
AGAUUGUAUUGAGAAGGCAGUUCAGUU	chr17:40141350-40141593(-)$1	243	87	114	12.3693
GCAAGAGUGGGACUUAACCUCUUUUUG	chr19:3977963-3978230(-)$1	267	30	57	14.9214
AAGUGAGUGGCUUCAUUGUCCUUAUUU	chr3:50144158-50144381(+)$1	223	137	164	13.0520
UGGAUGAAUGGAGAGGACCGCAACAUC	chr2:170003196-170003442(-)$1	246	22	49	14.3581
UGUGACAGAUGAAUAUGCAGGUCACCU	chr13:42876892-42877163(+)$1	271	9	36	13.5786
CUUAGCUAGCAAGAAUGUGAAGGCUGA	chr2:25965426-25965658(-)$1	232	127	154	14.2062
UCUGCCCACUUCUAAACAGGUUGGUGA	chr4:24529339-24529763(-)$1	424	80	107	13.3216
CUCCGUAUUACAAGGUGCUGUUGCUGG	chr14:102467771-102468034(+)$1	263	233	260	12.6582
UUCCUAGUCAUCAUUUUAUGCCAGGAA	chr3:135870195-135870437(-)$1	242	27	54	13.8833
AUGAGAUCAUUGUAAUAAAUGAACUUC	chr18:47906385-47906649(+)$1	264	152	179	12.3446
UGGUUUCUUUGUAUGUUCUUUUAGACC	chr6:36442495-36442797(+)$1	302	46	73	12.8922
GAUGUUCAAAUGAGAGAAUUUGAAGUG	chr12:64853887-64854140(+)$1	253	141	168	14.1050
ACUAAGACAAAGCCCCAUUUGUUUUAU	chr14:39648513-39648753(+)$1	240	62	89	14.3787
UUAUCUUUUGACAUGUAUUAAGAGAAU	chr14:39782444-39782684(+)$1	240	50	77	11.9457
AUAAUAUGGAUUUAAAUAUUCUGUUAU	chr1:242021837-242022120(+)$1	283	248	275	13.3482
ACCCACUAUUCCAGAACGAAAGGAAGU	chr19:30505835-30506116(+)$1	281	38	65	12.9064
UGAAGGGUUUUGGUCUAAGGACCAGUC	chr20:49508006-49508278(-)$1	272	135	162	13.6928
AAGGACUCUGUGAAAAAACUGGGAACU	chr1:155451556-155451845(-)$1	289	88	115	14.6862
CUUGUAAGUAUCauuauauauuuauau	chr11:92887181-92887411(-)$1	230	135	162	11.7412
UCCUAAAAUGCACCGAAGACGUUCCAG	chr16:19548048-19548499(+)$1	451	58	85	13.0325
UGGAAGUAUUUUAUGUUGAAUGCUGUC	chr1:46080610-46080840(+)$1	230	15	42	13.7420
UCCAAAGAAGGUGUUAUCCAUUUUUUG	chr1:234603238-234603462(-)$1	224	140	167	14.6248
GGUACGUGUUUAAAUCCAAAGAUGUAC	chr1:91967243-91967480(+)$1	237	144	171	12.1833
AGAGUAUACCUGGGAAGAGGUAUUUAU	chr10:94366864-94367092(+)$1	228	111	138	12.3577
GUAUCUAUCUCUUCAUUGGCAUGGGCA	chr1:113456615-113456901(-)$1	286	186	213	13.5342
ACUCGCUGAAGAACAUGCUCAGCGAUA	chr6:64356450-64356674(+)$1	224	133	160	11.6453
GAUAUCCUGGUUGGAACACCAGGUCGU	chr10:70726793-70727055(+)$1	262	3	30	13.5653
ACAGGAAUUUGACAAAGUAUAUUGCUG	chr17:30678470-30678744(+)$1	274	73	100	14.5739
GUAAGGAAUGCGGGAAGGCCUUCAGAC	chr19:36883818-36884065(-)$1	247	94	121	14.5801
UCUCAGGCUUCAACAUCGAAUACGCCG	chrM:3762-4035(+)$1	273	167	194	12.6875
GGUGAGGGCUUCAGUCAGGGCUCACAU	chr19:44777544-44777806(+)$1	262	226	253	12.8086
AGUUGGUUACAGCGCUGUGUGAUAUCA	chr15:78837111-78837396(+)$1	285	137	164	13.6778
AGGCGAGCAGCUUUCCCGCAGCUACGG	chr1:8923886-8924114(-)$1	228	179	206	14.2165
GAAAAUUUAAAGAAAUAUUUAGAACUC	chr4:71889215-71889521(+)$1	306	236	263	13.5878
CACUGGUCUCCUUCGUUGGAUGGACCA	chr10:70515148-70515382(+)$1	234	26	53	12.7044
UCAGUUAAAUGGUCUGACAUUUACUAU	chr6:34825457-34825713(+)$1	256	65	92	13.9216
GAAAACGCUGAAGAAACUCAAAAUGUG	chr10:91479158-91479459(+)$1	301	200	227	14.4670
GGAUGAAGUUUGCAUAAAAAGAAAUCC	chr22:22153209-22153463(-)$1	254	167	194	13.8035
GAGAUGUGCUUUAUGACGAGUACAUUC	chr1:156696626-156696871(-)$1	245	49	76	12.7230
CAGUUAAACACAAUUUGGAUGUGGUGA	chr14:32562037-32562280(+)$1	243	104	131	13.0295
GGGGUGAAGUACGGAAAUAUUUGAGUA	chr5:138704329-138704576(+)$1	247	134	161	13.2328
GCCUUGGGGUGCUUGAACAAUUCAUAC	chr9:74300062-74300316(-)$1	254	85	112	13.0326

#DB
(((((((.(((......))))))..))	chr12:57107220-57107481(-)$1	1	170	197	14.9454
.((((((((((......)))))...))	chr17:40010858-40011223(-)$1	1	240	267	13.0732
..((..(((((......)))))))..)	chr14:54894419-54894655(-)$1	1	56	83	11.9228
(((((((((((......))))))))..	chrX:153998940-153999183(+)$1	1	21	48	11.7305
(((((..((((......))))..))))	chr2:239186344-239186586(-)$1	1	147	174	13.0287
((.((((.(((......))).))))..	chr2:44457644-44457880(+)$1	1	191	218	13.3510
(((((((((((......))..))))))	chr4:24541694-24542016(-)$1	1	264	291	14.1712
(.(((....((......)).))).)))	chr19:57802538-57802795(+)$1	1	75	102	13.9081
((((((.((((......)))).))).)	chr17:40141350-40141593(-)$1	1	87	114	12.3693
(((((((.(((......))).))))))	chr19:3977963-3978230(-)$1	1	30	57	14.9214
((.((((.(((......))))))))))	chr3:50144158-50144381(+)$1	1	137	164	13.0520
.(((((..(((......)))...))))	chr2:170003196-170003442(-)$1	1	22	49	14.3581
.(((((...((......)).)))))))	chr13:42876892-42877163(+)$1	1	9	36	13.5786
(((((((..((......))..))))))	chr2:25965426-25965658(-)$1	1	127	154	14.2062
(..(((.((((......)))).)))))	chr4:24529339-24529763(-)$1	1	80	107	13.3216
(((((((..(((......)))))).))	chr14:102467771-102468034(+)$1	1	233	260	12.6582
(((((.(.(((......)))).)))))	chr3:135870195-135870437(-)$1	1	27	54	13.8833
))(((.(((((......))))).))).	chr18:47906385-47906649(+)$1	1	152	179	12.3446
.(((((....(......)....)))))	chr6:36442495-36442797(+)$1	1	46	73	12.8922
))))(((((((......)))))))(((	chr12:64853887-64854140(+)$1	1	141	168	14.1050
(.(((((((((......))))))))).	chr14:39648513-39648753(+)$1	1	62	89	14.3787
(..((((((((......))))))))))	chr14:39782444-39782684(+)$1	1	50	77	11.9457
((((((.((((......))))))))))	chr1:242021837-242022120(+)$1	1	248	275	13.3482
((...((.(((......)))))...))	chr19:30505835-30506116(+)$1	1	38	65	12.9064
(((..((((((......))))))..))	chr20:49508006-49508278(-)$1	1	135	162	13.6928
..(..(((.((......)).)))..))	chr1:155451556-155451845(-)$1	1	88	115	14.6862
..(((((((((......))))))))).	chr11:92887181-92887411(-)$1	1	135	162	11.7412
((((..(((((......).))))..))	chr16:19548048-19548499(+)$1	1	58	85	13.0325
(((((((((((......))))))).))	chr1:46080610-46080840(+)$1	1	15	42	13.7420
(((((((((((......)).)))))))	chr1:234603238-234603462(-)$1	1	140	167	14.6248
(((((((.(((......))).))))))	chr1:91967243-91967480(+)$1	1	144	171	12.1833
(.(((((((((......)))))..)))	chr10:94366864-94367092(+)$1	1	111	138	12.3577
((.(((((.((......)).))))).)	chr1:113456615-113456901(-)$1	1	186	213	13.5342
))(((((((.(......))))))))..	chr6:64356450-64356674(+)$1	1	133	160	11.6453
(((((((((((......))))))..))	chr10:70726793-70727055(+)$1	1	3	30	13.5653
.(((.(((.((......)).))).)))	chr17:30678470-30678744(+)$1	1	73	100	14.5739
(((..(((.((......)).)))....	chr19:36883818-36884065(-)$1	1	94	121	14.5801
)))).((((((......)))...))))	chrM:3762-4035(+)$1	1	167	194	12.6875
((((.((((((......)))))).)))	chr19:44777544-44777806(+)$1	1	226	253	12.8086
..(((((((((......))))))..))	chr15:78837111-78837396(+)$1	1	137	164	13.6778
((((((((.((......)).))).).)	chr1:8923886-8924114(-)$1	1	179	206	14.2165
(((((((((((......))))))....	chr4:71889215-71889521(+)$1	1	236	263	13.5878
))(((((((((......)))..)))))	chr10:70515148-70515382(+)$1	1	26	53	12.7044
(((..((((((......))))))...)	chr6:34825457-34825713(+)$1	1	65	92	13.9216
(....((((((......)))....)))	chr10:91479158-91479459(+)$1	1	200	227	14.4670
((((....(((......)))...))))	chr22:22153209-22153463(-)$1	1	167	194	13.8035
).(((((((((......)))))))))(	chr1:156696626-156696871(-)$1	1	49	76	12.7230
((.....((((......).)))..)))	chr14:32562037-32562280(+)$1	1	104	131	13.0295
..(.(.(((((......))))).).).	chr5:138704329-138704576(+)$1	1	134	161	13.2328
....((((.((......)).))))..)	chr9:74300062-74300316(-)$1	1	85	112	13.0326

#PSSM
e : 0.18	g : 0.14	c : 0.14	d : 0.12	[ : 0.06	= : 0.06	# : 0.06	! : 0.04	i : 0.04	" : 0.04	f : 0.02	h : 0.02	b : 0.02	: : 0.02	D : 0.02	F : 0.02	
e : 0.21	g : 0.12	c : 0.10	! : 0.08	d : 0.08	= : 0.06	[ : 0.06	# : 0.06	f : 0.04	i : 0.04	: : 0.04	a : 0.02	h : 0.02	b : 0.02	F : 0.02	" : 0.02	
e : 0.19	g : 0.14	c : 0.12	d : 0.10	i : 0.10	[ : 0.06	= : 0.04	! : 0.04	a : 0.04	f : 0.04	# : 0.04	b : 0.02	h : 0.02	" : 0.02	$ : 0.02	
e : 0.19	g : 0.14	d : 0.14	c : 0.12	i : 0.10	! : 0.08	h : 0.04	f : 0.04	# : 0.04	b : 0.02	" : 0.02	= : 0.02	$ : 0.02	[ : 0.02	
g : 0.16	c : 0.14	! : 0.12	d : 0.10	i : 0.10	e : 0.10	h : 0.04	f : 0.04	[ : 0.04	a : 0.04	# : 0.04	" : 0.02	: : 0.02	= : 0.02	$ : 0.02	
c : 0.19	f : 0.16	g : 0.12	d : 0.10	i : 0.10	e : 0.08	! : 0.06	[ : 0.06	h : 0.04	# : 0.04	b : 0.02	$ : 0.02	
c : 0.16	f : 0.16	e : 0.12	i : 0.10	g : 0.10	d : 0.08	# : 0.06	[ : 0.06	h : 0.04	! : 0.04	" : 0.02	a : 0.02	b : 0.02	$ : 0.02	
[ : 0.14	f : 0.14	c : 0.14	e : 0.12	d : 0.12	i : 0.10	# : 0.06	! : 0.06	g : 0.06	h : 0.04	" : 0.02	
c : 0.25	f : 0.12	[ : 0.12	e : 0.10	d : 0.10	i : 0.10	g : 0.06	h : 0.04	# : 0.04	! : 0.04	" : 0.02	
c : 0.27	b : 0.21	f : 0.12	e : 0.10	d : 0.10	i : 0.06	h : 0.04	g : 0.04	# : 0.02	[ : 0.02	
c : 0.25	b : 0.21	f : 0.12	e : 0.10	d : 0.08	a : 0.08	i : 0.06	h : 0.04	g : 0.04	
o : 0.98	c : 0.02	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
c : 0.23	b : 0.21	f : 0.12	e : 0.10	d : 0.08	a : 0.08	i : 0.06	h : 0.04	g : 0.04	o : 0.02	
c : 0.25	b : 0.21	f : 0.12	e : 0.10	d : 0.08	g : 0.06	i : 0.06	h : 0.04	] : 0.04	4 : 0.02	
c : 0.27	] : 0.18	f : 0.12	e : 0.10	d : 0.10	g : 0.06	i : 0.06	h : 0.04	2 : 0.04	4 : 0.02	
c : 0.16	e : 0.14	d : 0.14	f : 0.12	i : 0.08	] : 0.06	2 : 0.06	3 : 0.06	g : 0.06	h : 0.04	4 : 0.04	a : 0.02	b : 0.02	
c : 0.16	e : 0.14	f : 0.14	g : 0.12	i : 0.10	d : 0.08	] : 0.06	3 : 0.06	h : 0.04	2 : 0.04	4 : 0.04	b : 0.02	
c : 0.18	f : 0.16	g : 0.12	3 : 0.10	i : 0.10	d : 0.08	e : 0.08	2 : 0.06	h : 0.04	] : 0.04	b : 0.02	4 : 0.02	
2 : 0.16	g : 0.14	i : 0.10	c : 0.10	e : 0.10	d : 0.08	] : 0.08	3 : 0.06	4 : 0.06	h : 0.04	f : 0.04	b : 0.02	a : 0.02	
2 : 0.16	c : 0.16	d : 0.12	g : 0.10	i : 0.10	e : 0.10	3 : 0.06	] : 0.06	h : 0.04	f : 0.04	4 : 0.04	a : 0.02	
c : 0.18	d : 0.16	g : 0.14	i : 0.10	e : 0.10	2 : 0.06	] : 0.06	3 : 0.04	a : 0.04	f : 0.04	4 : 0.04	b : 0.02	: : 0.02	
d : 0.18	c : 0.18	g : 0.14	e : 0.14	: : 0.06	4 : 0.06	b : 0.04	2 : 0.04	i : 0.04	f : 0.04	3 : 0.02	h : 0.02	E : 0.02	B : 0.02	

#score	668.2547698309461
#seq	50
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_transcript_m1_run2.txt

#BEAR
bb"""ffffff$$$$$cccooooooccc]ffffff333b	chrX:107975760-107976003(-)$1	243	134	173	12.2701
ff"""ccc!!cccbb!!bbmmmmbb4444bb]ccc22cc	chr20:62585731-62585956(-)$1	225	49	88	11.6297
[bb"""iiiiiiiii[bboooooobbiiiiiiiii4444	chr7:45144409-45144635(-)$1	226	74	113	15.7854
eeee!!ccc!!a[ddddllldddd]a22ccceeeee>>>	chr15:41021956-41022225(+)$1	269	29	68	10.8768
ddccc[ddddgggggggooooooggggggg333ddddcc	chr15:96289011-96289242(+)$1	231	17	56	13.7806
!ccc!!ggggggg"""bbmmmmbb333gggggggccca2	chr12:65000385-65000620(+)$1	235	141	180	13.7850
[a!!a[ccc"""ccc[bbnnnnnbbccc4444ccc22a2	chr11:661030-661251(-)$1	221	55	94	14.1355
dd[bb!!eeeee[ddddoooooodddd]eeeee]bb]dd	chr6:153741527-153741762(+)$1	235	88	127	11.4290
[ccc!!ggggggg[bbbbmmmmbb]bbgggggggccc22	chr3:184382458-184382687(-)$1	229	130	169	12.1793
eeee[ccc!!ccc!!cccnnnnnccc22ccc22ccceee	chr6:26988035-26988258(+)$1	223	155	194	13.7543
!!bb!!eeeee####bbnnnnnbb333eeeee]bb333f	chr17:33923535-33923756(+)$1	221	114	153	13.3740
[eeeee!!==========mmmm==========22eeeee	chr5:140098431-140098696(+)$1	265	178	217	12.7658
d!!eeeee[ccc"""cccoooooocccccceeeee22dd	chr10:112650275-112650499(+)$1	224	38	77	14.2701
:bb[cccgggggggbboooooobb]ggggggg]ccc]bb	chr4:54922368-54922589(-)$1	221	180	219	11.6400
eeee!!dddd"""gggggggmmmmgggggggdddd333e	chr14:103988440-103988659(-)$1	219	90	129	12.2981
dddd!!bb####cccooooooccc333bb333dddd22b	chr11:64955987-64956221(+)$1	234	140	179	12.3194
gg!!ggggggg[eeeeeooooooeeeee]ggggggg22g	chr1:117214309-117214528(+)$1	219	73	112	14.1102
cc[a!!ccc[a[ffffffammmma]ffffffa]ccca]c	chr17:47026701-47026927(-)$1	226	125	164	12.3782
$ccc"""ggggggg"""ccclllccc333ggggggg555	chr3:156871237-156871470(+)$1	233	124	163	13.0034
iiii$$$$$ccc"""bboooooobb333ccciiiiiiii	chr10:61890882-61891101(-)$1	219	179	218	15.0269
gggccc"""eeeee[cccnnnnnccc]eeeee]ccc]gg	chr19:4361302-4361523(-)$1	221	23	62	12.8015
eeee[dddd[ddddcccooooooccc333dddddddd]e	chr20:34135082-34135313(+)$1	231	56	95	13.5314
g[ccc[dddd[gggggggnnnnnggggggg333ddddcc	chr17:7245259-7245484(+)$1	225	77	116	12.4812
Eccc!!bb[ccc!!cccooooooccc]ccc]bb22ccce	chr11:62620701-62620965(-)$1	264	59	98	13.5865
:ccc!!============mmmm============22ccc	chr4:87516807-87517042(+)$1	235	135	174	14.0775
eeee!!dddd[bb[cccnnnnncccbbdddd]eeeee33	chr16:29998948-29999181(+)$1	233	63	102	11.4378
eeeee:ccc"""eeeeeooooooeeeee333ccceeeee	chr1:6324677-6324906(-)$1	229	31	70	12.3129
bb[===========[bboooooobb]===========22	chr8:28928983-28929202(-)$1	219	77	116	16.0963
:iiiiiiiii"""ccccccmmmmccc22ccc]iiiiiii	chr9:131565432-131565653(+)$1	221	20	59	12.9596
""==========####cccmmmmccc==========]ii	chr1:198827955-198828176(-)$1	221	112	151	14.9432
eeee[ccc####eeeeeccclllccc22eeeee4444cc	chr7:151329101-151329320(-)$1	219	45	84	12.7759
dddd[ccc!!ffffff[ccclllccc]ffffff]ccc]d	chr6:31804789-31805018(+)$1	229	71	110	11.4969
b[ccc[dddd!!bbcccooooooccc]bb22dddd22cc	chr1:25621010-25621234(-)$1	224	136	175	13.8548
!!bb[cccffffff!!cccmmmmccc22ffffff]ccc]	chr1:17066919-17067276(+)$1	357	220	259	11.2507
hh[hhhhhhhh"""cccooooooccc333hhhhhhhh99	chr15:47564748-47564975(+)$1	227	40	79	12.4044
iccc"""gggggggcccooooooccc]gggggggccc]i	chr20:26189247-26189467(-)$1	220	63	102	16.4222
eeee!!==========[annnnna]==========333e	chr1:93306177-93306399(+)$1	222	2	41	16.8816
Edddd!!bb####eeeeeooooooeeeee4444bb22dd	chr1:31372864-31373091(-)$1	227	80	119	11.3242
#ccc!!iiiiiiiii[cccmmmmccciiiiiiiiiccc]	chr16:33965408-33965630(+)$1	222	179	218	14.4119
eeee[ccc[a"""eeeeennnnneeeee333a]ccc]ee	chr16:2204956-2205206(-)$1	250	151	190	13.1164
c]ddddiiiiiiiiirrrrrrrrriiiiiiiiiffffff	chr10:112404901-112405125(+)$1	224	79	118	10.4029
ccc!!ggggggg[a[bboooooobbagggggggccc22d	chr13:43529781-43530017(+)$1	236	89	128	15.7969
cc"""eeeee[a"""bboooooobb333a]eeeee333c	chr20:62550748-62550970(+)$1	222	23	62	16.7467
eee"""eeeeebb[cccooooooccc]bb]eeeee4444	chr12:93738331-93738556(+)$1	225	47	86	15.1842
f[ccc[eeeee####cccnnnnnccc4444eeeee]ccc	chr16:53967888-53968122(+)$1	234	81	120	14.1192
cffffffggggggg[cccooooooccc]ggggggg7777	chr14:21971816-21972039(+)$1	223	40	79	12.5267
ee[bb[===========rrrrrrrrr===========]b	chr12:83458335-83458569(-)$1	234	89	128	13.1721
b!!a[ccc!!ccc[fffffflllffffffcccccc22a2	chr19:50311852-50312075(+)$1	223	137	176	11.6689
eeeee[ccc[bb[a[bboooooobb]a]bbccc]eeeee	chr19:16474171-16474398(-)$1	227	115	154	13.1221
ff[bb"""gggggggcccmmmmccc22ggggggg4444b	chr5:141691324-141691547(-)$1	223	110	149	12.8942
c"""bb[ccc!!bb!!bbnnnnnbb]bb]ccc]bb333c	chr19:55738165-55738386(-)$1	221	132	171	12.4153
:ccc!!dddd####cccooooooccc4444dddd]ccc:	chr20:30386136-30386374(+)$1	238	193	232	14.2939
$eeeeeeeeee"""bb[annnnna]bb333eeeee]eee	chr5:55256153-55256392(-)$1	239	59	98	12.1023
"""dddd$$$$$eeeeeooooooeeeee333dddd333b	chr13:52585247-52585470(-)$1	223	30	69	12.9686

#otherMatches

#Seq PSSM
GACACUCACGUGAGAAUGGAUUUUGCCAGACGUGAUAAU	chrX:107975760-107976003(-)$1	243	134	173	12.2701
GCCCCUCUUCAACCUCUGCUGCUGCCCUUAGUGUUCCAG	chr20:62585731-62585956(-)$1	225	49	88	11.6297
CAUGGGCCCUGGGUCACCUACCCUGGGACCUGGGGAUAA	chr7:45144409-45144635(-)$1	226	74	113	15.7854
UGGCAGCAUUAAGGCUUUUGGAGUGUCUAUGGCCACAAA	chr15:41021956-41022225(+)$1	269	29	68	10.8768
aucuaucacuucuuggccuuuuagcuaagaucaagugua	chr15:96289011-96289242(+)$1	231	17	56	13.7806
agagguugcagugagcugagaucauagcacugcacucca	chr12:65000385-65000620(+)$1	235	141	180	13.7850
UGUUGUUGGCCAUGCUGCCCUGAGCGCAAACCCCAUUCC	chr11:661030-661251(-)$1	221	55	94	14.1355
cucggaagcuaagcagggucgggccugguuaguacuugg	chr6:153741527-153741762(+)$1	235	88	127	11.4290
agagcuugcagugagccgagaucgcgccacugcacucca	chr3:184382458-184382687(-)$1	229	130	169	12.1793
guugugaguucgagccucaccuggagcaUUGUUUUCCAA	chr6:26988035-26988258(+)$1	223	155	194	13.7543
CAGCCUGCCUCAUCAGGGCCUUCCGCGGAGGCCGCCCCG	chr17:33923535-33923756(+)$1	221	114	153	13.3740
UCAGCUCCUUUUCCAUGGGGAAccauggagaaauggcug	chr5:140098431-140098696(+)$1	265	178	217	12.7658
AGCUGCUCUGGAUAAGGCUACCGUGCUUCUGAGUAUGUC	chr10:112650275-112650499(+)$1	224	38	77	14.2701
AGUUAGUUAUACUGUGCAUUUUCAUCAGUAUACACUUAU	chr4:54922368-54922589(-)$1	221	180	219	11.6400
CGCGCUCGGGCCCGGCAGUGACGUCACUGUCCCCGUCCC	chr14:103988440-103988659(-)$1	219	90	129	12.2981
AGAGCCGGACCAUCCGCAAAUGGAACACCACACUCUACG	chr11:64955987-64956221(+)$1	234	140	179	12.3194
UCUUUCUAGUUCUUCCUAGAGUGAGGAAAAGCUGGGUUG	chr1:117214309-117214528(+)$1	219	73	112	14.1102
gccgacucgcgauuuccccaaaugugggaaacucgacug	chr17:47026701-47026927(-)$1	226	125	164	12.3782
cagaacuuacuaauaucagugucacuaaaguugguauac	chr3:156871237-156871470(+)$1	233	124	163	13.0034
GAUAAUUUUAGCAUUGAUAAUUUUCUUAGCUUAUCACUG	chr10:61890882-61891101(-)$1	219	179	218	15.0269
UCUGAGCCUGCCGGCGCCACCUGGGCCCCGGCCCUUGAG	chr19:4361302-4361523(-)$1	221	23	62	12.8015
CCUCUGCUUCUCCCCUCCCCUUAGAGCUUGGGAAAGUCG	chr20:34135082-34135313(+)$1	231	56	95	13.5314
UCGGCAUUUGUGACCUGGCCCGCCUGGGUCCACCAGAGC	chr17:7245259-7245484(+)$1	225	77	116	12.4812
AAGUCUUUGAUCUCCUGAACCACCAGUGAUGAAUUGCUG	chr11:62620701-62620965(-)$1	264	59	98	13.5865
ACuaauuauaaauuuuaagauuuuaaaauuuauauCUAG	chr4:87516807-87517042(+)$1	235	135	174	14.0775
CCCAACACCCAUUAGCUCUGUUGGCAAGGGUCUGGGUCC	chr16:29998948-29999181(+)$1	233	63	102	11.4378
CAUGCACCAGGGGUGGGGCAGAUCCCACGGGUGGGGGGC	chr1:6324677-6324906(-)$1	229	31	70	12.3129
GCACUCCGGGCUCCAGGGUGGUGCCGGGGGUCUGGGGAA	chr8:28928983-28929202(-)$1	219	77	116	16.0963
aagugcugggauuucaggcaugagccacUGACCCCAGCA	chr9:131565432-131565653(+)$1	221	20	59	12.9596
UGUCGGUGGGUUGAACUGUGUGGACAAGCUCACUGAACA	chr1:198827955-198828176(-)$1	221	112	151	14.9432
gggACGAGCGUCGCAGCUCAUGCUGAUCGCUGUCCUCCU	chr7:151329101-151329320(-)$1	219	45	84	12.7759
UGAUUUCACAGACUAGAGUCUCCGAUGCUGGUCAUGAUG	chr6:31804789-31805018(+)$1	229	71	110	11.4969
GCCCAAGGAGGCCGAGCUCUGUUGCUGCGAACUCCAGUG	chr1:25621010-25621234(-)$1	224	136	175	13.8548
gugguagugggggacugcguucgcgcuuuccccugACUU	chr1:17066919-17067276(+)$1	357	220	259	11.2507
uuuacAgaugugagggugaucuggcugcgacaucuguca	chr15:47564748-47564975(+)$1	227	40	79	12.4044
CCUCAGCUUCCCCCUCGACGGGGUGACGGGGGGAGAGCG	chr20:26189247-26189467(-)$1	220	63	102	16.4222
GAAGUUAAAAAGAAGAGGUAUGUCGUCUUUUUUUUUGUC	chr1:93306177-93306399(+)$1	222	2	41	16.8816
agguugagcaaugugcccacaguggggcaguuagcagga	chr1:31372864-31373091(-)$1	227	80	119	11.3242
AGUAGUCCCCGGGGGUGCCUCCGGGCUCCUCGGGGUGCA	chr16:33965408-33965630(+)$1	222	179	218	14.4119
UGCAGUCUGAUUAUUUAGCAAGACUGAGGCUUGAGGGUG	chr16:2204956-2205206(-)$1	250	151	190	13.1164
CCUGUGCGACUUGGGUCGUGAAUUCUCAGGUCGGCCUUC	chr10:112404901-112405125(+)$1	224	79	118	10.4029
gagguugcaaugagucaagaucgugccauugcacuccag	chr13:43529781-43530017(+)$1	236	89	128	15.7969
CAGCGCCACGGAAGAGGACACACCCGGCUGUGUGGACAU	chr20:62550748-62550970(+)$1	222	23	62	16.7467
ugcccaggcuggaguacaauagcgugaucucagcucacu	chr12:93738331-93738556(+)$1	225	47	86	15.1842
UCCUUGCCUCGCUCACUGCACGCCAGAACCUGAGGAGAG	chr16:53967888-53968122(+)$1	234	81	120	14.1192
CCAGAUCAGAGAGGUGGUGUAGCAACUUCUUCUCUAACU	chr14:21971816-21972039(+)$1	223	40	79	12.5267
Uaucuugucugaucuuggaagcuaagcaggguugggcug	chr12:83458335-83458569(-)$1	234	89	128	13.1721
GAAGGGGGAAGCCACUGGGCAGCGCCCGGGGUCCCAACG	chr19:50311852-50312075(+)$1	223	137	176	11.6689
UGGAGAGGGACCGAGGCUGGCCUGUGUGGGCUCGUUCUA	chr19:16474171-16474398(-)$1	227	115	154	13.1221
CCUGACUUUUUGUGUACAUACUUGUAAACACGGAUUUUU	chr5:141691324-141691547(-)$1	223	110	149	12.8942
GCCCCACAGCCUGCCCGCCCCCUGCUGCUGCUCUGAAUC	chr19:55738165-55738386(-)$1	221	132	171	12.4153
AGCUGGCCAGGCUACGGAGAGAACUGGUAACUGGGAGCA	chr20:30386136-30386374(+)$1	238	193	232	14.2939
ACCUUUUACAGAAUAUGUGUUUAGGAUUCGCUGUAUGAA	chr5:55256153-55256392(-)$1	239	59	98	12.1023
GAAGGGGCCAGUCGGAAAGUGAGUUUUGUUCCCCCGCGU	chr13:52585247-52585470(-)$1	223	30	69	12.9686

#DB
((...((((((.....(((......))).))))))...)	chrX:107975760-107976003(-)$1	1	134	173	12.2701
((...(((..(((((..((....))....)).)))..))	chr20:62585731-62585956(-)$1	1	49	88	11.6297
.((...(((((((((.((......)))))))))))....	chr7:45144409-45144635(-)$1	1	74	113	15.7854
((((..(((..(.((((...)))).)..))))))))...	chr15:41021956-41022225(+)$1	1	29	68	10.8768
(((((.(((((((((((......)))))))...))))))	chr15:96289011-96289242(+)$1	1	17	56	13.7806
.(((..(((((((...((....))...))))))))))).	chr12:65000385-65000620(+)$1	1	141	180	13.7850
.(..(.(((...(((.((.....)))))....)))..).	chr11:661030-661251(-)$1	1	55	94	14.1355
((.((..(((((.((((......)))).))))).)).))	chr6:153741527-153741762(+)$1	1	88	127	11.4290
.(((..(((((((.((((....)).))))))))))))..	chr3:184382458-184382687(-)$1	1	130	169	12.1793
((((.(((..(((..(((.....)))..)))..))))))	chr6:26988035-26988258(+)$1	1	155	194	13.7543
..((..(((((....((.....))...))))).))...)	chr17:33923535-33923756(+)$1	1	114	153	13.3740
.(((((..((((((((((....))))))))))..)))))	chr5:140098431-140098696(+)$1	1	178	217	12.7658
(..(((((.(((...(((......)))))))))))..))	chr10:112650275-112650499(+)$1	1	38	77	14.2701
.((.((((((((((((......)).))))))).))).))	chr4:54922368-54922589(-)$1	1	180	219	11.6400
((((..((((...(((((((....)))))))))))...)	chr14:103988440-103988659(-)$1	1	90	129	12.2981
((((..((....(((......)))...))...))))..)	chr11:64955987-64956221(+)$1	1	140	179	12.3194
((..(((((((.(((((......))))).)))))))..)	chr1:117214309-117214528(+)$1	1	73	112	14.1102
((.(..(((.(.(((((((....).))))))).)))).)	chr17:47026701-47026927(-)$1	1	125	164	12.3782
.(((...(((((((...(((...)))...)))))))...	chr3:156871237-156871470(+)$1	1	124	163	13.0034
((((.....(((...((......))...)))))))))))	chr10:61890882-61891101(-)$1	1	179	218	15.0269
((((((...(((((.(((.....))).))))).))).))	chr19:4361302-4361523(-)$1	1	23	62	12.8015
((((.((((.(((((((......)))...)))))))).)	chr20:34135082-34135313(+)$1	1	56	95	13.5314
(.(((.((((.(((((((.....)))))))...))))))	chr17:7245259-7245484(+)$1	1	77	116	12.4812
((((..((.(((..(((......))).))).))..)))(	chr11:62620701-62620965(-)$1	1	59	98	13.5865
.(((..((((((((((((....))))))))))))..)))	chr4:87516807-87517042(+)$1	1	135	174	14.0775
((((..((((.((.(((.....))))))))).)))))..	chr16:29998948-29999181(+)$1	1	63	102	11.4378
))))).(((...(((((......)))))...)))(((((	chr1:6324677-6324906(-)$1	1	31	70	12.3129
((.(((((((((((.((......)).)))))))))))..	chr8:28928983-28929202(-)$1	1	77	116	16.0963
.(((((((((...((((((....)))..))).)))))))	chr9:131565432-131565653(+)$1	1	20	59	12.9596
..((((((((((....(((....))))))))))))).))	chr1:198827955-198828176(-)$1	1	112	151	14.9432
((((.(((....((((((((...)))..)))))....))	chr7:151329101-151329320(-)$1	1	45	84	12.7759
((((.(((..((((((.(((...))).)))))).))).)	chr6:31804789-31805018(+)$1	1	71	110	11.4969
(.(((.((((..(((((......))).))..))))..))	chr1:25621010-25621234(-)$1	1	136	175	13.8548
..((.(((((((((..(((....)))..)))))).))).	chr1:17066919-17067276(+)$1	1	220	259	11.2507
((.((((((((...(((......)))...))))))))..	chr15:47564748-47564975(+)$1	1	40	79	12.4044
((((...((((((((((......))).)))))))))).)	chr20:26189247-26189467(-)$1	1	63	102	16.4222
((((..((((((((((.(.....).))))))))))...)	chr1:93306177-93306399(+)$1	1	2	41	16.8816
)((((..((....(((((......)))))....))..))	chr1:31372864-31373091(-)$1	1	80	119	11.3242
.(((..(((((((((.(((....))))))))))))))).	chr16:33965408-33965630(+)$1	1	179	218	14.4119
((((.(((.(...(((((.....)))))...).))).))	chr16:2204956-2205206(-)$1	1	151	190	13.1164
).))))(((((((((.........)))))))))((((((	chr10:112404901-112405125(+)$1	1	79	118	10.4029
(((..(((((((.(.((......)))))))))))))..)	chr13:43529781-43530017(+)$1	1	89	128	15.7969
((...(((((.(...((......))...).)))))...)	chr20:62550748-62550970(+)$1	1	23	62	16.7467
(((...(((((((.(((......))).)).)))))....	chr12:93738331-93738556(+)$1	1	47	86	15.1842
(.(((.(((((....(((.....)))....))))).)))	chr16:53967888-53968122(+)$1	1	81	120	14.1192
((((((((((((((.(((......))).)))))))....	chr14:21971816-21972039(+)$1	1	40	79	12.5267
((.((.(((((((((((.........))))))))))).)	chr12:83458335-83458569(-)$1	1	89	128	13.1721
(..(.(((..(((.((((((...))))))))))))..).	chr19:50311852-50312075(+)$1	1	137	176	11.6689
(((((.(((.((.(.((......)).).))))).)))))	chr19:16474171-16474398(-)$1	1	115	154	13.1221
((.((...((((((((((....)))..)))))))....)	chr5:141691324-141691547(-)$1	1	110	149	12.8942
(...((.(((..((..((.....)).)).))).))...)	chr19:55738165-55738386(-)$1	1	132	171	12.4153
.(((..((((....(((......)))....)))).))).	chr20:30386136-30386374(+)$1	1	193	232	14.2939
.((((((((((...((.(.....).))...))))).)))	chr5:55256153-55256392(-)$1	1	59	98	12.1023
...((((.....(((((......)))))...))))...)	chr13:52585247-52585470(-)$1	1	30	69	12.9686

#PSSM
e : 0.22	c : 0.11	d : 0.09	b : 0.07	[ : 0.07	: : 0.07	f : 0.05	! : 0.05	g : 0.05	$ : 0.03	i : 0.03	E : 0.03	" : 0.03	h : 0.01	# : 0.01	
e : 0.25	c : 0.20	d : 0.09	b : 0.07	! : 0.07	f : 0.05	[ : 0.05	" : 0.05	g : 0.03	i : 0.03	a : 0.01	h : 0.01	] : 0.01	
e : 0.24	c : 0.24	[ : 0.11	" : 0.09	b : 0.07	! : 0.07	d : 0.07	i : 0.03	g : 0.01	= : 0.01	f : 0.01	
e : 0.24	c : 0.24	" : 0.11	b : 0.09	d : 0.09	! : 0.05	a : 0.03	i : 0.03	= : 0.03	[ : 0.01	h : 0.01	f : 0.01	
! : 0.25	" : 0.12	[ : 0.12	c : 0.11	e : 0.09	b : 0.07	d : 0.05	= : 0.03	a : 0.01	g : 0.01	$ : 0.01	i : 0.01	h : 0.01	f : 0.01	
! : 0.27	c : 0.16	[ : 0.12	" : 0.09	e : 0.07	d : 0.05	f : 0.03	g : 0.03	= : 0.03	$ : 0.01	: : 0.01	i : 0.01	h : 0.01	b : 0.01	
c : 0.24	d : 0.14	e : 0.11	= : 0.09	i : 0.07	g : 0.07	" : 0.07	! : 0.05	f : 0.03	b : 0.03	$ : 0.01	h : 0.01	[ : 0.01	
c : 0.24	g : 0.14	d : 0.12	e : 0.12	= : 0.09	i : 0.07	b : 0.05	$ : 0.03	" : 0.03	f : 0.01	! : 0.01	h : 0.01	
g : 0.16	d : 0.12	c : 0.11	e : 0.11	= : 0.11	! : 0.07	i : 0.07	[ : 0.05	f : 0.03	# : 0.03	$ : 0.03	" : 0.01	h : 0.01	b : 0.01	
g : 0.16	e : 0.12	d : 0.11	= : 0.11	! : 0.09	i : 0.07	c : 0.07	# : 0.05	[ : 0.05	f : 0.03	" : 0.03	h : 0.01	a : 0.01	$ : 0.01	
g : 0.18	c : 0.11	e : 0.11	= : 0.11	" : 0.09	# : 0.07	f : 0.05	i : 0.05	! : 0.05	[ : 0.05	a : 0.01	d : 0.01	h : 0.01	b : 0.01	$ : 0.01	
g : 0.18	" : 0.12	c : 0.11	# : 0.11	= : 0.11	i : 0.05	b : 0.05	$ : 0.03	a : 0.03	e : 0.03	[ : 0.03	f : 0.03	! : 0.03	d : 0.01	
g : 0.16	" : 0.14	c : 0.09	# : 0.09	= : 0.09	e : 0.09	[ : 0.07	b : 0.07	i : 0.05	f : 0.05	$ : 0.01	d : 0.01	! : 0.01	
g : 0.14	e : 0.12	" : 0.11	= : 0.09	[ : 0.07	# : 0.07	b : 0.05	i : 0.05	d : 0.05	c : 0.05	f : 0.05	! : 0.03	a : 0.03	$ : 0.01	
c : 0.20	e : 0.11	" : 0.09	[ : 0.09	b : 0.07	g : 0.07	= : 0.07	i : 0.05	! : 0.05	# : 0.05	f : 0.05	d : 0.03	$ : 0.01	
c : 0.27	b : 0.16	e : 0.11	= : 0.07	! : 0.05	[ : 0.05	g : 0.05	f : 0.05	d : 0.03	" : 0.03	$ : 0.01	o : 0.01	# : 0.01	r : 0.01	
c : 0.35	b : 0.20	e : 0.11	g : 0.05	= : 0.05	[ : 0.05	d : 0.03	o : 0.03	f : 0.03	! : 0.01	" : 0.01	r : 0.01	
o : 0.35	c : 0.25	b : 0.11	n : 0.03	= : 0.03	g : 0.03	f : 0.03	a : 0.03	e : 0.03	r : 0.03	l : 0.01	
o : 0.42	n : 0.20	c : 0.14	m : 0.09	r : 0.03	b : 0.01	l : 0.01	g : 0.01	a : 0.01	f : 0.01	
o : 0.44	m : 0.20	n : 0.20	c : 0.05	r : 0.03	l : 0.01	g : 0.01	f : 0.01	
o : 0.44	m : 0.22	n : 0.20	l : 0.07	r : 0.03	d : 0.01	
o : 0.42	m : 0.22	n : 0.20	l : 0.07	r : 0.03	d : 0.01	c : 0.01	
o : 0.40	n : 0.16	m : 0.12	b : 0.07	l : 0.07	c : 0.05	= : 0.03	r : 0.03	d : 0.01	
c : 0.37	b : 0.22	o : 0.09	e : 0.07	a : 0.05	d : 0.03	g : 0.03	= : 0.03	r : 0.03	m : 0.01	f : 0.01	
c : 0.38	b : 0.16	] : 0.11	e : 0.09	g : 0.05	3 : 0.05	= : 0.03	o : 0.01	d : 0.01	i : 0.01	r : 0.01	f : 0.01	
c : 0.38	3 : 0.09	e : 0.09	b : 0.07	g : 0.07	= : 0.05	] : 0.05	a : 0.03	f : 0.03	4 : 0.01	d : 0.01	i : 0.01	r : 0.01	2 : 0.01	
3 : 0.14	2 : 0.11	= : 0.11	] : 0.11	g : 0.09	e : 0.09	c : 0.07	b : 0.07	4 : 0.05	i : 0.05	f : 0.03	d : 0.01	a : 0.01	
g : 0.16	e : 0.12	= : 0.11	3 : 0.11	2 : 0.09	c : 0.07	b : 0.07	4 : 0.05	i : 0.05	] : 0.05	f : 0.05	d : 0.01	
g : 0.18	3 : 0.12	c : 0.11	= : 0.11	e : 0.09	4 : 0.07	b : 0.07	f : 0.07	] : 0.05	i : 0.05	d : 0.01	a : 0.01	
g : 0.22	c : 0.14	= : 0.11	3 : 0.09	f : 0.07	4 : 0.07	e : 0.07	i : 0.05	b : 0.03	d : 0.03	] : 0.03	2 : 0.01	h : 0.01	
g : 0.18	e : 0.16	c : 0.12	3 : 0.11	= : 0.11	f : 0.07	i : 0.05	d : 0.05	4 : 0.03	b : 0.01	] : 0.01	2 : 0.01	h : 0.01	
e : 0.18	g : 0.16	= : 0.11	d : 0.09	i : 0.07	c : 0.07	f : 0.05	] : 0.05	3 : 0.05	4 : 0.03	a : 0.03	2 : 0.01	b : 0.01	h : 0.01	
e : 0.16	g : 0.14	] : 0.11	d : 0.11	c : 0.09	i : 0.09	= : 0.09	f : 0.05	3 : 0.03	2 : 0.03	b : 0.01	h : 0.01	4 : 0.01	
c : 0.18	d : 0.14	e : 0.12	g : 0.12	= : 0.09	i : 0.07	f : 0.05	] : 0.05	b : 0.05	2 : 0.03	4 : 0.01	h : 0.01	
c : 0.24	e : 0.18	d : 0.12	i : 0.07	b : 0.07	= : 0.07	g : 0.05	f : 0.03	2 : 0.03	4 : 0.03	] : 0.03	h : 0.01	
c : 0.25	3 : 0.12	2 : 0.12	e : 0.09	4 : 0.07	d : 0.07	= : 0.05	g : 0.03	i : 0.03	] : 0.03	b : 0.01	h : 0.01	f : 0.01	7 : 0.01	
c : 0.18	2 : 0.16	3 : 0.12	e : 0.11	] : 0.09	4 : 0.07	d : 0.05	i : 0.03	= : 0.03	> : 0.01	a : 0.01	5 : 0.01	h : 0.01	f : 0.01	7 : 0.01	
c : 0.20	3 : 0.14	e : 0.11	2 : 0.09	] : 0.09	4 : 0.05	a : 0.05	d : 0.05	i : 0.05	> : 0.01	b : 0.01	5 : 0.01	g : 0.01	9 : 0.01	f : 0.01	7 : 0.01	
c : 0.18	e : 0.18	b : 0.11	2 : 0.09	d : 0.09	i : 0.07	4 : 0.03	f : 0.03	g : 0.03	] : 0.03	> : 0.01	5 : 0.01	3 : 0.01	9 : 0.01	7 : 0.01	: : 0.01	

#score	716.3950918904393
#seq	54
#width	39
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_CDS_m2_run1.txt

#BEAR
[cccqqqqqqqqccc]	chr22:18383526-18383766(-)$1	240	5	21	13.8182
:cccqqqqqqqqccc:	chr5:133725938-133726178(+)$1	240	9	25	12.0056
eeeeqqqqqqqqeeee	chr10:5768762-5769002(+)$1	240	183	199	13.7645
eeeeqqqqqqqqeeee	chr5:74893735-74893975(+)$1	240	88	104	13.7645
[cccqqqqqqqqccc2	chr15:48434387-48434667(-)$1	280	15	31	13.6424
ggggqqqqqqqqgggg	chr8:95392363-95392605(-)$1	242	179	195	13.0912
[cccqqqqqqqqcccg	chr11:62348556-62348975(-)$1	419	45	61	13.7142
ddddqqqqqqqqdddd	chr5:72798690-72798930(+)$1	240	146	162	13.8834
ddddqqqqqqqqdddd	chr10:103920169-103920409(+)$1	240	32	48	13.8834
ffffqqqqqqqqffff	chr18:29218560-29218800(-)$1	240	3	19	12.4434
ddddqqqqqqqqdddd	chr3:73006363-73006603(+)$1	240	113	129	13.8834
d[bbqqqqqqqqbb]d	chr8:66651693-66651933(-)$1	240	151	167	12.2075
!cccqqqqqqqqccc4	chr3:184018053-184018293(+)$1	240	62	78	13.7760
ddddqqqqqqqqdddd	chr16:66651141-66651381(-)$1	240	192	208	13.8834
ddddqqqqqqqqdddd	chr19:21307623-21307864(+)$1	241	28	44	13.8834
ddddqqqqqqqqdddd	chr14:69695545-69695785(+)$1	240	98	114	13.8834
eeeeqqqqqqqqeeee	chr13:73335965-73336205(-)$1	240	75	91	13.7645
ddddqqqqqqqqdddd	chr7:112423818-112424070(-)$1	252	45	61	13.8834
ddddqqqqqqqqdddd	chr12:76446887-76447127(-)$1	240	67	83	13.8834
ddddqqqqqqqqdddd	chr2:37428757-37428997(-)$1	240	213	229	13.8834
!!bbqqqqqqqqbbff	chr5:178138974-178139214(-)$1	240	53	69	12.0623
ddddqqqqqqqqdddd	chr1:109472457-109472697(+)$1	240	98	114	13.8834
eeeeqqqqqqqqeeee	chr1:197112086-197112326(-)$1	240	218	234	13.7645
eeeeqqqqqqqqeeee	chr11:62346034-62346456(-)$1	422	62	78	13.7645
gcccqqqqqqqqccc3	chr5:131008405-131008645(-)$1	240	143	159	13.7429
:cccqqqqqqqqccc:	chr18:214495-214735(-)$1	240	77	93	12.0056
eeeeqqqqqqqqeeee	chr3:56682928-56683168(-)$1	240	109	125	13.7645
eeeeqqqqqqqqeeee	chr11:19191975-19192215(+)$1	240	217	233	13.7645
c[bbqqqqqqqqbbcc	chr14:39536342-39536582(-)$1	240	192	208	12.2023
====qqqqqqqq====	chr10:98286905-98287145(-)$1	240	84	100	13.1574
ddddqqqqqqqqdddd	chr10:124921783-124922023(+)$1	240	39	55	13.8834
ddddqqqqqqqqdddd	chr2:55805282-55805522(-)$1	240	84	100	13.8834
eeeeqqqqqqqqeeee	chr21:43413824-43414064(-)$1	240	104	120	13.7645
eeeeqqqqqqqqeeee	chr11:62343511-62343791(-)$1	280	197	213	13.7645
ccccqqqqqqqqccc]	chr6:146126254-146126494(-)$1	240	16	32	13.7594
ddddqqqqqqqqdddd	chr1:53699171-53699411(-)$1	240	53	69	13.8834
ffffqqqqqqqqffff	chr12:120899731-120899971(-)$1	240	191	207	12.4434
ggggqqqqqqqqgggg	chr1:100174500-100174740(-)$1	240	107	123	13.0912
eeeeqqqqqqqqeeee	chr12:92537801-92538041(-)$1	240	49	65	13.7645
ecccqqqqqqqqccc2	chr12:88542115-88542355(+)$1	240	43	59	13.6995
eeeeqqqqqqqqeeee	chr11:62346261-62346597(-)$1	336	203	219	13.7645
gggaqqqqqqqqa]gg	chr20:10389237-10389477(-)$1	240	143	159	12.8604
[cccqqqqqqqqccc]	chr13:26788511-26788751(-)$1	240	174	190	13.8182
eeeeqqqqqqqqeeee	chr18:28667554-28667797(-)$1	243	203	219	13.7645
ddddqqqqqqqqdddd	chr16:24551850-24552099(+)$1	249	32	48	13.8834
:cccqqqqqqqqccc:	chr3:108298112-108298352(-)$1	240	76	92	12.0056
:cccqqqqqqqqccc:	chr2:48033313-48033553(+)$1	240	92	108	12.0056
eeeeqqqqqqqqeeee	chr8:121502606-121502846(+)$1	240	95	111	13.7645
ffffqqqqqqqqffff	chr6:97246739-97246979(-)$1	240	4	20	12.4434
====qqqqqqqq====	chr5:133295131-133295371(-)$1	240	102	118	13.1574
:cccqqqqqqqqccc:	chr14:55510767-55511007(+)$1	240	127	143	12.0056
ddddqqqqqqqqdddd	chr3:182605294-182605534(+)$1	240	163	179	13.8834
ffffqqqqqqqqffff	chr20:20617934-20618174(-)$1	240	2	18	12.4434
ggggqqqqqqqqgggg	chr6:112395867-112396107(-)$1	240	72	88	13.0912
"cccqqqqqqqqccc2	chr4:24556351-24556591(-)$1	240	133	149	13.5645
!cccqqqqqqqqccc2	chr2:198256909-198257149(-)$1	240	78	94	13.6782
ddddqqqqqqqqdddd	chr1:62907803-62908043(+)$1	240	78	94	13.8834
ddddqqqqqqqqdddd	chr6:5260852-5261103(-)$1	251	209	225	13.8834
ddddqqqqqqqqdddd	chr14:31107239-31107479(+)$1	240	67	83	13.8834
d[bbqqqqqqqqbb22	chr6:56918530-56918770(+)$1	240	151	167	11.8146
eeeeqqqqqqqqeeee	chr11:62343313-62343700(-)$1	387	106	122	13.7645
ddddqqqqqqqqdddd	chr14:60600792-60601032(+)$1	240	151	167	13.8834
eeeeqqqqqqqqeeee	chr6:70410619-70410859(-)$1	240	95	111	13.7645
"cccqqqqqqqqccc3	chr1:165697120-165697363(-)$1	243	151	167	13.7123
!cccqqqqqqqqccc]	chr6:26285516-26285756(-)$1	240	35	51	13.8540
eeeeqqqqqqqqeeee	chr5:43502387-43502627(-)$1	240	214	230	13.7645
eeeeqqqqqqqqeeee	chr12:46758071-46758311(-)$1	240	204	220	13.7645
eeeeqqqqqqqqeeee	chr22:46712159-46712399(+)$1	240	81	97	13.7645
bcccqqqqqqqqccc]	chr7:91503266-91503506(-)$1	240	179	195	13.5269
:cccqqqqqqqqccc:	chr11:43515349-43515589(+)$1	240	55	71	12.0056
bcccqqqqqqqqccc:	chr14:20840855-20841095(-)$1	240	161	177	12.6230
ffffqqqqqqqqffff	chr3:16411595-16411835(-)$1	240	68	84	12.4434
ddddqqqqqqqqdddd	chr2:85769938-85770178(+)$1	240	99	115	13.8834

#otherMatches

#Seq PSSM
UUUCGUCGGAAAGAAU	chr22:18383526-18383766(-)$1	240	5	21	13.8182
AGCCAAUAGCCAGGCA	chr5:133725938-133726178(+)$1	240	9	25	12.0056
AUAUUUUUCAUUAUGU	chr10:5768762-5769002(+)$1	240	183	199	13.7645
UUGAUAUAUUUUUUAA	chr5:74893735-74893975(+)$1	240	88	104	13.7645
UUCUAAGGUUCAAGAU	chr15:48434387-48434667(-)$1	280	15	31	13.6424
GGAUCUCACUUAAUUC	chr8:95392363-95392605(-)$1	242	179	195	13.0912
UCCGAGGCCGAGCGGC	chr11:62348556-62348975(-)$1	419	45	61	13.7142
GCUGAGACAAAGCAGC	chr5:72798690-72798930(+)$1	240	146	162	13.8834
UGUCUAGACUCUGACA	chr10:103920169-103920409(+)$1	240	32	48	13.8834
GGAUUGAUUUUUAUCC	chr18:29218560-29218800(-)$1	240	3	19	12.4434
uaaauauuauuuuuua	chr3:73006363-73006603(+)$1	240	113	129	13.8834
AUUGAGUACUUCCAUU	chr8:66651693-66651933(-)$1	240	151	167	12.2075
CAGAUUCGUUCUUCUA	chr3:184018053-184018293(+)$1	240	62	78	13.7760
ACUUGCCUAGAAAAGU	chr16:66651141-66651381(-)$1	240	192	208	13.8834
gaaauauuaaucuuuc	chr19:21307623-21307864(+)$1	241	28	44	13.8834
CCAAGAACGUUAUUGG	chr14:69695545-69695785(+)$1	240	98	114	13.8834
UGGAUAAUGAUUUUCA	chr13:73335965-73336205(-)$1	240	75	91	13.7645
AGAGACACUCACCUCU	chr7:112423818-112424070(-)$1	252	45	61	13.8834
GGACGUGGGACAGUUC	chr12:76446887-76447127(-)$1	240	67	83	13.8834
CUAUAAAUAAAAAUAG	chr2:37428757-37428997(-)$1	240	213	229	13.8834
CUGGAGAGAAACCCUA	chr5:178138974-178139214(-)$1	240	53	69	12.0623
CCAUUAGUUACUAUGG	chr1:109472457-109472697(+)$1	240	98	114	13.8834
CUCCUGAAGAUUGGAG	chr1:197112086-197112326(-)$1	240	218	234	13.7645
CCUGCUUCUCCCCAGG	chr11:62346034-62346456(-)$1	422	62	78	13.7645
CUCUGAACUUCAAGAA	chr5:131008405-131008645(-)$1	240	143	159	13.7429
AGUCUAACUAAUGACA	chr18:214495-214735(-)$1	240	77	93	12.0056
AGGAUACCUUUUUCUU	chr3:56682928-56683168(-)$1	240	109	125	13.7645
agaagaugcacauucu	chr11:19191975-19192215(+)$1	240	217	233	13.7645
CGCUAGAAAUAAAGGU	chr14:39536342-39536582(-)$1	240	192	208	12.2023
UUUGUUUUAUUUCAGG	chr10:98286905-98287145(-)$1	240	84	100	13.1574
GAAGAAGUAUGCCUUC	chr10:124921783-124922023(+)$1	240	39	55	13.8834
auguaccccuucacau	chr2:55805282-55805522(-)$1	240	84	100	13.8834
AUGUUUUAAACUACAU	chr21:43413824-43414064(-)$1	240	104	120	13.7645
GGUCUGCGCCUUGGCC	chr11:62343511-62343791(-)$1	280	197	213	13.7645
UCAUGCCAGAUGAUGA	chr6:146126254-146126494(-)$1	240	16	32	13.7594
ACAACAUACAUUUUGU	chr1:53699171-53699411(-)$1	240	53	69	13.8834
GAGCUGCUUUGUGCUC	chr12:120899731-120899971(-)$1	240	191	207	12.4434
GGAAUGUUACUUUUCU	chr1:100174500-100174740(-)$1	240	107	123	13.0912
CCUCACCAGCAGGAGG	chr12:92537801-92538041(-)$1	240	49	65	13.7645
AGCCUCUUUUGUGGUU	chr12:88542115-88542355(+)$1	240	43	59	13.6995
CCUGCUUCUCCCCAGG	chr11:62346261-62346597(-)$1	336	203	219	13.7645
CAACAAUCUGCAGCUU	chr20:10389237-10389477(-)$1	240	143	159	12.8604
GGUCAAUUUUAAGGCA	chr13:26788511-26788751(-)$1	240	174	190	13.8182
GUGUUUCAAUUCAUAC	chr18:28667554-28667797(-)$1	243	203	219	13.7645
UAUAAAUAUACGUAUA	chr16:24551850-24552099(+)$1	249	32	48	13.8834
AAGCUAUUCCAUGCUC	chr3:108298112-108298352(-)$1	240	76	92	12.0056
AGACUAUAAAAUGUCG	chr2:48033313-48033553(+)$1	240	92	108	12.0056
GGUUUUCCUUUUGACU	chr8:121502606-121502846(+)$1	240	95	111	13.7645
UCCUUUAGCCGUAGGA	chr6:97246739-97246979(-)$1	240	4	20	12.4434
GGAAGACAGCCAUUUC	chr5:133295131-133295371(-)$1	240	102	118	13.1574
CUCCCUUAAUUCGGAC	chr14:55510767-55511007(+)$1	240	127	143	12.0056
CAUGUAGACCCUCAUG	chr3:182605294-182605534(+)$1	240	163	179	13.8834
AUGUUCUUUUCCACAU	chr20:20617934-20618174(-)$1	240	2	18	12.4434
GUCCCUUAAUAUGGAC	chr6:112395867-112396107(-)$1	240	72	88	13.0912
ACUCCAGAACCAGAGA	chr4:24556351-24556591(-)$1	240	133	149	13.5645
GAUAAGAACACCUAUA	chr2:198256909-198257149(-)$1	240	78	94	13.6782
CCGGUUUUAAAUCUGG	chr1:62907803-62908043(+)$1	240	78	94	13.8834
GCCUACAAUUACAGGU	chr6:5260852-5261103(-)$1	251	209	225	13.8834
AUAAAGUUUUCAUUGU	chr14:31107239-31107479(+)$1	240	67	83	13.8834
UAGGAACUGUAGCUAA	chr6:56918530-56918770(+)$1	240	151	167	11.8146
GGUCUGCGCCUUGGCC	chr11:62343313-62343700(-)$1	387	106	122	13.7645
CAUUUUGACUGUAAUG	chr14:60600792-60601032(+)$1	240	151	167	13.8834
CAGGUUUUCCCUCUUG	chr6:70410619-70410859(-)$1	240	95	111	13.7645
UCAGACUGGCAACUGU	chr1:165697120-165697363(-)$1	243	151	167	13.7123
GGCCGUGGUAAAGGUG	chr6:26285516-26285756(-)$1	240	35	51	13.8540
UCCAAAUAUAUAUGGG	chr5:43502387-43502627(-)$1	240	214	230	13.7645
UCCCAGGGUAAAGGGA	chr12:46758071-46758311(-)$1	240	204	220	13.7645
GUCUAAAUUCCAAGAC	chr22:46712159-46712399(+)$1	240	81	97	13.7645
UCAACUUUCAAUUUGA	chr7:91503266-91503506(-)$1	240	179	195	13.5269
AGACCAUCCAGUGUCA	chr11:43515349-43515589(+)$1	240	55	71	12.0056
GGCAAGUGAAACUGCG	chr14:20840855-20841095(-)$1	240	161	177	12.6230
UUUCAACAAACCGAAG	chr3:16411595-16411835(-)$1	240	68	84	12.4434
UGGAGUUUCUCAUCCA	chr2:85769938-85770178(+)$1	240	99	115	13.8834

#DB
.(((........))).	chr22:18383526-18383766(-)$1	1	5	21	13.8182
.(((........))).	chr5:133725938-133726178(+)$1	1	9	25	12.0056
((((........))))	chr10:5768762-5769002(+)$1	1	183	199	13.7645
((((........))))	chr5:74893735-74893975(+)$1	1	88	104	13.7645
.(((........))).	chr15:48434387-48434667(-)$1	1	15	31	13.6424
((((........))))	chr8:95392363-95392605(-)$1	1	179	195	13.0912
.(((........))))	chr11:62348556-62348975(-)$1	1	45	61	13.7142
((((........))))	chr5:72798690-72798930(+)$1	1	146	162	13.8834
((((........))))	chr10:103920169-103920409(+)$1	1	32	48	13.8834
((((........))))	chr18:29218560-29218800(-)$1	1	3	19	12.4434
((((........))))	chr3:73006363-73006603(+)$1	1	113	129	13.8834
(.((........)).)	chr8:66651693-66651933(-)$1	1	151	167	12.2075
.(((........))).	chr3:184018053-184018293(+)$1	1	62	78	13.7760
((((........))))	chr16:66651141-66651381(-)$1	1	192	208	13.8834
((((........))))	chr19:21307623-21307864(+)$1	1	28	44	13.8834
((((........))))	chr14:69695545-69695785(+)$1	1	98	114	13.8834
((((........))))	chr13:73335965-73336205(-)$1	1	75	91	13.7645
((((........))))	chr7:112423818-112424070(-)$1	1	45	61	13.8834
((((........))))	chr12:76446887-76447127(-)$1	1	67	83	13.8834
((((........))))	chr2:37428757-37428997(-)$1	1	213	229	13.8834
..((........))))	chr5:178138974-178139214(-)$1	1	53	69	12.0623
((((........))))	chr1:109472457-109472697(+)$1	1	98	114	13.8834
((((........))))	chr1:197112086-197112326(-)$1	1	218	234	13.7645
((((........))))	chr11:62346034-62346456(-)$1	1	62	78	13.7645
((((........))).	chr5:131008405-131008645(-)$1	1	143	159	13.7429
.(((........))).	chr18:214495-214735(-)$1	1	77	93	12.0056
((((........))))	chr3:56682928-56683168(-)$1	1	109	125	13.7645
((((........))))	chr11:19191975-19192215(+)$1	1	217	233	13.7645
(.((........))))	chr14:39536342-39536582(-)$1	1	192	208	12.2023
((((........))))	chr10:98286905-98287145(-)$1	1	84	100	13.1574
((((........))))	chr10:124921783-124922023(+)$1	1	39	55	13.8834
((((........))))	chr2:55805282-55805522(-)$1	1	84	100	13.8834
((((........))))	chr21:43413824-43414064(-)$1	1	104	120	13.7645
((((........))))	chr11:62343511-62343791(-)$1	1	197	213	13.7645
((((........))).	chr6:146126254-146126494(-)$1	1	16	32	13.7594
((((........))))	chr1:53699171-53699411(-)$1	1	53	69	13.8834
((((........))))	chr12:120899731-120899971(-)$1	1	191	207	12.4434
((((........))))	chr1:100174500-100174740(-)$1	1	107	123	13.0912
((((........))))	chr12:92537801-92538041(-)$1	1	49	65	13.7645
((((........))).	chr12:88542115-88542355(+)$1	1	43	59	13.6995
((((........))))	chr11:62346261-62346597(-)$1	1	203	219	13.7645
((((........).))	chr20:10389237-10389477(-)$1	1	143	159	12.8604
.(((........))).	chr13:26788511-26788751(-)$1	1	174	190	13.8182
((((........))))	chr18:28667554-28667797(-)$1	1	203	219	13.7645
((((........))))	chr16:24551850-24552099(+)$1	1	32	48	13.8834
.(((........))).	chr3:108298112-108298352(-)$1	1	76	92	12.0056
.(((........))).	chr2:48033313-48033553(+)$1	1	92	108	12.0056
((((........))))	chr8:121502606-121502846(+)$1	1	95	111	13.7645
((((........))))	chr6:97246739-97246979(-)$1	1	4	20	12.4434
((((........))))	chr5:133295131-133295371(-)$1	1	102	118	13.1574
.(((........))).	chr14:55510767-55511007(+)$1	1	127	143	12.0056
((((........))))	chr3:182605294-182605534(+)$1	1	163	179	13.8834
((((........))))	chr20:20617934-20618174(-)$1	1	2	18	12.4434
((((........))))	chr6:112395867-112396107(-)$1	1	72	88	13.0912
.(((........))).	chr4:24556351-24556591(-)$1	1	133	149	13.5645
.(((........))).	chr2:198256909-198257149(-)$1	1	78	94	13.6782
((((........))))	chr1:62907803-62908043(+)$1	1	78	94	13.8834
((((........))))	chr6:5260852-5261103(-)$1	1	209	225	13.8834
((((........))))	chr14:31107239-31107479(+)$1	1	67	83	13.8834
(.((........))..	chr6:56918530-56918770(+)$1	1	151	167	11.8146
((((........))))	chr11:62343313-62343700(-)$1	1	106	122	13.7645
((((........))))	chr14:60600792-60601032(+)$1	1	151	167	13.8834
((((........))))	chr6:70410619-70410859(-)$1	1	95	111	13.7645
.(((........))).	chr1:165697120-165697363(-)$1	1	151	167	13.7123
.(((........))).	chr6:26285516-26285756(-)$1	1	35	51	13.8540
((((........))))	chr5:43502387-43502627(-)$1	1	214	230	13.7645
((((........))))	chr12:46758071-46758311(-)$1	1	204	220	13.7645
((((........))))	chr22:46712159-46712399(+)$1	1	81	97	13.7645
((((........))).	chr7:91503266-91503506(-)$1	1	179	195	13.5269
.(((........))).	chr11:43515349-43515589(+)$1	1	55	71	12.0056
)(((........))).	chr14:20840855-20841095(-)$1	1	161	177	12.6230
((((........))))	chr3:16411595-16411835(-)$1	1	68	84	12.4434
((((........))))	chr2:85769938-85770178(+)$1	1	99	115	13.8834

#PSSM
d : 0.30	e : 0.26	: : 0.08	g : 0.06	f : 0.06	[ : 0.05	! : 0.05	c : 0.02	= : 0.02	" : 0.02	b : 0.02	
c : 0.27	d : 0.27	e : 0.24	f : 0.06	g : 0.05	[ : 0.04	= : 0.02	! : 0.01	
c : 0.27	d : 0.27	e : 0.24	f : 0.06	g : 0.05	b : 0.05	= : 0.02	
c : 0.27	d : 0.27	e : 0.24	f : 0.06	b : 0.05	g : 0.04	= : 0.02	a : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.27	d : 0.27	e : 0.24	f : 0.06	b : 0.05	g : 0.04	= : 0.02	a : 0.01	
c : 0.27	d : 0.27	e : 0.24	f : 0.06	b : 0.05	g : 0.04	= : 0.02	] : 0.01	
c : 0.28	d : 0.27	e : 0.24	f : 0.08	g : 0.05	= : 0.02	] : 0.01	2 : 0.01	
d : 0.28	e : 0.24	: : 0.09	f : 0.08	] : 0.06	2 : 0.06	g : 0.06	3 : 0.02	= : 0.02	4 : 0.01	c : 0.01	

#score	977.3481767423459
#seq	73
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_UTR_m2_run1.txt

#BEAR
hhhh[bbuuuuuuuuuuuubb]hh	chr20:34319770-34320004(-)$1	234	193	217	20.6800
dddeeeeevvvvvvvvvvvvveee	chr17:45903992-45904225(-)$1	233	71	95	21.7116
======[attttttttttta]===	chr12:56704133-56704361(-)$1	228	104	128	23.6683
ff[eeeeettttttttttteeeee	chr17:28792346-28792579(+)$1	233	66	90	22.7792
g!!eeeeettttttttttteeeee	chr19:56171442-56171681(+)$1	239	49	73	23.1735
dd"""ccctttttttttttccc44	chr1:155290317-155290547(+)$1	230	51	75	23.3001
dffffffuuuuuuuuuuuufffff	chr1:234741663-234741883(-)$1	220	106	130	21.0738
d"""ddddtttttttttttdddd3	chr19:3976290-3976513(-)$1	223	116	140	23.7496
iiiiiiiitttttttttttiiiii	chr6:144415962-144416204(-)$1	242	99	123	22.8768
eeeeddddwwwwwwwwwwwwwwdd	chr1:1477284-1477532(-)$1	248	184	208	20.4937
=bb[dddduuuuuuuuuuuudddd	chr12:49666384-49666612(+)$1	228	110	134	23.3287
$$$$$ccctttttttttttccc55	chr19:41836359-41836594(+)$1	235	146	170	21.1004
!ffffffwwwwwwwwwwwwwwfff	chr19:3976123-3976354(-)$1	231	116	140	20.2879
cc[eeeeeuuuuuuuuuuuueeee	chr19:14231193-14231446(-)$1	253	77	101	22.9972
&&&&ddddtttttttttttdddd7	chr17:76395459-76395683(+)$1	224	103	127	20.8139
ccceeeeeuuuuuuuuuuuueeee	chr12:48357907-48358131(+)$1	224	135	159	22.9100
[eeeeeyyyyyyyyyyyyyyyyee	chr1:218504823-218505061(+)$1	238	68	92	21.2506
ii:dddduuuuuuuuuuuudddd:	chr1:212859741-212859964(-)$1	223	150	174	21.0401
[ffffffvvvvvvvvvvvvvffff	chr16:2303334-2303565(-)$1	231	3	27	21.2749
gggggggvvvvvvvvvvvvvgggg	chr7:92190070-92190294(-)$1	224	58	82	22.1663
!eeeeevvvvvvvvvvvvveeeee	chr15:77759442-77759678(+)$1	236	186	210	21.3458
dd[eeeeettttttttttteeeee	chr5:180665108-180665338(-)$1	230	33	57	22.8756
:bb[ddddtttttttttttdddd]	chr3:128620054-128620281(+)$1	227	32	56	22.6120
eee[cccwwwwwwwwwwwwwwccc	chr3:49397436-49397665(-)$1	229	92	116	21.0363
ddddddddtttttttttttdddd5	chr14:24680621-24680850(-)$1	229	106	130	22.4080
"""eeeeeuuuuuuuuuuuueeee	chr22:18220839-18221084(-)$1	245	145	169	23.1806
[bb[cccuuuuuuuuuuuuccc]b	chr17:20914450-20914690(-)$1	240	68	92	22.6277
[a!!bbwwwwwwwwwwwwwwbb22	chr11:8709652-8709896(+)$1	244	88	112	20.3707
ffff!!bbuuuuuuuuuuuubb22	chr19:42751698-42751926(-)$1	228	38	62	21.6256
!!eeeeewwwwwwwwwwwwwweee	chr1:231155232-231155459(-)$1	227	123	147	21.3747
!ccc[abbtttttttttttbb]a]	chr19:18054552-18054772(+)$1	220	156	180	22.5956
===[dddduuuuuuuuuuuudddd	chr19:39334541-39334791(-)$1	250	154	178	23.7009
!bb[ddddtttttttttttdddd2	chr17:4851457-4851700(-)$1	243	75	99	23.6383
$$ccc!!attttttttttta22cc	chr7:135322674-135322898(+)$1	224	76	100	22.4985
ccc[dddduuuuuuuuuuuudddd	chr3:24019296-24019522(+)$1	226	149	173	23.5303
hhhhhhhhttttttttttthhhhh	chr12:64843785-64844010(+)$1	225	32	56	20.5795
$$$$$cccuuuuuuuuuuuuccc5	chr3:42826292-42826538(-)$1	246	170	194	21.7585
ddd[cccuuuuuuuuuuuuccc]d	chr8:19709192-19709429(+)$1	237	76	100	22.5857
ggggggguuuuuuuuuuuuggggg	chr12:57392563-57392787(-)$1	224	34	58	22.2447
Hbb[dddduuuuuuuuuuuudddd	chr16:69170509-69170729(+)$1	220	37	61	22.6043
"ffffffavvvvvvvvvvvvva]f	chr1:1189600-1189826(-)$1	226	104	128	21.5239
c"""ddddyyyyyyyyyyyyyyyy	chr12:6857072-6857351(-)$1	279	210	234	21.1238
dd!!ddddtttttttttttdddd2	chr12:57395011-57395255(-)$1	244	104	128	23.5619
ddd[ddddyyyyyyyyyyyyyyyy	chr2:98264472-98264697(+)$1	225	92	116	20.8610
hhhhhhhhuuuuuuuuuuuuhhhh	chr19:47673055-47673280(+)$1	225	62	86	20.7358
[bbeeeeevvvvvvvvvvvvveee	chr12:6601336-6601663(-)$1	327	111	135	21.9387
ddddddduuuuuuuuuuuudddd5	chr2:217365986-217366224(+)$1	238	55	79	21.8025
ccc[bbbbuuuuuuuuuuuubb]b	chr19:2269555-2269814(+)$1	259	98	122	21.8224
[bb[bbbbuuuuuuuuuuuubb]b	chr19:54656606-54656833(+)$1	227	43	67	21.7402
$$$$dddduuuuuuuuuuuudddd	chr22:38229622-38229847(-)$1	225	160	184	22.8114
!!ddddvvvvvvvvvvvvvdddd3	chr6:34256359-34256580(-)$1	221	139	163	21.8704
bb::ddddtttttttttttdddd:	chr1:238107407-238107637(-)$1	230	199	223	20.2721
dddd!!bbtttttttttttbb]dd	chr19:1585000-1585251(-)$1	251	178	202	22.0278
dddddd[auuuuuuuuuuuuaddd	chr22:30165703-30165953(+)$1	250	151	175	22.8764
ccc!!ccctttttttttttccc22	chr12:9094205-9094454(-)$1	249	166	190	23.3403
Iffffffuuuuuuuuuuuufffff	chr19:39327021-39327249(-)$1	228	72	96	19.9808
iiiiiiiitttttttttttiiiii	chr19:1418220-1418462(+)$1	242	69	93	22.8768
ccccyyyyyyyyyyyyyyyyccc]	chr1:16723869-16724120(+)$1	251	168	192	20.7618
iiiiiiiitttttttttttiiiii	chr7:44922694-44922916(-)$1	222	44	68	22.8768
fff[ddddtttttttttttddddf	chr6:18225151-18225403(-)$1	252	58	82	23.2024
:eeeeebbtttttttttttbb]ee	chr19:34303609-34303854(+)$1	245	61	85	21.3927
"gggggggyyyyyyyyyyyyyyyy	chr3:119182217-119182456(-)$1	239	108	132	20.6636
========ttttttttttt=====	chr12:56119241-56119501(-)$1	260	183	207	23.3329

#otherMatches

#Seq PSSM
AGAUGGCAGUUUAACUUGAGUGAU	chr20:34319770-34320004(-)$1	234	193	217	20.6800
UUCCCAGGUCCUGAAGCCCUUCCU	chr17:45903992-45904225(-)$1	233	71	95	21.7116
GUUUUUACUGAAAUUAACUGAAAA	chr12:56704133-56704361(-)$1	228	104	128	23.6683
CCUGUUCCAAGGCUAGAUCGGAAC	chr17:28792346-28792579(+)$1	233	66	90	22.7792
GACGAGGGUCCCCAGUCACCCCUC	chr19:56171442-56171681(+)$1	239	49	73	23.1735
UUGCGCGCAAAAUCUACAAGCGGA	chr1:155290317-155290547(+)$1	230	51	75	23.3001
CUUGGGCAUAUCAGUGACAGCCCA	chr1:234741663-234741883(-)$1	220	106	130	21.0738
ACACUUGAUGCCGUUUCUUUCAAU	chr19:3976290-3976513(-)$1	223	116	140	23.7496
GCGCUGGAGUGAGAUGGGAUUUGG	chr6:144415962-144416204(-)$1	242	99	123	22.8768
GGUAGCAUUACCCAAAUAAACUGU	chr1:1477284-1477532(-)$1	248	184	208	20.4937
GAGAAAGCCUACCACGAACAGCUU	chr12:49666384-49666612(+)$1	228	110	134	23.3287
CUCCUCCcuuaaccucucugggcu	chr19:41836359-41836594(+)$1	235	146	170	21.1004
UAAUUUUAACAAACGCAUUAAGAG	chr19:3976123-3976354(-)$1	231	116	140	20.2879
GGCUGCGGCCUCCCACUCAACUGC	chr19:14231193-14231446(-)$1	253	77	101	22.9972
AUCGGCCUCCAGCACAUUAAGGUG	chr17:76395459-76395683(+)$1	224	103	127	20.8139
UGCUCGCCCCUCCUCCUGCAGGCG	chr12:48357907-48358131(+)$1	224	135	159	22.9100
CCuauauaauaaaauuuaaaauua	chr1:218504823-218505061(+)$1	238	68	92	21.2506
CUCUCCCUUCUCCAGUUCUGGGAA	chr1:212859741-212859964(-)$1	223	150	174	21.0401
GAGCUGCCCCAGGCUUUAGUGCAG	chr16:2303334-2303565(-)$1	231	3	27	21.2749
AUCAGGUAACAUGACAUACAACUU	chr7:92190070-92190294(-)$1	224	58	82	22.1663
CUGCCUCCUGAGGAAAAACAGGUA	chr15:77759442-77759678(+)$1	236	186	210	21.3458
UUGAGAUGGGCAGAAUUAACAUCU	chr5:180665108-180665338(-)$1	230	33	57	22.8756
UCAGAUGAUAUCUUAAAUUUCAUG	chr3:128620054-128620281(+)$1	227	32	56	22.6120
UUACUGGCCUUUUUCAUUUAUCUA	chr3:49397436-49397665(-)$1	229	92	116	21.0363
CUGACGGGACAUUAUCCACCCUGG	chr14:24680621-24680850(-)$1	229	106	130	22.4080
AGACAUGGAGAAGGAGAAGACCAU	chr22:18220839-18221084(-)$1	245	145	169	23.1806
UGGAGUCUCCACCACCAUCGACCC	chr17:20914450-20914690(-)$1	240	68	92	22.6277
ACGGCAUAAUGGACGGGACUUGGA	chr11:8709652-8709896(+)$1	244	88	112	20.3707
GGGUGCCCUGAAACCAAACUGGAA	chr19:42751698-42751926(-)$1	228	38	62	21.6256
AAUGAGAAUAUAACAAGAGGAUCU	chr1:231155232-231155459(-)$1	227	123	147	21.3747
CCAUCCCCUCCCAUCCCCCGGCGC	chr19:18054552-18054772(+)$1	220	156	180	22.5956
GAGGUGACUGACUGCCCCUUGUCA	chr19:39334541-39334791(-)$1	250	154	178	23.7009
UCGUGGGCUACAAGGACUCGCCCU	chr17:4851457-4851700(-)$1	243	75	99	23.6383
AAUGUGGAGGGAGAUAAAGUAAGC	chr7:135322674-135322898(+)$1	224	76	100	22.4985
UGAUGGUGUCCCCAAUGCCCCACC	chr3:24019296-24019522(+)$1	226	149	173	23.5303
aaugaguuaaacuugaaaagacuu	chr12:64843785-64844010(+)$1	225	32	56	20.5795
AAUUCAACUUUUGUCUGCCUGUUU	chr3:42826292-42826538(-)$1	246	170	194	21.7585
AGGUUCUGCAUUAAUGAGAAGAUC	chr8:19709192-19709429(+)$1	237	76	100	22.5857
AAAGUUUUGUAUAUUUUGUAAACU	chr12:57392563-57392787(-)$1	224	34	58	22.2447
CCGGUACCUGAUGAAUUUGUGGUA	chr16:69170509-69170729(+)$1	220	37	61	22.6043
CGGGGGCCUCCCUCACAUCCCGUG	chr1:1189600-1189826(-)$1	226	104	128	21.5239
ACUUUUGAUCUUUUCCUGUUCAAU	chr12:6857072-6857351(-)$1	279	210	234	21.1238
CCCUGGUGGGAUUCAGCAACACCC	chr12:57395011-57395255(-)$1	244	104	128	23.5619
ACACUGAGCACCUGCACUAAAUUA	chr2:98264472-98264697(+)$1	225	92	116	20.8610
GGAGCAGUGAGAAAGCAAAGGCUG	chr19:47673055-47673280(+)$1	225	62	86	20.7358
GUAUCCGAAAGAGGAAAAUGGUUG	chr12:6601336-6601663(-)$1	327	111	135	21.9387
GAAACUGAAUCUUUCUUUCCAGUA	chr2:217365986-217366224(+)$1	238	55	79	21.8025
GGAAGGGGAUAAACCCAGCGCCAC	chr19:2269555-2269814(+)$1	259	98	122	21.8224
CAGAUGCCACCCCCACACUCGGAC	chr19:54656606-54656833(+)$1	227	43	67	21.7402
AGCAUGUCAGAAGUCACUAAGACA	chr22:38229622-38229847(-)$1	225	160	184	22.8114
AGGCCUCCUCUUUCAAAUAAGGCA	chr6:34256359-34256580(-)$1	221	139	163	21.8704
CCUCGGAGUAUAAUUCAACCUCCA	chr1:238107407-238107637(-)$1	230	199	223	20.2721
ACUCCUCCAACCAGGUCAAGGUGA	chr19:1585000-1585251(-)$1	251	178	202	22.0278
AAACAGACUCUUUACCUUCUGCUG	chr22:30165703-30165953(+)$1	250	151	175	22.8764
GCUUUUGAUUUGCAUCUUCUCACU	chr12:9094205-9094454(-)$1	249	166	190	23.3403
AGGGAGAGGGGAACUGUUAUCUCC	chr19:39327021-39327249(-)$1	228	72	96	19.9808
UUGGGUUUGUCAAAUUUAAAGACC	chr19:1418220-1418462(+)$1	242	69	93	22.8768
AGGCUGCUGCCCCUUUAUCUGCCU	chr1:16723869-16724120(+)$1	251	168	192	20.7618
AACUGAAGUCUUAAUUUACCUUCA	chr7:44922694-44922916(-)$1	222	44	68	22.8768
AUAUAAAGUUUUUUUAUUUCUUUU	chr6:18225151-18225403(-)$1	252	58	82	23.2024
UGACCUCUGUUUCUUCCUGGGCAG	chr19:34303609-34303854(+)$1	245	61	85	21.3927
AGCCUGGACACCUUUUCUUGAUUC	chr3:119182217-119182456(-)$1	239	108	132	20.6636
CUGGGGGAGUGGAAUAGUAUCCUC	chr12:56119241-56119501(-)$1	260	183	207	23.3329

#DB
((((.((............)).))	chr20:34319770-34320004(-)$1	1	193	217	20.6800
((((((((.............)))	chr17:45903992-45904225(-)$1	1	71	95	21.7116
((((((.(...........).)))	chr12:56704133-56704361(-)$1	1	104	128	23.6683
((.(((((...........)))))	chr17:28792346-28792579(+)$1	1	66	90	22.7792
(..(((((...........)))))	chr19:56171442-56171681(+)$1	1	49	73	23.1735
((...(((...........)))..	chr1:155290317-155290547(+)$1	1	51	75	23.3001
(((((((............)))))	chr1:234741663-234741883(-)$1	1	106	130	21.0738
(...((((...........)))).	chr19:3976290-3976513(-)$1	1	116	140	23.7496
((((((((...........)))))	chr6:144415962-144416204(-)$1	1	99	123	22.8768
))))((((..............))	chr1:1477284-1477532(-)$1	1	184	208	20.4937
(((.((((............))))	chr12:49666384-49666612(+)$1	1	110	134	23.3287
.....(((...........)))..	chr19:41836359-41836594(+)$1	1	146	170	21.1004
.((((((..............)))	chr19:3976123-3976354(-)$1	1	116	140	20.2879
((.(((((............))))	chr19:14231193-14231446(-)$1	1	77	101	22.9972
....((((...........)))).	chr17:76395459-76395683(+)$1	1	103	127	20.8139
((((((((............))))	chr12:48357907-48358131(+)$1	1	135	159	22.9100
.(((((................))	chr1:218504823-218505061(+)$1	1	68	92	21.2506
)).((((............)))).	chr1:212859741-212859964(-)$1	1	150	174	21.0401
.((((((.............))))	chr16:2303334-2303565(-)$1	1	3	27	21.2749
(((((((.............))))	chr7:92190070-92190294(-)$1	1	58	82	22.1663
.(((((.............)))))	chr15:77759442-77759678(+)$1	1	186	210	21.3458
((.(((((...........)))))	chr5:180665108-180665338(-)$1	1	33	57	22.8756
.((.((((...........)))).	chr3:128620054-128620281(+)$1	1	32	56	22.6120
(((.(((..............)))	chr3:49397436-49397665(-)$1	1	92	116	21.0363
((((((((...........)))).	chr14:24680621-24680850(-)$1	1	106	130	22.4080
...(((((............))))	chr22:18220839-18221084(-)$1	1	145	169	23.1806
.((.(((............))).)	chr17:20914450-20914690(-)$1	1	68	92	22.6277
.(..((..............))..	chr11:8709652-8709896(+)$1	1	88	112	20.3707
((((..((............))..	chr19:42751698-42751926(-)$1	1	38	62	21.6256
..(((((..............)))	chr1:231155232-231155459(-)$1	1	123	147	21.3747
.(((.(((...........)).).	chr19:18054552-18054772(+)$1	1	156	180	22.5956
(((.((((............))))	chr19:39334541-39334791(-)$1	1	154	178	23.7009
.((.((((...........)))).	chr17:4851457-4851700(-)$1	1	75	99	23.6383
..(((..(...........)..))	chr7:135322674-135322898(+)$1	1	76	100	22.4985
(((.((((............))))	chr3:24019296-24019522(+)$1	1	149	173	23.5303
((((((((...........)))))	chr12:64843785-64844010(+)$1	1	32	56	20.5795
.....(((............))).	chr3:42826292-42826538(-)$1	1	170	194	21.7585
(((.(((............))).)	chr8:19709192-19709429(+)$1	1	76	100	22.5857
(((((((............)))))	chr12:57392563-57392787(-)$1	1	34	58	22.2447
(((.((((............))))	chr16:69170509-69170729(+)$1	1	37	61	22.6043
.(((((((.............).)	chr1:1189600-1189826(-)$1	1	104	128	21.5239
(...((((................	chr12:6857072-6857351(-)$1	1	210	234	21.1238
((..((((...........)))).	chr12:57395011-57395255(-)$1	1	104	128	23.5619
(((.((((................	chr2:98264472-98264697(+)$1	1	92	116	20.8610
((((((((............))))	chr19:47673055-47673280(+)$1	1	62	86	20.7358
.(((((((.............)))	chr12:6601336-6601663(-)$1	1	111	135	21.9387
(((((((............)))).	chr2:217365986-217366224(+)$1	1	55	79	21.8025
(((.((((............)).)	chr19:2269555-2269814(+)$1	1	98	122	21.8224
.((.((((............)).)	chr19:54656606-54656833(+)$1	1	43	67	21.7402
....((((............))))	chr22:38229622-38229847(-)$1	1	160	184	22.8114
..((((.............)))).	chr6:34256359-34256580(-)$1	1	139	163	21.8704
))..((((...........)))).	chr1:238107407-238107637(-)$1	1	199	223	20.2721
((((..((...........)).))	chr19:1585000-1585251(-)$1	1	178	202	22.0278
((((((.(............))))	chr22:30165703-30165953(+)$1	1	151	175	22.8764
(((..(((...........)))..	chr12:9094205-9094454(-)$1	1	166	190	23.3403
(((((((............)))))	chr19:39327021-39327249(-)$1	1	72	96	19.9808
((((((((...........)))))	chr19:1418220-1418462(+)$1	1	69	93	22.8768
((((................))).	chr1:16723869-16724120(+)$1	1	168	192	20.7618
((((((((...........)))))	chr7:44922694-44922916(-)$1	1	44	68	22.8768
(((.((((...........)))))	chr6:18225151-18225403(-)$1	1	58	82	23.2024
.(((((((...........)).))	chr19:34303609-34303854(+)$1	1	61	85	21.3927
.(((((((................	chr3:119182217-119182456(-)$1	1	108	132	20.6636
((((((((...........)))))	chr12:56119241-56119501(-)$1	1	183	207	23.3329

#PSSM
d : 0.19	c : 0.11	! : 0.09	[ : 0.09	= : 0.06	i : 0.06	$ : 0.06	h : 0.04	f : 0.04	g : 0.04	" : 0.04	e : 0.03	: : 0.03	& : 0.01	H : 0.01	b : 0.01	I : 0.01	
d : 0.15	f : 0.12	b : 0.12	c : 0.11	e : 0.07	i : 0.06	$ : 0.06	h : 0.04	= : 0.04	! : 0.04	" : 0.04	g : 0.04	& : 0.01	a : 0.01	
d : 0.12	f : 0.11	b : 0.11	c : 0.11	e : 0.09	" : 0.06	h : 0.04	= : 0.04	[ : 0.04	! : 0.04	i : 0.04	$ : 0.04	g : 0.04	: : 0.03	& : 0.01	
e : 0.20	[ : 0.20	f : 0.09	d : 0.09	h : 0.04	" : 0.04	i : 0.04	$ : 0.04	g : 0.04	! : 0.04	c : 0.04	= : 0.03	& : 0.01	: : 0.01	
d : 0.31	e : 0.19	f : 0.07	c : 0.06	i : 0.04	g : 0.04	b : 0.04	! : 0.04	[ : 0.03	= : 0.03	$ : 0.03	h : 0.03	" : 0.01	y : 0.01	
d : 0.31	e : 0.19	c : 0.11	f : 0.07	b : 0.06	i : 0.04	g : 0.04	! : 0.04	= : 0.03	h : 0.03	a : 0.01	y : 0.01	
d : 0.28	e : 0.14	b : 0.11	c : 0.11	f : 0.07	i : 0.04	g : 0.04	[ : 0.03	y : 0.03	v : 0.03	h : 0.03	w : 0.01	! : 0.01	= : 0.01	
d : 0.25	u : 0.12	e : 0.12	b : 0.09	a : 0.06	c : 0.06	w : 0.06	v : 0.06	i : 0.04	y : 0.03	h : 0.03	g : 0.01	= : 0.01	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
t : 0.38	u : 0.34	v : 0.11	w : 0.07	y : 0.07	
u : 0.22	d : 0.17	v : 0.07	c : 0.07	w : 0.07	y : 0.07	b : 0.06	e : 0.06	i : 0.04	a : 0.03	f : 0.03	h : 0.01	g : 0.01	= : 0.01	
d : 0.25	b : 0.12	e : 0.11	c : 0.11	w : 0.06	y : 0.06	v : 0.04	f : 0.04	i : 0.04	g : 0.03	h : 0.03	] : 0.01	2 : 0.01	a : 0.01	= : 0.01	
d : 0.26	e : 0.15	c : 0.12	] : 0.06	f : 0.06	y : 0.06	b : 0.06	i : 0.04	= : 0.03	g : 0.03	h : 0.03	w : 0.01	2 : 0.01	a : 0.01	
d : 0.30	e : 0.19	] : 0.07	f : 0.06	c : 0.06	h : 0.04	i : 0.04	2 : 0.04	y : 0.04	= : 0.03	g : 0.03	4 : 0.01	5 : 0.01	a : 0.01	
e : 0.19	d : 0.14	f : 0.09	2 : 0.07	5 : 0.06	h : 0.04	i : 0.04	] : 0.04	b : 0.04	y : 0.04	= : 0.03	3 : 0.03	: : 0.03	g : 0.03	c : 0.03	4 : 0.01	7 : 0.01	

#score	1389.2694197720439
#seq	63
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_UTR_m2_run2.txt

#BEAR
Feeeeepppppppeeeee:	chr20:2128916-2129155(+)$1	239	14	33	11.9442
ccc[bbpppppppbb]ccc	chr4:113108853-113109074(+)$1	221	136	155	11.8706
ggggggpppppppgggggg	chr1:203771393-203771613(+)$1	220	3	22	13.6643
gg[cccpppppppccc]gg	chr18:74071653-74071876(-)$1	223	81	100	13.7695
iicccrrrrrrrrrccc]i	chr20:43128231-43128461(-)$1	230	29	48	11.1991
[a[cccrrrrrrrrrccca	chr3:141166991-141167214(+)$1	223	88	107	10.9599
b[ddddpppppppdddd]b	chr9:116080691-116080915(-)$1	224	127	146	12.1581
ffffffpppppppffffff	chr19:973418-973644(+)$1	226	89	108	13.8048
======ppppppp======	chr2:74331239-74331470(+)$1	231	126	145	14.0774
[eeeeerrrrrrrrreeee	chr21:18966134-18966368(-)$1	234	144	163	11.0534
ggggggpppppppgggggg	chr17:46138158-46138381(+)$1	223	47	66	13.6643
iiiiiipppppppiiiiii	chr6:144184743-144184977(+)$1	234	6	25	13.6061
ffffffpppppppffffff	chr18:48605588-48605836(+)$1	248	93	112	13.8048
[eeeeepppppppeeeeef	chr1:75229741-75229963(+)$1	222	137	156	13.5644
cc[cccrrrrrrrrrccc]	chr19:20005018-20005237(+)$1	219	70	89	11.0434
""ddddpppppppdddd44	chr11:47799664-47799883(-)$1	219	191	210	12.4878
ffffffpppppppffffff	chr4:26436130-26436357(+)$1	227	53	72	13.8048
fffffrrrrrrrrrfffff	chr12:9840485-9840707(+)$1	222	90	109	11.4163
ffffffpppppppffffff	chr17:40852199-40852418(-)$1	219	164	183	13.8048
eeeeeepppppppeeeee2	chr1:111489932-111490160(-)$1	228	57	76	13.0768
c[ddddpppppppdddd22	chr2:204296513-204296743(+)$1	230	192	211	12.3109
ffffffpppppppffffff	chr22:24967918-24968139(+)$1	221	6	25	13.8048
[eeeeepppppppeeeee]	chr4:762588-762806(+)$1	218	139	158	13.6639
======ppppppp======	chr8:97242859-97243074(-)$1	215	94	113	14.0774
iiiiiipppppppiiiiii	chr21:30716900-30717165(+)$1	265	9	28	13.6061
======ppppppp======	chr10:70173778-70174003(-)$1	225	200	219	14.0774
dd[cccpppppppccc]dd	chr8:124089261-124089497(+)$1	236	67	86	12.6888
"""cccpppppppccc]ee	chr3:98234611-98234841(-)$1	230	126	145	13.2396
eeeeerrrrrrrrreeeee	chr15:52843242-52843511(-)$1	269	170	189	10.9012
fffffrrrrrrrrrfffff	chr12:121202331-121202549(-)$1	218	64	83	11.4163
ffffffpppppppffffff	chr6:163994768-163994990(+)$1	222	96	115	13.8048
fffffrrrrrrrrrfffff	chr15:60783197-60783439(-)$1	242	171	190	11.4163
====rrrrrrrrr======	chrX:135046950-135047181(-)$1	231	187	206	11.2746
fffffrrrrrrrrrfffff	chr9:16417779-16417988(-)$1	209	117	136	11.4163
eeeeerrrrrrrrreeeee	chr1:114516619-114516843(+)$1	224	53	72	10.9012
fff[bbpppppppbbffff	chr18:44390557-44390814(-)$1	257	155	174	12.5088
ffffffpppppppffffff	chr2:10141313-10141535(+)$1	222	166	185	13.8048
e[ddddpppppppddddee	chr1:150548117-150548469(-)$1	352	89	108	12.5757
iiiiiipppppppiiiiii	chr5:173387039-173387264(+)$1	225	182	201	13.6061
##ddddpppppppdddd22	chr15:90378675-90378899(-)$1	224	159	178	12.1470
ggggggrrrrrrrrrgggg	chr13:30779177-30779406(-)$1	229	150	169	11.2941
[ddddrrrrrrrrrdddd]	chr16:69400156-69400386(-)$1	230	96	115	10.5285
======ppppppp======	chr3:140698649-140698872(+)$1	223	31	50	14.0774
!eeeeerrrrrrrrreeee	chr14:31363696-31363958(-)$1	262	126	145	10.9544
ggggggpppppppgggggg	chr5:76736550-76736772(-)$1	222	111	130	13.6643
ffffffpppppppffffff	chr19:16757409-16757632(-)$1	223	161	180	13.8048
Feeeeepppppppeeeee:	chr9:14083275-14083500(-)$1	225	31	50	11.9442
gg[cccpppppppcccggg	chr4:159589764-159589982(-)$1	218	166	185	13.8189
ggggggpppppppgggggg	chr15:81604915-81605136(-)$1	221	191	210	13.6643
###cccpppppppccc444	chr4:79839898-79840119(-)$1	221	39	58	12.9434
ffffffpppppppffffff	chr1:205683354-205683584(-)$1	230	107	126	13.8048
ccddddpppppppdddd]c	chr18:32823255-32823476(+)$1	221	147	166	12.5481
ffffffpppppppffffff	chr17:48799979-48800206(+)$1	227	110	129	13.8048
fffffrrrrrrrrrfffff	chr1:146626638-146626873(-)$1	235	206	225	11.4163
[ddddrrrrrrrrrdddd]	chr19:8027205-8027437(-)$1	232	166	185	10.5285
ggggggpppppppgggggg	chr2:135711360-135711599(+)$1	239	9	28	13.6643
ggggggpppppppgggggg	chr17:41363335-41363555(+)$1	220	20	39	13.6643
[ddddrrrrrrrrrdddd]	chr15:81047410-81047619(+)$1	209	147	166	10.5285
==[cccpppppppccc333	chr17:40175978-40176209(+)$1	231	194	213	13.7284
[eeeeepppppppeeeee]	chr17:60020238-60020468(-)$1	230	139	158	13.6639
eeeerrrrrrrrreeeeeg	chr15:65738806-65739039(-)$1	233	114	133	10.5990
c[ddddpppppppdddd]c	chr14:105476261-105476490(-)$1	229	117	136	12.6908
[eeeeerrrrrrrrreeee	chr4:2251209-2251438(-)$1	229	63	82	11.0534
cc[cccrrrrrrrrrccc]	chr7:97922248-97922478(-)$1	230	132	151	11.0434

#otherMatches

#Seq PSSM
GUUAGUUUCCAAUACUAGU	chr20:2128916-2129155(+)$1	239	14	33	11.9442
UAUUUCCUAUCUUGACAUG	chr4:113108853-113109074(+)$1	221	136	155	11.8706
UUUUGUGGGCUGGGCAAAA	chr1:203771393-203771613(+)$1	220	3	22	13.6643
CCUUUUUUUUUCCGAAUGG	chr18:74071653-74071876(-)$1	223	81	100	13.7695
GGAUCGUAUAUGUGGGUCC	chr20:43128231-43128461(-)$1	230	29	48	11.1991
AGACCAAAGUAAAUAUGGC	chr3:141166991-141167214(+)$1	223	88	107	10.9599
UGCAAGGUGAAGAUUUGGA	chr9:116080691-116080915(-)$1	224	127	146	12.1581
GGGAUGAAUGUGGCGUCUC	chr19:973418-973644(+)$1	226	89	108	13.8048
UAAAGUUGCAUUUAUUUUA	chr2:74331239-74331470(+)$1	231	126	145	14.0774
GUUUGAGAAAUUUUAUUAA	chr21:18966134-18966368(-)$1	234	144	163	11.0534
CCCUGUUUCACUUAUAGGG	chr17:46138158-46138381(+)$1	223	47	66	13.6643
UUGCCAUUUUUACUGGCAG	chr6:144184743-144184977(+)$1	234	6	25	13.6061
GUUUUGUAUUUUUUAAAAC	chr18:48605588-48605836(+)$1	248	93	112	13.8048
UGAGUGUAUCAGCCAUUCA	chr1:75229741-75229963(+)$1	222	137	156	13.5644
UACAGCUUUCACAUUGCUU	chr19:20005018-20005237(+)$1	219	70	89	11.0434
ACAUUAUAUACUUUAAUUA	chr11:47799664-47799883(-)$1	219	191	210	12.4878
AGGGUUUCUGUUUAACCCU	chr4:26436130-26436357(+)$1	227	53	72	13.8048
GAAAGUGUUUCUAUUUUUC	chr12:9840485-9840707(+)$1	222	90	109	11.4163
GGAUCCAGGGAUGGGGUCC	chr17:40852199-40852418(-)$1	219	164	183	13.8048
CCAUUGUUUUUUUUAAUGU	chr1:111489932-111490160(-)$1	228	57	76	13.0768
UAUUAUGAGUUGAGUAAAA	chr2:204296513-204296743(+)$1	230	192	211	12.3109
AUCUUUCAAAAGCGAAGAU	chr22:24967918-24968139(+)$1	221	6	25	13.8048
GUAGCAUUUAUUUUGCUAA	chr4:762588-762806(+)$1	218	139	158	13.6639
CGUAAGUUACAUCCUUAUG	chr8:97242859-97243074(-)$1	215	94	113	14.0774
UCAGGGAGAAUAAUUCUGA	chr21:30716900-30717165(+)$1	265	9	28	13.6061
AUUAUUAAUACUGAAUAAU	chr10:70173778-70174003(-)$1	225	200	219	14.0774
UUUGGGUUUUUUUCUUUGA	chr8:124089261-124089497(+)$1	236	67	86	12.6888
ACAAGGUAAAAUUCCUCAA	chr3:98234611-98234841(-)$1	230	126	145	13.2396
UGUGCCAACCAGAAGCACA	chr15:52843242-52843511(-)$1	269	170	189	10.9012
UGUUUAAAAACUGAAAACA	chr12:121202331-121202549(-)$1	218	64	83	11.4163
UGUUUAAUUAAAAUAAACA	chr6:163994768-163994990(+)$1	222	96	115	13.8048
UUUGAAAUCUCAUAUUAAA	chr15:60783197-60783439(-)$1	242	171	190	11.4163
AAUGAGUCUUUGGUAUUUC	chrX:135046950-135047181(-)$1	231	187	206	11.2746
AUGUUAUUAGAAUCAACAU	chr9:16417779-16417988(-)$1	209	117	136	11.4163
GUUUAUUGGACAUUUAAAC	chr1:114516619-114516843(+)$1	224	53	72	10.9012
UGUUGAUUUAAAUUCAUAU	chr18:44390557-44390814(-)$1	257	155	174	12.5088
UGCAUUGUAUAUAAGUGCA	chr2:10141313-10141535(+)$1	222	166	185	13.8048
UUGAUGUUUGUUCUAUCAG	chr1:150548117-150548469(-)$1	352	89	108	12.5757
AUAGUUUGCAAAUGACUAU	chr5:173387039-173387264(+)$1	225	182	201	13.6061
AGUAUUGGCCUGAAAUAGA	chr15:90378675-90378899(-)$1	224	159	178	12.1470
UACAUUUAUUUGAAUAAUG	chr13:30779177-30779406(-)$1	229	150	169	11.2941
CAAGUUCAGUGAAUACUUA	chr16:69400156-69400386(-)$1	230	96	115	10.5285
ACAUGGCUGUAAAUUAUGU	chr3:140698649-140698872(+)$1	223	31	50	14.0774
UGUCUUCAUAAACCAAGGA	chr14:31363696-31363958(-)$1	262	126	145	10.9544
CAUCAUUUCACAUGUGAUG	chr5:76736550-76736772(-)$1	222	111	130	13.6643
UCCACAGAAGACAUGUGGA	chr19:16757409-16757632(-)$1	223	161	180	13.8048
GCUAUUCAAGUUCAAUAGU	chr9:14083275-14083500(-)$1	225	31	50	11.9442
UGCAAUGCAUCAAAUUUAA	chr4:159589764-159589982(-)$1	218	166	185	13.8189
UUUCAUGUCCUCGGUGAAA	chr15:81604915-81605136(-)$1	221	191	210	13.6643
AUCCAUAUGUUAAGUGAUA	chr4:79839898-79840119(-)$1	221	39	58	12.9434
UGUGCAUACACUUUGUACA	chr1:205683354-205683584(-)$1	230	107	126	13.8048
UAUUCACCCCUCAUGAAUU	chr18:32823255-32823476(+)$1	221	147	166	12.5481
ACCAUUUAUUUGUAAUGGU	chr17:48799979-48800206(+)$1	227	110	129	13.8048
GAUGACUGAUUAUAUUAUC	chr1:146626638-146626873(-)$1	235	206	225	11.4163
UGCCUUGACAuuuuggguu	chr19:8027205-8027437(-)$1	232	166	185	10.5285
GAUCUCGAUGUAAGGGAUC	chr2:135711360-135711599(+)$1	239	9	28	13.6643
GAUAGUUAAUAGUAUUAUC	chr17:41363335-41363555(+)$1	220	20	39	13.6643
UACAUUUUGUUAAUAUGUU	chr15:81047410-81047619(+)$1	209	147	166	10.5285
UGUGGGUCACUGUCCCUUC	chr17:40175978-40176209(+)$1	231	194	213	13.7284
UAAAACAUCUUUAGUUUUC	chr17:60020238-60020468(-)$1	230	139	158	13.6639
UAUUUUCACUUUUAAUAGU	chr15:65738806-65739039(-)$1	233	114	133	10.5990
CCCCUUAACCAAAAAGGUG	chr14:105476261-105476490(-)$1	229	117	136	12.6908
AGGCUGGUUAAGUUGCAGC	chr4:2251209-2251438(-)$1	229	63	82	11.0534
AAAUACUAUAUAAAUGUAA	chr7:97922248-97922478(-)$1	230	132	151	11.0434

#DB
((((((.......))))).	chr20:2128916-2129155(+)$1	1	14	33	11.9442
(((.((.......)).)))	chr4:113108853-113109074(+)$1	1	136	155	11.8706
((((((.......))))))	chr1:203771393-203771613(+)$1	1	3	22	13.6643
((.(((.......))).))	chr18:74071653-74071876(-)$1	1	81	100	13.7695
(((((.........))).)	chr20:43128231-43128461(-)$1	1	29	48	11.1991
.(.(((.........))))	chr3:141166991-141167214(+)$1	1	88	107	10.9599
(.((((.......)))).)	chr9:116080691-116080915(-)$1	1	127	146	12.1581
((((((.......))))))	chr19:973418-973644(+)$1	1	89	108	13.8048
((((((.......))))))	chr2:74331239-74331470(+)$1	1	126	145	14.0774
.(((((.........))))	chr21:18966134-18966368(-)$1	1	144	163	11.0534
((((((.......))))))	chr17:46138158-46138381(+)$1	1	47	66	13.6643
((((((.......))))))	chr6:144184743-144184977(+)$1	1	6	25	13.6061
((((((.......))))))	chr18:48605588-48605836(+)$1	1	93	112	13.8048
.(((((.......))))))	chr1:75229741-75229963(+)$1	1	137	156	13.5644
((.(((.........))).	chr19:20005018-20005237(+)$1	1	70	89	11.0434
..((((.......))))..	chr11:47799664-47799883(-)$1	1	191	210	12.4878
((((((.......))))))	chr4:26436130-26436357(+)$1	1	53	72	13.8048
(((((.........)))))	chr12:9840485-9840707(+)$1	1	90	109	11.4163
((((((.......))))))	chr17:40852199-40852418(-)$1	1	164	183	13.8048
((((((.......))))).	chr1:111489932-111490160(-)$1	1	57	76	13.0768
(.((((.......))))..	chr2:204296513-204296743(+)$1	1	192	211	12.3109
((((((.......))))))	chr22:24967918-24968139(+)$1	1	6	25	13.8048
.(((((.......))))).	chr4:762588-762806(+)$1	1	139	158	13.6639
((((((.......))))))	chr8:97242859-97243074(-)$1	1	94	113	14.0774
((((((.......))))))	chr21:30716900-30717165(+)$1	1	9	28	13.6061
((((((.......))))))	chr10:70173778-70174003(-)$1	1	200	219	14.0774
((.(((.......))).))	chr8:124089261-124089497(+)$1	1	67	86	12.6888
...(((.......))).))	chr3:98234611-98234841(-)$1	1	126	145	13.2396
(((((.........)))))	chr15:52843242-52843511(-)$1	1	170	189	10.9012
(((((.........)))))	chr12:121202331-121202549(-)$1	1	64	83	11.4163
((((((.......))))))	chr6:163994768-163994990(+)$1	1	96	115	13.8048
(((((.........)))))	chr15:60783197-60783439(-)$1	1	171	190	11.4163
((((.........))))))	chrX:135046950-135047181(-)$1	1	187	206	11.2746
(((((.........)))))	chr9:16417779-16417988(-)$1	1	117	136	11.4163
(((((.........)))))	chr1:114516619-114516843(+)$1	1	53	72	10.9012
(((.((.......))))))	chr18:44390557-44390814(-)$1	1	155	174	12.5088
((((((.......))))))	chr2:10141313-10141535(+)$1	1	166	185	13.8048
(.((((.......))))))	chr1:150548117-150548469(-)$1	1	89	108	12.5757
((((((.......))))))	chr5:173387039-173387264(+)$1	1	182	201	13.6061
..((((.......))))..	chr15:90378675-90378899(-)$1	1	159	178	12.1470
((((((.........))))	chr13:30779177-30779406(-)$1	1	150	169	11.2941
.((((.........)))).	chr16:69400156-69400386(-)$1	1	96	115	10.5285
((((((.......))))))	chr3:140698649-140698872(+)$1	1	31	50	14.0774
.(((((.........))))	chr14:31363696-31363958(-)$1	1	126	145	10.9544
((((((.......))))))	chr5:76736550-76736772(-)$1	1	111	130	13.6643
((((((.......))))))	chr19:16757409-16757632(-)$1	1	161	180	13.8048
((((((.......))))).	chr9:14083275-14083500(-)$1	1	31	50	11.9442
((.(((.......))))))	chr4:159589764-159589982(-)$1	1	166	185	13.8189
((((((.......))))))	chr15:81604915-81605136(-)$1	1	191	210	13.6643
...(((.......)))...	chr4:79839898-79840119(-)$1	1	39	58	12.9434
((((((.......))))))	chr1:205683354-205683584(-)$1	1	107	126	13.8048
((((((.......)))).)	chr18:32823255-32823476(+)$1	1	147	166	12.5481
((((((.......))))))	chr17:48799979-48800206(+)$1	1	110	129	13.8048
(((((.........)))))	chr1:146626638-146626873(-)$1	1	206	225	11.4163
.((((.........)))).	chr19:8027205-8027437(-)$1	1	166	185	10.5285
((((((.......))))))	chr2:135711360-135711599(+)$1	1	9	28	13.6643
((((((.......))))))	chr17:41363335-41363555(+)$1	1	20	39	13.6643
.((((.........)))).	chr15:81047410-81047619(+)$1	1	147	166	10.5285
((.(((.......)))...	chr17:40175978-40176209(+)$1	1	194	213	13.7284
.(((((.......))))).	chr17:60020238-60020468(-)$1	1	139	158	13.6639
((((.........)))))(	chr15:65738806-65739039(-)$1	1	114	133	10.5990
(.((((.......)))).)	chr14:105476261-105476490(-)$1	1	117	136	12.6908
.(((((.........))))	chr4:2251209-2251438(-)$1	1	63	82	11.0534
((.(((.........))).	chr7:97922248-97922478(-)$1	1	132	151	11.0434

#PSSM
f : 0.25	g : 0.14	[ : 0.14	c : 0.09	= : 0.09	e : 0.07	i : 0.06	F : 0.03	" : 0.03	# : 0.03	b : 0.01	d : 0.01	! : 0.01	
f : 0.25	e : 0.18	g : 0.14	= : 0.09	c : 0.06	i : 0.06	[ : 0.06	d : 0.06	" : 0.03	# : 0.03	a : 0.01	
f : 0.25	e : 0.18	d : 0.15	g : 0.10	[ : 0.10	= : 0.07	i : 0.04	c : 0.03	" : 0.01	# : 0.01	
f : 0.23	e : 0.18	c : 0.15	d : 0.15	g : 0.10	= : 0.07	i : 0.04	[ : 0.03	
f : 0.23	e : 0.17	c : 0.15	d : 0.15	g : 0.10	= : 0.06	i : 0.04	b : 0.03	r : 0.03	
r : 0.20	f : 0.15	e : 0.14	c : 0.14	g : 0.10	d : 0.10	= : 0.06	i : 0.04	b : 0.03	
p : 0.68	r : 0.31	
p : 0.68	r : 0.31	
p : 0.68	r : 0.31	
p : 0.68	r : 0.31	
p : 0.68	r : 0.31	
p : 0.68	r : 0.31	
p : 0.68	r : 0.31	
r : 0.28	f : 0.15	e : 0.10	d : 0.10	g : 0.09	c : 0.09	= : 0.07	i : 0.04	b : 0.03	
f : 0.23	d : 0.15	e : 0.14	c : 0.10	r : 0.10	g : 0.09	= : 0.07	i : 0.04	b : 0.03	
f : 0.25	e : 0.18	c : 0.15	d : 0.15	g : 0.10	= : 0.07	i : 0.04	] : 0.01	
f : 0.25	e : 0.18	d : 0.15	g : 0.12	c : 0.07	= : 0.07	] : 0.04	i : 0.04	4 : 0.01	3 : 0.01	
f : 0.25	e : 0.21	g : 0.14	= : 0.07	c : 0.06	] : 0.06	d : 0.06	i : 0.04	4 : 0.03	2 : 0.03	3 : 0.01	
f : 0.26	g : 0.15	e : 0.10	] : 0.10	= : 0.07	i : 0.06	c : 0.04	2 : 0.04	: : 0.03	4 : 0.03	a : 0.01	b : 0.01	d : 0.01	3 : 0.01	

#score	807.452890381454
#seq	64
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_UTR_m1_run1.txt

#BEAR
hhhhhwwwwwwwwwwwwwwhhhhhhh	chr6:75963147-75963377(-)$1	230	141	167	22.3693
++cccwwwwwwwwwwwwwwccc>>>>	chr3:69105084-69105307(-)$1	223	90	116	22.1449
!!ddddvvvvvvvvvvvvvdddd22c	chr12:49087597-49087827(-)$1	230	66	92	23.0380
e"""bbvvvvvvvvvvvvvbb333ee	chr17:65105539-65105760(-)$1	221	18	44	22.9296
""cccvvvvvvvvvvvvvccc]iiii	chr8:17152778-17153000(+)$1	222	177	203	23.5307
fffffwwwwwwwwwwwwwwffffffb	chr12:74932190-74932420(+)$1	230	20	46	23.4621
eeeeewwwwwwwwwwwwwweeeee]b	chr2:37375979-37376209(+)$1	230	45	71	24.6659
gggggwwwwwwwwwwwwwwggggggg	chr1:167388246-167388469(+)$1	223	159	185	24.6863
!!eeeeeuuuuuuuuuuuueeeee]d	chr16:24835411-24835641(+)$1	230	116	142	23.3813
iiiiiwwwwwwwwwwwwwwiiiiiii	chr9:36337562-36337792(-)$1	230	28	54	24.7632
ddbbbbvvvvvvvvvvvvvbb]bb]d	chr16:47733157-47733382(+)$1	225	196	222	22.0616
fffffyyyyyyyyyyyyyyyyfffff	chr12:92537686-92537903(-)$1	217	175	201	21.6197
eeeeexxxxxxxxxxxxxxxeeeeee	chr3:49019008-49019232(+)$1	224	54	80	21.3795
ee!!bbvvvvvvvvvvvvvbb22eee	chr12:42706083-42706306(-)$1	223	160	186	22.7428
[ffffffuuuuuuuuuuuuffffff]	chr5:6756669-6756899(+)$1	230	165	191	22.2095
ccc[cccuuuuuuuuuuuucccccc4	chr2:61416870-61417089(-)$1	219	95	121	23.0128
=======uuuuuuuuuuuu=======	chr2:162092505-162092735(+)$1	230	113	139	23.4754
eeeeevvvvvvvvvvvvveeeee:cc	chr6:114182250-114182471(+)$1	221	151	177	22.3157
======vvvvvvvvvvvvv=======	chr6:28347556-28347780(-)$1	224	43	69	24.2446
eeeeeyyyyyyyyyyyyyyyyeeeee	chr7:45953845-45954070(-)$1	225	182	208	22.5023
fffffwwwwwwwwwwwwwwffffff4	chr11:67924141-67924367(-)$1	226	38	64	23.6194
ccccccvvvvvvvvvvvvvccc]ccc	chr4:48862973-48863196(+)$1	223	77	103	23.6832
eeeeeuuuuuuuuuuuueeeee]ggg	chr4:38774597-38774820(-)$1	223	177	203	22.3752
eeeeeyyyyyyyyyyyyyyyyeeeee	chr14:93706884-93707108(-)$1	224	29	55	22.5023
ee[dddduuuuuuuuuuuudddd]ee	chr5:89812595-89812820(-)$1	225	118	144	22.3219
gggggwwwwwwwwwwwwwwggggggg	chr3:20025860-20026090(+)$1	230	62	88	24.6863
"cccxxxxxxxxxxxxxxxccc333f	chr3:47386449-47386679(+)$1	230	61	87	20.9680
ddddddvvvvvvvvvvvvvdddd]dd	chr2:96808816-96809089(-)$1	273	28	54	22.5900
eeecccvvvvvvvvvvvvvccc4444	chrX:123046056-123046286(+)$1	230	136	162	23.8621
gggggwwwwwwwwwwwwwwggggggg	chr12:27573372-27573599(+)$1	227	182	208	24.6863
!!ddddvvvvvvvvvvvvvdddd22f	chr12:31540137-31540357(-)$1	220	116	142	22.9289
!!cccxxxxxxxxxxxxxxxccc]dd	chr3:124947050-124947268(-)$1	218	96	122	21.1647
eeeeeuuuuuuuuuuuueeeeeccc[	chr14:74178655-74178885(-)$1	230	59	85	22.0443
fffffauuuuuuuuuuuua]ffffff	chr12:80168167-80168397(-)$1	230	96	122	23.0162
eeeeewwwwwwwwwwwwwweeeee::	chr18:9547006-9547227(-)$1	221	190	216	22.9342
eeeeeeeuuuuuuuuuuuueeeee:I	chr12:121785552-121785777(-)$1	225	181	207	21.0169
eeeeeyyyyyyyyyyyyyyyyeeeee	chr6:111588943-111589170(+)$1	227	95	121	22.5023
:eeeeevvvvvvvvvvvvveeeee::	chr10:91068366-91068596(+)$1	230	191	217	21.1550
gggggwwwwwwwwwwwwwwggggggg	chr17:38438523-38438753(+)$1	230	40	66	24.6863
hhhhyyyyyyyyyyyyyyyyhhhhhh	chr17:47132252-47132482(+)$1	230	120	146	20.4381
[eeeeevvvvvvvvvvvvveeeee22	chr11:62609019-62609250(-)$1	231	121	147	23.8583
[bb[bbvvvvvvvvvvvvvbb]bb]c	chr5:78622679-78622905(+)$1	226	109	135	22.5590
fffffwwwwwwwwwwwwwwffffff:	chr16:67132805-67133025(+)$1	220	3	29	22.8171
eeeeeyyyyyyyyyyyyyyyyeeeee	chr3:160152516-160152737(+)$1	221	40	66	22.5023
dd[bbyyyyyyyyyyyyyyyybbddd	chr18:5289648-5289878(-)$1	230	85	111	20.6073
ddddxxxxxxxxxxxxxxxdddd333	chr15:89744326-89744556(+)$1	230	88	114	20.3056
::cccwwwwwwwwwwwwwwccceeee	chr20:52199303-52199522(-)$1	219	122	148	22.3719
fffffwwwwwwwwwwwwwwffffff:	chr17:17748082-17748301(-)$1	219	170	196	22.8171
gggggwwwwwwwwwwwwwwggggggg	chr4:42118919-42119143(-)$1	224	2	28	24.6863
======vvvvvvvvvvvvv=======	chr5:114859295-114859518(-)$1	223	67	93	24.2446
[eeeeevvvvvvvvvvvvveeeee]b	chr8:57078617-57078847(-)$1	230	92	118	24.0898
[bb[axxxxxxxxxxxxxxxa]bb]d	chr9:114980893-114981123(-)$1	230	143	169	20.3338
##cccwwwwwwwwwwwwwwcccbb]h	chr6:56973823-56974045(+)$1	222	173	199	23.9332
[ddddvvvvvvvvvvvvvddddgggg	chr6:36654199-36654422(+)$1	223	140	166	22.7557
###bbvvvvvvvvvvvvvbb333bb]	chr3:47777428-47777658(-)$1	230	30	56	21.6216
iicccyyyyyyyyyyyyyyyyccc33	chr1:243666765-243666995(-)$1	230	21	47	22.4146
ggggggvvvvvvvvvvvvvggggggg	chr3:33431533-33431753(-)$1	220	60	86	23.8635
iiiiixxxxxxxxxxxxxxxiiiiii	chr2:55894043-55894273(-)$1	230	149	175	21.5275
!!dddduuuuuuuuuuuuddddffff	chr7:6728732-6728962(-)$1	230	191	217	22.3636
eeeeexxxxxxxxxxxxxxxeeeee:	chr2:69546974-69547196(-)$1	222	3	29	20.5748
iiiiiivvvvvvvvvvvvviiiiiii	chr17:61666533-61666754(+)$1	221	27	53	23.9432
dddbbwwwwwwwwwwwwwwbb]dddd	chrX:54842264-54842504(+)$1	240	163	189	22.8569

#otherMatches

#Seq PSSM
CAGGUUUUAACUUCUUCAUGCCUGGA	chr6:75963147-75963377(-)$1	230	141	167	22.3693
UAGGCAAAUGAAAUCUCCAGCCAUCA	chr3:69105084-69105307(-)$1	223	90	116	22.1449
CAAUGUGAAGUCACAAUAUGCAUAUG	chr12:49087597-49087827(-)$1	230	66	92	23.0380
CCCAGUACCAAAUUUCCUCGCAAAGA	chr17:65105539-65105760(-)$1	221	18	44	22.9296
AACUUUCAAAAGCAAUUUAAGAUAUU	chr8:17152778-17153000(+)$1	222	177	203	23.5307
GCCAGGACAAUAACAUAGACUGGUCC	chr12:74932190-74932420(+)$1	230	20	46	23.4621
CACGCAGAUAAUCACGGAAGUGUGGA	chr2:37375979-37376209(+)$1	230	45	71	24.6659
UAAGAUACUCAAAUUUAACUUUUAGC	chr1:167388246-167388469(+)$1	223	159	185	24.6863
AAUGAUGUUCUCUCCGUCUCAUCGGC	chr16:24835411-24835641(+)$1	230	116	142	23.3813
UAGGAUAUCCCUCACCUGUUCCUGAU	chr9:36337562-36337792(-)$1	230	28	54	24.7632
CAGCCAUUAAUAUACGAACUGAGCAU	chr16:47733157-47733382(+)$1	225	196	222	22.0616
AGAAUGGuaaaaaaaaaaaaaauuuu	chr12:92537686-92537903(-)$1	217	175	201	21.6197
ACAGGUUCCUUCUCUUCUCUCCUGUU	chr3:49019008-49019232(+)$1	224	54	80	21.3795
uaauugucuauuuuuuuuccauguau	chr12:42706083-42706306(-)$1	223	160	186	22.7428
CUGUAGGCCUGUACUAAUCUCUACGC	chr5:6756669-6756899(+)$1	230	165	191	22.2095
UCCUAGAAUAAUGGAACACUCUGGAA	chr2:61416870-61417089(-)$1	219	95	121	23.0128
UACAUGGCUUUAAUUUUUACUGUGUG	chr2:162092505-162092735(+)$1	230	113	139	23.4754
AGUUCAUUUAAACCAUAGGAACUUUU	chr6:114182250-114182471(+)$1	221	151	177	22.3157
CCUGGAUGAUUAUCUCUGUUUUGGGA	chr6:28347556-28347780(-)$1	224	43	69	24.2446
UGGCuaauauaauuuuaauaaaguua	chr7:45953845-45954070(-)$1	225	182	208	22.5023
AACUACAGCUAUCUUAAUUUGGUUCU	chr11:67924141-67924367(-)$1	226	38	64	23.6194
UAACUCUUAAAAAACCGUCGAGAUUA	chr4:48862973-48863196(+)$1	223	77	103	23.6832
aggauuucuaagaauguauccuauag	chr4:38774597-38774820(-)$1	223	177	203	22.3752
UACUCUCCAAUGUAAAUAUAUGAGUA	chr14:93706884-93707108(-)$1	224	29	55	22.5023
UGUACUUUGAAAUUGUUAUGGGUUCG	chr5:89812595-89812820(-)$1	225	118	144	22.3219
GGGGUAAAAAUCAAAUGCAACCCCAU	chr3:20025860-20026090(+)$1	230	62	88	24.6863
UGUGAUUACCUCCUACUGCCACCAUG	chr3:47386449-47386679(+)$1	230	61	87	20.9680
UGGCGCUGGAAAAUUAUUUGUGCUCA	chr2:96808816-96809089(-)$1	273	28	54	22.5900
AAAUGCAAAAAAAAAAAAAGCAAUUA	chrX:123046056-123046286(+)$1	230	136	162	23.8621
UAUUGUUUGUAUCUUUUAUUAAUGUU	chr12:27573372-27573599(+)$1	227	182	208	24.6863
AAAAUAAGUAGCUUAAAAAUGUUGGG	chr12:31540137-31540357(-)$1	220	116	142	22.9289
UCUGUACUCACUUUCACUAAGCAUUG	chr3:124947050-124947268(-)$1	218	96	122	21.1647
UUCCAGAUUUAUAUUAAUGGAAGGAA	chr14:74178655-74178885(-)$1	230	59	85	22.0443
ACUGUCUCCUUAACCACUGAACAGUU	chr12:80168167-80168397(-)$1	230	96	122	23.0162
GUGCAACUUCUUCACAUACUGUACAU	chr18:9547006-9547227(-)$1	221	190	216	22.9342
CAUUUUCUUCUUUAUAUAUGAAAAGG	chr12:121785552-121785777(-)$1	225	181	207	21.0169
AGGUAUUUUUAUUAAUUGCUUUACCU	chr6:111588943-111589170(+)$1	227	95	121	22.5023
UGUGUUAUUUUCUGUAUUAAACAUCU	chr10:91068366-91068596(+)$1	230	191	217	21.1550
AGUGGUCUUAAAUCUCAUUCCACUGG	chr17:38438523-38438753(+)$1	230	40	66	24.6863
UCUACCUCUUAGCAAAACAAUAGAUA	chr17:47132252-47132482(+)$1	230	120	146	20.4381
accugguauugcaguacuuccaggaa	chr11:62609019-62609250(-)$1	231	121	147	23.8583
UACCAUGAAAUCUCCAGUAAUCGUUU	chr5:78622679-78622905(+)$1	226	109	135	22.5590
GCAGUAAUAGACAUCACAAACUGCCA	chr16:67132805-67133025(+)$1	220	3	29	22.8171
UGCCCUAGCUGUUAAAUUUCUGGGUA	chr3:160152516-160152737(+)$1	221	40	66	22.5023
CUUACGUAUUUCAAGUAAAAAGUAGA	chr18:5289648-5289878(-)$1	230	85	111	20.6073
AGGUUUAUCCGAAUAUGCUACCUUUC	chr15:89744326-89744556(+)$1	230	88	114	20.3056
ACUCCAGAAAUUGCCCAACGGAACUU	chr20:52199303-52199522(-)$1	219	122	148	22.3719
AAUGUGUUUAACCCUUUCUGCGUUCA	chr17:17748082-17748301(-)$1	219	170	196	22.8171
AGGGACAAGAAGCAAACAUUCUCUUA	chr4:42118919-42119143(-)$1	224	2	28	24.6863
UGUAUGUUAGCAUAUUUUCUAUGCAG	chr5:114859295-114859518(-)$1	223	67	93	24.2446
CCUAGAUGACCAUUUUUAUUUUAGUG	chr8:57078617-57078847(-)$1	230	92	118	24.0898
UCUGUGGCAUUGGAAAAAAAGGAGUC	chr9:114980893-114981123(-)$1	230	143	169	20.3338
UUCUGUUUCCAUUCAUUUUCAGCACU	chr6:56973823-56974045(+)$1	222	173	199	23.9332
CAGCUACCCUUUUUCUCCAGCUGGGC	chr6:36654199-36654422(+)$1	223	140	166	22.7557
UUUCAUCCUCAGAACAAUUGUUUGAC	chr3:47777428-47777658(-)$1	230	30	56	21.6216
CCCAGAUUCCAACAUUUCUCACUGAA	chr1:243666765-243666995(-)$1	230	21	47	22.4146
CCUUUCUAAUGAGCUGUAUGAGAGGU	chr3:33431533-33431753(-)$1	220	60	86	23.8635
UAAUUUAUAUAAAAAGCUCUAAUUAU	chr2:55894043-55894273(-)$1	230	149	175	21.5275
auuuaggaugcucuauuacuaauaac	chr7:6728732-6728962(-)$1	230	191	217	22.3636
GCUUGCUCCAUUGUUAUCUUCAAGUA	chr2:69546974-69547196(-)$1	222	3	29	20.5748
AGGGGCUUUUGUAUUUCCUGCCUCUG	chr17:61666533-61666754(+)$1	221	27	53	23.9432
aaaucuauuugccauuucugAGUUUA	chrX:54842264-54842504(+)$1	240	163	189	22.8569

#DB
(((((..............)))))))	chr6:75963147-75963377(-)$1	1	141	167	22.3693
..(((..............)))....	chr3:69105084-69105307(-)$1	1	90	116	22.1449
..((((.............))))..)	chr12:49087597-49087827(-)$1	1	66	92	23.0380
(...((.............))...))	chr17:65105539-65105760(-)$1	1	18	44	22.9296
..(((.............))).))))	chr8:17152778-17153000(+)$1	1	177	203	23.5307
(((((..............)))))))	chr12:74932190-74932420(+)$1	1	20	46	23.4621
(((((..............))))).)	chr2:37375979-37376209(+)$1	1	45	71	24.6659
(((((..............)))))))	chr1:167388246-167388469(+)$1	1	159	185	24.6863
..(((((............))))).)	chr16:24835411-24835641(+)$1	1	116	142	23.3813
(((((..............)))))))	chr9:36337562-36337792(-)$1	1	28	54	24.7632
((((((.............)).)).)	chr16:47733157-47733382(+)$1	1	196	222	22.0616
(((((................)))))	chr12:92537686-92537903(-)$1	1	175	201	21.6197
(((((...............)))))(	chr3:49019008-49019232(+)$1	1	54	80	21.3795
((..((.............))..)))	chr12:42706083-42706306(-)$1	1	160	186	22.7428
.((((((............)))))).	chr5:6756669-6756899(+)$1	1	165	191	22.2095
(((.(((............)))))).	chr2:61416870-61417089(-)$1	1	95	121	23.0128
(((((((............)))))))	chr2:162092505-162092735(+)$1	1	113	139	23.4754
(((((.............))))).((	chr6:114182250-114182471(+)$1	1	151	177	22.3157
((((((.............)))))))	chr6:28347556-28347780(-)$1	1	43	69	24.2446
(((((................)))))	chr7:45953845-45954070(-)$1	1	182	208	22.5023
(((((..............)))))).	chr11:67924141-67924367(-)$1	1	38	64	23.6194
((((((.............))).)))	chr4:48862973-48863196(+)$1	1	77	103	23.6832
(((((............))))).)))	chr4:38774597-38774820(-)$1	1	177	203	22.3752
(((((................)))))	chr14:93706884-93707108(-)$1	1	29	55	22.5023
((.((((............)))).))	chr5:89812595-89812820(-)$1	1	118	144	22.3219
(((((..............)))))))	chr3:20025860-20026090(+)$1	1	62	88	24.6863
.(((...............)))...)	chr3:47386449-47386679(+)$1	1	61	87	20.9680
((((((.............)))).))	chr2:96808816-96809089(-)$1	1	28	54	22.5900
((((((.............)))....	chrX:123046056-123046286(+)$1	1	136	162	23.8621
(((((..............)))))))	chr12:27573372-27573599(+)$1	1	182	208	24.6863
..((((.............))))..)	chr12:31540137-31540357(-)$1	1	116	142	22.9289
..(((...............))).))	chr3:124947050-124947268(-)$1	1	96	122	21.1647
(((((............)))))(((.	chr14:74178655-74178885(-)$1	1	59	85	22.0443
((((((............).))))))	chr12:80168167-80168397(-)$1	1	96	122	23.0162
(((((..............)))))..	chr18:9547006-9547227(-)$1	1	190	216	22.9342
))(((((............))))).)	chr12:121785552-121785777(-)$1	1	181	207	21.0169
(((((................)))))	chr6:111588943-111589170(+)$1	1	95	121	22.5023
.(((((.............)))))..	chr10:91068366-91068596(+)$1	1	191	217	21.1550
(((((..............)))))))	chr17:38438523-38438753(+)$1	1	40	66	24.6863
((((................))))))	chr17:47132252-47132482(+)$1	1	120	146	20.4381
.(((((.............)))))..	chr11:62609019-62609250(-)$1	1	121	147	23.8583
.((.((.............)).)).)	chr5:78622679-78622905(+)$1	1	109	135	22.5590
(((((..............)))))).	chr16:67132805-67133025(+)$1	1	3	29	22.8171
(((((................)))))	chr3:160152516-160152737(+)$1	1	40	66	22.5023
((.((................)))))	chr18:5289648-5289878(-)$1	1	85	111	20.6073
((((...............))))...	chr15:89744326-89744556(+)$1	1	88	114	20.3056
..(((..............)))((((	chr20:52199303-52199522(-)$1	1	122	148	22.3719
(((((..............)))))).	chr17:17748082-17748301(-)$1	1	170	196	22.8171
(((((..............)))))))	chr4:42118919-42119143(-)$1	1	2	28	24.6863
((((((.............)))))))	chr5:114859295-114859518(-)$1	1	67	93	24.2446
.(((((.............))))).)	chr8:57078617-57078847(-)$1	1	92	118	24.0898
.((.(...............).)).)	chr9:114980893-114981123(-)$1	1	143	169	20.3338
..(((..............))))).)	chr6:56973823-56974045(+)$1	1	173	199	23.9332
.((((.............))))))))	chr6:36654199-36654422(+)$1	1	140	166	22.7557
...((.............))...)).	chr3:47777428-47777658(-)$1	1	30	56	21.6216
(((((................)))..	chr1:243666765-243666995(-)$1	1	21	47	22.4146
((((((.............)))))))	chr3:33431533-33431753(-)$1	1	60	86	23.8635
(((((...............))))))	chr2:55894043-55894273(-)$1	1	149	175	21.5275
..((((............))))))))	chr7:6728732-6728962(-)$1	1	191	217	22.3636
(((((...............))))).	chr2:69546974-69547196(-)$1	1	3	29	20.5748
((((((.............)))))))	chr17:61666533-61666754(+)$1	1	27	53	23.9432
(((((..............)).))))	chrX:54842264-54842504(+)$1	1	163	189	22.8569

#PSSM
e : 0.25	f : 0.09	g : 0.09	[ : 0.09	! : 0.08	d : 0.08	i : 0.06	= : 0.04	h : 0.03	" : 0.03	c : 0.03	: : 0.03	# : 0.03	+ : 0.01	
e : 0.29	f : 0.11	g : 0.09	d : 0.09	! : 0.08	i : 0.06	c : 0.04	= : 0.04	h : 0.03	" : 0.03	b : 0.03	# : 0.03	+ : 0.01	: : 0.01	
e : 0.27	c : 0.14	d : 0.11	f : 0.11	g : 0.09	i : 0.04	b : 0.04	= : 0.04	h : 0.03	[ : 0.03	" : 0.01	! : 0.01	# : 0.01	
e : 0.25	c : 0.14	d : 0.11	f : 0.11	g : 0.09	b : 0.06	i : 0.04	[ : 0.04	= : 0.04	h : 0.03	" : 0.01	! : 0.01	
e : 0.25	c : 0.14	b : 0.11	f : 0.11	d : 0.09	g : 0.09	i : 0.04	= : 0.04	x : 0.03	h : 0.01	y : 0.01	a : 0.01	
w : 0.27	y : 0.12	x : 0.11	d : 0.08	e : 0.08	b : 0.06	v : 0.06	c : 0.04	= : 0.04	u : 0.03	f : 0.01	a : 0.01	g : 0.01	i : 0.01	
v : 0.32	w : 0.27	y : 0.12	x : 0.11	u : 0.06	e : 0.03	f : 0.01	c : 0.01	= : 0.01	d : 0.01	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.16	y : 0.12	x : 0.11	
v : 0.32	w : 0.27	u : 0.12	y : 0.12	x : 0.11	e : 0.03	
w : 0.27	v : 0.25	y : 0.12	x : 0.11	u : 0.09	e : 0.04	d : 0.03	c : 0.01	a : 0.01	b : 0.01	
e : 0.16	c : 0.12	y : 0.12	d : 0.11	b : 0.09	g : 0.09	f : 0.08	x : 0.08	= : 0.04	i : 0.03	h : 0.01	] : 0.01	
e : 0.19	c : 0.14	d : 0.11	y : 0.11	f : 0.09	g : 0.09	b : 0.08	i : 0.04	= : 0.04	h : 0.03	a : 0.01	3 : 0.01	
e : 0.25	c : 0.14	d : 0.11	f : 0.11	g : 0.09	] : 0.08	i : 0.04	= : 0.04	h : 0.03	3 : 0.03	2 : 0.01	b : 0.01	
e : 0.24	f : 0.12	g : 0.11	d : 0.09	b : 0.08	i : 0.06	c : 0.06	3 : 0.04	= : 0.04	h : 0.03	] : 0.03	> : 0.01	2 : 0.01	4 : 0.01	
e : 0.24	f : 0.12	g : 0.12	b : 0.08	i : 0.06	c : 0.06	3 : 0.04	= : 0.04	] : 0.04	h : 0.03	2 : 0.03	d : 0.03	> : 0.01	: : 0.01	4 : 0.01	
e : 0.16	f : 0.12	g : 0.12	] : 0.11	i : 0.06	c : 0.06	d : 0.06	2 : 0.04	= : 0.04	3 : 0.04	: : 0.04	h : 0.03	> : 0.01	4 : 0.01	b : 0.01	
e : 0.14	g : 0.12	d : 0.11	f : 0.08	: : 0.08	c : 0.06	i : 0.06	h : 0.04	b : 0.04	4 : 0.04	= : 0.04	] : 0.03	3 : 0.03	> : 0.01	[ : 0.01	I : 0.01	2 : 0.01	

#score	1410.7674213503
#seq	62
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_CDS_m3_run2.txt

#BEAR
cc[cccooooooccc]cc	chr6:56357701-56357971(-)$1	270	78	96	12.6118
ffffffooooooffffff	chr13:98668920-98669141(+)$1	221	82	100	10.7619
ccccccooooooccc444	chr5:176707687-176707922(+)$1	235	147	165	12.2638
bb[cccooooooccc]bb	chr17:7506131-7506366(-)$1	235	70	88	11.9418
ccccccoooooocccddd	chr19:53057781-53058020(+)$1	239	135	153	11.9084
"""cccooooooccc333	chr17:35608835-35609058(-)$1	223	190	208	12.7419
[bb[bboooooobb]bb]	chr17:62496741-62496970(-)$1	229	165	183	9.8988
)eeeeeooooooeeeee>	chr1:227842512-227842733(+)$1	221	152	170	9.7124
!bbcccooooooccc]bb	chr10:88939826-88940051(+)$1	225	167	185	11.7945
ffffffooooooffffff	chr4:17825198-17825430(+)$1	232	135	153	10.7619
ffffffooooooffffff	chr13:28003927-28004155(+)$1	228	65	83	10.7619
ggggggoooooogggggg	chr6:57012042-57012269(+)$1	227	157	175	11.4925
b!!cccooooooccc22b	chr2:62106012-62106244(-)$1	232	159	177	12.0555
bb[cccooooooccc]bb	chr7:92731302-92731534(-)$1	232	75	93	11.9418
ffffffooooooffffff	chr21:43413502-43413740(-)$1	238	142	160	10.7619
""ddddoooooodddd33	chr10:22617508-22617727(+)$1	219	48	66	10.9483
ffffffooooooffffff	chr19:38189110-38189329(-)$1	219	168	186	10.7619
c[ddddoooooodddd44	chr1:203768736-203768961(+)$1	225	73	91	10.7773
bb[cccooooooccc]bb	chr5:37351284-37351507(-)$1	223	156	174	11.9418
d!!cccoooooocccddd	chr1:82450920-82451139(+)$1	219	48	66	12.0678
d[ddddoooooodddd44	chr17:27024824-27025053(+)$1	229	85	103	10.6286
[eeeeeooooooeeeee]	chr17:26961930-26962163(-)$1	233	210	228	10.4347
ggggggoooooogggggg	chrX:119388831-119389059(+)$1	228	129	147	11.4925
eeecccooooooccc:dd	chr10:5790889-5791116(+)$1	227	48	66	10.9108
ee[cccooooooccc]ee	chr2:71582761-71582984(+)$1	223	130	148	12.3680
ggggggoooooogggggg	chr5:31484923-31485147(-)$1	224	189	207	11.4925
!!ddddoooooodddd22	chr22:29693723-29693975(+)$1	252	183	201	10.5782
ffffffooooooffffff	chr2:10186412-10186640(+)$1	228	44	62	10.7619
dddd[aooooooa]dddd	chr8:145948278-145948500(-)$1	222	136	154	10.3423
e!!cccooooooccc22e	chr21:34926425-34926660(+)$1	235	56	74	12.2670
bb[cccooooooccc]bb	chr4:83860753-83860985(-)$1	232	67	85	11.9418
ggggggoooooogggggg	chr3:101390772-101390997(-)$1	225	158	176	11.4925
""ddddoooooodddd77	chr4:78081984-78082210(+)$1	226	34	52	9.8125
eee[bboooooobb22ee	chr16:72142119-72142341(+)$1	222	82	100	10.2519
ccccccooooooccc]cc	chr9:35059449-35059670(-)$1	221	77	95	12.3763
ee!!bboooooobbeeee	chr19:3976153-3976397(-)$1	244	44	62	10.5646
[ccc[bboooooobb22c	chrX:123020157-123020385(+)$1	228	122	140	9.0071
ffffffooooooffffff	chr17:3572563-3572796(+)$1	233	163	181	10.7619
[eeeeeooooooeeeee]	chr6:56393539-56393764(-)$1	225	26	44	10.4347
!!ddddoooooodddd]e	chrM:15658-15983(+)$1	325	86	104	10.8403
c!!cccooooooccc]cc	chr16:75664249-75664477(-)$1	228	90	108	12.6844
ggggggoooooogggggg	chr13:33110271-33110492(-)$1	221	179	197	11.4925
!ddddaooooooa]dddd	chr16:19548049-19548277(+)$1	228	62	80	10.5937
ccc!!aooooooa22ccc	chr10:5791258-5791505(+)$1	247	39	57	10.5019
eee[bboooooobb]eee	chr17:60061546-60061767(-)$1	221	20	38	10.3586
dd[cccoooooocccddd	chr10:102710345-102710566(+)$1	221	14	32	11.8493
#bbcccooooooccc]bb	chr13:46563062-46563285(-)$1	223	57	75	11.7061
[a[cccooooooccca]e	chr1:55608561-55608782(-)$1	221	135	153	12.4174
"""cccoooooocccddd	chr17:44143932-44144165(-)$1	233	70	88	12.1428
iiiiiiooooooiiiiii	chrM:9508-9747(-)$1	239	169	187	11.2856
ggg[bboooooobbgggg	chr14:32561379-32561607(+)$1	228	154	172	10.9544
g]acccooooooccc:::	chr20:5095854-5096100(-)$1	246	227	245	9.2546
dd!!bboooooobb22dd	chr5:54456014-54456257(+)$1	243	138	156	10.2770
ff[cccooooooccc]ff	chr17:80014103-80014323(+)$1	220	77	95	12.4731
ggggggoooooogggggg	chr1:179815453-179815676(-)$1	223	36	54	11.4925
ccacccooooooccc22a	chr17:1584123-1584357(-)$1	234	122	140	12.0820

#otherMatches

#Seq PSSM
UUGCAGACUAAACUGGAA	chr6:56357701-56357971(-)$1	270	78	96	12.6118
UCUGACCAAAGUGUCAGA	chr13:98668920-98669141(+)$1	221	82	100	10.7619
GGUUAGAAAAAGCUAAAU	chr5:176707687-176707922(+)$1	235	147	165	12.2638
AGAGUUCAAGAAAGCCCU	chr17:7506131-7506366(-)$1	235	70	88	11.9418
CACGUCAUCGUAGACUUC	chr19:53057781-53058020(+)$1	239	135	153	11.9084
CUCAAAGACCCAUUUAUU	chr17:35608835-35609058(-)$1	223	190	208	12.7419
AGUACCAAAACAGGCACA	chr17:62496741-62496970(-)$1	229	165	183	9.8988
AUGCAAAGAAUGUUGCAA	chr1:227842512-227842733(+)$1	221	152	170	9.7124
AUGAGAACAGGAUCUACA	chr10:88939826-88940051(+)$1	225	167	185	11.7945
UCUUUUCUUGUUGAAAGA	chr4:17825198-17825430(+)$1	232	135	153	10.7619
AUAACUUCUUACAGUUGU	chr13:28003927-28004155(+)$1	228	65	83	10.7619
GGAGUGCAUUGCCAUUCC	chr6:57012042-57012269(+)$1	227	157	175	11.4925
CUUGACUGACAUGUCUCG	chr2:62106012-62106244(-)$1	232	159	177	12.0555
GGUCUUGGAUCAAAGUUC	chr7:92731302-92731534(-)$1	232	75	93	11.9418
UUAACUGAAAAGAGUUGG	chr21:43413502-43413740(-)$1	238	142	160	10.7619
CAGCAGCAAUGACUGUGA	chr10:22617508-22617727(+)$1	219	48	66	10.9483
AGGCAUUUCACUGUGCCU	chr19:38189110-38189329(-)$1	219	168	186	10.7619
CCUUUCCCUGCAGAAACU	chr1:203768736-203768961(+)$1	225	73	91	10.7773
GAUAAUGGCAGAAUUUUC	chr5:37351284-37351507(-)$1	223	156	174	11.9418
UACUGUGAGAAAACAAUC	chr1:82450920-82451139(+)$1	219	48	66	12.0678
CAUUCUACCCCCAGAAAU	chr17:27024824-27025053(+)$1	229	85	103	10.6286
UGUUUUUGAGGUGAAACU	chr17:26961930-26962163(-)$1	233	210	228	10.4347
UUAUGUCUUCACAUAUAA	chrX:119388831-119389059(+)$1	228	129	147	11.4925
AGAGGUAGUUACACCAGG	chr10:5790889-5791116(+)$1	227	48	66	10.9108
GUCGACAGUUACGUCAAC	chr2:71582761-71582984(+)$1	223	130	148	12.3680
GUGUUUAUGGAAGAACAU	chr5:31484923-31485147(-)$1	224	189	207	11.4925
AGGGCAGAGGCAUGCCAC	chr22:29693723-29693975(+)$1	252	183	201	10.5782
GUCUCUGACUCUGGGGAU	chr2:10186412-10186640(+)$1	228	44	62	10.7619
CCAGAGAAGUCACACUGG	chr8:145948278-145948500(-)$1	222	136	154	10.3423
GGUGGUAGUGAAGCUGAC	chr21:34926425-34926660(+)$1	235	56	74	12.2670
GGUCAUUGAUAUAUGUCC	chr4:83860753-83860985(-)$1	232	67	85	11.9418
AAACAUGAACUUGUGUUU	chr3:101390772-101390997(-)$1	225	158	176	11.4925
UGGAAAAAAUAAUUUCAG	chr4:78081984-78082210(+)$1	226	34	52	9.8125
UUUACCUGCAGUGGAAGA	chr16:72142119-72142341(+)$1	222	82	100	10.2519
UCAGACCUGGCCGUCUUG	chr9:35059449-35059670(-)$1	221	77	95	12.3763
GGCAGCAGACACGCCCUC	chr19:3976153-3976397(-)$1	244	44	62	10.5646
UCCAAGAAAUCCAUCCAU	chrX:123020157-123020385(+)$1	228	122	140	9.0071
ACGUCCUGUUCUGGACGU	chr17:3572563-3572796(+)$1	233	163	181	10.7619
UACCUGUGUUUUCAGGUU	chr6:56393539-56393764(-)$1	225	26	44	10.4347
UCAUUCUAACCUGAAUCG	chrM:15658-15983(+)$1	325	86	104	10.8403
AAGUGACUUGCAUCAAUC	chr16:75664249-75664477(-)$1	228	90	108	12.6844
UUUGAACUAUCAUUUAAA	chr13:33110271-33110492(-)$1	221	179	197	11.4925
AAAUGCACCGAAGACGUU	chr16:19548049-19548277(+)$1	228	62	80	10.5937
CAGAACACUUUAGACCUG	chr10:5791258-5791505(+)$1	247	39	57	10.5019
UACCAUCUUUAUAUUGUA	chr17:60061546-60061767(-)$1	221	20	38	10.3586
ccuaauguguaaauugga	chr10:102710345-102710566(+)$1	221	14	32	11.8493
ACUUCCCCAGCAGGACAG	chr13:46563062-46563285(-)$1	223	57	75	11.7061
GUAUCUAAGGAAAGAAGU	chr1:55608561-55608782(-)$1	221	135	153	12.4174
UCAGCCUGUCUUGGCAGA	chr17:44143932-44144165(-)$1	233	70	88	12.1428
AGCGGGGUGAUGCCUGUU	chrM:9508-9747(-)$1	239	169	187	11.2856
UAAAGAAACAUGUCUUAG	chr14:32561379-32561607(+)$1	228	154	172	10.9544
UGCCAGCAUAUACUGAAG	chr20:5095854-5096100(-)$1	246	227	245	9.2546
AACAGCUUUUAUGCCUUU	chr5:54456014-54456257(+)$1	243	138	156	10.2770
GAGCUGGAGCCACAGGUC	chr17:80014103-80014323(+)$1	220	77	95	12.4731
CCCAUUCAGAUUGAUGGG	chr1:179815453-179815676(-)$1	223	36	54	11.4925
UCCACCUCACCUGGUAAG	chr17:1584123-1584357(-)$1	234	122	140	12.0820

#DB
((.(((......))).))	chr6:56357701-56357971(-)$1	1	78	96	12.6118
((((((......))))))	chr13:98668920-98669141(+)$1	1	82	100	10.7619
((((((......)))...	chr5:176707687-176707922(+)$1	1	147	165	12.2638
((.(((......))).))	chr17:7506131-7506366(-)$1	1	70	88	11.9418
)))(((......)))(((	chr19:53057781-53058020(+)$1	1	135	153	11.9084
...(((......)))...	chr17:35608835-35609058(-)$1	1	190	208	12.7419
.((.((......)).)).	chr17:62496741-62496970(-)$1	1	165	183	9.8988
.(((((......))))).	chr1:227842512-227842733(+)$1	1	152	170	9.7124
.(((((......))).))	chr10:88939826-88940051(+)$1	1	167	185	11.7945
((((((......))))))	chr4:17825198-17825430(+)$1	1	135	153	10.7619
((((((......))))))	chr13:28003927-28004155(+)$1	1	65	83	10.7619
((((((......))))))	chr6:57012042-57012269(+)$1	1	157	175	11.4925
(..(((......)))..)	chr2:62106012-62106244(-)$1	1	159	177	12.0555
((.(((......))).))	chr7:92731302-92731534(-)$1	1	75	93	11.9418
((((((......))))))	chr21:43413502-43413740(-)$1	1	142	160	10.7619
..((((......))))..	chr10:22617508-22617727(+)$1	1	48	66	10.9483
((((((......))))))	chr19:38189110-38189329(-)$1	1	168	186	10.7619
(.((((......))))..	chr1:203768736-203768961(+)$1	1	73	91	10.7773
((.(((......))).))	chr5:37351284-37351507(-)$1	1	156	174	11.9418
(..(((......))))))	chr1:82450920-82451139(+)$1	1	48	66	12.0678
(.((((......))))..	chr17:27024824-27025053(+)$1	1	85	103	10.6286
.(((((......))))).	chr17:26961930-26962163(-)$1	1	210	228	10.4347
((((((......))))))	chrX:119388831-119389059(+)$1	1	129	147	11.4925
)))(((......))).((	chr10:5790889-5791116(+)$1	1	48	66	10.9108
((.(((......))).))	chr2:71582761-71582984(+)$1	1	130	148	12.3680
((((((......))))))	chr5:31484923-31485147(-)$1	1	189	207	11.4925
..((((......))))..	chr22:29693723-29693975(+)$1	1	183	201	10.5782
((((((......))))))	chr2:10186412-10186640(+)$1	1	44	62	10.7619
((((.(......).))))	chr8:145948278-145948500(-)$1	1	136	154	10.3423
(..(((......)))..)	chr21:34926425-34926660(+)$1	1	56	74	12.2670
((.(((......))).))	chr4:83860753-83860985(-)$1	1	67	85	11.9418
((((((......))))))	chr3:101390772-101390997(-)$1	1	158	176	11.4925
..((((......))))..	chr4:78081984-78082210(+)$1	1	34	52	9.8125
(((.((......))..))	chr16:72142119-72142341(+)$1	1	82	100	10.2519
((((((......))).))	chr9:35059449-35059670(-)$1	1	77	95	12.3763
((..((......))))))	chr19:3976153-3976397(-)$1	1	44	62	10.5646
.(((.((......))..)	chrX:123020157-123020385(+)$1	1	122	140	9.0071
((((((......))))))	chr17:3572563-3572796(+)$1	1	163	181	10.7619
.(((((......))))).	chr6:56393539-56393764(-)$1	1	26	44	10.4347
..((((......)))).)	chrM:15658-15983(+)$1	1	86	104	10.8403
(..(((......))).))	chr16:75664249-75664477(-)$1	1	90	108	12.6844
((((((......))))))	chr13:33110271-33110492(-)$1	1	179	197	11.4925
.(((((......).))))	chr16:19548049-19548277(+)$1	1	62	80	10.5937
(((..(......)..)))	chr10:5791258-5791505(+)$1	1	39	57	10.5019
(((.((......)).)))	chr17:60061546-60061767(-)$1	1	20	38	10.3586
((.(((......))))))	chr10:102710345-102710566(+)$1	1	14	32	11.8493
.(((((......))).))	chr13:46563062-46563285(-)$1	1	57	75	11.7061
.(.(((......)))).)	chr1:55608561-55608782(-)$1	1	135	153	12.4174
...(((......))))))	chr17:44143932-44144165(-)$1	1	70	88	12.1428
((((((......))))))	chrM:9508-9747(-)$1	1	169	187	11.2856
(((.((......))))))	chr14:32561379-32561607(+)$1	1	154	172	10.9544
).)(((......)))...	chr20:5095854-5096100(-)$1	1	227	245	9.2546
((..((......))..))	chr5:54456014-54456257(+)$1	1	138	156	10.2770
((.(((......))).))	chr17:80014103-80014323(+)$1	1	77	95	12.4731
((((((......))))))	chr1:179815453-179815676(-)$1	1	36	54	11.4925
((((((......)))..)	chr17:1584123-1584357(-)$1	1	122	140	12.0820

#PSSM
c : 0.14	f : 0.14	g : 0.14	e : 0.10	b : 0.08	[ : 0.08	d : 0.08	" : 0.07	! : 0.07	) : 0.01	# : 0.01	i : 0.01	
f : 0.14	e : 0.14	c : 0.12	b : 0.12	g : 0.12	! : 0.10	" : 0.07	d : 0.07	[ : 0.03	a : 0.01	i : 0.01	] : 0.01	
[ : 0.16	d : 0.14	f : 0.12	g : 0.12	e : 0.10	! : 0.10	c : 0.08	b : 0.05	" : 0.03	a : 0.03	i : 0.01	
c : 0.42	d : 0.14	f : 0.12	g : 0.10	[ : 0.07	e : 0.05	! : 0.05	i : 0.01	
c : 0.41	f : 0.12	d : 0.12	b : 0.10	g : 0.10	e : 0.05	[ : 0.03	! : 0.01	i : 0.01	
c : 0.41	f : 0.12	b : 0.12	g : 0.10	d : 0.10	e : 0.05	a : 0.05	i : 0.01	
o : 0.98	b : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
c : 0.41	f : 0.12	b : 0.10	g : 0.10	d : 0.10	e : 0.05	a : 0.05	o : 0.01	i : 0.01	
c : 0.41	f : 0.12	b : 0.12	g : 0.10	d : 0.10	e : 0.05	] : 0.03	2 : 0.01	i : 0.01	
c : 0.41	d : 0.14	f : 0.12	g : 0.12	e : 0.07	2 : 0.05	] : 0.03	b : 0.01	i : 0.01	
d : 0.21	] : 0.19	f : 0.12	g : 0.12	2 : 0.10	e : 0.08	: : 0.03	4 : 0.01	3 : 0.01	b : 0.01	c : 0.01	a : 0.01	i : 0.01	
f : 0.14	d : 0.14	b : 0.12	e : 0.12	g : 0.12	2 : 0.08	c : 0.07	4 : 0.05	3 : 0.03	] : 0.03	7 : 0.01	i : 0.01	: : 0.01	
f : 0.14	d : 0.14	b : 0.12	g : 0.12	e : 0.12	c : 0.08	4 : 0.05	] : 0.05	3 : 0.03	> : 0.01	2 : 0.01	7 : 0.01	i : 0.01	: : 0.01	a : 0.01	

#score	628.2368793898094
#seq	56
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_CDS_m2_run2.txt

#BEAR
b[cccooooooccc]bb	chr16:24801966-24802181(+)$1	215	21	38	10.1306
gggggoooooogggggg	chr2:32689760-32689982(+)$1	222	198	215	10.1504
[ddddoooooodddd22	chr17:65722548-65722767(+)$1	219	95	112	12.1269
eeeeeooooooeeeeeg	chr6:135538976-135539197(+)$1	221	118	135	10.8353
eee[aooooooa]eeee	chr8:17817504-17817724(+)$1	220	73	90	10.4461
"ddddoooooodddd44	chr6:87969020-87969242(+)$1	222	176	193	12.3957
eeeeeooooooeeeee:	chr3:23929038-23929280(+)$1	242	6	23	10.3550
gggggoooooogggggg	chr3:140692550-140692761(+)$1	211	20	37	10.1504
:ddddoooooodddd::	chr1:183602132-183602352(-)$1	220	53	70	10.0070
eeeeeooooooeeeee:	chr10:5827086-5827328(-)$1	242	186	203	10.3550
eeeeeooooooeeeee4	chr2:152135254-152135473(-)$1	219	28	45	11.0134
!ddddoooooodddd22	chr19:50188157-50188381(+)$1	224	7	24	12.1907
e"""aooooooa]eeee	chr2:135711360-135711599(+)$1	239	40	57	10.0631
eeeeeooooooeeeeeB	chr10:97816751-97816981(+)$1	230	187	204	10.3047
eeeeeooooooeeeee:	chr10:32324385-32324615(-)$1	230	54	71	10.3550
:ddddooooooddddHH	chr1:109957858-109958081(-)$1	223	21	38	10.2957
d[cccooooooccc]dd	chr3:44670528-44670754(+)$1	226	33	50	10.3408
eeeeeooooooeeeee:	chr12:133503222-133503441(-)$1	219	195	212	10.3550
%ddddooooooddddff	chr6:21198210-21198425(+)$1	215	153	170	11.2681
eeeeeooooooeeeee:	chr6:36454812-36455042(+)$1	230	71	88	10.3550
eeeeeooooooeeeee:	chr2:71368327-71368541(+)$1	214	169	186	10.3550
:ddddooooooddddee	chr10:121658213-121658436(+)$1	223	111	128	11.1349
[ddddoooooodddd]b	chr9:115593025-115593265(+)$1	240	12	29	12.1112
iddddoooooodddd33	chr7:104703699-104703917(+)$1	218	65	82	12.4504
!ddddoooooodddd33	chr14:23346418-23346644(+)$1	226	163	180	12.6724
"bbbboooooobb4444	chr5:137534020-137534243(-)$1	223	138	155	9.5094
gg[bboooooobb333g	chr11:102248241-102248464(+)$1	223	86	103	9.8450
#ddddoooooodddd44	chr3:155545884-155546107(-)$1	223	178	195	12.3814
:ddddooooooddddff	chr22:28254363-28254585(-)$1	222	120	137	10.9778
[ddddooooooddddee	chr12:66717734-66717957(+)$1	223	62	79	11.9857
eeeeeooooooeeeee4	chrX:118797417-118797639(-)$1	222	18	35	11.0134
gddddoooooodddd]g	chr8:126088526-126088750(-)$1	224	147	164	12.0679
#ddddooooooddddgg	chr12:50484005-50484231(+)$1	226	195	212	12.0447
ddd[aooooooa]dddd	chr1:200529839-200530059(-)$1	220	184	201	10.6360
!!cccooooooccc333	chr19:44980894-44981115(-)$1	221	146	163	11.5503
ffcccooooooccc]ff	chr12:4383229-4383450(+)$1	221	9	26	10.1555
fddddoooooodddd66	chr1:111494640-111494873(-)$1	233	89	106	11.3706
!!cccooooooccc22d	chr1:15844588-15844812(-)$1	224	118	135	10.7177
:ddddoooooodddd:e	chr5:75901957-75902174(+)$1	217	64	81	10.3971
dd[bboooooobb]ddd	chr1:145595054-145595284(-)$1	230	133	150	9.5575
cccbboooooobb]ccc	chr1:149898479-149898700(-)$1	221	113	130	9.5064
[ddddoooooodddd]c	chr1:76226924-76227141(+)$1	217	111	128	12.2393
cc[bboooooobbccc]	chr11:126073310-126073533(-)$1	223	164	181	9.6826
ggcccooooooccc]gg	chr5:87493449-87493672(-)$1	223	120	137	10.7034
:ddddoooooodddd::	chr11:73915280-73915506(+)$1	226	185	202	10.0070
ggg[aooooooaggggg	chr12:8201212-8201423(+)$1	211	148	165	10.2305
!ddddoooooodddd]c	chr4:185556409-185556634(-)$1	225	180	197	12.3031
:ddddoooooodddd::	chr1:234742812-234743031(-)$1	219	47	64	10.0070
bbcccooooooccc333	chr21:38852907-38853124(+)$1	217	13	30	10.7538
:ddddooooooddddGG	chr16:28855195-28855414(-)$1	219	137	154	10.5378
gggggoooooogggggg	chr4:76903057-76903277(-)$1	220	44	61	10.1504
eddddoooooodddd::	chr8:96047652-96047882(+)$1	230	134	151	10.6956
!!cccooooooccc333	chr16:84163084-84163308(-)$1	224	35	52	11.5503
d[cccoooooocccddd	chr11:125513649-125513866(+)$1	217	137	154	10.5288
iiiiiooooooiiiiii	chr3:15064667-15064874(+)$1	207	183	200	10.1675
###bboooooobb4444	chrX:44928924-44929149(+)$1	225	32	49	9.8646

#otherMatches

#Seq PSSM
UACAGAAAGCACUGGAC	chr16:24801966-24802181(+)$1	215	21	38	10.1306
AGAAGGCAAAAUUUUUA	chr2:32689760-32689982(+)$1	222	198	215	10.1504
UUAGUUAAAUCACUGCU	chr17:65722548-65722767(+)$1	219	95	112	12.1269
UCAGCCCGGACGCUGGU	chr6:135538976-135539197(+)$1	221	118	135	10.8353
UCUACCCAGCAGAAGAA	chr8:17817504-17817724(+)$1	220	73	90	10.4461
AGUACCUACAUGUACAA	chr6:87969020-87969242(+)$1	222	176	193	12.3957
GUAUUAUUCACAGUGCU	chr3:23929038-23929280(+)$1	242	6	23	10.3550
AGGCGAAUGGGUGCUUU	chr3:140692550-140692761(+)$1	211	20	37	10.1504
CUUCCAUCACAGGAAAC	chr1:183602132-183602352(-)$1	220	53	70	10.0070
CUCUAUGGCCUUGGAGA	chr10:5827086-5827328(-)$1	242	186	203	10.3550
UGACAGCCAGUUGUCAA	chr2:152135254-152135473(-)$1	219	28	45	11.0134
GCCUGCCUCCCCAGGGU	chr19:50188157-50188381(+)$1	224	7	24	12.1907
CCCAGGUAGAACAGCAG	chr2:135711360-135711599(+)$1	239	40	57	10.0631
AAGACUACAUCGUCUUA	chr10:97816751-97816981(+)$1	230	187	204	10.3047
GAAUCCUUCAAGAUUCA	chr10:32324385-32324615(-)$1	230	54	71	10.3550
ACAGAGAGCUAUCUGGU	chr1:109957858-109958081(-)$1	223	21	38	10.2957
GUAGAUGAUACUCUCCA	chr3:44670528-44670754(+)$1	226	33	50	10.3408
GGUUCAUCAAAGAACUC	chr12:133503222-133503441(-)$1	219	195	212	10.3550
UUCUCCAAAGUGAGAAA	chr6:21198210-21198425(+)$1	215	153	170	11.2681
CAAGUGGAUGAACUUGA	chr6:36454812-36455042(+)$1	230	71	88	10.3550
CAGGUGAGGAAGCCUGU	chr2:71368327-71368541(+)$1	214	169	186	10.3550
CGCCAUACCCCUGGCAG	chr10:121658213-121658436(+)$1	223	111	128	11.1349
GUGGAUCGUUUUUCAGA	chr9:115593025-115593265(+)$1	240	12	29	12.1112
AAUAUUGUGCUAUAUUU	chr7:104703699-104703917(+)$1	218	65	82	12.4504
UGCCCAGCCUGGGGCCC	chr14:23346418-23346644(+)$1	226	163	180	12.6724
UUCCCUUGCUUGGAUUU	chr5:137534020-137534243(-)$1	223	138	155	9.5094
AAACAGGAACAUGAUAU	chr11:102248241-102248464(+)$1	223	86	103	9.8450
AGUGCACAGGAGUAUAA	chr3:155545884-155546107(-)$1	223	178	195	12.3814
CCAGCUUUUUUGUUGGA	chr22:28254363-28254585(-)$1	222	120	137	10.9778
GAUAAAAUUUGUUGUAC	chr12:66717734-66717957(+)$1	223	62	79	11.9857
GUCCACCCUCAUGGACA	chrX:118797417-118797639(-)$1	222	18	35	11.0134
UUCCAGAUAAUUGGGCA	chr8:126088526-126088750(-)$1	224	147	164	12.0679
AUUCUUUUGCUAGAAUC	chr12:50484005-50484231(+)$1	226	195	212	12.0447
GUAACAAUAAAGCUGCC	chr1:200529839-200530059(-)$1	220	184	201	10.6360
UAUGAAUGUAAUCAGUG	chr19:44980894-44981115(-)$1	221	146	163	11.5503
CCGCAGGGCCGUGCGGG	chr12:4383229-4383450(+)$1	221	9	26	10.1555
UAGUUACCAAGAACUUU	chr1:111494640-111494873(-)$1	233	89	106	11.3706
UGCUCAGACCAGAGAUU	chr1:15844588-15844812(-)$1	224	118	135	10.7177
CUCUGUUAAACUAGAAG	chr5:75901957-75902174(+)$1	217	64	81	10.3971
GCUGCCCGAAUGUUGUU	chr1:145595054-145595284(-)$1	230	133	150	9.5575
CCCCAAAAUUAUGCGGG	chr1:149898479-149898700(-)$1	221	113	130	9.5064
GGGAUGCCAAAAUCUAU	chr1:76226924-76227141(+)$1	217	111	128	12.2393
AUGCCAAAUGAGGAUCA	chr11:126073310-126073533(-)$1	223	164	181	9.6826
AUUGCACUGCAGUAUGU	chr5:87493449-87493672(-)$1	223	120	137	10.7034
UGCCCUUUCUUGGGCUG	chr11:73915280-73915506(+)$1	226	185	202	10.0070
AAUUGGUCCAGCAUUGA	chr12:8201212-8201423(+)$1	211	148	165	10.2305
AGCACUGGUAUGUGUCU	chr4:185556409-185556634(-)$1	225	180	197	12.3031
UGCCCUCUUGUGGGCUC	chr1:234742812-234743031(-)$1	219	47	64	10.0070
CUAUGUAUUCUCAUUUC	chr21:38852907-38853124(+)$1	217	13	30	10.7538
GGCCCAGGUGAGGGCUC	chr16:28855195-28855414(-)$1	219	137	154	10.5378
CAUGUAAUACAAUGUGA	chr4:76903057-76903277(-)$1	220	44	61	10.1504
GCCAUUGAACUAUGGAA	chr8:96047652-96047882(+)$1	230	134	151	10.6956
CAGCAACUUUCUGCACA	chr16:84163084-84163308(-)$1	224	35	52	11.5503
UGCUUCUAGGUAAGACU	chr11:125513649-125513866(+)$1	217	137	154	10.5288
CAAGGUCAGUCCCUUGU	chr3:15064667-15064874(+)$1	207	183	200	10.1675
CUAGCAAUUCAGUAACA	chrX:44928924-44929149(+)$1	225	32	49	9.8646

#DB
(.(((......))).))	chr16:24801966-24802181(+)$1	1	21	38	10.1306
(((((......))))))	chr2:32689760-32689982(+)$1	1	198	215	10.1504
.((((......))))..	chr17:65722548-65722767(+)$1	1	95	112	12.1269
(((((......))))))	chr6:135538976-135539197(+)$1	1	118	135	10.8353
(((.(......).))))	chr8:17817504-17817724(+)$1	1	73	90	10.4461
.((((......))))..	chr6:87969020-87969242(+)$1	1	176	193	12.3957
(((((......))))).	chr3:23929038-23929280(+)$1	1	6	23	10.3550
(((((......))))))	chr3:140692550-140692761(+)$1	1	20	37	10.1504
.((((......))))..	chr1:183602132-183602352(-)$1	1	53	70	10.0070
(((((......))))).	chr10:5827086-5827328(-)$1	1	186	203	10.3550
(((((......))))).	chr2:152135254-152135473(-)$1	1	28	45	11.0134
.((((......))))..	chr19:50188157-50188381(+)$1	1	7	24	12.1907
(...(......).))))	chr2:135711360-135711599(+)$1	1	40	57	10.0631
(((((......))))))	chr10:97816751-97816981(+)$1	1	187	204	10.3047
(((((......))))).	chr10:32324385-32324615(-)$1	1	54	71	10.3550
.((((......))))((	chr1:109957858-109958081(-)$1	1	21	38	10.2957
(.(((......))).))	chr3:44670528-44670754(+)$1	1	33	50	10.3408
(((((......))))).	chr12:133503222-133503441(-)$1	1	195	212	10.3550
.((((......))))))	chr6:21198210-21198425(+)$1	1	153	170	11.2681
(((((......))))).	chr6:36454812-36455042(+)$1	1	71	88	10.3550
(((((......))))).	chr2:71368327-71368541(+)$1	1	169	186	10.3550
.((((......))))((	chr10:121658213-121658436(+)$1	1	111	128	11.1349
.((((......)))).)	chr9:115593025-115593265(+)$1	1	12	29	12.1112
(((((......))))..	chr7:104703699-104703917(+)$1	1	65	82	12.4504
.((((......))))..	chr14:23346418-23346644(+)$1	1	163	180	12.6724
.((((......))....	chr5:137534020-137534243(-)$1	1	138	155	9.5094
((.((......))...)	chr11:102248241-102248464(+)$1	1	86	103	9.8450
.((((......))))..	chr3:155545884-155546107(-)$1	1	178	195	12.3814
.((((......))))((	chr22:28254363-28254585(-)$1	1	120	137	10.9778
.((((......))))))	chr12:66717734-66717957(+)$1	1	62	79	11.9857
(((((......))))).	chrX:118797417-118797639(-)$1	1	18	35	11.0134
(((((......)))).)	chr8:126088526-126088750(-)$1	1	147	164	12.0679
.((((......))))))	chr12:50484005-50484231(+)$1	1	195	212	12.0447
(((.(......).))))	chr1:200529839-200530059(-)$1	1	184	201	10.6360
..(((......)))...	chr19:44980894-44981115(-)$1	1	146	163	11.5503
(((((......))).))	chr12:4383229-4383450(+)$1	1	9	26	10.1555
(((((......))))..	chr1:111494640-111494873(-)$1	1	89	106	11.3706
..(((......)))..)	chr1:15844588-15844812(-)$1	1	118	135	10.7177
.((((......)))).(	chr5:75901957-75902174(+)$1	1	64	81	10.3971
((.((......)).)))	chr1:145595054-145595284(-)$1	1	133	150	9.5575
(((((......)).)))	chr1:149898479-149898700(-)$1	1	113	130	9.5064
.((((......)))).)	chr1:76226924-76227141(+)$1	1	111	128	12.2393
((.((......))))).	chr11:126073310-126073533(-)$1	1	164	181	9.6826
(((((......))).))	chr5:87493449-87493672(-)$1	1	120	137	10.7034
.((((......))))..	chr11:73915280-73915506(+)$1	1	185	202	10.0070
(((.(......))))))	chr12:8201212-8201423(+)$1	1	148	165	10.2305
.((((......)))).)	chr4:185556409-185556634(-)$1	1	180	197	12.3031
.((((......))))..	chr1:234742812-234743031(-)$1	1	47	64	10.0070
(((((......)))...	chr21:38852907-38853124(+)$1	1	13	30	10.7538
.((((......))))))	chr16:28855195-28855414(-)$1	1	137	154	10.5378
(((((......))))))	chr4:76903057-76903277(-)$1	1	44	61	10.1504
)((((......))))..	chr8:96047652-96047882(+)$1	1	134	151	10.6956
..(((......)))...	chr16:84163084-84163308(-)$1	1	35	52	11.5503
(.(((......))))))	chr11:125513649-125513866(+)$1	1	137	154	10.5288
(((((......))))))	chr3:15064667-15064874(+)$1	1	183	200	10.1675
...((......))....	chrX:44928924-44929149(+)$1	1	32	49	9.8646

#PSSM
e : 0.23	: : 0.14	g : 0.12	! : 0.10	[ : 0.07	d : 0.07	# : 0.05	b : 0.03	" : 0.03	i : 0.03	f : 0.03	c : 0.03	% : 0.01	
d : 0.44	e : 0.19	g : 0.10	[ : 0.05	! : 0.05	b : 0.03	c : 0.03	" : 0.01	f : 0.01	i : 0.01	# : 0.01	
d : 0.42	e : 0.19	c : 0.17	g : 0.07	[ : 0.05	" : 0.01	b : 0.01	i : 0.01	# : 0.01	
d : 0.41	e : 0.17	c : 0.16	b : 0.10	g : 0.05	[ : 0.05	" : 0.01	i : 0.01	
d : 0.41	e : 0.17	c : 0.16	b : 0.10	a : 0.07	g : 0.05	i : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
d : 0.41	e : 0.17	c : 0.16	b : 0.10	a : 0.07	g : 0.05	i : 0.01	
d : 0.41	e : 0.17	c : 0.16	b : 0.10	g : 0.07	] : 0.05	i : 0.01	
d : 0.42	e : 0.21	c : 0.17	g : 0.07	4 : 0.03	] : 0.03	3 : 0.01	i : 0.01	
d : 0.46	e : 0.21	] : 0.07	g : 0.07	3 : 0.07	4 : 0.03	c : 0.03	2 : 0.01	i : 0.01	
e : 0.24	g : 0.10	3 : 0.10	: : 0.08	4 : 0.07	d : 0.07	] : 0.07	2 : 0.05	f : 0.05	c : 0.03	b : 0.01	H : 0.01	6 : 0.01	G : 0.01	i : 0.01	
: : 0.17	g : 0.16	4 : 0.10	e : 0.08	d : 0.08	3 : 0.08	f : 0.05	c : 0.05	b : 0.03	2 : 0.03	B : 0.01	H : 0.01	6 : 0.01	] : 0.01	G : 0.01	i : 0.01	

#score	605.3590215973036
#seq	56
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_CDS_m2_run1.txt

#BEAR
fff[bbtttttttttttbb22ff	chr1:23645032-23645266(-)$1	234	176	199	21.9599
eeeewwwwwwwwwwwwwweeeee	chr2:61705818-61706059(-)$1	241	24	47	20.9697
hhhhhhuuuuuuuuuuuuhhhhh	chr10:102703738-102703959(+)$1	221	187	210	21.1309
ddddwwwwwwwwwwwwwwdddd]	chr6:138655909-138656131(+)$1	222	127	150	20.5773
fffffftttttttttttffffff	chr1:204378705-204378946(-)$1	241	165	188	22.9945
dddyyyyyyyyyyyyyyyydddd	chr4:166215492-166215712(+)$1	220	188	211	18.9421
==ddddtttttttttttdddd::	chr12:6701809-6702029(-)$1	220	124	147	21.0068
ffffffuuuuuuuuuuuufffff	chr22:39710069-39710313(-)$1	244	86	109	22.5769
[eeeeettttttttttteeeee]	chr3:41267080-41267315(+)$1	235	87	110	23.5123
ggggggtttttttttttgggggg	chr5:78611897-78612117(+)$1	220	83	106	23.6148
hhhhhhuuuuuuuuuuuuhhhhh	chr11:32975349-32975574(+)$1	225	177	200	21.1309
cc[ccctttttttttttcccccc	chr5:37307333-37307580(-)$1	247	39	62	23.6696
ccccvvvvvvvvvvvvvccc]cc	chr3:88104531-88104751(-)$1	220	159	182	22.3008
ee[ccctttttttttttccc]ee	chr6:33669023-33669252(-)$1	229	180	203	23.6748
eeeeevvvvvvvvvvvvveeeee	chr16:24802560-24802788(+)$1	228	93	116	22.6618
fffffftttttttttttffffff	chr1:173916407-173916645(-)$1	238	34	57	22.9945
ccdddduuuuuuuuuuuudddd:	chr5:5463795-5464027(+)$1	232	190	213	21.5233
ggggggtttttttttttgggggg	chr17:58533593-58533818(-)$1	225	7	30	23.6148
eeeeeuuuuuuuuuuuueeeee3	chr1:24078090-24078312(+)$1	222	44	67	22.5942
ggg[bbtttttttttttbbgggg	chr16:72992891-72993122(-)$1	231	92	115	22.9460
cc[ccctttttttttttccc22c	chr14:92623936-92624172(+)$1	236	143	166	23.4605
ccc[bbuuuuuuuuuuuubb]cc	chr6:149700408-149700634(+)$1	226	141	164	22.0994
====bbuuuuuuuuuuuubb22=	chrM:10186-10611(-)$1	425	84	107	21.9163
:eeeeettttttttttteeeee:	chr1:40704184-40704409(+)$1	225	121	144	21.4158
:eeeeettttttttttteeeee:	chr2:192279155-192279388(+)$1	233	22	45	21.4158
eeeeevvvvvvvvvvvvveeeee	chr17:7403936-7404190(+)$1	254	77	100	22.6618
"cccwwwwwwwwwwwwwwccc33	chr4:10445608-10445837(-)$1	229	133	156	21.2352
eeeevvvvvvvvvvvvveeeee]	chr10:5791592-5791824(+)$1	232	185	208	22.3354
ddddvvvvvvvvvvvvvdddd]e	chr17:40010827-40011048(-)$1	221	186	209	21.5183
ggggggtttttttttttgggggg	chr6:21000365-21000594(+)$1	229	88	111	23.6148
ffffffvvvvvvvvvvvvvffff	chr1:54262329-54262562(-)$1	233	173	196	22.1634
ffffffvvvvvvvvvvvvvffff	chr4:187538143-187538364(-)$1	221	170	193	22.1634
ggggggtttttttttttgggggg	chr5:38530533-38530762(-)$1	229	109	132	23.6148
fffffftttttttttttffffff	chrX:53658433-53658658(-)$1	225	201	224	22.9945
g[ddddvvvvvvvvvvvvvdddd	chr17:60042440-60042662(-)$1	222	69	92	21.8642
eeeewwwwwwwwwwwwwweeeee	chr16:24573235-24573466(+)$1	231	154	177	20.9697
c[dddduuuuuuuuuuuudddd]	chr6:76380174-76380398(+)$1	224	39	62	22.6241
ccc[bbvvvvvvvvvvvvvbb33	chr12:123780441-123780661(-)$1	220	95	118	21.7703
dddccctttttttttttccc]dd	chr5:139917683-139917913(+)$1	230	63	86	23.1232
ffffffuuuuuuuuuuuufffff	chrM:8007-8242(+)$1	235	65	88	22.5769
=====uuuuuuuuuuuu======	chr9:6012365-6012597(-)$1	232	36	59	22.5985
eeeeevvvvvvvvvvvvveeeee	chr1:85116000-85116224(-)$1	224	45	68	22.6618
ggggguuuuuuuuuuuugggggg	chr3:148788995-148789220(-)$1	225	121	144	22.7613
###ccctttttttttttccc444	chr3:160150817-160151037(+)$1	220	138	161	23.1296
e!!cccuuuuuuuuuuuuccc22	chr7:127013434-127013658(-)$1	224	46	69	23.0478
!!ddddtttttttttttdddd22	chr1:109952485-109952709(-)$1	224	29	52	22.8132
ffddddtttttttttttdddd22	chrX:24006430-24006668(-)$1	238	49	72	22.7235
:eeeeettttttttttteeeee:	chr1:40704210-40704449(+)$1	239	95	118	21.4158
fffcccvvvvvvvvvvvvvccc:	chr3:107517315-107517547(+)$1	232	34	57	21.6938
hhh[bbtttttttttttbb]hhh	chr6:82941338-82941564(-)$1	226	27	50	21.5841
###ccctttttttttttccc333	chrX:47062904-47063130(+)$1	226	128	151	23.5001
ggggggtttttttttttgggggg	chr13:79942803-79943030(-)$1	227	81	104	23.6148
ccccccuuuuuuuuuuuuccc22	chr6:105526353-105526583(+)$1	230	92	115	23.0503
ffffffuuuuuuuuuuuufffff	chr19:40541275-40541501(-)$1	226	19	42	22.5769
hhhhhhttttttttttthhhhhh	chr16:58581369-58581595(-)$1	226	79	102	21.3506
$$$ccctttttttttttccc333	chr8:116427176-116427402(-)$1	226	189	212	22.9383
iiiiiitttttttttttiiiiii	chr2:198257011-198257243(-)$1	232	31	54	23.2893
ggggggtttttttttttgggggg	chr5:65349342-65349566(+)$1	224	186	209	23.6148
:eeeeettttttttttteeeeeh	chr16:89351681-89351913(-)$1	232	82	105	22.0744
fffffftttttttttttffffff	chr1:36752691-36752927(+)$1	236	88	111	22.9945
ddddwwwwwwwwwwwwwwdddd]	chr17:26960822-26961049(-)$1	227	84	107	20.5773
cccccctttttttttttccc:::	chr5:31526505-31526736(-)$1	231	182	205	20.7645
!!ddddtttttttttttdddd]d	chr10:119043756-119043976(-)$1	220	4	27	22.7852
dddddduuuuuuuuuuuudddd]	chrM:14733-15002(+)$1	269	240	263	22.2885
ggggggtttttttttttgggggg	chr3:88189839-88190065(+)$1	226	15	38	23.6148
ffffffvvvvvvvvvvvvvffff	chr15:90814321-90814554(+)$1	233	140	163	22.1634
eeeevvvvvvvvvvvvveeeee]	chr21:34926912-34927180(+)$1	268	172	195	22.3354
fffffftttttttttttffffff	chr19:44376892-44377119(-)$1	227	124	147	22.9945

#otherMatches

#Seq PSSM
AGCAGCACAAGCCAGACGCCGGC	chr1:23645032-23645266(-)$1	234	176	199	21.9599
GAUGAAGAGAAACAUAAACGUCA	chr2:61705818-61706059(-)$1	241	24	47	20.9697
ACCAUUUAGUCUGUGGUUAAUGG	chr10:102703738-102703959(+)$1	221	187	210	21.1309
CGACAAGACCAUUUCAAAGUUGA	chr6:138655909-138656131(+)$1	222	127	150	20.5773
GACUCAAAGACCCCAUCUGAGUC	chr1:204378705-204378946(-)$1	241	165	188	22.9945
CACUUUUUUUUAUAGCUUUGUGA	chr4:166215492-166215712(+)$1	220	188	211	18.9421
GAGUUGUUUCAUCUGCUCAACUU	chr12:6701809-6702029(-)$1	220	124	147	21.0068
UCUUGUUCAUUCAGAUUUAUAAG	chr22:39710069-39710313(-)$1	244	86	109	22.5769
UGUUGUUUUAUGCCAUUACAACU	chr3:41267080-41267315(+)$1	235	87	110	23.5123
AAGGAUGUUUUGAGAGAAUCCUU	chr5:78611897-78612117(+)$1	220	83	106	23.6148
ucuggaaaauauaagCUCUUCAG	chr11:32975349-32975574(+)$1	225	177	200	21.1309
CCAUCAGUGAGAUUUUAUGAGGG	chr5:37307333-37307580(-)$1	247	39	62	23.6696
AAAUGUGGAGUAUUAAAGUUAUG	chr3:88104531-88104751(-)$1	220	159	182	22.3008
AUAAGAAUGAGUGAAAAUCUGAU	chr6:33669023-33669252(-)$1	229	180	203	23.6748
UUGGGGAAACAACAUAAAUCCAA	chr16:24802560-24802788(+)$1	228	93	116	22.6618
GGUUUGGUGCCAUCUCACGAACU	chr1:173916407-173916645(-)$1	238	34	57	22.9945
ACCCGUUAAGCCUAGUAUAUGGA	chr5:5463795-5464027(+)$1	232	190	213	21.5233
UGAUUUUUAAAAUUCCUAAAUCA	chr17:58533593-58533818(-)$1	225	7	30	23.6148
GCUUUGACACAGGAAAAGGAGCA	chr1:24078090-24078312(+)$1	222	44	67	22.5942
UUUCUGGAACCAAAAAACAAAAA	chr16:72992891-72993122(-)$1	231	92	115	22.9460
CACGACAGUUGAUCAUCGUCCAU	chr14:92623936-92624172(+)$1	236	143	166	23.4605
CCGAGAAUAUUCAGCACCUCACG	chr6:149700408-149700634(+)$1	226	141	164	22.0994
UAUUCCUAGAAGUGAGAUGGUAA	chrM:10186-10611(-)$1	425	84	107	21.9163
AUUGUAUUCAUAAAACUUGCAAC	chr1:40704184-40704409(+)$1	225	121	144	21.4158
AACUCAUGGACCAUUUUUGAGUA	chr2:192279155-192279388(+)$1	233	22	45	21.4158
GCCGGCCAUCCUAAAGCCCCGGC	chr17:7403936-7404190(+)$1	254	77	100	22.6618
AUGGCAGUAAUAGGAAAACCAAA	chr4:10445608-10445837(-)$1	229	133	156	21.2352
GACAAAGAGCUAAAUGAUGUUUC	chr10:5791592-5791824(+)$1	232	185	208	22.3354
UGCUAAAACUGUAGAAAGGUAUA	chr17:40010827-40011048(-)$1	221	186	209	21.5183
UAAGGAAAUGGCAAAAAUCCUUA	chr6:21000365-21000594(+)$1	229	88	111	23.6148
UUCAUGGAUUCAGAAUAAACGUG	chr1:54262329-54262562(-)$1	233	173	196	22.1634
CUGGAUGCAAAUGACAACAGUCC	chr4:187538143-187538364(-)$1	221	170	193	22.1634
UUUAUUCUUCUAUAUCUAAUGAA	chr5:38530533-38530762(-)$1	229	109	132	23.6148
CUAUAUCUUUUUUUUUAAUGUAG	chrX:53658433-53658658(-)$1	225	201	224	22.9945
UCUUCAUCAUCCUCCAACUUGAA	chr17:60042440-60042662(-)$1	222	69	92	21.8642
UGGAAAUCCGUCUUCUGCUCCAG	chr16:24573235-24573466(+)$1	231	154	177	20.9697
GCUUGCAGCCUUAUUUUAGUAAA	chr6:76380174-76380398(+)$1	224	39	62	22.6241
UCUUGUAAAUCUCCUAUCAACUU	chr12:123780441-123780661(-)$1	220	95	118	21.7703
CUCCCAACAUCAGCCAAUGGAGA	chr5:139917683-139917913(+)$1	230	63	86	23.1232
UGAGCUGUCCCCACAUUAGGCUU	chrM:8007-8242(+)$1	235	65	88	22.5769
AAGCUAUUCAGACUUUGAGUUUU	chr9:6012365-6012597(-)$1	232	36	59	22.5985
GAGGCAGCCGCAAAAGAAGCCUC	chr1:85116000-85116224(-)$1	224	45	68	22.6618
UUCUGAGAAGGACCGACCAGAAA	chr3:148788995-148789220(-)$1	225	121	144	22.7613
CUUGAUUUUAAAAAUGUGUCCAU	chr3:160150817-160151037(+)$1	220	138	161	23.1296
CUAACUCUCCUAGUAAAAAGUAU	chr7:127013434-127013658(-)$1	224	46	69	23.0478
UUGUGCAUAAUUAAUAGGCAUCU	chr1:109952485-109952709(-)$1	224	29	52	22.8132
UAUCCAGUUAACAAAUAUGGACA	chrX:24006430-24006668(-)$1	238	49	72	22.7235
AUUGUAUUCAUAAAACUUGCAAC	chr1:40704210-40704449(+)$1	239	95	118	21.4158
CAUGGUAUUUCCUAUUUCAGCCA	chr3:107517315-107517547(+)$1	232	34	57	21.6938
GGGCGAUAAUACAAAUUUUACCC	chr6:82941338-82941564(-)$1	226	27	50	21.5841
AUGGACACCAUUGAGAAGUCAAA	chrX:47062904-47063130(+)$1	226	128	151	23.5001
UGGUCUGAAUUUCAUGAAGACCA	chr13:79942803-79943030(-)$1	227	81	104	23.6148
GAAGCAGAAUCCCAGCCAUGCAC	chr6:105526353-105526583(+)$1	230	92	115	23.0503
UGGUGCAAAUCUUAUUCAGCAUC	chr19:40541275-40541501(-)$1	226	19	42	22.5769
GGCUAGGAAUGAUCACAUUAGCU	chr16:58581369-58581595(-)$1	226	79	102	21.3506
CAGCUCAACAAACAGCAGAGGGG	chr8:116427176-116427402(-)$1	226	189	212	22.9383
AAUAAUGUAACCGUUCAAUUAUU	chr2:198257011-198257243(-)$1	232	31	54	23.2893
UUUUUAAGCAUUAAUUCUAAAGA	chr5:65349342-65349566(+)$1	224	186	209	23.6148
AGAAACGAAAUCCAAUAGUUUUA	chr16:89351681-89351913(-)$1	232	82	105	22.0744
GUGGGUAAGAGUCCACCAUCCAC	chr1:36752691-36752927(+)$1	236	88	111	22.9945
CGUGGCAGUGGAGAGGAACAUGC	chr17:26960822-26961049(-)$1	227	84	107	20.5773
GCAGGUUAAUUAUCAGUACCCUC	chr5:31526505-31526736(-)$1	231	182	205	20.7645
GAAGCCCCCUCACCUAAGGCUAU	chr10:119043756-119043976(-)$1	220	4	27	22.7852
GCUGAAUCAUCCGCUACCUUCAC	chrM:14733-15002(+)$1	269	240	263	22.2885
UGUUGUACCACAAGAACACAACA	chr3:88189839-88190065(+)$1	226	15	38	23.6148
GUUGGCUGAAGGCUUUGAUGUCA	chr15:90814321-90814554(+)$1	233	140	163	22.1634
AGAUCAUCUAAGUCCAAGUCUCA	chr21:34926912-34927180(+)$1	268	172	195	22.3354
UCAGACAAUUCAUACUGGUUUGA	chr19:44376892-44377119(-)$1	227	124	147	22.9945

#DB
(((.((...........))..))	chr1:23645032-23645266(-)$1	1	176	199	21.9599
((((..............)))))	chr2:61705818-61706059(-)$1	1	24	47	20.9697
((((((............)))))	chr10:102703738-102703959(+)$1	1	187	210	21.1309
((((..............)))).	chr6:138655909-138656131(+)$1	1	127	150	20.5773
((((((...........))))))	chr1:204378705-204378946(-)$1	1	165	188	22.9945
(((................))))	chr4:166215492-166215712(+)$1	1	188	211	18.9421
))((((...........))))..	chr12:6701809-6702029(-)$1	1	124	147	21.0068
((((((............)))))	chr22:39710069-39710313(-)$1	1	86	109	22.5769
.(((((...........))))).	chr3:41267080-41267315(+)$1	1	87	110	23.5123
((((((...........))))))	chr5:78611897-78612117(+)$1	1	83	106	23.6148
((((((............)))))	chr11:32975349-32975574(+)$1	1	177	200	21.1309
((.(((...........))))))	chr5:37307333-37307580(-)$1	1	39	62	23.6696
((((.............))).))	chr3:88104531-88104751(-)$1	1	159	182	22.3008
((.(((...........))).))	chr6:33669023-33669252(-)$1	1	180	203	23.6748
(((((.............)))))	chr16:24802560-24802788(+)$1	1	93	116	22.6618
((((((...........))))))	chr1:173916407-173916645(-)$1	1	34	57	22.9945
))((((............)))).	chr5:5463795-5464027(+)$1	1	190	213	21.5233
((((((...........))))))	chr17:58533593-58533818(-)$1	1	7	30	23.6148
(((((............))))).	chr1:24078090-24078312(+)$1	1	44	67	22.5942
(((.((...........))))))	chr16:72992891-72993122(-)$1	1	92	115	22.9460
((.(((...........)))..)	chr14:92623936-92624172(+)$1	1	143	166	23.4605
(((.((............)).))	chr6:149700408-149700634(+)$1	1	141	164	22.0994
((((((............))..)	chrM:10186-10611(-)$1	1	84	107	21.9163
.(((((...........))))).	chr1:40704184-40704409(+)$1	1	121	144	21.4158
.(((((...........))))).	chr2:192279155-192279388(+)$1	1	22	45	21.4158
(((((.............)))))	chr17:7403936-7404190(+)$1	1	77	100	22.6618
.(((..............)))..	chr4:10445608-10445837(-)$1	1	133	156	21.2352
((((.............))))).	chr10:5791592-5791824(+)$1	1	185	208	22.3354
((((.............)))).)	chr17:40010827-40011048(-)$1	1	186	209	21.5183
((((((...........))))))	chr6:21000365-21000594(+)$1	1	88	111	23.6148
((((((.............))))	chr1:54262329-54262562(-)$1	1	173	196	22.1634
((((((.............))))	chr4:187538143-187538364(-)$1	1	170	193	22.1634
((((((...........))))))	chr5:38530533-38530762(-)$1	1	109	132	23.6148
((((((...........))))))	chrX:53658433-53658658(-)$1	1	201	224	22.9945
(.((((.............))))	chr17:60042440-60042662(-)$1	1	69	92	21.8642
((((..............)))))	chr16:24573235-24573466(+)$1	1	154	177	20.9697
(.((((............)))).	chr6:76380174-76380398(+)$1	1	39	62	22.6241
(((.((.............))..	chr12:123780441-123780661(-)$1	1	95	118	21.7703
((((((...........))).))	chr5:139917683-139917913(+)$1	1	63	86	23.1232
((((((............)))))	chrM:8007-8242(+)$1	1	65	88	22.5769
(((((............))))))	chr9:6012365-6012597(-)$1	1	36	59	22.5985
(((((.............)))))	chr1:85116000-85116224(-)$1	1	45	68	22.6618
(((((............))))))	chr3:148788995-148789220(-)$1	1	121	144	22.7613
...(((...........)))...	chr3:160150817-160151037(+)$1	1	138	161	23.1296
(..(((............)))..	chr7:127013434-127013658(-)$1	1	46	69	23.0478
..((((...........))))..	chr1:109952485-109952709(-)$1	1	29	52	22.8132
((((((...........))))..	chrX:24006430-24006668(-)$1	1	49	72	22.7235
.(((((...........))))).	chr1:40704210-40704449(+)$1	1	95	118	21.4158
)))(((.............))).	chr3:107517315-107517547(+)$1	1	34	57	21.6938
(((.((...........)).)))	chr6:82941338-82941564(-)$1	1	27	50	21.5841
...(((...........)))...	chrX:47062904-47063130(+)$1	1	128	151	23.5001
((((((...........))))))	chr13:79942803-79943030(-)$1	1	81	104	23.6148
((((((............)))..	chr6:105526353-105526583(+)$1	1	92	115	23.0503
((((((............)))))	chr19:40541275-40541501(-)$1	1	19	42	22.5769
((((((...........))))))	chr16:58581369-58581595(-)$1	1	79	102	21.3506
...(((...........)))...	chr8:116427176-116427402(-)$1	1	189	212	22.9383
((((((...........))))))	chr2:198257011-198257243(-)$1	1	31	54	23.2893
((((((...........))))))	chr5:65349342-65349566(+)$1	1	186	209	23.6148
.(((((...........)))))(	chr16:89351681-89351913(-)$1	1	82	105	22.0744
((((((...........))))))	chr1:36752691-36752927(+)$1	1	88	111	22.9945
((((..............)))).	chr17:26960822-26961049(-)$1	1	84	107	20.5773
)))(((...........)))...	chr5:31526505-31526736(-)$1	1	182	205	20.7645
..((((...........)))).)	chr10:119043756-119043976(-)$1	1	4	27	22.7852
((((((............)))).	chrM:14733-15002(+)$1	1	240	263	22.2885
((((((...........))))))	chr3:88189839-88190065(+)$1	1	15	38	23.6148
((((((.............))))	chr15:90814321-90814554(+)$1	1	140	163	22.1634
((((.............))))).	chr21:34926912-34927180(+)$1	1	172	195	22.3354
((((((...........))))))	chr19:44376892-44377119(-)$1	1	124	147	22.9945

#PSSM
f : 0.20	e : 0.14	g : 0.14	c : 0.13	d : 0.08	h : 0.05	: : 0.05	= : 0.04	# : 0.02	! : 0.02	[ : 0.01	" : 0.01	$ : 0.01	i : 0.01	
f : 0.20	e : 0.20	g : 0.13	c : 0.13	d : 0.08	h : 0.05	= : 0.04	! : 0.04	[ : 0.02	# : 0.02	$ : 0.01	i : 0.01	
f : 0.19	e : 0.19	d : 0.19	g : 0.13	c : 0.08	h : 0.05	[ : 0.04	= : 0.02	# : 0.02	! : 0.01	$ : 0.01	i : 0.01	
e : 0.19	c : 0.19	d : 0.16	f : 0.16	g : 0.11	[ : 0.07	h : 0.04	= : 0.02	y : 0.01	i : 0.01	
f : 0.16	c : 0.16	e : 0.13	d : 0.11	g : 0.11	b : 0.08	w : 0.07	v : 0.05	h : 0.04	y : 0.01	= : 0.01	i : 0.01	
f : 0.16	c : 0.16	d : 0.11	g : 0.10	v : 0.10	b : 0.08	w : 0.07	e : 0.07	h : 0.04	u : 0.04	y : 0.01	i : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
t : 0.50	u : 0.22	v : 0.19	w : 0.07	y : 0.01	
u : 0.17	c : 0.13	v : 0.13	e : 0.11	g : 0.11	w : 0.07	f : 0.07	d : 0.07	b : 0.04	y : 0.01	= : 0.01	h : 0.01	i : 0.01	
e : 0.19	c : 0.17	d : 0.14	f : 0.11	g : 0.11	v : 0.08	b : 0.07	h : 0.04	y : 0.01	= : 0.01	i : 0.01	
e : 0.19	c : 0.19	d : 0.17	f : 0.16	g : 0.13	h : 0.04	b : 0.04	2 : 0.01	= : 0.01	] : 0.01	i : 0.01	
e : 0.19	d : 0.17	f : 0.16	g : 0.13	c : 0.07	h : 0.05	] : 0.05	2 : 0.04	3 : 0.02	b : 0.01	= : 0.01	4 : 0.01	i : 0.01	: : 0.01	
e : 0.20	f : 0.17	g : 0.13	d : 0.11	2 : 0.08	h : 0.05	c : 0.05	3 : 0.05	: : 0.02	] : 0.02	= : 0.01	4 : 0.01	i : 0.01	
f : 0.17	g : 0.13	e : 0.10	] : 0.10	: : 0.10	h : 0.07	3 : 0.07	d : 0.05	c : 0.05	2 : 0.05	= : 0.02	4 : 0.01	i : 0.01	

#score	1520.8941960876923
#seq	68
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_UTR_m3_run2.txt

#BEAR
ffffffqqqqqqqqfffff	chr19:54649385-54649619(+)$1	234	79	98	13.8263
""ddddqqqqqqqqdddd5	chr16:87865933-87866157(-)$1	224	174	193	13.1504
e[ddddqqqqqqqqdddd]	chrX:153713738-153713977(-)$1	239	22	41	13.8390
$a[cccqqqqqqqqccc]a	chr1:153781797-153782026(-)$1	229	74	93	14.0442
b[ddddqqqqqqqqdddd]	chr15:48434265-48434487(-)$1	222	136	155	13.7502
iiiiiiqqqqqqqqiiiii	chr11:94904323-94904547(-)$1	224	28	47	14.1148
beeeeeqqqqqqqqeeeee	chr19:12754604-12754825(-)$1	221	172	191	14.9304
!eeeeeqqqqqqqqeeeee	chr15:50792076-50792298(+)$1	222	63	82	15.3142
Ieeeeeqqqqqqqqeeeee	chr1:29444228-29444459(+)$1	231	49	68	13.9778
ffffffqqqqqqqqfffff	chr6:4061265-4061486(+)$1	221	91	110	13.8263
[eeeeeqqqqqqqqeeeee	chr16:46692864-46693085(-)$1	221	20	39	15.2854
ffffbbqqqqqqqqbb]ff	chr19:18679956-18680175(+)$1	219	169	188	13.2941
ffffffqqqqqqqqfffff	chr2:86718054-86718280(+)$1	226	181	200	13.8263
ii!!bbqqqqqqqqbb]ii	chr11:43364740-43364959(+)$1	219	145	164	13.5206
ggggggqqqqqqqqggggg	chr2:28002283-28002506(+)$1	223	170	189	14.2567
======qqqqqqqq=====	chr1:60340623-60340846(+)$1	223	98	117	14.4301
:eeeeeqqqqqqqqeeeee	chr1:24117495-24117735(+)$1	240	52	71	14.2993
!eeeeeqqqqqqqqeeeee	chr5:87491368-87491589(-)$1	221	151	170	15.3142
ggggggqqqqqqqqggggg	chr7:75957824-75958064(-)$1	240	146	165	14.2567
$$$cccqqqqqqqqccc33	chr7:5105937-5106159(+)$1	222	68	87	13.5042
fff[bbqqqqqqqqbb]ff	chr1:244219164-244219385(+)$1	221	192	211	13.3506
!eeeeeqqqqqqqqeeeee	chr22:21983211-21983432(-)$1	221	104	123	15.3142
ceeeeeqqqqqqqqeeeee	chrX:150576034-150576264(+)$1	230	17	36	15.1026
dddcccqqqqqqqqccc]d	chr16:19128659-19128898(+)$1	239	8	27	13.7667
eee[bbqqqqqqqqbb333	chr5:65374780-65375002(+)$1	222	103	122	13.6545
ccccccqqqqqqqqccc]c	chrX:153774160-153774382(-)$1	222	37	56	13.9383
dd[cccqqqqqqqqccc22	chr1:113455475-113455703(-)$1	228	6	25	13.5279
ffffffqqqqqqqqfffff	chr22:18218102-18218325(-)$1	223	172	191	13.8263
$eeeeeqqqqqqqqeeeee	chr22:29450359-29450589(+)$1	230	71	90	15.0728
eee[bbqqqqqqqqbb]ee	chr4:89578096-89578324(+)$1	228	9	28	13.8837
ffffffqqqqqqqqfffff	chr20:37203549-37203773(+)$1	224	171	190	13.8263
ddd[bbqqqqqqqqbb]dd	chr15:75893132-75893352(-)$1	220	106	125	13.0668
!eeeeeqqqqqqqqeeeee	chr3:48199442-48199661(-)$1	219	57	76	15.3142
!!ddddqqqqqqqqdddd]	chr6:71270469-71270695(+)$1	226	85	104	14.1205
#eeeeeqqqqqqqqeeeee	chr16:24930958-24931180(-)$1	222	98	117	15.2506
ffddddqqqqqqqqdddd:	chr9:101914000-101914219(+)$1	219	45	64	12.7381
ddddbbqqqqqqqqbb]dd	chr13:77454557-77454782(-)$1	225	80	99	12.9944
da[cccqqqqqqqqccc]a	chr19:2233219-2233441(-)$1	222	133	152	13.9603
ddddddqqqqqqqqdddd:	chr12:120779992-120780222(-)$1	230	84	103	12.5832
ggggggqqqqqqqqggggg	chr12:46756298-46756535(-)$1	237	109	128	14.2567
:eeeeeqqqqqqqqeeeee	chr8:87570972-87571199(+)$1	227	129	148	14.2993
""ddddqqqqqqqqdddd5	chr8:64125176-64125398(+)$1	222	81	100	13.1504
#eeeeeqqqqqqqqeeeee	chr4:2939566-2939790(-)$1	224	109	128	15.2506
:eeeeeqqqqqqqqeeeee	chr1:118410870-118411089(-)$1	219	20	39	14.2993
:eeeeeqqqqqqqqeeeee	chr13:115091933-115092152(+)$1	219	1	20	14.2993
iiiiiiqqqqqqqqiiiii	chr1:220871967-220872192(+)$1	225	162	181	14.1148
======qqqqqqqq=====	chr1:154554592-154554819(-)$1	227	105	124	14.4301
ffffffqqqqqqqqfffff	chr12:79984187-79984419(-)$1	232	66	85	13.8263
g[acccqqqqqqqqccc]a	chr1:145472212-145472433(+)$1	221	153	172	14.1028
ggggggqqqqqqqqggggg	chr3:184052932-184053159(+)$1	227	33	52	14.2567
ccc[bbqqqqqqqqbb]cc	chr10:102724270-102724489(+)$1	219	134	153	13.2047
b!!cccqqqqqqqqccc44	chr12:120661988-120662209(-)$1	221	94	113	13.9798
eeddddqqqqqqqqdddd]	chr20:17922551-17922772(-)$1	221	109	128	13.8833
:eeeeeqqqqqqqqeeeee	chr5:177637581-177637808(+)$1	227	125	144	14.2993
eeee[aqqqqqqqqa]eee	chr16:23478163-23478398(-)$1	235	32	51	14.3446
[eeeeeqqqqqqqqeeeee	chr19:50000458-50000698(+)$1	240	22	41	15.2854
ffffffqqqqqqqqfffff	chr11:125453789-125454016(+)$1	227	51	70	13.8263
dd[cccqqqqqqqqccc]d	chr19:17355985-17356211(-)$1	226	172	191	13.8412
ffffffqqqqqqqqfffff	chr22:38227206-38227427(-)$1	221	30	49	13.8263
deeeeeqqqqqqqqeeeee	chr19:39966946-39967166(+)$1	220	32	51	14.9890
ggggggqqqqqqqqggggg	chr19:48956843-48957067(+)$1	224	123	142	14.2567
!!ddddqqqqqqqqdddd2	chr5:151174987-151175229(+)$1	242	166	185	13.8726
ffffffqqqqqqqqfffff	chr7:156474875-156475104(-)$1	229	188	207	13.8263
deeeeeqqqqqqqqeeeee	chr1:235274456-235274679(-)$1	223	202	221	14.9890
[eeeeeqqqqqqqqeeeee	chr1:231155231-231155459(-)$1	228	26	45	15.2854
ffffffqqqqqqqqfffff	chr19:3538216-3538435(-)$1	219	115	134	13.8263
[a!!bbqqqqqqqqbb22a	chr6:36842475-36842704(-)$1	229	71	90	13.0183
iiiiiiqqqqqqqqiiiii	chr1:23634781-23635004(-)$1	223	112	131	14.1148
###cccqqqqqqqqccc44	chr10:116192635-116192863(-)$1	228	181	200	13.9943
!!ddddqqqqqqqqdddd]	chr12:21670584-21670805(+)$1	221	81	100	14.1205
:eeeeeqqqqqqqqeeeee	chr3:140698303-140698526(+)$1	223	106	125	14.2993
"eeeeeqqqqqqqqeeeee	chr15:55832558-55832779(-)$1	221	182	201	15.2771

#otherMatches

#Seq PSSM
CGACGUUGAGUACUAUGUU	chr19:54649385-54649619(+)$1	234	79	98	13.8263
GGUGGGUGAUUCCUCCCAG	chr16:87865933-87866157(-)$1	224	174	193	13.1504
GACGACAUCGAACGGUUGG	chrX:153713738-153713977(-)$1	239	22	41	13.8390
AUGAGGGGAAAGAGCCUGG	chr1:153781797-153782026(-)$1	229	74	93	14.0442
UGCUGUUUACUUCUGCAGG	chr15:48434265-48434487(-)$1	222	136	155	13.7502
UGGUUUAUUUAAAGAGAUU	chr11:94904323-94904547(-)$1	224	28	47	14.1148
UGAUGCCAAGAUUCGCAUU	chr19:12754604-12754825(-)$1	221	172	191	14.9304
AAUGCCGGGAGUCAGGCAU	chr15:50792076-50792298(+)$1	222	63	82	15.3142
GGGUUACUUCUGUCUGAUC	chr1:29444228-29444459(+)$1	231	49	68	13.9778
GUGUGCAGCAUUCAGUACA	chr6:4061265-4061486(+)$1	221	91	110	13.8263
cagaggccuaaguuccuuu	chr16:46692864-46693085(-)$1	221	20	39	15.2854
CGAUGUUUACAGAUGCUGU	chr19:18679956-18680175(+)$1	219	169	188	13.2941
UACUGAUAUAUUACUUGGU	chr2:86718054-86718280(+)$1	226	181	200	13.8263
UUUAGGUUUUUACUCCCAG	chr11:43364740-43364959(+)$1	219	145	164	13.5206
AAUCACUGCCUCCUGUGAU	chr2:28002283-28002506(+)$1	223	170	189	14.2567
UAUUUAACAUUUUCUAAAU	chr1:60340623-60340846(+)$1	223	98	117	14.4301
AGCUUCUAUCCAGCGAAGC	chr1:24117495-24117735(+)$1	240	52	71	14.2993
CUGCUGCUUGAGAAUAGCA	chr5:87491368-87491589(-)$1	221	151	170	15.3142
GGGCGUUUCCUACUGCGCC	chr7:75957824-75958064(-)$1	240	146	165	14.2567
GUAAGAUAAGAUUUUCUAA	chr7:5105937-5106159(+)$1	222	68	87	13.5042
UACUGUUAUUGUAUACUGU	chr1:244219164-244219385(+)$1	221	192	211	13.3506
CGUGGGCCCCUUCUCCCGC	chr22:21983211-21983432(-)$1	221	104	123	15.3142
AGAUAUAACUUGAAGUGUC	chrX:150576034-150576264(+)$1	230	17	36	15.1026
UCCCUGGUCGUGGGCAGAG	chr16:19128659-19128898(+)$1	239	8	27	13.7667
GGUGGGUUCACUUUCCAAG	chr5:65374780-65375002(+)$1	222	103	122	13.6545
GGACCCAGGUGUGCGGGAU	chrX:153774160-153774382(-)$1	222	37	56	13.9383
UUAGUAUUAAAAUCUACAG	chr1:113455475-113455703(-)$1	228	6	25	13.5279
UGAAUGAAAAUGUCCAUUU	chr22:18218102-18218325(-)$1	223	172	191	13.8263
UUGGCUGAGGUCCAGGUCA	chr22:29450359-29450589(+)$1	230	71	90	15.0728
AUUUUGGUAUAUAACAUGA	chr4:89578096-89578324(+)$1	228	9	28	13.8837
CUGUUUAAUCACCAGAAUA	chr20:37203549-37203773(+)$1	224	171	190	13.8263
ucccucaucuuacagaugg	chr15:75893132-75893352(-)$1	220	106	125	13.0668
UUGGCUGGUAUAGGAGCCA	chr3:48199442-48199661(-)$1	219	57	76	15.3142
CAUGUUAAAGAUGGAACAA	chr6:71270469-71270695(+)$1	226	85	104	14.1205
CGUUAACUAUCUAUUUAAU	chr16:24930958-24931180(-)$1	222	98	117	15.2506
CACAAUUGGCUGAUAUUGA	chr9:101914000-101914219(+)$1	219	45	64	12.7381
AUCUGCUAGACAAUGUAAG	chr13:77454557-77454782(-)$1	225	80	99	12.9944
CAGAGCCAGACAAAGCUGU	chr19:2233219-2233441(-)$1	222	133	152	13.9603
CAGGCCUCAGCUGUGGCCA	chr12:120779992-120780222(-)$1	230	84	103	12.5832
uGCAGAUCCGGAGUUCUGU	chr12:46756298-46756535(-)$1	237	109	128	14.2567
CCUGUAACUCUGUAUACAG	chr8:87570972-87571199(+)$1	227	129	148	14.2993
GUUAGGUGAGAUUUUCUGU	chr8:64125176-64125398(+)$1	222	81	100	13.1504
UUUUCAAUUAUAAAUGAAA	chr4:2939566-2939790(-)$1	224	109	128	15.2506
AUGUUUAGUAACACAAGCA	chr1:118410870-118411089(-)$1	219	20	39	14.2993
GUGACUAUCUUGUAAGUCA	chr13:115091933-115092152(+)$1	219	1	20	14.2993
UCUUAAGAAUCUGGUUAAG	chr1:220871967-220872192(+)$1	225	162	181	14.1148
GGAGUCUUGGUUGUGACUC	chr1:154554592-154554819(-)$1	227	105	124	14.4301
UGAAUUUUCUAUUUAAUUC	chr12:79984187-79984419(-)$1	232	66	85	13.8263
GAGCAGUUUGGUGCCUGAC	chr1:145472212-145472433(+)$1	221	153	172	14.1028
GGGGCACCAACGCCUGCCC	chr3:184052932-184053159(+)$1	227	33	52	14.2567
GGCGUGUUAUCAUCCAGGC	chr10:102724270-102724489(+)$1	219	134	153	13.2047
GAGGAGACCCCCUACUCAU	chr12:120661988-120662209(-)$1	221	94	113	13.9798
CUACAAACCCAUGAUUGUC	chr20:17922551-17922772(-)$1	221	109	128	13.8833
UGGCAAACUUUCUAUUGCC	chr5:177637581-177637808(+)$1	227	125	144	14.2993
UUCUUGUGUGUGUUCUGGA	chr16:23478163-23478398(-)$1	235	32	51	14.3446
AUCUUUCAAAACAAGAAGA	chr19:50000458-50000698(+)$1	240	22	41	15.2854
CAGUCCCUGUGCCUGGACU	chr11:125453789-125454016(+)$1	227	51	70	13.8263
CCCUGGGGCUAUGGCCAUG	chr19:17355985-17356211(-)$1	226	172	191	13.8412
GACCUUAAAAAUACAAGGU	chr22:38227206-38227427(-)$1	221	30	49	13.8263
CCUUGAUGAGCAGCUCAAG	chr19:39966946-39967166(+)$1	220	32	51	14.9890
UGGAGGUGUGGGUUCCUCC	chr19:48956843-48957067(+)$1	224	123	142	14.2567
ACAUGUCCGGGGCUGCAUA	chr5:151174987-151175229(+)$1	242	166	185	13.8726
CUAAACUUUUCAGUGUUUA	chr7:156474875-156475104(-)$1	229	188	207	13.8263
AAUUGAUGUUUUUUUUAAU	chr1:235274456-235274679(-)$1	223	202	221	14.9890
UCUGCUUUGAUGGCAGCAG	chr1:231155231-231155459(-)$1	228	26	45	15.2854
gguagauuuuguauuUUAC	chr19:3538216-3538435(-)$1	219	115	134	13.8263
GGAAGUGUGCAGCAGCGAC	chr6:36842475-36842704(-)$1	229	71	90	13.0183
AAAUAAAAUUUGAGUUGUU	chr1:23634781-23635004(-)$1	223	112	131	14.1148
UGCAUCUACAUUUUGGUUU	chr10:116192635-116192863(-)$1	228	181	200	13.9943
UUUUCAGUUUUAAAUGAGU	chr12:21670584-21670805(+)$1	221	81	100	14.1205
AUACAUAAAAUACAAUGUA	chr3:140698303-140698526(+)$1	223	106	125	14.2993
CUACUAAAAUUAUAUAGUA	chr15:55832558-55832779(-)$1	221	182	201	15.2771

#DB
((((((........)))))	chr19:54649385-54649619(+)$1	1	79	98	13.8263
..((((........)))).	chr16:87865933-87866157(-)$1	1	174	193	13.1504
(.((((........)))).	chrX:153713738-153713977(-)$1	1	22	41	13.8390
.(.(((........))).)	chr1:153781797-153782026(-)$1	1	74	93	14.0442
(.((((........)))).	chr15:48434265-48434487(-)$1	1	136	155	13.7502
((((((........)))))	chr11:94904323-94904547(-)$1	1	28	47	14.1148
)(((((........)))))	chr19:12754604-12754825(-)$1	1	172	191	14.9304
.(((((........)))))	chr15:50792076-50792298(+)$1	1	63	82	15.3142
((((((........)))))	chr1:29444228-29444459(+)$1	1	49	68	13.9778
((((((........)))))	chr6:4061265-4061486(+)$1	1	91	110	13.8263
.(((((........)))))	chr16:46692864-46693085(-)$1	1	20	39	15.2854
((((((........)).))	chr19:18679956-18680175(+)$1	1	169	188	13.2941
((((((........)))))	chr2:86718054-86718280(+)$1	1	181	200	13.8263
((..((........)).))	chr11:43364740-43364959(+)$1	1	145	164	13.5206
((((((........)))))	chr2:28002283-28002506(+)$1	1	170	189	14.2567
((((((........)))))	chr1:60340623-60340846(+)$1	1	98	117	14.4301
.(((((........)))))	chr1:24117495-24117735(+)$1	1	52	71	14.2993
.(((((........)))))	chr5:87491368-87491589(-)$1	1	151	170	15.3142
((((((........)))))	chr7:75957824-75958064(-)$1	1	146	165	14.2567
...(((........)))..	chr7:5105937-5106159(+)$1	1	68	87	13.5042
(((.((........)).))	chr1:244219164-244219385(+)$1	1	192	211	13.3506
.(((((........)))))	chr22:21983211-21983432(-)$1	1	104	123	15.3142
((((((........)))))	chrX:150576034-150576264(+)$1	1	17	36	15.1026
((((((........))).)	chr16:19128659-19128898(+)$1	1	8	27	13.7667
(((.((........))...	chr5:65374780-65375002(+)$1	1	103	122	13.6545
((((((........))).)	chrX:153774160-153774382(-)$1	1	37	56	13.9383
((.(((........)))..	chr1:113455475-113455703(-)$1	1	6	25	13.5279
((((((........)))))	chr22:18218102-18218325(-)$1	1	172	191	13.8263
.(((((........)))))	chr22:29450359-29450589(+)$1	1	71	90	15.0728
(((.((........)).))	chr4:89578096-89578324(+)$1	1	9	28	13.8837
((((((........)))))	chr20:37203549-37203773(+)$1	1	171	190	13.8263
(((.((........)).))	chr15:75893132-75893352(-)$1	1	106	125	13.0668
.(((((........)))))	chr3:48199442-48199661(-)$1	1	57	76	15.3142
..((((........)))).	chr6:71270469-71270695(+)$1	1	85	104	14.1205
.(((((........)))))	chr16:24930958-24931180(-)$1	1	98	117	15.2506
))((((........)))).	chr9:101914000-101914219(+)$1	1	45	64	12.7381
((((((........)).))	chr13:77454557-77454782(-)$1	1	80	99	12.9944
)(.(((........))).)	chr19:2233219-2233441(-)$1	1	133	152	13.9603
))((((........)))).	chr12:120779992-120780222(-)$1	1	84	103	12.5832
((((((........)))))	chr12:46756298-46756535(-)$1	1	109	128	14.2567
.(((((........)))))	chr8:87570972-87571199(+)$1	1	129	148	14.2993
..((((........)))).	chr8:64125176-64125398(+)$1	1	81	100	13.1504
.(((((........)))))	chr4:2939566-2939790(-)$1	1	109	128	15.2506
.(((((........)))))	chr1:118410870-118411089(-)$1	1	20	39	14.2993
.(((((........)))))	chr13:115091933-115092152(+)$1	1	1	20	14.2993
((((((........)))))	chr1:220871967-220872192(+)$1	1	162	181	14.1148
((((((........)))))	chr1:154554592-154554819(-)$1	1	105	124	14.4301
((((((........)))))	chr12:79984187-79984419(-)$1	1	66	85	13.8263
(.((((........))).)	chr1:145472212-145472433(+)$1	1	153	172	14.1028
((((((........)))))	chr3:184052932-184053159(+)$1	1	33	52	14.2567
(((.((........)).))	chr10:102724270-102724489(+)$1	1	134	153	13.2047
(..(((........)))..	chr12:120661988-120662209(-)$1	1	94	113	13.9798
((((((........)))).	chr20:17922551-17922772(-)$1	1	109	128	13.8833
.(((((........)))))	chr5:177637581-177637808(+)$1	1	125	144	14.2993
((((.(........).)))	chr16:23478163-23478398(-)$1	1	32	51	14.3446
.(((((........)))))	chr19:50000458-50000698(+)$1	1	22	41	15.2854
((((((........)))))	chr11:125453789-125454016(+)$1	1	51	70	13.8263
((.(((........))).)	chr19:17355985-17356211(-)$1	1	172	191	13.8412
((((((........)))))	chr22:38227206-38227427(-)$1	1	30	49	13.8263
)(((((........)))))	chr19:39966946-39967166(+)$1	1	32	51	14.9890
((((((........)))))	chr19:48956843-48957067(+)$1	1	123	142	14.2567
..((((........)))).	chr5:151174987-151175229(+)$1	1	166	185	13.8726
((((((........)))))	chr7:156474875-156475104(-)$1	1	188	207	13.8263
)(((((........)))))	chr1:235274456-235274679(-)$1	1	202	221	14.9890
.(((((........)))))	chr1:231155231-231155459(-)$1	1	26	45	15.2854
((((((........)))))	chr19:3538216-3538435(-)$1	1	115	134	13.8263
.(..((........))..)	chr6:36842475-36842704(-)$1	1	71	90	13.0183
((((((........)))))	chr1:23634781-23635004(-)$1	1	112	131	14.1148
...(((........)))..	chr10:116192635-116192863(-)$1	1	181	200	13.9943
..((((........)))).	chr12:21670584-21670805(+)$1	1	81	100	14.1205
.(((((........)))))	chr3:140698303-140698526(+)$1	1	106	125	14.2993
.(((((........)))))	chr15:55832558-55832779(-)$1	1	182	201	15.2771

#PSSM
f : 0.18	d : 0.12	! : 0.09	g : 0.08	: : 0.08	e : 0.06	i : 0.05	[ : 0.05	" : 0.04	$ : 0.04	b : 0.04	c : 0.04	# : 0.04	= : 0.02	I : 0.01	
e : 0.36	f : 0.18	d : 0.08	g : 0.06	i : 0.05	! : 0.05	[ : 0.04	a : 0.04	" : 0.02	= : 0.02	c : 0.02	$ : 0.01	# : 0.01	
e : 0.34	d : 0.18	f : 0.16	g : 0.06	[ : 0.05	i : 0.04	! : 0.04	= : 0.02	c : 0.02	$ : 0.01	a : 0.01	# : 0.01	
e : 0.31	f : 0.15	d : 0.15	c : 0.13	g : 0.06	[ : 0.06	i : 0.04	! : 0.02	= : 0.02	
e : 0.30	f : 0.13	d : 0.13	c : 0.13	b : 0.12	g : 0.06	i : 0.04	= : 0.02	[ : 0.01	
e : 0.30	f : 0.13	d : 0.13	c : 0.13	b : 0.12	g : 0.06	i : 0.04	= : 0.02	a : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.30	f : 0.13	d : 0.13	c : 0.13	b : 0.12	g : 0.06	i : 0.04	= : 0.02	a : 0.01	
e : 0.30	f : 0.13	d : 0.13	c : 0.13	b : 0.12	g : 0.06	i : 0.04	= : 0.02	] : 0.01	
e : 0.31	f : 0.13	d : 0.13	c : 0.13	] : 0.09	g : 0.06	i : 0.04	= : 0.02	3 : 0.01	2 : 0.01	
e : 0.33	f : 0.16	d : 0.16	] : 0.08	g : 0.06	i : 0.05	= : 0.02	3 : 0.02	2 : 0.02	4 : 0.02	c : 0.01	
e : 0.33	f : 0.16	] : 0.06	g : 0.06	a : 0.05	i : 0.05	d : 0.05	5 : 0.02	= : 0.02	3 : 0.02	c : 0.02	2 : 0.02	: : 0.02	4 : 0.02	

#score	1016.7033558442234
#seq	72
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_UTR_m1_run2.txt

#BEAR
e:gggggggtttttttttttggggggg	chr4:7061703-7061951(-)$1	248	101	128	21.8701
$$ffffffvvvvvvvvvvvvvffffff	chr1:2239331-2239601(+)$1	270	18	45	23.5012
eee!!ddddtttttttttttdddd444	chr7:87835374-87835602(-)$1	228	58	85	21.8345
eeeccc[bbtttttttttttbbccc]e	chr13:110407705-110407960(-)$1	255	204	231	21.6769
dd!!eeeeettttttttttteeeeedd	chr8:64124343-64124638(+)$1	295	29	56	22.4798
eeeeeyyyyyyyyyyyyyyyyeeeee]	chrX:72906261-72906534(+)$1	273	101	128	22.2877
====!!bbuuuuuuuuuuuubb22===	chr22:40731103-40731347(+)$1	244	92	119	22.7330
eee!!cccuuuuuuuuuuuuccc22ee	chr8:38020889-38021123(-)$1	234	187	214	23.3124
c!!ddddwwwwwwwwwwwwwwdddd22	chr3:149683737-149683973(-)$1	236	49	76	22.5379
fffffyyyyyyyyyyyyyyyyffffff	chr6:148870807-148871068(+)$1	261	5	32	21.7478
::ffffffuuuuuuuuuuuuffffffC	chr8:105502232-105502461(-)$1	229	200	227	21.2715
$$$$eeeeettttttttttteeeee44	chr2:215592529-215592807(-)$1	278	66	93	22.6922
[ddddyyyyyyyyyyyyyyyydddd]e	chr3:57557468-57557797(-)$1	329	187	214	21.4251
"gggggggvvvvvvvvvvvvvgggggg	chr1:164819643-164819872(+)$1	229	66	93	24.2172
ggggggxxxxxxxxxxxxxxxgggggg	chrX:73808232-73808548(-)$1	316	96	123	19.0907
fffffyyyyyyyyyyyyyyyyffffff	chr5:126172092-126172367(+)$1	275	78	105	21.7478
:ddddcccuuuuuuuuuuuuccc]ddd	chrX:47088536-47088789(+)$1	253	73	100	22.5122
:gggggggvvvvvvvvvvvvvgggggg	chr5:83238615-83238915(-)$1	300	25	52	23.4483
========uuuuuuuuuuuu=======	chr4:17609251-17609481(+)$1	230	16	43	24.1140
$$$$$cccuuuuuuuuuuuuccc4444	chr5:34907637-34907870(-)$1	233	52	79	23.2892
d[ccc[bbvvvvvvvvvvvvvbb]ccc	chr1:204522191-204522451(+)$1	260	99	126	22.8198
e[ffffffuuuuuuuuuuuuffffff]	chr9:77598196-77598430(-)$1	234	105	132	23.7685
ffcccyyyyyyyyyyyyyyyyccc]ff	chr8:95892755-95892982(-)$1	227	40	67	21.6968
%%%cccyyyyyyyyyyyyyyyyccc66	chr11:47489660-47489893(-)$1	233	160	187	20.0191
hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr7:5567008-5567282(-)$1	274	95	122	20.6965
:::eeeeeuuuuuuuuuuuueeeee::	chr10:32299904-32300210(-)$1	306	150	177	20.2870
gggggg[auuuuuuuuuuuuagggggg	chr17:30326211-30326458(+)$1	247	143	170	24.6105
e####cccuuuuuuuuuuuuccc333e	chr1:91381348-91381577(-)$1	229	128	155	23.9446
dddd[cccuuuuuuuuuuuucccdddd	chr5:58269777-58270015(-)$1	238	17	44	23.0117
::ffffffvvvvvvvvvvvvvffffff	chr1:15994854-15995109(+)$1	255	120	147	22.1725
b[cccbbwwwwwwwwwwwwwwbb]ccc	chr5:90666463-90666713(-)$1	250	92	119	21.9249
CCffffffvvvvvvvvvvvvvffffff	chr1:179811594-179811862(-)$1	268	23	50	21.6627
!!gggggggtttttttttttggggggg	chr20:30753451-30753694(+)$1	243	21	48	23.0343
d::eeeeeuuuuuuuuuuuueeeeedd	chr19:4046762-4047001(-)$1	239	55	82	22.2701
:eeeeeyyyyyyyyyyyyyyyyeeeee	chr17:65336262-65336502(-)$1	240	112	139	21.4581
###eeeeettttttttttteeeee333	chr9:125670568-125670800(-)$1	232	141	168	23.1982
GG:eeeeevvvvvvvvvvvvveeeeeE	chr17:60021955-60022188(-)$1	233	14	41	21.5430
!!ccc[bbvvvvvvvvvvvvvbb]ccc	chr6:159054856-159055085(+)$1	229	191	218	23.2250
[ffffffvvvvvvvvvvvvvffffff]	chr6:11136517-11136771(+)$1	254	167	194	23.1236
eee!!cccvvvvvvvvvvvvvccc444	chr4:101945524-101945754(-)$1	230	162	189	23.6757
ff[eeeeevvvvvvvvvvvvveeeee2	chr11:62609087-62609329(-)$1	242	198	225	23.9071
!bb!!ddddtttttttttttdddd22b	chr17:30809117-30809375(+)$1	258	133	160	21.2878
###ddddwwwwwwwwwwwwwwdddd22	chr6:111982400-111982635(-)$1	235	32	59	22.6234
"""eeeeeuuuuuuuuuuuueeeeeee	chr1:101441402-101441657(+)$1	255	108	135	24.5651
hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr4:124236165-124236397(+)$1	232	75	102	20.6965
eeee[ddddtttttttttttdddd]ee	chr11:73723718-73723965(-)$1	247	188	215	21.6652
!gggggggvvvvvvvvvvvvvgggggg	chr6:144150871-144151126(+)$1	255	65	92	24.2437
::ffffffuuuuuuuuuuuuffffff:	chr3:49396490-49396769(-)$1	279	31	58	21.4806
::dddd[avvvvvvvvvvvvva]dddd	chr17:4848859-4849109(-)$1	250	158	185	21.5786
gggggggwwwwwwwwwwwwwwgggggg	chrX:150574363-150574632(+)$1	269	177	204	23.3011
ccc[eeeeettttttttttteeeee22	chr3:49020750-49020990(+)$1	240	27	54	22.8702
fffffyyyyyyyyyyyyyyyyffffff	chr6:7287074-7287319(-)$1	245	17	44	21.7478
""eeeeevvvvvvvvvvvvveeeee33	chr11:62283775-62284036(-)$1	261	59	86	24.2400
"""eeeeeuuuuuuuuuuuueeeeehh	chr18:9401609-9401836(+)$1	227	10	37	24.2081
:::eeeeeuuuuuuuuuuuueeeee::	chr4:77035728-77036025(-)$1	297	103	130	20.2870
fffffffwwwwwwwwwwwwwwffffff	chr10:93043819-93044112(+)$1	293	104	131	22.5191
:eeeee[awwwwwwwwwwwwwwa]eee	chr11:73387400-73387695(-)$1	295	241	268	21.9970
bb[eeeeeuuuuuuuuuuuueeeee22	chr3:149087211-149087477(-)$1	266	124	151	24.0523
d[ffffffuuuuuuuuuuuuffffff2	chr2:209101472-209101711(-)$1	239	77	104	23.5846
[ggggggguuuuuuuuuuuuggggggg	chr7:127010610-127010880(-)$1	270	137	164	24.2368
ccceeeeeuuuuuuuuuuuueeeee]c	chr9:136897332-136897621(-)$1	289	196	223	24.3497
(((ddddwwwwwwwwwwwwwwdddd88	chr11:12962159-12962396(+)$1	237	179	206	20.2508

#otherMatches

#Seq PSSM
ACUUUAAAUGUUAAUGuuuaauuuaaa	chr4:7061703-7061951(-)$1	248	101	128	21.8701
UUCUGUGCCUUCCAGCAUCUUGUACAG	chr1:2239331-2239601(+)$1	270	18	45	23.5012
UUUUCUUGCUAAAACUCUAUGUAAAUU	chr7:87835374-87835602(-)$1	228	58	85	21.8345
UCAGAUGUCUCUGCUCUCCUGAAUCUU	chr13:110407705-110407960(-)$1	255	204	231	21.6769
cuggauuucuaaucuuaagugaaaugg	chr8:64124343-64124638(+)$1	295	29	56	22.4798
AAUAAUUUCUCAAAUGUUCUUUUAUUU	chrX:72906261-72906534(+)$1	273	101	128	22.2877
CAUAGAGGUUUAAUCAAACUCCCAUAU	chr22:40731103-40731347(+)$1	244	92	119	22.7330
UUAUAUUGUUCUUCAUAUCCCAAAUUA	chr8:38020889-38021123(-)$1	234	187	214	23.3124
UCUUCAUCAACAACCCUAAUUAUGGUC	chr3:149683737-149683973(-)$1	236	49	76	22.5379
UUAUCCUUCUUUUUUUAUUUAGAUAAU	chr6:148870807-148871068(+)$1	261	5	32	21.7478
UAAUGUUGACUUUAAUACUCUAACAUG	chr8:105502232-105502461(-)$1	229	200	227	21.2715
CAUGGUACAUAUUUUUAUUCUGUACAU	chr2:215592529-215592807(-)$1	278	66	93	22.6922
UUAUCCCCUUGCUACUUUACUGAUACC	chr3:57557468-57557797(-)$1	329	187	214	21.4251
AAAAAAUGUUUUGUUUUGUGUUAUUUU	chr1:164819643-164819872(+)$1	229	66	93	24.2172
GGAAAAGUACCAAAACCCAAAUUUUCU	chrX:73808232-73808548(-)$1	316	96	123	19.0907
UGAACUUAAUAACUGUGUACUGUUCGG	chr5:126172092-126172367(+)$1	275	78	105	21.7478
UGCCCCACCUGCCUCAUAUUGUGUGGG	chrX:47088536-47088789(+)$1	253	73	100	22.5122
AUAAGAGCAAGAGUUGAUAGAGCUUUU	chr5:83238615-83238915(-)$1	300	25	52	23.4483
AGGUUUUUGAAUAAAUGGAUGAAAAUC	chr4:17609251-17609481(+)$1	230	16	43	24.1140
GUUACAGGUUUUCUUCUUCUUCUCAAA	chr5:34907637-34907870(-)$1	233	52	79	23.2892
gcgcccagcUUAAACUAUUUUCUUGGU	chr1:204522191-204522451(+)$1	260	99	126	22.8198
AUAAUAAUCUUCCUUUUUUUGUUGUUU	chr9:77598196-77598430(-)$1	234	105	132	23.7685
UUUCUAAAUUCCUCCAUUGUGAGAUAA	chr8:95892755-95892982(-)$1	227	40	67	21.6968
CCUGGAUAUCCCGCCUGCCCCUUCCCC	chr11:47489660-47489893(-)$1	233	160	187	20.0191
CAAAGUUCACAAUGUGGCCGAGGACUU	chr7:5567008-5567282(-)$1	274	95	122	20.6965
CUUGUUUUUCUUUUCCUAUUAAAACGU	chr10:32299904-32300210(-)$1	306	150	177	20.2870
UAUGAACGGCUGUUUUUCUACUUUGUA	chr17:30326211-30326458(+)$1	247	143	170	24.6105
GAAAUGUAAUUAAUAAACAAUGCUCAC	chr1:91381348-91381577(-)$1	229	128	155	23.9446
UUCAAGUCUUCCUGAUACAUGACUGAA	chr5:58269777-58270015(-)$1	238	17	44	23.0117
UUGAUUUGUUCAUUUUUAUUUCAAAUC	chr1:15994854-15995109(+)$1	255	120	147	22.1725
AAUUGUGGAUUUAUUUACAAACAUCAA	chr5:90666463-90666713(-)$1	250	92	119	21.9249
UUGUCAAAGAUAAUUUGCUUAUUUGAC	chr1:179811594-179811862(-)$1	268	23	50	21.6627
UUGCUUUUUCUUCAGUGCUAAGAAAGU	chr20:30753451-30753694(+)$1	243	21	48	23.0343
UCAGGGCGCCCCCCCACCCCCGCCCGG	chr19:4046762-4047001(-)$1	239	55	82	22.2701
AGACUUUUUUUUUUUUUUUUUUGAGUC	chr17:65336262-65336502(-)$1	240	112	139	21.4581
UGAUCUCCAAACAUUCCUAGGAGAGUG	chr9:125670568-125670800(-)$1	232	141	168	23.1982
UCGCCGAGUCUACCUAGCUUUCUUGGA	chr17:60021955-60022188(-)$1	233	14	41	21.5430
ACUAGAACUUUUUAAAACUUUGUCCUA	chr6:159054856-159055085(+)$1	229	191	218	23.2250
CAAAAUAUCUAUUUAACCUCUAUUUUA	chr6:11136517-11136771(+)$1	254	167	194	23.1236
GCCUUUGUAAUUUGACUUCUGACAUGU	chr4:101945524-101945754(-)$1	230	162	189	23.6757
cgaccugguauugcaguacuuccagga	chr11:62609087-62609329(-)$1	242	198	225	23.9071
UCUCAACAUCUUUCCCCAUCAUGUCUA	chr17:30809117-30809375(+)$1	258	133	160	21.2878
UAUGUGAUUUUAACUCUGUCUUCACCU	chr6:111982400-111982635(-)$1	235	32	59	22.6234
UAUGAACAUUUUUCUUUUAUUGUUUUA	chr1:101441402-101441657(+)$1	255	108	135	24.5651
AAUGCUUUUAAUAAAUCAUAUGAAGCA	chr4:124236165-124236397(+)$1	232	75	102	20.6965
UAUUGGUGUUUGUAAUCUGUGCACAAG	chr11:73723718-73723965(-)$1	247	188	215	21.6652
AUAAAGGUGGUUAUAUUGUAAGCUUUU	chr6:144150871-144151126(+)$1	255	65	92	24.2437
UCACAGUGCUCUUUUCUCCUCACUGUA	chr3:49396490-49396769(-)$1	279	31	58	21.4806
AACAAGGUGCUGUGUGAUUUGAGCUUG	chr17:4848859-4849109(-)$1	250	158	185	21.5786
AAAAACACUCCCACAAGUAuuuguuuu	chrX:150574363-150574632(+)$1	269	177	204	23.3011
GCUCUGCCUUUCAUGACCCCAGGCAAC	chr3:49020750-49020990(+)$1	240	27	54	22.8702
ACUGAAAUAAUUUUUUAAAACUCAGUG	chr6:7287074-7287319(-)$1	245	17	44	21.7478
UUAAGAUUUCAUAUAUAUAUAUUUUUU	chr11:62283775-62284036(-)$1	261	59	86	24.2400
UGGCUUAUUUUUUCUGAUUUAUGAGGG	chr18:9401609-9401836(+)$1	227	10	37	24.2081
UAACAAAACUACUUAACCAUUUUUGCA	chr4:77035728-77036025(-)$1	297	103	130	20.2870
GCUAGAUACUUUUUUUUUUUAAUCUGG	chr10:93043819-93044112(+)$1	293	104	131	22.5191
AACACUGCAAACAAAUAUACUAGGAGU	chr11:73387400-73387695(-)$1	295	241	268	21.9970
GUUUUGGAUAAAAAUAACAUUCCAAUC	chr3:149087211-149087477(-)$1	266	124	151	24.0523
UAUUGCCACCUUUGUGAACAUGGCAAG	chr2:209101472-209101711(-)$1	239	77	104	23.5846
UUAGUUAUUUGUGUCAAAUUAUAAUUA	chr7:127010610-127010880(-)$1	270	137	164	24.2368
CAGUUAUAUAAUAUAAACUUUGUAAUC	chr9:136897332-136897621(-)$1	289	196	223	24.3497
ucugggcuucuucuaguuucuGCCUUA	chr11:12962159-12962396(+)$1	237	179	206	20.2508

#DB
).(((((((...........)))))))	chr4:7061703-7061951(-)$1	1	101	128	21.8701
..((((((.............))))))	chr1:2239331-2239601(+)$1	1	18	45	23.5012
(((..((((...........))))...	chr7:87835374-87835602(-)$1	1	58	85	21.8345
((((((.((...........))))).)	chr13:110407705-110407960(-)$1	1	204	231	21.6769
((..(((((...........)))))))	chr8:64124343-64124638(+)$1	1	29	56	22.4798
(((((................))))).	chrX:72906261-72906534(+)$1	1	101	128	22.2877
((((..((............))..)))	chr22:40731103-40731347(+)$1	1	92	119	22.7330
(((..(((............)))..))	chr8:38020889-38021123(-)$1	1	187	214	23.3124
(..((((..............))))..	chr3:149683737-149683973(-)$1	1	49	76	22.5379
(((((................))))))	chr6:148870807-148871068(+)$1	1	5	32	21.7478
..((((((............)))))))	chr8:105502232-105502461(-)$1	1	200	227	21.2715
....(((((...........)))))..	chr2:215592529-215592807(-)$1	1	66	93	22.6922
.((((................)))).)	chr3:57557468-57557797(-)$1	1	187	214	21.4251
.(((((((.............))))))	chr1:164819643-164819872(+)$1	1	66	93	24.2172
((((((...............))))))	chrX:73808232-73808548(-)$1	1	96	123	19.0907
(((((................))))))	chr5:126172092-126172367(+)$1	1	78	105	21.7478
.(((((((............))).)))	chrX:47088536-47088789(+)$1	1	73	100	22.5122
.(((((((.............))))))	chr5:83238615-83238915(-)$1	1	25	52	23.4483
((((((((............)))))))	chr4:17609251-17609481(+)$1	1	16	43	24.1140
.....(((............)))....	chr5:34907637-34907870(-)$1	1	52	79	23.2892
(.(((.((.............)).)))	chr1:204522191-204522451(+)$1	1	99	126	22.8198
(.((((((............)))))).	chr9:77598196-77598430(-)$1	1	105	132	23.7685
(((((................))).))	chr8:95892755-95892982(-)$1	1	40	67	21.6968
...(((................)))..	chr11:47489660-47489893(-)$1	1	160	187	20.0191
((((((((.............))))))	chr7:5567008-5567282(-)$1	1	95	122	20.6965
...(((((............)))))..	chr10:32299904-32300210(-)$1	1	150	177	20.2870
((((((.(............)))))))	chr17:30326211-30326458(+)$1	1	143	170	24.6105
(....(((............)))...)	chr1:91381348-91381577(-)$1	1	128	155	23.9446
((((.(((............)))))))	chr5:58269777-58270015(-)$1	1	17	44	23.0117
..((((((.............))))))	chr1:15994854-15995109(+)$1	1	120	147	22.1725
(.(((((..............)).)))	chr5:90666463-90666713(-)$1	1	92	119	21.9249
((((((((.............))))))	chr1:179811594-179811862(-)$1	1	23	50	21.6627
..(((((((...........)))))))	chr20:30753451-30753694(+)$1	1	21	48	23.0343
)..(((((............)))))((	chr19:4046762-4047001(-)$1	1	55	82	22.2701
.(((((................)))))	chr17:65336262-65336502(-)$1	1	112	139	21.4581
...(((((...........)))))...	chr9:125670568-125670800(-)$1	1	141	168	23.1982
((.(((((.............)))))(	chr17:60021955-60022188(-)$1	1	14	41	21.5430
..(((.((.............)).)))	chr6:159054856-159055085(+)$1	1	191	218	23.2250
.((((((.............)))))).	chr6:11136517-11136771(+)$1	1	167	194	23.1236
(((..(((.............)))...	chr4:101945524-101945754(-)$1	1	162	189	23.6757
((.(((((.............))))).	chr11:62609087-62609329(-)$1	1	198	225	23.9071
.((..((((...........))))..)	chr17:30809117-30809375(+)$1	1	133	160	21.2878
...((((..............))))..	chr6:111982400-111982635(-)$1	1	32	59	22.6234
...(((((............)))))))	chr1:101441402-101441657(+)$1	1	108	135	24.5651
((((((((.............))))))	chr4:124236165-124236397(+)$1	1	75	102	20.6965
((((.((((...........)))).))	chr11:73723718-73723965(-)$1	1	188	215	21.6652
.(((((((.............))))))	chr6:144150871-144151126(+)$1	1	65	92	24.2437
..((((((............)))))).	chr3:49396490-49396769(-)$1	1	31	58	21.4806
..((((.(.............).))))	chr17:4848859-4849109(-)$1	1	158	185	21.5786
(((((((..............))))))	chrX:150574363-150574632(+)$1	1	177	204	23.3011
(((.(((((...........)))))..	chr3:49020750-49020990(+)$1	1	27	54	22.8702
(((((................))))))	chr6:7287074-7287319(-)$1	1	17	44	21.7478
..(((((.............)))))..	chr11:62283775-62284036(-)$1	1	59	86	24.2400
...(((((............)))))))	chr18:9401609-9401836(+)$1	1	10	37	24.2081
...(((((............)))))..	chr4:77035728-77036025(-)$1	1	103	130	20.2870
(((((((..............))))))	chr10:93043819-93044112(+)$1	1	104	131	22.5191
.(((((.(..............).)))	chr11:73387400-73387695(-)$1	1	241	268	21.9970
((.(((((............)))))..	chr3:149087211-149087477(-)$1	1	124	151	24.0523
(.((((((............)))))).	chr2:209101472-209101711(-)$1	1	77	104	23.5846
.(((((((............)))))))	chr7:127010610-127010880(-)$1	1	137	164	24.2368
((((((((............))))).)	chr9:136897332-136897621(-)$1	1	196	223	24.3497
...((((..............))))..	chr11:12962159-12962396(+)$1	1	179	206	20.2508

#PSSM
: : 0.16	e : 0.14	f : 0.09	d : 0.08	" : 0.06	! : 0.06	$ : 0.04	c : 0.04	[ : 0.04	g : 0.04	= : 0.03	h : 0.03	b : 0.03	# : 0.03	% : 0.01	C : 0.01	G : 0.01	( : 0.01	
: : 0.12	e : 0.12	f : 0.11	g : 0.11	d : 0.06	[ : 0.06	$ : 0.04	! : 0.04	# : 0.04	" : 0.04	= : 0.03	h : 0.03	b : 0.03	c : 0.03	% : 0.01	C : 0.01	G : 0.01	( : 0.01	
f : 0.19	g : 0.14	e : 0.14	c : 0.09	d : 0.06	: : 0.06	# : 0.04	! : 0.03	= : 0.03	$ : 0.03	h : 0.03	[ : 0.03	" : 0.03	% : 0.01	b : 0.01	( : 0.01	
e : 0.24	f : 0.19	g : 0.14	d : 0.11	c : 0.09	! : 0.08	= : 0.03	$ : 0.03	h : 0.03	# : 0.01	[ : 0.01	
e : 0.27	f : 0.19	g : 0.14	c : 0.09	d : 0.09	! : 0.08	h : 0.03	[ : 0.03	= : 0.01	$ : 0.01	# : 0.01	
e : 0.25	g : 0.14	f : 0.14	c : 0.12	d : 0.11	y : 0.09	[ : 0.03	h : 0.03	! : 0.01	= : 0.01	b : 0.01	
e : 0.22	f : 0.14	y : 0.12	g : 0.11	d : 0.09	c : 0.09	[ : 0.06	b : 0.06	h : 0.03	x : 0.01	= : 0.01	
e : 0.20	y : 0.12	f : 0.11	g : 0.09	c : 0.09	w : 0.09	b : 0.06	d : 0.04	a : 0.04	h : 0.03	v : 0.03	x : 0.01	= : 0.01	
u : 0.32	v : 0.25	y : 0.12	w : 0.11	d : 0.04	e : 0.04	g : 0.03	b : 0.01	x : 0.01	t : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.16	y : 0.12	w : 0.11	x : 0.01	
u : 0.32	v : 0.25	t : 0.14	y : 0.12	w : 0.11	x : 0.01	e : 0.01	
v : 0.22	e : 0.19	y : 0.12	w : 0.11	c : 0.08	f : 0.08	g : 0.04	d : 0.04	b : 0.03	x : 0.01	= : 0.01	a : 0.01	
e : 0.24	f : 0.19	g : 0.14	d : 0.11	c : 0.11	b : 0.08	y : 0.03	h : 0.03	= : 0.01	a : 0.01	w : 0.01	
e : 0.25	f : 0.19	g : 0.14	c : 0.14	d : 0.11	b : 0.04	h : 0.03	2 : 0.01	= : 0.01	] : 0.01	a : 0.01	
e : 0.25	f : 0.19	g : 0.14	d : 0.14	] : 0.08	c : 0.06	2 : 0.03	h : 0.03	= : 0.01	4 : 0.01	3 : 0.01	
e : 0.25	f : 0.19	g : 0.14	d : 0.11	c : 0.08	4 : 0.04	= : 0.03	2 : 0.03	] : 0.03	h : 0.03	3 : 0.03	
f : 0.20	g : 0.14	e : 0.12	d : 0.08	2 : 0.08	4 : 0.06	] : 0.04	c : 0.04	h : 0.04	3 : 0.04	= : 0.03	: : 0.03	6 : 0.01	8 : 0.01	
g : 0.14	f : 0.12	e : 0.12	2 : 0.09	d : 0.08	4 : 0.06	c : 0.06	] : 0.04	h : 0.04	: : 0.04	= : 0.03	3 : 0.03	C : 0.01	6 : 0.01	E : 0.01	b : 0.01	8 : 0.01	

#score	1395.6280036022865
#seq	62
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_UTR_m2_run1.txt

#BEAR
Ceeeeeuuuuuuuuuuuueeeee	chr15:49418004-49418231(-)$1	227	140	163	22.2257
iiiiiivvvvvvvvvvvvviiii	chr2:207178867-207179101(+)$1	234	122	145	22.5941
cc!!bbuuuuuuuuuuuubb22c	chr4:106198286-106198516(+)$1	230	9	32	21.8154
:fffffftttttttttttfffff	chr3:167401000-167401225(-)$1	225	1	24	20.9470
iiiiiiitttttttttttiiiii	chr13:45605426-45605647(+)$1	221	170	193	21.9855
ffffffwwwwwwwwwwwwwwfff	chrX:11140906-11141136(+)$1	230	167	190	20.7634
ffffffuuuuuuuuuuuufffff	chr1:147116002-147116227(-)$1	225	101	124	22.4835
dd"""bbtttttttttttbb333	chr19:13265273-13265493(+)$1	220	114	137	20.9767
[fffffftttttttttttfffff	chr6:111349158-111349394(+)$1	236	79	102	21.8577
gggggggtttttttttttggggg	chr12:53808242-53808474(+)$1	232	118	141	22.1911
!ddddwwwwwwwwwwwwwwdddd	chr14:21732413-21732644(-)$1	231	94	117	21.1428
[eeeeeuuuuuuuuuuuueeeee	chr3:123632894-123633112(-)$1	218	159	182	23.3842
b!!cccvvvvvvvvvvvvvccc]	chr14:92527525-92527746(-)$1	221	93	116	22.7960
""ddddtttttttttttdddd33	chr19:24127030-24127261(+)$1	231	142	165	21.5592
[fffffftttttttttttfffff	chr4:177250487-177250716(+)$1	229	44	67	21.8577
======yyyyyyyyyyyyyyyy=	chr19:53888282-53888510(+)$1	228	140	163	20.6474
gggggggtttttttttttggggg	chr12:38716162-38716397(+)$1	235	26	49	22.1911
$$$cccuuuuuuuuuuuuccc22	chr4:56291844-56292071(+)$1	227	61	84	22.4491
[ddddwwwwwwwwwwwwwwdddd	chr18:43846075-43846298(+)$1	223	62	85	21.1271
c[ddddwwwwwwwwwwwwwwddd	chr10:126676796-126677025(+)$1	229	157	180	21.2029
gggggggtttttttttttggggg	chr9:134372242-134372465(+)$1	223	119	142	22.1911
!eeeeewwwwwwwwwwwwwweee	chr2:208466169-208466395(+)$1	226	84	107	21.6432
ffdddduuuuuuuuuuuudddd3	chr19:38122781-38123004(-)$1	223	161	184	22.9390
:eeeeewwwwwwwwwwwwwweee	chr16:69732638-69732865(+)$1	227	133	156	20.7167
fffawwwwwwwwwwwwwwa]fff	chr17:49254907-49255132(-)$1	225	5	28	20.3882
dd[cccvvvvvvvvvvvvvccc]	chr4:77968942-77969164(-)$1	222	52	75	22.5288
!eeeeeuuuuuuuuuuuueeeee	chrX:132436225-132436452(-)$1	227	169	192	23.3999
fffa[bbtttttttttttbb]a]	chr17:27876799-27877019(+)$1	220	164	187	21.2988
=======ttttttttttt=====	chr1:158069841-158070068(+)$1	227	162	185	22.4694
:cccccctttttttttttccc]c	chr12:101789040-101789258(-)$1	218	4	27	21.6925
eeecccwwwwwwwwwwwwwwccc	chr15:59387707-59387943(+)$1	236	171	194	21.1510
c[dddduuuuuuuuuuuudddd]	chr21:30716216-30716437(+)$1	221	118	141	23.2060
[cccwwwwwwwwwwwwwwccc]e	chr12:24966449-24966684(-)$1	235	153	176	20.9542
dddddduuuuuuuuuuuudddd:	chr8:41789578-41789808(-)$1	230	57	80	21.6674
c!!ddddtttttttttttdddd2	chr13:20593819-20594044(+)$1	225	38	61	22.1297
ffffffuuuuuuuuuuuufffff	chr9:114983715-114983936(-)$1	221	121	144	22.4835
ggyyyyyyyyyyyyyyyyggggg	chr16:75478594-75478820(-)$1	226	100	123	20.1034
##eeeeettttttttttteeeee	chr2:74362196-74362425(-)$1	229	14	37	22.3435
fff[bbwwwwwwwwwwwwwwbbf	chr12:69015131-69015351(+)$1	220	22	45	20.0630
gggggggtttttttttttggggg	chr1:35320091-35320333(-)$1	242	18	41	22.1911
###ddddtttttttttttdddd2	chr11:85372659-85372878(-)$1	219	45	68	21.9554
$fffffftttttttttttfffff	chr7:63814873-63815103(+)$1	230	123	146	21.6371
[ddddyyyyyyyyyyyyyyyydd	chr4:186070448-186070665(+)$1	217	94	117	20.6053
======wwwwwwwwwwwwww===	chr2:11322921-11323155(-)$1	234	41	64	21.5528
d[dddduuuuuuuuuuuudddd]	chr1:173906536-173906768(-)$1	232	94	117	23.0206
:eeeeeuuuuuuuuuuuueeeee	chr5:137087687-137087922(-)$1	235	0	23	22.4735
bb[ccctttttttttttccc]bb	chr3:184086198-184086425(+)$1	227	0	23	20.7625
[eeeeeuuuuuuuuuuuueeeee	chr3:119242643-119242867(+)$1	224	103	126	23.3842
hhh[ccctttttttttttccc]h	chr18:59711711-59711932(-)$1	221	102	125	21.7254
:eeeeevvvvvvvvvvvvveeee	chr20:42935104-42935331(-)$1	227	52	75	21.9750
ffyyyyyyyyyyyyyyyyfffff	chr3:170111697-170111921(+)$1	224	27	50	19.6719
b!!ddddtttttttttttdddd3	chr16:85955018-85955247(+)$1	229	21	44	22.1791
ffffffuuuuuuuuuuuufffff	chr12:72184001-72184221(+)$1	220	80	103	22.4835
hhh[bbvvvvvvvvvvvvvbb]h	chr5:133940626-133940852(-)$1	226	103	126	20.8534
:eeeeeyyyyyyyyyyyyyyyye	chr1:179811598-179811840(-)$1	242	94	117	19.8201
!!eeeeettttttttttteeeee	chr12:69665505-69665726(+)$1	221	27	50	22.5678
ggyyyyyyyyyyyyyyyyggggg	chr8:37613965-37614196(+)$1	231	183	206	20.1034
::cccwwwwwwwwwwwwwwccc:	chr6:33268879-33269101(-)$1	222	123	146	18.4474
!!ddddtttttttttttddddff	chr10:102724340-102724571(+)$1	231	139	162	21.6193
:eeeeevvvvvvvvvvvvveeee	chr5:102543272-102543500(+)$1	228	64	87	21.9750
$ddddwwwwwwwwwwwwwwdddd	chr3:18389785-18390005(-)$1	220	147	170	20.9065
ee[ccctttttttttttccc]ee	chr2:122484590-122484814(-)$1	224	116	139	21.7648
!!ddddvvvvvvvvvvvvvdddd	chr10:102120777-102121002(+)$1	225	96	119	22.6755
:eeeeewwwwwwwwwwwwwweee	chr11:62656126-62656361(+)$1	235	10	33	20.7167
ggdddduuuuuuuuuuuudddd3	chr11:117041539-117041765(+)$1	226	63	86	23.1390
gggggguuuuuuuuuuuuggggg	chr16:19132533-19132751(+)$1	218	47	70	23.1826

#otherMatches

#Seq PSSM
CUGUGCUAUCUUUGCUUUGUACA	chr15:49418004-49418231(-)$1	227	140	163	22.2257
UUUUUUUUUUUUUUUGGUUAAAG	chr2:207178867-207179101(+)$1	234	122	145	22.5941
AAUAGCUAAAAAUUUAAUGCCUU	chr4:106198286-106198516(+)$1	230	9	32	21.8154
UGAGUGUUAAUAUUAUAUACACU	chr3:167401000-167401225(-)$1	225	1	24	20.9470
UUCUUUGUUUUCCUCAUUUAAAG	chr13:45605426-45605647(+)$1	221	170	193	21.9855
UCUGUGGGUGAUUAAUUUGGUAU	chrX:11140906-11141136(+)$1	230	167	190	20.7634
UAAAAACUUUUUACuuucuuuuu	chr1:147116002-147116227(-)$1	225	101	124	22.4835
CUCAAGUUUUUCUCAUCUGCAUU	chr19:13265273-13265493(+)$1	220	114	137	20.9767
GAAAGCAUUUUGGUUAUUUGUUU	chr6:111349158-111349394(+)$1	236	79	102	21.8577
AUAUAUAUUUUUUGCUUUUGUAU	chr12:53808242-53808474(+)$1	232	118	141	22.1911
AAUGUGCUCCUUAUUUAAAACAU	chr14:21732413-21732644(-)$1	231	94	117	21.1428
GCUAACAGAUAAGCUAUAGUUGG	chr3:123632894-123633112(-)$1	218	159	182	23.3842
AUCUUGGCCAAAUAAUUUACAAU	chr14:92527525-92527746(-)$1	221	93	116	22.7960
aaugaugagacuuuuaaaucaaa	chr19:24127030-24127261(+)$1	231	142	165	21.5592
acucagaucuucuaauuuucuga	chr4:177250487-177250716(+)$1	229	44	67	21.8577
uagGAcaagggaucuucaagaag	chr19:53888282-53888510(+)$1	228	140	163	20.6474
ucaugggauacuuuucaguccau	chr12:38716162-38716397(+)$1	235	26	49	22.1911
CCAUGCAAUUUUCUUUCAGCACU	chr4:56291844-56292071(+)$1	227	61	84	22.4491
UGUAGUCAUUUGUUCAUCUUUAC	chr18:43846075-43846298(+)$1	223	62	85	21.1271
CUUUACAAUAAACAAAUACAGUA	chr10:126676796-126677025(+)$1	229	157	180	21.2029
UCCGGAGCCUGCUGCUUUCUCUG	chr9:134372242-134372465(+)$1	223	119	142	22.1911
AAAAUAACUCAAGUGCAUAAUAU	chr2:208466169-208466395(+)$1	226	84	107	21.6432
GGCUGGCAAAACGAAAAUCUAGA	chr19:38122781-38123004(-)$1	223	161	184	22.9390
CCAGAGCUACUUUAUAAAUUCUC	chr16:69732638-69732865(+)$1	227	133	156	20.7167
UCCCUGGGCAAAUCUUUUGAGGA	chr17:49254907-49255132(-)$1	225	5	28	20.3882
UGUCAGUUGCACUUUUUUUCUGC	chr4:77968942-77969164(-)$1	222	52	75	22.5288
AGAUUGUAUUCAAAGCAUCAAUC	chrX:132436225-132436452(-)$1	227	169	192	23.3999
GUCCAAGAAUAAUCCAAGCUAGA	chr17:27876799-27877019(+)$1	220	164	187	21.2988
uauauauuuaauuuuuuuauaua	chr1:158069841-158070068(+)$1	227	162	185	22.4694
GAGGGAUAAUUUGAUCGAAUCAC	chr12:101789040-101789258(-)$1	218	4	27	21.6925
GAUGAACACUAAAUAUUAAUUUC	chr15:59387707-59387943(+)$1	236	171	194	21.1510
UUGGACAUUUAAAGAUCAGUCUU	chr21:30716216-30716437(+)$1	221	118	141	23.2060
GAAUUCUUUUCAAACAAUGUUGA	chr12:24966449-24966684(-)$1	235	153	176	20.9542
CACUCAACGGACCUUACAUGAGA	chr8:41789578-41789808(-)$1	230	57	80	21.6674
AUAUUAAAAUUUCCAAACUUAAA	chr13:20593819-20594044(+)$1	225	38	61	22.1297
GGCACUAUUAUAAUUUUCAGUGC	chr9:114983715-114983936(-)$1	221	121	144	22.4835
UUAUCUACUCUUUUAAAAAACUA	chr16:75478594-75478820(-)$1	226	100	123	20.1034
CUGUUUCUUCCCCUCCACGAAAC	chr2:74362196-74362425(-)$1	229	14	37	22.3435
AGUUGCUAGUUGAAAAUAUUGCA	chr12:69015131-69015351(+)$1	220	22	45	20.0630
auaacaaccguuaacauuuuguu	chr1:35320091-35320333(-)$1	242	18	41	22.1911
AUAUGGUGUCAUAAUAAAACCAG	chr11:85372659-85372878(-)$1	219	45	68	21.9554
UUCUUUGUAUAAUCACCUCAGAG	chr7:63814873-63815103(+)$1	230	123	146	21.6371
GUGCACAUUAUCUACAUUCUCUG	chr4:186070448-186070665(+)$1	217	94	117	20.6053
uauauaaacacacacacauauau	chr2:11322921-11323155(-)$1	234	41	64	21.5528
AAGGUUUUUUUUUUUUUUAAUUC	chr1:173906536-173906768(-)$1	232	94	117	23.0206
CCUAGUUUCAUCCCUCUUACUGG	chr5:137087687-137087922(-)$1	235	0	23	22.4735
GGCGGCAUCUUUAACUGGCCUCC	chr3:184086198-184086425(+)$1	227	0	23	20.7625
UUUCUUUUCUUUUUAACUAAGAA	chr3:119242643-119242867(+)$1	224	103	126	23.3842
uuucuuaauuucuauuuaugaug	chr18:59711711-59711932(-)$1	221	102	125	21.7254
AGUUACAAGAAAUAAAAGAGUAA	chr20:42935104-42935331(-)$1	227	52	75	21.9750
CAUAUCCAAAAAGAAUUUUGUAC	chr3:170111697-170111921(+)$1	224	27	50	19.6719
AGACGUUUAAUACGAAGUGGCGG	chr16:85955018-85955247(+)$1	229	21	44	22.1791
UGAUACUUUCUGGCAACUGUAUC	chr12:72184001-72184221(+)$1	220	80	103	22.4835
UCACUUUCAUCUUCUUUCUAAAU	chr5:133940626-133940852(-)$1	226	103	126	20.8534
UUACAGAACAACUUUCAUUACAC	chr1:179811598-179811840(-)$1	242	94	117	19.8201
UAAAGGUGAAAAUUGCAGGCCUU	chr12:69665505-69665726(+)$1	221	27	50	22.5678
GCAAAAUCAUGAAAAUCAGCUGU	chr8:37613965-37614196(+)$1	231	183	206	20.1034
gaccucuuaaaaaucaucaagga	chr6:33268879-33269101(-)$1	222	123	146	18.4474
UGGCCAGUAAUAAUGUGUGGCGU	chr10:102724340-102724571(+)$1	231	139	162	21.6193
AGUGUAUUUUUUCCUCUACUGCA	chr5:102543272-102543500(+)$1	228	64	87	21.9750
GUCUUAAAAGUUUUAAAUAGAGA	chr3:18389785-18390005(-)$1	220	147	170	20.9065
UUAUACCAGUAUCAUCAGUGAAG	chr2:122484590-122484814(-)$1	224	116	139	21.7648
CUGAUAUUAUUUCUUCUCUUAUC	chr10:102120777-102121002(+)$1	225	96	119	22.6755
UGCUGCUCCGCUUCCCCUACGCG	chr11:62656126-62656361(+)$1	235	10	33	20.7167
CCCAGGUUUCUUGGUGUUCCUGC	chr11:117041539-117041765(+)$1	226	63	86	23.1390
CUUUUUGCUUUUGAAAAAAAAAG	chr16:19132533-19132751(+)$1	218	47	70	23.1826

#DB
((((((............)))))	chr15:49418004-49418231(-)$1	1	140	163	22.2257
((((((.............))))	chr2:207178867-207179101(+)$1	1	122	145	22.5941
((..((............))..)	chr4:106198286-106198516(+)$1	1	9	32	21.8154
.((((((...........)))))	chr3:167401000-167401225(-)$1	1	1	24	20.9470
(((((((...........)))))	chr13:45605426-45605647(+)$1	1	170	193	21.9855
((((((..............)))	chrX:11140906-11141136(+)$1	1	167	190	20.7634
((((((............)))))	chr1:147116002-147116227(-)$1	1	101	124	22.4835
((...((...........))...	chr19:13265273-13265493(+)$1	1	114	137	20.9767
.((((((...........)))))	chr6:111349158-111349394(+)$1	1	79	102	21.8577
(((((((...........)))))	chr12:53808242-53808474(+)$1	1	118	141	22.1911
.((((..............))))	chr14:21732413-21732644(-)$1	1	94	117	21.1428
.(((((............)))))	chr3:123632894-123633112(-)$1	1	159	182	23.3842
(..(((.............))).	chr14:92527525-92527746(-)$1	1	93	116	22.7960
..((((...........))))..	chr19:24127030-24127261(+)$1	1	142	165	21.5592
.((((((...........)))))	chr4:177250487-177250716(+)$1	1	44	67	21.8577
((((((................)	chr19:53888282-53888510(+)$1	1	140	163	20.6474
(((((((...........)))))	chr12:38716162-38716397(+)$1	1	26	49	22.1911
...(((............)))..	chr4:56291844-56292071(+)$1	1	61	84	22.4491
.((((..............))))	chr18:43846075-43846298(+)$1	1	62	85	21.1271
(.((((..............)))	chr10:126676796-126677025(+)$1	1	157	180	21.2029
(((((((...........)))))	chr9:134372242-134372465(+)$1	1	119	142	22.1911
.(((((..............)))	chr2:208466169-208466395(+)$1	1	84	107	21.6432
((((((............)))).	chr19:38122781-38123004(-)$1	1	161	184	22.9390
.(((((..............)))	chr16:69732638-69732865(+)$1	1	133	156	20.7167
((((..............).)))	chr17:49254907-49255132(-)$1	1	5	28	20.3882
((.(((.............))).	chr4:77968942-77969164(-)$1	1	52	75	22.5288
.(((((............)))))	chrX:132436225-132436452(-)$1	1	169	192	23.3999
((((.((...........)).).	chr17:27876799-27877019(+)$1	1	164	187	21.2988
(((((((...........)))))	chr1:158069841-158070068(+)$1	1	162	185	22.4694
.((((((...........))).)	chr12:101789040-101789258(-)$1	1	4	27	21.6925
((((((..............)))	chr15:59387707-59387943(+)$1	1	171	194	21.1510
(.((((............)))).	chr21:30716216-30716437(+)$1	1	118	141	23.2060
.(((..............))).)	chr12:24966449-24966684(-)$1	1	153	176	20.9542
))((((............)))).	chr8:41789578-41789808(-)$1	1	57	80	21.6674
(..((((...........)))).	chr13:20593819-20594044(+)$1	1	38	61	22.1297
((((((............)))))	chr9:114983715-114983936(-)$1	1	121	144	22.4835
((................)))))	chr16:75478594-75478820(-)$1	1	100	123	20.1034
..(((((...........)))))	chr2:74362196-74362425(-)$1	1	14	37	22.3435
(((.((..............)))	chr12:69015131-69015351(+)$1	1	22	45	20.0630
(((((((...........)))))	chr1:35320091-35320333(-)$1	1	18	41	22.1911
...((((...........)))).	chr11:85372659-85372878(-)$1	1	45	68	21.9554
.((((((...........)))))	chr7:63814873-63815103(+)$1	1	123	146	21.6371
.((((................))	chr4:186070448-186070665(+)$1	1	94	117	20.6053
((((((..............)))	chr2:11322921-11323155(-)$1	1	41	64	21.5528
(.((((............)))).	chr1:173906536-173906768(-)$1	1	94	117	23.0206
.(((((............)))))	chr5:137087687-137087922(-)$1	1	0	23	22.4735
((.(((...........))).))	chr3:184086198-184086425(+)$1	1	0	23	20.7625
.(((((............)))))	chr3:119242643-119242867(+)$1	1	103	126	23.3842
(((.(((...........))).)	chr18:59711711-59711932(-)$1	1	102	125	21.7254
.(((((.............))))	chr20:42935104-42935331(-)$1	1	52	75	21.9750
((................)))))	chr3:170111697-170111921(+)$1	1	27	50	19.6719
(..((((...........)))).	chr16:85955018-85955247(+)$1	1	21	44	22.1791
((((((............)))))	chr12:72184001-72184221(+)$1	1	80	103	22.4835
(((.((.............)).)	chr5:133940626-133940852(-)$1	1	103	126	20.8534
.(((((................)	chr1:179811598-179811840(-)$1	1	94	117	19.8201
..(((((...........)))))	chr12:69665505-69665726(+)$1	1	27	50	22.5678
((................)))))	chr8:37613965-37614196(+)$1	1	183	206	20.1034
..(((..............))).	chr6:33268879-33269101(-)$1	1	123	146	18.4474
..((((...........))))))	chr10:102724340-102724571(+)$1	1	139	162	21.6193
.(((((.............))))	chr5:102543272-102543500(+)$1	1	64	87	21.9750
.((((..............))))	chr3:18389785-18390005(-)$1	1	147	170	20.9065
((.(((...........))).))	chr2:122484590-122484814(-)$1	1	116	139	21.7648
..((((.............))))	chr10:102120777-102121002(+)$1	1	96	119	22.6755
.(((((..............)))	chr11:62656126-62656361(+)$1	1	10	33	20.7167
((((((............)))).	chr11:117041539-117041765(+)$1	1	63	86	23.1390
((((((............)))))	chr16:19132533-19132751(+)$1	1	47	70	23.1826

#PSSM
: : 0.13	f : 0.13	g : 0.12	[ : 0.10	! : 0.09	c : 0.06	d : 0.06	b : 0.04	= : 0.04	$ : 0.04	i : 0.03	e : 0.03	# : 0.03	h : 0.03	C : 0.01	" : 0.01	
e : 0.19	f : 0.19	g : 0.12	d : 0.10	! : 0.09	c : 0.04	= : 0.04	[ : 0.04	i : 0.03	# : 0.03	h : 0.03	" : 0.01	$ : 0.01	b : 0.01	: : 0.01	
e : 0.21	d : 0.19	f : 0.16	g : 0.07	! : 0.06	= : 0.04	[ : 0.04	c : 0.04	y : 0.04	i : 0.03	h : 0.03	" : 0.01	$ : 0.01	# : 0.01	
d : 0.24	e : 0.19	c : 0.13	f : 0.12	g : 0.07	= : 0.04	y : 0.04	[ : 0.04	i : 0.03	a : 0.03	! : 0.01	" : 0.01	
d : 0.24	e : 0.19	c : 0.13	f : 0.12	g : 0.07	b : 0.04	= : 0.04	y : 0.04	i : 0.03	w : 0.03	" : 0.01	[ : 0.01	
e : 0.19	d : 0.18	f : 0.12	c : 0.12	w : 0.09	b : 0.07	g : 0.07	y : 0.06	= : 0.04	i : 0.03	
u : 0.24	w : 0.21	v : 0.10	y : 0.09	f : 0.06	g : 0.06	t : 0.06	d : 0.04	b : 0.03	c : 0.03	e : 0.03	i : 0.01	= : 0.01	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.34	u : 0.24	w : 0.21	v : 0.10	y : 0.09	
t : 0.28	u : 0.24	w : 0.21	v : 0.10	y : 0.09	d : 0.03	c : 0.03	
w : 0.18	d : 0.15	f : 0.12	e : 0.10	v : 0.10	g : 0.10	c : 0.09	b : 0.04	y : 0.04	i : 0.01	a : 0.01	= : 0.01	
d : 0.21	e : 0.13	c : 0.13	f : 0.12	w : 0.12	g : 0.10	b : 0.06	y : 0.04	i : 0.03	] : 0.01	= : 0.01	
d : 0.22	e : 0.18	f : 0.15	c : 0.12	g : 0.10	y : 0.04	] : 0.04	i : 0.03	= : 0.03	b : 0.03	2 : 0.01	3 : 0.01	
d : 0.21	e : 0.19	f : 0.16	g : 0.10	c : 0.06	] : 0.06	i : 0.03	2 : 0.03	3 : 0.03	y : 0.03	= : 0.03	b : 0.03	a : 0.01	
e : 0.22	f : 0.18	g : 0.10	d : 0.09	3 : 0.07	] : 0.07	c : 0.04	= : 0.04	2 : 0.04	i : 0.03	: : 0.03	h : 0.03	b : 0.01	

#score	1432.9589568523695
#seq	66
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_UTR_m2_run1.txt

#BEAR
eee[cccwwwwwwwwwwwwwwccc2	chr1:26798929-26799209(+)$1	280	167	192	22.3058
ccc:ddddvvvvvvvvvvvvvdddd	chr15:23005470-23005710(-)$1	240	167	192	21.5042
fffddddvvvvvvvvvvvvvdddd4	chr3:122143087-122143327(-)$1	240	125	150	22.0812
::eeeeevvvvvvvvvvvvveeeee	chr12:46754582-46754858(-)$1	276	26	51	20.3077
gggccc[bbtttttttttttbb]cc	chr17:7220677-7220917(-)$1	240	67	92	21.2267
gggeeeeewwwwwwwwwwwwwweee	chr22:43563795-43564035(-)$1	240	185	210	21.9894
c!!eeeeeyyyyyyyyyyyyyyyye	chr6:82455581-82455821(-)$1	240	190	215	21.3752
b[ffffffuuuuuuuuuuuufffff	chr6:31506448-31506708(-)$1	260	205	230	22.2434
]bbddddwwwwwwwwwwwwwwdddd	chr7:149171259-149171499(-)$1	240	187	212	21.4965
gggggggxxxxxxxxxxxxxxxggg	chr17:53853558-53853798(+)$1	240	144	169	18.7251
=:ffffffuuuuuuuuuuuufffff	chr2:70437613-70437853(-)$1	240	108	133	21.4680
:gggggggtttttttttttgggggg	chr10:35338550-35338790(-)$1	240	2	27	20.6633
fffddddwwwwwwwwwwwwwwdddd	chrX:119391951-119392191(+)$1	240	32	57	21.8266
%%%%%cccuuuuuuuuuuuuccc66	chr18:19155592-19155832(-)$1	240	73	98	19.7346
ddddyyyyyyyyyyyyyyyydddd]	chr17:62225787-62226027(-)$1	240	87	112	20.5615
eeeee[ccctttttttttttcccee	chr14:67801476-67801716(+)$1	240	112	137	22.1104
&&&&dddduuuuuuuuuuuudddd9	chr1:27634276-27634516(+)$1	240	56	81	20.3150
========wwwwwwwwwwwwww===	chr10:27399441-27399681(-)$1	240	150	175	22.7050
""ffffffuuuuuuuuuuuufffff	chr7:135611551-135611803(-)$1	252	77	102	22.2827
ccceeeeeyyyyyyyyyyyyyyyye	chr5:36193769-36194009(-)$1	240	39	64	21.1868
d[bb[cccuuuuuuuuuuuuccc]b	chr2:27353633-27353873(-)$1	240	208	233	23.2471
!gggggggwwwwwwwwwwwwwwggg	chr17:40125965-40126205(+)$1	240	159	184	22.3985
eeeee[ccctttttttttttccc]e	chr11:9469143-9469383(+)$1	240	118	143	22.2024
========yyyyyyyyyyyyyyyy=	chr8:57876139-57876379(-)$1	240	171	196	21.8457
dddda[bbuuuuuuuuuuuubb]a]	chr19:10802766-10803055(+)$1	289	150	175	22.5756
::ddddwwwwwwwwwwwwwwdddd:	chr6:36198824-36199064(+)$1	240	4	29	18.9227
cc!!dddduuuuuuuuuuuudddd2	chr18:74682165-74682405(+)$1	240	145	170	23.4683
ddd[bbyyyyyyyyyyyyyyyybb]	chr6:41902793-41903038(-)$1	245	147	172	20.5317
fff:ddddvvvvvvvvvvvvvdddd	chr11:93914138-93914378(+)$1	240	63	88	21.2091
iiiiiiiiyyyyyyyyyyyyyyyyi	chr6:137518895-137519136(-)$1	241	187	212	21.6518
========uuuuuuuuuuuu=====	chr5:157183303-157183543(+)$1	240	86	111	23.9690
::ffffffuuuuuuuuuuuufffff	chr1:38061331-38061571(-)$1	240	167	192	20.6478
========uuuuuuuuuuuu=====	chr3:52082958-52083205(-)$1	247	179	204	23.9690
hhhhhhhhuuuuuuuuuuuuhhhhh	chr7:6062875-6063115(+)$1	240	113	138	21.0617
ee[cccxxxxxxxxxxxxxxxccc]	chr6:159058097-159058337(-)$1	240	129	154	18.5674
dddddddduuuuuuuuuuuudddd2	chr7:112460378-112460618(-)$1	240	196	221	22.9642
a[bb[cccuuuuuuuuuuuuccc]b	chrX:106957355-106957656(-)$1	301	111	136	23.3363
eeee[cccvvvvvvvvvvvvvccc]	chr1:28169639-28169879(+)$1	240	43	68	23.0023
[cccyyyyyyyyyyyyyyyycccdd	chr5:157216321-157216566(-)$1	245	141	166	20.8727
gg####ccctttttttttttccc55	chr7:26252197-26252437(+)$1	240	116	141	20.5371
)))eeeeeuuuuuuuuuuuueeeee	chr18:32467779-32468019(+)$1	240	177	202	21.7789
iiiiii[avvvvvvvvvvvvva]ii	chr12:1019946-1020186(+)$1	240	112	137	23.0183
eeeecccwwwwwwwwwwwwwwccc]	chr10:99216910-99217190(+)$1	280	73	98	22.4664
d!!ddddvvvvvvvvvvvvvdddd3	chr19:12841513-12841753(-)$1	240	17	42	22.5634
:::eeeeeuuuuuuuuuuuueeeee	chr3:185209088-185209384(-)$1	296	22	47	20.3707
bccc[cccuuuuuuuuuuuuccc22	chr1:25227750-25227993(-)$1	243	100	125	23.5293
dd!!ddddtttttttttttdddd]d	chr2:131906025-131906265(+)$1	240	39	64	21.4169
bdddd[bbvvvvvvvvvvvvvbb]d	chr17:47126802-47127083(+)$1	281	131	156	21.5059
eee"""bbtttttttttttbb]eee	chr19:55602427-55602667(-)$1	240	89	114	20.5303
bb[bb[ccctttttttttttccc]b	chr12:57647504-57647744(-)$1	240	195	220	21.3830
iiiiiiiixxxxxxxxxxxxxxxii	chr1:203276722-203276962(+)$1	240	132	157	18.6086
dddd[ddddtttttttttttdddd]	chr3:52886562-52886802(-)$1	240	62	87	21.5349
hhhhhhhhuuuuuuuuuuuuhhhhh	chr11:13750686-13750926(+)$1	240	177	202	21.0617
dd[ddddvvvvvvvvvvvvvdddd]	chr17:40176732-40176972(+)$1	240	72	97	22.4154
fff[ddddtttttttttttdddd]f	chr6:93952793-93953039(-)$1	246	193	218	21.2431
ccceeeeevvvvvvvvvvvvveeee	chr12:121766091-121766331(-)$1	240	9	34	22.3093
!!ccc[bbuuuuuuuuuuuubbccc	chr12:125627295-125627535(+)$1	240	50	75	23.0617
hhgggggggtttttttttttggggg	chr12:68055551-68055791(+)$1	240	213	238	21.2114
ffffff[auuuuuuuuuuuua]fff	chr5:162886942-162887182(-)$1	240	107	132	22.7247
!gggggggwwwwwwwwwwwwwwggg	chr14:54944085-54944325(-)$1	240	37	62	22.3985
:ggggggguuuuuuuuuuuuggggg	chr10:75008510-75008750(-)$1	240	191	216	22.7028

#otherMatches

#Seq PSSM
CGCCACCAUGCCCAAGAGAAAGGUA	chr1:26798929-26799209(+)$1	280	167	192	22.3058
GGCUGGGUUUAUUCUUCAGUUACCC	chr15:23005470-23005710(-)$1	240	167	192	21.5042
GUAACUGUAUAUCCUGUUUUUAGUU	chr3:122143087-122143327(-)$1	240	125	150	22.0812
UAUGAAAUUUCACCUAAUGUUUUCA	chr12:46754582-46754858(-)$1	276	26	51	20.3077
GCACAUGGCAUAUCACGGGAGCAAU	chr17:7220677-7220917(-)$1	240	67	92	21.2267
GAGCACAGCAUCCUCCUCUCACCUG	chr22:43563795-43564035(-)$1	240	185	210	21.9894
UUGGGUCACUCUUUUGGAAUAUUUU	chr6:82455581-82455821(-)$1	240	190	215	21.3752
GGCAAGUUGGAGGGAUAAGAAACUU	chr6:31506448-31506708(-)$1	260	205	230	22.2434
CAGCUGCCACCUCUAAACCAAGUAG	chr7:149171259-149171499(-)$1	240	187	212	21.4965
UGGGCUGGGCUGCCUUCUUCUACAG	chr17:53853558-53853798(+)$1	240	144	169	18.7251
AAAUAGUUUUCUUUCAUUUUGACUA	chr2:70437613-70437853(-)$1	240	108	133	21.4680
CUUUUGAUGAGUAUUUUUAGUUAAA	chr10:35338550-35338790(-)$1	240	2	27	20.6633
UGUACCAAAAAGAUAAAAAAAUGGU	chrX:119391951-119392191(+)$1	240	32	57	21.8266
AAAAAACCCUUUUUCUUUCAGGUGC	chr18:19155592-19155832(-)$1	240	73	98	19.7346
AGUGGACUUUUUCACUUCUAUACUU	chr17:62225787-62226027(-)$1	240	87	112	20.5615
CAAUGGAGUUUUGUGAUCCUGCUUA	chr14:67801476-67801716(+)$1	240	112	137	22.1104
CUCUCUUCUAGCUUGGUAAUGAAGU	chr1:27634276-27634516(+)$1	240	56	81	20.3150
UUUUGUGAAUAUGAACAUGCUGUUA	chr10:27399441-27399681(-)$1	240	150	175	22.7050
AAUGGAGAAACAAUCAUAUCUUUCU	chr7:135611551-135611803(-)$1	252	77	102	22.2827
acagacucuauccuuauacaauuug	chr5:36193769-36194009(-)$1	240	39	64	21.1868
UGAUAUUUAAUAAACAAGGAAAGAG	chr2:27353633-27353873(-)$1	240	208	233	23.2471
AUGCUCACGCUCCCAACACAAGGUG	chr17:40125965-40126205(+)$1	240	159	184	22.3985
AUAUUAGCAUAAAUCACUUUUGUAA	chr11:9469143-9469383(+)$1	240	118	143	22.2024
UUUCCCUGUAAUAGAAUGCAAAAUC	chr8:57876139-57876379(-)$1	240	171	196	21.8457
GCUUCUGGAUUCCAUCUGCACCUGU	chr19:10802766-10803055(+)$1	289	150	175	22.5756
CCAAGCUCACACUCUCUCCCGCUUA	chr6:36198824-36199064(+)$1	240	4	29	18.9227
CUAGAGCCUACUUUUAUUUUGGUUA	chr18:74682165-74682405(+)$1	240	145	170	23.4683
GGGUCAUGCCCUCCUCUCCCAUUGU	chr6:41902793-41903038(-)$1	245	147	172	20.5317
UAUGGAAGAAUGGUUUAUGAACUUC	chr11:93914138-93914378(+)$1	240	63	88	21.2091
UAACUUAUGAACCUUUACAUCCAGA	chr6:137518895-137519136(-)$1	241	187	212	21.6518
UCUGUGCUUUUUCAAUCACUAGUGC	chr5:157183303-157183543(+)$1	240	86	111	23.9690
AAGGACGGAGCACCAUCAACCCGUC	chr1:38061331-38061571(-)$1	240	167	192	20.6478
uauauauacacacacauacauauau	chr3:52082958-52083205(-)$1	247	179	204	23.9690
AGGGAACAUUGCACGUUUCUUGUUC	chr7:6062875-6063115(+)$1	240	113	138	21.0617
GCUGGAUUACACACAGCAAGUUCCU	chr6:159058097-159058337(-)$1	240	129	154	18.5674
AGGAAACUUGCAUUUUCAAUAGUUG	chr7:112460378-112460618(-)$1	240	196	221	22.9642
UUGCAUGGGGCCUAGUAACACCAAG	chrX:106957355-106957656(-)$1	301	111	136	23.3363
GAACCCUGGCUUAGAACCUGACAGA	chr1:28169639-28169879(+)$1	240	43	68	23.0023
AUGCAGCCUUCCAAACCCCAGCAGC	chr5:157216321-157216566(-)$1	245	141	166	20.8727
CUGAGAUGCCAUUAUUCCAAGCAAA	chr7:26252197-26252437(+)$1	240	116	141	20.5371
UCAAGAAGGAAAAAAAAAGACUUCU	chr18:32467779-32468019(+)$1	240	177	202	21.7789
UUCUCUGCUUGUAUUUCUUGUGGAG	chr12:1019946-1020186(+)$1	240	112	137	23.0183
CUGUCUGAAAAAACACCUGACUAGU	chr10:99216910-99217190(+)$1	280	73	98	22.4664
CGAUGUACAUAACUAUUUAAUGCAG	chr19:12841513-12841753(-)$1	240	17	42	22.5634
GUACUGCUAAUCAUAUACACAGUAG	chr3:185209088-185209384(-)$1	296	22	47	20.3707
AGGAAAGCACCUACAGACCGGCUCC	chr1:25227750-25227993(-)$1	243	100	125	23.5293
UUUUCCUGAAAAUACACUCCAGGUA	chr2:131906025-131906265(+)$1	240	39	64	21.4169
CCACUUGAUUGAGAAAGAUGUUCCA	chr17:47126802-47127083(+)$1	281	131	156	21.5059
UGAGGACCAAGAAGUGCAAGGAUCA	chr19:55602427-55602667(-)$1	240	89	114	20.5303
GGACAUCAGUCACUGUUUCUCUGUU	chr12:57647504-57647744(-)$1	240	195	220	21.3830
UAGCCAAGGAGAAGUGGGAGACGUU	chr1:203276722-203276962(+)$1	240	132	157	18.6086
AACCAGUGCUGGUUUAUUUUGUACA	chr3:52886562-52886802(-)$1	240	62	87	21.5349
GAAAGAGAUGUUCUCAUUUUUCUUU	chr11:13750686-13750926(+)$1	240	177	202	21.0617
aaaaaUUCCCCACCCCUACCAAUUG	chr17:40176732-40176972(+)$1	240	72	97	22.4154
UUUAAAAUGUACAUAAAGAAUUUAA	chr6:93952793-93953039(-)$1	246	193	218	21.2431
GUGGGUAUAUCUGUCCCCUUAGUAC	chr12:121766091-121766331(-)$1	240	9	34	22.3093
UGUGCGUCACCCGUCAACCAGAGCG	chr12:125627295-125627535(+)$1	240	50	75	23.0617
AAGCCACUUUUAAACUUAAUGGGUG	chr12:68055551-68055791(+)$1	240	213	238	21.2114
GGCCGGGAGGGACUGGAUUAUGUCG	chr5:162886942-162887182(-)$1	240	107	132	22.7247
CUUUGGUUUCCUGUAUCUUUUUAAU	chr14:54944085-54944325(-)$1	240	37	62	22.3985
AUGUAUUUGAAUACCUUAAAAAAUA	chr10:75008510-75008750(-)$1	240	191	216	22.7028

#DB
(((.(((..............))).	chr1:26798929-26799209(+)$1	1	167	192	22.3058
))).((((.............))))	chr15:23005470-23005710(-)$1	1	167	192	21.5042
(((((((.............)))).	chr3:122143087-122143327(-)$1	1	125	150	22.0812
..(((((.............)))))	chr12:46754582-46754858(-)$1	1	26	51	20.3077
((((((.((...........)).))	chr17:7220677-7220917(-)$1	1	67	92	21.2267
)))(((((..............)))	chr22:43563795-43564035(-)$1	1	185	210	21.9894
(..(((((................)	chr6:82455581-82455821(-)$1	1	190	215	21.3752
(.((((((............)))))	chr6:31506448-31506708(-)$1	1	205	230	22.2434
.))((((..............))))	chr7:149171259-149171499(-)$1	1	187	212	21.4965
(((((((...............)))	chr17:53853558-53853798(+)$1	1	144	169	18.7251
).((((((............)))))	chr2:70437613-70437853(-)$1	1	108	133	21.4680
.(((((((...........))))))	chr10:35338550-35338790(-)$1	1	2	27	20.6633
)))((((..............))))	chrX:119391951-119392191(+)$1	1	32	57	21.8266
.....(((............)))..	chr18:19155592-19155832(-)$1	1	73	98	19.7346
((((................)))).	chr17:62225787-62226027(-)$1	1	87	112	20.5615
(((((.(((...........)))))	chr14:67801476-67801716(+)$1	1	112	137	22.1104
....((((............)))).	chr1:27634276-27634516(+)$1	1	56	81	20.3150
((((((((..............)))	chr10:27399441-27399681(-)$1	1	150	175	22.7050
..((((((............)))))	chr7:135611551-135611803(-)$1	1	77	102	22.2827
((((((((................)	chr5:36193769-36194009(-)$1	1	39	64	21.1868
(.((.(((............))).)	chr2:27353633-27353873(-)$1	1	208	233	23.2471
.(((((((..............)))	chr17:40125965-40126205(+)$1	1	159	184	22.3985
(((((.(((...........))).)	chr11:9469143-9469383(+)$1	1	118	143	22.2024
((((((((................)	chr8:57876139-57876379(-)$1	1	171	196	21.8457
(((((.((............)).).	chr19:10802766-10803055(+)$1	1	150	175	22.5756
..((((..............)))).	chr6:36198824-36199064(+)$1	1	4	29	18.9227
((..((((............)))).	chr18:74682165-74682405(+)$1	1	145	170	23.4683
(((.((................)).	chr6:41902793-41903038(-)$1	1	147	172	20.5317
))).((((.............))))	chr11:93914138-93914378(+)$1	1	63	88	21.2091
((((((((................)	chr6:137518895-137519136(-)$1	1	187	212	21.6518
((((((((............)))))	chr5:157183303-157183543(+)$1	1	86	111	23.9690
..((((((............)))))	chr1:38061331-38061571(-)$1	1	167	192	20.6478
((((((((............)))))	chr3:52082958-52083205(-)$1	1	179	204	23.9690
((((((((............)))))	chr7:6062875-6063115(+)$1	1	113	138	21.0617
((.(((...............))).	chr6:159058097-159058337(-)$1	1	129	154	18.5674
((((((((............)))).	chr7:112460378-112460618(-)$1	1	196	221	22.9642
(.((.(((............))).)	chrX:106957355-106957656(-)$1	1	111	136	23.3363
((((.(((.............))).	chr1:28169639-28169879(+)$1	1	43	68	23.0023
.(((................)))))	chr5:157216321-157216566(-)$1	1	141	166	20.8727
((....(((...........)))..	chr7:26252197-26252437(+)$1	1	116	141	20.5371
...(((((............)))))	chr18:32467779-32468019(+)$1	1	177	202	21.7789
((((((.(.............).))	chr12:1019946-1020186(+)$1	1	112	137	23.0183
(((((((..............))).	chr10:99216910-99217190(+)$1	1	73	98	22.4664
(..((((.............)))).	chr19:12841513-12841753(-)$1	1	17	42	22.5634
...(((((............)))))	chr3:185209088-185209384(-)$1	1	22	47	20.3707
((((.(((............)))..	chr1:25227750-25227993(-)$1	1	100	125	23.5293
((..((((...........)))).)	chr2:131906025-131906265(+)$1	1	39	64	21.4169
(((((.((.............)).)	chr17:47126802-47127083(+)$1	1	131	156	21.5059
(((...((...........)).)))	chr19:55602427-55602667(-)$1	1	89	114	20.5303
((.((.(((...........))).)	chr12:57647504-57647744(-)$1	1	195	220	21.3830
((((((((...............))	chr1:203276722-203276962(+)$1	1	132	157	18.6086
((((.((((...........)))).	chr3:52886562-52886802(-)$1	1	62	87	21.5349
((((((((............)))))	chr11:13750686-13750926(+)$1	1	177	202	21.0617
((.((((.............)))).	chr17:40176732-40176972(+)$1	1	72	97	22.4154
(((.((((...........)))).)	chr6:93952793-93953039(-)$1	1	193	218	21.2431
((((((((.............))))	chr12:121766091-121766331(-)$1	1	9	34	22.3093
..(((.((............)))))	chr12:125627295-125627535(+)$1	1	50	75	23.0617
))(((((((...........)))))	chr12:68055551-68055791(+)$1	1	213	238	21.2114
((((((.(............).)))	chr5:162886942-162887182(-)$1	1	107	132	22.7247
.(((((((..............)))	chr14:54944085-54944325(-)$1	1	37	62	22.3985
.(((((((............)))))	chr10:75008510-75008750(-)$1	1	191	216	22.7028

