
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_transcript_m3_run1.txt

#BEAR
FF:ccc!!a[ddddmmmmdddd]a333cc	chr5:15877897-15878134(+)$1	237	197	226	12.0504
!ggggggg!!ddddmmmmddddggggggg	chr5:124951445-124951696(-)$1	251	28	57	12.8232
:=============mmmm===========	chrX:80653176-80653413(+)$1	237	144	173	11.2948
"""ffffff[ddddmmmmdddd]ffffff	chr12:55960170-55960414(-)$1	244	96	125	11.7719
ccc####gggggggmmmmggggggg22cc	chr2:32087351-32087589(+)$1	238	36	65	11.1169
cc[ffffff!!cccmmmmccc22ffffff	chr6:30249969-30250204(-)$1	235	72	101	10.9206
dd[bb[ccc[ddddmmmmdddd22ccc]b	chr13:60807317-60807555(+)$1	238	70	99	11.8989
h[a[ccc[bb[cccmmmmccc]bb]ccc]	chrX:71549761-71549996(+)$1	235	182	211	11.0775
$$$$dddd!!ddddoooooodddd333dd	chr7:122797650-122797885(-)$1	235	185	214	9.4245
:===========[allla]==========	chr15:79365502-79365737(-)$1	235	191	220	9.0440
dd[bb!!gggggggmmmmggggggg]bb]	chr1:180181907-180182144(+)$1	237	25	54	9.8679
####ccc"""ddddmmmmddddccc333d	chr4:6322128-6322363(+)$1	235	203	232	14.0219
dddd[ccc"""cccmmmmccc333ccc22	chr14:60898841-60899085(+)$1	244	117	146	12.0422
bb[ccc[a[ddddnnnnndddd]a]ccc]	chr7:3298086-3298324(+)$1	238	108	137	9.0490
:ffffff[ccccccmmmmccc22ccc]ff	chr5:20264762-20265003(-)$1	241	95	124	10.1331
h[cccddddeeeeemmmmeeeee333ddd	chr1:36879850-36880085(-)$1	235	126	155	10.8017
dd####ddddddddmmmmdddd]dddd33	chr9:30957160-30957421(-)$1	261	2	31	11.3191
a[bb[ccc!!eeeeellleeeee]ccc]b	chr6:32910948-32911183(-)$1	235	188	217	8.9781
cccccc[ccc[cccmmmmccc]ccc]ccc	chr12:16992172-16992410(+)$1	238	203	232	11.8197
eeee$$$$$eeeeemmmmeeeee333eee	chr11:29642168-29642473(+)$1	305	197	226	10.8088
eeee$$$$$eeeeemmmmeeeee333eee	chrX:98835693-98835928(+)$1	235	67	96	10.8088
[eeeee"""bbcccmmmmccc]bb]eeee	chr9:102445317-102445562(+)$1	245	42	71	10.6295
"""ffffff!!cccmmmmccc22ffffff	chr7:138588944-138589179(+)$1	235	96	125	11.2374
ccccc!!ddddcccmmmmccc]dddd22c	chr9:72510245-72510480(+)$1	235	104	133	10.7238
ccc"""eeeee!!ammmma22eeeeeccc	chr15:103023875-103024111(-)$1	236	89	118	9.9073
!!ccc[bb!!ddddmmmmdddd22bb]cc	chr19:6389709-6389944(+)$1	235	140	169	12.3242
!!eeeee[ffffffmmmmffffff]eeee	chr4:126706308-126706556(+)$1	248	169	198	9.6478
dd[eeeee[ddddoooooodddd]eeeee	chr1:54702798-54703044(-)$1	246	60	89	8.4550
#bb[bb"""eeeeemmmmeeeee]bb]bb	chr5:122903502-122903739(-)$1	237	80	109	10.0039
ccc[ccc"""ddddmmmmddddccc22cc	chr17:10406395-10406643(-)$1	248	164	193	13.2784
bbggggggg"""bbmmmmbb333gggggg	chr17:27716430-27716665(-)$1	235	95	124	10.0483
bgggggggffffffmmmmffffff333gg	chr15:27396439-27396677(+)$1	238	88	117	10.1814
###dddd"""ddddmmmmdddd333dddd	chr2:130101955-130102202(+)$1	247	32	61	13.3318
e[eeeee"""ddddmmmmdddd]eeeee]	chr19:12843634-12843875(-)$1	241	41	70	12.3619
fbb!!ccc!!ddddllldddd22ccc22b	chr7:20144330-20144565(-)$1	235	159	188	9.7172
gggggg!!ffffffmmmmffffff333gg	chr13:29999174-29999409(-)$1	235	76	105	10.6981
iiiiii[a[bb!!ammmma22bba]iiii	chr15:76001656-76001898(-)$1	242	198	227	9.7714
ff!!ccc[ccc[cccmmmmccc22ccc]c	chr3:60433367-60433602(+)$1	235	16	45	9.9873
bb[eeeee"""cccmmmmccceeeee]bb	chr1:135554227-135554464(-)$1	237	197	226	10.9606
$$$$dddd!!ddddmmmmdddd]dddd]a	chr18:61500318-61500556(-)$1	238	113	142	11.7323
cc[ccc!!ffffffmmmmffffff22ccc	chr7:88679712-88679947(-)$1	235	21	50	10.4284
eeeeeeee!!ddddmmmmdddd22eeeee	chr15:38224969-38225206(-)$1	237	115	144	11.8097
ee"""dddd[ddddmmmmdddd]dddd44	chr3:104260867-104261102(-)$1	235	115	144	11.6554
!ccc[iiiiiiiiimmmmiiiiiiiiicc	chr5:136385263-136385509(-)$1	246	118	147	11.3709
!!eeeee!!eeeeemmmmeeeee333eee	chr5:36944678-36944920(-)$1	242	155	184	12.0841
:::ccc####ddddmmmmdddd4444ccc	chr9:74906055-74906290(+)$1	235	141	170	11.0836
fffeeeee"""cccmmmmccc333eeeee	chr13:30801749-30801999(+)$1	250	103	132	11.7242
iii[ccc[bb[cccmmmmcccbbccc]ii	chr9:107950750-107950985(+)$1	235	193	222	11.0018
[a!!dddd"""cccmmmmccc4444dddd	chr11:4667759-4668018(-)$1	259	201	230	12.3118
ccc"""ccceeeeemmmmeeeee22ccc3	chr14:60248649-60248884(+)$1	235	126	155	11.3961
""ccc[ccc[ddddllldddd]ccc22cc	chr7:52399799-52400034(-)$1	235	103	132	10.3661
d####ccca[ddddmmmmdddd]a]ccc4	chr14:31846068-31846303(+)$1	235	191	220	13.2771

#otherMatches

#Seq PSSM
GUCUAGGGAGAGUAAUUUUACUGUAAGCU	chr5:15877897-15878134(+)$1	237	197	226	12.0504
GGUUCUCCUUGGGCAGGGGUUUGGGGAGC	chr5:124951445-124951696(-)$1	251	28	57	12.8232
uaaguuagggcucugaagagggcuuugau	chrX:80653176-80653413(+)$1	237	144	173	11.2948
GUGGCUUUUUGGUAAGGCUGCUUAGAAGC	chr12:55960170-55960414(-)$1	244	96	125	11.7719
ACCUAUGCAGCCUCAAAGGAGGCUGGUGG	chr2:32087351-32087589(+)$1	238	36	65	11.1169
GCUUGCUAGAAUUUAAAGAAAAGCUGGUG	chr6:30249969-30250204(-)$1	235	72	101	10.9206
AUUGCCCAUUGCAUUUAugugugugugug	chr13:60807317-60807555(+)$1	238	70	99	11.8989
AAAGACUGCCUGUCAAGAGGCCGGAGGUG	chrX:71549761-71549996(+)$1	235	182	211	11.0775
GAUCAGGUAAUGGAUAUCCUUCCAAAAGC	chr7:122797650-122797885(-)$1	235	185	214	9.4245
accuuaggcaagagauucauuuguuugag	chr15:79365502-79365737(-)$1	235	191	220	9.0440
CAGUAAUAGAUCAGAUAGUUGGUUUCUGG	chr1:180181907-180182144(+)$1	237	25	54	9.8679
UAAAAGCCAAAAUAGAAUUAUUGCUGCCU	chr4:6322128-6322363(+)$1	235	203	232	14.0219
CUGACCACUUCUGGAUGCCCACUUGUGAU	chr14:60898841-60899085(+)$1	244	117	146	12.0422
guguguguguUAAGGGGAUUGGGAAGCAG	chr7:3298086-3298324(+)$1	238	108	137	9.0490
UGCUUUAGGUUGCAGCUGUGUUUAACGUA	chr5:20264762-20265003(-)$1	241	95	124	10.1331
UCGCUGACCUGCUUCCCCAAGCACAUGGU	chr1:36879850-36880085(-)$1	235	126	155	10.8017
UGUGUAGCUGGAGUUCACGCUCACAGCCU	chr9:30957160-30957421(-)$1	261	2	31	11.3191
UGAAAGUUCAUCAGGUAGCUUGAAAACAU	chr6:32910948-32911183(-)$1	235	188	217	8.9781
ACAAUAAUGGAUUCUAUUGAAACUAAUGU	chr12:16992172-16992410(+)$1	238	203	232	11.8197
AACCCUUUUCACAGUGUACUGUGUUUGGU	chr11:29642168-29642473(+)$1	305	197	226	10.8088
GGCAUUACUGAGCUCUCGAGUUCUACUGC	chrX:98835693-98835928(+)$1	235	67	96	10.8088
CUAUGUAAAUCCAAGGUAUUGUGAAACGU	chr9:102445317-102445562(+)$1	245	42	71	10.6295
AAGUAUUUUGGUGCUUUUGCAAAAGGAUA	chr7:138588944-138589179(+)$1	235	96	125	11.2374
GCGCUUCGUCCAGCAUGAGCUCGGACAUG	chr9:72510245-72510480(+)$1	235	104	133	10.7238
CCUUUGGGUGUCACAGGAGGAAUGCCAGG	chr15:103023875-103024111(-)$1	236	89	118	9.9073
CAUCAACAUGGCACACCUGUGCAUUGCUG	chr19:6389709-6389944(+)$1	235	140	169	12.3242
UUAAGUGGAAAAAACUAUUUUUUUGUGCU	chr4:126706308-126706556(+)$1	248	169	198	9.6478
UUGAUGAGCCCAUCCCUUUGUGGUCUUGU	chr1:54702798-54703044(-)$1	246	60	89	8.4550
CGUCAGUUCAGUUGCUCACAGCUUCUCAC	chr5:122903502-122903739(-)$1	237	80	109	10.0039
AUGAAUGCAAUAUUGAUAGAUACAUGACA	chr17:10406395-10406643(-)$1	248	164	193	13.2784
GGUUGGUAUUUUAUAGAGGUUUUGUGCCG	chr17:27716430-27716665(-)$1	235	95	124	10.0483
UUUCUCCCCGGCAGAUCUUUGUUGUGUGG	chr15:27396439-27396677(+)$1	238	88	117	10.1814
ACCACAGGCUGUGUUCCUACACUGACUGU	chr2:130101955-130102202(+)$1	247	32	61	13.3318
UGGCUGAAAGAUAGGGCUCUGUGUCAGUG	chr19:12843634-12843875(-)$1	241	41	70	12.3619
CAGCUCUGAAGGACUGGGUCUACCAGUAC	chr7:20144330-20144565(-)$1	235	159	188	9.7172
AAGUAGAUGAGUACUACAGUAUUUUUGUU	chr13:29999174-29999409(-)$1	235	76	105	10.6981
UCUGGGUGCUGCUGCCCACCUCACUCCCA	chr15:76001656-76001898(-)$1	242	198	227	9.7714
CAAUGGCCACUUGUUUAAUGACUUGGUUG	chr3:60433367-60433602(+)$1	235	16	45	9.9873
CCAGCUUCCAUGGAAGAAUCUGAAGCAGG	chr1:135554227-135554464(-)$1	237	197	226	10.9606
UGAUGGGUGGGGCUGGGGAGCUGACCCCU	chr18:61500318-61500556(-)$1	238	113	142	11.7323
AUCUGCAAUGGCAUUUCAAUGCCAAAGCA	chr7:88679712-88679947(-)$1	235	21	50	10.4284
UGUGGGGGAGCCAAAGGAUUGGAACCCUC	chr15:38224969-38225206(-)$1	237	115	144	11.8097
UGUCUGGUUACUGUAUGGGCAGCGGCUUC	chr3:104260867-104261102(-)$1	235	115	144	11.6554
CUGGAGAACUCAUGGUCUCGUGGGUUCCC	chr5:136385263-136385509(-)$1	246	118	147	11.3709
UUAGAGACUUACAGAAUACUGUGCUUUCU	chr5:36944678-36944920(-)$1	242	155	184	12.0841
UUCGGACACAUUUAUUAUUAGAGCUCUCC	chr9:74906055-74906290(+)$1	235	141	170	11.0836
UGAGAAUGUUUGUCAUGUGACUAUUGUUU	chr13:30801749-30801999(+)$1	250	103	132	11.7242
UGGAUGCAUACGUGGCUCCACUGGCGCUU	chr9:107950750-107950985(+)$1	235	193	222	11.0018
GCUACCCACUCCCCAACUGGGCUUCUGGG	chr11:4667759-4668018(-)$1	259	201	230	12.3118
GAACAAUGUGUAUGUCAACAUGCCCACAA	chr14:60248649-60248884(+)$1	235	126	155	11.3961
ACUCCAGACAUGGGGCACCCGGGUUCAGG	chr7:52399799-52400034(-)$1	235	103	132	10.3661
UGAAAGGAAGUGAGACAGCUCAGUGUCCA	chr14:31846068-31846303(+)$1	235	191	220	13.2771

#DB
)).(((..(.((((....)))).)...))	chr5:15877897-15878134(+)$1	1	197	226	12.0504
.(((((((..((((....)))))))))))	chr5:124951445-124951696(-)$1	1	28	57	12.8232
.(((((((((((((....)))))))))))	chrX:80653176-80653413(+)$1	1	144	173	11.2948
...((((((.((((....)))).))))))	chr12:55960170-55960414(-)$1	1	96	125	11.7719
(((....(((((((....)))))))..))	chr2:32087351-32087589(+)$1	1	36	65	11.1169
((.((((((..(((....)))..))))))	chr6:30249969-30250204(-)$1	1	72	101	10.9206
((.((.(((.((((....))))..))).)	chr13:60807317-60807555(+)$1	1	70	99	11.8989
(.(.(((.((.(((....))).)).))).	chrX:71549761-71549996(+)$1	1	182	211	11.0775
....((((..((((......))))...))	chr7:122797650-122797885(-)$1	1	185	214	9.4245
.(((((((((((.(...).))))))))))	chr15:79365502-79365737(-)$1	1	191	220	9.0440
((.((..(((((((....))))))).)).	chr1:180181907-180182144(+)$1	1	25	54	9.8679
....(((...((((....)))))))...)	chr4:6322128-6322363(+)$1	1	203	232	14.0219
((((.(((...(((....)))...)))..	chr14:60898841-60899085(+)$1	1	117	146	12.0422
((.(((.(.((((.....)))).).))).	chr7:3298086-3298324(+)$1	1	108	137	9.0490
.((((((.((((((....)))..))).))	chr5:20264762-20265003(-)$1	1	95	124	10.1331
(.((((((((((((....)))))...)))	chr1:36879850-36880085(-)$1	1	126	155	10.8017
((....((((((((....)))).))))..	chr9:30957160-30957421(-)$1	1	2	31	11.3191
(.((.(((..(((((...))))).))).)	chr6:32910948-32911183(-)$1	1	188	217	8.9781
((((((.(((.(((....))).))).)))	chr12:16992172-16992410(+)$1	1	203	232	11.8197
((((.....(((((....)))))...)))	chr11:29642168-29642473(+)$1	1	197	226	10.8088
((((.....(((((....)))))...)))	chrX:98835693-98835928(+)$1	1	67	96	10.8088
.(((((...(((((....))).)).))))	chr9:102445317-102445562(+)$1	1	42	71	10.6295
...((((((..(((....)))..))))))	chr7:138588944-138589179(+)$1	1	96	125	11.2374
))(((..(((((((....))).))))..)	chr9:72510245-72510480(+)$1	1	104	133	10.7238
(((...(((((..(....)..))))))))	chr15:103023875-103024111(-)$1	1	89	118	9.9073
..(((.((..((((....))))..)).))	chr19:6389709-6389944(+)$1	1	140	169	12.3242
..(((((.((((((....)))))).))))	chr4:126706308-126706556(+)$1	1	169	198	9.6478
((.(((((.((((......)))).)))))	chr1:54702798-54703044(-)$1	1	60	89	8.4550
.((.((...(((((....))))).)).))	chr5:122903502-122903739(-)$1	1	80	109	10.0039
(((.(((...((((....)))))))..))	chr17:10406395-10406643(-)$1	1	164	193	13.2784
(((((((((...((....))...))))))	chr17:27716430-27716665(-)$1	1	95	124	10.0483
((((((((((((((....))))))...))	chr15:27396439-27396677(+)$1	1	88	117	10.1814
...((((...((((....))))...))))	chr2:130101955-130102202(+)$1	1	32	61	13.3318
(.(((((...((((....)))).))))).	chr19:12843634-12843875(-)$1	1	41	70	12.3619
(((..(((..((((...))))..)))..)	chr7:20144330-20144565(-)$1	1	159	188	9.7172
((((((..((((((....))))))...))	chr13:29999174-29999409(-)$1	1	76	105	10.6981
((((((.(.((..(....)..))).))))	chr15:76001656-76001898(-)$1	1	198	227	9.7714
((..(((.(((.(((....)))..))).)	chr3:60433367-60433602(+)$1	1	16	45	9.9873
((.(((((...(((....)))))))).))	chr1:135554227-135554464(-)$1	1	197	226	10.9606
....((((..((((....)))).)))).)	chr18:61500318-61500556(-)$1	1	113	142	11.7323
((.(((..((((((....))))))..)))	chr7:88679712-88679947(-)$1	1	21	50	10.4284
)))(((((..((((....))))..)))))	chr15:38224969-38225206(-)$1	1	115	144	11.8097
((...((((.((((....)))).))))..	chr3:104260867-104261102(-)$1	1	115	144	11.6554
.(((.(((((((((....)))))))))))	chr5:136385263-136385509(-)$1	1	118	147	11.3709
..(((((..(((((....)))))...)))	chr5:36944678-36944920(-)$1	1	155	184	12.0841
...(((....((((....))))....)))	chr9:74906055-74906290(+)$1	1	141	170	11.0836
)))(((((...(((....)))...)))))	chr13:30801749-30801999(+)$1	1	103	132	11.7242
(((.(((.((.(((....)))))))).))	chr9:107950750-107950985(+)$1	1	193	222	11.0018
.(..((((...(((....)))....))))	chr11:4667759-4668018(-)$1	1	201	230	12.3118
(((...((((((((....)))))..))).	chr14:60248649-60248884(+)$1	1	126	155	11.3961
..(((.(((.((((...)))).)))..))	chr7:52399799-52400034(-)$1	1	103	132	10.3661
(....((((.((((....)))).).))).	chr14:31846068-31846303(+)$1	1	191	220	13.2771

#PSSM
c : 0.15	d : 0.11	! : 0.09	e : 0.09	: : 0.07	b : 0.07	" : 0.05	# : 0.05	f : 0.05	h : 0.03	$ : 0.03	[ : 0.03	i : 0.03	F : 0.01	a : 0.01	g : 0.01	
c : 0.17	d : 0.09	b : 0.09	e : 0.09	[ : 0.07	g : 0.05	" : 0.05	# : 0.05	f : 0.05	! : 0.05	= : 0.03	$ : 0.03	i : 0.03	F : 0.01	: : 0.01	a : 0.01	
c : 0.19	[ : 0.13	e : 0.13	g : 0.07	# : 0.07	" : 0.05	b : 0.05	: : 0.03	= : 0.03	$ : 0.03	f : 0.03	i : 0.03	! : 0.03	a : 0.01	d : 0.01	
c : 0.19	e : 0.19	g : 0.07	f : 0.07	# : 0.07	[ : 0.07	b : 0.05	" : 0.05	! : 0.05	= : 0.03	$ : 0.03	d : 0.03	i : 0.01	
c : 0.26	e : 0.15	g : 0.07	f : 0.07	d : 0.07	# : 0.05	b : 0.05	[ : 0.05	" : 0.05	= : 0.03	$ : 0.03	! : 0.01	i : 0.01	
c : 0.26	e : 0.15	d : 0.11	g : 0.07	f : 0.07	[ : 0.05	= : 0.03	# : 0.03	! : 0.03	$ : 0.03	" : 0.03	i : 0.03	b : 0.01	
c : 0.23	e : 0.15	d : 0.13	! : 0.09	f : 0.07	g : 0.05	[ : 0.05	= : 0.03	# : 0.03	$ : 0.03	" : 0.03	b : 0.01	i : 0.01	
c : 0.15	d : 0.13	" : 0.11	g : 0.09	[ : 0.09	e : 0.09	! : 0.07	f : 0.05	= : 0.03	a : 0.03	$ : 0.03	b : 0.01	i : 0.01	# : 0.01	
" : 0.19	! : 0.15	f : 0.13	c : 0.11	d : 0.07	g : 0.05	[ : 0.05	a : 0.03	= : 0.03	b : 0.03	$ : 0.03	e : 0.01	i : 0.01	# : 0.01	
! : 0.17	" : 0.17	e : 0.13	[ : 0.11	b : 0.07	d : 0.07	f : 0.07	c : 0.05	= : 0.03	g : 0.03	i : 0.01	# : 0.01	
d : 0.40	e : 0.15	" : 0.09	f : 0.07	[ : 0.05	= : 0.03	g : 0.03	! : 0.03	c : 0.03	b : 0.03	i : 0.01	
d : 0.38	c : 0.23	e : 0.13	f : 0.07	= : 0.03	g : 0.03	! : 0.03	" : 0.01	[ : 0.01	i : 0.01	
d : 0.38	c : 0.24	e : 0.13	f : 0.07	g : 0.03	! : 0.03	= : 0.01	[ : 0.01	b : 0.01	i : 0.01	
d : 0.34	c : 0.24	e : 0.13	f : 0.07	a : 0.05	g : 0.03	= : 0.01	n : 0.01	o : 0.01	b : 0.01	i : 0.01	
m : 0.84	l : 0.05	o : 0.03	n : 0.01	e : 0.01	c : 0.01	
m : 0.86	l : 0.07	o : 0.03	n : 0.01	
m : 0.86	l : 0.07	o : 0.03	n : 0.01	
m : 0.86	o : 0.03	d : 0.03	a : 0.01	n : 0.01	l : 0.01	
d : 0.34	c : 0.23	e : 0.13	f : 0.07	g : 0.03	o : 0.03	a : 0.03	= : 0.01	] : 0.01	b : 0.01	m : 0.01	i : 0.01	
d : 0.36	c : 0.24	e : 0.13	f : 0.07	= : 0.03	g : 0.03	2 : 0.03	o : 0.01	b : 0.01	i : 0.01	
d : 0.38	c : 0.24	e : 0.13	f : 0.07	= : 0.03	g : 0.03	2 : 0.03	3 : 0.01	i : 0.01	
d : 0.34	e : 0.17	] : 0.09	2 : 0.07	f : 0.07	3 : 0.05	= : 0.03	g : 0.03	b : 0.03	c : 0.01	i : 0.01	4 : 0.01	
e : 0.17	] : 0.15	2 : 0.15	b : 0.07	c : 0.07	3 : 0.07	f : 0.07	g : 0.05	d : 0.05	= : 0.03	4 : 0.03	i : 0.01	
f : 0.13	c : 0.13	3 : 0.13	2 : 0.09	d : 0.09	a : 0.07	g : 0.07	] : 0.05	e : 0.05	= : 0.03	b : 0.03	4 : 0.03	i : 0.01	
c : 0.21	3 : 0.17	] : 0.11	e : 0.11	g : 0.07	d : 0.07	f : 0.05	= : 0.03	b : 0.03	2 : 0.03	4 : 0.03	i : 0.01	
c : 0.21	3 : 0.17	e : 0.15	d : 0.11	2 : 0.07	f : 0.05	g : 0.03	= : 0.03	] : 0.03	b : 0.03	i : 0.03	4 : 0.01	
c : 0.23	e : 0.17	d : 0.11	3 : 0.09	2 : 0.09	] : 0.09	f : 0.05	g : 0.03	= : 0.03	i : 0.03	b : 0.01	
c : 0.26	e : 0.17	g : 0.07	f : 0.07	] : 0.07	d : 0.07	b : 0.05	2 : 0.05	= : 0.03	3 : 0.03	i : 0.03	4 : 0.01	
c : 0.23	e : 0.15	b : 0.09	d : 0.09	g : 0.07	f : 0.07	] : 0.07	= : 0.03	3 : 0.03	i : 0.03	4 : 0.03	2 : 0.01	a : 0.01	

#score	574.5826994616174
#seq	52
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_transcript_m1_run1.txt

#BEAR
iiiiiiiiitttttttttttiiiiiiiii	chr11:121168857-121169093(+)$1	236	43	72	23.1162
[cccddddtttttttttttdddd]ccc33	chr4:107902633-107902868(-)$1	235	48	77	22.6361
!dddd[bbuuuuuuuuuuuubb333dddd	chr4:154530416-154530651(-)$1	235	178	207	23.8928
=="""cccwwwwwwwwwwwwwwccc====	chr2:154519610-154519845(+)$1	235	57	86	23.3994
ddd[ddddvvvvvvvvvvvvvdddddddd	chr14:35227157-35227392(-)$1	235	1	30	22.8488
gggeeeeeuuuuuuuuuuuueeeee]ggg	chr5:136384536-136384800(-)$1	264	223	252	25.0191
[eeeee[bbtttttttttttbbeeeee22	chr9:120869129-120869380(+)$1	251	61	90	23.1158
!gggggggvvvvvvvvvvvvvggggggg2	chr11:6255709-6255944(+)$1	235	145	174	24.0429
ggggggyyyyyyyyyyyyyyyyggggggg	chr18:4994934-4995169(+)$1	235	163	192	23.3990
eeeeeyyyyyyyyyyyyyyyyeeeeebbd	chr11:87793883-87794158(-)$1	275	111	140	22.2693
[ddddyyyyyyyyyyyyyyyydddd]ccc	chr3:60812561-60812821(+)$1	260	162	191	22.5098
a[bb[cccuuuuuuuuuuuuccc]bb]a]	chr11:17100124-17100379(+)$1	255	20	49	23.7550
gggg!!ayyyyyyyyyyyyyyyya22ggg	chr13:55422845-55423080(-)$1	235	103	132	22.9862
dd"""cccuuuuuuuuuuuuccc333ddd	chr12:111820777-111821023(+)$1	246	51	80	24.8700
e####cccwwwwwwwwwwwwwwccc5555	chr2:113875924-113876162(-)$1	238	6	35	20.1269
gggggggvvvvvvvvvvvvvgggggggdd	chr18:78021187-78021422(+)$1	235	53	82	23.7961
::eeeeevvvvvvvvvvvvveeeee:ccc	chr1:196519484-196519719(+)$1	235	187	216	21.0269
cc[eeeeexxxxxxxxxxxxxxxeeeee4	chr9:121364093-121364352(+)$1	259	201	230	19.0795
ddffffffuuuuuuuuuuuuffffff:BB	chr2:109773964-109774199(+)$1	235	130	159	21.0032
!!ffffffuuuuuuuuuuuuffffff22b	chr2:136607662-136607914(+)$1	252	119	148	23.8652
ddffffffuuuuuuuuuuuuffffff22d	chr14:76907113-76907357(+)$1	244	19	48	23.6173
iiieeeeeuuuuuuuuuuuueeeee]iii	chr5:136384420-136384663(-)$1	243	86	115	25.0308
##eeeeevvvvvvvvvvvvveeeee22hh	chr2:104268783-104269022(-)$1	239	163	192	23.4537
eeee!!bbvvvvvvvvvvvvvbb]eeeee	chr9:71352180-71352416(-)$1	236	59	88	23.3079
ffffffyyyyyyyyyyyyyyyyffffff:	chr2:6462887-6463179(-)$1	292	260	289	21.6435
dddd[ccctttttttttttcccdddd22e	chr5:122906679-122906924(-)$1	245	45	74	22.3454
fffff[bbuuuuuuuuuuuubb]ffffff	chr8:107740674-107740915(+)$1	241	139	168	23.4467
"""eeeeeyyyyyyyyyyyyyyyyeeeee	chr11:87793793-87794058(-)$1	265	8	37	22.5516
!!bbyyyyyyyyyyyyyyyybb22eeeee	chr18:31941014-31941249(+)$1	235	119	148	21.2207
ee!!dddduuuuuuuuuuuudddd22eee	chr4:134772502-134772737(-)$1	235	45	74	23.8973
ccc"""ccctttttttttttccc333ccc	chr18:6789456-6789691(+)$1	235	45	74	23.7334
========uuuuuuuuuuuu=========	chr13:74459848-74460091(-)$1	243	19	48	25.3017
eee[eeeeettttttttttteeeee]eee	chr14:37691621-37691860(-)$1	239	188	217	23.5534
e[gggggggtttttttttttggggggg]e	chr18:34505313-34505548(-)$1	235	125	154	23.3071
dd[a[cccvvvvvvvvvvvvvccca]ddd	chr3:103544754-103544989(-)$1	235	191	220	23.9221
eeee!!bbvvvvvvvvvvvvvbb22eeee	chr13:34284748-34284983(-)$1	235	135	164	22.9437
##ffffffwwwwwwwwwwwwwwffffff4	chr1:174127269-174127504(-)$1	235	39	68	22.7128
geeeee[bbtttttttttttbb]eeeee:	chr5:92481829-92482064(-)$1	235	97	126	22.2810
eeeeeeeewwwwwwwwwwwwwweeeeeDD	chr15:53066784-53067019(-)$1	235	88	117	21.2141
d[gggggggtttttttttttggggggg]d	chr5:122941662-122941901(-)$1	239	21	50	23.3112
gggggggxxxxxxxxxxxxxxxggggggg	chr8:85837495-85837730(-)$1	235	186	215	19.5126
d"""cccvvvvvvvvvvvvvccc333ddd	chr8:87784680-87784921(-)$1	241	44	73	24.0838
ddd[dddduuuuuuuuuuuudddd22ddd	chr17:81785531-81785767(-)$1	236	99	128	23.6527
ccc[eeeeettttttttttteeeee]ccc	chr1:172958025-172958260(+)$1	235	125	154	23.6043
accc!!bbuuuuuuuuuuuubb22ccc]a	chr16:28827388-28827623(-)$1	235	79	108	23.7315
E:ddddwwwwwwwwwwwwwwddddfffff	chr2:72245089-72245325(+)$1	236	14	43	19.7705
ffff[cccuuuuuuuuuuuuccc>>>>>>	chr2:71190389-71190626(-)$1	237	130	159	23.4396
iiiiiiiiwwwwwwwwwwwwwwiiiiiii	chr11:62215867-62216106(-)$1	239	161	190	23.2414
[ffffffwwwwwwwwwwwwwwffffff]c	chr11:50108530-50108781(-)$1	251	99	128	22.8906
%%%ccc[auuuuuuuuuuuua]ccc4444	chr5:73704943-73705180(+)$1	237	119	148	23.0274
fffddddwwwwwwwwwwwwwwdddd]fff	chr2:90962846-90963083(+)$1	237	75	104	22.2474
""a[eeeeettttttttttteeeee]agg	chr14:60843740-60843975(-)$1	235	51	80	23.7960
##eeeeevvvvvvvvvvvvveeeee4444	chr2:163842323-163842558(+)$1	235	193	222	24.2866
!!fffffftttttttttttffffff333d	chr6:30404433-30404668(+)$1	235	113	142	23.1702
gggggg[bbtttttttttttbb]gggggg	chr2:155973180-155973415(-)$1	235	94	123	23.2355
d!!eeeeettttttttttteeeeedddd]	chr12:54249968-54250203(+)$1	235	84	113	22.9145
dddeeeeeuuuuuuuuuuuueeeee]ddd	chr6:83757592-83757834(-)$1	242	206	235	24.5843
[dddd[ccctttttttttttccc]dddd]	chr1:89088986-89089221(+)$1	235	84	113	23.1738
========vvvvvvvvvvvvv========	chr15:4104066-4104302(+)$1	236	93	122	24.5617
ffffffyyyyyyyyyyyyyyyyffffff:	chr2:104269211-104269455(-)$1	244	82	111	21.6435
!!fffffftttttttttttffffff4444	chr4:154933049-154933289(+)$1	240	15	44	22.9893
eee[dddduuuuuuuuuuuudddd]eeee	chrX:102993034-102993276(-)$1	242	7	36	23.9485
:a[ddddvvvvvvvvvvvvvdddd]addd	chr13:12153525-12153765(-)$1	240	111	140	22.0864

#otherMatches

#Seq PSSM
GUGGGAUGGUUUGCUCUAGUCUGUCCUGC	chr11:121168857-121169093(+)$1	236	43	72	23.1162
AGAUAAGUAAAUAUACCAAACUUAAUCAA	chr4:107902633-107902868(-)$1	235	48	77	22.6361
CCAGUCCCUUCUUACUCCCCGGUUAACUG	chr4:154530416-154530651(-)$1	235	178	207	23.8928
CUGUAUCCACAGCCAAGAAGAAGGAAGAG	chr2:154519610-154519845(+)$1	235	57	86	23.3994
UACUCACUAUCCUGUCCAUAAAGUGGUGC	chr14:35227157-35227392(-)$1	235	1	30	22.8488
CAGUGUUAGCUUACUCUUAAUAAUGUCUG	chr5:136384536-136384800(-)$1	264	223	252	25.0191
UUUGCUUGCUUUUAUUUUUUGCAGUAACU	chr9:120869129-120869380(+)$1	251	61	90	23.1158
CCAGCCUGUGCCGACUUCUCUCAGGCUGC	chr11:6255709-6255944(+)$1	235	145	174	24.0429
GUUCCUGGCCCCUCUCACUUAGAGGAACA	chr18:4994934-4995169(+)$1	235	163	192	23.3990
UACGUUUGUGUUUGUCUGUGUGCGUGUGU	chr11:87793883-87794158(-)$1	275	111	140	22.2693
CCAUGUUUCUGUGACUUUGCUCgugugug	chr3:60812561-60812821(+)$1	260	162	191	22.5098
CUCUUGCUUGUGCAUAUCUUGGCUGGCGU	chr11:17100124-17100379(+)$1	255	20	49	23.7550
GGGCAAGGAAUACGUGGGCAAGACGAGCC	chr13:55422845-55423080(-)$1	235	103	132	22.9862
ACCUUCACUCUUUCCAAAACGUGUCUGUG	chr12:111820777-111821023(+)$1	246	51	80	24.8700
CUGAAGCCCCGCUGAACCCCAAGGCCAAC	chr2:113875924-113876162(-)$1	238	6	35	20.1269
UCCAUACUGUGUGCUAGUUUGUGUGGGGG	chr18:78021187-78021422(+)$1	235	53	82	23.7961
ACUCUAACAACUCUCAACAUUUGGAACAG	chr1:196519484-196519719(+)$1	235	187	216	21.0269
GGAUGGAGGCCAGCCUGUUUAGACUCCAC	chr9:121364093-121364352(+)$1	259	201	230	19.0795
gggccugguggauuauaaauucaggcacu	chr2:109773964-109774199(+)$1	235	130	159	21.0032
AACUAUGUGAAAUGGAUGUAAUAUAGGGU	chr2:136607662-136607914(+)$1	252	119	148	23.8652
AUAUUUGUGUAUGUAGUGUAACGAAUUUG	chr14:76907113-76907357(+)$1	244	19	48	23.6173
CAGUGUUAGCUUACUCUUAAUAAUGUCUG	chr5:136384420-136384663(-)$1	243	86	115	25.0308
UUUUUGGUUUUUGGUUAUUUUUAAGUAUU	chr2:104268783-104269022(-)$1	239	163	192	23.4537
AGCUGAGAUCACUAUAUUUAUUCAAGCUG	chr9:71352180-71352416(-)$1	236	59	88	23.3079
UAAUACUUGUUUCUCUCUCUGCGUGUUGU	chr2:6462887-6463179(-)$1	292	260	289	21.6435
CUCAUACUUGUACAAAGAUAGUUGAGCCA	chr5:122906679-122906924(-)$1	245	45	74	22.3454
AUGAAGAUGAGUCUUAGAAAAUGUUCAUC	chr8:107740674-107740915(+)$1	241	139	168	23.4467
GUGUACGUUUGUGUUUGUCUGUGUGCGUG	chr11:87793793-87794058(-)$1	265	8	37	22.5516
AGCCUGCUGAGGAAUGGAAUGGAGAUGCC	chr18:31941014-31941249(+)$1	235	119	148	21.2207
GGCAGAACUUGAGGUGCUAUGUUCCACCA	chr4:134772502-134772737(-)$1	235	45	74	23.8973
AUGACUGUCUGUAUCUUAAUGGCUUCCAU	chr18:6789456-6789691(+)$1	235	45	74	23.7334
AUAUGUCCAUGUUUAUUUGAGGGCGUAug	chr13:74459848-74460091(-)$1	243	19	48	25.3017
CCAGUGAGGAAAGACCAGGCUUUUAGUGG	chr14:37691621-37691860(-)$1	239	188	217	23.5534
CUGUGGCCCUAGCGUAAUAUGGGUCACUG	chr18:34505313-34505548(-)$1	235	125	154	23.3071
AGACAUAGUUUUACAUUCAUUCUGGCCUG	chr3:103544754-103544989(-)$1	235	191	220	23.9221
AGCAGAGGUGCUGCCCUAUAUCCCAUGCU	chr13:34284748-34284983(-)$1	235	135	164	22.9437
ACACAUUUCAACUAACCACAACAAAUGUU	chr1:174127269-174127504(-)$1	235	39	68	22.7128
UGUGGACACAGAUUUUUGUAGUUUCCAUU	chr5:92481829-92482064(-)$1	235	97	126	22.2810
GGGAGCCAUCUCCACUUCCUCUUGGCUGG	chr15:53066784-53067019(-)$1	235	88	117	21.2141
UACAUAAUGUUUUAUCCUUUUAUUAUGAA	chr5:122941662-122941901(-)$1	239	21	50	23.3112
GUCCCUUGAGAAUAUUCAGCAAAAGGGAU	chr8:85837495-85837730(-)$1	235	186	215	19.5126
CCUUAACUCACUUCAUAAUUGUUUAAGUC	chr8:87784680-87784921(-)$1	241	44	73	24.0838
AGAAGAGCUAAUUAGCCGGUGUUUAGUCU	chr17:81785531-81785767(-)$1	236	99	128	23.6527
ggcucacccauugcacuuuggggugugcu	chr1:172958025-172958260(+)$1	235	125	154	23.6043
CUUGCUUGCUUUCUGUCCCACACCCAGUG	chr16:28827388-28827623(-)$1	235	79	108	23.7315
AUGUGGAUAAUUAUUUCAAACUACAGUUC	chr2:72245089-72245325(+)$1	236	14	43	19.7705
cuguacccuacacugaccuugggcuugcu	chr2:71190389-71190626(-)$1	237	130	159	23.4396
UUAGUAAACAUUGAACAUUUUAUUUACUA	chr11:62215867-62216106(-)$1	239	161	190	23.2414
UGUCUAUUUCUUUUACUCUGUGUAGACUU	chr11:50108530-50108781(-)$1	251	99	128	22.8906
GGGAGGGGGGAGCAAGCACACGCCUAGGG	chr5:73704943-73705180(+)$1	237	119	148	23.0274
ggagaggaagggaagggaAGACCUCAUCC	chr2:90962846-90963083(+)$1	237	75	104	22.2474
UUGCCAAUGUGAAGUCUUGUCAUUGUCAG	chr14:60843740-60843975(-)$1	235	51	80	23.7960
CCUUUGUGCGAUAAACAAAAACAAAAAAU	chr2:163842323-163842558(+)$1	235	193	222	24.2866
UUGGAAGAAAAAAAAAAUAUCUUCCCUUG	chr6:30404433-30404668(+)$1	235	113	142	23.1702
AUUUUUUCAAUUAAUGUCUCUGUAAAAGU	chr2:155973180-155973415(-)$1	235	94	123	23.2355
CUAAUUUAUUUUAAAUAUUUGAAUGGUUU	chr12:54249968-54250203(+)$1	235	84	113	22.9145
CCUGUCCUGAUCGUACUCCGAGGACAAGG	chr6:83757592-83757834(-)$1	242	206	235	24.5843
UCGUUCCAGAUUUCUUAUGCCUGCAAUGU	chr1:89088986-89089221(+)$1	235	84	113	23.1738
AUCUUUUACCUUCCUCUGUUUUGAGAGAU	chr15:4104066-4104302(+)$1	236	93	122	24.5617
UACUCUUUCCUUUCCUUUCAGUAGAGUAA	chr2:104269211-104269455(-)$1	244	82	111	21.6435
UCUGUGGGCCCUCCCCUCCCCCAUAUCCU	chr4:154933049-154933289(+)$1	240	15	44	22.9893
UUGUGAUAUUGUAUCUGUUUUGUCCCGGU	chrX:102993034-102993276(-)$1	242	7	36	23.9485
GGGGGUUGAAGGAGAGAGGGAGCUGUGGU	chr13:12153525-12153765(-)$1	240	111	140	22.0864

#DB
(((((((((...........)))))))))	chr11:121168857-121169093(+)$1	1	43	72	23.1162
.(((((((...........)))).)))..	chr4:107902633-107902868(-)$1	1	48	77	22.6361
.((((.((............))...))))	chr4:154530416-154530651(-)$1	1	178	207	23.8928
((...(((..............)))))))	chr2:154519610-154519845(+)$1	1	57	86	23.3994
(((.((((.............))))))))	chr14:35227157-35227392(-)$1	1	1	30	22.8488
((((((((............))))).)))	chr5:136384536-136384800(-)$1	1	223	252	25.0191
.(((((.((...........)))))))..	chr9:120869129-120869380(+)$1	1	61	90	23.1158
.(((((((.............))))))).	chr11:6255709-6255944(+)$1	1	145	174	24.0429
((((((................)))))))	chr18:4994934-4995169(+)$1	1	163	192	23.3990
(((((................))))))))	chr11:87793883-87794158(-)$1	1	111	140	22.2693
.((((................)))).)))	chr3:60812561-60812821(+)$1	1	162	191	22.5098
(.((.(((............))).)).).	chr11:17100124-17100379(+)$1	1	20	49	23.7550
((((..(................)..)))	chr13:55422845-55423080(-)$1	1	103	132	22.9862
((...(((............)))...)))	chr12:111820777-111821023(+)$1	1	51	80	24.8700
(....(((..............)))....	chr2:113875924-113876162(-)$1	1	6	35	20.1269
(((((((.............)))))))((	chr18:78021187-78021422(+)$1	1	53	82	23.7961
..(((((.............))))).(((	chr1:196519484-196519719(+)$1	1	187	216	21.0269
((.(((((...............))))).	chr9:121364093-121364352(+)$1	1	201	230	19.0795
))((((((............)))))).))	chr2:109773964-109774199(+)$1	1	130	159	21.0032
..((((((............))))))..)	chr2:136607662-136607914(+)$1	1	119	148	23.8652
((((((((............))))))..)	chr14:76907113-76907357(+)$1	1	19	48	23.6173
((((((((............))))).)))	chr5:136384420-136384663(-)$1	1	86	115	25.0308
..(((((.............)))))..))	chr2:104268783-104269022(-)$1	1	163	192	23.4537
((((..((.............)).)))))	chr9:71352180-71352416(-)$1	1	59	88	23.3079
((((((................)))))).	chr2:6462887-6463179(-)$1	1	260	289	21.6435
((((.(((...........)))))))..)	chr5:122906679-122906924(-)$1	1	45	74	22.3454
(((((.((............)).))))))	chr8:107740674-107740915(+)$1	1	139	168	23.4467
...(((((................)))))	chr11:87793793-87794058(-)$1	1	8	37	22.5516
..((................))..)))))	chr18:31941014-31941249(+)$1	1	119	148	21.2207
((..((((............))))..)))	chr4:134772502-134772737(-)$1	1	45	74	23.8973
(((...(((...........)))...)))	chr18:6789456-6789691(+)$1	1	45	74	23.7334
((((((((............)))))))))	chr13:74459848-74460091(-)$1	1	19	48	25.3017
(((.(((((...........))))).)))	chr14:37691621-37691860(-)$1	1	188	217	23.5534
(.(((((((...........))))))).)	chr18:34505313-34505548(-)$1	1	125	154	23.3071
((.(.(((.............)))).)))	chr3:103544754-103544989(-)$1	1	191	220	23.9221
((((..((.............))..))))	chr13:34284748-34284983(-)$1	1	135	164	22.9437
..((((((..............)))))).	chr1:174127269-174127504(-)$1	1	39	68	22.7128
)(((((.((...........)).))))).	chr5:92481829-92482064(-)$1	1	97	126	22.2810
)))(((((..............)))))))	chr15:53066784-53067019(-)$1	1	88	117	21.2141
(.(((((((...........))))))).)	chr5:122941662-122941901(-)$1	1	21	50	23.3112
(((((((...............)))))))	chr8:85837495-85837730(-)$1	1	186	215	19.5126
(...(((.............)))...)))	chr8:87784680-87784921(-)$1	1	44	73	24.0838
(((.((((............))))..)))	chr17:81785531-81785767(-)$1	1	99	128	23.6527
(((.(((((...........))))).)))	chr1:172958025-172958260(+)$1	1	125	154	23.6043
((((..((............))..))).)	chr16:28827388-28827623(-)$1	1	79	108	23.7315
(.((((..............))))(((((	chr2:72245089-72245325(+)$1	1	14	43	19.7705
((((.(((............)))......	chr2:71190389-71190626(-)$1	1	130	159	23.4396
((((((((..............)))))))	chr11:62215867-62216106(-)$1	1	161	190	23.2414
.((((((..............)))))).)	chr11:50108530-50108781(-)$1	1	99	128	22.8906
...(((.(............).)))....	chr5:73704943-73705180(+)$1	1	119	148	23.0274
(((((((..............)))).)))	chr2:90962846-90963083(+)$1	1	75	104	22.2474
..(.(((((...........))))).)))	chr14:60843740-60843975(-)$1	1	51	80	23.7960
..(((((.............)))))....	chr2:163842323-163842558(+)$1	1	193	222	24.2866
..((((((...........))))))...)	chr6:30404433-30404668(+)$1	1	113	142	23.1702
((((((.((...........)).))))))	chr2:155973180-155973415(-)$1	1	94	123	23.2355
(..(((((...........))))))))).	chr12:54249968-54250203(+)$1	1	84	113	22.9145
((((((((............))))).)))	chr6:83757592-83757834(-)$1	1	206	235	24.5843
.((((.(((...........))).)))).	chr1:89088986-89089221(+)$1	1	84	113	23.1738
((((((((.............))))))))	chr15:4104066-4104302(+)$1	1	93	122	24.5617
((((((................)))))).	chr2:104269211-104269455(-)$1	1	82	111	21.6435
..((((((...........))))))....	chr4:154933049-154933289(+)$1	1	15	44	22.9893
(((.((((............)))).))))	chrX:102993034-102993276(-)$1	1	7	36	23.9485
.(.((((.............)))).)(((	chr13:12153525-12153765(-)$1	1	111	140	22.0864

#PSSM
d : 0.17	e : 0.14	g : 0.11	! : 0.09	[ : 0.07	f : 0.07	i : 0.04	= : 0.04	c : 0.04	# : 0.04	a : 0.03	: : 0.03	" : 0.03	E : 0.01	% : 0.01	
d : 0.17	e : 0.14	g : 0.11	f : 0.09	c : 0.07	! : 0.07	# : 0.06	i : 0.04	= : 0.04	[ : 0.04	" : 0.04	: : 0.03	% : 0.01	a : 0.01	
f : 0.19	e : 0.17	g : 0.14	d : 0.12	c : 0.06	" : 0.06	i : 0.04	[ : 0.04	b : 0.03	! : 0.03	= : 0.03	# : 0.01	% : 0.01	a : 0.01	
e : 0.23	f : 0.17	g : 0.12	d : 0.11	[ : 0.09	" : 0.06	c : 0.04	i : 0.03	b : 0.03	= : 0.03	# : 0.01	! : 0.01	a : 0.01	
e : 0.25	d : 0.17	f : 0.15	g : 0.11	[ : 0.06	! : 0.06	" : 0.04	i : 0.03	= : 0.03	c : 0.03	# : 0.01	y : 0.01	
e : 0.23	c : 0.14	f : 0.14	d : 0.12	g : 0.11	! : 0.06	[ : 0.04	y : 0.04	i : 0.03	= : 0.03	" : 0.01	
e : 0.20	c : 0.15	d : 0.11	f : 0.11	y : 0.09	b : 0.07	g : 0.07	[ : 0.06	i : 0.03	= : 0.03	a : 0.01	w : 0.01	
e : 0.15	c : 0.14	b : 0.12	y : 0.11	v : 0.09	f : 0.09	d : 0.07	g : 0.04	w : 0.04	i : 0.03	= : 0.03	x : 0.01	a : 0.01	
u : 0.26	v : 0.19	w : 0.12	y : 0.12	t : 0.07	b : 0.04	e : 0.04	x : 0.03	c : 0.03	g : 0.03	i : 0.01	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	t : 0.25	v : 0.19	w : 0.12	y : 0.12	x : 0.03	
u : 0.26	v : 0.19	t : 0.17	w : 0.12	y : 0.12	x : 0.03	f : 0.03	d : 0.01	c : 0.01	e : 0.01	
e : 0.15	b : 0.11	w : 0.11	y : 0.11	c : 0.11	d : 0.09	v : 0.09	f : 0.07	g : 0.04	x : 0.03	i : 0.01	= : 0.01	a : 0.01	
e : 0.17	d : 0.14	b : 0.14	c : 0.12	f : 0.09	w : 0.07	y : 0.07	g : 0.06	x : 0.03	= : 0.03	i : 0.01	] : 0.01	
e : 0.20	d : 0.15	c : 0.15	f : 0.14	g : 0.09	] : 0.04	i : 0.03	y : 0.03	b : 0.03	2 : 0.03	= : 0.03	3 : 0.01	x : 0.01	
e : 0.23	f : 0.15	d : 0.14	g : 0.11	] : 0.06	3 : 0.06	c : 0.06	2 : 0.04	i : 0.03	= : 0.03	a : 0.01	y : 0.01	> : 0.01	
e : 0.26	f : 0.17	g : 0.11	d : 0.09	c : 0.07	3 : 0.06	2 : 0.06	i : 0.03	= : 0.03	] : 0.03	b : 0.01	a : 0.01	> : 0.01	
e : 0.15	] : 0.14	f : 0.14	g : 0.11	d : 0.07	2 : 0.06	3 : 0.06	= : 0.04	4 : 0.04	i : 0.03	c : 0.03	b : 0.01	5 : 0.01	: : 0.01	> : 0.01	a : 0.01	
e : 0.17	d : 0.15	g : 0.14	f : 0.11	c : 0.09	2 : 0.06	i : 0.04	= : 0.04	4 : 0.04	b : 0.01	] : 0.01	5 : 0.01	: : 0.01	> : 0.01	a : 0.01	3 : 0.01	
d : 0.17	e : 0.14	g : 0.11	f : 0.09	2 : 0.06	c : 0.06	] : 0.06	i : 0.04	= : 0.04	4 : 0.04	3 : 0.03	b : 0.01	a : 0.01	5 : 0.01	B : 0.01	h : 0.01	D : 0.01	> : 0.01	
d : 0.20	e : 0.14	g : 0.09	c : 0.07	4 : 0.07	i : 0.04	= : 0.04	] : 0.04	: : 0.04	f : 0.04	2 : 0.03	3 : 0.01	5 : 0.01	B : 0.01	b : 0.01	h : 0.01	D : 0.01	a : 0.01	> : 0.01	

#score	1449.1489502946151
#seq	63
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_CDS_m3_run2.txt

#BEAR
!!a[bbqqqqqqqqbb]a22f	chr13:23513897-23514113(-)$1	216	156	177	13.5494
iiiiiiqqqqqqqqiiiiiii	chrX:70083595-70083817(+)$1	222	101	122	14.2700
bbddddqqqqqqqqdddd]bb	chr17:90762119-90762342(-)$1	223	157	178	13.8230
ccccccqqqqqqqqccc]ccc	chr4:108764159-108764379(+)$1	220	50	71	14.3901
:eeeeeqqqqqqqqeeeeehh	chr14:25279068-25279291(+)$1	223	13	34	13.5911
gggg[aqqqqqqqqa]ggggg	chr1:74725897-74726128(+)$1	231	61	82	14.4303
$$ddddqqqqqqqqdddd666	chr8:124922055-124922278(+)$1	223	147	168	13.2181
bbddddqqqqqqqqdddd]bb	chr3:5412876-5413107(+)$1	231	156	177	13.8230
c[ddddqqqqqqqqddddccc	chr3:88566312-88566539(-)$1	227	139	160	14.5654
ggggggqqqqqqqqggggggg	chr6:43223529-43223749(-)$1	220	129	150	14.4214
gggcccqqqqqqqqccc]ggg	chr15:81733816-81734090(+)$1	274	53	74	14.6555
ee[cccqqqqqqqqccc333e	chr15:89201321-89201563(-)$1	242	112	133	14.8652
:eeeeeqqqqqqqqeeeee::	chr11:70757313-70757541(-)$1	228	160	181	12.6395
ffff[aqqqqqqqqa]fffff	chr10:86283567-86283785(+)$1	218	169	190	13.8697
ffffffqqqqqqqqffffffe	chr4:150519027-150519265(-)$1	238	81	102	13.6383
!eeeeeqqqqqqqqeeeee22	chrM:4212-4453(+)$1	241	76	97	14.8534
[eeeeeqqqqqqqqeeeee22	chr11:105784811-105785036(+)$1	225	88	109	14.8113
======qqqqqqqq=======	chr4:40207104-40207331(-)$1	227	172	193	14.7339
ffffffqqqqqqqqffffff]	chr4:131760874-131761102(-)$1	228	195	216	13.8036
(eeeeeqqqqqqqqeeeee77	chr2:76745882-76746104(-)$1	222	165	186	13.6405
eeddddqqqqqqqqdddd444	chr11:75309881-75310113(+)$1	232	156	177	14.7278
iiiiiiqqqqqqqqiiiiiii	chrX:91784074-91784308(-)$1	234	168	189	14.2700
)eeeeeqqqqqqqqeeeee99	chr3:103135476-103135711(+)$1	235	88	109	13.6687
ffffffqqqqqqqqffffff:	chr7:118224326-118224548(-)$1	222	132	153	12.9911
eebb[aqqqqqqqqa]bb]ee	chr6:124696670-124696913(-)$1	243	20	41	12.9158
ccccccqqqqqqqqccc]ccc	chr2:155232208-155232451(-)$1	243	45	66	14.3901
ffffffqqqqqqqqffffff]	chr7:129897904-129898125(+)$1	221	97	118	13.8036
c!!cccqqqqqqqqccc]ccc	chr2:35033870-35034107(+)$1	237	141	162	14.7123
eee[bbqqqqqqqqbb22eee	chr8:111457737-111457961(+)$1	224	195	216	13.2142
""ddddqqqqqqqqdddd333	chr14:68423749-68423971(-)$1	222	127	148	15.1240
deeeeeqqqqqqqqeeeee]d	chr8:108703143-108703360(+)$1	217	97	118	14.6624
b!!cccqqqqqqqqcccbbee	chr4:126427026-126427247(-)$1	221	32	53	13.6849
eeeeeeqqqqqqqqeeeee66	chr5:125516319-125516540(-)$1	221	4	25	14.2566
cc!!bbqqqqqqqqbb22ccc	chr16:31007771-31007987(-)$1	216	83	104	13.2804
cc!!bbqqqqqqqqbb22ccc	chr9:21080911-21081137(+)$1	226	84	105	13.2804
ggggggqqqqqqqqggggggg	chr19:31158647-31158873(-)$1	226	28	49	14.4214
eeee[aqqqqqqqqa]eeeee	chr11:3943827-3944049(-)$1	222	1	22	14.4323
FFddddqqqqqqqqddddGGG	chr10:122568040-122568262(-)$1	222	41	62	12.2638
c[ddddqqqqqqqqdddd22c	chr1:63782003-63782226(-)$1	223	27	48	14.5198
ffffffqqqqqqqqffffff3	chrX:157681242-157681482(+)$1	240	175	196	13.8888
b[a!!aqqqqqqqqa22a]bb	chr17:67038614-67038838(-)$1	224	175	196	13.4813
======qqqqqqqq=======	chr15:4046400-4046625(+)$1	225	15	36	14.7339
"""cccqqqqqqqqccc22bb	chr1:107617775-107618023(+)$1	248	53	74	14.0454
ff[cccqqqqqqqqcccffff	chr11:86100031-86100273(-)$1	242	37	58	14.3036
:eeeeeqqqqqqqqeeeee::	chr2:66346471-66346689(+)$1	218	93	114	12.6395
####bbqqqqqqqqbb333gg	chrX:154291158-154291390(-)$1	232	159	180	13.7588
!!ddddqqqqqqqqdddd22a	chr18:35741541-35741766(+)$1	225	15	36	14.6160
"eeeeeqqqqqqqqeeeee]f	chr1:172129928-172130155(-)$1	227	101	122	14.9907
eeeeeaqqqqqqqqa]eeeee	chr5:33164655-33164886(-)$1	231	2	23	14.4866
eeeebbqqqqqqqqbb]eeee	chr9:57601272-57601495(+)$1	223	66	87	13.6729
dd[cccqqqqqqqqccc]ddd	chr3:96511589-96511809(+)$1	220	173	194	13.7597
d[ddddqqqqqqqqdddd]dd	chr13:55560157-55560388(+)$1	231	127	148	14.2225
:eeeeeqqqqqqqqeeeee::	chr9:48640306-48640527(+)$1	221	12	33	12.6395
[eeeeeqqqqqqqqeeeee]c	chr5:65535760-65535984(+)$1	224	167	188	15.0778
!!ddddqqqqqqqqdddd333	chr11:50046726-50046971(+)$1	245	209	230	15.2379
eeddddqqqqqqqqdddd::e	chr1:12933921-12934143(-)$1	222	156	177	12.7449
:eeeeeqqqqqqqqeeeee:=	chr11:69589971-69590230(+)$1	259	197	218	13.4039
ggggggqqqqqqqqggggggg	chr18:10483101-10483331(-)$1	230	170	191	14.4214
bb[cccqqqqqqqqccc]bb2	chr6:134871186-134871412(+)$1	226	191	212	13.6200
ffffffqqqqqqqqffffff7	chr2:72808391-72808623(-)$1	232	156	177	13.3516
ceeeeeqqqqqqqqeeeee]c	chr13:89830211-89830441(-)$1	230	98	119	15.0052
####bbqqqqqqqqbb4444c	chr1:135190499-135190720(-)$1	221	44	65	13.6490
ffffffqqqqqqqqffffff]	chr2:119872789-119873010(+)$1	221	43	64	13.8036
""ddddqqqqqqqqddddbb]	chr16:33210039-33210265(+)$1	226	13	34	14.2251
ffddddqqqqqqqqdddd]ff	chr7:135024559-135024779(+)$1	220	81	102	14.4216
c[ddddqqqqqqqqdddd]cc	chr6:120909385-120909608(-)$1	223	40	61	14.7492

#otherMatches

#Seq PSSM
GAGGGCGGGAAAGAGCACGGC	chr13:23513897-23514113(-)$1	216	156	177	13.5494
AGGGUUCUCUUUUCAGCUCUU	chrX:70083595-70083817(+)$1	222	101	122	14.2700
UCGGAUUUAGCACUGUCCAGA	chr17:90762119-90762342(-)$1	223	157	178	13.8230
CAGGCUGGUUAUAAGGCUCUG	chr4:108764159-108764379(+)$1	220	50	71	14.3901
UUAUCUGGCUAGUGAGAUACU	chr14:25279068-25279291(+)$1	223	13	34	13.5911
GAAUCUUUCUGCUUGCGUUCC	chr1:74725897-74726128(+)$1	231	61	82	14.4303
AACGUGGACUCCGACAUGCAA	chr8:124922055-124922278(+)$1	223	147	168	13.2181
UGAGCUGAGCCAGAAGCUACA	chr3:5412876-5413107(+)$1	231	156	177	13.8230
GUGUGGACGUGCUGCCACCAG	chr3:88566312-88566539(-)$1	227	139	160	14.5654
CUGUGGAAUAUCAGCCACAGA	chr6:43223529-43223749(-)$1	220	129	150	14.4214
AGACUUCUAAGCUUAAGAUCU	chr15:81733816-81734090(+)$1	274	53	74	14.6555
GCUCUAGUCCCCAAUAGCACG	chr15:89201321-89201563(-)$1	242	112	133	14.8652
AGUACGUUUACUGUUGUGCGA	chr11:70757313-70757541(-)$1	228	160	181	12.6395
UUCUUCAAUGACAAGCGGAGG	chr10:86283567-86283785(+)$1	218	169	190	13.8697
GGCUGUAAGUUCUGACGGCCA	chr4:150519027-150519265(-)$1	238	81	102	13.6383
AUAGGACUUAUUCUUCUUACA	chrM:4212-4453(+)$1	241	76	97	14.8534
AGGUGGCACGGACCCUACCAG	chr11:105784811-105785036(+)$1	225	88	109	14.8113
CAUCUAUUGCAGUCUAGAUGA	chr4:40207104-40207331(-)$1	227	172	193	14.7339
AAAGCCCCCUCACAGGCUUUG	chr4:131760874-131761102(-)$1	228	195	216	13.8036
CAUCUUAAUGGCUGAGGAUCC	chr2:76745882-76746104(-)$1	222	165	186	13.6405
GAACCUACAGAAUGAGGUACA	chr11:75309881-75310113(+)$1	232	156	177	14.7278
UGGUCAAUGCCUCCUGACUGG	chrX:91784074-91784308(-)$1	234	168	189	14.2700
UGUUGUAUCAGCACACAACCC	chr3:103135476-103135711(+)$1	235	88	109	13.6687
ACAGGUAUGGUAAAACUUGUA	chr7:118224326-118224548(-)$1	222	132	153	12.9911
GGGGUCAAUCUACAGCCCACC	chr6:124696670-124696913(-)$1	243	20	41	12.9158
GGUCAGCUCUAACACUGCACC	chr2:155232208-155232451(-)$1	243	45	66	14.3901
UCCUGUCUGUUUUCACAGGAG	chr7:129897904-129898125(+)$1	221	97	118	13.8036
CAAUCAAGAUCCUGUGAAGAC	chr2:35033870-35034107(+)$1	237	141	162	14.7123
CUGUGGCCUUUCCUCCUUCAG	chr8:111457737-111457961(+)$1	224	195	216	13.2142
CGGCAGAAACUUAACUGCAUG	chr14:68423749-68423971(-)$1	222	127	148	15.1240
GGGUGUCCUCAAGUACACUGC	chr8:108703143-108703360(+)$1	217	97	118	14.6624
CAGUCCCUGCUUAAGGAGCCA	chr4:126427026-126427247(-)$1	221	32	53	13.6849
UCACCCACAGAUCCGGGUGCC	chr5:125516319-125516540(-)$1	221	4	25	14.2566
UGACCUGAAGUAUAAGACCAA	chr16:31007771-31007987(-)$1	216	83	104	13.2804
ACACGCACCUUCUAGCCCGUC	chr9:21080911-21081137(+)$1	226	84	105	13.2804
AGUCUCCAUCCCUCGAGAUUC	chr19:31158647-31158873(-)$1	226	28	49	14.4214
CACUGAUGACCUCCUGAGUGG	chr11:3943827-3944049(-)$1	222	1	22	14.4323
GUGGUUGCUGAAGAAGCCUGG	chr10:122568040-122568262(-)$1	222	41	62	12.2638
ACAGGCCAAAGACAGCUUUUU	chr1:63782003-63782226(-)$1	223	27	48	14.5198
AGCCUUUCAGACGUGAGGCUC	chrX:157681242-157681482(+)$1	240	175	196	13.8888
GGGAAGGAAAUAGACAACGCA	chr17:67038614-67038838(-)$1	224	175	196	13.4813
CAGGGGGAAAUGUGCUUCUGU	chr15:4046400-4046625(+)$1	225	15	36	14.7339
ACCCCUUAUAUUUCAGGAAGG	chr1:107617775-107618023(+)$1	248	53	74	14.0454
CUAUGACAAUGACUUCAGGUG	chr11:86100031-86100273(-)$1	242	37	58	14.3036
CAGCUCACUUACCAGAGCUCC	chr2:66346471-66346689(+)$1	218	93	114	12.6395
GAGAGCGAGAGGAUGCAAGUG	chrX:154291158-154291390(-)$1	232	159	180	13.7588
CAUUUUGUUUUUAAAGAAACC	chr18:35741541-35741766(+)$1	225	15	36	14.6160
ACAUUCUACCCGCUGAGUGCC	chr1:172129928-172130155(-)$1	227	101	122	14.9907
UUGGCCUCCAUCAUGUGCCAG	chr5:33164655-33164886(-)$1	231	2	23	14.4866
GAAUUCACAAACAAGAUGUUC	chr9:57601272-57601495(+)$1	223	66	87	13.6729
UUGUUGUCUUCCACCAGGGAC	chr3:96511589-96511809(+)$1	220	173	194	13.7597
GAAUGAGGUAGGGAUUAUCCU	chr13:55560157-55560388(+)$1	231	127	148	14.2225
CCUGAGAUGCUAGACUCAGCU	chr9:48640306-48640527(+)$1	221	12	33	12.6395
GAUUCGGUCCUUCGCGGAUGC	chr5:65535760-65535984(+)$1	224	167	188	15.0778
GUGGCACUCAUGUCUGUUGUA	chr11:50046726-50046971(+)$1	245	209	230	15.2379
GUCCCCAGCAAAAAGGGGGAA	chr1:12933921-12934143(-)$1	222	156	177	12.7449
UGGGCUUCAGAGAUGGCCCUG	chr11:69589971-69590230(+)$1	259	197	218	13.4039
AUGUUUCUAUUAAAGAACAUC	chr18:10483101-10483331(-)$1	230	170	191	14.4214
GUGUCCAGGGAUGAGGAAGCG	chr6:134871186-134871412(+)$1	226	191	212	13.6200
ACUUGGCAAACAUUUCAAGUA	chr2:72808391-72808623(-)$1	232	156	177	13.3516
GAGAGGCUUUGCCUCCUCUAC	chr13:89830211-89830441(-)$1	230	98	119	15.0052
UAGGCCUAUUACCUGGAUUUG	chr1:135190499-135190720(-)$1	221	44	65	13.6490
CCUGGACUUUGGCCUCCAGGU	chr2:119872789-119873010(+)$1	221	43	64	13.8036
UAGUGGUAAUUCUCCCAUAUC	chr16:33210039-33210265(+)$1	226	13	34	14.2251
GUCCUGCCACCCUCCAGGCAU	chr7:135024559-135024779(+)$1	220	81	102	14.4216
UACUCCCGUGGACCGGAGCAA	chr6:120909385-120909608(-)$1	223	40	61	14.7492

#DB
..(.((........)).)..)	chr13:23513897-23514113(-)$1	1	156	177	13.5494
((((((........)))))))	chrX:70083595-70083817(+)$1	1	101	122	14.2700
((((((........)))).))	chr17:90762119-90762342(-)$1	1	157	178	13.8230
((((((........))).)))	chr4:108764159-108764379(+)$1	1	50	71	14.3901
.(((((........)))))((	chr14:25279068-25279291(+)$1	1	13	34	13.5911
((((.(........).)))))	chr1:74725897-74726128(+)$1	1	61	82	14.4303
..((((........))))...	chr8:124922055-124922278(+)$1	1	147	168	13.2181
((((((........)))).))	chr3:5412876-5413107(+)$1	1	156	177	13.8230
(.((((........)))))))	chr3:88566312-88566539(-)$1	1	139	160	14.5654
((((((........)))))))	chr6:43223529-43223749(-)$1	1	129	150	14.4214
((((((........))).)))	chr15:81733816-81734090(+)$1	1	53	74	14.6555
((.(((........)))...)	chr15:89201321-89201563(-)$1	1	112	133	14.8652
.(((((........)))))..	chr11:70757313-70757541(-)$1	1	160	181	12.6395
((((.(........).)))))	chr10:86283567-86283785(+)$1	1	169	190	13.8697
((((((........)))))))	chr4:150519027-150519265(-)$1	1	81	102	13.6383
.(((((........)))))..	chrM:4212-4453(+)$1	1	76	97	14.8534
.(((((........)))))..	chr11:105784811-105785036(+)$1	1	88	109	14.8113
((((((........)))))))	chr4:40207104-40207331(-)$1	1	172	193	14.7339
((((((........)))))).	chr4:131760874-131761102(-)$1	1	195	216	13.8036
.(((((........)))))..	chr2:76745882-76746104(-)$1	1	165	186	13.6405
((((((........))))...	chr11:75309881-75310113(+)$1	1	156	177	14.7278
((((((........)))))))	chrX:91784074-91784308(-)$1	1	168	189	14.2700
.(((((........)))))..	chr3:103135476-103135711(+)$1	1	88	109	13.6687
((((((........)))))).	chr7:118224326-118224548(-)$1	1	132	153	12.9911
((((.(........).)).))	chr6:124696670-124696913(-)$1	1	20	41	12.9158
((((((........))).)))	chr2:155232208-155232451(-)$1	1	45	66	14.3901
((((((........)))))).	chr7:129897904-129898125(+)$1	1	97	118	13.8036
(..(((........))).)))	chr2:35033870-35034107(+)$1	1	141	162	14.7123
(((.((........))..)))	chr8:111457737-111457961(+)$1	1	195	216	13.2142
..((((........))))...	chr14:68423749-68423971(-)$1	1	127	148	15.1240
((((((........))))).)	chr8:108703143-108703360(+)$1	1	97	118	14.6624
(..(((........)))))))	chr4:126427026-126427247(-)$1	1	32	53	13.6849
((((((........)))))..	chr5:125516319-125516540(-)$1	1	4	25	14.2566
((..((........))..)))	chr16:31007771-31007987(-)$1	1	83	104	13.2804
((..((........))..)))	chr9:21080911-21081137(+)$1	1	84	105	13.2804
((((((........)))))))	chr19:31158647-31158873(-)$1	1	28	49	14.4214
((((.(........).)))))	chr11:3943827-3944049(-)$1	1	1	22	14.4323
((((((........))))(((	chr10:122568040-122568262(-)$1	1	41	62	12.2638
(.((((........))))..)	chr1:63782003-63782226(-)$1	1	27	48	14.5198
((((((........)))))).	chrX:157681242-157681482(+)$1	1	175	196	13.8888
(.(..(........)..).))	chr17:67038614-67038838(-)$1	1	175	196	13.4813
((((((........)))))))	chr15:4046400-4046625(+)$1	1	15	36	14.7339
...(((........)))..))	chr1:107617775-107618023(+)$1	1	53	74	14.0454
((.(((........)))))))	chr11:86100031-86100273(-)$1	1	37	58	14.3036
.(((((........)))))..	chr2:66346471-66346689(+)$1	1	93	114	12.6395
....((........))...))	chrX:154291158-154291390(-)$1	1	159	180	13.7588
..((((........))))..)	chr18:35741541-35741766(+)$1	1	15	36	14.6160
.(((((........))))).)	chr1:172129928-172130155(-)$1	1	101	122	14.9907
((((((........).)))))	chr5:33164655-33164886(-)$1	1	2	23	14.4866
((((((........)).))))	chr9:57601272-57601495(+)$1	1	66	87	13.6729
((.(((........))).)))	chr3:96511589-96511809(+)$1	1	173	194	13.7597
(.((((........)))).))	chr13:55560157-55560388(+)$1	1	127	148	14.2225
.(((((........)))))..	chr9:48640306-48640527(+)$1	1	12	33	12.6395
.(((((........))))).)	chr5:65535760-65535984(+)$1	1	167	188	15.0778
..((((........))))...	chr11:50046726-50046971(+)$1	1	209	230	15.2379
))((((........))))..(	chr1:12933921-12934143(-)$1	1	156	177	12.7449
.(((((........))))).(	chr11:69589971-69590230(+)$1	1	197	218	13.4039
((((((........)))))))	chr18:10483101-10483331(-)$1	1	170	191	14.4214
((.(((........))).)).	chr6:134871186-134871412(+)$1	1	191	212	13.6200
((((((........)))))).	chr2:72808391-72808623(-)$1	1	156	177	13.3516
((((((........))))).)	chr13:89830211-89830441(-)$1	1	98	119	15.0052
....((........))....)	chr1:135190499-135190720(-)$1	1	44	65	13.6490
((((((........)))))).	chr2:119872789-119873010(+)$1	1	43	64	13.8036
..((((........)))))).	chr16:33210039-33210265(+)$1	1	13	34	14.2251
((((((........)))).))	chr7:135024559-135024779(+)$1	1	81	102	14.4216
(.((((........)))).))	chr6:120909385-120909608(-)$1	1	40	61	14.7492

#PSSM
f : 0.15	c : 0.13	e : 0.13	b : 0.07	: : 0.07	g : 0.07	! : 0.06	" : 0.06	d : 0.04	i : 0.03	[ : 0.03	= : 0.03	# : 0.03	$ : 0.01	( : 0.01	) : 0.01	F : 0.01	
e : 0.33	f : 0.15	! : 0.07	g : 0.07	[ : 0.07	c : 0.06	b : 0.04	" : 0.04	i : 0.03	= : 0.03	# : 0.03	$ : 0.01	F : 0.01	d : 0.01	
e : 0.27	d : 0.22	f : 0.12	g : 0.07	[ : 0.06	! : 0.06	a : 0.03	i : 0.03	c : 0.03	= : 0.03	# : 0.03	b : 0.01	" : 0.01	
e : 0.25	d : 0.22	c : 0.15	f : 0.12	g : 0.06	! : 0.04	[ : 0.03	i : 0.03	= : 0.03	# : 0.03	b : 0.01	
d : 0.22	e : 0.22	c : 0.15	b : 0.10	f : 0.10	[ : 0.06	g : 0.04	i : 0.03	= : 0.03	! : 0.01	
d : 0.22	e : 0.21	c : 0.15	b : 0.10	f : 0.10	a : 0.09	g : 0.04	i : 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	
d : 0.22	e : 0.21	c : 0.15	b : 0.10	f : 0.10	a : 0.09	g : 0.04	i : 0.03	= : 0.03	
d : 0.22	e : 0.21	c : 0.15	b : 0.10	f : 0.10	] : 0.07	g : 0.04	i : 0.03	= : 0.03	2 : 0.01	
e : 0.24	d : 0.22	c : 0.15	f : 0.12	g : 0.06	2 : 0.06	] : 0.03	i : 0.03	= : 0.03	b : 0.01	3 : 0.01	4 : 0.01	
e : 0.25	d : 0.22	f : 0.13	] : 0.09	g : 0.06	2 : 0.06	a : 0.03	i : 0.03	3 : 0.03	= : 0.03	b : 0.03	4 : 0.01	
e : 0.27	f : 0.13	] : 0.10	c : 0.09	g : 0.07	2 : 0.06	3 : 0.06	b : 0.04	i : 0.03	= : 0.03	4 : 0.03	6 : 0.01	G : 0.01	d : 0.01	: : 0.01	
f : 0.15	c : 0.10	b : 0.09	g : 0.09	e : 0.09	2 : 0.07	: : 0.07	] : 0.06	3 : 0.04	i : 0.03	6 : 0.03	= : 0.03	4 : 0.03	d : 0.03	h : 0.01	7 : 0.01	9 : 0.01	G : 0.01	
c : 0.16	e : 0.13	g : 0.09	f : 0.07	b : 0.06	: : 0.06	] : 0.06	2 : 0.04	= : 0.04	3 : 0.04	d : 0.04	i : 0.03	6 : 0.03	7 : 0.03	h : 0.01	4 : 0.01	9 : 0.01	G : 0.01	a : 0.01	

#score	925.1661468439329
#seq	66
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_CDS_m1_run2.txt

#BEAR
cc[bb####gggggggaooooooa]ggggggg333bbc	chr10:79003199-79003474(-)$1	275	86	124	16.0102
&&===========[ddddllldddd333==========	chr3:68731531-68731816(-)$1	285	214	252	13.4077
"dddd[ccc!!eeeeeooooooeeeee4444ccc]ddd	chr4:98746129-98746407(-)$1	278	20	58	14.3221
::::iiiiiiiii[cccooooooccc22iiiiiiiii:	chr8:98293552-98293831(-)$1	279	160	198	13.7527
$$$$ccc!!ddddddddoooooodddd]dddd]cccee	chr1:34237182-34237462(+)$1	280	55	93	13.4350
===========[a[cccooooooccc]a22========	chr8:72273597-72273870(-)$1	273	161	199	19.2460
gggggg"""===========lll===========gggg	chr9:59518339-59518625(+)$1	286	64	102	14.7786
ccc!!ccc!!cccbboooooobb]ccc22ccc]cccdd	chr17:56452228-56452499(+)$1	271	67	105	15.1301
d!!bb####ffffff[aooooooaffffffbb22dddd	chr11:55094677-55094948(-)$1	271	198	236	13.8560
hhh!!ccc"""bb[cccooooooccc]bb22ccchhhh	chr4:116276459-116276741(-)$1	282	69	107	16.1181
ddd$$$$$eeeee[cccooooooccceeeee22dddd2	chr9:21605583-21605854(-)$1	271	65	103	13.9283
iiiiii[ccc[eeeeeooooooeeeee22ccc333iii	chr11:51414477-51414900(-)$1	423	248	286	15.8294
[bb"""cccccc####cccmmmmccc333ccc]ccc44	chr4:126001328-126001601(-)$1	273	132	170	13.7138
hh]cccccc!!ccc!!cccmmmmccc333ccc333ccc	chr15:75901151-75901448(-)$1	297	216	254	13.6981
e"""dddd!!gggggggooooooggggggg333dddd3	chr10:127996178-127996446(-)$1	268	8	46	15.6969
dddd!!iiiiiiiiicccnnnnnccc22iiiiiiiii]	chr6:124914634-124914905(-)$1	271	41	79	14.3919
eeggggggg[ccc[bboooooobb]ccc]ggggggg]e	chr5:54226283-54226567(+)$1	284	197	235	15.5681
ffff[ccc"""bb"""bboooooobb22bb333ccc]f	chr11:3876178-3876459(+)$1	281	159	197	15.0110
"gggggggffffffooooooffffff333ggggggg]f	chr3:68376417-68376689(+)$1	272	166	204	13.0493
bb[ggggggg[bb[aooooooa]bbggggggg]bb444	chr15:36529074-36529355(-)$1	281	18	56	13.8781
!!dddd$$$$$a[ddddoooooodddd]a22dddd22d	chrX:131507372-131507647(-)$1	275	70	108	13.6476
[ggggggg!!dddd[bboooooobb]dddd4444gggg	chr12:117818792-117819060(+)$1	268	135	173	14.8869
ccc[ccc$$$$$ccc!!bboooooobb22ccc]ccc22	chr17:47734273-47734551(+)$1	278	151	189	13.3893
gggggggggggg[a[cccnnnnnccc]a]ggggggg]g	chr4:135892160-135892446(+)$1	286	168	206	14.0172
fffff[ccc####cccammmma]ccc333cccffffff	chr9:58094835-58095109(-)$1	274	150	188	12.8060
ffffccc[eeeee[cccooooooccc]eeeee]ccchh	chr11:78959574-78959840(-)$1	266	123	161	15.2769
ggggggccc[ccc[cccooooooccc333ccc]ccc]g	chr11:97539648-97540030(+)$1	382	54	92	19.5978
ddd[a[ffffff[bb[aooooooabbffffff]adddd	chr10:75180013-75180297(-)$1	284	137	175	13.5043
iiiiiiii!!ccc[bbnnnnnbb]ccc]iiiiiiiii2	chr15:76072437-76072711(-)$1	274	27	65	13.1900
bb[ggggggg!!ddddoooooodddd333ggggggg]b	chr7:53313672-53313945(+)$1	273	92	130	15.8361
==========bb[ddddoooooodddd]bb]=======	chr13:100820819-100821087(-)$1	268	114	152	15.9273
ffff!!a[a"""bbcccooooooccc4444bb4444a]	chr4:151701462-151701751(+)$1	289	201	239	17.0433
gg[ddddccc!!a!!bboooooobb333a22ccc]ddd	chr1:177908569-177908838(-)$1	269	28	66	15.8249
===============bboooooobb4444=========	chr1:84746916-84747201(-)$1	285	24	62	18.4193
==========ccc[ccclllcccccc333=========	chr11:40505833-40506118(-)$1	285	37	75	16.1028
[hhhhhhhh$$$$$cccooooooccc333hhhhhhhh]	chr6:125094247-125094519(+)$1	272	181	219	15.3648
##dddd!!a[ffffffooooooffffff]a22dddd22	chr2:152562325-152562608(+)$1	283	160	198	13.5112
e####ccc!!cccbboooooobb]ccc22ccc4444ee	chr11:120440387-120440672(-)$1	285	92	130	14.4707
!ccc!!ccc[ffffffooooooffffff]ccc]ccc22	chr2:154394744-154395013(-)$1	269	128	166	15.7435
hhhhhh[cccgggggggooooooggggggg]ccc]hhh	chr1:75498514-75498799(-)$1	285	194	232	14.8294
eeee####ggggggg[bboooooobb22ggggggg22e	chr16:20681481-20681762(+)$1	281	127	165	14.7378
cc::ggggggg[bbcccooooooccc]bb]ggggggg:	chr17:24703988-24704260(+)$1	272	193	231	13.3851
dddd[a!!ccc[a[cccooooooccc]a]ccc22a]dd	chr1:37486648-37486922(-)$1	274	64	102	17.2020
ddccc####dddd[cccoooooocccdddd22ccc333	chr4:41153153-41153424(-)$1	271	40	78	15.8039
[eeeee$$$$$ffffffooooooffffffeeeee]a]c	chr19:5279391-5279667(-)$1	276	150	188	13.5098
dddd[============oooooo============333	chrX:98744311-98744584(+)$1	273	9	47	18.1904

#otherMatches

#Seq PSSM
GCCUGCACUCCCCACCCUGUGCCGUGGUGGGGCCUCAG	chr10:79003199-79003474(-)$1	275	86	124	16.0102
AAUUUCUUUUUGAAAUAAUAGUUAUACCUUAAGAAGGA	chr3:68731531-68731816(-)$1	285	214	252	13.4077
CUAUAAGAGAGUAGUUUUAGUUAACUAAUAAUUCAUAU	chr4:98746129-98746407(-)$1	278	20	58	14.3221
AGGAUUAACAGACGGUAUUCCAUUACAGGUUUGUUGAA	chr8:98293552-98293831(-)$1	279	160	198	13.7527
ACUAGAGACGAUGAGGGAGCAAGCCCUGCAUCCCUCCA	chr1:34237182-34237462(+)$1	280	55	93	13.4350
CAGGUGGAGAGGAGUGGCAGCUAUCGGUAGCUCUUCGC	chr8:72273597-72273870(-)$1	273	161	199	19.2460
GGUGGAGCAGGAUGUGGACAUGGUGUUUGCAUCUUUCA	chr9:59518339-59518625(+)$1	286	64	102	14.7786
UCAGCUCAACAACUGUCGGAUCAUGUUUGUGGAUGAAG	chr17:56452228-56452499(+)$1	271	67	105	15.1301
UUUGACCAUGGACAGACCAUCCAGCUGUCCUCUCAGGC	chr11:55094677-55094948(-)$1	271	198	236	13.8560
UUGUAGCUGUACUCCAUGAGCAGAUGAAGGAGGCCGAA	chr4:116276459-116276741(-)$1	282	69	107	16.1181
UCUAACCCCUCAGGUGCGAGGAUGCACUGAGAAAGAAC	chr9:21605583-21605854(-)$1	271	65	103	13.9283
GUCUAUUUCCUGUUGCCGCUCUGCAGCCUGGACCUGUG	chr11:51414477-51414900(-)$1	423	248	286	15.8294
GGCGGGGGGGCGACCGGAGCACACUCACAUGCACCCGG	chr4:126001328-126001601(-)$1	273	132	170	13.7138
UCGGGCAGCAGUGCUCGCCACAUGGUCAUGCAAAAGCU	chr15:75901151-75901448(-)$1	297	216	254	13.6981
UAAAUAACUUUUUGCUUUCCCAUAGGUGAAUUUGUUGC	chr10:127996178-127996446(-)$1	268	8	46	15.6969
CAGUUUCUGCUCCUUGCCAAGUCGGCUAAGGGGGCGGC	chr6:124914634-124914905(-)$1	271	41	79	14.3919
GAAAGGUACAUUAACAUUUUUCUGCUGAAGUAUCUUAU	chr5:54226283-54226567(+)$1	284	197	235	15.5681
GGAAAAGCACAAGAAACUCUUUGAAGGCCUGAAGUUCU	chr11:3876178-3876459(+)$1	281	159	197	15.0110
AGGUAAGGUUGGAAGCUUGAUUCUGAGGCCCUUACCCU	chr3:68376417-68376689(+)$1	272	166	204	13.0493
ACAGGAUGGUUCUAGCAUUAACAAGAUUAUUUGGUUCA	chr15:36529074-36529355(-)$1	281	18	56	13.8781
AAUGCCAGUGCCCAUGAAACAAGUCAUAGAAGGCGACG	chrX:131507372-131507647(-)$1	275	70	108	13.6476
UACGGAUUAUGCUUGGGGCAUUGCUGAAGUUUUGGAUC	chr12:117818792-117819060(+)$1	268	135	173	14.8869
GCACGACUUCCUGGCCUUGAUUCUGCACCGCCUGUCUC	chr17:47734273-47734551(+)$1	278	151	189	13.3893
CGUUCAUUUUGAGGACAGGGGAGCUGCUGUUAAGGUAG	chr4:135892160-135892446(+)$1	286	168	206	14.0172
UCGAGUGUGAACAGCUCAUUUGCAGCAAGUGCUUCGAA	chr9:58094835-58095109(-)$1	274	150	188	12.8060
ccgcggcggacgggggcgcaggggccgccgUCAGCCGG	chr11:78959574-78959840(-)$1	266	123	161	15.2769
CUCCAGCAGAGCCCGGCUACUCUGCCCUUGGCCCUGCC	chr11:97539648-97540030(+)$1	382	54	92	19.5978
GGAUGUCGGGGCAGGAGGGUCCACCCGCUCUGUCUCCU	chr10:75180013-75180297(-)$1	284	137	175	13.5043
GAUGUCUUAGAGCCAGAAGCGCUCGCUGAGGGCGUCAG	chr15:76072437-76072711(-)$1	274	27	65	13.1900
CCCCAUGUGUUGGCUUUGCAGUAAGCAUCAUGCAUGAG	chr7:53313672-53313945(+)$1	273	92	130	15.8361
UCCAGGGAUGAGACUGCGAAAGAGCAGCCUACAUCUUU	chr13:100820819-100821087(-)$1	268	114	152	15.9273
AGAAGAUGGAAUCAUGGAUGCUGCCAAUUUUGUAAGUG	chr4:151701462-151701751(+)$1	289	201	239	17.0433
CACUGGAGUCCACGAAGAAGCCACUGAAGAAGACAUCC	chr1:177908569-177908838(-)$1	269	28	66	15.8249
GAAAUAUCUUACAUUUCUAAUCUGACUUUGGUGUAGGG	chr1:84746916-84747201(-)$1	285	24	62	18.4193
GCUUGCGGUCGCGACUGAAGCGGCGCAAAGACUGCGGG	chr11:40505833-40506118(-)$1	285	37	75	16.1028
GCCCCAAGGCCUAAGGACUGUGCUCCAUCCCUUGGGGA	chr6:125094247-125094519(+)$1	272	181	219	15.3648
GGUCCGAGGCAGAGUAUUACAUUAUUCUUCAGUGGGAA	chr2:152562325-152562608(+)$1	283	160	198	13.5112
UGGAAUCUCACCAUCAAAAAGGAGUGGAAGGACUGAGC	chr11:120440387-120440672(-)$1	285	92	130	14.4707
ugguggggcugauauuugaacugaugucugcuggcuug	chr2:154394744-154395013(-)$1	269	128	166	15.7435
ACCGGGACAGUGGGGCCCUGGUUGGCUUCAGCUGCCCU	chr1:75498514-75498799(-)$1	285	194	232	14.8294
GCCCCCGAGGGGUGGGCCAGGUGGGGAGCUGCCCCGAG	chr16:20681481-20681762(+)$1	281	127	165	14.7378
CACACCCAGCCACAGCAGAGCAUUGUGUGCGGUUGGGG	chr17:24703988-24704260(+)$1	272	193	231	13.3851
GACCGAGGGCCGUGAUCCAGUGUGGUGAGGGCGGUGGG	chr1:37486648-37486922(-)$1	274	64	102	17.2020
GUCACUGAUGAGCUCUGCUUUCCUAGGUUCCUGUGUCC	chr4:41153153-41153424(-)$1	271	40	78	15.8039
CGAUGAAGACAAGCCAGAUGAGACUGGCUUCAUCACAC	chr19:5279391-5279667(-)$1	276	150	188	13.5098
ACGUUUUGGUAUUGUCUCAGAUUGGAUGAUAUCAGUGU	chrX:98744311-98744584(+)$1	273	9	47	18.1904

#DB
((.((....((((((((......).)))))))...)))	chr10:79003199-79003474(-)$1	1	86	124	16.0102
..(((((((((((.((((...))))...))))))))))	chr3:68731531-68731816(-)$1	1	214	252	13.4077
.((((.(((..(((((......)))))....))).)))	chr4:98746129-98746407(-)$1	1	20	58	14.3221
....(((((((((.(((......)))..))))))))).	chr8:98293552-98293831(-)$1	1	160	198	13.7527
....(((..((((((((......)))).)))).)))))	chr1:34237182-34237462(+)$1	1	55	93	13.4350
(((((((((((.(.(((......))).)..))))))))	chr8:72273597-72273870(-)$1	1	161	199	19.2460
((((((...(((((((((((...)))))))))))))))	chr9:59518339-59518625(+)$1	1	64	102	14.7786
(((..(((..(((((......)).)))..))).)))))	chr17:56452228-56452499(+)$1	1	67	105	15.1301
(..((....((((((.(......)))))))))..))))	chr11:55094677-55094948(-)$1	1	198	236	13.8560
(((..(((...((.(((......))).))..)))))))	chr4:116276459-116276741(-)$1	1	69	107	16.1181
(((.....(((((.(((......))))))))..)))).	chr9:21605583-21605854(-)$1	1	65	103	13.9283
((((((.(((.(((((......)))))..)))...)))	chr11:51414477-51414900(-)$1	1	248	286	15.8294
.((...((((((....(((....)))...))).)))..	chr4:126001328-126001601(-)$1	1	132	170	13.7138
)).)))(((..(((..(((....)))...)))...)))	chr15:75901151-75901448(-)$1	1	216	254	13.6981
(...((((..(((((((......)))))))...)))).	chr10:127996178-127996446(-)$1	1	8	46	15.6969
((((..((((((((((((.....)))..))))))))).	chr6:124914634-124914905(-)$1	1	41	79	14.3919
(((((((((.(((.((......)).))).))))))).)	chr5:54226283-54226567(+)$1	1	197	235	15.5681
((((.(((...((...((......))..))...))).)	chr11:3876178-3876459(+)$1	1	159	197	15.0110
.(((((((((((((......))))))...))))))).)	chr3:68376417-68376689(+)$1	1	166	204	13.0493
((.(((((((.((.(......).))))))))).))...	chr15:36529074-36529355(-)$1	1	18	56	13.8781
..((((.....(.((((......)))).)..))))..)	chrX:131507372-131507647(-)$1	1	70	108	13.6476
.(((((((..((((.((......)).))))....))))	chr12:117818792-117819060(+)$1	1	135	173	14.8869
(((.(((.....(((..((......))..))).)))..	chr17:47734273-47734551(+)$1	1	151	189	13.3893
((((((((((((.(.(((.....))).).))))))).)	chr4:135892160-135892446(+)$1	1	168	206	14.0172
(((((.(((....((((....).)))...)))))))))	chr9:58094835-58095109(-)$1	1	150	188	12.8060
))))(((.(((((.(((......))).))))).)))((	chr11:78959574-78959840(-)$1	1	123	161	15.2769
(((((((((.(((.(((......)))...))).))).)	chr11:97539648-97540030(+)$1	1	54	92	19.5978
(((.(.((((((.((.(......))))))))).)))))	chr10:75180013-75180297(-)$1	1	137	175	13.5043
((((((((..(((.((.....)).))).))))))))).	chr15:76072437-76072711(-)$1	1	27	65	13.1900
((.(((((((..((((......))))...))))))).)	chr7:53313672-53313945(+)$1	1	92	130	15.8361
((((((((((((.((((......)))).)).)))))))	chr13:100820819-100821087(-)$1	1	114	152	15.9273
((((..(.(...(((((......)))....))....).	chr4:151701462-151701751(+)$1	1	201	239	17.0433
((.(((((((..(..((......))...)..))).)))	chr1:177908569-177908838(-)$1	1	28	66	15.8249
(((((((((((((((((......))....)))))))))	chr1:84746916-84747201(-)$1	1	24	62	18.4193
(((((((((((((.(((...))))))...)))))))))	chr11:40505833-40506118(-)$1	1	37	75	16.1028
.((((((((.....(((......)))...)))))))).	chr6:125094247-125094519(+)$1	1	181	219	15.3648
..((((..(.((((((......)))))).)..))))..	chr2:152562325-152562608(+)$1	1	160	198	13.5112
(....(((..(((((......)).)))..)))....))	chr11:120440387-120440672(-)$1	1	92	130	14.4707
.(((..(((.((((((......)))))).))).)))..	chr2:154394744-154395013(-)$1	1	128	166	15.7435
((((((.((((((((((......))))))).))).)))	chr1:75498514-75498799(-)$1	1	194	232	14.8294
((((....(((((((.((......))..)))))))..)	chr16:20681481-20681762(+)$1	1	127	165	14.7378
))..(((((((.(((((......))).)).))))))).	chr17:24703988-24704260(+)$1	1	193	231	13.3851
((((.(..(((.(.(((......))).).)))..).))	chr1:37486648-37486922(-)$1	1	64	102	17.2020
(((((....((((.(((......)))))))..)))...	chr4:41153153-41153424(-)$1	1	40	78	15.8039
.(((((.....((((((......))))))))))).).)	chr19:5279391-5279667(-)$1	1	150	188	13.5098
((((.((((((((((((......))))))))))))...	chrX:98744311-98744584(+)$1	1	9	47	18.1904

#PSSM
d : 0.15	c : 0.08	= : 0.08	g : 0.08	[ : 0.08	e : 0.08	f : 0.08	h : 0.06	" : 0.04	i : 0.04	b : 0.04	! : 0.04	& : 0.02	: : 0.02	$ : 0.02	# : 0.02	
d : 0.15	g : 0.13	c : 0.10	= : 0.08	h : 0.08	f : 0.08	b : 0.06	e : 0.06	! : 0.04	i : 0.04	# : 0.04	& : 0.02	: : 0.02	$ : 0.02	" : 0.02	
d : 0.17	g : 0.13	= : 0.10	[ : 0.08	c : 0.08	f : 0.08	h : 0.06	: : 0.04	i : 0.04	e : 0.04	$ : 0.02	! : 0.02	b : 0.02	] : 0.02	" : 0.02	# : 0.02	
g : 0.17	d : 0.15	= : 0.10	f : 0.08	c : 0.06	b : 0.04	: : 0.04	$ : 0.04	! : 0.04	i : 0.04	" : 0.04	[ : 0.04	h : 0.04	e : 0.04	# : 0.02	
g : 0.19	= : 0.10	d : 0.10	c : 0.10	! : 0.10	i : 0.06	[ : 0.06	b : 0.04	h : 0.04	# : 0.04	$ : 0.02	" : 0.02	f : 0.02	a : 0.02	e : 0.02	
g : 0.19	c : 0.17	= : 0.13	# : 0.08	d : 0.08	[ : 0.06	i : 0.06	! : 0.06	h : 0.04	$ : 0.02	" : 0.02	a : 0.02	e : 0.02	
c : 0.28	g : 0.15	= : 0.13	# : 0.08	i : 0.06	$ : 0.06	[ : 0.04	d : 0.04	! : 0.04	" : 0.02	f : 0.02	a : 0.02	h : 0.02	
c : 0.28	g : 0.15	= : 0.13	# : 0.08	$ : 0.08	i : 0.06	! : 0.06	[ : 0.04	" : 0.02	d : 0.02	f : 0.02	h : 0.02	
c : 0.21	= : 0.13	! : 0.13	g : 0.13	# : 0.06	" : 0.06	$ : 0.06	i : 0.04	e : 0.04	f : 0.04	a : 0.04	h : 0.02	
= : 0.15	! : 0.15	g : 0.13	c : 0.10	[ : 0.08	$ : 0.08	f : 0.06	" : 0.06	i : 0.04	d : 0.04	e : 0.04	# : 0.02	
c : 0.17	g : 0.13	= : 0.10	f : 0.10	! : 0.08	$ : 0.08	d : 0.06	" : 0.06	i : 0.04	e : 0.04	[ : 0.04	# : 0.02	b : 0.02	
c : 0.17	f : 0.13	g : 0.10	= : 0.08	e : 0.08	b : 0.08	d : 0.06	[ : 0.06	i : 0.04	$ : 0.04	! : 0.04	a : 0.02	# : 0.02	" : 0.02	
c : 0.17	f : 0.10	b : 0.10	g : 0.08	= : 0.08	e : 0.08	d : 0.08	[ : 0.08	a : 0.06	i : 0.04	# : 0.04	$ : 0.02	
[ : 0.28	d : 0.10	b : 0.10	f : 0.10	g : 0.08	= : 0.06	c : 0.06	e : 0.04	# : 0.02	i : 0.02	" : 0.02	a : 0.02	! : 0.02	$ : 0.02	
c : 0.30	d : 0.10	b : 0.10	g : 0.08	f : 0.08	= : 0.06	e : 0.04	! : 0.04	[ : 0.04	# : 0.02	i : 0.02	" : 0.02	o : 0.02	a : 0.02	
c : 0.32	d : 0.10	b : 0.10	o : 0.08	g : 0.06	[ : 0.06	f : 0.06	e : 0.04	= : 0.04	! : 0.04	# : 0.02	" : 0.02	
c : 0.34	o : 0.21	b : 0.10	a : 0.08	d : 0.08	= : 0.04	g : 0.04	! : 0.02	n : 0.02	f : 0.02	
o : 0.73	c : 0.08	b : 0.06	d : 0.02	= : 0.02	m : 0.02	n : 0.02	l : 0.02	
o : 0.78	n : 0.06	l : 0.04	c : 0.04	= : 0.02	b : 0.02	m : 0.02	
o : 0.80	m : 0.06	n : 0.06	l : 0.04	= : 0.02	
o : 0.78	m : 0.06	n : 0.06	l : 0.04	f : 0.02	c : 0.02	
o : 0.71	b : 0.06	m : 0.04	n : 0.04	a : 0.04	d : 0.02	l : 0.02	f : 0.02	c : 0.02	
o : 0.58	b : 0.08	f : 0.06	d : 0.04	e : 0.04	m : 0.04	n : 0.04	] : 0.04	l : 0.02	c : 0.02	
c : 0.36	d : 0.10	b : 0.10	f : 0.08	a : 0.06	] : 0.06	o : 0.06	e : 0.04	= : 0.04	g : 0.04	
c : 0.43	b : 0.15	d : 0.10	f : 0.10	] : 0.04	e : 0.04	= : 0.04	g : 0.04	o : 0.02	
c : 0.45	f : 0.10	g : 0.08	d : 0.08	b : 0.08	3 : 0.04	e : 0.04	= : 0.04	] : 0.02	4 : 0.02	
3 : 0.21	] : 0.13	d : 0.10	f : 0.10	g : 0.08	2 : 0.08	c : 0.08	e : 0.06	= : 0.04	4 : 0.04	b : 0.02	
3 : 0.21	2 : 0.17	f : 0.10	g : 0.08	] : 0.08	4 : 0.06	a : 0.06	= : 0.04	b : 0.04	e : 0.04	d : 0.04	c : 0.02	
3 : 0.17	g : 0.10	2 : 0.10	] : 0.10	b : 0.08	= : 0.06	4 : 0.06	i : 0.06	d : 0.06	f : 0.06	e : 0.04	a : 0.04	
c : 0.21	g : 0.19	= : 0.10	2 : 0.08	i : 0.06	d : 0.06	e : 0.06	4 : 0.04	f : 0.04	b : 0.04	h : 0.02	a : 0.02	] : 0.02	
c : 0.21	g : 0.17	= : 0.13	2 : 0.10	i : 0.06	e : 0.06	4 : 0.04	b : 0.04	3 : 0.04	] : 0.04	d : 0.02	f : 0.02	h : 0.02	
c : 0.30	g : 0.17	= : 0.15	i : 0.06	2 : 0.06	d : 0.04	b : 0.04	3 : 0.04	e : 0.04	4 : 0.02	f : 0.02	h : 0.02	
] : 0.19	= : 0.15	g : 0.13	3 : 0.10	c : 0.10	i : 0.06	2 : 0.06	4 : 0.06	d : 0.04	f : 0.02	h : 0.02	e : 0.02	
c : 0.28	= : 0.15	g : 0.13	d : 0.08	3 : 0.06	i : 0.06	4 : 0.06	2 : 0.04	b : 0.02	f : 0.02	a : 0.02	h : 0.02	e : 0.02	
c : 0.19	g : 0.17	= : 0.13	d : 0.13	] : 0.08	3 : 0.06	i : 0.06	h : 0.04	4 : 0.04	b : 0.02	f : 0.02	a : 0.02	
c : 0.19	d : 0.15	g : 0.15	= : 0.10	i : 0.08	h : 0.06	4 : 0.06	2 : 0.04	3 : 0.04	b : 0.02	f : 0.02	] : 0.02	a : 0.02	
d : 0.17	] : 0.15	= : 0.10	2 : 0.10	i : 0.08	h : 0.08	g : 0.06	e : 0.04	4 : 0.04	3 : 0.04	b : 0.02	c : 0.02	f : 0.02	a : 0.02	
d : 0.15	= : 0.10	2 : 0.10	e : 0.08	g : 0.08	c : 0.06	h : 0.06	3 : 0.06	] : 0.06	f : 0.06	: : 0.04	4 : 0.04	i : 0.02	b : 0.02	

#score	691.042339136613
#seq	46
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_CDS_m2_run2.txt

#BEAR
:gggggggooooooggggggg:	chr8:105158131-105158332(-)$1	201	1	23	10.4281
ccc"""bboooooobb333ccc	chr5:37671743-37671944(+)$1	201	14	36	12.6462
iii!!cccaooooooa]ccc22	chr15:85206916-85207117(+)$1	201	51	73	11.6707
eeee[cccooooooccceeeee	chr19:21351387-21351588(+)$1	201	116	138	11.8809
c!!cccoooooocccccc====	chr2:107136218-107136419(+)$1	201	127	149	9.1634
d!!eeeeeooooooeeeeeddd	chr15:96528558-96528759(-)$1	201	154	176	11.1865
eeee!!bboooooobb]eeeee	chr14:122027885-122028086(-)$1	201	35	57	11.9329
eebbddddoooooodddd333b	chrX:132336164-132336365(+)$1	201	73	95	10.1822
!!ffffffooooooffffff33	chr1:196633627-196633828(+)$1	201	147	169	12.2340
bb[eeeeeooooooeeeee]bb	chr11:60970621-60970822(-)$1	201	123	145	10.9579
dd[eeeeeooooooeeeee]dd	chr5:4083122-4083323(-)$1	201	131	153	11.1959
!!bb[cccooooooccc]bb22	chr10:59763433-59763634(+)$1	201	129	151	11.7050
d!!eeeeeooooooeeeeeddd	chr15:96528559-96528760(-)$1	201	155	177	11.1865
ff"""cccccclllccc]ccc2	chr16:34016444-34016645(-)$1	201	167	189	7.4589
cc"""cccooooooccc]ccc:	chr4:155089572-155089773(+)$1	201	127	149	12.2093
eeee!!bboooooobb]eeeee	chr14:122027884-122028085(-)$1	201	34	56	11.9329
iiiiii[aooooooaiiiiiii	chr17:24196152-24196353(-)$1	201	11	33	11.9979
:gggggggoooooogggggggF	chr16:37536060-37536261(-)$1	201	168	190	10.6881
ff[cccbboooooobb]ccc]f	chr3:8545575-8545776(+)$1	201	102	124	12.4210
ff[cccbboooooobb]ccc]f	chr3:8545573-8545774(+)$1	201	104	126	12.4210
b[bb!!bboooooobb]bb]bb	chr9:77640841-77641042(+)$1	201	18	40	11.0468
[eeeee[aooooooa]eeeee]	chr17:85464973-85465174(-)$1	201	40	62	11.5073
eeee[cccooooooccceeeee	chr18:49857946-49858147(-)$1	201	57	79	11.8809
bb[eeeeeooooooeeeee]bb	chr1:63206271-63206472(-)$1	201	121	143	10.9579
ddd!!cccrrrrrrrrrccc22	chr2:60071963-60072164(+)$1	201	145	167	7.4372
ccc[bb[aooooooa]bb]ccc	chr3:25335266-25335467(-)$1	201	127	149	10.9600
ffffffbboooooobb]fffff	chr10:19997979-19998180(+)$1	201	121	143	11.6718
!!ffffffooooooffffff33	chr1:196633637-196633838(+)$1	201	137	159	12.2340
ddccccccooooooccc]ccc]	chr2:121128803-121129004(+)$1	201	106	128	12.3777
ccc[bb[aooooooa]bb]ccc	chr3:25335265-25335466(-)$1	201	126	148	10.9600
!!ffffffooooooffffff33	chr1:196633638-196633839(+)$1	201	136	158	12.2340
:gggggggooooooggggggg:	chr10:57247502-57247703(-)$1	201	120	142	10.4281
bb[eeeeeooooooeeeee]bb	chr11:60970622-60970823(-)$1	201	124	146	10.9579
ccccccbboooooobb]ccc]c	chr11:83822136-83822337(+)$1	201	10	32	12.5708
bb[eeeeeooooooeeeee]bb	chr1:63206272-63206473(-)$1	201	122	144	10.9579
ffffddddoooooodddd22ff	chr2:80180560-80180761(+)$1	201	111	133	9.8108
!!ffffffooooooffffff33	chr1:196633636-196633837(+)$1	201	138	160	12.2340
Dccc!!bboooooobb22cccf	chr6:86057319-86057520(+)$1	201	151	173	11.3609
!ccc!!bboooooobb333ccc	chr3:55804395-55804596(-)$1	201	167	189	12.7996
##ffffffooooooffffff22	chr14:58728297-58728498(+)$1	201	33	55	11.6154
fffff[bboooooobbffffff	chr10:57236929-57237130(-)$1	201	170	192	11.5874
ddd!!cccrrrrrrrrrccc22	chr2:60071962-60072163(+)$1	201	146	168	7.4372
dd"""cccooooooccc22ddd	chr9:58471459-58471660(+)$1	201	116	138	11.5875
ccccccbboooooobb]ccc]c	chr11:83822137-83822338(+)$1	201	9	31	12.5708
[ccc[cccooooooccc]ccc3	chr13:114384775-114384976(-)$1	201	166	188	13.0213
cc"""cccooooooccc]ccc:	chr4:155089571-155089772(+)$1	201	128	150	12.2093

#otherMatches

#Seq PSSM
GGAGUCUGCCACGACAGACUCA	chr8:105158131-105158332(-)$1	201	1	23	10.4281
CCACUACUGGAGCAAGAACUGG	chr5:37671743-37671944(+)$1	201	14	36	12.6462
UGGCAGGUCUUGCUUGAACCAU	chr15:85206916-85207117(+)$1	201	51	73	11.6707
CUGCAUCUGUACAGAGAGCAGA	chr19:21351387-21351588(+)$1	201	116	138	11.8809
GACCUGGCCCAACAGCAGGGGG	chr2:107136218-107136419(+)$1	201	127	149	9.1634
AACAGUACUGUUAUGUGCUUGG	chr15:96528558-96528759(-)$1	201	154	176	11.1865
GUGCCCUGCAUACCCAAGCACA	chr14:122027885-122028086(-)$1	201	35	57	11.9329
CAGUAUUCAAGCAGGAGUAAAG	chrX:132336164-132336365(+)$1	201	73	95	10.1822
CCAUCAAGUACAUGUUUGAUUU	chr1:196633627-196633828(+)$1	201	147	169	12.2340
GGACAUGACGCCCUUCAUGGCC	chr11:60970621-60970822(-)$1	201	123	145	10.9579
UGAAUUAUACAACAAUGAUCCA	chr5:4083122-4083323(-)$1	201	131	153	11.1959
AACCGAGAAGUGUGUCUGGGGC	chr10:59763433-59763634(+)$1	201	129	151	11.7050
AACAGUACUGUUAUGUGCUUGG	chr15:96528559-96528760(-)$1	201	155	177	11.1865
GGUAAGUGGCAGCUUGCUCAUG	chr16:34016444-34016645(-)$1	201	167	189	7.4589
GAAAGACAAAGAACUGUAUCCC	chr4:155089572-155089773(+)$1	201	127	149	12.2093
GUGCCCUGCAUACCCAAGCACA	chr14:122027884-122028085(-)$1	201	34	56	11.9329
UCAGGGACGUAUCUGCUUUGGU	chr17:24196152-24196353(-)$1	201	11	33	11.9979
UGAUCGGAAGCAACUUCGAUCC	chr16:37536060-37536261(-)$1	201	168	190	10.6881
CAAAGAAGAAAGACCUGUCUCU	chr3:8545575-8545776(+)$1	201	102	124	12.4210
CAAAGAAGAAAGACCUGUCUCU	chr3:8545573-8545774(+)$1	201	104	126	12.4210
UGUUGCCAGGUGGAUGAGAGAG	chr9:77640841-77641042(+)$1	201	18	40	11.0468
GAUGGUGGGUAAUAUGACUGUA	chr17:85464973-85465174(-)$1	201	40	62	11.5073
UCAGCAAGGAAUAUCUUCUGAG	chr18:49857946-49858147(-)$1	201	57	79	11.8809
AGAUGCACUCUCUCGUGUAGCU	chr1:63206271-63206472(-)$1	201	121	143	10.9579
CUUUCAGAUCACAUUUUUCUCC	chr2:60071963-60072164(+)$1	201	145	167	7.4372
GGUGAUGUAAUACCAGAUGACC	chr3:25335266-25335467(-)$1	201	127	149	10.9600
CACUUGGGCCCCUACCUCAGGU	chr10:19997979-19998180(+)$1	201	121	143	11.6718
CCAUCAAGUACAUGUUUGAUUU	chr1:196633637-196633838(+)$1	201	137	159	12.2340
UCCCACAGAUGAGGCUGCUGGA	chr2:121128803-121129004(+)$1	201	106	128	12.3777
GGUGAUGUAAUACCAGAUGACC	chr3:25335265-25335466(-)$1	201	126	148	10.9600
CCAUCAAGUACAUGUUUGAUUU	chr1:196633638-196633839(+)$1	201	136	158	12.2340
CCAGUGGGAACAACUCCACUGU	chr10:57247502-57247703(-)$1	201	120	142	10.4281
GGACAUGACGCCCUUCAUGGCC	chr11:60970622-60970823(-)$1	201	124	146	10.9579
CAGGAACCGAUGAUGGCUUCAC	chr11:83822136-83822337(+)$1	201	10	32	12.5708
AGAUGCACUCUCUCGUGUAGCU	chr1:63206272-63206473(-)$1	201	122	144	10.9579
GUGUUAAUUCUCAUGUUACCAC	chr2:80180560-80180761(+)$1	201	111	133	9.8108
CCAUCAAGUACAUGUUUGAUUU	chr1:196633636-196633837(+)$1	201	138	160	12.2340
GAGCCUGCUCUCCUGCCUGCUU	chr6:86057319-86057520(+)$1	201	151	173	11.3609
UCAGCAGCUACAUCGCCAACUG	chr3:55804395-55804596(-)$1	201	167	189	12.7996
CCAGAAAUUUACACAUUUUUUA	chr14:58728297-58728498(+)$1	201	33	55	11.6154
GGGAUGUCUGGCAUGAGUCCCA	chr10:57236929-57237130(-)$1	201	170	192	11.5874
CUUUCAGAUCACAUUUUUCUCC	chr2:60071962-60072163(+)$1	201	146	168	7.4372
CUCUCACACCCUUAUGUACAGC	chr9:58471459-58471660(+)$1	201	116	138	11.5875
CAGGAACCGAUGAUGGCUUCAC	chr11:83822137-83822338(+)$1	201	9	31	12.5708
CACAUGGGACCGCGCUCUUGUU	chr13:114384775-114384976(-)$1	201	166	188	13.0213
GAAAGACAAAGAACUGUAUCCC	chr4:155089571-155089772(+)$1	201	128	150	12.2093