#PSSM
d : 0.14	e : 0.11	: : 0.09	c : 0.08	f : 0.08	= : 0.08	g : 0.06	b : 0.06	! : 0.04	i : 0.04	h : 0.04	] : 0.01	% : 0.01	& : 0.01	" : 0.01	a : 0.01	[ : 0.01	) : 0.01	
g : 0.13	d : 0.13	e : 0.11	c : 0.09	f : 0.08	: : 0.08	= : 0.06	! : 0.04	[ : 0.04	i : 0.04	h : 0.04	b : 0.03	% : 0.01	& : 0.01	" : 0.01	) : 0.01	
f : 0.14	g : 0.13	e : 0.11	d : 0.11	c : 0.09	! : 0.06	= : 0.06	b : 0.04	i : 0.04	[ : 0.04	h : 0.03	% : 0.01	& : 0.01	# : 0.01	) : 0.01	: : 0.01	
d : 0.18	e : 0.18	g : 0.09	c : 0.08	f : 0.08	= : 0.06	[ : 0.04	b : 0.04	i : 0.04	: : 0.03	! : 0.03	h : 0.03	% : 0.01	& : 0.01	# : 0.01	" : 0.01	
d : 0.22	e : 0.14	g : 0.09	c : 0.08	f : 0.08	[ : 0.08	= : 0.06	i : 0.04	y : 0.03	b : 0.03	h : 0.03	% : 0.01	a : 0.01	# : 0.01	" : 0.01	
d : 0.22	c : 0.14	e : 0.11	g : 0.09	[ : 0.09	f : 0.08	= : 0.06	i : 0.04	y : 0.03	h : 0.03	b : 0.01	# : 0.01	" : 0.01	
d : 0.21	c : 0.18	e : 0.11	g : 0.09	f : 0.06	= : 0.06	b : 0.06	[ : 0.04	y : 0.04	i : 0.03	h : 0.03	w : 0.01	x : 0.01	
c : 0.14	d : 0.13	e : 0.09	w : 0.08	b : 0.08	g : 0.08	v : 0.06	f : 0.06	= : 0.06	y : 0.04	x : 0.03	i : 0.03	h : 0.03	a : 0.03	
u : 0.34	v : 0.16	w : 0.14	y : 0.11	t : 0.06	c : 0.06	x : 0.04	b : 0.01	d : 0.01	g : 0.01	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	t : 0.18	v : 0.16	w : 0.14	y : 0.11	x : 0.04	
u : 0.34	v : 0.16	w : 0.14	t : 0.11	y : 0.11	x : 0.04	d : 0.03	g : 0.01	b : 0.01	
d : 0.18	c : 0.14	w : 0.13	v : 0.09	y : 0.08	b : 0.06	f : 0.06	e : 0.04	x : 0.04	g : 0.04	= : 0.03	h : 0.03	a : 0.01	
d : 0.24	c : 0.21	y : 0.08	e : 0.06	b : 0.06	w : 0.06	f : 0.06	g : 0.04	x : 0.03	= : 0.03	h : 0.03	] : 0.03	a : 0.01	
d : 0.24	c : 0.22	e : 0.09	g : 0.09	f : 0.08	y : 0.06	] : 0.04	= : 0.04	b : 0.03	h : 0.03	x : 0.01	
d : 0.22	e : 0.11	] : 0.11	c : 0.09	g : 0.09	f : 0.08	y : 0.06	= : 0.04	h : 0.03	i : 0.03	6 : 0.01	a : 0.01	b : 0.01	5 : 0.01	2 : 0.01	
e : 0.16	] : 0.13	d : 0.11	f : 0.09	g : 0.09	2 : 0.06	= : 0.06	b : 0.04	i : 0.04	c : 0.03	h : 0.03	4 : 0.01	6 : 0.01	9 : 0.01	: : 0.01	5 : 0.01	3 : 0.01	

#score	1320.9277150040637
#seq	61
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_CDS_m1_run2.txt

#BEAR
:eeeeebbvvvvvvvvvvvvvbb]eee	chr13:32911363-32911584(+)$1	221	181	208	22.8435
iiiiiiiivvvvvvvvvvvvviiiiii	chr13:23915541-23915761(-)$1	220	92	119	25.0427
iiiiiiiiitttttttttttiiiiiii	chr12:12356048-12356282(-)$1	234	110	137	23.0438
:gggggggvvvvvvvvvvvvvgggggg	chr1:155450543-155450778(-)$1	235	44	71	23.8385
"gggggggvvvvvvvvvvvvvgggggg	chr17:26961930-26962163(-)$1	233	64	91	24.7550
iiiiiiiiitttttttttttiiiiiii	chr2:198266056-198266292(-)$1	236	21	48	23.0438
iiiiiiiiitttttttttttiiiiiii	chr3:56597663-56597884(+)$1	221	189	216	23.0438
hhhh!!bbuuuuuuuuuuuubb22hhh	chr17:26955423-26955661(-)$1	238	182	209	21.5155
eeeeeyyyyyyyyyyyyyyyyeeeee:	chrX:53613689-53613938(-)$1	249	217	244	20.1292
ggg####cccuuuuuuuuuuuuccc22	chr2:55252294-55252525(-)$1	231	50	77	22.0723
d"""dddduuuuuuuuuuuudddd333	chr13:42874297-42874532(+)$1	235	145	172	24.2405
e!!eeeeeyyyyyyyyyyyyyyyyeee	chr7:157000058-157000284(+)$1	226	134	161	21.6714
c:ffffffvvvvvvvvvvvvvffffff	chr4:187538143-187538364(-)$1	221	168	195	22.2116
eeeeecccvvvvvvvvvvvvvccc]ee	chr3:150873881-150874123(+)$1	242	96	123	24.5366
ggeeeeewwwwwwwwwwwwwweeeee3	chr2:61705818-61706059(-)$1	241	21	48	23.3578
!gggggggtttttttttttggggggg2	chr13:23905551-23905775(-)$1	224	78	105	22.1070
iiiiiiiiyyyyyyyyyyyyyyyyiii	chr7:151884260-151884494(-)$1	234	200	227	22.0656
]a::dddduuuuuuuuuuuuddddccc	chr5:176686990-176687210(+)$1	220	36	63	21.1577
ccc[bbyyyyyyyyyyyyyyyybb]cc	chr10:5790889-5791116(+)$1	227	189	216	21.1550
e::eeeeewwwwwwwwwwwwwweeeee	chr16:20809905-20810134(-)$1	229	74	101	21.1769
b!!eeeeevvvvvvvvvvvvveeeee]	chr21:34926912-34927180(+)$1	268	168	195	24.7623
cceeeee[attttttttttta]eeeee	chr5:145640214-145640436(+)$1	222	181	208	23.2076
!dddd[bbvvvvvvvvvvvvvbb]ddd	chr5:130980263-130980494(-)$1	231	10	37	23.3214
ccc[dddduuuuuuuuuuuudddd]cc	chr6:76380174-76380398(+)$1	224	37	64	23.6462
#ffffffwwwwwwwwwwwwwwffffff	chrM:10262-10502(+)$1	240	52	79	21.7944
###eeeeeuuuuuuuuuuuueeeee44	chr14:31576156-31576383(-)$1	227	6	33	23.9250
ffccccccvvvvvvvvvvvvvccc]cc	chr7:27788145-27788385(+)$1	240	38	65	24.6383
fccc[cccuuuuuuuuuuuucccccc]	chr10:92982560-92982781(+)$1	221	139	166	24.2209
%%%%%cccvvvvvvvvvvvvvccc444	chr2:153535808-153536046(-)$1	238	54	81	22.6060
!!a[eeeeettttttttttteeeee]a	chr15:59910664-59910893(-)$1	229	97	124	23.0476
cc[bb[bbvvvvvvvvvvvvvbb]bb]	chr1:204378960-204379205(-)$1	245	114	141	23.3249
=========uuuuuuuuuuuu======	chr18:47016781-47017016(-)$1	235	60	87	24.4207
f"""ddddwwwwwwwwwwwwwwdddd]	chr17:26960822-26961049(-)$1	227	80	107	23.4953
!!ffffffuuuuuuuuuuuuffffff2	chr19:48887387-48887613(-)$1	226	105	132	22.6049
cc"""cccvvvvvvvvvvvvvccc22c	chr2:179422835-179423056(+)$1	221	163	190	25.1032
"""cccyyyyyyyyyyyyyyyyccc44	chr9:127912068-127912296(-)$1	228	96	123	22.5931
iii"""cccuuuuuuuuuuuuccc]ii	chr9:98229449-98229680(-)$1	231	181	208	24.6081
f$$$$$ccctttttttttttccc4444	chr19:38126809-38127032(-)$1	223	185	212	22.8856
ff:ccc[ccctttttttttttcccccc	chr16:27549025-27549248(-)$1	223	66	93	21.3455
"""eeeeeuuuuuuuuuuuueeeee33	chr4:126370793-126371017(+)$1	224	85	112	24.2584
bbcccdddduuuuuuuuuuuudddd:e	chr17:7404044-7404267(+)$1	223	131	158	21.8148
!!eeeeebbuuuuuuuuuuuubb]eee	chr6:87967119-87967346(+)$1	227	40	67	23.2762
bb[ccc[bbuuuuuuuuuuuubb]ccc	chr17:17158135-17158359(-)$1	224	113	140	22.9216
$eeeeeyyyyyyyyyyyyyyyyeeeee	chr2:32698093-32698320(+)$1	227	92	119	21.4001
ddd[ddddwwwwwwwwwwwwwwddddd	chr2:55785835-55786072(-)$1	237	169	196	22.5497
gg!!ddddvvvvvvvvvvvvvdddd]g	chr19:12222958-12223177(+)$1	219	171	198	24.8264
cc[eeeeevvvvvvvvvvvvveeeee]	chr1:16256977-16257208(+)$1	231	199	226	24.7515
g$$$$$cccuuuuuuuuuuuuccc666	chr17:41329874-41330097(+)$1	223	16	43	22.2990
ggg[ddddvvvvvvvvvvvvvdddd22	chr17:60042440-60042662(-)$1	222	67	94	24.5568
:ggggggguuuuuuuuuuuuggggggg	chr9:135202889-135203109(-)$1	220	129	156	22.8204
%%%%%cccuuuuuuuuuuuuccc4444	chr16:2811786-2812009(+)$1	223	50	77	21.7471
=======bbuuuuuuuuuuuubb22==	chrM:10186-10611(-)$1	425	81	108	23.4135
hhh"""bbvvvvvvvvvvvvvbb333h	chr1:31438862-31439109(-)$1	247	183	210	23.8301
[dddd[ddddtttttttttttdddd33	chr5:71493868-71494088(+)$1	220	89	116	21.8413
dddd[cccvvvvvvvvvvvvvccc]dd	chrX:71426868-71427091(-)$1	223	16	43	24.1778
dd[eeeeevvvvvvvvvvvvveeeee]	chr2:32640558-32640782(+)$1	224	139	166	24.4331
dddd[dddduuuuuuuuuuuudddd22	chr10:119043756-119043976(-)$1	220	103	130	22.7699
hhh[bb[awwwwwwwwwwwwwwa]bb]	chr14:102505308-102505550(+)$1	242	206	233	22.1972
::a"""cccuuuuuuuuuuuuccc333	chr4:74005653-74005911(-)$1	258	123	150	23.1185
e[cccccctttttttttttccc]ccc3	chr7:5104376-5104598(+)$1	222	158	185	22.6941
fffffcccvvvvvvvvvvvvvccc:::	chr3:107517315-107517547(+)$1	232	32	59	21.4697
gggggggccctttttttttttccc]gg	chr2:29164320-29164541(+)$1	221	67	94	22.8997
dd!!ddddvvvvvvvvvvvvvdddd]d	chr15:65892045-65892281(-)$1	236	48	75	24.2995
ccc[cccyyyyyyyyyyyyyyyycccc	chr5:41917261-41917488(+)$1	227	96	123	22.1601
cggggggguuuuuuuuuuuuggggggg	chr4:187530317-187530539(-)$1	222	164	191	23.6810
b"""ddddtttttttttttdddd]bb3	chr16:28845589-28845814(+)$1	225	127	154	21.8002
::eeeeewwwwwwwwwwwwwweeeeef	chr6:100965792-100966021(-)$1	229	127	154	21.1430
hhhhhhhhwwwwwwwwwwwwwwhhhhh	chr5:74077160-74077388(+)$1	228	92	119	21.2658

#otherMatches

#Seq PSSM
AGCUCUCUGAACAUAACAUUAAGAAGA	chr13:32911363-32911584(+)$1	221	181	208	22.8435
UUGGAAAAAUCUUUAUAUACAUUUUUC	chr13:23915541-23915761(-)$1	220	92	119	25.0427
UUUCAUCCACAAAUCAAAUCUGGAUGG	chr12:12356048-12356282(-)$1	234	110	137	23.0438
AUUCCAAGAAUAAGCUCUUCCCUUGGA	chr1:155450543-155450778(-)$1	235	44	71	23.8385
CGAACUCUAGAUGAGGCUGUGGGAGUU	chr17:26961930-26962163(-)$1	233	64	91	24.7550
UUACUAUUUCUUAACCUUUUAGGUGGU	chr2:198266056-198266292(-)$1	236	21	48	23.0438
GGUGAAAAAAAUGGAAUGACUUUUUCA	chr3:56597663-56597884(+)$1	221	189	216	23.0438
CUUUGGGUUAUAUGAUGGGUACAAAAA	chr17:26955423-26955661(-)$1	238	182	209	21.5155
CCUAGUUUCGUUUCUAUUUCCCUGGGA	chrX:53613689-53613938(-)$1	249	217	244	20.1292
UUUGAAGAACAUACAACCCAAAGUUGA	chr2:55252294-55252525(-)$1	231	50	77	22.0723
GGAGAAAAUAAAACUGUAACUUUUAAG	chr13:42874297-42874532(+)$1	235	145	172	24.2405
UUAGUCAUUCACUAAUUUCCAUACAUG	chr7:157000058-157000284(+)$1	226	134	161	21.6714
UUCUGGAUGCAAAUGACAACAGUCCAG	chr4:187538143-187538364(-)$1	221	168	195	22.2116
GAGAGCAGUUGGCCAAGAUUUCUGACU	chr3:150873881-150874123(+)$1	242	96	123	24.5366
GCUGAUGAAGAGAAACAUAAACGUCAA	chr2:61705818-61706059(-)$1	241	21	48	23.3578
UAAAUCAGCAACUGACAAUUUGAUUUC	chr13:23905551-23905775(-)$1	224	78	105	22.1070
ACCUUUUUUUUUUUUAACUGCAAUAGA	chr7:151884260-151884494(-)$1	234	200	227	22.0656
CCACGCCAAUGACUUUUGCCUGGCUGC	chr5:176686990-176687210(+)$1	220	36	63	21.1577
ACUGCUGCGGUAAAGAAAGAAGAGAAG	chr10:5790889-5791116(+)$1	227	189	216	21.1550
AAAGCAAGGAAAAAAUGAACAUCUUGC	chr16:20809905-20810134(-)$1	229	74	101	21.1769
AAAGAGAUCAUCUAAGUCCAAGUCUCA	chr21:34926912-34927180(+)$1	268	168	195	24.7623
GAAUUGAACAACAUUACCAAGCUCAAU	chr5:145640214-145640436(+)$1	222	181	208	23.2076
ACUGACAUUUUUUUCCCCUUUAUUUCA	chr5:130980263-130980494(-)$1	231	10	37	23.3214
UAGCUUGCAGCCUUAUUUUAGUAAAUU	chr6:76380174-76380398(+)$1	224	37	64	23.6462
CUAAUAGUUAUGUCAUCCCUCUUAUUA	chrM:10262-10502(+)$1	240	52	79	21.7944
AUAGUGAUGAGCUUGAAAGGAUCACGA	chr14:31576156-31576383(-)$1	227	6	33	23.9250
UUGCCCAUGUCAUCUUUCAAAAUGUGG	chr7:27788145-27788385(+)$1	240	38	65	24.6383
UCUGAUCAAGCCAACAACAGUGACGGA	chr10:92982560-92982781(+)$1	221	139	166	24.2209
UUUCAGCAACUCUUAUCUAAAUGCCCC	chr2:153535808-153536046(-)$1	238	54	81	22.6060
AUGAACUUCCUUUCAGCCUUGAAGUGC	chr15:59910664-59910893(-)$1	229	97	124	23.0476
UGUAGAUCCUUAUAAUCCCCAGAACUU	chr1:204378960-204379205(-)$1	245	114	141	23.3249
AGGAAAAUGACUCAUCAUCUCCAUUUU	chr18:47016781-47017016(-)$1	235	60	87	24.4207
GUAACGUGGCAGUGGAGAGGAACAUGC	chr17:26960822-26961049(-)$1	227	80	107	23.4953
UUCUACCUCUAUAUCACCAAAGGUAGC	chr19:48887387-48887613(-)$1	226	105	132	22.6049
GUUUCUGAAAAUUAACAUAAAUCAAUG	chr2:179422835-179423056(+)$1	221	163	190	25.1032
UUUGUUCAUAUCAACAACUUAAAACUC	chr9:127912068-127912296(-)$1	228	96	123	22.5931
ACGACCUACACAGGAGUUUCAGUAACG	chr9:98229449-98229680(-)$1	231	181	208	24.6081
GCCCACCUCAGUCGACAUCAGAGAAUU	chr19:38126809-38127032(-)$1	223	185	212	22.8856
GUCCCAUGUGAUCCGAUUACCCACUGG	chr16:27549025-27549248(-)$1	223	66	93	21.3455
CAAAUGGACAAGUGUUUUAUUUCAUAA	chr4:126370793-126371017(+)$1	224	85	112	24.2584
UGGCUUCUGGAUAUGUGAGGACAGAAU	chr17:7404044-7404267(+)$1	223	131	158	21.8148
AAUGUCUCUCUUCCCUUCACCAGCAGA	chr6:87967119-87967346(+)$1	227	40	67	23.2762
UAUCAUUACAAGAUAUGGCAAGUCGUG	chr17:17158135-17158359(-)$1	224	113	140	22.9216
AGUGGAGUUUUAUUAACAAUAAUCUAC	chr2:32698093-32698320(+)$1	227	92	119	21.4001
AAACAGCAUUACACACAAACUUUGCUU	chr2:55785835-55786072(-)$1	237	169	196	22.5497
AUGUGGGAAAUCAUACUAUAGUUCUGG	chr19:12222958-12223177(+)$1	219	171	198	24.8264
AAAAGGUUGACUCUGCUCCAAGACCUA	chr1:16256977-16257208(+)$1	231	199	226	24.7515
UUUUUUUACUUUGACUUCUGUGUACAU	chr17:41329874-41330097(+)$1	223	16	43	22.2990
CAUCUUCAUCAUCCUCCAACUUGAAUA	chr17:60042440-60042662(-)$1	222	67	94	24.5568
UGUCAGAAAUAAUAAGAAACUUCUGAC	chr9:135202889-135203109(-)$1	220	129	156	22.8204
UUCCCCAGAAAGUCCUAAACCUGCUCC	chr16:2811786-2812009(+)$1	223	50	77	21.7471
UAGUAUUCCUAGAAGUGAGAUGGUAAA	chrM:10186-10611(-)$1	425	81	108	23.4135
GGGCUCUGCCCAGCCUGCCAACACAUC	chr1:31438862-31439109(-)$1	247	183	210	23.8301
GUCUGUUGUGCAAACACCUACCACAUU	chr5:71493868-71494088(+)$1	220	89	116	21.8413
GGAACGAGAAAAAAGAAUUAACUUAUU	chrX:71426868-71427091(-)$1	223	16	43	24.1778
GGAAAGGUGAGCUGGAAUCAAAUCUUG	chr2:32640558-32640782(+)$1	224	139	166	24.4331
AUUCACUUCAAAUAUUUGAAAGAAGGA	chr10:119043756-119043976(-)$1	220	103	130	22.7699
AGACCGUGUCCCAGCAGUACCUCCCGC	chr14:102505308-102505550(+)$1	242	206	233	22.1972
GAGGAGCUCAACAAAACAAGGGAGGAA	chr4:74005653-74005911(-)$1	258	123	150	23.1185
AAUCCCAUGAAUGUAGUGAAUGUGGAA	chr7:5104376-5104598(+)$1	222	158	185	22.6941
UGCAUGGUAUUUCCUAUUUCAGCCAUA	chr3:107517315-107517547(+)$1	232	32	59	21.4697
CUUUUCAGAAACUUUCACACCUUCAUG	chr2:29164320-29164541(+)$1	221	67	94	22.8997
GUAGAGGGUCACUGCGACAUUCCCUAG	chr15:65892045-65892281(-)$1	236	48	75	24.2995
AUGCAAAACAAAUUUUAAACUUCUUUC	chr5:41917261-41917488(+)$1	227	96	123	22.1601
GGAGAAGUCAAAGUGACCAAACUUCUC	chr4:187530317-187530539(-)$1	222	164	191	23.6810
CAAGUACCGGGGAGCAAAAGGUGAGCA	chr16:28845589-28845814(+)$1	225	127	154	21.8002
UAGAAAACCAUCAUCUUCACCUUUUCA	chr6:100965792-100966021(-)$1	229	127	154	21.1430
GAAGAGGAUUUAUCAUCCACUUUCUUC	chr5:74077160-74077388(+)$1	228	92	119	21.2658

#DB
.(((((((.............)).)))	chr13:32911363-32911584(+)$1	1	181	208	22.8435
((((((((.............))))))	chr13:23915541-23915761(-)$1	1	92	119	25.0427
(((((((((...........)))))))	chr12:12356048-12356282(-)$1	1	110	137	23.0438
.(((((((.............))))))	chr1:155450543-155450778(-)$1	1	44	71	23.8385
.(((((((.............))))))	chr17:26961930-26962163(-)$1	1	64	91	24.7550
(((((((((...........)))))))	chr2:198266056-198266292(-)$1	1	21	48	23.0438
(((((((((...........)))))))	chr3:56597663-56597884(+)$1	1	189	216	23.0438
((((..((............))..)))	chr17:26955423-26955661(-)$1	1	182	209	21.5155
(((((................))))).	chrX:53613689-53613938(-)$1	1	217	244	20.1292
(((....(((............)))..	chr2:55252294-55252525(-)$1	1	50	77	22.0723
(...((((............))))...	chr13:42874297-42874532(+)$1	1	145	172	24.2405
(..(((((................)))	chr7:157000058-157000284(+)$1	1	134	161	21.6714
).((((((.............))))))	chr4:187538143-187538364(-)$1	1	168	195	22.2116
((((((((.............))).))	chr3:150873881-150874123(+)$1	1	96	123	24.5366
(((((((..............))))).	chr2:61705818-61706059(-)$1	1	21	48	23.3578
.(((((((...........))))))).	chr13:23905551-23905775(-)$1	1	78	105	22.1070
((((((((................)))	chr7:151884260-151884494(-)$1	1	200	227	22.0656
.)..((((............))))(((	chr5:176686990-176687210(+)$1	1	36	63	21.1577
(((.((................)).))	chr10:5790889-5791116(+)$1	1	189	216	21.1550
)..(((((..............)))))	chr16:20809905-20810134(-)$1	1	74	101	21.1769
(..(((((.............))))).	chr21:34926912-34927180(+)$1	1	168	195	24.7623
))(((((.(...........).)))))	chr5:145640214-145640436(+)$1	1	181	208	23.2076
.((((.((.............)).)))	chr5:130980263-130980494(-)$1	1	10	37	23.3214
(((.((((............)))).))	chr6:76380174-76380398(+)$1	1	37	64	23.6462
.((((((..............))))))	chrM:10262-10502(+)$1	1	52	79	21.7944
...(((((............)))))..	chr14:31576156-31576383(-)$1	1	6	33	23.9250
((((((((.............))).))	chr7:27788145-27788385(+)$1	1	38	65	24.6383
((((.(((............)))))).	chr10:92982560-92982781(+)$1	1	139	166	24.2209
.....(((.............)))...	chr2:153535808-153536046(-)$1	1	54	81	22.6060
..(.(((((...........))))).)	chr15:59910664-59910893(-)$1	1	97	124	23.0476
((.((.((.............)).)).	chr1:204378960-204379205(-)$1	1	114	141	23.3249
(((((((((............))))))	chr18:47016781-47017016(-)$1	1	60	87	24.4207
(...((((..............)))).	chr17:26960822-26961049(-)$1	1	80	107	23.4953
..((((((............)))))).	chr19:48887387-48887613(-)$1	1	105	132	22.6049
((...(((.............)))..)	chr2:179422835-179423056(+)$1	1	163	190	25.1032
...(((................)))..	chr9:127912068-127912296(-)$1	1	96	123	22.5931
(((...(((............))).))	chr9:98229449-98229680(-)$1	1	181	208	24.6081
(.....(((...........)))....	chr19:38126809-38127032(-)$1	1	185	212	22.8856
)).(((.(((...........))))))	chr16:27549025-27549248(-)$1	1	66	93	21.3455
...(((((............)))))..	chr4:126370793-126371017(+)$1	1	85	112	24.2584
)))))((((............)))).(	chr17:7404044-7404267(+)$1	1	131	158	21.8148
..(((((((............)).)))	chr6:87967119-87967346(+)$1	1	40	67	23.2762
((.(((.((............)).)))	chr17:17158135-17158359(-)$1	1	113	140	22.9216
.(((((................)))))	chr2:32698093-32698320(+)$1	1	92	119	21.4001
(((.((((..............)))))	chr2:55785835-55786072(-)$1	1	169	196	22.5497
((..((((.............)))).)	chr19:12222958-12223177(+)$1	1	171	198	24.8264
((.(((((.............))))).	chr1:16256977-16257208(+)$1	1	199	226	24.7515
(.....(((............)))...	chr17:41329874-41330097(+)$1	1	16	43	22.2990
(((.((((.............))))..	chr17:60042440-60042662(-)$1	1	67	94	24.5568
.(((((((............)))))))	chr9:135202889-135203109(-)$1	1	129	156	22.8204
.....(((............)))....	chr16:2811786-2812009(+)$1	1	50	77	21.7471
(((((((((............))..))	chrM:10186-10611(-)$1	1	81	108	23.4135
(((...((.............))...)	chr1:31438862-31439109(-)$1	1	183	210	23.8301
.((((.((((...........))))..	chr5:71493868-71494088(+)$1	1	89	116	21.8413
((((.(((.............))).))	chrX:71426868-71427091(-)$1	1	16	43	24.1778
((.(((((.............))))).	chr2:32640558-32640782(+)$1	1	139	166	24.4331
((((.((((............))))..	chr10:119043756-119043976(-)$1	1	103	130	22.7699
(((.((.(..............).)).	chr14:102505308-102505550(+)$1	1	206	233	22.1972
..(...(((............)))...	chr4:74005653-74005911(-)$1	1	123	150	23.1185
(.((((((...........))).))).	chr7:5104376-5104598(+)$1	1	158	185	22.6941
)))))(((.............)))...	chr3:107517315-107517547(+)$1	1	32	59	21.4697
((((((((((...........))).))	chr2:29164320-29164541(+)$1	1	67	94	22.8997
((..((((.............)))).)	chr15:65892045-65892281(-)$1	1	48	75	24.2995
(((.(((................))))	chr5:41917261-41917488(+)$1	1	96	123	22.1601
)(((((((............)))))))	chr4:187530317-187530539(-)$1	1	164	191	23.6810
(...((((...........)))).)).	chr16:28845589-28845814(+)$1	1	127	154	21.8002
..(((((..............)))))(	chr6:100965792-100966021(-)$1	1	127	154	21.1430
((((((((..............)))))	chr5:74077160-74077388(+)$1	1	92	119	21.2658

#PSSM
c : 0.13	i : 0.08	g : 0.08	d : 0.08	f : 0.08	: : 0.07	e : 0.07	! : 0.07	h : 0.05	b : 0.05	" : 0.04	# : 0.02	% : 0.02	= : 0.02	] : 0.01	$ : 0.01	[ : 0.01	
g : 0.14	c : 0.11	d : 0.10	i : 0.08	" : 0.07	! : 0.07	e : 0.05	h : 0.05	: : 0.05	f : 0.05	% : 0.02	= : 0.02	$ : 0.02	b : 0.02	a : 0.01	# : 0.01	[ : 0.01	
e : 0.11	g : 0.11	c : 0.10	i : 0.08	" : 0.08	d : 0.07	h : 0.05	! : 0.05	f : 0.05	[ : 0.05	: : 0.04	% : 0.02	a : 0.02	= : 0.02	$ : 0.02	# : 0.01	
e : 0.22	" : 0.10	[ : 0.10	c : 0.10	g : 0.08	i : 0.07	f : 0.05	d : 0.05	h : 0.02	% : 0.02	= : 0.02	$ : 0.02	! : 0.02	# : 0.01	: : 0.01	b : 0.01	
e : 0.23	d : 0.16	c : 0.10	g : 0.08	i : 0.07	f : 0.05	" : 0.05	b : 0.04	[ : 0.04	% : 0.02	= : 0.02	$ : 0.02	! : 0.01	# : 0.01	h : 0.01	
e : 0.20	c : 0.19	d : 0.16	g : 0.08	i : 0.07	f : 0.04	[ : 0.04	" : 0.04	b : 0.02	= : 0.02	$ : 0.02	! : 0.01	y : 0.01	# : 0.01	h : 0.01	
c : 0.20	d : 0.17	e : 0.17	g : 0.08	b : 0.07	i : 0.07	y : 0.05	f : 0.04	[ : 0.04	= : 0.02	# : 0.01	h : 0.01	
c : 0.23	d : 0.17	b : 0.11	e : 0.11	i : 0.07	g : 0.07	y : 0.07	w : 0.04	f : 0.02	[ : 0.01	= : 0.01	a : 0.01	h : 0.01	
v : 0.29	u : 0.16	w : 0.11	y : 0.10	c : 0.10	i : 0.04	t : 0.04	d : 0.04	b : 0.04	a : 0.01	e : 0.01	= : 0.01	
v : 0.29	u : 0.29	t : 0.13	w : 0.11	y : 0.10	c : 0.04	d : 0.01	
u : 0.30	v : 0.29	t : 0.17	w : 0.11	y : 0.10	
u : 0.30	v : 0.29	t : 0.17	w : 0.11	y : 0.10	
u : 0.30	v : 0.29	t : 0.17	w : 0.11	y : 0.10	
u : 0.30	v : 0.29	t : 0.17	w : 0.11	y : 0.10	
u : 0.30	v : 0.29	t : 0.17	w : 0.11	y : 0.10	
u : 0.30	v : 0.29	t : 0.17	w : 0.11	y : 0.10	
u : 0.30	v : 0.29	t : 0.17	w : 0.11	y : 0.10	
u : 0.30	v : 0.29	t : 0.17	w : 0.11	y : 0.10	
u : 0.30	v : 0.29	t : 0.17	w : 0.11	y : 0.10	
u : 0.30	v : 0.29	t : 0.13	w : 0.11	y : 0.10	g : 0.01	c : 0.01	d : 0.01	
v : 0.29	u : 0.14	w : 0.11	y : 0.10	d : 0.05	c : 0.05	i : 0.04	g : 0.04	e : 0.04	t : 0.04	b : 0.01	a : 0.01	f : 0.01	
c : 0.22	d : 0.14	e : 0.13	b : 0.11	y : 0.08	g : 0.07	w : 0.07	i : 0.05	f : 0.04	u : 0.01	] : 0.01	= : 0.01	
c : 0.23	e : 0.17	d : 0.17	b : 0.11	g : 0.07	i : 0.05	y : 0.04	f : 0.04	2 : 0.01	= : 0.01	a : 0.01	] : 0.01	h : 0.01	
c : 0.23	e : 0.17	d : 0.16	] : 0.10	g : 0.07	i : 0.05	f : 0.04	2 : 0.02	y : 0.02	4 : 0.02	b : 0.01	= : 0.01	3 : 0.01	h : 0.01	
e : 0.22	d : 0.13	c : 0.11	] : 0.10	i : 0.07	g : 0.07	3 : 0.04	f : 0.04	4 : 0.04	b : 0.04	h : 0.02	2 : 0.02	= : 0.01	6 : 0.01	: : 0.01	
e : 0.19	c : 0.13	i : 0.08	g : 0.08	3 : 0.07	4 : 0.07	2 : 0.05	d : 0.05	f : 0.04	] : 0.04	b : 0.04	h : 0.02	= : 0.02	: : 0.02	6 : 0.01	
e : 0.11	c : 0.11	3 : 0.10	] : 0.10	i : 0.08	g : 0.08	2 : 0.07	4 : 0.07	d : 0.05	h : 0.04	f : 0.04	: : 0.02	= : 0.02	a : 0.01	6 : 0.01	

#score	1562.97900922311
#seq	68
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011c_hg19_CDS_m1_run2.txt

#BEAR
c[cccyyyyyyyyyyyyyyyyccccc	chr5:41917261-41917491(+)$1	230	98	124	21.1297
ggggggvvvvvvvvvvvvvggggggg	chr12:65564702-65564941(+)$1	239	31	57	24.5704
gg[dddduuuuuuuuuuuudddd]gg	chr19:37368022-37368242(+)$1	220	92	118	23.8358
)eeeeevvvvvvvvvvvvveeeee]d	chr2:85866338-85866567(+)$1	229	174	200	23.8455
===[cccvvvvvvvvvvvvvccc===	chr2:179469606-179469827(+)$1	221	51	77	24.2663
deeeeevvvvvvvvvvvvveeeeehh	chr4:85742464-85742681(-)$1	217	68	94	23.8508
:gggggggtttttttttttggggggg	chr2:179407143-179407366(+)$1	223	173	199	22.3244
ffffyyyyyyyyyyyyyyyyffffff	chr2:74399746-74399970(-)$1	224	103	129	21.1696
""eeeeevvvvvvvvvvvvveeeee2	chr4:85730962-85731187(-)$1	225	97	123	24.4771
ggggcccvvvvvvvvvvvvvccc]gg	chr2:197710587-197710810(-)$1	223	11	37	24.3508
ddddddduuuuuuuuuuuudddd]dd	chr11:10821619-10821847(-)$1	228	56	82	22.7217
gggggwwwwwwwwwwwwwwggggggg	chr21:38131928-38132148(-)$1	220	150	176	23.0813
ggggggvvvvvvvvvvvvvggggggg	chr6:160501085-160501305(+)$1	220	100	126	24.5704
!ffffffuuuuuuuuuuuuffffff2	chr10:127413862-127414082(+)$1	220	115	141	24.2056
e[cccwwwwwwwwwwwwwwccc]eee	chr2:55825475-55825714(-)$1	239	48	74	22.5140
eeee[bbtttttttttttbb]eeeee	chr20:34832632-34832867(+)$1	235	92	118	22.1508
ffffffwwwwwwwwwwwwwwffffff	chr14:31917466-31917687(-)$1	221	56	82	22.9683
dd[ddddtttttttttttdddddddd	chr22:38621455-38621675(-)$1	220	168	194	21.3379
dd:dddduuuuuuuuuuuuddddfff	chr1:85790373-85790598(-)$1	225	170	196	22.0774
!!eeeeewwwwwwwwwwwwwweeeee	chr12:25261496-25261719(-)$1	223	69	95	23.1538
:eeeeewwwwwwwwwwwwwweeeee:	chr1:197111564-197111783(-)$1	219	43	69	21.6458
:fffffftttttttttttffffffFF	chr17:7489273-7489496(+)$1	223	188	214	21.2718
dgggggggtttttttttttggggggg	chr15:35273888-35274113(-)$1	225	92	118	23.1132
eefffffftttttttttttffffff:	chr1:229577536-229577760(-)$1	224	191	217	21.9819
ffffyyyyyyyyyyyyyyyyffffff	chr17:53040596-53040824(-)$1	228	99	125	21.1696
eeeeeeeuuuuuuuuuuuueeeee]e	chr4:68511555-68511776(-)$1	221	176	202	24.3753
dgggggggtttttttttttggggggg	chr2:55449287-55449505(-)$1	218	141	167	23.1132
======awwwwwwwwwwwwwwa]===	chr15:77363133-77363366(-)$1	233	78	104	22.8217
cceeeeevvvvvvvvvvvvveeeee:	chr7:79841993-79842220(+)$1	227	85	111	23.5396
ggggggguuuuuuuuuuuuggggggg	chr5:40777446-40777666(-)$1	220	167	193	24.6342
hha[ddddtttttttttttdddd]a]	chr16:31201267-31201506(+)$1	239	135	161	21.7542
b[eeeeeuuuuuuuuuuuueeeeebb	chr1:150469971-150470201(+)$1	230	12	38	24.0709
####cccuuuuuuuuuuuuccc4444	chr17:47118743-47118963(+)$1	220	86	112	23.5602
===bb[bbtttttttttttbbbb]==	chr4:83349339-83349559(-)$1	220	64	90	21.1652
gggggwwwwwwwwwwwwwwggggggg	chr22:50280697-50280920(+)$1	223	13	39	23.0813
!ffffffuuuuuuuuuuuuffffff5	chrM:8007-8281(+)$1	274	64	90	23.5546
e[eeeeevvvvvvvvvvvvveeeee3	chr14:62203529-62203750(+)$1	221	7	33	24.6918
dddd[bbtttttttttttbb]ddddf	chr3:167402004-167402243(-)$1	239	123	149	20.8765
ffffffvvvvvvvvvvvvvffffffc	chr5:133295549-133295778(-)$1	229	108	134	24.0134
eeeeeyyyyyyyyyyyyyyyyeeeee	chr16:56536479-56536699(+)$1	220	151	177	21.5732
b[eeeeettttttttttteeeee]bb	chr5:64881805-64882023(+)$1	218	55	81	22.6339
""eeeeeuuuuuuuuuuuueeeee33	chr19:37185646-37185872(+)$1	226	158	184	24.7554
ffffffbbtttttttttttbb]ffff	chr1:227841937-227842160(+)$1	223	186	212	22.0813
gbb[cccvvvvvvvvvvvvvccc]bb	chr8:28385197-28385419(+)$1	222	150	176	22.9450
cffffffvvvvvvvvvvvvvffffff	chr2:128522276-128522500(-)$1	224	41	67	24.0180
cffffffvvvvvvvvvvvvvffffff	chr5:59934498-59934722(-)$1	224	193	219	24.0180
f!!ddddwwwwwwwwwwwwwwdddd2	chr12:664472-664696(+)$1	224	95	121	21.6709
gggeeeeettttttttttteeeeeBB	chrX:119387409-119387630(+)$1	221	150	176	21.5858
!!fffffftttttttttttffffff2	chr10:104860944-104861164(-)$1	220	10	36	23.1113
=======uuuuuuuuuuuu=======	chr19:34951333-34951553(+)$1	220	113	139	24.5925
i[eeeeeuuuuuuuuuuuueeeeeii	chr15:49935584-49935812(+)$1	228	84	110	24.8185
ggggggvvvvvvvvvvvvvggggggg	chr1:91405644-91405871(-)$1	227	105	131	24.5704
dd[dddduuuuuuuuuuuuddddddd	chr1:183497980-183498199(+)$1	219	46	72	22.7675
$$eeeeevvvvvvvvvvvvveeeee6	chr2:231657841-231658068(+)$1	227	106	132	23.8005
ggggggvvvvvvvvvvvvvggggggg	chr17:56060330-56060550(-)$1	220	95	121	24.5704
BeeeeevvvvvvvvvvvvveeeeeEE	chr6:116599824-116600046(-)$1	222	154	180	21.6233
ffffffvvvvvvvvvvvvvffffffg	chr1:214794002-214794225(+)$1	223	110	136	24.0935
ggggggguuuuuuuuuuuuggggggg	chr1:115282378-115282601(-)$1	223	171	197	24.6342
eeeeeyyyyyyyyyyyyyyyyeeeee	chr10:88220898-88221123(-)$1	225	69	95	21.5732
#ffffffuuuuuuuuuuuuffffff3	chr3:180321959-180322182(+)$1	223	181	207	24.3436
cc[ddddtttttttttttdddd]ccc	chr17:1438664-1438887(-)$1	223	2	28	21.9621
e"""cccuuuuuuuuuuuuccc]eee	chr6:26156601-26156835(+)$1	234	70	96	23.9419
##eeeeeyyyyyyyyyyyyyyyyeee	chr16:31193857-31194086(+)$1	229	166	192	20.6567
%%%%cccuuuuuuuuuuuuccc4444	chr16:2811786-2812009(+)$1	223	51	77	21.0394
ggggggvvvvvvvvvvvvvggggggg	chr4:120428641-120428864(+)$1	223	59	85	24.5704

#otherMatches

#Seq PSSM
GCAAAACAAAUUUUAAACUUCUUUCA	chr5:41917261-41917491(+)$1	230	98	124	21.1297
UUCUCCAGCAAUUUAAACGGGAGGAG	chr12:65564702-65564941(+)$1	239	31	57	24.5704
GUAGUGGCUCAAACCUUACUCACCAU	chr19:37368022-37368242(+)$1	220	92	118	23.8358
AGGUAGCCCAUUAACACACCUGCCCU	chr2:85866338-85866567(+)$1	229	174	200	23.8455
GCAAUUCUUAAACAGACACUGGAUGC	chr2:179469606-179469827(+)$1	221	51	77	24.2663
UGCUAUCACAAAUAUUUACAUGGCUG	chr4:85742464-85742681(-)$1	217	68	94	23.8508
UUAAUUUUUACUUCAAAUCAAAAUUG	chr2:179407143-179407366(+)$1	223	173	199	22.3244
UUCUAAAACAUUCAAACCAAAGAAGA	chr2:74399746-74399970(-)$1	224	103	129	21.1696
CAGUAAACUUUUUAUUUAUCUUUACA	chr4:85730962-85731187(-)$1	225	97	123	24.4771
AUGUGACuauauaaauauuuguuaau	chr2:197710587-197710810(-)$1	223	11	37	24.3508
GGUGAGCAUUUCAGAACUAGCUCAAC	chr11:10821619-10821847(-)$1	228	56	82	22.7217
UUUUAGAUUAAUAAAACAAUAAAAAU	chr21:38131928-38132148(-)$1	220	150	176	23.0813
CUUCCCCUUCAUAUUCAAUGGGAAGA	chr6:160501085-160501305(+)$1	220	100	126	24.5704
AAAAGGCAAUUCUUUCCAAGUUUUUA	chr10:127413862-127414082(+)$1	220	115	141	24.2056
ACAGUACAUUCAGGACAUCAUUUUGC	chr2:55825475-55825714(-)$1	239	48	74	22.5140
GAUGAAGCACCACACCCUCUACAUCA	chr20:34832632-34832867(+)$1	235	92	118	22.1508
GAGACAGAAAAUGGCAAGCAUGUCUC	chr14:31917466-31917687(-)$1	221	56	82	22.9683
GGAGCUGCUCAGCCCCUACAGCCCCG	chr22:38621455-38621675(-)$1	220	168	194	21.3379
GCAAAGGUAAAAAAAUAUCCCUUCUG	chr1:85790373-85790598(-)$1	225	170	196	22.0774
AUUUUCUGAAGCACUUAAAGAAGAAA	chr12:25261496-25261719(-)$1	223	69	95	23.1538
AUAGAUCCAAUAUUAAGUAAAUCUAA	chr1:197111564-197111783(-)$1	219	43	69	21.6458
AGGUUACAAGGCAGCAAAGUggccgg	chr17:7489273-7489496(+)$1	223	188	214	21.2718
UUUGGAAACUUCAACAAUCUUUCUAA	chr15:35273888-35274113(-)$1	225	92	118	23.1132
UUUGUACAAUUUCAUAACAUGUAUAG	chr1:229577536-229577760(-)$1	224	191	217	21.9819
GAAUUUCUACAUACAAUAUUGUUCCA	chr17:53040596-53040824(-)$1	228	99	125	21.1696
UAAUUCAUUAAAACAAAUUUGAGUCU	chr4:68511555-68511776(-)$1	221	176	202	24.3753
UAAAGCUUUUAAGACAAUUAAGUUUU	chr2:55449287-55449505(-)$1	218	141	167	23.1132
GUGCGGCAUCACCUCCUCCAAGACCG	chr15:77363133-77363366(-)$1	233	78	104	22.8217
CAAGUGGUUUACAGAUACAUCCAUUA	chr7:79841993-79842220(+)$1	227	85	111	23.5396
UUUGUUAACCUACUUAAUGUGACAAG	chr5:40777446-40777666(-)$1	220	167	193	24.6342
CUCGCCGGGCAGACUUUAAUCGGGGU	chr16:31201267-31201506(+)$1	239	135	161	21.7542
AUGUCUGUACCCUCCUCUCCAGGCUG	chr1:150469971-150470201(+)$1	230	12	38	24.0709
GCAAGAUACCGAGACAAAAAUCACCA	chr17:47118743-47118963(+)$1	220	86	112	23.5602
CAGUCACUGGGAGAUCAAGAGGAUUU	chr4:83349339-83349559(-)$1	220	64	90	21.1652
UGUUCAACACACCCACUGAGAACGGU	chr22:50280697-50280920(+)$1	223	13	39	23.0813
AUGAGCUGUCCCCACAUUAGGCUUAA	chrM:8007-8281(+)$1	274	64	90	23.5546
UCACAGUCUCCCUUCCCCUCACUGUA	chr14:62203529-62203750(+)$1	221	7	33	24.6918
UCAGACCUUCAAAACUGUGGCCUGAA	chr3:167402004-167402243(-)$1	239	123	149	20.8765
UCACAUAUUUCUACCCCAAAUGUGAA	chr5:133295549-133295778(-)$1	229	108	134	24.0134
CCGGUAAUCUCCCUCUACCACACCGG	chr16:56536479-56536699(+)$1	220	151	177	21.5732
UGGUAUGGGAGGAGAAAGCAUAUGGG	chr5:64881805-64882023(+)$1	218	55	81	22.6339
CUGAAAGUCUUUUUUUUUUUUUUUUU	chr19:37185646-37185872(+)$1	226	158	184	24.7554
GCUGGGGCCUUGACAAUUUGCACUUA	chr1:227841937-227842160(+)$1	223	186	212	22.0813
UAGUGGCGUGUGUUUUGUUGGCCUCU	chr8:28385197-28385419(+)$1	222	150	176	22.9450
CGAACAUGAACAACGUCAAGAUGUUC	chr2:128522276-128522500(-)$1	224	41	67	24.0180
CGUUUCAUUUUUCACUAUUUUGAGAC	chr5:59934498-59934722(-)$1	224	193	219	24.0180
guagaaucuauuaaacacuucauucc	chr12:664472-664696(+)$1	224	95	121	21.6709
UGCUUGAUGAGUUAAUUAAAUCAGGG	chrX:119387409-119387630(+)$1	221	150	176	21.5858
UGAAUAAUGCUAUUUCCCaauuauua	chr10:104860944-104861164(-)$1	220	10	36	23.1113
UCUUCCGAAGAGGGAGAGACGGAAGG	chr19:34951333-34951553(+)$1	220	113	139	24.5925
ACAGAGGGCAAUAUGACAAUCUUUUA	chr15:49935584-49935812(+)$1	228	84	110	24.8185
UUCUUUCAAAUACCUUAAAAAAGAAA	chr1:91405644-91405871(-)$1	227	105	131	24.5704
GUCAGCCUUAUAAUCAGUUGGCUAUC	chr1:183497980-183498199(+)$1	219	46	72	22.7675
AAUUUUCAACAAUAUUCUCAGAAGAC	chr2:231657841-231658068(+)$1	227	106	132	23.8005
GGUGGUUCCCCUUAUCUCUACCAUCG	chr17:56060330-56060550(-)$1	220	95	121	24.5704
CGCAGAAACCAAGACCUCAUCUGCAG	chr6:116599824-116600046(-)$1	222	154	180	21.6233
CUAAUUCUCAAAGAACUCCAAUUAGG	chr1:214794002-214794225(+)$1	223	110	136	24.0935
GGGGUUAUUGAAAAACUGUUAACCUC	chr1:115282378-115282601(-)$1	223	171	197	24.6342
UGGUUUUUAGACUGGGCAUUUAGCUA	chr10:88220898-88221123(-)$1	225	69	95	21.5732
auuuuuguuuuuauuaauuuaaaaaa	chr3:180321959-180322182(+)$1	223	181	207	24.3436
GAAAGAUCUGUUCUCCCCAUCUCUCA	chr17:1438664-1438887(-)$1	223	2	28	21.9621
UCCCGUGAAGAAGAAGGCCCGCAAGU	chr6:26156601-26156835(+)$1	234	70	96	23.9419
CUGAAUAUUGCuuuucuuuuucuugu	chr16:31193857-31194086(+)$1	229	166	192	20.6567
UCCCCAGAAAGUCCUAAACCUGCUCC	chr16:2811786-2812009(+)$1	223	51	77	21.0394
UUUGAAACAAUGAAAAGACUUCAAAU	chr4:120428641-120428864(+)$1	223	59	85	24.5704

#DB
(.(((................)))))	chr5:41917261-41917491(+)$1	1	98	124	21.1297
((((((.............)))))))	chr12:65564702-65564941(+)$1	1	31	57	24.5704
((.((((............)))).))	chr19:37368022-37368242(+)$1	1	92	118	23.8358
.(((((.............))))).)	chr2:85866338-85866567(+)$1	1	174	200	23.8455
(((.(((.............))))))	chr2:179469606-179469827(+)$1	1	51	77	24.2663
)(((((.............)))))((	chr4:85742464-85742681(-)$1	1	68	94	23.8508
.(((((((...........)))))))	chr2:179407143-179407366(+)$1	1	173	199	22.3244
((((................))))))	chr2:74399746-74399970(-)$1	1	103	129	21.1696
..(((((.............))))).	chr4:85730962-85731187(-)$1	1	97	123	24.4771
(((((((.............))).))	chr2:197710587-197710810(-)$1	1	11	37	24.3508
(((((((............)))).))	chr11:10821619-10821847(-)$1	1	56	82	22.7217
(((((..............)))))))	chr21:38131928-38132148(-)$1	1	150	176	23.0813
((((((.............)))))))	chr6:160501085-160501305(+)$1	1	100	126	24.5704
.((((((............)))))).	chr10:127413862-127414082(+)$1	1	115	141	24.2056
(.(((..............))).)))	chr2:55825475-55825714(-)$1	1	48	74	22.5140
((((.((...........)).)))))	chr20:34832632-34832867(+)$1	1	92	118	22.1508
((((((..............))))))	chr14:31917466-31917687(-)$1	1	56	82	22.9683
((.((((...........))))))))	chr22:38621455-38621675(-)$1	1	168	194	21.3379
)).((((............))))(((	chr1:85790373-85790598(-)$1	1	170	196	22.0774
..(((((..............)))))	chr12:25261496-25261719(-)$1	1	69	95	23.1538
.(((((..............))))).	chr1:197111564-197111783(-)$1	1	43	69	21.6458
.((((((...........))))))))	chr17:7489273-7489496(+)$1	1	188	214	21.2718
((((((((...........)))))))	chr15:35273888-35274113(-)$1	1	92	118	23.1132
))((((((...........)))))).	chr1:229577536-229577760(-)$1	1	191	217	21.9819
((((................))))))	chr17:53040596-53040824(-)$1	1	99	125	21.1696
(((((((............))))).)	chr4:68511555-68511776(-)$1	1	176	202	24.3753
((((((((...........)))))))	chr2:55449287-55449505(-)$1	1	141	167	23.1132
(((((((..............).)))	chr15:77363133-77363366(-)$1	1	78	104	22.8217
))(((((.............))))).	chr7:79841993-79842220(+)$1	1	85	111	23.5396
(((((((............)))))))	chr5:40777446-40777666(-)$1	1	167	193	24.6342
(((.((((...........)))).).	chr16:31201267-31201506(+)$1	1	135	161	21.7542
(.(((((............)))))))	chr1:150469971-150470201(+)$1	1	12	38	24.0709
....(((............)))....	chr17:47118743-47118963(+)$1	1	86	112	23.5602
(((((.((...........)))).))	chr4:83349339-83349559(-)$1	1	64	90	21.1652
(((((..............)))))))	chr22:50280697-50280920(+)$1	1	13	39	23.0813
.((((((............)))))).	chrM:8007-8281(+)$1	1	64	90	23.5546
(.(((((.............))))).	chr14:62203529-62203750(+)$1	1	7	33	24.6918
((((.((...........)).)))))	chr3:167402004-167402243(-)$1	1	123	149	20.8765
((((((.............))))))(	chr5:133295549-133295778(-)$1	1	108	134	24.0134
(((((................)))))	chr16:56536479-56536699(+)$1	1	151	177	21.5732
(.(((((...........))))).))	chr5:64881805-64882023(+)$1	1	55	81	22.6339
..(((((............)))))..	chr19:37185646-37185872(+)$1	1	158	184	24.7554
((((((((...........)).))))	chr1:227841937-227842160(+)$1	1	186	212	22.0813
(((.(((.............))).))	chr8:28385197-28385419(+)$1	1	150	176	22.9450
(((((((.............))))))	chr2:128522276-128522500(-)$1	1	41	67	24.0180
)((((((.............))))))	chr5:59934498-59934722(-)$1	1	193	219	24.0180
(..((((..............)))).	chr12:664472-664696(+)$1	1	95	121	21.6709
)))(((((...........)))))))	chrX:119387409-119387630(+)$1	1	150	176	21.5858
..((((((...........)))))).	chr10:104860944-104861164(-)$1	1	10	36	23.1113
(((((((............)))))))	chr19:34951333-34951553(+)$1	1	113	139	24.5925
(.(((((............)))))))	chr15:49935584-49935812(+)$1	1	84	110	24.8185
((((((.............)))))))	chr1:91405644-91405871(-)$1	1	105	131	24.5704
((.((((............)))))))	chr1:183497980-183498199(+)$1	1	46	72	22.7675
..(((((.............))))).	chr2:231657841-231658068(+)$1	1	106	132	23.8005
((((((.............)))))))	chr17:56060330-56060550(-)$1	1	95	121	24.5704
)(((((.............)))))))	chr6:116599824-116600046(-)$1	1	154	180	21.6233
((((((.............)))))))	chr1:214794002-214794225(+)$1	1	110	136	24.0935
(((((((............)))))))	chr1:115282378-115282601(-)$1	1	171	197	24.6342
(((((................)))))	chr10:88220898-88221123(-)$1	1	69	95	21.5732
.((((((............)))))).	chr3:180321959-180322182(+)$1	1	181	207	24.3436
((.((((...........)))).)))	chr17:1438664-1438887(-)$1	1	2	28	21.9621
(...(((............))).)))	chr6:26156601-26156835(+)$1	1	70	96	23.9419
..(((((................)))	chr16:31193857-31194086(+)$1	1	166	192	20.6567
....(((............)))....	chr16:2811786-2812009(+)$1	1	51	77	21.0394
((((((.............)))))))	chr4:120428641-120428864(+)$1	1	59	85	24.5704

#PSSM
g : 0.20	d : 0.12	e : 0.12	f : 0.10	c : 0.07	= : 0.06	! : 0.06	: : 0.04	# : 0.04	" : 0.03	b : 0.03	) : 0.01	h : 0.01	i : 0.01	$ : 0.01	B : 0.01	% : 0.01	
g : 0.23	f : 0.18	e : 0.13	[ : 0.09	d : 0.07	= : 0.06	" : 0.04	! : 0.04	c : 0.03	# : 0.03	h : 0.01	b : 0.01	$ : 0.01	% : 0.01	
e : 0.27	g : 0.21	f : 0.21	[ : 0.06	= : 0.06	c : 0.03	d : 0.03	: : 0.01	a : 0.01	# : 0.01	b : 0.01	! : 0.01	" : 0.01	% : 0.01	
e : 0.29	f : 0.21	g : 0.20	d : 0.12	[ : 0.04	c : 0.03	= : 0.03	# : 0.01	b : 0.01	" : 0.01	% : 0.01	
e : 0.27	g : 0.18	f : 0.18	c : 0.12	d : 0.12	y : 0.03	[ : 0.03	= : 0.03	b : 0.01	
e : 0.24	f : 0.18	g : 0.15	d : 0.12	c : 0.09	y : 0.07	w : 0.04	b : 0.03	= : 0.03	[ : 0.01	
e : 0.18	v : 0.15	d : 0.12	f : 0.12	c : 0.09	y : 0.07	g : 0.07	w : 0.07	b : 0.06	a : 0.01	= : 0.01	
v : 0.29	u : 0.26	w : 0.12	y : 0.09	t : 0.09	g : 0.04	f : 0.03	b : 0.03	d : 0.01	e : 0.01	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.23	w : 0.12	y : 0.09	
v : 0.29	u : 0.26	t : 0.13	w : 0.12	y : 0.09	b : 0.03	d : 0.03	f : 0.01	e : 0.01	
g : 0.18	e : 0.13	v : 0.13	f : 0.12	d : 0.10	y : 0.09	w : 0.07	c : 0.06	b : 0.06	= : 0.01	
e : 0.21	f : 0.20	g : 0.18	d : 0.10	c : 0.10	y : 0.06	w : 0.04	] : 0.03	b : 0.03	= : 0.01	
e : 0.27	f : 0.20	g : 0.18	d : 0.13	c : 0.12	a : 0.01	b : 0.01	] : 0.01	= : 0.01	y : 0.01	
e : 0.27	f : 0.21	g : 0.18	d : 0.12	c : 0.06	] : 0.06	4 : 0.03	b : 0.01	= : 0.01	y : 0.01	
e : 0.30	f : 0.23	g : 0.18	] : 0.10	d : 0.06	= : 0.04	c : 0.03	4 : 0.03	
g : 0.21	f : 0.21	e : 0.18	d : 0.07	= : 0.06	b : 0.04	c : 0.03	] : 0.03	4 : 0.03	h : 0.01	F : 0.01	a : 0.01	3 : 0.01	B : 0.01	i : 0.01	E : 0.01	
g : 0.23	f : 0.12	e : 0.12	d : 0.06	= : 0.06	2 : 0.06	c : 0.04	: : 0.04	b : 0.04	3 : 0.04	4 : 0.03	h : 0.01	F : 0.01	] : 0.01	5 : 0.01	B : 0.01	i : 0.01	6 : 0.01	E : 0.01	

#score	1498.9903923742686
#seq	65
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_CDS_m2_run2.txt

#BEAR
bb"""ccc[ffffff[bboooooobb333ffffff22	chr12:53848518-53848748(+)$1	230	45	82	10.8292
hhhhhh[gggggggddddnnnnndddd4444gggggg	chr4:20621930-20622180(+)$1	250	23	60	13.2929
!ccc!!ccciiiiiiiiiooooooiiiiiiiii22cc	chr1:16255782-16256028(+)$1	246	163	200	13.0365
=======[ccc####ddddmmmmdddd22ccc=====	chr1:204375180-204375417(-)$1	237	105	142	14.6400
##ccc$$$$$eeeeecccnnnnnccc22eeeee4444	chr1:113231618-113231856(+)$1	238	33	70	11.5172
ggggggg####gggggggooooooggggggggggggg	chr5:133292429-133292673(-)$1	244	23	60	12.7071
ffffffdddd$$$$$ddddmmmmdddd4444dddd]f	chr13:25670763-25671001(+)$1	238	148	185	11.7077
hhhhhh"""ccc"""cccooooooccc4444ccc>>>	chr6:111621215-111621445(-)$1	230	15	52	15.7666
fff!!bbdddd####cccmmmmccc4444dddd4444	chr2:48033601-48033847(+)$1	246	103	140	12.4623
iiiiiiiiidddd!!bbmmmmbbdddd22iiiiiiii	chr1:115269495-115269731(-)$1	236	132	169	10.6663
Fdddd!!bb[ccc[ddddoooooodddd333ccc]bb	chrX:53561399-53561635(-)$1	236	187	224	13.3597
:iiiiiiiii!!bb[cccmmmmcccbb22iiiiiiii	chr9:19376152-19376396(-)$1	244	153	190	11.7747
=========="""eeeee[a[acccccclllccc]cc	chr1:115280525-115280752(-)$1	227	144	181	9.7839
ddd[bb"""eeeeeddddnnnnndddd]eeeee]bb]	chr1:243827980-243828220(-)$1	240	98	135	10.8523
dd[bb!!bb!!a[eeeeemmmmeeeee]a22bb333b	chr17:45757867-45758131(+)$1	264	22	59	10.3094
::ggggggg[ccc[ddddmmmmdddd4444ccc]ggg	chr5:167988314-167988589(-)$1	275	0	37	11.6933
ggg:bb!!iiiiiiiii[ammmma]iiiiiiiii22b	chrX:84525986-84526211(+)$1	225	133	170	10.3892
===========^^^^^^^^^^^^^^^^^^========	chr5:61645791-61646036(-)$1	245	65	102	9.7782
gggeeeeeeeeee!!cccmmmmccc4444eeeee333	chr8:29921239-29921462(-)$1	223	66	103	12.4694
dd[ccc####ccc!!ddddmmmmdddd]ccc4444cc	chr1:113456670-113456906(-)$1	236	5	42	12.9202
dddd[eeeee$$$$$cccooooooccc666666eeee	chr12:53776648-53776893(+)$1	245	169	206	10.9787
====eeeeebb[eeeeeddddllldddd333eeeeeb	chr15:75212527-75212768(-)$1	241	83	120	9.5014
f[ccc####bb[ccccccooooooccc55555ccc]b	chr22:39918010-39918233(+)$1	223	109	146	11.9288
:hhhhhhhh[a####cccnnnnnccc4444a]hhhhh	chr1:24294040-24294285(-)$1	245	101	138	12.3988
""bb[ggggggg"""cccnnnnnccc333ggggggg]	chr1:244217765-244217998(+)$1	233	7	44	14.5644
$$$$$ffffff"""ddddoooooodddd22ffffff3	chr3:56673965-56674194(-)$1	229	115	152	12.1661
c!!bb"""eeeee"""bbnnnnnbb333eeeee333b	chr6:56513267-56513515(-)$1	248	159	196	11.9650
""eeeee!!gggggggooooooggggggg]eeeee]e	chr4:122737900-122738140(-)$1	240	7	44	10.1374
ddd22cccccc[cccddddnnnnndddd22ccc]ccc	chr17:76220614-76220825(+)$1	211	105	142	10.5407
hhhhhhhh####a[ddddmmmmdddd]a333hhhhhh	chr3:149682868-149683101(-)$1	233	119	156	11.2726
eee[ccc!!ddddddddoooooodddd4444dddd22	chr1:16260532-16260752(+)$1	220	62	99	13.1634
:==========####cccnnnnnccc55555======	chr1:113232572-113232820(+)$1	248	203	240	12.9808
!iiiiiiiii$$$$$ddddmmmmdddd]iiiiiiiii	chr10:119042721-119042955(-)$1	234	3	40	13.5361
&&a[dddd!!dddd[cccooooooccc]dddd]dddd	chr7:128412479-128412737(+)$1	258	96	133	10.4066
dddeeeee[ddddddddoooooodddd4444ddddee	chr15:41961733-41961961(+)$1	228	187	224	12.0451
cc[ccc[eeeee"""cccmmmmccceeeeecccccce	chr2:44547605-44547830(-)$1	225	86	123	11.4791
%%%%iiiiiiiii!!cccnnnnnccc22iiiiiiiii	chr1:113231532-113231752(+)$1	220	76	113	11.7365
:ccc"""ffffff!!cccoooooocccffffff]ccc	chr14:103986509-103986751(-)$1	242	132	169	11.8788
e!!iiiiiiiiibbddddoooooodddd]bb]iiiii	chr5:162866393-162866622(+)$1	229	13	50	13.1506
fffff[bb"""ccc[cccnnnnnccc4444ccc333b	chr21:34924837-34925063(+)$1	226	133	170	14.2027
==========$$$$$cccnnnnnccc4444=======	chr17:40010436-40010681(-)$1	245	65	102	16.1553
eeeeedddd####eeeeemmmmeeeee333dddd333	chr3:133306639-133306898(+)$1	259	147	184	11.1836
gggggg"""bb####cccooooooccc4444bb333g	chr15:32916491-32916717(+)$1	226	31	68	17.1838
gg"""ccc[ccc!!ddddoooooodddd22ccc]ccc	chr12:69995044-69995285(+)$1	241	86	123	14.5593
fffff####eeeee!!ddddllldddd22eeeee444	chr4:83347644-83347869(-)$1	225	124	161	11.4255
##eeeee"""dddd[cccooooooccc]dddd4444e	chr1:113232001-113232220(+)$1	219	149	186	12.9945
!ccc!!ccciiiiiiiiiooooooiiiiiiiii22cc	chr1:16255832-16256071(+)$1	239	113	150	13.0365
eeeee!!ccca"""eeeeemmmmeeeee333a]ccc2	chr16:88495610-88495831(-)$1	221	47	84	11.7911
=====####ccc!!a[cccnnnnnccc]a22ccc666	chr2:61483906-61484157(-)$1	251	87	124	12.6360
bb[bb!!ffffff!!ddddllldddd333ffffff]b	chrX:84525892-84526133(+)$1	241	108	145	11.6950
f!!ffffffbb$$$$$cccnnnnnccc4444bb]fff	chr10:7844165-7844424(+)$1	259	144	181	11.6576
ccc:bb[===========oooooo===========]b	chr9:131456794-131457034(+)$1	240	106	143	13.1430
hhhhhbb[dddd"""ddddmmmmdddd4444dddd]b	chr1:46654253-46654494(-)$1	241	74	111	12.3776

#otherMatches

#Seq PSSM
CUCCCCAGAACACUGCUCGACAUGGACACCGGUGUGA	chr12:53848518-53848748(+)$1	230	45	82	10.8292
UUGCUGCUAAAUUACAAUGUAGAAUUGAUAAUGGUUU	chr4:20621930-20622180(+)$1	250	23	60	13.2929
AGUAUUUCUGUUGGGUCUGGCUCAAGGCCCAGCUCAG	chr1:16255782-16256028(+)$1	246	163	200	13.0365
GGAUAUUGCUUGACAUUUGAACACAGAGAAAGAAUGU	chr1:204375180-204375417(-)$1	237	105	142	14.6400
GACUCGACCGCUGGGCCGACGUGCGGUUCCCAGAAAA	chr1:113231618-113231856(+)$1	238	33	70	11.5172
GUGAUGGCCUUUGUUCCAAAACAGUGGAAUACCAUCG	chr5:133292429-133292673(-)$1	244	23	60	12.7071
UGUUUACAUCAAGAAUUUUGGAGAAGACAUGGAUGAU	chr13:25670763-25671001(+)$1	238	148	185	11.7077
UAAAAAUUUGUUGUUUGCAUACACGCAUAAAAACUUU	chr6:111621215-111621445(-)$1	230	15	52	15.7666
GCUAAUCUCCCAGAGGAAGUUAUUCAAAAGGGACAUA	chr2:48033601-48033847(+)$1	246	103	140	12.4623
GAUAAUUCUGCUCAUUCGAGAGAGGGUUAAGAGUUGU	chr1:115269495-115269731(-)$1	236	132	169	10.6663
AUGGUCCUCUUACCCUAGGCAACGCUAGUUUGUGUGA	chrX:53561399-53561635(-)$1	236	187	224	13.3597
ACUUUUCAUUGCUGAUAGAAAACUACAUAAAUGAAGA	chr9:19376152-19376396(-)$1	244	153	190	11.7747
CCCUGAAGAACGAAUGAAUGGACAAGUUAGUGACUUU	chr1:115280525-115280752(-)$1	227	144	181	9.7839
GGACUACUGUUAUAGAGAGAACAUUUCAUGUAGAUAC	chr1:243827980-243828220(-)$1	240	98	135	10.8523
UUUGGGAAGGAUGUACUGAAAUUAGUAGAAGCUAGGC	chr17:45757867-45758131(+)$1	264	22	59	10.3094
AUAUCUGUUAAUACGUAAAAUGUUGCUUUUUAUCAGC	chr5:167988314-167988589(-)$1	275	0	37	11.6933
GAGAACCCAUACUGGUGAGAAGCCAUAUCAGUGUCAG	chrX:84525986-84526211(+)$1	225	133	170	10.3892
UUAAGAGAUAAAUUUUUACUUUACCUCUAUUAUCUCU	chr5:61645791-61646036(-)$1	245	65	102	9.7782
AGUUGGAGUCAAACACUGGAUGCAGAAAUUUUGGAUU	chr8:29921239-29921462(-)$1	223	66	103	12.4694
GACUCUUUAAAGAUUGGAUUGACAUCUUUCUGAAUGG	chr1:113456670-113456906(-)$1	236	5	42	12.9202
CAGGGGUCUGAUGCUCUGAACAUCCAGCAAAACCAGA	chr12:53776648-53776893(+)$1	245	169	206	10.9787
CUUUAUUGAGUACCAAGCCAUGUAAUGGUAACUUGGA	chr15:75212527-75212768(-)$1	241	83	120	9.5014
AAGGAGAUAGGAAGCCAGACUACACUGCUUACGUUGC	chr22:39918010-39918233(+)$1	223	109	146	11.9288
guucugcuuacuacacuucaagaaagaucugaaagcg	chr1:24294040-24294285(-)$1	245	101	138	12.3988
CAGAGGUCUGUCACCUCCGUGAGGGAUUCGGCAGAUG	chr1:244217765-244217998(+)$1	233	7	44	14.5644
GACAACAGUCUAAGUCAAAUAAUGUUGAAGAGACUGA	chr3:56673965-56674194(-)$1	229	115	152	12.1661
UGUAGAAAUUACAUAGGAUUGAUUCAAUUGUAAACCC	chr6:56513267-56513515(-)$1	248	159	196	11.9650
AACUAUUUUUAAAAUCCUGCUAGAUUUUAUAAUGGAU	chr4:122737900-122738140(-)$1	240	7	44	10.1374
CUGGAAACCUCUGGAGGUCAUCUCGGCUGUUCCUGAG	chr17:76220614-76220825(+)$1	211	105	142	10.5407
GUUAAAAUGAACUGUUGCUAUUGUGAGAUGGAUUUUA	chr3:149682868-149683101(-)$1	233	119	156	11.2726
UGUUAUUAGCCGGAUGCCUGUCAGCAUUGACCUGGAA	chr1:16260532-16260752(+)$1	220	62	99	13.1634
CAGGGCUUUGGGAAGAGCACAGAGCUGGGAGCCAGAG	chr1:113232572-113232820(+)$1	248	203	240	12.9808
AUUGAAGAUAUAGAAACUUUAGAAAGUCUGUCUUUAG	chr10:119042721-119042955(-)$1	234	3	40	13.5361
CAGGCCAAUAUUGGGUCCUCAGUUGGGGCCAACUUGG	chr7:128412479-128412737(+)$1	258	96	133	10.4066
UCUGACCAAGAAGGGAAUAAUAUUUCCAGUUCUUCUG	chr15:41961733-41961961(+)$1	228	187	224	12.0451
GAAUAGCAUGCUCGAUUGGAAACAAAGCAUCUAUCUC	chr2:44547605-44547830(-)$1	225	86	123	11.4791
GCAAAUCUGGCCUACGUCACCAAGACUCGGGUCAGGU	chr1:113231532-113231752(+)$1	220	76	113	11.7365
UGAGUUCAUGUGGAACCCUCACCUGGGCUACAUCCUC	chr14:103986509-103986751(-)$1	242	132	169	11.8788
GCAAGACUAAGGGACUUUGAAGUAAAAGAUCUUCUUA	chr5:162866393-162866622(+)$1	229	13	50	13.1506
UGGUGCCACCUUUGCCUCCUGAAGAGCCCCCAACAAU	chr21:34924837-34925063(+)$1	226	133	170	14.2027
CCGGUUUGUAUACAUUGCCGCCCGCACUCCUGUAGAC	chr17:40010436-40010681(-)$1	245	65	102	16.1553
GAGGUAGGGAUGAGGUUUCAAAAAACCAGGCCCUUAA	chr3:133306639-133306898(+)$1	259	147	184	11.1836
AGAGGAAAAGAAUAAAGCUACACUGUUGCUCUCCUGU	chr15:32916491-32916717(+)$1	226	31	68	17.1838
GGACCAGUUUCUAGCAAAGUUGUGUUUGAAAGAUACU	chr12:69995044-69995285(+)$1	241	86	123	14.5593
GAUCAAGGAUAUGGAAAUUACAAUAGUGCCUAUGGUG	chr4:83347644-83347869(-)$1	225	124	161	11.4255
CCUGAGGCUUCGGAAUGGCGGAACCCAGUCUGUUACC	chr1:113232001-113232220(+)$1	219	149	186	12.9945
AGUAUUUCUGUUGGGUCUGGCUCAAGGCCCAGCUCAG	chr1:16255832-16256071(+)$1	239	113	150	13.0365
GGAAGAAGGCCGAGGGCCCGAGGGGGCCGGGGAGCUG	chr16:88495610-88495831(-)$1	221	47	84	11.7911
AGUCAAACUGCUGAAGAGUUUUAUACUGUGAGGUGCC	chr2:61483906-61484157(-)$1	251	87	124	12.6360
ACUGCAGAACAAGGACUGUUAAACAGGCAUUUGUUGG	chrX:84525892-84526133(+)$1	241	108	145	11.6950
UACUACUCUCUGAAGGAGUCCACCACUAGUGAGCAGA	chr10:7844165-7844424(+)$1	259	144	181	11.6576
UGCCCACUUUUUCUUUCAGGAGGAUGAAGGAGAAGAU	chr9:131456794-131457034(+)$1	240	106	143	13.1430
CUCUUUGUCCAGAUUUCCAAAGCUGGAUAAGUUGGUC	chr1:46654253-46654494(-)$1	241	74	111	12.3776

#DB
((...(((.((((((.((......))...))))))..	chr12:53848518-53848748(+)$1	1	45	82	10.8292
((((((.(((((((((((.....))))....))))))	chr4:20621930-20622180(+)$1	1	23	60	13.2929
.(((..((((((((((((......)))))))))..))	chr1:16255782-16256028(+)$1	1	163	200	13.0365
(((((((.(((....((((....))))..))))))))	chr1:204375180-204375417(-)$1	1	105	142	14.6400
..(((.....((((((((.....)))..)))))....	chr1:113231618-113231856(+)$1	1	33	70	11.5172
(((((((....(((((((......)))))))))))))	chr5:133292429-133292673(-)$1	1	23	60	12.7071
((((((((((.....((((....))))....)))).)	chr13:25670763-25671001(+)$1	1	148	185	11.7077
((((((...(((...(((......)))....)))...	chr6:111621215-111621445(-)$1	1	15	52	15.7666
(((..((((((....(((....)))....))))....	chr2:48033601-48033847(+)$1	1	103	140	12.4623
(((((((((((((..((....))))))..))))))))	chr1:115269495-115269731(-)$1	1	132	169	10.6663
)((((..((.(((.((((......))))...))).))	chrX:53561399-53561635(-)$1	1	187	224	13.3597
.(((((((((..((.(((....)))))..))))))))	chr9:19376152-19376396(-)$1	1	153	190	11.7747
((((((((((...(((((.(.(((((((...))).))	chr1:115280525-115280752(-)$1	1	144	181	9.7839
(((.((...(((((((((.....)))).))))).)).	chr1:243827980-243828220(-)$1	1	98	135	10.8523
((.((..((..(.(((((....))))).)..))...)	chr17:45757867-45758131(+)$1	1	22	59	10.3094
..(((((((.(((.((((....))))....))).)))	chr5:167988314-167988589(-)$1	1	0	37	11.6933
))).((..(((((((((.(....).)))))))))..)	chrX:84525986-84526211(+)$1	1	133	170	10.3892
(((((((((((..................))))))))	chr5:61645791-61646036(-)$1	1	65	102	9.7782
(((((((((((((..(((....)))....)))))...	chr8:29921239-29921462(-)$1	1	66	103	12.4694
((.(((....(((..((((....)))).)))....))	chr1:113456670-113456906(-)$1	1	5	42	12.9202
((((.(((((.....(((......)))......))))	chr12:53776648-53776893(+)$1	1	169	206	10.9787
(((((((((((.(((((((((...))))...))))))	chr15:75212527-75212768(-)$1	1	83	120	9.5014
(.(((....((.((((((......))).....))).)	chr22:39918010-39918233(+)$1	1	109	146	11.9288
.((((((((.(....(((.....)))....).)))))	chr1:24294040-24294285(-)$1	1	101	138	12.3988
..((.(((((((...(((.....)))...))))))).	chr1:244217765-244217998(+)$1	1	7	44	14.5644
.....((((((...((((......))))..)))))).	chr3:56673965-56674194(-)$1	1	115	152	12.1661
(..((...(((((...((.....))...)))))...)	chr6:56513267-56513515(-)$1	1	159	196	11.9650
..(((((..(((((((......))))))).))))).)	chr4:122737900-122738140(-)$1	1	7	44	10.1374
)))..)))(((.(((((((.....))))..))).)))	chr17:76220614-76220825(+)$1	1	105	142	10.5407
((((((((....(.((((....)))).)...))))))	chr3:149682868-149683101(-)$1	1	119	156	11.2726
(((.(((..((((((((......))))....))))..	chr1:16260532-16260752(+)$1	1	62	99	13.1634
.((((((((((....(((.....))).....))))))	chr1:113232572-113232820(+)$1	1	203	240	12.9808
.(((((((((.....((((....)))).)))))))))	chr10:119042721-119042955(-)$1	1	3	40	13.5361
..(.((((..((((.(((......))).)))).))))	chr7:128412479-128412737(+)$1	1	96	133	10.4066
)))(((((.((((((((......))))....))))))	chr15:41961733-41961961(+)$1	1	187	224	12.0451
((.(((.(((((...(((....)))))))))))))))	chr2:44547605-44547830(-)$1	1	86	123	11.4791
....(((((((((..(((.....)))..)))))))))	chr1:113231532-113231752(+)$1	1	76	113	11.7365
.(((...((((((..(((......))))))))).)))	chr14:103986509-103986751(-)$1	1	132	169	11.8788
(..(((((((((((((((......)))).)).)))))	chr5:162866393-162866622(+)$1	1	13	50	13.1506
(((((.((...(((.(((.....)))....)))...)	chr21:34924837-34925063(+)$1	1	133	170	14.2027
((((((((((.....(((.....)))....)))))))	chr17:40010436-40010681(-)$1	1	65	102	16.1553
(((((((((....(((((....)))))...))))...	chr3:133306639-133306898(+)$1	1	147	184	11.1836
((((((...((....(((......)))....))...)	chr15:32916491-32916717(+)$1	1	31	68	17.1838
((...(((.(((..((((......))))..))).)))	chr12:69995044-69995285(+)$1	1	86	123	14.5593
(((((....(((((..((((...))))..)))))...	chr4:83347644-83347869(-)$1	1	124	161	11.4255
..(((((...((((.(((......))).))))....)	chr1:113232001-113232220(+)$1	1	149	186	12.9945
.(((..((((((((((((......)))))))))..))	chr1:16255832-16256071(+)$1	1	113	150	13.0365
(((((..((((...(((((....)))))...).))).	chr16:88495610-88495831(-)$1	1	47	84	11.7911
(((((....(((..(.(((.....))).)..)))...	chr2:61483906-61484157(-)$1	1	87	124	12.6360
((.((..((((((..((((...))))...)))))).)	chrX:84525892-84526133(+)$1	1	108	145	11.6950
(..((((((((.....(((.....)))....)).)))	chr10:7844165-7844424(+)$1	1	144	181	11.6576
))).((.(((((((((((......))))))))))).)	chr9:131456794-131457034(+)$1	1	106	143	13.1430
(((((((.((((...((((....))))....)))).)	chr1:46654253-46654494(-)$1	1	74	111	12.3776

#PSSM
= : 0.11	f : 0.11	d : 0.11	g : 0.09	: : 0.09	h : 0.07	e : 0.07	! : 0.05	c : 0.05	b : 0.03	# : 0.03	" : 0.03	i : 0.01	F : 0.01	$ : 0.01	& : 0.01	% : 0.01	
= : 0.13	d : 0.13	h : 0.09	c : 0.09	g : 0.09	f : 0.07	i : 0.05	! : 0.05	e : 0.05	b : 0.03	# : 0.03	" : 0.03	: : 0.01	[ : 0.01	$ : 0.01	& : 0.01	% : 0.01	
= : 0.13	c : 0.11	h : 0.09	g : 0.09	d : 0.09	e : 0.09	f : 0.07	[ : 0.07	i : 0.05	! : 0.05	" : 0.03	b : 0.01	$ : 0.01	a : 0.01	% : 0.01	
c : 0.13	= : 0.13	e : 0.11	h : 0.09	f : 0.07	i : 0.07	b : 0.07	g : 0.05	[ : 0.05	" : 0.03	d : 0.03	: : 0.03	! : 0.01	$ : 0.01	2 : 0.01	% : 0.01	
e : 0.13	= : 0.11	b : 0.11	h : 0.09	c : 0.09	i : 0.09	f : 0.07	" : 0.05	! : 0.05	g : 0.05	d : 0.03	[ : 0.03	$ : 0.01	2 : 0.01	
c : 0.11	! : 0.11	e : 0.11	= : 0.09	b : 0.09	i : 0.09	h : 0.07	g : 0.07	f : 0.05	# : 0.05	" : 0.03	d : 0.03	$ : 0.01	[ : 0.01	
c : 0.11	e : 0.11	= : 0.09	" : 0.09	i : 0.09	! : 0.09	# : 0.07	[ : 0.05	g : 0.05	d : 0.05	b : 0.05	h : 0.03	f : 0.03	$ : 0.01	
c : 0.11	# : 0.09	" : 0.09	i : 0.09	= : 0.09	e : 0.09	d : 0.07	f : 0.07	g : 0.05	b : 0.05	! : 0.05	[ : 0.03	h : 0.03	$ : 0.01	
# : 0.11	i : 0.11	c : 0.09	" : 0.09	= : 0.09	e : 0.09	d : 0.07	f : 0.07	[ : 0.05	g : 0.05	! : 0.05	b : 0.03	$ : 0.01	h : 0.01	
i : 0.13	c : 0.11	d : 0.11	e : 0.11	= : 0.09	f : 0.07	# : 0.07	b : 0.07	g : 0.05	[ : 0.05	! : 0.03	" : 0.03	$ : 0.01	
c : 0.15	d : 0.13	e : 0.11	i : 0.09	f : 0.07	$ : 0.07	b : 0.07	g : 0.05	# : 0.05	= : 0.05	! : 0.03	" : 0.03	a : 0.03	
# : 0.13	c : 0.13	e : 0.11	d : 0.11	i : 0.09	$ : 0.09	g : 0.07	f : 0.05	" : 0.05	[ : 0.05	! : 0.01	a : 0.01	^ : 0.01	= : 0.01	
" : 0.13	# : 0.11	e : 0.11	c : 0.11	$ : 0.09	d : 0.09	i : 0.07	f : 0.05	g : 0.05	b : 0.03	! : 0.03	[ : 0.01	^ : 0.01	a : 0.01	= : 0.01	
! : 0.15	e : 0.13	" : 0.13	# : 0.09	$ : 0.09	d : 0.07	g : 0.05	i : 0.05	[ : 0.05	c : 0.05	b : 0.03	f : 0.01	^ : 0.01	= : 0.01	
d : 0.18	! : 0.13	e : 0.11	# : 0.09	$ : 0.09	" : 0.09	[ : 0.07	i : 0.05	g : 0.03	c : 0.03	f : 0.01	^ : 0.01	a : 0.01	= : 0.01	
c : 0.33	d : 0.32	e : 0.09	i : 0.05	[ : 0.03	g : 0.03	b : 0.01	^ : 0.01	" : 0.01	! : 0.01	$ : 0.01	= : 0.01	
c : 0.37	d : 0.33	e : 0.09	b : 0.05	i : 0.05	g : 0.01	^ : 0.01	o : 0.01	= : 0.01	
c : 0.37	d : 0.32	e : 0.07	o : 0.05	b : 0.03	i : 0.03	g : 0.01	m : 0.01	[ : 0.01	^ : 0.01	= : 0.01	
o : 0.35	n : 0.18	d : 0.16	m : 0.16	c : 0.03	[ : 0.01	a : 0.01	^ : 0.01	e : 0.01	
o : 0.35	m : 0.30	n : 0.24	d : 0.03	a : 0.01	^ : 0.01	l : 0.01	
o : 0.35	m : 0.30	n : 0.24	l : 0.03	[ : 0.01	^ : 0.01	d : 0.01	
o : 0.35	m : 0.28	n : 0.24	l : 0.05	b : 0.01	a : 0.01	^ : 0.01	
o : 0.33	n : 0.24	m : 0.13	c : 0.09	d : 0.05	e : 0.03	l : 0.03	b : 0.01	^ : 0.01	g : 0.01	
o : 0.30	d : 0.26	c : 0.22	e : 0.05	n : 0.05	a : 0.01	^ : 0.01	l : 0.01	b : 0.01	g : 0.01	
c : 0.39	d : 0.37	e : 0.05	b : 0.03	i : 0.03	g : 0.03	] : 0.01	^ : 0.01	= : 0.01	
d : 0.37	c : 0.32	e : 0.07	i : 0.05	b : 0.03	g : 0.03	4 : 0.03	^ : 0.01	3 : 0.01	= : 0.01	
d : 0.32	c : 0.18	4 : 0.11	3 : 0.07	e : 0.07	i : 0.05	2 : 0.03	g : 0.03	b : 0.01	^ : 0.01	] : 0.01	5 : 0.01	= : 0.01	
4 : 0.26	] : 0.13	2 : 0.11	d : 0.11	3 : 0.09	i : 0.05	g : 0.03	5 : 0.03	e : 0.03	c : 0.01	^ : 0.01	6 : 0.01	a : 0.01	f : 0.01	= : 0.01	
4 : 0.26	3 : 0.15	2 : 0.13	i : 0.09	e : 0.07	g : 0.03	a : 0.03	5 : 0.03	d : 0.03	l : 0.01	^ : 0.01	c : 0.01	6 : 0.01	f : 0.01	] : 0.01	= : 0.01	
4 : 0.22	i : 0.13	e : 0.11	3 : 0.09	2 : 0.09	f : 0.05	d : 0.05	c : 0.03	g : 0.03	= : 0.03	5 : 0.03	l : 0.01	6 : 0.01	] : 0.01	b : 0.01	
4 : 0.15	i : 0.13	c : 0.13	e : 0.11	f : 0.07	d : 0.07	3 : 0.07	= : 0.05	g : 0.03	2 : 0.03	5 : 0.03	l : 0.01	6 : 0.01	a : 0.01	b : 0.01	
c : 0.18	d : 0.15	i : 0.13	e : 0.13	f : 0.07	= : 0.07	g : 0.05	b : 0.05	] : 0.03	4 : 0.01	6 : 0.01	5 : 0.01	h : 0.01	a : 0.01	
c : 0.18	i : 0.15	e : 0.13	d : 0.11	= : 0.09	f : 0.07	g : 0.05	b : 0.05	4 : 0.03	h : 0.03	] : 0.03	6 : 0.01	
c : 0.13	d : 0.11	i : 0.11	] : 0.11	= : 0.09	e : 0.09	4 : 0.07	3 : 0.07	f : 0.05	g : 0.05	2 : 0.03	h : 0.03	
3 : 0.11	c : 0.11	= : 0.09	4 : 0.09	d : 0.09	i : 0.09	f : 0.07	g : 0.07	2 : 0.05	e : 0.05	] : 0.03	h : 0.03	> : 0.01	b : 0.01	6 : 0.01	
c : 0.16	] : 0.11	3 : 0.11	i : 0.09	g : 0.07	= : 0.07	4 : 0.07	2 : 0.05	e : 0.05	b : 0.03	h : 0.03	f : 0.03	> : 0.01	d : 0.01	6 : 0.01	
b : 0.18	c : 0.13	i : 0.09	e : 0.09	g : 0.07	= : 0.07	2 : 0.05	4 : 0.05	3 : 0.05	f : 0.03	] : 0.03	h : 0.03	> : 0.01	d : 0.01	6 : 0.01	

#score	649.8311399166789
#seq	53
#width	37
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_CDS_m2_run2.txt

#BEAR
eee!!dddd[aooooooadddd22eeee	chr11:62156509-62156728(+)$1	219	35	63	9.5660
ggg[ccc[cccooooooccccccggggg	chr12:49398216-49398444(-)$1	228	127	155	13.6014
b[ccc[ccc[aooooooa]ccc]ccc]b	chr8:27685583-27685808(-)$1	225	122	150	11.8161
gggggg!!cccnnnnnccc333gggggg	chr4:26422085-26422317(+)$1	232	125	153	13.1197
f[eeeee!!bboooooobb333eeeee]	chr14:32560333-32560568(+)$1	235	153	181	12.4531
fff[ccc!!aqqqqqqqqa22ccc]fff	chr19:38125771-38126000(-)$1	229	136	164	8.5256
cc!!bb[ddddoooooodddd]bb22cc	chr10:38407622-38407845(+)$1	223	3	31	9.7945
cc[cccacccooooooccc22a]ccc]c	chr17:1584133-1584371(-)$1	238	132	160	12.5747
"ccc[ffffffooooooffffff22ccc	chr8:21857037-21857269(+)$1	232	130	158	9.9472
ddddddd!!cccmmmmccc333dddd33	chr14:61442493-61442728(-)$1	235	65	93	9.2621
fffff####bbnnnnnbb4444ffffff	chr12:120534657-120534878(-)$1	221	36	64	9.3864
gggggg!!ddddnnnnndddd]gggggg	chr14:75520044-75520266(-)$1	222	59	87	9.8888
=========rrrrrrrrr==========	chr14:101350950-101351175(+)$1	225	116	144	10.6316
c[gggggggcccnnnnnccc]ggggggg	chr7:155094393-155094625(+)$1	232	21	49	11.3849
ii!!gggggggooooooggggggg4444	chr5:36183943-36184165(+)$1	222	150	178	12.0892
####ccc[a[ccclllccc]a]ccc444	chr8:25364803-25365036(+)$1	233	135	163	10.3720
b!!ccc[ddddoooooodddd]ccc22b	chr19:37210742-37210962(+)$1	220	124	152	10.4588
ffff!!eeeeeooooooeeeeeffffff	chrX:123019842-123020063(+)$1	221	31	59	9.2977
ggggggg!!ccclllccc333ggggggg	chr19:3980554-3980782(-)$1	228	18	46	12.3323
gggggg!!ddddllldddd333gggggg	chr6:18226306-18226530(-)$1	224	53	81	10.8946
g####ccc!!bbnnnnnbb22ccc4444	chr12:104341332-104341559(+)$1	227	178	206	10.1482
fff!!cccrrrrrrrrrccc22ffffff	chr3:56660975-56661204(-)$1	229	57	85	9.2199
hhhh$$$$$bboooooobb22hhhhhhh	chr16:23646844-23647065(-)$1	221	68	96	10.4605
ccc[ccc[cccooooooccc]ccc22cc	chr19:21992389-21992616(-)$1	227	165	193	13.0750
h"""bb!!cccooooooccc22bbhhhh	chr7:135612228-135612460(-)$1	232	194	222	12.0437
==========rrrrrrrrr=========	chr14:95592845-95593072(-)$1	227	66	94	10.6306
:ffffff[cccooooooccc]ffffff:	chr17:7319241-7319467(+)$1	226	131	159	10.2018
##ccc[ccc[bbnnnnnbb]ccc]ccc2	chr18:33689475-33689704(-)$1	229	30	58	9.3460
b[ccc"""ccclllcccccc]bb]cccb	chr4:184930616-184930838(+)$1	222	65	93	9.4843
ggggggccccccmmmmccc]ccc]gggg	chr2:55479527-55479755(-)$1	228	61	89	10.0958
ccggggggg"""bblllbb]ggggggg2	chr7:27211562-27211782(-)$1	220	177	205	8.6773
eeeeeffffffooooooffffff333ee	chr12:72289712-72289940(+)$1	228	81	109	9.6592
[a[bb####bboooooobb333bb]a]a	chrX:75397711-75397951(+)$1	240	184	212	12.6303
:ggggggg[bboooooobb22ggggggg	chr5:126171845-126172068(+)$1	223	14	42	12.4289
!!ffffff!!aooooooa333ffffff]	chr1:93312662-93312885(-)$1	223	38	66	12.6666
ddd[bb!!cccooooooccc22bbdddd	chr16:2303814-2304050(-)$1	236	165	193	11.4284
ggggccc[cccooooooccc]ccc]ggg	chr21:26957879-26958135(-)$1	256	132	160	13.8796
eeee####cccooooooccc333eeeee	chr19:37618917-37619139(+)$1	222	162	190	12.7645
ggggggg[ccclllccc4444ggggggg	chr17:27612909-27613142(-)$1	233	28	56	11.0184
ggggggg!!bboooooobb22ggggggg	chr13:43918720-43918940(-)$1	220	153	181	13.8893
iiiiiiiiirrrrrrrrriiiiiiiii:	chr3:139071465-139071696(+)$1	231	54	82	9.1716
[cccccc!!cccmmmmccc22ccc]ccc	chr2:113079283-113079504(+)$1	221	157	185	10.9148
##eeeeecccooooooccc22eeeee44	chr7:129832327-129832568(-)$1	241	50	78	11.4179
!eeeee"""cccmmmmccc22eeeee]e	chr16:820140-820363(+)$1	223	139	167	9.8145
$$iiiiiiiiiooooooiiiiiiiii55	chrX:38128765-38129003(-)$1	238	149	177	10.6489
:==========oooooo==========e	chr18:77737561-77737785(-)$1	224	65	93	12.1965
"""gggggggrrrrrrrrrggggggg]b	chr19:11548649-11548878(+)$1	229	48	76	9.6972
cdddd"""cccnnnnnccc333dddd33	chr1:85790371-85790605(-)$1	234	141	169	10.9740
hhhhhh####aooooooa333hhhhhhh	chr16:47733159-47733381(+)$1	222	145	173	11.9884
gggg[ccc[cccnnnnnccccccggggg	chr13:31232110-31232361(+)$1	251	157	185	10.9594
"eeeee!!cccnnnnnccc333eeeeed	chr17:34044133-34044358(+)$1	225	186	214	11.1475
ggggg[a[arrrrrrrrraa]ggggggg	chr5:118280172-118280404(-)$1	232	75	103	10.7426
======!!cccnnnnnccc22=======	chr1:243827980-243828203(-)$1	223	187	215	12.8980
eee:dddd!!aooooooa22ddddcccg	chr16:19518945-19519176(-)$1	231	129	157	9.4783
==!!ccc!!cccmmmmccc22ccc333=	chr3:41280725-41280946(+)$1	221	166	194	11.5704

#otherMatches

#Seq PSSM
UGGUUAUGGUGUUCAUUCUCAUUUUCAG	chr11:62156509-62156728(+)$1	219	35	63	9.5660
GCGCAUUCUGAAGUUCCUCAAAUUGUUU	chr12:49398216-49398444(-)$1	228	127	155	13.6014
CCGGCCUCUCCGUUUAUGCAGAAGCUUG	chr8:27685583-27685808(-)$1	225	122	150	11.8161
AGACAAGCGAAAGCACUUCAUGUUGUCU	chr4:26422085-26422317(+)$1	232	125	153	13.1197
CGUGGAUCAUUAUCUUAGAGAAGUUCAG	chr14:32560333-32560568(+)$1	235	153	181	12.4531
CCUUUGCGAAUUUUAUGUUGAGCAUAGG	chr19:38125771-38126000(-)$1	229	136	164	8.5256
CACACACAGGGGAGAAACCCUAUGAAUG	chr10:38407622-38407845(+)$1	223	3	31	9.7945
CAUGUCCACCUCACCUGGUAAGAGACCU	chr17:1584133-1584371(-)$1	238	132	160	12.5747
AAGGACUUACUGCACUUGGUAAGCACCU	chr8:21857037-21857269(+)$1	232	130	158	9.9472
CCAAUGAUCUCAAUCCUGAAUCUCAUAA	chr14:61442493-61442728(-)$1	235	65	93	9.2621
GUGCCCCCUCCUCCCCGGCCAAGGCGCC	chr12:120534657-120534878(-)$1	221	36	64	9.3864
CUUCAACAAUGAAAAAGUCAUCUUGAAG	chr14:75520044-75520266(-)$1	222	59	87	9.8888
GAUGAUGGAUUCUUAUGCUCCAUCAUCG	chr14:101350950-101351175(+)$1	225	116	144	10.6316
GUGAAAUUGACUGCUAAGGUACAGUUUC	chr7:155094393-155094625(+)$1	232	21	49	11.3849
GACUUGUUUUAAAACAAUAAAACACAUU	chr5:36183943-36184165(+)$1	222	150	178	12.0892
CAAAAGAAGAACAAUAUGUACAUUUGAC	chr8:25364803-25365036(+)$1	233	135	163	10.3720
CUCAUACAGGGGAAAAGCCCUAUAUUUG	chr19:37210742-37210962(+)$1	220	124	152	10.4588
UGGGAAGCAGAGAUCAUUUUGCCUUAGA	chrX:123019842-123020063(+)$1	221	31	59	9.2977
GUUCCAGAAGGCUGAGCUGCACUGGAAU	chr19:3980554-3980782(-)$1	228	18	46	12.3323
AUAGGUCUAUGAAAAUUAUCCUACUUAU	chr6:18226306-18226530(-)$1	224	53	81	10.8946
GACUUGUUUUGGAUGCCCCCUAAUCCCC	chr12:104341332-104341559(+)$1	227	178	206	10.1482
CUUGAGGAACUUAGUACUCCAGAAGGAA	chr3:56660975-56661204(-)$1	229	57	85	9.2199
GGCACAAGGCAAAAAAAUGACUGUCUCU	chr16:23646844-23647065(-)$1	221	68	96	10.4605
GGUUAUAAUGGAUUUAACCAAUGUUUGC	chr19:21992389-21992616(-)$1	227	165	193	13.0750
AAGUUUUGUUCUCCACUGAAGUAAUACU	chr7:135612228-135612460(-)$1	232	194	222	12.0437
AUGGAAUUAGAAGAAGCACUUAAUUUUA	chr14:95592845-95593072(-)$1	227	66	94	10.6306
CGUCAUGCUCAGUGCCGUGGUCAUGACC	chr17:7319241-7319467(+)$1	226	131	159	10.2018
AUGGAUGUAGCCGCUGGGGGUAUUUCUU	chr18:33689475-33689704(-)$1	229	30	58	9.3460
CUGUGCCAGGUGCCACCCACUGAAAAGA	chr4:184930616-184930838(+)$1	222	65	93	9.4843
AUUGUCGUAUUGGUUGUAGCUGCAGAUG	chr2:55479527-55479755(-)$1	228	61	89	10.0958
CUGGUUUCAGAACCGCAGGAUGAAACUG	chr7:27211562-27211782(-)$1	220	177	205	8.6773
ACAUUGAUUCUGAAGGAAGAAUUUUAAA	chr12:72289712-72289940(+)$1	228	81	109	9.6592
UGCUCUGGUCAUUCCCUUGUAUGAACUG	chrX:75397711-75397951(+)$1	240	184	212	12.6303
GAAUACUGUGAUCUAUUUCUUUAGUAUU	chr5:126171845-126172068(+)$1	223	14	42	12.4289
GAUUUUGGAACUGAAUUGGAACCAAGAA	chr1:93312662-93312885(-)$1	223	38	66	12.6666
CAGUAGGAAAGCAAACCCUUGACUCUGG	chr16:2303814-2304050(-)$1	236	165	193	11.4284
uaaauauguauaauaaaauaaauguuuu	chr21:26957879-26958135(-)$1	256	132	160	13.8796
GUGGAAAGAUGUUUAGUCAUGGCUCACA	chr19:37618917-37619139(+)$1	222	162	190	12.7645
CUUUGUUAGGCUCUGCCAAAGAACAGAG	chr17:27612909-27613142(-)$1	233	28	56	11.0184
AGUCGGCCAACAGCCACGUCCGCCGGCU	chr13:43918720-43918940(-)$1	220	153	181	13.8893
AACGUGGAAAAUAUGACCUUUUACGUUC	chr3:139071465-139071696(+)$1	231	54	82	9.1716
AAGUGAGUAAUAUUUUUGUACCUUGAUU	chr2:113079283-113079504(+)$1	221	157	185	10.9148
GAACUUUGGAUACUUUUCUCAGAAGUGA	chr7:129832327-129832568(-)$1	241	50	78	11.4179
ACAUCCAGGCUCUGCGGAGAGGGGUGGG	chr16:820140-820363(+)$1	223	139	167	9.8145
ACCAAGUGUAUUGUAAUGUAUACUUGAA	chrX:38128765-38129003(-)$1	238	149	177	10.6489
UUUUUUAAUCUCCUUUUAGGUUAAAAAU	chr18:77737561-77737785(-)$1	224	65	93	12.1965
CACGGCUGCCUGUCCUAAUGGCAGCUUC	chr19:11548649-11548878(+)$1	229	48	76	9.6972
UUGCUGCACCGAACCCCGGAAGAGUAUC	chr1:85790371-85790605(-)$1	234	141	169	10.9740
GACACAUGUUCUGAAGUGUGUUGUGUUU	chr16:47733159-47733381(+)$1	222	145	173	11.9884
CUGGUCUUAUACAGGGAGUGAAGUCAGU	chr13:31232110-31232361(+)$1	251	157	185	10.9594
UUGGAUUUUGGCCGAACUACGUAUCCAG	chr17:34044133-34044358(+)$1	225	186	214	11.1475
GUGUUUGUGUCCAUUUCUCCCAGCGCAC	chr5:118280172-118280404(-)$1	232	75	103	10.7426
UUUGUAUCUGACuuuauuauuuguaaau	chr1:243827980-243828203(-)$1	223	187	215	12.8980
AGUGUGGUCUGUUCUUUCUUGCCAGAAG	chr16:19518945-19519176(-)$1	231	129	157	9.4783
CCUACAGAACUUCAGAAAGACUUGGUUG	chr3:41280725-41280946(+)$1	221	166	194	11.5704

#DB
(((..((((.(......)))))..))))	chr11:62156509-62156728(+)$1	1	35	63	9.5660
(((.(((.(((......)))))))))))	chr12:49398216-49398444(-)$1	1	127	155	13.6014
(.(((.(((.(......).))).))).)	chr8:27685583-27685808(-)$1	1	122	150	11.8161
((((((..(((.....)))...))))))	chr4:26422085-26422317(+)$1	1	125	153	13.1197
(.(((((..((......))...))))).	chr14:32560333-32560568(+)$1	1	153	181	12.4531
(((.(((..(........)..))).)))	chr19:38125771-38126000(-)$1	1	136	164	8.5256
((..((.((((......)))).))..))	chr10:38407622-38407845(+)$1	1	3	31	9.7945
((.(((((((......)))..).))).)	chr17:1584133-1584371(-)$1	1	132	160	12.5747
.(((.((((((......))))))..)))	chr8:21857037-21857269(+)$1	1	130	158	9.9472
(((((((..(((....)))...))))..	chr14:61442493-61442728(-)$1	1	65	93	9.2621
(((((....((.....))....))))))	chr12:120534657-120534878(-)$1	1	36	64	9.3864
((((((..((((.....)))).))))))	chr14:75520044-75520266(-)$1	1	59	87	9.8888
(((((((((.........))))))))))	chr14:101350950-101351175(+)$1	1	116	144	10.6316
(.((((((((((.....))).)))))))	chr7:155094393-155094625(+)$1	1	21	49	11.3849
((..(((((((......)))))))....	chr5:36183943-36184165(+)$1	1	150	178	12.0892
....(((.(.(((...))).).)))...	chr8:25364803-25365036(+)$1	1	135	163	10.3720
(..(((.((((......)))).)))..)	chr19:37210742-37210962(+)$1	1	124	152	10.4588
((((..(((((......)))))))))))	chrX:123019842-123020063(+)$1	1	31	59	9.2977
(((((((..(((...)))...)))))))	chr19:3980554-3980782(-)$1	1	18	46	12.3323
((((((..((((...))))...))))))	chr6:18226306-18226530(-)$1	1	53	81	10.8946
(....(((..((.....))..)))....	chr12:104341332-104341559(+)$1	1	178	206	10.1482
(((..(((.........)))..))))))	chr3:56660975-56661204(-)$1	1	57	85	9.2199
((((.....((......))..)))))))	chr16:23646844-23647065(-)$1	1	68	96	10.4605
(((.(((.(((......))).)))..))	chr19:21992389-21992616(-)$1	1	165	193	13.0750
(...((..(((......)))..))))))	chr7:135612228-135612460(-)$1	1	194	222	12.0437
((((((((((.........)))))))))	chr14:95592845-95593072(-)$1	1	66	94	10.6306
.((((((.(((......))).)))))).	chr17:7319241-7319467(+)$1	1	131	159	10.2018
..(((.(((.((.....)).))).))).	chr18:33689475-33689704(-)$1	1	30	58	9.3460
(.(((...(((...)))))).)).)))(	chr4:184930616-184930838(+)$1	1	65	93	9.4843
((((((((((((....))).))).))))	chr2:55479527-55479755(-)$1	1	61	89	10.0958
(((((((((...((...)).))))))).	chr7:27211562-27211782(-)$1	1	177	205	8.6773
(((((((((((......))))))...))	chr12:72289712-72289940(+)$1	1	81	109	9.6592
.(.((....((......))...)).).)	chrX:75397711-75397951(+)$1	1	184	212	12.6303
.(((((((.((......))..)))))))	chr5:126171845-126172068(+)$1	1	14	42	12.4289
..((((((..(......)...)))))).	chr1:93312662-93312885(-)$1	1	38	66	12.6666
(((.((..(((......)))..))))))	chr16:2303814-2304050(-)$1	1	165	193	11.4284
(((((((.(((......))).))).)))	chr21:26957879-26958135(-)$1	1	132	160	13.8796
((((....(((......)))...)))))	chr19:37618917-37619139(+)$1	1	162	190	12.7645
(((((((.(((...)))....)))))))	chr17:27612909-27613142(-)$1	1	28	56	11.0184
(((((((..((......))..)))))))	chr13:43918720-43918940(-)$1	1	153	181	13.8893
(((((((((.........))))))))).	chr3:139071465-139071696(+)$1	1	54	82	9.1716
.((((((..(((....)))..))).)))	chr2:113079283-113079504(+)$1	1	157	185	10.9148
..((((((((......)))..)))))..	chr7:129832327-129832568(-)$1	1	50	78	11.4179
.(((((...(((....)))..))))).)	chr16:820140-820363(+)$1	1	139	167	9.8145
..(((((((((......)))))))))..	chrX:38128765-38129003(-)$1	1	149	177	10.6489
.((((((((((......))))))))))(	chr18:77737561-77737785(-)$1	1	65	93	12.1965
...(((((((.........))))))).)	chr19:11548649-11548878(+)$1	1	48	76	9.6972
(((((...(((.....)))...))))..	chr1:85790371-85790605(-)$1	1	141	169	10.9740
((((((....(......)...)))))))	chr16:47733159-47733381(+)$1	1	145	173	11.9884
((((.(((.(((.....)))))))))))	chr13:31232110-31232361(+)$1	1	157	185	10.9594
.(((((..(((.....)))...))))))	chr17:34044133-34044358(+)$1	1	186	214	11.1475
(((((.(.(.........)).)))))))	chr5:118280172-118280404(-)$1	1	75	103	10.7426
((((((..(((.....)))..)))))))	chr1:243827980-243828203(-)$1	1	187	215	12.8980
))).((((..(......)..))))((((	chr16:19518945-19519176(-)$1	1	129	157	9.4783
((..(((..(((....)))..)))...)	chr3:41280725-41280946(+)$1	1	166	194	11.5704

#PSSM
g : 0.21	c : 0.10	f : 0.09	e : 0.07	= : 0.07	b : 0.05	" : 0.05	# : 0.05	h : 0.05	: : 0.05	d : 0.03	i : 0.03	[ : 0.03	! : 0.03	$ : 0.01	
g : 0.21	e : 0.10	c : 0.10	f : 0.09	= : 0.09	[ : 0.07	# : 0.07	d : 0.05	i : 0.03	! : 0.03	h : 0.03	" : 0.03	a : 0.01	$ : 0.01	
g : 0.25	e : 0.14	c : 0.10	f : 0.10	! : 0.07	= : 0.07	d : 0.05	[ : 0.03	# : 0.03	h : 0.03	" : 0.03	i : 0.03	
g : 0.25	c : 0.12	e : 0.10	! : 0.09	[ : 0.07	f : 0.07	= : 0.07	d : 0.03	# : 0.03	h : 0.03	i : 0.03	" : 0.01	b : 0.01	: : 0.01	
g : 0.23	c : 0.21	e : 0.09	b : 0.07	= : 0.07	! : 0.05	d : 0.05	f : 0.05	[ : 0.03	# : 0.03	i : 0.03	$ : 0.01	h : 0.01	
c : 0.21	g : 0.21	e : 0.07	f : 0.07	= : 0.07	d : 0.05	[ : 0.05	b : 0.05	# : 0.05	" : 0.03	i : 0.03	! : 0.01	$ : 0.01	h : 0.01	
c : 0.23	g : 0.14	! : 0.12	f : 0.07	# : 0.07	d : 0.05	e : 0.05	= : 0.05	" : 0.05	[ : 0.03	a : 0.03	i : 0.03	$ : 0.01	
! : 0.25	c : 0.14	[ : 0.12	g : 0.09	d : 0.07	# : 0.07	f : 0.05	= : 0.05	" : 0.05	i : 0.03	e : 0.01	$ : 0.01	
c : 0.32	! : 0.18	d : 0.09	g : 0.07	# : 0.05	= : 0.05	f : 0.03	a : 0.03	[ : 0.03	i : 0.03	e : 0.01	r : 0.01	$ : 0.01	" : 0.01	
c : 0.41	b : 0.10	[ : 0.07	d : 0.07	r : 0.07	! : 0.05	f : 0.03	g : 0.03	= : 0.03	a : 0.01	e : 0.01	" : 0.01	i : 0.01	# : 0.01	
c : 0.40	b : 0.14	r : 0.10	a : 0.09	d : 0.07	o : 0.03	f : 0.03	q : 0.01	g : 0.01	e : 0.01	" : 0.01	i : 0.01	= : 0.01	
o : 0.49	c : 0.16	r : 0.10	n : 0.09	d : 0.03	b : 0.03	l : 0.03	q : 0.01	" : 0.01	
o : 0.49	n : 0.18	r : 0.10	m : 0.09	l : 0.07	q : 0.01	c : 0.01	b : 0.01	
o : 0.49	n : 0.18	r : 0.10	m : 0.09	l : 0.09	q : 0.01	b : 0.01	
o : 0.49	n : 0.18	r : 0.10	m : 0.09	l : 0.07	c : 0.03	q : 0.01	
o : 0.49	n : 0.18	r : 0.10	m : 0.09	c : 0.05	l : 0.03	q : 0.01	d : 0.01	
o : 0.45	c : 0.27	r : 0.10	n : 0.09	q : 0.01	b : 0.01	d : 0.01	l : 0.01	
c : 0.43	b : 0.16	a : 0.09	r : 0.09	d : 0.07	f : 0.03	q : 0.01	g : 0.01	e : 0.01	4 : 0.01	i : 0.01	= : 0.01	
c : 0.41	b : 0.14	d : 0.09	3 : 0.05	a : 0.03	f : 0.03	4 : 0.03	= : 0.03	r : 0.03	i : 0.03	] : 0.01	g : 0.01	e : 0.01	2 : 0.01	
c : 0.21	2 : 0.21	3 : 0.18	d : 0.07	] : 0.07	= : 0.05	f : 0.03	4 : 0.03	g : 0.03	i : 0.03	e : 0.01	a : 0.01	
2 : 0.25	3 : 0.20	] : 0.10	d : 0.09	c : 0.09	= : 0.05	g : 0.05	f : 0.03	4 : 0.03	i : 0.03	a : 0.01	e : 0.01	
c : 0.20	g : 0.16	3 : 0.14	] : 0.07	f : 0.07	= : 0.07	e : 0.05	2 : 0.05	d : 0.03	h : 0.03	i : 0.03	a : 0.01	4 : 0.01	b : 0.01	
c : 0.21	g : 0.21	f : 0.12	b : 0.09	e : 0.07	= : 0.07	d : 0.05	] : 0.03	h : 0.03	i : 0.03	2 : 0.01	3 : 0.01	
g : 0.25	c : 0.18	e : 0.09	f : 0.09	b : 0.07	= : 0.07	d : 0.05	] : 0.05	2 : 0.03	h : 0.03	i : 0.03	3 : 0.01	
g : 0.25	c : 0.12	e : 0.10	f : 0.09	] : 0.07	= : 0.07	2 : 0.05	d : 0.05	h : 0.05	4 : 0.03	3 : 0.03	i : 0.03	
g : 0.27	c : 0.12	e : 0.10	f : 0.10	= : 0.07	2 : 0.05	d : 0.05	4 : 0.05	h : 0.05	3 : 0.03	i : 0.03	a : 0.01	
g : 0.25	c : 0.12	f : 0.10	e : 0.09	] : 0.09	= : 0.07	4 : 0.07	3 : 0.05	h : 0.05	2 : 0.01	d : 0.01	i : 0.01	5 : 0.01	
g : 0.25	e : 0.09	c : 0.09	b : 0.07	f : 0.07	= : 0.07	4 : 0.07	h : 0.05	] : 0.03	3 : 0.03	: : 0.03	2 : 0.03	d : 0.03	a : 0.01	5 : 0.01	

#score	604.7683034743475
#seq	55
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_CDS_m1_run1.txt

#BEAR
::ccctttttttttttcccggggg	chr21:16336901-16337141(-)$1	240	31	55	20.2880
ddddyyyyyyyyyyyyyyyydddd	chr8:412990-413230(+)$1	240	79	103	20.6103
[ddddwwwwwwwwwwwwwwdddd]	chr12:51386500-51386740(-)$1	240	208	232	21.6074
[bbwwwwwwwwwwwwwwbbccc]e	chrX:53595607-53595847(-)$1	240	169	193	21.0247
ddbbvvvvvvvvvvvvvbb]dddd	chr19:50985680-50985920(+)$1	240	176	200	22.2416
hhhhhvvvvvvvvvvvvvhhhhhh	chr4:144135589-144135869(+)$1	280	179	203	20.9631
[cccvvvvvvvvvvvvvccc]ccc	chr16:58559022-58559263(-)$1	241	75	99	23.0163
d!!bbtttttttttttbb22dddd	chr1:55223616-55223856(-)$1	240	138	162	21.0581
fffffftttttttttttffffff2	chr11:87847148-87847388(-)$1	240	20	44	20.6429
g[ccctttttttttttccc]gggg	chr3:63981323-63981563(+)$1	240	191	215	22.4574
fffffuuuuuuuuuuuuffffff:	chr19:9677596-9677838(-)$1	242	119	143	21.1776
f!!bbuuuuuuuuuuuubb333ff	chr1:28862394-28862634(+)$1	240	181	205	23.0191
ddd[bbtttttttttttbbddddc	chr15:43814458-43814698(+)$1	240	140	164	21.7671
[ddddvvvvvvvvvvvvvdddd]b	chr1:70614084-70614324(-)$1	240	110	134	22.5797
fffffwwwwwwwwwwwwwwfffff	chr3:52558569-52558809(-)$1	240	200	224	20.7416
eeeeeuuuuuuuuuuuueeeee::	chr6:64422974-64423214(+)$1	240	77	101	21.2366
cccwwwwwwwwwwwwwwccc22ff	chr16:68156016-68156256(+)$1	240	118	142	20.9600
eee[attttttttttta]eeeeee	chr21:46271278-46271518(-)$1	240	203	227	22.5212
"""bbuuuuuuuuuuuubb]eeee	chr9:37780653-37780893(-)$1	240	107	131	23.3004
[ddddtttttttttttdddd]eee	chr14:89042144-89042384(+)$1	240	153	177	21.5644
##cccyyyyyyyyyyyyyyyyccc	chr2:64862998-64863238(-)$1	240	107	131	20.4911
eeeeevvvvvvvvvvvvveeeee:	chr21:34926614-34926854(+)$1	240	5	29	22.1600
fff[bbtttttttttttbb]ffff	chr22:46704649-46704894(+)$1	245	219	243	21.4666
eeeeeuuuuuuuuuuuueeeee22	chr3:9486692-9486932(+)$1	240	28	52	22.6621
ieeeeettttttttttteeeee]i	chr5:145602890-145603130(+)$1	240	21	45	21.9326
fyyyyyyyyyyyyyyyyffffffd	chr10:124697235-124697475(-)$1	240	122	146	19.5610
eeeeewwwwwwwwwwwwwweeeee	chr7:6639624-6639864(+)$1	240	10	34	21.8831
[cccvvvvvvvvvvvvvccc]bbe	chr7:107398706-107398946(+)$1	240	158	182	22.4510
eeebbuuuuuuuuuuuubb]eeee	chr17:46654178-46654418(-)$1	240	77	101	23.4290
eeewwwwwwwwwwwwwweeeeeee	chr1:173751182-173751422(+)$1	240	17	41	21.4094
eeeeewwwwwwwwwwwwwweeeee	chr17:70120265-70120505(+)$1	240	186	210	21.8831
iiiiiitttttttttttiiiiiii	chr10:104557710-104557950(+)$1	240	24	48	21.8773
::cccuuuuuuuuuuuucccdddd	chr21:34925742-34926040(+)$1	298	61	85	21.3094
=====vvvvvvvvvvvvv======	chr6:43607789-43608029(+)$1	240	117	141	23.1720
"ddddvvvvvvvvvvvvvdddd33	chr1:180382452-180382692(-)$1	240	147	171	22.6398
d[ddddtttttttttttddddddd	chr5:112176878-112177118(+)$1	240	128	152	21.3789
gyyyyyyyyyyyyyyyyggggggg	chr11:28098493-28098733(-)$1	240	197	221	20.2524
eeeeevvvvvvvvvvvvveeeee:	chr20:39832895-39833135(-)$1	240	97	121	22.1600
!!cccuuuuuuuuuuuuccc22cc	chr13:39264990-39265230(+)$1	240	105	129	23.3286
hhhhhvvvvvvvvvvvvvhhhhhh	chr2:86344115-86344355(+)$1	240	191	215	20.9631
gggggwwwwwwwwwwwwwwggggg	chr2:201759946-201760186(+)$1	240	200	224	21.7165
fffffwwwwwwwwwwwwwwfffff	chr1:153610781-153611021(+)$1	240	66	90	20.7416
ggggggtttttttttttggggggg	chr10:98292738-98292978(-)$1	240	28	52	21.7313
c[bbvvvvvvvvvvvvvbbccc]c	chr17:38458140-38458380(+)$1	240	118	142	22.4192
e[bbvvvvvvvvvvvvvbbeeeee	chr12:14631266-14631506(+)$1	240	71	95	22.7670
""ccctttttttttttccc333bb	chr17:56428701-56428941(-)$1	240	189	213	21.7641
!bbwwwwwwwwwwwwwwbb22eee	chr4:44689968-44690208(+)$1	240	101	125	20.9521
[cccvvvvvvvvvvvvvccc]fff	chr1:114483374-114483614(+)$1	240	187	211	22.8357
ggddddtttttttttttdddd22g	chr2:136614292-136614532(-)$1	240	104	128	21.1115
eeeeevvvvvvvvvvvvveeeeeC	chrX:53575863-53576103(-)$1	240	81	105	22.0150
geeeeettttttttttteeeee:h	chr2:60773018-60773258(-)$1	240	68	92	20.7737
eeeeevvvvvvvvvvvvveeeee2	chr6:160176498-160176738(+)$1	240	200	224	22.8448
cccccyyyyyyyyyyyyyyyyccc	chr22:40706824-40707064(+)$1	240	118	142	20.4317
!!cccuuuuuuuuuuuuccc22bb	chr19:8002924-8003164(-)$1	240	122	146	22.8772
eeeyyyyyyyyyyyyyyyyeeeee	chr16:4921053-4921293(+)$1	240	149	173	21.5587
i!!bbuuuuuuuuuuuubb]iiii	chr14:81744732-81744972(-)$1	240	106	130	23.3885
eeeyyyyyyyyyyyyyyyyeeeee	chr1:197072741-197072981(-)$1	240	58	82	21.5587
&ddddvvvvvvvvvvvvvddddbb	chr11:122930353-122930593(-)$1	240	201	225	21.5017
gggggvvvvvvvvvvvvvgggggg	chr14:73464709-73464949(-)$1	240	106	130	22.8859
ddd[bbtttttttttttbb]dddd	chr16:20807704-20807944(-)$1	240	205	229	21.8249
iyyyyyyyyyyyyyyyyiiiiiii	chr16:47005226-47005466(-)$1	240	140	164	20.3294
ccc[bbtttttttttttbb]ccc]	chr2:74757444-74757684(+)$1	240	122	146	22.0132
"ddddvvvvvvvvvvvvvdddd33	chr4:160262959-160263199(+)$1	240	181	205	22.6398
dddyyyyyyyyyyyyyyyydddd]	chr1:231471192-231471451(-)$1	259	104	128	21.0392
d!!bbuuuuuuuuuuuubb22ddd	chr11:59361003-59361243(-)$1	240	149	173	22.7426

#otherMatches

#Seq PSSM
GCCCACACAGCGCAAAUGGAGAAG	chr21:16336901-16337141(-)$1	240	31	55	20.2880
CUUCAGAAACAUUACCCAGCGAAG	chr8:412990-413230(+)$1	240	79	103	20.6103
uucuuuuuuuuuuuuuuuugagau	chr12:51386500-51386740(-)$1	240	208	232	21.6074
AGUACCUCACAGCUUAGACCUGUC	chrX:53595607-53595847(-)$1	240	169	193	21.0247
GGGAACAUGCCGCCUUCUCUCCAG	chr19:50985680-50985920(+)$1	240	176	200	22.2416
UCUGGCAUUAGCAUCCUCCCAGAG	chr4:144135589-144135869(+)$1	280	179	203	20.9631
AUUGCGCACAUCCACAACAAGGGC	chr16:58559022-58559263(-)$1	241	75	99	23.0163
UGCCUCAUCCCCCCUAAGAAGGGC	chr1:55223616-55223856(-)$1	240	138	162	21.0581
UGCUCUAGCAUUAUUUCAGAGUAU	chr11:87847148-87847388(-)$1	240	20	44	20.6429
AAAUUGAAAUCCAGCAAAUCUUUG	chr3:63981323-63981563(+)$1	240	191	215	22.4574
UCAUGCCUUAAUGCACACAUGGGA	chr19:9677596-9677838(-)$1	242	119	143	21.1776
ccugcguuccuguccuggcucugc	chr1:28862394-28862634(+)$1	240	181	205	23.0191
CCCAGCAAAAUCAAACAGCGGGCU	chr15:43814458-43814698(+)$1	240	140	164	21.7671
CCUCUUACAAAUUCCACCAGAGCU	chr1:70614084-70614324(-)$1	240	110	134	22.5797
CGUGGACUUCACCUUCUACCCACG	chr3:52558569-52558809(-)$1	240	200	224	20.7416
ACCUGUUGUUCAUCUCCCAGGUCA	chr6:64422974-64423214(+)$1	240	77	101	21.2366
UCUCCUAACUGUCAUCAAGAAUUA	chr16:68156016-68156256(+)$1	240	118	142	20.9600
UGACCUUCUAUUCCCUGUUCAUCU	chr21:46271278-46271518(-)$1	240	203	227	22.5212
AAGGCAAAAACCAUCCAGCAGACU	chr9:37780653-37780893(-)$1	240	107	131	23.3004
AUUAUGUUUACACUUGGUAAGACA	chr14:89042144-89042384(+)$1	240	153	177	21.5644
CCCCAAGUCAGCCUUUCAAAAUGG	chr2:64862998-64863238(-)$1	240	107	131	20.4911
CUGCUCAGCCCUAAAGAAAGUAGU	chr21:34926614-34926854(+)$1	240	5	29	22.1600
GGGAGCCCCCACUCCUUGCCCCUC	chr22:46704649-46704894(+)$1	245	219	243	21.4666
CUUUGGAGCAGUAAUUAUAAAGUG	chr3:9486692-9486932(+)$1	240	28	52	22.6621
ucaaauuuuuguuuuuUGUUUGCG	chr5:145602890-145603130(+)$1	240	21	45	21.9326
CAAAUAUACCCAACUCCGAGUUGC	chr10:124697235-124697475(-)$1	240	122	146	19.5610
GGCUUAUAAAAGGAAAAAGAAGCC	chr7:6639624-6639864(+)$1	240	10	34	21.8831
AUGCCACCACCUCCUUUGCAACAU	chr7:107398706-107398946(+)$1	240	158	182	22.4510
ACCGCCUACACGCGCCAGCAGGUC	chr17:46654178-46654418(-)$1	240	77	101	23.4290
GUCUAUAAUUUCCUUACGAUUGUC	chr1:173751182-173751422(+)$1	240	17	41	21.4094
GGGUCCCUUCCAUCCCGCAGACCC	chr17:70120265-70120505(+)$1	240	186	210	21.8831
UUUUUAAUUUUUUAGGAUAAGGAA	chr10:104557710-104557950(+)$1	240	24	48	21.8773
GCGGUGUCAGUCCUUCAACCUUCU	chr21:34925742-34926040(+)$1	298	61	85	21.3094
UGGGGGCAAUGCCCUAAGCCCCAA	chr6:43607789-43608029(+)$1	240	117	141	23.1720
GCCAUCAAAUCGAAAAAUGUGGAU	chr1:180382452-180382692(-)$1	240	147	171	22.6398
UCAGCUAAUAAGACACAAGCUAUU	chr5:112176878-112177118(+)$1	240	128	152	21.3789
aauuaaauuuuaGAAAGUAUAAAA	chr11:28098493-28098733(-)$1	240	197	221	20.2524
UGAUGGACAGGCAGAAAUCAUCAU	chr20:39832895-39833135(-)$1	240	97	121	22.1600
UCUGGUAAUUGAUACACCCAUUCU	chr13:39264990-39265230(+)$1	240	105	129	23.3286
UACAUAAUACUAUUUUAAAUGUAA	chr2:86344115-86344355(+)$1	240	191	215	20.9631
ACUGUGCACACAUUUUCUAACAgu	chr2:201759946-201760186(+)$1	240	200	224	21.7165
CCAGUGCCAGAAACAGAAGACUGG	chr1:153610781-153611021(+)$1	240	66	90	20.7416
CAGGUGGCCGUUUGUUGCAUCUGU	chr10:98292738-98292978(-)$1	240	28	52	21.7313
UCUCUUACACCCCACCCGAAAGUA	chr17:38458140-38458380(+)$1	240	118	142	22.4192
CGCCUCUUCAACCAUCUGGGGUGC	chr12:14631266-14631506(+)$1	240	71	95	22.7670
UCAGUUUCCAUCAUUCACUUCUGC	chr17:56428701-56428941(-)$1	240	189	213	21.7641
ACUGAAGCGCAAAUAGGAGAUACA	chr4:44689968-44690208(+)$1	240	101	125	20.9521
UGACCAAUAGCUAUGAAGUCUUGG	chr1:114483374-114483614(+)$1	240	187	211	22.8357
UUUUGGCAGCAGCAAACCCAAUCA	chr2:136614292-136614532(-)$1	240	104	128	21.1115
UACCGAGAAGCAUGCAAGCGGUGG	chrX:53575863-53576103(-)$1	240	81	105	22.0150
GUUGGCAUCCAGGUCACGCCAGAG	chr2:60773018-60773258(-)$1	240	68	92	20.7737
CAGAAAAUUAAUGCAUACUUUUGU	chr6:160176498-160176738(+)$1	240	200	224	22.8448
UCUCCACCAACAAAUAAAAUCGGA	chr22:40706824-40707064(+)$1	240	118	142	20.4317
CCGGCUUGCUAGAUAAUGUCAAAC	chr19:8002924-8003164(-)$1	240	122	146	22.8772
UGGAGAGGAACAACAAAGCCCAGG	chr16:4921053-4921293(+)$1	240	149	173	21.5587
AGAUGUACCUUAUAAUUCAAUGGG	chr14:81744732-81744972(-)$1	240	106	130	23.3885
CUAAUCAAACAACAAUCUAUAGCU	chr1:197072741-197072981(-)$1	240	58	82	21.5587
AGAACUGAAUGCUGACCUGUUCCG	chr11:122930353-122930593(-)$1	240	201	225	21.5017
UGGGCAGCCUAUGACCCAGUUCAC	chr14:73464709-73464949(-)$1	240	106	130	22.8859
AUCAUGUGACUUGUAAUCAGGAUU	chr16:20807704-20807944(-)$1	240	205	229	21.8249
CAUGGGCAAUCAGAGUAGAAGUCG	chr16:47005226-47005466(-)$1	240	140	164	20.3294
GUCAGUACAACUUCAUCGCAGAUG	chr2:74757444-74757684(+)$1	240	122	146	22.0132
AGAUUUAAAAUAUGUAUCAGUCCA	chr4:160262959-160263199(+)$1	240	181	205	22.6398
UGUGAAUCCUGAAAGUACAACAUC	chr1:231471192-231471451(-)$1	259	104	128	21.0392
UCUCCAUUAUGCCCCUCGGUAAGG	chr11:59361003-59361243(-)$1	240	149	173	22.7426

#DB
..(((...........)))(((((	chr21:16336901-16337141(-)$1	1	31	55	20.2880
((((................))))	chr8:412990-413230(+)$1	1	79	103	20.6103
.((((..............)))).	chr12:51386500-51386740(-)$1	1	208	232	21.6074
.((..............))))).)	chrX:53595607-53595847(-)$1	1	169	193	21.0247
((((.............)).))))	chr19:50985680-50985920(+)$1	1	176	200	22.2416
(((((.............))))))	chr4:144135589-144135869(+)$1	1	179	203	20.9631
.(((.............))).)))	chr16:58559022-58559263(-)$1	1	75	99	23.0163
(..((...........))..))))	chr1:55223616-55223856(-)$1	1	138	162	21.0581
((((((...........)))))).	chr11:87847148-87847388(-)$1	1	20	44	20.6429
(.(((...........))).))))	chr3:63981323-63981563(+)$1	1	191	215	22.4574
(((((............)))))).	chr19:9677596-9677838(-)$1	1	119	143	21.1776
(..((............))...))	chr1:28862394-28862634(+)$1	1	181	205	23.0191
(((.((...........)))))))	chr15:43814458-43814698(+)$1	1	140	164	21.7671
.((((.............)))).)	chr1:70614084-70614324(-)$1	1	110	134	22.5797
(((((..............)))))	chr3:52558569-52558809(-)$1	1	200	224	20.7416
(((((............)))))..	chr6:64422974-64423214(+)$1	1	77	101	21.2366
(((..............)))..))	chr16:68156016-68156256(+)$1	1	118	142	20.9600
(((.(...........).))))))	chr21:46271278-46271518(-)$1	1	203	227	22.5212
...((............)).))))	chr9:37780653-37780893(-)$1	1	107	131	23.3004
.((((...........)))).)))	chr14:89042144-89042384(+)$1	1	153	177	21.5644
..(((................)))	chr2:64862998-64863238(-)$1	1	107	131	20.4911
(((((.............))))).	chr21:34926614-34926854(+)$1	1	5	29	22.1600
(((.((...........)).))))	chr22:46704649-46704894(+)$1	1	219	243	21.4666
(((((............)))))..	chr3:9486692-9486932(+)$1	1	28	52	22.6621
((((((...........))))).)	chr5:145602890-145603130(+)$1	1	21	45	21.9326
(................))))))(	chr10:124697235-124697475(-)$1	1	122	146	19.5610
(((((..............)))))	chr7:6639624-6639864(+)$1	1	10	34	21.8831
.(((.............))).)))	chr7:107398706-107398946(+)$1	1	158	182	22.4510
(((((............)).))))	chr17:46654178-46654418(-)$1	1	77	101	23.4290
(((..............)))))))	chr1:173751182-173751422(+)$1	1	17	41	21.4094
(((((..............)))))	chr17:70120265-70120505(+)$1	1	186	210	21.8831
((((((...........)))))))	chr10:104557710-104557950(+)$1	1	24	48	21.8773
..(((............)))((((	chr21:34925742-34926040(+)$1	1	61	85	21.3094
(((((.............))))))	chr6:43607789-43608029(+)$1	1	117	141	23.1720
.((((.............))))..	chr1:180382452-180382692(-)$1	1	147	171	22.6398
(.((((...........)))))))	chr5:112176878-112177118(+)$1	1	128	152	21.3789
(................)))))))	chr11:28098493-28098733(-)$1	1	197	221	20.2524
(((((.............))))).	chr20:39832895-39833135(-)$1	1	97	121	22.1600
..(((............)))..))	chr13:39264990-39265230(+)$1	1	105	129	23.3286
(((((.............))))))	chr2:86344115-86344355(+)$1	1	191	215	20.9631
(((((..............)))))	chr2:201759946-201760186(+)$1	1	200	224	21.7165
(((((..............)))))	chr1:153610781-153611021(+)$1	1	66	90	20.7416
((((((...........)))))))	chr10:98292738-98292978(-)$1	1	28	52	21.7313
(.((.............))))).)	chr17:38458140-38458380(+)$1	1	118	142	22.4192
(.((.............)))))))	chr12:14631266-14631506(+)$1	1	71	95	22.7670
..(((...........)))...))	chr17:56428701-56428941(-)$1	1	189	213	21.7641
.((..............))..)))	chr4:44689968-44690208(+)$1	1	101	125	20.9521
.(((.............))).)))	chr1:114483374-114483614(+)$1	1	187	211	22.8357
((((((...........))))..)	chr2:136614292-136614532(-)$1	1	104	128	21.1115
(((((.............)))))(	chrX:53575863-53576103(-)$1	1	81	105	22.0150
)(((((...........))))).(	chr2:60773018-60773258(-)$1	1	68	92	20.7737
(((((.............))))).	chr6:160176498-160176738(+)$1	1	200	224	22.8448
))(((................)))	chr22:40706824-40707064(+)$1	1	118	142	20.4317
..(((............)))..))	chr19:8002924-8003164(-)$1	1	122	146	22.8772
(((................)))))	chr16:4921053-4921293(+)$1	1	149	173	21.5587
(..((............)).))))	chr14:81744732-81744972(-)$1	1	106	130	23.3885
(((................)))))	chr1:197072741-197072981(-)$1	1	58	82	21.5587
.((((.............))))))	chr11:122930353-122930593(-)$1	1	201	225	21.5017
(((((.............))))))	chr14:73464709-73464949(-)$1	1	106	130	22.8859
(((.((...........)).))))	chr16:20807704-20807944(-)$1	1	205	229	21.8249
(................)))))))	chr16:47005226-47005466(-)$1	1	140	164	20.3294
(((.((...........)).))).	chr2:74757444-74757684(+)$1	1	122	146	22.0132
.((((.............))))..	chr4:160262959-160263199(+)$1	1	181	205	22.6398
(((................)))).	chr1:231471192-231471451(-)$1	1	104	128	21.0392
(..((............))..)))	chr11:59361003-59361243(-)$1	1	149	173	22.7426

#PSSM
e : 0.21	d : 0.12	[ : 0.10	f : 0.10	g : 0.10	c : 0.06	" : 0.06	i : 0.06	! : 0.04	: : 0.03	h : 0.03	# : 0.01	= : 0.01	& : 0.01	
e : 0.23	d : 0.16	c : 0.09	! : 0.09	f : 0.07	[ : 0.06	g : 0.06	y : 0.04	: : 0.03	b : 0.03	h : 0.03	" : 0.03	# : 0.01	i : 0.01	= : 0.01	
e : 0.23	c : 0.20	d : 0.18	b : 0.07	f : 0.07	! : 0.06	y : 0.04	g : 0.04	h : 0.03	" : 0.01	i : 0.01	= : 0.01	
c : 0.16	e : 0.15	d : 0.13	b : 0.13	y : 0.09	[ : 0.07	w : 0.06	f : 0.06	g : 0.04	h : 0.03	i : 0.01	= : 0.01	
b : 0.15	e : 0.15	c : 0.12	d : 0.12	y : 0.10	v : 0.09	w : 0.06	f : 0.06	g : 0.04	h : 0.03	a : 0.01	i : 0.01	= : 0.01	
v : 0.27	u : 0.16	w : 0.15	y : 0.13	t : 0.09	b : 0.06	e : 0.03	d : 0.03	f : 0.01	i : 0.01	g : 0.01	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.26	u : 0.16	w : 0.15	y : 0.13	
v : 0.27	t : 0.16	u : 0.16	w : 0.15	y : 0.13	c : 0.04	b : 0.01	a : 0.01	d : 0.01	
b : 0.23	v : 0.18	c : 0.15	y : 0.09	w : 0.09	e : 0.07	f : 0.04	d : 0.04	i : 0.03	g : 0.03	] : 0.01	
b : 0.21	c : 0.15	e : 0.15	d : 0.10	y : 0.09	w : 0.09	f : 0.04	g : 0.04	h : 0.03	i : 0.03	2 : 0.01	= : 0.01	
e : 0.23	d : 0.15	c : 0.13	] : 0.12	g : 0.07	f : 0.07	y : 0.04	2 : 0.04	h : 0.03	3 : 0.03	i : 0.03	= : 0.01	
e : 0.26	d : 0.21	g : 0.09	f : 0.09	2 : 0.07	] : 0.06	c : 0.04	i : 0.04	h : 0.03	3 : 0.03	y : 0.03	= : 0.01	
e : 0.29	d : 0.21	f : 0.10	g : 0.09	c : 0.09	2 : 0.06	i : 0.04	h : 0.03	3 : 0.03	b : 0.01	= : 0.01	
e : 0.23	d : 0.15	f : 0.13	g : 0.09	c : 0.07	] : 0.06	b : 0.06	i : 0.04	h : 0.03	: : 0.03	2 : 0.03	3 : 0.03	= : 0.01	
e : 0.20	d : 0.12	g : 0.10	c : 0.09	f : 0.09	: : 0.06	b : 0.06	i : 0.06	] : 0.04	h : 0.04	2 : 0.04	3 : 0.03	= : 0.01	C : 0.01	

#score	1415.6552362159523
#seq	65
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_UTR_m1_run2.txt

#BEAR
:bbccctttttttttttccc]bb	chr17:1248029-1248256(-)$1	227	110	133	20.6671
[cccwwwwwwwwwwwwwwccc]a	chr4:76568065-76568290(-)$1	225	2	25	22.1497
bbcccvvvvvvvvvvvvvccc]b	chr2:232264363-232264590(+)$1	227	8	31	22.5437
eeeeeuuuuuuuuuuuueeeee2	chr7:20453655-20453889(+)$1	234	20	43	22.8549
ggggvvvvvvvvvvvvvgggggg	chr16:23533473-23533696(-)$1	223	36	59	23.1115
fffffvvvvvvvvvvvvvfffff	chr19:37001952-37002176(-)$1	224	89	112	22.2031
eeeeeuuuuuuuuuuuueeeee:	chr2:89156636-89156859(-)$1	223	66	89	22.1055
fffccctttttttttttccc]ff	chr17:7363424-7363654(-)$1	230	53	76	22.4189
hh[ccctttttttttttccc]hh	chr8:6616539-6616769(+)$1	230	86	109	22.2947
!dddduuuuuuuuuuuudddd22	chr19:10243997-10244230(-)$1	233	85	108	22.5064
!!ddddtttttttttttdddddd	chr1:150974591-150974816(-)$1	225	148	171	21.5873
eeeeeyyyyyyyyyyyyyyyyee	chr17:47787746-47787976(-)$1	230	183	206	19.7051
eeeeettttttttttteeeee::	chr1:27205786-27206016(-)$1	230	74	97	19.6492
#eeeeettttttttttteeeee4	chr10:102317508-102317730(-)$1	222	87	110	21.9675
cyyyyyyyyyyyyyyyyccc22c	chr8:123986293-123986524(+)$1	231	98	121	19.7759
fffffuuuuuuuuuuuuffffff	chr8:124232205-124232438(-)$1	233	27	50	22.3631
fffffvvvvvvvvvvvvvfffff	chr15:63558783-63559007(+)$1	224	192	215	22.2031
!!bbwwwwwwwwwwwwwwbb22g	chr11:244624-244862(+)$1	238	22	45	21.3165
ee[bbuuuuuuuuuuuubb]eee	chr3:178740218-178740449(-)$1	231	186	209	22.4861
###bbtttttttttttbb4444g	chr1:154680325-154680555(-)$1	230	171	194	20.8901
iiiiiitttttttttttiiiiii	chr10:23730032-23730262(+)$1	230	113	136	22.2230
=====vvvvvvvvvvvvv=====	chr15:78461243-78461473(+)$1	230	140	163	23.2542
cyyyyyyyyyyyyyyyyccc333	chr2:187542356-187542586(+)$1	230	99	122	20.0921
!ddddtttttttttttdddd22f	chr5:132216122-132216349(-)$1	227	80	103	21.1867
ggg[bbtttttttttttbbgggg	chr10:70743920-70744150(+)$1	230	20	43	21.8369
fffffvvvvvvvvvvvvvfffff	chr16:24836037-24836267(+)$1	230	149	172	22.2031
fffffuuuuuuuuuuuuffffff	chr1:203276943-203277173(+)$1	230	57	80	22.3631
ddddvvvvvvvvvvvvvdddd]c	chr14:75598409-75598639(-)$1	230	39	62	22.3206
ggggvvvvvvvvvvvvvgggggg	chr9:465092-465318(+)$1	226	154	177	23.1115
eeeeeuuuuuuuuuuuueeeee:	chr20:30824548-30824773(+)$1	225	105	128	22.1055
ggggggtttttttttttgggggg	chr1:92978921-92979146(-)$1	225	193	216	22.2807
iiiwwwwwwwwwwwwwwiiiiii	chr11:113668598-113668828(-)$1	230	53	76	21.6081
"eeeeettttttttttteeeee]	chr1:52486055-52486291(-)$1	236	26	49	22.1284
##ccctttttttttttccc333i	chr15:50791592-50791821(+)$1	229	182	205	22.4106
eeeewwwwwwwwwwwwwweeeee	chr16:69732593-69732823(+)$1	230	180	203	21.6729
&&cccvvvvvvvvvvvvvccc]d	chr17:56589670-56589900(-)$1	230	97	120	22.0010
eeeeeuuuuuuuuuuuueeeee:	chr9:115060025-115060255(-)$1	230	7	30	22.1055
gggggyyyyyyyyyyyyyyyygg	chr17:65071797-65072022(-)$1	225	28	51	20.0619
b[bbvvvvvvvvvvvvvbb]bb]	chr19:54652106-54652336(+)$1	230	87	110	21.3921
##cccvvvvvvvvvvvvvccc44	chr20:46284655-46284877(+)$1	222	126	149	23.1155
g[bbwwwwwwwwwwwwwwbbggg	chr7:20452592-20452822(+)$1	230	38	61	21.3745
eeeeevvvvvvvvvvvvveeeee	chr4:142654206-142654426(+)$1	220	86	109	22.7623
eeewwwwwwwwwwwwwweeeee]	chr20:34844710-34844940(+)$1	230	182	205	21.3154
hhhhhuuuuuuuuuuuuhhhhhh	chr3:156422988-156423222(+)$1	234	82	105	21.6304
fffffftttttttttttffffff	chr10:124923574-124923804(+)$1	230	96	119	21.3091
hhhhhuuuuuuuuuuuuhhhhhh	chr7:6442949-6443172(+)$1	223	132	155	21.6304
i[cccuuuuuuuuuuuuccc22i	chr18:32917310-32917530(-)$1	220	161	184	23.7354
dd[bbvvvvvvvvvvvvvbb]dd	chr7:5567266-5567491(-)$1	225	94	117	21.8427
ggggguuuuuuuuuuuugggggg	chr7:23683299-23683529(+)$1	230	206	229	23.4308
ddddvvvvvvvvvvvvvdddd]d	chr6:83906960-83907183(+)$1	223	84	107	22.1984
hhhhhuuuuuuuuuuuuhhhhhh	chr12:69232987-69233217(+)$1	230	11	34	21.6304
dd[ccctttttttttttccc]dd	chr3:41281494-41281726(+)$1	232	167	190	22.2895
hhhhhyyyyyyyyyyyyyyyyhh	chr17:74730109-74730336(-)$1	227	151	174	18.9018
c[ddddtttttttttttdddd]c	chr6:82924080-82924310(-)$1	230	185	208	21.8467
[dddduuuuuuuuuuuuddddee	chr14:81942172-81942397(-)$1	225	194	217	22.6200
ggggguuuuuuuuuuuugggggg	chr15:89740542-89740767(+)$1	225	53	76	23.4308
''cccuuuuuuuuuuuuccc000	chr5:65375988-65376213(+)$1	225	79	102	21.0865
!!cccuuuuuuuuuuuuccc22f	chr7:105195516-105195748(+)$1	232	63	86	23.7221
eeeewwwwwwwwwwwwwweeeee	chr9:87636439-87636669(+)$1	230	206	229	21.6729
d[bbvvvvvvvvvvvvvbbdddd	chrX:15848393-15848623(-)$1	230	57	80	21.7767

#otherMatches

#Seq PSSM
CGUGGCUGCUCAUUCUUGCCUAC	chr17:1248029-1248256(-)$1	227	110	133	20.6671
UGGAGUUUUAACAUUUUGUCCUC	chr4:76568065-76568290(-)$1	225	2	25	22.1497
CUGCUGACCCCCACCCCAGGCAA	chr2:232264363-232264590(+)$1	227	8	31	22.5437
uuucaauuuaacaucucugaaau	chr7:20453655-20453889(+)$1	234	20	43	22.8549
GGAUGACUCUGCUCAAGGUUCAG	chr16:23533473-23533696(-)$1	223	36	59	23.1115
UUAAAUAUAUUAAUUUCUUUUAA	chr19:37001952-37002176(-)$1	224	89	112	22.2031
GGACCUACCCCUAUUGCGGUCCU	chr2:89156636-89156859(-)$1	223	66	89	22.1055
UCCCUGAAUGUUAACCACAGAGG	chr17:7363424-7363654(-)$1	230	53	76	22.4189
GGUAAAACUUAUGAAAAUUUCCU	chr8:6616539-6616769(+)$1	230	86	109	22.2947
CUGGAUUUUAAAAGUUUUUUAUU	chr19:10243997-10244230(-)$1	233	85	108	22.5064
CAUGAACAUCCUCUUUCUUCAGU	chr1:150974591-150974816(-)$1	225	148	171	21.5873
AAGAAUGUUAAUGUUCGAGUUUU	chr17:47787746-47787976(-)$1	230	183	206	19.7051
ACCAGAAAGUCGAGCACUGGUCC	chr1:27205786-27206016(-)$1	230	74	97	19.6492
GCUUCCUAAGAAGAAAUGGAGGA	chr10:102317508-102317730(-)$1	222	87	110	21.9675
GUUUUCAUUUCUCUUCUUCACUG	chr8:123986293-123986524(+)$1	231	98	121	19.7759
AGAAAGAUCAAAGACCAUUUCUG	chr8:124232205-124232438(-)$1	233	27	50	22.3631
UAAGAGAUUAUAACUCCAUUUUA	chr15:63558783-63559007(+)$1	224	192	215	22.2031
UUUCUUGUUUUUGUUUUUGAUGU	chr11:244624-244862(+)$1	238	22	45	21.3165
UAGUUUUUUUCCUCCAUAGGUAG	chr3:178740218-178740449(-)$1	231	186	209	22.4861
CUUUGCCAUCAAGAAACAUUCAG	chr1:154680325-154680555(-)$1	230	171	194	20.8901
AAAUGUAUUUUUGCACAACAUUU	chr10:23730032-23730262(+)$1	230	113	136	22.2230
AUGGACACCACAUGAACCUCUGU	chr15:78461243-78461473(+)$1	230	140	163	23.2542
UUAAUACAUAUUACACUACAGUU	chr2:187542356-187542586(+)$1	230	99	122	20.0921
GGUUCGUCUAAAAUAAGGACAUA	chr5:132216122-132216349(-)$1	227	80	103	21.1867
UGCUAGGAAAUUUAAAGCUGCAU	chr10:70743920-70744150(+)$1	230	20	43	21.8369
UUUCUCUGCCAAAAAAAAAGAAA	chr16:24836037-24836267(+)$1	230	149	172	22.2031
GCCAGACACCUGCAUCCCUGGCU	chr1:203276943-203277173(+)$1	230	57	80	22.3631
CCUAAACUUAAGCUUUGUAGGAG	chr14:75598409-75598639(-)$1	230	39	62	22.3206
CAAGCUAAAUGUUUCCCUUUGCA	chr9:465092-465318(+)$1	226	154	177	23.1115
uccuucucuuucugcacaaggaa	chr20:30824548-30824773(+)$1	225	105	128	22.1055
UGAAUAUUAAUGUUUCUUGUUUA	chr1:92978921-92979146(-)$1	225	193	216	22.2807
GCAAAACUAUAUAUAUAUGUAUA	chr11:113668598-113668828(-)$1	230	53	76	21.6081
CCCACUUUACUCACCUUAGUGGU	chr1:52486055-52486291(-)$1	236	26	49	22.1284
UUGCUUUUUUUCUUUCAGCCUAU	chr15:50791592-50791821(+)$1	229	182	205	22.4106
AGAGCUACUUUAUAAAUUCUCUG	chr16:69732593-69732823(+)$1	230	180	203	21.6729
UUGCCAUCUCUAACUACCGGCUG	chr17:56589670-56589900(-)$1	230	97	120	22.0010
GACCAUUAUCUAAAACUUGGUUU	chr9:115060025-115060255(-)$1	230	7	30	22.1055
UUAUUUCUAAAAACUAAAAAUAA	chr17:65071797-65072022(-)$1	225	28	51	20.0619
cagcggagguggagggagcagca	chr19:54652106-54652336(+)$1	230	87	110	21.3921
CCCCAUUUUUUCAAACCUUGGUA	chr20:46284655-46284877(+)$1	222	126	149	23.1155
AAUGAUUUAUAAAUGUGCCAUAC	chr7:20452592-20452822(+)$1	230	38	61	21.3745
AGUGUUGUUUUUUAAGUUGCACU	chr4:142654206-142654426(+)$1	220	86	109	22.7623
CUGAUCUCCAGAGCAGCCAGGCU	chr20:34844710-34844940(+)$1	230	182	205	21.3154
UAAAAAAAAAAUACAAGUUUUAA	chr3:156422988-156423222(+)$1	234	82	105	21.6304
GUGUAAUAAAAAUCCCUUUGCAU	chr10:124923574-124923804(+)$1	230	96	119	21.3091
AUUAUAAAAUCUUUCUGAUAAUG	chr7:6442949-6443172(+)$1	223	132	155	21.6304
UGUGGGAAAGCCUUUAGCCAGAA	chr18:32917310-32917530(-)$1	220	161	184	23.7354
CCACCGCAAAUGCUUCUAGGCGG	chr7:5567266-5567491(-)$1	225	94	117	21.8427
UCAUGAUUUUUCACAUACAUGAA	chr7:23683299-23683529(+)$1	230	206	229	23.4308
GGAAAAAAAAAAUCUAAUUCUAC	chr6:83906960-83907183(+)$1	223	84	107	22.1984
UGACUGAGCAGUUAAAGGGUUAC	chr12:69232987-69233217(+)$1	230	11	34	21.6304
UUGUAUAAAAUAGACAAAUAGAA	chr3:41281494-41281726(+)$1	232	167	190	22.2895
CUUUUUUUCCCCCAUUUAUUUGA	chr17:74730109-74730336(-)$1	227	151	174	18.9018
GAAGAUGAUAACCAGAAGUCUGC	chr6:82924080-82924310(-)$1	230	185	208	21.8467
UCAGGUAUCUUUUUAUUUCUGAU	chr14:81942172-81942397(-)$1	225	194	217	22.6200
ACUGGCACUUUACCCUCUCAGUU	chr15:89740542-89740767(+)$1	225	53	76	23.4308
AGCACUUUUAAAAAUAUGUGAAC	chr5:65375988-65376213(+)$1	225	79	102	21.0865
AAGAGACUAGAGCUUCCCUUGGC	chr7:105195516-105195748(+)$1	232	63	86	23.7221
AUUCUUACCCUUUCUUUUGAAUC	chr9:87636439-87636669(+)$1	230	206	229	21.6729
GACCAAACUUAGUAUUAGGCAGG	chrX:15848393-15848623(-)$1	230	57	80	21.7767

#DB
.(((((...........))).))	chr17:1248029-1248256(-)$1	1	110	133	20.6671
.(((..............))).)	chr4:76568065-76568290(-)$1	1	2	25	22.1497
(((((.............))).)	chr2:232264363-232264590(+)$1	1	8	31	22.5437
(((((............))))).	chr7:20453655-20453889(+)$1	1	20	43	22.8549
((((.............))))))	chr16:23533473-23533696(-)$1	1	36	59	23.1115
(((((.............)))))	chr19:37001952-37002176(-)$1	1	89	112	22.2031
(((((............))))).	chr2:89156636-89156859(-)$1	1	66	89	22.1055
((((((...........))).))	chr17:7363424-7363654(-)$1	1	53	76	22.4189
((.(((...........))).))	chr8:6616539-6616769(+)$1	1	86	109	22.2947
.((((............))))..	chr19:10243997-10244230(-)$1	1	85	108	22.5064
..((((...........))))))	chr1:150974591-150974816(-)$1	1	148	171	21.5873
(((((................))	chr17:47787746-47787976(-)$1	1	183	206	19.7051
(((((...........)))))..	chr1:27205786-27206016(-)$1	1	74	97	19.6492
.(((((...........))))).	chr10:102317508-102317730(-)$1	1	87	110	21.9675
(................)))..)	chr8:123986293-123986524(+)$1	1	98	121	19.7759
(((((............))))))	chr8:124232205-124232438(-)$1	1	27	50	22.3631
(((((.............)))))	chr15:63558783-63559007(+)$1	1	192	215	22.2031
..((..............))..)	chr11:244624-244862(+)$1	1	22	45	21.3165
((.((............)).)))	chr3:178740218-178740449(-)$1	1	186	209	22.4861
...((...........))....)	chr1:154680325-154680555(-)$1	1	171	194	20.8901
((((((...........))))))	chr10:23730032-23730262(+)$1	1	113	136	22.2230
(((((.............)))))	chr15:78461243-78461473(+)$1	1	140	163	23.2542
(................)))...	chr2:187542356-187542586(+)$1	1	99	122	20.0921
.((((...........))))..)	chr5:132216122-132216349(-)$1	1	80	103	21.1867
(((.((...........))))))	chr10:70743920-70744150(+)$1	1	20	43	21.8369
(((((.............)))))	chr16:24836037-24836267(+)$1	1	149	172	22.2031
(((((............))))))	chr1:203276943-203277173(+)$1	1	57	80	22.3631
((((.............)))).)	chr14:75598409-75598639(-)$1	1	39	62	22.3206
((((.............))))))	chr9:465092-465318(+)$1	1	154	177	23.1115
(((((............))))).	chr20:30824548-30824773(+)$1	1	105	128	22.1055
((((((...........))))))	chr1:92978921-92979146(-)$1	1	193	216	22.2807
(((..............))))))	chr11:113668598-113668828(-)$1	1	53	76	21.6081
.(((((...........))))).	chr1:52486055-52486291(-)$1	1	26	49	22.1284
..(((...........)))...)	chr15:50791592-50791821(+)$1	1	182	205	22.4106
((((..............)))))	chr16:69732593-69732823(+)$1	1	180	203	21.6729
..(((.............))).)	chr17:56589670-56589900(-)$1	1	97	120	22.0010
(((((............))))).	chr9:115060025-115060255(-)$1	1	7	30	22.1055
(((((................))	chr17:65071797-65072022(-)$1	1	28	51	20.0619
(.((.............)).)).	chr19:54652106-54652336(+)$1	1	87	110	21.3921
..(((.............)))..	chr20:46284655-46284877(+)$1	1	126	149	23.1155
(.((..............)))))	chr7:20452592-20452822(+)$1	1	38	61	21.3745
(((((.............)))))	chr4:142654206-142654426(+)$1	1	86	109	22.7623
(((..............))))).	chr20:34844710-34844940(+)$1	1	182	205	21.3154
(((((............))))))	chr3:156422988-156423222(+)$1	1	82	105	21.6304
((((((...........))))))	chr10:124923574-124923804(+)$1	1	96	119	21.3091
(((((............))))))	chr7:6442949-6443172(+)$1	1	132	155	21.6304
(.(((............)))..)	chr18:32917310-32917530(-)$1	1	161	184	23.7354
((.((.............)).))	chr7:5567266-5567491(-)$1	1	94	117	21.8427
(((((............))))))	chr7:23683299-23683529(+)$1	1	206	229	23.4308
((((.............)))).)	chr6:83906960-83907183(+)$1	1	84	107	22.1984
(((((............))))))	chr12:69232987-69233217(+)$1	1	11	34	21.6304
((.(((...........))).))	chr3:41281494-41281726(+)$1	1	167	190	22.2895
(((((................))	chr17:74730109-74730336(-)$1	1	151	174	18.9018
(.((((...........)))).)	chr6:82924080-82924310(-)$1	1	185	208	21.8467
.((((............))))))	chr14:81942172-81942397(-)$1	1	194	217	22.6200
(((((............))))))	chr15:89740542-89740767(+)$1	1	53	76	23.4308
..(((............)))...	chr5:65375988-65376213(+)$1	1	79	102	21.0865
..(((............)))..)	chr7:105195516-105195748(+)$1	1	63	86	23.7221
((((..............)))))	chr9:87636439-87636669(+)$1	1	206	229	21.6729
(.((.............))))))	chrX:15848393-15848623(-)$1	1	57	80	21.7767

#PSSM
e : 0.18	g : 0.13	f : 0.11	h : 0.08	! : 0.08	d : 0.08	# : 0.06	c : 0.05	i : 0.05	[ : 0.03	b : 0.03	: : 0.01	= : 0.01	" : 0.01	& : 0.01	' : 0.01	
e : 0.21	g : 0.11	f : 0.11	d : 0.11	h : 0.08	[ : 0.08	! : 0.05	# : 0.05	b : 0.03	y : 0.03	i : 0.03	c : 0.01	= : 0.01	& : 0.01	' : 0.01	
e : 0.19	c : 0.13	g : 0.11	f : 0.11	d : 0.11	b : 0.08	[ : 0.06	h : 0.06	y : 0.03	i : 0.03	# : 0.01	= : 0.01	
c : 0.19	e : 0.18	d : 0.11	b : 0.11	g : 0.09	f : 0.09	h : 0.06	y : 0.03	w : 0.03	i : 0.01	= : 0.01	[ : 0.01	
c : 0.18	e : 0.15	w : 0.11	v : 0.09	f : 0.09	d : 0.08	b : 0.06	g : 0.06	h : 0.06	y : 0.03	i : 0.01	= : 0.01	
u : 0.28	v : 0.24	w : 0.11	y : 0.08	c : 0.06	t : 0.06	d : 0.03	e : 0.03	i : 0.01	b : 0.01	g : 0.01	f : 0.01	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	t : 0.26	v : 0.24	w : 0.11	y : 0.08	
u : 0.28	v : 0.24	t : 0.19	w : 0.11	y : 0.08	e : 0.01	b : 0.01	d : 0.01	c : 0.01	
c : 0.16	v : 0.15	e : 0.13	d : 0.11	w : 0.08	g : 0.08	b : 0.08	y : 0.05	f : 0.05	h : 0.05	i : 0.03	
c : 0.23	e : 0.18	d : 0.11	b : 0.11	f : 0.09	g : 0.08	y : 0.05	h : 0.05	i : 0.03	4 : 0.01	= : 0.01	
c : 0.21	e : 0.18	d : 0.13	g : 0.09	f : 0.09	y : 0.05	b : 0.05	h : 0.05	] : 0.03	i : 0.03	4 : 0.01	= : 0.01	3 : 0.01	
e : 0.19	g : 0.11	d : 0.11	f : 0.09	] : 0.08	2 : 0.08	c : 0.06	y : 0.05	h : 0.05	i : 0.03	3 : 0.03	4 : 0.01	= : 0.01	b : 0.01	0 : 0.01	
e : 0.21	g : 0.13	f : 0.11	] : 0.09	2 : 0.09	h : 0.08	d : 0.06	b : 0.03	4 : 0.03	i : 0.03	3 : 0.03	: : 0.01	= : 0.01	0 : 0.01	
g : 0.16	f : 0.15	d : 0.09	e : 0.09	h : 0.08	: : 0.06	i : 0.06	c : 0.05	] : 0.05	b : 0.03	2 : 0.03	4 : 0.03	a : 0.01	= : 0.01	3 : 0.01	0 : 0.01	

#score	1314.4825008476132
#seq	60
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_CDS_m1_run2.txt

#BEAR
dddduuuuuuuuuuuudddde	chr10:104436559-104436789(-)$1	230	39	60	23.5995
dddbbtttttttttttbb]dd	chr9:5763482-5763705(+)$1	223	37	58	21.2321
:ddddtttttttttttdddd:	chr2:179590463-179590684(-)$1	221	45	66	20.8711
eeeeyyyyyyyyyyyyyyyye	chr9:34241602-34241832(+)$1	230	97	118	20.1916
dddduuuuuuuuuuuudddd=	chr19:1620902-1621132(-)$1	230	127	148	23.5826
!cccvvvvvvvvvvvvvccc2	chr15:52675228-52675455(-)$1	227	6	27	22.1351
#cccuuuuuuuuuuuuccc33	chr17:11811-12032(-)$1	221	28	49	22.7982
cyyyyyyyyyyyyyyyyccc5	chr16:24815986-24816216(+)$1	230	53	74	19.4843
:ddddtttttttttttdddd:	chr17:35550222-35550452(-)$1	230	51	72	20.8711
ddwwwwwwwwwwwwwwdddd]	chr17:71232068-71232298(+)$1	230	112	133	21.3879
dddvvvvvvvvvvvvvdddd:	chr13:41894775-41895000(+)$1	225	190	211	22.0696
iiiiuuuuuuuuuuuuiiiii	chr14:78221342-78221563(-)$1	221	60	81	22.3135
eee[attttttttttta]eee	chr2:44003823-44004046(+)$1	223	198	219	22.4177
eeeevvvvvvvvvvvvveeee	chr19:18965834-18966064(+)$1	230	136	157	22.5184
yyyyyyyyyyyyyyyybbbb]	chrX:53240876-53241106(-)$1	230	57	78	18.7779
ddccctttttttttttccc]d	chr7:6505622-6505844(-)$1	222	95	116	22.0523
yyyyyyyyyyyyyyyydddd]	chr1:231471278-231471508(-)$1	230	164	185	20.3067
[cccuuuuuuuuuuuucccff	chr13:25841827-25842052(-)$1	225	91	112	22.6679
dddduuuuuuuuuuuudddd:	chr17:38572634-38572864(-)$1	230	38	59	22.8721
eeeettttttttttteeeeed	chr7:97488542-97488763(-)$1	221	16	37	21.5169
eeeeuuuuuuuuuuuueeeee	chr15:25584273-25584503(-)$1	230	42	63	23.0825
:ccctttttttttttccc===	chr1:55330905-55331135(-)$1	230	27	48	20.6499
dddvvvvvvvvvvvvvdddd]	chr4:3502399-3502620(+)$1	221	123	144	22.9163
!!bbuuuuuuuuuuuubb22f	chr2:191760295-191760525(+)$1	230	83	104	21.0445
eeeevvvvvvvvvvvvveeee	chr15:65759321-65759551(-)$1	230	112	133	22.5184
ddbbuuuuuuuuuuuubb]dd	chr17:1580801-1581031(-)$1	230	177	198	21.9398
dddvvvvvvvvvvvvvddddb	chr11:122930362-122930592(-)$1	230	202	223	22.5314
dddvvvvvvvvvvvvvdddd:	chr22:47107965-47108188(-)$1	223	2	23	22.0696
eeeeettttttttttteeeee	chr9:107564315-107564536(-)$1	221	135	156	22.0475
eeeeettttttttttteeeee	chr2:204275913-204276143(+)$1	230	26	47	22.0475
!cccuuuuuuuuuuuuccc22	chr15:69561359-69561589(+)$1	230	36	57	22.5588
[ddddtttttttttttdddd]	chr10:121596347-121596577(-)$1	230	78	99	22.6043
ccccuuuuuuuuuuuuccc]c	chr6:32808681-32808902(-)$1	221	4	25	22.7377
====uuuuuuuuuuuu=====	chr3:45763425-45763655(+)$1	230	46	67	22.5954
ffffwwwwwwwwwwwwwwfff	chrX:13726759-13726989(+)$1	230	43	64	19.9625
ggggwwwwwwwwwwwwwwggg	chr15:45656900-45657130(-)$1	230	3	24	20.5081
dddduuuuuuuuuuuudddd3	chr7:105192022-105192244(+)$1	222	69	90	23.6974
:ccctttttttttttcccccc	chr11:134038272-134038498(-)$1	226	30	51	20.6105
dddduuuuuuuuuuuuddddd	chr3:138724754-138724975(+)$1	221	49	70	23.4855
dddduuuuuuuuuuuudddda	chr1:110563335-110563565(+)$1	230	49	70	23.5907
dddyyyyyyyyyyyyyyyydd	chr1:145595054-145595284(-)$1	230	178	199	20.6549
eeeettttttttttteeeee:	chr9:108226471-108226701(+)$1	230	55	76	20.9035
dddduuuuuuuuuuuudddd2	chr14:51192487-51192714(-)$1	227	122	143	23.4962
=====ttttttttttt=====	chr5:74077602-74077832(-)$1	230	87	108	21.4718
eeeewwwwwwwwwwwwwweee	chr2:25972518-25972748(-)$1	230	177	198	21.2610
eeeevvvvvvvvvvvvveeee	chr12:110878036-110878266(-)$1	230	194	215	22.5184
ffffwwwwwwwwwwwwwwfff	chr15:59408995-59409217(+)$1	222	89	110	19.9625
eeeevvvvvvvvvvvvveeee	chr2:219114040-219114270(+)$1	230	181	202	22.5184
c[ccctttttttttttccccc	chr12:53701600-53701830(-)$1	230	100	121	21.8155
dddduuuuuuuuuuuudddda	chr16:24820675-24820905(+)$1	230	72	93	23.5907
eeeevvvvvvvvvvvvveeee	chr4:122737905-122738128(-)$1	223	167	188	22.5184
eeeeuuuuuuuuuuuueeeee	chr8:27311595-27311825(+)$1	230	80	101	23.0825
fffvvvvvvvvvvvvvfffff	chr15:42579824-42580049(+)$1	225	107	128	20.8375
cccvvvvvvvvvvvvvcccgg	chr8:38646160-38646385(+)$1	225	108	129	22.0070
eeeeyyyyyyyyyyyyyyyye	chr5:150072425-150072649(-)$1	224	15	36	20.1916
dddduuuuuuuuuuuudddd:	chr6:97339027-97339250(-)$1	223	143	164	22.8721
ffffftttttttttttfffff	chr12:55356379-55356609(-)$1	230	145	166	20.4070
ffffwwwwwwwwwwwwwwfff	chr20:47705692-47705917(+)$1	225	71	92	19.9625
dddwwwwwwwwwwwwwwdddd	chr22:41363707-41363931(+)$1	224	97	118	21.6221
:ddddtttttttttttdddd:	chr4:73956607-73956831(-)$1	224	120	141	20.8711
eeeeuuuuuuuuuuuueeeee	chrX:44870137-44870362(+)$1	225	107	128	23.0825
[ddddtttttttttttdddd]	chr7:156974216-156974451(+)$1	235	161	182	22.6043
dddduuuuuuuuuuuudddd6	chr7:6063011-6063236(+)$1	225	38	59	23.2238

#otherMatches

#Seq PSSM
UGGUGCUUUUCUUAUAACUAA	chr10:104436559-104436789(-)$1	230	39	60	23.5995
UCUACGUCAACUUCUGGUCAG	chr9:5763482-5763705(+)$1	223	37	58	21.2321
AGCAAGAAAUACAAGAUUGCA	chr2:179590463-179590684(-)$1	221	45	66	20.8711
AGCCUCUUCAUAAACCCAAUG	chr9:34241602-34241832(+)$1	230	97	118	20.1916
GCCCUUCUACCCCCGUGGGCU	chr19:1620902-1621132(-)$1	230	127	148	23.5826
UGUUUUACCUCACCUUUGACU	chr15:52675228-52675455(-)$1	227	6	27	22.1351
AAGAUCAUUUUUCUCUUCUCC	chr17:11811-12032(-)$1	221	28	49	22.7982
AGAUGAAUCCCAAAACAUGCA	chr16:24815986-24816216(+)$1	230	53	74	19.4843
AUGUCUAUGAACUACUGACAC	chr17:35550222-35550452(-)$1	230	51	72	20.8711
GAAAAUAUUCCUCAACUCUAC	chr17:71232068-71232298(+)$1	230	112	133	21.3879
UACUUCAUUCUUAAAUGUACA	chr13:41894775-41895000(+)$1	225	190	211	22.0696
AGUUUUUUAAAUUUCUGACUU	chr14:78221342-78221563(-)$1	221	60	81	22.3135
UUGGCAGUAAAAAUGGGGUAA	chr2:44003823-44004046(+)$1	223	198	219	22.4177
CCUGAUCCAGGGCCCGCCAGG	chr19:18965834-18966064(+)$1	230	136	157	22.5184
GCUACCCGGGAAUACACUCUG	chrX:53240876-53241106(-)$1	230	57	78	18.7779
UCCAGACCAUCCUAUACUGUG	chr7:6505622-6505844(-)$1	222	95	116	22.0523
GAAUCCUGAAAGUACAACAUC	chr1:231471278-231471508(-)$1	230	164	185	20.3067
AUUGCCAUGAUAUUUACAACU	chr13:25841827-25842052(-)$1	225	91	112	22.6679
UCAUGAUAACAGAACAAUGAA	chr17:38572634-38572864(-)$1	230	38	59	22.8721
ACCUAAUUUGAAUAAAGGUAU	chr7:97488542-97488763(-)$1	221	16	37	21.5169
AAGUGUAUUUCCCAUGACUUA	chr15:25584273-25584503(-)$1	230	42	63	23.0825
UGGCAAUUACUACAAGCCGUG	chr1:55330905-55331135(-)$1	230	27	48	20.6499
CUGGAGCAGAGGAAGGCAGCC	chr4:3502399-3502620(+)$1	221	123	144	22.9163
GUAUGGAUAUGUUAAGAUUAA	chr2:191760295-191760525(+)$1	230	83	104	21.0445
UGGCUACUCACAUUCUUGCUG	chr15:65759321-65759551(-)$1	230	112	133	22.5184
GUGGUUUUCUCUGUGUCCAAC	chr17:1580801-1581031(-)$1	230	177	198	21.9398
AACUGAAUGCUGACCUGUUCC	chr11:122930362-122930592(-)$1	230	202	223	22.5314
CAGACCAAAGCAUUUACUGGU	chr22:47107965-47108188(-)$1	223	2	23	22.0696
ACUUCCUCCGAGUCAAGAAGU	chr9:107564315-107564536(-)$1	221	135	156	22.0475
UAUUAUCCUUUCCUUUUAAUG	chr2:204275913-204276143(+)$1	230	26	47	22.0475
CAGGAACCAUCUAUGACCUCC	chr15:69561359-69561589(+)$1	230	36	57	22.5588
AGAAGGUGGAUUAUGACUUCA	chr10:121596347-121596577(-)$1	230	78	99	22.6043
UUCAACAUAACAUCAGUGACA	chr6:32808681-32808902(-)$1	221	4	25	22.7377
UUAAUUUUUUUUCUAUUUAGG	chr3:45763425-45763655(+)$1	230	46	67	22.5954
GUAUAAAGGAAUGUAAUGGUG	chrX:13726759-13726989(+)$1	230	43	64	19.9625
AUUAGAGACUAAUAAUAAUAA	chr15:45656900-45657130(-)$1	230	3	24	20.5081
UGGAUGAAAUGAAAGUUCCAG	chr7:105192022-105192244(+)$1	222	69	90	23.6974
AGUCAAACAAAGAGAGACGAA	chr11:134038272-134038498(-)$1	226	30	51	20.6105
CCUCUGGGAUCAGGAUGAGGG	chr3:138724754-138724975(+)$1	221	49	70	23.4855
UUUGAUGCCCACCUUACAGAG	chr1:110563335-110563565(+)$1	230	49	70	23.5907
GGACCUUCUCCCCAUUUCCUC	chr1:145595054-145595284(-)$1	230	178	199	20.6549
AGAGGAUCAUUUCAACUCUGG	chr9:108226471-108226701(+)$1	230	55	76	20.9035
UAACUCGUUAACUUAUGUUGU	chr14:51192487-51192714(-)$1	227	122	143	23.4962
CAAGAAAGAAAGCACAUCUUG	chr5:74077602-74077832(-)$1	230	87	108	21.4718
UCUCAAGGUAAGAGAAUGGAG	chr2:25972518-25972748(-)$1	230	177	198	21.2610
gauaauaccaaccuugcuauc	chr12:110878036-110878266(-)$1	230	194	215	22.5184
UGCCACUACACUUCUUAAGGC	chr15:59408995-59409217(+)$1	222	89	110	19.9625
CUGGGUCUUUUCCUCCACCAG	chr2:219114040-219114270(+)$1	230	181	202	22.5184
CUCACCUUUUCUUCUAGUGGC	chr12:53701600-53701830(-)$1	230	100	121	21.8155
ACAGUGGACAGCAUUUCUGUG	chr16:24820675-24820905(+)$1	230	72	93	23.5907
GUGCUUUUUCUUGUUUUGCAC	chr4:122737905-122738128(-)$1	223	167	188	22.5184
CCAGCCCACAGCUAACCUGGA	chr8:27311595-27311825(+)$1	230	80	101	23.0825
UCAGGCUUAAAAUUAAUGAAG	chr15:42579824-42580049(+)$1	225	107	128	20.8375
UCCGAUCACCUUUCAAGGAGU	chr8:38646160-38646385(+)$1	225	108	129	22.0070
CACAAUUGUUCUCCCCUCUAU	chr5:150072425-150072649(-)$1	224	15	36	20.1916
CUGCUGAGAAAAUAAUGCAGG	chr6:97339027-97339250(-)$1	223	143	164	22.8721
AGCUCAGAUAAGGAGAGAGCU	chr12:55356379-55356609(-)$1	230	145	166	20.4070
UUUUUUUUUUUUAAUUUCAGA	chr20:47705692-47705917(+)$1	225	71	92	19.9625
UGCUUUUCACUUCCACUGCAU	chr22:41363707-41363931(+)$1	224	97	118	21.6221
CACAGUGUUCCCUCUUCUGUC	chr4:73956607-73956831(-)$1	224	120	141	20.8711
CAUUAUAAUGCAUUUCAGUGG	chrX:44870137-44870362(+)$1	225	107	128	23.0825
UGGAUUUAUUGAUUUUGUCCU	chr7:156974216-156974451(+)$1	235	161	182	22.6043
ACCCUUAUAGAUAGCUGGGUA	chr7:6063011-6063236(+)$1	225	38	59	23.2238

#DB
((((............)))))	chr10:104436559-104436789(-)$1	1	39	60	23.5995
(((((...........)).))	chr9:5763482-5763705(+)$1	1	37	58	21.2321
.((((...........)))).	chr2:179590463-179590684(-)$1	1	45	66	20.8711
((((................)	chr9:34241602-34241832(+)$1	1	97	118	20.1916
((((............))))(	chr19:1620902-1621132(-)$1	1	127	148	23.5826
.(((.............))).	chr15:52675228-52675455(-)$1	1	6	27	22.1351
.(((............)))..	chr17:11811-12032(-)$1	1	28	49	22.7982
(................))).	chr16:24815986-24816216(+)$1	1	53	74	19.4843
.((((...........)))).	chr17:35550222-35550452(-)$1	1	51	72	20.8711
((..............)))).	chr17:71232068-71232298(+)$1	1	112	133	21.3879
(((.............)))).	chr13:41894775-41895000(+)$1	1	190	211	22.0696
((((............)))))	chr14:78221342-78221563(-)$1	1	60	81	22.3135
(((.(...........).)))	chr2:44003823-44004046(+)$1	1	198	219	22.4177
((((.............))))	chr19:18965834-18966064(+)$1	1	136	157	22.5184
................)))).	chrX:53240876-53241106(-)$1	1	57	78	18.7779
(((((...........))).)	chr7:6505622-6505844(-)$1	1	95	116	22.0523
................)))).	chr1:231471278-231471508(-)$1	1	164	185	20.3067
.(((............)))))	chr13:25841827-25842052(-)$1	1	91	112	22.6679
((((............)))).	chr17:38572634-38572864(-)$1	1	38	59	22.8721
((((...........)))))(	chr7:97488542-97488763(-)$1	1	16	37	21.5169
((((............)))))	chr15:25584273-25584503(-)$1	1	42	63	23.0825
.(((...........)))(((	chr1:55330905-55331135(-)$1	1	27	48	20.6499
(((.............)))).	chr4:3502399-3502620(+)$1	1	123	144	22.9163
..((............))..)	chr2:191760295-191760525(+)$1	1	83	104	21.0445
((((.............))))	chr15:65759321-65759551(-)$1	1	112	133	22.5184
((((............)).))	chr17:1580801-1581031(-)$1	1	177	198	21.9398
(((.............)))))	chr11:122930362-122930592(-)$1	1	202	223	22.5314
(((.............)))).	chr22:47107965-47108188(-)$1	1	2	23	22.0696
(((((...........)))))	chr9:107564315-107564536(-)$1	1	135	156	22.0475
(((((...........)))))	chr2:204275913-204276143(+)$1	1	26	47	22.0475
.(((............)))..	chr15:69561359-69561589(+)$1	1	36	57	22.5588
.((((...........)))).	chr10:121596347-121596577(-)$1	1	78	99	22.6043
((((............))).)	chr6:32808681-32808902(-)$1	1	4	25	22.7377
((((............)))))	chr3:45763425-45763655(+)$1	1	46	67	22.5954
((((..............)))	chrX:13726759-13726989(+)$1	1	43	64	19.9625
((((..............)))	chr15:45656900-45657130(-)$1	1	3	24	20.5081
((((............)))).	chr7:105192022-105192244(+)$1	1	69	90	23.6974
.(((...........)))(((	chr11:134038272-134038498(-)$1	1	30	51	20.6105
((((............))))(	chr3:138724754-138724975(+)$1	1	49	70	23.4855
((((............)))))	chr1:110563335-110563565(+)$1	1	49	70	23.5907
(((................))	chr1:145595054-145595284(-)$1	1	178	199	20.6549
((((...........))))).	chr9:108226471-108226701(+)$1	1	55	76	20.9035
((((............)))).	chr14:51192487-51192714(-)$1	1	122	143	23.4962
(((((...........)))))	chr5:74077602-74077832(-)$1	1	87	108	21.4718
((((..............)))	chr2:25972518-25972748(-)$1	1	177	198	21.2610
((((.............))))	chr12:110878036-110878266(-)$1	1	194	215	22.5184
((((..............)))	chr15:59408995-59409217(+)$1	1	89	110	19.9625
((((.............))))	chr2:219114040-219114270(+)$1	1	181	202	22.5184
(.(((...........)))))	chr12:53701600-53701830(-)$1	1	100	121	21.8155
((((............)))))	chr16:24820675-24820905(+)$1	1	72	93	23.5907
((((.............))))	chr4:122737905-122738128(-)$1	1	167	188	22.5184
((((............)))))	chr8:27311595-27311825(+)$1	1	80	101	23.0825
(((.............)))))	chr15:42579824-42580049(+)$1	1	107	128	20.8375
(((.............)))((	chr8:38646160-38646385(+)$1	1	108	129	22.0070
((((................)	chr5:150072425-150072649(-)$1	1	15	36	20.1916
((((............)))).	chr6:97339027-97339250(-)$1	1	143	164	22.8721
(((((...........)))))	chr12:55356379-55356609(-)$1	1	145	166	20.4070
((((..............)))	chr20:47705692-47705917(+)$1	1	71	92	19.9625
(((..............))))	chr22:41363707-41363931(+)$1	1	97	118	21.6221
.((((...........)))).	chr4:73956607-73956831(-)$1	1	120	141	20.8711
((((............)))))	chrX:44870137-44870362(+)$1	1	107	128	23.0825
.((((...........)))).	chr7:156974216-156974451(+)$1	1	161	182	22.6043
((((............)))).	chr7:6063011-6063236(+)$1	1	38	59	23.2238

#PSSM
d : 0.31	e : 0.25	: : 0.07	f : 0.07	c : 0.06	! : 0.04	[ : 0.04	y : 0.03	= : 0.03	# : 0.01	i : 0.01	g : 0.01	
d : 0.39	e : 0.25	c : 0.12	f : 0.07	y : 0.04	= : 0.03	i : 0.01	! : 0.01	g : 0.01	[ : 0.01	
d : 0.34	e : 0.25	c : 0.15	f : 0.07	y : 0.04	b : 0.03	= : 0.03	w : 0.01	i : 0.01	g : 0.01	
d : 0.23	e : 0.23	c : 0.14	v : 0.09	y : 0.06	f : 0.06	b : 0.04	w : 0.03	= : 0.03	i : 0.01	[ : 0.01	g : 0.01	
u : 0.33	v : 0.19	w : 0.11	y : 0.09	d : 0.07	t : 0.06	c : 0.03	e : 0.03	b : 0.01	a : 0.01	= : 0.01	f : 0.01	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.26	v : 0.19	w : 0.11	y : 0.09	
u : 0.33	t : 0.20	v : 0.19	w : 0.11	y : 0.09	e : 0.03	c : 0.03	
d : 0.33	c : 0.14	e : 0.11	v : 0.09	w : 0.09	b : 0.06	y : 0.06	= : 0.03	f : 0.03	i : 0.01	a : 0.01	
d : 0.34	e : 0.19	c : 0.17	w : 0.07	b : 0.06	y : 0.04	= : 0.03	f : 0.03	i : 0.01	] : 0.01	
d : 0.34	e : 0.22	c : 0.15	f : 0.07	y : 0.04	= : 0.04	] : 0.03	i : 0.01	b : 0.01	2 : 0.01	g : 0.01	
d : 0.39	e : 0.22	f : 0.09	c : 0.06	= : 0.04	y : 0.03	] : 0.03	2 : 0.03	g : 0.03	3 : 0.01	i : 0.01	b : 0.01	
e : 0.23	: : 0.12	d : 0.11	f : 0.11	] : 0.09	= : 0.06	2 : 0.04	c : 0.04	3 : 0.03	g : 0.03	a : 0.03	5 : 0.01	i : 0.01	b : 0.01	6 : 0.01	

#score	1378.3434604035613
#seq	63
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_UTR_m3_run1.txt

#BEAR
!!eeeeeqqqqqqqqeeeee22a2	chr6:97679374-97679614(-)$1	240	106	130	15.6862
ggggcccqqqqqqqqccc333ggg	chr7:100028783-100029052(+)$1	269	215	239	16.6189
fff[cccqqqqqqqqcccffffff	chr12:90049473-90049858(-)$1	385	201	225	15.5637
c!!ddddqqqqqqqqdddd22ccc	chr1:115248025-115248349(-)$1	324	107	131	15.2946
ggggg[aqqqqqqqqa]ggggggg	chr6:36570104-36570396(+)$1	292	44	68	16.1608
"bb!!bbqqqqqqqqbb22bb333	chr12:54635146-54635413(-)$1	267	51	75	14.2026
[ccc[bbqqqqqqqqbb]ccc]cc	chr5:179041714-179042009(-)$1	295	153	177	15.2015
fffff[aqqqqqqqqa]ffffff:	chr3:27415271-27415514(-)$1	243	29	53	14.4009
hffffffqqqqqqqqffffffccc	chr1:203839406-203839637(+)$1	231	129	153	15.2162
##eeeeeqqqqqqqqeeeeeeeee	chr22:36906860-36907089(-)$1	229	55	79	15.2274
gggggggqqqqqqqqggggggg]f	chr11:115045235-115045529(-)$1	294	48	72	16.2843
ggggcccqqqqqqqqccc22gggg	chr1:212793395-212793707(+)$1	312	80	104	16.0885
c[eeeeeqqqqqqqqeeeee]ccc	chr12:57031869-57032126(-)$1	257	219	243	15.6656
gggggggqqqqqqqqggggggg::	chr12:76440425-76440677(-)$1	252	187	211	14.7004
###bb[aqqqqqqqqa]bb22eee	chr6:139498480-139498812(+)$1	332	16	40	14.1434
ddeeeeeqqqqqqqqeeeee]ddd	chr2:97476856-97477110(+)$1	254	117	141	14.5960
b[eeeeeqqqqqqqqeeeee333b	chr1:114516525-114516910(+)$1	385	19	43	15.6661
!ccccccqqqqqqqqccc]ccc33	chr1:162497276-162497557(+)$1	281	171	195	16.4682
=======qqqqqqqq=========	chr8:38827437-38827696(+)$1	259	80	104	16.5609
[a[ddddqqqqqqqqdddd4444a	chr6:34741340-34741570(+)$1	230	122	146	15.5229
=======qqqqqqqq=========	chr12:131361224-131361557(+)$1	333	44	68	16.5609
h!!ddddqqqqqqqqdddd>>>>>	chr17:42875880-42876203(-)$1	323	31	55	14.5339
iiiiiiiqqqqqqqqiiiiiiiii	chr12:94701897-94702148(-)$1	251	70	94	16.0547
cc[ddddqqqqqqqqdddd22ccc	chr6:97338658-97338903(-)$1	245	160	184	15.1361
[ffffffqqqqqqqqffffffbb9	chrX:70279008-70279314(-)$1	306	25	49	14.4546
eee!!bbqqqqqqqqbb22eeeee	chr13:21548153-21548400(-)$1	247	126	150	14.1721
!!ccc[aqqqqqqqqa]ccc22gg	chr2:105963562-105963894(+)$1	332	13	37	15.9007
dffffffqqqqqqqqffffff444	chr9:74969467-74969721(-)$1	254	96	120	15.4089
"""ddddqqqqqqqqddddfffff	chr3:44483195-44483435(-)$1	240	63	87	15.0371
cffffffqqqqqqqqffffff444	chr9:23691660-23691932(-)$1	272	35	59	15.5785
i"""cccqqqqqqqqccc333iii	chr13:36878167-36878487(-)$1	320	197	221	16.4654
cccddddqqqqqqqqdddd]ccc4	chr8:28423201-28423488(+)$1	287	95	119	15.1862
!ddddbbqqqqqqqqbb]dddd22	chr21:15745812-15746117(-)$1	305	48	72	13.9145
eee[cccqqqqqqqqccceeeee]	chr7:131173353-131173693(+)$1	340	186	210	15.5945
!ccc[bbqqqqqqqqbb]ccc22c	chr1:171561228-171561610(+)$1	382	259	283	15.0573
gggggggqqqqqqqqggggggg]c	chrX:20143252-20143519(-)$1	267	164	188	16.3901
cceeeeeqqqqqqqqeeeeeccc"	chr6:109687919-109688196(-)$1	277	35	59	15.0882
!ccccccqqqqqqqqccc]ccc33	chr17:73773609-73773851(-)$1	242	72	96	16.4682
[ffffffqqqqqqqqffffff333	chr12:109524240-109524588(+)$1	348	208	232	16.0897
ee!!cccqqqqqqqqccc22eeee	chr14:56764949-56765203(+)$1	254	5	29	15.3644
ee!!cccqqqqqqqqccc333eee	chr11:126133583-126133820(-)$1	237	14	38	16.0459
"ffffffqqqqqqqqffffff444	chr2:69552647-69552922(-)$1	275	77	101	15.7054
gggggggqqqqqqqqgggggggHH	chr4:139089077-139089317(-)$1	240	0	24	15.0721
e!!ddddqqqqqqqqddddeeeee	chr1:111489970-111490209(-)$1	239	19	43	14.9772
bb[ddddqqqqqqqqdddd]bb]d	chr2:234201833-234202075(+)$1	242	106	130	14.0206
d[eeeeeqqqqqqqqeeeee22dd	chr1:53152879-53153145(-)$1	266	215	239	15.0690
[ffffffqqqqqqqqffffff]a2	chr5:150088819-150089053(-)$1	234	71	95	15.5487
f[eeeeeqqqqqqqqeeeee22ff	chr13:41131580-41131838(-)$1	258	167	191	15.2712
fffffbbqqqqqqqqbb]ffffff	chr3:176738447-176738710(-)$1	263	167	191	14.5396
g[eeeeeqqqqqqqqeeeee]ggg	chr3:48964677-48964923(+)$1	246	201	225	15.8204
:ffffffqqqqqqqqffffffccc	chr5:133291976-133292278(-)$1	302	195	219	14.3344
=======qqqqqqqq=========	chr11:61066940-61067180(-)$1	240	15	39	16.5609
ggggg[aqqqqqqqqaggggggg:	chr1:179070350-179070610(-)$1	260	221	245	15.5122
e[bb[bbqqqqqqqqbbbb333ee	chr12:49522521-49522759(-)$1	238	46	70	14.3079
gggggggqqqqqqqqgggggggii	chr7:44841192-44841458(+)$1	266	146	170	16.3178
eee[cccqqqqqqqqccc]eeeee	chr3:150260294-150260741(-)$1	447	223	247	15.5560
ccc[cccqqqqqqqqccc]cccgg	chr10:70482127-70482381(+)$1	254	145	169	16.0276
gggggggqqqqqqqqgggggggff	chr18:32917196-32917492(-)$1	296	236	260	16.1175
###ddddqqqqqqqqdddd22ggg	chr15:100254117-100254397(+)$1	280	116	140	15.2150
+ccc[bbqqqqqqqqbb]ccc>>>	chr6:18224349-18224667(-)$1	318	181	205	13.9441
ccc[cccqqqqqqqqccc]ccc::	chr5:14693983-14694236(+)$1	253	102	126	14.4039
[bb[cccqqqqqqqqccc]bb]a:	chr11:117038773-117039100(+)$1	327	272	296	14.4212
e!!ddddqqqqqqqqddddeeeee	chr15:99505599-99505839(+)$1	240	42	66	14.9772
gggggggqqqqqqqqggggggg22	chr12:74932795-74933200(+)$1	405	253	277	16.2091
gggggggqqqqqqqqggggggg::	chr5:65476493-65476796(+)$1	303	26	50	14.7004
i[eeeeeqqqqqqqqeeeeeiiii	chr5:178032217-178032485(-)$1	268	64	88	15.7508
gggggggqqqqqqqqgggggggdd	chr17:61667977-61668220(+)$1	243	40	64	15.9887

#otherMatches

#Seq PSSM
UUGGCUUCCUUUUAAAGGCCUUGC	chr6:97679374-97679614(-)$1	240	106	130	15.6862
AUGUGGGCCAUCUGACCCUGAGCA	chr7:100028783-100029052(+)$1	269	215	239	16.6189
GACAUGGCAAACAACUCAGUUGCU	chr12:90049473-90049858(-)$1	385	201	225	15.5637
UAGGUGUGAAUUUUGGCACAAAGG	chr1:115248025-115248349(-)$1	324	107	131	15.2946
AGCUGGGAUAUAGGCUGCAGCUAU	chr6:36570104-36570396(+)$1	292	44	68	16.1608
UUAAUGAUAAGUGUCUCUCUGUGA	chr12:54635146-54635413(-)$1	267	51	75	14.2026
GGAUGGGGAAUGUAAUUGAUCGAU	chr5:179041714-179042009(-)$1	295	153	177	15.2015
ACACAGUCUUUCUAAAGUGUGUGU	chr3:27415271-27415514(-)$1	243	29	53	14.4009
UGCUCAACACUCUCAUUGAGUCAC	chr1:203839406-203839637(+)$1	231	129	153	15.2162
AACCAGUGAUGUGGAGCUGGAGUU	chr22:36906860-36907089(-)$1	229	55	79	15.2274
uauauauauauauaaauauauauu	chr11:115045235-115045529(-)$1	294	48	72	16.2843
CAGAUCUGGUUUCUAAGAGUUUUG	chr1:212793395-212793707(+)$1	312	80	104	16.0885
UAUUUAAuuuuaguuuuagagaca	chr12:57031869-57032126(-)$1	257	219	243	15.6656
AAAAUUACAUUGAAUUGAUUUUUA	chr12:76440425-76440677(-)$1	252	187	211	14.7004
AUGCAGCUUUAAGAUGGUGGGGAG	chr6:139498480-139498812(+)$1	332	16	40	14.1434
AAAAAAGACACCAGACUUUUGUUC	chr2:97476856-97477110(+)$1	254	117	141	14.5960
UGGUCAGGAAAAAUGCUGAUAGAA	chr1:114516525-114516910(+)$1	385	19	43	15.6661
UUACCAAAUGACUGCUUGAGUGUU	chr1:162497276-162497557(+)$1	281	171	195	16.4682
AAUUUGGGGAAGUCACUAGGUUAG	chr8:38827437-38827696(+)$1	259	80	104	16.5609
GUCCUAUGAAAGAGAAUAGUUUUG	chr6:34741340-34741570(+)$1	230	122	146	15.5229
GCAGGAGGUUGGGAAUUCUUGCUG	chr12:131361224-131361557(+)$1	333	44	68	16.5609
AUUAUACUCUCAAUUGUGUUUUAA	chr17:42875880-42876203(-)$1	323	31	55	14.5339
UAAAGAGCUUAAUUUUUUUUUAAU	chr12:94701897-94702148(-)$1	251	70	94	16.0547
CUGUACCUUUAUUAUGGUGAAAGA	chr6:97338658-97338903(-)$1	245	160	184	15.1361
AUUUGUAUCCUCUGUUAUAGACAU	chrX:70279008-70279314(-)$1	306	25	49	14.4546
UCUUUAAAUGAGGUGUUCUAGACA	chr13:21548153-21548400(-)$1	247	126	150	14.1721
UUAAUCAUUCUGCCUUUAUUCCAA	chr2:105963562-105963894(+)$1	332	13	37	15.9007
CCUGUUUUCAUCUGUAAAUAGUUA	chr9:74969467-74969721(-)$1	254	96	120	15.4089
GAAAUGAGUAUAAAAUCAUGUAUU	chr3:44483195-44483435(-)$1	240	63	87	15.0371
UAUUUUUAUAAAAAAGAAAAUUUG	chr9:23691660-23691932(-)$1	272	35	59	15.5785
UCUCAAGUUUAUUUUUUUCCAAGU	chr13:36878167-36878487(-)$1	320	197	221	16.4654
AGCAGUUUUAAGUCUAACUAGCUU	chr8:28423201-28423488(+)$1	287	95	119	15.1862
UCUGUAGACCCUGACCUAGCAGUA	chr21:15745812-15746117(-)$1	305	48	72	13.9145
GUCCAGUGGUAUACAACUGACAGG	chr7:131173353-131173693(+)$1	340	186	210	15.5945
AGCCUUAUUUUUUAUUAUGGCAGC	chr1:171561228-171561610(+)$1	382	259	283	15.0573
UGCAAGUUGCUAGGUACUUGUGAG	chrX:20143252-20143519(-)$1	267	164	188	16.3901
CCUGACACACAUUCAUGUCAACAU	chr6:109687919-109688196(-)$1	277	35	59	15.0882
ACCGAAGUUCUUUUUCUUGUGGCA	chr17:73773609-73773851(-)$1	242	72	96	16.4682
AUGUAAUUACACUGUAUUAUAAAA	chr12:109524240-109524588(+)$1	348	208	232	16.0897
CAAACUAAAUUUAAGUGGGAUGAU	chr14:56764949-56765203(+)$1	254	5	29	15.3644
GCUCUUGCCCAAUACCAAAUCGCC	chr11:126133583-126133820(-)$1	237	14	38	16.0459
UUGAAAUUUGUUUCUGUUUUGUUU	chr2:69552647-69552922(-)$1	275	77	101	15.7054
uuuguugaagaagaccagcaaagu	chr4:139089077-139089317(-)$1	240	0	24	15.0721
AUCAGCUCCAAACUUAGCUUUUCC	chr1:111489970-111490209(-)$1	239	19	43	14.9772
GCUCUCUGUAUAUCUGGAGUGUGC	chr2:234201833-234202075(+)$1	242	106	130	14.0206
GAACGUAUCUUGGUUUACGUAAUU	chr1:53152879-53153145(-)$1	266	215	239	15.0690
GCUCCAUAUUUGCCAGUGGAGGAA	chr5:150088819-150089053(-)$1	234	71	95	15.5487
UGUUCAUAAGUUCAGAUGGGUAGC	chr13:41131580-41131838(-)$1	258	167	191	15.2712
UAUGUUGGCUGUGUACAUAUAUAA	chr3:176738447-176738710(-)$1	263	167	191	14.5396
UUUUUUCCUCCCUUAGAAGACAAA	chr3:48964677-48964923(+)$1	246	201	225	15.8204
UUCCAAGAAAACUGCUUUGGAUAU	chr5:133291976-133292278(-)$1	302	195	219	14.3344
UUUCAUUGUCUGUGAAGUGAGACC	chr11:61066940-61067180(-)$1	240	15	39	16.5609
GGUCAUGAUUCAAAGCUGACUUGG	chr1:179070350-179070610(-)$1	260	221	245	15.5122
GUGCACCGGUCUUCAGGGCUUCUU	chr12:49522521-49522759(-)$1	238	46	70	14.3079
UACUUUCCAGUCCCAGGAAGUGUC	chr7:44841192-44841458(+)$1	266	146	170	16.3178
UGUUUGUGUUUUUUAAUGUACAAU	chr3:150260294-150260741(-)$1	447	223	247	15.5560
UGGAGGACAGAAGAAUCCGCCAUG	chr10:70482127-70482381(+)$1	254	145	169	16.0276
UCUUUUUAGACAUCAGAGAAGACA	chr18:32917196-32917492(-)$1	296	236	260	16.1175
UUUAAUUAUUAGCCCAGUUUUUUC	chr15:100254117-100254397(+)$1	280	116	140	15.2150
UGAGACCUAAUAAUUGGCCUUCGA	chr6:18224349-18224667(-)$1	318	181	205	13.9441
UCCACCUGCUUUCAGAGGAGGAAC	chr5:14693983-14694236(+)$1	253	102	126	14.4039
GAGGGUAUUAUUUUUUAUGCUGCU	chr11:117038773-117039100(+)$1	327	272	296	14.4212
ACCAGUGGCGAAAGACACUUUCUU	chr15:99505599-99505839(+)$1	240	42	66	14.9772
AGUAGGGCGGUCAUUUCCUACUCU	chr12:74932795-74933200(+)$1	405	253	277	16.2091
UCAGCCACAUACGGUUGGCUGGUA	chr5:65476493-65476796(+)$1	303	26	50	14.7004
AUGGAGAGUACUAAAUUUCUUUUU	chr5:178032217-178032485(-)$1	268	64	88	15.7508
GGGGAAAGUUGGCUGUUUCCUUGC	chr17:61667977-61668220(+)$1	243	40	64	15.9887

#DB
..(((((........)))))..).	chr6:97679374-97679614(-)$1	1	106	130	15.6862
(((((((........)))...)))	chr7:100028783-100029052(+)$1	1	215	239	16.6189
(((.(((........)))))))))	chr12:90049473-90049858(-)$1	1	201	225	15.5637
(..((((........))))..)))	chr1:115248025-115248349(-)$1	1	107	131	15.2946
(((((.(........).)))))))	chr6:36570104-36570396(+)$1	1	44	68	16.1608
.((..((........))..))...	chr12:54635146-54635413(-)$1	1	51	75	14.2026
.(((.((........)).))).))	chr5:179041714-179042009(-)$1	1	153	177	15.2015
(((((.(........).)))))).	chr3:27415271-27415514(-)$1	1	29	53	14.4009
)((((((........))))))(((	chr1:203839406-203839637(+)$1	1	129	153	15.2162
..(((((........)))))))))	chr22:36906860-36907089(-)$1	1	55	79	15.2274
(((((((........))))))).)	chr11:115045235-115045529(-)$1	1	48	72	16.2843
(((((((........)))..))))	chr1:212793395-212793707(+)$1	1	80	104	16.0885
(.(((((........))))).)))	chr12:57031869-57032126(-)$1	1	219	243	15.6656
(((((((........)))))))..	chr12:76440425-76440677(-)$1	1	187	211	14.7004
...((.(........).))..)))	chr6:139498480-139498812(+)$1	1	16	40	14.1434
(((((((........))))).)))	chr2:97476856-97477110(+)$1	1	117	141	14.5960
(.(((((........)))))...)	chr1:114516525-114516910(+)$1	1	19	43	15.6661
.((((((........))).)))..	chr1:162497276-162497557(+)$1	1	171	195	16.4682
(((((((........)))))))))	chr8:38827437-38827696(+)$1	1	80	104	16.5609
.(.((((........))))....)	chr6:34741340-34741570(+)$1	1	122	146	15.5229
(((((((........)))))))))	chr12:131361224-131361557(+)$1	1	44	68	16.5609
(..((((........)))).....	chr17:42875880-42876203(-)$1	1	31	55	14.5339
(((((((........)))))))))	chr12:94701897-94702148(-)$1	1	70	94	16.0547
((.((((........))))..)))	chr6:97338658-97338903(-)$1	1	160	184	15.1361
.((((((........)))))))).	chrX:70279008-70279314(-)$1	1	25	49	14.4546
(((..((........))..)))))	chr13:21548153-21548400(-)$1	1	126	150	14.1721
..(((.(........).)))..))	chr2:105963562-105963894(+)$1	1	13	37	15.9007
(((((((........))))))...	chr9:74969467-74969721(-)$1	1	96	120	15.4089
...((((........)))))))))	chr3:44483195-44483435(-)$1	1	63	87	15.0371
(((((((........))))))...	chr9:23691660-23691932(-)$1	1	35	59	15.5785
(...(((........)))...)))	chr13:36878167-36878487(-)$1	1	197	221	16.4654
(((((((........)))).))).	chr8:28423201-28423488(+)$1	1	95	119	15.1862
.((((((........)).))))..	chr21:15745812-15746117(-)$1	1	48	72	13.9145
(((.(((........)))))))).	chr7:131173353-131173693(+)$1	1	186	210	15.5945
.(((.((........)).)))..)	chr1:171561228-171561610(+)$1	1	259	283	15.0573
(((((((........))))))).)	chrX:20143252-20143519(-)$1	1	164	188	16.3901
))(((((........)))))(((.	chr6:109687919-109688196(-)$1	1	35	59	15.0882
.((((((........))).)))..	chr17:73773609-73773851(-)$1	1	72	96	16.4682
.((((((........))))))...	chr12:109524240-109524588(+)$1	1	208	232	16.0897
((..(((........)))..))))	chr14:56764949-56765203(+)$1	1	5	29	15.3644
((..(((........)))...)))	chr11:126133583-126133820(-)$1	1	14	38	16.0459
.((((((........))))))...	chr2:69552647-69552922(-)$1	1	77	101	15.7054
(((((((........)))))))((	chr4:139089077-139089317(-)$1	1	0	24	15.0721
(..((((........)))))))))	chr1:111489970-111490209(-)$1	1	19	43	14.9772
((.((((........)))).)).)	chr2:234201833-234202075(+)$1	1	106	130	14.0206
(.(((((........)))))..))	chr1:53152879-53153145(-)$1	1	215	239	15.0690
.((((((........)))))).).	chr5:150088819-150089053(-)$1	1	71	95	15.5487
(.(((((........)))))..))	chr13:41131580-41131838(-)$1	1	167	191	15.2712
(((((((........)).))))))	chr3:176738447-176738710(-)$1	1	167	191	14.5396
(.(((((........))))).)))	chr3:48964677-48964923(+)$1	1	201	225	15.8204
.((((((........))))))(((	chr5:133291976-133292278(-)$1	1	195	219	14.3344
(((((((........)))))))))	chr11:61066940-61067180(-)$1	1	15	39	16.5609
(((((.(........)))))))).	chr1:179070350-179070610(-)$1	1	221	245	15.5122
(.((.((........))))...))	chr12:49522521-49522759(-)$1	1	46	70	14.3079
(((((((........)))))))((	chr7:44841192-44841458(+)$1	1	146	170	16.3178
(((.(((........))).)))))	chr3:150260294-150260741(-)$1	1	223	247	15.5560
(((.(((........))).)))))	chr10:70482127-70482381(+)$1	1	145	169	16.0276
(((((((........)))))))((	chr18:32917196-32917492(-)$1	1	236	260	16.1175
...((((........))))..)))	chr15:100254117-100254397(+)$1	1	116	140	15.2150
.(((.((........)).)))...	chr6:18224349-18224667(-)$1	1	181	205	13.9441
(((.(((........))).)))..	chr5:14693983-14694236(+)$1	1	102	126	14.4039
.((.(((........))).)).).	chr11:117038773-117039100(+)$1	1	272	296	14.4212
(..((((........)))))))))	chr15:99505599-99505839(+)$1	1	42	66	14.9772
(((((((........)))))))..	chr12:74932795-74933200(+)$1	1	253	277	16.2091
(((((((........)))))))..	chr5:65476493-65476796(+)$1	1	26	50	14.7004
(.(((((........)))))))))	chr5:178032217-178032485(-)$1	1	64	88	15.7508
(((((((........)))))))))	chr17:61667977-61668220(+)$1	1	40	64	15.9887

#PSSM
g : 0.20	c : 0.11	e : 0.11	! : 0.08	[ : 0.08	f : 0.05	" : 0.04	# : 0.04	d : 0.04	= : 0.04	i : 0.04	h : 0.02	b : 0.02	: : 0.01	+ : 0.01	
g : 0.19	f : 0.16	c : 0.14	[ : 0.10	! : 0.08	e : 0.07	b : 0.04	# : 0.04	= : 0.04	d : 0.02	" : 0.02	a : 0.01	i : 0.01	
e : 0.19	g : 0.19	f : 0.16	c : 0.13	! : 0.08	b : 0.04	= : 0.04	[ : 0.04	# : 0.02	" : 0.02	i : 0.01	d : 0.01	
g : 0.19	d : 0.16	e : 0.14	f : 0.14	[ : 0.08	c : 0.08	! : 0.05	= : 0.04	b : 0.02	i : 0.01	" : 0.01	
c : 0.20	d : 0.16	g : 0.16	e : 0.14	f : 0.14	[ : 0.05	= : 0.04	! : 0.02	b : 0.01	i : 0.01	
c : 0.19	e : 0.14	d : 0.14	g : 0.13	b : 0.11	f : 0.11	[ : 0.07	= : 0.04	i : 0.01	
c : 0.19	e : 0.14	d : 0.14	g : 0.13	b : 0.11	f : 0.11	a : 0.07	= : 0.04	i : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.19	e : 0.14	d : 0.14	g : 0.13	b : 0.11	f : 0.11	a : 0.07	= : 0.04	i : 0.01	
c : 0.19	e : 0.14	d : 0.14	g : 0.14	b : 0.11	f : 0.11	] : 0.05	= : 0.04	i : 0.01	
c : 0.20	g : 0.16	e : 0.14	d : 0.14	f : 0.13	] : 0.07	= : 0.04	2 : 0.02	b : 0.02	i : 0.01	
e : 0.16	f : 0.16	d : 0.16	g : 0.16	] : 0.08	2 : 0.05	c : 0.05	3 : 0.04	= : 0.04	b : 0.02	i : 0.01	
e : 0.22	f : 0.17	g : 0.16	c : 0.11	2 : 0.08	3 : 0.05	= : 0.04	b : 0.02	] : 0.02	4 : 0.01	> : 0.01	i : 0.01	d : 0.01	
f : 0.17	g : 0.17	c : 0.13	2 : 0.11	e : 0.10	3 : 0.07	b : 0.04	] : 0.04	= : 0.04	i : 0.02	4 : 0.01	> : 0.01	d : 0.01	
g : 0.22	c : 0.16	e : 0.13	2 : 0.07	f : 0.05	3 : 0.05	4 : 0.05	] : 0.04	= : 0.04	i : 0.04	d : 0.02	> : 0.02	b : 0.02	
e : 0.14	g : 0.11	c : 0.11	f : 0.08	3 : 0.07	4 : 0.05	i : 0.05	a : 0.04	] : 0.04	: : 0.04	d : 0.04	= : 0.04	2 : 0.04	> : 0.02	b : 0.01	H : 0.01	
e : 0.13	c : 0.11	g : 0.10	f : 0.08	: : 0.08	2 : 0.05	3 : 0.05	d : 0.05	i : 0.05	4 : 0.05	= : 0.04	> : 0.02	b : 0.01	a : 0.01	9 : 0.01	] : 0.01	" : 0.01	H : 0.01	

#score	1030.1433260613353
#seq	67
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_CDS_m1_run1.txt

#BEAR
deeeeeuuuuuuuuuuuueeeee]d	chr17:38080184-38080414(-)$1	230	14	39	22.0200
####ccctttttttttttccc333f	chr6:149699581-149699811(+)$1	230	176	201	23.6289
eee[ccctttttttttttccceeee	chr5:43628360-43628590(+)$1	230	129	154	23.2508
iiiiiiiwwwwwwwwwwwwwwiiii	chr9:115232614-115232839(+)$1	225	29	54	22.3262
cccddddvvvvvvvvvvvvvdddd]	chr1:155448238-155448468(-)$1	230	176	201	23.2204
$ccc[bbuuuuuuuuuuuubb]ccc	chr18:60016946-60017186(+)$1	240	63	88	22.6528
a!!ddddwwwwwwwwwwwwwwdddd	chr7:72892773-72892997(-)$1	224	102	127	22.1268
======uuuuuuuuuuuu=======	chr12:120899750-120899980(-)$1	230	73	98	23.0228
cc[dddduuuuuuuuuuuudddd]c	chr9:131765080-131765304(+)$1	224	89	114	24.0506
d"""cccvvvvvvvvvvvvvccc22	chr3:101572448-101572678(+)$1	230	93	118	23.0941
fff!!bbuuuuuuuuuuuubb22ff	chr2:191760294-191760524(+)$1	230	81	106	22.2442
##dddduuuuuuuuuuuudddd22h	chr14:51192487-51192714(-)$1	227	120	145	22.2461
iiiiiiyyyyyyyyyyyyyyyyiii	chr2:3481415-3481645(+)$1	230	138	163	21.6405
#fffffftttttttttttffffff6	chr11:118242143-118242373(+)$1	230	80	105	21.5778
gggggggtttttttttttggggggg	chr19:53304297-53304527(-)$1	230	178	203	23.1434
gggggggwwwwwwwwwwwwwwgggg	chr14:51273396-51273626(-)$1	230	199	224	22.1624
c[eeeeettttttttttteeeeecc	chr1:32541244-32541474(+)$1	230	136	161	22.6920
"ddddbbwwwwwwwwwwwwwwbb]d	chr1:109823569-109823790(-)$1	221	81	106	21.1151
[bb[cccuuuuuuuuuuuuccc]bb	chr3:122418718-122418943(+)$1	225	48	73	23.0830
ee[ddddwwwwwwwwwwwwwwdddd	chr4:122741751-122741977(-)$1	226	32	57	21.8530
eeeeeyyyyyyyyyyyyyyyyeeee	chr9:34241602-34241832(+)$1	230	96	121	20.6275
dddddddyyyyyyyyyyyyyyyydd	chr6:138198248-138198478(+)$1	230	113	138	20.4976
ccc[cccvvvvvvvvvvvvvccc]c	chr1:43830773-43831003(-)$1	230	20	45	23.8881
c!!ddddtttttttttttdddd333	chr19:2222435-2222665(+)$1	230	69	94	23.6998
dddd[bbwwwwwwwwwwwwwwbb]d	chr15:49426497-49426727(-)$1	230	69	94	20.8853
hhhhhhhttttttttttthhhhhhh	chr21:34635527-34635760(+)$1	233	150	175	20.8205
ggggggguuuuuuuuuuuugggggg	chr11:47827685-47827915(-)$1	230	180	205	23.6916
cccdddduuuuuuuuuuuudddd]c	chr11:64009908-64010130(+)$1	222	49	74	23.8568
::eeeeeuuuuuuuuuuuueeeeeD	chr12:44165889-44166119(+)$1	230	175	200	19.9597
##bbcccvvvvvvvvvvvvvccc]b	chr1:46032182-46032407(+)$1	225	145	170	22.7944
g!!ddddwwwwwwwwwwwwwwdddd	chrX:47087867-47088097(+)$1	230	99	124	22.1367
hhhhhhhvvvvvvvvvvvvvhhhhh	chr11:32994966-32995196(+)$1	230	45	70	21.4932
:ffffffuuuuuuuuuuuuffffff	chr1:175958484-175958714(-)$1	230	76	101	21.6409
===[ccctttttttttttccc22==	chr7:86541303-86541533(-)$1	230	33	58	23.7415
[ffffffuuuuuuuuuuuuffffff	chr3:15471323-15471553(+)$1	230	92	117	22.6398
fff[cccvvvvvvvvvvvvvccc]f	chr21:33038678-33038901(+)$1	223	57	82	23.4855
"""ddddyyyyyyyyyyyyyyyydd	chr1:212519149-212519375(+)$1	226	54	79	20.9324
eeeeewwwwwwwwwwwwwweeeee]	chr22:24133956-24134180(+)$1	224	140	165	20.7449
gg!!cccuuuuuuuuuuuuccc333	chr22:22161993-22162223(-)$1	230	118	143	24.4982
::dddduuuuuuuuuuuuddddggg	chr22:50716923-50717151(-)$1	228	90	115	20.6991
dd!!ccctttttttttttccc333d	chr6:32410337-32410562(+)$1	225	140	165	23.7389
cc[dddduuuuuuuuuuuudddd33	chr7:98513295-98513525(+)$1	230	49	74	23.9729
a[eeeeettttttttttteeeee]a	chr3:41267073-41267306(+)$1	233	93	118	22.7807
hhhhhhhwwwwwwwwwwwwwwhhhh	chr3:48510707-48510937(-)$1	230	152	177	20.4713
c!!ddddtttttttttttdddd]cc	chr22:46098489-46098719(+)$1	230	200	225	23.5793
iiiiiiitttttttttttiiiiiii	chr12:69210493-69210723(+)$1	230	35	60	23.2357
dddd[bbtttttttttttbb]dddd	chr18:67531531-67531755(-)$1	224	40	65	21.8668
==[dddduuuuuuuuuuuudddd]=	chr19:39334567-39334791(-)$1	224	155	180	24.1308
hhhhhhhttttttttttthhhhhhh	chr1:169437790-169438014(-)$1	224	163	188	20.8205
iiiiiiitttttttttttiiiiiii	chr5:100147494-100147724(-)$1	230	157	182	23.2357
ddd[ccctttttttttttccc]ddd	chr16:67174366-67174592(+)$1	226	23	48	23.1612
ff[ddddtttttttttttdddd]ff	chr4:106155729-106155959(+)$1	230	56	81	23.1361
ee[ddddtttttttttttdddd]ee	chr14:89042158-89042384(+)$1	226	137	162	23.0850
ccc[bbwwwwwwwwwwwwwwbb]cc	chr5:80600720-80600950(+)$1	230	33	58	21.2946
b[ddddwwwwwwwwwwwwwwdddd]	chr17:71232068-71232298(+)$1	230	108	133	21.7309
=======ttttttttttt=======	chr12:113405793-113406023(+)$1	230	80	105	23.5234
ffffffuuuuuuuuuuuuffffff]	chr12:62777823-62778049(+)$1	226	152	177	21.5353
gggggggtttttttttttggggggg	chr15:35273886-35274116(-)$1	230	96	121	23.1434
#ddddvvvvvvvvvvvvvdddd333	chr17:56589670-56589900(-)$1	230	179	204	21.7218
cc[ddddtttttttttttdddd]cc	chr1:1325813-1326043(-)$1	230	165	190	23.5174
ffffffwwwwwwwwwwwwwwfffff	chr1:150436992-150437222(+)$1	230	163	188	21.0009
ddd[ccctttttttttttccc]ddd	chr17:961907-962132(-)$1	225	168	193	23.1612
!ffffffwwwwwwwwwwwwwwffff	chr19:3976158-3976388(-)$1	230	150	175	21.2585
cffffffuuuuuuuuuuuuffffff	chr12:65133080-65133310(-)$1	230	182	207	22.5958
:ffffffuuuuuuuuuuuuffffff	chr5:36183944-36184164(+)$1	220	187	212	21.6409

#otherMatches

#Seq PSSM
CCGUGGCAUCUGGCUCUCCUACGUG	chr17:38080184-38080414(-)$1	230	14	39	22.0200
UAUCUCAGUUUAAUCCCAUGAACCC	chr6:149699581-149699811(+)$1	230	176	201	23.6289
GUAUGCCAUUAAGUAAACGGUUAUU	chr5:43628360-43628590(+)$1	230	129	154	23.2508
GUUCUUAAAGCAAUAUAUCCCUAAG	chr9:115232614-115232839(+)$1	225	29	54	22.3262
AGGACUCCCCUCCUUUCCAUGAGUA	chr1:155448238-155448468(-)$1	230	176	201	23.2204
uugAUGGUUGCAUUUUUCUCCCUCA	chr18:60016946-60017186(+)$1	240	63	88	22.6528
UGACUCUCAACCCUUCUACUAAGAG	chr7:72892773-72892997(-)$1	224	102	127	22.1268
GGUCUCGGUCUGGGUCAAGGGGCCG	chr12:120899750-120899980(-)$1	230	73	98	23.0228
GGAGCAGCUGCUCAAAACUCUGCGC	chr9:131765080-131765304(+)$1	224	89	114	24.0506
CCUCUGACUCUUCAAACACUUCACU	chr3:101572448-101572678(+)$1	230	93	118	23.0941
AGUGUAUGGAUAUGUUAAGAUUAAC	chr2:191760294-191760524(+)$1	230	81	106	22.2442
AUUAACUCGUUAACUUAUGUUGUCU	chr14:51192487-51192714(-)$1	227	120	145	22.2461
UUUUGAUGAACAGGUAAAUAUUUUA	chr2:3481415-3481645(+)$1	230	138	163	21.6405
UAUAGGCCCUCUUCGCUCGCUUAUU	chr11:118242143-118242373(+)$1	230	80	105	21.5778
AGGUAUUUAAUCAGAAGCGAUACCU	chr19:53304297-53304527(-)$1	230	178	203	23.1434
CUUCCCCUUUAAAAGUUGUCCGGGG	chr14:51273396-51273626(-)$1	230	199	224	22.1624
GUGGUGGUAUCCACCUUCCCACCCA	chr1:32541244-32541474(+)$1	230	136	161	22.6920
UGUGGGAUUGACCCUGAAAUUUCUC	chr1:109823569-109823790(-)$1	221	81	106	21.1151
ACUACUCAAAAAAUUAAAAGGGAAG	chr3:122418718-122418943(+)$1	225	48	73	23.0830
ACACUAUAAAUAAUUUUCUCAAUAG	chr4:122741751-122741977(-)$1	226	32	57	21.8530
AAGCCUCUUCAUAAACCCAAUGGCU	chr9:34241602-34241832(+)$1	230	96	121	20.6275
CAUGGCACAACUCAUCUCAUCAAUG	chr6:138198248-138198478(+)$1	230	113	138	20.4976
CUACGUGUACUUCGUUCUCUCACUU	chr1:43830773-43831003(-)$1	230	20	45	23.8881
GUCGCUGGCCUUUUCACACAGCCUU	chr19:2222435-2222665(+)$1	230	69	94	23.6998
UGCUUUGGAAAUUCAAAUGUACACA	chr15:49426497-49426727(-)$1	230	69	94	20.8853
GGGAAGGGACACAGCCAACCUUUCC	chr21:34635527-34635760(+)$1	233	150	175	20.8205
CUGCAAUUACCAGUUAUUUAUUGCA	chr11:47827685-47827915(-)$1	230	180	205	23.6916
CGGGGUCAAGAAGCGGGUGGACCAC	chr11:64009908-64010130(+)$1	222	49	74	23.8568
AGACAGGACAUUGAUGACACCUGUG	chr12:44165889-44166119(+)$1	230	175	200	19.9597
GAGGCCCUGAAGGAGGACGUGGGAC	chr1:46032182-46032407(+)$1	225	145	170	22.7944
UACUUCCAUAUUUGCACUAAAGGAG	chrX:47087867-47088097(+)$1	230	99	124	22.1367
GCUAUUUCUAAAAUCAAAAUGAAUG	chr11:32994966-32995196(+)$1	230	45	70	21.4932
UAUCUAAUUUUGUUUUGUUUUAGAU	chr1:175958484-175958714(-)$1	230	76	101	21.6409
ACUAUGACUUUAGCAACCUCAGCAG	chr7:86541303-86541533(-)$1	230	33	58	23.7415
UUAGAUGAUUUUAAACCAGCAUCUA	chr3:15471323-15471553(+)$1	230	92	117	22.6398
CUUUUUUUUCUUCUUCUUAUAAAUA	chr21:33038678-33038901(+)$1	223	57	82	23.4855
GCACCGAAUUUAUGGGAAAUUUCUU	chr1:212519149-212519375(+)$1	226	54	79	20.9324
GGUUUGUAAACCUGUUUCAAAACCA	chr22:24133956-24134180(+)$1	224	140	165	20.7449
AGUAGCUAUCAAGAAAAUCAGCCCC	chr22:22161993-22162223(-)$1	230	118	143	24.4982
CCGGUGGAAGCGCGUCAACACCCUU	chr22:50716923-50717151(-)$1	228	90	115	20.6991
CCUCUCUGCUGCACUCCUGGACAUG	chr6:32410337-32410562(+)$1	225	140	165	23.7389
GCCUCACUUGCACAAGAUUGUGAAC	chr7:98513295-98513525(+)$1	230	49	74	23.9729
GUGUUGUUUUAUGCCAUUACAACUC	chr3:41267073-41267306(+)$1	233	93	118	22.7807
ACCGGCCUACCACGAGACCCUGGCU	chr3:48510707-48510937(-)$1	230	152	177	20.4713
AUAGAUGCUUACCAAAAACAUCCUG	chr22:46098489-46098719(+)$1	230	200	225	23.5793
UAAAUGUAUUUACAACUAACAUUUA	chr12:69210493-69210723(+)$1	230	35	60	23.2357
GCAGUGAAUUAUUGACACUCUCUGC	chr18:67531531-67531755(-)$1	224	40	65	21.8668
AGGUGACUGACUGCCCCUUGUCAGC	chr19:39334567-39334791(-)$1	224	155	180	24.1308
AAAAAUUGUAACAGGAUAAAUUUUU	chr1:169437790-169438014(-)$1	224	163	188	20.8205
AGUGUGUAAAGCAAUAAAGCACAUU	chr5:100147494-100147724(-)$1	230	157	182	23.2357
UUUAUGGUUAUUUUUUCCCUACAGA	chr16:67174366-67174592(+)$1	226	23	48	23.1612
ACUGUCUCAAUAUUAUCCAGAUUGU	chr4:106155729-106155959(+)$1	230	56	81	23.1361
GUAUUAUGUUUACACUUGGUAAGAC	chr14:89042158-89042384(+)$1	226	137	162	23.0850
AAGAACAAAAAGAAAAAAGAGUACU	chr5:80600720-80600950(+)$1	230	33	58	21.2946
GAUAGAAAAUAUUCCUCAACUCUAC	chr17:71232068-71232298(+)$1	230	108	133	21.7309
AGCUGGUCACCCAGUACCGCCAGCU	chr12:113405793-113406023(+)$1	230	80	105	23.5234
GUAACAUUUGAUCCUUUUUGUUACU	chr12:62777823-62778049(+)$1	226	152	177	21.5353
UUGGAAACUUCAACAAUCUUUCUAA	chr15:35273886-35274116(-)$1	230	96	121	23.1434
AAGCUAGAAUCCCUAUGAAGUUCAA	chr17:56589670-56589900(-)$1	230	179	204	21.7218
AAUCUGCUUAAAGAUCUUGCAGCUU	chr1:1325813-1326043(-)$1	230	165	190	23.5174
UGUCUGCACUUUCCAAAACCCAGAC	chr1:150436992-150437222(+)$1	230	163	188	21.0009
GACCAAGACAGCCCCUUCCUUAGUC	chr17:961907-962132(-)$1	225	168	193	23.1612
UAAUUUUAACAAACGCAUUAAGAGG	chr19:3976158-3976388(-)$1	230	150	175	21.2585
UUGAGAAUAUGUCUUUCCUUUUUCA	chr12:65133080-65133310(-)$1	230	182	207	22.5958
UGAGUGCUUAAACUAAGUUGUAUUC	chr5:36183944-36184164(+)$1	220	187	212	21.6409

#DB
((((((............))))).)	chr17:38080184-38080414(-)$1	1	14	39	22.0200
....(((...........)))...)	chr6:149699581-149699811(+)$1	1	176	201	23.6289
(((.(((...........)))))))	chr5:43628360-43628590(+)$1	1	129	154	23.2508
(((((((..............))))	chr9:115232614-115232839(+)$1	1	29	54	22.3262
(((((((.............)))).	chr1:155448238-155448468(-)$1	1	176	201	23.2204
.(((.((............)).)))	chr18:60016946-60017186(+)$1	1	63	88	22.6528
(..((((..............))))	chr7:72892773-72892997(-)$1	1	102	127	22.1268
((((((............)))))))	chr12:120899750-120899980(-)$1	1	73	98	23.0228
((.((((............)))).)	chr9:131765080-131765304(+)$1	1	89	114	24.0506
(...(((.............)))..	chr3:101572448-101572678(+)$1	1	93	118	23.0941
(((..((............))..))	chr2:191760294-191760524(+)$1	1	81	106	22.2442
..((((............))))..)	chr14:51192487-51192714(-)$1	1	120	145	22.2461
((((((................)))	chr2:3481415-3481645(+)$1	1	138	163	21.6405
.((((((...........)))))).	chr11:118242143-118242373(+)$1	1	80	105	21.5778
(((((((...........)))))))	chr19:53304297-53304527(-)$1	1	178	203	23.1434
(((((((..............))))	chr14:51273396-51273626(-)$1	1	199	224	22.1624
(.(((((...........)))))))	chr1:32541244-32541474(+)$1	1	136	161	22.6920
.((((((..............)).)	chr1:109823569-109823790(-)$1	1	81	106	21.1151
.((.(((............))).))	chr3:122418718-122418943(+)$1	1	48	73	23.0830
((.((((..............))))	chr4:122741751-122741977(-)$1	1	32	57	21.8530
(((((................))))	chr9:34241602-34241832(+)$1	1	96	121	20.6275
)))((((................))	chr6:138198248-138198478(+)$1	1	113	138	20.4976
(((.(((.............))).)	chr1:43830773-43831003(-)$1	1	20	45	23.8881
(..((((...........))))...	chr19:2222435-2222665(+)$1	1	69	94	23.6998
((((.((..............)).)	chr15:49426497-49426727(-)$1	1	69	94	20.8853
(((((((...........)))))))	chr21:34635527-34635760(+)$1	1	150	175	20.8205
(((((((............))))))	chr11:47827685-47827915(-)$1	1	180	205	23.6916
(((((((............)))).)	chr11:64009908-64010130(+)$1	1	49	74	23.8568
..(((((............))))))	chr12:44165889-44166119(+)$1	1	175	200	19.9597
..(((((.............))).)	chr1:46032182-46032407(+)$1	1	145	170	22.7944
(..((((..............))))	chrX:47087867-47088097(+)$1	1	99	124	22.1367
(((((((.............)))))	chr11:32994966-32995196(+)$1	1	45	70	21.4932
.((((((............))))))	chr1:175958484-175958714(-)$1	1	76	101	21.6409
(((.(((...........)))..))	chr7:86541303-86541533(-)$1	1	33	58	23.7415
.((((((............))))))	chr3:15471323-15471553(+)$1	1	92	117	22.6398
(((.(((.............))).)	chr21:33038678-33038901(+)$1	1	57	82	23.4855
...((((................))	chr1:212519149-212519375(+)$1	1	54	79	20.9324
(((((..............))))).	chr22:24133956-24134180(+)$1	1	140	165	20.7449
((..(((............)))...	chr22:22161993-22162223(-)$1	1	118	143	24.4982
..((((............))))(((	chr22:50716923-50717151(-)$1	1	90	115	20.6991
((..(((...........)))...)	chr6:32410337-32410562(+)$1	1	140	165	23.7389
((.((((............))))..	chr7:98513295-98513525(+)$1	1	49	74	23.9729
(.(((((...........))))).)	chr3:41267073-41267306(+)$1	1	93	118	22.7807
(((((((..............))))	chr3:48510707-48510937(-)$1	1	152	177	20.4713
(..((((...........)))).))	chr22:46098489-46098719(+)$1	1	200	225	23.5793
(((((((...........)))))))	chr12:69210493-69210723(+)$1	1	35	60	23.2357
((((.((...........)).))))	chr18:67531531-67531755(-)$1	1	40	65	21.8668
((.((((............)))).)	chr19:39334567-39334791(-)$1	1	155	180	24.1308
(((((((...........)))))))	chr1:169437790-169438014(-)$1	1	163	188	20.8205
(((((((...........)))))))	chr5:100147494-100147724(-)$1	1	157	182	23.2357
(((.(((...........))).)))	chr16:67174366-67174592(+)$1	1	23	48	23.1612
((.((((...........)))).))	chr4:106155729-106155959(+)$1	1	56	81	23.1361
((.((((...........)))).))	chr14:89042158-89042384(+)$1	1	137	162	23.0850
(((.((..............)).))	chr5:80600720-80600950(+)$1	1	33	58	21.2946
(.((((..............)))).	chr17:71232068-71232298(+)$1	1	108	133	21.7309
(((((((...........)))))))	chr12:113405793-113406023(+)$1	1	80	105	23.5234
((((((............)))))).	chr12:62777823-62778049(+)$1	1	152	177	21.5353
(((((((...........)))))))	chr15:35273886-35274116(-)$1	1	96	121	23.1434
.((((.............))))...	chr17:56589670-56589900(-)$1	1	179	204	21.7218
((.((((...........)))).))	chr1:1325813-1326043(-)$1	1	165	190	23.5174
((((((..............)))))	chr1:150436992-150437222(+)$1	1	163	188	21.0009
(((.(((...........))).)))	chr17:961907-962132(-)$1	1	168	193	23.1612
.((((((..............))))	chr19:3976158-3976388(-)$1	1	150	175	21.2585
)((((((............))))))	chr12:65133080-65133310(-)$1	1	182	207	22.5958
.((((((............))))))	chr5:36183944-36184164(+)$1	1	187	212	21.6409

#PSSM
c : 0.16	d : 0.12	g : 0.09	# : 0.07	e : 0.07	f : 0.07	i : 0.06	= : 0.06	h : 0.06	: : 0.06	a : 0.03	" : 0.03	[ : 0.03	$ : 0.01	b : 0.01	! : 0.01	
f : 0.16	c : 0.12	d : 0.12	e : 0.09	g : 0.07	i : 0.06	! : 0.06	= : 0.06	h : 0.06	# : 0.04	[ : 0.04	" : 0.03	: : 0.03	b : 0.01	
f : 0.15	d : 0.15	e : 0.10	[ : 0.10	! : 0.09	c : 0.07	i : 0.06	g : 0.06	h : 0.06	= : 0.04	" : 0.03	b : 0.03	# : 0.01	
d : 0.33	[ : 0.12	f : 0.12	e : 0.09	i : 0.06	g : 0.06	h : 0.06	! : 0.04	= : 0.03	# : 0.01	c : 0.01	" : 0.01	b : 0.01	
d : 0.30	c : 0.18	f : 0.12	e : 0.09	i : 0.06	g : 0.06	h : 0.06	[ : 0.04	= : 0.03	! : 0.01	b : 0.01	
d : 0.27	c : 0.18	f : 0.12	b : 0.09	e : 0.06	i : 0.06	g : 0.06	h : 0.06	= : 0.03	y : 0.01	w : 0.01	v : 0.01	
d : 0.23	c : 0.18	f : 0.09	u : 0.07	b : 0.07	g : 0.06	h : 0.06	w : 0.06	i : 0.04	e : 0.04	y : 0.03	= : 0.01	v : 0.01	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
t : 0.33	u : 0.29	w : 0.20	v : 0.10	y : 0.06	
u : 0.21	w : 0.20	d : 0.12	c : 0.09	v : 0.09	y : 0.06	e : 0.04	= : 0.03	f : 0.03	g : 0.03	h : 0.03	i : 0.03	b : 0.01	
w : 0.18	d : 0.18	c : 0.12	v : 0.09	f : 0.09	e : 0.07	y : 0.06	b : 0.04	g : 0.04	= : 0.03	h : 0.03	i : 0.03	
d : 0.21	c : 0.18	w : 0.13	f : 0.10	e : 0.07	y : 0.06	b : 0.04	g : 0.04	h : 0.04	= : 0.03	i : 0.03	] : 0.01	
d : 0.27	f : 0.12	e : 0.10	c : 0.09	g : 0.06	h : 0.06	i : 0.04	] : 0.04	y : 0.04	b : 0.04	3 : 0.03	= : 0.03	2 : 0.03	
d : 0.18	f : 0.12	e : 0.10	] : 0.09	3 : 0.07	c : 0.07	g : 0.07	i : 0.06	h : 0.06	2 : 0.04	= : 0.03	b : 0.03	y : 0.03	
] : 0.15	d : 0.15	f : 0.15	3 : 0.09	e : 0.07	c : 0.07	g : 0.07	i : 0.06	h : 0.06	= : 0.04	2 : 0.03	b : 0.01	
d : 0.18	f : 0.15	c : 0.12	h : 0.07	g : 0.07	i : 0.06	] : 0.06	= : 0.06	3 : 0.06	e : 0.04	b : 0.03	2 : 0.01	6 : 0.01	D : 0.01	a : 0.01	

#score	1457.2264358821565
#seq	65
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_UTR_m1_run1.txt

#BEAR
a[cccccc"""cccnnnnnccc333ccc]cc	chr9:138900866-138901092(-)$1	226	162	193	16.4073
eeeebbccc[ddddnnnnnddddccc4444b	chr11:66393990-66394207(+)$1	217	106	137	12.0613
ffff"""gggggggooooooggggggg4444	chr3:150276124-150276338(+)$1	214	131	162	10.6146
!ffffff####cccnnnnnccc4444fffff	chr19:32876849-32877078(+)$1	229	73	104	15.0113
da!!ccc####cccnnnnnccc333ccc22a	chr19:1434651-1434885(+)$1	234	57	88	15.9037
==========!!bboooooobb22=======	chr19:10941991-10942212(+)$1	221	33	64	12.6506
!eeeee!!a[ddddnnnnndddd]a]eeeee	chr15:75189781-75190002(+)$1	221	111	142	13.3343
ee"""dddd[ddddnnnnndddd]ddddeee	chr3:15482345-15482562(+)$1	217	47	78	11.8730
hhh"""dddd[cccnnnnncccdddd]hhhh	chr21:45179709-45179935(+)$1	226	55	86	11.6900
hh[eeeee####bbnnnnnbb4444eeeee2	chr7:111846160-111846381(-)$1	221	144	175	13.3114
::eeeee"""ddddnnnnndddd333eeeee	chr13:30423766-30423994(-)$1	228	145	176	12.2090
cggggggg"""ccclllccc]ggggggg]cc	chr14:23299302-23299523(+)$1	221	41	72	11.4978
""ffffff!!a[bboooooobba22ffffff	chr12:133348736-133348958(-)$1	222	83	114	10.9551
"eeeee!!ffffffnnnnnffffff333eee	chr21:45181149-45181368(+)$1	219	35	66	11.5583
eee!!dddd[bb[annnnna]bb]dddd444	chrX:41782216-41782440(-)$1	224	119	150	11.5856
]ccc==========nnnnn==========::	chr1:203769128-203769355(+)$1	227	121	152	12.7858
ccc[a[gggggggccclllccc]ggggggg]	chr1:233115903-233116121(+)$1	218	26	57	10.7571
!!ccc[ccc!!ddddmmmmdddd22ccc]cc	chr6:11581089-11581307(+)$1	218	97	128	9.9644
:ffffff"""a[bbnnnnnbba333ffffff	chr7:151874682-151874907(-)$1	225	183	214	13.2378
=========[ddddnnnnndddd========	chr12:53682779-53683006(+)$1	227	10	41	14.7351
ddd!!ffffffcccnnnnnccc]ffffff33	chr6:64404391-64404605(+)$1	214	147	178	12.7012
!ddddaccc[cccooooooccc]ccc]a]dd	chr1:231501840-231502060(-)$1	220	60	91	10.9638
hhhhhh[bb"""bbnnnnnbb333bb]hhhh	chr20:55949592-55949817(+)$1	225	179	210	11.8643
eeeeeeee"""cccnnnnnccc333eeeee4	chr14:102547631-102547851(-)$1	220	156	187	15.2193
ggggggg####cccoooooocccggggggg3	chr16:3632056-3632284(-)$1	228	29	60	13.0723
!!ccc####eeeeennnnneeeeecccffff	chr22:18037250-18037463(+)$1	213	56	87	12.1360
ddd!!iiiiiiiiinnnnniiiiiiiii]dd	chr8:98737406-98737622(+)$1	216	29	60	13.8443
cc[bb[ccc!!cccnnnnncccccc]bb]cc	chr12:121000656-121000875(+)$1	219	13	44	13.8017
d####ccc"""ccclllccc4444ccc22dd	chr12:124498514-124498731(+)$1	217	63	94	10.9473
ee####bb!!ddddnnnnndddd22bbeeee	chr11:105961966-105962183(+)$1	217	79	110	12.6433
hhhhhh$$$$$cccooooooccc4444hhhh	chr10:104839259-104839484(+)$1	225	182	213	10.2676
[ggggggga[cccammmma]ccc]a4444gg	chr1:90309120-90309347(+)$1	227	140	171	10.7292
ccc[eeeeeacccooooooccc]a333eeee	chr11:130005430-130005647(+)$1	217	149	180	11.3125
eeeee[bb[cccbbnnnnnbb]cccbbeeee	chr6:34393717-34393943(-)$1	226	67	98	11.7635
b[ffffff!!bb[annnnna]bb]ffffff]	chr10:126308371-126308583(-)$1	212	93	124	12.2683
"""ffffff"""bbnnnnnbb333ffffff3	chr9:79933290-79933509(+)$1	219	156	187	13.8131
$$ffffff[cccbbnnnnnbb]cccffffff	chr16:56465138-56465362(-)$1	224	105	136	11.9512
ee[iiiiiiiii[annnnna]iiiiiiiii]	chr1:6682094-6682320(+)$1	226	111	142	14.3814
$$bb[iiiiiiiiinnnnniiiiiiiii]bb	chr22:36138682-36138902(-)$1	220	139	170	13.1529
!ccc[iiiiiiiiinnnnniiiiiiiii22c	chr9:115631672-115631915(+)$1	243	29	60	14.3218
#ggggggg"""cccnnnnnccc55555gggg	chr9:21862354-21862579(+)$1	225	43	74	12.4090
""eeeee"""ddddoooooodddd333eeee	chr3:190024340-190024569(-)$1	229	171	202	11.5417
::ggggggg####ccclllccc333gggggg	chr3:113440013-113440240(-)$1	227	48	79	10.3835
:a[===========nnnnn===========]	chr11:119171803-119172021(+)$1	218	94	125	14.6564
eggggggg!!a[bbnnnnnbb]a22gggggg	chr19:36258664-36258881(+)$1	217	35	66	14.3550
ggggggg[ccc[cccmmmmccc]ccc22ggg	chr3:184041643-184041865(+)$1	222	132	163	9.5471
#ccc"""gggggggnnnnngggggggccc44	chr1:166822667-166822887(+)$1	220	175	206	13.3596
b!!ccc!!ccc!!ccclllccc22ccc22cc	chr6:31508779-31509053(-)$1	274	12	43	10.4276
=========[ddddnnnnndddd]=======	chr5:171299794-171300014(-)$1	220	146	177	14.8888
eee"""ccceeeeennnnneeeee]ccc333	chr19:44090014-44090247(-)$1	233	138	169	12.1881
a[eeeee[a[ddddnnnnnddddaeeeee]a	chr17:1324331-1324566(-)$1	235	121	152	12.7930
="""==========nnnnn==========66	chr1:237061076-237061302(+)$1	226	35	66	14.5325
fffa!!dddd[cccnnnnnccc22dddd22a	chr19:19617058-19617290(+)$1	232	81	112	12.5293
!!iiiiiiiiicccooooooccc22iiiiii	chr17:41602399-41602650(+)$1	251	208	239	13.1583
b[ccc[bb[a[cccoooooocccabb22ccc	chr6:33663493-33663714(+)$1	221	58	89	10.6279

#otherMatches

#Seq PSSM
UGCCCCCCCACCCUUGGCCAGGACAGGGAGG	chr9:138900866-138901092(-)$1	226	162	193	16.4073
GCGGGCGGCUCAGAUGCACUCUGGCUACCAG	chr11:66393990-66394207(+)$1	217	106	137	12.0613
GUUCAUUUACAUAACAUAUUUUGUGUGUCAC	chr3:150276124-150276338(+)$1	214	131	162	10.6146
AUUCUGAUCAUUAUAAAGAAUACUUUUCAGG	chr19:32876849-32877078(+)$1	229	73	104	15.0113
CCGAGCUCACAGGACUUUCUCCCCCAGCAGG	chr19:1434651-1434885(+)$1	234	57	88	15.9037
GCCUGGGGGGGACUCUACCAAGGUCUUCUUG	chr19:10941991-10942212(+)$1	221	33	64	12.6506
ACUCUGCCAGCAUCCUCCUGAUGGUACAGGG	chr15:75189781-75190002(+)$1	221	111	142	13.3343
ACUUGAAUUGUUACUGGAUGUAGGAAUUGUU	chr3:15482345-15482562(+)$1	217	47	78	11.8730
GCCGAGGGGGCUCCCAGAAGGACCCCAGGCC	chr21:45179709-45179935(+)$1	226	55	86	11.6900
GCGCGGGGAUUACAAAGCCUGAAGACCCCGG	chr7:111846160-111846381(-)$1	221	144	175	13.3114
AACCAGAACCUCGGCCUGACCGGCACUUUGG	chr13:30423766-30423994(-)$1	228	145	176	12.2090
GGGGGACCAGAAGCUGGGCUAGGUCCUCACA	chr14:23299302-23299523(+)$1	221	41	72	11.4978
uuacaggcgugagccccugcgcccggccUGU	chr12:133348736-133348958(-)$1	222	83	114	10.9551
UUGUCCAACAGGAAACCCAUUUCUGGUGGGA	chr21:45181149-45181368(+)$1	219	35	66	11.5583
GGGCUGGGCACUGAGCUCUUGGGCGCCCCCA	chrX:41782216-41782440(-)$1	224	119	150	11.5856
UGGAUGAGUACUUCAAAGAGAAGUAUUCAGA	chr1:203769128-203769355(+)$1	227	121	152	12.7858
UAUGUGGGGUGGGAGUGUCACUGCCUACUUG	chr1:233115903-233116121(+)$1	218	26	57	10.7571
GGAGCUCUGGUCUGUGUAGGCAGUACAGUGU	chr6:11581089-11581307(+)$1	218	97	128	9.9644
CAGACCCCAUGCGACGACCUCCCCAGGGUCU	chr7:151874682-151874907(-)$1	225	183	214	13.2378
AUAGGGACUGUUCCUUCUUGGAAAGUUCCUA	chr12:53682779-53683006(+)$1	227	10	41	14.7351
UCUUCGUAAGAUGGGACAACCAGUUUUACCU	chr6:64404391-64404605(+)$1	214	147	178	12.7012
UUUGACUGCUGUGACUUUGUACUGCAUGAUC	chr1:231501840-231502060(-)$1	220	60	91	10.9638
AACAGUUAGAUCAGCCCAUCUCAGCUUGCUG	chr20:55949592-55949817(+)$1	225	179	210	11.8643
CUUGAUGUUUAGAAAAGUAUUCGUUACAUCU	chr14:102547631-102547851(-)$1	220	156	187	15.2193
UCAGGCCUCCACAGGCAUUUCUGGGCCUGGG	chr16:3632056-3632284(-)$1	228	29	60	13.0723
AACUCUAACGUCAGAACGGCUGACGAGCAGU	chr22:18037250-18037463(+)$1	213	56	87	12.1360
UGUUUAACUAAACUGUCAUGGUUUAGUUUAC	chr8:98737406-98737622(+)$1	216	29	60	13.8443
AUUCUAAGCCCUUGCCCUUCAAGCUAAGUGU	chr12:121000656-121000875(+)$1	219	13	44	13.8017
cugaugagacagacaaggucccuacucuugu	chr12:124498514-124498731(+)$1	217	63	94	10.9473
CUUAAGGAAAGCUUCAUAAAAGCCAUUGGUG	chr11:105961966-105962183(+)$1	217	79	110	12.6433
GAUGAAAUUUUAGCCGCCAAGUUCGUAUUCA	chr10:104839259-104839484(+)$1	225	182	213	10.2676
CCGUGGUUCCAGCCUCCGGAGCUCGCCCAAG	chr1:90309120-90309347(+)$1	227	140	171	10.7292
CACCCCUUCCCAGCCCUACCUGAGAACGAAG	chr11:130005430-130005647(+)$1	217	149	180	11.3125
GGAAGAGACGCAGCACCGCGCAUGCUCCUUC	chr6:34393717-34393943(-)$1	226	67	98	11.7635
CUGCGGGCUCUGCCUUGGUGUCAUGCCUGCU	chr10:126308371-126308583(-)$1	212	93	124	12.2683
UUCAGGGGAAGGCAAAAACUGGAGUUCCCUA	chr9:79933290-79933509(+)$1	219	156	187	13.8131
CUUCAUGGUAGGUGAGCACCAGUCUCCAUGA	chr16:56465138-56465362(-)$1	224	105	136	11.9512
CUGCCUCAGCUGCUGCCUGACCGGCUGGGGG	chr1:6682094-6682320(+)$1	226	111	142	14.3814
CAAGGUAGGAGGGAGUGUUUCUCUUCUAGCU	chr22:36138682-36138902(-)$1	220	139	170	13.1529
CUUACUGUUUCUGUUUCACAUAGGGACAUUU	chr9:115631672-115631915(+)$1	243	29	60	14.3218
guaaauugguacaguauuucuggagggcaau	chr9:21862354-21862579(+)$1	225	43	74	12.4090
caaggcauuuggcugcuguaagcuuauugcu	chr3:190024340-190024569(-)$1	229	171	202	11.5417
GUGUGUUUGUGGUACUUUGGGUUUUUAAACA	chr3:113440013-113440240(-)$1	227	48	79	10.3835
CUGUAAUUACUGUGUUCUUCACGGUAAUUAG	chr11:119171803-119172021(+)$1	218	94	125	14.6564
CCAAGGCCGAGUCUCUGAAAGCCAAGGCCUU	chr19:36258664-36258881(+)$1	217	35	66	14.3550
AGUGGGUUCUAAAUCUAAUGGUCUGGUUGCC	chr3:184041643-184041865(+)$1	222	132	163	9.5471
UAAGUUUGAGUGUUACGAAAACAUUCCUUUA	chr1:166822667-166822887(+)$1	220	175	206	13.3596
CAUGCUAAUUACACAAGGCUUGCUUAAACAG	chr6:31508779-31509053(-)$1	274	12	43	10.4276
GAAGUUGGUGUGCUGACAGAGCAGGCUGAUU	chr5:171299794-171300014(-)$1	220	146	177	14.8888
AUAAAAAUGAAUAGAAAUCCUAUUGCGUGUC	chr19:44090014-44090247(-)$1	233	138	169	12.1881
UGUUGAGUGUGGCAGUUAAUGCCCCUCAAGA	chr17:1324331-1324566(-)$1	235	121	152	12.7930
UCCUGCAGUGCCUGGAAAACAGGCGCUGUUU	chr1:237061076-237061302(+)$1	226	35	66	14.5325
CAGCAGCCCUGAGCAGAAAGCUGGAGGGGGG	chr19:19617058-19617290(+)$1	232	81	112	12.5293
CCUUAUGUUAUUAGUAAGUUCUGAAGUGAUG	chr17:41602399-41602650(+)$1	251	208	239	13.1583
CGCUGAGGAGAGCCACCGAAGGCCCCAACAG	chr6:33663493-33663714(+)$1	221	58	89	10.6279

#DB
(.((((((...(((.....)))...))).))	chr9:138900866-138901092(-)$1	1	162	193	16.4073
(((((((((.((((.....)))))))....)	chr11:66393990-66394207(+)$1	1	106	137	12.0613
((((...(((((((......)))))))....	chr3:150276124-150276338(+)$1	1	131	162	10.6146
.((((((....(((.....)))....)))))	chr19:32876849-32877078(+)$1	1	73	104	15.0113
((..(((....(((.....)))...)))..)	chr19:1434651-1434885(+)$1	1	57	88	15.9037
((((((((((..((......))..)))))))	chr19:10941991-10942212(+)$1	1	33	64	12.6506
.(((((..(.((((.....)))).).)))))	chr15:75189781-75190002(+)$1	1	111	142	13.3343
((...((((.((((.....)))).)))))))	chr3:15482345-15482562(+)$1	1	47	78	11.8730
(((...((((.(((.....))))))).))))	chr21:45179709-45179935(+)$1	1	55	86	11.6900
((.(((((....((.....))....))))).	chr7:111846160-111846381(-)$1	1	144	175	13.3114
..(((((...((((.....))))...)))))	chr13:30423766-30423994(-)$1	1	145	176	12.2090
((((((((...(((...))).))))))).))	chr14:23299302-23299523(+)$1	1	41	72	11.4978
..((((((..(.((......)))..))))))	chr12:133348736-133348958(-)$1	1	83	114	10.9551
.(((((..((((((.....))))))...)))	chr21:45181149-45181368(+)$1	1	35	66	11.5583
(((..((((.((.(.....).)).))))...	chrX:41782216-41782440(-)$1	1	119	150	11.5856
.)))((((((((((.....))))))))))..	chr1:203769128-203769355(+)$1	1	121	152	12.7858
(((.(.((((((((((...))).))))))).	chr1:233115903-233116121(+)$1	1	26	57	10.7571
..(((.(((..((((....))))..))).))	chr6:11581089-11581307(+)$1	1	97	128	9.9644
.((((((...(.((.....)))...))))))	chr7:151874682-151874907(-)$1	1	183	214	13.2378
(((((((((.((((.....))))))))))))	chr12:53682779-53683006(+)$1	1	10	41	14.7351
(((..(((((((((.....))).))))))..	chr6:64404391-64404605(+)$1	1	147	178	12.7012
.((((((((.(((......))).))).).))	chr1:231501840-231502060(-)$1	1	60	91	10.9638
((((((.((...((.....))...)).))))	chr20:55949592-55949817(+)$1	1	179	210	11.8643
((((((((...(((.....)))...))))).	chr14:102547631-102547851(-)$1	1	156	187	15.2193
(((((((....(((......)))))))))).	chr16:3632056-3632284(-)$1	1	29	60	13.0723
..(((....(((((.....))))))))))))	chr22:18037250-18037463(+)$1	1	56	87	12.1360
(((..(((((((((.....))))))))).))	chr8:98737406-98737622(+)$1	1	29	60	13.8443
((.((.(((..(((.....)))))).)).))	chr12:121000656-121000875(+)$1	1	13	44	13.8017
(....(((...(((...)))....)))..))	chr12:124498514-124498731(+)$1	1	63	94	10.9473
((....((..((((.....))))..))))))	chr11:105961966-105962183(+)$1	1	79	110	12.6433
((((((.....(((......)))....))))	chr10:104839259-104839484(+)$1	1	182	213	10.2676
.((((((((.((((....).))).)....))	chr1:90309120-90309347(+)$1	1	140	171	10.7292
(((.(((((((((......))).)...))))	chr11:130005430-130005647(+)$1	1	149	180	11.3125
(((((.((.(((((.....)).)))))))))	chr6:34393717-34393943(-)$1	1	67	98	11.7635
(.((((((..((.(.....).)).)))))).	chr10:126308371-126308583(-)$1	1	93	124	12.2683
...((((((...((.....))...)))))).	chr9:79933290-79933509(+)$1	1	156	187	13.8131
..((((((.(((((.....)).)))))))))	chr16:56465138-56465362(-)$1	1	105	136	11.9512
((.(((((((((.(.....).))))))))).	chr1:6682094-6682320(+)$1	1	111	142	14.3814
..((.(((((((((.....))))))))).))	chr22:36138682-36138902(-)$1	1	139	170	13.1529
.(((.(((((((((.....)))))))))..)	chr9:115631672-115631915(+)$1	1	29	60	14.3218
.(((((((...(((.....))).....))))	chr9:21862354-21862579(+)$1	1	43	74	12.4090
..(((((...((((......))))...))))	chr3:190024340-190024569(-)$1	1	171	202	11.5417
..(((((((....(((...)))...))))))	chr3:113440013-113440240(-)$1	1	48	79	10.3835
.(.(((((((((((.....))))))))))).	chr11:119171803-119172021(+)$1	1	94	125	14.6564
((((((((..(.((.....)).)..))))))	chr19:36258664-36258881(+)$1	1	35	66	14.3550
(((((((.(((.(((....))).)))..)))	chr3:184041643-184041865(+)$1	1	132	163	9.5471
.(((...(((((((.....))))))))))..	chr1:166822667-166822887(+)$1	1	175	206	13.3596
(..(((..(((..(((...)))..)))..))	chr6:31508779-31509053(-)$1	1	12	43	10.4276
(((((((((.((((.....)))).)))))))	chr5:171299794-171300014(-)$1	1	146	177	14.8888
(((...((((((((.....))))).)))...	chr19:44090014-44090247(-)$1	1	138	169	12.1881
(.(((((.(.((((.....)))))))))).)	chr17:1324331-1324566(-)$1	1	121	152	12.7930
(...((((((((((.....))))))))))..	chr1:237061076-237061302(+)$1	1	35	66	14.5325
((((..((((.(((.....)))..))))..)	chr19:19617058-19617290(+)$1	1	81	112	12.5293
..((((((((((((......)))..))))))	chr17:41602399-41602650(+)$1	1	208	239	13.1583
(.(((.((.(.(((......))))))..)))	chr6:33663493-33663714(+)$1	1	58	89	10.6279

#PSSM
e : 0.16	! : 0.12	d : 0.07	= : 0.07	h : 0.07	: : 0.07	c : 0.07	" : 0.07	b : 0.05	a : 0.03	f : 0.03	g : 0.03	$ : 0.03	# : 0.03	] : 0.01	[ : 0.01	
e : 0.18	g : 0.10	c : 0.10	[ : 0.07	f : 0.07	h : 0.07	" : 0.07	! : 0.07	= : 0.05	d : 0.05	a : 0.03	: : 0.03	$ : 0.03	# : 0.01	
e : 0.18	c : 0.16	f : 0.12	g : 0.12	[ : 0.07	= : 0.05	" : 0.05	h : 0.05	d : 0.05	! : 0.03	# : 0.03	b : 0.01	i : 0.01	
e : 0.16	c : 0.14	f : 0.12	g : 0.12	! : 0.07	= : 0.07	" : 0.07	[ : 0.03	h : 0.03	b : 0.03	# : 0.03	i : 0.03	d : 0.01	a : 0.01	
e : 0.16	g : 0.12	c : 0.10	f : 0.10	= : 0.10	" : 0.09	! : 0.07	b : 0.03	h : 0.03	# : 0.03	i : 0.03	[ : 0.03	a : 0.01	d : 0.01	
e : 0.14	f : 0.12	g : 0.12	= : 0.10	[ : 0.09	i : 0.09	c : 0.07	" : 0.07	d : 0.03	h : 0.03	# : 0.03	b : 0.01	a : 0.01	! : 0.01	
c : 0.14	g : 0.14	f : 0.12	= : 0.10	e : 0.10	i : 0.09	d : 0.07	! : 0.05	b : 0.05	" : 0.03	[ : 0.01	# : 0.01	$ : 0.01	
g : 0.14	c : 0.12	= : 0.10	f : 0.09	i : 0.09	# : 0.07	d : 0.07	b : 0.07	! : 0.05	e : 0.05	" : 0.05	[ : 0.03	$ : 0.01	
" : 0.14	c : 0.12	= : 0.10	# : 0.09	i : 0.09	g : 0.07	d : 0.07	! : 0.07	a : 0.05	f : 0.05	[ : 0.05	b : 0.01	$ : 0.01	e : 0.01	
" : 0.18	[ : 0.16	! : 0.10	# : 0.09	i : 0.09	= : 0.07	c : 0.07	g : 0.05	d : 0.03	f : 0.03	e : 0.03	a : 0.03	$ : 0.01	
d : 0.16	" : 0.12	c : 0.12	# : 0.09	i : 0.09	g : 0.05	! : 0.05	[ : 0.05	a : 0.05	= : 0.05	f : 0.03	b : 0.03	e : 0.03	$ : 0.01	
c : 0.36	d : 0.18	[ : 0.07	i : 0.07	g : 0.05	= : 0.05	! : 0.03	# : 0.03	b : 0.03	" : 0.03	e : 0.03	f : 0.01	
c : 0.34	d : 0.18	b : 0.16	g : 0.05	[ : 0.05	= : 0.05	i : 0.05	e : 0.03	f : 0.01	# : 0.01	! : 0.01	
c : 0.34	d : 0.18	b : 0.16	a : 0.07	= : 0.05	i : 0.05	g : 0.03	o : 0.03	e : 0.03	f : 0.01	
n : 0.67	o : 0.18	c : 0.07	l : 0.03	d : 0.01	m : 0.01	
n : 0.67	o : 0.18	c : 0.05	m : 0.05	l : 0.03	
n : 0.67	o : 0.18	l : 0.09	m : 0.05	
n : 0.67	o : 0.18	l : 0.05	m : 0.05	c : 0.03	
n : 0.67	o : 0.18	l : 0.05	c : 0.03	m : 0.03	a : 0.01	
c : 0.30	d : 0.16	o : 0.14	b : 0.12	a : 0.05	= : 0.05	i : 0.05	e : 0.03	f : 0.01	] : 0.01	g : 0.01	
c : 0.36	d : 0.18	b : 0.16	] : 0.07	= : 0.05	i : 0.05	g : 0.03	e : 0.03	f : 0.01	4 : 0.01	
c : 0.36	d : 0.18	b : 0.07	i : 0.07	g : 0.05	= : 0.05	] : 0.05	4 : 0.03	3 : 0.03	e : 0.03	f : 0.01	a : 0.01	
d : 0.20	c : 0.14	3 : 0.12	] : 0.09	i : 0.07	g : 0.05	4 : 0.05	2 : 0.05	= : 0.05	a : 0.03	b : 0.03	e : 0.03	f : 0.01	5 : 0.01	
3 : 0.14	2 : 0.14	c : 0.10	] : 0.10	g : 0.09	4 : 0.07	= : 0.07	i : 0.07	a : 0.05	d : 0.03	f : 0.03	e : 0.03	5 : 0.01	
c : 0.16	3 : 0.14	= : 0.10	g : 0.09	2 : 0.09	d : 0.07	f : 0.07	i : 0.07	4 : 0.05	a : 0.03	b : 0.03	5 : 0.01	] : 0.01	e : 0.01	
c : 0.18	g : 0.12	= : 0.10	f : 0.10	i : 0.09	d : 0.07	3 : 0.07	b : 0.07	4 : 0.05	e : 0.05	] : 0.03	5 : 0.01	
c : 0.14	f : 0.12	g : 0.10	= : 0.10	e : 0.09	i : 0.09	4 : 0.05	d : 0.05	] : 0.05	3 : 0.05	b : 0.05	2 : 0.03	5 : 0.01	
e : 0.16	f : 0.14	= : 0.10	g : 0.10	c : 0.09	i : 0.09	2 : 0.07	4 : 0.05	d : 0.05	h : 0.05	3 : 0.01	a : 0.01	b : 0.01	
e : 0.20	f : 0.14	] : 0.12	= : 0.10	g : 0.10	2 : 0.09	4 : 0.07	h : 0.05	i : 0.03	c : 0.03	3 : 0.01	
e : 0.18	f : 0.12	g : 0.12	c : 0.10	4 : 0.07	= : 0.07	2 : 0.05	h : 0.05	d : 0.05	3 : 0.03	i : 0.03	: : 0.01	b : 0.01	] : 0.01	6 : 0.01	
e : 0.14	c : 0.12	f : 0.09	g : 0.09	4 : 0.07	] : 0.07	3 : 0.07	a : 0.05	= : 0.05	h : 0.05	d : 0.05	b : 0.03	2 : 0.01	: : 0.01	6 : 0.01	i : 0.01	

#score	690.699274125653
#seq	55
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_CDS_m2_run2.txt

#BEAR
::ddddoooooodddd	chr2:55277171-55277406(-)$1	235	199	215	11.2518
cc[cccooooooccc]	chr20:47710663-47710883(+)$1	220	75	91	10.9606
i[ddddoooooodddd	chr11:3744493-3744720(-)$1	227	87	103	12.3128
ggggggoooooogggg	chr14:75143227-75143450(-)$1	223	148	164	9.8002
bb[cccooooooccc]	chr5:37351250-37351483(-)$1	233	132	148	10.7172
eeee[aooooooaeee	chr1:55349269-55349496(-)$1	227	158	174	10.1765
e[ddddoooooodddd	chrM:12637-12875(+)$1	238	138	154	12.2237
e[ddddoooooodddd	chrM:12568-12832(+)$1	264	207	223	12.2237
dddcccooooooccc]	chr12:7044800-7045032(+)$1	232	76	92	10.9658
ccddddoooooodddd	chr19:6415577-6415800(-)$1	223	7	23	12.2403
iiiiiiooooooiiii	chr6:53135290-53135516(-)$1	226	162	178	10.0066
::ddddoooooodddd	chr3:167402014-167402247(-)$1	233	166	182	11.2518
::ddddoooooodddd	chr19:9639222-9639454(-)$1	232	124	140	11.2518
::ddddoooooodddd	chrM:13039-13295(+)$1	256	217	233	11.2518
:eeeeeooooooeeee	chr17:46937673-46937905(+)$1	232	27	43	10.2162
dd[cccooooooccc]	chr1:54704657-54704889(-)$1	232	161	177	10.7674
iiicccooooooccc:	chrM:6442-6670(+)$1	228	136	152	9.7611
dddcccooooooccc]	chr1:161009666-161009898(-)$1	232	105	121	10.9658
::ddddoooooodddd	chr19:37382561-37382786(-)$1	225	94	110	11.2518
:eeeeeooooooeeee	chr11:129992230-129992462(+)$1	232	183	199	10.2162
iiiiiiooooooiiii	chr13:77672142-77672374(-)$1	232	88	104	10.0066
ccddddoooooodddd	chr7:127222909-127223141(-)$1	232	6	22	12.2403
::ddddoooooodddd	chr21:33740611-33740847(-)$1	236	123	139	11.2518
!a[cccooooooccc]	chr1:11983351-11983584(-)$1	233	44	60	11.1474
eeddddoooooodddd	chr19:56206593-56206827(+)$1	234	145	161	12.0598
:eeeeeooooooeeee	chrM:13008-13250(-)$1	242	203	219	10.2162
::ddddoooooodddd	chrM:11700-11927(+)$1	227	85	101	11.2518
###cccooooooccc]	chr16:11643218-11643445(-)$1	227	121	137	10.9899
$$ddddoooooodddd	chr2:152314250-152314480(+)$1	230	138	154	12.1353
::ddddoooooodddd	chr19:49118500-49118722(-)$1	222	107	123	11.2518
::ddddoooooodddd	chr17:80529586-80529818(+)$1	232	153	169	11.2518
eeddddoooooodddd	chrM:8330-8586(+)$1	256	200	216	12.0598
$$$cccooooooccc4	chr7:127017170-127017401(-)$1	231	192	208	10.3979
dd[cccooooooccc]	chr17:38151397-38151629(+)$1	232	173	189	10.7674
c:ddddoooooodddd	chrM:12853-13092(+)$1	239	174	190	11.6753
:eeeeeooooooeeee	chr4:104057269-104057501(-)$1	232	41	57	10.2162
ddddbboooooobb]d	chr8:110587774-110588004(-)$1	230	161	177	9.4695
:eeeeeooooooeeee	chr22:39917914-39918146(+)$1	232	125	141	10.2162
!!ddddoooooodddd	chr1:241797965-241798198(-)$1	233	146	162	12.5496
cc[cccooooooccc3	chr14:104200893-104201125(-)$1	232	25	41	10.8435
"eeeeeooooooeeee	chr15:65982778-65983010(-)$1	232	143	159	10.7390
d[ddddoooooodddd	chr19:59060808-59061031(+)$1	223	51	67	12.2657
[eeeeeooooooeeee	chrM:12800-13024(+)$1	224	175	191	10.6572
iiiiiiooooooiiii	chr10:71977550-71977774(-)$1	224	68	84	10.0066
cc[cccooooooccc]	chr1:110882951-110883183(+)$1	232	139	155	10.9606
::ddddoooooodddd	chr12:123086048-123086272(+)$1	224	18	34	11.2518
f!!cccooooooccc4	chr19:21240490-21240723(+)$1	233	137	153	10.7915
!!ddddoooooodddd	chrM:15524-15783(+)$1	259	220	236	12.5496
b[ddddoooooodddd	chrX:53223695-53223940(-)$1	245	10	26	12.3099
"eeeeeooooooeeee	chr2:183866834-183867073(-)$1	239	83	99	10.7390
!!ddddoooooodddd	chrM:15712-15965(+)$1	253	32	48	12.5496
b[ddddoooooodddd	chr1:27874612-27874844(-)$1	232	173	189	12.3099
dddcccooooooccc]	chrM:9702-10036(+)$1	334	85	101	10.9658
::ddddoooooodddd	chrM:15422-15654(+)$1	232	175	191	11.2518
c[ddddoooooodddd	chr1:39888352-39888581(+)$1	229	66	82	12.3864
[eeeeeooooooeeee	chr2:73678097-73678329(+)$1	232	148	164	10.6572
====[aooooooa]==	chr17:33463352-33463576(-)$1	224	145	161	9.8666
ddddddoooooodddd	chr2:176959212-176959435(+)$1	223	15	31	12.0470

#otherMatches

#Seq PSSM
CCCUGAUGGACUUCGG	chr2:55277171-55277406(-)$1	235	199	215	11.2518
UAGAGAAAAAGAUCUG	chr20:47710663-47710883(+)$1	220	75	91	10.9606
GAAGAUUCCCUUGUUU	chr11:3744493-3744720(-)$1	227	87	103	12.3128
CCUUGUCCAUUCAUGA	chr14:75143227-75143450(-)$1	223	148	164	9.8002
GAUAAUGGCAGAAUUU	chr5:37351250-37351483(-)$1	233	132	148	10.7172
AUCAUGAUCAACCUGA	chr1:55349269-55349496(-)$1	227	158	174	10.1765
GUAGGAAUUAUAUCCU	chrM:12637-12875(+)$1	238	138	154	12.2237
GUAGGAAUUAUAUCCU	chrM:12568-12832(+)$1	264	207	223	12.2237
UGGCCUGUCCCAGGGC	chr12:7044800-7045032(+)$1	232	76	92	10.9658
GGCAGGCCCUGUUCUG	chr19:6415577-6415800(-)$1	223	7	23	12.2403
GCCUUUACCAACAAAG	chr6:53135290-53135516(-)$1	226	162	178	10.0066
AAGAGAUGUACUUCUC	chr3:167402014-167402247(-)$1	233	166	182	11.2518
AAAUUCACAUGCGAAU	chr19:9639222-9639454(-)$1	232	124	140	11.2518
CAAGUCAACUAGGACU	chrM:13039-13295(+)$1	256	217	233	11.2518
UGCUCAGUUACAUGGG	chr17:46937673-46937905(+)$1	232	27	43	10.2162
AAGCAAGUUUAAUUGA	chr1:54704657-54704889(-)$1	232	161	177	10.7674
AGGAGACCCCAUUCUA	chrM:6442-6670(+)$1	228	136	152	9.7611
GAUCUUAAAAACAAGA	chr1:161009666-161009898(-)$1	232	105	121	10.9658
AUAGUGCCUCAACACU	chr19:37382561-37382786(-)$1	225	94	110	11.2518
CCCAUGUAGAGCCAUG	chr11:129992230-129992462(+)$1	232	183	199	10.2162
AGAAAAAUCGAGUUUU	chr13:77672142-77672374(-)$1	232	88	104	10.0066
CAUGGAGAGGAGUCCA	chr7:127222909-127223141(-)$1	232	6	22	12.2403
ACUACUAAACAAGGUA	chr21:33740611-33740847(-)$1	236	123	139	11.2518
AAAUGAAGAAGAUCAC	chr1:11983351-11983584(-)$1	233	44	60	11.1474
GCCUGGCUCCAUCCGG	chr19:56206593-56206827(+)$1	234	145	161	12.0598
AUGGCUGAGGGGAGUC	chrM:13008-13250(-)$1	242	203	219	10.2162
AAUCCUCUCUCAAGGA	chrM:11700-11927(+)$1	227	85	101	11.2518
CCCCAGAAAUUGCUGC	chr16:11643218-11643445(-)$1	227	121	137	10.9899
AAGAAUAAACAGAUUC	chr2:152314250-152314480(+)$1	230	138	154	12.1353
UCUCUUAUUAAAAAGA	chr19:49118500-49118722(-)$1	222	107	123	11.2518
CUGGCAGGUAAAUGCC	chr17:80529586-80529818(+)$1	232	153	169	11.2518
AACGAAAAUCUGUUCG	chrM:8330-8586(+)$1	256	200	216	12.0598
UUUUACAGCUAAGUAU	chr7:127017170-127017401(-)$1	231	192	208	10.3979
CUGUUGGAGGAGCAGA	chr17:38151397-38151629(+)$1	232	173	189	10.7674
CCCUGACUCCCCUCAG	chrM:12853-13092(+)$1	239	174	190	11.6753
GUCUCUUGACUUGGAG	chr4:104057269-104057501(-)$1	232	41	57	10.2162
GCUACUGGUAGGAGAU	chr8:110587774-110588004(-)$1	230	161	177	9.4695
UCCCCUUUCCCCAGGG	chr22:39917914-39918146(+)$1	232	125	141	10.2162
ACUGCACUCAAUUGCA	chr1:241797965-241798198(-)$1	233	146	162	12.5496
GCCUGCUCCCCUGCGA	chr14:104200893-104201125(-)$1	232	25	41	10.8435
ACUAGUACCUAAACUA	chr15:65982778-65983010(-)$1	232	143	159	10.7390
GAGGGUACCUCAGCCC	chr19:59060808-59061031(+)$1	223	51	67	12.2657
ACUAGGCCUCCUCCUA	chrM:12800-13024(+)$1	224	175	191	10.6572
UGAAAUUUUCUUAUUU	chr10:71977550-71977774(-)$1	224	68	84	10.0066
CUGCUCCUUUCAGAGA	chr1:110882951-110883183(+)$1	232	139	155	10.9606
UUUUGUUUUUAUACAG	chr12:123086048-123086272(+)$1	224	18	34	11.2518
UAACUCAUAUUGGAGA	chr19:21240490-21240723(+)$1	233	137	153	10.7915
UCAUUCUAACCUGAAU	chrM:15524-15783(+)$1	259	220	236	12.5496
GGUAUGGCAGAUCGUG	chrX:53223695-53223940(-)$1	245	10	26	12.3099
ACUUUGAUUUAACAAA	chr2:183866834-183867073(-)$1	239	83	99	10.7390
UCAUUCUAACCUGAAU	chrM:15712-15965(+)$1	253	32	48	12.5496
GGGACAGCAGCAUGUC	chr1:27874612-27874844(-)$1	232	173	189	12.3099
GCUCAACAUUUUUUGU	chrM:9702-10036(+)$1	334	85	101	10.9658
UCCCUAACAAACUAGG	chrM:15422-15654(+)$1	232	175	191	11.2518
ACAGCUACAGGAAGCU	chr1:39888352-39888581(+)$1	229	66	82	12.3864
GCAGUUUCUACCAACU	chr2:73678097-73678329(+)$1	232	148	164	10.6572
CCUUUGAACCUGCUGA	chr17:33463352-33463576(-)$1	224	145	161	9.8666
CCGGACAUGUGCGUCU	chr2:176959212-176959435(+)$1	223	15	31	12.0470

#DB
..((((......))))	chr2:55277171-55277406(-)$1	1	199	215	11.2518
((.(((......))).	chr20:47710663-47710883(+)$1	1	75	91	10.9606
(.((((......))))	chr11:3744493-3744720(-)$1	1	87	103	12.3128
((((((......))))	chr14:75143227-75143450(-)$1	1	148	164	9.8002
((.(((......))).	chr5:37351250-37351483(-)$1	1	132	148	10.7172
((((.(......))))	chr1:55349269-55349496(-)$1	1	158	174	10.1765
(.((((......))))	chrM:12637-12875(+)$1	1	138	154	12.2237
(.((((......))))	chrM:12568-12832(+)$1	1	207	223	12.2237
((((((......))).	chr12:7044800-7045032(+)$1	1	76	92	10.9658
((((((......))))	chr19:6415577-6415800(-)$1	1	7	23	12.2403
((((((......))))	chr6:53135290-53135516(-)$1	1	162	178	10.0066
..((((......))))	chr3:167402014-167402247(-)$1	1	166	182	11.2518
..((((......))))	chr19:9639222-9639454(-)$1	1	124	140	11.2518
..((((......))))	chrM:13039-13295(+)$1	1	217	233	11.2518
.(((((......))))	chr17:46937673-46937905(+)$1	1	27	43	10.2162
((.(((......))).	chr1:54704657-54704889(-)$1	1	161	177	10.7674
)))(((......))).	chrM:6442-6670(+)$1	1	136	152	9.7611
((((((......))).	chr1:161009666-161009898(-)$1	1	105	121	10.9658
..((((......))))	chr19:37382561-37382786(-)$1	1	94	110	11.2518
.(((((......))))	chr11:129992230-129992462(+)$1	1	183	199	10.2162
((((((......))))	chr13:77672142-77672374(-)$1	1	88	104	10.0066
((((((......))))	chr7:127222909-127223141(-)$1	1	6	22	12.2403
..((((......))))	chr21:33740611-33740847(-)$1	1	123	139	11.2518
.(.(((......))).	chr1:11983351-11983584(-)$1	1	44	60	11.1474
((((((......))))	chr19:56206593-56206827(+)$1	1	145	161	12.0598
.(((((......))))	chrM:13008-13250(-)$1	1	203	219	10.2162
..((((......))))	chrM:11700-11927(+)$1	1	85	101	11.2518
...(((......))).	chr16:11643218-11643445(-)$1	1	121	137	10.9899
..((((......))))	chr2:152314250-152314480(+)$1	1	138	154	12.1353
..((((......))))	chr19:49118500-49118722(-)$1	1	107	123	11.2518
..((((......))))	chr17:80529586-80529818(+)$1	1	153	169	11.2518
((((((......))))	chrM:8330-8586(+)$1	1	200	216	12.0598
...(((......))).	chr7:127017170-127017401(-)$1	1	192	208	10.3979
((.(((......))).	chr17:38151397-38151629(+)$1	1	173	189	10.7674
).((((......))))	chrM:12853-13092(+)$1	1	174	190	11.6753
.(((((......))))	chr4:104057269-104057501(-)$1	1	41	57	10.2162
((((((......)).)	chr8:110587774-110588004(-)$1	1	161	177	9.4695
.(((((......))))	chr22:39917914-39918146(+)$1	1	125	141	10.2162
..((((......))))	chr1:241797965-241798198(-)$1	1	146	162	12.5496
((.(((......))).	chr14:104200893-104201125(-)$1	1	25	41	10.8435
.(((((......))))	chr15:65982778-65983010(-)$1	1	143	159	10.7390
(.((((......))))	chr19:59060808-59061031(+)$1	1	51	67	12.2657
.(((((......))))	chrM:12800-13024(+)$1	1	175	191	10.6572
((((((......))))	chr10:71977550-71977774(-)$1	1	68	84	10.0066
((.(((......))).	chr1:110882951-110883183(+)$1	1	139	155	10.9606
..((((......))))	chr12:123086048-123086272(+)$1	1	18	34	11.2518
(..(((......))).	chr19:21240490-21240723(+)$1	1	137	153	10.7915
..((((......))))	chrM:15524-15783(+)$1	1	220	236	12.5496
(.((((......))))	chrX:53223695-53223940(-)$1	1	10	26	12.3099
.(((((......))))	chr2:183866834-183867073(-)$1	1	83	99	10.7390
..((((......))))	chrM:15712-15965(+)$1	1	32	48	12.5496
(.((((......))))	chr1:27874612-27874844(-)$1	1	173	189	12.3099
((((((......))).	chrM:9702-10036(+)$1	1	85	101	10.9658
..((((......))))	chrM:15422-15654(+)$1	1	175	191	11.2518
(.((((......))))	chr1:39888352-39888581(+)$1	1	66	82	12.3864
.(((((......))))	chr2:73678097-73678329(+)$1	1	148	164	10.6572
((((.(......).))	chr17:33463352-33463576(-)$1	1	145	161	9.8666
))((((......))))	chr2:176959212-176959435(+)$1	1	15	31	12.0470

#PSSM
: : 0.27	d : 0.13	c : 0.12	i : 0.08	e : 0.08	! : 0.06	b : 0.05	$ : 0.03	" : 0.03	[ : 0.03	g : 0.01	# : 0.01	f : 0.01	= : 0.01	
: : 0.20	e : 0.20	[ : 0.12	d : 0.12	c : 0.08	i : 0.06	! : 0.06	$ : 0.03	g : 0.01	b : 0.01	a : 0.01	# : 0.01	= : 0.01	
d : 0.55	e : 0.17	[ : 0.12	i : 0.06	g : 0.01	# : 0.01	$ : 0.01	! : 0.01	= : 0.01	
d : 0.49	c : 0.24	e : 0.17	i : 0.05	g : 0.01	= : 0.01	
d : 0.48	c : 0.24	e : 0.15	i : 0.05	[ : 0.03	g : 0.01	b : 0.01	
d : 0.48	c : 0.24	e : 0.15	i : 0.05	a : 0.03	g : 0.01	b : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
d : 0.48	c : 0.24	e : 0.15	i : 0.05	a : 0.03	g : 0.01	b : 0.01	
d : 0.48	c : 0.24	e : 0.17	i : 0.05	g : 0.01	b : 0.01	] : 0.01	
d : 0.48	c : 0.24	e : 0.17	i : 0.05	g : 0.01	] : 0.01	= : 0.01	
d : 0.49	] : 0.17	e : 0.17	i : 0.05	4 : 0.03	g : 0.01	: : 0.01	3 : 0.01	= : 0.01	

#score	646.1199361742155
#seq	58
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_UTR_m3_run1.txt

#BEAR
[aeeeeerrrrrrrrreeeee4	chr16:4918732-4918962(+)$1	230	145	167	8.6139
cc"""cccqqqqqqqqcccccc	chr3:49049417-49049643(+)$1	226	195	217	14.5935
ccc"""bbqqqqqqqqbb333c	chr19:15348425-15348651(-)$1	226	150	172	13.7764
ccbb[cccqqqqqqqqccc]bb	chr14:64494384-64494600(+)$1	216	73	95	13.8252
b[ffffffqqqqqqqqffffff	chr6:35824954-35825172(-)$1	218	148	170	13.6694
iiiiiiiirrrrrrrrriiiii	chr4:7032214-7032440(+)$1	226	94	116	9.5211
c"""ddddqqqqqqqqddddcc	chr19:14626295-14626515(-)$1	220	189	211	13.0729
##aeeeeeqqqqqqqqeeeee]	chr17:54965827-54966074(-)$1	247	44	66	13.5687
fcccddddqqqqqqqqdddd]c	chr17:27401744-27401967(-)$1	223	196	218	12.9113
eee!!cccqqqqqqqqccceee	chr2:128047247-128047461(-)$1	214	104	126	14.2550
eeeeeeeeqqqqqqqqeeeee:	chr2:109335898-109336120(+)$1	222	112	134	12.1742
gggggggaqqqqqqqqa]gggg	chr20:39831069-39831287(-)$1	218	13	35	14.4823
ccc[cccrrrrrrrrrccc]cc	chr16:66655640-66655861(-)$1	221	192	214	9.8794
""ffffffqqqqqqqqffffff	chr7:133978866-133979091(-)$1	225	105	127	13.9123
:gggggggqqqqqqqqgggggg	chr2:219315091-219315301(-)$1	210	152	174	13.8113
###eeeeeqqqqqqqqeeeee3	chr10:97818273-97818494(+)$1	221	109	131	13.6321
fffbbcccqqqqqqqqccc]bb	chr19:1581080-1581303(-)$1	223	48	70	13.4301
#gggggggqqqqqqqqgggggg	chr14:56765030-56765251(+)$1	221	51	73	14.7248
[gggggggqqqqqqqqgggggg	chr12:122756909-122757127(-)$1	218	136	158	14.6962
eeccccccqqqqqqqqccc22c	chr11:119170728-119170958(+)$1	230	50	72	14.1348
[gggggggrrrrrrrrrggggg	chr8:37557348-37557595(+)$1	247	37	59	9.9257
fffffcccqqqqqqqqccc]ff	chr21:34775762-34775992(+)$1	230	84	106	14.4945
""bb[cccrrrrrrrrrccc]b	chr6:32936382-32936602(+)$1	220	55	77	9.2100
ddd!!cccqqqqqqqqccc22d	chr8:38130237-38130467(-)$1	230	173	195	13.8552
"ccc[cccqqqqqqqqccc]cc	chr5:6755128-6755344(+)$1	216	159	181	15.0367
g:ffffffqqqqqqqqffffff	chr3:27475369-27475585(-)$1	216	124	146	12.7754
ee!!ddddqqqqqqqqdddd55	chr2:85548894-85549113(-)$1	219	112	134	11.2338
ddddddbbqqqqqqqqbb]ddd	chr2:219503377-219503589(-)$1	212	131	153	12.0834
ggggg[bbqqqqqqqqbb]ggg	chr1:151263247-151263468(+)$1	221	184	206	14.0100
ccccc[bbqqqqqqqqbb]ccc	chr9:123525650-123525881(-)$1	231	145	167	13.5852
b!!eeeeeqqqqqqqqeeeee2	chr17:61907708-61907935(+)$1	227	130	152	13.2601
!!ffffffrrrrrrrrrfffff	chr10:76936697-76936907(+)$1	210	116	138	9.2181
:gggggggqqqqqqqqgggggg	chr1:15993104-15993327(+)$1	223	199	221	13.8113
:gggggggqqqqqqqqgggggg	chr1:6283679-6283897(-)$1	218	174	196	13.8113
dd[ccc[aqqqqqqqqa]ccc]	chr10:92665012-92665233(+)$1	221	89	111	13.7383
ccc"""bbqqqqqqqqbb22cc	chr17:48211196-48211407(-)$1	211	18	40	13.2572
"gggggggqqqqqqqqgggggg	chr12:46757627-46757849(-)$1	222	113	135	14.7265
fffff[bbqqqqqqqqbb]fff	chr1:116239168-116239395(+)$1	227	155	177	13.3545
::ccccccqqqqqqqqccc]cc	chr2:242168637-242168867(-)$1	230	202	224	13.0116
fffffcccqqqqqqqqccc333	chr3:44485772-44485996(-)$1	224	183	205	14.6552
c[eeeeerrrrrrrrreeeee]	chrX:153236759-153236993(-)$1	234	89	111	8.7055
eeee[cccqqqqqqqqccceee	chr7:131173430-131173645(+)$1	215	108	130	14.1501
#gggggggqqqqqqqqgggggg	chr10:21070990-21071216(-)$1	226	160	182	14.7248
((ffffffqqqqqqqqffffff	chr7:86824896-86825119(+)$1	223	50	72	12.5138
d####cccqqqqqqqqccc444	chr22:45591945-45592160(-)$1	215	151	173	14.2962
ggga[cccqqqqqqqqccc22a	chr19:14520561-14520776(-)$1	215	165	187	14.4918
gggggggssssssssssggggg	chrX:54096079-54096297(-)$1	218	110	132	8.4228
bddddcccqqqqqqqqccc]dd	chr14:75483622-75483841(-)$1	219	49	71	13.5477
iiiiiiiirrrrrrrrriiiii	chr6:138658261-138658478(+)$1	217	166	188	9.5211
fffff[bbqqqqqqqqbb]fff	chr14:73686055-73686277(+)$1	222	36	58	13.3545
bb[eeeeeqqqqqqqqeeeee]	chr7:133977676-133977904(-)$1	228	201	223	13.1309

#otherMatches

#Seq PSSM
CCAGGAUAUUAAUGGAAUCCUA	chr16:4918732-4918962(+)$1	230	145	167	8.6139
UCAUACCUGGAAAGCAAGGGAU	chr3:49049417-49049643(+)$1	226	195	217	14.5935
GAGGCCACCAACCAAAGUCAGU	chr19:15348425-15348651(-)$1	226	150	172	13.7764
GAGCCUUGGCUGGAAAUAAAGC	chr14:64494384-64494600(+)$1	216	73	95	13.8252
CCCUUGGCUUUCACUUGUUAAG	chr6:35824954-35825172(-)$1	218	148	170	13.6694
GCAGCUCAGUGGAAGGAUGAGC	chr4:7032214-7032440(+)$1	226	94	116	9.5211
GUUUGUGCUUUAUUCUGUAUUU	chr19:14626295-14626515(-)$1	220	189	211	13.0729
gacagucuaacugugggggcua	chr17:54965827-54966074(-)$1	247	44	66	13.5687
GCAGCCCUCUCACCCCAGGGCC	chr17:27401744-27401967(-)$1	223	196	218	12.9113
CUCCAGGACCCCGUGAUCCGAG	chr2:128047247-128047461(-)$1	214	104	126	14.2550
UGCGGGCCUGAGCGCUGGUCUC	chr2:109335898-109336120(+)$1	222	112	134	12.1742
GCAGCUCCCAGGCAAAGUGAGC	chr20:39831069-39831287(-)$1	218	13	35	14.4823
GUCGUGUGUAUUUGUAACAAGA	chr16:66655640-66655861(-)$1	221	192	214	9.8794
UAGUGGGACUCCUCUUUCCCAC	chr7:133978866-133979091(-)$1	225	105	127	13.9123
UUCAGAGUGACUUUUGAUUCUG	chr2:219315091-219315301(-)$1	210	152	174	13.8113
UAUGGACUUGCCAAACAGUCUU	chr10:97818273-97818494(+)$1	221	109	131	13.6321
CUGCACGGAUGAGACGCUGCUG	chr19:1581080-1581303(-)$1	223	48	70	13.4301
CAUAGGAGCUCCACCAUUCCUG	chr14:56765030-56765251(+)$1	221	51	73	14.7248
AAAAAUGUGCCAUUUUGCAUUU	chr12:122756909-122757127(-)$1	218	136	158	14.6962
AGAAAGCUAUAGAACAAGUAUU	chr11:119170728-119170958(+)$1	230	50	72	14.1348
UGGACCCCCCAGCGACUGGGGU	chr8:37557348-37557595(+)$1	247	37	59	9.9257
GCCAUGCGAccgacgcugcugu	chr21:34775762-34775992(+)$1	230	84	106	14.4945
GACUGCGGGAUAGGAAGCUGGG	chr6:32936382-32936602(+)$1	220	55	77	9.2100
UAUUUGUUAACUUUUAAAUCUA	chr8:38130237-38130467(-)$1	230	173	195	13.8552
CCAGGAUUCUUCCUUCAGUGCU	chr5:6755128-6755344(+)$1	216	159	181	15.0367
UCUUUUGCAGAUAUAGGCAAGA	chr3:27475369-27475585(-)$1	216	124	146	12.7754
ACUUUUUGAAAUAGGGCAAGUU	chr2:85548894-85549113(-)$1	219	112	134	11.2338
GACCCGGCAUCGAGAAGCACGG	chr2:219503377-219503589(-)$1	212	131	153	12.0834
GUUUCAUCAGCCACAAGAAGAG	chr1:151263247-151263468(+)$1	221	184	206	14.0100
AGUAUGCUAUACUAGAAGGAUA	chr9:123525650-123525881(-)$1	231	145	167	13.5852
CACUGGGCAUUGCUCAGCCCAA	chr17:61907708-61907935(+)$1	227	130	152	13.2601
AGUCAAGAAAUAAUAUGUUUUG	chr10:76936697-76936907(+)$1	210	116	138	9.2181
UAUUUUAAAAGUCAUAUUAGAG	chr1:15993104-15993327(+)$1	223	199	221	13.8113
gaagaacaaugucaaauguuuu	chr1:6283679-6283897(-)$1	218	174	196	13.8113
cugggaaguuuugucuccucug	chr10:92665012-92665233(+)$1	221	89	111	13.7383
GACUUCGAUCAGUAUUUCUUGU	chr17:48211196-48211407(-)$1	211	18	40	13.2572
UGUUCUUCCCAUCUAUGAAGAA	chr12:46757627-46757849(-)$1	222	113	135	14.7265
AAUAAGCCUCUUUAGUGGGUUG	chr1:116239168-116239395(+)$1	227	155	177	13.3545
CCUCAGGAAAUAAACGUCCUUG	chr2:242168637-242168867(-)$1	230	202	224	13.0116
CCUCUAGGACCAGGGCCCUCUC	chr3:44485772-44485996(-)$1	224	183	205	14.6552
CCCGCCUCCAUUCGUUAGGUGU	chrX:153236759-153236993(-)$1	234	89	111	8.7055
UGUCCAGUGGUAUACAACUGAC	chr7:131173430-131173645(+)$1	215	108	130	14.1501
CUCUAAAGAUUUAGAACUUUAG	chr10:21070990-21071216(-)$1	226	160	182	14.7248
UAGAGACCUAGGAGGUGGUCUU	chr7:86824896-86825119(+)$1	223	50	72	12.5138
UGAAGGCGUUUCCAUCUGCAAG	chr22:45591945-45592160(-)$1	215	151	173	14.2962
AGACAGUGAGAAGAACCGCAAG	chr19:14520561-14520776(-)$1	215	165	187	14.4918
UUUGGGUAGACUUUAAAGCCCA	chrX:54096079-54096297(-)$1	218	110	132	8.4228
CACCAUGAGAACAGAAUCACUG	chr14:75483622-75483841(-)$1	219	49	71	13.5477
GUUUGUUUCCAUCCCCAAGGCA	chr6:138658261-138658478(+)$1	217	166	188	9.5211
AAGUCAAGAUUCCCGGCUGGAC	chr14:73686055-73686277(+)$1	222	36	58	13.3545
cggguuuuuguuacuuaaaaug	chr7:133977676-133977904(-)$1	228	201	223	13.1309

#DB
.((((((.........))))).	chr16:4918732-4918962(+)$1	1	145	167	8.6139
((...(((........))))))	chr3:49049417-49049643(+)$1	1	195	217	14.5935
(((...((........))...)	chr19:15348425-15348651(-)$1	1	150	172	13.7764
((((.(((........))).))	chr14:64494384-64494600(+)$1	1	73	95	13.8252
(.((((((........))))))	chr6:35824954-35825172(-)$1	1	148	170	13.6694
((((((((.........)))))	chr4:7032214-7032440(+)$1	1	94	116	9.5211
(...((((........))))))	chr19:14626295-14626515(-)$1	1	189	211	13.0729
..((((((........))))).	chr17:54965827-54966074(-)$1	1	44	66	13.5687
)(((((((........)))).)	chr17:27401744-27401967(-)$1	1	196	218	12.9113
(((..(((........))))))	chr2:128047247-128047461(-)$1	1	104	126	14.2550
)))(((((........))))).	chr2:109335898-109336120(+)$1	1	112	134	12.1742
((((((((........).))))	chr20:39831069-39831287(-)$1	1	13	35	14.4823
(((.(((.........))).))	chr16:66655640-66655861(-)$1	1	192	214	9.8794
..((((((........))))))	chr7:133978866-133979091(-)$1	1	105	127	13.9123
.(((((((........))))))	chr2:219315091-219315301(-)$1	1	152	174	13.8113
...(((((........))))).	chr10:97818273-97818494(+)$1	1	109	131	13.6321
((((((((........))).))	chr19:1581080-1581303(-)$1	1	48	70	13.4301
.(((((((........))))))	chr14:56765030-56765251(+)$1	1	51	73	14.7248
.(((((((........))))))	chr12:122756909-122757127(-)$1	1	136	158	14.6962
((((((((........)))..)	chr11:119170728-119170958(+)$1	1	50	72	14.1348
.(((((((.........)))))	chr8:37557348-37557595(+)$1	1	37	59	9.9257
((((((((........))).))	chr21:34775762-34775992(+)$1	1	84	106	14.4945
..((.(((.........))).)	chr6:32936382-32936602(+)$1	1	55	77	9.2100
(((..(((........)))..)	chr8:38130237-38130467(-)$1	1	173	195	13.8552
.(((.(((........))).))	chr5:6755128-6755344(+)$1	1	159	181	15.0367
).((((((........))))))	chr3:27475369-27475585(-)$1	1	124	146	12.7754
((..((((........))))..	chr2:85548894-85549113(-)$1	1	112	134	11.2338
((((((((........)).)))	chr2:219503377-219503589(-)$1	1	131	153	12.0834
(((((.((........)).)))	chr1:151263247-151263468(+)$1	1	184	206	14.0100
(((((.((........)).)))	chr9:123525650-123525881(-)$1	1	145	167	13.5852
(..(((((........))))).	chr17:61907708-61907935(+)$1	1	130	152	13.2601
..((((((.........)))))	chr10:76936697-76936907(+)$1	1	116	138	9.2181
.(((((((........))))))	chr1:15993104-15993327(+)$1	1	199	221	13.8113
.(((((((........))))))	chr1:6283679-6283897(-)$1	1	174	196	13.8113
((.(((.(........).))).	chr10:92665012-92665233(+)$1	1	89	111	13.7383
(((...((........))..))	chr17:48211196-48211407(-)$1	1	18	40	13.2572
.(((((((........))))))	chr12:46757627-46757849(-)$1	1	113	135	14.7265
(((((.((........)).)))	chr1:116239168-116239395(+)$1	1	155	177	13.3545
..((((((........))).))	chr2:242168637-242168867(-)$1	1	202	224	13.0116
((((((((........)))...	chr3:44485772-44485996(-)$1	1	183	205	14.6552
(.(((((.........))))).	chrX:153236759-153236993(-)$1	1	89	111	8.7055
((((.(((........))))))	chr7:131173430-131173645(+)$1	1	108	130	14.1501
.(((((((........))))))	chr10:21070990-21071216(-)$1	1	160	182	14.7248
..((((((........))))))	chr7:86824896-86825119(+)$1	1	50	72	12.5138
(....(((........)))...	chr22:45591945-45592160(-)$1	1	151	173	14.2962
((((.(((........)))..)	chr19:14520561-14520776(-)$1	1	165	187	14.4918
(((((((..........)))))	chrX:54096079-54096297(-)$1	1	110	132	8.4228
((((((((........))).))	chr14:75483622-75483841(-)$1	1	49	71	13.5477
((((((((.........)))))	chr6:138658261-138658478(+)$1	1	166	188	9.5211
(((((.((........)).)))	chr14:73686055-73686277(+)$1	1	36	58	13.3545
((.(((((........))))).	chr7:133977676-133977904(-)$1	1	201	223	13.1309

#PSSM
c : 0.15	f : 0.11	e : 0.09	g : 0.09	b : 0.07	# : 0.07	" : 0.07	: : 0.07	d : 0.07	[ : 0.05	i : 0.03	! : 0.01	( : 0.01	
g : 0.23	c : 0.15	e : 0.09	f : 0.09	d : 0.07	" : 0.05	# : 0.05	[ : 0.03	i : 0.03	: : 0.03	! : 0.03	a : 0.01	( : 0.01	b : 0.01	
g : 0.23	f : 0.19	c : 0.15	e : 0.09	d : 0.05	" : 0.03	b : 0.03	i : 0.03	# : 0.03	! : 0.03	[ : 0.03	a : 0.01	
g : 0.21	f : 0.17	e : 0.15	c : 0.11	" : 0.07	b : 0.05	! : 0.05	i : 0.03	d : 0.03	[ : 0.01	# : 0.01	a : 0.01	
g : 0.21	f : 0.17	e : 0.13	[ : 0.09	d : 0.09	c : 0.09	" : 0.05	i : 0.03	! : 0.03	b : 0.01	# : 0.01	
c : 0.33	g : 0.19	e : 0.13	f : 0.09	d : 0.07	[ : 0.07	" : 0.03	i : 0.03	
c : 0.31	g : 0.19	e : 0.13	b : 0.13	f : 0.09	d : 0.05	i : 0.03	[ : 0.01	
c : 0.29	g : 0.15	b : 0.13	f : 0.09	e : 0.09	r : 0.05	d : 0.05	i : 0.03	a : 0.03	s : 0.01	
q : 0.82	r : 0.15	s : 0.01	
q : 0.82	r : 0.15	s : 0.01	
q : 0.82	r : 0.15	s : 0.01	
q : 0.82	r : 0.15	s : 0.01	
q : 0.82	r : 0.15	s : 0.01	
q : 0.82	r : 0.15	s : 0.01	
q : 0.82	r : 0.15	s : 0.01	
q : 0.82	r : 0.15	s : 0.01	
c : 0.29	e : 0.13	b : 0.13	g : 0.13	r : 0.09	f : 0.07	d : 0.05	a : 0.03	s : 0.01	
c : 0.31	g : 0.17	e : 0.13	b : 0.13	f : 0.09	d : 0.05	i : 0.03	] : 0.03	
c : 0.33	g : 0.19	e : 0.13	f : 0.09	] : 0.09	d : 0.05	i : 0.03	3 : 0.01	2 : 0.01	
g : 0.21	e : 0.17	] : 0.13	f : 0.13	c : 0.07	d : 0.07	2 : 0.07	3 : 0.03	i : 0.03	4 : 0.01	
g : 0.21	e : 0.17	c : 0.15	f : 0.15	2 : 0.05	3 : 0.03	b : 0.03	i : 0.03	] : 0.03	d : 0.03	5 : 0.01	4 : 0.01	
g : 0.21	c : 0.19	f : 0.15	] : 0.07	b : 0.05	d : 0.05	4 : 0.03	i : 0.03	e : 0.03	3 : 0.03	: : 0.01	5 : 0.01	2 : 0.01	a : 0.01	

#score	658.6005512515649
#seq	51
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_CDS_m3_run1.txt