#DB
.(((((((......))))))).	chr8:105158131-105158332(-)$1	1	1	23	10.4281
(((...((......))...)))	chr5:37671743-37671944(+)$1	1	14	36	12.6462
(((..((((......).)))..	chr15:85206916-85207117(+)$1	1	51	73	11.6707
((((.(((......))))))))	chr19:21351387-21351588(+)$1	1	116	138	11.8809
(..(((......))))))((((	chr2:107136218-107136419(+)$1	1	127	149	9.1634
(..(((((......))))))))	chr15:96528558-96528759(-)$1	1	154	176	11.1865
((((..((......)).)))))	chr14:122027885-122028086(-)$1	1	35	57	11.9329
((((((((......))))...)	chrX:132336164-132336365(+)$1	1	73	95	10.1822
..((((((......))))))..	chr1:196633627-196633828(+)$1	1	147	169	12.2340
((.(((((......))))).))	chr11:60970621-60970822(-)$1	1	123	145	10.9579
((.(((((......))))).))	chr5:4083122-4083323(-)$1	1	131	153	11.1959
..((.(((......))).))..	chr10:59763433-59763634(+)$1	1	129	151	11.7050
(..(((((......))))))))	chr15:96528559-96528760(-)$1	1	155	177	11.1865
((...((((((...))).))).	chr16:34016444-34016645(-)$1	1	167	189	7.4589
((...(((......))).))).	chr4:155089572-155089773(+)$1	1	127	149	12.2093
((((..((......)).)))))	chr14:122027884-122028085(-)$1	1	34	56	11.9329
((((((.(......))))))))	chr17:24196152-24196353(-)$1	1	11	33	11.9979
.(((((((......))))))))	chr16:37536060-37536261(-)$1	1	168	190	10.6881
((.(((((......)).))).)	chr3:8545575-8545776(+)$1	1	102	124	12.4210
((.(((((......)).))).)	chr3:8545573-8545774(+)$1	1	104	126	12.4210
(.((..((......)).)).))	chr9:77640841-77641042(+)$1	1	18	40	11.0468
.(((((.(......).))))).	chr17:85464973-85465174(-)$1	1	40	62	11.5073
((((.(((......))))))))	chr18:49857946-49858147(-)$1	1	57	79	11.8809
((.(((((......))))).))	chr1:63206271-63206472(-)$1	1	121	143	10.9579
(((..(((.........)))..	chr2:60071963-60072164(+)$1	1	145	167	7.4372
(((.((.(......).)).)))	chr3:25335266-25335467(-)$1	1	127	149	10.9600
((((((((......)).)))))	chr10:19997979-19998180(+)$1	1	121	143	11.6718
..((((((......))))))..	chr1:196633637-196633838(+)$1	1	137	159	12.2340
((((((((......))).))).	chr2:121128803-121129004(+)$1	1	106	128	12.3777
(((.((.(......).)).)))	chr3:25335265-25335466(-)$1	1	126	148	10.9600
..((((((......))))))..	chr1:196633638-196633839(+)$1	1	136	158	12.2340
.(((((((......))))))).	chr10:57247502-57247703(-)$1	1	120	142	10.4281
((.(((((......))))).))	chr11:60970622-60970823(-)$1	1	124	146	10.9579
((((((((......)).))).)	chr11:83822136-83822337(+)$1	1	10	32	12.5708
((.(((((......))))).))	chr1:63206272-63206473(-)$1	1	122	144	10.9579
((((((((......))))..))	chr2:80180560-80180761(+)$1	1	111	133	9.8108
..((((((......))))))..	chr1:196633636-196633837(+)$1	1	138	160	12.2340
)(((..((......))..)))(	chr6:86057319-86057520(+)$1	1	151	173	11.3609
.(((..((......))...)))	chr3:55804395-55804596(-)$1	1	167	189	12.7996
..((((((......))))))..	chr14:58728297-58728498(+)$1	1	33	55	11.6154
(((((.((......))))))))	chr10:57236929-57237130(-)$1	1	170	192	11.5874
(((..(((.........)))..	chr2:60071962-60072163(+)$1	1	146	168	7.4372
((...(((......)))..)))	chr9:58471459-58471660(+)$1	1	116	138	11.5875
((((((((......)).))).)	chr11:83822137-83822338(+)$1	1	9	31	12.5708
.(((.(((......))).))).	chr13:114384775-114384976(-)$1	1	166	188	13.0213
((...(((......))).))).	chr4:155089571-155089772(+)$1	1	128	150	12.2093

#PSSM
c : 0.17	d : 0.15	! : 0.13	f : 0.13	e : 0.10	b : 0.10	: : 0.06	i : 0.04	[ : 0.04	D : 0.02	# : 0.02	
c : 0.21	! : 0.17	e : 0.13	f : 0.13	d : 0.10	b : 0.08	g : 0.06	i : 0.04	[ : 0.02	# : 0.02	
c : 0.19	f : 0.17	[ : 0.15	e : 0.10	" : 0.08	g : 0.06	! : 0.06	b : 0.06	i : 0.04	d : 0.04	
e : 0.26	c : 0.19	f : 0.17	" : 0.10	g : 0.06	! : 0.06	b : 0.06	[ : 0.04	i : 0.02	
! : 0.17	e : 0.17	f : 0.15	c : 0.13	" : 0.10	[ : 0.08	g : 0.06	d : 0.04	b : 0.04	i : 0.02	
c : 0.36	e : 0.17	f : 0.13	! : 0.10	g : 0.06	d : 0.04	b : 0.04	" : 0.02	i : 0.02	[ : 0.02	
b : 0.26	c : 0.26	e : 0.15	f : 0.10	[ : 0.08	g : 0.06	d : 0.04	o : 0.02	
b : 0.26	c : 0.26	e : 0.15	f : 0.10	a : 0.08	g : 0.06	d : 0.04	o : 0.02	
o : 0.91	r : 0.04	a : 0.02	c : 0.02	
o : 0.93	r : 0.04	c : 0.02	
o : 0.93	r : 0.04	c : 0.02	
o : 0.93	r : 0.04	l : 0.02	
o : 0.91	r : 0.04	c : 0.02	l : 0.02	
o : 0.91	r : 0.04	c : 0.02	l : 0.02	
b : 0.26	c : 0.21	e : 0.15	f : 0.10	a : 0.08	g : 0.06	d : 0.04	r : 0.04	o : 0.02	
b : 0.26	c : 0.21	e : 0.15	f : 0.10	g : 0.06	] : 0.06	d : 0.04	r : 0.04	a : 0.02	i : 0.02	
c : 0.21	] : 0.19	e : 0.17	f : 0.13	g : 0.06	3 : 0.04	d : 0.04	r : 0.04	b : 0.04	i : 0.02	2 : 0.02	
e : 0.26	c : 0.17	f : 0.15	] : 0.13	g : 0.06	b : 0.06	3 : 0.04	d : 0.04	2 : 0.04	i : 0.02	
c : 0.28	e : 0.26	f : 0.15	g : 0.06	3 : 0.06	b : 0.04	] : 0.04	2 : 0.04	= : 0.02	i : 0.02	
c : 0.36	f : 0.15	] : 0.13	e : 0.10	g : 0.06	d : 0.06	= : 0.02	3 : 0.02	b : 0.02	i : 0.02	2 : 0.02	
c : 0.21	2 : 0.10	e : 0.10	3 : 0.10	b : 0.10	d : 0.08	] : 0.08	g : 0.06	f : 0.06	= : 0.02	i : 0.02	
c : 0.13	2 : 0.13	b : 0.13	f : 0.13	3 : 0.10	: : 0.08	e : 0.08	d : 0.08	] : 0.04	= : 0.02	i : 0.02	F : 0.02	

#score	519.9176731218802
#seq	46
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_CDS_m2_run2.txt

#BEAR
gggggg[bb"""eeeeennnnneeeee333bb]ggg	chr9:118741782-118741999(+)$1	217	63	99	11.1796
[dddd[ffffffcccooooooccc]ffffffdddd2	chr11:84029345-84029565(+)$1	220	5	41	12.7332
===========[cccooooooccc]===========	chr15:98762106-98762331(-)$1	225	166	202	17.5677
"ccc####bb[cccooooooccc]bb22ccc4444d	chr8:113840294-113840510(+)$1	216	83	119	14.7189
deeeee[bb"""eeeeemmmmeeeee333bb]eeee	chr3:122207777-122207994(+)$1	217	55	91	11.6025
!==========[cccqqqqqqqqccc==========	chr9:107239350-107239581(-)$1	231	168	204	11.8995
cccccffffff[ddddoooooodddd333ffffff:	chr7:149268628-149268893(-)$1	265	97	133	12.5682
ggggg!!bbdddd[aooooooa]dddd]bbgggggg	chr5:115995588-115995812(+)$1	224	179	215	13.2958
b[ccc[ccc!!ccc[bblllbb]ccc22ccccccbb	chr11:109528850-109529081(+)$1	231	20	56	11.9449
cc[eeeeebb[ccccccooooooccc333ccc]bb2	chr14:60919167-60919402(+)$1	235	161	197	13.2219
"""ccc[bb[a[cccmmmmccc]a]bb22ccceeee	chr3:133130348-133130566(-)$1	218	177	213	11.2469
==========ccc!!ammmma22ccc]=========	chr5:34091279-34091501(+)$1	222	25	61	13.1086
hhhhhhhh!!a[cccooooooccc]a22hhhhhhhh	chr17:35292896-35293152(-)$1	256	187	223	13.3864
eeee"""bb!!cccaooooooa]ccc22bb333eee	chr8:73109750-73109972(+)$1	222	142	178	16.0766
ddd!!a!!ccc[cccnnnnncccccc22a22dddd:	chr5:92734727-92734964(-)$1	237	155	191	11.2433
"""ggggggg[ddddoooooodddd]ggggggg]cc	chr6:41566677-41566931(+)$1	254	196	232	14.3879
)ffffff"""eeeeeooooooeeeee4444ffffff	chr1:156340435-156340656(+)$1	221	112	148	12.2779
eeeeeccc"""a[ddddllldddd]a333ccc]eee	chr3:89021747-89021980(+)$1	233	127	163	13.4778
eeee"""ccc!!ccc[bblllbbcccccceeeee]d	chr14:21549096-21549317(-)$1	221	161	197	11.9811
========="""cccooooooccc4444========	chr17:34788715-34788956(+)$1	241	10	46	18.5859
ggg####dddd!!cccmmmmcccddddggggggg44	chr7:133591404-133591628(+)$1	224	63	99	11.5736
ffccc[eeeee[cccooooooccc]eeeee333ccc	chr2:181118008-181118227(+)$1	219	169	205	14.2972
=====[bb####cccooooooccc]bb]========	chr17:25965278-25965500(+)$1	222	22	58	17.0422
========####ddddmmmmdddd==========cc	chr2:26066471-26066732(-)$1	261	129	165	13.5301
eeee!!a[bbcccooooooccc22bb]a22eeeee]	chr2:69752390-69752625(+)$1	235	116	152	10.8809
eeee!!eeeeeddddoooooodddd333eeeee]ee	chr1:71100169-71100391(-)$1	222	48	84	14.3661
d[bb####ccc!!ddddmmmmdddd333ccc4444b	chr1:54421833-54422058(-)$1	225	43	79	12.5178
!!ccc[ccc[eeeeeooooooeeeee]ccc22ccc]	chr12:29376105-29376327(+)$1	222	41	77	13.9125
c[ggggggg"""eeeeellleeeeeggggggg]ccc	chr2:26296721-26296960(-)$1	239	145	181	11.8758
===========[cccooooooccc]===========	chr15:98780538-98780783(-)$1	245	166	202	17.5677
ggggg[dddd"""cccnnnnnccc333ddddggggg	chr15:9043491-9043706(-)$1	215	62	98	12.4624
[ccc!!iiiiiiiii"""aooooooa333iiiiiii	chr9:20722610-20722843(-)$1	233	34	70	13.0982
:eeeee[ccc!!ddddnnnnndddd333ccc]eeee	chr17:13959254-13959475(+)$1	221	74	110	12.1842
dd[bb[ccc"""ccc[bblllbb]ccc]cccbb]dd	chr15:95471042-95471265(-)$1	223	150	186	11.1441
:ccc####ffffffooooooffffff4444ccc:cc	chr1:22278465-22278684(-)$1	219	74	110	10.7004
eeee!!ccc[ccc[cccmmmmccc]cccccceeeee	chr3:31123033-31123249(-)$1	216	147	183	12.2586
eee22gggggggcccoooooocccffffff!!dddd	chr3:27045758-27045976(+)$1	218	54	90	12.1876
eee[dddd####eeeeemmmmeeeee333ddddeee	chr2:128501743-128501978(-)$1	235	24	60	11.0722
[ccc"""ccc[ccclllccc]cccccciiiiiiiii	chr12:72265406-72265629(-)$1	223	133	169	11.7369
bb####cccccc[cccmmmmcccccc333ccc4444	chr8:114525505-114525732(-)$1	227	45	81	13.1408
bb"""eeeee!!ddddoooooodddd22eeeee333	chr6:115204553-115204778(+)$1	225	47	83	13.4294
fffff!!ccc[ddddoooooodddd]ccc]ffffff	chr7:36397378-36397597(-)$1	219	39	75	13.3561
#dddd[ccc"""cccooooooccc333ccc333ddd	chr11:51934381-51934612(+)$1	231	160	196	16.9462
eeee!!ccc[a[aooooooaaccc]eeeee4444ff	chr2:32082383-32082624(+)$1	241	44	80	13.2022
ccceeeee[a!!ddddoooooodddd22a]eeeee:	chr1:95466416-95466638(+)$1	222	164	200	13.0746
fggggggg"""eeeeeooooooeeeee]ggggggg4	chr17:34253058-34253282(-)$1	224	111	147	13.7556
d[ccc[gggggggbboooooobb4444ggggggg66	chr14:104063681-104063902(+)$1	221	125	161	13.0233
ddd"""dddd[acccooooooccc]a]dddd333dd	chr11:116460266-116460489(-)$1	223	99	135	14.7288
"dddd[ccc####ddddmmmmdddd22ccc22dddd	chr10:80714055-80714278(-)$1	223	90	126	11.2915
[ccc"""bb"""cccoooooocccbb333ccc]ggg	chr2:158271751-158271972(+)$1	221	73	109	18.0380
========[bb[cccoooooocccbb]=========	chr2:90730352-90730573(-)$1	221	138	174	16.3959
dddd"""ggggggg!!bboooooobb333ggggggg	chr7:35988203-35988422(-)$1	219	172	208	12.1063
$$$dddd[ccc[cccooooooccc]ccc]dddd444	chr7:120694669-120694897(+)$1	228	133	169	13.6604

#otherMatches

#Seq PSSM
UUUCAGGAGGAGAUGGGCAUUUCCUGUGAGCUGCUG	chr9:118741782-118741999(+)$1	217	63	99	11.1796
AAUGGUAUUGCAGCAGUGAAAUGCAUGCGAUCUAUC	chr11:84029345-84029565(+)$1	220	5	41	12.7332
CGUGCCUUUGUGCACUGGUAUGUGGGUGAGGGCAUG	chr15:98762106-98762331(-)$1	225	166	202	17.5677
UGGAAUUCUGUGUUUUGCUUAACUCAAAUCCUGCAA	chr8:113840294-113840510(+)$1	216	83	119	14.7189
UCUGUGUUGCAGUUCUCCAAGGAGAGGCACAUCAUG	chr3:122207777-122207994(+)$1	217	55	91	11.6025
ACGGGUCUUUGAGGAAAGAGGUAUCCCAGAGGCCCG	chr9:107239350-107239581(-)$1	231	168	204	11.8995
GGCCCGGCAGCAGGCAUCCCACUGCCCCGGCUGCCA	chr7:149268628-149268893(-)$1	265	97	133	12.5682
GUGGAGAGCCUCUUGGAUGAACUGGAGAGUUCCGUG	chr5:115995588-115995812(+)$1	224	179	215	13.2958
GCGGAACAUCCAGCAGUACAACAGCUUCGUGUCCCU	chr11:109528850-109529081(+)$1	231	20	56	11.9449
GAGUACGGGGUGGCCAGAAUGACUUGUUAGCCUCCU	chr14:60919167-60919402(+)$1	235	161	197	13.2219
ACACGAUCUACAGCUACACGGCAGCAGCUUCGGGGA	chr3:133130348-133130566(-)$1	218	177	213	11.2469
GAUGAGCUCCCACAGCUGUGGAGGUGAGGGGCUCAU	chr5:34091279-34091501(+)$1	222	25	61	13.1086
CCAUGUCUCGAGCUGGCAACAUGGGUGUAGGCAUGG	chr17:35292896-35293152(-)$1	256	187	223	13.3864
ACCUACUGCCCCUGCACUACCGCCAGAUGCCCCAGG	chr8:73109750-73109972(+)$1	222	142	178	16.0766
CCAAAUAAGCCCAGCAAAGAGCUGGCAGAGCUGGUG	chr5:92734727-92734964(-)$1	237	155	191	11.2433
AUGGGGGCAAAGUCUAUUUUCAGACAUUGCCUCAAG	chr6:41566677-41566931(+)$1	254	196	232	14.3879
CUGUGGACAACAAGGACAGUCCCUUGAAUUUUCAUA	chr1:156340435-156340656(+)$1	221	112	148	12.2779
CCUCUGGUUUGGGGAACAUGGUUUGUAGCACCAAGA	chr3:89021747-89021980(+)$1	233	127	163	13.4778
AACAACUCGAACGGAACCUGUGGUCCUUGUGUUUGU	chr14:21549096-21549317(-)$1	221	161	197	11.9811
GAAGGCAGGCCCGAGACCACACUCACCUCCUGUCUU	chr17:34788715-34788956(+)$1	241	10	46	18.5859
GGUUGAAUCCCAGGGCAGUAGCCGGGAGCCCAUCAG	chr7:133591404-133591628(+)$1	224	63	99	11.5736
CUUACAUCCUGUCUUUAACAUGAGUUAGGAAGAGUA	chr2:181118008-181118227(+)$1	219	169	205	14.2972
GGGAGGUUGGAAGGGAGGCAGCCCAGAGCUCCCCAG	chr17:25965278-25965500(+)$1	222	22	58	17.0422
UAAGGAGGCCAAGGCAGUUGUGCCCUUCCUUGGGGU	chr2:26066471-26066732(-)$1	261	129	165	13.5301
UAUUCCCUGUGUCCCCAAAGACUUACUGAUGAUGUC	chr2:69752390-69752625(+)$1	235	116	152	10.8809
AAGUUACACAUUUUAUUUACUUAAACCCAUGUGCAC	chr1:71100169-71100391(-)$1	222	48	84	14.3661
CAGCCACUAGUCUCAGCUCCUGCUGCUUAUUUCUCG	chr1:54421833-54422058(-)$1	225	43	79	12.5178
CAAGUGUCUGCAGGUACAGAGACCUGGAGGGAACUA	chr12:29376105-29376327(+)$1	222	41	77	13.9125
ACAUGGGGCUCCAGGCUGCCAGCUUGCCCCAUUUUC	chr2:26296721-26296960(-)$1	239	145	181	11.8758
CGUGCCUUUGUGCACUGGUAUGUGGGUGAGGGCAUG	chr15:98780538-98780783(-)$1	245	166	202	17.5677
AAUUUGCUCUUCCUUUGCAGUGAACUUGGAGAAAUU	chr15:9043491-9043706(-)$1	215	62	98	12.4624
UGGUUACAUGAGACAUUUCUUCCCCGUCCUGUCUUA	chr9:20722610-20722843(-)$1	233	34	70	13.0982
UCUUGACGAUGAUGAAUGUCCUUUACAAAUCUUCAG	chr17:13959254-13959475(+)$1	221	74	110	12.1842
UGCGGUGGGUCCUGCAGGCGCCCAGCAUCCCCCACA	chr15:95471042-95471265(-)$1	223	150	186	11.1441
UUGUUCCCUCCAUCCUCCCUGGUGGAUCCCACACUC	chr1:22278465-22278684(-)$1	219	74	110	10.7004
UGUCUUGCUUCUUCGGUAUCAACCUGAGAGCGACAU	chr3:31123033-31123249(-)$1	216	147	183	12.2586
AGCCUUGUAUAAGUCAUUGAAGACAGAAUUCUGGAA	chr3:27045758-27045976(+)$1	218	54	90	12.1876
GUUGUAGAUCCAGCAGUGAAAAUUGUGUUUCUGAAC	chr2:128501743-128501978(-)$1	235	24	60	11.0722
CGGAGAACUGAAUCUGAGAUACGGUCCUUUCUUAAG	chr12:72265406-72265629(-)$1	223	133	169	11.7369
GAGCUGAGCAUCAUCCCCCAGGAGAUCACGCUGCUG	chr8:114525505-114525732(-)$1	227	45	81	13.1408
CCAUUAGGUCAAAGUGGAAAAUCACUACGACUUCCA	chr6:115204553-115204778(+)$1	225	47	83	13.4294
AUGGGUGUUGAUGUCAUCUGGGACAGCAAGUUCAUC	chr7:36397378-36397597(-)$1	219	39	75	13.3561
UAAGUAUUCUUUGUAAGUAUCUACUCUGAGCUAGCU	chr11:51934381-51934612(+)$1	231	160	196	16.9462
GCCGCUGAAUGACUCUUUUGCUUCUUGGCCACUCUA	chr2:32082383-32082624(+)$1	241	44	80	13.2022
GUGUCCUGGUGUUCCAGGUAGGUGGAUGGGCAGGAA	chr1:95466416-95466638(+)$1	222	164	200	13.0746
UGUUUACCAACUGUUACAUUUAUAACAAGGUAAGCU	chr17:34253058-34253282(-)$1	224	111	147	13.7556
CUGGCCAGUGUCUCCUUGCGUGGCCCAAGAUGCUAU	chr14:104063681-104063902(+)$1	221	125	161	13.0233
CUUUCCCUUCACCAGCCGCUUCUGUGAGAAGUACGA	chr11:116460266-116460489(-)$1	223	99	135	14.7288
AUGACUGGCUCAAGGCAGCCCUGCUGUGCCCUGUCG	chr10:80714055-80714278(-)$1	223	90	126	11.2915
UGUAUGUCAUGUAACUUCUUUGUUUGUUUUACUAUU	chr2:158271751-158271972(+)$1	221	73	109	18.0380
GUGGUUGCUGUAGGCGCCAUAGCCAUCGUGAUCGUG	chr2:90730352-90730573(-)$1	221	138	174	16.3959
CCGUUUCCCUGGAGAAAGAUCUCACUACAUUCCAGG	chr7:35988203-35988422(-)$1	219	172	208	12.1063
CUCGUUCCUGUAGAUGUAGUGGUCAACACGAGCCUU	chr7:120694669-120694897(+)$1	228	133	169	13.6604

#DB
((((((.((...(((((.....)))))...)).)))	chr9:118741782-118741999(+)$1	1	63	99	11.1796
.((((.(((((((((......))).)))))))))).	chr11:84029345-84029565(+)$1	1	5	41	12.7332
(((((((((((.(((......))).)))))))))))	chr15:98762106-98762331(-)$1	1	166	202	17.5677
.(((....((.(((......))).))..)))....)	chr8:113840294-113840510(+)$1	1	83	119	14.7189
)(((((.((...(((((....)))))...)).))))	chr3:122207777-122207994(+)$1	1	55	91	11.6025
.((((((((((.(((........)))))))))))))	chr9:107239350-107239581(-)$1	1	168	204	11.8995
)))))((((((.((((......))))...)))))).	chr7:149268628-149268893(-)$1	1	97	133	12.5682
(((((..((((((.(......).)))).))))))))	chr5:115995588-115995812(+)$1	1	179	215	13.2958
(.(((.(((..(((.((...)).)))..))))))))	chr11:109528850-109529081(+)$1	1	20	56	11.9449
((.(((((((.((((((......)))...))).)).	chr14:60919167-60919402(+)$1	1	161	197	13.2219
...(((.((.(.(((....))).).))..)))))))	chr3:133130348-133130566(-)$1	1	177	213	11.2469
(((((((((((((..(....)..))).)))))))))	chr5:34091279-34091501(+)$1	1	25	61	13.1086
((((((((..(.(((......))).)..))))))))	chr17:35292896-35293152(-)$1	1	187	223	13.3864
((((...((..((((......).)))..))...)))	chr8:73109750-73109972(+)$1	1	142	178	16.0766
(((..(..(((.(((.....))))))..)..)))).	chr5:92734727-92734964(-)$1	1	155	191	11.2433
...(((((((.((((......)))).))))))).))	chr6:41566677-41566931(+)$1	1	196	232	14.3879
.((((((...(((((......)))))....))))))	chr1:156340435-156340656(+)$1	1	112	148	12.2779
((((((((...(.((((...)))).)...))).)))	chr3:89021747-89021980(+)$1	1	127	163	13.4778
((((...(((..(((.((...))))))))))))).)	chr14:21549096-21549317(-)$1	1	161	197	11.9811
(((((((((...(((......)))....))))))))	chr17:34788715-34788956(+)$1	1	10	46	18.5859
(((....((((..(((....))))))))))))))..	chr7:133591404-133591628(+)$1	1	63	99	11.5736
(((((.(((((.(((......))).)))))...)))	chr2:181118008-181118227(+)$1	1	169	205	14.2972
(((((.((....(((......))).)).))))))))	chr17:25965278-25965500(+)$1	1	22	58	17.0422
((((((((....((((....))))))))))))))))	chr2:26066471-26066732(-)$1	1	129	165	13.5301
((((..(.(((((......)))..)).)..))))).	chr2:69752390-69752625(+)$1	1	116	152	10.8809
((((..(((((((((......))))...))))).))	chr1:71100169-71100391(-)$1	1	48	84	14.3661
(.((....(((..((((....))))...)))....)	chr1:54421833-54422058(-)$1	1	43	79	12.5178
..(((.(((.(((((......))))).)))..))).	chr12:29376105-29376327(+)$1	1	41	77	13.9125
(.(((((((...(((((...)))))))))))).)))	chr2:26296721-26296960(-)$1	1	145	181	11.8758
(((((((((((.(((......))).)))))))))))	chr15:98780538-98780783(-)$1	1	166	202	17.5677
(((((.((((...(((.....)))...)))))))))	chr15:9043491-9043706(-)$1	1	62	98	12.4624
.(((..(((((((((...(......)...)))))))	chr9:20722610-20722843(-)$1	1	34	70	13.0982
.(((((.(((..((((.....))))...))).))))	chr17:13959254-13959475(+)$1	1	74	110	12.1842
((.((.(((...(((.((...)).))).))))).))	chr15:95471042-95471265(-)$1	1	150	186	11.1441
.(((....((((((......))))))....))).((	chr1:22278465-22278684(-)$1	1	74	110	10.7004
((((..(((.(((.(((....))).)))))))))))	chr3:31123033-31123249(-)$1	1	147	183	12.2586
)))..)))))))(((......)))((((((..((((	chr3:27045758-27045976(+)$1	1	54	90	12.1876
(((.((((....(((((....)))))...)))))))	chr2:128501743-128501978(-)$1	1	24	60	11.0722
.(((...(((.(((...))).)))))))))))))))	chr12:72265406-72265629(-)$1	1	133	169	11.7369
((....((((((.(((....))))))...)))....	chr8:114525505-114525732(-)$1	1	45	81	13.1408
((...(((((..((((......))))..)))))...	chr6:115204553-115204778(+)$1	1	47	83	13.4294
(((((..(((.((((......)))).))).))))))	chr7:36397378-36397597(-)$1	1	39	75	13.3561
.((((.(((...(((......)))...)))...)))	chr11:51934381-51934612(+)$1	1	160	196	16.9462
((((..(((.(.(......))))).)))))....))	chr2:32082383-32082624(+)$1	1	44	80	13.2022
)))(((((.(..((((......))))..).))))).	chr1:95466416-95466638(+)$1	1	164	200	13.0746
((((((((...(((((......))))).))))))).	chr17:34253058-34253282(-)$1	1	111	147	13.7556
(.(((.(((((((((......))....)))))))..	chr14:104063681-104063902(+)$1	1	125	161	13.0233
(((...((((.((((......))).).))))...))	chr11:116460266-116460489(-)$1	1	99	135	14.7288
.((((.(((....((((....))))..)))..))))	chr10:80714055-80714278(-)$1	1	90	126	11.2915
.(((...((...(((......)))))...))).)))	chr2:158271751-158271972(+)$1	1	73	109	18.0380
((((((((.((.(((......))))).)))))))))	chr2:90730352-90730573(-)$1	1	138	174	16.3959
((((...(((((((..((......))...)))))))	chr7:35988203-35988422(-)$1	1	172	208	12.1063
...((((.(((.(((......))).))).))))...	chr7:120694669-120694897(+)$1	1	133	169	13.6604

#PSSM
e : 0.16	= : 0.13	d : 0.13	g : 0.07	[ : 0.07	" : 0.07	c : 0.07	b : 0.05	f : 0.05	! : 0.03	: : 0.03	h : 0.01	) : 0.01	# : 0.01	$ : 0.01	
e : 0.20	= : 0.15	c : 0.15	d : 0.13	g : 0.09	[ : 0.07	f : 0.05	" : 0.03	b : 0.03	h : 0.01	! : 0.01	$ : 0.01	
c : 0.20	e : 0.20	= : 0.15	g : 0.11	d : 0.11	" : 0.05	[ : 0.03	f : 0.03	h : 0.01	b : 0.01	# : 0.01	$ : 0.01	
c : 0.20	e : 0.20	= : 0.15	g : 0.11	d : 0.09	f : 0.03	# : 0.03	b : 0.03	" : 0.03	h : 0.01	! : 0.01	2 : 0.01	[ : 0.01	
= : 0.15	" : 0.13	g : 0.11	c : 0.11	! : 0.11	d : 0.09	# : 0.09	e : 0.09	f : 0.03	h : 0.01	b : 0.01	2 : 0.01	
[ : 0.18	= : 0.13	! : 0.13	" : 0.11	g : 0.09	# : 0.09	e : 0.09	f : 0.03	c : 0.03	d : 0.03	h : 0.01	a : 0.01	
c : 0.16	= : 0.13	e : 0.09	" : 0.09	g : 0.09	[ : 0.07	# : 0.07	d : 0.07	f : 0.05	! : 0.05	h : 0.01	b : 0.01	a : 0.01	i : 0.01	
c : 0.24	b : 0.13	= : 0.13	g : 0.11	e : 0.09	d : 0.07	# : 0.05	f : 0.03	[ : 0.03	h : 0.01	! : 0.01	" : 0.01	i : 0.01	
c : 0.28	b : 0.16	= : 0.09	g : 0.09	f : 0.05	" : 0.05	d : 0.05	e : 0.05	# : 0.05	[ : 0.03	! : 0.01	i : 0.01	
" : 0.18	c : 0.15	= : 0.07	b : 0.07	d : 0.07	[ : 0.07	g : 0.07	# : 0.07	f : 0.05	! : 0.05	e : 0.05	i : 0.01	a : 0.01	
" : 0.18	c : 0.13	[ : 0.11	! : 0.11	e : 0.07	# : 0.07	f : 0.05	= : 0.05	a : 0.05	g : 0.05	d : 0.03	i : 0.01	b : 0.01	
[ : 0.20	c : 0.16	" : 0.15	! : 0.11	d : 0.07	# : 0.07	e : 0.05	g : 0.05	f : 0.03	a : 0.03	i : 0.01	
c : 0.49	d : 0.16	e : 0.13	[ : 0.03	! : 0.03	g : 0.03	" : 0.01	i : 0.01	f : 0.01	a : 0.01	# : 0.01	
c : 0.49	d : 0.20	e : 0.13	[ : 0.03	o : 0.03	! : 0.01	i : 0.01	f : 0.01	b : 0.01	g : 0.01	
c : 0.43	d : 0.20	e : 0.13	o : 0.07	a : 0.03	! : 0.03	[ : 0.01	i : 0.01	l : 0.01	b : 0.01	
o : 0.47	d : 0.15	e : 0.09	c : 0.09	[ : 0.03	q : 0.01	b : 0.01	m : 0.01	a : 0.01	n : 0.01	" : 0.01	l : 0.01	! : 0.01	
o : 0.54	m : 0.09	e : 0.07	b : 0.07	n : 0.05	d : 0.05	c : 0.03	q : 0.01	" : 0.01	l : 0.01	
o : 0.56	m : 0.18	n : 0.07	l : 0.05	b : 0.05	q : 0.01	" : 0.01	c : 0.01	
o : 0.58	m : 0.18	l : 0.09	n : 0.07	q : 0.01	a : 0.01	c : 0.01	
o : 0.56	m : 0.16	l : 0.09	n : 0.07	c : 0.05	q : 0.01	a : 0.01	
o : 0.52	c : 0.11	m : 0.09	n : 0.05	a : 0.03	d : 0.03	l : 0.03	q : 0.01	b : 0.01	e : 0.01	f : 0.01	] : 0.01	
c : 0.43	d : 0.15	o : 0.13	e : 0.09	b : 0.07	a : 0.03	n : 0.01	q : 0.01	2 : 0.01	f : 0.01	
c : 0.39	d : 0.20	e : 0.13	] : 0.07	o : 0.05	b : 0.05	2 : 0.03	q : 0.01	f : 0.01	
c : 0.47	d : 0.24	e : 0.13	] : 0.03	o : 0.03	a : 0.01	2 : 0.01	f : 0.01	4 : 0.01	
] : 0.22	d : 0.20	c : 0.18	e : 0.13	b : 0.09	4 : 0.03	3 : 0.03	f : 0.03	= : 0.01	o : 0.01	
c : 0.22	e : 0.15	b : 0.13	d : 0.09	3 : 0.09	a : 0.07	f : 0.05	= : 0.05	] : 0.03	4 : 0.03	g : 0.01	2 : 0.01	
3 : 0.26	2 : 0.15	c : 0.11	] : 0.09	e : 0.07	= : 0.07	4 : 0.07	f : 0.03	d : 0.03	b : 0.03	g : 0.03	
3 : 0.24	2 : 0.15	c : 0.13	= : 0.11	] : 0.07	g : 0.07	4 : 0.05	f : 0.03	e : 0.03	d : 0.03	a : 0.01	i : 0.01	
c : 0.20	3 : 0.18	= : 0.15	g : 0.09	e : 0.07	f : 0.03	b : 0.03	2 : 0.03	a : 0.03	4 : 0.03	d : 0.03	h : 0.01	i : 0.01	] : 0.01	
c : 0.26	= : 0.15	g : 0.11	e : 0.09	d : 0.07	f : 0.05	b : 0.05	2 : 0.03	4 : 0.03	i : 0.03	] : 0.03	3 : 0.01	h : 0.01	
c : 0.22	= : 0.15	g : 0.13	e : 0.09	f : 0.07	d : 0.07	3 : 0.05	2 : 0.05	b : 0.03	i : 0.03	h : 0.01	! : 0.01	4 : 0.01	
= : 0.15	g : 0.15	c : 0.13	e : 0.11	d : 0.07	3 : 0.07	4 : 0.05	f : 0.05	b : 0.03	] : 0.03	2 : 0.03	i : 0.03	h : 0.01	! : 0.01	
e : 0.16	= : 0.15	g : 0.13	d : 0.11	] : 0.09	4 : 0.07	3 : 0.07	f : 0.05	c : 0.05	i : 0.03	h : 0.01	b : 0.01	
e : 0.18	g : 0.15	= : 0.15	d : 0.09	4 : 0.09	c : 0.07	f : 0.05	] : 0.05	i : 0.03	3 : 0.03	b : 0.01	h : 0.01	: : 0.01	
e : 0.18	d : 0.13	= : 0.13	g : 0.11	c : 0.11	4 : 0.09	f : 0.07	b : 0.03	i : 0.03	h : 0.01	] : 0.01	3 : 0.01	6 : 0.01	
e : 0.15	= : 0.13	d : 0.13	g : 0.09	c : 0.09	4 : 0.07	: : 0.05	f : 0.05	2 : 0.03	b : 0.03	] : 0.03	i : 0.03	h : 0.01	3 : 0.01	6 : 0.01	

#score	707.0649732916584
#seq	53
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_CDS_m2_run2.txt

#BEAR
e"""ddddwwwwwwwwwwwwwwddd	chr4:43687279-43687507(+)$1	228	190	215	22.4756
iiiiiiiiitttttttttttiiiii	chr11:96774940-96775160(+)$1	220	94	119	21.6708
f"""ddddtttttttttttdddd22	chrX:54171297-54171520(+)$1	223	121	146	23.2856
dddd[ccctttttttttttcccddd	chr9:14814514-14814737(-)$1	223	103	128	22.6285
ggg:eeeeettttttttttteeeee	chr11:69468855-69469078(-)$1	223	53	78	20.9128
ddd[ddddtttttttttttdddd]d	chr3:127248963-127249189(+)$1	226	142	167	23.1606
#gggggggtttttttttttgggggg	chr8:74981852-74982072(-)$1	220	141	166	22.0798
[ccceeeeettttttttttteeeee	chr9:89998438-89998657(-)$1	219	104	129	21.7705
ddd[ddddtttttttttttdddddd	chr9:35493494-35493713(+)$1	219	112	137	23.1973
ggffffffwwwwwwwwwwwwwwfff	chr17:38442266-38442487(+)$1	221	152	177	20.6035
ccbb[cccuuuuuuuuuuuuccc33	chr4:138981677-138981896(-)$1	219	62	87	23.5351
ffff[cccuuuuuuuuuuuuccc]f	chr11:86893645-86893888(-)$1	243	144	169	23.3753
:eeeeewwwwwwwwwwwwwweeeee	chr7:148464397-148464619(-)$1	222	120	145	19.6031
ccfffffftttttttttttffffff	chr1:75544811-75545033(+)$1	222	100	125	21.1921
ee[bb[ccctttttttttttccc]b	chr9:30269702-30269923(+)$1	221	125	150	21.5018
$$$$dddduuuuuuuuuuuudddd5	chr6:29367925-29368151(+)$1	226	55	80	23.0033
ccffffffyyyyyyyyyyyyyyyyf	chr8:97532193-97532435(+)$1	242	88	113	20.4991
c"""cccvvvvvvvvvvvvvccc33	chr18:37975608-37975828(+)$1	220	72	97	23.1412
ii[fffffftttttttttttfffff	chr9:115159835-115160057(-)$1	222	89	114	21.0536
ffffdddduuuuuuuuuuuudddd2	chr15:34455904-34456124(-)$1	220	27	52	23.7960
========vvvvvvvvvvvvv====	chr7:135152567-135152790(-)$1	223	7	32	22.8887
eee[ddddwwwwwwwwwwwwwwddd	chr7:115224876-115225100(+)$1	224	56	81	22.0600
b"""ddddwwwwwwwwwwwwwwddd	chr2:165208130-165208353(-)$1	223	83	108	22.4159
fff[cccyyyyyyyyyyyyyyyycc	chr9:118981510-118981731(+)$1	221	175	200	21.3631
dddeeeeeuuuuuuuuuuuueeeee	chr11:87706374-87706598(+)$1	224	172	197	22.7726
::dddd[auuuuuuuuuuuua]ddd	chr17:15089618-15089849(-)$1	231	198	223	21.7218
cc!!dddduuuuuuuuuuuudddd]	chr9:4537598-4537815(+)$1	217	161	186	24.7096
ddddyyyyyyyyyyyyyyyydddd6	chr11:95625097-95625321(+)$1	224	68	93	20.0181
gggggggwwwwwwwwwwwwwwgggg	chr1:164612422-164612648(-)$1	226	2	27	21.4143
[ccccccxxxxxxxxxxxxxxxccc	chr3:7437380-7437600(+)$1	220	76	101	17.1836
bb!!ddddtttttttttttddddbb	chr10:77640398-77640624(-)$1	226	168	193	22.6655
gggggggvvvvvvvvvvvvvggggg	chrX:156005842-156006060(-)$1	218	17	42	22.2207
b"""ddddvvvvvvvvvvvvvdddd	chr14:14921719-14921956(+)$1	237	69	94	23.5072
####dddduuuuuuuuuuuudddd>	chr8:111317640-111317861(+)$1	221	77	102	24.4056
ff:eeeeeuuuuuuuuuuuueeeee	chr19:6982382-6982605(-)$1	223	38	63	21.9343
!!ffffffvvvvvvvvvvvvvffff	chr2:29633041-29633261(-)$1	220	15	40	21.6414
===[ddddtttttttttttdddd22	chr18:56935580-56935801(-)$1	221	46	71	23.3903
dd!!ddddyyyyyyyyyyyyyyyyd	chr18:38050188-38050409(-)$1	221	96	121	21.8421
ggg[dddduuuuuuuuuuuudddd2	chr3:90191214-90191436(+)$1	222	34	59	24.4837
========uuuuuuuuuuuu=====	chr9:109987045-109987266(-)$1	221	38	63	23.8194
ffffffwwwwwwwwwwwwwwfffff	chr7:3610915-3611161(-)$1	246	1	26	19.8727
[bb[ddddxxxxxxxxxxxxxxxdd	chr1:90141492-90141710(-)$1	218	141	166	17.3926
:gggggggtttttttttttgggggg	chr6:7972164-7972386(+)$1	222	37	62	21.2277
iiiiiiiiitttttttttttiiiii	chr17:35032999-35033224(+)$1	225	120	145	21.6708
dddd[cccuuuuuuuuuuuucccdd	chr2:75819627-75819859(-)$1	232	39	64	23.4236
dddd[ccctttttttttttccc]dd	chr6:85428317-85428532(-)$1	215	185	210	22.4122
d####ccctttttttttttccc444	chr1:37688671-37688889(-)$1	218	130	155	22.8509
EEE:dddduuuuuuuuuuuuddddF	chr4:123140754-123140972(-)$1	218	148	173	20.1152
e:::dddduuuuuuuuuuuudddd:	chrX:43682757-43682982(+)$1	225	139	164	20.5252
ee!!ddddtttttttttttdddd22	chr11:116299222-116299453(+)$1	231	28	53	23.1523
b[fffffftttttttttttffffff	chr10:118296602-118296837(-)$1	235	186	211	21.1272
"bb[dddduuuuuuuuuuuuddddb	chr10:58511973-58512197(+)$1	224	185	210	23.8458
b[ddddbbuuuuuuuuuuuubb]dd	chr5:96642737-96642969(+)$1	232	110	135	22.4131
gg::ddddtttttttttttddddhh	chr8:83508828-83509051(+)$1	223	91	116	21.0353
=========ttttttttttt=====	chr6:34834246-34834468(-)$1	222	123	148	22.1919
ddddddddtttttttttttdddd]d	chr8:108948741-108948961(+)$1	220	0	25	22.7684
hhhhhhhhuuuuuuuuuuuuhhhhh	chr2:49113053-49113272(+)$1	219	6	31	20.6607
c[cccabbwwwwwwwwwwwwwwbb]	chr7:28314668-28314890(-)$1	222	151	176	20.4427

#otherMatches

#Seq PSSM
UCUUGGCUGCCCACCUUCCCCAAGC	chr4:43687279-43687507(+)$1	228	190	215	22.4756
GUGUUGAUUUUUUCCCGGAUGGUCA	chr11:96774940-96775160(+)$1	220	94	119	21.6708
GCUAUUCUGCCCACAUUUGAGAAAA	chrX:54171297-54171520(+)$1	223	121	146	23.2856
UCUGCAGCUCCACACCUCUGCUCAG	chr9:14814514-14814737(-)$1	223	103	128	22.6285
UGGGCCGCUUCACCUUCUCCAGCGG	chr11:69468855-69469078(-)$1	223	53	78	20.9128
AGCUGGAUGCUUCCACCUUGUCCCG	chr3:127248963-127249189(+)$1	226	142	167	23.1606
UGGGUGCUGGGUCCACAUAAGCACC	chr8:74981852-74982072(-)$1	220	141	166	22.0798
UAGCCCUUUUUCCUGUUCCUGAAGG	chr9:89998438-89998657(-)$1	219	104	129	21.7705
UCCUCUGGUGCAAUUUUCUCCAGGG	chr9:35493494-35493713(+)$1	219	112	137	23.1973
UUUGUUUUAUCCUCAGCUCUAGAAA	chr17:38442266-38442487(+)$1	221	152	177	20.6035
UCCUCGUGAUUUAUUUCCAGCACAU	chr4:138981677-138981896(-)$1	219	62	87	23.5351
AGCCACAUUAUGCUCAACUUAUGAG	chr11:86893645-86893888(-)$1	243	144	169	23.3753
AGCUGGAUUCCUAAAGUGCCCCAGC	chr7:148464397-148464619(-)$1	222	120	145	19.6031
GAUGACAGCCCAGGCCUUCCUGUCA	chr1:75544811-75545033(+)$1	222	100	125	21.1921
GCAGGUGGCUAAUCUAACAUGUCCC	chr9:30269702-30269923(+)$1	221	125	150	21.5018
AGGCCCUGUACCAAGUGAGCCAGGA	chr6:29367925-29368151(+)$1	226	55	80	23.0033
AGAGGUAGAAGCCACUCACAAACAC	chr8:97532193-97532435(+)$1	242	88	113	20.4991
UGGGAGCAAUUCCAUUAGCAGCUAC	chr18:37975608-37975828(+)$1	220	72	97	23.1412
UCCGGGGACGAUAUCAACAAGUUCC	chr9:115159835-115160057(-)$1	222	89	114	21.0536
AGACUGAGAAUCGUUCCUUCCUUAC	chr15:34455904-34456124(-)$1	220	27	52	23.7960
GGAGGCCUUUCCCUGUGUCUUGGGC	chr7:135152567-135152790(-)$1	223	7	32	22.8887
GAGCACGCUCUCUACGAUCAUUGUG	chr7:115224876-115225100(+)$1	224	56	81	22.0600
CAAACCAGAUGUGAUCUUAAAACUG	chr2:165208130-165208353(-)$1	223	83	108	22.4159
CAGCACAUACCCACAACCUCCAUUG	chr9:118981510-118981731(+)$1	221	175	200	21.3631
UCCUGGUUCCUGAGCGUGUAGAUCA	chr11:87706374-87706598(+)$1	224	172	197	22.7726
GAGAAGCGGAAGAAUAAAGGCACUU	chr17:15089618-15089849(-)$1	231	198	223	21.7218
CACUGACAUGCCAUCCAUUCUGUCC	chr9:4537598-4537815(+)$1	217	161	186	24.7096
GAGACCCGUCCCGCACCCUUUCUCA	chr11:95625097-95625321(+)$1	224	68	93	20.0181
GUACUUACACUACCUCUUCAUUGAG	chr1:164612422-164612648(-)$1	226	2	27	21.4143
AAGUGGCAACAGCAAUGAAUUAGCC	chr3:7437380-7437600(+)$1	220	76	101	17.1836
GAGCUGGUUUUCUCCUGUUACCAUC	chr10:77640398-77640624(-)$1	226	168	193	22.6655
UUAAAAGACUACAAAAAUAACUUUU	chrX:156005842-156006060(-)$1	218	17	42	22.2207
UGUCCUGCUACUAUGAGCUCUGCAG	chr14:14921719-14921956(+)$1	237	69	94	23.5072
ACCUUGCUCUCUCAAACCAAAGCAU	chr8:111317640-111317861(+)$1	221	77	102	24.4056
GAACCGGGAAAGAAGGUGAACUUGG	chr19:6982382-6982605(-)$1	223	38	63	21.9343
AAGCUGGGCCACCAUCAGCUCCCCA	chr2:29633041-29633261(-)$1	220	15	40	21.6414
UUAGGUACCACUGUCGAUUGUACAA	chr18:56935580-56935801(-)$1	221	46	71	23.3903
CCUCCUCCCCCUCCCCCUUUUCCUG	chr18:38050188-38050409(-)$1	221	96	121	21.8421
UGUCAUGCCAUACGUCUCCAGUAUC	chr3:90191214-90191436(+)$1	222	34	59	24.4837
GUACCCCUCCCACCAUUCCAAGGGG	chr9:109987045-109987266(-)$1	221	38	63	23.8194
AUUGGGUACACUAGCCAUACCCCAG	chr7:3610915-3611161(-)$1	246	1	26	19.8727
GUUGGUGACCUGCACAACACUCUUC	chr1:90141492-90141710(-)$1	218	141	166	17.3926
UGAAAACAAAUAUCUUGCCUGUUUU	chr6:7972164-7972386(+)$1	222	37	62	21.2277
GGGCAGGGGGUAGCCGGGGACCUCU	chr17:35032999-35033224(+)$1	225	120	145	21.6708
UAGCACGCGCUACAAUUUUGGCGGC	chr2:75819627-75819859(-)$1	232	39	64	23.4236
GGCCCAAGACUAGUAACCCCUUCGG	chr6:85428317-85428532(-)$1	215	185	210	22.4122
CACGACAGUAUUUUCUUUCCUGAAU	chr1:37688671-37688889(-)$1	218	130	155	22.8509
UGCAGGGCCAUCUUCAGCAAGUCCA	chr4:123140754-123140972(-)$1	218	148	173	20.1152
UCCCCUGCAUCCUCAACAAAGCAGU	chrX:43682757-43682982(+)$1	225	139	164	20.5252
GCACCAGGAUCCUGCCUUCCCUGCA	chr11:116299222-116299453(+)$1	231	28	53	23.1523
GGAAUAUUCAGCAGAGGACAGUGUU	chr10:118296602-118296837(-)$1	235	186	211	21.1272
AGAAGCGCCACUCCUUCACUGCGCU	chr10:58511973-58512197(+)$1	224	185	210	23.8458
CCCAGGCAUCUCUUUACCCUUGUUC	chr5:96642737-96642969(+)$1	232	110	135	22.4131
UUAACUGGCAACUCCAAAACCAGAG	chr8:83508828-83509051(+)$1	223	91	116	21.0353
GUGUCUGAGUCCAACCUCCCUUCAG	chr6:34834246-34834468(-)$1	222	123	148	22.1919
GGGAGGGCAUUUGGUCAGAGCCCAU	chr8:108948741-108948961(+)$1	220	0	25	22.7684
GCUAGCAAAUCAAAACAAACUUGCU	chr2:49113053-49113272(+)$1	219	6	31	20.6607
UCGUGCGGCCUUCUCCUUCCUCCCA	chr7:28314668-28314890(-)$1	222	151	176	20.4427

#DB
(...((((..............)))	chr4:43687279-43687507(+)$1	1	190	215	22.4756
(((((((((...........)))))	chr11:96774940-96775160(+)$1	1	94	119	21.6708
(...((((...........))))..	chrX:54171297-54171520(+)$1	1	121	146	23.2856
((((.(((...........))))))	chr9:14814514-14814737(-)$1	1	103	128	22.6285
))).(((((...........)))))	chr11:69468855-69469078(-)$1	1	53	78	20.9128
(((.((((...........)))).)	chr3:127248963-127249189(+)$1	1	142	167	23.1606
.(((((((...........))))))	chr8:74981852-74982072(-)$1	1	141	166	22.0798
.((((((((...........)))))	chr9:89998438-89998657(-)$1	1	104	129	21.7705
(((.((((...........))))))	chr9:35493494-35493713(+)$1	1	112	137	23.1973
((((((((..............)))	chr17:38442266-38442487(+)$1	1	152	177	20.6035
((((.(((............)))..	chr4:138981677-138981896(-)$1	1	62	87	23.5351
((((.(((............))).)	chr11:86893645-86893888(-)$1	1	144	169	23.3753
.(((((..............)))))	chr7:148464397-148464619(-)$1	1	120	145	19.6031
))((((((...........))))))	chr1:75544811-75545033(+)$1	1	100	125	21.1921
((.((.(((...........))).)	chr9:30269702-30269923(+)$1	1	125	150	21.5018
....((((............)))).	chr6:29367925-29368151(+)$1	1	55	80	23.0033
))((((((................)	chr8:97532193-97532435(+)$1	1	88	113	20.4991
(...(((.............)))..	chr18:37975608-37975828(+)$1	1	72	97	23.1412
((.((((((...........)))))	chr9:115159835-115160057(-)$1	1	89	114	21.0536
((((((((............)))).	chr15:34455904-34456124(-)$1	1	27	52	23.7960
((((((((.............))))	chr7:135152567-135152790(-)$1	1	7	32	22.8887
(((.((((..............)))	chr7:115224876-115225100(+)$1	1	56	81	22.0600
(...((((..............)))	chr2:165208130-165208353(-)$1	1	83	108	22.4159
(((.(((................))	chr9:118981510-118981731(+)$1	1	175	200	21.3631
((((((((............)))))	chr11:87706374-87706598(+)$1	1	172	197	22.7726
..((((.(............).)))	chr17:15089618-15089849(-)$1	1	198	223	21.7218
((..((((............)))).	chr9:4537598-4537815(+)$1	1	161	186	24.7096
((((................)))).	chr11:95625097-95625321(+)$1	1	68	93	20.0181
(((((((..............))))	chr1:164612422-164612648(-)$1	1	2	27	21.4143
.((((((...............)))	chr3:7437380-7437600(+)$1	1	76	101	17.1836
((..((((...........))))))	chr10:77640398-77640624(-)$1	1	168	193	22.6655
(((((((.............)))))	chrX:156005842-156006060(-)$1	1	17	42	22.2207
(...((((.............))))	chr14:14921719-14921956(+)$1	1	69	94	23.5072
....((((............)))).	chr8:111317640-111317861(+)$1	1	77	102	24.4056
)).(((((............)))))	chr19:6982382-6982605(-)$1	1	38	63	21.9343
..((((((.............))))	chr2:29633041-29633261(-)$1	1	15	40	21.6414
(((.((((...........))))..	chr18:56935580-56935801(-)$1	1	46	71	23.3903
((..((((................)	chr18:38050188-38050409(-)$1	1	96	121	21.8421
(((.((((............)))).	chr3:90191214-90191436(+)$1	1	34	59	24.4837
((((((((............)))))	chr9:109987045-109987266(-)$1	1	38	63	23.8194
((((((..............)))))	chr7:3610915-3611161(-)$1	1	1	26	19.8727
.((.((((...............))	chr1:90141492-90141710(-)$1	1	141	166	17.3926
.(((((((...........))))))	chr6:7972164-7972386(+)$1	1	37	62	21.2277
(((((((((...........)))))	chr17:35032999-35033224(+)$1	1	120	145	21.6708
((((.(((............)))))	chr2:75819627-75819859(-)$1	1	39	64	23.4236
((((.(((...........))).))	chr6:85428317-85428532(-)$1	1	185	210	22.4122
(....(((...........)))...	chr1:37688671-37688889(-)$1	1	130	155	22.8509
))).((((............)))))	chr4:123140754-123140972(-)$1	1	148	173	20.1152
)...((((............)))).	chrX:43682757-43682982(+)$1	1	139	164	20.5252
((..((((...........))))..	chr11:116299222-116299453(+)$1	1	28	53	23.1523
(.((((((...........))))))	chr10:118296602-118296837(-)$1	1	186	211	21.1272
.((.((((............)))))	chr10:58511973-58512197(+)$1	1	185	210	23.8458
(.((((((............)).))	chr5:96642737-96642969(+)$1	1	110	135	22.4131
))..((((...........))))((	chr8:83508828-83509051(+)$1	1	91	116	21.0353
(((((((((...........)))))	chr6:34834246-34834468(-)$1	1	123	148	22.1919
((((((((...........)))).)	chr8:108948741-108948961(+)$1	1	0	25	22.7684
((((((((............)))))	chr2:49113053-49113272(+)$1	1	6	31	20.6607
(.((((((..............)).	chr7:28314668-28314890(-)$1	1	151	176	20.4427

#PSSM
d : 0.17	f : 0.10	g : 0.10	c : 0.10	e : 0.08	b : 0.08	= : 0.06	i : 0.05	[ : 0.05	: : 0.05	# : 0.03	$ : 0.01	! : 0.01	E : 0.01	" : 0.01	h : 0.01	
d : 0.15	g : 0.13	c : 0.10	" : 0.08	f : 0.08	e : 0.06	= : 0.06	i : 0.05	b : 0.05	[ : 0.05	: : 0.03	# : 0.03	$ : 0.01	! : 0.01	E : 0.01	h : 0.01	
d : 0.17	f : 0.15	g : 0.10	" : 0.08	= : 0.06	! : 0.06	c : 0.05	b : 0.05	: : 0.05	i : 0.03	e : 0.03	[ : 0.03	# : 0.03	$ : 0.01	E : 0.01	h : 0.01	
f : 0.15	[ : 0.13	d : 0.12	" : 0.08	: : 0.06	g : 0.06	! : 0.06	c : 0.05	e : 0.05	= : 0.05	i : 0.03	b : 0.03	# : 0.03	$ : 0.01	h : 0.01	
d : 0.41	f : 0.12	[ : 0.08	e : 0.08	g : 0.06	c : 0.06	= : 0.05	i : 0.03	b : 0.01	y : 0.01	# : 0.01	h : 0.01	
d : 0.41	c : 0.15	f : 0.12	e : 0.08	g : 0.06	= : 0.05	i : 0.03	[ : 0.01	y : 0.01	h : 0.01	a : 0.01	
d : 0.37	c : 0.17	f : 0.10	e : 0.06	g : 0.06	= : 0.05	i : 0.03	w : 0.03	b : 0.03	[ : 0.01	y : 0.01	h : 0.01	
d : 0.37	c : 0.12	f : 0.10	e : 0.06	w : 0.05	= : 0.05	i : 0.03	g : 0.03	v : 0.03	y : 0.03	b : 0.03	a : 0.01	x : 0.01	h : 0.01	
u : 0.29	t : 0.25	w : 0.13	v : 0.08	y : 0.06	i : 0.03	e : 0.03	x : 0.03	c : 0.01	f : 0.01	= : 0.01	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
t : 0.37	u : 0.29	w : 0.13	v : 0.08	y : 0.06	x : 0.03	
u : 0.29	w : 0.13	d : 0.13	t : 0.12	v : 0.08	y : 0.06	c : 0.05	g : 0.03	f : 0.03	x : 0.03	
d : 0.29	c : 0.13	w : 0.10	e : 0.08	f : 0.06	g : 0.05	y : 0.05	v : 0.05	i : 0.03	x : 0.03	= : 0.03	a : 0.01	b : 0.01	h : 0.01	
d : 0.31	c : 0.13	w : 0.08	e : 0.08	f : 0.08	g : 0.06	y : 0.05	= : 0.05	i : 0.03	x : 0.03	] : 0.01	b : 0.01	h : 0.01	
d : 0.39	f : 0.10	c : 0.10	e : 0.08	g : 0.06	y : 0.05	= : 0.05	i : 0.03	] : 0.03	x : 0.01	4 : 0.01	h : 0.01	b : 0.01	
d : 0.34	f : 0.10	e : 0.08	] : 0.06	g : 0.06	2 : 0.05	= : 0.05	i : 0.03	3 : 0.03	y : 0.03	c : 0.03	b : 0.03	h : 0.03	4 : 0.01	
d : 0.24	f : 0.13	2 : 0.08	e : 0.08	g : 0.06	b : 0.05	= : 0.05	i : 0.03	3 : 0.03	c : 0.03	] : 0.03	h : 0.03	5 : 0.01	6 : 0.01	> : 0.01	4 : 0.01	F : 0.01	: : 0.01	

#score	1276.0749336035283
#seq	58
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_UTR_m2_run1.txt

#BEAR
[eeeeewwwwwwwwwwwwwweeee	chr5:137967098-137967380(+)$1	282	51	75	19.0710
!ffffffssssssssssffffff2	chr15:79655049-79655353(-)$1	304	236	260	14.4162
#ffffffssssssssssffffff]	chr16:91227830-91228116(+)$1	286	94	118	14.5918
GGddddtttttttttttdddd::D	chr1:181447940-181448228(-)$1	288	78	102	16.5652
!!ddddtttttttttttdddd22d	chr5:31924703-31924994(+)$1	291	245	269	20.9023
iiiiiissssssssssiiiiiiii	chr4:63211330-63211606(+)$1	276	98	122	14.7750
ggggguuuuuuuuuuuuggggggg	chr4:33125089-33125364(+)$1	275	127	151	19.7585
ddddvvvvvvvvvvvvvdddd]gg	chr14:99472877-99473151(+)$1	274	116	140	18.7215
b[ddddyyyyyyyyyyyyyyyydd	chr15:81678793-81679067(-)$1	274	24	48	17.1641
a[ddddvvvvvvvvvvvvvdddd]	chr13:73773790-73774082(+)$1	292	212	236	19.4557
eeee[bbssssssssssbb]eeee	chr19:8907655-8907942(+)$1	287	176	200	14.5149
::ddddtttttttttttddddhhh	chr5:123807810-123808084(+)$1	274	113	137	18.3653
ff[ccctttttttttttccc]fff	chr17:37114860-37115135(-)$1	275	203	227	20.0215
dd[ddddssssssssssdddd]dd	chr14:121941982-121942255(-)$1	273	211	235	15.5027
eeeewwwwwwwwwwwwwweeeee]	chr2:144232685-144232977(+)$1	292	97	121	18.7325
"""ddddssssssssssdddd444	chr3:108706698-108706973(-)$1	275	191	215	15.9182
iiiiiivvvvvvvvvvvvviiiii	chr2:30882339-30882614(-)$1	275	135	159	18.9672
ffffbbtttttttttttbb]ffff	chr4:99324900-99325179(+)$1	279	22	46	18.6641
&eeeeettttttttttteeeee88	chr2:31071139-31071426(+)$1	287	60	84	18.8458
dddd[awwwwwwwwwwwwwwa]dd	chr13:5869145-5869421(+)$1	276	152	176	18.7442
=======ssssssssss=======	chr5:93697524-93697808(+)$1	284	165	189	15.3043
a[ddddtttttttttttdddd]a2	chr19:46147231-46147507(+)$1	276	58	82	20.8899
ffffffuuuuuuuuuuuuffffff	chr12:113887155-113887428(+)$1	273	151	175	19.2246
d!!cccssssssssssccc]dddd	chr7:16451276-16451548(-)$1	272	35	59	15.4949
####cccssssssssssccc333h	chr2:168780769-168781049(-)$1	280	43	67	15.7425
fffffftttttttttttffffff:	chr15:81535366-81535658(-)$1	292	165	189	18.2333
fffffftttttttttttffffff]	chr17:46305889-46306172(+)$1	283	95	119	19.2221
:dddduuuuuuuuuuuuddddccc	chr4:126421180-126421460(-)$1	280	102	126	19.2680
!!ddddssssssssssdddd22ee	chr5:76641535-76641823(-)$1	288	224	248	15.8719
!!ccctttttttttttccc22ddd	chr8:74842841-74843113(+)$1	272	115	139	18.5324
!!ddddtttttttttttdddd]dd	chr16:91227771-91228065(+)$1	294	89	113	21.2320
c[eeeeerrrrrrrrreeeee]cc	chr6:54767244-54767517(+)$1	273	40	64	11.3080
[bbwwwwwwwwwwwwwwbb]bbff	chr8:125096545-125096859(+)$1	314	47	71	16.6012
:eeeeevvvvvvvvvvvvveeeee	chr5:67078040-67078309(+)$1	269	217	241	18.2564
"""cccssssssssssccchhhhh	chr2:173526976-173527252(+)$1	276	228	252	15.1534
[a[ddddrrrrrrrrrdddda]ee	chr15:80766809-80767079(+)$1	270	87	111	11.5527
[eeeeesssssssssseeeee22g	chr11:117828673-117828945(-)$1	272	173	197	15.4729
c[eeeeerrrrrrrrreeeee]cc	chr2:32162847-32163126(+)$1	279	216	240	11.3080
iiiiiixxxxxxxxxxxxxxxiii	chr6:30079454-30079729(+)$1	275	225	249	14.4842
eeeyyyyyyyyyyyyyyyyeeeee	chr16:98170644-98170921(-)$1	277	2	26	17.2444
!!cccvvvvvvvvvvvvvccc22g	chr3:121969333-121969622(+)$1	289	21	45	19.5055
iiiiiitttttttttttiiiiiii	chr4:83921329-83921604(-)$1	275	114	138	19.9847
c[ddddwwwwwwwwwwwwwwdddd	chr15:75831591-75831877(-)$1	286	218	242	19.0037
bdddduuuuuuuuuuuudddd]bb	chr3:145309905-145310179(-)$1	274	122	146	19.6769
iiddddtttttttttttdddd22i	chr5:137968786-137969068(+)$1	282	11	35	20.5312
"""cccuuuuuuuuuuuuccc333	chr2:32134292-32134590(-)$1	298	165	189	21.0601
fffffftttttttttttffffff:	chr6:124998807-124999094(+)$1	287	237	261	18.2333
hhhhhhttttttttttthhhhhhh	chr18:75555293-75555568(+)$1	275	59	83	17.6035
eeeeewwwwwwwwwwwwwweeeee	chr19:45079711-45079992(-)$1	281	67	91	18.9693
cc[cccuuuuuuuuuuuucccccc	chr4:151560200-151560489(+)$1	289	249	273	20.3195
[bb[bbvvvvvvvvvvvvvbb]bb	chr3:90057072-90057343(+)$1	271	213	237	17.4567
!eeeeeuuuuuuuuuuuueeeee2	chr6:56728726-56729000(-)$1	274	11	35	20.4646
&&ddddssssssssssddddeeee	chr14:71003925-71004195(-)$1	270	83	107	14.8076
''ddddxxxxxxxxxxxxxxxddd	chr3:122242260-122242557(-)$1	297	221	245	13.6496
[bb[auuuuuuuuuuuua]bb]ee	chr4:49669033-49669321(+)$1	288	178	202	19.4017

#otherMatches

#Seq PSSM
CCUCUUUAAUUUUAAACAUUAGGA	chr5:137967098-137967380(+)$1	282	51	75	19.0710
GAAAACUUAAGGGUUUUAGUUUUG	chr15:79655049-79655353(-)$1	304	236	260	14.4162
AGGAAGUCUAAAAACUAACUUUCC	chr16:91227830-91228116(+)$1	286	94	118	14.5918
GCAGUCAGAAAACACGAGACUCAA	chr1:181447940-181448228(-)$1	288	78	102	16.5652
CAGAGACCACAUAUUUAUCUCCCU	chr5:31924703-31924994(+)$1	291	245	269	20.9023
UUUUUAAUUAGUCUAGUAGGAAAA	chr4:63211330-63211606(+)$1	276	98	122	14.7750
AUUCCGAUUUUGAUGGAGGAGUUU	chr4:33125089-33125364(+)$1	275	127	151	19.7585
ACUGUGCCUACUUCCCUCAGUAAU	chr14:99472877-99473151(+)$1	274	116	140	18.7215
CUCACCCAGGAGCAAAACAGAAGG	chr15:81678793-81679067(-)$1	274	24	48	17.1641
GUCUAUCACAUUUGCUCUCAUGGU	chr13:73773790-73774082(+)$1	292	212	236	19.4557
ACUCGCUGGUAUUAGAAAGGGAGU	chr19:8907655-8907942(+)$1	287	176	200	14.5149
UUGCAUUUAUUUAUUUUGUGUGUG	chr5:123807810-123808084(+)$1	274	113	137	18.3653
UGUUAACUUUAUUAUUUUUAUCAU	chr17:37114860-37115135(-)$1	275	203	227	20.0215
UUGUGUCUAAUUUUGAUGACGGAA	chr14:121941982-121942255(-)$1	273	211	235	15.5027
AUUCUCUUCCCAUACAAUGAGUGA	chr2:144232685-144232977(+)$1	292	97	121	18.7325
UUUUUUCCCCCCAAGUUGAGAUUG	chr3:108706698-108706973(-)$1	275	191	215	15.9182
GGGGGAAGGGAAUGCAGGAUUUCC	chr2:30882339-30882614(-)$1	275	135	159	18.9672
CGGAGCAAACUCAACCCGCGUCCG	chr4:99324900-99325179(+)$1	279	22	46	18.6641
AGGGACUCUUUCUCCUCGUUCCgu	chr2:31071139-31071426(+)$1	287	60	84	18.8458
CGUCUCACUUAUGAAACACAGCGA	chr13:5869145-5869421(+)$1	276	152	176	18.7442
GUUCAGCUUUUCGGAUUGUUGAAC	chr5:93697524-93697808(+)$1	284	165	189	15.3043
UGGGAUUUUUAAGUGGUAUUUGGU	chr19:46147231-46147507(+)$1	276	58	82	20.8899
UGUUAUGUUUUAUACCCAGUAACA	chr12:113887155-113887428(+)$1	273	151	175	19.2246
ccugggcuacauaaaacccuguug	chr7:16451276-16451548(-)$1	272	35	59	15.4949
CAUCUGCGAAGGAAUGAGCGUCUC	chr2:168780769-168781049(-)$1	280	43	67	15.7425
GUGUCAUAUUGGUCCUUUGAUACU	chr15:81535366-81535658(-)$1	292	165	189	18.2333
CCAUGCUUUUUCAGAUUGUGUGGU	chr17:46305889-46306172(+)$1	283	95	119	19.2221
UGUCCUUAUCCCUGCUUGGACACC	chr4:126421180-126421460(-)$1	280	102	126	19.2680
AAUGAGCCUGUUUAUUUUCAGAGG	chr5:76641535-76641823(-)$1	288	224	248	15.8719
CAGCACACACAGUCCCUGCCAUGG	chr8:74842841-74843113(+)$1	272	115	139	18.5324
CAUUGUACAAAACGGCCACAACGC	chr16:91227771-91228065(+)$1	294	89	113	21.2320
CUUCAGCAUCCCCAGCGCUGGCGG	chr6:54767244-54767517(+)$1	273	40	64	11.3080
CGCACUUACGCCUUUAAGCCUCGC	chr8:125096545-125096859(+)$1	314	47	71	16.6012
AGCUGUCUUCUUGCGUUCUACAGC	chr5:67078040-67078309(+)$1	269	217	241	18.2564
CGAUGGGGUACAGAAGCUACCUGG	chr2:173526976-173527252(+)$1	276	228	252	15.1534
GAUGGAGCAGCCUUACCUUCUGUG	chr15:80766809-80767079(+)$1	270	87	111	11.5527
AGCUCCCAGUGAGCCAGGGGCAGA	chr11:117828673-117828945(-)$1	272	173	197	15.4729
GGGCUUCCAUCUUUUUGAGGCACU	chr2:32162847-32163126(+)$1	279	216	240	11.3080
guugcauuaucaguauuacuuugu	chr6:30079454-30079729(+)$1	275	225	249	14.4842
UGGGAUGAAUUAAUACUGGCUAGA	chr16:98170644-98170921(-)$1	277	2	26	17.2444
UGGAACAUAAGAUACAAAUUCAUG	chr3:121969333-121969622(+)$1	289	21	45	19.5055
UUUUCCUUUAUAGUUUUGGGAGAG	chr4:83921329-83921604(-)$1	275	114	138	19.9847
UAGGGCUCCCCACCCUCCCCGCCU	chr15:75831591-75831877(-)$1	286	218	242	19.0037
CUUUUGGGGAGGGAGGGGAAAUGU	chr3:145309905-145310179(-)$1	274	122	146	19.6769
GGAGGGCACUUGUCUCUUCCUACC	chr5:137968786-137969068(+)$1	282	11	35	20.5312
GGGUGGGUAUUGUCAAUGUUAAGG	chr2:32134292-32134590(-)$1	298	165	189	21.0601
UGUUUAAGUAUAUGUGGUAAGCAU	chr6:124998807-124999094(+)$1	287	237	261	18.2333
UGUAAAUAUAAAGACGUUUUAUAA	chr18:75555293-75555568(+)$1	275	59	83	17.6035
GACUUCAAAACACAUGAAAGAGUC	chr19:45079711-45079992(-)$1	281	67	91	18.9693
CAGAGCAGAUCACCAAAAGCUUGG	chr4:151560200-151560489(+)$1	289	249	273	20.3195
AGUGAGAGAAAAGUAGGUACUGAC	chr3:90057072-90057343(+)$1	271	213	237	17.4567
ACUUUAUCCAUCCUGUCUUGAAGA	chr6:56728726-56729000(-)$1	274	11	35	20.4646
GUGCCUGUCCACCCAAAGGCUCCA	chr14:71003925-71004195(-)$1	270	83	107	14.8076
UAAUUUUUUCCAAUGCUAUUUGAA	chr3:122242260-122242557(-)$1	297	221	245	13.6496
GGAGUGAAUUUUUGAUAAGUUAUC	chr4:49669033-49669321(+)$1	288	178	202	19.4017

#DB
.(((((..............))))	chr5:137967098-137967380(+)$1	1	51	75	19.0710
.((((((..........)))))).	chr15:79655049-79655353(-)$1	1	236	260	14.4162
.((((((..........)))))).	chr16:91227830-91228116(+)$1	1	94	118	14.5918
))((((...........))))..(	chr1:181447940-181448228(-)$1	1	78	102	16.5652
..((((...........))))..)	chr5:31924703-31924994(+)$1	1	245	269	20.9023
((((((..........))))))))	chr4:63211330-63211606(+)$1	1	98	122	14.7750
(((((............)))))))	chr4:33125089-33125364(+)$1	1	127	151	19.7585
((((.............)))).))	chr14:99472877-99473151(+)$1	1	116	140	18.7215
(.((((................))	chr15:81678793-81679067(-)$1	1	24	48	17.1641
(.((((.............)))).	chr13:73773790-73774082(+)$1	1	212	236	19.4557
((((.((..........)).))))	chr19:8907655-8907942(+)$1	1	176	200	14.5149
..((((...........))))(((	chr5:123807810-123808084(+)$1	1	113	137	18.3653
((.(((...........))).)))	chr17:37114860-37115135(-)$1	1	203	227	20.0215
((.((((..........)))).))	chr14:121941982-121942255(-)$1	1	211	235	15.5027
((((..............))))).	chr2:144232685-144232977(+)$1	1	97	121	18.7325
...((((..........))))...	chr3:108706698-108706973(-)$1	1	191	215	15.9182
((((((.............)))))	chr2:30882339-30882614(-)$1	1	135	159	18.9672
((((((...........)).))))	chr4:99324900-99325179(+)$1	1	22	46	18.6641
.(((((...........)))))..	chr2:31071139-31071426(+)$1	1	60	84	18.8458
((((.(..............).))	chr13:5869145-5869421(+)$1	1	152	176	18.7442
(((((((..........)))))))	chr5:93697524-93697808(+)$1	1	165	189	15.3043
(.((((...........)))).).	chr19:46147231-46147507(+)$1	1	58	82	20.8899
((((((............))))))	chr12:113887155-113887428(+)$1	1	151	175	19.2246
(..(((..........))).))))	chr7:16451276-16451548(-)$1	1	35	59	15.4949
....(((..........)))...)	chr2:168780769-168781049(-)$1	1	43	67	15.7425
((((((...........)))))).	chr15:81535366-81535658(-)$1	1	165	189	18.2333
((((((...........)))))).	chr17:46305889-46306172(+)$1	1	95	119	19.2221
.((((............))))(((	chr4:126421180-126421460(-)$1	1	102	126	19.2680
..((((..........))))..))	chr5:76641535-76641823(-)$1	1	224	248	15.8719
..(((...........)))..)))	chr8:74842841-74843113(+)$1	1	115	139	18.5324
..((((...........)))).))	chr16:91227771-91228065(+)$1	1	89	113	21.2320
(.(((((.........))))).))	chr6:54767244-54767517(+)$1	1	40	64	11.3080
.((..............)).))((	chr8:125096545-125096859(+)$1	1	47	71	16.6012
.(((((.............)))))	chr5:67078040-67078309(+)$1	1	217	241	18.2564
...(((..........))))))))	chr2:173526976-173527252(+)$1	1	228	252	15.1534
.(.((((.........))))).))	chr15:80766809-80767079(+)$1	1	87	111	11.5527
.(((((..........)))))..)	chr11:117828673-117828945(-)$1	1	173	197	15.4729
(.(((((.........))))).))	chr2:32162847-32163126(+)$1	1	216	240	11.3080
((((((...............)))	chr6:30079454-30079729(+)$1	1	225	249	14.4842
(((................)))))	chr16:98170644-98170921(-)$1	1	2	26	17.2444
..(((.............)))..)	chr3:121969333-121969622(+)$1	1	21	45	19.5055
((((((...........)))))))	chr4:83921329-83921604(-)$1	1	114	138	19.9847
(.((((..............))))	chr15:75831591-75831877(-)$1	1	218	242	19.0037
(((((............)))).))	chr3:145309905-145310179(-)$1	1	122	146	19.6769
((((((...........))))..)	chr5:137968786-137969068(+)$1	1	11	35	20.5312
...(((............)))...	chr2:32134292-32134590(-)$1	1	165	189	21.0601
((((((...........)))))).	chr6:124998807-124999094(+)$1	1	237	261	18.2333
((((((...........)))))))	chr18:75555293-75555568(+)$1	1	59	83	17.6035
(((((..............)))))	chr19:45079711-45079992(-)$1	1	67	91	18.9693
((.(((............))))))	chr4:151560200-151560489(+)$1	1	249	273	20.3195
.((.((.............)).))	chr3:90057072-90057343(+)$1	1	213	237	17.4567
.(((((............))))).	chr6:56728726-56729000(-)$1	1	11	35	20.4646
..((((..........))))))))	chr14:71003925-71004195(-)$1	1	83	107	14.8076
..((((...............)))	chr3:122242260-122242557(-)$1	1	221	245	13.6496
.((.(............).)).))	chr4:49669033-49669321(+)$1	1	178	202	19.4017

#PSSM
! : 0.12	[ : 0.10	f : 0.10	i : 0.09	d : 0.07	e : 0.07	c : 0.07	: : 0.05	" : 0.05	# : 0.03	b : 0.03	a : 0.03	& : 0.03	G : 0.01	g : 0.01	= : 0.01	h : 0.01	' : 0.01	
e : 0.16	f : 0.14	! : 0.10	[ : 0.10	i : 0.09	d : 0.09	" : 0.05	b : 0.05	G : 0.01	g : 0.01	: : 0.01	= : 0.01	# : 0.01	a : 0.01	h : 0.01	c : 0.01	& : 0.01	' : 0.01	
d : 0.29	e : 0.20	f : 0.12	i : 0.07	[ : 0.07	" : 0.05	b : 0.05	c : 0.03	g : 0.01	= : 0.01	! : 0.01	# : 0.01	h : 0.01	
d : 0.34	e : 0.18	f : 0.12	c : 0.12	i : 0.07	[ : 0.03	g : 0.01	= : 0.01	# : 0.01	w : 0.01	y : 0.01	h : 0.01	
d : 0.30	e : 0.14	c : 0.14	f : 0.10	i : 0.07	[ : 0.03	w : 0.03	b : 0.03	g : 0.01	v : 0.01	= : 0.01	y : 0.01	h : 0.01	a : 0.01	
d : 0.27	e : 0.12	f : 0.10	c : 0.10	i : 0.07	u : 0.07	b : 0.05	w : 0.05	v : 0.03	a : 0.01	= : 0.01	t : 0.01	y : 0.01	h : 0.01	
t : 0.27	u : 0.14	w : 0.10	s : 0.10	v : 0.10	d : 0.05	f : 0.03	y : 0.03	e : 0.03	x : 0.03	b : 0.01	= : 0.01	c : 0.01	
t : 0.27	s : 0.23	u : 0.14	w : 0.10	v : 0.10	r : 0.05	y : 0.03	x : 0.03	
t : 0.27	s : 0.23	u : 0.14	w : 0.10	v : 0.10	r : 0.05	y : 0.03	x : 0.03	
t : 0.27	s : 0.23	u : 0.14	w : 0.10	v : 0.10	r : 0.05	y : 0.03	x : 0.03	
t : 0.27	s : 0.23	u : 0.14	w : 0.10	v : 0.10	r : 0.05	y : 0.03	x : 0.03	
t : 0.27	s : 0.23	u : 0.14	w : 0.10	v : 0.10	r : 0.05	y : 0.03	x : 0.03	
t : 0.27	s : 0.23	u : 0.14	w : 0.10	v : 0.10	r : 0.05	y : 0.03	x : 0.03	
t : 0.27	s : 0.23	u : 0.14	w : 0.10	v : 0.10	r : 0.05	y : 0.03	x : 0.03	
t : 0.27	s : 0.23	u : 0.14	w : 0.10	v : 0.10	r : 0.05	y : 0.03	x : 0.03	
t : 0.27	s : 0.23	u : 0.14	w : 0.10	v : 0.10	r : 0.05	y : 0.03	x : 0.03	
t : 0.25	u : 0.14	s : 0.12	w : 0.10	v : 0.10	c : 0.05	d : 0.05	e : 0.05	y : 0.03	x : 0.03	i : 0.01	
d : 0.25	w : 0.09	f : 0.09	v : 0.09	c : 0.09	e : 0.07	u : 0.07	b : 0.05	i : 0.03	y : 0.03	x : 0.03	g : 0.01	= : 0.01	h : 0.01	a : 0.01	
d : 0.25	c : 0.14	f : 0.10	e : 0.10	w : 0.07	v : 0.07	b : 0.05	i : 0.03	y : 0.03	x : 0.03	g : 0.01	= : 0.01	h : 0.01	] : 0.01	
d : 0.27	e : 0.16	f : 0.10	c : 0.09	] : 0.07	w : 0.05	i : 0.05	h : 0.03	x : 0.03	b : 0.03	g : 0.01	y : 0.01	= : 0.01	2 : 0.01	
d : 0.25	e : 0.21	f : 0.12	i : 0.05	b : 0.05	c : 0.05	a : 0.03	2 : 0.03	h : 0.03	x : 0.03	g : 0.01	y : 0.01	] : 0.01	= : 0.01	3 : 0.01	
] : 0.20	e : 0.16	f : 0.14	2 : 0.09	d : 0.09	i : 0.07	h : 0.05	3 : 0.03	c : 0.03	: : 0.01	g : 0.01	y : 0.01	4 : 0.01	= : 0.01	b : 0.01	
e : 0.20	f : 0.16	d : 0.16	2 : 0.07	i : 0.07	c : 0.07	h : 0.05	g : 0.03	3 : 0.03	b : 0.03	: : 0.01	4 : 0.01	8 : 0.01	= : 0.01	a : 0.01	
e : 0.16	d : 0.16	i : 0.09	] : 0.07	g : 0.07	h : 0.07	f : 0.07	c : 0.07	2 : 0.05	: : 0.03	b : 0.03	D : 0.01	4 : 0.01	8 : 0.01	= : 0.01	3 : 0.01	

#score	964.7654039628543
#seq	55
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_CDS_m2_run1.txt

#BEAR
eeeee"""cccssssssssssccc4444e	chr6:29411059-29411294(+)$1	235	156	185	12.5309
""ccc[a!!ccc[ddddllldddd]ccc]	chr15:102797233-102797477(+)$1	244	82	111	7.5798
dddd[cccwwwwwwwwwwwwwwcccdddd	chr11:6523715-6523950(-)$1	235	174	203	10.9013
[dddd####cccqqqqqqqqcccdddd22	chr14:60248649-60248884(+)$1	235	85	114	11.3761
"ccc[ccc[ddddllldddd]ccc22ccc	chr7:52399799-52400034(-)$1	235	104	133	8.0811
hhhhhh[bb[cccqqqqqqqqccc]bb]h	chr4:132851049-132851284(-)$1	235	62	91	9.8358
hh[ccc"""ddddllldddd]ccc]hhhh	chr4:129523617-129523873(+)$1	256	184	213	7.8340
dabb[a!!addddnnnnndddd]a22a]b	chr7:74904121-74904374(-)$1	253	38	67	8.2366
a[bb[a####cccpppppppccc333a]b	chr1:174215791-174216027(-)$1	236	76	105	11.3912
dddd!!a[bbvvvvvvvvvvvvvbb]a33	chr9:59525865-59526101(+)$1	236	184	213	9.8439
ffff####ddddrrrrrrrrrdddd22ff	chr9:109934542-109934779(+)$1	237	23	52	12.3385
chhhhhhhh[cccqqqqqqqqccc]hhhh	chr15:97962359-97962622(+)$1	263	163	192	9.1406
[dddd####ddddpppppppdddd333dd	chr7:133592024-133592270(-)$1	246	200	229	10.6311
ff!!bb!!eeeeerrrrrrrrreeeee]b	chr10:19329021-19329256(+)$1	235	119	148	10.1030
ccc!!cccvvvvvvvvvvvvvccc22ccc	chr17:34406174-34406409(+)$1	235	115	144	10.9902
ffff[gggggggrrrrrrrrrggggggg]	chr7:134356893-134357130(+)$1	237	82	111	10.4050
dd[ccc[eeeeesssssssssseeeee]c	chr2:76561979-76562240(-)$1	261	120	149	9.8152
ggggg[a!!cccrrrrrrrrrccc22a]g	chr1:36879850-36880085(-)$1	235	64	93	14.7310
GG:ccc!!ddddqqqqqqqqdddd4444c	chr2:76606134-76606371(-)$1	237	79	108	9.8304
:gggggggddddqqqqqqqqdddd]gggg	chr2:67350602-67350837(+)$1	235	198	227	9.4175
ddddbb####bbqqqqqqqqbb4444bb]	chr4:129522281-129522528(+)$1	247	83	112	9.7889
eeee[a!!cccssssssssssccc22aee	chr5:29761756-29761991(+)$1	235	22	51	13.0455
d[ccc"""a!!ddddnnnnndddd22a22	chr2:76689541-76689776(-)$1	235	126	155	8.8138

#otherMatches

#Seq PSSM
GAAGUAUUGCCCCCCAGACCAGGCCCCCA	chr6:29411059-29411294(+)$1	235	156	185	12.5309
AACUCGUACGCGGAGCCCUUGGCUGCGCC	chr15:102797233-102797477(+)$1	244	82	111	7.5798
AGCCACUGGUAAUGACUGUAGACAGGGCU	chr11:6523715-6523950(-)$1	235	174	203	10.9013
ACGAGAUCACAGACCAAUUGCUGCUUGCC	chr14:60248649-60248884(+)$1	235	85	114	11.3761
CUCCAGACAUGGGGCACCCGGGUUCAGGA	chr7:52399799-52400034(-)$1	235	104	133	8.0811
UGCAGGGGGAUGAGUCCAUUGUCAACUGC	chr4:132851049-132851284(-)$1	235	62	91	9.8358
GUUCAGAAACUUGAAGCGGGGCUGUGCGU	chr4:129523617-129523873(+)$1	256	184	213	7.8340
ACGCCGAGGAGGCGCGCAGCCUACGACAG	chr7:74904121-74904374(-)$1	253	38	67	8.2366
CCGUGACACUGAAUUCUCUUUUCUUCUGG	chr1:174215791-174216027(-)$1	236	76	105	11.3912
AGGGAAUGAUGAAGUGCUAAUAAAUGGGG	chr9:59525865-59526101(+)$1	236	184	213	9.8439
UUGAUGACCACAUUUAAAAACUGUGUUUC	chr9:109934542-109934779(+)$1	237	23	52	12.3385
ACCAUGGUCAGCUCACACCCUGGUAGAUC	chr15:97962359-97962622(+)$1	263	163	192	9.1406
ACGAUGAGAUCACAGCCAUGGUGAGAAGU	chr7:133592024-133592270(-)$1	246	200	229	10.6311
GGAAGCACGUCUGCCAUGACCCCAGACAG	chr10:19329021-19329256(+)$1	235	119	148	10.1030
GAUCuguaguaaaccaauguaugcuuauc	chr17:34406174-34406409(+)$1	235	115	144	10.9902
GAAGCCAGUGGGCCCAUCAACUUCACUGU	chr7:134356893-134357130(+)$1	237	82	111	10.4050
UUCCGUGUGUUGGCCAAGAACGCAGCAGG	chr2:76561979-76562240(-)$1	261	120	149	9.8152
UGGUCUGCCUCUUUCCUCCAUAGAUCCUG	chr1:36879850-36880085(-)$1	235	64	93	14.7310
GCAGGAAGCAGUAAGCUGAAGCUGAAGGU	chr2:76606134-76606371(-)$1	237	79	108	9.8304
CCUUCGGUCUUUAAUAGAAGAAAGAACUG	chr2:67350602-67350837(+)$1	235	198	227	9.4175
CCUGUUAAAAACCAAAUUUCGUGAAGAGC	chr4:129522281-129522528(+)$1	247	83	112	9.7889
CGAGAGAUCCGAAAGCUGGAACGGUGCCU	chr5:29761756-29761991(+)$1	235	22	51	13.0455
AGGUGGAGCACUAUGAAGAGCAUGAGGAA	chr2:76689541-76689776(-)$1	235	126	155	8.8138

#DB
(((((...(((..........)))....)	chr6:29411059-29411294(+)$1	1	156	185	12.5309
..(((.(..(((.((((...)))).))).	chr15:102797233-102797477(+)$1	1	82	111	7.5798
((((.(((..............)))))))	chr11:6523715-6523950(-)$1	1	174	203	10.9013
.((((....(((........)))))))..	chr14:60248649-60248884(+)$1	1	85	114	11.3761
.(((.(((.((((...)))).)))..)))	chr7:52399799-52400034(-)$1	1	104	133	8.0811
((((((.((.(((........))).)).)	chr4:132851049-132851284(-)$1	1	62	91	9.8358
((.(((...((((...)))).))).))))	chr4:129523617-129523873(+)$1	1	184	213	7.8340
((((.(..(((((.....)))).)..).)	chr7:74904121-74904374(-)$1	1	38	67	8.2366
(.((.(....(((.......)))...).)	chr1:174215791-174216027(-)$1	1	76	105	11.3912
((((..(.((.............)).)..	chr9:59525865-59526101(+)$1	1	184	213	9.8439
((((....((((.........))))..))	chr9:109934542-109934779(+)$1	1	23	52	12.3385
(((((((((.(((........))).))))	chr15:97962359-97962622(+)$1	1	163	192	9.1406
.((((....((((.......))))...))	chr7:133592024-133592270(-)$1	1	200	229	10.6311
((..((..(((((.........))))).)	chr10:19329021-19329256(+)$1	1	119	148	10.1030
(((..(((.............)))..)))	chr17:34406174-34406409(+)$1	1	115	144	10.9902
((((.(((((((.........))))))).	chr7:134356893-134357130(+)$1	1	82	111	10.4050
((.(((.(((((..........))))).)	chr2:76561979-76562240(-)$1	1	120	149	9.8152
(((((.(..(((.........)))..).)	chr1:36879850-36880085(-)$1	1	64	93	14.7310
((.(((..((((........))))....)	chr2:76606134-76606371(-)$1	1	79	108	9.8304
.(((((((((((........)))).))))	chr2:67350602-67350837(+)$1	1	198	227	9.4175
((((((....((........))....)).	chr4:129522281-129522528(+)$1	1	83	112	9.7889
((((.(..(((..........)))..)))	chr5:29761756-29761991(+)$1	1	22	51	13.0455
(.(((...(..((((.....))))..)..	chr2:76689541-76689776(-)$1	1	126	155	8.8138

#PSSM
d : 0.26	f : 0.13	e : 0.08	" : 0.08	[ : 0.08	h : 0.08	c : 0.08	a : 0.04	g : 0.04	G : 0.04	: : 0.04	
d : 0.26	h : 0.13	f : 0.13	e : 0.08	c : 0.08	[ : 0.08	g : 0.08	" : 0.04	a : 0.04	G : 0.04	
d : 0.21	c : 0.17	e : 0.08	h : 0.08	[ : 0.08	b : 0.08	f : 0.08	g : 0.08	! : 0.04	: : 0.04	
c : 0.26	d : 0.21	e : 0.08	h : 0.08	b : 0.08	f : 0.08	! : 0.08	g : 0.08	
[ : 0.26	c : 0.21	d : 0.08	h : 0.08	! : 0.08	b : 0.08	g : 0.08	e : 0.04	# : 0.04	
c : 0.26	# : 0.13	a : 0.13	" : 0.08	[ : 0.08	h : 0.08	b : 0.08	g : 0.08	! : 0.04	
# : 0.21	! : 0.17	" : 0.13	a : 0.13	c : 0.13	[ : 0.08	g : 0.08	h : 0.04	
! : 0.26	# : 0.21	" : 0.13	c : 0.13	g : 0.08	b : 0.04	[ : 0.04	h : 0.04	e : 0.04	
# : 0.17	d : 0.13	c : 0.08	! : 0.08	b : 0.08	a : 0.08	e : 0.08	w : 0.04	[ : 0.04	" : 0.04	h : 0.04	v : 0.04	g : 0.04	
d : 0.30	c : 0.21	[ : 0.08	# : 0.08	e : 0.08	w : 0.04	b : 0.04	v : 0.04	g : 0.04	! : 0.04	
c : 0.34	d : 0.30	v : 0.08	e : 0.08	w : 0.04	g : 0.04	b : 0.04	! : 0.04	
d : 0.34	c : 0.26	s : 0.08	v : 0.08	e : 0.08	w : 0.04	g : 0.04	b : 0.04	
d : 0.21	q : 0.17	s : 0.13	c : 0.13	r : 0.13	v : 0.08	[ : 0.04	w : 0.04	e : 0.04	
q : 0.26	r : 0.17	s : 0.13	d : 0.08	l : 0.08	p : 0.08	v : 0.08	w : 0.04	n : 0.04	
q : 0.26	r : 0.17	s : 0.13	d : 0.08	l : 0.08	p : 0.08	v : 0.08	w : 0.04	n : 0.04	
q : 0.26	r : 0.17	s : 0.13	l : 0.08	n : 0.08	p : 0.08	v : 0.08	d : 0.04	w : 0.04	
q : 0.26	r : 0.17	s : 0.13	d : 0.13	n : 0.08	p : 0.08	v : 0.08	w : 0.04	
q : 0.26	r : 0.17	s : 0.13	d : 0.08	n : 0.08	p : 0.08	v : 0.08	l : 0.04	w : 0.04	
q : 0.26	r : 0.17	s : 0.13	d : 0.13	p : 0.08	v : 0.08	l : 0.04	w : 0.04	n : 0.04	
q : 0.26	r : 0.17	s : 0.13	d : 0.13	p : 0.08	v : 0.08	l : 0.04	w : 0.04	n : 0.04	
d : 0.26	r : 0.17	s : 0.13	c : 0.08	] : 0.08	q : 0.08	v : 0.08	w : 0.04	b : 0.04	
c : 0.43	d : 0.30	w : 0.04	v : 0.04	r : 0.04	g : 0.04	s : 0.04	b : 0.04	
c : 0.47	d : 0.26	e : 0.08	] : 0.04	v : 0.04	g : 0.04	4 : 0.04	
c : 0.39	d : 0.30	e : 0.08	a : 0.04	3 : 0.04	b : 0.04	g : 0.04	4 : 0.04	
2 : 0.26	] : 0.21	4 : 0.13	d : 0.08	3 : 0.08	e : 0.08	c : 0.04	b : 0.04	g : 0.04	
2 : 0.30	4 : 0.13	d : 0.08	h : 0.08	3 : 0.08	e : 0.08	g : 0.08	c : 0.04	b : 0.04	] : 0.04	
a : 0.26	c : 0.13	4 : 0.08	d : 0.08	b : 0.08	h : 0.08	e : 0.08	g : 0.08	2 : 0.04	3 : 0.04	
] : 0.26	c : 0.13	4 : 0.08	d : 0.08	2 : 0.08	h : 0.08	g : 0.08	3 : 0.04	f : 0.04	b : 0.04	e : 0.04	
c : 0.17	] : 0.13	h : 0.13	b : 0.13	e : 0.08	d : 0.08	2 : 0.08	g : 0.08	3 : 0.04	f : 0.04	

#score	236.66252419084788
#seq	23
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_UTR_m2_run1.txt

#BEAR
ffffff"""ddddooooooddddfffff	chr9:64034181-64034381(-)$1	200	8	36	10.5845
:eeeee[ffffffooooooffffff]ee	chr14:70186070-70186305(-)$1	235	156	184	10.8586
[eeeee[ffffffooooooffffff444	chr15:75779600-75779807(-)$1	207	87	115	12.1248
ddd"""gggggggooooooggggggg]d	chr14:56357793-56358002(-)$1	209	25	53	13.0558
##dddd####cccnnnnnccc22dddd3	chr11:109528873-109529073(+)$1	200	23	51	9.4175
+++dddd!!cccooooooccc22dddd>	chr19:7353206-7353417(-)$1	211	137	165	10.0203
d"""ffffff[bboooooobbffffff7	chr19:56672112-56672321(+)$1	209	164	192	12.9722
dddd####ddddoooooodddd22dddd	chr6:114266412-114266616(+)$1	204	61	89	9.9484
e[eeeee[bb[bboooooobb]bb]eee	chr3:151895545-151895750(+)$1	205	74	102	12.8238
===[iiiiiiiiiooooooiiiiiiiii	chr1:175266017-175266234(-)$1	217	166	194	13.5900
ee!!ffffffcccooooooccc4444ff	chr11:77349686-77349893(-)$1	207	157	185	12.9200
ddddgggggggcccmmmmccc333gggg	chr6:119875390-119875592(-)$1	202	142	170	9.1484
cdddd[ccc!!bboooooobb22ccc]d	chr4:41685596-41685805(+)$1	209	89	117	14.7746
fff:eeeee!!bboooooobb]eeeee:	chr15:89116577-89116792(+)$1	215	187	215	11.3923
#dddd!!ddddoooooodddd22dddd3	chr17:85463561-85463767(-)$1	206	30	58	9.3550
=============oooooo=========	chr8:109895338-109895541(+)$1	203	161	189	14.2433
bbeeeeeccc[bboooooobb333ccc]	chr3:96435952-96436163(+)$1	211	156	184	14.5160
===========[ammmma==========	chr4:149100964-149101178(-)$1	214	162	190	9.7590
eee####ccc[bboooooobbccc333e	chr19:7502119-7502326(+)$1	207	94	122	14.1721
$$$$gggggggbboooooobb22ggggg	chr17:15943601-15943801(-)$1	200	67	95	14.2780
eee"""bb!!cccooooooccc22bb33	chr10:107936142-107936348(-)$1	206	67	95	13.2374
$eeeee####cccooooooccc4444ee	chr7:117037227-117037433(+)$1	206	114	142	12.9366
33ddddccc!!bboooooobb333ccc:	chr7:126117223-126117423(-)$1	200	93	121	13.3759
###dddd[bb[bboooooobb333bb22	chr11:74713857-74714088(+)$1	231	112	140	13.7006
bb####ccc!!cccmmmmccc22ccc33	chr3:100009989-100010202(-)$1	213	68	96	9.9419
ii[bb[dddd[bboooooobb]ddddbb	chr1:90595242-90595466(+)$1	224	103	131	12.1622
e!!iiiiiiiiiccclllccc]iiiiii	chr1:9537149-9537367(+)$1	218	83	111	9.5228
eeeffffff!!bboooooobb22fffff	chr16:92297768-92297991(+)$1	223	178	206	14.1217
ffff"""ffffffooooooffffff>>>	chrX:96661501-96661701(-)$1	200	47	75	11.1454
ccc[eeeee!!bboooooobbeeeeecc	chr7:126117333-126117540(-)$1	207	46	74	13.3205
gccc!!cccddddoooooodddd]ccc2	chr1:11586522-11586725(+)$1	203	12	40	11.7522
ccc"""cccddddoooooodddd]ccc3	chrX:153882680-153882885(-)$1	205	166	194	12.1772
!!eeeee[ccc!!aooooooa22ccc]e	chr17:14041936-14042137(+)$1	201	32	60	12.7593
:::ffffff!!bboooooobb22fffff	chr11:20725570-20725770(+)$1	200	82	110	11.4960
d!!cccccc[cccoooooocccccc22c	chr7:3637294-3637512(-)$1	218	101	129	12.9251
========"""bblllbb]=========	chr2:132135197-132135400(-)$1	203	146	174	9.5118
eeeeeccc!!cccooooooccc]ccc88	chr1:176751781-176751993(+)$1	212	25	53	12.7315
eee!!eeeee[bboooooobb]eeeeee	chr13:43498700-43498900(+)$1	200	162	190	13.6599
bb[bb!!ffffffooooooffffff22b	chr17:35970877-35971094(-)$1	217	26	54	10.8581
ddd[ddddcccbboooooobb22ccc]d	chr2:75504899-75505113(+)$1	214	103	131	14.0316
ddd:iiiiiiiiiooooooiiiiiiiii	chr10:13869983-13870186(+)$1	203	151	179	12.1512
$$$iiiiiiiii[aooooooa22iiiii	chr1:122239522-122239739(-)$1	217	115	143	12.6281
=======[bb!!bbnnnnnbb22bb]==	chr11:90139629-90139830(-)$1	201	32	60	9.8951
bb!!ccc[eeeeeooooooeeeeeccc2	chr14:73762473-73762674(+)$1	201	37	65	11.4031
eee!!eeeee[bboooooobb]eeeee5	chr9:58044041-58044250(-)$1	209	126	154	13.2076
"ffffff"""cccnnnnnccc22fffff	chr15:98780317-98780522(+)$1	205	38	66	9.2287
hhhh!!gggggggooooooggggggg]h	chr2:155052105-155052314(+)$1	209	36	64	11.9328
ddd[ccc[bb[bboooooobb]bb333c	chr9:20451099-20451318(-)$1	219	81	109	13.4542
$$$ffffff[cccooooooccc]fffff	chr9:56343854-56344055(+)$1	201	17	45	12.3708
::a!!dddd[cccooooooccc]dddd2	chr15:5168034-5168239(+)$1	205	79	107	11.0062
ddd!!gggggggbbnnnnnbb]gggggg	chr2:71739246-71739452(+)$1	206	170	198	9.8612
ccc[bbeeeeebboooooobb22eeeee	chr11:97576479-97576679(-)$1	200	26	54	13.1434

#otherMatches

#Seq PSSM
ACACAGCAUGUGCCAAAUUGUACUUGUG	chr9:64034181-64034381(-)$1	200	8	36	10.5845
ACGGGAUGUGCGUGGGGCAAUGUGCUUC	chr14:70186070-70186305(-)$1	235	156	184	10.8586
GAUUGUGGUAUUUAAUAGCAAGUACAGU	chr15:75779600-75779807(-)$1	207	87	115	12.1248
CAUUCUGGGGGCUCUGGUAGGUUCUUUG	chr14:56357793-56358002(-)$1	209	25	53	13.0558
UCGUGUCCCUGUCCGUCUGACCCGCGCC	chr11:109528873-109529073(+)$1	200	23	51	9.4175
AUAGCCCCCAGUAUUCCAGCUCUGGGCA	chr19:7353206-7353417(-)$1	211	137	165	10.0203
GUCAAAACUAAUCAUGCCAGAUAGUUUA	chr19:56672112-56672321(+)$1	209	164	192	12.9722
GGACUCCCAUGUAGCAAAGCGUAUGUCU	chr6:114266412-114266616(+)$1	204	61	89	9.9484
AUGUAUUUGCAACUAUUAUGUGGUCGAU	chr3:151895545-151895750(+)$1	205	74	102	12.8238
guguguauguguguguguguacguguau	chr1:175266017-175266234(-)$1	217	166	194	13.5900
ACAAACUAGUGACCAAAUUGUCAUCUGC	chr11:77349686-77349893(-)$1	207	157	185	12.9200
GGGUAUGUGGAAAGAAAUCUUAGGUCCA	chr6:119875390-119875592(-)$1	202	142	170	9.1484
CAUUUGCAUAGCAGGGGAGUGGAAUGGA	chr4:41685596-41685805(+)$1	209	89	117	14.7746
CAGAUGGACCUGGCCACUCCCUGUCCAG	chr15:89116577-89116792(+)$1	215	187	215	11.3923
AGGAGAACAGGAGAACGCCUGGCCUCCC	chr17:85463561-85463767(-)$1	206	30	58	9.3550
UUCUUUUAGUUUUCAUGGAGAAGCUGAA	chr8:109895338-109895541(+)$1	203	161	189	14.2433
GCUUAGCCUACUCUAUGUUGAAUAUGGU	chr3:96435952-96436163(+)$1	211	156	184	14.5160
CGAGGGUGUAGACUGCUGCUGUACCCUU	chr4:149100964-149101178(-)$1	214	162	190	9.7590
AACCAAACUCUAGCUGACACUGAGCAAG	chr19:7502119-7502326(+)$1	207	94	122	14.1721
AUUUGGAGGUGACUAGUUUGUACCGCCU	chr17:15943601-15943801(-)$1	200	67	95	14.2780
UAGCAAACUGAAGCAACCUCUUAUGUAC	chr10:107936142-107936348(-)$1	206	67	95	13.2374
AGUUGCAAAACAACAUAAAUUGAACAGU	chr7:117037227-117037433(+)$1	206	114	142	12.9366
ACACUCGAAUCGCUACAUUGCUUUUUCU	chr7:126117223-126117423(-)$1	200	93	121	13.3759
UCGUUGGACACGGUGAUUUCCAAAUGAA	chr11:74713857-74714088(+)$1	231	112	140	13.7006
CUAUGAACAAUGGUGGCGGCCUAUGUAA	chr3:100009989-100010202(-)$1	213	68	96	9.9419
UGAGCACAGGAAAGCUACAUUAUUUGGC	chr1:90595242-90595466(+)$1	224	103	131	12.1622
AUAAUAUUAAAAGUAUAGUGCUUUUUGG	chr1:9537149-9537367(+)$1	218	83	111	9.5228
GCUUAUUUUCACACAUAUUUGACAAGAU	chr16:92297768-92297991(+)$1	223	178	206	14.1217
AACAUACAUUUUCUAACCUGAAAGUUGA	chrX:96661501-96661701(-)$1	200	47	75	11.1454
CCUGAGCAAGUCAUUCCUUUGUUGCUAG	chr7:126117333-126117540(-)$1	207	46	74	13.3205
UUAGAACUUUAUGAAGUUGCAUGUAAGA	chr1:11586522-11586725(+)$1	203	12	40	11.7522
guauguagcccagucuaaccuggagcuu	chrX:153882680-153882885(-)$1	205	166	194	12.1772
UAAACUUUGCACUGUCAAUCCUCUGCUG	chr17:14041936-14042137(+)$1	201	32	60	12.7593
UAGCAAUUUAUGUCAAGAAGCCAAAGUU	chr11:20725570-20725770(+)$1	200	82	110	11.4960
CCUUCCGCAUGCGCUUCUACGUUGCCUG	chr7:3637294-3637512(-)$1	218	101	129	12.9251
UCUUCAAACAGCCAAUGGAUUUGAGGAU	chr2:132135197-132135400(-)$1	203	146	174	9.5118
UACUUGACUUCUGCUUAUACAGUGUCUA	chr1:176751781-176751993(+)$1	212	25	53	12.7315
AGAGCCGGUCUACUUCCAUGUUGACUGU	chr13:43498700-43498900(+)$1	200	162	190	13.6599
CCACACUUGGGAAAGUAUGUUUCCACCU	chr17:35970877-35971094(-)$1	217	26	54	10.8581
GGGGGAAUGGGGCGUGCUAGUAUUUCAA	chr2:75504899-75505113(+)$1	214	103	131	14.0316
AAGCAAGAUAUUUAAACUAGAAUAUCUU	chr10:13869983-13870186(+)$1	203	151	179	12.1512
GCAUUUCGGGUCACAAAAAGGGAGGUCC	chr1:122239522-122239739(-)$1	217	115	143	12.6281
UUAAAUGAAUCCACAAAAAGUUAAUAUA	chr11:90139629-90139830(-)$1	201	32	60	9.8951
UUAGGCAUCUUUCCCUCAUGGAAGUGCA	chr14:73762473-73762674(+)$1	201	37	65	11.4031
AAAUAAUCGAUUUGAACAGGACUCGGUG	chr9:58044041-58044250(-)$1	209	126	154	13.2076
CUGUAUGAAAGCACACAUUGCCACAUAC	chr15:98780317-98780522(+)$1	205	38	66	9.2287
AGUCCUGGCCCUAGUUCUAUAGGGCUUG	chr2:155052105-155052314(+)$1	209	36	64	11.9328
GUAUGACAGCAGCAAAGCAGCAGCCAAG	chr9:20451099-20451318(-)$1	219	81	109	13.4542
ACUGCUGCACAGCCAGCCAGCUUUGCAG	chr9:56343854-56344055(+)$1	201	17	45	12.3708
UUGUUGUGCUAAUGUUCUAAUUUGUGCU	chr15:5168034-5168239(+)$1	205	79	107	11.0062
GACACCUGGGUUCUCUCUCAGUGACCCA	chr2:71739246-71739452(+)$1	206	170	198	9.8612
AUGUGACUUGUCCAUUUCCGGCUGCAAG	chr11:97576479-97576679(-)$1	200	26	54	13.1434

#DB
((((((...((((......)))))))))	chr9:64034181-64034381(-)$1	1	8	36	10.5845
.(((((.((((((......)))))).))	chr14:70186070-70186305(-)$1	1	156	184	10.8586
.(((((.((((((......))))))...	chr15:75779600-75779807(-)$1	1	87	115	12.1248
(((...(((((((......))))))).)	chr14:56357793-56358002(-)$1	1	25	53	13.0558
..((((....(((.....)))..)))).	chr11:109528873-109529073(+)$1	1	23	51	9.4175
...((((..(((......)))..)))).	chr19:7353206-7353417(-)$1	1	137	165	10.0203
(...((((((.((......)))))))).	chr19:56672112-56672321(+)$1	1	164	192	12.9722
((((....((((......))))..))))	chr6:114266412-114266616(+)$1	1	61	89	9.9484
(.(((((.((.((......)).)).)))	chr3:151895545-151895750(+)$1	1	74	102	12.8238
(((.(((((((((......)))))))))	chr1:175266017-175266234(-)$1	1	166	194	13.5900
((..(((((((((......)))....))	chr11:77349686-77349893(-)$1	1	157	185	12.9200
((((((((((((((....)))...))))	chr6:119875390-119875592(-)$1	1	142	170	9.1484
)((((.(((..((......))..))).)	chr4:41685596-41685805(+)$1	1	89	117	14.7746
))).(((((..((......)).))))).	chr15:89116577-89116792(+)$1	1	187	215	11.3923
.((((..((((......))))..)))).	chr17:85463561-85463767(-)$1	1	30	58	9.3550
(((((((((((((......)))))))))	chr8:109895338-109895541(+)$1	1	161	189	14.2433
))((((((((.((......))...))).	chr3:96435952-96436163(+)$1	1	156	184	14.5160
(((((((((((.(....)))))))))))	chr4:149100964-149101178(-)$1	1	162	190	9.7590
(((....(((.((......)))))...)	chr19:7502119-7502326(+)$1	1	94	122	14.1721
....(((((((((......))..)))))	chr17:15943601-15943801(-)$1	1	67	95	14.2780
(((...((..(((......)))..))..	chr10:107936142-107936348(-)$1	1	67	95	13.2374
.(((((....(((......)))....))	chr7:117037227-117037433(+)$1	1	114	142	12.9366
..))))(((..((......))...))).	chr7:126117223-126117423(-)$1	1	93	121	13.3759
...((((.((.((......))...))..	chr11:74713857-74714088(+)$1	1	112	140	13.7006
((....(((..(((....)))..)))..	chr3:100009989-100010202(-)$1	1	68	96	9.9419
((.((.((((.((......)).))))))	chr1:90595242-90595466(+)$1	1	103	131	12.1622
(..((((((((((((...))).))))))	chr1:9537149-9537367(+)$1	1	83	111	9.5228
(((((((((..((......))..)))))	chr16:92297768-92297991(+)$1	1	178	206	14.1217
((((...((((((......))))))...	chrX:96661501-96661701(-)$1	1	47	75	11.1454
(((.(((((..((......)))))))))	chr7:126117333-126117540(-)$1	1	46	74	13.3205
((((..(((((((......)))).))).	chr1:11586522-11586725(+)$1	1	12	40	11.7522
(((...(((((((......)))).))).	chrX:153882680-153882885(-)$1	1	166	194	12.1772
..(((((.(((..(......)..))).)	chr17:14041936-14042137(+)$1	1	32	60	12.7593
...((((((..((......))..)))))	chr11:20725570-20725770(+)$1	1	82	110	11.4960
(..((((((.(((......))))))..)	chr7:3637294-3637512(-)$1	1	101	129	12.9251
((((((((...((...)).)))))))))	chr2:132135197-132135400(-)$1	1	146	174	9.5118
((((((((..(((......))).)))..	chr1:176751781-176751993(+)$1	1	25	53	12.7315
(((..(((((.((......)).))))))	chr13:43498700-43498900(+)$1	1	162	190	13.6599
((.((..((((((......))))))..)	chr17:35970877-35971094(-)$1	1	26	54	10.8581
(((.(((((((((......))..))).)	chr2:75504899-75505113(+)$1	1	103	131	14.0316
))).(((((((((......)))))))))	chr10:13869983-13870186(+)$1	1	151	179	12.1512
...(((((((((.(......)..)))))	chr1:122239522-122239739(-)$1	1	115	143	12.6281
(((((((.((..((.....))..)).))	chr11:90139629-90139830(-)$1	1	32	60	9.8951
((..(((.(((((......)))))))).	chr14:73762473-73762674(+)$1	1	37	65	11.4031
(((..(((((.((......)).))))).	chr9:58044041-58044250(-)$1	1	126	154	13.2076
.((((((...(((.....)))..)))))	chr15:98780317-98780522(+)$1	1	38	66	9.2287
((((..(((((((......))))))).)	chr2:155052105-155052314(+)$1	1	36	64	11.9328
(((.(((.((.((......)).))...)	chr9:20451099-20451318(-)$1	1	81	109	13.4542
...((((((.(((......))).)))))	chr9:56343854-56344055(+)$1	1	17	45	12.3708
..(..((((.(((......))).)))).	chr15:5168034-5168239(+)$1	1	79	107	11.0062
(((..(((((((((.....)).))))))	chr2:71739246-71739452(+)$1	1	170	198	9.8612
(((.(((((((((......))..)))))	chr11:97576479-97576679(-)$1	1	26	54	13.1434