#BEAR
[ddddqqqqqqqqdddd]	chr9:139369326-139369555(-)$1	229	157	175	13.2845
fffffqqqqqqqqfffff	chr1:32502424-32502684(+)$1	260	86	104	13.7853
cc!!aqqqqqqqqa22cc	chr15:40917416-40917631(+)$1	215	48	66	13.7927
fffffqqqqqqqqfffff	chr8:124266378-124266603(-)$1	225	113	131	13.7853
bb[bbqqqqqqqqbbbb]	chr3:48219255-48219490(-)$1	235	15	33	12.5775
dd[bbqqqqqqqqbb]dd	chr19:36218687-36218922(+)$1	235	171	189	13.3124
fddddqqqqqqqqdddd]	chr4:159780148-159780366(+)$1	218	64	82	13.2167
##cccqqqqqqqqcccff	chr19:19609228-19609447(+)$1	219	74	92	14.0591
eeeeeqqqqqqqqeeeee	chr20:47734781-47735011(-)$1	230	198	216	13.9906
eeeeeqqqqqqqqeeeee	chr11:65546329-65546547(-)$1	218	193	211	13.9906
fffffqqqqqqqqfffff	chr6:32945168-32945436(+)$1	268	33	51	13.7853
fffffqqqqqqqqfffff	chr7:133984846-133985077(-)$1	231	70	88	13.7853
===[aqqqqqqqqa====	chr7:43918674-43918909(-)$1	235	90	108	14.4668
b[cccqqqqqqqqccc33	chr8:94935651-94935873(+)$1	222	84	102	14.1948
eeeeeqqqqqqqqeeeee	chr6:4937705-4937941(+)$1	236	30	48	13.9906
eeeeeqqqqqqqqeeeee	chr19:56206065-56206286(+)$1	221	186	204	13.9906
dd[bbqqqqqqqqbbddd	chrX:10534979-10535198(-)$1	219	169	187	13.2068
c[cccqqqqqqqqccc]c	chr6:117888008-117888228(-)$1	220	172	190	14.2901
fffffqqqqqqqqfffff	chr15:91420290-91420509(+)$1	219	161	179	13.7853
fff[aqqqqqqqqa]fff	chr2:73677681-73677907(+)$1	226	180	198	14.2643
eeeeeqqqqqqqqeeeee	chr10:15256443-15256667(-)$1	224	33	51	13.9906
b!!bbqqqqqqqqbb444	chr17:65959373-65959590(+)$1	217	184	202	13.7340
gggggqqqqqqqqggggg	chr1:220358880-220359098(+)$1	218	43	61	13.9061
eeeeeqqqqqqqqeeeee	chr17:61912701-61912921(-)$1	220	125	143	13.9906
eeeeeqqqqqqqqeeeee	chr14:23548000-23548221(-)$1	221	96	114	13.9906
eeeeeqqqqqqqqeeeee	chr17:1556781-1557079(-)$1	298	86	104	13.9906
fffffqqqqqqqqfffff	chr1:6292005-6292252(-)$1	247	211	229	13.7853
gggggqqqqqqqqggggg	chr10:115674769-115674989(+)$1	220	190	208	13.9061
"""bbqqqqqqqqbb444	chr1:55624514-55624724(-)$1	210	17	35	13.7798
c!!bbqqqqqqqqbb22c	chr18:2729211-2729427(+)$1	216	128	146	13.5762
f!!bbqqqqqqqqbb444	chr22:50187770-50187989(-)$1	219	172	190	14.0079
""cccqqqqqqqqccc22	chr17:63010602-63010843(-)$1	241	156	174	13.9004
eeebbqqqqqqqqbb]ee	chr16:4910894-4911122(+)$1	228	35	53	13.7342
fff[aqqqqqqqqa]fff	chr10:7866294-7866508(+)$1	214	47	65	14.2643
[a!!aqqqqqqqqa22a]	chr22:41569631-41569848(+)$1	217	77	95	13.9789
gggggqqqqqqqqggggg	chr11:17390358-17390590(+)$1	232	141	159	13.9061
ccc[aqqqqqqqqa]ccc	chr10:112724287-112724513(+)$1	226	93	111	14.1993
eeeeeqqqqqqqqeeeee	chr6:127611212-127611436(-)$1	224	45	63	13.9906
eeeeeqqqqqqqqeeeee	chr14:61180137-61180359(-)$1	222	15	33	13.9906
!!cccqqqqqqqqccc22	chr5:112178904-112179122(+)$1	218	116	134	14.0645
!!a[aqqqqqqqqa]a]=	chr17:1264286-1264516(-)$1	230	160	178	14.5320
!!cccqqqqqqqqccc44	chr8:25364494-25364719(+)$1	225	193	211	14.4107
dddddqqqqqqqqdddd]	chr19:39962202-39962429(+)$1	227	186	204	13.0742
""cccqqqqqqqqccc66	chr3:78710257-78710475(-)$1	218	108	126	13.2751
eeeeeqqqqqqqqeeeee	chr6:76420996-76421213(+)$1	217	133	151	13.9906
cc[bbqqqqqqqqbb22c	chrX:53426503-53426750(-)$1	247	83	101	13.4013
ddd[aqqqqqqqqadddd	chr19:44739899-44740148(+)$1	249	118	136	13.5421
fffffqqqqqqqqfffff	chr11:108191970-108192190(+)$1	220	85	103	13.7853
c[cccqqqqqqqqccc]c	chr2:44559551-44559777(-)$1	226	6	24	14.2901
d[cccqqqqqqqqccc]d	chr2:20135896-20136113(-)$1	217	41	59	14.0736
eeeeeqqqqqqqqeeeee	chr16:19548210-19548432(+)$1	222	203	221	13.9906
eeeeeqqqqqqqqeeeee	chr18:57005696-57005920(-)$1	224	84	102	13.9906
cc[aaqqqqqqqqa]a]c	chr22:38694725-38694994(-)$1	269	181	199	14.2975
cddddqqqqqqqqdddd2	chrX:39914537-39914865(-)$1	328	178	196	12.9494
ggg[aqqqqqqqqa]ggg	chr17:80529606-80529842(+)$1	236	154	172	14.3365
b[cccqqqqqqqqccc]b	chr8:77768303-77768514(+)$1	211	171	189	13.7462
[ddddqqqqqqqqdddd]	chr19:38135466-38135677(-)$1	211	38	56	13.2845
f!!bbqqqqqqqqbb333	chr6:53363455-53363674(-)$1	219	161	179	14.1808
fff[aqqqqqqqqa]fff	chr20:61525765-61525984(-)$1	219	89	107	14.2643
dd[bbqqqqqqqqbb]dd	chr9:131515011-131515228(-)$1	217	42	60	13.3124
!!cccqqqqqqqqcccbb	chr8:48830769-48831028(-)$1	259	183	201	13.6365
fffffqqqqqqqqfffff	chr14:45581536-45581746(+)$1	210	52	70	13.7853
####aqqqqqqqqa333h	chr8:95894950-95895170(-)$1	220	168	186	14.0352
[cccaqqqqqqqqa]ccc	chr19:7975772-7975988(+)$1	216	39	57	14.2578
fffffqqqqqqqqfffff	chr5:147790199-147790423(+)$1	224	48	66	13.7853
eeeeeqqqqqqqqeeeee	chr11:82644057-82644273(+)$1	216	76	94	13.9906

#otherMatches

#Seq PSSM
CAGCUCUGUCCUUAGCUU	chr9:139369326-139369555(-)$1	229	157	175	13.2845
GAUAUGAUGGAUGAUAUC	chr1:32502424-32502684(+)$1	260	86	104	13.7853
UUGAUGACCUGGAACAGA	chr15:40917416-40917631(+)$1	215	48	66	13.7927
ACUUUACUCCCCAAAAGU	chr8:124266378-124266603(-)$1	225	113	131	13.7853
UCCUCAAAUGAAAGAGAU	chr3:48219255-48219490(-)$1	235	15	33	12.5775
AGGCCAGAUGAAGGGGCU	chr19:36218687-36218922(+)$1	235	171	189	13.3124
ACUGAUGAGACAUUCAGC	chr4:159780148-159780366(+)$1	218	64	82	13.2167
UCCACCCCCACUAGUGUG	chr19:19609228-19609447(+)$1	219	74	92	14.0591
UCCUGAAUAACAGCAGGA	chr20:47734781-47735011(-)$1	230	198	216	13.9906
UUUGCUGGCACCUGCAAA	chr11:65546329-65546547(-)$1	218	193	211	13.9906
GCUGCCUCCUUCUGCAGC	chr6:32945168-32945436(+)$1	268	33	51	13.7853
GGGCAUUGACUUUUGCUC	chr7:133984846-133985077(-)$1	231	70	88	13.7853
CCUAGAGACGUACCAGGU	chr7:43918674-43918909(-)$1	235	90	108	14.4668
UCGCCACGCUGUGGGCAA	chr8:94935651-94935873(+)$1	222	84	102	14.1948
aaaaUGCUUUAAGAUUUU	chr6:4937705-4937941(+)$1	236	30	48	13.9906
GGGGCCCAAUGCAGCCCU	chr19:56206065-56206286(+)$1	221	186	204	13.9906
UGUGUGACCGAUGACCAG	chrX:10534979-10535198(-)$1	219	169	187	13.2068
AGUUGCAAAGACACAAGU	chr6:117888008-117888228(-)$1	220	172	190	14.2901
GCAGGCCCCGGUCUCUGC	chr15:91420290-91420509(+)$1	219	161	179	13.7853
AAGAGGCUAAGAACGUUU	chr2:73677681-73677907(+)$1	226	180	198	14.2643
AAUCUUUGGCUUUGGAUU	chr10:15256443-15256667(-)$1	224	33	51	13.9906
CGGGCACAAGAGGGCAGC	chr17:65959373-65959590(+)$1	217	184	202	13.7340
GCUUUCUAUAAUCAGAGU	chr1:220358880-220359098(+)$1	218	43	61	13.9061
AGUGGAAGGAAAACUGCU	chr17:61912701-61912921(-)$1	220	125	143	13.9906
GAGGACUUCCACCUCCUC	chr14:23548000-23548221(-)$1	221	96	114	13.9906
CCCUGCCUGUUUUUAGGG	chr17:1556781-1557079(-)$1	298	86	104	13.9906
CUCUGGUGACCAGUGGAG	chr1:6292005-6292252(-)$1	247	211	229	13.7853
UCUGUUGAAAGCCACAGG	chr10:115674769-115674989(+)$1	220	190	208	13.9061
AUUGGUUAGCAUCCCUGA	chr1:55624514-55624724(-)$1	210	17	35	13.7798
CAGGAUCUGCAAUUCAAG	chr18:2729211-2729427(+)$1	216	128	146	13.5762
AAGCUGCUCAAAAAGGAA	chr22:50187770-50187989(-)$1	219	172	190	14.0079
AAUCGUCAAUAACCGGGU	chr17:63010602-63010843(-)$1	241	156	174	13.9004
GAUUUGGACUUGGAGCAU	chr16:4910894-4911122(+)$1	228	35	53	13.7342
UCUACAUGAACUAGAAGA	chr10:7866294-7866508(+)$1	214	47	65	14.2643
ACAAGAAGAAACCCGGGA	chr22:41569631-41569848(+)$1	217	77	95	13.9789
CCUUGGAAAAAGGUAAGG	chr11:17390358-17390590(+)$1	232	141	159	13.9061
GAGGUGAUUAAAGAGCUC	chr10:112724287-112724513(+)$1	226	93	111	14.1993
GUCCACAAAGAGAUGGGC	chr6:127611212-127611436(-)$1	224	45	63	13.9906
AGAACAUCGUUUGGUUCU	chr14:61180137-61180359(-)$1	222	15	33	13.9906
CAUCAGAAUCCAGUGAAA	chr5:112178904-112179122(+)$1	218	116	134	14.0645
AGCGUGAAAGUUAAGGGG	chr17:1264286-1264516(-)$1	230	160	178	14.5320
UAUUCUGAUGGUCGAAGU	chr8:25364494-25364719(+)$1	225	193	211	14.4107
GACCCUGUGCGUUGGGUA	chr19:39962202-39962429(+)$1	227	186	204	13.0742
UCGGCCAUCUGGAGCCAA	chr3:78710257-78710475(-)$1	218	108	126	13.2751
ACAGUAAGCAUUAACUGU	chr6:76420996-76421213(+)$1	217	133	151	13.9906
CACCUUUAUACACAGUUU	chrX:53426503-53426750(-)$1	247	83	101	13.4013
CUGCAUAUUCAUUUCAGA	chr19:44739899-44740148(+)$1	249	118	136	13.5421
CGCAGCCUUGAGUCUGUG	chr11:108191970-108192190(+)$1	220	85	103	13.7853
AUAAUGGAUACAAAUUCU	chr2:44559551-44559777(-)$1	226	6	24	14.2901
GCUCCUGAAAACUGGAUC	chr2:20135896-20136113(-)$1	217	41	59	14.0736
CAUGGACUUGUUACUGUG	chr16:19548210-19548432(+)$1	222	203	221	13.9906
UGUUGUGAAAACUCAGCA	chr18:57005696-57005920(-)$1	224	84	102	13.9906
UUGACUGGAACAUGCUGA	chr22:38694725-38694994(-)$1	269	181	199	14.2975
GCUACGUACUCAGGUAGA	chrX:39914537-39914865(-)$1	328	178	196	12.9494
UUUGUUGUUAAAUAGAGG	chr17:80529606-80529842(+)$1	236	154	172	14.3365
AGUCCUUCUCCCCGGAAU	chr8:77768303-77768514(+)$1	211	171	189	13.7462
AGGAUUUGGUGAUGUUCA	chr19:38135466-38135677(-)$1	211	38	56	13.2845
UACAGUACCAUGCCUCUC	chr6:53363455-53363674(-)$1	219	161	179	14.1808
GCAAGAGUCAGCACGUGC	chr20:61525765-61525984(-)$1	219	89	107	14.2643
CAAGGCAGCCCCACCCUG	chr9:131515011-131515228(-)$1	217	42	60	13.3124
CUUUCAUCAGUAAGAAGU	chr8:48830769-48831028(-)$1	259	183	201	13.6365
AAAUAUCCUAAAUUGUUU	chr14:45581536-45581746(+)$1	210	52	70	13.7853
CUCUCUAUUUGUUGUCUU	chr8:95894950-95895170(-)$1	220	168	186	14.0352
UGGCCUUGGGUCUGUGCC	chr19:7975772-7975988(+)$1	216	39	57	14.2578
CUGCCCUAAAGAUGGCAG	chr5:147790199-147790423(+)$1	224	48	66	13.7853
UUUCAGAAAUGAAUGAAA	chr11:82644057-82644273(+)$1	216	76	94	13.9906

#DB
.((((........)))).	chr9:139369326-139369555(-)$1	1	157	175	13.2845
(((((........)))))	chr1:32502424-32502684(+)$1	1	86	104	13.7853
((..(........)..))	chr15:40917416-40917631(+)$1	1	48	66	13.7927
(((((........)))))	chr8:124266378-124266603(-)$1	1	113	131	13.7853
((.((........)))).	chr3:48219255-48219490(-)$1	1	15	33	12.5775
((.((........)).))	chr19:36218687-36218922(+)$1	1	171	189	13.3124
(((((........)))).	chr4:159780148-159780366(+)$1	1	64	82	13.2167
..(((........)))))	chr19:19609228-19609447(+)$1	1	74	92	14.0591
(((((........)))))	chr20:47734781-47735011(-)$1	1	198	216	13.9906
(((((........)))))	chr11:65546329-65546547(-)$1	1	193	211	13.9906
(((((........)))))	chr6:32945168-32945436(+)$1	1	33	51	13.7853
(((((........)))))	chr7:133984846-133985077(-)$1	1	70	88	13.7853
(((.(........)))))	chr7:43918674-43918909(-)$1	1	90	108	14.4668
(.(((........)))..	chr8:94935651-94935873(+)$1	1	84	102	14.1948
(((((........)))))	chr6:4937705-4937941(+)$1	1	30	48	13.9906
(((((........)))))	chr19:56206065-56206286(+)$1	1	186	204	13.9906
((.((........)))))	chrX:10534979-10535198(-)$1	1	169	187	13.2068
(.(((........))).)	chr6:117888008-117888228(-)$1	1	172	190	14.2901
(((((........)))))	chr15:91420290-91420509(+)$1	1	161	179	13.7853
(((.(........).)))	chr2:73677681-73677907(+)$1	1	180	198	14.2643
(((((........)))))	chr10:15256443-15256667(-)$1	1	33	51	13.9906
(..((........))...	chr17:65959373-65959590(+)$1	1	184	202	13.7340
(((((........)))))	chr1:220358880-220359098(+)$1	1	43	61	13.9061
(((((........)))))	chr17:61912701-61912921(-)$1	1	125	143	13.9906
(((((........)))))	chr14:23548000-23548221(-)$1	1	96	114	13.9906
(((((........)))))	chr17:1556781-1557079(-)$1	1	86	104	13.9906
(((((........)))))	chr1:6292005-6292252(-)$1	1	211	229	13.7853
(((((........)))))	chr10:115674769-115674989(+)$1	1	190	208	13.9061
...((........))...	chr1:55624514-55624724(-)$1	1	17	35	13.7798
(..((........))..)	chr18:2729211-2729427(+)$1	1	128	146	13.5762
(..((........))...	chr22:50187770-50187989(-)$1	1	172	190	14.0079
..(((........)))..	chr17:63010602-63010843(-)$1	1	156	174	13.9004
(((((........)).))	chr16:4910894-4911122(+)$1	1	35	53	13.7342
(((.(........).)))	chr10:7866294-7866508(+)$1	1	47	65	14.2643
.(..(........)..).	chr22:41569631-41569848(+)$1	1	77	95	13.9789
(((((........)))))	chr11:17390358-17390590(+)$1	1	141	159	13.9061
(((.(........).)))	chr10:112724287-112724513(+)$1	1	93	111	14.1993
(((((........)))))	chr6:127611212-127611436(-)$1	1	45	63	13.9906
(((((........)))))	chr14:61180137-61180359(-)$1	1	15	33	13.9906
..(((........)))..	chr5:112178904-112179122(+)$1	1	116	134	14.0645
..(.(........).).)	chr17:1264286-1264516(-)$1	1	160	178	14.5320
..(((........)))..	chr8:25364494-25364719(+)$1	1	193	211	14.4107
(((((........)))).	chr19:39962202-39962429(+)$1	1	186	204	13.0742
..(((........)))..	chr3:78710257-78710475(-)$1	1	108	126	13.2751
(((((........)))))	chr6:76420996-76421213(+)$1	1	133	151	13.9906
((.((........))..)	chrX:53426503-53426750(-)$1	1	83	101	13.4013
(((.(........)))))	chr19:44739899-44740148(+)$1	1	118	136	13.5421
(((((........)))))	chr11:108191970-108192190(+)$1	1	85	103	13.7853
(.(((........))).)	chr2:44559551-44559777(-)$1	1	6	24	14.2901
(.(((........))).)	chr2:20135896-20136113(-)$1	1	41	59	14.0736
(((((........)))))	chr16:19548210-19548432(+)$1	1	203	221	13.9906
(((((........)))))	chr18:57005696-57005920(-)$1	1	84	102	13.9906
((.((........).).)	chr22:38694725-38694994(-)$1	1	181	199	14.2975
(((((........)))).	chrX:39914537-39914865(-)$1	1	178	196	12.9494
(((.(........).)))	chr17:80529606-80529842(+)$1	1	154	172	14.3365
(.(((........))).)	chr8:77768303-77768514(+)$1	1	171	189	13.7462
.((((........)))).	chr19:38135466-38135677(-)$1	1	38	56	13.2845
(..((........))...	chr6:53363455-53363674(-)$1	1	161	179	14.1808
(((.(........).)))	chr20:61525765-61525984(-)$1	1	89	107	14.2643
((.((........)).))	chr9:131515011-131515228(-)$1	1	42	60	13.3124
..(((........)))))	chr8:48830769-48831028(-)$1	1	183	201	13.6365
(((((........)))))	chr14:45581536-45581746(+)$1	1	52	70	13.7853
....(........)...)	chr8:95894950-95895170(-)$1	1	168	186	14.0352
.((((........).)))	chr19:7975772-7975988(+)$1	1	39	57	14.2578
(((((........)))))	chr5:147790199-147790423(+)$1	1	48	66	13.7853
(((((........)))))	chr11:82644057-82644273(+)$1	1	76	94	13.9906

#PSSM
f : 0.22	e : 0.22	c : 0.12	d : 0.09	[ : 0.06	b : 0.06	g : 0.06	! : 0.06	" : 0.04	# : 0.03	= : 0.01	
e : 0.22	f : 0.18	d : 0.13	! : 0.12	c : 0.07	[ : 0.07	g : 0.06	" : 0.04	# : 0.03	b : 0.01	= : 0.01	a : 0.01	
e : 0.22	c : 0.19	f : 0.18	d : 0.09	! : 0.09	[ : 0.09	g : 0.06	= : 0.01	" : 0.01	a : 0.01	# : 0.01	
e : 0.21	c : 0.18	b : 0.16	f : 0.13	[ : 0.12	d : 0.07	g : 0.04	! : 0.03	a : 0.01	# : 0.01	
e : 0.21	a : 0.19	b : 0.16	c : 0.16	f : 0.13	d : 0.07	g : 0.04	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.21	a : 0.19	b : 0.16	c : 0.16	f : 0.13	d : 0.07	g : 0.04	
e : 0.21	b : 0.16	c : 0.16	f : 0.13	] : 0.12	d : 0.09	g : 0.04	2 : 0.03	= : 0.01	3 : 0.01	
e : 0.21	c : 0.19	f : 0.18	d : 0.10	2 : 0.06	g : 0.06	] : 0.04	4 : 0.04	a : 0.03	3 : 0.03	b : 0.01	= : 0.01	
e : 0.22	f : 0.19	d : 0.13	] : 0.09	4 : 0.06	g : 0.06	2 : 0.06	c : 0.04	3 : 0.04	b : 0.03	= : 0.01	a : 0.01	6 : 0.01	
e : 0.22	f : 0.19	c : 0.12	] : 0.09	d : 0.07	4 : 0.06	g : 0.06	2 : 0.04	= : 0.03	3 : 0.03	b : 0.03	6 : 0.01	h : 0.01	

#score	914.4635924141468
#seq	66
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_UTR_m2_run1.txt

#BEAR
e[a[cccwwwwwwwwwwwwwwccc	chr12:54653134-54653374(-)$1	240	74	98	22.8033
:ffffffuuuuuuuuuuuufffff	chr17:6524125-6524365(-)$1	240	213	237	21.8854
gg[dddduuuuuuuuuuuudddd6	chr15:83686057-83686377(-)$1	320	27	51	22.9947
g[a[cccwwwwwwwwwwwwwwccc	chr12:118852103-118852348(+)$1	245	186	210	22.8815
cc!!ccctttttttttttccc22c	chr12:76462601-76462842(-)$1	241	130	154	21.3800
###dddduuuuuuuuuuuudddd3	chr17:47127479-47127808(+)$1	329	112	136	23.2911
gggggggvvvvvvvvvvvvvgggg	chr2:242291918-242292238(+)$1	320	16	40	23.1021
[ffffffuuuuuuuuuuuufffff	chr16:46998507-46998787(-)$1	280	190	214	22.9346
iiiiiiiwwwwwwwwwwwwwwiii	chr5:157213659-157213899(-)$1	240	96	120	22.5682
iii!!bbyyyyyyyyyyyyyyyyb	chr17:60022422-60022662(-)$1	240	149	173	20.0204
iiiiiiiitttttttttttiiiii	chr19:37128822-37129062(-)$1	240	128	152	21.3113
ffffffvvvvvvvvvvvvvfffff	chr2:30866450-30866690(+)$1	240	142	166	22.2712
cc[cccwwwwwwwwwwwwwwccc]	chr16:22297211-22297451(+)$1	240	163	187	23.0896
"""dddduuuuuuuuuuuudddd2	chr1:179870337-179870588(+)$1	251	186	210	23.1621
iiiiiiiuuuuuuuuuuuuiiiii	chr16:89711750-89712011(-)$1	261	20	44	23.5204
ggggggguuuuuuuuuuuuggggg	chr10:120792983-120793230(+)$1	247	128	152	23.5124
=======uuuuuuuuuuuu=====	chr22:42479092-42479332(+)$1	240	18	42	23.9282
!eeeeevvvvvvvvvvvvveeeee	chr7:139060742-139060982(+)$1	240	37	61	23.1612
ddd[cccwwwwwwwwwwwwwwccc	chr17:80684601-80684841(+)$1	240	58	82	22.5171
========ttttttttttt=====	chr8:18385221-18385461(-)$1	240	192	216	21.9120
dddddddwwwwwwwwwwwwwwddd	chr6:151790205-151790445(+)$1	240	53	77	21.8883
[ffffffuuuuuuuuuuuufffff	chr13:103493337-103493577(+)$1	240	146	170	22.9346
gg[bbwwwwwwwwwwwwwwbb]gg	chr10:855511-855759(-)$1	248	168	192	21.7332
fff[cccuuuuuuuuuuuucccff	chr11:63721925-63722165(+)$1	240	12	36	23.7033
gggggyyyyyyyyyyyyyyyyggg	chr1:146629278-146629518(-)$1	240	207	231	21.8362
!ffffffuuuuuuuuuuuufffff	chr1:36389637-36389877(+)$1	240	36	60	22.9715
ggggggxxxxxxxxxxxxxxxggg	chr1:184356140-184356387(+)$1	247	1	25	19.4417
""cccxxxxxxxxxxxxxxxccc3	chr11:47638902-47639182(-)$1	280	217	241	19.3836
gggggg[attttttttttta]ggg	chr1:28527145-28527390(-)$1	245	73	97	22.3985
eeeeewwwwwwwwwwwwwweeeee	chr10:11373597-11373837(+)$1	240	38	62	22.3588
ee[bbwwwwwwwwwwwwwwbb]ee	chr16:732535-732815(+)$1	280	45	69	21.5781
==!!cccwwwwwwwwwwwwwwccc	chr11:19245627-19245867(-)$1	240	39	63	23.0299
dddd[bbuuuuuuuuuuuubb333	chr19:42734572-42734890(-)$1	318	183	207	22.5588
'ffffffuuuuuuuuuuuufffff	chr3:57546667-57546917(+)$1	250	132	156	22.2449
!!cccyyyyyyyyyyyyyyyyccc	chr2:203633211-203633451(+)$1	240	194	218	21.8892
:eeeeevvvvvvvvvvvvveeeee	chr18:45362603-45362843(-)$1	240	42	66	22.0751
eeee[ccctttttttttttcccee	chr2:74383559-74383866(-)$1	307	270	294	22.0950
::ddddwwwwwwwwwwwwwwdddd	chr3:136060212-136060452(-)$1	240	4	28	20.3340
ddddcccwwwwwwwwwwwwwwccc	chr1:151670111-151670351(+)$1	240	132	156	22.3988
eeee[bbuuuuuuuuuuuubb]ee	chr20:61920978-61921219(+)$1	241	115	139	22.9249
e"""ddddtttttttttttdddd4	chr17:691178-691418(+)$1	240	4	28	21.2435
cc[dddduuuuuuuuuuuudddd]	chr17:74731227-74731467(-)$1	240	85	109	23.4445
ggg"""bbtttttttttttbbggg	chr2:233433659-233433939(+)$1	280	63	87	21.1455
ddeeeeeuuuuuuuuuuuueeeee	chr2:160623975-160624216(+)$1	241	60	84	23.2985
dddddyyyyyyyyyyyyyyyyddd	chr3:160095128-160095368(-)$1	240	69	93	21.1148
eeeeewwwwwwwwwwwwwweeeee	chr16:79630990-79631231(-)$1	241	24	48	22.3588
fff[cccwwwwwwwwwwwwwwccc	chr17:61498379-61498619(+)$1	240	200	224	22.6372
eeeeewwwwwwwwwwwwwweeeee	chr17:36924102-36924351(-)$1	249	210	234	22.3588
ddd[cccvvvvvvvvvvvvvccc]	chr5:173383277-173383532(+)$1	255	214	238	23.2213
!!eeeeettttttttttteeeee]	chr14:104171541-104171781(-)$1	240	114	138	21.6709
e!!ddddvvvvvvvvvvvvvdddd	chr6:36199288-36199528(+)$1	240	131	155	22.8893
cc[ddddtttttttttttdddd]c	chr6:32945445-32945733(+)$1	288	85	109	21.1505
!!cccxxxxxxxxxxxxxxxccc2	chr17:66526319-66526576(+)$1	257	67	91	19.3164
ffeeeeeuuuuuuuuuuuueeeee	chr5:89813128-89813370(-)$1	242	184	208	23.3625
!eeeeevvvvvvvvvvvvveeeee	chr22:22274272-22274560(-)$1	288	33	57	23.1612
!cccyyyyyyyyyyyyyyyycccd	chr12:12629189-12629469(-)$1	280	199	223	21.2684
ccceeeeettttttttttteeeee	chr3:93722561-93722801(+)$1	240	138	162	21.4849
ddddddduuuuuuuuuuuudddd]	chr3:98516933-98517173(-)$1	240	160	184	23.0300
ff[ddddvvvvvvvvvvvvvdddd	chr12:122270052-122270292(+)$1	240	48	72	22.7482
ffffffvvvvvvvvvvvvvfffff	chr16:47116072-47116312(-)$1	240	153	177	22.2712
:eeeeevvvvvvvvvvvvveeeee	chr5:114950379-114950747(-)$1	368	308	332	22.0751

#otherMatches

#Seq PSSM
GCGAUCCGGUAGGUAAAGGAGGGA	chr12:54653134-54653374(-)$1	240	74	98	22.8033
CACAGGAAACAAGUCGACCUUCUG	chr17:6524125-6524365(-)$1	240	213	237	21.8854
AUUUCAGAAAAUUAAGAAGCUGAC	chr15:83686057-83686377(-)$1	320	27	51	22.9947
UGUUUUGUUUCGUUUUCUCCUUAA	chr12:118852103-118852348(+)$1	245	186	210	22.8815
CUGGUGAAGAAACAAAACUCAAAG	chr12:76462601-76462842(-)$1	241	130	154	21.3800
UCCCGUGUAGGUUUCACAUUAUGU	chr17:47127479-47127808(+)$1	329	112	136	23.2911
UCUGUUAACCAAAUAAAACAUAAU	chr2:242291918-242292238(+)$1	320	16	40	23.1021
ACUGGGGAAGCAGACCAGGCCCCA	chr16:46998507-46998787(-)$1	280	190	214	22.9346
AGaaaaauauuuauuuuauuuuuu	chr5:157213659-157213899(-)$1	240	96	120	22.5682
AGAACCAUUUUUUAAACUUCCCUU	chr17:60022422-60022662(-)$1	240	149	173	20.0204
UCUAUUGUGCAGAUUCCCAACAGU	chr19:37128822-37129062(-)$1	240	128	152	21.3113
UACAUUUCUUUAUACAAAUAAUGU	chr2:30866450-30866690(+)$1	240	142	166	22.2712
caguguguacccuuaaaugaacaa	chr16:22297211-22297451(+)$1	240	163	187	23.0896
GUAAUAUUGCUUUAUAUACAUAUG	chr1:179870337-179870588(+)$1	251	186	210	23.1621
UGCCACCCAACGCUGUCCUGGUGG	chr16:89711750-89712011(-)$1	261	20	44	23.5204
CUUUGUAUUUUAAUUUUCCUACAA	chr10:120792983-120793230(+)$1	247	128	152	23.5124
CCUUUCUUACAGGAAUUACAGAAA	chr22:42479092-42479332(+)$1	240	18	42	23.9282
GAAUGUUAUUAACUCUUCUAUAUU	chr7:139060742-139060982(+)$1	240	37	61	23.1612
UCAUGCACGCGUUGAUCAAUUUGC	chr17:80684601-80684841(+)$1	240	58	82	22.5171
AUGCCGUCUUCUAGAAAACGAUGG	chr8:18385221-18385461(-)$1	240	192	216	21.9120
CUCUCAGUUGCAUAGAAAGAUCUG	chr6:151790205-151790445(+)$1	240	53	77	21.8883
UGUUGGUUUUUCUUCUGCUGCCAA	chr13:103493337-103493577(+)$1	240	146	170	22.9346
UACAUGUAAACUAUUGGUAAUUUA	chr10:855511-855759(-)$1	248	168	192	21.7332
GCUGCUGCCACUGAACUCUCAGAG	chr11:63721925-63722165(+)$1	240	12	36	23.7033
AUCCUAUUAUAACCAACUCUCAGG	chr1:146629278-146629518(-)$1	240	207	231	21.8362
AUGGGGAAAUGUCUCUGGAUCCCC	chr1:36389637-36389877(+)$1	240	36	60	22.9715
AGGAGCUCCCCUCCCUCGCUCGCU	chr1:184356140-184356387(+)$1	247	1	25	19.4417
uucaauauuacuaucugcauuugu	chr11:47638902-47639182(-)$1	280	217	241	19.3836
CUGGGUGUGCUCCCUUCGAAGGCC	chr1:28527145-28527390(-)$1	245	73	97	22.3985
GAAAUUGUUAUUGUUUGUUAUUUC	chr10:11373597-11373837(+)$1	240	38	62	22.3588
ACCGCUUCCCCCAAGUUCUGCUGU	chr16:732535-732815(+)$1	280	45	69	21.5781
UUCCCUUAAACAUUUUGCACAAAG	chr11:19245627-19245867(-)$1	240	39	63	23.0299
GAGGACCUCCUACCCCCUUGGCCC	chr19:42734572-42734890(-)$1	318	183	207	22.5588
AGGAUGCAAGCACAAUUUAGUAUU	chr3:57546667-57546917(+)$1	250	132	156	22.2449
GUUGGUUUCUAAAGUUACACUCCA	chr2:203633211-203633451(+)$1	240	194	218	21.8892
AUACCAUUUUUUGGCAACUUGGUA	chr18:45362603-45362843(-)$1	240	42	66	22.0751
CAGGAUAAAAAGAUACCCAUUGCC	chr2:74383559-74383866(-)$1	307	270	294	22.0950
AUUAGCUAAAUUCAUCAUCUGCUG	chr3:136060212-136060452(-)$1	240	4	28	20.3340
CCCAGACUUCUUUUGCAAUUUGUC	chr1:151670111-151670351(+)$1	240	132	156	22.3988
GGAAGGCGCGGACCUGACAGCAUU	chr20:61920978-61921219(+)$1	241	115	139	22.9249
ACCACCUGUUUUGUUUCCUCAGGG	chr17:691178-691418(+)$1	240	4	28	21.2435
UUGGGCCUUUUAAAAACAUGGCUG	chr17:74731227-74731467(-)$1	240	85	109	23.4445
CAUGACCCUCUCCCUCUCUGGAUG	chr2:233433659-233433939(+)$1	280	63	87	21.1455
UCUGCUGGACUUUUUAACAUAGCA	chr2:160623975-160624216(+)$1	241	60	84	23.2985
AGAGUGGAAAAAAGUGUAGAAGCU	chr3:160095128-160095368(-)$1	240	69	93	21.1148
UAUAAUUUAAUUCUAGUUUUUAUA	chr16:79630990-79631231(-)$1	241	24	48	22.3588
AUGUGUCGCAUUUAAUCAGAAGAC	chr17:61498379-61498619(+)$1	240	200	224	22.6372
GGUCUGAACAACUGCCGCAAGACC	chr17:36924102-36924351(-)$1	249	210	234	22.3588
auuguuaauaauauaacauauaag	chr5:173383277-173383532(+)$1	255	214	238	23.2213
CCGGUUCCACCUGCUUCCGAGCCU	chr14:104171541-104171781(-)$1	240	114	138	21.6709
CCUGCCACCAAACAUCUUCCUGGC	chr6:36199288-36199528(+)$1	240	131	155	22.8893
UAGGAUGUAUUUGAGUUCCGUUAU	chr6:32945445-32945733(+)$1	288	85	109	21.1505
UUAGCCUGUUACCCAUCUUUGCUU	chr17:66526319-66526576(+)$1	257	67	91	19.3164
GGCAUUAUUUCCUAAUUGUUGAUG	chr5:89813128-89813370(-)$1	242	184	208	23.3625
AUUAGUGUCUAUUCUUAAAAUUAA	chr22:22274272-22274560(-)$1	288	33	57	23.1612
UUCACAAACCCACGCUCACCUGAC	chr12:12629189-12629469(-)$1	280	199	223	21.2684
GCUAUGUCAGAAAUGCUAAGACAU	chr3:93722561-93722801(+)$1	240	138	162	21.4849
AUAUGUCACCUAGGGAACAGACAU	chr3:98516933-98517173(-)$1	240	160	184	23.0300
GGAAGGGACCCUUGCCUCACCCCU	chr12:122270052-122270292(+)$1	240	48	72	22.7482
CCAGUUAAAAUUCCUUAGAAAUUG	chr16:47116072-47116312(-)$1	240	153	177	22.2712
AAUGCAUAUAUAUACUUCUUGCAU	chr5:114950379-114950747(-)$1	368	308	332	22.0751

#DB
(.(.(((..............)))	chr12:54653134-54653374(-)$1	1	74	98	22.8033
.((((((............)))))	chr17:6524125-6524365(-)$1	1	213	237	21.8854
((.((((............)))).	chr15:83686057-83686377(-)$1	1	27	51	22.9947
(.(.(((..............)))	chr12:118852103-118852348(+)$1	1	186	210	22.8815
((..(((...........)))..)	chr12:76462601-76462842(-)$1	1	130	154	21.3800
...((((............)))).	chr17:47127479-47127808(+)$1	1	112	136	23.2911
(((((((.............))))	chr2:242291918-242292238(+)$1	1	16	40	23.1021
.((((((............)))))	chr16:46998507-46998787(-)$1	1	190	214	22.9346
(((((((..............)))	chr5:157213659-157213899(-)$1	1	96	120	22.5682
(((..((................)	chr17:60022422-60022662(-)$1	1	149	173	20.0204
((((((((...........)))))	chr19:37128822-37129062(-)$1	1	128	152	21.3113
((((((.............)))))	chr2:30866450-30866690(+)$1	1	142	166	22.2712
((.(((..............))).	chr16:22297211-22297451(+)$1	1	163	187	23.0896
...((((............)))).	chr1:179870337-179870588(+)$1	1	186	210	23.1621
(((((((............)))))	chr16:89711750-89712011(-)$1	1	20	44	23.5204
(((((((............)))))	chr10:120792983-120793230(+)$1	1	128	152	23.5124
(((((((............)))))	chr22:42479092-42479332(+)$1	1	18	42	23.9282
.(((((.............)))))	chr7:139060742-139060982(+)$1	1	37	61	23.1612
(((.(((..............)))	chr17:80684601-80684841(+)$1	1	58	82	22.5171
((((((((...........)))))	chr8:18385221-18385461(-)$1	1	192	216	21.9120
(((((((..............)))	chr6:151790205-151790445(+)$1	1	53	77	21.8883
.((((((............)))))	chr13:103493337-103493577(+)$1	1	146	170	22.9346
((.((..............)).))	chr10:855511-855759(-)$1	1	168	192	21.7332
(((.(((............)))))	chr11:63721925-63722165(+)$1	1	12	36	23.7033
(((((................)))	chr1:146629278-146629518(-)$1	1	207	231	21.8362
.((((((............)))))	chr1:36389637-36389877(+)$1	1	36	60	22.9715
((((((...............)))	chr1:184356140-184356387(+)$1	1	1	25	19.4417
..(((...............))).	chr11:47638902-47639182(-)$1	1	217	241	19.3836
((((((.(...........).)))	chr1:28527145-28527390(-)$1	1	73	97	22.3985
(((((..............)))))	chr10:11373597-11373837(+)$1	1	38	62	22.3588
((.((..............)).))	chr16:732535-732815(+)$1	1	45	69	21.5781
((..(((..............)))	chr11:19245627-19245867(-)$1	1	39	63	23.0299
((((.((............))...	chr19:42734572-42734890(-)$1	1	183	207	22.5588
.((((((............)))))	chr3:57546667-57546917(+)$1	1	132	156	22.2449
..(((................)))	chr2:203633211-203633451(+)$1	1	194	218	21.8892
.(((((.............)))))	chr18:45362603-45362843(-)$1	1	42	66	22.0751
((((.(((...........)))))	chr2:74383559-74383866(-)$1	1	270	294	22.0950
..((((..............))))	chr3:136060212-136060452(-)$1	1	4	28	20.3340
(((((((..............)))	chr1:151670111-151670351(+)$1	1	132	156	22.3988
((((.((............)).))	chr20:61920978-61921219(+)$1	1	115	139	22.9249
(...((((...........)))).	chr17:691178-691418(+)$1	1	4	28	21.2435
((.((((............)))).	chr17:74731227-74731467(-)$1	1	85	109	23.4445
(((...((...........)))))	chr2:233433659-233433939(+)$1	1	63	87	21.1455
))(((((............)))))	chr2:160623975-160624216(+)$1	1	60	84	23.2985
)((((................)))	chr3:160095128-160095368(-)$1	1	69	93	21.1148
(((((..............)))))	chr16:79630990-79631231(-)$1	1	24	48	22.3588
(((.(((..............)))	chr17:61498379-61498619(+)$1	1	200	224	22.6372
(((((..............)))))	chr17:36924102-36924351(-)$1	1	210	234	22.3588
(((.(((.............))).	chr5:173383277-173383532(+)$1	1	214	238	23.2213
..(((((...........))))).	chr14:104171541-104171781(-)$1	1	114	138	21.6709
(..((((.............))))	chr6:36199288-36199528(+)$1	1	131	155	22.8893
((.((((...........)))).)	chr6:32945445-32945733(+)$1	1	85	109	21.1505
..(((...............))).	chr17:66526319-66526576(+)$1	1	67	91	19.3164
(((((((............)))))	chr5:89813128-89813370(-)$1	1	184	208	23.3625
.(((((.............)))))	chr22:22274272-22274560(-)$1	1	33	57	23.1612
.(((................))))	chr12:12629189-12629469(-)$1	1	199	223	21.2684
)))(((((...........)))))	chr3:93722561-93722801(+)$1	1	138	162	21.4849
(((((((............)))).	chr3:98516933-98517173(-)$1	1	160	184	23.0300
((.((((.............))))	chr12:122270052-122270292(+)$1	1	48	72	22.7482
((((((.............)))))	chr16:47116072-47116312(-)$1	1	153	177	22.2712
.(((((.............)))))	chr5:114950379-114950747(-)$1	1	308	332	22.0751

#PSSM
e : 0.14	g : 0.14	d : 0.13	! : 0.11	f : 0.09	c : 0.08	: : 0.06	i : 0.06	= : 0.04	[ : 0.03	" : 0.03	# : 0.01	' : 0.01	
f : 0.18	e : 0.16	g : 0.13	d : 0.13	c : 0.09	i : 0.06	! : 0.06	" : 0.04	= : 0.04	[ : 0.03	# : 0.01	: : 0.01	
e : 0.19	f : 0.14	d : 0.13	[ : 0.11	g : 0.09	c : 0.08	i : 0.06	! : 0.04	a : 0.03	" : 0.03	= : 0.03	# : 0.01	
d : 0.21	e : 0.21	f : 0.11	[ : 0.09	g : 0.08	c : 0.08	! : 0.04	i : 0.04	= : 0.03	b : 0.03	" : 0.03	
c : 0.21	d : 0.19	e : 0.18	f : 0.11	g : 0.08	i : 0.04	[ : 0.04	= : 0.03	b : 0.03	! : 0.01	" : 0.01	y : 0.01	
c : 0.18	d : 0.18	e : 0.13	f : 0.11	w : 0.08	g : 0.06	y : 0.06	i : 0.04	b : 0.04	= : 0.03	x : 0.03	" : 0.01	
c : 0.16	d : 0.16	w : 0.11	v : 0.09	f : 0.08	b : 0.06	y : 0.06	e : 0.06	i : 0.04	x : 0.04	g : 0.03	= : 0.03	[ : 0.01	
u : 0.29	w : 0.24	v : 0.16	y : 0.08	t : 0.04	x : 0.04	i : 0.01	= : 0.01	a : 0.01	c : 0.01	d : 0.01	b : 0.01	e : 0.01	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	t : 0.16	v : 0.16	y : 0.08	x : 0.04	
u : 0.29	w : 0.24	v : 0.16	t : 0.11	y : 0.08	x : 0.04	c : 0.01	e : 0.01	d : 0.01	
e : 0.18	w : 0.16	f : 0.11	d : 0.11	y : 0.08	b : 0.08	v : 0.06	c : 0.04	x : 0.04	i : 0.03	= : 0.03	g : 0.01	a : 0.01	
e : 0.18	d : 0.16	w : 0.13	c : 0.13	f : 0.11	b : 0.08	y : 0.06	g : 0.03	i : 0.03	= : 0.03	x : 0.01	] : 0.01	
c : 0.22	d : 0.19	e : 0.18	f : 0.11	g : 0.09	i : 0.04	] : 0.04	= : 0.03	2 : 0.01	y : 0.01	3 : 0.01	
e : 0.22	c : 0.19	d : 0.18	f : 0.13	g : 0.11	i : 0.04	= : 0.03	2 : 0.01	y : 0.01	3 : 0.01	] : 0.01	
e : 0.21	c : 0.14	f : 0.13	g : 0.11	d : 0.09	] : 0.08	3 : 0.04	i : 0.04	2 : 0.03	= : 0.03	6 : 0.01	b : 0.01	4 : 0.01	

#score	1357.2797987182194
#seq	61
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_CDS_m3_run2.txt

#BEAR
[ddddqqqqqqqqddddh	chr1:197057397-197057616(-)$1	219	194	212	14.1338
eeeeeqqqqqqqqeeeee	chr3:180680750-180680978(+)$1	228	108	126	14.7794
cccccqqqqqqqqccc]c	chr11:58893014-58893231(+)$1	217	115	133	14.2686
$ddddqqqqqqqqdddd5	chr17:2228531-2228749(-)$1	218	124	142	13.5507
''cccqqqqqqqqccc22	chr1:16254555-16254779(+)$1	224	158	176	13.5296
eeeeeqqqqqqqqeeeee	chr17:7404828-7405045(+)$1	217	138	156	14.7794
eeeeeqqqqqqqqeeeee	chr13:108862986-108863206(-)$1	220	107	125	14.7794
gggggqqqqqqqqggggg	chr2:201438393-201438613(+)$1	220	74	92	13.8422
fffffqqqqqqqqfffff	chr10:119042972-119043189(-)$1	217	94	112	13.2430
fffffqqqqqqqqfffff	chr3:4703782-4703999(+)$1	217	146	164	13.2430
gggggqqqqqqqqggggg	chr8:38194725-38194946(-)$1	221	79	97	13.8422
h[cccqqqqqqqqccc]h	chr13:25901046-25901272(+)$1	226	187	205	14.1312
b[cccqqqqqqqqccc>>	chr4:187541448-187541665(-)$1	217	160	178	13.9395
eeeeeqqqqqqqqeeeee	chr2:46986983-46987202(+)$1	219	49	67	14.7794
c[cccqqqqqqqqccc]c	chr10:34690658-34690876(-)$1	218	164	182	14.4529
cccccqqqqqqqqccc22	chr12:98927120-98927333(+)$1	213	155	173	14.3752
fffffqqqqqqqqfffff	chr1:214815809-214816027(+)$1	218	157	175	13.2430
cddddqqqqqqqqdddd]	chr1:227842512-227842735(+)$1	223	14	32	14.2321
""cccqqqqqqqqccc33	chr17:76219647-76219865(+)$1	218	122	140	15.0413
fffffqqqqqqqqfffff	chr13:23905551-23905768(-)$1	217	171	189	13.2430
eeeeeqqqqqqqqeeeee	chr6:31848438-31848655(-)$1	217	146	164	14.7794
$$cccqqqqqqqqccc44	chr21:30338975-30339201(-)$1	226	96	114	14.4406
!ddddqqqqqqqqdddd4	chr6:64421800-64422022(+)$1	222	182	200	14.5735
""cccqqqqqqqqccc33	chr2:44428665-44428884(+)$1	219	11	29	15.0413
eeeeeqqqqqqqqeeeee	chr1:193038444-193038675(+)$1	231	42	60	14.7794
eeeeeqqqqqqqqeeeee	chr21:34926955-34927174(+)$1	219	26	44	14.7794
eeeeeqqqqqqqqeeeee	chr16:2814923-2815154(+)$1	231	170	188	14.7794
!!cccqqqqqqqqcccdd	chr19:52519413-52519631(-)$1	218	128	146	14.6588
[ddddqqqqqqqqdddd2	chr6:30521091-30521316(-)$1	225	71	89	14.5218
!!cccqqqqqqqqccc22	chr13:46563088-46563310(-)$1	222	172	190	14.9137
eeeeaqqqqqqqqa]eee	chr1:111999186-111999405(+)$1	219	73	91	14.2367
&&cccqqqqqqqqccc44	chr21:30331849-30332068(-)$1	219	106	124	13.5808
$ddddqqqqqqqqdddd3	chr5:137735506-137735730(+)$1	224	34	52	14.4429
eeeeeqqqqqqqqeeeee	chr11:3741912-3742133(-)$1	221	152	170	14.7794
!!cccqqqqqqqqccc22	chr1:222801447-222801665(+)$1	218	107	125	14.9137
#ddddqqqqqqqqdddd3	chr10:94413442-94413661(+)$1	219	72	90	14.6161
eeeeeqqqqqqqqeeeee	chr13:42877219-42877438(+)$1	219	52	70	14.7794
eeeeeqqqqqqqqeeeee	chr10:27458891-27459112(+)$1	221	2	20	14.7794
!ddddqqqqqqqqdddd2	chr8:48749787-48750009(-)$1	222	106	124	14.5670
fffffqqqqqqqqfffff	chr11:9597458-9597678(+)$1	220	11	29	13.2430
[ddddqqqqqqqqdddd]	chr3:180685756-180685973(+)$1	217	39	57	14.5132
eeeeeqqqqqqqqeeeee	chr19:57765083-57765300(+)$1	217	153	171	14.7794
"ddddqqqqqqqqdddd4	chr12:98927329-98927552(+)$1	223	37	55	14.5066
gggggqqqqqqqqggggg	chr19:44418937-44419160(-)$1	223	3	21	13.8422
!ddddqqqqqqqqdddd2	chr12:27066836-27067055(-)$1	219	178	196	14.5670
eeeeeqqqqqqqqeeeee	chr9:135204451-135204668(-)$1	217	142	160	14.7794
[ddddqqqqqqqqdddd]	chr7:64863480-64863702(+)$1	222	125	143	14.5132
eeeeeqqqqqqqqeeeee	chr19:44680522-44680747(+)$1	225	170	188	14.7794
eeeeeqqqqqqqqeeeee	chr1:114308872-114309090(-)$1	218	164	182	14.7794
eeeeeqqqqqqqqeeeee	chr16:71483266-71483489(-)$1	223	158	176	14.7794
!a!!aqqqqqqqqa22a2	chr12:110783785-110783999(+)$1	214	22	40	13.1332
c[cccqqqqqqqqccccc	chr5:71493868-71494088(+)$1	220	180	198	14.2998
!!cccqqqqqqqqccc22	chr12:99020192-99020411(-)$1	219	106	124	14.9137
fffffqqqqqqqqfffff	chr11:10825617-10825839(-)$1	222	113	131	13.2430
!!cccqqqqqqqqcccdd	chr2:44550400-44550616(-)$1	216	21	39	14.6588
$$cccqqqqqqqqccc22	chr6:87968398-87968617(+)$1	219	161	179	14.3483
[ddddqqqqqqqqddddc	chr19:32845272-32845490(+)$1	218	17	35	14.3047
##cccqqqqqqqqccc33	chr1:220151788-220152011(-)$1	223	166	184	14.9947
bbcccqqqqqqqqccc]b	chr5:32387581-32387799(-)$1	218	156	174	13.4495
gggggqqqqqqqqggggg	chr1:220195607-220195827(-)$1	220	144	162	13.8422
eeeeeqqqqqqqqeeeee	chr22:32112107-32112326(-)$1	219	119	137	14.7794
fffffqqqqqqqqfffff	chr2:230670455-230670672(-)$1	217	25	43	13.2430
e[cccqqqqqqqqccc]e	chr10:115609587-115609811(-)$1	224	161	179	14.7058
gddddqqqqqqqqdddd:	chr3:57545398-57545618(+)$1	220	116	134	13.2572
eeeeeqqqqqqqqeeeee	chr5:177632796-177633013(+)$1	217	169	187	14.7794
""cccqqqqqqqqccc33	chr1:207966801-207967017(+)$1	216	26	44	15.0413
eeeeeqqqqqqqqeeeee	chr9:37357026-37357242(+)$1	216	60	78	14.7794
eeeeeqqqqqqqqeeeee	chr10:14939070-14939287(+)$1	217	140	158	14.7794

#otherMatches

#Seq PSSM
GUUGGCUAUUUUACUGAA	chr1:197057397-197057616(-)$1	219	194	212	14.1338
UAAUUACACCUCCGGUUA	chr3:180680750-180680978(+)$1	228	108	126	14.7794
AGAGUUCUGCCCUACUCC	chr11:58893014-58893231(+)$1	217	115	133	14.2686
GUGCUGCUUUUCAAGCAA	chr17:2228531-2228749(-)$1	218	124	142	13.5507
AAUGGGAAACUUACCAAG	chr1:16254555-16254779(+)$1	224	158	176	13.5296
UCAGAAAUCCCUGUCUGA	chr17:7404828-7405045(+)$1	217	138	156	14.7794
AACUUAUAACUCAGAGUU	chr13:108862986-108863206(-)$1	220	107	125	14.7794
AAAGGCAUUUAGAUCUUU	chr2:201438393-201438613(+)$1	220	74	92	13.8422
AGUUGGAACACAAUAAUU	chr10:119042972-119043189(-)$1	217	94	112	13.2430
GAGCACUCCCGCAUGCUC	chr3:4703782-4703999(+)$1	217	146	164	13.2430
CAAGUGAUCCCCAGCUUG	chr8:38194725-38194946(-)$1	221	79	97	13.8422
UAUAAUAGGUAUUUUGGA	chr13:25901046-25901272(+)$1	226	187	205	14.1312
CCGGUGUUUGUCAACCUU	chr4:187541448-187541665(-)$1	217	160	178	13.9395
UUUUAGAACAUUAUAAAG	chr2:46986983-46987202(+)$1	219	49	67	14.7794
UAGCAUCAUUAAUUGCAG	chr10:34690658-34690876(-)$1	218	164	182	14.4529
AGUCUAAGUUUCAAGAAA	chr12:98927120-98927333(+)$1	213	155	173	14.3752
GCUCUAAAAUGUCAGAGC	chr1:214815809-214816027(+)$1	218	157	175	13.2430
GUGGUCACAACUAACUAG	chr1:227842512-227842735(+)$1	223	14	32	14.2321
UUCAACUGUGCUCUUGUU	chr17:76219647-76219865(+)$1	218	122	140	15.0413
GGAGUGAAAUAUGACUCU	chr13:23905551-23905768(-)$1	217	171	189	13.2430
GCGAUUUCCACGCAUCGC	chr6:31848438-31848655(-)$1	217	146	164	14.7794
ACUGAACCUUCUCUCACU	chr21:30338975-30339201(-)$1	226	96	114	14.4406
AUGAGCAGACCAACUCAA	chr6:64421800-64422022(+)$1	222	182	200	14.5735
UGAUGAAUACAUGCGUAA	chr2:44428665-44428884(+)$1	219	11	29	15.0413
GUGCUCCGACAUAAGCAC	chr1:193038444-193038675(+)$1	231	42	60	14.7794
GAAGAAAAGAGACUCUUC	chr21:34926955-34927174(+)$1	219	26	44	14.7794
CAGUUGAUCAGAAAACUG	chr16:2814923-2815154(+)$1	231	170	188	14.7794
ACAGGAGAAAAACCCUAU	chr19:52519413-52519631(-)$1	218	128	146	14.6588
CCCGCCAGCUCUUGUGGU	chr6:30521091-30521316(-)$1	225	71	89	14.5218
CCUUCUCCUCGUCGAAAA	chr13:46563088-46563310(-)$1	222	172	190	14.9137
UGCCCAACUAGAAGAGGC	chr1:111999186-111999405(+)$1	219	73	91	14.2367
UAUUCAAAACAAAGAAAU	chr21:30331849-30332068(-)$1	219	106	124	13.5808
UCCACCAGAGAAAGUGGC	chr5:137735506-137735730(+)$1	224	34	52	14.4429
GGAGAGUGCAUUGUCUCU	chr11:3741912-3742133(-)$1	221	152	170	14.7794
UACCUUUACAGAUGGGGA	chr1:222801447-222801665(+)$1	218	107	125	14.9137
AAGAGCAGAUUACCUCUG	chr10:94413442-94413661(+)$1	219	72	90	14.6161
AGCAUAACAAAAGAUGCU	chr13:42877219-42877438(+)$1	219	52	70	14.7794
CCAACAAUGAUGAGUUGG	chr10:27458891-27459112(+)$1	221	2	20	14.7794
CCUUAUAUUCUCCUAAGA	chr8:48749787-48750009(-)$1	222	106	124	14.5670
CUCUGUUAAACUCCGGGG	chr11:9597458-9597678(+)$1	220	11	29	13.2430
UUUUAUAGAAAUCUAAGU	chr3:180685756-180685973(+)$1	217	39	57	14.5132
GGUCUUCAAACACAGAUC	chr19:57765083-57765300(+)$1	217	153	171	14.7794
CUUUGUGGCAUUUCAGAA	chr12:98927329-98927552(+)$1	223	37	55	14.5066
GAUUCAGUAAUCAGAGUU	chr19:44418937-44419160(-)$1	223	3	21	13.8422
GAUCACAUUUACUUGAUA	chr12:27066836-27067055(-)$1	219	178	196	14.5670
UUGAGAGUUUCUAUUCAA	chr9:135204451-135204668(-)$1	217	142	160	14.7794
AAUUCAUACUAGAGAGUA	chr7:64863480-64863702(+)$1	222	125	143	14.5132
GGGCUUCAUUUGUAGCUC	chr19:44680522-44680747(+)$1	225	170	188	14.7794
AGCCUGGCAUAUAAGGCU	chr1:114308872-114309090(-)$1	218	164	182	14.7794
GGAGUGUGGCAAAGCUUU	chr16:71483266-71483489(-)$1	223	158	176	14.7794
UGUCCGAAAACCAGUCCU	chr12:110783785-110783999(+)$1	214	22	40	13.1332
GAUUUCUCCCCUAAAACU	chr5:71493868-71494088(+)$1	220	180	198	14.2998
UAUACAUUCUCAAGUAAC	chr12:99020192-99020411(-)$1	219	106	124	14.9137
AAAUUACAAGAUGAAUUU	chr11:10825617-10825839(-)$1	222	113	131	13.2430
ACCAACCUCUUACUUGAA	chr2:44550400-44550616(-)$1	216	21	39	14.6588
CUUCAAUAAAUUCUGAUU	chr6:87968398-87968617(+)$1	219	161	179	14.3483
UGGAGAUAUAAACCUUUU	chr19:32845272-32845490(+)$1	218	17	35	14.3047
UUGAGUUUAGAUUUUCCU	chr1:220151788-220152011(-)$1	223	166	184	14.9947
GGAAAUGUUCAUUUUUAC	chr5:32387581-32387799(-)$1	218	156	174	13.4495
UAUAUCUCCUUCAAUAUG	chr1:220195607-220195827(-)$1	220	144	162	13.8422
GACUGUAACUCCUUAGUC	chr22:32112107-32112326(-)$1	219	119	137	14.7794
UAGAUUUCUCAAUGUUUA	chr2:230670455-230670672(-)$1	217	25	43	13.2430
GUGAUUUUGUGUUGUUUC	chr10:115609587-115609811(-)$1	224	161	179	14.7058
CAAGCUGAAAAGUGCUUG	chr3:57545398-57545618(+)$1	220	116	134	13.2572
AGGGUUUGGGUUUAUCCU	chr5:177632796-177633013(+)$1	217	169	187	14.7794
UUAUCUUUGACAUGAUCU	chr1:207966801-207967017(+)$1	216	26	44	15.0413
GUUUUAAAACCCAGAAGC	chr9:37357026-37357242(+)$1	216	60	78	14.7794
AGCUUAGUCAAUGAAGCU	chr10:14939070-14939287(+)$1	217	140	158	14.7794

#DB
.((((........)))))	chr1:197057397-197057616(-)$1	1	194	212	14.1338
(((((........)))))	chr3:180680750-180680978(+)$1	1	108	126	14.7794
(((((........))).)	chr11:58893014-58893231(+)$1	1	115	133	14.2686
.((((........)))).	chr17:2228531-2228749(-)$1	1	124	142	13.5507
..(((........)))..	chr1:16254555-16254779(+)$1	1	158	176	13.5296
(((((........)))))	chr17:7404828-7405045(+)$1	1	138	156	14.7794
(((((........)))))	chr13:108862986-108863206(-)$1	1	107	125	14.7794
(((((........)))))	chr2:201438393-201438613(+)$1	1	74	92	13.8422
(((((........)))))	chr10:119042972-119043189(-)$1	1	94	112	13.2430
(((((........)))))	chr3:4703782-4703999(+)$1	1	146	164	13.2430
(((((........)))))	chr8:38194725-38194946(-)$1	1	79	97	13.8422
(.(((........))).)	chr13:25901046-25901272(+)$1	1	187	205	14.1312
(.(((........)))..	chr4:187541448-187541665(-)$1	1	160	178	13.9395
(((((........)))))	chr2:46986983-46987202(+)$1	1	49	67	14.7794
(.(((........))).)	chr10:34690658-34690876(-)$1	1	164	182	14.4529
(((((........)))..	chr12:98927120-98927333(+)$1	1	155	173	14.3752
(((((........)))))	chr1:214815809-214816027(+)$1	1	157	175	13.2430
(((((........)))).	chr1:227842512-227842735(+)$1	1	14	32	14.2321
..(((........)))..	chr17:76219647-76219865(+)$1	1	122	140	15.0413
(((((........)))))	chr13:23905551-23905768(-)$1	1	171	189	13.2430
(((((........)))))	chr6:31848438-31848655(-)$1	1	146	164	14.7794
..(((........)))..	chr21:30338975-30339201(-)$1	1	96	114	14.4406
.((((........)))).	chr6:64421800-64422022(+)$1	1	182	200	14.5735
..(((........)))..	chr2:44428665-44428884(+)$1	1	11	29	15.0413
(((((........)))))	chr1:193038444-193038675(+)$1	1	42	60	14.7794
(((((........)))))	chr21:34926955-34927174(+)$1	1	26	44	14.7794
(((((........)))))	chr16:2814923-2815154(+)$1	1	170	188	14.7794
..(((........)))))	chr19:52519413-52519631(-)$1	1	128	146	14.6588
.((((........)))).	chr6:30521091-30521316(-)$1	1	71	89	14.5218
..(((........)))..	chr13:46563088-46563310(-)$1	1	172	190	14.9137
(((((........).)))	chr1:111999186-111999405(+)$1	1	73	91	14.2367
..(((........)))..	chr21:30331849-30332068(-)$1	1	106	124	13.5808
.((((........)))).	chr5:137735506-137735730(+)$1	1	34	52	14.4429
(((((........)))))	chr11:3741912-3742133(-)$1	1	152	170	14.7794
..(((........)))..	chr1:222801447-222801665(+)$1	1	107	125	14.9137
.((((........)))).	chr10:94413442-94413661(+)$1	1	72	90	14.6161
(((((........)))))	chr13:42877219-42877438(+)$1	1	52	70	14.7794
(((((........)))))	chr10:27458891-27459112(+)$1	1	2	20	14.7794
.((((........)))).	chr8:48749787-48750009(-)$1	1	106	124	14.5670
(((((........)))))	chr11:9597458-9597678(+)$1	1	11	29	13.2430
.((((........)))).	chr3:180685756-180685973(+)$1	1	39	57	14.5132
(((((........)))))	chr19:57765083-57765300(+)$1	1	153	171	14.7794
.((((........)))).	chr12:98927329-98927552(+)$1	1	37	55	14.5066
(((((........)))))	chr19:44418937-44419160(-)$1	1	3	21	13.8422
.((((........)))).	chr12:27066836-27067055(-)$1	1	178	196	14.5670
(((((........)))))	chr9:135204451-135204668(-)$1	1	142	160	14.7794
.((((........)))).	chr7:64863480-64863702(+)$1	1	125	143	14.5132
(((((........)))))	chr19:44680522-44680747(+)$1	1	170	188	14.7794
(((((........)))))	chr1:114308872-114309090(-)$1	1	164	182	14.7794
(((((........)))))	chr16:71483266-71483489(-)$1	1	158	176	14.7794
.(..(........)..).	chr12:110783785-110783999(+)$1	1	22	40	13.1332
(.(((........)))))	chr5:71493868-71494088(+)$1	1	180	198	14.2998
..(((........)))..	chr12:99020192-99020411(-)$1	1	106	124	14.9137
(((((........)))))	chr11:10825617-10825839(-)$1	1	113	131	13.2430
..(((........)))))	chr2:44550400-44550616(-)$1	1	21	39	14.6588
..(((........)))..	chr6:87968398-87968617(+)$1	1	161	179	14.3483
.((((........)))))	chr19:32845272-32845490(+)$1	1	17	35	14.3047
..(((........)))..	chr1:220151788-220152011(-)$1	1	166	184	14.9947
(((((........))).)	chr5:32387581-32387799(-)$1	1	156	174	13.4495
(((((........)))))	chr1:220195607-220195827(-)$1	1	144	162	13.8422
(((((........)))))	chr22:32112107-32112326(-)$1	1	119	137	14.7794
(((((........)))))	chr2:230670455-230670672(-)$1	1	25	43	13.2430
(.(((........))).)	chr10:115609587-115609811(-)$1	1	161	179	14.7058
)((((........)))).	chr3:57545398-57545618(+)$1	1	116	134	13.2572
(((((........)))))	chr5:177632796-177633013(+)$1	1	169	187	14.7794
..(((........)))..	chr1:207966801-207967017(+)$1	1	26	44	15.0413
(((((........)))))	chr9:37357026-37357242(+)$1	1	60	78	14.7794
(((((........)))))	chr10:14939070-14939287(+)$1	1	140	158	14.7794

#PSSM
e : 0.32	! : 0.13	f : 0.10	[ : 0.07	c : 0.07	g : 0.07	$ : 0.05	" : 0.05	b : 0.02	# : 0.02	' : 0.01	h : 0.01	& : 0.01	
e : 0.30	d : 0.20	f : 0.10	[ : 0.07	! : 0.07	g : 0.05	" : 0.04	c : 0.02	$ : 0.02	' : 0.01	& : 0.01	a : 0.01	# : 0.01	b : 0.01	
e : 0.30	c : 0.30	d : 0.20	f : 0.10	g : 0.05	! : 0.01	
e : 0.30	c : 0.30	d : 0.20	f : 0.10	g : 0.05	! : 0.01	
c : 0.30	e : 0.29	d : 0.20	f : 0.10	g : 0.05	a : 0.02	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.30	e : 0.29	d : 0.20	f : 0.10	g : 0.05	a : 0.02	
c : 0.30	e : 0.29	d : 0.20	f : 0.10	g : 0.05	] : 0.01	2 : 0.01	
e : 0.30	c : 0.30	d : 0.20	f : 0.10	g : 0.05	2 : 0.01	
e : 0.30	d : 0.23	f : 0.10	2 : 0.08	] : 0.07	g : 0.05	3 : 0.05	4 : 0.02	> : 0.01	a : 0.01	c : 0.01	
e : 0.32	2 : 0.14	f : 0.10	3 : 0.08	c : 0.05	g : 0.05	4 : 0.05	] : 0.04	h : 0.02	d : 0.02	5 : 0.01	> : 0.01	b : 0.01	: : 0.01	

#score	975.0291309370687
#seq	68
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_UTR_m1_run1.txt

#BEAR
!!gggggggvvvvvvvvvvvvvggggggg	chr1:27106504-27106723(+)$1	219	177	206	23.7142
==========uuuuuuuuuuuu=======	chr12:69666156-69666373(+)$1	217	83	112	24.6979
3eeeeeeeeeettttttttttteeeee::	chr18:48701020-48701236(-)$1	216	80	109	21.3913
"ffffffddddwwwwwwwwwwwwwwdddd	chr10:856891-857110(-)$1	219	39	68	21.4326
f####fffffftttttttttttffffff3	chr5:178508904-178509124(+)$1	220	81	110	23.0693
iiiiiiiiiwwwwwwwwwwwwwwiiiiii	chr3:169811001-169811220(-)$1	219	129	158	23.1334
bb!!gggggggtttttttttttggggggg	chr7:138983426-138983652(+)$1	226	48	77	23.3652
eeee[eeeeeuuuuuuuuuuuueeeee]e	chr19:57804453-57804680(+)$1	227	104	133	24.1604
gggggffffffuuuuuuuuuuuuffffff	chrX:103435382-103435601(+)$1	219	110	139	23.5058
eeeee[bbwwwwwwwwwwwwwwbbeeeee	chr10:14945374-14945596(+)$1	222	137	166	21.1716
ffiiiiiiiiitttttttttttiiiiiii	chr5:71502967-71503187(+)$1	220	169	198	23.2925
dd!!ccc[ccctttttttttttccc]ccc	chr10:22619285-22619504(+)$1	219	74	103	24.0995
:::ffffffwwwwwwwwwwwwwwffffff	chr15:100256046-100256267(+)$1	221	2	31	19.6473
:ccc[cccccctttttttttttccc22cc	chr1:156281794-156282014(-)$1	220	3	32	22.8382
::iiiiiiiiitttttttttttiiiiiii	chr20:61510195-61510417(-)$1	222	33	62	21.6725
ggggggg[ccctttttttttttccc]ggg	chr5:135513780-135513997(+)$1	217	114	143	24.5307
effffff[ccctttttttttttccc22ff	chr19:38229825-38230044(-)$1	219	181	210	23.4721
"eeeee[cccuuuuuuuuuuuuccc]eee	chr8:144735477-144735698(+)$1	221	51	80	24.4632
!!bb####bbuuuuuuuuuuuubb22bb2	chr5:32355848-32356068(-)$1	220	116	145	21.9415
####ddddccctttttttttttccc]ddd	chr4:76569874-76570101(-)$1	227	30	59	23.2983
DD:ggggggguuuuuuuuuuuuggggggg	chr18:48606593-48606813(+)$1	220	83	112	21.2806
dd!!bb[bbbbuuuuuuuuuuuubb]bb]	chr12:12273435-12273652(-)$1	217	74	103	22.1630
ddd[eeeeexxxxxxxxxxxxxxxeeeee	chr2:242293172-242293394(+)$1	222	58	87	18.8582
ccc[dddd[bbuuuuuuuuuuuubb]ddd	chr5:41920406-41920632(+)$1	226	98	127	22.6686
ccc!!cccwwwwwwwwwwwwwwccc22cc	chr1:157091437-157091654(-)$1	217	9	38	22.2741
dddd[eeeeewwwwwwwwwwwwwweeeee	chr7:44918482-44918713(-)$1	231	127	156	22.7584
ffffff[ddddtttttttttttdddd22f	chrX:39910694-39910918(-)$1	224	50	79	22.7032
"gggggggyyyyyyyyyyyyyyyyggggg	chr18:48581124-48581345(+)$1	221	143	172	23.1514
ccc[a[eeeeettttttttttteeeee]a	chr8:82627200-82627418(-)$1	218	150	179	24.1742
gggggg[ddddvvvvvvvvvvvvvddddg	chr17:40993923-40994141(+)$1	218	110	139	22.8843
dddd:eeeeewwwwwwwwwwwwwweeeee	chr1:224346960-224347184(+)$1	224	86	115	21.6075
eeeeeeeeexxxxxxxxxxxxxxxeeeee	chr18:43845193-43845412(+)$1	219	137	166	18.6817
gggggffffffvvvvvvvvvvvvvfffff	chr3:101369548-101369769(-)$1	221	53	82	22.7959
!ddddfffffftttttttttttffffff6	chr12:42478924-42479142(-)$1	218	9	38	22.3308
ffffffeeeeettttttttttteeeee::	chr8:95443852-95444072(-)$1	220	87	116	21.7389
ccccc!!cccwwwwwwwwwwwwwwccc22	chr1:157091523-157091747(-)$1	224	100	129	22.9857
ddd!!eeeeevvvvvvvvvvvvveeeee]	chr2:152693047-152693275(-)$1	228	141	170	23.7837
fff[eeeeevvvvvvvvvvvvveeeee]f	chr12:64844351-64844570(+)$1	219	58	87	23.3207
iii!!ccc[bbuuuuuuuuuuuubbccci	chr3:160155336-160155556(-)$1	220	62	91	23.5646
eeee[cccyyyyyyyyyyyyyyyycccee	chrX:123235938-123236158(+)$1	220	58	87	22.2411
e$$$$$eeeeettttttttttteeeee44	chr2:215592530-215592753(-)$1	223	10	39	23.0067
fffff!!ddddtttttttttttdddd22f	chr5:132216087-132216311(-)$1	224	36	65	22.7297
[dddd"""cccwwwwwwwwwwwwwwccc3	chr6:17616084-17616305(-)$1	221	90	119	22.0459
ffffffeeeeettttttttttteeeee>>	chr21:34948810-34949031(+)$1	221	52	81	23.2752
!!ffffff[bbwwwwwwwwwwwwwwbb]f	chr1:225683023-225683242(-)$1	219	116	145	21.6717
cffffffddddtttttttttttdddd]ff	chr20:49507538-49507762(-)$1	224	74	103	22.8816
ggggg"""ccctttttttttttccc4444	chr1:229458901-229459122(-)$1	221	44	73	24.2547
ccc####ddddtttttttttttddddccc	chr1:68168747-68168971(-)$1	224	90	119	23.0919
!dddd[eeeeettttttttttteeeeedd	chr5:81569763-81569985(-)$1	222	54	83	23.3597
"eeeeecccxxxxxxxxxxxxxxxccc33	chr7:139787338-139787558(-)$1	220	41	70	19.1007
$$$ggggggguuuuuuuuuuuuggggggg	chr21:28209349-28209572(-)$1	223	19	48	23.7937
#ffffffcccuuuuuuuuuuuuccc]fff	chr3:196313913-196314132(+)$1	219	132	161	24.3532
"""ccceeeeeuuuuuuuuuuuueeeee6	chr1:224605911-224606131(-)$1	220	96	125	23.9422
!!a[bb[cccuuuuuuuuuuuucccbb]a	chr1:150548057-150548273(-)$1	216	62	91	23.9290
iiiiiiiiixxxxxxxxxxxxxxxiiiii	chr3:87303141-87303362(+)$1	221	125	154	19.1939
dddd"""ddddtttttttttttdddd333	chr19:3976291-3976513(-)$1	222	113	142	23.1255
!!ffffffyyyyyyyyyyyyyyyyfffff	chr2:131805459-131805679(-)$1	220	127	156	22.5502
"ggggggg[bbtttttttttttbbggggg	chr11:32998702-32998924(+)$1	222	27	56	23.7957
b"""eeeeevvvvvvvvvvvvveeeee33	chr12:110973530-110973746(-)$1	216	14	43	23.5470
e!!bb####bbwwwwwwwwwwwwwwbb44	chr19:44635158-44635377(+)$1	219	10	39	20.8763

#otherMatches

#Seq PSSM
AAGCCCAGGACCCCUUUUCCACCCUGGGC	chr1:27106504-27106723(+)$1	219	177	206	23.7142
UAUGUAUUUAACUGUGCCAAUCUAAAUAC	chr12:69666156-69666373(+)$1	217	83	112	24.6979
AUAGUUUAGUAUUUGCUAAUUUUACUACA	chr18:48701020-48701236(-)$1	216	80	109	21.3913
UUGGAAAGUCUUAUUAAAAGCCUCCAGAU	chr10:856891-857110(-)$1	219	39	68	21.4326
ugaaaguagagaaaaaagaaaacucuaua	chr5:178508904-178509124(+)$1	220	81	110	23.0693
UCCAAGAAAACCAUGAAAACUUCUUUCUU	chr3:169811001-169811220(-)$1	219	129	158	23.1334
UGCUUUGCUGCUUUUAGCCCUUGCAGCAA	chr7:138983426-138983652(+)$1	226	48	77	23.3652
AAUUCACCUCAACAAUUUUCUAGAGGUCA	chr19:57804453-57804680(+)$1	227	104	133	24.1604
UAUAAAUUGCUAGAAAUAUACAGAGCAAU	chrX:103435382-103435601(+)$1	219	110	139	23.5058
AAGUAAUCUAUAUUUUUGAACUGAUACUU	chr10:14945374-14945596(+)$1	222	137	166	21.1716
CUAUGUUAGUUAUUUAUUUCAAAAUUAAC	chr5:71502967-71503187(+)$1	220	169	198	23.2925
AGUCUGUUCCAUUAGAAGCAAUUGGCACA	chr10:22619285-22619504(+)$1	219	74	103	24.0995
CACAGGUGGUCCCAAUCAAAACUCCAUCU	chr15:100256046-100256267(+)$1	221	2	31	19.6473
GCCUGUGGGGCCCGGAUAGUCAGCCGACC	chr1:156281794-156282014(-)$1	220	3	32	22.8382
UAUUUCCAUUUAAAAUUAAAAGAAAUGGG	chr20:61510195-61510417(-)$1	222	33	62	21.6725
CUGUCAUAAGCAUUACUUUAUAGCUAGUG	chr5:135513780-135513997(+)$1	217	114	143	24.5307
CAUGGAUAUCUUAAUCAACAUCAGAAAAU	chr19:38229825-38230044(-)$1	219	181	210	23.4721
CUGGAAAAUCAGCAUUACUAGAGAUGUUU	chr8:144735477-144735698(+)$1	221	51	80	24.4632
AACAGGAAACGAAGAAGAGAUAGUGAUGG	chr5:32355848-32356068(-)$1	220	116	145	21.9415
UUCUUUUCCAGUAGAAAAUAGUUUGUGAA	chr4:76569874-76570101(-)$1	227	30	59	23.2983
CUCAUUUGUACUCUUGAUUACUUACAAAU	chr18:48606593-48606813(+)$1	220	83	112	21.2806
UAAGAAAUGAUGAAAGGAAAAAAAUGCAA	chr12:12273435-12273652(-)$1	217	74	103	22.1630
GGAGGGAGGACCCACACUGCUACACUUCU	chr2:242293172-242293394(+)$1	222	58	87	18.8582
GUACUACACUAAauucacucaacuauugu	chr5:41920406-41920632(+)$1	226	98	127	22.6686
UUAAACCCAACUCACUAACACAGGGAAUG	chr1:157091437-157091654(-)$1	217	9	38	22.2741
ACUUAGAAAAAACAAAGUCCUUAAUUUUC	chr7:44918482-44918713(-)$1	231	127	156	22.7584
GUGUGUAAUAUAAAUUCAAACCAUAUCCA	chrX:39910694-39910918(-)$1	224	50	79	22.7032
CGACAGAGACAUACAGCACCCCAGCUCUG	chr18:48581124-48581345(+)$1	221	143	172	23.1514
CUUGUGGCAGUUAUAUGUCCUUAUUGUGA	chr8:82627200-82627418(-)$1	218	150	179	24.1742
CUCACAUGAGGUUACUGUUUCUUUCCUCU	chr17:40993923-40994141(+)$1	218	110	139	22.8843
UCACCAAAUGAAGCUUUUUCUAUCCAUUU	chr1:224346960-224347184(+)$1	224	86	115	21.6075
UGACAUAUUUUCUUCAUAGUCCCUAAUAU	chr18:43845193-43845412(+)$1	219	137	166	18.6817
AAUGACUGUACUGAAUUUAAAACCGUACA	chr3:101369548-101369769(-)$1	221	53	82	22.7959
CAUGUUGUGGCUUAUUUACACUGUCACAC	chr12:42478924-42479142(-)$1	218	9	38	22.3308
UCUAAUUUAGGAGCUAUACUAACCUAAUA	chr8:95443852-95444072(-)$1	220	87	116	21.7389
CAUUAAACCCAACUCACUAACACAGGGAA	chr1:157091523-157091747(-)$1	224	100	129	22.9857
GUUUUGCUUUGCAUUCUUAUUCAAAAGCU	chr2:152693047-152693275(-)$1	228	141	170	23.7837
GUUGCCUAGAGCACCAUCACAGCUAGGAA	chr12:64844351-64844570(+)$1	219	58	87	23.3207
UUGCUGUGACAUUUAAACAUUCUUGUACC	chr3:160155336-160155556(-)$1	220	62	91	23.5646
AGUCAUGGUUAAUAACAAAUGAAUCCAGA	chrX:123235938-123236158(+)$1	220	58	87	22.2411
CUCAUGGUACAUAUUUUUAUUCUGUACAU	chr2:215592530-215592753(-)$1	223	10	39	23.0067
AGAAUUGGUUCGUCUAAAAUAAGGACAUA	chr5:132216087-132216311(-)$1	224	36	65	22.7297
UUAAUUUUGGAAUUUUCCUCCUUUCUCUU	chr6:17616084-17616305(-)$1	221	90	119	22.0459
GGAGUGCCUCACGUAGAUAGAUUGAGGUU	chr21:34948810-34949031(+)$1	221	52	81	23.2752
CCCAGAUUGCUAAAUGUUCUUUCCAAGAA	chr1:225683023-225683242(-)$1	219	116	145	21.6717
GGAAAAGCAGAGGUUUAUUUUAUCUGCCU	chr20:49507538-49507762(-)$1	224	74	103	22.8816
UAGACUUUGAACCGCCAGACUUUUCUCUU	chr1:229458901-229459122(-)$1	221	44	73	24.2547
AGGCUAUGAGUAUAAAUACAUAACUUCCU	chr1:68168747-68168971(-)$1	224	90	119	23.0919
cuuccauuugucaaagaccaaaacaaagg	chr5:81569763-81569985(-)$1	222	54	83	23.3597
gaccugggcuuuugucgaaguucugccau	chr7:139787338-139787558(-)$1	220	41	70	19.1007
UCCUGGUACUUAUCAAAUACUUAGUAUCA	chr21:28209349-28209572(-)$1	223	19	48	23.7937
CUGAGACAGGCUGUUUUAAUUACCUGGUU	chr3:196313913-196314132(+)$1	219	132	161	24.3532
UGCCUAUAUCACAAUACCAAACUUGAUAA	chr1:224605911-224606131(-)$1	220	96	125	23.9422
AACCUGAGUGACCCUCCCUCCCCACCAAG	chr1:150548057-150548273(-)$1	216	62	91	23.9290
UUUAUGUUCUAAAUCUUUUUCACUGAAUA	chr3:87303141-87303362(+)$1	221	125	154	19.1939
AUAACACUUGAUGCCGUUUCUUUCAAUAU	chr19:3976291-3976513(-)$1	222	113	142	23.1255
GAUGAGAUGAGCUCAGAUUUAAAAAUCUC	chr2:131805459-131805679(-)$1	220	127	156	22.5502
UCAAUUGUACAUUUUAUUUCACUGAUAGU	chr11:32998702-32998924(+)$1	222	27	56	23.7957
AAUUACCCCACAUGGAAAUUUAGGGGUUU	chr12:110973530-110973746(-)$1	216	14	43	23.5470
UGAUGCAGGACUAUCUAUAAUUCACGUAA	chr19:44635158-44635377(+)$1	219	10	39	20.8763

#DB
..(((((((.............)))))))	chr1:27106504-27106723(+)$1	1	177	206	23.7142
((((((((((............)))))))	chr12:69666156-69666373(+)$1	1	83	112	24.6979
.)))))(((((...........)))))..	chr18:48701020-48701236(-)$1	1	80	109	21.3913
.((((((((((..............))))	chr10:856891-857110(-)$1	1	39	68	21.4326
(....((((((...........)))))).	chr5:178508904-178509124(+)$1	1	81	110	23.0693
(((((((((..............))))))	chr3:169811001-169811220(-)$1	1	129	158	23.1334
((..(((((((...........)))))))	chr7:138983426-138983652(+)$1	1	48	77	23.3652
((((.(((((............))))).)	chr19:57804453-57804680(+)$1	1	104	133	24.1604
)))))((((((............))))))	chrX:103435382-103435601(+)$1	1	110	139	23.5058
(((((.((..............)))))))	chr10:14945374-14945596(+)$1	1	137	166	21.1716
))(((((((((...........)))))))	chr5:71502967-71503187(+)$1	1	169	198	23.2925
((..(((.(((...........))).)))	chr10:22619285-22619504(+)$1	1	74	103	24.0995
...((((((..............))))))	chr15:100256046-100256267(+)$1	1	2	31	19.6473
.(((.((((((...........)))..))	chr1:156281794-156282014(-)$1	1	3	32	22.8382
..(((((((((...........)))))))	chr20:61510195-61510417(-)$1	1	33	62	21.6725
(((((((.(((...........))).)))	chr5:135513780-135513997(+)$1	1	114	143	24.5307
)((((((.(((...........)))..))	chr19:38229825-38230044(-)$1	1	181	210	23.4721
.(((((.(((............))).)))	chr8:144735477-144735698(+)$1	1	51	80	24.4632
..((....((............))..)).	chr5:32355848-32356068(-)$1	1	116	145	21.9415
....(((((((...........))).)))	chr4:76569874-76570101(-)$1	1	30	59	23.2983
((.(((((((............)))))))	chr18:48606593-48606813(+)$1	1	83	112	21.2806
((..((.((((............)).)).	chr12:12273435-12273652(-)$1	1	74	103	22.1630
(((.(((((...............)))))	chr2:242293172-242293394(+)$1	1	58	87	18.8582
(((.((((.((............)).)))	chr5:41920406-41920632(+)$1	1	98	127	22.6686
(((..(((..............)))..))	chr1:157091437-157091654(-)$1	1	9	38	22.2741
((((.(((((..............)))))	chr7:44918482-44918713(-)$1	1	127	156	22.7584
((((((.((((...........))))..)	chrX:39910694-39910918(-)$1	1	50	79	22.7032
.(((((((................)))))	chr18:48581124-48581345(+)$1	1	143	172	23.1514
(((.(.(((((...........))))).)	chr8:82627200-82627418(-)$1	1	150	179	24.1742
((((((.((((.............)))))	chr17:40993923-40994141(+)$1	1	110	139	22.8843
)))).(((((..............)))))	chr1:224346960-224347184(+)$1	1	86	115	21.6075
(((((((((...............)))))	chr18:43845193-43845412(+)$1	1	137	166	18.6817
(((((((((((.............)))))	chr3:101369548-101369769(-)$1	1	53	82	22.7959
.((((((((((...........)))))).	chr12:42478924-42479142(-)$1	1	9	38	22.3308
))))))(((((...........)))))..	chr8:95443852-95444072(-)$1	1	87	116	21.7389
(((((..(((..............)))..	chr1:157091523-157091747(-)$1	1	100	129	22.9857
(((..(((((.............))))).	chr2:152693047-152693275(-)$1	1	141	170	23.7837
(((.(((((.............))))).)	chr12:64844351-64844570(+)$1	1	58	87	23.3207
(((..(((.((............))))))	chr3:160155336-160155556(-)$1	1	62	91	23.5646
((((.(((................)))))	chrX:123235938-123236158(+)$1	1	58	87	22.2411
(.....(((((...........)))))..	chr2:215592530-215592753(-)$1	1	10	39	23.0067
(((((..((((...........))))..)	chr5:132216087-132216311(-)$1	1	36	65	22.7297
.((((...(((..............))).	chr6:17616084-17616305(-)$1	1	90	119	22.0459
(((((((((((...........)))))..	chr21:34948810-34949031(+)$1	1	52	81	23.2752
..((((((.((..............)).)	chr1:225683023-225683242(-)$1	1	116	145	21.6717
)((((((((((...........)))).))	chr20:49507538-49507762(-)$1	1	74	103	22.8816
(((((...(((...........)))....	chr1:229458901-229459122(-)$1	1	44	73	24.2547
(((....((((...........)))))))	chr1:68168747-68168971(-)$1	1	90	119	23.0919
.((((.(((((...........)))))))	chr5:81569763-81569985(-)$1	1	54	83	23.3597
.((((((((...............)))..	chr7:139787338-139787558(-)$1	1	41	70	19.1007
...(((((((............)))))))	chr21:28209349-28209572(-)$1	1	19	48	23.7937
.(((((((((............))).)))	chr3:196313913-196314132(+)$1	1	132	161	24.3532
...((((((((............))))).	chr1:224605911-224606131(-)$1	1	96	125	23.9422
..(.((.(((............))))).)	chr1:150548057-150548273(-)$1	1	62	91	23.9290
(((((((((...............)))))	chr3:87303141-87303362(+)$1	1	125	154	19.1939
((((...((((...........))))...	chr19:3976291-3976513(-)$1	1	113	142	23.1255
..((((((................)))))	chr2:131805459-131805679(-)$1	1	127	156	22.5502
.(((((((.((...........)))))))	chr11:32998702-32998924(+)$1	1	27	56	23.7957
(...(((((.............)))))..	chr12:110973530-110973746(-)$1	1	14	43	23.5470
(..((....((..............))..	chr19:44635158-44635377(+)$1	1	10	39	20.8763

#PSSM
! : 0.11	f : 0.11	e : 0.11	d : 0.11	" : 0.09	c : 0.09	g : 0.08	i : 0.05	: : 0.05	b : 0.03	# : 0.03	= : 0.01	3 : 0.01	D : 0.01	[ : 0.01	$ : 0.01	
f : 0.16	d : 0.16	e : 0.11	g : 0.11	! : 0.09	c : 0.09	i : 0.05	# : 0.03	: : 0.03	$ : 0.03	" : 0.03	= : 0.01	b : 0.01	D : 0.01	
f : 0.18	g : 0.13	d : 0.13	e : 0.11	c : 0.09	i : 0.08	! : 0.06	# : 0.03	: : 0.03	$ : 0.03	" : 0.03	= : 0.01	b : 0.01	a : 0.01	
f : 0.18	g : 0.16	e : 0.11	! : 0.09	d : 0.09	[ : 0.08	i : 0.06	# : 0.05	c : 0.05	b : 0.03	= : 0.01	$ : 0.01	" : 0.01	
g : 0.18	f : 0.18	e : 0.13	d : 0.08	i : 0.06	[ : 0.06	# : 0.05	c : 0.05	b : 0.05	! : 0.05	= : 0.01	a : 0.01	: : 0.01	$ : 0.01	" : 0.01	
f : 0.23	e : 0.18	g : 0.13	c : 0.09	i : 0.06	[ : 0.05	# : 0.05	" : 0.05	d : 0.03	b : 0.03	! : 0.03	= : 0.01	$ : 0.01	
e : 0.24	f : 0.18	g : 0.11	c : 0.09	[ : 0.08	i : 0.06	# : 0.05	" : 0.05	d : 0.03	! : 0.03	= : 0.01	b : 0.01	
e : 0.24	d : 0.15	c : 0.15	f : 0.11	g : 0.09	i : 0.06	[ : 0.05	b : 0.03	# : 0.03	" : 0.03	= : 0.01	
e : 0.24	c : 0.19	d : 0.11	f : 0.08	g : 0.06	i : 0.06	[ : 0.06	y : 0.05	w : 0.03	b : 0.03	= : 0.01	# : 0.01	
e : 0.18	c : 0.18	d : 0.11	b : 0.11	f : 0.06	w : 0.06	x : 0.06	v : 0.05	g : 0.05	y : 0.05	i : 0.03	= : 0.01	
u : 0.13	e : 0.11	d : 0.11	w : 0.11	c : 0.11	b : 0.09	v : 0.06	f : 0.06	x : 0.06	y : 0.05	i : 0.03	g : 0.01	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
t : 0.38	u : 0.21	w : 0.18	v : 0.09	x : 0.06	y : 0.05	
c : 0.16	e : 0.15	w : 0.15	u : 0.08	d : 0.08	g : 0.06	x : 0.06	b : 0.05	y : 0.05	v : 0.05	f : 0.03	i : 0.03	= : 0.01	
e : 0.18	c : 0.16	w : 0.11	b : 0.09	d : 0.08	g : 0.06	f : 0.06	x : 0.06	i : 0.05	y : 0.05	v : 0.03	= : 0.01	
e : 0.26	c : 0.21	g : 0.09	f : 0.09	d : 0.09	w : 0.06	i : 0.06	b : 0.05	= : 0.01	2 : 0.01	
e : 0.26	d : 0.11	] : 0.11	g : 0.09	f : 0.09	c : 0.08	i : 0.06	2 : 0.06	b : 0.05	= : 0.01	4 : 0.01	
e : 0.28	g : 0.11	f : 0.11	c : 0.11	2 : 0.08	b : 0.08	d : 0.06	i : 0.06	= : 0.01	] : 0.01	4 : 0.01	3 : 0.01	
f : 0.15	e : 0.15	g : 0.11	c : 0.09	d : 0.08	] : 0.08	i : 0.06	2 : 0.05	4 : 0.05	3 : 0.05	: : 0.03	b : 0.03	= : 0.01	> : 0.01	
f : 0.18	g : 0.13	e : 0.13	3 : 0.08	i : 0.08	d : 0.06	c : 0.06	4 : 0.05	: : 0.03	2 : 0.03	] : 0.03	a : 0.03	6 : 0.03	= : 0.01	> : 0.01	

#score	1359.391862001075
#seq	60
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_UTR_m1_run1.txt

#BEAR
c!!ffffff####cccddddllldddd]cccffffff333	chr20:42089757-42089981(+)$1	224	173	213	11.7555
dddd[ccc!!ccc!!bboooooobb333ccc22ccc]ddd	chr16:68961421-68961643(+)$1	222	120	160	12.9944
"""============rrrrrrrrr============22bb	chr2:61708230-61708451(-)$1	221	138	178	12.5433
ee[ccc"""bb[dddd[allla]dddd]bbccc]eeeeeF	chr1:32110351-32110572(-)$1	221	147	187	11.9833
ee!!eeeee####bb[aooooooa]bb4444eeeee22ee	chr2:96949590-96949816(-)$1	226	25	65	14.7639
eeeeccceeeee!!ddddnnnnndddd4444eeeee]ccc	chr6:43738688-43738915(+)$1	227	117	157	14.4788
cc!!dddd[cccbbddddnnnnndddd4444bb]cccddd	chr17:1303301-1303545(-)$1	244	133	173	12.7097
gggg[ddddccceeeeeooooooeeeee4444ccc]dddd	chr17:48814249-48814487(+)$1	238	151	191	14.8084
eee[a!!ccc"""ddddnnnnndddd4444ccc22a]eee	chr4:152024911-152025141(+)$1	230	159	199	14.5043
=====####dddd[aooooooa]dddd4444=========	chr19:583209-583432(+)$1	223	86	126	16.8601
d[ccc!!eeeee[ddddoooooodddd333eeeee4444c	chr16:46705549-46705769(-)$1	220	139	179	17.0845
iiiiiiii!!gggggggnnnnnggggggg22iiiiiiiii	chr10:116622008-116622231(+)$1	223	126	166	11.3616
dddd[a!!ccc[ddddddddllldddd]dddd]ccc22ad	chr1:228682256-228682480(+)$1	224	139	179	12.5024
==!!ccc[dddd[eeeeerrrrrrrrreeeeedddd]ccc	chr17:28444048-28444271(+)$1	223	70	110	10.8844
c[ffffff[dddd[cccoooooocccddddffffff]ccc	chr2:99225028-99225253(+)$1	225	2	42	13.0778
ffeeeee####ffffffooooooffffff22eeeee333f	chrX:54070418-54070641(-)$1	223	61	101	12.1178
ggg!!bb!!ccceeeeeooooooeeeee]ccc]bb]gggg	chr12:6660509-6660735(-)$1	226	112	152	14.0287
gg####dddd[dddd[aooooooadddd22ddddgggggg	chr13:37633645-37633869(-)$1	224	142	182	14.9527
bb[bb[dddd"""ddddoooooodddd]dddd]bb]bb22	chr10:13213022-13213250(+)$1	228	38	78	13.9830
ee[ccceeeee!!ddddoooooodddd4444eeeee]ccc	chr10:58117809-58118039(-)$1	230	162	202	17.5178
ggggg]aeeeee[ddddoooooodddd]eeeee::eeeee	chr11:19138681-19138920(+)$1	239	121	161	12.4581
:===========[ddddoooooodddd===========::	chr2:216197089-216197310(+)$1	221	172	212	14.3806
dddd####dddd[ddddoooooodddddddd22dddd999	chr1:27216574-27216803(-)$1	229	172	212	12.8705
a[bb####dddd[ddddmmmmdddd]dddd4444bb]a]e	chr5:65440085-65440317(+)$1	232	132	172	11.8975
fff"""dddd####ddddllldddddddd22ffffffccc	chr20:36661928-36662160(+)$1	232	78	118	12.2766
ii[a[aa####ccccccooooooccc]ccc4444a]a]a]	chr19:30433101-30433346(+)$1	245	140	180	16.1855
e[bb!!ffffff[eeeeeooooooeeeeeffffff22bb]	chr19:10217198-10217420(+)$1	222	62	102	10.8692
ggg[bb[eeeee!!cccooooooccc4444eeeee]bb]g	chr2:101888049-101888275(-)$1	226	112	152	15.2750
ggggggg!!bb####cccnnnnnccc4444bb4444gggg	chr17:27066032-27066265(+)$1	233	168	208	13.4361
====ccc[ddddddddrrrrrrrrrdddd333dddd]ccc	chr3:52321754-52321979(+)$1	225	158	198	13.6385
iiiii[dddd[a!!cccooooooccc22addddiiiiiii	chr15:93443595-93443814(+)$1	219	176	216	15.0493
$$$ccc!!dddd[ccclllccc]dddd4444ccc333a22	chr9:139820483-139820711(+)$1	228	56	96	12.7520
ffffff[ccc"""cccrrrrrrrrrccc333ccc]fffff	chr11:60670835-60671059(-)$1	224	124	164	12.4860
dddd[dddd"""ccc[aooooooa]ccc333dddddddd:	chr19:57803650-57803879(+)$1	229	154	194	13.5548
!ccc!!ccc[cccccccccnnnnnccc]ccc]ccc22ccc	chr13:30169466-30169689(-)$1	223	73	113	11.8385
ddd[a####ffffffooooooffffff4444a]ddddccc	chrX:122820306-122820531(-)$1	225	58	98	12.5841
hhhhhhh"""bb!!cccooooooccc22bb333hhhhhhh	chr14:103800665-103800907(+)$1	242	39	79	12.3163
!bb[dddd$$$$$ddddoooooodddd55555dddd]bb2	chr10:94352944-94353169(+)$1	225	176	216	12.2526
dddd"""dddd!!cccmmmmccc]dddd4444dddd22ee	chr3:9466070-9466296(+)$1	226	11	51	11.8927
"ccc"""eeeee^^^^^^^^^^^^^^^^^^^eeeee333c	chr9:95012368-95012598(-)$1	230	98	138	10.3419
EEggggggg"""cccrrrrrrrrrccc4444ggggggg:e	chr3:49713511-49713737(+)$1	226	44	84	11.1891
cc[bb!!dddd[eeeeeooooooeeeeedddd22bb]ccc	chr2:48032686-48032906(+)$1	220	6	46	13.1576
ddd####cccccc[ddddnnnnndddd]ccc]ccc22ddd	chr2:190329848-190330069(+)$1	221	121	161	13.3008
c[ddddccc[ddddrrrrrrrrrdddd]ccc]dddd]ccc	chr1:38187245-38187481(-)$1	236	14	54	12.1311
===========ddddddddmmmmdddd]dddd]=======	chr1:11072622-11072873(+)$1	251	4	44	12.5934
=====####ccc[ddddlllddddccc4444=========	chr5:177631522-177631746(+)$1	224	27	67	15.5292
[dddda!!ccc####cccnnnnnccc333ccc22a4444d	chr19:1434639-1434880(+)$1	241	65	105	13.1365
ggggggg[ccceeeeeooooooeeeee88888888cccgg	chr14:105886270-105886498(+)$1	228	121	161	11.7089
ee####===========vvvvvvvvvvvvv==========	chr11:74353244-74353471(+)$1	227	106	146	11.3428
eebb####ccc!!bboooooobb22ccc4444bb]eeeee	chr6:151206694-151206916(+)$1	222	138	178	12.0136
gggggggbb####ddddoooooodddd666666bb]gggg	chr9:95033773-95033998(-)$1	225	141	181	14.7730
gggggg"""eeeeea[ddddllldddd]a]eeeee333gg	chr1:115280549-115280778(-)$1	229	106	146	13.0417

#otherMatches

#Seq PSSM
UUUUGAGCUAACGUAACUUUUGUAAAGAUUAAGCUCAUUU	chr20:42089757-42089981(+)$1	224	173	213	11.7555
UGAUCCGGUCAUCCAAGAACUCGCUGUUGAUCUCCGCAUC	chr16:68961421-68961643(+)$1	222	120	160	12.9944
AUUUAUUUGCUCUUGCAGAAAUAUUAGGGGUAGAUGUGAC	chr2:61708230-61708451(-)$1	221	138	178	12.5433
CCCGCGAAUCCAGGUAGCGGCGGUGCCAGGCGCAGGCCCG	chr1:32110351-32110572(-)$1	221	147	187	11.9833
GGAUGGGAGCCUUGGCCUGCAGUGACCCUCCCUCCCUCCC	chr2:96949590-96949816(-)$1	226	25	65	14.7639
UGAGGCGGCGGUGUGCGCAGACAGUGCUCCAGCCGCGCGC	chr6:43738688-43738915(+)$1	227	117	157	14.4788
CUGCCGCUAUGGAUGAUCGAGAGGAUCUGGUGUACCAGGC	chr17:1303301-1303545(-)$1	244	133	173	12.7097
CUGUGUAACUUUUAUCAAAUUUAUGAUAUUUAAAAUGUUG	chr17:48814249-48814487(+)$1	238	151	191	14.8084
gguguaauggaaaaagcauaaggcuuggacucagaagacu	chr4:152024911-152025141(+)$1	230	159	199	14.5043
CCUCCUUGUCUGUGCAUCCGGGGGCAGCUCUGGAGGGGGU	chr19:583209-583432(+)$1	223	86	126	16.8601
ACCAGCAGUACUUGGUAUGAGUUUACCCUUAGUAUAUCCC	chr16:46705549-46705769(-)$1	220	139	179	17.0845
GAAAAUUGCUUUAUAAAAUUGCUUUAUAAUUUGAUUUUCU	chr10:116622008-116622231(+)$1	223	126	166	11.3616
GCAAAGCUUGUAGCAGUAGCUCAGUUGCCUGCAGCAUCCU	chr1:228682256-228682480(+)$1	224	139	179	12.5024
GCAGAGAGCGAGACUUUUCUAUUUUCCAAAAGCUCGGUCU	chr17:28444048-28444271(+)$1	223	70	110	10.8844
GGCGCGUCCGCGGCGGAAGUCGGUUCCCGUGACGCGGCGC	chr2:99225028-99225253(+)$1	225	2	42	13.0778
GGUCUCCAGUAGGCCCGAACGGCCGGGCCGAGGGGAAUGU	chrX:54070418-54070641(-)$1	223	61	101	12.1178
CUCGACGAGCUCUGUUCUGGUGCGGGCAGGAGGCGGGAGC	chr12:6660509-6660735(-)$1	226	112	152	14.0287
CUUGGGGCCUAGCGGCGAGGCGACCCGCACAGGUGGGCGG	chr13:37633645-37633869(-)$1	224	142	182	14.9527
CGGCGACGGUGAAUCUUAUACAGAAGAGGCUGAUGAUGGA	chr10:13213022-13213250(+)$1	228	38	78	13.9830
UUCUGACUACAUCCCAGCAAGCUCUGGCAUCUGUGGAUUA	chr10:58117809-58118039(-)$1	230	162	202	17.5178
GGGCCGGGGCUGGGCUCGCAGGUGAGUGCGGCCGGGCGGU	chr11:19138681-19138920(+)$1	239	121	161	12.4581
UUGUUCGAAAGGCAUUUCUUCUUAAAUUUUUUUGAAUAUU	chr2:216197089-216197310(+)$1	221	172	212	14.3806
CCGUUUUCCCUGUGAGUUGACCUGCUCCGGGCCGCGGGCC	chr1:27216574-27216803(-)$1	229	172	212	12.8705
GCGGCUUCGGUUUGGGCUUAGGCUUCGGCCUCACCCCCAC	chr5:65440085-65440317(+)$1	232	132	172	11.8975
CUGUCUCCUUCGAAGUGCUCUGCGCGAGGUUCAGAGCGGC	chr20:36661928-36662160(+)$1	232	78	118	12.2766
GCGGGGCGGCGGCGGCGGGGACAUGCACGUGUGAGAUGCG	chr19:30433101-30433346(+)$1	245	140	180	16.1855
ACGCGAGGCUGCACGGGUCGCAACAUCCGGCAGCUCAGCC	chr19:10217198-10217420(+)$1	222	62	102	10.8692
AAAAGAAUUCAAGGCAUCUUAACGUGACAGUUGAACUCAU	chr2:101888049-101888275(-)$1	226	112	152	15.2750
UGGGGCCGUGGAGACAGCGGUAAGCUCCAGCCUUUAGGCC	chr17:27066032-27066265(+)$1	233	168	208	13.4361
CUCGCAUGGCCUUCAGAAGCGGUCCCUGGGCUGGGCGAUG	chr3:52321754-52321979(+)$1	225	158	198	13.6385
AAGAAGCAGCCGUACUGAGAGCCCAGGUCGUUGUUUUUUC	chr15:93443595-93443814(+)$1	219	176	216	15.0493
UUCAGAGACUGCGGAGGGGCUUGGCAGACGGUCUUAGCCA	chr9:139820483-139820711(+)$1	228	56	96	12.7520
AGUGGGUGAGUUCCUGCAAGAGAAUCAGCAUCUUCCCCAC	chr11:60670835-60671059(-)$1	224	124	164	12.4860
AUGUUAGAAAUUGACACAGCCAAGAGUCUUAUUCUACAUC	chr19:57803650-57803879(+)$1	229	154	194	13.5548
CCUUGAGCGCGUCCGACAGUCUGUCUGUUCGCGAUCCUGC	chr13:30169466-30169689(-)$1	223	73	113	11.8385
GUUAGAAUCUUACAUGAGUAUGUGUGAACCGCAAACACUG	chrX:122820306-122820531(-)$1	225	58	98	12.5841
GGCGCCGUCUCUCCGCGCCAGGUCGCCCAGCUCCGGCGCU	chr14:103800665-103800907(+)$1	242	39	79	12.3163
GCGGGGACCGUCAUGGCGUCGCAGCCAAAUUCGUCUGCGA	chr10:94352944-94353169(+)$1	225	176	216	12.2526
AGAAUUCCAUUCUGUGUGUUCAUCAAUGUUAUUUCUUUCU	chr3:9466070-9466296(+)$1	226	11	51	11.8927
UGAUCAGAGACCGAAAAACUAUUCCCAUAAAGGUUUGAAA	chr9:95012368-95012598(-)$1	230	98	138	10.3419
CCCCAAGGCCGAGUCCUUCUUUCAGACCAAAGCCUUGGAC	chr3:49713511-49713737(+)$1	226	44	84	11.1891
AAGAUGAAUUUAUGUAAUAUGAUUUGCAAAAUGAGUAUUC	chr2:48032686-48032906(+)$1	220	6	46	13.1576
AAAACACAAGGGUAAUACUAUCUGUGUAGCCACUUAAUUU	chr2:190329848-190330069(+)$1	221	121	161	13.3008
GAGCUGCUCGUAGCCGUGCAUAUGCUGAGGGACAGCGCCU	chr1:38187245-38187481(-)$1	236	14	54	12.1311
CUCUCGUCGGUGCCUUCCACCUCUGGACAGGCAACCGGUG	chr1:11072622-11072873(+)$1	251	4	44	12.5934
CGGGACGGAGCUUGGCUGUUGGUCGGUGGGUUCCCGUGCG	chr5:177631522-177631746(+)$1	224	27	67	15.5292
CGCCCCGAGCUCACAGGACUUUCUCCCCCAGCAGGUUACG	chr19:1434639-1434880(+)$1	241	65	105	13.1365
GGGUCGGAGGUAAGGCCGCACCGCCUUUAUgcccggcccc	chr14:105886270-105886498(+)$1	228	121	161	11.7089
CAAAACCCUUCUUUUUAAAAGGAAAAAGGAUGGAGAGAAG	chr11:74353244-74353471(+)$1	227	106	146	11.3428
UGUUGCCAAAGCUGUAAUUGAACUUCUUGAAAAAUCAGGU	chr6:151206694-151206916(+)$1	222	138	178	12.0136
CUUCACAACGGAGGUGACAGAUUUCGCAGGACAGUAUGUG	chr9:95033773-95033998(-)$1	225	141	181	14.7730
CAUCGGACCGACGGACUGGGAAACCCAUUGCUGUUAAACU	chr1:115280549-115280778(-)$1	229	106	146	13.0417

#DB
(..((((((....(((((((...)))).)))))))))...	chr20:42089757-42089981(+)$1	1	173	213	11.7555
((((.(((..(((..((......))...)))..))).)))	chr16:68961421-68961643(+)$1	1	120	160	12.9944
...((((((((((((.........))))))))))))..))	chr2:61708230-61708451(-)$1	1	138	178	12.5433
((.(((...((.((((.(...).)))).))))).))))))	chr1:32110351-32110572(-)$1	1	147	187	11.9833
((..(((((....((.(......).))....)))))..))	chr2:96949590-96949816(-)$1	1	25	65	14.7639
))))((((((((..((((.....))))....))))).)))	chr6:43738688-43738915(+)$1	1	117	157	14.4788
((..((((.(((((((((.....))))....)).))))))	chr17:1303301-1303545(-)$1	1	133	173	12.7097
((((.((((((((((((......)))))....))).))))	chr17:48814249-48814487(+)$1	1	151	191	14.8084
(((.(..(((...((((.....))))....)))..).)))	chr4:152024911-152025141(+)$1	1	159	199	14.5043
(((((....((((.(......).))))....)))))))))	chr19:583209-583432(+)$1	1	86	126	16.8601
(.(((..(((((.((((......))))...)))))....)	chr16:46705549-46705769(-)$1	1	139	179	17.0845
((((((((..(((((((.....)))))))..)))))))))	chr10:116622008-116622231(+)$1	1	126	166	11.3616
((((.(..(((.((((((((...)))).)))).)))..))	chr1:228682256-228682480(+)$1	1	139	179	12.5024
((..(((.((((.(((((.........))))))))).)))	chr17:28444048-28444271(+)$1	1	70	110	10.8844
(.((((((.((((.(((......))))))))))))).)))	chr2:99225028-99225253(+)$1	1	2	42	13.0778
(((((((....((((((......))))))..)))))...)	chrX:54070418-54070641(-)$1	1	61	101	12.1178
(((..((..((((((((......))))).))).)).))))	chr12:6660509-6660735(-)$1	1	112	152	14.0287
((....((((.((((.(......)))))..))))))))))	chr13:37633645-37633869(-)$1	1	142	182	14.9527
((.((.((((...((((......)))).)))).)).))..	chr10:13213022-13213250(+)$1	1	38	78	13.9830
((.((((((((..((((......))))....))))).)))	chr10:58117809-58118039(-)$1	1	162	202	17.5178
))))).)(((((.((((......)))).)))))..(((((	chr11:19138681-19138920(+)$1	1	121	161	12.4581
.(((((((((((.((((......)))))))))))))))..	chr2:216197089-216197310(+)$1	1	172	212	14.3806
((((....((((.((((......))))))))..))))...	chr1:27216574-27216803(-)$1	1	172	212	12.8705
(.((....((((.((((....)))).))))....)).).)	chr5:65440085-65440317(+)$1	1	132	172	11.8975
(((...((((....((((...))))))))..))))))(((	chr20:36661928-36662160(+)$1	1	78	118	12.2766
((.(.((....((((((......))).)))....).).).	chr19:30433101-30433346(+)$1	1	140	180	16.1855
(.((..((((((.(((((......)))))))))))..)).	chr19:10217198-10217420(+)$1	1	62	102	10.8692
(((.((.(((((..(((......)))....))))).)).)	chr2:101888049-101888275(-)$1	1	112	152	15.2750
(((((((..((....(((.....)))....))....))))	chr17:27066032-27066265(+)$1	1	168	208	13.4361
(((((((.((((((((.........))))...)))).)))	chr3:52321754-52321979(+)$1	1	158	198	13.6385
(((((.((((.(..(((......)))..))))))))))))	chr15:93443595-93443814(+)$1	1	176	216	15.0493
...(((..((((.(((...))).))))....)))...)..	chr9:139820483-139820711(+)$1	1	56	96	12.7520
((((((.(((...(((.........)))...))).)))))	chr11:60670835-60671059(-)$1	1	124	164	12.4860
((((.((((...(((.(......).)))...)))))))).	chr19:57803650-57803879(+)$1	1	154	194	13.5548
.(((..(((.(((((((((.....))).))).)))..)))	chr13:30169466-30169689(-)$1	1	73	113	11.8385
(((.(....((((((......))))))....).))))(((	chrX:122820306-122820531(-)$1	1	58	98	12.5841
(((((((...((..(((......)))..))...)))))))	chr14:103800665-103800907(+)$1	1	39	79	12.3163
.((.((((.....((((......)))).....)))).)).	chr10:94352944-94353169(+)$1	1	176	216	12.2526
((((...((((..(((....))).))))....))))..))	chr3:9466070-9466296(+)$1	1	11	51	11.8927
.(((...(((((...................)))))...)	chr9:95012368-95012598(-)$1	1	98	138	10.3419
(((((((((...(((.........)))....))))))).(	chr3:49713511-49713737(+)$1	1	44	84	11.1891
((.((..((((.(((((......)))))))))..)).)))	chr2:48032686-48032906(+)$1	1	6	46	13.1576
(((....((((((.((((.....)))).))).)))..)))	chr2:190329848-190330069(+)$1	1	121	161	13.3008
(.(((((((.((((.........)))).))).)))).)))	chr1:38187245-38187481(-)$1	1	14	54	12.1311
(((((((((((((((((((....)))).)))).)))))))	chr1:11072622-11072873(+)$1	1	4	44	12.5934
(((((....(((.((((...)))))))....)))))))))	chr5:177631522-177631746(+)$1	1	27	67	15.5292
.(((((..(((....(((.....)))...)))..)....)	chr19:1434639-1434880(+)$1	1	65	105	13.1365
(((((((.((((((((......)))))........)))))	chr14:105886270-105886498(+)$1	1	121	161	11.7089
((....(((((((((((.............))))))))))	chr11:74353244-74353471(+)$1	1	106	146	11.3428
((((....(((..((......))..)))....)).)))))	chr6:151206694-151206916(+)$1	1	138	178	12.0136
(((((((((....((((......))))......)).))))	chr9:95033773-95033998(-)$1	1	141	181	14.7730
((((((...((((((.((((...)))).).)))))...))	chr1:115280549-115280778(-)$1	1	106	146	13.0417

#PSSM
g : 0.17	d : 0.15	e : 0.15	c : 0.09	= : 0.09	i : 0.05	f : 0.05	" : 0.03	! : 0.03	b : 0.01	: : 0.01	a : 0.01	$ : 0.01	h : 0.01	E : 0.01	[ : 0.01	
g : 0.17	d : 0.15	e : 0.13	= : 0.11	[ : 0.09	c : 0.07	i : 0.05	f : 0.05	b : 0.03	! : 0.01	" : 0.01	$ : 0.01	h : 0.01	E : 0.01	
d : 0.17	g : 0.17	[ : 0.09	= : 0.09	! : 0.07	b : 0.07	e : 0.05	c : 0.05	f : 0.05	i : 0.03	# : 0.03	" : 0.01	$ : 0.01	h : 0.01	
d : 0.13	g : 0.13	= : 0.11	c : 0.11	b : 0.09	! : 0.07	[ : 0.07	f : 0.05	# : 0.05	e : 0.03	i : 0.03	" : 0.01	a : 0.01	h : 0.01	
c : 0.13	# : 0.11	g : 0.11	[ : 0.09	= : 0.09	d : 0.07	f : 0.05	! : 0.05	b : 0.05	" : 0.05	e : 0.03	a : 0.03	i : 0.03	h : 0.01	
# : 0.17	c : 0.13	d : 0.09	! : 0.09	g : 0.09	f : 0.05	= : 0.05	a : 0.05	" : 0.05	e : 0.03	b : 0.03	[ : 0.03	i : 0.01	] : 0.01	h : 0.01	
d : 0.15	# : 0.13	c : 0.11	! : 0.11	= : 0.07	" : 0.07	g : 0.07	f : 0.05	e : 0.05	a : 0.03	[ : 0.03	i : 0.01	b : 0.01	h : 0.01	
d : 0.19	# : 0.15	e : 0.13	c : 0.11	! : 0.09	= : 0.07	f : 0.05	" : 0.05	[ : 0.05	i : 0.01	g : 0.01	b : 0.01	
d : 0.24	c : 0.17	e : 0.13	# : 0.09	! : 0.07	= : 0.07	" : 0.05	f : 0.03	[ : 0.03	$ : 0.01	g : 0.01	b : 0.01	
d : 0.24	c : 0.21	e : 0.13	# : 0.09	= : 0.07	" : 0.05	! : 0.03	b : 0.03	f : 0.03	[ : 0.03	$ : 0.01	
c : 0.21	d : 0.19	e : 0.13	# : 0.11	" : 0.09	= : 0.07	b : 0.05	[ : 0.03	f : 0.03	g : 0.01	$ : 0.01	
d : 0.19	c : 0.15	e : 0.13	# : 0.11	" : 0.09	= : 0.05	[ : 0.05	f : 0.05	! : 0.05	g : 0.01	a : 0.01	b : 0.01	$ : 0.01	
[ : 0.17	d : 0.15	! : 0.13	# : 0.11	c : 0.11	e : 0.09	" : 0.05	= : 0.03	f : 0.03	b : 0.01	g : 0.01	$ : 0.01	^ : 0.01	
d : 0.32	c : 0.15	e : 0.13	! : 0.09	b : 0.05	[ : 0.05	# : 0.05	= : 0.03	f : 0.03	g : 0.01	^ : 0.01	
d : 0.38	c : 0.23	e : 0.11	= : 0.03	b : 0.03	a : 0.03	f : 0.03	# : 0.03	! : 0.01	g : 0.01	^ : 0.01	r : 0.01	
d : 0.36	c : 0.23	e : 0.11	[ : 0.07	r : 0.05	o : 0.05	b : 0.01	g : 0.01	f : 0.01	^ : 0.01	= : 0.01	
d : 0.36	c : 0.15	r : 0.09	e : 0.09	o : 0.07	a : 0.05	b : 0.01	[ : 0.01	g : 0.01	f : 0.01	l : 0.01	m : 0.01	^ : 0.01	= : 0.01	
o : 0.48	d : 0.15	r : 0.09	c : 0.05	n : 0.03	e : 0.03	m : 0.03	l : 0.03	a : 0.01	^ : 0.01	v : 0.01	
o : 0.49	n : 0.13	r : 0.11	d : 0.07	l : 0.07	m : 0.03	c : 0.01	^ : 0.01	v : 0.01	
o : 0.49	n : 0.15	r : 0.11	d : 0.05	l : 0.05	m : 0.05	c : 0.01	^ : 0.01	v : 0.01	
o : 0.49	n : 0.15	r : 0.11	l : 0.09	m : 0.03	c : 0.03	^ : 0.01	d : 0.01	v : 0.01	
o : 0.44	n : 0.15	r : 0.11	l : 0.05	d : 0.05	a : 0.03	c : 0.03	f : 0.01	^ : 0.01	m : 0.01	v : 0.01	b : 0.01	
o : 0.42	r : 0.11	n : 0.11	d : 0.07	l : 0.05	] : 0.05	g : 0.01	f : 0.01	c : 0.01	^ : 0.01	m : 0.01	e : 0.01	v : 0.01	b : 0.01	
d : 0.44	c : 0.13	r : 0.09	e : 0.07	a : 0.05	f : 0.03	b : 0.01	g : 0.01	o : 0.01	n : 0.01	] : 0.01	^ : 0.01	v : 0.01	2 : 0.01	
d : 0.46	c : 0.19	e : 0.09	r : 0.05	] : 0.03	f : 0.03	b : 0.01	= : 0.01	g : 0.01	^ : 0.01	v : 0.01	2 : 0.01	
d : 0.46	c : 0.24	e : 0.09	f : 0.03	3 : 0.01	= : 0.01	b : 0.01	g : 0.01	r : 0.01	] : 0.01	^ : 0.01	v : 0.01	
d : 0.48	c : 0.11	e : 0.09	4 : 0.05	3 : 0.03	f : 0.03	2 : 0.03	= : 0.01	b : 0.01	g : 0.01	r : 0.01	] : 0.01	^ : 0.01	v : 0.01	
4 : 0.23	] : 0.19	d : 0.13	e : 0.09	c : 0.07	3 : 0.05	= : 0.03	2 : 0.03	g : 0.01	f : 0.01	5 : 0.01	^ : 0.01	8 : 0.01	v : 0.01	6 : 0.01	
4 : 0.28	d : 0.17	c : 0.11	3 : 0.07	e : 0.05	= : 0.03	b : 0.03	a : 0.03	g : 0.01	f : 0.01	] : 0.01	2 : 0.01	5 : 0.01	^ : 0.01	8 : 0.01	v : 0.01	6 : 0.01	
4 : 0.28	c : 0.15	d : 0.15	3 : 0.07	2 : 0.07	= : 0.03	b : 0.03	e : 0.03	f : 0.01	5 : 0.01	^ : 0.01	8 : 0.01	v : 0.01	6 : 0.01	] : 0.01	
4 : 0.26	c : 0.17	d : 0.13	e : 0.09	3 : 0.07	= : 0.05	2 : 0.05	f : 0.03	b : 0.01	5 : 0.01	^ : 0.01	8 : 0.01	6 : 0.01	
e : 0.19	d : 0.13	c : 0.11	= : 0.09	4 : 0.09	f : 0.07	] : 0.05	2 : 0.03	b : 0.03	3 : 0.03	i : 0.01	a : 0.01	5 : 0.01	g : 0.01	8 : 0.01	6 : 0.01	
e : 0.17	d : 0.15	c : 0.13	= : 0.09	] : 0.09	f : 0.07	2 : 0.07	4 : 0.05	b : 0.03	i : 0.01	3 : 0.01	g : 0.01	8 : 0.01	6 : 0.01	
d : 0.17	e : 0.15	c : 0.13	= : 0.11	f : 0.07	b : 0.07	2 : 0.05	4 : 0.05	] : 0.03	i : 0.03	: : 0.01	h : 0.01	g : 0.01	8 : 0.01	
e : 0.17	d : 0.15	c : 0.11	= : 0.11	b : 0.09	f : 0.07	i : 0.03	g : 0.03	a : 0.03	] : 0.03	2 : 0.01	: : 0.01	4 : 0.01	3 : 0.01	h : 0.01	8 : 0.01	
e : 0.15	d : 0.15	= : 0.11	] : 0.11	f : 0.07	c : 0.07	4 : 0.05	2 : 0.05	i : 0.03	g : 0.03	b : 0.03	3 : 0.03	a : 0.01	h : 0.01	
] : 0.21	2 : 0.13	= : 0.09	g : 0.09	d : 0.07	3 : 0.07	f : 0.05	e : 0.05	c : 0.03	4 : 0.03	i : 0.03	b : 0.03	a : 0.01	h : 0.01	
c : 0.21	d : 0.09	= : 0.09	g : 0.09	3 : 0.07	2 : 0.07	e : 0.07	b : 0.07	4 : 0.03	i : 0.03	a : 0.03	9 : 0.01	] : 0.01	f : 0.01	h : 0.01	
c : 0.19	e : 0.11	g : 0.11	d : 0.09	= : 0.07	3 : 0.05	b : 0.05	4 : 0.03	i : 0.03	a : 0.03	2 : 0.03	: : 0.03	] : 0.03	9 : 0.01	f : 0.01	h : 0.01	
c : 0.23	e : 0.13	g : 0.13	d : 0.11	= : 0.07	2 : 0.05	i : 0.03	f : 0.03	: : 0.03	] : 0.03	3 : 0.01	b : 0.01	F : 0.01	9 : 0.01	h : 0.01	

#score	687.1884824105733
#seq	52
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_transcript_m2_run2.txt

#BEAR
###eeeeeuuuuuuuuuuuueeeee33	chr11:62620701-62620965(-)$1	264	123	150	24.8383
ddeeeeevvvvvvvvvvvvveeeee]d	chr1:161500080-161500318(-)$1	238	114	141	24.1083
!!eeeeevvvvvvvvvvvvveeeee]d	chr7:144546847-144547071(-)$1	224	118	145	24.7537
[ddddyyyyyyyyyyyyyyyydddd]b	chr16:70605660-70605910(+)$1	250	191	218	20.3487
c[bb[cccwwwwwwwwwwwwwwccc]b	chr5:180687234-180687468(-)$1	234	92	119	22.4560
+eeeeewwwwwwwwwwwwwweeeeedd	chr3:170858103-170858323(+)$1	220	118	145	22.8036
[a!!dddduuuuuuuuuuuudddd]a]	chr13:50616726-50616978(-)$1	252	93	120	23.8573
ffffffwwwwwwwwwwwwwwffffff:	chr6:3148866-3149088(-)$1	222	67	94	22.0546
ggggggwwwwwwwwwwwwwwggggggg	chr7:13381602-13381828(+)$1	226	40	67	23.4847
""ffffffuuuuuuuuuuuuffffff3	chr11:58646066-58646285(+)$1	219	132	159	23.5925
$$$$dddduuuuuuuuuuuudddd777	chr6:53084029-53084271(+)$1	242	5	32	21.5285
:::eeeeeuuuuuuuuuuuueeeee::	chr10:75548227-75548447(+)$1	220	2	29	20.3261
ffff[cccuuuuuuuuuuuuccc]fff	chr15:96289011-96289242(+)$1	231	189	216	23.7290
fgggggggtttttttttttgggggggi	chr10:61890882-61891101(-)$1	219	148	175	21.6195
eeee[cccvvvvvvvvvvvvvccc]ee	chr15:41022040-41022270(+)$1	230	158	185	23.3137
GGG:dddduuuuuuuuuuuudddd:ee	chr10:135085262-135085481(-)$1	219	21	48	20.1055
gggg[cccvvvvvvvvvvvvvccc]gg	chr6:31630195-31630419(-)$1	224	142	169	23.8659
ggggggwwwwwwwwwwwwwwggggggg	chr9:72926430-72926663(-)$1	233	79	106	23.4847
iiiiiiiiuuuuuuuuuuuuiiiiiii	chr1:228205380-228205610(+)$1	230	144	171	23.5768
fff[dddduuuuuuuuuuuudddd333	chr15:32940288-32940509(+)$1	221	129	156	23.8533
DDeeeeevvvvvvvvvvvvveeeee::	chr11:31391978-31392199(+)$1	221	39	66	20.7497
:ffffffvvvvvvvvvvvvvffffff:	chr2:32299495-32299721(+)$1	226	49	76	21.7769
ggggggwwwwwwwwwwwwwwggggggg	chr6:117996611-117996835(+)$1	224	38	65	23.4847
"""eeeeeuuuuuuuuuuuueeeee33	chr9:4850244-4850465(+)$1	221	28	55	24.9375
f[cccddddtttttttttttdddd22c	chr2:204389888-204390124(-)$1	236	34	61	21.1512
ffffffxxxxxxxxxxxxxxxffffff	chrY:10036442-10036705(+)$1	263	216	243	18.4421
ggggggwwwwwwwwwwwwwwggggggg	chr14:19696243-19696465(+)$1	222	130	157	23.4847
:ddddcccvvvvvvvvvvvvvccc22d	chr14:50320244-50320725(-)$1	481	428	455	21.9575
%%eeeeevvvvvvvvvvvvveeeee55	chr8:141434578-141434813(+)$1	235	193	220	22.2850
f!!ddddwwwwwwwwwwwwwwdddd33	chr17:5196796-5197029(+)$1	233	152	179	23.4283
iiffffffuuuuuuuuuuuuffffff6	chr16:84749497-84749727(+)$1	230	106	133	23.0748
eeeee[bbuuuuuuuuuuuubb]eeee	chr2:20601349-20601585(-)$1	236	82	109	22.7428
========xxxxxxxxxxxxxxx====	chr1:161500802-161501054(+)$1	252	173	200	18.3311
::cccccctttttttttttccc]ccc:	chr1:178146720-178146940(+)$1	220	141	168	19.5638
H:eeeeevvvvvvvvvvvvveeeee::	chr16:59765159-59765390(+)$1	231	177	204	21.6218
hhhhhhhhuuuuuuuuuuuuhhhhhhh	chr9:9441987-9442388(+)$1	401	299	326	20.6205
f[ddddxxxxxxxxxxxxxxxdddd]f	chr18:9475836-9476060(+)$1	224	140	167	18.7526
bb[eeeeettttttttttteeeeebbD	chr1:78840782-78841015(-)$1	233	169	196	20.5057
e!!ddddvvvvvvvvvvvvvdddd444	chr15:72394775-72395016(+)$1	241	128	155	23.7557
"ggggggguuuuuuuuuuuuggggggg	chr4:151443603-151443822(-)$1	219	176	203	24.0125
b[bb[bbvvvvvvvvvvvvvbb]bb]b	chr2:232326262-232326527(-)$1	265	95	122	21.7272
[bb[eeeeettttttttttteeeeebb	chr16:3749054-3749277(-)$1	223	159	186	21.4974
[ffffffwwwwwwwwwwwwwwffffff	chr17:41084827-41085059(-)$1	232	188	215	22.7158
gggg[cccuuuuuuuuuuuucccgggg	chr22:43548277-43548500(+)$1	223	60	87	24.4591
ee[a!!bbtttttttttttbb]a]eee	chr1:7243682-7243905(+)$1	223	10	37	20.4888
ggg[ddddtttttttttttddddgggg	chr11:6703432-6703659(-)$1	227	64	91	21.7797
eeee[cccuuuuuuuuuuuuccceeee	chr17:27188466-27188685(-)$1	219	164	191	23.9884
eeeeexxxxxxxxxxxxxxxeeeee66	chr16:13158150-13158380(-)$1	230	25	52	18.6426
hhhheeeeettttttttttteeeee::	chr4:39472779-39473007(+)$1	228	54	81	20.0133
dddd[cccwwwwwwwwwwwwwwccc]d	chr9:35757446-35757668(+)$1	222	55	82	22.2715
c[ffffffuuuuuuuuuuuuffffffc	chr1:149822849-149823099(+)$1	250	120	147	23.3744

#otherMatches

#Seq PSSM
CCCCAGUCUGAUCAAUGUGUGACUGAA	chr11:62620701-62620965(-)$1	264	123	150	24.8383
ccgagcggucuaaggcgcugcguucag	chr1:161500080-161500318(-)$1	238	114	141	24.1083
aaacaagcucucaaaauccauuuguag	chr7:144546847-144547071(-)$1	224	118	145	24.7537
UUUCCCCUCAGCUCUUCUCCUGGAAUG	chr16:70605660-70605910(+)$1	250	191	218	20.3487
GUCUACCGAGAAGAAGAAAUACUGGAA	chr5:180687234-180687468(-)$1	234	92	119	22.4560
CGGCGCAUCUGCUCCUCAUAGUGCCGG	chr3:170858103-170858323(+)$1	220	118	145	22.8036
ggcuggucucuagaacuccugaccucg	chr13:50616726-50616978(-)$1	252	93	120	23.8573
GUUUUUGAAAUAUUAAUACAAAAGACU	chr6:3148866-3149088(-)$1	222	67	94	22.0546
gaucauuuuuauaacacaguaugguca	chr7:13381602-13381828(+)$1	226	40	67	23.4847
auuuuagguaaaaauggaauccugaau	chr11:58646066-58646285(+)$1	219	132	159	23.5925
UCAGAGAAGAAAAGACCAAGUUCUaua	chr6:53084029-53084271(+)$1	242	5	32	21.5285
CCAGCUCCCCUUUCCCAUAUGGAGCCU	chr10:75548227-75548447(+)$1	220	2	29	20.3261
ccuccaggaacagugcacccccucgag	chr15:96289011-96289242(+)$1	231	189	216	23.7290
GUAGGAAAUCAUUGAUCAUUUUCUUAG	chr10:61890882-61891101(-)$1	219	148	175	21.6195
CUUUUCGGAAUGUCAUAUUAACUGUGA	chr15:41022040-41022270(+)$1	230	158	185	23.3137
AGGACCACAGCAAGAACCCCGUGGGCG	chr10:135085262-135085481(-)$1	219	21	48	20.1055
GGGCCGUGCCAAUCCCAUCCCCACUGU	chr6:31630195-31630419(-)$1	224	142	169	23.8659
acuaacauagugucauuaaaguuggua	chr9:72926430-72926663(-)$1	233	79	106	23.4847
UCAGAUCCUUCUCCUUCUCUGGGUCUG	chr1:228205380-228205610(+)$1	230	144	171	23.5768
uuaaguaauuuauuucauuuuuaucuc	chr15:32940288-32940509(+)$1	221	129	156	23.8533
UAAUGCUGUUCAUUAAUUAAAGUAUAA	chr11:31391978-31392199(+)$1	221	39	66	20.7497
uaagcuguuuuucucuuucucaGCuuu	chr2:32299495-32299721(+)$1	226	49	76	21.7769
CUGCCAAGGGAGGAGGAAGAUGGCGGC	chr6:117996611-117996835(+)$1	224	38	65	23.4847
AUAUUCAGGUAGAUAUGAGACUGAACU	chr9:4850244-4850465(+)$1	221	28	55	24.9375
cucuacuaaaaauacaaaaauuggcau	chr2:204389888-204390124(-)$1	236	34	61	21.1512
ggaaguaaaagucauaacaaaauuucc	chrY:10036442-10036705(+)$1	263	216	243	18.4421
gcagugagccuagaucacaccacugcg	chr14:19696243-19696465(+)$1	222	130	157	23.4847
AUGCAUCUAUCCUAAGACAAAAGAAAU	chr14:50320244-50320725(-)$1	481	428	455	21.9575
AAAAAACACAAGAAAAAAGAGUUUUAA	chr8:141434578-141434813(+)$1	235	193	220	22.2850
gccucaguuucccaaaguucuuugauu	chr17:5196796-5197029(+)$1	233	152	179	23.4283
cccuuugggucgucccucaaccagagc	chr16:84749497-84749727(+)$1	230	106	133	23.0748
GGUCGAAGUAAUAAUCUGgccuacggc	chr2:20601349-20601585(-)$1	236	82	109	22.7428
GGGUUUUUGUCUUUCCUUCUACGAAAA	chr1:161500802-161501054(+)$1	252	173	200	18.3311
gagccaggaaaguaaggagccuaggca	chr1:178146720-178146940(+)$1	220	141	168	19.5638
uggaugggagaaaagacagaccauuau	chr16:59765159-59765390(+)$1	231	177	204	21.6218
aucaguagAAGUCUGUAAUGCUACUGG	chr9:9441987-9442388(+)$1	401	299	326	20.6205
CGGGGGUGGAGAGUUAGGAGUCCCCAG	chr18:9475836-9476060(+)$1	224	140	167	18.7526
GUGAGGAAGAGGAGAUUGAUUCCUGCU	chr1:78840782-78841015(-)$1	233	169	196	20.5057
gacucugaauccagAAAUAACAGAUAU	chr15:72394775-72395016(+)$1	241	128	155	23.7557
acucaaagaucucugaaaugcuuuggg	chr4:151443603-151443822(-)$1	219	176	203	24.0125
CAGugaugaagaggaggaugaugacag	chr2:232326262-232326527(-)$1	265	95	122	21.7272
GUGUGUGGUGUCACAUUCAAACUAUCA	chr16:3749054-3749277(-)$1	223	159	186	21.4974
ggauuAAGAAAAAAAGAAACAUUAGUU	chr17:41084827-41085059(-)$1	232	188	215	22.7158
GGGCUACGGGAUACCAGCAGCGUGCCC	chr22:43548277-43548500(+)$1	223	60	87	24.4591
augcaacugugaaaaagaaagaggaug	chr1:7243682-7243905(+)$1	223	10	37	20.4888
CCCUCGGUACAAAGAUCAAACUGGGGG	chr11:6703432-6703659(-)$1	227	64	91	21.7797
GAGAUGCUGCAAGCCCAAGAAGCUCUC	chr17:27188466-27188685(-)$1	219	164	191	23.9884
AAAAUUCUUGUAUUAUUAUUAuuuuuc	chr16:13158150-13158380(-)$1	230	25	52	18.6426
AUUUGUGCUUUUCUUCCUACAGCACUU	chr4:39472779-39473007(+)$1	228	54	81	20.0133
UUGGGGUGAGAGAGGAAGGAAGCACGC	chr9:35757446-35757668(+)$1	222	55	82	22.2715
UGCUGGGCAAAGUCACCAUCGCCCAGG	chr1:149822849-149823099(+)$1	250	120	147	23.3744

#DB
...(((((............)))))..	chr11:62620701-62620965(-)$1	1	123	150	24.8383
(((((((.............))))).)	chr1:161500080-161500318(-)$1	1	114	141	24.1083
..(((((.............))))).)	chr7:144546847-144547071(-)$1	1	118	145	24.7537
.((((................)))).)	chr16:70605660-70605910(+)$1	1	191	218	20.3487
(.((.(((..............))).)	chr5:180687234-180687468(-)$1	1	92	119	22.4560
.(((((..............)))))))	chr3:170858103-170858323(+)$1	1	118	145	22.8036
.(..((((............)))).).	chr13:50616726-50616978(-)$1	1	93	120	23.8573
((((((..............)))))).	chr6:3148866-3149088(-)$1	1	67	94	22.0546
((((((..............)))))))	chr7:13381602-13381828(+)$1	1	40	67	23.4847
..((((((............)))))).	chr11:58646066-58646285(+)$1	1	132	159	23.5925
....((((............))))...	chr6:53084029-53084271(+)$1	1	5	32	21.5285
...(((((............)))))..	chr10:75548227-75548447(+)$1	1	2	29	20.3261
((((.(((............))).)))	chr15:96289011-96289242(+)$1	1	189	216	23.7290
)(((((((...........)))))))(	chr10:61890882-61891101(-)$1	1	148	175	21.6195
((((.(((.............))).))	chr15:41022040-41022270(+)$1	1	158	185	23.3137
(((.((((............)))).((	chr10:135085262-135085481(-)$1	1	21	48	20.1055
((((.(((.............))).))	chr6:31630195-31630419(-)$1	1	142	169	23.8659
((((((..............)))))))	chr9:72926430-72926663(-)$1	1	79	106	23.4847
((((((((............)))))))	chr1:228205380-228205610(+)$1	1	144	171	23.5768
(((.((((............))))...	chr15:32940288-32940509(+)$1	1	129	156	23.8533
(((((((.............)))))..	chr11:31391978-31392199(+)$1	1	39	66	20.7497
.((((((.............)))))).	chr2:32299495-32299721(+)$1	1	49	76	21.7769
((((((..............)))))))	chr6:117996611-117996835(+)$1	1	38	65	23.4847
...(((((............)))))..	chr9:4850244-4850465(+)$1	1	28	55	24.9375
(.(((((((...........))))..)	chr2:204389888-204390124(-)$1	1	34	61	21.1512
((((((...............))))))	chrY:10036442-10036705(+)$1	1	216	243	18.4421
((((((..............)))))))	chr14:19696243-19696465(+)$1	1	130	157	23.4847
.(((((((.............)))..)	chr14:50320244-50320725(-)$1	1	428	455	21.9575
..(((((.............)))))..	chr8:141434578-141434813(+)$1	1	193	220	22.2850
(..((((..............))))..	chr17:5196796-5197029(+)$1	1	152	179	23.4283
((((((((............)))))).	chr16:84749497-84749727(+)$1	1	106	133	23.0748
(((((.((............)).))))	chr2:20601349-20601585(-)$1	1	82	109	22.7428
((((((((...............))))	chr1:161500802-161501054(+)$1	1	173	200	18.3311
..((((((...........))).))).	chr1:178146720-178146940(+)$1	1	141	168	19.5638
).(((((.............)))))..	chr16:59765159-59765390(+)$1	1	177	204	21.6218
((((((((............)))))))	chr9:9441987-9442388(+)$1	1	299	326	20.6205
(.((((...............)))).)	chr18:9475836-9476060(+)$1	1	140	167	18.7526
((.(((((...........))))))))	chr1:78840782-78841015(-)$1	1	169	196	20.5057
(..((((.............))))...	chr15:72394775-72395016(+)$1	1	128	155	23.7557
.(((((((............)))))))	chr4:151443603-151443822(-)$1	1	176	203	24.0125
(.((.((.............)).)).)	chr2:232326262-232326527(-)$1	1	95	122	21.7272
.((.(((((...........)))))))	chr16:3749054-3749277(-)$1	1	159	186	21.4974
.((((((..............))))))	chr17:41084827-41085059(-)$1	1	188	215	22.7158
((((.(((............)))))))	chr22:43548277-43548500(+)$1	1	60	87	24.4591
((.(..((...........)).).)))	chr1:7243682-7243905(+)$1	1	10	37	20.4888
(((.((((...........))))))))	chr11:6703432-6703659(-)$1	1	64	91	21.7797
((((.(((............)))))))	chr17:27188466-27188685(-)$1	1	164	191	23.9884
(((((...............)))))..	chr16:13158150-13158380(-)$1	1	25	52	18.6426
))))(((((...........)))))..	chr4:39472779-39473007(+)$1	1	54	81	20.0133
((((.(((..............))).)	chr9:35757446-35757668(+)$1	1	55	82	22.2715
(.((((((............)))))))	chr1:149822849-149823099(+)$1	1	120	147	23.3744

#PSSM
f : 0.15	g : 0.13	e : 0.11	[ : 0.07	: : 0.07	" : 0.05	d : 0.03	c : 0.03	i : 0.03	h : 0.03	b : 0.03	# : 0.01	! : 0.01	+ : 0.01	$ : 0.01	G : 0.01	D : 0.01	% : 0.01	= : 0.01	H : 0.01	
g : 0.17	e : 0.11	f : 0.11	[ : 0.09	d : 0.07	! : 0.05	: : 0.05	" : 0.03	i : 0.03	h : 0.03	b : 0.03	# : 0.01	a : 0.01	$ : 0.01	G : 0.01	D : 0.01	% : 0.01	= : 0.01	
e : 0.19	f : 0.17	g : 0.17	d : 0.07	b : 0.05	! : 0.05	c : 0.03	h : 0.03	[ : 0.03	# : 0.01	$ : 0.01	: : 0.01	G : 0.01	i : 0.01	" : 0.01	= : 0.01	
e : 0.27	f : 0.15	g : 0.15	d : 0.11	[ : 0.05	b : 0.03	c : 0.03	h : 0.03	! : 0.01	$ : 0.01	: : 0.01	i : 0.01	= : 0.01	a : 0.01	
e : 0.27	d : 0.19	[ : 0.15	f : 0.13	g : 0.11	c : 0.03	i : 0.01	= : 0.01	h : 0.01	! : 0.01	
e : 0.23	c : 0.17	d : 0.17	f : 0.13	g : 0.11	y : 0.01	i : 0.01	[ : 0.01	= : 0.01	h : 0.01	b : 0.01	! : 0.01	x : 0.01	
e : 0.21	c : 0.17	d : 0.15	w : 0.11	f : 0.09	x : 0.05	b : 0.05	g : 0.03	y : 0.01	i : 0.01	= : 0.01	h : 0.01	
c : 0.17	v : 0.15	w : 0.15	e : 0.11	d : 0.11	f : 0.05	x : 0.05	g : 0.03	b : 0.03	y : 0.01	i : 0.01	= : 0.01	h : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.09	x : 0.07	e : 0.03	y : 0.01	d : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	t : 0.15	x : 0.07	y : 0.01	
u : 0.33	v : 0.21	w : 0.19	x : 0.07	t : 0.05	y : 0.01	g : 0.01	c : 0.01	e : 0.01	b : 0.01	d : 0.01	
e : 0.25	d : 0.13	g : 0.11	f : 0.09	w : 0.07	c : 0.07	v : 0.05	x : 0.05	b : 0.05	y : 0.01	i : 0.01	h : 0.01	
e : 0.25	d : 0.19	f : 0.13	c : 0.13	g : 0.11	w : 0.03	b : 0.03	i : 0.01	x : 0.01	h : 0.01	] : 0.01	
e : 0.25	d : 0.19	c : 0.15	f : 0.13	g : 0.11	] : 0.05	i : 0.01	x : 0.01	h : 0.01	a : 0.01	
e : 0.29	d : 0.17	g : 0.15	f : 0.13	c : 0.11	] : 0.03	i : 0.01	= : 0.01	h : 0.01	b : 0.01	
e : 0.29	f : 0.15	g : 0.15	d : 0.05	c : 0.05	] : 0.05	2 : 0.03	b : 0.03	7 : 0.01	: : 0.01	i : 0.01	3 : 0.01	= : 0.01	h : 0.01	4 : 0.01	
g : 0.17	f : 0.15	] : 0.13	e : 0.09	3 : 0.07	: : 0.07	2 : 0.03	b : 0.03	d : 0.01	a : 0.01	7 : 0.01	i : 0.01	5 : 0.01	= : 0.01	c : 0.01	h : 0.01	4 : 0.01	6 : 0.01	
g : 0.15	: : 0.13	3 : 0.09	d : 0.09	e : 0.09	b : 0.07	f : 0.07	i : 0.03	c : 0.03	6 : 0.03	] : 0.01	7 : 0.01	5 : 0.01	= : 0.01	h : 0.01	D : 0.01	4 : 0.01	

#score	1133.3402062586467
#seq	51
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_CDS_m2_run2.txt

#BEAR
[a!!a!!aqqqqqqqqa22a]a]	chr12:122254959-122255182(+)$1	223	4	27	15.3938
c####cccqqqqqqqqccc22cc	chr9:37860058-37860289(+)$1	231	164	187	16.8915
fff[bb[aqqqqqqqqa]bbfff	chr9:21971012-21971244(-)$1	232	200	223	13.6570
[dddd[bbqqqqqqqqbb333dd	chr2:74590021-74590261(-)$1	240	93	116	15.3393
fff!!cccqqqqqqqqccc]fff	chr20:32880077-32880327(-)$1	250	214	237	16.4656
hhhhddddqqqqqqqqdddd]hh	chr19:18685784-18686027(+)$1	243	30	53	13.5148
ddd[bb[aqqqqqqqqa]bbddd	chr17:4575805-4576044(-)$1	239	87	110	13.4644
gccc[cccqqqqqqqqccc]ccc	chr16:29821468-29821692(+)$1	224	41	64	16.4999
fff!!cccqqqqqqqqccc22ff	chr16:31201267-31201489(+)$1	222	86	109	16.6440
b[bb[cccqqqqqqqqccc]bbb	chr1:149824291-149824553(+)$1	262	102	125	15.4392
dd[a[cccqqqqqqqqccc333a	chr20:43882998-43883218(-)$1	220	168	191	17.0581
:gggggggqqqqqqqqggggggg	chr15:82821095-82821356(-)$1	261	7	30	14.1814
hhheeeeeqqqqqqqqeeeeeff	chr12:109530284-109530507(-)$1	223	108	131	13.5299
eeee[cccqqqqqqqqccc]eee	chr3:45530113-45530341(+)$1	228	189	212	16.1540
e[ffffffqqqqqqqqffffff]	chr1:35854422-35854662(+)$1	240	172	195	14.0305
ebb[ddddqqqqqqqqdddd]bb	chr4:119606599-119606852(-)$1	253	80	103	14.2267
c"""ddddqqqqqqqqdddd333	chr16:2815919-2816139(+)$1	220	193	216	15.7696
dd[eeeeeqqqqqqqqeeeeedd	chr4:129192433-129192653(-)$1	220	181	204	13.9627
cdddd[bbqqqqqqqqbb]dddd	chr21:38538723-38538950(+)$1	227	195	218	14.3449
f"""a[bbqqqqqqqqbb]a333	chr3:39425096-39425318(+)$1	222	148	171	16.0376
:gggggggqqqqqqqqggggggg	chr11:47587361-47587592(+)$1	231	184	207	14.1814
eeee[cccqqqqqqqqccc22ee	chr11:62344558-62344793(-)$1	235	134	157	16.3300
eeee"""aqqqqqqqqa4444ee	chr15:75194952-75195185(-)$1	233	196	219	15.4382
h####cccqqqqqqqqccc4444	chr12:101017828-101018071(-)$1	243	106	129	16.9738
gggggcccqqqqqqqqccc]ggg	chr1:156169961-156170183(+)$1	222	141	164	16.2803
e"""ddddqqqqqqqqdddd888	chr9:135975580-135975809(-)$1	229	143	166	14.3329
####ddddqqqqqqqqdddd777	chr17:46993338-46993563(+)$1	225	34	57	13.8723
!bb!!cccqqqqqqqqccc22bb	chr7:96746921-96747151(+)$1	230	30	53	16.1939
eeeeddddqqqqqqqqdddd]ee	chr6:3154703-3154927(-)$1	224	192	215	14.5338
bdddd!!aqqqqqqqqa22dddd	chr2:55277167-55277421(-)$1	254	46	69	13.9676
:ccc[cccqqqqqqqqccc]ccc	chr17:36884157-36884413(+)$1	256	6	29	15.6095
eee!!cccqqqqqqqqccc22ee	chr16:29818521-29818746(+)$1	225	140	163	16.6566
b"""ddddqqqqqqqqdddd333	chr15:81557947-81558166(-)$1	219	150	173	15.5942
$$bb[cccqqqqqqqqccc]bb>	chr3:127298483-127298705(-)$1	222	145	168	15.2674
bdddd[bbqqqqqqqqbbdddd]	chr6:137540305-137540528(-)$1	223	27	50	14.1947
ccceeeeeqqqqqqqqeeeee]c	chr4:44449608-44449828(+)$1	220	80	103	14.2809
gg"""cccqqqqqqqqccc22gg	chr17:66033394-66033655(+)$1	261	27	50	16.9669
$ccc[cccqqqqqqqqcccccc5	chr6:30314178-30314410(+)$1	232	112	135	15.3334
e[bb[cccqqqqqqqqccc]bb9	chr2:32770683-32770902(+)$1	219	179	202	15.3303
cgggggggqqqqqqqqggggggg	chr3:186506884-186507120(+)$1	236	164	187	15.0643
========qqqqqqqq=======	chr15:40707027-40707249(+)$1	222	145	168	15.7618
eeddddbbqqqqqqqqbb]dddd	chr11:62457997-62458219(-)$1	222	178	201	14.2210
eeeeeeeeqqqqqqqqeeeee44	chr1:46032517-46032777(+)$1	260	159	182	14.2921
fffffcccqqqqqqqqccc333f	chr9:139720140-139720367(+)$1	227	87	110	16.3560
eeeee[bbqqqqqqqqbb]eeee	chr9:95076644-95076869(-)$1	225	19	42	14.4851
ff"""cccqqqqqqqqccc333f	chr19:41784915-41785177(+)$1	262	136	159	17.3122
[ccc[cccqqqqqqqqccc]ccc	chr12:1702079-1702313(-)$1	234	142	165	16.5517
ffffffbbqqqqqqqqbb]ffff	chr11:65658390-65658620(+)$1	230	180	203	14.0487
mddddcccqqqqqqqqcccffff	chr1:36056209-36056458(-)$1	249	200	223	14.7983
ddd!!cccqqqqqqqqccc22dd	chr7:5568018-5568240(-)$1	222	133	156	16.5015
!!ccccccqqqqqqqqccc333c	chr6:30691666-30691892(+)$1	226	47	70	17.0101
dddd!!bbqqqqqqqqbb22ddd	chr16:66919570-66919791(+)$1	221	80	103	14.6504
ccceeeeeqqqqqqqqeeeee33	chr19:37676087-37676311(-)$1	224	44	67	14.5088
ee####bbqqqqqqqqbb333ee	chr12:10875563-10875791(-)$1	228	158	181	15.8996
:dddd[bbqqqqqqqqbb]dddd	chr19:19293337-19293568(-)$1	231	146	169	13.4620
fff[ddddqqqqqqqqdddd]ff	chr1:44084905-44085150(+)$1	245	79	102	14.7627
###eeeeeqqqqqqqqeeeee]b	chr11:810198-810443(+)$1	245	69	92	14.1575
ccc!!cccqqqqqqqqccc333c	chr12:125478274-125478508(+)$1	234	13	36	17.4643
b[bb!!bbqqqqqqqqbb22bb3	chr19:18053399-18053627(+)$1	228	89	112	14.5434
dd"""cccqqqqqqqqcccdddd	chr12:80083799-80084022(-)$1	223	71	94	16.1101
""ffffffqqqqqqqqffffffd	chr6:157099414-157099637(-)$1	223	129	152	13.9112
ffbb[cccqqqqqqqqcccbb]f	chr3:49049818-49050056(+)$1	238	192	215	15.2403
========qqqqqqqq=======	chr1:20978895-20979120(-)$1	225	184	207	15.7618
!bb!!cccqqqqqqqqccc4444	chr8:144898655-144898897(-)$1	242	162	185	16.9292
f[a!!cccqqqqqqqqcccafff	chr16:28834617-28834843(+)$1	226	52	75	16.5534
Fgggggggqqqqqqqqggggggg	chr3:40502864-40503091(+)$1	227	199	222	14.6686

#otherMatches

#Seq PSSM
GCGAGCACAAGGACGAGGACAGG	chr12:122254959-122255182(+)$1	223	4	27	15.3938
CUCAUUGGACAAAUUGCCAUUGC	chr9:37860058-37860289(+)$1	231	164	187	16.8915
ACGUGCGCGAUGCCUGGGGCCGU	chr9:21971012-21971244(-)$1	232	200	223	13.6570
AAUUGAGCACACACACGCACGUA	chr2:74590021-74590261(-)$1	240	93	116	15.3393
UGUUUGCCCACAUGAUGGCCGCA	chr20:32880077-32880327(-)$1	250	214	237	16.4656
GGGCUGCCGGAGUCGGGGUAUGC	chr19:18685784-18686027(+)$1	243	30	53	13.5148
GAGAUCUCCUUGGAAAGUGACUC	chr17:4575805-4576044(-)$1	239	87	110	13.4644
GGUGCCUGUGAGCUCUCAGCCAC	chr16:29821468-29821692(+)$1	224	41	64	16.4999
UCUCUAGGUAAAGAAUUCUCCGG	chr16:31201267-31201489(+)$1	222	86	109	16.6440
GAGCUGCUGAUCCGCAAGCUGCC	chr1:149824291-149824553(+)$1	262	102	125	15.4392
GGUCUCCUUGUGGUGUGGGUGUG	chr20:43882998-43883218(-)$1	220	168	191	17.0581
CUGGGGUCCACUCACAGAUCUCA	chr15:82821095-82821356(-)$1	261	7	30	14.1814
CUGGACUGCAGUUACACAGUCCU	chr12:109530284-109530507(-)$1	223	108	131	13.5299
AGGUUGGUGACUAAGAACUUACU	chr3:45530113-45530341(+)$1	228	189	212	16.1540
CCAAAUUGGUACAGAAUAAUUUA	chr1:35854422-35854662(+)$1	240	172	195	14.0305
ACACCAGGGCCGCGGACCUGCUG	chr4:119606599-119606852(-)$1	253	80	103	14.2267
AAACGCUCUAGAUCUCGAGCCUC	chr16:2815919-2816139(+)$1	220	193	216	15.7696
GAACUUUGUAAACAACCAAAGUC	chr4:129192433-129192653(-)$1	220	181	204	13.9627
UAAGAGUUAAAUAGAAAAGUCUU	chr21:38538723-38538950(+)$1	227	195	218	14.3449
GCAACCCCAAGAUGUCGGAGACA	chr3:39425096-39425318(+)$1	222	148	171	16.0376
ACCGGGCCGAGGGGCAGGCUCGG	chr11:47587361-47587592(+)$1	231	184	207	14.1814
UGUCAGGUGAGAAUGGAUCAGGA	chr11:62344558-62344793(-)$1	235	134	157	16.3300
GGGGACUCUUCUUCCUGUACCCU	chr15:75194952-75195185(-)$1	233	196	219	15.4382
AAAAGUGUGGACUCGGGCAGAUC	chr12:101017828-101018071(-)$1	243	106	129	16.9738
AGAGGGACAAGGGGUAGUUGCCU	chr1:156169961-156170183(+)$1	222	141	164	16.2803
CAGAUGACCGGAGUAAGUCAGAA	chr9:135975580-135975809(-)$1	229	143	166	14.3329
CCCCAGGGUACUUGUUCCCUAUU	chr17:46993338-46993563(+)$1	225	34	57	13.8723
GGUUCACUAAUACGCAAGUUCGC	chr7:96746921-96747151(+)$1	230	30	53	16.1939
AGCGGGGUCACCACCUGCCUGCG	chr6:3154703-3154927(-)$1	224	192	215	14.5338
CCGCGUUCAAGUACCAGUUCGUG	chr2:55277167-55277421(-)$1	254	46	69	13.9676
UGGGAAGAGAAGUAAGUCUACCC	chr17:36884157-36884413(+)$1	256	6	29	15.6095
AGCAAGGGGCCCUACAUCUGCGC	chr16:29818521-29818746(+)$1	225	140	163	16.6566
GCAAUAGGGAUUAACACCUAAAC	chr15:81557947-81558166(-)$1	219	150	173	15.5942
aaaagccaacuccaacuggguua	chr3:127298483-127298705(-)$1	222	145	168	15.2674
GCGCUCGGGGUUGGAGCCAGCGA	chr6:137540305-137540528(-)$1	223	27	50	14.1947
GGACAGGCGAUCAAAGGCCUGCU	chr4:44449608-44449828(+)$1	220	80	103	14.2809
UAGCAACAAAAACUGGUGUGAUA	chr17:66033394-66033655(+)$1	261	27	50	16.9669
ACUCUGGGGAGACAGGCCUGAGG	chr6:30314178-30314410(+)$1	232	112	135	15.3334
UCUGUCUCUCUGCUUUGAGCCAC	chr2:32770683-32770902(+)$1	219	179	202	15.3303
CCUUAUUUAAUUCCUGGGAUGAG	chr3:186506884-186507120(+)$1	236	164	187	15.0643
GCCUCUUGGGUAAGUGUGAGAGG	chr15:40707027-40707249(+)$1	222	145	168	15.7618
UAAUCUAAUAUCCCAUUUGAGAU	chr11:62457997-62458219(-)$1	222	178	201	14.2210
GGCCUUAUGCCUUUGAGUGAGCC	chr1:46032517-46032777(+)$1	260	159	182	14.2921
CAGCCACGGAUGACAUCGUGAAG	chr9:139720140-139720367(+)$1	227	87	110	16.3560
CAAAGACUCACAACAUAGGCUUU	chr9:95076644-95076869(-)$1	225	19	42	14.4851
GGUCCCUGGACUCCUGCAGCACC	chr19:41784915-41785177(+)$1	262	136	159	17.3122
CCUGAGCCAACUCACCGGCAUAG	chr12:1702079-1702313(-)$1	234	142	165	16.5517
CCCGGGCCGUGCGCGAGGACCUG	chr11:65658390-65658620(+)$1	230	180	203	14.0487
CUCGGGCCAGGUGCACGGCCUCU	chr1:36056209-36056458(-)$1	249	200	223	14.7983
ACGGCCGAGCGGGAAAUCGUGCG	chr7:5568018-5568240(-)$1	222	133	156	16.5015
AGGUCUUCGAUGCCAAGAACAUG	chr6:30691666-30691892(+)$1	226	47	70	17.0101
GGCAGAGCGGCUGGCGGCGAUGC	chr16:66919570-66919791(+)$1	221	80	103	14.6504
GAAGGCCUUUAGCAACAGGUCCA	chr19:37676087-37676311(-)$1	224	44	67	14.5088
UCCCCAGGACCCCGCGCCCAAGA	chr12:10875563-10875791(-)$1	228	158	181	15.8996
AGCAUCCGGGACCAUAUGAAUGC	chr19:19293337-19293568(-)$1	231	146	169	13.4620
UCAUCGUGAUUGAUGCCAUGUUG	chr1:44084905-44085150(+)$1	245	79	102	14.7627
CUAGGGGGCAACUCCUCCCCCAG	chr11:810198-810443(+)$1	245	69	92	14.1575
GCGCACGGCCCUCACCCCGCAUC	chr12:125478274-125478508(+)$1	234	13	36	17.4643
GACCAGCUGGAACGUAAGAAGGA	chr19:18053399-18053627(+)$1	228	89	112	14.5434
CGAAACGCGAGAAGAUGCGCGCC	chr12:80083799-80084022(-)$1	223	71	94	16.1101
GAggcgcgccgccgcccgcgccg	chr6:157099414-157099637(-)$1	223	129	152	13.9112
AGGUACACUCAAGGCUGUGACUC	chr3:49049818-49050056(+)$1	238	192	215	15.2403
UGCUGGGGCUCUUCAUCUUCAGC	chr1:20978895-20979120(-)$1	225	184	207	15.7618
AGUGUACGACCAGGAGCGUUUUG	chr8:144898655-144898897(-)$1	242	162	185	16.9292
CACCAGCCCUCCCAACGGCGGCC	chr16:28834617-28834843(+)$1	226	52	75	16.5534
GGGAUAAUUUUUAUUUGUUGUUU	chr3:40502864-40503091(+)$1	227	199	222	14.6686

#DB
.(..(..(........)..).).	chr12:122254959-122255182(+)$1	1	4	27	15.3938
(....(((........)))..))	chr9:37860058-37860289(+)$1	1	164	187	16.8915
(((.((.(........).)))))	chr9:21971012-21971244(-)$1	1	200	223	13.6570
.((((.((........))...))	chr2:74590021-74590261(-)$1	1	93	116	15.3393
(((..(((........))).)))	chr20:32880077-32880327(-)$1	1	214	237	16.4656
((((((((........)))).))	chr19:18685784-18686027(+)$1	1	30	53	13.5148
(((.((.(........).)))))	chr17:4575805-4576044(-)$1	1	87	110	13.4644
((((.(((........))).)))	chr16:29821468-29821692(+)$1	1	41	64	16.4999
(((..(((........)))..))	chr16:31201267-31201489(+)$1	1	86	109	16.6440
(.((.(((........))).)))	chr1:149824291-149824553(+)$1	1	102	125	15.4392
((.(.(((........)))...)	chr20:43882998-43883218(-)$1	1	168	191	17.0581
.(((((((........)))))))	chr15:82821095-82821356(-)$1	1	7	30	14.1814
)))(((((........)))))((	chr12:109530284-109530507(-)$1	1	108	131	13.5299
((((.(((........))).)))	chr3:45530113-45530341(+)$1	1	189	212	16.1540
(.((((((........)))))).	chr1:35854422-35854662(+)$1	1	172	195	14.0305
)((.((((........)))).))	chr4:119606599-119606852(-)$1	1	80	103	14.2267
(...((((........))))...	chr16:2815919-2816139(+)$1	1	193	216	15.7696
((.(((((........)))))))	chr4:129192433-129192653(-)$1	1	181	204	13.9627
)((((.((........)).))))	chr21:38538723-38538950(+)$1	1	195	218	14.3449
(...(.((........)).)...	chr3:39425096-39425318(+)$1	1	148	171	16.0376
.(((((((........)))))))	chr11:47587361-47587592(+)$1	1	184	207	14.1814
((((.(((........)))..))	chr11:62344558-62344793(-)$1	1	134	157	16.3300
((((...(........)....))	chr15:75194952-75195185(-)$1	1	196	219	15.4382
(....(((........)))....	chr12:101017828-101018071(-)$1	1	106	129	16.9738
((((((((........))).)))	chr1:156169961-156170183(+)$1	1	141	164	16.2803
(...((((........))))...	chr9:135975580-135975809(-)$1	1	143	166	14.3329
....((((........))))...	chr17:46993338-46993563(+)$1	1	34	57	13.8723
.((..(((........)))..))	chr7:96746921-96747151(+)$1	1	30	53	16.1939
((((((((........)))).))	chr6:3154703-3154927(-)$1	1	192	215	14.5338
(((((..(........)..))))	chr2:55277167-55277421(-)$1	1	46	69	13.9676
.(((.(((........))).)))	chr17:36884157-36884413(+)$1	1	6	29	15.6095
(((..(((........)))..))	chr16:29818521-29818746(+)$1	1	140	163	16.6566
(...((((........))))...	chr15:81557947-81558166(-)$1	1	150	173	15.5942
..((.(((........))).)).	chr3:127298483-127298705(-)$1	1	145	168	15.2674
(((((.((........)))))).	chr6:137540305-137540528(-)$1	1	27	50	14.1947
((((((((........))))).)	chr4:44449608-44449828(+)$1	1	80	103	14.2809
((...(((........)))..))	chr17:66033394-66033655(+)$1	1	27	50	16.9669
.(((.(((........)))))).	chr6:30314178-30314410(+)$1	1	112	135	15.3334
(.((.(((........))).)).	chr2:32770683-32770902(+)$1	1	179	202	15.3303
((((((((........)))))))	chr3:186506884-186507120(+)$1	1	164	187	15.0643
((((((((........)))))))	chr15:40707027-40707249(+)$1	1	145	168	15.7618
))((((((........)).))))	chr11:62457997-62458219(-)$1	1	178	201	14.2210
((((((((........)))))..	chr1:46032517-46032777(+)$1	1	159	182	14.2921
((((((((........)))...)	chr9:139720140-139720367(+)$1	1	87	110	16.3560
(((((.((........)).))))	chr9:95076644-95076869(-)$1	1	19	42	14.4851
((...(((........)))...)	chr19:41784915-41785177(+)$1	1	136	159	17.3122
.(((.(((........))).)))	chr12:1702079-1702313(-)$1	1	142	165	16.5517
((((((((........)).))))	chr11:65658390-65658620(+)$1	1	180	203	14.0487
.))))(((........)))((((	chr1:36056209-36056458(-)$1	1	200	223	14.7983
(((..(((........)))..))	chr7:5568018-5568240(-)$1	1	133	156	16.5015
..((((((........)))...)	chr6:30691666-30691892(+)$1	1	47	70	17.0101
((((..((........))..)))	chr16:66919570-66919791(+)$1	1	80	103	14.6504
((((((((........)))))..	chr19:37676087-37676311(-)$1	1	44	67	14.5088
((....((........))...))	chr12:10875563-10875791(-)$1	1	158	181	15.8996
.((((.((........)).))))	chr19:19293337-19293568(-)$1	1	146	169	13.4620
(((.((((........)))).))	chr1:44084905-44085150(+)$1	1	79	102	14.7627
...(((((........))))).)	chr11:810198-810443(+)$1	1	69	92	14.1575
(((..(((........)))...)	chr12:125478274-125478508(+)$1	1	13	36	17.4643
(.((..((........))..)).	chr19:18053399-18053627(+)$1	1	89	112	14.5434
((...(((........)))))))	chr12:80083799-80084022(-)$1	1	71	94	16.1101
..((((((........)))))))	chr6:157099414-157099637(-)$1	1	129	152	13.9112
((((.(((........))))).)	chr3:49049818-49050056(+)$1	1	192	215	15.2403
((((((((........)))))))	chr1:20978895-20979120(-)$1	1	184	207	15.7618
.((..(((........)))....	chr8:144898655-144898897(-)$1	1	162	185	16.9292
(.(..(((........)))))))	chr16:28834617-28834843(+)$1	1	52	75	16.5534
)(((((((........)))))))	chr3:40502864-40503091(+)$1	1	199	222	14.6686

#PSSM
e : 0.19	f : 0.15	c : 0.10	d : 0.09	b : 0.07	: : 0.06	[ : 0.04	h : 0.04	g : 0.04	! : 0.04	# : 0.03	$ : 0.03	= : 0.03	m : 0.01	" : 0.01	F : 0.01	
d : 0.18	e : 0.13	f : 0.12	c : 0.10	g : 0.09	[ : 0.07	" : 0.07	# : 0.06	b : 0.04	h : 0.03	= : 0.03	a : 0.01	$ : 0.01	! : 0.01	
d : 0.15	f : 0.12	c : 0.12	b : 0.12	e : 0.10	" : 0.10	# : 0.07	g : 0.07	h : 0.03	[ : 0.03	= : 0.03	! : 0.01	a : 0.01	
e : 0.16	! : 0.13	d : 0.12	" : 0.10	c : 0.07	b : 0.07	g : 0.07	# : 0.06	[ : 0.06	f : 0.06	= : 0.03	h : 0.01	a : 0.01	
d : 0.22	[ : 0.16	! : 0.15	e : 0.10	g : 0.07	f : 0.06	" : 0.06	# : 0.04	a : 0.03	b : 0.03	= : 0.03	c : 0.01	
c : 0.42	d : 0.13	[ : 0.09	e : 0.09	! : 0.06	g : 0.06	f : 0.04	b : 0.03	= : 0.03	" : 0.01	# : 0.01	
c : 0.42	b : 0.16	d : 0.12	e : 0.09	g : 0.06	! : 0.03	[ : 0.03	f : 0.03	= : 0.03	" : 0.01	
c : 0.42	b : 0.16	d : 0.12	e : 0.09	a : 0.07	g : 0.06	f : 0.03	= : 0.03	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.42	b : 0.16	d : 0.12	e : 0.09	a : 0.07	g : 0.06	f : 0.03	= : 0.03	
c : 0.42	b : 0.16	d : 0.12	e : 0.09	g : 0.06	2 : 0.03	] : 0.03	f : 0.03	= : 0.03	4 : 0.01	
c : 0.42	d : 0.13	e : 0.09	] : 0.09	2 : 0.06	g : 0.06	b : 0.03	3 : 0.03	f : 0.03	= : 0.03	4 : 0.01	
d : 0.21	2 : 0.13	] : 0.13	3 : 0.10	e : 0.10	g : 0.06	f : 0.06	a : 0.04	b : 0.04	4 : 0.04	= : 0.03	c : 0.01	
3 : 0.15	d : 0.12	e : 0.12	2 : 0.10	f : 0.10	] : 0.07	b : 0.07	g : 0.07	c : 0.06	4 : 0.04	= : 0.03	8 : 0.01	7 : 0.01	
d : 0.16	f : 0.15	3 : 0.13	e : 0.10	b : 0.09	g : 0.09	c : 0.07	4 : 0.04	] : 0.04	= : 0.03	a : 0.01	h : 0.01	8 : 0.01	7 : 0.01	
f : 0.16	d : 0.16	c : 0.10	e : 0.10	g : 0.09	3 : 0.07	b : 0.06	] : 0.04	4 : 0.04	= : 0.03	h : 0.01	a : 0.01	8 : 0.01	7 : 0.01	> : 0.01	5 : 0.01	9 : 0.01	

#score	1008.9724500183147
#seq	66
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_CDS_m3_run1.txt

#BEAR
d!!cccqqqqqqqqccc333	chr19:37210297-37210498(+)$1	201	146	166	15.0942
dd[cccqqqqqqqqcccddd	chr5:176335563-176335764(-)$1	201	114	134	14.1437
e[ddddqqqqqqqqddddee	chr15:41337115-41337316(-)$1	201	86	106	14.7925
ffffffqqqqqqqqffffff	chr3:137982499-137982700(+)$1	201	26	46	13.4384
!bbcccqqqqqqqqccc]bb	chr15:82443899-82444100(-)$1	201	139	159	13.5457
cc[cccqqqqqqqqccc333	chr10:27332370-27332571(-)$1	201	10	30	15.0411
ggggggqqqqqqqqgggggg	chr12:108919852-108920053(-)$1	201	122	142	14.1186
ddd[bbqqqqqqqqbb]ddd	chr17:65720132-65720333(+)$1	201	82	102	13.0723
:eeeeeqqqqqqqqeeeee:	chr17:7139175-7139376(-)$1	201	120	140	12.8528
ffffffqqqqqqqqffffff	chr1:109857255-109857456(-)$1	201	54	74	13.4384
""ddddqqqqqqqqdddd44	chr19:21299615-21299816(+)$1	201	153	173	15.2675
c[ddddqqqqqqqqddddcc	chr1:197072902-197073103(-)$1	201	44	64	15.0275
d!!cccqqqqqqqqccc333	chr10:31815762-31815963(+)$1	201	114	134	15.0942
ggddddqqqqqqqqdddd55	chr21:45507566-45507767(+)$1	201	141	161	13.6870
+eeeeeqqqqqqqqeeeee3	chr2:114476705-114476906(-)$1	201	140	160	14.1388
!!ddddqqqqqqqqdddd22	chrX:133551204-133551405(+)$1	201	24	44	15.0363
ccc[bbqqqqqqqqbbcccD	chr11:46817154-46817355(-)$1	201	93	113	12.5315
ggggggqqqqqqqqgggggg	chr16:461450-461651(+)$1	201	17	37	14.1186
##ddddqqqqqqqqdddd44	chr11:46839899-46840100(-)$1	201	65	85	15.2110
:eeeeeqqqqqqqqeeeee:	chr7:158464161-158464362(-)$1	201	179	199	12.8528
ccddddqqqqqqqqdddd]c	chr5:94927035-94927236(+)$1	201	164	184	14.9731
ccc[bbqqqqqqqqbb]ccc	chr22:18377967-18378168(-)$1	201	147	167	13.4000
ggggggqqqqqqqqgggggg	chr9:131356453-131356654(+)$1	201	153	173	14.1186
iiiiiiqqqqqqqqiiiiii	chr1:75217981-75218182(+)$1	201	13	33	14.0492
ffffffqqqqqqqqffffff	chr1:153733259-153733460(+)$1	201	54	74	13.4384
ffff[aqqqqqqqqafffff	chr4:6862567-6862768(+)$1	201	127	147	13.5378
ffffffqqqqqqqqffffff	chr11:93429803-93430004(+)$1	201	144	164	13.4384
ccc[bbqqqqqqqqbbccc:	chr10:101606648-101606849(+)$1	201	29	49	12.8125
[eeeeeqqqqqqqqeeeee3	chrX:23803832-23804033(+)$1	201	16	36	14.7731
ddddddqqqqqqqqdddd]d	chr10:70958149-70958350(+)$1	201	9	29	14.5907
b[ddddqqqqqqqqddddbb	chr12:6701855-6702056(-)$1	201	102	122	14.3499
""ddddqqqqqqqqdddd]b	chr8:68200110-68200311(-)$1	201	85	105	14.9606
iiiiiiqqqqqqqqiiiiii	chr11:3714477-3714678(-)$1	201	10	30	14.0492
eeddddqqqqqqqqdddd]e	chr18:20562227-20562428(+)$1	201	35	55	14.7638
bb[cccqqqqqqqqccc]bb	chr3:197562460-197562661(+)$1	201	181	201	13.6251
#eeeeeqqqqqqqqeeeee4	chr11:33127039-33127240(-)$1	201	5	25	14.6504
ggggggqqqqqqqqgggggg	chr21:30342916-30343117(-)$1	201	71	91	14.1186
e[ddddqqqqqqqqdddd33	chr7:107545805-107546006(+)$1	201	115	135	15.3670
[eeeeeqqqqqqqqeeeee]	chr3:52941122-52941323(-)$1	201	59	79	14.6207
h[ddddqqqqqqqqddddhh	chr14:53341898-53342099(-)$1	201	163	183	14.2500
:eeeeeqqqqqqqqeeeee:	chr17:45012342-45012543(+)$1	201	111	131	12.8528
[eeeeeqqqqqqqqeeeee]	chr22:36682692-36682893(-)$1	201	138	158	14.6207
a[ddddqqqqqqqqdddd]a	chr1:1563949-1564150(+)$1	201	47	67	15.2042
d[ddddqqqqqqqqdddd]d	chr8:48809708-48809909(-)$1	201	52	72	14.9210
c[ddddqqqqqqqqdddd]c	chr3:66436484-66436685(-)$1	201	114	134	15.1969
ffffffqqqqqqqqffffff	chr5:37183584-37183785(-)$1	201	102	122	13.4384
b[ddddqqqqqqqqdddd]b	chr14:100705563-100705764(+)$1	201	51	71	14.7943
dd[cccqqqqqqqqcccddd	chr12:121747565-121747766(-)$1	201	84	104	14.1437
ddddddqqqqqqqqdddd:i	chr11:9435800-9436001(+)$1	201	105	125	13.6794
$$ddddqqqqqqqqddddcc	chr13:77655935-77656136(-)$1	201	173	193	14.5507
ffffffqqqqqqqqffffff	chr10:104103719-104103920(+)$1	201	69	89	13.4384
eeee[aqqqqqqqqa]eeee	chr14:31077105-31077306(+)$1	201	179	199	13.9051
ffffffqqqqqqqqffffff	chr5:72377667-72377868(+)$1	201	24	44	13.4384
!!acccqqqqqqqqccc]a3	chr2:230923904-230924105(-)$1	201	109	129	14.9784
:eeeeeqqqqqqqqeeeee:	chr17:28512555-28512756(+)$1	201	95	115	12.8528
!eeeeeqqqqqqqqeeeee2	chr2:74594103-74594304(-)$1	201	139	159	14.5392
###cccqqqqqqqqccc444	chr11:9167173-9167374(-)$1	201	81	101	14.7808
cc[cccqqqqqqqqcccccc	chr12:70297417-70297618(+)$1	201	49	69	14.5615
eee[bbqqqqqqqqbb333e	chr22:24493984-24494185(+)$1	201	171	191	13.4928
$a[cccqqqqqqqqccc]a2	chr11:134048718-134048919(-)$1	201	148	168	14.4189
#eeeeeqqqqqqqqeeeee]	chr19:18420184-18420385(-)$1	201	138	158	14.5926
ccc[bbqqqqqqqqbbccc3	chr2:71627163-71627364(+)$1	201	112	132	13.7885
ee!!bbqqqqqqqqbb22ee	chr8:53569565-53569766(-)$1	201	120	140	12.8233
ffddddqqqqqqqqdddd55	chr3:160231820-160232021(-)$1	201	103	123	13.5484
ffff[aqqqqqqqqa]ffff	chr21:37744630-37744831(+)$1	201	145	165	13.4626
d!!cccqqqqqqqqccc22d	chr8:97270620-97270821(-)$1	201	171	191	14.2305

#otherMatches

#Seq PSSM
GAAUUCACUCAGAAGAAAAA	chr19:37210297-37210498(+)$1	201	146	166	15.0942
GUAUCAGUGUCAUGUGGACU	chr5:176335563-176335764(-)$1	201	114	134	14.1437
CAUCAGCUACGCUCCUGGGG	chr15:41337115-41337316(-)$1	201	86	106	14.7925
GUGAAGUUUGUCACCUUCAU	chr3:137982499-137982700(+)$1	201	26	46	13.4384
AAGGAGAAUCUCCACUCACU	chr15:82443899-82444100(-)$1	201	139	159	13.5457
UACCACUUCUGUAUGUGCUA	chr10:27332370-27332571(-)$1	201	10	30	15.0411
GGAGGCCAAUGUUUGUUUCC	chr12:108919852-108920053(-)$1	201	122	142	14.1186
CAAAUAUACACUCUUACUUG	chr17:65720132-65720333(+)$1	201	82	102	13.0723
AGAAUCAGGUGAGAGGUUCG	chr17:7139175-7139376(-)$1	201	120	140	12.8528
AGAAUUCCAAGUCAAAUUCU	chr1:109857255-109857456(-)$1	201	54	74	13.4384
AAGGUUAUGAACUAAACCAG	chr19:21299615-21299816(+)$1	201	153	173	15.2675
GUAUAAAGCAAUUAUUGUCA	chr1:197072902-197073103(-)$1	201	44	64	15.0275
CGACUCGGACGAGAGAGAGA	chr10:31815762-31815963(+)$1	201	114	134	15.0942
GCACUCGGAGGGGAGAGUGA	chr21:45507566-45507767(+)$1	201	141	161	13.6870
AUUUGCUUUUAUAUGCAGAA	chr2:114476705-114476906(-)$1	201	140	160	14.1388
ACUAUUGGAUGUGAAAUAAA	chrX:133551204-133551405(+)$1	201	24	44	15.0363
AGAAGGAAUUCAAACCUCUG	chr11:46817154-46817355(-)$1	201	93	113	12.5315
GCUUCCUACGUGACGGGGGC	chr16:461450-461651(+)$1	201	17	37	14.1186
GUGGGUAUGAAGAGGCCCUG	chr11:46839899-46840100(-)$1	201	65	85	15.2110
ACUUAUGACAUGAAAUAGGG	chr7:158464161-158464362(-)$1	201	179	199	12.8528
CAGUUUUAUAAAAUGAGCAU	chr5:94927035-94927236(+)$1	201	164	184	14.9731
UGGGCCCAUCUGCAGGACCA	chr22:18377967-18378168(-)$1	201	147	167	13.4000
GGAGCAGGUUGAGGUGCUCC	chr9:131356453-131356654(+)$1	201	153	173	14.1186
GCUUAGAAGUUCCAUUAAGC	chr1:75217981-75218182(+)$1	201	13	33	14.0492
CUUCUAUCCACCAUUGGAGG	chr1:153733259-153733460(+)$1	201	54	74	13.4384
AACAAGUCUAAAGUCUGUUC	chr4:6862567-6862768(+)$1	201	127	147	13.5378
ACUGAUUCUGUUAUAUCAGU	chr11:93429803-93430004(+)$1	201	144	164	13.4384
GGCAUGAGCCCCAACAGCCC	chr10:101606648-101606849(+)$1	201	29	49	12.8125
AAUGGAAUGAACCAUCCAUC	chrX:23803832-23804033(+)$1	201	16	36	14.7731
CUGUGCUGGACCAUGCACUA	chr10:70958149-70958350(+)$1	201	9	29	14.5907
CCAGCACAAGCUGUUGCUGA	chr12:6701855-6702056(-)$1	201	102	122	14.3499
AACAUUGUAGAAGAAAUGGU	chr8:68200110-68200311(-)$1	201	85	105	14.9606
UAUUGCACACACAGGUAAUA	chr11:3714477-3714678(-)$1	201	10	30	14.0492
UCUGGCGUUAACCGGCUACG	chr18:20562227-20562428(+)$1	201	35	55	14.7638
CCUUAGUUCACAGUUUAUGG	chr3:197562460-197562661(+)$1	201	181	201	13.6251
GCUGUAGGAUCUUAUGCAGA	chr11:33127039-33127240(-)$1	201	5	25	14.6504
AAUGCAAAAAAGAGUGUGUU	chr21:30342916-30343117(-)$1	201	71	91	14.1186
CAGAAGUUACUCCUUUUCCU	chr7:107545805-107546006(+)$1	201	115	135	15.3670
ACAUCCGAGCAGCAGGAUGA	chr3:52941122-52941323(-)$1	201	59	79	14.6207
GGUGAAUCUUUUUUUUUACC	chr14:53341898-53342099(-)$1	201	163	183	14.2500
AGUUCACAACGGCAUGGAUG	chr17:45012342-45012543(+)$1	201	111	131	12.8528
GGCUGCAAUGGAGAGCGGCA	chr22:36682692-36682893(-)$1	201	138	158	14.6207
GGAGGGGGACACAGCCCUGC	chr1:1563949-1564150(+)$1	201	47	67	15.2042
CAGAGGAUUUCCACCUUCCG	chr8:48809708-48809909(-)$1	201	52	72	14.9210
CAUGGAGAACUUUGUCCACG	chr3:66436484-66436685(-)$1	201	114	134	15.1969
ACACUUCCUGUAAUAGGUGU	chr5:37183584-37183785(-)$1	201	102	122	13.4384
GACGGCUCGGAGAUGCCGGC	chr14:100705563-100705764(+)$1	201	51	71	14.7943
GAUGUUUCUUUUUCAGCUCA	chr12:121747565-121747766(-)$1	201	84	104	14.1437
AGUCUGUCCUCAUCCAGAAA	chr11:9435800-9436001(+)$1	201	105	125	13.6794
UUUCAGUUAUUAUCCUGGUU	chr13:77655935-77656136(-)$1	201	173	193	14.5507
UCUGUGUAUUUUCUUGCAGA	chr10:104103719-104103920(+)$1	201	69	89	13.4384
GUAUCUGUUUAUUAAAAUGC	chr14:31077105-31077306(+)$1	201	179	199	13.9051
UGGAUUAUAAAUACAAUCCA	chr5:72377667-72377868(+)$1	201	24	44	13.4384
CACCCAAACAUUGAUGGCGG	chr2:230923904-230924105(-)$1	201	109	129	14.9784
CGGGUUAAUGCAAAGACCUA	chr17:28512555-28512756(+)$1	201	95	115	12.8528
ACACAUCUAGAUCUGUGUGA	chr2:74594103-74594304(-)$1	201	139	159	14.5392
GGAUCUGUAUAUCAGGAGAA	chr11:9167173-9167374(-)$1	201	81	101	14.7808
GGCAGCGAGGACAAGUUCCA	chr12:70297417-70297618(+)$1	201	49	69	14.5615
GUACAGUCCCUGUUCUCCCU	chr22:24493984-24494185(+)$1	201	171	191	13.4928
CGCAUCUUCCUUCUGAUUCA	chr11:134048718-134048919(-)$1	201	148	168	14.4189
ccucaguuuccccucugaga	chr19:18420184-18420385(-)$1	201	138	158	14.5926
AGCCACUGAAAACUGUGCUA	chr2:71627163-71627364(+)$1	201	112	132	13.7885
UUGGUUAAACAUGAAAAAGA	chr8:53569565-53569766(-)$1	201	120	140	12.8233
CAGGCAGUAAUUGAUGCCAA	chr3:160231820-160232021(-)$1	201	103	123	13.5484
UGUUUCAACAUCAAGUAACA	chr21:37744630-37744831(+)$1	201	145	165	13.4626
CCAUGAAUGAACAGUCACAG	chr8:97270620-97270821(-)$1	201	171	191	14.2305

#DB
(..(((........)))...	chr19:37210297-37210498(+)$1	1	146	166	15.0942
((.(((........))))))	chr5:176335563-176335764(-)$1	1	114	134	14.1437
(.((((........))))))	chr15:41337115-41337316(-)$1	1	86	106	14.7925
((((((........))))))	chr3:137982499-137982700(+)$1	1	26	46	13.4384
.(((((........))).))	chr15:82443899-82444100(-)$1	1	139	159	13.5457
((.(((........)))...	chr10:27332370-27332571(-)$1	1	10	30	15.0411
((((((........))))))	chr12:108919852-108920053(-)$1	1	122	142	14.1186
(((.((........)).)))	chr17:65720132-65720333(+)$1	1	82	102	13.0723
.(((((........))))).	chr17:7139175-7139376(-)$1	1	120	140	12.8528
((((((........))))))	chr1:109857255-109857456(-)$1	1	54	74	13.4384
..((((........))))..	chr19:21299615-21299816(+)$1	1	153	173	15.2675
(.((((........))))))	chr1:197072902-197073103(-)$1	1	44	64	15.0275
(..(((........)))...	chr10:31815762-31815963(+)$1	1	114	134	15.0942
((((((........))))..	chr21:45507566-45507767(+)$1	1	141	161	13.6870
.(((((........))))).	chr2:114476705-114476906(-)$1	1	140	160	14.1388
..((((........))))..	chrX:133551204-133551405(+)$1	1	24	44	15.0363
(((.((........)))))(	chr11:46817154-46817355(-)$1	1	93	113	12.5315
((((((........))))))	chr16:461450-461651(+)$1	1	17	37	14.1186
..((((........))))..	chr11:46839899-46840100(-)$1	1	65	85	15.2110
.(((((........))))).	chr7:158464161-158464362(-)$1	1	179	199	12.8528
((((((........)))).)	chr5:94927035-94927236(+)$1	1	164	184	14.9731
(((.((........)).)))	chr22:18377967-18378168(-)$1	1	147	167	13.4000
((((((........))))))	chr9:131356453-131356654(+)$1	1	153	173	14.1186
((((((........))))))	chr1:75217981-75218182(+)$1	1	13	33	14.0492
((((((........))))))	chr1:153733259-153733460(+)$1	1	54	74	13.4384
((((.(........))))))	chr4:6862567-6862768(+)$1	1	127	147	13.5378
((((((........))))))	chr11:93429803-93430004(+)$1	1	144	164	13.4384
(((.((........))))).	chr10:101606648-101606849(+)$1	1	29	49	12.8125
.(((((........))))).	chrX:23803832-23804033(+)$1	1	16	36	14.7731
((((((........)))).)	chr10:70958149-70958350(+)$1	1	9	29	14.5907
(.((((........))))))	chr12:6701855-6702056(-)$1	1	102	122	14.3499
..((((........)))).)	chr8:68200110-68200311(-)$1	1	85	105	14.9606
((((((........))))))	chr11:3714477-3714678(-)$1	1	10	30	14.0492
((((((........)))).)	chr18:20562227-20562428(+)$1	1	35	55	14.7638
((.(((........))).))	chr3:197562460-197562661(+)$1	1	181	201	13.6251
.(((((........))))).	chr11:33127039-33127240(-)$1	1	5	25	14.6504
((((((........))))))	chr21:30342916-30343117(-)$1	1	71	91	14.1186
(.((((........))))..	chr7:107545805-107546006(+)$1	1	115	135	15.3670
.(((((........))))).	chr3:52941122-52941323(-)$1	1	59	79	14.6207
(.((((........))))))	chr14:53341898-53342099(-)$1	1	163	183	14.2500
.(((((........))))).	chr17:45012342-45012543(+)$1	1	111	131	12.8528
.(((((........))))).	chr22:36682692-36682893(-)$1	1	138	158	14.6207
(.((((........)))).)	chr1:1563949-1564150(+)$1	1	47	67	15.2042
(.((((........)))).)	chr8:48809708-48809909(-)$1	1	52	72	14.9210
(.((((........)))).)	chr3:66436484-66436685(-)$1	1	114	134	15.1969
((((((........))))))	chr5:37183584-37183785(-)$1	1	102	122	13.4384
(.((((........)))).)	chr14:100705563-100705764(+)$1	1	51	71	14.7943
((.(((........))))))	chr12:121747565-121747766(-)$1	1	84	104	14.1437
))((((........)))).(	chr11:9435800-9436001(+)$1	1	105	125	13.6794
..((((........))))))	chr13:77655935-77656136(-)$1	1	173	193	14.5507
((((((........))))))	chr10:104103719-104103920(+)$1	1	69	89	13.4384
((((.(........).))))	chr14:31077105-31077306(+)$1	1	179	199	13.9051
((((((........))))))	chr5:72377667-72377868(+)$1	1	24	44	13.4384
..((((........))).).	chr2:230923904-230924105(-)$1	1	109	129	14.9784
.(((((........))))).	chr17:28512555-28512756(+)$1	1	95	115	12.8528
.(((((........))))).	chr2:74594103-74594304(-)$1	1	139	159	14.5392
...(((........)))...	chr11:9167173-9167374(-)$1	1	81	101	14.7808
((.(((........))))))	chr12:70297417-70297618(+)$1	1	49	69	14.5615
(((.((........))...)	chr22:24493984-24494185(+)$1	1	171	191	13.4928
.(.(((........))).).	chr11:134048718-134048919(-)$1	1	148	168	14.4189
.(((((........))))).	chr19:18420184-18420385(-)$1	1	138	158	14.5926
(((.((........))))).	chr2:71627163-71627364(+)$1	1	112	132	13.7885
((..((........))..))	chr8:53569565-53569766(-)$1	1	120	140	12.8233
((((((........))))..	chr3:160231820-160232021(-)$1	1	103	123	13.5484
((((.(........).))))	chr21:37744630-37744831(+)$1	1	145	165	13.4626
(..(((........)))..)	chr8:97270620-97270821(-)$1	1	171	191	14.2305

#PSSM
f : 0.15	d : 0.13	c : 0.13	e : 0.09	g : 0.07	! : 0.06	: : 0.06	# : 0.06	[ : 0.04	b : 0.04	" : 0.03	i : 0.03	$ : 0.03	+ : 0.01	h : 0.01	a : 0.01	
e : 0.22	f : 0.15	[ : 0.13	c : 0.10	! : 0.07	d : 0.07	g : 0.07	b : 0.03	" : 0.03	# : 0.03	i : 0.03	$ : 0.01	a : 0.01	
d : 0.31	e : 0.19	f : 0.13	[ : 0.09	! : 0.06	g : 0.06	c : 0.06	i : 0.03	b : 0.01	a : 0.01	# : 0.01	
d : 0.30	c : 0.18	e : 0.18	f : 0.13	[ : 0.09	g : 0.06	i : 0.03	! : 0.01	
d : 0.30	c : 0.18	e : 0.16	f : 0.10	b : 0.10	g : 0.06	[ : 0.04	i : 0.03	
d : 0.30	c : 0.18	e : 0.16	f : 0.10	b : 0.10	g : 0.06	a : 0.04	i : 0.03	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
d : 0.30	c : 0.18	e : 0.16	f : 0.10	b : 0.10	g : 0.06	a : 0.04	i : 0.03	
d : 0.30	c : 0.18	e : 0.16	f : 0.12	b : 0.10	g : 0.06	i : 0.03	] : 0.03	
d : 0.30	c : 0.22	e : 0.18	f : 0.13	g : 0.06	] : 0.03	i : 0.03	3 : 0.01	2 : 0.01	
d : 0.34	e : 0.18	f : 0.13	c : 0.07	3 : 0.06	] : 0.06	g : 0.06	i : 0.03	2 : 0.03	4 : 0.01	
e : 0.21	f : 0.13	] : 0.12	c : 0.10	3 : 0.07	g : 0.06	d : 0.04	b : 0.04	4 : 0.04	5 : 0.03	2 : 0.03	i : 0.03	a : 0.03	h : 0.01	: : 0.01	
f : 0.13	3 : 0.12	d : 0.09	c : 0.09	e : 0.07	b : 0.07	: : 0.07	g : 0.06	4 : 0.06	2 : 0.04	i : 0.04	] : 0.04	5 : 0.03	D : 0.01	h : 0.01	a : 0.01	

#score	932.647605880198
#seq	66
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_CDS_m1_run2.txt

#BEAR
ggggggg[a[aooooooa]a]gggggg	chr3:12880818-12881069(-)$1	251	170	197	9.7908
ee####ffffffnnnnnffffffeeee	chr9:21968045-21968316(-)$1	271	188	215	11.4813
###dddd!!cccnnnnnccc333dddd	chr4:147103976-147104231(+)$1	255	62	89	13.3152
fff:eeeeecccnnnnnccc22eeeee	chr22:24236858-24237115(+)$1	257	117	144	11.8685
+ffffff"""annnnna333ffffff3	chr21:34924584-34924967(+)$1	383	35	62	11.3177
fff[ccc[ddddoooooodddd]ccc]	chr1:118476995-118477226(+)$1	231	116	143	9.1900
ggggggg[cccooooooccc]gggggg	chr16:2011405-2011691(+)$1	286	173	200	10.2561
c"""eeeee[bbnnnnnbb]eeeee33	chr4:74005417-74005659(-)$1	242	190	217	11.5462
eeeee####cccnnnnnccc333eeee	chr1:67880870-67881098(-)$1	228	118	145	14.5100
[bb!!cccddddnnnnndddd]ccc22	chr19:58199165-58199395(+)$1	230	169	196	11.7298
cccccc[addddnnnnndddd]a]ccc	chr20:2448193-2448451(-)$1	258	132	159	12.5529
"dddd[bb[cccnnnnnccc]bb]ddd	chr14:51561116-51561356(-)$1	240	148	175	11.9673
fff!!dddd[bbnnnnnbb22ddddff	chr1:113471635-113471892(-)$1	257	177	204	11.1125
=ffffff!!cccnnnnncccffffff3	chr11:47444346-47444576(-)$1	230	144	171	14.1645
#ccc[gggggggoooooogggggggcc	chr1:150550837-150551066(-)$1	229	126	153	8.9126
ba[eeeee[cccnnnnnccceeeee]a	chr2:27008946-27009191(+)$1	245	90	117	12.6222
fff"""dddd[annnnna]ddddffff	chr1:87329063-87329288(-)$1	225	47	74	12.1944
dffffff"""bbnnnnnbb22ffffff	chr10:51592492-51592716(-)$1	224	172	199	12.7299
ee:ggggggg[annnnna]ggggggg:	chr15:69745096-69745423(+)$1	327	226	253	10.5459
fffff"""ddddnnnnnddddffffff	chr19:39926387-39926679(-)$1	292	155	182	13.3217
[ffffff"""ccclllccc4444ffff	chr7:75689678-75689916(+)$1	238	121	148	10.0528
!dddd[ffffffnnnnnffffff]ddd	chr21:27097534-27097760(-)$1	226	57	84	10.8756
###ccc[eeeeennnnneeeee]ccc7	chr16:70597694-70597947(+)$1	253	168	195	11.1004
d[ccc!!addddnnnnndddd]a22cc	chr6:27100234-27100536(-)$1	302	140	167	12.4206
eeeee[bb[cccnnnnnccc]bbeeee	chr2:242206181-242206423(-)$1	242	115	142	12.6664
###ccc[eeeeennnnneeeeeccc]e	chr1:169094024-169094254(+)$1	230	164	191	11.5513
ffffff[bb!!annnnna22bb]ffff	chr2:198285682-198285912(-)$1	230	119	146	11.6093
ccc!!eeeeebbnnnnnbb333eeeee	chr1:24022205-24022432(+)$1	227	55	82	12.2461
ddd!!gggggggnnnnnggggggg]dd	chrX:70782675-70782899(+)$1	224	84	111	11.9800
:===========nnnnn==========	chr17:62497990-62498233(-)$1	243	162	189	12.2451
ffffff"""cccnnnnncccffffff5	chr12:133778924-133779152(+)$1	228	100	127	13.4191
ccc[ccc"""bbnnnnnbb333ccccc	chr19:50358012-50358236(+)$1	224	181	208	13.1228
[eeeee"""cccnnnnnccc4444eee	chr11:57099216-57099452(-)$1	236	70	97	14.4401
ggggg!!eeeeennnnneeeeeggggg	chr5:82849097-82849328(+)$1	231	4	31	12.1110
:ffffff[cccooooooccc]ffffff	chr1:87569103-87569324(+)$1	221	177	204	9.3546
ffff!!ffffffnnnnnffffff22ff	chr12:6601333-6601613(-)$1	280	8	35	11.7076
eeeee####cccnnnnnccc22eeeee	chr1:32495809-32496033(+)$1	224	92	119	13.7809
d!!dddd!!cccnnnnnccc]dddd22	chr17:7478337-7478604(+)$1	267	182	209	12.3295
!dddd####cccooooooccc4444dd	chr20:30386183-30386426(+)$1	243	151	178	9.7489
eeeeegggggggnnnnnggggggg333	chr17:30696542-30696797(+)$1	255	98	125	12.3790
g[eeeee!!ccclllccc4444eeeee	chrX:107978308-107978536(-)$1	228	62	89	9.3181
fffff!!eeeeennnnneeeee22fff	chr6:34826446-34826673(+)$1	227	197	224	12.0114
c[ffffff[cccnnnnnccc]ffffff	chr22:29727687-29727921(-)$1	234	104	131	13.8565
d[ffffff[cccnnnnnccc]ffffff	chr6:41062089-41062318(+)$1	229	105	132	13.7411
fff!!bb[ddddnnnnnddddbb22ff	chr14:96010333-96010595(+)$1	262	69	96	11.8650
gg"""ccc[ccclllccc]ccc]gggg	chr16:81053646-81053879(+)$1	233	50	77	8.9543
gggggg!!ddddnnnnndddd333ggg	chr19:57802407-57802630(+)$1	223	21	48	13.6451
hhh[bb[ccc[annnnna]cccbb]hh	chr1:24019066-24019291(+)$1	225	89	116	10.5793
bb"""bb[ddddnnnnndddd]bbbb]	chr16:30002372-30002621(+)$1	249	197	224	10.7368
=="""ccc[cccnnnnncccccc22==	chr12:49666504-49666739(+)$1	235	85	112	13.1583
eeeee####cccnnnnnccc4444eee	chr5:134007401-134007622(+)$1	221	165	192	14.3071
!!eeeee"""aooooooa333eeeee2	chr3:139092511-139092740(-)$1	229	195	222	9.8285
""ffffffddddnnnnndddd333fff	chr19:42462790-42463037(-)$1	247	42	69	13.0988
eeeee"""ddddnnnnndddd333eee	chr19:50002691-50003021(+)$1	330	147	174	13.5013
fffff"""ddddnnnnndddd4444ff	chr16:71482090-71482315(-)$1	225	131	158	13.4809
!ffffff"""bbnnnnnbb4444ffff	chr19:40741075-40741311(-)$1	236	79	106	13.5662
ddd!!gggggggnnnnngggggggddd	chr10:43882107-43882390(-)$1	283	42	69	11.8679
fffffff"""bbnnnnnbbffffffdd	chr13:41705205-41705443(-)$1	238	40	67	12.4576
ee[dddd[ddddnnnnndddd]dddd]	chr7:26232866-26233092(-)$1	226	85	112	11.7141

#otherMatches

#Seq PSSM
AGUUCCUGGUCCACAACGUCAAGGAGC	chr3:12880818-12881069(-)$1	251	170	197	9.7908
UUCGUAGUUUUCAUUUAGAAAAUAGAG	chr9:21968045-21968316(-)$1	271	188	215	11.4813
UGUUCCUUUUCAUAUUUUGAUUUAGGA	chr4:147103976-147104231(+)$1	255	62	89	13.3152
GGUCCCGGACCAGCUCAUGGCCUUCGG	chr22:24236858-24237115(+)$1	257	117	144	11.8685
UGGCUGAACGCUCUAUGAUGUCAGCCU	chr21:34924584-34924967(+)$1	383	35	62	11.3177
GGCUUAAACAAGAAGUUACUUGCUUAU	chr1:118476995-118477226(+)$1	231	116	143	9.1900
GAACUGUAUCAAGGAAGUGGAGCAGUU	chr16:2011405-2011691(+)$1	286	173	200	10.2561
CUCUGGCGAUGCCUCAAGCUUUGCCUC	chr4:74005417-74005659(-)$1	242	190	217	11.5462
CCAGCAAAUGAUAUAACGUCUCAGCUG	chr1:67880870-67881098(-)$1	228	118	145	14.5100
UGGAAAGUCUUUUAGCCAAAGUGCUAG	chr19:58199165-58199395(+)$1	230	169	196	11.7298
CCUUCAAGGCUUUUGACAAGCACAUGA	chr20:2448193-2448451(-)$1	258	132	159	12.5529
ACUGGAAGGGGUAAUUGACCGCUACCA	chr14:51561116-51561356(-)$1	240	148	175	11.9673
AGGUAAGUACCCAUUAAGGCCUGCUCU	chr1:113471635-113471892(-)$1	257	177	204	11.1125
CCCAGGGACGGGGAAGACCCUCCUGGC	chr11:47444346-47444576(-)$1	230	144	171	14.1645
ACGAAGACGAUGUGAAAUCGUUGUCUC	chr1:150550837-150551066(-)$1	229	126	153	8.9126
CGGGCGCCAGCACCCUCUGCGGCGUGU	chr2:27008946-27009191(+)$1	245	90	117	12.6222
GAACAUUGCUGAAGAACUGAGCAUUCU	chr1:87329063-87329288(-)$1	225	47	74	12.1944
GGGAGCACAUGAAAGGCUCCUUGCUCC	chr10:51592492-51592716(-)$1	224	172	199	12.7299
GGCCCUCAUUCUGCACGACGAUGAGGU	chr15:69745096-69745423(+)$1	327	226	253	10.5459
GGGCCCGCUGCAGUCUGUGCAGGUCUU	chr19:39926387-39926679(-)$1	292	155	182	13.3217
UUGUUGCAGAGCUGAAGGUAAGGGCGG	chr7:75689678-75689916(+)$1	238	121	148	10.0528
UAGUACACAAAAUUAAUUUUUGUUUGC	chr21:27097534-27097760(-)$1	226	57	84	10.8756
CCCUGAGAGUAACAACCUUAUUAUCAU	chr16:70597694-70597947(+)$1	253	168	195	11.1004
UUCUGAAGCAGGUCCACCCUGACACCG	chr6:27100234-27100536(-)$1	302	140	167	12.4206
UUGUGUGUAGGUGUGAGAUCAACCAUG	chr2:242206181-242206423(-)$1	242	115	142	12.6664
UGAGGCAUAUGUACUGAACAUAGUUAG	chr1:169094024-169094254(+)$1	230	164	191	11.5513
CUGUGGCAUUGCUUAAUGAUAUACCAC	chr2:198285682-198285912(-)$1	230	119	146	11.6093
GGUGACUGUUGGUUAUUCCUGGGACAG	chr1:24022205-24022432(+)$1	227	55	82	12.2461
CAGGAAACUUCGCCAGCUGAAGUUGCU	chrX:70782675-70782899(+)$1	224	84	111	11.9800
UUUAAAGAAAGUUUAUUGCUUUCUUUA	chr17:62497990-62498233(-)$1	243	162	189	12.2451
UAUUGAAUCUGGAAAAACCGUCAAUAA	chr12:133778924-133779152(+)$1	228	100	127	13.4191
GGCUGACCCAGCUGUCUGUCCUGUCGC	chr19:50358012-50358236(+)$1	224	181	208	13.1228
UCCCUGCACCCUCUGUCAGGCACUCAG	chr11:57099216-57099452(-)$1	236	70	97	14.4401
UAUCCUACUAACACUUGGUUGGGGGUG	chr5:82849097-82849328(+)$1	231	4	31	12.1110
AGGAAGGGUUUCUUUUUAAAGCUUUCU	chr1:87569103-87569324(+)$1	221	177	204	9.3546
GAUCAGGGGGCCCAUAUGGCUUCGAGG	chr12:6601333-6601613(-)$1	280	8	35	11.7076
UUGAGAAGAUUCAGAAAGGAGACUCAA	chr1:32495809-32496033(+)$1	224	92	119	13.7809
GAUCUAAAAGCCACCCAGGCCUUGGUC	chr17:7478337-7478604(+)$1	267	182	209	12.3295
GCCAGGCUACGGAGAGAACUGGUAACU	chr20:30386183-30386426(+)$1	243	151	178	9.7489
GGCAUGCCAGGAUACCUUCCUGGUGCU	chr17:30696542-30696797(+)$1	255	98	125	12.3790
GCCGGGAGGCUGGCUCAGAAGGUCCCG	chrX:107978308-107978536(-)$1	228	62	89	9.3181
UCUGCUUCGCCUGAAGGAGGUGCUGCA	chr6:34826446-34826673(+)$1	227	197	224	12.0114
GUGGGCUCGGUCAUGAAGAUGGAGCCU	chr22:29727687-29727921(-)$1	234	104	131	13.8565
CGAUUUUUCUCUCCAAAGGAAAAGGAU	chr6:41062089-41062318(+)$1	229	105	132	13.7411
AAAAAGCUGGGGAUCCACUCCGCCCUU	chr14:96010333-96010595(+)$1	262	69	96	11.8650
UUAAUAAGGUGACAGUCAGCUUCAGAG	chr16:81053646-81053879(+)$1	233	50	77	8.9543
GAGGAAAUGUUUAAUGAGAAUUGCUUC	chr19:57802407-57802630(+)$1	223	21	48	13.6451
CUCAACAUCUGUGUUGGGGAGAGUGGA	chr1:24019066-24019291(+)$1	225	89	116	10.5793
GUCCCGUUCCCCGUUCUGGGGCACACU	chr16:30002372-30002621(+)$1	249	197	224	10.7368
UAAAUACAUGGCUUGCUGCCUGUUAUA	chr12:49666504-49666739(+)$1	235	85	112	13.1583
GGCUUAUUGGGUGAGAUGCUAUGAAAG	chr5:134007401-134007622(+)$1	221	165	192	14.3071
UCGCUUUGGGCUAUGAUGAAGGGAGCA	chr3:139092511-139092740(-)$1	229	195	222	9.8285
CUCACGGCCCCGCAACCUGGGAGAGCU	chr19:42462790-42463037(-)$1	247	42	69	13.0988
GUGCUCAAGGUCACCAAGGCUGCCGGC	chr19:50002691-50003021(+)$1	330	147	174	13.5013
CACACUGGGGAGAAACCCUUCAGAUGU	chr16:71482090-71482315(-)$1	225	131	158	13.4809
AAGGAGGUCAUGGAGCACAGGUUCUUC	chr19:40741075-40741311(-)$1	236	79	106	13.5662
GGUGAAGCAGAUGUUGAGUUUGCUACU	chr10:43882107-43882390(-)$1	283	42	69	11.8679
GCAGCAACUUGCAGAUCGCUUGCUGUG	chr13:41705205-41705443(-)$1	238	40	67	12.4576
CAAUUUUUUAAUAGGAAAUUAUGGAAG	chr7:26232866-26233092(-)$1	226	85	112	11.7141

#DB
(((((((.(.(......).).))))))	chr3:12880818-12881069(-)$1	1	170	197	9.7908
((....((((((.....))))))))))	chr9:21968045-21968316(-)$1	1	188	215	11.4813
...((((..(((.....)))...))))	chr4:147103976-147104231(+)$1	1	62	89	13.3152
))).((((((((.....)))..)))))	chr22:24236858-24237115(+)$1	1	117	144	11.8685
.((((((...(.....)...)))))).	chr21:34924584-34924967(+)$1	1	35	62	11.3177
(((.(((.((((......)))).))).	chr1:118476995-118477226(+)$1	1	116	143	9.1900
(((((((.(((......))).))))))	chr16:2011405-2011691(+)$1	1	173	200	10.2561
(...(((((.((.....)).)))))..	chr4:74005417-74005659(-)$1	1	190	217	11.5462
(((((....(((.....)))...))))	chr1:67880870-67881098(-)$1	1	118	145	14.5100
.((..(((((((.....)))).)))..	chr19:58199165-58199395(+)$1	1	169	196	11.7298
)))(((.(((((.....)))).).)))	chr20:2448193-2448451(-)$1	1	132	159	12.5529
.((((.((.(((.....))).)).)))	chr14:51561116-51561356(-)$1	1	148	175	11.9673
(((..((((.((.....))..))))))	chr1:113471635-113471892(-)$1	1	177	204	11.1125
(((((((..(((.....))))))))).	chr11:47444346-47444576(-)$1	1	144	171	14.1645
.(((.(((((((......)))))))))	chr1:150550837-150551066(-)$1	1	126	153	8.9126
((.(((((.(((.....)))))))).)	chr2:27008946-27009191(+)$1	1	90	117	12.6222
(((...((((.(.....).))))))))	chr1:87329063-87329288(-)$1	1	47	74	12.1944
(((((((...((.....))..))))))	chr10:51592492-51592716(-)$1	1	172	199	12.7299
)).(((((((.(.....).))))))).	chr15:69745096-69745423(+)$1	1	226	253	10.5459
(((((...((((.....))))))))))	chr19:39926387-39926679(-)$1	1	155	182	13.3217
.((((((...(((...)))....))))	chr7:75689678-75689916(+)$1	1	121	148	10.0528
.((((.((((((.....)))))).)))	chr21:27097534-27097760(-)$1	1	57	84	10.8756
...(((.(((((.....))))).))).	chr16:70597694-70597947(+)$1	1	168	195	11.1004
(.(((..(((((.....)))).)..))	chr6:27100234-27100536(-)$1	1	140	167	12.4206
(((((.((.(((.....))).))))))	chr2:242206181-242206423(-)$1	1	115	142	12.6664
...(((.(((((.....)))))))).)	chr1:169094024-169094254(+)$1	1	164	191	11.5513
((((((.((..(.....)..)).))))	chr2:198285682-198285912(-)$1	1	119	146	11.6093
(((..(((((((.....))...)))))	chr1:24022205-24022432(+)$1	1	55	82	12.2461
(((..(((((((.....))))))).))	chrX:70782675-70782899(+)$1	1	84	111	11.9800
.(((((((((((.....))))))))))	chr17:62497990-62498233(-)$1	1	162	189	12.2451
((((((...(((.....))))))))).	chr12:133778924-133779152(+)$1	1	100	127	13.4191
(((.(((...((.....))...)))))	chr19:50358012-50358236(+)$1	1	181	208	13.1228
.(((((...(((.....)))....)))	chr11:57099216-57099452(-)$1	1	70	97	14.4401
(((((..(((((.....))))))))))	chr5:82849097-82849328(+)$1	1	4	31	12.1110
.((((((.(((......))).))))))	chr1:87569103-87569324(+)$1	1	177	204	9.3546
((((..((((((.....))))))..))	chr12:6601333-6601613(-)$1	1	8	35	11.7076
(((((....(((.....)))..)))))	chr1:32495809-32496033(+)$1	1	92	119	13.7809
(..((((..(((.....))).))))..	chr17:7478337-7478604(+)$1	1	182	209	12.3295
.((((....(((......)))....))	chr20:30386183-30386426(+)$1	1	151	178	9.7489
((((((((((((.....)))))))...	chr17:30696542-30696797(+)$1	1	98	125	12.3790
(.(((((..(((...)))....)))))	chrX:107978308-107978536(-)$1	1	62	89	9.3181
(((((..(((((.....)))))..)))	chr6:34826446-34826673(+)$1	1	197	224	12.0114
(.((((((.(((.....))).))))))	chr22:29727687-29727921(-)$1	1	104	131	13.8565
(.((((((.(((.....))).))))))	chr6:41062089-41062318(+)$1	1	105	132	13.7411
(((..((.((((.....))))))..))	chr14:96010333-96010595(+)$1	1	69	96	11.8650
((...(((.(((...))).))).))))	chr16:81053646-81053879(+)$1	1	50	77	8.9543
((((((..((((.....))))...)))	chr19:57802407-57802630(+)$1	1	21	48	13.6451
(((.((.(((.(.....).))))).))	chr1:24019066-24019291(+)$1	1	89	116	10.5793
((...((.((((.....)))).)))).	chr16:30002372-30002621(+)$1	1	197	224	10.7368
((...(((.(((.....))))))..))	chr12:49666504-49666739(+)$1	1	85	112	13.1583
(((((....(((.....)))....)))	chr5:134007401-134007622(+)$1	1	165	192	14.3071
..(((((...(......)...))))).	chr3:139092511-139092740(-)$1	1	195	222	9.8285
..((((((((((.....))))...)))	chr19:42462790-42463037(-)$1	1	42	69	13.0988
(((((...((((.....))))...)))	chr19:50002691-50003021(+)$1	1	147	174	13.5013
(((((...((((.....))))....))	chr16:71482090-71482315(-)$1	1	131	158	13.4809
.((((((...((.....))....))))	chr19:40741075-40741311(-)$1	1	79	106	13.5662
(((..(((((((.....))))))))))	chr10:43882107-43882390(-)$1	1	42	69	11.8679
)((((((...((.....))))))))((	chr13:41705205-41705443(-)$1	1	40	67	12.4576
((.((((.((((.....)))).)))).	chr7:26232866-26233092(-)$1	1	85	112	11.7141

#PSSM
f : 0.20	e : 0.15	g : 0.10	d : 0.10	c : 0.08	# : 0.06	! : 0.06	[ : 0.05	" : 0.03	= : 0.03	b : 0.03	: : 0.03	+ : 0.01	h : 0.01	
f : 0.30	e : 0.16	g : 0.08	d : 0.08	c : 0.06	[ : 0.06	# : 0.05	" : 0.03	b : 0.03	= : 0.03	! : 0.03	a : 0.01	h : 0.01	
f : 0.35	e : 0.15	c : 0.08	d : 0.08	g : 0.06	# : 0.06	" : 0.06	[ : 0.03	b : 0.01	: : 0.01	= : 0.01	! : 0.01	h : 0.01	
f : 0.27	e : 0.16	d : 0.10	! : 0.10	g : 0.08	" : 0.08	c : 0.08	[ : 0.05	# : 0.01	: : 0.01	= : 0.01	
f : 0.25	e : 0.20	! : 0.11	d : 0.10	c : 0.10	g : 0.08	" : 0.06	# : 0.01	[ : 0.01	= : 0.01	b : 0.01	
f : 0.20	g : 0.13	c : 0.13	e : 0.11	# : 0.08	d : 0.06	" : 0.06	! : 0.06	[ : 0.05	b : 0.05	= : 0.01	
f : 0.22	g : 0.11	e : 0.10	d : 0.08	c : 0.08	[ : 0.08	" : 0.08	# : 0.06	b : 0.06	! : 0.06	= : 0.01	
" : 0.20	e : 0.13	[ : 0.11	f : 0.10	! : 0.08	g : 0.08	# : 0.06	c : 0.06	b : 0.05	a : 0.03	d : 0.03	= : 0.01	
d : 0.23	" : 0.15	e : 0.11	[ : 0.11	g : 0.08	! : 0.06	# : 0.06	f : 0.05	c : 0.05	a : 0.01	b : 0.01	= : 0.01	
c : 0.35	d : 0.22	" : 0.11	g : 0.08	e : 0.08	[ : 0.05	f : 0.05	! : 0.01	= : 0.01	
c : 0.35	d : 0.20	b : 0.11	g : 0.06	e : 0.06	a : 0.05	f : 0.05	[ : 0.05	! : 0.01	= : 0.01	
c : 0.32	d : 0.20	b : 0.11	o : 0.06	g : 0.06	a : 0.06	e : 0.06	f : 0.05	n : 0.01	= : 0.01	
n : 0.83	o : 0.11	l : 0.03	c : 0.01	
n : 0.83	o : 0.11	l : 0.05	
n : 0.83	o : 0.11	l : 0.05	
n : 0.83	o : 0.11	c : 0.03	l : 0.01	
n : 0.81	o : 0.11	c : 0.05	a : 0.01	
c : 0.33	d : 0.18	b : 0.11	a : 0.10	e : 0.06	f : 0.05	o : 0.05	g : 0.05	3 : 0.01	= : 0.01	
c : 0.32	d : 0.20	b : 0.11	] : 0.08	g : 0.06	e : 0.06	f : 0.05	3 : 0.03	2 : 0.01	= : 0.01	4 : 0.01	
c : 0.33	d : 0.22	g : 0.08	f : 0.06	3 : 0.06	e : 0.06	2 : 0.05	4 : 0.05	a : 0.01	] : 0.01	= : 0.01	
d : 0.22	] : 0.13	f : 0.11	e : 0.10	3 : 0.08	g : 0.08	4 : 0.08	2 : 0.06	c : 0.06	b : 0.01	= : 0.01	
f : 0.20	g : 0.11	3 : 0.11	e : 0.11	4 : 0.11	] : 0.08	d : 0.06	b : 0.06	c : 0.05	2 : 0.03	= : 0.01	
f : 0.20	g : 0.13	e : 0.11	4 : 0.10	3 : 0.08	b : 0.08	] : 0.06	c : 0.06	d : 0.06	a : 0.03	= : 0.01	2 : 0.01	
f : 0.22	e : 0.16	g : 0.15	c : 0.08	2 : 0.08	d : 0.06	4 : 0.06	] : 0.05	3 : 0.05	b : 0.03	= : 0.01	
f : 0.25	e : 0.22	g : 0.11	d : 0.11	c : 0.10	2 : 0.06	] : 0.03	4 : 0.03	= : 0.01	3 : 0.01	b : 0.01	
f : 0.30	e : 0.18	d : 0.13	g : 0.10	c : 0.10	3 : 0.03	2 : 0.03	] : 0.03	= : 0.03	h : 0.01	b : 0.01	
f : 0.25	e : 0.18	d : 0.11	g : 0.08	3 : 0.06	c : 0.06	] : 0.05	2 : 0.05	= : 0.03	a : 0.01	: : 0.01	7 : 0.01	5 : 0.01	h : 0.01	

#score	705.9619914641046
#seq	59
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_UTR_m3_run1.txt

#BEAR
iiiiiiooooooiiiii	chr1:201847793-201847994(+)$1	201	64	81	10.5028
:eeeeeooooooeeeee	chr19:3053720-3053921(-)$1	201	171	188	11.9063
:eeeeeooooooeeeee	chr10:70252812-70253013(-)$1	201	22	39	11.9063
ceeeeeooooooeeeee	chr1:100614520-100614721(-)$1	201	116	133	12.6470
ccc!!aooooooa22cc	chr16:547251-547452(+)$1	201	110	127	9.8102
ee[cccoooooocccee	chr5:71482454-71482655(+)$1	201	159	176	11.1297
ggggggooooooggggg	chr11:129939853-129940054(+)$1	201	90	107	10.9054
ffffffoooooofffff	chr16:22334078-22334279(+)$1	201	54	71	10.5915
f[ddddoooooodddd2	chr19:56614676-56614877(-)$1	201	90	107	10.7672
Deeeeeooooooeeeee	chr9:139743235-139743436(+)$1	201	183	200	11.7352
ffffffoooooofffff	chr21:45749400-45749601(-)$1	201	39	56	10.5915
c[ddddoooooodddd]	chr14:24028075-24028276(+)$1	201	52	69	11.1395
:eeeeeooooooeeeee	chr16:731974-732175(-)$1	201	179	196	11.9063
eeeeeeooooooeeeee	chr16:89350359-89350560(-)$1	201	179	196	12.5023
%eeeeeooooooeeeee	chr6:11138712-11138913(+)$1	201	152	169	12.1616
eeee[aooooooaeeee	chr2:48033626-48033827(+)$1	201	2	19	11.9623
hhhcccooooooccc]h	chr13:79886367-79886568(-)$1	201	130	147	9.8191
:eeeeeooooooeeeee	chr10:74631139-74631340(+)$1	201	7	24	11.9063
ffffffoooooofffff	chr14:24910091-24910292(-)$1	201	43	60	10.5915
[eeeeeooooooeeeee	chr2:8943094-8943295(-)$1	201	182	199	12.7459
ccccccooooooccc]c	chr13:30087763-30087964(-)$1	201	139	156	10.5162
!ccc[aooooooa]ccc	chr5:65455052-65455253(+)$1	201	45	62	10.6028
ffff[aooooooaffff	chr16:30771915-30772116(+)$1	201	174	191	10.6235
ffffffoooooofffff	chr8:95853648-95853849(+)$1	201	9	26	10.5915
ggggggooooooggggg	chr15:83687429-83687630(-)$1	201	76	93	10.9054
Jeeeeeooooooeeeee	chr3:195792315-195792516(-)$1	201	38	55	11.3463
!!ddddooooooddddd	chr1:53516281-53516482(+)$1	201	91	108	11.1202
[eeeeeooooooeeeee	chr3:12876977-12877178(-)$1	201	97	114	12.7459
!eeeeeooooooeeeee	chr16:87732864-87733065(-)$1	201	150	167	12.7753
!eeeeeooooooeeeee	chr2:207025672-207025873(+)$1	201	16	33	12.7753
ffffffoooooofffff	chr17:79532298-79532499(-)$1	201	126	143	10.5915
:eeeeeooooooeeeee	chr5:176980578-176980779(-)$1	201	31	48	11.9063
dddd[aooooooa]ddd	chr20:3764841-3765042(-)$1	201	76	93	10.4675
bbddddooooooddddc	chr10:75557132-75557333(+)$1	201	108	125	10.4422
ffffffoooooofffff	chr19:55897389-55897590(+)$1	201	115	132	10.5915
[eeeeeooooooeeeee	chrX:64738120-64738321(-)$1	201	13	30	12.7459
:eeeeeooooooeeeee	chr17:61907681-61907882(+)$1	201	5	22	11.9063
ffffffoooooofffff	chr15:72499414-72499615(-)$1	201	175	192	10.5915
[eeeeeooooooeeeee	chr1:76199149-76199350(+)$1	201	34	51	12.7459
d[ddddoooooodddd]	chr8:82571567-82571768(-)$1	201	106	123	10.9733
d[ddddoooooodddd9	chr17:29556282-29556483(+)$1	201	63	80	10.2311
deeeeeooooooeeeee	chr3:44839006-44839207(+)$1	201	110	127	12.4808
!!ddddoooooodddd]	chr3:42662828-42663029(+)$1	201	64	81	11.2324
:eeeeeooooooeeeee	chr10:5807881-5808082(-)$1	201	31	48	11.9063
cc[cccooooooccc]c	chr16:31225253-31225454(+)$1	201	121	138	10.5513
#eeeeeooooooeeeee	chr11:3756377-3756578(-)$1	201	103	120	12.6906
eee[bboooooobb]ee	chr1:166821936-166822137(+)$1	201	97	114	10.0501
""ddddoooooodddd4	chr20:54944803-54945004(-)$1	201	136	153	10.9587
ffffffoooooofffff	chr2:48025687-48025888(+)$1	201	179	196	10.5915
""ddddooooooddddb	chr3:121150999-121151200(-)$1	201	80	97	10.7017
ggggggooooooggggg	chr19:3536313-3536514(+)$1	201	143	160	10.9054
ccddddoooooodddd:	chr3:108285280-108285481(-)$1	201	138	155	10.0007
ccddddoooooodddd2	chr12:132623502-132623703(-)$1	201	120	137	10.7651
ggggggooooooggggg	chr1:43637815-43638016(-)$1	201	5	22	10.9054
$eeeeeooooooeeeee	chr21:30428611-30428812(-)$1	201	48	65	12.5343
ee[cccoooooocccee	chr19:17322946-17323147(+)$1	201	154	171	11.1297

#otherMatches

#Seq PSSM
gaguggauauucccauu	chr1:201847793-201847994(+)$1	201	64	81	10.5028
AUGUUUAGCACAAGACA	chr19:3053720-3053921(-)$1	201	171	188	11.9063
AUGUAAUCUCACUUGCA	chr10:70252812-70253013(-)$1	201	22	39	11.9063
AUGGAUAAUAUAAUUCA	chr1:100614520-100614721(-)$1	201	116	133	12.6470
GUUCUUACCGAAAUAAA	chr16:547251-547452(+)$1	201	110	127	9.8102
AGUGGCUUGGUUGCCUU	chr5:71482454-71482655(+)$1	201	159	176	11.1297
GGCGCCUGCCUUGGCGC	chr11:129939853-129940054(+)$1	201	90	107	10.9054
GGCAGGGACUGACCUGC	chr16:22334078-22334279(+)$1	201	54	71	10.5915
GGCCCCUGCAGUGGGGA	chr19:56614676-56614877(-)$1	201	90	107	10.7672
GGAGGGGGGAGGCCUUC	chr9:139743235-139743436(+)$1	201	183	200	11.7352
CUCCCGCACCCAUGGGA	chr21:45749400-45749601(-)$1	201	39	56	10.5915
AGUGUCCCUUCUGACAG	chr14:24028075-24028276(+)$1	201	52	69	11.1395
UUGGGGGAGACACCCCA	chr16:731974-732175(-)$1	201	179	196	11.9063
AGCUGGGACUCGCCAGU	chr16:89350359-89350560(-)$1	201	179	196	12.5023
UGUUUUUGUUUUAAAAC	chr6:11138712-11138913(+)$1	201	152	169	12.1616
GGAGACUAUUACGUUCC	chr2:48033626-48033827(+)$1	201	2	19	11.9623
UGGGUAUGAUGCUACUU	chr13:79886367-79886568(-)$1	201	130	147	9.8191
AUUAGCAGAAAAGCUGA	chr10:74631139-74631340(+)$1	201	7	24	11.9063
GUCUCCAAAUGGGGAGA	chr14:24910091-24910292(-)$1	201	43	60	10.5915
GAGAUUGUGCAGGAUCU	chr2:8943094-8943295(-)$1	201	182	199	12.7459
GCCGUCUCCCCCGACUG	chr13:30087763-30087964(-)$1	201	139	156	10.5162
CCAUGACAAGUCUGAUG	chr5:65455052-65455253(+)$1	201	45	62	10.6028
cugggcucuuuugccag	chr16:30771915-30772116(+)$1	201	174	191	10.6235
UAAAGUAAAAAAACUUU	chr8:95853648-95853849(+)$1	201	9	26	10.5915
AGUUGUGAUGGGACAGC	chr15:83687429-83687630(-)$1	201	76	93	10.9054
AUUCUAGGAAUAUGGAA	chr3:195792315-195792516(-)$1	201	38	55	11.3463
CUGAAGAACUCCCUUUG	chr1:53516281-53516482(+)$1	201	91	108	11.1202
GUAAUCCACCACGGUUA	chr3:12876977-12877178(-)$1	201	97	114	12.7459
GAUCCAAAAGAAUGGAU	chr16:87732864-87733065(-)$1	201	150	167	12.7753
accucuggggugagagg	chr2:207025672-207025873(+)$1	201	16	33	12.7753
CUGCCAGGCACGUGGCA	chr17:79532298-79532499(-)$1	201	126	143	10.5915
CCCAGCAGAGCAGUUGG	chr5:176980578-176980779(-)$1	201	31	48	11.9063
UCUGCCAUCCACGUCAG	chr20:3764841-3765042(-)$1	201	76	93	10.4675
AGGUCAGGACAGUGACA	chr10:75557132-75557333(+)$1	201	108	125	10.4422
GCAGCUAGUCUCGGCUG	chr19:55897389-55897590(+)$1	201	115	132	10.5915
GAGCAGGAGAAGCUGCU	chrX:64738120-64738321(-)$1	201	13	30	12.7459
CCUGCCCAACAAGGUAG	chr17:61907681-61907882(+)$1	201	5	22	11.9063
CAUGUGCACACUCGCAU	chr15:72499414-72499615(-)$1	201	175	192	10.5915
CAAUGUGUUGAAACAUU	chr1:76199149-76199350(+)$1	201	34	51	12.7459
CAAAUAAUAGAAUAUUA	chr8:82571567-82571768(-)$1	201	106	123	10.9733
AACCAUGAGAAAGUGGG	chr17:29556282-29556483(+)$1	201	63	80	10.2311
AAAACAGAGACAUGUUU	chr3:44839006-44839207(+)$1	201	110	127	12.4808
CUGACAAAUUUGUGUUU	chr3:42662828-42663029(+)$1	201	64	81	11.2324
ACAUCUAUAAGAGGAUG	chr10:5807881-5808082(-)$1	201	31	48	11.9063
UUGGGCAGGGCAGCUAA	chr16:31225253-31225454(+)$1	201	121	138	10.5513
UGGAGACUCUCCUCUCU	chr11:3756377-3756578(-)$1	201	103	120	12.6906
CAUUUCAUCAGAGACAU	chr1:166821936-166822137(+)$1	201	97	114	10.0501
CCCUGACCCCGAUCAGU	chr20:54944803-54945004(-)$1	201	136	153	10.9587
AGGGUCAUAUCAGAUUC	chr2:48025687-48025888(+)$1	201	179	196	10.5915
GCCUGUGCAGAUGCAGU	chr3:121150999-121151200(-)$1	201	80	97	10.7017
GUUUUUAAAUAAGAAAA	chr19:3536313-3536514(+)$1	201	143	160	10.9054
GUGAGUAUAUAAACUCU	chr3:108285280-108285481(-)$1	201	138	155	10.0007
GCGGGCAAUGAAGCCUU	chr12:132623502-132623703(-)$1	201	120	137	10.7651
AAACCGGAAGUAUGGUU	chr1:43637815-43638016(-)$1	201	5	22	10.9054
UGUAUUUGUAGUAGUAC	chr21:30428611-30428812(-)$1	201	48	65	12.5343
GGGCCAGACCAAUGGCU	chr19:17322946-17323147(+)$1	201	154	171	11.1297

#DB
((((((......)))))	chr1:201847793-201847994(+)$1	1	64	81	10.5028
.(((((......)))))	chr19:3053720-3053921(-)$1	1	171	188	11.9063
.(((((......)))))	chr10:70252812-70253013(-)$1	1	22	39	11.9063
)(((((......)))))	chr1:100614520-100614721(-)$1	1	116	133	12.6470
(((..(......)..))	chr16:547251-547452(+)$1	1	110	127	9.8102
((.(((......)))))	chr5:71482454-71482655(+)$1	1	159	176	11.1297
((((((......)))))	chr11:129939853-129940054(+)$1	1	90	107	10.9054
((((((......)))))	chr16:22334078-22334279(+)$1	1	54	71	10.5915
(.((((......)))).	chr19:56614676-56614877(-)$1	1	90	107	10.7672
)(((((......)))))	chr9:139743235-139743436(+)$1	1	183	200	11.7352
((((((......)))))	chr21:45749400-45749601(-)$1	1	39	56	10.5915
(.((((......)))).	chr14:24028075-24028276(+)$1	1	52	69	11.1395
.(((((......)))))	chr16:731974-732175(-)$1	1	179	196	11.9063
)(((((......)))))	chr16:89350359-89350560(-)$1	1	179	196	12.5023
.(((((......)))))	chr6:11138712-11138913(+)$1	1	152	169	12.1616
((((.(......)))))	chr2:48033626-48033827(+)$1	1	2	19	11.9623
((((((......))).)	chr13:79886367-79886568(-)$1	1	130	147	9.8191
.(((((......)))))	chr10:74631139-74631340(+)$1	1	7	24	11.9063
((((((......)))))	chr14:24910091-24910292(-)$1	1	43	60	10.5915
.(((((......)))))	chr2:8943094-8943295(-)$1	1	182	199	12.7459
((((((......))).)	chr13:30087763-30087964(-)$1	1	139	156	10.5162
.(((.(......).)))	chr5:65455052-65455253(+)$1	1	45	62	10.6028
((((.(......)))))	chr16:30771915-30772116(+)$1	1	174	191	10.6235
((((((......)))))	chr8:95853648-95853849(+)$1	1	9	26	10.5915
((((((......)))))	chr15:83687429-83687630(-)$1	1	76	93	10.9054
((((((......)))))	chr3:195792315-195792516(-)$1	1	38	55	11.3463
..((((......)))))	chr1:53516281-53516482(+)$1	1	91	108	11.1202
.(((((......)))))	chr3:12876977-12877178(-)$1	1	97	114	12.7459
.(((((......)))))	chr16:87732864-87733065(-)$1	1	150	167	12.7753
.(((((......)))))	chr2:207025672-207025873(+)$1	1	16	33	12.7753
((((((......)))))	chr17:79532298-79532499(-)$1	1	126	143	10.5915
.(((((......)))))	chr5:176980578-176980779(-)$1	1	31	48	11.9063
((((.(......).)))	chr20:3764841-3765042(-)$1	1	76	93	10.4675
))((((......))))(	chr10:75557132-75557333(+)$1	1	108	125	10.4422
((((((......)))))	chr19:55897389-55897590(+)$1	1	115	132	10.5915
.(((((......)))))	chrX:64738120-64738321(-)$1	1	13	30	12.7459
.(((((......)))))	chr17:61907681-61907882(+)$1	1	5	22	11.9063
((((((......)))))	chr15:72499414-72499615(-)$1	1	175	192	10.5915
.(((((......)))))	chr1:76199149-76199350(+)$1	1	34	51	12.7459
(.((((......)))).	chr8:82571567-82571768(-)$1	1	106	123	10.9733
(.((((......)))).	chr17:29556282-29556483(+)$1	1	63	80	10.2311
((((((......)))))	chr3:44839006-44839207(+)$1	1	110	127	12.4808
..((((......)))).	chr3:42662828-42663029(+)$1	1	64	81	11.2324
.(((((......)))))	chr10:5807881-5808082(-)$1	1	31	48	11.9063
((.(((......))).)	chr16:31225253-31225454(+)$1	1	121	138	10.5513
.(((((......)))))	chr11:3756377-3756578(-)$1	1	103	120	12.6906
(((.((......)).))	chr1:166821936-166822137(+)$1	1	97	114	10.0501
..((((......)))).	chr20:54944803-54945004(-)$1	1	136	153	10.9587
((((((......)))))	chr2:48025687-48025888(+)$1	1	179	196	10.5915
..((((......)))))	chr3:121150999-121151200(-)$1	1	80	97	10.7017
((((((......)))))	chr19:3536313-3536514(+)$1	1	143	160	10.9054
))((((......)))).	chr3:108285280-108285481(-)$1	1	138	155	10.0007
((((((......)))).	chr12:132623502-132623703(-)$1	1	120	137	10.7651
((((((......)))))	chr1:43637815-43638016(-)$1	1	5	22	10.9054
.(((((......)))))	chr21:30428611-30428812(-)$1	1	48	65	12.5343
((.(((......)))))	chr19:17322946-17323147(+)$1	1	154	171	11.1297

#PSSM
f : 0.17	: : 0.12	c : 0.12	e : 0.08	! : 0.08	g : 0.07	[ : 0.07	d : 0.07	" : 0.03	i : 0.01	D : 0.01	% : 0.01	h : 0.01	J : 0.01	b : 0.01	# : 0.01	$ : 0.01	
e : 0.44	f : 0.16	c : 0.10	g : 0.07	[ : 0.07	! : 0.03	" : 0.03	i : 0.01	h : 0.01	d : 0.01	b : 0.01	
e : 0.41	d : 0.21	f : 0.16	g : 0.07	c : 0.05	[ : 0.05	i : 0.01	h : 0.01	
e : 0.39	d : 0.21	f : 0.16	c : 0.10	g : 0.07	i : 0.01	! : 0.01	[ : 0.01	
e : 0.37	d : 0.19	f : 0.14	c : 0.08	g : 0.07	[ : 0.07	i : 0.01	! : 0.01	b : 0.01	
e : 0.37	d : 0.19	f : 0.14	a : 0.08	c : 0.08	g : 0.07	i : 0.01	b : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
e : 0.37	d : 0.19	f : 0.14	a : 0.08	c : 0.08	g : 0.07	i : 0.01	b : 0.01	
e : 0.39	d : 0.19	f : 0.16	c : 0.08	g : 0.07	] : 0.03	i : 0.01	2 : 0.01	b : 0.01	
e : 0.39	d : 0.21	f : 0.16	c : 0.10	g : 0.07	i : 0.01	2 : 0.01	] : 0.01	
e : 0.44	d : 0.21	f : 0.16	g : 0.07	] : 0.05	c : 0.03	i : 0.01	
e : 0.44	f : 0.16	c : 0.08	g : 0.07	] : 0.05	2 : 0.03	d : 0.03	i : 0.01	h : 0.01	9 : 0.01	4 : 0.01	b : 0.01	: : 0.01	

#score	631.8299670916609
#seq	56
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_CDS_m2_run1.txt

#BEAR
FFccc!!ddddoooooodddd22cccccc	chr12:57038522-57038732(-)$1	210	41	70	12.3169
[bb[bb[ddddoooooodddd]bb]bb]d	chr16:67997282-67997499(-)$1	217	146	175	11.4871
c!!ccc[ddddoooooodddd22ccc333	chr16:2499780-2500005(+)$1	225	142	171	13.7592
=========[bbnnnnnbb]=========	chr16:28856604-28856825(-)$1	221	20	49	11.4838
d!!ccc[bbbboooooobb]bb]ccc]dd	chr15:22969232-22969452(-)$1	220	132	161	11.9996
ffffccc[cccooooooccc22ccc]fff	chr11:62400049-62400268(+)$1	219	108	137	13.0645
g####dddd[aooooooaddddggggggg	chr7:107558290-107558510(+)$1	220	33	62	13.1401
d[ggggggg[cccmmmmccc]gggggggd	chr9:139734082-139734308(+)$1	226	180	209	9.4894
eeee"""ddddooooooddddeeeee777	chr1:212985514-212985734(+)$1	220	55	84	10.7747
[a!!eeeeebboooooobb]eeeee22a]	chr10:1089832-1090055(-)$1	223	179	208	12.0417
ee"""gggggggnnnnnggggggg]eeee	chr11:57449831-57450050(+)$1	219	187	216	9.5294
ffff!!eeeeeooooooeeeeeffffff:	chr2:220404408-220404637(-)$1	229	185	214	10.8193
eeebbbb[cccooooooccc]bb22bb]e	chr5:37351248-37351483(-)$1	235	127	156	11.4759
d[ggggggg[aooooooa]gggggggddd	chr6:32939524-32939754(+)$1	230	78	107	13.3519
:==========oooooo==========::	chr17:30666827-30667057(-)$1	230	89	118	12.3349
ddd[gggggggoooooogggggggddddc	chr1:76256892-76257112(+)$1	220	83	112	12.3899
===========rrrrrrrrr=========	chr1:193038640-193038863(+)$1	223	115	144	10.6879
"""bb####bboooooobb22bb333===	chr12:69232989-69233213(+)$1	224	61	90	13.2402
[ggggggg[bboooooobb333ggggggg	chr20:43610381-43610599(+)$1	218	132	161	14.0416
"""ccc"""cccnnnnnccc22ccc333g	chr5:33458635-33458857(+)$1	222	145	174	11.4123
##ccc"""cccooooooccc4444ccc33	chr4:154517416-154517637(+)$1	221	89	118	15.2850
===========oooooo============	chr17:57288802-57289026(+)$1	224	37	66	15.4039
b"""ccc!!cccnnnnnccc333cccbbf	chr22:41921154-41921374(+)$1	220	99	128	10.8450
eeee"""eeeeennnnneeeee333eeee	chr3:88184118-88184341(+)$1	223	19	48	9.3340
ggggg[a!!aaooooooa]a22a]ggggg	chr6:57011911-57012135(+)$1	224	62	91	14.1972
:iiiiiiiiiooooooiiiiiiiii:===	chr1:244582079-244582301(-)$1	222	4	33	11.2185
fffff[eeeeeooooooeeeeeffffff:	chr1:205687341-205687558(-)$1	217	155	184	10.5120
d"""eeeee[aooooooa]eeeee]dddd	chr2:37873306-37873536(-)$1	230	8	37	12.3629
hhhhhhh[cccooooooccc]hhhhhhhh	chr10:32304427-32304654(-)$1	227	116	145	11.2565
==========[bbmmmmbb]=========	chr11:34112103-34112323(+)$1	220	28	57	10.1433
[dddd"""cccooooooccc4444dddd3	chr6:33414438-33414656(+)$1	218	160	189	13.8737
aa!!ccc[ddddnnnnndddd4444ccc2	chr11:121358711-121358941(+)$1	230	44	73	10.1648
##iiiiiiiiiooooooiiiiiiiii22a	chr2:135891437-135891663(+)$1	226	64	93	14.1017
iiiiiii"""cccmmmmccciiiiiiiii	chr10:31809770-31810004(+)$1	234	85	114	10.3977
!!dddd[ddddooooooddddddddccc]	chr7:138764593-138764812(-)$1	219	70	99	12.1432
[ccc[bb[cccooooooccc]bbccc]dd	chr17:60032706-60032924(-)$1	218	75	104	13.0296
gggggg####bbnnnnnbb333ggggggg	chr19:21990988-21991218(-)$1	230	57	86	10.7289
c"""bb[ddddooooooddddbb22ccc]	chr16:18893470-18893700(-)$1	230	65	94	12.5938
ddd!!ffffffooooooffffff]dddd]	chr5:127483234-127483460(+)$1	226	66	95	11.0138
:eeeee[ddddooooooddddeeeeeccc	chr6:3267800-3268030(+)$1	230	119	148	10.9965
fffff[ccc[aooooooa]ccc]ffffff	chr2:74437010-74437230(+)$1	220	34	63	12.3084
=========!!bbmmmmbb333=======	chr3:122447063-122447282(+)$1	219	79	108	10.5094
iiii####cccammmma]ccc333iiiii	chr1:89426982-89427212(-)$1	230	52	81	11.3334
#dddd"""cccooooooccc333dddd44	chr1:116941263-116941482(+)$1	219	146	175	13.9624
gggg!!eeeeeooooooeeeee333gggg	chr11:134127025-134127246(+)$1	221	140	169	13.6532
hhhhh"""cccooooooccchhhhhhhh6	chr12:121001084-121001306(+)$1	222	39	68	11.6717
"""ccc!!cccooooooccc333ccc]cc	chr22:32352528-32352751(+)$1	223	65	94	15.3987
ccc!!ccc[bboooooobb]ccc22ccce	chr12:56221312-56221542(-)$1	230	24	53	12.5709
ffffffeeeeeooooooeeeee4444fff	chr14:51107410-51107631(-)$1	221	134	163	11.5412
"eeeee[cccaooooooa]ccceeeee33	chr6:88187040-88187259(+)$1	219	7	36	12.8419
[bb"""eeeeeooooooeeeee]bb]bb2	chr22:18226642-18226862(-)$1	220	38	67	11.5580

#otherMatches

#Seq PSSM
UUAGAGGCCAGAAAGUACUGGAUUCUGGU	chr12:57038522-57038732(-)$1	210	41	70	12.3169
AUUUUGGGCCACAGGUUUGGCACACAGAG	chr16:67997282-67997499(-)$1	217	146	175	11.4871
UUUggccgggcgcagaggcucaugccugu	chr16:2499780-2500005(+)$1	225	142	171	13.7592
UUAGUUCUAGCUGAGGGAGGUGGGGCUAA	chr16:28856604-28856825(-)$1	221	20	49	11.4838
UAGUUGAGCUCCCAGAAGACGUGCAGGGU	chr15:22969232-22969452(-)$1	220	132	161	11.9996
GGGUUGUACAGCUCAUACUGGAACACAUC	chr11:62400049-62400268(+)$1	219	108	137	13.0645
ACUUUUCUGGCAGUUACGUAGAUUCUUUU	chr7:107558290-107558510(+)$1	220	33	62	13.1401
GACCUCUUCGGGCUGGGGCUGGAGGAGGC	chr9:139734082-139734308(+)$1	226	180	209	9.4894
UGCUUUCUCUUUUCUCUAAGAAGCAGAAA	chr1:212985514-212985734(+)$1	220	55	84	10.7747
AAGAGCACUCUGUUCAAGGAAGUGCAGUC	chr10:1089832-1090055(-)$1	223	179	208	12.0417
AGAUCUGCUUCUCUCUUAGAAGCACCUUA	chr11:57449831-57450050(+)$1	219	187	216	9.5294
GAGCUGGGCCGUGACACUGGCCGCUUUGA	chr2:220404408-220404637(-)$1	229	185	214	10.8193
CCACUGAUAAUGGCAGAAUUUUCUUGGCU	chr5:37351248-37351483(-)$1	235	127	156	11.4759
CUGGAGGCUCUGGGGCGAUGGCUUCCGCA	chr6:32939524-32939754(+)$1	230	78	107	13.3519
CAUUUGUCAAGCCUCUCCUUGGCAGAUAC	chr17:30666827-30667057(-)$1	230	89	118	12.3349
UUGACACAAGAUUCUCUUUUUGUGCGGUG	chr1:76256892-76257112(+)$1	220	83	112	12.3899
CCAGUGAAGGUAAGCAUAAGAUCUUCAUU	chr1:193038640-193038863(+)$1	223	115	144	10.6879
AAGGACUAUUGGAAAUGCACUUCAUGCAA	chr12:69232989-69233213(+)$1	224	61	90	13.2402
ACUUAUGGAUCGUUAUGGAGUACUGUGGG	chr20:43610381-43610599(+)$1	218	132	161	14.0416
UUAUUGCUUUCUUCUUUAGAUUUAGGAUA	chr5:33458635-33458857(+)$1	222	145	174	11.4123
UAUGGAAAAGUUACCUCACUCAUACUAAU	chr4:154517416-154517637(+)$1	221	89	118	15.2850
UAAGAUUUUAAGCAGUAUUAAAGUCUUGG	chr17:57288802-57289026(+)$1	224	37	66	15.4039
CAUGUGGACGUGAGCCCCACCAGCCAGCG	chr22:41921154-41921374(+)$1	220	99	128	10.8450
CAGGGAAAGAUAGCUAAUGUCUGUAUUUG	chr3:88184118-88184341(+)$1	223	19	48	9.3340
GUCCAGAUUGCAAUCAAGUCUUUGUGGAU	chr6:57011911-57012135(+)$1	224	62	91	14.1972
UGCAGAAUUGUAACGGUAAUUCUGUUUUA	chr1:244582079-244582301(-)$1	222	4	33	11.2185
GAUGAUGGUCUGGGGAGAGAUUUUAUUaa	chr1:205687341-205687558(-)$1	217	155	184	10.5120
GAAACCAGGAGAAAGCACACCUGGGCCAG	chr2:37873306-37873536(-)$1	230	8	37	12.3629
AAGUGCAAUUCGUGGAGGAGGUGCAUUUG	chr10:32304427-32304654(-)$1	227	116	145	11.2565
GUCUCAGCCUCAAGUAUUUCAGGCUGGGA	chr11:34112103-34112323(+)$1	220	28	57	10.1433
AGCCUGAGGCUGGAGAGAGCAAGUGGGUG	chr6:33414438-33414656(+)$1	218	160	189	13.8737
GCUUAUGCCCAGUACCUCUGGAUCACGUU	chr11:121358711-121358941(+)$1	230	44	73	10.1648
GAUCAAUUUUUACCAUGGAGGGUUGAAAG	chr2:135891437-135891663(+)$1	226	64	93	14.1017
UCUUCUGUGUGAUGAUUGUCCAGGAGAUA	chr10:31809770-31810004(+)$1	234	85	114	10.3977
UACUGAUCUUGGAGGAACAAGUCAGGCCG	chr7:138764593-138764812(-)$1	219	70	99	12.1432
UACAUCAUGUACUCAUAUACUUGUGUUUC	chr17:60032706-60032924(-)$1	218	75	104	13.0296
CAUACUGGAGAGAAACCCUACAAGUGUGA	chr19:21990988-21991218(-)$1	230	57	86	10.7289
AAUCAGUGGAUGAAGAUGUCCCUCCUCCA	chr16:18893470-18893700(-)$1	230	65	94	12.5938
ACUUUUAUUUAAGGUAAUGAGUAUGGUGU	chr5:127483234-127483460(+)$1	226	66	95	11.0138
AUGGAGGCUUUCCCCGAAAAGUUCUAGCU	chr6:3267800-3268030(+)$1	230	119	148	10.9965
AUGUCAAUACAUAUAUUUUUAUAGGCAUU	chr2:74437010-74437230(+)$1	220	34	63	12.3084
UUCUUUUCACAGCUGUGGCAUAUGGAAAG	chr3:122447063-122447282(+)$1	219	79	108	10.5094
UUCUGACUGGACAUUAGAUCCUCAAGAAC	chr1:89426982-89427212(-)$1	230	52	81	11.3334
AGGUGAGAGCUAUUUAAGGUGUACACCAA	chr1:116941263-116941482(+)$1	219	146	175	13.9624
UUGGAAGGCACAAUGAAGUGCUCACUCGG	chr11:134127025-134127246(+)$1	221	140	169	13.6532
UGUUGACUUAGAGUUUGCUGCAACAGGGU	chr12:121001084-121001306(+)$1	222	39	68	11.6717
AUCCAGAAUGCACCUGAGCAAGCCUGCCU	chr22:32352528-32352751(+)$1	223	65	94	15.3987
CUAAGCCAGGGGUUUUACUGUGGAGUAGG	chr12:56221312-56221542(-)$1	230	24	53	12.5709
GCUUCAGGUUUACGCACGAGCCCCUGUGA	chr14:51107410-51107631(-)$1	221	134	163	11.5412
UAAGUAAUGUCUUUGUUGCACGUAUUUUC	chr6:88187040-88187259(+)$1	219	7	36	12.8419
UGGCCUGGCUGAAGUCCCGGCUUCCUGAC	chr22:18226642-18226862(-)$1	220	38	67	11.5580

#DB
(((((..((((......))))..)))(((	chr12:57038522-57038732(-)$1	1	41	70	12.3169
.((.((.((((......)))).)).)).)	chr16:67997282-67997499(-)$1	1	146	175	11.4871
(..(((.((((......))))..)))...	chr16:2499780-2500005(+)$1	1	142	171	13.7592
(((((((((.((.....)).)))))))))	chr16:28856604-28856825(-)$1	1	20	49	11.4838
(..(((.((((......)).)).))).))	chr15:22969232-22969452(-)$1	1	132	161	11.9996
(((((((.(((......)))..))).)))	chr11:62400049-62400268(+)$1	1	108	137	13.0645
(....((((.(......))))))))))))	chr7:107558290-107558510(+)$1	1	33	62	13.1401
(.(((((((.(((....))).))))))))	chr9:139734082-139734308(+)$1	1	180	209	9.4894
((((...((((......)))))))))...	chr1:212985514-212985734(+)$1	1	55	84	10.7747
.(..(((((((......)).)))))..).	chr10:1089832-1090055(-)$1	1	179	208	12.0417
((...(((((((.....))))))).))))	chr11:57449831-57450050(+)$1	1	187	216	9.5294
((((..(((((......))))))))))).	chr2:220404408-220404637(-)$1	1	185	214	10.8193
(((((((.(((......))).))..)).)	chr5:37351248-37351483(-)$1	1	127	156	11.4759
(.(((((((.(......).))))))))))	chr6:32939524-32939754(+)$1	1	78	107	13.3519
.((((((((((......))))))))))..	chr17:30666827-30667057(-)$1	1	89	118	12.3349
(((.(((((((......)))))))))))(	chr1:76256892-76257112(+)$1	1	83	112	12.3899
(((((((((((.........)))))))))	chr1:193038640-193038863(+)$1	1	115	144	10.6879
...((....((......))..))...)))	chr12:69232989-69233213(+)$1	1	61	90	13.2402
.(((((((.((......))...)))))))	chr20:43610381-43610599(+)$1	1	132	161	14.0416
...(((...(((.....)))..)))...)	chr5:33458635-33458857(+)$1	1	145	174	11.4123
..(((...(((......)))....)))..	chr4:154517416-154517637(+)$1	1	89	118	15.2850
(((((((((((......))))))))))))	chr17:57288802-57289026(+)$1	1	37	66	15.4039
(...(((..(((.....)))...))))))	chr22:41921154-41921374(+)$1	1	99	128	10.8450
((((...(((((.....)))))...))))	chr3:88184118-88184341(+)$1	1	19	48	9.3340
(((((.(..((......).)..).)))))	chr6:57011911-57012135(+)$1	1	62	91	14.1972
.(((((((((......))))))))).(((	chr1:244582079-244582301(-)$1	1	4	33	11.2185
(((((.(((((......))))))))))).	chr1:205687341-205687558(-)$1	1	155	184	10.5120
(...(((((.(......).))))).))))	chr2:37873306-37873536(-)$1	1	8	37	12.3629
(((((((.(((......))).))))))))	chr10:32304427-32304654(-)$1	1	116	145	11.2565
((((((((((.((....)).)))))))))	chr11:34112103-34112323(+)$1	1	28	57	10.1433
.((((...(((......)))....)))).	chr6:33414438-33414656(+)$1	1	160	189	13.8737
((..(((.((((.....))))....))).	chr11:121358711-121358941(+)$1	1	44	73	10.1648
..(((((((((......)))))))))..)	chr2:135891437-135891663(+)$1	1	64	93	14.1017
(((((((...(((....))))))))))))	chr10:31809770-31810004(+)$1	1	85	114	10.3977
..((((.((((......))))))))))).	chr7:138764593-138764812(-)$1	1	70	99	12.1432
.(((.((.(((......))).))))).))	chr17:60032706-60032924(-)$1	1	75	104	13.0296
((((((....((.....))...)))))))	chr19:21990988-21991218(-)$1	1	57	86	10.7289
(...((.((((......))))))..))).	chr16:18893470-18893700(-)$1	1	65	94	12.5938
(((..((((((......)))))).)))).	chr5:127483234-127483460(+)$1	1	66	95	11.0138
.(((((.((((......)))))))))(((	chr6:3267800-3268030(+)$1	1	119	148	10.9965
(((((.(((.(......).))).))))))	chr2:74437010-74437230(+)$1	1	34	63	12.3084
(((((((((..((....))...)))))))	chr3:122447063-122447282(+)$1	1	79	108	10.5094
((((....((((....).)))...)))))	chr1:89426982-89427212(-)$1	1	52	81	11.3334
.((((...(((......)))...))))..	chr1:116941263-116941482(+)$1	1	146	175	13.9624
((((..(((((......)))))...))))	chr11:134127025-134127246(+)$1	1	140	169	13.6532
(((((...(((......))))))))))).	chr12:121001084-121001306(+)$1	1	39	68	11.6717
...(((..(((......)))...))).))	chr22:32352528-32352751(+)$1	1	65	94	15.3987
(((..(((.((......)).)))..))))	chr12:56221312-56221542(-)$1	1	24	53	12.5709
(((((((((((......)))))....)))	chr14:51107410-51107631(-)$1	1	134	163	11.5412
.(((((.((((......).))))))))..	chr6:88187040-88187259(+)$1	1	7	36	12.8419
.((...(((((......))))).)).)).	chr22:18226642-18226862(-)$1	1	38	67	11.5580

#PSSM
[ : 0.11	d : 0.11	= : 0.09	f : 0.09	g : 0.07	e : 0.07	" : 0.07	c : 0.05	: : 0.05	# : 0.05	h : 0.03	i : 0.03	F : 0.01	b : 0.01	a : 0.01	! : 0.01	
= : 0.11	e : 0.11	" : 0.11	f : 0.09	d : 0.07	g : 0.07	! : 0.05	# : 0.05	i : 0.05	b : 0.03	[ : 0.03	a : 0.03	h : 0.03	c : 0.03	F : 0.01	
" : 0.13	= : 0.11	g : 0.11	f : 0.09	e : 0.09	d : 0.09	c : 0.07	! : 0.07	i : 0.07	b : 0.03	h : 0.03	# : 0.01	
c : 0.13	= : 0.11	g : 0.11	f : 0.09	" : 0.09	e : 0.07	! : 0.07	i : 0.07	d : 0.05	[ : 0.03	b : 0.03	h : 0.03	# : 0.01	
c : 0.17	= : 0.11	g : 0.11	b : 0.07	" : 0.07	e : 0.07	! : 0.07	i : 0.05	f : 0.05	d : 0.05	# : 0.03	h : 0.03	[ : 0.01	
c : 0.15	" : 0.13	= : 0.11	g : 0.11	b : 0.07	e : 0.07	! : 0.05	[ : 0.05	i : 0.05	d : 0.03	# : 0.03	f : 0.03	h : 0.01	
[ : 0.13	" : 0.13	e : 0.13	= : 0.11	c : 0.09	g : 0.09	# : 0.05	i : 0.05	! : 0.03	b : 0.03	d : 0.01	a : 0.01	h : 0.01	f : 0.01	
d : 0.15	e : 0.15	= : 0.11	" : 0.11	[ : 0.09	g : 0.09	# : 0.05	! : 0.05	c : 0.05	i : 0.03	b : 0.01	f : 0.01	
c : 0.23	d : 0.17	e : 0.15	= : 0.11	g : 0.07	# : 0.03	[ : 0.03	" : 0.03	! : 0.03	i : 0.03	b : 0.01	f : 0.01	
c : 0.25	d : 0.15	[ : 0.11	e : 0.11	b : 0.09	= : 0.07	g : 0.03	i : 0.03	a : 0.01	" : 0.01	# : 0.01	f : 0.01	! : 0.01	
c : 0.27	d : 0.15	b : 0.13	a : 0.11	e : 0.11	= : 0.05	g : 0.03	o : 0.01	[ : 0.01	i : 0.01	f : 0.01	! : 0.01	
o : 0.74	b : 0.07	c : 0.07	g : 0.01	r : 0.01	e : 0.01	d : 0.01	a : 0.01	
o : 0.74	n : 0.13	c : 0.03	b : 0.03	r : 0.01	m : 0.01	
o : 0.74	n : 0.13	m : 0.09	r : 0.01	
o : 0.74	n : 0.13	m : 0.09	r : 0.01	
o : 0.74	n : 0.13	m : 0.09	r : 0.01	
o : 0.72	n : 0.13	m : 0.07	r : 0.01	i : 0.01	a : 0.01	
c : 0.25	b : 0.17	d : 0.15	a : 0.11	e : 0.11	g : 0.03	= : 0.03	i : 0.03	r : 0.01	f : 0.01	] : 0.01	
c : 0.27	d : 0.17	b : 0.17	e : 0.11	] : 0.09	g : 0.03	= : 0.03	i : 0.03	r : 0.01	f : 0.01	
c : 0.31	d : 0.17	e : 0.13	] : 0.09	g : 0.05	3 : 0.05	= : 0.03	i : 0.03	r : 0.01	2 : 0.01	a : 0.01	f : 0.01	
d : 0.17	e : 0.15	3 : 0.11	= : 0.09	2 : 0.07	] : 0.07	c : 0.07	g : 0.05	i : 0.05	4 : 0.03	b : 0.01	f : 0.01	h : 0.01	
e : 0.19	3 : 0.13	2 : 0.09	= : 0.09	b : 0.09	g : 0.07	4 : 0.05	i : 0.05	c : 0.05	d : 0.03	h : 0.03	] : 0.01	f : 0.01	
g : 0.13	= : 0.11	3 : 0.11	b : 0.09	e : 0.09	4 : 0.07	] : 0.05	c : 0.05	f : 0.05	i : 0.05	2 : 0.03	h : 0.03	a : 0.01	d : 0.01	
c : 0.15	g : 0.13	= : 0.11	e : 0.09	3 : 0.07	4 : 0.07	f : 0.05	2 : 0.05	i : 0.05	b : 0.03	] : 0.03	h : 0.03	d : 0.03	
c : 0.17	= : 0.11	g : 0.11	d : 0.09	e : 0.07	i : 0.07	] : 0.05	f : 0.05	2 : 0.05	3 : 0.05	h : 0.03	4 : 0.03	b : 0.01	
c : 0.21	g : 0.13	= : 0.11	e : 0.09	d : 0.09	f : 0.05	i : 0.05	b : 0.03	] : 0.03	3 : 0.03	h : 0.03	2 : 0.01	: : 0.01	4 : 0.01	
= : 0.15	c : 0.13	g : 0.11	d : 0.11	f : 0.09	b : 0.07	] : 0.05	e : 0.05	3 : 0.03	2 : 0.03	h : 0.03	i : 0.03	7 : 0.01	
c : 0.13	= : 0.13	d : 0.13	g : 0.11	f : 0.09	3 : 0.07	] : 0.03	e : 0.03	b : 0.03	h : 0.03	i : 0.03	7 : 0.01	a : 0.01	: : 0.01	2 : 0.01	4 : 0.01	
= : 0.13	d : 0.11	g : 0.11	c : 0.07	3 : 0.07	f : 0.07	] : 0.07	e : 0.07	: : 0.05	2 : 0.03	i : 0.03	7 : 0.01	h : 0.01	a : 0.01	4 : 0.01	6 : 0.01	

#score	615.7938174054354
#seq	51
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_UTR_m2_run1.txt

#BEAR
ee!!bboooooobb22eee	chr2:44586801-44587034(-)$1	233	117	136	10.5918
ggggggooooooggggggg	chrX:73805432-73805664(-)$1	232	186	205	12.5881
ggggggooooooggggggg	chr20:61536257-61536479(-)$1	222	30	49	12.5881
e[acccooooooccc]a]e	chr1:179075177-179075400(-)$1	223	51	70	12.1308
ffffffooooooffffff:	chr4:83274331-83274553(-)$1	222	8	27	11.0160
ggg!!aooooooa22gggg	chr1:166826149-166826372(-)$1	223	87	106	11.9187
hhhhhhoooooohhhhhhh	chr21:34949626-34949853(+)$1	227	34	53	9.8622
gg!!bboooooobb22ggg	chr11:10819062-10819281(-)$1	219	114	133	11.2077
"""cccoooooocccccc]	chr10:111894983-111895220(+)$1	237	52	71	12.3364
======oooooo=======	chr3:169714398-169714622(+)$1	224	56	75	12.4180
####bboooooobb333gg	chr1:10365594-10365815(+)$1	221	48	67	11.1845
ffffffooooooffffffd	chr12:79985478-79985714(-)$1	236	23	42	11.6444
ccccccooooooccc333c	chr15:72875588-72875812(+)$1	224	20	39	12.3137
"""cccoooooocccccc3	chr2:179379295-179379523(+)$1	228	56	75	12.3759
ffffffooooooffffff2	chrX:54096157-54096394(-)$1	237	134	153	11.7524
"""cccooooooccc333f	chr6:89322114-89322335(-)$1	221	150	169	12.4659
c!!cccoooooocccccc7	chr13:25881883-25882108(+)$1	225	60	79	11.8893
ffffffooooooffffff:	chr14:75600503-75600729(-)$1	226	195	214	11.0160
ffffffooooooffffff2	chr2:170608262-170608493(+)$1	231	56	75	11.7524
hhhhhhoooooohhhhhhh	chr3:172539131-172539360(+)$1	229	53	72	9.8622
[eeeeeooooooeeeee]a	chr8:94743348-94743593(-)$1	245	191	210	11.5004
ccccccooooooccc]ccc	chr7:22981453-22981682(-)$1	229	22	41	12.1334
ggggggooooooggggggg	chr1:150192533-150192754(-)$1	221	79	98	12.5881
cc[cccooooooccc]ccc	chr6:111628591-111628823(-)$1	232	142	161	12.3594
eeee[aooooooa]eeeee	chr14:100744871-100745097(+)$1	226	64	83	11.6293
ggggggooooooggggggg	chr14:105477116-105477338(-)$1	222	113	132	12.5881
ggggggooooooggggggg	chr19:37001767-37001998(-)$1	231	137	156	12.5881
eeee[aooooooa]eeeee	chr22:41832092-41832313(-)$1	221	79	98	11.6293
d[ddddoooooodddd]dd	chrX:123236303-123236533(+)$1	230	37	56	10.1768
ggggggooooooggggggg	chr13:30086470-30086720(-)$1	250	200	219	12.5881
ffff[aooooooa]fffff	chr11:117040212-117040439(+)$1	227	114	133	11.9568
"""cccooooooccc333b	chr8:64122332-64122559(+)$1	227	56	75	12.3468
(eeeeeooooooeeeeecc	chr17:63009960-63010196(-)$1	236	49	68	10.7142
g!!cccooooooccc4444	chr22:32081409-32081633(-)$1	224	122	141	12.3886
ffffffooooooffffff:	chr14:32624870-32625101(+)$1	231	83	102	11.0160
ggggggooooooggggggg	chr2:187373413-187373637(+)$1	224	18	37	12.5881
c[ddddoooooodddd]cc	chr2:238007622-238007854(+)$1	232	207	226	10.7679
ffffffooooooffffff:	chr14:57756019-57756243(+)$1	224	44	63	11.0160
eeee[aooooooaeeeee:	chr1:94351979-94352203(-)$1	224	32	51	10.8366
ffffffooooooffffff=	chr1:241793086-241793312(-)$1	226	27	46	11.8402
ffffffooooooffffff:	chr3:42661589-42661810(+)$1	221	74	93	11.0160
d!!a[aooooooa]a333d	chr12:46581403-46581629(-)$1	226	203	222	12.0573
fff!!aooooooa]fffff	chr1:23636763-23637014(-)$1	251	146	165	11.9524
eee[bboooooobb]eeee	chr1:211918794-211919038(-)$1	244	20	39	10.6997
"eeeeeooooooeeeee33	chr14:81940805-81941046(-)$1	241	98	117	11.6403
ggggggooooooggggggg	chr15:42708555-42708789(-)$1	234	94	113	12.5881
ggggggooooooggggggg	chr12:116397831-116398053(-)$1	222	156	175	12.5881
iiiiiaooooooa]iiiii	chr12:54633363-54633595(-)$1	232	35	54	12.3151
ff[cccoooooocccffff	chr10:60157870-60158123(+)$1	253	222	241	12.2666
cc[cccooooooccc]ccc	chr2:202488606-202488830(-)$1	224	25	44	12.3594
$eeeeeooooooeeeeeee	chr17:27590962-27591191(-)$1	229	94	113	11.0307
a!!cccooooooccc22a]	chr3:196076940-196077164(-)$1	224	85	104	12.1831
$eeeeeooooooeeeee44	chr1:228286589-228286818(+)$1	229	117	136	11.1718
"eeeeeooooooeeeee22	chr9:125609225-125609448(-)$1	223	166	185	11.1870
a[ddddoooooodddd]a2	chr2:179371274-179371496(+)$1	222	188	207	10.6097
======oooooo=======	chr2:69549449-69549670(-)$1	221	94	113	12.4180

#otherMatches

#Seq PSSM
ACCUAUAAAAUCAUUCGUG	chr2:44586801-44587034(-)$1	233	117	136	10.5918
UUGUUUAAAGCAAAACAAG	chrX:73805432-73805664(-)$1	232	186	205	12.5881
UUCAAACAGAUCUUUGAAA	chr20:61536257-61536479(-)$1	222	30	49	12.5881
AUCGGGUCUAAUUCCAGUU	chr1:179075177-179075400(-)$1	223	51	70	12.1308
CUGUGGUGGACUUCAUAGA	chr4:83274331-83274553(-)$1	222	8	27	11.0160
GGUAGCCCCUGAGAAAUUU	chr1:166826149-166826372(-)$1	223	87	106	11.9187
AAAGUUUAUGUUAAUUUUU	chr21:34949626-34949853(+)$1	227	34	53	9.8622
UUUUAGGAGUAUCUUUAAU	chr11:10819062-10819281(-)$1	219	114	133	11.2077
UUAUGUUGUAUUACAAUGU	chr10:111894983-111895220(+)$1	237	52	71	12.3364
GGCUCUUCUCCUGGGGUUG	chr3:169714398-169714622(+)$1	224	56	75	12.4180
GAAAUAGUGAAAUAAAAGU	chr1:10365594-10365815(+)$1	221	48	67	11.1845
AUGUAAAAUUUCUUAUGUA	chr12:79985478-79985714(-)$1	236	23	42	11.6444
UCUGUGGGAGUACAUUGAG	chr15:72875588-72875812(+)$1	224	20	39	12.3137
AUUCAAAGACCCUUGUCAC	chr2:179379295-179379523(+)$1	228	56	75	12.3759
GUCCAGUCUGGUCUGGACC	chrX:54096157-54096394(-)$1	237	134	153	11.7524
GAAGAUUGAAAUAUCCAAA	chr6:89322114-89322335(-)$1	221	150	169	12.4659
CAACCCUUCUGUGGGGCUC	chr13:25881883-25882108(+)$1	225	60	79	11.8893
gcaguuccuuuugauugcu	chr14:75600503-75600729(-)$1	226	195	214	11.0160
GAAUGACuuuauuuauuua	chr2:170608262-170608493(+)$1	231	56	75	11.7524
AGUAAAUGACUCUUUGCUA	chr3:172539131-172539360(+)$1	229	53	72	9.8622
Guuuuauuauuuuaagagu	chr8:94743348-94743593(-)$1	245	191	210	11.5004
AUUUGCGUUUAGGCACAAU	chr7:22981453-22981682(-)$1	229	22	41	12.1334
GGUGUAGUAUGGUGCAUUU	chr1:150192533-150192754(-)$1	221	79	98	12.5881
UGAUGACCUAACUCAGCAU	chr6:111628591-111628823(-)$1	232	142	161	12.3594
CAAUUACAGUGAUUAUUGA	chr14:100744871-100745097(+)$1	226	64	83	11.6293
UUACCUUUAGAUAGGUGAA	chr14:105477116-105477338(-)$1	222	113	132	12.5881
UGCCCAUGUGCUUGGGUAG	chr19:37001767-37001998(-)$1	231	137	156	12.5881
AAAUGUACAAAAAGAUUUU	chr22:41832092-41832313(-)$1	221	79	98	11.6293
CCUACAGUAUGUUGUAUGU	chrX:123236303-123236533(+)$1	230	37	56	10.1768
AUGGGCGCCAUGGCUCAUU	chr13:30086470-30086720(-)$1	250	200	219	12.5881
ACAUACUUUUUUGAAUGUA	chr11:117040212-117040439(+)$1	227	114	133	11.9568
ACAAAGUUGACUCUUCUCG	chr8:64122332-64122559(+)$1	227	56	75	12.3468
UGGCUUCUAUUCAAGUCCA	chr17:63009960-63010196(-)$1	236	49	68	10.7142
AAGCGAUUCAGUUUGAGGG	chr22:32081409-32081633(-)$1	224	122	141	12.3886
AUCuaauauauuuuagaua	chr14:32624870-32625101(+)$1	231	83	102	11.0160
AAUUAAAUACACUUGAUUU	chr2:187373413-187373637(+)$1	224	18	37	12.5881
gaucuccagAGUGAGAACA	chr2:238007622-238007854(+)$1	232	207	226	10.7679
GUACUAAGCUCCUAGUAUA	chr14:57756019-57756243(+)$1	224	44	63	11.0160
CUUGACAAAGAAGCAAGAC	chr1:94351979-94352203(-)$1	224	32	51	10.8366
AUAAUUGUAAUAAAUUAUU	chr1:241793086-241793312(-)$1	226	27	46	11.8402
GUGUAUUAUUUCAUACAUG	chr3:42661589-42661810(+)$1	221	74	93	11.0160
CCCGUCUCAACUGUCCAUG	chr12:46581403-46581629(-)$1	226	203	222	12.0573
UAACUGUUUCAUCUUUAAG	chr1:23636763-23637014(-)$1	251	146	165	11.9524
CCUGGGAAUAAGCUGAGGG	chr1:211918794-211919038(-)$1	244	20	39	10.6997
GGUUUUUCUCCUAAAAUAA	chr14:81940805-81941046(-)$1	241	98	117	11.6403
GAGGUGUACCUUUAUCUUC	chr15:42708555-42708789(-)$1	234	94	113	12.5881
UAAAAAAAUGCCUUUUUAA	chr12:116397831-116398053(-)$1	222	156	175	12.5881
UGGAACAAUGAAGCUUUUG	chr12:54633363-54633595(-)$1	232	35	54	12.3151
GUCAUGAAUAGGCAUACAG	chr10:60157870-60158123(+)$1	253	222	241	12.2666
UAAACAUUAAUUUGUCUAG	chr2:202488606-202488830(-)$1	224	25	44	12.3594
AGAAUGAUUCAACAUUUUC	chr17:27590962-27591191(-)$1	229	94	113	11.0307
GGGCAAUCCAAUUUGAACU	chr3:196076940-196077164(-)$1	224	85	104	12.1831
UUUUGUAUUUUGAUAAACA	chr1:228286589-228286818(+)$1	229	117	136	11.1718
UGUUUCUGUGUUGAGAUUA	chr9:125609225-125609448(-)$1	223	166	185	11.1870
GAGCCUUGAUCUGGGUACU	chr2:179371274-179371496(+)$1	222	188	207	10.6097
UGUUUGCUUUAACAAACAU	chr2:69549449-69549670(-)$1	221	94	113	12.4180

#DB
((..((......))..)))	chr2:44586801-44587034(-)$1	1	117	136	10.5918
((((((......)))))))	chrX:73805432-73805664(-)$1	1	186	205	12.5881
((((((......)))))))	chr20:61536257-61536479(-)$1	1	30	49	12.5881
(.((((......))).).)	chr1:179075177-179075400(-)$1	1	51	70	12.1308
((((((......)))))).	chr4:83274331-83274553(-)$1	1	8	27	11.0160
(((..(......)..))))	chr1:166826149-166826372(-)$1	1	87	106	11.9187
((((((......)))))))	chr21:34949626-34949853(+)$1	1	34	53	9.8622
((..((......))..)))	chr11:10819062-10819281(-)$1	1	114	133	11.2077
...(((......)))))).	chr10:111894983-111895220(+)$1	1	52	71	12.3364
((((((......)))))))	chr3:169714398-169714622(+)$1	1	56	75	12.4180
....((......))...))	chr1:10365594-10365815(+)$1	1	48	67	11.1845
((((((......))))))(	chr12:79985478-79985714(-)$1	1	23	42	11.6444
((((((......)))...)	chr15:72875588-72875812(+)$1	1	20	39	12.3137
...(((......)))))).	chr2:179379295-179379523(+)$1	1	56	75	12.3759
((((((......)))))).	chrX:54096157-54096394(-)$1	1	134	153	11.7524
...(((......)))...)	chr6:89322114-89322335(-)$1	1	150	169	12.4659
(..(((......)))))).	chr13:25881883-25882108(+)$1	1	60	79	11.8893
((((((......)))))).	chr14:75600503-75600729(-)$1	1	195	214	11.0160
((((((......)))))).	chr2:170608262-170608493(+)$1	1	56	75	11.7524
((((((......)))))))	chr3:172539131-172539360(+)$1	1	53	72	9.8622
.(((((......))))).)	chr8:94743348-94743593(-)$1	1	191	210	11.5004
((((((......))).)))	chr7:22981453-22981682(-)$1	1	22	41	12.1334
((((((......)))))))	chr1:150192533-150192754(-)$1	1	79	98	12.5881
((.(((......))).)))	chr6:111628591-111628823(-)$1	1	142	161	12.3594
((((.(......).)))))	chr14:100744871-100745097(+)$1	1	64	83	11.6293
((((((......)))))))	chr14:105477116-105477338(-)$1	1	113	132	12.5881
((((((......)))))))	chr19:37001767-37001998(-)$1	1	137	156	12.5881
((((.(......).)))))	chr22:41832092-41832313(-)$1	1	79	98	11.6293
(.((((......)))).))	chrX:123236303-123236533(+)$1	1	37	56	10.1768
((((((......)))))))	chr13:30086470-30086720(-)$1	1	200	219	12.5881
((((.(......).)))))	chr11:117040212-117040439(+)$1	1	114	133	11.9568
...(((......)))...)	chr8:64122332-64122559(+)$1	1	56	75	12.3468
.(((((......)))))))	chr17:63009960-63010196(-)$1	1	49	68	10.7142
(..(((......)))....	chr22:32081409-32081633(-)$1	1	122	141	12.3886
((((((......)))))).	chr14:32624870-32625101(+)$1	1	83	102	11.0160
((((((......)))))))	chr2:187373413-187373637(+)$1	1	18	37	12.5881
(.((((......)))).))	chr2:238007622-238007854(+)$1	1	207	226	10.7679
((((((......)))))).	chr14:57756019-57756243(+)$1	1	44	63	11.0160
((((.(......)))))).	chr1:94351979-94352203(-)$1	1	32	51	10.8366
((((((......))))))(	chr1:241793086-241793312(-)$1	1	27	46	11.8402
((((((......)))))).	chr3:42661589-42661810(+)$1	1	74	93	11.0160
(..(.(......).)...)	chr12:46581403-46581629(-)$1	1	203	222	12.0573
(((..(......).)))))	chr1:23636763-23637014(-)$1	1	146	165	11.9524
(((.((......)).))))	chr1:211918794-211919038(-)$1	1	20	39	10.6997
.(((((......)))))..	chr14:81940805-81941046(-)$1	1	98	117	11.6403
((((((......)))))))	chr15:42708555-42708789(-)$1	1	94	113	12.5881
((((((......)))))))	chr12:116397831-116398053(-)$1	1	156	175	12.5881
((((((......).)))))	chr12:54633363-54633595(-)$1	1	35	54	12.3151
((.(((......)))))))	chr10:60157870-60158123(+)$1	1	222	241	12.2666
((.(((......))).)))	chr2:202488606-202488830(-)$1	1	25	44	12.3594
.(((((......)))))))	chr17:27590962-27591191(-)$1	1	94	113	11.0307
(..(((......)))..).	chr3:196076940-196077164(-)$1	1	85	104	12.1831
.(((((......)))))..	chr1:228286589-228286818(+)$1	1	117	136	11.1718
.(((((......)))))..	chr9:125609225-125609448(-)$1	1	166	185	11.1870
(.((((......)))).).	chr2:179371274-179371496(+)$1	1	188	207	10.6097
((((((......)))))))	chr2:69549449-69549670(-)$1	1	94	113	12.4180

#PSSM
g : 0.21	f : 0.21	e : 0.10	" : 0.10	c : 0.10	h : 0.03	= : 0.03	d : 0.03	$ : 0.03	a : 0.03	# : 0.01	[ : 0.01	( : 0.01	i : 0.01	
f : 0.21	e : 0.19	g : 0.19	[ : 0.07	" : 0.07	c : 0.07	! : 0.07	h : 0.03	= : 0.03	# : 0.01	i : 0.01	
f : 0.19	g : 0.17	e : 0.17	! : 0.10	" : 0.07	[ : 0.05	d : 0.05	h : 0.03	= : 0.03	c : 0.03	a : 0.01	# : 0.01	i : 0.01	
c : 0.23	f : 0.17	g : 0.16	e : 0.16	! : 0.07	d : 0.05	h : 0.03	= : 0.03	# : 0.01	a : 0.01	[ : 0.01	i : 0.01	
c : 0.23	g : 0.16	f : 0.16	e : 0.10	[ : 0.08	b : 0.07	d : 0.05	! : 0.03	h : 0.03	= : 0.03	i : 0.01	
c : 0.23	g : 0.16	f : 0.16	a : 0.14	e : 0.10	b : 0.07	d : 0.05	h : 0.03	= : 0.03	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
c : 0.23	g : 0.16	f : 0.16	a : 0.14	e : 0.10	b : 0.07	d : 0.05	h : 0.03	= : 0.03	
c : 0.23	g : 0.16	f : 0.16	e : 0.12	] : 0.10	b : 0.07	d : 0.05	h : 0.03	= : 0.03	2 : 0.01	
c : 0.23	f : 0.19	g : 0.16	e : 0.16	2 : 0.05	d : 0.05	h : 0.03	= : 0.03	3 : 0.01	a : 0.01	] : 0.01	i : 0.01	
f : 0.21	g : 0.17	e : 0.17	3 : 0.08	] : 0.07	2 : 0.05	c : 0.05	d : 0.05	h : 0.03	= : 0.03	4 : 0.01	i : 0.01	
f : 0.21	e : 0.19	g : 0.19	c : 0.10	3 : 0.08	] : 0.05	h : 0.03	= : 0.03	a : 0.01	4 : 0.01	i : 0.01	2 : 0.01	
g : 0.21	f : 0.21	c : 0.14	e : 0.10	3 : 0.08	] : 0.03	h : 0.03	= : 0.03	4 : 0.03	a : 0.03	d : 0.01	i : 0.01	2 : 0.01	
g : 0.21	e : 0.10	: : 0.10	c : 0.10	2 : 0.07	f : 0.07	= : 0.05	d : 0.05	h : 0.03	] : 0.03	3 : 0.03	4 : 0.03	7 : 0.01	a : 0.01	b : 0.01	i : 0.01	

#score	656.2528848736341
#seq	56
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_CDS_m3_run1.txt

#BEAR
eeeeemmmmeeee	chr12:69995124-69995392(+)$1	268	161	174	9.6946
eeeeellleeeee	chr1:203786117-203786345(+)$1	228	21	34	8.3462
eeeeennnnneee	chr4:123814223-123814474(+)$1	251	91	104	7.5562
eeeooooooeeee	chr1:63884952-63885186(+)$1	234	75	88	7.2602
gggggmmmmgggg	chr6:64286617-64286893(+)$1	276	77	90	5.8601
gggggmmmmgggg	chr12:46756783-46757013(-)$1	230	162	175	5.8601
eeeeammmma]ee	chr4:108829724-108829954(+)$1	230	53	66	8.3366
eeeeemmmmeeee	chr1:28177069-28177295(+)$1	226	0	13	9.6946
eeeeemmmmeeee	chr8:97285473-97285703(+)$1	230	50	63	9.6946
eeeeemmmmeeee	chr5:58571073-58571357(-)$1	284	54	67	9.6946
[ddddmmmmdddd	chr15:64458148-64458407(-)$1	259	83	96	5.7010
eeeeemmmmeeee	chr1:160247861-160248110(-)$1	249	160	173	9.6946
eeeeemmmmeeee	chr7:112423829-112424057(-)$1	228	70	83	9.6946
eeeooooooeeee	chr5:14758562-14758791(-)$1	229	14	27	7.2602
eeeeennnnneee	chr17:48941213-48941459(-)$1	246	86	99	7.5562
eeeeemmmmeeee	chr7:112423936-112424159(-)$1	223	172	185	9.6946
eeeeellleeeee	chr17:48940650-48940874(-)$1	224	88	101	8.3462
[ddddmmmmdddd	chr2:242276798-242277025(+)$1	227	59	72	5.7010
eeeeemmmmeeee	chr2:182766402-182766665(+)$1	263	0	13	9.6946
eeeeemmmmeeee	chr14:73959656-73959886(+)$1	230	90	103	9.6946
eeeeemmmmeeee	chr6:122777572-122777804(-)$1	232	4	17	9.6946
eeeeemmmmeeee	chr4:123813799-123814102(+)$1	303	264	277	9.6946
eeeeemmmmeeee	chr2:38523149-38523459(-)$1	310	17	30	9.6946
eeeeemmmmeeee	chr20:34213906-34214176(-)$1	270	112	125	9.6946
eeeeennnnneee	chr17:34893889-34894126(+)$1	237	6	19	7.5562
eeeooooooeeee	chr8:38961084-38961386(+)$1	302	76	89	7.2602
e[cccmmmmccce	chrM:14381-14653(-)$1	272	95	108	6.0341
eeeeellleeeee	chr6:170105105-170105331(+)$1	226	71	84	8.3462
eeeeemmmmeeee	chr7:91743055-91743284(-)$1	229	193	206	9.6946
gggggmmmmgggg	chr17:34893429-34893666(+)$1	237	219	232	5.8601
eeeeemmmmeeee	chr2:38522989-38523244(-)$1	255	181	194	9.6946
eeeeennnnneee	chr7:148523495-148523722(-)$1	227	82	95	7.5562
eeeeemmmmeeee	chr13:96443144-96443447(+)$1	303	112	125	9.6946
eeeeennnnneee	chr14:54896879-54897115(-)$1	236	156	169	7.5562
eeeeellleeeee	chrX:48435824-48436083(+)$1	259	44	57	8.3462
gggggmmmmgggg	chr19:18390706-18390940(-)$1	234	123	136	5.8601
eeeeennnnneee	chr2:42936144-42936371(+)$1	227	30	43	7.5562
eeeeemmmmeeee	chr13:45010577-45010808(-)$1	231	96	109	9.6946
eeeeemmmmeeee	chr9:123367816-123368090(-)$1	274	126	139	9.6946
eeeeellleeeee	chr5:134192921-134193147(+)$1	226	43	56	8.3462

#otherMatches

#Seq PSSM
AAAUCAGUUGAUU	chr12:69995124-69995392(+)$1	268	161	174	9.6946
GCUUUGAGGAAGC	chr1:203786117-203786345(+)$1	228	21	34	8.3462
UCAGGACGGACCU	chr4:123814223-123814474(+)$1	251	91	104	7.5562
UUUUUUCUUAAAG	chr1:63884952-63885186(+)$1	234	75	88	7.2602
UGAAGUAGACUUC	chr6:64286617-64286893(+)$1	276	77	90	5.8601
GCUGUGUUAAUGG	chr12:46756783-46757013(-)$1	230	162	175	5.8601
GGAUCAUCUGCAU	chr4:108829724-108829954(+)$1	230	53	66	8.3366
AUGUCUCCUGGCA	chr1:28177069-28177295(+)$1	226	0	13	9.6946
CAGGGAUGACUCU	chr8:97285473-97285703(+)$1	230	50	63	9.6946
UCUUUGCAGAAAG	chr5:58571073-58571357(-)$1	284	54	67	9.6946
CUGAUUAUUGUUA	chr15:64458148-64458407(-)$1	259	83	96	5.7010
GGGUCUACGGACC	chr1:160247861-160248110(-)$1	249	160	173	9.6946
UUCCAUUUUUGGA	chr7:112423829-112424057(-)$1	228	70	83	9.6946
UUUGAAACAAAAA	chr5:14758562-14758791(-)$1	229	14	27	7.2602
GCUUGAAAUCCAA	chr17:48941213-48941459(-)$1	246	86	99	7.5562
UUCCAUUUUUGGA	chr7:112423936-112424159(-)$1	223	172	185	9.6946
GCAACAAGGUUGC	chr17:48940650-48940874(-)$1	224	88	101	8.3462
GGCUUGAACAGGC	chr2:242276798-242277025(+)$1	227	59	72	5.7010
UUUGGAAUUCUAA	chr2:182766402-182766665(+)$1	263	0	13	9.6946
AGCAUCAGUGUGC	chr14:73959656-73959886(+)$1	230	90	103	9.6946
UCUAGAUUCCUGG	chr6:122777572-122777804(-)$1	232	4	17	9.6946
UGGAAGUUCUUCC	chr4:123813799-123814102(+)$1	303	264	277	9.6946
GUAAUUUUUGUUG	chr2:38523149-38523459(-)$1	310	17	30	9.6946
GUAUUUUUUGAUA	chr20:34213906-34214176(-)$1	270	112	125	9.6946
CACAUGGCUGGUG	chr17:34893889-34894126(+)$1	237	6	19	7.5562
GAAACUUAAUUCC	chr8:38961084-38961386(+)$1	302	76	89	7.2602
GUGUGUUAUUAUU	chrM:14381-14653(-)$1	272	95	108	6.0341
UGGGAGAGUCUCA	chr6:170105105-170105331(+)$1	226	71	84	8.3462
UUCGUUUAUAUGA	chr7:91743055-91743284(-)$1	229	193	206	9.6946
AGUUCACUGGAAC	chr17:34893429-34893666(+)$1	237	219	232	5.8601
UAAACCAAAGUUU	chr2:38522989-38523244(-)$1	255	181	194	9.6946
UGUUCAGAGAGAG	chr7:148523495-148523722(-)$1	227	82	95	7.5562
AUUUAGAUUUAAA	chr13:96443144-96443447(+)$1	303	112	125	9.6946
UGAAAUAUGCUUU	chr14:54896879-54897115(-)$1	236	156	169	7.5562
UUCUGAUCCAGGA	chrX:48435824-48436083(+)$1	259	44	57	8.3462
UUUCUACUCGGGA	chr19:18390706-18390940(-)$1	234	123	136	5.8601
GCUGCGGCAGGCA	chr2:42936144-42936371(+)$1	227	30	43	7.5562
UGAGACAUUUUUC	chr13:45010577-45010808(-)$1	231	96	109	9.6946
AGAUAAUUUUGUC	chr9:123367816-123368090(-)$1	274	126	139	9.6946
GCACAUGUUGUGU	chr5:134192921-134193147(+)$1	226	43	56	8.3462

#DB
(((((....))))	chr12:69995124-69995392(+)$1	1	161	174	9.6946
(((((...)))))	chr1:203786117-203786345(+)$1	1	21	34	8.3462
(((((.....)))	chr4:123814223-123814474(+)$1	1	91	104	7.5562
(((......))))	chr1:63884952-63885186(+)$1	1	75	88	7.2602
(((((....))))	chr6:64286617-64286893(+)$1	1	77	90	5.8601
(((((....))))	chr12:46756783-46757013(-)$1	1	162	175	5.8601
(((((....).))	chr4:108829724-108829954(+)$1	1	53	66	8.3366
(((((....))))	chr1:28177069-28177295(+)$1	1	0	13	9.6946
(((((....))))	chr8:97285473-97285703(+)$1	1	50	63	9.6946
(((((....))))	chr5:58571073-58571357(-)$1	1	54	67	9.6946
.((((....))))	chr15:64458148-64458407(-)$1	1	83	96	5.7010
(((((....))))	chr1:160247861-160248110(-)$1	1	160	173	9.6946
(((((....))))	chr7:112423829-112424057(-)$1	1	70	83	9.6946
(((......))))	chr5:14758562-14758791(-)$1	1	14	27	7.2602
(((((.....)))	chr17:48941213-48941459(-)$1	1	86	99	7.5562
(((((....))))	chr7:112423936-112424159(-)$1	1	172	185	9.6946
(((((...)))))	chr17:48940650-48940874(-)$1	1	88	101	8.3462
.((((....))))	chr2:242276798-242277025(+)$1	1	59	72	5.7010
(((((....))))	chr2:182766402-182766665(+)$1	1	0	13	9.6946
(((((....))))	chr14:73959656-73959886(+)$1	1	90	103	9.6946
(((((....))))	chr6:122777572-122777804(-)$1	1	4	17	9.6946
(((((....))))	chr4:123813799-123814102(+)$1	1	264	277	9.6946
(((((....))))	chr2:38523149-38523459(-)$1	1	17	30	9.6946
(((((....))))	chr20:34213906-34214176(-)$1	1	112	125	9.6946
(((((.....)))	chr17:34893889-34894126(+)$1	1	6	19	7.5562
(((......))))	chr8:38961084-38961386(+)$1	1	76	89	7.2602
(.(((....))))	chrM:14381-14653(-)$1	1	95	108	6.0341
(((((...)))))	chr6:170105105-170105331(+)$1	1	71	84	8.3462
(((((....))))	chr7:91743055-91743284(-)$1	1	193	206	9.6946
(((((....))))	chr17:34893429-34893666(+)$1	1	219	232	5.8601
(((((....))))	chr2:38522989-38523244(-)$1	1	181	194	9.6946
(((((.....)))	chr7:148523495-148523722(-)$1	1	82	95	7.5562
(((((....))))	chr13:96443144-96443447(+)$1	1	112	125	9.6946
(((((.....)))	chr14:54896879-54897115(-)$1	1	156	169	7.5562
(((((...)))))	chrX:48435824-48436083(+)$1	1	44	57	8.3462
(((((....))))	chr19:18390706-18390940(-)$1	1	123	136	5.8601
(((((.....)))	chr2:42936144-42936371(+)$1	1	30	43	7.5562
(((((....))))	chr13:45010577-45010808(-)$1	1	96	109	9.6946
(((((....))))	chr9:123367816-123368090(-)$1	1	126	139	9.6946
(((((...)))))	chr5:134192921-134193147(+)$1	1	43	56	8.3462

#PSSM
e : 0.85	g : 0.10	[ : 0.05	
e : 0.82	g : 0.10	d : 0.05	[ : 0.02	
e : 0.82	g : 0.10	d : 0.05	c : 0.02	
e : 0.75	g : 0.10	o : 0.07	d : 0.05	c : 0.02	
e : 0.72	g : 0.10	o : 0.07	d : 0.05	a : 0.02	c : 0.02	
m : 0.65	n : 0.15	l : 0.12	o : 0.07	
m : 0.65	n : 0.15	l : 0.12	o : 0.07	
m : 0.65	n : 0.15	l : 0.12	o : 0.07	
m : 0.65	n : 0.15	e : 0.12	o : 0.07	
e : 0.65	n : 0.15	g : 0.10	d : 0.05	a : 0.02	c : 0.02	
e : 0.80	g : 0.10	d : 0.05	] : 0.02	c : 0.02	
e : 0.82	g : 0.10	d : 0.05	c : 0.02	
e : 0.85	g : 0.10	d : 0.05	

#score	332.56768074801766
#seq	40
#width	13
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_UTR_m2_run1.txt

#BEAR
dccc"""ddddoooooodddd22ccc99	chr1:205682908-205683167(-)$1	259	143	171	15.4561
b[eeeeeddddoooooodddd]eeeeeb	chr15:51294927-51295153(+)$1	226	175	203	14.7190
$==========oooooo==========]	chr14:36767818-36768050(-)$1	232	175	203	15.0690
iiiiii[ddddoooooodddd]iiiiii	chr11:65763986-65764215(-)$1	229	194	222	17.3508
$$$$$a[ddddoooooodddd]accc]b	chr17:77767460-77767710(-)$1	250	126	154	15.9287
cccddddddddoooooodddd333dddd	chr6:26027027-26027330(-)$1	303	108	136	15.2852
e[ccc!!ddddoooooodddd22ccc]e	chr11:85373957-85374191(-)$1	234	56	84	16.9717
cciiiiiiiiiooooooiiiiiiiii]c	chr6:4115912-4116139(-)$1	227	50	78	14.6370
gggg####cccooooooccc22gggggg	chr12:110784960-110785209(+)$1	249	60	88	15.6766
ccc!!ffffffooooooffffff22ccc	chr8:66539468-66539693(-)$1	225	120	148	12.1338
cc[eeeeecccooooooccc333eeeee	chr19:10265486-10265708(-)$1	222	182	210	14.5865
eeeee!!ddddoooooodddd22eeeee	chr1:229729084-229729316(-)$1	232	136	164	15.7072
dbb[bb[ddddooooooddddbb]bb33	chr15:76634690-76634914(+)$1	224	147	175	14.5651
ffffff!!cccooooooccc333fffff	chr19:12924295-12924554(+)$1	259	163	191	15.0339
:==========oooooo==========:	chr6:15521314-15521554(+)$1	240	189	217	13.4713
!!bb####cccooooooccc333bb22c	chr1:156701898-156702120(+)$1	222	114	142	14.8736
[bb[bb[ddddoooooodddd]bb22bb	chr13:100638311-100638547(+)$1	236	25	53	14.8585
======!!cccooooooccc333=====	chr4:139085312-139085533(-)$1	221	111	139	16.9269
b[ccc[cccbboooooobb]ccc22ccc	chr19:44100483-44100706(+)$1	223	47	75	12.6578
dd!!gggggggooooooggggggg22dd	chr12:122734363-122734589(-)$1	226	181	209	13.2443
ddd"""eeeeeooooooeeeee4444dd	chr11:27520018-27520279(-)$1	261	179	207	13.3231
gggggg[a!!aooooooa22aggggggg	chr16:30094963-30095196(+)$1	233	4	32	13.9253
bb!!bb[ddddoooooodddd]bbbb22	chr11:64889724-64889944(+)$1	220	87	115	15.0989
ffffff[ddddoooooodddd22fffff	chr5:74075723-74075943(-)$1	220	12	40	15.8605
GG:ccc[ddddooooooddddcccccc#	chr19:44501530-44501794(+)$1	264	29	57	13.8639
hhhhhh[ddddoooooodddd]hhhhhh	chr17:30696724-30696972(+)$1	248	198	226	14.6863
dddd"""ddddoooooodddd4444ddd	chr20:54944724-54944986(-)$1	262	113	141	15.7429
ffffff[ddddoooooodddd]ffffff	chr10:98281091-98281327(-)$1	236	100	128	15.6598
###ccc[ddddoooooodddd]cccfff	chr6:150004271-150004497(-)$1	226	191	219	16.5781
dd!!abbddddoooooodddd]bb]a22	chr16:68160250-68160471(+)$1	221	117	145	14.9702
ii$$$$$ddddooooooddddiiiiiii	chr12:54763240-54763486(-)$1	246	51	79	15.9618
ffffff[ddddoooooodddd]ffffff	chr21:34106891-34107117(-)$1	226	160	188	15.6598
cc[eeeee[bboooooobbeeeee]ccc	chr1:26450384-26450616(+)$1	232	177	205	12.2326
ggggggg[ddddnnnnndddd]gggggg	chr6:150111066-150111287(+)$1	221	104	132	11.4476
===========oooooo===========	chr11:118394129-118394372(+)$1	243	173	201	15.4099
cc[ccc!!cccooooooccc22ccc22c	chr1:7839616-7839850(+)$1	234	136	164	15.2438
ggggg"""cccooooooccc333ggggg	chr19:46268227-46268450(-)$1	223	108	136	16.4231
gggggg[ddddoooooodddd]gggggg	chr19:4044586-4044818(-)$1	232	192	220	17.1661
iii####acccooooooccc]a4444ii	chr19:10505653-10505886(-)$1	233	55	83	15.4469
ccc[cccddddoooooodddd22ccc]c	chr4:146055791-146056024(-)$1	233	168	196	16.6235
ggggggg[cccooooooccc]ggggggg	chr1:145441268-145441488(+)$1	220	141	169	15.1119
bb[ccc[ddddooooooddddccc]bbF	chr15:69561833-69562062(+)$1	229	179	207	15.2052
eeeee[eeeeeooooooeeeee22eeee	chr5:138221825-138222043(+)$1	218	136	164	12.7298
b"""ccc[cccooooooccc]cccbbff	chr19:18554363-18554595(-)$1	232	60	88	14.0165
!!ccc[eeeeeooooooeeeee22ccc3	chr6:485405-485637(-)$1	232	26	54	13.9982