#PSSM
d : 0.17	e : 0.17	= : 0.09	c : 0.07	b : 0.07	$ : 0.07	f : 0.05	: : 0.05	# : 0.05	[ : 0.01	+ : 0.01	3 : 0.01	i : 0.01	g : 0.01	! : 0.01	" : 0.01	h : 0.01	
e : 0.19	d : 0.17	= : 0.09	f : 0.07	b : 0.07	c : 0.07	$ : 0.05	! : 0.05	# : 0.03	: : 0.03	+ : 0.01	" : 0.01	[ : 0.01	3 : 0.01	i : 0.01	h : 0.01	
e : 0.23	d : 0.21	= : 0.09	f : 0.07	! : 0.07	c : 0.07	$ : 0.05	# : 0.03	[ : 0.03	+ : 0.01	" : 0.01	: : 0.01	h : 0.01	a : 0.01	
d : 0.15	e : 0.13	f : 0.11	! : 0.11	[ : 0.09	" : 0.07	= : 0.07	: : 0.03	# : 0.03	b : 0.03	i : 0.03	c : 0.03	$ : 0.01	h : 0.01	
e : 0.17	f : 0.13	d : 0.13	! : 0.11	" : 0.07	i : 0.07	= : 0.07	# : 0.05	b : 0.05	c : 0.05	g : 0.03	
e : 0.19	f : 0.13	d : 0.11	" : 0.07	i : 0.07	! : 0.07	= : 0.07	c : 0.07	# : 0.05	g : 0.05	[ : 0.03	b : 0.01	
c : 0.17	e : 0.15	f : 0.11	g : 0.09	d : 0.09	# : 0.07	i : 0.07	= : 0.07	" : 0.03	[ : 0.03	! : 0.03	b : 0.01	
f : 0.17	c : 0.17	[ : 0.11	g : 0.09	e : 0.09	i : 0.07	d : 0.07	# : 0.05	= : 0.05	" : 0.03	! : 0.01	b : 0.01	
c : 0.19	f : 0.17	e : 0.11	g : 0.09	d : 0.07	b : 0.07	i : 0.07	" : 0.05	! : 0.05	# : 0.03	= : 0.03	
! : 0.17	d : 0.11	f : 0.11	g : 0.09	c : 0.09	b : 0.07	i : 0.07	e : 0.07	[ : 0.05	# : 0.03	= : 0.03	" : 0.03	
c : 0.23	[ : 0.17	! : 0.15	d : 0.09	g : 0.09	f : 0.07	i : 0.07	= : 0.03	e : 0.03	" : 0.01	
b : 0.36	c : 0.23	d : 0.07	f : 0.07	i : 0.07	g : 0.05	! : 0.03	o : 0.01	= : 0.01	[ : 0.01	e : 0.01	
b : 0.40	c : 0.23	f : 0.07	d : 0.05	o : 0.05	g : 0.03	i : 0.03	= : 0.01	a : 0.01	! : 0.01	[ : 0.01	e : 0.01	
o : 0.78	c : 0.05	n : 0.03	a : 0.03	b : 0.03	m : 0.01	l : 0.01	
o : 0.82	n : 0.07	m : 0.05	c : 0.01	l : 0.01	
o : 0.82	n : 0.07	m : 0.05	l : 0.03	
o : 0.82	n : 0.07	m : 0.05	l : 0.01	b : 0.01	
o : 0.80	n : 0.07	m : 0.03	d : 0.01	a : 0.01	l : 0.01	b : 0.01	
o : 0.76	c : 0.11	d : 0.03	n : 0.03	= : 0.01	] : 0.01	
b : 0.38	c : 0.24	d : 0.09	f : 0.07	= : 0.05	g : 0.03	i : 0.03	o : 0.03	e : 0.01	
b : 0.38	c : 0.24	d : 0.09	f : 0.07	= : 0.05	g : 0.03	i : 0.03	a : 0.03	e : 0.01	
2 : 0.26	] : 0.15	c : 0.15	f : 0.09	d : 0.07	3 : 0.07	= : 0.05	g : 0.03	i : 0.03	e : 0.03	
2 : 0.30	f : 0.09	e : 0.09	d : 0.07	3 : 0.07	g : 0.05	i : 0.05	= : 0.05	] : 0.05	b : 0.03	4 : 0.03	c : 0.03	
f : 0.19	c : 0.13	e : 0.11	d : 0.09	g : 0.07	i : 0.07	3 : 0.07	b : 0.05	= : 0.05	2 : 0.03	4 : 0.03	] : 0.03	
c : 0.21	f : 0.19	d : 0.11	g : 0.09	e : 0.09	i : 0.07	= : 0.05	b : 0.05	4 : 0.03	3 : 0.03	] : 0.01	
c : 0.19	f : 0.11	d : 0.11	e : 0.11	g : 0.09	i : 0.07	4 : 0.05	= : 0.05	] : 0.03	3 : 0.03	b : 0.03	2 : 0.03	> : 0.01	
f : 0.13	e : 0.13	c : 0.11	] : 0.09	d : 0.09	i : 0.07	= : 0.07	3 : 0.07	g : 0.05	2 : 0.05	4 : 0.01	b : 0.01	> : 0.01	8 : 0.01	
e : 0.13	f : 0.11	3 : 0.09	d : 0.07	i : 0.07	= : 0.07	2 : 0.07	g : 0.05	c : 0.05	> : 0.03	: : 0.03	b : 0.03	4 : 0.01	7 : 0.01	] : 0.01	8 : 0.01	5 : 0.01	h : 0.01	

#score	625.6073411746117
#seq	52
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_transcript_m2_run2.txt

#BEAR
[ggggggg"""ccclllccc333ggggggg	chr13:5862414-5862667(+)$1	253	140	170	12.1853
c!!ggggggg[bboooooobb]ggggggg2	chr10:117187834-117188071(-)$1	237	47	77	13.7276
a[gggggggddddnnnnndddd22gggggg	chr5:144178998-144179245(+)$1	247	49	79	11.1274
dggggggg[dddd[aooooooa]ddddggg	chr3:109398330-109398565(+)$1	235	127	157	11.2579
fffffccc[ddddoooooodddd]ccc22f	chr5:101195404-101195645(-)$1	241	49	79	12.3403
eee[ccc!!ddddoooooodddd22ccc]e	chr4:155031015-155031252(-)$1	237	116	146	13.6818
ddccc$$$$$cccoooooocccccc333dd	chr11:70799268-70799546(-)$1	278	138	168	13.7612
dddd!!gggggggoooooogggggggdddd	chr2:90844960-90845220(+)$1	260	20	50	12.5738
hhiiiiiiiiicccnnnnnccc]iiiiiii	chr5:52550096-52550337(-)$1	241	146	176	11.1876
d####bb[bbcccooooooccc]bb]bb44	chr19:38046573-38046827(-)$1	254	192	222	12.2333
eeeeggggggg[aooooooa]ggggggg66	chr14:47572988-47573223(+)$1	235	9	39	12.6274
[ffffff"""cccooooooccc333fffff	chr12:25684069-25684309(+)$1	240	80	110	15.1015
eeeeeeee[ddddooooooddddeeeee33	chr4:57722048-57722289(+)$1	241	42	72	12.5119
[dddd[gggggggooooooggggggg]ddd	chr12:52495841-52496085(+)$1	244	187	217	12.7218
!dddd"""eeeeeooooooeeeee22dddd	chr15:96213872-96214122(+)$1	250	78	108	11.3846
!!ffffff!!cccnnnnnccc333ffffff	chr8:111253241-111253489(+)$1	248	139	169	11.3531
b####gggggggaooooooa]ggggggg44	chr19:55852007-55852254(+)$1	247	51	81	13.5540
ggggggg$$$$$cccmmmmccc333ggggg	chr10:109198210-109198447(-)$1	237	34	64	10.7834
=======ddddbboooooobb]dddd]===	chr8:13119681-13119997(+)$1	316	203	233	12.3093
####bb[bb[cccooooooccc]bb]bbdd	chr10:79742090-79742336(+)$1	246	140	170	12.3798
d[eeeee[eeeeeooooooeeeeeeeeee]	chr1:94004890-94005127(-)$1	237	94	124	11.6919
:::ccc####cccooooooccc4444ccc:	chr9:49325241-49325535(-)$1	294	58	88	12.0738
ccc[ccc####bboooooobb22ccc]ccc	chr4:125846408-125846691(-)$1	283	123	153	14.0531
:ggggggg!!cccmmmmccc4444gggggg	chr15:82984262-82984510(-)$1	248	206	236	10.7485
ddd[ccc[eeeeeooooooeeeee]cccdd	chr7:6659898-6660159(-)$1	261	212	242	11.7841
:::eeeee!!cccooooooccc22eeeee:	chr11:21941404-21941641(-)$1	237	80	110	11.0422
!bbeeeee[bb[aooooooa]bb]eeeee4	chr12:52743922-52744167(-)$1	245	66	96	11.3860
gggg[ccc!!cccnnnnnccc22cccgggg	chr19:56510075-56510311(+)$1	236	177	207	11.8749
!!ccc!!ffffffooooooffffff]ccc2	chr10:127001593-127001855(-)$1	262	221	251	12.0647
##a"""bb[ddddoooooodddd]bb333a	chr5:90658083-90658318(-)$1	235	84	114	12.7570
:eeeee####cccooooooccc333eeeee	chr10:59822869-59823120(+)$1	251	31	61	14.8762
bb[ccc####cccooooooccc4444ccc]	chr11:108027333-108027583(-)$1	250	124	154	15.4323
HHHeeeeea[cccooooooccc]a]eeeee	chr5:151911420-151911657(-)$1	237	201	231	12.1011
"""eeeee!!cccooooooccc22eeeee]	chr15:78924050-78924285(+)$1	235	15	45	14.9299
cc[==========lll==========]ccc	chr15:53140124-53140376(-)$1	252	221	251	11.5368
a[dddd"""ddddoooooodddd22dddd]	chr4:132688126-132688370(+)$1	244	120	150	13.2135
=============nnnnn============	chr2:157382318-157382598(-)$1	280	18	48	11.9757
hhhhccc[a!!bboooooobb22a]ccc22	chr17:69563744-69563979(+)$1	235	179	209	13.0108
ggggggg####cccmmmmccc22ggggggg	chr17:24689391-24689639(+)$1	248	75	105	11.5417
dggggggg!!cccooooooccc]ggggggg	chr6:52709601-52709849(+)$1	248	153	183	15.8867
d[ccc####ddddoooooodddd333ccc2	chr1:140505902-140506175(-)$1	273	86	116	14.5801
cc!!gggggggrrrrrrrrrggggggg22c	chr17:56560597-56560878(-)$1	281	89	119	9.3760
iiiiiiii"""bboooooobb333iiiiii	chr15:80844511-80844753(-)$1	242	172	202	15.5104
Giiiiiiiiirrrrrrrrriiiiiiiiicc	chr3:57261778-57262015(-)$1	237	10	40	9.4766
gggggg####cccmmmmccc4444gggggg	chr15:53049662-53049899(-)$1	237	191	221	11.7730
ccccc!!bb!!bboooooobb22bb22ccc	chr10:82350717-82351005(+)$1	288	13	43	12.3321
iia[bb"""ddddoooooodddd]bb]a]i	chr8:11349779-11350042(+)$1	263	156	186	13.3389
:ggggggg!!cccooooooccc22gggggg	chr11:74887102-74887345(+)$1	243	155	185	15.4855
gggggggg!!ddddmmmmdddd22gggggg	chr5:35178235-35178503(+)$1	268	87	117	10.8187
eeee"""a[ddddoooooodddd]a333ee	chr3:57269027-57269267(-)$1	240	144	174	13.5635
eeeee$$$$$cccooooooccc333eeeee	chr13:113280282-113280518(+)$1	236	79	109	14.6760
cc[==========nnnnn==========]c	chr17:13985293-13985550(+)$1	257	49	79	11.8072

#otherMatches

#Seq PSSM
GGAUGUGUAUACUGUGAUAGAAGGCACAUU	chr13:5862414-5862667(+)$1	253	140	170	12.1853
GGUGUUUUCUAAGGAAGAACUAAGGAAACU	chr10:117187834-117188071(-)$1	237	47	77	13.7276
GUGUUAGGAACAGCCGCACUGUGCUUCUAA	chr5:144178998-144179245(+)$1	247	49	79	11.1274
uccucgguauuuccauugcauuugaaagcu	chr3:109398330-109398565(+)$1	235	127	157	11.2579
UUCCAGGUCCUGUGGAGGAACAGAACCGAU	chr5:101195404-101195645(-)$1	241	49	79	12.3403
UGCAGUGGAUGCUCGGAAUGGCACACGCAG	chr4:155031015-155031252(-)$1	237	116	146	13.6818
GGGGACAAUUAGCUUUGCUGCUUCCUAACC	chr11:70799268-70799546(-)$1	278	138	168	13.7612
CUGGCUGGUCUGAACACACUUGGACCCCAG	chr2:90844960-90845220(+)$1	260	20	50	12.5738
UUGAGAAUGAACAUACAGAGUGUUUUAUUU	chr5:52550096-52550337(-)$1	241	146	176	11.1876
GGACUCAAUGCUUCUAGAAAAGACAAUGUC	chr19:38046573-38046827(-)$1	254	192	222	12.2333
CACAGAGCUUCAGGGAUUGCAGGAGCUUCA	chr14:47572988-47573223(+)$1	235	9	39	12.6274
GCCACCAAGAUGAGAAAUAUUGAAGUGGUG	chr12:25684069-25684309(+)$1	240	80	110	15.1015
CUGAGAUACGAUGACUGUGCAUUUGUCUUC	chr4:57722048-57722289(+)$1	241	42	72	12.5119
uagcugucuucugacgcaccagaagagggu	chr12:52495841-52496085(+)$1	244	187	217	12.7218
AGCCUUUAGUUUAGACGCGUGGACGCAGGU	chr15:96213872-96214122(+)$1	250	78	108	11.3846
AAUAGAUUCAGCUCCCUUGGCCAAGAUCUG	chr8:111253241-111253489(+)$1	248	139	169	11.3531
AUAAAACAAGGCCUACUGUGCGUCUUGUCA	chr19:55852007-55852254(+)$1	247	51	81	13.5540
UGUUUAGUUCUGAUCAUGUGAUGUUCUAAA	chr10:109198210-109198447(-)$1	237	34	64	10.7834
CACACUUGGCAAGCUUCUCCUCUGUCUGGG	chr8:13119681-13119997(+)$1	316	203	233	12.3093
CUUUGGGGCUGGCGUGUGGGCCUGUGUCCU	chr10:79742090-79742336(+)$1	246	140	170	12.3798
CCACUUUGAUUUGAGAAGCCAGAUGAGGUU	chr1:94004890-94005127(-)$1	237	94	124	11.6919
acaugcacacgcgcacacacgcacacgcac	chr9:49325241-49325535(-)$1	294	58	88	12.0738
gcuagaggaagucgggacaggaacucaagc	chr4:125846408-125846691(-)$1	283	123	153	14.0531
UGACACCCAAAGGUUUUCUUAGGAGGGUGU	chr15:82984262-82984510(-)$1	248	206	236	10.7485
UCCAUUUCAUCUAAGUAACUAGAUUGAGGG	chr7:6659898-6660159(-)$1	261	212	242	11.7841
uggcccacaccuaaaauccuagcagugggg	chr11:21941404-21941641(-)$1	237	80	110	11.0422
AGGGGUGAAGAGUAAGUGCAGUUAUCACUA	chr12:52743922-52744167(-)$1	245	66	96	11.3860
GCUUCUUUCUGUGUAUcucacuuaaaaagc	chr19:56510075-56510311(+)$1	236	177	207	11.8749
GCAGGACGUUGGGCCCAGCCCCAGCACCUA	chr10:127001593-127001855(-)$1	262	221	251	12.0647
UGCUCCCAAAUCAUUCUACUGAUGUGCUUG	chr5:90658083-90658318(-)$1	235	84	114	12.7570
CUUGGGUUUUGAUGUUUAAAUCCUCCCCAG	chr10:59822869-59823120(+)$1	251	31	61	14.8762
CUGGAGAAAAUGGAAGAGGCUAGAGGCUUG	chr11:108027333-108027583(-)$1	250	124	154	15.4323
UGAUGUUUCUUUUUAAUGUGAAUGAAAACA	chr5:151911420-151911657(-)$1	237	201	231	12.1011
UUUCCCUUCCUGGUAUUUCCUAAUAAGGGU	chr15:78924050-78924285(+)$1	235	15	45	14.9299
AAGUAACGUUUGCACUGCAAAUGUUAAUUG	chr15:53140124-53140376(-)$1	252	221	251	11.5368
CCGGGCCAUGUGGGAGGCACCGCUUGCCCA	chr4:132688126-132688370(+)$1	244	120	150	13.2135
CUGCAGUUUUUAUUUAGCAUGGGGAUUGCA	chr2:157382318-157382598(-)$1	280	18	48	11.9757
guucuggucuucuauaggcagcuguccacu	chr17:69563744-69563979(+)$1	235	179	209	13.0108
CUGAGAGCAUAGCUUCCCAGCGUUUCUUGG	chr17:24689391-24689639(+)$1	248	75	105	11.5417
UAGCGUCUUGGGCUCAUUUGCUGAGAUGCU	chr6:52709601-52709849(+)$1	248	153	183	15.8867
UUCAGAUAAGGUGAAAUCCCGCCCCCUUGC	chr1:140505902-140506175(-)$1	273	86	116	14.5801
CUCUGUCCUUGAAGCAAACGCAAGGACUCA	chr17:56560597-56560878(-)$1	281	89	119	9.3760
ggcauugcauuucccuaaugaccagugaug	chr15:80844511-80844753(-)$1	242	172	202	15.5104
ACUCUGUAAUUUUGUAGCUAUUACAGAGGG	chr3:57261778-57262015(-)$1	237	10	40	9.4766
CUGAGGCUGGUCUGUGGAGAAAUCCCUCGG	chr15:53049662-53049899(-)$1	237	191	221	11.7730
auuuauuuauuuauuuauuuauuuauuuaA	chr10:82350717-82351005(+)$1	288	13	43	12.3321
UGGCGUUCUGCUGUUCUCUCAGCUGCCCAC	chr8:11349779-11350042(+)$1	263	156	186	13.3389
UGAUUCUCUCCACUUACCUGUGCUGGGGAU	chr11:74887102-74887345(+)$1	243	155	185	15.4855
AGGGCACAUGUGGUGCUUGCUGUUUGUGCU	chr5:35178235-35178503(+)$1	268	87	117	10.8187
ugggaaugcgcugagcuaccagccccugcc	chr3:57269027-57269267(-)$1	240	144	174	13.5635
CAGGCUCUCAACUUCAGAUAGUGUUGCCUG	chr13:113280282-113280518(+)$1	236	79	109	14.6760
CUCGUCUGUUUUUCUCCAGGAAGUAGACCA	chr17:13985293-13985550(+)$1	257	49	79	11.8072

#DB
.(((((((...(((...)))...)))))))	chr13:5862414-5862667(+)$1	1	140	170	12.1853
(..(((((((.((......)).))))))).	chr10:117187834-117188071(-)$1	1	47	77	13.7276
(.(((((((((((.....))))..))))))	chr5:144178998-144179245(+)$1	1	49	79	11.1274
((((((((.((((.(......).)))))))	chr3:109398330-109398565(+)$1	1	127	157	11.2579
((((((((.((((......)))).)))..)	chr5:101195404-101195645(-)$1	1	49	79	12.3403
(((.(((..((((......))))..))).)	chr4:155031015-155031252(-)$1	1	116	146	13.6818
(((((.....(((......))))))...))	chr11:70799268-70799546(-)$1	1	138	168	13.7612
((((..(((((((......)))))))))))	chr2:90844960-90845220(+)$1	1	20	50	12.5738
((((((((((((((.....))).)))))))	chr5:52550096-52550337(-)$1	1	146	176	11.1876
(....((.(((((......))).)).))..	chr19:38046573-38046827(-)$1	1	192	222	12.2333
(((((((((((.(......).)))))))..	chr14:47572988-47573223(+)$1	1	9	39	12.6274
.((((((...(((......)))...)))))	chr12:25684069-25684309(+)$1	1	80	110	15.1015
((((((((.((((......)))))))))..	chr4:57722048-57722289(+)$1	1	42	72	12.5119
.((((.(((((((......))))))).)))	chr12:52495841-52496085(+)$1	1	187	217	12.7218
.((((...(((((......)))))..))))	chr15:96213872-96214122(+)$1	1	78	108	11.3846
..((((((..(((.....)))...))))))	chr8:111253241-111253489(+)$1	1	139	169	11.3531
(....((((((((......).)))))))..	chr19:55852007-55852254(+)$1	1	51	81	13.5540
(((((((.....(((....)))...)))))	chr10:109198210-109198447(-)$1	1	34	64	10.7834
(((((((((((((......)).)))).)))	chr8:13119681-13119997(+)$1	1	203	233	12.3093
....((.((.(((......))).)).))))	chr10:79742090-79742336(+)$1	1	140	170	12.3798
(.(((((.(((((......)))))))))).	chr1:94004890-94005127(-)$1	1	94	124	11.6919
...(((....(((......)))....))).	chr9:49325241-49325535(-)$1	1	58	88	12.0738
(((.(((....((......))..))).)))	chr4:125846408-125846691(-)$1	1	123	153	14.0531
.(((((((..(((....)))....))))))	chr15:82984262-82984510(-)$1	1	206	236	10.7485
(((.(((.(((((......))))).)))))	chr7:6659898-6660159(-)$1	1	212	242	11.7841
...(((((..(((......)))..))))).	chr11:21941404-21941641(-)$1	1	80	110	11.0422
.(((((((.((.(......).)).))))).	chr12:52743922-52744167(-)$1	1	66	96	11.3860
((((.(((..(((.....)))..)))))))	chr19:56510075-56510311(+)$1	1	177	207	11.8749
..(((..((((((......)))))).))).	chr10:127001593-127001855(-)$1	1	221	251	12.0647
..(...((.((((......)))).))...)	chr5:90658083-90658318(-)$1	1	84	114	12.7570
.(((((....(((......)))...)))))	chr10:59822869-59823120(+)$1	1	31	61	14.8762
((.(((....(((......)))....))).	chr11:108027333-108027583(-)$1	1	124	154	15.4323
)))((((((.(((......))).).)))))	chr5:151911420-151911657(-)$1	1	201	231	12.1011
...(((((..(((......)))..))))).	chr15:78924050-78924285(+)$1	1	15	45	14.9299
((.((((((((((...)))))))))).)))	chr15:53140124-53140376(-)$1	1	221	251	11.5368
(.((((...((((......))))..)))).	chr4:132688126-132688370(+)$1	1	120	150	13.2135
(((((((((((((.....))))))))))))	chr2:157382318-157382598(-)$1	1	18	48	11.9757
(((((((.(..((......))..).)))..	chr17:69563744-69563979(+)$1	1	179	209	13.0108
(((((((....(((....)))..)))))))	chr17:24689391-24689639(+)$1	1	75	105	11.5417
)(((((((..(((......))).)))))))	chr6:52709601-52709849(+)$1	1	153	183	15.8867
(.(((....((((......))))...))).	chr1:140505902-140506175(-)$1	1	86	116	14.5801
((..(((((((.........)))))))..)	chr17:56560597-56560878(-)$1	1	89	119	9.3760
((((((((...((......))...))))))	chr15:80844511-80844753(-)$1	1	172	202	15.5104
((((((((((.........)))))))))((	chr3:57261778-57262015(-)$1	1	10	40	9.4766
((((((....(((....)))....))))))	chr15:53049662-53049899(-)$1	1	191	221	11.7730
(((((..((..((......))..))..)))	chr10:82350717-82351005(+)$1	1	13	43	12.3321
(((.((...((((......)))).)).).)	chr8:11349779-11350042(+)$1	1	156	186	13.3389
.(((((((..(((......)))..))))))	chr11:74887102-74887345(+)$1	1	155	185	15.4855
((((((((..((((....))))..))))))	chr5:35178235-35178503(+)$1	1	87	117	10.8187
((((...(.((((......)))).)...))	chr3:57269027-57269267(-)$1	1	144	174	13.5635
(((((.....(((......)))...)))))	chr13:113280282-113280518(+)$1	1	79	109	14.6760
((.((((((((((.....)))))))))).)	chr17:13985293-13985550(+)$1	1	49	79	11.8072

#PSSM
d : 0.15	c : 0.11	e : 0.09	g : 0.09	: : 0.09	! : 0.07	[ : 0.05	a : 0.03	h : 0.03	b : 0.03	= : 0.03	# : 0.03	i : 0.03	f : 0.01	H : 0.01	" : 0.01	G : 0.01	
g : 0.19	e : 0.11	d : 0.09	c : 0.09	[ : 0.07	# : 0.07	! : 0.05	i : 0.05	f : 0.03	h : 0.03	= : 0.03	: : 0.03	b : 0.03	H : 0.01	" : 0.01	
g : 0.21	e : 0.13	c : 0.09	d : 0.09	f : 0.05	i : 0.05	# : 0.05	[ : 0.05	! : 0.03	= : 0.03	: : 0.03	a : 0.03	b : 0.01	H : 0.01	" : 0.01	h : 0.01	
g : 0.23	e : 0.19	c : 0.11	[ : 0.07	d : 0.07	= : 0.07	f : 0.05	i : 0.05	# : 0.05	" : 0.01	h : 0.01	! : 0.01	
g : 0.24	c : 0.19	e : 0.15	= : 0.07	f : 0.05	i : 0.05	d : 0.05	# : 0.03	b : 0.03	" : 0.03	! : 0.01	[ : 0.01	
g : 0.26	c : 0.15	e : 0.13	= : 0.07	! : 0.05	i : 0.05	b : 0.05	" : 0.05	$ : 0.03	f : 0.03	[ : 0.01	d : 0.01	# : 0.01	
g : 0.28	c : 0.11	e : 0.11	# : 0.09	" : 0.07	= : 0.07	i : 0.05	$ : 0.03	b : 0.03	f : 0.03	! : 0.03	[ : 0.01	
g : 0.24	# : 0.13	e : 0.09	[ : 0.07	" : 0.07	$ : 0.05	i : 0.05	b : 0.05	= : 0.05	c : 0.03	f : 0.03	! : 0.01	d : 0.01	a : 0.01	
! : 0.17	g : 0.13	# : 0.13	[ : 0.11	" : 0.09	$ : 0.05	b : 0.05	e : 0.05	= : 0.05	i : 0.03	a : 0.03	d : 0.01	f : 0.01	
d : 0.21	! : 0.19	g : 0.11	# : 0.11	" : 0.05	$ : 0.05	e : 0.05	= : 0.05	i : 0.03	b : 0.03	[ : 0.03	f : 0.01	
c : 0.32	d : 0.23	g : 0.09	e : 0.05	= : 0.05	" : 0.03	# : 0.03	! : 0.03	[ : 0.01	i : 0.01	$ : 0.01	b : 0.01	f : 0.01	r : 0.01	
c : 0.38	d : 0.21	b : 0.11	g : 0.05	e : 0.05	= : 0.05	[ : 0.03	r : 0.03	$ : 0.01	f : 0.01	
c : 0.40	d : 0.21	b : 0.11	a : 0.05	e : 0.05	= : 0.05	g : 0.03	r : 0.03	f : 0.01	
o : 0.69	n : 0.09	c : 0.07	m : 0.03	r : 0.03	[ : 0.01	l : 0.01	d : 0.01	
o : 0.69	n : 0.11	m : 0.07	l : 0.03	r : 0.03	a : 0.01	c : 0.01	
o : 0.71	n : 0.11	m : 0.09	l : 0.03	r : 0.03	
o : 0.71	n : 0.11	m : 0.09	r : 0.03	l : 0.01	= : 0.01	
o : 0.71	n : 0.11	c : 0.05	m : 0.05	r : 0.03	= : 0.01	
o : 0.71	c : 0.11	= : 0.05	d : 0.03	r : 0.03	n : 0.01	m : 0.01	
c : 0.40	d : 0.19	b : 0.11	a : 0.05	e : 0.05	= : 0.05	g : 0.03	o : 0.01	f : 0.01	r : 0.01	i : 0.01	
c : 0.34	d : 0.19	b : 0.11	g : 0.05	] : 0.05	e : 0.05	= : 0.05	4 : 0.03	3 : 0.01	o : 0.01	f : 0.01	i : 0.01	
c : 0.28	d : 0.19	g : 0.09	2 : 0.09	3 : 0.05	e : 0.05	= : 0.05	] : 0.03	4 : 0.03	a : 0.01	b : 0.01	f : 0.01	i : 0.01	
2 : 0.19	d : 0.17	3 : 0.13	g : 0.11	] : 0.11	4 : 0.07	e : 0.05	= : 0.05	c : 0.01	b : 0.01	f : 0.01	i : 0.01	
g : 0.17	2 : 0.13	3 : 0.13	] : 0.09	e : 0.07	4 : 0.07	c : 0.05	b : 0.05	= : 0.05	d : 0.03	i : 0.03	a : 0.03	f : 0.01	
g : 0.26	b : 0.09	3 : 0.09	e : 0.09	c : 0.07	2 : 0.05	i : 0.05	] : 0.05	= : 0.05	d : 0.03	f : 0.03	4 : 0.03	a : 0.01	
g : 0.28	e : 0.15	c : 0.11	d : 0.05	3 : 0.05	i : 0.05	] : 0.05	= : 0.05	f : 0.03	2 : 0.03	4 : 0.03	b : 0.03	
g : 0.26	c : 0.15	e : 0.15	] : 0.09	d : 0.07	3 : 0.05	i : 0.05	b : 0.03	f : 0.03	= : 0.03	2 : 0.01	
g : 0.26	c : 0.19	e : 0.15	d : 0.07	3 : 0.05	i : 0.05	= : 0.05	2 : 0.03	b : 0.03	f : 0.03	a : 0.01	
g : 0.23	e : 0.15	c : 0.15	d : 0.13	2 : 0.05	] : 0.05	i : 0.03	4 : 0.03	f : 0.03	3 : 0.03	= : 0.03	6 : 0.01	
g : 0.21	d : 0.11	c : 0.11	e : 0.09	2 : 0.07	] : 0.07	f : 0.05	i : 0.05	4 : 0.05	= : 0.03	: : 0.03	6 : 0.01	3 : 0.01	a : 0.01	

#score	655.5243777209021
#seq	52
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_CDS_m3_run2.txt

#BEAR
eeeee####ddddmmmmdddd666666eee	chr19:12014201-12014402(+)$1	201	69	99	11.6350
eeeee[ddddcccooooooccc]ddddeee	chr15:85206916-85207117(+)$1	201	106	136	8.4457
ccccc####ddddmmmmdddd4444ccc]c	chr3:55804395-55804596(-)$1	201	62	92	15.2621
[bbeeeee[ddddmmmmdddd22eeeee]b	chr2:138109392-138109593(+)$1	201	12	42	10.3328
dd[ccc[a[ddddnnnnndddd22a]ccc]	chr4:140529513-140529714(+)$1	201	148	178	12.2885
cc"""ccceeeeennnnneeeee22ccc22	chr2:25324426-25324627(-)$1	201	161	191	9.5919
dddd[ccc"""cccmmmmccc333ccc22d	chr14:60898834-60899035(+)$1	201	124	154	10.7382
!!ccc[a"""ddddllldddda]ccc]ccc	chr1:174209728-174209929(-)$1	201	17	47	13.3678
ccc[ccc"""ddddlllddddcccccc22b	chr14:58728297-58728498(+)$1	201	111	141	12.4106
cc[bb"""eeeeemmmmeeeee]bbccc33	chr17:17715849-17716050(-)$1	201	158	188	10.2711
c"""dddd!!cccnnnnnccc4444dddd2	chr9:120483174-120483375(+)$1	201	165	195	10.6057
eee####a[bbcccmmmmccc]bb]a333e	chr9:58491415-58491616(+)$1	201	136	166	9.2899
!!dddd####cccnnnnnccc4444dddd]	chr3:36943623-36943824(+)$1	201	145	175	12.0740
##eeeee!!ddddmmmmdddd]eeeee333	chr13:9150200-9150401(+)$1	201	14	44	11.5765
hhhhh####ddddlllddddhhhhhhhh]c	chr17:57220840-57221041(-)$1	201	107	137	9.7786
####eeeeeddddoooooodddd22eeeee	chr9:58471459-58471660(+)$1	201	147	177	10.3471
c[ccc####ddddnnnnndddd333ccc]c	chr18:20824956-20825157(+)$1	201	126	156	15.2431
"dddd####eeeeellleeeee666666dd	chr12:105940975-105941176(-)$1	201	56	86	9.8507
[bb"""ggggggglllggggggg333bb]d	chr18:20823886-20824087(+)$1	201	166	196	8.9509
cc!!a"""eeeeemmmmeeeee333a22cc	chr6:141481094-141481295(+)$1	201	31	61	11.8897
dddd$$$$$eeeeellleeeee22dddd]c	chr6:124997803-124998004(+)$1	201	108	138	10.6989
%%dddd"""ccclllcccdddd]ggggggg	chr17:21088240-21088441(+)$1	201	159	189	9.1240
[dddd[dddd[ddddllldddd22dddddd	chr3:8545575-8545776(+)$1	201	14	44	10.0939
f!!dddd!!ddddnnnnndddd22dddd22	chr6:113712738-113712939(-)$1	201	141	171	12.2302
[bb"""ggggggglllggggggg333bb]d	chr18:20823889-20824090(+)$1	201	163	193	8.9509
ddccc####ddddmmmmdddd4444ccc]d	chr9:3759759-3759960(+)$1	201	5	35	15.0185
####eeeeeddddoooooodddd22eeeee	chr9:58471460-58471661(+)$1	201	146	176	10.3471
fffbb####eeeeellleeeeebb]fffff	chr1:16993931-16994132(-)$1	201	151	181	9.4905
::ccc!!ddddcccmmmmccc333dddd22	chr2:104098479-104098680(-)$1	201	13	43	9.0738
ccc[ccc"""ddddlllddddcccccc22b	chr14:58728298-58728499(+)$1	201	110	140	12.4106
ff[ccc"""ddddllldddd]ccc]fffff	chr10:107686417-107686618(+)$1	201	150	180	11.6240
!!bb[bb[a[ddddmmmmdddd]a]bb]bb	chr3:55791875-55792076(-)$1	201	137	167	9.7342
!ffffff####ddddllldddd333fffff	chrX:34142070-34142271(+)$1	201	71	101	11.3188
e"""ccc!!ddddnnnnndddd4444ccc2	chr1:157179242-157179443(-)$1	201	49	79	13.3988
dddd[ccc"""cccmmmmccc333ccc22d	chr14:60898835-60899036(+)$1	201	123	153	10.7382
========ddddoooooodddd]=======	chr17:24196151-24196352(-)$1	201	53	83	11.2455
eeee[ccc[ddddmmmmddddccc]eeeee	chr3:25334949-25335150(-)$1	201	91	121	10.9303
ccccc####ddddmmmmdddd4444ccc]c	chr3:55804393-55804594(-)$1	201	60	90	15.2621
eeeee####ddddmmmmdddd666666eee	chr19:12014202-12014403(+)$1	201	68	98	11.6350
%%dddd"""ccclllcccdddd]ggggggg	chr17:21088241-21088442(+)$1	201	158	188	9.1240
[dddd[dddd[ddddllldddd22dddddd	chr3:8545573-8545774(+)$1	201	16	46	10.0939
fffff####ddddmmmmdddd4444fffff	chr12:76823578-76823779(-)$1	201	127	157	13.5091

#otherMatches

#Seq PSSM
AGAGUGCAAGUGCACCAGCGCCCUCCAACU	chr19:12014201-12014402(+)$1	201	69	99	11.6350
AUUCUGUUCACAUCUCUUAAUGCUGAAAGG	chr15:85206916-85207117(+)$1	201	106	136	8.4457
GUCAACAGCAAUGAAAACAUUAUAUUUGUA	chr3:55804395-55804596(-)$1	201	62	92	15.2621
GCCCAGGCCGAGUUAGCGCUCAAGUCUGAG	chr2:138109392-138109593(+)$1	201	12	42	10.3328
GUAUCUGCAGUCCAUCGAGGACCGGGAGAA	chr4:140529513-140529714(+)$1	201	148	178	12.2885
GGCUUGGUCCCUUACUUCAAGGGCAAUCUA	chr2:25324426-25324627(-)$1	201	161	191	9.5919
CUGACCACUUCUGGAUGCCCACUUGUGAUU	chr14:60898834-60899035(+)$1	201	124	154	10.7382
AGGCUGACAUUGGCAUUGCCAUGGGCAUCU	chr1:174209728-174209929(-)$1	201	17	47	13.3678
AAGCUGACAAAGACAGUGUCUUCACUUGAG	chr14:58728297-58728498(+)$1	201	111	141	12.4106
CUACAAACGGGAAAGUGUUCCCAUGGGCUC	chr17:17715849-17716050(-)$1	201	158	188	10.2711
UAAAGUCCCAGCCAAGAAGGCCACAGGACC	chr9:120483174-120483375(+)$1	201	165	195	10.6057
CUUGUGGUGAUCAUUGUUGUGUAUGAGAAG	chr9:58491415-58491616(+)$1	201	136	166	9.2899
UUCCAGCUUUUAUUCUUUGUGUCUUCUGGC	chr3:36943623-36943824(+)$1	201	145	175	12.0740
AAAUGUUCUCAUGGGAACAUGUAACAUCUU	chr13:9150200-9150401(+)$1	201	14	44	11.5765
UCACCCAAGGUGUCUGACACGGUGGUGGAG	chr17:57220840-57221041(-)$1	201	107	137	9.7786
AGGAAUGGGGUAGAACUCACUGCCACCCGU	chr9:58471459-58471660(+)$1	201	147	177	10.3471
UCUGGGUAAGCUUGUAGAAAGCCCACCAUG	chr18:20824956-20825157(+)$1	201	126	156	15.2431
AUAAAAACCUUGCCAAUGGCAGUUAUGAUU	chr12:105940975-105941176(-)$1	201	56	86	9.8507
GAUAAAGAAGAAGUGCCUUCUUCCAGAUGU	chr18:20823886-20824087(+)$1	201	166	196	8.9509
GCUAGUCUGGUUAUGUGUAACUUUUCGUGC	chr6:141481094-141481295(+)$1	201	31	61	11.8897
GUCACCAGGUCUCCUAUGGAGAGAUGAUUG	chr6:124997803-124998004(+)$1	201	108	138	10.6989
AAGCAUUCCUGGGACCCAAUGCAGUGAGGA	chr17:21088240-21088441(+)$1	201	159	189	9.1240
AUCAACAAGCGGGCCUCUGGCCAGGCUUUU	chr3:8545575-8545776(+)$1	201	14	44	10.0939
GGCGGUGAUCGUGGCCUUCACGGGCGCCUG	chr6:113712738-113712939(-)$1	201	141	171	12.2302
GAUAAAGAAGAAGUGCCUUCUUCCAGAUGU	chr18:20823889-20824090(+)$1	201	163	193	8.9509
GACAUUGUGGGCUUUACAGCCAUAUGUGCU	chr9:3759759-3759960(+)$1	201	5	35	15.0185
AGGAAUGGGGUAGAACUCACUGCCACCCGU	chr9:58471460-58471661(+)$1	201	146	176	10.3471
AGCCAACUCUGUAAGUCUUGCAUGAGCUUU	chr1:16993931-16994132(-)$1	201	151	181	9.4905
AGGGACAGACAAUCUACAGAUACAUGUCAC	chr2:104098479-104098680(-)$1	201	13	43	9.0738
AAGCUGACAAAGACAGUGUCUUCACUUGAG	chr14:58728298-58728499(+)$1	201	110	140	12.4106
GCUUCGAAAGACUGGCAGUUACGGUGCCCU	chr10:107686417-107686618(+)$1	201	150	180	11.6240
UUCAGGAUGUUGAUAUCAAUCGCCUUCGUG	chr3:55791875-55792076(-)$1	201	137	167	9.7342
AGAGAUGCAUCCAGGGGCCUUGCCACAUUU	chrX:34142070-34142271(+)$1	201	71	101	11.3188
CACCUGUCCCACGAGGAGCGUGUCCAACAU	chr1:157179242-157179443(-)$1	201	49	79	13.3988
CUGACCACUUCUGGAUGCCCACUUGUGAUU	chr14:60898835-60899036(+)$1	201	123	153	10.7382
UUUUUAACCUCUAUUUCAGGAGUGUUGGAA	chr17:24196151-24196352(-)$1	201	53	83	11.2455
AUUGUUGGCUUUGUUUACGGACCAUCAAUG	chr3:25334949-25335150(-)$1	201	91	121	10.9303
GUCAACAGCAAUGAAAACAUUAUAUUUGUA	chr3:55804393-55804594(-)$1	201	60	90	15.2621
AGAGUGCAAGUGCACCAGCGCCCUCCAACU	chr19:12014202-12014403(+)$1	201	68	98	11.6350
AAGCAUUCCUGGGACCCAAUGCAGUGAGGA	chr17:21088241-21088442(+)$1	201	158	188	9.1240
AUCAACAAGCGGGCCUCUGGCCAGGCUUUU	chr3:8545573-8545774(+)$1	201	16	46	10.0939
UGCAUUCUAUCCUGGUAAGGAGACugugug	chr12:76823578-76823779(-)$1	201	127	157	13.5091

#DB
(((((....((((....))))......)))	chr19:12014201-12014402(+)$1	1	69	99	11.6350
(((((.(((((((......))).)))))))	chr15:85206916-85207117(+)$1	1	106	136	8.4457
(((((....((((....))))....))).)	chr3:55804395-55804596(-)$1	1	62	92	15.2621
.(((((((.((((....))))..))))).)	chr2:138109392-138109593(+)$1	1	12	42	10.3328
((.(((.(.((((.....))))..).))).	chr4:140529513-140529714(+)$1	1	148	178	12.2885
((...((((((((.....)))))..)))..	chr2:25324426-25324627(-)$1	1	161	191	9.5919
((((.(((...(((....)))...)))..)	chr14:60898834-60899035(+)$1	1	124	154	10.7382
..(((.(...((((...))))).))).)))	chr1:174209728-174209929(-)$1	1	17	47	13.3678
(((.(((...((((...))))))))))..)	chr14:58728297-58728498(+)$1	1	111	141	12.4106
((.((...(((((....))))).)))))..	chr17:17715849-17716050(-)$1	1	158	188	10.2711
(...((((..(((.....)))....)))).	chr9:120483174-120483375(+)$1	1	165	195	10.6057
(((....(.(((((....))).)).)...)	chr9:58491415-58491616(+)$1	1	136	166	9.2899
..((((....(((.....)))....)))).	chr3:36943623-36943824(+)$1	1	145	175	12.0740
..(((((..((((....)))).)))))...	chr13:9150200-9150401(+)$1	1	14	44	11.5765
(((((....((((...)))))))))))).)	chr17:57220840-57221041(-)$1	1	107	137	9.7786
....(((((((((......))))..)))))	chr9:58471459-58471660(+)$1	1	147	177	10.3471
(.(((....((((.....))))...))).)	chr18:20824956-20825157(+)$1	1	126	156	15.2431
.((((....(((((...)))))......))	chr12:105940975-105941176(-)$1	1	56	86	9.8507
.((...(((((((...)))))))...)).)	chr18:20823886-20824087(+)$1	1	166	196	8.9509
((..(...(((((....)))))...)..))	chr6:141481094-141481295(+)$1	1	31	61	11.8897
((((.....(((((...)))))..)))).)	chr6:124997803-124998004(+)$1	1	108	138	10.6989
..((((...(((...))))))).)))))))	chr17:21088240-21088441(+)$1	1	159	189	9.1240
.((((.((((.((((...))))..))))))	chr3:8545575-8545776(+)$1	1	14	44	10.0939
(..((((..((((.....))))..))))..	chr6:113712738-113712939(-)$1	1	141	171	12.2302
.((...(((((((...)))))))...)).)	chr18:20823889-20824090(+)$1	1	163	193	8.9509
(((((....((((....))))....))).)	chr9:3759759-3759960(+)$1	1	5	35	15.0185
....(((((((((......))))..)))))	chr9:58471460-58471661(+)$1	1	146	176	10.3471
(((((....(((((...))))))).)))))	chr1:16993931-16994132(-)$1	1	151	181	9.4905
..(((..(((((((....)))...))))..	chr2:104098479-104098680(-)$1	1	13	43	9.0738
(((.(((...((((...))))))))))..)	chr14:58728298-58728499(+)$1	1	110	140	12.4106
((.(((...((((...)))).))).)))))	chr10:107686417-107686618(+)$1	1	150	180	11.6240
..((.((.(.((((....)))).).)).))	chr3:55791875-55792076(-)$1	1	137	167	9.7342
.((((((....((((...))))...)))))	chrX:34142070-34142271(+)$1	1	71	101	11.3188
(...(((..((((.....))))....))).	chr1:157179242-157179443(-)$1	1	49	79	13.3988
((((.(((...(((....)))...)))..)	chr14:60898835-60899036(+)$1	1	123	153	10.7382
((((((((((((......)))).)))))))	chr17:24196151-24196352(-)$1	1	53	83	11.2455
((((.(((.((((....))))))).)))))	chr3:25334949-25335150(-)$1	1	91	121	10.9303
(((((....((((....))))....))).)	chr3:55804393-55804594(-)$1	1	60	90	15.2621
(((((....((((....))))......)))	chr19:12014202-12014403(+)$1	1	68	98	11.6350
..((((...(((...))))))).)))))))	chr17:21088241-21088442(+)$1	1	158	188	9.1240
.((((.((((.((((...))))..))))))	chr3:8545573-8545774(+)$1	1	16	46	10.0939
(((((....((((....))))....)))))	chr12:76823578-76823779(-)$1	1	127	157	13.5091

#PSSM
c : 0.21	e : 0.14	[ : 0.11	d : 0.11	! : 0.09	f : 0.09	# : 0.07	% : 0.04	h : 0.02	" : 0.02	: : 0.02	= : 0.02	
d : 0.19	c : 0.16	e : 0.11	! : 0.09	f : 0.09	b : 0.07	# : 0.07	" : 0.04	% : 0.04	h : 0.02	[ : 0.02	: : 0.02	= : 0.02	
d : 0.21	c : 0.19	e : 0.14	b : 0.09	[ : 0.07	" : 0.07	f : 0.07	# : 0.04	! : 0.04	h : 0.02	= : 0.02	
d : 0.23	c : 0.19	e : 0.14	" : 0.11	b : 0.07	# : 0.07	[ : 0.04	f : 0.04	h : 0.02	! : 0.02	= : 0.02	
c : 0.26	d : 0.19	e : 0.16	[ : 0.09	" : 0.07	b : 0.04	f : 0.04	# : 0.02	h : 0.02	a : 0.02	$ : 0.02	= : 0.02	
# : 0.26	c : 0.21	d : 0.11	[ : 0.09	e : 0.09	" : 0.09	$ : 0.02	! : 0.02	b : 0.02	f : 0.02	= : 0.02	
# : 0.28	c : 0.16	d : 0.11	" : 0.11	e : 0.09	g : 0.04	[ : 0.02	a : 0.02	$ : 0.02	! : 0.02	b : 0.02	f : 0.02	= : 0.02	
# : 0.28	" : 0.19	d : 0.11	c : 0.09	e : 0.07	! : 0.07	a : 0.04	g : 0.04	$ : 0.02	[ : 0.02	= : 0.02	
# : 0.28	" : 0.19	d : 0.11	e : 0.11	[ : 0.09	! : 0.09	g : 0.04	$ : 0.02	a : 0.02	
d : 0.52	e : 0.14	" : 0.11	# : 0.04	g : 0.04	c : 0.04	! : 0.02	b : 0.02	[ : 0.02	
d : 0.54	e : 0.14	c : 0.11	" : 0.04	g : 0.04	[ : 0.04	b : 0.02	# : 0.02	
d : 0.59	c : 0.21	e : 0.14	g : 0.04	
d : 0.57	c : 0.16	e : 0.14	g : 0.04	l : 0.04	o : 0.02	
m : 0.26	n : 0.16	d : 0.16	l : 0.14	o : 0.09	c : 0.09	e : 0.07	
m : 0.38	l : 0.28	n : 0.16	o : 0.09	d : 0.07	
m : 0.38	l : 0.30	n : 0.16	o : 0.09	c : 0.04	
m : 0.38	l : 0.21	n : 0.16	o : 0.09	d : 0.04	g : 0.04	c : 0.04	
d : 0.33	n : 0.16	m : 0.11	e : 0.11	o : 0.09	l : 0.07	g : 0.04	c : 0.04	
d : 0.59	e : 0.14	c : 0.14	o : 0.07	g : 0.04	
d : 0.64	c : 0.16	e : 0.14	g : 0.04	
d : 0.59	c : 0.16	e : 0.14	g : 0.04	h : 0.02	] : 0.02	
d : 0.30	4 : 0.14	e : 0.14	c : 0.11	3 : 0.07	6 : 0.04	] : 0.04	g : 0.04	2 : 0.02	a : 0.02	h : 0.02	
] : 0.16	4 : 0.16	2 : 0.14	3 : 0.14	c : 0.09	6 : 0.07	e : 0.04	b : 0.04	d : 0.04	g : 0.04	h : 0.02	
2 : 0.19	3 : 0.19	4 : 0.16	c : 0.11	6 : 0.07	b : 0.07	e : 0.04	g : 0.04	d : 0.02	h : 0.02	a : 0.02	= : 0.02	
4 : 0.16	d : 0.14	c : 0.11	] : 0.11	3 : 0.11	6 : 0.07	2 : 0.07	e : 0.04	g : 0.04	a : 0.02	b : 0.02	h : 0.02	= : 0.02	
c : 0.26	d : 0.19	e : 0.11	f : 0.09	6 : 0.07	a : 0.04	3 : 0.04	g : 0.04	] : 0.02	h : 0.02	b : 0.02	4 : 0.02	= : 0.02	
c : 0.28	d : 0.19	e : 0.11	f : 0.09	6 : 0.07	b : 0.07	g : 0.04	] : 0.02	3 : 0.02	h : 0.02	2 : 0.02	= : 0.02	
c : 0.21	e : 0.16	d : 0.16	2 : 0.11	f : 0.09	3 : 0.04	b : 0.04	g : 0.04	h : 0.02	6 : 0.02	] : 0.02	= : 0.02	
] : 0.21	2 : 0.16	e : 0.14	d : 0.11	c : 0.09	f : 0.09	3 : 0.07	g : 0.04	b : 0.02	= : 0.02	
d : 0.19	e : 0.16	c : 0.16	2 : 0.11	b : 0.09	f : 0.09	] : 0.04	3 : 0.04	g : 0.04	= : 0.02	

#score	470.00445610939283
#seq	42
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_UTR_m1_run1.txt

#BEAR
gg!!ddddtttttttttttdddd22	chr11:80216395-80216631(+)$1	236	82	107	22.3481
gggggggtttttttttttggggggg	chr10:98488280-98488519(+)$1	239	166	191	23.7433
hhhhhhwwwwwwwwwwwwwwhhhhh	chr3:106377564-106377824(+)$1	260	96	121	21.1431
iiii[bbuuuuuuuuuuuubb]iii	chr7:51612652-51612887(+)$1	235	161	186	23.9829
ccc[ddddtttttttttttddddcc	chr11:51935880-51936142(+)$1	262	111	136	22.2644
ggggggguuuuuuuuuuuugggggg	chr12:109152922-109153254(-)$1	332	199	224	25.2114
d[ddddwwwwwwwwwwwwwwdddd]	chr2:126719268-126719499(-)$1	231	43	68	21.4859
gggggggvvvvvvvvvvvvvggggg	chr18:31598254-31598643(-)$1	389	2	27	24.8070
[fffffftttttttttttffffff]	chr6:38558567-38558836(+)$1	269	29	54	22.4558
!!ddddwwwwwwwwwwwwwwdddd]	chr3:122242557-122242825(-)$1	268	69	94	21.7348
GGeeeeeuuuuuuuuuuuueeeee:	chr3:22110437-22110674(+)$1	237	73	98	22.0910
bbb[bbvvvvvvvvvvvvvbb]bb]	chr15:58774336-58774707(-)$1	371	279	304	21.0430
!ffffffwwwwwwwwwwwwwwffff	chr2:119852921-119853176(+)$1	255	81	106	22.1891
gggggggtttttttttttggggggg	chr19:16459118-16459405(+)$1	287	144	169	23.7433
gggggggwwwwwwwwwwwwwwgggg	chr9:55983772-55984018(-)$1	246	58	83	23.5606
=======wwwwwwwwwwwwww====	chr7:73318202-73318485(+)$1	283	197	222	23.2619
ffffffbbtttttttttttbb]fff	chr17:87833164-87833407(-)$1	243	134	159	21.9167
hhhhhhhvvvvvvvvvvvvvhhhhh	chr7:152086646-152086905(+)$1	259	88	113	22.4163
gggggggyyyyyyyyyyyyyyyygg	chr1:66488988-66489246(+)$1	258	15	40	22.3062
::eeeeeuuuuuuuuuuuueeeeeB	chr5:144664571-144664802(+)$1	231	117	142	20.8256
ddd!!bbuuuuuuuuuuuubb22dd	chr2:120181681-120181916(-)$1	235	178	203	21.9241
f[eeeeevvvvvvvvvvvvveeeee	chr10:43303185-43303453(+)$1	268	40	65	23.5093
gggggg[attttttttttta]gggg	chr15:96517704-96517954(-)$1	250	156	181	24.5004
gggggggtttttttttttggggggg	chr2:90857624-90857893(+)$1	269	127	152	23.7433
gggggccctttttttttttccc]gg	chr1:5152360-5152624(+)$1	264	80	105	23.8549
ggeeeeeuuuuuuuuuuuueeeee]	chr5:136384423-136384850(-)$1	427	274	299	24.3469
::eeeeeuuuuuuuuuuuueeeeeH	chr1:4835581-4835831(+)$1	250	170	195	21.2311
ebb[ddddtttttttttttdddd]b	chr13:3881793-3882038(-)$1	245	72	97	21.4704
ffffcccwwwwwwwwwwwwwwccc2	chr9:70448740-70449007(-)$1	267	93	118	22.0492
cc[dddduuuuuuuuuuuuddddcc	chr1:162151860-162152101(-)$1	241	200	225	23.3849
iiiii[avvvvvvvvvvvvva]iii	chr2:131879136-131879378(-)$1	242	191	216	24.3771
hh!!cccvvvvvvvvvvvvvccc44	chr10:116784492-116784737(-)$1	245	133	158	23.3296
gggggggtttttttttttggggggg	chr16:46447988-46448248(-)$1	260	113	138	23.7433
=======yyyyyyyyyyyyyyyy==	chr17:31982112-31982365(-)$1	253	81	106	22.0480
========ttttttttttt======	chr19:37344859-37345118(-)$1	259	141	166	23.6165
hhhhhhhuuuuuuuuuuuuhhhhhh	chr4:149994451-149994686(+)$1	235	195	220	22.5747
d!!dddduuuuuuuuuuuudddd]d	chr15:3933818-3934057(-)$1	239	211	236	23.2304
e[eeeeeyyyyyyyyyyyyyyyyee	chr16:92084791-92085022(+)$1	231	149	174	21.1792
%%eeeeettttttttttteeeee33	chr8:12868340-12868607(+)$1	267	9	34	21.1907
"""dddduuuuuuuuuuuuddddff	chr11:107070286-107070540(-)$1	254	138	163	23.2052
gggg[bbuuuuuuuuuuuubb]ggg	chrX:91973223-91973455(+)$1	232	166	191	24.1577
========ttttttttttt======	chr6:12261510-12261764(-)$1	254	63	88	23.6165
ggggggguuuuuuuuuuuugggggg	chr7:118215642-118215940(-)$1	298	149	174	25.2114
gggggggtttttttttttggggggg	chr4:82447613-82447869(-)$1	256	72	97	23.7433
ggggggguuuuuuuuuuuugggggg	chr4:56890861-56891097(-)$1	236	134	159	25.2114
[ffffffwwwwwwwwwwwwwwffff	chr13:83803058-83803294(+)$1	236	14	39	22.2070
gggdddduuuuuuuuuuuudddd]g	chr12:120089540-120089793(+)$1	253	189	214	23.9504
c[eeeeeuuuuuuuuuuuueeeee]	chr5:92481693-92481934(-)$1	241	152	177	24.2065
ddeeeeeuuuuuuuuuuuueeeee]	chr14:106291283-106291555(-)$1	272	75	100	23.6710
iiiiiiivvvvvvvvvvvvviiiii	chr9:20239073-20239339(-)$1	266	225	250	24.5284
c!!eeeeettttttttttteeeee2	chr19:32748081-32748343(-)$1	262	191	216	22.7440
:ffffffuuuuuuuuuuuuffffff	chr13:18958248-18958479(+)$1	231	86	111	22.4832
gggggggtttttttttttggggggg	chr1:77363846-77364084(-)$1	238	148	173	23.7433
[ffffffwwwwwwwwwwwwwwffff	chr2:126717614-126717872(-)$1	258	137	162	22.2070
ffffffvvvvvvvvvvvvvffffff	chr1:33853022-33853263(-)$1	241	137	162	22.5057
dd!!ddddtttttttttttdddddd	chr18:9315375-9315606(-)$1	231	136	161	21.6713
iiiicccuuuuuuuuuuuuccc::D	chr4:82446363-82446643(-)$1	280	166	191	21.0423
fff!!ccctttttttttttccc22f	chr11:116711135-116711412(-)$1	277	209	234	22.5033
[ffffffwwwwwwwwwwwwwwffff	chrX:138753261-138753521(-)$1	260	106	131	22.2070
ggggggguuuuuuuuuuuugggggg	chr6:13034865-13035119(+)$1	254	31	56	25.2114
ggggggguuuuuuuuuuuugggggg	chr10:36721480-36721761(+)$1	281	11	36	25.2114
hhhhhhhuuuuuuuuuuuuhhhhhh	chrX:53915331-53915604(+)$1	273	5	30	22.5747
gggggggyyyyyyyyyyyyyyyygg	chr12:70475848-70476102(+)$1	254	51	76	22.3062
==eeeeevvvvvvvvvvvvveeeee	chr13:107751829-107752080(-)$1	251	114	139	23.6633
!ffffffuuuuuuuuuuuuffffff	chr16:52251412-52251643(-)$1	231	135	160	23.6256

#otherMatches

#Seq PSSM
AAAAGAGAGAGAAGAAAUAUUUUGA	chr11:80216395-80216631(+)$1	236	82	107	22.3481
AGGAUGAGUUACGUCUUGUCAUCUU	chr10:98488280-98488519(+)$1	239	166	191	23.7433
GAUUAGUUUUGAUCAUAUAUUUAGU	chr3:106377564-106377824(+)$1	260	96	121	21.1431
CAGGGACUCUGCUAAAACUGUGCCU	chr7:51612652-51612887(+)$1	235	161	186	23.9829
GUUGUUCUUUGUUACUGUCAGAAAA	chr11:51935880-51936142(+)$1	262	111	136	22.2644
UUACUUUGUCCUGAAAUGAAAAGUG	chr12:109152922-109153254(-)$1	332	199	224	25.2114
UAUGUAACUUUUAACCCCUCUACAG	chr2:126719268-126719499(-)$1	231	43	68	21.4859
UAAGAUAGCUUAAAUUAUCGUGUCU	chr18:31598254-31598643(-)$1	389	2	27	24.8070
CUUGCAGUUUUUGAACAUUUGUAAA	chr6:38558567-38558836(+)$1	269	29	54	22.4558
UUCCCCCUUCACCUUUUAACGGGGU	chr3:122242557-122242825(-)$1	268	69	94	21.7348
CCAGAUUCCAGUAUUAAAAAAUCUC	chr3:22110437-22110674(+)$1	237	73	98	22.0910
AGUACGCAGAGAAGGAAACCGGACA	chr15:58774336-58774707(-)$1	371	279	304	21.0430
UUGAAAGCCCCUUAUUUAUAACUUU	chr2:119852921-119853176(+)$1	255	81	106	22.1891
UUUAUUCUCCUUACGUUCGAGUGAA	chr19:16459118-16459405(+)$1	287	144	169	23.7433
GUCUUUGUUCAUCUUCAAAAUCAGA	chr9:55983772-55984018(-)$1	246	58	83	23.5606
AUUUUUACAUUCCCGUCUUACUAAA	chr7:73318202-73318485(+)$1	283	197	222	23.2619
UACUGUCAAAAAAUAUGCAUGUAUA	chr17:87833164-87833407(-)$1	243	134	159	21.9167
CAUGAUAUUUAUAAGUAAUUUAUUG	chr7:152086646-152086905(+)$1	259	88	113	22.4163
GGGUUCUUUCUUCUGAUAAUUCUAG	chr1:66488988-66489246(+)$1	258	15	40	22.3062
AUAAGUGACUAGCCCUUUCCGCUUU	chr5:144664571-144664802(+)$1	231	117	142	20.8256
UUAAGGAACUAUAGAUCUAUCAGUG	chr2:120181681-120181916(-)$1	235	178	203	21.9241
GAUUGGAACCCAUCCCCAAGUCCAG	chr10:43303185-43303453(+)$1	268	40	65	23.5093
UUCUGGGUAAUGAGUUGAGGGCCAG	chr15:96517704-96517954(-)$1	250	156	181	24.5004
UCAAGAUUGUAUCGUUUUAUUUUGA	chr2:90857624-90857893(+)$1	269	127	152	23.7433
GAGAAAUAUUACUGUUACUUAUAUU	chr1:5152360-5152624(+)$1	264	80	105	23.8549
AGUGUUAGCUUACUCUUAAUAAUGU	chr5:136384423-136384850(-)$1	427	274	299	24.3469
UCUGUCAUAUAUUUUAUUUUGACAU	chr1:4835581-4835831(+)$1	250	170	195	21.2311
AUACUGGCAAUCAGUUCAAGUCAUU	chr13:3881793-3882038(-)$1	245	72	97	21.4704
AUUCGGUAAGUUAGUGUCAAGACCA	chr9:70448740-70449007(-)$1	267	93	118	22.0492
gacaucacaacAGCUAAAAUGAUUC	chr1:162151860-162152101(-)$1	241	200	225	23.3849
UGGUGAGUUUAAUCUUCAGUCAUAC	chr2:131879136-131879378(-)$1	242	191	216	24.3771
AAAAAUGGAAUCAAAAAAUACAUAU	chr10:116784492-116784737(-)$1	245	133	158	23.3296
UAUAAUCUCAAGUAUAAUGAUUGUG	chr16:46447988-46448248(-)$1	260	113	138	23.7433
UAGGAAACAGACACUACUUAUUUUU	chr17:31982112-31982365(-)$1	253	81	106	22.0480
AGAAAGAUAUCCCAAUACAGUCUUU	chr19:37344859-37345118(-)$1	259	141	166	23.6165
GCACAUGAAAGACCUACAACAUGUG	chr4:149994451-149994686(+)$1	235	195	220	22.5747
CUUUGCACACACUGUUCAUUGCAUG	chr15:3933818-3934057(-)$1	239	211	236	23.2304
UAGUAAGCUUUCUCUGUUUUAAACU	chr16:92084791-92085022(+)$1	231	149	174	21.1792
AAGAUACGUAUGUUGGAAGUAUUAU	chr8:12868340-12868607(+)$1	267	9	34	21.1907
UUAUGCUGUAGUAAGAGAAAGCAAA	chr11:107070286-107070540(-)$1	254	138	163	23.2052
gaaucugccacauuccuuccaaauu	chrX:91973223-91973455(+)$1	232	166	191	24.1577
GAGAUGUAAUGUGCUUUUCUACAUU	chr6:12261510-12261764(-)$1	254	63	88	23.6165
GUUACAGAAAAAUUCUUAACUGUAA	chr7:118215642-118215940(-)$1	298	149	174	25.2114
uuuuaaacaaaauuuauuuuuaaaa	chr4:82447613-82447869(-)$1	256	72	97	23.7433
GGGAAGAGGUUUUACGGAAUUUUCC	chr4:56890861-56891097(-)$1	236	134	159	25.2114
CAGUCCUGUAAAAACCCACCAAGGA	chr13:83803058-83803294(+)$1	236	14	39	22.2070
GAGGUGCAGAGCCACACACGCACUU	chr12:120089540-120089793(+)$1	253	189	214	23.9504
GUGUAAUUUUUCUUUUGUUAUUAUU	chr5:92481693-92481934(-)$1	241	152	177	24.2065
AUCAAUCAGUAUGUUUUUAGAUUGU	chr14:106291283-106291555(-)$1	272	75	100	23.6710
ugucagcucuaaaauucuuugcugg	chr9:20239073-20239339(-)$1	266	225	250	24.5284
GGUUGUCAGGAGAAUCAGAUGACAA	chr19:32748081-32748343(-)$1	262	191	216	22.7440
AGUGACUUCGUUAUACCCUAGUUAC	chr13:18958248-18958479(+)$1	231	86	111	22.4832
UAUUUUGUUUUUAUUUGUCAAGGUA	chr1:77363846-77364084(-)$1	238	148	173	23.7433
aguacuugccuaccauguucaaagu	chr2:126717614-126717872(-)$1	258	137	162	22.2070
AAGGuauuuuuuauuuauuuauuuu	chr1:33853022-33853263(-)$1	241	137	162	22.5057
GAAUUUUAUAUGCUUCCUUUAAAUC	chr18:9315375-9315606(-)$1	231	136	161	21.6713
GUUAGACUUAUUUUUUUCUGUUAUG	chr4:82446363-82446643(-)$1	280	166	191	21.0423
CUUUUGUUUCCCUCAUUUUAAUCCA	chr11:116711135-116711412(-)$1	277	209	234	22.5033
UUUCCAAUAUAUGUAUCCCAUUUGG	chrX:138753261-138753521(-)$1	260	106	131	22.2070
AUGGUUGCAUAAUAUUUACCAACCA	chr6:13034865-13035119(+)$1	254	31	56	25.2114
GCUUGUUUUUGUUUUUCUUGGCAAG	chr10:36721480-36721761(+)$1	281	11	36	25.2114
CAGGUGUAUAUCGUUCAGGGCACUU	chrX:53915331-53915604(+)$1	273	5	30	22.5747
GUGUCUGAAAAUUAAAAUCAAGCCG	chr12:70475848-70476102(+)$1	254	51	76	22.3062
UUUCAUUUGCCCAAAUAAAUAGUGA	chr13:107751829-107752080(-)$1	251	114	139	23.6633
UAAGGGUUUCUUUCAGUUUGCCUUU	chr16:52251412-52251643(-)$1	231	135	160	23.6256

#DB
((..((((...........))))..	chr11:80216395-80216631(+)$1	1	82	107	22.3481
(((((((...........)))))))	chr10:98488280-98488519(+)$1	1	166	191	23.7433
((((((..............)))))	chr3:106377564-106377824(+)$1	1	96	121	21.1431
((((.((............)).)))	chr7:51612652-51612887(+)$1	1	161	186	23.9829
(((.((((...........))))))	chr11:51935880-51936142(+)$1	1	111	136	22.2644
(((((((............))))))	chr12:109152922-109153254(-)$1	1	199	224	25.2114
(.((((..............)))).	chr2:126719268-126719499(-)$1	1	43	68	21.4859
(((((((.............)))))	chr18:31598254-31598643(-)$1	1	2	27	24.8070
.((((((...........)))))).	chr6:38558567-38558836(+)$1	1	29	54	22.4558
..((((..............)))).	chr3:122242557-122242825(-)$1	1	69	94	21.7348
(((((((............))))).	chr3:22110437-22110674(+)$1	1	73	98	22.0910
(((.((.............)).)).	chr15:58774336-58774707(-)$1	1	279	304	21.0430
.((((((..............))))	chr2:119852921-119853176(+)$1	1	81	106	22.1891
(((((((...........)))))))	chr19:16459118-16459405(+)$1	1	144	169	23.7433
(((((((..............))))	chr9:55983772-55984018(-)$1	1	58	83	23.5606
(((((((..............))))	chr7:73318202-73318485(+)$1	1	197	222	23.2619
((((((((...........)).)))	chr17:87833164-87833407(-)$1	1	134	159	21.9167
(((((((.............)))))	chr7:152086646-152086905(+)$1	1	88	113	22.4163
(((((((................))	chr1:66488988-66489246(+)$1	1	15	40	22.3062
..(((((............))))))	chr5:144664571-144664802(+)$1	1	117	142	20.8256
(((..((............))..))	chr2:120181681-120181916(-)$1	1	178	203	21.9241
(.(((((.............)))))	chr10:43303185-43303453(+)$1	1	40	65	23.5093
((((((.(...........).))))	chr15:96517704-96517954(-)$1	1	156	181	24.5004
(((((((...........)))))))	chr2:90857624-90857893(+)$1	1	127	152	23.7433
((((((((...........))).))	chr1:5152360-5152624(+)$1	1	80	105	23.8549
(((((((............))))).	chr5:136384423-136384850(-)$1	1	274	299	24.3469
..(((((............))))))	chr1:4835581-4835831(+)$1	1	170	195	21.2311
(((.((((...........)))).)	chr13:3881793-3882038(-)$1	1	72	97	21.4704
(((((((..............))).	chr9:70448740-70449007(-)$1	1	93	118	22.0492
((.((((............))))))	chr1:162151860-162152101(-)$1	1	200	225	23.3849
(((((.(.............).)))	chr2:131879136-131879378(-)$1	1	191	216	24.3771
((..(((.............)))..	chr10:116784492-116784737(-)$1	1	133	158	23.3296
(((((((...........)))))))	chr16:46447988-46448248(-)$1	1	113	138	23.7433
(((((((................))	chr17:31982112-31982365(-)$1	1	81	106	22.0480
((((((((...........))))))	chr19:37344859-37345118(-)$1	1	141	166	23.6165
(((((((............))))))	chr4:149994451-149994686(+)$1	1	195	220	22.5747
(..((((............)))).)	chr15:3933818-3934057(-)$1	1	211	236	23.2304
(.(((((................))	chr16:92084791-92085022(+)$1	1	149	174	21.1792
..(((((...........)))))..	chr8:12868340-12868607(+)$1	1	9	34	21.1907
...((((............))))))	chr11:107070286-107070540(-)$1	1	138	163	23.2052
((((.((............)).)))	chrX:91973223-91973455(+)$1	1	166	191	24.1577
((((((((...........))))))	chr6:12261510-12261764(-)$1	1	63	88	23.6165
(((((((............))))))	chr7:118215642-118215940(-)$1	1	149	174	25.2114
(((((((...........)))))))	chr4:82447613-82447869(-)$1	1	72	97	23.7433
(((((((............))))))	chr4:56890861-56891097(-)$1	1	134	159	25.2114
.((((((..............))))	chr13:83803058-83803294(+)$1	1	14	39	22.2070
(((((((............)))).)	chr12:120089540-120089793(+)$1	1	189	214	23.9504
(.(((((............))))).	chr5:92481693-92481934(-)$1	1	152	177	24.2065
(((((((............))))).	chr14:106291283-106291555(-)$1	1	75	100	23.6710
(((((((.............)))))	chr9:20239073-20239339(-)$1	1	225	250	24.5284
(..(((((...........))))).	chr19:32748081-32748343(-)$1	1	191	216	22.7440
.((((((............))))))	chr13:18958248-18958479(+)$1	1	86	111	22.4832
(((((((...........)))))))	chr1:77363846-77364084(-)$1	1	148	173	23.7433
.((((((..............))))	chr2:126717614-126717872(-)$1	1	137	162	22.2070
((((((.............))))))	chr1:33853022-33853263(-)$1	1	137	162	22.5057
((..((((...........))))))	chr18:9315375-9315606(-)$1	1	136	161	21.6713
))))(((............)))..)	chr4:82446363-82446643(-)$1	1	166	191	21.0423
(((..(((...........)))..)	chr11:116711135-116711412(-)$1	1	209	234	22.5033
.((((((..............))))	chrX:138753261-138753521(-)$1	1	106	131	22.2070
(((((((............))))))	chr6:13034865-13035119(+)$1	1	31	56	25.2114
(((((((............))))))	chr10:36721480-36721761(+)$1	1	11	36	25.2114
(((((((............))))))	chrX:53915331-53915604(+)$1	1	5	30	22.5747
(((((((................))	chr12:70475848-70476102(+)$1	1	51	76	22.3062
))(((((.............)))))	chr13:107751829-107752080(-)$1	1	114	139	23.6633
.((((((............))))))	chr16:52251412-52251643(-)$1	1	135	160	23.6256

#PSSM
g : 0.32	h : 0.07	d : 0.07	= : 0.07	f : 0.07	i : 0.06	c : 0.06	[ : 0.06	! : 0.04	: : 0.04	e : 0.03	G : 0.01	b : 0.01	% : 0.01	" : 0.01	
g : 0.32	f : 0.16	h : 0.07	= : 0.07	i : 0.06	[ : 0.06	! : 0.04	d : 0.04	c : 0.03	b : 0.03	: : 0.03	G : 0.01	% : 0.01	" : 0.01	
g : 0.29	f : 0.16	e : 0.15	! : 0.07	h : 0.06	i : 0.06	= : 0.06	d : 0.04	b : 0.03	c : 0.01	[ : 0.01	" : 0.01	
g : 0.27	e : 0.16	f : 0.15	d : 0.09	! : 0.07	h : 0.06	i : 0.06	= : 0.06	[ : 0.04	
g : 0.26	e : 0.16	d : 0.15	f : 0.13	h : 0.06	= : 0.06	c : 0.04	[ : 0.03	! : 0.03	i : 0.03	b : 0.01	
g : 0.24	e : 0.16	d : 0.15	f : 0.13	c : 0.07	h : 0.06	b : 0.06	= : 0.06	[ : 0.01	i : 0.01	
g : 0.23	e : 0.16	d : 0.12	f : 0.10	c : 0.07	b : 0.06	= : 0.06	w : 0.04	h : 0.04	v : 0.03	[ : 0.01	a : 0.01	i : 0.01	
u : 0.35	w : 0.15	v : 0.13	t : 0.12	d : 0.06	y : 0.06	c : 0.03	= : 0.03	b : 0.01	a : 0.01	e : 0.01	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.29	w : 0.15	v : 0.13	y : 0.06	
u : 0.35	t : 0.16	w : 0.15	v : 0.13	g : 0.09	y : 0.06	f : 0.01	e : 0.01	
g : 0.16	w : 0.15	d : 0.12	e : 0.12	v : 0.10	b : 0.07	f : 0.06	y : 0.06	c : 0.04	= : 0.03	h : 0.03	a : 0.01	
g : 0.18	d : 0.15	e : 0.15	w : 0.10	b : 0.07	h : 0.06	f : 0.06	y : 0.06	c : 0.06	= : 0.03	] : 0.01	a : 0.01	i : 0.01	
g : 0.21	d : 0.15	e : 0.15	f : 0.12	] : 0.07	c : 0.07	h : 0.06	y : 0.06	= : 0.04	2 : 0.01	i : 0.01	
g : 0.23	d : 0.15	e : 0.15	f : 0.13	h : 0.06	y : 0.06	i : 0.04	= : 0.04	2 : 0.03	c : 0.03	b : 0.01	] : 0.01	: : 0.01	
g : 0.27	f : 0.15	e : 0.15	h : 0.06	d : 0.06	= : 0.06	i : 0.04	c : 0.04	] : 0.04	2 : 0.03	b : 0.01	4 : 0.01	3 : 0.01	: : 0.01	
g : 0.29	f : 0.15	] : 0.10	h : 0.06	= : 0.06	2 : 0.04	i : 0.04	d : 0.04	e : 0.04	c : 0.03	: : 0.01	B : 0.01	H : 0.01	b : 0.01	4 : 0.01	3 : 0.01	D : 0.01	

#score	1495.2463646557087
#seq	65
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_UTR_m1_run1.txt

#BEAR
""ggggggg####bbnnnnnbb4444ggggggg4	chr5:108863240-108863508(-)$1	268	62	96	11.0870
ccffffff####cccnnnnnccc]ffffff]ccc	chr10:86297866-86298144(+)$1	278	136	170	10.4906
dd[a[eeeee!!cccooooooccc55555eeeee	chr15:79658142-79658416(-)$1	274	99	133	11.4392
========####cccooooooccc333=======	chr15:44595248-44595531(-)$1	283	153	187	18.3468
=======$$$$$cccooooooccc]=========	chr7:107985018-107985335(+)$1	317	69	103	16.7219
b####ccc"""ddddoooooodddd]ccc4444b	chr8:11834139-11834413(+)$1	274	108	142	13.9721
ccc[ggggggg!!ddddllldddd333ggggggg	chr8:74842841-74843113(+)$1	272	74	108	11.6977
f:dddd"""ffffffooooooffffff]ddddcc	chr11:32327052-32327325(+)$1	273	200	234	10.3296
b!!ccc[a[a[a[bboooooobb]aa]a]ccc]b	chr15:75900547-75900820(-)$1	273	206	240	13.2605
[ccc"""ccc[ddddoooooodddd22ccc333c	chr15:79655896-79656195(-)$1	299	243	277	14.2793
ccc####dddd[cccooooooccc]ddddcccHH	chr18:24443321-24443593(+)$1	272	226	260	12.6059
======[a####eeeeemmmmeeeee4444a]==	chr18:34930961-34931234(+)$1	273	37	71	11.0292
ddd[bb$$$$$ddddccclllccc]dddd4444b	chr15:81535417-81535702(-)$1	285	106	140	10.0593
eee[a!!ddddddddoooooodddd4444dddda	chr13:69138016-69138287(-)$1	271	148	182	12.7990
f!!ccc"""cccrrrrrrrrrccc333ccc333f	chr17:34791800-34792094(+)$1	294	158	192	12.9550
=============!!bbmmmmbb22=========	chr2:157382615-157382901(-)$1	286	152	186	11.2118
dddd####cccddddccclllccc4444dddd]c	chr11:79506359-79506633(+)$1	274	42	76	11.1611
eee[eeeee[cccrrrrrrrrrccc]eeeee333	chr6:124863939-124864209(-)$1	270	55	89	11.2064
[dddd[ccc!!ddddoooooodddd333ccc22d	chr16:91227771-91228058(+)$1	287	20	54	13.8783
eeeeedddd!!ddddoooooodddd]dddd]eee	chr15:101926286-101926567(+)$1	281	218	252	12.2801
:gggggggddddcccooooooccc]dddd22ggg	chr10:116510443-116510718(-)$1	275	235	269	13.0312
b!!ffffff"""cccnnnnnccc4444ffffff2	chr3:121969333-121969624(+)$1	291	210	244	10.9874
fff!!eeeee!!cccooooooccc22eeeeefff	chr12:113887155-113887428(+)$1	273	75	109	14.5290
!cccdddd"""cccrrrrrrrrrccc]dddd]cc	chr5:141098323-141098602(-)$1	279	50	84	11.2634
iiiiii[ccc!!cccooooooccc]ccc22iiii	chr11:97574608-97574878(+)$1	270	55	89	15.9425
b[eeeeeeeeeecccooooooccc]eeeee22ee	chr7:117008957-117009223(-)$1	266	82	116	13.3142
dddd[==========oooooo==========]dd	chr16:98170652-98170921(-)$1	269	111	145	14.8948
======"""ddddqqqqqqqqdddd333======	chr12:114059359-114059639(-)$1	280	154	188	10.8018
======!!dddd[bboooooobb]dddd22====	chr4:83921329-83921604(-)$1	275	14	48	13.1593
ddd"""iiiiiiiiiooooooiiiiiiiii4444	chr19:5456434-5456714(-)$1	280	69	103	14.1681
cc[ddddccc!!cccooooooccc22ccc22ddd	chr1:62843167-62843435(+)$1	268	153	187	14.3100
cc:hhhhhhhhacccooooooccc]a4444hhhh	chr6:56728726-56729000(-)$1	274	108	142	11.7762
[ddddccc####cccmmmmcccccc]dddd]bb]	chr11:117828172-117828460(-)$1	288	166	200	10.3997
c[ffffff[===========lll===========	chr3:133126987-133127268(-)$1	281	181	215	10.0524
dddd[eeeee"""ccclllccc333eeeeedddd	chr8:123178705-123178982(-)$1	277	170	204	10.6893
iiiiiiiiivvvvvvvvvvvvviiiiiiiii]dd	chr2:30882339-30882614(-)$1	275	132	166	9.7774
ddd[dddd$$$$$cccmmmmccc4444dddd333	chr10:80611569-80611846(+)$1	277	48	82	10.9115
ggggggg[eeeee[cccmmmmccc22eeeee]gg	chr7:25670028-25670303(+)$1	275	55	89	10.7535
iiiiiiii!!cccqqqqqqqqccc333iiiiiii	chr15:102261444-102261729(+)$1	285	195	229	11.9618
:::===========rrrrrrrrr===========	chr6:140543072-140543349(+)$1	277	199	233	9.9209
d[eeeee####ddddooooooddddeeeeedddd	chr8:74844691-74844960(+)$1	269	148	182	12.8612
============bbccclllccc22bb]======	chr5:137968786-137969068(+)$1	282	79	113	12.1197
:ccc[eeeee!!cccooooooccc22eeeee]cc	chr16:98014687-98014959(-)$1	272	228	262	14.5841
FFccc[gggggggbboooooobb]ggggggg]cc	chr10:116509619-116509901(-)$1	282	93	127	11.9665
iiii[a[a[eeeee[ccclllccc22eeeee]a]	chr14:55505758-55506035(+)$1	277	57	91	11.5502
ff[bb[eeeee[cccooooooccc]eeeee]bbf	chr11:69813257-69813539(+)$1	282	182	216	13.1399
!!gggggggffffffooooooffffff22ggggg	chr15:81535368-81535654(-)$1	286	243	277	11.9228
iiii[cccccc[cccoooooocccccc22ccc22	chr5:123807810-123808084(+)$1	274	193	227	14.1946

#otherMatches

#Seq PSSM
AGGAGGCGGCUUUCAUUCUCUGUCUUCCGCCUCA	chr5:108863240-108863508(-)$1	268	62	96	11.0870
ugggcuggccuuggacucaauccuccggccucag	chr10:86297866-86298144(+)$1	278	136	170	10.4906
UGUGCUUAGCUUGCCUCAGAUGGCUCAGUGUUGA	chr15:79658142-79658416(-)$1	274	99	133	11.4392
GUGUGAUGUUCAGAGAAAAAccuuagguaucaug	chr15:44595248-44595531(-)$1	283	153	187	18.3468
CAGGCUCAGAACCUGGGAAAGCAGAGAGUUUGGG	chr7:107985018-107985335(+)$1	317	69	103	16.7219
CCCCCGCCCACCCACCCACCUGUGGAGGUUUCUG	chr8:11834139-11834413(+)$1	274	108	142	13.9721
CUGUGCCUGCCGCGCCUAUAAGGCCUGGGUGGGC	chr8:74842841-74843113(+)$1	272	74	108	11.6977
GCUCCUAACUUGCUAAGGUUCUAGCAGCAGGACU	chr11:32327052-32327325(+)$1	273	200	234	10.3296
GAAGUCCCUGUGUCUGAAAUUGGUCCUGUGACCC	chr15:75900547-75900820(-)$1	273	206	240	13.2605
AAGAUGCGAGCCUGCCAAUGAGCAGCCCUCUUCU	chr15:79655896-79656195(-)$1	299	243	277	14.2793
GUGCGACUGCAAAGUAGCGAGACUGUGCACACUG	chr18:24443321-24443593(+)$1	272	226	260	12.6059
cgcauggguguguacuugugugagugugugugug	chr18:34930961-34931234(+)$1	273	37	71	11.0292
UCCCUCGCCCUGCCCCAGUGACUGAGGGUCUUGG	chr15:81535417-81535702(-)$1	285	106	140	10.0593
UGCGGGACCGCGCCGAggcggcggcagcagcggc	chr13:69138016-69138287(-)$1	271	148	182	12.7990
UGUGUGUGCGUAUCuuuuuuuuauuauuauuaaa	chr17:34791800-34792094(+)$1	294	158	192	12.9550
uguauguaugugugcacuagugucagcguguaug	chr2:157382615-157382901(-)$1	286	152	186	11.2118
ACGAAGAAAGAUGCAGGCUUUGCCCACAUGCACU	chr11:79506359-79506633(+)$1	274	42	76	11.1611
AGGUGGGGCGGGAACACACAAAUCCAGCCCCCUU	chr6:124863939-124864209(-)$1	270	55	89	11.2064
UGGAGAGAUGCGUUCGUUCCAGAACCUGGUUGAC	chr16:91227771-91228058(+)$1	287	20	54	13.8783
UCAUUUCUGGAUGAGGAAGCACUUAACAGGUAGU	chr15:101926286-101926567(+)$1	281	218	252	12.2801
ACCAGUCAGCACCUCUGUCUUGAGUGUGCUGUGA	chr10:116510443-116510718(-)$1	275	235	269	13.0312
UUGUUUUCUAACGGAAAUCGUCUAUAAAGAAAAA	chr3:121969333-121969624(+)$1	291	210	244	10.9874
GCUAUGUUUGAAGCCUGAGGUGGCCACAGACAGC	chr12:113887155-113887428(+)$1	273	75	109	14.5290
ACUUUCCUCUCGGUUUCAUUCUCACCCAGGACAA	chr5:141098323-141098602(-)$1	279	50	84	11.2634
GAGAGACAGUAGACGUGACUCUGUGACUUUUCUC	chr11:97574608-97574878(+)$1	270	55	89	15.9425
CUGCCGCCGCAGGCUCUACGCGGCUCUGCGCUGC	chr7:117008957-117009223(-)$1	266	82	116	13.3142
UUUGGUUUCUGAGUAGUGGGAUGCUUGGGAAGUG	chr16:98170652-98170921(-)$1	269	111	145	14.8948
UCCUUUUGUGUGACAUUGGACUCACUGUGGAGGA	chr12:114059359-114059639(-)$1	280	154	188	10.8018
UGUACAUAUGUGUGCCUCUGUGUCUACACUUGUG	chr4:83921329-83921604(-)$1	275	14	48	13.1593
UCCUUGCUCUUGCUGGCAGAGCAGCAGGGGAAAU	chr19:5456434-5456714(-)$1	280	69	103	14.1681
AUCUCCAGGUACCUAGACAAAUAGAGACCAUUGG	chr1:62843167-62843435(+)$1	268	153	187	14.3100
GUUGCACUUCCGCCUGUAUAGGGGACUUGAGGGA	chr6:56728726-56729000(-)$1	274	108	142	11.7762
AAGAGAGCUAUACUGGUGCCAGGCUCCUCUCCAU	chr11:117828172-117828460(-)$1	288	166	200	10.3997
GAUCAAGUGGGAGGCAGAUCUGUGAUUUGCUUCU	chr3:133126987-133127268(-)$1	281	181	215	10.0524
CCCGUGGAUUAGAAAGCAGCUUGGAAGUCCUGGG	chr8:123178705-123178982(-)$1	277	170	204	10.6893
CUGGGGGGAAGGGAAUGCAGGAUUUCCCCAGAAG	chr2:30882339-30882614(-)$1	275	132	166	9.7774
GCCUGUGGCCUCCGCAUCUCUGCACAUCCACCCU	chr10:80611569-80611846(+)$1	277	48	82	10.9115
UUGGUGUUGACCUGGACCCACGUCAGGGGUUUGC	chr7:25670028-25670303(+)$1	275	55	89	10.7535
CACUGGUGACUCCUUGAAAAUGGAAAAUAUUAGU	chr15:102261444-102261729(+)$1	285	195	229	11.9618
AAAAAGUUAUUUUUGUGCCUUUAAAAAAUGACUU	chr6:140543072-140543349(+)$1	277	199	233	9.9209
CAUGCGCGACUGUGGCAGGUUCCACGCGCGGGGC	chr8:74844691-74844960(+)$1	269	148	182	12.8612
GGAGAGGCCUUAACCCUGUGAGGAAGUGUGGGGC	chr5:137968786-137969068(+)$1	282	79	113	12.1197
UCCCCAUGGUAACAGGCCAGGCUGCCAUCAUAGG	chr16:98014687-98014959(-)$1	272	228	262	14.5841
CUCCCUGCUCUGCUGUCCUCCCACGUGGAGCUGG	chr10:116509619-116509901(-)$1	282	93	127	11.9665
CCUAGAAUGUGGCAUCAUAUCGUGCUUGCUAGAA	chr14:55505758-55506035(+)$1	277	57	91	11.5502
ACUGUUGGCCGGCUGCUCAGACAGACGGCCUGCG	chr11:69813257-69813539(+)$1	282	182	216	13.1399
UCUCCCUGCUGGACUAACCCAAGUCCACUGUGGG	chr15:81535368-81535654(-)$1	286	243	277	11.9228
aaguagguuccagggaucgaacucggaucaucaa	chr5:123807810-123808084(+)$1	274	193	227	14.1946

#DB
..(((((((....((.....))....))))))).	chr5:108863240-108863508(-)$1	1	62	96	11.0870
((((((((....(((.....))).)))))).)))	chr10:86297866-86298144(+)$1	1	136	170	10.4906
((.(.(((((..(((......))).....)))))	chr15:79658142-79658416(-)$1	1	99	133	11.4392
((((((((....(((......)))...)))))))	chr15:44595248-44595531(-)$1	1	153	187	18.3468
(((((((.....(((......))).)))))))))	chr7:107985018-107985335(+)$1	1	69	103	16.7219
(....(((...((((......)))).)))....)	chr8:11834139-11834413(+)$1	1	108	142	13.9721
(((.(((((((..((((...))))...)))))))	chr8:74842841-74843113(+)$1	1	74	108	11.6977
).((((...((((((......)))))).))))((	chr11:32327052-32327325(+)$1	1	200	234	10.3296
(..(((.(.(.(.((......)).)).).))).)	chr15:75900547-75900820(-)$1	1	206	240	13.2605
.(((...(((.((((......))))..)))...)	chr15:79655896-79656195(-)$1	1	243	277	14.2793
(((....((((.(((......))).)))))))))	chr18:24443321-24443593(+)$1	1	226	260	12.6059
((((((.(....(((((....)))))....).))	chr18:34930961-34931234(+)$1	1	37	71	11.0292
(((.((.....(((((((...))).))))....)	chr15:81535417-81535702(-)$1	1	106	140	10.0593
(((.(..((((((((......))))....)))))	chr13:69138016-69138287(-)$1	1	148	182	12.7990
(..(((...(((.........)))...)))...)	chr17:34791800-34792094(+)$1	1	158	192	12.9550
(((((((((((((..((....))..)))))))))	chr2:157382615-157382901(-)$1	1	152	186	11.2118
((((....((((((((((...)))....)))).)	chr11:79506359-79506633(+)$1	1	42	76	11.1611
(((.(((((.(((.........))).)))))...	chr6:124863939-124864209(-)$1	1	55	89	11.2064
.((((.(((..((((......))))...)))..)	chr16:91227771-91228058(+)$1	1	20	54	13.8783
(((((((((..((((......)))).)))).)))	chr15:101926286-101926567(+)$1	1	218	252	12.2801
.((((((((((((((......))).))))..)))	chr10:116510443-116510718(-)$1	1	235	269	13.0312
(..((((((...(((.....)))....)))))).	chr3:121969333-121969624(+)$1	1	210	244	10.9874
(((..(((((..(((......)))..))))))))	chr12:113887155-113887428(+)$1	1	75	109	14.5290
.(((((((...(((.........))).)))).))	chr5:141098323-141098602(-)$1	1	50	84	11.2634
((((((.(((..(((......))).)))..))))	chr11:97574608-97574878(+)$1	1	55	89	15.9425
(.(((((((((((((......))).)))))..))	chr7:117008957-117009223(-)$1	1	82	116	13.3142
((((.((((((((((......)))))))))).))	chr16:98170652-98170921(-)$1	1	111	145	14.8948
((((((...((((........))))...))))))	chr12:114059359-114059639(-)$1	1	154	188	10.8018
((((((..((((.((......)).))))..))))	chr4:83921329-83921604(-)$1	1	14	48	13.1593
(((...(((((((((......)))))))))....	chr19:5456434-5456714(-)$1	1	69	103	14.1681
((.(((((((..(((......)))..)))..)))	chr1:62843167-62843435(+)$1	1	153	187	14.3100
)).((((((((((((......))).)....))))	chr6:56728726-56729000(-)$1	1	108	142	11.7762
.(((((((....(((....)))))).)))).)).	chr11:117828172-117828460(-)$1	1	166	200	10.3997
(.((((((.(((((((((((...)))))))))))	chr3:133126987-133127268(-)$1	1	181	215	10.0524
((((.(((((...(((...)))...)))))))))	chr8:123178705-123178982(-)$1	1	170	204	10.6893
(((((((((.............))))))))).))	chr2:30882339-30882614(-)$1	1	132	166	9.7774
(((.((((.....(((....)))....))))...	chr10:80611569-80611846(+)$1	1	48	82	10.9115
(((((((.(((((.(((....)))..))))).))	chr7:25670028-25670303(+)$1	1	55	89	10.7535
((((((((..(((........)))...)))))))	chr15:102261444-102261729(+)$1	1	195	229	11.9618
...(((((((((((.........)))))))))))	chr6:140543072-140543349(+)$1	1	199	233	9.9209
(.(((((....((((......)))))))))))))	chr8:74844691-74844960(+)$1	1	148	182	12.8612
(((((((((((((((((...)))..)).))))))	chr5:137968786-137969068(+)$1	1	79	113	12.1197
.(((.(((((..(((......)))..))))).))	chr16:98014687-98014959(-)$1	1	228	262	14.5841
))(((.(((((((((......)).))))))).))	chr10:116509619-116509901(-)$1	1	93	127	11.9665
((((.(.(.(((((.(((...)))..))))).).	chr14:55505758-55506035(+)$1	1	57	91	11.5502
((.((.(((((.(((......))).))))).)))	chr11:69813257-69813539(+)$1	1	182	216	13.1399
..(((((((((((((......))))))..)))))	chr15:81535368-81535654(-)$1	1	243	277	11.9228
((((.((((((.(((......))))))..)))..	chr5:123807810-123808084(+)$1	1	193	227	14.1946

#PSSM
d : 0.16	= : 0.14	c : 0.12	i : 0.10	b : 0.08	f : 0.08	[ : 0.06	e : 0.06	: : 0.06	! : 0.04	" : 0.02	g : 0.02	F : 0.02	
d : 0.18	c : 0.16	= : 0.14	i : 0.10	! : 0.08	e : 0.06	[ : 0.06	: : 0.04	g : 0.04	f : 0.04	" : 0.02	# : 0.02	F : 0.02	
d : 0.18	= : 0.14	c : 0.12	e : 0.10	i : 0.10	g : 0.08	f : 0.06	[ : 0.06	! : 0.06	: : 0.04	# : 0.02	
= : 0.16	d : 0.14	c : 0.12	[ : 0.10	i : 0.10	g : 0.08	f : 0.06	e : 0.06	# : 0.04	a : 0.02	! : 0.02	" : 0.02	h : 0.02	b : 0.02	
= : 0.16	[ : 0.12	d : 0.12	g : 0.10	e : 0.08	f : 0.06	# : 0.06	c : 0.06	i : 0.06	" : 0.04	b : 0.04	a : 0.02	! : 0.02	h : 0.02	
= : 0.18	e : 0.14	g : 0.10	c : 0.10	d : 0.10	f : 0.06	[ : 0.06	i : 0.06	" : 0.04	# : 0.04	b : 0.02	! : 0.02	h : 0.02	a : 0.02	
e : 0.16	g : 0.12	= : 0.12	c : 0.08	" : 0.08	[ : 0.08	d : 0.08	f : 0.06	i : 0.06	# : 0.04	! : 0.04	$ : 0.02	h : 0.02	
e : 0.14	c : 0.14	g : 0.10	= : 0.10	d : 0.10	f : 0.06	" : 0.06	a : 0.06	i : 0.06	$ : 0.04	# : 0.04	! : 0.02	h : 0.02	[ : 0.02	
e : 0.16	c : 0.12	# : 0.10	" : 0.10	d : 0.10	g : 0.08	= : 0.08	$ : 0.06	[ : 0.06	i : 0.04	f : 0.02	h : 0.02	! : 0.02	
e : 0.16	# : 0.12	c : 0.12	d : 0.10	= : 0.10	$ : 0.06	" : 0.06	! : 0.06	g : 0.04	f : 0.04	a : 0.02	[ : 0.02	i : 0.02	h : 0.02	v : 0.02	
! : 0.14	# : 0.12	d : 0.10	c : 0.10	= : 0.10	" : 0.08	e : 0.08	$ : 0.06	g : 0.04	f : 0.04	[ : 0.04	i : 0.02	h : 0.02	v : 0.02	
d : 0.22	! : 0.12	# : 0.10	= : 0.10	c : 0.08	[ : 0.06	e : 0.06	$ : 0.04	f : 0.04	a : 0.04	" : 0.04	i : 0.02	v : 0.02	g : 0.02	
c : 0.39	d : 0.18	= : 0.08	e : 0.06	f : 0.04	[ : 0.04	# : 0.02	! : 0.02	r : 0.02	i : 0.02	" : 0.02	v : 0.02	$ : 0.02	b : 0.02	g : 0.02	
c : 0.39	d : 0.18	b : 0.10	= : 0.06	f : 0.04	e : 0.04	r : 0.04	q : 0.04	! : 0.02	i : 0.02	v : 0.02	[ : 0.02	
c : 0.41	d : 0.18	b : 0.08	r : 0.08	f : 0.04	= : 0.04	q : 0.04	e : 0.02	! : 0.02	i : 0.02	v : 0.02	[ : 0.02	
o : 0.54	c : 0.14	r : 0.08	n : 0.06	q : 0.04	d : 0.02	e : 0.02	b : 0.02	m : 0.02	= : 0.02	v : 0.02	
o : 0.54	c : 0.10	r : 0.08	n : 0.06	q : 0.04	m : 0.04	d : 0.02	e : 0.02	b : 0.02	= : 0.02	l : 0.02	v : 0.02	
o : 0.54	m : 0.10	r : 0.08	n : 0.06	l : 0.06	c : 0.06	q : 0.04	= : 0.02	v : 0.02	
o : 0.54	l : 0.12	m : 0.10	r : 0.08	n : 0.06	q : 0.04	= : 0.02	v : 0.02	
o : 0.54	l : 0.10	m : 0.08	r : 0.08	n : 0.06	q : 0.04	c : 0.04	= : 0.02	v : 0.02	
o : 0.54	c : 0.12	l : 0.08	r : 0.08	m : 0.06	q : 0.04	b : 0.02	d : 0.02	v : 0.02	
c : 0.52	d : 0.16	b : 0.10	r : 0.06	f : 0.04	e : 0.02	= : 0.02	i : 0.02	l : 0.02	v : 0.02	
c : 0.52	d : 0.16	b : 0.08	f : 0.04	r : 0.04	i : 0.04	4 : 0.02	e : 0.02	= : 0.02	l : 0.02	3 : 0.02	
c : 0.45	d : 0.16	] : 0.08	4 : 0.06	= : 0.06	f : 0.04	2 : 0.04	i : 0.04	e : 0.02	3 : 0.02	
] : 0.16	d : 0.16	2 : 0.14	3 : 0.10	4 : 0.08	c : 0.08	f : 0.06	= : 0.06	i : 0.04	5 : 0.02	a : 0.02	e : 0.02	g : 0.02	
3 : 0.12	2 : 0.12	4 : 0.10	= : 0.10	e : 0.10	] : 0.08	d : 0.08	f : 0.06	c : 0.06	a : 0.04	i : 0.04	5 : 0.02	b : 0.02	g : 0.02	
e : 0.18	3 : 0.12	d : 0.12	4 : 0.12	= : 0.10	c : 0.08	f : 0.06	g : 0.04	] : 0.04	i : 0.04	5 : 0.02	2 : 0.02	b : 0.02	
e : 0.18	d : 0.16	= : 0.12	c : 0.10	4 : 0.08	g : 0.06	i : 0.06	f : 0.04	] : 0.04	3 : 0.04	2 : 0.04	5 : 0.02	a : 0.02	
d : 0.18	e : 0.18	= : 0.16	c : 0.10	2 : 0.08	g : 0.06	4 : 0.06	i : 0.06	f : 0.04	5 : 0.02	] : 0.02	
e : 0.20	= : 0.16	d : 0.14	c : 0.12	g : 0.08	4 : 0.08	2 : 0.08	i : 0.06	f : 0.04	
= : 0.18	d : 0.14	e : 0.12	g : 0.08	] : 0.08	c : 0.08	4 : 0.06	2 : 0.06	i : 0.06	3 : 0.04	a : 0.02	f : 0.02	h : 0.02	
= : 0.16	] : 0.16	d : 0.12	g : 0.08	c : 0.08	3 : 0.08	4 : 0.06	e : 0.04	2 : 0.04	f : 0.04	i : 0.04	b : 0.04	h : 0.02	
= : 0.18	d : 0.12	g : 0.10	c : 0.10	3 : 0.08	e : 0.06	4 : 0.06	] : 0.04	2 : 0.04	f : 0.04	i : 0.04	b : 0.04	H : 0.02	h : 0.02	a : 0.02	
= : 0.18	c : 0.14	d : 0.12	g : 0.08	e : 0.06	b : 0.06	f : 0.06	4 : 0.04	3 : 0.04	2 : 0.04	i : 0.04	] : 0.04	H : 0.02	a : 0.02	h : 0.02	

#score	595.796933841625
#seq	48
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_UTR_m3_run1.txt

#BEAR
e"""ddddqqqqqqqqdddd333	chr4:53774453-53774673(+)$1	220	130	153	15.1623
:gggggggqqqqqqqqggggggg	chr1:194997455-194997675(+)$1	220	72	95	15.0563
iiiiiiiiqqqqqqqqiiiiiii	chr3:58326310-58326530(-)$1	220	150	173	15.9866
dddd[cccqqqqqqqqccc]ddd	chr19:60603961-60604183(-)$1	222	38	61	14.6243
dd"""cccqqqqqqqqccc22dd	chr4:125386907-125387127(+)$1	220	96	119	14.8616
========qqqqqqqq=======	chr6:28478842-28479069(+)$1	227	118	141	16.3934
bb[eeeeeqqqqqqqqeeeee]b	chr8:119481991-119482264(+)$1	273	29	52	14.4739
cc[eeeeeqqqqqqqqeeeee]c	chr2:25206074-25206313(+)$1	239	139	162	14.8968
gggggg[aqqqqqqqqagggggg	chr11:51414141-51414380(-)$1	239	190	213	16.0107
"""eeeeeqqqqqqqqeeeee44	chr7:36475304-36475539(-)$1	235	148	171	14.9180
gbb[ddddqqqqqqqqddddbb]	chr9:50443803-50444023(-)$1	220	186	209	14.3021
##ffffffqqqqqqqqffffff3	chr16:50195693-50195926(-)$1	233	26	49	15.0217
b[ffffffqqqqqqqqffffff]	chr16:17045054-17045274(+)$1	220	98	121	14.8617
fff[ddddqqqqqqqqddddfff	chrX:20437664-20437890(-)$1	226	101	124	14.7620
eeeee[bbqqqqqqqqbbeeeee	chr16:84839299-84839531(+)$1	232	163	186	14.3104
!gggggggqqqqqqqqggggggg	chr3:94301892-94302125(-)$1	233	99	122	16.0661
a[ffffffqqqqqqqqffffff]	chr11:115885624-115885844(-)$1	220	128	151	15.0479
ff[ccc[aqqqqqqqqacccfff	chr18:66141453-66141721(-)$1	268	126	149	15.4798
iiiiiiiiqqqqqqqqiiiiiii	chr2:140245634-140245857(+)$1	223	98	121	15.9866
ee!!bbbbqqqqqqqqbb]bb22	chr18:38748059-38748279(-)$1	220	99	122	13.5523
:gggggggqqqqqqqqggggggg	chr11:48619828-48620062(-)$1	234	176	199	15.0563
ffffffbbqqqqqqqqbb]ffff	chr16:57152745-57152966(+)$1	221	169	192	14.5127
gggggcccqqqqqqqqccc4444	chr1:37474054-37474274(-)$1	220	75	98	15.8167
bb[eeeeeqqqqqqqqeeeee]b	chr13:101505964-101506184(-)$1	220	144	167	14.4739
hh[ccc[aqqqqqqqqaccc]hh	chr3:9433802-9434022(-)$1	220	97	120	15.1547
[bb!!cccqqqqqqqqcccbb]h	chr14:21274531-21274756(-)$1	225	104	127	15.1454
eeeee[bbqqqqqqqqbb]eeee	chr16:64858839-64859059(+)$1	220	9	32	14.3884
ddd[ddddqqqqqqqqddddddd	chr12:80276444-80276678(-)$1	234	38	61	13.8634
!!a[ddddqqqqqqqqdddd]a2	chrX:70331690-70331910(-)$1	220	103	126	15.1830
h!!ccc[aqqqqqqqqa]ccc22	chr19:29686671-29686893(-)$1	222	31	54	15.1213
ggccccccqqqqqqqqccc]ccc	chr3:88713501-88713721(-)$1	220	179	202	15.7259
accc!!bbqqqqqqqqbb22ccc	chr5:117733297-117733517(-)$1	220	102	125	14.7079
iiiiiiiiqqqqqqqqiiiiiii	chr15:98980138-98980358(+)$1	220	19	42	15.9866
b[ffffffqqqqqqqqffffff]	chr7:128785962-128786199(-)$1	237	197	220	14.8617
!!a[ddddqqqqqqqqdddda]c	chr2:105542151-105542376(-)$1	225	92	115	15.2533
eeee"""aqqqqqqqqa333eee	chr5:148359632-148359852(+)$1	220	96	119	14.9463
ff####bbqqqqqqqqbb]ffff	chr7:133938806-133939080(-)$1	274	67	90	14.7256
:gggggggqqqqqqqqggggggg	chr5:102263345-102263572(-)$1	227	41	64	15.0563
!gggggggqqqqqqqqggggggg	chr8:109710411-109710635(+)$1	224	19	42	16.0661
iiiiiiiiqqqqqqqqiiiiiii	chr11:75518638-75518869(+)$1	231	67	90	15.9866
"""eeeeeqqqqqqqqeeeee33	chr7:3154673-3154893(-)$1	220	110	133	15.1479
!bb[ddddqqqqqqqqdddd]bb	chr13:113295040-113295260(+)$1	220	26	49	14.5701
c[bb[cccqqqqqqqqccc22bb	chr10:126935754-126935975(+)$1	221	72	95	14.8597
eeee!!bbqqqqqqqqbb22eee	chr1:39053263-39053484(+)$1	221	152	175	14.2877
::ccccccqqqqqqqqccc]ccc	chr11:54724800-54725020(-)$1	220	152	175	13.8185
fffff!!aqqqqqqqqa22ffff	chr11:51506674-51506894(-)$1	220	129	152	14.6228
========qqqqqqqq=======	chr3:88882382-88882604(+)$1	222	150	173	16.3934
""bbddddqqqqqqqqdddd]bb	chr6:124666624-124666844(+)$1	220	92	115	14.2472
ccc[ddddqqqqqqqqdddd]cc	chr11:4081564-4081819(+)$1	255	160	183	14.9717
"gggggggqqqqqqqqggggggg	chr17:6239695-6239917(+)$1	222	46	69	16.0062
bb[eeeeeqqqqqqqqeeeee]b	chr5:31442993-31443232(-)$1	239	84	107	14.4739
ggg"""bbqqqqqqqqbbggggg	chr2:154698015-154698235(-)$1	220	147	170	15.4269
eee!!cccqqqqqqqqccc]eee	chr1:167523412-167523647(-)$1	235	174	197	15.6074
eeffffffqqqqqqqqffffff:	chr11:40564158-40564379(-)$1	221	81	104	13.7251
fff!!cccqqqqqqqqccc]fff	chr13:55419252-55419472(+)$1	220	112	135	15.8749
cddddcccqqqqqqqqccc4444	chr17:45738064-45738286(-)$1	222	137	160	14.8954
e[bb[a[aqqqqqqqqa]a]bbe	chr11:102264379-102264601(-)$1	222	168	191	14.5579
ffff[cccqqqqqqqqcccffff	chr14:21204271-21204502(-)$1	231	130	153	15.5431
hhhh[cccqqqqqqqqccchhhh	chr9:54796638-54796858(+)$1	220	47	70	14.5737
[bb[ddddqqqqqqqqdddd]bb	chr13:12487569-12487811(+)$1	242	195	218	14.5273
!bb"""bbqqqqqqqqbb333bb	chr9:57390322-57390542(+)$1	220	76	99	14.7352
:gggggggqqqqqqqqggggggg	chr3:30517201-30517421(+)$1	220	41	64	15.0563
!!ffffffqqqqqqqqffffff2	chr6:97182875-97183115(+)$1	240	125	148	14.9976

#otherMatches

#Seq PSSM
AUUUUUAAAAUGUUAAUUAAUCU	chr4:53774453-53774673(+)$1	220	130	153	15.1623
AAGAAUGUUGAAAAAUAUGUUCU	chr1:194997455-194997675(+)$1	220	72	95	15.0563
CUUUCCUGUAUCGGACCAGGAAA	chr3:58326310-58326530(-)$1	220	150	173	15.9866
UCACCCGAUAUCAGCCUCGAGUG	chr19:60603961-60604183(-)$1	222	38	61	14.6243
CACAUGUGAUCACUCCCACCAUG	chr4:125386907-125387127(+)$1	220	96	119	14.8616
GUGGACUGGUCAAUUGCAGUUUA	chr6:28478842-28479069(+)$1	227	118	141	16.3934
CCGACUGGGGAUGUAGUCAGUGG	chr8:119481991-119482264(+)$1	273	29	52	14.4739
CAGUUUCAACUUUUCAUGAAGGU	chr2:25206074-25206313(+)$1	239	139	162	14.8968
UUUCAGUCAAGUACAAGUUGAAA	chr11:51414141-51414380(-)$1	239	190	213	16.0107
UCUUGUUAAAAUUUUAUAACAUU	chr7:36475304-36475539(-)$1	235	148	171	14.9180
CUGUACAUGGACCCGAGUGUCAC	chr9:50443803-50444023(-)$1	220	186	209	14.3021
GAAAAACAUAGAGGUUUGUUUUG	chr16:50195693-50195926(-)$1	233	26	49	15.0217
UUGUAUUCCAUGAAGAGAAUGCU	chr16:17045054-17045274(+)$1	220	98	121	14.8617
CGCCUGUGGUAAUGCGUACAGUG	chrX:20437664-20437890(-)$1	226	101	124	14.7620
UCAGUAUGCCACGUUACAGCUGA	chr16:84839299-84839531(+)$1	232	163	186	14.3104
CAGUUGGAUGGGUUGCUUUAACU	chr3:94301892-94302125(-)$1	233	99	122	16.0661
CAAGGGCCCCAGACUCGGCUUUG	chr11:115885624-115885844(-)$1	220	128	151	15.0479
GCCAGAACUCCUUCAUGUCUGUA	chr18:66141453-66141721(-)$1	268	126	149	15.4798
UCUGUUUUGAAGAAGAAAAACAG	chr2:140245634-140245857(+)$1	223	98	121	15.9866
GCCCGUCCAGUGGGUAGGUACUU	chr18:38748059-38748279(-)$1	220	99	122	13.5523
AAAAGCAAAGCAGAGAUUGUUUU	chr11:48619828-48620062(-)$1	234	176	199	15.0563
CACUGUCAUAAAUUGUUGAACGG	chr16:57152745-57152966(+)$1	221	169	192	14.5127
agcuuugcccuuugaugcauuuu	chr1:37474054-37474274(-)$1	220	75	98	15.8167
GGUCAGCUGCCCCACAAGCUGCC	chr13:101505964-101506184(-)$1	220	144	167	14.4739
AAGUGUAGAUAUGGCACACAGUU	chr3:9433802-9434022(-)$1	220	97	120	15.1547
ugugaacuauugugugagugcug	chr14:21274531-21274756(-)$1	225	104	127	15.1454
UGUACAUGAAUGUUAACAAGUAC	chr16:64858839-64859059(+)$1	220	9	32	14.3884
CUGAGACACUUUUCUAUGUCCAG	chr12:80276444-80276678(-)$1	234	38	61	13.8634
AACUUAGAAUGUUUUGUUUGUGG	chrX:70331690-70331910(-)$1	220	103	126	15.1830
GGCUAAGUACUGUAUGGGUUAAA	chr19:29686671-29686893(-)$1	222	31	54	15.1213
ACAUGACAUACGCAUUUGUACAU	chr3:88713501-88713721(-)$1	220	179	202	15.7259
CCCAUUCUCAGCAACAAGUCUGG	chr5:117733297-117733517(-)$1	220	102	125	14.7079
AGAAUCUUAAACAACCAGGAUUU	chr15:98980138-98980358(+)$1	220	19	42	15.9866
CCAAAAUGUGUUuuuuuguuuuu	chr7:128785962-128786199(-)$1	237	197	220	14.8617
AGGACUUGAUGGGAAGCAGGCAG	chr2:105542151-105542376(-)$1	225	92	115	15.2533
AUCUGAGAGUAUCGAAUGAAGGA	chr5:148359632-148359852(+)$1	220	96	119	14.9463
UGUCAAGGAAAGUAUACCCCAAG	chr7:133938806-133939080(-)$1	274	67	90	14.7256
UGGUACAACAGUGACCUUGUACC	chr5:102263345-102263572(-)$1	227	41	64	15.0563
UGACCUGUGGGCGUGGGCAGGUU	chr8:109710411-109710635(+)$1	224	19	42	16.0661
AUUGUGUAAAUCCAAAUGCACAG	chr11:75518638-75518869(+)$1	231	67	90	15.9866
GAUGAAAACAUUAAAUUUUUUUA	chr7:3154673-3154893(-)$1	220	110	133	15.1479
AUUAUGUCAUCUAGAAGACGAAA	chr13:113295040-113295260(+)$1	220	26	49	14.5701
ACGGACAGACGGAUGACUGGCCC	chr10:126935754-126935975(+)$1	221	72	95	14.8597
AUGUAACUCUAUAGAAAGGAAUG	chr1:39053263-39053484(+)$1	221	152	175	14.2877
GACCAGGGAGAAUCCACCCAUGG	chr11:54724800-54725020(-)$1	220	152	175	13.8185
GGGAAACCUUCCUCGUGCCUUCC	chr11:51506674-51506894(-)$1	220	129	152	14.6228
AGAAAAUAGUUUGGAGUAUUUUC	chr3:88882382-88882604(+)$1	222	150	173	16.3934
UCGGGGGUCAAGCACAGCCCACC	chr6:124666624-124666844(+)$1	220	92	115	14.2472
GAUAAGCUGUAAACAAAGCUGGU	chr11:4081564-4081819(+)$1	255	160	183	14.9717
GCUGUCCUGUGAGCUGGGGACAG	chr17:6239695-6239917(+)$1	222	46	69	16.0062
cacaugguggcucacaaccaucu	chr5:31442993-31443232(-)$1	239	84	107	14.4739
UUGAUUCCUGGGCUGUGGCAAGU	chr2:154698015-154698235(-)$1	220	147	170	15.4269
UUCAGAGUCAUUUCUAGCUGGAA	chr1:167523412-167523647(-)$1	235	174	197	15.6074
GAAUUGAAAUACUAUCUUCAAUA	chr11:40564158-40564379(-)$1	221	81	104	13.7251
GGUCUCCAGGUUGUGGUGGUGCC	chr13:55419252-55419472(+)$1	220	112	135	15.8749
CCUCUGCCUUAUCUCUGGCCUCC	chr17:45738064-45738286(-)$1	222	137	160	14.8954
GUACGUGUGCACGUUUGGGGGUC	chr11:102264379-102264601(-)$1	222	168	191	14.5579
GUCUGACAUUUGCUUUUGUGGGC	chr14:21204271-21204502(-)$1	231	130	153	15.5431
GACUCAGGUCUAGACCCCUAGUC	chr9:54796638-54796858(+)$1	220	47	70	14.5737
GCGGCCGUGACUUGGAACGGGUG	chr13:12487569-12487811(+)$1	242	195	218	14.5273
AGGGAAGGAACACAGACCAUAUC	chr9:57390322-57390542(+)$1	220	76	99	14.7352
AGUAUGAAAUACCACCUUUGUAC	chr3:30517201-30517421(+)$1	220	41	64	15.0563
UUUAGCGGUAUUAUUUUUGUUGU	chr6:97182875-97183115(+)$1	240	125	148	14.9976