#otherMatches

#Seq PSSM
AACUCCCAGUCUUCCUUGAUUUUAGUCC	chr1:205682908-205683167(-)$1	259	143	171	15.4561
CUGCUAAUGAUUUAUAUAUCACUUAGUG	chr15:51294927-51295153(+)$1	226	175	203	14.7190
aaaaauuuauugacugaaaugaauUUUA	chr14:36767818-36768050(-)$1	232	175	203	15.0690
AAGAUAUGUAUGUGUGUGUAUCUAUCUU	chr11:65763986-65764215(-)$1	229	194	222	17.3508
CGAAAUGCCAGGAUAAAUUGGGAGGAUU	chr17:77767460-77767710(-)$1	250	126	154	15.9287
GUGGUUUACGCGCUCAAGCGUCAAGGAC	chr6:26027027-26027330(-)$1	303	108	136	15.2852
AUUUGGGGCAUGCACAAAUGUGAUAGUU	chr11:85373957-85374191(-)$1	234	56	84	16.9717
AAAGCAUGUCCAAGGAAGGAUGUGCUGU	chr6:4115912-4116139(-)$1	227	50	78	14.6370
GUCUAAUGUAUUUUAUUGUAACAGACAU	chr12:110784960-110785209(+)$1	249	60	88	15.6766
UUACGGGAUCUAGCAGCAGAUCCGUUAA	chr8:66539468-66539693(-)$1	225	120	148	12.1338
GAACCAGCAGACACUGUUCUUCAGUUGG	chr19:10265486-10265708(-)$1	222	182	210	14.5865
AUUAUGAUAAAGAAUAAUUUGGAGUAAU	chr1:229729084-229729316(-)$1	232	136	164	15.7072
GUUGGCGCGGCGGGAGGGCCGGCGGAGG	chr15:76634690-76634914(+)$1	224	147	175	14.5651
AUUUGGUUUGAUUUUUUUCAUUUUUAAa	chr19:12924295-12924554(+)$1	259	163	191	15.0339
UUGAAUGUGAAAAUGCAUUUGCGUUCAU	chr6:15521314-15521554(+)$1	240	189	217	13.4713
AACUGCUGCACUCAGAUGUGAUGGGACU	chr1:156701898-156702120(+)$1	222	114	142	14.8736
UGUAUAGAAGUUUGUCCAUUUGUAAAAC	chr13:100638311-100638547(+)$1	236	25	53	14.8585
GUGCAAUAUGAUGUCAUUCAACUUUGCA	chr4:139085312-139085533(-)$1	221	111	139	16.9269
GACCCCUCCCGUUAUUUUGAGGACCGGG	chr19:44100483-44100706(+)$1	223	47	75	12.6578
UGACAUCUGUUUUCACUAAUAGGUAAUA	chr12:122734363-122734589(-)$1	226	181	209	13.2443
CAAACAAAUUUAUCAUGAAAUUCUCCUU	chr11:27520018-27520279(-)$1	261	179	207	13.3231
CCCUGUAGAUCUUCUGCGUGCACGGGGG	chr16:30094963-30095196(+)$1	233	4	32	13.9253
GGUAAAGAUGGCAGCUACCAUGUUCCGG	chr11:64889724-64889944(+)$1	220	87	115	15.0989
UUUUGUAAUUUAUUUAAAAAUGGACAAA	chr5:74075723-74075943(-)$1	220	12	40	15.8605
UGGGAGACGCUACAAGAGGCGCUUGAAU	chr19:44501530-44501794(+)$1	264	29	57	13.8639
AUUUUACAUGGGAAAAAUUAUUUGGAAU	chr17:30696724-30696972(+)$1	248	198	226	14.6863
CUCUGCCCUGACCCCGAUCAGUUAAGGA	chr20:54944724-54944986(-)$1	262	113	141	15.7429
AUUUAGAUAAACUACAUUUUAACUGAAU	chr10:98281091-98281327(-)$1	236	100	128	15.6598
AAUUCUUUAUGGAGCAACAUGUAGAAAA	chr6:150004271-150004497(-)$1	226	191	219	16.5781
CACUAGACUGGCCUUUACCAGCUCAUUU	chr16:68160250-68160471(+)$1	221	117	145	14.9702
CCGGCACUUGGGUGGGACCAAGGAGAUG	chr12:54763240-54763486(-)$1	246	51	79	15.9618
GUGUAAUUAUGCAUAUAUAUAUUUAUAC	chr21:34106891-34107117(-)$1	226	160	188	15.6598
GAAAUUAUUGAUAGCUUUCAUAAUCUCA	chr1:26450384-26450616(+)$1	232	177	205	12.2326
CUUACUGCAUGUUUUGCACGUAUGGUAA	chr6:150111066-150111287(+)$1	221	104	132	11.4476
UUUUCUAUGAGAAGCACUUCAUAGGGAG	chr11:118394129-118394372(+)$1	243	173	201	15.4099
UUUUGACUUAGAACCUGCUAUAUUAUCA	chr1:7839616-7839850(+)$1	234	136	164	15.2438
GCCUGGAAUCCGAAGGUGGAGGACAGGC	chr19:46268227-46268450(-)$1	223	108	136	16.4231
UGCGUGGACGCGUGUGUGCGUGUGUGCA	chr19:4044586-4044818(-)$1	232	192	220	17.1661
UCUUCCUGGCAGAAAUGUGCACUCAUGG	chr19:10505653-10505886(-)$1	233	55	83	15.4469
AUCUGUGUAGUCCUCAUACUGUUUACUG	chr4:146055791-146056024(-)$1	233	168	196	16.6235
AGCGCCCAUGUUGUGAUACAGGGGUGUU	chr1:145441268-145441488(+)$1	220	141	169	15.1119
GUAACACAGUAAAUAUGUACUUGUAGCC	chr15:69561833-69562062(+)$1	229	179	207	15.2052
CCAGGGACUUGCGUAGACAGGUAAUCUG	chr5:138221825-138222043(+)$1	218	136	164	12.7298
CUGGGGAGCCAGGAGGAUGGGUCUGCCU	chr19:18554363-18554595(-)$1	232	60	88	14.0165
CACCGGGACUUCUCUCAGAGUCAGCGGC	chr6:485405-485637(-)$1	232	26	54	13.9982

#DB
((((...((((......))))..)))..	chr1:205682908-205683167(-)$1	1	143	171	15.4561
(.(((((((((......)))).))))))	chr15:51294927-51295153(+)$1	1	175	203	14.7190
.((((((((((......)))))))))).	chr14:36767818-36768050(-)$1	1	175	203	15.0690
((((((.((((......)))).))))))	chr11:65763986-65764215(-)$1	1	194	222	17.3508
.....(.((((......)))).)))).)	chr17:77767460-77767710(-)$1	1	126	154	15.9287
(((((((((((......))))...))))	chr6:26027027-26027330(-)$1	1	108	136	15.2852
(.(((..((((......))))..))).)	chr11:85373957-85374191(-)$1	1	56	84	16.9717
(((((((((((......))))))))).)	chr6:4115912-4116139(-)$1	1	50	78	14.6370
((((....(((......)))..))))))	chr12:110784960-110785209(+)$1	1	60	88	15.6766
(((..((((((......))))))..)))	chr8:66539468-66539693(-)$1	1	120	148	12.1338
((.((((((((......)))...)))))	chr19:10265486-10265708(-)$1	1	182	210	14.5865
(((((..((((......))))..)))))	chr1:229729084-229729316(-)$1	1	136	164	15.7072
(((.((.((((......)))))).))..	chr15:76634690-76634914(+)$1	1	147	175	14.5651
((((((..(((......)))...)))))	chr19:12924295-12924554(+)$1	1	163	191	15.0339
.((((((((((......)))))))))).	chr6:15521314-15521554(+)$1	1	189	217	13.4713
..((....(((......)))...))..)	chr1:156701898-156702120(+)$1	1	114	142	14.8736
.((.((.((((......)))).))..))	chr13:100638311-100638547(+)$1	1	25	53	14.8585
((((((..(((......)))...)))))	chr4:139085312-139085533(-)$1	1	111	139	16.9269
(.(((.(((((......)).)))..)))	chr19:44100483-44100706(+)$1	1	47	75	12.6578
((..(((((((......)))))))..))	chr12:122734363-122734589(-)$1	1	181	209	13.2443
(((...(((((......)))))....))	chr11:27520018-27520279(-)$1	1	179	207	13.3231
((((((.(..(......)..))))))))	chr16:30094963-30095196(+)$1	1	4	32	13.9253
((..((.((((......)))).))))..	chr11:64889724-64889944(+)$1	1	87	115	15.0989
((((((.((((......))))..)))))	chr5:74075723-74075943(-)$1	1	12	40	15.8605
((.(((.((((......)))))))(((.	chr19:44501530-44501794(+)$1	1	29	57	13.8639
((((((.((((......)))).))))))	chr17:30696724-30696972(+)$1	1	198	226	14.6863
((((...((((......))))....)))	chr20:54944724-54944986(-)$1	1	113	141	15.7429
((((((.((((......)))).))))))	chr10:98281091-98281327(-)$1	1	100	128	15.6598
...(((.((((......)))).))))))	chr6:150004271-150004497(-)$1	1	191	219	16.5781
((..(((((((......)))).)).)..	chr16:68160250-68160471(+)$1	1	117	145	14.9702
((.....((((......)))))))))))	chr12:54763240-54763486(-)$1	1	51	79	15.9618
((((((.((((......)))).))))))	chr21:34106891-34107117(-)$1	1	160	188	15.6598
((.(((((.((......))))))).)))	chr1:26450384-26450616(+)$1	1	177	205	12.2326
(((((((.((((.....)))).))))))	chr6:150111066-150111287(+)$1	1	104	132	11.4476
(((((((((((......)))))))))))	chr11:118394129-118394372(+)$1	1	173	201	15.4099
((.(((..(((......)))..)))..)	chr1:7839616-7839850(+)$1	1	136	164	15.2438
(((((...(((......)))...)))))	chr19:46268227-46268450(-)$1	1	108	136	16.4231
((((((.((((......)))).))))))	chr19:4044586-4044818(-)$1	1	192	220	17.1661
(((....((((......))).)....))	chr19:10505653-10505886(-)$1	1	55	83	15.4469
(((.(((((((......))))..))).)	chr4:146055791-146056024(-)$1	1	168	196	16.6235
(((((((.(((......))).)))))))	chr1:145441268-145441488(+)$1	1	141	169	15.1119
((.(((.((((......))))))).)))	chr15:69561833-69562062(+)$1	1	179	207	15.2052
(((((.(((((......)))))..))))	chr5:138221825-138222043(+)$1	1	136	164	12.7298
(...(((.(((......))).)))))))	chr19:18554363-18554595(-)$1	1	60	88	14.0165
..(((.(((((......)))))..))).	chr6:485405-485637(-)$1	1	26	54	13.9982

#PSSM
c : 0.15	d : 0.13	g : 0.13	b : 0.11	f : 0.08	i : 0.06	e : 0.06	$ : 0.04	! : 0.04	= : 0.04	: : 0.02	[ : 0.02	G : 0.02	h : 0.02	# : 0.02	
c : 0.17	g : 0.13	= : 0.08	b : 0.08	f : 0.08	d : 0.08	[ : 0.06	i : 0.06	e : 0.04	! : 0.04	$ : 0.02	G : 0.02	h : 0.02	# : 0.02	" : 0.02	
c : 0.15	g : 0.13	= : 0.08	[ : 0.08	f : 0.08	e : 0.06	i : 0.06	b : 0.06	! : 0.06	$ : 0.04	d : 0.04	: : 0.02	h : 0.02	# : 0.02	" : 0.02	
c : 0.17	g : 0.13	e : 0.11	= : 0.08	! : 0.08	f : 0.08	[ : 0.06	i : 0.04	$ : 0.04	d : 0.04	" : 0.04	b : 0.02	h : 0.02	# : 0.02	
c : 0.20	g : 0.13	e : 0.11	= : 0.08	f : 0.08	" : 0.06	# : 0.06	b : 0.06	i : 0.04	$ : 0.04	d : 0.02	! : 0.02	h : 0.02	a : 0.02	
c : 0.13	f : 0.11	g : 0.11	" : 0.08	= : 0.08	b : 0.08	e : 0.06	# : 0.06	[ : 0.06	i : 0.04	! : 0.04	a : 0.02	d : 0.02	h : 0.02	$ : 0.02	
[ : 0.31	e : 0.13	! : 0.11	" : 0.06	= : 0.06	# : 0.06	c : 0.06	g : 0.06	d : 0.02	i : 0.02	f : 0.02	b : 0.02	$ : 0.02	
d : 0.48	e : 0.11	= : 0.06	! : 0.06	[ : 0.06	# : 0.04	a : 0.04	i : 0.02	f : 0.02	c : 0.02	g : 0.02	" : 0.02	
d : 0.51	c : 0.24	= : 0.06	e : 0.06	i : 0.02	f : 0.02	g : 0.02	! : 0.02	[ : 0.02	
d : 0.51	c : 0.22	= : 0.06	e : 0.06	b : 0.04	i : 0.02	f : 0.02	g : 0.02	! : 0.02	
d : 0.51	c : 0.22	= : 0.06	e : 0.06	b : 0.04	i : 0.02	f : 0.02	g : 0.02	a : 0.02	
o : 0.97	d : 0.02	
o : 0.97	n : 0.02	
o : 0.97	n : 0.02	
o : 0.97	n : 0.02	
o : 0.97	n : 0.02	
o : 0.97	n : 0.02	
d : 0.51	c : 0.22	= : 0.06	e : 0.06	b : 0.04	i : 0.02	f : 0.02	g : 0.02	a : 0.02	
d : 0.51	c : 0.22	= : 0.06	e : 0.06	b : 0.04	i : 0.02	f : 0.02	g : 0.02	2 : 0.02	
d : 0.51	c : 0.22	e : 0.08	= : 0.06	i : 0.02	f : 0.02	] : 0.02	g : 0.02	2 : 0.02	
d : 0.51	3 : 0.11	e : 0.08	= : 0.06	] : 0.06	2 : 0.04	i : 0.02	f : 0.02	c : 0.02	g : 0.02	a : 0.02	
] : 0.26	2 : 0.15	3 : 0.13	c : 0.08	e : 0.08	= : 0.06	g : 0.06	i : 0.04	f : 0.02	b : 0.02	4 : 0.02	a : 0.02	
2 : 0.15	3 : 0.13	g : 0.13	c : 0.13	b : 0.08	= : 0.06	i : 0.06	f : 0.06	4 : 0.06	e : 0.04	a : 0.02	h : 0.02	
c : 0.20	g : 0.15	e : 0.08	= : 0.08	2 : 0.08	f : 0.08	b : 0.08	i : 0.06	4 : 0.06	3 : 0.02	] : 0.02	h : 0.02	
c : 0.17	g : 0.13	e : 0.08	= : 0.08	2 : 0.08	b : 0.08	f : 0.08	i : 0.06	4 : 0.06	] : 0.06	d : 0.02	h : 0.02	
c : 0.20	g : 0.13	f : 0.11	e : 0.08	= : 0.08	b : 0.08	2 : 0.08	i : 0.06	d : 0.04	4 : 0.04	h : 0.02	a : 0.02	
g : 0.13	f : 0.13	c : 0.11	e : 0.08	= : 0.08	] : 0.08	d : 0.08	2 : 0.08	i : 0.06	b : 0.04	9 : 0.02	3 : 0.02	h : 0.02	
c : 0.15	g : 0.13	f : 0.13	d : 0.08	e : 0.08	b : 0.06	i : 0.06	3 : 0.04	= : 0.04	2 : 0.04	9 : 0.02	] : 0.02	: : 0.02	# : 0.02	h : 0.02	F : 0.02	

#score	671.5409972364515
#seq	45
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_UTR_m3_run1.txt

#BEAR
ddddqqqqqqqqddd	chrX:106367075-106367320(-)$1	245	90	105	12.8774
""bbqqqqqqqqbb4	chr16:30096203-30096514(+)$1	311	164	179	13.2757
:cccqqqqqqqqccc	chr20:62270995-62271217(-)$1	222	85	100	13.1098
ecccqqqqqqqqccc	chr12:118469457-118469678(+)$1	221	188	203	13.7751
ffffqqqqqqqqfff	chr14:103986166-103986434(-)$1	268	116	131	12.2805
:cccqqqqqqqqccc	chr12:16046883-16047113(+)$1	230	185	200	13.1098
iiiiqqqqqqqqiii	chr19:7747370-7747594(+)$1	224	41	56	12.9726
e[bbqqqqqqqqbb]	chr5:68473332-68473562(+)$1	230	81	96	13.2308
b[bbqqqqqqqqbbb	chrX:23804082-23804312(+)$1	230	53	68	12.7149
:cccqqqqqqqqccc	chr3:52558478-52558704(-)$1	226	21	36	13.1098
iiiiqqqqqqqqiii	chr19:7747276-7747539(+)$1	263	135	150	12.9726
ffffqqqqqqqqfff	chr12:120992425-120992670(+)$1	245	143	158	12.2805
b[bbqqqqqqqqbb]	chr12:54630891-54631134(-)$1	243	88	103	13.0951
[cccqqqqqqqqccc	chr19:50185145-50185382(+)$1	237	85	100	13.9453
ddddqqqqqqqqddd	chr11:65421936-65422185(-)$1	249	173	188	12.8774
e[bbqqqqqqqqbb]	chr19:1278953-1279207(+)$1	254	32	47	13.2308
e[bbqqqqqqqqbb]	chr2:74442197-74442439(+)$1	242	176	191	13.2308
ddddqqqqqqqqddd	chr10:38346057-38346304(+)$1	247	36	51	12.8774
!cccqqqqqqqqccc	chr9:130647755-130647998(-)$1	243	108	123	14.0051
!cccqqqqqqqqccc	chr16:1822066-1822313(-)$1	247	86	101	14.0051
ddddqqqqqqqqddd	chr10:22825038-22825261(-)$1	223	120	135	12.8774
:cccqqqqqqqqccc	chr16:18804490-18804715(-)$1	225	175	190	13.1098
ddddqqqqqqqqddd	chr9:131458179-131458420(+)$1	241	88	103	12.8774
i[bbqqqqqqqqbb]	chr19:18054445-18054681(+)$1	236	179	194	13.2554
[cccqqqqqqqqccc	chr5:138705118-138705344(+)$1	226	14	29	13.9453
:cccqqqqqqqqccc	chr11:61171847-61172087(-)$1	240	195	210	13.1098
ddddqqqqqqqqddd	chr16:2820869-2821112(+)$1	243	55	70	12.8774
ffffqqqqqqqqfff	chr19:1435161-1435384(+)$1	223	92	107	12.2805
ffffqqqqqqqqfff	chr5:31554638-31554887(+)$1	249	89	104	12.2805
:cccqqqqqqqqccc	chr20:60775863-60776108(+)$1	245	74	89	13.1098
[cccqqqqqqqqccc	chr19:3985275-3985518(-)$1	243	51	66	13.9453
ddddqqqqqqqqddd	chr7:148979841-148980070(+)$1	229	97	112	12.8774
eeeeqqqqqqqqeee	chr12:56119861-56120091(-)$1	230	1	16	12.3231
ddddqqqqqqqqddd	chr1:39500132-39500364(+)$1	232	160	175	12.8774
:cccqqqqqqqqccc	chr6:160169898-160170121(+)$1	223	127	142	13.1098
Gcccqqqqqqqqccc	chr3:23960597-23960825(+)$1	228	141	156	13.3686
[cccqqqqqqqqccc	chr17:905132-905353(+)$1	221	69	84	13.9453
eeeeqqqqqqqqeee	chr7:97482337-97482564(-)$1	227	198	213	12.3231
ecccqqqqqqqqccc	chr7:23240042-23240268(+)$1	226	92	107	13.7751
eebbqqqqqqqqbb]	chr18:57571122-57571368(+)$1	246	224	239	13.0295
!cccqqqqqqqqccc	chr2:176974159-176974390(+)$1	231	183	198	14.0051
c[bbqqqqqqqqbb]	chr7:6502182-6502424(-)$1	242	23	38	13.2319
ddddqqqqqqqqddd	chr12:4409067-4409305(+)$1	238	41	56	12.8774
!cccqqqqqqqqccc	chr11:4156350-4156579(+)$1	229	65	80	14.0051
ddddqqqqqqqqddd	chr20:34293097-34293348(-)$1	251	107	122	12.8774
%cccqqqqqqqqccc	chr11:47440276-47440508(-)$1	232	168	183	13.3812
ddddqqqqqqqqddd	chr10:73993042-73993263(+)$1	221	90	105	12.8774
!!bbqqqqqqqqbb3	chr1:115260342-115260574(-)$1	232	23	38	13.4576
"cccqqqqqqqqccc	chr19:56179984-56180220(+)$1	236	148	163	13.9568
a[bbqqqqqqqqbb]	chr22:50637431-50637664(+)$1	233	202	217	13.2981
!!bbqqqqqqqqbb2	chr3:53263209-53263462(-)$1	253	127	142	13.1794
""bbqqqqqqqqbb3	chr22:29176952-29177175(+)$1	223	56	71	13.3244
ffffqqqqqqqqfff	chr19:34718464-34718686(+)$1	222	19	34	12.2805
b[bbqqqqqqqqbb]	chr19:58595630-58595873(-)$1	243	84	99	13.0951
ddddqqqqqqqqddd	chr3:128888986-128889240(-)$1	254	113	128	12.8774
eeeeqqqqqqqqeee	chr6:17609184-17609415(+)$1	231	105	120	12.3231
ddddqqqqqqqqddd	chr1:226332740-226332989(-)$1	249	137	152	12.8774
gcccqqqqqqqqccc	chr11:118964518-118964746(-)$1	228	102	117	13.7885
b[bbqqqqqqqqbb]	chr19:39374197-39374434(-)$1	237	136	151	13.0951
ddbbqqqqqqqqbb3	chr5:98191421-98191662(-)$1	241	105	120	13.1186
[cccqqqqqqqqccc	chr4:38702432-38702663(+)$1	231	159	174	13.9453
:cccqqqqqqqqccc	chr12:50157232-50157489(+)$1	257	138	153	13.1098
ddddqqqqqqqqddd	chr14:75599503-75599726(-)$1	223	133	148	12.8774
ggggqqqqqqqqggg	chr2:241070156-241070415(-)$1	259	233	248	12.8277
$cccqqqqqqqqccc	chr3:127842464-127842690(-)$1	226	29	44	13.7541
[cccqqqqqqqqccc	chr19:50185089-50185338(+)$1	249	141	156	13.9453
eeeeqqqqqqqqeee	chr1:109780519-109780743(+)$1	224	175	190	12.3231
h[bbqqqqqqqqbbh	chr11:65622654-65622897(-)$1	243	129	144	12.8143
"""aqqqqqqqqa33	chr17:74732913-74733158(-)$1	245	205	220	12.9928
:cccqqqqqqqqccc	chr19:47712541-47712786(+)$1	245	71	86	13.1098
!cccqqqqqqqqccc	chr2:70437666-70437894(-)$1	228	193	208	14.0051
"cccqqqqqqqqccc	chr17:46703541-46703770(-)$1	229	43	58	13.9568
:cccqqqqqqqqccc	chr3:127799876-127800103(-)$1	227	0	15	13.1098
eeeeqqqqqqqqeee	chr12:56145359-56145589(+)$1	230	82	97	12.3231
====qqqqqqqq===	chr7:27202728-27202967(-)$1	239	127	142	13.1566
eeeeqqqqqqqqeee	chr17:16285922-16286155(+)$1	233	70	85	12.3231
ddddqqqqqqqqddd	chr8:99057495-99057716(-)$1	221	202	217	12.8774
##bbqqqqqqqqbb3	chr19:40029651-40029890(-)$1	239	58	73	13.2497
iiiiqqqqqqqqiii	chr14:75593603-75593828(-)$1	225	39	54	12.9726

#otherMatches

#Seq PSSM
GUAAUUUAUGUCUUA	chrX:106367075-106367320(-)$1	245	90	105	12.8774
CGACUACUUCCUGUG	chr16:30096203-30096514(+)$1	311	164	179	13.2757
CCACGUAGUAAAGUG	chr20:62270995-62271217(-)$1	222	85	100	13.1098
GCAGGUUCCAAAUUG	chr12:118469457-118469678(+)$1	221	188	203	13.7751
CUUCUCAGAGGUGGA	chr14:103986166-103986434(-)$1	268	116	131	12.2805
AACUGUUCGGUAAGU	chr12:16046883-16047113(+)$1	230	185	200	13.1098
CGCCGUGUGGAAGGC	chr19:7747370-7747594(+)$1	224	41	56	12.9726
UCUGCACUAGUUCAA	chr5:68473332-68473562(+)$1	230	81	96	13.2308
GGCAAUCUCAGAUGC	chrX:23804082-23804312(+)$1	230	53	68	12.7149
ACCUACUUCUCAAGG	chr3:52558478-52558704(-)$1	226	21	36	13.1098
CGCCGUGUGGAAGGC	chr19:7747276-7747539(+)$1	263	135	150	12.9726
UGAUCCUGAUACAUU	chr12:120992425-120992670(+)$1	245	143	158	12.2805
CUUGUUUUUCUUCGC	chr12:54630891-54631134(-)$1	243	88	103	13.0951
UCUUCAAGGACAAGG	chr19:50185145-50185382(+)$1	237	85	100	13.9453
AGGCUAUAACUCGCC	chr11:65421936-65422185(-)$1	249	173	188	12.8774
CCUCGCCUCCUGGAU	chr19:1278953-1279207(+)$1	254	32	47	13.2308
UCUUUCUUUUUUAAU	chr2:74442197-74442439(+)$1	242	176	191	13.2308
ACUUUUACAUUUGAG	chr10:38346057-38346304(+)$1	247	36	51	12.8774
CGACCCUCUGUCGUC	chr9:130647755-130647998(-)$1	243	108	123	14.0051
GUCUAGAAUGCCAGA	chr16:1822066-1822313(-)$1	247	86	101	14.0051
CUGUUACCAAAUGCA	chr10:22825038-22825261(-)$1	223	120	135	12.8774
ACCCAUUGCCCCGGG	chr16:18804490-18804715(-)$1	225	175	190	13.1098
UCAGUAAGAAGUCUG	chr9:131458179-131458420(+)$1	241	88	103	12.8774
GGCCAAGGCGCCGGG	chr19:18054445-18054681(+)$1	236	179	194	13.2554
AGUCUAACAUAUGAC	chr5:138705118-138705344(+)$1	226	14	29	13.9453
AUGGUGCUUUGUCCA	chr11:61171847-61172087(-)$1	240	195	210	13.1098
UUCUUCCCCAGCAGA	chr16:2820869-2821112(+)$1	243	55	70	12.8774
UGUUAAAGAAAAAAU	chr19:1435161-1435384(+)$1	223	92	107	12.2805
AUUUUGCGUGCUAAA	chr5:31554638-31554887(+)$1	249	89	104	12.2805
CGUCGCAAACAAGAU	chr20:60775863-60776108(+)$1	245	74	89	13.1098
AGCGUUCUCUUCCGC	chr19:3985275-3985518(-)$1	243	51	66	13.9453
AGUUGUUAAUGGAAC	chr7:148979841-148980070(+)$1	229	97	112	12.8774
GGUUCACUUAACAAC	chr12:56119861-56120091(-)$1	230	1	16	12.3231
UCUAUUUUCUCUUGG	chr1:39500132-39500364(+)$1	232	160	175	12.8774
AAUCAAAUAAUAGAU	chr6:160169898-160170121(+)$1	223	127	142	13.1098
UUGGUGAAGAUUCCA	chr3:23960597-23960825(+)$1	228	141	156	13.3686
UGUGAAGGGUCCUGC	chr17:905132-905353(+)$1	221	69	84	13.9453
AUGUCUUUAAAAACA	chr7:97482337-97482564(-)$1	227	198	213	12.3231
CGGGCUCACAUUCUC	chr7:23240042-23240268(+)$1	226	92	107	13.7751
UGGAAAAUUACCUCA	chr18:57571122-57571368(+)$1	246	224	239	13.0295
UGAAUAAAUGGUUUC	chr2:176974159-176974390(+)$1	231	183	198	14.0051
AUGAAAUUGUACUCC	chr7:6502182-6502424(-)$1	242	23	38	13.2319
AUCCAAGUCGGAGGA	chr12:4409067-4409305(+)$1	238	41	56	12.8774
UGAUCAAAGCCAAUC	chr11:4156350-4156579(+)$1	229	65	80	14.0051
UUGGAUGGGAUACCG	chr20:34293097-34293348(-)$1	251	107	122	12.8774
AGAUGGUUUAGGGUC	chr11:47440276-47440508(-)$1	232	168	183	13.3812
GGGUUAAGAGAUACU	chr10:73993042-73993263(+)$1	221	90	105	12.8774
UAUCAAUUUUAGGAG	chr1:115260342-115260574(-)$1	232	23	38	13.4576
ACGUGGACAUCAACG	chr19:56179984-56180220(+)$1	236	148	163	13.9568
GCGUGCAGCCAAACA	chr22:50637431-50637664(+)$1	233	202	217	13.2981
AACAUCAACCUCUGC	chr3:53263209-53263462(-)$1	253	127	142	13.1794
CAUCAGGAUGUAGAG	chr22:29176952-29177175(+)$1	223	56	71	13.3244
UCAUCUUAAAACAUG	chr19:34718464-34718686(+)$1	222	19	34	12.2805
CAGCCAUUUAGUGCC	chr19:58595630-58595873(-)$1	243	84	99	13.0951
AACUACAAAAAAAGU	chr3:128888986-128889240(-)$1	254	113	128	12.8774
GUAAGUUAGUGAUUA	chr6:17609184-17609415(+)$1	231	105	120	12.3231
GCAGUGCUUAAUUUG	chr1:226332740-226332989(-)$1	249	137	152	12.8774
CCUUAGGCAUUGGGG	chr11:118964518-118964746(-)$1	228	102	117	13.7885
CCGGCACGAAUACCC	chr19:39374197-39374434(-)$1	237	136	151	13.0951
GUACUUAUAUCUGUA	chr5:98191421-98191662(-)$1	241	105	120	13.1186
CAGUCCUCAUAUACU	chr4:38702432-38702663(+)$1	231	159	174	13.9453
AGACUAAUUCUUGUC	chr12:50157232-50157489(+)$1	257	138	153	13.1098
GGAGUUUAUCCUUUC	chr14:75599503-75599726(-)$1	223	133	148	12.8774
GUGUUUGUGUGUGCA	chr2:241070156-241070415(-)$1	259	233	248	12.8277
UGCCCUAGUAACGGC	chr3:127842464-127842690(-)$1	226	29	44	13.7541
UCUUCAAGGACAAGG	chr19:50185089-50185338(+)$1	249	141	156	13.9453
AUCAUUGAUGACUGA	chr1:109780519-109780743(+)$1	224	175	190	12.3231
CACACCUGCCCUUGG	chr11:65622654-65622897(-)$1	243	129	144	12.8143
ACUCACACCACAGCC	chr17:74732913-74733158(-)$1	245	205	220	12.9928
AUUGGCCCGAUACAA	chr19:47712541-47712786(+)$1	245	71	86	13.1098
UUAUUAUCCAGCAUA	chr2:70437666-70437894(-)$1	228	193	208	14.0051
AGCCCUCACACCGGU	chr17:46703541-46703770(-)$1	229	43	58	13.9568
ACAUGAAGUGAGAUG	chr3:127799876-127800103(-)$1	227	0	15	13.1098
GGAGUUGAGAAUCUC	chr12:56145359-56145589(+)$1	230	82	97	12.3231
AUAGUUUUUAGUCUG	chr7:27202728-27202967(-)$1	239	127	142	13.1566
UUACAAGUUUCAGUA	chr17:16285922-16286155(+)$1	233	70	85	12.3231
GGGCAGAUGUGAGCC	chr8:99057495-99057716(-)$1	221	202	217	12.8774
AAAGCAUUAUAACUG	chr19:40029651-40029890(-)$1	239	58	73	13.2497
AACACAGAGAACUGU	chr14:75593603-75593828(-)$1	225	39	54	12.9726

#DB
((((........)))	chrX:106367075-106367320(-)$1	1	90	105	12.8774
..((........)).	chr16:30096203-30096514(+)$1	1	164	179	13.2757
.(((........)))	chr20:62270995-62271217(-)$1	1	85	100	13.1098
)(((........)))	chr12:118469457-118469678(+)$1	1	188	203	13.7751
((((........)))	chr14:103986166-103986434(-)$1	1	116	131	12.2805
.(((........)))	chr12:16046883-16047113(+)$1	1	185	200	13.1098
((((........)))	chr19:7747370-7747594(+)$1	1	41	56	12.9726
(.((........)).	chr5:68473332-68473562(+)$1	1	81	96	13.2308
(.((........)))	chrX:23804082-23804312(+)$1	1	53	68	12.7149
.(((........)))	chr3:52558478-52558704(-)$1	1	21	36	13.1098
((((........)))	chr19:7747276-7747539(+)$1	1	135	150	12.9726
((((........)))	chr12:120992425-120992670(+)$1	1	143	158	12.2805
(.((........)).	chr12:54630891-54631134(-)$1	1	88	103	13.0951
.(((........)))	chr19:50185145-50185382(+)$1	1	85	100	13.9453
((((........)))	chr11:65421936-65422185(-)$1	1	173	188	12.8774
(.((........)).	chr19:1278953-1279207(+)$1	1	32	47	13.2308
(.((........)).	chr2:74442197-74442439(+)$1	1	176	191	13.2308
((((........)))	chr10:38346057-38346304(+)$1	1	36	51	12.8774
.(((........)))	chr9:130647755-130647998(-)$1	1	108	123	14.0051
.(((........)))	chr16:1822066-1822313(-)$1	1	86	101	14.0051
((((........)))	chr10:22825038-22825261(-)$1	1	120	135	12.8774
.(((........)))	chr16:18804490-18804715(-)$1	1	175	190	13.1098
((((........)))	chr9:131458179-131458420(+)$1	1	88	103	12.8774
(.((........)).	chr19:18054445-18054681(+)$1	1	179	194	13.2554
.(((........)))	chr5:138705118-138705344(+)$1	1	14	29	13.9453
.(((........)))	chr11:61171847-61172087(-)$1	1	195	210	13.1098
((((........)))	chr16:2820869-2821112(+)$1	1	55	70	12.8774
((((........)))	chr19:1435161-1435384(+)$1	1	92	107	12.2805
((((........)))	chr5:31554638-31554887(+)$1	1	89	104	12.2805
.(((........)))	chr20:60775863-60776108(+)$1	1	74	89	13.1098
.(((........)))	chr19:3985275-3985518(-)$1	1	51	66	13.9453
((((........)))	chr7:148979841-148980070(+)$1	1	97	112	12.8774
((((........)))	chr12:56119861-56120091(-)$1	1	1	16	12.3231
((((........)))	chr1:39500132-39500364(+)$1	1	160	175	12.8774
.(((........)))	chr6:160169898-160170121(+)$1	1	127	142	13.1098
((((........)))	chr3:23960597-23960825(+)$1	1	141	156	13.3686
.(((........)))	chr17:905132-905353(+)$1	1	69	84	13.9453
((((........)))	chr7:97482337-97482564(-)$1	1	198	213	12.3231
)(((........)))	chr7:23240042-23240268(+)$1	1	92	107	13.7751
((((........)).	chr18:57571122-57571368(+)$1	1	224	239	13.0295
.(((........)))	chr2:176974159-176974390(+)$1	1	183	198	14.0051
(.((........)).	chr7:6502182-6502424(-)$1	1	23	38	13.2319
((((........)))	chr12:4409067-4409305(+)$1	1	41	56	12.8774
.(((........)))	chr11:4156350-4156579(+)$1	1	65	80	14.0051
((((........)))	chr20:34293097-34293348(-)$1	1	107	122	12.8774
.(((........)))	chr11:47440276-47440508(-)$1	1	168	183	13.3812
((((........)))	chr10:73993042-73993263(+)$1	1	90	105	12.8774
..((........)).	chr1:115260342-115260574(-)$1	1	23	38	13.4576
.(((........)))	chr19:56179984-56180220(+)$1	1	148	163	13.9568
(.((........)).	chr22:50637431-50637664(+)$1	1	202	217	13.2981
..((........)).	chr3:53263209-53263462(-)$1	1	127	142	13.1794
..((........)).	chr22:29176952-29177175(+)$1	1	56	71	13.3244
((((........)))	chr19:34718464-34718686(+)$1	1	19	34	12.2805
(.((........)).	chr19:58595630-58595873(-)$1	1	84	99	13.0951
((((........)))	chr3:128888986-128889240(-)$1	1	113	128	12.8774
((((........)))	chr6:17609184-17609415(+)$1	1	105	120	12.3231
((((........)))	chr1:226332740-226332989(-)$1	1	137	152	12.8774
((((........)))	chr11:118964518-118964746(-)$1	1	102	117	13.7885
(.((........)).	chr19:39374197-39374434(-)$1	1	136	151	13.0951
((((........)).	chr5:98191421-98191662(-)$1	1	105	120	13.1186
.(((........)))	chr4:38702432-38702663(+)$1	1	159	174	13.9453
.(((........)))	chr12:50157232-50157489(+)$1	1	138	153	13.1098
((((........)))	chr14:75599503-75599726(-)$1	1	133	148	12.8774
((((........)))	chr2:241070156-241070415(-)$1	1	233	248	12.8277
.(((........)))	chr3:127842464-127842690(-)$1	1	29	44	13.7541
.(((........)))	chr19:50185089-50185338(+)$1	1	141	156	13.9453
((((........)))	chr1:109780519-109780743(+)$1	1	175	190	12.3231
(.((........)))	chr11:65622654-65622897(-)$1	1	129	144	12.8143
...(........)..	chr17:74732913-74733158(-)$1	1	205	220	12.9928
.(((........)))	chr19:47712541-47712786(+)$1	1	71	86	13.1098
.(((........)))	chr2:70437666-70437894(-)$1	1	193	208	14.0051
.(((........)))	chr17:46703541-46703770(-)$1	1	43	58	13.9568
.(((........)))	chr3:127799876-127800103(-)$1	1	0	15	13.1098
((((........)))	chr12:56145359-56145589(+)$1	1	82	97	12.3231
((((........)))	chr7:27202728-27202967(-)$1	1	127	142	13.1566
((((........)))	chr17:16285922-16286155(+)$1	1	70	85	12.3231
((((........)))	chr8:99057495-99057716(-)$1	1	202	217	12.8774
..((........)).	chr19:40029651-40029890(-)$1	1	58	73	13.2497
((((........)))	chr14:75593603-75593828(-)$1	1	39	54	12.9726

#PSSM
d : 0.20	e : 0.15	: : 0.12	! : 0.08	[ : 0.07	" : 0.06	f : 0.06	i : 0.05	b : 0.05	g : 0.02	G : 0.01	c : 0.01	% : 0.01	a : 0.01	$ : 0.01	h : 0.01	= : 0.01	# : 0.01	
c : 0.36	d : 0.20	[ : 0.13	e : 0.08	f : 0.06	" : 0.03	i : 0.03	! : 0.02	g : 0.01	= : 0.01	# : 0.01	
c : 0.36	b : 0.22	d : 0.18	e : 0.07	f : 0.06	i : 0.03	g : 0.01	" : 0.01	= : 0.01	
c : 0.36	b : 0.22	d : 0.18	e : 0.07	f : 0.06	i : 0.03	g : 0.01	a : 0.01	= : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.36	b : 0.22	d : 0.18	e : 0.07	f : 0.06	i : 0.03	g : 0.01	a : 0.01	= : 0.01	
c : 0.36	b : 0.22	d : 0.18	e : 0.07	f : 0.06	i : 0.03	g : 0.01	3 : 0.01	= : 0.01	
c : 0.36	d : 0.18	] : 0.12	e : 0.07	f : 0.06	3 : 0.06	i : 0.03	4 : 0.01	b : 0.01	2 : 0.01	g : 0.01	h : 0.01	= : 0.01	

#score	1037.8797210134767
#seq	79
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_UTR_m3_run2.txt

#BEAR
ddd!!bb[attttttttttta]bb22d	chr19:49611467-49611715(+)$1	248	38	65	21.5206
e[a[ddddvvvvvvvvvvvvvdddda]	chr19:44417327-44417542(-)$1	215	27	54	24.6380
""a!!eeeeettttttttttteeeee2	chr8:37612342-37612560(+)$1	218	8	35	21.9192
ggggggg[atttttttttttagggggg	chr6:74225417-74225679(-)$1	262	71	98	24.5394
[ggggggguuuuuuuuuuuuggggggg	chr6:117002349-117002580(+)$1	231	69	96	24.7116
eeeeddddvvvvvvvvvvvvvdddd22	chr22:50216504-50216761(-)$1	257	139	166	24.0517
[gggggggtttttttttttggggggga	chr1:154247771-154248035(+)$1	264	83	110	22.8128
[ccc[cccyyyyyyyyyyyyyyyyccc	chr7:97835894-97836121(+)$1	227	119	146	20.8770
"""eeeeebbtttttttttttbb]eee	chr22:21244510-21244738(+)$1	228	57	84	21.4395
dggggggguuuuuuuuuuuuggggggg	chr1:114472396-114472619(+)$1	223	196	223	24.3599
:ffffffvvvvvvvvvvvvvffffff:	chr19:30501993-30502223(+)$1	230	0	27	20.9025
gggggggxxxxxxxxxxxxxxxggggg	chr1:242011951-242012165(+)$1	214	161	188	18.9026
:gggggggvvvvvvvvvvvvvgggggg	chr5:135516314-135516536(+)$1	222	74	101	24.8392
iiiiiiiivvvvvvvvvvvvviiiiii	chr4:2243174-2243397(-)$1	223	173	200	25.6894
iiiiiiiiitttttttttttiiiiiii	chr5:71503136-71503377(+)$1	241	2	29	23.2164
gggggggyyyyyyyyyyyyyyyygggg	chr19:39889302-39889520(+)$1	218	143	170	21.9275
hhhhhhh[auuuuuuuuuuuuahhhhh	chr11:120959544-120959766(+)$1	222	149	176	23.2433
ee[eeeeevvvvvvvvvvvvveeeee]	chr17:37077072-37077294(+)$1	222	17	44	24.9134
!gggggggtttttttttttggggggg2	chr2:55254494-55254717(-)$1	223	81	108	22.7937
fff[acccuuuuuuuuuuuuccc]a]f	chr15:64980467-64980684(-)$1	217	21	48	23.5569
ccffffffvvvvvvvvvvvvvffffff	chr7:143078673-143078893(+)$1	220	52	79	24.0192
hhhhhhhhuuuuuuuuuuuuhhhhhhh	chr6:44414932-44415152(+)$1	220	74	101	22.1680
==========ttttttttttt======	chr3:195778731-195778998(-)$1	267	158	185	22.6060
d[dddd!!bbtttttttttttbbdddd	chr5:139930151-139930369(-)$1	218	43	70	20.6610
dd[eeeeettttttttttteeeeeddd	chr11:6424926-6425152(-)$1	226	64	91	21.4094
ee[eeeeeuuuuuuuuuuuueeeee]e	chrX:54097675-54097887(-)$1	212	3	30	23.6128
[a[fffffftttttttttttffffff]	chr17:40717994-40718236(+)$1	242	34	61	22.2354
fff[ddddvvvvvvvvvvvvvddddff	chr17:40724845-40725070(-)$1	225	180	207	24.3082
:ffffffwwwwwwwwwwwwwwffffff	chr5:135513957-135514208(+)$1	251	169	196	21.7865
e[ffffffwwwwwwwwwwwwwwfffff	chr7:155573331-155573541(+)$1	210	78	105	22.7547
ffffff[bbuuuuuuuuuuuubbffff	chr2:27355133-27355351(-)$1	218	77	104	22.3493
:ffffffwwwwwwwwwwwwwwffffff	chr12:49229905-49230124(-)$1	219	162	189	21.7865
f!!eeeeevvvvvvvvvvvvveeeee2	chr19:15532427-15532648(-)$1	221	117	144	24.8100
[ffffff[bbtttttttttttbb]fff	chr16:67596471-67596683(+)$1	212	162	189	21.3072
b]bbdddduuuuuuuuuuuuddddeee	chr10:72186870-72187084(+)$1	214	49	76	22.2667
f:eeeeewwwwwwwwwwwwwweeeee:	chr19:10427715-10427937(-)$1	222	105	132	21.2493
hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr14:77253642-77253863(-)$1	221	184	211	23.6277
ggggddddwwwwwwwwwwwwwwdddd]	chr17:80037253-80037487(-)$1	234	18	45	23.4685
[dddddddduuuuuuuuuuuudddd]d	chr17:44834356-44834579(+)$1	223	160	187	22.7134
Hgggggggvvvvvvvvvvvvvgggggg	chr12:69115563-69115781(+)$1	218	137	164	25.1266
hhhhhhhhuuuuuuuuuuuuhhhhhhh	chr14:61186668-61186899(-)$1	231	37	64	22.1680
!bb[ddddvvvvvvvvvvvvvdddd]b	chr19:16345660-16345893(+)$1	233	173	200	24.1731
========vvvvvvvvvvvvv======	chr11:47492253-47492476(-)$1	223	81	108	25.5696
bbccc[bbvvvvvvvvvvvvvbb]ccc	chr1:16265896-16266214(+)$1	318	234	261	23.4791
h"""ddddwwwwwwwwwwwwwwddddh	chr20:50700798-50701020(-)$1	222	30	57	22.6689
[bb!!bbavvvvvvvvvvvvva]bb22	chr20:4835012-4835230(-)$1	218	15	42	23.4775
hhhhhhhhwwwwwwwwwwwwwwhhhhh	chr12:49085434-49085661(-)$1	227	85	112	22.3956
dbb!!dddduuuuuuuuuuuudddd22	chr16:28845298-28845528(+)$1	230	187	214	22.6076
eeeeeyyyyyyyyyyyyyyyyeeeeed	chr5:138269440-138269665(+)$1	225	77	104	20.3074
###eeeeewwwwwwwwwwwwwweeeee	chr10:98593084-98593306(+)$1	222	128	155	23.2433
[ggggggguuuuuuuuuuuuggggggg	chr12:4413652-4413872(+)$1	220	51	78	24.7116
bgggggggvvvvvvvvvvvvvgggggg	chr19:15465564-15465820(-)$1	256	185	212	25.5275
ccc[ddddvvvvvvvvvvvvvdddd]c	chr1:78030124-78030344(-)$1	220	186	213	24.6709
[ccc[ccctttttttttttccc]ccc]	chr2:73301909-73302143(-)$1	234	54	81	22.5856
eeeee[bbuuuuuuuuuuuubb]eeee	chr11:57584651-57584870(+)$1	219	38	65	22.6603
gggggdddduuuuuuuuuuuudddd33	chr11:117041490-117041708(+)$1	218	109	136	23.7102
::eeeeewwwwwwwwwwwwwweeeee:	chr19:7979156-7979381(+)$1	225	178	205	20.4701
iiiiiiiiiuuuuuuuuuuuuiiiiii	chr1:28608743-28609024(+)$1	281	151	178	24.2493

#otherMatches

#Seq PSSM
cgugaccgcgagcacaaacggggggag	chr19:49611467-49611715(+)$1	248	38	65	21.5206
GGUGCUGAAAUAUUUUAAUAAUCAGAG	chr19:44417327-44417542(-)$1	215	27	54	24.6380
UUGUUUUUUUUUUUUCUUCUCAAAAAU	chr8:37612342-37612560(+)$1	218	8	35	21.9192
UCAGUUUACUUGCAUAUACUGAGAUUG	chr6:74225417-74225679(-)$1	262	71	98	24.5394
AGUGGCGGCCCUUCUGUUACCCGCCAC	chr6:117002349-117002580(+)$1	231	69	96	24.7116
CGCUCCUUAUAUUCCCCCGCAGAGGUA	chr22:50216504-50216761(-)$1	257	139	166	24.0517
ACUUCUCUUUGUAGAUAGUGGAGGAGC	chr1:154247771-154248035(+)$1	264	83	110	22.8128
CUUGAGCUUUAAAAAAACCUCCACAGC	chr7:97835894-97836121(+)$1	227	119	146	20.8770
ACCCUCUAGACUAGACACAUUUCAUGG	chr22:21244510-21244738(+)$1	228	57	84	21.4395
CGGGGAGCGACUUCCCCUCAGCUCCCU	chr1:114472396-114472619(+)$1	223	196	223	24.3599
AUUUUAGGUCCGAAUAAAUACUGGAAA	chr19:30501993-30502223(+)$1	230	0	27	20.9025
UGGUGCUGUUAUUGUUACCUCGAGUGC	chr1:242011951-242012165(+)$1	214	161	188	18.9026
GUAUUGUUGCUAUAUAAAAAAAAUAAU	chr5:135516314-135516536(+)$1	222	74	101	24.8392
GAAGAUGUGCCAUGCUUAUUUGCGUCU	chr4:2243174-2243397(-)$1	223	173	200	25.6894
AUGUUAGUUAUUUAUUUCAAAAUUAAC	chr5:71503136-71503377(+)$1	241	2	29	23.2164
GCCAUGGUUCCCACAUUCGCACUCCAU	chr19:39889302-39889520(+)$1	218	143	170	21.9275
UUUCCUGACAGAUUUUUGGAAGUAGGA	chr11:120959544-120959766(+)$1	222	149	176	23.2433
UUCUGUUUCCUCUUGAUCUCAAAGCAC	chr17:37077072-37077294(+)$1	222	17	44	24.9134
UGUCCAUGGUCACAGAAAAUAUGGACU	chr2:55254494-55254717(-)$1	223	81	108	22.7937
UUAGAAGCUUUCUAAACUGCGCUGUGU	chr15:64980467-64980684(-)$1	217	21	48	23.5569
CCCCGCAGAAGAAGUUCGGCCCUGUGG	chr7:143078673-143078893(+)$1	220	52	79	24.0192
UUUUUUUGUUAAUAUCACUUUAAAGAA	chr6:44414932-44415152(+)$1	220	74	101	22.1680
CGUUUGGGACAUUGACAAUGAGUUUUA	chr3:195778731-195778998(-)$1	267	158	185	22.6060
GAGAAGAACCAUACCAUACCAGGCUUC	chr5:139930151-139930369(-)$1	218	43	70	20.6610
GGUAGGCUGACCCUCACCAAGCCUCCC	chr11:6424926-6425152(-)$1	226	64	91	21.4094
ACUAUUUGAUUUUACACGCCUAGAUUG	chrX:54097675-54097887(-)$1	212	3	30	23.6128
CGACCCCGUGGUGAGGAGAAAUGGGGG	chr17:40717994-40718236(+)$1	242	34	61	22.2354
UUCCUGCUACUUUCACCUUUAAGCAGA	chr17:40724845-40725070(-)$1	225	180	207	24.3082
ACUGCAAUUUAUAGAUUACAUUUGUAG	chr5:135513957-135514208(+)$1	251	169	196	21.7865
CUCAGCCUUGAGAACUCCACGUGGGCU	chr7:155573331-155573541(+)$1	210	78	105	22.7547
CAGGUUUGGGCAGGUUCCAGACCAGCC	chr2:27355133-27355351(-)$1	218	77	104	22.3493
ACAGCAGCCUUCCUCAUCCCUCUGCUG	chr12:49229905-49230124(-)$1	219	162	189	21.7865
GGGCCAGUGGGGUUGUAGAGAGCUGGA	chr19:15532427-15532648(-)$1	221	117	144	24.8100
GGGCCCGGGGUGGAGGAGGUUUCGCGG	chr16:67596471-67596683(+)$1	212	162	189	21.3072
AUGGGCAGCUAUAGAUUAAUCUGCAAA	chr10:72186870-72187084(+)$1	214	49	76	22.2667
CCGGAGCCCUCCUGCCUCAUUGCUCCU	chr19:10427715-10427937(-)$1	222	105	132	21.2493
UUGCUUUCUUGUUUCUGUUUUGAAAGU	chr14:77253642-77253863(-)$1	221	184	211	23.6277
CUGCCGCUGAAGGGCCUAGAGGAGCGU	chr17:80037253-80037487(-)$1	234	18	45	23.4685
AUCUUGCCAUUUGUAUACUUUUGGUGG	chr17:44834356-44834579(+)$1	223	160	187	22.7134
GAUCCAGACAUCAGUAGCAACUCUGGA	chr12:69115563-69115781(+)$1	218	137	164	25.1266
GUGGCAUUGAACCCACCAAAAAUGUCA	chr14:61186668-61186899(-)$1	231	37	64	22.1680
AGCGGGCCAUUUACACGUCGAGGCUGG	chr19:16345660-16345893(+)$1	233	173	200	24.1731
GCCUCUGCUCUAAGAAGUGCUGUGGGG	chr11:47492253-47492476(-)$1	223	81	108	25.5696
GCCCAAGGACACAUCACCAACCCAUGG	chr1:16265896-16266214(+)$1	318	234	261	23.4791
GGCUGGCCGCUCCAACUUCACAGGCCU	chr20:50700798-50701020(-)$1	222	30	57	22.6689
GCCAACCCAAUAAUUCUGUCCGAGGAG	chr20:4835012-4835230(-)$1	218	15	42	23.4775
CUCAAGUUUUUGCAGCCUAUAUGACUU	chr12:49085434-49085661(-)$1	227	85	112	22.3956
AGUACAUCUCCUACAUACCUCAGAUCC	chr16:28845298-28845528(+)$1	230	187	214	22.6076
GCAGCCAAGAACUUGAUGAAUGCUGUG	chr5:138269440-138269665(+)$1	225	77	104	20.3074
AUAUAUUUAACCCCCCUCCAAAAAGUA	chr10:98593084-98593306(+)$1	222	128	155	23.2433
GAUUCUGGAUUCUAAACAACCCAGAAU	chr12:4413652-4413872(+)$1	220	51	78	24.7116
CCCAGAAUAUGCUGUAAUCUAAUUUUG	chr19:15465564-15465820(-)$1	256	185	212	25.5275
GAUUUUGGAUUUUUUUUUUUACCAGUG	chr1:78030124-78030344(-)$1	220	186	213	24.6709
CCAGUCUCUGCCAUGUCCUGAGUCUGC	chr2:73301909-73302143(-)$1	234	54	81	22.5856
GAAACUGGCUUCCCCACUCCCCCGUUU	chr11:57584651-57584870(+)$1	219	38	65	22.6603
UCCCCCAGGUUUCUUGGUGUUCCUGCU	chr11:117041490-117041708(+)$1	218	109	136	23.7102
UUGAGAAUAAACCCCUUCCUUUUCUUC	chr19:7979156-7979381(+)$1	225	178	205	20.4701
CACUGGGUGGGUAGGGAGUGGUAUCCA	chr1:28608743-28609024(+)$1	281	151	178	24.2493

#DB
(((..((.(...........).))..)	chr19:49611467-49611715(+)$1	1	38	65	21.5206
(.(.((((.............))))).	chr19:44417327-44417542(-)$1	1	27	54	24.6380
..(..(((((...........))))).	chr8:37612342-37612560(+)$1	1	8	35	21.9192
(((((((.(...........)))))))	chr6:74225417-74225679(-)$1	1	71	98	24.5394
.(((((((............)))))))	chr6:117002349-117002580(+)$1	1	69	96	24.7116
((((((((.............))))..	chr22:50216504-50216761(-)$1	1	139	166	24.0517
.(((((((...........))))))))	chr1:154247771-154248035(+)$1	1	83	110	22.8128
.(((.(((................)))	chr7:97835894-97836121(+)$1	1	119	146	20.8770
...(((((((...........)).)))	chr22:21244510-21244738(+)$1	1	57	84	21.4395
)(((((((............)))))))	chr1:114472396-114472619(+)$1	1	196	223	24.3599
.((((((.............)))))).	chr19:30501993-30502223(+)$1	1	0	27	20.9025
(((((((...............)))))	chr1:242011951-242012165(+)$1	1	161	188	18.9026
.(((((((.............))))))	chr5:135516314-135516536(+)$1	1	74	101	24.8392
((((((((.............))))))	chr4:2243174-2243397(-)$1	1	173	200	25.6894
(((((((((...........)))))))	chr5:71503136-71503377(+)$1	1	2	29	23.2164
(((((((................))))	chr19:39889302-39889520(+)$1	1	143	170	21.9275
(((((((.(............))))))	chr11:120959544-120959766(+)$1	1	149	176	23.2433
((.(((((.............))))).	chr17:37077072-37077294(+)$1	1	17	44	24.9134
.(((((((...........))))))).	chr2:55254494-55254717(-)$1	1	81	108	22.7937
(((.((((............))).).)	chr15:64980467-64980684(-)$1	1	21	48	23.5569
((((((((.............))))))	chr7:143078673-143078893(+)$1	1	52	79	24.0192
((((((((............)))))))	chr6:44414932-44415152(+)$1	1	74	101	22.1680
((((((((((...........))))))	chr3:195778731-195778998(-)$1	1	158	185	22.6060
(.((((..((...........))))))	chr5:139930151-139930369(-)$1	1	43	70	20.6610
((.(((((...........))))))))	chr11:6424926-6425152(-)$1	1	64	91	21.4094
((.(((((............))))).)	chrX:54097675-54097887(-)$1	1	3	30	23.6128
.(.((((((...........)))))).	chr17:40717994-40718236(+)$1	1	34	61	22.2354
(((.((((.............))))))	chr17:40724845-40725070(-)$1	1	180	207	24.3082
.((((((..............))))))	chr5:135513957-135514208(+)$1	1	169	196	21.7865
(.((((((..............)))))	chr7:155573331-155573541(+)$1	1	78	105	22.7547
((((((.((............))))))	chr2:27355133-27355351(-)$1	1	77	104	22.3493
.((((((..............))))))	chr12:49229905-49230124(-)$1	1	162	189	21.7865
(..(((((.............))))).	chr19:15532427-15532648(-)$1	1	117	144	24.8100
.((((((.((...........)).)))	chr16:67596471-67596683(+)$1	1	162	189	21.3072
).))((((............))))(((	chr10:72186870-72187084(+)$1	1	49	76	22.2667
).(((((..............))))).	chr19:10427715-10427937(-)$1	1	105	132	21.2493
((((((((.............))))))	chr14:77253642-77253863(-)$1	1	184	211	23.6277
((((((((..............)))).	chr17:80037253-80037487(-)$1	1	18	45	23.4685
.((((((((............)))).)	chr17:44834356-44834579(+)$1	1	160	187	22.7134
)(((((((.............))))))	chr12:69115563-69115781(+)$1	1	137	164	25.1266
((((((((............)))))))	chr14:61186668-61186899(-)$1	1	37	64	22.1680
.((.((((.............)))).)	chr19:16345660-16345893(+)$1	1	173	200	24.1731
((((((((.............))))))	chr11:47492253-47492476(-)$1	1	81	108	25.5696
))(((.((.............)).)))	chr1:16265896-16266214(+)$1	1	234	261	23.4791
(...((((..............)))))	chr20:50700798-50701020(-)$1	1	30	57	22.6689
.((..(((.............).))..	chr20:4835012-4835230(-)$1	1	15	42	23.4775
((((((((..............)))))	chr12:49085434-49085661(-)$1	1	85	112	22.3956
(((..((((............))))..	chr16:28845298-28845528(+)$1	1	187	214	22.6076
(((((................)))))(	chr5:138269440-138269665(+)$1	1	77	104	20.3074
...(((((..............)))))	chr10:98593084-98593306(+)$1	1	128	155	23.2433
.(((((((............)))))))	chr12:4413652-4413872(+)$1	1	51	78	24.7116
((((((((.............))))))	chr19:15465564-15465820(-)$1	1	185	212	25.5275
(((.((((.............)))).)	chr1:78030124-78030344(-)$1	1	186	213	24.6709
.(((.(((...........))).))).	chr2:73301909-73302143(-)$1	1	54	81	22.5856
(((((.((............)).))))	chr11:57584651-57584870(+)$1	1	38	65	22.6603
(((((((((............))))..	chr11:117041490-117041708(+)$1	1	109	136	23.7102
..(((((..............))))).	chr19:7979156-7979381(+)$1	1	178	205	20.4701
(((((((((............))))))	chr1:28608743-28609024(+)$1	1	151	178	24.2493

#PSSM
[ : 0.15	e : 0.12	h : 0.10	d : 0.08	g : 0.08	: : 0.08	f : 0.08	i : 0.05	b : 0.05	" : 0.03	! : 0.03	c : 0.03	= : 0.03	H : 0.01	# : 0.01	
g : 0.22	f : 0.12	e : 0.08	h : 0.08	c : 0.06	b : 0.06	d : 0.05	[ : 0.05	" : 0.05	i : 0.05	= : 0.03	: : 0.03	a : 0.01	! : 0.01	] : 0.01	# : 0.01	
g : 0.22	f : 0.15	e : 0.08	h : 0.08	c : 0.06	[ : 0.06	b : 0.06	d : 0.05	i : 0.05	a : 0.03	" : 0.03	= : 0.03	! : 0.01	# : 0.01	
g : 0.22	e : 0.18	f : 0.13	[ : 0.08	h : 0.08	! : 0.06	c : 0.05	i : 0.05	= : 0.03	d : 0.03	b : 0.01	" : 0.01	
g : 0.20	d : 0.17	e : 0.17	f : 0.13	h : 0.08	! : 0.06	i : 0.05	[ : 0.03	= : 0.03	a : 0.01	c : 0.01	
d : 0.20	g : 0.18	e : 0.15	f : 0.13	h : 0.08	c : 0.05	i : 0.05	b : 0.03	= : 0.03	[ : 0.03	y : 0.01	
d : 0.18	g : 0.18	e : 0.15	f : 0.12	h : 0.08	b : 0.06	c : 0.05	i : 0.05	= : 0.03	! : 0.01	[ : 0.01	y : 0.01	
d : 0.18	g : 0.13	e : 0.12	[ : 0.06	h : 0.06	w : 0.06	c : 0.05	i : 0.05	f : 0.05	b : 0.05	y : 0.03	= : 0.03	v : 0.01	x : 0.01	! : 0.01	a : 0.01	
v : 0.29	u : 0.15	w : 0.15	t : 0.06	b : 0.06	a : 0.05	y : 0.05	d : 0.05	i : 0.03	e : 0.01	x : 0.01	= : 0.01	f : 0.01	
v : 0.29	u : 0.25	w : 0.15	t : 0.13	y : 0.05	b : 0.05	e : 0.01	x : 0.01	= : 0.01	
v : 0.29	u : 0.25	t : 0.22	w : 0.15	y : 0.05	x : 0.01	
v : 0.29	u : 0.25	t : 0.22	w : 0.15	y : 0.05	x : 0.01	
v : 0.29	u : 0.25	t : 0.22	w : 0.15	y : 0.05	x : 0.01	
v : 0.29	u : 0.25	t : 0.22	w : 0.15	y : 0.05	x : 0.01	
v : 0.29	u : 0.25	t : 0.22	w : 0.15	y : 0.05	x : 0.01	
v : 0.29	u : 0.25	t : 0.22	w : 0.15	y : 0.05	x : 0.01	
v : 0.29	u : 0.25	t : 0.22	w : 0.15	y : 0.05	x : 0.01	
v : 0.29	u : 0.25	t : 0.22	w : 0.15	y : 0.05	x : 0.01	
v : 0.29	u : 0.25	t : 0.22	w : 0.15	y : 0.05	x : 0.01	
v : 0.29	u : 0.25	t : 0.15	w : 0.15	y : 0.05	g : 0.03	x : 0.01	e : 0.01	c : 0.01	
v : 0.27	w : 0.15	u : 0.10	t : 0.08	g : 0.08	y : 0.05	a : 0.03	f : 0.03	c : 0.03	h : 0.03	e : 0.03	x : 0.01	i : 0.01	d : 0.01	b : 0.01	
d : 0.15	g : 0.15	e : 0.13	b : 0.10	f : 0.08	w : 0.08	i : 0.05	h : 0.05	y : 0.03	a : 0.03	c : 0.03	= : 0.03	] : 0.01	x : 0.01	
d : 0.18	g : 0.17	e : 0.15	b : 0.10	f : 0.10	h : 0.08	i : 0.05	] : 0.05	y : 0.03	= : 0.03	c : 0.01	
d : 0.20	g : 0.18	e : 0.17	f : 0.12	h : 0.08	] : 0.06	i : 0.05	b : 0.03	= : 0.03	y : 0.01	c : 0.01	
d : 0.20	e : 0.18	g : 0.18	f : 0.13	h : 0.08	c : 0.05	i : 0.05	= : 0.03	2 : 0.01	a : 0.01	b : 0.01	
g : 0.18	e : 0.17	f : 0.15	h : 0.08	] : 0.08	2 : 0.06	d : 0.06	c : 0.05	i : 0.05	= : 0.03	a : 0.01	3 : 0.01	
g : 0.15	f : 0.13	2 : 0.10	h : 0.10	d : 0.08	] : 0.08	e : 0.08	c : 0.05	: : 0.05	i : 0.05	= : 0.03	a : 0.01	b : 0.01	3 : 0.01	

#score	1333.7994790605173
#seq	58
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_CDS_m2_run2.txt

#BEAR
fff"""a[eeeeebbmmmmbb]eeeee]a333ff	chr5:154187924-154188150(+)$1	226	117	151	10.1783
fffffa!!ccc[cccmmmmcccccc22a]fffff	chr6:157528207-157528432(+)$1	225	160	194	12.6058
eeeee[bb"""ddddmmmmdddd4444bb]eeee	chr11:47772386-47772603(-)$1	217	52	86	12.6766
ii####ccc!!cccnnnnnccc22ccc333iiii	chr3:58097809-58098026(+)$1	217	115	149	12.1776
ffffggggggg!!bbmmmmbbggggggg]fffff	chrX:153582202-153582422(-)$1	220	59	93	11.6384
d!!eeeeeccc[bboooooobb]ccc4444eeee	chr9:134038403-134038623(+)$1	220	177	211	10.9116
eee[ggggggg[ccclllccc]ggggggg]eeee	chr14:31642777-31642999(-)$1	222	108	142	12.2201
eee[ccc[a####bbmmmmbb333a]ccceeeee	chr8:104427159-104427381(-)$1	222	19	53	13.1525
fdddd[ccc"""ddddllldddd333cccdddd]	chr5:70840856-70841075(+)$1	219	170	204	12.4305
ffffffccc"""bboooooobb4444ccc]ffff	chr6:30681792-30682023(-)$1	231	91	125	12.6160
ggggg"""bba[cccmmmmccc]a]bb333gggg	chr1:114512511-114512746(+)$1	235	156	190	13.3457
!==========[aooooooa]==========]dd	chr5:67592012-67592230(+)$1	218	84	118	13.1415
##dddd!!ccc[cccmmmmcccccc22ddddfff	chr22:50169628-50169874(-)$1	246	185	219	11.7969
!!ggggggg[bb[bbmmmmbb]bb]ggggggg22	chr2:242062164-242062389(-)$1	225	110	144	10.5293
:a[============lll============]a:d	chr1:27102052-27102266(+)$1	214	166	200	11.0087
dddddddd####cccmmmmccc4444dddd]ddd	chr4:183600729-183600950(+)$1	221	103	137	12.3970
:ggggggg[ddddoooooodddd333ggggggg:	chr22:50191621-50191840(-)$1	219	138	172	10.6644
:ggggggg[cccddddllldddd333ccc]gggg	chr11:57457436-57457658(+)$1	222	91	125	12.0511
:iiiiiiiiicccooooooccc4444iiiiiiii	chrX:47104169-47104389(+)$1	220	37	71	12.1709
ggggggg[bb[ddddmmmmddddbbgggggggdd	chr17:79935450-79935673(+)$1	223	165	199	11.6359
f"""dddd####ddddllldddd333ddddffff	chr3:44488669-44488891(-)$1	222	165	199	12.4410
eee===========mmmm===========]eeee	chr14:23495416-23495640(-)$1	224	114	148	12.6770
C==========[ddddllldddd]==========	chr8:22885145-22885360(-)$1	215	34	68	12.3571
gggggg####eeeeemmmmeeeee22ggggggg:	chr8:27957304-27957524(+)$1	220	10	44	10.6843
ccc####a[a[ddddmmmmdddda]a333ccc]f	chr19:15367699-15367962(-)$1	263	14	48	12.9771
ddeeeee"""eeeeemmmmeeeee4444eeeee]	chr11:66482645-66482855(-)$1	210	41	75	11.1744
hhh"""ccc"""ccclllcccccc333hhhhhhh	chrX:46917799-46918015(+)$1	216	109	143	11.9912
ff!!ccc"""eeeeennnnneeeee]ccc]ffff	chr3:127324936-127325156(+)$1	220	149	183	10.1139
[ffffff####ddddmmmmddddffffff]ccc>	chr16:18847655-18847872(-)$1	217	135	169	11.7117
ee!!ggggggg[cccmmmmcccggggggg]eeee	chr4:74017051-74017270(-)$1	219	133	167	13.5301
ddccc!!ccc[ddddllldddd]cccccc]dddd	chr10:75535222-75535451(+)$1	229	112	146	10.9168
ffffff!!ccc[ccclllccc22ccc333fffff	chr17:16004866-16005091(-)$1	225	65	99	11.8860
!eeeeebb"""ddddmmmmdddd22bb]eeeee]	chr12:120615434-120615655(-)$1	221	149	183	11.9296
dd!!ccc"""ddddnnnnndddd333ccc]dddd	chr3:107938288-107938503(-)$1	215	114	148	11.8209
c!!ffffff"""cccoooooocccffffff22cc	chr21:47835922-47836142(+)$1	220	77	111	11.0030
ff"""ffffff[aooooooaffffff22ffffff	chr19:3119164-3119385(+)$1	221	164	198	9.8749
===========[aooooooa]=============	chr3:41275183-41275405(+)$1	222	171	205	13.3713
cc"""eeeee!!cccnnnnnccc22eeeeecccd	chr7:73534840-73535057(+)$1	217	106	140	10.5620
ggbb!!dddd!!cccmmmmccc22dddd333bb3	chr19:7687598-7687830(-)$1	232	62	96	11.2164
ee[eeeee[bb[cccmmmmccc]bb22eeeeeee	chr16:1836512-1836738(+)$1	226	180	214	11.5147
:ffffffbb[a[cccmmmmccc]a]bb]ffffff	chr16:3778746-3778963(-)$1	217	69	103	11.1806
b[=============nnnnn=============]	chr15:69747700-69747922(+)$1	222	49	83	12.1886
"""dddd$$$$$cccmmmmccc333dddd22fff	chr20:31023522-31023750(+)$1	228	125	159	12.4000
dcccggggggg[bbnnnnnbb]ggggggg]ccc]	chr9:135554368-135554597(+)$1	229	12	46	10.3675
ccc[eeeee"""cccmmmmccc4444eeeee]cc	chr6:15487644-15487866(+)$1	222	138	172	13.6897
cc[ggggggg!!aooooooa22ggggggg]ccc:	chr3:49065105-49065337(-)$1	232	29	63	10.9769
ff"""ccc"""ddddmmmmdddd4444cccffff	chr19:34292070-34292298(+)$1	228	88	122	14.0574
a[eeeeeccc!!cccoooooocccccc]eeeee]	chr9:96214288-96214512(+)$1	224	112	146	11.7723
c####ccc[bb[bbmmmmbbbb333ccc22ccce	chr12:49431812-49432048(-)$1	236	41	75	10.7969
eeeee!!ccc"""bbmmmmbb333ccc22eeeee	chr5:122726725-122726947(-)$1	222	140	174	12.3870
ffffcccccc"""bbmmmmbb22ccc]ccc]fff	chr8:144681155-144681374(+)$1	219	182	216	11.7870
d[dddd[bb"""cccmmmmcccbb333dddd]dd	chr19:7619351-7619569(+)$1	218	29	63	12.3413
hhhccc!!bb!!cccmmmmccc22bb4444ccc2	chr11:72408383-72408593(-)$1	210	12	46	12.0708
c[ggggggg!!ddddmmmmdddd333gggggggc	chr19:10218102-10218317(+)$1	215	13	47	14.3396
!!==========ddddllldddd]==========	chr1:149878168-149878386(-)$1	218	101	135	13.1108
fffffffffff[cccmmmmccc]ffffff22fff	chr19:42409017-42409236(+)$1	219	7	41	11.0294
dd"""dddda[ddddmmmmdddd22a]dddd333	chr11:118374502-118374721(+)$1	219	120	154	11.4515

#otherMatches

#Seq PSSM
CAGUCUCAGGAGAUGAACACACUCUUCCGCUUCU	chr5:154187924-154188150(+)$1	226	117	151	10.1783
UUCCGGGCAGCUAGACUUGUCUGCUUACACGGAA	chr6:157528207-157528432(+)$1	225	160	194	12.6058
ACAGACAUAUAUUCUAAGGAGAAAACGAUUUCUG	chr11:47772386-47772603(-)$1	217	52	86	12.6766
UGGGAAAGCCCCGCUCAACGUGCAGUUCAACAGC	chr3:58097809-58098026(+)$1	217	115	149	12.1776
CUGCCUAUGGGCCUGGCCUCACCCAUGGAGUAGU	chrX:153582202-153582422(-)$1	220	59	93	11.6384
CAAUAAAUAUGGGUGAAUGAAUGCAUGAACAUUU	chr9:134038403-134038623(+)$1	220	177	211	10.9116
CUGCUGGUGGUACUGUUUCAGGACCAUCAUCAGC	chr14:31642777-31642999(-)$1	222	108	142	12.2201
GUGUCUGUGCCCCGUUCUUGCCCCCUCAGUACUA	chr8:104427159-104427381(-)$1	222	19	53	13.1525
UUACACUUCCUGUGCCAGAGGUAAAAGAAUGUAC	chr5:70840856-70841075(+)$1	219	170	204	12.4305
GGUAGGCCGAAUGCCUGACUGCUCUGUGGCCCUG	chr6:30681792-30682023(-)$1	231	91	125	12.6160
CACUGAUACCCUGAGUGCUCUCCGAGGCAAUAGU	chr1:114512511-114512746(+)$1	235	156	190	13.3457
UGCGAGGGAAGCGAGAUGGCACUUUUCUUGUCCG	chr5:67592012-67592230(+)$1	218	84	118	13.1415
GGCUCUCGUGGCGCCUGCGGGUCCAGAGGAGGCU	chr22:50169628-50169874(-)$1	246	185	219	11.7969
CAAGGCUGUGGAACUGGAGGGGUUGGCGGCCUGU	chr2:242062164-242062389(-)$1	225	110	144	10.5293
AAGAUUGAGAGGGUUUGGGAUCUUCUUAGUGUAG	chr1:27102052-27102266(+)$1	214	166	200	11.0087
GCUCCUGGAUGGCAGCAGGCUGAUUGCCAGAGAG	chr4:183600729-183600950(+)$1	221	103	137	12.3970
GAAGCUCAAGGGUAUAAAAACCUCCAUGAGUUUG	chr22:50191621-50191840(-)$1	219	138	172	10.6644
UGAAUAACUGUAUUGGUCGCCGGAACUACCGUUA	chr11:57457436-57457658(+)$1	222	91	125	12.0511
AUUGCCUUGGCACAUCUCAGUGGCCCCCAAGGCG	chrX:47104169-47104389(+)$1	220	37	71	12.1709
CUGCUUCAGGUgcggccgcccgcccggggcggac	chr17:79935450-79935673(+)$1	223	165	199	11.6359
UCUCUUCAAAAACAGUAUGAUUGCCAUGAAAGUG	chr3:44488669-44488891(-)$1	222	165	199	12.4410
UUCUGGCUCUGUGUAUGCAUAUGGGGUCAUGGAU	chr14:23495416-23495640(-)$1	224	114	148	12.6770
UGGGAGGGGGGUGCUUCAUGGGCCCCUCCCUUCC	chr8:22885145-22885360(-)$1	215	34	68	12.3571
UCUUGAUAAUGUGAGAUGCUUUACUUUCAGGGUG	chr8:27957304-27957524(+)$1	220	10	44	10.6843
GAGCCUGAGGAGCCAGUGGUGGCCGUGUCCUCCC	chr19:15367699-15367962(-)$1	263	14	48	12.9771
AGGCACUGCAGUUCCUCAAGGAGCAGAAAGUGCA	chr11:66482645-66482855(-)$1	210	41	75	11.1744
GUCACUGGGAAAGCCUCUGGUCCUUCAGGCUGCC	chrX:46917799-46918015(+)$1	216	109	143	11.9912
GUACUGGCCAUGUACCCCAAGUACGACCGCAUCA	chr3:127324936-127325156(+)$1	220	149	183	10.1139
AGAAGCAACACAGCUUGCAAGCUUGCUUCAAGAG	chr16:18847655-18847872(-)$1	217	135	169	11.7117
GUGAAAUAUGUCAAAUAUGUUUAUAUAUUAACCA	chr4:74017051-74017270(-)$1	219	133	167	13.5301
UCUGGACCAGGGGGAAGCUCUCACUGCCAUGAUC	chr10:75535222-75535451(+)$1	229	112	146	10.9168
CUCGAGGAAACACAGAACCUGCGGUUGAGCUUGA	chr17:16004866-16005091(-)$1	225	65	99	11.8860
AGCCUCCGAAGUACCUGUUGGUGAGCGAGAGGUG	chr12:120615434-120615655(-)$1	221	149	183	11.9296
CGAACAGUUCUACAUGUUUUGUACUCUUGCUGCU	chr3:107938288-107938503(-)$1	215	114	148	11.8209
GGAAGAUUGUCAGCUGCCGAAGGUCGAUCUCGUA	chr21:47835922-47836142(+)$1	220	77	111	11.0030
CCUGGUGGACUACUUCCCCGAGUUCGAUGGUGCG	chr19:3119164-3119385(+)$1	221	164	198	9.8749
AAAGGUAAAUUGUCAAAGUAGAAUUUACCUUUGU	chr3:41275183-41275405(+)$1	222	171	205	13.3713
CUUUGGGAUCGUCCUGUGCGAGGUAGGUCCAGGG	chr7:73534840-73535057(+)$1	217	106	140	10.5620
CCUGGAGAAGGCCACCAAGGUGAACUUCAAGCAG	chr19:7687598-7687830(-)$1	232	62	96	11.2164
CAGCUGCCCGCAUCCCGGUGGAGGCCUGGCGGUG	chr16:1836512-1836738(+)$1	226	180	214	11.5147
CGGAUGCCCAGCGUGCAGCCACCCAGGAGCAUCU	chr16:3778746-3778963(-)$1	217	69	103	11.1806
UGACUUUUUUUUUCUAGCUGAGGAGAAGAAAGUG	chr15:69747700-69747922(+)$1	222	49	83	12.1886
AAGGUGAAUGGUGACAUGCGUCUGGUUACAAGGA	chr20:31023522-31023750(+)$1	228	125	159	12.4000
UUGAAGUUUGAACACCAGUUGAUUAAACUCUCAG	chr9:135554368-135554597(+)$1	229	12	46	10.3675
AGCAGGGGUGCCUACAUGUGUGCCAGACCCCAGU	chr6:15487644-15487866(+)$1	222	138	172	13.6897
CCCCAAGGAUCGCGUGCGGGAUGUUUUUGAGGCC	chr3:49065105-49065337(-)$1	232	29	63	10.9769
ACCAAGUCCAAUGCACCUGUGCACAUCGAUGUGG	chr19:34292070-34292298(+)$1	228	88	122	14.0574
CGGCCAGUGGAACCACAUGCUUGGCUACCUGGCG	chr9:96214288-96214512(+)$1	224	112	146	11.7723
AGACGAGUUUGACCUGCUGGCAUAUACUGAUCCU	chr12:49431812-49432048(-)$1	236	41	75	10.7969
CCAGGCAAGUAGUGGCCCUCCUUCAUUCCCCUGG	chr5:122726725-122726947(-)$1	222	140	174	12.3870
UGGCCGCCUUCAAACAGCUGUACAAGCGCGAGCU	chr8:144681155-144681374(+)$1	219	182	216	11.7870
UCGGGGAGCACACUGACCCCAGGCCAACCCCAGG	chr19:7619351-7619569(+)$1	218	29	63	12.3413
CAGGGUGGGAUAGGUGUAGGCCCCUCAGUGACUG	chr11:72408383-72408593(-)$1	210	12	46	12.0708
UCAGCUUAUAGUUGUCACAACAAGGGAUAAGCUA	chr19:10218102-10218317(+)$1	215	13	47	14.3396
GCUUCCUGGGGACACUGGCAGUGCUUCCUGGGAA	chr1:149878168-149878386(-)$1	218	101	135	13.1108
CUCCAGCUUGUGCUUAGGGAGGGGCAGGCACUGG	chr19:42409017-42409236(+)$1	219	7	41	11.0294
UGACUUAAGCACUUCAGAUGAAGACGACUUAUAC	chr11:118374502-118374721(+)$1	219	120	154	11.4515

#DB
(((...(.(((((((....)).))))).)...))	chr5:154187924-154188150(+)$1	1	117	151	10.1783
((((((..(((.(((....))))))..).)))))	chr6:157528207-157528432(+)$1	1	160	194	12.6058
(((((.((...((((....))))....)).))))	chr11:47772386-47772603(-)$1	1	52	86	12.6766
((....(((..(((.....)))..)))...))))	chr3:58097809-58098026(+)$1	1	115	149	12.1776
(((((((((((..((....))))))))).)))))	chrX:153582202-153582422(-)$1	1	59	93	11.6384
(..((((((((.((......)).)))....))))	chr9:134038403-134038623(+)$1	1	177	211	10.9116
(((.(((((((.(((...))).))))))).))))	chr14:31642777-31642999(-)$1	1	108	142	12.2201
(((.(((.(....((....))...).))))))))	chr8:104427159-104427381(-)$1	1	19	53	13.1525
(((((.(((...((((...))))...))))))).	chr5:70840856-70841075(+)$1	1	170	204	12.4305
(((((((((...((......))....))).))))	chr6:30681792-30682023(-)$1	1	91	125	12.6160
(((((...(((.(((....))).).))...))))	chr1:114512511-114512746(+)$1	1	156	190	13.3457
.((((((((((.(......).)))))))))).))	chr5:67592012-67592230(+)$1	1	84	118	13.1415
..((((..(((.(((....))))))..)))))))	chr22:50169628-50169874(-)$1	1	185	219	11.7969
..(((((((.((.((....)).)).)))))))..	chr2:242062164-242062389(-)$1	1	110	144	10.5293
.(.((((((((((((...)))))))))))).).(	chr1:27102052-27102266(+)$1	1	166	200	11.0087
((((((((....(((....)))....)))).)))	chr4:183600729-183600950(+)$1	1	103	137	12.3970
.(((((((.((((......))))...))))))).	chr22:50191621-50191840(-)$1	1	138	172	10.6644
.(((((((.(((((((...))))...))).))))	chr11:57457436-57457658(+)$1	1	91	125	12.0511
.((((((((((((......)))....))))))))	chrX:47104169-47104389(+)$1	1	37	71	12.1709
(((((((.((.((((....)))))))))))))))	chr17:79935450-79935673(+)$1	1	165	199	11.6359
(...((((....((((...))))...))))))))	chr3:44488669-44488891(-)$1	1	165	199	12.4410
((((((((((((((....))))))))))).))))	chr14:23495416-23495640(-)$1	1	114	148	12.6770
(((((((((((.((((...)))).))))))))))	chr8:22885145-22885360(-)$1	1	34	68	12.3571
((((((....(((((....)))))..))))))).	chr8:27957304-27957524(+)$1	1	10	44	10.6843
(((....(.(.((((....))))).)...))).)	chr19:15367699-15367962(-)$1	1	14	48	12.9771
(((((((...(((((....)))))....))))).	chr11:66482645-66482855(-)$1	1	41	75	11.1744
(((...(((...(((...))))))...)))))))	chrX:46917799-46918015(+)$1	1	109	143	11.9912
((..(((...(((((.....))))).))).))))	chr3:127324936-127325156(+)$1	1	149	183	10.1139
.((((((....((((....)))))))))).))).	chr16:18847655-18847872(-)$1	1	135	169	11.7117
((..(((((((.(((....)))))))))).))))	chr4:74017051-74017270(-)$1	1	133	167	13.5301
(((((..(((.((((...)))).)))))).))))	chr10:75535222-75535451(+)$1	1	112	146	10.9168
((((((..(((.(((...)))..)))...)))))	chr17:16004866-16005091(-)$1	1	65	99	11.8860
.(((((((...((((....))))..)).))))).	chr12:120615434-120615655(-)$1	1	149	183	11.9296
((..(((...((((.....))))...))).))))	chr3:107938288-107938503(-)$1	1	114	148	11.8209
(..((((((...(((......)))))))))..))	chr21:47835922-47836142(+)$1	1	77	111	11.0030
((...((((((.(......)))))))..))))))	chr19:3119164-3119385(+)$1	1	164	198	9.8749
(((((((((((.(......).)))))))))))))	chr3:41275183-41275405(+)$1	1	171	205	13.3713
((...(((((..(((.....)))..))))))))(	chr7:73534840-73535057(+)$1	1	106	140	10.5620
((((..((((..(((....)))..))))...)).	chr19:7687598-7687830(-)$1	1	62	96	11.2164
((.(((((.((.(((....))).))..)))))))	chr16:1836512-1836738(+)$1	1	180	214	11.5147
.((((((((.(.(((....))).).)).))))))	chr16:3778746-3778963(-)$1	1	69	103	11.1806
(.(((((((((((((.....))))))))))))).	chr15:69747700-69747922(+)$1	1	49	83	12.1886
...((((.....(((....)))...))))..)))	chr20:31023522-31023750(+)$1	1	125	159	12.4000
(((((((((((.((.....)).))))))).))).	chr9:135554368-135554597(+)$1	1	12	46	10.3675
(((.(((((...(((....)))....))))).))	chr6:15487644-15487866(+)$1	1	138	172	13.6897
((.(((((((..(......)..))))))).))).	chr3:49065105-49065337(-)$1	1	29	63	10.9769
((...(((...((((....))))....)))))))	chr19:34292070-34292298(+)$1	1	88	122	14.0574
(.((((((((..(((......)))))).))))).	chr9:96214288-96214512(+)$1	1	112	146	11.7723
(....(((.((.((....))))...)))..))))	chr12:49431812-49432048(-)$1	1	41	75	10.7969
(((((..(((...((....))...)))..)))))	chr5:122726725-122726947(-)$1	1	140	174	12.3870
((((((((((...((....))..))).))).)))	chr8:144681155-144681374(+)$1	1	182	216	11.7870
(.((((.((...(((....)))))...)))).))	chr19:7619351-7619569(+)$1	1	29	63	12.3413
((((((..((..(((....)))..))....))).	chr11:72408383-72408593(-)$1	1	12	46	12.0708
(.(((((((..((((....))))...))))))))	chr19:10218102-10218317(+)$1	1	13	47	14.3396
..((((((((((((((...)))).))))))))))	chr1:149878168-149878386(-)$1	1	101	135	13.1108
(((((((((((.(((....))).))))))..)))	chr19:42409017-42409236(+)$1	1	7	41	11.0294
((...(((((.((((....))))..).))))...	chr11:118374502-118374721(+)$1	1	120	154	11.4515

#PSSM
f : 0.21	d : 0.14	e : 0.12	c : 0.12	: : 0.08	g : 0.07	! : 0.07	h : 0.03	i : 0.01	# : 0.01	C : 0.01	[ : 0.01	= : 0.01	b : 0.01	" : 0.01	a : 0.01	
f : 0.21	e : 0.14	d : 0.10	g : 0.10	c : 0.08	! : 0.07	[ : 0.07	= : 0.05	i : 0.03	# : 0.03	" : 0.03	h : 0.03	a : 0.01	
f : 0.15	e : 0.14	g : 0.12	" : 0.10	! : 0.08	= : 0.08	d : 0.07	c : 0.07	[ : 0.05	# : 0.03	h : 0.03	i : 0.01	b : 0.01	
f : 0.15	g : 0.14	" : 0.12	e : 0.12	= : 0.12	d : 0.08	# : 0.05	[ : 0.05	! : 0.05	c : 0.05	i : 0.01	b : 0.01	
g : 0.21	e : 0.14	f : 0.12	= : 0.12	" : 0.10	c : 0.10	d : 0.10	# : 0.05	i : 0.01	! : 0.01	
g : 0.19	e : 0.12	c : 0.12	f : 0.12	= : 0.12	d : 0.10	" : 0.05	! : 0.05	[ : 0.03	# : 0.03	a : 0.01	i : 0.01	
c : 0.17	g : 0.17	= : 0.12	! : 0.10	e : 0.10	d : 0.08	f : 0.08	b : 0.03	# : 0.03	a : 0.01	" : 0.01	i : 0.01	[ : 0.01	
c : 0.17	g : 0.15	= : 0.12	! : 0.07	b : 0.07	e : 0.07	" : 0.07	d : 0.07	[ : 0.05	f : 0.05	# : 0.03	i : 0.01	a : 0.01	$ : 0.01	
c : 0.21	g : 0.12	= : 0.12	" : 0.10	b : 0.08	[ : 0.08	# : 0.07	e : 0.05	f : 0.05	d : 0.03	a : 0.01	i : 0.01	$ : 0.01	
" : 0.21	c : 0.15	= : 0.12	g : 0.08	# : 0.08	b : 0.08	e : 0.03	! : 0.03	[ : 0.03	d : 0.03	a : 0.03	f : 0.03	i : 0.01	$ : 0.01	
" : 0.19	! : 0.12	= : 0.12	c : 0.10	e : 0.07	g : 0.07	# : 0.07	[ : 0.07	b : 0.05	a : 0.03	d : 0.03	f : 0.03	$ : 0.01	
[ : 0.28	d : 0.19	" : 0.14	! : 0.10	e : 0.07	= : 0.07	c : 0.05	# : 0.05	b : 0.01	$ : 0.01	
c : 0.36	d : 0.28	e : 0.07	b : 0.07	a : 0.07	= : 0.05	" : 0.03	! : 0.01	# : 0.01	[ : 0.01	
c : 0.35	d : 0.26	b : 0.17	o : 0.10	= : 0.05	e : 0.05	
c : 0.33	d : 0.24	o : 0.14	b : 0.10	n : 0.05	e : 0.05	= : 0.03	m : 0.03	
m : 0.54	o : 0.17	n : 0.10	l : 0.08	d : 0.08	
m : 0.54	o : 0.17	l : 0.17	n : 0.10	
m : 0.54	o : 0.17	l : 0.17	n : 0.10	
m : 0.50	o : 0.17	n : 0.10	l : 0.08	c : 0.05	= : 0.03	d : 0.01	b : 0.01	
c : 0.31	d : 0.28	b : 0.14	o : 0.07	a : 0.07	n : 0.05	= : 0.03	e : 0.03	
c : 0.33	d : 0.28	b : 0.17	= : 0.05	e : 0.05	] : 0.03	o : 0.03	f : 0.01	2 : 0.01	
c : 0.33	d : 0.28	= : 0.08	] : 0.07	b : 0.05	e : 0.05	2 : 0.05	3 : 0.03	g : 0.01	f : 0.01	
d : 0.26	c : 0.10	] : 0.10	2 : 0.08	g : 0.08	= : 0.08	e : 0.07	3 : 0.07	4 : 0.07	b : 0.03	f : 0.01	
3 : 0.17	c : 0.15	4 : 0.10	2 : 0.10	g : 0.08	= : 0.08	e : 0.07	b : 0.07	a : 0.05	f : 0.05	] : 0.03	
3 : 0.17	c : 0.15	4 : 0.12	= : 0.12	g : 0.08	] : 0.07	2 : 0.07	f : 0.07	b : 0.05	e : 0.03	a : 0.01	d : 0.01	
c : 0.14	3 : 0.14	4 : 0.12	g : 0.12	= : 0.12	2 : 0.07	b : 0.07	f : 0.07	e : 0.03	] : 0.03	a : 0.03	d : 0.03	
c : 0.19	g : 0.17	= : 0.12	4 : 0.08	2 : 0.07	d : 0.07	3 : 0.07	e : 0.05	b : 0.05	f : 0.05	] : 0.03	i : 0.01	
g : 0.17	c : 0.17	= : 0.12	d : 0.12	] : 0.07	3 : 0.07	4 : 0.05	f : 0.05	e : 0.05	2 : 0.03	a : 0.01	b : 0.01	i : 0.01	h : 0.01	
g : 0.15	c : 0.15	= : 0.12	d : 0.10	e : 0.10	3 : 0.08	f : 0.08	] : 0.03	4 : 0.03	2 : 0.03	a : 0.01	b : 0.01	i : 0.01	h : 0.01	
] : 0.21	e : 0.14	f : 0.10	d : 0.10	= : 0.10	g : 0.08	3 : 0.07	c : 0.05	2 : 0.05	4 : 0.03	i : 0.01	h : 0.01	
e : 0.21	f : 0.15	g : 0.12	c : 0.12	d : 0.10	= : 0.08	] : 0.05	2 : 0.05	3 : 0.03	i : 0.03	h : 0.01	
f : 0.22	e : 0.19	g : 0.12	c : 0.12	d : 0.07	= : 0.07	] : 0.05	3 : 0.03	i : 0.03	a : 0.01	h : 0.01	2 : 0.01	b : 0.01	
f : 0.24	e : 0.19	c : 0.14	d : 0.12	g : 0.08	= : 0.07	i : 0.03	2 : 0.01	: : 0.01	] : 0.01	h : 0.01	b : 0.01	3 : 0.01	
f : 0.26	e : 0.15	d : 0.14	] : 0.10	: : 0.05	= : 0.05	c : 0.05	i : 0.03	g : 0.03	2 : 0.03	3 : 0.03	h : 0.01	> : 0.01	

#score	679.0520561361453
#seq	57
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_transcript_m3_run2.txt

#BEAR
iiiiiiqqqqqqqqiiiii	chr14:67095236-67095466(+)$1	230	50	69	14.0552
=[ddddqqqqqqqqdddd4	chr17:58730889-58731124(+)$1	235	12	31	13.6245
bb[cccqqqqqqqqcccbb	chr7:93529378-93529607(+)$1	229	30	49	13.3144
!eeeeeqqqqqqqqeeeee	chr1:184709182-184709409(-)$1	227	104	123	15.1104
:eeeeeqqqqqqqqeeeee	chr12:39743710-39743942(-)$1	232	0	19	14.4132
deeeeeqqqqqqqqeeeee	chr12:26279231-26279452(+)$1	221	74	93	14.7796
ffffffqqqqqqqqfffff	chr7:113772062-113772294(+)$1	232	142	161	13.5368
:eeeeeqqqqqqqqeeeee	chr8:77602000-77602232(+)$1	232	195	214	14.4132
dd[cccqqqqqqqqccc]d	chr13:50318450-50318682(-)$1	232	36	55	13.8650
Feeeeeqqqqqqqqeeeee	chr9:34087538-34087769(-)$1	231	79	98	14.7170
eeee[aqqqqqqqqaeeee	chr4:77080948-77081176(-)$1	228	81	100	14.4759
======qqqqqqqq=====	chr7:106860200-106860432(-)$1	232	24	43	14.3673
gggg[aqqqqqqqqa]ggg	chr1:155884077-155884320(-)$1	243	186	205	14.0562
:eeeeeqqqqqqqqeeeee	chr14:67262564-67262796(+)$1	232	158	177	14.4132
ccccbbqqqqqqqqbb]cc	chr1:167510526-167510758(-)$1	232	177	196	12.9787
"""cccqqqqqqqqccc44	chr22:29449672-29449904(+)$1	232	144	163	14.3250
:eeeeeqqqqqqqqeeeee	chr22:40945576-40945808(-)$1	232	123	142	14.4132
cc[cccqqqqqqqqccc]c	chr13:37598315-37598545(-)$1	230	85	104	14.2506
##bb[aqqqqqqqqa]bb2	chr5:140994382-140994614(-)$1	232	74	93	12.5224
fff[bbqqqqqqqqbb333	chr2:96851580-96851812(-)$1	232	65	84	13.2219
[eeeeeqqqqqqqqeeeee	chr1:87363257-87363489(-)$1	232	75	94	15.0594
ggggggqqqqqqqqggggg	chr2:213254899-213255140(-)$1	241	54	73	14.3103
bb!!bbqqqqqqqqbb22b	chr2:77408698-77408932(-)$1	234	139	158	12.3067
+++cccqqqqqqqqccc22	chr12:71837645-71837885(+)$1	240	147	166	12.2209
fffcccqqqqqqqqccc22	chr9:80036180-80036412(+)$1	232	24	43	13.7855
bb[cccqqqqqqqqccc]b	chr1:8663508-8663740(-)$1	232	204	223	13.7057
"eeeeeqqqqqqqqeeeee	chr4:6644303-6644536(+)$1	233	202	221	15.1224
ffffffqqqqqqqqfffff	chr1:52882424-52882650(+)$1	226	84	103	13.5368
:eeeeeqqqqqqqqeeeee	chr6:38334900-38335135(-)$1	235	188	207	14.4132
c[ddddqqqqqqqqdddd]	chr4:80833037-80833269(-)$1	232	123	142	13.6261
ggggggqqqqqqqqggggg	chr16:78603810-78604032(+)$1	222	176	195	14.3103
ggggggqqqqqqqqggggg	chr20:33128629-33128858(+)$1	229	99	118	14.3103
""ddddqqqqqqqqdddd3	chr3:17555528-17555753(-)$1	225	161	180	13.7639
ffffffqqqqqqqqfffff	chr13:25908676-25908907(+)$1	231	148	167	13.5368
[eeeeeqqqqqqqqeeeee	chr19:9767237-9767469(-)$1	232	147	166	15.0594
cc!!bbqqqqqqqqbb22c	chr13:37583399-37583631(+)$1	232	211	230	12.8516
ggggggqqqqqqqqggggg	chr3:196440892-196441124(+)$1	232	73	92	14.3103
:eeeeeqqqqqqqqeeeee	chr1:220707646-220707879(+)$1	233	33	52	14.4132
:eeeeeqqqqqqqqeeeee	chr2:10013721-10013952(+)$1	231	167	186	14.4132
:eeeeeqqqqqqqqeeeee	chr2:148690057-148690289(-)$1	232	72	91	14.4132
$$$cccqqqqqqqqccc77	chr21:41092693-41092925(+)$1	232	191	210	12.4475
ffffffqqqqqqqqfffff	chr3:179084498-179084731(+)$1	233	37	56	13.5368
ggggggqqqqqqqqggggg	chr14:97329544-97329782(+)$1	238	166	185	14.3103
ffffffqqqqqqqqfffff	chr18:72624036-72624267(+)$1	231	68	87	13.5368
:eeeeeqqqqqqqqeeeee	chr15:72117704-72117935(-)$1	231	85	104	14.4132
##ddddqqqqqqqqdddd3	chr18:37081049-37081274(-)$1	225	183	202	13.7251
#eeeeeqqqqqqqqeeeee	chr1:76553686-76553918(+)$1	232	78	97	15.1115
=!!cccqqqqqqqqccc33	chr12:59310362-59310594(-)$1	232	67	86	14.5479
:eeeeeqqqqqqqqeeeee	chr9:33900412-33900637(+)$1	225	85	104	14.4132
a[ddddqqqqqqqqdddd]	chr17:73163941-73164174(-)$1	233	17	36	13.6883
dd[cccqqqqqqqqcccdd	chr22:35671788-35672020(+)$1	232	40	59	13.7398
ggggggqqqqqqqqggggg	chr19:13251623-13251855(+)$1	232	146	165	14.3103
ccc[bbqqqqqqqqbb]cc	chr17:26653630-26653862(+)$1	232	141	160	12.9637

#otherMatches

#Seq PSSM
gugaaggccuaggacuuua	chr14:67095236-67095466(+)$1	230	50	69	14.0552
aauucugagcuuaaagaaa	chr17:58730889-58731124(+)$1	235	12	31	13.6245
gcuagccuccaacagcugc	chr7:93529378-93529607(+)$1	229	30	49	13.3144
uaauuauauuuuauuaauu	chr1:184709182-184709409(-)$1	227	104	123	15.1104
AGUGAAGAAAAUAAUUUAU	chr12:39743710-39743942(-)$1	232	0	19	14.4132
UUUCCUGCACAGAGAGGGA	chr12:26279231-26279452(+)$1	221	74	93	14.7796
AGUUUACAUUUUAAUAAAC	chr7:113772062-113772294(+)$1	232	142	161	13.5368
ACAUCAUAAUGUCCUGAUG	chr8:77602000-77602232(+)$1	232	195	214	14.4132
CAAUGGAUUAACAACUAAU	chr13:50318450-50318682(-)$1	232	36	55	13.8650
AAAUCUUUUUAGUUAGAUU	chr9:34087538-34087769(-)$1	231	79	98	14.7170
CAUGUCUUAAUUAUGCAUG	chr4:77080948-77081176(-)$1	228	81	100	14.4759
augaguuaacauauauUUG	chr7:106860200-106860432(-)$1	232	24	43	14.3673
GGGUUGUUUUUUCUCUAUU	chr1:155884077-155884320(-)$1	243	186	205	14.0562
ugguaaccaucuuuuuacc	chr14:67262564-67262796(+)$1	232	158	177	14.4132
GCUGCUACAAUCUAAGUCA	chr1:167510526-167510758(-)$1	232	177	196	12.9787
UCCGAGUCCUUUGCCUCUU	chr22:29449672-29449904(+)$1	232	144	163	14.3250
cacaacuuauaaguguugu	chr22:40945576-40945808(-)$1	232	123	142	14.4132
UUUUUUGCAGUCUAGAAUA	chr13:37598315-37598545(-)$1	230	85	104	14.2506
AGUGGAGUUGUUCGUGCAG	chr5:140994382-140994614(-)$1	232	74	93	12.5224
AAUCGGCCAGUUCUUCUAU	chr2:96851580-96851812(-)$1	232	65	84	13.2219
AAGGAUUGUUGUUUGUCCU	chr1:87363257-87363489(-)$1	232	75	94	15.0594
UAAAUAAAACUUGAUAUUU	chr2:213254899-213255140(-)$1	241	54	73	14.3103
AAUCUGUUCUUAUUCAAUU	chr2:77408698-77408932(-)$1	234	139	158	12.3067
GAAUGGAACAAAAGCCACA	chr12:71837645-71837885(+)$1	240	147	166	12.2209
ACAGCCUCUGCCUUGGUUU	chr9:80036180-80036412(+)$1	232	24	43	13.7855
GAUGUAACUGUUACUGCUU	chr1:8663508-8663740(-)$1	232	204	223	13.7057
AAUCUGCUGUCUCCCAGAU	chr4:6644303-6644536(+)$1	233	202	221	15.1224
AGGUGCUGAGUUUUGUAUC	chr1:52882424-52882650(+)$1	226	84	103	13.5368
AGUUUUGGAAGGGGAAAGC	chr6:38334900-38335135(-)$1	235	188	207	14.4132
auuaacuaaauguuguuau	chr4:80833037-80833269(-)$1	232	123	142	13.6261
UUCUUUAUUGGUAAAAGGG	chr16:78603810-78604032(+)$1	222	176	195	14.3103
GUUUUUCUUUAACUAAAAA	chr20:33128629-33128858(+)$1	229	99	118	14.3103
UUUAAAAAUAAAACUUUAC	chr3:17555528-17555753(-)$1	225	161	180	13.7639
GAAAAUUAUAAAAUAUUUU	chr13:25908676-25908907(+)$1	231	148	167	13.5368
UUUCUGCUUAACUUCAGAA	chr19:9767237-9767469(-)$1	232	147	166	15.0594
CUUAGGCAAACCAACCCUA	chr13:37583399-37583631(+)$1	232	211	230	12.8516
CUAAUUUAAUUUAUAGUUG	chr3:196440892-196441124(+)$1	232	73	92	14.3103
ugauuaguuaacuauaguc	chr1:220707646-220707879(+)$1	233	33	52	14.4132
cuuugacucugccuuuaaa	chr2:10013721-10013952(+)$1	231	167	186	14.4132
UCUGUUUAGACGAUAAUAG	chr2:148690057-148690289(-)$1	232	72	91	14.4132
AAAGAGAACACAGCCUUAU	chr21:41092693-41092925(+)$1	232	191	210	12.4475
AGAUUUAUUUUUGCAAGUC	chr3:179084498-179084731(+)$1	233	37	56	13.5368
gucucuagggcuacggaga	chr14:97329544-97329782(+)$1	238	166	185	14.3103
CCAAGCUCUCUGCUGUUUG	chr18:72624036-72624267(+)$1	231	68	87	13.5368
AAGGUUUUUAAUAUGACCU	chr15:72117704-72117935(-)$1	231	85	104	14.4132
UUUCAUGUGCUCCAGUGGU	chr18:37081049-37081274(-)$1	225	183	202	13.7251
aaggacuaggcauuguucu	chr1:76553686-76553918(+)$1	232	78	97	15.1115
CCAGCUGAGCUCUGGGUAC	chr12:59310362-59310594(-)$1	232	67	86	14.5479
AGAUUUUCAAGCCUGAAUC	chr9:33900412-33900637(+)$1	225	85	104	14.4132
GUGAAAAUACCCCCUUUCU	chr17:73163941-73164174(-)$1	233	17	36	13.6883
UCACAUGUAGUUAAGUGGA	chr22:35671788-35672020(+)$1	232	40	59	13.7398
GACAGGCUGCCCACCCUGU	chr19:13251623-13251855(+)$1	232	146	165	14.3103
UUGCGGAGCCCCUACUACA	chr17:26653630-26653862(+)$1	232	141	160	12.9637

#DB
((((((........)))))	chr14:67095236-67095466(+)$1	1	50	69	14.0552
(.((((........)))).	chr17:58730889-58731124(+)$1	1	12	31	13.6245
((.(((........)))))	chr7:93529378-93529607(+)$1	1	30	49	13.3144
.(((((........)))))	chr1:184709182-184709409(-)$1	1	104	123	15.1104
.(((((........)))))	chr12:39743710-39743942(-)$1	1	0	19	14.4132
)(((((........)))))	chr12:26279231-26279452(+)$1	1	74	93	14.7796
((((((........)))))	chr7:113772062-113772294(+)$1	1	142	161	13.5368
.(((((........)))))	chr8:77602000-77602232(+)$1	1	195	214	14.4132
((.(((........))).)	chr13:50318450-50318682(-)$1	1	36	55	13.8650
((((((........)))))	chr9:34087538-34087769(-)$1	1	79	98	14.7170
((((.(........)))))	chr4:77080948-77081176(-)$1	1	81	100	14.4759
((((((........)))))	chr7:106860200-106860432(-)$1	1	24	43	14.3673
((((.(........).)))	chr1:155884077-155884320(-)$1	1	186	205	14.0562
.(((((........)))))	chr14:67262564-67262796(+)$1	1	158	177	14.4132
((((((........)).))	chr1:167510526-167510758(-)$1	1	177	196	12.9787
...(((........)))..	chr22:29449672-29449904(+)$1	1	144	163	14.3250
.(((((........)))))	chr22:40945576-40945808(-)$1	1	123	142	14.4132
((.(((........))).)	chr13:37598315-37598545(-)$1	1	85	104	14.2506
..((.(........).)).	chr5:140994382-140994614(-)$1	1	74	93	12.5224
(((.((........))...	chr2:96851580-96851812(-)$1	1	65	84	13.2219
.(((((........)))))	chr1:87363257-87363489(-)$1	1	75	94	15.0594
((((((........)))))	chr2:213254899-213255140(-)$1	1	54	73	14.3103
((..((........))..)	chr2:77408698-77408932(-)$1	1	139	158	12.3067
...(((........)))..	chr12:71837645-71837885(+)$1	1	147	166	12.2209
((((((........)))..	chr9:80036180-80036412(+)$1	1	24	43	13.7855
((.(((........))).)	chr1:8663508-8663740(-)$1	1	204	223	13.7057
.(((((........)))))	chr4:6644303-6644536(+)$1	1	202	221	15.1224
((((((........)))))	chr1:52882424-52882650(+)$1	1	84	103	13.5368
.(((((........)))))	chr6:38334900-38335135(-)$1	1	188	207	14.4132
(.((((........)))).	chr4:80833037-80833269(-)$1	1	123	142	13.6261
((((((........)))))	chr16:78603810-78604032(+)$1	1	176	195	14.3103
((((((........)))))	chr20:33128629-33128858(+)$1	1	99	118	14.3103
..((((........)))).	chr3:17555528-17555753(-)$1	1	161	180	13.7639
((((((........)))))	chr13:25908676-25908907(+)$1	1	148	167	13.5368
.(((((........)))))	chr19:9767237-9767469(-)$1	1	147	166	15.0594
((..((........))..)	chr13:37583399-37583631(+)$1	1	211	230	12.8516
((((((........)))))	chr3:196440892-196441124(+)$1	1	73	92	14.3103
.(((((........)))))	chr1:220707646-220707879(+)$1	1	33	52	14.4132
.(((((........)))))	chr2:10013721-10013952(+)$1	1	167	186	14.4132
.(((((........)))))	chr2:148690057-148690289(-)$1	1	72	91	14.4132
...(((........)))..	chr21:41092693-41092925(+)$1	1	191	210	12.4475
((((((........)))))	chr3:179084498-179084731(+)$1	1	37	56	13.5368
((((((........)))))	chr14:97329544-97329782(+)$1	1	166	185	14.3103
((((((........)))))	chr18:72624036-72624267(+)$1	1	68	87	13.5368
.(((((........)))))	chr15:72117704-72117935(-)$1	1	85	104	14.4132
..((((........)))).	chr18:37081049-37081274(-)$1	1	183	202	13.7251
.(((((........)))))	chr1:76553686-76553918(+)$1	1	78	97	15.1115
(..(((........)))..	chr12:59310362-59310594(-)$1	1	67	86	14.5479
.(((((........)))))	chr9:33900412-33900637(+)$1	1	85	104	14.4132
(.((((........)))).	chr17:73163941-73164174(-)$1	1	17	36	13.6883
((.(((........)))))	chr22:35671788-35672020(+)$1	1	40	59	13.7398
((((((........)))))	chr19:13251623-13251855(+)$1	1	146	165	14.3103
(((.((........)).))	chr17:26653630-26653862(+)$1	1	141	160	12.9637

#PSSM
: : 0.18	f : 0.13	g : 0.13	c : 0.09	= : 0.05	b : 0.05	d : 0.05	" : 0.05	# : 0.05	[ : 0.03	i : 0.01	! : 0.01	F : 0.01	e : 0.01	+ : 0.01	$ : 0.01	a : 0.01	
e : 0.33	f : 0.13	g : 0.13	c : 0.07	[ : 0.05	b : 0.05	d : 0.03	" : 0.03	# : 0.03	i : 0.01	= : 0.01	+ : 0.01	$ : 0.01	! : 0.01	
e : 0.33	f : 0.13	g : 0.13	d : 0.09	[ : 0.09	! : 0.05	c : 0.03	i : 0.01	= : 0.01	" : 0.01	b : 0.01	+ : 0.01	$ : 0.01	
e : 0.33	c : 0.20	g : 0.13	d : 0.09	f : 0.09	[ : 0.03	! : 0.03	i : 0.01	= : 0.01	b : 0.01	
e : 0.32	c : 0.18	g : 0.11	d : 0.09	f : 0.09	b : 0.09	[ : 0.05	i : 0.01	= : 0.01	
e : 0.32	c : 0.18	g : 0.11	d : 0.09	f : 0.09	b : 0.09	a : 0.05	i : 0.01	= : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.32	c : 0.18	g : 0.11	d : 0.09	f : 0.09	b : 0.09	a : 0.05	i : 0.01	= : 0.01	
e : 0.33	c : 0.18	g : 0.11	d : 0.09	f : 0.09	b : 0.09	] : 0.03	i : 0.01	= : 0.01	
e : 0.33	c : 0.18	g : 0.13	d : 0.09	f : 0.09	] : 0.03	2 : 0.03	i : 0.01	= : 0.01	b : 0.01	3 : 0.01	
e : 0.33	g : 0.13	d : 0.11	f : 0.09	2 : 0.07	] : 0.05	b : 0.03	c : 0.03	3 : 0.03	i : 0.01	= : 0.01	4 : 0.01	7 : 0.01	
e : 0.33	g : 0.13	f : 0.09	c : 0.07	3 : 0.07	b : 0.05	2 : 0.05	4 : 0.03	d : 0.03	] : 0.03	i : 0.01	= : 0.01	7 : 0.01	

#score	741.0704245203751
#seq	53
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_CDS_m2_run1.txt

#BEAR
d[eeeeeuuuuuuuuuuuueeeee	chr2:55252584-55252824(-)$1	240	11	35	23.2462
hhhhhhhvvvvvvvvvvvvvhhhh	chr2:86344115-86344355(+)$1	240	189	213	21.2587
dddd!!bbtttttttttttbb22d	chr16:66592064-66592304(+)$1	240	97	121	19.8449
###ddddtttttttttttdddd33	chr14:60600792-60601032(+)$1	240	12	36	20.6420
Ifffffftttttttttttffffff	chr5:70860605-70860845(+)$1	240	211	235	20.2787
ggggggxxxxxxxxxxxxxxxggg	chr2:85262097-85262337(+)$1	240	80	104	18.2947
"""bbwwwwwwwwwwwwwwbbggg	chr10:75299143-75299383(-)$1	240	195	219	21.4517
ee[bbwwwwwwwwwwwwwwbb]ee	chr22:39917913-39918153(+)$1	240	159	183	21.0963
iiiiiiivvvvvvvvvvvvviiii	chr1:245019722-245019962(-)$1	240	104	128	23.3717
b[fffffftttttttttttfffff	chr17:60060310-60060550(-)$1	240	117	141	21.4784
iiiiiiivvvvvvvvvvvvviiii	chr11:8974745-8974985(-)$1	240	77	101	23.3717
eeeee[bbtttttttttttbb]ee	chr5:176562801-176563041(+)$1	240	61	85	21.1053
iiiiiiivvvvvvvvvvvvviiii	chr5:87502859-87503099(-)$1	240	157	181	23.3717
:ffffffvvvvvvvvvvvvvffff	chrX:135080182-135080424(+)$1	242	98	122	22.2333
e[eeeeeuuuuuuuuuuuueeeee	chr8:105509837-105510077(-)$1	240	120	144	23.3151
""eeeeettttttttttteeeeeh	chr1:64038061-64038301(+)$1	240	133	157	21.6052
gggggyyyyyyyyyyyyyyyyggg	chr11:121177751-121177991(+)$1	240	63	87	21.4811
%gggggggtttttttttttggggg	chr5:38530532-38530772(-)$1	240	117	141	21.1260
Effffffuuuuuuuuuuuufffff	chr11:69458598-69458838(+)$1	240	46	70	22.1448
!!bb!!bbtttttttttttbb22b	chr3:182605294-182605534(+)$1	240	113	137	20.2525
h!!eeeeettttttttttteeeee	chr19:34916921-34917161(+)$1	240	110	134	21.6814
ggggggxxxxxxxxxxxxxxxggg	chr7:6513726-6513972(-)$1	246	34	58	18.2947
gg[eeeeettttttttttteeeee	chr14:50081039-50081279(+)$1	240	146	170	21.8313
a[eeeeeuuuuuuuuuuuueeeee	chr12:102154933-102155173(-)$1	240	118	142	23.4460
[bb[bbvvvvvvvvvvvvvbb]bb	chr3:148765778-148766018(-)$1	240	147	171	21.2197
ffff[bbtttttttttttbbffff	chrX:100667781-100668021(+)$1	240	99	123	20.9226
=======uuuuuuuuuuuu=====	chr18:48702602-48702842(-)$1	240	6	30	23.5912
f[cccyyyyyyyyyyyyyyyyccc	chr6:96034241-96034481(+)$1	240	31	55	20.9166
cc!!cccvvvvvvvvvvvvvccc2	chr1:100174500-100174740(-)$1	240	43	67	22.9286
hh[bbwwwwwwwwwwwwwwbb]hh	chr9:110091831-110092080(+)$1	249	75	99	20.7215
beeeeevvvvvvvvvvvvveeeee	chr19:57803351-57803591(+)$1	240	64	88	22.5832
"eeeeevvvvvvvvvvvvveeeee	chr16:29822345-29822585(+)$1	240	51	75	22.7908
gggggyyyyyyyyyyyyyyyyggg	chr8:141561299-141561539(-)$1	240	61	85	21.4811
gggggggwwwwwwwwwwwwwwggg	chr1:197112086-197112326(-)$1	240	151	175	22.7332
ggggggxxxxxxxxxxxxxxxggg	chr13:21721358-21721608(+)$1	250	121	145	18.2947
ffffffwwwwwwwwwwwwwwffff	chr8:95780589-95780829(+)$1	240	148	172	22.1811
!ddddyyyyyyyyyyyyyyyyddd	chr6:80626366-80626606(-)$1	240	128	152	19.9619
!a[eeeeettttttttttteeeee	chr1:154524467-154524707(-)$1	240	201	225	21.7889
####cccvvvvvvvvvvvvvccc4	chr5:67593224-67593464(+)$1	240	35	59	22.9773
gggggggwwwwwwwwwwwwwwggg	chr12:112568218-112568458(+)$1	240	30	54	22.7332
bfffffftttttttttttffffff	chr14:69695545-69695785(+)$1	240	158	182	21.2368
d[eeeeevvvvvvvvvvvvveeee	chr11:62343125-62343407(-)$1	282	200	224	23.1979
ggggggxxxxxxxxxxxxxxxggg	chr6:109689987-109690227(-)$1	240	125	149	18.2947
gggggbbuuuuuuuuuuuubb]gg	chr8:27680565-27680805(-)$1	240	182	206	23.2183
b"""cccuuuuuuuuuuuuccc44	chr14:60585107-60585347(+)$1	240	37	61	22.8933
e[fffffftttttttttttfffff	chr11:9459608-9459848(+)$1	240	66	90	21.4968
dd[ddddwwwwwwwwwwwwwwddd	chr15:76209549-76209789(+)$1	240	187	211	20.9973
:ffffffuuuuuuuuuuuufffff	chr1:214816452-214816692(+)$1	240	34	58	22.2390
::cccyyyyyyyyyyyyyyyyccc	chrX:71425350-71425590(-)$1	240	19	43	18.9398
gggggggvvvvvvvvvvvvvgggg	chr2:203071820-203072101(-)$1	281	45	69	23.6112
gggggggwwwwwwwwwwwwwwggg	chr10:1038365-1038605(+)$1	240	33	57	22.7332
HH:ddddvvvvvvvvvvvvvdddd	chr13:48938928-48939168(+)$1	240	68	92	19.8431
bb[ddddtttttttttttddddbb	chr11:43515349-43515589(+)$1	240	26	50	19.8131
fffffffvvvvvvvvvvvvvffff	chr11:125770034-125770274(+)$1	240	159	183	22.9077
eee[ccctttttttttttccc]ee	chr5:76342233-76342473(+)$1	240	116	140	21.7999
:eeeeevvvvvvvvvvvvveeeee	chr10:69676226-69676466(+)$1	240	72	96	21.9152
b!!ddddtttttttttttddddbb	chr1:28792834-28793074(+)$1	240	207	231	20.2642
[ffffffvvvvvvvvvvvvvffff	chr12:12814039-12814279(-)$1	240	183	207	23.1462
e[cccwwwwwwwwwwwwwwccc]e	chr2:55825477-55825717(-)$1	240	51	75	21.9151
!ffffffuuuuuuuuuuuufffff	chr19:48887386-48887626(-)$1	240	119	143	23.1923
:ffffffuuuuuuuuuuuufffff	chr7:108155191-108155431(-)$1	240	72	96	22.2390
a[eeeeettttttttttteeeee]	chr3:41267075-41267315(+)$1	240	91	115	21.7921
!!cccwwwwwwwwwwwwwwcccii	chr20:20617934-20618174(-)$1	240	141	165	22.2049
!!eeeeeuuuuuuuuuuuueeeee	chr16:3367545-3367785(+)$1	240	68	92	23.5336
hhhhhhhwwwwwwwwwwwwwwhhh	chr20:47768143-47768383(-)$1	240	118	142	20.6143
f[cccwwwwwwwwwwwwwwccc]f	chr2:48033313-48033553(+)$1	240	119	143	21.8952
h"""ccctttttttttttccc]hh	chr4:166254616-166254856(+)$1	240	20	44	21.5673
gggg!!avvvvvvvvvvvvva22g	chr1:55557613-55557853(-)$1	240	133	157	23.1705
fff[cccvvvvvvvvvvvvvccc]	chr12:70206507-70206747(+)$1	240	79	103	23.0821

#otherMatches

#Seq PSSM
GAUAACACAAAAGAUACCCUGUUA	chr2:55252584-55252824(-)$1	240	11	35	23.2462
UUUACAUAAUACUAUUUUAAAUGU	chr2:86344115-86344355(+)$1	240	189	213	21.2587
GGAUUUGAAGUCACCGUUAUCUUA	chr16:66592064-66592304(+)$1	240	97	121	19.8449
ACAAACGAUGAUGAAGAACGUUAU	chr14:60600792-60601032(+)$1	240	12	36	20.6420
UUUAGGUUGAUUUUGAAUACUUAA	chr5:70860605-70860845(+)$1	240	211	235	20.2787
CACAGUCUUUUACUUGUCCCUAUU	chr2:85262097-85262337(+)$1	240	80	104	18.2947
AGUCCUUUUUGAAGUGUUUGGUGA	chr10:75299143-75299383(-)$1	240	195	219	21.4517
AGAUCAUUCCUUUAGUUUAGAGCU	chr22:39917913-39918153(+)$1	240	159	183	21.0963
GUAGUUUGCCCAAAAGAUGAAGAC	chr1:245019722-245019962(-)$1	240	104	128	23.3717
ACCUCAAACUCAUACUUCUUUUGG	chr17:60060310-60060550(-)$1	240	117	141	21.4784
AACUUAAUUUUCAAUUUCCUUUAG	chr11:8974745-8974985(-)$1	240	77	101	23.3717
UCUCCCAGCCCCCUUUUCACUAGG	chr5:176562801-176563041(+)$1	240	61	85	21.1053
AGAUCUGUUUGUGUCACCUUUGGA	chr5:87502859-87503099(-)$1	240	157	181	23.3717
AGAAGUAUUUUUCAACAUAUUACU	chrX:135080182-135080424(+)$1	242	98	122	22.2333
UAUCCAGACUUUUAUCCUCCUGGA	chr8:105509837-105510077(-)$1	240	120	144	23.3151
UACUUAGAACUUACCAAACUAAGA	chr1:64038061-64038301(+)$1	240	133	157	21.6052
GUCAUGCUUUUCACCCUAUUGAUG	chr11:121177751-121177991(+)$1	240	63	87	21.4811
CAUUUAUUCUUCUAUAUCUAAUGA	chr5:38530532-38530772(-)$1	240	117	141	21.1260
GCAAUGACCCCGCACGAUUUCAUU	chr11:69458598-69458838(+)$1	240	46	70	22.1448
AUAUUUGUUUUACUUCCCUACCUA	chr3:182605294-182605534(+)$1	240	113	137	20.2525
UCCuuuuauuaauauaaauuaaaa	chr19:34916921-34917161(+)$1	240	110	134	21.6814
AUACUUCCCUUCUGUUUCUCUAGG	chr7:6513726-6513972(-)$1	246	34	58	18.2947
AUGUUAAUUCCUCUGAUAUGUUAA	chr14:50081039-50081279(+)$1	240	146	170	21.8313
CUCUUAUUUUUAUUAUCUCAUGAG	chr12:102154933-102155173(-)$1	240	118	142	23.4460
AUGGUGGCAUAGAACAAUACAGCG	chr3:148765778-148766018(-)$1	240	147	171	21.2197
AGAAUGAUAUUUAUAAUUUCUUCU	chrX:100667781-100668021(+)$1	240	99	123	20.9226
CAUGUGGCCACAACCUCUUCUGCA	chr18:48702602-48702842(-)$1	240	6	30	23.5912
UGCAGCAAAACACUUACUAUUUUG	chr6:96034241-96034481(+)$1	240	31	55	20.9166
AUAUCUCAAUUUUUCUUUCAGGGU	chr1:100174500-100174740(-)$1	240	43	67	22.9286
UCUUCUACAGCAGAACUUUGAUGA	chr9:110091831-110092080(+)$1	249	75	99	20.7215
UCCCACGAACCCAUCCAGAGUGGG	chr19:57803351-57803591(+)$1	240	64	88	22.5832
UCGUGUUCCUGUGUCCCCUGCAUG	chr16:29822345-29822585(+)$1	240	51	75	22.7908
CACACGGGCAUCGAGAUCAAGGUG	chr8:141561299-141561539(-)$1	240	61	85	21.4811
UAUAUGUGUACAUCUCAGCAAACA	chr1:197112086-197112326(-)$1	240	151	175	22.7332
AAAUUCUAUUUACUAUUUGUUGAA	chr13:21721358-21721608(+)$1	250	121	145	18.2947
AUUUGUUUUCUUUCUAUGUUGCAA	chr8:95780589-95780829(+)$1	240	148	172	22.1811
CUUCUACAUUCGGACAUACAAAGA	chr6:80626366-80626606(-)$1	240	128	152	19.9619
UGUGGAGGAUGCUGGCCUCCCUCC	chr1:154524467-154524707(-)$1	240	201	225	21.7889
AUUGUGUCAUAAACAAAACAGCAA	chr5:67593224-67593464(+)$1	240	35	59	22.9773
UUUUUGCAUGUCAUCUUUAAAGCA	chr12:112568218-112568458(+)$1	240	30	54	22.7332
UCAGAAGAUGCCAGCAAGCUUCUG	chr14:69695545-69695785(+)$1	240	158	182	21.2368
AAAGUAGAUGGACAGAAAAACUGC	chr11:62343125-62343407(-)$1	282	200	224	23.1979
UCUUUAUAAAUUCUGCAAAUCUAA	chr6:109689987-109690227(-)$1	240	125	149	18.2947
UGAAGCUAAGAUUUUGAAAAGCCU	chr8:27680565-27680805(-)$1	240	182	206	23.2183
AAAAACAACUGCCACUUUAUGUAU	chr14:60585107-60585347(+)$1	240	37	61	22.8933
UAUGGAACAGAUACCCCAAGUUUU	chr11:9459608-9459848(+)$1	240	66	90	21.4968
UAAGUUACUUUUAUUUAUCAUUAA	chr15:76209549-76209789(+)$1	240	187	211	20.9973
UUUGUCAGAAAAUGAACAGUGGCA	chr1:214816452-214816692(+)$1	240	34	58	22.2390
AAAGCAAAAAUCAGAAGUAAAGCU	chrX:71425350-71425590(-)$1	240	19	43	18.9398
UUCCUCUUACAGCUGGGAAUGGAG	chr2:203071820-203072101(-)$1	281	45	69	23.6112
GUAAUUAUGUUUUAUUUUCUUUAA	chr10:1038365-1038605(+)$1	240	33	57	22.7332
UUAAUGAUCAUGUUGUAACUUCAU	chr13:48938928-48939168(+)$1	240	68	92	19.8431
CGAGUUUGUCCCAGCCAAGAACCG	chr11:43515349-43515589(+)$1	240	26	50	19.8131
UGAGAUAACCUAGCUCUUUAUAUC	chr11:125770034-125770274(+)$1	240	159	183	22.9077
UCUCUAAUUCAACAUCAUUUAAAG	chr5:76342233-76342473(+)$1	240	116	140	21.7999
AUCUGUGAAACAGGAAGUAACAGA	chr10:69676226-69676466(+)$1	240	72	96	21.9152
GCAAGGUUCAUCAUCUCCACCUCC	chr1:28792834-28793074(+)$1	240	207	231	20.2642
AAGCUUUAACUAUAAAAACAGAAG	chr12:12814039-12814279(-)$1	240	183	207	23.1462
ACAGUACAUUCAGGACAUCAUUUU	chr2:55825477-55825717(-)$1	240	51	75	21.9151
UCUACCUCUAUAUCACCAAAGGUA	chr19:48887386-48887626(-)$1	240	119	143	23.1923
ACAAGUUCUAUAACCACAAAAUUU	chr7:108155191-108155431(-)$1	240	72	96	22.2390
GUGUUGUUUUAUGCCAUUACAACU	chr3:41267075-41267315(+)$1	240	91	115	21.7921
UAACAAACAUCUACAAACCUGUAC	chr20:20617934-20618174(-)$1	240	141	165	22.2049
AGGAAUAAAACCAUAUAAAUGUUC	chr16:3367545-3367785(+)$1	240	68	92	23.5336
GUUCCACCUUUACUUUAUCAAGUG	chr20:47768143-47768383(-)$1	240	118	142	20.6143
CAACUCACUACCAUUCAUUAGUAG	chr2:48033313-48033553(+)$1	240	119	143	21.8952
UAUAUGUUGAAUAAUUAUACAAAG	chr4:166254616-166254856(+)$1	240	20	44	21.5673
AUCUACGGACAAAGAAGAAACUCA	chr1:55557613-55557853(-)$1	240	133	157	23.1705
CCUGUAAACACAGAAUUAAAUUAG	chr12:70206507-70206747(+)$1	240	79	103	23.0821

#DB
(.(((((............)))))	chr2:55252584-55252824(-)$1	1	11	35	23.2462
(((((((.............))))	chr2:86344115-86344355(+)$1	1	189	213	21.2587
((((..((...........))..)	chr16:66592064-66592304(+)$1	1	97	121	19.8449
...((((...........))))..	chr14:60600792-60601032(+)$1	1	12	36	20.6420
)((((((...........))))))	chr5:70860605-70860845(+)$1	1	211	235	20.2787
((((((...............)))	chr2:85262097-85262337(+)$1	1	80	104	18.2947
...((..............)))))	chr10:75299143-75299383(-)$1	1	195	219	21.4517
((.((..............)).))	chr22:39917913-39918153(+)$1	1	159	183	21.0963
(((((((.............))))	chr1:245019722-245019962(-)$1	1	104	128	23.3717
(.((((((...........)))))	chr17:60060310-60060550(-)$1	1	117	141	21.4784
(((((((.............))))	chr11:8974745-8974985(-)$1	1	77	101	23.3717
(((((.((...........)).))	chr5:176562801-176563041(+)$1	1	61	85	21.1053
(((((((.............))))	chr5:87502859-87503099(-)$1	1	157	181	23.3717
.((((((.............))))	chrX:135080182-135080424(+)$1	1	98	122	22.2333
(.(((((............)))))	chr8:105509837-105510077(-)$1	1	120	144	23.3151
..(((((...........))))))	chr1:64038061-64038301(+)$1	1	133	157	21.6052
(((((................)))	chr11:121177751-121177991(+)$1	1	63	87	21.4811
.(((((((...........)))))	chr5:38530532-38530772(-)$1	1	117	141	21.1260
(((((((............)))))	chr11:69458598-69458838(+)$1	1	46	70	22.1448
..((..((...........))..)	chr3:182605294-182605534(+)$1	1	113	137	20.2525
(..(((((...........)))))	chr19:34916921-34917161(+)$1	1	110	134	21.6814
((((((...............)))	chr7:6513726-6513972(-)$1	1	34	58	18.2947
((.(((((...........)))))	chr14:50081039-50081279(+)$1	1	146	170	21.8313
(.(((((............)))))	chr12:102154933-102155173(-)$1	1	118	142	23.4460
.((.((.............)).))	chr3:148765778-148766018(-)$1	1	147	171	21.2197
((((.((...........))))))	chrX:100667781-100668021(+)$1	1	99	123	20.9226
(((((((............)))))	chr18:48702602-48702842(-)$1	1	6	30	23.5912
(.(((................)))	chr6:96034241-96034481(+)$1	1	31	55	20.9166
((..(((.............))).	chr1:100174500-100174740(-)$1	1	43	67	22.9286
((.((..............)).))	chr9:110091831-110092080(+)$1	1	75	99	20.7215
((((((.............)))))	chr19:57803351-57803591(+)$1	1	64	88	22.5832
.(((((.............)))))	chr16:29822345-29822585(+)$1	1	51	75	22.7908
(((((................)))	chr8:141561299-141561539(-)$1	1	61	85	21.4811
(((((((..............)))	chr1:197112086-197112326(-)$1	1	151	175	22.7332
((((((...............)))	chr13:21721358-21721608(+)$1	1	121	145	18.2947
((((((..............))))	chr8:95780589-95780829(+)$1	1	148	172	22.1811
.((((................)))	chr6:80626366-80626606(-)$1	1	128	152	19.9619
.(.(((((...........)))))	chr1:154524467-154524707(-)$1	1	201	225	21.7889
....(((.............))).	chr5:67593224-67593464(+)$1	1	35	59	22.9773
(((((((..............)))	chr12:112568218-112568458(+)$1	1	30	54	22.7332
(((((((...........))))))	chr14:69695545-69695785(+)$1	1	158	182	21.2368
(.(((((.............))))	chr11:62343125-62343407(-)$1	1	200	224	23.1979
((((((...............)))	chr6:109689987-109690227(-)$1	1	125	149	18.2947
(((((((............)).))	chr8:27680565-27680805(-)$1	1	182	206	23.2183
(...(((............)))..	chr14:60585107-60585347(+)$1	1	37	61	22.8933
(.((((((...........)))))	chr11:9459608-9459848(+)$1	1	66	90	21.4968
((.((((..............)))	chr15:76209549-76209789(+)$1	1	187	211	20.9973
.((((((............)))))	chr1:214816452-214816692(+)$1	1	34	58	22.2390
..(((................)))	chrX:71425350-71425590(-)$1	1	19	43	18.9398
(((((((.............))))	chr2:203071820-203072101(-)$1	1	45	69	23.6112
(((((((..............)))	chr10:1038365-1038605(+)$1	1	33	57	22.7332
((.((((.............))))	chr13:48938928-48939168(+)$1	1	68	92	19.8431
((.((((...........))))))	chr11:43515349-43515589(+)$1	1	26	50	19.8131
(((((((.............))))	chr11:125770034-125770274(+)$1	1	159	183	22.9077
(((.(((...........))).))	chr5:76342233-76342473(+)$1	1	116	140	21.7999
.(((((.............)))))	chr10:69676226-69676466(+)$1	1	72	96	21.9152
(..((((...........))))))	chr1:28792834-28793074(+)$1	1	207	231	20.2642
.((((((.............))))	chr12:12814039-12814279(-)$1	1	183	207	23.1462
(.(((..............))).)	chr2:55825477-55825717(-)$1	1	51	75	21.9151
.((((((............)))))	chr19:48887386-48887626(-)$1	1	119	143	23.1923
.((((((............)))))	chr7:108155191-108155431(-)$1	1	72	96	22.2390
(.(((((...........))))).	chr3:41267075-41267315(+)$1	1	91	115	21.7921
..(((..............)))))	chr20:20617934-20618174(-)$1	1	141	165	22.2049
..(((((............)))))	chr16:3367545-3367785(+)$1	1	68	92	23.5336
(((((((..............)))	chr20:47768143-47768383(-)$1	1	118	142	20.6143
(.(((..............))).)	chr2:48033313-48033553(+)$1	1	119	143	21.8952
(...(((...........))).))	chr4:166254616-166254856(+)$1	1	20	44	21.5673
((((..(.............)..)	chr1:55557613-55557853(-)$1	1	133	157	23.1705
(((.(((.............))).	chr12:70206507-70206747(+)$1	1	79	103	23.0821

#PSSM
g : 0.18	e : 0.08	b : 0.08	! : 0.08	f : 0.08	h : 0.07	: : 0.07	d : 0.05	" : 0.04	i : 0.04	# : 0.02	a : 0.02	[ : 0.02	I : 0.01	% : 0.01	E : 0.01	= : 0.01	c : 0.01	H : 0.01	
g : 0.20	f : 0.17	[ : 0.14	e : 0.08	! : 0.07	" : 0.05	h : 0.04	d : 0.04	i : 0.04	# : 0.02	b : 0.02	= : 0.01	c : 0.01	a : 0.01	: : 0.01	H : 0.01	
f : 0.20	g : 0.18	e : 0.17	[ : 0.08	c : 0.07	" : 0.04	i : 0.04	! : 0.04	h : 0.02	d : 0.02	# : 0.02	b : 0.02	= : 0.01	: : 0.01	
e : 0.20	f : 0.18	g : 0.18	d : 0.10	c : 0.07	b : 0.05	i : 0.04	[ : 0.04	h : 0.02	" : 0.02	= : 0.01	! : 0.01	# : 0.01	
e : 0.20	f : 0.17	g : 0.17	c : 0.15	d : 0.08	b : 0.05	! : 0.04	i : 0.04	h : 0.02	[ : 0.01	= : 0.01	
e : 0.18	f : 0.17	g : 0.13	w : 0.08	c : 0.08	d : 0.07	y : 0.07	! : 0.04	i : 0.04	b : 0.04	h : 0.02	[ : 0.01	= : 0.01	
f : 0.15	e : 0.14	w : 0.10	c : 0.08	b : 0.07	d : 0.07	y : 0.07	g : 0.07	x : 0.05	v : 0.05	i : 0.04	h : 0.02	= : 0.01	a : 0.01	
v : 0.26	w : 0.17	u : 0.15	t : 0.14	y : 0.07	x : 0.05	b : 0.04	e : 0.04	f : 0.02	g : 0.01	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
t : 0.27	v : 0.26	w : 0.17	u : 0.15	y : 0.07	x : 0.05	
v : 0.26	w : 0.17	u : 0.15	t : 0.13	y : 0.07	x : 0.05	d : 0.04	f : 0.02	e : 0.02	c : 0.02	b : 0.01	
v : 0.20	e : 0.17	b : 0.13	f : 0.11	w : 0.08	c : 0.08	y : 0.07	x : 0.05	d : 0.04	g : 0.01	= : 0.01	
e : 0.18	f : 0.18	c : 0.13	b : 0.11	y : 0.07	w : 0.07	d : 0.05	x : 0.05	i : 0.04	g : 0.02	h : 0.01	= : 0.01	a : 0.01	
e : 0.18	f : 0.18	g : 0.17	c : 0.13	] : 0.10	d : 0.08	2 : 0.04	i : 0.04	h : 0.02	= : 0.01	
e : 0.23	f : 0.18	g : 0.18	c : 0.07	h : 0.05	i : 0.05	2 : 0.04	b : 0.04	d : 0.04	] : 0.02	3 : 0.01	= : 0.01	4 : 0.01	
e : 0.21	f : 0.20	g : 0.20	h : 0.07	d : 0.05	i : 0.05	b : 0.05	c : 0.02	4 : 0.02	] : 0.02	3 : 0.01	= : 0.01	2 : 0.01	

#score	1497.806354012917
#seq	69
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_UTR_m2_run1.txt

#BEAR
========####ddddssssssssssdddd4444======	chr5:58267361-58267645(-)$1	284	146	186	13.9814
"ccc!!ccc"""eeeeellleeeee]ccc]ccc4444ccc	chrX:12841261-12841520(+)$1	259	198	238	14.5952
=========22eeeee4444ccceeeee333ccc333ggg	chr18:73001474-73001724(+)$1	250	157	197	13.6962
==========[eeeeepppppppeeeee333=========	chr10:112771899-112772227(+)$1	328	163	203	15.4422
fffff!!bb[ccc[cccooooooccc]ccc]bb22fffff	chr15:69740284-69740572(+)$1	288	33	73	13.1028
[==========zzzzzzzzzzzzzzzzz==========]b	chr1:211746496-211746728(-)$1	232	97	137	13.5004
iiiii[ccc[a[cccqqqqqqqqccc]a22ccc]iiiiii	chr2:38522757-38522999(-)$1	242	124	164	13.1935
eeeeeeecccccc[cccooooooccc]ccc]ccc]eeeee	chr16:56463678-56463971(-)$1	293	188	228	13.9922
cc"""============oooooo============]ccc:	chr11:118394291-118394518(+)$1	227	5	45	17.7090
###ccc[ccc[ccc[ccclllccc]ccc333ccc333ccc	chr5:159829420-159829683(-)$1	263	26	66	14.3341
bb####dddd[ccc[bboooooobbccc]dddd]bb]fff	chr17:57292397-57292648(+)$1	251	191	231	12.3714
bdddd============oooooo============22ddd	chr8:17423601-17423833(+)$1	232	150	190	16.7546
#ggggggg####eeeeemmmmeeeee4444gggggggggg	chr14:21820003-21820237(-)$1	234	174	214	15.1041
g[eeeee[ccc!!eeeeemmmmeeeee333ccc]eeeee2	chr14:53108691-53108914(-)$1	223	45	85	13.2822
gggg[ffffff[bb[bboooooobb]bb]ffffff22ggg	chr13:28868851-28869102(+)$1	251	159	199	12.5958
ccc!!ggggggg[ddddnnnnndddd]ggggggg22cccc	chr18:48701288-48701591(-)$1	303	166	206	14.0385
iiiiiiiiiddddddddnnnnndddd]dddd4444iiiii	chr3:176739169-176739401(-)$1	232	32	72	14.6703
:::==========!!ddddllldddd333==========:	chr3:123210461-123210727(-)$1	266	108	148	12.9937
gg=================lll=================:	chr4:52781339-52781573(+)$1	234	48	88	16.6418
[gggggggbb"""ddddnnnnndddd333bb]ggggggg]	chr1:113455390-113455754(-)$1	364	248	288	15.3815
hhhhh!!dddd!!ddddoooooodddddddd4444hhhhh	chr3:160218902-160219172(-)$1	270	133	173	13.7407
====[bb[ccc!!ddddmmmmddddccc]bb]========	chr7:17384930-17385161(+)$1	231	148	188	14.5128
!!ccc[dddd!!eeeeennnnneeeeedddd]ccc4444h	chr9:33110562-33110811(-)$1	249	162	202	13.6468
eeeee"""ccc[eeeeennnnneeeeeccc333eeeee22	chr1:71529388-71529618(-)$1	230	77	117	13.5855
:=================mmmm=================:	chr7:101901135-101901394(+)$1	259	20	60	14.8587
================[bbmmmmbb]==============	chr2:232319507-232319739(-)$1	232	169	209	14.9945
ddd!!=============nnnnn=============333d	chr11:130102627-130102853(-)$1	226	99	139	16.0482
iiiiiiiii####eeeeellleeeee]iiiiiiiii333a	chr1:25169438-25169699(+)$1	261	83	123	16.8326
=========!!ccc[bbrrrrrrrrrbb]ccc]=======	chr6:109689011-109689241(-)$1	230	91	131	14.8387
!!ccc$$$$$ccc[cccoooooocccccc333ccc22bbc	chr1:193054896-193055146(+)$1	250	55	95	14.6861
c####bb$$$$$eeeeeooooooeeeee4444bb333ccc	chr1:6284096-6284342(-)$1	246	76	116	16.5840
=========="""ddddoooooodddd22===========	chr3:171904616-171904846(+)$1	230	75	115	20.5360
g####ccc!!a[eeeeennnnneeeeea22cccggggggg	chr1:179075430-179075694(-)$1	264	177	217	15.4740
===========[cccssssssssssccc]===========	chr5:40761481-40761715(-)$1	234	150	190	15.2577
eeeee[bbiiiiiiiiiooooooiiiiiiiii22bb22ee	chr5:175935057-175935287(+)$1	230	185	225	13.8783
#dddd####bb[eeeeeooooooeeeee]bb333dddd55	chr3:32523752-32523990(-)$1	238	63	103	13.2244
==========!!eeeeeooooooeeeee88888888====	chr15:45009828-45010063(+)$1	235	76	116	16.0516
eeeeegggggggeeeeeooooooeeeee]ggggggggggg	chr2:191798356-191798659(+)$1	303	16	56	16.5202
c[iiiiiiiii"""cccooooooccc333iiiiiiiii]c	chr3:123212617-123212871(-)$1	254	95	135	19.1033
ffffff[ccc"""ddddoooooodddd333ccc333ffff	chr2:233721814-233722076(+)$1	262	21	61	16.8727
========="""eeeeeooooooeeeee22==========	chr12:40152560-40152810(-)$1	250	48	88	20.9896
[cccffffff"""ddddoooooodddd333ffffff]ccc	chr15:59955926-59956162(-)$1	236	180	220	16.0121
b!!ggggggg!!eeeeeooooooeeeee22ggggggg22b	chr18:11852544-11852923(+)$1	379	273	313	17.2647
hh####eeeee[bbcccooooooccc]bb333eeeeehhh	chr1:28149174-28149407(+)$1	233	49	89	13.3517
eeee[eeeee!!eeeeeooooooeeeee]eeeee]eeeee	chr4:108832169-108832412(+)$1	243	142	182	14.7793
iiiiiiiii"""ddddoooooodddd4444iiiiiiiii]	chr14:51722163-51722393(+)$1	230	91	131	19.0103
ggggggg[dddd[ddddnnnnndddd]dddd]ggggggg3	chr5:151184120-151184391(+)$1	271	97	137	13.4376

#otherMatches

#Seq PSSM
UGUUUUAUAUCAGUUAAAAUUCACAAUAAUGUAGAUAGAA	chr5:58267361-58267645(-)$1	284	146	186	13.9814
CAGUUUCAGAUAAACCAUCUUGGUUACUGUGCUUAAUUUG	chrX:12841261-12841520(+)$1	259	198	238	14.5952
AAUGUAAAACCACAAUUUUUGAAUAAAAUUUAGUUCCUGC	chr18:73001474-73001724(+)$1	250	157	197	13.6962
GAGUAAAUCACUGGAUUUCUUUUGUUUGUUUUGAUUUGCU	chr10:112771899-112772227(+)$1	328	163	203	15.4422
AGACAACUAGUAUUCAACAAACCUUGUAUAGUAUAUGUUU	chr15:69740284-69740572(+)$1	288	33	73	13.1028
UUGAGUUAUUUCACUUUUCAUAAUUUUUAAGUAGCUUAUA	chr1:211746496-211746728(-)$1	232	97	137	13.5004
UUUACUUAAUCUAAUGUUAGUGAAUUUGUCUUAUGUAAAA	chr2:38522757-38522999(-)$1	242	124	164	13.1935
ACUUGAGAUGAAAUGCUUGGGGUAGCUUUUCCAUCCUCAA	chr16:56463678-56463971(-)$1	293	188	228	13.9922
GUAUAUUUUUCUAUGAGAAGCACUUCAUAGGGAGAAGCAC	chr11:118394291-118394518(+)$1	227	5	45	17.7090
CAAACUUUAUUGCUUCGAUUUUUGUGGCCCUAUAUUUAGU	chr5:159829420-159829683(-)$1	263	26	66	14.3341
GAAUAUAAAAUACAUGGAUGAUACCUGUUUUUUCUCGUUU	chr17:57292397-57292648(+)$1	251	191	231	12.3714
UCUGUUUCUUUUGUCUUGUCUUAGAGAUGAGGGGGCUACA	chr8:17423601-17423833(+)$1	232	150	190	16.7546
AAUGUAGAGGAAGGCUCAAAGGAGUCAACAUUUAUAUCUG	chr14:21820003-21820237(-)$1	234	174	214	15.1041
AAGCUAUUUGAAGGGGUUUAGGAAUUUAUAUCACAUGGUA	chr14:53108691-53108914(-)$1	223	45	85	13.2822
UUUCAAAGAACUCUCAGUUCUGCCUAGGUGUUUUUGGGGG	chr13:28868851-28869102(+)$1	251	159	199	12.5958
AACGGUUUUUAUUUUGAUUUUUUCAGUAUAAAAAAAGUUG	chr18:48701288-48701591(-)$1	303	166	206	14.0385
ACAUUUAAUAUCAGUUUUUUUUAAACAUGAUUCUAGUUAA	chr3:176739169-176739401(-)$1	232	32	72	14.6703
AAUUGUAAUUUUAUAAGUCUUUGAUUCACuaaaauuauau	chr3:123210461-123210727(-)$1	266	108	148	12.9937
AAAUUUUGUAUGUAUAUACAGUGUGUGUGUAUACAAAAUC	chr4:52781339-52781573(+)$1	234	48	88	16.6418
UUAUAUCUGCUUCUAGCUUAGUGCUAUGUGUGAGAUAUGU	chr1:113455390-113455754(-)$1	364	248	288	15.3815
UUUUUUUAGUUGCUUCUCAAGUCAGAAAACUUUUCAGGAA	chr3:160218902-160219172(-)$1	270	133	173	13.7407
GAAAAAAUUUGUCUGAAACAUUUCAUAAUUUGUUUCCAGC	chr7:17384930-17385161(+)$1	231	148	188	14.5128
AUCUUUGUAACUGCAGGUGGUUUCUGUUUGCCAGGUGUAA	chr9:33110562-33110811(-)$1	249	162	202	13.6468
UUUUUCCGUAACAUUGUCUGCUGCAAUUUAAAUAAAAAUU	chr1:71529388-71529618(-)$1	230	77	117	13.5855
AAAAGGAAAAAAAAAAAGUCGUCUUUUUUUUUUUUUUUUG	chr7:101901135-101901394(+)$1	259	20	60	14.8587
uuuuuuuuuuUUUGCGUUCGUGGGGUUGUAAAAGAAAAGA	chr2:232319507-232319739(-)$1	232	169	209	14.9945
gguuaacuucauuuuuauuuuuuguagagaugaggucuca	chr11:130102627-130102853(-)$1	226	99	139	16.0482
GAUGAAAAUUCAUUUUGAAACUCAAAUAUUUUCAUUUUGG	chr1:25169438-25169699(+)$1	261	83	123	16.8326
AGUAUAGAGCUAAAUUGAUUUAAUUACACUUUCCUUUGUA	chr6:109689011-109689241(-)$1	230	91	131	14.8387
AAGGCAAUUUUUGAGUAGCAUAUUACCAGCUAGCCAGUCA	chr1:193054896-193055146(+)$1	250	55	95	14.6861
UCUCCGUUUAUUUGGGAUUUGAUUCUCAUUUUACCAUAGC	chr1:6284096-6284342(-)$1	246	76	116	16.5840
AAGUAAAAUUACCAUCAACAAUGUGAUUCAAUUUUAUUUU	chr3:171904616-171904846(+)$1	230	75	115	20.5360
UUUCAGGGAGCACCAGGUAGACCCUGGGAACCUAAUGACU	chr1:179075430-179075694(-)$1	264	177	217	15.4740
AUGCAUAUAUAUGCAUAUAUGUGUUUGUUUGuguauguau	chr5:40761481-40761715(-)$1	234	150	190	15.2577
UGGUAAUGGGUACAUGGGUCAGGCCAUGUAUUAACAGAUG	chr5:175935057-175935287(+)$1	230	185	225	13.8783
UAUUUGAAACAGUGGAAUCAUGUUUCCAGUGAUAAAGUUU	chr3:32523752-32523990(-)$1	238	63	103	13.2244
AGGGUUAUAAUAAUGUUAACAUGGACAUGAUCUUCUUUAU	chr15:45009828-45010063(+)$1	235	76	116	16.0516
UCUUCAAGUGAAUUGUUCACCUAAACAAUUUUAUUUUCAU	chr2:191798356-191798659(+)$1	303	16	56	16.5202
UCAGGAAUAGAUUUAUACACCAUUAUUGUUUUAUUUUUAA	chr3:123212617-123212871(-)$1	254	95	135	19.1033
AGGCAGCAUGUGUUCACUGUGCUGUGAUUUCAUCUACUGU	chr2:233721814-233722076(+)$1	262	21	61	16.8727
UAAUAAAAAUAAUGGGACUUUUUUCUUAACUUUUUAUUAG	chr12:40152560-40152810(-)$1	250	48	88	20.9896
UUAUUGAAUGAUGCAUCUUCUUCGGUGAAAUAUUUAUAUG	chr15:59955926-59956162(-)$1	236	180	220	16.0121
AUCUGGAAAAAUUAAAUUUGUUCAUUUAUAUUUUCUACUU	chr18:11852544-11852923(+)$1	379	273	313	17.2647
UUACUUUCUGGUACCCAGUAUAUUGGAGUCUGUCAGAAAC	chr1:28149174-28149407(+)$1	233	49	89	13.3517
uuuuguuuuUAAAAGAUCAUUUUAUCUUAAAAAGGAAAGC	chr4:108832169-108832412(+)$1	243	142	182	14.7793
UUGUAUAUGUCUUAAAUGUAUUUUUGUCCUCAUAUACAGA	chr14:51722163-51722393(+)$1	230	91	131	19.0103
UAGAAUUUUUUUUUGAUAAAGGAUCACAAAACAAUUCUAA	chr5:151184120-151184391(+)$1	271	97	137	13.4376

#DB
((((((((....((((..........))))....))))))	chr5:58267361-58267645(-)$1	1	146	186	13.9814
.(((..(((...(((((...))))).))).)))....)))	chrX:12841261-12841520(+)$1	1	198	238	14.5952
)))))))))..)))))....))))))))...)))...)))	chr18:73001474-73001724(+)$1	1	157	197	13.6962
((((((((((.(((((.......)))))...)))))))))	chr10:112771899-112772227(+)$1	1	163	203	15.4422
(((((..((.(((.(((......))).))).))..)))))	chr15:69740284-69740572(+)$1	1	33	73	13.1028
.((((((((((.................)))))))))).)	chr1:211746496-211746728(-)$1	1	97	137	13.5004
(((((.(((.(.(((........))).)..))).))))))	chr2:38522757-38522999(-)$1	1	124	164	13.1935
))(((((((((((.(((......))).))).))).)))))	chr16:56463678-56463971(-)$1	1	188	228	13.9922
((...((((((((((((......)))))))))))).))).	chr11:118394291-118394518(+)$1	1	5	45	17.7090
...(((.(((.(((.(((...))).)))...)))...)))	chr5:159829420-159829683(-)$1	1	26	66	14.3341
((....((((.(((.((......))))).)))).)).)))	chr17:57292397-57292648(+)$1	1	191	231	12.3714
(((((((((((((((((......))))))))))))..)))	chr8:17423601-17423833(+)$1	1	150	190	16.7546
.(((((((....(((((....)))))....))))))))))	chr14:21820003-21820237(-)$1	1	174	214	15.1041
(.(((((.(((..(((((....)))))...))).))))).	chr14:53108691-53108914(-)$1	1	45	85	13.2822
((((.((((((.((.((......)).)).))))))..)))	chr13:28868851-28869102(+)$1	1	159	199	12.5958
(((..(((((((.((((.....)))).)))))))..)))(	chr18:48701288-48701591(-)$1	1	166	206	14.0385
(((((((((((((((((.....)))).))))....)))))	chr3:176739169-176739401(-)$1	1	32	72	14.6703
...((((((((((..((((...))))...)))))))))).	chr3:123210461-123210727(-)$1	1	108	148	12.9937
))(((((((((((((((((...))))))))))))))))).	chr4:52781339-52781573(+)$1	1	48	88	16.6418
.(((((((((...((((.....))))...)).))))))).	chr1:113455390-113455754(-)$1	1	248	288	15.3815
(((((..((((..((((......))))))))....)))))	chr3:160218902-160219172(-)$1	1	133	173	13.7407
((((.((.(((..((((....))))))).)).))))))))	chr7:17384930-17385161(+)$1	1	148	188	14.5128
..(((.((((..(((((.....))))))))).)))....)	chr9:33110562-33110811(-)$1	1	162	202	13.6468
(((((...(((.(((((.....))))))))...)))))..	chr1:71529388-71529618(-)$1	1	77	117	13.5855
.(((((((((((((((((....))))))))))))))))).	chr7:101901135-101901394(+)$1	1	20	60	14.8587
((((((((((((((((.((....)).))))))))))))))	chr2:232319507-232319739(-)$1	1	169	209	14.9945
(((..(((((((((((((.....)))))))))))))...)	chr11:130102627-130102853(-)$1	1	99	139	16.0482
(((((((((....(((((...))))).)))))))))...)	chr1:25169438-25169699(+)$1	1	83	123	16.8326
(((((((((..(((.((.........)).))).)))))))	chr6:109689011-109689241(-)$1	1	91	131	14.8387
..(((.....(((.(((......))))))...)))..)))	chr1:193054896-193055146(+)$1	1	55	95	14.6861
(....((.....(((((......)))))....))...)))	chr1:6284096-6284342(-)$1	1	76	116	16.5840
((((((((((...((((......))))..)))))))))))	chr3:171904616-171904846(+)$1	1	75	115	20.5360
(....(((..(.(((((.....))))))..))))))))))	chr1:179075430-179075694(-)$1	1	177	217	15.4740
(((((((((((.(((..........))).)))))))))))	chr5:40761481-40761715(-)$1	1	150	190	15.2577
(((((.(((((((((((......)))))))))..))..))	chr5:175935057-175935287(+)$1	1	185	225	13.8783
.((((....((.(((((......))))).))...))))..	chr3:32523752-32523990(-)$1	1	63	103	13.2244
((((((((((..(((((......)))))........))))	chr15:45009828-45010063(+)$1	1	76	116	16.0516
)))))((((((((((((......))))).)))))))((((	chr2:191798356-191798659(+)$1	1	16	56	16.5202
(.(((((((((...(((......)))...))))))))).)	chr3:123212617-123212871(-)$1	1	95	135	19.1033
((((((.(((...((((......))))...)))...))))	chr2:233721814-233722076(+)$1	1	21	61	16.8727
(((((((((...(((((......)))))..))))))))))	chr12:40152560-40152810(-)$1	1	48	88	20.9896
.(((((((((...((((......))))...)))))).)))	chr15:59955926-59956162(-)$1	1	180	220	16.0121
(..(((((((..(((((......)))))..)))))))..)	chr18:11852544-11852923(+)$1	1	273	313	17.2647
((....(((((.(((((......))).))...))))))))	chr1:28149174-28149407(+)$1	1	49	89	13.3517
((((.(((((..(((((......))))).))))).)))))	chr4:108832169-108832412(+)$1	1	142	182	14.7793
(((((((((...((((......))))....))))))))).	chr14:51722163-51722393(+)$1	1	91	131	19.0103
(((((((.((((.((((.....)))).)))).))))))).	chr5:151184120-151184391(+)$1	1	97	137	13.4376

#PSSM
= : 0.21	e : 0.10	g : 0.10	i : 0.08	c : 0.08	[ : 0.06	# : 0.06	b : 0.06	f : 0.04	: : 0.04	h : 0.04	! : 0.04	" : 0.02	d : 0.02	
= : 0.25	e : 0.10	g : 0.10	c : 0.08	i : 0.08	# : 0.06	d : 0.06	! : 0.06	f : 0.04	[ : 0.04	h : 0.04	b : 0.02	: : 0.02	
= : 0.27	e : 0.12	c : 0.10	i : 0.10	# : 0.10	g : 0.08	d : 0.06	f : 0.04	" : 0.02	: : 0.02	h : 0.02	! : 0.02	
= : 0.29	e : 0.12	c : 0.10	i : 0.10	g : 0.10	# : 0.08	f : 0.04	d : 0.04	! : 0.04	" : 0.02	h : 0.02	
= : 0.27	i : 0.10	e : 0.10	# : 0.08	g : 0.08	! : 0.06	f : 0.06	c : 0.06	[ : 0.06	d : 0.04	" : 0.02	h : 0.02	
= : 0.34	g : 0.12	i : 0.08	! : 0.06	[ : 0.06	e : 0.06	# : 0.06	f : 0.06	c : 0.04	b : 0.04	" : 0.02	$ : 0.02	
= : 0.34	g : 0.12	e : 0.08	i : 0.08	c : 0.06	b : 0.06	! : 0.04	[ : 0.04	d : 0.04	f : 0.04	" : 0.02	$ : 0.02	# : 0.02	
= : 0.34	c : 0.12	g : 0.10	i : 0.08	d : 0.06	[ : 0.06	b : 0.04	f : 0.04	$ : 0.04	e : 0.04	" : 0.02	# : 0.02	
= : 0.31	c : 0.17	i : 0.10	d : 0.08	# : 0.06	g : 0.06	b : 0.04	f : 0.04	$ : 0.04	e : 0.04	! : 0.02	
= : 0.25	c : 0.12	d : 0.10	# : 0.06	" : 0.06	g : 0.06	[ : 0.04	f : 0.04	b : 0.04	! : 0.04	$ : 0.04	i : 0.04	e : 0.04	2 : 0.02	
= : 0.19	" : 0.14	c : 0.12	! : 0.10	# : 0.06	[ : 0.06	d : 0.06	a : 0.04	g : 0.04	i : 0.04	2 : 0.02	f : 0.02	$ : 0.02	b : 0.02	e : 0.02	
" : 0.17	[ : 0.14	= : 0.14	! : 0.14	c : 0.12	# : 0.06	e : 0.04	g : 0.04	d : 0.04	z : 0.02	$ : 0.02	i : 0.02	
e : 0.29	c : 0.17	= : 0.14	" : 0.10	d : 0.06	! : 0.06	b : 0.04	[ : 0.04	z : 0.02	# : 0.02	i : 0.02	
e : 0.34	d : 0.23	= : 0.12	c : 0.10	[ : 0.06	b : 0.04	z : 0.02	! : 0.02	i : 0.02	" : 0.02	
e : 0.34	d : 0.23	c : 0.14	= : 0.12	[ : 0.08	z : 0.02	! : 0.02	i : 0.02	
e : 0.34	d : 0.25	c : 0.12	= : 0.12	b : 0.06	z : 0.02	q : 0.02	s : 0.02	i : 0.02	
e : 0.29	d : 0.21	c : 0.12	= : 0.10	b : 0.06	s : 0.04	4 : 0.02	p : 0.02	z : 0.02	q : 0.02	[ : 0.02	i : 0.02	o : 0.02	
o : 0.46	n : 0.14	= : 0.06	s : 0.04	m : 0.04	e : 0.04	l : 0.02	4 : 0.02	p : 0.02	z : 0.02	q : 0.02	c : 0.02	d : 0.02	b : 0.02	r : 0.02	
o : 0.46	n : 0.17	m : 0.08	l : 0.06	s : 0.04	4 : 0.02	p : 0.02	z : 0.02	q : 0.02	d : 0.02	= : 0.02	b : 0.02	r : 0.02	
o : 0.46	n : 0.17	l : 0.10	m : 0.10	s : 0.04	4 : 0.02	p : 0.02	z : 0.02	q : 0.02	r : 0.02	
o : 0.46	n : 0.17	m : 0.10	l : 0.08	s : 0.04	e : 0.02	c : 0.02	p : 0.02	z : 0.02	q : 0.02	r : 0.02	
o : 0.46	n : 0.17	e : 0.06	m : 0.06	s : 0.04	c : 0.04	l : 0.04	p : 0.02	z : 0.02	q : 0.02	d : 0.02	r : 0.02	
o : 0.44	e : 0.14	d : 0.14	s : 0.04	c : 0.04	= : 0.04	p : 0.02	z : 0.02	q : 0.02	m : 0.02	n : 0.02	r : 0.02	
e : 0.34	d : 0.23	c : 0.14	= : 0.10	b : 0.06	s : 0.04	z : 0.02	r : 0.02	i : 0.02	
e : 0.34	d : 0.23	c : 0.12	= : 0.10	b : 0.06	s : 0.04	z : 0.02	] : 0.02	r : 0.02	i : 0.02	
e : 0.31	c : 0.21	d : 0.21	= : 0.10	] : 0.06	s : 0.02	z : 0.02	r : 0.02	i : 0.02	
e : 0.27	] : 0.17	c : 0.12	= : 0.12	d : 0.10	3 : 0.06	4 : 0.04	b : 0.04	z : 0.02	i : 0.02	
c : 0.19	e : 0.19	= : 0.12	3 : 0.12	d : 0.10	b : 0.06	a : 0.04	4 : 0.04	i : 0.04	z : 0.02	g : 0.02	2 : 0.02	
3 : 0.19	] : 0.17	= : 0.14	d : 0.10	c : 0.10	2 : 0.10	4 : 0.06	i : 0.04	g : 0.02	8 : 0.02	b : 0.02	
= : 0.21	3 : 0.17	d : 0.12	c : 0.08	2 : 0.08	4 : 0.06	b : 0.06	i : 0.06	g : 0.04	] : 0.02	f : 0.02	8 : 0.02	e : 0.02	
= : 0.23	c : 0.12	3 : 0.12	d : 0.10	g : 0.08	i : 0.08	b : 0.06	4 : 0.04	] : 0.04	f : 0.04	8 : 0.02	e : 0.02	
= : 0.25	c : 0.19	4 : 0.08	g : 0.08	] : 0.08	3 : 0.08	i : 0.08	f : 0.04	b : 0.02	d : 0.02	8 : 0.02	e : 0.02	
= : 0.27	c : 0.21	g : 0.12	4 : 0.06	i : 0.06	b : 0.04	f : 0.04	3 : 0.04	e : 0.04	d : 0.02	] : 0.02	2 : 0.02	8 : 0.02	
= : 0.29	g : 0.14	c : 0.10	4 : 0.08	] : 0.06	e : 0.06	i : 0.06	2 : 0.04	f : 0.04	3 : 0.04	b : 0.02	8 : 0.02	
= : 0.31	g : 0.12	3 : 0.08	i : 0.08	4 : 0.06	e : 0.06	2 : 0.04	] : 0.04	b : 0.04	f : 0.04	c : 0.04	d : 0.02	8 : 0.02	
= : 0.27	g : 0.12	i : 0.10	e : 0.10	3 : 0.08	2 : 0.08	4 : 0.04	f : 0.04	b : 0.04	] : 0.02	h : 0.02	d : 0.02	8 : 0.02	
= : 0.27	g : 0.12	3 : 0.10	e : 0.10	i : 0.08	2 : 0.08	4 : 0.04	f : 0.04	c : 0.04	] : 0.04	h : 0.02	d : 0.02	
= : 0.27	g : 0.14	c : 0.12	i : 0.08	e : 0.08	f : 0.06	d : 0.04	h : 0.04	3 : 0.04	2 : 0.04	4 : 0.02	b : 0.02	
= : 0.25	g : 0.14	c : 0.12	e : 0.08	f : 0.06	i : 0.06	] : 0.04	h : 0.04	2 : 0.04	3 : 0.04	d : 0.02	4 : 0.02	b : 0.02	5 : 0.02	
= : 0.19	c : 0.14	g : 0.10	: : 0.08	f : 0.06	e : 0.06	h : 0.06	b : 0.04	i : 0.04	d : 0.04	2 : 0.04	] : 0.04	a : 0.02	5 : 0.02	3 : 0.02	

#score	713.4753081373426
#seq	47
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_UTR_m2_run2.txt

#BEAR
ffff[bbeeeeeooooooeeeee333bb]f	chrX:128580417-128580645(-)$1	228	189	219	12.1455
=======!!cccooooooccc]========	chr18:59854007-59854229(-)$1	222	12	42	17.5670
hhhhh!!bb[aooooooa]bb22hhhhhhh	chr1:68168981-68169202(-)$1	221	86	116	11.4489
========eeeeemmmmeeeee]=======	chr8:77895093-77895322(-)$1	229	160	190	10.9945
=========cccooooooccc22=======	chr6:26599185-26599406(+)$1	221	163	193	17.4169
f[eeeee!!cccooooooccc22eeeee]f	chr2:175937635-175937854(-)$1	219	126	156	14.7648
============lll============333	chr11:88026700-88026926(-)$1	226	134	164	13.3792
!!ccc####cccooooooccc333ccc22e	chr1:244871171-244871407(+)$1	236	132	162	16.3669
=========[bboooooobb]=========	chr16:11444883-11445105(+)$1	222	159	189	16.7262
ccc####ddddoooooodddd333cccbbm	chr5:146772702-146772925(-)$1	223	153	183	12.0948
eeeee####cccooooooccceeeee333g	chr5:130761633-130761853(-)$1	220	73	103	15.2948
ddd[ccc!!cccoooooocccccc]dddd:	chr12:96672801-96673020(-)$1	219	186	216	12.8268
!!ggggggg[bboooooobb4444gggggg	chr17:54944348-54944581(+)$1	233	166	196	15.6171
++ggggggg[bboooooobb]gggggggbb	chr6:31478011-31478234(+)$1	223	121	151	12.8624
feeeeeccc[bboooooobb333ccc]eee	chr11:94864504-94864731(+)$1	227	12	42	14.0193
gggg"""eeeeeooooooeeeee]gggggg	chr2:32248989-32249210(-)$1	221	6	36	14.8652
B:==========oooooo==========bb	chr3:96336543-96336789(-)$1	246	135	165	14.2561
!!==========oooooo==========22	chr11:86519858-86520089(+)$1	231	55	85	16.8315
iiiiii[eeeeeooooooeeeee]iiiiii	chr9:86276343-86276571(-)$1	228	10	40	15.1207
eee!!iiiiiiiiillliiiiiiiii333e	chr4:140394905-140395133(+)$1	228	2	32	11.9604
dd!!dddd[cccooooooccc]dddd22dd	chr19:10221869-10222093(-)$1	224	124	154	13.0677
e!!dddd"""bboooooobb333dddd22e	chr5:102423430-102423650(-)$1	220	124	154	14.1833
ggggg!!eeeeeooooooeeeee333gggg	chr1:62916788-62917011(+)$1	223	133	163	14.7515
eee!!iiiiiiiiimmmmiiiiiiiiieee	chr21:46190599-46190837(-)$1	238	204	234	10.9102
"""iiiiiiiiiooooooiiiiiiiii22h	chr12:81188157-81188381(-)$1	224	112	142	15.7145
ddd"""ffffffooooooffffffddddff	chr11:33163080-33163311(-)$1	231	128	158	11.7687
iiiiiiiiicccooooooccc22iiiiiii	chr17:57188946-57189168(-)$1	222	135	165	16.8621
d[dddd!!ddddoooooodddd]dddd]dd	chr10:8058099-8058322(+)$1	223	139	169	12.5204
#eeeee"""cccooooooccc333eeeee4	chrX:46741274-46741506(+)$1	232	159	189	15.6073
:eeeee"""cccooooooccc]eeeee:cc	chr7:100881950-100882169(-)$1	219	167	197	12.8228
iiiiii"""ddddmmmmdddd333iiiiii	chr11:107975784-107976007(+)$1	223	21	51	11.8020
fff"""ffffffooooooffffff]fffff	chr19:1435223-1435443(+)$1	220	160	190	12.1507
gg$$$$$ccc[aooooooacccggggggg6	chr19:58005675-58005895(+)$1	220	111	141	13.5696
iiiiiii[ddddoooooodddd>>>>>>>>	chr19:58064279-58064504(+)$1	225	71	101	12.3222
ggggggg[bb[aooooooa]bb]ggggggg	chr17:28444013-28444271(+)$1	258	204	234	14.1120
ggccc!!eeeeeooooooeeeeeccc]ggg	chr8:81432875-81433102(+)$1	227	126	156	14.0462
iiiiiiiiicccooooooccc333iiiiii	chr1:227844399-227844634(+)$1	235	59	89	17.3581
bb####bb[cccooooooccc]bb]bb]gg	chr1:46506525-46506749(-)$1	224	136	166	13.2476
eeeee$$$$$bboooooobb333eeeeeee	chr19:13064318-13064550(-)$1	232	67	97	13.7555
e[eeeee!!cccooooooccc333eeeee]	chr1:25688707-25688939(+)$1	232	112	142	15.4266
ccc===========lll===========]c	chr14:35180747-35180977(-)$1	230	67	97	13.0410
hhhhhhheeeeeooooooeeeeeffffff"	chr7:91741671-91741897(-)$1	226	124	154	11.4888
eee!!iiiiiiiiimmmmiiiiiiiii22e	chr14:95556492-95556724(-)$1	232	64	94	11.1172
gg[dddd"""bboooooobb]ddddggggg	chr16:8878001-8878225(+)$1	224	87	117	13.6837
gggggg!!ddddnnnnndddd22ggggggg	chr6:143382640-143382859(-)$1	219	175	205	10.8261
eggggggg!!bboooooobb]ggggggga[	chr1:11080442-11080691(-)$1	249	79	109	14.9231

#otherMatches

#Seq PSSM
AGUAGAAAGUAGUUGUGUUUACUGAAUUGU	chrX:128580417-128580645(-)$1	228	189	219	12.1455
GGUGGCUUAGGAAUACCCUCCCGGCUAUCG	chr18:59854007-59854229(-)$1	222	12	42	17.5670
UAUUUAUAAUGUAGCUUCUUUCAAAAUAUU	chr1:68168981-68169202(-)$1	221	86	116	11.4489
CUCUGGGAUGAGUGUGCAUUUAUUUUCAGA	chr8:77895093-77895322(-)$1	229	160	190	10.9945
aaauaaaaauauuuuuauGUGCCUUUUUAU	chr6:26599185-26599406(+)$1	221	163	193	17.4169
UCUCAGUGCCAUCUCCUAAUGAGACUGACA	chr2:175937635-175937854(-)$1	219	126	156	14.7648
uauuuuuaaaauaaaguuuuaaaaauaaCU	chr11:88026700-88026926(-)$1	226	134	164	13.3792
CAAGAAAUGUCUUCCUUUAGAAAAUCUCAU	chr1:244871171-244871407(+)$1	236	132	162	16.3669
GCCCAUGGUGAuuaaagugugguuaugggc	chr16:11444883-11445105(+)$1	222	159	189	16.7262
GCCAGCAGCUGAGAACAUAGCACAGGCCCA	chr5:146772702-146772925(-)$1	223	153	183	12.0948
CAUACUUUUCCAGCCUCAUGGGUAUGGCAC	chr5:130761633-130761853(-)$1	220	73	103	15.2948
AAACUAUAAAUCUUAAUUGGUAUAUUUUGA	chr12:96672801-96673020(-)$1	219	186	216	12.8268
AGCCCAGAAAGGUACAUUCCAGGGUUCUGG	chr17:54944348-54944581(+)$1	233	166	196	15.6171
cgaagggcuguggaagaucagagcccuugu	chr6:31478011-31478234(+)$1	223	121	151	12.8624
AAGAAUCCUGCUGGAUAAAGAAAAGGAAUU	chr11:94864504-94864731(+)$1	227	12	42	14.0193
AUUAAGAGGCAGCUUUAAUUGCCAUGAUCA	chr2:32248989-32249210(-)$1	221	6	36	14.8652
UAGUCCAAAGAGGAACAGCUCUUUGGACAC	chr3:96336543-96336789(-)$1	246	135	165	14.2561
UGGCGUGCACACgugugugugugugugugu	chr11:86519858-86520089(+)$1	231	55	85	16.8315
GUACAGUAAGAUGUGUGGGUUUUUCUGUAU	chr9:86276343-86276571(-)$1	228	10	40	15.1207
GGAUAAGAAGGCAUAGAAUGUUUUCUGGUU	chr4:140394905-140395133(+)$1	228	2	32	11.9604
CCAAUUCAGUUCUUUACUGGAGUGGAAGGG	chr19:10221869-10222093(-)$1	224	124	154	13.0677
UAUAGAAGAAGUAUCUUGACACAUUCUUAA	chr5:102423430-102423650(-)$1	220	124	154	14.1833
AACACUUGGAUUUACACCAGUCUUUUGUGU	chr1:62916788-62917011(+)$1	223	133	163	14.7515
UUggccaggugcggugguucgugccuguaa	chr21:46190599-46190837(-)$1	238	204	234	10.9102
UAAACAUCUAUAGAUAUGUGUGGAUGUGUG	chr12:81188157-81188381(-)$1	224	112	142	15.7145
UCAGUAUUGCAGCAUUCACUGUAGUGAUAG	chr11:33163080-33163311(-)$1	231	128	158	11.7687
GAACAGCAUGAACUUGCUUUCUGAUGCUGU	chr17:57188946-57189168(-)$1	222	135	165	16.8621
AAAUGCCAAGUAAAUUGAUAUUAGUGUAUG	chr10:8058099-8058322(+)$1	223	139	169	12.5204
UAAGACCUUUUACCCAUUUAAUUUGUCUUU	chrX:46741274-46741506(+)$1	232	159	189	15.6073
UUAGCCACAGGAUCACGCUCCAGGCUGUUG	chr7:100881950-100882169(-)$1	219	167	197	12.8228
UUUAAAUAUGGCUGGAAAGCUUGUUUUGAA	chr11:107975784-107976007(+)$1	223	21	51	11.8020
CCCCUCGCUCCUGGCUUUGGGGGUUGGGAC	chr19:1435223-1435443(+)$1	220	160	190	12.1507
CUAAAUAUGCACAcuggaggcaagaugaga	chr19:58005675-58005895(+)$1	220	111	141	13.5696
gaggccacaaggguggagccuuaaucugau	chr19:58064279-58064504(+)$1	225	71	101	12.3222
CAGGGGCAGUGUGAAGAGAGACAGUUCCUG	chr17:28444013-28444271(+)$1	258	204	234	14.1120
GAGAAGCUUUAUUAUUCUAUAAAUUCUUCA	chr8:81432875-81433102(+)$1	227	126	156	14.0462
AAGAUAAUACAGUAGCUUUUGAAAUGUUAU	chr1:227844399-227844634(+)$1	235	59	89	17.3581
AGCUUUCAUCACAGAACAGUGUUGUCUCCA	chr1:46506525-46506749(-)$1	224	136	166	13.2476
AGCCCCAGCAGGCACAGACCAUAGGGCUAG	chr19:13064318-13064550(-)$1	232	67	97	13.7555
AUUUUAAACUUAUUAAAUUGACUCUUAAAC	chr1:25688707-25688939(+)$1	232	112	142	15.4266
UAUCUGAUUUGUUCUCUGGAUAAAUUAGCA	chr14:35180747-35180977(-)$1	230	67	97	13.0410
AUGUGAGAUCAGUGAACUCUGGUUUUAAGA	chr7:91741671-91741897(-)$1	226	124	154	11.4888
AAAUUUUGGAACUAAUUGUAGUUUUAGUUU	chr14:95556492-95556724(-)$1	232	64	94	11.1172
AGCAAGUCUUAGUACAUCCUCACUUUUAUU	chr16:8878001-8878225(+)$1	224	87	117	13.6837
AUUUGGUUCUUUCAGGUGAAGUUCCAAAUC	chr6:143382640-143382859(-)$1	219	175	205	10.8261
UGGGGAUGAAGACAUCCAUCACAUCCCCGU	chr1:11080442-11080691(-)$1	249	79	109	14.9231

#DB
((((.(((((((......)))))...)).)	chrX:128580417-128580645(-)$1	1	189	219	12.1455
(((((((..(((......))).))))))))	chr18:59854007-59854229(-)$1	1	12	42	17.5670
(((((..((.(......).))..)))))))	chr1:68168981-68169202(-)$1	1	86	116	11.4489
(((((((((((((....))))).)))))))	chr8:77895093-77895322(-)$1	1	160	190	10.9945
((((((((((((......)))..)))))))	chr6:26599185-26599406(+)$1	1	163	193	17.4169
(.(((((..(((......)))..))))).)	chr2:175937635-175937854(-)$1	1	126	156	14.7648
((((((((((((...))))))))))))...	chr11:88026700-88026926(-)$1	1	134	164	13.3792
..(((....(((......)))...)))..)	chr1:244871171-244871407(+)$1	1	132	162	16.3669
(((((((((.((......)).)))))))))	chr16:11444883-11445105(+)$1	1	159	189	16.7262
(((....((((......))))...)))((.	chr5:146772702-146772925(-)$1	1	153	183	12.0948
(((((....(((......))))))))...)	chr5:130761633-130761853(-)$1	1	73	103	15.2948
(((.(((..(((......)))))).)))).	chr12:96672801-96673020(-)$1	1	186	216	12.8268
..(((((((.((......))....))))))	chr17:54944348-54944581(+)$1	1	166	196	15.6171
..(((((((.((......)).)))))))))	chr6:31478011-31478234(+)$1	1	121	151	12.8624
(((((((((.((......))...))).)))	chr11:94864504-94864731(+)$1	1	12	42	14.0193
((((...(((((......))))).))))))	chr2:32248989-32249210(-)$1	1	6	36	14.8652
(.((((((((((......))))))))))((	chr3:96336543-96336789(-)$1	1	135	165	14.2561
..((((((((((......))))))))))..	chr11:86519858-86520089(+)$1	1	55	85	16.8315
((((((.(((((......))))).))))))	chr9:86276343-86276571(-)$1	1	10	40	15.1207
(((..(((((((((...)))))))))...)	chr4:140394905-140395133(+)$1	1	2	32	11.9604
((..((((.(((......))).))))..))	chr19:10221869-10222093(-)$1	1	124	154	13.0677
(..((((...((......))...))))..)	chr5:102423430-102423650(-)$1	1	124	154	14.1833
(((((..(((((......)))))...))))	chr1:62916788-62917011(+)$1	1	133	163	14.7515
(((..(((((((((....))))))))))))	chr21:46190599-46190837(-)$1	1	204	234	10.9102
...(((((((((......)))))))))..)	chr12:81188157-81188381(-)$1	1	112	142	15.7145
(((...((((((......))))))))))))	chr11:33163080-33163311(-)$1	1	128	158	11.7687
((((((((((((......)))..)))))))	chr17:57188946-57189168(-)$1	1	135	165	16.8621
(.((((..((((......)))).)))).))	chr10:8058099-8058322(+)$1	1	139	169	12.5204
.(((((...(((......)))...))))).	chrX:46741274-46741506(+)$1	1	159	189	15.6073
.(((((...(((......))).))))).((	chr7:100881950-100882169(-)$1	1	167	197	12.8228
((((((...((((....))))...))))))	chr11:107975784-107976007(+)$1	1	21	51	11.8020
(((...((((((......)))))).)))))	chr19:1435223-1435443(+)$1	1	160	190	12.1507
((.....(((.(......))))))))))).	chr19:58005675-58005895(+)$1	1	111	141	13.5696
(((((((.((((......))))........	chr19:58064279-58064504(+)$1	1	71	101	12.3222
(((((((.((.(......).)).)))))))	chr17:28444013-28444271(+)$1	1	204	234	14.1120
(((((..(((((......)))))))).)))	chr8:81432875-81433102(+)$1	1	126	156	14.0462
((((((((((((......)))...))))))	chr1:227844399-227844634(+)$1	1	59	89	17.3581
((....((.(((......))).)).)).))	chr1:46506525-46506749(-)$1	1	136	166	13.2476
(((((.....((......))...)))))((	chr19:13064318-13064550(-)$1	1	67	97	13.7555
(.(((((..(((......)))...))))).	chr1:25688707-25688939(+)$1	1	112	142	15.4266
((((((((((((((...))))))))))).)	chr14:35180747-35180977(-)$1	1	67	97	13.0410
)))))))(((((......)))))((((((.	chr7:91741671-91741897(-)$1	1	124	154	11.4888
(((..(((((((((....)))))))))..)	chr14:95556492-95556724(-)$1	1	64	94	11.1172
((.((((...((......)).)))))))))	chr16:8878001-8878225(+)$1	1	87	117	13.6837
((((((..((((.....))))..)))))))	chr6:143382640-143382859(-)$1	1	175	205	10.8261
)(((((((..((......)).)))))))(.	chr1:11080442-11080691(-)$1	1	79	109	14.9231

#PSSM
e : 0.17	g : 0.15	= : 0.10	i : 0.10	f : 0.08	d : 0.08	! : 0.06	h : 0.04	c : 0.04	+ : 0.02	B : 0.02	" : 0.02	# : 0.02	: : 0.02	b : 0.02	
e : 0.17	g : 0.17	= : 0.10	i : 0.10	! : 0.08	[ : 0.06	d : 0.06	f : 0.04	h : 0.04	c : 0.04	+ : 0.02	: : 0.02	" : 0.02	b : 0.02	
e : 0.21	= : 0.15	g : 0.15	i : 0.10	c : 0.08	d : 0.06	f : 0.04	h : 0.04	! : 0.04	" : 0.02	$ : 0.02	# : 0.02	[ : 0.02	
= : 0.17	e : 0.15	g : 0.15	i : 0.13	! : 0.08	d : 0.06	h : 0.04	c : 0.04	# : 0.04	" : 0.04	f : 0.02	[ : 0.02	$ : 0.02	
= : 0.17	e : 0.15	g : 0.13	i : 0.13	d : 0.08	c : 0.06	" : 0.06	! : 0.06	h : 0.04	# : 0.04	[ : 0.02	$ : 0.02	
i : 0.19	= : 0.17	e : 0.10	g : 0.10	# : 0.08	d : 0.08	! : 0.06	" : 0.06	$ : 0.04	b : 0.02	c : 0.02	h : 0.02	
= : 0.17	i : 0.15	! : 0.10	g : 0.08	" : 0.08	# : 0.06	d : 0.06	b : 0.04	e : 0.04	c : 0.04	f : 0.04	$ : 0.04	[ : 0.02	h : 0.02	
= : 0.15	e : 0.13	! : 0.13	i : 0.13	" : 0.10	g : 0.06	b : 0.04	# : 0.04	d : 0.04	c : 0.04	f : 0.04	[ : 0.04	$ : 0.02	
e : 0.15	= : 0.13	i : 0.13	! : 0.10	" : 0.10	d : 0.08	b : 0.04	# : 0.04	g : 0.04	c : 0.04	[ : 0.04	f : 0.04	$ : 0.02	
c : 0.30	e : 0.15	[ : 0.10	d : 0.10	= : 0.08	i : 0.08	" : 0.04	f : 0.04	b : 0.02	$ : 0.02	! : 0.02	
c : 0.28	b : 0.17	e : 0.15	d : 0.10	= : 0.08	i : 0.08	f : 0.04	[ : 0.04	a : 0.02	
c : 0.28	b : 0.17	e : 0.15	= : 0.08	i : 0.08	d : 0.08	o : 0.04	f : 0.04	a : 0.04	
o : 0.82	i : 0.06	e : 0.02	l : 0.02	d : 0.02	= : 0.02	n : 0.02	
o : 0.82	i : 0.06	m : 0.04	l : 0.02	= : 0.02	n : 0.02	
o : 0.82	m : 0.08	l : 0.06	n : 0.02	
o : 0.82	m : 0.08	l : 0.04	= : 0.02	n : 0.02	
o : 0.82	m : 0.08	l : 0.04	= : 0.02	n : 0.02	
o : 0.78	d : 0.06	= : 0.04	m : 0.04	a : 0.02	e : 0.02	i : 0.02	
c : 0.28	b : 0.17	e : 0.15	d : 0.10	= : 0.08	i : 0.08	f : 0.04	a : 0.04	] : 0.02	
c : 0.30	b : 0.19	e : 0.15	d : 0.10	= : 0.08	i : 0.08	f : 0.04	] : 0.02	
c : 0.30	e : 0.15	d : 0.10	= : 0.08	] : 0.08	i : 0.08	3 : 0.06	b : 0.04	f : 0.04	4 : 0.02	
3 : 0.19	e : 0.17	2 : 0.10	= : 0.10	] : 0.08	i : 0.08	d : 0.06	c : 0.04	g : 0.04	f : 0.04	4 : 0.02	b : 0.02	
3 : 0.19	e : 0.17	= : 0.13	2 : 0.10	i : 0.08	] : 0.06	g : 0.06	d : 0.04	f : 0.04	c : 0.02	4 : 0.02	> : 0.02	b : 0.02	
3 : 0.17	= : 0.17	g : 0.10	i : 0.10	e : 0.08	d : 0.08	c : 0.06	f : 0.06	] : 0.04	h : 0.02	4 : 0.02	> : 0.02	b : 0.02	
= : 0.17	i : 0.17	g : 0.15	e : 0.13	d : 0.10	c : 0.08	] : 0.06	3 : 0.04	h : 0.02	> : 0.02	f : 0.02	
= : 0.17	g : 0.17	i : 0.17	e : 0.13	d : 0.10	c : 0.08	3 : 0.04	f : 0.04	h : 0.02	> : 0.02	b : 0.02	
g : 0.19	= : 0.17	i : 0.15	e : 0.10	d : 0.08	b : 0.04	c : 0.04	3 : 0.04	] : 0.04	f : 0.04	h : 0.02	2 : 0.02	> : 0.02	
g : 0.21	= : 0.15	e : 0.13	2 : 0.10	i : 0.08	3 : 0.06	b : 0.04	d : 0.04	] : 0.04	f : 0.04	h : 0.02	: : 0.02	> : 0.02	
g : 0.19	2 : 0.10	e : 0.10	= : 0.08	i : 0.08	] : 0.06	3 : 0.06	b : 0.06	d : 0.06	f : 0.06	h : 0.02	c : 0.02	> : 0.02	a : 0.02	
g : 0.19	e : 0.15	f : 0.08	= : 0.08	i : 0.08	h : 0.04	b : 0.04	d : 0.04	c : 0.04	3 : 0.02	m : 0.02	: : 0.02	2 : 0.02	4 : 0.02	6 : 0.02	> : 0.02	] : 0.02	" : 0.02	[ : 0.02	

#score	637.6401554178389
#seq	46
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_UTR_m1_run2.txt

#BEAR
fff!!bbvvvvvvvvvvvvvbb22fffff	chrX:41055455-41055703(+)$1	248	128	157	22.7789
bb[ccc[bbtttttttttttbb]ccc22b	chr19:58489683-58489905(-)$1	222	23	52	22.3061
========uuuuuuuuuuuu=========	chr14:96852426-96852657(+)$1	231	107	136	26.4026
hhhhhhhhuuuuuuuuuuuuhhhhhhhh:	chr17:27876131-27876360(+)$1	229	54	83	21.3423
eeee[cccwwwwwwwwwwwwwwccc]eee	chr4:76567882-76568104(-)$1	222	189	218	23.5288
hhhhhhhhuuuuuuuuuuuuhhhhhhhh3	chr17:27587911-27588131(-)$1	220	168	197	22.3443
d!!fffffftttttttttttffffffddd	chr5:112176034-112176255(+)$1	221	186	215	22.5768
dffffffyyyyyyyyyyyyyyyyffffff	chr4:108832312-108832532(+)$1	220	65	94	22.3967
hhhh[cccvvvvvvvvvvvvvccchhhhh	chr8:26228117-26228345(+)$1	228	183	212	23.7040
========uuuuuuuuuuuu=========	chr3:185204669-185204914(+)$1	245	47	76	26.4026
d!!eeeeevvvvvvvvvvvvveeeeeddd	chr7:128142285-128142513(+)$1	228	95	124	23.8546
:gggggggwwwwwwwwwwwwwwggggggg	chr15:56385038-56385264(-)$1	226	175	204	23.8937
iiiiiiiiitttttttttttiiiiiiiii	chr3:196311927-196312156(+)$1	229	37	66	24.6055
!!ffffffvvvvvvvvvvvvvffffff22	chr19:37006283-37006517(-)$1	234	173	202	24.3917
========vvvvvvvvvvvvv========	chr19:24312005-24312250(+)$1	245	34	63	26.2633
========ttttttttttt==========	chr8:64123606-64123844(+)$1	238	165	194	24.6615
ccffffffvvvvvvvvvvvvvffffff]c	chr15:90814321-90814554(+)$1	233	138	167	24.4647
e[eeeee[attttttttttta]eeeee22	chr6:11135683-11135923(+)$1	240	78	107	23.6954
e[ffffffvvvvvvvvvvvvvffffff]e	chr3:142776528-142776753(+)$1	225	82	111	24.4398
eee!!cccuuuuuuuuuuuuccc4444ee	chr17:30703131-30703373(+)$1	242	44	73	24.3950
iiiiiiixxxxxxxxxxxxxxxiiiiiii	chr11:120356492-120356714(+)$1	222	133	162	20.2784
[eeeeeyyyyyyyyyyyyyyyyeeeee]c	chr5:71503549-71503778(+)$1	229	29	58	22.9904
========uuuuuuuuuuuu=========	chr5:34906990-34907218(-)$1	228	7	36	26.4026
ffccccccvvvvvvvvvvvvvccc]ccc2	chr7:27788145-27788385(+)$1	240	38	67	24.3993
dddd!!bbtttttttttttbb22ddddff	chr7:135612573-135612809(-)$1	236	98	127	20.7798
:ffffffyyyyyyyyyyyyyyyyffffff	chr1:151431674-151431912(-)$1	238	29	58	21.6391
ffffffyyyyyyyyyyyyyyyyffffff]	chr22:24765096-24765320(+)$1	224	47	76	22.6903
bb[fffffftttttttttttffffff22b	chr6:101100503-101100731(-)$1	228	156	185	22.3580
bb"""ddddtttttttttttdddd333bb	chr5:162879420-162879655(-)$1	235	161	190	21.9647
$$$$dddduuuuuuuuuuuudddd66666	chr14:91924548-91924782(-)$1	234	191	220	20.5105
f[ffffffvvvvvvvvvvvvvffffff]f	chr1:154179645-154179876(-)$1	231	13	42	24.4324
ccc!!ddddtttttttttttdddd22ccc	chr1:167390652-167390876(+)$1	224	133	162	22.5879
c!!eeeeeuuuuuuuuuuuueeeee22cc	chrX:114884305-114884529(+)$1	224	100	129	24.3265
!!ddddyyyyyyyyyyyyyyyydddd22a	chr5:135515315-135515562(+)$1	247	95	124	22.1386
:ffffffvvvvvvvvvvvvvffffffccc	chr2:61719089-61719310(-)$1	221	84	113	22.7597
======bbuuuuuuuuuuuubb]======	chr7:138985546-138985781(+)$1	235	144	173	25.4317
[gggggggwwwwwwwwwwwwwwggggggg	chr19:48832524-48832757(+)$1	233	181	210	24.9097
##eeeeevvvvvvvvvvvvveeeee333g	chr4:129785146-129785371(+)$1	225	58	87	24.1984
!!gggggggtttttttttttggggggg]e	chr10:14945827-14946058(+)$1	231	159	188	24.3744
fffffcccuuuuuuuuuuuuccc]fffff	chr2:131808795-131809040(-)$1	245	94	123	24.4620
hh:eeeeevvvvvvvvvvvvveeeeeGGG	chr22:32081409-32081633(-)$1	224	176	205	21.1501
ccc[dddduuuuuuuuuuuudddd]ccc:	chr8:98737575-98737806(+)$1	231	96	125	23.1503
iiiiiiiiuuuuuuuuuuuuiiiiiiiii	chr9:125608248-125608472(-)$1	224	74	103	26.0690
=======xxxxxxxxxxxxxxx=======	chr2:242026416-242026638(-)$1	222	188	217	20.5011
[eeeeeyyyyyyyyyyyyyyyyeeeee22	chrX:133559554-133559790(+)$1	236	166	195	22.6451
iiiiiiyyyyyyyyyyyyyyyyiiiiiii	chr18:48610891-48611135(+)$1	244	28	57	24.2872
cc[ddddvvvvvvvvvvvvvdddd]cccg	chr5:78622450-78622672(+)$1	222	119	148	23.5535
:gggggggwwwwwwwwwwwwwwggggggg	chr2:120736328-120736557(+)$1	229	9	38	23.8937
========vvvvvvvvvvvvv========	chr18:45362689-45362943(-)$1	254	60	89	26.2633
hhhhhhhhuuuuuuuuuuuuhhhhhhhhH	chr1:39471359-39471580(+)$1	221	174	203	21.6589
dddcccyyyyyyyyyyyyyyyyccc]ddd	chr10:101465696-101465920(+)$1	224	188	217	22.1742
c[ffffffvvvvvvvvvvvvvffffff]c	chr6:91224892-91225117(-)$1	225	40	69	24.6507
fdddd[cccuuuuuuuuuuuuccc]dddd	chr22:38363654-38363879(+)$1	225	195	224	22.5772
&&eeeeevvvvvvvvvvvvveeeee333c	chr14:75600055-75600278(-)$1	223	102	131	22.8382
"ggggggguuuuuuuuuuuuggggggg]i	chr1:42643439-42643660(-)$1	221	106	135	25.8199
:gggggggvvvvvvvvvvvvvgggggggg	chr10:119038047-119038267(-)$1	220	96	125	24.7500
ee!!ddddvvvvvvvvvvvvvdddd22ee	chr6:43149090-43149325(+)$1	235	113	142	23.3864
eee!!bbvvvvvvvvvvvvvbb22eeeee	chr16:56463636-56463858(-)$1	222	47	76	22.5744
iggggggguuuuuuuuuuuuggggggg44	chr15:45010146-45010371(+)$1	225	92	121	25.5866
cc"""ddddtttttttttttdddd22ccc	chr8:124220251-124220476(-)$1	225	176	205	22.3840
"gggggggwwwwwwwwwwwwwwggggggg	chr2:139330063-139330295(+)$1	232	96	125	24.8502

#otherMatches

#Seq PSSM
UCAUUACUCUACUCUUUACUGUUUUGGGG	chrX:41055455-41055703(+)$1	248	128	157	22.7789
CCUUAUUGUACACCUAAGAAACCAUACUG	chr19:58489683-58489905(-)$1	222	23	52	22.3061
AAUCUAUUUAUAUUACUAAUAAUGGAUUA	chr14:96852426-96852657(+)$1	231	107	136	26.4026
UUCUGGAACAUUUUUCCUAUUUCCAGAGU	chr17:27876131-27876360(+)$1	229	54	83	21.3423
CCCAGUUGCAUUUCAUACAAACUAAGUGG	chr4:76567882-76568104(-)$1	222	189	218	23.5288
CCCUUCCUCCUCUACUUUCUAGGAGGGGA	chr17:27587911-27588131(-)$1	220	168	197	22.3443
GUUGAAGGGACACCUAUAAACUUUUCCAC	chr5:112176034-112176255(+)$1	221	186	215	22.5768
GACACACCCCACAGAUUUUACAUGUGUGU	chr4:108832312-108832532(+)$1	220	65	94	22.3967
AUCCUCAUUACUGUAUCAUUUGUGGGGUA	chr8:26228117-26228345(+)$1	228	183	212	23.7040
GAUGCUAGCUCUAUUGUAAACUGGCGUCU	chr3:185204669-185204914(+)$1	245	47	76	26.4026
AUUGUAAACCUUAAACCACCAUUUAUUUC	chr7:128142285-128142513(+)$1	228	95	124	23.8546
UUCAGGUUAUUAUAAAUAUUUAGGCUUGA	chr15:56385038-56385264(-)$1	226	175	204	23.8937
GUUUUUACUCUCAAAAUCAUAGUAAAGAU	chr3:196311927-196312156(+)$1	229	37	66	24.6055
AUGUUACAUUUUAUCCCUUUUUGUAAUCA	chr19:37006283-37006517(-)$1	234	173	202	24.3917
UAUUUUAUUAAUUGUACUUCUAUGAAAUA	chr19:24312005-24312250(+)$1	245	34	63	26.2633
ACUGUAUUCAAGUGAAAAAAAUACAGUAU	chr8:64123606-64123844(+)$1	238	165	194	24.6615
AGGUUGGCUGAAGGCUUUGAUGUCAGCAC	chr15:90814321-90814554(+)$1	233	138	167	24.4647
cccacugccauuaaacagaagacaguguu	chr6:11135683-11135923(+)$1	240	78	107	23.6954
UAUUUUGAUUUAGCUUGCUUUUUAAAAAA	chr3:142776528-142776753(+)$1	225	82	111	24.4398
UAUUAUGGAUCUAAUUCAAACCAAUAUGU	chr17:30703131-30703373(+)$1	242	44	73	24.3950
CAAAUUUUAUUUUCUUGACUAUAAAUUUG	chr11:120356492-120356714(+)$1	222	133	162	20.2784
GAAGAAAACCAGAUUUUUAGCCUUCUUGC	chr5:71503549-71503778(+)$1	229	29	58	22.9904
UUCCCAGGCAUAUGGACAAUUCUGGGAGG	chr5:34906990-34907218(-)$1	228	7	36	26.4026
UUGCCCAUGUCAUCUUUCAAAAUGUGGCC	chr7:27788145-27788385(+)$1	240	38	67	24.3993
UGAAUUUUUCCCUUUAUAUAAUUUUCACC	chr7:135612573-135612809(-)$1	236	98	127	20.7798
UGGCCCCCCCACCCCCCUCCCUCGGGGCC	chr1:151431674-151431912(-)$1	238	29	58	21.6391
CCCAAACAAAAAAUAUUUCAACUUUGGGU	chr22:24765096-24765320(+)$1	224	47	76	22.6903
GAUUUUAGAUGCAAAUACUUUCUAGACUU	chr6:101100503-101100731(-)$1	228	156	185	22.3580
cauuggugcucaaaauuauuguacauuug	chr5:162879420-162879655(-)$1	235	161	190	21.9647
AUAAAGUUUUCCUCUUUUUUAACUGUUCC	chr14:91924548-91924782(-)$1	234	191	220	20.5105
CCGGGCCGCCCUCGGAACAUCUGGCCCAG	chr1:154179645-154179876(-)$1	231	13	42	24.4324
GUUUUGGCCCUUCUACUCUUGGCCUUAGC	chr1:167390652-167390876(+)$1	224	133	162	22.5879
UUUUCUUAUUCUUUUAUUCUUAAGAUCAG	chrX:114884305-114884529(+)$1	224	100	129	24.3265
UUUGCUUACUUGAUAGAACUUUGGCAUUU	chr5:135515315-135515562(+)$1	247	95	124	22.1386
AUUGAUGAAAUUUUGAACAACAUUAACAC	chr2:61719089-61719310(-)$1	221	84	113	22.7597
AGGUCAGAGGGUAAAUGAAAUCGUGAUUU	chr7:138985546-138985781(+)$1	235	144	173	25.4317
AGGAGGUCUCUUCUAUGCCACCGGCCUCU	chr19:48832524-48832757(+)$1	233	181	210	24.9097
AAACAGGGAAUAAAUCAGGAUUUGUGUGU	chr4:129785146-129785371(+)$1	225	58	87	24.1984
AGAUUCUGUUAACCAAAAUUGCAGAAUGG	chr10:14945827-14946058(+)$1	231	159	188	24.3744
AAUGAGUUAAAAGGGAACAAAACUUUAUU	chr2:131808795-131809040(-)$1	245	94	123	24.4620
uuggguuuuuuuuuuuuuuuuGGACCUCC	chr22:32081409-32081633(-)$1	224	176	205	21.1501
AGGCAAAAUCCAAUUUACAUUUUUCCCUU	chr8:98737575-98737806(+)$1	231	96	125	23.1503
UUCAAAUGGGAUCAUUUAAACAUUUGAAA	chr9:125608248-125608472(-)$1	224	74	103	26.0690
UUUCUGUUUUUCUGGGUAUUUCACAGAGA	chr2:242026416-242026638(-)$1	222	188	217	20.5011
UGAAUAAGACAUCCAUAACUACUAUUCUU	chrX:133559554-133559790(+)$1	236	166	195	22.6451
AGCUGGAGAGGAAGGGAUGAAACCAGCUG	chr18:48610891-48611135(+)$1	244	28	57	24.2872
UAGCUUUGUGCAAUAUUAUAAAAGGUAGA	chr5:78622450-78622672(+)$1	222	119	148	23.5535
CAAAUGGCAGAUAUUUUGGAAAGCCAUUU	chr2:120736328-120736557(+)$1	229	9	38	23.8937
UGUCUGUGUACAUUUUCCUUUCAUGGACA	chr18:45362689-45362943(-)$1	254	60	89	26.2633
AACAAAUAAAAUACUUAAGCUAUUUGUUU	chr1:39471359-39471580(+)$1	221	174	203	21.6589
GUAGAAUUCUUCAAAAAUAAAUUUCAUAC	chr10:101465696-101465920(+)$1	224	188	217	22.1742
UAAUUUUGCUACCAAAACCUUCAGAAUAA	chr6:91224892-91225117(-)$1	225	40	69	24.6507
CUUCCCCGUUACCGCCAUGCUGCGUGGAG	chr22:38363654-38363879(+)$1	225	195	224	22.5772
uuuaucuuaaccauucacauagaugugug	chr14:75600055-75600278(-)$1	223	102	131	22.8382
AAAUCACUUUAAUUAGCCUUAGUGAUUCU	chr1:42643439-42643660(-)$1	221	106	135	25.8199
GAAGUUAACACAAACACAAUCUUAGCUUA	chr10:119038047-119038267(-)$1	220	96	125	24.7500
AAAAAUACUCUUUCAAUAAAUGUAUCAUU	chr6:43149090-43149325(+)$1	235	113	142	23.3864
ACUUUAUUUUUACAGUACUUGUUCAGUCA	chr16:56463636-56463858(-)$1	222	47	76	22.5744
AUAUAAGAUUCAUAUUUACUUCUUAUACA	chr15:45010146-45010371(+)$1	225	92	121	25.5866
GUUUACCCAUUUGUAAAACUUGGGCUGCA	chr8:124220251-124220476(-)$1	225	176	205	22.3840
UGGAUAAAAUAAAAAUAUUCAAUUUAUUC	chr2:139330063-139330295(+)$1	232	96	125	24.8502

#DB
(((..((.............))..)))))	chrX:41055455-41055703(+)$1	1	128	157	22.7789
((.(((.((...........)).)))..)	chr19:58489683-58489905(-)$1	1	23	52	22.3061
((((((((............)))))))))	chr14:96852426-96852657(+)$1	1	107	136	26.4026
((((((((............)))))))).	chr17:27876131-27876360(+)$1	1	54	83	21.3423
((((.(((..............))).)))	chr4:76567882-76568104(-)$1	1	189	218	23.5288
((((((((............)))))))).	chr17:27587911-27588131(-)$1	1	168	197	22.3443
(..((((((...........)))))))))	chr5:112176034-112176255(+)$1	1	186	215	22.5768
)((((((................))))))	chr4:108832312-108832532(+)$1	1	65	94	22.3967
((((.(((.............))))))))	chr8:26228117-26228345(+)$1	1	183	212	23.7040
((((((((............)))))))))	chr3:185204669-185204914(+)$1	1	47	76	26.4026
(..(((((.............))))))))	chr7:128142285-128142513(+)$1	1	95	124	23.8546
.(((((((..............)))))))	chr15:56385038-56385264(-)$1	1	175	204	23.8937
(((((((((...........)))))))))	chr3:196311927-196312156(+)$1	1	37	66	24.6055
..((((((.............))))))..	chr19:37006283-37006517(-)$1	1	173	202	24.3917
((((((((.............))))))))	chr19:24312005-24312250(+)$1	1	34	63	26.2633
((((((((...........))))))))))	chr8:64123606-64123844(+)$1	1	165	194	24.6615
((((((((.............)))))).)	chr15:90814321-90814554(+)$1	1	138	167	24.4647
(.(((((.(...........).)))))..	chr6:11135683-11135923(+)$1	1	78	107	23.6954
(.((((((.............)))))).)	chr3:142776528-142776753(+)$1	1	82	111	24.4398
(((..(((............)))....))	chr17:30703131-30703373(+)$1	1	44	73	24.3950
(((((((...............)))))))	chr11:120356492-120356714(+)$1	1	133	162	20.2784
.(((((................))))).)	chr5:71503549-71503778(+)$1	1	29	58	22.9904
((((((((............)))))))))	chr5:34906990-34907218(-)$1	1	7	36	26.4026
((((((((.............))).))).	chr7:27788145-27788385(+)$1	1	38	67	24.3993
((((..((...........))..))))))	chr7:135612573-135612809(-)$1	1	98	127	20.7798
.((((((................))))))	chr1:151431674-151431912(-)$1	1	29	58	21.6391
((((((................)))))).	chr22:24765096-24765320(+)$1	1	47	76	22.6903
((.((((((...........))))))..)	chr6:101100503-101100731(-)$1	1	156	185	22.3580
((...((((...........))))...))	chr5:162879420-162879655(-)$1	1	161	190	21.9647
....((((............)))).....	chr14:91924548-91924782(-)$1	1	191	220	20.5105
(.((((((.............)))))).)	chr1:154179645-154179876(-)$1	1	13	42	24.4324
(((..((((...........))))..)))	chr1:167390652-167390876(+)$1	1	133	162	22.5879
(..(((((............)))))..))	chrX:114884305-114884529(+)$1	1	100	129	24.3265
..((((................))))..)	chr5:135515315-135515562(+)$1	1	95	124	22.1386
.((((((.............))))))(((	chr2:61719089-61719310(-)$1	1	84	113	22.7597
((((((((............)).))))))	chr7:138985546-138985781(+)$1	1	144	173	25.4317
.(((((((..............)))))))	chr19:48832524-48832757(+)$1	1	181	210	24.9097
..(((((.............)))))...)	chr4:129785146-129785371(+)$1	1	58	87	24.1984
..(((((((...........))))))).)	chr10:14945827-14946058(+)$1	1	159	188	24.3744
((((((((............))).)))))	chr2:131808795-131809040(-)$1	1	94	123	24.4620
)).(((((.............))))))))	chr22:32081409-32081633(-)$1	1	176	205	21.1501
(((.((((............)))).))).	chr8:98737575-98737806(+)$1	1	96	125	23.1503
((((((((............)))))))))	chr9:125608248-125608472(-)$1	1	74	103	26.0690
(((((((...............)))))))	chr2:242026416-242026638(-)$1	1	188	217	20.5011
.(((((................)))))..	chrX:133559554-133559790(+)$1	1	166	195	22.6451
((((((................)))))))	chr18:48610891-48611135(+)$1	1	28	57	24.2872
((.((((.............)))).)))(	chr5:78622450-78622672(+)$1	1	119	148	23.5535
.(((((((..............)))))))	chr2:120736328-120736557(+)$1	1	9	38	23.8937
((((((((.............))))))))	chr18:45362689-45362943(-)$1	1	60	89	26.2633
((((((((............)))))))))	chr1:39471359-39471580(+)$1	1	174	203	21.6589
((((((................))).)))	chr10:101465696-101465920(+)$1	1	188	217	22.1742
(.((((((.............)))))).)	chr6:91224892-91225117(-)$1	1	40	69	24.6507
)((((.(((............))).))))	chr22:38363654-38363879(+)$1	1	195	224	22.5772
..(((((.............)))))...)	chr14:75600055-75600278(-)$1	1	102	131	22.8382
.(((((((............))))))).)	chr1:42643439-42643660(-)$1	1	106	135	25.8199
.(((((((.............)))))))(	chr10:119038047-119038267(-)$1	1	96	125	24.7500
((..((((.............))))..))	chr6:43149090-43149325(+)$1	1	113	142	23.3864
(((..((.............))..)))))	chr16:56463636-56463858(-)$1	1	47	76	22.5744
((((((((............)))))))..	chr15:45010146-45010371(+)$1	1	92	121	25.5866
((...((((...........))))..)))	chr8:124220251-124220476(-)$1	1	176	205	22.3840
.(((((((..............)))))))	chr2:139330063-139330295(+)$1	1	96	125	24.8502

#PSSM
= : 0.13	c : 0.11	f : 0.09	e : 0.09	h : 0.08	d : 0.08	: : 0.08	i : 0.08	b : 0.04	! : 0.04	[ : 0.04	" : 0.03	$ : 0.01	# : 0.01	& : 0.01	
= : 0.13	f : 0.11	g : 0.11	e : 0.09	! : 0.09	h : 0.08	c : 0.08	i : 0.06	[ : 0.06	b : 0.04	d : 0.04	$ : 0.01	# : 0.01	& : 0.01	
f : 0.18	= : 0.13	e : 0.13	g : 0.13	h : 0.06	! : 0.06	i : 0.06	d : 0.06	[ : 0.04	c : 0.04	" : 0.03	$ : 0.01	: : 0.01	
f : 0.19	e : 0.14	= : 0.13	g : 0.13	! : 0.08	h : 0.06	i : 0.06	d : 0.06	c : 0.04	" : 0.03	$ : 0.01	[ : 0.01	
f : 0.19	= : 0.13	e : 0.13	g : 0.13	d : 0.09	! : 0.08	i : 0.06	c : 0.04	h : 0.04	[ : 0.03	" : 0.03	
f : 0.18	= : 0.13	e : 0.13	g : 0.13	d : 0.13	c : 0.11	i : 0.06	h : 0.04	b : 0.03	! : 0.01	[ : 0.01	
f : 0.16	g : 0.13	= : 0.11	d : 0.11	c : 0.09	e : 0.09	y : 0.09	b : 0.06	h : 0.04	i : 0.04	[ : 0.01	
y : 0.13	g : 0.13	f : 0.11	v : 0.09	= : 0.09	c : 0.09	d : 0.09	b : 0.04	h : 0.04	e : 0.04	i : 0.03	x : 0.03	[ : 0.01	
v : 0.31	u : 0.24	y : 0.13	w : 0.08	d : 0.04	f : 0.03	t : 0.03	x : 0.03	b : 0.01	i : 0.01	a : 0.01	g : 0.01	c : 0.01	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.18	y : 0.13	w : 0.08	x : 0.03	
v : 0.31	u : 0.26	t : 0.14	y : 0.13	w : 0.08	x : 0.03	= : 0.01	b : 0.01	
v : 0.21	y : 0.13	d : 0.09	b : 0.08	w : 0.08	= : 0.06	h : 0.04	f : 0.04	e : 0.04	g : 0.04	i : 0.03	c : 0.03	x : 0.03	a : 0.01	u : 0.01	
f : 0.13	y : 0.13	d : 0.11	= : 0.09	w : 0.08	c : 0.08	e : 0.08	b : 0.06	g : 0.06	h : 0.04	i : 0.03	x : 0.03	] : 0.01	2 : 0.01	
f : 0.14	e : 0.13	g : 0.13	d : 0.13	= : 0.11	c : 0.11	i : 0.06	2 : 0.04	h : 0.04	] : 0.03	y : 0.03	
f : 0.18	d : 0.14	= : 0.13	e : 0.13	g : 0.13	c : 0.09	i : 0.06	h : 0.04	2 : 0.03	4 : 0.01	] : 0.01	
f : 0.21	e : 0.14	= : 0.13	g : 0.13	h : 0.06	i : 0.06	] : 0.06	c : 0.04	d : 0.04	2 : 0.03	4 : 0.01	3 : 0.01	6 : 0.01	
f : 0.21	= : 0.13	g : 0.13	e : 0.09	c : 0.06	h : 0.06	i : 0.06	2 : 0.06	d : 0.04	3 : 0.04	] : 0.03	4 : 0.01	6 : 0.01	
f : 0.16	= : 0.13	g : 0.13	c : 0.09	2 : 0.08	e : 0.08	d : 0.08	h : 0.06	i : 0.06	3 : 0.04	4 : 0.01	6 : 0.01	G : 0.01	
= : 0.13	] : 0.11	c : 0.11	f : 0.09	2 : 0.09	g : 0.08	h : 0.06	e : 0.06	d : 0.06	i : 0.06	3 : 0.03	b : 0.01	6 : 0.01	G : 0.01	4 : 0.01	
= : 0.13	c : 0.13	g : 0.11	f : 0.09	e : 0.09	i : 0.08	d : 0.06	2 : 0.06	b : 0.04	: : 0.03	3 : 0.01	h : 0.01	] : 0.01	6 : 0.01	a : 0.01	G : 0.01	H : 0.01	4 : 0.01	

#score	1436.849960937609
#seq	61
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_UTR_m2_run2.txt

#BEAR
eee[eeeeennnnneeeee]eee	chr9:35056061-35056290(-)$1	229	199	222	11.0222
ggggg[cccnnnnncccgggggg	chr19:37238458-37238688(-)$1	230	188	211	12.0794
d####ddddnnnnndddd22ddd	chr11:95564385-95564615(+)$1	230	191	214	11.3311
fffff[cccnnnnnccc]fffff	chr1:19234701-19234931(-)$1	230	130	153	10.7279
gggg[cccooooooccc]ggggg	chr2:191798220-191798450(+)$1	230	40	63	10.3504
iiiiiiiiinnnnniiiiiiiii	chrX:19934507-19934730(-)$1	223	46	69	11.6746
!!gggggggooooooggggggg2	chr10:74127839-74128069(-)$1	230	22	45	9.5765
eeee[ddddoooooodddd22ee	chr11:129770019-129770240(-)$1	221	58	81	10.2234
gggg!!cccnnnnncccgggggg	chr5:72801129-72801359(+)$1	230	117	140	12.3691
ff!!eeeeennnnneeeeeffff	chr12:22842149-22842379(+)$1	230	16	39	10.4143
$$$ccc[bbnnnnnbbccc4444	chr19:1038850-1039065(+)$1	215	34	57	8.9828
c[a!!ddddoooooodddd22a]	chr5:137524506-137524736(-)$1	230	27	50	10.3337
cc"""ddddnnnnndddd4444c	chr11:57428891-57429114(+)$1	223	43	66	12.0401
ffffffcccnnnnnccceeeeel	chr16:50139411-50139633(+)$1	222	78	101	10.2723
eeee[ddddoooooodddd]eee	chrX:110931117-110931356(+)$1	239	163	186	10.5431
ffff[ddddnnnnndddd22fff	chr11:111933312-111933539(+)$1	227	67	90	11.4208
dd!!eeeeennnnneeeeedddd	chr17:40465548-40465771(-)$1	223	79	102	9.9840
ffffeeeeennnnneeeee4444	chr19:53302531-53302756(-)$1	225	2	25	10.4334
ggggg[cccnnnnnccc]ggggg	chr5:72205772-72206002(+)$1	230	73	96	12.1655
eeeeeeeeennnnneeeee]eee	chr10:89727488-89727718(+)$1	230	190	213	10.7866
!!gggggggnnnnnggggggg22	chr5:36177233-36177463(+)$1	230	3	26	10.8229
eee!!ddddnnnnnddddeeeee	chr10:115673012-115673242(+)$1	230	131	154	12.0471
iiiiiiiiiooooooiiiiiiii	chr8:38709533-38709763(+)$1	230	113	136	10.1092
ggggeeeeennnnneeeee]ggg	chr19:2428073-2428303(-)$1	230	35	58	11.2411
dddd[ddddoooooodddd]ddd	chr6:64408309-64408539(+)$1	230	29	52	9.5357
iiiiiiiiiooooooiiiiiiii	chr1:197126027-197126250(-)$1	223	9	32	10.1092
eeeeeeeeennnnneeeee333e	chr16:87443108-87443338(-)$1	230	26	49	11.0132
ecccddddooooooddddccc[e	chr3:182637874-182638104(+)$1	230	93	116	9.0389
hhhh[ddddnnnnndddd]hhhh	chr8:98740319-98740541(+)$1	222	153	176	10.6304
h####ddddoooooodddd4444	chr4:110631261-110631484(-)$1	223	129	152	10.2633
gggg!!ccclllccc333ggggg	chr7:151877809-151878034(-)$1	225	7	30	8.4654
!!cccddddnnnnndddd]ccc7	chr1:160579430-160579672(-)$1	242	79	102	10.9216
"ccc[ddddoooooodddd]ccc	chr17:27082990-27083212(-)$1	222	181	204	10.3528
ffff!!cccnnnnnccc22ffff	chr12:12795129-12795363(+)$1	234	209	232	11.0597
bb"""ddddoooooodddd333b	chr12:53460260-53460487(-)$1	227	169	192	9.9157
eeeee[cccnnnnnccc]eeeee	chr4:13571103-13571333(-)$1	230	78	101	11.4329
iiiiii[bbnnnnnbb]iiiiii	chr10:50666386-50666616(-)$1	230	135	158	10.3834
e####ddddnnnnndddd4444e	chr17:66528504-66528728(+)$1	224	166	189	12.0590
g$$$$$cccnnnnncccgggggg	chr9:72325910-72326134(-)$1	224	22	45	10.9388
ddgggggggnnnnnggggggg]d	chr12:109041132-109041362(-)$1	230	48	71	10.6762
==========lll==========	chr11:87034413-87034643(+)$1	230	30	53	9.2742
===========lll=========	chr6:71270305-71270545(+)$1	240	162	185	9.2445
!!bb[ddddoooooodddd4444	chr9:88967759-88967989(-)$1	230	52	75	10.0383
eeee[cccooooooccc]eeeee	chr7:73654243-73654469(-)$1	226	152	175	9.7374
ccc[a[cccnnnnnccca]ccc:	chr13:42806563-42806793(+)$1	230	91	114	10.4078
eeee[ddddnnnnndddd333ee	chr16:23678568-23678798(+)$1	230	141	164	12.4270
=========nnnnn=========	chr3:63819551-63819775(-)$1	224	88	111	12.2490
eeee!!cccnnnnnccc22eeee	chr10:8057720-8057951(+)$1	231	47	70	11.5356
[eeeeecccnnnnnccc]eeeee	chr1:36067499-36067723(-)$1	224	5	28	11.3599
gggg[ddddnnnnnddddggggg	chr17:27876714-27876936(+)$1	222	65	88	12.4445
ccc"""cccnnnnnccc333ccc	chr11:102207739-102207969(+)$1	230	126	149	12.0399
=========oooooo========	chr9:125611149-125611390(-)$1	241	70	93	10.6255
eee[a[cccnnnnnccc]a]eee	chr8:91634704-91634934(-)$1	230	43	66	11.9610
ffff[ddddooooooddddffff	chr6:56323572-56323799(-)$1	227	149	172	9.7309
ggg!!ddddoooooodddd]ggg	chr15:52015670-52015891(-)$1	221	4	27	11.0801
ggggggg[aooooooa]gggggg	chr12:96673588-96673810(-)$1	222	29	52	9.5550
"dddd[cccnnnnnccc22dddd	chr5:108672062-108672292(-)$1	230	172	195	9.9655

#otherMatches

#Seq PSSM
uaaaaaaaaaaaacuuuuuguua	chr9:35056061-35056290(-)$1	229	199	222	11.0222
aguggcgcuaucucggcucacug	chr19:37238458-37238688(-)$1	230	188	211	12.0794
CAGGAUGACUCAAUGUUAAAGCA	chr11:95564385-95564615(+)$1	230	191	214	11.3311
GCAGACUUCUGUGCGGACUUUGC	chr1:19234701-19234931(-)$1	230	130	153	10.7279
GUGUCUUAUGUUACUAAAACAUU	chr2:191798220-191798450(+)$1	230	40	63	10.3504
AUUUUUAAAGGCUUUUUAAAAAU	chrX:19934507-19934730(-)$1	223	46	69	11.6746
AAAAGCCCAAAGACAUGGGUUUC	chr10:74127839-74128069(-)$1	230	22	45	9.5765
GCGGAUGGCAGUCGAGCCAAAUC	chr11:129770019-129770240(-)$1	221	58	81	10.2234
UUUGCAGCUAAUUAAGCCGAAGA	chr5:72801129-72801359(+)$1	230	117	140	12.3691
GUGCUUAUAAGAACUGUAAACUG	chr12:22842149-22842379(+)$1	230	16	39	10.4143
UUAAGGAGCCCCCAGCCCUCCUC	chr19:1038850-1039065(+)$1	215	34	57	8.9828
ACGCAGAGUUUCUCCACUCAACU	chr5:137524506-137524736(-)$1	230	27	50	10.3337
GGACAUAGAGAUCAUCUGGCCAC	chr11:57428891-57429114(+)$1	223	43	66	12.0401
gucucacugcugcccaggcugua	chr16:50139411-50139633(+)$1	222	78	101	10.2723
UGUGauuaaaucaaauuaaauac	chrX:110931117-110931356(+)$1	239	163	186	10.5431
UCCAGAUAAGUUAUUUAUAAUGG	chr11:111933312-111933539(+)$1	227	67	90	11.4208
CCUUAGGUAGCAUGUAUCUGGUC	chr17:40465548-40465771(-)$1	223	79	102	9.9840
AAGGUUUUUAAUCAAAAAACAAC	chr19:53302531-53302756(-)$1	225	2	25	10.4334
UGAAAAAUGAUUGCUAUAUUUCA	chr5:72205772-72206002(+)$1	230	73	96	12.1655
AUAGAAUUUGACAAGAAUUGCUA	chr10:89727488-89727718(+)$1	230	190	213	10.7866
CUAGGAUCAAUGUGUGAUUUUCA	chr5:36177233-36177463(+)$1	230	3	26	10.8229
UGUUAUUCAGACCUUGGAACAGU	chr10:115673012-115673242(+)$1	230	131	154	12.0471
AAGAUUGCACUUUUUUGUAGUUU	chr8:38709533-38709763(+)$1	230	113	136	10.1092
AAGAUGCAUGCCUAAUGUGUUCU	chr19:2428073-2428303(-)$1	230	35	58	11.2411
ACUUACAGACUCAAAUUUGAAGG	chr6:64408309-64408539(+)$1	230	29	52	9.5357
AAAUAUAAUAAUAUAAUUGUAUU	chr1:197126027-197126250(-)$1	223	9	32	10.1092
ACUCCAAUAAUCCAUAUUGAAAG	chr16:87443108-87443338(-)$1	230	26	49	11.0132
AGCUCGCCUAUAAUGGUGCUUAA	chr3:182637874-182638104(+)$1	230	93	116	9.0389
UAAAACAAACCAUUUUUGAUUUG	chr8:98740319-98740541(+)$1	222	153	176	10.6304
UUCAAAAUUCAUAGAAAUUACUU	chr4:110631261-110631484(-)$1	223	129	152	10.2633
AAGAUCUCAGUCUGACUCUUUUG	chr7:151877809-151878034(-)$1	225	7	30	8.4654
UCAAGGUCUUUCCUAGGCACUUU	chr1:160579430-160579672(-)$1	242	79	102	10.9216
GAUUAUUAUAAACCAGUAAAAAU	chr17:27082990-27083212(-)$1	222	181	204	10.3528
UUUUGAUUGCCCUACAAAGAGAA	chr12:12795129-12795363(+)$1	234	209	232	11.0597
CCGAGGGUGGAAAGGCACCACAG	chr12:53460260-53460487(-)$1	227	169	192	9.9157
GUAUUUUACUCUAUGUAUGAUGC	chr4:13571103-13571333(-)$1	230	78	101	11.4329
AGGUCUUACAUUCAGUCAGACCU	chr10:50666386-50666616(-)$1	230	135	158	10.3834
GAAUUGGCAUAAUUUGUCUUAGU	chr17:66528504-66528728(+)$1	224	166	189	12.0590
AAAAUAAUGGAAUGCAUUCUUAG	chr9:72325910-72326134(-)$1	224	22	45	10.9388
UUUUUUGUUUUCUUAGCAAAAUG	chr12:109041132-109041362(-)$1	230	48	71	10.6762
AAACACAAAGAAACUUUGUGUUU	chr11:87034413-87034643(+)$1	230	30	53	9.2742
aauuuaugaaauacuuuuaugaa	chr6:71270305-71270545(+)$1	240	162	185	9.2445
AACUAUGGGAAUACCCCCAGAAA	chr9:88967759-88967989(-)$1	230	52	75	10.0383
AUGACGGCCUAGAAGCCAUCAUC	chr7:73654243-73654469(-)$1	226	152	175	9.7374
GGUUGCUGAAAUUCUCACUGCCU	chr13:42806563-42806793(+)$1	230	91	114	10.4078
UUGUACCAUUAUCUGUGGAACAC	chr16:23678568-23678798(+)$1	230	141	164	12.4270
GUAUGAAUGUAUUUCAUUCAUAU	chr3:63819551-63819775(-)$1	224	88	111	12.2490
UAAAUUUCUUUGACAGACUUUUA	chr10:8057720-8057951(+)$1	231	47	70	11.5356
cucaagcagucugccugccuugg	chr1:36067499-36067723(-)$1	224	5	28	11.3599
UGUCCUGGUGUAUUGCCAGACAG	chr17:27876714-27876936(+)$1	222	65	88	12.4445
UUAAUUUAUUAAAUGUAUUAUAA	chr11:102207739-102207969(+)$1	230	126	149	12.0399
GCAUUAUAUGUAGGAGUGUGGUG	chr9:125611149-125611390(-)$1	241	70	93	10.6255
UAUCCCCAGCAUUCCUGUGUGUG	chr8:91634704-91634934(-)$1	230	43	66	11.9610
UCUGUAUAAUUUUUUUUGUCAGA	chr6:56323572-56323799(-)$1	227	149	172	9.7309
AGUUCUAAACUCUGAUUUAUGCU	chr15:52015670-52015891(-)$1	221	4	27	11.0801
CAGCUAUUGAUGUAACUAUAGCU	chr12:96673588-96673810(-)$1	222	29	52	9.5550
UGGCACAUUUGUUUAAUAUUGCU	chr5:108672062-108672292(-)$1	230	172	195	9.9655

#DB
(((.(((((.....))))).)))	chr9:35056061-35056290(-)$1	1	199	222	11.0222
(((((.(((.....)))))))))	chr19:37238458-37238688(-)$1	1	188	211	12.0794
(....((((.....))))..)))	chr11:95564385-95564615(+)$1	1	191	214	11.3311
(((((.(((.....))).)))))	chr1:19234701-19234931(-)$1	1	130	153	10.7279
((((.(((......))).)))))	chr2:191798220-191798450(+)$1	1	40	63	10.3504
(((((((((.....)))))))))	chrX:19934507-19934730(-)$1	1	46	69	11.6746
..(((((((......))))))).	chr10:74127839-74128069(-)$1	1	22	45	9.5765
((((.((((......))))..))	chr11:129770019-129770240(-)$1	1	58	81	10.2234
((((..(((.....)))))))))	chr5:72801129-72801359(+)$1	1	117	140	12.3691
((..(((((.....)))))))))	chr12:22842149-22842379(+)$1	1	16	39	10.4143
...(((.((.....)))))....	chr19:1038850-1039065(+)$1	1	34	57	8.9828
(.(..((((......))))..).	chr5:137524506-137524736(-)$1	1	27	50	10.3337
((...((((.....))))....)	chr11:57428891-57429114(+)$1	1	43	66	12.0401
))))))(((.....)))(((((.	chr16:50139411-50139633(+)$1	1	78	101	10.2723
((((.((((......)))).)))	chrX:110931117-110931356(+)$1	1	163	186	10.5431
((((.((((.....))))..)))	chr11:111933312-111933539(+)$1	1	67	90	11.4208
((..(((((.....)))))))))	chr17:40465548-40465771(-)$1	1	79	102	9.9840
(((((((((.....)))))....	chr19:53302531-53302756(-)$1	1	2	25	10.4334
(((((.(((.....))).)))))	chr5:72205772-72206002(+)$1	1	73	96	12.1655
(((((((((.....))))).)))	chr10:89727488-89727718(+)$1	1	190	213	10.7866
..(((((((.....)))))))..	chr5:36177233-36177463(+)$1	1	3	26	10.8229
(((..((((.....)))))))))	chr10:115673012-115673242(+)$1	1	131	154	12.0471
(((((((((......))))))))	chr8:38709533-38709763(+)$1	1	113	136	10.1092
(((((((((.....))))).)))	chr19:2428073-2428303(-)$1	1	35	58	11.2411
((((.((((......)))).)))	chr6:64408309-64408539(+)$1	1	29	52	9.5357
(((((((((......))))))))	chr1:197126027-197126250(-)$1	1	9	32	10.1092
(((((((((.....)))))...)	chr16:87443108-87443338(-)$1	1	26	49	11.0132
))))((((......))))(((.(	chr3:182637874-182638104(+)$1	1	93	116	9.0389
((((.((((.....)))).))))	chr8:98740319-98740541(+)$1	1	153	176	10.6304
(....((((......))))....	chr4:110631261-110631484(-)$1	1	129	152	10.2633
((((..(((...)))...)))))	chr7:151877809-151878034(-)$1	1	7	30	8.4654
..(((((((.....)))).))).	chr1:160579430-160579672(-)$1	1	79	102	10.9216
.(((.((((......)))).)))	chr17:27082990-27083212(-)$1	1	181	204	10.3528
((((..(((.....)))..))))	chr12:12795129-12795363(+)$1	1	209	232	11.0597
((...((((......))))...)	chr12:53460260-53460487(-)$1	1	169	192	9.9157
(((((.(((.....))).)))))	chr4:13571103-13571333(-)$1	1	78	101	11.4329
((((((.((.....)).))))))	chr10:50666386-50666616(-)$1	1	135	158	10.3834
(....((((.....))))....)	chr17:66528504-66528728(+)$1	1	166	189	12.0590
(.....(((.....)))))))))	chr9:72325910-72326134(-)$1	1	22	45	10.9388
(((((((((.....))))))).)	chr12:109041132-109041362(-)$1	1	48	71	10.6762
((((((((((...))))))))))	chr11:87034413-87034643(+)$1	1	30	53	9.2742
(((((((((((...)))))))))	chr6:71270305-71270545(+)$1	1	162	185	9.2445
..((.((((......))))....	chr9:88967759-88967989(-)$1	1	52	75	10.0383
((((.(((......))).)))))	chr7:73654243-73654469(-)$1	1	152	175	9.7374
(((.(.(((.....)))).))).	chr13:42806563-42806793(+)$1	1	91	114	10.4078
((((.((((.....))))...))	chr16:23678568-23678798(+)$1	1	141	164	12.4270
(((((((((.....)))))))))	chr3:63819551-63819775(-)$1	1	88	111	12.2490
((((..(((.....)))..))))	chr10:8057720-8057951(+)$1	1	47	70	11.5356
.((((((((.....))).)))))	chr1:36067499-36067723(-)$1	1	5	28	11.3599
((((.((((.....)))))))))	chr17:27876714-27876936(+)$1	1	65	88	12.4445
(((...(((.....)))...)))	chr11:102207739-102207969(+)$1	1	126	149	12.0399
(((((((((......))))))))	chr9:125611149-125611390(-)$1	1	70	93	10.6255
(((.(.(((.....))).).)))	chr8:91634704-91634934(-)$1	1	43	66	11.9610
((((.((((......))))))))	chr6:56323572-56323799(-)$1	1	149	172	9.7309
(((..((((......)))).)))	chr15:52015670-52015891(-)$1	1	4	27	11.0801
(((((((.(......).))))))	chr12:96673588-96673810(-)$1	1	29	52	9.5550
.((((.(((.....)))..))))	chr5:108672062-108672292(-)$1	1	172	195	9.9655

#PSSM
e : 0.22	g : 0.17	f : 0.12	d : 0.07	i : 0.07	! : 0.07	c : 0.07	= : 0.07	h : 0.03	" : 0.03	$ : 0.01	b : 0.01	[ : 0.01	
e : 0.21	g : 0.15	f : 0.12	c : 0.08	i : 0.07	! : 0.07	d : 0.07	= : 0.07	# : 0.05	$ : 0.03	[ : 0.01	h : 0.01	b : 0.01	
e : 0.21	g : 0.21	f : 0.10	c : 0.08	i : 0.07	= : 0.07	# : 0.05	! : 0.03	$ : 0.03	" : 0.03	d : 0.03	a : 0.01	h : 0.01	b : 0.01	
g : 0.19	e : 0.15	f : 0.10	! : 0.08	i : 0.07	c : 0.07	= : 0.07	[ : 0.05	# : 0.05	" : 0.05	d : 0.03	h : 0.01	$ : 0.01	b : 0.01	
[ : 0.21	e : 0.15	! : 0.12	g : 0.10	i : 0.07	= : 0.07	# : 0.05	" : 0.05	f : 0.03	c : 0.03	d : 0.03	a : 0.03	$ : 0.01	
d : 0.35	e : 0.14	[ : 0.12	i : 0.07	g : 0.07	! : 0.07	= : 0.07	c : 0.05	f : 0.01	$ : 0.01	" : 0.01	
d : 0.35	c : 0.29	e : 0.12	g : 0.07	= : 0.07	i : 0.05	[ : 0.03	
d : 0.35	c : 0.29	e : 0.12	= : 0.07	i : 0.05	g : 0.05	b : 0.03	[ : 0.01	
d : 0.33	c : 0.26	e : 0.12	= : 0.07	o : 0.05	i : 0.05	g : 0.05	b : 0.03	a : 0.01	
n : 0.63	o : 0.31	= : 0.03	l : 0.01	
n : 0.63	o : 0.31	l : 0.03	= : 0.01	
n : 0.63	o : 0.31	l : 0.05	
n : 0.63	o : 0.31	l : 0.03	c : 0.01	
n : 0.63	o : 0.31	c : 0.01	= : 0.01	l : 0.01	
c : 0.29	o : 0.26	d : 0.17	e : 0.12	= : 0.05	b : 0.03	g : 0.03	i : 0.01	
d : 0.35	c : 0.28	e : 0.12	= : 0.07	i : 0.05	g : 0.05	b : 0.03	3 : 0.01	a : 0.01	
d : 0.35	c : 0.29	e : 0.12	= : 0.07	i : 0.05	g : 0.05	] : 0.03	3 : 0.01	
d : 0.35	e : 0.14	g : 0.12	] : 0.12	i : 0.07	= : 0.07	2 : 0.05	3 : 0.03	c : 0.01	a : 0.01	
e : 0.21	g : 0.19	d : 0.17	2 : 0.08	i : 0.07	= : 0.07	] : 0.05	c : 0.03	4 : 0.03	3 : 0.03	f : 0.01	a : 0.01	
g : 0.19	] : 0.14	4 : 0.10	e : 0.10	2 : 0.07	f : 0.07	i : 0.07	3 : 0.07	= : 0.07	c : 0.05	d : 0.03	h : 0.01	
g : 0.22	e : 0.17	4 : 0.10	f : 0.08	c : 0.08	d : 0.07	i : 0.07	= : 0.07	3 : 0.05	2 : 0.03	h : 0.01	
e : 0.21	g : 0.19	4 : 0.10	f : 0.08	d : 0.07	i : 0.07	c : 0.07	= : 0.07	3 : 0.03	a : 0.01	2 : 0.01	[ : 0.01	h : 0.01	] : 0.01	
e : 0.24	g : 0.17	d : 0.08	f : 0.08	i : 0.07	4 : 0.07	= : 0.07	c : 0.05	2 : 0.03	] : 0.01	l : 0.01	h : 0.01	7 : 0.01	b : 0.01	: : 0.01	

#score	611.4266226477806
#seq	57
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_UTR_m1_run1.txt

#BEAR
""eeeee[dddd[cccooooooccc]dddd333eeeee	chr19:32874084-32874316(+)$1	232	123	161	15.5035
!ccc"""ffffffcccooooooccc]ffffffccc22c	chr16:29846982-29847207(+)$1	225	68	106	14.9186
ggggggg####ddddoooooodddd22ggggggg:ccc	chr1:27106579-27106789(+)$1	210	10	48	13.5021
eeeee"""bb!!ddddoooooodddd22bb333eeeee	chrX:153589738-153589963(-)$1	225	115	153	15.0397
[dddd[ccc"""ffffffooooooffffff22ccc]dd	chr2:10193211-10193441(+)$1	230	185	223	12.6996
eeee!!dddd"""cccooooooccc333dddd]eeeee	chr7:151163359-151163598(-)$1	239	189	227	15.5529
======!!eeeee[cccmmmmccceeeee333======	chr2:37073874-37074093(-)$1	219	60	98	13.1398
!!ggggggg[cccrrrrrrrrrccc]ggggggg4444f	chr1:156280856-156281075(-)$1	219	22	60	12.4785
=======ccc!!ccc!!aooooooa22ccc4444ccc]	chr3:49022560-49022804(+)$1	244	37	75	15.7234
ebb[dddd!!bb[cccoooooocccbb]ddddbb]eee	chr17:76396707-76396960(+)$1	253	102	140	12.3699
==[dddd!!bb!!cccmmmmcccbb22dddd22=====	chr8:42256197-42256431(+)$1	234	188	226	12.4592
mdddda[dddd!!cccooooooccc22dddd]addddn	chr12:42476315-42476536(-)$1	221	25	63	14.4405
dddaccc[dddd!!cccmmmmccc]dddd333ccc]a]	chr4:42116110-42116324(-)$1	214	118	156	12.3561
bcccccc!!bb[cccooooooccc]bb]ccc]ccc]bb	chr20:32699889-32700116(-)$1	227	183	221	13.7300
d[a[eeeeeffffff[ccclllccc22ffffff333ee	chr22:21804321-21804557(+)$1	236	115	153	11.2936
c!!ccc"""eeeeeooooooeeeee22ccc22ccc]cc	chr21:34635253-34635480(+)$1	227	116	154	14.3648
[cccccc[a[ffffffooooooffffff]a]ccc]ccc	chr17:47131351-47131686(+)$1	335	142	180	13.7306
fffff"""bb!!bbrrrrrrrrrbb22bb333ffffff	chrX:153582528-153582757(-)$1	229	31	69	11.7517
d####ccc"""ddddoooooodddd22ccc666666dd	chr20:54944581-54944802(-)$1	221	170	208	12.3046
dddd!!ccc[a[a[ddddllldddd333a]a]ccc]dd	chr19:3463322-3463532(+)$1	210	31	69	13.0295
ee[ccc!!bb"""cccooooooccc333bb22ccceee	chr19:49965081-49965307(+)$1	226	154	192	18.0417
ddd[ccciiiiiiiiinnnnniiiiiiiii]ccc22dd	chr7:35293229-35293456(-)$1	227	58	96	11.2319
gg!!abb[cccbb[cccnnnnnccc22bb22ccc]bb]	chr17:12852415-12852628(+)$1	213	6	44	12.2061
ggggcccffffffcccooooooccc]ffffff]ccc]g	chr9:140084507-140084729(+)$1	222	41	79	14.6065
hccc[ffffff"""cccnnnnnccc333ffffff]ccc	chr20:48569467-48569696(+)$1	229	112	150	12.2240
ee:ccc[eeeee[cccooooooccc]eeeee]ccc:::	chr17:78109026-78109248(-)$1	222	148	186	11.6767
gggggg"""a!!ddddoooooodddd22a22ggggggg	chr6:30569114-30569333(-)$1	219	123	161	15.3732
=====[bb[a[ddddoooooodddd22a]bb]======	chr7:140035014-140035242(-)$1	228	83	121	14.4408
eee!!bb!!ccc[cccooooooccc]cccbb22eeeee	chr9:35099909-35100134(-)$1	225	129	167	15.2460
c[dddd!!ggggggg[ammmma]ggggggg333dddd]	chr1:114472396-114472619(+)$1	223	15	53	11.8352
========="""cccpppppppccc333==========	chr8:22477381-22477616(+)$1	235	117	155	12.6845
]ddddddddccc[cccooooooccc]ccc333dddd::	chr20:30823935-30824170(+)$1	235	113	151	13.2735
"""ffffff[bb[cccooooooccc22bb]ffffff44	chr16:11945204-11945462(-)$1	258	152	190	14.5941
:ffffff!!ccc"""cccmmmmccc22ccc22ffffff	chr15:22928058-22928278(+)$1	220	113	151	10.9955
bb!!ccc"""bb[ddddmmmmdddd22bb333ccc22b	chr17:37881288-37881521(+)$1	233	137	175	12.4453
d[a[a[eeeee!!cccnnnnnccc22eeeee]a]a]dd	chr22:18210099-18210313(+)$1	214	74	112	12.4686
a[dddd[bb####cccooooooccc4444bbdddd]ab	chr2:27263514-27263738(+)$1	224	160	198	14.6543
"""ccc!!bb!!eeeeeooooooeeeeebb]ccc333h	chr1:32663457-32663750(+)$1	293	142	180	14.0945
!!ccc"""ccc!!cccooooooccc22ccc22ccc]dd	chr12:6603178-6603404(+)$1	226	114	152	19.1070
[ccc!!dddd!!cccammmma]ccc22dddd22ccc]b	chr19:56170490-56170700(+)$1	210	131	169	12.8160
#bb!!bb[ccc!!eeeeeooooooeeeee333ccc]bb	chr11:57077249-57077471(-)$1	222	60	98	12.8459
ggg[a!!dddd!!eeeeellleeeeedddd22a]gggg	chr1:23413553-23413785(-)$1	232	19	57	11.3413
===========[ccc!!bbmmmmbb22ccc========	chr10:135234258-135234485(+)$1	227	153	191	11.7012
gggccc[a[ddddarrrrrrrrra]dddd]a]ccc]gg	chr12:125432089-125432347(-)$1	258	107	145	11.4464
##==========!!bboooooobb22==========]g	chr1:179074174-179074444(-)$1	270	76	114	15.2329
egggggggccc[bboooooobb]ccc]ggggggg22ee	chr17:26941772-26942007(-)$1	235	157	195	11.5499
c[dddd!!a[eeeeerrrrrrrrreeeee333a22ddd	chr8:20078842-20079075(+)$1	233	130	168	11.4117
[dddd!!dddd[eeeeeooooooeeeeedddd4444dd	chr11:62396210-62396422(-)$1	212	97	135	12.2440
ee!!a[ffffff[cccooooooccc]ffffff]a22ee	chr17:76420147-76420367(+)$1	220	66	104	14.8201
eee!!bb[bb"""ddddoooooodddd]bb22bb333e	chr12:117582424-117582704(-)$1	280	232	270	13.7808
iiiii!!bb[ffffffooooooffffffbb22iiiiii	chr6:135308723-135308943(-)$1	220	79	117	14.0153

#otherMatches

#Seq PSSM
AAAGAGGAAGUAGAGGUGUAAUCCUGUAUUAACCCUCU	chr19:32874084-32874316(+)$1	232	123	161	15.5035
GGGGCGUACCUCCCAGCGGUGUUUGAGGAGGUUCUGGA	chr16:29846982-29847207(+)$1	225	68	106	14.9186
CUCGGGGCAGUUGGACCUAUCUCCAUACCCCGAGAGCA	chr1:27106579-27106789(+)$1	210	10	48	13.5021
CGGGUGCAGCGGUGCCCUGCAAGGUGGAGCCAGGCCUG	chrX:153589738-153589963(-)$1	225	115	153	15.0397
ACCAGUACUUGCUGCAGGAUCUAGUCUGUAAUAGUCUU	chr2:10193211-10193441(+)$1	230	185	223	12.6996
ACAGGAGAUGAUUGAGAACAGCCUUGCCUGUCACUGUC	chr7:151163359-151163598(-)$1	239	189	227	15.5529
GAAAAUUAGCGGGAGGUUUGGAUCCCUGCCUUAUUUUC	chr2:37073874-37074093(-)$1	219	60	98	13.1398
CUUUUGGUGCCUCCGAUUUUAUGAGUCAUCAAGCUUUG	chr1:156280856-156281075(-)$1	219	22	60	12.4785
CUCUGCACCCUAAAUCACACCCUGGGCAUUGUCUGGGC	chr3:49022560-49022804(+)$1	244	37	75	15.7234
CUGCAGGACUGUGCGGAGAUUGCCGACUUCUUCACGGA	chr17:76396707-76396960(+)$1	253	102	140	12.3699
AGAGAACGCAUUAGAAGUUAUUCAUAGGUUCAAUUUAU	chr8:42256197-42256431(+)$1	234	188	226	12.4592
ccaagaguuugagaccagccuaggugacaaagugagac	chr12:42476315-42476536(-)$1	221	25	63	14.4405
AGGGGACCAGUAUUUUGCAAGCAGUUACUAAAGUCACA	chr4:42116110-42116324(-)$1	214	118	156	12.3561
CCACUCGAGCCGCAGCCAUGUCUGGGGACGAGGUGAGG	chr20:32699889-32700116(-)$1	227	183	221	13.7300
GAGUGAGCGGGUGGCAGGCCGGGCUCCGCCACUGCAUG	chr22:21804321-21804557(+)$1	236	115	153	11.2936
UGAGGUUGAUGUGGAGCUCCCCACGAUGCCAAAGGACA	chr21:34635253-34635480(+)$1	227	116	154	14.3648
AGGCCUCAUGUCUGAAGGGGGAUUUAGGGGCGAGAGCC	chr17:47131351-47131686(+)$1	335	142	180	13.7306
GCUCGGGAGCCAAGGAGGCCAGACUGUGCCAAUGAGCU	chrX:153582528-153582757(-)$1	229	31	69	11.7517
UUAACCACUUAUCUCCCAUAUGAGAGUGUGAAAAAUAG	chr20:54944581-54944802(-)$1	221	170	208	12.3046
ACCCCGGCCGGGCAGCGGAGACCGCAGAGGCGGGCAGG	chr19:3463322-3463532(+)$1	210	31	69	13.0295
GGACGUAGACUCGGCCGUGGAGGGUGUCGUGGACGCCG	chr19:49965081-49965307(+)$1	226	154	192	18.0417
CAGUGUGCAGCUCUGGAGUCGUUGGAGCUGACACUUCU	chr7:35293229-35293456(-)$1	227	58	96	11.2319
AGUUGCUGUGCGCUGACCCUCUGUCCUGUUGGUAGGGA	chr17:12852415-12852628(+)$1	213	6	44	12.2061
GUCCUCGCUUCAUGCUCACACAGGCUAUGGGGAUGGUG	chr9:140084507-140084729(+)$1	222	41	79	14.6065
GACUCAGCGGAUACUAGUUCUUUUACCUUCUGCUUGGU	chr20:48569467-48569696(+)$1	229	112	150	12.2240
AUUGUUCUAAGUCUUUUUCAUUAAAAAUUUAAAACUUU	chr17:78109026-78109248(-)$1	222	148	186	11.6767
GCCCCCUCAGUUCCCACUUGCUUGGGUUCCUGGGGGUU	chr6:30569114-30569333(-)$1	219	123	161	15.3732
GCUUCGAGUCUGCCCUAAUUUGGGUUUGUCUAGGAGCU	chr7:140035014-140035242(-)$1	228	83	121	14.4408
GGGAACAAGGAAGCAGAUUUUCCUGAUUCUGGCUCUAG	chr9:35099909-35100134(-)$1	225	129	167	15.2460
cgcggggacggcuccggggggcgggggccggggcccgg	chr1:114472396-114472619(+)$1	223	15	53	11.8352
UCUCCUGUCCUCUUCCAGUUUAGAAUAAGACAGGGGAG	chr8:22477381-22477616(+)$1	235	117	155	12.6845
CUGGCUGGCUGAUUUCAUUUUGGAAUUCAUUUGCCAUC	chr20:30823935-30824170(+)$1	235	113	151	13.2735
GACUCCAGCGGCCCCGACAGCACGGAAGCAGCUGGAUA	chr16:11945204-11945462(-)$1	258	152	190	14.5941
ACACCUGGAGGAGCUGCUCCCGGGCCAUCCCACAGGUG	chr15:22928058-22928278(+)$1	220	113	151	10.9955
ACGAGACAGAGUACCAUGCAGAUGGGGGCAAGGUUAGG	chr17:37881288-37881521(+)$1	233	137	175	12.4453
CCCCGCCGGUGAGAUGAAGCCCAUGCCGCUGUCUGAGG	chr22:18210099-18210313(+)$1	214	74	112	12.4686
CUGGGCACUUGCCCUGAUAUCCCAGCAGUAGGCCCUGC	chr2:27263514-27263738(+)$1	224	160	198	14.6543
CAAGGCCUGCUGAGCUGAUUCUCCAGCUGCUGCCCCAG	chr1:32663457-32663750(+)$1	293	142	180	14.0945
GAAUCAGAGCCGCGGGUGAGAUCCCCAGGUAAGAUGUG	chr12:6603178-6603404(+)$1	226	114	152	19.1070
UCGGAGCCGGGACCGCAAACGCCGGAGCCGGAGCCGCG	chr19:56170490-56170700(+)$1	210	131	169	12.8160
AGCAGGACUGGGAGUUUCAGAAGAGAGAUGUGUCACUC	chr11:57077249-57077471(-)$1	222	60	98	12.8459
UCUGUAUGUUUUAAUCUCAUGGGGAUGAGCUCAGAGAA	chr1:23413553-23413785(-)$1	232	19	57	11.3413
UAGUGGGGCUGAGAGAUGUGGGGGCCCCUCCAGCCCCA	chr10:135234258-135234485(+)$1	227	153	191	11.7012
UCAGGAAGUGGGUCAAGCCCUGGGAACCCUCAUCCAUG	chr12:125432089-125432347(-)$1	258	107	145	11.4464
GUUUUCUUGCCCAACAACAAUCUGAAGGGUAGGGGGUG	chr1:179074174-179074444(-)$1	270	76	114	15.2329
CAGGGAAUGGGCCCAGGGCAGGACCCUAUUCCCUUGGG	chr17:26941772-26942007(-)$1	235	157	195	11.5499
GCGAUCUUCUAUGCAGUUCUGCCAUGCGUCCUGUUGGU	chr8:20078842-20079075(+)$1	233	130	168	11.4117
AUGCCUUGGGCCAGCGAUAUUCUUUGCUGCCCUUCUGG	chr11:62396210-62396422(-)$1	212	97	135	12.2440
UCUGGGUGUCCCAGCGAGCCCCUGCAGGGACAGUAUGG	chr17:76420147-76420367(+)$1	220	66	104	14.8201
ACUUUGCUCUCAACAUUUAAAAUAAUGCAGUUGCUCUA	chr12:117582424-117582704(-)$1	280	232	270	13.7808
AGGACAAACACGAGAGCAUGGACUCUUGGUCCGUUCUC	chr6:135308723-135308943(-)$1	220	79	117	14.0153

#DB
..(((((.((((.(((......))).))))...)))))	chr19:32874084-32874316(+)$1	1	123	161	15.5035
.(((...(((((((((......))).)))))))))..)	chr16:29846982-29847207(+)$1	1	68	106	14.9186
(((((((....((((......))))..))))))).(((	chr1:27106579-27106789(+)$1	1	10	48	13.5021
(((((...((..((((......))))..))...)))))	chrX:153589738-153589963(-)$1	1	115	153	15.0397
.((((.(((...((((((......))))))..))).))	chr2:10193211-10193441(+)$1	1	185	223	12.6996
((((..((((...(((......)))...)))).)))))	chr7:151163359-151163598(-)$1	1	189	227	15.5529
((((((..(((((.(((....))))))))...))))))	chr2:37073874-37074093(-)$1	1	60	98	13.1398
..(((((((.(((.........))).)))))))....)	chr1:156280856-156281075(-)$1	1	22	60	12.4785
((((((((((..(((..(......)..)))....))).	chr3:49022560-49022804(+)$1	1	37	75	15.7234
(((.((((..((.(((......))))).)))))).)))	chr17:76396707-76396960(+)$1	1	102	140	12.3699
((.((((..((..(((....)))))..))))..)))))	chr8:42256197-42256431(+)$1	1	188	226	12.4592
.))))(.((((..(((......)))..)))).)((((.	chr12:42476315-42476536(-)$1	1	25	63	14.4405
(((((((.((((..(((....))).))))...))).).	chr4:42116110-42116324(-)$1	1	118	156	12.3561
(((((((..((.(((......))).)).))).))).))	chr20:32699889-32700116(-)$1	1	183	221	13.7300
(.(.(((((((((((.(((...)))..))))))...))	chr22:21804321-21804557(+)$1	1	115	153	11.2936
(..(((...(((((......)))))..)))..))).))	chr21:34635253-34635480(+)$1	1	116	154	14.3648
.((((((.(.((((((......)))))).).))).)))	chr17:47131351-47131686(+)$1	1	142	180	13.7306
(((((...((..((.........))..))...))))))	chrX:153582528-153582757(-)$1	1	31	69	11.7517
(....(((...((((......))))..)))......))	chr20:54944581-54944802(-)$1	1	170	208	12.3046
((((..(((.(.(.((((...))))...).).))).))	chr19:3463322-3463532(+)$1	1	31	69	13.0295
((.(((..((...(((......)))...))..))))))	chr19:49965081-49965307(+)$1	1	154	192	18.0417
(((.((((((((((((.....))))))))).)))..))	chr7:35293229-35293456(-)$1	1	58	96	11.2319
((..(((.(((((.(((.....)))..))..))).)).	chr17:12852415-12852628(+)$1	1	6	44	12.2061
((((((((((((((((......))).)))))).))).)	chr9:140084507-140084729(+)$1	1	41	79	14.6065
)(((.((((((...(((.....)))...)))))).)))	chr20:48569467-48569696(+)$1	1	112	150	12.2240
)).(((.(((((.(((......))).))))).)))...	chr17:78109026-78109248(-)$1	1	148	186	11.6767
((((((...(..((((......))))..)..)))))))	chr6:30569114-30569333(-)$1	1	123	161	15.3732
(((((.((.(.((((......))))..).)).))))))	chr7:140035014-140035242(-)$1	1	83	121	14.4408
(((..((..(((.(((......))).)))))..)))))	chr9:35099909-35100134(-)$1	1	129	167	15.2460
(.((((..(((((((.(....).)))))))...)))).	chr1:114472396-114472619(+)$1	1	15	53	11.8352
(((((((((...(((.......)))...))))))))))	chr8:22477381-22477616(+)$1	1	117	155	12.6845
.))))(((((((.(((......))).)))...))))..	chr20:30823935-30824170(+)$1	1	113	151	13.2735
...((((((.((.(((......)))..)).))))))..	chr16:11945204-11945462(-)$1	1	152	190	14.5941
.((((((..(((...(((....)))..)))..))))))	chr15:22928058-22928278(+)$1	1	113	151	10.9955
((..(((...((.((((....))))..))...)))..)	chr17:37881288-37881521(+)$1	1	137	175	12.4453
(.(.(.(((((..(((.....)))..))))).).).))	chr22:18210099-18210313(+)$1	1	74	112	12.4686
(.((((.((....(((......)))....)))))).))	chr2:27263514-27263738(+)$1	1	160	198	14.6543
...(((..((..(((((......))))))).)))...)	chr1:32663457-32663750(+)$1	1	142	180	14.0945
..(((...(((..(((......)))..)))..))).))	chr12:6603178-6603404(+)$1	1	114	152	19.1070
.(((..((((..((((....).)))..))))..))).)	chr19:56170490-56170700(+)$1	1	131	169	12.8160
.((..((.(((..(((((......)))))...))).))	chr11:57077249-57077471(-)$1	1	60	98	12.8459
(((.(..((((..(((((...)))))))))..).))))	chr1:23413553-23413785(-)$1	1	19	57	11.3413
(((((((((((.(((..((....))..)))))))))))	chr10:135234258-135234485(+)$1	1	153	191	11.7012
((((((.(.(((((.........).)))).).))).))	chr12:125432089-125432347(-)$1	1	107	145	11.4464
..((((((((((..((......))..)))))))))).)	chr1:179074174-179074444(-)$1	1	76	114	15.2329
(((((((((((.((......)).))).)))))))..))	chr17:26941772-26942007(-)$1	1	157	195	11.5499
(.((((..(.(((((.........)))))...)..)))	chr8:20078842-20079075(+)$1	1	130	168	11.4117
.((((..((((.(((((......)))))))))....))	chr11:62396210-62396422(-)$1	1	97	135	12.2440
((..(.((((((.(((......))).)))))).)..))	chr17:76420147-76420367(+)$1	1	66	104	14.8201
(((..((.((...((((......)))).))..))...)	chr12:117582424-117582704(-)$1	1	232	270	13.7808
(((((..((.((((((......))))))))..))))))	chr6:135308723-135308943(-)$1	1	79	117	14.0153

#PSSM
e : 0.17	g : 0.11	= : 0.11	d : 0.11	[ : 0.07	" : 0.05	! : 0.05	c : 0.05	b : 0.03	# : 0.03	m : 0.01	f : 0.01	h : 0.01	] : 0.01	: : 0.01	a : 0.01	i : 0.01	
g : 0.13	e : 0.13	d : 0.13	= : 0.11	c : 0.09	[ : 0.09	" : 0.05	! : 0.05	b : 0.05	f : 0.03	# : 0.03	i : 0.01	
d : 0.19	g : 0.13	c : 0.11	= : 0.11	e : 0.09	! : 0.07	b : 0.03	[ : 0.03	a : 0.03	f : 0.03	" : 0.03	# : 0.01	: : 0.01	i : 0.01	
c : 0.21	d : 0.17	= : 0.11	! : 0.11	g : 0.09	[ : 0.09	e : 0.05	f : 0.05	a : 0.01	# : 0.01	i : 0.01	
c : 0.23	d : 0.17	! : 0.11	= : 0.11	g : 0.07	a : 0.07	e : 0.05	f : 0.05	" : 0.01	# : 0.01	[ : 0.01	i : 0.01	
c : 0.23	! : 0.11	d : 0.11	= : 0.09	" : 0.07	g : 0.07	[ : 0.07	b : 0.07	f : 0.05	e : 0.03	a : 0.01	
c : 0.17	! : 0.15	" : 0.11	d : 0.09	b : 0.09	= : 0.07	[ : 0.07	f : 0.07	e : 0.05	g : 0.05	
! : 0.17	d : 0.13	[ : 0.11	" : 0.11	f : 0.09	c : 0.07	e : 0.05	b : 0.05	= : 0.05	g : 0.03	# : 0.01	i : 0.01	a : 0.01	
d : 0.15	b : 0.13	c : 0.13	f : 0.09	! : 0.09	e : 0.07	" : 0.07	= : 0.05	g : 0.03	a : 0.03	[ : 0.03	# : 0.01	i : 0.01	
d : 0.15	c : 0.15	b : 0.13	[ : 0.11	f : 0.09	" : 0.07	e : 0.07	# : 0.03	a : 0.03	= : 0.03	! : 0.01	i : 0.01	g : 0.01	
c : 0.15	f : 0.13	d : 0.11	! : 0.11	" : 0.11	e : 0.09	b : 0.09	# : 0.03	= : 0.03	a : 0.01	i : 0.01	[ : 0.01	g : 0.01	
! : 0.23	d : 0.11	f : 0.11	" : 0.11	[ : 0.09	e : 0.07	c : 0.07	b : 0.07	i : 0.01	g : 0.01	# : 0.01	= : 0.01	
[ : 0.15	! : 0.15	f : 0.11	d : 0.11	c : 0.11	" : 0.09	e : 0.09	b : 0.05	a : 0.01	i : 0.01	g : 0.01	# : 0.01	
c : 0.41	d : 0.13	e : 0.11	f : 0.07	[ : 0.05	! : 0.03	b : 0.03	" : 0.03	r : 0.01	i : 0.01	g : 0.01	a : 0.01	
c : 0.49	d : 0.15	e : 0.09	f : 0.07	r : 0.05	o : 0.03	i : 0.01	g : 0.01	" : 0.01	b : 0.01	
c : 0.41	o : 0.11	d : 0.09	r : 0.07	e : 0.07	f : 0.05	! : 0.03	[ : 0.03	i : 0.01	p : 0.01	a : 0.01	b : 0.01	
o : 0.49	c : 0.11	r : 0.07	e : 0.07	d : 0.05	! : 0.03	m : 0.03	n : 0.03	f : 0.01	a : 0.01	p : 0.01	
o : 0.54	m : 0.11	r : 0.07	n : 0.07	c : 0.03	e : 0.03	f : 0.01	a : 0.01	d : 0.01	p : 0.01	b : 0.01	
o : 0.60	m : 0.13	r : 0.07	n : 0.07	l : 0.03	c : 0.01	p : 0.01	b : 0.01	
o : 0.60	m : 0.15	r : 0.07	n : 0.07	l : 0.05	p : 0.01	
o : 0.56	m : 0.11	r : 0.07	n : 0.07	l : 0.05	c : 0.01	e : 0.01	p : 0.01	a : 0.01	b : 0.01	
o : 0.49	d : 0.09	c : 0.09	r : 0.07	e : 0.03	n : 0.03	m : 0.03	l : 0.01	i : 0.01	a : 0.01	p : 0.01	] : 0.01	b : 0.01	
c : 0.50	d : 0.13	o : 0.11	r : 0.05	e : 0.03	f : 0.03	] : 0.03	i : 0.01	m : 0.01	b : 0.01	
c : 0.50	d : 0.15	b : 0.07	e : 0.07	o : 0.05	f : 0.03	i : 0.01	g : 0.01	a : 0.01	r : 0.01	
c : 0.43	d : 0.15	e : 0.13	f : 0.05	b : 0.05	] : 0.05	2 : 0.03	a : 0.01	i : 0.01	g : 0.01	
2 : 0.35	] : 0.15	e : 0.11	d : 0.09	3 : 0.09	f : 0.05	b : 0.03	i : 0.01	g : 0.01	4 : 0.01	c : 0.01	
2 : 0.35	e : 0.13	f : 0.11	d : 0.09	3 : 0.09	g : 0.03	b : 0.03	c : 0.03	i : 0.01	4 : 0.01	= : 0.01	] : 0.01	
c : 0.15	d : 0.13	f : 0.13	e : 0.13	3 : 0.09	g : 0.07	b : 0.07	] : 0.05	2 : 0.03	i : 0.01	a : 0.01	4 : 0.01	= : 0.01	
d : 0.19	b : 0.17	c : 0.17	f : 0.11	e : 0.09	g : 0.07	] : 0.03	a : 0.03	= : 0.03	i : 0.01	4 : 0.01	
d : 0.15	b : 0.15	3 : 0.13	c : 0.13	f : 0.11	g : 0.07	] : 0.05	2 : 0.03	e : 0.03	= : 0.03	a : 0.01	i : 0.01	
3 : 0.19	2 : 0.19	f : 0.11	d : 0.11	g : 0.05	] : 0.05	b : 0.05	= : 0.05	a : 0.03	e : 0.03	4 : 0.01	c : 0.01	6 : 0.01	
2 : 0.21	3 : 0.19	] : 0.13	f : 0.11	g : 0.07	d : 0.07	c : 0.07	= : 0.05	4 : 0.01	6 : 0.01	
c : 0.31	= : 0.09	f : 0.09	g : 0.07	a : 0.07	3 : 0.05	] : 0.05	2 : 0.05	4 : 0.03	b : 0.03	d : 0.03	6 : 0.01	i : 0.01	
c : 0.35	= : 0.11	e : 0.07	d : 0.07	f : 0.07	g : 0.05	4 : 0.05	b : 0.03	] : 0.03	3 : 0.01	6 : 0.01	2 : 0.01	a : 0.01	i : 0.01	
c : 0.29	= : 0.11	e : 0.07	] : 0.07	d : 0.07	2 : 0.07	3 : 0.05	f : 0.05	4 : 0.03	g : 0.03	: : 0.01	6 : 0.01	a : 0.01	i : 0.01	
] : 0.19	e : 0.11	c : 0.11	= : 0.11	2 : 0.09	d : 0.07	3 : 0.05	f : 0.05	4 : 0.03	g : 0.03	6 : 0.01	b : 0.01	: : 0.01	i : 0.01	
d : 0.19	e : 0.17	c : 0.09	= : 0.09	b : 0.05	] : 0.05	g : 0.05	2 : 0.03	4 : 0.03	a : 0.03	f : 0.03	: : 0.03	3 : 0.03	i : 0.01	
e : 0.19	d : 0.15	c : 0.09	= : 0.09	b : 0.09	g : 0.09	] : 0.07	f : 0.05	: : 0.03	n : 0.01	4 : 0.01	h : 0.01	i : 0.01	

#score	684.7960695196375
#seq	51
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011c_hg19_CDS_m2_run1.txt

#BEAR
eeeee"""ccc[cccnnnnnccc]ccc22ee	chr2:128522276-128522500(-)$1	224	90	121	10.5195
gggg[a!!ccccccooooooccc4444ccc2	chr2:44566345-44566566(-)$1	221	171	202	12.8250
Eiiiiiiiii[bboooooobb]iiiiiiiii	chr10:70765399-70765624(+)$1	225	45	76	11.2055
!ggggggg!!eeeeellleeeee22gggggg	chr11:118889474-118889703(+)$1	229	52	83	10.9898
gggccc!!eeeeeooooooeeeeeccc]ggg	chr2:176972456-176972680(+)$1	224	33	64	10.6956
eeeccc!!bb[bboooooobb]bb22ccc33	chr9:114676874-114677096(+)$1	222	60	91	10.0541
ffffff[ccc!!cccmmmmccc22cccffff	chr5:133723979-133724204(+)$1	225	145	176	10.6750
[ccc####a[ddddmmmmdddd]a4444ccc	chr6:170159888-170160115(+)$1	227	170	201	10.4263
gggggeeeee!!ccclllccc333eeeeeff	chr12:88554498-88554718(+)$1	220	28	59	11.9624
=========cccooooooccc]=========	chr2:210893562-210893786(+)$1	224	62	93	13.3883
ggggggg"""eeeeellleeeee333ggggg	chr6:64415924-64416149(+)$1	225	111	142	12.0422
==========[ddddllldddd]========	chr10:86130952-86131176(+)$1	224	182	213	12.6570
dd!!bb####ddddmmmmdddd333bb333d	chr19:40877504-40877724(+)$1	220	38	69	10.0969
ggg####ccc!!bbnnnnnbb22cccggggg	chr10:124922046-124922280(+)$1	234	24	55	11.3258
===========[bbmmmmbb]==========	chr17:29663783-29664004(+)$1	221	159	190	11.8554
dddd[a[ccc!!cccmmmmccc22cccaddd	chr1:231471759-231471979(-)$1	220	10	41	10.7589
====$$$$$cccooooooccc4444======	chr11:85977134-85977358(+)$1	224	40	71	12.8177
iiiiiiiii[a[bboooooobba]iiiiiii	chr2:105893988-105894209(-)$1	221	3	34	12.2165
g!!ccc!!ccc[annnnna]ccccccggggg	chr11:130013190-130013425(+)$1	235	124	155	11.6632
!!dddd!!ccc[ccclllcccccc4444ddd	chrX:119387409-119387630(+)$1	221	85	116	12.0571
b!!gggggggcccnnnnnccc]ggggggg22	chr1:8927073-8927295(-)$1	222	155	186	10.6902
ddd####dddd[cccooooooccc4444ddd	chr2:238991835-238992057(+)$1	222	37	68	10.3011
ffffffccc!!cccmmmmccc22ccc]ffff	chr2:187626384-187626605(+)$1	221	32	63	9.9683
cccccc[bb[a[cccmmmmccc]a]bb333c	chr19:42365453-42365674(+)$1	221	15	46	10.8472
fff"""eeeee[cccmmmmccc4444eeeee	chr5:59982689-59982907(-)$1	218	110	141	10.5093
iiiiiiiii"""bbmmmmbb333iiiiiiii	chr15:49431625-49431846(-)$1	221	45	76	11.8051
b[==========rrrrrrrrr==========	chr22:40660937-40661160(+)$1	223	59	90	10.8263
gggggg!!ccc[ccclllccc]ccc]ggggg	chr19:9949020-9949244(+)$1	224	174	205	13.8029
d[ggggggg"""bbnnnnnbb333ggggggg	chr8:30565489-30565714(-)$1	225	29	60	11.8035
cc[bb"""cccooooooccc333bb]cccbb	chr11:3383679-3383920(-)$1	241	78	109	9.4632
ccffffff[cccooooooccc]ffffff]cc	chr7:107224286-107224511(+)$1	225	158	189	9.8728
ffffff!!bb!!ccclllccc4444bb22ff	chr1:27623486-27623708(+)$1	222	185	216	11.4653
=========[eeeeellleeeee333=====	chr6:146239173-146239393(-)$1	220	121	152	12.6559
[ccc!!ccc!!ddddllldddd22ccc]ccc	chr13:101320849-101321069(-)$1	220	117	148	11.1973
"bb"""eeeee[ccclllccc333eeeeebb	chr1:53158403-53158621(-)$1	218	47	78	10.9806
[bb[bb[ccccccooooooccc4444cccbb	chr11:105880616-105880838(-)$1	222	27	58	11.3291
iiiii[ccc[a[annnnna]a]ccc]iiiii	chr7:158482420-158482644(-)$1	224	123	154	11.9085
[ggggggg!!cccnnnnnccc22ggggggg]	chr14:56125209-56125431(+)$1	222	20	51	11.6322
dd[ccc!!a!!cccmmmmccc]a22ccc22d	chr3:9483728-9483949(+)$1	221	140	171	11.5071
dddd[ccc"""a[bbmmmmbb]a333ccc]d	chrX:107977028-107977257(-)$1	229	140	171	10.2606
iiiii"""ccceeeeeooooooeeeee333c	chrX:123185117-123185337(+)$1	220	37	68	9.6902
iiiiiii$$$$$cccooooooccc]iiiiii	chr7:6731936-6732156(-)$1	220	119	150	11.9778
ggggggaccc[bbcccooooooccc]bb]cc	chr19:36036579-36036807(+)$1	228	3	34	9.2808
ee"""ffffff[ccclllccc]ffffff22e	chr13:33016779-33017011(-)$1	232	127	158	10.3888
"""ggggggg[ddddllldddd22ggggggg	chrX:23803758-23803982(+)$1	224	49	80	11.2285
cc[eeeee!!eeeeellleeeee333eeeee	chr15:43814295-43814516(+)$1	221	122	153	9.9484
gggggg"""bb[cccooooooccc333bb44	chr9:94123835-94124066(+)$1	231	27	58	11.6936
dd[a[eeeee!!cccnnnnnccc333eeeee	chr3:23931990-23932227(+)$1	237	199	230	10.4328
[dddd"""ccc[bbnnnnnbb]ccc]dddd=	chr5:179688658-179688881(-)$1	223	161	192	10.1906
ggggg####ffffffmmmmffffffgggggg	chr10:70721766-70722013(+)$1	247	152	183	9.7011
ddeeeee"""cccooooooccceeeee]ddd	chr9:130438094-130438314(+)$1	220	131	162	10.3534
!!eeeee"""cccnnnnnccc]eeeeeccc]	chr15:75165469-75165689(-)$1	220	53	84	10.3072
&&iiiiiiiii[cccmmmmccciiiiiiiii	chr19:9048169-9048401(-)$1	232	69	100	10.9873
:::iiiiiiiiiccclllccc]iiiiiiiii	chr20:37202722-37202948(+)$1	226	169	200	10.0570
d"""ffffff!!cccmmmmcccffffff333	chr13:50283622-50283855(-)$1	233	148	179	10.0645
####ccc[ggggggglllggggggg]ccc44	chr1:245023645-245023867(-)$1	222	144	175	10.6896

#otherMatches

#Seq PSSM
AGAGGCCAGGUUUAUACACAAUAUACCAUUU	chr2:128522276-128522500(-)$1	224	90	121	10.5195
ACCCACCAGUACUUAUCCAGAAGCGAAUACA	chr2:44566345-44566566(-)$1	221	171	202	12.8250
aaguaaaccauuacacaaauauugguuUAUU	chr10:70765399-70765624(+)$1	225	45	76	11.2055
GUGGUGAACAAAGCUGGCGGCUUGAUUUACC	chr11:118889474-118889703(+)$1	229	52	83	10.9898
ggccggACGUGCUCUUCAAGGCGCCUGAGCC	chr2:176972456-176972680(+)$1	224	33	64	10.6956
UCCCAGGUGUCUCUCUUCUGAAACCACUGAA	chr9:114676874-114677096(+)$1	222	60	91	10.0541
AUUAUAAUUUGUCAGUAUUCUGUAGGAUAUA	chr5:133723979-133724204(+)$1	225	145	176	10.6750
UUGUUUUUCCUGGUAAGUACUAUGUUUCACA	chr6:170159888-170160115(+)$1	227	170	201	10.4263
GCUGCAGACACUAGUAAAACUCAUUGUCUUG	chr12:88554498-88554718(+)$1	220	28	59	11.9624
UGACAUGGGAAUCACAAUGUUAUCUAUGUCA	chr2:210893562-210893786(+)$1	224	62	93	13.3883
CCUCAAAUAUUUUGGCUUCUGAAUUCUUUGA	chr6:64415924-64416149(+)$1	225	111	142	12.0422
GAUAAAGGGAGGUUUGAAAAGUGUUUCUUUA	chr10:86130952-86131176(+)$1	224	182	213	12.6570
GGCCGCUAUCGCUGAGCUCAGCACUGCCCUC	chr19:40877504-40877724(+)$1	220	38	69	10.0969
GGUUAUUUCUGUAUCUGGUGUUAAGAACCAU	chr10:124922046-124922280(+)$1	234	24	55	11.3258
GGAAAGGAAUUUGUGUUUACCAGUUCCUUUC	chr17:29663783-29664004(+)$1	221	159	190	11.8554
UGUUUGAUAGUAAGGAGAGCCUCUCUACAGC	chr1:231471759-231471979(-)$1	220	10	41	10.7589
UCUUAAACUUUGGAGGAUCAAUUCAAAGAGA	chr11:85977134-85977358(+)$1	224	40	71	12.8177
CUGGGGGUGUCACUGUGUGAAGGUCGCCUCC	chr2:105893988-105894209(-)$1	221	3	34	12.2165
ACAAAUACCUGGAGCAGAUGCAGAUUUAGGU	chr11:130013190-130013425(+)$1	235	124	155	11.6632
AGAGAUCUUUGCAGAAAUUCUCAAUUAUAUC	chrX:119387409-119387630(+)$1	221	85	116	12.0571
UGGGGGUUUCAGCUUGCUGUUGGGGACCCGA	chr1:8927073-8927295(-)$1	222	155	186	10.6902
CAACUUUUCCUUCCAGUUUUAUGGUCCCAGG	chr2:238991835-238992057(+)$1	222	37	68	10.3011
AGAGUUUCCAUGGUAAAAACUCGGGACGAUU	chr2:187626384-187626605(+)$1	221	32	63	9.9683
GAGCUUUGUGAGAGGAGGACCUGUGGCUUUG	chr19:42365453-42365674(+)$1	221	15	46	10.8472
CUUAUACAGGUAAUGGCAACAUGUAAACCUG	chr5:59982689-59982907(-)$1	218	110	141	10.5093
UUCGGAGUGCAGUCACAAGAAAUUAUUCUGA	chr15:49431625-49431846(-)$1	221	45	76	11.8051
AAUCUUGGGGUCUGGAAAUCUGACCCUAAGG	chr22:40660937-40661160(+)$1	223	59	90	10.8263
GGGCAGGGGGAGCCUGCCAGGGUCCGCUGCU	chr19:9949020-9949244(+)$1	224	174	205	13.8029
UGAAUACUGACUUGGGUUUCAUUGCAGUGUU	chr8:30565489-30565714(-)$1	225	29	60	11.8035
ugucuuauagguauuuucuuugugguuacca	chr11:3383679-3383920(-)$1	241	78	109	9.4632
UCUUUGaauaaauauaacuuuuuuuaaauga	chr7:107224286-107224511(+)$1	225	158	189	9.8728
CCUCCAAGCCCCAGUUACACUAUAUGGACUG	chr1:27623486-27623708(+)$1	222	185	216	11.4653
GAGAAGGUAUUGUUUCUAAGACAUGCUACUU	chr6:146239173-146239393(-)$1	220	121	152	12.6559
UCUGUUCUUCCUCCAUUCUGGGCUAAGUUAG	chr13:101320849-101321069(-)$1	220	117	148	11.1973
AGACAUGAAGAACAACCCUUGCCCUCUUCUC	chr1:53158403-53158621(-)$1	218	47	78	10.9806
GUUGUCAUCCGUCAUACCAGAUUCCAGGAGA	chr11:105880616-105880838(-)$1	222	27	58	11.3291
AGAAAGAAGAGGUAAAUAGGUAUUUGUUUUU	chr7:158482420-158482644(-)$1	224	123	154	11.9085
UUUAGAUACUGAUGUUUAAUUUUUAUUUAAU	chr14:56125209-56125431(+)$1	222	20	51	11.6322
UGCCCGUACUUUCGGUAAUGAUGCUCGGUUC	chr3:9483728-9483949(+)$1	221	140	171	11.5071
UUGGGACAGAAUGACAACAGUGAGUAUGUGC	chrX:107977028-107977257(-)$1	229	140	171	10.2606
uuGUCCUUAGGAUAGAAUUGUGUCUAUGACC	chrX:123185117-123185337(+)$1	220	37	68	9.6902
AGCUUGAGAAAACUCAUCCAGGAGAUCAAGC	chr7:6731936-6732156(-)$1	220	119	150	11.9778
CCGCUCCCGGAGACGCCGCCUCGCGAUcccc	chr19:36036579-36036807(+)$1	228	3	34	9.2808
CUUUUGUGCUACAUAAUUUAUCUAGUAUUUG	chr13:33016779-33017011(-)$1	232	127	158	10.3888
AAUGAGGUGUCGCUGCAGCAGCAUGCACUUC	chrX:23803758-23803982(+)$1	224	49	80	11.2285
UCUGGUGGUCUGGCUACCAGCCAAUCCCACU	chr15:43814295-43814516(+)$1	221	122	153	9.9484
CGAGCGGCCGCCCGCUGCCCCGCGCCUGCCC	chr9:94123835-94124066(+)$1	231	27	58	11.6936
GAGUAGGGUAUUUCUAUAACAGAUAUUAUUC	chr3:23931990-23932227(+)$1	237	199	230	10.4328
UAUUAAACAUCUGCAUUCAGCUGGUAUAAUU	chr5:179688658-179688881(-)$1	223	161	192	10.1906
GUUCUUGGAAAUAUCGUAUGAUGUUAGAACG	chr10:70721766-70722013(+)$1	247	152	183	9.7011
GGCUGUGGGACCUAGAGGAAGGCACAGACCC	chr9:130438094-130438314(+)$1	220	131	162	10.3534
AGCAGCGUUCGCGGAGUUCGCCCGCUGGCCC	chr15:75165469-75165689(-)$1	220	53	84	10.3072
CUCUGGUCACUAGUUCCAGGGCAGUGACCAG	chr19:9048169-9048401(-)$1	232	69	100	10.9873
UAUGGUCAUCCCUCUUGUGGAUGGGAUGAUU	chr20:37202722-37202948(+)$1	226	169	200	10.0570
GUAAGGCAUAUAAUGUCCUCAUUAUGCUAUU	chr13:50283622-50283855(-)$1	233	148	179	10.0645
CUUACAAUGGAGAGUUUUGCUUUUCUUUGGG	chr1:245023645-245023867(-)$1	222	144	175	10.6896

#DB
(((((...(((.(((.....))).)))..))	chr2:128522276-128522500(-)$1	1	90	121	10.5195
((((.(..((((((......)))....))).	chr2:44566345-44566566(-)$1	1	171	202	12.8250
((((((((((.((......)).)))))))))	chr10:70765399-70765624(+)$1	1	45	76	11.2055
.(((((((..(((((...)))))..))))))	chr11:118889474-118889703(+)$1	1	52	83	10.9898
((((((..(((((......)))))))).)))	chr2:176972456-176972680(+)$1	1	33	64	10.6956
((((((..((.((......)).))..)))..	chr9:114676874-114677096(+)$1	1	60	91	10.0541
((((((.(((..(((....)))..)))))))	chr5:133723979-133724204(+)$1	1	145	176	10.6750
.(((....(.((((....)))).)....)))	chr6:170159888-170160115(+)$1	1	170	201	10.4263
)))))(((((..(((...)))...)))))((	chr12:88554498-88554718(+)$1	1	28	59	11.9624
((((((((((((......))).)))))))))	chr2:210893562-210893786(+)$1	1	62	93	13.3883
(((((((...(((((...)))))...)))))	chr6:64415924-64416149(+)$1	1	111	142	12.0422
((((((((((.((((...)))).))))))))	chr10:86130952-86131176(+)$1	1	182	213	12.6570
((..((....((((....))))...))...)	chr19:40877504-40877724(+)$1	1	38	69	10.0969
(((....(((..((.....))..))))))))	chr10:124922046-124922280(+)$1	1	24	55	11.3258
(((((((((((.((....)).))))))))))	chr17:29663783-29664004(+)$1	1	159	190	11.8554
((((.(.(((..(((....)))..)))))))	chr1:231471759-231471979(-)$1	1	10	41	10.7589
((((.....(((......)))....))))))	chr11:85977134-85977358(+)$1	1	40	71	12.8177
(((((((((.(.((......))).)))))))	chr2:105893988-105894209(-)$1	1	3	34	12.2165
(..(((..(((.(.....).)))))))))))	chr11:130013190-130013425(+)$1	1	124	155	11.6632
..((((..(((.(((...))))))....)))	chrX:119387409-119387630(+)$1	1	85	116	12.0571
(..((((((((((.....))).)))))))..	chr1:8927073-8927295(-)$1	1	155	186	10.6902
(((....((((.(((......)))....)))	chr2:238991835-238992057(+)$1	1	37	68	10.3011
(((((((((..(((....)))..))).))))	chr2:187626384-187626605(+)$1	1	32	63	9.9683
((((((.((.(.(((....))).).))...)	chr19:42365453-42365674(+)$1	1	15	46	10.8472
(((...(((((.(((....)))....)))))	chr5:59982689-59982907(-)$1	1	110	141	10.5093
(((((((((...((....))...))))))))	chr15:49431625-49431846(-)$1	1	45	76	11.8051
(.((((((((((.........))))))))))	chr22:40660937-40661160(+)$1	1	59	90	10.8263
((((((..(((.(((...))).))).)))))	chr19:9949020-9949244(+)$1	1	174	205	13.8029
(.(((((((...((.....))...)))))))	chr8:30565489-30565714(-)$1	1	29	60	11.8035
((.((...(((......)))...)).)))))	chr11:3383679-3383920(-)$1	1	78	109	9.4632
((((((((.(((......))).)))))).))	chr7:107224286-107224511(+)$1	1	158	189	9.8728
((((((..((..(((...)))....))..))	chr1:27623486-27623708(+)$1	1	185	216	11.4653
(((((((((.(((((...)))))...)))))	chr6:146239173-146239393(-)$1	1	121	152	12.6559
.(((..(((..((((...))))..))).)))	chr13:101320849-101321069(-)$1	1	117	148	11.1973
.((...(((((.(((...)))...)))))))	chr1:53158403-53158621(-)$1	1	47	78	10.9806
.((.((.((((((......)))....)))))	chr11:105880616-105880838(-)$1	1	27	58	11.3291
(((((.(((.(.(.....).).))).)))))	chr7:158482420-158482644(-)$1	1	123	154	11.9085
.(((((((..(((.....)))..))))))).	chr14:56125209-56125431(+)$1	1	20	51	11.6322
((.(((..(..(((....))).)..)))..)	chr3:9483728-9483949(+)$1	1	140	171	11.5071
((((.(((...(.((....)).)...))).)	chrX:107977028-107977257(-)$1	1	140	171	10.2606
(((((...((((((((......)))))...)	chrX:123185117-123185337(+)$1	1	37	68	9.6902
(((((((.....(((......))).))))))	chr7:6731936-6732156(-)$1	1	119	150	11.9778
((((((((((.(((((......))).)).))	chr19:36036579-36036807(+)$1	1	3	34	9.2808
((...((((((.(((...))).))))))..)	chr13:33016779-33017011(-)$1	1	127	158	10.3888
...(((((((.((((...))))..)))))))	chrX:23803758-23803982(+)$1	1	49	80	11.2285
((.(((((..(((((...)))))...)))))	chr15:43814295-43814516(+)$1	1	122	153	9.9484
((((((...((.(((......)))...))..	chr9:94123835-94124066(+)$1	1	27	58	11.6936
((.(.(((((..(((.....)))...)))))	chr3:23931990-23932227(+)$1	1	199	230	10.4328
.((((...(((.((.....)).))).)))))	chr5:179688658-179688881(-)$1	1	161	192	10.1906
(((((....((((((....))))))))))))	chr10:70721766-70722013(+)$1	1	152	183	9.7011
(((((((...(((......)))))))).)))	chr9:130438094-130438314(+)$1	1	131	162	10.3534
..(((((...(((.....))).)))))))).	chr15:75165469-75165689(-)$1	1	53	84	10.3072
..(((((((((.(((....))))))))))))	chr19:9048169-9048401(-)$1	1	69	100	10.9873
...((((((((((((...))).)))))))))	chr20:37202722-37202948(+)$1	1	169	200	10.0570
(...((((((..(((....)))))))))...	chr13:50283622-50283855(-)$1	1	148	179	10.0645
....(((.(((((((...))))))).)))..	chr1:245023645-245023867(-)$1	1	144	175	10.6896

#PSSM
g : 0.17	d : 0.16	[ : 0.08	= : 0.08	i : 0.08	f : 0.07	c : 0.07	e : 0.05	! : 0.05	b : 0.03	" : 0.03	E : 0.01	& : 0.01	: : 0.01	# : 0.01	
g : 0.19	d : 0.14	i : 0.10	c : 0.10	= : 0.08	f : 0.07	! : 0.07	e : 0.05	[ : 0.03	b : 0.03	" : 0.03	& : 0.01	: : 0.01	# : 0.01	
g : 0.21	i : 0.12	= : 0.10	f : 0.08	d : 0.08	e : 0.07	[ : 0.07	c : 0.05	! : 0.05	" : 0.05	b : 0.03	: : 0.01	# : 0.01	
g : 0.21	i : 0.14	c : 0.12	= : 0.10	e : 0.07	f : 0.07	d : 0.07	" : 0.07	# : 0.05	! : 0.01	b : 0.01	[ : 0.01	a : 0.01	
g : 0.19	i : 0.14	c : 0.10	f : 0.08	= : 0.08	e : 0.07	[ : 0.07	# : 0.05	b : 0.05	" : 0.05	d : 0.03	$ : 0.01	! : 0.01	
g : 0.16	c : 0.12	" : 0.10	i : 0.10	f : 0.10	e : 0.08	= : 0.08	# : 0.07	a : 0.03	b : 0.03	$ : 0.01	d : 0.01	! : 0.01	[ : 0.01	
! : 0.14	e : 0.12	i : 0.10	g : 0.10	" : 0.08	# : 0.08	= : 0.08	c : 0.08	[ : 0.07	f : 0.05	$ : 0.01	a : 0.01	
c : 0.16	" : 0.14	! : 0.14	i : 0.08	g : 0.08	e : 0.08	= : 0.08	# : 0.05	f : 0.05	$ : 0.03	d : 0.01	b : 0.01	[ : 0.01	
c : 0.28	i : 0.08	e : 0.08	= : 0.08	" : 0.08	g : 0.07	! : 0.05	b : 0.05	a : 0.03	# : 0.03	$ : 0.03	f : 0.03	d : 0.01	[ : 0.01	
c : 0.28	! : 0.10	" : 0.10	e : 0.08	[ : 0.08	i : 0.05	b : 0.05	= : 0.05	g : 0.05	f : 0.05	# : 0.01	d : 0.01	$ : 0.01	
c : 0.28	! : 0.17	e : 0.12	[ : 0.08	d : 0.05	a : 0.05	" : 0.05	= : 0.03	f : 0.03	i : 0.03	$ : 0.01	b : 0.01	g : 0.01	
[ : 0.26	c : 0.19	! : 0.12	e : 0.10	d : 0.08	b : 0.05	" : 0.03	= : 0.01	o : 0.01	a : 0.01	$ : 0.01	f : 0.01	i : 0.01	g : 0.01	
c : 0.46	b : 0.16	e : 0.10	d : 0.08	o : 0.07	a : 0.03	r : 0.01	[ : 0.01	f : 0.01	g : 0.01	
c : 0.39	o : 0.16	b : 0.12	e : 0.08	d : 0.08	n : 0.08	r : 0.01	f : 0.01	g : 0.01	
c : 0.33	o : 0.19	n : 0.14	m : 0.10	e : 0.08	d : 0.05	r : 0.01	b : 0.01	f : 0.01	g : 0.01	
l : 0.26	o : 0.24	m : 0.24	n : 0.17	r : 0.01	e : 0.01	c : 0.01	
o : 0.28	l : 0.26	m : 0.24	n : 0.17	r : 0.01	
o : 0.26	l : 0.26	m : 0.24	n : 0.17	r : 0.01	c : 0.01	
c : 0.28	o : 0.21	m : 0.14	n : 0.08	d : 0.08	e : 0.07	b : 0.03	a : 0.03	r : 0.01	g : 0.01	
c : 0.42	b : 0.14	o : 0.12	e : 0.08	d : 0.08	n : 0.03	] : 0.03	r : 0.01	f : 0.01	g : 0.01	
c : 0.48	b : 0.12	e : 0.08	d : 0.08	o : 0.08	3 : 0.03	] : 0.01	r : 0.01	a : 0.01	f : 0.01	g : 0.01	
c : 0.28	] : 0.23	e : 0.08	d : 0.08	3 : 0.08	2 : 0.05	= : 0.03	4 : 0.03	o : 0.03	b : 0.01	f : 0.01	g : 0.01	
c : 0.21	e : 0.14	2 : 0.12	3 : 0.10	4 : 0.07	f : 0.07	i : 0.05	] : 0.05	= : 0.05	a : 0.05	g : 0.03	b : 0.01	
c : 0.19	3 : 0.16	2 : 0.10	4 : 0.08	i : 0.07	e : 0.07	= : 0.07	f : 0.07	g : 0.05	] : 0.03	b : 0.03	a : 0.03	
c : 0.21	4 : 0.14	3 : 0.12	i : 0.08	e : 0.08	g : 0.08	= : 0.07	f : 0.07	2 : 0.05	] : 0.03	b : 0.01	
c : 0.16	4 : 0.10	i : 0.10	g : 0.10	3 : 0.10	] : 0.10	e : 0.08	= : 0.08	b : 0.05	f : 0.05	2 : 0.01	
c : 0.19	g : 0.17	e : 0.14	i : 0.12	= : 0.10	4 : 0.07	b : 0.07	f : 0.05	] : 0.01	3 : 0.01	d : 0.01	
g : 0.17	c : 0.14	i : 0.12	= : 0.10	f : 0.08	e : 0.08	] : 0.05	4 : 0.05	3 : 0.05	2 : 0.03	b : 0.03	a : 0.01	d : 0.01	
g : 0.19	c : 0.16	i : 0.12	= : 0.10	e : 0.08	d : 0.08	2 : 0.07	3 : 0.07	f : 0.03	] : 0.03	b : 0.01	
g : 0.17	i : 0.12	c : 0.10	= : 0.10	3 : 0.08	d : 0.08	e : 0.07	f : 0.07	2 : 0.05	b : 0.05	4 : 0.03	] : 0.01	
g : 0.16	i : 0.12	= : 0.12	d : 0.12	c : 0.10	e : 0.08	f : 0.07	b : 0.05	2 : 0.03	3 : 0.03	] : 0.03	4 : 0.03	

#score	620.053268296332
#seq	56
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_UTR_m2_run1.txt

#BEAR
ggggggguuuuuuuuuuuuggggg	chr1:65694486-65694711(+)$1	225	68	92	24.5425
dd[cccvvvvvvvvvvvvvccc]d	chr2:198416963-198417195(+)$1	232	2	26	23.1005
cc[cccwwwwwwwwwwwwwwcccc	chr10:112658763-112658988(+)$1	225	93	117	22.4166
eeeeyyyyyyyyyyyyyyyyeeee	chr18:77897426-77897659(+)$1	233	15	39	22.0529
====cccuuuuuuuuuuuuccc]=	chr7:94921490-94921722(+)$1	232	6	30	24.5434
###ddddvvvvvvvvvvvvvdddd	chr11:33766136-33766366(-)$1	230	86	110	22.4435
========ttttttttttt=====	chr1:117645223-117645481(+)$1	258	91	115	23.2531
###ddddvvvvvvvvvvvvvdddd	chr16:85709401-85709628(+)$1	227	172	196	22.4435
[ddddyyyyyyyyyyyyyyyyddd	chr7:27211304-27211536(-)$1	232	57	81	21.6563
ggggggguuuuuuuuuuuuggggg	chr12:57392695-57392922(-)$1	227	169	193	24.5425
ggggggvvvvvvvvvvvvvggggg	chr8:48974455-48974698(+)$1	243	118	142	23.8463
hhhhhhhuuuuuuuuuuuuhhhhh	chr20:44039116-44039343(+)$1	227	158	182	22.0765
cc[cccwwwwwwwwwwwwwwcccc	chr5:132213789-132214016(-)$1	227	184	208	22.4166
hh"""ccctttttttttttccc88	chr17:54942088-54942338(+)$1	250	157	181	21.2733
ffff[bbuuuuuuuuuuuubb]ff	chr4:77968486-77968718(-)$1	232	130	154	22.9098
$ffffffyyyyyyyyyyyyyyyyf	chr12:46582371-46582603(-)$1	232	173	197	20.5294
cceeeeeuuuuuuuuuuuueeeee	chr17:7560490-7560725(+)$1	235	96	120	23.7619
ddddccctttttttttttccc]dd	chr1:85490940-85491172(-)$1	232	156	180	22.3265
dd!!ccctttttttttttccc22d	chr10:75572160-75572390(-)$1	230	24	48	22.1979
""eeeeettttttttttteeeee4	chr10:94213293-94213521(-)$1	228	67	91	22.5599
gggggwwwwwwwwwwwwwwggggg	chr15:66787387-66787616(-)$1	229	95	119	22.7094
&ffffffuuuuuuuuuuuufffff	chr3:158983400-158983640(+)$1	240	120	144	22.7772
fff[cccuuuuuuuuuuuuccc]f	chr2:152658801-152659026(-)$1	225	98	122	24.0766
========ttttttttttt=====	chr1:117645287-117645514(+)$1	227	27	51	23.2531
e[ddddvvvvvvvvvvvvvdddd]	chr11:35828228-35828452(+)$1	224	126	150	22.7056
ggggggguuuuuuuuuuuuggggg	chr15:63136648-63136880(+)$1	232	18	42	24.5425
[ddddyyyyyyyyyyyyyyyyddd	chr13:111372459-111372686(+)$1	227	27	51	21.6563
[ccc[ccctttttttttttccccc	chr14:92530123-92530357(-)$1	234	77	101	23.1140
[ffffffwwwwwwwwwwwwwwfff	chr1:67874558-67874787(-)$1	229	79	103	21.6321
!!eeeeeuuuuuuuuuuuueeeee	chr5:132028934-132029168(-)$1	234	28	52	24.1207
ggggggguuuuuuuuuuuuggggg	chr5:167983608-167983849(-)$1	241	77	101	24.5425
iiiii[attttttttttta]iiii	chr1:182353230-182353463(-)$1	233	57	81	23.7081
[ffffffvvvvvvvvvvvvvffff	chr3:183704507-183704733(-)$1	226	160	184	22.7920
f"""bbvvvvvvvvvvvvvbb22f	chr11:134019114-134019340(+)$1	226	113	137	21.6446
hhhhhhhuuuuuuuuuuuuhhhhh	chr1:53517065-53517296(+)$1	231	37	61	22.0765
ggggggguuuuuuuuuuuuggggg	chr2:24290445-24290691(-)$1	246	75	99	24.5425
eeee[bbuuuuuuuuuuuubbeee	chr7:94921929-94922155(+)$1	226	94	118	23.1862
[ffffffuuuuuuuuuuuufffff	chr7:70256364-70256594(+)$1	230	107	131	23.5971
iiiiiiiuuuuuuuuuuuuiiiii	chr12:74934417-74934649(+)$1	232	57	81	24.4848
e[ddddvvvvvvvvvvvvvdddd]	chr11:35828281-35828506(+)$1	225	73	97	22.7056
ggggggguuuuuuuuuuuuggggg	chr7:150777232-150777458(-)$1	226	70	94	24.5425
ggggggguuuuuuuuuuuuggggg	chr1:244871121-244871348(+)$1	227	22	46	24.5425
eeeeyyyyyyyyyyyyyyyyeeee	chr5:179264182-179264409(-)$1	227	100	124	22.0529
eeeeyyyyyyyyyyyyyyyyeeee	chr5:142659928-142660157(-)$1	229	100	124	22.0529
eee[cccuuuuuuuuuuuucccee	chr3:123330177-123330421(+)$1	244	41	65	24.1702
:ffffffuuuuuuuuuuuufffff	chr12:42475561-42475790(-)$1	229	52	76	22.3014
eeeeyyyyyyyyyyyyyyyyeeee	chr3:125165648-125165880(-)$1	232	1	25	22.0529
[ffffffuuuuuuuuuuuufffff	chr1:153615504-153615729(+)$1	225	30	54	23.5971
eee[bbvvvvvvvvvvvvvbb]ee	chr19:13251623-13251855(+)$1	232	198	222	22.3641
ffffffwwwwwwwwwwwwwwffff	chr17:1247743-1247975(-)$1	232	188	212	21.8168
[gggggggtttttttttttggggg	chr17:65335414-65335670(-)$1	256	132	156	23.3053
"""ddddtttttttttttdddd]d	chr2:86440218-86440451(+)$1	233	22	46	22.1381
!gggggggtttttttttttggggg	chr11:119205397-119205629(+)$1	232	179	203	23.2594
cceeeeevvvvvvvvvvvvveeee	chr8:56980333-56980565(-)$1	232	63	87	22.9300
ffffcccuuuuuuuuuuuuccc33	chr2:70166528-70166760(+)$1	232	49	73	23.8916
ggggggvvvvvvvvvvvvvggggg	chr5:124080847-124081079(-)$1	232	194	218	23.8463
b[eeeeettttttttttteeeee]	chr2:87003827-87004059(+)$1	232	75	99	22.3921
d[eeeeeuuuuuuuuuuuueeeee	chr12:42852054-42852286(-)$1	232	140	164	23.7626
gggyyyyyyyyyyyyyyyyggggg	chr17:47127285-47127514(+)$1	229	67	91	21.9948
iiiiiiiitttttttttttiiiii	chr15:72879516-72879740(+)$1	224	190	214	22.9008
[ddddwwwwwwwwwwwwwwdddd]	chr4:103746435-103746667(-)$1	232	126	150	21.7569
cc[dddduuuuuuuuuuuuddddc	chr7:134654455-134654675(+)$1	220	60	84	23.3602
[eeeeevvvvvvvvvvvvveeeee	chr18:723131-723364(-)$1	233	193	217	23.3821
###ddddtttttttttttddddcc	chr1:68168746-68168971(-)$1	225	94	118	22.0441
[dddd[auuuuuuuuuuuuadddd	chr8:25700816-25701047(-)$1	231	43	67	23.7494
##eeeeettttttttttteeeee]	chr5:140064780-140065012(-)$1	232	72	96	22.6526

#otherMatches

#Seq PSSM
UCUUUCUUACUUAGAACUUGGAAA	chr1:65694486-65694711(+)$1	225	68	92	24.5425
CACAGUGAAAGGAAUGAUGACUUU	chr2:198416963-198417195(+)$1	232	2	26	23.1005
GUAUGAGAAAAUAUUACCAAUUAA	chr10:112658763-112658988(+)$1	225	93	117	22.4166
AUUUUCCCUUUUGAUAUGCUAAGU	chr18:77897426-77897659(+)$1	233	15	39	22.0529
GAUACUCUAUUAAUGUCUUGAGAU	chr7:94921490-94921722(+)$1	232	6	30	24.5434
UUAUUAGUUUUCguuuccuucuaa	chr11:33766136-33766366(-)$1	230	86	110	22.4435
AGUAUUUGGuacaaucuaauaaau	chr1:117645223-117645481(+)$1	258	91	115	23.2531
ACCCUGUGCUUAAUUCUAUAACAG	chr16:85709401-85709628(+)$1	227	172	196	22.4435
GCUGGUCCCCUCCCUCUGUCUUCA	chr7:27211304-27211536(-)$1	232	57	81	21.6563
AAAGUUUUGUAUAUUUUGUAAACU	chr12:57392695-57392922(-)$1	227	169	193	24.5425
CGUAUUCUCUACUCUAACAAAUAU	chr8:48974455-48974698(+)$1	243	118	142	23.8463
AAGAUAUCAAACCCACUACAUGUC	chr20:44039116-44039343(+)$1	227	158	182	22.0765
AGAGCAUCCAGCCCAUUCCUUGCC	chr5:132213789-132214016(-)$1	227	184	208	22.4166
GAACAGGCUUAUGUAAAAUGCCCU	chr17:54942088-54942338(+)$1	250	157	181	21.2733
UGAUAGUUUUCACUCAUUUAUAAU	chr4:77968486-77968718(-)$1	232	130	154	22.9098
CAUGAUAUACAAUAAUGUUUAUUU	chr12:46582371-46582603(-)$1	232	173	197	20.5294
CAAGUUAUCAACUAAUCACUAACU	chr17:7560490-7560725(+)$1	235	96	120	23.7619
UCAAACUUAUGUUUCCCUAGUCUU	chr1:85490940-85491172(-)$1	232	156	180	22.3265
AAAUAAUUUAAAAAUAGUGUUUGU	chr10:75572160-75572390(-)$1	230	24	48	22.1979
CCAUGAGUUUUACUUUUCCUCAUC	chr10:94213293-94213521(-)$1	228	67	91	22.5599
GGUGGCAACUCUCCAUUAACCACC	chr15:66787387-66787616(-)$1	229	95	119	22.7094
ACCUCUAACACAACCUUAAUGGAG	chr3:158983400-158983640(+)$1	240	120	144	22.7772
UGAAUAAAUUAUUAAUCCAUUAAU	chr2:152658801-152659026(-)$1	225	98	122	24.0766
AGUAUUUGGuacaaucuaauaaau	chr1:117645287-117645514(+)$1	227	27	51	23.2531
CAUAUUGAAGCAUGAAAUAAAUGA	chr11:35828228-35828452(+)$1	224	126	150	22.7056
GAGGCUGGGUCUCAUUCAGCGGCC	chr15:63136648-63136880(+)$1	232	18	42	24.5425
CAUUUUAGAAACUACAAAUAUAGG	chr13:111372459-111372686(+)$1	227	27	51	21.6563
UGGCUCACAUCAUGUAAUAGUGGC	chr14:92530123-92530357(-)$1	234	77	101	23.1140
ugcagugagccaagaucauagcac	chr1:67874558-67874787(-)$1	229	79	103	21.6321
CUCUUUUCCCUUUAAUUUAAAAAG	chr5:132028934-132029168(-)$1	234	28	52	24.1207
GUUUUGGUCAUAUAUACAUUCAGA	chr5:167983608-167983849(-)$1	241	77	101	24.5425
GUUAAUCUUGCUUUCUUUGUUUGG	chr1:182353230-182353463(-)$1	233	57	81	23.7081
GUGUUAUGUAAUUUACCAAAAUGG	chr3:183704507-183704733(-)$1	226	160	184	22.7920
UUACUCUAACAAGCCACAUGAAUA	chr11:134019114-134019340(+)$1	226	113	137	21.6446
UAUAACGUUCUCAGUCCUUUGUUA	chr1:53517065-53517296(+)$1	231	37	61	22.0765
UCAUUUGGACUAAAUCCCACGAAU	chr2:24290445-24290691(-)$1	246	75	99	24.5425
AGUGAGUUAUUUUAACAUUACCAC	chr7:94921929-94922155(+)$1	226	94	118	23.1862
AUACAUUAAUACUUCUUAAAAUGU	chr7:70256364-70256594(+)$1	230	107	131	23.5971
UACUUCCUAACAAUGUCUUGGAAG	chr12:74934417-74934649(+)$1	232	57	81	24.4848
CAUAUUGAAGCAUGAAAUAAAUGA	chr11:35828281-35828506(+)$1	225	73	97	22.7056
gacugggcgcgaccacuaacccgg	chr7:150777232-150777458(-)$1	226	70	94	24.5425
UGUUGUAUUUACUUUCAUCUGCAG	chr1:244871121-244871348(+)$1	227	22	46	24.5425
UAAGAACCAUUAACAAUAAACUUA	chr5:179264182-179264409(-)$1	227	100	124	22.0529
UAAACUCAAAACUUAACAUAUUUA	chr5:142659928-142660157(-)$1	229	100	124	22.0529
UGGCUGCCAAUAAUGAACUGCACC	chr3:123330177-123330421(+)$1	244	41	65	24.1702
UAGAGGAGUUUUCAGUUCAUCCUC	chr12:42475561-42475790(-)$1	229	52	76	22.3014
AGCCUAAAUUUACUCUGCUUGGCU	chr3:125165648-125165880(-)$1	232	1	25	22.0529
UGAUUGAAUAAAGAGUAGCUUAAU	chr1:153615504-153615729(+)$1	225	30	54	23.5971
GCCGAGCCCCCACCCCUCCCUGGG	chr19:13251623-13251855(+)$1	232	198	222	22.3641
CAAACACACUGACAGUAUUAUGUU	chr17:1247743-1247975(-)$1	232	188	212	21.8168
AUCUUUUUAAAACUAACCAAAAAA	chr17:65335414-65335670(-)$1	256	132	156	23.3053
CUUGGGAUCCUGUGUAUUUCCCUG	chr2:86440218-86440451(+)$1	233	22	46	22.1381
AUGUUUGGCCUCUUCCCUCCCAAA	chr11:119205397-119205629(+)$1	232	179	203	23.2594
caacaaauauccagaaaucuuuug	chr8:56980333-56980565(-)$1	232	63	87	22.9300
UUGUAGCAUUUUUAUUUAAGCUAA	chr2:70166528-70166760(+)$1	232	49	73	23.8916
UUUUCCCCCCCCCUUCACAGGAAA	chr5:124080847-124081079(-)$1	232	194	218	23.8463
CAUCACUAGGAUGUAUAAGGUGAC	chr2:87003827-87004059(+)$1	232	75	99	22.3921
GAAUAUAAAUCUUUGCAAAUGUAU	chr12:42852054-42852286(-)$1	232	140	164	23.7626
GACUCAAGGGAAAAGAACUGUCAG	chr17:47127285-47127514(+)$1	229	67	91	21.9948
UUAGAGGUUGCUCUAUACUAUCUC	chr15:72879516-72879740(+)$1	224	190	214	22.9008
UUAAACUGUAUUUCCCUUUUUUGU	chr4:103746435-103746667(-)$1	232	126	150	21.7569
GAACUUAUUAUAUAGCCUCUAAGU	chr7:134654455-134654675(+)$1	220	60	84	23.3602
UUUUUAUGUAAAACAUUUUUAGAA	chr18:723131-723364(-)$1	233	193	217	23.3821
UAUGAGUAUAAAUACAUAACUUCC	chr1:68168746-68168971(-)$1	225	94	118	22.0441
CCACCACUCCCUCCGCUUUGGGUG	chr8:25700816-25701047(-)$1	231	43	67	23.7494
uuuuucaucauccccaauugaaac	chr5:140064780-140065012(-)$1	232	72	96	22.6526

#DB
(((((((............)))))	chr1:65694486-65694711(+)$1	1	68	92	24.5425
((.(((.............))).)	chr2:198416963-198417195(+)$1	1	2	26	23.1005
((.(((..............))))	chr10:112658763-112658988(+)$1	1	93	117	22.4166
((((................))))	chr18:77897426-77897659(+)$1	1	15	39	22.0529
(((((((............))).)	chr7:94921490-94921722(+)$1	1	6	30	24.5434
...((((.............))))	chr11:33766136-33766366(-)$1	1	86	110	22.4435
((((((((...........)))))	chr1:117645223-117645481(+)$1	1	91	115	23.2531
...((((.............))))	chr16:85709401-85709628(+)$1	1	172	196	22.4435
.((((................)))	chr7:27211304-27211536(-)$1	1	57	81	21.6563
(((((((............)))))	chr12:57392695-57392922(-)$1	1	169	193	24.5425
((((((.............)))))	chr8:48974455-48974698(+)$1	1	118	142	23.8463
(((((((............)))))	chr20:44039116-44039343(+)$1	1	158	182	22.0765
((.(((..............))))	chr5:132213789-132214016(-)$1	1	184	208	22.4166
((...(((...........)))..	chr17:54942088-54942338(+)$1	1	157	181	21.2733
((((.((............)).))	chr4:77968486-77968718(-)$1	1	130	154	22.9098
.((((((................)	chr12:46582371-46582603(-)$1	1	173	197	20.5294
(((((((............)))))	chr17:7560490-7560725(+)$1	1	96	120	23.7619
(((((((...........))).))	chr1:85490940-85491172(-)$1	1	156	180	22.3265
((..(((...........)))..)	chr10:75572160-75572390(-)$1	1	24	48	22.1979
..(((((...........))))).	chr10:94213293-94213521(-)$1	1	67	91	22.5599
(((((..............)))))	chr15:66787387-66787616(-)$1	1	95	119	22.7094
.((((((............)))))	chr3:158983400-158983640(+)$1	1	120	144	22.7772
(((.(((............))).)	chr2:152658801-152659026(-)$1	1	98	122	24.0766
((((((((...........)))))	chr1:117645287-117645514(+)$1	1	27	51	23.2531
(.((((.............)))).	chr11:35828228-35828452(+)$1	1	126	150	22.7056
(((((((............)))))	chr15:63136648-63136880(+)$1	1	18	42	24.5425
.((((................)))	chr13:111372459-111372686(+)$1	1	27	51	21.6563
.(((.(((...........)))))	chr14:92530123-92530357(-)$1	1	77	101	23.1140
.((((((..............)))	chr1:67874558-67874787(-)$1	1	79	103	21.6321
..(((((............)))))	chr5:132028934-132029168(-)$1	1	28	52	24.1207
(((((((............)))))	chr5:167983608-167983849(-)$1	1	77	101	24.5425
(((((.(...........).))))	chr1:182353230-182353463(-)$1	1	57	81	23.7081
.((((((.............))))	chr3:183704507-183704733(-)$1	1	160	184	22.7920
(...((.............))..)	chr11:134019114-134019340(+)$1	1	113	137	21.6446
(((((((............)))))	chr1:53517065-53517296(+)$1	1	37	61	22.0765
(((((((............)))))	chr2:24290445-24290691(-)$1	1	75	99	24.5425
((((.((............)))))	chr7:94921929-94922155(+)$1	1	94	118	23.1862
.((((((............)))))	chr7:70256364-70256594(+)$1	1	107	131	23.5971
(((((((............)))))	chr12:74934417-74934649(+)$1	1	57	81	24.4848
(.((((.............)))).	chr11:35828281-35828506(+)$1	1	73	97	22.7056
(((((((............)))))	chr7:150777232-150777458(-)$1	1	70	94	24.5425
(((((((............)))))	chr1:244871121-244871348(+)$1	1	22	46	24.5425
((((................))))	chr5:179264182-179264409(-)$1	1	100	124	22.0529
((((................))))	chr5:142659928-142660157(-)$1	1	100	124	22.0529
(((.(((............)))))	chr3:123330177-123330421(+)$1	1	41	65	24.1702
.((((((............)))))	chr12:42475561-42475790(-)$1	1	52	76	22.3014
((((................))))	chr3:125165648-125165880(-)$1	1	1	25	22.0529
.((((((............)))))	chr1:153615504-153615729(+)$1	1	30	54	23.5971
(((.((.............)).))	chr19:13251623-13251855(+)$1	1	198	222	22.3641
((((((..............))))	chr17:1247743-1247975(-)$1	1	188	212	21.8168
.(((((((...........)))))	chr17:65335414-65335670(-)$1	1	132	156	23.3053
...((((...........)))).)	chr2:86440218-86440451(+)$1	1	22	46	22.1381
.(((((((...........)))))	chr11:119205397-119205629(+)$1	1	179	203	23.2594
(((((((.............))))	chr8:56980333-56980565(-)$1	1	63	87	22.9300
(((((((............)))..	chr2:70166528-70166760(+)$1	1	49	73	23.8916
((((((.............)))))	chr5:124080847-124081079(-)$1	1	194	218	23.8463
(.(((((...........))))).	chr2:87003827-87004059(+)$1	1	75	99	22.3921
(.(((((............)))))	chr12:42852054-42852286(-)$1	1	140	164	23.7626
(((................)))))	chr17:47127285-47127514(+)$1	1	67	91	21.9948
((((((((...........)))))	chr15:72879516-72879740(+)$1	1	190	214	22.9008
.((((..............)))).	chr4:103746435-103746667(-)$1	1	126	150	21.7569
((.((((............)))))	chr7:134654455-134654675(+)$1	1	60	84	23.3602
.(((((.............)))))	chr18:723131-723364(-)$1	1	193	217	23.3821
...((((...........))))))	chr1:68168746-68168971(-)$1	1	94	118	22.0441
.((((.(............)))))	chr8:25700816-25701047(-)$1	1	43	67	23.7494
..(((((...........))))).	chr5:140064780-140065012(-)$1	1	72	96	22.6526

#PSSM
g : 0.16	[ : 0.16	e : 0.13	c : 0.07	f : 0.07	d : 0.06	# : 0.06	= : 0.04	h : 0.04	i : 0.04	" : 0.03	! : 0.03	$ : 0.01	& : 0.01	: : 0.01	b : 0.01	
g : 0.19	f : 0.16	e : 0.12	d : 0.10	c : 0.09	# : 0.06	[ : 0.06	= : 0.04	h : 0.04	" : 0.04	i : 0.04	! : 0.01	
e : 0.22	g : 0.19	f : 0.16	d : 0.10	[ : 0.06	= : 0.04	# : 0.04	" : 0.04	i : 0.04	h : 0.03	! : 0.01	c : 0.01	
e : 0.19	g : 0.18	d : 0.18	f : 0.15	c : 0.06	= : 0.04	[ : 0.04	i : 0.04	h : 0.03	" : 0.03	! : 0.01	y : 0.01	
g : 0.18	d : 0.16	c : 0.13	f : 0.12	e : 0.12	y : 0.07	[ : 0.04	i : 0.04	= : 0.03	h : 0.03	b : 0.03	" : 0.01	
g : 0.16	c : 0.16	f : 0.12	e : 0.12	y : 0.10	d : 0.10	b : 0.06	= : 0.03	h : 0.03	w : 0.03	[ : 0.03	i : 0.03	
g : 0.13	v : 0.12	c : 0.12	y : 0.10	f : 0.10	e : 0.10	w : 0.07	d : 0.07	= : 0.03	h : 0.03	b : 0.03	a : 0.03	i : 0.03	
u : 0.37	v : 0.18	y : 0.12	t : 0.12	w : 0.09	= : 0.03	c : 0.03	g : 0.03	i : 0.01	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	t : 0.22	v : 0.18	y : 0.12	w : 0.09	
u : 0.37	v : 0.18	y : 0.12	t : 0.10	w : 0.09	e : 0.04	c : 0.03	d : 0.03	a : 0.01	
g : 0.19	c : 0.13	y : 0.10	e : 0.10	d : 0.09	w : 0.06	v : 0.06	b : 0.06	f : 0.06	= : 0.03	h : 0.03	i : 0.03	] : 0.01	a : 0.01	
g : 0.19	e : 0.18	c : 0.16	d : 0.13	f : 0.09	b : 0.06	y : 0.04	i : 0.04	= : 0.03	h : 0.03	w : 0.01	
g : 0.19	e : 0.19	d : 0.16	c : 0.13	f : 0.10	] : 0.04	i : 0.04	= : 0.03	h : 0.03	2 : 0.03	y : 0.01	
e : 0.22	g : 0.19	d : 0.15	f : 0.12	] : 0.06	c : 0.06	i : 0.04	= : 0.03	h : 0.03	2 : 0.03	8 : 0.01	y : 0.01	3 : 0.01	
g : 0.19	e : 0.18	f : 0.16	d : 0.13	c : 0.07	] : 0.07	= : 0.04	i : 0.04	h : 0.03	8 : 0.01	4 : 0.01	3 : 0.01	

#score	1515.6232139221752
#seq	66
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_CDS_m2_run2.txt

#BEAR
ee!!ccc^^^^^^^^^^^^^^^^^^ccc333ee	chr11:92532947-92533171(+)$1	224	70	103	33.9067
cccccc^^^^^^^^^^^^^^^^^^^^^ccc]cc	chr5:145890093-145890328(+)$1	235	57	90	36.7747
ee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr9:100760787-100761020(+)$1	233	43	76	40.5089
d!!dddd^^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:135496579-135496813(+)$1	234	80	113	37.9971
ggg[dddd^^^^^^^^^^^^^^^^^^ddddggg	chr4:6863362-6863590(+)$1	228	134	167	32.3432
eee[ccc^^^^^^^^^^^^^^^^^^^^^cccee	chr19:53209121-53209356(-)$1	235	92	125	37.0316
bb:dddd^^^^^^^^^^^^^^^^^^^^^^dddd	chr16:24580005-24580233(+)$1	228	161	194	35.0591
iiiiii^^^^^^^^^^^^^^^^^^^^^^^^iii	chr1:206589159-206589396(+)$1	237	64	97	37.9227
eeeee^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr2:8871796-8872024(-)$1	228	2	35	38.1379
d^^^^^^^^^^^^^^^^^^^^^^^^^^dddddd	chr1:97236241-97236462(+)$1	221	98	131	37.5929
ggggggg^^^^^^^^^^^^^^^^^^^^^^^ggg	chr19:44739410-44739641(+)$1	231	100	133	37.3362
==ggggggg^^^^^^^^^^^^^^^^^^gggggg	chr3:194168494-194168716(-)$1	222	166	199	32.1909
c"""eeeee^^^^^^^^^^^^^^^^^^eeeee5	chr1:78097598-78097830(-)$1	232	114	147	32.3817
:ffffff^^^^^^^^^^^^^^^^^^^^ffffff	chr3:156262056-156262290(-)$1	234	180	213	33.7298
ggggggg^^^^^^^^^^^^^^^^^^^ggggggg	chr2:201438380-201438614(+)$1	234	187	220	33.6047
eeee^^^^^^^^^^^^^^^^^^^^^^^eeeee]	chr1:165712392-165712623(-)$1	231	40	73	37.1828
ee^^^^^^^^^^^^^^^^^^^^^^^^^eeeee3	chr4:77979635-77979860(-)$1	225	125	158	38.1541
ff^^^^^^^^^^^^^^^^^^^^^^^^^^fffff	chrM:3639-3877(+)$1	238	109	142	38.6562
fffff^^^^^^^^^^^^^^^^^^^^^^^^ffff	chr3:160149425-160149645(+)$1	220	95	128	37.8682
!!bb[bb^^^^^^^^^^^^^^^^^^^^bb]bb2	chr19:53117366-53117603(-)$1	237	180	213	34.3702
^^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd]	chr17:18220099-18220320(+)$1	221	92	125	38.7658
d^^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd	chr6:57018589-57018813(+)$1	224	84	117	39.2109
iiiiiiii^^^^^^^^^^^^^^^^^^^iiiiii	chr1:220197639-220197858(-)$1	219	112	145	33.4743
fffff[ccc^^^^^^^^^^^^^^^^^^ccc]ff	chr15:65864561-65864794(+)$1	233	14	47	32.9492
c[dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr6:27420082-27420316(-)$1	234	91	124	38.4372
d^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr19:21476350-21476578(-)$1	228	190	223	40.5224
d[a[ccc^^^^^^^^^^^^^^^^^^^^ccc]a]	chr5:159820727-159820949(-)$1	222	157	190	36.9181
dd^^^^^^^^^^^^^^^^^^^^^^^^^^dddd]	chr2:61722623-61722844(-)$1	221	98	131	38.6613
ff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:71494456-71494686(+)$1	230	60	93	40.4759
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^a]	chr5:5462232-5462454(+)$1	222	97	130	40.3497
[ffffff^^^^^^^^^^^^^^^^^^^^^fffff	chr19:37239765-37239987(-)$1	222	22	55	35.7284
!!eeeee^^^^^^^^^^^^^^^^^^^^^^^eee	chr1:155450543-155450778(-)$1	235	88	121	37.4081
bb!!ccc^^^^^^^^^^^^^^^^^^^^^ccc22	chrM:13661-13963(+)$1	302	64	97	36.7711
e^^^^^^^^^^^^^^^^^^^^^^^^^^^^^eee	chr15:68378787-68379017(+)$1	230	192	225	40.0519
ddd[ccc^^^^^^^^^^^^^^^^^^^^ccc22d	chr4:110441470-110441694(+)$1	224	165	198	35.5198
!ggggggg^^^^^^^^^^^^^^^^^^^gggggg	chr1:40713742-40713970(-)$1	228	159	192	33.8401
hhhhhhh^^^^^^^^^^^^^^^^^^^^^^^hhh	chr11:34118656-34118882(+)$1	226	13	46	34.3985
ff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr12:48468055-48468280(-)$1	225	93	126	40.4759
$$$$ccc^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:8966-9202(+)$1	236	100	133	38.1283
eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee3	chr3:31621298-31621538(+)$1	240	110	143	36.7851
ccc!!bb^^^^^^^^^^^^^^^^^^^^^^^^^b	chr1:54262329-54262562(-)$1	233	94	127	37.8429
c^^^^^^^^^^^^^^^^^^^^^^^^^^ccc]cc	chrM:10402-10737(+)$1	335	128	161	38.4641
bb^^^^^^^^^^^^^^^^^^^^^^^^^^bb]ff	chr17:7404265-7404496(+)$1	231	102	135	38.2293
^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd22	chr13:50129638-50129857(-)$1	219	119	152	37.5396
e^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^e	chr19:1010752-1010985(-)$1	233	91	124	40.4507
ccc[dddd^^^^^^^^^^^^^^^^^^^dddd33	chr15:100252519-100252754(+)$1	235	44	77	34.2305
d"""bb^^^^^^^^^^^^^^^^^^^^^^^^bb]	chr5:112177077-112177298(+)$1	221	140	173	38.2010
ff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr2:153535808-153536046(-)$1	238	103	136	40.4759
fffff^^^^^^^^^^^^^^^^^^^^^^^^ffff	chr13:79929255-79929475(-)$1	220	81	114	37.8682
f[ccc^^^^^^^^^^^^^^^^^^^^^^cccfff	chr11:92881719-92881948(-)$1	229	143	176	37.1830
eee[bb^^^^^^^^^^^^^^^^^^^^^^bb]ee	chr17:1557129-1557370(-)$1	241	20	53	36.8506
b"""dddd^^^^^^^^^^^^^^^^^^dddd22b	chr5:61747584-61747804(+)$1	220	120	153	32.0133
c[bb^^^^^^^^^^^^^^^^^^^^^^^bbccc:	chr9:134454881-134455108(-)$1	227	179	212	36.0171
!!eeeee^^^^^^^^^^^^^^^^^^^^^eeeee	chr10:1038459-1038696(+)$1	237	124	157	36.3187
d^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr14:95570287-95570521(-)$1	234	100	133	40.5224
ee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr12:80189379-80189603(-)$1	224	57	90	40.5089
!!eeeee^^^^^^^^^^^^^^^^^^^^^eeeee	chr5:132220682-132220911(-)$1	229	21	54	36.3187
c"""dddd^^^^^^^^^^^^^^^^^^^^dddd]	chr10:129903295-129903514(-)$1	219	91	124	35.4098
ff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:71494430-71494651(+)$1	221	86	119	40.4759
e!!bb^^^^^^^^^^^^^^^^^^^^^^^^^bb2	chr1:171526993-171527228(+)$1	235	21	54	38.3570
fffff^^^^^^^^^^^^^^^^^^^^^^ffffff	chr16:2811815-2812065(+)$1	250	118	151	36.2030
ddd[ccc^^^^^^^^^^^^^^^^^^^^ccc]dd	chr19:58489683-58489905(-)$1	222	174	207	35.7919
cc!!ccc^^^^^^^^^^^^^^^^^^^^^^^^^^	chrM:4606-4870(+)$1	264	65	98	38.8177
eee!!ccc^^^^^^^^^^^^^^^^^^^ccc]ee	chr11:118343401-118343626(+)$1	225	18	51	35.2543
ee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:214791882-214792123(+)$1	241	108	141	40.5089
ff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^f	chr6:17649313-17649557(-)$1	244	110	143	40.3403
ccc[dddd^^^^^^^^^^^^^^^^^^^^dddd]	chr7:104742453-104742686(+)$1	233	159	192	34.9916
ff^^^^^^^^^^^^^^^^^^^^^^^^^ffffff	chrM:3440-3707(+)$1	267	168	201	37.6584
dffffff^^^^^^^^^^^^^^^^^^^^^^^^^f	chr17:65908531-65908754(+)$1	223	84	117	37.3560
hhhhhhh^^^^^^^^^^^^^^^^^^^^^^^hhh	chr19:24309427-24309671(+)$1	244	186	219	34.3985

#otherMatches

#Seq PSSM
UAAAUGACAACCCCCCUAUUUUCGAUCAGCCUA	chr11:92532947-92533171(+)$1	224	70	103	33.9067
GGGUCCACCCCCACCUCCCACAGCAUCGGAGCC	chr5:145890093-145890328(+)$1	235	57	90	36.7747
CUUGCAGCUUGAACUCAGUGAAAAUAGAAUCUU	chr9:100760787-100761020(+)$1	233	43	76	40.5089
UCCAGAUUCUUUCCACCAGCCCAACAACACUCC	chr5:135496579-135496813(+)$1	234	80	113	37.9971
GUACUUUCAUUGAUGGUCAUUUUGUAGAAAUGC	chr4:6863362-6863590(+)$1	228	134	167	32.3432
UGACAAGGCUUUUAAUCAACAAUCACAACUUUC	chr19:53209121-53209356(-)$1	235	92	125	37.0316
UCAGCCGCUCACAUUCUCGUUCCUAUUCACGGU	chr16:24580005-24580233(+)$1	228	161	194	35.0591
UCUUUUUCCUCCUCCUCUCUUACAGAAAAUGAA	chr1:206589159-206589396(+)$1	237	64	97	37.9227
GAGUAUAGAGAUGCCUAUAGAGAAUACAUUGCU	chr2:8871796-8872024(-)$1	228	2	35	38.1379
GUAACCAACCAAUAUAUAUCCAGUACUCGAAUC	chr1:97236241-97236462(+)$1	221	98	131	37.5929
UCUUUUCAUUCUUAUCAAUCUAAUCAUACAGGA	chr19:44739410-44739641(+)$1	231	100	133	37.3362
AACCUCAAUUAUUUAUcauaugcagcuauugag	chr3:194168494-194168716(-)$1	222	166	199	32.1909
UGUGACUCUCAAAAUAAUGGAAGUGAAGGAGUA	chr1:78097598-78097830(-)$1	232	114	147	32.3817
UUCAACCCCACAGUGUAUCCUUUUCAAGGUUGA	chr3:156262056-156262290(-)$1	234	180	213	33.7298
GGUAAAAAUGUGAUAAUAAAAGAAAAUUUUGCC	chr2:201438380-201438614(+)$1	234	187	220	33.6047
AAGAUAACAAUUCUUUUUUUUUUUUUUUCUUUU	chr1:165712392-165712623(-)$1	231	40	73	37.1828
GUACCAAUUCAACCUUUACCCAGAAACAUUUGC	chr4:77979635-77979860(-)$1	225	125	158	38.1541
AUCAUUCUACUAUCAACAUUACUAAUAAGUGGC	chrM:3639-3877(+)$1	238	109	142	38.6562
CCAGAUUCUAUAACAAAUCAAAUUGCACUUUUG	chr3:160149425-160149645(+)$1	220	95	128	37.8682
AAAAAUCAAACCUUGCAAGUCAUCAAAGAAUUC	chr19:53117366-53117603(-)$1	237	180	213	34.3702
ACAACAGCAUAUAACAAACUUUCUCUUUGAAGA	chr17:18220099-18220320(+)$1	221	92	125	38.7658
GAACAACUACCCAAGCAAAUUCCUUUCACCAUC	chr6:57018589-57018813(+)$1	224	84	117	39.2109
AUACUUCGGAUCAUUUUGAAACUAUAAUGAAGU	chr1:220197639-220197858(-)$1	219	112	145	33.4743
UCUCAGUGAUUCAGUCCAUUCCAAUAUUCAAUG	chr15:65864561-65864794(+)$1	233	14	47	32.9492
CACCAGGAGCACACACCUUACUCAACAUCAAAA	chr6:27420082-27420316(-)$1	234	91	124	38.4372
CUCAAAUUUUACUAAUCAUAAAAAAAUUCAUAC	chr19:21476350-21476578(-)$1	228	190	223	40.5224
guguggcuauuucaaaaaaaguuccucguuucu	chr5:159820727-159820949(-)$1	222	157	190	36.9181
GCUUCCUUUAAAUACCAAUAUUCGACUUGCGUA	chr2:61722623-61722844(-)$1	221	98	131	38.6613
UCUCCAAAAUCUGAUAUCUCUCCACUCACCCCA	chr5:71494456-71494686(+)$1	230	60	93	40.4759
UGAAAAUAUCCUCAUCCAAAACCAAGACAUUGU	chr5:5462232-5462454(+)$1	222	97	130	40.3497
ACUCACCCAACAUCACAGAAUUCACACUGGUGA	chr19:37239765-37239987(-)$1	222	22	55	35.7284
UUCUGAAUCCAGCAUUCAUACUAUUACUCCUUC	chr1:155450543-155450778(-)$1	235	88	121	37.4081
CGCAGGAUUUCUCAUUACUAACAACAUUUCCCC	chrM:13661-13963(+)$1	302	64	97	36.7711
GAACUCCCACAUCUUACAUCAGCUCUUCACCCA	chr15:68378787-68379017(+)$1	230	192	225	40.0519
AGAUGGUAAGCAGUCAGUAAAAUAAAAGCCUUU	chr4:110441470-110441694(+)$1	224	165	198	35.5198
GGAGCAAGAUUAUCUAAUAGUCCCAAACUUGUU	chr1:40713742-40713970(-)$1	228	159	192	33.8401
UCUUCAUUAAUAAAAAAGUAAAAAUUCCUUGUG	chr11:34118656-34118882(+)$1	226	13	46	34.3985
GUACUCUUCAUCAUCCCCAUCAUCACCACUCUG	chr12:48468055-48468280(-)$1	225	93	126	40.4759
AAUAUCAACCAUUAACCUUCCCUCUACACUUAU	chrM:8966-9202(+)$1	236	100	133	38.1283
AGCGGCCUUACAUCUAUAUCUACUUUCCUGCUU	chr3:31621298-31621538(+)$1	240	110	143	36.7851
UGACUGAAUUUUCUAAUCCUUCUCCAUCUACCU	chr1:54262329-54262562(-)$1	233	94	127	37.8429
GUAUAUCGCUCACACCUCAUAUCCUCCCUACUA	chrM:10402-10737(+)$1	335	128	161	38.4641
UCACUCGCCUCUUCUACUCCAACAUUCAGACUG	chr17:7404265-7404496(+)$1	231	102	135	38.2293
AAAAGUUACAAACUGUUUACAUAUUAAGAGGGU	chr13:50129638-50129857(-)$1	219	119	152	37.5396
CAUUCCAUGAUCUACUUCUUCCACCACUACGAG	chr19:1010752-1010985(-)$1	233	91	124	40.4507
CCAUCUGACCUCUCUCUUUUUUUUCCUUCAGUG	chr15:100252519-100252754(+)$1	235	44	77	34.2305
ACCAAGAAAACAACAAUAAAGAAAAUGAACCUA	chr5:112177077-112177298(+)$1	221	140	173	38.2010
CUGGAAAGCCUUACUAUUAUAAUUCUCAAACAA	chr2:153535808-153536046(-)$1	238	103	136	40.4759
AGAAGGAAGCACCCAACAGUUACAAACUACUUC	chr13:79929255-79929475(-)$1	220	81	114	37.8682
UGUUGAAGAAAUUAUUUAUCCUACUCCCAAAGU	chr11:92881719-92881948(-)$1	229	143	176	37.1830
GGAAGGGAUCCUUGUAAUAUAACCCACACCAUC	chr17:1557129-1557370(-)$1	241	20	53	36.8506
UUACCAAGACACUGGCAUCUAAACGACUUGCUG	chr5:61747584-61747804(+)$1	220	120	153	32.0133
CAGGAACAUAACAAGGAGAAAAACAGACCGGGA	chr9:134454881-134455108(-)$1	227	179	212	36.0171
UUUCCCCAAAUUGGAUGUAAGUGACUUAGGGGA	chr10:1038459-1038696(+)$1	237	124	157	36.3187
CAAAUCUUUCAUCUCAAUUUCUAACUCCUCUUC	chr14:95570287-95570521(-)$1	234	100	133	40.5224
UUAACagagggagaaaaaagagaagaggagaaa	chr12:80189379-80189603(-)$1	224	57	90	40.5089
AAGCUUUUAAAUAUAUUUAGAACUUCUUAAAGU	chr5:132220682-132220911(-)$1	229	21	54	36.3187
CCCAGUGGGUACCCCAACAAUCUUCAAGCCACA	chr10:129903295-129903514(-)$1	219	91	124	35.4098
UCUCCAAAAUCUGAUAUCUCUCCACUCACCCCA	chr5:71494430-71494651(+)$1	221	86	119	40.4759
ucagccccaaauccugccccaccugccccagcc	chr1:171526993-171527228(+)$1	235	21	54	38.3570
CGGGAUAAAUCACAUUCUCAUACCCCCUCCCGU	chr16:2811815-2812065(+)$1	250	118	151	36.2030
UUUAGUGGUCACUCAGCCCUACUUCAACACCAG	chr19:58489683-58489905(-)$1	222	174	207	35.7919
AUAAUCCUUCUAAUAGCUAUCCUCUUCAACAAU	chrM:4606-4870(+)$1	264	65	98	38.8177
UCCCAGUCCCCAGAAAAUGAGAGUAAUGAUAGG	chr11:118343401-118343626(+)$1	225	18	51	35.2543
ACAAAAAAUUUUUACAACUCCACUAACACCAAG	chr1:214791882-214792123(+)$1	241	108	141	40.5089
AUCACAACUUCCUCUCCAUCACCCAUCAAUUCG	chr6:17649313-17649557(-)$1	244	110	143	40.3403
GUCCUACCAAGUACCCCAAAACAAAGAAGGUAU	chr7:104742453-104742686(+)$1	233	159	192	34.9916
GCCUCCUAUUUAUUCUAGCCACCUCUAGCCUAG	chrM:3440-3707(+)$1	267	168	201	37.6584
CAGAAGUUAAGAAAGUUACUUCAUCACCUAUUA	chr17:65908531-65908754(+)$1	223	84	117	37.3560
GUGGUGAAGCUUUUAAUCGAUCCUCAAAUCUUA	chr19:24309427-24309671(+)$1	244	186	219	34.3985

#DB
((..(((..................)))...))	chr11:92532947-92533171(+)$1	1	70	103	33.9067
((((((.....................))).))	chr5:145890093-145890328(+)$1	1	57	90	36.7747
((...............................	chr9:100760787-100761020(+)$1	1	43	76	40.5089
(..((((..........................	chr5:135496579-135496813(+)$1	1	80	113	37.9971
(((.((((..................)))))))	chr4:6863362-6863590(+)$1	1	134	167	32.3432
(((.(((.....................)))))	chr19:53209121-53209356(-)$1	1	92	125	37.0316
)).((((......................))))	chr16:24580005-24580233(+)$1	1	161	194	35.0591
((((((........................)))	chr1:206589159-206589396(+)$1	1	64	97	37.9227
(((((........................))))	chr2:8871796-8872024(-)$1	1	2	35	38.1379
(..........................))))))	chr1:97236241-97236462(+)$1	1	98	131	37.5929
(((((((.......................)))	chr19:44739410-44739641(+)$1	1	100	133	37.3362
))(((((((..................))))))	chr3:194168494-194168716(-)$1	1	166	199	32.1909
(...(((((..................))))).	chr1:78097598-78097830(-)$1	1	114	147	32.3817
.((((((....................))))))	chr3:156262056-156262290(-)$1	1	180	213	33.7298
(((((((...................)))))))	chr2:201438380-201438614(+)$1	1	187	220	33.6047
((((.......................))))).	chr1:165712392-165712623(-)$1	1	40	73	37.1828
((.........................))))).	chr4:77979635-77979860(-)$1	1	125	158	38.1541
((..........................)))))	chrM:3639-3877(+)$1	1	109	142	38.6562
(((((........................))))	chr3:160149425-160149645(+)$1	1	95	128	37.8682
..((.((....................)).)).	chr19:53117366-53117603(-)$1	1	180	213	34.3702
............................)))).	chr17:18220099-18220320(+)$1	1	92	125	38.7658
(............................))))	chr6:57018589-57018813(+)$1	1	84	117	39.2109
((((((((...................))))))	chr1:220197639-220197858(-)$1	1	112	145	33.4743
(((((.(((..................))).))	chr15:65864561-65864794(+)$1	1	14	47	32.9492
(.((((...........................	chr6:27420082-27420316(-)$1	1	91	124	38.4372
(................................	chr19:21476350-21476578(-)$1	1	190	223	40.5224
(.(.(((....................))).).	chr5:159820727-159820949(-)$1	1	157	190	36.9181
((..........................)))).	chr2:61722623-61722844(-)$1	1	98	131	38.6613
((...............................	chr5:71494456-71494686(+)$1	1	60	93	40.4759
...............................).	chr5:5462232-5462454(+)$1	1	97	130	40.3497
.((((((.....................)))))	chr19:37239765-37239987(-)$1	1	22	55	35.7284
..(((((.......................)))	chr1:155450543-155450778(-)$1	1	88	121	37.4081
((..(((.....................)))..	chrM:13661-13963(+)$1	1	64	97	36.7711
(.............................)))	chr15:68378787-68379017(+)$1	1	192	225	40.0519
(((.(((....................)))..)	chr4:110441470-110441694(+)$1	1	165	198	35.5198
.(((((((...................))))))	chr1:40713742-40713970(-)$1	1	159	192	33.8401
(((((((.......................)))	chr11:34118656-34118882(+)$1	1	13	46	34.3985
((...............................	chr12:48468055-48468280(-)$1	1	93	126	40.4759
....(((..........................	chrM:8966-9202(+)$1	1	100	133	38.1283
(((((......................))))).	chr3:31621298-31621538(+)$1	1	110	143	36.7851
(((..((.........................)	chr1:54262329-54262562(-)$1	1	94	127	37.8429
(..........................))).))	chrM:10402-10737(+)$1	1	128	161	38.4641
((..........................)).))	chr17:7404265-7404496(+)$1	1	102	135	38.2293
...........................))))..	chr13:50129638-50129857(-)$1	1	119	152	37.5396
(...............................)	chr19:1010752-1010985(-)$1	1	91	124	40.4507
(((.((((...................))))..	chr15:100252519-100252754(+)$1	1	44	77	34.2305
(...((........................)).	chr5:112177077-112177298(+)$1	1	140	173	38.2010
((...............................	chr2:153535808-153536046(-)$1	1	103	136	40.4759
(((((........................))))	chr13:79929255-79929475(-)$1	1	81	114	37.8682
(.(((......................))))))	chr11:92881719-92881948(-)$1	1	143	176	37.1830
(((.((......................)).))	chr17:1557129-1557370(-)$1	1	20	53	36.8506
(...((((..................))))..)	chr5:61747584-61747804(+)$1	1	120	153	32.0133
(.((.......................))))).	chr9:134454881-134455108(-)$1	1	179	212	36.0171
..(((((.....................)))))	chr10:1038459-1038696(+)$1	1	124	157	36.3187
(................................	chr14:95570287-95570521(-)$1	1	100	133	40.5224
((...............................	chr12:80189379-80189603(-)$1	1	57	90	40.5089
..(((((.....................)))))	chr5:132220682-132220911(-)$1	1	21	54	36.3187
(...((((....................)))).	chr10:129903295-129903514(-)$1	1	91	124	35.4098
((...............................	chr5:71494430-71494651(+)$1	1	86	119	40.4759
(..((.........................)).	chr1:171526993-171527228(+)$1	1	21	54	38.3570
(((((......................))))))	chr16:2811815-2812065(+)$1	1	118	151	36.2030
(((.(((....................))).))	chr19:58489683-58489905(-)$1	1	174	207	35.7919
((..(((..........................	chrM:4606-4870(+)$1	1	65	98	38.8177
(((..(((...................))).))	chr11:118343401-118343626(+)$1	1	18	51	35.2543
((...............................	chr1:214791882-214792123(+)$1	1	108	141	40.5089
((..............................)	chr6:17649313-17649557(-)$1	1	110	143	40.3403
(((.((((....................)))).	chr7:104742453-104742686(+)$1	1	159	192	34.9916
((.........................))))))	chrM:3440-3707(+)$1	1	168	201	37.6584
(((((((.........................)	chr17:65908531-65908754(+)$1	1	84	117	37.3560
(((((((.......................)))	chr19:24309427-24309671(+)$1	1	186	219	34.3985

#PSSM
e : 0.20	f : 0.17	d : 0.15	c : 0.14	! : 0.07	b : 0.05	g : 0.04	^ : 0.04	i : 0.02	h : 0.02	= : 0.01	: : 0.01	[ : 0.01	$ : 0.01	
f : 0.20	e : 0.15	^ : 0.14	! : 0.08	c : 0.07	g : 0.05	" : 0.05	[ : 0.05	b : 0.04	d : 0.04	i : 0.02	h : 0.02	= : 0.01	$ : 0.01	
^ : 0.32	e : 0.12	f : 0.10	! : 0.07	c : 0.07	g : 0.07	" : 0.05	d : 0.04	i : 0.02	b : 0.02	h : 0.02	: : 0.01	a : 0.01	$ : 0.01	
^ : 0.32	[ : 0.11	f : 0.10	e : 0.08	! : 0.07	g : 0.05	" : 0.05	d : 0.04	b : 0.04	c : 0.02	i : 0.02	h : 0.02	$ : 0.01	
^ : 0.35	c : 0.14	d : 0.11	f : 0.10	e : 0.08	g : 0.05	b : 0.04	i : 0.02	h : 0.02	! : 0.02	[ : 0.01	
^ : 0.45	c : 0.14	d : 0.11	g : 0.05	e : 0.05	b : 0.05	f : 0.04	i : 0.02	h : 0.02	[ : 0.01	
^ : 0.52	c : 0.14	d : 0.10	g : 0.05	e : 0.05	f : 0.04	b : 0.02	h : 0.02	i : 0.01	
^ : 0.84	d : 0.07	g : 0.02	c : 0.02	e : 0.01	i : 0.01	
^ : 0.95	g : 0.01	e : 0.01	c : 0.01	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.98	c : 0.01	
^ : 0.94	d : 0.02	c : 0.01	g : 0.01	
^ : 0.61	c : 0.12	d : 0.07	e : 0.05	g : 0.04	f : 0.04	b : 0.02	i : 0.01	
^ : 0.44	c : 0.14	d : 0.12	e : 0.08	f : 0.07	b : 0.05	g : 0.04	3 : 0.01	i : 0.01	
^ : 0.37	c : 0.15	d : 0.15	e : 0.10	f : 0.10	g : 0.04	b : 0.02	3 : 0.01	] : 0.01	i : 0.01	
^ : 0.25	d : 0.12	e : 0.12	] : 0.11	f : 0.11	g : 0.07	c : 0.04	b : 0.04	i : 0.02	2 : 0.02	h : 0.02	3 : 0.01	
^ : 0.24	e : 0.18	f : 0.14	d : 0.11	g : 0.07	2 : 0.05	c : 0.04	b : 0.04	i : 0.02	a : 0.02	h : 0.02	3 : 0.01	
^ : 0.18	f : 0.17	e : 0.14	] : 0.11	g : 0.07	d : 0.07	2 : 0.05	3 : 0.04	c : 0.02	i : 0.02	h : 0.02	b : 0.02	5 : 0.01	: : 0.01	

#score	2596.222929282967
#seq	70
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_UTR_m2_run1.txt

#BEAR
ddeeeeea[cccooooooccc]a]eeeeefff	chr1:232534417-232534657(-)$1	240	50	82	10.0315
:ccc!!dddd[cccmmmmccc]dddd]cccff	chr19:50551661-50551901(+)$1	240	65	97	11.5434
===========cccmmmmccc]==========	chr12:14651028-14651268(+)$1	240	85	117	15.8216
eeeee[gggggggooooooggggggg333eee	chr20:58513213-58513453(-)$1	240	138	170	10.4181
d$$$$$gggggggooooooggggggg333ddd	chr15:64673508-64673748(-)$1	240	76	108	9.7211
e[ccc"""ffffffmmmmffffff]ccceeee	chr17:34894379-34894619(+)$1	240	151	183	10.3780
gg!!ccc[ccc[ccclllccc]ccccccgggg	chrX:12842191-12842431(+)$1	240	183	215	12.5039
ggg!!bb!!eeeeemmmmeeeee]bb]ggggg	chr11:63677329-63677569(+)$1	240	39	71	11.4408
ccc[ccc[ccc[bbmmmmbbccc22ccc]ccc	chr1:16722681-16722924(+)$1	243	210	242	12.1746
$ccc[cccccccccmmmmccc22ccc]ccccc	chr17:61770929-61771169(+)$1	240	105	137	13.0424
ggggggccca[cccmmmmccc]a]ccc22ggg	chr10:60155281-60155521(+)$1	240	16	48	14.2698
cc[ffffff!!cccmmmmcccffffff4444c	chr1:43849772-43850012(-)$1	240	169	201	11.6752
ccc!!cccddddbbmmmmbb333dddd]ccc3	chr11:67163343-67163583(+)$1	240	35	67	11.7711
"iiiiiiiii!!bbmmmmbb22iiiiiiiii]	chr16:67778120-67778360(-)$1	240	144	176	13.3570
:eeeeeccc"""bbmmmmbb333ccc]eeeee	chr1:28608574-28608869(+)$1	295	81	113	10.7190
gg[bb####eeeeellleeeee333bb333gg	chr20:60756358-60756638(+)$1	280	188	220	10.5432
eeedddd####cccmmmmccc333dddd22ee	chr8:105509553-105509892(-)$1	339	16	48	13.0603
$ccc[ccc[a[ddddmmmmddddaccc]cccd	chr7:129126102-129126342(+)$1	240	194	226	10.4651
======####ddddmmmmdddd==========	chr6:93950047-93950287(-)$1	240	60	92	14.3793
[eeeee[bbccc[ammmma]ccc]bbeeeee]	chr15:89741648-89741888(+)$1	240	136	168	10.5279
hhhhhhh####cccmmmmccc4444hhhhhhh	chr10:91179384-91179624(+)$1	240	33	65	12.6558
gggg[bb"""eeeeellleeeee333bb]ggg	chr12:115120956-115121196(-)$1	240	187	219	10.5159
=======####ddddllldddd4444======	chr6:75964149-75964389(-)$1	240	148	180	13.2834
cccdddd[a[cccooooooccca]dddd]ccc	chr11:71146440-71146680(-)$1	240	201	233	11.3062
bb"""ccc"""cccmmmmccc333ccc]bb]g	chr3:188596332-188596572(+)$1	240	130	162	14.3563
=======bb"""bbnnnnnbb333bb]=====	chr22:20761747-20761987(+)$1	240	37	69	11.4304
ccc[dddd"""cccmmmmccc333dddd]ccc	chr12:57396241-57396489(-)$1	248	37	69	13.9880
iiiiiiiii[cccammmma]ccciiiiiiiii	chr3:48506883-48507123(+)$1	240	60	92	14.3367
bb!!ccc"""ddddmmmmdddd4444cccbb]	chr19:47113848-47114133(+)$1	285	110	142	12.1784
=====[dddd!!bbmmmmbb22dddd]=====	chr2:87003340-87003580(+)$1	240	19	51	12.0774
dddd####a[cccnnnnnccc]adddd4444d	chr12:56664100-56664342(+)$1	242	130	162	10.7369
iiiiiiii[ddddoooooodddd]iiiiiiii	chr3:88101994-88102247(-)$1	253	66	98	12.1369
====####eeeeennnnneeeee]========	chr1:15987695-15987975(+)$1	280	206	238	10.9249
ggg!!dddd[cccnnnnnccc]dddd4444gg	chr5:108671516-108671813(-)$1	297	4	36	11.0073
gggggggccc[cccmmmmccc]ccc]gggggg	chr11:32999385-32999625(+)$1	240	100	132	13.7980
dddd[bb####cccmmmmccc333bbdddd22	chr2:159530368-159530608(+)$1	240	70	102	12.3735
====####ffffffmmmmffffff========	chr16:84157286-84157526(-)$1	240	57	89	12.3837
e"""==========mmmm==========4444	chr4:164440798-164441040(+)$1	242	135	167	14.2504
""ccc$$$$$ddddmmmmdddd333ccc]eee	chr11:61567141-61567383(-)$1	242	11	43	12.0924
:iiiiiiiii[ccclllccc]iiiiiiiiiee	chr3:71005628-71005868(-)$1	240	53	85	11.9382
e!!ccc[a!!cccnnnnnccc]a]ccc4444e	chr8:41402032-41402272(+)$1	240	14	46	12.3911
ggggg[bb[ccc[ammmmacccbb]ggggggg	chr9:125670248-125670531(-)$1	283	30	62	12.3552
e####ccc"""cccmmmmccc4444ccc4444	chr12:56635474-56635714(-)$1	240	114	146	14.7715
!ccc[bb[ccccccmmmmccc]ccc]bbccc]	chr5:180670766-180671006(-)$1	240	13	45	12.7082
:===========oooooo===========FFF	chr2:61705670-61705910(-)$1	240	74	106	10.8443
:=============mmmm=============c	chr21:18938745-18939006(+)$1	261	120	152	13.9942
cc"""iiiiiiiiimmmmiiiiiiiii22ccc	chr12:56710961-56711201(-)$1	240	133	165	13.3518
[eeeee"""cccddddllldddd]ccc333ee	chr15:40759188-40759428(+)$1	240	170	202	9.8388
"ggggggg####bbmmmmbb4444ggggggg]	chr8:94936990-94937230(+)$1	240	76	108	13.3915
hhhhhh$$$$$cccmmmmccc4444hhhhhhh	chr18:5290551-5290791(-)$1	240	98	130	11.8527
==============mmmm==============	chr10:116623781-116624021(+)$1	240	77	109	15.0869
c"""iiiiiiiiiooooooiiiiiiiii]ccc	chr16:18803159-18803399(-)$1	240	8	40	12.4962
ggggccca[ddddmmmmdddd]a]ccc]gggg	chr12:110890576-110890816(-)$1	240	150	182	11.4457
cc!!a[dddd[ccclllccc]dddd]a22ccc	chr3:73432387-73432627(-)$1	240	163	195	10.6445
hhhhhhdddd[cccmmmmccc]ddddgggggg	chr9:71396502-71396742(+)$1	240	46	78	11.7221

#otherMatches

#Seq PSSM
UUUUAGACUCUGCUAAAACAGUGCUCUGGCUU	chr1:232534417-232534657(-)$1	240	50	82	10.0315
UGGGAACCUGUUGGCUAACCAUUGGGGCCUUA	chr19:50551661-50551901(+)$1	240	65	97	11.5434
UGGACAGAUGUGUGUAUACACUACAUUUGUUU	chr12:14651028-14651268(+)$1	240	85	117	15.8216
UGAUUUCAUGUAUUUCUCUGUACAUGUUUGAU	chr20:58513213-58513453(-)$1	240	138	170	10.4181
CAAUAUAAACUGUGGCGGGAUAGUUUUCGGGU	chr15:64673508-64673748(-)$1	240	76	108	9.7211
UUGUGCUUUUGGCAACAGUGUUAACCAUAUUU	chr17:34894379-34894619(+)$1	240	151	183	10.3780
UUGACGGAGUGAUGUGUUGCAGUACCUGAAAA	chrX:12842191-12842431(+)$1	240	183	215	12.5039
GCUGCUGAGGCUGGAGGGCCGGCACAAGGCUC	chr11:63677329-63677569(+)$1	240	39	71	11.4408
GACUGGUUCCUCAGAGGCCUAGGCUACCCGUC	chr1:16722681-16722924(+)$1	243	210	242	12.1746
UGAACAUGGCCGGGACUUCCUGAGGCGCAUUU	chr17:61770929-61771169(+)$1	240	105	137	13.0424
UAUAAUUCACAUUGUAUUCAGAGUUGAUGGUU	chr10:60155281-60155521(+)$1	240	16	48	14.2698
CGACUUUGGCCAGGAUUUCCUUCAAAGAAAAC	chr1:43849772-43850012(-)$1	240	169	201	11.6752
ACAGACAGCACUGCCAAAGCCAUGGUGACUGA	chr11:67163343-67163583(+)$1	240	35	67	11.7711
CUACACCAAGAAUGGCCACAGCCUUGGUGUGU	chr16:67778120-67778360(-)$1	240	144	176	13.3570
UGUGCCUCCUCUCUGACCAGUUUGGAGGGCAC	chr1:28608574-28608869(+)$1	295	81	113	10.7190
UUAAGUGCUGUAUUAAUAAUACUUUCUGAAAG	chr20:60756358-60756638(+)$1	280	188	220	10.5432
ACUGACUUUAAACUUGAUGGUACUGGUUAUGG	chr8:105509553-105509892(-)$1	339	16	48	13.0603
AUAUUCAAUGUGAAAAUUAUUUCCUUGUGUAC	chr7:129126102-129126342(+)$1	240	194	226	10.4651
GGUGGUUUAUGCUUGUCAGAGCACUAUUAGUU	chr6:93950047-93950287(-)$1	240	60	92	14.3793
ACUUACUGGGAACCUUAUGAUUCACCGUAAGA	chr15:89741648-89741888(+)$1	240	136	168	10.5279
UGUGAAAUUUUCAGAAUGUUGUUUUUUUCAUG	chr10:91179384-91179624(+)$1	240	33	65	12.6558
GUGGAUGAGCCUCUCCAUGAGAGAUCCGGUCA	chr12:115120956-115121196(-)$1	240	187	219	10.5159
UUAAAAGAAUGUGUGUUUCAUAAUGACUUUUA	chr6:75964149-75964389(-)$1	240	148	180	13.2834
GGGACUGGGAGCGCUACACCGCCGCAGUGCCU	chr11:71146440-71146680(-)$1	240	201	233	11.3062
UACUAUGAAUAUUCCACUGAAGAGUCAAUGAU	chr3:188596332-188596572(+)$1	240	130	162	14.3563
ugcagugagccaugauucacagcacugcacug	chr22:20761747-20761987(+)$1	240	37	69	11.4304
UCUGUUCUGUGUUGUGUUUAAAGAAGAAAAGA	chr12:57396241-57396489(-)$1	248	37	69	13.9880
GUGUGGCUGAGGCCCUGAGUGUCCAGCCACAU	chr3:48506883-48507123(+)$1	240	60	92	14.3367
ACCGGGCAAUAUUGUGUUCAGUUCAAGCUGUG	chr19:47113848-47114133(+)$1	285	110	142	12.1784
AUCACAGAUGCUAUUUCUGUUUUAUUGGUGAU	chr2:87003340-87003580(+)$1	240	19	51	12.0774
CCAGAAAUUGGGUUCUAUGCUGGCUGGAAAUG	chr12:56664100-56664342(+)$1	242	130	162	10.7369
UAUAAGUUGUAUGCAUAAACAUAAGAUUUGUA	chr3:88101994-88102247(-)$1	253	66	98	12.1369
UUUGUCAUCCAAUUUCAUAUUGGUUAAAGACU	chr1:15987695-15987975(+)$1	280	206	238	10.9249
GGGCACAUAAAAGGAAUAUUUAUAUGGCUUCC	chr5:108671516-108671813(-)$1	297	4	36	11.0073
UUUGAGUUAACAGGCCAACUUUUUAUACUUAA	chr11:32999385-32999625(+)$1	240	100	132	13.7980
GGAGCGAGACCGAUUCAAAUCACAUCCUUCCU	chr2:159530368-159530608(+)$1	240	70	102	12.3735
UCUGCUAUGGAAUGAACUUAUUCCUAGAUUUG	chr16:84157286-84157526(-)$1	240	57	89	12.3837
AACUAAGGACAAAAAAUGUUUUGUUUUUCUUG	chr4:164440798-164441040(+)$1	242	135	167	14.2504
AAUGGUAAAAUGAGUGAUCUCAAAUCCACUGA	chr11:61567141-61567383(-)$1	242	11	43	12.0924
UCUAAACUGAGUGGUUGCUGGUUAGUUUGGUA	chr3:71005628-71005868(-)$1	240	53	85	11.9382
AGCCCAAGUUCAUUUAGUAUGUCAUGGUUAAU	chr8:41402032-41402272(+)$1	240	14	46	12.3911
AUGAAAAGUGUUUGAGUUCAGCCUCUUCAUUU	chr9:125670248-125670531(-)$1	283	30	62	12.3552
CAGUUUUCUCUCUAAAUGUAGCAUUGAAUUUG	chr12:56635474-56635714(-)$1	240	114	146	14.7715
CGCCAUCUUGAGCAGAAAUGUAUCAUGGGGCU	chr5:180670766-180671006(-)$1	240	13	45	12.7082
UUUUCUUAUGUGUUUUUUUGUAUAAGAAAUUU	chr2:61705670-61705910(-)$1	240	74	106	10.8443
GGUGAUAUUUUUCUUAUUAGAAAAAUAUUAUA	chr21:18938745-18939006(+)$1	261	120	152	13.9942
CUGUAAGUUCCUAGCUGGCUAGGGAUUGAAGU	chr12:56710961-56711201(-)$1	240	133	165	13.3518
CUGCAGCCACUUGCUCUAGGAGCUAAGGACUU	chr15:40759188-40759428(+)$1	240	170	202	9.8388
CUGAUGCUUAAUAGAAUACUUAGUGGCAUCAA	chr8:94936990-94937230(+)$1	240	76	108	13.3915
AAUGGUGUUCCUCAGUUCUGACCAAACCGUUU	chr18:5290551-5290791(-)$1	240	98	130	11.8527
GUGUGuguauauauguauauauguauauauau	chr10:116623781-116624021(+)$1	240	77	109	15.0869
GAAAUCUUUAGGAAUGAACUUCUGAGGGCCAA	chr16:18803159-18803399(-)$1	240	8	40	12.4962
UGUUUAAAGUGGAAUCUUUUAGUAUUAUAACA	chr12:110890576-110890816(-)$1	240	150	182	11.4457
AAUUCCUGCCUCGUUCAAUGCGGCAAGUUUUU	chr3:73432387-73432627(-)$1	240	163	195	10.6445
CAAAUUAAGUAUAUAAAAGUAAACUUUUAAGA	chr9:71396502-71396742(+)$1	240	46	78	11.7221

#DB
))((((((.(((......))).).)))))(((	chr1:232534417-232534657(-)$1	1	50	82	10.0315
.(((..((((.(((....))).)))).)))((	chr19:50551661-50551901(+)$1	1	65	97	11.5434
((((((((((((((....))).))))))))))	chr12:14651028-14651268(+)$1	1	85	117	15.8216
(((((.(((((((......)))))))...)))	chr20:58513213-58513453(-)$1	1	138	170	10.4181
(.....(((((((......)))))))...)))	chr15:64673508-64673748(-)$1	1	76	108	9.7211
(.(((...((((((....)))))).)))))))	chr17:34894379-34894619(+)$1	1	151	183	10.3780
((..(((.(((.(((...))).))))))))))	chrX:12842191-12842431(+)$1	1	183	215	12.5039
(((..((..(((((....))))).)).)))))	chr11:63677329-63677569(+)$1	1	39	71	11.4408
(((.(((.(((.((....)))))..))).)))	chr1:16722681-16722924(+)$1	1	210	242	12.1746
.(((.(((((((((....)))..))).)))))	chr17:61770929-61771169(+)$1	1	105	137	13.0424
((((((((((.(((....))).).)))..)))	chr10:60155281-60155521(+)$1	1	16	48	14.2698
((.((((((..(((....)))))))))....)	chr1:43849772-43850012(-)$1	1	169	201	11.6752
(((..(((((((((....))...)))).))).	chr11:67163343-67163583(+)$1	1	35	67	11.7711
.(((((((((..((....))..))))))))).	chr16:67778120-67778360(-)$1	1	144	176	13.3570
.((((((((...((....))...))).)))))	chr1:28608574-28608869(+)$1	1	81	113	10.7190
((.((....(((((...)))))...))...))	chr20:60756358-60756638(+)$1	1	188	220	10.5432
(((((((....(((....)))...))))..))	chr8:105509553-105509892(-)$1	1	16	48	13.0603
.(((.(((.(.((((....)))))))).))))	chr7:129126102-129126342(+)$1	1	194	226	10.4651
((((((....((((....))))))))))))))	chr6:93950047-93950287(-)$1	1	60	92	14.3793
.(((((.(((((.(....).))).))))))).	chr15:89741648-89741888(+)$1	1	136	168	10.5279
(((((((....(((....)))....)))))))	chr10:91179384-91179624(+)$1	1	33	65	12.6558
((((.((...(((((...)))))...)).)))	chr12:115120956-115121196(-)$1	1	187	219	10.5159
(((((((....((((...))))....))))))	chr6:75964149-75964389(-)$1	1	148	180	13.2834
(((((((.(.(((......)))).)))).)))	chr11:71146440-71146680(-)$1	1	201	233	11.3062
((...(((...(((....)))...))).)).)	chr3:188596332-188596572(+)$1	1	130	162	14.3563
(((((((((...((.....))...)).)))))	chr22:20761747-20761987(+)$1	1	37	69	11.4304
(((.((((...(((....)))...)))).)))	chr12:57396241-57396489(-)$1	1	37	69	13.9880
(((((((((.((((....).))))))))))))	chr3:48506883-48507123(+)$1	1	60	92	14.3367
((..(((...((((....))))....))))).	chr19:47113848-47114133(+)$1	1	110	142	12.1784
(((((.((((..((....))..)))).)))))	chr2:87003340-87003580(+)$1	1	19	51	12.0774
((((....(.(((.....))).)))))....)	chr12:56664100-56664342(+)$1	1	130	162	10.7369
((((((((.((((......)))).))))))))	chr3:88101994-88102247(-)$1	1	66	98	12.1369
((((....(((((.....))))).))))))))	chr1:15987695-15987975(+)$1	1	206	238	10.9249
(((..((((.(((.....))).))))....))	chr5:108671516-108671813(-)$1	1	4	36	11.0073
((((((((((.(((....))).))).))))))	chr11:32999385-32999625(+)$1	1	100	132	13.7980
((((.((....(((....)))...))))))..	chr2:159530368-159530608(+)$1	1	70	102	12.3735
((((....((((((....))))))))))))))	chr16:84157286-84157526(-)$1	1	57	89	12.3837
(...((((((((((....))))))))))....	chr4:164440798-164441040(+)$1	1	135	167	14.2504
..(((.....((((....))))...))).)))	chr11:61567141-61567383(-)$1	1	11	43	12.0924
.(((((((((.(((...))).)))))))))((	chr3:71005628-71005868(-)$1	1	53	85	11.9382
(..(((.(..(((.....))).).)))....)	chr8:41402032-41402272(+)$1	1	14	46	12.3911
(((((.((.(((.(....)))))).)))))))	chr9:125670248-125670531(-)$1	1	30	62	12.3552
(....(((...(((....)))....)))....	chr12:56635474-56635714(-)$1	1	114	146	14.7715
.(((.((.((((((....))).))).))))).	chr5:180670766-180671006(-)$1	1	13	45	12.7082
.(((((((((((......))))))))))))))	chr2:61705670-61705910(-)$1	1	74	106	10.8443
.(((((((((((((....)))))))))))))(	chr21:18938745-18939006(+)$1	1	120	152	13.9942
((...(((((((((....)))))))))..)))	chr12:56710961-56711201(-)$1	1	133	165	13.3518
.(((((...(((((((...)))).)))...))	chr15:40759188-40759428(+)$1	1	170	202	9.8388
.(((((((....((....))....))))))).	chr8:94936990-94937230(+)$1	1	76	108	13.3915
((((((.....(((....)))....)))))))	chr18:5290551-5290791(-)$1	1	98	130	11.8527
((((((((((((((....))))))))))))))	chr10:116623781-116624021(+)$1	1	77	109	15.0869
(...(((((((((......))))))))).)))	chr16:18803159-18803399(-)$1	1	8	40	12.4962
((((((((.((((....)))).).))).))))	chr12:110890576-110890816(-)$1	1	150	182	11.4457
((..(.((((.(((...))).)))).)..)))	chr3:73432387-73432627(-)$1	1	163	195	10.6445
))))))((((.(((....))).))))((((((	chr9:71396502-71396742(+)$1	1	46	78	11.7221

#PSSM
g : 0.16	= : 0.14	c : 0.14	e : 0.10	: : 0.09	d : 0.07	" : 0.05	h : 0.05	$ : 0.03	[ : 0.03	b : 0.03	i : 0.03	! : 0.01	
c : 0.20	= : 0.18	g : 0.18	e : 0.09	i : 0.07	d : 0.05	h : 0.05	" : 0.05	b : 0.03	$ : 0.01	[ : 0.01	! : 0.01	# : 0.01	
c : 0.18	= : 0.18	g : 0.14	e : 0.10	! : 0.07	i : 0.07	" : 0.07	h : 0.05	[ : 0.03	d : 0.03	$ : 0.01	# : 0.01	
= : 0.18	c : 0.12	! : 0.10	g : 0.10	e : 0.09	i : 0.07	d : 0.07	" : 0.07	h : 0.05	[ : 0.03	$ : 0.01	f : 0.01	b : 0.01	# : 0.01	
= : 0.16	c : 0.12	e : 0.09	[ : 0.09	i : 0.09	! : 0.07	g : 0.07	# : 0.07	d : 0.05	h : 0.05	" : 0.03	$ : 0.01	f : 0.01	b : 0.01	a : 0.01	
c : 0.18	= : 0.14	i : 0.10	e : 0.07	[ : 0.07	b : 0.07	# : 0.07	d : 0.07	g : 0.05	h : 0.05	$ : 0.03	! : 0.01	" : 0.01	f : 0.01	
c : 0.20	d : 0.14	= : 0.12	i : 0.10	b : 0.09	# : 0.09	g : 0.07	" : 0.03	[ : 0.03	$ : 0.03	e : 0.01	f : 0.01	h : 0.01	
# : 0.16	c : 0.14	d : 0.10	i : 0.10	= : 0.09	" : 0.07	[ : 0.07	a : 0.05	g : 0.05	b : 0.05	$ : 0.03	! : 0.01	f : 0.01	
c : 0.12	# : 0.12	d : 0.10	" : 0.10	[ : 0.09	= : 0.09	i : 0.09	f : 0.05	g : 0.03	! : 0.03	b : 0.03	a : 0.03	$ : 0.03	e : 0.01	
c : 0.16	d : 0.12	" : 0.12	# : 0.10	= : 0.09	i : 0.07	[ : 0.07	e : 0.05	g : 0.03	f : 0.03	a : 0.03	! : 0.03	$ : 0.03	
c : 0.23	[ : 0.12	d : 0.10	= : 0.09	" : 0.09	# : 0.09	e : 0.07	! : 0.05	g : 0.03	f : 0.03	i : 0.03	$ : 0.01	
c : 0.47	d : 0.14	e : 0.07	= : 0.07	g : 0.03	f : 0.03	[ : 0.03	! : 0.03	" : 0.03	i : 0.03	# : 0.01	
c : 0.41	d : 0.14	b : 0.12	e : 0.07	= : 0.05	o : 0.03	g : 0.03	f : 0.03	[ : 0.03	i : 0.03	
c : 0.32	o : 0.12	b : 0.12	d : 0.10	n : 0.07	e : 0.05	a : 0.05	= : 0.05	f : 0.03	i : 0.01	m : 0.01	
m : 0.63	o : 0.12	n : 0.09	l : 0.05	d : 0.05	c : 0.01	e : 0.01	
m : 0.65	o : 0.12	l : 0.10	n : 0.09	d : 0.01	
m : 0.65	o : 0.12	l : 0.12	n : 0.09	
m : 0.63	o : 0.12	n : 0.09	l : 0.07	c : 0.03	e : 0.01	d : 0.01	
c : 0.40	b : 0.10	o : 0.09	d : 0.09	e : 0.07	= : 0.07	a : 0.05	f : 0.03	m : 0.01	n : 0.01	i : 0.01	l : 0.01	
c : 0.43	d : 0.14	b : 0.12	e : 0.07	= : 0.07	g : 0.03	f : 0.03	] : 0.03	i : 0.03	
c : 0.45	d : 0.14	e : 0.07	= : 0.07	g : 0.03	f : 0.03	3 : 0.03	2 : 0.03	] : 0.03	i : 0.03	b : 0.01	4 : 0.01	
] : 0.21	d : 0.14	3 : 0.12	c : 0.09	e : 0.07	4 : 0.07	= : 0.07	f : 0.05	2 : 0.05	i : 0.05	g : 0.03	
3 : 0.16	d : 0.14	a : 0.10	= : 0.10	c : 0.10	4 : 0.10	i : 0.07	f : 0.05	e : 0.05	g : 0.03	2 : 0.01	b : 0.01	
] : 0.18	3 : 0.14	d : 0.12	= : 0.10	4 : 0.10	c : 0.09	i : 0.09	f : 0.05	g : 0.03	2 : 0.01	a : 0.01	b : 0.01	
c : 0.20	d : 0.18	= : 0.14	i : 0.10	4 : 0.09	b : 0.07	g : 0.05	3 : 0.05	] : 0.03	e : 0.01	2 : 0.01	f : 0.01	
c : 0.23	d : 0.16	= : 0.14	i : 0.10	b : 0.09	g : 0.07	] : 0.05	h : 0.03	4 : 0.03	e : 0.01	f : 0.01	3 : 0.01	
c : 0.21	= : 0.16	] : 0.10	d : 0.10	i : 0.10	g : 0.07	b : 0.05	e : 0.03	3 : 0.03	h : 0.03	f : 0.01	4 : 0.01	a : 0.01	
= : 0.20	c : 0.14	g : 0.09	i : 0.09	3 : 0.07	4 : 0.07	] : 0.07	d : 0.07	e : 0.05	2 : 0.05	h : 0.03	b : 0.03	
= : 0.18	g : 0.12	c : 0.10	] : 0.10	4 : 0.10	e : 0.07	3 : 0.07	2 : 0.07	i : 0.07	h : 0.03	b : 0.01	d : 0.01	
c : 0.20	= : 0.16	g : 0.16	4 : 0.10	e : 0.09	i : 0.07	d : 0.03	3 : 0.03	h : 0.03	b : 0.03	f : 0.01	2 : 0.01	F : 0.01	
g : 0.20	c : 0.18	= : 0.16	e : 0.14	4 : 0.09	i : 0.05	f : 0.03	h : 0.03	d : 0.01	] : 0.01	b : 0.01	2 : 0.01	F : 0.01	
g : 0.20	c : 0.16	= : 0.14	e : 0.14	] : 0.09	d : 0.05	f : 0.03	h : 0.03	i : 0.03	4 : 0.03	3 : 0.01	2 : 0.01	F : 0.01	

#score	672.5113034537219
#seq	55
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_UTR_m2_run2.txt

#BEAR
============!!cccmmmmccc=============	chr1:35649830-35650080(-)$1	250	119	156	14.2623
a[dddd!!eeeee[cccrrrrrrrrrccc22eeeee]	chr3:184040099-184040323(+)$1	224	160	197	10.6928
eeee####bb"""ddddnnnnndddd22bb22eeeee	chr19:2271805-2272039(+)$1	234	56	93	13.4285
iii####bb####ddddnnnnndddd333bb]iiiii	chr3:156870792-156871022(-)$1	230	152	189	14.0034
bb[ccc[ffffff[cccooooooccc22ffffff22c	chr12:54679635-54679880(+)$1	245	86	123	11.9879
!ggggggg####bb[bboooooobb]bbggggggg22	chr17:80363132-80363361(-)$1	229	11	48	13.1554
!!ggggggg[ccc[cccnnnnnccccccggggggg22	chr17:40925407-40925647(+)$1	240	74	111	15.3530
[eeeee$$$$$ccc[bboooooobb]ccc4444eeee	chr3:12625786-12626028(-)$1	242	2	39	13.2068
fiiiiiiiiiffffffooooooffffff333iiiiii	chr5:33457373-33457596(+)$1	223	163	200	13.1390
gggggg!!ccc!!ddddmmmmdddd]ccc333ggggg	chr19:38873895-38874144(+)$1	249	108	145	13.7491
[a[ddddccc"""bboooooobb333ccc22dddd]a	chr17:5344268-5344497(-)$1	229	64	101	12.2350
ddd!!============nnnnn============22d	chrX:23802422-23802650(+)$1	228	2	39	14.9365
$ddddffffffccc[bboooooobb]ccc22ffffff	chr12:112513437-112513670(-)$1	233	114	151	11.7990
hhhhh[dddd"""ccc[aooooooa]ccc333dddd2	chr16:30775480-30775733(+)$1	253	163	200	13.5032
"dddd[eeeeebb[cccooooooccc]bb]eeeee]d	chr4:83275088-83275348(-)$1	260	32	69	12.3772
!!dddd[ccc[a[bboooooobb]a]ccc333dddd]	chr5:137088338-137088580(-)$1	242	8	45	12.9780
iiiiiiiii[ccc!!cccmmmmccc]ccc]iiiiiii	chr2:47630363-47630607(+)$1	244	202	239	13.6218
eee[ccc!!ccc!!bboooooobb22ccc22ccc]ee	chr19:10250257-10250481(-)$1	224	177	214	14.4672
a[ccc!!ccc[ccc[cccmmmmccc]ccc]ccc22cc	chr19:12826400-12826631(-)$1	231	11	48	12.4818
ggggg[dddd####cccnnnnnccc22ddddgggggg	chr12:67706793-67707051(+)$1	258	152	189	14.8983
ccccceeeeeccc[bboooooobbccc4444eeeee:	chr19:50000449-50000685(+)$1	236	193	230	11.8738
!!cccccc[bb"""cccnnnnnccc333bb]ccc]cc	chr10:124190327-124190555(+)$1	228	89	126	15.6104
eee"""eeeeea!!cccooooooccc22a]eeeeeee	chr19:1816412-1816645(-)$1	233	123	160	13.9232
!ggggggg[bb"""cccnnnnnccc22bbggggggg2	chr17:48829451-48829709(+)$1	258	92	129	15.3718
fff:===========[ccclllccc]===========	chr12:105536887-105537119(+)$1	232	117	154	12.4426
ccc[eeeee[bb!!cccnnnnnccc]bbeeeee]ccc	chr10:58118049-58118292(-)$1	243	104	141	13.4622
[eeeee"""ccc!!cccnnnnnccc22ccc22eeeee	chr3:131221645-131221874(-)$1	229	2	39	16.0001
cc"""ccc####eeeeemmmmeeeeeccc333ccc22	chr17:73773731-73773959(-)$1	228	148	185	11.1663
d!!dddd"""gggggggnnnnngggggggdddddddd	chr1:220445604-220445828(-)$1	224	49	86	11.7184
iiiiiiiii!!aa[cccnnnnnccc]a]a22iiiiii	chr1:10511792-10512018(+)$1	226	88	125	16.7905
)ccc!!ccc[ccc[bbnnnnnbb]cccccc22ccchh	chr17:80386388-80386615(+)$1	227	55	92	12.0417
[ccc####ccc!!ddddnnnnndddd]ccccccdddd	chr1:113454941-113455171(-)$1	230	100	137	14.0482
!!ccc[dddd####bboooooobb22dddd]ccc22a	chr7:44608629-44608855(-)$1	226	67	104	13.0104
hhhh[ddddccc!!cccmmmmccc22ccc333dddd4	chr15:89169297-89169531(+)$1	234	113	150	12.4872
dddccc[a[dddd[cccnnnnnccc]dddd]a]ccc]	chr22:38879599-38879828(-)$1	229	81	118	13.6180
GGggggggg####cccooooooccc333ggggggg::	chr5:68473421-68473652(+)$1	231	36	73	12.5807
dddd[ggggggg!!cccnnnnnccc22ggggggg22d	chr3:156874689-156874922(-)$1	233	52	89	15.0459
ffffff!!ccc"""cccmmmmccc333ccc]ffffff	chr2:61711072-61711310(-)$1	238	85	122	12.8008
gggggg!!dddd[ddddnnnnndddddddd333gggg	chr12:57905365-57905619(+)$1	254	96	133	13.5498
ffff[ccc"""ffffffnnnnnffffff22cccffff	chr2:37430442-37430667(+)$1	225	66	103	11.4666
eee"""ffffff[ddddnnnnndddd]ffffff4444	chr9:95032074-95032313(-)$1	239	61	98	11.9913
ccc!!dddd"""eeeeeooooooeeeee333dddd]c	chr7:135611490-135611722(-)$1	232	138	175	12.2923
gggg####ffffffrrrrrrrrrffffff333ggggg	chr1:154179615-154179849(-)$1	234	69	106	10.7184
gccc"""a[ccc!!cccnnnnnccc]ccc]accc]gg	chr15:89803908-89804138(+)$1	230	60	97	16.6172
:iiiiiiiii[a!!ddddmmmmdddd22a22iiiiii	chr22:29191097-29191324(-)$1	227	81	118	11.7325
dddd"""ccceeeeebboooooobb]eeeee333ccc	chr1:180082180-180082409(+)$1	229	107	144	11.9804
ffffff[cccccc[cccnnnnnccc]ccc4444ccc]	chr19:10370436-10370663(+)$1	227	120	157	15.4123
b[==========####ammmma333==========22	chr22:39131879-39132111(-)$1	232	163	200	13.1749
e[eeeeeggggggg[bbnnnnnbbggggggg333eee	chr3:195776360-195776595(-)$1	235	170	207	13.2726
b[eeeeeccc[bb[bboooooobb]bb]ccc333eee	chr20:34330029-34330261(-)$1	232	128	165	12.0273
ggggddddccc"""cccnnnnnccc333ccc4444dd	chr1:91990856-91991081(+)$1	225	163	200	15.6889
ee]bb:ggggggg[cccooooooccc333ggggggg:	chr11:62283971-62284202(-)$1	231	150	187	12.0206
eee!!iiiiiiiii[bboooooobb]iiiiiiiii]e	chr19:54382494-54382712(-)$1	218	86	123	14.1966
dddd[ggggggg[ddddnnnnnddddggggggg22dd	chr14:20926027-20926257(-)$1	230	136	173	12.7508
fffff"""ccc####bbnnnnnbb22ccc22ffffff	chr20:36685896-36686133(+)$1	237	182	219	14.1909
=======####bb[ddddllldddd]bb333======	chr19:10796097-10796374(+)$1	277	191	228	13.2868
eeeee[eeeee!!ddddnnnnndddd22eeeee]eee	chrX:150157052-150157294(+)$1	242	152	189	12.2825
"eeeee####bb[ddddoooooodddd]bb4444eee	chr9:91093476-91093704(+)$1	228	67	104	12.5389

#otherMatches

#Seq PSSM
UAUGGAUGUUAGCAGUUUAUUGACCUAAUAUUUGUAA	chr1:35649830-35650080(-)$1	250	119	156	14.2623
GGGGAGAGGGCCAAGUUGAGGUAUGGAGCAGUGGUCA	chr3:184040099-184040323(+)$1	224	160	197	10.6928
GCCAAACGCAUUAACUGGCGAACAGUGCUGAGUGGCG	chr19:2271805-2272039(+)$1	234	56	93	13.4285
GCUAAAGGAGUUGGGAUUUUGUGUUCAUGUCAAGCAU	chr3:156870792-156871022(-)$1	230	152	189	14.0034
GAGUUUGCAAUAGCAGGUGGAACCCUAACUAUUGAGG	chr12:54679635-54679880(+)$1	245	86	123	11.9879
AUUUUCAGGGACUUGAGGAAUGGCUGAACUGAAAGGA	chr17:80363132-80363361(-)$1	229	11	48	13.1554
UGGGCUACUACGAUGGCGAUGAGUUUCGAGUGGCCGU	chr17:40925407-40925647(+)$1	240	74	111	15.3530
UGCCUGUCUUCUAGUUGACUUUGCACCUGUCUUCAGG	chr3:12625786-12626028(-)$1	242	2	39	13.2068
ACUGAGUUUUCUUCAACUUCAUUUGAAGUUUGAAAUU	chr5:33457373-33457596(+)$1	223	163	200	13.1390
GCCCGGCAGCUGGAGAUGAUCGUCUGAGCCCCCCGGG	chr19:38873895-38874144(+)$1	249	108	145	13.7491
UGUGAUAGUAGGCCAUGCAUCUGAGAUACGAUAUUCC	chr17:5344268-5344497(-)$1	229	64	101	12.2350
CUUCGCCAUGUACAUGGCCCUUCCGUGUACAUGGAUG	chrX:23802422-23802650(+)$1	228	2	39	14.9365
AUGCAUGGCUAUGUACAAGAAGCUGAGCAGGUGGCCA	chr12:112513437-112513670(-)$1	233	114	151	11.7990
UAGAGGCCUCAGACCGCCUACAGCGCCGGGUGGAGGA	chr16:30775480-30775733(+)$1	253	163	200	13.5032
UGUCUCCAGGUGGUGAAGCAGUAUUUUCCAAUUUGAA	chr4:83275088-83275348(-)$1	260	32	69	12.3772
UUGGACCUUGGUCGUUUUUAUACUAGCAAAAUGUCUU	chr5:137088338-137088580(-)$1	242	8	45	12.9780
GGGGAGGGACCCGGGGCCUUGUGGCGCGGCUCCUUUC	chr2:47630363-47630607(+)$1	244	202	239	13.6218
CCCGGCCAGCAGCCAGCCAUCCCUUACUGAAGGCAGG	chr19:10250257-10250481(-)$1	224	177	214	14.4672
GUGGGAGGGGGAGGUGCUAGGCAGCCCCUGCCCAGCC	chr19:12826400-12826631(-)$1	231	11	48	12.4818
AAUUUUGUGACCAUGAAUUUCUUUCUUUUAUAAAUUU	chr12:67706793-67707051(+)$1	258	152	189	14.8983
GAGUUGCCCUGCCUGCAUCUAAGUGGCUUCUGGGGCU	chr19:50000449-50000685(+)$1	236	193	230	11.8738
UAAACAUUGUGAUAAAAUUAAUUUUCAGUAGAAUAGU	chr10:124190327-124190555(+)$1	228	89	126	15.6104
CUGCGUGACGUCCAGGCCGUUCUGCUGAGCAUGUUCA	chr19:1816412-1816645(-)$1	233	123	160	13.9232
CAAAUUUUGCGUUGUAGGACUACUGUUCGAAGAUUUU	chr17:48829451-48829709(+)$1	258	92	129	15.3718
UGGAAAUUUUAAAUGAGGUAACAUCAUAUUUGAGAUU	chr12:105536887-105537119(+)$1	232	117	154	12.4426
UUUGCCAUGACUUCCUGGAGGACAGCAGCAUGGAGAA	chr10:58118049-58118292(-)$1	243	104	141	13.4622
UGCCCGGAGUUCAUUGUAAAACGCACCGGAAGUGGGU	chr3:131221645-131221874(-)$1	229	2	39	16.0001
GUUGAGUUUUUCUCCUCUGCUGAGGAAACAGUACCGA	chr17:73773731-73773959(-)$1	228	148	185	11.1663
CUUGGCUAGAGCUAUUGGGGCUCGGUGGCGGCCGCAG	chr1:220445604-220445828(-)$1	224	49	86	11.7184
GGGCUUUUCUUCUGAUGUUCAUUAUGGUGCUGGGAAG	chr1:10511792-10512018(+)$1	226	88	125	16.7905
AUCAAAGAGAUCUUGCAUCUGGCUGGACUCAAUGAGC	chr17:80386388-80386615(+)$1	227	55	92	12.0417
AUUUAAAAUACCACUGUAAUUGACAGAGUAAAAGUAU	chr1:113454941-113455171(-)$1	230	100	137	14.0482
AUUCUGCUCCCCUACCAGUUCCGGAUGGAGGAGAUCG	chr7:44608629-44608855(-)$1	226	67	104	13.0104
UCCCUUGCCCCAAGCAGUGAGCUGACUGGAAUGGUAC	chr15:89169297-89169531(+)$1	234	113	150	12.4872
GGAAAGGGUUCCAAUGUAUUAAGCAAUGGGCUGCUUC	chr22:38879599-38879828(-)$1	229	81	118	13.6180
ACUUGUAAACUUGAGUUGGAGUACUAUAUUUACAAAU	chr5:68473421-68473652(+)$1	231	36	73	12.5807
ACCAGCUACAUUUACCAAAGCCUGGGUGAUGUGGAGU	chr3:156874689-156874922(-)$1	233	52	89	15.0459
CCUGAACAUAGAACGAACUUUUUCUUACUACUUCAGG	chr2:61711072-61711310(-)$1	238	85	122	12.8008
UCUUUCUCCGUUAUCUCAGCUGGAGAAGCGACUGGAG	chr12:57905365-57905619(+)$1	254	96	133	13.5498
UAGUUCAGGGGUCUUUAGAUUGUAAAGAAAUUGACUG	chr2:37430442-37430667(+)$1	225	66	103	11.4666
CUAAUUUACAAAGCAGUGCCCAGCUGGUUUGUGCGAG	chr9:95032074-95032313(-)$1	239	61	98	11.9913
CAUCCGAAUGCUAAAUAAUACUGUGUUUUAAGUUUUG	chr7:135611490-135611722(-)$1	232	138	175	12.2923
UGUGUCUAAAGGGUAAUUCCCCAACCCUUCCUUAUGA	chr1:154179615-154179849(-)$1	234	69	106	10.7184
AACACUUAGGAGACGUAAGAUAUACACUUGUUGUAUC	chr15:89803908-89804138(+)$1	230	60	97	16.6172
AUGUCCUCUCUGCUUGGUGUAAACCAUUCUUGGGAGG	chr22:29191097-29191324(-)$1	227	81	118	11.7325
GUUAUUUGGAAGACAGAAAAACAUCUUGUCUACAUCC	chr1:180082180-180082409(+)$1	229	107	144	11.9804
CCUUCGAGGAAGGUGUCACCUGGACCCCUUCAUUCCA	chr19:10370436-10370663(+)$1	227	120	157	15.4123
GGCUGGUGCCUGGGAGCUGAUGAAGCAGGUGCCAGGG	chr22:39131879-39132111(-)$1	232	163	200	13.1749
AAAUAUCAGACUAGUGACAAGCUCCUGGUCUUGAGAU	chr3:195776360-195776595(-)$1	235	170	207	13.2726
GGAGCUUGUCGACGCUGUCGCAGGGGUGGAUCCUGAG	chr20:34330029-34330261(-)$1	232	128	165	12.0273
GUUUAUAUUCAGAAAUGGUAUAUAUCAAUGACAGCAU	chr1:91990856-91991081(+)$1	225	163	200	15.6889
GGCUCCUGGAACUAUACAGAUAGGUAAAGAGUUCCAA	chr11:62283971-62284202(-)$1	231	150	187	12.0206
GGACUUUUCAGGGGUUCGGGGCGGGUUUCCUGGGAUU	chr19:54382494-54382712(-)$1	218	86	123	14.1966
ACCCCCCCAGUUGCAGUAUUUAACUGGGCUGGGUAGG	chr14:20926027-20926257(-)$1	230	136	173	12.7508
UGGCUUAAAGUGACCUCUAGUUGAAGACUAUGGCCAC	chr20:36685896-36686133(+)$1	237	182	219	14.1909
UUUAAAACUUUGAUUGCAUGAUGUAUUUUUUUUUUAG	chr19:10796097-10796374(+)$1	277	191	228	13.2868
GUUUUUGAAGUUAAAUAAACAGUAUUACAUUUUUAAA	chrX:150157052-150157294(+)$1	242	152	189	12.2825
UUUUUAUAAUUAUGAUGUAACUCUAUCUUAUCCUUAA	chr9:91093476-91093704(+)$1	228	67	104	12.5389

#DB
((((((((((((..(((....))))))))))))))))	chr1:35649830-35650080(-)$1	1	119	156	14.2623
(.((((..(((((.(((.........)))..))))).	chr3:184040099-184040323(+)$1	1	160	197	10.6928
((((....((...((((.....))))..))..)))))	chr19:2271805-2272039(+)$1	1	56	93	13.4285
(((....((....((((.....))))...)).)))))	chr3:156870792-156871022(-)$1	1	152	189	14.0034
((.(((.((((((.(((......)))..))))))..)	chr12:54679635-54679880(+)$1	1	86	123	11.9879
.(((((((....((.((......)).)))))))))..	chr17:80363132-80363361(-)$1	1	11	48	13.1554
..(((((((.(((.(((.....)))))))))))))..	chr17:40925407-40925647(+)$1	1	74	111	15.3530
.(((((.....(((.((......)).)))....))))	chr3:12625786-12626028(-)$1	1	2	39	13.2068
)(((((((((((((((......))))))...))))))	chr5:33457373-33457596(+)$1	1	163	200	13.1390
((((((..(((..((((....)))).)))...)))))	chr19:38873895-38874144(+)$1	1	108	145	13.7491
.(.(((((((...((......))...)))..)))).)	chr17:5344268-5344497(-)$1	1	64	101	12.2350
(((..((((((((((((.....))))))))))))..)	chrX:23802422-23802650(+)$1	1	2	39	14.9365
.(((((((((((((.((......)).)))..))))))	chr12:112513437-112513670(-)$1	1	114	151	11.7990
(((((.((((...(((.(......).)))...)))).	chr16:30775480-30775733(+)$1	1	163	200	13.5032
.((((.(((((((.(((......))).)).))))).)	chr4:83275088-83275348(-)$1	1	32	69	12.3772
..((((.(((.(.((......)).).)))...)))).	chr5:137088338-137088580(-)$1	1	8	45	12.9780
(((((((((.(((..(((....))).))).)))))))	chr2:47630363-47630607(+)$1	1	202	239	13.6218
(((.(((..(((..((......))..)))..))).))	chr19:10250257-10250481(-)$1	1	177	214	14.4672
(.(((..(((.(((.(((....))).))).)))..))	chr19:12826400-12826631(-)$1	1	11	48	12.4818
(((((.((((....(((.....)))..))))))))))	chr12:67706793-67707051(+)$1	1	152	189	14.8983
)))))((((((((.((......)))))....))))).	chr19:50000449-50000685(+)$1	1	193	230	11.8738
..((((((.((...(((.....)))...)).))).))	chr10:124190327-124190555(+)$1	1	89	126	15.6104
(((...((((((..(((......)))..).)))))))	chr19:1816412-1816645(-)$1	1	123	160	13.9232
.(((((((.((...(((.....)))..))))))))).	chr17:48829451-48829709(+)$1	1	92	129	15.3718
))).(((((((((((.(((...))).)))))))))))	chr12:105536887-105537119(+)$1	1	117	154	12.4426
(((.(((((.((..(((.....))).))))))).)))	chr10:58118049-58118292(-)$1	1	104	141	13.4622
.(((((...(((..(((.....)))..)))..)))))	chr3:131221645-131221874(-)$1	1	2	39	16.0001
((...(((....(((((....))))))))...)))..	chr17:73773731-73773959(-)$1	1	148	185	11.1663
(..((((...(((((((.....)))))))))))))))	chr1:220445604-220445828(-)$1	1	49	86	11.7184
(((((((((..((.(((.....))).).)..))))))	chr1:10511792-10512018(+)$1	1	88	125	16.7905
.(((..(((.(((.((.....)).))))))..)))))	chr17:80386388-80386615(+)$1	1	55	92	12.0417
.(((....(((..((((.....)))).))))))))))	chr1:113454941-113455171(-)$1	1	100	137	14.0482
..(((.((((....((......))..)))).)))..)	chr7:44608629-44608855(-)$1	1	67	104	13.0104
((((.(((((((..(((....)))..)))...)))).	chr15:89169297-89169531(+)$1	1	113	150	12.4872
((((((.(.((((.(((.....))).)))).).))).	chr22:38879599-38879828(-)$1	1	81	118	13.6180
(((((((((....(((......)))...)))))))..	chr5:68473421-68473652(+)$1	1	36	73	12.5807
((((.(((((((..(((.....)))..)))))))..)	chr3:156874689-156874922(-)$1	1	52	89	15.0459
((((((..(((...(((....)))...))).))))))	chr2:61711072-61711310(-)$1	1	85	122	12.8008
((((((..((((.((((.....))))))))...))))	chr12:57905365-57905619(+)$1	1	96	133	13.5498
((((.(((...((((((.....))))))..)))))))	chr2:37430442-37430667(+)$1	1	66	103	11.4666
(((...((((((.((((.....)))).))))))....	chr9:95032074-95032313(-)$1	1	61	98	11.9913
(((..((((...(((((......)))))...)))).)	chr7:135611490-135611722(-)$1	1	138	175	12.2923
((((....((((((.........))))))...)))))	chr1:154179615-154179849(-)$1	1	69	106	10.7184
((((...(.(((..(((.....))).))).)))).))	chr15:89803908-89804138(+)$1	1	60	97	16.6172
.(((((((((.(..((((....))))..)..))))))	chr22:29191097-29191324(-)$1	1	81	118	11.7325
((((...((((((((((......)).)))))...)))	chr1:180082180-180082409(+)$1	1	107	144	11.9804
((((((.((((((.(((.....))).)))....))).	chr19:10370436-10370663(+)$1	1	120	157	15.4123
(.((((((((((....(....)...))))))))))..	chr22:39131879-39132111(-)$1	1	163	200	13.1749
(.((((((((((((.((.....)))))))))...)))	chr3:195776360-195776595(-)$1	1	170	207	13.2726
(.((((((((.((.((......)).)).)))...)))	chr20:34330029-34330261(-)$1	1	128	165	12.0273
(((((((((((...(((.....)))...)))....))	chr1:91990856-91991081(+)$1	1	163	200	15.6889
)).)).(((((((.(((......)))...))))))).	chr11:62283971-62284202(-)$1	1	150	187	12.0206
(((..(((((((((.((......)).))))))))).)	chr19:54382494-54382712(-)$1	1	86	123	14.1966
((((.(((((((.((((.....)))))))))))..))	chr14:20926027-20926257(-)$1	1	136	173	12.7508
(((((...(((....((.....))..)))..))))))	chr20:36685896-36686133(+)$1	1	182	219	14.1909
(((((((....((.((((...)))).))...))))))	chr19:10796097-10796374(+)$1	1	191	228	13.2868
(((((.(((((..((((.....))))..))))).)))	chrX:150157052-150157294(+)$1	1	152	189	12.2825
.(((((....((.((((......)))).))....)))	chr9:91093476-91093704(+)$1	1	67	104	12.5389

#PSSM
e : 0.13	! : 0.10	f : 0.10	g : 0.10	d : 0.10	[ : 0.06	c : 0.06	i : 0.05	b : 0.05	= : 0.03	a : 0.03	h : 0.03	" : 0.03	$ : 0.01	) : 0.01	G : 0.01	: : 0.01	
e : 0.17	g : 0.12	d : 0.12	c : 0.12	[ : 0.08	i : 0.08	! : 0.08	f : 0.08	= : 0.03	h : 0.03	b : 0.01	a : 0.01	G : 0.01	
e : 0.18	d : 0.15	g : 0.15	c : 0.15	i : 0.08	f : 0.08	= : 0.05	[ : 0.03	h : 0.03	" : 0.01	! : 0.01	] : 0.01	
d : 0.15	c : 0.15	g : 0.15	e : 0.12	i : 0.06	f : 0.06	= : 0.05	! : 0.05	" : 0.05	h : 0.03	[ : 0.03	# : 0.01	: : 0.01	b : 0.01	
d : 0.12	c : 0.12	g : 0.12	e : 0.12	" : 0.08	= : 0.06	# : 0.06	i : 0.06	! : 0.06	[ : 0.06	f : 0.05	h : 0.01	b : 0.01	
g : 0.13	d : 0.12	e : 0.12	c : 0.10	= : 0.08	i : 0.08	[ : 0.08	" : 0.08	# : 0.06	f : 0.05	! : 0.03	: : 0.01	
d : 0.13	g : 0.12	e : 0.12	= : 0.08	! : 0.08	# : 0.08	i : 0.08	c : 0.08	[ : 0.06	" : 0.06	f : 0.03	$ : 0.01	
c : 0.17	g : 0.13	d : 0.10	! : 0.08	# : 0.08	i : 0.08	e : 0.08	= : 0.06	f : 0.05	" : 0.05	a : 0.03	b : 0.01	$ : 0.01	
c : 0.20	e : 0.10	g : 0.10	d : 0.10	i : 0.08	= : 0.06	f : 0.06	# : 0.06	[ : 0.06	" : 0.05	b : 0.03	$ : 0.01	! : 0.01	
c : 0.25	# : 0.10	e : 0.08	d : 0.08	= : 0.06	f : 0.06	[ : 0.06	g : 0.06	b : 0.05	i : 0.05	" : 0.05	$ : 0.01	! : 0.01	
c : 0.24	# : 0.12	e : 0.08	" : 0.08	f : 0.08	g : 0.08	= : 0.06	[ : 0.06	b : 0.06	d : 0.03	$ : 0.01	! : 0.01	i : 0.01	
c : 0.20	" : 0.13	# : 0.12	f : 0.08	b : 0.08	g : 0.08	= : 0.06	a : 0.06	! : 0.05	e : 0.03	d : 0.03	i : 0.01	
! : 0.20	c : 0.13	" : 0.12	# : 0.10	[ : 0.08	e : 0.06	f : 0.06	b : 0.06	g : 0.05	= : 0.03	a : 0.01	d : 0.01	i : 0.01	
[ : 0.20	! : 0.17	d : 0.15	c : 0.08	# : 0.06	" : 0.06	b : 0.05	f : 0.05	e : 0.05	= : 0.03	g : 0.03	i : 0.01	
c : 0.37	d : 0.18	b : 0.12	[ : 0.10	e : 0.05	f : 0.03	= : 0.03	# : 0.03	! : 0.01	g : 0.01	r : 0.01	
c : 0.41	b : 0.20	d : 0.18	f : 0.03	o : 0.03	e : 0.03	= : 0.01	[ : 0.01	g : 0.01	r : 0.01	# : 0.01	
c : 0.39	d : 0.18	o : 0.13	b : 0.12	e : 0.03	= : 0.01	[ : 0.01	g : 0.01	n : 0.01	f : 0.01	r : 0.01	a : 0.01	
n : 0.43	o : 0.32	m : 0.10	c : 0.05	r : 0.03	d : 0.03	a : 0.01	
n : 0.43	o : 0.34	m : 0.15	r : 0.03	c : 0.01	l : 0.01	
n : 0.43	o : 0.34	m : 0.15	r : 0.03	l : 0.03	
n : 0.43	o : 0.34	m : 0.15	r : 0.03	l : 0.03	
n : 0.41	o : 0.31	c : 0.05	b : 0.05	m : 0.05	r : 0.03	d : 0.03	l : 0.01	e : 0.01	a : 0.01	
c : 0.32	o : 0.20	d : 0.17	b : 0.15	r : 0.03	f : 0.03	= : 0.01	e : 0.01	g : 0.01	3 : 0.01	
c : 0.39	d : 0.18	b : 0.18	f : 0.05	3 : 0.03	] : 0.03	e : 0.03	r : 0.01	= : 0.01	o : 0.01	g : 0.01	
c : 0.37	d : 0.18	b : 0.08	2 : 0.06	f : 0.05	3 : 0.05	= : 0.03	a : 0.03	e : 0.03	g : 0.03	r : 0.01	] : 0.01	
] : 0.29	d : 0.15	2 : 0.13	c : 0.12	3 : 0.08	= : 0.05	f : 0.05	e : 0.03	g : 0.03	r : 0.01	b : 0.01	
c : 0.31	2 : 0.15	3 : 0.10	= : 0.06	b : 0.06	d : 0.06	f : 0.05	] : 0.05	g : 0.05	e : 0.03	a : 0.01	i : 0.01	
c : 0.34	2 : 0.08	3 : 0.08	b : 0.08	= : 0.06	f : 0.06	d : 0.06	g : 0.06	] : 0.05	e : 0.03	4 : 0.01	i : 0.01	
c : 0.36	g : 0.12	b : 0.08	3 : 0.08	= : 0.06	d : 0.06	f : 0.05	a : 0.05	e : 0.05	4 : 0.01	2 : 0.01	i : 0.01	
3 : 0.15	2 : 0.13	g : 0.13	c : 0.10	] : 0.08	d : 0.08	= : 0.06	b : 0.06	4 : 0.05	e : 0.05	f : 0.03	i : 0.01	
2 : 0.17	3 : 0.17	g : 0.13	e : 0.08	c : 0.08	= : 0.06	4 : 0.06	] : 0.06	f : 0.03	i : 0.03	d : 0.03	b : 0.01	a : 0.01	
3 : 0.17	g : 0.13	c : 0.12	e : 0.10	= : 0.08	f : 0.08	i : 0.08	4 : 0.06	2 : 0.05	d : 0.05	] : 0.01	a : 0.01	
g : 0.17	c : 0.15	e : 0.13	i : 0.10	d : 0.10	= : 0.08	f : 0.08	4 : 0.06	3 : 0.06	] : 0.01	
g : 0.17	c : 0.13	e : 0.12	d : 0.12	i : 0.10	= : 0.08	f : 0.08	4 : 0.05	3 : 0.05	2 : 0.03	] : 0.03	
e : 0.18	g : 0.15	d : 0.12	i : 0.10	2 : 0.10	c : 0.10	= : 0.06	f : 0.06	] : 0.05	4 : 0.03	
e : 0.18	2 : 0.13	g : 0.12	d : 0.12	c : 0.10	i : 0.08	] : 0.06	f : 0.06	= : 0.05	h : 0.01	: : 0.01	4 : 0.01	
e : 0.17	d : 0.12	c : 0.10	2 : 0.10	i : 0.08	g : 0.08	] : 0.06	f : 0.06	= : 0.05	: : 0.05	a : 0.03	4 : 0.03	h : 0.01	

#score	771.4628757172827
#seq	58
#width	37
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_UTR_m2_run1.txt

#BEAR
ccc[attttttttttta]ccc	chr18:25531103-25531343(-)$1	240	6	27	22.2178
[cccavvvvvvvvvvvvva]c	chr11:9467689-9467929(+)$1	240	138	159	22.7758
eeeeuuuuuuuuuuuueeeee	chr10:12206782-12207022(+)$1	240	123	144	22.5427
=====wwwwwwwwwwwwww==	chr12:124082283-124082523(+)$1	240	159	180	20.6738
idddduuuuuuuuuuuudddd	chr7:135613228-135613471(-)$1	243	208	229	22.2757
fffwwwwwwwwwwwwwwffff	chr15:23048414-23048655(-)$1	241	12	33	20.4563
:cccwwwwwwwwwwwwwwccc	chr4:75972462-75972702(+)$1	240	59	80	20.1309
ddddvvvvvvvvvvvvvdddd	chr14:58839039-58839279(+)$1	240	159	180	22.9135
gggggvvvvvvvvvvvvvggg	chr5:143538374-143538614(-)$1	240	43	64	22.8696
[ddddtttttttttttdddd6	chr10:94112187-94112427(+)$1	240	150	171	21.5725
eeeeettttttttttteeeee	chr5:82349686-82349926(-)$1	240	33	54	22.6690
ddddvvvvvvvvvvvvvdddd	chr7:148700649-148700890(-)$1	241	194	215	22.9135
!ddddtttttttttttdddd]	chr8:125325831-125326071(-)$1	240	84	105	22.1846
eewwwwwwwwwwwwwweeeee	chr1:228880527-228880767(+)$1	240	54	75	20.5124
ggwwwwwwwwwwwwwwggggg	chr17:65073719-65074016(-)$1	297	163	184	20.2632
gggggtttttttttttggggg	chr8:79514515-79514755(+)$1	240	140	161	22.2301
eeeeuuuuuuuuuuuueeeee	chr6:17609417-17609657(+)$1	240	15	36	22.5427
ddddwwwwwwwwwwwwwwddd	chr10:90973898-90974138(-)$1	240	109	130	21.2658
gggguuuuuuuuuuuuggggg	chr16:18803518-18803758(-)$1	240	18	39	22.1875
gggggtttttttttttggggg	chr12:96672445-96672685(-)$1	240	28	49	22.2301
ddddvvvvvvvvvvvvvdddd	chrX:102006763-102007003(+)$1	240	80	101	22.9135
eeeeevvvvvvvvvvvvveee	chr11:111934327-111934567(+)$1	240	94	115	23.2107
gggguuuuuuuuuuuuggggg	chr4:52780878-52781118(+)$1	240	123	144	22.1875
eeeeettttttttttteeeee	chr7:129805426-129805666(-)$1	240	202	223	22.6690
fffffvvvvvvvvvvvvvfff	chr1:159997850-159998099(-)$1	249	204	225	22.1092
[ddddtttttttttttdddd]	chr15:99506283-99506563(+)$1	280	87	108	22.2350
[cccuuuuuuuuuuuuccc]e	chr14:55511093-55511333(+)$1	240	84	105	22.1884
$dddduuuuuuuuuuuudddd	chr13:107144129-107144369(-)$1	240	124	145	21.9023
ddddvvvvvvvvvvvvvdddd	chr7:44921675-44921915(-)$1	240	122	143	22.9135
[ddddtttttttttttdddd]	chr4:122738597-122738837(-)$1	240	78	99	22.2350
eeeeuuuuuuuuuuuueeeee	chr18:60244444-60244684(+)$1	240	55	76	22.5427
fffffvvvvvvvvvvvvvfff	chr3:150301688-150301928(+)$1	240	129	150	22.1092
eeeeevvvvvvvvvvvvveee	chr6:7610508-7610748(+)$1	240	113	134	23.2107
ggwwwwwwwwwwwwwwggggg	chr15:43619940-43620180(-)$1	240	203	224	20.2632
ffffftttttttttttfffff	chr10:102723538-102723778(+)$1	240	54	75	21.3950
eeeeettttttttttteeeee	chr17:56081654-56081894(-)$1	240	89	110	22.6690
:cccvvvvvvvvvvvvvccc:	chr5:107006308-107006611(-)$1	303	13	34	20.7492
ggwwwwwwwwwwwwwwggggg	chr1:46126563-46126803(-)$1	240	159	180	20.2632
ggwwwwwwwwwwwwwwggggg	chr7:26230663-26230943(-)$1	280	45	66	20.2632
gggggtttttttttttggggg	chr16:87863942-87864182(-)$1	240	210	231	22.2301
eeeeettttttttttteeeee	chr2:54092218-54092458(-)$1	240	53	74	22.6690
ddddvvvvvvvvvvvvvdddd	chr17:54942866-54943106(+)$1	240	57	78	22.9135
hhhhhwwwwwwwwwwwwwwhh	chr14:57670964-57671204(-)$1	240	96	117	19.4193
eddddvvvvvvvvvvvvvddd	chr9:116025630-116025873(+)$1	243	27	48	22.7598
eeeeettttttttttteeeee	chr9:125002560-125002800(-)$1	240	22	43	22.6690
ee[bbtttttttttttbb22e	chr7:108214901-108215141(+)$1	240	214	235	20.5930
ffffftttttttttttfffff	chr13:42894006-42894246(+)$1	240	79	100	21.3950
eeeeettttttttttteeeee	chr5:151184722-151185002(+)$1	280	177	198	22.6690
eeeeeuuuuuuuuuuuueeee	chr15:35148798-35149038(-)$1	240	218	239	22.7625
ffffftttttttttttfffff	chr8:121548629-121548872(-)$1	243	59	80	21.3950
=====ttttttttttt=====	chr5:145890488-145890728(+)$1	240	84	105	22.3633
eeeeevvvvvvvvvvvvveee	chr15:65953603-65953843(-)$1	240	21	42	23.2107
ddddvvvvvvvvvvvvvdddd	chr12:2998092-2998332(+)$1	240	90	111	22.9135
eeeeevvvvvvvvvvvvveee	chr20:57608260-57608500(-)$1	240	213	234	23.2107
iiiiivvvvvvvvvvvvviii	chr1:212276447-212276687(+)$1	240	97	118	22.6681
[ddddtttttttttttdddde	chr15:70341743-70341983(-)$1	240	148	169	22.3009
[ddddtttttttttttdddd]	chr1:100550374-100550615(-)$1	241	172	193	22.2350
iiiiuuuuuuuuuuuuiiiii	chrX:154284672-154284931(+)$1	259	64	85	22.0596
hhhhhvvvvvvvvvvvvvhhh	chr5:118583548-118583788(+)$1	240	17	38	21.4084
hhhhhuuuuuuuuuuuuhhhh	chr1:151220741-151220981(+)$1	240	33	54	20.7016
eeeeettttttttttteeeee	chr5:71503647-71503927(+)$1	280	27	48	22.6690
ggwwwwwwwwwwwwwwggggg	chr2:230899611-230899851(-)$1	240	8	29	20.2632
fffffvvvvvvvvvvvvvfff	chr5:135517430-135517675(+)$1	245	155	176	22.1092
b[bbwwwwwwwwwwwwwwbb]	chr5:173316207-173316447(+)$1	240	31	52	19.7467
=====uuuuuuuuuuuu====	chr3:52082889-52083129(-)$1	240	106	127	22.4124

#otherMatches

#Seq PSSM
AUGGAUUCAGGUUUUUUGCAU	chr18:25531103-25531343(-)$1	240	6	27	22.2178
UGGCCUGUUUUUAAUCCUGUG	chr11:9467689-9467929(+)$1	240	138	159	22.7758
UACUUUUUUAACUCAUGGUAU	chr10:12206782-12207022(+)$1	240	123	144	22.5427
AGuuuuauauaauuaauuuaa	chr12:124082283-124082523(+)$1	240	159	180	20.6738
ACCUCAAAUUUUUAGGGGAGG	chr7:135613228-135613471(-)$1	243	208	229	22.2757
GCCCAAACGUCCCCAACGGUU	chr15:23048414-23048655(-)$1	241	12	33	20.4563
CUGCAAUUACUCAACGAGGCA	chr4:75972462-75972702(+)$1	240	59	80	20.1309
GAACUGCCAAAGUAUAUGUUC	chr14:58839039-58839279(+)$1	240	159	180	22.9135
UAGAAAAACUGUCUCUGAUUC	chr5:143538374-143538614(-)$1	240	43	64	22.8696
UGCAUGUCAAUAAUAAAUGUU	chr10:94112187-94112427(+)$1	240	150	171	21.5725
ACUUUUCCAAGUUUACAGAGU	chr5:82349686-82349926(-)$1	240	33	54	22.6690
guccagauuuuuacagaggau	chr7:148700649-148700890(-)$1	241	194	215	22.9135
AUGCUUUUUCAUCAAUAGCAG	chr8:125325831-125326071(-)$1	240	84	105	22.1846
GUGGCCACAAAAACAGAUGCU	chr1:228880527-228880767(+)$1	240	54	75	20.5124
AGCUUUUUUUUUUUUUUUGGU	chr17:65073719-65074016(-)$1	297	163	184	20.2632
GGCUGUCUUUUCAUUUUAGUU	chr8:79514515-79514755(+)$1	240	140	161	22.2301
ACUGUAAAAGUAUUCCCAGUA	chr6:17609417-17609657(+)$1	240	15	36	22.5427
GAUGCUAACAAUUAAUUUUAU	chr10:90973898-90974138(-)$1	240	109	130	21.2658
ACUGGCAAAAGGACAGCAGUC	chr16:18803518-18803758(-)$1	240	18	39	22.1875
GUGGAUUUUUGUAUAUUUCAU	chr12:96672445-96672685(-)$1	240	28	49	22.2301
UUGCUUUUUUCCUCCUUGCGA	chrX:102006763-102007003(+)$1	240	80	101	22.9135
UAGGUUGCUACUUUAUUUGCC	chr11:111934327-111934567(+)$1	240	94	115	23.2107
UUUUUUUGCCAUUCUUGAGGA	chr4:52780878-52781118(+)$1	240	123	144	22.1875
UUAAGUUUAUGuauauuuuaa	chr7:129805426-129805666(-)$1	240	202	223	22.6690
UGUAUAUUCACAUUAUAAAUA	chr1:159997850-159998099(-)$1	249	204	225	22.1092
UUUAUAAUUGCCGAAAAUAAU	chr15:99506283-99506563(+)$1	280	87	108	22.2350
UGGUGUCCAAAAUAAAAUCUC	chr14:55511093-55511333(+)$1	240	84	105	22.1884
AUUUUAUUAAACACAGGGAAA	chr13:107144129-107144369(-)$1	240	124	145	21.9023
GAACAAAUUCCUAAAUAGUUU	chr7:44921675-44921915(-)$1	240	122	143	22.9135
AAUCACUCAAAGUAUAUGGUG	chr4:122738597-122738837(-)$1	240	78	99	22.2350
AUAUGAAACUGAAAAAAUAUG	chr18:60244444-60244684(+)$1	240	55	76	22.5427
AUUUAUCCAAGAUUCUACUAA	chr3:150301688-150301928(+)$1	240	129	150	22.1092
UAAAUAUAUAAAAUCCACAUU	chr6:7610508-7610748(+)$1	240	113	134	23.2107
UCAAUUCAUUUUGCACGGGGU	chr15:43619940-43620180(-)$1	240	203	224	20.2632
UCAAAUUUAAAACCACUUUGA	chr10:102723538-102723778(+)$1	240	54	75	21.3950
UGGGAAUACUUUUAAGUCUCA	chr17:56081654-56081894(-)$1	240	89	110	22.6690
ACGCUUCUCUCCAUCUUGUGA	chr5:107006308-107006611(-)$1	303	13	34	20.7492
CUCUGAAUUUAUAAAUAGUAA	chr1:46126563-46126803(-)$1	240	159	180	20.2632
UAAUUUUUAUAAACCCUGUUU	chr7:26230663-26230943(-)$1	280	45	66	20.2632
GUGCAUUUUCAGUCGUUGUGC	chr16:87863942-87864182(-)$1	240	210	231	22.2301
GAACUCAUUAAGAAACAGUUU	chr2:54092218-54092458(-)$1	240	53	74	22.6690
GGUUUUCUGCAACAAUUAGCU	chr17:54942866-54943106(+)$1	240	57	78	22.9135
GGGUUUUAAAAGCUGUCAUAA	chr14:57670964-57671204(-)$1	240	96	117	19.4193
AAUGAUUUCAUUAACUUUUCA	chr9:116025630-116025873(+)$1	243	27	48	22.7598
ACUUAACAUCUUCCCAUGAGU	chr9:125002560-125002800(-)$1	240	22	43	22.6690
UUUCCUCUUUAGGCGUGGUUG	chr7:108214901-108215141(+)$1	240	214	235	20.5930
uAAGGGAGUACUUUAACCUUG	chr13:42894006-42894246(+)$1	240	79	100	21.3950
CUGGAAGAAAAUUUAAUCUGG	chr5:151184722-151185002(+)$1	280	177	198	22.6690
AACAAUUCUAGUUUCAUUUGU	chr15:35148798-35149038(-)$1	240	218	239	22.7625
AUUUUUCCCCCAAGUUAAAAU	chr8:121548629-121548872(-)$1	243	59	80	21.3950
UCCAAGAAAACCCGAGUUGGG	chr5:145890488-145890728(+)$1	240	84	105	22.3633
AUGAACGUAUUUCCUGUUUUC	chr15:65953603-65953843(-)$1	240	21	42	23.2107
UGGUCUUUGUUUCCUUAACCA	chr12:2998092-2998332(+)$1	240	90	111	22.9135
GUUCAUAAAUGAAACCCUUGG	chr20:57608260-57608500(-)$1	240	213	234	23.2107
AUAGUCUUCACUUUUUAAAUU	chr1:212276447-212276687(+)$1	240	97	118	22.6681
ACCUGGGAAGAGGAGACAGGG	chr15:70341743-70341983(-)$1	240	148	169	22.3009
UGAGGGAAAAUGAUUACCUCU	chr1:100550374-100550615(-)$1	241	172	193	22.2350
caagguucacaucguauuugc	chrX:154284672-154284931(+)$1	259	64	85	22.0596
AAAACUGGUUUUUCAUGUGUU	chr5:118583548-118583788(+)$1	240	17	38	21.4084
CUUUCUCUCUGACUCCUGGAA	chr1:151220741-151220981(+)$1	240	33	54	20.7016
AAUGUAUUUAACCUGAACAUU	chr5:71503647-71503927(+)$1	280	27	48	22.6690
UAUUUCCUGUUUAUGUUAUUU	chr2:230899611-230899851(-)$1	240	8	29	20.2632
GCUAUAUAAUAAUUGCUAGUA	chr5:135517430-135517675(+)$1	245	155	176	22.1092
GAACGUAUUCCCCUCUUAGUC	chr5:173316207-173316447(+)$1	240	31	52	19.7467
auauacacacacauacauaua	chr3:52082889-52083129(-)$1	240	106	127	22.4124

#DB
(((.(...........).)))	chr18:25531103-25531343(-)$1	1	6	27	22.2178
.((((.............).)	chr11:9467689-9467929(+)$1	1	138	159	22.7758
((((............)))))	chr10:12206782-12207022(+)$1	1	123	144	22.5427
(((((..............))	chr12:124082283-124082523(+)$1	1	159	180	20.6738
)((((............))))	chr7:135613228-135613471(-)$1	1	208	229	22.2757
(((..............))))	chr15:23048414-23048655(-)$1	1	12	33	20.4563
.(((..............)))	chr4:75972462-75972702(+)$1	1	59	80	20.1309
((((.............))))	chr14:58839039-58839279(+)$1	1	159	180	22.9135
(((((.............)))	chr5:143538374-143538614(-)$1	1	43	64	22.8696
.((((...........)))).	chr10:94112187-94112427(+)$1	1	150	171	21.5725
(((((...........)))))	chr5:82349686-82349926(-)$1	1	33	54	22.6690
((((.............))))	chr7:148700649-148700890(-)$1	1	194	215	22.9135
.((((...........)))).	chr8:125325831-125326071(-)$1	1	84	105	22.1846
((..............)))))	chr1:228880527-228880767(+)$1	1	54	75	20.5124
((..............)))))	chr17:65073719-65074016(-)$1	1	163	184	20.2632
(((((...........)))))	chr8:79514515-79514755(+)$1	1	140	161	22.2301
((((............)))))	chr6:17609417-17609657(+)$1	1	15	36	22.5427
((((..............)))	chr10:90973898-90974138(-)$1	1	109	130	21.2658
((((............)))))	chr16:18803518-18803758(-)$1	1	18	39	22.1875
(((((...........)))))	chr12:96672445-96672685(-)$1	1	28	49	22.2301
((((.............))))	chrX:102006763-102007003(+)$1	1	80	101	22.9135
(((((.............)))	chr11:111934327-111934567(+)$1	1	94	115	23.2107
((((............)))))	chr4:52780878-52781118(+)$1	1	123	144	22.1875
(((((...........)))))	chr7:129805426-129805666(-)$1	1	202	223	22.6690
(((((.............)))	chr1:159997850-159998099(-)$1	1	204	225	22.1092
.((((...........)))).	chr15:99506283-99506563(+)$1	1	87	108	22.2350
.(((............))).)	chr14:55511093-55511333(+)$1	1	84	105	22.1884
.((((............))))	chr13:107144129-107144369(-)$1	1	124	145	21.9023
((((.............))))	chr7:44921675-44921915(-)$1	1	122	143	22.9135
.((((...........)))).	chr4:122738597-122738837(-)$1	1	78	99	22.2350
((((............)))))	chr18:60244444-60244684(+)$1	1	55	76	22.5427
(((((.............)))	chr3:150301688-150301928(+)$1	1	129	150	22.1092
(((((.............)))	chr6:7610508-7610748(+)$1	1	113	134	23.2107
((..............)))))	chr15:43619940-43620180(-)$1	1	203	224	20.2632
(((((...........)))))	chr10:102723538-102723778(+)$1	1	54	75	21.3950
(((((...........)))))	chr17:56081654-56081894(-)$1	1	89	110	22.6690
.(((.............))).	chr5:107006308-107006611(-)$1	1	13	34	20.7492
((..............)))))	chr1:46126563-46126803(-)$1	1	159	180	20.2632
((..............)))))	chr7:26230663-26230943(-)$1	1	45	66	20.2632
(((((...........)))))	chr16:87863942-87864182(-)$1	1	210	231	22.2301
(((((...........)))))	chr2:54092218-54092458(-)$1	1	53	74	22.6690
((((.............))))	chr17:54942866-54943106(+)$1	1	57	78	22.9135
(((((..............))	chr14:57670964-57671204(-)$1	1	96	117	19.4193
(((((.............)))	chr9:116025630-116025873(+)$1	1	27	48	22.7598
(((((...........)))))	chr9:125002560-125002800(-)$1	1	22	43	22.6690
((.((...........))..)	chr7:108214901-108215141(+)$1	1	214	235	20.5930
(((((...........)))))	chr13:42894006-42894246(+)$1	1	79	100	21.3950
(((((...........)))))	chr5:151184722-151185002(+)$1	1	177	198	22.6690
(((((............))))	chr15:35148798-35149038(-)$1	1	218	239	22.7625
(((((...........)))))	chr8:121548629-121548872(-)$1	1	59	80	21.3950
(((((...........)))))	chr5:145890488-145890728(+)$1	1	84	105	22.3633
(((((.............)))	chr15:65953603-65953843(-)$1	1	21	42	23.2107
((((.............))))	chr12:2998092-2998332(+)$1	1	90	111	22.9135
(((((.............)))	chr20:57608260-57608500(-)$1	1	213	234	23.2107
(((((.............)))	chr1:212276447-212276687(+)$1	1	97	118	22.6681
.((((...........)))))	chr15:70341743-70341983(-)$1	1	148	169	22.3009
.((((...........)))).	chr1:100550374-100550615(-)$1	1	172	193	22.2350
((((............)))))	chrX:154284672-154284931(+)$1	1	64	85	22.0596
(((((.............)))	chr5:118583548-118583788(+)$1	1	17	38	21.4084
(((((............))))	chr1:151220741-151220981(+)$1	1	33	54	20.7016
(((((...........)))))	chr5:71503647-71503927(+)$1	1	27	48	22.6690
((..............)))))	chr2:230899611-230899851(-)$1	1	8	29	20.2632
(((((.............)))	chr5:135517430-135517675(+)$1	1	155	176	22.1092
(.((..............)).	chr5:173316207-173316447(+)$1	1	31	52	19.7467
(((((............))))	chr3:52082889-52083129(-)$1	1	106	127	22.4124

#PSSM
e : 0.27	g : 0.16	[ : 0.10	f : 0.10	d : 0.10	= : 0.04	i : 0.04	h : 0.04	: : 0.03	c : 0.01	! : 0.01	$ : 0.01	b : 0.01	
e : 0.26	d : 0.24	g : 0.16	f : 0.10	c : 0.07	= : 0.04	h : 0.04	i : 0.03	[ : 0.01	
d : 0.24	e : 0.23	f : 0.10	g : 0.09	w : 0.09	c : 0.07	= : 0.04	h : 0.04	i : 0.03	[ : 0.01	b : 0.01	
d : 0.24	e : 0.23	w : 0.10	g : 0.09	f : 0.09	c : 0.06	= : 0.04	h : 0.04	b : 0.03	i : 0.03	[ : 0.01	
e : 0.18	w : 0.15	d : 0.13	u : 0.10	v : 0.10	f : 0.09	g : 0.06	= : 0.04	h : 0.04	a : 0.03	b : 0.01	i : 0.01	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
t : 0.33	v : 0.29	u : 0.18	w : 0.18	
v : 0.29	e : 0.16	g : 0.15	w : 0.09	d : 0.09	u : 0.07	f : 0.04	a : 0.01	c : 0.01	b : 0.01	= : 0.01	i : 0.01	
d : 0.21	v : 0.18	e : 0.18	g : 0.15	w : 0.07	f : 0.06	c : 0.03	= : 0.03	] : 0.01	b : 0.01	i : 0.01	h : 0.01	
e : 0.24	d : 0.24	g : 0.16	f : 0.10	c : 0.06	w : 0.03	= : 0.03	i : 0.03	h : 0.03	a : 0.01	2 : 0.01	b : 0.01	
e : 0.24	d : 0.24	g : 0.16	f : 0.10	c : 0.04	= : 0.04	h : 0.04	] : 0.03	i : 0.03	2 : 0.01	b : 0.01	
e : 0.29	g : 0.16	d : 0.15	f : 0.10	] : 0.07	c : 0.04	= : 0.04	h : 0.04	i : 0.03	6 : 0.01	: : 0.01	

#score	1427.207679716754
#seq	65
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_UTR_m3_run1.txt

#BEAR
c[eeeeennnnneeeee]	chr1:24293222-24293483(-)$1	261	160	178	10.9154
iiiiiiiooooooiiiii	chr11:9467429-9467647(+)$1	218	116	134	6.9825
gg[ddddnnnnndddd]g	chr12:107367513-107367724(+)$1	211	187	205	10.1394
e"""cccnnnnnccc333	chr1:90498565-90498834(+)$1	269	208	226	10.7076
gggggggnnnnngggggg	chr10:76941173-76941398(+)$1	225	192	210	11.6975
gggggggooooooggggg	chr5:148875277-148875548(-)$1	271	0	18	7.5239
fff[abbnnnnnbb]a]f	chr5:82877411-82877651(+)$1	240	196	214	9.7295
!!eeeeennnnneeeee2	chr7:139249862-139250086(-)$1	224	159	177	10.9316
effffffnnnnnffffff	chr5:64886468-64886741(-)$1	273	33	51	10.5478
:ffffffnnnnnffffff	chr12:112944324-112944535(+)$1	211	55	73	9.7317
eee[cccnnnnnccc]ee	chr18:33571584-33571821(-)$1	237	132	150	10.7802
iiiiiiinnnnniiiiii	chr6:7285358-7285597(-)$1	239	98	116	11.1378
gggggggnnnnngggggg	chr9:123522247-123522491(-)$1	244	95	113	11.6975
cceeeeennnnneeeee:	chr1:94027579-94027816(-)$1	237	50	68	9.6192
!!eeeeennnnneeeee>	chr10:60156342-60156568(+)$1	226	112	130	10.8450
gggggggnnnnngggggg	chr6:75965590-75965813(-)$1	223	92	110	11.6975
&ccccccnnnnnccc]cc	chr14:53108349-53108632(-)$1	283	233	251	10.0999
c[eeeeennnnneeeeec	chr18:721650-721888(-)$1	238	207	225	10.7842
##eeeeennnnneeeee5	chr1:166823092-166823346(+)$1	254	223	241	9.9549
gggggggnnnnngggggg	chr16:81079884-81080138(+)$1	254	86	104	11.6975
eeee[bbnnnnnbb]eee	chr1:28527127-28527395(-)$1	268	195	213	9.7991
a!!ddddnnnnndddd22	chr2:223807631-223807864(+)$1	233	84	102	9.6506
gggggggnnnnngggggg	chr13:99104818-99105031(-)$1	213	1	19	11.6975
:ccccccnnnnnccc444	chr6:116599120-116599347(-)$1	227	6	24	9.5143
effffffnnnnnffffff	chr1:33323410-33323663(+)$1	253	98	116	10.5478
[ffffffnnnnnffffff	chr7:92234750-92234982(-)$1	232	111	129	10.7772
eeee[bbnnnnnbb22ee	chr5:140894634-140894865(-)$1	231	41	59	9.3404
[bb[cccnnnnncccbb]	chr22:38687702-38687949(-)$1	247	146	164	9.8097
gggggggnnnnngggggg	chr5:135515822-135516059(+)$1	237	179	197	11.6975
"""ddddnnnnndddd]f	chr19:16213365-16213593(+)$1	228	44	62	9.8510
!ffffffnnnnnffffff	chr20:42091111-42091323(+)$1	212	189	207	10.8144
hhhhhhhnnnnnhhhhhh	chr3:38532646-38532879(+)$1	233	5	23	9.0709
!!eeeeennnnneeeee2	chr1:23632204-23632415(-)$1	211	149	167	10.9316
"""ddddnnnnndddd44	chr11:9469454-9469715(+)$1	261	103	121	9.6313
gggg[bbnnnnnbbgggg	chr1:150548569-150548792(-)$1	223	144	162	10.6705
ddd[cccnnnnnccc]dd	chr1:28865311-28865522(+)$1	211	70	88	9.9648
!ffffffnnnnnffffff	chr6:89872908-89873142(+)$1	234	20	38	10.8144
d!!ddddnnnnndddd]d	chr1:47141882-47142161(-)$1	279	80	98	9.6028
eee!!bbnnnnnbb22ee	chr3:41281490-41281712(+)$1	222	27	45	9.3030
fffff[annnnna]ffff	chr3:160153965-160154188(-)$1	223	55	73	10.2740
&ccc[bbnnnnnbb]ccc	chr1:241792362-241792574(-)$1	212	51	69	9.1293
gggggggnnnnngggggg	chr10:11373933-11374157(+)$1	224	114	132	11.6975
:ffffffnnnnnffffff	chr5:133738007-133738248(-)$1	241	206	224	9.7317
gggggggnnnnngggggg	chr8:8642436-8642667(-)$1	231	202	220	11.6975
gggggggooooooggggg	chrX:70794609-70794843(+)$1	234	31	49	7.5239
ggg[cccnnnnnccc]gg	chr1:23633523-23633758(-)$1	235	36	54	11.4297
cceeeeennnnneeeee9	chr8:56737286-56737515(+)$1	229	28	46	10.0057
hhhhhhhnnnnnhhhhhh	chr1:47842837-47843058(+)$1	221	145	163	9.0709
eeeecccnnnnnccc]ee	chr10:31816410-31816632(+)$1	222	121	139	10.7037
gggggggnnnnngggggg	chr21:40195823-40196058(+)$1	235	55	73	11.6975
gggggggooooooggggg	chr6:64292298-64292513(+)$1	215	53	71	7.5239
b[eeeeennnnneeeee]	chr1:160967899-160968128(-)$1	229	47	65	10.6712
c[eeeeennnnneeeeec	chr7:135612051-135612299(-)$1	248	14	32	10.7842
:ffffffnnnnnffffff	chr12:46579830-46580069(-)$1	239	27	45	9.7317
!ffffffnnnnnffffff	chr4:26433113-26433368(+)$1	255	142	160	10.8144
gggggggooooooggggg	chr2:178086152-178086367(+)$1	215	24	42	7.5239
i!!ddddnnnnndddd22	chr6:47199682-47199964(-)$1	282	222	240	9.7120
[bb[cccnnnnnccc333	chr15:99505043-99505265(+)$1	222	118	136	10.5858
gggggggnnnnngggggg	chr4:77081392-77081641(-)$1	249	105	123	11.6975

#otherMatches

#Seq PSSM
GUGUGGUUAUCUGCCAUU	chr1:24293222-24293483(-)$1	261	160	178	10.9154
AGUGGUAUUUCAUUGCUG	chr11:9467429-9467647(+)$1	218	116	134	6.9825
UUGUAUUAAAGGGAUGGG	chr12:107367513-107367724(+)$1	211	187	205	10.1394
aauauaugacagauacug	chr1:90498565-90498834(+)$1	269	208	226	10.7076
GCAUAAGGAAAGUUUGUG	chr10:76941173-76941398(+)$1	225	192	210	11.6975
AAGGAAAUGAGAUUUUUU	chr5:148875277-148875548(-)$1	271	0	18	7.5239
AGUGACUGCUGAAGAUGA	chr5:82877411-82877651(+)$1	240	196	214	9.7295
UCUUACACAAACUGUGAC	chr7:139249862-139250086(-)$1	224	159	177	10.9316
UGGCUUUAUUUAAAAGCU	chr5:64886468-64886741(-)$1	273	33	51	10.5478
UGACCAGUGUUUUUGGUC	chr12:112944324-112944535(+)$1	211	55	73	9.7317
AAUAGUUCUUUUAACAAU	chr18:33571584-33571821(-)$1	237	132	150	10.7802
AGUCAAAGAUGUUUUGAC	chr6:7285358-7285597(-)$1	239	98	116	11.1378
CUUGGUUUAGACAACCAA	chr9:123522247-123522491(-)$1	244	95	113	11.6975
UCAAGUUUCCCCAGCUUC	chr1:94027579-94027816(-)$1	237	50	68	9.6192
AUAUGCACUUUAUGCGUU	chr10:60156342-60156568(+)$1	226	112	130	10.8450
GAAGUUGGCACAUAACUU	chr6:75965590-75965813(-)$1	223	92	110	11.6975
UGGCCAUUUUUUGUGUGU	chr14:53108349-53108632(-)$1	283	233	251	10.0999
UAUUCUUCCAUUGAGAAA	chr18:721650-721888(-)$1	238	207	225	10.7842
UUCUCUUGCUUUGGGAGC	chr1:166823092-166823346(+)$1	254	223	241	9.9549
AGUAUCUAGCAAGGAUAU	chr16:81079884-81080138(+)$1	254	86	104	11.6975
UGGCAUGAGGCCCACGCC	chr1:28527127-28527395(-)$1	268	195	213	9.7991
GGACUUAAAUCAUAGGCA	chr2:223807631-223807864(+)$1	233	84	102	9.6506
GCUGGAGAAUCGCUCUGG	chr13:99104818-99105031(-)$1	213	1	19	11.6975
UGCUGUCACUUGGAUUUC	chr6:116599120-116599347(-)$1	227	6	24	9.5143
UGUUUUAAAUUCUGGGGC	chr1:33323410-33323663(+)$1	253	98	116	10.5478
CCUUCCUAUCUGAGGAGG	chr7:92234750-92234982(-)$1	232	111	129	10.7772
AGGGCGUCUGUUGCUCCC	chr5:140894634-140894865(-)$1	231	41	59	9.3404
GAGAUGCCCUCAGCACUG	chr22:38687702-38687949(-)$1	247	146	164	9.8097
AUUCUAGCACCACUAGAA	chr5:135515822-135516059(+)$1	237	179	197	11.6975
AAUUCCUUCUUUGGGACC	chr19:16213365-16213593(+)$1	228	44	62	9.8510
UUCACAGAGUAGCUGUGA	chr20:42091111-42091323(+)$1	212	189	207	10.8144
UGuauuuuaaauaaauau	chr3:38532646-38532879(+)$1	233	5	23	9.0709
GUGUUUUGUGUGAAAGCU	chr1:23632204-23632415(-)$1	211	149	167	10.9316
AAAAAUGGAUUACAUUAG	chr11:9469454-9469715(+)$1	261	103	121	9.6313
CUGAAUGGAACUCAUUAG	chr1:150548569-150548792(-)$1	223	144	162	10.6705
AGCAACUUGUACAGUGGC	chr1:28865311-28865522(+)$1	211	70	88	9.9648
UUCGUGGAUGGACCAUGA	chr6:89872908-89873142(+)$1	234	20	38	10.8144
CCUUAACUCUUUGUUGUG	chr1:47141882-47142161(-)$1	279	80	98	9.6028
UAAGUCUCUCGUAGUGUU	chr3:41281490-41281712(+)$1	222	27	45	9.3030
CUCUUGGAUCACCGAAGA	chr3:160153965-160154188(-)$1	223	55	73	10.2740
AAGAAAGAAAAGCUAUUU	chr1:241792362-241792574(-)$1	212	51	69	9.1293
UUGGGAAAAGAAUUCCUA	chr10:11373933-11374157(+)$1	224	114	132	11.6975
gaggugagcagaucaccu	chr5:133738007-133738248(-)$1	241	206	224	9.7317
AUAAUCCCACACGGGUUA	chr8:8642436-8642667(-)$1	231	202	220	11.6975
UAUUUCUUUCAGCAGAAA	chrX:70794609-70794843(+)$1	234	31	49	7.5239
UAUUAAUUGUGCAUUUGU	chr1:23633523-23633758(-)$1	235	36	54	11.4297
GAGACAUUUGGCAUGUCU	chr8:56737286-56737515(+)$1	229	28	46	10.0057
ACAACUUGUACAAAGUUG	chr1:47842837-47843058(+)$1	221	145	163	9.0709
GAUAUGCAUCUGGCAUUG	chr10:31816410-31816632(+)$1	222	121	139	10.7037
AAAAUAAGAAUAUUAUUU	chr21:40195823-40196058(+)$1	235	55	73	11.6975
GAUGAAAUUUGCUUUUUA	chr6:64292298-64292513(+)$1	215	53	71	7.5239
CUGACAUUGACUGUGUCU	chr1:160967899-160968128(-)$1	229	47	65	10.6712
CAUUAGCGAAAGGUUAAG	chr7:135612051-135612299(-)$1	248	14	32	10.7842
CUUAAUGUUACUUAUUGG	chr12:46579830-46580069(-)$1	239	27	45	9.7317
AUGACUUUUCAUGAGUCA	chr4:26433113-26433368(+)$1	255	142	160	10.8144
GGUUAAUUGUACUGUUAA	chr2:178086152-178086367(+)$1	215	24	42	7.5239
UCAGGAUUUGCUAUUUAA	chr6:47199682-47199964(-)$1	282	222	240	9.7120
ACUGUGGAACUACCAAAU	chr15:99505043-99505265(+)$1	222	118	136	10.5858
UUAAGGGCAUUUUCUUUG	chr4:77081392-77081641(-)$1	249	105	123	11.6975

#DB
(.(((((.....))))).	chr1:24293222-24293483(-)$1	1	160	178	10.9154
(((((((......)))))	chr11:9467429-9467647(+)$1	1	116	134	6.9825
((.((((.....)))).)	chr12:107367513-107367724(+)$1	1	187	205	10.1394
(...(((.....)))...	chr1:90498565-90498834(+)$1	1	208	226	10.7076
(((((((.....))))))	chr10:76941173-76941398(+)$1	1	192	210	11.6975
(((((((......)))))	chr5:148875277-148875548(-)$1	1	0	18	7.5239
(((.(((.....)).).)	chr5:82877411-82877651(+)$1	1	196	214	9.7295
..(((((.....))))).	chr7:139249862-139250086(-)$1	1	159	177	10.9316
(((((((.....))))))	chr5:64886468-64886741(-)$1	1	33	51	10.5478
.((((((.....))))))	chr12:112944324-112944535(+)$1	1	55	73	9.7317
(((.(((.....))).))	chr18:33571584-33571821(-)$1	1	132	150	10.7802
(((((((.....))))))	chr6:7285358-7285597(-)$1	1	98	116	11.1378
(((((((.....))))))	chr9:123522247-123522491(-)$1	1	95	113	11.6975
))(((((.....))))).	chr1:94027579-94027816(-)$1	1	50	68	9.6192
..(((((.....))))).	chr10:60156342-60156568(+)$1	1	112	130	10.8450
(((((((.....))))))	chr6:75965590-75965813(-)$1	1	92	110	11.6975
.((((((.....))).))	chr14:53108349-53108632(-)$1	1	233	251	10.0999
(.(((((.....))))))	chr18:721650-721888(-)$1	1	207	225	10.7842
..(((((.....))))).	chr1:166823092-166823346(+)$1	1	223	241	9.9549
(((((((.....))))))	chr16:81079884-81080138(+)$1	1	86	104	11.6975
((((.((.....)).)))	chr1:28527127-28527395(-)$1	1	195	213	9.7991
(..((((.....))))..	chr2:223807631-223807864(+)$1	1	84	102	9.6506
(((((((.....))))))	chr13:99104818-99105031(-)$1	1	1	19	11.6975
.((((((.....)))...	chr6:116599120-116599347(-)$1	1	6	24	9.5143
(((((((.....))))))	chr1:33323410-33323663(+)$1	1	98	116	10.5478
.((((((.....))))))	chr7:92234750-92234982(-)$1	1	111	129	10.7772
((((.((.....))..))	chr5:140894634-140894865(-)$1	1	41	59	9.3404
.((.(((.....))))).	chr22:38687702-38687949(-)$1	1	146	164	9.8097
(((((((.....))))))	chr5:135515822-135516059(+)$1	1	179	197	11.6975
...((((.....)))).)	chr19:16213365-16213593(+)$1	1	44	62	9.8510
.((((((.....))))))	chr20:42091111-42091323(+)$1	1	189	207	10.8144
(((((((.....))))))	chr3:38532646-38532879(+)$1	1	5	23	9.0709
..(((((.....))))).	chr1:23632204-23632415(-)$1	1	149	167	10.9316
...((((.....))))..	chr11:9469454-9469715(+)$1	1	103	121	9.6313
((((.((.....))))))	chr1:150548569-150548792(-)$1	1	144	162	10.6705
(((.(((.....))).))	chr1:28865311-28865522(+)$1	1	70	88	9.9648
.((((((.....))))))	chr6:89872908-89873142(+)$1	1	20	38	10.8144
(..((((.....)))).)	chr1:47141882-47142161(-)$1	1	80	98	9.6028
(((..((.....))..))	chr3:41281490-41281712(+)$1	1	27	45	9.3030
(((((.(.....).))))	chr3:160153965-160154188(-)$1	1	55	73	10.2740
.(((.((.....)).)))	chr1:241792362-241792574(-)$1	1	51	69	9.1293
(((((((.....))))))	chr10:11373933-11374157(+)$1	1	114	132	11.6975
.((((((.....))))))	chr5:133738007-133738248(-)$1	1	206	224	9.7317
(((((((.....))))))	chr8:8642436-8642667(-)$1	1	202	220	11.6975
(((((((......)))))	chrX:70794609-70794843(+)$1	1	31	49	7.5239
(((.(((.....))).))	chr1:23633523-23633758(-)$1	1	36	54	11.4297
(((((((.....))))).	chr8:56737286-56737515(+)$1	1	28	46	10.0057
(((((((.....))))))	chr1:47842837-47843058(+)$1	1	145	163	9.0709
(((((((.....))).))	chr10:31816410-31816632(+)$1	1	121	139	10.7037
(((((((.....))))))	chr21:40195823-40196058(+)$1	1	55	73	11.6975
(((((((......)))))	chr6:64292298-64292513(+)$1	1	53	71	7.5239
(.(((((.....))))).	chr1:160967899-160968128(-)$1	1	47	65	10.6712
(.(((((.....))))))	chr7:135612051-135612299(-)$1	1	14	32	10.7842
.((((((.....))))))	chr12:46579830-46580069(-)$1	1	27	45	9.7317
.((((((.....))))))	chr4:26433113-26433368(+)$1	1	142	160	10.8144
(((((((......)))))	chr2:178086152-178086367(+)$1	1	24	42	7.5239
(..((((.....))))..	chr6:47199682-47199964(-)$1	1	222	240	9.7120
.((.(((.....)))...	chr15:99505043-99505265(+)$1	1	118	136	10.5858
(((((((.....))))))	chr4:77081392-77081641(-)$1	1	105	123	11.6975

#PSSM
g : 0.28	e : 0.13	! : 0.10	c : 0.08	: : 0.06	i : 0.05	[ : 0.05	f : 0.03	& : 0.03	" : 0.03	h : 0.03	d : 0.03	# : 0.01	a : 0.01	b : 0.01	
g : 0.28	f : 0.18	! : 0.10	e : 0.08	c : 0.08	[ : 0.06	" : 0.05	i : 0.03	b : 0.03	h : 0.03	# : 0.01	d : 0.01	
g : 0.27	e : 0.25	f : 0.18	" : 0.05	c : 0.05	! : 0.05	i : 0.03	b : 0.03	h : 0.03	[ : 0.01	d : 0.01	
g : 0.25	e : 0.22	f : 0.16	d : 0.10	[ : 0.10	c : 0.05	i : 0.03	h : 0.03	" : 0.01	! : 0.01	
g : 0.23	e : 0.16	f : 0.16	c : 0.15	d : 0.10	[ : 0.06	i : 0.03	h : 0.03	a : 0.01	! : 0.01	
g : 0.23	e : 0.16	c : 0.15	f : 0.15	d : 0.10	b : 0.10	i : 0.03	h : 0.03	[ : 0.01	
g : 0.23	e : 0.16	c : 0.15	f : 0.15	d : 0.10	b : 0.10	i : 0.03	h : 0.03	a : 0.01	
n : 0.91	o : 0.08	
n : 0.91	o : 0.08	
n : 0.91	o : 0.08	
n : 0.91	o : 0.08	
n : 0.91	o : 0.08	
e : 0.16	g : 0.16	c : 0.15	f : 0.15	d : 0.10	b : 0.10	o : 0.08	h : 0.03	i : 0.01	a : 0.01	
g : 0.23	e : 0.16	c : 0.15	f : 0.15	d : 0.10	b : 0.10	i : 0.03	h : 0.03	] : 0.01	
g : 0.25	e : 0.16	f : 0.16	c : 0.15	d : 0.10	] : 0.05	i : 0.03	2 : 0.03	h : 0.03	
g : 0.25	e : 0.18	f : 0.16	d : 0.10	] : 0.08	i : 0.03	3 : 0.03	2 : 0.03	h : 0.03	a : 0.01	4 : 0.01	b : 0.01	c : 0.01	
g : 0.27	e : 0.25	f : 0.16	] : 0.06	i : 0.03	3 : 0.03	c : 0.03	2 : 0.03	4 : 0.03	h : 0.03	b : 0.01	d : 0.01	
g : 0.28	f : 0.20	e : 0.08	2 : 0.06	c : 0.06	] : 0.05	i : 0.03	3 : 0.03	4 : 0.03	h : 0.03	d : 0.03	: : 0.01	> : 0.01	5 : 0.01	9 : 0.01	

#score	602.7192272220841
#seq	59
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_UTR_m2_run2.txt

#BEAR
dd[ddddtttttttttttdddd]dd	chr12:4410382-4410622(+)$1	240	39	64	22.7804
cccddddwwwwwwwwwwwwwwdddd	chr4:129192025-129192265(-)$1	240	56	81	20.7894
ccc[bbwwwwwwwwwwwwwwbbccc	chr17:46626897-46627137(-)$1	240	49	74	21.0525
=====wwwwwwwwwwwwww======	chr12:124082283-124082523(+)$1	240	159	184	22.8919
b!!ddddtttttttttttdddd22b	chr4:169848027-169848267(+)$1	240	119	144	22.5617
gggggggtttttttttttggggggg	chr10:70931586-70931826(+)$1	240	110	135	24.5367
hhhhhhhttttttttttthhhhhhh	chr11:27387504-27387744(-)$1	240	64	89	21.8451
eeeeevvvvvvvvvvvvveeeee00	chrX:15844721-15844961(-)$1	240	45	70	21.6219
dd[ddddwwwwwwwwwwwwwwdddd	chr10:74767232-74767472(-)$1	240	140	165	20.7378
dd!!ccctttttttttttcccdddd	chr1:101444663-101444903(+)$1	240	73	98	23.4271
ffffffvvvvvvvvvvvvvffffff	chr16:4506546-4506786(+)$1	240	127	152	23.4522
!ffffffuuuuuuuuuuuuffffff	chr6:7288989-7289229(-)$1	240	151	176	23.3744
iiiiiiiuuuuuuuuuuuuiiiiii	chr13:37583547-37583787(-)$1	240	121	146	24.4650
###dddduuuuuuuuuuuudddd55	chr5:132215252-132215492(-)$1	240	151	176	21.5441
ggggggguuuuuuuuuuuugggggg	chr1:118408515-118408755(-)$1	240	137	162	24.5584
iiiiibbtttttttttttbb]iiii	chr1:153920072-153920312(-)$1	240	199	224	23.4533
!fffffftttttttttttffffff2	chr3:136667565-136667805(+)$1	240	200	225	23.4088
ccc[ccctttttttttttccc]ccc	chr1:85020351-85020591(-)$1	240	95	120	24.0143
eeeee[atttttttttttaeeeee:	chr10:322873-323113(-)$1	240	56	81	22.6765
ee!!ccctttttttttttccc22ee	chr21:15745504-15745744(-)$1	240	63	88	23.3254
gggggggtttttttttttggggggg	chr2:37478903-37479143(-)$1	240	134	159	24.5367
eee[cccuuuuuuuuuuuuccc444	chr3:160154549-160154789(-)$1	240	18	43	23.5722
bb!!cccvvvvvvvvvvvvvccc22	chr11:63677999-63678239(+)$1	240	118	143	23.1539
ddeeeeettttttttttteeeee]d	chr10:105048813-105049053(+)$1	240	124	149	22.9048
ggggggwwwwwwwwwwwwwwggggg	chr17:65073719-65074016(-)$1	297	159	184	23.0331
hffffffuuuuuuuuuuuuffffff	chr6:82456506-82456746(-)$1	240	144	169	23.1399
iiiiiiitttttttttttiiiiiii	chr11:20530493-20530733(+)$1	240	92	117	24.3558
ggggbbvvvvvvvvvvvvvbb]ggg	chr17:71203947-71204187(-)$1	240	136	161	23.5428
iiiiiiitttttttttttiiiiiii	chr16:83845119-83845359(+)$1	240	138	163	24.3558
bb[ddddtttttttttttddddbb:	chr11:43515349-43515589(+)$1	240	26	51	21.4067
ffffffuuuuuuuuuuuuffffff2	chr8:104455227-104455480(+)$1	253	77	102	22.7014
ffffffuuuuuuuuuuuuffffff:	chr9:72333089-72333329(-)$1	240	193	218	21.9016
ffffffuuuuuuuuuuuuffffff:	chr1:160186700-160186940(-)$1	240	67	92	21.9016
hhhhhhhttttttttttthhhhhhh	chr2:70506482-70506722(+)$1	240	206	231	21.8451
!!eeeeeuuuuuuuuuuuueeeee>	chr18:66342916-66343156(-)$1	240	90	115	23.2841
gggggggtttttttttttggggggg	chr16:46990491-46990731(-)$1	240	13	38	24.5367
!!eeeeeuuuuuuuuuuuueeeee]	chr5:132028928-132029171(-)$1	243	31	56	23.5202
bb[dddduuuuuuuuuuuudddd]b	chr18:12986670-12986911(+)$1	241	168	193	22.6780
ffffffvvvvvvvvvvvvvffffff	chr14:103808447-103808687(+)$1	240	120	145	23.4522
###ddddtttttttttttdddd333	chr12:53807935-53808175(+)$1	240	36	61	23.3389
ggggggguuuuuuuuuuuugggggg	chr5:167983609-167983850(-)$1	241	78	103	24.5584
iiiiivvvvvvvvvvvvviiiiiii	chr5:60047699-60047939(-)$1	240	115	140	23.5119
"""ddddtttttttttttdddd444	chr1:154243122-154243363(+)$1	241	144	169	23.0794
cffffffuuuuuuuuuuuuffffff	chr6:117883766-117884006(-)$1	240	159	184	23.2399
=====vvvvvvvvvvvvv=======	chr10:98716164-98716404(+)$1	240	177	202	23.7061
ggggggguuuuuuuuuuuugggggg	chr2:209222676-209222916(+)$1	240	23	48	24.5584
ee[cccuuuuuuuuuuuuccc]eee	chr14:55511006-55511246(+)$1	240	169	194	23.1942
ddd[ccctttttttttttccc]ddd	chr3:41281493-41281733(+)$1	240	167	192	23.2270
ggggggwwwwwwwwwwwwwwggggg	chr3:107881087-107881327(-)$1	240	67	92	23.0331
iiiiiiitttttttttttiiiiiii	chr7:111367013-111367253(-)$1	240	37	62	24.3558
c[ddddvvvvvvvvvvvvvddddcc	chr17:60022362-60022602(-)$1	240	169	194	23.2166
ggggggguuuuuuuuuuuugggggg	chr15:26812706-26812946(-)$1	240	76	101	24.5584
ggggggvvvvvvvvvvvvvgggggg	chr5:173385282-173385602(+)$1	320	70	95	24.8212
gggggggtttttttttttggggggg	chr6:99848105-99848347(-)$1	242	59	84	24.5367
"cccwwwwwwwwwwwwwwccc333h	chr19:1554792-1555087(-)$1	295	179	204	20.9045
&eeeeevvvvvvvvvvvvveeeee5	chr2:153617083-153617326(+)$1	243	83	108	22.1532
ggggggwwwwwwwwwwwwwwggggg	chr1:111726911-111727151(+)$1	240	106	131	23.0331
cc[ddddvvvvvvvvvvvvvdddd]	chr18:319407-319650(-)$1	243	161	186	23.1733
ggggggvvvvvvvvvvvvvgggggg	chr22:21305539-21305779(+)$1	240	210	235	24.8212
ffffffvvvvvvvvvvvvvffffff	chr12:10851591-10851831(-)$1	240	209	234	23.4522
=======uuuuuuuuuuuu======	chr17:58523227-58523467(-)$1	240	22	47	24.6120
!!eeeeettttttttttteeeee22	chr18:51681172-51681412(-)$1	240	141	166	23.2647
:ddddbbuuuuuuuuuuuubb]ddd	chr10:104417499-104417739(+)$1	240	160	185	20.9207
dd!!cccvvvvvvvvvvvvvccc33	chr6:158932293-158932533(+)$1	240	165	190	23.7388
hhhhhhhttttttttttthhhhhhh	chr20:33098809-33099049(+)$1	240	32	57	21.8451
gggggggtttttttttttggggggg	chr4:164441352-164441632(+)$1	280	29	54	24.5367
!ffffffuuuuuuuuuuuuffffff	chr8:105501602-105501842(-)$1	240	141	166	23.3744
bb[ddddvvvvvvvvvvvvvdddd]	chr11:107662173-107662413(-)$1	240	1	26	22.7425
:fffffftttttttttttffffff:	chr1:211836075-211836315(-)$1	240	160	185	21.4918
###ddddtttttttttttdddd333	chr14:60600792-60601032(+)$1	240	12	37	23.3389
[eeeeeuuuuuuuuuuuueeeee]e	chr19:57804440-57804680(+)$1	240	121	146	22.8063
iiiiiiitttttttttttiiiiiii	chr5:60454444-60454704(-)$1	260	165	190	24.3558

#otherMatches

#Seq PSSM
AUCUCUAUACUUCUCCUUUGGACAU	chr12:4410382-4410622(+)$1	240	39	64	22.7804
AAGAAAGUCACAAUAUUACuucuuu	chr4:129192025-129192265(-)$1	240	56	81	20.7894
CCCAUCAAUUACAGUUUUUAGAGGG	chr17:46626897-46627137(-)$1	240	49	74	21.0525
AGuuuuauauaauuaauuuaaauuu	chr12:124082283-124082523(+)$1	240	159	184	22.8919
UUAACAUUUUUUUUCUUUAUGUGUA	chr4:169848027-169848267(+)$1	240	119	144	22.5617
UAUGGCCUUCUUUUUUUUGGCCAUA	chr10:70931586-70931826(+)$1	240	110	135	24.5367
AGAAACUCCUAAUUAAAAGGUUUUU	chr11:27387504-27387744(-)$1	240	64	89	21.8451
CCUUUUUUUUUUUUUUUUAAAGGAC	chrX:15844721-15844961(-)$1	240	45	70	21.6219
AAAGUCCUGCAUAACAACACUGGGC	chr10:74767232-74767472(-)$1	240	140	165	20.7378
CUAUUUCUAACUCUUCAUGAAAGCA	chr1:101444663-101444903(+)$1	240	73	98	23.4271
CACUAAAAUAAAGCAUCUAUUAGUG	chr16:4506546-4506786(+)$1	240	127	152	23.4522
UGUUGAUAUAACCUUUUUAGUUAAC	chr6:7288989-7289229(-)$1	240	151	176	23.3744
CAUUUUUAAAUAAAAACAGGGAAAU	chr13:37583547-37583787(-)$1	240	121	146	24.4650
UUUGGUGUGCCUUAAAUCUUACCUU	chr5:132215252-132215492(-)$1	240	151	176	21.5441
augcaugcacacacacauauaugca	chr1:118408515-118408755(-)$1	240	137	162	24.5584
AUCUAGGGAGUUAUAGGGCCAUGGG	chr1:153920072-153920312(-)$1	240	199	224	23.4533
GUGGAAAAUUAGAAAUUAUUUCCAG	chr3:136667565-136667805(+)$1	240	200	225	23.4088
AGGCAAGAAGCAAGUCAACUUACCU	chr1:85020351-85020591(-)$1	240	95	120	24.0143
GAAGGACUUUGGAUUACUGCCUUCA	chr10:322873-323113(-)$1	240	56	81	22.6765
GUAUGGAUAACUAUAUUUUCUGGAU	chr21:15745504-15745744(-)$1	240	63	88	23.3254
CAAAAGUAAAAGAACaaaacuuuug	chr2:37478903-37479143(-)$1	240	134	159	24.5367
UCUUGGAUUAAAAACUCAUUCUUAU	chr3:160154549-160154789(-)$1	240	18	43	23.5722
uauuuuauuuuuuuuuuuuuugauu	chr11:63677999-63678239(+)$1	240	118	143	23.1539
CCAUAUAUCCUUUUCUUCUAUGUAG	chr10:105048813-105049053(+)$1	240	124	149	22.9048
UAUCAGCUUUUUUUUUUUUUUUGGU	chr17:65073719-65074016(-)$1	297	159	184	23.0331
UACUAUAGUCUUGUGCAUAUGUAGU	chr6:82456506-82456746(-)$1	240	144	169	23.1399
GAUUUCUAGUACUGCCCAGGAAAUC	chr11:20530493-20530733(+)$1	240	92	117	24.3558
AAAGCCAGAUACUUGACAAGGAUUU	chr17:71203947-71204187(-)$1	240	136	161	23.5428
UGGCGGUUCUUGCAUAACAUUGUCA	chr16:83845119-83845359(+)$1	240	138	163	24.3558
CGAGUUUGUCCCAGCCAAGAACCGA	chr11:43515349-43515589(+)$1	240	26	51	21.4067
UCUGCAUUCUUCUUUCAUUGUAGAA	chr8:104455227-104455480(+)$1	253	77	102	22.7014
UGAAAGUCCAUAGUAAAUCUUUCAU	chr9:72333089-72333329(-)$1	240	193	218	21.9016
UCCCAGAAUCCUAUUUUCCUGGGAA	chr1:160186700-160186940(-)$1	240	67	92	21.9016
gucaggagaucaagaccauccuggc	chr2:70506482-70506722(+)$1	240	206	231	21.8451
CUGUCACCCAUUUCGUCAAGUGACC	chr18:66342916-66343156(-)$1	240	90	115	23.2841
UGAAAGGAAACAAGACUCCCUUUCA	chr16:46990491-46990731(-)$1	240	13	38	24.5367
CUCUUUUCCCUUUAAUUUAAAAAGU	chr5:132028928-132029171(-)$1	243	31	56	23.5202
guuccugucuucauuguuuCAGGUA	chr18:12986670-12986911(+)$1	241	168	193	22.6780
AUAUUUUUUACUUCACAUUGAAUAU	chr14:103808447-103808687(+)$1	240	120	145	23.4522
UUUGAAUGAGUUUUUUAAAUUUUUU	chr12:53807935-53808175(+)$1	240	36	61	23.3389
GUUUUGGUCAUAUAUACAUUCAGAA	chr5:167983609-167983850(-)$1	241	78	103	24.5584
auauuauaaauaaauacaaauauag	chr5:60047699-60047939(-)$1	240	115	140	23.5119
UGUGUCCUCAAAUUUAAUGGAUUAA	chr1:154243122-154243363(+)$1	241	144	169	23.0794
UUGCAUUUCAGCUUUAUUCAAUGCA	chr6:117883766-117884006(-)$1	240	159	184	23.2399
UGGUGGAAAAUGUGCACACACUACC	chr10:98716164-98716404(+)$1	240	177	202	23.7061
UUUUUCUAAUUCUGACCUAAGAAAA	chr2:209222676-209222916(+)$1	240	23	48	24.5584
AGUGGUGUCCAAAAUAAAAUCUCUG	chr14:55511006-55511246(+)$1	240	169	194	23.1942
UUUGUAUAAAAUAGACAAAUAGAAA	chr3:41281493-41281733(+)$1	240	167	192	23.2270
CAUAGAUUUCAAAACAUAAUUUUAU	chr3:107881087-107881327(-)$1	240	67	92	23.0331
GCAUCUUAGGUCUAGAUAGGGAUGC	chr7:111367013-111367253(-)$1	240	37	62	24.3558
GUCUGUACUUUUCUAUAACACAGCU	chr17:60022362-60022602(-)$1	240	169	194	23.2166
UCGACUGUCACUGAGCUUUCGGUUG	chr15:26812706-26812946(-)$1	240	76	101	24.5584
GCAAUACCUCAAUUUUUCAUAUUGC	chr5:173385282-173385602(+)$1	320	70	95	24.8212
AAUGUUAGAAAUCCuauauaauauu	chr6:99848105-99848347(-)$1	242	59	84	24.5367
uuacuuuuUACCUCUUGUGUAUAUG	chr19:1554792-1555087(-)$1	295	179	204	20.9045
UGAAAUUUUUACUAUUUCUGUUUCC	chr2:153617083-153617326(+)$1	243	83	108	22.1532
UAUAAUUUAUAAUAAUCAAUGUUGU	chr1:111726911-111727151(+)$1	240	106	131	23.0331
GGAGCCAAAGAAAACAAUAAUGGUA	chr18:319407-319650(-)$1	243	161	186	23.1733
UGUGGUUCAUCCAUCAUCUGCUGCA	chr22:21305539-21305779(+)$1	240	210	235	24.8212
UUUACUUGACUUGAUUAAUAGUAAA	chr12:10851591-10851831(-)$1	240	209	234	23.4522
UGUUGAAUUUUAGUUUUCUUUUAAC	chr17:58523227-58523467(-)$1	240	22	47	24.6120
AAGGGGACACCUGUACAUUCUUCCA	chr18:51681172-51681412(-)$1	240	141	166	23.2647
UCUCCUCACCAUCUUCCCAGACGGA	chr10:104417499-104417739(+)$1	240	160	185	20.9207
UGCAUAGGCCCCAGACCAAACUAGA	chr6:158932293-158932533(+)$1	240	165	190	23.7388
UAUAUCCUUUCCUGUUGUGGAUGUA	chr20:33098809-33099049(+)$1	240	32	57	21.8451
GAUUAGGGAACCAGUGAUUUUAAUU	chr4:164441352-164441632(+)$1	280	29	54	24.5367
UGCGGUUUAUUUAUUCUUUAACUGU	chr8:105501602-105501842(-)$1	240	141	166	23.3744
gcccaggcuaaucucaaauuccuga	chr11:107662173-107662413(-)$1	240	1	26	22.7425
CUUCUUUCCCACUAAAUAAAAGAAU	chr1:211836075-211836315(-)$1	240	160	185	21.4918
ACAAACGAUGAUGAAGAACGUUAUA	chr14:60600792-60601032(+)$1	240	12	37	23.3389
CACCUCAACAAUUUUCUAGAGGUCA	chr19:57804440-57804680(+)$1	240	121	146	22.8063
AUUAAUGUUUUCUGUACCCAUUAAU	chr5:60454444-60454704(-)$1	260	165	190	24.3558

#DB
((.((((...........)))).))	chr12:4410382-4410622(+)$1	1	39	64	22.7804
(((((((..............))))	chr4:129192025-129192265(-)$1	1	56	81	20.7894
(((.((..............)))))	chr17:46626897-46627137(-)$1	1	49	74	21.0525
(((((..............))))))	chr12:124082283-124082523(+)$1	1	159	184	22.8919
(..((((...........))))..)	chr4:169848027-169848267(+)$1	1	119	144	22.5617
(((((((...........)))))))	chr10:70931586-70931826(+)$1	1	110	135	24.5367
(((((((...........)))))))	chr11:27387504-27387744(-)$1	1	64	89	21.8451
(((((.............)))))..	chrX:15844721-15844961(-)$1	1	45	70	21.6219
((.((((..............))))	chr10:74767232-74767472(-)$1	1	140	165	20.7378
((..(((...........)))))))	chr1:101444663-101444903(+)$1	1	73	98	23.4271
((((((.............))))))	chr16:4506546-4506786(+)$1	1	127	152	23.4522
.((((((............))))))	chr6:7288989-7289229(-)$1	1	151	176	23.3744
(((((((............))))))	chr13:37583547-37583787(-)$1	1	121	146	24.4650
...((((............))))..	chr5:132215252-132215492(-)$1	1	151	176	21.5441
(((((((............))))))	chr1:118408515-118408755(-)$1	1	137	162	24.5584
(((((((...........)).))))	chr1:153920072-153920312(-)$1	1	199	224	23.4533
.((((((...........)))))).	chr3:136667565-136667805(+)$1	1	200	225	23.4088
(((.(((...........))).)))	chr1:85020351-85020591(-)$1	1	95	120	24.0143
(((((.(...........)))))).	chr10:322873-323113(-)$1	1	56	81	22.6765
((..(((...........)))..))	chr21:15745504-15745744(-)$1	1	63	88	23.3254
(((((((...........)))))))	chr2:37478903-37479143(-)$1	1	134	159	24.5367
(((.(((............)))...	chr3:160154549-160154789(-)$1	1	18	43	23.5722
((..(((.............)))..	chr11:63677999-63678239(+)$1	1	118	143	23.1539
(((((((...........))))).)	chr10:105048813-105049053(+)$1	1	124	149	22.9048
((((((..............)))))	chr17:65073719-65074016(-)$1	1	159	184	23.0331
(((((((............))))))	chr6:82456506-82456746(-)$1	1	144	169	23.1399
(((((((...........)))))))	chr11:20530493-20530733(+)$1	1	92	117	24.3558
((((((.............)).)))	chr17:71203947-71204187(-)$1	1	136	161	23.5428
(((((((...........)))))))	chr16:83845119-83845359(+)$1	1	138	163	24.3558
((.((((...........)))))).	chr11:43515349-43515589(+)$1	1	26	51	21.4067
((((((............)))))).	chr8:104455227-104455480(+)$1	1	77	102	22.7014
((((((............)))))).	chr9:72333089-72333329(-)$1	1	193	218	21.9016
((((((............)))))).	chr1:160186700-160186940(-)$1	1	67	92	21.9016
(((((((...........)))))))	chr2:70506482-70506722(+)$1	1	206	231	21.8451
..(((((............))))).	chr18:66342916-66343156(-)$1	1	90	115	23.2841
(((((((...........)))))))	chr16:46990491-46990731(-)$1	1	13	38	24.5367
..(((((............))))).	chr5:132028928-132029171(-)$1	1	31	56	23.5202
((.((((............)))).)	chr18:12986670-12986911(+)$1	1	168	193	22.6780
((((((.............))))))	chr14:103808447-103808687(+)$1	1	120	145	23.4522
...((((...........))))...	chr12:53807935-53808175(+)$1	1	36	61	23.3389
(((((((............))))))	chr5:167983609-167983850(-)$1	1	78	103	24.5584
(((((.............)))))))	chr5:60047699-60047939(-)$1	1	115	140	23.5119
...((((...........))))...	chr1:154243122-154243363(+)$1	1	144	169	23.0794
)((((((............))))))	chr6:117883766-117884006(-)$1	1	159	184	23.2399
(((((.............)))))))	chr10:98716164-98716404(+)$1	1	177	202	23.7061
(((((((............))))))	chr2:209222676-209222916(+)$1	1	23	48	24.5584
((.(((............))).)))	chr14:55511006-55511246(+)$1	1	169	194	23.1942
(((.(((...........))).)))	chr3:41281493-41281733(+)$1	1	167	192	23.2270
((((((..............)))))	chr3:107881087-107881327(-)$1	1	67	92	23.0331
(((((((...........)))))))	chr7:111367013-111367253(-)$1	1	37	62	24.3558
(.((((.............))))))	chr17:60022362-60022602(-)$1	1	169	194	23.2166
(((((((............))))))	chr15:26812706-26812946(-)$1	1	76	101	24.5584
((((((.............))))))	chr5:173385282-173385602(+)$1	1	70	95	24.8212
(((((((...........)))))))	chr6:99848105-99848347(-)$1	1	59	84	24.5367
.(((..............)))...)	chr19:1554792-1555087(-)$1	1	179	204	20.9045
.(((((.............))))).	chr2:153617083-153617326(+)$1	1	83	108	22.1532
((((((..............)))))	chr1:111726911-111727151(+)$1	1	106	131	23.0331
((.((((.............)))).	chr18:319407-319650(-)$1	1	161	186	23.1733
((((((.............))))))	chr22:21305539-21305779(+)$1	1	210	235	24.8212
((((((.............))))))	chr12:10851591-10851831(-)$1	1	209	234	23.4522
(((((((............))))))	chr17:58523227-58523467(-)$1	1	22	47	24.6120
..(((((...........)))))..	chr18:51681172-51681412(-)$1	1	141	166	23.2647
.((((((............)).)))	chr10:104417499-104417739(+)$1	1	160	185	20.9207
((..(((.............)))..	chr6:158932293-158932533(+)$1	1	165	190	23.7388
(((((((...........)))))))	chr20:33098809-33099049(+)$1	1	32	57	21.8451
(((((((...........)))))))	chr4:164441352-164441632(+)$1	1	29	54	24.5367
.((((((............))))))	chr8:105501602-105501842(-)$1	1	141	166	23.3744
((.((((.............)))).	chr11:107662173-107662413(-)$1	1	1	26	22.7425
.((((((...........)))))).	chr1:211836075-211836315(-)$1	1	160	185	21.4918
...((((...........))))...	chr14:60600792-60601032(+)$1	1	12	37	23.3389
.(((((............))))).)	chr19:57804440-57804680(+)$1	1	121	146	22.8063
(((((((...........)))))))	chr5:60454444-60454704(-)$1	1	165	190	24.3558

#PSSM
g : 0.20	i : 0.09	d : 0.08	c : 0.08	f : 0.08	! : 0.08	b : 0.06	e : 0.06	h : 0.05	= : 0.04	# : 0.04	" : 0.02	: : 0.02	& : 0.01	[ : 0.01	
g : 0.20	f : 0.16	d : 0.09	e : 0.09	i : 0.09	c : 0.06	! : 0.05	b : 0.05	= : 0.04	h : 0.04	# : 0.04	" : 0.01	[ : 0.01	
g : 0.20	f : 0.16	e : 0.12	[ : 0.09	i : 0.09	! : 0.06	c : 0.05	= : 0.04	h : 0.04	# : 0.04	d : 0.04	" : 0.01	
g : 0.20	d : 0.19	f : 0.16	e : 0.11	i : 0.09	[ : 0.05	! : 0.05	= : 0.04	h : 0.04	c : 0.02	
d : 0.19	g : 0.19	f : 0.16	e : 0.11	c : 0.11	i : 0.09	= : 0.04	h : 0.04	b : 0.02	w : 0.01	
g : 0.19	d : 0.18	f : 0.16	c : 0.11	e : 0.08	i : 0.06	b : 0.05	h : 0.04	v : 0.04	w : 0.02	[ : 0.01	= : 0.01	
d : 0.16	v : 0.15	g : 0.12	c : 0.09	w : 0.08	f : 0.08	i : 0.06	u : 0.06	e : 0.05	h : 0.04	b : 0.02	a : 0.01	= : 0.01	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
t : 0.38	u : 0.29	v : 0.20	w : 0.11	
u : 0.22	v : 0.16	w : 0.09	d : 0.08	c : 0.08	g : 0.06	f : 0.06	i : 0.06	e : 0.05	h : 0.04	b : 0.01	a : 0.01	= : 0.01	
f : 0.16	g : 0.15	d : 0.12	e : 0.11	c : 0.09	w : 0.08	i : 0.08	v : 0.05	= : 0.04	h : 0.04	b : 0.04	
g : 0.19	f : 0.16	d : 0.15	c : 0.12	e : 0.11	i : 0.08	b : 0.04	= : 0.04	h : 0.04	w : 0.02	] : 0.01	
d : 0.19	g : 0.19	f : 0.16	e : 0.11	i : 0.09	] : 0.06	= : 0.04	h : 0.04	c : 0.04	b : 0.01	2 : 0.01	3 : 0.01	
g : 0.20	f : 0.16	d : 0.13	e : 0.12	i : 0.09	c : 0.05	= : 0.04	h : 0.04	3 : 0.04	2 : 0.02	4 : 0.02	] : 0.01	b : 0.01	
g : 0.20	f : 0.16	d : 0.11	i : 0.09	e : 0.08	3 : 0.05	c : 0.04	= : 0.04	2 : 0.04	h : 0.04	] : 0.04	4 : 0.02	0 : 0.01	5 : 0.01	b : 0.01	
g : 0.20	d : 0.09	f : 0.09	i : 0.09	: : 0.06	h : 0.05	2 : 0.05	c : 0.04	= : 0.04	e : 0.04	] : 0.04	3 : 0.04	b : 0.02	5 : 0.02	4 : 0.02	0 : 0.01	> : 0.01	

#score	1667.844394958923
#seq	72
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_CDS_m2_run1.txt

#BEAR
fffffvvvvvvvvvvvvvfffff	chr1:114483870-114484083(+)$1	213	174	197	22.0446
gggggggtttttttttttggggg	chr19:33697080-33697350(+)$1	270	216	239	22.1337
ccc[bbyyyyyyyyyyyyyyyyb	chr19:14628960-14629177(-)$1	217	104	127	19.6767
Eeeeeeuuuuuuuuuuuueeeee	chr7:116339429-116339639(+)$1	210	175	198	21.6368
fffffftttttttttttffffff	chr5:154254776-154254997(+)$1	221	174	197	21.2449
cc[ddddtttttttttttdddd]	chr13:23928784-23929036(-)$1	252	52	75	21.9154
======uuuuuuuuuuuu=====	chr3:41279405-41279666(+)$1	261	19	42	23.4149
:eeeeeuuuuuuuuuuuueeeee	chr12:110977610-110977854(-)$1	244	188	211	21.6422
d[cccvvvvvvvvvvvvvcccdd	chr12:80211111-80211324(-)$1	213	51	74	22.6617
ggggggwwwwwwwwwwwwwwggg	chr12:118480966-118481206(-)$1	240	173	196	21.0345
f!!ccctttttttttttccc22f	chr11:65484073-65484297(+)$1	224	129	152	21.8377
[cccwwwwwwwwwwwwwwcccee	chr16:3841913-3842159(-)$1	246	83	106	21.6009
ffffffuuuuuuuuuuuufffff	chr17:57290819-57291038(+)$1	219	68	91	22.5285
:ddddvvvvvvvvvvvvvdddd:	chr12:6691961-6692186(-)$1	225	129	152	20.3921
bbddddtttttttttttdddd22	chr16:30616384-30616595(-)$1	211	161	184	20.5727
gggggggtttttttttttggggg	chr11:66488510-66488741(-)$1	231	41	64	22.1337
g[cccvvvvvvvvvvvvvcccgg	chr17:63553840-63554052(-)$1	212	116	139	23.1001
[bb[ccctttttttttttcccbb	chr19:15228701-15228918(-)$1	217	151	174	21.6863
gggggvvvvvvvvvvvvvggggg	chr1:202912883-202913116(-)$1	233	198	221	22.7454
hhhawwwwwwwwwwwwwwa]hhh	chr3:124482411-124482629(-)$1	218	65	88	20.0648
gggggggtttttttttttggggg	chr19:44680585-44680797(+)$1	212	80	103	22.1337
dcccwwwwwwwwwwwwwwccc]d	chr13:111926091-111926316(+)$1	225	113	136	21.2511
:ddddwwwwwwwwwwwwwwdddd	chrX:138878367-138878587(-)$1	220	131	154	20.0471
fffffftttttttttttffffff	chr11:46774111-46774332(-)$1	221	115	138	21.2449
bb[cccuuuuuuuuuuuuccc]b	chr11:118343191-118343422(+)$1	231	129	152	22.9593
ffff[bbtttttttttttbb]ff	chr7:151845601-151845811(-)$1	210	131	154	21.3131
"""cccuuuuuuuuuuuuccc]g	chr17:45740356-45740583(+)$1	227	53	76	23.4495
[ccc[bbtttttttttttbb]cc	chr12:6636920-6637150(+)$1	230	83	106	21.7960
======uuuuuuuuuuuu=====	chr5:16676131-16676360(-)$1	229	18	41	23.4149
gggddddtttttttttttdddd2	chr19:59067973-59068193(-)$1	220	10	33	21.6951
cccyyyyyyyyyyyyyyyyccc]	chrX:153220786-153221055(-)$1	269	31	54	21.2296
::dddduuuuuuuuuuuudddd:	chr16:19553154-19553377(+)$1	223	74	97	20.0029
fffffvvvvvvvvvvvvvfffff	chrX:80049135-80049353(-)$1	218	24	47	22.0446
ccc[ccctttttttttttccccc	chr7:151884315-151884532(-)$1	217	3	26	22.6399
ff:cccuuuuuuuuuuuuccc::	chr10:77159995-77160220(-)$1	225	37	60	20.5071
!ddddvvvvvvvvvvvvvddddf	chr7:92133995-92134223(-)$1	228	118	141	22.2147
fffffftttttttttttffffff	chr11:120312361-120312580(+)$1	219	184	207	21.2449
gggggguuuuuuuuuuuuggggg	chr5:112154733-112154956(+)$1	223	45	68	23.2611
c[dddduuuuuuuuuuuudddd3	chr9:104238146-104238402(-)$1	256	62	85	22.7917
ggggggwwwwwwwwwwwwwwggg	chr15:35275039-35275256(-)$1	217	76	99	21.0345
hhhhwwwwwwwwwwwwwwhhhhh	chr8:95902582-95902795(-)$1	213	49	72	19.5330
eecccvvvvvvvvvvvvvccc]e	chr17:34854860-34855081(-)$1	221	122	145	22.7199
:eeeeettttttttttteeeeeb	chr1:6679848-6680089(+)$1	241	134	157	20.2014
"cccyyyyyyyyyyyyyyyyccc	chr1:101705114-101705329(+)$1	215	65	88	21.2937
""dddduuuuuuuuuuuuddddd	chr1:152277124-152277340(+)$1	216	96	119	22.5701
:ddddvvvvvvvvvvvvvddddE	chr4:10105420-10105653(-)$1	233	53	76	20.3596
=======ttttttttttt=====	chr1:147091818-147092032(+)$1	214	131	154	22.3511
[eeeeeyyyyyyyyyyyyyyyye	chr11:4140985-4141205(+)$1	220	28	51	19.9570
eeyyyyyyyyyyyyyyyyeeeee	chr17:61492840-61493067(+)$1	227	184	207	20.2094
ffffffuuuuuuuuuuuufffff	chr3:50327049-50327291(-)$1	242	77	100	22.5285
!cccwwwwwwwwwwwwwwccc==	chr2:113316881-113317105(+)$1	224	149	172	21.7151
a!!cccvvvvvvvvvvvvvccc2	chr18:19321472-19321699(+)$1	227	137	160	22.4165
[ddddyyyyyyyyyyyyyyyydd	chr11:64082202-64082425(+)$1	223	119	142	20.6442
cc[cccvvvvvvvvvvvvvcccc	chr17:40149108-40149332(-)$1	224	93	116	22.6070
ddyyyyyyyyyyyyyyyydddd]	chrX:41029208-41029430(+)$1	222	18	41	20.2691
gggggggtttttttttttggggg	chr11:62286576-62286838(-)$1	262	67	90	22.1337
fffffwwwwwwwwwwwwwwffff	chr3:45784942-45785164(+)$1	222	28	51	20.9196
eeee[bbtttttttttttbb]ee	chr5:176562681-176562900(+)$1	219	182	205	21.2068
f!!cccuuuuuuuuuuuuccc22	chr6:30297350-30297567(+)$1	217	167	190	23.1651
fffffftttttttttttffffff	chr4:111539424-111539646(-)$1	222	115	138	21.2449
[ccc[auuuuuuuuuuuua]ccc	chr1:38041936-38042159(-)$1	223	38	61	23.5556
fffffftttttttttttffffff	chr2:44428301-44428522(+)$1	221	189	212	21.2449
ee[ddddtttttttttttdddd]	chr1:155288368-155288599(+)$1	231	32	55	21.7436
dd[bbvvvvvvvvvvvvvbb]dd	chr12:53664446-53664676(+)$1	230	29	52	21.3120
::eeeeettttttttttteeeee	chr19:1106483-1106713(+)$1	230	50	73	19.6595
gggggvvvvvvvvvvvvvggggg	chr10:34400349-34400576(-)$1	227	163	186	22.7454
iii[bbuuuuuuuuuuuubb]ii	chr10:3143554-3143779(+)$1	225	149	172	22.4716
[ddddyyyyyyyyyyyyyyyydd	chr5:37064589-37064820(+)$1	231	6	29	20.6442
:::cccuuuuuuuuuuuucccff	chr2:183829325-183829552(-)$1	227	86	109	20.6566
:eeeeettttttttttteeeeed	chr20:34294992-34295213(-)$1	221	135	158	20.3041
e[ddddwwwwwwwwwwwwwwddd	chr14:72138984-72139197(+)$1	213	52	75	20.4171
[ayyyyyyyyyyyyyyyya]iii	chr1:215781383-215781603(+)$1	220	62	85	20.8018
eeeddddtttttttttttdddd:	chr1:154573490-154573711(-)$1	221	109	132	20.6493

#otherMatches

#Seq PSSM
CUGUGUGCUCAACCUACUUACAG	chr1:114483870-114484083(+)$1	213	174	197	22.0446
CGGGCUUCUUCAUCACCCAGGCU	chr19:33697080-33697350(+)$1	270	216	239	22.1337
GCUACCACCCGGACAAGAACAAG	chr19:14628960-14629177(-)$1	217	104	127	19.6767
CGGAGGUUCACUGCAUAUUCUCC	chr7:116339429-116339639(+)$1	210	175	198	21.6368
CCAGGAGAAGAUGAGCAUCCUGG	chr5:154254776-154254997(+)$1	221	174	197	21.2449
UGUGCUCAACUACCUCCAGAGCU	chr13:23928784-23929036(-)$1	252	52	75	21.9154
UAUGCUUUAAAAAAAAUUAGUGU	chr3:41279405-41279666(+)$1	261	19	42	23.4149
GCCUGAUUAUAUGAUUCUUCAGG	chr12:110977610-110977854(-)$1	244	188	211	21.6422
AACUAAUGCCAACACUUCUAGUA	chr12:80211111-80211324(-)$1	213	51	74	22.6617
GGGCACGCCACCACCCCCAAGUG	chr12:118480966-118481206(-)$1	240	173	196	21.0345
CACAGACCCUUUCCUCUUCUACG	chr11:65484073-65484297(+)$1	224	129	152	21.8377
ACGACAAAUCAUCUCUCAUUGGA	chr16:3841913-3842159(-)$1	246	83	106	21.6009
CCUCAUUAUGCUCAACUUAUGAG	chr17:57290819-57291038(+)$1	219	68	91	22.5285
AGCCAUUGCCUCCUCUGUUGGCC	chr12:6691961-6692186(-)$1	225	129	152	20.3921
GAACCUCUCCCAGCACCAGGUCA	chr16:30616384-30616595(-)$1	211	161	184	20.5727
GCUGUCACCCACAGACUUUGACA	chr11:66488510-66488741(-)$1	231	41	64	22.1337
ACAGUGGAUACAGGUAAGACUUU	chr17:63553840-63554052(-)$1	212	116	139	23.1001
AUCAUCGUCAAUCGUAAUCGGGA	chr19:15228701-15228918(-)$1	217	151	174	21.6863
UUGCCACUCCUAAGCACCGGCAG	chr1:202912883-202913116(-)$1	233	198	221	22.7454
CUUCAAAUCCAUUAUACAGAAAG	chr3:124482411-124482629(-)$1	218	65	88	20.0648
ACCAUACAAAUGUGAGGAGUGUG	chr19:44680585-44680797(+)$1	212	80	103	22.1337
CUGGGAUUCUCGUGCUGACCACG	chr13:111926091-111926316(+)$1	225	113	136	21.2511
AGACCUUAAUGAAGAACUUGGUC	chrX:138878367-138878587(-)$1	220	131	154	20.0471
AGUUCUCCCAAAUUCUCAGAGCU	chr11:46774111-46774332(-)$1	221	115	138	21.2449
AGUGUUGAUACCUCCACAGACUC	chr11:118343191-118343422(+)$1	231	129	152	22.9593
UGGUGCCUUAAUAAAUGUGGAGC	chr7:151845601-151845811(-)$1	210	131	154	21.3131
UGCGUUGUUAUUUUAGUAAACUA	chr17:45740356-45740583(+)$1	227	53	76	23.4495
ACACAGAGGCAGAACUAAUCCGU	chr12:6636920-6637150(+)$1	230	83	106	21.7960
AUAUUUGAGAGUCUUGAAAAAUA	chr5:16676131-16676360(-)$1	229	18	41	23.4149
UCUCUCUUUUCUUUUCCUGGAGC	chr19:59067973-59068193(-)$1	220	10	33	21.6951
CACUAACUCUCCUCCUCGUGUGU	chrX:153220786-153221055(-)$1	269	31	54	21.2296
AAUGUUAAAAGAGAAGAAGGCAA	chr16:19553154-19553377(+)$1	223	74	97	20.0029
UUUAUAUUUUUAAACCAAAUAAA	chrX:80049135-80049353(-)$1	218	24	47	22.0446
GUGAUCCUAACAACUCUUGGACA	chr7:151884315-151884532(-)$1	217	3	26	22.6399
UUCCACUUCUUUCUCUGUGUGAC	chr10:77159995-77160220(-)$1	225	37	60	20.5071
CUGCUGUCCCGGAACAUGAGCAC	chr7:92133995-92134223(-)$1	228	118	141	22.2147
AGCAGAUUCAGAGUUCUUCUGUU	chr11:120312361-120312580(+)$1	219	184	207	21.2449
UGGAUGUCUUCCUCUCCUCAUCC	chr5:112154733-112154956(+)$1	223	45	68	23.2611
CCGGACCCUCACCUACCUGUCCC	chr9:104238146-104238402(-)$1	256	62	85	22.7917
CAUGAAAAGAAGAAAGAAUAUUC	chr15:35275039-35275256(-)$1	217	76	99	21.0345
UGUUAAAAAAGGAGAGCAGAUAU	chr8:95902582-95902795(-)$1	213	49	72	19.5330
CAGCUGCCACAGUCAUCAAGCGU	chr17:34854860-34855081(-)$1	221	122	145	22.7199
CGCUGCUUUAGCCACCUGCAGCC	chr1:6679848-6680089(+)$1	241	134	157	20.2014
CUGCUCUCCAUCGUCAUUCUGUA	chr1:101705114-101705329(+)$1	215	65	88	21.2937
CAGACCUUCCCCCUGACCGGUCA	chr1:152277124-152277340(+)$1	216	96	119	22.5701
UUGCUGACAUCUACACAGAGCAC	chr4:10105420-10105653(-)$1	233	53	76	20.3596
AGGCUCCCAGCGCCACAUGGAGC	chr1:147091818-147092032(+)$1	214	131	154	22.3511
CCAUUUUUUUCUUUUCUUUGCUG	chr11:4140985-4141205(+)$1	220	28	51	19.9570
GGAAAAUGAACGUAAGUCCCUGU	chr17:61492840-61493067(+)$1	227	184	207	20.2094
GCAUUGCCCUUCUCCCAACAGUG	chr3:50327049-50327291(-)$1	242	77	100	22.5285
UGUCCCGUGCAUACCCCAGACGG	chr2:113316881-113317105(+)$1	224	149	172	21.7151
GGACUGGAAGUGGGGGAAGCAGG	chr18:19321472-19321699(+)$1	227	137	160	22.4165
CCUCUGUGACCUCUUUGACCGAG	chr11:64082202-64082425(+)$1	223	119	142	20.6442
CUAGCUAUUAUGGUAAUCGAGCA	chr17:40149108-40149332(-)$1	224	93	116	22.6070
UGUCUUUCUUUUUCCCCCCAGAG	chrX:41029208-41029430(+)$1	222	18	41	20.2691
CAGGGAUUUGACCUGAAUGUUCC	chr11:62286576-62286838(-)$1	262	67	90	22.1337
GGGUCUGAUAUCAACAAACGACU	chr3:45784942-45785164(+)$1	222	28	51	20.9196
CUCCCAGCCCCCUUUUCACUAGG	chr5:176562681-176562900(+)$1	219	182	205	21.2068
CCACUGGACGAUGCUACACAGGA	chr6:30297350-30297567(+)$1	217	167	190	23.1651
CGGGCUCCAGUCUCAACAGCCUG	chr4:111539424-111539646(-)$1	222	115	138	21.2449
AUUGGCUAUCCAAAUGUUGGCAA	chr1:38041936-38042159(-)$1	223	38	61	23.5556
AGACUGGUCAUUUUUUGCAGUUU	chr2:44428301-44428522(+)$1	221	189	212	21.2449
GGGUUUCGCAUAUCUGGAGAAAG	chr1:155288368-155288599(+)$1	231	32	55	21.7436
UGACCUGACCCAACUAGUGGACA	chr12:53664446-53664676(+)$1	230	29	52	21.3120
GACAGGUGAUAGAGAAGGACCUG	chr19:1106483-1106713(+)$1	230	50	73	19.6595
GUGCCAAAGAGAACCCCAGGUAC	chr10:34400349-34400576(-)$1	227	163	186	22.7454
CGGAAGGAGUGGAGUGGGCUGCU	chr10:3143554-3143779(+)$1	225	149	172	22.4716
CUUGGUCUUUUUUCCCCCCUCCC	chr5:37064589-37064820(+)$1	231	6	29	20.6442
AUUGCAUUUCCACUACUUUGCAC	chr2:183829325-183829552(-)$1	227	86	109	20.6566
AAUGUUUCCAACUCUCUAACAUG	chr20:34294992-34295213(-)$1	221	135	158	20.3041
CCACAGUAUCUUUUAUUUCCUUG	chr14:72138984-72139197(+)$1	213	52	75	20.4171
CGUCAUUCAAGAUACUAUCCCUG	chr1:215781383-215781603(+)$1	220	62	85	20.8018
AGCGGGCUGUUAGAAUAUGCCCA	chr1:154573490-154573711(-)$1	221	109	132	20.6493

#DB
(((((.............)))))	chr1:114483870-114484083(+)$1	1	174	197	22.0446
(((((((...........)))))	chr19:33697080-33697350(+)$1	1	216	239	22.1337
(((.((................)	chr19:14628960-14629177(-)$1	1	104	127	19.6767
)(((((............)))))	chr7:116339429-116339639(+)$1	1	175	198	21.6368
((((((...........))))))	chr5:154254776-154254997(+)$1	1	174	197	21.2449
((.((((...........)))).	chr13:23928784-23929036(-)$1	1	52	75	21.9154
((((((............)))))	chr3:41279405-41279666(+)$1	1	19	42	23.4149
.(((((............)))))	chr12:110977610-110977854(-)$1	1	188	211	21.6422
(.(((.............)))))	chr12:80211111-80211324(-)$1	1	51	74	22.6617
((((((..............)))	chr12:118480966-118481206(-)$1	1	173	196	21.0345
(..(((...........)))..)	chr11:65484073-65484297(+)$1	1	129	152	21.8377
.(((..............)))))	chr16:3841913-3842159(-)$1	1	83	106	21.6009
((((((............)))))	chr17:57290819-57291038(+)$1	1	68	91	22.5285
.((((.............)))).	chr12:6691961-6692186(-)$1	1	129	152	20.3921
((((((...........))))..	chr16:30616384-30616595(-)$1	1	161	184	20.5727
(((((((...........)))))	chr11:66488510-66488741(-)$1	1	41	64	22.1337
(.(((.............)))))	chr17:63553840-63554052(-)$1	1	116	139	23.1001
.((.(((...........)))))	chr19:15228701-15228918(-)$1	1	151	174	21.6863
(((((.............)))))	chr1:202912883-202913116(-)$1	1	198	221	22.7454
((((..............).)))	chr3:124482411-124482629(-)$1	1	65	88	20.0648
(((((((...........)))))	chr19:44680585-44680797(+)$1	1	80	103	22.1337
((((..............))).)	chr13:111926091-111926316(+)$1	1	113	136	21.2511
.((((..............))))	chrX:138878367-138878587(-)$1	1	131	154	20.0471
((((((...........))))))	chr11:46774111-46774332(-)$1	1	115	138	21.2449
((.(((............))).)	chr11:118343191-118343422(+)$1	1	129	152	22.9593
((((.((...........)).))	chr7:151845601-151845811(-)$1	1	131	154	21.3131
...(((............))).)	chr17:45740356-45740583(+)$1	1	53	76	23.4495
.(((.((...........)).))	chr12:6636920-6637150(+)$1	1	83	106	21.7960
((((((............)))))	chr5:16676131-16676360(-)$1	1	18	41	23.4149
(((((((...........)))).	chr19:59067973-59068193(-)$1	1	10	33	21.6951
(((................))).	chrX:153220786-153221055(-)$1	1	31	54	21.2296
..((((............)))).	chr16:19553154-19553377(+)$1	1	74	97	20.0029
(((((.............)))))	chrX:80049135-80049353(-)$1	1	24	47	22.0446
(((.(((...........)))))	chr7:151884315-151884532(-)$1	1	3	26	22.6399
)).(((............)))..	chr10:77159995-77160220(-)$1	1	37	60	20.5071
.((((.............)))))	chr7:92133995-92134223(-)$1	1	118	141	22.2147
((((((...........))))))	chr11:120312361-120312580(+)$1	1	184	207	21.2449
((((((............)))))	chr5:112154733-112154956(+)$1	1	45	68	23.2611
(.((((............)))).	chr9:104238146-104238402(-)$1	1	62	85	22.7917
((((((..............)))	chr15:35275039-35275256(-)$1	1	76	99	21.0345
((((..............)))))	chr8:95902582-95902795(-)$1	1	49	72	19.5330
(((((.............))).)	chr17:34854860-34855081(-)$1	1	122	145	22.7199
.(((((...........)))))(	chr1:6679848-6680089(+)$1	1	134	157	20.2014
.(((................)))	chr1:101705114-101705329(+)$1	1	65	88	21.2937
..((((............)))))	chr1:152277124-152277340(+)$1	1	96	119	22.5701
.((((.............))))(	chr4:10105420-10105653(-)$1	1	53	76	20.3596
(((((((...........)))))	chr1:147091818-147092032(+)$1	1	131	154	22.3511
.(((((................)	chr11:4140985-4141205(+)$1	1	28	51	19.9570
((................)))))	chr17:61492840-61493067(+)$1	1	184	207	20.2094
((((((............)))))	chr3:50327049-50327291(-)$1	1	77	100	22.5285
.(((..............)))))	chr2:113316881-113317105(+)$1	1	149	172	21.7151
(..(((.............))).	chr18:19321472-19321699(+)$1	1	137	160	22.4165
.((((................))	chr11:64082202-64082425(+)$1	1	119	142	20.6442
((.(((.............))))	chr17:40149108-40149332(-)$1	1	93	116	22.6070
((................)))).	chrX:41029208-41029430(+)$1	1	18	41	20.2691
(((((((...........)))))	chr11:62286576-62286838(-)$1	1	67	90	22.1337
(((((..............))))	chr3:45784942-45785164(+)$1	1	28	51	20.9196
((((.((...........)).))	chr5:176562681-176562900(+)$1	1	182	205	21.2068
(..(((............)))..	chr6:30297350-30297567(+)$1	1	167	190	23.1651
((((((...........))))))	chr4:111539424-111539646(-)$1	1	115	138	21.2449
.(((.(............).)))	chr1:38041936-38042159(-)$1	1	38	61	23.5556
((((((...........))))))	chr2:44428301-44428522(+)$1	1	189	212	21.2449
((.((((...........)))).	chr1:155288368-155288599(+)$1	1	32	55	21.7436
((.((.............)).))	chr12:53664446-53664676(+)$1	1	29	52	21.3120
..(((((...........)))))	chr19:1106483-1106713(+)$1	1	50	73	19.6595
(((((.............)))))	chr10:34400349-34400576(-)$1	1	163	186	22.7454
(((.((............)).))	chr10:3143554-3143779(+)$1	1	149	172	22.4716
.((((................))	chr5:37064589-37064820(+)$1	1	6	29	20.6442
...(((............)))((	chr2:183829325-183829552(-)$1	1	86	109	20.6566
.(((((...........)))))(	chr20:34294992-34295213(-)$1	1	135	158	20.3041
(.((((..............)))	chr14:72138984-72139197(+)$1	1	52	75	20.4171
.(................).)))	chr1:215781383-215781603(+)$1	1	62	85	20.8018
)))((((...........)))).	chr1:154573490-154573711(-)$1	1	109	132	20.6493

#PSSM
f : 0.19	g : 0.15	: : 0.12	[ : 0.10	c : 0.08	e : 0.08	d : 0.05	= : 0.04	" : 0.04	b : 0.02	h : 0.02	! : 0.02	E : 0.01	a : 0.01	i : 0.01	
f : 0.16	c : 0.15	g : 0.13	e : 0.13	d : 0.10	[ : 0.05	= : 0.04	! : 0.04	b : 0.04	: : 0.04	h : 0.02	" : 0.02	i : 0.01	a : 0.01	
c : 0.16	f : 0.15	d : 0.15	g : 0.13	e : 0.10	[ : 0.06	= : 0.04	! : 0.04	y : 0.04	h : 0.02	: : 0.02	b : 0.01	" : 0.01	i : 0.01	
c : 0.23	d : 0.20	f : 0.15	g : 0.12	e : 0.09	[ : 0.05	y : 0.05	= : 0.04	a : 0.01	h : 0.01	b : 0.01	
d : 0.20	c : 0.17	f : 0.13	g : 0.12	e : 0.08	w : 0.06	y : 0.06	[ : 0.05	b : 0.04	= : 0.04	
v : 0.15	c : 0.13	d : 0.12	g : 0.09	f : 0.09	w : 0.09	y : 0.09	e : 0.08	b : 0.06	= : 0.04	a : 0.01	
u : 0.23	v : 0.17	w : 0.13	y : 0.12	t : 0.12	g : 0.05	d : 0.05	b : 0.04	c : 0.02	= : 0.01	e : 0.01	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
t : 0.32	u : 0.23	v : 0.17	w : 0.13	y : 0.12	
u : 0.23	t : 0.20	v : 0.17	w : 0.13	y : 0.12	f : 0.06	e : 0.02	c : 0.01	d : 0.01	
c : 0.19	d : 0.16	f : 0.12	g : 0.09	y : 0.08	e : 0.08	w : 0.06	b : 0.06	= : 0.04	a : 0.04	v : 0.02	h : 0.01	
c : 0.23	d : 0.17	f : 0.13	g : 0.09	e : 0.08	y : 0.06	b : 0.06	= : 0.04	w : 0.04	] : 0.04	h : 0.01	
c : 0.24	d : 0.19	f : 0.13	g : 0.12	e : 0.08	] : 0.06	y : 0.05	= : 0.04	h : 0.02	2 : 0.01	i : 0.01	
d : 0.23	f : 0.16	g : 0.13	e : 0.10	c : 0.09	= : 0.05	] : 0.05	2 : 0.04	y : 0.02	h : 0.02	i : 0.02	b : 0.01	: : 0.01	
f : 0.19	g : 0.15	d : 0.12	e : 0.10	c : 0.06	b : 0.05	] : 0.05	= : 0.05	: : 0.05	2 : 0.05	h : 0.02	i : 0.02	3 : 0.01	E : 0.01	

#score	1574.5982711892984
#seq	73
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_CDS_m3_run1.txt

#BEAR
"ccc[bb"""bb[ccc[allla]cccbb333bb]ccc3	chrX:53659381-53659600(-)$1	219	119	157	12.5977
ff!!a!!bba[eeeeellleeeee]a22bb333a22ff	chr11:47446069-47446299(-)$1	230	132	170	11.0324
fff####eeeee[a[ccclllccc]a]eeeeeffffff	chr1:93812236-93812459(+)$1	223	165	203	11.5326
##ccc[gggggggcccnnnnnccc55555gggggggcc	chr2:113330044-113330274(+)$1	230	47	85	12.3506
[ggggggg^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chr11:32953336-32953562(+)$1	226	95	133	9.8620
==========!!eeeeemmmmeeeee22==========	chr11:64878077-64878302(+)$1	225	39	77	12.8024
fgggggggdddd[cccmmmmccc22dddd4444ggggg	chr1:212194384-212194604(-)$1	220	138	176	10.8096
cc==========ddddnnnnndddd4444=========	chr20:58519665-58519891(+)$1	226	166	204	15.0625
"eeeee"""a!!a!!bbnnnnnbb]a22a]eeeee]dd	chr1:27097519-27097749(+)$1	230	86	124	12.4404
bb[ccc[ffffffcccnnnnnccc]ffffff22cccbb	chr14:95562165-95562389(-)$1	224	71	109	11.9194
c"""ffffff[bb[ddddllldddd333bb]ffffff3	chr11:107682300-107682524(-)$1	224	11	49	11.3365
g[bb[ccc[ccc[cccnnnnnccc]ccc333ccc22bb	chr11:61080903-61081128(-)$1	225	147	185	15.2868
[ffffff!!ccc[cccnnnnnccc22ccc4444fffff	chr9:32558821-32559051(-)$1	230	123	161	14.6964
###bb[cccccc[cccooooooccc22ccc]ccc]bb5	chr16:4707169-4707394(+)$1	225	150	188	13.5394
[ccc!!ccc"""cccooooooccc4444ccc333cccc	chr2:24524756-24524980(-)$1	224	40	78	15.7610
2eeeeeiiiiiiiiixxxxxxxxxxxxxxxiiiiiiii	chr2:55894043-55894273(-)$1	230	139	177	11.1290
GGGggggggg!!cccooooooccc4444gggggggfff	chr9:130511544-130511766(-)$1	222	7	45	13.4788
""ggggggg!!bb[bboooooobb]bb333ggggggg2	chr2:149541172-149541402(+)$1	230	73	111	13.3991
iiiiiccc[a"""cccnnnnnccc]a]ccc]iiiiiii	chr1:28148707-28148934(+)$1	227	19	57	17.3666
###dddd[ccc!!cccnnnnnccc22ccc]dddd333i	chr14:23745776-23746002(-)$1	226	152	190	14.1805
"eeeee$$$$$ccc[annnnna]ccc22eeeee333gg	chr3:179051425-179051646(+)$1	221	167	205	13.4691
##ffffff[cccrrrrrrrrrccc]ffffffggggggg	chr19:52719167-52719391(+)$1	224	30	68	10.6498
======$$$$$ggggggglllggggggg333=======	chr17:5336527-5336750(-)$1	223	36	74	13.2263
iiiiii[ccceeeeellleeeee4444ccc]iiiiiii	chr5:87502862-87503092(-)$1	230	34	72	11.2627
========!!bb[cccooooooccc22bb22=======	chr15:66832414-66832644(+)$1	230	7	45	15.6027
===========!!eeeeellleeeee22==========	chr15:77346449-77346679(-)$1	230	151	189	13.6319
ddd!!eeeee"""cccooooooccc333eeeee22ddd	chr7:98984214-98984444(+)$1	230	116	154	13.0582
=====eeeee"""bbnnnnnbb333eeeee]=======	chr17:62496741-62496964(-)$1	223	22	60	12.6219
b[ffffff"""eeeeennnnneeeee333ffffff]bb	chr20:34242929-34243159(-)$1	230	24	62	12.4780
b[ccc[ccc[bb[cccmmmmcccbb22ccc]ccc]bb4	chr14:95574155-95574385(-)$1	230	26	64	11.9447
ccc[ccc[bb[ccc[cccmmmmccccccbb]ccc333c	chr3:143691151-143691371(+)$1	220	116	154	11.1730
""ggggggg!!bb[cccmmmmccc]bb22ggggggg33	chr5:43655861-43656091(+)$1	230	50	88	12.9905
ffffff"""ccc[cccnnnnnccc333ccc333fffff	chr7:20418616-20418835(+)$1	219	49	87	16.1272
ee[cccxxxxxxxxxxxxxxxccc]eeeee]ccc22cc	chr9:86300816-86301046(-)$1	230	30	68	10.7830
e!!ggggggg"""a[annnnna]a333ggggggg]eee	chr13:108862560-108862790(-)$1	230	188	226	15.9248
iiiiiiiii^^^^^^^^^^^^^^^^^^^^iiiiiiiii	chr4:89381196-89381422(+)$1	226	96	134	10.5594
eee"""ggggggg[cccmmmmccc]ggggggg]eeeee	chr7:154738162-154738387(-)$1	225	178	216	11.6332
eeee"""ccc[bb[bbnnnnnbb]bb]ccc]eeeeedd	chr14:102550167-102550391(-)$1	224	20	58	11.5434
eeeebb"""gggggggnnnnnggggggg333bb]eeee	chr9:79971671-79971892(-)$1	221	130	168	12.1107
[ggggggg!!gggggggmmmmggggggg22ggggggg]	chr2:32734721-32734946(+)$1	225	49	87	11.4028
cc[ccccccbbddddoooooodddd22bb22ccc]ccc	chrX:117530919-117531146(+)$1	227	61	99	11.6946
ee!!ggggggg!!cccnnnnnccc]gggggggeeeee:	chr10:93024110-93024340(+)$1	230	3	41	13.7336
f!!cccccc"""cccooooooccc333ccc]ccc>>>>	chr8:125498101-125498323(+)$1	222	70	108	15.4153
ddd$$$$$ccc!!cccnnnnnccc4444ccc4444ddd	chr11:122930305-122930526(-)$1	221	166	204	14.2040
eee!!ccc[cccacccooooooccc22a]ccc]ccc>>	chr17:1584135-1584365(-)$1	230	120	158	13.8244
bb!!ccc!!bb[bb[ccclllccc]bb]bb]cccbb]g	chr5:156746765-156746985(-)$1	220	146	184	11.4303
d[ccc!!eeeee[cccnnnnnccc]eeeee22cccddd	chr13:41303495-41303725(-)$1	230	116	154	13.1573
ggggggg[bb"""cccbblllbb]cccbb22ggggggg	chr19:20989811-20990041(+)$1	230	45	83	12.0400
iccc[a$$$$$bb[bboooooobb]bb22a]ccc]iii	chr18:46448047-46448269(-)$1	222	174	212	12.3685
""bb"""iiiiiiiiinnnnniiiiiiiii333bb333	chr6:18258096-18258320(-)$1	224	57	95	13.6242
ee!!ffffffa!!cccmmmmccc22a]ffffff4444e	chr16:2256422-2256652(+)$1	230	36	74	11.2858
e[bb[ccc[bb!!ddddnnnnndddd22bb]ccc333b	chr4:183720778-183721001(+)$1	223	91	129	12.3495
ffff[ccc####ddddllldddd4444cccffffffdd	chr10:43882292-43882522(-)$1	230	24	62	11.5268

#otherMatches

#Seq PSSM
AUUCUAUGCAGAUCCUGGGGCCGAGGUCAAAAUUGAGA	chrX:53659381-53659600(-)$1	219	119	157	12.5977
UACACGACAGGUGAGCGUGGCUCAGCAAUGAGAGACUG	chr11:47446069-47446299(-)$1	230	132	170	11.0324
CACCAGAGCAUGUCAUACAAGGUAAGUCGUGUGUGAGA	chr1:93812236-93812459(+)$1	223	165	203	11.5326
CAAGAUGAAAGCAGCAGAAAAUGCUAAGAUGUUUUUUC	chr2:113330044-113330274(+)$1	230	47	85	12.3506
CAGGAUUCAACUUUUAACACUACAUCAAAUGGAAUUUU	chr11:32953336-32953562(+)$1	226	95	133	9.8620
AGGGCGAGGGUGCAGGGCGGGCUCUGAUUCCUUGUCUU	chr11:64878077-64878302(+)$1	225	39	77	12.8024
CAAUUCUGCAUUCCUAAAGUUAGCUGAUGUUUUCAGAG	chr1:212194384-212194604(-)$1	220	138	176	10.8096
GUUUUGUUCUCAGAGGCAAACCCUUGAAAUGAGGACAG	chr20:58519665-58519891(+)$1	226	166	204	15.0625
ACAGGUCAACAAGAACAAAAAAUGGCGGGAACUUGCAA	chr1:27097519-27097749(+)$1	230	86	124	12.4404
AGAUGUAUGUUUGAUCAUCCAGAUGCAGAUAAAACACU	chr14:95562165-95562389(-)$1	224	71	109	11.9194
UAACCUUUUAGUAAUCUUGAAAAGAAAAUGGUGGAAGU	chr11:107682300-107682524(-)$1	224	11	49	11.3365
UAUCCUGACAGGUGAGUCUCUUUUUCCUUAUUUAAUGA	chr11:61080903-61081128(-)$1	225	147	185	15.2868
AAGAAGUCCAGAAUAUUCCCUGUAAGUCUUAACACUUC	chr9:32558821-32559051(-)$1	230	123	161	14.6964
CUGCCCUCCUUCAAGAUUGACUUCUCGGAAUGGAAGGA	chr16:4707169-4707394(+)$1	225	150	188	13.5394
CUAAAAGCAGAAGAGUUUAUUCUUGCAAUGCACCUUAC	chr2:24524756-24524980(-)$1	224	40	78	15.7610
CAAACACAGGUAAUUUAUAUAAAAAGCUCUAAUUAUUU	chr2:55894043-55894273(-)$1	230	139	177	11.1290
UGACCACGUGCCCGCCCUCGUGCGCUAUCAUGUGGGCA	chr9:130511544-130511766(-)$1	222	7	45	13.4788
ACCUGUUCCAAGUCGCAGUGAGGUAGCCAAGGAACAGA	chr2:149541172-149541402(+)$1	230	73	111	13.3991
UAUUUCUUUCCUCAGAAAAAAUCUCGCAAGAAGAUGUG	chr1:28148707-28148934(+)$1	227	19	57	17.3666
AGAGUCACCAGAAAUUAAAGGAGUCCCUGAUGACACCU	chr14:23745776-23746002(-)$1	226	152	190	14.1805
GACACCCAUUUUAGUGAUCACCUCUAUUGGUGUGAACA	chr3:179051425-179051646(+)$1	221	167	205	13.4691
GGAGGUGGAACUAGCACAUCAGGUCUCACUUCCCUUUG	chr19:52719167-52719391(+)$1	224	30	68	10.6498
GAGAGUGACAUCUUCUCUAUCAGGGAAGUUAGCUUUCA	chr17:5336527-5336750(-)$1	223	36	74	13.2263
GAUCAUUGUGUAUAGCUCCUAUAAAUUUAUUGUGGUUU	chr5:87502862-87503092(-)$1	230	34	72	11.2627
UAUUCUUUCCUUAGUGAGAAGCCACAGAAAUGGAGAGU	chr15:66832414-66832644(+)$1	230	7	45	15.6027
CAGAGACAGGUGAGCUUUCUUGAGGCAGAUUUGUUUUU	chr15:77346449-77346679(-)$1	230	151	189	13.6319
CAUGAGGUGCAUAUCUAUGAAAAGAGCGGUGCCAAAUG	chr7:98984214-98984444(+)$1	230	116	154	13.0582
GUGUGCAAAACUCCGUACAUUGCUAUUUUGCCACACUG	chr17:62496741-62496964(-)$1	223	22	60	12.6219
GGGGUGAACUGGGUGAGGCUUUCAUCGUUUUUGCCACU	chr20:34242929-34243159(-)$1	230	24	62	12.4780
CAUGUUGUCUCUACAAAUGCUUGAGUUGAUUACAAGAC	chr14:95574155-95574385(-)$1	230	26	64	11.9447
UCGCCGUCGCUGCUCGCCUCUUGGCAGCGCAACGAACU	chr3:143691151-143691371(+)$1	220	116	154	11.1730
UUUUAAUUUAUUUUUGACCUUUCAUAACAGGAUUGACA	chr5:43655861-43656091(+)$1	230	50	88	12.9905
UGAACUAGGAGCCGAAGCUAAUUUUAUGCUGAAAGUUC	chr7:20418616-20418835(+)$1	219	49	87	16.1272
AUAUUUGCUGGAAAAAUUUUGAAAGAUCAAGAUACCUU	chr9:86300816-86301046(-)$1	230	30	68	10.7830
ACACAAACUUUCAUGCAAAAGGGAACUAAGUUUGAUAU	chr13:108862560-108862790(-)$1	230	188	226	15.9248
GAGAUUACCAUUCUCUUGCACUCUCAAAAGGUAAUUUU	chr4:89381196-89381422(+)$1	226	96	134	10.5594
GCUUACCUGUGUGAGUAUGUGUGCACGCACAGCAGUGG	chr7:154738162-154738387(-)$1	225	178	216	11.6332
CCAGUUUUGUCCUUGGAAUGACUCAGUGCAUUUGGUUU	chr14:102550167-102550391(-)$1	224	20	58	11.5434
AAUAACCUUAUCUUCUGAAGGAGAAGAUUCAGUAUAUU	chr9:79971671-79971892(-)$1	221	130	168	12.1107
UAUAUUGAUCAUACAAGUCAUUUUGUAUUUUCAGUAUU	chr2:32734721-32734946(+)$1	225	49	87	11.4028
AUACCUUUGAGUCUUGCAGAAGAGAAACUACCAACAGG	chrX:117530919-117531146(+)$1	227	61	99	11.6946
AAAUUUCAAAAAAUAUGCAAAAUACUUUUGAAUUCAAC	chr10:93024110-93024340(+)$1	230	3	41	13.7336
GGUGAAUUAUUAUGCUUCUUUGCACAUUGACUUCUAUG	chr8:125498101-125498323(+)$1	222	70	108	15.4153
UGGACCCAGUAGAGAAAGCCCUUCGAGAUGCCAAACUA	chr11:122930305-122930526(-)$1	221	166	204	14.2040
CCACACCAUGUCCACCUCACCUGGUAAGAGACCUGGAA	chr17:1584135-1584365(-)$1	230	120	158	13.8244
UGAUGGCCUGGUUGAAGACGCUCUCCAUCCUGCCCAUG	chr5:156746765-156746985(-)$1	220	146	184	11.4303
UAUCUUAGUGUUAAACAGAAGGUUGAACACAUAGAGUG	chr13:41303495-41303725(-)$1	230	116	154	13.1573
AAGAAUGUGGCAAGGCCUUUAAGUGCUCCUCUAUUCUU	chr19:20989811-20990041(+)$1	230	45	83	12.0400
GUGCAGAAGGUGCGGAGCAAAAUCGGCUGCGGCAUCCA	chr18:46448047-46448269(-)$1	222	174	212	12.3685
GGAUACAUUUUUUUCUAAGUAAGAAGAAAACCGAUGAA	chr6:18258096-18258320(-)$1	224	57	95	13.6242
CUCAGCACAGCCAAGCUUCAGUUCAGCCUGUGUCCCUA	chr16:2256422-2256652(+)$1	230	36	74	11.2858
UCGCCACGGUCAAGUCGCUGAUCGGCAAGGGCGUCAUG	chr4:183720778-183721001(+)$1	223	91	129	12.3495
AGUGAGUUCACAGUGCAGAGCACCACAGGCCACUGUGU	chr10:43882292-43882522(-)$1	230	24	62	11.5268

#DB
.(((.((...((.(((.(...).)))))...)).))).	chrX:53659381-53659600(-)$1	1	119	157	12.5977
((..(..(((.(((((...))))).)..))...)..))	chr11:47446069-47446299(-)$1	1	132	170	11.0324
(((....(((((.(.(((...))).).)))))))))))	chr1:93812236-93812459(+)$1	1	165	203	11.5326
..(((.((((((((((.....))).....)))))))))	chr2:113330044-113330274(+)$1	1	47	85	12.3506
.(((((((.......................)))))))	chr11:32953336-32953562(+)$1	1	95	133	9.8620
((((((((((..(((((....)))))..))))))))))	chr11:64878077-64878302(+)$1	1	39	77	12.8024
((((((((((((.(((....)))..))))....)))))	chr1:212194384-212194604(-)$1	1	138	176	10.8096
))((((((((((((((.....))))....)))))))))	chr20:58519665-58519891(+)$1	1	166	204	15.0625
.(((((...(..(..((.....)).)..).))))).))	chr1:27097519-27097749(+)$1	1	86	124	12.4404
((.(((.(((((((((.....))).))))))..)))))	chr14:95562165-95562389(-)$1	1	71	109	11.9194
(...((((((.((.((((...))))...)).)))))).	chr11:107682300-107682524(-)$1	1	11	49	11.3365
(.((.(((.(((.(((.....))).)))...)))..))	chr11:61080903-61081128(-)$1	1	147	185	15.2868
.((((((..(((.(((.....)))..)))....)))))	chr9:32558821-32559051(-)$1	1	123	161	14.6964
...((.((((((.(((......)))..))).))).)).	chr16:4707169-4707394(+)$1	1	150	188	13.5394
.(((..(((...(((......)))....)))...))))	chr2:24524756-24524980(-)$1	1	40	78	15.7610
.)))))(((((((((...............))))))))	chr2:55894043-55894273(-)$1	1	139	177	11.1290
((((((((((..(((......)))....)))))))(((	chr9:130511544-130511766(-)$1	1	7	45	13.4788
..(((((((..((.((......)).))...))))))).	chr2:149541172-149541402(+)$1	1	73	111	13.3991
((((((((.(...(((.....))).).))).)))))))	chr1:28148707-28148934(+)$1	1	19	57	17.3666
...((((.(((..(((.....)))..))).))))...)	chr14:23745776-23746002(-)$1	1	152	190	14.1805
.(((((.....(((.(.....).)))..)))))...))	chr3:179051425-179051646(+)$1	1	167	205	13.4691
..((((((.(((.........))).)))))))))))))	chr19:52719167-52719391(+)$1	1	30	68	10.6498
((((((.....(((((((...)))))))...)))))))	chr17:5336527-5336750(-)$1	1	36	74	13.2263
((((((.((((((((...)))))....))).)))))))	chr5:87502862-87503092(-)$1	1	34	72	11.2627
((((((((..((.(((......)))..))..)))))))	chr15:66832414-66832644(+)$1	1	7	45	15.6027
(((((((((((..(((((...)))))..))))))))))	chr15:77346449-77346679(-)$1	1	151	189	13.6319
(((..(((((...(((......)))...)))))..)))	chr7:98984214-98984444(+)$1	1	116	154	13.0582
((((((((((...((.....))...))))).)))))))	chr17:62496741-62496964(-)$1	1	22	60	12.6219
(.((((((...(((((.....)))))...)))))).))	chr20:34242929-34243159(-)$1	1	24	62	12.4780
(.(((.(((.((.(((....)))))..))).))).)).	chr14:95574155-95574385(-)$1	1	26	64	11.9447
(((.(((.((.(((.(((....)))))))).)))...)	chr3:143691151-143691371(+)$1	1	116	154	11.1730
..(((((((..((.(((....))).))..)))))))..	chr5:43655861-43656091(+)$1	1	50	88	12.9905
((((((...(((.(((.....)))...)))...)))))	chr7:20418616-20418835(+)$1	1	49	87	16.1272
((.(((...............))).))))).)))..))	chr9:86300816-86301046(-)$1	1	30	68	10.7830
(..(((((((...(.(.....).)...))))))).)))	chr13:108862560-108862790(-)$1	1	188	226	15.9248
(((((((((....................)))))))))	chr4:89381196-89381422(+)$1	1	96	134	10.5594
(((...(((((((.(((....))).))))))).)))))	chr7:154738162-154738387(-)$1	1	178	216	11.6332
((((...(((.((.((.....)).)).))).)))))))	chr14:102550167-102550391(-)$1	1	20	58	11.5434
((((((...(((((((.....)))))))...)).))))	chr9:79971671-79971892(-)$1	1	130	168	12.1107
.(((((((..(((((((....)))))))..))))))).	chr2:32734721-32734946(+)$1	1	49	87	11.4028
((.((((((((((((......))))..))..))).)))	chrX:117530919-117531146(+)$1	1	61	99	11.6946
((..(((((((..(((.....))).)))))))))))).	chr10:93024110-93024340(+)$1	1	3	41	13.7336
(..((((((...(((......)))...))).)))....	chr8:125498101-125498323(+)$1	1	70	108	15.4153
(((.....(((..(((.....)))....)))....)))	chr11:122930305-122930526(-)$1	1	166	204	14.2040
(((..(((.(((((((......)))..).))).)))..	chr17:1584135-1584365(-)$1	1	120	158	13.8244
((..(((..((.((.(((...))).)).)).))))).)	chr5:156746765-156746985(-)$1	1	146	184	11.4303
(.(((..(((((.(((.....))).)))))..))))))	chr13:41303495-41303725(-)$1	1	116	154	13.1573
(((((((.((...(((((...)).)))))..)))))))	chr19:20989811-20990041(+)$1	1	45	83	12.0400
((((.(.....((.((......)).))..).))).)))	chr18:46448047-46448269(-)$1	1	174	212	12.3685
..((...(((((((((.....)))))))))...))...	chr6:18258096-18258320(-)$1	1	57	95	13.6242
((..(((((((..(((....)))..).))))))....)	chr16:2256422-2256652(+)$1	1	36	74	11.2858
(.((.(((.((..((((.....))))..)).)))...)	chr4:183720778-183721001(+)$1	1	91	129	12.3495
((((.(((....((((...))))....)))))))))((	chr10:43882292-43882522(-)$1	1	24	62	11.5268

#PSSM
e : 0.16	" : 0.11	f : 0.11	= : 0.09	# : 0.07	[ : 0.07	c : 0.07	b : 0.07	i : 0.07	d : 0.05	g : 0.03	2 : 0.01	G : 0.01	
e : 0.18	c : 0.11	f : 0.09	= : 0.09	[ : 0.09	# : 0.07	g : 0.07	" : 0.07	i : 0.05	b : 0.03	d : 0.03	! : 0.03	G : 0.01	
c : 0.13	e : 0.13	! : 0.11	f : 0.11	g : 0.11	= : 0.11	[ : 0.05	b : 0.05	i : 0.05	# : 0.03	d : 0.03	" : 0.01	G : 0.01	
c : 0.18	g : 0.15	! : 0.11	= : 0.11	e : 0.09	f : 0.09	b : 0.07	i : 0.05	" : 0.03	# : 0.01	d : 0.01	[ : 0.01	$ : 0.01	
c : 0.16	g : 0.16	= : 0.11	f : 0.11	[ : 0.09	e : 0.05	! : 0.05	i : 0.05	" : 0.05	b : 0.03	a : 0.01	# : 0.01	d : 0.01	$ : 0.01	
c : 0.20	g : 0.16	f : 0.11	= : 0.09	e : 0.09	! : 0.05	[ : 0.05	" : 0.05	b : 0.03	i : 0.03	# : 0.01	d : 0.01	$ : 0.01	a : 0.01	
c : 0.22	g : 0.20	" : 0.09	f : 0.09	= : 0.07	$ : 0.07	! : 0.03	[ : 0.03	i : 0.03	e : 0.03	b : 0.01	# : 0.01	d : 0.01	x : 0.01	
c : 0.22	g : 0.18	f : 0.09	" : 0.07	e : 0.07	= : 0.07	$ : 0.07	i : 0.05	[ : 0.05	! : 0.03	b : 0.01	x : 0.01	
c : 0.16	g : 0.13	" : 0.09	[ : 0.09	e : 0.07	! : 0.07	b : 0.05	= : 0.05	f : 0.05	i : 0.05	$ : 0.05	^ : 0.01	d : 0.01	x : 0.01	# : 0.01	
c : 0.18	g : 0.11	b : 0.09	" : 0.07	e : 0.07	! : 0.07	a : 0.05	= : 0.05	f : 0.05	$ : 0.05	^ : 0.03	i : 0.03	d : 0.01	[ : 0.01	x : 0.01	# : 0.01	
c : 0.15	" : 0.15	b : 0.11	g : 0.09	! : 0.09	[ : 0.07	e : 0.05	$ : 0.05	^ : 0.03	= : 0.03	i : 0.03	d : 0.01	f : 0.01	x : 0.01	a : 0.01	# : 0.01	
! : 0.16	b : 0.15	c : 0.15	" : 0.13	e : 0.09	g : 0.09	^ : 0.03	d : 0.03	i : 0.03	= : 0.01	f : 0.01	x : 0.01	[ : 0.01	# : 0.01	
[ : 0.18	b : 0.11	! : 0.11	g : 0.09	c : 0.09	" : 0.09	e : 0.07	d : 0.05	^ : 0.03	a : 0.03	i : 0.03	f : 0.01	r : 0.01	x : 0.01	
c : 0.45	[ : 0.11	e : 0.09	d : 0.07	g : 0.05	a : 0.03	^ : 0.03	i : 0.03	b : 0.03	! : 0.01	r : 0.01	x : 0.01	
c : 0.45	e : 0.09	[ : 0.09	d : 0.09	b : 0.07	g : 0.05	^ : 0.03	i : 0.03	! : 0.01	r : 0.01	x : 0.01	
c : 0.45	e : 0.07	d : 0.07	b : 0.07	o : 0.07	g : 0.05	^ : 0.03	x : 0.03	a : 0.03	r : 0.01	l : 0.01	n : 0.01	i : 0.01	
n : 0.33	o : 0.18	c : 0.09	l : 0.05	m : 0.05	^ : 0.03	e : 0.03	b : 0.03	d : 0.03	x : 0.03	g : 0.03	[ : 0.01	r : 0.01	
n : 0.37	o : 0.18	m : 0.13	l : 0.05	c : 0.05	^ : 0.03	x : 0.03	a : 0.01	d : 0.01	r : 0.01	g : 0.01	e : 0.01	b : 0.01	
n : 0.37	o : 0.18	l : 0.16	m : 0.15	^ : 0.03	x : 0.03	r : 0.01	e : 0.01	
n : 0.37	o : 0.18	m : 0.15	l : 0.13	e : 0.03	^ : 0.03	x : 0.03	r : 0.01	d : 0.01	
n : 0.35	o : 0.18	l : 0.13	m : 0.09	c : 0.05	e : 0.03	^ : 0.03	x : 0.03	r : 0.01	b : 0.01	d : 0.01	
c : 0.41	o : 0.11	e : 0.09	d : 0.07	a : 0.05	g : 0.05	b : 0.05	^ : 0.03	n : 0.03	x : 0.01	m : 0.01	i : 0.01	
c : 0.50	e : 0.09	d : 0.09	b : 0.09	] : 0.05	g : 0.05	^ : 0.03	x : 0.01	3 : 0.01	i : 0.01	
c : 0.49	e : 0.07	d : 0.07	b : 0.07	g : 0.05	^ : 0.03	2 : 0.03	4 : 0.03	] : 0.03	x : 0.01	3 : 0.01	a : 0.01	i : 0.01	
] : 0.28	c : 0.15	4 : 0.09	2 : 0.07	d : 0.07	3 : 0.07	e : 0.05	g : 0.05	^ : 0.03	b : 0.03	5 : 0.01	x : 0.01	i : 0.01	
2 : 0.13	e : 0.11	4 : 0.11	c : 0.09	a : 0.09	3 : 0.09	b : 0.09	g : 0.09	^ : 0.03	d : 0.03	f : 0.03	5 : 0.01	x : 0.01	i : 0.01	
2 : 0.20	4 : 0.11	3 : 0.11	b : 0.09	c : 0.09	g : 0.09	] : 0.07	e : 0.05	^ : 0.03	f : 0.03	5 : 0.01	d : 0.01	x : 0.01	i : 0.01	
c : 0.22	2 : 0.15	g : 0.11	b : 0.07	e : 0.07	4 : 0.07	3 : 0.07	f : 0.05	^ : 0.03	5 : 0.01	d : 0.01	x : 0.01	a : 0.01	] : 0.01	i : 0.01	
c : 0.22	b : 0.15	3 : 0.11	e : 0.11	g : 0.07	f : 0.05	2 : 0.05	^ : 0.03	= : 0.03	5 : 0.01	d : 0.01	4 : 0.01	a : 0.01	x : 0.01	] : 0.01	i : 0.01	
c : 0.20	e : 0.11	g : 0.11	3 : 0.09	b : 0.09	f : 0.07	2 : 0.07	= : 0.05	4 : 0.03	] : 0.03	i : 0.03	^ : 0.01	x : 0.01	a : 0.01	
] : 0.24	g : 0.15	3 : 0.13	f : 0.09	e : 0.07	2 : 0.07	= : 0.05	c : 0.05	4 : 0.03	i : 0.03	^ : 0.01	d : 0.01	
g : 0.20	c : 0.20	= : 0.11	e : 0.09	3 : 0.07	f : 0.07	i : 0.07	4 : 0.05	b : 0.03	2 : 0.03	d : 0.01	
c : 0.20	g : 0.16	= : 0.11	f : 0.09	e : 0.09	3 : 0.07	i : 0.07	4 : 0.05	b : 0.03	] : 0.03	2 : 0.01	d : 0.01	
c : 0.24	g : 0.18	f : 0.11	= : 0.11	e : 0.07	i : 0.07	] : 0.03	3 : 0.03	4 : 0.03	a : 0.01	d : 0.01	2 : 0.01	b : 0.01	
g : 0.16	f : 0.11	= : 0.11	c : 0.09	e : 0.09	] : 0.09	2 : 0.07	i : 0.07	3 : 0.07	4 : 0.03	b : 0.03	> : 0.01	
g : 0.15	f : 0.11	= : 0.11	c : 0.09	i : 0.09	3 : 0.09	e : 0.09	2 : 0.05	b : 0.05	d : 0.05	] : 0.03	> : 0.01	4 : 0.01	
g : 0.13	f : 0.11	= : 0.11	d : 0.11	c : 0.09	b : 0.09	i : 0.09	3 : 0.09	e : 0.07	> : 0.03	] : 0.01	4 : 0.01	
g : 0.11	= : 0.11	d : 0.11	i : 0.11	f : 0.09	c : 0.09	3 : 0.07	b : 0.07	e : 0.07	> : 0.03	5 : 0.01	2 : 0.01	4 : 0.01	] : 0.01	: : 0.01	

#score	679.4339320847808
#seq	53
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_UTR_m1_run1.txt

#BEAR
eeeeeeewwwwwwwwwwwwwweeeee:::	chr12:110477443-110477683(-)$1	240	170	199	20.5080
gggg[bbtttttttttttbb]ggggggg2	chr7:141361597-141361858(-)$1	261	109	138	22.9705
ggggggxxxxxxxxxxxxxxxgggggggf	chr13:31725033-31725272(-)$1	239	12	41	20.3452
iiicccwwwwwwwwwwwwwwccc]iiiii	chr17:48832300-48832579(+)$1	279	79	108	24.0271
ggg!!bbwwwwwwwwwwwwwwbb]ggggg	chr5:71501925-71502282(+)$1	357	26	55	22.9674
!!fffffftttttttttttffffff333c	chr17:73017160-73017434(+)$1	274	224	253	23.1238
eeeeebbwwwwwwwwwwwwwwbb]eeeee	chr10:103922292-103922567(+)$1	275	203	232	22.1124
eeeeeewwwwwwwwwwwwwweeeee]eee	chr6:4061913-4062150(+)$1	237	31	60	23.5159
gggggggvvvvvvvvvvvvvggggggg::	chr19:50129252-50129485(+)$1	233	1	30	22.9269
ffffffwwwwwwwwwwwwwwffffffeee	chr7:97481367-97481644(-)$1	277	210	239	22.9752
!!a!!ccctttttttttttccc22a4444	chr1:244870699-244871138(+)$1	439	83	112	22.9476
====yyyyyyyyyyyyyyyy=========	chr18:33572302-33572559(-)$1	257	20	49	23.3235
[eeeeexxxxxxxxxxxxxxxeeeee]ag	chr8:1951859-1952130(+)$1	271	193	222	20.2153
hhddddyyyyyyyyyyyyyyyydddd22h	chr7:99130373-99130607(+)$1	234	18	47	21.3861
d[cccwwwwwwwwwwwwwwccc]dddd44	chr3:182990907-182991182(+)$1	275	129	158	22.1257
[eeeeexxxxxxxxxxxxxxxeeeee22h	chr15:68585590-68585879(+)$1	289	61	90	20.0930
ggggggwwwwwwwwwwwwwwggggggg22	chr17:42475105-42475337(-)$1	232	19	48	24.5603
======wwwwwwwwwwwwww=========	chr6:150132368-150132605(+)$1	237	118	147	24.4773
cc[eeeeettttttttttteeeee]ccc:	chr7:157209571-157209834(+)$1	263	102	131	22.1105
hhhhccctttttttttttccc]hhhhhhh	chr1:25167474-25167765(+)$1	291	112	141	21.0497
cc[eeeeettttttttttteeeeeccc33	chr13:21721784-21722027(+)$1	243	162	191	23.3845
"""eeeeettttttttttteeeee]hhhh	chr22:32353157-32353414(+)$1	257	84	113	22.2802
fff[bbuuuuuuuuuuuubb]ffffff]b	chr1:224345043-224345266(+)$1	223	92	121	22.2832
ggcccbbvvvvvvvvvvvvvbb]ccc]gg	chr17:30701609-30701927(+)$1	318	45	74	23.2538
ggggggwwwwwwwwwwwwwwggggggg]b	chr2:73471025-73471258(+)$1	233	99	128	24.4020
!!ddddvvvvvvvvvvvvvdddd22gggg	chr3:137965093-137965373(+)$1	280	35	64	22.7180
$eeeeexxxxxxxxxxxxxxxeeeee22e	chr14:99864183-99864412(-)$1	229	18	47	19.9099
fffff[auuuuuuuuuuuua]ffffff22	chr14:61179646-61179919(-)$1	273	197	226	24.7603
:eeeeeyyyyyyyyyyyyyyyyeeeee::	chr12:56366157-56366449(+)$1	292	208	237	20.1555
gggggyyyyyyyyyyyyyyyygggggggb	chr5:37289706-37289965(-)$1	259	129	158	23.4548
hhhhhhwwwwwwwwwwwwwwhhhhhhhh:	chr19:58199815-58200114(+)$1	299	156	185	20.6825
"fffffftttttttttttffffff22ccc	chrX:21890052-21890281(+)$1	229	139	168	21.6856
"ffffffvvvvvvvvvvvvvffffff555	chr21:34728692-34728923(+)$1	231	8	37	21.8163
ee[eeeeettttttttttteeeee333ee	chr17:40723801-40724055(+)$1	254	51	80	22.9673
!gggggggtttttttttttggggggg22f	chr15:45007752-45007990(+)$1	238	188	217	23.2793
e[bb[ccctttttttttttcccbbeeeee	chrX:10417268-10417506(-)$1	238	179	208	21.4915
gggggggvvvvvvvvvvvvvggggggg33	chr12:56388293-56388544(+)$1	251	69	98	25.1132
"eeeeeyyyyyyyyyyyyyyyyeeeee]c	chr4:183815617-183815858(-)$1	241	114	143	23.1758
ddddyyyyyyyyyyyyyyyyddddeeeee	chr17:78441652-78441971(-)$1	319	97	126	20.9915
[ffffffuuuuuuuuuuuuffffff]fff	chr2:206867332-206867614(-)$1	282	228	257	23.7173
bb[ddddtttttttttttdddd]bb]ggg	chr12:53582977-53583261(+)$1	284	224	253	20.6663
bb[eeeeettttttttttteeeee]bb66	chr18:29710348-29710650(+)$1	302	112	141	21.2904
d"""cccuuuuuuuuuuuuccc4444ddd	chr2:179296845-179297078(-)$1	233	57	86	23.0634
cc[dddduuuuuuuuuuuudddd]ccc44	chr9:125621251-125621481(-)$1	230	17	46	23.6372
gggggggvvvvvvvvvvvvvggggggg22	chr10:75542116-75542350(+)$1	234	124	153	24.7874
fffff[auuuuuuuuuuuua]ffffff33	chr1:20234702-20235130(+)$1	428	328	357	25.0861
=====bbtttttttttttbb]========	chr6:89874053-89874295(+)$1	242	49	78	23.0698
f[eeeeevvvvvvvvvvvvveeeee333f	chr3:58303724-58303984(+)$1	260	81	110	24.6420
=====bbuuuuuuuuuuuubb]=======	chr17:58740885-58741163(+)$1	278	223	252	24.4843
hhhhhhwwwwwwwwwwwwwwhhhhhhhh:	chr22:39258148-39258380(-)$1	232	174	203	20.6825
!ffffffvvvvvvvvvvvvvffffff22e	chr2:27016914-27017172(+)$1	258	81	110	23.8966
========ttttttttttt==========	chr21:27096760-27097010(-)$1	250	75	104	23.4625
ffff!!attttttttttta22ffffff22	chr1:198289679-198289933(+)$1	254	87	116	22.8803
d"""ddddtttttttttttdddd22dddd	chr5:133533207-133533475(-)$1	268	42	71	20.3639
[eeeeewwwwwwwwwwwwwweeeee333c	chr1:145500845-145501148(+)$1	303	172	201	24.6128
%fffffftttttttttttffffff4444d	chr8:38068328-38068554(+)$1	226	80	109	21.3464
""eeeeeuuuuuuuuuuuueeeee4444h	chrX:123234686-123234925(+)$1	239	96	125	24.4429
ffff!!awwwwwwwwwwwwwwa22fffff	chr4:41957062-41957285(+)$1	223	146	175	22.3507
hhhh[avvvvvvvvvvvvva]hhhhhhhh	chr6:7281617-7281864(-)$1	247	135	164	22.2746
bgggggggtttttttttttggggggg]bb	chr5:81571515-81571755(-)$1	240	64	93	22.3830

#otherMatches

#Seq PSSM
UGGGCUUCCCUUACCCCACAAGAGCCAGU	chr12:110477443-110477683(-)$1	240	170	199	20.5080
GUCUGAACCUUCCUCUUCUUGGGAUGAAU	chr7:141361597-141361858(-)$1	261	109	138	22.9705
UUGUGCAGAAUUUAAAACUAAGUACAAGU	chr13:31725033-31725272(-)$1	239	12	41	20.3452
UGAAACAAAAAACACUUGAAGUUAUUAUG	chr17:48832300-48832579(+)$1	279	79	108	24.0271
AUUAACUGAAGCAAAUACCAAAGCAGUUG	chr5:71501925-71502282(+)$1	357	26	55	22.9674
UCAGAAAACAAUUCCUACCUUUUCUCUCA	chr17:73017160-73017434(+)$1	274	224	253	23.1238
CCCUCCUUCCCUCAAAACCCUAGAGAGGG	chr10:103922292-103922567(+)$1	275	203	232	22.1124
CUUUACCUUUUAUUUCUUUUGUAAAUGAA	chr6:4061913-4062150(+)$1	237	31	60	23.5159
GGGGGACCCCUUCCCCCCAAGUCCCCCCU	chr19:50129252-50129485(+)$1	233	1	30	22.9269
GCUGUAGUCAUUUAUGUUCAUGCAGUCUC	chr7:97481367-97481644(-)$1	277	210	239	22.9752
GAAGAAAGGAAUAUAUGAACUUAAUGAGA	chr1:244870699-244871138(+)$1	439	83	112	22.9476
GCAGAUGAAAGUCUAGAGAACUGUUCCUU	chr18:33572302-33572559(-)$1	257	20	49	23.3235
UCUAUCUAAAAAGCAAUCUUUGAUAGUCC	chr8:1951859-1952130(+)$1	271	193	222	20.2153
AGCAUUAACCCCUUUGAAAAGAAAUGGAC	chr7:99130373-99130607(+)$1	234	18	47	21.3861
UUGCAUCUUUUUUCCAUAUUGUUAAUUUU	chr3:182990907-182991182(+)$1	275	129	158	22.1257
uuauuuaaaCAUCAAAACUUAAAAUAUCA	chr15:68585590-68585879(+)$1	289	61	90	20.0930
AGCAUGCCAUCCUACAACAUCAUGCUGCC	chr17:42475105-42475337(-)$1	232	19	48	24.5603
AGCUGUGUCCUAGUUCUUGAACAGUUUAU	chr6:150132368-150132605(+)$1	237	118	147	24.4773
CAUGAUGUAUUGCUUCUUCACGUUUUGUU	chr7:157209571-157209834(+)$1	263	102	131	22.1105
AAUAUACACUCCUAAGCAGUAUUAUUUUA	chr1:25167474-25167765(+)$1	291	112	141	21.0497
GCUGCGGCAAGUUGAAGAAGCUGUGUUGG	chr13:21721784-21722027(+)$1	243	162	191	23.3845
ACAGAGAGACAACUUGCUCCUUUCCAUCA	chr22:32353157-32353414(+)$1	257	84	113	22.2802
GCAGCAGGUUAAAACAAAUGGUGCUGGCG	chr1:224345043-224345266(+)$1	223	92	121	22.2832
GAGCCCUGUAAAGGUGGGAAGGUGGUGUC	chr17:30701609-30701927(+)$1	318	45	74	23.2538
GCAGUUAACAAGAUCAAAGAGAUUGCUGU	chr2:73471025-73471258(+)$1	233	99	128	24.4020
UUUCAGUUAACAAGAUACUUUGACUUGAA	chr3:137965093-137965373(+)$1	280	35	64	22.7180
uaGUGAUUUCUAAAGAUUUGUUUACUUUU	chr14:99864183-99864412(-)$1	229	18	47	19.9099
CUUUUACUCCAUGGGCAUUGAAAAGGUUA	chr14:61179646-61179919(-)$1	273	197	226	24.7603
UUGGCUUUUUUUUUUUUUUUUUGGUCAUA	chr12:56366157-56366449(+)$1	292	208	237	20.1555
GUUGUUAUAUAUACUCAGCUCACAACAUU	chr5:37289706-37289965(-)$1	259	129	158	23.4548
CUUGGGGAAAUUAUUAAUAGCCCAAGCAU	chr19:58199815-58200114(+)$1	299	156	185	20.6825
CCAUCUUCCAAAACUUUUAAGAUGACAGA	chrX:21890052-21890281(+)$1	229	139	168	21.6856
AGUAGCUUACCCUAGAAAACAGCUGCAAA	chr21:34728692-34728923(+)$1	231	8	37	21.8163
AGCCUUCCCCCCACUCCAUGGAAGUCCUU	chr17:40723801-40724055(+)$1	254	51	80	22.9673
UGAGUAGUCAUAUCAUAAAGCUGCUUUGA	chr15:45007752-45007990(+)$1	238	188	217	23.2793
CAUGAGUGUAAUGAAAUCUCACCAGAAGU	chrX:10417268-10417506(-)$1	238	179	208	21.4915
UGUUUUUGUUUUGCUUCUGAGAAAGCAUU	chr12:56388293-56388544(+)$1	251	69	98	25.1132
CUGAAUGCCAUCAUGAACAAAAAUUCGAC	chr4:183815617-183815858(-)$1	241	114	143	23.1758
CUGAAUAAUACAUGCCUCUCUCAGGUAAG	chr17:78441652-78441971(-)$1	319	97	126	20.9915
UGAAAGCUUUUCUUUCUCUGCUUUUUAAA	chr2:206867332-206867614(-)$1	282	228	257	23.7173
UACCAGCAAUGAUUCCUGGCUGUUACCUA	chr12:53582977-53583261(+)$1	284	224	253	20.6663
AGAGUGGAUUUGCUGACAUUCCAUACUAA	chr18:29710348-29710650(+)$1	302	112	141	21.2904
UAUUGGACAUUAAUCGUCAUCCUUGAAUG	chr2:179296845-179297078(-)$1	233	57	86	23.0634
AAGGGCUGCCUUAGAUUUAAGCCAUUAUA	chr9:125621251-125621481(-)$1	230	17	46	23.6372
GGGGAGAUAGAAGUAAUGAUUCUCCCUGC	chr10:75542116-75542350(+)$1	234	124	153	24.7874
UUCUGGAAUUCUGAUAGUGUGUAGAGCAG	chr1:20234702-20235130(+)$1	428	328	357	25.0861
GCUAAGAUUAACAUAAUUUCUUUGGUUUU	chr6:89874053-89874295(+)$1	242	49	78	23.0698
GGCUGGGUUAAAGUUAUGGUUCCAGAAGC	chr3:58303724-58303984(+)$1	260	81	110	24.6420
AAGUUGCUGUAAAAUUUGUGUAAAUUUGU	chr17:58740885-58741163(+)$1	278	223	252	24.4843
CCUCCGCCCCCUGCAAUCUUUGGAGGAGU	chr22:39258148-39258380(-)$1	232	174	203	20.6825
UUAUUAUUUUAGCUCUUUCUGUAAUAUUU	chr2:27016914-27017172(+)$1	258	81	110	23.8966
UUAAUCUGGUAAUUUGUCACGGAUUAGUU	chr21:27096760-27097010(-)$1	250	75	104	23.4625
GCCACUCUGUAUGCAUAUGUUUGGUCUUG	chr1:198289679-198289933(+)$1	254	87	116	22.8803
UGAACCAUAUAUCGACCUAAUGGAAAUGG	chr5:133533207-133533475(-)$1	268	42	71	20.3639
CAAUUGGACUUCCCACUUAACAAUUAUAC	chr1:145500845-145501148(+)$1	303	172	201	24.6128
UGUCACAUUUUUGUACAUUGUGACUGCUU	chr8:38068328-38068554(+)$1	226	80	109	21.3464
UAUGAAUUCUCUUACAUUUAUUUACUGGU	chrX:123234686-123234925(+)$1	239	96	125	24.4429
AUCUGACUUAAAAGGUUAAAUGGAAGGUU	chr4:41957062-41957285(+)$1	223	146	175	22.3507
GUUUUCUAUUUGAGUGCUUGCAAACUCAA	chr6:7281617-7281864(-)$1	247	135	164	22.2746
CAUCCUGUGGAAUAAGAAAAUGGGAUAGA	chr5:81571515-81571755(-)$1	240	64	93	22.3830

#DB
))(((((..............)))))...	chr12:110477443-110477683(-)$1	1	170	199	20.5080
((((.((...........)).))))))).	chr7:141361597-141361858(-)$1	1	109	138	22.9705
((((((...............)))))))(	chr13:31725033-31725272(-)$1	1	12	41	20.3452
((((((..............))).)))))	chr17:48832300-48832579(+)$1	1	79	108	24.0271
(((..((..............)).)))))	chr5:71501925-71502282(+)$1	1	26	55	22.9674
..((((((...........))))))...)	chr17:73017160-73017434(+)$1	1	224	253	23.1238
(((((((..............)).)))))	chr10:103922292-103922567(+)$1	1	203	232	22.1124
((((((..............))))).)))	chr6:4061913-4062150(+)$1	1	31	60	23.5159
(((((((.............)))))))..	chr19:50129252-50129485(+)$1	1	1	30	22.9269
((((((..............))))))(((	chr7:97481367-97481644(-)$1	1	210	239	22.9752
..(..(((...........)))..)....	chr1:244870699-244871138(+)$1	1	83	112	22.9476
((((................)))))))))	chr18:33572302-33572559(-)$1	1	20	49	23.3235
.(((((...............))))).))	chr8:1951859-1952130(+)$1	1	193	222	20.2153
((((((................))))..)	chr7:99130373-99130607(+)$1	1	18	47	21.3861
(.(((..............))).))))..	chr3:182990907-182991182(+)$1	1	129	158	22.1257
.(((((...............)))))..)	chr15:68585590-68585879(+)$1	1	61	90	20.0930
((((((..............)))))))..	chr17:42475105-42475337(-)$1	1	19	48	24.5603
((((((..............)))))))))	chr6:150132368-150132605(+)$1	1	118	147	24.4773
((.(((((...........))))).))).	chr7:157209571-157209834(+)$1	1	102	131	22.1105
(((((((...........))).)))))))	chr1:25167474-25167765(+)$1	1	112	141	21.0497
((.(((((...........))))))))..	chr13:21721784-21722027(+)$1	1	162	191	23.3845
...(((((...........))))).))))	chr22:32353157-32353414(+)$1	1	84	113	22.2802
(((.((............)).)))))).)	chr1:224345043-224345266(+)$1	1	92	121	22.2832
(((((((.............)).))).))	chr17:30701609-30701927(+)$1	1	45	74	23.2538
((((((..............))))))).)	chr2:73471025-73471258(+)$1	1	99	128	24.4020
..((((.............))))..))))	chr3:137965093-137965373(+)$1	1	35	64	22.7180
.(((((...............)))))..)	chr14:99864183-99864412(-)$1	1	18	47	19.9099
(((((.(............).))))))..	chr14:61179646-61179919(-)$1	1	197	226	24.7603
.(((((................)))))..	chr12:56366157-56366449(+)$1	1	208	237	20.1555
(((((................))))))))	chr5:37289706-37289965(-)$1	1	129	158	23.4548
((((((..............)))))))).	chr19:58199815-58200114(+)$1	1	156	185	20.6825
.((((((...........))))))..)))	chrX:21890052-21890281(+)$1	1	139	168	21.6856
.((((((.............))))))...	chr21:34728692-34728923(+)$1	1	8	37	21.8163
((.(((((...........)))))...))	chr17:40723801-40724055(+)$1	1	51	80	22.9673
.(((((((...........)))))))..)	chr15:45007752-45007990(+)$1	1	188	217	23.2793
(.((.(((...........))))))))))	chrX:10417268-10417506(-)$1	1	179	208	21.4915
(((((((.............)))))))..	chr12:56388293-56388544(+)$1	1	69	98	25.1132
.(((((................))))).)	chr4:183815617-183815858(-)$1	1	114	143	23.1758
((((................)))))))))	chr17:78441652-78441971(-)$1	1	97	126	20.9915
.((((((............)))))).)))	chr2:206867332-206867614(-)$1	1	228	257	23.7173
((.((((...........)))).)).)))	chr12:53582977-53583261(+)$1	1	224	253	20.6663
((.(((((...........))))).))..	chr18:29710348-29710650(+)$1	1	112	141	21.2904
(...(((............)))....)))	chr2:179296845-179297078(-)$1	1	57	86	23.0634
((.((((............)))).)))..	chr9:125621251-125621481(-)$1	1	17	46	23.6372
(((((((.............)))))))..	chr10:75542116-75542350(+)$1	1	124	153	24.7874
(((((.(............).))))))..	chr1:20234702-20235130(+)$1	1	328	357	25.0861
(((((((...........)).))))))))	chr6:89874053-89874295(+)$1	1	49	78	23.0698
(.(((((.............)))))...)	chr3:58303724-58303984(+)$1	1	81	110	24.6420
(((((((............)).)))))))	chr17:58740885-58741163(+)$1	1	223	252	24.4843
((((((..............)))))))).	chr22:39258148-39258380(-)$1	1	174	203	20.6825
.((((((.............))))))..)	chr2:27016914-27017172(+)$1	1	81	110	23.8966
((((((((...........))))))))))	chr21:27096760-27097010(-)$1	1	75	104	23.4625
((((..(...........)..))))))..	chr1:198289679-198289933(+)$1	1	87	116	22.8803
(...((((...........))))..))))	chr5:133533207-133533475(-)$1	1	42	71	20.3639
.(((((..............)))))...)	chr1:145500845-145501148(+)$1	1	172	201	24.6128
.((((((...........))))))....)	chr8:38068328-38068554(+)$1	1	80	109	21.3464
..(((((............)))))....)	chrX:123234686-123234925(+)$1	1	96	125	24.4429
((((..(..............)..)))))	chr4:41957062-41957285(+)$1	1	146	175	22.3507
((((.(.............).))))))))	chr6:7281617-7281864(-)$1	1	135	164	22.2746
((((((((...........))))))).))	chr5:81571515-81571755(-)$1	1	64	93	22.3830

#PSSM
g : 0.16	f : 0.11	e : 0.08	! : 0.08	= : 0.08	h : 0.08	" : 0.08	[ : 0.06	d : 0.06	c : 0.05	b : 0.05	i : 0.01	$ : 0.01	: : 0.01	% : 0.01	
g : 0.19	f : 0.18	e : 0.16	= : 0.08	h : 0.08	" : 0.06	! : 0.05	[ : 0.05	c : 0.05	b : 0.03	i : 0.01	d : 0.01	
f : 0.19	e : 0.18	g : 0.18	[ : 0.09	= : 0.08	h : 0.06	d : 0.05	" : 0.05	c : 0.03	i : 0.01	a : 0.01	b : 0.01	
e : 0.26	f : 0.18	g : 0.16	= : 0.08	d : 0.08	h : 0.06	c : 0.05	! : 0.03	" : 0.03	[ : 0.01	b : 0.01	
e : 0.26	g : 0.15	f : 0.15	c : 0.08	d : 0.08	! : 0.06	= : 0.06	[ : 0.05	y : 0.03	h : 0.03	b : 0.01	
e : 0.24	g : 0.13	b : 0.11	f : 0.11	c : 0.08	d : 0.08	y : 0.05	= : 0.03	[ : 0.03	h : 0.03	! : 0.03	w : 0.01	a : 0.01	
w : 0.16	e : 0.13	b : 0.09	f : 0.09	y : 0.09	g : 0.08	x : 0.06	c : 0.06	a : 0.06	d : 0.05	v : 0.03	u : 0.01	= : 0.01	
w : 0.23	v : 0.15	u : 0.13	t : 0.11	y : 0.09	e : 0.08	x : 0.06	c : 0.03	g : 0.03	f : 0.01	= : 0.01	d : 0.01	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
t : 0.31	w : 0.23	v : 0.15	u : 0.13	y : 0.09	x : 0.06	
w : 0.23	t : 0.19	v : 0.15	u : 0.11	y : 0.09	x : 0.06	b : 0.05	f : 0.03	c : 0.01	d : 0.01	a : 0.01	
w : 0.21	v : 0.11	y : 0.09	e : 0.09	c : 0.08	b : 0.06	x : 0.06	f : 0.06	d : 0.06	a : 0.05	g : 0.03	= : 0.01	2 : 0.01	
e : 0.15	f : 0.11	g : 0.11	] : 0.09	c : 0.09	d : 0.08	w : 0.06	x : 0.06	y : 0.06	= : 0.05	b : 0.03	h : 0.03	2 : 0.01	
e : 0.21	f : 0.18	g : 0.16	c : 0.08	d : 0.08	= : 0.06	b : 0.05	y : 0.05	h : 0.05	] : 0.03	a : 0.01	
e : 0.24	f : 0.18	g : 0.16	= : 0.08	d : 0.08	h : 0.06	b : 0.05	] : 0.05	2 : 0.03	c : 0.01	4 : 0.01	
e : 0.24	f : 0.18	g : 0.16	= : 0.08	] : 0.06	2 : 0.06	h : 0.06	d : 0.05	b : 0.03	c : 0.01	4 : 0.01	
e : 0.19	g : 0.18	f : 0.16	= : 0.08	h : 0.06	] : 0.05	c : 0.05	2 : 0.05	4 : 0.05	d : 0.03	i : 0.01	a : 0.01	3 : 0.01	b : 0.01	
g : 0.19	e : 0.15	f : 0.13	= : 0.08	h : 0.08	3 : 0.06	4 : 0.06	c : 0.06	] : 0.05	d : 0.05	i : 0.01	2 : 0.01	b : 0.01	
g : 0.18	e : 0.11	f : 0.09	= : 0.08	2 : 0.08	h : 0.08	3 : 0.06	c : 0.06	4 : 0.05	] : 0.05	d : 0.05	: : 0.01	i : 0.01	5 : 0.01	b : 0.01	
2 : 0.15	g : 0.11	3 : 0.09	e : 0.09	4 : 0.08	= : 0.08	h : 0.08	: : 0.05	] : 0.05	c : 0.03	f : 0.03	d : 0.03	i : 0.01	a : 0.01	5 : 0.01	6 : 0.01	b : 0.01	
e : 0.13	: : 0.09	h : 0.09	2 : 0.08	f : 0.08	g : 0.08	= : 0.08	c : 0.06	b : 0.06	4 : 0.05	3 : 0.05	d : 0.05	i : 0.01	5 : 0.01	6 : 0.01	

#score	1358.7099953405761
#seq	60
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_CDS_m1_run1.txt

#BEAR
eeeeettttttttttteeeee:	chr16:2813393-2813624(+)$1	231	135	157	22.3392
b[ccctttttttttttccc]bb	chr1:115266476-115266708(-)$1	232	170	192	22.1546
dddduuuuuuuuuuuuddddff	chr1:85790373-85790598(-)$1	225	173	195	22.1748
ffffftttttttttttffffff	chr1:36752691-36752927(+)$1	236	89	111	22.6397
eeeeuuuuuuuuuuuueeeee:	chr3:51457315-51457536(-)$1	221	75	97	22.1620
eeeeeyyyyyyyyyyyyyyyye	chr15:91510267-91510490(-)$1	223	75	97	19.0814
Hddddtttttttttttdddd:F	chr2:152319539-152319781(+)$1	242	11	33	20.4062
gggggtttttttttttgggggg	chr13:23905551-23905775(-)$1	224	81	103	22.8960
gggguuuuuuuuuuuugggggg	chr9:135202889-135203109(-)$1	220	133	155	22.8028
!dddduuuuuuuuuuuudddd2	chr6:109484004-109484237(+)$1	233	67	89	21.6365
ffffvvvvvvvvvvvvvfffff	chr1:214794052-214794275(+)$1	223	62	84	21.7440
====uuuuuuuuuuuu======	chr12:120899732-120899958(-)$1	226	53	75	22.6706
ffffuuuuuuuuuuuuffffff	chr13:32912764-32912985(+)$1	221	74	96	22.4785
eeeeuuuuuuuuuuuueeeee:	chr10:91479089-91479309(+)$1	220	37	59	22.1620
b[ccctttttttttttcccbbd	chrX:123224393-123224625(+)$1	232	135	157	21.9140
cdddduuuuuuuuuuuudddd:	chr5:5463795-5464027(+)$1	232	191	213	20.8189
eeevvvvvvvvvvvvveeeee]	chr13:48947446-48947671(+)$1	225	75	97	21.9389
[dddduuuuuuuuuuuudddd2	chr5:112178706-112178926(+)$1	220	150	172	21.6491
eeeeettttttttttteeeee]	chr17:34050569-34050806(+)$1	237	160	182	23.2323
eeeeuuuuuuuuuuuueeeee2	chr16:53272191-53272422(+)$1	231	88	110	22.9019
eeeeuuuuuuuuuuuueeeee4	chr14:55510780-55511037(+)$1	257	28	50	22.9857
ffffftttttttttttffffff	chr9:135204301-135204521(-)$1	220	140	162	22.6397
##cccuuuuuuuuuuuuccc22	chr2:55252294-55252525(-)$1	231	55	77	21.7125
!cccwwwwwwwwwwwwwwccc5	chr17:65908210-65908445(+)$1	235	12	34	19.8639
dddduuuuuuuuuuuudddd]c	chr6:76380174-76380398(+)$1	224	41	63	22.1936
"""bbtttttttttttbb333g	chr2:20508142-20508404(-)$1	262	118	140	21.3898
ffffvvvvvvvvvvvvvfffff	chr2:61719089-61719310(-)$1	221	87	109	21.7440
gggguuuuuuuuuuuugggggg	chr1:54269533-54269754(-)$1	221	38	60	22.8028
eeevvvvvvvvvvvvveeeee]	chr16:58559031-58559282(-)$1	251	34	56	21.9389
ffffftttttttttttffffff	chr21:38877489-38877728(+)$1	239	67	89	22.6397
ccc[ayyyyyyyyyyyyyyyya	chr5:92920938-92921162(+)$1	224	104	126	19.3165
iiiyyyyyyyyyyyyyyyyiii	chr19:23406295-23406519(-)$1	224	13	35	20.2997
eeeeettttttttttteeeee5	chr19:53209121-53209356(-)$1	235	155	177	22.5348
cc[bbvvvvvvvvvvvvvbb33	chr12:123780441-123780661(-)$1	220	96	118	20.1853
gg!!ayyyyyyyyyyyyyyyya	chr9:100760787-100761020(+)$1	233	177	199	19.4102
eeeeettttttttttteeeee]	chr3:56682929-56683156(-)$1	227	191	213	23.2323
ffffftttttttttttffffff	chr9:125613561-125613784(-)$1	223	2	24	22.6397
eeeeettttttttttteeeee:	chr16:24582657-24582899(+)$1	242	58	80	22.3392
eyyyyyyyyyyyyyyyyeeeee	chr7:64168093-64168320(+)$1	227	116	138	20.1400
ccwwwwwwwwwwwwwwccc]cc	chr2:180809744-180809969(-)$1	225	14	36	19.8443
hhhhuuuuuuuuuuuuhhhhhh	chr10:102703738-102703959(+)$1	221	189	211	20.6954
ffffwwwwwwwwwwwwwwffff	chr8:95862185-95862410(+)$1	225	187	209	20.3265
cccvvvvvvvvvvvvvccc000	chrX:71425351-71425591(-)$1	240	89	111	20.3823
hhhhhttttttttttthhhhhh	chr14:23239348-23239578(+)$1	230	181	203	20.6376
eeeeuuuuuuuuuuuueeeee:	chr2:74437010-74437234(+)$1	224	185	207	22.1620
!dddduuuuuuuuuuuudddd2	chr17:45740418-45740642(+)$1	224	17	39	21.6365
!!ccctttttttttttccceee	chrX:71425275-71425497(-)$1	222	62	84	22.9747
gggggtttttttttttgggggg	chr5:78611897-78612117(+)$1	220	84	106	22.8960
ddddvvvvvvvvvvvvvdddd:	chr4:87693919-87694150(+)$1	231	7	29	20.6007
eyyyyyyyyyyyyyyyyeeeee	chr10:75557562-75557793(+)$1	231	39	61	20.1400
ffffftttttttttttffffff	chr21:40587062-40587284(-)$1	222	49	71	22.6397
ffffvvvvvvvvvvvvvfffff	chr3:132387609-132387831(+)$1	222	14	36	21.7440
dddduuuuuuuuuuuudddd66	chr20:34309600-34309826(-)$1	226	27	49	21.4931
e!!bbvvvvvvvvvvvvvbb22	chr6:71235578-71235800(+)$1	222	70	92	19.8589
""ccctttttttttttccc333	chr2:73678956-73679180(+)$1	224	151	173	22.9234
ffffftttttttttttffffff	chr10:27455974-27456195(+)$1	221	163	185	22.6397
gggguuuuuuuuuuuugggggg	chr9:72967123-72967353(+)$1	230	118	140	22.8028
ffffftttttttttttffffff	chr1:171553052-171553276(+)$1	224	146	168	22.6397
eeeeettttttttttteeeeee	chr19:38125803-38126037(-)$1	234	142	164	22.9592
dddduuuuuuuuuuuudddd33	chr13:42874297-42874532(+)$1	235	149	171	22.4399
=bbvvvvvvvvvvvvvbb]===	chrM:3639-3877(+)$1	238	29	51	20.3782
dddduuuuuuuuuuuudddd33	chrM:13433-13705(+)$1	272	145	167	22.4399
eeeeettttttttttteeeee:	chr10:32324387-32324616(-)$1	229	75	97	22.3392
ffffftttttttttttffffff	chr11:9459618-9459862(+)$1	244	59	81	22.6397
ba!!attttttttttta22a]b	chr9:128099715-128099943(+)$1	228	40	62	21.8332
hhhhhttttttttttthhhhhh	chr2:73761918-73762149(+)$1	231	47	69	20.6376
!ddddtttttttttttdddd55	chr15:42743364-42743590(-)$1	226	35	57	21.1149
ffffuuuuuuuuuuuuffffff	chr19:37239921-37240145(-)$1	224	2	24	22.4785
ffffuuuuuuuuuuuuffffff	chr12:100502192-100502426(-)$1	234	66	88	22.4785
gggggtttttttttttgggggg	chr5:38530533-38530762(-)$1	229	110	132	22.8960
hhhhhttttttttttthhhhhh	chr3:25670301-25670538(-)$1	237	189	211	20.6376
dddduuuuuuuuuuuudddd]d	chrM:14733-15002(+)$1	269	242	264	22.0067
gggggtttttttttttgggggg	chr4:88015975-88016207(+)$1	232	194	216	22.8960
[cccuuuuuuuuuuuuccc]ff	chr1:85630187-85630419(-)$1	232	72	94	22.7130

#otherMatches

#Seq PSSM
GGCCCAAACUCCACCGGGGCCA	chr16:2813393-2813624(+)$1	231	135	157	22.3392
UGAGUACCAAGGAAUGAUUGAG	chr1:115266476-115266708(-)$1	232	170	192	22.1546
AAGGUAAAAAAAUAUCCCUUCU	chr1:85790373-85790598(-)$1	225	173	195	22.1748
UGGGUAAGAGUCCACCAUCCAC	chr1:36752691-36752927(+)$1	236	89	111	22.6397
CAGCCAUAAAAAAACAGCUGGA	chr3:51457315-51457536(-)$1	221	75	97	22.1620
UUCCAAAUCUGAUGCUACUUCU	chr15:91510267-91510490(-)$1	223	75	97	19.0814
AGAAAAAAAGCUUUAAUUUCAU	chr2:152319539-152319781(+)$1	242	11	33	20.4062
AUCAGCAACUGACAAUUUGAUU	chr13:23905551-23905775(-)$1	224	81	103	22.8960
AGAAAUAAUAAGAAACUUCUGA	chr9:135202889-135203109(-)$1	220	133	155	22.8028
ACUGACACUAACCUUUUUCAGA	chr6:109484004-109484237(+)$1	233	67	89	21.6365
AAUUCUCAAAGAACUCCAAUUA	chr1:214794052-214794275(+)$1	223	62	84	21.7440
UCUCGGUCUGGGUCAAGGGGCC	chr12:120899732-120899958(-)$1	226	53	75	22.6706
CUUUGAUCAGAAACCAGAAGAA	chr13:32912764-32912985(+)$1	221	74	96	22.4785
ACAGUUCUUGUCUUUUCUGUUU	chr10:91479089-91479309(+)$1	220	37	59	22.1620
GAGCCCAAAAGAUUACGGCCUG	chrX:123224393-123224625(+)$1	232	135	157	21.9140
CCCGUUAAGCCUAGUAUAUGGA	chr5:5463795-5464027(+)$1	232	191	213	20.8189
CUAUUUUUAUCCCCUCUAGGAC	chr13:48947446-48947671(+)$1	225	75	97	21.9389
AGCAAAGCGCCAUGAUAUUGCA	chr5:112178706-112178926(+)$1	220	150	172	21.6491
CAGUACCCUUCAACCAUGCUGU	chr17:34050569-34050806(+)$1	237	160	182	23.2323
AUGGGUCUUGGCAAAACUAUUC	chr16:53272191-53272422(+)$1	231	88	110	22.9019
UGUCUUCCAUUCUCCUGACAUU	chr14:55510780-55511037(+)$1	257	28	50	22.9857
AUUAAAGAAUGAAGAAUUAGUU	chr9:135204301-135204521(-)$1	220	140	162	22.6397
AGAACAUACAACCCAAAGUUGA	chr2:55252294-55252525(-)$1	231	55	77	21.7125
AUGGAAAAGAUAAUAAACCCAA	chr17:65908210-65908445(+)$1	235	12	34	19.8639
UUGCAGCCUUAUUUUAGUAAAU	chr6:76380174-76380398(+)$1	224	41	63	22.1936
AUACUAAUCCCUCAGAAGGACU	chr2:20508142-20508404(-)$1	262	118	140	21.3898
GAUGAAAUUUUGAACAACAUUA	chr2:61719089-61719310(-)$1	221	87	109	21.7440
aaauuaaauaauauGUGUUUUU	chr1:54269533-54269754(-)$1	221	38	60	22.8028
GGGAAUCGCUACAACCUCCAGC	chr16:58559031-58559282(-)$1	251	34	56	21.9389
GAGAAAGCCUUUCAUCUUCUCU	chr21:38877489-38877728(+)$1	239	67	89	22.6397
GCUGCAAAAGUUUCUUCAAGAG	chr5:92920938-92921162(+)$1	224	104	126	19.3165
GUUCUUUCACACCUAACUCAAC	chr19:23406295-23406519(-)$1	224	13	35	20.2997
UUACAAAUGUGAAGAAUGUGAC	chr19:53209121-53209356(-)$1	235	155	177	22.5348
CUUGUAAAUCUCCUAUCAACUU	chr12:123780441-123780661(-)$1	220	96	118	20.1853
GUAACUGAGAAUUUGGAAACUG	chr9:100760787-100761020(+)$1	233	177	199	19.4102
UUAGUUAAAACACAUUGCUAAU	chr3:56682929-56683156(-)$1	227	191	213	23.2323
cauggggagagggagaccaugg	chr9:125613561-125613784(-)$1	223	2	24	22.6397
GUCUCAAUCUUCCAAAGAGGCU	chr16:24582657-24582899(+)$1	242	58	80	22.3392
CAACUUACUAGACAUAAGAUAG	chr7:64168093-64168320(+)$1	227	116	138	20.1400
GAGACGAUGGGAAAAAUCUAGC	chr2:180809744-180809969(-)$1	225	14	36	19.8443
CAUUUAGUCUGUGGUUAAUGGU	chr10:102703738-102703959(+)$1	221	189	211	20.6954
AAAUUAACCUUGAAAUAUAUUU	chr8:95862185-95862410(+)$1	225	187	209	20.3265
GAUACCUCAAGCAUAAAUCCAU	chrX:71425351-71425591(-)$1	240	89	111	20.3823
GAAAUUUCCUCUCUGUGUUUCA	chr14:23239348-23239578(+)$1	230	181	203	20.6376
GGAACACUGUCCUUUUUUCCCC	chr2:74437010-74437234(+)$1	224	185	207	22.1620
GAUCUGCUGUUCAUAAAAGGUA	chr17:45740418-45740642(+)$1	224	17	39	21.6365
CUUCAACUCCCAAAAAUGACAU	chrX:71425275-71425497(-)$1	222	62	84	22.9747
AGGAUGUUUUGAGAGAAUCCUU	chr5:78611897-78612117(+)$1	220	84	106	22.8960
GUAGUAAUCCUUCCCCUCUACC	chr4:87693919-87694150(+)$1	231	7	29	20.6007
UGCACACUUCUACUUCGAGCUG	chr10:75557562-75557793(+)$1	231	39	61	20.1400
CAUUUAACGAACCUGAGAGUGU	chr21:40587062-40587284(-)$1	222	49	71	22.6397
GUAUGUUUUUCAUCAGAAUACC	chr3:132387609-132387831(+)$1	222	14	36	21.7440
GCAGAAAAAAACAGAGCUGCAG	chr20:34309600-34309826(-)$1	226	27	49	21.4931
UGAUAAAUCUAAUAACUCUACA	chr6:71235578-71235800(+)$1	222	70	92	19.8589
AGAGUUGCCGCAUUUUACUGAA	chr2:73678956-73679180(+)$1	224	151	173	22.9234
CACACCUUCAUAUCCAGUGUGG	chr10:27455974-27456195(+)$1	221	163	185	22.6397
UCUUAAUAAAAGUAAAGAGAGG	chr9:72967123-72967353(+)$1	230	118	140	22.8028
AGGCACAAUCCGGUCUUGCCUU	chr1:171553052-171553276(+)$1	224	146	168	22.6397
AUAAUGUAACUUAAUAAUUAUU	chr19:38125803-38126037(-)$1	234	142	164	22.9592
AAAAUAAAACUGUAACUUUUAA	chr13:42874297-42874532(+)$1	235	149	171	22.4399
GAGCAUCAAACUCAAACUACGC	chrM:3639-3877(+)$1	238	29	51	20.3782
CGCUACCUCCCUGACAAGCGCC	chrM:13433-13705(+)$1	272	145	167	22.4399
GGUGGCAACUGUAGAACCACUA	chr10:32324387-32324616(-)$1	229	75	97	22.3392
GGAACAGAUACCCCAAGUUUUA	chr11:9459618-9459862(+)$1	244	59	81	22.6397
UCCAGGAAAUGAAGAGCGAGAA	chr9:128099715-128099943(+)$1	228	40	62	21.8332
UGCCAUAUAAGCCUUCUGGUAG	chr2:73761918-73762149(+)$1	231	47	69	20.6376
GCAAGAAAAUGACAAACUUGGU	chr15:42743364-42743590(-)$1	226	35	57	21.1149
UUGGCUCAACACUACUUCAACA	chr19:37239921-37240145(-)$1	224	2	24	22.4785
ACAUAAAUAAAUGUCAAUGUGU	chr12:100502192-100502426(-)$1	234	66	88	22.4785
UUAUUCUUCUAUAUCUAAUGAA	chr5:38530533-38530762(-)$1	229	110	132	22.8960
AGUACUAUAAAGGUUUGUAUUU	chr3:25670301-25670538(-)$1	237	189	211	20.6376
UGAAUCAUCCGCUACCUUCACG	chrM:14733-15002(+)$1	269	242	264	22.0067
AAUGUCUCAUGUCAAUGCAUUG	chr4:88015975-88016207(+)$1	232	194	216	22.8960
GGACCAGUAUUAUUAAGUCAGA	chr1:85630187-85630419(-)$1	232	72	94	22.7130

#DB
(((((...........))))).	chr16:2813393-2813624(+)$1	1	135	157	22.3392
(.(((...........))).))	chr1:115266476-115266708(-)$1	1	170	192	22.1546
((((............))))((	chr1:85790373-85790598(-)$1	1	173	195	22.1748
(((((...........))))))	chr1:36752691-36752927(+)$1	1	89	111	22.6397
((((............))))).	chr3:51457315-51457536(-)$1	1	75	97	22.1620
(((((................)	chr15:91510267-91510490(-)$1	1	75	97	19.0814
(((((...........)))).(	chr2:152319539-152319781(+)$1	1	11	33	20.4062
(((((...........))))))	chr13:23905551-23905775(-)$1	1	81	103	22.8960
((((............))))))	chr9:135202889-135203109(-)$1	1	133	155	22.8028
.((((............)))).	chr6:109484004-109484237(+)$1	1	67	89	21.6365
((((.............)))))	chr1:214794052-214794275(+)$1	1	62	84	21.7440
((((............))))))	chr12:120899732-120899958(-)$1	1	53	75	22.6706
((((............))))))	chr13:32912764-32912985(+)$1	1	74	96	22.4785
((((............))))).	chr10:91479089-91479309(+)$1	1	37	59	22.1620
(.(((...........)))))(	chrX:123224393-123224625(+)$1	1	135	157	21.9140
)((((............)))).	chr5:5463795-5464027(+)$1	1	191	213	20.8189
(((.............))))).	chr13:48947446-48947671(+)$1	1	75	97	21.9389
.((((............)))).	chr5:112178706-112178926(+)$1	1	150	172	21.6491
(((((...........))))).	chr17:34050569-34050806(+)$1	1	160	182	23.2323
((((............))))).	chr16:53272191-53272422(+)$1	1	88	110	22.9019
((((............))))).	chr14:55510780-55511037(+)$1	1	28	50	22.9857
(((((...........))))))	chr9:135204301-135204521(-)$1	1	140	162	22.6397
..(((............)))..	chr2:55252294-55252525(-)$1	1	55	77	21.7125
.(((..............))).	chr17:65908210-65908445(+)$1	1	12	34	19.8639
((((............)))).)	chr6:76380174-76380398(+)$1	1	41	63	22.1936
...((...........))...)	chr2:20508142-20508404(-)$1	1	118	140	21.3898
((((.............)))))	chr2:61719089-61719310(-)$1	1	87	109	21.7440
((((............))))))	chr1:54269533-54269754(-)$1	1	38	60	22.8028
(((.............))))).	chr16:58559031-58559282(-)$1	1	34	56	21.9389
(((((...........))))))	chr21:38877489-38877728(+)$1	1	67	89	22.6397
(((.(................)	chr5:92920938-92921162(+)$1	1	104	126	19.3165
(((................)))	chr19:23406295-23406519(-)$1	1	13	35	20.2997
(((((...........))))).	chr19:53209121-53209356(-)$1	1	155	177	22.5348
((.((.............))..	chr12:123780441-123780661(-)$1	1	96	118	20.1853
((..(................)	chr9:100760787-100761020(+)$1	1	177	199	19.4102
(((((...........))))).	chr3:56682929-56683156(-)$1	1	191	213	23.2323
(((((...........))))))	chr9:125613561-125613784(-)$1	1	2	24	22.6397
(((((...........))))).	chr16:24582657-24582899(+)$1	1	58	80	22.3392
(................)))))	chr7:64168093-64168320(+)$1	1	116	138	20.1400
((..............))).))	chr2:180809744-180809969(-)$1	1	14	36	19.8443
((((............))))))	chr10:102703738-102703959(+)$1	1	189	211	20.6954
((((..............))))	chr8:95862185-95862410(+)$1	1	187	209	20.3265
(((.............)))...	chrX:71425351-71425591(-)$1	1	89	111	20.3823
(((((...........))))))	chr14:23239348-23239578(+)$1	1	181	203	20.6376
((((............))))).	chr2:74437010-74437234(+)$1	1	185	207	22.1620
.((((............)))).	chr17:45740418-45740642(+)$1	1	17	39	21.6365
..(((...........))))))	chrX:71425275-71425497(-)$1	1	62	84	22.9747
(((((...........))))))	chr5:78611897-78612117(+)$1	1	84	106	22.8960
((((.............)))).	chr4:87693919-87694150(+)$1	1	7	29	20.6007
(................)))))	chr10:75557562-75557793(+)$1	1	39	61	20.1400
(((((...........))))))	chr21:40587062-40587284(-)$1	1	49	71	22.6397
((((.............)))))	chr3:132387609-132387831(+)$1	1	14	36	21.7440
((((............))))..	chr20:34309600-34309826(-)$1	1	27	49	21.4931
(..((.............))..	chr6:71235578-71235800(+)$1	1	70	92	19.8589
..(((...........)))...	chr2:73678956-73679180(+)$1	1	151	173	22.9234
(((((...........))))))	chr10:27455974-27456195(+)$1	1	163	185	22.6397
((((............))))))	chr9:72967123-72967353(+)$1	1	118	140	22.8028
(((((...........))))))	chr1:171553052-171553276(+)$1	1	146	168	22.6397
(((((...........)))))(	chr19:38125803-38126037(-)$1	1	142	164	22.9592
((((............))))..	chr13:42874297-42874532(+)$1	1	149	171	22.4399
(((.............)).)))	chrM:3639-3877(+)$1	1	29	51	20.3782
((((............))))..	chrM:13433-13705(+)$1	1	145	167	22.4399
(((((...........))))).	chr10:32324387-32324616(-)$1	1	75	97	22.3392
(((((...........))))))	chr11:9459618-9459862(+)$1	1	59	81	22.6397
((..(...........)..).)	chr9:128099715-128099943(+)$1	1	40	62	21.8332
(((((...........))))))	chr2:73761918-73762149(+)$1	1	47	69	20.6376
.((((...........))))..	chr15:42743364-42743590(-)$1	1	35	57	21.1149
((((............))))))	chr19:37239921-37240145(-)$1	1	2	24	22.4785
((((............))))))	chr12:100502192-100502426(-)$1	1	66	88	22.4785
(((((...........))))))	chr5:38530533-38530762(-)$1	1	110	132	22.8960
(((((...........))))))	chr3:25670301-25670538(-)$1	1	189	211	20.6376
((((............)))).)	chrM:14733-15002(+)$1	1	242	264	22.0067
(((((...........))))))	chr4:88015975-88016207(+)$1	1	194	216	22.8960
.(((............))).))	chr1:85630187-85630419(-)$1	1	72	94	22.7130

#PSSM
e : 0.24	f : 0.20	g : 0.10	d : 0.09	! : 0.06	c : 0.06	h : 0.05	b : 0.04	= : 0.02	[ : 0.02	" : 0.02	H : 0.01	# : 0.01	i : 0.01	
e : 0.20	f : 0.20	d : 0.17	g : 0.10	c : 0.08	h : 0.05	[ : 0.02	" : 0.02	y : 0.02	! : 0.02	= : 0.01	# : 0.01	i : 0.01	b : 0.01	a : 0.01	
e : 0.20	f : 0.20	d : 0.17	c : 0.12	g : 0.09	h : 0.05	! : 0.04	y : 0.02	= : 0.01	" : 0.01	i : 0.01	[ : 0.01	w : 0.01	b : 0.01	
f : 0.20	e : 0.17	d : 0.17	c : 0.09	g : 0.09	v : 0.05	h : 0.05	b : 0.04	y : 0.04	! : 0.02	= : 0.01	[ : 0.01	w : 0.01	
u : 0.27	e : 0.10	f : 0.10	v : 0.10	d : 0.08	c : 0.06	g : 0.05	w : 0.04	b : 0.04	a : 0.04	y : 0.04	h : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
t : 0.40	u : 0.33	v : 0.13	y : 0.08	w : 0.04	
e : 0.18	f : 0.14	d : 0.10	c : 0.09	g : 0.09	y : 0.08	v : 0.08	u : 0.06	h : 0.05	w : 0.02	b : 0.02	= : 0.01	a : 0.01	
e : 0.21	f : 0.18	d : 0.17	c : 0.10	g : 0.09	y : 0.05	h : 0.05	w : 0.02	b : 0.02	v : 0.02	= : 0.01	2 : 0.01	
e : 0.21	f : 0.20	d : 0.17	c : 0.12	g : 0.09	y : 0.05	h : 0.05	b : 0.02	= : 0.01	3 : 0.01	] : 0.01	2 : 0.01	
e : 0.22	f : 0.20	d : 0.17	g : 0.09	h : 0.05	] : 0.04	y : 0.04	b : 0.04	= : 0.02	c : 0.02	3 : 0.02	i : 0.01	0 : 0.01	a : 0.01	
e : 0.22	f : 0.22	g : 0.09	d : 0.06	3 : 0.06	h : 0.05	y : 0.04	] : 0.04	b : 0.02	= : 0.02	2 : 0.02	c : 0.02	: : 0.01	i : 0.01	0 : 0.01	6 : 0.01	5 : 0.01	
f : 0.22	: : 0.10	g : 0.10	2 : 0.08	e : 0.06	] : 0.05	3 : 0.05	h : 0.05	5 : 0.04	b : 0.02	= : 0.02	d : 0.02	c : 0.02	a : 0.02	F : 0.01	4 : 0.01	i : 0.01	0 : 0.01	6 : 0.01	

#score	1611.7408837221067
#seq	74
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_CDS_m1_run1.txt

#BEAR
c"""cccvvvvvvvvvvvvvccc22c	chr2:109411016-109411234(+)$1	218	59	85	22.9836
iiiiiiiitttttttttttiiiiiii	chr8:124349940-124350156(-)$1	216	57	83	22.7996
[bbddddtttttttttttdddd333b	chr15:42529594-42529814(-)$1	220	146	172	21.6407
gccccccvvvvvvvvvvvvvccc]cc	chr6:43481067-43481279(-)$1	212	132	158	23.2983
iiiiiiixxxxxxxxxxxxxxxiiii	chr3:125295061-125295283(-)$1	222	35	61	19.3339
ddd"""bbtttttttttttbb333dd	chr18:28650675-28650908(-)$1	233	125	151	21.4912
gggggggvvvvvvvvvvvvvgggggg	chrM:5909-6130(+)$1	221	139	165	23.1745
!ffffffuuuuuuuuuuuuffffff2	chr22:42610086-42610317(-)$1	231	64	90	22.2680
gg:eeeeettttttttttteeeee::	chr1:27875083-27875296(-)$1	213	69	95	19.4364
ddddddduuuuuuuuuuuudddd:::	chr12:110784127-110784392(+)$1	265	204	230	20.4525
e[ddddvvvvvvvvvvvvvdddd]ee	chr13:96529955-96530176(-)$1	221	170	196	21.9527
=======uuuuuuuuuuuu=======	chr17:45755578-45755873(+)$1	295	257	283	24.9506
ddd[cccuuuuuuuuuuuuccc22dd	chr22:42608631-42608859(-)$1	228	62	88	23.6251
ddddcccvvvvvvvvvvvvvccc22d	chr8:141551167-141551433(-)$1	266	119	145	22.3738
!dddd[bbtttttttttttbb22ddd	chr9:88957910-88958126(-)$1	216	138	164	21.0844
gggg[bbuuuuuuuuuuuubbggggg	chr19:2185804-2186022(+)$1	218	187	213	23.6184
ccc[bbwwwwwwwwwwwwwwbbccc:	chr2:219130482-219130706(-)$1	224	193	219	20.8359
eeeeeeettttttttttteeeee]ee	chr21:30426362-30426574(+)$1	212	54	80	21.3427
##fffffftttttttttttffffff4	chr1:197128427-197128668(-)$1	241	180	206	20.9989
dddd[bbwwwwwwwwwwwwwwbbddd	chr9:13192046-13192270(-)$1	224	56	82	20.8168
=======uuuuuuuuuuuu=======	chr10:32327609-32327834(-)$1	225	165	191	24.9506
=======xxxxxxxxxxxxxxx====	chr10:93008160-93008415(+)$1	255	197	223	19.5862
c!!dddduuuuuuuuuuuudddd22c	chr10:28897150-28897373(+)$1	223	72	98	23.4299
iiiiiiiuuuuuuuuuuuuiiiiiii	chr11:118369041-118369293(+)$1	252	223	249	24.5888
eeeeeeeuuuuuuuuuuuueeeee66	chr2:201681738-201681977(+)$1	239	164	190	22.1816
fbb[cccvvvvvvvvvvvvvccc]bb	chr17:78302125-78302346(+)$1	221	77	103	22.7740
e!!bbccctttttttttttccc]bb3	chr19:39421142-39421360(-)$1	218	145	171	21.9297
ddddyyyyyyyyyyyyyyyydddd::	chr1:29319792-29320002(+)$1	210	155	181	19.4198
c[a[cccuuuuuuuuuuuuccca]cc	chr6:109690087-109690308(-)$1	221	20	46	24.6119
$$$eeeeettttttttttteeeee55	chr19:23405376-23405606(-)$1	230	71	97	19.9052
ggggggguuuuuuuuuuuuggggggg	chr5:70754306-70754534(+)$1	228	45	71	24.1262
bb[dddduuuuuuuuuuuudddd]bb	chr2:210887619-210887841(+)$1	222	55	81	23.0283
eeeeeyyyyyyyyyyyyyyyyeeeee	chr12:85255643-85255873(-)$1	230	132	158	21.5846
""eeeeewwwwwwwwwwwwwweeeee	chr17:12823021-12823240(+)$1	219	139	165	22.1428
gggggggxxxxxxxxxxxxxxxgggg	chr14:21834499-21834735(-)$1	236	10	36	18.9497
cccdddduuuuuuuuuuuudddd]cc	chr3:47883013-47883304(+)$1	291	176	202	23.6028
=======yyyyyyyyyyyyyyyy===	chr1:186296601-186296825(-)$1	224	6	32	23.4012
!bb[ddddtttttttttttdddd]bb	chr22:26895010-26895225(-)$1	215	162	188	21.9883
::eeeeeuuuuuuuuuuuueeeeebb	chr19:41800224-41800461(+)$1	237	165	191	21.1135
hhhhh[bbtttttttttttbb333hh	chr20:17950554-17950790(+)$1	236	50	76	21.3794
=======uuuuuuuuuuuu=======	chr2:152321192-152321403(+)$1	211	35	61	24.9506
[gggggggtttttttttttggggggg	chr2:48047460-48047679(-)$1	219	171	197	22.6414
[bb[cccuuuuuuuuuuuuccc]bb]	chr13:60557838-60558056(-)$1	218	103	129	23.7892
###dddduuuuuuuuuuuuddddeee	chr12:56143310-56143533(+)$1	223	139	165	23.1964
[bb!!ccctttttttttttccc22bb	chr1:91404691-91404914(-)$1	223	116	142	22.5276
gggggggxxxxxxxxxxxxxxxgggg	chr5:1341819-1342040(-)$1	221	74	100	18.9497
=======xxxxxxxxxxxxxxx====	chr5:93978997-93979213(+)$1	216	8	34	19.5862
hhhhhhhwwwwwwwwwwwwwwhhhhh	chr4:53463656-53464006(-)$1	350	76	102	20.7791
gggggggtttttttttttggggggg:	chr12:110778622-110778875(+)$1	253	208	234	21.2471
ggg[cccuuuuuuuuuuuucccgggg	chr17:8273187-8273447(-)$1	260	14	40	24.6618
[gggggggtttttttttttggggggg	chr5:5464173-5464414(+)$1	241	151	177	22.6414
[ffffffwwwwwwwwwwwwwwfffff	chr6:157454095-157454313(+)$1	218	10	36	21.3729
ccc[bbvvvvvvvvvvvvvbb]ccc:	chr15:52356078-52356293(+)$1	215	120	146	20.9303
=======uuuuuuuuuuuu=======	chr6:34835236-34835466(+)$1	230	21	47	24.9506
hhhhh[ayyyyyyyyyyyyyyyyahh	chr1:78098189-78098403(-)$1	214	28	54	21.4483
a[eeeeeyyyyyyyyyyyyyyyyeee	chr15:50862001-50862211(-)$1	210	79	105	21.9313
[ddddwwwwwwwwwwwwwwdddd]bb	chr3:47889245-47889481(+)$1	236	45	71	21.4906
####ccctttttttttttccc4444d	chr12:132496044-132496264(+)$1	220	19	45	22.2804

#otherMatches

#Seq PSSM
GUCAGCUGUCCAAAAUCUAAAGCAUC	chr2:109411016-109411234(+)$1	218	59	85	22.9836
UGGAGGAGCAGUAACUAAAUUCUUCC	chr8:124349940-124350156(-)$1	216	57	83	22.7996
AUGCGGAAUUUCAGAAUAUCCGAUAC	chr15:42529594-42529814(-)$1	220	146	172	21.6407
ACUCUGGUUGCUAUCCUACUCCAUGG	chr6:43481067-43481279(-)$1	212	132	158	23.2983
AAGAAGAAAACAAAAGGAAUGAUUUU	chr3:125295061-125295283(-)$1	222	35	61	19.3339
GGACGUCUAAACAACCAAAAGUAAUU	chr18:28650675-28650908(-)$1	233	125	151	21.4912
GGUAACGACCACAUCUACAACGUUAU	chrM:5909-6130(+)$1	221	139	165	23.1745
UGUGAGGUCCCCCAUGCAGUUUCACC	chr22:42610086-42610317(-)$1	231	64	90	22.2680
UGCCACGUCAGCGAGCCCAACGUGAU	chr1:27875083-27875296(-)$1	213	69	95	19.4364
UAAAGCAACUGUCUAUUUCUGCUGAA	chr12:110784127-110784392(+)$1	265	204	230	20.4525
ACUAGGCACAAAAAAUAAACCUGCUG	chr13:96529955-96530176(-)$1	221	170	196	21.9527
GGGCUAUGUCUGUCAUUCUGUAGCUC	chr17:45755578-45755873(+)$1	295	257	283	24.9506
UAUCCAAUUCCCAGAAAGUUUGAAAU	chr22:42608631-42608859(-)$1	228	62	88	23.6251
CACCCGCAUCAUCUUCUACCGCGACG	chr8:141551167-141551433(-)$1	266	119	145	22.3738
UAAGUACAAAAUGAAAUGCUGGCACU	chr9:88957910-88958126(-)$1	216	138	164	21.0844
AGGACGCAUCCUAUAAUUAGCUCUUC	chr19:2185804-2186022(+)$1	218	187	213	23.6184
GACUCCUCUCCUUCCUUCCUGGGUCU	chr2:219130482-219130706(-)$1	224	193	219	20.8359
UUCACAUCAGCGACACACAUGUGCAA	chr21:30426362-30426574(+)$1	212	54	80	21.3427
GUAAAUCUAAACAUUCCACAGAUUUU	chr1:197128427-197128668(-)$1	241	180	206	20.9989
GGUGUGCUGUCGUCGAACUGUGCCAC	chr9:13192046-13192270(-)$1	224	56	82	20.8168
UCUGUUAAUUCCUUUUUAAUAAUAGA	chr10:32327609-32327834(-)$1	225	165	191	24.9506
UGAAAUCAACACUUCUAUUAAAGAUU	chr10:93008160-93008415(+)$1	255	197	223	19.5862
UCCCUGUUUCUCCUGUUCCACAGUCG	chr10:28897150-28897373(+)$1	223	72	98	23.4299
UAAAAAAAAAAaaaaagacuuuuuua	chr11:118369041-118369293(+)$1	252	223	249	24.5888
UAAUGGAACACUUAAUGCAUCCAUUC	chr2:201681738-201681977(+)$1	239	164	190	22.1816
UACUUCUAAAGAAAGAGAAAAGAUGU	chr17:78302125-78302346(+)$1	221	77	103	22.7740
ACUCCCUCAGCUGGACAUAGAGCGGU	chr19:39421142-39421360(-)$1	218	145	171	21.9297
AAGCAGAAACAGAAUUAAAAGCUUCC	chr1:29319792-29320002(+)$1	210	155	181	19.4198
UGCAUCUUUAAAUUACAAUAGAGGAC	chr6:109690087-109690308(-)$1	221	20	46	24.6119
ACCCUACAAAUGUAAAGAAUGUGGCA	chr19:23405376-23405606(-)$1	230	71	97	19.9052
GCAUGUGUAACAGAAGAUUCAUGUGC	chr5:70754306-70754534(+)$1	228	45	71	24.1262
ACCUAUUUUUUUUAACAUUAGUAAGU	chr2:210887619-210887841(+)$1	222	55	81	23.0283
UUGUGUCUCUCUGGUUGUCUUUGCAA	chr12:85255643-85255873(-)$1	230	132	158	21.5846
UACUUUCUUUUUUGCUUCUUUGAAGG	chr17:12823021-12823240(+)$1	219	139	165	22.1428
AAGAUACUUUAAUAUCUCCUUUGUGU	chr14:21834499-21834735(-)$1	236	10	36	18.9497
AGGUGAUUCAGAUUGCAACGUCAUCC	chr3:47883013-47883304(+)$1	291	176	202	23.6028
UCUUUUUUAACUUUUUUAUUUUUAAA	chr1:186296601-186296825(-)$1	224	6	32	23.4012
UGCUGGGAAAAUCAACCUAUCCCUGC	chr22:26895010-26895225(-)$1	215	162	188	21.9883
UUACUCACCUCCAACCUACUGAGUGC	chr19:41800224-41800461(+)$1	237	165	191	21.1135
UGUGGCCGGAAGAAAAAAGUGAACCC	chr20:17950554-17950790(+)$1	236	50	76	21.3794
UGUGAUUGCUGUGGGGAAAAAUCACA	chr2:152321192-152321403(+)$1	211	35	61	24.9506
UUUAUGUGGUAAGUUAAUGUAUAUAG	chr2:48047460-48047679(-)$1	219	171	197	22.6414
CAGACUUCACAUAUCGAAAAAGACUA	chr13:60557838-60558056(-)$1	218	103	129	23.7892
CAAGGCCAACUACUGCUCCGGCCAGU	chr12:56143310-56143533(+)$1	223	139	165	23.1964
CCUCAUAAGAAUGUUACAAUUAAAAG	chr1:91404691-91404914(-)$1	223	116	142	22.5276
UGUUUCUGUACCAAAGAAAACGAGAA	chr5:1341819-1342040(-)$1	221	74	100	18.9497
AUUUUACCAAAAAGUUCACCAAGUGG	chr5:93978997-93979213(+)$1	216	8	34	19.5862
GUUUUCUUUCUCCUUUAUUGCAGAAA	chr4:53463656-53464006(-)$1	350	76	102	20.7791
AGGCUACACAAGCACAUAGUAGCCUC	chr12:110778622-110778875(+)$1	253	208	234	21.2471
UGUACAGGGCACAGAGAAACUGAUAG	chr17:8273187-8273447(-)$1	260	14	40	24.6618
AGAGGUGGGGCCUCCUUUGCCGCCUC	chr5:5464173-5464414(+)$1	241	151	177	22.6414
UAUGCAGAGAUUAUGAAACACCUGCA	chr6:157454095-157454313(+)$1	218	10	36	21.3729
GAUGAAGAAGAAGUACAAGUUGAUCC	chr15:52356078-52356293(+)$1	215	120	146	20.9303
CUGAAGGUGAAUGAGGUGUCUUUUGG	chr6:34835236-34835466(+)$1	230	21	47	24.9506
GGAACACUAAACAAAAUAGCAUUGGU	chr1:78098189-78098403(-)$1	214	28	54	21.4483
AGAGCAAAACAUCACUGUAAUUCUUG	chr15:50862001-50862211(-)$1	210	79	105	21.9313
AUGGAUCAGAAGGCCAUAUUCCAGCA	chr3:47889245-47889481(+)$1	236	45	71	21.4906
UUGUUGUGAGAAGUUGUAACAUACUC	chr12:132496044-132496264(+)$1	220	19	45	22.2804