#DB
(...((((........))))...	chr4:53774453-53774673(+)$1	1	130	153	15.1623
.(((((((........)))))))	chr1:194997455-194997675(+)$1	1	72	95	15.0563
((((((((........)))))))	chr3:58326310-58326530(-)$1	1	150	173	15.9866
((((.(((........))).)))	chr19:60603961-60604183(-)$1	1	38	61	14.6243
((...(((........)))..))	chr4:125386907-125387127(+)$1	1	96	119	14.8616
((((((((........)))))))	chr6:28478842-28479069(+)$1	1	118	141	16.3934
((.(((((........))))).)	chr8:119481991-119482264(+)$1	1	29	52	14.4739
((.(((((........))))).)	chr2:25206074-25206313(+)$1	1	139	162	14.8968
((((((.(........)))))))	chr11:51414141-51414380(-)$1	1	190	213	16.0107
...(((((........)))))..	chr7:36475304-36475539(-)$1	1	148	171	14.9180
(((.((((........)))))).	chr9:50443803-50444023(-)$1	1	186	209	14.3021
..((((((........)))))).	chr16:50195693-50195926(-)$1	1	26	49	15.0217
(.((((((........)))))).	chr16:17045054-17045274(+)$1	1	98	121	14.8617
(((.((((........)))))))	chrX:20437664-20437890(-)$1	1	101	124	14.7620
(((((.((........)))))))	chr16:84839299-84839531(+)$1	1	163	186	14.3104
.(((((((........)))))))	chr3:94301892-94302125(-)$1	1	99	122	16.0661
(.((((((........)))))).	chr11:115885624-115885844(-)$1	1	128	151	15.0479
((.(((.(........)))))))	chr18:66141453-66141721(-)$1	1	126	149	15.4798
((((((((........)))))))	chr2:140245634-140245857(+)$1	1	98	121	15.9866
((..((((........)).))..	chr18:38748059-38748279(-)$1	1	99	122	13.5523
.(((((((........)))))))	chr11:48619828-48620062(-)$1	1	176	199	15.0563
((((((((........)).))))	chr16:57152745-57152966(+)$1	1	169	192	14.5127
((((((((........)))....	chr1:37474054-37474274(-)$1	1	75	98	15.8167
((.(((((........))))).)	chr13:101505964-101506184(-)$1	1	144	167	14.4739
((.(((.(........)))).))	chr3:9433802-9434022(-)$1	1	97	120	15.1547
.((..(((........))))).)	chr14:21274531-21274756(-)$1	1	104	127	15.1454
(((((.((........)).))))	chr16:64858839-64859059(+)$1	1	9	32	14.3884
(((.((((........)))))))	chr12:80276444-80276678(-)$1	1	38	61	13.8634
..(.((((........)))).).	chrX:70331690-70331910(-)$1	1	103	126	15.1830
(..(((.(........).)))..	chr19:29686671-29686893(-)$1	1	31	54	15.1213
))((((((........))).)))	chr3:88713501-88713721(-)$1	1	179	202	15.7259
((((..((........))..)))	chr5:117733297-117733517(-)$1	1	102	125	14.7079
((((((((........)))))))	chr15:98980138-98980358(+)$1	1	19	42	15.9866
(.((((((........)))))).	chr7:128785962-128786199(-)$1	1	197	220	14.8617
..(.((((........))))).)	chr2:105542151-105542376(-)$1	1	92	115	15.2533
((((...(........)...)))	chr5:148359632-148359852(+)$1	1	96	119	14.9463
((....((........)).))))	chr7:133938806-133939080(-)$1	1	67	90	14.7256
.(((((((........)))))))	chr5:102263345-102263572(-)$1	1	41	64	15.0563
.(((((((........)))))))	chr8:109710411-109710635(+)$1	1	19	42	16.0661
((((((((........)))))))	chr11:75518638-75518869(+)$1	1	67	90	15.9866
...(((((........)))))..	chr7:3154673-3154893(-)$1	1	110	133	15.1479
.((.((((........)))).))	chr13:113295040-113295260(+)$1	1	26	49	14.5701
(.((.(((........)))..))	chr10:126935754-126935975(+)$1	1	72	95	14.8597
((((..((........))..)))	chr1:39053263-39053484(+)$1	1	152	175	14.2877
..((((((........))).)))	chr11:54724800-54725020(-)$1	1	152	175	13.8185
(((((..(........)..))))	chr11:51506674-51506894(-)$1	1	129	152	14.6228
((((((((........)))))))	chr3:88882382-88882604(+)$1	1	150	173	16.3934
..((((((........)))).))	chr6:124666624-124666844(+)$1	1	92	115	14.2472
(((.((((........)))).))	chr11:4081564-4081819(+)$1	1	160	183	14.9717
.(((((((........)))))))	chr17:6239695-6239917(+)$1	1	46	69	16.0062
((.(((((........))))).)	chr5:31442993-31443232(-)$1	1	84	107	14.4739
(((...((........)))))))	chr2:154698015-154698235(-)$1	1	147	170	15.4269
(((..(((........))).)))	chr1:167523412-167523647(-)$1	1	174	197	15.6074
))((((((........)))))).	chr11:40564158-40564379(-)$1	1	81	104	13.7251
(((..(((........))).)))	chr13:55419252-55419472(+)$1	1	112	135	15.8749
((((((((........)))....	chr17:45738064-45738286(-)$1	1	137	160	14.8954
(.((.(.(........).).)))	chr11:102264379-102264601(-)$1	1	168	191	14.5579
((((.(((........)))))))	chr14:21204271-21204502(-)$1	1	130	153	15.5431
((((.(((........)))))))	chr9:54796638-54796858(+)$1	1	47	70	14.5737
.((.((((........)))).))	chr13:12487569-12487811(+)$1	1	195	218	14.5273
.((...((........))...))	chr9:57390322-57390542(+)$1	1	76	99	14.7352
.(((((((........)))))))	chr3:30517201-30517421(+)$1	1	41	64	15.0563
..((((((........)))))).	chr6:97182875-97183115(+)$1	1	125	148	14.9976

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

#score	946.729668607134
#seq	63
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_CDS_m1_run1.txt

#BEAR
ggggggtttttttttttgggg	chr19:10058959-10059195(+)$1	236	212	233	17.0877
!dddduuuuuuuuuuuudddd	chr9:95945897-95946132(+)$1	235	113	134	20.6594
[ddddxxxxxxxxxxxxxxxd	chr10:41239320-41239558(+)$1	238	89	110	16.8914
dddwwwwwwwwwwwwwwdddd	chr15:99351509-99351763(-)$1	254	41	62	19.3289
eeeeevvvvvvvvvvvvveee	chr10:53063680-53063917(+)$1	237	73	94	19.3721
ggggguuuuuuuuuuuugggg	chr11:86602657-86602898(-)$1	241	170	191	19.5364
e[cccuuuuuuuuuuuuccce	chr10:106256389-106256638(+)$1	249	30	51	20.4486
fdddduuuuuuuuuuuudddd	chr15:31418450-31418687(-)$1	237	63	84	20.2583
$$ddddtttttttttttdddd	chr8:41532325-41532562(+)$1	237	121	142	17.7890
!ccc^^^^^^^^^^^^^^^^^	chr11:70483254-70483493(-)$1	239	50	71	16.2115
[dddd^^^^^^^^^^^^^^^^	chr5:72015103-72015349(-)$1	246	133	154	15.9984
eeeee^^^^^^^^^^^^^^^^	chr3:95023988-95024224(-)$1	236	187	208	15.3913
cddddwwwwwwwwwwwwwwdd	chr15:83666718-83666956(+)$1	238	71	92	20.0418
!ccc^^^^^^^^^^^^^^^^^	chr12:21315974-21316209(+)$1	235	169	190	16.2115
!ccc^^^^^^^^^^^^^^^^^	chr11:55208949-55209192(-)$1	243	159	180	16.2115
===bbvvvvvvvvvvvvvbb]	chr5:138398460-138398701(-)$1	241	139	160	18.8453
ccc[cccsssssssssscccc	chr2:6468061-6468303(-)$1	242	164	185	13.0211
eeeeettttttttttteeeee	chr7:137872027-137872262(+)$1	235	69	90	17.1894
eeeeettttttttttteeeee	chr1:59927210-59927447(+)$1	237	94	115	17.1894
GGcccvvvvvvvvvvvvvccc	chr5:104508405-104508686(-)$1	281	15	36	19.0746
DDddddtttttttttttdddd	chr2:34631511-34631748(+)$1	237	18	39	16.3392
fffffuuuuuuuuuuuuffff	chr7:20150502-20150751(-)$1	249	163	184	18.7732
dddwwwwwwwwwwwwwwdddd	chr7:148337524-148337759(+)$1	235	140	161	19.3289
!cccxxxxxxxxxxxxxxxcc	chr11:109528789-109529095(+)$1	306	224	245	17.1011
gggggyyyyyyyyyyyyyyyy	chr11:31917577-31917812(+)$1	235	105	126	18.6170
''ddddtttttttttttdddd	chr18:46664687-46664922(-)$1	235	62	83	17.0666
^^^^^^^^^^^^^^^^^dddd	chr15:27701031-27701272(-)$1	241	164	185	14.9576
^^^^^^^^^^^^^^^^^ffff	chr6:4706066-4706310(+)$1	244	187	208	14.2632
fffffyyyyyyyyyyyyyyyy	chr5:34186114-34186353(+)$1	239	134	155	18.1536
[axxxxxxxxxxxxxxxa]dd	chr7:65047791-65048042(+)$1	251	45	66	16.2776
ddddcccssssssssssccc]	chr16:35299447-35299697(+)$1	250	79	100	13.0215
^^^^^^^^^^^^^^^^^ccc]	chr14:31989531-31989766(-)$1	235	97	118	15.1004
^^^^^^^^^^^^^^^^^gggg	chr12:4637380-4637615(+)$1	235	27	48	14.5629
:ddddtttttttttttddddC	chr5:90646461-90646698(-)$1	237	214	235	15.9097
[ddddyyyyyyyyyyyyyyyy	chr19:47331845-47332080(+)$1	235	57	78	19.2850
""cccvvvvvvvvvvvvvccc	chr4:126707015-126707250(+)$1	235	164	185	20.3043
eeeeeuuuuuuuuuuuueeee	chr2:181041975-181042222(-)$1	247	222	243	19.6959
!bbxxxxxxxxxxxxxxxbb2	chr11:41946818-41947090(-)$1	272	91	112	15.4959
"dddd^^^^^^^^^^^^^^^^	chr4:148761180-148761417(-)$1	237	60	81	15.9962
"""bbvvvvvvvvvvvvvbb5	chr8:47292820-47293064(-)$1	244	131	152	18.1906
::ccctttttttttttccc:e	chr13:78336959-78337194(-)$1	235	25	46	15.5077
ffffftttttttttttfffff	chr8:46095312-46095551(+)$1	239	146	167	16.1746
[dddduuuuuuuuuuuudddd	chr11:115667985-115668222(-)$1	237	46	67	20.5991
gg[ccctttttttttttccc]	chr8:63391717-63391957(-)$1	240	169	190	18.2404
eeeeevvvvvvvvvvvvveee	chrX:148326258-148326496(+)$1	238	121	142	19.3721
#ddddwwwwwwwwwwwwwwdd	chr19:10058581-10058825(+)$1	244	120	141	20.2451
:dddduuuuuuuuuuuudddd	chr3:146395453-146395688(-)$1	235	60	81	19.5606
ggg[cccsssssssssscccg	chr12:73675052-73675287(+)$1	235	105	126	12.7879
ddcccwwwwwwwwwwwwwwcc	chr1:75212189-75212442(-)$1	253	177	198	20.0378
hhhhvvvvvvvvvvvvvhhhh	chr19:10058659-10058899(+)$1	240	65	86	17.1567
!ccc^^^^^^^^^^^^^^^^^	chr11:70483294-70483530(-)$1	236	87	108	16.2115
[axxxxxxxxxxxxxxxa]dd	chr19:7289793-7290030(-)$1	237	35	56	16.2776
eecccwwwwwwwwwwwwwwcc	chr16:11134462-11134700(-)$1	238	58	79	19.9909
cccccvvvvvvvvvvvvvccc	chr6:4591853-4592090(+)$1	237	70	91	20.1269
ccc[cccssssssssssccc]	chr11:78335201-78335436(+)$1	235	51	72	12.9911
ddddvvvvvvvvvvvvvdddd	chr11:72025341-72025578(-)$1	237	178	199	19.4987
======ttttttttttt====	chr2:181041364-181041632(-)$1	268	188	209	17.5110

#otherMatches

#Seq PSSM
CCACGUGAGUAUCGGAAACGU	chr19:10058959-10059195(+)$1	236	212	233	17.0877
UGAACUUUCUCGAAUUUGUUC	chr9:95945897-95946132(+)$1	235	113	134	20.6594
CAGCCCAACAUCACCACCCUG	chr10:41239320-41239558(+)$1	238	89	110	16.8914
CCUCUACCCACCUACCCAGGC	chr15:99351509-99351763(-)$1	254	41	62	19.3289
CAGAACCUAUUUAUCAAUUUC	chr10:53063680-53063917(+)$1	237	73	94	19.3721
AACUAGUUUGACAUCUGUAGU	chr11:86602657-86602898(-)$1	241	170	191	19.5364
CAGAUGACACCAGCCAAAUCG	chr10:106256389-106256638(+)$1	249	30	51	20.4486
AUGUUCUCCUCCCUUUCAGCA	chr15:31418450-31418687(-)$1	237	63	84	20.2583
UCUGGUCAUACUGGAAAACCA	chr8:41532325-41532562(+)$1	237	121	142	17.7890
UGCACCUUCUCCAUAUCCCCG	chr11:70483254-70483493(-)$1	239	50	71	16.2115
GCUGCUGUCAACUAUUUCACC	chr5:72015103-72015349(-)$1	246	133	154	15.9984
CCACUUUAAUCUUGUUCUCUU	chr3:95023988-95024224(-)$1	236	187	208	15.3913
AGGACUUUUAUUAUUUCCCGU	chr15:83666718-83666956(+)$1	238	71	92	20.0418
AGGUACAGACUCUCUCAUACU	chr12:21315974-21316209(+)$1	235	169	190	16.2115
CCCAUUACCCCCUUGUUUAAA	chr11:55208949-55209192(-)$1	243	159	180	16.2115
UUUUGGAGGAUAUACAAGCAC	chr5:138398460-138398701(-)$1	241	139	160	18.8453
CUUACUGAUCCUAACCCCAGA	chr2:6468061-6468303(-)$1	242	164	185	13.0211
AAGGAAGCCCUUUCCGUCCUU	chr7:137872027-137872262(+)$1	235	69	90	17.1894
AGAUAUAGGAAUGAAUUGUCU	chr1:59927210-59927447(+)$1	237	94	115	17.1894
AUGACUUUCUAAAACUUUGUC	chr5:104508405-104508686(-)$1	281	15	36	19.0746
AGGAACUAGAAGAAAUUGUUC	chr2:34631511-34631748(+)$1	237	18	39	16.3392
CCAGGCCUCUGACUAUUCCUG	chr7:20150502-20150751(-)$1	249	163	184	18.7732
CCCUUUCCACAACAUCUGGGU	chr7:148337524-148337759(+)$1	235	140	161	19.3289
UCUUGUCUCUUUAUACUAAAA	chr11:109528789-109529095(+)$1	306	224	245	17.1011
GGAACAGAGGAACAAAGGGAA	chr11:31917577-31917812(+)$1	235	105	126	18.6170
UUUGAUACAGCCCAUAAAUCA	chr18:46664687-46664922(-)$1	235	62	83	17.0666
UUCUUCGUUCCGUUCAUCUCA	chr15:27701031-27701272(-)$1	241	164	185	14.9576
caucacccuccacaucaggau	chr6:4706066-4706310(+)$1	244	187	208	14.2632
UCAGAAGAAAACGAACAAAAA	chr5:34186114-34186353(+)$1	239	134	155	18.1536
UGUUCCUGCUUCUCUCUCCUG	chr7:65047791-65048042(+)$1	251	45	66	16.2776
CCUUCUGUCUAGAUCAUCAGU	chr16:35299447-35299697(+)$1	250	79	100	13.0215
UCGUUACCGCCAUCUUUGUGC	chr14:31989531-31989766(-)$1	235	97	118	15.1004
UUUAGUAACAAAGUUUUAAAU	chr12:4637380-4637615(+)$1	235	27	48	14.5629
UUGGGGAUUCCUUUUACCCAC	chr5:90646461-90646698(-)$1	237	214	235	15.9097
UCAGGGACAGCCCCCAACUCA	chr19:47331845-47332080(+)$1	235	57	78	19.2850
AAGGGCCAAAUAAAAAACCCC	chr4:126707015-126707250(+)$1	235	164	185	20.3043
AGCUCAACUACAAGAUGGAGC	chr2:181041975-181042222(-)$1	247	222	243	19.6959
CCCCACACCCCAUCAAUAGGU	chr11:41946818-41947090(-)$1	272	91	112	15.4959
GUCCUUUCUCUCUUUUUGCCU	chr4:148761180-148761417(-)$1	237	60	81	15.9962
AUUGCAAAAGAUGAAGGAGCC	chr8:47292820-47293064(-)$1	244	131	152	18.1906
ccggcuccuccaccccgcccG	chr13:78336959-78337194(-)$1	235	25	46	15.5077
GGAGAAUAUGACAUUCUUUCC	chr8:46095312-46095551(+)$1	239	146	167	16.1746
AUGCGCCCCCUACACUAUGCA	chr11:115667985-115668222(-)$1	237	46	67	20.5991
UUCUUUCAAAAAAAAAAAAAA	chr8:63391717-63391957(-)$1	240	169	190	18.2404
UAUGGUGACUGUUCUAAUCCG	chrX:148326258-148326496(+)$1	238	121	142	19.3721
UGAAGAACUUUGCCAAAUACU	chr19:10058581-10058825(+)$1	244	120	141	20.2451
ACUUCGAUGACUAUGAAGAAG	chr3:146395453-146395688(-)$1	235	60	81	19.5606
UGGAGGUCUAACUCCACACCC	chr12:73675052-73675287(+)$1	235	105	126	12.7879
GCCCUGGAAAAAGAUUAUGAG	chr1:75212189-75212442(-)$1	253	177	198	20.0378
CUCCACCAAUCUCAUGAGGAG	chr19:10058659-10058899(+)$1	240	65	86	17.1567
UGCACCUUCUCCAUAUCCCCG	chr11:70483294-70483530(-)$1	236	87	108	16.2115
UCUUUCUUGUACUCUGUGUAG	chr19:7289793-7290030(-)$1	237	35	56	16.2776
GCGGCAGCGACGGUAUAAAGC	chr16:11134462-11134700(-)$1	238	58	79	19.9909
CCGACACUCAACAUCAUCGUC	chr6:4591853-4592090(+)$1	237	70	91	20.1269
GUUCAGACCUUACUCCCUCUA	chr11:78335201-78335436(+)$1	235	51	72	12.9911
CAGCAGGGAAAUGAAGAGCUG	chr11:72025341-72025578(-)$1	237	178	199	19.4987
AGAACGUUUUCGGGUUUUGUU	chr2:181041364-181041632(-)$1	268	188	209	17.5110

#DB
((((((...........))))	chr19:10058959-10059195(+)$1	1	212	233	17.0877
.((((............))))	chr9:95945897-95946132(+)$1	1	113	134	20.6594
.((((...............)	chr10:41239320-41239558(+)$1	1	89	110	16.8914
(((..............))))	chr15:99351509-99351763(-)$1	1	41	62	19.3289
(((((.............)))	chr10:53063680-53063917(+)$1	1	73	94	19.3721
(((((............))))	chr11:86602657-86602898(-)$1	1	170	191	19.5364
(.(((............))))	chr10:106256389-106256638(+)$1	1	30	51	20.4486
(((((............))))	chr15:31418450-31418687(-)$1	1	63	84	20.2583
..((((...........))))	chr8:41532325-41532562(+)$1	1	121	142	17.7890
.(((.................	chr11:70483254-70483493(-)$1	1	50	71	16.2115
.((((................	chr5:72015103-72015349(-)$1	1	133	154	15.9984
(((((................	chr3:95023988-95024224(-)$1	1	187	208	15.3913
(((((..............))	chr15:83666718-83666956(+)$1	1	71	92	20.0418
.(((.................	chr12:21315974-21316209(+)$1	1	169	190	16.2115
.(((.................	chr11:55208949-55209192(-)$1	1	159	180	16.2115
(((((.............)).	chr5:138398460-138398701(-)$1	1	139	160	18.8453
(((.(((..........))))	chr2:6468061-6468303(-)$1	1	164	185	13.0211
(((((...........)))))	chr7:137872027-137872262(+)$1	1	69	90	17.1894
(((((...........)))))	chr1:59927210-59927447(+)$1	1	94	115	17.1894
(((((.............)))	chr5:104508405-104508686(-)$1	1	15	36	19.0746
((((((...........))))	chr2:34631511-34631748(+)$1	1	18	39	16.3392
(((((............))))	chr7:20150502-20150751(-)$1	1	163	184	18.7732
(((..............))))	chr7:148337524-148337759(+)$1	1	140	161	19.3289
.(((...............))	chr11:109528789-109529095(+)$1	1	224	245	17.1011
(((((................	chr11:31917577-31917812(+)$1	1	105	126	18.6170
..((((...........))))	chr18:46664687-46664922(-)$1	1	62	83	17.0666
.................))))	chr15:27701031-27701272(-)$1	1	164	185	14.9576
.................))))	chr6:4706066-4706310(+)$1	1	187	208	14.2632
(((((................	chr5:34186114-34186353(+)$1	1	134	155	18.1536
.(...............).))	chr7:65047791-65048042(+)$1	1	45	66	16.2776
(((((((..........))).	chr16:35299447-35299697(+)$1	1	79	100	13.0215
.................))).	chr14:31989531-31989766(-)$1	1	97	118	15.1004
.................))))	chr12:4637380-4637615(+)$1	1	27	48	14.5629
.((((...........)))))	chr5:90646461-90646698(-)$1	1	214	235	15.9097
.((((................	chr19:47331845-47332080(+)$1	1	57	78	19.2850
..(((.............)))	chr4:126707015-126707250(+)$1	1	164	185	20.3043
(((((............))))	chr2:181041975-181042222(-)$1	1	222	243	19.6959
.((...............)).	chr11:41946818-41947090(-)$1	1	91	112	15.4959
.((((................	chr4:148761180-148761417(-)$1	1	60	81	15.9962
...((.............)).	chr8:47292820-47293064(-)$1	1	131	152	18.1906
..(((...........))).(	chr13:78336959-78337194(-)$1	1	25	46	15.5077
(((((...........)))))	chr8:46095312-46095551(+)$1	1	146	167	16.1746
.((((............))))	chr11:115667985-115668222(-)$1	1	46	67	20.5991
((.(((...........))).	chr8:63391717-63391957(-)$1	1	169	190	18.2404
(((((.............)))	chrX:148326258-148326496(+)$1	1	121	142	19.3721
.((((..............))	chr19:10058581-10058825(+)$1	1	120	141	20.2451
.((((............))))	chr3:146395453-146395688(-)$1	1	60	81	19.5606
(((.(((..........))))	chr12:73675052-73675287(+)$1	1	105	126	12.7879
(((((..............))	chr1:75212189-75212442(-)$1	1	177	198	20.0378
((((.............))))	chr19:10058659-10058899(+)$1	1	65	86	17.1567
.(((.................	chr11:70483294-70483530(-)$1	1	87	108	16.2115
.(...............).))	chr19:7289793-7290030(-)$1	1	35	56	16.2776
(((((..............))	chr16:11134462-11134700(-)$1	1	58	79	19.9909
))(((.............)))	chr6:4591853-4592090(+)$1	1	70	91	20.1269
(((.(((..........))).	chr11:78335201-78335436(+)$1	1	51	72	12.9911
((((.............))))	chr11:72025341-72025578(-)$1	1	178	199	19.4987
((((((...........))))	chr2:181041364-181041632(-)$1	1	188	209	17.5110

#PSSM
e : 0.14	! : 0.12	[ : 0.10	g : 0.08	d : 0.08	f : 0.07	c : 0.07	^ : 0.07	: : 0.05	" : 0.05	= : 0.03	$ : 0.01	G : 0.01	D : 0.01	' : 0.01	# : 0.01	h : 0.01	
d : 0.28	c : 0.14	e : 0.12	g : 0.08	^ : 0.07	f : 0.05	= : 0.03	a : 0.03	" : 0.03	[ : 0.01	$ : 0.01	G : 0.01	D : 0.01	' : 0.01	b : 0.01	: : 0.01	h : 0.01	
d : 0.31	c : 0.24	e : 0.10	g : 0.07	^ : 0.07	f : 0.05	= : 0.03	x : 0.03	b : 0.01	" : 0.01	[ : 0.01	h : 0.01	
d : 0.28	c : 0.22	e : 0.10	^ : 0.07	g : 0.05	[ : 0.05	f : 0.05	x : 0.05	w : 0.03	b : 0.03	h : 0.01	= : 0.01	
d : 0.24	c : 0.21	^ : 0.14	e : 0.10	x : 0.07	g : 0.05	f : 0.05	w : 0.03	b : 0.03	v : 0.03	= : 0.01	
^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	c : 0.08	t : 0.08	d : 0.05	y : 0.05	g : 0.01	= : 0.01	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	c : 0.07	y : 0.05	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	s : 0.07	y : 0.05	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	s : 0.07	y : 0.05	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	s : 0.07	y : 0.05	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	s : 0.07	y : 0.05	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	s : 0.07	y : 0.05	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	s : 0.07	y : 0.05	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	s : 0.07	y : 0.05	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	s : 0.07	y : 0.05	
t : 0.19	^ : 0.19	v : 0.15	u : 0.14	w : 0.10	x : 0.08	s : 0.07	y : 0.05	
^ : 0.19	v : 0.15	u : 0.14	t : 0.10	w : 0.10	x : 0.08	s : 0.07	y : 0.05	e : 0.03	d : 0.01	c : 0.01	f : 0.01	
d : 0.21	c : 0.14	v : 0.12	^ : 0.12	w : 0.07	g : 0.05	x : 0.05	e : 0.05	f : 0.05	y : 0.05	a : 0.03	h : 0.01	= : 0.01	
d : 0.21	c : 0.19	^ : 0.12	e : 0.08	w : 0.07	g : 0.05	b : 0.05	f : 0.05	y : 0.05	x : 0.03	] : 0.03	h : 0.01	= : 0.01	
d : 0.28	c : 0.22	^ : 0.12	e : 0.08	g : 0.05	b : 0.05	f : 0.05	y : 0.05	x : 0.01	: : 0.01	h : 0.01	= : 0.01	
d : 0.28	e : 0.12	^ : 0.12	c : 0.12	] : 0.08	g : 0.07	f : 0.05	y : 0.05	C : 0.01	2 : 0.01	5 : 0.01	h : 0.01	= : 0.01	

#score	997.4902511627922
#seq	57
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_CDS_m3_run2.txt