#DB
(...(((.............)))..)	chr2:109411016-109411234(+)$1	1	59	85	22.9836
((((((((...........)))))))	chr8:124349940-124350156(-)$1	1	57	83	22.7996
.((((((...........))))...)	chr15:42529594-42529814(-)$1	1	146	172	21.6407
(((((((.............))).))	chr6:43481067-43481279(-)$1	1	132	158	23.2983
(((((((...............))))	chr3:125295061-125295283(-)$1	1	35	61	19.3339
(((...((...........))...))	chr18:28650675-28650908(-)$1	1	125	151	21.4912
(((((((.............))))))	chrM:5909-6130(+)$1	1	139	165	23.1745
.((((((............)))))).	chr22:42610086-42610317(-)$1	1	64	90	22.2680
)).(((((...........)))))..	chr1:27875083-27875296(-)$1	1	69	95	19.4364
)))((((............))))...	chr12:110784127-110784392(+)$1	1	204	230	20.4525
(.((((.............)))).))	chr13:96529955-96530176(-)$1	1	170	196	21.9527
(((((((............)))))))	chr17:45755578-45755873(+)$1	1	257	283	24.9506
(((.(((............)))..))	chr22:42608631-42608859(-)$1	1	62	88	23.6251
(((((((.............)))..)	chr8:141551167-141551433(-)$1	1	119	145	22.3738
.((((.((...........))..)))	chr9:88957910-88958126(-)$1	1	138	164	21.0844
((((.((............)))))))	chr19:2185804-2186022(+)$1	1	187	213	23.6184
(((.((..............))))).	chr2:219130482-219130706(-)$1	1	193	219	20.8359
(((((((...........))))).))	chr21:30426362-30426574(+)$1	1	54	80	21.3427
..((((((...........)))))).	chr1:197128427-197128668(-)$1	1	180	206	20.9989
((((.((..............)))))	chr9:13192046-13192270(-)$1	1	56	82	20.8168
(((((((............)))))))	chr10:32327609-32327834(-)$1	1	165	191	24.9506
(((((((...............))))	chr10:93008160-93008415(+)$1	1	197	223	19.5862
(..((((............))))..)	chr10:28897150-28897373(+)$1	1	72	98	23.4299
(((((((............)))))))	chr11:118369041-118369293(+)$1	1	223	249	24.5888
(((((((............)))))..	chr2:201681738-201681977(+)$1	1	164	190	22.1816
(((.(((.............))).))	chr17:78302125-78302346(+)$1	1	77	103	22.7740
(..(((((...........))).)).	chr19:39421142-39421360(-)$1	1	145	171	21.9297
((((................))))..	chr1:29319792-29320002(+)$1	1	155	181	19.4198
(.(.(((............)))).))	chr6:109690087-109690308(-)$1	1	20	46	24.6119
...(((((...........)))))..	chr19:23405376-23405606(-)$1	1	71	97	19.9052
(((((((............)))))))	chr5:70754306-70754534(+)$1	1	45	71	24.1262
((.((((............)))).))	chr2:210887619-210887841(+)$1	1	55	81	23.0283
(((((................)))))	chr12:85255643-85255873(-)$1	1	132	158	21.5846
..(((((..............)))))	chr17:12823021-12823240(+)$1	1	139	165	22.1428
(((((((...............))))	chr14:21834499-21834735(-)$1	1	10	36	18.9497
(((((((............)))).))	chr3:47883013-47883304(+)$1	1	176	202	23.6028
(((((((................)))	chr1:186296601-186296825(-)$1	1	6	32	23.4012
.((.((((...........)))).))	chr22:26895010-26895225(-)$1	1	162	188	21.9883
..(((((............)))))((	chr19:41800224-41800461(+)$1	1	165	191	21.1135
(((((.((...........))...))	chr20:17950554-17950790(+)$1	1	50	76	21.3794
(((((((............)))))))	chr2:152321192-152321403(+)$1	1	35	61	24.9506
.(((((((...........)))))))	chr2:48047460-48047679(-)$1	1	171	197	22.6414
.((.(((............))).)).	chr13:60557838-60558056(-)$1	1	103	129	23.7892
...((((............)))))))	chr12:56143310-56143533(+)$1	1	139	165	23.1964
.((..(((...........)))..))	chr1:91404691-91404914(-)$1	1	116	142	22.5276
(((((((...............))))	chr5:1341819-1342040(-)$1	1	74	100	18.9497
(((((((...............))))	chr5:93978997-93979213(+)$1	1	8	34	19.5862
(((((((..............)))))	chr4:53463656-53464006(-)$1	1	76	102	20.7791
(((((((...........))))))).	chr12:110778622-110778875(+)$1	1	208	234	21.2471
(((.(((............)))))))	chr17:8273187-8273447(-)$1	1	14	40	24.6618
.(((((((...........)))))))	chr5:5464173-5464414(+)$1	1	151	177	22.6414
.((((((..............)))))	chr6:157454095-157454313(+)$1	1	10	36	21.3729
(((.((.............)).))).	chr15:52356078-52356293(+)$1	1	120	146	20.9303
(((((((............)))))))	chr6:34835236-34835466(+)$1	1	21	47	24.9506
(((((.(................)))	chr1:78098189-78098403(-)$1	1	28	54	21.4483
(.(((((................)))	chr15:50862001-50862211(-)$1	1	79	105	21.9313
.((((..............)))).))	chr3:47889245-47889481(+)$1	1	45	71	21.4906
....(((...........)))....)	chr12:132496044-132496264(+)$1	1	19	45	22.2804

#PSSM
g : 0.15	[ : 0.12	= : 0.12	c : 0.10	d : 0.10	e : 0.08	i : 0.05	! : 0.05	# : 0.05	h : 0.05	f : 0.01	$ : 0.01	b : 0.01	" : 0.01	: : 0.01	a : 0.01	
g : 0.17	d : 0.13	= : 0.12	b : 0.10	c : 0.06	i : 0.05	[ : 0.05	e : 0.05	# : 0.05	h : 0.05	" : 0.03	f : 0.03	! : 0.03	$ : 0.01	: : 0.01	
d : 0.15	g : 0.15	= : 0.12	e : 0.10	b : 0.08	c : 0.06	i : 0.05	f : 0.05	h : 0.05	! : 0.03	# : 0.03	" : 0.01	: : 0.01	a : 0.01	$ : 0.01	[ : 0.01	
d : 0.20	g : 0.13	e : 0.13	[ : 0.13	= : 0.12	i : 0.05	f : 0.05	h : 0.05	" : 0.03	c : 0.01	b : 0.01	! : 0.01	# : 0.01	
d : 0.17	c : 0.15	e : 0.13	g : 0.12	= : 0.12	i : 0.05	f : 0.05	b : 0.05	h : 0.05	[ : 0.03	" : 0.01	y : 0.01	! : 0.01	
c : 0.18	d : 0.13	g : 0.12	e : 0.12	= : 0.12	b : 0.06	i : 0.05	f : 0.05	[ : 0.05	y : 0.03	" : 0.01	h : 0.01	w : 0.01	
c : 0.18	d : 0.12	g : 0.12	e : 0.12	= : 0.12	b : 0.08	i : 0.05	f : 0.05	v : 0.03	w : 0.03	y : 0.03	h : 0.01	a : 0.01	
u : 0.32	v : 0.12	w : 0.10	x : 0.08	y : 0.08	t : 0.06	b : 0.05	e : 0.03	c : 0.03	g : 0.03	i : 0.01	f : 0.01	d : 0.01	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.27	v : 0.12	w : 0.10	x : 0.08	y : 0.08	
u : 0.32	t : 0.20	v : 0.12	w : 0.10	x : 0.08	y : 0.08	d : 0.01	e : 0.01	g : 0.01	c : 0.01	
d : 0.15	c : 0.12	v : 0.08	x : 0.08	b : 0.08	e : 0.08	w : 0.08	y : 0.08	= : 0.06	g : 0.06	i : 0.03	f : 0.03	
c : 0.18	d : 0.17	b : 0.10	x : 0.08	g : 0.08	e : 0.08	= : 0.06	w : 0.06	y : 0.06	i : 0.03	f : 0.03	
c : 0.17	d : 0.17	e : 0.12	g : 0.10	x : 0.08	= : 0.06	f : 0.05	y : 0.05	i : 0.03	3 : 0.03	b : 0.03	2 : 0.01	h : 0.01	] : 0.01	4 : 0.01	
g : 0.15	d : 0.15	e : 0.12	c : 0.10	= : 0.10	i : 0.05	3 : 0.05	f : 0.05	2 : 0.05	y : 0.05	] : 0.03	b : 0.01	a : 0.01	h : 0.01	4 : 0.01	
] : 0.15	g : 0.15	e : 0.13	= : 0.12	2 : 0.08	i : 0.05	3 : 0.05	f : 0.05	d : 0.05	c : 0.03	b : 0.03	: : 0.01	h : 0.01	a : 0.01	4 : 0.01	
g : 0.15	b : 0.13	= : 0.12	e : 0.10	c : 0.08	d : 0.06	2 : 0.05	i : 0.05	f : 0.05	: : 0.05	h : 0.05	3 : 0.01	6 : 0.01	5 : 0.01	4 : 0.01	
g : 0.13	b : 0.12	= : 0.12	d : 0.10	: : 0.10	e : 0.10	c : 0.08	i : 0.05	h : 0.05	2 : 0.01	4 : 0.01	6 : 0.01	3 : 0.01	5 : 0.01	] : 0.01	f : 0.01	

#score	1282.5508363801428
#seq	58
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_UTR_m1_run2.txt

#BEAR
c[ddddwwwwwwwwwwwwwwdddd]ccc	chrX:68749673-68749913(+)$1	240	35	63	21.9490
hhhhhhhhttttttttttthhhhhhhh:	chr7:148767190-148767431(-)$1	241	202	230	20.6377
gggggg[auuuuuuuuuuuuaggggggg	chrX:128580895-128581135(-)$1	240	19	47	24.7978
eeee[bbvvvvvvvvvvvvvbb]eeeee	chr1:242012363-242012603(+)$1	240	22	50	22.8301
!eeeee[auuuuuuuuuuuua]eeeee]	chr12:76441649-76441896(-)$1	247	87	115	24.4684
gggggg[auuuuuuuuuuuua]gggggg	chr7:70256785-70257027(+)$1	242	190	218	24.7430
eeeee[bbwwwwwwwwwwwwwwbb]eee	chr1:226420045-226420297(-)$1	252	163	191	21.4289
"ddddccctttttttttttccc]dddd6	chr16:58554750-58555043(-)$1	293	186	214	23.0835
$$$$$ccctttttttttttccc4444dd	chr12:122064413-122064653(+)$1	240	99	127	22.0880
hhhhhhhuuuuuuuuuuuuhhhhhhhh:	chr10:103346982-103347222(-)$1	240	87	115	20.6275
eee[ddddtttttttttttddddeeeee	chr3:183528706-183528953(+)$1	247	163	191	22.8605
[gggggggtttttttttttggggggg]a	chr7:45758154-45758394(+)$1	240	57	85	24.0283
eeeeddddyyyyyyyyyyyyyyyydddd	chr2:224743062-224743302(-)$1	240	61	89	20.6467
hhhhhhhhvvvvvvvvvvvvvhhhhhhh	chr18:44634152-44634392(-)$1	240	59	87	21.3197
eeeee[bbuuuuuuuuuuuubb]eeeee	chr16:67063531-67063814(+)$1	283	209	237	23.5548
iiiiiiiiyyyyyyyyyyyyyyyyiiii	chr8:103216990-103217234(-)$1	244	159	187	21.8909
ggggggwwwwwwwwwwwwwwgggggggE	chr12:22839737-22839979(+)$1	242	8	36	21.7388
"ddddcccvvvvvvvvvvvvvccc]ddd	chr10:75531437-75531681(+)$1	244	157	185	22.9801
ddddddddtttttttttttdddd]dddd	chr5:71516556-71516804(-)$1	248	190	218	22.0653
ee"""cccvvvvvvvvvvvvvccc>>>>	chr6:117881429-117881669(-)$1	240	147	175	22.3788
eeee!!bbwwwwwwwwwwwwwwbb22ee	chrX:17764052-17764292(+)$1	240	83	111	21.1392
========yyyyyyyyyyyyyyyy====	chr13:107142621-107142861(-)$1	240	61	89	22.0753
=========ssssssssss=========	chr22:21802020-21802260(+)$1	240	42	70	16.7396
hhhhhhhyyyyyyyyyyyyyyyyhhhhh	chr1:204523259-204523499(+)$1	240	207	235	20.5352
fffeeeeettttttttttteeeee::::	chr17:76989212-76989453(-)$1	241	83	111	19.3197
========yyyyyyyyyyyyyyyy====	chr22:44359086-44359326(+)$1	240	168	196	22.0753
[ccc[ccctttttttttttccc]ccc]f	chr11:102267510-102267800(-)$1	290	140	168	23.9954
========ttttttttttt=========	chr7:139257071-139257311(-)$1	240	53	81	24.4468
ccddddwwwwwwwwwwwwwwdddd22cc	chr17:4636355-4636648(+)$1	293	264	292	21.4733
f!!ddddvvvvvvvvvvvvvddddffff	chrX:48436101-48436391(+)$1	290	81	109	22.5059
""fffffftttttttttttffffff>>>	chr2:113287741-113288065(+)$1	324	40	68	22.1142
eee[ddddvvvvvvvvvvvvvdddd]ee	chr16:1709830-1710070(+)$1	240	56	84	22.5788
ffffffwwwwwwwwwwwwwwffffff]h	chr6:21596675-21596920(+)$1	245	17	45	20.7729
ggggg[bbuuuuuuuuuuuubb]ggggg	chr3:44483068-44483320(-)$1	252	64	92	24.0657
c[ccc[bbwwwwwwwwwwwwwwbbcccc	chr6:7286592-7286832(-)$1	240	94	122	21.3388
ccfffffftttttttttttffffff]cc	chr6:82457177-82457425(-)$1	248	76	104	22.4649
#ffffffuuuuuuuuuuuuffffff444	chr19:57869595-57869835(+)$1	240	37	65	22.3032
dddeeeeettttttttttteeeee]ddd	chr20:23352959-23353208(+)$1	249	201	229	22.8923
b!!eeeeeuuuuuuuuuuuueeeee22b	chr13:96276968-96277248(-)$1	280	144	172	23.4119
"""eeeeettttttttttteeeeeeeee	chr15:81296004-81296284(+)$1	280	224	252	23.2357
=====abbuuuuuuuuuuuubb]a]===	chr17:45700054-45700294(+)$1	240	198	226	24.1736
h[cccccctttttttttttccc]ccc33	chr10:72640516-72640806(+)$1	290	231	259	24.0054
f:eeeeewwwwwwwwwwwwwweeeee::	chr1:150448515-150448755(+)$1	240	208	236	19.4854
cc!!dddduuuuuuuuuuuudddd]ccc	chr17:27240872-27241112(-)$1	240	57	85	23.6112
##ddddvvvvvvvvvvvvvdddd333ff	chr5:56224548-56224788(-)$1	240	118	146	21.7545
hhhhhhhuuuuuuuuuuuuhhhhhhhh>	chr1:53516999-53517286(+)$1	287	103	131	21.3608
bffffffuuuuuuuuuuuuffffff]bb	chr9:134350472-134350712(+)$1	240	173	201	21.5472
ggggggwwwwwwwwwwwwwwggggggg6	chr3:153998306-153998546(-)$1	240	72	100	22.3688
a!!eeeeettttttttttteeeee]a22	chr9:108370082-108370322(+)$1	240	61	89	23.4437
))eeeeeuuuuuuuuuuuueeeee6666	chr3:172117995-172118235(+)$1	240	85	113	20.4282
iiiiiiiitttttttttttiiiiiiiii	chr15:44063455-44063703(+)$1	248	144	172	24.1244
eeee[bbuuuuuuuuuuuubb]eeeee4	chr17:28792763-28793089(+)$1	326	209	237	22.8071
!eeeeewwwwwwwwwwwwwweeeee22c	chr5:40761489-40761746(-)$1	257	83	111	22.2026
dddd[ccctttttttttttccc]dddd]	chr4:170015437-170015678(-)$1	241	86	114	23.3105
iiiiiiiiuuuuuuuuuuuuiiiiiiii	chr7:100468106-100468346(+)$1	240	200	228	24.6491

#otherMatches

#Seq PSSM
CGUGGUGUCCUUCUCCAGCAACCAGGGU	chrX:68749673-68749913(+)$1	240	35	63	21.9490
UUAUAAAACAAGGACAUAAUUUUAUGAA	chr7:148767190-148767431(-)$1	241	202	230	20.6377
UGGGAAACUGCUAUUUUCUUGUUCCCAU	chrX:128580895-128581135(-)$1	240	19	47	24.7978
UGCUUUGUUUAAAAUUCAUUCACAGCAG	chr1:242012363-242012603(+)$1	240	22	50	22.8301
GCUGUGCCUUUCAUUACUUUGUUACAGA	chr12:76441649-76441896(-)$1	247	87	115	24.4684
GUGUGUCCUAUUUCAUACCUGUACACAC	chr7:70256785-70257027(+)$1	242	190	218	24.7430
UUCCAACACCAAAUAACCUAACUGCUGG	chr1:226420045-226420297(-)$1	252	163	191	21.4289
AACUGCAUCUCUGUUGUACGUGUCAGUC	chr16:58554750-58555043(-)$1	293	186	214	23.0835
UUCUUCGACCUCGUCCUCCUCGUCCUGU	chr12:122064413-122064653(+)$1	240	99	127	22.0880
GGAUCCAGCCAUACUUCAAUGGAUCCCA	chr10:103346982-103347222(-)$1	240	87	115	20.6275
CUGUACUCUGAGCCCAAGUGAGUCAGCU	chr3:183528706-183528953(+)$1	247	163	191	22.8605
GUGUCCGUAGUUGGCAAAAAUGGGCAGU	chr7:45758154-45758394(+)$1	240	57	85	24.0283
GUUUUGGGGCAUUUGUGGAACUUACCCA	chr2:224743062-224743302(-)$1	240	61	89	20.6467
uguaaaauuaaaacuaucaguauuuuac	chr18:44634152-44634392(-)$1	240	59	87	21.3197
CGCGGGUCACUUGUUGCGCGGGGCCGCG	chr16:67063531-67063814(+)$1	283	209	237	23.5548
AAUAAGGUCACAAUAUUCUUACAUACUU	chr8:103216990-103217234(-)$1	244	159	187	21.8909
CAUUUUCAUAAAACAGAUAAAGAAUGUG	chr12:22839737-22839979(+)$1	242	8	36	21.7388
AGAGCCAGUUCACAUCCCACUCUGAGCU	chr10:75531437-75531681(+)$1	244	157	185	22.9801
UAUGUGCCCUACAUGGCAAGGCACCAUG	chr5:71516556-71516804(-)$1	248	190	218	22.0653
UAUUAGCCUGUAAAUAAAGAUGGCAUCU	chr6:117881429-117881669(-)$1	240	147	175	22.3788
AGGAACCGAAUAUUGUAUCUGACGCAUC	chrX:17764052-17764292(+)$1	240	83	111	21.1392
UUCUGUGCGUCUGUUUUGUGUCUGGUGC	chr13:107142621-107142861(-)$1	240	61	89	22.0753
gugcgugcguguguguguguguaugugc	chr22:21802020-21802260(+)$1	240	42	70	16.7396
AUUGUUCAGAACUAUAUCCUAACGAGCA	chr1:204523259-204523499(+)$1	240	207	235	20.5352
CUGGGUCGUUUCUUCCAUCCGACCUCGU	chr17:76989212-76989453(-)$1	241	83	111	19.3197
GGAAAUUCUUGAAAACAAAGAUGUGAGU	chr22:44359086-44359326(+)$1	240	168	196	22.0753
AGUCAGUCAGAACUUCGUAGACCGACCU	chr11:102267510-102267800(-)$1	290	140	168	23.9954
UUUGAAGAACUUUAUGAACUUUUCAAAG	chr7:139257071-139257311(-)$1	240	53	81	24.4468
GUGGGCAUGGAAAAACUGAAGCCCGAGC	chr17:4636355-4636648(+)$1	293	264	292	21.4733
AUCCAGGGACAUUUUAAAAACCUGUACA	chrX:48436101-48436391(+)$1	290	81	109	22.5059
AAGAGGAGAAAAUCAAUGCCUCCUUGAA	chr2:113287741-113288065(+)$1	324	40	68	22.1142
GCUCUGGAAGCAAACACCAUCUCUACAG	chr16:1709830-1710070(+)$1	240	56	84	22.5788
GGGGAGAACCCAGCGCACCCCUCCCCCC	chr6:21596675-21596920(+)$1	245	17	45	20.7729
UUUGUUUUUUUCUAAAAAUUGAUGCAGA	chr3:44483068-44483320(-)$1	252	64	92	24.0657
CACACACAAACAAGAUUCUUACUGGUGG	chr6:7286592-7286832(-)$1	240	94	122	21.3388
CACGGGAGAAAAAAAUAUCCUCCUGUUG	chr6:82457177-82457425(-)$1	248	76	104	22.4649
UUGAGGGUCCUCAUCUUUUCCCUCAUGA	chr19:57869595-57869835(+)$1	240	37	65	22.3032
GCCACUUUCUUCAAUGUAAAAAGUAGGC	chr20:23352959-23353208(+)$1	249	201	229	22.8923
UAGUUGAUGAAAUGGAAAAAGUCAAGGA	chr13:96276968-96277248(-)$1	280	144	172	23.4119
AGCGUGUGUUUUUUUAAUUUACACUAUA	chr15:81296004-81296284(+)$1	280	224	252	23.2357
UUCUCCCGGUUCAUUUUAUGCGUGCGAG	chr17:45700054-45700294(+)$1	240	198	226	24.1736
UAGCCACCAACUGUACCUGGGUAGGCAA	chr10:72640516-72640806(+)$1	290	231	259	24.0054
CCUAUCGAGAUAAUGUGAAUACGAUAAA	chr1:150448515-150448755(+)$1	240	208	236	19.4854
GUUCCUGAUGCUAUAAAAUCUCAGUACC	chr17:27240872-27241112(-)$1	240	57	85	23.6112
CGGAAGAAGAAUGCCGAAGCUUUGAACA	chr5:56224548-56224788(-)$1	240	118	146	21.7545
UAUAACGUUCUCAGUCCUUUGUUAUAAU	chr1:53516999-53517286(+)$1	287	103	131	21.3608
AUGAAGAGAAAUAACUGGAUCUUUAUUG	chr9:134350472-134350712(+)$1	240	173	201	21.5472
UUCUCACCCCCCAUAGAUAAUGAGAAGA	chr3:153998306-153998546(-)$1	240	72	100	22.3688
UUCCAAAGGAUCCAAUGCACUUUGUAGA	chr9:108370082-108370322(+)$1	240	61	89	23.4437
AAAGAGAUUUUUUGCAUAUUCUCUGCCU	chr3:172117995-172118235(+)$1	240	85	113	20.4282
CAGGACCAGUUUAUGUUUGUGGUUUUGG	chr15:44063455-44063703(+)$1	248	144	172	24.1244
UUUUUGAUCAACCAAUUUUUCUAAAAGU	chr17:28792763-28793089(+)$1	326	209	237	22.8071
uugguaagcacauguauaucuaccauuu	chr5:40761489-40761746(-)$1	257	83	111	22.2026
UAGGUAAUAUAAUGUAUGGGUUUUCUAU	chr4:170015437-170015678(-)$1	241	86	114	23.3105
UUCGCGGCCAGCAUUUCUACGCCGUGGA	chr7:100468106-100468346(+)$1	240	200	228	24.6491

#DB
(.((((..............)))).)))	chrX:68749673-68749913(+)$1	1	35	63	21.9490
((((((((...........)))))))).	chr7:148767190-148767431(-)$1	1	202	230	20.6377
((((((.(............))))))))	chrX:128580895-128581135(-)$1	1	19	47	24.7978
((((.((.............)).)))))	chr1:242012363-242012603(+)$1	1	22	50	22.8301
.(((((.(............).))))).	chr12:76441649-76441896(-)$1	1	87	115	24.4684
((((((.(............).))))))	chr7:70256785-70257027(+)$1	1	190	218	24.7430
(((((.((..............)).)))	chr1:226420045-226420297(-)$1	1	163	191	21.4289
.(((((((...........))).)))).	chr16:58554750-58555043(-)$1	1	186	214	23.0835
.....(((...........)))....))	chr12:122064413-122064653(+)$1	1	99	127	22.0880
(((((((............)))))))).	chr10:103346982-103347222(-)$1	1	87	115	20.6275
(((.((((...........)))))))))	chr3:183528706-183528953(+)$1	1	163	191	22.8605
.(((((((...........))))))).)	chr7:45758154-45758394(+)$1	1	57	85	24.0283
))))((((................))))	chr2:224743062-224743302(-)$1	1	61	89	20.6467
((((((((.............)))))))	chr18:44634152-44634392(-)$1	1	59	87	21.3197
(((((.((............)).)))))	chr16:67063531-67063814(+)$1	1	209	237	23.5548
((((((((................))))	chr8:103216990-103217234(-)$1	1	159	187	21.8909
((((((..............)))))))(	chr12:22839737-22839979(+)$1	1	8	36	21.7388
.(((((((.............))).)))	chr10:75531437-75531681(+)$1	1	157	185	22.9801
((((((((...........)))).))))	chr5:71516556-71516804(-)$1	1	190	218	22.0653
((...(((.............)))....	chr6:117881429-117881669(-)$1	1	147	175	22.3788
((((..((..............))..))	chrX:17764052-17764292(+)$1	1	83	111	21.1392
((((((((................))))	chr13:107142621-107142861(-)$1	1	61	89	22.0753
(((((((((..........)))))))))	chr22:21802020-21802260(+)$1	1	42	70	16.7396
(((((((................)))))	chr1:204523259-204523499(+)$1	1	207	235	20.5352
)))(((((...........)))))....	chr17:76989212-76989453(-)$1	1	83	111	19.3197
((((((((................))))	chr22:44359086-44359326(+)$1	1	168	196	22.0753
.(((.(((...........))).))).)	chr11:102267510-102267800(-)$1	1	140	168	23.9954
((((((((...........)))))))))	chr7:139257071-139257311(-)$1	1	53	81	24.4468
((((((..............))))..))	chr17:4636355-4636648(+)$1	1	264	292	21.4733
(..((((.............))))))))	chrX:48436101-48436391(+)$1	1	81	109	22.5059
..((((((...........))))))...	chr2:113287741-113288065(+)$1	1	40	68	22.1142
(((.((((.............)))).))	chr16:1709830-1710070(+)$1	1	56	84	22.5788
((((((..............)))))).)	chr6:21596675-21596920(+)$1	1	17	45	20.7729
(((((.((............)).)))))	chr3:44483068-44483320(-)$1	1	64	92	24.0657
(.(((.((..............))))))	chr6:7286592-7286832(-)$1	1	94	122	21.3388
((((((((...........)))))).))	chr6:82457177-82457425(-)$1	1	76	104	22.4649
.((((((............))))))...	chr19:57869595-57869835(+)$1	1	37	65	22.3032
((((((((...........))))).)))	chr20:23352959-23353208(+)$1	1	201	229	22.8923
(..(((((............)))))..)	chr13:96276968-96277248(-)$1	1	144	172	23.4119
...(((((...........)))))))))	chr15:81296004-81296284(+)$1	1	224	252	23.2357
((((((((............)).).)))	chr17:45700054-45700294(+)$1	1	198	226	24.1736
(.((((((...........))).)))..	chr10:72640516-72640806(+)$1	1	231	259	24.0054
).(((((..............)))))..	chr1:150448515-150448755(+)$1	1	208	236	19.4854
((..((((............)))).)))	chr17:27240872-27241112(-)$1	1	57	85	23.6112
..((((.............))))...))	chr5:56224548-56224788(-)$1	1	118	146	21.7545
(((((((............)))))))).	chr1:53516999-53517286(+)$1	1	103	131	21.3608
(((((((............)))))).))	chr9:134350472-134350712(+)$1	1	173	201	21.5472
((((((..............))))))).	chr3:153998306-153998546(-)$1	1	72	100	22.3688
(..(((((...........))))).)..	chr9:108370082-108370322(+)$1	1	61	89	23.4437
..(((((............)))))....	chr3:172117995-172118235(+)$1	1	85	113	20.4282
((((((((...........)))))))))	chr15:44063455-44063703(+)$1	1	144	172	24.1244
((((.((............)).))))).	chr17:28792763-28793089(+)$1	1	209	237	22.8071
.(((((..............)))))..)	chr5:40761489-40761746(-)$1	1	83	111	22.2026
((((.(((...........))).)))).	chr4:170015437-170015678(-)$1	1	86	114	23.3105
((((((((............))))))))	chr7:100468106-100468346(+)$1	1	200	228	24.6491

#PSSM
e : 0.16	h : 0.10	c : 0.09	g : 0.09	= : 0.09	" : 0.07	f : 0.07	i : 0.05	d : 0.05	! : 0.03	[ : 0.03	# : 0.03	b : 0.03	$ : 0.01	a : 0.01	) : 0.01	
e : 0.20	g : 0.10	h : 0.09	d : 0.09	= : 0.09	f : 0.07	c : 0.07	[ : 0.05	i : 0.05	! : 0.05	" : 0.03	$ : 0.01	: : 0.01	# : 0.01	) : 0.01	
e : 0.21	d : 0.14	g : 0.10	f : 0.10	h : 0.09	= : 0.09	! : 0.07	i : 0.05	c : 0.05	" : 0.03	$ : 0.01	
e : 0.27	d : 0.14	g : 0.10	h : 0.09	= : 0.09	f : 0.09	i : 0.05	c : 0.05	[ : 0.03	$ : 0.01	" : 0.01	! : 0.01	
d : 0.20	e : 0.20	g : 0.10	h : 0.09	= : 0.09	f : 0.09	[ : 0.07	i : 0.05	c : 0.03	$ : 0.01	" : 0.01	! : 0.01	
d : 0.16	e : 0.16	c : 0.12	h : 0.09	g : 0.09	f : 0.09	[ : 0.07	= : 0.07	i : 0.05	b : 0.03	! : 0.01	a : 0.01	
b : 0.14	c : 0.12	e : 0.12	w : 0.10	d : 0.10	h : 0.09	= : 0.07	f : 0.07	[ : 0.05	i : 0.05	g : 0.01	v : 0.01	
w : 0.12	c : 0.12	b : 0.10	u : 0.10	d : 0.09	e : 0.09	= : 0.07	a : 0.05	v : 0.05	i : 0.05	h : 0.03	f : 0.03	g : 0.01	y : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	= : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
t : 0.30	u : 0.27	w : 0.18	v : 0.12	y : 0.09	s : 0.01	
w : 0.18	u : 0.16	v : 0.10	c : 0.09	y : 0.09	e : 0.09	f : 0.07	h : 0.05	d : 0.05	= : 0.03	g : 0.01	i : 0.01	b : 0.01	
d : 0.12	e : 0.12	b : 0.09	c : 0.09	y : 0.09	f : 0.09	w : 0.07	v : 0.07	h : 0.05	a : 0.05	g : 0.05	= : 0.03	i : 0.03	
d : 0.14	e : 0.14	c : 0.12	y : 0.09	f : 0.09	h : 0.07	g : 0.07	b : 0.07	] : 0.05	w : 0.05	= : 0.03	i : 0.03	
e : 0.18	d : 0.14	] : 0.14	g : 0.09	y : 0.09	f : 0.09	h : 0.07	b : 0.05	c : 0.03	= : 0.03	i : 0.03	4 : 0.01	
e : 0.23	d : 0.12	g : 0.10	h : 0.09	f : 0.09	y : 0.07	c : 0.07	b : 0.05	= : 0.03	i : 0.03	4 : 0.01	] : 0.01	a : 0.01	3 : 0.01	
e : 0.16	] : 0.12	g : 0.10	f : 0.10	h : 0.09	d : 0.09	= : 0.07	i : 0.05	c : 0.05	2 : 0.03	4 : 0.01	> : 0.01	: : 0.01	3 : 0.01	6 : 0.01	
e : 0.14	g : 0.10	d : 0.10	c : 0.09	h : 0.09	= : 0.09	2 : 0.07	i : 0.05	] : 0.05	4 : 0.03	> : 0.03	f : 0.03	: : 0.01	3 : 0.01	a : 0.01	6 : 0.01	
e : 0.16	d : 0.12	c : 0.09	h : 0.09	g : 0.09	= : 0.09	] : 0.05	i : 0.05	2 : 0.05	> : 0.03	: : 0.03	f : 0.03	4 : 0.01	3 : 0.01	b : 0.01	6 : 0.01	
e : 0.12	c : 0.10	d : 0.09	= : 0.09	: : 0.07	g : 0.05	6 : 0.05	h : 0.05	i : 0.05	> : 0.05	f : 0.05	] : 0.03	4 : 0.03	b : 0.03	a : 0.01	E : 0.01	3 : 0.01	2 : 0.01	

#score	1228.877338539517
#seq	55
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_CDS_m2_run1.txt

#BEAR
eeeecccwwwwwwwwwwwwwwccc22	chr7:128846078-128846299(+)$1	221	3	29	22.2183
ggggcccyyyyyyyyyyyyyyyyccc	chr16:30734830-30735052(+)$1	222	136	162	22.0137
e[eeeeeuuuuuuuuuuuueeeee]e	chr17:62496686-62496940(-)$1	254	162	188	24.7765
ff[cccyyyyyyyyyyyyyyyyccc2	chr9:33948356-33948580(-)$1	224	38	64	22.0734
f"""ccctttttttttttccc22fff	chr22:21272164-21272387(+)$1	223	169	195	22.7045
[gggggggtttttttttttggggggg	chr1:154247782-154248009(+)$1	227	72	98	22.7374
DDeeeeettttttttttteeeeeddd	chr2:176043747-176043981(-)$1	234	76	102	20.5698
cc!!cccuuuuuuuuuuuuccc22cc	chr12:62775178-62775398(+)$1	220	192	218	24.1576
!!cccwwwwwwwwwwwwwwccc]ccc	chr19:39879313-39879550(-)$1	237	66	92	22.6439
ggggggguuuuuuuuuuuuggggggg	chr19:36107952-36108181(+)$1	229	86	112	24.0980
""bb[bbtttttttttttbbbbffff	chr1:110882314-110882542(+)$1	228	99	125	21.2584
[cccyyyyyyyyyyyyyyyycccggg	chr10:120829021-120829244(-)$1	223	151	177	22.3219
###dddduuuuuuuuuuuuddddeee	chr17:8158789-8159012(+)$1	223	157	183	23.6791
=======uuuuuuuuuuuu=======	chr21:33067054-33067305(-)$1	251	181	207	24.4212
[a!!dddduuuuuuuuuuuudddd22	chr5:138654497-138654721(+)$1	224	137	163	22.1837
hhhhhwwwwwwwwwwwwwwhhhhhhh	chr12:95442754-95443010(-)$1	256	154	180	19.9019
hha[ddddtttttttttttdddd]a]	chr16:31201266-31201489(+)$1	223	136	162	22.1246
eeeeeyyyyyyyyyyyyyyyyeeeee	chr17:71232994-71233222(+)$1	228	139	165	22.7442
::eeeeeuuuuuuuuuuuueeeee::	chr19:53304799-53305028(-)$1	229	15	41	20.9194
gggg[ccctttttttttttccc]ggg	chr10:111881882-111882109(+)$1	227	145	171	23.4195
ddd[ccctttttttttttccc]dddd	chr1:224619290-224619514(-)$1	224	35	61	22.5519
""eeeeeuuuuuuuuuuuueeeee]c	chr5:178309740-178309968(+)$1	228	124	150	24.8817
hhh[cccuuuuuuuuuuuuccc4444	chr14:24658559-24658787(-)$1	228	131	157	24.1879
effffffwwwwwwwwwwwwwwfffff	chr17:48814249-48814487(+)$1	238	33	59	21.3639
bb[ddddtttttttttttdddd]bb4	chr20:21312135-21312360(+)$1	225	123	149	21.4939
eeeeebbtttttttttttbb]eeeee	chr7:150731384-150731605(+)$1	221	40	66	22.6196
abb[cccuuuuuuuuuuuucccbb]a	chr1:11315991-11316234(-)$1	243	125	151	23.5963
##eeeeeuuuuuuuuuuuueeeee44	chr16:2813239-2813481(+)$1	242	135	161	24.9134
"eeeeevvvvvvvvvvvvveeeeeff	chr19:39421220-39421461(-)$1	241	157	183	23.5430
gga[cccvvvvvvvvvvvvvccc]a]	chr7:23224774-23224998(+)$1	224	148	174	23.6633
d[eeeeeuuuuuuuuuuuueeeee]d	chr22:37887273-37887494(-)$1	221	39	65	24.6003
fbb[cccuuuuuuuuuuuuccc]bb]	chr22:45599737-45599963(-)$1	226	145	171	23.7381
ggggggguuuuuuuuuuuuggggggg	chr1:36291495-36291724(+)$1	229	146	172	24.0980
!!eeeeettttttttttteeeee444	chrX:53658282-53658506(-)$1	224	145	171	23.7016
ee[eeeeettttttttttteeeee44	chr19:45899567-45899786(-)$1	219	39	65	23.3037
e[ddddvvvvvvvvvvvvvdddd]ee	chr6:33634937-33635157(+)$1	220	159	185	22.5094
$$$$$ccctttttttttttccc4444	chr13:75923272-75923500(-)$1	228	50	76	22.2193
ddd[cccuuuuuuuuuuuuccc]ddd	chr21:44299502-44299724(-)$1	222	10	36	23.9827
ceeeeewwwwwwwwwwwwwweeeee]	chrX:100667652-100667875(+)$1	223	89	115	23.0071
!ffffffuuuuuuuuuuuuffffff2	chr15:41313127-41313368(-)$1	241	50	76	23.5352
eeeeeeevvvvvvvvvvvvveeeee]	chr17:7842802-7843031(+)$1	229	156	182	23.7033
d[bb[bbtttttttttttbb]bbddd	chr9:140008884-140009106(-)$1	222	126	152	20.7921
::eeeeevvvvvvvvvvvvveeeee:	chr1:204379521-204379765(-)$1	244	149	175	20.8759
[ffffffyyyyyyyyyyyyyyyyfff	chr17:26918704-26918955(-)$1	251	180	206	21.3966
ggggyyyyyyyyyyyyyyyygggggg	chr17:30685446-30685681(+)$1	235	66	92	22.3295
[eeeeeauuuuuuuuuuuua]eeeee	chr7:1526573-1526800(-)$1	227	85	111	24.8510
!!eeeeeuuuuuuuuuuuueeeeebb	chr3:152163169-152163399(+)$1	230	182	208	24.4235
e[cccwwwwwwwwwwwwwwccc]eee	chr13:75936601-75936826(-)$1	225	59	85	22.5492
fffffwwwwwwwwwwwwwwffffff2	chr19:3976160-3976388(-)$1	228	152	178	21.3792
ee!!bbvvvvvvvvvvvvvbb22eee	chr17:48263927-48264156(-)$1	229	92	118	21.9667
!ffffffuuuuuuuuuuuuffffff2	chr10:127413873-127414097(+)$1	224	104	130	23.5352

#otherMatches

#Seq PSSM
GCCUGGCACACUUCCUUCAAAGCCCU	chr7:128846078-128846299(+)$1	221	3	29	22.2183
CCUGGGCCAGCCUCUUCUCCAAUGCC	chr16:30734830-30735052(+)$1	222	136	162	22.0137
UUCUUUACACCUAAUAACAUAAAGCA	chr17:62496686-62496940(-)$1	254	162	188	24.7765
AAAUGGCAAACAUCACCAGCUCCCAG	chr9:33948356-33948580(-)$1	224	38	64	22.0734
GUCCGCGAUUCUUCCACCUGCCCUGG	chr22:21272164-21272387(+)$1	223	169	195	22.7045
ACUUCUCUUUGUAGAUAGUGGAGGAG	chr1:154247782-154248009(+)$1	227	72	98	22.7374
UCAGCAGAGACAUUGAUACUGCUGCC	chr2:176043747-176043981(-)$1	234	76	102	20.5698
CUAAAUCUUAUGCCGAACUGAUCAAG	chr12:62775178-62775398(+)$1	220	192	218	24.1576
CAGGUGAUCUUUGACUCAGACCCAGC	chr19:39879313-39879550(-)$1	237	66	92	22.6439
GAUGUGACCUUUGGAUCCCUCACGUC	chr19:36107952-36108181(+)$1	229	86	112	24.0980
GAGCACCAAAAAUUCUUCGGGCGGGG	chr1:110882314-110882542(+)$1	228	99	125	21.2584
UGGCAAAUUACUAUAACAAAGUCUCA	chr10:120829021-120829244(-)$1	223	151	177	22.3219
AUGGCCCUAUCAAUAUACUGGGUGAG	chr17:8158789-8159012(+)$1	223	157	183	23.6791
UAAAACUUUAUUCUCAGAUAGUUUUA	chr21:33067054-33067305(-)$1	251	181	207	24.4212
CGCAGUGGAUUAUUACACAACCACAC	chr5:138654497-138654721(+)$1	224	137	163	22.1837
UGUAGCUUUCAGGGUAUUUCUAUAUG	chr12:95442754-95443010(-)$1	256	154	180	19.9019
CUCGCCGGGCAGACUUUAAUCGGGGU	chr16:31201266-31201489(+)$1	223	136	162	22.1246
GGUAAACAAGCUUAUUUUCAAUUGCC	chr17:71232994-71233222(+)$1	228	139	165	22.7442
UCAGUAUUAUACACCAUCUGUACUUC	chr19:53304799-53305028(-)$1	229	15	41	20.9194
UUAUGAGGACUCUGGACAACUUGGUA	chr10:111881882-111882109(+)$1	227	145	171	23.4195
ACUGUUGAUCUCCUCAUGCAAGAGUC	chr1:224619290-224619514(-)$1	224	35	61	22.5519
AAUGAAAAUUUACAAAUAAUUUCAGU	chr5:178309740-178309968(+)$1	228	124	150	24.8817
AUCCGGUAUAUCUAUGUUAACCUCAA	chr14:24658559-24658787(-)$1	228	131	157	24.1879
CAAGCAAUUUUUUAAGUACCUUUGUU	chr17:48814249-48814487(+)$1	238	33	59	21.3639
AGAAGGCAAAGAGGUAAAGCUUACUU	chr20:21312135-21312360(+)$1	225	123	149	21.4939
CGUGGCCAAGUACACAAGGGACCACG	chr7:150731384-150731605(+)$1	221	40	66	22.6196
CUGUCUGAUUCUCACAACCCAGCGUG	chr1:11315991-11316234(-)$1	243	125	151	23.5963
GAAGCAGAUCAGUAUCUCCCUGCUCC	chr16:2813239-2813481(+)$1	242	135	161	24.9134
AUCUCCAACGAUAGUCCAAGGAGAAG	chr19:39421220-39421461(-)$1	241	157	183	23.5430
UGAAAGUUUUCAGGAAAAUUACUAUC	chr7:23224774-23224998(+)$1	224	148	174	23.6633
CGCUGCUCACUCUUCUCUCGGCAGGG	chr22:37887273-37887494(-)$1	221	39	65	24.6003
CUGGUGGCUAGUGACAAAACCAACAC	chr22:45599737-45599963(-)$1	226	145	171	23.7381
AUUUACCAAAGAAAUCAGAGGUAAGU	chr1:36291495-36291724(+)$1	229	146	172	24.0980
GAUGUGGCUUUAAAACAUCCACAGGA	chrX:53658282-53658506(-)$1	224	145	171	23.7016
AUCCGGGGCUCGCCACCCCUCCCGUC	chr19:45899567-45899786(-)$1	219	39	65	23.3037
UGGCUGCACGuuccuuccucagcaag	chr6:33634937-33635157(+)$1	220	159	185	22.5094
UUCUUCCUGUAGGUUGAUGAGGUAAU	chr13:75923272-75923500(-)$1	228	50	76	22.2193
CGUGGGGUAUACGUCAUCUCUCGGCG	chr21:44299502-44299724(-)$1	222	10	36	23.9827
GGGUCUGAUAGAUUUGGAAGAGACCU	chrX:100667652-100667875(+)$1	223	89	115	23.0071
CGCAGUGCCAUUGGAUUCUUACUGCA	chr15:41313127-41313368(-)$1	241	50	76	23.5352
GGCUGCCCUAGAAGAAGAACGGCAGA	chr17:7842802-7843031(+)$1	229	156	182	23.7033
GUCUGGACCACUUCAACUUCGAGCGC	chr9:140008884-140009106(-)$1	222	126	152	20.7921
CAAGGGGCAAGAUUUACCCACCCCUG	chr1:204379521-204379765(-)$1	244	149	175	20.8759
GCUGUCCCUCACCCAGAAACCCAGGA	chr17:26918704-26918955(-)$1	251	180	206	21.3966
UGUUGUUAGGUACAUAAAGAAACAAU	chr17:30685446-30685681(+)$1	235	66	92	22.3295
GGCUGGCGGACCUGGUACAGUCCAGC	chr7:1526573-1526800(-)$1	227	85	111	24.8510
CCUUGUUAGCAGUCAGAAAAGCAAAG	chr3:152163169-152163399(+)$1	230	182	208	24.4235
CAGGGUUUUAAUUUUUUCCCCCAGGU	chr13:75936601-75936826(-)$1	225	59	85	22.5492
AUUUUAACAAACGCAUUAAGAGGUUU	chr19:3976160-3976388(-)$1	228	152	178	21.3792
AGCCGCAAGAACCCCGCCCGCACCUG	chr17:48263927-48264156(-)$1	229	92	118	21.9667
AAAAGGCAAUUCUUUCCAAGUUUUUA	chr10:127413873-127414097(+)$1	224	104	130	23.5352

#DB
(((((((..............)))..	chr7:128846078-128846299(+)$1	1	3	29	22.2183
))))(((................)))	chr16:30734830-30735052(+)$1	1	136	162	22.0137
(.(((((............))))).)	chr17:62496686-62496940(-)$1	1	162	188	24.7765
((.(((................))).	chr9:33948356-33948580(-)$1	1	38	64	22.0734
(...(((...........)))..)))	chr22:21272164-21272387(+)$1	1	169	195	22.7045
.(((((((...........)))))))	chr1:154247782-154248009(+)$1	1	72	98	22.7374
(((((((...........)))))(((	chr2:176043747-176043981(-)$1	1	76	102	20.5698
((..(((............)))..))	chr12:62775178-62775398(+)$1	1	192	218	24.1576
..(((..............))).)))	chr19:39879313-39879550(-)$1	1	66	92	22.6439
(((((((............)))))))	chr19:36107952-36108181(+)$1	1	86	112	24.0980
..((.((...........))))))))	chr1:110882314-110882542(+)$1	1	99	125	21.2584
.(((................))))))	chr10:120829021-120829244(-)$1	1	151	177	22.3219
...((((............)))))))	chr17:8158789-8159012(+)$1	1	157	183	23.6791
(((((((............)))))))	chr21:33067054-33067305(-)$1	1	181	207	24.4212
.(..((((............))))..	chr5:138654497-138654721(+)$1	1	137	163	22.1837
(((((..............)))))))	chr12:95442754-95443010(-)$1	1	154	180	19.9019
(((.((((...........)))).).	chr16:31201266-31201489(+)$1	1	136	162	22.1246
(((((................)))))	chr17:71232994-71233222(+)$1	1	139	165	22.7442
..(((((............)))))..	chr19:53304799-53305028(-)$1	1	15	41	20.9194
((((.(((...........))).)))	chr10:111881882-111882109(+)$1	1	145	171	23.4195
(((.(((...........))).))))	chr1:224619290-224619514(-)$1	1	35	61	22.5519
..(((((............))))).)	chr5:178309740-178309968(+)$1	1	124	150	24.8817
(((.(((............)))....	chr14:24658559-24658787(-)$1	1	131	157	24.1879
(((((((..............)))))	chr17:48814249-48814487(+)$1	1	33	59	21.3639
((.((((...........)))).)).	chr20:21312135-21312360(+)$1	1	123	149	21.4939
(((((((...........)).)))))	chr7:150731384-150731605(+)$1	1	40	66	22.6196
(((.(((............))))).)	chr1:11315991-11316234(-)$1	1	125	151	23.5963
..(((((............)))))..	chr16:2813239-2813481(+)$1	1	135	161	24.9134
.(((((.............)))))))	chr19:39421220-39421461(-)$1	1	157	183	23.5430
(((.(((.............))).).	chr7:23224774-23224998(+)$1	1	148	174	23.6633
(.(((((............))))).)	chr22:37887273-37887494(-)$1	1	39	65	24.6003
(((.(((............))).)).	chr22:45599737-45599963(-)$1	1	145	171	23.7381
(((((((............)))))))	chr1:36291495-36291724(+)$1	1	146	172	24.0980
..(((((...........)))))...	chrX:53658282-53658506(-)$1	1	145	171	23.7016
((.(((((...........)))))..	chr19:45899567-45899786(-)$1	1	39	65	23.3037
(.((((.............)))).))	chr6:33634937-33635157(+)$1	1	159	185	22.5094
.....(((...........)))....	chr13:75923272-75923500(-)$1	1	50	76	22.2193
(((.(((............))).)))	chr21:44299502-44299724(-)$1	1	10	36	23.9827
((((((..............))))).	chrX:100667652-100667875(+)$1	1	89	115	23.0071
.((((((............)))))).	chr15:41313127-41313368(-)$1	1	50	76	23.5352
(((((((.............))))).	chr17:7842802-7843031(+)$1	1	156	182	23.7033
(.((.((...........)).)))))	chr9:140008884-140009106(-)$1	1	126	152	20.7921
..(((((.............))))).	chr1:204379521-204379765(-)$1	1	149	175	20.8759
.((((((................)))	chr17:26918704-26918955(-)$1	1	180	206	21.3966
((((................))))))	chr17:30685446-30685681(+)$1	1	66	92	22.3295
.((((((............).)))))	chr7:1526573-1526800(-)$1	1	85	111	24.8510
..(((((............)))))))	chr3:152163169-152163399(+)$1	1	182	208	24.4235
(.(((..............))).)))	chr13:75936601-75936826(-)$1	1	59	85	22.5492
(((((..............)))))).	chr19:3976160-3976388(-)$1	1	152	178	21.3792
((..((.............))..)))	chr17:48263927-48264156(-)$1	1	92	118	21.9667
.((((((............)))))).	chr10:127413873-127414097(+)$1	1	104	130	23.5352

#PSSM
e : 0.19	g : 0.11	[ : 0.09	! : 0.09	f : 0.07	d : 0.07	" : 0.05	h : 0.05	c : 0.03	# : 0.03	: : 0.03	D : 0.01	= : 0.01	b : 0.01	a : 0.01	$ : 0.01	
e : 0.17	g : 0.13	f : 0.11	[ : 0.09	" : 0.05	! : 0.05	h : 0.05	b : 0.05	c : 0.03	# : 0.03	: : 0.03	d : 0.03	D : 0.01	= : 0.01	a : 0.01	$ : 0.01	
e : 0.31	g : 0.11	f : 0.09	b : 0.07	[ : 0.05	! : 0.05	c : 0.05	d : 0.05	h : 0.03	a : 0.03	" : 0.01	# : 0.01	= : 0.01	$ : 0.01	
e : 0.33	[ : 0.13	g : 0.11	f : 0.09	c : 0.07	! : 0.05	d : 0.05	b : 0.03	" : 0.01	= : 0.01	h : 0.01	$ : 0.01	
e : 0.31	c : 0.25	d : 0.09	f : 0.09	g : 0.05	[ : 0.05	y : 0.03	= : 0.01	h : 0.01	$ : 0.01	b : 0.01	
e : 0.27	c : 0.25	d : 0.09	w : 0.07	b : 0.07	f : 0.07	g : 0.05	y : 0.05	= : 0.01	
c : 0.23	e : 0.21	w : 0.09	y : 0.07	d : 0.07	f : 0.07	g : 0.05	b : 0.05	v : 0.05	= : 0.01	a : 0.01	
u : 0.35	t : 0.15	w : 0.13	y : 0.11	v : 0.11	d : 0.03	c : 0.03	g : 0.01	e : 0.01	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	t : 0.25	w : 0.13	y : 0.11	v : 0.11	
u : 0.37	w : 0.13	y : 0.11	v : 0.11	t : 0.09	b : 0.05	c : 0.03	e : 0.03	d : 0.01	
c : 0.21	e : 0.19	y : 0.11	b : 0.07	d : 0.07	w : 0.05	g : 0.05	v : 0.05	f : 0.05	= : 0.01	u : 0.01	h : 0.01	a : 0.01	
e : 0.25	c : 0.25	d : 0.09	y : 0.07	g : 0.07	] : 0.05	f : 0.05	w : 0.03	b : 0.03	= : 0.01	h : 0.01	
e : 0.31	c : 0.23	d : 0.09	g : 0.07	f : 0.07	y : 0.05	2 : 0.03	b : 0.03	= : 0.01	h : 0.01	] : 0.01	
e : 0.31	] : 0.11	f : 0.09	d : 0.09	c : 0.07	g : 0.07	2 : 0.05	y : 0.03	4 : 0.03	b : 0.03	= : 0.01	h : 0.01	
e : 0.33	f : 0.13	g : 0.11	d : 0.09	c : 0.07	] : 0.05	4 : 0.05	b : 0.05	2 : 0.01	= : 0.01	h : 0.01	
e : 0.19	f : 0.15	g : 0.11	4 : 0.09	c : 0.07	] : 0.07	d : 0.07	b : 0.05	2 : 0.03	a : 0.03	= : 0.01	h : 0.01	: : 0.01	
e : 0.15	2 : 0.11	g : 0.11	4 : 0.11	f : 0.09	d : 0.09	] : 0.09	c : 0.07	: : 0.03	= : 0.01	h : 0.01	a : 0.01	b : 0.01	

#score	1166.2821272284332
#seq	51
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_CDS_m2_run2.txt

#BEAR
ggddddtttttttttttdddd]g	chr15:74750929-74751149(-)$1	220	9	32	21.3730
hhhhhvvvvvvvvvvvvvhhhhh	chr1:152279895-152280118(+)$1	223	35	58	21.3593
ffffffvvvvvvvvvvvvvffff	chr20:2641350-2641571(-)$1	221	104	127	23.3159
fffffftttttttttttffffff	chr9:131287396-131287639(+)$1	243	217	240	21.4812
dd[bbvvvvvvvvvvvvvbbddd	chr2:131103310-131103535(+)$1	225	24	47	22.4518
""eeeeettttttttttteeeee	chr7:139415870-139416096(-)$1	226	63	86	21.6007
g!!bbwwwwwwwwwwwwwwbb22	chr10:129907083-129907354(-)$1	271	39	62	21.2658
[cccwwwwwwwwwwwwwwccc]d	chr1:150940201-150940427(-)$1	226	98	121	22.1394
hhhhhhuuuuuuuuuuuuhhhhh	chr21:34038305-34038525(-)$1	220	121	144	20.5766
ffffffuuuuuuuuuuuufffff	chr8:21856184-21856408(+)$1	224	100	123	22.8565
a[eeeeettttttttttteeeee	chr3:127336747-127336975(+)$1	228	125	148	21.6200
!fffffftttttttttttfffff	chr6:33644446-33644677(+)$1	231	34	57	21.6887
e[dddduuuuuuuuuuuudddd]	chr11:94918487-94918731(-)$1	244	17	40	22.5980
#ddddwwwwwwwwwwwwwwdddd	chr17:8273038-8273268(-)$1	230	173	196	21.7370
ffffffuuuuuuuuuuuufffff	chr4:123844319-123844538(+)$1	219	7	30	22.8565
cc!!bbuuuuuuuuuuuubb22c	chr1:90399522-90399738(+)$1	216	53	76	22.0800
"eeeeevvvvvvvvvvvvveeee	chr1:892497-892721(-)$1	224	148	171	23.4858
Icccwwwwwwwwwwwwwwccccc	chr3:135870907-135871134(-)$1	227	26	49	20.7392
#eeeeevvvvvvvvvvvvveeee	chr17:1578358-1578580(-)$1	222	98	121	23.4508
!fffffftttttttttttfffff	chr4:30724014-30724308(+)$1	294	48	71	21.6887
cc[ccctttttttttttcccccc	chr5:37307333-37307580(-)$1	247	39	62	22.1892
ffffffuuuuuuuuuuuufffff	chr1:45216076-45216306(+)$1	230	125	148	22.8565
cc[cccuuuuuuuuuuuuccc]c	chr4:2514716-2514944(+)$1	228	34	57	23.5628
ffffffuuuuuuuuuuuufffff	chr1:16262120-16262370(+)$1	250	193	216	22.8565
F:ddddvvvvvvvvvvvvvdddd	chr10:329165-329386(-)$1	221	192	215	21.7209
c[cccvvvvvvvvvvvvvccc]c	chr9:135554797-135555105(+)$1	308	16	39	23.9593
"cccwwwwwwwwwwwwwwccc33	chr17:42882803-42883045(-)$1	242	117	140	22.2544
fffffftttttttttttffffff	chr7:99054152-99054367(+)$1	215	21	44	21.4812
!eeeeevvvvvvvvvvvvveeee	chr1:182353568-182353804(-)$1	236	160	183	23.5347
[a[bbwwwwwwwwwwwwwwbb]a	chrX:47065552-47065818(+)$1	266	235	258	21.5799
FFFccctttttttttttccc:dd	chr17:77758424-77758662(+)$1	238	39	62	19.8698
=======ttttttttttt=====	chr9:140093741-140093963(-)$1	222	114	137	21.5870
"""ccctttttttttttccc444	chr10:103900223-103900434(+)$1	211	58	81	22.0437
ff:ddddtttttttttttdddd:	chrX:76944287-76944512(-)$1	225	139	162	19.2920
ee!!bbuuuuuuuuuuuubb22e	chr19:4099243-4099481(-)$1	238	150	173	21.8686
c[ddddvvvvvvvvvvvvvdddd	chrX:47062082-47062296(+)$1	214	81	104	23.1516
f[ddddvvvvvvvvvvvvvdddd	chr17:2601599-2601860(-)$1	261	115	138	23.1445
EEEcccuuuuuuuuuuuucccgg	chr12:98992335-98992553(+)$1	218	110	133	20.5652
%cccwwwwwwwwwwwwwwccc66	chr3:101395518-101395740(-)$1	222	69	92	20.5697
ffffffuuuuuuuuuuuufffff	chr13:108882341-108882564(+)$1	223	130	153	22.8565
beeeeevvvvvvvvvvvvveeee	chr19:57803239-57803464(+)$1	225	176	199	23.1543
[eeeeettttttttttteeeee3	chr7:104747865-104748092(+)$1	227	8	31	21.7518
ddddccctttttttttttccc::	chr1:109492883-109493098(-)$1	215	100	123	19.8412
ff!!bbvvvvvvvvvvvvvbb55	chr19:45912066-45912287(+)$1	221	15	38	21.2954
ffffffvvvvvvvvvvvvvffff	chr20:42341563-42341822(+)$1	259	63	86	23.3159
dddd[bbtttttttttttbb]dd	chr1:35658011-35658235(-)$1	224	31	54	20.5960
ddddwwwwwwwwwwwwwwdddd3	chr5:140782550-140782767(+)$1	217	73	96	21.2718
!!dddduuuuuuuuuuuudddd2	chr1:155447655-155447883(-)$1	228	23	46	22.6996
!eeeeevvvvvvvvvvvvveeee	chr13:78293616-78293837(+)$1	221	84	107	23.5347
"""bbvvvvvvvvvvvvvbb333	chr19:10514029-10514259(-)$1	230	160	183	22.9179
hhhhhvvvvvvvvvvvvvhhhhh	chr7:97822475-97822698(+)$1	223	10	33	21.3593
::eeeeettttttttttteeeee	chr1:171755041-171755301(+)$1	260	19	42	19.6286
[eeeeewwwwwwwwwwwwwweee	chr15:68582144-68582382(+)$1	238	80	103	21.6421
gggggvvvvvvvvvvvvvggggg	chr1:202912800-202913073(-)$1	273	155	178	23.3745
ffffffuuuuuuuuuuuufffff	chr11:10774126-10774355(+)$1	229	71	94	22.8565
cccccvvvvvvvvvvvvvccc]c	chr12:48181736-48181957(-)$1	221	60	83	23.8905
fddddwwwwwwwwwwwwwwdddd	chr7:30671918-30672143(+)$1	225	67	90	21.6666
ccyyyyyyyyyyyyyyyyccc22	chr6:56392296-56392548(-)$1	252	65	88	18.4592
beeeeettttttttttteeeee3	chr1:11184505-11184722(-)$1	217	163	186	21.3673
ddddwwwwwwwwwwwwwwdddd4	chr17:43003427-43003664(-)$1	237	55	78	21.2038
ffff[avvvvvvvvvvvvva]ff	chr8:77895720-77895938(-)$1	218	24	47	23.3473

#otherMatches

#Seq PSSM
UCGGUUGCCAGAGACAGAACUGG	chr15:74750929-74751149(-)$1	220	9	32	21.3730
GUGGGAUCCCUGCCUUCCUCCAC	chr1:152279895-152280118(+)$1	223	35	58	21.3593
UGGACUUAUUUGCCAACGUAGUC	chr20:2641350-2641571(-)$1	221	104	127	23.3159
GCUGCAAGAGGCACAGAUGCAGC	chr9:131287396-131287639(+)$1	243	217	240	21.4812
CCACCUUUCCCCGCCAGUGGGGC	chr2:131103310-131103535(+)$1	225	24	47	22.4518
CCAGCACAAGAACCACACGUGCU	chr7:139415870-139416096(-)$1	226	63	86	21.6007
AGACAUAUAAGGAAAAUAUUGAA	chr10:129907083-129907354(-)$1	271	39	62	21.2658
UGCCUUCAUUGCCGGCAUGGCCG	chr1:150940201-150940427(-)$1	226	98	121	22.1394
CAACUGGAAAUAAGGGAGCAGUU	chr21:34038305-34038525(-)$1	220	121	144	20.5766
GAUGUCUCUUCCCCCAAUGGCAU	chr8:21856184-21856408(+)$1	224	100	123	22.8565
CUCACGCUUUGACAUCCUGUGUG	chr3:127336747-127336975(+)$1	228	125	148	21.6200
GAGGUCUCUAAGUGGCAUGGACC	chr6:33644446-33644677(+)$1	231	34	57	21.6887
AUUUCUUUGUAGCAUUCUAGAAU	chr11:94918487-94918731(-)$1	244	17	40	22.5980
AGUUCAUUUUAUACUACCAGGAU	chr17:8273038-8273268(-)$1	230	173	196	21.7370
GAACCAAAGCGCGGAAAAUGGUU	chr4:123844319-123844538(+)$1	219	7	30	22.8565
GCCAAGUUCAUUUUUAUUCUCUG	chr1:90399522-90399738(+)$1	216	53	76	22.0800
UGCAGGAGAAUGACCAGAGCCUG	chr1:892497-892721(-)$1	224	148	171	23.4858
UGGUAUAAAUAUUCCUUCACCUG	chr3:135870907-135871134(-)$1	227	26	49	20.7392
CAUGACAGCCAAGAACAACGUCG	chr17:1578358-1578580(-)$1	222	98	121	23.4508
ACGGGCAGAUCGAAUACGUGUUC	chr4:30724014-30724308(+)$1	294	48	71	21.6887
CCAUCAGUGAGAUUUUAUGAGGG	chr5:37307333-37307580(-)$1	247	39	62	22.1892
AGCUGCAAACUCCCGCAAGCAGU	chr1:45216076-45216306(+)$1	230	125	148	22.8565
AGGGUAUAAUAAAAUGUUUGCGU	chr4:2514716-2514944(+)$1	228	34	57	23.5628
GGAUGUGAGGAUCAUGGUGCAUC	chr1:16262120-16262370(+)$1	250	193	216	22.8565
CGGCCCCCCCCCAACAGAUGGGC	chr10:329165-329386(-)$1	221	192	215	21.7209
ACUCAAAAAUCUUACUAGUGGAU	chr9:135554797-135555105(+)$1	308	16	39	23.9593
UCCCUCUGUGAUGUACCUGGGCU	chr17:42882803-42883045(-)$1	242	117	140	22.2544
GUGCAUUUAACUGUUUCAUGCGC	chr7:99054152-99054367(+)$1	215	21	44	21.4812
CGUCGCCCCUCUGCCAACUGCGA	chr1:182353568-182353804(-)$1	236	160	183	23.5347
CCAUCCCCAUCUGUACCCUGAAG	chrX:47065552-47065818(+)$1	266	235	258	21.5799
ACAAGCAAAAGUGAGAAGCUGGC	chr17:77758424-77758662(+)$1	238	39	62	19.8698
CCUGGCUUGGCCAAGAAUAGCCG	chr9:140093741-140093963(-)$1	222	114	137	21.5870
CCUGUUCCUAAUGACCUGACUCC	chr10:103900223-103900434(+)$1	211	58	81	22.0437
GUCAAUCAUUUUCAAAAAGAUUC	chrX:76944287-76944512(-)$1	225	139	162	19.2920
GGAAGGUACCCCAUCCCCCCGCC	chr19:4099243-4099481(-)$1	238	150	173	21.8686
CACCCAUAAACGCCUUCAUUGGG	chrX:47062082-47062296(+)$1	214	81	104	23.1516
ACGUCCGAGACCACUACAAGGAC	chr17:2601599-2601860(-)$1	261	115	138	23.1445
AGCUCCCAAAAUGUAUAAGGAAG	chr12:98992335-98992553(+)$1	218	110	133	20.5652
AAGCGUAAAAUCCGAAAAGCUGC	chr3:101395518-101395740(-)$1	222	69	92	20.5697
GCAGUGCCAAGGCUAUUUCACUG	chr13:108882341-108882564(+)$1	223	130	153	22.8565
UCCCACGAACCCAUCCAGAGUGG	chr19:57803239-57803464(+)$1	225	176	199	23.1543
GGGUCUGCAAGAAAUAAAGACUA	chr7:104747865-104748092(+)$1	227	8	31	21.7518
AUGACUGGAUUGACCCCACAGAC	chr1:109492883-109493098(-)$1	215	100	123	19.8412
CCGACCAAAAAGAGAAAGAGGCA	chr19:45912066-45912287(+)$1	221	15	38	21.2954
UCUGCCAACCCCUAGCUGCGGCG	chr20:42341563-42341822(+)$1	259	63	86	23.3159
GACUCCGACCCCGCCGCCUGCAG	chr1:35658011-35658235(-)$1	224	31	54	20.5960
GCCUGAAGAGACAGAAAAGGGCU	chr5:140782550-140782767(+)$1	217	73	96	21.2718
GAUGAACAUACAAACCUUUUCAC	chr1:155447655-155447883(-)$1	228	23	46	22.6996
UCAGAGAAAUCCCUGACUCCUUU	chr13:78293616-78293837(+)$1	221	84	107	23.5347
GCACCCCAACAUCGACACGGCCA	chr19:10514029-10514259(-)$1	230	160	183	22.9179
UGCUGAUGACAUCCUUGCCAGCA	chr7:97822475-97822698(+)$1	223	10	33	21.3593
AGGGCCGGAAACAGCUGGCGGCC	chr1:171755041-171755301(+)$1	260	19	42	19.6286
CGUGCUGAUCCCAAUGCCAAAGC	chr15:68582144-68582382(+)$1	238	80	103	21.6421
UUGCCACUCCUAAGCACCGGCAG	chr1:202912800-202913073(-)$1	273	155	178	23.3745
GACCUACCUUUUGUAUUUUAGGU	chr11:10774126-10774355(+)$1	229	71	94	22.8565
UGUGCUCUACAUCUCCCUGCAUC	chr12:48181736-48181957(-)$1	221	60	83	23.8905
CAGUGAACAAGACCCCCCACACU	chr7:30671918-30672143(+)$1	225	67	90	21.6666
GUACAAAGACAUUACUAAACUGA	chr6:56392296-56392548(-)$1	252	65	88	18.4592
CUCAGGUAUUCAGAAACCCUGAA	chr1:11184505-11184722(-)$1	217	163	186	21.3673
AGCGUCACUUUCCUUCCUCGCUG	chr17:43003427-43003664(-)$1	237	55	78	21.2038
AGAACGUCUCCUAGGUAUUCAUU	chr8:77895720-77895938(-)$1	218	24	47	23.3473

#DB
((((((...........)))).)	chr15:74750929-74751149(-)$1	1	9	32	21.3730
(((((.............)))))	chr1:152279895-152280118(+)$1	1	35	58	21.3593
((((((.............))))	chr20:2641350-2641571(-)$1	1	104	127	23.3159
((((((...........))))))	chr9:131287396-131287639(+)$1	1	217	240	21.4812
((.((.............)))))	chr2:131103310-131103535(+)$1	1	24	47	22.4518
..(((((...........)))))	chr7:139415870-139416096(-)$1	1	63	86	21.6007
(..((..............))..	chr10:129907083-129907354(-)$1	1	39	62	21.2658
.(((..............))).)	chr1:150940201-150940427(-)$1	1	98	121	22.1394
((((((............)))))	chr21:34038305-34038525(-)$1	1	121	144	20.5766
((((((............)))))	chr8:21856184-21856408(+)$1	1	100	123	22.8565
(.(((((...........)))))	chr3:127336747-127336975(+)$1	1	125	148	21.6200
.((((((...........)))))	chr6:33644446-33644677(+)$1	1	34	57	21.6887
(.((((............)))).	chr11:94918487-94918731(-)$1	1	17	40	22.5980
.((((..............))))	chr17:8273038-8273268(-)$1	1	173	196	21.7370
((((((............)))))	chr4:123844319-123844538(+)$1	1	7	30	22.8565
((..((............))..)	chr1:90399522-90399738(+)$1	1	53	76	22.0800
.(((((.............))))	chr1:892497-892721(-)$1	1	148	171	23.4858
((((..............)))((	chr3:135870907-135871134(-)$1	1	26	49	20.7392
.(((((.............))))	chr17:1578358-1578580(-)$1	1	98	121	23.4508
.((((((...........)))))	chr4:30724014-30724308(+)$1	1	48	71	21.6887
((.(((...........))))))	chr5:37307333-37307580(-)$1	1	39	62	22.1892
((((((............)))))	chr1:45216076-45216306(+)$1	1	125	148	22.8565
((.(((............))).)	chr4:2514716-2514944(+)$1	1	34	57	23.5628
((((((............)))))	chr1:16262120-16262370(+)$1	1	193	216	22.8565
).((((.............))))	chr10:329165-329386(-)$1	1	192	215	21.7209
(.(((.............))).)	chr9:135554797-135555105(+)$1	1	16	39	23.9593
.(((..............)))..	chr17:42882803-42883045(-)$1	1	117	140	22.2544
((((((...........))))))	chr7:99054152-99054367(+)$1	1	21	44	21.4812
.(((((.............))))	chr1:182353568-182353804(-)$1	1	160	183	23.5347
.(.((..............)).)	chrX:47065552-47065818(+)$1	1	235	258	21.5799
((((((...........))).((	chr17:77758424-77758662(+)$1	1	39	62	19.8698
(((((((...........)))))	chr9:140093741-140093963(-)$1	1	114	137	21.5870
...(((...........)))...	chr10:103900223-103900434(+)$1	1	58	81	22.0437
)).((((...........)))).	chrX:76944287-76944512(-)$1	1	139	162	19.2920
((..((............))..)	chr19:4099243-4099481(-)$1	1	150	173	21.8686
(.((((.............))))	chrX:47062082-47062296(+)$1	1	81	104	23.1516
(.((((.............))))	chr17:2601599-2601860(-)$1	1	115	138	23.1445
)))(((............)))((	chr12:98992335-98992553(+)$1	1	110	133	20.5652
.(((..............)))..	chr3:101395518-101395740(-)$1	1	69	92	20.5697
((((((............)))))	chr13:108882341-108882564(+)$1	1	130	153	22.8565
((((((.............))))	chr19:57803239-57803464(+)$1	1	176	199	23.1543
.(((((...........))))).	chr7:104747865-104748092(+)$1	1	8	31	21.7518
))))(((...........)))..	chr1:109492883-109493098(-)$1	1	100	123	19.8412
((..((.............))..	chr19:45912066-45912287(+)$1	1	15	38	21.2954
((((((.............))))	chr20:42341563-42341822(+)$1	1	63	86	23.3159
((((.((...........)).))	chr1:35658011-35658235(-)$1	1	31	54	20.5960
((((..............)))).	chr5:140782550-140782767(+)$1	1	73	96	21.2718
..((((............)))).	chr1:155447655-155447883(-)$1	1	23	46	22.6996
.(((((.............))))	chr13:78293616-78293837(+)$1	1	84	107	23.5347
...((.............))...	chr19:10514029-10514259(-)$1	1	160	183	22.9179
(((((.............)))))	chr7:97822475-97822698(+)$1	1	10	33	21.3593
..(((((...........)))))	chr1:171755041-171755301(+)$1	1	19	42	19.6286
.(((((..............)))	chr15:68582144-68582382(+)$1	1	80	103	21.6421
(((((.............)))))	chr1:202912800-202913073(-)$1	1	155	178	23.3745
((((((............)))))	chr11:10774126-10774355(+)$1	1	71	94	22.8565
(((((.............))).)	chr12:48181736-48181957(-)$1	1	60	83	23.8905
)((((..............))))	chr7:30671918-30672143(+)$1	1	67	90	21.6666
((................)))..	chr6:56392296-56392548(-)$1	1	65	88	18.4592
((((((...........))))).	chr1:11184505-11184722(-)$1	1	163	186	21.3673
((((..............)))).	chr17:43003427-43003664(-)$1	1	55	78	21.2038
((((.(.............).))	chr8:77895720-77895938(-)$1	1	24	47	23.3473

#PSSM
f : 0.24	c : 0.11	d : 0.08	" : 0.08	! : 0.08	[ : 0.06	g : 0.04	h : 0.04	e : 0.03	# : 0.03	F : 0.03	b : 0.03	a : 0.01	I : 0.01	= : 0.01	E : 0.01	% : 0.01	: : 0.01	
f : 0.24	c : 0.14	e : 0.14	d : 0.11	[ : 0.08	h : 0.04	" : 0.04	g : 0.03	! : 0.03	: : 0.03	a : 0.01	F : 0.01	= : 0.01	E : 0.01	
f : 0.21	d : 0.19	e : 0.18	c : 0.09	[ : 0.06	! : 0.06	h : 0.04	" : 0.03	F : 0.01	= : 0.01	: : 0.01	E : 0.01	g : 0.01	y : 0.01	
d : 0.21	f : 0.21	e : 0.18	c : 0.18	b : 0.06	h : 0.04	! : 0.04	= : 0.01	g : 0.01	y : 0.01	
f : 0.19	e : 0.18	d : 0.14	c : 0.13	b : 0.11	w : 0.09	h : 0.04	[ : 0.03	= : 0.01	g : 0.01	y : 0.01	
f : 0.19	e : 0.18	w : 0.16	d : 0.11	v : 0.11	c : 0.09	b : 0.06	h : 0.01	= : 0.01	y : 0.01	a : 0.01	
v : 0.31	u : 0.21	w : 0.18	t : 0.13	e : 0.04	f : 0.03	= : 0.01	d : 0.01	c : 0.01	b : 0.01	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	t : 0.27	u : 0.21	w : 0.18	y : 0.01	
v : 0.31	u : 0.21	w : 0.18	t : 0.14	c : 0.04	f : 0.03	e : 0.03	d : 0.01	y : 0.01	
c : 0.21	v : 0.19	f : 0.16	d : 0.09	b : 0.08	e : 0.08	w : 0.08	h : 0.04	= : 0.01	g : 0.01	
c : 0.21	f : 0.19	d : 0.18	e : 0.16	b : 0.13	h : 0.04	= : 0.01	w : 0.01	g : 0.01	a : 0.01	
d : 0.19	f : 0.19	e : 0.18	c : 0.18	h : 0.04	b : 0.04	2 : 0.03	] : 0.03	: : 0.01	= : 0.01	4 : 0.01	3 : 0.01	g : 0.01	
f : 0.21	d : 0.21	e : 0.18	] : 0.09	2 : 0.06	h : 0.04	c : 0.03	3 : 0.03	g : 0.03	= : 0.01	4 : 0.01	6 : 0.01	: : 0.01	5 : 0.01	
f : 0.21	e : 0.16	d : 0.14	c : 0.09	3 : 0.08	g : 0.04	h : 0.04	2 : 0.04	4 : 0.03	: : 0.03	] : 0.01	a : 0.01	= : 0.01	6 : 0.01	5 : 0.01	

#score	1340.4866442426105
#seq	61
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_UTR_m2_run1.txt

#BEAR
ccc$$$$$ddddoooooodddd333cccGG	chr10:858360-858606(-)$1	246	150	180	15.3021
[===========nnnnn===========22	chrX:106894030-106894257(+)$1	227	36	66	11.1227
dddddd"""cccooooooccc333dddd]d	chr3:30049504-30049737(+)$1	233	145	175	13.7895
====="""ddddoooooodddd333=====	chr8:38830162-38830386(+)$1	224	183	213	18.7386
gggggg[cccrrrrrrrrrccc]ggggggg	chr6:11183947-11184168(-)$1	221	36	66	9.9781
[dddd"""ddddnnnnndddd333ddddbb	chr5:162880484-162880709(-)$1	225	35	65	12.2381
ggggg!!eeeeeooooooeeeeeggggggg	chr3:156260308-156260539(-)$1	231	58	88	14.1859
c[a!!dddd[annnnna]dddd22a333cc	chr5:36194780-36195005(-)$1	225	108	138	11.3093
d"""ccc[ddddooooooddddccc>>>>>	chrX:48436125-48436356(+)$1	231	153	183	13.6951
ddd"""ccc!!cccnnnnnccc22ccc333	chr10:14562563-14562794(-)$1	231	147	177	9.8303
=====[dddd[aooooooa]dddd======	chr14:64971820-64972045(+)$1	225	119	149	14.1698
:ffffff!!ddddnnnnndddd22ffffff	chr9:123363853-123364106(-)$1	253	103	133	10.3771
!!bb!!ccc[aooooooa]ccc22bb22a]	chr8:23118418-23118648(+)$1	230	138	168	12.6107
:hhhhhhhhcccooooooccc4444hhhhh	chr9:37865373-37865629(+)$1	256	81	111	11.4155
eeeee"""ddddoooooodddd22eeeee]	chr13:110802224-110802470(-)$1	246	8	38	16.7945
:ffffff[ddddoooooodddd]ffffff:	chr21:35476684-35476915(+)$1	231	171	201	12.2041
ii==========oooooo==========BB	chr12:12874363-12874620(+)$1	257	165	195	12.5394
====!!eeeeeooooooeeeee22======	chr5:89812218-89812489(-)$1	271	170	200	14.8340
ii!!ddddddddoooooodddd]dddd22i	chr5:159503084-159503311(-)$1	227	86	116	14.2342
!!ggggggg[ddddmmmmdddd]ggggggg	chr1:114306451-114306681(-)$1	230	91	121	10.3965
eeeee"""ddddoooooodddd333eeeee	chr14:104024442-104024726(-)$1	284	37	67	17.1963
[gggggggddddoooooodddd22gggggg	chr5:54460291-54460538(+)$1	247	125	155	16.8931
eggggggg[cccoooooocccggggggg]e	chr6:82456501-82456744(-)$1	243	23	53	13.4436
:dddd"""ddddoooooodddd333dddd:	chr3:113439734-113439990(-)$1	256	13	43	14.8112
eeee[bb[ddddoooooodddd333bb]ee	chr3:52028805-52029029(-)$1	224	169	199	16.0412
ffff[bb[ddddoooooodddd4444bb]f	chr11:57067113-57067372(-)$1	259	177	207	15.0322
[eeeee"""ddddnnnnndddd333eeeee	chr17:63007084-63007378(-)$1	294	198	228	13.0867
iiiiiii[ddddoooooodddd333iiiii	chr2:29170381-29170638(+)$1	257	178	208	18.0620
hhhhh!!eeeeeooooooeeeee4444hhh	chr15:52842587-52842831(-)$1	244	142	172	13.4474
iiiiiii[ddddoooooodddd333iiiii	chr2:131809053-131809281(-)$1	228	78	108	18.0620
gggggggeeeeennnnneeeee]ggggggg	chr10:120443479-120443702(-)$1	223	156	186	10.9196
dccc####ddddoooooodddd666666cc	chr1:87209017-87209248(+)$1	231	20	50	13.7523
e[ccc[a!!eeeeellleeeee22a]ccc]	chr2:208630471-208630702(-)$1	231	114	144	11.1487
eeeeeee[ddddoooooodddd]eeeeedd	chr10:112658008-112658240(+)$1	232	166	196	14.4347
dd[ccc[eeeeeooooooeeeee]cccddd	chr4:88084031-88084257(-)$1	226	179	209	12.8836
iii[bb[cccooooooccc]bb22iiiiii	chr3:39137447-39137673(+)$1	226	62	92	11.4790
eee"""ddddcccooooooccc22dddd55	chr5:32602605-32602845(+)$1	240	24	54	11.5913
gggg"""eeeeeooooooeeeee4444ggg	chr6:56969672-56969923(+)$1	251	121	151	15.0216
hhhhhhh[ddddoooooodddd22hhhhhh	chr7:26252075-26252295(+)$1	220	143	173	14.5961
===####eeeeennnnneeeee4444====	chr3:130720404-130720677(+)$1	273	15	45	12.4499
b[eeeee!!cccooooooccc333eeeee]	chr21:45113193-45113434(+)$1	241	115	145	14.3004
eee!!bb[ddddoooooodddd]bb22eee	chr1:38462405-38462643(-)$1	238	171	201	14.3982
e!!eeeeeddddoooooodddd22eeeee]	chr3:30048701-30048932(+)$1	231	17	47	15.6950
ccccc####cccooooooccc22ccc]ccc	chr12:107367208-107367433(+)$1	225	186	216	14.0573
===========oooooo===========:e	chr1:169433334-169433559(-)$1	225	100	130	12.6128

#otherMatches

#Seq PSSM
CUCUAGAACGUCCCCGCAGAUGAAUGAGGG	chr10:858360-858606(-)$1	246	150	180	15.3021
UAGCCUACUGCCACUGAGGCAGUAGGUUUU	chrX:106894030-106894257(+)$1	227	36	66	11.1227
UAUUAAUGAAAAGUGAAAUUUGAUUUAAUU	chr3:30049504-30049737(+)$1	233	145	175	13.7895
CCUUGCCUGAGUUGUGCUAUUUUCAUAAGG	chr8:38830162-38830386(+)$1	224	183	213	18.7386
AUGGGGCAGGUGAAAUACUUCUACCCCAUG	chr6:11183947-11184168(-)$1	221	36	66	9.9781
AGUAUAGAUCAUGUGAAAUGAAGGGUGCCU	chr5:162880484-162880709(-)$1	225	35	65	12.2381
UCUCUAAUUUUCCAACUAGAGGAAGAGAAA	chr3:156260308-156260539(-)$1	231	58	88	14.1859
CCCUUUCCUCCUAAUUGUGGGAUUGUCAGA	chr5:36194780-36195005(-)$1	225	108	138	11.3093
accaacauggugaaaccccaucuguacuaa	chrX:48436125-48436356(+)$1	231	153	183	13.6951
AGGAACGUGAAUGUCGAGCACAGCCACUAC	chr10:14562563-14562794(-)$1	231	147	177	9.8303
UCUCUGCCUUUAUUUUUUUCGAGGGGGGAG	chr14:64971820-64972045(+)$1	225	119	149	14.1698
AAAAUGACAUUUGAAAACUAAAGCUCAUUU	chr9:123363853-123364106(-)$1	253	103	133	10.3771
UGUCCCACUUGAUUUCACUGGUAAGAAUGA	chr8:23118418-23118648(+)$1	230	138	168	12.6107
AAGAGUAAAAUCUAAUCUGAUGUUUUUUAC	chr9:37865373-37865629(+)$1	256	81	111	11.4155
AUAUUUUCUGCAAUCCAAUGCACUGAUGUG	chr13:110802224-110802470(-)$1	246	8	38	16.7945
UAUAUCUGGUGUAGACUAAUAUGAGAUGUU	chr21:35476684-35476915(+)$1	231	171	201	12.2041
CAAGCUAUCUAAAGUUUGUUAGAUAGCUGC	chr12:12874363-12874620(+)$1	257	165	195	12.5394
GUUAUUGUUUAACAUUAUGGAUUUUAAUUG	chr5:89812218-89812489(-)$1	271	170	200	14.8340
GAUCAGGUUUUAAGUAUAUAAAUAUUUUUU	chr5:159503084-159503311(-)$1	227	86	116	14.2342
CUGUUAAAGCaaaaauuuuuuuuuuuuaau	chr1:114306451-114306681(-)$1	230	91	121	10.3965
CUUUAAACAGCUCAAAGUAGCUAGCUAAAG	chr14:104024442-104024726(-)$1	284	37	67	17.1963
ACAUUUUCUAGGACUGUACUUGAUGAAAAU	chr5:54460291-54460538(+)$1	247	125	155	16.8931
GGUUGGUAGCUUAGUUGGAAGUGCCAGCAC	chr6:82456501-82456744(-)$1	243	23	53	13.4436
AAGUAUUUGAGUUAAACUGCUUUUUUGCUA	chr3:113439734-113439990(-)$1	256	13	43	14.8112
CCUCUGGUCAGGGUGUAACCUGCCUCCUGA	chr3:52028805-52029029(-)$1	224	169	199	16.0412
UCUCCGUCUGCCCCGCCAGGUACCCCACAG	chr11:57067113-57067372(-)$1	259	177	207	15.0322
UAUGCUUUUGAUAAAAUGUAUUUUCAGCAU	chr17:63007084-63007378(-)$1	294	198	228	13.0867
aaauauuuuuauaauuaaauaauuuaauGU	chr2:29170381-29170638(+)$1	257	178	208	18.0620
UGUUUAAAUAAAAGGAACUUUAUAAUGAAA	chr15:52842587-52842831(-)$1	244	142	172	13.4474
UUAUAUGUCUUUAUUGGAAAAGUCCUAUGU	chr2:131809053-131809281(-)$1	228	78	108	18.0620
UGCAAAAUUUAGUUUCUCUAAAUUUUUGCA	chr10:120443479-120443702(-)$1	223	156	186	10.9196
UCAGAAACUGGCCUUUCUGCCAAUAAAGUU	chr1:87209017-87209248(+)$1	231	20	50	13.7523
UUAUUCCUCCUCUCCUGGAGAGCUGUGAUU	chr2:208630471-208630702(-)$1	231	114	144	11.1487
GACAGUGUUUUUUGUAGUAAAAUCACUGGU	chr10:112658008-112658240(+)$1	232	166	196	14.4347
agcuuauaggcuauaagaagccuuuaauuu	chr4:88084031-88084257(-)$1	226	179	209	12.8836
UCCACCAUAGCAGGGACUAGGGAGGGAGGC	chr3:39137447-39137673(+)$1	226	62	92	11.4790
UACCAAGUUUGAUUCAUACAUCUAAAACAU	chr5:32602605-32602845(+)$1	240	24	54	11.5913
GuuaauuuuuuauuauuuuaaaauCUCUGG	chr6:56969672-56969923(+)$1	251	121	151	15.0216
uguguguguguguguAUCCAUAAAAUGCAU	chr7:26252075-26252295(+)$1	220	143	173	14.5961
UGAAACUUUAUAAAGCAUAUGGUCAGUUAU	chr3:130720404-130720677(+)$1	273	15	45	12.4499
CGCUAUAAAUUAUACCUUUAAGAAUGUGGG	chr21:45113193-45113434(+)$1	241	115	145	14.3004
UCCAGAUUCUGCAAUAAAGCGGUGUGAGGA	chr1:38462405-38462643(-)$1	238	171	201	14.3982
UUUAAUCAACAAAAUAUAUUGUAGUGAuuu	chr3:30048701-30048932(+)$1	231	17	47	15.6950
GAGGUUCUUGUUGAAAUGAACUUACCAUCU	chr12:107367208-107367433(+)$1	225	186	216	14.0573
AUUUUAUUAAAUCUUUUUUUAAUGGAAUGU	chr1:169433334-169433559(-)$1	225	100	130	12.6128

#DB
(((.....((((......))))...)))))	chr10:858360-858606(-)$1	1	150	180	15.3021
.(((((((((((.....)))))))))))..	chrX:106894030-106894257(+)$1	1	36	66	11.1227
((((((...(((......)))...)))).)	chr3:30049504-30049737(+)$1	1	145	175	13.7895
(((((...((((......))))...)))))	chr8:38830162-38830386(+)$1	1	183	213	18.7386
((((((.(((.........))).)))))))	chr6:11183947-11184168(-)$1	1	36	66	9.9781
.((((...((((.....))))...))))))	chr5:162880484-162880709(-)$1	1	35	65	12.2381
(((((..(((((......))))))))))))	chr3:156260308-156260539(-)$1	1	58	88	14.1859
(.(..((((.(.....).))))..)...))	chr5:36194780-36195005(-)$1	1	108	138	11.3093
(...(((.((((......))))))).....	chrX:48436125-48436356(+)$1	1	153	183	13.6951
(((...(((..(((.....)))..)))...	chr10:14562563-14562794(-)$1	1	147	177	9.8303
(((((.((((.(......).))))))))))	chr14:64971820-64972045(+)$1	1	119	149	14.1698
.((((((..((((.....))))..))))))	chr9:123363853-123364106(-)$1	1	103	133	10.3771
..((..(((.(......).)))..))..).	chr8:23118418-23118648(+)$1	1	138	168	12.6107
.(((((((((((......)))....)))))	chr9:37865373-37865629(+)$1	1	81	111	11.4155
(((((...((((......))))..))))).	chr13:110802224-110802470(-)$1	1	8	38	16.7945
.((((((.((((......)))).)))))).	chr21:35476684-35476915(+)$1	1	171	201	12.2041
))((((((((((......))))))))))))	chr12:12874363-12874620(+)$1	1	165	195	12.5394
((((..(((((......)))))..))))))	chr5:89812218-89812489(-)$1	1	170	200	14.8340
((..((((((((......)))).))))..)	chr5:159503084-159503311(-)$1	1	86	116	14.2342
..(((((((.((((....)))).)))))))	chr1:114306451-114306681(-)$1	1	91	121	10.3965
(((((...((((......))))...)))))	chr14:104024442-104024726(-)$1	1	37	67	17.1963
.(((((((((((......))))..))))))	chr5:54460291-54460538(+)$1	1	125	155	16.8931
((((((((.(((......)))))))))).)	chr6:82456501-82456744(-)$1	1	23	53	13.4436
.((((...((((......))))...)))).	chr3:113439734-113439990(-)$1	1	13	43	14.8112
((((.((.((((......))))...)).))	chr3:52028805-52029029(-)$1	1	169	199	16.0412
((((.((.((((......))))....)).)	chr11:57067113-57067372(-)$1	1	177	207	15.0322
.(((((...((((.....))))...)))))	chr17:63007084-63007378(-)$1	1	198	228	13.0867
(((((((.((((......))))...)))))	chr2:29170381-29170638(+)$1	1	178	208	18.0620
(((((..(((((......)))))....)))	chr15:52842587-52842831(-)$1	1	142	172	13.4474
(((((((.((((......))))...)))))	chr2:131809053-131809281(-)$1	1	78	108	18.0620
((((((((((((.....))))).)))))))	chr10:120443479-120443702(-)$1	1	156	186	10.9196
((((....((((......))))......))	chr1:87209017-87209248(+)$1	1	20	50	13.7523
(.(((.(..(((((...)))))..).))).	chr2:208630471-208630702(-)$1	1	114	144	11.1487
))(((((.((((......)))).)))))((	chr10:112658008-112658240(+)$1	1	166	196	14.4347
((.(((.(((((......))))).))))))	chr4:88084031-88084257(-)$1	1	179	209	12.8836
(((.((.(((......))).))..))))))	chr3:39137447-39137673(+)$1	1	62	92	11.4790
(((...(((((((......)))..))))..	chr5:32602605-32602845(+)$1	1	24	54	11.5913
((((...(((((......)))))....)))	chr6:56969672-56969923(+)$1	1	121	151	15.0216
(((((((.((((......))))..))))))	chr7:26252075-26252295(+)$1	1	143	173	14.5961
(((....(((((.....)))))....))))	chr3:130720404-130720677(+)$1	1	15	45	12.4499
(.(((((..(((......)))...))))).	chr21:45113193-45113434(+)$1	1	115	145	14.3004
(((..((.((((......)))).))..)))	chr1:38462405-38462643(-)$1	1	171	201	14.3982
(..(((((((((......))))..))))).	chr3:30048701-30048932(+)$1	1	17	47	15.6950
(((((....(((......)))..))).)))	chr12:107367208-107367433(+)$1	1	186	216	14.0573
(((((((((((......))))))))))).(	chr1:169433334-169433559(-)$1	1	100	130	12.6128

#PSSM
e : 0.20	d : 0.11	= : 0.11	i : 0.11	[ : 0.08	g : 0.08	: : 0.08	c : 0.06	! : 0.04	h : 0.04	f : 0.02	b : 0.02	
e : 0.15	= : 0.13	g : 0.13	d : 0.11	i : 0.11	c : 0.06	[ : 0.06	f : 0.06	! : 0.06	h : 0.06	" : 0.02	
e : 0.17	= : 0.15	g : 0.15	c : 0.08	d : 0.08	f : 0.06	h : 0.06	i : 0.06	! : 0.04	a : 0.02	" : 0.02	b : 0.02	[ : 0.02	
g : 0.15	e : 0.15	= : 0.13	c : 0.08	d : 0.06	! : 0.06	" : 0.06	f : 0.06	h : 0.06	i : 0.04	$ : 0.02	b : 0.02	[ : 0.02	# : 0.02	
g : 0.13	e : 0.13	= : 0.11	d : 0.08	! : 0.08	c : 0.08	" : 0.06	h : 0.06	f : 0.04	[ : 0.04	i : 0.04	# : 0.04	$ : 0.02	b : 0.02	
" : 0.17	g : 0.11	! : 0.08	b : 0.08	e : 0.08	= : 0.06	d : 0.06	# : 0.06	c : 0.04	[ : 0.04	f : 0.04	h : 0.04	i : 0.04	$ : 0.02	
" : 0.17	d : 0.08	e : 0.08	g : 0.08	= : 0.06	[ : 0.06	c : 0.06	b : 0.06	# : 0.06	! : 0.04	f : 0.04	h : 0.04	i : 0.04	$ : 0.02	a : 0.02	
[ : 0.20	e : 0.17	" : 0.15	c : 0.08	d : 0.08	= : 0.06	! : 0.06	g : 0.06	# : 0.04	$ : 0.02	h : 0.02	
d : 0.48	e : 0.15	c : 0.08	= : 0.06	! : 0.06	" : 0.04	h : 0.02	g : 0.02	[ : 0.02	# : 0.02	
d : 0.51	e : 0.17	c : 0.15	= : 0.06	[ : 0.06	! : 0.02	
d : 0.48	e : 0.17	c : 0.13	= : 0.06	a : 0.04	r : 0.02	! : 0.02	[ : 0.02	o : 0.02	
d : 0.48	c : 0.15	e : 0.15	o : 0.08	= : 0.04	r : 0.02	n : 0.02	a : 0.02	
o : 0.73	n : 0.11	d : 0.06	c : 0.04	r : 0.02	e : 0.02	
o : 0.75	n : 0.15	r : 0.02	c : 0.02	d : 0.02	e : 0.02	
o : 0.75	n : 0.17	r : 0.02	m : 0.02	l : 0.02	
o : 0.75	n : 0.17	r : 0.02	m : 0.02	l : 0.02	
o : 0.73	n : 0.15	r : 0.02	a : 0.02	m : 0.02	l : 0.02	c : 0.02	
o : 0.66	e : 0.08	n : 0.06	= : 0.04	r : 0.02	d : 0.02	] : 0.02	a : 0.02	m : 0.02	c : 0.02	
d : 0.51	e : 0.17	c : 0.13	= : 0.06	r : 0.02	n : 0.02	a : 0.02	] : 0.02	o : 0.02	
d : 0.51	c : 0.20	e : 0.17	= : 0.06	] : 0.04	
d : 0.53	c : 0.20	e : 0.17	= : 0.06	b : 0.02	
d : 0.51	e : 0.17	c : 0.08	= : 0.06	3 : 0.06	4 : 0.02	g : 0.02	b : 0.02	2 : 0.02	
2 : 0.28	3 : 0.24	] : 0.15	e : 0.08	= : 0.06	4 : 0.06	c : 0.02	d : 0.02	g : 0.02	6 : 0.02	
2 : 0.26	3 : 0.24	g : 0.11	4 : 0.11	= : 0.06	c : 0.04	d : 0.04	f : 0.02	6 : 0.02	e : 0.02	] : 0.02	b : 0.02	
3 : 0.17	g : 0.13	= : 0.11	4 : 0.11	d : 0.08	c : 0.08	e : 0.08	a : 0.04	f : 0.04	b : 0.04	6 : 0.02	i : 0.02	h : 0.02	
= : 0.13	g : 0.13	e : 0.13	d : 0.11	c : 0.08	4 : 0.08	i : 0.06	f : 0.04	b : 0.04	h : 0.04	3 : 0.02	> : 0.02	6 : 0.02	] : 0.02	2 : 0.02	
= : 0.15	g : 0.13	e : 0.13	d : 0.11	c : 0.08	i : 0.06	f : 0.04	2 : 0.04	h : 0.04	b : 0.04	4 : 0.04	3 : 0.02	> : 0.02	6 : 0.02	] : 0.02	
= : 0.15	g : 0.15	e : 0.15	d : 0.11	c : 0.06	h : 0.06	i : 0.06	3 : 0.04	f : 0.04	2 : 0.04	> : 0.02	] : 0.02	b : 0.02	6 : 0.02	
e : 0.15	g : 0.13	= : 0.08	c : 0.08	] : 0.06	h : 0.06	d : 0.06	i : 0.06	2 : 0.04	f : 0.04	G : 0.02	b : 0.02	> : 0.02	3 : 0.02	a : 0.02	B : 0.02	5 : 0.02	: : 0.02	
g : 0.13	e : 0.13	] : 0.11	= : 0.08	i : 0.08	d : 0.06	c : 0.06	h : 0.06	f : 0.04	: : 0.04	G : 0.02	2 : 0.02	b : 0.02	> : 0.02	3 : 0.02	B : 0.02	5 : 0.02	

#score	615.1840906731909
#seq	45
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_CDS_m1_run1.txt

#BEAR
eeee^^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr1:100174500-100174740(-)$1	240	186	219	36.3230
iiiiiii^^^^^^^^^^^^^^^^^^^^^iiiii	chr1:62148993-62149233(-)$1	240	101	134	36.8511
###dddd^^^^^^^^^^^^^^^^^^dddd333b	chr19:37726559-37726799(+)$1	240	198	231	32.5822
!ffffff^^^^^^^^^^^^^^^^^^^^^^^^^^	chr2:179330366-179330606(-)$1	240	173	206	39.4747
""eeeee^^^^^^^^^^^^^^^^^^^^^^^eee	chr1:165712392-165712632(-)$1	240	46	79	38.7325
!bbdddd^^^^^^^^^^^^^^^^^^^^^^^ddd	chr19:30500106-30500346(+)$1	240	98	131	37.5114
c[eeeee^^^^^^^^^^^^^^^^^^^^^^eeee	chr20:47587730-47587973(+)$1	243	105	138	38.0504
eee[ccc^^^^^^^^^^^^^^^^^^^^^^^^^^	chr16:69725942-69726182(+)$1	240	94	127	39.4229
eeeee^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr12:27156098-27156338(-)$1	240	106	139	36.5704
iiiiii^^^^^^^^^^^^^^^^^^^^^^^iiii	chr7:94167019-94167261(+)$1	242	94	127	37.8321
gg!!abb^^^^^^^^^^^^^^^^^^^^^^^bb]	chr1:171481181-171481421(+)$1	240	122	155	37.8460
b"""ccc^^^^^^^^^^^^^^^^^^^^^^^^^^	chr3:169801936-169802176(+)$1	240	103	136	39.3570
:ffffff^^^^^^^^^^^^^^^^^^^^ffffff	chr6:87966405-87966645(+)$1	240	56	89	34.2996
gggggg^^^^^^^^^^^^^^^^^^^^^^^gggg	chr15:48434387-48434667(-)$1	280	113	146	37.9046
cc[dddd^^^^^^^^^^^^^^^^^^^^^^^^dd	chr13:21721358-21721608(+)$1	250	202	235	38.4871
a[a[ccc^^^^^^^^^^^^^^^^^^^^^^^^^^	chr2:42936006-42936246(+)$1	240	98	131	39.7426
::ffffff^^^^^^^^^^^^^^^^^^^^fffff	chr3:156262052-156262292(-)$1	240	181	214	33.2268
c[eeeee^^^^^^^^^^^^^^^^^^^^^^^eee	chr5:88018284-88018524(-)$1	240	193	226	38.6665
eeee[bb^^^^^^^^^^^^^^^^^^^^^^^bbe	chr12:50481050-50481290(+)$1	240	106	139	37.5322
"""ccc[bb^^^^^^^^^^^^^^^^^^bb]ccc	chr5:102440194-102440434(-)$1	240	135	168	32.6956
ii!!ccc^^^^^^^^^^^^^^^^^^^^^^ccc2	chr12:57458340-57458580(-)$1	240	56	89	38.1551
b[eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:155227030-155227270(-)$1	240	102	135	39.4930
eeedddd^^^^^^^^^^^^^^^^^^^^^^^^^^	chr18:61067712-61067953(-)$1	241	95	128	39.0089
[ffffff^^^^^^^^^^^^^^^^^^^^^^^^^^	chr13:39587141-39587381(-)$1	240	185	218	39.4252
##ffffff^^^^^^^^^^^^^^^^^^ffffff5	chr3:15288160-15288400(+)$1	240	114	147	31.9256
gggggg^^^^^^^^^^^^^^^^^^^^^^^gggg	chr19:44739401-44739641(+)$1	240	110	143	37.9046
dddd[bb^^^^^^^^^^^^^^^^^^^^^^^^^^	chr17:79535989-79536229(-)$1	240	119	152	38.5054
ffffffff^^^^^^^^^^^^^^^^^^^^fffff	chr18:357342-357582(-)$1	240	106	139	34.7921
=======^^^^^^^^^^^^^^^^^^^^^=====	chr8:29961732-29961973(+)$1	241	37	70	37.4635
ggggggg^^^^^^^^^^^^^^^^^^^^^^^^^^	chr14:91947843-91948083(-)$1	240	12	45	39.5619
hhhhhhh^^^^^^^^^^^^^^^^^^^^^^^^^^	chr8:66651693-66651933(-)$1	240	65	98	38.0585
[ffffff^^^^^^^^^^^^^^^^^^^^^^^^^f	chr12:46591440-46591680(-)$1	240	119	152	39.0894
[ffffff^^^^^^^^^^^^^^^^^^ffffff]d	chr10:98287068-98287308(-)$1	240	113	146	32.1482
:::dddd^^^^^^^^^^^^^^^^^^^^^dddd:	chr9:36356247-36356487(-)$1	240	81	114	32.6688
dd[dddd^^^^^^^^^^^^^^^^^^^dddd333	chr2:86344115-86344355(+)$1	240	91	124	33.9986
:ccc^^^^^^^^^^^^^^^^^^^^^^^^^ccc:	chr3:184018053-184018293(+)$1	240	102	135	35.7955
===[dddd^^^^^^^^^^^^^^^^^^dddd22=	chr18:214495-214735(-)$1	240	133	166	32.3100
""eeeee^^^^^^^^^^^^^^^^^^^^^^eeee	chr8:26218450-26218690(+)$1	240	110	143	38.1164
"ffffff^^^^^^^^^^^^^^^^^^^^^^^^^^	chr10:116623272-116623512(+)$1	240	90	123	39.4416
=======^^^^^^^^^^^^^^^^^^^^======	chr14:74363092-74363332(+)$1	240	24	57	36.2293
!ffffff^^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:71494446-71494686(+)$1	240	65	98	39.4747
d[ccc^^^^^^^^^^^^^^^^^^^^^^^^cccd	chr4:17825195-17825435(+)$1	240	99	132	37.6583
gg!!ccc^^^^^^^^^^^^^^^^^^^^^ccc]g	chr19:32930585-32930825(+)$1	240	114	147	37.4223
ccc!!bb^^^^^^^^^^^^^^^^^^^^^^^^^b	chr1:54262328-54262568(-)$1	240	100	133	38.5621
d!!dddd^^^^^^^^^^^^^^^^^^^^^^^^^^	chr12:46758071-46758311(-)$1	240	14	47	39.3229
ggg[eeeee^^^^^^^^^^^^^^^^^^^eeeee	chr8:17132178-17132418(+)$1	240	100	133	34.0298
CCeeeee^^^^^^^^^^^^^^^^^^^^^^^^^e	chr3:16411595-16411835(-)$1	240	20	53	37.0295
gggggg^^^^^^^^^^^^^^^^^^^^^^ggggg	chr19:9676516-9676756(-)$1	240	123	156	36.9684
hhhhhhh^^^^^^^^^^^^^^^^^^^hhhhhhh	chr14:90870955-90871195(+)$1	240	39	72	29.7903
ddddddd^^^^^^^^^^^^^^^^^^^^^dddd]	chrX:107937952-107938192(+)$1	240	48	81	35.9286
effffff^^^^^^^^^^^^^^^^^^^^^^^fff	chr8:77776365-77776605(+)$1	240	157	190	38.0056
dd!!ccc^^^^^^^^^^^^^^^^^^^cccdddd	chr3:150289858-150290098(+)$1	240	138	171	34.1112
b[eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^	chr11:32954039-32954279(+)$1	240	148	181	39.4930
##eeeee^^^^^^^^^^^^^^^^^^^^^^^^ee	chr5:112178191-112178431(+)$1	240	107	140	39.0870

#otherMatches

#Seq PSSM
AAGUGAUAAUUAUCAUCAAACCAAAGAAACUUG	chr1:100174500-100174740(-)$1	240	186	219	36.3230
UAGAAAAACGCAAUUAUAUCCAUAAAUAUUUUU	chr1:62148993-62149233(-)$1	240	101	134	36.8511
UGAAGCUUCAUCUUCAUCUUUCUUUGGCUGUUC	chr19:37726559-37726799(+)$1	240	198	231	32.5822
ACUUUUCUCCAAGUUGUAUUUGCUAUUUUUCCC	chr2:179330366-179330606(-)$1	240	173	206	39.4747
CCAAAGAUAACAAUUCUUUUUUUUUUUUUUUCU	chr1:165712392-165712632(-)$1	240	46	79	38.7325
UUGGAGAUAAUUCUAUACCAACAAUAUAUUUUU	chr19:30500106-30500346(+)$1	240	98	131	37.5114
CCAUUUUUCUUACUCUUCUUUCAAACUUUAAAA	chr20:47587730-47587973(+)$1	243	105	138	38.0504
CUUUACAGCAGCAGAUUUCAUCAAAUAUUUUUC	chr16:69725942-69726182(+)$1	240	94	127	39.4229
UGUGACUUUUCUUAUUUUCCAAAUACACUCACA	chr12:27156098-27156338(-)$1	240	106	139	36.5704
AAGGAAAACAAAUUUUAUACACAUUCAUCUUUC	chr7:94167019-94167261(+)$1	242	94	127	37.8321
ACAAGGGGAAAUCAUUAGAAACACAGAAAACCA	chr1:171481181-171481421(+)$1	240	122	155	37.8460
AUCUGCCUAUUUACUCAAAUUAUUUCCUUUACU	chr3:169801936-169802176(+)$1	240	103	136	39.3570
UUUCAAAACAAUUUACCAACUUCCAAAUUUGAA	chr6:87966405-87966645(+)$1	240	56	89	34.2996
AUAAUAUCAACCUCCACAGCCCCUUAUUUUAUU	chr15:48434387-48434667(-)$1	280	113	146	37.9046
GCCAUUAAGCCUUUAAAUUCUAAACAAAUUAUA	chr13:21721358-21721608(+)$1	250	202	235	38.4871
GCCAAGCUUUCUUCCUUCAUACUACAUAUUUCA	chr2:42936006-42936246(+)$1	240	98	131	39.7426
CUUCAACCCCACAGUGUAUCCUUUUCAAGGUUG	chr3:156262052-156262292(-)$1	240	181	214	33.2268
AUGUGCCGUGUGUGGAAAAAAAAAAAGUCAGGU	chr5:88018284-88018524(-)$1	240	193	226	38.6665
GCUGCGAAUUUUCAUUUCUAACACUUUCAAUCC	chr12:50481050-50481290(+)$1	240	106	139	37.5322
AUAUGGACCUCCUCAGAAAAUAAUAAUGGACCA	chr5:102440194-102440434(-)$1	240	135	168	32.6956
AGAAGUCAAAUUUUCUACUACUCUACUGGGAUG	chr12:57458340-57458580(-)$1	240	56	89	38.1551
UUCAUUCAAUUUCUUCGUUUUCUUCUUCAUUUU	chr1:155227030-155227270(-)$1	240	102	135	39.4930
CAACAGAAGCCAACAACUCAACAUUUUUUUCAA	chr18:61067712-61067953(-)$1	241	95	128	39.0089
CGCUGCCACCUCCACAUCUCUCCCUCAUCCUAG	chr13:39587141-39587381(-)$1	240	185	218	39.4252
CCUUCACCAUACACCUUAUCAAAACGGGUGAGA	chr3:15288160-15288400(+)$1	240	114	147	31.9256
CUUUUCAUUCUUAUCAAUCUAAUCAUACAGGAG	chr19:44739401-44739641(+)$1	240	110	143	37.9046
GUUUACACUUUUUCUAUUUCGCAAAAUCCAUUU	chr17:79535989-79536229(-)$1	240	119	152	38.5054
ACUGAAGUUUUCUAUCAUAUUAUUAUACAUUUU	chr18:357342-357582(-)$1	240	106	139	34.7921
AAAAUGACAUAGCAAAAAUUACAUUAACUUAUU	chr8:29961732-29961973(+)$1	241	37	70	37.4635
CUGAGCUGAAACAAAAAAUUCAUCAGACAUACA	chr14:91947843-91948083(-)$1	240	12	45	39.5619
UUUCCUACUAAUGUAAUGUCUCUUCUUUCUUUU	chr8:66651693-66651933(-)$1	240	65	98	38.0585
CAUCUCUUUAUUUAAAAAUCACAGACCAGGAUG	chr12:46591440-46591680(-)$1	240	119	152	39.0894
UUUUACUACUAUUUUUUCAAAACAAAGUAAGUG	chr10:98287068-98287308(-)$1	240	113	146	32.1482
CUAGUGAUCCAUUUCUUAUACAUCCUCCUCACC	chr9:36356247-36356487(-)$1	240	81	114	32.6688
GGAGAAUGUGGCCAAGUUUAUUAUUAAUUCAUA	chr2:86344115-86344355(+)$1	240	91	124	33.9986
AGCCUCUCAAAUUUCUGCGUCCACACUAUGGCA	chr3:184018053-184018293(+)$1	240	102	135	35.7955
AAAACUGUGAUAGAUUUUGUUACCAAGCAGCAU	chr18:214495-214735(-)$1	240	133	166	32.3100
AUAUCACAUCAACUCAAUUUCUAUUAAUAGUGA	chr8:26218450-26218690(+)$1	240	110	143	38.1164
UCUAAGUUUCUGUUUUUCAUCCCUUCUUUUUUC	chr10:116623272-116623512(+)$1	240	90	123	39.4416
AGAGCUCAGACUGUACAGAAAUCCCCGGAGUUU	chr14:74363092-74363332(+)$1	240	24	57	36.2293
AGCUCUCUCCAAAAUCUGAUAUCUCUCCACUCA	chr5:71494446-71494686(+)$1	240	65	98	39.4747
GAGAUUCUUAUUUUACCCACAAUCCCAAUAUCC	chr4:17825195-17825435(+)$1	240	99	132	37.6583
AUUUUCAUAUCAACUUUUCUCUUUAGUCUGACA	chr19:32930585-32930825(+)$1	240	114	147	37.4223
UGACUGAAUUUUCUAAUCCUUCUCCAUCUACCU	chr1:54262328-54262568(-)$1	240	100	133	38.5621
GCUUUGAUAAUUAACGAAACAAUAAACACCACC	chr12:46758071-46758311(-)$1	240	14	47	39.3229
UCUCAGGGUUUUCCAUUUCUUCCUCCAUAUCCU	chr8:17132178-17132418(+)$1	240	100	133	34.0298
CUCUCCACUCCCUUUACAAAUCCCAACAGAAAU	chr3:16411595-16411835(-)$1	240	20	53	37.0295
CAUUUAAAAACACACUGAAGAAAAACUCUGAAU	chr19:9676516-9676756(-)$1	240	123	156	36.9684
AAGAUAACCAAAAGUUACUAUUAUAUUUGUCUU	chr14:90870955-90871195(+)$1	240	39	72	29.7903
CUGUAGAUUAUGUUCCUUCUCCUUUUCCUUUAC	chrX:107937952-107938192(+)$1	240	48	81	35.9286
UCCUGGCCUAAUAUCCUUUUCCAAGCGUCUGCC	chr8:77776365-77776605(+)$1	240	157	190	38.0056
CGGUGGCUUCUGAUUCUACAUAUUUUGCUUGGU	chr3:150289858-150290098(+)$1	240	138	171	34.1112
CCAAGCCUUUUAUCAGUUAGUCAGUCCCAAAAU	chr11:32954039-32954279(+)$1	240	148	181	39.4930
AAGUCCUCCUAACAAAUUAUCUCAACUUCCAAG	chr5:112178191-112178431(+)$1	240	107	140	39.0870

#DB
((((........................)))))	chr1:100174500-100174740(-)$1	1	186	219	36.3230
(((((((.....................)))))	chr1:62148993-62149233(-)$1	1	101	134	36.8511
...((((..................))))...)	chr19:37726559-37726799(+)$1	1	198	231	32.5822
.((((((..........................	chr2:179330366-179330606(-)$1	1	173	206	39.4747
..(((((.......................)))	chr1:165712392-165712632(-)$1	1	46	79	38.7325
.((((((.......................)))	chr19:30500106-30500346(+)$1	1	98	131	37.5114
(.(((((......................))))	chr20:47587730-47587973(+)$1	1	105	138	38.0504
(((.(((..........................	chr16:69725942-69726182(+)$1	1	94	127	39.4229
(((((.......................)))))	chr12:27156098-27156338(-)$1	1	106	139	36.5704
((((((.......................))))	chr7:94167019-94167261(+)$1	1	94	127	37.8321
((..(((.......................)).	chr1:171481181-171481421(+)$1	1	122	155	37.8460
(...(((..........................	chr3:169801936-169802176(+)$1	1	103	136	39.3570
.((((((....................))))))	chr6:87966405-87966645(+)$1	1	56	89	34.2996
((((((.......................))))	chr15:48434387-48434667(-)$1	1	113	146	37.9046
((.((((........................))	chr13:21721358-21721608(+)$1	1	202	235	38.4871
(.(.(((..........................	chr2:42936006-42936246(+)$1	1	98	131	39.7426
..((((((....................)))))	chr3:156262052-156262292(-)$1	1	181	214	33.2268
(.(((((.......................)))	chr5:88018284-88018524(-)$1	1	193	226	38.6665
((((.((.......................)))	chr12:50481050-50481290(+)$1	1	106	139	37.5322
...(((.((..................)).)))	chr5:102440194-102440434(-)$1	1	135	168	32.6956
((..(((......................))).	chr12:57458340-57458580(-)$1	1	56	89	38.1551
(.(((((..........................	chr1:155227030-155227270(-)$1	1	102	135	39.4930
(((((((..........................	chr18:61067712-61067953(-)$1	1	95	128	39.0089
.((((((..........................	chr13:39587141-39587381(-)$1	1	185	218	39.4252
..((((((..................)))))).	chr3:15288160-15288400(+)$1	1	114	147	31.9256
((((((.......................))))	chr19:44739401-44739641(+)$1	1	110	143	37.9046
((((.((..........................	chr17:79535989-79536229(-)$1	1	119	152	38.5054
((((((((....................)))))	chr18:357342-357582(-)$1	1	106	139	34.7921
(((((((.....................)))))	chr8:29961732-29961973(+)$1	1	37	70	37.4635
(((((((..........................	chr14:91947843-91948083(-)$1	1	12	45	39.5619
(((((((..........................	chr8:66651693-66651933(-)$1	1	65	98	38.0585
.((((((.........................)	chr12:46591440-46591680(-)$1	1	119	152	39.0894
.((((((..................)))))).)	chr10:98287068-98287308(-)$1	1	113	146	32.1482
...((((.....................)))).	chr9:36356247-36356487(-)$1	1	81	114	32.6688
((.((((...................))))...	chr2:86344115-86344355(+)$1	1	91	124	33.9986
.(((.........................))).	chr3:184018053-184018293(+)$1	1	102	135	35.7955
(((.((((..................))))..)	chr18:214495-214735(-)$1	1	133	166	32.3100
..(((((......................))))	chr8:26218450-26218690(+)$1	1	110	143	38.1164
.((((((..........................	chr10:116623272-116623512(+)$1	1	90	123	39.4416
(((((((....................))))))	chr14:74363092-74363332(+)$1	1	24	57	36.2293
.((((((..........................	chr5:71494446-71494686(+)$1	1	65	98	39.4747
(.(((........................))))	chr4:17825195-17825435(+)$1	1	99	132	37.6583
((..(((.....................))).)	chr19:32930585-32930825(+)$1	1	114	147	37.4223
(((..((.........................)	chr1:54262328-54262568(-)$1	1	100	133	38.5621
(..((((..........................	chr12:46758071-46758311(-)$1	1	14	47	39.3229
(((.(((((...................)))))	chr8:17132178-17132418(+)$1	1	100	133	34.0298
(((((((.........................)	chr3:16411595-16411835(-)$1	1	20	53	37.0295
((((((......................)))))	chr19:9676516-9676756(-)$1	1	123	156	36.9684
(((((((...................)))))))	chr14:90870955-90871195(+)$1	1	39	72	29.7903
(((((((.....................)))).	chrX:107937952-107938192(+)$1	1	48	81	35.9286
)((((((.......................)))	chr8:77776365-77776605(+)$1	1	157	190	38.0056
((..(((...................)))))))	chr3:150289858-150290098(+)$1	1	138	171	34.1112
(.(((((..........................	chr11:32954039-32954279(+)$1	1	148	181	39.4930
..(((((........................))	chr5:112178191-112178431(+)$1	1	107	140	39.0870

#PSSM
g : 0.12	e : 0.11	d : 0.11	" : 0.07	c : 0.07	: : 0.07	i : 0.05	# : 0.05	! : 0.05	b : 0.05	[ : 0.05	= : 0.05	h : 0.03	a : 0.01	f : 0.01	C : 0.01	
f : 0.16	g : 0.12	[ : 0.11	e : 0.09	" : 0.07	d : 0.07	i : 0.05	# : 0.05	c : 0.05	= : 0.05	: : 0.03	h : 0.03	b : 0.01	! : 0.01	C : 0.01	
e : 0.24	f : 0.20	! : 0.09	g : 0.09	= : 0.05	c : 0.05	i : 0.03	" : 0.03	[ : 0.03	d : 0.03	h : 0.03	# : 0.01	b : 0.01	a : 0.01	: : 0.01	
e : 0.20	f : 0.20	d : 0.16	! : 0.09	[ : 0.07	g : 0.07	c : 0.05	i : 0.03	= : 0.03	h : 0.03	" : 0.01	
f : 0.20	e : 0.18	d : 0.16	c : 0.14	g : 0.07	^ : 0.03	i : 0.03	[ : 0.03	= : 0.03	h : 0.03	a : 0.01	! : 0.01	
f : 0.20	d : 0.16	e : 0.16	c : 0.12	^ : 0.07	b : 0.07	g : 0.07	i : 0.03	= : 0.03	h : 0.03	
f : 0.20	d : 0.16	e : 0.16	^ : 0.14	c : 0.11	b : 0.07	= : 0.03	h : 0.03	i : 0.01	[ : 0.01	g : 0.01	
^ : 0.88	f : 0.05	b : 0.01	d : 0.01	e : 0.01	
^ : 0.96	b : 0.01	e : 0.01	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.96	d : 0.01	f : 0.01	
^ : 0.87	d : 0.05	f : 0.03	h : 0.01	c : 0.01	
^ : 0.81	d : 0.05	f : 0.05	b : 0.01	= : 0.01	h : 0.01	c : 0.01	
^ : 0.61	d : 0.09	f : 0.09	e : 0.05	= : 0.03	c : 0.03	i : 0.01	b : 0.01	g : 0.01	h : 0.01	
^ : 0.46	e : 0.09	f : 0.09	d : 0.09	c : 0.07	g : 0.05	i : 0.03	= : 0.03	3 : 0.01	] : 0.01	h : 0.01	
^ : 0.35	e : 0.12	f : 0.11	c : 0.09	d : 0.07	g : 0.05	i : 0.03	3 : 0.03	b : 0.03	= : 0.03	2 : 0.01	h : 0.01	
^ : 0.31	e : 0.14	d : 0.09	f : 0.09	c : 0.07	g : 0.05	i : 0.03	3 : 0.03	b : 0.03	= : 0.03	] : 0.03	2 : 0.01	h : 0.01	
^ : 0.25	e : 0.18	d : 0.09	f : 0.09	g : 0.07	= : 0.05	i : 0.03	b : 0.03	] : 0.03	: : 0.03	c : 0.01	2 : 0.01	5 : 0.01	3 : 0.01	h : 0.01	

#score	1994.0867764329537
#seq	54
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_UTR_m3_run2.txt

#BEAR
eeeee^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr19:46214144-46214374(-)$1	230	97	130	38.3184
cc[ccc^^^^^^^^^^^^^^^^^^^^^cccccc	chr14:45394193-45394423(-)$1	230	116	149	37.3732
hhhhhh^^^^^^^^^^^^^^^^^^^^^hhhhhh	chr3:150176904-150177137(+)$1	233	17	50	34.1468
hhhh^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr13:39622802-39623029(+)$1	227	161	194	37.9931
gggggg^^^^^^^^^^^^^^^^^^^^ggggggg	chr4:48425197-48425427(+)$1	230	144	177	36.1229
e!!ffffff^^^^^^^^^^^^^^^^^^ffffff	chr15:38644951-38645176(+)$1	225	44	77	32.2948
ffffff^^^^^^^^^^^^^^^^^^^^ffffff:	chr8:71023373-71023603(-)$1	230	180	213	34.6506
ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr6:36198879-36199109(+)$1	230	23	56	38.3363
gggg^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr9:4663856-4664086(+)$1	230	44	77	38.8114
hhh[bb^^^^^^^^^^^^^^^^^^^^^bbhhhh	chr13:100215035-100215265(+)$1	230	69	102	35.1514
fffff^^^^^^^^^^^^^^^^^^^^^^ffffff	chr5:95222782-95223024(-)$1	242	112	145	37.6357
&&dddd^^^^^^^^^^^^^^^^^^^^^dddd99	chr10:38119672-38119902(-)$1	230	109	142	33.8125
dd[ccc^^^^^^^^^^^^^^^^^^^^^ccc]dd	chr3:8920428-8920651(-)$1	223	3	36	36.8817
gggggg^^^^^^^^^^^^^^^^^^ggggggg33	chr15:52202892-52203113(+)$1	221	81	114	33.0350
======^^^^^^^^^^^^^^^^^^^^^======	chr17:54968466-54968690(-)$1	224	95	128	37.6033
ggggg^^^^^^^^^^^^^^^^^^^^^^^^gggg	chr4:56298586-56298816(-)$1	230	124	157	39.0496
$$dddd^^^^^^^^^^^^^^^^^^^^^dddd44	chr6:136579479-136579709(-)$1	230	103	136	36.0264
""ffffff^^^^^^^^^^^^^^^^^^^ffffff	chr4:40425414-40425644(-)$1	230	11	44	33.8008
ddd[ccc^^^^^^^^^^^^^^^^^^^cccdddd	chr1:160455226-160455450(-)$1	224	96	129	34.1580
iiiiiii^^^^^^^^^^^^^^^^^^^^iiiiii	chr18:66343472-66343696(-)$1	224	166	199	35.6580
eeeee^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr1:85403424-85403654(-)$1	230	43	76	37.9167
fffff^^^^^^^^^^^^^^^^^^^^^^ffffff	chr10:97631884-97632107(+)$1	223	150	183	37.6357
ff[ccc^^^^^^^^^^^^^^^^^^^^^^^ccc]	chr13:45910962-45911187(-)$1	225	140	173	38.2849
hhhh^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr3:37029721-37029952(-)$1	231	106	139	37.9931
fffff^^^^^^^^^^^^^^^^^^^^^^^fffff	chr5:149781318-149781541(-)$1	223	189	222	38.2374
====^^^^^^^^^^^^^^^^^^^^^^^^^====	chr2:160176363-160176590(-)$1	227	154	187	39.0977
gggggg^^^^^^^^^^^^^^^^^^^^ggggggg	chr5:173383963-173384193(+)$1	230	13	46	36.1229
bb[dddd^^^^^^^^^^^^^^^^^^^^dddd33	chr1:180944454-180944678(-)$1	224	167	200	34.8237
cceeeee^^^^^^^^^^^^^^^^^^^^^eeeee	chr10:28884808-28885038(+)$1	230	24	57	35.8739
hhh^^^^^^^^^^^^^^^^^^^^^^^^^^^hhh	chr13:25916091-25916320(+)$1	229	94	127	37.4476
fff^^^^^^^^^^^^^^^^^^^^^^^^^^^^ff	chr7:5567266-5567491(-)$1	225	132	165	38.3850
ccc^^^^^^^^^^^^^^^^^^^^^^^^ccc22e	chr10:91100291-91100521(+)$1	230	20	53	37.4183
!!dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr19:47278061-47278291(-)$1	230	27	60	37.6054
!!ffffff^^^^^^^^^^^^^^^^^^^ffffff	chr6:86204693-86204920(+)$1	227	172	205	34.0572
e[dddd^^^^^^^^^^^^^^^^^^^^ddddeee	chr15:64463745-64463967(-)$1	222	145	178	35.0790
ggggg^^^^^^^^^^^^^^^^^^^^^^^ggggg	chr5:127524682-127524912(+)$1	230	89	122	38.7035
fffff^^^^^^^^^^^^^^^^^^^^^^^fffff	chr10:65382024-65382254(+)$1	230	150	183	38.2374
gggggg^^^^^^^^^^^^^^^^^^^^ggggggg	chr14:93705279-93705509(-)$1	230	186	219	36.1229
fffff^^^^^^^^^^^^^^^^^^^^^^^^ffff	chr11:47800241-47800471(-)$1	230	190	223	38.5873
d[dddd^^^^^^^^^^^^^^^^^^^^^dddddd	chr16:53359147-53359380(+)$1	233	39	72	36.1002
ddd^^^^^^^^^^^^^^^^^^^^^^^^^^dddd	chr7:6063959-6064186(-)$1	227	15	48	37.8057
eeee^^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr21:37748520-37748750(+)$1	230	139	172	38.4580
eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee]	chr4:153546755-153546979(-)$1	224	116	149	37.4015
=====^^^^^^^^^^^^^^^^^^^^^^^^====	chr4:185309183-185309407(-)$1	224	64	97	39.0365
#dddd^^^^^^^^^^^^^^^^^^^^^^^^dddd	chr4:129793416-129793643(+)$1	227	126	159	37.7400
ddd"""ccc^^^^^^^^^^^^^^^^^^^ccc55	chr12:118587574-118587804(-)$1	230	103	136	32.0966
fffff^^^^^^^^^^^^^^^^^^^^^^ffffff	chr13:39622975-39623205(+)$1	230	126	159	37.6357
fffffa^^^^^^^^^^^^^^^^^^^^^a]ffff	chr7:123324306-123324544(-)$1	238	87	120	37.5134
fffff^^^^^^^^^^^^^^^^^^^^^^ffffff	chr12:76749069-76749294(-)$1	225	95	128	37.6357
gggg^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr21:38884251-38884481(+)$1	230	96	129	38.8114
#dddd^^^^^^^^^^^^^^^^^^^^^^dddd33	chr3:112182851-112183081(-)$1	230	123	156	37.2139
eeccc^^^^^^^^^^^^^^^^^^^^^^^^ccc4	chr5:74880591-74880812(+)$1	221	35	68	38.7103
geeeee^^^^^^^^^^^^^^^^^^^^^^^eeee	chr6:33268925-33269159(-)$1	234	96	129	37.7464
ddddddd^^^^^^^^^^^^^^^^^^^dddd22d	chr5:35058195-35058425(-)$1	230	1	34	33.0061
eeeccc^^^^^^^^^^^^^^^^^^^^^^^ccc3	chr2:26357829-26358059(+)$1	230	182	215	38.2033
gggggg^^^^^^^^^^^^^^^^^^^^ggggggg	chr1:115247999-115248229(-)$1	230	171	204	36.1229
ggg[bb^^^^^^^^^^^^^^^^^^bb]gggggg	chr5:82349903-82350127(-)$1	224	56	89	32.7505
ffffff^^^^^^^^^^^^^^^^^^^^ffffff]	chr17:62119530-62119754(-)$1	224	77	110	35.6962
iiiiii^^^^^^^^^^^^^^^^^^^^^^iiiii	chr4:89182387-89182617(-)$1	230	146	179	37.7696
eeee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr12:59265856-59266086(-)$1	230	155	188	38.4167
[dddd^^^^^^^^^^^^^^^^^^^^^^dddd]d	chr21:40567658-40567888(-)$1	230	193	226	37.0309
iii^^^^^^^^^^^^^^^^^^^^^^^^^^iiii	chr5:167983613-167983848(-)$1	235	80	113	38.7876
ffffff^^^^^^^^^^^^^^^^^^ffffff22c	chr1:53292815-53293047(+)$1	232	98	131	31.9805
gg"""ccc^^^^^^^^^^^^^^^^^^^ccc333	chr5:159830019-159830249(-)$1	230	59	92	34.9368

#otherMatches

#Seq PSSM
AAGUAUAAAAACCCUCCUCCUCCCGUUAUUAUU	chr19:46214144-46214374(-)$1	230	97	130	38.3184
UUCUACUUCUUAACCUUUUUUCCCUUUGUAAAC	chr14:45394193-45394423(-)$1	230	116	149	37.3732
UUUUUUGAAUAAUUAUAAGUAUCAGUAAAGGAA	chr3:150176904-150177137(+)$1	233	17	50	34.1468
GAGCuuccuucucuuuuuuuuucuuuuucuuuc	chr13:39622802-39623029(+)$1	227	161	194	37.9931
AUGGCUCUUAAUAUAUCCUUGAAAUCGGCUAUU	chr4:48425197-48425427(+)$1	230	144	177	36.1229
UUAUCAGUUACAUUUUAUUUUUAUUUAAACUGG	chr15:38644951-38645176(+)$1	225	44	77	32.2948
UCAUGAUACUGGUAAUUUAUAAUAAUUCGUGAU	chr8:71023373-71023603(-)$1	230	180	213	34.6506
CAGUCUUGCUUUCUCUUUCCCAUAUUCCUUUUC	chr6:36198879-36199109(+)$1	230	23	56	38.3363
GAUUAUAAUACUUGUCUUUCUCUCCUCUCCCUC	chr9:4663856-4664086(+)$1	230	44	77	38.8114
UAUUGGCCUAGUAAUCCUUCAGAAACACCGUAA	chr13:100215035-100215265(+)$1	230	69	102	35.1514
UUUGCACUACAACUCUAUAACAUUACCGCAGAA	chr5:95222782-95223024(-)$1	242	112	145	37.6357
ucagcacucaucacuuccuaauuauuuugcuac	chr10:38119672-38119902(-)$1	230	109	142	33.8125
GAUCCAAAAUUGAAACUGAUAAACUUCUGGUUC	chr3:8920428-8920651(-)$1	223	3	36	36.8817
ugguuuuguuuuguuuuguuuuUUAAAUCAGUA	chr15:52202892-52203113(+)$1	221	81	114	33.0350
CAAUGUUACAUAAACUCCAUUACCCGCAUGUUG	chr17:54968466-54968690(-)$1	224	95	128	37.6033
UAAAGAUACCAAAUAGAAACACCUUCCAGCuuu	chr4:56298586-56298816(-)$1	230	124	157	39.0496
AUAAACUCCCUCAAACCUUUCUUUACUGUUuuu	chr6:136579479-136579709(-)$1	230	103	136	36.0264
ACCACCAAACUCCCUUAAAAACAAACAUUGGUG	chr4:40425414-40425644(-)$1	230	11	44	33.8008
cuagcauuacccuucugacacucucuauguagc	chr1:160455226-160455450(-)$1	224	96	129	34.1580
GUCUUGUGAUUGACUUUCGCAAAAUAAACAGGA	chr18:66343472-66343696(-)$1	224	166	199	35.6580
UGGGUUCUAAUAGCUACUUUUUCAUUUCACCCA	chr1:85403424-85403654(-)$1	230	43	76	37.9167
aagucaaccuccccaucagacauucaaggcuuu	chr10:97631884-97632107(+)$1	223	150	183	37.6357
GAAGAGAUUACCAAGAGAAUAAAAAGAGACUCA	chr13:45910962-45911187(-)$1	225	140	173	38.2849
ggcauuaccacuaccaaccauucauuuguccuu	chr3:37029721-37029952(-)$1	231	106	139	37.9931
CUUCCCUUUCCCCAGCAUCACUCCCCAAGGAAG	chr5:149781318-149781541(-)$1	223	189	222	38.2374
AUGGUUCUCCUUUCCCUCUCAAUAAAUAUCUAU	chr2:160176363-160176590(-)$1	227	154	187	39.0977
CUACCAAAGCUAGAAUUAAUGACAACUGGUGGG	chr5:173383963-173384193(+)$1	230	13	46	36.1229
CACUAAACUUUAACCUUCUGAUGACUUUUUAAA	chr1:180944454-180944678(-)$1	224	167	200	34.8237
GCACUGUUCCUUCUAGUCCAUUUACGCUACAGU	chr10:28884808-28885038(+)$1	230	24	57	35.8739
AAGGAAAAUUAUUUAUCUCUGAGCACUAAACUU	chr13:25916091-25916320(+)$1	229	94	127	37.4476
CGUUACACCCUUUCUUGACAAAACCUAACUUGC	chr7:5567266-5567491(-)$1	225	132	165	38.3850
cucaaaaaaaaaaaaaaaaaaaaaaaaGAGUUG	chr10:91100291-91100521(+)$1	230	20	53	37.4183
UCCCCUAUUCCCUCCACAAUAACAGAAACACUC	chr19:47278061-47278291(-)$1	230	27	60	37.6054
AAGAGGUAUACAUUUUUUAAGUCGCUCUGCCUC	chr6:86204693-86204920(+)$1	227	172	205	34.0572
UCAAGGACUGCUAUUCUCCUUCUUCCCCUUAGU	chr15:64463745-64463967(-)$1	222	145	178	35.0790
AUGUAAGAAGCUUUUCACUUAAAAAAAAUGCAU	chr5:127524682-127524912(+)$1	230	89	122	38.7035
UUCAGUUUUCUUCUCCCAACGUUUAAUUCUGAA	chr10:65382024-65382254(+)$1	230	150	183	38.2374
AAUUCUUGACAUUUAAAUCUUCUUAUAGAAUUC	chr14:93705279-93705509(-)$1	230	186	219	36.1229
GCAAAUCUUUUAAUUCUUCCCUAUCACCUUUUG	chr11:47800241-47800471(-)$1	230	190	223	38.5873
AUAAUUUACAGAUCAAAACUCAGCAAUAAUUUG	chr16:53359147-53359380(+)$1	233	39	72	36.1002
GCUGCCGUUCCUUCCCUUCCUGCCCCACAAGCU	chr7:6063959-6064186(-)$1	227	15	48	37.8057
AAAGUUUUAUCAUUGCUAUUUAUUUUUACCUUU	chr21:37748520-37748750(+)$1	230	139	172	38.4580
UCUCACCUGACuuuuuuuuuuuuuuuuugagau	chr4:153546755-153546979(-)$1	224	116	149	37.4015
CCUUCCCUCAAAGCUUCCAUUCCACAUCCGGAG	chr4:185309183-185309407(-)$1	224	64	97	39.0365
AGAUUAAUUUUUUUCCAGAGUCAUUUUUAAAUC	chr4:129793416-129793643(+)$1	227	126	159	37.7400
UUUAAAAACAAAACAAAACAUUUUUCAGGUUCC	chr12:118587574-118587804(-)$1	230	103	136	32.0966
AGAUGAUAAUUUCCUGCUUUCCUCCUACAUCUU	chr13:39622975-39623205(+)$1	230	126	159	37.6357
GUUGCCUUUUUUGCUUUUUUUUAAUCUGUGCAA	chr7:123324306-123324544(-)$1	238	87	120	37.5134
AAUAGACAUAAUUAAUUCAAUACACUACUGUUA	chr12:76749069-76749294(-)$1	225	95	128	37.6357
UGGUAACAGUUCccaucaccaucaccaccacca	chr21:38884251-38884481(+)$1	230	96	129	38.8114
CACUAUUAUUUACAUGGCUUAUUUCAUUAGUUU	chr3:112182851-112183081(-)$1	230	123	156	37.2139
CUUGGAAUUAUUACAUGUACAGAACUUUACCAA	chr5:74880591-74880812(+)$1	221	35	68	38.7103
AAUGCUUUUUUAAAAAACACACAUCUUAUGGCA	chr6:33268925-33269159(-)$1	234	96	129	37.7464
UGUCUUCUGUAAAGCCAUAUUGAAGUGAAGUUA	chr5:35058195-35058425(-)$1	230	1	34	33.0061
AGCCACCUAUUUUAUUUGUUCUUUCAUCUGUGA	chr2:26357829-26358059(+)$1	230	182	215	38.2033
UUUUGGUUUUUUUAAAGGUUACAUGUUCAAGAG	chr1:115247999-115248229(-)$1	230	171	204	36.1229
UCUUGUUAAUCCCUGUUCUACUGUGCCAGACAC	chr5:82349903-82350127(-)$1	224	56	89	32.7505
GUGAUCCUACAUCCUUAAAUCUCAUCGAUUACC	chr17:62119530-62119754(-)$1	224	77	110	35.6962
GUUUUAUGUCUCCUUUUUGCUCAUUUUCUAAGA	chr4:89182387-89182617(-)$1	230	146	179	37.7696
AGCCCCAUUUAUACAAUAACAAUUUUUAUUAUU	chr12:59265856-59266086(-)$1	230	155	188	38.4167
CGAGGUACCUACCACUUUUUUUUUUUUCUUCCC	chr21:40567658-40567888(-)$1	230	193	226	37.0309
UGGUCAUAUAUACAUUCAGAACUUUUAUUUUAA	chr5:167983613-167983848(-)$1	235	80	113	38.7876
GUAUUUUAAAUCAGGACAUCACUUAAGUAUUAA	chr1:53292815-53293047(+)$1	232	98	131	31.9805
UGCCUGGCUUUAAUAAAUAUUUCAGAUGCCUCA	chr5:159830019-159830249(-)$1	230	59	92	34.9368

#DB
(((((........................))))	chr19:46214144-46214374(-)$1	1	97	130	38.3184
((.(((.....................))))))	chr14:45394193-45394423(-)$1	1	116	149	37.3732
((((((.....................))))))	chr3:150176904-150177137(+)$1	1	17	50	34.1468
((((.............................	chr13:39622802-39623029(+)$1	1	161	194	37.9931
((((((....................)))))))	chr4:48425197-48425427(+)$1	1	144	177	36.1229
(..((((((..................))))))	chr15:38644951-38645176(+)$1	1	44	77	32.2948
((((((....................)))))).	chr8:71023373-71023603(-)$1	1	180	213	34.6506
(((..............................	chr6:36198879-36199109(+)$1	1	23	56	38.3363
((((.............................	chr9:4663856-4664086(+)$1	1	44	77	38.8114
(((.((.....................))))))	chr13:100215035-100215265(+)$1	1	69	102	35.1514
(((((......................))))))	chr5:95222782-95223024(-)$1	1	112	145	37.6357
..((((.....................))))..	chr10:38119672-38119902(-)$1	1	109	142	33.8125
((.(((.....................))).))	chr3:8920428-8920651(-)$1	1	3	36	36.8817
((((((..................)))))))..	chr15:52202892-52203113(+)$1	1	81	114	33.0350
((((((.....................))))))	chr17:54968466-54968690(-)$1	1	95	128	37.6033
(((((........................))))	chr4:56298586-56298816(-)$1	1	124	157	39.0496
..((((.....................))))..	chr6:136579479-136579709(-)$1	1	103	136	36.0264
..((((((...................))))))	chr4:40425414-40425644(-)$1	1	11	44	33.8008
(((.(((...................)))))))	chr1:160455226-160455450(-)$1	1	96	129	34.1580
(((((((....................))))))	chr18:66343472-66343696(-)$1	1	166	199	35.6580
(((((.......................)))))	chr1:85403424-85403654(-)$1	1	43	76	37.9167
(((((......................))))))	chr10:97631884-97632107(+)$1	1	150	183	37.6357
((.(((.......................))).	chr13:45910962-45911187(-)$1	1	140	173	38.2849
((((.............................	chr3:37029721-37029952(-)$1	1	106	139	37.9931
(((((.......................)))))	chr5:149781318-149781541(-)$1	1	189	222	38.2374
((((.........................))))	chr2:160176363-160176590(-)$1	1	154	187	39.0977
((((((....................)))))))	chr5:173383963-173384193(+)$1	1	13	46	36.1229
((.((((....................))))..	chr1:180944454-180944678(-)$1	1	167	200	34.8237
))(((((.....................)))))	chr10:28884808-28885038(+)$1	1	24	57	35.8739
(((...........................)))	chr13:25916091-25916320(+)$1	1	94	127	37.4476
(((............................))	chr7:5567266-5567491(-)$1	1	132	165	38.3850
(((........................)))..)	chr10:91100291-91100521(+)$1	1	20	53	37.4183
..((((...........................	chr19:47278061-47278291(-)$1	1	27	60	37.6054
..((((((...................))))))	chr6:86204693-86204920(+)$1	1	172	205	34.0572
(.((((....................)))))))	chr15:64463745-64463967(-)$1	1	145	178	35.0790
(((((.......................)))))	chr5:127524682-127524912(+)$1	1	89	122	38.7035
(((((.......................)))))	chr10:65382024-65382254(+)$1	1	150	183	38.2374
((((((....................)))))))	chr14:93705279-93705509(-)$1	1	186	219	36.1229
(((((........................))))	chr11:47800241-47800471(-)$1	1	190	223	38.5873
(.((((.....................))))))	chr16:53359147-53359380(+)$1	1	39	72	36.1002
(((..........................))))	chr7:6063959-6064186(-)$1	1	15	48	37.8057
((((.........................))))	chr21:37748520-37748750(+)$1	1	139	172	38.4580
(((((......................))))).	chr4:153546755-153546979(-)$1	1	116	149	37.4015
(((((........................))))	chr4:185309183-185309407(-)$1	1	64	97	39.0365
.((((........................))))	chr4:129793416-129793643(+)$1	1	126	159	37.7400
(((...(((...................)))..	chr12:118587574-118587804(-)$1	1	103	136	32.0966
(((((......................))))))	chr13:39622975-39623205(+)$1	1	126	159	37.6357
((((((.....................).))))	chr7:123324306-123324544(-)$1	1	87	120	37.5134
(((((......................))))))	chr12:76749069-76749294(-)$1	1	95	128	37.6357
((((.............................	chr21:38884251-38884481(+)$1	1	96	129	38.8114
.((((......................))))..	chr3:112182851-112183081(-)$1	1	123	156	37.2139
(((((........................))).	chr5:74880591-74880812(+)$1	1	35	68	38.7103
((((((.......................))))	chr6:33268925-33269159(-)$1	1	96	129	37.7464
(((((((...................))))..)	chr5:35058195-35058425(-)$1	1	1	34	33.0061
((((((.......................))).	chr2:26357829-26358059(+)$1	1	182	215	38.2033
((((((....................)))))))	chr1:115247999-115248229(-)$1	1	171	204	36.1229
(((.((..................)).))))))	chr5:82349903-82350127(-)$1	1	56	89	32.7505
((((((....................)))))).	chr17:62119530-62119754(-)$1	1	77	110	35.6962
((((((......................)))))	chr4:89182387-89182617(-)$1	1	146	179	37.7696
((((.............................	chr12:59265856-59266086(-)$1	1	155	188	38.4167
.((((......................)))).)	chr21:40567658-40567888(-)$1	1	193	226	37.0309
(((..........................))))	chr5:167983613-167983848(-)$1	1	80	113	38.7876
((((((..................))))))..)	chr1:53292815-53293047(+)$1	1	98	131	31.9805
((...(((...................)))...	chr5:159830019-159830249(-)$1	1	59	92	34.9368

#PSSM
f : 0.20	g : 0.18	e : 0.14	d : 0.09	h : 0.07	c : 0.06	= : 0.04	i : 0.04	! : 0.03	# : 0.03	& : 0.01	$ : 0.01	" : 0.01	b : 0.01	[ : 0.01	
f : 0.20	g : 0.17	e : 0.12	d : 0.12	h : 0.07	c : 0.06	! : 0.04	= : 0.04	i : 0.04	[ : 0.03	& : 0.01	$ : 0.01	" : 0.01	b : 0.01	
f : 0.21	d : 0.18	g : 0.15	e : 0.12	h : 0.07	[ : 0.06	c : 0.04	= : 0.04	i : 0.04	! : 0.01	" : 0.01	
f : 0.21	d : 0.15	g : 0.14	e : 0.10	^ : 0.09	c : 0.07	h : 0.04	[ : 0.04	= : 0.04	i : 0.03	" : 0.03	
f : 0.21	^ : 0.20	d : 0.15	g : 0.10	c : 0.09	e : 0.07	b : 0.03	= : 0.03	i : 0.03	" : 0.03	h : 0.01	
^ : 0.46	d : 0.10	c : 0.09	f : 0.09	g : 0.07	b : 0.03	i : 0.03	e : 0.03	h : 0.01	= : 0.01	" : 0.01	a : 0.01	
^ : 0.84	f : 0.04	c : 0.04	d : 0.03	i : 0.01	e : 0.01	
^ : 0.92	f : 0.04	c : 0.03	
^ : 0.96	f : 0.01	c : 0.01	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 0.95	g : 0.01	b : 0.01	f : 0.01	
^ : 0.95	g : 0.01	b : 0.01	f : 0.01	
^ : 0.81	g : 0.07	f : 0.04	d : 0.03	c : 0.01	] : 0.01	
^ : 0.45	f : 0.15	d : 0.12	g : 0.09	c : 0.07	h : 0.01	b : 0.01	= : 0.01	i : 0.01	e : 0.01	a : 0.01	
^ : 0.34	f : 0.18	d : 0.12	g : 0.10	c : 0.09	e : 0.04	i : 0.03	h : 0.01	b : 0.01	= : 0.01	] : 0.01	
f : 0.21	d : 0.17	^ : 0.14	c : 0.12	g : 0.12	e : 0.09	= : 0.04	i : 0.04	h : 0.03	
f : 0.20	d : 0.14	^ : 0.12	g : 0.12	e : 0.10	c : 0.07	h : 0.04	= : 0.04	i : 0.04	2 : 0.04	] : 0.01	3 : 0.01	
f : 0.21	e : 0.10	^ : 0.10	g : 0.10	d : 0.07	c : 0.06	3 : 0.06	h : 0.04	= : 0.04	i : 0.04	2 : 0.04	9 : 0.01	4 : 0.01	5 : 0.01	] : 0.01	
f : 0.18	e : 0.10	^ : 0.10	g : 0.10	d : 0.10	3 : 0.07	h : 0.04	= : 0.04	i : 0.04	] : 0.04	c : 0.03	4 : 0.03	: : 0.01	9 : 0.01	5 : 0.01	

#score	2347.0989896696365
#seq	64
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_UTR_m2_run1.txt

#BEAR
eeeewwwwwwwwwwwwwweeeee]ddd	chr14:104646016-104646242(+)$1	226	118	145	23.0163
eeeeeuuuuuuuuuuuueeeee4444f	chr19:7705539-7705763(+)$1	224	87	114	24.3336
eeeeevvvvvvvvvvvvveeeeeccc:	chrX:112019897-112020115(-)$1	218	191	218	23.4981
#dddduuuuuuuuuuuudddd333eee	chr18:56997461-56997686(-)$1	225	165	192	24.4344
&cccvvvvvvvvvvvvvcccdddd]ee	chr3:5259521-5259748(+)$1	227	83	110	23.3727
ggggguuuuuuuuuuuuggggggg22a	chr17:79804251-79804470(-)$1	219	116	143	23.6881
hhhhhuuuuuuuuuuuuhhhhhhhh44	chr19:52825189-52825402(+)$1	213	154	181	22.1458
fffwwwwwwwwwwwwwwffffffccce	chr17:7215046-7215293(+)$1	247	3	30	21.0317
!!cccuuuuuuuuuuuuccc22bb]cc	chr16:1749474-1749700(+)$1	226	160	187	24.1743
gggggvvvvvvvvvvvvvggggggg]f	chr19:39371982-39372197(-)$1	215	168	195	24.0304
&cccwwwwwwwwwwwwwwccc777777	chr3:127323825-127324068(+)$1	243	91	118	19.7294
dddbbtttttttttttbb]dddd]bb:	chr11:129992144-129992365(+)$1	221	144	171	20.3920
iiiiivvvvvvvvvvvvviiiiiiiii	chr17:73886325-73886549(-)$1	224	130	157	24.3383
[dddduuuuuuuuuuuudddd333ggg	chr3:113529074-113529302(+)$1	228	10	37	24.7295
ccc[bbtttttttttttbb]ccceeee	chr18:74073866-74074119(-)$1	253	186	213	21.4134
ddddvvvvvvvvvvvvvdddd:ddddp	chr10:32298559-32298779(-)$1	220	26	53	21.5219
[cccvvvvvvvvvvvvvcccdddd]cc	chrX:70504152-70504390(+)$1	238	175	202	24.3260
::cccvvvvvvvvvvvvvcccccc[ff	chr11:66393963-66394183(+)$1	220	92	119	21.8969
eexxxxxxxxxxxxxxxeeeee333a]	chr1:52378923-52379146(-)$1	223	49	76	17.5344
"dddduuuuuuuuuuuudddd4444bb	chr4:40440819-40441040(-)$1	221	61	88	23.8729
[a!!bbtttttttttttbb22abbeee	chr5:154237957-154238175(+)$1	218	27	54	20.9434
hhhhhuuuuuuuuuuuuhhhhhhhh22	chr8:21862965-21863208(+)$1	243	137	164	21.7780
dddwwwwwwwwwwwwwwdddd:::a[d	chr12:6602998-6603216(+)$1	218	115	142	19.2734
[cccvvvvvvvvvvvvvccc]hhhhhh	chr13:77457446-77457684(-)$1	238	53	80	23.4868
eeeeeyyyyyyyyyyyyyyyyeeeee:	chr14:75130312-75130537(-)$1	225	188	215	18.9051
e[cccuuuuuuuuuuuuccc]eeeee2	chr6:151239641-151239863(+)$1	222	25	52	23.9730
gggggtttttttttttggggggg:ddd	chr7:139248981-139249200(-)$1	219	176	203	21.7282
hhhhhvvvvvvvvvvvvvhhhhhhhh:	chr2:234202988-234203208(+)$1	220	161	188	21.6481
eeeeettttttttttteeeee4444cc	chrX:153667027-153667272(+)$1	245	111	138	23.4050
""ddddtttttttttttdddd22eeee	chr16:31478275-31478496(+)$1	221	41	68	22.1860
G:cccvvvvvvvvvvvvvccc::bb[d	chr14:100002266-100002489(-)$1	223	178	205	20.4212
=====wwwwwwwwwwwwww========	chr9:116169527-116169749(-)$1	222	83	110	22.9164
!!a[attttttttttta]a22bb22gg	chr6:28120960-28121183(+)$1	223	51	78	22.5184
[ddddvvvvvvvvvvvvvdddd]cccD	chr16:19126490-19126711(+)$1	221	24	51	23.6379
ccc[attttttttttta]ccc4444dd	chr7:50659886-50660107(-)$1	221	135	162	23.8157
[ddddvvvvvvvvvvvvvdddd22ddd	chr16:27495469-27495699(-)$1	230	91	118	24.2161
###ccctttttttttttccc333gggg	chr16:46715278-46715504(-)$1	226	65	92	23.2877
eeeeeuuuuuuuuuuuueeeee22ddd	chr5:112176427-112176644(+)$1	217	85	112	24.1137
eeeeettttttttttteeeee333ddd	chr3:49051360-49051588(+)$1	228	185	212	23.5050
hhhhhvvvvvvvvvvvvvhhhhhhhh:	chr12:120984183-120984411(+)$1	228	71	98	21.6481
eeyyyyyyyyyyyyyyyyeeeee]ddd	chr10:103565782-103566000(-)$1	218	111	138	20.5271
d[ccctttttttttttccc]ddddeee	chr14:75230027-75230265(+)$1	238	32	59	22.6704
ggggguuuuuuuuuuuugggggggddd	chr6:36654523-36654742(+)$1	219	24	51	23.8990
=====wwwwwwwwwwwwww========	chr5:112350856-112351088(+)$1	232	200	227	22.9164
[eeeeettttttttttteeeeeccc]c	chr16:2757781-2758004(+)$1	223	194	221	22.9076
[ddddvvvvvvvvvvvvvdddd22ccc	chr17:74039827-74040044(-)$1	217	169	196	24.3822
e[ccctttttttttttccceeeee]cc	chr12:49414659-49414886(-)$1	227	82	109	23.3905
!!cccuuuuuuuuuuuuccc22ccccc	chr17:73517442-73517655(+)$1	213	120	147	24.6076
"""ccctttttttttttccc333bb22	chr15:79614997-79615220(+)$1	223	156	183	22.5440
!cccwwwwwwwwwwwwwwccc======	chr2:113316907-113317132(+)$1	225	123	150	23.6030
eeeevvvvvvvvvvvvveeeee66666	chr5:141000713-141000933(-)$1	220	60	87	22.1448
eeeeettttttttttteeeeegggggg	chr3:9512105-9512324(+)$1	219	17	44	22.9303
ffffftttttttttttffffff]a]ff	chr16:249012-249243(-)$1	231	141	168	21.3399
eeeevvvvvvvvvvvvveeeeeccccc	chr17:57741107-57741368(+)$1	261	36	63	24.1773
ggggguuuuuuuuuuuuggggggg22f	chr2:153616210-153616449(+)$1	239	170	197	23.5559
eeeeettttttttttteeeee333ddd	chr12:49719449-49719676(+)$1	227	87	114	23.5050
[ddddwwwwwwwwwwwwwwdddd]bb]	chr14:96554407-96554633(+)$1	226	72	99	22.1596

#otherMatches

#Seq PSSM
CGCCGGACAAGAGGAGGGGGCGUGCAG	chr14:104646016-104646242(+)$1	226	118	145	23.0163
CCCUGAUCAAAGACUUCCAGGGGACCC	chr19:7705539-7705763(+)$1	224	87	114	24.3336
AGAAACCAAUCCCACUUCUUUCUAGGA	chrX:112019897-112020115(-)$1	218	191	218	23.4981
UAAGGAAUUUAUUUCUCCCUUUACUAC	chr18:56997461-56997686(-)$1	225	165	192	24.4344
UGCCUGUGAUUUCUCUUGGCGCUCCCC	chr3:5259521-5259748(+)$1	227	83	110	23.3727
CAGAGAGGAUCACAGAGUUCUGCCACC	chr17:79804251-79804470(-)$1	219	116	143	23.6881
CAUACCAGAGAGAAGCCGUAUGAAUGU	chr19:52825189-52825402(+)$1	213	154	181	22.1458
GCUUACUUUCUGCCCCUAGCCUGGCUC	chr17:7215046-7215293(+)$1	247	3	30	21.0317
CUGCCAUCUGAAACCUCGGCCUGAUCU	chr16:1749474-1749700(+)$1	226	160	187	24.1743
GGGUCCCCUCCUCCCCCUGACCCCCUC	chr19:39371982-39372197(-)$1	215	168	195	24.0304
CCGCUUCAAGAACUUCCUGCGCACUCA	chr3:127323825-127324068(+)$1	243	91	118	19.7294
uggaggaCCGAGAUUACUACUAUGACA	chr11:129992144-129992365(+)$1	221	144	171	20.3920
UUUAAUUUUUUGUAACAUUUGGAGAGA	chr17:73886325-73886549(-)$1	224	130	157	24.3383
caccauauuggucaggcuggucucgaa	chr3:113529074-113529302(+)$1	228	10	37	24.7295
UUAGUGGGUAUUUAAAAUAGUAAAUAA	chr18:74073866-74074119(-)$1	253	186	213	21.4134
GUUAUAAGUAAUAUAGUUAACAAGCAA	chr10:32298559-32298779(-)$1	220	26	53	21.5219
ugccagacaaaacaccgggcacccagu	chrX:70504152-70504390(+)$1	238	175	202	24.3260
UCCGAUUACGCACGCUAUUCGGGCUCC	chr11:66393963-66394183(+)$1	220	92	119	21.8969
ugaccaauuuuucaaucuaccacaGGA	chr1:52378923-52379146(-)$1	223	49	76	17.5344
CAGCGGUUCCCCACUCACGCUUCUUUC	chr4:40440819-40441040(-)$1	221	61	88	23.8729
ACAGGCAGAGCGAACACGCACGGAGUC	chr5:154237957-154238175(+)$1	218	27	54	20.9434
UGUGUGAGAGUGCAGAGAUAUAUUUAG	chr8:21862965-21863208(+)$1	243	137	164	21.7780
CCGUUGAGAUUUGAACUCGGUAUUUGU	chr12:6602998-6603216(+)$1	218	115	142	19.2734
AAUAAAUUCCCAAUGCAUAUCCUAUGU	chr13:77457446-77457684(-)$1	238	53	80	23.4868
CUGAUCCUAACACACAUAACCAUCAGC	chr14:75130312-75130537(-)$1	225	188	215	18.9051
AUGACAGUGUACUGAAAGUCUUUUUUU	chr6:151239641-151239863(+)$1	222	25	52	23.9730
AGGGGAGGACCAUAUACCCCUAUUCCC	chr7:139248981-139249200(-)$1	219	176	203	21.7282
AUUUCUGAAGAUUUGACUGAGGUCUCU	chr2:234202988-234203208(+)$1	220	161	188	21.6481
GGCCCCCUGAGUCGAUGGGCCGAGGCC	chrX:153667027-153667272(+)$1	245	111	138	23.4050
AGCGGUGAGAACAUGGAACCGGACUCC	chr16:31478275-31478496(+)$1	221	41	68	22.1860
CCAGCACCCACCCCUCCAGCUCACCCA	chr14:100002266-100002489(-)$1	223	178	205	20.4212
CGCUUUUUGUUUCUAAGUUGAGUGCUU	chr9:116169527-116169749(-)$1	222	83	110	22.9164
AGAGAGACGACAUAAAUGUGAUGAAUG	chr6:28120960-28121183(+)$1	223	51	78	22.5184
UCACCUCUCUGCUACUCUGGUGCUGCG	chr16:19126490-19126711(+)$1	221	24	51	23.6379
CAGUCAAGCAACCACAGUCUGUUAAUC	chr7:50659886-50660107(-)$1	221	135	162	23.8157
UUGGAUAAAACAUCUCAUUCCGUUGGA	chr16:27495469-27495699(-)$1	230	91	118	24.2161
UUUUUAGUCCUUAAUCAUAAUUAAAAG	chr16:46715278-46715504(-)$1	226	65	92	23.2877
UCCGUGUGAAAAAGAUAAUGGACCAGG	chr5:112176427-112176644(+)$1	217	85	112	24.1137
CCAGGUAAUAUAUGCUCCUGGGCAGGG	chr3:49051360-49051588(+)$1	228	185	212	23.5050
CUUUCCUACCCCAAAAAUGAAAGUUUU	chr12:120984183-120984411(+)$1	228	71	98	21.6481
ACUUUCUGUUAUCCAAAUGUGUCUCAG	chr10:103565782-103566000(-)$1	218	111	138	20.5271
GCGCGCUCCGUUUACACGCUCCGGGGC	chr14:75230027-75230265(+)$1	238	32	59	22.6704
CCCCCUCCUCUAGCUGUGGGGGUGAGG	chr6:36654523-36654742(+)$1	219	24	51	23.8990
UGUUUUUUUUUUUCUUUUUAAGUGCAU	chr5:112350856-112351088(+)$1	232	200	227	22.9164
AGAGAACUUUGUACCCCUUCUCUGUGU	chr16:2757781-2758004(+)$1	223	194	221	22.9076
GGCAGGUUAUGGAGUCAGCUGUGGAGG	chr17:74039827-74040044(-)$1	217	169	196	24.3822
CCUCACUGCCCUCUUCUGAGUGGGUGG	chr12:49414659-49414886(-)$1	227	82	109	23.3905
AAGAGAAAGAGGAGCAGCUCCAGCCCU	chr17:73517442-73517655(+)$1	213	120	147	24.6076
GUGGCUAAUAAAAACUAAGUGUGAGCG	chr15:79614997-79615220(+)$1	223	156	183	22.5440
UGUCCCGUGCAUACCCCAGACGGGGAG	chr2:113316907-113317132(+)$1	225	123	150	23.6030
CUUUUCCUCUCUCUCCCAAGGCCUGAC	chr5:141000713-141000933(-)$1	220	60	87	22.1448
GUUGAUUUUUAUUCUUUCAGCUUUGUC	chr3:9512105-9512324(+)$1	219	17	44	22.9303
UUGGGGUUCAUUCAGAUCCGAGAGAAG	chr16:249012-249243(-)$1	231	141	168	21.3399
ACUGCUCAUUUCUAAAACAGUUCAUGG	chr17:57741107-57741368(+)$1	261	36	63	24.1773
AAAACUUAAUCAUGAUUGUUUUGUAAU	chr2:153616210-153616449(+)$1	239	170	197	23.5559
GGGCCUCUGCAUAUUUGGCCCCCAGAA	chr12:49719449-49719676(+)$1	227	87	114	23.5050
GUGUAUAUUUAGAGACAAUUACAAGAA	chr14:96554407-96554633(+)$1	226	72	99	22.1596

#DB
((((..............))))).)))	chr14:104646016-104646242(+)$1	1	118	145	23.0163
(((((............)))))....)	chr19:7705539-7705763(+)$1	1	87	114	24.3336
(((((.............)))))))).	chrX:112019897-112020115(-)$1	1	191	218	23.4981
.((((............))))...)))	chr18:56997461-56997686(-)$1	1	165	192	24.4344
.(((.............))))))).))	chr3:5259521-5259748(+)$1	1	83	110	23.3727
(((((............)))))))..)	chr17:79804251-79804470(-)$1	1	116	143	23.6881
(((((............))))))))..	chr19:52825189-52825402(+)$1	1	154	181	22.1458
(((..............))))))((((	chr17:7215046-7215293(+)$1	1	3	30	21.0317
..(((............)))..)).))	chr16:1749474-1749700(+)$1	1	160	187	24.1743
(((((.............))))))).)	chr19:39371982-39372197(-)$1	1	168	195	24.0304
.(((..............)))......	chr3:127323825-127324068(+)$1	1	91	118	19.7294
(((((...........)).)))).)).	chr11:129992144-129992365(+)$1	1	144	171	20.3920
(((((.............)))))))))	chr17:73886325-73886549(-)$1	1	130	157	24.3383
.((((............))))...)))	chr3:113529074-113529302(+)$1	1	10	37	24.7295
(((.((...........)).)))))))	chr18:74073866-74074119(-)$1	1	186	213	21.4134
((((.............)))).((((.	chr10:32298559-32298779(-)$1	1	26	53	21.5219
.(((.............))))))).))	chrX:70504152-70504390(+)$1	1	175	202	24.3260
..(((.............)))(((.((	chr11:66393963-66394183(+)$1	1	92	119	21.8969
((...............)))))...).	chr1:52378923-52379146(-)$1	1	49	76	17.5344
.((((............))))....))	chr4:40440819-40441040(-)$1	1	61	88	23.8729
.(..((...........))..))))))	chr5:154237957-154238175(+)$1	1	27	54	20.9434
(((((............))))))))..	chr8:21862965-21863208(+)$1	1	137	164	21.7780
(((..............))))...(.(	chr12:6602998-6603216(+)$1	1	115	142	19.2734
.(((.............))).))))))	chr13:77457446-77457684(-)$1	1	53	80	23.4868
(((((................))))).	chr14:75130312-75130537(-)$1	1	188	215	18.9051
(.(((............))).))))).	chr6:151239641-151239863(+)$1	1	25	52	23.9730
(((((...........))))))).(((	chr7:139248981-139249200(-)$1	1	176	203	21.7282
(((((.............)))))))).	chr2:234202988-234203208(+)$1	1	161	188	21.6481
(((((...........)))))....))	chrX:153667027-153667272(+)$1	1	111	138	23.4050
..((((...........))))..))))	chr16:31478275-31478496(+)$1	1	41	68	22.1860
).(((.............)))..((.(	chr14:100002266-100002489(-)$1	1	178	205	20.4212
(((((..............))))))))	chr9:116169527-116169749(-)$1	1	83	110	22.9164
..(.(...........).)..))..))	chr6:28120960-28121183(+)$1	1	51	78	22.5184
.((((.............)))).)))(	chr16:19126490-19126711(+)$1	1	24	51	23.6379
(((.(...........).)))....))	chr7:50659886-50660107(-)$1	1	135	162	23.8157
.((((.............))))..)))	chr16:27495469-27495699(-)$1	1	91	118	24.2161
...(((...........)))...))))	chr16:46715278-46715504(-)$1	1	65	92	23.2877
(((((............)))))..)))	chr5:112176427-112176644(+)$1	1	85	112	24.1137
(((((...........)))))...)))	chr3:49051360-49051588(+)$1	1	185	212	23.5050
(((((.............)))))))).	chr12:120984183-120984411(+)$1	1	71	98	21.6481
((................))))).)))	chr10:103565782-103566000(-)$1	1	111	138	20.5271
(.(((...........))).))))(((	chr14:75230027-75230265(+)$1	1	32	59	22.6704
(((((............)))))))(((	chr6:36654523-36654742(+)$1	1	24	51	23.8990
(((((..............))))))))	chr5:112350856-112351088(+)$1	1	200	227	22.9164
.(((((...........)))))))).)	chr16:2757781-2758004(+)$1	1	194	221	22.9076
.((((.............))))..)))	chr17:74039827-74040044(-)$1	1	169	196	24.3822
(.(((...........)))))))).))	chr12:49414659-49414886(-)$1	1	82	109	23.3905
..(((............)))..)))))	chr17:73517442-73517655(+)$1	1	120	147	24.6076
...(((...........)))...))..	chr15:79614997-79615220(+)$1	1	156	183	22.5440
.(((..............)))))))))	chr2:113316907-113317132(+)$1	1	123	150	23.6030
((((.............))))).....	chr5:141000713-141000933(-)$1	1	60	87	22.1448
(((((...........)))))((((((	chr3:9512105-9512324(+)$1	1	17	44	22.9303
(((((...........)))))).).))	chr16:249012-249243(-)$1	1	141	168	21.3399
((((.............)))))(((((	chr17:57741107-57741368(+)$1	1	36	63	24.1773
(((((............)))))))..)	chr2:153616210-153616449(+)$1	1	170	197	23.5559
(((((...........)))))...)))	chr12:49719449-49719676(+)$1	1	87	114	23.5050
.((((..............)))).)).	chr14:96554407-96554633(+)$1	1	72	99	22.1596

#PSSM
e : 0.26	[ : 0.15	g : 0.08	h : 0.07	! : 0.07	d : 0.07	" : 0.05	# : 0.03	& : 0.03	f : 0.03	c : 0.03	= : 0.03	i : 0.01	: : 0.01	G : 0.01	
e : 0.24	d : 0.17	c : 0.12	g : 0.08	h : 0.07	! : 0.05	[ : 0.05	f : 0.03	: : 0.03	" : 0.03	= : 0.03	i : 0.01	a : 0.01	# : 0.01	
c : 0.24	e : 0.21	d : 0.19	g : 0.08	h : 0.07	f : 0.03	= : 0.03	i : 0.01	x : 0.01	! : 0.01	a : 0.01	# : 0.01	y : 0.01	" : 0.01	
c : 0.24	e : 0.21	d : 0.15	g : 0.08	h : 0.07	[ : 0.05	w : 0.03	= : 0.03	b : 0.01	i : 0.01	x : 0.01	! : 0.01	y : 0.01	f : 0.01	
e : 0.15	c : 0.15	d : 0.14	v : 0.10	w : 0.08	g : 0.08	h : 0.07	b : 0.05	= : 0.03	a : 0.03	i : 0.01	x : 0.01	y : 0.01	f : 0.01	
v : 0.28	u : 0.22	t : 0.19	w : 0.14	b : 0.03	y : 0.03	c : 0.03	x : 0.01	d : 0.01	e : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
t : 0.29	v : 0.28	u : 0.22	w : 0.14	y : 0.03	x : 0.01	
v : 0.28	u : 0.22	w : 0.14	t : 0.10	e : 0.07	y : 0.03	a : 0.03	c : 0.03	b : 0.01	x : 0.01	g : 0.01	f : 0.01	
e : 0.17	v : 0.17	c : 0.17	w : 0.10	d : 0.10	g : 0.07	b : 0.05	h : 0.03	f : 0.03	y : 0.03	] : 0.03	
c : 0.26	e : 0.22	d : 0.15	g : 0.08	h : 0.07	w : 0.05	f : 0.03	b : 0.03	] : 0.01	i : 0.01	y : 0.01	a : 0.01	
e : 0.24	c : 0.22	d : 0.19	g : 0.08	h : 0.07	f : 0.03	] : 0.03	2 : 0.03	= : 0.03	i : 0.01	y : 0.01	
e : 0.24	d : 0.24	c : 0.10	g : 0.08	h : 0.07	2 : 0.07	f : 0.03	] : 0.03	= : 0.03	3 : 0.03	i : 0.01	y : 0.01	
e : 0.21	d : 0.14	3 : 0.10	g : 0.10	h : 0.08	2 : 0.05	: : 0.05	4 : 0.05	= : 0.05	f : 0.03	c : 0.03	7 : 0.01	i : 0.01	a : 0.01	b : 0.01	
3 : 0.12	e : 0.10	d : 0.10	g : 0.10	h : 0.08	c : 0.08	4 : 0.07	2 : 0.07	b : 0.05	= : 0.05	: : 0.03	] : 0.03	f : 0.01	7 : 0.01	i : 0.01	6 : 0.01	
c : 0.12	g : 0.10	3 : 0.08	h : 0.08	e : 0.08	] : 0.07	4 : 0.07	d : 0.07	b : 0.07	2 : 0.07	= : 0.05	: : 0.03	7 : 0.01	i : 0.01	6 : 0.01	a : 0.01	
d : 0.15	c : 0.12	e : 0.12	] : 0.08	h : 0.08	4 : 0.07	g : 0.07	b : 0.07	2 : 0.05	= : 0.05	7 : 0.01	i : 0.01	[ : 0.01	3 : 0.01	a : 0.01	6 : 0.01	
d : 0.17	c : 0.17	e : 0.14	2 : 0.07	g : 0.07	b : 0.05	h : 0.05	= : 0.05	4 : 0.03	] : 0.03	f : 0.03	[ : 0.03	7 : 0.01	i : 0.01	a : 0.01	6 : 0.01	
d : 0.19	c : 0.14	e : 0.12	f : 0.08	: : 0.08	g : 0.07	2 : 0.05	= : 0.05	] : 0.03	a : 0.01	4 : 0.01	7 : 0.01	i : 0.01	p : 0.01	b : 0.01	h : 0.01	D : 0.01	6 : 0.01	

#score	1292.1509544590172
#seq	57
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_UTR_m1_run2.txt

#BEAR
ggggggg^^^^^^^^^^^^^^^^^^ggggggg	chr15:65870516-65870733(+)$1	217	135	167	32.5142
iiiiiii^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:109243368-109243583(+)$1	215	20	52	36.6680
#eeeee[bbyyyyyyyyyyyyyyyybb]eeee	chr6:52129282-52129504(-)$1	222	149	181	23.1129
c[eeeee^^^^^^^^^^^^^^^^^^^^^^^ee	chr1:162496027-162496247(+)$1	220	36	68	35.9353
ffffff!!bb^^^^^^^^^^^^^^^^^^bb22	chr12:123892489-123892710(+)$1	221	63	95	30.7688
hhhhhhh^^^^^^^^^^^^^^^^^^^^^^^^h	chr12:75893237-75893460(-)$1	223	16	48	34.8307
[ffffff^^^^^^^^^^^^^^^^^^^ffffff	chr4:83847824-83848048(-)$1	224	49	81	33.0524
ggggggg^^^^^^^^^^^^^^^^^^ggggggg	chr2:10022749-10022969(+)$1	220	58	90	32.5142
=======^^^^^^^^^^^^^^^^^^^^^^^^^	chr17:27589353-27589570(-)$1	217	144	176	36.8017
ee!!ccc^^^^^^^^^^^^^^^^^^^^^ccce	chr12:112578876-112579089(+)$1	213	85	117	35.3506
==eeeee^^^^^^^^^^^^^^^^^^^^^^eee	chr22:35690487-35690714(+)$1	227	95	127	35.8491
ggggggg^^^^^^^^^^^^^^^^^^ggggggg	chr10:72187409-72187623(+)$1	214	59	91	32.5142
ffffff^^^^^^^^^^^^^^^^^^^^^^ffff	chr13:79888853-79889076(-)$1	223	175	207	35.1138
ii!!ccc^^^^^^^^^^^^^^^^^^^^^^ccc	chr12:57458397-57458619(-)$1	222	95	127	36.1207
ggggggg^^^^^^^^^^^^^^^^^^^^ggggg	chr4:17846888-17847115(+)$1	227	27	59	35.1816
:eeeee^^^^^^^^^^^^^^^^^^^^^^eeee	chr17:45196505-45196728(-)$1	223	134	166	34.0720
=======^^^^^^^^^^^^^^^^^^^^^====	chr15:74923793-74924014(-)$1	221	112	144	36.4272
ggggggg^^^^^^^^^^^^^^^^^^^^^^^gg	chr6:118029676-118029896(+)$1	220	126	158	36.8114
eee####ccc^^^^^^^^^^^^^^^^^^ccc]	chr15:45899910-45900132(+)$1	222	103	135	31.1360
eeee^^^^^^^^^^^^^^^^^^^^^^^^^^ee	chr19:6414672-6414890(-)$1	218	164	196	35.2415
========^^^^^^^^^^^^^^^^^^^^====	chr10:121336527-121336743(-)$1	216	178	210	35.3100
iiiiiiiiiyyyyyyyyyyyyyyyyiiiiiii	chr1:144901957-144902173(-)$1	216	61	93	23.7123
!!ffffff^^^^^^^^^^^^^^^^^^^^ffff	chr1:231501613-231501823(-)$1	210	138	170	34.1611
ggggggg^^^^^^^^^^^^^^^^^^^^^^^^^	chr18:8718425-8718645(+)$1	220	78	110	36.7057
fff^^^^^^^^^^^^^^^^^^^^^^^^^ffff	chr3:5221129-5221349(+)$1	220	99	131	34.3689
((eeeee^^^^^^^^^^^^^^^^^^^eeeee9	chr7:11082267-11082486(+)$1	219	145	177	30.8392
hhhhhhh^^^^^^^^^^^^^^^^^^^^^hhhh	chr1:113456077-113456300(-)$1	223	181	213	33.2242
ff[dddd^^^^^^^^^^^^^^^^^^^^^^ddd	chr2:148692805-148693029(-)$1	224	26	58	34.8271
ddffffff^^^^^^^^^^^^^^^^^^ffffff	chr6:30667614-30667839(-)$1	225	180	212	31.2497
cc[dddd^^^^^^^^^^^^^^^^^^^^^^ddd	chr6:86321163-86321380(-)$1	217	69	101	34.8753
ggggggg^^^^^^^^^^^^^^^^^^^^^^ggg	chr6:42976064-42976283(+)$1	219	153	185	36.6539
$$gggggggyyyyyyyyyyyyyyyyggggggg	chr20:461867-462086(-)$1	219	151	183	23.4076
==========xxxxxxxxxxxxxxx=======	chr6:56971587-56971810(+)$1	223	132	164	22.6901
:ffffff^^^^^^^^^^^^^^^^^^^^fffff	chr19:36727071-36727305(+)$1	234	199	231	33.2130
!!dddd^^^^^^^^^^^^^^^^^^^^^^^^^d	chr14:93695396-93695620(+)$1	224	131	163	35.4653
dddd[bb^^^^^^^^^^^^^^^^^^^^^^^^b	chr20:34238765-34238981(-)$1	216	130	162	34.6156
cc!!ccc^^^^^^^^^^^^^^^^^^^^^^ccc	chr4:76570258-76570479(-)$1	221	72	104	35.8561
dffffff^^^^^^^^^^^^^^^^^^^ffffff	chrX:18258839-18259062(-)$1	223	165	197	32.7576
ff[dddd^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:225683451-225683676(-)$1	225	109	141	35.4479
:ffffff^^^^^^^^^^^^^^^^^^^^^ffff	chr8:87479178-87479403(+)$1	225	93	125	34.2804
eeeee^^^^^^^^^^^^^^^^^^^^^^^eeee	chr20:30922424-30922644(+)$1	220	2	34	34.7495
ggggggg^^^^^^^^^^^^^^^^^^^^^gggg	chr1:207222132-207222350(-)$1	218	120	152	36.2238
ggggggg^^^^^^^^^^^^^^^^^^^^ggggg	chr4:78087969-78088183(+)$1	214	156	188	35.1816
ggggggg^^^^^^^^^^^^^^^^^^^^^^^^^	chr19:37004526-37004752(-)$1	226	6	38	36.7057
iiiiiiiii^^^^^^^^^^^^^^^^^^iiiii	chr2:128057562-128057786(-)$1	224	18	50	32.2673
ggggggg^^^^^^^^^^^^^^^^^^^^^^^^^	chr12:109040746-109040966(-)$1	220	173	205	36.7057
:ffffff^^^^^^^^^^^^^^^^^^^ffffff	chr8:98731225-98731438(+)$1	213	75	107	31.9689
!!eeeee^^^^^^^^^^^^^^^^^^^^^^^ee	chr6:16146925-16147147(+)$1	222	167	199	36.0557
=======!!cccyyyyyyyyyyyyyyyyccc3	chr12:98928295-98928518(+)$1	223	33	65	24.2402
!!dddd^^^^^^^^^^^^^^^^^^^^^^^ddd	chrX:119660422-119660639(-)$1	217	107	139	34.9418
==========^^^^^^^^^^^^^^^^^^====	chr8:116424243-116424467(-)$1	224	17	49	32.6940
iiiiiii^^^^^^^^^^^^^^^^^^^^^^^^^	chr13:49783429-49783646(+)$1	217	91	123	36.6680

#otherMatches

#Seq PSSM
GAUUGUGUAUUUCUAUUAAAACAUUUACAAUC	chr15:65870516-65870733(+)$1	217	135	167	32.5142
UUUUCUUGAAUUCUUUCUCAGAUUUUAAAGUA	chr1:109243368-109243583(+)$1	215	20	52	36.6680
CGAGAGAGUUUGUUCUGUGUUUCCCACCCUCU	chr6:52129282-52129504(-)$1	222	149	181	23.1129
ACUUUUUUUUUUUUUUACAGUUAAUUUAAUGA	chr1:162496027-162496247(+)$1	220	36	68	35.9353
GGUUUUAGAGGAAAUAGUCAAACAUGAACUAG	chr12:123892489-123892710(+)$1	221	63	95	30.7688
auaaauuauauuauuauuguauuuuuugaaaa	chr12:75893237-75893460(-)$1	223	16	48	34.8307
CUAAGAGGUUUCAAACCAAAUCGCAACUCUUA	chr4:83847824-83848048(-)$1	224	49	81	33.0524
UAAACCUUUUUCUUUUUAAAAAUACAGGUUUG	chr2:10022749-10022969(+)$1	220	58	90	32.5142
uuuuuuuaaauaaaaauuuucaaaaaguuaaa	chr17:27589353-27589570(-)$1	217	144	176	36.8017
GUUUUCCACAAUAGAACUACCAACCAAAGGAA	chr12:112578876-112579089(+)$1	213	85	117	35.3506
AUUGCAAAAACAAAACAAAACUCACUCUCUUG	chr22:35690487-35690714(+)$1	227	95	127	35.8491
UGGAAAUAUUACUGAGAUGAAACACAUUUCCA	chr10:72187409-72187623(+)$1	214	59	91	32.5142
UAAAUGUUUUCUCCCCAUACUUUAUAGCCAUU	chr13:79888853-79889076(-)$1	223	175	207	35.1138
AGAAGUCAAAUUUUCUACUACUCUACUGGGAU	chr12:57458397-57458619(-)$1	222	95	127	36.1207
UUGCCUUUUCUUUCACCAAUUUGCUUCGAGGU	chr4:17846888-17847115(+)$1	227	27	59	35.1816
UUGGGAGAAAAUAAAUAUAAUGAAAAAUUCCC	chr17:45196505-45196728(-)$1	223	134	166	34.0720
CUGGGCUUUGAACCUUUUACAUUUGUCCAGUC	chr15:74923793-74924014(-)$1	221	112	144	36.4272
GACUUUUUUUUUUUGUUUUAAUUUAUUACUGA	chr6:118029676-118029896(+)$1	220	126	158	36.8114
CCAAAUACCCACUUUAUAGAUAAUUACAGGGA	chr15:45899910-45900132(+)$1	222	103	135	31.1360
GUUUUUGUUCUUUUUAUUCUUUUAUUUUUUAA	chr19:6414672-6414890(-)$1	218	164	196	35.2415
UAAGGUUUCCAUCUUACAUGUCACAUAAAAGC	chr10:121336527-121336743(-)$1	216	178	210	35.3100
ACUAGAUAGGGUCCUAUGUUUUUCACUAUUUA	chr1:144901957-144902173(-)$1	216	61	93	23.7123
ACUAUUAAAUUUUGCCCUAAAAGACCUCUUAA	chr1:231501613-231501823(-)$1	210	138	170	34.1611
UUCGGCGAGAACUGGACCGCGCUAAUAAAAAC	chr18:8718425-8718645(+)$1	220	78	110	36.7057
UUCCACCCAAUAUAAUAAAACCUGUUAAGAAU	chr3:5221129-5221349(+)$1	220	99	131	34.3689
AUGCCAAGAAAGACCAAAAACAGUUAUUGGUG	chr7:11082267-11082486(+)$1	219	145	177	30.8392
GAGGCAAAUCUAAAAUUUAAAAUUAAUCUUGC	chr1:113456077-113456300(-)$1	223	181	213	33.2242
GAUAUGCUAAACAUUCUAUAAACAUUCUUGUA	chr2:148692805-148693029(-)$1	224	26	58	34.8271
ccagcuuuuccaggauuuauaaaauuagagcu	chr6:30667614-30667839(-)$1	225	180	212	31.2497
GAUAGCUUAAAGUAAAAAGUGAAAAUUAUAGU	chr6:86321163-86321380(-)$1	217	69	101	34.8753
GCUGCCUUCCUCCUUAUAAUGUCCAACUCAGG	chr6:42976064-42976283(+)$1	219	153	185	36.6539
UUGAAGUGGUCCCUCCCCUCUUCCUCUGCUUU	chr20:461867-462086(-)$1	219	151	183	23.4076
GUUUUAUAAACCAUUAAAAUAUUAUUUUAUGA	chr6:56971587-56971810(+)$1	223	132	164	22.6901
AAGUAAAUCCUCACUCAUCAAGAAAUUUUUAC	chr19:36727071-36727305(+)$1	234	199	231	33.2130
UUCUGUAAAAUUUAAAUAAAACCAAUACAAAA	chr14:93695396-93695620(+)$1	224	131	163	35.4653
CGUUUGAAACAUCCCCAACAUUUCCUACAAAU	chr20:34238765-34238981(-)$1	216	130	162	34.6156
GACUUGGAGAAUUAAGGACUGAGAAAUGACCA	chr4:76570258-76570479(-)$1	221	72	104	35.8561
AUAUCAUCUUUUCUCAGAUAUUUUGUGUGAUA	chrX:18258839-18259062(-)$1	223	165	197	32.7576
AGCUAUCAUAAUUCAAGUAUACAUUUCUUUUU	chr1:225683451-225683676(-)$1	225	109	141	35.4479
AAACAGUUCAUCCUUUUCUACUUUAUUUAUUG	chr8:87479178-87479403(+)$1	225	93	125	34.2804
AGCCAUACUAAAAAUGCUCUGAGGGAACUGGC	chr20:30922424-30922644(+)$1	220	2	34	34.7495
ACACUGAAAUUCCUUGUUAAGAUUAAAAUUAG	chr1:207222132-207222350(-)$1	218	120	152	36.2238
UGUAUAUGAACAUGUAAAUCUUUUAAAAUGUA	chr4:78087969-78088183(+)$1	214	156	188	35.1816
AUAGUGUAAAGAAAACCCguacccccaaaacu	chr19:37004526-37004752(-)$1	226	6	38	36.7057
CUGUGUCUUUAUGUUUUAACUUCUUUCAAGAU	chr2:128057562-128057786(-)$1	224	18	50	32.2673
UGCUUUUUAUAUUUCUUUCUUUUUUAAUGUUG	chr12:109040746-109040966(-)$1	220	173	205	36.7057
AUUAGAGAAGACCUUCCAGUGAAUACCUCUAA	chr8:98731225-98731438(+)$1	213	75	107	31.9689
GAUGUUAAAAAAAAAAAAAAGGAAGAAAAAUA	chr6:16146925-16147147(+)$1	222	167	199	36.0557
CAAUUUAACGCUUUCUAGAUCACAUAUUAGUC	chr12:98928295-98928518(+)$1	223	33	65	24.2402
UUUUACUACCGAUGACCAAAUGAAGCAGUGUA	chrX:119660422-119660639(-)$1	217	107	139	34.9418
AAAAAGGGUAGCACUUAUUCAUUCCAAGUACu	chr8:116424243-116424467(-)$1	224	17	49	32.6940
UAAUCUUGAUUUUACCUCAUAUACUGUACAUU	chr13:49783429-49783646(+)$1	217	91	123	36.6680

#DB
(((((((..................)))))))	chr15:65870516-65870733(+)$1	1	135	167	32.5142
(((((((.........................	chr1:109243368-109243583(+)$1	1	20	52	36.6680
.(((((.((................)).))))	chr6:52129282-52129504(-)$1	1	149	181	23.1129
(.(((((.......................))	chr1:162496027-162496247(+)$1	1	36	68	35.9353
((((((..((..................))..	chr12:123892489-123892710(+)$1	1	63	95	30.7688
(((((((........................)	chr12:75893237-75893460(-)$1	1	16	48	34.8307
.((((((...................))))))	chr4:83847824-83848048(-)$1	1	49	81	33.0524
(((((((..................)))))))	chr2:10022749-10022969(+)$1	1	58	90	32.5142
(((((((.........................	chr17:27589353-27589570(-)$1	1	144	176	36.8017
((..(((.....................))))	chr12:112578876-112579089(+)$1	1	85	117	35.3506
(((((((......................)))	chr22:35690487-35690714(+)$1	1	95	127	35.8491
(((((((..................)))))))	chr10:72187409-72187623(+)$1	1	59	91	32.5142
((((((......................))))	chr13:79888853-79889076(-)$1	1	175	207	35.1138
((..(((......................)))	chr12:57458397-57458619(-)$1	1	95	127	36.1207
(((((((....................)))))	chr4:17846888-17847115(+)$1	1	27	59	35.1816
.(((((......................))))	chr17:45196505-45196728(-)$1	1	134	166	34.0720
(((((((.....................))))	chr15:74923793-74924014(-)$1	1	112	144	36.4272
(((((((.......................))	chr6:118029676-118029896(+)$1	1	126	158	36.8114
(((....(((..................))).	chr15:45899910-45900132(+)$1	1	103	135	31.1360
((((..........................))	chr19:6414672-6414890(-)$1	1	164	196	35.2415
((((((((....................))))	chr10:121336527-121336743(-)$1	1	178	210	35.3100
(((((((((................)))))))	chr1:144901957-144902173(-)$1	1	61	93	23.7123
..((((((....................))))	chr1:231501613-231501823(-)$1	1	138	170	34.1611
(((((((.........................	chr18:8718425-8718645(+)$1	1	78	110	36.7057
(((.........................))))	chr3:5221129-5221349(+)$1	1	99	131	34.3689
..(((((...................))))).	chr7:11082267-11082486(+)$1	1	145	177	30.8392
(((((((.....................))))	chr1:113456077-113456300(-)$1	1	181	213	33.2242
((.((((......................)))	chr2:148692805-148693029(-)$1	1	26	58	34.8271
((((((((..................))))))	chr6:30667614-30667839(-)$1	1	180	212	31.2497
((.((((......................)))	chr6:86321163-86321380(-)$1	1	69	101	34.8753
(((((((......................)))	chr6:42976064-42976283(+)$1	1	153	185	36.6539
..(((((((................)))))))	chr20:461867-462086(-)$1	1	151	183	23.4076
((((((((((...............)))))))	chr6:56971587-56971810(+)$1	1	132	164	22.6901
.((((((....................)))))	chr19:36727071-36727305(+)$1	1	199	231	33.2130
..((((.........................)	chr14:93695396-93695620(+)$1	1	131	163	35.4653
((((.((........................)	chr20:34238765-34238981(-)$1	1	130	162	34.6156
((..(((......................)))	chr4:76570258-76570479(-)$1	1	72	104	35.8561
(((((((...................))))))	chrX:18258839-18259062(-)$1	1	165	197	32.7576
((.((((.........................	chr1:225683451-225683676(-)$1	1	109	141	35.4479
.((((((.....................))))	chr8:87479178-87479403(+)$1	1	93	125	34.2804
(((((.......................))))	chr20:30922424-30922644(+)$1	1	2	34	34.7495
(((((((.....................))))	chr1:207222132-207222350(-)$1	1	120	152	36.2238
(((((((....................)))))	chr4:78087969-78088183(+)$1	1	156	188	35.1816
(((((((.........................	chr19:37004526-37004752(-)$1	1	6	38	36.7057
(((((((((..................)))))	chr2:128057562-128057786(-)$1	1	18	50	32.2673
(((((((.........................	chr12:109040746-109040966(-)$1	1	173	205	36.7057
.((((((...................))))))	chr8:98731225-98731438(+)$1	1	75	107	31.9689
..(((((.......................))	chr6:16146925-16147147(+)$1	1	167	199	36.0557
(((((((..(((................))).	chr12:98928295-98928518(+)$1	1	33	65	24.2402
..((((.......................)))	chrX:119660422-119660639(-)$1	1	107	139	34.9418
((((((((((..................))))	chr8:116424243-116424467(-)$1	1	17	49	32.6940
(((((((.........................	chr13:49783429-49783646(+)$1	1	91	123	36.6680

#PSSM
g : 0.21	= : 0.13	i : 0.09	f : 0.09	e : 0.07	: : 0.07	! : 0.07	c : 0.05	d : 0.05	h : 0.03	# : 0.01	[ : 0.01	( : 0.01	$ : 0.01	
g : 0.21	f : 0.19	= : 0.13	e : 0.11	i : 0.09	! : 0.07	h : 0.03	d : 0.03	c : 0.03	[ : 0.01	( : 0.01	$ : 0.01	
g : 0.23	f : 0.19	e : 0.17	= : 0.11	i : 0.07	! : 0.05	[ : 0.05	d : 0.05	h : 0.03	
g : 0.23	f : 0.17	e : 0.15	= : 0.11	d : 0.11	i : 0.07	! : 0.05	h : 0.03	# : 0.01	^ : 0.01	
g : 0.23	f : 0.17	e : 0.13	= : 0.11	d : 0.09	i : 0.07	c : 0.05	h : 0.03	^ : 0.03	# : 0.01	[ : 0.01	
g : 0.23	f : 0.17	e : 0.11	= : 0.11	d : 0.09	i : 0.07	c : 0.05	^ : 0.05	h : 0.03	# : 0.01	b : 0.01	
g : 0.23	f : 0.13	^ : 0.13	= : 0.11	i : 0.07	e : 0.07	c : 0.05	d : 0.05	h : 0.03	[ : 0.01	! : 0.01	# : 0.01	b : 0.01	
^ : 0.76	= : 0.05	! : 0.03	i : 0.03	f : 0.03	b : 0.01	c : 0.01	g : 0.01	
^ : 0.82	b : 0.03	i : 0.03	= : 0.03	c : 0.01	g : 0.01	! : 0.01	
^ : 0.84	y : 0.05	c : 0.03	= : 0.03	b : 0.01	
^ : 0.90	y : 0.05	x : 0.01	c : 0.01	
^ : 0.90	y : 0.05	x : 0.01	c : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.90	y : 0.07	x : 0.01	
^ : 0.84	g : 0.07	b : 0.01	i : 0.01	= : 0.01	y : 0.01	
^ : 0.75	g : 0.07	f : 0.07	b : 0.01	i : 0.01	e : 0.01	= : 0.01	y : 0.01	
^ : 0.67	g : 0.11	f : 0.09	i : 0.03	] : 0.01	e : 0.01	= : 0.01	y : 0.01	
^ : 0.40	f : 0.17	g : 0.13	e : 0.07	= : 0.07	c : 0.05	i : 0.03	b : 0.01	h : 0.01	
^ : 0.26	f : 0.17	g : 0.15	e : 0.09	c : 0.09	= : 0.07	d : 0.05	i : 0.03	b : 0.01	h : 0.01	
^ : 0.19	g : 0.17	f : 0.17	e : 0.15	c : 0.09	= : 0.07	d : 0.05	i : 0.03	2 : 0.01	h : 0.01	
g : 0.17	f : 0.17	e : 0.15	^ : 0.13	= : 0.07	d : 0.07	h : 0.03	c : 0.03	i : 0.03	2 : 0.01	] : 0.01	9 : 0.01	b : 0.01	3 : 0.01	

#score	1742.0815622738514
#seq	52
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_UTR_m2_run1.txt

#BEAR
bb!!ccc[bboooooobb22ccc22	chr1:162496340-162496577(+)$1	237	136	161	11.8586
dd"""eeeeeooooooeeeeedddd	chr22:47082838-47083068(-)$1	230	160	185	12.3959
cccgggggggooooooggggggg]c	chr22:29190586-29190811(-)$1	225	89	114	14.2133
fffff!!cccoooooocccffffff	chr11:118397365-118397589(+)$1	224	169	194	13.5016
[bb[ccc[bboooooobb]ccc]bb	chr6:117881780-117882014(-)$1	234	153	178	11.8231
h####eeeeeooooooeeeee22hh	chr5:68473584-68473813(+)$1	229	104	129	12.3809
ggggggg[bboooooobb]gggggg	chr1:212537757-212538002(-)$1	245	66	91	13.8679
fffff[ddddoooooodddd333ff	chr18:32721458-32721700(+)$1	242	196	221	13.3654
ffff!!ddddoooooodddd22fff	chr7:140419204-140419444(-)$1	240	102	127	13.0039
fffff[ddddooooooddddfffff	chr12:27846193-27846429(+)$1	236	177	202	12.7445
iiiiiii[bboooooobb22iiiii	chr12:50231540-50231786(-)$1	246	197	222	13.6692
eeee"""cccooooooccc4444ee	chr12:56431729-56431964(+)$1	235	180	205	13.6943
cc####ddddoooooodddd4444c	chr18:73000618-73000848(+)$1	230	47	72	13.2549
==========oooooo=========	chr10:70652497-70652729(+)$1	232	10	35	15.3329
ffff!!ddddooooooddddfffff	chr20:49506759-49506983(-)$1	224	163	188	13.0058
#iiiiiiiiiooooooiiiiiiiii	chr11:19245991-19246230(-)$1	239	125	150	14.6797
gggggg[cccooooooccc]ggggg	chr3:3189866-3190094(+)$1	228	77	102	14.8084
eeeee!!cccooooooccc22eeee	chr2:175937689-175937922(-)$1	233	196	221	13.3445
ffff[eeeeeooooooeeeee22ff	chr5:123973026-123973252(-)$1	226	9	34	12.8631
eeeee[ddddoooooodddd22eee	chr8:25699636-25699860(-)$1	224	66	91	12.5995
[ccc[eeeeeooooooeeeee]ccc	chr2:190535421-190535642(+)$1	221	166	191	13.4713
ee####ddddoooooodddd4444e	chr17:2287390-2287646(-)$1	256	64	89	13.0358
ggggggg[bboooooobbggggggg	chr12:117582991-117583224(-)$1	233	165	190	13.8970
cc[eeeee[aooooooa]eeeee22	chrX:118378153-118378381(+)$1	228	101	126	12.6773
d!!gggggggooooooggggggg]d	chr10:89513411-89513656(-)$1	245	114	139	14.1619
fffff[ddddoooooodddd]ffff	chr21:34106806-34107075(-)$1	269	119	144	12.8900
gggggg[cccoooooocccgggggg	chr9:34086413-34086666(-)$1	253	165	190	14.7652
c!!gggggggooooooggggggg]c	chr17:4175367-4175600(-)$1	233	85	110	14.4295
fccc[eeeeeooooooeeeeeccc:	chr13:95226363-95226586(-)$1	223	91	116	12.2036
dd[ccc!!bboooooobb]ccc22d	chrX:8496981-8497214(-)$1	233	41	66	12.4522
biiiiiiiiiooooooiiiiiiiii	chr15:29992671-29992919(-)$1	248	98	123	14.5143
eeeee!!cccooooooccc22eeee	chr2:10141413-10141667(+)$1	254	199	224	13.3445
ffffff[cccooooooccc]fffff	chr9:139334875-139335098(-)$1	223	129	154	13.3503
===========nnnnn=========	chr4:26433533-26433779(+)$1	246	190	215	10.5579
:iiiiiiiiiooooooiiiiiiiii	chr5:153433891-153434114(+)$1	223	17	42	13.7214
==========oooooo=========	chr12:123641033-123641263(-)$1	230	119	144	15.3329
==========oooooo=========	chr13:108882959-108883237(+)$1	278	57	82	15.3329
ggggg[a[bboooooobbagggggg	chr20:25428680-25428912(+)$1	232	26	51	13.8155
c[eeeee[bboooooobb]eeeee]	chr14:55833518-55833742(-)$1	224	18	43	12.6580
hhhh[eeeeeooooooeeeee]hhh	chr20:61827754-61828008(-)$1	254	20	45	12.3530
!!hhhhhhhhoooooohhhhhhhh2	chr17:56082278-56082513(-)$1	235	93	118	11.2767
eeee[eeeeeooooooeeeee]eee	chr7:130060684-130060908(-)$1	224	113	138	13.0016
gggggg[cccoooooocccgggggg	chr1:63906460-63906695(-)$1	235	138	163	14.7652
=====!!cccooooooccc4444==	chr11:19245630-19245864(-)$1	234	139	164	14.9642
!!dddd"""aooooooa333dddd2	chrX:148563514-148563741(-)$1	227	155	180	11.9378
##ddddddddoooooodddd4444d	chr12:26225550-26225825(+)$1	275	89	114	12.1860
d!!ccc[cccooooooccc]ccc22	chr4:177249986-177250241(+)$1	255	126	151	13.6873
edddd!!cccoooooocccdddd44	chr12:132284087-132284348(+)$1	261	20	45	12.9219
cc:gggggggoooooogggggggdd	chr12:110784444-110784681(+)$1	237	194	219	12.7732
ccc"""ddddoooooodddd333cc	chr6:136578412-136578636(-)$1	224	84	109	13.7085
==========oooooo=========	chr15:58007023-58007265(+)$1	242	43	68	15.3329
dd[a[eeeeeooooooeeeeeaddd	chr10:63952898-63953120(-)$1	222	102	127	12.6431
===gggggggooooooggggggg77	chr14:50575801-50576070(-)$1	269	56	81	13.1786
c[==========lll==========	chrX:24004543-24004764(-)$1	221	64	89	10.7545
:ccc[eeeeeooooooeeeee]ccc	chr1:113454881-113455107(-)$1	226	198	223	12.3761
ggggg!!cccoooooocccgggggg	chr2:203739844-203740068(-)$1	224	91	116	14.9357
dddgggggggooooooggggggg::	chr10:119042403-119042671(-)$1	268	237	262	11.6399
ffffff[cccooooooccc]fffff	chr7:44618454-44618691(-)$1	237	72	97	13.3503
$dddd!!cccooooooccc]ddddg	chr2:206861215-206861443(-)$1	228	194	219	12.8282

#otherMatches

#Seq PSSM
GUCUGCCUGGAAAUAGCCUUGGUUU	chr1:162496340-162496577(+)$1	237	136	161	11.8586
AUUUUAGAAGAAAACCCUUUUGUCA	chr22:47082838-47083068(-)$1	230	160	185	12.3959
UGCUGAGGGGGCUCUUUCCCUCAUG	chr22:29190586-29190811(-)$1	225	89	114	14.2133
GUUUAUUGCUGCACAUGGUUAAGCU	chr11:118397365-118397589(+)$1	224	169	194	13.5016
GAAUAUGAUGGAAAAGCAACAUUUU	chr6:117881780-117882014(-)$1	234	153	178	11.8231
AAUUGAUGUAUAUGUUUAUAUACUG	chr5:68473584-68473813(+)$1	229	104	129	12.3809
UGUUGAUGUAUGAGUUUAGAUUAAC	chr1:212537757-212538002(-)$1	245	66	91	13.8679
GAUGGUAUCCCUUCCUGGAUCAUUC	chr18:32721458-32721700(+)$1	242	196	221	13.3654
UUCUCAUGUAAAUUUGUAUAACAGA	chr7:140419204-140419444(-)$1	240	102	127	13.0039
GGACGAUGGUGAAAAGAUCACGUUU	chr12:27846193-27846429(+)$1	236	177	202	12.7445
aaaauuaaaagauaaauugauaauu	chr12:50231540-50231786(-)$1	246	197	222	13.6692
GAAGCAAGUGCAAUACCACCUCUCU	chr12:56431729-56431964(+)$1	235	180	205	13.6943
GCCUCUGAAAUCAGUCUUUCCUUUG	chr18:73000618-73000848(+)$1	230	47	72	13.2549
CUACUUUUUUCUUUAUAAAAAGGUA	chr10:70652497-70652729(+)$1	232	10	35	15.3329
CCAUAACUCUUUCAUCAGAGAUGGC	chr20:49506759-49506983(-)$1	224	163	188	13.0058
AUACGUUGGGGAUUUGUUCAAUGUG	chr11:19245991-19246230(-)$1	239	125	150	14.6797
GGACCUCUGUAGAACAACAAGGGUC	chr3:3189866-3190094(+)$1	228	77	102	14.8084
UCAGUGCCAUCUCCUAAUGAGACUG	chr2:175937689-175937922(-)$1	233	196	221	13.3445
AGUGUUAGCCACAAAAGGCUACUUA	chr5:123973026-123973252(-)$1	226	9	34	12.8631
UAAUUGUACAAAUGUGUGUAAGGAU	chr8:25699636-25699860(-)$1	224	66	91	12.5995
agagcuucuaaaaccauggaauuuc	chr2:190535421-190535642(+)$1	221	166	191	13.4713
GAGAUUUUUAUGUGUUUGGAUACAU	chr17:2287390-2287646(-)$1	256	64	89	13.0358
auCUACUUCAGUAUCAUGAGUAGGU	chr12:117582991-117583224(-)$1	233	165	190	13.8970
CUAUACAGUUGUAUGAAUUUGUAAA	chrX:118378153-118378381(+)$1	228	101	126	12.6773
GUUUCUUAAAUAUUAUUUUAAGGUU	chr10:89513411-89513656(-)$1	245	114	139	14.1619
UGUAAUUAUGCAUAUAUAUAUUUAU	chr21:34106806-34107075(-)$1	269	119	144	12.8900
UAUUGCUAGACCCUCUUCUGUAAUG	chr9:34086413-34086666(-)$1	253	165	190	14.7652
GCUUUCUUGUAGUAGAAUAAGAAUC	chr17:4175367-4175600(-)$1	233	85	110	14.4295
UGUGUAAAGUUUUUAUAUUUUCACA	chr13:95226363-95226586(-)$1	223	91	116	12.2036
GCUACCUUCUCAUCCAAGUGGUCUG	chrX:8496981-8497214(-)$1	233	41	66	12.4522
GGUUUGUAAAUUAACUUUUAUAAAC	chr15:29992671-29992919(-)$1	248	98	123	14.5143
GACUUUCCCUAGACAAAGGUUAAGU	chr2:10141413-10141667(+)$1	254	199	224	13.3445
AUUUCUGUAGGUUCUGCUGGAGGAA	chr9:139334875-139335098(-)$1	223	129	154	13.3503
UCAGCAGGGUAUUUUCUGCCUUGUU	chr4:26433533-26433779(+)$1	246	190	215	10.5579
CAUGUCUGUAGGGUUAUACAGAUGU	chr5:153433891-153434114(+)$1	223	17	42	13.7214
UAUUUAAAAAGCAUUAUUUUUAAAU	chr12:123641033-123641263(-)$1	230	119	144	15.3329
AAUGAAAUGCAUGAUGGUAUUUUAU	chr13:108882959-108883237(+)$1	278	57	82	15.3329
cagugagcugagaucacaccacugu	chr20:25428680-25428912(+)$1	232	26	51	13.8155
GAUCGAACCCUUUUGUGGUUUUGAA	chr14:55833518-55833742(-)$1	224	18	43	12.6580
CUCCAGUGUGUCGUCCCGUGCGGGG	chr20:61827754-61828008(-)$1	254	20	45	12.3530
UCAUGUGUCUUUCUGUAGACAUAUC	chr17:56082278-56082513(-)$1	235	93	118	11.2767
CUGUAUAUAAGUCAAGUUGUACAUA	chr7:130060684-130060908(-)$1	224	113	138	13.0016
UCUUUAAUGUAAGCCAACAUGGAGA	chr1:63906460-63906695(-)$1	235	138	163	14.7652
UGCAGUGUAUCUUUUUGUAAAGUUU	chr11:19245630-19245864(-)$1	234	139	164	14.9642
AGGAAAUUUGGUUAAACUUUUUUCA	chrX:148563514-148563741(-)$1	227	155	180	11.9378
CUUUGCUUAUGUACAAAUAAAUCUG	chr12:26225550-26225825(+)$1	275	89	114	12.1860
AUUAUUCUAAUUCAUUUUAAAAUCU	chr4:177249986-177250241(+)$1	255	126	151	13.6873
AUCCACCUGGCCGCCUCCAUGGACC	chr12:132284087-132284348(+)$1	261	20	45	12.9219
GUGUGGUUUUUUUUCUAAAACUAAA	chr12:110784444-110784681(+)$1	237	194	219	12.7732
CAAUGAUGGUAAUGAGACCAAACUU	chr6:136578412-136578636(-)$1	224	84	109	13.7085
AAUAUUGUGUUUAACCACAUGGUAU	chr15:58007023-58007265(+)$1	242	43	68	15.3329
CUUGUAUAUACAUAAUUAUGUCAGA	chr10:63952898-63953120(-)$1	222	102	127	12.6431
UUCAAACUAGUAAAUUUUAGUUUGU	chr14:50575801-50576070(-)$1	269	56	81	13.1786
UAAAAGCAUUUAUAAUAAGUGUUUU	chrX:24004543-24004764(-)$1	221	64	89	10.7545
UUCAUUUUGGGCCUUGCUAAAUUGA	chr1:113454881-113455107(-)$1	226	198	223	12.3761
UGUAUAAAGAUCAAUUUCUGUAUAU	chr2:203739844-203740068(-)$1	224	91	116	14.9357
AAUUAGUGUUAAAUAGAAUACUGUC	chr10:119042403-119042671(-)$1	268	237	262	11.6399
AGGAUUGAGAUGUUUUUCUAAAUCU	chr7:44618454-44618691(-)$1	237	72	97	13.3503
UCUGUAAGCCAGAGGAGGUGACAGU	chr2:206861215-206861443(-)$1	228	194	219	12.8282

#DB
((..(((.((......))..)))..	chr1:162496340-162496577(+)$1	1	136	161	11.8586
((...(((((......)))))))))	chr22:47082838-47083068(-)$1	1	160	185	12.3959
((((((((((......))))))).)	chr22:29190586-29190811(-)$1	1	89	114	14.2133
(((((..(((......)))))))))	chr11:118397365-118397589(+)$1	1	169	194	13.5016
.((.(((.((......)).))).))	chr6:117881780-117882014(-)$1	1	153	178	11.8231
(....(((((......)))))..))	chr5:68473584-68473813(+)$1	1	104	129	12.3809
(((((((.((......)).))))))	chr1:212537757-212538002(-)$1	1	66	91	13.8679
(((((.((((......))))...))	chr18:32721458-32721700(+)$1	1	196	221	13.3654
((((..((((......))))..)))	chr7:140419204-140419444(-)$1	1	102	127	13.0039
(((((.((((......)))))))))	chr12:27846193-27846429(+)$1	1	177	202	12.7445
(((((((.((......))..)))))	chr12:50231540-50231786(-)$1	1	197	222	13.6692
((((...(((......)))....))	chr12:56431729-56431964(+)$1	1	180	205	13.6943
((....((((......))))....)	chr18:73000618-73000848(+)$1	1	47	72	13.2549
((((((((((......)))))))))	chr10:70652497-70652729(+)$1	1	10	35	15.3329
((((..((((......)))))))))	chr20:49506759-49506983(-)$1	1	163	188	13.0058
.(((((((((......)))))))))	chr11:19245991-19246230(-)$1	1	125	150	14.6797
((((((.(((......))).)))))	chr3:3189866-3190094(+)$1	1	77	102	14.8084
(((((..(((......)))..))))	chr2:175937689-175937922(-)$1	1	196	221	13.3445
((((.(((((......)))))..))	chr5:123973026-123973252(-)$1	1	9	34	12.8631
(((((.((((......))))..)))	chr8:25699636-25699860(-)$1	1	66	91	12.5995
.(((.(((((......))))).)))	chr2:190535421-190535642(+)$1	1	166	191	13.4713
((....((((......))))....)	chr17:2287390-2287646(-)$1	1	64	89	13.0358
(((((((.((......)))))))))	chr12:117582991-117583224(-)$1	1	165	190	13.8970
((.(((((.(......).)))))..	chrX:118378153-118378381(+)$1	1	101	126	12.6773
(..(((((((......))))))).)	chr10:89513411-89513656(-)$1	1	114	139	14.1619
(((((.((((......)))).))))	chr21:34106806-34107075(-)$1	1	119	144	12.8900
((((((.(((......)))))))))	chr9:34086413-34086666(-)$1	1	165	190	14.7652
(..(((((((......))))))).)	chr17:4175367-4175600(-)$1	1	85	110	14.4295
)(((.(((((......)))))))).	chr13:95226363-95226586(-)$1	1	91	116	12.2036
((.(((..((......)).)))..)	chrX:8496981-8497214(-)$1	1	41	66	12.4522
((((((((((......)))))))))	chr15:29992671-29992919(-)$1	1	98	123	14.5143
(((((..(((......)))..))))	chr2:10141413-10141667(+)$1	1	199	224	13.3445
((((((.(((......))).)))))	chr9:139334875-139335098(-)$1	1	129	154	13.3503
(((((((((((.....)))))))))	chr4:26433533-26433779(+)$1	1	190	215	10.5579
.(((((((((......)))))))))	chr5:153433891-153434114(+)$1	1	17	42	13.7214
((((((((((......)))))))))	chr12:123641033-123641263(-)$1	1	119	144	15.3329
((((((((((......)))))))))	chr13:108882959-108883237(+)$1	1	57	82	15.3329
(((((.(.((......)))))))))	chr20:25428680-25428912(+)$1	1	26	51	13.8155
(.(((((.((......)).))))).	chr14:55833518-55833742(-)$1	1	18	43	12.6580
((((.(((((......))))).)))	chr20:61827754-61828008(-)$1	1	20	45	12.3530
..((((((((......)))))))).	chr17:56082278-56082513(-)$1	1	93	118	11.2767
((((.(((((......))))).)))	chr7:130060684-130060908(-)$1	1	113	138	13.0016
((((((.(((......)))))))))	chr1:63906460-63906695(-)$1	1	138	163	14.7652
(((((..(((......)))....))	chr11:19245630-19245864(-)$1	1	139	164	14.9642
..((((...(......)...)))).	chrX:148563514-148563741(-)$1	1	155	180	11.9378
..((((((((......))))....)	chr12:26225550-26225825(+)$1	1	89	114	12.1860
(..(((.(((......))).)))..	chr4:177249986-177250241(+)$1	1	126	151	13.6873
(((((..(((......)))))))..	chr12:132284087-132284348(+)$1	1	20	45	12.9219
)).(((((((......)))))))((	chr12:110784444-110784681(+)$1	1	194	219	12.7732
(((...((((......))))...))	chr6:136578412-136578636(-)$1	1	84	109	13.7085
((((((((((......)))))))))	chr15:58007023-58007265(+)$1	1	43	68	15.3329
((.(.(((((......)))))))))	chr10:63952898-63953120(-)$1	1	102	127	12.6431
((((((((((......)))))))..	chr14:50575801-50576070(-)$1	1	56	81	13.1786
(.((((((((((...))))))))))	chrX:24004543-24004764(-)$1	1	64	89	10.7545
.(((.(((((......))))).)))	chr1:113454881-113455107(-)$1	1	198	223	12.3761
(((((..(((......)))))))))	chr2:203739844-203740068(-)$1	1	91	116	14.9357
)))(((((((......)))))))..	chr10:119042403-119042671(-)$1	1	237	262	11.6399
((((((.(((......))).)))))	chr7:44618454-44618691(-)$1	1	72	97	13.3503
.((((..(((......))).)))))	chr2:206861215-206861443(-)$1	1	194	219	12.8282

#PSSM
f : 0.16	c : 0.13	g : 0.11	e : 0.11	= : 0.11	d : 0.10	b : 0.03	[ : 0.03	h : 0.03	# : 0.03	: : 0.03	! : 0.03	i : 0.01	$ : 0.01	
f : 0.15	c : 0.13	g : 0.11	= : 0.11	d : 0.10	e : 0.10	! : 0.08	i : 0.06	b : 0.03	# : 0.03	[ : 0.03	h : 0.01	
f : 0.15	= : 0.13	g : 0.11	e : 0.10	c : 0.08	d : 0.08	! : 0.06	i : 0.06	# : 0.05	[ : 0.05	h : 0.03	" : 0.01	b : 0.01	: : 0.01	
g : 0.22	f : 0.15	e : 0.11	= : 0.11	c : 0.08	i : 0.06	d : 0.06	# : 0.05	" : 0.03	h : 0.03	! : 0.01	[ : 0.01	a : 0.01	
g : 0.22	= : 0.11	[ : 0.11	f : 0.10	e : 0.08	c : 0.06	i : 0.06	d : 0.06	" : 0.05	# : 0.05	! : 0.03	h : 0.01	
e : 0.18	g : 0.18	! : 0.15	= : 0.10	[ : 0.08	c : 0.06	i : 0.06	" : 0.03	# : 0.03	f : 0.03	d : 0.03	h : 0.01	
e : 0.18	d : 0.16	g : 0.13	! : 0.13	= : 0.10	[ : 0.10	i : 0.06	c : 0.03	" : 0.03	a : 0.01	h : 0.01	
c : 0.23	e : 0.16	d : 0.16	[ : 0.11	g : 0.10	= : 0.10	i : 0.05	! : 0.01	h : 0.01	" : 0.01	
c : 0.23	d : 0.16	e : 0.15	b : 0.13	g : 0.10	= : 0.10	i : 0.05	[ : 0.01	h : 0.01	" : 0.01	
c : 0.23	d : 0.16	e : 0.15	b : 0.13	g : 0.10	= : 0.10	i : 0.05	a : 0.03	h : 0.01	
o : 0.96	= : 0.03	
o : 0.96	n : 0.01	= : 0.01	
o : 0.96	n : 0.01	l : 0.01	
o : 0.96	n : 0.01	l : 0.01	
o : 0.96	n : 0.01	l : 0.01	
o : 0.96	n : 0.01	= : 0.01	
c : 0.23	d : 0.16	e : 0.15	b : 0.13	g : 0.10	= : 0.10	i : 0.05	a : 0.03	h : 0.01	
c : 0.23	d : 0.16	e : 0.15	b : 0.13	g : 0.10	= : 0.10	i : 0.05	] : 0.01	h : 0.01	3 : 0.01	
c : 0.23	e : 0.16	d : 0.16	g : 0.11	= : 0.10	] : 0.06	i : 0.05	2 : 0.03	a : 0.01	h : 0.01	3 : 0.01	
g : 0.20	e : 0.18	d : 0.18	= : 0.10	] : 0.08	2 : 0.06	i : 0.05	c : 0.03	4 : 0.03	f : 0.01	h : 0.01	3 : 0.01	
g : 0.22	e : 0.18	= : 0.10	f : 0.08	4 : 0.08	c : 0.06	2 : 0.06	i : 0.06	d : 0.05	3 : 0.03	] : 0.01	h : 0.01	
g : 0.22	f : 0.10	= : 0.10	c : 0.08	4 : 0.08	d : 0.06	2 : 0.06	i : 0.06	e : 0.06	] : 0.06	3 : 0.03	h : 0.01	a : 0.01	
g : 0.22	f : 0.11	= : 0.10	e : 0.10	c : 0.08	d : 0.08	4 : 0.08	i : 0.06	2 : 0.05	3 : 0.03	h : 0.03	] : 0.01	
f : 0.15	g : 0.11	= : 0.11	e : 0.10	d : 0.08	2 : 0.06	i : 0.06	4 : 0.06	c : 0.06	] : 0.05	h : 0.05	b : 0.01	7 : 0.01	: : 0.01	
f : 0.15	g : 0.13	= : 0.11	d : 0.10	c : 0.10	e : 0.10	2 : 0.08	i : 0.06	h : 0.03	: : 0.03	b : 0.01	] : 0.01	4 : 0.01	7 : 0.01	

#score	783.6369126771906
#seq	59
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_CDS_m2_run2.txt

#BEAR
a[eeeeettttttttttteeeee]	chr3:41267080-41267314(+)$1	234	86	110	22.6960
:ffffffvvvvvvvvvvvvvffff	chr22:36157148-36157374(-)$1	226	106	130	22.3273
iiiiiiivvvvvvvvvvvvviiii	chr1:113471828-113472047(-)$1	219	92	116	23.5590
:gggggggtttttttttttggggg	chr2:179407143-179407366(+)$1	223	173	197	21.4238
::eeeeeuuuuuuuuuuuueeeee	chr20:18511244-18511469(+)$1	225	69	93	22.1547
ggg[cccvvvvvvvvvvvvvccc]	chr17:34893559-34893780(+)$1	221	119	143	24.1347
e[ddddwwwwwwwwwwwwwwdddd	chr5:5441162-5441385(+)$1	223	91	115	21.8500
e"""bbvvvvvvvvvvvvvbb]ee	chrM:10105-10356(+)$1	251	72	96	23.0701
dfffffftttttttttttffffff	chr21:34926035-34926255(+)$1	220	178	202	21.2479
[dddd[bbtttttttttttbb]dd	chr17:21101789-21102011(-)$1	222	64	88	21.1734
eeeeewwwwwwwwwwwwwweeeee	chr1:154226278-154226506(+)$1	228	96	120	22.2155
ccc[cccuuuuuuuuuuuuccccc	chr10:92982560-92982781(+)$1	221	140	164	23.7980
""cccwwwwwwwwwwwwwwccc33	chr7:107198392-107198619(-)$1	227	96	120	22.6710
Deeeeevvvvvvvvvvvvveeeee	chr2:176981675-176981893(+)$1	218	188	212	22.8833
eee[cccvvvvvvvvvvvvvccc]	chr6:114267163-114267388(-)$1	225	192	216	23.9364
ddddcccwwwwwwwwwwwwwwccc	chr21:37443229-37443455(+)$1	226	103	127	21.5199
cceeeeeuuuuuuuuuuuueeeee	chrX:69368512-69368733(+)$1	221	134	158	23.7289
d[eeeeeuuuuuuuuuuuueeeee	chr17:62496655-62496886(-)$1	231	108	132	23.8963
gggggggwwwwwwwwwwwwwwggg	chr3:52723102-52723322(+)$1	220	99	123	21.9457
#ffffffuuuuuuuuuuuufffff	chr5:177020587-177020811(+)$1	224	104	128	22.9563
iii[cccuuuuuuuuuuuuccc]i	chr1:54509051-54509274(-)$1	223	43	67	24.0278
==:eeeeettttttttttteeeee	chr17:40997852-40998082(+)$1	230	91	115	21.7131
iiiiiiiitttttttttttiiiii	chr2:198257019-198257242(-)$1	223	28	52	21.9260
"""bbwwwwwwwwwwwwwwbb333	chr1:231696798-231697025(+)$1	227	119	143	21.6079
%dddd[bbtttttttttttbb]dd	chr3:167402017-167402247(-)$1	230	126	150	20.6698
e!!ddddtttttttttttdddd]e	chr10:119043756-119043979(-)$1	223	6	30	21.9317
f[cccwwwwwwwwwwwwwwcccff	chr11:111941104-111941331(+)$1	227	39	63	22.2379
#ffffffuuuuuuuuuuuufffff	chr5:177020617-177020849(+)$1	232	74	98	22.9563
====[bbuuuuuuuuuuuubb]==	chr10:27415543-27415769(-)$1	226	25	49	23.0101
$$$ddddvvvvvvvvvvvvvdddd	chrX:24082236-24082456(+)$1	220	52	76	22.7527
!ffffffuuuuuuuuuuuufffff	chrM:8007-8242(+)$1	235	64	88	22.9954
h!!eeeeettttttttttteeeee	chr15:32929904-32930127(+)$1	223	158	182	22.6352
:::eeeeettttttttttteeeee	chr2:85769943-85770178(+)$1	235	49	73	20.0124
:::ddddvvvvvvvvvvvvvdddd	chr13:45841358-45841581(+)$1	223	197	221	20.4769
f!!cccvvvvvvvvvvvvvccc33	chr2:228401565-228401787(+)$1	222	101	125	24.2429
e"""cccuuuuuuuuuuuuccc33	chr18:77890913-77891135(+)$1	222	5	29	24.1259
f!!ddddtttttttttttdddd33	chr19:39878918-39879139(-)$1	221	162	186	21.9081
e!!bbwwwwwwwwwwwwwwbbeee	chr13:30109856-30110080(-)$1	224	105	129	21.6483
ffffddddtttttttttttdddd2	chrX:24006430-24006654(-)$1	224	33	57	21.2709
&&&dddduuuuuuuuuuuudddd7	chr6:35841949-35842169(-)$1	220	21	45	20.8174
####ccctttttttttttccc333	chr1:197112528-197112753(-)$1	225	112	136	22.7983
eeeeewwwwwwwwwwwwwweeeee	chr9:123949130-123949351(-)$1	221	136	160	22.2155
hhhhhhhuuuuuuuuuuuuhhhhh	chr5:118454529-118454757(+)$1	228	170	194	21.2183
:eeeeevvvvvvvvvvvvveeeee	chr7:79841993-79842221(+)$1	228	86	110	23.1595
!!bb[bbwwwwwwwwwwwwwwbbb	chr20:43135457-43135681(-)$1	224	93	117	20.3080
gggggggvvvvvvvvvvvvvgggg	chr11:20529827-20530048(+)$1	221	116	140	23.6387
beeeeevvvvvvvvvvvvveeeee	chr12:6601356-6601579(-)$1	223	29	53	23.7129
eeeeewwwwwwwwwwwwwweeeee	chr10:88939826-88940051(+)$1	225	12	36	22.2155
ccc[cccuuuuuuuuuuuuccccc	chr6:116973090-116973312(-)$1	222	71	95	23.7980
ggg[cccvvvvvvvvvvvvvccc]	chr19:38126223-38126444(-)$1	221	67	91	24.1347
ggggggguuuuuuuuuuuuggggg	chr5:40777446-40777666(-)$1	220	167	191	23.4794
e[cccwwwwwwwwwwwwwwccc]e	chr14:104026927-104027154(-)$1	227	103	127	22.5032
####cccuuuuuuuuuuuuccc44	chr17:16068277-16068499(-)$1	222	187	211	24.0486
b[ddddvvvvvvvvvvvvvdddd]	chr11:35006109-35006331(+)$1	222	11	35	23.2890
e[eeeeeuuuuuuuuuuuueeeee	chr12:27077191-27077418(-)$1	227	139	163	23.9772
gbb[cccvvvvvvvvvvvvvccc]	chr8:28385188-28385419(+)$1	231	159	183	23.5742
BB:eeeeettttttttttteeeee	chr1:220197639-220197858(-)$1	219	190	214	20.0238
fccc[ccctttttttttttccc]c	chr6:17602775-17603001(+)$1	226	66	90	22.4640
c[cccccctttttttttttccc22	chr1:156281794-156282010(-)$1	216	2	26	22.6863
ffff!!bbtttttttttttbb]ff	chr6:13617939-13618166(+)$1	227	55	79	21.2610
:ffffffvvvvvvvvvvvvvffff	chr1:23645046-23645263(-)$1	217	113	137	22.3273
a[eeeeettttttttttteeeee]	chr15:34519865-34520092(+)$1	227	108	132	22.6960
:fffffftttttttttttffffff	chr5:141364350-141364573(+)$1	223	125	149	20.6934
$$eeeeeuuuuuuuuuuuueeeee	chr7:26224373-26224596(-)$1	223	187	211	23.6897
eeee[bbuuuuuuuuuuuubb]ee	chr7:40172584-40172803(-)$1	219	73	97	22.8697
hhhhhhhuuuuuuuuuuuuhhhhh	chr11:10821626-10821852(-)$1	226	57	81	21.2183

#otherMatches

#Seq PSSM
GUGUUGUUUUAUGCCAUUACAACU	chr3:41267080-41267314(+)$1	234	86	110	22.6960
CACUUACAUUCCUUUAAUCAGUAA	chr22:36157148-36157374(-)$1	226	106	130	22.3273
AUUUUGGAAUUUAUCUACACUUAA	chr1:113471828-113472047(-)$1	219	92	116	23.5590
UUAAUUUUUACUUCAAAUCAAAAU	chr2:179407143-179407366(+)$1	223	173	197	21.4238
UCUUACCUAGAGGCUACAUGGUAA	chr20:18511244-18511469(+)$1	225	69	93	22.1547
AGUUGUGAAAUUGAUAACACCACU	chr17:34893559-34893780(+)$1	221	119	143	24.1347
AAGAGAUGCUUCAAAAAAUUUCUC	chr5:5441162-5441385(+)$1	223	91	115	21.8500
GCUUCGACCCUAUAUCCCCCGCCC	chrM:10105-10356(+)$1	251	72	96	23.0701
GGAAAUUGGUGAAGAGAAAAUUUU	chr21:34926035-34926255(+)$1	220	178	202	21.2479
CCGCCUGCCUCUUCACCCCGUUGG	chr17:21101789-21102011(-)$1	222	64	88	21.1734
GUGAAUCAUCCUCUACAAUUUCAU	chr1:154226278-154226506(+)$1	228	96	120	22.2155
CUGAUCAAGCCAACAACAGUGACG	chr10:92982560-92982781(+)$1	221	140	164	23.7980
AAAGACUUAUACUUCUCAAUCUAU	chr7:107198392-107198619(-)$1	227	96	120	22.6710
CUCCUUCACCACCAACAUUAAGGA	chr2:176981675-176981893(+)$1	218	188	212	22.8833
GCCCUUGAUUGUGAGAUUCCCAAU	chr6:114267163-114267388(-)$1	225	192	216	23.9364
ACUCCCUCUAAUAAAACCCCAAGG	chr21:37443229-37443455(+)$1	226	103	127	21.5199
CCAGUGAAACCCUUCAUUCUCACU	chrX:69368512-69368733(+)$1	221	134	158	23.7289
UUCUUUACACCUAAUAACAUAAAG	chr17:62496655-62496886(-)$1	231	108	132	23.8963
UACUUAUAUUAAAUAAAUCAGGUG	chr3:52723102-52723322(+)$1	220	99	123	21.9457
UUUCACUUCCCAUACCCCUGGUGA	chr5:177020587-177020811(+)$1	224	104	128	22.9563
uaauauauuucucauuauuuauuu	chr1:54509051-54509274(-)$1	223	43	67	24.0278
UUCGAAGGCACCACAAUUACCUUC	chr17:40997852-40998082(+)$1	230	91	115	21.7131
GAAAUAAUGUAACCGUUCAAUUAU	chr2:198257019-198257242(-)$1	223	28	52	21.9260
AAAACACGAUCAUUAAUUAGUAUG	chr1:231696798-231697025(+)$1	227	119	143	21.6079
UUCAGACCUUCAAAACUGUGGCCU	chr3:167402017-167402247(-)$1	230	126	150	20.6698
GGAAGCCCCCUCACCUAAGGCUAU	chr10:119043756-119043979(-)$1	223	6	30	21.9317
UAUCUAUUCAACUUACCUCAGAAA	chr11:111941104-111941331(+)$1	227	39	63	22.2379
UUUCACUUCCCAUACCCCUGGUGA	chr5:177020617-177020849(+)$1	232	74	98	22.9563
AAGUUAUUUGGAAAAUUGUGUCAC	chr10:27415543-27415769(-)$1	226	25	49	23.0101
UUUUGAUCUUUCUAAAUUUUGUCA	chrX:24082236-24082456(+)$1	220	52	76	22.7527
AUGAGCUGUCCCCACAUUAGGCUU	chrM:8007-8242(+)$1	235	64	88	22.9954
UUGUCAUUAAUGUAAAUAAAGUGA	chr15:32929904-32930127(+)$1	223	158	182	22.6352
ACUGAUUCUUACGACAUUUGAAUC	chr2:85769943-85770178(+)$1	235	49	73	20.0124
UUAACACGACAUUACUGAAAGUGU	chr13:45841358-45841581(+)$1	223	197	221	20.4769
UCUUCUACAAACCCAUUUCAGACC	chr2:228401565-228401787(+)$1	222	101	125	24.2429
GUUCUAAUUAAAUAUUUCUUUAUC	chr18:77890913-77891135(+)$1	222	5	29	24.1259
UACUCAGCACACUCCUAUCUGAUU	chr19:39878918-39879139(-)$1	221	162	186	21.9081
AAUCCUCUCCUACAUCAUCGGUAG	chr13:30109856-30110080(-)$1	224	105	129	21.6483
CUUAUCCAGUUAACAAAUAUGGAC	chrX:24006430-24006654(-)$1	224	33	57	21.2709
UGCCGUUUUUUCCCUCCUUAAUGA	chr6:35841949-35842169(-)$1	220	21	45	20.8174
CUCAUCUCUUCAUGCAUCAGAAAA	chr1:197112528-197112753(-)$1	225	112	136	22.7983
UCUUAUUACACAGAAAAUUUAAGA	chr9:123949130-123949351(-)$1	221	136	160	22.2155
GUGAGUGUUUUUGUUACAUUACUU	chr5:118454529-118454757(+)$1	228	170	194	21.2183
AAGUGGUUUACAGAUACAUCCAUU	chr7:79841993-79842221(+)$1	228	86	110	23.1595
CGGGCUGCUCUAUACAUAUUACAC	chr20:43135457-43135681(-)$1	224	93	117	20.3080
UUAUGGUCUCCAGUGAAACAGCCA	chr11:20529827-20530048(+)$1	221	116	140	23.6387
AUCCGAAAGAGGAAAAUGGUUGGA	chr12:6601356-6601579(-)$1	223	29	53	23.7129
UCUGAUUAAAGCCCAGAUUUCAGA	chr10:88939826-88940051(+)$1	225	12	36	22.2155
GUUGUGGUUACAGAAAUUUCCAAA	chr6:116973090-116973312(-)$1	222	71	95	23.7980
UUGUAAGGAAUGUGGGAAGACUUU	chr19:38126223-38126444(-)$1	221	67	91	24.1347
UUUGUUAACCUACUUAAUGUGACA	chr5:40777446-40777666(-)$1	220	167	191	23.4794
CACACUUUAACCAAAAUCUGUGCG	chr14:104026927-104027154(-)$1	227	103	127	22.5032
UUAAACUGAAAAAGAAACAAGUAA	chr17:16068277-16068499(-)$1	222	187	211	24.0486
UGCCAGAUGUUAAUGUAAGCUGGG	chr11:35006109-35006331(+)$1	222	11	35	23.2890
UUCUUUUUCCUGCUAUUUUGAAAG	chr12:27077191-27077418(-)$1	227	139	163	23.9772
UAGUGGCGUGUGUUUUGUUGGCCU	chr8:28385188-28385419(+)$1	231	159	183	23.5742
CUCCUGCUGAACAGAUGAAAGCAG	chr1:220197639-220197858(-)$1	219	190	214	20.0238
CCUUGGCCCACAGAUUUAUGGCAG	chr6:17602775-17603001(+)$1	226	66	90	22.4640
UGUGGGGCCCGGAUAGUCAGCCGA	chr1:156281794-156282010(-)$1	216	2	26	22.6863
UCCUUAGCAUCAAGAAAUCGCCAG	chr6:13617939-13618166(+)$1	227	55	79	21.2610
ACCCGAUGACAAAAAGAAGAAUCG	chr1:23645046-23645263(-)$1	217	113	137	22.3273
CUCCAUCUUCCCUACUAUGAUGGU	chr15:34519865-34520092(+)$1	227	108	132	22.6960
CCUGGUUCACCAUGUUUUAACCGG	chr5:141364350-141364573(+)$1	223	125	149	20.6934
AAUCCUGUCAAAUUAGUUCCAGGA	chr7:26224373-26224596(-)$1	223	187	211	23.6897
UGUAGUGGAUAUAAGCCAACAAUA	chr7:40172584-40172803(-)$1	219	73	97	22.8697
AGCUGGUGAGCAUUUCAGAACUAG	chr11:10821626-10821852(-)$1	226	57	81	21.2183

#DB
(.(((((...........))))).	chr3:41267080-41267314(+)$1	1	86	110	22.6960
.((((((.............))))	chr22:36157148-36157374(-)$1	1	106	130	22.3273
(((((((.............))))	chr1:113471828-113472047(-)$1	1	92	116	23.5590
.(((((((...........)))))	chr2:179407143-179407366(+)$1	1	173	197	21.4238
..(((((............)))))	chr20:18511244-18511469(+)$1	1	69	93	22.1547
(((.(((.............))).	chr17:34893559-34893780(+)$1	1	119	143	24.1347
(.((((..............))))	chr5:5441162-5441385(+)$1	1	91	115	21.8500
(...((.............)).))	chrM:10105-10356(+)$1	1	72	96	23.0701
(((((((...........))))))	chr21:34926035-34926255(+)$1	1	178	202	21.2479
.((((.((...........)).))	chr17:21101789-21102011(-)$1	1	64	88	21.1734
(((((..............)))))	chr1:154226278-154226506(+)$1	1	96	120	22.2155
(((.(((............)))))	chr10:92982560-92982781(+)$1	1	140	164	23.7980
..(((..............)))..	chr7:107198392-107198619(-)$1	1	96	120	22.6710
)(((((.............)))))	chr2:176981675-176981893(+)$1	1	188	212	22.8833
(((.(((.............))).	chr6:114267163-114267388(-)$1	1	192	216	23.9364
(((((((..............)))	chr21:37443229-37443455(+)$1	1	103	127	21.5199
(((((((............)))))	chrX:69368512-69368733(+)$1	1	134	158	23.7289
(.(((((............)))))	chr17:62496655-62496886(-)$1	1	108	132	23.8963
(((((((..............)))	chr3:52723102-52723322(+)$1	1	99	123	21.9457
.((((((............)))))	chr5:177020587-177020811(+)$1	1	104	128	22.9563
(((.(((............))).)	chr1:54509051-54509274(-)$1	1	43	67	24.0278
)).(((((...........)))))	chr17:40997852-40998082(+)$1	1	91	115	21.7131
((((((((...........)))))	chr2:198257019-198257242(-)$1	1	28	52	21.9260
...((..............))...	chr1:231696798-231697025(+)$1	1	119	143	21.6079
.((((.((...........)).))	chr3:167402017-167402247(-)$1	1	126	150	20.6698
(..((((...........)))).)	chr10:119043756-119043979(-)$1	1	6	30	21.9317
(.(((..............)))))	chr11:111941104-111941331(+)$1	1	39	63	22.2379
.((((((............)))))	chr5:177020617-177020849(+)$1	1	74	98	22.9563
((((.((............)).))	chr10:27415543-27415769(-)$1	1	25	49	23.0101
...((((.............))))	chrX:24082236-24082456(+)$1	1	52	76	22.7527
.((((((............)))))	chrM:8007-8242(+)$1	1	64	88	22.9954
(..(((((...........)))))	chr15:32929904-32930127(+)$1	1	158	182	22.6352
...(((((...........)))))	chr2:85769943-85770178(+)$1	1	49	73	20.0124
...((((.............))))	chr13:45841358-45841581(+)$1	1	197	221	20.4769
(..(((.............)))..	chr2:228401565-228401787(+)$1	1	101	125	24.2429
(...(((............)))..	chr18:77890913-77891135(+)$1	1	5	29	24.1259
(..((((...........))))..	chr19:39878918-39879139(-)$1	1	162	186	21.9081
(..((..............)))))	chr13:30109856-30110080(-)$1	1	105	129	21.6483
((((((((...........)))).	chrX:24006430-24006654(-)$1	1	33	57	21.2709
...((((............)))).	chr6:35841949-35842169(-)$1	1	21	45	20.8174
....(((...........)))...	chr1:197112528-197112753(-)$1	1	112	136	22.7983
(((((..............)))))	chr9:123949130-123949351(-)$1	1	136	160	22.2155
(((((((............)))))	chr5:118454529-118454757(+)$1	1	170	194	21.2183
.(((((.............)))))	chr7:79841993-79842221(+)$1	1	86	110	23.1595
..((.((..............)))	chr20:43135457-43135681(-)$1	1	93	117	20.3080
(((((((.............))))	chr11:20529827-20530048(+)$1	1	116	140	23.6387
((((((.............)))))	chr12:6601356-6601579(-)$1	1	29	53	23.7129
(((((..............)))))	chr10:88939826-88940051(+)$1	1	12	36	22.2155
(((.(((............)))))	chr6:116973090-116973312(-)$1	1	71	95	23.7980
(((.(((.............))).	chr19:38126223-38126444(-)$1	1	67	91	24.1347
(((((((............)))))	chr5:40777446-40777666(-)$1	1	167	191	23.4794
(.(((..............))).)	chr14:104026927-104027154(-)$1	1	103	127	22.5032
....(((............)))..	chr17:16068277-16068499(-)$1	1	187	211	24.0486
(.((((.............)))).	chr11:35006109-35006331(+)$1	1	11	35	23.2890
(.(((((............)))))	chr12:27077191-27077418(-)$1	1	139	163	23.9772
(((.(((.............))).	chr8:28385188-28385419(+)$1	1	159	183	23.5742
)).(((((...........)))))	chr1:220197639-220197858(-)$1	1	190	214	20.0238
((((.(((...........))).)	chr6:17602775-17603001(+)$1	1	66	90	22.4640
(.((((((...........)))..	chr1:156281794-156282010(-)$1	1	2	26	22.6863
((((..((...........)).))	chr6:13617939-13618166(+)$1	1	55	79	21.2610
.((((((.............))))	chr1:23645046-23645263(-)$1	1	113	137	22.3273
(.(((((...........))))).	chr15:34519865-34520092(+)$1	1	108	132	22.6960
.((((((...........))))))	chr5:141364350-141364573(+)$1	1	125	149	20.6934
..(((((............)))))	chr7:26224373-26224596(-)$1	1	187	211	23.6897
((((.((............)).))	chr7:40172584-40172803(-)$1	1	73	97	22.8697
(((((((............)))))	chr11:10821626-10821852(-)$1	1	57	81	21.2183

#PSSM
e : 0.18	: : 0.12	g : 0.09	f : 0.09	c : 0.06	# : 0.06	i : 0.04	d : 0.04	h : 0.04	a : 0.03	" : 0.03	= : 0.03	$ : 0.03	! : 0.03	b : 0.03	[ : 0.01	D : 0.01	% : 0.01	& : 0.01	B : 0.01	
[ : 0.13	f : 0.13	e : 0.12	g : 0.09	! : 0.09	" : 0.06	c : 0.06	i : 0.04	: : 0.04	d : 0.04	= : 0.03	$ : 0.03	# : 0.03	h : 0.03	& : 0.01	b : 0.01	B : 0.01	
e : 0.22	f : 0.13	c : 0.10	g : 0.09	d : 0.07	! : 0.07	: : 0.06	i : 0.04	" : 0.04	# : 0.03	h : 0.03	b : 0.03	= : 0.01	$ : 0.01	& : 0.01	
e : 0.27	d : 0.15	f : 0.13	[ : 0.10	c : 0.09	g : 0.06	b : 0.04	i : 0.03	" : 0.03	# : 0.03	h : 0.03	= : 0.01	
e : 0.25	c : 0.24	d : 0.15	f : 0.10	g : 0.06	[ : 0.06	b : 0.04	i : 0.03	h : 0.03	! : 0.01	
e : 0.21	c : 0.21	d : 0.12	w : 0.12	f : 0.10	g : 0.06	b : 0.06	i : 0.03	[ : 0.03	h : 0.03	! : 0.01	
c : 0.19	e : 0.16	w : 0.13	f : 0.10	v : 0.09	b : 0.09	d : 0.09	g : 0.06	i : 0.03	h : 0.03	
u : 0.28	v : 0.24	w : 0.18	t : 0.10	e : 0.06	b : 0.04	c : 0.03	g : 0.01	i : 0.01	d : 0.01	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
t : 0.28	u : 0.28	v : 0.24	w : 0.18	
u : 0.28	v : 0.24	t : 0.18	w : 0.18	e : 0.03	f : 0.03	d : 0.03	c : 0.01	
e : 0.25	c : 0.18	v : 0.15	b : 0.12	f : 0.07	d : 0.07	w : 0.06	g : 0.03	h : 0.03	i : 0.01	
e : 0.25	c : 0.24	d : 0.12	b : 0.12	f : 0.10	g : 0.04	w : 0.04	i : 0.03	h : 0.03	
e : 0.27	c : 0.24	d : 0.12	f : 0.10	] : 0.09	g : 0.06	i : 0.03	3 : 0.03	h : 0.03	b : 0.01	
e : 0.30	f : 0.13	d : 0.12	c : 0.10	3 : 0.09	g : 0.06	] : 0.06	i : 0.03	h : 0.03	= : 0.01	b : 0.01	4 : 0.01	2 : 0.01	
e : 0.30	f : 0.13	] : 0.10	3 : 0.09	d : 0.07	g : 0.06	c : 0.06	i : 0.04	2 : 0.03	h : 0.03	= : 0.01	7 : 0.01	b : 0.01	4 : 0.01	

#score	1484.1582669156985
#seq	66
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_UTR_m1_run1.txt

#BEAR
[ccc[bbuuuuuuuuuuuubb]cccbb	chr17:17158109-17158310(-)$1	201	66	93	22.9744
!!ddddwwwwwwwwwwwwwwdddd22e	chr9:95055645-95055846(-)$1	201	77	104	22.6422
ffffffvvvvvvvvvvvvvffffff22	chr16:67604955-67605156(+)$1	201	89	116	22.7226
:eeeeevvvvvvvvvvvvveeeee:::	chr7:24732323-24732524(+)$1	201	119	146	20.9539
:ccc[bbuuuuuuuuuuuubb]cccAK	chr9:95063930-95064131(-)$1	201	48	75	20.4734
&eeeeevvvvvvvvvvvvveeeee333	chr9:95076986-95077187(-)$1	201	23	50	23.8622
ggggggvvvvvvvvvvvvvggggggg:	chr6:42906463-42906664(+)$1	201	173	200	24.2699
cccdddduuuuuuuuuuuudddd]ccc	chr2:220011339-220011540(-)$1	201	17	44	23.0623
!!cccwwwwwwwwwwwwwwccc]gggg	chr7:44613863-44614064(-)$1	201	85	112	23.6096
ffffffvvvvvvvvvvvvvffffffcc	chr17:38320211-38320412(+)$1	201	24	51	22.9552
gggggggtttttttttttggggggg::	chr14:80971206-80971407(-)$1	201	102	129	20.6577
eeeeeeuuuuuuuuuuuueeeee]eee	chrX:107965577-107965778(-)$1	201	60	87	22.1333
ggggxxxxxxxxxxxxxxxggggggg2	chr5:135514686-135514887(+)$1	201	131	158	18.4080
$$$cccyyyyyyyyyyyyyyyyccc55	chr10:94297144-94297345(-)$1	201	68	95	18.9978
"eeeeettttttttttteeeee22ggg	chr9:139343367-139343568(-)$1	201	67	94	20.4174
hhhhhhvvvvvvvvvvvvvhhhhhhhh	chr18:673289-673490(+)$1	201	161	188	22.2435
ccc[cccuuuuuuuuuuuuccc]ccc]	chr7:99971087-99971288(+)$1	201	171	198	23.9167
$$$$cccuuuuuuuuuuuuccc66666	chrX:47074306-47074507(+)$1	201	46	73	20.8341
bb[eeeeettttttttttteeeee]bb	chr17:42960383-42960584(-)$1	201	1	28	20.7689
Ebb[bbvvvvvvvvvvvvvbb]bb:gg	chr4:6644199-6644400(+)$1	201	23	50	20.9257
####bbvvvvvvvvvvvvvbb55555i	chr3:15482577-15482778(+)$1	201	158	185	19.5754
ddddbbwwwwwwwwwwwwwwbb333dd	chr14:23388158-23388359(-)$1	201	89	116	22.0117
ggggggauuuuuuuuuuuua]gggggg	chr19:45409737-45409938(+)$1	201	131	158	24.1071
ddddddvvvvvvvvvvvvvdddd333d	chr22:38694031-38694232(-)$1	201	150	177	23.7869
e"""bbtttttttttttbb333eeeee	chr14:73572850-73573051(+)$1	201	68	95	19.7538
gggggggtttttttttttggggggg]b	chr7:124538239-124538440(-)$1	201	26	53	21.8357
ddddddddtttttttttttdddd22dd	chr19:9452312-9452513(+)$1	201	71	98	20.4947
h[ddddvvvvvvvvvvvvvdddd]hhh	chr18:13734406-13734607(+)$1	201	150	177	23.3174
ff[eeeeettttttttttteeeee444	chr1:6693474-6693675(+)$1	201	71	98	21.2890
b[fffffftttttttttttffffffbb	chr1:192983793-192983994(-)$1	201	114	141	20.0820
ggggggvvvvvvvvvvvvvggggggg:	chr20:36033395-36033596(+)$1	201	87	114	24.2699
#eeeeettttttttttteeeeeccc00	chr15:48450285-48450486(-)$1	201	113	140	20.4048
ddd[cccuuuuuuuuuuuucccdddd]	chr3:184043560-184043761(+)$1	201	32	59	23.1884
eeeeexxxxxxxxxxxxxxxeeeee44	chr14:23380595-23380796(-)$1	201	143	170	18.0402
dddd[ccctttttttttttccc]dddd	chr17:2323997-2324198(-)$1	201	32	59	21.2987
hhhhhwwwwwwwwwwwwwwhhhhhhhh	chr6:76333533-76333734(+)$1	201	31	58	21.3335
[bbyyyyyyyyyyyyyyyybbccc]bb	chr12:88497494-88497695(-)$1	201	93	120	20.0755
gggggwwwwwwwwwwwwwwggggggg:	chr3:152182787-152182988(+)$1	201	63	90	23.1683
ggggggvvvvvvvvvvvvvggggggg3	chr7:151859103-151859304(-)$1	201	120	147	24.8827
:::cccvvvvvvvvvvvvvccceeeee	chr16:89354790-89354991(-)$1	201	65	92	21.1178
!!ddddvvvvvvvvvvvvvdddd22cc	chr12:49087620-49087821(-)$1	201	60	87	24.0010
ggggggvvvvvvvvvvvvvggggggg:	chr20:61439207-61439408(+)$1	201	23	50	24.2699
ggggggguuuuuuuuuuuuggggggg:	chr8:25193731-25193932(+)$1	201	1	28	23.2528
ggggggvvvvvvvvvvvvvggggggg5	chr6:139229713-139229914(-)$1	201	124	151	24.3314
ggggggvvvvvvvvvvvvvggggggg:	chr7:151835597-151835798(-)$1	201	108	135	24.2699
eeeeeyyyyyyyyyyyyyyyyeeeee5	chr5:149420271-149420472(+)$1	201	14	41	20.2009
c[ddddwwwwwwwwwwwwwwdddd]cc	chr4:17824528-17824729(+)$1	201	143	170	22.9266
c[bbyyyyyyyyyyyyyyyybbccc::	chr19:12348800-12349001(+)$1	201	174	201	19.0176
#bbyyyyyyyyyyyyyyyybb22ffff	chr16:23680712-23680913(+)$1	201	125	152	19.1835
!!ddddwwwwwwwwwwwwwwdddd22f	chr15:40509629-40509830(+)$1	201	32	59	22.6129
eeeeewwwwwwwwwwwwwweeeee::G	chr12:133498444-133498645(-)$1	201	43	70	20.7278
[ccc[bbuuuuuuuuuuuubb]ccccc	chr1:97278505-97278706(+)$1	201	91	118	23.2745
ccc[bbwwwwwwwwwwwwwwbb]ccc]	chr4:54325392-54325593(+)$1	201	87	114	22.7205
gggggwwwwwwwwwwwwwwggggggg:	chr20:57022150-57022351(+)$1	201	123	150	23.1683
#bb[bbvvvvvvvvvvvvvbb]bb444	chr12:56680199-56680400(-)$1	201	36	63	23.0428
eeeeeyyyyyyyyyyyyyyyyeeeee:	chrX:84510636-84510837(+)$1	201	174	201	20.1394
hhhhhhvvvvvvvvvvvvvhhhhhhhh	chr17:61899076-61899277(-)$1	201	160	187	22.2435
ddd[cccuuuuuuuuuuuucccddddb	chr3:98309397-98309598(-)$1	201	34	61	23.0307
ccc[ddddtttttttttttdddd]ccc	chr15:42119550-42119751(+)$1	201	103	130	21.5300
ddd!!avvvvvvvvvvvvva22dddd4	chr11:62367575-62367776(-)$1	201	21	48	23.4890
h[ddddvvvvvvvvvvvvvdddd]hhh	chr22:38692606-38692807(-)$1	201	119	146	23.3174

#otherMatches

#Seq PSSM
UCAUUACAAGAUAUGGCAAGUCGUGUG	chr17:17158109-17158310(-)$1	201	66	93	22.9744
UCGUUCGUUUCCAGCCUCAGGAAUUUA	chr9:95055645-95055846(-)$1	201	77	104	22.6422
UUUUAGAAUGAUUACGGACCUGAAGCC	chr16:67604955-67605156(+)$1	201	89	116	22.7226
ACUGCAUACCUGAAAUCACUGCAGCCC	chr7:24732323-24732524(+)$1	201	119	146	20.9539
AAGGGAGGAAGCUGAGAAACUACCUGA	chr9:95063930-95064131(-)$1	201	48	75	20.4734
AAAGGAGUCAAUGAAAAAAUCCUUGAA	chr9:95076986-95077187(-)$1	201	23	50	23.8622
CUUGGCUGUGCCCUCUUCUGCCAAGGA	chr6:42906463-42906664(+)$1	201	173	200	24.2699
CAUCAGGUAAGAAACUCAUCCUGUAUG	chr2:220011339-220011540(-)$1	201	17	44	23.0623
CCGCCGGUCCUCUCUCUCAGGCAGUUG	chr7:44613863-44614064(-)$1	201	85	112	23.6096
GGACUGAUUCCAGCACCUCCAGUCCCA	chr17:38320211-38320412(+)$1	201	24	51	22.9552
GGCAGGAUCACAGUCGCUUCCUGUCUA	chr14:80971206-80971407(-)$1	201	102	129	20.6577
AAAAGUGAUGCUUAUGGAAUUUUAUCU	chrX:107965577-107965778(-)$1	201	60	87	22.1333
CCAUUUUUUAAGUACUUAUGUGGAAGC	chr5:135514686-135514887(+)$1	201	131	158	18.4080
UAAUCCAGCCAUCAAGAGAAUAGGAAA	chr10:94297144-94297345(-)$1	201	68	95	18.9978
CUAuuuaaaugacaguaaaauacacag	chr9:139343367-139343568(-)$1	201	67	94	20.4174
UAUAGUUGUUUUAUAUGUUGCUAUAAU	chr18:673289-673490(+)$1	201	161	188	22.2435
CCCCUGGAGAAGAACAAGGCCAUGGGU	chr7:99971087-99971288(+)$1	201	171	198	23.9167
CCCUUGUCCACCCCUCUCCACACCCCU	chrX:47074306-47074507(+)$1	201	46	73	20.8341
GGGCACAGUAAAUUUUCCUCUGUGGUC	chr17:42960383-42960584(-)$1	201	1	28	20.7689
UUGGCAUAAAAUGAAAGAUUGGCAAAG	chr4:6644199-6644400(+)$1	201	23	50	20.9257
UUCUGCCCUCUGCCCUCCAGCUUUACC	chr3:15482577-15482778(+)$1	201	158	185	19.5754
CUCCCCACAACAUACUCAAAGGAACGG	chr14:23388158-23388359(-)$1	201	89	116	22.0117
CACAGGCAGGAAGAUGAAGGUUCUGUG	chr19:45409737-45409938(+)$1	201	131	158	24.1071
UCUGGCUUUUCCAAAAUUUGCCACUUG	chr22:38694031-38694232(-)$1	201	150	177	23.7869
GAAAUCAGAGAACGAAAGAAAACCCGG	chr14:73572850-73573051(+)$1	201	68	95	19.7538
GGCUAGAUUUAUUGUUUUUUUAGCUUC	chr7:124538239-124538440(-)$1	201	26	53	21.8357
UUGGAGAGGAACUGUUUGACUUUAACC	chr19:9452312-9452513(+)$1	201	71	98	20.4947
ACCUAAGAAACUUUAAUAAUUGGAUGA	chr18:13734406-13734607(+)$1	201	150	177	23.3174
AGCCGCUCGGGGUUCUAAGGAGUGACU	chr1:6693474-6693675(+)$1	201	71	98	21.2890
gaucacuugauuucgacaaagguggca	chr1:192983793-192983994(-)$1	201	114	141	20.0820
AUGAAAUUUCAACUUUUCCUUUCAUAC	chr20:36033395-36033596(+)$1	201	87	114	24.2699
UGGUGAGUUCCUGUAUAUCACUUCAAC	chr15:48450285-48450486(-)$1	201	113	140	20.4048
GCUAGGAUUUAUUCAUUAUUCCAGUAU	chr3:184043560-184043761(+)$1	201	32	59	23.1884
AAUAUAAAACAGAUUCUUACAUAUUAA	chr14:23380595-23380796(-)$1	201	143	170	18.0402
ACCGAGAAAACCCAUAACAUUCGUGGU	chr17:2323997-2324198(-)$1	201	32	59	21.2987
AUAAGGAUUGUGAUUGCUACUUAUGUU	chr6:76333533-76333734(+)$1	201	31	58	21.3335
UGCCAAAAUGAGAUCUGAAGCGCUAUU	chr12:88497494-88497695(-)$1	201	93	120	20.0755
UCAUGACUGACAAAAACUCCAUGGGGC	chr3:152182787-152182988(+)$1	201	63	90	23.1683
AAACGACAACUUUUUUCUUUUGUUUUA	chr7:151859103-151859304(-)$1	201	120	147	24.8827
CCCCCGUUCUUCACACAUCCGGCCUGU	chr16:89354790-89354991(-)$1	201	65	92	21.1178
CAAUGUGAAGUCACAAUAUGCAUAUGC	chr12:49087620-49087821(-)$1	201	60	87	24.0010
UGUGGGGUCCGUGAUACCGCCCACACA	chr20:61439207-61439408(+)$1	201	23	50	24.2699
UUUUCUUUCUCAUUCUUCUAAGGAAAC	chr8:25193731-25193932(+)$1	201	1	28	23.2528
UCCUAGACACAUUUAAUUACUAGGAAG	chr6:139229713-139229914(-)$1	201	124	151	24.3314
GGCAGCUCUGUGAGCAUUUGCUGUCAC	chr7:151835597-151835798(-)$1	201	108	135	24.2699
CUUGUUGCCUCUUCUUAACCUGCAGGU	chr5:149420271-149420472(+)$1	201	14	41	20.2009
GAUGACAAAAGAAUUCAUAGGUCAACA	chr4:17824528-17824729(+)$1	201	143	170	22.9266
CAUGGAAAAAAGUUAUACUACAGCAAU	chr19:12348800-12349001(+)$1	201	174	201	19.0176
auggaauacaccaaauggacaggccug	chr16:23680712-23680913(+)$1	201	125	152	19.1835
UUUUUAUUAUCUCCUUCUCUUAAAUCU	chr15:40509629-40509830(+)$1	201	32	59	22.6129
UUUCCCAUCAGUUCUCACCGGAAAUAU	chr12:133498444-133498645(-)$1	201	43	70	20.7278
AGAAGAGGAUCUACGAACACUGUUCGC	chr1:97278505-97278706(+)$1	201	91	118	23.2745
GUCGCCAUGAAAGUGAAGAAGGAGAUA	chr4:54325392-54325593(+)$1	201	87	114	22.7205
AGUUUUAAAUUGGUAACUUAAGCUUCC	chr20:57022150-57022351(+)$1	201	123	150	23.1683
AGAAGACUAAGAAUAAGAAUCAUUGCG	chr12:56680199-56680400(-)$1	201	36	63	23.0428
AGUGAAACAUAAAGCCCAUAAUUACUC	chrX:84510636-84510837(+)$1	201	174	201	20.1394
UGCAGGAAGAACAAGCCAACCUGUGGU	chr17:61899076-61899277(-)$1	201	160	187	22.2435
GGGCGUGAGCUCUGUUAUCCACCCCAA	chr3:98309397-98309598(-)$1	201	34	61	23.0307
CUGCUGUGCCCCGACUUCCCACACCAG	chr15:42119550-42119751(+)$1	201	103	130	21.5300
uuuuuguuuuuuuccuccccuuagacu	chr11:62367575-62367776(-)$1	201	21	48	23.4890
GGAGCACCUCUCCACCCACUGCUGCUG	chr22:38692606-38692807(-)$1	201	119	146	23.3174

#DB
.(((.((............)).)))))	chr17:17158109-17158310(-)$1	1	66	93	22.9744
..((((..............))))..)	chr9:95055645-95055846(-)$1	1	77	104	22.6422
((((((.............))))))..	chr16:67604955-67605156(+)$1	1	89	116	22.7226
.(((((.............)))))...	chr7:24732323-24732524(+)$1	1	119	146	20.9539
.(((.((............)).)))(.	chr9:95063930-95064131(-)$1	1	48	75	20.4734
.(((((.............)))))...	chr9:95076986-95077187(-)$1	1	23	50	23.8622
((((((.............))))))).	chr6:42906463-42906664(+)$1	1	173	200	24.2699
(((((((............)))).)))	chr2:220011339-220011540(-)$1	1	17	44	23.0623
..(((..............))).))))	chr7:44613863-44614064(-)$1	1	85	112	23.6096
((((((.............))))))))	chr17:38320211-38320412(+)$1	1	24	51	22.9552
(((((((...........)))))))..	chr14:80971206-80971407(-)$1	1	102	129	20.6577
((((((............))))).)))	chrX:107965577-107965778(-)$1	1	60	87	22.1333
((((...............))))))).	chr5:135514686-135514887(+)$1	1	131	158	18.4080
...(((................)))..	chr10:94297144-94297345(-)$1	1	68	95	18.9978
.(((((...........)))))..)))	chr9:139343367-139343568(-)$1	1	67	94	20.4174
((((((.............))))))))	chr18:673289-673490(+)$1	1	161	188	22.2435
(((.(((............))).))).	chr7:99971087-99971288(+)$1	1	171	198	23.9167
....(((............))).....	chrX:47074306-47074507(+)$1	1	46	73	20.8341
((.(((((...........))))).))	chr17:42960383-42960584(-)$1	1	1	28	20.7689
(((.((.............)).)).((	chr4:6644199-6644400(+)$1	1	23	50	20.9257
....((.............)).....)	chr3:15482577-15482778(+)$1	1	158	185	19.5754
((((((..............))...))	chr14:23388158-23388359(-)$1	1	89	116	22.0117
(((((((............).))))))	chr19:45409737-45409938(+)$1	1	131	158	24.1071
((((((.............))))...)	chr22:38694031-38694232(-)$1	1	150	177	23.7869
(...((...........))...)))))	chr14:73572850-73573051(+)$1	1	68	95	19.7538
(((((((...........))))))).)	chr7:124538239-124538440(-)$1	1	26	53	21.8357
((((((((...........))))..))	chr19:9452312-9452513(+)$1	1	71	98	20.4947
(.((((.............)))).)))	chr18:13734406-13734607(+)$1	1	150	177	23.3174
((.(((((...........)))))...	chr1:6693474-6693675(+)$1	1	71	98	21.2890
(.((((((...........))))))))	chr1:192983793-192983994(-)$1	1	114	141	20.0820
((((((.............))))))).	chr20:36033395-36033596(+)$1	1	87	114	24.2699
.(((((...........))))))))..	chr15:48450285-48450486(-)$1	1	113	140	20.4048
(((.(((............))))))).	chr3:184043560-184043761(+)$1	1	32	59	23.1884
(((((...............)))))..	chr14:23380595-23380796(-)$1	1	143	170	18.0402
((((.(((...........))).))))	chr17:2323997-2324198(-)$1	1	32	59	21.2987
(((((..............))))))))	chr6:76333533-76333734(+)$1	1	31	58	21.3335
.((................))))).))	chr12:88497494-88497695(-)$1	1	93	120	20.0755
(((((..............))))))).	chr3:152182787-152182988(+)$1	1	63	90	23.1683
((((((.............))))))).	chr7:151859103-151859304(-)$1	1	120	147	24.8827
...(((.............)))(((((	chr16:89354790-89354991(-)$1	1	65	92	21.1178
..((((.............))))..))	chr12:49087620-49087821(-)$1	1	60	87	24.0010
((((((.............))))))).	chr20:61439207-61439408(+)$1	1	23	50	24.2699
(((((((............))))))).	chr8:25193731-25193932(+)$1	1	1	28	23.2528
((((((.............))))))).	chr6:139229713-139229914(-)$1	1	124	151	24.3314
((((((.............))))))).	chr7:151835597-151835798(-)$1	1	108	135	24.2699
(((((................))))).	chr5:149420271-149420472(+)$1	1	14	41	20.2009
(.((((..............)))).))	chr4:17824528-17824729(+)$1	1	143	170	22.9266
(.((................)))))..	chr19:12348800-12349001(+)$1	1	174	201	19.0176
.((................))..))))	chr16:23680712-23680913(+)$1	1	125	152	19.1835
..((((..............))))..)	chr15:40509629-40509830(+)$1	1	32	59	22.6129
(((((..............)))))..(	chr12:133498444-133498645(-)$1	1	43	70	20.7278
.(((.((............)).)))))	chr1:97278505-97278706(+)$1	1	91	118	23.2745
(((.((..............)).))).	chr4:54325392-54325593(+)$1	1	87	114	22.7205
(((((..............))))))).	chr20:57022150-57022351(+)$1	1	123	150	23.1683
.((.((.............)).))...	chr12:56680199-56680400(-)$1	1	36	63	23.0428
(((((................))))).	chrX:84510636-84510837(+)$1	1	174	201	20.1394
((((((.............))))))))	chr17:61899076-61899277(-)$1	1	160	187	22.2435
(((.(((............)))))))(	chr3:98309397-98309598(-)$1	1	34	61	23.0307
(((.((((...........)))).)))	chr15:42119550-42119751(+)$1	1	103	130	21.5300
(((..(.............)..)))).	chr11:62367575-62367776(-)$1	1	21	48	23.4890
(.((((.............)))).)))	chr22:38692606-38692807(-)$1	1	119	146	23.3174

#PSSM
g : 0.21	d : 0.11	c : 0.09	e : 0.09	h : 0.08	! : 0.06	# : 0.06	[ : 0.04	f : 0.04	: : 0.04	$ : 0.03	b : 0.03	& : 0.01	" : 0.01	E : 0.01	
g : 0.21	e : 0.14	c : 0.11	d : 0.11	b : 0.08	[ : 0.08	! : 0.06	f : 0.04	h : 0.04	$ : 0.03	# : 0.01	" : 0.01	: : 0.01	
d : 0.21	g : 0.21	e : 0.14	c : 0.13	b : 0.08	f : 0.04	h : 0.04	$ : 0.03	[ : 0.03	# : 0.01	" : 0.01	: : 0.01	
g : 0.21	d : 0.18	e : 0.18	[ : 0.11	c : 0.09	f : 0.04	h : 0.04	y : 0.03	$ : 0.01	# : 0.01	" : 0.01	b : 0.01	! : 0.01	
g : 0.19	e : 0.18	d : 0.16	c : 0.11	b : 0.09	[ : 0.06	f : 0.04	h : 0.04	y : 0.04	x : 0.01	! : 0.01	
d : 0.16	g : 0.16	b : 0.14	e : 0.11	c : 0.11	w : 0.08	y : 0.08	f : 0.04	x : 0.03	h : 0.03	a : 0.01	
v : 0.34	w : 0.16	y : 0.09	c : 0.08	b : 0.04	d : 0.04	g : 0.04	t : 0.04	x : 0.03	e : 0.03	u : 0.01	a : 0.01	f : 0.01	
v : 0.34	u : 0.18	w : 0.16	y : 0.09	t : 0.08	x : 0.03	e : 0.03	d : 0.03	f : 0.01	c : 0.01	
v : 0.34	u : 0.18	t : 0.18	w : 0.16	y : 0.09	x : 0.03	
v : 0.34	u : 0.18	t : 0.18	w : 0.16	y : 0.09	x : 0.03	
v : 0.34	u : 0.18	t : 0.18	w : 0.16	y : 0.09	x : 0.03	
v : 0.34	u : 0.18	t : 0.18	w : 0.16	y : 0.09	x : 0.03	
v : 0.34	u : 0.18	t : 0.18	w : 0.16	y : 0.09	x : 0.03	
v : 0.34	u : 0.18	t : 0.18	w : 0.16	y : 0.09	x : 0.03	
v : 0.34	u : 0.18	t : 0.18	w : 0.16	y : 0.09	x : 0.03	
v : 0.34	u : 0.18	t : 0.18	w : 0.16	y : 0.09	x : 0.03	
v : 0.34	u : 0.18	t : 0.18	w : 0.16	y : 0.09	x : 0.03	
v : 0.34	u : 0.18	w : 0.16	t : 0.13	y : 0.09	x : 0.03	e : 0.03	b : 0.01	
v : 0.34	u : 0.16	w : 0.16	y : 0.09	t : 0.09	e : 0.04	g : 0.03	x : 0.03	b : 0.01	
g : 0.19	b : 0.13	e : 0.13	d : 0.11	c : 0.11	w : 0.08	y : 0.06	f : 0.04	h : 0.04	a : 0.03	3 : 0.01	x : 0.01	
g : 0.19	b : 0.18	d : 0.16	e : 0.14	c : 0.11	f : 0.04	y : 0.04	h : 0.04	] : 0.01	3 : 0.01	2 : 0.01	
g : 0.21	e : 0.18	d : 0.16	c : 0.13	] : 0.08	f : 0.04	h : 0.04	b : 0.04	2 : 0.03	y : 0.01	5 : 0.01	3 : 0.01	
d : 0.21	g : 0.21	e : 0.18	c : 0.11	] : 0.06	f : 0.04	h : 0.04	2 : 0.03	b : 0.03	6 : 0.01	5 : 0.01	3 : 0.01	
g : 0.22	e : 0.16	c : 0.14	d : 0.11	] : 0.08	f : 0.06	2 : 0.04	h : 0.04	b : 0.03	3 : 0.03	6 : 0.01	5 : 0.01	
g : 0.24	c : 0.16	e : 0.09	h : 0.08	2 : 0.06	f : 0.06	d : 0.06	: : 0.04	3 : 0.04	] : 0.04	4 : 0.03	6 : 0.01	5 : 0.01	
g : 0.22	c : 0.13	d : 0.09	e : 0.08	h : 0.08	b : 0.06	: : 0.06	2 : 0.04	4 : 0.04	3 : 0.03	5 : 0.03	A : 0.01	6 : 0.01	] : 0.01	0 : 0.01	f : 0.01	
: : 0.18	b : 0.09	c : 0.09	h : 0.08	e : 0.06	g : 0.06	d : 0.06	4 : 0.06	5 : 0.04	] : 0.04	2 : 0.03	3 : 0.03	f : 0.03	K : 0.01	6 : 0.01	i : 0.01	0 : 0.01	G : 0.01	

#score	1341.6154921918192
#seq	61
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_UTR_m1_run1.txt

#BEAR
hhhhhhhvvvvvvvvvvvvvhhhhhh	chr11:125526253-125526475(+)$1	222	140	166	21.0771
fff[axxxxxxxxxxxxxxxa]ffff	chr6:30692857-30693077(+)$1	220	181	207	20.0527
!!cccattttttttttta]ccc22ee	chr10:12877375-12877595(+)$1	220	169	195	20.3893
[eeeeewwwwwwwwwwwwwweeeee]	chr6:11137763-11137983(+)$1	220	93	119	25.1471
ffffffwwwwwwwwwwwwwwffffff	chr5:140085581-140085813(+)$1	232	98	124	23.1347
hhcccyyyyyyyyyyyyyyyyccc]h	chr12:125627057-125627285(+)$1	228	26	52	21.4572
[bb[bbuuuuuuuuuuuubb]bb]bb	chr1:244572571-244572797(-)$1	226	128	154	20.4199
======wwwwwwwwwwwwww======	chr12:124082345-124082568(+)$1	223	96	122	24.8846
!!ddddtttttttttttdddd333cc	chr1:40090127-40090349(-)$1	222	93	119	19.8183
iiiiiiwwwwwwwwwwwwwwiiiiii	chr11:27519339-27519564(-)$1	225	88	114	24.7318
[a!!cccvvvvvvvvvvvvvccc22a	chr5:6607337-6607565(-)$1	228	87	113	23.7865
:eeeeevvvvvvvvvvvvveeeee::	chr19:36728104-36728328(+)$1	224	120	146	20.7374
feeeeewwwwwwwwwwwwwweeeee]	chr1:78030729-78030952(-)$1	223	12	38	24.8105
::dddduuuuuuuuuuuuddddiiii	chr6:32083239-32083465(-)$1	226	3	29	20.5098
ffddddwwwwwwwwwwwwwwdddd]f	chr1:7840547-7840774(+)$1	227	60	86	24.1920
c[eeeeevvvvvvvvvvvvveeeee3	chr20:48568706-48568927(+)$1	221	130	156	24.0157
"""dddduuuuuuuuuuuudddd333	chr6:111346910-111347136(+)$1	226	106	132	23.3433
==!!bbwwwwwwwwwwwwwwbb22==	chr12:54575824-54576064(-)$1	240	135	161	23.4199
ff[cccuuuuuuuuuuuucccfffff	chr8:37701414-37701635(-)$1	221	108	134	22.3330
hh[cccwwwwwwwwwwwwwwccc22h	chr19:21300179-21300405(+)$1	226	77	103	24.0284
gggggggvvvvvvvvvvvvvgggggg	chr11:57093710-57093952(-)$1	242	79	105	23.3132
iiiiiiivvvvvvvvvvvvviiiiii	chr1:33321651-33321873(+)$1	222	38	64	23.4358
"""bbuuuuuuuuuuuubb333dddd	chr5:115469717-115469937(+)$1	220	101	127	19.5152
Beeeeewwwwwwwwwwwwwweeeee:	chr1:168214340-168214565(+)$1	225	19	45	23.0147
ccc[cccvvvvvvvvvvvvvccc]cc	chr1:55315680-55315899(-)$1	219	86	112	23.6725
eee[cccvvvvvvvvvvvvvccc333	chr2:135713146-135713376(+)$1	230	161	187	24.0557
[cccyyyyyyyyyyyyyyyyccc]bb	chr5:123973068-123973291(-)$1	223	140	166	21.3046
iii[cccvvvvvvvvvvvvvccc]ii	chr1:38279499-38279730(-)$1	231	140	166	24.0860
"""dddduuuuuuuuuuuudddd333	chr16:23634274-23634494(-)$1	220	68	94	23.3433
======xxxxxxxxxxxxxxx=====	chr1:27203220-27203453(-)$1	233	23	49	21.3671
ggggggyyyyyyyyyyyyyyyygggg	chr1:179887949-179888176(+)$1	227	38	64	21.7391
c[ddddwwwwwwwwwwwwwwddddcc	chr1:225590705-225590925(-)$1	220	24	50	24.4380
cccddddvvvvvvvvvvvvvdddd]c	chr4:100469488-100469709(-)$1	221	22	48	23.2886
eeecccxxxxxxxxxxxxxxxccc33	chr9:5798794-5799021(-)$1	227	84	110	21.1928
ffffffuuuuuuuuuuuuffffff>>	chr12:110974303-110974525(-)$1	222	57	83	20.7368
[eeeeexxxxxxxxxxxxxxxeeeee	chr19:17631675-17631898(+)$1	223	64	90	21.3170
eeeee[bbtttttttttttbb]eeee	chr4:177250333-177250554(+)$1	221	23	49	19.7610
[eeeeevvvvvvvvvvvvveeeee]b	chr1:161493528-161493754(-)$1	226	163	189	23.7198
hhhhhhwwwwwwwwwwwwwwhhhhhh	chr12:124497897-124498139(+)$1	242	170	196	22.5599
##ddddwwwwwwwwwwwwwwdddd33	chr19:39889405-39889627(+)$1	222	143	169	24.7217
ccddddwwwwwwwwwwwwwwdddd]c	chr4:129192137-129192364(-)$1	227	156	182	24.4368
!!ddddwwwwwwwwwwwwwwdddd33	chr17:42928435-42928665(+)$1	230	109	135	24.9881
c[ddddxxxxxxxxxxxxxxxdddd]	chr3:160787056-160787277(+)$1	221	85	111	20.9036
[eeeeewwwwwwwwwwwwwweeeee]	chr6:26104413-26104654(+)$1	241	67	93	25.1471
dddcccxxxxxxxxxxxxxxxccc]d	chr6:46113365-46113584(+)$1	219	143	169	20.5245
:eeeeewwwwwwwwwwwwwweeeee:	chr20:31436853-31437084(+)$1	231	2	28	22.9570
[eeeeeyyyyyyyyyyyyyyyyeeee	chr15:55832558-55832779(-)$1	221	119	145	22.0224
b!!cccuuuuuuuuuuuuccc]bb]c	chr12:104742463-104742685(+)$1	222	95	121	22.3748
[ffffffvvvvvvvvvvvvvffffff	chr5:145668572-145668794(+)$1	222	30	56	22.2800
dddeeeeeuuuuuuuuuuuueeeee]	chr11:32879345-32879570(+)$1	225	40	66	22.3276
eeeeexxxxxxxxxxxxxxxeeeee:	chr12:25360606-25360829(-)$1	223	45	71	20.1278
""eeeeevvvvvvvvvvvvveeeee4	chr4:95585308-95585529(+)$1	221	22	48	23.9259
eeee[bbuuuuuuuuuuuubb]eeee	chr12:109040041-109040260(-)$1	219	25	51	22.3131
d[dddduuuuuuuuuuuudddddddd	chr16:56463879-56464118(-)$1	239	142	168	21.9403
ggggggguuuuuuuuuuuuggggggg	chr16:11962698-11962917(-)$1	219	67	93	22.7624
=======vvvvvvvvvvvvv======	chr16:4855082-4855308(-)$1	226	111	137	23.6977
f[cccxxxxxxxxxxxxxxxccc]ff	chr5:98129441-98129667(+)$1	226	30	56	20.8852
gggggggvvvvvvvvvvvvvgggggg	chr12:98941554-98941783(+)$1	229	47	73	23.3132

#otherMatches

#Seq PSSM
AAUAAAUUCAAACCUGUUUUAUUUAU	chr11:125526253-125526475(+)$1	222	140	166	21.0771
ACAUCUCAUUUCUUCCUUUUGCUGUU	chr6:30692857-30693077(+)$1	220	181	207	20.0527
AGAUGCUCAUUUCCUCUGUCAUGAGA	chr10:12877375-12877595(+)$1	220	169	195	20.3893
AGGUUGUUUUAUUUCCUUCCCAACCA	chr6:11137763-11137983(+)$1	220	93	119	25.1471
GAACAUCCCACCUUUAUCCUGUGUUC	chr5:140085581-140085813(+)$1	232	98	124	23.1347
CAGACACACUCCUGAGCCAAGGUCUU	chr12:125627057-125627285(+)$1	228	26	52	21.4572
UGCUCCUGCUGCUCUCAUGGUGCCAC	chr1:244572571-244572797(-)$1	226	128	154	20.4199
GAGuuuuauauaauuaauuuaaauuu	chr12:124082345-124082568(+)$1	223	96	122	24.8846
UUCCCCGUUAUCAUGAAGGGGCCCAC	chr1:40090127-40090349(-)$1	222	93	119	19.8183
UGUAAUUGAUAGCAUUACUUAUUACA	chr11:27519339-27519564(-)$1	225	88	114	24.7318
AGACCAGAGAAAGCACACAGCUGAGC	chr5:6607337-6607565(-)$1	228	87	113	23.7865
CCCCAUGAAAGCCUUGAAAGUGGGAA	chr19:36728104-36728328(+)$1	224	120	146	20.7374
UUUGUGAAAAUAGUUUUCAGCACAGA	chr1:78030729-78030952(-)$1	223	12	38	24.8105
GUGGGACUGUUUCAAAUUUCCCUGAU	chr6:32083239-32083465(-)$1	226	3	29	20.5098
GACUCUGACCGUCUCAUAAAAGAGUU	chr1:7840547-7840774(+)$1	227	60	86	24.1920
UCAGCCCUUCUCUUCCCUUUGGGCUC	chr20:48568706-48568927(+)$1	221	130	156	24.0157
CAAAUUCUUCUUUCUCAUUGGGUGGA	chr6:111346910-111347136(+)$1	226	106	132	23.3433
CCAAGGAAAGAUUGAAUGAGCUGGGG	chr12:54575824-54576064(-)$1	240	135	161	23.4199
CCUCAUAACAAAAGGACAGUGGGUAG	chr8:37701414-37701635(-)$1	221	108	134	22.3330
AAAGCUUUUAACCACCCUUCAGCCCU	chr19:21300179-21300405(+)$1	226	77	103	24.0284
GGAAGGUUCUCUUUGCGCUUGCCUUC	chr11:57093710-57093952(-)$1	242	79	105	23.3132
AGCAGCAUUUCAUGUUCUUUUGCUGU	chr1:33321651-33321873(+)$1	222	38	64	23.4358
AAACUAAAAUCUCCUCAAGCUGUGUU	chr5:115469717-115469937(+)$1	220	101	127	19.5152
ggaaggagaaaaaugaaaggccuuua	chr1:168214340-168214565(+)$1	225	19	45	23.0147
GGAAGGUAUUUUGGAAUCACACCCUC	chr1:55315680-55315899(-)$1	219	86	112	23.6725
UUUCAGGUAAAUGUAGUCUUCCUUAU	chr2:135713146-135713376(+)$1	230	161	187	24.0557
AUAUCCUUCACAUAUUUCCCAUAAGC	chr5:123973068-123973291(-)$1	223	140	166	21.3046
GUUGCAAUAAGUUAUCUCAUUUGGAA	chr1:38279499-38279730(-)$1	231	140	166	24.0860
GAAAGUGAAAAGCAAGUACUACUGAA	chr16:23634274-23634494(-)$1	220	68	94	23.3433
CUCUCACCAUAACAAACCAAAUGGGG	chr1:27203220-27203453(-)$1	233	23	49	21.3671
AGUUUAGUCAAACAUAGGUAUAUGAA	chr1:179887949-179888176(+)$1	227	38	64	21.7391
GUACUUUUUUUUUUCUUUUUGAGUCA	chr1:225590705-225590925(-)$1	220	24	50	24.4380
GCGCAUAUCUGUUCCUUCUUUAUGAU	chr4:100469488-100469709(-)$1	221	22	48	23.2886
GUUUGAUUAUACUGGAAUUUCUCACA	chr9:5798794-5799021(-)$1	227	84	110	21.1928
GUACAAGUCUAACACAAAUUGUACGU	chr12:110974303-110974525(-)$1	222	57	83	20.7368
CCCUCUUCUUCAGCGCAUUUUGGAGG	chr19:17631675-17631898(+)$1	223	64	90	21.3170
GUGGUAUGcuuuccauuuacaaacca	chr4:177250333-177250554(+)$1	221	23	49	19.7610
AUUAAUCACUCUUGAAUAAAUUAAAC	chr1:161493528-161493754(-)$1	226	163	189	23.7198
AGGUGACUCAUAAUUCCCAUUCACUU	chr12:124497897-124498139(+)$1	242	170	196	22.5599
AGUCCCCACACUGGAAAACUGGGAAA	chr19:39889405-39889627(+)$1	222	143	169	24.7217
AGAAAGUCACAAUAUUACuucuuucc	chr4:129192137-129192364(-)$1	227	156	182	24.4368
UCUGACAACACGAAGGCCACGUCAUA	chr17:42928435-42928665(+)$1	230	109	135	24.9881
AUGGUUUCUUCAUGUUUUCCCAACUC	chr3:160787056-160787277(+)$1	221	85	111	20.9036
CGGCUGAAUCUAAGAAUACGCGGUCU	chr6:26104413-26104654(+)$1	241	67	93	25.1471
ACGUUCUCAAAAUAUUAACUCGAAUU	chr6:46113365-46113584(+)$1	219	143	169	20.5245
CUCAGUGGAGAAAUGUAAAGACUGAA	chr20:31436853-31437084(+)$1	231	2	28	22.9570
CAGGUAUACUUUACUAAAUAAUUACC	chr15:55832558-55832779(-)$1	221	119	145	22.0224
GUUGAAUUUUUUUCUUUUUUCUCCAU	chr12:104742463-104742685(+)$1	222	95	121	22.3748
AUGUAAUGUUUGUUUUAUCAAUUACA	chr5:145668572-145668794(+)$1	222	30	56	22.2800
GUGGUCAUUUUAAAACAUGUGUGACA	chr11:32879345-32879570(+)$1	225	40	66	22.3276
GCCCUACAUCUUAUUUCCUCAGGGCU	chr12:25360606-25360829(-)$1	223	45	71	20.1278
CCUGAAGGAAUAAAUUCCAGCUUUAA	chr4:95585308-95585529(+)$1	221	22	48	23.9259
GGAAGACGUGUACUGCUGAGUGUUCC	chr12:109040041-109040260(-)$1	219	25	51	22.3131
AACACUGUAUUUGGACAAAGUGUGAC	chr16:56463879-56464118(-)$1	239	142	168	21.9403
AAACAAUAAUGCUAGCUGAGUUGUUU	chr16:11962698-11962917(-)$1	219	67	93	22.7624
UGACCCCCUCUUCCUCACAUGGGGUC	chr16:4855082-4855308(-)$1	226	111	137	23.6977
UUUGGuuuuuuauuuuuugucuauaa	chr5:98129441-98129667(+)$1	226	30	56	20.8852
AUUUUCUUCAUGUUGACCCUAGAAAA	chr12:98941554-98941783(+)$1	229	47	73	23.3132

#DB
(((((((.............))))))	chr11:125526253-125526475(+)$1	1	140	166	21.0771
(((.(...............).))))	chr6:30692857-30693077(+)$1	1	181	207	20.0527
..((((...........).)))..))	chr10:12877375-12877595(+)$1	1	169	195	20.3893
.(((((..............))))).	chr6:11137763-11137983(+)$1	1	93	119	25.1471
((((((..............))))))	chr5:140085581-140085813(+)$1	1	98	124	23.1347
(((((................))).)	chr12:125627057-125627285(+)$1	1	26	52	21.4572
.((.((............)).)).))	chr1:244572571-244572797(-)$1	1	128	154	20.4199
((((((..............))))))	chr12:124082345-124082568(+)$1	1	96	122	24.8846
..((((...........))))...))	chr1:40090127-40090349(-)$1	1	93	119	19.8183
((((((..............))))))	chr11:27519339-27519564(-)$1	1	88	114	24.7318
.(..(((.............)))..)	chr5:6607337-6607565(-)$1	1	87	113	23.7865
.(((((.............)))))..	chr19:36728104-36728328(+)$1	1	120	146	20.7374
((((((..............))))).	chr1:78030729-78030952(-)$1	1	12	38	24.8105
..((((............))))((((	chr6:32083239-32083465(-)$1	1	3	29	20.5098
((((((..............)))).)	chr1:7840547-7840774(+)$1	1	60	86	24.1920
(.(((((.............))))).	chr20:48568706-48568927(+)$1	1	130	156	24.0157
...((((............))))...	chr6:111346910-111347136(+)$1	1	106	132	23.3433
((..((..............))..))	chr12:54575824-54576064(-)$1	1	135	161	23.4199
((.(((............))))))))	chr8:37701414-37701635(-)$1	1	108	134	22.3330
((.(((..............)))..)	chr19:21300179-21300405(+)$1	1	77	103	24.0284
(((((((.............))))))	chr11:57093710-57093952(-)$1	1	79	105	23.3132
(((((((.............))))))	chr1:33321651-33321873(+)$1	1	38	64	23.4358
...((............))...))))	chr5:115469717-115469937(+)$1	1	101	127	19.5152
((((((..............))))).	chr1:168214340-168214565(+)$1	1	19	45	23.0147
(((.(((.............))).))	chr1:55315680-55315899(-)$1	1	86	112	23.6725
(((.(((.............)))...	chr2:135713146-135713376(+)$1	1	161	187	24.0557
.(((................))).))	chr5:123973068-123973291(-)$1	1	140	166	21.3046
(((.(((.............))).))	chr1:38279499-38279730(-)$1	1	140	166	24.0860
...((((............))))...	chr16:23634274-23634494(-)$1	1	68	94	23.3433
((((((...............)))))	chr1:27203220-27203453(-)$1	1	23	49	21.3671
((((((................))))	chr1:179887949-179888176(+)$1	1	38	64	21.7391
(.((((..............))))))	chr1:225590705-225590925(-)$1	1	24	50	24.4380
(((((((.............)))).)	chr4:100469488-100469709(-)$1	1	22	48	23.2886
((((((...............)))..	chr9:5798794-5799021(-)$1	1	84	110	21.1928
((((((............))))))..	chr12:110974303-110974525(-)$1	1	57	83	20.7368
.(((((...............)))))	chr19:17631675-17631898(+)$1	1	64	90	21.3170
(((((.((...........)).))))	chr4:177250333-177250554(+)$1	1	23	49	19.7610
.(((((.............))))).)	chr1:161493528-161493754(-)$1	1	163	189	23.7198
((((((..............))))))	chr12:124497897-124498139(+)$1	1	170	196	22.5599
..((((..............))))..	chr19:39889405-39889627(+)$1	1	143	169	24.7217
((((((..............)))).)	chr4:129192137-129192364(-)$1	1	156	182	24.4368
..((((..............))))..	chr17:42928435-42928665(+)$1	1	109	135	24.9881
(.((((...............)))).	chr3:160787056-160787277(+)$1	1	85	111	20.9036
.(((((..............))))).	chr6:26104413-26104654(+)$1	1	67	93	25.1471
((((((...............))).)	chr6:46113365-46113584(+)$1	1	143	169	20.5245
.(((((..............))))).	chr20:31436853-31437084(+)$1	1	2	28	22.9570
.(((((................))))	chr15:55832558-55832779(-)$1	1	119	145	22.0224
(..(((............))).)).)	chr12:104742463-104742685(+)$1	1	95	121	22.3748
.((((((.............))))))	chr5:145668572-145668794(+)$1	1	30	56	22.2800
((((((((............))))).	chr11:32879345-32879570(+)$1	1	40	66	22.3276
(((((...............))))).	chr12:25360606-25360829(-)$1	1	45	71	20.1278
..(((((.............))))).	chr4:95585308-95585529(+)$1	1	22	48	23.9259
((((.((............)).))))	chr12:109040041-109040260(-)$1	1	25	51	22.3131
(.((((............))))))))	chr16:56463879-56464118(-)$1	1	142	168	21.9403
(((((((............)))))))	chr16:11962698-11962917(-)$1	1	67	93	22.7624
(((((((.............))))))	chr16:4855082-4855308(-)$1	1	111	137	23.6977
(.(((...............))).))	chr5:98129441-98129667(+)$1	1	30	56	20.8852
(((((((.............))))))	chr12:98941554-98941783(+)$1	1	47	73	23.3132

#PSSM
[ : 0.15	f : 0.12	c : 0.10	e : 0.08	h : 0.06	= : 0.06	" : 0.06	g : 0.06	! : 0.05	i : 0.05	: : 0.05	d : 0.05	B : 0.01	# : 0.01	b : 0.01	
e : 0.24	f : 0.10	[ : 0.08	h : 0.06	! : 0.06	= : 0.06	" : 0.06	g : 0.06	c : 0.06	i : 0.05	d : 0.03	b : 0.01	a : 0.01	: : 0.01	# : 0.01	
e : 0.27	d : 0.18	c : 0.10	f : 0.06	g : 0.06	= : 0.05	i : 0.05	! : 0.05	" : 0.05	h : 0.03	[ : 0.03	b : 0.01	
e : 0.25	d : 0.20	c : 0.15	[ : 0.08	g : 0.06	f : 0.05	= : 0.05	h : 0.03	i : 0.03	! : 0.03	b : 0.01	
e : 0.24	c : 0.20	d : 0.20	g : 0.06	f : 0.05	b : 0.05	= : 0.05	h : 0.03	i : 0.03	a : 0.01	y : 0.01	[ : 0.01	
e : 0.20	d : 0.20	c : 0.15	g : 0.06	x : 0.05	f : 0.05	b : 0.05	= : 0.05	h : 0.03	y : 0.03	i : 0.03	a : 0.01	u : 0.01	[ : 0.01	
w : 0.27	x : 0.13	u : 0.12	y : 0.06	c : 0.06	e : 0.05	d : 0.05	g : 0.05	t : 0.03	v : 0.03	b : 0.03	h : 0.01	i : 0.01	f : 0.01	= : 0.01	
w : 0.27	v : 0.25	u : 0.18	x : 0.13	y : 0.06	t : 0.03	b : 0.01	e : 0.01	
w : 0.27	v : 0.25	u : 0.20	x : 0.13	y : 0.06	t : 0.05	
w : 0.27	v : 0.25	u : 0.20	x : 0.13	y : 0.06	t : 0.05	
w : 0.27	v : 0.25	u : 0.20	x : 0.13	y : 0.06	t : 0.05	
w : 0.27	v : 0.25	u : 0.20	x : 0.13	y : 0.06	t : 0.05	
w : 0.27	v : 0.25	u : 0.20	x : 0.13	y : 0.06	t : 0.05	
w : 0.27	v : 0.25	u : 0.20	x : 0.13	y : 0.06	t : 0.05	
w : 0.27	v : 0.25	u : 0.20	x : 0.13	y : 0.06	t : 0.05	
w : 0.27	v : 0.25	u : 0.20	x : 0.13	y : 0.06	t : 0.05	
w : 0.27	v : 0.25	u : 0.20	x : 0.13	y : 0.06	t : 0.05	
w : 0.27	v : 0.25	u : 0.18	x : 0.13	y : 0.06	a : 0.01	d : 0.01	b : 0.01	t : 0.01	
w : 0.27	v : 0.25	x : 0.13	u : 0.08	y : 0.06	d : 0.05	b : 0.03	c : 0.03	] : 0.01	f : 0.01	t : 0.01	
w : 0.27	v : 0.22	x : 0.13	d : 0.08	y : 0.06	c : 0.05	b : 0.05	e : 0.03	3 : 0.01	f : 0.01	u : 0.01	g : 0.01	
e : 0.18	d : 0.18	c : 0.17	x : 0.08	f : 0.05	y : 0.05	b : 0.05	g : 0.05	h : 0.03	= : 0.03	i : 0.03	a : 0.01	] : 0.01	3 : 0.01	
e : 0.20	c : 0.18	d : 0.18	] : 0.06	f : 0.06	= : 0.05	g : 0.05	h : 0.03	b : 0.03	3 : 0.03	i : 0.03	y : 0.03	
e : 0.25	d : 0.18	c : 0.17	f : 0.08	g : 0.06	= : 0.05	i : 0.05	h : 0.03	2 : 0.03	b : 0.03	3 : 0.01	
e : 0.25	d : 0.15	f : 0.08	] : 0.08	2 : 0.06	3 : 0.06	g : 0.06	c : 0.05	= : 0.05	i : 0.05	h : 0.03	b : 0.01	
e : 0.24	] : 0.12	3 : 0.10	f : 0.08	= : 0.06	i : 0.06	g : 0.06	c : 0.05	d : 0.05	h : 0.03	b : 0.03	2 : 0.03	: : 0.01	> : 0.01	
3 : 0.12	f : 0.10	c : 0.10	e : 0.08	] : 0.08	h : 0.06	= : 0.06	i : 0.06	: : 0.06	g : 0.06	b : 0.05	d : 0.05	a : 0.01	> : 0.01	4 : 0.01	

#score	1309.8029493439267
#seq	58
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_transcript_m2_run2.txt

#BEAR
"ffffffuuuuuuuuuuuuffffff2	chr15:67814676-67814902(+)$1	226	118	144	22.7442
!!eeeeeuuuuuuuuuuuueeeee22	chr8:54904310-54904559(-)$1	249	73	99	24.0587
fffffwwwwwwwwwwwwwwffffffe	chr4:157872478-157872710(-)$1	232	177	203	20.7413
gggggggwwwwwwwwwwwwwwggggg	chr5:129306967-129307198(+)$1	231	192	218	22.6085
"""eeeeettttttttttteeeee44	chr11:6204467-6204700(-)$1	233	163	189	22.8926
ccc!!bbwwwwwwwwwwwwwwbb22c	chr11:21000755-21000987(+)$1	232	64	90	21.8922
ee[ddddvvvvvvvvvvvvvddddee	chr1:175944335-175944567(-)$1	232	119	145	22.6709
iiiiiiiitttttttttttiiiiiii	chr1:22035812-22036044(-)$1	232	176	202	22.3966
##eeeeeuuuuuuuuuuuueeeee22	chr2:154302306-154302543(-)$1	237	182	208	23.9391
dddyyyyyyyyyyyyyyyydddd]cc	chr13:94000904-94001131(+)$1	227	53	79	20.5517
::eeeeewwwwwwwwwwwwwweeeee	chr1:208393666-208393899(-)$1	233	185	211	20.7070
c[bbcccuuuuuuuuuuuuccc]bbc	chrX:107976466-107976689(-)$1	223	64	90	23.4724
:ffffffuuuuuuuuuuuuffffff:	chr12:42475561-42475790(-)$1	229	52	78	21.0645
"""dddduuuuuuuuuuuudddd333	chr17:11927847-11928073(+)$1	226	105	131	24.5494
h"""ddddtttttttttttdddd22h	chr4:20463870-20464102(+)$1	232	9	35	22.1317
bb[ddddvvvvvvvvvvvvvdddd]b	chr12:95657936-95658169(+)$1	233	175	201	22.5225
d[eeeeeuuuuuuuuuuuueeeeedd	chr5:78693579-78693811(-)$1	232	118	144	23.4860
e"""cccuuuuuuuuuuuuccc333e	chr12:98995819-98996041(+)$1	222	20	46	24.8552
$$$ddddvvvvvvvvvvvvvdddd66	chr5:115479351-115479573(+)$1	222	89	115	21.7888
====cccuuuuuuuuuuuuccc]===	chr7:94921490-94921722(+)$1	232	6	32	24.9334
a[eeeeevvvvvvvvvvvvveeeee]	chr17:57910764-57911004(+)$1	240	36	62	23.3923
::cccwwwwwwwwwwwwwwcccbb!!	chr18:39568721-39568953(+)$1	232	33	59	19.3583
iiiiiiiyyyyyyyyyyyyyyyyiii	chr4:145662369-145662612(+)$1	243	68	94	22.1349
&eeeeevvvvvvvvvvvvveeeee33	chr14:75600057-75600290(-)$1	233	115	141	22.3983
[gggggggtttttttttttggggggg	chr17:65335414-65335670(-)$1	256	132	158	22.3685
eeeeebbyyyyyyyyyyyyyyyybb]	chr18:48415928-48416150(+)$1	222	93	119	21.1422
e!!dddduuuuuuuuuuuuddddeee	chr4:2677275-2677506(+)$1	231	54	80	23.7386
=======vvvvvvvvvvvvv======	chr1:198225038-198225268(+)$1	230	90	116	23.9105
gggggggvvvvvvvvvvvvvgggggg	chr13:94242763-94242995(+)$1	232	101	127	23.2707
eeeeeccctttttttttttccc:ddd	chr2:75884401-75884624(+)$1	223	24	50	21.5331
c!!ddddtttttttttttdddd22cc	chr3:183888827-183889083(+)$1	256	175	201	22.0484
gggg[ccctttttttttttccc22gg	chr5:82872155-82872385(+)$1	230	19	45	23.0518
H:eeeeevvvvvvvvvvvvveeeee:	chr1:59123723-59123947(-)$1	224	92	118	20.8042
ff"""bbwwwwwwwwwwwwwwbb22f	chr13:73424445-73424674(+)$1	229	198	224	21.5263
bbeeeeewwwwwwwwwwwwwweeeee	chr13:103421910-103422141(-)$1	231	167	193	22.0611
eeeyyyyyyyyyyyyyyyyeeeee44	chr4:20554720-20554959(+)$1	239	46	72	21.0929
d"""cccuuuuuuuuuuuuccc333d	chr1:36068776-36068999(-)$1	223	23	49	24.7286
ggg[cccvvvvvvvvvvvvvccc333	chr19:39369501-39369722(-)$1	221	24	50	24.2569
!bb[ddddtttttttttttdddd]bb	chr6:111640624-111640856(-)$1	232	169	195	21.6926
ggg"""bbtttttttttttbb]gggg	chr12:95702116-95702345(+)$1	229	119	145	21.7866
eeee[ccctttttttttttccc]eee	chr16:47720244-47720477(+)$1	233	107	133	22.7691
dbb[bbwwwwwwwwwwwwwwbb]bb]	chr11:22227269-22227500(+)$1	231	78	104	20.9266
=======uuuuuuuuuuuu=======	chr6:14128479-14128704(+)$1	225	135	161	24.6169
iii!!bbwwwwwwwwwwwwwwbb22i	chr6:125404202-125404434(+)$1	232	117	143	22.1442
::ddddyyyyyyyyyyyyyyyydddd	chr7:79825562-79825794(+)$1	232	145	171	19.7260
+eeeeeauuuuuuuuuuuua]eeeee	chr17:64378934-64379172(+)$1	238	29	55	23.2579
ggggggguuuuuuuuuuuuggggggg	chr7:151175577-151175805(-)$1	228	152	178	23.8731
ccc[cccuuuuuuuuuuuuccc]ccc	chr7:123714359-123714602(+)$1	243	160	186	24.3561
:ffffffvvvvvvvvvvvvvffffff	chr2:32521770-32522002(+)$1	232	29	55	21.2276
fffffbbyyyyyyyyyyyyyyyybb]	chr1:98249503-98249735(-)$1	232	121	147	20.8063
fffyyyyyyyyyyyyyyyyffffff]	chr3:155633970-155634201(+)$1	231	168	194	20.4907
b!!ddddyyyyyyyyyyyyyyyyddd	chr7:28742202-28742434(+)$1	232	93	119	21.5861
====[bbtttttttttttbb]=====	chr4:113569543-113569767(-)$1	224	80	106	22.2315
ccc[cccuuuuuuuuuuuucccccc9	chr12:108139640-108139872(-)$1	232	182	208	23.6215
b[eeeeeuuuuuuuuuuuueeeee22	chr14:57862421-57862653(+)$1	232	170	196	23.7833
ggggggguuuuuuuuuuuuggggggg	chr19:28287651-28287883(+)$1	232	12	38	23.8731
bb[dddduuuuuuuuuuuuddddbb]	chr9:123177427-123177654(-)$1	227	51	77	23.1723
ccc!!ccctttttttttttccc]ccc	chr17:67154245-67154482(-)$1	237	93	119	23.1310
e!!cccxxxxxxxxxxxxxxxccc33	chr12:1393090-1393343(+)$1	253	70	96	19.3856
[cccxxxxxxxxxxxxxxxccc]===	chr9:7041129-7041357(+)$1	228	101	127	18.6296
!bb[cccvvvvvvvvvvvvvccc]bb	chr9:80433304-80433537(-)$1	233	30	56	22.9166
c!!ddddtttttttttttdddd22cc	chr6:71401142-71401376(+)$1	234	201	227	22.0484

#otherMatches

#Seq PSSM
AUAAUCUGAUCGUCCAUUAAGGUUAA	chr15:67814676-67814902(+)$1	226	118	144	22.7442
UCAUACACUGuuauuuuuuuguauuu	chr8:54904310-54904559(-)$1	249	73	99	24.0587
AUUUACAAGCAAUUAUAUAUAAAUAC	chr4:157872478-157872710(-)$1	232	177	203	20.7413
UGUACUGUUAAUUUAAUUGCUUAGUA	chr5:129306967-129307198(+)$1	231	192	218	22.6085
uuauggaaguggccagaaauuccagu	chr11:6204467-6204700(-)$1	233	163	189	22.8926
GGUAACCAUGCUAUCAUAAAAGGAAA	chr11:21000755-21000987(+)$1	232	64	90	21.8922
ACACAUCUAAUGUAACUAAUGGUGGU	chr1:175944335-175944567(-)$1	232	119	145	22.6709
AAGUUUUCAUAGACUCACGGGAAAUU	chr1:22035812-22036044(-)$1	232	176	202	22.3966
ugacauuuuuccugacuauaauguau	chr2:154302306-154302543(-)$1	237	182	208	23.9391
UGCAAAAAUAUAAAGUUAAGCAGAUC	chr13:94000904-94001131(+)$1	227	53	79	20.5517
uauugucucauuuacugucaugacaa	chr1:208393666-208393899(-)$1	233	185	211	20.7070
CGUGCCAACCCCUUAUCUCUGGACAG	chrX:107976466-107976689(-)$1	223	64	90	23.4724
UAGAGGAGUUUUCAGUUCAUCCUCUU	chr12:42475561-42475790(-)$1	229	52	78	21.0645
AUACUCAAAUUAACUACUCUGAGAAA	chr17:11927847-11928073(+)$1	226	105	131	24.5494
AAAAUGAAUAAACCAGGUUUUCAAGU	chr4:20463870-20464102(+)$1	232	9	35	22.1317
GUUUACUAUUAACAUACAAAAGUAUA	chr12:95657936-95658169(+)$1	233	175	201	22.5225
AAGUUAUCCUAACCUUUCUAUGACUA	chr5:78693579-78693811(-)$1	232	118	144	23.4860
ACAAGGUAAACCAAAUUAGGCUGAUU	chr12:98995819-98996041(+)$1	222	20	46	24.8552
AAGUAAAUAUGCACUAACUUUUUAAA	chr5:115479351-115479573(+)$1	222	89	115	21.7888
GAUACUCUAUUAAUGUCUUGAGAUGU	chr7:94921490-94921722(+)$1	232	6	32	24.9334
ggccaggaauuugagacccaccuggg	chr17:57910764-57911004(+)$1	240	36	62	23.3923
AUUCCUAUAUACAUAAACUGGAAGGA	chr18:39568721-39568953(+)$1	232	33	59	19.3583
GAGAAGUUACUUCUUCCCUAUUUAUU	chr4:145662369-145662612(+)$1	243	68	94	22.1349
uuaucuuaaccauucacauagaugug	chr14:75600057-75600290(-)$1	233	115	141	22.3983
AUCUUUUUAAAACUAACCAAAAAAgg	chr17:65335414-65335670(-)$1	256	132	158	22.3685
uucugugacauauaacaauuuaacau	chr18:48415928-48416150(+)$1	222	93	119	21.1422
uccuucauugcuuacuuuuUGAAAAG	chr4:2677275-2677506(+)$1	231	54	80	23.7386
UUGAAGAAUGCUAACCUAACUCUUUA	chr1:198225038-198225268(+)$1	230	90	116	23.9105
AUAUUUAUACUAAUACUUACUAAAUA	chr13:94242763-94242995(+)$1	232	101	127	23.2707
CUCCUCCACAUGAAUAuuuugguuuu	chr2:75884401-75884624(+)$1	223	24	50	21.5331
GACUUUACCCCACAUUACUGAAACCA	chr3:183888827-183889083(+)$1	256	175	201	22.0484
gcauuauguuugugagauuuauucau	chr5:82872155-82872385(+)$1	230	19	45	23.0518
gcugugugaccuuaaucaaaacacau	chr1:59123723-59123947(-)$1	224	92	118	20.8042
GUUUUCAUUUCUCAUGUCCAUUGUUG	chr13:73424445-73424674(+)$1	229	198	224	21.5263
CAGAGCAAACAUAUAUAUAGCUGUUC	chr13:103421910-103422141(-)$1	231	167	193	22.0611
UAUUUUAUGUUCUUUcuuuguacuua	chr4:20554720-20554959(+)$1	239	46	72	21.0929
GCUCCAGAAACGCUUCAUCCUGAAUC	chr1:36068776-36068999(-)$1	223	23	49	24.7286
GCUCAGAACAUCCCCCAAUCUCUUAC	chr19:39369501-39369722(-)$1	221	24	50	24.2569
ACuuuuuuuuuuuuuuccugagacag	chr6:111640624-111640856(-)$1	232	169	195	21.6926
GGGAUCCCAGAUCAAACCAGGCCCCU	chr12:95702116-95702345(+)$1	229	119	145	21.7866
auaacaauaauuuacuaacauuuuua	chr16:47720244-47720477(+)$1	233	107	133	22.7691
gauaccaaaaagauaauaaaggaaua	chr11:22227269-22227500(+)$1	231	78	104	20.9266
CUGUGGAUAAACCCCAAAUUCCACAG	chr6:14128479-14128704(+)$1	225	135	161	24.6169
AAACAUCUAUAUCAUAACUCUGACCU	chr6:125404202-125404434(+)$1	232	117	143	22.1442
UAAGUAAUCCCUAUUCUUUUUCUACU	chr7:79825562-79825794(+)$1	232	145	171	19.7260
cauuaccaccaacaagaaagagugau	chr17:64378934-64379172(+)$1	238	29	55	23.2579
AGACAUAACUUCUUUUUUCUAUGUUU	chr7:151175577-151175805(-)$1	228	152	178	23.8731
aucaaccucuccucauuUUGGUAGAU	chr7:123714359-123714602(+)$1	243	160	186	24.3561
aaguuacuauuuuucucuuuguaauu	chr2:32521770-32522002(+)$1	232	29	55	21.2276
UACUUCUAUUACUAACAGCAAAAAGA	chr1:98249503-98249735(-)$1	232	121	147	20.8063
cagucacuccucguucuaccuguugu	chr3:155633970-155634201(+)$1	231	168	194	20.4907
gagauggauacuaaacaaaauaacca	chr7:28742202-28742434(+)$1	232	93	119	21.5861
GCUUUCUGUGACUUUAAAAGUAAGUG	chr4:113569543-113569767(-)$1	224	80	106	22.2315
ACACAACUUUAGAUCAAAUGUUUGUA	chr12:108139640-108139872(-)$1	232	182	208	23.6215
CUGAAAAUUUUUAAUUUUUUUUUCCU	chr14:57862421-57862653(+)$1	232	170	196	23.7833
UGAUUAUUCCAAAUGCAUUGUGAUCA	chr19:28287651-28287883(+)$1	232	12	38	23.8731
UGUGGGAAAUAGCUCACCCUCCCCAU	chr9:123177427-123177654(-)$1	227	51	77	23.1723
uggcuugaaucucuaaaaaucaucca	chr17:67154245-67154482(-)$1	237	93	119	23.1310
acuuacuccuucuaucuaacuguauu	chr12:1393090-1393343(+)$1	253	70	96	19.3856
auaacaauuuacauaucuuuuacauu	chr9:7041129-7041357(+)$1	228	101	127	18.6296
UAAUUUAGCUUAACUACUUAUAAUUU	chr9:80433304-80433537(-)$1	233	30	56	22.9166
ucuacucucuaucuccaugaguucaa	chr6:71401142-71401376(+)$1	234	201	227	22.0484

#DB
.((((((............)))))).	chr15:67814676-67814902(+)$1	1	118	144	22.7442
..(((((............)))))..	chr8:54904310-54904559(-)$1	1	73	99	24.0587
(((((..............)))))))	chr4:157872478-157872710(-)$1	1	177	203	20.7413
(((((((..............)))))	chr5:129306967-129307198(+)$1	1	192	218	22.6085
...(((((...........)))))..	chr11:6204467-6204700(-)$1	1	163	189	22.8926
(((..((..............))..)	chr11:21000755-21000987(+)$1	1	64	90	21.8922
((.((((.............))))))	chr1:175944335-175944567(-)$1	1	119	145	22.6709
((((((((...........)))))))	chr1:22035812-22036044(-)$1	1	176	202	22.3966
..(((((............)))))..	chr2:154302306-154302543(-)$1	1	182	208	23.9391
(((................)))).))	chr13:94000904-94001131(+)$1	1	53	79	20.5517
..(((((..............)))))	chr1:208393666-208393899(-)$1	1	185	211	20.7070
(.(((((............))).)))	chrX:107976466-107976689(-)$1	1	64	90	23.4724
.((((((............)))))).	chr12:42475561-42475790(-)$1	1	52	78	21.0645
...((((............))))...	chr17:11927847-11928073(+)$1	1	105	131	24.5494
(...((((...........))))..)	chr4:20463870-20464102(+)$1	1	9	35	22.1317
((.((((.............)))).)	chr12:95657936-95658169(+)$1	1	175	201	22.5225
(.(((((............)))))))	chr5:78693579-78693811(-)$1	1	118	144	23.4860
(...(((............)))...)	chr12:98995819-98996041(+)$1	1	20	46	24.8552
...((((.............))))..	chr5:115479351-115479573(+)$1	1	89	115	21.7888
(((((((............))).)))	chr7:94921490-94921722(+)$1	1	6	32	24.9334
(.(((((.............))))).	chr17:57910764-57911004(+)$1	1	36	62	23.3923
..(((..............)))((..	chr18:39568721-39568953(+)$1	1	33	59	19.3583
(((((((................)))	chr4:145662369-145662612(+)$1	1	68	94	22.1349
.(((((.............)))))..	chr14:75600057-75600290(-)$1	1	115	141	22.3983
.(((((((...........)))))))	chr17:65335414-65335670(-)$1	1	132	158	22.3685
(((((((................)).	chr18:48415928-48416150(+)$1	1	93	119	21.1422
(..((((............)))))))	chr4:2677275-2677506(+)$1	1	54	80	23.7386
(((((((.............))))))	chr1:198225038-198225268(+)$1	1	90	116	23.9105
(((((((.............))))))	chr13:94242763-94242995(+)$1	1	101	127	23.2707
)))))(((...........))).(((	chr2:75884401-75884624(+)$1	1	24	50	21.5331
(..((((...........))))..))	chr3:183888827-183889083(+)$1	1	175	201	22.0484
((((.(((...........)))..))	chr5:82872155-82872385(+)$1	1	19	45	23.0518
(.(((((.............))))).	chr1:59123723-59123947(-)$1	1	92	118	20.8042
((...((..............))..)	chr13:73424445-73424674(+)$1	1	198	224	21.5263
))(((((..............)))))	chr13:103421910-103422141(-)$1	1	167	193	22.0611
(((................)))))..	chr4:20554720-20554959(+)$1	1	46	72	21.0929
(...(((............)))...)	chr1:36068776-36068999(-)$1	1	23	49	24.7286
(((.(((.............)))...	chr19:39369501-39369722(-)$1	1	24	50	24.2569
.((.((((...........)))).))	chr6:111640624-111640856(-)$1	1	169	195	21.6926
(((...((...........)).))))	chr12:95702116-95702345(+)$1	1	119	145	21.7866
((((.(((...........))).)))	chr16:47720244-47720477(+)$1	1	107	133	22.7691
(((.((..............)).)).	chr11:22227269-22227500(+)$1	1	78	104	20.9266
(((((((............)))))))	chr6:14128479-14128704(+)$1	1	135	161	24.6169
(((..((..............))..)	chr6:125404202-125404434(+)$1	1	117	143	22.1442
..((((................))))	chr7:79825562-79825794(+)$1	1	145	171	19.7260
.((((((............).)))))	chr17:64378934-64379172(+)$1	1	29	55	23.2579
(((((((............)))))))	chr7:151175577-151175805(-)$1	1	152	178	23.8731
(((.(((............))).)))	chr7:123714359-123714602(+)$1	1	160	186	24.3561
.((((((.............))))))	chr2:32521770-32522002(+)$1	1	29	55	21.2276
(((((((................)).	chr1:98249503-98249735(-)$1	1	121	147	20.8063
(((................)))))).	chr3:155633970-155634201(+)$1	1	168	194	20.4907
(..((((................)))	chr7:28742202-28742434(+)$1	1	93	119	21.5861
((((.((...........)).)))))	chr4:113569543-113569767(-)$1	1	80	106	22.2315
(((.(((............)))))).	chr12:108139640-108139872(-)$1	1	182	208	23.6215
(.(((((............)))))..	chr14:57862421-57862653(+)$1	1	170	196	23.7833
(((((((............)))))))	chr19:28287651-28287883(+)$1	1	12	38	23.8731
((.((((............)))))).	chr9:123177427-123177654(-)$1	1	51	77	23.1723
(((..(((...........))).)))	chr17:67154245-67154482(-)$1	1	93	119	23.1310
(..(((...............)))..	chr12:1393090-1393343(+)$1	1	70	96	19.3856
.(((...............))).)))	chr9:7041129-7041357(+)$1	1	101	127	18.6296
.((.(((.............))).))	chr9:80433304-80433537(-)$1	1	30	56	22.9166
(..((((...........))))..))	chr6:71401142-71401376(+)$1	1	201	227	22.0484

#PSSM
e : 0.12	g : 0.11	c : 0.11	: : 0.08	b : 0.08	f : 0.06	d : 0.06	= : 0.06	" : 0.04	! : 0.04	i : 0.04	[ : 0.03	# : 0.01	h : 0.01	$ : 0.01	a : 0.01	& : 0.01	H : 0.01	+ : 0.01	
g : 0.12	f : 0.11	e : 0.11	! : 0.09	b : 0.09	" : 0.08	c : 0.08	: : 0.06	[ : 0.06	= : 0.06	i : 0.04	# : 0.01	d : 0.01	$ : 0.01	
e : 0.22	g : 0.12	f : 0.09	" : 0.09	c : 0.09	! : 0.08	b : 0.06	= : 0.06	[ : 0.04	i : 0.04	d : 0.03	$ : 0.01	
e : 0.22	d : 0.16	g : 0.09	[ : 0.09	f : 0.08	" : 0.08	= : 0.06	! : 0.04	y : 0.04	c : 0.04	i : 0.03	b : 0.01	
e : 0.20	d : 0.19	c : 0.16	f : 0.08	g : 0.08	! : 0.04	y : 0.04	[ : 0.04	i : 0.03	= : 0.03	" : 0.03	b : 0.01	x : 0.01	
c : 0.20	d : 0.19	e : 0.17	b : 0.11	g : 0.08	f : 0.04	y : 0.04	w : 0.03	i : 0.03	= : 0.03	" : 0.01	x : 0.01	
c : 0.19	d : 0.17	e : 0.14	b : 0.11	g : 0.08	y : 0.06	f : 0.04	w : 0.04	i : 0.03	= : 0.03	x : 0.03	v : 0.01	a : 0.01	
u : 0.30	v : 0.17	w : 0.14	y : 0.12	c : 0.06	t : 0.04	d : 0.03	x : 0.03	e : 0.01	i : 0.01	g : 0.01	b : 0.01	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	t : 0.20	v : 0.17	w : 0.14	y : 0.12	x : 0.03	
u : 0.30	v : 0.17	t : 0.16	w : 0.14	y : 0.12	d : 0.03	x : 0.03	b : 0.01	
c : 0.19	v : 0.16	d : 0.12	e : 0.11	w : 0.11	y : 0.08	f : 0.06	g : 0.04	b : 0.03	i : 0.01	= : 0.01	a : 0.01	x : 0.01	
c : 0.22	d : 0.17	e : 0.14	w : 0.09	f : 0.08	y : 0.08	g : 0.06	= : 0.03	b : 0.03	] : 0.03	i : 0.01	x : 0.01	
c : 0.24	e : 0.19	d : 0.17	f : 0.08	g : 0.08	y : 0.08	b : 0.06	= : 0.04	i : 0.01	] : 0.01	
e : 0.19	d : 0.16	] : 0.11	g : 0.09	f : 0.08	b : 0.06	y : 0.06	c : 0.06	= : 0.04	2 : 0.04	3 : 0.03	i : 0.01	: : 0.01	
e : 0.22	2 : 0.11	g : 0.09	d : 0.09	b : 0.09	f : 0.08	= : 0.08	3 : 0.06	c : 0.06	] : 0.04	i : 0.03	
e : 0.12	2 : 0.11	g : 0.11	b : 0.11	c : 0.09	3 : 0.09	f : 0.08	= : 0.08	d : 0.06	4 : 0.03	i : 0.03	] : 0.01	6 : 0.01	! : 0.01	
e : 0.12	g : 0.11	c : 0.11	] : 0.09	d : 0.08	= : 0.08	2 : 0.06	3 : 0.06	i : 0.04	b : 0.04	4 : 0.03	: : 0.03	f : 0.03	h : 0.01	6 : 0.01	! : 0.01	9 : 0.01	

#score	1388.87978239944
#seq	62
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_CDS_m1_run1.txt

#BEAR
fffffccctttttttttttccc]ff	chr20:21321263-21321483(+)$1	220	69	94	21.2043
!!dddduuuuuuuuuuuudddd22a	chr1:155447726-155447956(-)$1	230	96	121	22.4492
eeeeeuuuuuuuuuuuueeeee]gg	chr7:45009205-45009431(-)$1	226	181	206	22.5768
ee[ddddtttttttttttdddd]ee	chr9:79972573-79972795(+)$1	222	16	41	21.1687
fffffwwwwwwwwwwwwwwffffff	chr18:29488723-29488940(-)$1	217	142	167	23.2836
gggddddtttttttttttdddd]gg	chr9:135211598-135211828(-)$1	230	140	165	21.2000
eeeebbvvvvvvvvvvvvvbb]eee	chr1:89587445-89587662(-)$1	217	167	192	22.8990
[eeeeevvvvvvvvvvvvveeeeee	chr4:122737842-122738072(-)$1	230	109	134	23.9687
eeeyyyyyyyyyyyyyyyyeeeee]	chr10:88220899-88221123(-)$1	224	71	96	21.6812
ceeeeettttttttttteeeee]cc	chr5:134029500-134029722(-)$1	222	16	41	21.4389
:eeeeevvvvvvvvvvvvveeeee:	chr16:67178140-67178370(+)$1	230	11	36	21.8863
eddddvvvvvvvvvvvvvdddd]ee	chr3:63825249-63825470(-)$1	221	66	91	22.7050
dddddyyyyyyyyyyyyyyyydddd	chr6:138198248-138198478(+)$1	230	115	140	20.9085
fffffwwwwwwwwwwwwwwffffff	chrX:13726759-13726989(+)$1	230	42	67	23.2836
ccc[cccuuuuuuuuuuuuccc]cc	chr5:140810757-140810979(+)$1	222	195	220	23.4010
!eeeeevvvvvvvvvvvvveeeee2	chr16:57241872-57242102(+)$1	230	22	47	23.7041
g[cccyyyyyyyyyyyyyyyycccg	chr4:56283979-56284198(+)$1	219	94	119	21.9666
f[cccwwwwwwwwwwwwwwccc]ff	chr2:48033322-48033552(+)$1	230	110	135	24.1373
ddcccwwwwwwwwwwwwwwccc::e	chr14:31122642-31122863(+)$1	221	101	126	21.4492
b[cccyyyyyyyyyyyyyyyyccc2	chr6:99353410-99353628(-)$1	218	67	92	21.3482
eeeeewwwwwwwwwwwwwweeeeef	chr6:100965791-100966021(-)$1	230	129	154	24.0398
e[cccwwwwwwwwwwwwwwccc]ee	chr14:104026933-104027154(-)$1	221	103	128	24.2153
iiiiiiiuuuuuuuuuuuuiiiiii	chr11:73789580-73789799(-)$1	219	190	215	22.4163
====bbvvvvvvvvvvvvvbb]===	chrM:3537-3767(+)$1	230	128	153	22.7734
ggggggvvvvvvvvvvvvvgggggg	chr5:133292436-133292663(-)$1	227	100	125	23.4155
c[ddddtttttttttttddddcccc	chr2:28805205-28805419(-)$1	214	101	126	20.5651
d!!cccvvvvvvvvvvvvvccc22d	chr17:26913037-26913260(-)$1	223	102	127	23.3795
fffffwwwwwwwwwwwwwwffffff	chr10:22615361-22615591(+)$1	230	185	210	23.2836
eeeeewwwwwwwwwwwwwweeeee2	chr22:39477444-39477674(+)$1	230	10	35	23.7800
eeeeewwwwwwwwwwwwwweeeeeD	chr4:1725449-1725675(+)$1	226	133	158	22.9850
eeeeeyyyyyyyyyyyyyyyyeeee	chr13:73293029-73293253(-)$1	224	103	128	22.1168
eeeeexxxxxxxxxxxxxxxeeeee	chr15:78780973-78781203(+)$1	230	126	151	20.3261
!!cccwwwwwwwwwwwwwwccc22f	chr1:47110734-47110981(-)$1	247	127	152	23.7073
[ddddwwwwwwwwwwwwwwdddddd	chr2:26607749-26607975(+)$1	226	122	147	22.8741
[ffffffuuuuuuuuuuuuffffff	chr9:20789455-20789671(+)$1	216	78	103	22.5305
fffffwwwwwwwwwwwwwwffffff	chr18:33744360-33744585(+)$1	225	15	40	23.2836
e[cccxxxxxxxxxxxxxxxcccee	chr9:139820038-139820268(+)$1	230	57	82	20.2027
ddd[cccuuuuuuuuuuuuccc]dd	chr14:35271964-35272187(-)$1	223	49	74	22.9338
ggggggguuuuuuuuuuuugggggg	chr4:39291492-39291722(-)$1	230	9	34	22.6776
eeeeevvvvvvvvvvvvveeeee:D	chr3:124732204-124732425(-)$1	221	18	43	21.1972
[cccxxxxxxxxxxxxxxxccc]ee	chr9:86300825-86301046(-)$1	221	32	57	20.2375
c[cccwwwwwwwwwwwwwwccc]cc	chr1:115282378-115282601(-)$1	223	10	35	24.1398
!cccxxxxxxxxxxxxxxxccc22d	chr10:97444240-97444463(-)$1	223	181	206	19.6408
ggeeeeeuuuuuuuuuuuueeeee6	chr5:137759685-137759908(+)$1	223	113	138	22.7535
eeeeeuuuuuuuuuuuueeeee]bb	chr11:6631096-6631319(+)$1	223	50	75	22.0100
iiiiiavvvvvvvvvvvvva]iiii	chr6:25466003-25466228(+)$1	225	61	86	23.5122
hhh[bbvvvvvvvvvvvvvbb]hhh	chr15:74706855-74707078(-)$1	223	169	194	21.6142
ffffffvvvvvvvvvvvvvffffff	chr2:27820864-27821086(+)$1	222	2	27	23.1033
[ffffffuuuuuuuuuuuuffffff	chr3:45781001-45781222(+)$1	221	169	194	22.5305
=====yyyyyyyyyyyyyyyy====	chr2:48718074-48718292(+)$1	218	81	106	21.8456
ff[cccvvvvvvvvvvvvvccc]ff	chr22:38694816-38695036(-)$1	220	176	201	23.9375
eeeeeuuuuuuuuuuuueeeee22c	chr4:436932-437156(-)$1	224	27	52	22.1256
f[eeeeeuuuuuuuuuuuueeeeef	chr2:105696363-105696590(+)$1	227	92	117	23.3585
fffffuuuuuuuuuuuuffffff:c	chr17:27957758-27957988(-)$1	230	124	149	20.4726
hhhh[bbuuuuuuuuuuuubb]hhh	chr7:92151316-92151546(-)$1	230	55	80	20.9582
c!!ddddtttttttttttdddd22c	chr6:17629462-17629683(-)$1	221	181	206	20.6941
gggggggtttttttttttggggggg	chr12:6691764-6691983(-)$1	219	46	71	20.8446
%%dddduuuuuuuuuuuuddddddd	chr20:30753056-30753278(+)$1	222	50	75	20.6578
eeeeewwwwwwwwwwwwwweeeee4	chr1:46425000-46425220(+)$1	220	119	144	23.9438
ffffffvvvvvvvvvvvvvffffff	chr1:235599631-235599852(+)$1	221	69	94	23.1033
ffffffvvvvvvvvvvvvvffffff	chr15:40498289-40498519(+)$1	230	11	36	23.1033
beeeeevvvvvvvvvvvvveeeee:	chr2:219114040-219114278(+)$1	238	179	204	22.6517
c[cccuuuuuuuuuuuucccccc]b	chr6:116973147-116973377(-)$1	230	138	163	22.1709
c[bbyyyyyyyyyyyyyyyybb]cc	chr4:175237258-175237484(+)$1	226	138	163	20.8876
[ddddwwwwwwwwwwwwwwdddd]b	chr17:71232068-71232298(+)$1	230	109	134	22.8908

#otherMatches

#Seq PSSM
UUCUACAUUCAUUCCAUUUAUGUUA	chr20:21321263-21321483(+)$1	220	69	94	21.2043
GAUGAACAUACAAACCUUUUCACAA	chr1:155447726-155447956(-)$1	230	96	121	22.4492
AGGCACCAUGCUGCCCAUGCCUCGU	chr7:45009205-45009431(-)$1	226	181	206	22.5768
GGGGGACAUAUUUUUCAGGUUCGCC	chr9:79972573-79972795(+)$1	222	16	41	21.1687
AAUUCGACAGUUUAUACAAGAGUUC	chr18:29488723-29488940(-)$1	217	142	167	23.2836
GGUUAGGUGAGUAUUAUUCCUACAC	chr9:135211598-135211828(-)$1	230	140	165	21.2000
CCUACCUGAUGAACAAGCUGGCUGG	chr1:89587445-89587662(-)$1	217	167	192	22.8990
UGGUGCUUUUUCUUGUUUUGCACUG	chr4:122737842-122738072(-)$1	230	109	134	23.9687
GUUUUUAGACUGGGCAUUUAGCUAU	chr10:88220899-88221123(-)$1	224	71	96	21.6812
AAAUUUAAAGAAAAAACAAGUUCUA	chr5:134029500-134029722(-)$1	222	16	41	21.4389
CCUCAGUAACAUUCCCUCCUUGAGU	chr16:67178140-67178370(+)$1	230	11	36	21.8863
GAGAUGAUCGGAGAAUUAAUCUGCU	chr3:63825249-63825470(-)$1	221	66	91	22.7050
UGGCACAACUCAUCUCAUCAAUGCC	chr6:138198248-138198478(+)$1	230	115	140	20.9085
GGUAUAAAGGAAUGUAAUGGUGCCU	chrX:13726759-13726989(+)$1	230	42	67	23.2836
CCUGGUCCUUACGGCCUCCGACGGG	chr5:140810757-140810979(+)$1	222	195	220	23.4010
CUCCAGUUUGAAUUCUUAUUUGGAA	chr16:57241872-57242102(+)$1	230	22	47	23.7041
UCAAGCUCUUACAUUAACAUUCUUA	chr4:56283979-56284198(+)$1	219	94	119	21.9666
CAACUCACUACCAUUCAUUAGUAGA	chr2:48033322-48033552(+)$1	230	110	135	24.1373
ACUCCUUUACAUCAUACUUGGACAU	chr14:31122642-31122863(+)$1	221	101	126	21.4492
CUCUGUCUUAUUUAGCUUAUUCAGC	chr6:99353410-99353628(-)$1	218	67	92	21.3482
GAAAACCAUCAUCUUCACCUUUUCA	chr6:100965791-100966021(-)$1	230	129	154	24.0398
CACACUUUAACCAAAAUCUGUGCGG	chr14:104026933-104027154(-)$1	221	103	128	24.2153
UGGGCUGGAGCUUUGAGAACAGCCU	chr11:73789580-73789799(-)$1	219	190	215	22.4163
GGUGAGCAUCAAACUCAAACUACGC	chrM:3537-3767(+)$1	230	128	153	22.7734
AUUAUAUUUUUUAAAGCACUGUGAU	chr5:133292436-133292663(-)$1	227	100	125	23.4155
UUGACGAUCUCAAGCACCGUCACCA	chr2:28805205-28805419(-)$1	214	101	126	20.5651
CACCUAUCCCUGUUGCAUUUAGAAG	chr17:26913037-26913260(-)$1	223	102	127	23.3795
GAAUUUGAAAACUGUUAAUGAUUCC	chr10:22615361-22615591(+)$1	230	185	210	23.2836
GUUCUCUCUUCUUUUUCUUAGAAUU	chr22:39477444-39477674(+)$1	230	10	35	23.7800
GACACAGAAAGAGAAGUAAGUGUUG	chr4:1725449-1725675(+)$1	226	133	158	22.9850
UAACCCAGAAGCUUUAUCAUCGGUU	chr13:73293029-73293253(-)$1	224	103	128	22.1168
AAGAUAAAAUAGAAGUAAGAGUCUU	chr15:78780973-78781203(+)$1	230	126	151	20.3261
CACUGCACUUAUAAAUAUUCAGGUA	chr1:47110734-47110981(-)$1	247	127	152	23.7073
UAUGGUUCCCUUAUUUUCUCCAUGC	chr2:26607749-26607975(+)$1	226	122	147	22.8741
UUGAAGACAAAGGACAAAAUCUUCA	chr9:20789455-20789671(+)$1	216	78	103	22.5305
AAAUGUUUUCUCUUCAGUUUAUUUU	chr18:33744360-33744585(+)$1	225	15	40	23.2836
CACAGACCUGUGUCCCCUCCCUGGG	chr9:139820038-139820268(+)$1	230	57	82	20.2027
UGAUGAUCCACCCACAUUUAUCUUC	chr14:35271964-35272187(-)$1	223	49	74	22.9338
AAGAAUUGUUUGGGACUUAGAUUUU	chr4:39291492-39291722(-)$1	230	9	34	22.6776
AGGGCCUCCUUUGCCUCUGCCCUCU	chr3:124732204-124732425(-)$1	221	18	43	21.1972
AUUUGCUGGAAAAAUUUUGAAAGAU	chr9:86300825-86301046(-)$1	221	32	57	20.2375
UUAGUGACUUAUUAACCAGACUUAA	chr1:115282378-115282601(-)$1	223	10	35	24.1398
CAGCAACACUUCAUCCUUCGCUUCA	chr10:97444240-97444463(-)$1	223	181	206	19.6408
UGACCACAUCAUUGCCUCAGUGGUA	chr5:137759685-137759908(+)$1	223	113	138	22.7535
AUCUGUUUUCUCUUCCUCAGAUUGA	chr11:6631096-6631319(+)$1	223	50	75	22.0100
GAGCACUUUCAUGUACUUUGUUGUU	chr6:25466003-25466228(+)$1	225	61	86	23.5122
CAUGUGCUUUACCUAACUACAGGUG	chr15:74706855-74707078(-)$1	223	169	194	21.6142
GUAAAAGAAUGUAUAGAAAUUUUGC	chr2:27820864-27821086(+)$1	222	2	27	23.1033
AAUGUUGACCUUUCUUUUACAACAU	chr3:45781001-45781222(+)$1	221	169	194	22.5305
GAUUGCAUCCUUCUUCAGCAACAAU	chr2:48718074-48718292(+)$1	218	81	106	21.8456
CUUCCGCAACCUCUUCCACCGGCAG	chr22:38694816-38695036(-)$1	220	176	201	23.9375
UGAAUCAACACAAGAAAAUUCAUAC	chr4:436932-437156(-)$1	224	27	52	22.1256
AAGAUGGCCGUCCAUUUCACUAUCU	chr2:105696363-105696590(+)$1	227	92	117	23.3585
AUGUGAUUCUGAGCCUACACAUGUG	chr17:27957758-27957988(-)$1	230	124	149	20.4726
UAGUGAUCAAGGUGAAAAUGUGGCU	chr7:92151316-92151546(-)$1	230	55	80	20.9582
UAAGAAUGAUAAUUUUAAGUUUGGA	chr6:17629462-17629683(-)$1	221	181	206	20.6941
ACCUGGGUUUCUUCUUCCCCUAGGU	chr12:6691764-6691983(-)$1	219	46	71	20.8446
GUGGAGUUCAUCCCCUCUCUCCUCU	chr20:30753056-30753278(+)$1	222	50	75	20.6578
GGCCACACUCACCACUCCAUGGCCA	chr1:46425000-46425220(+)$1	220	119	144	23.9438
GUUAGAACAAUUAAUCCUCUCUGAC	chr1:235599631-235599852(+)$1	221	69	94	23.1033
ACUGAGCUAAUAUGUCUCUCUCAGU	chr15:40498289-40498519(+)$1	230	11	36	23.1033
CUCUGGGUCUUUUCCUCCACCAGAA	chr2:219114040-219114278(+)$1	238	179	204	22.6517
UGUGGUUACAGAAAUUUCCAAAUGC	chr6:116973147-116973377(-)$1	230	138	163	22.1709
AGAGCCUCUACUGUUAAUUACUGUG	chr4:175237258-175237484(+)$1	226	138	163	20.8876
AUAGAAAAUAUUCCUCAACUCUACC	chr17:71232068-71232298(+)$1	230	109	134	22.8908

#DB
((((((((...........))).))	chr20:21321263-21321483(+)$1	1	69	94	21.2043
..((((............))))..)	chr1:155447726-155447956(-)$1	1	96	121	22.4492
(((((............))))).))	chr7:45009205-45009431(-)$1	1	181	206	22.5768
((.((((...........)))).))	chr9:79972573-79972795(+)$1	1	16	41	21.1687
(((((..............))))))	chr18:29488723-29488940(-)$1	1	142	167	23.2836
(((((((...........)))).))	chr9:135211598-135211828(-)$1	1	140	165	21.2000
((((((.............)).)))	chr1:89587445-89587662(-)$1	1	167	192	22.8990
.(((((.............))))))	chr4:122737842-122738072(-)$1	1	109	134	23.9687
(((................))))).	chr10:88220899-88221123(-)$1	1	71	96	21.6812
((((((...........))))).))	chr5:134029500-134029722(-)$1	1	16	41	21.4389
.(((((.............))))).	chr16:67178140-67178370(+)$1	1	11	36	21.8863
(((((.............)))).))	chr3:63825249-63825470(-)$1	1	66	91	22.7050
)((((................))))	chr6:138198248-138198478(+)$1	1	115	140	20.9085
(((((..............))))))	chrX:13726759-13726989(+)$1	1	42	67	23.2836
(((.(((............))).))	chr5:140810757-140810979(+)$1	1	195	220	23.4010
.(((((.............))))).	chr16:57241872-57242102(+)$1	1	22	47	23.7041
(.(((................))))	chr4:56283979-56284198(+)$1	1	94	119	21.9666
(.(((..............))).))	chr2:48033322-48033552(+)$1	1	110	135	24.1373
))(((..............)))..(	chr14:31122642-31122863(+)$1	1	101	126	21.4492
(.(((................))).	chr6:99353410-99353628(-)$1	1	67	92	21.3482
(((((..............)))))(	chr6:100965791-100966021(-)$1	1	129	154	24.0398
(.(((..............))).))	chr14:104026933-104027154(-)$1	1	103	128	24.2153
(((((((............))))))	chr11:73789580-73789799(-)$1	1	190	215	22.4163
((((((.............)).)))	chrM:3537-3767(+)$1	1	128	153	22.7734
((((((.............))))))	chr5:133292436-133292663(-)$1	1	100	125	23.4155
(.((((...........))))))))	chr2:28805205-28805419(-)$1	1	101	126	20.5651
(..(((.............)))..)	chr17:26913037-26913260(-)$1	1	102	127	23.3795
(((((..............))))))	chr10:22615361-22615591(+)$1	1	185	210	23.2836
(((((..............))))).	chr22:39477444-39477674(+)$1	1	10	35	23.7800
(((((..............))))))	chr4:1725449-1725675(+)$1	1	133	158	22.9850
(((((................))))	chr13:73293029-73293253(-)$1	1	103	128	22.1168
(((((...............)))))	chr15:78780973-78781203(+)$1	1	126	151	20.3261
..(((..............)))..)	chr1:47110734-47110981(-)$1	1	127	152	23.7073
.((((..............))))))	chr2:26607749-26607975(+)$1	1	122	147	22.8741
.((((((............))))))	chr9:20789455-20789671(+)$1	1	78	103	22.5305
(((((..............))))))	chr18:33744360-33744585(+)$1	1	15	40	23.2836
(.(((...............)))))	chr9:139820038-139820268(+)$1	1	57	82	20.2027
(((.(((............))).))	chr14:35271964-35272187(-)$1	1	49	74	22.9338
(((((((............))))))	chr4:39291492-39291722(-)$1	1	9	34	22.6776
(((((.............))))).(	chr3:124732204-124732425(-)$1	1	18	43	21.1972
.(((...............))).))	chr9:86300825-86301046(-)$1	1	32	57	20.2375
(.(((..............))).))	chr1:115282378-115282601(-)$1	1	10	35	24.1398
.(((...............)))..)	chr10:97444240-97444463(-)$1	1	181	206	19.6408
(((((((............))))).	chr5:137759685-137759908(+)$1	1	113	138	22.7535
(((((............))))).))	chr11:6631096-6631319(+)$1	1	50	75	22.0100
((((((.............).))))	chr6:25466003-25466228(+)$1	1	61	86	23.5122
(((.((.............)).)))	chr15:74706855-74707078(-)$1	1	169	194	21.6142
((((((.............))))))	chr2:27820864-27821086(+)$1	1	2	27	23.1033
.((((((............))))))	chr3:45781001-45781222(+)$1	1	169	194	22.5305
(((((................))))	chr2:48718074-48718292(+)$1	1	81	106	21.8456
((.(((.............))).))	chr22:38694816-38695036(-)$1	1	176	201	23.9375
(((((............)))))..)	chr4:436932-437156(-)$1	1	27	52	22.1256
(.(((((............))))))	chr2:105696363-105696590(+)$1	1	92	117	23.3585
(((((............)))))).(	chr17:27957758-27957988(-)$1	1	124	149	20.4726
((((.((............)).)))	chr7:92151316-92151546(-)$1	1	55	80	20.9582
(..((((...........))))..)	chr6:17629462-17629683(-)$1	1	181	206	20.6941
(((((((...........)))))))	chr12:6691764-6691983(-)$1	1	46	71	20.8446
..((((............)))))))	chr20:30753056-30753278(+)$1	1	50	75	20.6578
(((((..............))))).	chr1:46425000-46425220(+)$1	1	119	144	23.9438
((((((.............))))))	chr1:235599631-235599852(+)$1	1	69	94	23.1033
((((((.............))))))	chr15:40498289-40498519(+)$1	1	11	36	23.1033
)(((((.............))))).	chr2:219114040-219114278(+)$1	1	179	204	22.6517
(.(((............)))))).)	chr6:116973147-116973377(-)$1	1	138	163	22.1709
(.((................)).))	chr4:175237258-175237484(+)$1	1	138	163	20.8876
.((((..............)))).)	chr17:71232068-71232298(+)$1	1	109	134	22.8908

#PSSM
e : 0.24	f : 0.18	c : 0.10	g : 0.09	[ : 0.09	! : 0.06	d : 0.06	b : 0.03	i : 0.03	= : 0.03	h : 0.03	: : 0.01	% : 0.01	
e : 0.27	f : 0.18	[ : 0.15	d : 0.09	g : 0.07	! : 0.06	c : 0.04	i : 0.03	= : 0.03	h : 0.03	% : 0.01	
e : 0.29	c : 0.18	f : 0.16	d : 0.12	g : 0.06	[ : 0.03	i : 0.03	= : 0.03	! : 0.03	h : 0.03	b : 0.01	
e : 0.27	c : 0.20	f : 0.16	d : 0.15	[ : 0.04	g : 0.04	i : 0.03	= : 0.03	y : 0.01	h : 0.01	b : 0.01	
e : 0.26	c : 0.20	f : 0.16	d : 0.15	b : 0.04	g : 0.04	y : 0.03	i : 0.03	x : 0.03	= : 0.01	[ : 0.01	
w : 0.23	e : 0.10	y : 0.10	d : 0.09	c : 0.07	u : 0.07	f : 0.07	b : 0.06	x : 0.06	g : 0.04	v : 0.03	i : 0.01	a : 0.01	
v : 0.24	w : 0.23	u : 0.10	y : 0.10	x : 0.06	c : 0.04	d : 0.04	t : 0.03	f : 0.03	g : 0.03	e : 0.03	i : 0.01	b : 0.01	
u : 0.24	v : 0.24	w : 0.23	y : 0.10	t : 0.09	x : 0.06	c : 0.01	
u : 0.24	v : 0.24	w : 0.23	t : 0.10	y : 0.10	x : 0.06	
u : 0.24	v : 0.24	w : 0.23	t : 0.10	y : 0.10	x : 0.06	
u : 0.24	v : 0.24	w : 0.23	t : 0.10	y : 0.10	x : 0.06	
u : 0.24	v : 0.24	w : 0.23	t : 0.10	y : 0.10	x : 0.06	
u : 0.24	v : 0.24	w : 0.23	t : 0.10	y : 0.10	x : 0.06	
u : 0.24	v : 0.24	w : 0.23	t : 0.10	y : 0.10	x : 0.06	
u : 0.24	v : 0.24	w : 0.23	t : 0.10	y : 0.10	x : 0.06	
u : 0.24	v : 0.24	w : 0.23	t : 0.10	y : 0.10	x : 0.06	
u : 0.24	v : 0.24	w : 0.23	t : 0.10	y : 0.10	x : 0.06	
v : 0.24	w : 0.23	u : 0.16	y : 0.10	t : 0.07	e : 0.06	x : 0.06	d : 0.01	f : 0.01	c : 0.01	
w : 0.23	v : 0.21	u : 0.13	d : 0.10	y : 0.10	e : 0.07	x : 0.06	t : 0.01	f : 0.01	g : 0.01	c : 0.01	
e : 0.24	c : 0.20	f : 0.15	d : 0.13	y : 0.09	b : 0.06	g : 0.04	x : 0.03	i : 0.01	a : 0.01	
e : 0.26	c : 0.21	f : 0.15	d : 0.13	b : 0.07	y : 0.07	g : 0.04	i : 0.01	] : 0.01	
e : 0.27	c : 0.26	f : 0.15	d : 0.13	] : 0.06	g : 0.04	i : 0.03	= : 0.01	b : 0.01	
] : 0.23	e : 0.23	f : 0.15	2 : 0.09	c : 0.07	d : 0.06	g : 0.04	i : 0.03	= : 0.03	h : 0.03	: : 0.01	
e : 0.29	f : 0.18	c : 0.10	2 : 0.09	g : 0.07	d : 0.06	: : 0.04	i : 0.03	= : 0.03	h : 0.03	] : 0.03	b : 0.01	
f : 0.23	e : 0.15	c : 0.12	g : 0.09	d : 0.09	2 : 0.04	b : 0.04	: : 0.03	i : 0.03	= : 0.03	D : 0.03	h : 0.03	a : 0.01	] : 0.01	6 : 0.01	4 : 0.01	

#score	1452.5538472864432
#seq	65
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_CDS_m3_run1.txt

#BEAR
gggggg[ddddnnnnndddd]ggggggg	chr1:29068822-29069055(+)$1	233	152	180	10.4517
ff####eeeeeooooooeeeee4444ff	chr20:5096019-5096248(-)$1	229	68	96	12.7300
a"""a!!ddddoooooodddd22a333a	chr2:136622483-136622733(-)$1	250	54	82	14.9338
h"""eeeee[aooooooa]eeeee22hh	chr4:87685682-87685914(+)$1	232	184	212	12.3714
"""eeeeecccooooooccc22eeeee4	chr5:123983379-123983623(-)$1	244	170	198	13.4852
ccc####ddddoooooodddd]ccc22b	chr13:42874991-42875230(+)$1	239	138	166	14.0989
bbbb!!eeeeeooooooeeeee22bb]b	chr10:5798549-5798770(+)$1	221	90	118	11.4165
iiiiii[ddddooooooddddiiiiiii	chr19:21719465-21719699(+)$1	234	38	66	14.7804
===========nnnnn===========:	chr2:183888494-183888725(-)$1	231	36	64	10.8637
===ccc[ddddoooooodddd22ccc]=	chr11:108384522-108384751(-)$1	229	14	42	14.3172
gggggg!!cccooooooccc]ggggggg	chr13:42875145-42875374(+)$1	229	176	204	15.5921
iiiiiiiddddoooooodddd333iiii	chr9:106894230-106894456(+)$1	226	46	74	14.8530
c[==========lll==========]cc	chr2:48027672-48027920(+)$1	248	3	31	11.6959
iiiccc!!cccooooooccc]ccceeee	chr5:53839079-53839314(+)$1	235	153	181	14.5803
c!!dddd!!bboooooobb22dddd22c	chr14:60749716-60749952(+)$1	236	69	97	12.0492
hccc[a[ddddoooooodddd]a]cccG	chr3:47162233-47162458(-)$1	225	46	74	13.3388
ggggg####cccnnnnnccc22gggggg	chr22:41645661-41645889(-)$1	228	56	84	10.4785
ffff[ffffffooooooffffff>>>>>	chr11:19256386-19256608(-)$1	222	121	149	10.7925
ebb[gggggggooooooggggggg]bb:	chr2:232324872-232325098(-)$1	226	109	137	12.5058
eee[dddd[bboooooobb]dddd]eee	chr19:21719640-21719867(+)$1	227	74	102	11.2845
a!!ccceeeeeooooooeeeee]ccc22	chr11:68305049-68305272(+)$1	223	122	150	13.4737
c!!gggggggbboooooobb]ggggggg	chr17:27977576-27977799(-)$1	223	39	67	12.7088
cc[ccc!!cccooooooccc22ccc22c	chr21:43413146-43413445(-)$1	299	158	186	15.0757
eeee[ccc[bboooooobb22ccc]eee	chrX:123020157-123020385(+)$1	228	118	146	12.0263
f============lll============	chr10:120489709-120489929(-)$1	220	130	158	11.5880
$$$$ccc[cccooooooccccccdddd2	chr10:5791345-5791571(+)$1	226	162	190	12.9029
c[iiiiiiiiiooooooiiiiiiiii22	chr14:39648514-39648741(+)$1	227	61	89	15.3368
ggggggg[cccooooooccc]ggggggg	chr1:155449453-155449693(-)$1	240	13	41	15.4054
:eeeee!!cccooooooccc22eeeee:	chr21:34926425-34926660(+)$1	235	51	79	11.8900
!!ggggggg[aooooooa]ggggggg22	chr10:5781814-5782041(+)$1	227	156	184	14.6844
f[bbgggggggooooooggggggg333b	chr15:65962286-65962507(-)$1	221	24	52	14.1919
cddddccc[bboooooobbccc22dddd	chr2:170402804-170403059(-)$1	255	19	47	11.2372
!!ccc[eeeeeooooooeeeeeccc22c	chr2:219093367-219093599(+)$1	232	9	37	13.4944
ffff"""ddddoooooodddd22fffff	chr13:32914697-32914915(+)$1	218	189	217	12.9969
cciiiiiiiiiooooooiiiiiiiii22	chr1:16255779-16256028(+)$1	249	173	201	15.1489
:cccccc[cccooooooccc]ccc]ccc	chr6:56357701-56357971(-)$1	270	73	101	13.6687
eeeee!!ddddooooooddddeeeeeee	chr9:74489596-74489826(-)$1	230	76	104	12.6267
cggggggg[arrrrrrrrra]ggggggg	chr3:142754787-142755011(+)$1	224	110	138	9.7778
ccc[bb[ddddoooooodddd]bb]ccc	chr20:57015873-57016099(+)$1	226	94	122	13.0955
::ccc!!ddddoooooodddd333ccc:	chr17:1559654-1559880(-)$1	226	55	83	11.8873
[a"""bb[cccooooooccc]bb333a]	chr1:203769485-203769713(+)$1	228	33	61	14.1652
fffff"""cccooooooccc]ffffff2	chr2:20482748-20482973(-)$1	225	176	204	13.5383
ggg"""a[cccooooooccc]a22gggg	chr9:133730348-133730569(+)$1	221	49	77	15.0112
===========lll===========333	chr17:27014012-27014241(+)$1	229	8	36	12.1496
GGiiiiiiiiiooooooiiiiiiiii::	chr6:149700408-149700634(+)$1	226	73	101	12.2862
c!!hhhhhhhhoooooohhhhhhhh22c	chr6:49459809-49460031(+)$1	222	172	200	12.4145
ggggggg[cccoooooocccggggggg5	chr1:35580249-35580471(+)$1	222	174	202	14.5544
ccc[gggggggooooooggggggg]ccc	chr3:56667308-56667535(-)$1	227	169	197	14.4371

#otherMatches

#Seq PSSM
GGCUUCUCCUAUUCUUUGGGUGAAGCUG	chr1:29068822-29069055(+)$1	233	152	180	10.4517
UGCACUGAGGUACCUGAACUUCUUUACA	chr20:5096019-5096248(-)$1	229	68	96	12.7300
CAAAUGACUGUGAAAGAAUGGGAGAAAG	chr2:136622483-136622733(-)$1	250	54	82	14.9338
UAAGUGUCACGGUACUGUUUGACAAGGU	chr4:87685682-87685914(+)$1	232	184	212	12.3714
GCAUGGCCAGUAUCAAAGCUGAGGCCGA	chr5:123983379-123983623(-)$1	244	170	198	13.4852
GCAAUUAUGGUGACAAAACCAGUGCAGG	chr13:42874991-42875230(+)$1	239	138	166	14.0989
GAGAGAAUGAUACACUAAUCAUCAUCAU	chr10:5798549-5798770(+)$1	221	90	118	11.4165
ACUAACCAUAAGAGAAUUUAUGUUGGUG	chr19:21719465-21719699(+)$1	234	38	66	14.7804
GAAGAAGGGUGCAUUUCACUUUUUUUUA	chr2:183888494-183888725(-)$1	231	36	64	10.8637
AUUCAGUUCUUCUGACAGAGACUUUGAA	chr11:108384522-108384751(-)$1	229	14	42	14.3172
GGUGAUUCUGCCCAAGUGCAUAUUGCCA	chr13:42875145-42875374(+)$1	229	176	204	15.5921
UUUUAUCUCAUAGUACAAUGACUUGAUG	chr9:106894230-106894456(+)$1	226	46	74	14.8530
AAGAAGAAGAUUAUUGAUUUUCUUUCUG	chr2:48027672-48027920(+)$1	248	3	31	11.6959
GAAGCUCUUCACAAAUAUGAUAGUGUUU	chr5:53839079-53839314(+)$1	235	153	181	14.5803
CAGAUAGAAGUGGGUCAACAGCUGUAGG	chr14:60749716-60749952(+)$1	236	69	97	12.0492
UUCCUCUUGUGAGAUACCACAUGUGGAU	chr3:47162233-47162458(-)$1	225	46	74	13.3388
UCUGCCCUACAGAUGCCCUGAUGCAGAA	chr22:41645661-41645889(-)$1	228	56	84	10.4785
UGGCACCUUGAAGAGCAUCGGGGAGGAG	chr11:19256386-19256608(-)$1	222	121	149	10.7925
CGGCUUUCAAUCUCUUUGUUGGAAACCU	chr2:232324872-232325098(-)$1	226	109	137	12.5058
GUGAUGAAUGUGGCAAAACCUUUAGCAU	chr19:21719640-21719867(+)$1	227	74	102	11.2845
GACACACUUCUAGAAAGAGAAGAUGUAA	chr11:68305049-68305272(+)$1	223	122	150	13.4737
GAGUAUCAUAACAUUCGGGUAUAUGAUG	chr17:27977576-27977799(-)$1	223	39	67	12.7088
CUUGUUGUACUAUUCAAAGUUAGGCUUA	chr21:43413146-43413445(-)$1	299	158	186	15.0757
AUCUUCCAAGAAAUCCAUCCAUGGCAGA	chrX:123020157-123020385(+)$1	228	118	146	12.0263
ACAGGUAAGUUAAGAUUUAAUUUGCUUG	chr10:120489709-120489929(-)$1	220	130	158	11.5880
ACAGUUGUGGAGUCAGAUCCCAGACCAC	chr10:5791345-5791571(+)$1	226	162	190	12.9029
ACUAAGACAAAGCCCCAUUUGUUUUAUA	chr14:39648514-39648741(+)$1	227	61	89	15.3368
GAAAGAAACUGUUGAAUCAGAUUCUUUC	chr1:155449453-155449693(-)$1	240	13	41	15.4054
CUAGUGGUGGUAGUGAAGCUGACAUUGA	chr21:34926425-34926660(+)$1	235	51	79	11.8900
UUAGCCAAGAUGAAGAAAGCUUGGUUCC	chr10:5781814-5782041(+)$1	227	156	184	14.6844
UUGUCCAUGAUGAGGAAAUCAUGGCUGG	chr15:65962286-65962507(-)$1	221	24	52	14.1919
GCAUGAUCACAUGUAUUUGGAUAAUAUG	chr2:170402804-170403059(-)$1	255	19	47	11.2372
UUGUGGCCUACGGCAAGGUAGGCGCUUG	chr2:219093367-219093599(+)$1	232	9	37	13.4944
UAUCAAAUAACUUAAAUGUUGAAGGUGG	chr13:32914697-32914915(+)$1	218	189	217	12.9969
CUGUUGGGUCUGGCUCAAGGCCCAGCUC	chr1:16255779-16256028(+)$1	249	173	201	15.1489
UGUCCUUGCAGACUAAACUGGAAGAGGC	chr6:56357701-56357971(-)$1	270	73	101	13.6687
UUUGUACGUUGUUCACCCAAUGCGAAAU	chr9:74489596-74489826(-)$1	230	76	104	12.6267
AAAUAUUUUCUUAGGACUUGUAAAUAUU	chr3:142754787-142755011(+)$1	224	110	138	9.7778
UGUAGAAAUAAAUAAAAUUAUAUCCACA	chr20:57015873-57016099(+)$1	226	94	122	13.0955
AAGGAUCGGAGCUCCAACUCCCUUUCCA	chr17:1559654-1559880(-)$1	226	55	83	11.8873
ACGUUGGUUCUGAGCUGGGAUCCUGAGC	chr1:203769485-203769713(+)$1	228	33	61	14.1652
GUCAACCUGGAAGUACAUCUCUUGGCUU	chr2:20482748-20482973(-)$1	225	176	204	13.5383
AGAGCAGUCCUGGCCAGAGGUCCAUCUC	chr9:133730348-133730569(+)$1	221	49	77	15.0112
GAUUUAAACCAGAAUGGUUUGGAUUUCC	chr17:27014012-27014241(+)$1	229	8	36	12.1496
ACCAGGGGUGGUGUCCCCUACCUUUGAA	chr6:149700408-149700634(+)$1	226	73	101	12.2862
AUCUUAAAGAGUGUUUUUUUUUUAGAUU	chr6:49459809-49460031(+)$1	222	172	200	12.4145
UAUUUAAAUGGAAUGAACCAUUAAAUGA	chr1:35580249-35580471(+)$1	222	174	202	14.5544
UUCCACUUCGGCUUUAACUGAAGUAGAA	chr3:56667308-56667535(-)$1	227	169	197	14.4371

#DB
((((((.((((.....)))).)))))))	chr1:29068822-29069055(+)$1	1	152	180	10.4517
((....(((((......)))))....))	chr20:5096019-5096248(-)$1	1	68	96	12.7300
(...(..((((......))))..)...)	chr2:136622483-136622733(-)$1	1	54	82	14.9338
(...(((((.(......).)))))..))	chr4:87685682-87685914(+)$1	1	184	212	12.3714
...((((((((......)))..))))).	chr5:123983379-123983623(-)$1	1	170	198	13.4852
(((....((((......)))).)))..)	chr13:42874991-42875230(+)$1	1	138	166	14.0989
((((..(((((......)))))..)).)	chr10:5798549-5798770(+)$1	1	90	118	11.4165
((((((.((((......)))))))))))	chr19:21719465-21719699(+)$1	1	38	66	14.7804
(((((((((((.....))))))))))).	chr2:183888494-183888725(-)$1	1	36	64	10.8637
((((((.((((......))))..))).)	chr11:108384522-108384751(-)$1	1	14	42	14.3172
((((((..(((......))).)))))))	chr13:42875145-42875374(+)$1	1	176	204	15.5921
(((((((((((......))))...))))	chr9:106894230-106894456(+)$1	1	46	74	14.8530
(.((((((((((...)))))))))).))	chr2:48027672-48027920(+)$1	1	3	31	11.6959
)))(((..(((......))).)))((((	chr5:53839079-53839314(+)$1	1	153	181	14.5803
(..((((..((......))..))))..)	chr14:60749716-60749952(+)$1	1	69	97	12.0492
)(((.(.((((......)))).).))))	chr3:47162233-47162458(-)$1	1	46	74	13.3388
(((((....(((.....)))..))))))	chr22:41645661-41645889(-)$1	1	56	84	10.4785
((((.((((((......)))))).....	chr11:19256386-19256608(-)$1	1	121	149	10.7925
)((.(((((((......))))))).)).	chr2:232324872-232325098(-)$1	1	109	137	12.5058
(((.((((.((......)).)))).)))	chr19:21719640-21719867(+)$1	1	74	102	11.2845
(..((((((((......))))).)))..	chr11:68305049-68305272(+)$1	1	122	150	13.4737
(..(((((((((......)).)))))))	chr17:27977576-27977799(-)$1	1	39	67	12.7088
((.(((..(((......)))..)))..)	chr21:43413146-43413445(-)$1	1	158	186	15.0757
((((.(((.((......))..))).)))	chrX:123020157-123020385(+)$1	1	118	146	12.0263
)((((((((((((...))))))))))))	chr10:120489709-120489929(-)$1	1	130	158	11.5880
....(((.(((......)))))))))).	chr10:5791345-5791571(+)$1	1	162	190	12.9029
(.(((((((((......)))))))))..	chr14:39648514-39648741(+)$1	1	61	89	15.3368
(((((((.(((......))).)))))))	chr1:155449453-155449693(-)$1	1	13	41	15.4054
.(((((..(((......)))..))))).	chr21:34926425-34926660(+)$1	1	51	79	11.8900
..(((((((.(......).)))))))..	chr10:5781814-5782041(+)$1	1	156	184	14.6844
(.(((((((((......)))))))...)	chr15:65962286-65962507(-)$1	1	24	52	14.1919
((((((((.((......)))))..))))	chr2:170402804-170403059(-)$1	1	19	47	11.2372
..(((.(((((......))))))))..)	chr2:219093367-219093599(+)$1	1	9	37	13.4944
((((...((((......))))..)))))	chr13:32914697-32914915(+)$1	1	189	217	12.9969
(((((((((((......)))))))))..	chr1:16255779-16256028(+)$1	1	173	201	15.1489
.((((((.(((......))).))).)))	chr6:56357701-56357971(-)$1	1	73	101	13.6687
(((((..((((......)))))))))))	chr9:74489596-74489826(-)$1	1	76	104	12.6267
((((((((.(.........).)))))))	chr3:142754787-142755011(+)$1	1	110	138	9.7778
(((.((.((((......)))).)).)))	chr20:57015873-57016099(+)$1	1	94	122	13.0955
..(((..((((......))))...))).	chr17:1559654-1559880(-)$1	1	55	83	11.8873
.(...((.(((......))).))...).	chr1:203769485-203769713(+)$1	1	33	61	14.1652
(((((...(((......))).)))))).	chr2:20482748-20482973(-)$1	1	176	204	13.5383
(((...(.(((......))).)..))))	chr9:133730348-133730569(+)$1	1	49	77	15.0112
(((((((((((...)))))))))))...	chr17:27014012-27014241(+)$1	1	8	36	12.1496
(((((((((((......)))))))))..	chr6:149700408-149700634(+)$1	1	73	101	12.2862
(..((((((((......))))))))..)	chr6:49459809-49460031(+)$1	1	172	200	12.4145
(((((((.(((......)))))))))).	chr1:35580249-35580471(+)$1	1	174	202	14.5544
(((.(((((((......))))))).)))	chr3:56667308-56667535(-)$1	1	169	197	14.4371

#PSSM
c : 0.25	g : 0.12	f : 0.12	e : 0.08	i : 0.06	= : 0.06	: : 0.06	a : 0.04	h : 0.04	! : 0.04	" : 0.02	b : 0.02	$ : 0.02	[ : 0.02	G : 0.02	
g : 0.14	c : 0.14	! : 0.12	f : 0.08	= : 0.08	e : 0.08	" : 0.06	i : 0.06	[ : 0.06	b : 0.04	$ : 0.02	d : 0.02	: : 0.02	a : 0.02	G : 0.02	
g : 0.16	c : 0.14	i : 0.12	= : 0.10	" : 0.08	! : 0.08	e : 0.08	b : 0.06	f : 0.06	# : 0.02	[ : 0.02	$ : 0.02	d : 0.02	
g : 0.16	c : 0.16	i : 0.10	" : 0.08	e : 0.08	= : 0.08	[ : 0.08	f : 0.06	# : 0.04	b : 0.04	d : 0.04	$ : 0.02	h : 0.02	
g : 0.22	c : 0.16	i : 0.10	e : 0.08	= : 0.08	d : 0.06	[ : 0.06	" : 0.06	# : 0.04	a : 0.02	! : 0.02	b : 0.02	f : 0.02	h : 0.02	
g : 0.20	c : 0.16	i : 0.10	! : 0.08	= : 0.08	# : 0.06	e : 0.06	" : 0.06	d : 0.04	b : 0.04	a : 0.02	f : 0.02	[ : 0.02	h : 0.02	
g : 0.16	! : 0.14	e : 0.12	[ : 0.10	= : 0.08	i : 0.08	c : 0.08	# : 0.04	d : 0.04	" : 0.04	f : 0.02	b : 0.02	a : 0.02	h : 0.02	
d : 0.25	e : 0.12	g : 0.12	[ : 0.12	! : 0.10	= : 0.08	i : 0.06	c : 0.04	# : 0.02	f : 0.02	" : 0.02	h : 0.02	
c : 0.25	d : 0.22	e : 0.10	g : 0.10	= : 0.08	[ : 0.08	i : 0.06	! : 0.02	# : 0.02	f : 0.02	h : 0.02	
c : 0.27	d : 0.22	e : 0.08	= : 0.08	b : 0.08	g : 0.08	i : 0.06	[ : 0.04	f : 0.02	a : 0.02	h : 0.02	
c : 0.27	d : 0.22	b : 0.10	e : 0.08	= : 0.08	g : 0.06	i : 0.06	a : 0.04	f : 0.02	r : 0.02	h : 0.02	
o : 0.83	n : 0.04	= : 0.04	c : 0.02	b : 0.02	r : 0.02	l : 0.02	
o : 0.85	n : 0.06	l : 0.04	= : 0.02	r : 0.02	
o : 0.85	n : 0.06	l : 0.06	r : 0.02	
o : 0.85	n : 0.06	l : 0.04	r : 0.02	= : 0.02	
o : 0.85	n : 0.06	= : 0.04	l : 0.02	r : 0.02	
o : 0.85	= : 0.08	d : 0.02	n : 0.02	r : 0.02	
c : 0.27	d : 0.22	e : 0.08	= : 0.08	b : 0.08	g : 0.06	i : 0.06	a : 0.04	f : 0.02	o : 0.02	r : 0.02	h : 0.02	
c : 0.27	d : 0.22	b : 0.10	e : 0.08	= : 0.08	g : 0.06	i : 0.06	] : 0.04	f : 0.02	r : 0.02	h : 0.02	
c : 0.29	d : 0.22	e : 0.10	= : 0.08	g : 0.08	i : 0.06	2 : 0.04	f : 0.02	] : 0.02	b : 0.02	a : 0.02	h : 0.02	
d : 0.22	] : 0.20	2 : 0.12	e : 0.10	g : 0.10	= : 0.08	i : 0.06	c : 0.04	f : 0.02	h : 0.02	
g : 0.20	2 : 0.14	e : 0.12	c : 0.10	i : 0.08	= : 0.08	] : 0.06	3 : 0.04	d : 0.04	f : 0.04	b : 0.02	a : 0.02	h : 0.02	
g : 0.22	c : 0.14	2 : 0.12	e : 0.08	i : 0.08	= : 0.08	3 : 0.04	d : 0.04	f : 0.04	b : 0.04	4 : 0.02	a : 0.02	] : 0.02	h : 0.02	
g : 0.22	c : 0.16	e : 0.08	i : 0.08	= : 0.08	2 : 0.06	3 : 0.06	d : 0.06	f : 0.04	4 : 0.02	a : 0.02	] : 0.02	> : 0.02	b : 0.02	h : 0.02	
g : 0.18	c : 0.14	] : 0.12	i : 0.10	e : 0.08	= : 0.08	3 : 0.06	d : 0.06	f : 0.04	4 : 0.02	2 : 0.02	b : 0.02	> : 0.02	h : 0.02	
g : 0.18	c : 0.14	2 : 0.12	e : 0.12	i : 0.10	3 : 0.08	b : 0.04	= : 0.04	d : 0.04	f : 0.04	4 : 0.02	] : 0.02	> : 0.02	
2 : 0.18	g : 0.16	e : 0.12	c : 0.12	f : 0.06	3 : 0.06	] : 0.04	i : 0.04	= : 0.04	d : 0.04	h : 0.02	> : 0.02	b : 0.02	a : 0.02	: : 0.02	
c : 0.16	g : 0.14	2 : 0.12	: : 0.10	e : 0.08	b : 0.06	f : 0.04	i : 0.04	= : 0.04	a : 0.02	h : 0.02	4 : 0.02	G : 0.02	> : 0.02	d : 0.02	] : 0.02	3 : 0.02	5 : 0.02	

#score	628.3954720823064
#seq	48
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_UTR_m3_run2.txt

#BEAR
========qqqqqqqq========	chr9:14617620-14617847(-)$1	227	185	209	16.6973
bb"""cccqqqqqqqqccc]bb::	chr17:46699108-46699328(-)$1	220	7	31	13.1465
eeee[cccqqqqqqqqccc]eeee	chr7:36493098-36493326(+)$1	228	75	99	15.4175
!gggggggqqqqqqqqggggggg2	chr9:114983369-114983595(-)$1	226	53	77	16.3644
iiiiiiiiqqqqqqqqiiiiiiii	chr15:64429982-64430229(+)$1	247	105	129	16.9553
cbb[ddddqqqqqqqqdddd]bb]	chr15:44854867-44855092(+)$1	225	57	81	14.7034
hhhhhhhhqqqqqqqqhhhhhhhh	chr4:129190487-129190727(-)$1	240	111	135	15.0088
####ddddqqqqqqqqddddbb22	chr6:105528965-105529197(+)$1	232	177	201	14.4055
dd!!ddddqqqqqqqqdddd333d	chr5:151186435-151186664(+)$1	229	3	27	15.1184
========qqqqqqqq========	chr1:158069882-158070140(+)$1	258	74	98	16.6973
hhhhhhhhqqqqqqqqhhhhhhhh	chr8:104084337-104084564(+)$1	227	125	149	15.0088
cc[cccbbqqqqqqqqbb]ccc]c	chr15:100252957-100253208(+)$1	251	77	101	15.3134
========qqqqqqqq========	chr8:38127321-38127547(-)$1	226	10	34	16.6973
$gggggggqqqqqqqqggggggg]	chr2:206861365-206861608(-)$1	243	55	79	16.2629
!!ffffffqqqqqqqqffffffcc	chrX:131761047-131761280(-)$1	233	36	60	14.5448
ggccc!!aqqqqqqqqa22ccc]g	chr20:52183640-52183863(-)$1	223	189	213	15.2019
ccffffffqqqqqqqqffffff77	chr1:243663001-243663233(-)$1	232	22	46	12.9754
ddd[ddddqqqqqqqqdddd]ddd	chr5:106713753-106713985(-)$1	232	176	200	14.5593
hhhh[cccqqqqqqqqccc333hh	chr4:38702484-38702754(+)$1	270	103	127	16.0016
ggg!!cccqqqqqqqqccc4444g	chr14:71577789-71578015(+)$1	226	190	214	16.0886
ddd[ddddqqqqqqqqdddd]ddd	chr2:118589746-118589974(+)$1	228	67	91	14.5593
ee!!ddddqqqqqqqqddddeeee	chr7:914214-914448(+)$1	234	40	64	14.8944
#bbeeeeeqqqqqqqqeeeee]bb	chr17:3629845-3630077(+)$1	232	22	46	14.1132
:gggggggqqqqqqqqggggggg:	chr22:45582409-45582641(+)$1	232	114	138	14.3835
ee[a[cccqqqqqqqqccc]a]ee	chr5:96370550-96370799(+)$1	249	205	229	15.8687
gggg!!bbqqqqqqqqbb22gggg	chr10:99435649-99435878(+)$1	229	59	83	15.4708
[bb[ddddqqqqqqqqdddd]bb2	chr4:31147489-31147715(+)$1	226	104	128	14.5976
hhhhhhhhqqqqqqqqhhhhhhhh	chr2:163217244-163217478(+)$1	234	68	92	15.0088
d[ccc[bbqqqqqqqqbbcccddd	chr14:35871067-35871310(-)$1	243	56	80	14.5365
cc[eeeeeqqqqqqqqeeeeeccc	chr13:25915962-25916183(+)$1	221	101	125	15.2393
hhhh[cccqqqqqqqqccc]hhhh	chr8:121549059-121549292(-)$1	233	100	124	16.0503
gggg!!bbqqqqqqqqbb]ggggg	chr4:39781133-39781366(+)$1	233	153	177	15.8438
[ccc!!bbqqqqqqqqbb22ccc3	chr1:206762192-206762424(+)$1	232	124	148	15.0681
b[ffffffqqqqqqqqffffff]b	chr3:72427116-72427343(-)$1	227	21	45	14.0042
$$$$ddddqqqqqqqqddddbb33	chr8:54879938-54880188(-)$1	250	126	150	13.9675
hhhhhhhhqqqqqqqqhhhhhhhh	chrX:51079176-51079406(+)$1	230	65	89	15.0088
++ffffffqqqqqqqqffffff44	chr10:88195098-88195344(-)$1	246	195	219	12.7930
"""eeeeeqqqqqqqqeeeeeiii	chr12:8928935-8929160(+)$1	225	184	208	15.3688
iiiiiiiiqqqqqqqqiiiiiiii	chr15:89745408-89745640(+)$1	232	84	108	16.9553
eeeeecccqqqqqqqqccc22eee	chr3:194123437-194123695(-)$1	258	208	232	14.8410
hhhhhh[aqqqqqqqqa]hhhhhh	chr14:35550413-35550644(+)$1	231	53	77	15.0312
"gggggggqqqqqqqqgggggggd	chr7:151164061-151164284(-)$1	223	180	204	16.2813
###eeeeeqqqqqqqqeeeee22d	chr3:15296352-15296589(-)$1	237	30	54	14.4665
eeeeecccqqqqqqqqccceeeee	chr4:39780141-39780406(+)$1	265	199	223	15.0561
hhhhhhhhqqqqqqqqhhhhhhhh	chr17:44839882-44840127(-)$1	245	76	100	15.0088
dd[eeeeeqqqqqqqqeeeee]dd	chr6:4955423-4955652(+)$1	229	41	65	14.6241
======bbqqqqqqqqbb]=====	chr7:23240338-23240560(+)$1	222	37	61	15.9313
((ffffffqqqqqqqqffffffgg	chr10:89513168-89513406(-)$1	238	26	50	13.0452
:ccc[cccqqqqqqqqccccccgg	chr7:102952842-102953097(-)$1	255	35	59	15.2951
ccc[ddddqqqqqqqqddddccc]	chr2:70506446-70506673(+)$1	227	97	121	15.5702
gggg!!bbqqqqqqqqbb22gggg	chr18:23971464-23971691(+)$1	227	143	167	15.4708
gg[eeeeeqqqqqqqqeeeee]gg	chr1:12569267-12569491(+)$1	224	113	137	15.4561
ccc[ddddqqqqqqqqdddd]ccc	chr15:100253720-100253951(+)$1	231	98	122	15.6068
hhhhhhhhqqqqqqqqhhhhhhhh	chr9:21332611-21332862(-)$1	251	170	194	15.0088
gggg[cccqqqqqqqqccc]gggg	chr17:65066471-65066701(-)$1	230	61	85	16.8154
b[bb[cccqqqqqqqqccc]bb]b	chr11:94905529-94905753(-)$1	224	185	209	14.9600
========qqqqqqqq========	chr3:133116476-133116708(+)$1	232	22	46	16.6973
iiiiiiiiqqqqqqqqiiiiiiii	chr6:79648285-79648526(-)$1	241	67	91	16.9553
ccc[ddddqqqqqqqqdddd]ccc	chr5:134061008-134061240(+)$1	232	33	57	15.6068

#otherMatches

#Seq PSSM
AAAAAACUCAGCUUUUAGUUUUUU	chr9:14617620-14617847(-)$1	227	185	209	16.6973
GGCCCUGCAUUCUUCCGCACCCUC	chr17:46699108-46699328(-)$1	220	7	31	13.1465
uuuaaaauuauaaaauauuGUAAA	chr7:36493098-36493326(+)$1	228	75	99	15.4175
AAGUGUAUAUACAUAAAUACACUC	chr9:114983369-114983595(-)$1	226	53	77	16.3644
AAUAUAUAAAUACAAAUGUAUAUU	chr15:64429982-64430229(+)$1	247	105	129	16.9553
UCAGUUUCUAACAAAUGAAAAUGU	chr15:44854867-44855092(+)$1	225	57	81	14.7034
AAUAUUUUCUAAACAAAAAAUGUU	chr4:129190487-129190727(-)$1	240	111	135	15.0088
GACACAGAUCAAAAUUUUUGAAUA	chr6:105528965-105529197(+)$1	232	177	201	14.4055
ugccuuccaaguagccggaacuac	chr5:151186435-151186664(+)$1	229	3	27	15.1184
AAAAAUAUUAUGUACUAUAUUUUU	chr1:158069882-158070140(+)$1	258	74	98	16.6973
AGCAAAUGUGAAACUUUAUUUGCU	chr8:104084337-104084564(+)$1	227	125	149	15.0088
AAAUCGGUAAAUAAGGACAUGAGU	chr15:100252957-100253208(+)$1	251	77	101	15.3134
UGUUUUAUUGCAUAGUGUGAAACG	chr8:38127321-38127547(-)$1	226	10	34	16.6973
UGGGAUUUGCUAGAAAAAAUUCUC	chr2:206861365-206861608(-)$1	243	55	79	16.2629
GAUAAUGUGUCUAAAAAUAUUGCU	chrX:131761047-131761280(-)$1	233	36	60	14.5448
UAUAUUUCAGCUUAAAGUUAUGUU	chr20:52183640-52183863(-)$1	223	189	213	15.2019
CCCACUGCAGGCUGAGGCGGUGUC	chr1:243663001-243663233(-)$1	232	22	46	12.9754
UCUUUUGUAAGUGAGAACAAUAGA	chr5:106713753-106713985(-)$1	232	176	200	14.5593
UGUACAGUCCUCAUAUACUAUAUA	chr4:38702484-38702754(+)$1	270	103	127	16.0016
UAAUUUGCAACUCUUAGCAUUUUU	chr14:71577789-71578015(+)$1	226	190	214	16.0886
GUACAUAAUCUAAUUUUUAUAUGC	chr2:118589746-118589974(+)$1	228	67	91	14.5593
UAGAAUUGGAACUAUGCAGUUAAG	chr7:914214-914448(+)$1	234	40	64	14.8944
ucccagcuacucgggaggcugagg	chr17:3629845-3630077(+)$1	232	22	46	14.1132
auaguuuauauauuuuuaaauuaG	chr22:45582409-45582641(+)$1	232	114	138	14.3835
AUGUACAUAAUGAAACAUGGAGGU	chr5:96370550-96370799(+)$1	249	205	229	15.8687
AGUGUUGCUGCCCCCUGUGUCAUU	chr10:99435649-99435878(+)$1	229	59	83	15.4708
GACACAUUUAUAAAUUAAUGAGUA	chr4:31147489-31147715(+)$1	226	104	128	14.5976
UCUGUAGUGAAAUAAGACUACAGA	chr2:163217244-163217478(+)$1	234	68	92	15.0088
GACUGUGUGUUUGGAGGCCAGCGU	chr14:35871067-35871310(-)$1	243	56	80	14.5365
CACACAUUUUUUGUAUAAUGUUGG	chr13:25915962-25916183(+)$1	221	101	125	15.2393
UAUUGUAAAUAACAUAUUAAAAUA	chr8:121549059-121549292(-)$1	233	100	124	16.0503
UAGUUUUGCAAGAUCACACACUAA	chr4:39781133-39781366(+)$1	233	153	177	15.8438
AUAUAGCUAUAUAUAAAGAGAUAA	chr1:206762192-206762424(+)$1	232	124	148	15.0681
AUAUGAUUUUCCUAACAAUCAUUU	chr3:72427116-72427343(-)$1	227	21	45	14.0042
UUCUUGUAAUUUCUUGUACAUGUA	chr8:54879938-54880188(-)$1	250	126	150	13.9675
CAAUGACUAUUCUCCAGGUUGUUG	chrX:51079176-51079406(+)$1	230	65	89	15.0088
UAUACAGUAUUUCUCAGCUGUGAU	chr10:88195098-88195344(-)$1	246	195	219	12.7930
AAUUUUUGUAUAUUGUUAAAAUUG	chr12:8928935-8929160(+)$1	225	184	208	15.3688
GUGGUGGUGAACAAAGAUCAUUAC	chr15:89745408-89745640(+)$1	232	84	108	16.9553
AUUGUACAUUCAGCAUUGUAAAUA	chr3:194123437-194123695(-)$1	258	208	232	14.8410
GUUUUUUUUUUUUAAUACAAAAAC	chr14:35550413-35550644(+)$1	231	53	77	15.0312
AACCUGAAAGAUAUCAUUUGGGUC	chr7:151164061-151164284(-)$1	223	180	204	16.2813
UUAAGAAAAUUUAGCAUUUCUAAA	chr3:15296352-15296589(-)$1	237	30	54	14.4665
UUAGCAGUGUACCAAGACUAGCAA	chr4:39780141-39780406(+)$1	265	199	223	15.0561
CUUUUUGAUUUUAUAUUCAAAAAG	chr17:44839882-44840127(-)$1	245	76	100	15.0088
GAUGCCUAUUAUUAGUUAGGCUUC	chr6:4955423-4955652(+)$1	229	41	65	14.6241
UAAAUACAAAAAAGAAUGAUGUUU	chr7:23240338-23240560(+)$1	222	37	61	15.9313
auuGUGCCCUAAGUCAGGUACAAA	chr10:89513168-89513406(-)$1	238	26	50	13.0452
AAGCUGCUCAAGAACAAGUGCUGA	chr7:102952842-102953097(-)$1	255	35	59	15.2951
UGGUAAAUACUAAUUAAUUUCCAU	chr2:70506446-70506673(+)$1	227	97	121	15.5702
UAUUCCAAAUACUUCauuaaaaua	chr18:23971464-23971691(+)$1	227	143	167	15.4708
AUGUACAACAGUGUGUUUGUAAAU	chr1:12569267-12569491(+)$1	224	113	137	15.4561
UGACUAUAUAUAAAAUUAUAUUCA	chr15:100253720-100253951(+)$1	231	98	122	15.6068
UCUUUGACUCCAAAAUGUCAGAGG	chr9:21332611-21332862(-)$1	251	170	194	15.0088
UGUUUUCAAAGAUUCAUGGUAACA	chr17:65066471-65066701(-)$1	230	61	85	16.8154
UUGGCACAUAUAAACCUGUACCCA	chr11:94905529-94905753(-)$1	224	185	209	14.9600
uauauGUAAUCAAAGAUACAUAUG	chr3:133116476-133116708(+)$1	232	22	46	16.6973
UGAAAAAUAAUUUCAAAUUUUUCA	chr6:79648285-79648526(-)$1	241	67	91	16.9553
GUUGUUAUGGAUUAAAAUAAGAAU	chr5:134061008-134061240(+)$1	232	33	57	15.6068

#DB
((((((((........))))))))	chr9:14617620-14617847(-)$1	1	185	209	16.6973
((...(((........))).))..	chr17:46699108-46699328(-)$1	1	7	31	13.1465
((((.(((........))).))))	chr7:36493098-36493326(+)$1	1	75	99	15.4175
.(((((((........))))))).	chr9:114983369-114983595(-)$1	1	53	77	16.3644
((((((((........))))))))	chr15:64429982-64430229(+)$1	1	105	129	16.9553
(((.((((........)))).)).	chr15:44854867-44855092(+)$1	1	57	81	14.7034
((((((((........))))))))	chr4:129190487-129190727(-)$1	1	111	135	15.0088
....((((........))))))..	chr6:105528965-105529197(+)$1	1	177	201	14.4055
((..((((........))))...)	chr5:151186435-151186664(+)$1	1	3	27	15.1184
((((((((........))))))))	chr1:158069882-158070140(+)$1	1	74	98	16.6973
((((((((........))))))))	chr8:104084337-104084564(+)$1	1	125	149	15.0088
((.(((((........)).))).)	chr15:100252957-100253208(+)$1	1	77	101	15.3134
((((((((........))))))))	chr8:38127321-38127547(-)$1	1	10	34	16.6973
.(((((((........))))))).	chr2:206861365-206861608(-)$1	1	55	79	16.2629
..((((((........))))))))	chrX:131761047-131761280(-)$1	1	36	60	14.5448
(((((..(........)..))).)	chr20:52183640-52183863(-)$1	1	189	213	15.2019
((((((((........))))))..	chr1:243663001-243663233(-)$1	1	22	46	12.9754
(((.((((........)))).)))	chr5:106713753-106713985(-)$1	1	176	200	14.5593
((((.(((........)))...))	chr4:38702484-38702754(+)$1	1	103	127	16.0016
(((..(((........)))....)	chr14:71577789-71578015(+)$1	1	190	214	16.0886
(((.((((........)))).)))	chr2:118589746-118589974(+)$1	1	67	91	14.5593
((..((((........))))))))	chr7:914214-914448(+)$1	1	40	64	14.8944
.(((((((........))))).))	chr17:3629845-3630077(+)$1	1	22	46	14.1132
.(((((((........))))))).	chr22:45582409-45582641(+)$1	1	114	138	14.3835
((.(.(((........))).).))	chr5:96370550-96370799(+)$1	1	205	229	15.8687
((((..((........))..))))	chr10:99435649-99435878(+)$1	1	59	83	15.4708
.((.((((........)))).)).	chr4:31147489-31147715(+)$1	1	104	128	14.5976
((((((((........))))))))	chr2:163217244-163217478(+)$1	1	68	92	15.0088
(.(((.((........))))))))	chr14:35871067-35871310(-)$1	1	56	80	14.5365
((.(((((........))))))))	chr13:25915962-25916183(+)$1	1	101	125	15.2393
((((.(((........))).))))	chr8:121549059-121549292(-)$1	1	100	124	16.0503
((((..((........)).)))))	chr4:39781133-39781366(+)$1	1	153	177	15.8438
.(((..((........))..))).	chr1:206762192-206762424(+)$1	1	124	148	15.0681
(.((((((........)))))).)	chr3:72427116-72427343(-)$1	1	21	45	14.0042
....((((........))))))..	chr8:54879938-54880188(-)$1	1	126	150	13.9675
((((((((........))))))))	chrX:51079176-51079406(+)$1	1	65	89	15.0088
..((((((........))))))..	chr10:88195098-88195344(-)$1	1	195	219	12.7930
...(((((........))))))))	chr12:8928935-8929160(+)$1	1	184	208	15.3688
((((((((........))))))))	chr15:89745408-89745640(+)$1	1	84	108	16.9553
((((((((........)))..)))	chr3:194123437-194123695(-)$1	1	208	232	14.8410
((((((.(........).))))))	chr14:35550413-35550644(+)$1	1	53	77	15.0312
.(((((((........))))))))	chr7:151164061-151164284(-)$1	1	180	204	16.2813
...(((((........)))))..)	chr3:15296352-15296589(-)$1	1	30	54	14.4665
)))))(((........)))(((((	chr4:39780141-39780406(+)$1	1	199	223	15.0561
((((((((........))))))))	chr17:44839882-44840127(-)$1	1	76	100	15.0088
((.(((((........))))).))	chr6:4955423-4955652(+)$1	1	41	65	14.6241
((((((((........)).)))))	chr7:23240338-23240560(+)$1	1	37	61	15.9313
..((((((........))))))))	chr10:89513168-89513406(-)$1	1	26	50	13.0452
.(((.(((........))))))((	chr7:102952842-102953097(-)$1	1	35	59	15.2951
(((.((((........))))))).	chr2:70506446-70506673(+)$1	1	97	121	15.5702
((((..((........))..))))	chr18:23971464-23971691(+)$1	1	143	167	15.4708
((.(((((........))))).))	chr1:12569267-12569491(+)$1	1	113	137	15.4561
(((.((((........)))).)))	chr15:100253720-100253951(+)$1	1	98	122	15.6068
((((((((........))))))))	chr9:21332611-21332862(-)$1	1	170	194	15.0088
((((.(((........))).))))	chr17:65066471-65066701(-)$1	1	61	85	16.8154
(.((.(((........))).)).)	chr11:94905529-94905753(-)$1	1	185	209	14.9600
((((((((........))))))))	chr3:133116476-133116708(+)$1	1	22	46	16.6973
((((((((........))))))))	chr6:79648285-79648526(-)$1	1	67	91	16.9553
(((.((((........)))).)))	chr5:134061008-134061240(+)$1	1	33	57	15.6068

#PSSM
h : 0.15	c : 0.11	g : 0.11	= : 0.08	e : 0.08	d : 0.08	b : 0.05	i : 0.05	# : 0.05	! : 0.03	$ : 0.03	: : 0.03	[ : 0.03	" : 0.03	+ : 0.01	( : 0.01	
g : 0.18	h : 0.15	c : 0.13	= : 0.08	e : 0.08	b : 0.06	d : 0.06	i : 0.05	[ : 0.05	# : 0.03	! : 0.01	$ : 0.01	+ : 0.01	" : 0.01	( : 0.01	
g : 0.15	h : 0.15	c : 0.11	= : 0.08	[ : 0.08	f : 0.08	b : 0.06	e : 0.05	i : 0.05	" : 0.03	# : 0.03	! : 0.03	d : 0.03	$ : 0.01	
e : 0.15	h : 0.15	g : 0.13	[ : 0.11	= : 0.08	c : 0.08	f : 0.08	i : 0.05	! : 0.05	" : 0.01	# : 0.01	a : 0.01	$ : 0.01	b : 0.01	
d : 0.18	e : 0.13	[ : 0.11	h : 0.11	= : 0.08	f : 0.08	! : 0.08	g : 0.06	i : 0.05	c : 0.05	" : 0.01	
c : 0.20	d : 0.18	h : 0.11	e : 0.10	= : 0.08	f : 0.08	! : 0.08	g : 0.06	i : 0.05	[ : 0.01	
c : 0.18	d : 0.18	b : 0.11	h : 0.10	e : 0.10	f : 0.08	= : 0.06	g : 0.06	i : 0.05	! : 0.01	[ : 0.01	
c : 0.18	d : 0.18	b : 0.11	h : 0.10	e : 0.10	f : 0.08	= : 0.06	g : 0.06	i : 0.05	a : 0.03	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.18	d : 0.18	b : 0.11	h : 0.10	e : 0.10	f : 0.08	= : 0.06	g : 0.06	i : 0.05	a : 0.03	
c : 0.18	d : 0.18	b : 0.11	h : 0.10	e : 0.10	f : 0.08	= : 0.06	g : 0.06	i : 0.05	2 : 0.01	] : 0.01	
c : 0.20	d : 0.18	h : 0.11	e : 0.10	f : 0.08	= : 0.06	g : 0.06	2 : 0.06	i : 0.05	] : 0.05	
d : 0.18	h : 0.11	e : 0.11	] : 0.10	= : 0.08	g : 0.08	f : 0.08	c : 0.06	2 : 0.06	i : 0.05	3 : 0.01	4 : 0.01	
e : 0.15	g : 0.13	h : 0.13	] : 0.10	c : 0.10	= : 0.08	f : 0.08	b : 0.06	i : 0.05	3 : 0.03	4 : 0.01	a : 0.01	2 : 0.01	
g : 0.13	h : 0.13	c : 0.13	b : 0.10	= : 0.08	f : 0.08	e : 0.06	i : 0.06	] : 0.06	d : 0.05	3 : 0.03	4 : 0.01	2 : 0.01	
g : 0.18	h : 0.15	c : 0.10	= : 0.08	e : 0.08	i : 0.06	] : 0.06	d : 0.06	b : 0.05	2 : 0.03	3 : 0.03	4 : 0.03	: : 0.01	7 : 0.01	
h : 0.15	g : 0.15	d : 0.11	= : 0.08	e : 0.08	c : 0.08	i : 0.06	2 : 0.05	] : 0.05	b : 0.05	: : 0.03	3 : 0.03	7 : 0.01	4 : 0.01	

#score	898.6317170769669
#seq	59
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_UTR_m1_run2.txt

#BEAR
[eeeeeyyyyyyyyyyyyyyyyeeeee]b	chr1:229460452-229460702(-)$1	250	149	178	22.1925
gggggbb^^^^^^^^^^^^^^^^^^^^^b	chr5:71501624-71501851(+)$1	227	53	82	26.3470
:gggggggvvvvvvvvvvvvvggggggg:	chr16:70606317-70606539(+)$1	222	99	128	19.0562
ggggggg^^^^^^^^^^^^^^^^^^^^^^	chr7:26706865-26707088(-)$1	223	77	106	27.1451
ccc"""bbwwwwwwwwwwwwwwbb333cc	chr22:44890030-44890265(-)$1	235	64	93	21.9139
beeeeeyyyyyyyyyyyyyyyyeeeee]b	chr3:128356670-128356900(-)$1	230	95	124	21.8547
iiiiiiiiwwwwwwwwwwwwwwiiiiiii	chr3:169711481-169711717(+)$1	236	9	38	22.3914
ffffff^^^^^^^^^^^^^^^^^^^^^^f	chr2:26614225-26614448(+)$1	223	94	123	25.6976
hhhhhhh^^^^^^^^^^^^^^^^^^^^^^	chr3:113437829-113438060(-)$1	231	177	206	25.7583
========wwwwwwwwwwwwww=======	chr12:70637670-70637893(+)$1	223	117	146	23.2157
"""dddd^^^^^^^^^^^^^^^^^^^^^^	chr1:33241384-33241620(-)$1	236	91	120	25.8450
=========uuuuuuuuuuuu========	chr5:34906990-34907218(-)$1	228	6	35	20.9550
ggggggg^^^^^^^^^^^^^^^^^^^^^^	chr2:29022490-29022725(+)$1	235	146	175	27.1451
dddd[cccvvvvvvvvvvvvvccc]dddd	chr5:133531659-133531898(-)$1	239	197	226	19.8587
ggggggg^^^^^^^^^^^^^^^^^^^^^^	chr2:182794489-182794722(+)$1	233	85	114	27.1451
eeeee^^^^^^^^^^^^^^^^^^^eeeee	chr5:142660690-142660927(-)$1	237	198	227	24.5695
=======^^^^^^^^^^^^^^^^^^^^^^	chr3:73118120-73118353(+)$1	233	90	119	27.2915
gggggggwwwwwwwwwwwwwwggggggg4	chr1:46126564-46126793(-)$1	229	144	173	22.3991
iiiiiiixxxxxxxxxxxxxxxiiiiiii	chr1:214528320-214528549(-)$1	229	91	120	22.3150
hhhhh[bbwwwwwwwwwwwwwwbb]hhhh	chr9:110091837-110092070(+)$1	233	66	95	19.8569
d[eeeeexxxxxxxxxxxxxxxeeeee22	chr2:242293172-242293394(+)$1	222	60	89	20.9129
:dddd^^^^^^^^^^^^^^^^^^^dddd:	chr2:8997088-8997309(-)$1	221	58	87	22.1137
=========uuuuuuuuuuuu========	chr12:25362020-25362269(-)$1	249	136	165	20.9550
cgggggggvvvvvvvvvvvvvggggggg3	chr2:29025533-29025753(+)$1	220	153	182	20.8833
eeeee^^^^^^^^^^^^^^^^^^^^^^^^	chr19:6414588-6414819(-)$1	231	92	121	26.4880
dddd^^^^^^^^^^^^^^^^^^^dddd22	chr20:34536257-34536484(+)$1	227	64	93	22.7544
gggggggwwwwwwwwwwwwwwgggggggf	chr8:101166019-101166251(+)$1	232	136	165	22.1239
ffffffa^^^^^^^^^^^^^^^^^^a]ff	chr17:47129126-47129361(+)$1	235	56	85	24.8220
"ccc^^^^^^^^^^^^^^^^^^^^^ccc6	chr4:48424987-48425208(+)$1	221	81	110	24.7644
iiiiiii^^^^^^^^^^^^^^^^^^^^ii	chr12:46758072-46758299(-)$1	227	84	113	26.7734
#ffffff^^^^^^^^^^^^^^^^^^^^^^	chr13:20714484-20714715(-)$1	231	35	64	25.9205
[gggggggvvvvvvvvvvvvvggggggg]	chr5:135516196-135516423(+)$1	227	169	198	20.8608
dd[dddd^^^^^^^^^^^^^^^^^^^^^^	chr19:57983225-57983442(-)$1	217	118	147	25.8998
eeee[bb^^^^^^^^^^^^^^^^^^^^^b	chr12:49330512-49330745(-)$1	233	20	49	25.9261
gggggggxxxxxxxxxxxxxxxggggggg	chr18:19445691-19445917(+)$1	226	61	90	22.3015
gggggggwwwwwwwwwwwwwwggggggg:	chr15:59147368-59147604(+)$1	236	207	236	21.5507
=======^^^^^^^^^^^^^^^^^^====	chr1:227848260-227848486(+)$1	226	99	128	26.4485
dffffff^^^^^^^^^^^^^^^^^^^^^^	chr1:109178089-109178309(+)$1	220	101	130	25.8565
::eeeeeyyyyyyyyyyyyyyyyeeeee:	chr17:49043456-49043685(-)$1	229	200	229	19.7155
c"""cccxxxxxxxxxxxxxxxccc22cc	chr13:41932609-41932831(+)$1	222	94	123	21.5372
eeeee^^^^^^^^^^^^^^^^^^^eeeee	chr12:54633877-54634098(-)$1	221	15	44	24.5695
:eeeeeyyyyyyyyyyyyyyyyeeeeeGG	chr10:111894983-111895220(+)$1	237	194	223	20.2439
[ggggggguuuuuuuuuuuuggggggg]d	chr12:4413568-4413794(+)$1	226	135	164	19.5192
iiiiiiiiwwwwwwwwwwwwwwiiiiiii	chr14:91924986-91925210(-)$1	224	124	153	22.3914
hh[dddd^^^^^^^^^^^^^^^^^^^^^^	chr1:179069505-179069733(-)$1	228	101	130	25.9754
eeeee^^^^^^^^^^^^^^^^^^^^^eee	chr2:139328551-139328791(+)$1	240	167	196	25.5406
eeedddd^^^^^^^^^^^^^^^^^^^^^d	chr1:36602097-36602320(-)$1	223	135	164	25.6696
iii[ccc^^^^^^^^^^^^^^^^^^^^^^	chr6:75964203-75964439(-)$1	236	38	67	27.0171
ggggggg^^^^^^^^^^^^^^^^^^^^^^	chr3:10192956-10193194(+)$1	238	118	147	27.1451
eeee[dddduuuuuuuuuuuudddd333e	chr19:11032771-11032999(-)$1	228	182	211	19.2712
ccc[ccc^^^^^^^^^^^^^^^^^^^^^^	chr14:97001030-97001261(+)$1	231	93	122	26.6259
gggg[bb^^^^^^^^^^^^^^^^^^^^^^	chr14:39651597-39651818(+)$1	221	42	71	26.6767
!bb[cccxxxxxxxxxxxxxxxccc333b	chr1:94351979-94352203(-)$1	224	92	121	21.9885
iiiiicccwwwwwwwwwwwwwwccc]iii	chr11:62284068-62284293(-)$1	225	137	166	22.8287
ggggggg^^^^^^^^^^^^^^^^^^^^gg	chr8:48974116-48974343(+)$1	227	98	127	26.7193
=========uuuuuuuuuuuu========	chr19:34951324-34951553(+)$1	229	120	149	20.9550
eeee!!cccvvvvvvvvvvvvvccc22ee	chr7:80373839-80374104(-)$1	265	108	137	20.5233
dddd^^^^^^^^^^^^^^^^^^^^^dddd	chr10:60158846-60159081(+)$1	235	97	126	24.0733
gggggggxxxxxxxxxxxxxxxggggggg	chr13:21721372-21721607(+)$1	235	106	135	22.3015
gggg"""cccuuuuuuuuuuuuccc22gg	chr10:116621615-116621848(+)$1	233	143	172	19.9663
hhhhhhh^^^^^^^^^^^^^^^^^^^^hh	chrX:107965567-107965801(-)$1	234	45	74	24.7273
bb[ddddwwwwwwwwwwwwwwdddd]bb:	chr8:28426920-28427142(+)$1	222	187	216	19.1601
dd[ccc^^^^^^^^^^^^^^^^^^^cccd	chr3:160789159-160789381(+)$1	222	189	218	25.0991
ccc[bb^^^^^^^^^^^^^^^^^^bb]cc	chr20:43126031-43126259(-)$1	228	52	81	24.0472
!eeeee[bbvvvvvvvvvvvvvbb]eeee	chr7:155568867-155569090(+)$1	223	148	177	19.7346
gggggggxxxxxxxxxxxxxxxggggggg	chr13:30778905-30779138(-)$1	233	105	134	22.3015
eee[cccxxxxxxxxxxxxxxxccc]eee	chr14:91927646-91927865(-)$1	219	20	49	21.8717

#otherMatches

#Seq PSSM
AGCAUAAGACUCGUUUUCCUUAUAUGCCG	chr1:229460452-229460702(-)$1	250	149	178	22.1925
CAAGUUGGCUAGAAGAAAGUAAAAAGAAC	chr5:71501624-71501851(+)$1	227	53	82	26.3470
UAUACCCACCCCUCUUCCCACUGGGUAUU	chr16:70606317-70606539(+)$1	222	99	128	19.0562
GGAGAGUUUUCUUUACACCCUUGACAAUA	chr7:26706865-26707088(-)$1	223	77	106	27.1451
AUCAGGCUAAGAAAGUGGGGGAAGGGAGA	chr22:44890030-44890265(-)$1	235	64	93	21.9139
AGGGGAACCAUUAUUUCUACUCUCCCUAU	chr3:128356670-128356900(-)$1	230	95	124	21.8547
CCAGCAGAGAAAGUGAACAGCAUUUGUUG	chr3:169711481-169711717(+)$1	236	9	38	22.3914
UCAUGCCAAUUACUAUAACAUUUCCAAAG	chr2:26614225-26614448(+)$1	223	94	123	25.6976
ACAUUGCUGUUACAUCUGAAAUAAACUUA	chr3:113437829-113438060(-)$1	231	177	206	25.7583
UACACGUAUAUCAUCUGCCAGUUAUGUGU	chr12:70637670-70637893(+)$1	223	117	146	23.2157
UCAGUCUGCUCCAUCCAUCACCCAUUUAC	chr1:33241384-33241620(-)$1	236	91	120	25.8450
CUUCCCAGGCAUAUGGACAAUUCUGGGAG	chr5:34906990-34907218(-)$1	228	6	35	20.9550
GGGAAGAGCUUUACAGACAUUCACCAACU	chr2:29022490-29022725(+)$1	235	146	175	27.1451
ACUGAACAAAUAGCUUAUCCAUGUGCAGU	chr5:133531659-133531898(-)$1	239	197	226	19.8587
UUGAAGACUUCCAGACUUAUCCAACUUAU	chr2:182794489-182794722(+)$1	233	85	114	27.1451
UUGACUCAAAUCUCCAGUAUUCUUGUCAA	chr5:142660690-142660927(-)$1	237	198	227	24.5695
AUUGGUUAGACUACAUCUUACUAUUUCAC	chr3:73118120-73118353(+)$1	233	90	119	27.2915
CUUUGCUCUGAAUUUAUAAAUAGUAAAGG	chr1:46126564-46126793(-)$1	229	144	173	22.3991
UAAGAGUUGUUCCACAUAUUUCACUUUUA	chr1:214528320-214528549(-)$1	229	91	120	22.3150
UUUUCUUCUACAGCAGAACUUUGAUGAAG	chr9:110091837-110092070(+)$1	233	66	95	19.8569
AGGGAGGACCCACACUGCUACACUUCUGA	chr2:242293172-242293394(+)$1	222	60	89	20.9129
UUUGCAAAUGAAGUUAAAGACAAGGCAAC	chr2:8997088-8997309(-)$1	221	58	87	22.1137
uuuuucuauaaaaagaaaaaaauGGAAAA	chr12:25362020-25362269(-)$1	249	136	165	20.9550
UUCAACCACUACCUUCUACAUUGGUUGAC	chr2:29025533-29025753(+)$1	220	153	182	20.8833
GGUUUUUGUUCUUUUUAUUCUUUUAUUUU	chr19:6414588-6414819(-)$1	231	92	121	26.4880
GACAGCUUCCCCGUUCUAUUUAAUGUCCA	chr20:34536257-34536484(+)$1	227	64	93	22.7544
aucugcaguccuuguuaaaaaugcagguu	chr8:101166019-101166251(+)$1	232	136	165	22.1239
GCAAUGCUUUUCAUUUUUUUUUUUUGUUA	chr17:47129126-47129361(+)$1	235	56	85	24.8220
GGGGGAAAAAAAUCUAUGCACUUAACCUA	chr4:48424987-48425208(+)$1	221	81	110	24.7644
AAAAUGACUCUUGCAGACCUCACUAUUUU	chr12:46758072-46758299(-)$1	227	84	113	26.7734
CUACUCACACUUUUCACCUCCAACUUCUA	chr13:20714484-20714715(-)$1	231	35	64	25.9205
GAAUAUAAAUAAUUUUUCACAUUGUAUUG	chr5:135516196-135516423(+)$1	227	169	198	20.8608
uuuccugauuccuuuuauauuuucucccu	chr19:57983225-57983442(-)$1	217	118	147	25.8998
CAGAUGCUUCCCUCCAUACUUUUUAUUUG	chr12:49330512-49330745(-)$1	233	20	49	25.9261
GGGUAUUAUUUAAACUGCCAACAAUAUCC	chr18:19445691-19445917(+)$1	226	61	90	22.3015
CAGUUACUAUUUAUUGACAAUGUGAUUGA	chr15:59147368-59147604(+)$1	236	207	236	21.5507
acaauuauuuucuuucuuuccaauuuggu	chr1:227848260-227848486(+)$1	226	99	128	26.4485
UAUAACUUAAACCCUAUAGAUUUUGUCAA	chr1:109178089-109178309(+)$1	220	101	130	25.8565
CCGUUCUACCAUAACAAUACAGAGGAACU	chr17:49043456-49043685(-)$1	229	200	229	19.7155
CCCUGAUAAUCUUUUUCUAAUAAUCCUGU	chr13:41932609-41932831(+)$1	222	94	123	21.5372
AAUACUUCGUUUUGGUUUCUUCUUGUGUU	chr12:54633877-54634098(-)$1	221	15	44	24.5695
AAUGCCUCUAUUUACUUGCUUUGGCAUAA	chr10:111894983-111895220(+)$1	237	194	223	20.2439
GAUUCUGGAUUCUAAACAACCCAGAAUGG	chr12:4413568-4413794(+)$1	226	135	164	19.5192
GGAUCAGUACCUGUUGAAAAAAACUGGUU	chr14:91924986-91925210(-)$1	224	124	153	22.3914
GAAUGGGACUUAAAUUUUCACAUAUAUGU	chr1:179069505-179069733(-)$1	228	101	130	25.9754
GAGGGUCUUAUAAGAAAACAAAAAUUCCC	chr2:139328551-139328791(+)$1	240	167	196	25.5406
AGUGAAAUCCCAAUCAUGUCCUGUUUUCU	chr1:36602097-36602320(-)$1	223	135	164	25.6696
AGAGUUUAUAUUUUCCUUCAGUUAUAUUU	chr6:75964203-75964439(-)$1	236	38	67	27.0171
UUCUACUCCUUCCCUAAUAGCUUUUUAAA	chr3:10192956-10193194(+)$1	238	118	147	27.1451
CCUGGCCAGGCUACCUUCCCACUGGAGAC	chr19:11032771-11032999(-)$1	228	182	211	19.2712
AUACAGAUUUUACUAACAUUUUAAUUUAU	chr14:97001030-97001261(+)$1	231	93	122	26.6259
AAAUCAUUUGCUAUUUUCUAUUCUCCCUU	chr14:39651597-39651818(+)$1	221	42	71	26.6767
UGAUGAGUUUUUACUUUUACCUCUCUACU	chr1:94351979-94352203(-)$1	224	92	121	21.9885
GUGUUCCUAUAUAAACUCCAAAGGGAAAC	chr11:62284068-62284293(-)$1	225	137	166	22.8287
GUAUACACACUUUUAUUUACCCUAUUUUG	chr8:48974116-48974343(+)$1	227	98	127	26.7193
UAUCUUCCGAAGAGGGAGAGACGGAAGGU	chr19:34951324-34951553(+)$1	229	120	149	20.9550
UAUAUUUAACUUAACCCAGAUUUUAUUUA	chr7:80373839-80374104(-)$1	265	108	137	20.5233
GGAAUUUUAAAUAAACUAAACAUUUUUUC	chr10:60158846-60159081(+)$1	235	97	126	24.0733
UAAAUUCUAUUUACUAUUUGUUGAAUUUA	chr13:21721372-21721607(+)$1	235	106	135	22.3015
UUAUCAAACAAAAUAUGAAAACUGUAAAU	chr10:116621615-116621848(+)$1	233	143	172	19.9663
UAGAGUGAUUAUAUUGCCACAAAAACACA	chrX:107965567-107965801(-)$1	234	45	74	24.7273
ACCUGUAUUAUUAACGUCAUUUACAUGUA	chr8:28426920-28427142(+)$1	222	187	216	19.1601
AGUGUAUAUAUCCUACUCCCAUUACUGCC	chr3:160789159-160789381(+)$1	222	189	218	25.0991
GGUCCUAAACUUCAAAAACAUUACAGUGC	chr20:43126031-43126259(-)$1	228	52	81	24.0472
CGAUUUCAUGUCACAUUUACUAAUAGAAU	chr7:155568867-155569090(+)$1	223	148	177	19.7346
CAGACUUUAUCUACACACUUUCGGGUCUG	chr13:30778905-30779138(-)$1	233	105	134	22.3015
CAGCCAGUCAUCUACAACAAAUCUGCCUG	chr14:91927646-91927865(-)$1	219	20	49	21.8717

#DB
.(((((................))))).)	chr1:229460452-229460702(-)$1	1	149	178	22.1925
(((((((.....................)	chr5:71501624-71501851(+)$1	1	53	82	26.3470
.(((((((.............))))))).	chr16:70606317-70606539(+)$1	1	99	128	19.0562
(((((((......................	chr7:26706865-26707088(-)$1	1	77	106	27.1451
(((...((..............))...))	chr22:44890030-44890265(-)$1	1	64	93	21.9139
((((((................))))).)	chr3:128356670-128356900(-)$1	1	95	124	21.8547
((((((((..............)))))))	chr3:169711481-169711717(+)$1	1	9	38	22.3914
((((((......................)	chr2:26614225-26614448(+)$1	1	94	123	25.6976
(((((((......................	chr3:113437829-113438060(-)$1	1	177	206	25.7583
((((((((..............)))))))	chr12:70637670-70637893(+)$1	1	117	146	23.2157
...((((......................	chr1:33241384-33241620(-)$1	1	91	120	25.8450
(((((((((............))))))))	chr5:34906990-34907218(-)$1	1	6	35	20.9550
(((((((......................	chr2:29022490-29022725(+)$1	1	146	175	27.1451
((((.(((.............))).))))	chr5:133531659-133531898(-)$1	1	197	226	19.8587
(((((((......................	chr2:182794489-182794722(+)$1	1	85	114	27.1451
(((((...................)))))	chr5:142660690-142660927(-)$1	1	198	227	24.5695
(((((((......................	chr3:73118120-73118353(+)$1	1	90	119	27.2915
(((((((..............))))))).	chr1:46126564-46126793(-)$1	1	144	173	22.3991
(((((((...............)))))))	chr1:214528320-214528549(-)$1	1	91	120	22.3150
(((((.((..............)).))))	chr9:110091837-110092070(+)$1	1	66	95	19.8569
(.(((((...............)))))..	chr2:242293172-242293394(+)$1	1	60	89	20.9129
.((((...................)))).	chr2:8997088-8997309(-)$1	1	58	87	22.1137
(((((((((............))))))))	chr12:25362020-25362269(-)$1	1	136	165	20.9550
((((((((.............))))))).	chr2:29025533-29025753(+)$1	1	153	182	20.8833
(((((........................	chr19:6414588-6414819(-)$1	1	92	121	26.4880
((((...................))))..	chr20:34536257-34536484(+)$1	1	64	93	22.7544
(((((((..............))))))))	chr8:101166019-101166251(+)$1	1	136	165	22.1239
(((((((..................).))	chr17:47129126-47129361(+)$1	1	56	85	24.8220
.(((.....................))).	chr4:48424987-48425208(+)$1	1	81	110	24.7644
(((((((....................))	chr12:46758072-46758299(-)$1	1	84	113	26.7734
.((((((......................	chr13:20714484-20714715(-)$1	1	35	64	25.9205
.(((((((.............))))))).	chr5:135516196-135516423(+)$1	1	169	198	20.8608
((.((((......................	chr19:57983225-57983442(-)$1	1	118	147	25.8998
((((.((.....................)	chr12:49330512-49330745(-)$1	1	20	49	25.9261
(((((((...............)))))))	chr18:19445691-19445917(+)$1	1	61	90	22.3015
(((((((..............))))))).	chr15:59147368-59147604(+)$1	1	207	236	21.5507
(((((((..................))))	chr1:227848260-227848486(+)$1	1	99	128	26.4485
(((((((......................	chr1:109178089-109178309(+)$1	1	101	130	25.8565
..(((((................))))).	chr17:49043456-49043685(-)$1	1	200	229	19.7155
(...(((...............)))..))	chr13:41932609-41932831(+)$1	1	94	123	21.5372
(((((...................)))))	chr12:54633877-54634098(-)$1	1	15	44	24.5695
.(((((................)))))))	chr10:111894983-111895220(+)$1	1	194	223	20.2439
.(((((((............))))))).)	chr12:4413568-4413794(+)$1	1	135	164	19.5192
((((((((..............)))))))	chr14:91924986-91925210(-)$1	1	124	153	22.3914
((.((((......................	chr1:179069505-179069733(-)$1	1	101	130	25.9754
(((((.....................)))	chr2:139328551-139328791(+)$1	1	167	196	25.5406
(((((((.....................)	chr1:36602097-36602320(-)$1	1	135	164	25.6696
(((.(((......................	chr6:75964203-75964439(-)$1	1	38	67	27.0171
(((((((......................	chr3:10192956-10193194(+)$1	1	118	147	27.1451
((((.((((............))))...)	chr19:11032771-11032999(-)$1	1	182	211	19.2712
(((.(((......................	chr14:97001030-97001261(+)$1	1	93	122	26.6259
((((.((......................	chr14:39651597-39651818(+)$1	1	42	71	26.6767
.((.(((...............)))...)	chr1:94351979-94352203(-)$1	1	92	121	21.9885
((((((((..............))).)))	chr11:62284068-62284293(-)$1	1	137	166	22.8287
(((((((....................))	chr8:48974116-48974343(+)$1	1	98	127	26.7193
(((((((((............))))))))	chr19:34951324-34951553(+)$1	1	120	149	20.9550
((((..(((.............)))..))	chr7:80373839-80374104(-)$1	1	108	137	20.5233
((((.....................))))	chr10:60158846-60159081(+)$1	1	97	126	24.0733
(((((((...............)))))))	chr13:21721372-21721607(+)$1	1	106	135	22.3015
((((...(((............)))..))	chr10:116621615-116621848(+)$1	1	143	172	19.9663
(((((((....................))	chrX:107965567-107965801(-)$1	1	45	74	24.7273
((.((((..............)))).)).	chr8:28426920-28427142(+)$1	1	187	216	19.1601
((.(((...................))))	chr3:160789159-160789381(+)$1	1	189	218	25.0991
(((.((..................)).))	chr20:43126031-43126259(-)$1	1	52	81	24.0472
.(((((.((.............)).))))	chr7:155568867-155569090(+)$1	1	148	177	19.7346
(((((((...............)))))))	chr13:30778905-30779138(-)$1	1	105	134	22.3015
(((.(((...............))).)))	chr14:91927646-91927865(-)$1	1	20	49	21.8717

#PSSM
g : 0.20	e : 0.13	d : 0.10	i : 0.08	= : 0.08	c : 0.07	: : 0.05	h : 0.05	[ : 0.04	b : 0.02	f : 0.02	" : 0.02	! : 0.02	# : 0.01	
g : 0.26	e : 0.19	i : 0.08	= : 0.08	d : 0.08	c : 0.05	f : 0.05	h : 0.05	" : 0.02	b : 0.02	[ : 0.01	: : 0.01	
g : 0.26	e : 0.22	i : 0.08	= : 0.08	c : 0.05	f : 0.05	d : 0.05	[ : 0.05	h : 0.04	" : 0.02	b : 0.01	
g : 0.26	e : 0.19	d : 0.13	= : 0.08	i : 0.07	[ : 0.07	f : 0.05	h : 0.04	" : 0.02	c : 0.02	
g : 0.23	e : 0.14	= : 0.08	d : 0.08	c : 0.08	i : 0.07	f : 0.05	[ : 0.05	h : 0.04	^ : 0.04	" : 0.02	! : 0.01	b : 0.01	
g : 0.22	c : 0.11	^ : 0.11	e : 0.08	= : 0.08	d : 0.08	b : 0.05	i : 0.05	f : 0.05	" : 0.02	h : 0.02	[ : 0.01	! : 0.01	
g : 0.22	^ : 0.16	c : 0.11	= : 0.08	d : 0.08	b : 0.07	i : 0.05	y : 0.04	h : 0.02	e : 0.02	f : 0.02	a : 0.01	" : 0.01	[ : 0.01	
^ : 0.49	x : 0.11	y : 0.05	g : 0.05	= : 0.05	c : 0.05	w : 0.05	b : 0.04	i : 0.02	d : 0.01	
^ : 0.49	w : 0.14	x : 0.11	y : 0.05	v : 0.05	= : 0.04	c : 0.02	u : 0.01	d : 0.01	b : 0.01	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.07	y : 0.05	c : 0.01	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.08	y : 0.05	
^ : 0.49	w : 0.14	x : 0.11	v : 0.08	u : 0.07	y : 0.05	g : 0.01	
^ : 0.49	x : 0.11	g : 0.10	w : 0.08	y : 0.05	= : 0.04	d : 0.02	v : 0.02	c : 0.01	u : 0.01	
^ : 0.49	g : 0.14	c : 0.10	e : 0.05	= : 0.05	b : 0.04	i : 0.04	d : 0.02	y : 0.01	
^ : 0.47	g : 0.14	c : 0.10	e : 0.07	= : 0.05	b : 0.04	i : 0.04	d : 0.04	
^ : 0.41	g : 0.14	e : 0.10	c : 0.08	= : 0.05	d : 0.05	i : 0.04	] : 0.04	3 : 0.01	b : 0.01	
^ : 0.34	g : 0.14	e : 0.11	= : 0.07	d : 0.05	3 : 0.04	i : 0.04	2 : 0.04	] : 0.04	c : 0.02	h : 0.01	a : 0.01	b : 0.01	
^ : 0.32	e : 0.14	g : 0.14	= : 0.07	i : 0.05	d : 0.05	3 : 0.04	2 : 0.04	] : 0.02	c : 0.02	h : 0.01	b : 0.01	
^ : 0.28	g : 0.16	e : 0.10	c : 0.07	i : 0.07	= : 0.07	] : 0.04	d : 0.04	h : 0.02	2 : 0.02	3 : 0.02	f : 0.01	G : 0.01	b : 0.01	
^ : 0.22	e : 0.10	b : 0.07	: : 0.07	i : 0.07	= : 0.07	d : 0.07	g : 0.07	c : 0.04	f : 0.04	h : 0.02	2 : 0.02	4 : 0.01	3 : 0.01	6 : 0.01	] : 0.01	G : 0.01	

#score	1568.5076022383405
#seq	67
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_CDS_m2_run2.txt

#BEAR
::bb!!gggggggooooooggggggg22	chr6:53787401-53787629(+)$1	228	144	172	11.7645
dggggggg!!ccclllccc333gggggg	chr7:151877809-151878034(-)$1	225	3	31	9.3131
'''cccccc!!bboooooobb333ccc6	chr7:92763027-92763245(-)$1	218	127	155	12.4827
eeeee####ddddoooooodddd]eeee	chr6:31508130-31508360(-)$1	230	149	177	12.4379
iiiiiiddddcccooooooccc]dddd:	chr14:31642315-31642535(-)$1	220	89	117	12.9460
[a[bb[ccc!!bboooooobbccc]bb]	chr16:66783070-66783300(-)$1	230	86	114	13.6331
[cccdddd!!cccoooooocccdddd88	chr1:16264002-16264232(+)$1	230	147	175	13.4159
ggggggg[eeeeeooooooeeeee]ggg	chr16:14041708-14041940(+)$1	232	158	186	12.8159
dddd!!a[a[cccooooooccc]aa]dd	chr3:38180132-38180362(+)$1	230	42	70	14.6933
[ccc"""bb[cccoooooocccbb333c	chr11:20419128-20419352(+)$1	224	45	73	14.2958
ddccc####ddddoooooodddd22ccc	chr5:43446297-43446527(-)$1	230	129	157	13.1096
cc::ggggggg[aooooooaggggggg:	chr15:78453929-78454159(+)$1	230	48	76	11.1535
::ccc[ccc[cccooooooccc]ccc]c	chr7:5103975-5104197(+)$1	222	39	67	13.5290
occca[gggggggooooooggggggga:	chr7:115580655-115580877(-)$1	222	25	53	12.6907
ddd"""a!!ddddoooooodddd22add	chr17:37657449-37657679(+)$1	230	75	103	13.4415
d[bb!!ccc[cccoooooocccccc22b	chr19:6380198-6380419(-)$1	221	61	89	14.3070
ee[bb[eeeee[aooooooa]eeeee]b	chr8:17817512-17817734(+)$1	222	57	85	12.4208
$$$$$ccc[a[bboooooobb]a]ccc5	chr17:76045575-76045808(+)$1	233	157	185	12.8224
$$$$ccc!!ddddooooooddddccc55	chr1:152059440-152059661(+)$1	221	175	203	12.0680
ccc[cccffffffooooooffffff]cc	chr2:183866833-183867063(-)$1	230	178	206	12.2637
$$$$$ddddddddoooooodddd]dddd	chr14:64988931-64989161(+)$1	230	113	141	11.9291
!!ccc####ddddoooooodddd]ccc2	chr13:42875006-42875236(+)$1	230	121	149	13.5549
C:ggggggg[bboooooobb]ggggggg	chr3:101284316-101284546(+)$1	230	194	222	10.1646
f####dddd!!bboooooobb4444ddd	chr2:20885284-20885515(-)$1	231	158	186	13.4722
bbb"""eeeee[aooooooaeeeee22b	chr3:33087607-33087826(+)$1	219	95	123	12.4950
ggggg[ccc[cccoooooocccccc]gg	chr5:54674156-54674380(+)$1	224	128	156	14.8676
eeeeeeeee[cccooooooccc]eeeee	chr6:2900689-2900911(-)$1	222	117	145	13.3534
eeee####cccbboooooobb]ccc777	chr3:194168485-194168716(-)$1	231	88	116	11.9625
:ggggggg"""bboooooobb333gggg	chr3:122287935-122288158(+)$1	223	2	30	13.3029
dd[eeeeea[cccooooooccc]a]eee	chr19:9677295-9677518(-)$1	223	87	115	14.0320
==========rrrrrrrrr=========	chr8:29961736-29961966(+)$1	230	181	209	9.4310
dddd!!ccc[bboooooobb]ccc4444	chr14:20818585-20818811(+)$1	226	131	159	12.4035
dd!!eeeee!!bboooooobb333eeee	chr17:47004351-47004581(+)$1	230	58	86	13.5262
cc!!ccc!!ddddoooooodddd22ccc	chr2:228197088-228197318(+)$1	230	120	148	13.7693
[bb!!bb[eeeeeooooooeeeee]bb2	chr6:136588127-136588357(-)$1	230	35	63	11.9093
[a[ffffff[cccoooooocccffffff	chr1:150201361-150201591(-)$1	230	111	139	13.3900
22ddddccc[cccoooooocccccceee	chr1:156281757-156281984(-)$1	227	171	199	12.7949
=========[cccooooooccc======	chr19:18284649-18284880(+)$1	231	41	69	15.4589
cc!!ccc[bbcccooooooccc333bb]	chr1:24981419-24981649(+)$1	230	34	62	14.4162
ddd[dddd!!cccooooooccc]dddd]	chr18:43467637-43467867(-)$1	230	74	102	13.9502
cc"""bb[eeeeeooooooeeeee22bb	chr1:38034404-38034634(-)$1	230	149	177	12.3227
###bb[eeeeebboooooobb]eeeee]	chr3:58303068-58303294(+)$1	226	18	46	12.7468
ggg$$$$$eeeeeooooooeeeee4444	chr4:113540244-113540469(-)$1	225	76	104	12.6666
ee####ddddcccooooooccc]dddde	chr11:47755489-47755719(-)$1	230	29	57	13.9586
bb"""ccc!!ccclllccc]ccc4444b	chr11:3038238-3038468(-)$1	230	132	160	9.9630
eggggggg"""cccnnnnnccc]ggggg	chr13:31233307-31233531(+)$1	224	156	184	9.6728
d!!==========oooooo=========	chr5:71654071-71654297(+)$1	226	152	180	14.7133
::ffffff!!cccooooooccc4444ff	chr9:108226463-108226693(+)$1	230	84	112	12.5601
%ddddccc!!cccooooooccc22ccc]	chr1:229683221-229683442(-)$1	221	62	90	13.8838
hhhhhffffff[aooooooa]ffffff>	chr3:44540888-44541118(-)$1	230	129	157	10.9741

#otherMatches

#Seq PSSM
AAACGAGGUCAAUCAUGCCAUUGACCGA	chr6:53787401-53787629(+)$1	228	144	172	11.7645
CUCCAAGAUCUCAGUCUGACUCUUUUGG	chr7:151877809-151878034(-)$1	225	3	31	9.3131
CACUGCUGGGCAGAGUCUCCUAAACCAA	chr7:92763027-92763245(-)$1	218	127	155	12.4827
GGAUGUCAAGGGCUCCUAUGUCUCCAUC	chr6:31508130-31508360(-)$1	230	149	177	12.4379
UCUGGGGAGCGCUCACAUCGGCAGCUUA	chr14:31642315-31642535(-)$1	220	89	117	12.9460
GAAGAUGGUUCUGGUAAAACAACCCUCA	chr16:66783070-66783300(-)$1	230	86	114	13.6331
AGCAGGGGCUGCCCUUCCUGGCCCCCAA	chr1:16264002-16264232(+)$1	230	147	175	13.4159
CUCCUCAUGCAACGGCGGAGUUGUUUGA	chr16:14041708-14041940(+)$1	232	158	186	12.8159
CUCCAGGACCGCCCGCCAUGGCUGCAGG	chr3:38180132-38180362(+)$1	230	42	70	14.6933
AUCUACUAGUGUCAUUGCGGACCUCCAG	chr11:20419128-20419352(+)$1	224	45	73	14.2958
UGUUCAUUCGUUAUGUAUUUAACAGGAA	chr5:43446297-43446527(-)$1	230	129	157	13.1096
CAAAACAUUUGACCUUUACGCGAAUGUC	chr15:78453929-78454159(+)$1	230	48	76	11.1535
UCACACUUAGAGGAGAAGCCCUAUAAAU	chr7:5103975-5104197(+)$1	222	39	67	13.5290
CUGUGUCUCAGGGGCCAAGCCCUGAGCU	chr7:115580655-115580877(-)$1	222	25	53	12.6907
GUAUAUGGACCAUGACUUAAUGGGACUG	chr17:37657449-37657679(+)$1	230	75	103	13.4415
CCUCAAGCGACUCAACCCCGAGCGCAAG	chr19:6380198-6380419(-)$1	221	61	89	14.3070
GGAUGAUUUCUACCCAGCAGAAGAAGAC	chr8:17817512-17817734(+)$1	222	57	85	12.4208
UCAAUGCAAUGCAGACAAAUGGACUGCC	chr17:76045575-76045808(+)$1	233	157	185	12.8224
UUGUUCUUAGGAUCAUUGUGUUCAGAUG	chr1:152059440-152059661(+)$1	221	175	203	12.0680
ACUAUGCCCAUGAAAUGACUCAUGGAGC	chr2:183866833-183867063(-)$1	230	178	206	12.2637
AAAACAUUUUCUGCACAGACGGACAAAU	chr14:64988931-64989161(+)$1	230	113	141	11.9291
AAGCAAUUAUGGUGACAAAACCAGUGCA	chr13:42875006-42875236(+)$1	230	121	149	13.5549
AAUGUUAUGACUACUUUCAGGCAUGACA	chr3:101284316-101284546(+)$1	230	194	222	10.1646
CCUAAAGCCCCCUGAUGAAAGAUUUGGC	chr2:20885284-20885515(-)$1	231	158	186	13.4722
GCUGCAUAGGGUGAGUUGGCCCCUAGAA	chr3:33087607-33087826(+)$1	219	95	123	12.4950
CCUUUUCUACAACCAGGUCGUUUGGUAA	chr5:54674156-54674380(+)$1	224	128	156	14.8676
AUACUGUGUCAAGAUAACCCUUCGCACA	chr6:2900689-2900911(-)$1	222	117	145	13.3534
GCUGGCAUUGGGUUUAUCUACACUAUUA	chr3:194168485-194168716(-)$1	231	88	116	11.9625
AAAGGAGAAAGGAGGCGAAUUAACUCUC	chr3:122287935-122288158(+)$1	223	2	30	13.3029
CAAUGUGGGAGAGCUUUUACUUACUCCA	chr19:9677295-9677518(-)$1	223	87	115	14.0320
UUGUAAGGAACUUGCCAUCUUUCUUACA	chr8:29961736-29961966(+)$1	230	181	209	9.4310
UCUGAUUCAGCUAUUAGAAGAUGAUGCC	chr14:20818585-20818811(+)$1	226	131	159	12.4035
AGGCUCCAUAAUGAGAAUGCAGAAAUGG	chr17:47004351-47004581(+)$1	230	58	86	13.5262
GCACUGAAAACACCACCUCGUGUACUUA	chr2:228197088-228197318(+)$1	230	120	148	13.7693
GUUAAUCAGUUUCGAAUUAGAGGCAGAG	chr6:136588127-136588357(-)$1	230	35	63	11.9093
CAGCAAAUCACAUACUUAGAUGGAUUUG	chr1:150201361-150201591(-)$1	230	111	139	13.3900
UAUGACCAGAUGAAGUAGAUCACUGAAC	chr1:156281757-156281984(-)$1	227	171	199	12.7949
cugcugcugcugGACGUCCCCACGGCGG	chr19:18284649-18284880(+)$1	231	41	69	15.4589
GAAAACUCGUAGGUUAUCUCCUUCAGCA	chr1:24981419-24981649(+)$1	230	34	62	14.4162
GAUUACGUCAGCGAUGAGACGCAGCGUC	chr18:43467637-43467867(-)$1	230	74	102	13.9502
ACAAAGCCAAAGCCAAAAAGUUUUCAGC	chr1:38034404-38034634(-)$1	230	149	177	12.3227
AAAACUGGGCAUGUUUCCCCAUUGCCCU	chr3:58303068-58303294(+)$1	226	18	46	12.7468
GAACUAAAUUCUGAGAUGACAGAGCAUU	chr4:113540244-113540469(-)$1	225	76	104	12.6666
GCAUUGUAGUUUCAGAUUGGAGAACUGG	chr11:47755489-47755719(-)$1	230	29	57	13.9586
GGUAAGCCAGGCCCCAGGCAGGCGUAUC	chr11:3038238-3038468(-)$1	230	132	160	9.9630
UUCGAUGAAUAUCUGUUUGAGAAUUAUU	chr13:31233307-31233531(+)$1	224	156	184	9.6728
GCCACUCAGCCAGUCCCUGUUGGCUGAG	chr5:71654071-71654297(+)$1	226	152	180	14.7133
CAAAUAAAAAUGAUGAAAUUCAGAACUU	chr9:108226463-108226693(+)$1	230	84	112	12.5601
UUUGACAAGACUCGCACAGGAGAAUUGA	chr1:229683221-229683442(-)$1	221	62	90	13.8838
UUAUACACCAGAGAAUUCACACUGGUGA	chr3:44540888-44541118(-)$1	230	129	157	10.9741

#DB
..((..(((((((......)))))))..	chr6:53787401-53787629(+)$1	1	144	172	11.7645
((((((((..(((...)))...))))))	chr7:151877809-151878034(-)$1	1	3	31	9.3131
...((((((..((......))...))).	chr7:92763027-92763245(-)$1	1	127	155	12.4827
(((((....((((......)))).))))	chr6:31508130-31508360(-)$1	1	149	177	12.4379
))))))(((((((......))).)))).	chr14:31642315-31642535(-)$1	1	89	117	12.9460
.(.((.(((..((......))))).)).	chr16:66783070-66783300(-)$1	1	86	114	13.6331
.(((((((..(((......)))))))..	chr1:16264002-16264232(+)$1	1	147	175	13.4159
(((((((.(((((......))))).)))	chr16:14041708-14041940(+)$1	1	158	186	12.8159
((((..(.(.(((......))).)).))	chr3:38180132-38180362(+)$1	1	42	70	14.6933
.(((...((.(((......)))))...)	chr11:20419128-20419352(+)$1	1	45	73	14.2958
(((((....((((......))))..)))	chr5:43446297-43446527(-)$1	1	129	157	13.1096
))..(((((((.(......)))))))).	chr15:78453929-78454159(+)$1	1	48	76	11.1535
..(((.(((.(((......))).))).)	chr7:5103975-5104197(+)$1	1	39	67	13.5290
.)))(.(((((((......)))))))).	chr7:115580655-115580877(-)$1	1	25	53	12.6907
(((...(..((((......))))..)))	chr17:37657449-37657679(+)$1	1	75	103	13.4415
(.((..(((.(((......))))))..)	chr19:6380198-6380419(-)$1	1	61	89	14.3070
((.((.(((((.(......).))))).)	chr8:17817512-17817734(+)$1	1	57	85	12.4208
.....(((.(.((......)).).))).	chr17:76045575-76045808(+)$1	1	157	185	12.8224
....(((..((((......)))))))..	chr1:152059440-152059661(+)$1	1	175	203	12.0680
(((.(((((((((......)))))).))	chr2:183866833-183867063(-)$1	1	178	206	12.2637
.....((((((((......)))).))))	chr14:64988931-64989161(+)$1	1	113	141	11.9291
..(((....((((......)))).))).	chr13:42875006-42875236(+)$1	1	121	149	13.5549
).(((((((.((......)).)))))))	chr3:101284316-101284546(+)$1	1	194	222	10.1646
(....((((..((......))....)))	chr2:20885284-20885515(-)$1	1	158	186	13.4722
(((...(((((.(......))))))..)	chr3:33087607-33087826(+)$1	1	95	123	12.4950
(((((.(((.(((......)))))).))	chr5:54674156-54674380(+)$1	1	128	156	14.8676
(((((((((.(((......))).)))))	chr6:2900689-2900911(-)$1	1	117	145	13.3534
((((....(((((......)).)))...	chr3:194168485-194168716(-)$1	1	88	116	11.9625
.(((((((...((......))...))))	chr3:122287935-122288158(+)$1	1	2	30	13.3029
((.((((((.(((......))).).)))	chr19:9677295-9677518(-)$1	1	87	115	14.0320
((((((((((.........)))))))))	chr8:29961736-29961966(+)$1	1	181	209	9.4310
((((..(((.((......)).)))....	chr14:20818585-20818811(+)$1	1	131	159	12.4035
((..(((((..((......))...))))	chr17:47004351-47004581(+)$1	1	58	86	13.5262
((..(((..((((......))))..)))	chr2:228197088-228197318(+)$1	1	120	148	13.7693
.((..((.(((((......))))).)).	chr6:136588127-136588357(-)$1	1	35	63	11.9093
.(.((((((.(((......)))))))))	chr1:150201361-150201591(-)$1	1	111	139	13.3900
..))))(((.(((......))))))(((	chr1:156281757-156281984(-)$1	1	171	199	12.7949
(((((((((.(((......)))))))))	chr19:18284649-18284880(+)$1	1	41	69	15.4589
((..(((.(((((......)))...)).	chr1:24981419-24981649(+)$1	1	34	62	14.4162
(((.((((..(((......))).)))).	chr18:43467637-43467867(-)$1	1	74	102	13.9502
((...((.(((((......)))))..))	chr1:38034404-38034634(-)$1	1	149	177	12.3227
...((.(((((((......)).))))).	chr3:58303068-58303294(+)$1	1	18	46	12.7468
(((.....(((((......)))))....	chr4:113540244-113540469(-)$1	1	76	104	12.6666
((....(((((((......))).)))))	chr11:47755489-47755719(-)$1	1	29	57	13.9586
((...(((..(((...))).)))....)	chr11:3038238-3038468(-)$1	1	132	160	9.9630
)(((((((...(((.....))).)))))	chr13:31233307-31233531(+)$1	1	156	184	9.6728
(..((((((((((......)))))))))	chr5:71654071-71654297(+)$1	1	152	180	14.7133
..((((((..(((......)))....))	chr9:108226463-108226693(+)$1	1	84	112	12.5601
.(((((((..(((......)))..))).	chr1:229683221-229683442(-)$1	1	62	90	13.8838
(((((((((((.(......).)))))).	chr3:44540888-44541118(-)$1	1	129	157	10.9741

#PSSM
d : 0.19	e : 0.12	[ : 0.10	c : 0.10	: : 0.08	g : 0.06	$ : 0.06	b : 0.04	= : 0.04	' : 0.02	i : 0.02	o : 0.02	! : 0.02	C : 0.02	f : 0.02	2 : 0.02	# : 0.02	% : 0.02	h : 0.02	
c : 0.16	d : 0.16	g : 0.12	e : 0.10	: : 0.08	$ : 0.06	b : 0.06	a : 0.04	! : 0.04	# : 0.04	= : 0.04	' : 0.02	i : 0.02	[ : 0.02	2 : 0.02	h : 0.02	
g : 0.14	c : 0.14	d : 0.12	b : 0.08	[ : 0.08	! : 0.08	e : 0.06	$ : 0.06	# : 0.06	= : 0.04	" : 0.04	' : 0.02	i : 0.02	: : 0.02	f : 0.02	h : 0.02	
c : 0.14	g : 0.12	b : 0.10	e : 0.08	d : 0.08	" : 0.08	$ : 0.08	! : 0.08	= : 0.06	[ : 0.04	# : 0.04	f : 0.04	i : 0.02	: : 0.02	h : 0.02	
c : 0.16	g : 0.14	! : 0.10	" : 0.10	e : 0.08	d : 0.08	b : 0.06	$ : 0.06	# : 0.06	= : 0.06	f : 0.04	i : 0.02	a : 0.02	h : 0.02	
c : 0.16	g : 0.12	[ : 0.12	# : 0.10	d : 0.10	! : 0.08	" : 0.06	e : 0.06	= : 0.06	f : 0.06	b : 0.04	i : 0.02	$ : 0.02	
c : 0.27	g : 0.16	d : 0.12	e : 0.12	# : 0.08	= : 0.06	f : 0.06	a : 0.04	b : 0.04	" : 0.02	$ : 0.02	
c : 0.19	g : 0.14	d : 0.12	e : 0.12	[ : 0.10	# : 0.08	f : 0.08	! : 0.06	= : 0.06	b : 0.02	$ : 0.02	
! : 0.18	e : 0.18	c : 0.16	g : 0.08	d : 0.08	# : 0.06	f : 0.06	= : 0.06	a : 0.04	b : 0.04	" : 0.04	[ : 0.02	
[ : 0.23	! : 0.19	d : 0.18	e : 0.14	g : 0.06	f : 0.04	" : 0.04	= : 0.04	a : 0.02	c : 0.02	b : 0.02	
c : 0.40	d : 0.14	e : 0.14	! : 0.08	g : 0.06	f : 0.04	b : 0.04	" : 0.04	[ : 0.02	r : 0.02	= : 0.02	
c : 0.40	b : 0.19	d : 0.14	e : 0.08	[ : 0.08	g : 0.04	f : 0.02	r : 0.02	= : 0.02	
c : 0.40	b : 0.16	d : 0.14	e : 0.08	a : 0.08	g : 0.04	o : 0.04	f : 0.02	r : 0.02	= : 0.02	
o : 0.92	l : 0.04	r : 0.02	c : 0.02	
o : 0.92	l : 0.04	r : 0.02	n : 0.02	
o : 0.92	l : 0.04	r : 0.02	n : 0.02	
o : 0.92	c : 0.04	r : 0.02	n : 0.02	
o : 0.92	c : 0.04	r : 0.02	n : 0.02	
o : 0.88	c : 0.04	b : 0.04	r : 0.02	n : 0.02	
c : 0.36	b : 0.19	d : 0.14	e : 0.08	a : 0.08	g : 0.04	= : 0.04	3 : 0.02	f : 0.02	] : 0.02	
c : 0.38	b : 0.16	d : 0.14	e : 0.10	] : 0.08	g : 0.06	= : 0.04	3 : 0.02	f : 0.02	
c : 0.42	d : 0.14	e : 0.12	g : 0.08	3 : 0.08	] : 0.06	f : 0.04	= : 0.04	4 : 0.02	
d : 0.16	] : 0.16	c : 0.14	e : 0.14	g : 0.10	3 : 0.08	f : 0.06	= : 0.06	4 : 0.04	b : 0.02	a : 0.02	2 : 0.02	
c : 0.16	e : 0.16	g : 0.12	3 : 0.08	] : 0.08	d : 0.08	2 : 0.08	f : 0.06	4 : 0.06	= : 0.06	a : 0.04	b : 0.02	
c : 0.19	g : 0.14	e : 0.12	d : 0.10	4 : 0.10	] : 0.08	2 : 0.08	f : 0.06	= : 0.06	3 : 0.04	a : 0.02	
g : 0.16	c : 0.16	e : 0.14	d : 0.12	4 : 0.08	b : 0.06	] : 0.06	2 : 0.06	= : 0.06	f : 0.04	3 : 0.02	a : 0.02	7 : 0.02	
g : 0.14	c : 0.14	d : 0.14	e : 0.12	b : 0.08	2 : 0.06	= : 0.06	4 : 0.06	f : 0.06	] : 0.04	8 : 0.02	3 : 0.02	a : 0.02	5 : 0.02	7 : 0.02	
g : 0.12	e : 0.12	] : 0.10	c : 0.10	b : 0.10	d : 0.08	2 : 0.06	: : 0.06	= : 0.06	5 : 0.04	4 : 0.04	f : 0.04	6 : 0.02	8 : 0.02	7 : 0.02	> : 0.02	

#score	639.2520719897923
#seq	50
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_CDS_m2_run1.txt

#BEAR
###cccqqqqqqqqccc22cc	chr21:34901112-34901342(-)$1	230	194	215	15.0624
ffddddqqqqqqqqddddbb!	chr12:46760961-46761204(-)$1	243	120	141	13.4800
c[ddddqqqqqqqqddddccc	chr17:29551989-29552215(+)$1	226	165	186	14.4985
d[ddddqqqqqqqqdddd]dd	chr1:28177069-28177295(+)$1	226	73	94	14.2777
cc[cccqqqqqqqqccc]ccc	chr16:58077027-58077250(+)$1	223	171	192	15.2059
e[ddddqqqqqqqqdddd]ee	chr4:139100298-139100525(-)$1	227	116	137	14.3867
###cccqqqqqqqqccc8888	chr19:9676694-9676930(-)$1	236	136	157	13.2692
!!ddddqqqqqqqqdddd22g	chr3:145806339-145806562(-)$1	223	28	49	14.5517
bb[cccqqqqqqqqccc]bb]	chr10:35857954-35858203(+)$1	249	184	205	14.0283
ggggggqqqqqqqqggggggg	chr19:13054678-13055125(+)$1	447	347	368	14.9428
eee[bbqqqqqqqqbb]eeee	chr4:123813799-123814102(+)$1	303	215	236	14.2546
ffffffqqqqqqqqffffff:	chr4:41951234-41951484(+)$1	250	133	154	13.3907
ffffffqqqqqqqqffffffh	chr6:79727143-79727370(-)$1	227	58	79	14.1066
eeeebbqqqqqqqqbb]eeee	chr5:132203050-132203288(+)$1	238	134	155	14.1582
ffffffqqqqqqqqffffff3	chr12:69995124-69995392(+)$1	268	84	105	14.3362
ffffffqqqqqqqqffffff:	chr3:145806271-145806498(-)$1	227	94	115	13.3907
:eeeeeqqqqqqqqeeeeedd	chr12:38714832-38715062(+)$1	230	125	146	13.4029
gg!!bbqqqqqqqqbbggggg	chr17:19844127-19844352(-)$1	225	112	133	14.6988
""ddddqqqqqqqqdddd333	chr1:40756545-40756767(+)$1	222	165	186	14.8342
ddd[bbqqqqqqqqbb]dddd	chr19:11660985-11661211(+)$1	226	140	161	13.6337
!!ddddqqqqqqqqdddd22c	chr3:158261839-158262081(+)$1	242	170	191	14.5609
[eeeeeqqqqqqqqeeeee]d	chr12:46591649-46591879(-)$1	230	39	60	14.6975
ggggggqqqqqqqqggggggg	chr3:195789361-195789588(-)$1	227	175	196	14.9428
eee[bbqqqqqqqqbbeeeee	chr7:888005-888229(+)$1	224	81	102	14.2330
[eeeeeqqqqqqqqeeeee22	chr12:46758071-46758302(-)$1	231	193	214	14.4678
d!!cccqqqqqqqqccc]ddd	chr6:72003168-72003389(+)$1	221	166	187	14.8941
FF:cccqqqqqqqqcccdddd	chr22:29916986-29917210(-)$1	224	18	39	12.7620
g[ddddqqqqqqqqdddd]gg	chr1:156109436-156109665(+)$1	229	112	133	14.7265
[eeeeeqqqqqqqqeeeee]d	chr5:33461205-33461451(+)$1	246	93	114	14.6975
ffffffqqqqqqqqffffffb	chr2:54150410-54150640(-)$1	230	147	168	14.0061
ffffffqqqqqqqqffffffg	chr1:185278074-185278309(-)$1	235	24	45	14.2945
e[ddddqqqqqqqqddddeee	chr5:179041835-179042065(-)$1	230	84	105	14.2873
d!!cccqqqqqqqqccc22dd	chr3:125725149-125725394(-)$1	245	138	159	14.8794
======qqqqqqqq=======	chr3:15480448-15480717(+)$1	269	22	43	15.2147
ggggggqqqqqqqqggggggg	chr1:23645045-23645266(-)$1	221	92	113	14.9428
======qqqqqqqq=======	chr17:56082192-56082461(-)$1	269	176	197	15.2147
ccccccqqqqqqqqccc]ccc	chr5:108672956-108673183(-)$1	227	184	205	15.0187
cc[cccqqqqqqqqccc]ccc	chr5:32789611-32789861(+)$1	250	178	199	15.2059
ggg[bbqqqqqqqqbb]gggg	chr6:36489493-36489716(-)$1	223	26	47	14.6431
======qqqqqqqq=======	chr14:62212413-62212635(+)$1	222	181	202	15.2147
!!ddddqqqqqqqqdddd22b	chr17:60060094-60060330(-)$1	236	60	81	14.2632
ggggggqqqqqqqqggggggg	chr3:170078527-170078746(+)$1	219	105	126	14.9428
ccc[bbqqqqqqqqbb22ccc	chr5:864404-864693(-)$1	289	34	55	14.0002
cc!!bbqqqqqqqqbb22ccc	chr3:150270010-150270252(+)$1	242	80	101	14.1277
dd[cccqqqqqqqqccc]ddd	chr11:61048069-61048292(-)$1	223	133	154	14.5797
ggggggqqqqqqqqggggggg	chr15:49935583-49935815(+)$1	232	176	197	14.9428
"""cccqqqqqqqqccc22gg	chr17:45748034-45748275(+)$1	241	95	116	15.1719
ffffffqqqqqqqqffffff]	chr18:9124775-9125019(+)$1	244	73	94	14.2668
====[aqqqqqqqqa]=====	chr4:187557162-187557386(-)$1	224	111	132	14.7935
ffffffqqqqqqqqffffffd	chr7:35674686-35674908(-)$1	222	186	207	14.2063
hhh[bbqqqqqqqqbb333hh	chr14:36781081-36781304(-)$1	223	104	125	13.6926
!eeeeeqqqqqqqqeeeee]f	chr5:43502387-43502615(-)$1	228	200	221	14.6071
iiiiiiqqqqqqqqiiiiiii	chr1:203786117-203786345(+)$1	228	95	116	14.7966
ffffffqqqqqqqqffffff:	chr12:2970363-2970591(-)$1	228	4	25	13.3907
cc[cccqqqqqqqqccc22cc	chr13:33110270-33110515(-)$1	245	78	99	15.0924
c[ddddqqqqqqqqdddd]cc	chr21:43413824-43414057(-)$1	233	121	142	14.6642
&eeeeeqqqqqqqqeeeee33	chr5:64766695-64766925(-)$1	230	107	128	14.2146
####bbqqqqqqqqbb4444c	chr12:6439711-6439953(-)$1	242	127	148	14.3274
feeeeeqqqqqqqqeeeee22	chr11:18428534-18428764(+)$1	230	143	164	14.3012
$eeeeeqqqqqqqqeeeee55	chr2:189876386-189876616(+)$1	230	178	199	12.9201
eee[bbqqqqqqqqbb]eeee	chr9:135554554-135554784(+)$1	230	131	152	14.2546
ffffffqqqqqqqqffffff2	chr6:71569770-71570011(+)$1	241	161	182	14.1162
caddddqqqqqqqqdddd]a4	chr1:62907804-62908027(+)$1	223	75	96	14.3322
$$$cccqqqqqqqqccc22dd	chr13:100206570-100206803(+)$1	233	113	134	14.2660
[eeeeeqqqqqqqqeeeeecc	chr4:103226083-103226306(-)$1	223	40	61	14.7566
gggcccqqqqqqqqccc333g	chr5:131008402-131008634(-)$1	232	130	151	15.5550
ee[cccqqqqqqqqccceeee	chr4:123813305-123813530(+)$1	225	32	53	14.9624
+eeeeeqqqqqqqqeeeee>>	chr4:89345683-89345906(+)$1	223	21	42	13.6268

#otherMatches

#Seq PSSM
CACCCACAUUACUAUGGAAGC	chr21:34901112-34901342(-)$1	230	194	215	15.0624
UGUUCAUCUCCUUUUGAAGAC	chr12:46760961-46761204(-)$1	243	120	141	13.4800
GUAGGAUGUGAUAUUCCUUCU	chr17:29551989-29552215(+)$1	226	165	186	14.4985
UCACAACACUUGCAUUGUAGA	chr1:28177069-28177295(+)$1	226	73	94	14.2777
UGACCGCAUUGACACGGCCAU	chr16:58077027-58077250(+)$1	223	171	192	15.2059
UAUGGGACAAGAAACCCAGGU	chr4:139100298-139100525(-)$1	227	116	137	14.3867
GAACUCACACUGGAGAGAAAC	chr19:9676694-9676930(-)$1	236	136	157	13.2692
UGAUAAUUUUAUUUUUAUGUU	chr3:145806339-145806562(-)$1	223	28	49	14.5517
UCCUUUAGUUUGAGAAAAGAC	chr10:35857954-35858203(+)$1	249	184	205	14.0283
CUCCCCUCCAACCUGGGGGGC	chr19:13054678-13055125(+)$1	447	347	368	14.9428
CUGGCAGUUCCUUAUGAUAGA	chr4:123813799-123814102(+)$1	303	215	236	14.2546
CUUCGAUAUUCGUCUCGAAGA	chr4:41951234-41951484(+)$1	250	133	154	13.3907
UAUUCUUCAUAGGUGGAAUGU	chr6:79727143-79727370(-)$1	227	58	79	14.1066
GUAGUGUUUUAUCUUAUCUAC	chr5:132203050-132203288(+)$1	238	134	155	14.1582
AUAUCCUUAAGUUUGGAUAUU	chr12:69995124-69995392(+)$1	268	84	105	14.3362
AAGAAGCACUUAAACUUUUUA	chr3:145806271-145806498(-)$1	227	94	115	13.3907
UCUGAACAAGACUUUUCAGUG	chr12:38714832-38715062(+)$1	230	125	146	13.4029
ACAUUCUCUUCUGUGAGUCAG	chr17:19844127-19844352(-)$1	225	112	133	14.6988
CUGCUUCAAAUCUAGAGCUUU	chr1:40756545-40756767(+)$1	222	165	186	14.8342
GCUGUAAAAUCUCCUGAGGCC	chr19:11660985-11661211(+)$1	226	140	161	13.6337
CAAGAGAUUAAUUGCUCUCCG	chr3:158261839-158262081(+)$1	242	170	191	14.5609
CGUUCAUCUUUAUUUGAACUG	chr12:46591649-46591879(-)$1	230	39	60	14.6975
AACuuuuuugagauggaguuu	chr3:195789361-195789588(-)$1	227	175	196	14.9428
UGGCUGGCCAGAUACACUGCA	chr7:888005-888229(+)$1	224	81	102	14.2330
ACUCCCAGGGUAAAGGGAGGA	chr12:46758071-46758302(-)$1	231	193	214	14.4678
UAAAUUGCACUUUAAAUAAUC	chr6:72003168-72003389(+)$1	221	166	187	14.8941
UUGGUCAUCAGUGAGACGUGG	chr22:29916986-29917210(-)$1	224	18	39	12.7620
UAUUUUAUUUAGACAAGAGAU	chr1:156109436-156109665(+)$1	229	112	133	14.7265
CGUACGGUAUAUAGCGUAUUU	chr5:33461205-33461451(+)$1	246	93	114	14.6975
CGCAUGGUGGCAGACAUGUGC	chr2:54150410-54150640(-)$1	230	147	168	14.0061
UAGCACACAGAGCAGUGCUAG	chr1:185278074-185278309(-)$1	235	24	45	14.2945
GUCAAAUUGAUCUCUUUGCAG	chr5:179041835-179042065(-)$1	230	84	105	14.2873
UAUUUAGAUUUCAAUAAUCAG	chr3:125725149-125725394(-)$1	245	138	159	14.8794
UGAUUUUCUUCCCUAAGUUGA	chr3:15480448-15480717(+)$1	269	22	43	15.2147
GGUGGACGUUAUUCUCUAUCA	chr1:23645045-23645266(-)$1	221	92	113	14.9428
UGGUAUGACUCCAAGUGCUAU	chr17:56082192-56082461(-)$1	269	176	197	15.2147
CAGCUCCUUCCUCUGAGCCUG	chr5:108672956-108673183(-)$1	227	184	205	15.0187
AUCACUUUCCUUUUAGUUAUG	chr5:32789611-32789861(+)$1	250	178	199	15.2059
AUACUUUUUCAGUUAAUUAUU	chr6:36489493-36489716(-)$1	223	26	47	14.6431
UUUAGGAGCUUUAAUCUAAGU	chr14:62212413-62212635(+)$1	222	181	202	15.2147
GGUUCAGUCAAAUAUGAAAAU	chr17:60060094-60060330(-)$1	236	60	81	14.2632
AAUUCUGUUCUCCGAGAAUUU	chr3:170078527-170078746(+)$1	219	105	126	14.9428
GGGAGCAGCCAGACGUCACCC	chr5:864404-864693(-)$1	289	34	55	14.0002
CUGAGUCUUUAUUAACAAAGU	chr3:150270010-150270252(+)$1	242	80	101	14.1277
UGUGAAGCUGCUUGUUCCCAC	chr11:61048069-61048292(-)$1	223	133	154	14.5797
AAAACUUACACAUUAGUUUUU	chr15:49935583-49935815(+)$1	232	176	197	14.9428
ACCAGCUACUUACUGCUUAUC	chr17:45748034-45748275(+)$1	241	95	116	15.1719
AGAGUGUUUAUUUGUAUUUUU	chr18:9124775-9125019(+)$1	244	73	94	14.2668
UUUACCUUUACUGUGAUGGAA	chr4:187557162-187557386(-)$1	224	111	132	14.7935
UUGUGGUUUAAUUUCUGCAAC	chr7:35674686-35674908(-)$1	222	186	207	14.2063
UUACCCCUUACCCCGGAUUUA	chr14:36781081-36781304(-)$1	223	104	125	13.6926
AUUCCAAAUAUAUAUGGGAAA	chr5:43502387-43502615(-)$1	228	200	221	14.6071
AGAAGACUGCUAUUUUUUUUU	chr1:203786117-203786345(+)$1	228	95	116	14.7966
uuuccauagguuuuuggggaa	chr12:2970363-2970591(-)$1	228	4	25	13.3907
CAGACAAAUAUCCCUGUAAUG	chr13:33110270-33110515(-)$1	245	78	99	15.0924
CCUCUCUAUUUGUUGAGAAGA	chr21:43413824-43414057(-)$1	233	121	142	14.6642
UAAGUUAUUUUUUAAACUUUC	chr5:64766695-64766925(-)$1	230	107	128	14.2146
CCCUCCUCUUCAUUGGUUUAA	chr12:6439711-6439953(-)$1	242	127	148	14.3274
AAAGGAUGAUGUCUUCCUUAG	chr11:18428534-18428764(+)$1	230	143	164	14.3012
UCUUGUCAACCAGUGCAAGUG	chr2:189876386-189876616(+)$1	230	178	199	12.9201
UUUGGAAAAAAAGAUUGAAAG	chr9:135554554-135554784(+)$1	230	131	152	14.2546
CAGUAGUGCAACCCCUACUGC	chr6:71569770-71570011(+)$1	241	161	182	14.1162
UCCCGGUUUUAAAUCUGGAGU	chr1:62907804-62908027(+)$1	223	75	96	14.3322
CUUUUCUUCAUUCUGAAUAGU	chr13:100206570-100206803(+)$1	233	113	134	14.2660
AUUUGGAUUUGAUCCCAAAGU	chr4:103226083-103226306(-)$1	223	40	61	14.7566
UGCUCUGAACUUCAAGAAACG	chr5:131008402-131008634(-)$1	232	130	151	15.5550
aaCAGGUAAUUCUUCCUUUAU	chr4:123813305-123813530(+)$1	225	32	53	14.9624
UGUUUUUAAUUAUCAAAACUA	chr4:89345683-89345906(+)$1	223	21	42	13.6268

#DB
...(((........)))..))	chr21:34901112-34901342(-)$1	1	194	215	15.0624
))((((........))))((.	chr12:46760961-46761204(-)$1	1	120	141	13.4800
(.((((........)))))))	chr17:29551989-29552215(+)$1	1	165	186	14.4985
(.((((........)))).))	chr1:28177069-28177295(+)$1	1	73	94	14.2777
((.(((........))).)))	chr16:58077027-58077250(+)$1	1	171	192	15.2059
(.((((........)))).))	chr4:139100298-139100525(-)$1	1	116	137	14.3867
...(((........)))....	chr19:9676694-9676930(-)$1	1	136	157	13.2692
..((((........))))..)	chr3:145806339-145806562(-)$1	1	28	49	14.5517
((.(((........))).)).	chr10:35857954-35858203(+)$1	1	184	205	14.0283
((((((........)))))))	chr19:13054678-13055125(+)$1	1	347	368	14.9428
(((.((........)).))))	chr4:123813799-123814102(+)$1	1	215	236	14.2546
((((((........)))))).	chr4:41951234-41951484(+)$1	1	133	154	13.3907
((((((........))))))(	chr6:79727143-79727370(-)$1	1	58	79	14.1066
((((((........)).))))	chr5:132203050-132203288(+)$1	1	134	155	14.1582
((((((........)))))).	chr12:69995124-69995392(+)$1	1	84	105	14.3362
((((((........)))))).	chr3:145806271-145806498(-)$1	1	94	115	13.3907
.(((((........)))))((	chr12:38714832-38715062(+)$1	1	125	146	13.4029
((..((........)))))))	chr17:19844127-19844352(-)$1	1	112	133	14.6988
..((((........))))...	chr1:40756545-40756767(+)$1	1	165	186	14.8342
(((.((........)).))))	chr19:11660985-11661211(+)$1	1	140	161	13.6337
..((((........))))..)	chr3:158261839-158262081(+)$1	1	170	191	14.5609
.(((((........))))).)	chr12:46591649-46591879(-)$1	1	39	60	14.6975
((((((........)))))))	chr3:195789361-195789588(-)$1	1	175	196	14.9428
(((.((........)))))))	chr7:888005-888229(+)$1	1	81	102	14.2330
.(((((........)))))..	chr12:46758071-46758302(-)$1	1	193	214	14.4678
(..(((........))).)))	chr6:72003168-72003389(+)$1	1	166	187	14.8941
((.(((........)))((((	chr22:29916986-29917210(-)$1	1	18	39	12.7620
(.((((........)))).))	chr1:156109436-156109665(+)$1	1	112	133	14.7265
.(((((........))))).)	chr5:33461205-33461451(+)$1	1	93	114	14.6975
((((((........)))))))	chr2:54150410-54150640(-)$1	1	147	168	14.0061
((((((........))))))(	chr1:185278074-185278309(-)$1	1	24	45	14.2945
(.((((........)))))))	chr5:179041835-179042065(-)$1	1	84	105	14.2873
(..(((........)))..))	chr3:125725149-125725394(-)$1	1	138	159	14.8794
((((((........)))))))	chr3:15480448-15480717(+)$1	1	22	43	15.2147
((((((........)))))))	chr1:23645045-23645266(-)$1	1	92	113	14.9428
((((((........)))))))	chr17:56082192-56082461(-)$1	1	176	197	15.2147
((((((........))).)))	chr5:108672956-108673183(-)$1	1	184	205	15.0187
((.(((........))).)))	chr5:32789611-32789861(+)$1	1	178	199	15.2059
(((.((........)).))))	chr6:36489493-36489716(-)$1	1	26	47	14.6431
((((((........)))))))	chr14:62212413-62212635(+)$1	1	181	202	15.2147
..((((........))))..)	chr17:60060094-60060330(-)$1	1	60	81	14.2632
((((((........)))))))	chr3:170078527-170078746(+)$1	1	105	126	14.9428
(((.((........))..)))	chr5:864404-864693(-)$1	1	34	55	14.0002
((..((........))..)))	chr3:150270010-150270252(+)$1	1	80	101	14.1277
((.(((........))).)))	chr11:61048069-61048292(-)$1	1	133	154	14.5797
((((((........)))))))	chr15:49935583-49935815(+)$1	1	176	197	14.9428
...(((........)))..))	chr17:45748034-45748275(+)$1	1	95	116	15.1719
((((((........)))))).	chr18:9124775-9125019(+)$1	1	73	94	14.2668
((((.(........).)))))	chr4:187557162-187557386(-)$1	1	111	132	14.7935
((((((........))))))(	chr7:35674686-35674908(-)$1	1	186	207	14.2063
(((.((........))...))	chr14:36781081-36781304(-)$1	1	104	125	13.6926
.(((((........))))).)	chr5:43502387-43502615(-)$1	1	200	221	14.6071
((((((........)))))))	chr1:203786117-203786345(+)$1	1	95	116	14.7966
((((((........)))))).	chr12:2970363-2970591(-)$1	1	4	25	13.3907
((.(((........)))..))	chr13:33110270-33110515(-)$1	1	78	99	15.0924
(.((((........)))).))	chr21:43413824-43414057(-)$1	1	121	142	14.6642
.(((((........)))))..	chr5:64766695-64766925(-)$1	1	107	128	14.2146
....((........))....)	chr12:6439711-6439953(-)$1	1	127	148	14.3274
((((((........)))))..	chr11:18428534-18428764(+)$1	1	143	164	14.3012
.(((((........)))))..	chr2:189876386-189876616(+)$1	1	178	199	12.9201
(((.((........)).))))	chr9:135554554-135554784(+)$1	1	131	152	14.2546
((((((........)))))).	chr6:71569770-71570011(+)$1	1	161	182	14.1162
((((((........)))).).	chr1:62907804-62908027(+)$1	1	75	96	14.3322
...(((........)))..))	chr13:100206570-100206803(+)$1	1	113	134	14.2660
.(((((........)))))))	chr4:103226083-103226306(-)$1	1	40	61	14.7566
((((((........)))...)	chr5:131008402-131008634(-)$1	1	130	151	15.5550
((.(((........)))))))	chr4:123813305-123813530(+)$1	1	32	53	14.9624
.(((((........)))))..	chr4:89345683-89345906(+)$1	1	21	42	13.6268

#PSSM
f : 0.17	c : 0.13	g : 0.13	e : 0.10	d : 0.07	! : 0.05	[ : 0.05	= : 0.05	# : 0.04	" : 0.02	$ : 0.02	b : 0.01	: : 0.01	F : 0.01	h : 0.01	i : 0.01	& : 0.01	+ : 0.01	
e : 0.22	f : 0.16	g : 0.11	[ : 0.08	c : 0.08	! : 0.07	= : 0.05	# : 0.04	" : 0.02	d : 0.02	b : 0.01	F : 0.01	h : 0.01	i : 0.01	a : 0.01	$ : 0.01	
e : 0.20	d : 0.19	f : 0.14	g : 0.10	[ : 0.08	! : 0.05	= : 0.05	# : 0.04	c : 0.02	: : 0.01	" : 0.01	h : 0.01	i : 0.01	$ : 0.01	
c : 0.22	d : 0.17	e : 0.16	f : 0.14	[ : 0.10	g : 0.07	= : 0.05	! : 0.02	i : 0.01	# : 0.01	
c : 0.22	d : 0.17	b : 0.16	f : 0.14	e : 0.14	g : 0.07	= : 0.04	[ : 0.01	i : 0.01	
c : 0.22	d : 0.17	b : 0.16	f : 0.14	e : 0.14	g : 0.07	= : 0.04	a : 0.01	i : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.22	d : 0.17	b : 0.16	f : 0.14	e : 0.14	g : 0.07	= : 0.04	a : 0.01	i : 0.01	
c : 0.22	d : 0.17	b : 0.16	f : 0.14	e : 0.14	g : 0.07	= : 0.04	] : 0.01	i : 0.01	
c : 0.22	d : 0.17	e : 0.16	f : 0.14	g : 0.08	] : 0.07	= : 0.05	2 : 0.02	3 : 0.01	i : 0.01	4 : 0.01	
e : 0.22	d : 0.20	f : 0.14	2 : 0.10	g : 0.10	] : 0.08	= : 0.05	3 : 0.02	8 : 0.01	i : 0.01	4 : 0.01	
e : 0.23	f : 0.14	2 : 0.11	g : 0.10	c : 0.08	] : 0.07	d : 0.05	= : 0.05	3 : 0.04	b : 0.02	8 : 0.01	i : 0.01	4 : 0.01	
c : 0.14	f : 0.14	g : 0.13	d : 0.11	e : 0.10	2 : 0.07	= : 0.05	3 : 0.04	] : 0.04	b : 0.02	8 : 0.01	h : 0.01	i : 0.01	4 : 0.01	5 : 0.01	a : 0.01	> : 0.01	
c : 0.17	g : 0.17	d : 0.16	e : 0.10	= : 0.05	: : 0.04	3 : 0.04	2 : 0.04	] : 0.02	h : 0.02	b : 0.02	! : 0.01	8 : 0.01	f : 0.01	i : 0.01	5 : 0.01	4 : 0.01	> : 0.01	

#score	979.9886618330175
#seq	68
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_CDS_m1_run2.txt

#BEAR
ffffffvvvvvvvvvvvvvfffff	chr19:14203497-14203755(-)$1	258	194	218	22.6624
[fffffftttttttttttffffff	chr12:46756739-46756982(-)$1	243	13	37	21.8598
"""ccctttttttttttccc]hhh	chr4:166254597-166254827(+)$1	230	40	64	21.1504
ffff[attttttttttta]fffff	chr3:120320995-120321218(+)$1	223	182	206	22.1680
:eeeeevvvvvvvvvvvvveeeee	chr21:44524383-44524610(-)$1	227	77	101	23.6414
ddddyyyyyyyyyyyyyyyydddd	chr15:44925561-44925787(-)$1	226	4	28	20.9332
ddeeeeettttttttttteeeee3	chr2:242276798-242277025(+)$1	227	169	193	22.9436
"ddddvvvvvvvvvvvvvdddd33	chr2:101885549-101885779(+)$1	230	108	132	22.4666
ceeeeeuuuuuuuuuuuueeeee2	chrX:48435773-48435996(+)$1	223	26	50	24.6499
:eeeeevvvvvvvvvvvvveeeee	chr7:86827213-86827439(-)$1	226	106	130	23.6414
:eeeeevvvvvvvvvvvvveeeee	chr14:62203523-62203750(+)$1	227	14	38	23.6414
[eeeeeyyyyyyyyyyyyyyyyee	chrM:13763-13992(-)$1	229	79	103	22.2534
[eeeeeuuuuuuuuuuuueeeeed	chr19:3121242-3121481(+)$1	239	110	134	25.0834
gggggggtttttttttttgggggg	chr13:37596337-37596590(-)$1	253	55	79	21.5210
:eeeeeuuuuuuuuuuuueeeee:	chr15:35271777-35272003(-)$1	226	182	206	23.2697
fff[bbuuuuuuuuuuuubb]fff	chr7:32598070-32598292(+)$1	222	179	203	22.3515
ddd[bbvvvvvvvvvvvvvbb]dd	chr7:5567242-5567523(-)$1	281	125	149	21.5613
gggyyyyyyyyyyyyyyyyggggg	chr9:88592141-88592388(+)$1	247	61	85	20.9256
""cccyyyyyyyyyyyyyyyyccc	chr10:99258025-99258252(-)$1	227	66	90	21.1844
[ddddvvvvvvvvvvvvvdddd]d	chr2:242187393-242187630(-)$1	237	146	170	22.4390
[eeeeeuuuuuuuuuuuueeeee]	chr1:120464889-120465121(-)$1	232	206	230	25.2202
ffffffvvvvvvvvvvvvvfffff	chr6:71569770-71570011(+)$1	241	0	24	22.6624
##ddddwwwwwwwwwwwwwwdddd	chr4:169227537-169227767(-)$1	230	186	210	21.8473
dddd[bbtttttttttttbb]ddd	chr6:111697037-111697277(-)$1	240	184	208	20.7318
[eeeeeyyyyyyyyyyyyyyyyee	chr7:26236914-26237140(-)$1	226	42	66	22.2534
fffffftttttttttttffffff3	chr15:101717722-101717946(-)$1	224	62	86	21.4986
[eeeeewwwwwwwwwwwwwweeee	chr15:55642864-55643083(+)$1	219	58	82	23.6427
ffffffuuuuuuuuuuuuffffff	chr11:12958526-12958756(+)$1	230	34	58	23.0738
:cccwwwwwwwwwwwwwwcccfff	chr1:204518696-204518963(+)$1	267	29	53	20.5308
$eeeeevvvvvvvvvvvvveeeee	chr1:204379804-204380030(-)$1	226	63	87	24.4136
ccddddwwwwwwwwwwwwwwdddd	chr9:103109491-103109713(-)$1	222	163	187	21.6566
iiiiiivvvvvvvvvvvvviiiii	chr11:8974754-8974984(-)$1	230	77	101	22.5853
""ddddwwwwwwwwwwwwwwdddd	chr22:45813446-45813691(+)$1	245	10	34	21.9144
ffffffuuuuuuuuuuuuffffff	chr12:124848114-124848336(-)$1	222	138	162	23.0738
"eeeeewwwwwwwwwwwwwweeee	chr5:889662-889892(-)$1	230	168	192	23.5780
[eeeeeuuuuuuuuuuuueeeeei	chr15:49935583-49935815(+)$1	232	86	110	25.1214
gggggggtttttttttttgggggg	chr11:33308927-33309148(+)$1	221	136	160	21.5210
!!dddduuuuuuuuuuuudddd22	chr22:23466374-23466618(+)$1	244	144	168	22.9782
ffffffuuuuuuuuuuuuffffff	chr10:70243158-70243379(-)$1	221	119	143	23.0738
c:eeeeettttttttttteeeee:	chr12:118471959-118472182(-)$1	223	85	109	21.2208
[ddddyyyyyyyyyyyyyyyyddd	chr12:105238218-105238449(-)$1	231	61	85	21.3944
ddd!!auuuuuuuuuuuua22ddd	chr1:47746285-47746512(-)$1	227	146	170	22.6555
Heeeeeuuuuuuuuuuuueeeee:	chr16:47733157-47733381(+)$1	224	7	31	23.5481
[eeeeeuuuuuuuuuuuueeeee]	chr5:37168800-37169028(-)$1	228	178	202	25.2202
[eeeeevvvvvvvvvvvvveeeee	chr4:122737873-122738103(-)$1	230	140	164	24.6971
ffff[awwwwwwwwwwwwwwa]ff	chr3:14513677-14513921(+)$1	244	52	76	21.8872
##ddddtttttttttttdddd444	chr10:5042652-5042876(-)$1	224	146	170	21.4218
=eeeeeuuuuuuuuuuuueeeee:	chr8:11695903-11696125(+)$1	222	158	182	24.0584
:eeeeeuuuuuuuuuuuueeeeee	chr5:79770405-79770639(+)$1	234	119	143	24.1374
[bb[bbyyyyyyyyyyyyyyyybb	chr1:78958924-78959152(+)$1	228	21	45	19.5252
ggdddduuuuuuuuuuuudddd]g	chr9:35099896-35100135(-)$1	239	125	149	23.1127
ffffwwwwwwwwwwwwwwffffff	chr3:194180500-194180739(-)$1	239	20	44	21.1609
[cccwwwwwwwwwwwwwwccc]ee	chr2:55825474-55825717(-)$1	243	52	76	21.8445
!cccwwwwwwwwwwwwwwccc]ff	chr20:34322902-34323158(-)$1	256	7	31	21.5627
[eeeeevvvvvvvvvvvvveeeee	chr1:16256986-16257208(+)$1	222	192	216	24.6971
"""ccctttttttttttccc333e	chr1:110888795-110889030(+)$1	235	81	105	21.7856
eeeeewwwwwwwwwwwwwweeeee	chrM:11252-11504(+)$1	252	221	245	23.1895
:eeeeeuuuuuuuuuuuueeeee:	chr12:69995124-69995392(+)$1	268	109	133	23.2697
dd[cccuuuuuuuuuuuuccc333	chr14:35592583-35592810(+)$1	227	190	214	23.0321
bb[cccuuuuuuuuuuuuccc]bb	chr8:94746337-94746558(-)$1	221	143	167	22.2555
ffffffuuuuuuuuuuuuffffff	chr2:207638849-207639073(+)$1	224	40	64	23.0738
eeeyyyyyyyyyyyyyyyyeeeee	chr16:29821588-29821869(+)$1	281	49	73	21.8143
[eeeeeuuuuuuuuuuuueeeee]	chr12:102154932-102155163(-)$1	231	109	133	25.2202
Geeeeeuuuuuuuuuuuueeeee:	chr12:16507144-16507367(+)$1	223	25	49	23.7036
:eeeeeuuuuuuuuuuuueeeee:	chr7:148700900-148701129(-)$1	229	7	31	23.2697

#otherMatches

#Seq PSSM
GGGGCUCACGCUUAACUCCAGCCC	chr19:14203497-14203755(-)$1	258	194	218	22.6624
UGAAAACAGCCAAUCAAAGUUUUU	chr12:46756739-46756982(-)$1	243	13	37	21.8598
AUAUGUUGAAUAAUUAUACAAAGU	chr4:166254597-166254827(+)$1	230	40	64	21.1504
AGUAGUUUCUCUUUCUUAGUAUUA	chr3:120320995-120321218(+)$1	223	182	206	22.1680
AGCUCUCAUUUUCCCUUACAGAGU	chr21:44524383-44524610(-)$1	227	77	101	23.6414
AGGAAAAUCUUUUUAAUCCAUCCU	chr15:44925561-44925787(-)$1	226	4	28	20.9332
CAUGGGUUUGUAAGUUUUACCCAA	chr2:242276798-242277025(+)$1	227	169	193	22.9436
UUUUUUUUUUCCUUUUUCAGAAUC	chr2:101885549-101885779(+)$1	230	108	132	22.4666
UUGUCAGCUGUUACUUCAUGACAU	chrX:48435773-48435996(+)$1	223	26	50	24.6499
CUCAACUACCUCCAAAACCGUUGA	chr7:86827213-86827439(-)$1	226	106	130	23.6414
CACAGUCUCCCUUCCCCUCACUGU	chr14:62203523-62203750(+)$1	227	14	38	23.6414
GUAUGUUGGAGAAAUAAAAUGUGC	chrM:13763-13992(-)$1	229	79	103	22.2534
AUGUACAUCUCUCCCUCCGUACAC	chr19:3121242-3121481(+)$1	239	110	134	25.0834
AAGUAAGAUUCCAUUAACCUUAUU	chr13:37596337-37596590(-)$1	253	55	79	21.5210
ACAGGUGAUUUUUAAGUAACUUGG	chr15:35271777-35272003(-)$1	226	182	206	23.2697
CAGCAGUAUCUACUCUUUCUUUUG	chr7:32598070-32598292(+)$1	222	179	203	22.3515
UCCACCGCAAAUGCUUCUAGGCGG	chr7:5567242-5567523(-)$1	281	125	149	21.5613
GUUAAUAUAUUUUAAAUGAAAUUC	chr9:88592141-88592388(+)$1	247	61	85	20.9256
UCGAGCCACCGCCCAUAUCCCCUC	chr10:99258025-99258252(-)$1	227	66	90	21.1844
GCUCAGAGGACCUAAGAAUGAGGU	chr2:242187393-242187630(-)$1	237	146	170	22.4390
AGAUGCAAGCAAUCACAAGCGUCG	chr1:120464889-120465121(-)$1	232	206	230	25.2202
GGUACUCUGUUUUUAUUCCAGUGC	chr6:71569770-71570011(+)$1	241	0	24	22.6624
UUAUGCAUACCUUCUUCCAAGCAU	chr4:169227537-169227767(-)$1	230	186	210	21.8473
AACCUGGCAAUAAACCAUCCCGGU	chr6:111697037-111697277(-)$1	240	184	208	20.7318
ACCCUUUGGUUUGAAAGGUAAUGA	chr7:26236914-26237140(-)$1	226	42	66	22.2534
GGGUGGCUUUGAUGUUUCCAUCCA	chr15:101717722-101717946(-)$1	224	62	86	21.4986
UGGAAGAAACCAGCUCUAAGUUUC	chr15:55642864-55643083(+)$1	219	58	82	23.6427
GACUUGUUCUUCUCCAAUUAAGUC	chr11:12958526-12958756(+)$1	230	34	58	23.0738
UGCCAGAAGACUAAAGAAGGCUGG	chr1:204518696-204518963(+)$1	267	29	53	20.5308
AUCCCGUCUGUACUCUAACCGGGA	chr1:204379804-204380030(-)$1	226	63	87	24.4136
UUUACAGAUAAAGAUGCUAAUGUA	chr9:103109491-103109713(-)$1	222	163	187	21.6566
ACUUAAUUUUCAAUUUCCUUUAGG	chr11:8974754-8974984(-)$1	230	77	101	22.5853
UAUGGAUAUGCUGUAUCUCUUCCA	chr22:45813446-45813691(+)$1	245	10	34	21.9144
AGAGUCCACCCUGACCUUGACUUU	chr12:124848114-124848336(-)$1	222	138	162	23.0738
CACUUCCUCCGCCAGCUUCAGAGG	chr5:889662-889892(-)$1	230	168	192	23.5780
CAGAGGGCAAUAUGACAAUCUUUU	chr15:49935583-49935815(+)$1	232	86	110	25.1214
AACAACUCCAUACUUUUUGGUUGU	chr11:33308927-33309148(+)$1	221	136	160	21.5210
GUGGUCUUUUUUGUGUCUGGCUUG	chr22:23466374-23466618(+)$1	244	144	168	22.9782
CGCUGUAUUCCCUCUCAAGCAGUG	chr10:70243158-70243379(-)$1	221	119	143	23.0738
CCGGAAAGCCCUUCGAAGUUUCCU	chr12:118471959-118472182(-)$1	223	85	109	21.2208
UAAGUCUGCUCAAGUUCUACUGCU	chr12:105238218-105238449(-)$1	231	61	85	21.3944
GAUACCUACUCCCCCACUGCCAUC	chr1:47746285-47746512(-)$1	227	146	170	22.6555
CUCCUCCCCUGGGAAAAAGAGGAA	chr16:47733157-47733381(+)$1	224	7	31	23.5481
CUAUUUUUUUCAUACCAUAAGUAC	chr5:37168800-37169028(-)$1	228	178	202	25.2202
UGGUGCUUUUUCUUGUUUUGCACU	chr4:122737873-122738103(-)$1	230	140	164	24.6971
AUUGCCUACCCAAAAGCUGUGACA	chr3:14513677-14513921(+)$1	244	52	76	21.8872
GUGUGAUCAAAUUAAUUUCACUUU	chr10:5042652-5042876(-)$1	224	146	170	21.4218
UACCUGACCACUCUCUCCCAGGUA	chr8:11695903-11696125(+)$1	222	158	182	24.0584
CUUCUUAUCAGUUUGCAAAAGAAA	chr5:79770405-79770639(+)$1	234	119	143	24.1374
GACAUCGAGACUAUAAAAUUCAGG	chr1:78958924-78959152(+)$1	228	21	45	19.5252
AGUCUGGGAACAAGGAAGCAGAUU	chr9:35099896-35100135(-)$1	239	125	149	23.1127
AUCCCUUUCUCUCUUUAAGGAUGA	chr3:194180500-194180739(-)$1	239	20	44	21.1609
CAGUACAUUCAGGACAUCAUUUUG	chr2:55825474-55825717(-)$1	243	52	76	21.8445
CAGCGUCCAUUCCGUUAAGCUCUU	chr20:34322902-34323158(-)$1	256	7	31	21.5627
AAGGUUGACUCUGCUCCAAGACCU	chr1:16256986-16257208(+)$1	222	192	216	24.6971
uuaauauuGUAAACAUUUGUACUG	chr1:110888795-110889030(+)$1	235	81	105	21.7856
AGGCGGCUAUGGUAUAAUACGCCU	chrM:11252-11504(+)$1	252	221	245	23.1895
UGACCUUCGCUUUAACAUAGGUCU	chr12:69995124-69995392(+)$1	268	109	133	23.2697
UGAGGAACACUAUUCAACUCCCAA	chr14:35592583-35592810(+)$1	227	190	214	23.0321
CCACCUCCAGAGCAUUUUAGGCGG	chr8:94746337-94746558(-)$1	221	143	167	22.2555
AAUUACUAUUAGCAUACUGUAAUU	chr2:207638849-207639073(+)$1	224	40	64	23.0738
CCUAUUUCCCUACCAACCAAGGAG	chr16:29821588-29821869(+)$1	281	49	73	21.8143
UCUUAUUUUUAUUAUCUCAUGAGU	chr12:102154932-102155163(-)$1	231	109	133	25.2202
AGACCAAAAUUGAAAAAAUGGUUG	chr12:16507144-16507367(+)$1	223	25	49	23.7036
CUGGCCAAGAAGUACAAGGGCCAA	chr7:148700900-148701129(-)$1	229	7	31	23.2697

#DB
((((((.............)))))	chr19:14203497-14203755(-)$1	1	194	218	22.6624
.((((((...........))))))	chr12:46756739-46756982(-)$1	1	13	37	21.8598
...(((...........))).)))	chr4:166254597-166254827(+)$1	1	40	64	21.1504
((((.(...........).)))))	chr3:120320995-120321218(+)$1	1	182	206	22.1680
.(((((.............)))))	chr21:44524383-44524610(-)$1	1	77	101	23.6414
((((................))))	chr15:44925561-44925787(-)$1	1	4	28	20.9332
(((((((...........))))).	chr2:242276798-242277025(+)$1	1	169	193	22.9436
.((((.............))))..	chr2:101885549-101885779(+)$1	1	108	132	22.4666
((((((............))))).	chrX:48435773-48435996(+)$1	1	26	50	24.6499
.(((((.............)))))	chr7:86827213-86827439(-)$1	1	106	130	23.6414
.(((((.............)))))	chr14:62203523-62203750(+)$1	1	14	38	23.6414
.(((((................))	chrM:13763-13992(-)$1	1	79	103	22.2534
.(((((............))))))	chr19:3121242-3121481(+)$1	1	110	134	25.0834
(((((((...........))))))	chr13:37596337-37596590(-)$1	1	55	79	21.5210
.(((((............))))).	chr15:35271777-35272003(-)$1	1	182	206	23.2697
(((.((............)).)))	chr7:32598070-32598292(+)$1	1	179	203	22.3515
(((.((.............)).))	chr7:5567242-5567523(-)$1	1	125	149	21.5613
(((................)))))	chr9:88592141-88592388(+)$1	1	61	85	20.9256
..(((................)))	chr10:99258025-99258252(-)$1	1	66	90	21.1844
.((((.............)))).)	chr2:242187393-242187630(-)$1	1	146	170	22.4390
.(((((............))))).	chr1:120464889-120465121(-)$1	1	206	230	25.2202
((((((.............)))))	chr6:71569770-71570011(+)$1	1	0	24	22.6624
..((((..............))))	chr4:169227537-169227767(-)$1	1	186	210	21.8473
((((.((...........)).)))	chr6:111697037-111697277(-)$1	1	184	208	20.7318
.(((((................))	chr7:26236914-26237140(-)$1	1	42	66	22.2534
((((((...........)))))).	chr15:101717722-101717946(-)$1	1	62	86	21.4986
.(((((..............))))	chr15:55642864-55643083(+)$1	1	58	82	23.6427
((((((............))))))	chr11:12958526-12958756(+)$1	1	34	58	23.0738
.(((..............)))(((	chr1:204518696-204518963(+)$1	1	29	53	20.5308
.(((((.............)))))	chr1:204379804-204380030(-)$1	1	63	87	24.4136
((((((..............))))	chr9:103109491-103109713(-)$1	1	163	187	21.6566
((((((.............)))))	chr11:8974754-8974984(-)$1	1	77	101	22.5853
..((((..............))))	chr22:45813446-45813691(+)$1	1	10	34	21.9144
((((((............))))))	chr12:124848114-124848336(-)$1	1	138	162	23.0738
.(((((..............))))	chr5:889662-889892(-)$1	1	168	192	23.5780
.(((((............))))))	chr15:49935583-49935815(+)$1	1	86	110	25.1214
(((((((...........))))))	chr11:33308927-33309148(+)$1	1	136	160	21.5210
..((((............))))..	chr22:23466374-23466618(+)$1	1	144	168	22.9782
((((((............))))))	chr10:70243158-70243379(-)$1	1	119	143	23.0738
).(((((...........))))).	chr12:118471959-118472182(-)$1	1	85	109	21.2208
.((((................)))	chr12:105238218-105238449(-)$1	1	61	85	21.3944
(((..(............)..)))	chr1:47746285-47746512(-)$1	1	146	170	22.6555
((((((............))))).	chr16:47733157-47733381(+)$1	1	7	31	23.5481
.(((((............))))).	chr5:37168800-37169028(-)$1	1	178	202	25.2202
.(((((.............)))))	chr4:122737873-122738103(-)$1	1	140	164	24.6971
((((.(..............).))	chr3:14513677-14513921(+)$1	1	52	76	21.8872
..((((...........))))...	chr10:5042652-5042876(-)$1	1	146	170	21.4218
)(((((............))))).	chr8:11695903-11696125(+)$1	1	158	182	24.0584
.(((((............)))))(	chr5:79770405-79770639(+)$1	1	119	143	24.1374
.((.((................))	chr1:78958924-78959152(+)$1	1	21	45	19.5252
((((((............)))).)	chr9:35099896-35100135(-)$1	1	125	149	23.1127
((((..............))))))	chr3:194180500-194180739(-)$1	1	20	44	21.1609
.(((..............))).))	chr2:55825474-55825717(-)$1	1	52	76	21.8445
.(((..............))).))	chr20:34322902-34323158(-)$1	1	7	31	21.5627
.(((((.............)))))	chr1:16256986-16257208(+)$1	1	192	216	24.6971
...(((...........)))...)	chr1:110888795-110889030(+)$1	1	81	105	21.7856
(((((..............)))))	chrM:11252-11504(+)$1	1	221	245	23.1895
.(((((............))))).	chr12:69995124-69995392(+)$1	1	109	133	23.2697
((.(((............)))...	chr14:35592583-35592810(+)$1	1	190	214	23.0321
((.(((............))).))	chr8:94746337-94746558(-)$1	1	143	167	22.2555
((((((............))))))	chr2:207638849-207639073(+)$1	1	40	64	23.0738
(((................)))))	chr16:29821588-29821869(+)$1	1	49	73	21.8143
.(((((............))))).	chr12:102154932-102155163(-)$1	1	109	133	25.2202
((((((............))))).	chr12:16507144-16507367(+)$1	1	25	49	23.7036
.(((((............))))).	chr7:148700900-148701129(-)$1	1	7	31	23.2697

#PSSM
[ : 0.23	f : 0.16	: : 0.12	" : 0.09	d : 0.09	g : 0.06	c : 0.04	# : 0.03	! : 0.03	e : 0.03	$ : 0.01	i : 0.01	H : 0.01	= : 0.01	b : 0.01	G : 0.01	
e : 0.38	f : 0.18	d : 0.13	" : 0.06	g : 0.06	c : 0.06	# : 0.03	b : 0.03	i : 0.01	! : 0.01	: : 0.01	
e : 0.41	d : 0.20	f : 0.18	c : 0.06	g : 0.04	" : 0.03	[ : 0.03	i : 0.01	b : 0.01	
e : 0.40	f : 0.16	d : 0.16	c : 0.12	[ : 0.04	g : 0.03	y : 0.03	i : 0.01	! : 0.01	
e : 0.40	d : 0.13	f : 0.12	c : 0.07	w : 0.06	[ : 0.04	y : 0.04	b : 0.04	g : 0.03	i : 0.01	! : 0.01	
e : 0.38	f : 0.12	d : 0.09	y : 0.07	w : 0.07	c : 0.06	b : 0.06	a : 0.04	v : 0.03	g : 0.03	i : 0.01	
u : 0.35	v : 0.18	w : 0.16	y : 0.12	t : 0.07	e : 0.03	g : 0.03	f : 0.01	b : 0.01	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	t : 0.16	w : 0.16	y : 0.12	
u : 0.35	v : 0.18	w : 0.16	y : 0.12	t : 0.09	c : 0.03	a : 0.01	f : 0.01	d : 0.01	
e : 0.23	v : 0.15	y : 0.12	f : 0.10	c : 0.10	w : 0.10	d : 0.07	g : 0.03	b : 0.03	] : 0.01	a : 0.01	
e : 0.35	f : 0.15	c : 0.10	y : 0.09	w : 0.09	d : 0.07	g : 0.04	b : 0.04	i : 0.01	2 : 0.01	
e : 0.38	f : 0.15	d : 0.13	y : 0.07	c : 0.07	] : 0.04	g : 0.04	b : 0.01	i : 0.01	2 : 0.01	a : 0.01	3 : 0.01	
e : 0.38	f : 0.18	d : 0.16	] : 0.07	y : 0.04	g : 0.04	3 : 0.03	h : 0.01	c : 0.01	i : 0.01	4 : 0.01	
e : 0.43	f : 0.21	d : 0.12	3 : 0.04	g : 0.04	] : 0.03	b : 0.03	h : 0.01	c : 0.01	i : 0.01	2 : 0.01	4 : 0.01	
e : 0.23	f : 0.20	d : 0.15	: : 0.10	3 : 0.06	g : 0.06	] : 0.04	2 : 0.03	i : 0.03	b : 0.03	h : 0.01	c : 0.01	4 : 0.01	

#score	1474.486073533755
#seq	65
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_CDS_m3_run1.txt

#BEAR
d!!bbqqqqqqqqbb22ddd	chr15:86253759-86253975(+)$1	216	108	128	14.1867
!!cccqqqqqqqqcccgggg	chr10:103546127-103546347(-)$1	220	180	200	15.6413
ddcccqqqqqqqqccc]ddd	chr9:140482119-140482336(-)$1	217	52	72	15.0305
[ddddqqqqqqqqdddd]ee	chr8:11687731-11687955(+)$1	224	184	204	13.7366
gggggqqqqqqqqggggggg	chr19:10334911-10335137(-)$1	226	198	218	14.5319
eeeeeqqqqqqqqeeeeebb	chr11:46783506-46783736(-)$1	230	30	50	13.3951
eeeeeqqqqqqqqeeeee22	chr13:73335968-73336198(-)$1	230	67	87	13.4862
gg[bbqqqqqqqqbb]gggg	chr7:151049824-151050046(+)$1	222	63	83	14.3948
c[cccqqqqqqqqccc]ccc	chr1:114500738-114500964(+)$1	226	162	182	15.8451
eeeeeqqqqqqqqeeeee22	chr1:207648317-207648547(+)$1	230	186	206	13.4862
fffffqqqqqqqqffffff3	chr2:135890406-135890630(+)$1	224	20	40	13.6032
"ddddqqqqqqqqdddd444	chr17:53491430-53491660(-)$1	230	93	113	14.0074
==[bbqqqqqqqqbb=====	chr1:153923642-153923862(-)$1	220	132	152	14.6589
eeeeeqqqqqqqqeeeee00	chr6:116720405-116720630(+)$1	225	129	149	13.0779
!!cccqqqqqqqqccc22bb	chr11:118354854-118355073(+)$1	219	39	59	15.1121
c[cccqqqqqqqqccc]ccc	chr20:43532544-43532764(+)$1	220	146	166	15.8451
""cccqqqqqqqqccc333c	chr6:150004719-150004941(-)$1	222	18	38	15.9127
fffffqqqqqqqqffffff:	chr1:63329686-63329906(+)$1	220	26	46	12.7568
=====qqqqqqqq=======	chr14:91957003-91957226(-)$1	223	151	171	14.9414
c[a[aqqqqqqqqa]accc]	chr9:117103725-117103943(-)$1	218	135	155	14.7586
bcccaqqqqqqqqa]ccc]b	chr20:34241966-34242184(-)$1	218	65	85	14.3908
ggg[aqqqqqqqqagggggg	chr7:128657938-128658161(-)$1	223	35	55	14.7268
dd!!aqqqqqqqqa22dddd	chr1:229794750-229794969(+)$1	219	170	190	13.7275
gggggqqqqqqqqggggggg	chr8:37704456-37704674(+)$1	218	41	61	14.5319
e[cccqqqqqqqqccceeee	chr8:103841548-103841770(-)$1	222	5	25	15.0287
gggggqqqqqqqqggggggg	chr12:8202012-8202233(+)$1	221	192	212	14.5319
[ddddqqqqqqqqdddd]bb	chr9:110086120-110086342(+)$1	222	178	198	13.6260
ddcccqqqqqqqqccc]ddd	chr1:155452101-155452325(-)$1	224	167	187	15.0305
eeeeeqqqqqqqqeeeee]b	chr5:177632796-177633009(+)$1	213	169	189	13.6595
[ddddqqqqqqqqddddccc	chr17:76676305-76676527(-)$1	222	41	61	14.1323
eeeeeqqqqqqqqeeeeedd	chr12:95396436-95396659(-)$1	223	46	66	13.6484
ddcccqqqqqqqqccc]ddd	chr1:192545832-192546047(+)$1	215	118	138	15.0305
eeeeeqqqqqqqqeeeee]b	chr10:103901127-103901357(+)$1	230	25	45	13.6595
###bbqqqqqqqqbb4444a	chr20:49510690-49510917(-)$1	227	185	205	14.5210
iiiiiqqqqqqqqiiiiiii	chr2:232322956-232323176(-)$1	220	61	81	14.5507
ggg[aqqqqqqqqagggggg	chr3:107789868-107790093(-)$1	225	154	174	14.7268
d[a[aqqqqqqqqa]a]ddd	chr5:179136927-179137168(+)$1	241	3	23	14.6401
fffffqqqqqqqqffffff:	chr19:38869800-38870017(+)$1	217	197	217	12.7568
c!!bbqqqqqqqqbb333cc	chr19:17430358-17430581(+)$1	223	104	124	15.1338
##cccqqqqqqqqccc4444	chrX:107381082-107381299(+)$1	217	145	165	15.5078
!!cccqqqqqqqqcccffff	chrX:153133216-153133439(+)$1	223	183	203	15.2453
c!!bbqqqqqqqqbb]ccc2	chr2:224642373-224642599(-)$1	226	13	33	14.4945
[ddddqqqqqqqqddddhhh	chr10:124895500-124895718(-)$1	218	55	75	13.4257
fffffqqqqqqqqffffffC	chr9:139945710-139945931(+)$1	221	3	23	12.7009
f!!bbqqqqqqqqbb22fff	chr14:31596959-31597179(-)$1	220	33	53	14.1431
cccbbqqqqqqqqbb]ccc]	chr16:30732564-30732794(+)$1	230	198	218	14.3574
[ddddqqqqqqqqddddddd	chr19:48640707-48640930(-)$1	223	41	61	13.7755
!ddddqqqqqqqqdddd22c	chrX:133551190-133551414(+)$1	224	39	59	13.7810
!!cccqqqqqqqqccc333c	chr8:56864513-56864739(+)$1	226	158	178	16.0900
eeeeeqqqqqqqqeeeee66	chr7:92146836-92147059(-)$1	223	43	63	12.9694
!!cccqqqqqqqqcccgggg	chr8:26248737-26248958(+)$1	221	88	108	15.6413
c[cccqqqqqqqqccc]ccc	chr17:75398138-75398359(+)$1	221	32	52	15.8451
d!!bbqqqqqqqqbb333dd	chr22:32179804-32180027(+)$1	223	134	154	14.7875
c[cccqqqqqqqqccc]ccc	chr11:119158499-119158721(+)$1	222	176	196	15.8451
cccccqqqqqqqqccc::dd	chr20:46279893-46280119(+)$1	226	23	43	13.1529
[bbbbqqqqqqqqbb22bb]	chr19:6586180-6586396(-)$1	216	28	48	13.1747
c[cccqqqqqqqqccc22cc	chr12:95397276-95397499(-)$1	223	35	55	15.4554
ddcccqqqqqqqqccc]ddd	chr18:48702862-48703085(-)$1	223	160	180	15.0305
bb!!aqqqqqqqqa22bb]c	chr5:134010316-134010536(+)$1	220	188	208	13.0599
a[cccqqqqqqqqcccabb:	chr1:155838205-155838430(+)$1	225	8	28	14.0891
f[cccqqqqqqqqccc]fff	chr1:39765796-39766016(+)$1	220	138	158	15.3283
cc[bbqqqqqqqqbbccc22	chr18:12720556-12720776(+)$1	220	111	131	14.0865
""cccqqqqqqqqccc]ccc	chr3:32525439-32525662(-)$1	223	197	217	15.8076
c[cccqqqqqqqqccc]ccc	chr2:42544497-42544715(+)$1	218	104	124	15.8451

#otherMatches

#Seq PSSM
GAAACAAGCGUAAGUAGCUC	chr15:86253759-86253975(+)$1	216	108	128	14.1867
GCACCUUGUGAAUGGUAGUU	chr10:103546127-103546347(-)$1	220	180	200	15.6413
CCUUCUCAGGCCCGAAUGGA	chr9:140482119-140482336(-)$1	217	52	72	15.0305
GUGCUAUUCCACAGGUAGGG	chr8:11687731-11687955(+)$1	224	184	204	13.7366
GUGGUCCGCUCAAGCCACGC	chr19:10334911-10335137(-)$1	226	198	218	14.5319
UGGCAUGAAUGUUUGCCAAC	chr11:46783506-46783736(-)$1	230	30	50	13.3951
AUGGAUAAUGAUUUUCAUCA	chr13:73335968-73336198(-)$1	230	67	87	13.4862
UAUUUUACAGAAUAGCUGAA	chr7:151049824-151050046(+)$1	222	63	83	14.3948
CCUGCGUUUCAAAGUAAGUG	chr1:114500738-114500964(+)$1	226	162	182	15.8451
AUUAGGUGUCAUACUGAUAA	chr1:207648317-207648547(+)$1	230	186	206	13.4862
UGGUCUAAAAUGUGAUUAUU	chr2:135890406-135890630(+)$1	224	20	40	13.6032
AUGGCCGCUACAAGCCAACU	chr17:53491430-53491660(-)$1	230	93	113	14.0074
CGUGGCUGCCUUCCCUGCAU	chr1:153923642-153923862(-)$1	220	132	152	14.6589
ACAGCCAUCCCAUGCUGUAC	chr6:116720405-116720630(+)$1	225	129	149	13.0779
UUAGGAAAAACCACCUCCGG	chr11:118354854-118355073(+)$1	219	39	59	15.1121
UACUUGAAAAUGAAAGGAGA	chr20:43532544-43532764(+)$1	220	146	166	15.8451
UCAGUCAUCUUCUGCUCCAG	chr6:150004719-150004941(-)$1	222	18	38	15.9127
UGGUCAUUCCAGAGACUAUG	chr1:63329686-63329906(+)$1	220	26	46	12.7568
UGUGUUUUAUCUUGCAUAUU	chr14:91957003-91957226(-)$1	223	151	171	14.9414
GAGCCUUCAUUCUGACCUUC	chr9:117103725-117103943(-)$1	218	135	155	14.7586
CCUGCCACAGAAAGACAGUG	chr20:34241966-34242184(-)$1	218	65	85	14.3908
UGAAGAUUCAGACCUCAUUU	chr7:128657938-128658161(-)$1	223	35	55	14.7268
UGACGUCCAGUUCCUGCGGG	chr1:229794750-229794969(+)$1	219	170	190	13.7275
GCCCCCAUUGUUAGGGGCCA	chr8:37704456-37704674(+)$1	218	41	61	14.5319
AAUACCUGCGUAAGUAUGAG	chr8:103841548-103841770(-)$1	222	5	25	15.0287
AUGUUGAAAAGGAAGCAUAG	chr12:8202012-8202233(+)$1	221	192	212	14.5319
GUGACUAAUCAGUGUCAGUU	chr9:110086120-110086342(+)$1	222	178	198	13.6260
AGGGAGAAAACAAUCCUUUG	chr1:155452101-155452325(-)$1	224	167	187	15.0305
AGGGUUUGGGUUUAUCCUGU	chr5:177632796-177633009(+)$1	213	169	189	13.6595
AUGUUUCUCAGUUAACAGCU	chr17:76676305-76676527(-)$1	222	41	61	14.1323
UUUUGGGUAUUCACAGGACA	chr12:95396436-95396659(-)$1	223	46	66	13.6484
UUCUUGCCAACCAAAGUAAG	chr1:192545832-192546047(+)$1	215	118	138	15.0305
GGGCACCCCCUCCUGCCCCA	chr10:103901127-103901357(+)$1	230	25	45	13.6595
AGAUCCUCUUUAUGAAAUAG	chr20:49510690-49510917(-)$1	227	185	205	14.5210
GUUUUUUUAAUCUAGAGCGA	chr2:232322956-232323176(-)$1	220	61	81	14.5507
GUAAGUAUUAUUUCUACUUU	chr3:107789868-107790093(-)$1	225	154	174	14.7268
GAGGACUAUAAACUGCACUU	chr5:179136927-179137168(+)$1	241	3	23	14.6401
GACAUACAGACCAAUGUCUA	chr19:38869800-38870017(+)$1	217	197	217	12.7568
UAAGACUCUCAACUCCACAG	chr19:17430358-17430581(+)$1	223	104	124	15.1338
CACUUCUUUCCCUGAGCCCA	chrX:107381082-107381299(+)$1	217	145	165	15.5078
CAGGGAUGUGAGCCCCGGCC	chrX:153133216-153133439(+)$1	223	183	203	15.2453
AUACAUUUCAUAUUGCUCUU	chr2:224642373-224642599(-)$1	226	13	33	14.4945
UGGAGAACGGGGACUCCUUG	chr10:124895500-124895718(-)$1	218	55	75	13.4257
CUCUUCCUGGCCCGAGAGGA	chr9:139945710-139945931(+)$1	221	3	23	12.7009
CUAUGUCAACAUCCAGUGUU	chr14:31596959-31597179(-)$1	220	33	53	14.1431
CAUUCUAUCUCCCGAUAUGC	chr16:30732564-30732794(+)$1	230	198	218	14.3574
GUGGCCGAGAACAGCCGCAG	chr19:48640707-48640930(-)$1	223	41	61	13.7755
CUAUUGGAUGUGAAAUAAAA	chrX:133551190-133551414(+)$1	224	39	59	13.7810
AAAGUAAGUAAAAACUGAAG	chr8:56864513-56864739(+)$1	226	158	178	16.0900
UGCAUUCAAAAAUAUGCAGU	chr7:92146836-92147059(-)$1	223	43	63	12.9694
GCUGGAACACGUACCAUCCU	chr8:26248737-26248958(+)$1	221	88	108	15.6413
UCGAGACACCCAACUCCACC	chr17:75398138-75398359(+)$1	221	32	52	15.8451
UGAGCUGUGAAAUGUGGGAU	chr22:32179804-32180027(+)$1	223	134	154	14.7875
AUUUUGUACAGUGGAGUUGU	chr11:119158499-119158721(+)$1	222	176	196	15.8451
CCCACCUCCUAAUGUGACUG	chr20:46279893-46280119(+)$1	226	23	43	13.1529
GCCGCUCCUUCCUGCAUGGA	chr19:6586180-6586396(-)$1	216	28	48	13.1747
GAGGCAAGAUGGAGUUAGUG	chr12:95397276-95397499(-)$1	223	35	55	15.4554
UGGUUCCACCUCUAGCUCAC	chr18:48702862-48703085(-)$1	223	160	180	15.0305
UGGUUUAAACUGUAUACACA	chr5:134010316-134010536(+)$1	220	188	208	13.0599
GUGGACUAUAACUUCCCGAA	chr1:155838205-155838430(+)$1	225	8	28	14.0891
GAGAUCAAAAACCAUCGUUC	chr1:39765796-39766016(+)$1	220	138	158	15.3283
ACUCUAUGAUGAAAGGUGAG	chr18:12720556-12720776(+)$1	220	111	131	14.0865
CACUUAAUGCCUAAAGACUC	chr3:32525439-32525662(-)$1	223	197	217	15.8076
UUUAUUUACCUCUAUGUAGU	chr2:42544497-42544715(+)$1	218	104	124	15.8451

#DB
(..((........))..)))	chr15:86253759-86253975(+)$1	1	108	128	14.1867
..(((........)))))))	chr10:103546127-103546347(-)$1	1	180	200	15.6413
(((((........))).)))	chr9:140482119-140482336(-)$1	1	52	72	15.0305
.((((........)))).))	chr8:11687731-11687955(+)$1	1	184	204	13.7366
(((((........)))))))	chr19:10334911-10335137(-)$1	1	198	218	14.5319
(((((........)))))))	chr11:46783506-46783736(-)$1	1	30	50	13.3951
(((((........)))))..	chr13:73335968-73336198(-)$1	1	67	87	13.4862
((.((........)).))))	chr7:151049824-151050046(+)$1	1	63	83	14.3948
(.(((........))).)))	chr1:114500738-114500964(+)$1	1	162	182	15.8451
(((((........)))))..	chr1:207648317-207648547(+)$1	1	186	206	13.4862
(((((........)))))).	chr2:135890406-135890630(+)$1	1	20	40	13.6032
.((((........))))...	chr17:53491430-53491660(-)$1	1	93	113	14.0074
((.((........)))))))	chr1:153923642-153923862(-)$1	1	132	152	14.6589
(((((........)))))..	chr6:116720405-116720630(+)$1	1	129	149	13.0779
..(((........)))..))	chr11:118354854-118355073(+)$1	1	39	59	15.1121
(.(((........))).)))	chr20:43532544-43532764(+)$1	1	146	166	15.8451
..(((........)))...)	chr6:150004719-150004941(-)$1	1	18	38	15.9127
(((((........)))))).	chr1:63329686-63329906(+)$1	1	26	46	12.7568
(((((........)))))))	chr14:91957003-91957226(-)$1	1	151	171	14.9414
(.(.(........).)))).	chr9:117103725-117103943(-)$1	1	135	155	14.7586
(((((........).))).)	chr20:34241966-34242184(-)$1	1	65	85	14.3908
(((.(........)))))))	chr7:128657938-128658161(-)$1	1	35	55	14.7268
((..(........)..))))	chr1:229794750-229794969(+)$1	1	170	190	13.7275
(((((........)))))))	chr8:37704456-37704674(+)$1	1	41	61	14.5319
(.(((........)))))))	chr8:103841548-103841770(-)$1	1	5	25	15.0287
(((((........)))))))	chr12:8202012-8202233(+)$1	1	192	212	14.5319
.((((........)))).))	chr9:110086120-110086342(+)$1	1	178	198	13.6260
(((((........))).)))	chr1:155452101-155452325(-)$1	1	167	187	15.0305
(((((........))))).)	chr5:177632796-177633009(+)$1	1	169	189	13.6595
.((((........)))))))	chr17:76676305-76676527(-)$1	1	41	61	14.1323
(((((........)))))((	chr12:95396436-95396659(-)$1	1	46	66	13.6484
(((((........))).)))	chr1:192545832-192546047(+)$1	1	118	138	15.0305
(((((........))))).)	chr10:103901127-103901357(+)$1	1	25	45	13.6595
...((........))....)	chr20:49510690-49510917(-)$1	1	185	205	14.5210
(((((........)))))))	chr2:232322956-232323176(-)$1	1	61	81	14.5507
(((.(........)))))))	chr3:107789868-107790093(-)$1	1	154	174	14.7268
(.(.(........).).)))	chr5:179136927-179137168(+)$1	1	3	23	14.6401
(((((........)))))).	chr19:38869800-38870017(+)$1	1	197	217	12.7568
(..((........))...))	chr19:17430358-17430581(+)$1	1	104	124	15.1338
..(((........)))....	chrX:107381082-107381299(+)$1	1	145	165	15.5078
..(((........)))))))	chrX:153133216-153133439(+)$1	1	183	203	15.2453
(..((........)).))).	chr2:224642373-224642599(-)$1	1	13	33	14.4945
.((((........)))))))	chr10:124895500-124895718(-)$1	1	55	75	13.4257
(((((........))))))(	chr9:139945710-139945931(+)$1	1	3	23	12.7009
(..((........))..)))	chr14:31596959-31597179(-)$1	1	33	53	14.1431
(((((........)).))).	chr16:30732564-30732794(+)$1	1	198	218	14.3574
.((((........)))))))	chr19:48640707-48640930(-)$1	1	41	61	13.7755
.((((........))))..)	chrX:133551190-133551414(+)$1	1	39	59	13.7810
..(((........)))...)	chr8:56864513-56864739(+)$1	1	158	178	16.0900
(((((........)))))..	chr7:92146836-92147059(-)$1	1	43	63	12.9694
..(((........)))))))	chr8:26248737-26248958(+)$1	1	88	108	15.6413
(.(((........))).)))	chr17:75398138-75398359(+)$1	1	32	52	15.8451
(..((........))...))	chr22:32179804-32180027(+)$1	1	134	154	14.7875
(.(((........))).)))	chr11:119158499-119158721(+)$1	1	176	196	15.8451
))(((........)))..((	chr20:46279893-46280119(+)$1	1	23	43	13.1529
.((((........))..)).	chr19:6586180-6586396(-)$1	1	28	48	13.1747
(.(((........)))..))	chr12:95397276-95397499(-)$1	1	35	55	15.4554
(((((........))).)))	chr18:48702862-48703085(-)$1	1	160	180	15.0305
((..(........)..)).)	chr5:134010316-134010536(+)$1	1	188	208	13.0599
(.(((........)))))).	chr1:155838205-155838430(+)$1	1	8	28	14.0891
(.(((........))).)))	chr1:39765796-39766016(+)$1	1	138	158	15.3283
((.((........)))))..	chr18:12720556-12720776(+)$1	1	111	131	14.0865
..(((........))).)))	chr3:32525439-32525662(-)$1	1	197	217	15.8076
(.(((........))).)))	chr2:42544497-42544715(+)$1	1	104	124	15.8451

#PSSM
c : 0.18	e : 0.14	d : 0.12	! : 0.09	[ : 0.09	g : 0.09	f : 0.09	" : 0.04	= : 0.03	b : 0.03	# : 0.03	i : 0.01	a : 0.01	
d : 0.18	[ : 0.17	! : 0.15	e : 0.12	g : 0.09	f : 0.06	c : 0.06	= : 0.03	" : 0.03	# : 0.03	b : 0.03	i : 0.01	
c : 0.37	e : 0.12	! : 0.10	d : 0.10	g : 0.07	f : 0.06	[ : 0.04	a : 0.03	= : 0.01	# : 0.01	i : 0.01	b : 0.01	
c : 0.35	b : 0.17	e : 0.12	d : 0.10	f : 0.06	[ : 0.06	g : 0.04	! : 0.03	= : 0.01	i : 0.01	
c : 0.34	b : 0.17	e : 0.12	d : 0.10	a : 0.10	f : 0.06	g : 0.04	= : 0.01	i : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.34	b : 0.17	e : 0.12	d : 0.10	a : 0.10	f : 0.06	g : 0.04	= : 0.01	i : 0.01	
c : 0.34	b : 0.17	e : 0.12	d : 0.10	g : 0.07	f : 0.06	] : 0.04	2 : 0.03	= : 0.01	i : 0.01	
c : 0.37	e : 0.12	d : 0.10	2 : 0.07	g : 0.07	f : 0.06	] : 0.04	= : 0.03	a : 0.03	3 : 0.03	4 : 0.01	i : 0.01	
] : 0.18	e : 0.14	g : 0.12	d : 0.12	2 : 0.07	f : 0.07	c : 0.07	3 : 0.06	= : 0.03	4 : 0.03	i : 0.01	: : 0.01	b : 0.01	a : 0.01	
c : 0.18	e : 0.14	d : 0.12	g : 0.12	f : 0.10	3 : 0.06	4 : 0.04	2 : 0.04	b : 0.04	] : 0.03	= : 0.03	i : 0.01	h : 0.01	: : 0.01	
c : 0.18	d : 0.17	g : 0.12	f : 0.10	b : 0.07	2 : 0.06	] : 0.06	4 : 0.04	e : 0.03	= : 0.03	3 : 0.03	0 : 0.01	i : 0.01	h : 0.01	6 : 0.01	
c : 0.20	d : 0.17	g : 0.12	b : 0.09	2 : 0.06	: : 0.04	] : 0.04	f : 0.04	e : 0.03	4 : 0.03	= : 0.03	3 : 0.01	0 : 0.01	a : 0.01	i : 0.01	h : 0.01	C : 0.01	6 : 0.01	

#score	924.1047699682873
#seq	64
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_CDS_m2_run2.txt

#BEAR
eeeeeqqqqqqqqeeeee	chr5:32403253-32403475(-)$1	222	13	31	14.9871
[ddddqqqqqqqqdddde	chr14:70990495-70990725(-)$1	230	159	177	14.3056
cc[bbqqqqqqqqbbccc	chr11:122930362-122930592(-)$1	230	63	81	12.8687
!!cccqqqqqqqqccc22	chr3:125725215-125725445(-)$1	230	190	208	13.7064
"ddddqqqqqqqqdddd2	chr6:80718074-80718297(+)$1	223	197	215	13.9270
:ddddqqqqqqqqddddc	chr6:27841149-27841374(-)$1	225	168	186	12.9204
gggggqqqqqqqqggggg	chr3:160148850-160149074(+)$1	224	180	198	13.8398
eeeeeqqqqqqqqeeeee	chr17:1384041-1384262(-)$1	221	30	48	14.9871
d[a[aqqqqqqqqa]a]d	chr17:4700667-4700891(+)$1	224	17	35	13.2953
d[cccqqqqqqqqccc]d	chr11:107682300-107682524(-)$1	224	118	136	13.7283
fffffqqqqqqqqfffff	chr12:51512352-51512582(-)$1	230	122	140	13.6036
fffffqqqqqqqqfffff	chr1:100525393-100525613(+)$1	220	70	88	13.6036
cccccqqqqqqqqccc]c	chr18:48584632-48584862(+)$1	230	170	188	13.7838
=====qqqqqqqq=====	chr8:41905879-41906104(-)$1	225	145	163	13.8718
dd[bbqqqqqqqqbb]dd	chr17:27805205-27805427(+)$1	222	96	114	12.8133
[ddddqqqqqqqqdddd]	chr9:5933733-5933963(-)$1	230	209	227	14.2435
gggggqqqqqqqqggggg	chr2:180838322-180838552(-)$1	230	163	181	13.8398
ccc[aqqqqqqqqa]ccc	chr1:120168481-120168704(-)$1	223	204	222	13.4777
[ddddqqqqqqqqddddd	chr15:59911190-59911420(+)$1	230	59	77	14.0810
fffffqqqqqqqqfffff	chr1:91382360-91382581(-)$1	221	142	160	13.6036
fffffqqqqqqqqfffff	chr5:74891977-74892207(+)$1	230	85	103	13.6036
eeeeaqqqqqqqqa]eee	chr14:103931975-103932197(+)$1	222	124	142	14.5531
eeeeeqqqqqqqqeeeee	chr20:48522085-48522305(+)$1	220	41	59	14.9871
e[cccqqqqqqqqcccee	chr8:11667167-11667397(+)$1	230	78	96	14.3110
[ddddqqqqqqqqdddd]	chr4:106155729-106155959(+)$1	230	200	218	14.2435
eeeeeqqqqqqqqeeeee	chr4:96073711-96073933(-)$1	222	115	133	14.9871
"ddddqqqqqqqqdddd3	chr11:61081034-61081260(-)$1	226	80	98	14.1205
eeeeeqqqqqqqqeeeee	chr2:184024144-184024374(+)$1	230	92	110	14.9871
f!!bbqqqqqqqqbb]ff	chr6:31475115-31475335(+)$1	220	161	179	12.9856
[ddddqqqqqqqqdddd]	chr1:220368542-220368772(-)$1	230	185	203	14.2435
fffffqqqqqqqqfffff	chr14:74976335-74976555(-)$1	220	34	52	13.6036
[ddddqqqqqqqqdddd]	chr4:148544989-148545215(+)$1	226	73	91	14.2435
eeeeeqqqqqqqqeeeee	chr12:100598643-100598873(+)$1	230	207	225	14.9871
eee[aqqqqqqqqa]eee	chr10:12126588-12126812(+)$1	224	119	137	14.3982
##cccqqqqqqqqccc44	chr5:74100306-74100530(-)$1	224	39	57	13.6949
eeeeeqqqqqqqqeeeee	chr20:61299319-61299544(+)$1	225	70	88	14.9871
[a[bbqqqqqqqqbbaee	chr1:32627443-32627668(+)$1	225	129	147	13.3015
!ddddqqqqqqqqdddd]	chr16:67262185-67262410(+)$1	225	128	146	14.2137
gggggqqqqqqqqggggg	chr6:72011310-72011532(+)$1	222	4	22	13.8398
eeeeeqqqqqqqqeeeee	chr6:100965790-100966021(-)$1	231	96	114	14.9871
eeeeeqqqqqqqqeeeee	chr7:97488542-97488763(-)$1	221	126	144	14.9871
eeeeeqqqqqqqqeeeee	chr4:103527638-103527865(+)$1	227	139	157	14.9871
ff[bbqqqqqqqqbb]ff	chr8:11687732-11687962(+)$1	230	60	78	12.9262
fffffqqqqqqqqfffff	chr11:111225123-111225349(-)$1	226	195	213	13.6036
eeeeeqqqqqqqqeeeee	chr2:75881917-75882141(+)$1	224	141	159	14.9871
eeeeeqqqqqqqqeeeee	chr1:101379132-101379356(+)$1	224	116	134	14.9871
eeeeeqqqqqqqqeeeee	chr10:64967736-64967957(-)$1	221	12	30	14.9871
eeeeeqqqqqqqqeeeee	chr8:17823801-17824026(+)$1	225	32	50	14.9871
c[cccqqqqqqqqccc]c	chr19:41257234-41257464(+)$1	230	195	213	13.8647
eeeeeqqqqqqqqeeeee	chr5:110097335-110097565(+)$1	230	172	190	14.9871
[ddddqqqqqqqqddddd	chrX:118763280-118763510(-)$1	230	97	115	14.0810
eeeeeqqqqqqqqeeeee	chr1:37947965-37948192(+)$1	227	4	22	14.9871
cccccqqqqqqqqccc]c	chr2:113330044-113330274(+)$1	230	137	155	13.7838
gggggqqqqqqqqggggg	chr19:52090675-52090905(+)$1	230	147	165	13.8398
eeeeeqqqqqqqqeeeee	chr20:25597084-25597314(-)$1	230	23	41	14.9871
cccbbqqqqqqqqbb]cc	chr3:49094938-49095168(-)$1	230	34	52	12.8165
"""bbqqqqqqqqbb333	chr11:3038238-3038468(-)$1	230	32	50	12.7747
dddddqqqqqqqqddddb	chr10:43882441-43882671(-)$1	230	150	168	13.5373
fffffqqqqqqqqfffff	chr14:39545172-39545394(-)$1	222	143	161	13.6036
fffffqqqqqqqqfffff	chr18:54283399-54283629(-)$1	230	210	228	13.6036
eeeeeqqqqqqqqeeeee	chr3:127340415-127340645(+)$1	230	1	19	14.9871
fffffqqqqqqqqfffff	chr11:35685186-35685411(+)$1	225	36	54	13.6036
!!cccqqqqqqqqccc22	chr5:132232221-132232444(-)$1	223	71	89	13.7064
eeeeeqqqqqqqqeeeee	chr8:90777536-90777766(+)$1	230	131	149	14.9871
fffffqqqqqqqqfffff	chr11:67926429-67926654(-)$1	225	188	206	13.6036
#ddddqqqqqqqqdddd2	chr1:23885585-23885815(-)$1	230	183	201	13.8887
eeeeeqqqqqqqqeeeee	chr7:77423530-77423760(-)$1	230	197	215	14.9871
eeeeeqqqqqqqqeeeee	chr8:17092216-17092446(-)$1	230	87	105	14.9871
"ddddqqqqqqqqdddd4	chr8:124267209-124267439(-)$1	230	23	41	14.0525
!!cccqqqqqqqqccc22	chr1:235295171-235295395(-)$1	224	111	129	13.7064
cddddqqqqqqqqdddd:	chr22:29912933-29913159(-)$1	226	121	139	12.9724

#otherMatches

#Seq PSSM
CAACAGAACCAAAUGUUG	chr5:32403253-32403475(-)$1	222	13	31	14.9871
ACAAGGCAUGAAGCUUGG	chr14:70990495-70990725(-)$1	230	159	177	14.3056
AGAGCUGUAAGACGCCUC	chr11:122930362-122930592(-)$1	230	63	81	12.8687
AUUUAGAUUUCAAUAAUC	chr3:125725215-125725445(-)$1	230	190	208	13.7064
AAUAUUAAAUCAUAUAUA	chr6:80718074-80718297(+)$1	223	197	215	13.9270
AGGGCAUCACCAAGCCCG	chr6:27841149-27841374(-)$1	225	168	186	12.9204
UCUUUAUGAAAAAGGAGG	chr3:160148850-160149074(+)$1	224	180	198	13.8398
GGGCUCUUUUCCCAGUCC	chr17:1384041-1384262(-)$1	221	30	48	14.9871
GGUGGAAGACAGGUGGGC	chr17:4700667-4700891(+)$1	224	17	35	13.2953
UAACCAGUGUCCAGGUAA	chr11:107682300-107682524(-)$1	224	118	136	13.7283
CUGCUACCUCUCCAGCAG	chr12:51512352-51512582(-)$1	230	122	140	13.6036
AUUGGUGCUCUUUCUGAU	chr1:100525393-100525613(+)$1	220	70	88	13.6036
UGCCGCCCCAUCCCGGAC	chr18:48584632-48584862(+)$1	230	170	188	13.7838
AGAGAGUUGUGAGUCUCU	chr8:41905879-41906104(-)$1	225	145	163	13.8718
CAGCAAUUACACAUGGUG	chr17:27805205-27805427(+)$1	222	96	114	12.8133
UGAGGUAAGUUUCCCUCC	chr9:5933733-5933963(-)$1	230	209	227	14.2435
UUCGAAAAGGCUAUCGAA	chr2:180838322-180838552(-)$1	230	163	181	13.8398
CAGGUGAGGAGAAAGCUG	chr1:120168481-120168704(-)$1	223	204	222	13.4777
AGUGAGAGACACAUUACA	chr15:59911190-59911420(+)$1	230	59	77	14.0810
GGUGGAAGUCACGUCACU	chr1:91382360-91382581(-)$1	221	142	160	13.6036
UUUUCCCAAUGAAGAGGA	chr5:74891977-74892207(+)$1	230	85	103	13.6036
CUCACUUCCCUUUGAUGG	chr14:103931975-103932197(+)$1	222	124	142	14.5531
CCCUUGGAGCUGGAAGGG	chr20:48522085-48522305(+)$1	220	41	59	14.9871
GUGGAAAAGAAGGUCCCG	chr8:11667167-11667397(+)$1	230	78	96	14.3110
ACAGACCUCUAACUCUGA	chr4:106155729-106155959(+)$1	230	200	218	14.2435
GGAAGCUGGUAUUCUUCC	chr4:96073711-96073933(-)$1	222	115	133	14.9871
AGGUCUGUUGAGCGACCG	chr11:61081034-61081260(-)$1	226	80	98	14.1205
AGAUGUGCUUUAUCAUCU	chr2:184024144-184024374(+)$1	230	92	110	14.9871
CAAGAAGAAAACAUCAGC	chr6:31475115-31475335(+)$1	220	161	179	12.9856
UUUAACUUAUAUUUUGAU	chr1:220368542-220368772(-)$1	230	185	203	14.2435
CUCUGCCUCAACACGGAG	chr14:74976335-74976555(-)$1	220	34	52	13.6036
UUGCAACACUUAGUGCAU	chr4:148544989-148545215(+)$1	226	73	91	14.2435
AUGUUUCAUUUCUAGCAU	chr12:100598643-100598873(+)$1	230	207	225	14.9871
AGAAGAGCGAAAACAUCU	chr10:12126588-12126812(+)$1	224	119	137	14.3982
AUGUUAGAGUUAAAACCA	chr5:74100306-74100530(-)$1	224	39	57	13.6949
UCAGAAUCUUUCCUCUGG	chr20:61299319-61299544(+)$1	225	70	88	14.9871
ACGAUGACACGGAAUGCA	chr1:32627443-32627668(+)$1	225	129	147	13.3015
CUGGGUAAGUAUCUCCAU	chr16:67262185-67262410(+)$1	225	128	146	14.2137
UCAGAGAACUUUAUCUGG	chr6:72011310-72011532(+)$1	222	4	22	13.8398
AAGGACUCUUCUCUUCUU	chr6:100965790-100966021(-)$1	231	96	114	14.9871
UUUGGAUUUAAAGCCAAA	chr7:97488542-97488763(-)$1	221	126	144	14.9871
AGGACAUGAUAAAGUUCU	chr4:103527638-103527865(+)$1	227	139	157	14.9871
AGCCGGAGAAUAUUGACU	chr8:11687732-11687962(+)$1	230	60	78	12.9262
UGGGCCCCAGUUUGUCCA	chr11:111225123-111225349(-)$1	226	195	213	13.6036
UUGAAACUAGAAGUUCAA	chr2:75881917-75882141(+)$1	224	141	159	14.9871
GUGCUCUAGAUCAGGCAC	chr1:101379132-101379356(+)$1	224	116	134	14.9871
AAGAUACCAGAACAUCUU	chr10:64967736-64967957(-)$1	221	12	30	14.9871
UAGACUCUAUCUUGUCUG	chr8:17823801-17824026(+)$1	225	32	50	14.9871
GCUGGccccucuuccguc	chr19:41257234-41257464(+)$1	230	195	213	13.8647
CUGGAAGAUAUAAUCUGG	chr5:110097335-110097565(+)$1	230	172	190	14.9871
AGGAUAAGAAGAAAUCCC	chrX:118763280-118763510(-)$1	230	97	115	14.0810
CUUCUCAGCAAUUAGAAG	chr1:37947965-37948192(+)$1	227	4	22	14.9871
AUCGGAUAACAAACUGUA	chr2:113330044-113330274(+)$1	230	137	155	13.7838
UACUGGUGAGAGACAGUA	chr19:52090675-52090905(+)$1	230	147	165	13.8398
UAGGAUCACAGCUUCCUA	chr20:25597084-25597314(-)$1	230	23	41	14.9871
GCUCAGAUCCAGGUGCAG	chr3:49094938-49095168(-)$1	230	34	52	12.8165
GUCAGUGCAACCUCUAUA	chr11:3038238-3038468(-)$1	230	32	50	12.7747
UGUAUGACCACAGAUACG	chr10:43882441-43882671(-)$1	230	150	168	13.5373
GUCCUGCUACUCAGGGGC	chr14:39545172-39545394(-)$1	222	143	161	13.6036
UAAAAUUAAAACUUUUUA	chr18:54283399-54283629(-)$1	230	210	228	13.6036
GGUGUCUGAAAGUGCACU	chr3:127340415-127340645(+)$1	230	1	19	14.9871
CUAUUGCCAGGAAGAUAG	chr11:35685186-35685411(+)$1	225	36	54	13.6036
CCUCAGAUUCAGAUGAAA	chr5:132232221-132232444(-)$1	223	71	89	13.7064
CUUCAUCAUGACUUGAAG	chr8:90777536-90777766(+)$1	230	131	149	14.9871
UUCAAAGAUAAAAUUGAG	chr11:67926429-67926654(-)$1	225	188	206	13.6036
CACCUUCCCAUCCAGGUA	chr1:23885585-23885815(-)$1	230	183	201	13.8887
GGAUAUUUGAUACUAUCC	chr7:77423530-77423760(-)$1	230	197	215	14.9871
UUUGGCUACUUAAUCAAA	chr8:17092216-17092446(-)$1	230	87	105	14.9871
UCCUGGAUUGGCACAGGU	chr8:124267209-124267439(-)$1	230	23	41	14.0525
AAUUAAAUAAUUCUGAAC	chr1:235295171-235295395(-)$1	224	111	129	13.7064
CGCUCAUCGAAAGGGGCA	chr22:29912933-29913159(-)$1	226	121	139	12.9724

#DB
(((((........)))))	chr5:32403253-32403475(-)$1	1	13	31	14.9871
.((((........)))))	chr14:70990495-70990725(-)$1	1	159	177	14.3056
((.((........)))))	chr11:122930362-122930592(-)$1	1	63	81	12.8687
..(((........)))..	chr3:125725215-125725445(-)$1	1	190	208	13.7064
.((((........)))).	chr6:80718074-80718297(+)$1	1	197	215	13.9270
.((((........))))(	chr6:27841149-27841374(-)$1	1	168	186	12.9204
(((((........)))))	chr3:160148850-160149074(+)$1	1	180	198	13.8398
(((((........)))))	chr17:1384041-1384262(-)$1	1	30	48	14.9871
(.(.(........).).)	chr17:4700667-4700891(+)$1	1	17	35	13.2953
(.(((........))).)	chr11:107682300-107682524(-)$1	1	118	136	13.7283
(((((........)))))	chr12:51512352-51512582(-)$1	1	122	140	13.6036
(((((........)))))	chr1:100525393-100525613(+)$1	1	70	88	13.6036
(((((........))).)	chr18:48584632-48584862(+)$1	1	170	188	13.7838
(((((........)))))	chr8:41905879-41906104(-)$1	1	145	163	13.8718
((.((........)).))	chr17:27805205-27805427(+)$1	1	96	114	12.8133
.((((........)))).	chr9:5933733-5933963(-)$1	1	209	227	14.2435
(((((........)))))	chr2:180838322-180838552(-)$1	1	163	181	13.8398
(((.(........).)))	chr1:120168481-120168704(-)$1	1	204	222	13.4777
.((((........)))))	chr15:59911190-59911420(+)$1	1	59	77	14.0810
(((((........)))))	chr1:91382360-91382581(-)$1	1	142	160	13.6036
(((((........)))))	chr5:74891977-74892207(+)$1	1	85	103	13.6036
(((((........).)))	chr14:103931975-103932197(+)$1	1	124	142	14.5531
(((((........)))))	chr20:48522085-48522305(+)$1	1	41	59	14.9871
(.(((........)))))	chr8:11667167-11667397(+)$1	1	78	96	14.3110
.((((........)))).	chr4:106155729-106155959(+)$1	1	200	218	14.2435
(((((........)))))	chr4:96073711-96073933(-)$1	1	115	133	14.9871
.((((........)))).	chr11:61081034-61081260(-)$1	1	80	98	14.1205
(((((........)))))	chr2:184024144-184024374(+)$1	1	92	110	14.9871
(..((........)).))	chr6:31475115-31475335(+)$1	1	161	179	12.9856
.((((........)))).	chr1:220368542-220368772(-)$1	1	185	203	14.2435
(((((........)))))	chr14:74976335-74976555(-)$1	1	34	52	13.6036
.((((........)))).	chr4:148544989-148545215(+)$1	1	73	91	14.2435
(((((........)))))	chr12:100598643-100598873(+)$1	1	207	225	14.9871
(((.(........).)))	chr10:12126588-12126812(+)$1	1	119	137	14.3982
..(((........)))..	chr5:74100306-74100530(-)$1	1	39	57	13.6949
(((((........)))))	chr20:61299319-61299544(+)$1	1	70	88	14.9871
.(.((........)))))	chr1:32627443-32627668(+)$1	1	129	147	13.3015
.((((........)))).	chr16:67262185-67262410(+)$1	1	128	146	14.2137
(((((........)))))	chr6:72011310-72011532(+)$1	1	4	22	13.8398
(((((........)))))	chr6:100965790-100966021(-)$1	1	96	114	14.9871
(((((........)))))	chr7:97488542-97488763(-)$1	1	126	144	14.9871
(((((........)))))	chr4:103527638-103527865(+)$1	1	139	157	14.9871
((.((........)).))	chr8:11687732-11687962(+)$1	1	60	78	12.9262
(((((........)))))	chr11:111225123-111225349(-)$1	1	195	213	13.6036
(((((........)))))	chr2:75881917-75882141(+)$1	1	141	159	14.9871
(((((........)))))	chr1:101379132-101379356(+)$1	1	116	134	14.9871
(((((........)))))	chr10:64967736-64967957(-)$1	1	12	30	14.9871
(((((........)))))	chr8:17823801-17824026(+)$1	1	32	50	14.9871
(.(((........))).)	chr19:41257234-41257464(+)$1	1	195	213	13.8647
(((((........)))))	chr5:110097335-110097565(+)$1	1	172	190	14.9871
.((((........)))))	chrX:118763280-118763510(-)$1	1	97	115	14.0810
(((((........)))))	chr1:37947965-37948192(+)$1	1	4	22	14.9871
(((((........))).)	chr2:113330044-113330274(+)$1	1	137	155	13.7838
(((((........)))))	chr19:52090675-52090905(+)$1	1	147	165	13.8398
(((((........)))))	chr20:25597084-25597314(-)$1	1	23	41	14.9871
(((((........)).))	chr3:49094938-49095168(-)$1	1	34	52	12.8165
...((........))...	chr11:3038238-3038468(-)$1	1	32	50	12.7747
)((((........))))(	chr10:43882441-43882671(-)$1	1	150	168	13.5373
(((((........)))))	chr14:39545172-39545394(-)$1	1	143	161	13.6036
(((((........)))))	chr18:54283399-54283629(-)$1	1	210	228	13.6036
(((((........)))))	chr3:127340415-127340645(+)$1	1	1	19	14.9871
(((((........)))))	chr11:35685186-35685411(+)$1	1	36	54	13.6036
..(((........)))..	chr5:132232221-132232444(-)$1	1	71	89	13.7064
(((((........)))))	chr8:90777536-90777766(+)$1	1	131	149	14.9871
(((((........)))))	chr11:67926429-67926654(-)$1	1	188	206	13.6036
.((((........)))).	chr1:23885585-23885815(-)$1	1	183	201	13.8887
(((((........)))))	chr7:77423530-77423760(-)$1	1	197	215	14.9871
(((((........)))))	chr8:17092216-17092446(-)$1	1	87	105	14.9871
.((((........)))).	chr8:124267209-124267439(-)$1	1	23	41	14.0525
..(((........)))..	chr1:235295171-235295395(-)$1	1	111	129	13.7064
)((((........)))).	chr22:29912933-29913159(-)$1	1	121	139	12.9724

#PSSM
e : 0.33	f : 0.16	[ : 0.11	c : 0.09	! : 0.05	" : 0.05	g : 0.05	d : 0.05	# : 0.02	: : 0.01	= : 0.01	
e : 0.32	d : 0.22	f : 0.15	c : 0.07	! : 0.05	g : 0.05	[ : 0.05	= : 0.01	# : 0.01	a : 0.01	" : 0.01	
e : 0.32	d : 0.21	c : 0.15	f : 0.14	[ : 0.05	g : 0.05	a : 0.01	= : 0.01	! : 0.01	" : 0.01	
e : 0.30	d : 0.21	f : 0.14	c : 0.12	b : 0.09	g : 0.05	[ : 0.04	= : 0.01	
e : 0.29	d : 0.21	f : 0.14	c : 0.12	b : 0.09	g : 0.05	a : 0.05	= : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.29	d : 0.21	f : 0.14	c : 0.12	b : 0.09	g : 0.05	a : 0.05	= : 0.01	
e : 0.29	d : 0.21	f : 0.14	c : 0.12	b : 0.09	g : 0.05	] : 0.05	= : 0.01	
e : 0.32	d : 0.21	c : 0.15	f : 0.14	g : 0.05	] : 0.05	a : 0.02	= : 0.01	3 : 0.01	
e : 0.35	d : 0.22	f : 0.16	] : 0.07	g : 0.05	c : 0.04	2 : 0.04	= : 0.01	4 : 0.01	3 : 0.01	
e : 0.36	f : 0.16	c : 0.09	2 : 0.07	d : 0.07	] : 0.07	g : 0.05	3 : 0.02	4 : 0.02	= : 0.01	b : 0.01	: : 0.01	

#score	999.5693298891762
#seq	71
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_UTR_m2_run2.txt

#BEAR
========"""cccooooooccc333======	chr1:114519934-114520158(+)$1	224	64	96	14.6607
Gggggggg!!cccooooooccc22ggggggg:	chrX:67754635-67754859(+)$1	224	9	41	12.2360
:dddd[ccceeeeennnnneeeee22ccc333	chr2:70523106-70523339(-)$1	233	48	80	11.3054
b!!==========oooooo==========22b	chr3:57913391-57913603(+)$1	212	168	200	13.4448
gggggg[ccc!!bbnnnnnbb333cccggggg	chr8:48889344-48889587(+)$1	243	1	33	13.3800
ccc[ccc[ddddbbnnnnnbb]dddd]ccccc	chr1:75231324-75231557(+)$1	233	186	218	11.5666
ggg$$$$$a!!cccnnnnnccc22aggggggg	chr3:195776888-195777170(-)$1	282	16	48	14.1232
ccc!!iiiiiiiiinnnnniiiiiiiii22cc	chr9:135569218-135569498(+)$1	280	209	241	13.8858
!!eeeee####cccooooooccceeeee333g	chr5:130761641-130761853(-)$1	212	71	103	12.9767
####ccc!!eeeeennnnneeeee22ccc]bb	chrX:135292047-135292258(+)$1	211	65	97	12.7521
ee"""ffffff[bbnnnnnbbffffff333ee	chr1:36321367-36321588(+)$1	221	81	113	11.9627
FFFFgggggggcccnnnnnccc>>>>>>>>>>	chr7:141173243-141173458(+)$1	215	12	44	10.9290
####ccc[ffffffnnnnnffffffccc22cc	chr10:88196272-88196498(-)$1	226	134	166	12.8983
:ggggggg!!ddddnnnnndddd]gggggggB	chrX:53405770-53406000(-)$1	230	83	115	12.0152
"""ggggggg[ddddmmmmdddd]ggggggg3	chr14:75142807-75143034(-)$1	227	30	62	9.8747
ffa[ccc[ffffffnnnnnffffffccc]a::	chr5:133530677-133530948(-)$1	271	151	183	10.6394
=======####ddddllldddd4444======	chr6:75964150-75964379(-)$1	229	138	170	11.5580
ffff[ddddbbcccnnnnnccc]bb22dddd]	chr4:123814160-123814390(+)$1	230	102	134	10.9215
b!!eeeee####bbnnnnnbb4444eeeee22	chrX:153292163-153292392(-)$1	229	58	90	12.6329
biiiiiiiii[cccooooooccciiiiiiiii	chr12:29655265-29655539(-)$1	274	52	84	12.7823
$$$$iiiiiiiiiooooooiiiiiiiii4444	chr9:123366437-123366651(-)$1	214	71	103	12.8030
feeeee[a!!cccooooooccc22a]eeeee:	chr14:92246643-92246865(-)$1	222	35	67	11.5344
gggggggg[eeeeennnnneeeee22gggggg	chr10:113912243-113912486(-)$1	243	47	79	12.5610
gggggg!!bbcccooooooccc]bb22ggggg	chr4:99960466-99960684(+)$1	218	68	100	11.8747
g[dddd[bb[cccooooooccc]bb]dddd]g	chr7:138986196-138986409(+)$1	213	61	93	10.8611
=$$$$$ffffffbbnnnnnbb]ffffff]===	chr3:5258001-5258229(+)$1	228	85	117	11.5631
ee"""dddd!!cccnnnnnccc22dddd]eee	chr8:94745229-94745458(-)$1	229	23	55	13.1042
####ccc[ccc[ccclllccc]cccccc4444	chr10:115672438-115672665(+)$1	227	143	175	11.3847
d[ffffff!!cccooooooccc22ffffff]d	chr3:138402431-138402664(-)$1	233	150	182	11.3569
eee"""dddd[cccnnnnncccddddeeeeec	chr12:22839958-22840178(+)$1	220	110	142	12.2659
cc"""eeeee[cccnnnnnccc]eeeee]ccc	chr7:141450097-141450316(+)$1	219	142	174	13.6559
ggggggg"""cccoooooocccggggggg333	chr9:23692127-23692357(-)$1	230	125	157	14.1002
ddd[ccc!!ddddoooooodddd>>>>>>>>>	chr3:42689004-42689233(+)$1	229	128	160	10.2312
!!eeeee####bboooooobb4444eeeee22	chr7:105182824-105183063(+)$1	239	36	68	11.7961
::eeeee"""ddddnnnnndddd333eeeee:	chr8:116420986-116421207(-)$1	221	146	178	10.7757
dd[a"""gggggggnnnnnggggggg4444a]	chr6:36462770-36462991(-)$1	221	144	176	13.3108
============[aooooooa===========	chr11:34121246-34121466(+)$1	220	106	138	13.3109
####ccc####cccnnnnnccc4444ccc444	chrX:10415882-10416102(-)$1	220	117	149	15.9878
dddd!!ccc!!cccnnnnnccc22ccc22ddd	chr3:169713981-169714195(+)$1	214	23	55	12.9511
####dddd[ddddoooooodddd]dddd4444	chrX:123236208-123236428(+)$1	220	125	157	11.4648
eeee[bb####cccooooooccc333bb]eee	chr11:12964878-12965093(+)$1	215	93	125	11.8442
ccc$$$$$ffffffnnnnnffffff4444ccc	chr6:89321142-89321391(-)$1	249	29	61	11.7217
fff[ccc[ffffffooooooffffff]ccc]f	chr1:14113586-14113813(+)$1	227	24	56	10.3713
cccdddd"""ddddnnnnndddd22dddd666	chr14:93704132-93704371(-)$1	239	49	81	11.2496
ff[a$$$$$eeeeennnnneeeeea]ffffff	chr1:218509223-218509440(+)$1	217	68	100	10.9165
gg!!a"""eeeeeooooooeeeee4444a22g	chr5:53840042-53840270(+)$1	228	35	67	11.7705
g[dddd[affffffnnnnnffffff]a]dddd	chr22:42301872-42302096(+)$1	224	163	195	11.0789
:============oooooo============:	chr17:1324001-1324221(-)$1	220	153	185	12.1834
ccc!!iiiiiiiiinnnnniiiiiiiii22cc	chr1:54231501-54231727(-)$1	226	139	171	13.8858
gggg[eeeee[cccnnnnnccc22eeeee]gg	chr22:20098524-20098754(+)$1	230	94	126	13.4396
iiiiii!!ccc[bbnnnnnbb]ccciiiiiii	chr7:101895715-101895945(+)$1	230	114	146	13.1800
:dddd!!ccc[cccnnnnncccccc22dddd:	chr3:25639730-25639955(-)$1	225	60	92	11.1217
cc:gggggggddddnnnnndddd]ggggggg:	chr16:15128258-15128503(+)$1	245	166	198	11.3357
#bb[ffffff[cccnnnnncccffffffbb33	chr1:45213004-45213231(+)$1	227	163	195	12.2620
"""bb!!gggggggnnnnngggggggbb]eee	chr16:90033257-90033472(+)$1	215	52	84	12.4154
""eeeee[a[ddddnnnnnddddaeeeee333	chr7:44917398-44917781(-)$1	383	164	196	13.1734
$$ggggggga[bboooooobb]a333gggggg	chr12:14651255-14651507(+)$1	252	153	185	12.3278

#otherMatches

#Seq PSSM
aAUGUUAGUAUUUCUGCUUUGAAUCCUUGAUA	chr1:114519934-114520158(+)$1	224	64	96	14.6607
GGACGGGGACUCCAACAAAGGAAACCCUGUUG	chrX:67754635-67754859(+)$1	224	9	41	12.2360
UGUGCAGCUGGCAGUGUUCCUGCCCCAGCAUG	chr2:70523106-70523339(-)$1	233	48	80	11.3054
UUUGAAAUAUAUACACAUAUAUAUAUUUUUUA	chr3:57913391-57913603(+)$1	212	168	200	13.4448
UGAGCAAGGAAGGCUCCCUGCAUGUCCUGCUU	chr8:48889344-48889587(+)$1	243	1	33	13.3800
AGAAUUAAGAAGAGAGGGGCUGCUUCCUAAUC	chr1:75231324-75231557(+)$1	233	186	218	11.5666
GGGUUUUUGUUACCUUUAUGGUUUCUCCAGGU	chr3:195776888-195777170(-)$1	282	16	48	14.1232
AGGUUUUGGAAAGGAGAUGCUUUUUCAAUUCU	chr9:135569218-135569498(+)$1	280	209	241	13.8858
GACAUACUUUUCCAGCCUCAUGGGUAUGGCAC	chr5:130761641-130761853(-)$1	212	71	103	12.9767
AAUCUGGCCAACAAGCGCUUUGUUUUCCACCA	chrX:135292047-135292258(+)$1	211	65	97	12.7521
GGAAUCCAAGAUGUGAAGAACUCUUGGUGACU	chr1:36321367-36321588(+)$1	221	81	113	11.9627
GUUUGAGGAUGCUGGCUCACAGACCUAUCAUU	chr7:141173243-141173458(+)$1	215	12	44	10.9290
AACAUGUAUAUUCUUCUAUAGAGUGACAGGAU	chr10:88196272-88196498(-)$1	226	134	166	12.8983
AUGCCCUGCUGACUGGGAAAGUUUCAGGGCAC	chrX:53405770-53406000(-)$1	230	83	115	12.0152
GAGUACUGGUGUCUCAUUUGAGAAAUCAGUAA	chr14:75142807-75143034(-)$1	227	30	62	9.8747
UAGUCGGUAUUUCUUAAAUAGAAGUUUGUCAA	chr5:133530677-133530948(-)$1	271	151	183	10.6394
UUAAAAGAAUGUGUGUUUCAUAAUGACUUUUA	chr6:75964150-75964379(-)$1	229	138	170	11.5580
UACAUAUCUGACUUCCCAAAAGCUCCAGGAUU	chr4:123814160-123814390(+)$1	230	102	134	10.9215
CCCCAGGUCUACCCCUCCCGGCCCUGCCUGCU	chrX:153292163-153292392(-)$1	229	58	90	12.6329
ACAAUUCCUCGUUCUCAGAUGGAGAGGAAUUG	chr12:29655265-29655539(-)$1	274	52	84	12.7823
AAUAUUGCUAGAGCUGGGACUCUGGUGAGCAU	chr9:123366437-123366651(-)$1	214	71	103	12.8030
AGUACUCCUAGGGAAAUGGCCUCUGAAGUAUA	chr14:92246643-92246865(-)$1	222	35	67	11.5344
AGCUGUUUCUUGGAAAUCCUCCAACCAAAUAG	chr10:113912243-113912486(-)$1	243	47	79	12.5610
AUCUGAACAGGCUCUUAAAGGUACUUCUCAGA	chr4:99960466-99960684(+)$1	218	68	100	11.8747
AAUGAACUUUGCCUGUAUUGGUUGACUUUAAU	chr7:138986196-138986409(+)$1	213	61	93	10.8611
ggauuacaggugagcaccacuguaccuggcua	chr3:5258001-5258229(+)$1	228	85	117	11.5631
AAUUUAAAAUUACACAUGCUGUUUUUUUCUUU	chr8:94745229-94745458(-)$1	229	23	55	13.1042
GAUGUUCACUUCUGUCAAACAAGGGGAAGUAG	chr10:115672438-115672665(+)$1	227	143	175	11.3847
UACUGAGAUUUUUAACAUCAAAUUUCUUAGAA	chr3:138402431-138402664(-)$1	233	150	182	11.3569
GAACAAAAUAAGAUAUCUAAUCUAUUUUCCCC	chr12:22839958-22840178(+)$1	220	110	142	12.2659
UAAAAUACUCUUUUACGUAAAAUGAGUAAUAA	chr7:141450097-141450316(+)$1	219	142	174	13.6559
GCCUUGAACCUGUGAGUAAAUAUUGAGGCUUU	chr9:23692127-23692357(-)$1	230	125	157	14.1002
GGAUACUGAAUACAAAACAGUAUGAUUUAUAU	chr3:42689004-42689233(+)$1	229	128	160	10.2312
ACAAUUUCAUCAGAAAUUCCUAAAAGAAUUCG	chr7:105182824-105183063(+)$1	239	36	68	11.7961
GAGGCAUGAGGGGGGAACAUCUCAAAAUGCCA	chr8:116420986-116421207(-)$1	221	146	178	10.7757
UUAGAAGGCCCAGAAAGUCUUUGGGCAUUGCC	chr6:36462770-36462991(-)$1	221	144	176	13.3108
UGGAGUGUGGUUUGGCAGAACAACUGCAUUUC	chr11:34121246-34121466(+)$1	220	106	138	13.3109
AAAUGGUUUCAAUUGCUAAAAUAUUUACCUGG	chrX:10415882-10416102(-)$1	220	117	149	15.9878
CUGUGACAUUUAUCUACCUGGUUUAUGGAAUA	chr3:169713981-169714195(+)$1	214	23	55	12.9511
AAAUAAACCUACAGUAUGUUGUAUGUUUUCUC	chrX:123236208-123236428(+)$1	220	125	157	11.4648
GCAUUGCAAAGGGUAGUUUCACUGAAGUCAUG	chr11:12964878-12965093(+)$1	215	93	125	11.8442
agacauuuauuuucaaagcgagaauucuaucu	chr6:89321142-89321391(-)$1	249	29	61	11.7217
AGAUUGGAUAUGGACUCUUUUUUAUGCCUAUU	chr1:14113586-14113813(+)$1	227	24	56	10.3713
AUGCACCACAUCUGUACUUCAGAGAGGUGGAA	chr14:93704132-93704371(-)$1	239	49	81	11.2496
UAUUUAUCAUCUGAGGCUUUCAGAAUUAAUGC	chr1:218509223-218509440(+)$1	217	68	100	10.9165
UCAGCAAACAUGUCUUACAACAUGAGGAGGAG	chr5:53840042-53840270(+)$1	228	35	67	11.7705
GACAGCAGUCUCUGAGCACCAGGGAGCAGUUG	chr22:42301872-42302096(+)$1	224	163	195	11.0789
AGCAUGUAUUGUAUAUGUUUAUAGUAUAUGUA	chr17:1324001-1324221(-)$1	220	153	185	12.1834
GGGAACUCCUCCUGUGUACUAGGAGGAGGACC	chr1:54231501-54231727(-)$1	226	139	171	13.8858
GCCUGUGACAGCGGUUUCUCUGGAUGUCAAAG	chr22:20098524-20098754(+)$1	230	94	126	13.4396
UUUUGCCAUUAACUUAGCUGGCUAAGCAGAGG	chr7:101895715-101895945(+)$1	230	114	146	13.1800
CUUCUCUGCCACGAACCGGUCGGGCUAGGAAA	chr3:25639730-25639955(-)$1	225	60	92	11.1217
CCUCUUCCCAGGUCUUGCUGACCUUGGGAGGU	chr16:15128258-15128503(+)$1	245	166	198	11.3357
GUCAUCUGGCUGCAGCCAGUGCGCCAGAGAAU	chr1:45213004-45213231(+)$1	227	163	195	12.2620
AGCCAAUGGCCUUUUGUUUGGGGGCCUGAGGU	chr16:90033257-90033472(+)$1	215	52	84	12.4154
AUUCUCUUGUAAAAUUCCUUUUUCAGAGACAU	chr7:44917398-44917781(-)$1	383	164	196	13.1734
AGGAUCUAUAGUAUCAUUUUAGUUAAGUGGGU	chr12:14651255-14651507(+)$1	252	153	185	12.3278

#DB
((((((((...(((......)))...))))))	chr1:114519934-114520158(+)$1	1	64	96	14.6607
((((((((..(((......)))..))))))).	chrX:67754635-67754859(+)$1	1	9	41	12.2360
.((((.((((((((.....)))))..)))...	chr2:70523106-70523339(-)$1	1	48	80	11.3054
(..((((((((((......))))))))))..)	chr3:57913391-57913603(+)$1	1	168	200	13.4448
((((((.(((..((.....))...))))))))	chr8:48889344-48889587(+)$1	1	1	33	13.3800
(((.(((.((((((.....)).)))).)))))	chr1:75231324-75231557(+)$1	1	186	218	11.5666
(((.....(..(((.....)))..))))))))	chr3:195776888-195777170(-)$1	1	16	48	14.1232
(((..(((((((((.....)))))))))..))	chr9:135569218-135569498(+)$1	1	209	241	13.8858
..(((((....(((......))))))))...)	chr5:130761641-130761853(-)$1	1	71	103	12.9767
....(((..(((((.....)))))..))).))	chrX:135292047-135292258(+)$1	1	65	97	12.7521
((...((((((.((.....))))))))...))	chr1:36321367-36321588(+)$1	1	81	113	11.9627
((((((((((((((.....)))..........	chr7:141173243-141173458(+)$1	1	12	44	10.9290
....(((.((((((.....)))))))))..))	chr10:88196272-88196498(-)$1	1	134	166	12.8983
.(((((((..((((.....)))).))))))))	chrX:53405770-53406000(-)$1	1	83	115	12.0152
...(((((((.((((....)))).))))))).	chr14:75142807-75143034(-)$1	1	30	62	9.8747
))(.(((.((((((.....))))))))).)..	chr5:133530677-133530948(-)$1	1	151	183	10.6394
(((((((....((((...))))....))))))	chr6:75964150-75964379(-)$1	1	138	170	11.5580
((((.(((((((((.....))).))..)))).	chr4:123814160-123814390(+)$1	1	102	134	10.9215
(..(((((....((.....))....)))))..	chrX:153292163-153292392(-)$1	1	58	90	12.6329
((((((((((.(((......))))))))))))	chr12:29655265-29655539(-)$1	1	52	84	12.7823
....(((((((((......)))))))))....	chr9:123366437-123366651(-)$1	1	71	103	12.8030
)(((((.(..(((......)))..).))))).	chr14:92246643-92246865(-)$1	1	35	67	11.5344
)(((((((.(((((.....)))))..))))))	chr10:113912243-113912486(-)$1	1	47	79	12.5610
((((((..(((((......))).))..)))))	chr4:99960466-99960684(+)$1	1	68	100	11.8747
(.((((.((.(((......))).)).)))).)	chr7:138986196-138986409(+)$1	1	61	93	10.8611
(.....((((((((.....)).)))))).)))	chr3:5258001-5258229(+)$1	1	85	117	11.5631
((...((((..(((.....)))..)))).)))	chr8:94745229-94745458(-)$1	1	23	55	13.1042
....(((.(((.(((...))).))))))....	chr10:115672438-115672665(+)$1	1	143	175	11.3847
(.((((((..(((......)))..)))))).)	chr3:138402431-138402664(-)$1	1	150	182	11.3569
(((...((((.(((.....))))))))))))(	chr12:22839958-22840178(+)$1	1	110	142	12.2659
((...(((((.(((.....))).))))).)))	chr7:141450097-141450316(+)$1	1	142	174	13.6559
(((((((...(((......))))))))))...	chr9:23692127-23692357(-)$1	1	125	157	14.1002
(((.(((..((((......)))).........	chr3:42689004-42689233(+)$1	1	128	160	10.2312
..(((((....((......))....)))))..	chr7:105182824-105183063(+)$1	1	36	68	11.7961
..(((((...((((.....))))...))))).	chr8:116420986-116421207(-)$1	1	146	178	10.7757
((.(...(((((((.....)))))))....).	chr6:36462770-36462991(-)$1	1	144	176	13.3108
((((((((((((.(......))))))))))))	chr11:34121246-34121466(+)$1	1	106	138	13.3109
....(((....(((.....)))....)))...	chrX:10415882-10416102(-)$1	1	117	149	15.9878
((((..(((..(((.....)))..)))..)))	chr3:169713981-169714195(+)$1	1	23	55	12.9511
....((((.((((......)))).))))....	chrX:123236208-123236428(+)$1	1	125	157	11.4648
((((.((....(((......)))...)).)))	chr11:12964878-12965093(+)$1	1	93	125	11.8442
(((.....((((((.....))))))....)))	chr6:89321142-89321391(-)$1	1	29	61	11.7217
(((.(((.((((((......)))))).))).)	chr1:14113586-14113813(+)$1	1	24	56	10.3713
(((((((...((((.....))))..))))...	chr14:93704132-93704371(-)$1	1	49	81	11.2496
((.(.....(((((.....)))))).))))))	chr1:218509223-218509440(+)$1	1	68	100	10.9165
((..(...(((((......)))))....)..)	chr5:53840042-53840270(+)$1	1	35	67	11.7705
(.((((.(((((((.....)))))).).))))	chr22:42301872-42302096(+)$1	1	163	195	11.0789
.((((((((((((......)))))))))))).	chr17:1324001-1324221(-)$1	1	153	185	12.1834
(((..(((((((((.....)))))))))..))	chr1:54231501-54231727(-)$1	1	139	171	13.8858
((((.(((((.(((.....)))..))))).))	chr22:20098524-20098754(+)$1	1	94	126	13.4396
((((((..(((.((.....)).))))))))))	chr7:101895715-101895945(+)$1	1	114	146	13.1800
.((((..(((.(((.....))))))..)))).	chr3:25639730-25639955(-)$1	1	60	92	11.1217
)).(((((((((((.....)))).))))))).	chr16:15128258-15128503(+)$1	1	166	198	11.3357
.((.((((((.(((.....)))))))))))..	chr1:45213004-45213231(+)$1	1	163	195	12.2620
...((..(((((((.....))))))))).)))	chr16:90033257-90033472(+)$1	1	52	84	12.4154
..(((((.(.((((.....))))))))))...	chr7:44917398-44917781(-)$1	1	164	196	13.1734
..((((((((.((......)).)...))))))	chr12:14651255-14651507(+)$1	1	153	185	12.3278

#PSSM
g : 0.15	c : 0.12	# : 0.10	: : 0.08	f : 0.08	= : 0.07	e : 0.07	d : 0.07	b : 0.05	" : 0.05	! : 0.03	$ : 0.03	G : 0.01	F : 0.01	i : 0.01	
g : 0.15	c : 0.12	d : 0.08	# : 0.08	e : 0.08	= : 0.07	! : 0.07	f : 0.07	" : 0.05	$ : 0.05	[ : 0.05	i : 0.03	F : 0.01	: : 0.01	b : 0.01	
g : 0.15	e : 0.12	d : 0.10	c : 0.08	# : 0.08	" : 0.08	= : 0.07	! : 0.05	f : 0.05	i : 0.03	$ : 0.03	[ : 0.03	F : 0.01	a : 0.01	: : 0.01	b : 0.01	
g : 0.17	e : 0.12	d : 0.10	= : 0.08	[ : 0.08	# : 0.08	$ : 0.07	" : 0.07	! : 0.05	f : 0.03	i : 0.03	a : 0.03	F : 0.01	b : 0.01	
g : 0.17	c : 0.14	d : 0.10	e : 0.10	= : 0.08	" : 0.08	$ : 0.07	! : 0.05	[ : 0.05	i : 0.05	f : 0.03	a : 0.01	b : 0.01	
g : 0.17	c : 0.14	e : 0.14	d : 0.10	= : 0.08	i : 0.08	$ : 0.07	f : 0.05	" : 0.05	! : 0.05	[ : 0.01	b : 0.01	
c : 0.17	g : 0.14	e : 0.12	= : 0.08	d : 0.08	[ : 0.07	i : 0.07	f : 0.07	! : 0.07	$ : 0.05	" : 0.03	b : 0.01	
g : 0.15	[ : 0.10	# : 0.08	= : 0.07	c : 0.07	i : 0.07	! : 0.07	f : 0.07	d : 0.07	" : 0.07	$ : 0.05	e : 0.05	a : 0.03	b : 0.01	
f : 0.14	! : 0.10	c : 0.10	# : 0.10	g : 0.10	" : 0.07	d : 0.07	i : 0.07	= : 0.05	e : 0.05	a : 0.03	[ : 0.03	b : 0.03	$ : 0.01	
f : 0.14	! : 0.12	e : 0.12	# : 0.10	g : 0.08	" : 0.07	c : 0.07	d : 0.07	i : 0.07	= : 0.05	b : 0.03	[ : 0.03	a : 0.01	
c : 0.14	d : 0.14	[ : 0.14	f : 0.12	# : 0.10	e : 0.08	! : 0.07	= : 0.05	i : 0.05	g : 0.05	" : 0.01	b : 0.01	
c : 0.36	d : 0.17	f : 0.10	e : 0.08	= : 0.05	i : 0.05	[ : 0.05	b : 0.03	g : 0.03	! : 0.01	# : 0.01	
c : 0.38	d : 0.15	b : 0.14	e : 0.08	f : 0.08	i : 0.05	= : 0.03	g : 0.03	[ : 0.01	
c : 0.28	o : 0.24	d : 0.12	b : 0.10	f : 0.08	e : 0.07	i : 0.03	g : 0.03	a : 0.01	
n : 0.59	o : 0.35	d : 0.03	c : 0.01	
n : 0.59	o : 0.35	l : 0.03	m : 0.01	
n : 0.59	o : 0.35	l : 0.03	m : 0.01	
n : 0.59	o : 0.35	l : 0.03	m : 0.01	
n : 0.59	o : 0.35	m : 0.01	d : 0.01	c : 0.01	
c : 0.31	d : 0.15	b : 0.14	o : 0.10	e : 0.08	f : 0.07	i : 0.05	= : 0.03	g : 0.03	
c : 0.38	d : 0.15	b : 0.14	e : 0.08	f : 0.08	i : 0.05	= : 0.03	g : 0.03	a : 0.01	
c : 0.36	d : 0.15	f : 0.10	e : 0.08	] : 0.08	= : 0.05	i : 0.05	4 : 0.03	g : 0.03	3 : 0.01	
d : 0.17	f : 0.14	c : 0.12	2 : 0.12	e : 0.08	4 : 0.07	] : 0.07	= : 0.05	i : 0.05	g : 0.05	3 : 0.01	> : 0.01	a : 0.01	
2 : 0.14	f : 0.14	e : 0.12	3 : 0.08	i : 0.07	] : 0.07	4 : 0.07	= : 0.05	b : 0.05	c : 0.05	g : 0.05	d : 0.03	> : 0.03	a : 0.01	
f : 0.15	g : 0.12	c : 0.08	4 : 0.08	3 : 0.07	2 : 0.07	d : 0.07	i : 0.07	e : 0.07	= : 0.05	a : 0.05	b : 0.05	> : 0.03	
g : 0.14	2 : 0.10	e : 0.10	c : 0.08	d : 0.08	i : 0.08	f : 0.08	3 : 0.07	4 : 0.07	] : 0.07	= : 0.05	> : 0.03	
e : 0.15	g : 0.14	c : 0.14	= : 0.08	i : 0.08	f : 0.08	d : 0.07	2 : 0.05	4 : 0.05	] : 0.03	> : 0.03	b : 0.03	a : 0.01	
g : 0.17	e : 0.15	c : 0.14	d : 0.10	= : 0.08	i : 0.08	f : 0.07	4 : 0.05	> : 0.03	b : 0.03	3 : 0.01	2 : 0.01	] : 0.01	
g : 0.17	e : 0.12	] : 0.10	= : 0.08	c : 0.08	d : 0.08	4 : 0.08	2 : 0.07	3 : 0.03	> : 0.03	i : 0.03	f : 0.03	a : 0.01	b : 0.01	
g : 0.15	e : 0.14	= : 0.08	3 : 0.08	2 : 0.08	d : 0.08	4 : 0.08	c : 0.07	] : 0.03	> : 0.03	i : 0.03	f : 0.03	a : 0.01	6 : 0.01	b : 0.01	
g : 0.17	e : 0.12	c : 0.10	= : 0.08	3 : 0.08	2 : 0.07	d : 0.07	4 : 0.07	] : 0.05	> : 0.03	i : 0.03	b : 0.01	: : 0.01	a : 0.01	6 : 0.01	f : 0.01	
g : 0.15	: : 0.12	c : 0.12	3 : 0.08	= : 0.07	e : 0.07	4 : 0.07	d : 0.05	b : 0.03	> : 0.03	] : 0.03	2 : 0.03	i : 0.03	f : 0.03	B : 0.01	6 : 0.01	

#score	697.7191011499119
#seq	57
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_UTR_m1_run2.txt

#BEAR
iiiiiii[ccctttttttttttccc333iiii	chr14:55513397-55513619(+)$1	222	70	102	26.2151
:gggggggccctttttttttttccc22ggggg	chr12:95676132-95676351(+)$1	219	156	188	24.8043
%%%ggggggguuuuuuuuuuuuggggggg555	chr7:138983993-138984217(+)$1	224	10	42	21.4333
eeee[cccyyyyyyyyyyyyyyyyccceeeee	chr9:123216002-123216229(-)$1	227	107	139	23.4827
c####fffffftttttttttttffffff4444	chr16:1726584-1726825(+)$1	241	23	55	24.1092
d[eeeee[bbtttttttttttbb]eeeee]dd	chr6:89321261-89321504(-)$1	243	122	154	22.4802
hhhhhhhhbbvvvvvvvvvvvvvbb]hhhhhh	chr7:65422987-65423206(+)$1	219	157	189	22.0173
eeee[eeeeewwwwwwwwwwwwwweeeee]ee	chr2:27016865-27017078(+)$1	213	115	147	24.2066
e"""ffffffvvvvvvvvvvvvvffffff333	chr9:72331480-72331708(-)$1	228	123	155	24.6297
!ccc[ffffffuuuuuuuuuuuuffffff]cc	chr12:46757477-46757703(-)$1	226	107	139	25.2284
ffeeeee!!bbuuuuuuuuuuuubb22eeeee	chr4:73986681-73986900(-)$1	219	5	37	23.6982
fffff"""ccctttttttttttccc333ffff	chr1:93308666-93308884(-)$1	218	106	138	24.4551
!!gggggggyyyyyyyyyyyyyyyyggggggg	chr1:70700337-70700556(+)$1	219	64	96	25.3163
dddd[eeeeeuuuuuuuuuuuueeeee22ddd	chr7:128410114-128410354(+)$1	240	191	223	23.9704
!!gggggggvvvvvvvvvvvvvggggggg]bb	chr5:65222294-65222519(+)$1	225	80	112	24.3981
ccc!!bb[ccctttttttttttccc]bb]ccc	chr2:100165515-100165734(-)$1	219	64	96	24.4803
fffffeeeeewwwwwwwwwwwwwweeeee:::	chr21:43409914-43410204(-)$1	290	198	230	20.7562
ggggggg!!bbvvvvvvvvvvvvvbb]ggggg	chr15:66181606-66181829(+)$1	223	0	32	24.1960
ffffffeeeeettttttttttteeeee00000	chr1:24797185-24797426(+)$1	241	105	137	21.8614
""bb[ddddyyyyyyyyyyyyyyyydddd333	chr2:64118266-64118498(+)$1	232	83	115	23.5445
iiiiiiiiiwwwwwwwwwwwwwwiiiiiiiii	chr4:42118953-42119193(-)$1	240	48	80	25.0523
bbccceeeeeuuuuuuuuuuuueeeee]ccc]	chr12:1600907-1601124(+)$1	217	104	136	24.5601
[ccc"""dddduuuuuuuuuuuudddd333cc	chr11:120203879-120204107(+)$1	228	15	47	25.0921
ff"""eeeeeuuuuuuuuuuuueeeee333ff	chr10:5807598-5807819(-)$1	221	66	98	25.2118
gggg[eeeeevvvvvvvvvvvvveeeee]ggg	chr1:42642376-42642609(-)$1	233	66	98	25.5883
:eeeee[dddduuuuuuuuuuuudddd333ee	chr14:57676213-57676431(-)$1	218	56	88	23.7992
===========ttttttttttt==========	chr7:30122029-30122245(+)$1	216	134	166	25.9280
#ccc[eeeeevvvvvvvvvvvvveeeeeccc2	chr8:57872191-57872409(-)$1	218	121	153	25.0437
gggggggdddduuuuuuuuuuuudddd333gg	chr11:117041539-117041765(+)$1	226	58	90	25.4883
::eeeee[ccctttttttttttccc]eeeeeh	chr11:34122599-34122828(+)$1	229	12	44	22.9180
ffff[ddddvvvvvvvvvvvvvdddd22ffff	chr19:58134501-58134725(+)$1	224	100	132	22.7528
hhhhhh!!ccctttttttttttccc22hhhhh	chr9:140194497-140194718(-)$1	221	165	197	23.3586
ee"""ffffffuuuuuuuuuuuuffffff22e	chr7:22984229-22984440(-)$1	211	132	164	24.2053
ggg!!ddddyyyyyyyyyyyyyyyyddddggg	chr1:226171898-226172129(-)$1	231	156	188	23.8712
dddd[ffffffuuuuuuuuuuuuffffff]dd	chr4:90164807-90165038(-)$1	231	92	124	24.2243
ggeeeeedddduuuuuuuuuuuudddd4444e	chr2:60685996-60686209(-)$1	213	139	171	24.3811
=======dddduuuuuuuuuuuudddd]====	chr1:78341233-78341453(+)$1	220	3	35	25.5226
:==========ttttttttttt==========	chr10:28897221-28897443(+)$1	222	167	199	25.0753
==========vvvvvvvvvvvvv=========	chr11:111954388-111954611(+)$1	223	118	150	26.1346
dddd[eeeeeattttttttttta]eeeee]dd	chr6:31508003-31508256(-)$1	253	105	137	24.9222
ooccc:dddduuuuuuuuuuuuddddffffff	chr5:140958563-140958796(-)$1	233	66	98	22.3134
$$$ggggggguuuuuuuuuuuugggggggiii	chr21:28209415-28209640(-)$1	225	87	119	25.2131
ee[ccc!!cccuuuuuuuuuuuuccc22ccce	chr9:97221540-97221761(+)$1	221	158	190	25.1115
::ffffffccctttttttttttccc]ffffff	chr14:69708607-69708831(+)$1	224	57	89	22.7167
##iiiiiiiiitttttttttttiiiiiiiii3	chr16:69338804-69339036(+)$1	232	171	203	25.5662
"ffffffyyyyyyyyyyyyyyyyffffff333	chr12:65089212-65089451(+)$1	239	98	130	23.2536
""hhhhhhhhvvvvvvvvvvvvvhhhhhhhh3	chr16:69338267-69338490(+)$1	223	132	164	22.6946
eeiiiiiiiiitttttttttttiiiiiiiii:	chr18:72912495-72912748(-)$1	253	72	104	24.1932
deeeee[cccayyyyyyyyyyyyyyyya]ccc	chr17:73942522-73942746(-)$1	224	132	164	22.7745
f$$$$$ddddwwwwwwwwwwwwwwddddffff	chr2:85545103-85545327(-)$1	224	73	105	22.0646
ffff[cccccctttttttttttccc22ccc]f	chr22:30426253-30426464(+)$1	211	156	188	24.5803
:iiiiiiiiivvvvvvvvvvvvviiiiiiiii	chr3:140697503-140697755(+)$1	252	211	243	25.0716
[bb!!ffffffuuuuuuuuuuuuffffffbbd	chr1:36389547-36389772(+)$1	225	122	154	23.7799
dddd####cccvvvvvvvvvvvvvccc22ddd	chr6:151678964-151679194(+)$1	230	72	104	22.8615
c####ffffffuuuuuuuuuuuuffffffccc	chr6:150570953-150571228(+)$1	275	221	253	24.7051
c[gggggggvvvvvvvvvvvvvggggggg]cc	chr2:208628494-208628704(-)$1	210	86	118	24.8526
a[hhhhhhhhwwwwwwwwwwwwwwhhhhhhhh	chr8:57871655-57871876(-)$1	221	58	90	21.9579
ffgggggggyyyyyyyyyyyyyyyyggggggg	chr6:72014015-72014232(+)$1	217	117	149	24.8823
ccc!!eeeeexxxxxxxxxxxxxxxeeeeecc	chr1:226820504-226820716(-)$1	212	161	193	19.8932
ddddeeeeexxxxxxxxxxxxxxxeeeee]dd	chr8:22477385-22477615(+)$1	230	49	81	19.0256
bcccffffffyyyyyyyyyyyyyyyyffffff	chr9:134374635-134374914(+)$1	279	53	85	23.0584
ggggggg!!bbtttttttttttbb22gggggg	chr9:123523504-123523737(-)$1	233	36	68	24.5549

#otherMatches

#Seq PSSM
AUUUGCUACAGUGAAAAGAAGUUUGGAAAGUA	chr14:55513397-55513619(+)$1	222	70	102	26.2151
UCGGUACUUUGAAACUCAGCACCAGUCAGUAC	chr12:95676132-95676351(+)$1	219	156	188	24.8043
CUCUAAAUGGUAUAAGCUUCAUCCAUUUAUAA	chr7:138983993-138984217(+)$1	224	10	42	21.4333
UGCUUCUGGGACAACUAUUCUUGACAGAGCAG	chr9:123216002-123216229(-)$1	227	107	139	23.4827
UGUAAUUAAGAUGAGAUCAGUUUCUUAGAAAA	chr16:1726584-1726825(+)$1	241	23	55	24.1092
acuaaauaucaaggaaaucaagacauuuauuu	chr6:89321261-89321504(-)$1	243	122	154	22.4802
CUACCCUUCCAUCAAACAAAAAGGGCAAGGGU	chr7:65422987-65423206(+)$1	219	157	189	22.0173
GAAAAGGCUAUGUACUUAUUAUUUUAGCUCUU	chr2:27016865-27017078(+)$1	213	115	147	24.2066
UUUACUUGCUAGGUAAUUUGUAAAGUGGGGAU	chr9:72331480-72331708(-)$1	228	123	155	24.6297
AGAAUGAUGAAUGUGUCCAAGAUUUCAUUUUU	chr12:46757477-46757703(-)$1	226	107	139	25.2284
AUUAGAAUUAUAUAUCAUCUCCAAUUUUUCUG	chr4:73986681-73986900(-)$1	219	5	37	23.6982
UAGGAUCAACAGGUCCCCAAGAUGUCAUUCCU	chr1:93308666-93308884(-)$1	218	106	138	24.4551
UUUGGGGGCUCCUACUCUUGAUCCUGCCCUUG	chr1:70700337-70700556(+)$1	219	64	96	25.3163
AGAGUGGGGAUUUUUUUCUUCUUCCCUUUCUC	chr7:128410114-128410354(+)$1	240	191	223	23.9704
AGUGAAAAGUUUUGUUUUUUUUUUUUUCGGCG	chr5:65222294-65222519(+)$1	225	80	112	24.3981
AGGCUUUGUUCUACCUACUCUUGAAGAAUCCU	chr2:100165515-100165734(-)$1	219	64	96	24.4803
CUGAUGUAAAAUUCUAAAUUACCAUUUACUUC	chr21:43409914-43410204(-)$1	290	198	230	20.7562
GCUGUAGUCAGUCAUUUUGGUUUUCUUCUAUA	chr15:66181606-66181829(+)$1	223	0	32	24.1960
GUCUUAACCACUUCUGUAUUGUGUGGUCUUAA	chr1:24797185-24797426(+)$1	241	105	137	21.8614
UUGGACCACUGAAAUGAAAAAUACUGUGGACA	chr2:64118266-64118498(+)$1	232	83	115	23.5445
GUUAAGGGACAAGAAGCAAACAUUCUCUUAAU	chr4:42118953-42119193(-)$1	240	48	80	25.0523
GGCAGGAACUUAACCCAAAUCUAGUUCUUUGA	chr12:1600907-1601124(+)$1	217	104	136	24.5601
UAAAAAAAAGAAAAAAAGCUGGCUCUUGAAUU	chr11:120203879-120204107(+)$1	228	15	47	25.0921
ACCAAACUGGCUUUUUUUUUUUCUAGUGAAGU	chr10:5807598-5807819(-)$1	221	66	98	25.2118
UAAUUUCAAAUGGAAUAGAGUAUUUUGAUAUU	chr1:42642376-42642609(-)$1	233	66	98	25.5883
GCAUCUUCAACAAUAUUCCUACAGUUGUAUGG	chr14:57676213-57676431(-)$1	218	56	88	23.7992
GAGGAGUGCAGCGGAAAAAAAUUUGCACUCUU	chr7:30122029-30122245(+)$1	216	134	166	25.9280
AAAGUAUGUUUUUUAUAAGAACUGGCAUCUUG	chr8:57872191-57872409(-)$1	218	121	153	25.0437
GGUCCCCCAGGUUUCUUGGUGUUCCUGCUUGG	chr11:117041539-117041765(+)$1	226	58	90	25.4883
AACAUUCCACAUUCAAAAGUUUUGUAGGGUGG	chr11:34122599-34122828(+)$1	229	12	44	22.9180
augaacaguccauuuuaaaauuacugagucau	chr19:58134501-58134725(+)$1	224	100	132	22.7528
GAGGCUGAAUUAUUCAAAUUUAAAUGAGGUUU	chr9:140194497-140194718(-)$1	221	165	197	23.3586
UGUAAAUCUUGCAACAUAGCUCUCAAGAUACC	chr7:22984229-22984440(-)$1	211	132	164	24.2053
cuaauuuucuuuuuuuuuucuuuuugagaugg	chr1:226171898-226172129(-)$1	231	156	188	23.8712
UAUAUGUGUUUUUAUUGAAAACUGGGCACUUG	chr4:90164807-90165038(-)$1	231	92	124	24.2243
UUUCCAUACACUGUGUGCUAUUUGUGUUAACA	chr2:60685996-60686209(-)$1	213	139	171	24.3811
AGUAAUGAUGUUUAAUAUGUACUGCAUACAUU	chr1:78341233-78341453(+)$1	220	3	35	25.5226
UUUAUUUGCAUUGUGCAAAGUUAUGUAAGUAG	chr10:28897221-28897443(+)$1	222	167	199	25.0753
CAGGGCAGCAACUGCCAUUUAAAUGUUGUCUU	chr11:111954388-111954611(+)$1	223	118	150	26.1346
GCCAGAGUUGCUCCGGGCCAUUGUCGACUGUG	chr6:31508003-31508256(-)$1	253	105	137	24.9222
AGCUGAGAUGGAUGAAGUGGAACGUUUCCAGC	chr5:140958563-140958796(-)$1	233	66	98	22.3134
UCCUGGUACUUAUCAAAUACUUAGUAUCAUGG	chr21:28209415-28209640(-)$1	225	87	119	25.2131
GGCAGAAAGUGGGAUUCUGCAUACGCCAUCUC	chr9:97221540-97221761(+)$1	221	158	190	25.1115
AUCAGAAUCAGUAUCAGUUCCCCUGUAUUCUG	chr14:69708607-69708831(+)$1	224	57	89	22.7167
GUGAGAAAAGGUUAUAAUAGAUUCUUUUUUUU	chr16:69338804-69339036(+)$1	232	171	203	25.5662
GCUUUUCAGUUAGGGGUAGUGGAGAAAGGGGU	chr12:65089212-65089451(+)$1	239	98	130	23.2536
Gauuauuuauuucuuauauuuuuauaaguaaa	chr16:69338267-69338490(+)$1	223	132	164	22.6946
UGAAAACUUACAUAGACAGAAAGUAGGUUUUG	chr18:72912495-72912748(-)$1	253	72	104	24.1932
UCAGAAAAAGCUUAAGAAAUGCGAUAUGACUU	chr17:73942522-73942746(-)$1	224	132	164	22.7745
UAUUUUUCAGUGCAUAAUGUUUUUCUGAGCUU	chr2:85545103-85545327(-)$1	224	73	105	22.0646
GUAGUGCUUGCCUAUUGUAACAGCAUUGGUUC	chr22:30426253-30426464(+)$1	211	156	188	24.5803
AGUUUUUAAAAAAUCGACUCAUGUUUAAAAAC	chr3:140697503-140697755(+)$1	252	211	243	25.0716
AUGGAUGGGGAAAUGUCUCUGGAUCCCCACAG	chr1:36389547-36389772(+)$1	225	122	154	23.7799
GACGUUUUUGUUUAAAUUCCACCCGCGUUUGU	chr6:151678964-151679194(+)$1	230	72	104	22.8615
AGCUCUUUGGAGAAGGAUCAAAAUUCAGAUGG	chr6:150570953-150571228(+)$1	275	221	253	24.7051
UGGGCAUGUACAAGCUUAAAUAACGUGCCGAC	chr2:208628494-208628704(-)$1	210	86	118	24.8526
GUGGGAAAAUGAGAUUUGUAAGUAGUUUUCUU	chr8:57871655-57871876(-)$1	221	58	90	21.9579
GCUGAAUUGUAGAACACAAAUAAUUUAAUUCA	chr6:72014015-72014232(+)$1	217	117	149	24.8823
cauuaauucagacguaaagauucuaugaauau	chr1:226820504-226820716(-)$1	212	161	193	19.8932
AGAAUGUCAUUUUGCCCUCAACCUUGGUAUUU	chr8:22477385-22477615(+)$1	230	49	81	19.0256
UGGUGGAGCCUUCUCCCUUGCCAUUUGGUUCC	chr9:134374635-134374914(+)$1	279	53	85	23.0584
UUCUCAUUUCUGAAAAAUUCUAAGUCAUGAGA	chr9:123523504-123523737(-)$1	233	36	68	24.5549

#DB
(((((((.(((...........)))...))))	chr14:55513397-55513619(+)$1	1	70	102	26.2151
.((((((((((...........)))..)))))	chr12:95676132-95676351(+)$1	1	156	188	24.8043
...(((((((............)))))))...	chr7:138983993-138984217(+)$1	1	10	42	21.4333
((((.(((................))))))))	chr9:123216002-123216229(-)$1	1	107	139	23.4827
(....((((((...........))))))....	chr16:1726584-1726825(+)$1	1	23	55	24.1092
(.(((((.((...........)).))))).))	chr6:89321261-89321504(-)$1	1	122	154	22.4802
((((((((((.............)).))))))	chr7:65422987-65423206(+)$1	1	157	189	22.0173
((((.(((((..............))))).))	chr2:27016865-27017078(+)$1	1	115	147	24.2066
(...((((((.............))))))...	chr9:72331480-72331708(-)$1	1	123	155	24.6297
.(((.((((((............)))))).))	chr12:46757477-46757703(-)$1	1	107	139	25.2284
(((((((..((............))..)))))	chr4:73986681-73986900(-)$1	1	5	37	23.6982
(((((...(((...........)))...))))	chr1:93308666-93308884(-)$1	1	106	138	24.4551
..(((((((................)))))))	chr1:70700337-70700556(+)$1	1	64	96	25.3163
((((.(((((............)))))..)))	chr7:128410114-128410354(+)$1	1	191	223	23.9704
..(((((((.............))))))).))	chr5:65222294-65222519(+)$1	1	80	112	24.3981
(((..((.(((...........))).)).)))	chr2:100165515-100165734(-)$1	1	64	96	24.4803
)))))(((((..............)))))...	chr21:43409914-43410204(-)$1	1	198	230	20.7562
(((((((..((.............)).)))))	chr15:66181606-66181829(+)$1	1	0	32	24.1960
(((((((((((...........))))).....	chr1:24797185-24797426(+)$1	1	105	137	21.8614
..((.((((................))))...	chr2:64118266-64118498(+)$1	1	83	115	23.5445
(((((((((..............)))))))))	chr4:42118953-42119193(-)$1	1	48	80	25.0523
((((((((((............))))).))).	chr12:1600907-1601124(+)$1	1	104	136	24.5601
.(((...((((............))))...))	chr11:120203879-120204107(+)$1	1	15	47	25.0921
((...(((((............)))))...))	chr10:5807598-5807819(-)$1	1	66	98	25.2118
((((.(((((.............))))).)))	chr1:42642376-42642609(-)$1	1	66	98	25.5883
.(((((.((((............))))...))	chr14:57676213-57676431(-)$1	1	56	88	23.7992
(((((((((((...........))))))))))	chr7:30122029-30122245(+)$1	1	134	166	25.9280
.(((.(((((.............)))))))).	chr8:57872191-57872409(-)$1	1	121	153	25.0437
(((((((((((............))))...))	chr11:117041539-117041765(+)$1	1	58	90	25.4883
..(((((.(((...........))).)))))(	chr11:34122599-34122828(+)$1	1	12	44	22.9180
((((.((((.............))))..))))	chr19:58134501-58134725(+)$1	1	100	132	22.7528
((((((..(((...........)))..)))))	chr9:140194497-140194718(-)$1	1	165	197	23.3586
((...((((((............))))))..)	chr7:22984229-22984440(-)$1	1	132	164	24.2053
(((..((((................)))))))	chr1:226171898-226172129(-)$1	1	156	188	23.8712
((((.((((((............)))))).))	chr4:90164807-90165038(-)$1	1	92	124	24.2243
))(((((((((............))))....)	chr2:60685996-60686209(-)$1	1	139	171	24.3811
(((((((((((............)))).))))	chr1:78341233-78341453(+)$1	1	3	35	25.5226
.((((((((((...........))))))))))	chr10:28897221-28897443(+)$1	1	167	199	25.0753
((((((((((.............)))))))))	chr11:111954388-111954611(+)$1	1	118	150	26.1346
((((.((((((...........).))))).))	chr6:31508003-31508256(-)$1	1	105	137	24.9222
..))).((((............))))((((((	chr5:140958563-140958796(-)$1	1	66	98	22.3134
...(((((((............))))))))))	chr21:28209415-28209640(-)$1	1	87	119	25.2131
((.(((..(((............)))..))))	chr9:97221540-97221761(+)$1	1	158	190	25.1115
..(((((((((...........))).))))))	chr14:69708607-69708831(+)$1	1	57	89	22.7167
..(((((((((...........))))))))).	chr16:69338804-69339036(+)$1	1	171	203	25.5662
.((((((................))))))...	chr12:65089212-65089451(+)$1	1	98	130	23.2536
..((((((((.............)))))))).	chr16:69338267-69338490(+)$1	1	132	164	22.6946
))(((((((((...........))))))))).	chr18:72912495-72912748(-)$1	1	72	104	24.1932
((((((.((((................).)))	chr17:73942522-73942746(-)$1	1	132	164	22.7745
(.....((((..............))))))))	chr2:85545103-85545327(-)$1	1	73	105	22.0646
((((.((((((...........)))..))).)	chr22:30426253-30426464(+)$1	1	156	188	24.5803
.(((((((((.............)))))))))	chr3:140697503-140697755(+)$1	1	211	243	25.0716
.((..((((((............)))))))))	chr1:36389547-36389772(+)$1	1	122	154	23.7799
((((....(((.............)))..)))	chr6:151678964-151679194(+)$1	1	72	104	22.8615
(....((((((............)))))))))	chr6:150570953-150571228(+)$1	1	221	253	24.7051
(.(((((((.............))))))).))	chr2:208628494-208628704(-)$1	1	86	118	24.8526
(.((((((((..............))))))))	chr8:57871655-57871876(-)$1	1	58	90	21.9579
))(((((((................)))))))	chr6:72014015-72014232(+)$1	1	117	149	24.8823
(((..(((((...............)))))))	chr1:226820504-226820716(-)$1	1	161	193	19.8932
(((((((((...............))))).))	chr8:22477385-22477615(+)$1	1	49	81	19.0256
((((((((((................))))))	chr9:134374635-134374914(+)$1	1	53	85	23.0584
(((((((..((...........))..))))))	chr9:123523504-123523737(-)$1	1	36	68	24.5549

#PSSM
f : 0.14	d : 0.11	: : 0.09	e : 0.09	g : 0.09	c : 0.08	! : 0.04	" : 0.04	= : 0.04	i : 0.03	h : 0.03	b : 0.03	[ : 0.03	# : 0.03	% : 0.01	o : 0.01	$ : 0.01	a : 0.01	
f : 0.14	g : 0.11	e : 0.11	c : 0.09	d : 0.08	= : 0.06	i : 0.04	# : 0.04	[ : 0.04	" : 0.04	h : 0.03	! : 0.03	b : 0.03	: : 0.03	$ : 0.03	% : 0.01	o : 0.01	
g : 0.16	e : 0.12	c : 0.12	f : 0.11	i : 0.08	d : 0.08	h : 0.06	= : 0.06	" : 0.04	# : 0.03	b : 0.03	$ : 0.03	% : 0.01	[ : 0.01	
g : 0.17	e : 0.12	c : 0.11	f : 0.11	i : 0.08	d : 0.08	h : 0.06	! : 0.06	= : 0.06	" : 0.04	# : 0.03	b : 0.01	$ : 0.01	
[ : 0.17	g : 0.16	e : 0.11	f : 0.11	i : 0.08	h : 0.06	! : 0.06	= : 0.06	# : 0.04	c : 0.04	" : 0.04	$ : 0.01	
e : 0.25	f : 0.17	g : 0.16	i : 0.08	h : 0.06	= : 0.06	c : 0.04	d : 0.04	" : 0.03	b : 0.01	: : 0.01	$ : 0.01	# : 0.01	
e : 0.24	g : 0.16	f : 0.16	i : 0.08	d : 0.08	= : 0.06	h : 0.04	c : 0.03	" : 0.03	[ : 0.03	! : 0.03	b : 0.01	# : 0.01	
e : 0.17	d : 0.16	f : 0.14	g : 0.11	! : 0.08	[ : 0.06	i : 0.06	c : 0.04	h : 0.04	= : 0.04	" : 0.01	y : 0.01	# : 0.01	
c : 0.17	e : 0.17	d : 0.16	f : 0.12	g : 0.09	i : 0.06	! : 0.04	= : 0.04	y : 0.03	b : 0.03	h : 0.03	
c : 0.17	e : 0.16	f : 0.12	d : 0.11	y : 0.09	b : 0.08	v : 0.04	= : 0.04	i : 0.04	g : 0.03	h : 0.03	w : 0.01	x : 0.01	
c : 0.16	v : 0.16	y : 0.11	u : 0.09	f : 0.09	w : 0.08	d : 0.08	b : 0.04	= : 0.03	a : 0.03	i : 0.03	x : 0.03	t : 0.01	e : 0.01	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.27	v : 0.19	y : 0.12	w : 0.08	x : 0.03	
u : 0.29	t : 0.25	v : 0.19	y : 0.12	w : 0.08	x : 0.03	b : 0.01	
u : 0.19	v : 0.14	c : 0.12	y : 0.12	w : 0.08	g : 0.06	e : 0.06	b : 0.03	= : 0.03	d : 0.03	i : 0.03	x : 0.03	f : 0.01	a : 0.01	
c : 0.14	f : 0.12	y : 0.11	d : 0.11	e : 0.09	g : 0.06	w : 0.06	i : 0.06	b : 0.04	= : 0.04	] : 0.03	v : 0.03	x : 0.03	h : 0.01	
c : 0.17	e : 0.17	f : 0.12	d : 0.12	y : 0.09	g : 0.06	i : 0.06	b : 0.04	= : 0.04	h : 0.03	x : 0.01	2 : 0.01	
e : 0.19	d : 0.16	f : 0.12	g : 0.09	2 : 0.08	] : 0.06	i : 0.06	c : 0.04	= : 0.04	3 : 0.03	h : 0.03	y : 0.03	b : 0.01	
e : 0.20	f : 0.17	d : 0.12	g : 0.11	2 : 0.09	i : 0.06	h : 0.04	= : 0.04	3 : 0.03	c : 0.03	b : 0.01	] : 0.01	y : 0.01	
e : 0.17	f : 0.17	g : 0.14	3 : 0.09	h : 0.06	2 : 0.06	i : 0.06	d : 0.04	= : 0.04	] : 0.03	b : 0.01	0 : 0.01	4 : 0.01	a : 0.01	c : 0.01	
f : 0.20	g : 0.14	e : 0.14	i : 0.08	h : 0.06	c : 0.06	3 : 0.06	= : 0.06	] : 0.04	4 : 0.03	2 : 0.03	d : 0.03	0 : 0.01	
] : 0.12	g : 0.11	3 : 0.11	c : 0.11	i : 0.09	f : 0.09	e : 0.06	h : 0.06	= : 0.06	4 : 0.03	d : 0.03	5 : 0.01	: : 0.01	0 : 0.01	2 : 0.01	b : 0.01	
c : 0.16	g : 0.12	f : 0.11	i : 0.09	d : 0.09	e : 0.08	h : 0.06	= : 0.06	3 : 0.04	4 : 0.03	b : 0.03	5 : 0.01	: : 0.01	0 : 0.01	2 : 0.01	] : 0.01	
g : 0.12	f : 0.12	e : 0.11	d : 0.11	c : 0.11	3 : 0.08	i : 0.06	h : 0.06	= : 0.06	: : 0.03	5 : 0.01	4 : 0.01	b : 0.01	0 : 0.01	] : 0.01	2 : 0.01	

#score	1483.5408776603174
#seq	62
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_CDS_m3_run2.txt

#BEAR
eewwwwwwwwwwwwwweee	chr3:23848777-23849003(+)$1	226	141	160	19.5311
eeeettttttttttteeee	chr2:42556976-42557201(+)$1	225	96	115	22.6691
eeeevvvvvvvvvvvvvee	chr14:92597235-92597462(+)$1	227	81	100	21.6275
f[bbtttttttttttbb]f	chr1:63955729-63955952(-)$1	223	150	169	21.4639
eeeettttttttttteeee	chr1:220197639-220197858(-)$1	219	194	213	22.6691
eeeettttttttttteeee	chr1:227843173-227843397(+)$1	224	74	93	22.6691
ccvvvvvvvvvvvvvccc:	chr1:150938533-150938763(-)$1	230	25	44	20.1885
fffftttttttttttffff	chr12:46756785-46757007(-)$1	222	41	60	21.8981
hccctttttttttttccc]	chr10:101978384-101978604(-)$1	220	109	128	22.7835
dddduuuuuuuuuuuuddd	chr4:187629196-187629417(-)$1	221	185	204	22.0520
eeeuuuuuuuuuuuueeee	chr8:145065312-145065549(+)$1	237	195	214	21.4402
"ccctttttttttttccc3	chr22:22142486-22142709(-)$1	223	136	155	22.7620
eewwwwwwwwwwwwwweee	chrX:70793422-70793645(+)$1	223	25	44	19.5311
ccbbtttttttttttbb]c	chr1:82408740-82408972(+)$1	232	14	33	21.7548
bwwwwwwwwwwwwwwbb33	chr1:150240403-150240625(-)$1	222	37	56	17.9923
iiiitttttttttttiiii	chr19:30503350-30503574(+)$1	224	152	171	22.2999
hhhhuuuuuuuuuuuuhhh	chr20:5096029-5096248(-)$1	219	159	178	20.5857
fffftttttttttttffff	chr6:146126255-146126485(-)$1	230	64	83	21.8981
ddddtttttttttttdddd	chr2:28268542-28268766(+)$1	224	81	100	22.8486
eeeettttttttttteeee	chr20:47704479-47704712(+)$1	233	47	66	22.6691
dddduuuuuuuuuuuuddd	chr15:34455673-34455893(-)$1	220	109	128	22.0520
ddddtttttttttttdddd	chr10:131964682-131964917(+)$1	235	176	195	22.8486
cccuuuuuuuuuuuuccc]	chr14:74363103-74363332(+)$1	229	190	209	21.6496
[ccctttttttttttccc4	chr6:149983055-149983287(-)$1	232	29	48	22.8440
ggggtttttttttttgggg	chr5:134079587-134079810(+)$1	223	174	193	22.3694
[ccctttttttttttccc3	chr5:59934498-59934721(-)$1	223	148	167	22.8918
ddddtttttttttttdddd	chrX:24006430-24006654(-)$1	224	37	56	22.8486
eeeevvvvvvvvvvvvvee	chr14:102323061-102323279(+)$1	218	7	26	21.6275
eebbtttttttttttbb]e	chr5:178310290-178310514(+)$1	224	160	179	21.8759
cccuuuuuuuuuuuuccc:	chr1:100614491-100614708(+)$1	217	4	23	20.6875
ddddtttttttttttdddd	chr11:46780417-46780646(-)$1	229	84	103	22.8486
ffffuuuuuuuuuuuufff	chr11:18536264-18536487(-)$1	223	77	96	21.1276
ddddvvvvvvvvvvvvvdd	chr11:125472631-125472857(+)$1	226	63	82	21.7753
:ccctttttttttttccc:	chr1:152006068-152006293(-)$1	225	15	34	20.9438
dddduuuuuuuuuuuuddd	chr6:35841949-35842169(-)$1	220	24	43	22.0520
hhhhttttttttttthhhh	chr13:53240899-53241122(+)$1	223	5	24	21.2074
:ccctttttttttttccc:	chr4:83769856-83770082(-)$1	226	205	224	20.9438
bbvvvvvvvvvvvvvbb22	chr6:71235578-71235800(+)$1	222	73	92	19.5013
ddddvvvvvvvvvvvvvdd	chrM:10105-10331(+)$1	226	137	156	21.7753
ddddtttttttttttdddd	chr1:114248599-114248820(-)$1	221	92	111	22.8486
ggggtttttttttttgggg	chr6:108544129-108544351(-)$1	222	54	73	22.3694
"ccctttttttttttccc3	chr9:114997039-114997267(-)$1	228	97	116	22.7620
ggggtttttttttttgggg	chr5:95124412-95124633(+)$1	221	130	149	22.3694
eeeevvvvvvvvvvvvvee	chr11:85361204-85361426(+)$1	222	43	62	21.6275
fffftttttttttttffff	chr12:93221601-93221819(-)$1	218	39	58	21.8981
ffffuuuuuuuuuuuufff	chr19:37239921-37240155(-)$1	234	12	31	21.1276
ddddtttttttttttdddd	chr6:17647976-17648197(-)$1	221	133	152	22.8486
iiiitttttttttttiiii	chr4:185552819-185553043(-)$1	224	121	140	22.2999
ddddvvvvvvvvvvvvvdd	chr17:40962777-40962998(-)$1	221	74	93	21.7753
hh[auuuuuuuuuuuua]h	chrX:153609405-153609630(+)$1	225	9	28	21.1895
ddddtttttttttttdddd	chr20:34241484-34241708(-)$1	224	32	51	22.8486
fffftttttttttttffff	chr10:27455974-27456195(+)$1	221	164	183	21.8981
ddddvvvvvvvvvvvvvdd	chr7:24689200-24689423(+)$1	223	198	217	21.7753
eeeettttttttttteeee	chr4:144447346-144447569(+)$1	223	180	199	22.6691
ddddtttttttttttdddd	chr5:179688658-179688881(-)$1	223	40	59	22.8486
ddddvvvvvvvvvvvvvdd	chr10:5496330-5496553(+)$1	223	122	141	21.7753

#otherMatches

#Seq PSSM
UGCUCUUUUUUUUUUCCAC	chr3:23848777-23849003(+)$1	226	141	160	19.5311
GUGUCAUCCAAUCUAAUAC	chr2:42556976-42557201(+)$1	225	96	115	22.6691
GGACCAAAAAAAAUGACGU	chr14:92597235-92597462(+)$1	227	81	100	21.6275
UCUCCCACAAGUUCUGAAG	chr1:63955729-63955952(-)$1	223	150	169	21.4639
UGCUGAACAGAUGAAAGCA	chr1:220197639-220197858(-)$1	219	194	213	22.6691
UACAAAUGUAAAGAAUGUG	chr1:227843173-227843397(+)$1	224	74	93	22.6691
GGAAGAAACAGAGAGCUCA	chr1:150938533-150938763(-)$1	230	25	44	20.1885
AAACAGCCAAUCAAAGUUU	chr12:46756785-46757007(-)$1	222	41	60	21.8981
UCAACCAAAUAGCCUUUGU	chr10:101978384-101978604(-)$1	220	109	128	22.7835
GUGGGAGAGCAAAUAACCA	chr4:187629196-187629417(-)$1	221	185	204	22.0520
GGCCCCUUACCCACAGCCC	chr8:145065312-145065549(+)$1	237	195	214	21.4402
AGGCUGUUCCCAAAUGCUG	chr22:22142486-22142709(-)$1	223	136	155	22.7620
GUUCUUGUUUUUUAUUACC	chrX:70793422-70793645(+)$1	223	25	44	19.5311
CAGAUAAAAUUUAUUUCAU	chr1:82408740-82408972(+)$1	232	14	33	21.7548
CUCCUUGAUUUCUCUGGCU	chr1:150240403-150240625(-)$1	222	37	56	17.9923
AUCUGAAAAGUCAUAAGAU	chr19:30503350-30503574(+)$1	224	152	171	22.2999
AUAAUAAAUUUGAACCUUG	chr20:5096029-5096248(-)$1	219	159	178	20.5857
ACGUGAAGAAUGUGGAUGU	chr6:146126255-146126485(-)$1	230	64	83	21.8981
GCUGCCCGUAGAUUUCAGC	chr2:28268542-28268766(+)$1	224	81	100	22.8486
CUGUUUUUGUAUUUUACAG	chr20:47704479-47704712(+)$1	233	47	66	22.6691
UUCACUAAUAAGAACAUGA	chr15:34455673-34455893(-)$1	220	109	128	22.0520
GGGACUCAAAGCCUAUUCC	chr10:131964682-131964917(+)$1	235	176	195	22.8486
GGCAUAUUUAACUUAGUCA	chr14:74363103-74363332(+)$1	229	190	209	21.6496
UGCUGAUGAAAUAAAAGCU	chr6:149983055-149983287(-)$1	232	29	48	22.8440
AAAUUUCGAUGAUGUGUUU	chr5:134079587-134079810(+)$1	223	174	193	22.3694
AGUUGGAAUAUAAUGAACA	chr5:59934498-59934721(-)$1	223	148	167	22.8918
UCCAGUUAACAAAUAUGGA	chrX:24006430-24006654(-)$1	224	37	56	22.8486
UCAGUGUUGCGUCCUCUUU	chr14:102323061-102323279(+)$1	218	7	26	21.6275
AGGCAUCCAGUUACAGCAC	chr5:178310290-178310514(+)$1	224	160	179	21.8759
GCCUCAUUAAACUUUGGUA	chr1:100614491-100614708(+)$1	217	4	23	20.6875
AUGCACAGUAAUACAGCAU	chr11:46780417-46780646(-)$1	229	84	103	22.8486
GAAGUUUCUAUUUCUUUUU	chr11:18536264-18536487(-)$1	223	77	96	21.1276
CAGGUUUAAUGAUCACCUC	chr11:125472631-125472857(+)$1	226	63	82	21.7753
AGGCAAAAAUCUCCAGCCC	chr1:152006068-152006293(-)$1	225	15	34	20.9438
CGUUUUUUCCCUCCUUAAU	chr6:35841949-35842169(-)$1	220	24	43	22.0520
AUAUACAUUUACAAAAUGU	chr13:53240899-53241122(+)$1	223	5	24	21.2074
GACCUUCUCUGAUAUGGUA	chr4:83769856-83770082(-)$1	226	205	224	20.9438
UAAAUCUAAUAACUCUACA	chr6:71235578-71235800(+)$1	222	73	92	19.5013
UUCUUAUUAUUUGAUCUAG	chrM:10105-10331(+)$1	226	137	156	21.7753
UGGAUUAGCAUUUUUUCCA	chr1:114248599-114248820(-)$1	221	92	111	22.8486
AAGUUUCCUUAAUGUGCUU	chr6:108544129-108544351(-)$1	222	54	73	22.3694
GGGUAUAAUUUCUUCACCA	chr9:114997039-114997267(-)$1	228	97	116	22.7620
UGAAUUUCAGGAUCUUUCA	chr5:95124412-95124633(+)$1	221	130	149	22.3694
UCUUUGUAUAAAUUCUUGA	chr11:85361204-85361426(+)$1	222	43	62	21.6275
AAGGAACAGAGACAGCUUU	chr12:93221601-93221819(-)$1	218	39	58	21.8981
UUGGCUCAACACUACUUCA	chr19:37239921-37240155(-)$1	234	12	31	21.1276
GAGGCAAAUGUACUACCUC	chr6:17647976-17648197(-)$1	221	133	152	22.8486
UCAGGUAAUGUCUAACUGA	chr4:185552819-185553043(-)$1	224	121	140	22.2999
AUUGAAGACACAGGAGGCA	chr17:40962777-40962998(-)$1	221	74	93	21.7753
CUGAAAACCGUGCUCCUGG	chrX:153609405-153609630(+)$1	225	9	28	21.1895
CUUCAGCUAUGACCAGAGG	chr20:34241484-34241708(-)$1	224	32	51	22.8486
ACACCUUCAUAUCCAGUGU	chr10:27455974-27456195(+)$1	221	164	183	21.8981
UCAGUACCCUAUUAAAUCU	chr7:24689200-24689423(+)$1	223	198	217	21.7753
UCUACAUUACACAACUGGA	chr4:144447346-144447569(+)$1	223	180	199	22.6691
CUGACCUUUUCUCCCUCAG	chr5:179688658-179688881(-)$1	223	40	59	22.8486
GAGCACCCUGAUGUUCAGC	chr10:5496330-5496553(+)$1	223	122	141	21.7753

#DB
((..............)))	chr3:23848777-23849003(+)$1	1	141	160	19.5311
((((...........))))	chr2:42556976-42557201(+)$1	1	96	115	22.6691
((((.............))	chr14:92597235-92597462(+)$1	1	81	100	21.6275
(.((...........)).)	chr1:63955729-63955952(-)$1	1	150	169	21.4639
((((...........))))	chr1:220197639-220197858(-)$1	1	194	213	22.6691
((((...........))))	chr1:227843173-227843397(+)$1	1	74	93	22.6691
((.............))).	chr1:150938533-150938763(-)$1	1	25	44	20.1885
((((...........))))	chr12:46756785-46757007(-)$1	1	41	60	21.8981
((((...........))).	chr10:101978384-101978604(-)$1	1	109	128	22.7835
((((............)))	chr4:187629196-187629417(-)$1	1	185	204	22.0520
(((............))))	chr8:145065312-145065549(+)$1	1	195	214	21.4402
.(((...........))).	chr22:22142486-22142709(-)$1	1	136	155	22.7620
((..............)))	chrX:70793422-70793645(+)$1	1	25	44	19.5311
((((...........)).)	chr1:82408740-82408972(+)$1	1	14	33	21.7548
(..............))..	chr1:150240403-150240625(-)$1	1	37	56	17.9923
((((...........))))	chr19:30503350-30503574(+)$1	1	152	171	22.2999
((((............)))	chr20:5096029-5096248(-)$1	1	159	178	20.5857
((((...........))))	chr6:146126255-146126485(-)$1	1	64	83	21.8981
((((...........))))	chr2:28268542-28268766(+)$1	1	81	100	22.8486
((((...........))))	chr20:47704479-47704712(+)$1	1	47	66	22.6691
((((............)))	chr15:34455673-34455893(-)$1	1	109	128	22.0520
((((...........))))	chr10:131964682-131964917(+)$1	1	176	195	22.8486
(((............))).	chr14:74363103-74363332(+)$1	1	190	209	21.6496
.(((...........))).	chr6:149983055-149983287(-)$1	1	29	48	22.8440
((((...........))))	chr5:134079587-134079810(+)$1	1	174	193	22.3694
.(((...........))).	chr5:59934498-59934721(-)$1	1	148	167	22.8918
((((...........))))	chrX:24006430-24006654(-)$1	1	37	56	22.8486
((((.............))	chr14:102323061-102323279(+)$1	1	7	26	21.6275
((((...........)).)	chr5:178310290-178310514(+)$1	1	160	179	21.8759
(((............))).	chr1:100614491-100614708(+)$1	1	4	23	20.6875
((((...........))))	chr11:46780417-46780646(-)$1	1	84	103	22.8486
((((............)))	chr11:18536264-18536487(-)$1	1	77	96	21.1276
((((.............))	chr11:125472631-125472857(+)$1	1	63	82	21.7753
.(((...........))).	chr1:152006068-152006293(-)$1	1	15	34	20.9438
((((............)))	chr6:35841949-35842169(-)$1	1	24	43	22.0520
((((...........))))	chr13:53240899-53241122(+)$1	1	5	24	21.2074
.(((...........))).	chr4:83769856-83770082(-)$1	1	205	224	20.9438
((.............))..	chr6:71235578-71235800(+)$1	1	73	92	19.5013
((((.............))	chrM:10105-10331(+)$1	1	137	156	21.7753
((((...........))))	chr1:114248599-114248820(-)$1	1	92	111	22.8486
((((...........))))	chr6:108544129-108544351(-)$1	1	54	73	22.3694
.(((...........))).	chr9:114997039-114997267(-)$1	1	97	116	22.7620
((((...........))))	chr5:95124412-95124633(+)$1	1	130	149	22.3694
((((.............))	chr11:85361204-85361426(+)$1	1	43	62	21.6275
((((...........))))	chr12:93221601-93221819(-)$1	1	39	58	21.8981
((((............)))	chr19:37239921-37240155(-)$1	1	12	31	21.1276
((((...........))))	chr6:17647976-17648197(-)$1	1	133	152	22.8486
((((...........))))	chr4:185552819-185553043(-)$1	1	121	140	22.2999
((((.............))	chr17:40962777-40962998(-)$1	1	74	93	21.7753
((.(............).)	chrX:153609405-153609630(+)$1	1	9	28	21.1895
((((...........))))	chr20:34241484-34241708(-)$1	1	32	51	22.8486
((((...........))))	chr10:27455974-27456195(+)$1	1	164	183	21.8981
((((.............))	chr7:24689200-24689423(+)$1	1	198	217	21.7753
((((...........))))	chr4:144447346-144447569(+)$1	1	180	199	22.6691
((((...........))))	chr5:179688658-179688881(-)$1	1	40	59	22.8486
((((.............))	chr10:5496330-5496553(+)$1	1	122	141	21.7753

#PSSM
d : 0.28	e : 0.21	f : 0.12	c : 0.07	h : 0.07	g : 0.05	" : 0.03	b : 0.03	i : 0.03	[ : 0.03	: : 0.03	
d : 0.28	e : 0.21	c : 0.19	f : 0.10	h : 0.05	g : 0.05	i : 0.03	[ : 0.01	w : 0.01	b : 0.01	
d : 0.28	e : 0.16	c : 0.16	f : 0.10	w : 0.05	b : 0.05	g : 0.05	v : 0.03	i : 0.03	h : 0.03	[ : 0.01	
d : 0.28	e : 0.14	c : 0.12	f : 0.10	w : 0.05	b : 0.05	u : 0.05	g : 0.05	v : 0.03	i : 0.03	h : 0.03	a : 0.01	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
t : 0.58	v : 0.17	u : 0.17	w : 0.05	
c : 0.17	v : 0.14	d : 0.14	u : 0.12	e : 0.10	b : 0.08	f : 0.07	g : 0.05	w : 0.03	i : 0.03	h : 0.01	
d : 0.19	c : 0.17	e : 0.14	v : 0.14	f : 0.10	b : 0.08	g : 0.05	i : 0.03	h : 0.03	a : 0.01	
d : 0.28	e : 0.19	c : 0.17	f : 0.10	] : 0.07	g : 0.05	i : 0.03	h : 0.03	3 : 0.01	2 : 0.01	
d : 0.28	e : 0.21	f : 0.12	: : 0.07	3 : 0.07	h : 0.05	g : 0.05	] : 0.03	i : 0.03	c : 0.01	4 : 0.01	2 : 0.01	

#score	1222.1374342600986
#seq	56
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_UTR_m1_run2.txt

#BEAR
eeeebbtttttttttttbb]eeee	chr14:75295855-75296056(+)$1	201	82	106	21.5467
""cccvvvvvvvvvvvvvccc333	chr13:96295242-96295443(-)$1	201	143	167	23.1035
b!!ddddtttttttttttdddd22	chr12:27467351-27467552(+)$1	201	48	72	21.6699
ffffffvvvvvvvvvvvvvfffff	chr14:68123117-68123318(-)$1	201	142	166	22.6695
:fffffftttttttttttffffff	chr16:71766502-71766703(-)$1	201	87	111	20.6905
iiiiiiuuuuuuuuuuuuiiiiii	chr16:89711840-89712041(-)$1	201	51	75	23.6418
:fffffftttttttttttffffff	chr8:144678729-144678930(-)$1	201	1	25	20.6905
c!!cccwwwwwwwwwwwwwwccc2	chr12:124107192-124107393(-)$1	201	165	189	22.4933
!a[cccvvvvvvvvvvvvvccc]a	chr19:48984182-48984383(+)$1	201	134	158	23.6234
ffffffuuuuuuuuuuuuffffff	chr2:61715225-61715426(-)$1	201	134	158	22.8313
ffff[ayyyyyyyyyyyyyyyya]	chr9:35100605-35100806(-)$1	201	51	75	21.4604
gggggggtttttttttttgggggg	chr9:114153988-114154189(-)$1	201	149	173	22.4027
eeeeeyyyyyyyyyyyyyyyyeee	chr9:103339056-103339257(+)$1	201	126	150	21.5707
gggggguuuuuuuuuuuugggggg	chr14:68244339-68244540(-)$1	201	161	185	23.7581
ggggggvvvvvvvvvvvvvggggg	chr9:35076385-35076586(-)$1	201	161	185	23.5649
cc!!bbuuuuuuuuuuuubb]ccc	chr2:62067001-62067202(-)$1	201	65	89	23.0418
eeeeeyyyyyyyyyyyyyyyyeee	chr19:50192481-50192682(+)$1	201	162	186	21.5707
ggggggwwwwwwwwwwwwwwgggg	chr19:49464018-49464219(+)$1	201	152	176	22.6160
b[eeeeettttttttttteeeee]	chr15:59189259-59189460(-)$1	201	64	88	22.0434
fff!!awwwwwwwwwwwwwwa22f	chr22:46689095-46689296(+)$1	201	134	158	22.0890
:eeeeevvvvvvvvvvvvveeeee	chr7:139137507-139137708(+)$1	201	60	84	22.1484
ggggggwwwwwwwwwwwwwwgggg	chr1:235273923-235274124(-)$1	201	81	105	22.6160
eeeeevvvvvvvvvvvvveeeeeE	chr17:60021973-60022174(-)$1	201	3	27	21.3251
ffffffwwwwwwwwwwwwwwffff	chr16:89805640-89805841(-)$1	201	143	167	21.7812
!!ddddvvvvvvvvvvvvvdddd]	chr13:111945371-111945572(+)$1	201	19	43	23.1224
ddddccctttttttttttccc22d	chr14:89087501-89087702(-)$1	201	158	182	22.1301
eee[bbuuuuuuuuuuuubbeeee	chr3:183900705-183900906(+)$1	201	171	195	23.1047
##dddduuuuuuuuuuuudddd33	chr5:179135218-179135419(+)$1	201	94	118	23.2942
))dddduuuuuuuuuuuudddd00	chr19:35988156-35988357(-)$1	201	107	131	21.2484
fffffftttttttttttffffffi	chr1:27055973-27056174(+)$1	201	75	99	21.3830
ceeeeeuuuuuuuuuuuueeeee2	chr16:30094687-30094888(+)$1	201	153	177	23.2339
ee!!bbyyyyyyyyyyyyyyyybb	chr7:116770492-116770693(+)$1	201	75	99	20.9226
!!dddduuuuuuuuuuuudddd22	chr11:110108240-110108441(-)$1	201	133	157	23.1634
ff!!bbtttttttttttbb22fff	chr7:107253709-107253910(+)$1	201	124	148	21.2049
iiddddvvvvvvvvvvvvvdddd]	chr3:3190120-3190321(+)$1	201	23	47	22.9149
!!dddduuuuuuuuuuuudddd]b	chr16:2499772-2499973(+)$1	201	107	131	23.0730
dd[cccuuuuuuuuuuuuccc]dd	chr3:9489994-9490195(+)$1	201	169	193	23.5270
gg!!bbvvvvvvvvvvvvvbb22g	chr17:78519390-78519591(+)$1	201	18	42	22.9875
c[a[bbvvvvvvvvvvvvvbb]ac	chr12:50394879-50395080(-)$1	201	114	138	22.8884
ddd[ccctttttttttttccc]dd	chr17:57109213-57109414(-)$1	201	55	79	22.3491
eeeeevvvvvvvvvvvvveeeee]	chr6:33589239-33589440(+)$1	201	144	168	22.4815
deeeeeuuuuuuuuuuuueeeee:	chr1:44436242-44436443(+)$1	201	36	60	22.3137
hhhhhhuuuuuuuuuuuuhhhhhh	chr10:103347080-103347281(-)$1	201	147	171	21.2773
"""cccuuuuuuuuuuuuccc333	chr12:122693085-122693286(-)$1	201	75	99	24.1827
[bba!!attttttttttta22a]b	chr9:128099724-128099925(+)$1	201	29	53	21.6295
""ddddtttttttttttdddd333	chrX:70794448-70794649(+)$1	201	149	173	22.0575
$$ddddtttttttttttdddd]cc	chr19:17328182-17328383(+)$1	201	130	154	21.3133
!eeeeeyyyyyyyyyyyyyyyyee	chr19:44341435-44341636(+)$1	201	156	180	21.6263
ee!!bbvvvvvvvvvvvvvbb22e	chr6:71235477-71235678(+)$1	201	170	194	22.7684
ffffffvvvvvvvvvvvvvfffff	chr5:180222620-180222821(-)$1	201	84	108	22.6695
dd[cccwwwwwwwwwwwwwwccc]	chr5:134147338-134147539(+)$1	201	156	180	22.3576
ddddyyyyyyyyyyyyyyyydddd	chr8:145748951-145749152(+)$1	201	175	199	20.6640
cc[cccuuuuuuuuuuuuccc]cc	chr7:129668735-129668936(-)$1	201	5	29	23.8966
ggggggyyyyyyyyyyyyyyyygg	chr9:108337180-108337381(+)$1	201	55	79	21.8757
hhhcccyyyyyyyyyyyyyyyycc	chr17:49269980-49270181(-)$1	201	16	40	21.1288
ee"""bbtttttttttttbb333e	chr14:73572848-73573049(+)$1	201	69	93	21.8577
d[ddddwwwwwwwwwwwwwwdddd	chr1:233388352-233388553(-)$1	201	29	53	21.7082
ggggggwwwwwwwwwwwwwwgggg	chr19:4174076-4174277(-)$1	201	174	198	22.6160
[eeeeevvvvvvvvvvvvveeeee	chr14:78186877-78187078(-)$1	201	126	150	23.2015
gggggggtttttttttttgggggg	chrX:102931929-102932130(-)$1	201	84	108	22.4027
!eeeeeuuuuuuuuuuuueeeee6	chr2:148653890-148654091(+)$1	201	112	136	23.0370
ffffffuuuuuuuuuuuuffffff	chr17:56423412-56423613(-)$1	201	64	88	22.8313
iiiiiiuuuuuuuuuuuuiiiiii	chr1:21071058-21071259(-)$1	201	73	97	23.6418
ddd[bbvvvvvvvvvvvvvbb]dd	chr16:75663280-75663481(-)$1	201	160	184	22.3936
gggggguuuuuuuuuuuugggggg	chr19:36593299-36593500(+)$1	201	24	48	23.7581
fa[cccuuuuuuuuuuuuccc]a]	chr15:42118212-42118413(+)$1	201	63	87	23.9859

#otherMatches

#Seq PSSM
UGGUACUAAAAGGAAACGUGACUG	chr14:75295855-75296056(+)$1	201	82	106	21.5467
UAAGGUAAAUACCAUGGCCCUGUA	chr13:96295242-96295443(-)$1	201	143	167	23.1035
UUUUCAAUAAUAAUAUAUUUGACU	chr12:27467351-27467552(+)$1	201	48	72	21.6699
AGCUGGGGGAACAACGAGACCAGU	chr14:68123117-68123318(-)$1	201	142	166	22.6695
UGGCGAAAAAACACUCACUUUGUC	chr16:71766502-71766703(-)$1	201	87	111	20.6905
GCCACCCAACGCUGUCCUGGUGGU	chr16:89711840-89712041(-)$1	201	51	75	23.6418
ACUUUCAGAGGCUUUAAGUGGAAG	chr8:144678729-144678930(-)$1	201	1	25	20.6905
CCGGCUCUUUCCACUAAACCAGCA	chr12:124107192-124107393(-)$1	201	165	189	22.4933
acguguuuggauugagguugcagg	chr19:48984182-48984383(+)$1	201	134	158	23.6234
AGAGAUGCUUUGCUUUUGAUUUCU	chr2:61715225-61715426(-)$1	201	134	158	22.8313
GAUCUCUGAUUUUUAUCCCCCUGU	chr9:35100605-35100806(-)$1	201	51	75	21.4604
GAUGGGUAAGUAUGCUAAAUCCAU	chr9:114153988-114154189(-)$1	201	149	173	22.4027
GUCAUAUCCACUUCUUCCACAAUG	chr9:103339056-103339257(+)$1	201	126	150	21.5707
UGGCCACUUCUCACUUCUUGGCCA	chr14:68244339-68244540(-)$1	201	161	185	23.7581
AGGUUCCCCUUGCUCACCUGAGCU	chr9:35076385-35076586(-)$1	201	161	185	23.5649
GCGAGCAGCCCGGGAAAAGCAGCU	chr2:62067001-62067202(-)$1	201	65	89	23.0418
CUGUCUACUAACCGGCUUCCCGAC	chr19:50192481-50192682(+)$1	201	162	186	21.5707
GGUGAGACUCCUCAAGCCUccuca	chr19:49464018-49464219(+)$1	201	152	176	22.6160
CAACUAAAAAUAUCUGGGUUAGUG	chr15:59189259-59189460(-)$1	201	64	88	22.0434
AGUCUCUGUUGUCUCAUUguguug	chr22:46689095-46689296(+)$1	201	134	158	22.0890
CUCUGAUUUCCUUUUUCACUCAGA	chr7:139137507-139137708(+)$1	201	60	84	22.1484
GAUUGACUUACAAACUCUUCUUAA	chr1:235273923-235274124(-)$1	201	81	105	22.6160
CCGAGUCUACCUAGCUUUCUUGGA	chr17:60021973-60022174(-)$1	201	3	27	21.3251
GUCUUCUCUCCUACUUCCAUGAAG	chr16:89805640-89805841(-)$1	201	143	167	21.7812
UCUUCACCCCAAACUUCCCUGAAU	chr13:111945371-111945572(+)$1	201	19	43	23.1224
CUGGGGACUAGCAACACAUCCUUC	chr14:89087501-89087702(-)$1	201	158	182	22.1301
AGUUCUUUCAAAAAACUUAGAUUG	chr3:183900705-183900906(+)$1	201	171	195	23.1047
CAAGCAUCAUGCCAUCUCUGCUAA	chr5:179135218-179135419(+)$1	201	94	118	23.2942
CAUACACCAGCAUCUUUCUGUACC	chr19:35988156-35988357(-)$1	201	107	131	21.2484
AUACAGACUAAAAAAACCUGUGUA	chr1:27055973-27056174(+)$1	201	75	99	21.3830
ACUGAGAUCUUUGACUACCUCAGC	chr16:30094687-30094888(+)$1	201	153	177	23.2339
AGCCUCUUACUUACUAUGACAUGA	chr7:116770492-116770693(+)$1	201	75	99	20.9226
AACGACUUGAAAAGGAGCGUCGAG	chr11:110108240-110108441(-)$1	201	133	157	23.1634
CGAAAGAAUAUGAUCAACUCCUGA	chr7:107253709-107253910(+)$1	201	124	148	21.2049
GUACUAAGAUCUUAAAAAGUGGUA	chr3:3190120-3190321(+)$1	201	23	47	22.9149
ACCUCAUUCCCUGCGUCUUGAGCC	chr16:2499772-2499973(+)$1	201	107	131	23.0730
GGCAACGACCCUAAACAUGUUACC	chr3:9489994-9490195(+)$1	201	169	193	23.5270
CCCCCACCCCCUCCCCCACUGAUG	chr17:78519390-78519591(+)$1	201	18	42	22.9875
GCAGUAGACCAGGUAAGAAUAGUC	chr12:50394879-50395080(-)$1	201	114	138	22.8884
CCAUUAAUUUUAAUACAUUUGUUG	chr17:57109213-57109414(-)$1	201	55	79	22.3491
GUGAAAUGUCCAGCUUUCUUCACA	chr6:33589239-33589440(+)$1	201	144	168	22.4815
GUUCCCUGACCAGCUAUUGGGAGA	chr1:44436242-44436443(+)$1	201	36	60	22.3137
GAUCCAGCCAUACUUCAAUGGAUC	chr10:103347080-103347281(-)$1	201	147	171	21.2773
ACAGCCACAGCACCCCCAGGCCAA	chr12:122693085-122693286(-)$1	201	75	99	24.1827
CGUCCAGGAAAUGAAGAGCGAGAA	chr9:128099724-128099925(+)$1	201	29	53	21.6295
CUAAAGUUUUUUUUUUUUUUUUUU	chrX:70794448-70794649(+)$1	201	149	173	22.0575
CUAGGACAAGACAUGUAUCCUUGC	chr19:17328182-17328383(+)$1	201	130	154	21.3133
UUAUAGAACAUUUAUUUCAUAACU	chr19:44341435-44341636(+)$1	201	156	180	21.6263
CUGAUAAAUCUAAUAACUCUACAG	chr6:71235477-71235678(+)$1	201	170	194	22.7684
GGCAAUAUCUACAUAUUUGAUUGU	chr5:180222620-180222821(-)$1	201	84	108	22.6695
UUGGUCUACAAGAUUCAGAUGAUG	chr5:134147338-134147539(+)$1	201	156	180	22.3576
CUGAAACCUCACAAGUCCUCUCAG	chr8:145748951-145749152(+)$1	201	175	199	20.6640
gccGUGUUUUUUAUUUUUUACAGU	chr7:129668735-129668936(-)$1	201	5	29	23.8966
UAUCUUCCUUUCCAAAUCCAAAAA	chr9:108337180-108337381(+)$1	201	55	79	21.8757
ACUACAGCCUCCAGCAUCACAGUG	chr17:49269980-49270181(-)$1	201	16	40	21.1288
GGAAAUCAGAGAACGAAAGAAAAC	chr14:73572848-73573049(+)$1	201	69	93	21.8577
CCAGGAAAAAAAGGAGGAAAUCCU	chr1:233388352-233388553(-)$1	201	29	53	21.7082
UCAGUGUGuuuacuuuauuuuauu	chr19:4174076-4174277(-)$1	201	174	198	22.6160
GAUGACAAAAAAAUUGGAAGUUGU	chr14:78186877-78187078(-)$1	201	126	150	23.2015
GCCUUUAUGAAACAUAGUUAAAGG	chrX:102931929-102932130(-)$1	201	84	108	22.4027
CUGGAAGAAUAUUUCUGGUUCCAU	chr2:148653890-148654091(+)$1	201	112	136	23.0370
GUUCUGGAACUAAAUGAACAGAAC	chr17:56423412-56423613(-)$1	201	64	88	22.8313
CUCCCCUAUGAACAUUGUGGGGAG	chr1:21071058-21071259(-)$1	201	73	97	23.6418
CAGGCCAAGGUGAGAAAGGGGACU	chr16:75663280-75663481(-)$1	201	160	184	22.3936
ugcuaauuuuuuguauuuuuagua	chr19:36593299-36593500(+)$1	201	24	48	23.7581
GCCCAGCAUUGUAUUUCCCUGUGA	chr15:42118212-42118413(+)$1	201	63	87	23.9859

#DB
((((((...........)).))))	chr14:75295855-75296056(+)$1	1	82	106	21.5467
..(((.............)))...	chr13:96295242-96295443(-)$1	1	143	167	23.1035
(..((((...........))))..	chr12:27467351-27467552(+)$1	1	48	72	21.6699
((((((.............)))))	chr14:68123117-68123318(-)$1	1	142	166	22.6695
.((((((...........))))))	chr16:71766502-71766703(-)$1	1	87	111	20.6905
((((((............))))))	chr16:89711840-89712041(-)$1	1	51	75	23.6418
.((((((...........))))))	chr8:144678729-144678930(-)$1	1	1	25	20.6905
(..(((..............))).	chr12:124107192-124107393(-)$1	1	165	189	22.4933
.(.(((.............))).)	chr19:48984182-48984383(+)$1	1	134	158	23.6234
((((((............))))))	chr2:61715225-61715426(-)$1	1	134	158	22.8313
((((.(................).	chr9:35100605-35100806(-)$1	1	51	75	21.4604
(((((((...........))))))	chr9:114153988-114154189(-)$1	1	149	173	22.4027
(((((................)))	chr9:103339056-103339257(+)$1	1	126	150	21.5707
((((((............))))))	chr14:68244339-68244540(-)$1	1	161	185	23.7581
((((((.............)))))	chr9:35076385-35076586(-)$1	1	161	185	23.5649
((..((............)).)))	chr2:62067001-62067202(-)$1	1	65	89	23.0418
(((((................)))	chr19:50192481-50192682(+)$1	1	162	186	21.5707
((((((..............))))	chr19:49464018-49464219(+)$1	1	152	176	22.6160
(.(((((...........))))).	chr15:59189259-59189460(-)$1	1	64	88	22.0434
(((..(..............)..)	chr22:46689095-46689296(+)$1	1	134	158	22.0890
.(((((.............)))))	chr7:139137507-139137708(+)$1	1	60	84	22.1484
((((((..............))))	chr1:235273923-235274124(-)$1	1	81	105	22.6160
(((((.............)))))(	chr17:60021973-60022174(-)$1	1	3	27	21.3251
((((((..............))))	chr16:89805640-89805841(-)$1	1	143	167	21.7812
..((((.............)))).	chr13:111945371-111945572(+)$1	1	19	43	23.1224
(((((((...........)))..)	chr14:89087501-89087702(-)$1	1	158	182	22.1301
(((.((............))))))	chr3:183900705-183900906(+)$1	1	171	195	23.1047
..((((............))))..	chr5:179135218-179135419(+)$1	1	94	118	23.2942
..((((............))))..	chr19:35988156-35988357(-)$1	1	107	131	21.2484
((((((...........))))))(	chr1:27055973-27056174(+)$1	1	75	99	21.3830
((((((............))))).	chr16:30094687-30094888(+)$1	1	153	177	23.2339
((..((................))	chr7:116770492-116770693(+)$1	1	75	99	20.9226
..((((............))))..	chr11:110108240-110108441(-)$1	1	133	157	23.1634
((..((...........))..)))	chr7:107253709-107253910(+)$1	1	124	148	21.2049
((((((.............)))).	chr3:3190120-3190321(+)$1	1	23	47	22.9149
..((((............)))).)	chr16:2499772-2499973(+)$1	1	107	131	23.0730
((.(((............))).))	chr3:9489994-9490195(+)$1	1	169	193	23.5270
((..((.............))..)	chr17:78519390-78519591(+)$1	1	18	42	22.9875
(.(.((.............)).))	chr12:50394879-50395080(-)$1	1	114	138	22.8884
(((.(((...........))).))	chr17:57109213-57109414(-)$1	1	55	79	22.3491
(((((.............))))).	chr6:33589239-33589440(+)$1	1	144	168	22.4815
)(((((............))))).	chr1:44436242-44436443(+)$1	1	36	60	22.3137
((((((............))))))	chr10:103347080-103347281(-)$1	1	147	171	21.2773
...(((............)))...	chr12:122693085-122693286(-)$1	1	75	99	24.1827
.(((..(...........)..).)	chr9:128099724-128099925(+)$1	1	29	53	21.6295
..((((...........))))...	chrX:70794448-70794649(+)$1	1	149	173	22.0575
..((((...........)))).))	chr19:17328182-17328383(+)$1	1	130	154	21.3133
.(((((................))	chr19:44341435-44341636(+)$1	1	156	180	21.6263
((..((.............))..)	chr6:71235477-71235678(+)$1	1	170	194	22.7684
((((((.............)))))	chr5:180222620-180222821(-)$1	1	84	108	22.6695
((.(((..............))).	chr5:134147338-134147539(+)$1	1	156	180	22.3576
((((................))))	chr8:145748951-145749152(+)$1	1	175	199	20.6640
((.(((............))).))	chr7:129668735-129668936(-)$1	1	5	29	23.8966
((((((................))	chr9:108337180-108337381(+)$1	1	55	79	21.8757
((((((................))	chr17:49269980-49270181(-)$1	1	16	40	21.1288
((...((...........))...)	chr14:73572848-73573049(+)$1	1	69	93	21.8577
(.((((..............))))	chr1:233388352-233388553(-)$1	1	29	53	21.7082
((((((..............))))	chr19:4174076-4174277(-)$1	1	174	198	22.6160
.(((((.............)))))	chr14:78186877-78187078(-)$1	1	126	150	23.2015
(((((((...........))))))	chrX:102931929-102932130(-)$1	1	84	108	22.4027
.(((((............))))).	chr2:148653890-148654091(+)$1	1	112	136	23.0370
((((((............))))))	chr17:56423412-56423613(-)$1	1	64	88	22.8313
((((((............))))))	chr1:21071058-21071259(-)$1	1	73	97	23.6418
(((.((.............)).))	chr16:75663280-75663481(-)$1	1	160	184	22.3936
((((((............))))))	chr19:36593299-36593500(+)$1	1	24	48	23.7581
((.(((............))).).	chr15:42118212-42118413(+)$1	1	63	87	23.9859

#PSSM
f : 0.15	g : 0.15	e : 0.13	d : 0.12	! : 0.09	c : 0.07	" : 0.04	: : 0.04	i : 0.04	b : 0.03	h : 0.03	[ : 0.03	# : 0.01	) : 0.01	$ : 0.01	
e : 0.22	f : 0.16	g : 0.15	d : 0.09	! : 0.07	" : 0.04	i : 0.04	[ : 0.04	a : 0.03	c : 0.03	h : 0.03	# : 0.01	) : 0.01	b : 0.01	$ : 0.01	
e : 0.19	d : 0.19	f : 0.15	g : 0.13	! : 0.10	[ : 0.07	i : 0.03	h : 0.03	" : 0.03	c : 0.01	a : 0.01	b : 0.01	
e : 0.18	d : 0.18	c : 0.13	f : 0.13	g : 0.13	! : 0.09	[ : 0.06	i : 0.03	h : 0.01	a : 0.01	" : 0.01	
c : 0.16	e : 0.16	d : 0.15	b : 0.13	g : 0.13	f : 0.12	i : 0.03	! : 0.03	[ : 0.01	h : 0.01	y : 0.01	" : 0.01	
b : 0.15	d : 0.15	c : 0.15	g : 0.13	f : 0.12	e : 0.10	v : 0.04	y : 0.04	i : 0.03	a : 0.03	h : 0.01	! : 0.01	
u : 0.30	v : 0.22	w : 0.12	y : 0.12	t : 0.07	f : 0.03	g : 0.03	c : 0.03	d : 0.01	e : 0.01	a : 0.01	b : 0.01	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	t : 0.22	v : 0.22	w : 0.12	y : 0.12	
u : 0.30	v : 0.22	t : 0.15	w : 0.12	y : 0.12	b : 0.03	d : 0.03	f : 0.01	
v : 0.18	w : 0.12	y : 0.12	c : 0.10	d : 0.10	e : 0.09	b : 0.07	f : 0.07	g : 0.06	i : 0.03	h : 0.01	a : 0.01	
d : 0.13	c : 0.12	w : 0.12	y : 0.12	e : 0.12	f : 0.10	b : 0.10	g : 0.07	i : 0.03	2 : 0.03	] : 0.01	h : 0.01	
d : 0.16	e : 0.15	c : 0.15	f : 0.12	g : 0.12	y : 0.10	b : 0.06	i : 0.03	2 : 0.03	] : 0.01	a : 0.01	h : 0.01	3 : 0.01	
e : 0.18	d : 0.13	f : 0.13	g : 0.12	] : 0.10	y : 0.07	3 : 0.06	c : 0.06	2 : 0.06	i : 0.03	h : 0.01	a : 0.01	
e : 0.19	f : 0.13	g : 0.13	d : 0.10	2 : 0.09	c : 0.09	3 : 0.07	] : 0.04	a : 0.04	i : 0.03	0 : 0.01	b : 0.01	h : 0.01	
g : 0.15	e : 0.13	f : 0.13	] : 0.10	d : 0.09	c : 0.07	3 : 0.06	2 : 0.06	i : 0.04	b : 0.04	a : 0.01	E : 0.01	0 : 0.01	: : 0.01	h : 0.01	6 : 0.01	

#score	1479.1757911343839
#seq	66
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_UTR_m3_run1.txt

#BEAR
ggggg$$$$$cccmmmmccc]gggggggBB	chr17:6023844-6024076(+)$1	232	84	114	12.0060
cc!!ccc!!ddddmmmmdddd]ccc333cc	chr16:11935509-11935740(-)$1	231	77	107	12.3965
b[eeeee!!ddddmmmmdddd]eeeee]bb	chr6:170886618-170886838(-)$1	220	113	143	11.0794
c!!dddd"""cccmmmmccc666666dddd	chr17:4789342-4789558(+)$1	216	122	152	11.3954
##ccc$$$$$cccmmmmccc4444cccddd	chr17:7839956-7840185(+)$1	229	22	52	13.4378
gggbb[ddddcccmmmmccc333dddd]bb	chr11:68196992-68197224(+)$1	232	179	209	12.9254
ee[ccc!!a[cccmmmmccca]ccceeeee	chr10:1176884-1177104(+)$1	220	175	205	14.0098
==!!a!!abbcccmmmmccc]bb]a22a22	chr15:28356776-28356986(-)$1	210	120	150	12.1560
ee[ccc####ccclllccc4444ccc]eee	chr19:41306614-41306849(+)$1	235	80	110	12.0857
!!ccc####ddddmmmmdddd]ccc22ccc	chrX:54095592-54095807(-)$1	215	147	177	11.5753
eeeffffff[cccmmmmccc]ffffff22e	chr17:36827962-36828183(-)$1	221	142	172	12.6406
ff[a[bb!!ddddmmmmdddd]bbafffff	chr3:141713763-141713982(-)$1	219	84	114	11.0412
(ffffff!!cccnnnnnccc333ffffffi	chr7:128587887-128588105(+)$1	218	80	110	10.1660
ffff[bb[a[cccmmmmccc]a]bbfffff	chr6:42985157-42985388(+)$1	231	10	40	13.1950
$dddd!!bb[cccmmmmccc]bb22dddd4	chr3:38532518-38532738(+)$1	220	38	68	11.3377
bb[dddd"""cccmmmmccc333dddd]bb	chr17:76221137-76221363(+)$1	226	61	91	14.4478
ffff[dddd[cccmmmmcccdddd]fffff	chr17:40731865-40732087(-)$1	222	82	112	12.4726
#bb[iiiiiiiiimmmmiiiiiiiii]bbe	chr6:33740403-33740645(-)$1	242	8	38	10.6395
b[ffffff[ddddmmmmdddd]ffffff]b	chr17:43184045-43184266(+)$1	221	185	215	11.2304
b:ggggggg[cccmmmmccc]ggggggg::	chr22:41575156-41575381(+)$1	225	127	157	11.3718
ggg"""gggggggmmmmggggggg333ggg	chr19:19101795-19102026(-)$1	231	142	172	11.3427
ee:ccc[ccc[ccclllccc333ccc]ccc	chr12:6640649-6640859(+)$1	210	105	135	10.6448
bffffff!!ddddmmmmdddd]ffffff]b	chr4:140432300-140432518(-)$1	218	83	113	11.5448
""ffffff!!cccmmmmccc22ffffff22	chr5:118824815-118825041(+)$1	226	63	93	13.7752
cc[dddd[a[cccmmmmccc]adddd]ccc	chr12:117582095-117582310(-)$1	215	176	206	13.7457
gggg[a[bb[cccmmmmcccbb]agggggg	chr17:64738737-64738961(+)$1	224	92	122	12.6460
ffffffddddcccmmmmccc]ddddbb[cc	chr12:50393305-50393592(-)$1	287	106	136	11.5278
cc!!dddd!!cccmmmmcccdddd22ccc3	chr7:99228542-99228766(+)$1	224	82	112	12.9591
b[eeeee!!acccmmmmccc22a22eeeee	chr6:107387782-107388009(-)$1	227	77	107	13.2616
gg[bb[a"""cccmmmmccc]abb]ggggg	chr19:50302576-50302814(+)$1	238	96	126	14.2276
ddd[dddd"""ccclllccc333dddd]dd	chr1:161011880-161012101(-)$1	221	3	33	11.2121
ee[a[bb"""cccmmmmccc]bb]a]eeee	chr8:105601008-105601227(-)$1	219	88	118	13.5019
c[ccc[bb"""bbmmmmbb333bb]ccc]c	chr5:157214732-157214965(-)$1	233	115	145	12.1117
bb!!dddd"""ccclllccc333dddd22b	chr17:65722591-65722849(+)$1	258	119	149	11.6109
ffff:ccc!!cccmmmmccc333ccciiii	chr12:133298532-133298751(+)$1	219	171	201	14.0817
::ggggggg[cccmmmmccc]gggggggbb	chr10:11299698-11299920(+)$1	222	50	80	12.0699
eee[ccc"""cccmmmmcccccc]eeeee3	chr5:14694362-14694607(+)$1	245	89	119	13.8397
C============mmmm============:	chr1:67875212-67875435(-)$1	223	53	83	10.7119
Cffffff[ccc[ammmmaccc22ffffffd	chr17:18149008-18149254(-)$1	246	86	116	11.0488
bb[eeeee"""bbmmmmbb4444eeeee]b	chr13:77791885-77792109(-)$1	224	16	46	11.8798
hhhh[a[ccccccmmmmccc]ccc]ahhhh	chr15:40913792-40914017(+)$1	225	82	112	11.9315
ccc[eeeee!!bbmmmmbb22eeeee]ccc	chr12:49229822-49230055(-)$1	233	129	159	10.4296
b[bb!!bb!!cccmmmmccc333bb333bb	chr15:42706716-42706958(-)$1	242	45	75	13.9074
ff[eeeee!!cccmmmmccc333eeeeeff	chrX:153588790-153589000(-)$1	210	129	159	14.5610
e[ffffff[ddddmmmmdddd333ffffff	chr10:119134667-119134890(-)$1	223	146	176	11.6942
dd[ffffff[cccmmmmcccffffff]ddd	chr1:26227133-26227358(-)$1	225	177	207	12.2368
ee!!eeeee[cccmmmmccc]eeeee22ee	chr12:112946025-112946237(+)$1	212	29	59	12.7032
c]ggggggg:cccmmmmccceeeee[ccc[	chr19:35770383-35770629(+)$1	246	141	171	11.0471
fff!!dddd[cccmmmmccc]ddddfffff	chr6:42988816-42989047(+)$1	231	153	183	12.8973
####dddd"""ccclllccc22dddd4444	chr13:20356804-20357030(-)$1	226	133	163	11.0359
ggccc[ccc[cccmmmmcccccc]ccc22g	chr17:43112136-43112365(-)$1	229	190	220	13.2238
!!ffffff!!cccmmmmccc333ffffff2	chr18:56063521-56063731(+)$1	210	36	66	14.7812
:bbccc[ccccccmmmmccc]ccc]ccc]b	chr22:24812970-24813187(+)$1	217	160	190	12.3083
==========[bbmmmmbb]==========	chr9:134372659-134372881(+)$1	222	105	135	11.6411
"""bbccc[ddddmmmmddddccc]bb333	chr1:19444258-19444501(-)$1	243	207	237	10.6026
eeeee[ccc[cccmmmmcccccceeeeedd	chr19:49654067-49654294(+)$1	227	119	149	12.6531

#otherMatches

#Seq PSSM
CCCUGCGUGACCACAACUGGACGGGGCUGC	chr17:6023844-6024076(+)$1	232	84	114	12.0060
GAAACUCCUGUUUGUGAAAACUGAGAAAUC	chr16:11935509-11935740(-)$1	231	77	107	12.3965
CUGUGCUGAGAGCUGCAGCUUGGGUACUGG	chr6:170886618-170886838(-)$1	220	113	143	11.0794
CCUCCGCCCAGGCUCAAGUCCAAGAAGUGG	chr17:4789342-4789558(+)$1	216	122	152	11.3954
AAAGUUAUUUUGAAAUUUCAUCUUACUUGC	chr17:7839956-7840185(+)$1	229	22	52	13.4378
GGUGUGACCUAGGUGCUCCUUUGGGGUGAU	chr11:68196992-68197224(+)$1	232	179	209	12.9254
GCUGUCCUGAGCGAACUUGCCUGAUGCAGG	chr10:1176884-1177104(+)$1	220	175	205	14.0098
GCAGAGCGCUCGCUGCUGUGUAGACUGUAG	chr15:28356776-28356986(-)$1	210	120	150	12.1560
CCAGCCCUCUUCGGGACGGUUUUGGCGGGC	chr19:41306614-41306849(+)$1	235	80	110	12.0857
UGGCUUAUUGCAGUAGUCUGCUGGUGCAGG	chrX:54095592-54095807(-)$1	215	147	177	11.5753
CUUUGUAAAAAGUUGUUAUUGUUUGCAUAG	chr17:36827962-36828183(-)$1	221	142	172	12.6406
AGACACACAUAGCAGAAGCUACUGGCUGGG	chr3:141713763-141713982(-)$1	219	84	114	11.0412
AAGCAGCGCUUCUACACGAACCAGCUGCUG	chr7:128587887-128588105(+)$1	218	80	110	10.1660
ACCAAGGGGAUUGGGGACAAACAUCUGGUU	chr6:42985157-42985388(+)$1	231	10	40	13.1950
ACCCACUAUCCACCAUAGUGCAUUUUGGGA	chr3:38532518-38532738(+)$1	220	38	68	11.3377
AGCUGGAAAAAAAUGGUUUUGUCUUCAACU	chr17:76221137-76221363(+)$1	226	61	91	14.4478
AACACCCCUGUACUUGGGUGAGGGAUGUUG	chr17:40731865-40732087(-)$1	222	82	112	12.4726
AUGUGUGCCCUUUGUAGGAGGGGCAUCCAC	chr6:33740403-33740645(-)$1	242	8	38	10.6395
UUGUGGUAGUGAUGGUUGUCAGUGCUGCCA	chr17:43184045-43184266(+)$1	221	185	215	11.2304
Guuuuauuauuuuuuuuaaauuaaugaaca	chr22:41575156-41575381(+)$1	225	127	157	11.3718
UGGCUUGUUUCCAUCACUGGAAAUCACUUA	chr19:19101795-19102026(-)$1	231	142	172	11.3427
ugagguagggaguucgagaccagccugacc	chr12:6640649-6640859(+)$1	210	105	135	10.6448
AGUGCAAAUUGUGUUAGCACACUUGCAUAU	chr4:140432300-140432518(-)$1	218	83	113	11.5448
UAUUUCAGAUCUUGUGGAAGCCCUGAAGCC	chr5:118824815-118825041(+)$1	226	63	93	13.7752
UCACAGCACCUGGCCCGCCAAGGUUGGGAG	chr12:117582095-117582310(-)$1	215	176	206	13.7457
AGUCACGACCAGGACCUUCUGUGGGACUCC	chr17:64738737-64738961(+)$1	224	92	122	12.6460
GUGACUGUUCCCAAUGAUGGCGGGCCCAUC	chr12:50393305-50393592(-)$1	287	106	136	11.5278
aggcccuguaacaaacaugucaggaacucu	chr7:99228542-99228766(+)$1	224	82	112	12.9591
CUCCCCCUUCCCACCGCUGGUUGUUGGGGG	chr6:107387782-107388009(-)$1	227	77	107	13.2616
GCAUGUGCACGCUGGCCAGCUCCGAGUUCU	chr19:50302576-50302814(+)$1	238	96	126	14.2276
UCCAAGGGAAGCUUUAUGAGGGGCCCUAGG	chr1:161011880-161012101(-)$1	221	3	33	11.2121
CAUCUGCUGUGGUUAUGGCCUGUCGCUGGA	chr8:105601008-105601227(-)$1	219	88	118	13.5019
UGGGAAUGGCCCCUCUUGGAAAUACUCCGA	chr5:157214732-157214965(-)$1	233	115	145	12.1117
CCCUGGAUCAGGAUCACGUCGCAGUCCUAG	chr17:65722591-65722849(+)$1	258	119	149	11.6109
GCUGAGGUGACACGCUAGUGACAGCCCAAU	chr12:133298532-133298751(+)$1	219	171	201	14.0817
AUGAGAACGACAUCAGGGUGAUGUUCUCUC	chr10:11299698-11299920(+)$1	222	50	80	12.0699
AUGGCCUGAAUUGUCCUCAAGGGGUGUGGA	chr5:14694362-14694607(+)$1	245	89	119	13.8397
UUGACUUUUAAGUUCAAAUUUGGAGGUUAU	chr1:67875212-67875435(-)$1	223	53	83	10.7119
GCAGGUUAUCAACGAAGGUGAGGAGCCUGA	chr17:18149008-18149254(-)$1	246	86	116	11.0488
GGGGAUGUCCCACUCUUGUUCAAGCAUUGC	chr13:77791885-77792109(-)$1	224	16	46	11.8798
UCUCACAGAGAAAACUAUUUAUUCCGGAGA	chr15:40913792-40914017(+)$1	225	82	112	11.9315
ACCACACUUCCCAAAAUUGACAGGUGAGGU	chr12:49229822-49230055(-)$1	233	129	159	10.4296
CCCUGCCUGACGAUGUAUCGAAAAGAUGAG	chr15:42706716-42706958(-)$1	242	45	75	13.9074
GGUGGCCUGGGCCUGACGGUGGAGGGCCCC	chrX:153588790-153589000(-)$1	210	129	159	14.5610
ggcgggAUGGGGCUGCUGCUCAUGAUCCUG	chr10:119134667-119134890(-)$1	223	146	176	11.6942
AUGUAGUGGCUUCUUUUGAACUGUUAGAUG	chr1:26227133-26227358(-)$1	225	177	207	12.2368
UGUAAACUUAGGCCAAGGCCAGAGUUAUCA	chr12:112946025-112946237(+)$1	212	29	59	12.7032
GAGCCUUUGGGGGGCCACCCGGGGCCUGGA	chr19:35770383-35770629(+)$1	246	141	171	11.0471
CUGUCGCUGUACUCUGAAGUUCAGCCAGCU	chr6:42988816-42989047(+)$1	231	153	183	12.8973
AUGAUGUUAAGAGGAAACCUGAAGCAAGUG	chr13:20356804-20357030(-)$1	226	133	163	11.0359
GCGGUGAUUGACGUGGACGUGAUGGCCCGG	chr17:43112136-43112365(-)$1	229	190	220	13.2238
AUUUGCCUAACAGACUUUUGCAGAGGCGAU	chr18:56063521-56063731(+)$1	210	36	66	14.7812
CUCUCGAUCCCAGGCUUCUGCGGACCGACG	chr22:24812970-24813187(+)$1	217	160	190	12.3083
GGGGACAGUUCAGGUUUCUCAGCUGUUCUU	chr9:134372659-134372881(+)$1	222	105	135	11.6411
CAGUCCUGAGGCCAAUAGGUCCAGUGGGAU	chr1:19444258-19444501(-)$1	243	207	237	10.6026
GGGGGACGGUGGGGGAGCCCUCGCCCCCGA	chr19:49654067-49654294(+)$1	227	119	149	12.6531

#DB
(((((.....(((....))).)))))))))	chr17:6023844-6024076(+)$1	1	84	114	12.0060
((..(((..((((....)))).)))...))	chr16:11935509-11935740(-)$1	1	77	107	12.3965
(.(((((..((((....)))).))))).))	chr6:170886618-170886838(-)$1	1	113	143	11.0794
(..((((...(((....)))......))))	chr17:4789342-4789558(+)$1	1	122	152	11.3954
..(((.....(((....)))....))))))	chr17:7839956-7840185(+)$1	1	22	52	13.4378
)))((.(((((((....)))...)))).))	chr11:68196992-68197224(+)$1	1	179	209	12.9254
((.(((..(.(((....)))).))))))))	chr10:1176884-1177104(+)$1	1	175	205	14.0098
((..(..((((((....))).)).)..)..	chr15:28356776-28356986(-)$1	1	120	150	12.1560
((.(((....(((...)))....))).)))	chr19:41306614-41306849(+)$1	1	80	110	12.0857
..(((....((((....)))).)))..)))	chrX:54095592-54095807(-)$1	1	147	177	11.5753
(((((((((.(((....))).))))))..)	chr17:36827962-36828183(-)$1	1	142	172	12.6406
((.(.((..((((....)))).))))))))	chr3:141713763-141713982(-)$1	1	84	114	11.0412
.((((((..(((.....)))...)))))))	chr7:128587887-128588105(+)$1	1	80	110	10.1660
((((.((.(.(((....))).).)))))))	chr6:42985157-42985388(+)$1	1	10	40	13.1950
.((((..((.(((....))).))..)))).	chr3:38532518-38532738(+)$1	1	38	68	11.3377
((.((((...(((....)))...)))).))	chr17:76221137-76221363(+)$1	1	61	91	14.4478
((((.((((.(((....))))))).)))))	chr17:40731865-40732087(-)$1	1	82	112	12.4726
.((.(((((((((....))))))))).)))	chr6:33740403-33740645(-)$1	1	8	38	10.6395
(.((((((.((((....)))).)))))).)	chr17:43184045-43184266(+)$1	1	185	215	11.2304
).(((((((.(((....))).)))))))..	chr22:41575156-41575381(+)$1	1	127	157	11.3718
(((...(((((((....)))))))...)))	chr19:19101795-19102026(-)$1	1	142	172	11.3427
)).(((.(((.(((...)))...))).)))	chr12:6640649-6640859(+)$1	1	105	135	10.6448
(((((((..((((....)))).)))))).)	chr4:140432300-140432518(-)$1	1	83	113	11.5448
..((((((..(((....)))..))))))..	chr5:118824815-118825041(+)$1	1	63	93	13.7752
((.((((.(.(((....))).))))).)))	chr12:117582095-117582310(-)$1	1	176	206	13.7457
((((.(.((.(((....))))).)))))))	chr17:64738737-64738961(+)$1	1	92	122	12.6460
))))))(((((((....))).))))((.((	chr12:50393305-50393592(-)$1	1	106	136	11.5278
((..((((..(((....)))))))..))).	chr7:99228542-99228766(+)$1	1	82	112	12.9591
(.(((((..((((....)))..)..)))))	chr6:107387782-107388009(-)$1	1	77	107	13.2616
((.((.(...(((....))).))).)))))	chr19:50302576-50302814(+)$1	1	96	126	14.2276
(((.((((...(((...)))...)))).))	chr1:161011880-161012101(-)$1	1	3	33	11.2121
((.(.((...(((....))).)).).))))	chr8:105601008-105601227(-)$1	1	88	118	13.5019
(.(((.((...((....))...)).))).)	chr5:157214732-157214965(-)$1	1	115	145	12.1117
((..((((...(((...)))...))))..)	chr17:65722591-65722849(+)$1	1	119	149	11.6109
)))).(((..(((....)))...)))((((	chr12:133298532-133298751(+)$1	1	171	201	14.0817
..(((((((.(((....))).)))))))((	chr10:11299698-11299920(+)$1	1	50	80	12.0699
(((.(((...(((....)))))).))))).	chr5:14694362-14694607(+)$1	1	89	119	13.8397
(((((((((((((....)))))))))))).	chr1:67875212-67875435(-)$1	1	53	83	10.7119
(((((((.(((.(....))))..))))))(	chr17:18149008-18149254(-)$1	1	86	116	11.0488
((.(((((...((....))....))))).)	chr13:77791885-77792109(-)$1	1	16	46	11.8798
((((.(.((((((....))).))).)))))	chr15:40913792-40914017(+)$1	1	82	112	11.9315
(((.(((((..((....))..))))).)))	chr12:49229822-49230055(-)$1	1	129	159	10.4296
(.((..((..(((....)))...))...))	chr15:42706716-42706958(-)$1	1	45	75	13.9074
((.(((((..(((....)))...)))))))	chrX:153588790-153589000(-)$1	1	129	159	14.5610
(.((((((.((((....))))...))))))	chr10:119134667-119134890(-)$1	1	146	176	11.6942
((.((((((.(((....))))))))).)))	chr1:26227133-26227358(-)$1	1	177	207	12.2368
((..(((((.(((....))).)))))..))	chr12:112946025-112946237(+)$1	1	29	59	12.7032
).))))))).(((....)))(((((.(((.	chr19:35770383-35770629(+)$1	1	141	171	11.0471
(((..((((.(((....))).)))))))))	chr6:42988816-42989047(+)$1	1	153	183	12.8973
....((((...(((...)))..))))....	chr13:20356804-20357030(-)$1	1	133	163	11.0359
(((((.(((.(((....)))))).)))..)	chr17:43112136-43112365(-)$1	1	190	220	13.2238
..((((((..(((....)))...)))))).	chr18:56063521-56063731(+)$1	1	36	66	14.7812
.(((((.((((((....))).))).))).)	chr22:24812970-24813187(+)$1	1	160	190	12.3083
((((((((((.((....)).))))))))))	chr9:134372659-134372881(+)$1	1	105	135	11.6411
...(((((.((((....))))))).))...	chr1:19444258-19444501(-)$1	1	207	237	10.6026
(((((.(((.(((....)))))))))))((	chr19:49654067-49654294(+)$1	1	119	149	12.6531

#PSSM
b : 0.16	e : 0.16	c : 0.12	f : 0.12	g : 0.10	# : 0.05	= : 0.03	! : 0.03	" : 0.03	d : 0.03	: : 0.03	C : 0.03	( : 0.01	$ : 0.01	h : 0.01	
f : 0.17	e : 0.14	g : 0.10	[ : 0.10	b : 0.08	c : 0.07	! : 0.05	= : 0.05	d : 0.05	# : 0.03	: : 0.03	" : 0.03	h : 0.01	] : 0.01	
f : 0.21	[ : 0.17	g : 0.12	! : 0.10	e : 0.08	c : 0.08	b : 0.05	d : 0.03	= : 0.03	: : 0.01	h : 0.01	# : 0.01	" : 0.01	
f : 0.23	c : 0.14	! : 0.10	g : 0.08	e : 0.08	d : 0.07	b : 0.07	[ : 0.07	a : 0.03	= : 0.03	" : 0.01	h : 0.01	# : 0.01	
c : 0.17	f : 0.17	d : 0.14	e : 0.12	[ : 0.10	g : 0.07	b : 0.05	= : 0.03	! : 0.03	a : 0.01	i : 0.01	" : 0.01	: : 0.01	
f : 0.17	d : 0.16	c : 0.14	e : 0.10	[ : 0.08	! : 0.05	b : 0.05	g : 0.05	$ : 0.03	a : 0.03	= : 0.03	# : 0.01	i : 0.01	" : 0.01	
d : 0.19	f : 0.16	c : 0.10	e : 0.10	b : 0.08	g : 0.07	[ : 0.07	! : 0.05	$ : 0.03	# : 0.03	= : 0.03	i : 0.01	a : 0.01	
d : 0.14	! : 0.12	c : 0.12	f : 0.10	" : 0.08	b : 0.07	g : 0.07	e : 0.07	[ : 0.05	$ : 0.03	# : 0.03	= : 0.03	a : 0.01	i : 0.01	
! : 0.21	" : 0.17	c : 0.10	d : 0.07	g : 0.07	a : 0.05	b : 0.05	[ : 0.05	$ : 0.03	# : 0.03	f : 0.03	= : 0.03	e : 0.03	i : 0.01	
[ : 0.24	d : 0.17	" : 0.17	! : 0.12	c : 0.08	$ : 0.03	= : 0.03	b : 0.01	# : 0.01	i : 0.01	g : 0.01	a : 0.01	: : 0.01	
c : 0.66	d : 0.14	" : 0.08	[ : 0.03	i : 0.01	g : 0.01	= : 0.01	! : 0.01	
c : 0.71	d : 0.14	b : 0.07	i : 0.01	g : 0.01	= : 0.01	[ : 0.01	
c : 0.69	d : 0.14	b : 0.07	n : 0.01	i : 0.01	g : 0.01	= : 0.01	a : 0.01	
m : 0.89	c : 0.07	l : 0.01	n : 0.01	
m : 0.89	l : 0.08	n : 0.01	
m : 0.89	l : 0.08	n : 0.01	
m : 0.89	l : 0.07	c : 0.01	n : 0.01	
c : 0.71	d : 0.14	b : 0.07	i : 0.01	g : 0.01	= : 0.01	a : 0.01	
c : 0.73	d : 0.14	b : 0.07	i : 0.01	g : 0.01	= : 0.01	
c : 0.71	d : 0.14	4 : 0.03	i : 0.01	g : 0.01	3 : 0.01	= : 0.01	2 : 0.01	] : 0.01	
] : 0.26	3 : 0.19	d : 0.17	2 : 0.07	c : 0.07	4 : 0.05	= : 0.03	6 : 0.01	a : 0.01	i : 0.01	g : 0.01	b : 0.01	f : 0.01	e : 0.01	
3 : 0.21	] : 0.12	c : 0.10	g : 0.07	b : 0.07	d : 0.07	2 : 0.07	4 : 0.05	a : 0.05	e : 0.05	f : 0.03	= : 0.03	6 : 0.01	i : 0.01	
3 : 0.19	c : 0.16	b : 0.10	d : 0.10	f : 0.08	g : 0.07	e : 0.07	4 : 0.05	] : 0.03	= : 0.03	6 : 0.01	i : 0.01	a : 0.01	2 : 0.01	
d : 0.17	c : 0.16	f : 0.14	e : 0.12	b : 0.08	g : 0.07	] : 0.07	2 : 0.03	= : 0.03	6 : 0.01	4 : 0.01	i : 0.01	a : 0.01	3 : 0.01	
f : 0.16	c : 0.14	e : 0.14	d : 0.14	] : 0.10	g : 0.07	a : 0.05	2 : 0.05	b : 0.03	= : 0.03	6 : 0.01	i : 0.01	3 : 0.01	
f : 0.23	e : 0.16	c : 0.12	d : 0.12	g : 0.08	3 : 0.05	2 : 0.05	b : 0.03	= : 0.03	6 : 0.01	i : 0.01	] : 0.01	a : 0.01	[ : 0.01	
f : 0.21	e : 0.14	d : 0.10	c : 0.10	] : 0.10	g : 0.08	3 : 0.05	2 : 0.05	b : 0.03	= : 0.03	i : 0.01	h : 0.01	4 : 0.01	
f : 0.19	e : 0.14	c : 0.14	g : 0.10	] : 0.07	d : 0.07	2 : 0.07	3 : 0.05	= : 0.03	a : 0.01	b : 0.01	[ : 0.01	i : 0.01	h : 0.01	4 : 0.01	
f : 0.16	c : 0.14	b : 0.10	d : 0.10	e : 0.10	2 : 0.08	] : 0.08	g : 0.05	= : 0.03	B : 0.01	: : 0.01	i : 0.01	h : 0.01	4 : 0.01	3 : 0.01	
b : 0.17	c : 0.12	e : 0.12	d : 0.10	f : 0.10	g : 0.07	2 : 0.05	3 : 0.05	i : 0.03	4 : 0.03	: : 0.03	B : 0.01	h : 0.01	[ : 0.01	= : 0.01	

#score	687.0104898835104
#seq	56
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_CDS_m1_run2.txt

#BEAR
gggggwwwwwwwwwwwwwwggggg	chr15:29561336-29561563(-)$1	227	2	26	22.2861
ddddyyyyyyyyyyyyyyyydddd	chr3:47957446-47957657(-)$1	211	37	61	19.8680
!fffffftttttttttttffffff	chr16:47462596-47462826(-)$1	230	155	179	22.7028
ffffffwwwwwwwwwwwwwwffff	chr12:57909628-57909852(+)$1	224	160	184	22.0987
ffffffwwwwwwwwwwwwwwffff	chr16:31288221-31288443(-)$1	222	127	151	22.0987
dd[ccctttttttttttccc]ddd	chr1:17355084-17355308(-)$1	224	142	166	22.1683
bb[cccwwwwwwwwwwwwwwccc]	chr4:144468481-144468698(+)$1	217	104	128	21.8805
ff[cccuuuuuuuuuuuucccfff	chr13:21995117-21995335(-)$1	218	35	59	24.0989
h!!ccctttttttttttccc]hhh	chr17:27085375-27085598(-)$1	223	96	120	21.9484
bddddwwwwwwwwwwwwwwdddd:	chr15:69747755-69747975(+)$1	220	192	216	19.9569
eeeeyyyyyyyyyyyyyyyyeeee	chrX:74523172-74523390(+)$1	218	128	152	20.7147
ccccccwwwwwwwwwwwwwwccc]	chr11:95712946-95713175(-)$1	229	159	183	22.1410
:eeeeeuuuuuuuuuuuueeeeeD	chr2:271814-272034(+)$1	220	147	171	21.2234
:eeeeevvvvvvvvvvvvveeeee	chr12:105538422-105538643(+)$1	221	67	91	22.1474
hhhhhhuuuuuuuuuuuuhhhhhh	chr11:118390319-118390542(+)$1	223	53	77	21.1898
"ddddwwwwwwwwwwwwwwdddd6	chr10:28906510-28906732(+)$1	222	61	85	20.7050
iiiiiiitttttttttttiiiiii	chr12:56601937-56602157(-)$1	220	178	202	22.1265
ee[cccuuuuuuuuuuuuccc22e	chr11:763659-763885(+)$1	226	105	129	23.3142
fffcccuuuuuuuuuuuuccc]ff	chr17:61784590-61784812(-)$1	222	14	38	23.9660
bbddddvvvvvvvvvvvvvdddd]	chr8:124042822-124043047(-)$1	225	46	70	21.9535
ffffffuuuuuuuuuuuuffffff	chr12:65133079-65133309(-)$1	230	182	206	23.6605
!!eeeeettttttttttteeeee]	chr7:38816228-38816458(-)$1	230	59	83	22.4953
[ddddwwwwwwwwwwwwwwdddd]	chr1:52246879-52247099(+)$1	220	50	74	21.3611
ggeeeeettttttttttteeeee:	chr12:123805015-123805234(-)$1	219	27	51	21.3493
iiiiiiuuuuuuuuuuuuiiiiii	chrX:107371914-107372138(+)$1	224	4	28	23.5604
cfffffftttttttttttffffff	chr4:78663346-78663570(-)$1	224	94	118	22.5879
###bbvvvvvvvvvvvvvbb22bb	chr17:1268167-1268391(-)$1	224	80	104	21.0855
fffa[bbtttttttttttbb]a]f	chr7:45141851-45142066(-)$1	215	153	177	22.0576
gggggwwwwwwwwwwwwwwggggg	chr11:93471273-93471495(-)$1	222	196	220	22.2861
====wwwwwwwwwwwwww======	chr16:23101994-23102219(-)$1	225	53	77	21.7577
gggggguuuuuuuuuuuugggggg	chr6:90051943-90052169(-)$1	226	37	61	23.7333
!eeeeevvvvvvvvvvvvveeeee	chr16:57241878-57242108(+)$1	230	16	40	23.2049
gggggggtttttttttttgggggg	chr4:122604448-122604665(-)$1	217	152	176	22.4749
ff[ccctttttttttttccc]fff	chr8:94745693-94745911(-)$1	218	12	36	22.8503
[eeeeeuuuuuuuuuuuueeeeed	chr3:179051951-179052172(+)$1	221	132	156	23.3560
eeeeewwwwwwwwwwwwwweeeee	chr19:47503644-47503861(+)$1	217	72	96	21.8527
eee[ccctttttttttttccceee	chr1:154557365-154557585(-)$1	220	66	90	22.7334
======uuuuuuuuuuuu======	chr11:108119590-108119820(+)$1	230	57	81	23.8325
ccc!!bbtttttttttttbb22cc	chr17:61498767-61498991(+)$1	224	79	103	21.5629
eeeeeeettttttttttteeeee2	chr17:10596104-10596323(-)$1	219	35	59	21.9325
###cccuuuuuuuuuuuuccc444	chr1:203768481-203768720(+)$1	239	57	81	23.4360
[fffffftttttttttttffffff	chr3:113442754-113442977(-)$1	223	163	187	22.7072
ffffffwwwwwwwwwwwwwwffff	chr17:56780568-56780790(+)$1	222	21	45	22.0987
$ccc[avvvvvvvvvvvvva]ccc	chr16:24829843-24830120(+)$1	277	135	159	23.2446
ffffffuuuuuuuuuuuuffffff	chr22:29182207-29182436(+)$1	229	205	229	23.6605
[bb[bbuuuuuuuuuuuubbbb]c	chr1:78207272-78207498(-)$1	226	70	94	21.9570
:fffffftttttttttttffffff	chr8:126194351-126194576(+)$1	225	17	41	21.6453
ffffffuuuuuuuuuuuuffffff	chr19:9492131-9492352(+)$1	221	92	116	23.6605
hh"""bbtttttttttttbb22hh	chr10:112058351-112058575(-)$1	224	106	130	20.6074
%fffffftttttttttttffffff	chr14:102552331-102552554(-)$1	223	127	151	22.0000
dd[cccwwwwwwwwwwwwwwccc]	chr10:111637477-111637698(-)$1	221	96	120	22.0575
ceeeeevvvvvvvvvvvvveeeee	chr1:84955279-84955499(+)$1	220	47	71	23.0900
ffffffuuuuuuuuuuuuffffff	chr11:822330-822547(+)$1	217	79	103	23.6605
d[eeeeettttttttttteeeee]	chr1:150116925-150117142(+)$1	217	62	86	22.2754
##bbwwwwwwwwwwwwwwbb333c	chr1:150240403-150240625(-)$1	222	34	58	20.5920
"bbccctttttttttttccc]bb2	chr7:30538426-30538643(-)$1	217	146	170	21.3787
Deeeeeuuuuuuuuuuuueeeee:	chr22:24951647-24951869(-)$1	222	22	46	21.3039
g[dddduuuuuuuuuuuudddd44	chr17:37618406-37618653(+)$1	247	87	111	22.4368
ccc[bbuuuuuuuuuuuubb]ccc	chr2:198338391-198338617(+)$1	226	202	226	23.0640
d!!ccctttttttttttccc]ddd	chr10:22828834-22829083(-)$1	249	136	160	22.2428
ffffyyyyyyyyyyyyyyyyffff	chr10:7840941-7841150(+)$1	209	106	130	21.0029
hhhhhhvvvvvvvvvvvvvhhhhh	chr18:9561942-9562166(-)$1	224	94	118	21.1684
ffffffuuuuuuuuuuuuffffff	chr1:179959620-179959839(+)$1	219	6	30	23.6605
dd[ccctttttttttttccc]ddd	chr3:47770421-47770656(-)$1	235	198	222	22.1683

#otherMatches

#Seq PSSM
GGGGACUACAAGGACAUCUUCCCC	chr15:29561336-29561563(-)$1	227	2	26	22.2861
UGGCCAACAAUGUGACUCCAGCCA	chr3:47957446-47957657(-)$1	211	37	61	19.8680
AGUAUGGGAUUUUAUUUACUGUAC	chr16:47462596-47462826(-)$1	230	155	179	22.7028
GGCUGUGCCCUCGCUCCACAACAG	chr12:57909628-57909852(+)$1	224	160	184	22.0987
UUUUCUCCUUUGAUGUAUAUAGAA	chr16:31288221-31288443(-)$1	222	127	151	22.0987
GACACCAACCUCAAUAAGGUCUCA	chr1:17355084-17355308(-)$1	224	142	166	22.1683
UGGCUCAGAUUGAAAGGGGAGAGG	chr4:144468481-144468698(+)$1	217	104	128	21.8805
AGACCGUUGUUUACCUUGUGGCUU	chr13:21995117-21995335(-)$1	218	35	59	24.0989
GGGCCCACUACCGAGCAGGGACCG	chr17:27085375-27085598(-)$1	223	96	120	21.9484
UUGGCUUUCAGCCUAUUCUGCCAU	chr15:69747755-69747975(+)$1	220	192	216	19.9569
UGUUGCACCUACACAUUUUGGACA	chrX:74523172-74523390(+)$1	218	128	152	20.7147
GAAUGCCAUCAUUAUCUACAGCAG	chr11:95712946-95713175(-)$1	229	159	183	22.1410
AAGAGGCCAACCUGAACUCCUCUG	chr2:271814-272034(+)$1	220	147	171	21.2234
UGGUAGCUUACGUAACUCACUACC	chr12:105538422-105538643(+)$1	221	67	91	22.1474
AGUUGUGUUCCUCAUUGAGCAGCU	chr11:118390319-118390542(+)$1	223	53	77	21.1898
UUCUUUAAUUACAGGCAUCAAGAU	chr10:28906510-28906732(+)$1	222	61	85	20.7050
UCAGCUGAACACAAACACCAGCUG	chr12:56601937-56602157(-)$1	220	178	202	22.1265
AAAUCUACAACUACUACAAGAAGU	chr11:763659-763885(+)$1	226	105	129	23.3142
CACCCUCCCCGCUUCCCCAGGAGU	chr17:61784590-61784812(-)$1	222	14	38	23.9660
CAGGCUUACAGAAACUAACAGCUG	chr8:124042822-124043047(-)$1	225	46	70	21.9535
UGAGAAUAUGUCUUUCCUUUUUCA	chr12:65133079-65133309(-)$1	230	182	206	23.6605
UCCUGUAUCCCUUUUGUUUGCAGU	chr7:38816228-38816458(-)$1	230	59	83	22.4953
AAAAAGCCAUACAAUCCCAUUUUG	chr1:52246879-52247099(+)$1	220	50	74	21.3611
AAACAAAAAUAUUUAAACUUUGUA	chr12:123805015-123805234(-)$1	219	27	51	21.3493
GUUAUUUGAAAUUAAGUUAGUAGC	chrX:107371914-107372138(+)$1	224	4	28	23.5604
UAGAUGAUAACUUUUCUUUCAUCU	chr4:78663346-78663570(-)$1	224	94	118	22.5879
GAGCUGACAGUUGAAGAAAGAAAC	chr17:1268167-1268391(-)$1	224	80	104	21.0855
GGGAAACUGCCUGGUCUUGUCUGC	chr7:45141851-45142066(-)$1	215	153	177	22.0576
UUGGAGAAAAAUUUUAACGUUUGA	chr11:93471273-93471495(-)$1	222	196	220	22.2861
AUUUUGAAGAGAUAAAAUGAGUUG	chr16:23101994-23102219(-)$1	225	53	77	21.7577
GACUCCGAUUUUGAUGGAGGAGUU	chr6:90051943-90052169(-)$1	226	37	61	23.7333
CUCCAGUUUGAAUUCUUAUUUGGA	chr16:57241878-57242108(+)$1	230	16	40	23.2049
AAGGAUGAGUGAAAGGAACAUUCU	chr4:122604448-122604665(-)$1	217	152	176	22.4749
GAUCCAAAAAUAAAUUGUGGUUCA	chr8:94745693-94745911(-)$1	218	12	36	22.8503
AGAUCUUAAAAUUCAUCUAGAUUU	chr3:179051951-179052172(+)$1	221	132	156	23.3560
CAUUGAACUCUUUAUCCAGCAGUG	chr19:47503644-47503861(+)$1	217	72	96	21.8527
GCCACGGAAUGAAUUGUCCCGGGU	chr1:154557365-154557585(-)$1	220	66	90	22.7334
UUUAUUUUACAGGUUUUUAAUGAA	chr11:108119590-108119820(+)$1	230	57	81	23.8325
GUGAGCCCACCCGAUCCAGGACCA	chr17:61498767-61498991(+)$1	224	79	103	21.5629
UCUCCUUAAGAGUUAGAGAAGGAA	chr17:10596104-10596323(-)$1	219	35	59	21.9325
AAAAUGAUCACCAACUUCCAUGGA	chr1:203768481-203768720(+)$1	239	57	81	23.4360
CAAAACUUGGUAUAAUAUAGUUUU	chr3:113442754-113442977(-)$1	223	163	187	22.7072
AUAAUAUUCUUUCUCAUAUUUAUU	chr17:56780568-56780790(+)$1	222	21	45	22.0987
AACUACAACGUUCCCCUCAGCAGU	chr16:24829843-24830120(+)$1	277	135	159	23.2446
CGGGUGUAAUAAUAUCUCCACCUG	chr22:29182207-29182436(+)$1	229	205	229	23.6605
ACCUCAUUUUGAAAGUCUUGGGAA	chr1:78207272-78207498(-)$1	226	70	94	21.9570
AUACCAGAUUUAAAAUUAUUGGUA	chr8:126194351-126194576(+)$1	225	17	41	21.6453
GCACAGGCUCUUACCUUAUUGUGC	chr19:9492131-9492352(+)$1	221	92	116	23.6605
CUCAACCUACUCAUUCAUGGAAAG	chr10:112058351-112058575(-)$1	224	106	130	20.6074
AUCCCAGUAAAUUAGACUCUGGGA	chr14:102552331-102552554(-)$1	223	127	151	22.0000
UGAGCUUCCCAACAAUUUCCAGUA	chr10:111637477-111637698(-)$1	221	96	120	22.0575
UGAAGCUACAGAUGAAUUUGCUUC	chr1:84955279-84955499(+)$1	220	47	71	23.0900
GUGGCAUUUCAGACAACCUGCCAC	chr11:822330-822547(+)$1	217	79	103	23.6605
GGAAGGGCACAGCUUCCUCUCUUG	chr1:150116925-150117142(+)$1	217	62	86	22.2754
UCCCUCCUUGAUUUCUCUGGCUCC	chr1:150240403-150240625(-)$1	222	34	58	20.5920
AGAAGGAAAAGAAAUAACCUGUCG	chr7:30538426-30538643(-)$1	217	146	170	21.3787
GGCUGGGAAACUAGGGCACCAGUA	chr22:24951647-24951869(-)$1	222	22	46	21.3039
CCCCCGAAGCAGCAUCCCUGGGCA	chr17:37618406-37618653(+)$1	247	87	111	22.4368
UCCAGAAACAAAUAUACCUCGGGA	chr2:198338391-198338617(+)$1	226	202	226	23.0640
GAUGCAAAAAAGAAAGCUGCCCAU	chr10:22828834-22829083(-)$1	249	136	160	22.2428
CAUUCCUCCAUUGCUAAACAGAUG	chr10:7840941-7841150(+)$1	209	106	130	21.0029
AUAUGGACUCCACUCUUCACUAUA	chr18:9561942-9562166(-)$1	224	94	118	21.1684
GUGUUUAAACUUUAGCUGAGACAC	chr1:179959620-179959839(+)$1	219	6	30	23.6605
UAUGUCAUACCCCCAAAGACUUAA	chr3:47770421-47770656(-)$1	235	198	222	22.1683

#DB
(((((..............)))))	chr15:29561336-29561563(-)$1	1	2	26	22.2861
((((................))))	chr3:47957446-47957657(-)$1	1	37	61	19.8680
.((((((...........))))))	chr16:47462596-47462826(-)$1	1	155	179	22.7028
((((((..............))))	chr12:57909628-57909852(+)$1	1	160	184	22.0987
((((((..............))))	chr16:31288221-31288443(-)$1	1	127	151	22.0987
((.(((...........))).)))	chr1:17355084-17355308(-)$1	1	142	166	22.1683
((.(((..............))).	chr4:144468481-144468698(+)$1	1	104	128	21.8805
((.(((............))))))	chr13:21995117-21995335(-)$1	1	35	59	24.0989
(..(((...........))).)))	chr17:27085375-27085598(-)$1	1	96	120	21.9484
)((((..............)))).	chr15:69747755-69747975(+)$1	1	192	216	19.9569
((((................))))	chrX:74523172-74523390(+)$1	1	128	152	20.7147
((((((..............))).	chr11:95712946-95713175(-)$1	1	159	183	22.1410
.(((((............))))))	chr2:271814-272034(+)$1	1	147	171	21.2234
.(((((.............)))))	chr12:105538422-105538643(+)$1	1	67	91	22.1474
((((((............))))))	chr11:118390319-118390542(+)$1	1	53	77	21.1898
.((((..............)))).	chr10:28906510-28906732(+)$1	1	61	85	20.7050
(((((((...........))))))	chr12:56601937-56602157(-)$1	1	178	202	22.1265
((.(((............)))..)	chr11:763659-763885(+)$1	1	105	129	23.3142
((((((............))).))	chr17:61784590-61784812(-)$1	1	14	38	23.9660
((((((.............)))).	chr8:124042822-124043047(-)$1	1	46	70	21.9535
((((((............))))))	chr12:65133079-65133309(-)$1	1	182	206	23.6605
..(((((...........))))).	chr7:38816228-38816458(-)$1	1	59	83	22.4953
.((((..............)))).	chr1:52246879-52247099(+)$1	1	50	74	21.3611
))(((((...........))))).	chr12:123805015-123805234(-)$1	1	27	51	21.3493
((((((............))))))	chrX:107371914-107372138(+)$1	1	4	28	23.5604
(((((((...........))))))	chr4:78663346-78663570(-)$1	1	94	118	22.5879
...((.............))..))	chr17:1268167-1268391(-)$1	1	80	104	21.0855
((((.((...........)).).)	chr7:45141851-45142066(-)$1	1	153	177	22.0576
(((((..............)))))	chr11:93471273-93471495(-)$1	1	196	220	22.2861
((((..............))))))	chr16:23101994-23102219(-)$1	1	53	77	21.7577
((((((............))))))	chr6:90051943-90052169(-)$1	1	37	61	23.7333
.(((((.............)))))	chr16:57241878-57242108(+)$1	1	16	40	23.2049
(((((((...........))))))	chr4:122604448-122604665(-)$1	1	152	176	22.4749
((.(((...........))).)))	chr8:94745693-94745911(-)$1	1	12	36	22.8503
.(((((............))))))	chr3:179051951-179052172(+)$1	1	132	156	23.3560
(((((..............)))))	chr19:47503644-47503861(+)$1	1	72	96	21.8527
(((.(((...........))))))	chr1:154557365-154557585(-)$1	1	66	90	22.7334
((((((............))))))	chr11:108119590-108119820(+)$1	1	57	81	23.8325
(((..((...........))..))	chr17:61498767-61498991(+)$1	1	79	103	21.5629
(((((((...........))))).	chr17:10596104-10596323(-)$1	1	35	59	21.9325
...(((............)))...	chr1:203768481-203768720(+)$1	1	57	81	23.4360
.((((((...........))))))	chr3:113442754-113442977(-)$1	1	163	187	22.7072
((((((..............))))	chr17:56780568-56780790(+)$1	1	21	45	22.0987
.(((.(.............).)))	chr16:24829843-24830120(+)$1	1	135	159	23.2446
((((((............))))))	chr22:29182207-29182436(+)$1	1	205	229	23.6605
.((.((............)))).)	chr1:78207272-78207498(-)$1	1	70	94	21.9570
.((((((...........))))))	chr8:126194351-126194576(+)$1	1	17	41	21.6453
((((((............))))))	chr19:9492131-9492352(+)$1	1	92	116	23.6605
((...((...........))..))	chr10:112058351-112058575(-)$1	1	106	130	20.6074
.((((((...........))))))	chr14:102552331-102552554(-)$1	1	127	151	22.0000
((.(((..............))).	chr10:111637477-111637698(-)$1	1	96	120	22.0575
)(((((.............)))))	chr1:84955279-84955499(+)$1	1	47	71	23.0900
((((((............))))))	chr11:822330-822547(+)$1	1	79	103	23.6605
(.(((((...........))))).	chr1:150116925-150117142(+)$1	1	62	86	22.2754
..((..............))...)	chr1:150240403-150240625(-)$1	1	34	58	20.5920
.(((((...........))).)).	chr7:30538426-30538643(-)$1	1	146	170	21.3787
((((((............))))).	chr22:24951647-24951869(-)$1	1	22	46	21.3039
(.((((............))))..	chr17:37618406-37618653(+)$1	1	87	111	22.4368
(((.((............)).)))	chr2:198338391-198338617(+)$1	1	202	226	23.0640
(..(((...........))).)))	chr10:22828834-22829083(-)$1	1	136	160	22.2428
((((................))))	chr10:7840941-7841150(+)$1	1	106	130	21.0029
((((((.............)))))	chr18:9561942-9562166(-)$1	1	94	118	21.1684
((((((............))))))	chr1:179959620-179959839(+)$1	1	6	30	23.6605
((.(((...........))).)))	chr3:47770421-47770656(-)$1	1	198	222	22.1683

#PSSM
f : 0.20	g : 0.09	d : 0.09	e : 0.07	c : 0.07	h : 0.06	[ : 0.06	! : 0.04	b : 0.04	: : 0.04	# : 0.04	" : 0.03	i : 0.03	= : 0.03	$ : 0.01	% : 0.01	D : 0.01	
f : 0.28	e : 0.17	d : 0.10	g : 0.07	b : 0.06	c : 0.06	! : 0.04	h : 0.04	# : 0.04	i : 0.03	= : 0.03	[ : 0.03	
f : 0.25	e : 0.20	[ : 0.10	d : 0.09	g : 0.06	c : 0.06	b : 0.04	! : 0.03	h : 0.03	i : 0.03	# : 0.03	= : 0.03	" : 0.01	
f : 0.21	c : 0.21	e : 0.18	d : 0.09	g : 0.06	[ : 0.04	h : 0.03	i : 0.03	b : 0.03	= : 0.03	a : 0.01	! : 0.01	" : 0.01	
c : 0.21	f : 0.20	e : 0.17	d : 0.07	g : 0.06	y : 0.04	b : 0.04	h : 0.03	i : 0.03	[ : 0.03	w : 0.03	= : 0.01	! : 0.01	" : 0.01	
c : 0.21	f : 0.20	e : 0.15	w : 0.12	b : 0.07	y : 0.04	h : 0.03	i : 0.03	d : 0.03	g : 0.03	v : 0.01	= : 0.01	a : 0.01	
u : 0.29	w : 0.21	v : 0.10	t : 0.09	f : 0.07	e : 0.06	y : 0.04	b : 0.04	i : 0.01	g : 0.01	c : 0.01	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
t : 0.32	u : 0.29	w : 0.21	v : 0.10	y : 0.04	
u : 0.29	t : 0.23	w : 0.21	v : 0.10	c : 0.09	y : 0.04	
w : 0.18	c : 0.17	f : 0.15	e : 0.10	b : 0.10	v : 0.09	y : 0.04	i : 0.03	= : 0.03	g : 0.03	h : 0.01	d : 0.01	
c : 0.17	e : 0.17	f : 0.15	b : 0.10	w : 0.09	d : 0.07	g : 0.06	y : 0.04	h : 0.03	i : 0.03	= : 0.03	a : 0.01	
f : 0.21	e : 0.18	] : 0.14	c : 0.12	d : 0.09	g : 0.06	2 : 0.04	h : 0.03	i : 0.03	= : 0.03	b : 0.01	3 : 0.01	
f : 0.25	e : 0.20	d : 0.14	c : 0.07	g : 0.06	2 : 0.06	h : 0.04	i : 0.03	= : 0.03	b : 0.03	] : 0.01	a : 0.01	4 : 0.01	3 : 0.01	
f : 0.26	e : 0.20	d : 0.12	c : 0.09	g : 0.06	h : 0.06	i : 0.03	b : 0.03	] : 0.03	= : 0.03	4 : 0.03	2 : 0.01	3 : 0.01	
f : 0.28	] : 0.10	e : 0.10	d : 0.07	c : 0.07	g : 0.06	h : 0.06	: : 0.04	i : 0.03	= : 0.03	2 : 0.03	4 : 0.03	D : 0.01	6 : 0.01	b : 0.01	

#score	1423.4460982611497
#seq	64
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_CDS_m2_run2.txt

#BEAR
hccc[bbqqqqqqqqbb]ccc	chr17:26653650-26653865(+)$1	215	120	141	14.4226
gggggggqqqqqqqqgggggg	chr6:152570236-152570463(-)$1	227	164	185	14.9055
b"""cccqqqqqqqqccc333	chr3:130463620-130463840(-)$1	220	176	197	15.5595
#ffffffqqqqqqqqffffff	chr4:162307118-162307348(-)$1	230	185	206	14.0316
ccc[cccqqqqqqqqccc]cc	chr3:47163952-47164175(-)$1	223	56	77	15.4049
%%eeeeeqqqqqqqqeeeee2	chr12:12871662-12871880(+)$1	218	53	74	13.3778
iieeeeeqqqqqqqqeeeee]	chr17:80588695-80588925(-)$1	230	72	93	14.4527
%%eeeeeqqqqqqqqeeeee7	chr12:1137139-1137369(+)$1	230	166	187	12.9288
h"""cccqqqqqqqqccc333	chr2:44428655-44428884(+)$1	229	19	40	15.5813
ddeeeeeqqqqqqqqeeeee:	chr9:95077990-95078220(-)$1	230	72	93	13.2059
%%%%cccqqqqqqqqccc333	chr1:110134715-110134937(+)$1	222	140	161	13.3845
gggggggqqqqqqqqgggggg	chr3:56707547-56707765(-)$1	218	156	177	14.9055
[ccc!!aqqqqqqqqa22ccc	chr3:97596609-97596839(+)$1	230	37	58	14.6450
ggg!!bbqqqqqqqqbb22gg	chr20:50768635-50768853(-)$1	218	122	143	14.9215
dddd!!aqqqqqqqqa22ddd	chr12:57567481-57567699(+)$1	218	139	160	13.7431
!!eeeeeqqqqqqqqeeeee2	chr12:120636881-120637101(-)$1	220	29	50	14.6857
ebb[cccqqqqqqqqcccbb:	chr6:46107518-46107739(+)$1	221	110	131	13.0844
c[cccbbqqqqqqqqbb22cc	chr5:149786745-149786965(-)$1	220	195	216	14.6856
"ffffffqqqqqqqqffffff	chr11:93429784-93430002(+)$1	218	162	183	14.0408
fccc!!aqqqqqqqqa4444c	chr1:161751666-161751889(+)$1	223	76	97	14.6951
:ddddbbqqqqqqqqbb]ddd	chr5:139908150-139908380(+)$1	230	112	133	12.9004
hhh!!bbqqqqqqqqbb22hh	chr7:92901886-92902109(+)$1	223	100	121	13.8698
eee[cccqqqqqqqqccceee	chr12:109017075-109017288(-)$1	213	41	62	15.0347
:bb[cccqqqqqqqqccc]bb	chr12:39761593-39761816(-)$1	223	111	132	13.4572
!!eeeeeqqqqqqqqeeeee2	chr6:96034242-96034481(+)$1	239	123	144	14.6857
gggggggqqqqqqqqgggggg	chr19:52090681-52090911(+)$1	230	139	160	14.9055
"ccc[bbqqqqqqqqbb]ccc	chr18:47009854-47010091(-)$1	237	75	96	14.7706
ff!!cccqqqqqqqqccc22f	chr12:32900102-32900332(-)$1	230	12	33	14.9100
####cccqqqqqqqqccc22d	chr22:24964019-24964237(+)$1	218	191	212	15.1706
ee[ddddqqqqqqqqdddd]e	chr9:86297802-86298034(-)$1	232	196	217	13.5734
:ffffffqqqqqqqqffffff	chr1:109338869-109339086(+)$1	217	176	197	13.0437
ddd[cccqqqqqqqqccc]dd	chr7:151884402-151884626(-)$1	224	66	87	14.8586
!!bbcccqqqqqqqqccc]bb	chr6:32943119-32943345(+)$1	226	114	135	14.4547
!!cccbbqqqqqqqqbb]ccc	chr8:74893433-74893663(+)$1	230	90	111	14.9802
#ffffffqqqqqqqqffffff	chr12:105589151-105589371(-)$1	220	78	99	14.0316
ddd[cccqqqqqqqqccc]dd	chr5:140963632-140963862(-)$1	230	197	218	14.8586
h"""cccqqqqqqqqccc333	chr6:41756877-41757097(+)$1	220	188	209	15.5813
ffff[bbqqqqqqqqbbffff	chr9:104170432-104170653(+)$1	221	3	24	13.9535
eee"""aqqqqqqqqa333ee	chr4:143094779-143094999(-)$1	220	161	182	14.9246
b[eeeeeqqqqqqqqeeeee]	chr15:75212638-75212853(-)$1	215	92	113	14.3616
ee[a[bbqqqqqqqqbb]a]e	chr2:225370630-225370853(-)$1	223	176	197	14.4475
eeee!!aqqqqqqqqa22eee	chrX:30872503-30872733(-)$1	230	81	102	14.3103
#ccc[bbqqqqqqqqbb]ccc	chr17:65850530-65850748(+)$1	218	65	86	14.7614
gggggggqqqqqqqqgggggg	chr20:10388170-10388394(-)$1	224	115	136	14.9055
gggggggqqqqqqqqgggggg	chr2:48061856-48062076(-)$1	220	163	184	14.9055
ddd[cccqqqqqqqqccc]dd	chr7:102743756-102743986(-)$1	230	112	133	14.8586
iiiddddqqqqqqqqdddd]i	chr2:74086276-74086507(+)$1	231	170	191	13.8026
ddd!!bbqqqqqqqqbb22dd	chr8:67590334-67590564(+)$1	230	151	172	14.2316
gggggggqqqqqqqqgggggg	chr10:75897841-75898095(-)$1	254	50	71	14.9055
gggggggqqqqqqqqgggggg	chr16:31200419-31200649(+)$1	230	8	29	14.9055
!!eeeeeqqqqqqqqeeeee2	chr8:70488143-70488363(+)$1	220	28	49	14.6857
ee[ddddqqqqqqqqdddd]e	chr1:155218138-155218361(-)$1	223	10	31	13.5734
####cccqqqqqqqqccc444	chr5:74100306-74100530(-)$1	224	37	58	15.4790
!!eeeeeqqqqqqqqeeeee]	chr3:145788749-145788970(-)$1	221	22	43	14.8184
ccc[cccqqqqqqqqcccccc	chr15:72873165-72873385(+)$1	220	141	162	15.2058
dddddddqqqqqqqqdddd]d	chr6:80751768-80751987(+)$1	219	149	170	13.2944
####cccqqqqqqqqccc]hh	chr7:135611955-135612198(-)$1	243	175	196	15.1858
b[eeeeeqqqqqqqqeeeee3	chr11:104900363-104900599(-)$1	236	8	29	14.4393
ffff[bbqqqqqqqqbb22ff	chr1:37959259-37959480(-)$1	221	49	70	14.1135
e:eeeeeqqqqqqqqeeeee:	chr14:105236991-105237220(-)$1	229	141	162	12.4366
:ffffffqqqqqqqqffffff	chr6:125397744-125397967(+)$1	223	106	127	13.0437
gggggggqqqqqqqqgggggg	chr1:220195606-220195844(-)$1	238	159	180	14.9055
e[ccc[aqqqqqqqqa]ccc3	chr19:52793539-52793764(+)$1	225	83	104	14.9077

#otherMatches

#Seq PSSM
GUUGCGGAGCCCCUACUACAA	chr17:26653650-26653865(+)$1	215	120	141	14.4226
AGAGGUAUUUAUAGCUGCCUU	chr6:152570236-152570463(-)$1	227	164	185	14.9055
GACAGCUGUGGACCAAGCACA	chr3:130463620-130463840(-)$1	220	176	197	15.5595
AAGCACACAAACUGAUGUGCU	chr4:162307118-162307348(-)$1	230	185	206	14.0316
AGAAUUAAAUAUAAAUGGAUC	chr3:47163952-47164175(-)$1	223	56	77	15.4049
AUAAAGAUUGUGUGUUCUUUU	chr12:12871662-12871880(+)$1	218	53	74	13.3778
GCAACUAUUUAGCUUUAGUUG	chr17:80588695-80588925(-)$1	230	72	93	14.4527
UGUGGGUUCAGAAACACCUAA	chr12:1137139-1137369(+)$1	230	166	187	12.9288
AUUGAUGAAUACAUGCGUAAC	chr2:44428655-44428884(+)$1	229	19	40	15.5813
UGCACAAAAAAGAACUUGUGA	chr9:95077990-95078220(-)$1	230	72	93	13.2059
GAAGCAUGGAUGUUAGUGAAA	chr1:110134715-110134937(+)$1	222	140	161	13.3845
AGGUAUGUUUUAAAUUAUACU	chr3:56707547-56707765(-)$1	218	156	177	14.9055
UACUACCUCCAAUCUGCAAGU	chr3:97596609-97596839(+)$1	230	37	58	14.6450
CAGCCCAUCCAGCUUUGCUCU	chr20:50768635-50768853(-)$1	218	122	143	14.9215
GGACGAGGAGAACUGCGAGUC	chr12:57567481-57567699(+)$1	218	139	160	13.7431
CGUCUCCCUCUUCCUGGAGAA	chr12:120636881-120637101(-)$1	220	29	50	14.6857
UGACUCUAAUGACAAGGAUCC	chr6:46107518-46107739(+)$1	221	110	131	13.0844
GACAGUCACCUCCCAGAACCU	chr5:149786745-149786965(-)$1	220	195	216	14.6856
AACUGAUUCUGUUAUAUCAGU	chr11:93429784-93430002(+)$1	218	162	183	14.0408
GCCUUGGGAGUCAGACAUUUG	chr1:161751666-161751889(+)$1	223	76	97	14.6951
GCCGUCUACCUAACCAGAACG	chr5:139908150-139908380(+)$1	230	112	133	12.9004
UUGACAUUAACCAUUAUACCA	chr7:92901886-92902109(+)$1	223	100	121	13.8698
AAGAGGUCUGUUCAUACCCUU	chr12:109017075-109017288(-)$1	213	41	62	15.0347
ACUGUGAAUACAGAAUCAGAG	chr12:39761593-39761816(-)$1	223	111	132	13.4572
AUUUAUUUUCUCUCUGAUGAU	chr6:96034242-96034481(+)$1	239	123	144	14.6857
CAUACUGGUGAGAGACAGUAU	chr19:52090681-52090911(+)$1	230	139	160	14.9055
AUAUGGCCUAAGAAAGCAAUA	chr18:47009854-47010091(-)$1	237	75	96	14.7706
UACUAAACGUUUCUAUUUUUU	chr12:32900102-32900332(-)$1	230	12	33	14.9100
AUUACUGCCUGGAGACAGAGA	chr22:24964019-24964237(+)$1	218	191	212	15.1706
GAUGGGAAAAAAUACUCCUUU	chr9:86297802-86298034(-)$1	232	196	217	13.5734
AAUCUUUGAAAACUGAAAGAU	chr1:109338869-109339086(+)$1	217	176	197	13.0437
GAUAAAAAUUCAGCCUUUAAU	chr7:151884402-151884626(-)$1	224	66	87	14.8586
GGGCUGCUUCAGAGUGUAUGC	chr6:32943119-32943345(+)$1	226	114	135	14.4547
UUUACGGUGAUCACCCCAGUG	chr8:74893433-74893663(+)$1	230	90	111	14.9802
AAUGUCCUCUACAGUGGAUAU	chr12:105589151-105589371(-)$1	220	78	99	14.0316
ACAUGGGAGACUGUGCCCUUG	chr5:140963632-140963862(-)$1	230	197	218	14.8586
GCCAAGUAGGUAAGCACUGAA	chr6:41756877-41757097(+)$1	220	188	209	15.5813
UGUUCAGAGAAAACACUAACA	chr9:104170432-104170653(+)$1	221	3	24	13.9535
AGCCAGCAUUCUCCAGACAGC	chr4:143094779-143094999(-)$1	220	161	182	14.9246
UGACAUUGCUACUUGAGUGUG	chr15:75212638-75212853(-)$1	215	92	113	14.3616
AAGGGGUAAGUAGUAAUGCAU	chr2:225370630-225370853(-)$1	223	176	197	14.4475
GGACAGCAAUUAAUAGGAGUC	chrX:30872503-30872733(-)$1	230	81	102	14.3103
GGGUGAUACAGUAUGAUGACC	chr17:65850530-65850748(+)$1	218	65	86	14.7614
AUAUAUCAGACACAAGGUAUG	chr20:10388170-10388394(-)$1	224	115	136	14.9055
UUAUUUUUAUGACUUAAAAUG	chr2:48061856-48062076(-)$1	220	163	184	14.9055
AAAUGUGAGCACAGGCACUUU	chr7:102743756-102743986(-)$1	230	112	133	14.8586
AUGUUGCCAGAGUCAGUAGCC	chr2:74086276-74086507(+)$1	231	170	191	13.8026
CAUAACAAAAGAAACUGAAAU	chr8:67590334-67590564(+)$1	230	151	172	14.2316
UUUCUUUGAAGCUCAAGAGAA	chr10:75897841-75898095(-)$1	254	50	71	14.9055
UCUGUUCAACAAGCAGAACAG	chr16:31200419-31200649(+)$1	230	8	29	14.9055
UUUGCUAAACAAUGCUGGCAC	chr8:70488143-70488363(+)$1	220	28	49	14.6857
CUCUGGGCUUGAGUUCCCACA	chr1:155218138-155218361(-)$1	223	10	31	13.5734
CAAUGUUAGAGUUAAAACCAA	chr5:74100306-74100530(-)$1	224	37	58	15.4790
GCACUACUGAAUUUUGUAGUA	chr3:145788749-145788970(-)$1	221	22	43	14.8184
AGAAUAACCAGUCCAUUAUCU	chr15:72873165-72873385(+)$1	220	141	162	15.2058
GAUUUGCAGUUAUUCGUAAUG	chr6:80751768-80751987(+)$1	219	149	170	13.2944
AAACCCAGUUAAGCAUGGAAG	chr7:135611955-135612198(-)$1	243	175	196	15.1858
CCCAGAGCACAAGACCUCUGA	chr11:104900363-104900599(-)$1	236	8	29	14.4393
GUUUCUCCCUUCUUAGAAUGA	chr1:37959259-37959480(-)$1	221	49	70	14.1135
GAGGGGCCACUGCCUGCCCCC	chr14:105236991-105237220(-)$1	229	141	162	12.4366
UGUAACACUAAUUUUUGUUAC	chr6:125397744-125397967(+)$1	223	106	127	13.0437
AGUAUAUCUCCUUCAAUAUGC	chr1:220195606-220195844(-)$1	238	159	180	14.9055
CAAAGUCUUCAGAGUGUCUUC	chr19:52793539-52793764(+)$1	225	83	104	14.9077

#DB
((((.((........)).)))	chr17:26653650-26653865(+)$1	1	120	141	14.4226
(((((((........))))))	chr6:152570236-152570463(-)$1	1	164	185	14.9055
(...(((........)))...	chr3:130463620-130463840(-)$1	1	176	197	15.5595
.((((((........))))))	chr4:162307118-162307348(-)$1	1	185	206	14.0316
(((.(((........))).))	chr3:47163952-47164175(-)$1	1	56	77	15.4049
..(((((........))))).	chr12:12871662-12871880(+)$1	1	53	74	13.3778
(((((((........))))).	chr17:80588695-80588925(-)$1	1	72	93	14.4527
..(((((........))))).	chr12:1137139-1137369(+)$1	1	166	187	12.9288
(...(((........)))...	chr2:44428655-44428884(+)$1	1	19	40	15.5813
))(((((........))))).	chr9:95077990-95078220(-)$1	1	72	93	13.2059
....(((........)))...	chr1:110134715-110134937(+)$1	1	140	161	13.3845
(((((((........))))))	chr3:56707547-56707765(-)$1	1	156	177	14.9055
.(((..(........)..)))	chr3:97596609-97596839(+)$1	1	37	58	14.6450
(((..((........))..))	chr20:50768635-50768853(-)$1	1	122	143	14.9215
((((..(........)..)))	chr12:57567481-57567699(+)$1	1	139	160	13.7431
..(((((........))))).	chr12:120636881-120637101(-)$1	1	29	50	14.6857
)((.(((........))))).	chr6:46107518-46107739(+)$1	1	110	131	13.0844
(.(((((........))..))	chr5:149786745-149786965(-)$1	1	195	216	14.6856
.((((((........))))))	chr11:93429784-93430002(+)$1	1	162	183	14.0408
((((..(........)....)	chr1:161751666-161751889(+)$1	1	76	97	14.6951
.((((((........)).)))	chr5:139908150-139908380(+)$1	1	112	133	12.9004
(((..((........))..))	chr7:92901886-92902109(+)$1	1	100	121	13.8698
(((.(((........))))))	chr12:109017075-109017288(-)$1	1	41	62	15.0347
.((.(((........))).))	chr12:39761593-39761816(-)$1	1	111	132	13.4572
..(((((........))))).	chr6:96034242-96034481(+)$1	1	123	144	14.6857
(((((((........))))))	chr19:52090681-52090911(+)$1	1	139	160	14.9055
.(((.((........)).)))	chr18:47009854-47010091(-)$1	1	75	96	14.7706
((..(((........)))..)	chr12:32900102-32900332(-)$1	1	12	33	14.9100
....(((........)))..)	chr22:24964019-24964237(+)$1	1	191	212	15.1706
((.((((........)))).)	chr9:86297802-86298034(-)$1	1	196	217	13.5734
.((((((........))))))	chr1:109338869-109339086(+)$1	1	176	197	13.0437
(((.(((........))).))	chr7:151884402-151884626(-)$1	1	66	87	14.8586
..(((((........))).))	chr6:32943119-32943345(+)$1	1	114	135	14.4547
..(((((........)).)))	chr8:74893433-74893663(+)$1	1	90	111	14.9802
.((((((........))))))	chr12:105589151-105589371(-)$1	1	78	99	14.0316
(((.(((........))).))	chr5:140963632-140963862(-)$1	1	197	218	14.8586
(...(((........)))...	chr6:41756877-41757097(+)$1	1	188	209	15.5813
((((.((........))))))	chr9:104170432-104170653(+)$1	1	3	24	13.9535
(((...(........)...))	chr4:143094779-143094999(-)$1	1	161	182	14.9246
(.(((((........))))).	chr15:75212638-75212853(-)$1	1	92	113	14.3616
((.(.((........)).).)	chr2:225370630-225370853(-)$1	1	176	197	14.4475
((((..(........)..)))	chrX:30872503-30872733(-)$1	1	81	102	14.3103
.(((.((........)).)))	chr17:65850530-65850748(+)$1	1	65	86	14.7614
(((((((........))))))	chr20:10388170-10388394(-)$1	1	115	136	14.9055
(((((((........))))))	chr2:48061856-48062076(-)$1	1	163	184	14.9055
(((.(((........))).))	chr7:102743756-102743986(-)$1	1	112	133	14.8586
(((((((........)))).)	chr2:74086276-74086507(+)$1	1	170	191	13.8026
(((..((........))..))	chr8:67590334-67590564(+)$1	1	151	172	14.2316
(((((((........))))))	chr10:75897841-75898095(-)$1	1	50	71	14.9055
(((((((........))))))	chr16:31200419-31200649(+)$1	1	8	29	14.9055
..(((((........))))).	chr8:70488143-70488363(+)$1	1	28	49	14.6857
((.((((........)))).)	chr1:155218138-155218361(-)$1	1	10	31	13.5734
....(((........)))...	chr5:74100306-74100530(-)$1	1	37	58	15.4790
..(((((........))))).	chr3:145788749-145788970(-)$1	1	22	43	14.8184
(((.(((........))))))	chr15:72873165-72873385(+)$1	1	141	162	15.2058
(((((((........)))).)	chr6:80751768-80751987(+)$1	1	149	170	13.2944
....(((........))).))	chr7:135611955-135612198(-)$1	1	175	196	15.1858
(.(((((........))))).	chr11:104900363-104900599(-)$1	1	8	29	14.4393
((((.((........))..))	chr1:37959259-37959480(-)$1	1	49	70	14.1135
).(((((........))))).	chr14:105236991-105237220(-)$1	1	141	162	12.4366
.((((((........))))))	chr6:125397744-125397967(+)$1	1	106	127	13.0437
(((((((........))))))	chr1:220195606-220195844(-)$1	1	159	180	14.9055
(.(((.(........).))).	chr19:52793539-52793764(+)$1	1	83	104	14.9077

#PSSM
g : 0.14	e : 0.14	d : 0.11	# : 0.09	! : 0.09	h : 0.06	f : 0.06	: : 0.06	b : 0.04	c : 0.04	% : 0.04	i : 0.03	" : 0.03	[ : 0.01	
g : 0.14	f : 0.12	d : 0.12	c : 0.11	! : 0.09	e : 0.09	[ : 0.06	" : 0.04	% : 0.04	# : 0.04	i : 0.03	b : 0.03	h : 0.01	: : 0.01	
e : 0.22	c : 0.15	g : 0.14	f : 0.11	d : 0.11	" : 0.04	b : 0.04	# : 0.04	[ : 0.04	% : 0.01	h : 0.01	! : 0.01	i : 0.01	
e : 0.19	c : 0.12	g : 0.12	[ : 0.12	f : 0.11	d : 0.09	" : 0.06	! : 0.06	# : 0.04	% : 0.01	b : 0.01	a : 0.01	
c : 0.31	e : 0.17	g : 0.12	! : 0.11	[ : 0.09	f : 0.07	d : 0.07	" : 0.01	
c : 0.26	b : 0.19	e : 0.17	g : 0.12	f : 0.07	! : 0.06	d : 0.06	" : 0.01	[ : 0.01	
c : 0.26	b : 0.19	e : 0.17	g : 0.12	a : 0.09	f : 0.07	d : 0.06	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.26	b : 0.19	e : 0.17	g : 0.12	a : 0.09	f : 0.07	d : 0.06	
c : 0.26	b : 0.19	e : 0.17	g : 0.12	f : 0.07	d : 0.06	2 : 0.04	4 : 0.01	3 : 0.01	] : 0.01	
c : 0.28	e : 0.17	g : 0.12	2 : 0.12	] : 0.09	f : 0.09	d : 0.06	4 : 0.01	3 : 0.01	
e : 0.20	g : 0.12	c : 0.11	] : 0.11	2 : 0.11	f : 0.09	d : 0.09	3 : 0.07	4 : 0.03	b : 0.01	a : 0.01	
e : 0.22	c : 0.14	g : 0.14	f : 0.11	d : 0.09	] : 0.07	3 : 0.06	b : 0.04	4 : 0.03	h : 0.03	2 : 0.03	
c : 0.14	g : 0.14	f : 0.12	d : 0.12	3 : 0.09	e : 0.09	2 : 0.06	] : 0.04	: : 0.04	h : 0.03	b : 0.03	7 : 0.01	i : 0.01	4 : 0.01	

#score	907.1137033460114
#seq	63
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_CDS_m1_run1.txt

#BEAR
hhhhhhuuuuuuuuuuuuhhhhhh	chr16:66592077-66592311(+)$1	234	200	224	15.5013
^^^^^^^^^^^^^^^^^^eeeee3	chr1:32384562-32384836(-)$1	274	221	245	20.9079
[fffffftttttttttttffffff	chr12:46756783-46757013(-)$1	230	44	68	16.4791
^^^^^^^^^^^^^^^^^^gggggg	chr2:42936144-42936371(+)$1	227	98	122	21.0152
^^^^^^^^^^^^^^^^^^dddd]d	chr9:123367816-123368090(-)$1	274	76	100	20.4014
fffffvvvvvvvvvvvvvffffff	chr1:63884952-63885186(+)$1	234	30	54	20.6417
gggggguuuuuuuuuuuugggggg	chr2:38522989-38523244(-)$1	255	144	168	19.2225
:eeeeeuuuuuuuuuuuueeeee:	chr12:69995124-69995392(+)$1	268	109	133	17.4879
^^^^^^^^^^^^^^^^^^hhhhhh	chr9:86584253-86584496(-)$1	243	121	145	19.6097
"ccc^^^^^^^^^^^^^^^^^^cc	chr11:62291708-62291936(-)$1	228	75	99	18.4277
iiiiiiitttttttttttiiiiii	chrX:48435824-48436083(+)$1	259	195	219	15.6115
Dfffffftttttttttttffffff	chr8:71499064-71499290(-)$1	226	18	42	15.4625
ddcccwwwwwwwwwwwwwwccc55	chrX:48432839-48433062(+)$1	223	19	43	17.9491
ffffftttttttttttffffff]e	chr11:9459623-9459853(+)$1	230	54	78	15.3257
fffffvvvvvvvvvvvvvffffff	chr13:96443144-96443447(+)$1	303	213	237	20.6417
^^^^^^^^^^^^^^^^^^dddd22	chr2:135711881-135712106(+)$1	225	104	128	20.2511
eeeeevvvvvvvvvvvvveeeee:	chr6:64286617-64286893(+)$1	276	252	276	19.4612
"""bbvvvvvvvvvvvvvbb]eee	chrM:10104-10389(+)$1	285	74	98	19.9781
fffxxxxxxxxxxxxxxxffffff	chr1:68947115-68947340(-)$1	225	183	207	17.4150
^^^^^^^^^^^^^^^^^^ffffff	chr2:198256869-198257170(-)$1	301	133	157	20.9090
dddxxxxxxxxxxxxxxxdddd]c	chr15:41643036-41643288(+)$1	252	127	151	16.7181
^^^^^^^^^^^^^^^^^^ddddcc	chr17:48941213-48941459(-)$1	246	24	48	20.4330
gggggvvvvvvvvvvvvvgggggg	chr2:128521990-128522277(-)$1	287	220	244	20.6211
^^^^^^^^^^^^^^^^^^eeeee3	chr9:19096605-19096838(-)$1	233	51	75	20.9079
^^^^^^^^^^^^^^^^^^bb]ggg	chr11:9444498-9444740(+)$1	242	119	143	20.4464
:dddd^^^^^^^^^^^^^^^^^^d	chr1:28177069-28177295(+)$1	226	155	179	15.9877
ffffffuuuuuuuuuuuuffffff	chr7:91743055-91743284(-)$1	229	29	53	19.2775
^^^^^^^^^^^^^^^^^^dddd44	chr8:38961084-38961386(+)$1	302	244	268	20.4145
fffffwwwwwwwwwwwwwwfffff	chr4:123813799-123814102(+)$1	303	177	201	19.8473
^^^^^^^^^^^^^^^^^^dddd22	chr6:64289828-64290064(+)$1	236	114	138	20.2511
^^^^^^^^^^^^^^^^^^gggggg	chr7:148523495-148523722(-)$1	227	107	131	21.0152
gggggggtttttttttttgggggg	chr10:98292798-98293027(-)$1	229	76	100	16.2154
eeeeevvvvvvvvvvvvveeeee:	chr14:62203523-62203750(+)$1	227	15	39	19.4612

#otherMatches

#Seq PSSM
UUUACUUUUUCCUACCAUAGUGAG	chr16:66592077-66592311(+)$1	234	200	224	15.5013
AUAACUCACAACCCUACCAAUGCU	chr1:32384562-32384836(-)$1	274	221	245	20.9079
UGAAAACAGCCAAUCAAAGUUUUU	chr12:46756783-46757013(-)$1	230	44	68	16.4791
UGCUUUUAAAUUCUUAACCUUAUA	chr2:42936144-42936371(+)$1	227	98	122	21.0152
UACAUCAACAUUCACUCCCAUGCG	chr9:123367816-123368090(-)$1	274	76	100	20.4014
ACUUGAUAUGCUAUUUCACAAGUU	chr1:63884952-63885186(+)$1	234	30	54	20.6417
UUUCAUGCUUGCUGUACAAUGAGA	chr2:38522989-38523244(-)$1	255	144	168	19.2225
UGACCUUCGCUUUAACAUAGGUCU	chr12:69995124-69995392(+)$1	268	109	133	17.4879
UUUUUUCUUUUCUUUUAUAGUGUG	chr9:86584253-86584496(-)$1	243	121	145	19.6097
UCGAAGGCAAGUCAAAGAAAUCUC	chr11:62291708-62291936(-)$1	228	75	99	18.4277
UUUAAAUUUUUUCUGCCUAUUUAA	chrX:48435824-48436083(+)$1	259	195	219	15.6115
UAAUUAAUAUUCCCAUUUUUAAUU	chr8:71499064-71499290(-)$1	226	18	42	15.4625
CUACGUACUCUUUAUCAAUCGUCU	chrX:48432839-48433062(+)$1	223	19	43	17.9491
GGAACAGAUACCCCAAGUUUUAAA	chr11:9459623-9459853(+)$1	230	54	78	15.3257
GAAAAAAAAUUUCAAAUCUUUUCA	chr13:96443144-96443447(+)$1	303	213	237	20.6417
AUAUAUCCUCUCACAACUCUGUUU	chr2:135711881-135712106(+)$1	225	104	128	20.2511
ACCUUAAACAAAUUUAUAGAGGUA	chr6:64286617-64286893(+)$1	276	252	276	19.4612
CUUCGACCCUAUAUCCCCCGCCCG	chrM:10104-10389(+)$1	285	74	98	19.9781
CCAAACUUCAUGAUGCAAUGGGUA	chr1:68947115-68947340(-)$1	225	183	207	17.4150
AUAUCUUAUAAUUUUAUUGUUUAU	chr2:198256869-198257170(-)$1	301	133	157	20.9090
UAUUUCCUUUUUAAAUUUGUAGCA	chr15:41643036-41643288(+)$1	252	127	151	16.7181
uuuuuuuuuuuuuuuuuuGGUGGG	chr17:48941213-48941459(-)$1	246	24	48	20.4330
UCAGUCUUUAAUUAUGCAACUGAA	chr2:128521990-128522277(-)$1	287	220	244	20.6211
AUUUCAUUUUUAACCACUAGGAAC	chr9:19096605-19096838(-)$1	233	51	75	20.9079
GACAUUAAAUUAUAUUAAUCAAGG	chr11:9444498-9444740(+)$1	242	119	143	20.4464
CUCCUUUCUUUCUCCCACUUUCUA	chr1:28177069-28177295(+)$1	226	155	179	15.9877
ACAUUUGCUGUUCAUCUAAAAUGU	chr7:91743055-91743284(-)$1	229	29	53	19.2775
AAACACCACAAAACAGACUUCACU	chr8:38961084-38961386(+)$1	302	244	268	20.4145
GUGAAUUUAAUCAAUUCCUUUCAU	chr4:123813799-123814102(+)$1	303	177	201	19.8473
UUUUUUUUUUUCCUCCCAGAAAGC	chr6:64289828-64290064(+)$1	236	114	138	20.2511
UCCUUUCAUACGCUUUUCUGUAGG	chr7:148523495-148523722(-)$1	227	107	131	21.0152
ACAGGUGGCCGUUUGUUGCAUCUG	chr10:98292798-98293027(-)$1	229	76	100	16.2154
ACAGUCUCCCUUCCCCUCACUGUA	chr14:62203523-62203750(+)$1	227	15	39	19.4612

#DB
((((((............))))))	chr16:66592077-66592311(+)$1	1	200	224	15.5013
..................))))).	chr1:32384562-32384836(-)$1	1	221	245	20.9079
.((((((...........))))))	chr12:46756783-46757013(-)$1	1	44	68	16.4791
..................))))))	chr2:42936144-42936371(+)$1	1	98	122	21.0152
..................)))).)	chr9:123367816-123368090(-)$1	1	76	100	20.4014
(((((.............))))))	chr1:63884952-63885186(+)$1	1	30	54	20.6417
((((((............))))))	chr2:38522989-38523244(-)$1	1	144	168	19.2225
.(((((............))))).	chr12:69995124-69995392(+)$1	1	109	133	17.4879
..................))))))	chr9:86584253-86584496(-)$1	1	121	145	19.6097
.(((..................))	chr11:62291708-62291936(-)$1	1	75	99	18.4277
(((((((...........))))))	chrX:48435824-48436083(+)$1	1	195	219	15.6115
(((((((...........))))))	chr8:71499064-71499290(-)$1	1	18	42	15.4625
(((((..............)))..	chrX:48432839-48433062(+)$1	1	19	43	17.9491
(((((...........)))))).)	chr11:9459623-9459853(+)$1	1	54	78	15.3257
(((((.............))))))	chr13:96443144-96443447(+)$1	1	213	237	20.6417
..................))))..	chr2:135711881-135712106(+)$1	1	104	128	20.2511
(((((.............))))).	chr6:64286617-64286893(+)$1	1	252	276	19.4612
...((.............)).)))	chrM:10104-10389(+)$1	1	74	98	19.9781
(((...............))))))	chr1:68947115-68947340(-)$1	1	183	207	17.4150
..................))))))	chr2:198256869-198257170(-)$1	1	133	157	20.9090
(((...............)))).)	chr15:41643036-41643288(+)$1	1	127	151	16.7181
..................))))((	chr17:48941213-48941459(-)$1	1	24	48	20.4330
(((((.............))))))	chr2:128521990-128522277(-)$1	1	220	244	20.6211
..................))))).	chr9:19096605-19096838(-)$1	1	51	75	20.9079
..................)).)))	chr11:9444498-9444740(+)$1	1	119	143	20.4464
.((((..................)	chr1:28177069-28177295(+)$1	1	155	179	15.9877
((((((............))))))	chr7:91743055-91743284(-)$1	1	29	53	19.2775
..................))))..	chr8:38961084-38961386(+)$1	1	244	268	20.4145
(((((..............)))))	chr4:123813799-123814102(+)$1	1	177	201	19.8473
..................))))..	chr6:64289828-64290064(+)$1	1	114	138	20.2511
..................))))))	chr7:148523495-148523722(-)$1	1	107	131	21.0152
(((((((...........))))))	chr10:98292798-98293027(-)$1	1	76	100	16.2154
(((((.............))))).	chr14:62203523-62203750(+)$1	1	15	39	19.4612

#PSSM
^ : 0.36	f : 0.18	g : 0.09	: : 0.06	" : 0.06	d : 0.06	e : 0.06	h : 0.03	[ : 0.03	i : 0.03	D : 0.03	
^ : 0.36	f : 0.24	g : 0.09	e : 0.09	d : 0.09	h : 0.03	c : 0.03	i : 0.03	" : 0.03	
^ : 0.36	f : 0.24	g : 0.09	e : 0.09	c : 0.06	d : 0.06	h : 0.03	i : 0.03	" : 0.03	
^ : 0.36	f : 0.21	g : 0.09	e : 0.09	c : 0.06	x : 0.06	h : 0.03	i : 0.03	b : 0.03	d : 0.03	
^ : 0.39	f : 0.21	g : 0.09	e : 0.09	x : 0.06	h : 0.03	i : 0.03	c : 0.03	b : 0.03	d : 0.03	
^ : 0.42	v : 0.18	f : 0.09	g : 0.06	w : 0.06	x : 0.06	h : 0.03	e : 0.03	i : 0.03	t : 0.03	
^ : 0.42	v : 0.18	u : 0.12	f : 0.06	w : 0.06	x : 0.06	i : 0.03	t : 0.03	g : 0.03	
^ : 0.42	v : 0.18	t : 0.15	u : 0.12	w : 0.06	x : 0.06	
^ : 0.42	v : 0.18	t : 0.15	u : 0.12	w : 0.06	x : 0.06	
^ : 0.42	v : 0.18	t : 0.15	u : 0.12	w : 0.06	x : 0.06	
^ : 0.42	v : 0.18	t : 0.15	u : 0.12	w : 0.06	x : 0.06	
^ : 0.42	v : 0.18	t : 0.15	u : 0.12	w : 0.06	x : 0.06	
^ : 0.42	v : 0.18	t : 0.15	u : 0.12	w : 0.06	x : 0.06	
^ : 0.42	v : 0.18	t : 0.15	u : 0.12	w : 0.06	x : 0.06	
^ : 0.42	v : 0.18	t : 0.15	u : 0.12	w : 0.06	x : 0.06	
^ : 0.42	v : 0.18	t : 0.15	u : 0.12	w : 0.06	x : 0.06	
^ : 0.42	v : 0.18	u : 0.12	t : 0.12	w : 0.06	x : 0.06	f : 0.03	
^ : 0.42	v : 0.18	u : 0.12	t : 0.12	w : 0.06	x : 0.06	f : 0.03	
f : 0.24	d : 0.18	e : 0.15	g : 0.15	h : 0.06	^ : 0.06	w : 0.06	b : 0.06	i : 0.03	
f : 0.27	d : 0.18	e : 0.15	g : 0.15	h : 0.06	^ : 0.06	b : 0.06	i : 0.03	c : 0.03	
f : 0.27	d : 0.18	e : 0.15	g : 0.15	h : 0.06	^ : 0.06	] : 0.06	i : 0.03	c : 0.03	
f : 0.27	e : 0.18	g : 0.18	d : 0.18	h : 0.06	^ : 0.06	i : 0.03	c : 0.03	
f : 0.24	e : 0.18	g : 0.18	] : 0.09	h : 0.06	c : 0.06	2 : 0.06	i : 0.03	5 : 0.03	^ : 0.03	4 : 0.03	
f : 0.24	g : 0.18	: : 0.09	c : 0.09	h : 0.06	3 : 0.06	d : 0.06	e : 0.06	2 : 0.06	i : 0.03	5 : 0.03	4 : 0.03	

#score	624.2974066728545
#seq	33
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_CDS_m3_run2.txt

#BEAR
c####eeeee[ammmma]eeeee22cc	chr18:54353093-54353333(+)$1	240	136	163	10.5130
ee!!ccc!!cccmmmmccc22ccc]ee	chr12:123687443-123687683(-)$1	240	199	226	13.7618
[ggggggg[cccmmmmccc]ggggggg	chr17:48445381-48445672(-)$1	291	214	241	13.6362
ddd[eeeee[bbmmmmbb22eeeee]d	chr19:50295173-50295413(+)$1	240	49	76	10.2418
ii!!ccc!!cccmmmmccc]ccciiii	chr1:242020636-242020876(+)$1	240	67	94	14.2466
iiiii[bbddddmmmmdddd22bb]ii	chr2:207655237-207655477(+)$1	240	131	158	10.6638
dd"""ccc[cccmmmmccc22ccc]dd	chr11:68707012-68707252(+)$1	240	184	211	13.1741
CCeeeee!!cccmmmmccc333eeeee	chr12:85677346-85677586(+)$1	240	134	161	11.2382
b[gggggggcccmmmmccc]ggggggg	chr2:136615375-136615655(-)$1	280	36	63	13.2481
ddd[bb[a[cccmmmmccca]bb]ddd	chr21:38269116-38269356(-)$1	240	210	237	11.7687
d[cccgggggggmmmmggggggg22cc	chr3:45636344-45636584(+)$1	240	138	165	11.4333
iiiiii[a!!bbmmmmbb]a]iiiiii	chr1:47101374-47101615(-)$1	241	25	52	12.6830
eeeee[a!!cccmmmmccc22aeeeee	chr1:54262546-54262786(-)$1	240	78	105	13.2117
bb[iiiiiiiiimmmmiiiiiiiii]b	chr6:89856150-89856390(+)$1	240	212	239	11.7936
b[eeeee[acccmmmmccc]a]eeeee	chr17:74732838-74733192(-)$1	354	55	82	12.4200
ddd[a!!eeeeemmmmeeeee22addd	chrX:119565134-119565374(-)$1	240	94	121	10.4010
eeee!!a!!cccmmmmccc22a22eee	chr1:46494463-46494704(+)$1	241	20	47	13.6714
:ccc!!bb[cccmmmmccc]bb22ccc	chrX:24190738-24190986(+)$1	248	1	28	11.4978
c####gggggggmmmmggggggg]ccc	chr15:99671610-99671850(+)$1	240	52	79	11.9478
ee"""ccc!!bbmmmmbb22ccc4444	chr11:35747419-35747665(+)$1	246	86	113	11.8298
ggg"""ffffffmmmmffffff333gg	chr3:37100265-37100505(-)$1	240	52	79	11.0150
ccc[ccc!!cccmmmmccc333ccc]c	chr5:176959427-176959669(-)$1	242	51	78	14.4260
hhhhhhhh[cccmmmmccc]hhhhhhh	chr5:112348995-112349235(+)$1	240	68	95	10.9225
ddd"""dddd[ammmma]dddd4444d	chrX:18961727-18961967(-)$1	240	23	50	10.4477
$$a[bb!!ddddmmmmdddd333bb]a	chr14:94545340-94545595(-)$1	255	166	193	10.8468
eeee[bb!!cccmmmmccc4444bb]e	chr1:160247833-160248073(-)$1	240	22	49	12.7934
gggggg!!ddddmmmmdddd4444ggg	chrX:53574826-53575106(-)$1	280	248	275	12.0111
d[bb[bb!!cccmmmmccc]bb22bb]	chr20:60879431-60879690(+)$1	259	178	205	11.5749
eeeee!!eeeeemmmmeeeee22eeee	chr1:161816206-161816446(+)$1	240	80	107	10.3593
ggggg####cccmmmmccc4444gggg	chr1:229779249-229779529(+)$1	280	32	59	14.0315
====bb####bbmmmmbb333bb333=	chr12:6958822-6959062(-)$1	240	134	161	12.4258
Bffffff!!cccmmmmccc22ffffff	chr11:122930581-122930821(-)$1	240	23	50	11.0898
:===========mmmm===========	chr1:62253403-62253643(+)$1	240	2	29	12.6198
#ccca!!eeeeemmmmeeeee22a]cc	chr17:40120504-40120784(+)$1	280	188	215	10.8555
b[==========mmmm==========]	chr7:77549627-77549867(+)$1	240	187	214	13.2961
iiiiiiieeeeemmmmeeeee]iiiii	chr11:95591628-95591868(-)$1	240	54	81	11.5688
""ccc!!eeeeemmmmeeeee22cccc	chr3:107474353-107474593(+)$1	240	195	222	10.7686
ccc[dddd[cccmmmmccc]dddd]cc	chr1:155217809-155218089(-)$1	280	206	233	12.1060
eeeee####cccmmmmccc]eeeee]h	chr10:105201979-105202219(+)$1	240	150	177	12.9698
""gggggggcccmmmmccc]ggggggg	chr17:56772191-56772431(+)$1	240	84	111	13.3174
iiiiiiii[cccmmmmccc]iiiiiii	chr12:42853565-42853805(-)$1	240	181	208	14.3928
d[a[ccca!!bbmmmmbb22a]ccca]	chr19:13135914-13136154(+)$1	240	86	113	11.8296
ccc!!gggggggmmmmggggggg]ccc	chr4:76571482-76571722(-)$1	240	162	189	12.0634
eee!!ddddcccmmmmccc22dddd44	chr20:62614406-62614655(+)$1	249	15	42	11.8406
iii[a"""ddddmmmmdddd4444a]i	chr6:3085484-3085729(+)$1	245	125	152	12.4527
iiiiiii!!cccmmmmccciiiiiiii	chr12:125466963-125467203(-)$1	240	177	204	14.3371
======!!ddddmmmmdddd=======	chr3:195006430-195006673(-)$1	243	79	106	12.7666
iiiiiiiiicccmmmmccc]iiiiiii	chr8:37729983-37730223(-)$1	240	112	139	14.0977
ff"""ccc[cccmmmmccc]ccc333f	chr1:214500930-214501170(+)$1	240	143	170	13.5042
gggeeeee!!bbmmmmbbeeeee4444	chr19:19648191-19648431(+)$1	240	7	34	10.8199
============mmmm===========	chr6:118015197-118015437(+)$1	240	163	190	13.5788
"eeeee####bbmmmmbb333eeeee]	chr1:182823089-182823329(+)$1	240	128	155	11.6712
eeeee####cccmmmmccc333eeeee	chr10:101165430-101165670(-)$1	240	74	101	13.5982

#otherMatches

#Seq PSSM
CUGGAUUGUUACCUCGGAAAUAAGUGA	chr18:54353093-54353333(+)$1	240	136	163	10.5130
AUAGACUCAUUUUCACAAGCAAGUAAU	chr12:123687443-123687683(-)$1	240	199	226	13.7618
CUUUGAUGUCCUGUUGAGGCCAUCGGA	chr17:48445381-48445672(-)$1	291	214	241	13.6362
GCCCUGUGCCUCCUUCGACUGUACAAG	chr19:50295173-50295413(+)$1	240	49	76	10.2418
UUGGCCUAUCUUAACAAAGCGGGAAUU	chr1:242020636-242020876(+)$1	240	67	94	14.2466
AAAAUGCGGCAUUUGAAUGCAAUGGGU	chr2:207655237-207655477(+)$1	240	131	158	10.6638
UGACCGGCCGCAUCCUUGCACGCCCCG	chr11:68707012-68707252(+)$1	240	184	211	13.1741
GGGGAUAAAUGUGAUAGCAAUGUAUCC	chr12:85677346-85677586(+)$1	240	134	161	11.2382
ccagcuUGAAAGACAGCUUCUUAGGCU	chr2:136615375-136615655(-)$1	280	36	63	13.2481
AGGUCUGCAUCUGCUCAGAGGAGUCCU	chr21:38269116-38269356(-)$1	240	210	237	11.7687
AACCCCGAGUUUGAGGAAACUCGCAGG	chr3:45636344-45636584(+)$1	240	138	165	11.4333
CUGAUCGGAAAGAGACCUACGGGUUAG	chr1:47101374-47101615(-)$1	241	25	52	12.6830
GAGCCCAUUUGGGACCCCAUUUGGCUC	chr1:54262546-54262786(-)$1	240	78	105	13.2117
CUGCCCGGGUCGGGGGCGACCCGGGAA	chr6:89856150-89856390(+)$1	240	212	239	11.7936
AAGUACGGGCGCGUCGGCGACGUGUAC	chr17:74732838-74733192(-)$1	354	55	82	12.4200
GCCCAUAGCGGUGGGAGCUGCCUUGGC	chrX:119565134-119565374(-)$1	240	94	121	10.4010
CCAGGGCUAUGGGAAGCCAGUGGACUG	chr1:46494463-46494704(+)$1	241	20	47	13.6714
UUGAGUGUCUCAGAAAUGAAACUAUCA	chrX:24190738-24190986(+)$1	248	1	28	11.4978
CGGUGGUUCGGGAGAGCCUGAGCAGGC	chr15:99671610-99671850(+)$1	240	52	79	11.9478
AGGAAUUUAAGAAAGUUCAGAAAGUGA	chr11:35747419-35747665(+)$1	246	86	113	11.8298
GGCUUCAUUUGAGAGAUUGGAUCUUGC	chr3:37100265-37100505(-)$1	240	52	79	11.0150
GUUUGCACACAGUGGCCUGGCUUGCCA	chr5:176959427-176959669(-)$1	242	51	78	14.4260
ACAUGCUGAGGGACAGCCCGUGGCAUG	chr5:112348995-112349235(+)$1	240	68	95	10.9225
UCAUACCUGUGUUUGUAGGCAGCUCUU	chrX:18961727-18961967(-)$1	240	23	50	10.4477
CCUGACCUUGGCACCUGCCAUCCGUGA	chr14:94545340-94545595(-)$1	255	166	193	10.8468
UAACCUUUUACAUUAUUGUUAUUAAUG	chr1:160247833-160248073(-)$1	240	22	49	12.7934
AAGCACAGGCUAAUUCUGGCAGCGGUG	chrX:53574826-53575106(-)$1	280	248	275	12.0111
AAGCGGCUUUUCUUCUGGAUGCAGGUA	chr20:60879431-60879690(+)$1	259	178	205	11.5749
AAAUCAAAGGAGGCACCUUCUAGGAUU	chr1:161816206-161816446(+)$1	240	80	107	10.3593
CCUGAAAUUCCUGUUCAGGUCACUCAG	chr1:229779249-229779529(+)$1	280	32	59	14.0315
GGCACCUUUAUCUUCUGAAUUGGACUU	chr12:6958822-6959062(-)$1	240	134	161	12.4258
CGGAUUAUUUUAAGAUUAAUUUGAUCC	chr11:122930581-122930821(-)$1	240	23	50	11.0898
AUUUUGUCUUUUUCUUGAAGGAUGGAA	chr1:62253403-62253643(+)$1	240	2	29	12.6198
AAGCCGGCCAGGUCUUCCUGGAAGAGC	chr17:40120504-40120784(+)$1	280	188	215	10.8555
UGAUUUUAUAUUAGCCAAUGUAAAGUG	chr7:77549627-77549867(+)$1	240	187	214	13.2961
UUCCUAAAUCUUUUCUAGGAUAUUAGG	chr11:95591628-95591868(-)$1	240	54	81	11.5688
GAUAAGAUCUGCAGAGGUGGAAAUUAC	chr3:107474353-107474593(+)$1	240	195	222	10.7686
AGCCCCAGACCCCAGUGGGACUGGAGC	chr1:155217809-155218089(-)$1	280	206	233	12.1060
UGCAGUACAUGGCUUUCCACCUGCAGG	chr10:105201979-105202219(+)$1	240	150	177	12.9698
CUUAUUUUACUUUCAGAAGUUGGGAUA	chr17:56772191-56772431(+)$1	240	84	111	13.3174
GUAUUAUUUCUUAACCAAGUAGUGAUG	chr12:42853565-42853805(-)$1	240	181	208	14.3928
CCGAGAUCAAGCAGAAGUGGGCAUCCC	chr19:13135914-13136154(+)$1	240	86	113	11.8296
GAUGACUCUGAACCAGUUCAGAGAAUC	chr4:76571482-76571722(-)$1	240	162	189	12.0634
UCAGACAUUGGGCCCGCCCGUGAUGCA	chr20:62614406-62614655(+)$1	249	15	42	11.8406
AAGCGAAUCCGGAAGCUCGGCCGACAU	chr6:3085484-3085729(+)$1	245	125	152	12.4527
CCUCCCUCCAGGGCCCCCUAGGGAGGG	chr12:125466963-125467203(-)$1	240	177	204	14.3371
AUUUUUAGGUUACGUUUAGCAAGAAUG	chr3:195006430-195006673(-)$1	243	79	106	12.7666
GCUGUGAGCCCUGUUGGGGAGCUUGCA	chr8:37729983-37730223(-)$1	240	112	139	14.0977
UCAUGGCUAUGGGUGGCUGCAGCAGGG	chr1:214500930-214501170(+)$1	240	143	170	13.5042
CCCAAGCGCUGCGCUGGCCGCUUCUCC	chr19:19648191-19648431(+)$1	240	7	34	10.8199
uauauacauauauauguauauguaugu	chr6:118015197-118015437(+)$1	240	163	190	13.5788
CUUGGAAAAUGCUAAAGCUCGUCUAAA	chr1:182823089-182823329(+)$1	240	128	155	11.6712
GUUGUCCUCCACGCCUGUGCACACAAC	chr10:101165430-101165670(-)$1	240	74	101	13.5982

#DB
(....(((((.(....).)))))..))	chr18:54353093-54353333(+)$1	1	136	163	10.5130
((..(((..(((....)))..))).))	chr12:123687443-123687683(-)$1	1	199	226	13.7618
.(((((((.(((....))).)))))))	chr17:48445381-48445672(-)$1	1	214	241	13.6362
(((.(((((.((....))..))))).)	chr19:50295173-50295413(+)$1	1	49	76	10.2418
((..(((..(((....))).)))))))	chr1:242020636-242020876(+)$1	1	67	94	14.2466
(((((.((((((....))))..)).))	chr2:207655237-207655477(+)$1	1	131	158	10.6638
((...(((.(((....)))..))).))	chr11:68707012-68707252(+)$1	1	184	211	13.1741
(((((((..(((....)))...)))))	chr12:85677346-85677586(+)$1	1	134	161	11.2382
(.((((((((((....))).)))))))	chr2:136615375-136615655(-)$1	1	36	63	13.2481
(((.((.(.(((....)))).)).)))	chr21:38269116-38269356(-)$1	1	210	237	11.7687
(.((((((((((....)))))))..))	chr3:45636344-45636584(+)$1	1	138	165	11.4333
((((((.(..((....)).).))))))	chr1:47101374-47101615(-)$1	1	25	52	12.6830
(((((.(..(((....)))..))))))	chr1:54262546-54262786(-)$1	1	78	105	13.2117
((.(((((((((....))))))))).)	chr6:89856150-89856390(+)$1	1	212	239	11.7936
(.(((((.((((....))).).)))))	chr17:74732838-74733192(-)$1	1	55	82	12.4200
(((.(..(((((....)))))..))))	chrX:119565134-119565374(-)$1	1	94	121	10.4010
((((..(..(((....)))..)..)))	chr1:46494463-46494704(+)$1	1	20	47	13.6714
.(((..((.(((....))).))..)))	chrX:24190738-24190986(+)$1	1	1	28	11.4978
(....(((((((....))))))).)))	chr15:99671610-99671850(+)$1	1	52	79	11.9478
((...(((..((....))..)))....	chr11:35747419-35747665(+)$1	1	86	113	11.8298
(((...((((((....))))))...))	chr3:37100265-37100505(-)$1	1	52	79	11.0150
(((.(((..(((....)))...))).)	chr5:176959427-176959669(-)$1	1	51	78	14.4260
((((((((.(((....))).)))))))	chr5:112348995-112349235(+)$1	1	68	95	10.9225
(((...((((.(....).))))....)	chrX:18961727-18961967(-)$1	1	23	50	10.4477
..(.((..((((....))))...)).)	chr14:94545340-94545595(-)$1	1	166	193	10.8468
((((.((..(((....)))....)).)	chr1:160247833-160248073(-)$1	1	22	49	12.7934
((((((..((((....))))....)))	chrX:53574826-53575106(-)$1	1	248	275	12.0111
(.((.((..(((....))).))..)).	chr20:60879431-60879690(+)$1	1	178	205	11.5749
(((((..(((((....)))))..))))	chr1:161816206-161816446(+)$1	1	80	107	10.3593
(((((....(((....)))....))))	chr1:229779249-229779529(+)$1	1	32	59	14.0315
((((((....((....))...))...)	chr12:6958822-6959062(-)$1	1	134	161	12.4258
(((((((..(((....)))..))))))	chr11:122930581-122930821(-)$1	1	23	50	11.0898
.(((((((((((....)))))))))))	chr1:62253403-62253643(+)$1	1	2	29	12.6198
.((((..(((((....)))))..).))	chr17:40120504-40120784(+)$1	1	188	215	10.8555
(.((((((((((....)))))))))).	chr7:77549627-77549867(+)$1	1	187	214	13.2961
((((((((((((....))))).)))))	chr11:95591628-95591868(-)$1	1	54	81	11.5688
..(((..(((((....)))))..))))	chr3:107474353-107474593(+)$1	1	195	222	10.7686
(((.((((.(((....))).)))).))	chr1:155217809-155218089(-)$1	1	206	233	12.1060
(((((....(((....))).))))).)	chr10:105201979-105202219(+)$1	1	150	177	12.9698
..((((((((((....))).)))))))	chr17:56772191-56772431(+)$1	1	84	111	13.3174
((((((((.(((....))).)))))))	chr12:42853565-42853805(-)$1	1	181	208	14.3928
(.(.((((..((....))..).)))).	chr19:13135914-13136154(+)$1	1	86	113	11.8296
(((..(((((((....))))))).)))	chr4:76571482-76571722(-)$1	1	162	189	12.0634
(((..(((((((....)))..))))..	chr20:62614406-62614655(+)$1	1	15	42	11.8406
(((.(...((((....))))....).)	chr6:3085484-3085729(+)$1	1	125	152	12.4527
(((((((..(((....)))))))))))	chr12:125466963-125467203(-)$1	1	177	204	14.3371
((((((..((((....)))))))))))	chr3:195006430-195006673(-)$1	1	79	106	12.7666
((((((((((((....))).)))))))	chr8:37729983-37730223(-)$1	1	112	139	14.0977
((...(((.(((....))).)))...)	chr1:214500930-214501170(+)$1	1	143	170	13.5042
((((((((..((....)))))))....	chr19:19648191-19648431(+)$1	1	7	34	10.8199
((((((((((((....)))))))))))	chr6:118015197-118015437(+)$1	1	163	190	13.5788
.(((((....((....))...))))).	chr1:182823089-182823329(+)$1	1	128	155	11.6712
(((((....(((....)))...)))))	chr10:101165430-101165670(-)$1	1	74	101	13.5982

#PSSM
e : 0.16	d : 0.15	i : 0.15	c : 0.09	b : 0.07	g : 0.07	= : 0.05	" : 0.05	: : 0.03	[ : 0.01	C : 0.01	h : 0.01	$ : 0.01	B : 0.01	# : 0.01	f : 0.01	
e : 0.18	i : 0.15	[ : 0.11	g : 0.09	d : 0.09	c : 0.09	= : 0.07	# : 0.03	f : 0.03	" : 0.03	C : 0.01	b : 0.01	h : 0.01	$ : 0.01	
e : 0.18	g : 0.13	i : 0.13	c : 0.13	= : 0.09	d : 0.07	" : 0.05	# : 0.03	! : 0.03	a : 0.03	[ : 0.01	h : 0.01	b : 0.01	f : 0.01	
e : 0.18	[ : 0.15	i : 0.13	g : 0.09	" : 0.09	= : 0.09	! : 0.07	c : 0.07	# : 0.03	h : 0.01	b : 0.01	f : 0.01	
e : 0.16	i : 0.13	c : 0.11	g : 0.09	" : 0.09	! : 0.07	= : 0.07	b : 0.05	a : 0.05	# : 0.03	[ : 0.03	h : 0.01	f : 0.01	d : 0.01	
c : 0.13	g : 0.13	e : 0.11	i : 0.11	! : 0.11	b : 0.09	= : 0.07	" : 0.05	# : 0.05	[ : 0.03	d : 0.03	h : 0.01	f : 0.01	
c : 0.13	! : 0.13	g : 0.11	e : 0.09	i : 0.09	# : 0.09	b : 0.07	d : 0.05	= : 0.05	[ : 0.03	a : 0.03	f : 0.03	h : 0.01	" : 0.01	
! : 0.24	e : 0.15	g : 0.11	# : 0.09	c : 0.05	a : 0.05	i : 0.05	d : 0.05	= : 0.05	b : 0.03	[ : 0.01	f : 0.01	h : 0.01	" : 0.01	
! : 0.26	[ : 0.15	e : 0.13	d : 0.13	g : 0.09	# : 0.09	= : 0.05	i : 0.03	a : 0.01	f : 0.01	
c : 0.49	e : 0.11	d : 0.11	! : 0.07	g : 0.05	= : 0.05	# : 0.03	[ : 0.01	i : 0.01	f : 0.01	
c : 0.49	b : 0.13	d : 0.09	e : 0.09	g : 0.05	= : 0.05	[ : 0.03	i : 0.01	f : 0.01	
c : 0.49	b : 0.13	d : 0.09	e : 0.09	g : 0.05	= : 0.05	a : 0.03	i : 0.01	f : 0.01	
m : 0.99	
m : 0.99	
m : 0.99	
m : 0.99	
c : 0.49	b : 0.13	d : 0.09	e : 0.09	g : 0.05	= : 0.05	a : 0.03	i : 0.01	f : 0.01	
c : 0.49	b : 0.13	d : 0.09	e : 0.09	g : 0.05	= : 0.05	] : 0.03	i : 0.01	f : 0.01	
c : 0.49	e : 0.13	d : 0.11	2 : 0.05	g : 0.05	= : 0.05	3 : 0.03	] : 0.01	i : 0.01	f : 0.01	
] : 0.24	2 : 0.16	e : 0.13	d : 0.11	3 : 0.09	g : 0.05	= : 0.05	a : 0.03	i : 0.03	4 : 0.03	f : 0.01	
e : 0.16	2 : 0.13	g : 0.11	3 : 0.11	i : 0.07	4 : 0.07	= : 0.07	c : 0.05	] : 0.03	a : 0.03	b : 0.03	d : 0.03	f : 0.01	h : 0.01	
g : 0.11	e : 0.09	c : 0.09	2 : 0.09	i : 0.09	3 : 0.07	b : 0.07	4 : 0.07	= : 0.07	] : 0.05	d : 0.05	a : 0.03	f : 0.03	h : 0.01	
e : 0.16	c : 0.13	2 : 0.13	g : 0.11	i : 0.11	4 : 0.09	= : 0.07	b : 0.05	3 : 0.03	d : 0.03	h : 0.01	f : 0.01	
e : 0.15	i : 0.13	2 : 0.09	c : 0.09	4 : 0.09	g : 0.07	= : 0.07	b : 0.05	] : 0.05	3 : 0.05	a : 0.03	d : 0.03	h : 0.01	f : 0.01	
e : 0.16	i : 0.13	c : 0.11	] : 0.09	g : 0.09	= : 0.07	d : 0.05	4 : 0.05	3 : 0.05	b : 0.05	2 : 0.03	h : 0.01	f : 0.01	a : 0.01	
c : 0.15	e : 0.15	] : 0.13	i : 0.13	g : 0.11	4 : 0.07	= : 0.07	d : 0.05	3 : 0.03	h : 0.01	b : 0.01	f : 0.01	a : 0.01	
c : 0.16	e : 0.15	i : 0.15	g : 0.11	d : 0.09	] : 0.07	= : 0.07	4 : 0.05	h : 0.03	f : 0.03	b : 0.01	a : 0.01	

#score	649.7827208993374
#seq	53
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_CDS_m3_run2.txt

#BEAR
[eeeeellleeeee	chr2:44547429-44547654(-)$1	225	117	131	9.7969
eeeeemmmmeeeee	chr3:160155801-160156039(-)$1	238	135	149	10.5030
!eeeeellleeeee	chr10:99629097-99629319(-)$1	222	44	58	9.8123
eeeeennnnneeee	chr1:154197459-154197702(+)$1	243	168	182	9.3473
eeeeennnnneeee	chr14:95592845-95593072(-)$1	227	164	178	9.3473
eeeeennnnneeee	chr1:62148997-62149222(-)$1	225	172	186	9.3473
eeeeennnnneeee	chr10:70204616-70204848(-)$1	232	30	44	9.3473
eeeeellleeeee3	chr3:152017853-152018085(+)$1	232	88	102	9.2775
eeeeeooooooeee	chr6:56919214-56919447(+)$1	233	158	172	8.9039
eeeeemmmmeeeee	chr7:150554567-150554786(+)$1	219	81	95	10.5030
eeeeennnnneeee	chr14:24408825-24409062(-)$1	237	116	130	9.3473
eeeeemmmmeeeee	chr8:126034041-126034264(+)$1	223	64	78	10.5030
eeeeellleeeee]	chr6:13620998-13621223(+)$1	225	188	202	9.3605
eeeeellleeeeed	chr10:133769322-133769552(+)$1	230	158	172	9.4091
:eeeeellleeeee	chr12:72289712-72289940(+)$1	228	52	66	8.8409
eeeeemmmmeeeee	chr10:38407622-38407845(+)$1	223	141	155	10.5030
eeeeeooooooeee	chr16:19518945-19519176(-)$1	231	35	49	8.9039
:eeeeellleeeee	chr1:205683351-205683596(-)$1	245	222	236	8.8409
[eeeeellleeeee	chr17:34894305-34894538(+)$1	233	126	140	9.7969
eeeeemmmmeeeee	chr12:95365161-95365389(-)$1	228	116	130	10.5030
eeeeemmmmeeeee	chr8:67577088-67577309(-)$1	221	142	156	10.5030
eeeeemmmmeeeee	chr19:21992389-21992616(-)$1	227	128	142	10.5030
eeeeeooooooeee	chr3:179051424-179051656(+)$1	232	78	92	8.9039
eeeeemmmmeeeee	chr19:44591305-44591531(+)$1	226	114	128	10.5030
:eeeeellleeeee	chrX:138879342-138879566(-)$1	224	188	202	8.8409
[eeeeellleeeee	chr17:33679289-33679524(-)$1	235	58	72	9.7969
eeeeennnnneeee	chr20:47686683-47686915(+)$1	232	97	111	9.3473
eeeeeooooooeee	chr3:69072256-69072483(-)$1	227	131	145	8.9039
eeeee4444eeeee	chr3:56707578-56707805(-)$1	227	114	128	8.8489
eeeeemmmmeeeee	chr17:34044133-34044358(+)$1	225	102	116	10.5030
eeeeemmmmeeeee	chr3:73432403-73432627(-)$1	224	19	33	10.5030
eeeeennnnneeee	chr15:41672279-41672572(+)$1	293	238	252	9.3473
eeeeellleeeeeh	chr13:45007945-45008224(-)$1	279	120	134	9.2473
eeeeemmmmeeeee	chrX:107976286-107976529(-)$1	243	5	19	10.5030
eeeeemmmmeeeee	chrM:11097-11374(+)$1	277	57	71	10.5030
eeeeemmmmeeeee	chr7:64863384-64863612(+)$1	228	148	162	10.5030
eeeeellleeeee]	chr1:54678086-54678318(+)$1	232	201	215	9.3605
eeeeemmmmeeeee	chr19:37210742-37210962(+)$1	220	199	213	10.5030
eeeeemmmmeeeee	chrX:73815594-73815821(-)$1	227	0	14	10.5030
eeeeemmmmeeeee	chrX:18264707-18264939(-)$1	232	124	138	10.5030
:eeeeellleeeee	chr18:77737561-77737785(-)$1	224	145	159	8.8409
eeeeemmmmeeeee	chr15:83686713-83686938(-)$1	225	23	37	10.5030
eeeeemmmmeeeee	chr12:120534657-120534878(-)$1	221	92	106	10.5030
eeeeemmmmeeeee	chr9:78808124-78808363(+)$1	239	83	97	10.5030
eeeeennnnneeee	chr12:25362603-25362855(-)$1	252	38	52	9.3473
deeeeellleeeee	chr6:138727075-138727309(+)$1	234	74	88	9.7631
eeeeemmmmeeeee	chrX:23803365-23803586(+)$1	221	149	163	10.5030
eeeeemmmmeeeee	chr11:61188861-61189094(-)$1	233	170	184	10.5030
eeeeemmmmeeeee	chr12:50535760-50535987(-)$1	227	57	71	10.5030
eeeeemmmmeeeee	chr18:77893409-77893655(+)$1	246	9	23	10.5030
eeeeennnnneeee	chr1:109952484-109952709(-)$1	225	0	14	9.3473
!eeeeellleeeee	chr22:46725152-46725378(+)$1	226	23	37	9.8123
eeeee4444eeeee	chrM:7153-7384(+)$1	231	116	130	8.8489

#otherMatches

#Seq PSSM
UUUAACAGUGUUGA	chr2:44547429-44547654(-)$1	225	117	131	9.7969
AAGUGAAAUCACUU	chr3:160155801-160156039(-)$1	238	135	149	10.5030
GCAGGAGCUUCCUG	chr10:99629097-99629319(-)$1	222	44	58	9.8123
CCCGGGGAAACUGG	chr1:154197459-154197702(+)$1	243	168	182	9.3473
AUACCAAGUAGGUA	chr14:95592845-95593072(-)$1	227	164	178	9.3473
UAUAUUAUUCAUAU	chr1:62148997-62149222(-)$1	225	172	186	9.3473
GAUGGCAUUCUCAU	chr10:70204616-70204848(-)$1	232	30	44	9.3473
UUGGUUUCACUGAA	chr3:152017853-152018085(+)$1	232	88	102	9.2775
AGCUAAAAAGAUAG	chr6:56919214-56919447(+)$1	233	158	172	8.9039
CUGCAGGCAUGCAG	chr7:150554567-150554786(+)$1	219	81	95	10.5030
guaauuuuccauua	chr14:24408825-24409062(-)$1	237	116	130	9.3473
CAGUAGUGGUGCUG	chr8:126034041-126034264(+)$1	223	64	78	10.5030
AUUCUUCUGGAGUA	chr6:13620998-13621223(+)$1	225	188	202	9.3605
AGGACCAAGUCUUG	chr10:133769322-133769552(+)$1	230	158	172	9.4091
ACCGGUAUCACUGG	chr12:72289712-72289940(+)$1	228	52	66	8.8409
GAAGUCAGAACUUU	chr10:38407622-38407845(+)$1	223	141	155	10.5030
UUUAAUCAAUUUUA	chr16:19518945-19519176(-)$1	231	35	49	8.9039
GGGGUAUAGUACUC	chr1:205683351-205683596(-)$1	245	222	236	8.8409
AUAUUUGCAAGAUA	chr17:34894305-34894538(+)$1	233	126	140	9.7969
UUCUACCACUAGAA	chr12:95365161-95365389(-)$1	228	116	130	10.5030
UUGGAGAUGUUCAA	chr8:67577088-67577309(-)$1	221	142	156	10.5030
CCAUAAAAGUGUGG	chr19:21992389-21992616(-)$1	227	128	142	10.5030
CAUGCCAAACUGCA	chr3:179051424-179051656(+)$1	232	78	92	8.9039
uccauauuuauggg	chr19:44591305-44591531(+)$1	226	114	128	10.5030
CUUGGUAUAACCAA	chrX:138879342-138879566(-)$1	224	188	202	8.8409
CAGCUGACCCAGCU	chr17:33679289-33679524(-)$1	235	58	72	9.7969
AUGAAUAAUUUUCA	chr20:47686683-47686915(+)$1	232	97	111	9.3473
ACUUUUAAGACAAA	chr3:69072256-69072483(-)$1	227	131	145	8.9039
UCUUCUUACCUUGA	chr3:56707578-56707805(-)$1	227	114	128	8.8489
AAACAACAAUGUUU	chr17:34044133-34044358(+)$1	225	102	116	10.5030
UGGAUGACGAUCCA	chr3:73432403-73432627(-)$1	224	19	33	10.5030
CAUGGGUUCUUCAU	chr15:41672279-41672572(+)$1	293	238	252	9.3473
GUAGUGUAACUAUU	chr13:45007945-45008224(-)$1	279	120	134	9.2473
UGAAGUAAUUUUCA	chrX:107976286-107976529(-)$1	243	5	19	10.5030
UCAUCACCCGAUGA	chrM:11097-11374(+)$1	277	57	71	10.5030
GAAAGAAACCUUUC	chr7:64863384-64863612(+)$1	228	148	162	10.5030
UUGCUUUUGGCAGU	chr1:54678086-54678318(+)$1	232	201	215	9.3605
AUGAGAAAACUCAU	chr19:37210742-37210962(+)$1	220	199	213	10.5030
UUCAUCAAUAUGGA	chrX:73815594-73815821(-)$1	227	0	14	10.5030
AGUCUCCCAGGAUU	chrX:18264707-18264939(-)$1	232	124	138	10.5030
UGUAUGAGUUAUAC	chr18:77737561-77737785(-)$1	224	145	159	8.8409
AAGCAAGACUGUUU	chr15:83686713-83686938(-)$1	225	23	37	10.5030
GCGGACUGAUUCGC	chr12:120534657-120534878(-)$1	221	92	106	10.5030
UCUGUGCCAACGGA	chr9:78808124-78808363(+)$1	239	83	97	10.5030
UUCGAGAAAUUCGA	chr12:25362603-25362855(-)$1	252	38	52	9.3473
AGCCUGGUUCAGGU	chr6:138727075-138727309(+)$1	234	74	88	9.7631
UGAGGACUUCUUCG	chrX:23803365-23803586(+)$1	221	149	163	10.5030
CUGUAUACCUACAG	chr11:61188861-61189094(-)$1	233	170	184	10.5030
UGGACAUUUGUCUA	chr12:50535760-50535987(-)$1	227	57	71	10.5030
AGUCCUCAGGGACU	chr18:77893409-77893655(+)$1	246	9	23	10.5030
AAAGGGAAAAUCUU	chr1:109952484-109952709(-)$1	225	0	14	9.3473
AUGAGCAAAGCUCA	chr22:46725152-46725378(+)$1	226	23	37	9.8123
GUAGGCUCAUUCAU	chrM:7153-7384(+)$1	231	116	130	8.8489

#DB
.(((((...)))))	chr2:44547429-44547654(-)$1	1	117	131	9.7969
(((((....)))))	chr3:160155801-160156039(-)$1	1	135	149	10.5030
.(((((...)))))	chr10:99629097-99629319(-)$1	1	44	58	9.8123
(((((.....))))	chr1:154197459-154197702(+)$1	1	168	182	9.3473
(((((.....))))	chr14:95592845-95593072(-)$1	1	164	178	9.3473
(((((.....))))	chr1:62148997-62149222(-)$1	1	172	186	9.3473
(((((.....))))	chr10:70204616-70204848(-)$1	1	30	44	9.3473
(((((...))))).	chr3:152017853-152018085(+)$1	1	88	102	9.2775
(((((......)))	chr6:56919214-56919447(+)$1	1	158	172	8.9039
(((((....)))))	chr7:150554567-150554786(+)$1	1	81	95	10.5030
(((((.....))))	chr14:24408825-24409062(-)$1	1	116	130	9.3473
(((((....)))))	chr8:126034041-126034264(+)$1	1	64	78	10.5030
(((((...))))).	chr6:13620998-13621223(+)$1	1	188	202	9.3605
(((((...)))))(	chr10:133769322-133769552(+)$1	1	158	172	9.4091
.(((((...)))))	chr12:72289712-72289940(+)$1	1	52	66	8.8409
(((((....)))))	chr10:38407622-38407845(+)$1	1	141	155	10.5030
(((((......)))	chr16:19518945-19519176(-)$1	1	35	49	8.9039
.(((((...)))))	chr1:205683351-205683596(-)$1	1	222	236	8.8409
.(((((...)))))	chr17:34894305-34894538(+)$1	1	126	140	9.7969
(((((....)))))	chr12:95365161-95365389(-)$1	1	116	130	10.5030
(((((....)))))	chr8:67577088-67577309(-)$1	1	142	156	10.5030
(((((....)))))	chr19:21992389-21992616(-)$1	1	128	142	10.5030
(((((......)))	chr3:179051424-179051656(+)$1	1	78	92	8.9039
(((((....)))))	chr19:44591305-44591531(+)$1	1	114	128	10.5030
.(((((...)))))	chrX:138879342-138879566(-)$1	1	188	202	8.8409
.(((((...)))))	chr17:33679289-33679524(-)$1	1	58	72	9.7969
(((((.....))))	chr20:47686683-47686915(+)$1	1	97	111	9.3473
(((((......)))	chr3:69072256-69072483(-)$1	1	131	145	8.9039
)))))....)))))	chr3:56707578-56707805(-)$1	1	114	128	8.8489
(((((....)))))	chr17:34044133-34044358(+)$1	1	102	116	10.5030
(((((....)))))	chr3:73432403-73432627(-)$1	1	19	33	10.5030
(((((.....))))	chr15:41672279-41672572(+)$1	1	238	252	9.3473
(((((...)))))(	chr13:45007945-45008224(-)$1	1	120	134	9.2473
(((((....)))))	chrX:107976286-107976529(-)$1	1	5	19	10.5030
(((((....)))))	chrM:11097-11374(+)$1	1	57	71	10.5030
(((((....)))))	chr7:64863384-64863612(+)$1	1	148	162	10.5030
(((((...))))).	chr1:54678086-54678318(+)$1	1	201	215	9.3605
(((((....)))))	chr19:37210742-37210962(+)$1	1	199	213	10.5030
(((((....)))))	chrX:73815594-73815821(-)$1	1	0	14	10.5030
(((((....)))))	chrX:18264707-18264939(-)$1	1	124	138	10.5030
.(((((...)))))	chr18:77737561-77737785(-)$1	1	145	159	8.8409
(((((....)))))	chr15:83686713-83686938(-)$1	1	23	37	10.5030
(((((....)))))	chr12:120534657-120534878(-)$1	1	92	106	10.5030
(((((....)))))	chr9:78808124-78808363(+)$1	1	83	97	10.5030
(((((.....))))	chr12:25362603-25362855(-)$1	1	38	52	9.3473
)(((((...)))))	chr6:138727075-138727309(+)$1	1	74	88	9.7631
(((((....)))))	chrX:23803365-23803586(+)$1	1	149	163	10.5030
(((((....)))))	chr11:61188861-61189094(-)$1	1	170	184	10.5030
(((((....)))))	chr12:50535760-50535987(-)$1	1	57	71	10.5030
(((((....)))))	chr18:77893409-77893655(+)$1	1	9	23	10.5030
(((((.....))))	chr1:109952484-109952709(-)$1	1	0	14	9.3473
.(((((...)))))	chr22:46725152-46725378(+)$1	1	23	37	9.8123
)))))....)))))	chrM:7153-7384(+)$1	1	116	130	8.8489

#PSSM
e : 0.81	: : 0.07	[ : 0.05	! : 0.03	d : 0.01	
e : 0.99	
e : 0.99	
e : 0.99	
e : 0.99	
m : 0.43	e : 0.18	n : 0.16	l : 0.09	o : 0.07	4 : 0.03	
m : 0.43	l : 0.28	n : 0.16	o : 0.07	4 : 0.03	
m : 0.43	l : 0.28	n : 0.16	o : 0.07	4 : 0.03	
m : 0.43	l : 0.18	n : 0.16	e : 0.09	o : 0.07	4 : 0.03	
e : 0.75	n : 0.16	o : 0.07	
e : 0.92	o : 0.07	
e : 0.99	
e : 0.99	
e : 0.90	] : 0.03	3 : 0.01	d : 0.01	h : 0.01	

#score	519.8068085577604
#seq	53
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_UTR_m1_run1.txt

#BEAR
hhhh[cccuuuuuuuuuuuuccchhhhh	chr17:74035541-74035774(-)$1	233	36	64	24.7250
eeeee[ccctttttttttttccc]eeee	chr11:59341950-59342192(-)$1	242	82	110	23.5957
fbb[dddduuuuuuuuuuuudddd]bb5	chr17:1946526-1946751(+)$1	225	29	57	22.4995
c[ffffffwwwwwwwwwwwwwwffffff	chr1:33066881-33067108(+)$1	227	130	158	22.1155
gggggggyyyyyyyyyyyyyyyyggggg	chr15:90226752-90227003(+)$1	251	29	57	22.8719
hhhhh[bbuuuuuuuuuuuubb]hhhhh	chr17:21433870-21434093(-)$1	223	46	74	23.7474
:ddddcccuuuuuuuuuuuuccc]dddd	chr3:121435560-121435780(-)$1	220	134	162	22.9225
[ccc[ccctttttttttttccc22ccc]	chr11:74352074-74352296(+)$1	222	166	194	23.8001
gggggggwwwwwwwwwwwwwwggggggg	chr7:40165944-40166191(-)$1	247	79	107	24.1203
!!a!!cccyyyyyyyyyyyyyyyyccc2	chr12:53805620-53805841(+)$1	221	121	149	22.4666
ggggggggvvvvvvvvvvvvvggggggg	chr11:65766728-65766951(-)$1	223	191	219	25.2475
!!eeeeeattttttttttta]eeeeeff	chr5:140956980-140957200(-)$1	220	132	160	23.1764
$ffffffvvvvvvvvvvvvvffffffcc	chr5:61683216-61683441(+)$1	225	21	49	22.7550
"ccc[cccuuuuuuuuuuuuccc]ccc]	chr7:100027371-100027599(+)$1	228	15	43	25.5833
==[bb[bbuuuuuuuuuuuubbbb====	chr17:27209560-27209789(-)$1	229	50	78	23.9204
===[dddduuuuuuuuuuuudddd22==	chr15:69739112-69739342(+)$1	230	61	89	24.6276
hhhhhhhhvvvvvvvvvvvvvhhhhhhh	chr3:97661540-97661769(-)$1	229	74	102	23.4626
=======wwwwwwwwwwwwww=======	chr17:7481088-7481311(+)$1	223	79	107	24.3925
dd!!eeeeettttttttttteeeee22d	chr5:169010973-169011209(+)$1	236	77	105	22.7380
ccc!!bbwwwwwwwwwwwwwwbb22ccc	chr5:80597313-80597554(+)$1	241	1	29	23.1511
d[eeeeeyyyyyyyyyyyyyyyyeeeee	chr3:136062593-136062816(-)$1	223	159	187	21.4892
F::eeeeewwwwwwwwwwwwwweeeee:	chr20:34329904-34330135(-)$1	231	74	102	19.3099
+++eeeeeuuuuuuuuuuuueeeee444	chr2:118588346-118588576(+)$1	230	109	137	22.0989
gggg[ddddtttttttttttdddd22gg	chr7:35840748-35840967(+)$1	219	6	34	23.6427
"""eeeeeuuuuuuuuuuuueeeee333	chr2:25962859-25963082(-)$1	223	126	154	24.4924
fffffcccvvvvvvvvvvvvvccc22ff	chr16:30680935-30681159(+)$1	224	110	138	24.1969
=====[bbvvvvvvvvvvvvvbb]====	chr19:58806200-58806432(+)$1	232	62	90	25.0545
iiiiiii[attttttttttta]iiiiii	chr9:129646911-129647140(+)$1	229	12	40	25.1857
hh[a!!bbuuuuuuuuuuuubb22a]hh	chr16:3740731-3740983(-)$1	252	123	151	24.1636
========uuuuuuuuuuuu========	chr7:133979614-133979841(-)$1	227	27	55	25.7009
#ddddbbvvvvvvvvvvvvvbb]dddd3	chr17:79637171-79637399(+)$1	228	83	111	22.4999
fffff[ccctttttttttttccc333ff	chr3:58307729-58307980(+)$1	251	36	64	23.9031
eeeee[bbuuuuuuuuuuuubbeeeeed	chr1:109475476-109475725(-)$1	249	35	63	23.5450
hhh[ddddvvvvvvvvvvvvvdddd]hh	chr22:38692541-38692813(-)$1	272	123	151	23.9195
ccc!!cccuuuuuuuuuuuuccc22ccc	chr17:47482212-47482437(-)$1	225	22	50	25.4827
da!!ddddyyyyyyyyyyyyyyyydddd	chr4:99428728-99428970(-)$1	242	130	158	20.9347
[ffffffvvvvvvvvvvvvvffffff]c	chr14:103807652-103807891(+)$1	239	22	50	23.0526
'ccc!!ccctttttttttttccc22ccc	chr1:3800120-3800368(-)$1	248	171	199	23.8937
c[eeeeevvvvvvvvvvvvveeeee333	chr7:98258983-98259219(+)$1	236	121	149	24.0986
hhhhhhhhvvvvvvvvvvvvvhhhhhhh	chr15:76136254-76136487(+)$1	233	162	190	23.4626
[bb"""bbvvvvvvvvvvvvvbb333bb	chr16:58315506-58315745(+)$1	239	117	145	23.8480
dhhhhhhhhttttttttttthhhhhhhh	chr17:21730999-21731227(+)$1	228	90	118	21.8116
:bb!!ddddtttttttttttdddd22bb	chr8:98864588-98864807(+)$1	219	97	125	21.6478
hhhhhhhhuuuuuuuuuuuuhhhhhhhh	chr19:41786969-41787194(+)$1	225	76	104	23.2482
gggbbddddtttttttttttdddd]bb>	chr9:125636081-125636332(-)$1	251	171	199	22.0209
gggggg[avvvvvvvvvvvvva]ggggg	chr8:38707431-38707650(+)$1	219	51	79	25.3391
gg"""cccwwwwwwwwwwwwwwccc333	chr5:37290190-37290443(-)$1	253	87	115	24.1051
========uuuuuuuuuuuu========	chr6:135284477-135284719(-)$1	242	86	114	25.7009
hhhhhhhhwwwwwwwwwwwwwwhhhhhh	chr3:43732370-43732600(+)$1	230	118	146	22.3773
bb[fffffftttttttttttffffff]b	chr10:104499540-104499760(+)$1	220	65	93	21.8972
iiiiiiiiitttttttttttiiiiiiii	chr6:31765217-31765447(-)$1	230	113	141	24.4436
dd[eeeeeuuuuuuuuuuuueeeee333	chr17:80215954-80216189(-)$1	235	183	211	24.3302
ee"""cccuuuuuuuuuuuuccc333ee	chr3:63985556-63985776(+)$1	220	118	146	25.0372
bb[eeeeevvvvvvvvvvvvveeeeebb	chr15:64973983-64974204(+)$1	221	77	105	23.4542
ccgggggggtttttttttttggggggg]	chr9:125703243-125703470(+)$1	227	178	206	24.0070
:cccdddduuuuuuuuuuuudddd]ccc	chr2:164592384-164592606(-)$1	222	128	156	23.2850
[ccc[cccvvvvvvvvvvvvvcccccc]	chr14:21955547-21955766(+)$1	219	97	125	25.4265
gggggggyyyyyyyyyyyyyyyyggggg	chr17:47127263-47127484(+)$1	221	85	113	22.8719
ffccc[bbuuuuuuuuuuuubbccc]ff	chr6:105530660-105530880(+)$1	220	81	109	24.0785
#bb[cccvvvvvvvvvvvvvcccbb333	chr5:132441091-132441316(+)$1	225	104	132	24.0214

#otherMatches

#Seq PSSM
UGUGAGAAAAUCCCAGCAAGUUCCAUGA	chr17:74035541-74035774(-)$1	233	36	64	24.7250
GAGAAUUCCCCAACUAAAUUGGACUUCU	chr11:59341950-59342192(-)$1	242	82	110	23.5957
CCUGCCCUGUACUGAAGAAAAGGGGAGC	chr17:1946526-1946751(+)$1	225	29	57	22.4995
uugcagugagccgagaucacaccauugc	chr1:33066881-33067108(+)$1	227	130	158	22.1155
CUGCUUCAGAGAUCGGAAUAAAAGAAGU	chr15:90226752-90227003(+)$1	251	29	57	22.8719
UUUUUAUUGAAAUAAAAUGGGAAAAGAA	chr17:21433870-21434093(-)$1	223	46	74	23.7474
AGCUUCUCCAAGAUAAGAAUGAGCAAGC	chr3:121435560-121435780(-)$1	220	134	162	22.9225
UGGAUACGUUUACCCCUCUUGUCUUCCU	chr11:74352074-74352296(+)$1	222	166	194	23.8001
ugcagugagccaagaucucaccacugca	chr7:40165944-40166191(-)$1	247	79	107	24.1203
UUGCCGUCUCAUCUUCUCUCAUCUGAUC	chr12:53805620-53805841(+)$1	221	121	149	22.4666
UGAGGGAAAAAUAGAGCCUUCUUUCCUC	chr11:65766728-65766951(-)$1	223	191	219	25.2475
CUUGGUCCGAAAUGACUAUGAGGCCAGG	chr5:140956980-140957200(-)$1	220	132	160	23.1764
AGAUGAUUAGCUUCAAAUUUAUUAUUUG	chr5:61683216-61683441(+)$1	225	21	49	22.7550
AGUGGCGGAGGAGAAAGGGGUCGGCGCA	chr7:100027371-100027599(+)$1	228	15	43	25.5833
GGAGCCAGCCCUUGAUCCCUCUGCCCCC	chr17:27209560-27209789(-)$1	229	50	78	23.9204
GAGCUGAUCUUUUUCCUCUUGUCAUUUU	chr15:69739112-69739342(+)$1	230	61	89	24.6276
UGACCUUGCUGAAUUCAAAAACAAGGUU	chr3:97661540-97661769(-)$1	229	74	102	23.4626
ACGAGACGUGAUUAUGAGGGAGUUUCGU	chr17:7481088-7481311(+)$1	223	79	107	24.3925
AGCCGGUCUUAUCUUCCGCUGGACCACC	chr5:169010973-169011209(+)$1	236	77	105	22.7380
ACUAAGCGCGCCACAAACUCAGCCCAGU	chr5:80597313-80597554(+)$1	241	1	29	23.1511
UGUCUUUUUCACAAAAAGCCUUUAAAGA	chr3:136062593-136062816(-)$1	223	159	187	21.4892
UUCUCUAAUUCCAUUGUUUUUUUUAGAU	chr20:34329904-34330135(-)$1	231	74	102	19.3099
CACGUCUCUCUUUUAUUUCUGGGAUAUA	chr2:118588346-118588576(+)$1	230	109	137	22.0989
GUAGGCGCCUUUGGAGAAUCGGCGGGCU	chr7:35840748-35840967(+)$1	219	6	34	23.6427
ACACAGCUAAGAGAUAAGAAGGCUGCAA	chr2:25962859-25963082(-)$1	223	126	154	24.4924
GCUGGAGGGCAAAGGUCAUAACCUCACC	chr16:30680935-30681159(+)$1	224	110	138	24.1969
CACUGGGGAGAAGCCAUACACCUGCAGU	chr19:58806200-58806432(+)$1	232	62	90	25.0545
CCAUAUAGACCUGCGUAuuuugugugug	chr9:129646911-129647140(+)$1	229	12	40	25.1857
ACUCGAUUAUCAGCAGCACAGAGAGCGU	chr16:3740731-3740983(-)$1	252	123	151	24.1636
GUGUGUUUAUCCUCACCACAGAAUGCGC	chr7:133979614-133979841(-)$1	227	27	55	25.7009
CCCAGGUGACCUUCAGAAAGACAUUGGA	chr17:79637171-79637399(+)$1	228	83	111	22.4999
auagaugguaaauguuuuagaccuuuuu	chr3:58307729-58307980(+)$1	251	36	64	23.9031
ggcuauguacuaaaaauaaaacuagcca	chr1:109475476-109475725(-)$1	249	35	63	23.5450
CAGGAGCACCUCUCCACCCACUGCUGCU	chr22:38692541-38692813(-)$1	272	123	151	23.9195
GCUCUCGGAACAUCACCUACCUGCCAGC	chr17:47482212-47482437(-)$1	225	22	50	25.4827
UGGAAUGAAAAAGUAAGUUGAAUAUCAU	chr4:99428728-99428970(-)$1	242	130	158	20.9347
GGUUUGAUUUUGGUCGUUCUUCAGAUGU	chr14:103807652-103807891(+)$1	239	22	50	23.0526
GUGCACUAGUUUUAGGUUCUCUGAGGUA	chr1:3800120-3800368(-)$1	248	171	199	23.8937
GACAUGCCCAUCCUGACAUUGUAUGCUA	chr7:98258983-98259219(+)$1	236	121	149	24.0986
UGGGGGCUUCUGGCCCAUCUCGGUCCCC	chr15:76136254-76136487(+)$1	233	162	190	23.4626
AUGGGGCCGCAAUUAACAACAGGAAACA	chr16:58315506-58315745(+)$1	239	117	145	23.8480
GUCUUUCUGACUACAACAUCCAGAAAGA	chr17:21730999-21731227(+)$1	228	90	118	21.8116
CGCUUUUUACCUUGACUACCUGAAUUGC	chr8:98864588-98864807(+)$1	219	97	125	21.6478
CUUUGCCUAUUUCUUCCGUCAGGCGAAG	chr19:41786969-41787194(+)$1	225	76	104	23.2482
uggcgccacuauacuccuguguggacga	chr9:125636081-125636332(-)$1	251	171	199	22.0209
GCUAAAUCUUUUUGCUGCUGUGUUUUGG	chr8:38707431-38707650(+)$1	219	51	79	25.3391
cugcccgccuccaccucccaaaguguug	chr5:37290190-37290443(-)$1	253	87	115	24.1051
ugcagugagccaugaucacaucacugca	chr6:135284477-135284719(-)$1	242	86	114	25.7009
CGGCGGAGGAGGAGGAGGUGGACUCUGC	chr3:43732370-43732600(+)$1	230	118	146	22.3773
guuguggugagccaagauugcgccacug	chr10:104499540-104499760(+)$1	220	65	93	21.8972
GGCUGGGAAACUUCAAAGCCUUCCCAGU	chr6:31765217-31765447(-)$1	230	113	141	24.4436
ggccuaagccauccucccaccuuagccu	chr17:80215954-80216189(-)$1	235	183	211	24.3302
AUUAGGCUUUAGAUUUUGAUAGCAAUGU	chr3:63985556-63985776(+)$1	220	118	146	25.0372
CUACCUGACCCUACCUCUUCCUCAGGAG	chr15:64973983-64974204(+)$1	221	77	105	23.4542
CCCAGGGGUAUUUUCCGACGGCCCCUGC	chr9:125703243-125703470(+)$1	227	178	206	24.0070
CGUCUUCCCUUCAAAAACUUGGAAUGAU	chr2:164592384-164592606(-)$1	222	128	156	23.2850
UGAAAUCCCACCUAUCUCCUUGGAUUCU	chr14:21955547-21955766(+)$1	219	97	125	25.4265
UAUUGACUCAAGGGAAAAGAACUGUCAG	chr17:47127263-47127484(+)$1	221	85	113	22.8719
GGUGUUGACUACCUCUUGAAUCACAUCU	chr6:105530660-105530880(+)$1	220	81	109	24.0785
ACAACACCUCAUUCUUAACUGUGUGGCC	chr5:132441091-132441316(+)$1	225	104	132	24.0214

#DB
((((.(((............))))))))	chr17:74035541-74035774(-)$1	1	36	64	24.7250
(((((.(((...........))).))))	chr11:59341950-59342192(-)$1	1	82	110	23.5957
(((.((((............)))).)).	chr17:1946526-1946751(+)$1	1	29	57	22.4995
(.((((((..............))))))	chr1:33066881-33067108(+)$1	1	130	158	22.1155
(((((((................)))))	chr15:90226752-90227003(+)$1	1	29	57	22.8719
(((((.((............)).)))))	chr17:21433870-21434093(-)$1	1	46	74	23.7474
.(((((((............))).))))	chr3:121435560-121435780(-)$1	1	134	162	22.9225
.(((.(((...........)))..))).	chr11:74352074-74352296(+)$1	1	166	194	23.8001
(((((((..............)))))))	chr7:40165944-40166191(-)$1	1	79	107	24.1203
..(..(((................))).	chr12:53805620-53805841(+)$1	1	121	149	22.4666
)(((((((.............)))))))	chr11:65766728-65766951(-)$1	1	191	219	25.2475
..((((((...........).)))))))	chr5:140956980-140957200(-)$1	1	132	160	23.1764
.((((((.............))))))))	chr5:61683216-61683441(+)$1	1	21	49	22.7550
.(((.(((............))).))).	chr7:100027371-100027599(+)$1	1	15	43	25.5833
((.((.((............))))))))	chr17:27209560-27209789(-)$1	1	50	78	23.9204
(((.((((............))))..))	chr15:69739112-69739342(+)$1	1	61	89	24.6276
((((((((.............)))))))	chr3:97661540-97661769(-)$1	1	74	102	23.4626
(((((((..............)))))))	chr17:7481088-7481311(+)$1	1	79	107	24.3925
((..(((((...........)))))..)	chr5:169010973-169011209(+)$1	1	77	105	22.7380
(((..((..............))..)))	chr5:80597313-80597554(+)$1	1	1	29	23.1511
(.(((((................)))))	chr3:136062593-136062816(-)$1	1	159	187	21.4892
(..(((((..............))))).	chr20:34329904-34330135(-)$1	1	74	102	19.3099
...(((((............)))))...	chr2:118588346-118588576(+)$1	1	109	137	22.0989
((((.((((...........))))..))	chr7:35840748-35840967(+)$1	1	6	34	23.6427
...(((((............)))))...	chr2:25962859-25963082(-)$1	1	126	154	24.4924
((((((((.............)))..))	chr16:30680935-30681159(+)$1	1	110	138	24.1969
(((((.((.............)).))))	chr19:58806200-58806432(+)$1	1	62	90	25.0545
(((((((.(...........).))))))	chr9:129646911-129647140(+)$1	1	12	40	25.1857
((.(..((............))..).))	chr16:3740731-3740983(-)$1	1	123	151	24.1636
((((((((............))))))))	chr7:133979614-133979841(-)$1	1	27	55	25.7009
.((((((.............)).)))).	chr17:79637171-79637399(+)$1	1	83	111	22.4999
(((((.(((...........)))...))	chr3:58307729-58307980(+)$1	1	36	64	23.9031
(((((.((............)))))))(	chr1:109475476-109475725(-)$1	1	35	63	23.5450
(((.((((.............)))).))	chr22:38692541-38692813(-)$1	1	123	151	23.9195
(((..(((............)))..)))	chr17:47482212-47482437(-)$1	1	22	50	25.4827
((..((((................))))	chr4:99428728-99428970(-)$1	1	130	158	20.9347
.((((((.............)))))).)	chr14:103807652-103807891(+)$1	1	22	50	23.0526
.(((..(((...........)))..)))	chr1:3800120-3800368(-)$1	1	171	199	23.8937
(.(((((.............)))))...	chr7:98258983-98259219(+)$1	1	121	149	24.0986
((((((((.............)))))))	chr15:76136254-76136487(+)$1	1	162	190	23.4626
.((...((.............))...))	chr16:58315506-58315745(+)$1	1	117	145	23.8480
(((((((((...........))))))))	chr17:21730999-21731227(+)$1	1	90	118	21.8116
.((..((((...........))))..))	chr8:98864588-98864807(+)$1	1	97	125	21.6478
((((((((............))))))))	chr19:41786969-41787194(+)$1	1	76	104	23.2482
(((((((((...........)))).)).	chr9:125636081-125636332(-)$1	1	171	199	22.0209
((((((.(.............).)))))	chr8:38707431-38707650(+)$1	1	51	79	25.3391
((...(((..............)))...	chr5:37290190-37290443(-)$1	1	87	115	24.1051
((((((((............))))))))	chr6:135284477-135284719(-)$1	1	86	114	25.7009
((((((((..............))))))	chr3:43732370-43732600(+)$1	1	118	146	22.3773
((.((((((...........)))))).)	chr10:104499540-104499760(+)$1	1	65	93	21.8972
(((((((((...........))))))))	chr6:31765217-31765447(-)$1	1	113	141	24.4436
((.(((((............)))))...	chr17:80215954-80216189(-)$1	1	183	211	24.3302
((...(((............)))...))	chr3:63985556-63985776(+)$1	1	118	146	25.0372
((.(((((.............)))))))	chr15:64973983-64974204(+)$1	1	77	105	23.4542
(((((((((...........))))))).	chr9:125703243-125703470(+)$1	1	178	206	24.0070
.(((((((............)))).)))	chr2:164592384-164592606(-)$1	1	128	156	23.2850
.(((.(((.............)))))).	chr14:21955547-21955766(+)$1	1	97	125	25.4265
(((((((................)))))	chr17:47127263-47127484(+)$1	1	85	113	22.8719
(((((.((............))))).))	chr6:105530660-105530880(+)$1	1	81	109	24.0785
.((.(((.............)))))...	chr5:132441091-132441316(+)$1	1	104	132	24.0214

#PSSM
h : 0.13	g : 0.13	= : 0.09	c : 0.08	d : 0.08	f : 0.06	[ : 0.06	e : 0.05	: : 0.05	! : 0.03	" : 0.03	i : 0.03	# : 0.03	b : 0.03	$ : 0.01	F : 0.01	+ : 0.01	' : 0.01	
h : 0.15	g : 0.13	c : 0.13	b : 0.09	= : 0.09	f : 0.08	d : 0.06	e : 0.05	[ : 0.05	! : 0.03	i : 0.03	: : 0.01	+ : 0.01	" : 0.01	a : 0.01	
h : 0.13	g : 0.13	c : 0.13	e : 0.08	f : 0.08	[ : 0.08	= : 0.08	b : 0.06	" : 0.05	d : 0.03	! : 0.03	i : 0.03	a : 0.01	: : 0.01	+ : 0.01	
e : 0.16	h : 0.11	g : 0.11	f : 0.09	c : 0.09	! : 0.09	[ : 0.06	= : 0.06	" : 0.05	d : 0.03	b : 0.03	i : 0.03	a : 0.01	
e : 0.18	d : 0.11	f : 0.09	g : 0.09	h : 0.09	! : 0.09	[ : 0.08	= : 0.06	" : 0.05	b : 0.03	i : 0.03	c : 0.03	
c : 0.18	e : 0.15	d : 0.13	[ : 0.11	g : 0.09	h : 0.08	f : 0.06	= : 0.05	b : 0.03	i : 0.03	! : 0.03	" : 0.01	
c : 0.23	b : 0.15	e : 0.15	d : 0.13	g : 0.08	h : 0.08	f : 0.06	= : 0.05	i : 0.03	[ : 0.01	
c : 0.21	d : 0.13	b : 0.11	e : 0.09	v : 0.08	h : 0.08	y : 0.05	w : 0.05	f : 0.03	g : 0.03	a : 0.03	= : 0.03	[ : 0.01	i : 0.01	
u : 0.31	v : 0.24	w : 0.11	y : 0.08	c : 0.05	d : 0.05	t : 0.03	e : 0.01	a : 0.01	h : 0.01	f : 0.01	i : 0.01	g : 0.01	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.23	w : 0.11	y : 0.08	
u : 0.31	v : 0.24	t : 0.19	w : 0.11	y : 0.08	c : 0.01	a : 0.01	
c : 0.16	v : 0.16	w : 0.11	d : 0.09	b : 0.09	y : 0.08	e : 0.08	f : 0.05	= : 0.03	h : 0.03	] : 0.01	a : 0.01	i : 0.01	g : 0.01	
c : 0.19	b : 0.15	d : 0.11	e : 0.11	y : 0.08	w : 0.06	h : 0.06	g : 0.05	f : 0.05	= : 0.05	] : 0.01	a : 0.01	i : 0.01	
c : 0.21	e : 0.15	d : 0.11	y : 0.08	h : 0.08	f : 0.06	b : 0.06	] : 0.05	g : 0.05	= : 0.05	2 : 0.03	i : 0.03	
e : 0.16	d : 0.13	h : 0.11	g : 0.09	2 : 0.08	] : 0.06	f : 0.06	c : 0.06	= : 0.05	3 : 0.05	y : 0.03	b : 0.03	i : 0.03	
e : 0.18	h : 0.11	2 : 0.11	g : 0.09	c : 0.09	= : 0.08	f : 0.06	d : 0.06	] : 0.05	3 : 0.05	i : 0.03	a : 0.01	b : 0.01	
c : 0.13	3 : 0.13	h : 0.11	e : 0.09	g : 0.09	= : 0.08	2 : 0.08	f : 0.06	d : 0.05	] : 0.05	b : 0.03	i : 0.03	4 : 0.01	
h : 0.15	c : 0.15	g : 0.11	= : 0.09	e : 0.08	b : 0.08	f : 0.08	3 : 0.08	d : 0.05	i : 0.03	] : 0.03	2 : 0.01	4 : 0.01	
h : 0.15	g : 0.09	c : 0.09	= : 0.09	3 : 0.09	f : 0.08	d : 0.06	] : 0.06	b : 0.06	e : 0.05	i : 0.03	5 : 0.01	2 : 0.01	: : 0.01	4 : 0.01	> : 0.01	

#score	1415.0006379165225
#seq	60
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_CDS_m3_run2.txt

#BEAR
ccccc!!a[ccclllccc]a22ccc]ccc	chr15:69732978-69733207(+)$1	229	124	153	11.6642
ggggggg[cccooooooccc]ggggggg:	chr3:194180500-194180739(-)$1	239	50	79	11.6366
ffffff"""cccnnnnnccc]ffffff]b	chr11:62291708-62291936(-)$1	228	155	184	12.6385
gggg[a"""cccmmmmccca]gggggggb	chr3:15480448-15480717(+)$1	269	193	222	11.8141
Edddd####cccnnnnnccc4444dddd:	chrM:6823-7055(+)$1	232	28	57	12.1618
iiii"""eeeeennnnneeeee]iiiiii	chr15:44941092-44941331(-)$1	239	146	175	10.9615
fff!!ccc[cccnnnnnccc]ccc22fff	chr2:196544704-196544931(+)$1	227	37	66	12.3424
ddddccc!!cccooooooccc]ccc]ddd	chr5:134231912-134232136(+)$1	224	194	223	12.4576
!dddd[a!!cccooooooccc22a]dddd	chr6:5260863-5261088(-)$1	225	152	181	12.6296
c!!dddd!!cccnnnnnccc22dddd22c	chr6:149900965-149901184(+)$1	219	179	208	12.6382
ffffff"""cccmmmmccc]ffffff333	chr9:115014911-115015138(-)$1	227	99	128	10.0475
ggggggg!!ddddllldddd22ggggggg	chr5:86705034-86705269(-)$1	235	25	54	10.6893
ccc[ccc!!cccooooooccc22cccccc	chr20:30345164-30345410(+)$1	246	195	224	13.4549
====$$$$$cccnnnnnccc4444=====	chr19:6413627-6413870(-)$1	243	208	237	14.5336
eee!!gggggggnnnnngggggggeeeee	chr5:74639979-74640200(+)$1	221	177	206	10.7546
ccc[bb"""bboooooobb333bb]ccc:	chr2:223773482-223773728(+)$1	246	0	29	11.1915
iiiiiiiiicccnnnnnccc]iiiiiiii	chr1:94363311-94363536(-)$1	225	187	216	13.4435
ccc!!gggggggnnnnngggggggccc22	chr5:134235167-134235401(+)$1	234	66	95	11.2444
hhhhh"""ddddnnnnndddd4444hhhh	chr5:131008402-131008634(-)$1	232	62	91	11.2921
!!dddd"""cccnnnnncccdddddddd:	chr6:109689956-109690212(-)$1	256	188	217	12.1089
eee[ccc!!cccoooooocccccceeeee	chr1:93307318-93307575(+)$1	257	2	31	12.3879
dddd$$$$$cccooooooccc333dddd:	chr19:13318765-13318994(-)$1	229	58	87	11.8612
==============lll============	chr3:120320995-120321218(+)$1	223	40	69	11.1701
dddccc####bbnnnnnbb4444ccc]dd	chr17:34173964-34174190(+)$1	226	35	64	12.5094
####dddd[cccnnnnnccc]dddd22ee	chr13:100206570-100206803(+)$1	233	7	36	11.0838
d!!dddd"""bbnnnnnbb333dddd444	chr16:11940512-11940749(-)$1	237	111	140	11.8191
[bb!!ccccccaooooooa]ccc22ccc2	chr19:48887386-48887613(-)$1	227	33	62	10.7772
ffggggggg[bbnnnnnbb22ggggggg:	chr5:179149803-179150055(+)$1	252	163	192	10.0237
ee[bb"""ddddnnnnndddd]bb]eeee	chr12:75893488-75893721(+)$1	233	58	87	10.9620
g####gggggggooooooggggggggggg	chr5:133292569-133292858(-)$1	289	214	243	11.0429
iiiii####ccclllccc333iiiiiiii	chr8:95392368-95392596(-)$1	228	131	160	13.1721
f[ccc####ccclllccc333ccc]ffff	chr15:42823584-42823827(+)$1	243	13	42	12.3041
hh"""gggggggnnnnnggggggg]hhhh	chr12:102313839-102314071(+)$1	232	43	72	10.5920
!!ccc####ccclllccc22ccc]fffff	chr20:34240416-34240640(-)$1	224	78	107	11.3134
gggggggccc[bblllbbccc333ggggg	chr6:74472043-74472269(+)$1	226	82	111	10.0547
eeeee"""ddddnnnnndddd333eeeee	chr6:64289828-64290064(+)$1	236	204	233	12.0870
hh[ccc"""cccmmmmccc4444ccc22h	chr13:100214819-100215045(+)$1	226	21	50	11.6007
""dddd!!ddddnnnnndddd22dddd22	chr12:124071276-124071507(+)$1	231	146	175	10.9990
ggggggg[ddddoooooodddd22ggggg	chr6:64421573-64421797(+)$1	224	86	115	10.8386
gggggg"""cccmmmmccc333ggggggg	chr3:129274266-129274510(-)$1	244	85	114	12.8686
+bb[ccc[ddddnnnnndddd]ccc]bb2	chr5:43502387-43502615(-)$1	228	109	138	10.0282
======"""bboooooobb333=======	chr21:34962011-34962238(-)$1	227	172	201	13.7781
[dddd####cccooooooccc333dddd]	chr14:50625220-50625452(-)$1	232	132	161	13.8768
ddd]eeeeecccnnnnncccddddccc[b	chr6:87968446-87968674(+)$1	228	75	104	9.7761
==========oooooo==========ccc	chr4:83368973-83369194(+)$1	221	28	57	11.1760
eee!!ccc[cccoooooocccccc22eee	chr3:32578419-32578641(-)$1	222	161	190	11.7122
gbb!!bb!!cccnnnnnccc22bb22bb]	chr5:79284280-79284509(-)$1	229	121	150	12.0133
=======[ddddnnnnndddd]=======	chr8:124042757-124042989(-)$1	232	138	167	12.5825
####ccc!!cccooooooccc22ccc333	chr8:28837513-28837755(+)$1	242	27	56	13.5322
hhh[ccc[ddddnnnnndddd22ccc]hh	chr6:7845405-7845643(+)$1	238	69	98	11.1651
fffff####bboooooobb333ffffff:	chr9:79874920-79875148(+)$1	228	195	224	10.8972
ee"""ccc[cccoooooocccccc333ee	chr1:32381487-32381717(-)$1	230	51	80	12.2447
!!dddd####cccmmmmccc333dddd77	chr7:6502591-6502824(-)$1	233	37	66	10.0620
c[ccc####ccclllccc4444ccc]ccc	chr17:34892967-34893208(+)$1	241	176	205	12.9258
fffff####cccmmmmccc4444ffffff	chr18:54278163-54278397(-)$1	234	180	209	11.0485
!!bb[gggggggooooooggggggg]bb3	chr11:46689311-46689537(+)$1	226	146	175	10.2623

#otherMatches

#Seq PSSM
CUAGCUUUCUAGUAACUAUAUUGCUCAGA	chr15:69732978-69733207(+)$1	229	124	153	11.6642
AAUGUGGUUUUGUGCAAAAAUUCGCGUUC	chr3:194180500-194180739(-)$1	239	50	79	11.6366
GAUGUCAAAGGUAAAAAGCCAGAUAUUGA	chr11:62291708-62291936(-)$1	228	155	184	12.6385
GGCAGUGACAGUGAUGACUAGUGCUGGAU	chr3:15480448-15480717(+)$1	269	193	222	11.8141
CGGCGUCAAAGUAUUUAGCUGACUCGCCA	chrM:6823-7055(+)$1	232	28	57	12.1618
UUGGUUUGACUCAAGAAGAGUUUUUAAAC	chr15:44941092-44941331(-)$1	239	146	175	10.9615
UUAAAUCUCUUUAGGAAAAAUAGAAAUGA	chr2:196544704-196544931(+)$1	227	37	66	12.3424
UCAGACAGGUAUGUGGAAGUAAUGUGCUG	chr5:134231912-134232136(+)$1	224	194	223	12.4576
UCUCUGUACCGGGCGAUGCUGAGAGAGAG	chr6:5260863-5261088(-)$1	225	152	181	12.6296
AUUUAAAGUAUUAAGGAGAUUAUUUAUUU	chr6:149900965-149901184(+)$1	219	179	208	12.6382
GAUUAUCACCUUUACAAAGAAUAAUCAGU	chr9:115014911-115015138(-)$1	227	99	128	10.0475
UCACAAAAUUUAACAUUUAACAUUUGUGA	chr5:86705034-86705269(-)$1	235	25	54	10.6893
UACUCAAAACAUAGAUUCAUGGUUUGGUA	chr20:30345164-30345410(+)$1	246	195	224	13.4549
GAAAAAAAAAAGUCACUCUUGCUAUUUCU	chr19:6413627-6413870(-)$1	243	208	237	14.5336
AGUAAGUAUUUAAAACCUAAAUAUACUUU	chr5:74639979-74640200(+)$1	221	177	206	10.7546
GAGUACUUAUGAAUAACCACGUGUCUUCA	chr2:223773482-223773728(+)$1	246	0	29	11.1915
AGUAUAGGUGUAUUAGUUAUAACUUGUGC	chr1:94363311-94363536(-)$1	225	187	216	13.4435
UCCCAGCACUUUGAUAAAAAGUGUGGACU	chr5:134235167-134235401(+)$1	234	66	95	11.2444
CUGUGGUAGUUGGCAAACGACAAGACAUG	chr5:131008402-131008634(-)$1	232	62	91	11.2921
GAUUCAUUUGUGUAACUCACUGAAGCCAA	chr6:109689956-109690212(-)$1	256	188	217	12.1089
AGGUGGAACCGUCCCAAAAUGUCCCUUGC	chr1:93307318-93307575(+)$1	257	2	31	12.3879
CAAUCCCGUGUCUCCUUUGAUUUUGUUGU	chr19:13318765-13318994(-)$1	229	58	87	11.8612
UUUUUUUCUGUCUUUACAGGAUAGGAAAG	chr3:120320995-120321218(+)$1	223	40	69	11.1701
CCAGAGUUUUGCCUGCUGCUUUCCUCGUG	chr17:34173964-34174190(+)$1	226	35	64	12.5094
AACCAAUCAGAUUCCACGUCAGAUUCCUG	chr13:100206570-100206803(+)$1	233	7	36	11.0838
GAGCAGUUUUGAUUUCUUCCUUACUGAUG	chr16:11940512-11940749(-)$1	237	111	140	11.8191
CAUUUCGAGGGCUUCUUCGACCUCAUCGC	chr19:48887386-48887613(-)$1	227	33	62	10.7772
GAUUGGGCCAAUGAUGGAUGGGGCCUGAA	chr5:179149803-179150055(+)$1	252	163	192	10.0237
UUUACAAAAGGAGAUAGUUCUAGUCAAGG	chr12:75893488-75893721(+)$1	233	58	87	10.9620
GCCUUUGUUCCAAAACAGUGGAAUACCAU	chr5:133292569-133292858(-)$1	289	214	243	11.0429
AGUUCAAAAGCUGGUGGUGUAGGACUUAA	chr8:95392368-95392596(-)$1	228	131	160	13.1721
UCUUGUUUUUCAGGCUGACACCAACAGAG	chr15:42823584-42823827(+)$1	243	13	42	12.3041
UUAGGAUUAUGUAUAUCACGUAGUGAGUG	chr12:102313839-102314071(+)$1	232	43	72	10.5920
AUGCCCACAGGUGAAGCCAUGGUGGCCUU	chr20:34240416-34240640(-)$1	224	78	107	11.3134
GUGAAAGGAGACGUAACGCUUACAUUUUU	chr6:74472043-74472269(+)$1	226	82	111	10.0547
GUUUCAAAGAUUCCAACGGUCAUAGAAAC	chr6:64289828-64290064(+)$1	236	204	233	12.0870
GUUUUGCGACUUUUUUAAGGAACCAGUCA	chr13:100214819-100215045(+)$1	226	21	50	11.6007
AAAAUAGUGAUGUUCACCAUUGAUAUUGG	chr12:124071276-124071507(+)$1	231	146	175	10.9990
AGAGGAAGAAAAUGACUUUUUUAAUUCUU	chr6:64421573-64421797(+)$1	224	86	115	10.8386
AAAGUGUUUCUAAAGAUAGCACCACUUUU	chr3:129274266-129274510(-)$1	244	85	114	12.8686
ACUUAUUAUUCUAUUCAAGAAGGAUCAGG	chr5:43502387-43502615(-)$1	228	109	138	10.0282
CUUUGGAAAUUGUUGAGAAAAACCAAGGA	chr21:34962011-34962238(-)$1	227	172	201	13.7781
UGUAAACCACAGGAAUUGCUGAGCUUACU	chr14:50625220-50625452(-)$1	232	132	161	13.8768
UGGUGAUUCCCAAAUGAUGGCUUUGAAUU	chr6:87968446-87968674(+)$1	228	75	104	9.7761
UUGUGGAAGAACUGGAUCUUUUACAACUG	chr4:83368973-83369194(+)$1	221	28	57	11.1760
UGAUUCAGUGUAUCACUUUACCUGUUUUA	chr3:32578419-32578641(-)$1	222	161	190	11.7122
UGAGUUUGAUCCUGCCUGGAAGAAUGUCU	chr5:79284280-79284509(-)$1	229	121	150	12.0133
GAAACAGGUAUGUUACCCAUAGUUGUUUU	chr8:124042757-124042989(-)$1	232	138	167	12.5825
UUCUACCUUCAACAUACAUUGUUGGUCUU	chr8:28837513-28837755(+)$1	242	27	56	13.5322
UCCGCAUCUACAAGGACUGUGUUAUGGGG	chr6:7845405-7845643(+)$1	238	69	98	11.1651
AUCUGCCCCUGUCAAAUCAUUCCAGGUAA	chr9:79874920-79875148(+)$1	228	195	224	10.8972
ccUAUAAUAGUACAUUUCUACAUUUUUGG	chr1:32381487-32381717(-)$1	230	51	80	12.2447
CAGUUUGCCAGCAUAAGUGCCAAAGACCA	chr7:6502591-6502824(-)$1	233	37	66	10.0620
UAGUUCCCAUGGUAGCCACUUUGACCAUU	chr17:34892967-34893208(+)$1	241	176	205	12.9258
UUGCUUAAAUGAUACUUCGGGAUAGUAAA	chr18:54278163-54278397(-)$1	234	180	209	11.0485
ACCUGUGAGAAUGUCUGAGUUCUUAGAGU	chr11:46689311-46689537(+)$1	226	146	175	10.2623

#DB
(((((..(.(((...))).)..))).)))	chr15:69732978-69733207(+)$1	1	124	153	11.6642
(((((((.(((......))).))))))).	chr3:194180500-194180739(-)$1	1	50	79	11.6366
((((((...(((.....))).)))))).)	chr11:62291708-62291936(-)$1	1	155	184	12.6385
((((.(...(((....)))).))))))))	chr3:15480448-15480717(+)$1	1	193	222	11.8141
(((((....(((.....)))....)))).	chrM:6823-7055(+)$1	1	28	57	12.1618
((((...(((((.....))))).))))))	chr15:44941092-44941331(-)$1	1	146	175	10.9615
(((..(((.(((.....))).)))..)))	chr2:196544704-196544931(+)$1	1	37	66	12.3424
(((((((..(((......))).))).)))	chr5:134231912-134232136(+)$1	1	194	223	12.4576
.((((.(..(((......)))..).))))	chr6:5260863-5261088(-)$1	1	152	181	12.6296
(..((((..(((.....)))..))))..)	chr6:149900965-149901184(+)$1	1	179	208	12.6382
((((((...(((....))).))))))...	chr9:115014911-115015138(-)$1	1	99	128	10.0475
(((((((..((((...))))..)))))))	chr5:86705034-86705269(-)$1	1	25	54	10.6893
(((.(((..(((......)))..))))))	chr20:30345164-30345410(+)$1	1	195	224	13.4549
((((.....(((.....)))....)))))	chr19:6413627-6413870(-)$1	1	208	237	14.5336
(((..(((((((.....))))))))))))	chr5:74639979-74640200(+)$1	1	177	206	10.7546
(((.((...((......))...)).))).	chr2:223773482-223773728(+)$1	1	0	29	11.1915
((((((((((((.....))).))))))))	chr1:94363311-94363536(-)$1	1	187	216	13.4435
(((..(((((((.....))))))))))..	chr5:134235167-134235401(+)$1	1	66	95	11.2444
(((((...((((.....))))....))))	chr5:131008402-131008634(-)$1	1	62	91	11.2921
..((((...(((.....))))))))))).	chr6:109689956-109690212(-)$1	1	188	217	12.1089
(((.(((..(((......)))))))))))	chr1:93307318-93307575(+)$1	1	2	31	12.3879
((((.....(((......)))...)))).	chr19:13318765-13318994(-)$1	1	58	87	11.8612
((((((((((((((...))))))))))))	chr3:120320995-120321218(+)$1	1	40	69	11.1701
((((((....((.....))....))).))	chr17:34173964-34174190(+)$1	1	35	64	12.5094
....((((.(((.....))).))))..))	chr13:100206570-100206803(+)$1	1	7	36	11.0838
(..((((...((.....))...))))...	chr16:11940512-11940749(-)$1	1	111	140	11.8191
.((..(((((((......).)))..))).	chr19:48887386-48887613(-)$1	1	33	62	10.7772
))(((((((.((.....))..))))))).	chr5:179149803-179150055(+)$1	1	163	192	10.0237
((.((...((((.....)))).)).))))	chr12:75893488-75893721(+)$1	1	58	87	10.9620
(....(((((((......)))))))))))	chr5:133292569-133292858(-)$1	1	214	243	11.0429
(((((....(((...)))...))))))))	chr8:95392368-95392596(-)$1	1	131	160	13.1721
(.(((....(((...)))...))).))))	chr15:42823584-42823827(+)$1	1	13	42	12.3041
((...(((((((.....))))))).))))	chr12:102313839-102314071(+)$1	1	43	72	10.5920
..(((....(((...)))..))).)))))	chr20:34240416-34240640(-)$1	1	78	107	11.3134
((((((((((.((...)))))...)))))	chr6:74472043-74472269(+)$1	1	82	111	10.0547
(((((...((((.....))))...)))))	chr6:64289828-64290064(+)$1	1	204	233	12.0870
((.(((...(((....)))....)))..)	chr13:100214819-100215045(+)$1	1	21	50	11.6007
..((((..((((.....))))..))))..	chr12:124071276-124071507(+)$1	1	146	175	10.9990
(((((((.((((......))))..)))))	chr6:64421573-64421797(+)$1	1	86	115	10.8386
((((((...(((....)))...)))))))	chr3:129274266-129274510(-)$1	1	85	114	12.8686
.((.(((.((((.....)))).))).)).	chr5:43502387-43502615(-)$1	1	109	138	10.0282
((((((...((......))...)))))))	chr21:34962011-34962238(-)$1	1	172	201	13.7781
.((((....(((......)))...)))).	chr14:50625220-50625452(-)$1	1	132	161	13.8768
))).)))))(((.....)))(((((((.(	chr6:87968446-87968674(+)$1	1	75	104	9.7761
((((((((((......))))))))))(((	chr4:83368973-83369194(+)$1	1	28	57	11.1760
(((..(((.(((......))))))..)))	chr3:32578419-32578641(-)$1	1	161	190	11.7122
(((..((..(((.....)))..))..)).	chr5:79284280-79284509(-)$1	1	121	150	12.0133
(((((((.((((.....)))).)))))))	chr8:124042757-124042989(-)$1	1	138	167	12.5825
....(((..(((......)))..)))...	chr8:28837513-28837755(+)$1	1	27	56	13.5322
(((.(((.((((.....))))..))).))	chr6:7845405-7845643(+)$1	1	69	98	11.1651
(((((....((......))...)))))).	chr9:79874920-79875148(+)$1	1	195	224	10.8972
((...(((.(((......))))))...))	chr1:32381487-32381717(-)$1	1	51	80	12.2447
..((((....(((....)))...))))..	chr7:6502591-6502824(-)$1	1	37	66	10.0620
(.(((....(((...)))....))).)))	chr17:34892967-34893208(+)$1	1	176	205	12.9258
(((((....(((....)))....))))))	chr18:54278163-54278397(-)$1	1	180	209	11.0485
..((.(((((((......))))))).)).	chr11:46689311-46689537(+)$1	1	146	175	10.2623

#PSSM
g : 0.14	f : 0.12	c : 0.10	e : 0.10	d : 0.08	! : 0.08	= : 0.08	h : 0.07	i : 0.05	# : 0.03	[ : 0.03	E : 0.01	" : 0.01	+ : 0.01	
d : 0.12	g : 0.10	f : 0.10	! : 0.10	e : 0.10	= : 0.08	c : 0.07	h : 0.07	i : 0.05	# : 0.05	b : 0.05	[ : 0.03	" : 0.01	
d : 0.17	c : 0.12	g : 0.12	f : 0.08	= : 0.08	e : 0.07	b : 0.07	i : 0.05	# : 0.05	! : 0.03	h : 0.03	[ : 0.03	" : 0.03	
d : 0.17	g : 0.12	c : 0.10	! : 0.10	[ : 0.08	= : 0.08	f : 0.07	i : 0.05	# : 0.05	b : 0.03	" : 0.03	h : 0.01	e : 0.01	] : 0.01	
c : 0.21	d : 0.16	g : 0.10	! : 0.10	f : 0.07	= : 0.07	" : 0.05	[ : 0.03	$ : 0.03	b : 0.03	i : 0.03	e : 0.03	h : 0.01	# : 0.01	
c : 0.21	g : 0.19	# : 0.14	d : 0.10	" : 0.07	= : 0.07	f : 0.03	$ : 0.03	b : 0.03	! : 0.01	a : 0.01	[ : 0.01	i : 0.01	e : 0.01	
" : 0.21	g : 0.17	# : 0.17	c : 0.17	d : 0.05	= : 0.05	! : 0.03	$ : 0.03	a : 0.01	i : 0.01	e : 0.01	b : 0.01	
" : 0.21	# : 0.17	! : 0.16	g : 0.10	[ : 0.08	c : 0.08	e : 0.03	$ : 0.03	= : 0.03	a : 0.01	i : 0.01	d : 0.01	
# : 0.17	" : 0.16	! : 0.14	d : 0.14	g : 0.10	[ : 0.08	c : 0.05	e : 0.03	$ : 0.03	= : 0.03	i : 0.01	
c : 0.57	d : 0.16	g : 0.08	b : 0.05	= : 0.03	# : 0.03	e : 0.01	" : 0.01	[ : 0.01	
c : 0.57	d : 0.16	b : 0.10	g : 0.08	e : 0.01	= : 0.01	[ : 0.01	o : 0.01	
c : 0.53	d : 0.16	o : 0.08	g : 0.08	b : 0.07	e : 0.01	= : 0.01	a : 0.01	
n : 0.42	o : 0.32	l : 0.08	m : 0.08	d : 0.01	= : 0.01	b : 0.01	c : 0.01	
n : 0.42	o : 0.32	l : 0.12	m : 0.10	= : 0.01	
n : 0.42	o : 0.32	l : 0.14	m : 0.10	
n : 0.42	o : 0.32	m : 0.10	c : 0.08	l : 0.05	
n : 0.42	o : 0.30	c : 0.17	d : 0.01	l : 0.01	b : 0.01	= : 0.01	m : 0.01	
c : 0.39	o : 0.23	d : 0.14	b : 0.12	g : 0.05	= : 0.03	e : 0.01	
c : 0.48	d : 0.16	b : 0.10	g : 0.08	= : 0.03	3 : 0.03	] : 0.01	e : 0.01	a : 0.01	2 : 0.01	4 : 0.01	
c : 0.39	d : 0.16	3 : 0.12	g : 0.08	4 : 0.07	a : 0.03	] : 0.03	= : 0.03	2 : 0.03	e : 0.01	
c : 0.21	d : 0.17	3 : 0.14	] : 0.10	4 : 0.10	2 : 0.08	g : 0.08	= : 0.03	e : 0.01	f : 0.01	
3 : 0.17	2 : 0.16	g : 0.14	4 : 0.12	c : 0.12	] : 0.07	d : 0.07	f : 0.03	i : 0.03	= : 0.03	e : 0.01	
c : 0.19	g : 0.17	4 : 0.10	2 : 0.10	d : 0.08	3 : 0.08	= : 0.07	f : 0.05	b : 0.05	i : 0.03	] : 0.01	
c : 0.24	g : 0.17	d : 0.12	f : 0.07	3 : 0.07	= : 0.07	4 : 0.05	i : 0.05	b : 0.05	2 : 0.03	a : 0.01	] : 0.01	
c : 0.19	g : 0.16	d : 0.16	f : 0.08	] : 0.08	= : 0.08	2 : 0.07	i : 0.05	e : 0.05	4 : 0.01	3 : 0.01	
d : 0.16	c : 0.16	g : 0.14	f : 0.10	] : 0.08	= : 0.08	2 : 0.07	e : 0.07	i : 0.05	h : 0.03	3 : 0.01	
c : 0.14	g : 0.14	d : 0.14	f : 0.10	e : 0.08	= : 0.07	i : 0.05	2 : 0.05	3 : 0.05	b : 0.05	h : 0.03	] : 0.03	4 : 0.01	
g : 0.14	d : 0.12	e : 0.12	c : 0.10	f : 0.08	2 : 0.07	= : 0.07	i : 0.05	h : 0.05	b : 0.05	3 : 0.03	] : 0.01	4 : 0.01	[ : 0.01	7 : 0.01	
: : 0.12	e : 0.12	c : 0.08	g : 0.08	f : 0.07	= : 0.07	2 : 0.07	h : 0.07	b : 0.05	i : 0.05	d : 0.05	3 : 0.05	] : 0.03	4 : 0.01	7 : 0.01	

#score	656.2563248264803
#seq	56
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_CDS_m2_run1.txt

#BEAR
#cccvvvvvvvvvvvvvccc]	chr10:115885640-115885863(-)$1	223	95	116	21.8105
#eeeeettttttttttteeee	chr17:1257454-1257681(-)$1	227	141	162	23.1714
ccc[bbuuuuuuuuuuuubb]	chr6:149700408-149700634(+)$1	226	141	162	21.4503
:ddddvvvvvvvvvvvvvddd	chr6:34212942-34213161(+)$1	219	185	206	21.6254
c[ddddvvvvvvvvvvvvvdd	chr13:31835020-31835240(+)$1	220	89	110	22.6999
g!!ccctttttttttttccc2	chr7:6621189-6621409(+)$1	220	139	160	23.1833
cc[cccvvvvvvvvvvvvvcc	chr10:60560582-60560877(-)$1	295	8	29	22.3165
""ddddtttttttttttdddd	chr16:31200940-31201172(-)$1	232	7	28	23.2550
ggggggvvvvvvvvvvvvvgg	chr11:46568701-46568921(-)$1	220	53	74	22.1830
e[ddddvvvvvvvvvvvvvdd	chr5:130498239-130498462(-)$1	223	141	162	22.6491
fffffftttttttttttffff	chr5:96506817-96507037(-)$1	220	28	49	22.2876
======ttttttttttt====	chr10:7841755-7841978(+)$1	223	180	201	23.0388
fffffftttttttttttffff	chr1:11076874-11077143(-)$1	269	24	45	22.2876
::ddddtttttttttttdddd	chr4:17813774-17813995(+)$1	221	198	219	21.2896
eeeebbtttttttttttbb]e	chr2:9618361-9618584(+)$1	223	49	70	22.2074
deeeeettttttttttteeee	chr20:46268344-46268565(+)$1	221	28	49	22.9689
ffddddtttttttttttdddd	chrX:24006430-24006668(-)$1	238	49	70	23.0634
[eeeeettttttttttteeee	chr3:196866942-196867167(-)$1	225	88	109	23.2182
ff!!bbuuuuuuuuuuuubb2	chr17:57760237-57760475(+)$1	238	138	159	21.2229
eee[bbvvvvvvvvvvvvvbb	chr12:14631261-14631481(+)$1	220	74	95	21.2775
!!dddduuuuuuuuuuuuddd	chr13:108861539-108861762(-)$1	223	102	123	22.8196
c[cccuuuuuuuuuuuucccc	chr6:116973157-116973377(-)$1	220	138	159	22.3910
eeeeeuuuuuuuuuuuueeee	chr10:88827759-88827993(-)$1	234	211	232	22.1493
eedddduuuuuuuuuuuuddd	chr2:54044985-54045208(+)$1	223	113	134	22.5432
:dddduuuuuuuuuuuudddd	chr6:97339027-97339247(-)$1	220	139	160	21.2331
[eeeeevvvvvvvvvvvvvee	chr5:175810934-175811153(-)$1	219	99	120	22.5436
f!!ccctttttttttttccc]	chr17:26687679-26687902(+)$1	223	29	50	23.3445
c[dddduuuuuuuuuuuuddd	chr1:156756733-156756955(+)$1	222	168	189	22.7660
ggg[bbtttttttttttbb]g	chr6:142519476-142519705(+)$1	229	33	54	22.1457
ggggggtttttttttttgggg	chr9:88692255-88692491(-)$1	236	44	65	22.7383
eeeeeuuuuuuuuuuuueeee	chr10:60566242-60566480(+)$1	238	144	165	22.1493
!!ddddvvvvvvvvvvvvvdd	chr12:124071278-124071497(+)$1	219	177	198	22.7535
[eeeeettttttttttteeee	chr7:27788145-27788385(+)$1	240	201	222	23.2182
bbcccuuuuuuuuuuuuccc]	chr1:241767466-241767686(-)$1	220	151	172	21.7475
ggggggtttttttttttgggg	chr2:179407143-179407366(+)$1	223	175	196	22.7383
gggggguuuuuuuuuuuuggg	chr1:100573098-100573318(-)$1	220	135	156	22.2075
e[ddddtttttttttttdddd	chr7:124481038-124481259(-)$1	221	152	173	23.2896
:eeeeettttttttttteeee	chr1:220197639-220197858(-)$1	219	192	213	22.3285
eeeeeuuuuuuuuuuuueeee	chrX:122747415-122747637(-)$1	222	184	205	22.1493
fffffuuuuuuuuuuuuffff	chr9:112900063-112900282(+)$1	219	104	125	21.4295
b[cccuuuuuuuuuuuuccc]	chr2:203378343-203378563(+)$1	220	102	123	22.2791
ccccccuuuuuuuuuuuuccc	chr1:100546019-100546241(+)$1	222	156	177	22.4309
iii!!avvvvvvvvvvvvva2	chr20:7967915-7968136(-)$1	221	48	69	21.9918
:cccvvvvvvvvvvvvvcccG	chr7:27168824-27169060(-)$1	236	79	100	20.3211
:eeeeettttttttttteeee	chr1:244579183-244579403(-)$1	220	169	190	22.3285
###cccuuuuuuuuuuuuccc	chr17:47118743-47118963(+)$1	220	87	108	22.4073
fffccctttttttttttccc:	chr13:97986472-97986693(+)$1	221	198	219	22.0574
======uuuuuuuuuuuu===	chr18:12794164-12794384(-)$1	220	31	52	22.4528
fffffftttttttttttffff	chr19:12924082-12924303(+)$1	221	93	114	22.2876
d[ddddvvvvvvvvvvvvvdd	chr4:24550462-24550681(-)$1	219	167	188	22.5398
cc[ccctttttttttttcccc	chr9:35102651-35102870(-)$1	219	15	36	23.1275
eedddduuuuuuuuuuuuddd	chr2:61722569-61722788(-)$1	219	139	160	22.5432
beeeeevvvvvvvvvvvvvee	chr12:6601355-6601579(-)$1	224	29	50	22.2877
fffffftttttttttttffff	chr1:90400655-90400878(+)$1	223	93	114	22.2876
e[ddddvvvvvvvvvvvvvdd	chr4:83276374-83276602(-)$1	228	25	46	22.6491
+dddduuuuuuuuuuuudddd	chrM:13446-13699(+)$1	253	131	152	21.5323
""bbvvvvvvvvvvvvvbb]e	chrM:10105-10454(+)$1	349	74	95	20.6520
g"""bbtttttttttttbb33	chr2:20508172-20508391(-)$1	219	104	125	21.9211
fffffftttttttttttffff	chr2:32639934-32640156(+)$1	222	158	179	22.2876
'eeeeettttttttttteeee	chr4:106196440-106196665(+)$1	225	161	182	22.6352
d[ddddtttttttttttdddd	chr10:131964682-131964917(+)$1	235	174	195	23.1803
iiiiiuuuuuuuuuuuuiiii	chrM:7741-8036(-)$1	295	140	161	21.8333

#otherMatches

#Seq PSSM
CAUGGCAUCUUUAUAUACAUC	chr10:115885640-115885863(-)$1	223	95	116	21.8105
AUCUGACACUAUGGACUUCAG	chr17:1257454-1257681(-)$1	227	141	162	23.1714
CCGAGAAUAUUCAGCACCUCA	chr6:149700408-149700634(+)$1	226	141	162	21.4503
UGGCACGCCCUACUCCACUGC	chr6:34212942-34213161(+)$1	219	185	206	21.6254
GAUGAAGAAGCUACAAUAAUU	chr13:31835020-31835240(+)$1	220	89	110	22.6999
UUUAAAUAUUCUCCUCUUUUC	chr7:6621189-6621409(+)$1	220	139	160	23.1833
AGUUGAGAACAAAUAUAUAUC	chr10:60560582-60560877(-)$1	295	8	29	22.3165
UUGCUGCCCUAUAUCCCCAGC	chr16:31200940-31201172(-)$1	232	7	28	23.2550
GUUCUACUCUUUGAUUUUCUA	chr11:46568701-46568921(-)$1	220	53	74	22.1830
GUGAUACCCAAGAAACAUAUA	chr5:130498239-130498462(-)$1	223	141	162	22.6491
GAGAUUUUAAUGAAUUUAAUC	chr5:96506817-96507037(-)$1	220	28	49	22.2876
AAAUAACAGUUUAAAAAUUAU	chr10:7841755-7841978(+)$1	223	180	201	23.0388
UGCUAGAUACUCAUUCACUGG	chr1:11076874-11077143(-)$1	269	24	45	22.2876
CAAUCAGAUAUGGAAGAUGAU	chr4:17813774-17813995(+)$1	221	198	219	21.2896
CCUUCCAAGAUUAAUCAGGAA	chr2:9618361-9618584(+)$1	223	49	70	22.2074
GGGCUUACCAAACUCAAAGGC	chr20:46268344-46268565(+)$1	221	28	49	22.9689
UAUCCAGUUAACAAAUAUGGA	chrX:24006430-24006668(-)$1	238	49	70	23.0634
AGAUGACUCAAGUAUUUUCAU	chr3:196866942-196867167(-)$1	225	88	109	23.2182
GUAUUAACGAGACUUUUAUAU	chr17:57760237-57760475(+)$1	238	138	159	21.2229
ACCGCCUCUUCAACCAUCUGG	chr12:14631261-14631481(+)$1	220	74	95	21.2775
AACAAAAUUUCUAAUAUAUUU	chr13:108861539-108861762(-)$1	223	102	123	22.8196
UGUGGUUACAGAAAUUUCCAA	chr6:116973157-116973377(-)$1	220	138	159	22.3910
GCUGUCUACAAGAAUUAACAG	chr10:88827759-88827993(-)$1	234	211	232	22.1493
CCAACUAAAGGAUAUUAAAGU	chr2:54044985-54045208(+)$1	223	113	134	22.5432
ACUGCUGAGAAAAUAAUGCAG	chr6:97339027-97339247(-)$1	220	139	160	21.2331
GCUCCAAUUUAUAUUCAUCUG	chr5:175810934-175811153(-)$1	219	99	120	22.5436
UCCUAGAGAAUGUUGAACUAA	chr17:26687679-26687902(+)$1	223	29	50	23.3445
ACGACUACAGCUACAAUCAGU	chr1:156756733-156756955(+)$1	222	168	189	22.7660
AUAAGAAUACCUAGCACUUGU	chr6:142519476-142519705(+)$1	229	33	54	22.1457
GGAGCUGAAGAAGAACGAGUU	chr9:88692255-88692491(-)$1	236	44	65	22.7383
UGUAAUACACUAAUAACUUAC	chr10:60566242-60566480(+)$1	238	144	165	22.1493
GCUCCAAAAGGACAAGAUAUG	chr12:124071278-124071497(+)$1	219	177	198	22.7535
AAAUUUUCUUUUAAAACAGAU	chr7:27788145-27788385(+)$1	240	201	222	23.2182
CUCCCAAACCACAUCCAGGGU	chr1:241767466-241767686(-)$1	220	151	172	21.7475
AAUUUUUACUUCAAAUCAAAA	chr2:179407143-179407366(+)$1	223	175	196	22.7383
GUUUGUUUUAAAAAUUUUAUA	chr1:100573098-100573318(-)$1	220	135	156	22.2075
AAGGACGAAAAGUAGCAGUUC	chr7:124481038-124481259(-)$1	221	152	173	23.2896
CCUGCUGAACAGAUGAAAGCA	chr1:220197639-220197858(-)$1	219	192	213	22.3285
GAAGUGAAUUGGAAAAGGCUU	chrX:122747415-122747637(-)$1	222	184	205	22.1493
UCCCCUUCCUCCACGCUGGGG	chr9:112900063-112900282(+)$1	219	104	125	21.4295
ACCUCAUUCAUUUAACCGAGA	chr2:203378343-203378563(+)$1	220	102	123	22.2791
CUUGGGAACAAACACAAGCCC	chr1:100546019-100546241(+)$1	222	156	177	22.4309
AUUUUUGGUUCUCUUAAAAAU	chr20:7967915-7968136(-)$1	221	48	69	21.9918
CUGCCCAACACCAAGAUGCGA	chr7:27168824-27169060(-)$1	236	79	100	20.3211
UAGAGCAGUUUCAUAAAGCUC	chr1:244579183-244579403(-)$1	220	169	190	22.3285
CAAGAUACCGAGACAAAAAUC	chr17:47118743-47118963(+)$1	220	87	108	22.4073
CCAGGAACACCACUUCAUCCA	chr13:97986472-97986693(+)$1	221	198	219	22.0574
AGAUGGGGUUUAUGUCAGUCA	chr18:12794164-12794384(-)$1	220	31	52	22.4528
AGGAAGAUCACAUCCUACUUC	chr19:12924082-12924303(+)$1	221	93	114	22.2876
ACCUCCCAAAAAACAGAAUGG	chr4:24550462-24550681(-)$1	219	167	188	22.5398
GAUGGGAUCUCUGCUCACCCU	chr9:35102651-35102870(-)$1	219	15	36	23.1275
CUUAAGGAACAUGAUCAACUU	chr2:61722569-61722788(-)$1	219	139	160	22.5432
AUCCGAAAGAGGAAAAUGGUU	chr12:6601355-6601579(-)$1	224	29	50	22.2877
UUGGAGUCACUUUAUUUCUCU	chr1:90400655-90400878(+)$1	223	93	114	22.2876
UUCUAACACUUGUUUUAUUUU	chr4:83276374-83276602(-)$1	228	25	46	22.6491
UCGCUACCUCCCUGACAAGCG	chrM:13446-13699(+)$1	253	131	152	21.5323
UUCGACCCUAUAUCCCCCGCC	chrM:10105-10454(+)$1	349	74	95	20.6520
AAUACUAAUCCCUCAGAAGGA	chr2:20508172-20508391(-)$1	219	104	125	21.9211
UGCUACCUCACCCAUUAGUAG	chr2:32639934-32640156(+)$1	222	158	179	22.2876
UCUGGGUUCCUAUUCUCCCCA	chr4:106196440-106196665(+)$1	225	161	182	22.6352
CAGGGACUCAAAGCCUAUUCC	chr10:131964682-131964917(+)$1	235	174	195	23.1803
AUUGGUGGCCAAUUGAUUUGA	chrM:7741-8036(-)$1	295	140	161	21.8333

#DB
.(((.............))).	chr10:115885640-115885863(-)$1	1	95	116	21.8105
.(((((...........))))	chr17:1257454-1257681(-)$1	1	141	162	23.1714
(((.((............)).	chr6:149700408-149700634(+)$1	1	141	162	21.4503
.((((.............)))	chr6:34212942-34213161(+)$1	1	185	206	21.6254
(.((((.............))	chr13:31835020-31835240(+)$1	1	89	110	22.6999
(..(((...........))).	chr7:6621189-6621409(+)$1	1	139	160	23.1833
((.(((.............))	chr10:60560582-60560877(-)$1	1	8	29	22.3165
..((((...........))))	chr16:31200940-31201172(-)$1	1	7	28	23.2550
((((((.............))	chr11:46568701-46568921(-)$1	1	53	74	22.1830
(.((((.............))	chr5:130498239-130498462(-)$1	1	141	162	22.6491
((((((...........))))	chr5:96506817-96507037(-)$1	1	28	49	22.2876
((((((...........))))	chr10:7841755-7841978(+)$1	1	180	201	23.0388
((((((...........))))	chr1:11076874-11077143(-)$1	1	24	45	22.2876
..((((...........))))	chr4:17813774-17813995(+)$1	1	198	219	21.2896
((((((...........)).)	chr2:9618361-9618584(+)$1	1	49	70	22.2074
)(((((...........))))	chr20:46268344-46268565(+)$1	1	28	49	22.9689
((((((...........))))	chrX:24006430-24006668(-)$1	1	49	70	23.0634
.(((((...........))))	chr3:196866942-196867167(-)$1	1	88	109	23.2182
((..((............)).	chr17:57760237-57760475(+)$1	1	138	159	21.2229
(((.((.............))	chr12:14631261-14631481(+)$1	1	74	95	21.2775
..((((............)))	chr13:108861539-108861762(-)$1	1	102	123	22.8196
(.(((............))))	chr6:116973157-116973377(-)$1	1	138	159	22.3910
(((((............))))	chr10:88827759-88827993(-)$1	1	211	232	22.1493
((((((............)))	chr2:54044985-54045208(+)$1	1	113	134	22.5432
.((((............))))	chr6:97339027-97339247(-)$1	1	139	160	21.2331
.(((((.............))	chr5:175810934-175811153(-)$1	1	99	120	22.5436
(..(((...........))).	chr17:26687679-26687902(+)$1	1	29	50	23.3445
(.((((............)))	chr1:156756733-156756955(+)$1	1	168	189	22.7660
(((.((...........)).)	chr6:142519476-142519705(+)$1	1	33	54	22.1457
((((((...........))))	chr9:88692255-88692491(-)$1	1	44	65	22.7383
(((((............))))	chr10:60566242-60566480(+)$1	1	144	165	22.1493
..((((.............))	chr12:124071278-124071497(+)$1	1	177	198	22.7535
.(((((...........))))	chr7:27788145-27788385(+)$1	1	201	222	23.2182
(((((............))).	chr1:241767466-241767686(-)$1	1	151	172	21.7475
((((((...........))))	chr2:179407143-179407366(+)$1	1	175	196	22.7383
((((((............)))	chr1:100573098-100573318(-)$1	1	135	156	22.2075
(.((((...........))))	chr7:124481038-124481259(-)$1	1	152	173	23.2896
.(((((...........))))	chr1:220197639-220197858(-)$1	1	192	213	22.3285
(((((............))))	chrX:122747415-122747637(-)$1	1	184	205	22.1493
(((((............))))	chr9:112900063-112900282(+)$1	1	104	125	21.4295
(.(((............))).	chr2:203378343-203378563(+)$1	1	102	123	22.2791
)))(((............)))	chr1:100546019-100546241(+)$1	1	156	177	22.4309
(((..(.............).	chr20:7967915-7968136(-)$1	1	48	69	21.9918
.(((.............))))	chr7:27168824-27169060(-)$1	1	79	100	20.3211
.(((((...........))))	chr1:244579183-244579403(-)$1	1	169	190	22.3285
...(((............)))	chr17:47118743-47118963(+)$1	1	87	108	22.4073
)))(((...........))).	chr13:97986472-97986693(+)$1	1	198	219	22.0574
((((((............)))	chr18:12794164-12794384(-)$1	1	31	52	22.4528
((((((...........))))	chr19:12924082-12924303(+)$1	1	93	114	22.2876
(.((((.............))	chr4:24550462-24550681(-)$1	1	167	188	22.5398
((.(((...........))))	chr9:35102651-35102870(-)$1	1	15	36	23.1275
((((((............)))	chr2:61722569-61722788(-)$1	1	139	160	22.5432
((((((.............))	chr12:6601355-6601579(-)$1	1	29	50	22.2877
((((((...........))))	chr1:90400655-90400878(+)$1	1	93	114	22.2876
(.((((.............))	chr4:83276374-83276602(-)$1	1	25	46	22.6491
.((((............))))	chrM:13446-13699(+)$1	1	131	152	21.5323
..((.............)).)	chrM:10105-10454(+)$1	1	74	95	20.6520
(...((...........))..	chr2:20508172-20508391(-)$1	1	104	125	21.9211
((((((...........))))	chr2:32639934-32640156(+)$1	1	158	179	22.2876
.(((((...........))))	chr4:106196440-106196665(+)$1	1	161	182	22.6352
(.((((...........))))	chr10:131964682-131964917(+)$1	1	174	195	23.1803
(((((............))))	chrM:7741-8036(-)$1	1	140	161	21.8333

#PSSM
e : 0.16	f : 0.16	c : 0.11	g : 0.11	: : 0.09	# : 0.04	d : 0.04	[ : 0.04	b : 0.04	" : 0.03	= : 0.03	! : 0.03	i : 0.03	+ : 0.01	' : 0.01	
e : 0.25	[ : 0.14	f : 0.14	c : 0.09	g : 0.08	! : 0.06	d : 0.04	" : 0.04	= : 0.03	i : 0.03	: : 0.01	b : 0.01	# : 0.01	
d : 0.27	e : 0.22	c : 0.11	f : 0.11	g : 0.08	! : 0.04	[ : 0.03	= : 0.03	i : 0.03	# : 0.01	b : 0.01	" : 0.01	
d : 0.27	e : 0.20	c : 0.19	f : 0.09	g : 0.06	[ : 0.04	= : 0.03	! : 0.03	b : 0.01	" : 0.01	i : 0.01	
d : 0.27	e : 0.19	c : 0.16	b : 0.09	f : 0.09	g : 0.06	v : 0.04	= : 0.03	! : 0.01	i : 0.01	
d : 0.22	u : 0.16	e : 0.14	c : 0.11	b : 0.09	f : 0.08	v : 0.06	g : 0.06	= : 0.03	a : 0.01	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
t : 0.43	u : 0.32	v : 0.24	
v : 0.19	e : 0.16	u : 0.16	c : 0.14	d : 0.11	f : 0.09	b : 0.06	g : 0.03	= : 0.01	i : 0.01	
d : 0.19	c : 0.17	v : 0.17	e : 0.16	b : 0.09	f : 0.09	g : 0.04	= : 0.03	i : 0.01	
d : 0.27	c : 0.19	e : 0.19	f : 0.09	g : 0.06	b : 0.04	] : 0.04	= : 0.03	a : 0.01	3 : 0.01	i : 0.01	
d : 0.27	e : 0.22	f : 0.09	] : 0.08	c : 0.08	g : 0.08	2 : 0.04	= : 0.03	b : 0.01	G : 0.01	: : 0.01	3 : 0.01	i : 0.01	

#score	1383.9278755447865
#seq	62
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_UTR_m1_run2.txt

#BEAR
fff!!cccyyyyyyyyyyyyyyyyccc2	chr1:113454941-113455171(-)$1	230	35	63	23.2715
:gggggggxxxxxxxxxxxxxxxggggg	chr16:15960316-15960571(-)$1	255	127	155	19.7548
iiiiiiiiuuuuuuuuuuuuiiiiiiii	chr16:89711921-89712169(-)$1	248	177	205	23.9434
eeeee[bbwwwwwwwwwwwwwwbb]eee	chr1:45101601-45101850(+)$1	249	177	205	22.2532
!gggggggwwwwwwwwwwwwwwgggggg	chr17:48459508-48459756(-)$1	248	177	205	23.2435
dddddddduuuuuuuuuuuudddd]ddd	chr5:138650265-138650504(+)$1	239	162	190	22.6510
ccc!!ddddtttttttttttdddd22cc	chr1:70717510-70717751(+)$1	241	151	179	21.6044
ee!!dddduuuuuuuuuuuudddd22ee	chr1:26226967-26227230(-)$1	263	222	250	23.3415
gggg!!bbwwwwwwwwwwwwwwbb22gg	chr22:35660668-35660897(+)$1	229	48	76	22.3070
bb####bbvvvvvvvvvvvvvbb333bb	chr3:47777419-47777657(-)$1	238	26	54	21.4387
eeee!!bbwwwwwwwwwwwwwwbb]eee	chr5:33457373-33457596(+)$1	223	56	84	22.3668
ff!!ddddtttttttttttddddfffff	chr15:68584755-68584985(+)$1	230	74	102	21.1728
iiiiiiiiuuuuuuuuuuuuiiiiiiii	chr1:6285064-6285340(-)$1	276	20	48	23.9434
eeeeyyyyyyyyyyyyyyyyeeeeeccc	chr1:161009615-161009845(-)$1	230	157	185	21.4671
##ddddbbuuuuuuuuuuuubb4444dd	chr19:47990824-47991047(-)$1	223	62	90	22.7611
c!!fffffftttttttttttffffff22	chr11:124496707-124496931(+)$1	224	30	58	21.3179
eeeeeee[attttttttttta]eeeee:	chr12:50157272-50157507(+)$1	235	108	136	21.6511
b!!eeeeeyyyyyyyyyyyyyyyyeeee	chr12:42841491-42841718(+)$1	227	19	47	23.3091
cceeeeewwwwwwwwwwwwwweeeee]c	chr18:55268488-55268736(-)$1	248	218	246	22.6134
eeeeeddddtttttttttttdddd]eee	chr11:68658789-68659016(-)$1	227	89	117	21.6450
eeee[cccuuuuuuuuuuuuccceeeee	chr9:95030368-95030599(-)$1	231	22	50	24.2657
bb[eeeeevvvvvvvvvvvvveeeeebb	chr17:42283801-42284026(-)$1	225	75	103	21.8885
ccc!!cccxxxxxxxxxxxxxxxccc22	chr14:103985973-103986218(-)$1	245	18	46	20.1089
ffff!!bbvvvvvvvvvvvvvbb]ffff	chr1:150594945-150595171(-)$1	226	162	190	22.1330
"""eeeeeuuuuuuuuuuuueeeee333	chr12:89983904-89984140(-)$1	236	179	207	24.1401
d[ffffffvvvvvvvvvvvvvffffff]	chr20:3185197-3185421(-)$1	224	187	215	22.2483
Bcccyyyyyyyyyyyyyyyycccbbeee	chr19:33872241-33872464(+)$1	223	48	76	20.5384
b[eeeeexxxxxxxxxxxxxxxeeeee]	chr19:15348209-15348467(-)$1	258	96	124	20.2318
!ggggggguuuuuuuuuuuuggggggg5	chr9:138396100-138396331(+)$1	231	164	192	23.3961
ggggg!!bbtttttttttttbb22gggg	chr8:27667434-27667664(-)$1	230	79	107	21.6102
ffffffbbuuuuuuuuuuuubb]fffff	chr2:47387689-47387937(-)$1	248	113	141	22.9275
hhhhhhhwwwwwwwwwwwwwwhhhhhhh	chr3:52741840-52742069(+)$1	229	54	82	19.8334
::gggggggtttttttttttggggggg:	chr18:673276-673499(+)$1	223	1	29	19.5216
:ggggggguuuuuuuuuuuugggggggE	chr14:103808305-103808532(+)$1	227	6	34	22.3530
:gggggggwwwwwwwwwwwwwwgggggg	chr9:95027677-95027926(-)$1	249	14	42	22.4770
####ddddxxxxxxxxxxxxxxxdddd4	chr1:45212303-45212528(+)$1	225	93	121	19.5933
dd[ddddwwwwwwwwwwwwwwdddd]dd	chr7:935534-935764(+)$1	230	58	86	21.8277
eeeeecccuuuuuuuuuuuuccc]eeee	chr12:1017882-1018104(+)$1	222	147	175	24.1876
b!!fffffftttttttttttffffff22	chr17:73773731-73773959(-)$1	228	82	110	21.2479
iiiiiiyyyyyyyyyyyyyyyyiiiiii	chr5:133292426-133292667(-)$1	241	89	117	23.5393
eeeeddddvvvvvvvvvvvvvdddd:::	chr4:39784149-39784373(+)$1	224	58	86	19.2468
"""cccwwwwwwwwwwwwwwccc]ccc]	chr1:150190896-150191121(-)$1	225	186	214	22.3237
###eeeeeuuuuuuuuuuuueeeee444	chr1:228286743-228286972(+)$1	229	143	171	23.8039
c"""ddddyyyyyyyyyyyyyyyydddd	chr20:44445445-44445686(+)$1	241	63	91	22.6951
d[ffffffyyyyyyyyyyyyyyyyffff	chr6:151685654-151685884(-)$1	230	29	57	22.8811
b####ddddtttttttttttddddbb]d	chr1:154179615-154179849(-)$1	234	18	46	21.0410
+ggggggguuuuuuuuuuuuggggggg7	chr8:41367261-41367499(+)$1	238	171	199	23.0916
[eeeeewwwwwwwwwwwwwweeeeeggg	chr10:70742698-70742923(+)$1	225	176	204	21.9008
========vvvvvvvvvvvvv=======	chr8:145748272-145748496(+)$1	224	179	207	23.2102
effffffyyyyyyyyyyyyyyyyfffff	chr17:48829451-48829709(+)$1	258	32	60	23.1284
fffff[ccctttttttttttccc333ff	chr18:12814105-12814332(-)$1	227	77	105	22.4190
===!!cccyyyyyyyyyyyyyyyyccc3	chr12:98928225-98928449(+)$1	224	107	135	23.8607
ddd[eeeeettttttttttteeeee]dd	chr19:36259374-36259600(+)$1	226	117	145	21.4577
ccc[cccwwwwwwwwwwwwwwccc]ccc	chr17:27246071-27246297(-)$1	226	31	59	22.9369
:ffffffyyyyyyyyyyyyyyyyfffff	chr6:109688167-109688395(-)$1	228	83	111	22.4877
CCffffffwwwwwwwwwwwwwwffffff	chr17:12046019-12046243(+)$1	224	196	224	20.4115
bb[cccwwwwwwwwwwwwwwccc]bb]e	chr17:74731148-74731379(-)$1	231	117	145	21.3628
ddd!!ddddtttttttttttdddd22dd	chr3:10192894-10193122(+)$1	228	104	132	21.0909
dffffffxxxxxxxxxxxxxxxffffff	chr5:180665991-180666219(-)$1	228	16	44	19.5857
Fccc[cccxxxxxxxxxxxxxxxccc]c	chr19:12242400-12242629(-)$1	229	189	217	19.8526
((fffffftttttttttttffffffbb]	chr3:195776360-195776595(-)$1	235	92	120	19.1743
ee"""cccuuuuuuuuuuuuccc]eeee	chr6:26156510-26156749(+)$1	239	160	188	24.2951
"dddd[ccctttttttttttcccdddd]	chr17:40277221-40277458(-)$1	237	57	85	21.8138

#otherMatches

#Seq PSSM
UUUAACCUAAUAUCACUUAAAUCGAGGC	chr1:113454941-113455171(-)$1	230	35	63	23.2715
UUGUUUGGGCUCCGAAACUCUUACCAAA	chr16:15960316-15960571(-)$1	255	127	155	19.7548
GUGCCACCCAACGCUGUCCUGGUGGUAU	chr16:89711921-89712169(-)$1	248	177	205	23.9434
GUGGUGUGGACAGAAGCGGAUACGGGCC	chr1:45101601-45101850(+)$1	249	177	205	22.2532
CAGAUUUCACGACUCAGAGAUAGAAAUC	chr17:48459508-48459756(-)$1	248	177	205	23.2435
AGGAGUUUGAAAUACCUUUAAAACAUCC	chr5:138650265-138650504(+)$1	239	162	190	22.6510
UGAUAAUAAAACCCUUAAACUUAUGUUC	chr1:70717510-70717751(+)$1	241	151	179	21.6044
CCUCCUGGUUGAUACUUGUUCCAGAUGG	chr1:26226967-26227230(-)$1	263	222	250	23.3415
GUUGAAAGCUAUCACUUCCCCACUGGCA	chr22:35660668-35660897(+)$1	229	48	76	22.3070
UCUUUUCAUCCUCAGAACAAUUGUUUGA	chr3:47777419-47777657(-)$1	238	26	54	21.4387
CCCAGAUCCUAAAAUGUUGAAAGAGUGG	chr5:33457373-33457596(+)$1	223	56	84	22.3668
AUUCAAGUGAAAGUUAUAUGCUUAUUUC	chr15:68584755-68584985(+)$1	230	74	102	21.1728
GAUGCUGUGUAACCCCAUCUGCGGCGUC	chr1:6285064-6285340(-)$1	276	20	48	23.9434
GGGCCCAAGAACUGCAGAUAGCCCAGGA	chr1:161009615-161009845(-)$1	230	157	185	21.4671
ACACCUGCUCCUUCCCUAAUGCUUUGAG	chr19:47990824-47991047(-)$1	223	62	90	22.7611
GAAACUGGACUUCUAAAUUCUUCAGUGA	chr11:124496707-124496931(+)$1	224	30	58	21.3179
UUGUCAGGCAUUUUUGAAAAGGCUGAUU	chr12:50157272-50157507(+)$1	235	108	136	21.6511
GGCCUCUACUGAUAAUACCUACCCUAGA	chr12:42841491-42841718(+)$1	227	19	47	23.3091
UAACUUAUCUUUCUGUCCUUUUAAGUGU	chr18:55268488-55268736(-)$1	248	218	246	22.6134
CCCUGCUGUAACUGAUGACAACAGUCAG	chr11:68658789-68659016(-)$1	227	89	117	21.6450
CAGAGUUGGUACGAGAAAAACGAUUUGG	chr9:95030368-95030599(-)$1	231	22	50	24.2657
CCGUCUCUGUUGUCAUUUCUGGGAGAGG	chr17:42283801-42284026(-)$1	225	75	103	21.8885
AGCCCGGCCCACACCCGACACCAGCCCU	chr14:103985973-103986218(-)$1	245	18	46	20.1089
AGGGCUUGGAGUUGGUAAAAACAUUCCU	chr1:150594945-150595171(-)$1	226	162	190	22.1330
CUGUUUAAUUUUUAAAAUUUUUGAAAAC	chr12:89983904-89984140(-)$1	236	179	207	24.1401
CUAGUCGGCUUUAUCCUCUUCCUGACUC	chr20:3185197-3185421(-)$1	224	187	215	22.2483
GUCCUUCUGAAUGUAAAACUGGAGCCCA	chr19:33872241-33872464(+)$1	223	48	76	20.5384
UGGCACUGCUUAUCUCCGAAAUGGUGUG	chr19:15348209-15348467(-)$1	258	96	124	20.2318
UGCUGCUGUCCCUGUGAUCCCAGCAGCC	chr9:138396100-138396331(+)$1	231	164	192	23.3961
CUGCUCAUGCUGACUUAAAACACUAGCA	chr8:27667434-27667664(-)$1	230	79	107	21.6102
UACUGUCAAAAAAAUAUGCAUGUAUAGU	chr2:47387689-47387937(-)$1	248	113	141	22.9275
UAAGAGCUAAAACCACCUAAUGCUCUUA	chr3:52741840-52742069(+)$1	229	54	82	19.8334
AUGUAUGUGCAUUUCAAUCCCACGUACU	chr18:673276-673499(+)$1	223	1	29	19.5216
ACAUACUGUAUUUUUUCGUUCAGUGUGG	chr14:103808305-103808532(+)$1	227	6	34	22.3530
UGCAUGCUAUAUAAAUUAACUCAGUAUG	chr9:95027677-95027926(-)$1	249	14	42	22.4770
GGCUUGGAAAUCAGAAACCCAUAUCCAU	chr1:45212303-45212528(+)$1	225	93	121	19.5933
CUGCGCCACAUCCUCACGCUCGGUGGAG	chr7:935534-935764(+)$1	230	58	86	21.8277
GUAGCCUAUAUACUAACUACUAGUGCUG	chr12:1017882-1018104(+)$1	222	147	175	24.1876
UUAACUAACAUUCUGAACUAGUUAGUGC	chr17:73773731-73773959(-)$1	228	82	110	21.2479
UGAAGAUUACCAAUGAUUAUAUUUUUUA	chr5:133292426-133292667(-)$1	241	89	117	23.5393
AUGGGUGGGUUACCAGAAAUACCAUUGA	chr4:39784149-39784373(+)$1	224	58	86	19.2468
CUCAAGAAUCUCCUUAAAAACUUUGAAG	chr1:150190896-150191121(-)$1	225	186	214	22.3237
UUAGAAUAAAAUCUCUUAACUAUUUCAC	chr1:228286743-228286972(+)$1	229	143	171	23.8039
UAUUUUUGUUUUGUUUUUGUCUUUUAAA	chr20:44445445-44445686(+)$1	241	63	91	22.6951
UACUAUUCUAUAAAUUGCCUUUCUGAAU	chr6:151685654-151685884(-)$1	230	29	57	22.8811
GCCCAGACUGUAUCCAUCCAAGUUCCCG	chr1:154179615-154179849(-)$1	234	18	46	21.0410
AUUGGUUCUCUUCAUUCCUUGGGCCAGC	chr8:41367261-41367499(+)$1	238	171	199	23.0916
GUGAGUUCACCUGUCUUUAUACUCAAAA	chr10:70742698-70742923(+)$1	225	176	204	21.9008
GGCCCAGCAACCCGCCUUCUAGCUGGGC	chr8:145748272-145748496(+)$1	224	179	207	23.2102
GGGCCAACACUUUCUCAUAAAAAUUGGC	chr17:48829451-48829709(+)$1	258	32	60	23.1284
UACAUGGCUAUAAUAGAAGGAGCAAAAU	chr18:12814105-12814332(-)$1	227	77	105	22.4190
UUAACGCUUUCUAGAUCACAUAUUAGUC	chr12:98928225-98928449(+)$1	224	107	135	23.8607
UUCAUACAGUUACUGGUUAUCUGUGAGA	chr19:36259374-36259600(+)$1	226	117	145	21.4577
GUGUGACUAUUGCCCUCUCCUGUUUCAC	chr17:27246071-27246297(-)$1	226	31	59	22.9369
AGGUACCUCACAAAAUGUAUUAUGGUGC	chr6:109688167-109688395(-)$1	228	83	111	22.4877
GAUGCCAUUACAGAACCAAAUCGUGGCA	chr17:12046019-12046243(+)$1	224	196	224	20.4115
ACUUCUUUCUUUUCAAACCUAGAUGUAU	chr17:74731148-74731379(-)$1	231	117	145	21.3628
AGAUUCAUUAACUCAAAUUCAAUGCUUC	chr3:10192894-10193122(+)$1	228	104	132	21.0909
CACCUGUCAACCGCACGUCUAUGCAGGU	chr5:180665991-180666219(-)$1	228	16	44	19.5857
CAUGUGGAUGUCAGGCAUAUUUUUCCUC	chr19:12242400-12242629(-)$1	229	189	217	19.8526
AAAACCCUUUUCUACAGUUAGGGUUGAG	chr3:195776360-195776595(-)$1	235	92	120	19.1743
CUCCCGUGAAGAAGAAGGCCCGCAAGUC	chr6:26156510-26156749(+)$1	239	160	188	24.2951
UCCACAUCCUCACUUUGUUCGGAGUGGU	chr17:40277221-40277458(-)$1	237	57	85	21.8138

#DB
(((..(((................))).	chr1:113454941-113455171(-)$1	1	35	63	23.2715
.(((((((...............)))))	chr16:15960316-15960571(-)$1	1	127	155	19.7548
((((((((............))))))))	chr16:89711921-89712169(-)$1	1	177	205	23.9434
(((((.((..............)).)))	chr1:45101601-45101850(+)$1	1	177	205	22.2532
.(((((((..............))))))	chr17:48459508-48459756(-)$1	1	177	205	23.2435
((((((((............)))).)))	chr5:138650265-138650504(+)$1	1	162	190	22.6510
(((..((((...........))))..))	chr1:70717510-70717751(+)$1	1	151	179	21.6044
((..((((............))))..))	chr1:26226967-26227230(-)$1	1	222	250	23.3415
((((..((..............))..))	chr22:35660668-35660897(+)$1	1	48	76	22.3070
((....((.............))...))	chr3:47777419-47777657(-)$1	1	26	54	21.4387
((((..((..............)).)))	chr5:33457373-33457596(+)$1	1	56	84	22.3668
((..((((...........)))))))))	chr15:68584755-68584985(+)$1	1	74	102	21.1728
((((((((............))))))))	chr1:6285064-6285340(-)$1	1	20	48	23.9434
((((................)))))(((	chr1:161009615-161009845(-)$1	1	157	185	21.4671
..((((((............))....))	chr19:47990824-47991047(-)$1	1	62	90	22.7611
(..((((((...........))))))..	chr11:124496707-124496931(+)$1	1	30	58	21.3179
))(((((.(...........).))))).	chr12:50157272-50157507(+)$1	1	108	136	21.6511
(..(((((................))))	chr12:42841491-42841718(+)$1	1	19	47	23.3091
(((((((..............))))).)	chr18:55268488-55268736(-)$1	1	218	246	22.6134
(((((((((...........)))).)))	chr11:68658789-68659016(-)$1	1	89	117	21.6450
((((.(((............))))))))	chr9:95030368-95030599(-)$1	1	22	50	24.2657
((.(((((.............)))))))	chr17:42283801-42284026(-)$1	1	75	103	21.8885
(((..(((...............)))..	chr14:103985973-103986218(-)$1	1	18	46	20.1089
((((..((.............)).))))	chr1:150594945-150595171(-)$1	1	162	190	22.1330
...(((((............)))))...	chr12:89983904-89984140(-)$1	1	179	207	24.1401
(.((((((.............)))))).	chr20:3185197-3185421(-)$1	1	187	215	22.2483
((((................)))(((((	chr19:33872241-33872464(+)$1	1	48	76	20.5384
(.(((((...............))))).	chr19:15348209-15348467(-)$1	1	96	124	20.2318
.(((((((............))))))).	chr9:138396100-138396331(+)$1	1	164	192	23.3961
(((((..((...........))..))))	chr8:27667434-27667664(-)$1	1	79	107	21.6102
((((((((............)).)))))	chr2:47387689-47387937(-)$1	1	113	141	22.9275
(((((((..............)))))))	chr3:52741840-52742069(+)$1	1	54	82	19.8334
..(((((((...........))))))).	chr18:673276-673499(+)$1	1	1	29	19.5216
.(((((((............)))))))(	chr14:103808305-103808532(+)$1	1	6	34	22.3530
.(((((((..............))))))	chr9:95027677-95027926(-)$1	1	14	42	22.4770
....((((...............)))).	chr1:45212303-45212528(+)$1	1	93	121	19.5933
((.((((..............)))).))	chr7:935534-935764(+)$1	1	58	86	21.8277
((((((((............))).))))	chr12:1017882-1018104(+)$1	1	147	175	24.1876
(..((((((...........))))))..	chr17:73773731-73773959(-)$1	1	82	110	21.2479
((((((................))))))	chr5:133292426-133292667(-)$1	1	89	117	23.5393
))))((((.............))))...	chr4:39784149-39784373(+)$1	1	58	86	19.2468
...(((..............))).))).	chr1:150190896-150191121(-)$1	1	186	214	22.3237
...(((((............)))))...	chr1:228286743-228286972(+)$1	1	143	171	23.8039
(...((((................))))	chr20:44445445-44445686(+)$1	1	63	91	22.6951
(.((((((................))))	chr6:151685654-151685884(-)$1	1	29	57	22.8811
(....((((...........)))))).)	chr1:154179615-154179849(-)$1	1	18	46	21.0410
.(((((((............))))))).	chr8:41367261-41367499(+)$1	1	171	199	23.0916
.(((((..............))))))))	chr10:70742698-70742923(+)$1	1	176	204	21.9008
((((((((.............)))))))	chr8:145748272-145748496(+)$1	1	179	207	23.2102
)((((((................)))))	chr17:48829451-48829709(+)$1	1	32	60	23.1284
(((((.(((...........)))...))	chr18:12814105-12814332(-)$1	1	77	105	22.4190
(((..(((................))).	chr12:98928225-98928449(+)$1	1	107	135	23.8607
(((.(((((...........))))).))	chr19:36259374-36259600(+)$1	1	117	145	21.4577
(((.(((..............))).)))	chr17:27246071-27246297(-)$1	1	31	59	22.9369
.((((((................)))))	chr6:109688167-109688395(-)$1	1	83	111	22.4877
))((((((..............))))))	chr17:12046019-12046243(+)$1	1	196	224	20.4115
((.(((..............))).)).)	chr17:74731148-74731379(-)$1	1	117	145	21.3628
(((..((((...........))))..))	chr3:10192894-10193122(+)$1	1	104	132	21.0909
)((((((...............))))))	chr5:180665991-180666219(-)$1	1	16	44	19.5857
)(((.(((...............))).)	chr19:12242400-12242629(-)$1	1	189	217	19.8526
..((((((...........)))))))).	chr3:195776360-195776595(-)$1	1	92	120	19.1743
((...(((............))).))))	chr6:26156510-26156749(+)$1	1	160	188	24.2951
.((((.(((...........))))))).	chr17:40277221-40277458(-)$1	1	57	85	21.8138

#PSSM
e : 0.17	d : 0.11	b : 0.11	c : 0.09	f : 0.07	: : 0.07	i : 0.04	# : 0.04	" : 0.04	! : 0.03	g : 0.03	= : 0.03	B : 0.01	h : 0.01	+ : 0.01	[ : 0.01	C : 0.01	F : 0.01	( : 0.01	
e : 0.17	f : 0.12	g : 0.12	c : 0.09	d : 0.07	# : 0.06	i : 0.04	b : 0.04	! : 0.04	" : 0.04	[ : 0.04	= : 0.03	h : 0.01	: : 0.01	C : 0.01	( : 0.01	
f : 0.17	e : 0.17	g : 0.14	d : 0.07	c : 0.07	! : 0.07	# : 0.06	" : 0.06	i : 0.04	[ : 0.04	= : 0.03	h : 0.01	
e : 0.23	f : 0.19	g : 0.14	! : 0.11	d : 0.06	c : 0.06	i : 0.04	# : 0.04	" : 0.03	[ : 0.03	h : 0.01	= : 0.01	
e : 0.19	f : 0.17	d : 0.14	! : 0.12	g : 0.12	i : 0.04	c : 0.04	# : 0.03	y : 0.03	[ : 0.03	h : 0.01	= : 0.01	" : 0.01	
d : 0.19	c : 0.15	f : 0.15	e : 0.14	g : 0.11	! : 0.06	i : 0.04	[ : 0.04	y : 0.03	# : 0.01	h : 0.01	= : 0.01	
d : 0.17	c : 0.15	f : 0.14	e : 0.12	g : 0.11	b : 0.11	y : 0.04	w : 0.04	i : 0.03	! : 0.01	h : 0.01	= : 0.01	
d : 0.15	c : 0.14	b : 0.12	g : 0.11	w : 0.11	f : 0.09	y : 0.07	e : 0.07	i : 0.03	x : 0.03	[ : 0.01	= : 0.01	
u : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	d : 0.06	t : 0.03	f : 0.03	c : 0.03	a : 0.01	b : 0.01	g : 0.01	e : 0.01	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	t : 0.22	w : 0.20	y : 0.15	x : 0.09	v : 0.09	
u : 0.22	w : 0.20	t : 0.19	y : 0.15	x : 0.09	v : 0.09	d : 0.01	f : 0.01	
w : 0.15	y : 0.12	c : 0.12	d : 0.11	x : 0.09	v : 0.09	e : 0.07	g : 0.06	b : 0.04	f : 0.04	i : 0.03	a : 0.01	
d : 0.14	c : 0.14	y : 0.12	e : 0.11	x : 0.09	w : 0.09	b : 0.07	f : 0.06	g : 0.06	i : 0.03	] : 0.01	h : 0.01	= : 0.01	
d : 0.14	e : 0.14	c : 0.14	y : 0.11	g : 0.09	f : 0.09	b : 0.07	x : 0.06	i : 0.04	4 : 0.01	2 : 0.01	] : 0.01	h : 0.01	= : 0.01	
d : 0.15	f : 0.15	e : 0.15	g : 0.11	y : 0.07	] : 0.07	b : 0.06	i : 0.04	c : 0.04	3 : 0.03	4 : 0.01	2 : 0.01	h : 0.01	= : 0.01	
e : 0.20	f : 0.19	g : 0.12	c : 0.07	] : 0.07	d : 0.07	2 : 0.06	i : 0.04	b : 0.04	3 : 0.03	4 : 0.01	h : 0.01	= : 0.01	
e : 0.19	f : 0.17	g : 0.14	c : 0.11	d : 0.06	2 : 0.06	i : 0.04	3 : 0.04	b : 0.04	4 : 0.03	] : 0.03	h : 0.01	: : 0.01	= : 0.01	
e : 0.17	g : 0.15	f : 0.15	d : 0.12	c : 0.09	] : 0.06	i : 0.04	b : 0.04	2 : 0.04	3 : 0.01	h : 0.01	: : 0.01	4 : 0.01	= : 0.01	
e : 0.15	f : 0.14	d : 0.11	g : 0.09	c : 0.07	] : 0.07	2 : 0.06	i : 0.04	: : 0.04	b : 0.03	3 : 0.03	4 : 0.03	5 : 0.01	h : 0.01	E : 0.01	7 : 0.01	= : 0.01	

#score	1388.2001604605232
#seq	63
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_UTR_m1_run1.txt

#BEAR
:eeeeeyyyyyyyyyyyyyyyyeeeee	chr6:114181919-114182144(+)$1	225	17	44	19.7202
g[ffffffvvvvvvvvvvvvvffffff	chr6:170715826-170716052(+)$1	226	84	111	23.3566
=======uuuuuuuuuuuu========	chr8:30401916-30402240(+)$1	324	112	139	24.6028
cggggggguuuuuuuuuuuuggggggg	chr6:163993032-163993254(+)$1	222	43	70	24.2653
ffffffwwwwwwwwwwwwwwffffff:	chr17:48459887-48460106(-)$1	219	86	113	20.2737
hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr13:97928267-97928487(+)$1	220	153	180	21.9304
b[ffffffvvvvvvvvvvvvvffffff	chr20:48569764-48569996(+)$1	232	102	129	23.1122
""ddddvvvvvvvvvvvvvddddiiii	chr8:38103298-38103519(+)$1	221	165	192	22.9161
gggggggvvvvvvvvvvvvvggggggg	chr12:98941566-98941788(+)$1	222	35	62	24.5049
===eeeeewwwwwwwwwwwwwweeeee	chr2:55402728-55402951(-)$1	223	41	68	21.7324
:eeeeevvvvvvvvvvvvveeeeebbn	chr2:211298429-211298661(-)$1	232	3	30	20.6772
f[aeeeeettttttttttteeeee]a]	chr1:218507208-218507432(+)$1	224	184	211	23.8627
!!fffffftttttttttttffffff]e	chr2:70131363-70131582(+)$1	219	36	63	23.8632
eeeeyyyyyyyyyyyyyyyyeeeee]d	chr6:160177073-160177294(+)$1	221	34	61	20.0159
eeeeddddvvvvvvvvvvvvvdddd]e	chr8:22279290-22279509(+)$1	219	77	104	23.0298
ggggggyyyyyyyyyyyyyyyyggggg	chr14:67801078-67801299(+)$1	221	178	205	21.5801
hhhhhhhhuuuuuuuuuuuuhhhhhhh	chr2:153511452-153511674(-)$1	222	27	54	21.7443
"ggggggguuuuuuuuuuuuggggggg	chr2:20518209-20518434(-)$1	225	162	189	24.2964
b!!eeeeettttttttttteeeee22b	chr2:20449974-20450196(-)$1	222	164	191	23.2876
========ttttttttttt========	chr1:218504588-218504808(+)$1	220	10	37	25.3102
####ddddtttttttttttddddcccf	chr14:32315624-32315846(+)$1	222	83	110	23.4529
f!!cccvvvvvvvvvvvvvccc22fff	chr21:34730131-34730358(+)$1	227	61	88	23.0743
eeee[ccctttttttttttccc]eeee	chr9:19375881-19376102(-)$1	221	88	115	24.2146
ccc[ddddvvvvvvvvvvvvvdddd]c	chrX:24095676-24095905(+)$1	229	165	192	23.2726
e[ffffffwwwwwwwwwwwwwwfffff	chr15:75950347-75950570(+)$1	223	82	109	21.3358
=======uuuuuuuuuuuu========	chr18:12794164-12794384(-)$1	220	30	57	24.6028
hhhhddddtttttttttttdddd>>>>	chr12:110929353-110929574(-)$1	221	141	168	21.8777
eeeeddddtttttttttttdddd22ee	chr1:149913439-149913661(-)$1	222	182	209	22.8702
ggggggguuuuuuuuuuuuggggggg2	chr17:56081070-56081291(-)$1	221	129	156	23.7009
c[fffffftttttttttttffffff]c	chr17:5335894-5336115(+)$1	221	91	118	23.8192
ffffffvvvvvvvvvvvvvffffff::	chr14:68123090-68123319(-)$1	229	143	170	20.4650
hhhhhhhhttttttttttthhhhhhhh	chr7:90044442-90044668(+)$1	226	0	27	21.8488
iiiiiiiitttttttttttiiiiiiii	chr17:7417700-7417919(+)$1	219	186	213	25.0108
iiiiiiivvvvvvvvvvvvviiiiiii	chr2:113091590-113091817(+)$1	227	190	217	24.8582
#eeeeebbvvvvvvvvvvvvvbb]eee	chr13:53206458-53206683(+)$1	225	138	165	22.6531
ggggddddtttttttttttdddd]ggg	chr7:158433249-158433469(-)$1	220	99	126	24.0200
d[ccc[cccvvvvvvvvvvvvvccc]c	chr1:210416009-210416233(+)$1	224	91	118	21.8822
ffff[cccwwwwwwwwwwwwwwccc]f	chr19:2430743-2430963(-)$1	220	93	120	21.8219
ccbb[cccvvvvvvvvvvvvvcccbb:	chr10:60129297-60129520(+)$1	223	148	175	21.7785
========ttttttttttt========	chr2:10269444-10269666(+)$1	222	100	127	25.3102
fffff[bbuuuuuuuuuuuubbfffff	chr10:89312911-89313134(+)$1	223	7	34	22.5626
iiiiiiivvvvvvvvvvvvviiiiiii	chr11:68381563-68381786(+)$1	223	117	144	24.8582
hhhhhhhhuuuuuuuuuuuuhhhhhhh	chr2:68406806-68407027(-)$1	221	1	28	21.7443
dddd[ccctttttttttttccc]dddd	chr16:70504994-70505227(+)$1	233	86	113	23.2943
b[ddddbbtttttttttttbb]dddd]	chr11:129992201-129992424(+)$1	223	84	111	22.7684
:::eeeeettttttttttteeeeeddd	chr22:33255548-33255771(+)$1	223	128	155	20.2005
!!eeeeewwwwwwwwwwwwwweeeee2	chr10:104624231-104624466(+)$1	235	93	120	22.0364
cccc[ccctttttttttttccc22ccc	chr20:35237972-35238193(+)$1	221	51	78	24.0552
!ccc[ccctttttttttttccc]ccc2	chr15:66841210-66841439(+)$1	229	31	58	24.3275
f"""bbvvvvvvvvvvvvvbb333fff	chr14:97032608-97032839(+)$1	231	131	158	22.3266
iiiiiiivvvvvvvvvvvvviiiiiii	chr19:32874989-32875210(+)$1	221	93	120	24.8582
e"""ddddtttttttttttdddd333e	chr19:6414395-6414617(-)$1	222	85	112	23.6780
%ffffffuuuuuuuuuuuuffffff]h	chr3:87304128-87304354(+)$1	226	165	192	22.1505
iiiiiiiiuuuuuuuuuuuuiiiiiii	chr1:232174690-232174920(+)$1	230	187	214	24.6837
:ffffffuuuuuuuuuuuuffffff:f	chr6:126251701-126251931(+)$1	230	144	171	20.7346
f"""bbbbtttttttttttbb]bbfff	chr18:47920026-47920251(+)$1	225	104	131	22.3276
gggg!!bbtttttttttttbb22gggg	chr12:88589979-88590200(+)$1	221	55	82	23.7527
dddd!!bbtttttttttttbb22dddd	chr13:34411133-34411365(+)$1	232	64	91	22.0007
eeeeeccctttttttttttccc4444e	chr11:43876813-43877034(+)$1	221	183	210	23.9460
gg"""ccctttttttttttccc4444g	chr1:229458901-229459122(-)$1	221	47	74	24.2590
iiiiiiiitttttttttttiiiiiiii	chr5:151185066-151185286(+)$1	220	91	118	25.0108
c[ccc[bbtttttttttttbb]ccccc	chr2:9017113-9017335(-)$1	222	68	95	23.7764
$$$eeeeettttttttttteeeeeiii	chr1:212277874-212278104(+)$1	230	126	153	23.5028
f"""ddddvvvvvvvvvvvvvdddd]f	chr12:64538838-64539061(+)$1	223	94	121	23.2395
eee[ddddtttttttttttddddeeee	chr15:70341784-70342013(-)$1	229	175	202	23.2734
$$$eeeeettttttttttteeeee22c	chr15:49282276-49282500(-)$1	224	131	158	22.9203

#otherMatches

#Seq PSSM
CACAGAUCCCAUCUCAAAUCAUUCUGU	chr6:114181919-114182144(+)$1	225	17	44	19.7202
UCUGUGAAAAUUGUUUUCUCCUUCAUA	chr6:170715826-170716052(+)$1	226	84	111	23.3566
CACUUUACCCCAGUAGCCCUGAAGUGU	chr8:30401916-30402240(+)$1	324	112	139	24.6028
CCAAAUCUGAUACUGUGAAAAGAUUUG	chr6:163993032-163993254(+)$1	222	43	70	24.2653
UAAAUGGUCAGCUGUCACUACAUUUAU	chr17:48459887-48460106(-)$1	219	86	113	20.2737
UGGAAUCAUUAGAACUUGGAUUGAUUU	chr13:97928267-97928487(+)$1	220	153	180	21.9304
UCAUAUUUCACAAAUAUUAAUAAAUAU	chr20:48569764-48569996(+)$1	232	102	129	23.1122
UUUAGGUAACAAAAUGAGUUCUGUGUG	chr8:38103298-38103519(+)$1	221	165	192	22.9161
AUUUUCUUCAUGUUGACCCUAGAAAAU	chr12:98941566-98941788(+)$1	222	35	62	24.5049
AGCUGAGGGAGCUUGUACAACACCUUA	chr2:55402728-55402951(-)$1	223	41	68	21.7324
AUAUCAUUUUUUAAAUUCUUGAUGCCU	chr2:211298429-211298661(-)$1	232	3	30	20.6772
GGUUGAUGUUCUUAGUAUUUAUCAUAG	chr1:218507208-218507432(+)$1	224	184	211	23.8627
GAAAAGGUGGAUUCAACAGACCUUUGG	chr2:70131363-70131582(+)$1	219	36	63	23.8632
GUUUUUUAUCACUAAAAGUUGGACUCA	chr6:160177073-160177294(+)$1	221	34	61	20.0159
UAGGGUGUUUUCCCUUUUUGUGCACAC	chr8:22279290-22279509(+)$1	219	77	104	23.0298
CUACAUAAUUUUAUUUGAACAAAUGUA	chr14:67801078-67801299(+)$1	221	178	205	21.5801
CAGACUAUUUUAGAGAGGCUGUGGUUU	chr2:153511452-153511674(-)$1	222	27	54	21.7443
AUUGUGAAUAUAUUUAGCAUUUUAUAA	chr2:20518209-20518434(-)$1	225	162	189	24.2964
AGUAUGAACCAGCUUUCUUUUUAUUAU	chr2:20449974-20450196(-)$1	222	164	191	23.2876
AAUUAUAUUUUAAACCCUUGUAUAAUU	chr1:218504588-218504808(+)$1	220	10	37	25.3102
UCCAGUGUCCAAAAUGUAAACACAAAA	chr14:32315624-32315846(+)$1	222	83	110	23.4529
GGAGCAUAUCAUGACUGCCUGCCACCA	chr21:34730131-34730358(+)$1	227	61	88	23.0743
GAAAUGAUGAGGACUAUUAAUCUUUUU	chr9:19375881-19376102(-)$1	221	88	115	24.2146
AAGUUAUCUCCCUCUCCCUGUGAUGCC	chrX:24095676-24095905(+)$1	229	165	192	23.2726
GCAGGGGACCAUUGCAGCAUCCUCCCC	chr15:75950347-75950570(+)$1	223	82	109	21.3358
AAGAUGGGGUUUAUGUCAGUCAUUUUG	chr18:12794164-12794384(-)$1	220	30	57	24.6028
AUUUAUACUUUGAUAACCUGuauuuaa	chr12:110929353-110929574(-)$1	221	141	168	21.8777
aaauaguauuuaucuugguuacugggu	chr1:149913439-149913661(-)$1	222	182	209	22.8702
CAAAGAUUUUUUUUUUCCUAUUUUUGA	chr17:56081070-56081291(-)$1	221	129	156	23.7009
UUGUAUUGAAACUUUUAAACAAUACUG	chr17:5335894-5336115(+)$1	221	91	118	23.8192
AGCUGGGGGAACAACGAGACCAGUUAG	chr14:68123090-68123319(-)$1	229	143	170	20.4650
UAUAUAGCGAAUAAAUCUAGUUGUAUA	chr7:90044442-90044668(+)$1	226	0	27	21.8488
UUUUAUUUUUUUGAAGUUUAAAUAAAG	chr17:7417700-7417919(+)$1	219	186	213	25.0108
UUUGUUGUUAAUUGAGAAGUCAAUAAA	chr2:113091590-113091817(+)$1	227	190	217	24.8582
AUUAUGGCAGUUACUAAAGAAGCACGU	chr13:53206458-53206683(+)$1	225	138	165	22.6531
gcaacuaauucucuuaauuuugguuug	chr7:158433249-158433469(-)$1	220	99	126	24.0200
UCUAUAUGAUACAAUAUUUUUUUUAAA	chr1:210416009-210416233(+)$1	224	91	118	21.8822
GCCACUGAAAACUAUUUUUAUAUCAUU	chr19:2430743-2430963(-)$1	220	93	120	21.8219
CAGAUCUAUUUUGUUUGCCAUUAGUCA	chr10:60129297-60129520(+)$1	223	148	175	21.7785
UUUUUUUUUUCCAUCUCAUAAGAAAAA	chr2:10269444-10269666(+)$1	222	100	127	25.3102
GUUUGGACAAUUAGCAACAAGUCAGAU	chr10:89312911-89313134(+)$1	223	7	34	22.5626
AACCAGUGUAUUUUUUUAGAACUGGUU	chr11:68381563-68381786(+)$1	223	117	144	24.8582
AUGUAUGUAUCUAAACACCCACAUAUA	chr2:68406806-68407027(-)$1	221	1	28	21.7443
CCAGGGCCCCAUUCACAUAGGCGCUGG	chr16:70504994-70505227(+)$1	233	86	113	23.2943
ugguggaggaCCGAGAUUACUACUAUG	chr11:129992201-129992424(+)$1	223	84	111	22.7684
CAAAAAUGAAAAACUACUCCAUUUGAG	chr22:33255548-33255771(+)$1	223	128	155	20.2005
UAUGUGAUAAAAUAAUACCUUUCACAA	chr10:104624231-104624466(+)$1	235	93	120	22.0364
GAGUCCUGUACCUCUACUUCAGCAAUU	chr20:35237972-35238193(+)$1	221	51	78	24.0552
UUAGCAGCCAUAUUCCACAGUUCCUAU	chr15:66841210-66841439(+)$1	229	31	58	24.3275
UGUUGAUAAACUUACUCUUUCUGAAUC	chr14:97032608-97032839(+)$1	231	131	158	22.3266
UGUUUGUAAAAAUUUUAAUAACAAAUA	chr19:32874989-32875210(+)$1	221	93	120	24.8582
gcgugaagaucguugccaccuuccaac	chr19:6414395-6414617(-)$1	222	85	112	23.6780
CAUUUUGGGCUAAUACUGACAAAAUAC	chr3:87304128-87304354(+)$1	226	165	192	22.1505
UUAUAAUUGUGUCUAAAGAAAAUUAUG	chr1:232174690-232174920(+)$1	230	187	214	24.6837
UGCUAUAAAAUUUUAAAUCUGUAGCCU	chr6:126251701-126251931(+)$1	230	144	171	20.7346
aaauuccuuuaaauuucccagugauag	chr18:47920026-47920251(+)$1	225	104	131	22.3276
UUUAAAUGUAAUUUUUAAUCAGGUAAA	chr12:88589979-88590200(+)$1	221	55	82	23.7527
GUGACAGACUCCGAACAAUUCCUUUAC	chr13:34411133-34411365(+)$1	232	64	91	22.0007
UUUGAAGUUUAAUAUAAAUGCUCAUAU	chr11:43876813-43877034(+)$1	221	183	210	23.9460
ACUUUGAACCGCCAGACUUUUCUCUUG	chr1:229458901-229459122(-)$1	221	47	74	24.2590
UUGCUGUGAUGGUUAAGACCACAGUGA	chr5:151185066-151185286(+)$1	220	91	118	25.0108
UACAAAGACUACAUUACUUUCAUUGAA	chr2:9017113-9017335(-)$1	222	68	95	23.7764
ACUGAGUGAAAUUGGGAUACAUUUGGC	chr1:212277874-212278104(+)$1	230	126	153	23.5028
GUAAGAAUUCUUAAAAACCAUAUUCCU	chr12:64538838-64539061(+)$1	223	94	121	23.2395
CUCACCUGGGAAGAGGAGACAGGGAGG	chr15:70341784-70342013(-)$1	229	175	202	23.2734
AAUUGUCAUUUUAGAUUUUUGACAUUU	chr15:49282276-49282500(-)$1	224	131	158	22.9203

#DB
.(((((................)))))	chr6:114181919-114182144(+)$1	1	17	44	19.7202
(.((((((.............))))))	chr6:170715826-170716052(+)$1	1	84	111	23.3566
(((((((............))))))))	chr8:30401916-30402240(+)$1	1	112	139	24.6028
)(((((((............)))))))	chr6:163993032-163993254(+)$1	1	43	70	24.2653
((((((..............)))))).	chr17:48459887-48460106(-)$1	1	86	113	20.2737
((((((((.............))))))	chr13:97928267-97928487(+)$1	1	153	180	21.9304
(.((((((.............))))))	chr20:48569764-48569996(+)$1	1	102	129	23.1122
..((((.............))))))))	chr8:38103298-38103519(+)$1	1	165	192	22.9161
(((((((.............)))))))	chr12:98941566-98941788(+)$1	1	35	62	24.5049
((((((((..............)))))	chr2:55402728-55402951(-)$1	1	41	68	21.7324
.(((((.............)))))((.	chr2:211298429-211298661(-)$1	1	3	30	20.6772
(.((((((...........))))).).	chr1:218507208-218507432(+)$1	1	184	211	23.8627
..((((((...........)))))).)	chr2:70131363-70131582(+)$1	1	36	63	23.8632
((((................))))).)	chr6:160177073-160177294(+)$1	1	34	61	20.0159
((((((((.............)))).)	chr8:22279290-22279509(+)$1	1	77	104	23.0298
((((((................)))))	chr14:67801078-67801299(+)$1	1	178	205	21.5801
((((((((............)))))))	chr2:153511452-153511674(-)$1	1	27	54	21.7443
.(((((((............)))))))	chr2:20518209-20518434(-)$1	1	162	189	24.2964
(..(((((...........)))))..)	chr2:20449974-20450196(-)$1	1	164	191	23.2876
((((((((...........))))))))	chr1:218504588-218504808(+)$1	1	10	37	25.3102
....((((...........))))))))	chr14:32315624-32315846(+)$1	1	83	110	23.4529
(..(((.............)))..)))	chr21:34730131-34730358(+)$1	1	61	88	23.0743
((((.(((...........))).))))	chr9:19375881-19376102(-)$1	1	88	115	24.2146
(((.((((.............)))).)	chrX:24095676-24095905(+)$1	1	165	192	23.2726
(.((((((..............)))))	chr15:75950347-75950570(+)$1	1	82	109	21.3358
(((((((............))))))))	chr18:12794164-12794384(-)$1	1	30	57	24.6028
((((((((...........))))....	chr12:110929353-110929574(-)$1	1	141	168	21.8777
((((((((...........))))..))	chr1:149913439-149913661(-)$1	1	182	209	22.8702
(((((((............))))))).	chr17:56081070-56081291(-)$1	1	129	156	23.7009
(.((((((...........)))))).)	chr17:5335894-5336115(+)$1	1	91	118	23.8192
((((((.............))))))..	chr14:68123090-68123319(-)$1	1	143	170	20.4650
((((((((...........))))))))	chr7:90044442-90044668(+)$1	1	0	27	21.8488
((((((((...........))))))))	chr17:7417700-7417919(+)$1	1	186	213	25.0108
(((((((.............)))))))	chr2:113091590-113091817(+)$1	1	190	217	24.8582
.(((((((.............)).)))	chr13:53206458-53206683(+)$1	1	138	165	22.6531
((((((((...........)))).)))	chr7:158433249-158433469(-)$1	1	99	126	24.0200
(.(((.(((.............))).)	chr1:210416009-210416233(+)$1	1	91	118	21.8822
((((.(((..............))).)	chr19:2430743-2430963(-)$1	1	93	120	21.8219
))((.(((.............))))).	chr10:60129297-60129520(+)$1	1	148	175	21.7785
((((((((...........))))))))	chr2:10269444-10269666(+)$1	1	100	127	25.3102
(((((.((............)))))))	chr10:89312911-89313134(+)$1	1	7	34	22.5626
(((((((.............)))))))	chr11:68381563-68381786(+)$1	1	117	144	24.8582
((((((((............)))))))	chr2:68406806-68407027(-)$1	1	1	28	21.7443
((((.(((...........))).))))	chr16:70504994-70505227(+)$1	1	86	113	23.2943
(.((((((...........)).)))).	chr11:129992201-129992424(+)$1	1	84	111	22.7684
...(((((...........)))))(((	chr22:33255548-33255771(+)$1	1	128	155	20.2005
..(((((..............))))).	chr10:104624231-104624466(+)$1	1	93	120	22.0364
((((.(((...........)))..)))	chr20:35237972-35238193(+)$1	1	51	78	24.0552
.(((.(((...........))).))).	chr15:66841210-66841439(+)$1	1	31	58	24.3275
(...((.............))...)))	chr14:97032608-97032839(+)$1	1	131	158	22.3266
(((((((.............)))))))	chr19:32874989-32875210(+)$1	1	93	120	24.8582
(...((((...........))))...)	chr19:6414395-6414617(-)$1	1	85	112	23.6780
.((((((............)))))).)	chr3:87304128-87304354(+)$1	1	165	192	22.1505
((((((((............)))))))	chr1:232174690-232174920(+)$1	1	187	214	24.6837
.((((((............)))))).(	chr6:126251701-126251931(+)$1	1	144	171	20.7346
(...((((...........)).)))))	chr18:47920026-47920251(+)$1	1	104	131	22.3276
((((..((...........))..))))	chr12:88589979-88590200(+)$1	1	55	82	23.7527
((((..((...........))..))))	chr13:34411133-34411365(+)$1	1	64	91	22.0007
((((((((...........)))....)	chr11:43876813-43877034(+)$1	1	183	210	23.9460
((...(((...........)))....)	chr1:229458901-229459122(-)$1	1	47	74	24.2590
((((((((...........))))))))	chr5:151185066-151185286(+)$1	1	91	118	25.0108
(.(((.((...........)).)))))	chr2:9017113-9017335(-)$1	1	68	95	23.7764
...(((((...........))))))))	chr1:212277874-212278104(+)$1	1	126	153	23.5028
(...((((.............)))).)	chr12:64538838-64539061(+)$1	1	94	121	23.2395
(((.((((...........))))))))	chr15:70341784-70342013(-)$1	1	175	202	23.2734
...(((((...........)))))..)	chr15:49282276-49282500(-)$1	1	131	158	22.9203

#PSSM
f : 0.13	e : 0.12	g : 0.10	c : 0.09	i : 0.09	= : 0.07	h : 0.07	: : 0.06	b : 0.04	! : 0.04	d : 0.04	" : 0.03	# : 0.03	$ : 0.03	% : 0.01	
e : 0.13	[ : 0.12	g : 0.12	f : 0.09	i : 0.09	= : 0.07	h : 0.07	" : 0.07	! : 0.06	c : 0.06	d : 0.03	$ : 0.03	# : 0.01	: : 0.01	
f : 0.16	e : 0.15	g : 0.10	i : 0.09	= : 0.07	h : 0.07	c : 0.07	" : 0.07	d : 0.06	! : 0.03	$ : 0.03	a : 0.01	# : 0.01	b : 0.01	: : 0.01	
e : 0.22	f : 0.16	g : 0.10	i : 0.09	h : 0.07	c : 0.07	" : 0.07	= : 0.06	d : 0.06	[ : 0.03	# : 0.01	b : 0.01	
e : 0.16	d : 0.16	f : 0.15	[ : 0.09	i : 0.09	g : 0.07	= : 0.06	h : 0.06	c : 0.04	b : 0.03	! : 0.03	y : 0.01	" : 0.01	
d : 0.16	e : 0.15	f : 0.13	c : 0.13	i : 0.09	g : 0.07	= : 0.06	h : 0.06	[ : 0.04	b : 0.03	! : 0.03	y : 0.01	
d : 0.13	c : 0.13	f : 0.10	e : 0.10	b : 0.10	i : 0.09	v : 0.07	= : 0.06	g : 0.06	h : 0.06	y : 0.04	w : 0.01	
v : 0.13	d : 0.13	c : 0.13	b : 0.10	e : 0.09	f : 0.07	u : 0.07	h : 0.06	y : 0.04	i : 0.04	g : 0.03	w : 0.03	= : 0.03	
t : 0.43	v : 0.25	u : 0.16	w : 0.07	y : 0.04	c : 0.01	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
t : 0.43	v : 0.27	u : 0.16	w : 0.07	y : 0.04	
v : 0.19	d : 0.10	c : 0.10	u : 0.09	e : 0.09	b : 0.09	w : 0.07	f : 0.07	= : 0.06	y : 0.04	i : 0.03	g : 0.01	h : 0.01	
v : 0.13	d : 0.10	e : 0.10	c : 0.10	b : 0.10	f : 0.09	i : 0.09	= : 0.06	g : 0.06	w : 0.06	h : 0.04	y : 0.03	
d : 0.15	f : 0.12	e : 0.12	c : 0.12	i : 0.09	= : 0.06	g : 0.06	h : 0.06	w : 0.04	] : 0.04	y : 0.03	b : 0.03	2 : 0.03	v : 0.01	3 : 0.01	
d : 0.16	e : 0.15	f : 0.15	i : 0.09	g : 0.07	= : 0.06	h : 0.06	2 : 0.06	c : 0.06	] : 0.04	b : 0.03	4 : 0.03	3 : 0.01	
e : 0.18	f : 0.15	i : 0.10	g : 0.09	d : 0.09	c : 0.09	= : 0.06	h : 0.06	2 : 0.04	] : 0.03	3 : 0.03	4 : 0.03	> : 0.01	b : 0.01	
f : 0.19	i : 0.12	e : 0.10	g : 0.10	d : 0.10	c : 0.09	= : 0.06	h : 0.06	2 : 0.04	b : 0.03	4 : 0.03	] : 0.01	> : 0.01	3 : 0.01	
] : 0.13	f : 0.12	i : 0.12	e : 0.10	g : 0.10	= : 0.06	h : 0.06	c : 0.06	d : 0.06	b : 0.03	2 : 0.03	: : 0.03	4 : 0.03	a : 0.01	> : 0.01	3 : 0.01	
f : 0.16	e : 0.15	i : 0.12	g : 0.10	c : 0.09	h : 0.07	= : 0.06	d : 0.06	: : 0.04	2 : 0.04	] : 0.03	n : 0.01	b : 0.01	> : 0.01	

#score	1518.2429679936033
#seq	66
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000