#BEAR
}BB}CCC}DDDDFFFFFFf	chr9:107159263-107159531(-)$1	268	220	239	8.1196
}A}EEEEEYYBBYYEEEEE	chr5:108863235-108863508(-)$1	273	254	273	10.9915
FFYYEEEEEZZZDDDD:::	chr19:29086354-29086641(+)$1	287	198	217	9.2274
}BB}EEEEEEEEEEZZZDD	chr14:52760735-52761006(+)$1	271	222	241	9.2988
CCC}EEEEE}CCC}GGGGG	chr5:123244330-123244627(-)$1	297	182	201	11.4495
:BB}EEEEE}DDDDBBAZZ	chr3:108706698-108706973(-)$1	275	226	245	9.5363
BBBBYYCCC}AZZZJJJJJ	chr19:8964904-8965185(+)$1	281	137	156	8.6550
CCCYYEEEEEZZZGGGGGG	chr11:70466238-70466523(-)$1	285	182	201	10.5437
CCC}EEEEE}A}GGGGGGG	chr17:32498275-32498549(-)$1	274	163	182	11.1421
YYAYYFFFFFFYYEEEEED	chr13:73773754-73774025(+)$1	271	135	154	9.6182
}BB}EEEEEYYFFFFFF}C	chr3:95464619-95464908(+)$1	289	260	279	12.3863
BBYYEEEEECCCHHHHHHH	chrX:147007026-147007294(-)$1	268	161	180	10.6141
DDDD~~~~A}CCCFFFFFF	chr5:75006662-75006928(-)$1	266	217	236	9.5702
CCC}EEEEE}DDDDYYDDD	chr19:46681119-46681390(+)$1	271	229	248	9.6893
YYAYYDDDD~~~~A}IIII	chr5:92391562-92391834(-)$1	272	181	200	10.5671
::EEEEE}CCCYYEEEEE:	chr17:6084525-6084804(+)$1	279	258	277	8.6759
YBB}EEEEE}DDDD}BB::	chr1:93275013-93275289(-)$1	276	232	251	10.7131
CC~~~~CCC}CCC}DDDD}	chr6:51413984-51414268(-)$1	284	210	229	8.6290
EEEE}FFFFFFYYGGGGGG	chr1:77503123-77503392(-)$1	269	241	260	8.7190
GGG}DDDDZZZA}GGGGGG	chr5:93697524-93697808(+)$1	284	257	276	7.8045
YBB}EEEEEYYEEEEEYYB	chr8:74842841-74843113(+)$1	272	248	267	11.7370
YBB}EEEEE}AYYHHHHHH	chr10:79879360-79879636(-)$1	276	240	259	13.3689
EYYEEEEE?????GGGGGG	chr2:31615419-31615714(+)$1	295	266	285	8.9006
EEE}EEEEEZZZFFFFFF:	chr2:163884354-163884637(-)$1	283	262	281	12.0357
::EEEEEEEEEEFFFFFFY	chr18:36908130-36908409(+)$1	279	255	274	10.0477
DDDDEEEEE}AYYEEEEE~	chr11:102978351-102978633(+)$1	282	222	241	10.5559
~~~~FFFFFFZZZFFFFFF	chr8:95850590-95850858(-)$1	268	153	172	9.9057
EEEEYYEEEEEYYJJJJJJ	chr17:37114860-37115135(-)$1	275	168	187	9.9841
:BB}DDDDZZZIIIIIIII	chr9:97269861-97270130(-)$1	269	237	256	8.5205
FFFFFF}AYYCCCGGGGGG	chr11:120481895-120482204(-)$1	309	275	294	8.1581
EEE}EEEEE}CCCCCC:::	chr6:54767244-54767517(+)$1	273	68	87	9.5879
}BB}CCCZZZDDDD}GGGG	chr7:25670028-25670303(+)$1	275	247	266	8.7637
C}A}EEEEE}FFFFFF:::	chr11:117828707-117828977(-)$1	270	225	244	10.5802
:BB}EEEEE}BBYYCCC}C	chr2:156359444-156359715(+)$1	271	247	266	11.0756
EEEEEEEEEEEEEEE::::	chr9:64825922-64826205(+)$1	283	261	280	8.8875
FFFYYDDDD}FFFFFF}CC	chr2:34678076-34678352(-)$1	276	228	247	9.0469
IIII}ACCC}AYYA}FFFF	chr7:28151313-28151603(-)$1	290	162	181	9.0229
EEE}EEEEE}CCC}BBEEE	chr2:174125832-174126111(+)$1	279	252	271	11.1729
}BB}EEEEE}GGGGGGG??	chr8:63405926-63406223(-)$1	297	163	182	8.4299
:BBFFFFFF}AYYGGGGGG	chr12:85733283-85733552(-)$1	269	242	261	9.8032

#otherMatches

#Seq PSSM
AGGAUGUCAGUGACUGCCC	chr9:107159263-107159531(-)$1	268	220	239	8.1196
UGGGACUGCUGGCUGUGGU	chr5:108863235-108863508(-)$1	273	254	273	10.9915
AAAAGGGGGUAUUGAUUAC	chr19:29086354-29086641(+)$1	287	198	217	9.2274
AGUACUUUGUUUCCAUCUU	chr14:52760735-52761006(+)$1	271	222	241	9.2988
CCAACAGUCAGCACGCCCA	chr5:123244330-123244627(-)$1	297	182	201	11.4495
UGCACUCUGAGCUCCCCGU	chr3:108706698-108706973(-)$1	275	226	245	9.5363
ACAGCACUGAGAAAGAUUU	chr19:8964904-8965185(+)$1	281	137	156	8.6550
GAGCACCGGAGGAGCCCCC	chr11:70466238-70466523(-)$1	285	182	201	10.5437
GCUGAGGGGGGUGCUGGGG	chr17:32498275-32498549(-)$1	274	163	182	11.1421
CUGUACUGGGUAUGAAUGA	chr13:73773754-73774025(+)$1	271	135	154	9.6182
AGCAAAAAGAAAGUGGCUA	chr3:95464619-95464908(+)$1	289	260	279	12.3863
GGAUAGCUACCGCUACUUG	chrX:147007026-147007294(-)$1	268	161	180	10.6141
AGCUUCUAAGGUGAGGGCC	chr5:75006662-75006928(-)$1	266	217	236	9.5702
GCCUUGUUUUGUCAGCCAG	chr19:46681119-46681390(+)$1	271	229	248	9.6893
GACGACUUUAGAGGGUACC	chr5:92391562-92391834(-)$1	272	181	200	10.5671
AGCCCCUAACUGAUUUGGU	chr17:6084525-6084804(+)$1	279	258	277	8.6759
GACCCCCAAUGACAGGUAA	chr1:93275013-93275289(-)$1	276	232	251	10.7131
AUUGGGAAGUCAUGGAAGU	chr6:51413984-51414268(-)$1	284	210	229	8.6290
GCACGAGGAGCAGAAUGGU	chr1:77503123-77503392(-)$1	269	241	260	8.7190
GGAGGUAAAUUUGAGAAUU	chr5:93697524-93697808(+)$1	284	257	276	7.8045
ACCAGGCUACAGGGUGCAG	chr8:74842841-74843113(+)$1	272	248	267	11.7370
CGCACCACUGCAGAUCUAC	chr10:79879360-79879636(-)$1	276	240	259	13.3689
UGCCCUGUGUGUUCUAGGU	chr2:31615419-31615714(+)$1	295	266	285	8.9006
UUUUGGGGACUUGAGAGCA	chr2:163884354-163884637(-)$1	283	262	281	12.0357
GAUCCUAAGGCCUGUUUUC	chr18:36908130-36908409(+)$1	279	255	274	10.0477
GUCCCUCGUGCAGCCAGGU	chr11:102978351-102978633(+)$1	282	222	241	10.5559
UCAAUCCUUGCCUUUUUGG	chr8:95850590-95850858(-)$1	268	153	172	9.9057
UUCUCUGCCUUUAUCCUCC	chr17:37114860-37115135(-)$1	275	168	187	9.9841
UCGUUUGGCUAUGUUGGCU	chr9:97269861-97270130(-)$1	269	237	256	8.5205
GGAUUGAGCAUGUUGCUGG	chr11:120481895-120482204(-)$1	309	275	294	8.1581
GGCGGCCCGUACGGCUCAC	chr6:54767244-54767517(+)$1	273	68	87	9.5879
UGUGUCAUUAAUCCCUCUG	chr7:25670028-25670303(+)$1	275	247	266	8.7637
CAGAUUGGCUUCUUCCUCA	chr11:117828707-117828977(-)$1	270	225	244	10.5802
ACCAUUUGCAGAUGCCCAU	chr2:156359444-156359715(+)$1	271	247	266	11.0756
CUUCCCUUUCCUGCCAUAC	chr9:64825922-64826205(+)$1	283	261	280	8.8875
UGCCAGAGUGUAUGCACUU	chr2:34678076-34678352(-)$1	276	228	247	9.0469
AGUGGCUGCAGCAGAGUGA	chr7:28151313-28151603(-)$1	290	162	181	9.0229
ACCGCGGUGGGCUAGGGCC	chr2:174125832-174126111(+)$1	279	252	271	11.1729
GUAUGCCAUGGUUGGGGCU	chr8:63405926-63406223(-)$1	297	163	182	8.4299
AGGAGCCCGUCAGAGUGGC	chr12:85733283-85733552(-)$1	269	242	261	9.8032

#DB
.)).))).))))))))))(	chr9:107159263-107159531(-)$1	1	220	239	8.1196
.).)))))..))..)))))	chr5:108863235-108863508(-)$1	1	254	273	10.9915
))..)))))...))))...	chr19:29086354-29086641(+)$1	1	198	217	9.2274
.)).))))))))))...))	chr14:52760735-52761006(+)$1	1	222	241	9.2988
))).))))).))).)))))	chr5:123244330-123244627(-)$1	1	182	201	11.4495
.)).))))).)))))))..	chr3:108706698-108706973(-)$1	1	226	245	9.5363
))))..))).)...)))))	chr19:8964904-8965185(+)$1	1	137	156	8.6550
)))..)))))...))))))	chr11:70466238-70466523(-)$1	1	182	201	10.5437
))).))))).).)))))))	chr17:32498275-32498549(-)$1	1	163	182	11.1421
..)..))))))..))))))	chr13:73773754-73774025(+)$1	1	135	154	9.6182
.)).)))))..)))))).)	chr3:95464619-95464908(+)$1	1	260	279	12.3863
))..)))))))))))))))	chrX:147007026-147007294(-)$1	1	161	180	10.6141
))))....).)))))))))	chr5:75006662-75006928(-)$1	1	217	236	9.5702
))).))))).))))..)))	chr19:46681119-46681390(+)$1	1	229	248	9.6893
..)..))))....).))))	chr5:92391562-92391834(-)$1	1	181	200	10.5671
..))))).)))..))))).	chr17:6084525-6084804(+)$1	1	258	277	8.6759
.)).))))).)))).))..	chr1:93275013-93275289(-)$1	1	232	251	10.7131
))....))).))).)))).	chr6:51413984-51414268(-)$1	1	210	229	8.6290
)))).))))))..))))))	chr1:77503123-77503392(-)$1	1	241	260	8.7190
))).))))...).))))))	chr5:93697524-93697808(+)$1	1	257	276	7.8045
.)).)))))..)))))..)	chr8:74842841-74843113(+)$1	1	248	267	11.7370
.)).))))).)..))))))	chr10:79879360-79879636(-)$1	1	240	259	13.3689
)..))))).....))))))	chr2:31615419-31615714(+)$1	1	266	285	8.9006
))).)))))...)))))).	chr2:163884354-163884637(-)$1	1	262	281	12.0357
..)))))))))))))))).	chr18:36908130-36908409(+)$1	1	255	274	10.0477
))))))))).)..))))).	chr11:102978351-102978633(+)$1	1	222	241	10.5559
....))))))...))))))	chr8:95850590-95850858(-)$1	1	153	172	9.9057
))))..)))))..))))))	chr17:37114860-37115135(-)$1	1	168	187	9.9841
.)).))))...))))))))	chr9:97269861-97270130(-)$1	1	237	256	8.5205
)))))).)..)))))))))	chr11:120481895-120482204(-)$1	1	275	294	8.1581
))).))))).))))))...	chr6:54767244-54767517(+)$1	1	68	87	9.5879
.)).)))...)))).))))	chr7:25670028-25670303(+)$1	1	247	266	8.7637
).).))))).))))))...	chr11:117828707-117828977(-)$1	1	225	244	10.5802
.)).))))).))..))).)	chr2:156359444-156359715(+)$1	1	247	266	11.0756
)))))))))))))))....	chr9:64825922-64826205(+)$1	1	261	280	8.8875
)))..)))).)))))).))	chr2:34678076-34678352(-)$1	1	228	247	9.0469
)))).)))).)..).))))	chr7:28151313-28151603(-)$1	1	162	181	9.0229
))).))))).))).)))))	chr2:174125832-174126111(+)$1	1	252	271	11.1729
.)).))))).)))))))..	chr8:63405926-63406223(-)$1	1	163	182	8.4299
.)))))))).)..))))))	chr12:85733283-85733552(-)$1	1	242	261	9.8032

#PSSM
E : 0.17	} : 0.15	C : 0.15	: : 0.15	Y : 0.12	F : 0.07	B : 0.05	D : 0.05	G : 0.02	~ : 0.02	I : 0.02	
B : 0.35	E : 0.15	C : 0.12	F : 0.07	Y : 0.07	D : 0.05	: : 0.05	A : 0.02	G : 0.02	~ : 0.02	} : 0.02	I : 0.02	
B : 0.32	E : 0.19	C : 0.10	Y : 0.07	A : 0.07	D : 0.05	~ : 0.05	F : 0.05	} : 0.02	G : 0.02	I : 0.02	
} : 0.47	E : 0.17	Y : 0.15	D : 0.05	~ : 0.05	F : 0.05	B : 0.02	I : 0.02	
E : 0.57	Y : 0.15	F : 0.07	C : 0.05	~ : 0.05	} : 0.05	D : 0.05	
E : 0.60	F : 0.12	D : 0.10	C : 0.05	Y : 0.05	~ : 0.05	A : 0.02	
E : 0.62	C : 0.12	F : 0.10	D : 0.10	~ : 0.02	} : 0.02	
E : 0.60	F : 0.10	D : 0.10	C : 0.07	} : 0.05	~ : 0.02	A : 0.02	Z : 0.02	
E : 0.55	C : 0.10	F : 0.10	D : 0.07	Z : 0.07	Y : 0.05	A : 0.02	? : 0.02	
} : 0.45	Z : 0.12	E : 0.12	Y : 0.10	F : 0.07	C : 0.05	D : 0.02	~ : 0.02	? : 0.02	
C : 0.19	Z : 0.15	A : 0.15	D : 0.12	E : 0.10	F : 0.10	B : 0.05	Y : 0.05	~ : 0.02	? : 0.02	G : 0.02	
Y : 0.19	C : 0.17	D : 0.12	Z : 0.12	E : 0.10	F : 0.07	B : 0.05	} : 0.02	~ : 0.02	A : 0.02	? : 0.02	I : 0.02	G : 0.02	
Y : 0.24	F : 0.15	C : 0.15	D : 0.12	E : 0.07	Z : 0.07	G : 0.05	H : 0.02	~ : 0.02	} : 0.02	? : 0.02	I : 0.02	
F : 0.19	G : 0.19	E : 0.15	D : 0.12	} : 0.07	Y : 0.05	H : 0.05	A : 0.05	Z : 0.02	J : 0.02	I : 0.02	C : 0.02	
G : 0.22	F : 0.19	E : 0.15	} : 0.10	D : 0.05	B : 0.05	J : 0.05	H : 0.05	C : 0.05	Z : 0.02	Y : 0.02	I : 0.02	
G : 0.24	F : 0.22	E : 0.12	B : 0.07	D : 0.05	J : 0.05	H : 0.05	I : 0.05	C : 0.05	Z : 0.02	Y : 0.02	: : 0.02	
G : 0.24	F : 0.17	E : 0.12	: : 0.10	J : 0.05	H : 0.05	D : 0.05	I : 0.05	Z : 0.02	A : 0.02	B : 0.02	Y : 0.02	C : 0.02	} : 0.02	
G : 0.22	F : 0.15	E : 0.12	: : 0.12	D : 0.07	J : 0.05	} : 0.05	H : 0.05	I : 0.05	Z : 0.02	Y : 0.02	C : 0.02	? : 0.02	
G : 0.22	: : 0.17	D : 0.07	C : 0.07	F : 0.07	E : 0.05	J : 0.05	H : 0.05	I : 0.05	f : 0.02	Z : 0.02	} : 0.02	B : 0.02	Y : 0.02	~ : 0.02	? : 0.02	

#score	395.53732294065
#seq	40
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_CDS_m1_run1.txt

#BEAR
ggggggg"""ddddoooooodddd22ggggggg	chr6:113678312-113678549(-)$1	237	202	235	15.8025
]ccccccggggggg[ammmma]ggggggg]ccc	chr6:29402139-29402374(+)$1	235	193	226	10.3289
ccc[eeeee[a[cccmmmmccc]a]eeeee333	chr8:23678766-23679001(+)$1	235	47	80	10.5507
gggg[bb!!bbcccmmmmccc]bb22bb]gggg	chr14:37935173-37935433(-)$1	260	223	256	11.6554
iiiiiiiiffffffmmmmffffff333iiiiii	chr5:122941662-122941901(-)$1	239	95	128	11.5757
eggggggg[addddmmmmdddd]a]ggggggg]	chr4:126425743-126425995(-)$1	252	6	39	11.9562
======[a!!ddddoooooodddd22a======	chr13:55422845-55423080(-)$1	235	24	57	16.3076
iiiiiiii!!ddddoooooodddd22iiiiiii	chr2:121373570-121373818(-)$1	248	26	59	16.1549
cc[ccc[a[ccccccnnnnnccc]cccaccc]c	chr10:128243637-128243873(+)$1	236	187	220	11.9142
]==========333eeeee]dddd22ggggggg	chr7:26443554-26443792(-)$1	238	147	180	10.5040
:iiiiiiiii[cccooooooccc]iiiiiiiii	chr1:172771744-172771979(-)$1	235	12	45	14.4808
ccc[ccc!!ccc[bblllbb]ccc22ccccccb	chr11:109528792-109529029(+)$1	237	80	113	11.4024
iiiiiiiii[eeeeennnnneeeee]iiiiiii	chr13:11843033-11843270(-)$1	237	100	133	11.6974
e[ccc[bb[a[cccooooooccc]a]bbccc]e	chr1:43180304-43180550(-)$1	246	167	200	13.8031
ddd!!eeeee[cccooooooccc]eeeee22dd	chr7:50553444-50553683(-)$1	239	112	145	11.3302
[ggggggg"""cccmmmmcccggggggg333a]	chr2:156795708-156795945(-)$1	237	16	49	12.7920
dddd==========cccmmmmccc22=======	chr2:164824339-164824574(+)$1	235	108	141	11.2719
ccccc[bb!!ddddoooooodddd]bb]ccchh	chr14:55565114-55565368(-)$1	254	120	153	12.8004
eeeeea[ccc[cccooooooccc]ccc]a]eee	chr1:137747212-137747452(+)$1	240	58	91	12.3038
ffggggggg[bbccclllccc]bb333gggggg	chr19:57229539-57229774(-)$1	235	71	104	12.6606
a!!ccc####cccddddllldddd]ccc22ccc	chr5:122950679-122950926(-)$1	247	151	184	11.1697
======="""cccwwwwwwwwwwwwwwccc===	chr2:154519610-154519845(+)$1	235	52	85	9.7366
gggg!!dddd!!bblllbb]dddd22ggggggg	chr14:55566891-55567130(-)$1	239	38	71	11.1717
gggggggeeeee[ammmma]eeeee]ggggggg	chr2:76648356-76648591(-)$1	235	158	191	11.0813
ggggg!!a####cccnnnnnccc4444a22ggg	chr15:100233580-100233815(-)$1	235	81	114	13.3673
d"""dddd"""cccooooooccc4444dddd55	chr11:115940745-115940980(-)$1	235	107	140	11.6362

#otherMatches

#Seq PSSM
GUGACAGCACAGGCAGCCUGGCCUUCCUGUUAC	chr6:113678312-113678549(-)$1	237	202	235	15.8025
AUCCGCUUUGGGGGCGAACACAUCCCCAACAGC	chr6:29402139-29402374(+)$1	235	193	226	10.3289
GCCCGUGGCUGGACUCUUCAGUGCUGCUAUCAU	chr8:23678766-23679001(+)$1	235	47	80	10.5507
GUUUAAAAUGUGCAGUAAUGCGACCCUUCAGGC	chr14:37935173-37935433(-)$1	260	223	256	11.6554
UUUUCCUUUUAGGUUUUGGCUUGGUUCGAGGAA	chr5:122941662-122941901(-)$1	239	95	128	11.5757
GUUUCACUGGGGUCUUGUGACCACAGGUGGGGC	chr4:126425743-126425995(-)$1	252	6	39	11.9562
GGCCGCGCGGACCCUGAAGUGGGUGAGGCGGCC	chr13:55422845-55423080(-)$1	235	24	57	16.3076
UUUGUUUGUUUUUGUUUUUUCAAAUCUGAGCAG	chr2:121373570-121373818(-)$1	248	26	59	16.1549
GUGUCCAGUGGAAAGAAACCCUUGUCCCGGAGG	chr10:128243637-128243873(+)$1	236	187	220	11.9142
AUCUGAGCCCCACGGGGUCUUUCUUAGGGAGAA	chr7:26443554-26443792(-)$1	238	147	180	10.5040
UUAAUUUUUUGUGUUUCACUGCAGGAGGAGUUG	chr1:172771744-172771979(-)$1	235	12	45	14.4808
GGAACAUCCAGCAGUACAACAGCUUCGUGUCCC	chr11:109528792-109529029(+)$1	237	80	113	11.4024
AAGUCGGUGGCGGGAGGGCUUCCUGGUGCCGGC	chr13:11843033-11843270(-)$1	237	100	133	11.6974
UCCUGACUGUGGAAAGGAUAUUUGAAGGCGGCA	chr1:43180304-43180550(-)$1	246	167	200	13.8031
uuucugugggaaguccuuuugcucuccaucuga	chr7:50553444-50553683(-)$1	239	112	145	11.3302
UCGUGUUUCCAAUGCCAGCGUAAGCAUGUUUCC	chr2:156795708-156795945(-)$1	237	16	49	12.7920
GCCAGUGGCAGGGCUGGAGGGCCACUGCCCUGU	chr2:164824339-164824574(+)$1	235	108	141	11.2719
GAGCUGCGGGCUGUGGUGGAGCAGACGGAGCGG	chr14:55565114-55565368(-)$1	254	120	153	12.8004
CUCACCAUCCCCUUCAGACAGAGCGGAAGAGUG	chr1:137747212-137747452(+)$1	240	58	91	12.3038
GAGGUGGUAACUGCCCUGGGCAAGACCUACCAC	chr19:57229539-57229774(-)$1	235	71	104	12.6606
GUUAGAAUUUUACUGCUGGCAGCAUGUAUAUCU	chr5:122950679-122950926(-)$1	247	151	184	11.1697
UUUUUCUGUAUCCACAGCCAAGAAGAAGGAAGA	chr2:154519610-154519845(+)$1	235	52	85	9.7366
AAGGGAAGUGGGGCAAGGCAUAUUGAUCUUUCU	chr14:55566891-55567130(-)$1	239	38	71	11.1717
UCAUCAAGGAUGGCACCAGGCAUUCAUUGGUGA	chr2:76648356-76648591(-)$1	235	158	191	11.0813
CGGGAAGCCAAUAAGUACUUCUUCAUCGAGUCC	chr15:100233580-100233815(-)$1	235	81	114	13.3673
ACAAGAAGACCCAGUAGACCCUGCCCACUUCCC	chr11:115940745-115940980(-)$1	235	107	140	11.6362

#DB
(((((((...((((......))))..)))))))	chr6:113678312-113678549(-)$1	1	202	235	15.8025
.)))((((((((((.(....).))))))).)))	chr6:29402139-29402374(+)$1	1	193	226	10.3289
(((.(((((.(.(((....))).).)))))...	chr8:23678766-23679001(+)$1	1	47	80	10.5507
((((.((..(((((....))).))..)).))))	chr14:37935173-37935433(-)$1	1	223	256	11.6554
((((((((((((((....))))))...))))))	chr5:122941662-122941901(-)$1	1	95	128	11.5757
((((((((.(((((....)))).).))))))).	chr4:126425743-126425995(-)$1	1	6	39	11.9562
((((((.(..((((......))))..)))))))	chr13:55422845-55423080(-)$1	1	24	57	16.3076
((((((((..((((......))))..)))))))	chr2:121373570-121373818(-)$1	1	26	59	16.1549
((.(((.(.((((((.....))).))))))).)	chr10:128243637-128243873(+)$1	1	187	220	11.9142
.))))))))))...))))).))))..)))))))	chr7:26443554-26443792(-)$1	1	147	180	10.5040
.(((((((((.(((......))).)))))))))	chr1:172771744-172771979(-)$1	1	12	45	14.4808
(((.(((..(((.((...)).)))..)))))))	chr11:109528792-109529029(+)$1	1	80	113	11.4024
(((((((((.(((((.....))))).)))))))	chr13:11843033-11843270(-)$1	1	100	133	11.6974
(.(((.((.(.(((......))).).))))).)	chr1:43180304-43180550(-)$1	1	167	200	13.8031
(((..(((((.(((......))).)))))..))	chr7:50553444-50553683(-)$1	1	112	145	11.3302
.(((((((...(((....))))))))))...).	chr2:156795708-156795945(-)$1	1	16	49	12.7920
(((((((((((((((((....)))..)))))))	chr2:164824339-164824574(+)$1	1	108	141	11.2719
))(((.((..((((......)))).)).)))((	chr14:55565114-55565368(-)$1	1	120	153	12.8004
((((((.(((.(((......))).))).).)))	chr1:137747212-137747452(+)$1	1	58	91	12.3038
(((((((((.(((((...))).))...))))))	chr19:57229539-57229774(-)$1	1	71	104	12.6606
(..(((....(((((((...)))).)))..)))	chr5:122950679-122950926(-)$1	1	151	184	11.1697
(((((((...(((..............))))))	chr2:154519610-154519845(+)$1	1	52	85	9.7366
((((..((((..((...)).))))..)))))))	chr14:55566891-55567130(-)$1	1	38	71	11.1717
((((((((((((.(....).))))).)))))))	chr2:76648356-76648591(-)$1	1	158	191	11.0813
(((((..(....(((.....)))....)..)))	chr15:100233580-100233815(-)$1	1	81	114	13.3673
(...((((...(((......)))....))))..	chr11:115940745-115940980(-)$1	1	107	140	11.6362

#PSSM
g : 0.19	c : 0.15	i : 0.11	e : 0.11	d : 0.11	] : 0.07	= : 0.07	: : 0.03	[ : 0.03	f : 0.03	a : 0.03	
g : 0.26	c : 0.19	i : 0.15	= : 0.11	d : 0.07	[ : 0.03	e : 0.03	f : 0.03	! : 0.03	" : 0.03	
g : 0.30	c : 0.19	i : 0.15	= : 0.11	d : 0.07	[ : 0.03	e : 0.03	! : 0.03	" : 0.03	
g : 0.30	c : 0.19	i : 0.15	= : 0.11	[ : 0.07	! : 0.03	d : 0.03	e : 0.03	" : 0.03	
g : 0.23	c : 0.23	i : 0.15	= : 0.15	e : 0.07	! : 0.07	[ : 0.03	d : 0.03	
g : 0.19	c : 0.15	i : 0.15	= : 0.15	e : 0.07	[ : 0.07	! : 0.07	b : 0.03	a : 0.03	d : 0.03	
g : 0.19	i : 0.15	b : 0.11	[ : 0.11	= : 0.11	c : 0.07	e : 0.07	d : 0.07	# : 0.03	! : 0.03	
g : 0.15	i : 0.15	e : 0.11	a : 0.11	" : 0.07	! : 0.07	= : 0.07	b : 0.07	d : 0.07	c : 0.03	# : 0.03	
! : 0.19	" : 0.15	e : 0.11	[ : 0.11	g : 0.07	= : 0.07	i : 0.07	# : 0.07	f : 0.03	c : 0.03	d : 0.03	
" : 0.15	[ : 0.11	! : 0.11	c : 0.11	a : 0.07	= : 0.07	e : 0.07	# : 0.07	g : 0.03	b : 0.03	f : 0.03	i : 0.03	d : 0.03	
d : 0.19	c : 0.15	[ : 0.15	b : 0.07	= : 0.07	e : 0.07	" : 0.07	g : 0.03	a : 0.03	f : 0.03	! : 0.03	# : 0.03	
c : 0.42	d : 0.19	e : 0.07	g : 0.03	[ : 0.03	f : 0.03	3 : 0.03	= : 0.03	b : 0.03	! : 0.03	# : 0.03	
c : 0.49	d : 0.19	[ : 0.07	g : 0.03	f : 0.03	3 : 0.03	e : 0.03	= : 0.03	b : 0.03	
c : 0.42	d : 0.23	b : 0.07	g : 0.03	f : 0.03	3 : 0.03	e : 0.03	= : 0.03	w : 0.03	a : 0.03	
o : 0.34	c : 0.19	m : 0.19	e : 0.07	[ : 0.03	b : 0.03	d : 0.03	w : 0.03	l : 0.03	
o : 0.34	m : 0.23	n : 0.11	l : 0.11	a : 0.03	e : 0.03	c : 0.03	d : 0.03	w : 0.03	
o : 0.34	m : 0.26	n : 0.11	l : 0.11	e : 0.03	c : 0.03	d : 0.03	w : 0.03	
o : 0.34	m : 0.30	n : 0.11	l : 0.11	e : 0.03	w : 0.03	b : 0.03	
o : 0.34	m : 0.11	c : 0.11	n : 0.11	b : 0.07	f : 0.03	d : 0.03	e : 0.03	l : 0.03	w : 0.03	a : 0.03	
o : 0.34	c : 0.15	n : 0.11	] : 0.11	m : 0.07	f : 0.03	d : 0.03	b : 0.03	l : 0.03	w : 0.03	
c : 0.42	d : 0.30	e : 0.07	a : 0.03	f : 0.03	] : 0.03	m : 0.03	w : 0.03	
c : 0.38	d : 0.30	] : 0.11	e : 0.07	f : 0.03	g : 0.03	w : 0.03	
c : 0.34	d : 0.26	g : 0.07	] : 0.07	b : 0.07	e : 0.07	f : 0.03	w : 0.03	
d : 0.26	] : 0.19	g : 0.07	a : 0.07	b : 0.07	c : 0.07	e : 0.07	4 : 0.07	f : 0.03	w : 0.03	
2 : 0.30	] : 0.15	e : 0.11	g : 0.07	3 : 0.07	c : 0.07	4 : 0.07	i : 0.03	a : 0.03	w : 0.03	
2 : 0.30	g : 0.11	c : 0.11	] : 0.11	e : 0.07	3 : 0.07	4 : 0.07	i : 0.03	b : 0.03	w : 0.03	
g : 0.26	c : 0.15	b : 0.11	i : 0.11	e : 0.07	3 : 0.07	4 : 0.07	a : 0.03	= : 0.03	w : 0.03	
g : 0.30	i : 0.15	c : 0.11	e : 0.07	b : 0.07	= : 0.07	a : 0.07	] : 0.07	d : 0.03	
g : 0.26	c : 0.19	i : 0.15	e : 0.07	= : 0.07	2 : 0.07	] : 0.03	3 : 0.03	a : 0.03	d : 0.03	
g : 0.26	c : 0.19	i : 0.15	2 : 0.11	] : 0.07	= : 0.07	e : 0.03	3 : 0.03	d : 0.03	
g : 0.30	c : 0.23	i : 0.15	= : 0.11	3 : 0.07	2 : 0.03	e : 0.03	d : 0.03	
g : 0.30	i : 0.15	c : 0.11	= : 0.11	] : 0.07	3 : 0.03	d : 0.03	a : 0.03	h : 0.03	e : 0.03	5 : 0.03	
g : 0.26	i : 0.15	c : 0.11	= : 0.11	] : 0.07	e : 0.07	3 : 0.03	b : 0.03	d : 0.03	h : 0.03	5 : 0.03	

#score	319.45693940445
#seq	26
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_transcript_m3_run2.txt

#BEAR
eeeeeooooooeeeee:	chrX:35550059-35550260(+)$1	201	24	41	9.6837
""cccooooooccc444	chr2:102628349-102628550(+)$1	201	79	96	12.2190
b[cccooooooccc]bb	chr12:37297529-37297730(+)$1	201	54	71	11.6222
eeeeeooooooeeeee3	chr14:124475150-124475351(-)$1	201	157	174	10.6968
ff!!aooooooa22fff	chr11:51931425-51931626(+)$1	201	150	167	10.2490
ddddoooooodddd]a3	chr10:111835816-111836017(+)$1	201	27	44	9.1431
b!!bboooooobb22bb	chr9:34320917-34321118(+)$1	201	28	45	9.6033
bddddoooooodddd22	chr5:9475569-9475770(-)$1	201	179	196	10.0079
gggggoooooogggggg	chr4:109886332-109886533(-)$1	201	47	64	11.2259
dd[bboooooobb22dd	chr4:70094272-70094473(-)$1	201	170	187	9.5547
d[cccoooooocccddd	chr8:97974618-97974819(-)$1	201	144	161	11.4694
""cccooooooccc]cc	chrX:92259225-92259426(-)$1	201	118	135	12.3271
fffffooooooffffff	chr15:92170414-92170615(+)$1	201	43	60	10.4941
eeeeeooooooeeeee:	chr7:4779206-4779407(-)$1	201	72	89	9.6837
h[cccooooooccchhh	chr6:124966972-124967173(+)$1	201	36	53	11.1595
eeeeeooooooeeeee]	chr6:45303747-45303948(+)$1	201	150	167	10.6343
fffffooooooffffff	chr17:90470222-90470423(-)$1	201	130	147	10.4941
"""bboooooobb]eee	chr14:31853768-31853969(+)$1	201	134	151	10.3171
$$cccooooooccc333	chr16:96242655-96242856(-)$1	201	163	180	12.0856
iiiiiooooooiiiiii	chr14:125035840-125036041(-)$1	201	162	179	11.0307
eeeeeooooooeeeee]	chr5:132636804-132637005(-)$1	201	103	120	10.6343
ddcccooooooccc]dd	chr8:68757310-68757511(+)$1	201	18	35	11.6030
""cccooooooccc444	chr2:104849255-104849456(-)$1	201	165	182	12.2190
c[cccooooooccc]cc	chr12:100060284-100060485(-)$1	201	182	199	12.2763
gggggoooooogggggg	chr5:118699237-118699438(+)$1	201	144	161	11.2259
"""bboooooobb333e	chr1:172255662-172255863(-)$1	201	91	108	10.7059
gggggoooooogggggg	chr6:80231164-80231365(+)$1	201	2	19	11.2259
a[cccooooooccc]a]	chr5:18867413-18867614(+)$1	201	46	63	12.3913
$ddddoooooodddd33	chr10:121220663-121220864(-)$1	201	43	60	10.5665
!!cccooooooccc]ee	chr1:82748253-82748454(+)$1	201	114	131	12.4247
dddddoooooodddd22	chr9:43855425-43855626(+)$1	201	94	111	10.0801
e[cccooooooccc]ee	chr9:52485033-52485234(-)$1	201	54	71	12.2229
!!cccoooooocccccc	chr8:96492922-96493123(+)$1	201	140	157	12.0797
gggggoooooogggggg	chr3:136566059-136566260(+)$1	201	3	20	11.2259
eee[aooooooa]eeee	chr19:43806706-43806907(+)$1	201	116	133	10.6237
!!cccooooooccc22e	chr9:14108500-14108701(+)$1	201	150	167	12.0055
c!!bboooooobbccc:	chr6:108751091-108751292(+)$1	201	2	19	9.7203
!!cccooooooccc444	chr19:58870275-58870476(-)$1	201	80	97	12.3450
ddcccooooooccc]dd	chr5:68186859-68187060(-)$1	201	131	148	11.6030
fffffooooooffffff	chr6:12265894-12266095(-)$1	201	161	178	10.4941
gggggoooooogggggg	chr2:29886490-29886691(+)$1	201	37	54	11.2259
cccccooooooccc333	chr11:97607315-97607516(-)$1	201	48	65	12.2266
fffffooooooffffff	chr2:19927213-19927414(+)$1	201	10	27	10.4941
bb!!aooooooa22bb]	chr5:49667400-49667601(-)$1	201	129	146	9.4026
gggggoooooogggggg	chr5:77428190-77428391(+)$1	201	168	185	11.2259
::cccoooooocccfff	chr10:76756818-76757019(-)$1	201	1	18	9.8051
c[cccooooooccc]cc	chr10:80644947-80645148(+)$1	201	51	68	12.2763
bbcccooooooccc]bb	chr8:34524868-34525069(+)$1	201	160	177	11.1127
eeeeeooooooeeeee5	chr16:44085559-44085760(-)$1	201	168	185	9.8652
ffcccooooooccc]ff	chr9:56327517-56327718(+)$1	201	112	129	11.9467
ffcccooooooccc]ff	chr2:44436219-44436420(-)$1	201	115	132	11.9467
fffffooooooffffff	chr6:42266240-42266441(-)$1	201	51	68	10.4941
eeeeaooooooa]eeee	chr2:77267061-77267262(-)$1	201	76	93	10.6067
!ddddoooooodddd]d	chrX:40513245-40513446(-)$1	201	173	190	10.3947
gggggoooooogggggg	chr4:8534168-8534369(+)$1	201	166	183	11.2259
fffffooooooffffff	chr1:59037515-59037716(+)$1	201	173	190	10.4941
eeeeeooooooeeeee:	chr7:117117257-117117458(-)$1	201	119	136	9.6837
[ddddoooooodddd22	chr8:128901377-128901578(+)$1	201	33	50	10.3070
cccccooooooccc]cc	chr8:4289368-4289569(-)$1	201	166	183	12.0208
%ddddooooooddddff	chr15:63800859-63801060(-)$1	201	143	160	9.8043
!!cccooooooccc]ee	chr3:55930208-55930409(-)$1	201	51	68	12.4247

#otherMatches

#Seq PSSM
AUGAAACCUUGUUCAUU	chrX:35550059-35550260(+)$1	201	24	41	9.6837
UAGCUAAUUAGAGCACA	chr2:102628349-102628550(+)$1	201	79	96	12.2190
GAUUAUAUUGCUAGCCU	chr12:37297529-37297730(+)$1	201	54	71	11.6222
ccauugaugaaaguggu	chr14:124475150-124475351(-)$1	201	157	174	10.6968
UUAAGGAAAUACGGAAA	chr11:51931425-51931626(+)$1	201	150	167	10.2490
AUGCUGUUAUGCAUGAU	chr10:111835816-111836017(+)$1	201	27	44	9.1431
ACUGGAAGCUACCCUUG	chr9:34320917-34321118(+)$1	201	28	45	9.6033
cucagacacugcugaua	chr5:9475569-9475770(-)$1	201	179	196	10.0079
GUGACAACAAGGUCACA	chr4:109886332-109886533(-)$1	201	47	64	11.2259
GUACCAAAAUCGGAAAC	chr4:70094272-70094473(-)$1	201	170	187	9.5547
UGCCUAUGACAAGGACU	chr8:97974618-97974819(-)$1	201	144	161	11.4694
UAGCAAUAUAAUGCAUU	chrX:92259225-92259426(-)$1	201	118	135	12.3271
GCCUAUAUGUUUGGGUU	chr15:92170414-92170615(+)$1	201	43	60	10.4941
GAGUCUCUCGUGACUCC	chr7:4779206-4779407(-)$1	201	72	89	9.6837
aucuugccccaaagucc	chr6:124966972-124967173(+)$1	201	36	53	11.1595
AAAUAAAAUGAUGUUUG	chr6:45303747-45303948(+)$1	201	150	167	10.6343
gugaaaauaacuuuacu	chr17:90470222-90470423(-)$1	201	130	147	10.4941
ucuacuuuucugucugu	chr14:31853768-31853969(+)$1	201	134	151	10.3171
AACCUCGUUAAAGGAAU	chr16:96242655-96242856(-)$1	201	163	180	12.0856
GUGUGUAACUUUACACU	chr14:125035840-125036041(-)$1	201	162	179	11.0307
CACAGAGCAAGCUGUGC	chr5:132636804-132637005(-)$1	201	103	120	10.6343
cugauauuuaaaucuag	chr8:68757310-68757511(+)$1	201	18	35	11.6030
UCUGUCUGCAAACAUCA	chr2:104849255-104849456(-)$1	201	165	182	12.2190
UUUCACAGACAUGAUAA	chr12:100060284-100060485(-)$1	201	182	199	12.2763
GUCCUUUUCUUAGGACU	chr5:118699237-118699438(+)$1	201	144	161	11.2259
CCAGAUUCAUUUCACAA	chr1:172255662-172255863(-)$1	201	91	108	10.7059
uuggggguuagccuggg	chr6:80231164-80231365(+)$1	201	2	19	11.2259
uguccuucacuggaggu	chr5:18867413-18867614(+)$1	201	46	63	12.3913
AUUCCACUGCAGGAAAA	chr10:121220663-121220864(-)$1	201	43	60	10.5665
UUUGCAUCAUCGUAUGA	chr1:82748253-82748454(+)$1	201	114	131	12.4247
UUCAUUUCUCUGUGACU	chr9:43855425-43855626(+)$1	201	94	111	10.0801
CCAGAAAAACGUUUAGG	chr9:52485033-52485234(-)$1	201	54	71	12.2229
AUUUCAAUAAAGGAGGC	chr8:96492922-96493123(+)$1	201	140	157	12.0797
UUAGCUGCAGUGUUGAA	chr3:136566059-136566260(+)$1	201	3	20	11.2259
AUAGCUGUCUUGGUGUG	chr19:43806706-43806907(+)$1	201	116	133	10.6237
CUGAAUCCAUUUUCUAG	chr9:14108500-14108701(+)$1	201	150	167	12.0055
cauccucacuugggccc	chr6:108751091-108751292(+)$1	201	2	19	9.7203
AUGGAACAAUAUCCUAA	chr19:58870275-58870476(-)$1	201	80	97	12.3450
GCCAGUUGACUCUGUGU	chr5:68186859-68187060(-)$1	201	131	148	11.6030
GAUAAAUAAUCUUGUCC	chr6:12265894-12266095(-)$1	201	161	178	10.4941
ACAUGAAGCCCUAUGUG	chr2:29886490-29886691(+)$1	201	37	54	11.2259
CCUCAUUUGUUUGACCA	chr11:97607315-97607516(-)$1	201	48	65	12.2266
uauauuuccuuguguga	chr2:19927213-19927414(+)$1	201	10	27	10.4941
GCUUUGUGUCGAUUGCC	chr5:49667400-49667601(-)$1	201	129	146	9.4026
GAGAUCAUCAUAUUUCU	chr5:77428190-77428391(+)$1	201	168	185	11.2259
AUGUGAAAGAGCACGAG	chr10:76756818-76757019(-)$1	201	1	18	9.8051
GGCUGGACUGGCAGGCU	chr10:80644947-80645148(+)$1	201	51	68	12.2763
UGGCCCCAUUUGGCACA	chr8:34524868-34525069(+)$1	201	160	177	11.1127
AAGAUUUCACUAUCUUU	chr16:44085559-44085760(-)$1	201	168	185	9.8652
GACAUUCCCUCGUGAUU	chr9:56327517-56327718(+)$1	201	112	129	11.9467
CAUGUCACACUGCACUG	chr2:44436219-44436420(-)$1	201	115	132	11.9467
AGGGUCUCUUUGCCUUG	chr6:42266240-42266441(-)$1	201	51	68	10.4941
gaaucuguuguguauuc	chr2:77267061-77267262(-)$1	201	76	93	10.6067
uguuucaguuuagacuu	chrX:40513245-40513446(-)$1	201	173	190	10.3947
GUUAACCUGUUUUAAUG	chr4:8534168-8534369(+)$1	201	166	183	11.2259
GUGUUUCUUCCAGCAUA	chr1:59037515-59037716(+)$1	201	173	190	10.4941
GCGAUUGCUCUGUUGCC	chr7:117117257-117117458(-)$1	201	119	136	9.6837
UGGAGCUCUGUCUCCUC	chr8:128901377-128901578(+)$1	201	33	50	10.3070
GACAUGUUCAAAUGCUU	chr8:4289368-4289569(-)$1	201	166	183	12.0208
UAGACAUUGCAGUCUCU	chr15:63800859-63801060(-)$1	201	143	160	9.8043
aggugaaucaauacaug	chr3:55930208-55930409(-)$1	201	51	68	12.4247

#DB
(((((......))))).	chrX:35550059-35550260(+)$1	1	24	41	9.6837
..(((......)))...	chr2:102628349-102628550(+)$1	1	79	96	12.2190
(.(((......))).))	chr12:37297529-37297730(+)$1	1	54	71	11.6222
(((((......))))).	chr14:124475150-124475351(-)$1	1	157	174	10.6968
((..(......)..)))	chr11:51931425-51931626(+)$1	1	150	167	10.2490
((((......)))).).	chr10:111835816-111836017(+)$1	1	27	44	9.1431
(..((......))..))	chr9:34320917-34321118(+)$1	1	28	45	9.6033
(((((......))))..	chr5:9475569-9475770(-)$1	1	179	196	10.0079
(((((......))))))	chr4:109886332-109886533(-)$1	1	47	64	11.2259
((.((......))..))	chr4:70094272-70094473(-)$1	1	170	187	9.5547
(.(((......))))))	chr8:97974618-97974819(-)$1	1	144	161	11.4694
..(((......))).))	chrX:92259225-92259426(-)$1	1	118	135	12.3271
(((((......))))))	chr15:92170414-92170615(+)$1	1	43	60	10.4941
(((((......))))).	chr7:4779206-4779407(-)$1	1	72	89	9.6837
(.(((......))))))	chr6:124966972-124967173(+)$1	1	36	53	11.1595
(((((......))))).	chr6:45303747-45303948(+)$1	1	150	167	10.6343
(((((......))))))	chr17:90470222-90470423(-)$1	1	130	147	10.4941
...((......)).)))	chr14:31853768-31853969(+)$1	1	134	151	10.3171
..(((......)))...	chr16:96242655-96242856(-)$1	1	163	180	12.0856
(((((......))))))	chr14:125035840-125036041(-)$1	1	162	179	11.0307
(((((......))))).	chr5:132636804-132637005(-)$1	1	103	120	10.6343
(((((......))).))	chr8:68757310-68757511(+)$1	1	18	35	11.6030
..(((......)))...	chr2:104849255-104849456(-)$1	1	165	182	12.2190
(.(((......))).))	chr12:100060284-100060485(-)$1	1	182	199	12.2763
(((((......))))))	chr5:118699237-118699438(+)$1	1	144	161	11.2259
...((......))...)	chr1:172255662-172255863(-)$1	1	91	108	10.7059
(((((......))))))	chr6:80231164-80231365(+)$1	1	2	19	11.2259
(.(((......))).).	chr5:18867413-18867614(+)$1	1	46	63	12.3913
.((((......))))..	chr10:121220663-121220864(-)$1	1	43	60	10.5665
..(((......))).))	chr1:82748253-82748454(+)$1	1	114	131	12.4247
(((((......))))..	chr9:43855425-43855626(+)$1	1	94	111	10.0801
(.(((......))).))	chr9:52485033-52485234(-)$1	1	54	71	12.2229
..(((......))))))	chr8:96492922-96493123(+)$1	1	140	157	12.0797
(((((......))))))	chr3:136566059-136566260(+)$1	1	3	20	11.2259
(((.(......).))))	chr19:43806706-43806907(+)$1	1	116	133	10.6237
..(((......)))..)	chr9:14108500-14108701(+)$1	1	150	167	12.0055
(..((......))))).	chr6:108751091-108751292(+)$1	1	2	19	9.7203
..(((......)))...	chr19:58870275-58870476(-)$1	1	80	97	12.3450
(((((......))).))	chr5:68186859-68187060(-)$1	1	131	148	11.6030
(((((......))))))	chr6:12265894-12266095(-)$1	1	161	178	10.4941
(((((......))))))	chr2:29886490-29886691(+)$1	1	37	54	11.2259
(((((......)))...	chr11:97607315-97607516(-)$1	1	48	65	12.2266
(((((......))))))	chr2:19927213-19927414(+)$1	1	10	27	10.4941
((..(......)..)).	chr5:49667400-49667601(-)$1	1	129	146	9.4026
(((((......))))))	chr5:77428190-77428391(+)$1	1	168	185	11.2259
..(((......)))(((	chr10:76756818-76757019(-)$1	1	1	18	9.8051
(.(((......))).))	chr10:80644947-80645148(+)$1	1	51	68	12.2763
(((((......))).))	chr8:34524868-34525069(+)$1	1	160	177	11.1127
(((((......))))).	chr16:44085559-44085760(-)$1	1	168	185	9.8652
(((((......))).))	chr9:56327517-56327718(+)$1	1	112	129	11.9467
(((((......))).))	chr2:44436219-44436420(-)$1	1	115	132	11.9467
(((((......))))))	chr6:42266240-42266441(-)$1	1	51	68	10.4941
(((((......).))))	chr2:77267061-77267262(-)$1	1	76	93	10.6067
.((((......)))).)	chrX:40513245-40513446(-)$1	1	173	190	10.3947
(((((......))))))	chr4:8534168-8534369(+)$1	1	166	183	11.2259
(((((......))))))	chr1:59037515-59037716(+)$1	1	173	190	10.4941
(((((......))))).	chr7:117117257-117117458(-)$1	1	119	136	9.6837
.((((......))))..	chr8:128901377-128901578(+)$1	1	33	50	10.3070
(((((......))).))	chr8:4289368-4289569(-)$1	1	166	183	12.0208
.((((......))))))	chr15:63800859-63801060(-)$1	1	143	160	9.8043
..(((......))).))	chr3:55930208-55930409(-)$1	1	51	68	12.4247

#PSSM
e : 0.16	f : 0.14	g : 0.11	d : 0.09	! : 0.09	" : 0.08	b : 0.08	c : 0.08	$ : 0.03	h : 0.01	i : 0.01	a : 0.01	: : 0.01	[ : 0.01	% : 0.01	
d : 0.16	e : 0.14	f : 0.14	[ : 0.11	! : 0.11	g : 0.11	" : 0.08	c : 0.03	b : 0.03	$ : 0.01	i : 0.01	: : 0.01	
c : 0.39	e : 0.14	d : 0.11	g : 0.11	f : 0.09	! : 0.06	" : 0.03	[ : 0.01	i : 0.01	
c : 0.39	e : 0.13	d : 0.11	g : 0.11	f : 0.09	b : 0.08	! : 0.03	i : 0.01	[ : 0.01	
c : 0.39	e : 0.11	g : 0.11	d : 0.09	f : 0.09	b : 0.08	a : 0.06	o : 0.01	i : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 0.98	d : 0.01	
c : 0.39	e : 0.11	d : 0.11	g : 0.11	f : 0.09	b : 0.08	a : 0.06	i : 0.01	
c : 0.39	e : 0.11	d : 0.11	g : 0.11	f : 0.09	b : 0.08	2 : 0.03	] : 0.03	i : 0.01	
c : 0.40	e : 0.14	d : 0.11	g : 0.11	f : 0.09	2 : 0.06	] : 0.01	i : 0.01	3 : 0.01	
] : 0.24	e : 0.16	f : 0.13	d : 0.11	g : 0.11	4 : 0.04	2 : 0.04	3 : 0.04	c : 0.03	h : 0.01	i : 0.01	b : 0.01	
e : 0.21	f : 0.18	g : 0.11	c : 0.09	b : 0.06	2 : 0.06	d : 0.06	3 : 0.06	4 : 0.04	a : 0.03	h : 0.01	i : 0.01	] : 0.01	
f : 0.18	e : 0.13	g : 0.11	3 : 0.08	d : 0.08	c : 0.08	: : 0.06	] : 0.06	4 : 0.04	b : 0.04	2 : 0.04	h : 0.01	i : 0.01	5 : 0.01	

#score	670.3607883373344
#seq	61
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_UTR_m3_run2.txt

#BEAR
[ffffffbbqqqqqqqqbb]fffff	chr4:34035605-34035842(+)$1	237	205	230	15.1558
"dddd!!bbqqqqqqqqbb22dddd	chr1:179693655-179693886(-)$1	231	21	46	14.3766
eeeee[cccqqqqqqqqccc22eee	chr4:154932870-154933122(+)$1	252	67	92	15.2890
!eeeee[bbqqqqqqqqbbeeeee2	chr15:81149437-81149690(-)$1	253	63	88	15.1554
d[gggggggqqqqqqqqggggggg2	chr1:183106021-183106270(-)$1	249	136	161	16.2708
hdddd[cccqqqqqqqqccc]dddd	chr6:107519540-107519785(+)$1	245	27	52	15.0127
!!cccddddqqqqqqqqdddd8888	chr9:66803104-66803336(-)$1	232	16	41	14.3805
eeeeeddddqqqqqqqqdddd]eee	chr15:27660338-27660609(-)$1	271	145	170	14.9464
:ccc[ddddqqqqqqqqddddccc:	chr2:17266437-17266677(-)$1	240	185	210	13.9726
gg!!eeeeeqqqqqqqqeeeee>>>	chr12:55746999-55747278(-)$1	279	106	131	15.6030
[ffffffbbqqqqqqqqbb]fffff	chr11:74488957-74489391(-)$1	434	215	240	15.1558
#a[ffffffqqqqqqqqffffff]a	chr3:122561805-122562045(+)$1	240	179	204	15.5674
!!ccc[cccqqqqqqqqcccccc]b	chr16:27449498-27449730(+)$1	232	109	134	16.4454
=========qqqqqqqq========	chr6:124908758-124908998(-)$1	240	92	117	17.1733
ddd[eeeeeqqqqqqqqeeeeeddd	chr9:75420614-75420883(-)$1	269	197	222	15.1504
iiiiiiiiiqqqqqqqqiiiiiiii	chr6:113338975-113339207(+)$1	232	177	202	16.5589
ccgggggggqqqqqqqqggggggg:	chr8:47292471-47292715(-)$1	244	137	162	15.4939
e"""eeeeeqqqqqqqqeeeee22e	chr6:94554491-94554722(-)$1	231	141	166	15.6177
Cbb[eeeeeqqqqqqqqeeeee444	chr7:73317663-73317929(+)$1	266	62	87	14.4991
ffffff[bbqqqqqqqqbb]fffff	chr5:136266011-136266276(+)$1	265	1	26	14.9796
f"""eeeeeqqqqqqqqeeeee22f	chr4:97779062-97779336(+)$1	274	103	128	15.5397
dddd[ddddqqqqqqqqdddd]ddd	chr1:133185406-133185659(-)$1	253	22	47	14.9042
dd[ccc[bbqqqqqqqqbb]ccc]d	chr1:16632733-16632985(-)$1	252	143	168	15.4879
[ccceeeeeqqqqqqqqeeeee]cc	chr2:4544840-4545071(-)$1	231	113	138	16.1242
""gggggggqqqqqqqqggggggg6	chr17:10399552-10399793(-)$1	241	156	181	16.3005
ee####cccqqqqqqqqccc333ee	chr4:149022852-149023111(+)$1	259	116	141	15.9598
::gggggggqqqqqqqqgggggggd	chr4:134300592-134300828(-)$1	236	134	159	14.3112
ffffffcccqqqqqqqqccc]ffff	chr11:86936263-86936511(+)$1	248	202	227	15.4856
Fccc!!cccqqqqqqqqccc333cc	chr11:87044238-87044469(-)$1	231	204	229	16.2298
eeeccc!!aqqqqqqqqa22ccc]e	chr1:87746246-87746585(+)$1	339	92	117	14.9594
ddd[eeeeeqqqqqqqqeeeee]dd	chr12:70412531-70412783(+)$1	252	117	142	15.3367
!ccc[ddddqqqqqqqqdddd]ccc	chr9:99380774-99381018(-)$1	244	151	176	16.1397
====eeeeeqqqqqqqqeeeeeccc	chr18:10816740-10816974(+)$1	234	132	157	16.2632
ccc"""cccqqqqqqqqccc]ccc3	chr1:38850771-38851021(-)$1	250	89	114	16.3706
iiiiiiiiiqqqqqqqqiiiiiiii	chr4:97778422-97778671(+)$1	249	19	44	16.5589
"""ffffffqqqqqqqqffffff44	chr8:70215589-70215825(-)$1	236	121	146	15.8192
[ccc[ddddqqqqqqqqdddd]ccc	chr9:75066880-75067121(+)$1	241	145	170	16.1217
e[gggggggqqqqqqqqggggggg>	chr5:66692431-66692676(-)$1	245	25	50	16.3852
=====ddddqqqqqqqqdddd4444	chr7:88746392-88746643(-)$1	251	28	53	16.3215
cccbbddddqqqqqqqqdddd22bb	chr11:96799668-96799912(-)$1	244	151	176	14.3756
gg!!ddddaqqqqqqqqa]dddd]g	chr12:109151010-109151274(-)$1	264	214	239	15.4514
iiiiiiiiiqqqqqqqqiiiiiiii	chr4:63211254-63211503(+)$1	249	211	236	16.5589
##gggggggqqqqqqqqggggggg]	chr15:58614412-58614687(-)$1	275	160	185	16.5327
=========qqqqqqqq========	chr4:149994279-149994511(+)$1	232	14	39	17.1733
%%ddddcccqqqqqqqqccc22ddd	chr15:99846399-99846665(+)$1	266	132	157	13.9431
gggggg[bbqqqqqqqqbb]ggggg	chrX:71278472-71278707(-)$1	235	170	195	16.0772
cccc!!cccqqqqqqqqccc22ccc	chr4:130336972-130337233(+)$1	261	180	205	16.2027
=========qqqqqqqq========	chr9:108000180-108000445(-)$1	265	24	49	17.1733
gggggg[bbqqqqqqqqbb]ggggg	chr11:77345498-77345740(-)$1	242	51	76	16.0772
dd:ffffffqqqqqqqqffffffgg	chr1:60041702-60041962(+)$1	260	87	112	14.0598
ee"""ddddqqqqqqqqdddd333e	chr10:86300012-86300243(+)$1	231	43	68	15.8326
=========qqqqqqqq========	chr5:96505163-96505416(-)$1	253	52	77	17.1733
===ffffffqqqqqqqqffffff44	chr13:56840174-56840416(+)$1	242	95	120	15.8221
[ffffff[aqqqqqqqqa]ffffff	chr4:85034018-85034271(+)$1	253	21	46	15.2062
!!bb[ddddqqqqqqqqdddd]bb2	chr18:20119658-20119895(-)$1	237	208	233	15.0096
!ccc!!cccqqqqqqqqccc22ccc	chr19:16460523-16460757(+)$1	234	175	200	16.4203
iiiffffffqqqqqqqqffffff:f	chr19:41992311-41992556(+)$1	245	170	195	14.5170
hhccc[cccqqqqqqqqccc]ccc3	chr13:55698755-55699034(+)$1	279	184	209	16.1136
bb[ccc[bbqqqqqqqqbb]ccc]b	chr14:61985536-61985784(-)$1	248	25	50	15.1128
e[bbeeeeeqqqqqqqqeeeee]bb	chr10:12898359-12898624(-)$1	265	117	142	14.9888
e"""eeeeeqqqqqqqqeeeee333	chr1:182531055-182531299(+)$1	244	73	98	16.3849
c[dddd[bbqqqqqqqqbb]ddddc	chr1:80263151-80263412(-)$1	261	116	141	14.9039

#otherMatches

#Seq PSSM
CCUUUGAAUUCUGCCUUGUAUCAAA	chr4:34035605-34035842(+)$1	237	205	230	15.1558
AACCAUUGCAAAAUUGAGCUUUGGU	chr1:179693655-179693886(-)$1	231	21	46	14.3766
CUUCCUGGAAGCCUUCCUCCCUGGA	chr4:154932870-154933122(+)$1	252	67	92	15.2890
AUCAUGACUGUGCCAUGGGCAUGAC	chr15:81149437-81149690(-)$1	253	63	88	15.1554
AAAUCAGAGAAAUCCUGUUUUGAUA	chr1:183106021-183106270(-)$1	249	136	161	16.2708
GCUGGUGGUGACUCUCAGCUUCCAG	chr6:107519540-107519785(+)$1	245	27	52	15.0127
UCUAAUUGCUUAAUUUUGUAACUGC	chr9:66803104-66803336(-)$1	232	16	41	14.3805
UGAUGUAAAUAUUUUAUUUUGCCAU	chr15:27660338-27660609(-)$1	271	145	170	14.9464
UGCCUAUGAUAAUCUGUUUGUGGCU	chr2:17266437-17266677(-)$1	240	185	210	13.9726
AUUUGUACUUUGAUAUCAGUAUUUU	chr12:55746999-55747278(-)$1	279	106	131	15.6030
GAAAUGGUGCAUCUUAACAUUUGUU	chr11:74488957-74489391(-)$1	434	215	240	15.1558
UCAAUAUAUCUGAACAAAUAUAUAG	chr3:122561805-122562045(+)$1	240	179	204	15.5674
CCGACCUUUGAUUUAUAGAAGUCUG	chr16:27449498-27449730(+)$1	232	109	134	16.4454
auauauauGAAUAGGUCUAUAUAUA	chr6:124908758-124908998(-)$1	240	92	117	17.1733
GGCAUUGUGGUUAAUUAUAUAGGUU	chr9:75420614-75420883(-)$1	269	197	222	15.1504
CAGUGAUUGUACCUUAUUGGUCGCU	chr6:113338975-113339207(+)$1	232	177	202	16.5589
UGAUGCUGAAAAGUAACUCAGUGUG	chr8:47292471-47292715(-)$1	244	137	162	15.4939
UGAAGUGUCUAACAAAUGGCAUAAA	chr6:94554491-94554722(-)$1	231	141	166	15.6177
UGCUGUGGCUGUCACCUGUCACCUU	chr7:73317663-73317929(+)$1	266	62	87	14.4991
GAGGCUAUCCCUGAGCUGAAAGCCU	chr5:136266011-136266276(+)$1	265	1	26	14.9796
UUCUGUUAUCAAAGCACAUAACUCA	chr4:97779062-97779336(+)$1	274	103	128	15.5397
AGACAUAGGGACAUAAGCCUACGUC	chr1:133185406-133185659(-)$1	253	22	47	14.9042
UGUGUUUUGUUUAUUGCCACAACUC	chr1:16632733-16632985(-)$1	252	143	168	15.4879
GACUUGCUUUUCUUUCUAAGCAGAG	chr2:4544840-4545071(-)$1	231	113	138	16.1242
CACAAUUUUGAUAACUGAAAAUUGC	chr17:10399552-10399793(-)$1	241	156	181	16.3005
AAAGUGUAUGCGUUAUAAUAAAGUU	chr4:149022852-149023111(+)$1	259	116	141	15.9598
AUUAUUGGUAAUACAUAGCCAGUGG	chr4:134300592-134300828(-)$1	236	134	159	14.3112
ACACAUCUGCUAUUAUCCAGUGUGU	chr11:86936263-86936511(+)$1	248	202	227	15.4856
CCCUUAAAUGUACAUAGAUUGUUAG	chr11:87044238-87044469(-)$1	231	204	229	16.2298
AAGUGUAUAUAUGCUUUUUCACAGC	chr1:87746246-87746585(+)$1	339	92	117	14.9594
ACUAUGUAUUAGAUGUUAUAUACAG	chr12:70412531-70412783(+)$1	252	117	142	15.3367
CCACUUUGUGAGCAAGAAUGAugug	chr9:99380774-99381018(-)$1	244	151	176	16.1397
AUAAGCAAAUAUGCCAUUUUGUCUG	chr18:10816740-10816974(+)$1	234	132	157	16.2632
UCACUUGUGAUAUUUACCACCUGAC	chr1:38850771-38851021(-)$1	250	89	114	16.3706
CUCAAAGGGCAAUGGUUUUUUUUGG	chr4:97778422-97778671(+)$1	249	19	44	16.5589
AAAUAGUAACUAAAGUUUUAUUAAC	chr8:70215589-70215825(-)$1	236	121	146	15.8192
UCUUCAUUAUGAAAUCCUAGUUAAG	chr9:75066880-75067121(+)$1	241	145	170	16.1217
ACUAGAUGUGUUUUUAAACAUCUAU	chr5:66692431-66692676(-)$1	245	25	50	16.3852
AAGAGCUUUACACGAGAAAAGAUUC	chr7:88746392-88746643(-)$1	251	28	53	16.3215
GUUCUCUGAACUCCGAAUCAGUUAG	chr11:96799668-96799912(-)$1	244	151	176	14.3756
AGAAAGUGCUUAAUAUUGUUACUGC	chr12:109151010-109151274(-)$1	264	214	239	15.4514
AGAAGGGGAGUAAACUGUUCCCUUC	chr4:63211254-63211503(+)$1	249	211	236	16.5589
UUUUUUUUCUUUCUCUUGAAAAAGC	chr15:58614412-58614687(-)$1	275	160	185	16.5327
GUUUUAAGCAGGCAGGAGCUUGGGA	chr4:149994279-149994511(+)$1	232	14	39	17.1733
UCAGGUGUCCAUUGAAUGACGUAUC	chr15:99846399-99846665(+)$1	266	132	157	13.9431
UCCUGGCCAGUCCUUAGUGAUCAGG	chrX:71278472-71278707(-)$1	235	170	195	16.0772
UGCUCAGCGCCACCCCUUGUAAAGU	chr4:130336972-130337233(+)$1	261	180	205	16.2027
UUUAUCUGUGUACAAUAGCAGAUAA	chr9:108000180-108000445(-)$1	265	24	49	17.1733
ACAUUUUAGAAUUAAUACUUAAGUG	chr11:77345498-77345740(-)$1	242	51	76	16.0772
AAAGUUGAGAUUCACUCCUUAAUGC	chr1:60041702-60041962(+)$1	260	87	112	14.0598
cugcccccacaguguguugggauaa	chr10:86300012-86300243(+)$1	231	43	68	15.8326
UUGAAAGUAAAAUUUGGUAUUUUUA	chr5:96505163-96505416(-)$1	253	52	77	17.1733
GCCUCAUUUGCCUAUCAGAGUGAGA	chr13:56840174-56840416(+)$1	242	95	120	15.8221
AGAAAGUCCUUUUUGUUGCACUUUC	chr4:85034018-85034271(+)$1	253	21	46	15.2062
UCUUCUCACAUGUAUAGGUGAAAAU	chr18:20119658-20119895(-)$1	237	208	233	15.0096
AUACCAAGCUCAGAGCUGCUGAGUA	chr19:16460523-16460757(+)$1	234	175	200	16.4203
AGGUUCUCGGACCACAUCGAGGGAC	chr19:41992311-41992556(+)$1	245	170	195	14.5170
UUGGUGCUGGUUGGAAACAGAGCCU	chr13:55698755-55699034(+)$1	279	184	209	16.1136
GACCACUCACUUCAGCCUGUGUGUU	chr14:61985536-61985784(-)$1	248	25	50	15.1128
AUGUUGUAAGUUUAAUAUUACACGC	chr10:12898359-12898624(-)$1	265	117	142	14.9888
CUAUAUAGAUUUUCUUUUUUAUCUU	chr1:182531055-182531299(+)$1	244	73	98	16.3849
AUGCAAAAUUCCCAGUUAUCUUGCU	chr1:80263151-80263412(-)$1	261	116	141	14.9039

#DB
.((((((((........)).)))))	chr4:34035605-34035842(+)$1	1	205	230	15.1558
.((((..((........))..))))	chr1:179693655-179693886(-)$1	1	21	46	14.3766
(((((.(((........)))..)))	chr4:154932870-154933122(+)$1	1	67	92	15.2890
.(((((.((........))))))).	chr15:81149437-81149690(-)$1	1	63	88	15.1554
(.(((((((........))))))).	chr1:183106021-183106270(-)$1	1	136	161	16.2708
(((((.(((........))).))))	chr6:107519540-107519785(+)$1	1	27	52	15.0127
..(((((((........))))....	chr9:66803104-66803336(-)$1	1	16	41	14.3805
(((((((((........)))).)))	chr15:27660338-27660609(-)$1	1	145	170	14.9464
.(((.((((........))))))).	chr2:17266437-17266677(-)$1	1	185	210	13.9726
((..(((((........)))))...	chr12:55746999-55747278(-)$1	1	106	131	15.6030
.((((((((........)).)))))	chr11:74488957-74489391(-)$1	1	215	240	15.1558
.(.((((((........)))))).)	chr3:122561805-122562045(+)$1	1	179	204	15.5674
..(((.(((........)))))).)	chr16:27449498-27449730(+)$1	1	109	134	16.4454
(((((((((........))))))))	chr6:124908758-124908998(-)$1	1	92	117	17.1733
(((.(((((........))))))))	chr9:75420614-75420883(-)$1	1	197	222	15.1504
(((((((((........))))))))	chr6:113338975-113339207(+)$1	1	177	202	16.5589
))(((((((........))))))).	chr8:47292471-47292715(-)$1	1	137	162	15.4939
(...(((((........)))))..)	chr6:94554491-94554722(-)$1	1	141	166	15.6177
(((.(((((........)))))...	chr7:73317663-73317929(+)$1	1	62	87	14.4991
((((((.((........)).)))))	chr5:136266011-136266276(+)$1	1	1	26	14.9796
(...(((((........)))))..)	chr4:97779062-97779336(+)$1	1	103	128	15.5397
((((.((((........)))).)))	chr1:133185406-133185659(-)$1	1	22	47	14.9042
((.(((.((........)).))).)	chr1:16632733-16632985(-)$1	1	143	168	15.4879
.((((((((........))))).))	chr2:4544840-4545071(-)$1	1	113	138	16.1242
..(((((((........))))))).	chr17:10399552-10399793(-)$1	1	156	181	16.3005
((....(((........)))...))	chr4:149022852-149023111(+)$1	1	116	141	15.9598
..(((((((........)))))))(	chr4:134300592-134300828(-)$1	1	134	159	14.3112
(((((((((........))).))))	chr11:86936263-86936511(+)$1	1	202	227	15.4856
)(((..(((........)))...))	chr11:87044238-87044469(-)$1	1	204	229	16.2298
((((((..(........)..))).)	chr1:87746246-87746585(+)$1	1	92	117	14.9594
(((.(((((........))))).))	chr12:70412531-70412783(+)$1	1	117	142	15.3367
.(((.((((........)))).)))	chr9:99380774-99381018(-)$1	1	151	176	16.1397
))))(((((........)))))(((	chr18:10816740-10816974(+)$1	1	132	157	16.2632
(((...(((........))).))).	chr1:38850771-38851021(-)$1	1	89	114	16.3706
(((((((((........))))))))	chr4:97778422-97778671(+)$1	1	19	44	16.5589
...((((((........))))))..	chr8:70215589-70215825(-)$1	1	121	146	15.8192
.(((.((((........)))).)))	chr9:75066880-75067121(+)$1	1	145	170	16.1217
(.(((((((........))))))).	chr5:66692431-66692676(-)$1	1	25	50	16.3852
(((((((((........))))....	chr7:88746392-88746643(-)$1	1	28	53	16.3215
(((((((((........))))..))	chr11:96799668-96799912(-)$1	1	151	176	14.3756
((..(((((........).)))).)	chr12:109151010-109151274(-)$1	1	214	239	15.4514
(((((((((........))))))))	chr4:63211254-63211503(+)$1	1	211	236	16.5589
..(((((((........))))))).	chr15:58614412-58614687(-)$1	1	160	185	16.5327
(((((((((........))))))))	chr4:149994279-149994511(+)$1	1	14	39	17.1733
..(((((((........)))..)))	chr15:99846399-99846665(+)$1	1	132	157	13.9431
((((((.((........)).)))))	chrX:71278472-71278707(-)$1	1	170	195	16.0772
)(((..(((........)))..)))	chr4:130336972-130337233(+)$1	1	180	205	16.2027
(((((((((........))))))))	chr9:108000180-108000445(-)$1	1	24	49	17.1733
((((((.((........)).)))))	chr11:77345498-77345740(-)$1	1	51	76	16.0772
)).((((((........))))))((	chr1:60041702-60041962(+)$1	1	87	112	14.0598
((...((((........))))...)	chr10:86300012-86300243(+)$1	1	43	68	15.8326
(((((((((........))))))))	chr5:96505163-96505416(-)$1	1	52	77	17.1733
(((((((((........))))))..	chr13:56840174-56840416(+)$1	1	95	120	15.8221
.((((((.(........).))))))	chr4:85034018-85034271(+)$1	1	21	46	15.2062
..((.((((........)))).)).	chr18:20119658-20119895(-)$1	1	208	233	15.0096
.(((..(((........)))..)))	chr19:16460523-16460757(+)$1	1	175	200	16.4203
)))((((((........)))))).(	chr19:41992311-41992556(+)$1	1	170	195	14.5170
(((((.(((........))).))).	chr13:55698755-55699034(+)$1	1	184	209	16.1136
((.(((.((........)).))).)	chr14:61985536-61985784(-)$1	1	25	50	15.1128
(.(((((((........))))).))	chr10:12898359-12898624(-)$1	1	117	142	14.9888
(...(((((........)))))...	chr1:182531055-182531299(+)$1	1	73	98	16.3849
(.((((.((........)).)))))	chr1:80263151-80263412(-)$1	1	116	141	14.9039

#PSSM
e : 0.14	= : 0.11	! : 0.09	d : 0.09	[ : 0.08	c : 0.08	g : 0.06	i : 0.06	" : 0.04	f : 0.04	h : 0.03	: : 0.03	# : 0.03	C : 0.01	F : 0.01	% : 0.01	b : 0.01	
c : 0.16	d : 0.11	= : 0.11	e : 0.09	f : 0.08	" : 0.08	[ : 0.06	g : 0.06	i : 0.06	! : 0.04	b : 0.03	a : 0.01	: : 0.01	# : 0.01	% : 0.01	h : 0.01	
c : 0.19	g : 0.12	d : 0.11	= : 0.11	f : 0.08	" : 0.08	e : 0.06	i : 0.06	[ : 0.04	b : 0.04	! : 0.03	# : 0.01	: : 0.01	
c : 0.20	f : 0.16	g : 0.12	= : 0.09	d : 0.08	" : 0.08	e : 0.04	[ : 0.04	i : 0.04	b : 0.04	! : 0.03	# : 0.01	
e : 0.20	f : 0.16	g : 0.12	c : 0.09	d : 0.08	[ : 0.08	= : 0.08	i : 0.04	! : 0.04	" : 0.03	# : 0.01	b : 0.01	
d : 0.20	e : 0.17	f : 0.16	g : 0.12	! : 0.06	[ : 0.06	= : 0.06	i : 0.04	c : 0.04	# : 0.01	" : 0.01	
c : 0.17	d : 0.17	e : 0.16	f : 0.12	[ : 0.11	g : 0.09	= : 0.06	i : 0.04	! : 0.03	
c : 0.17	d : 0.17	b : 0.16	e : 0.16	g : 0.09	f : 0.08	= : 0.06	i : 0.04	! : 0.01	[ : 0.01	
c : 0.17	b : 0.16	d : 0.16	e : 0.16	g : 0.09	f : 0.08	= : 0.06	i : 0.04	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	
c : 0.17	b : 0.16	d : 0.16	e : 0.16	g : 0.09	f : 0.08	= : 0.06	i : 0.04	a : 0.04	
c : 0.17	b : 0.16	d : 0.16	e : 0.16	g : 0.09	f : 0.08	= : 0.06	i : 0.04	] : 0.03	2 : 0.01	
c : 0.17	e : 0.17	d : 0.17	] : 0.12	g : 0.09	f : 0.09	= : 0.06	i : 0.04	2 : 0.03	
d : 0.19	e : 0.17	f : 0.14	g : 0.12	2 : 0.08	] : 0.06	c : 0.06	= : 0.06	i : 0.04	3 : 0.03	
e : 0.17	f : 0.16	g : 0.12	c : 0.11	2 : 0.08	] : 0.08	d : 0.06	= : 0.06	i : 0.04	3 : 0.04	8 : 0.01	4 : 0.01	
c : 0.19	f : 0.16	g : 0.12	d : 0.11	= : 0.06	3 : 0.06	e : 0.04	i : 0.04	2 : 0.04	] : 0.04	4 : 0.03	8 : 0.01	> : 0.01	b : 0.01	
c : 0.16	g : 0.14	d : 0.11	] : 0.09	f : 0.08	e : 0.06	= : 0.06	4 : 0.06	i : 0.04	b : 0.04	2 : 0.03	3 : 0.03	8 : 0.01	> : 0.01	: : 0.01	
d : 0.12	c : 0.12	f : 0.11	e : 0.09	b : 0.06	= : 0.06	4 : 0.06	g : 0.06	2 : 0.04	i : 0.04	3 : 0.04	: : 0.03	> : 0.03	8 : 0.01	a : 0.01	6 : 0.01	] : 0.01	

#score	968.5364956901207
#seq	62
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_UTR_m1_run2.txt

#BEAR
cc^^^^^^^^^^^^^^^^^^^^^^^^ccc333g	chr16:65862445-65862646(+)$1	201	73	106	36.2383
gggggg^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr17:57219868-57220069(-)$1	201	83	116	39.1209
%%%bb^^^^^^^^^^^^^^^^^^^^^bb66666	chr4:128819875-128820076(+)$1	201	8	41	32.3515
[dddd^^^^^^^^^^^^^^^^^^^^^^^^^ddd	chr7:107789455-107789656(+)$1	201	4	37	38.0573
ffffff^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr2:121134454-121134655(+)$1	201	76	109	38.6160
ddd[bb^^^^^^^^^^^^^^^^^^^^bb]dddd	chr18:67649573-67649774(-)$1	201	141	174	34.3331
fffff^^^^^^^^^^^^^^^^^^^^^^^fffff	chr1:88439798-88439999(-)$1	201	73	106	37.2475
ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^ccc	chr9:95357532-95357733(-)$1	201	39	72	38.5364
$$$$bb^^^^^^^^^^^^^^^^^^^^^^bb444	chr15:25903137-25903338(+)$1	201	55	88	36.1610
[eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr18:67650028-67650229(-)$1	201	92	125	39.2473
[eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee	chrX:162825825-162826026(+)$1	201	89	122	37.9440
ccc^^^^^^^^^^^^^^^^^^^^^^^^^^ccc]	chr11:54723340-54723541(+)$1	201	80	113	38.2381
ffffff^^^^^^^^^^^^^^^^^^^ffffff::	chr5:82170020-82170221(+)$1	201	1	34	31.9894
eee^^^^^^^^^^^^^^^^^^^^^^^^eeeee:	chr18:25636119-25636320(-)$1	201	47	80	36.2950
gggg!!bb^^^^^^^^^^^^^^^^^^bb22ggg	chr11:75439643-75439844(+)$1	201	104	137	32.7304
eeeee^^^^^^^^^^^^^^^^^^^^^eeeeebb	chr12:75399194-75399395(+)$1	201	79	112	35.6494
fff!!bb^^^^^^^^^^^^^^^^^^^bb22fff	chrX:58437065-58437266(+)$1	201	110	143	33.6656
iii^^^^^^^^^^^^^^^^^^^^^^^^^^iiii	chr8:127434179-127434380(-)$1	201	97	130	38.1959
eee^^^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr11:66025316-66025517(-)$1	201	88	121	38.2817
hhhhhh^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr15:74401810-74402011(+)$1	201	72	105	37.8016
ggggggg^^^^^^^^^^^^^^^^^^^ggggggg	chr9:51896540-51896741(+)$1	201	103	136	34.1565
ffff[ccc^^^^^^^^^^^^^^^^^^cccffff	chr18:37680517-37680718(+)$1	201	150	183	32.7811
"ddddccc^^^^^^^^^^^^^^^^^^ccc22dd	chr15:84775799-84776000(-)$1	201	76	109	32.4061
:eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee	chr6:138311646-138311847(-)$1	201	127	160	36.7621
fffccc^^^^^^^^^^^^^^^^^^^^^ccc]ff	chr5:34537967-34538168(-)$1	201	80	113	36.6406
iiiiii^^^^^^^^^^^^^^^^^^^^^^iiiii	chr12:8758551-8758752(+)$1	201	157	190	37.3934
hhhhhh^^^^^^^^^^^^^^^^^^^^^^^^hhh	chr1:156239603-156239804(-)$1	201	132	165	36.4214
!eeeee^^^^^^^^^^^^^^^^^^^eeeee22b	chr2:156367422-156367623(+)$1	201	62	95	34.0669
!!dddd^^^^^^^^^^^^^^^^^^^^^^^^^dd	chr11:49697541-49697742(+)$1	201	73	106	38.3200
=====a^^^^^^^^^^^^^^^^^^^^^^^^^a]	chr3:100369109-100369310(-)$1	201	76	109	39.0585
"eeeee^^^^^^^^^^^^^^^^^^^^^eeeeed	chr8:26877614-26877815(-)$1	201	80	113	36.9146
eeeeee^^^^^^^^^^^^^^^^^^^^eeeee::	chr18:6026240-6026441(-)$1	201	107	140	34.3398
gggggg^^^^^^^^^^^^^^^^^^^^^^^^^gg	chr7:51613526-51613727(+)$1	201	72	105	38.8306
!eeeee^^^^^^^^^^^^^^^^^^^^eeeeeee	chr11:41723708-41723909(-)$1	201	162	195	36.0502
GGGccc^^^^^^^^^^^^^^^^^^^^^^^ccc:	chr17:36995197-36995398(+)$1	201	59	92	35.9427
gg[ccc^^^^^^^^^^^^^^^^^^^^^^ccc]g	chr13:83804489-83804690(+)$1	201	70	103	37.8561
gggggg^^^^^^^^^^^^^^^^^^^^ggggggg	chr6:126588458-126588659(-)$1	201	105	138	35.7087
gg[ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr19:41288794-41288995(-)$1	201	65	98	39.1487
a[dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr18:36450551-36450752(+)$1	201	73	106	38.6315
ccdddd^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr6:5111020-5111221(+)$1	201	57	90	38.5650
hhhhhh^^^^^^^^^^^^^^^^^^^^^^hhhhh	chr10:12103037-12103238(-)$1	201	6	39	34.8316
^^^^^^^^^^^^^^^^^^^^^^^^^^eeeee]b	chr16:37114978-37115179(-)$1	201	68	101	35.3417
=eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee	chr14:22613335-22613536(+)$1	201	59	92	37.8392
iiiiii^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr15:30958666-30958867(+)$1	201	151	184	38.9846
c[dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr8:63389593-63389794(-)$1	201	27	60	38.6568
[eeeee^^^^^^^^^^^^^^^^^^^^^^^eeee	chr4:56970802-56971003(-)$1	201	53	86	38.4474
ffffff^^^^^^^^^^^^^^^^^^^^ffffff:	chr13:89749944-89750145(+)$1	201	22	55	34.4469
ffffff^^^^^^^^^^^^^^^^^^^^^^fffff	chr11:105920293-105920494(+)$1	201	116	149	36.9947
^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff:	chr10:80484217-80484418(-)$1	201	146	179	34.3791

#otherMatches

#Seq PSSM
AAUUCUCACAACUCAUUUCCAAACAUUUCACUU	chr16:65862445-65862646(+)$1	201	73	106	36.2383
AGGUUGCUUCUAUUUGCUUCACCUUUAACUCCU	chr17:57219868-57220069(-)$1	201	83	116	39.1209
UGCGGCUCCUCCCACCUCCAUCUUCUCCUAUCA	chr4:128819875-128820076(+)$1	201	8	41	32.3515
AAGGUAACAAAAAUAACUUCAUACUUCCUCACC	chr7:107789455-107789656(+)$1	201	4	37	38.0573
CCAAGCUCCCCAAUCACUUAGUCUUCACCUACC	chr2:121134454-121134655(+)$1	201	76	109	38.6160
GACAACGACACCUCAGAAAUAUUCCAGUAGUCA	chr18:67649573-67649774(-)$1	201	141	174	34.3331
AGUGGCUUUUCUCCCAAAACCUCCAUCUUCACU	chr1:88439798-88439999(-)$1	201	73	106	37.2475
GGCCAUCUCACCUCCAACCUAUAAGUAUCAGCU	chr9:95357532-95357733(-)$1	201	39	72	38.5364
ACUUGCUUAUUUUUGAUUGACCUUCUAUGCUUA	chr15:25903137-25903338(+)$1	201	55	88	36.1610
UCAUACAUUUUCACCUACAUUUUCCAUAACUUU	chr18:67650028-67650229(-)$1	201	92	125	39.2473
ACAGUUUCAUAUCAACUAUCUAAAACCUAACUG	chrX:162825825-162826026(+)$1	201	89	122	37.9440
ACAACACCCUCAUAUUUUUUUCAGCUUUCUGUU	chr11:54723340-54723541(+)$1	201	80	113	38.2381
AUGACCUUGCUUUUUUUCCUACUAUGGUUAUCU	chr5:82170020-82170221(+)$1	201	1	34	31.9894
UGUAAAAAAACAAAAACAAAAAACCCAACAGCU	chr18:25636119-25636320(-)$1	201	47	80	36.2950
GAUGCCCUUUAACAUUGUGAACAAAUAGACCGU	chr11:75439643-75439844(+)$1	201	104	137	32.7304
GAUGUAAAAAUCCAUUUUAUUUCAAGACAUCGU	chr12:75399194-75399395(+)$1	201	79	112	35.6494
GAAAUCAACGUCUUCCCCAAAAUCCAUGUCUUC	chrX:58437065-58437266(+)$1	201	110	143	33.6656
UCAUUUCAUCUCUUUUUUAUAUCAAGUUUUGAA	chr8:127434179-127434380(-)$1	201	97	130	38.1959
AGUUUCUCCAUCACUCACAGGCCUCCAUUACUG	chr11:66025316-66025517(-)$1	201	88	121	38.2817
UGCCUGUCCAUCAUCUCCUCUAAUGCUCUCAUC	chr15:74401810-74402011(+)$1	201	72	105	37.8016
UAGUGAUUGCAUCAAUUAUAACAUUUAUCAUUA	chr9:51896540-51896741(+)$1	201	103	136	34.1565
UUUAAGUAUUUUUCCAAAUCUAUUGUUGCUGAA	chr18:37680517-37680718(+)$1	201	150	183	32.7811
ACUUCUGAUUUCUACAAAAAAACAUUUCAAUGA	chr15:84775799-84776000(-)$1	201	76	109	32.4061
CUGGACUCuuuuauuauuauuauuuuuuguuua	chr6:138311646-138311847(-)$1	201	127	160	36.7621
CCUCAACAACAUACAUCUCAUUUCCUUUUGAAG	chr5:34537967-34538168(-)$1	201	80	113	36.6406
GAAUAAUUCUCUUCUCCCCUUUUCUACUUUGUU	chr12:8758551-8758752(+)$1	201	157	190	37.3934
UUUUCUUAAUCCACGCUGUUUUCAUUAAUCAGA	chr1:156239603-156239804(-)$1	201	132	165	36.4214
CGGCAGUCCCAUCUCACUUCCUGUCCUGCUAAG	chr2:156367422-156367623(+)$1	201	62	95	34.0669
CCUUCUUUAUCACAAAGCACCCCAUCUCAAUAG	chr11:49697541-49697742(+)$1	201	73	106	38.3200
UAAACCUUAGUACUUUAGACUCCAUAUCAUUGU	chr3:100369109-100369310(-)$1	201	76	109	39.0585
UCCAUCCUUCCCACUUCUGCUUUUCAUGAUGGG	chr8:26877614-26877815(-)$1	201	80	113	36.9146
CUCUGACUAUCAGUAAACAUCAAAACUCAGAAU	chr18:6026240-6026441(-)$1	201	107	140	34.3398
GCCACCCCUAAGCCCUUACUCUCCCUCUCAUGG	chr7:51613526-51613727(+)$1	201	72	105	38.8306
UAGCAUAUGGACUUUUACAAUAAAAAAUGCUGC	chr11:41723708-41723909(-)$1	201	162	195	36.0502
ACACUGUCACCCUAUCCAUAUAUCUUACUCAGC	chr17:36995197-36995398(+)$1	201	59	92	35.9427
GUUAAAAACAAAAUAAAGACAUCAACCAUUUCA	chr13:83804489-83804690(+)$1	201	70	103	37.8561
AUCUGGUCCACUUCACACUCCCUUCCCCAGGUG	chr6:126588458-126588659(-)$1	201	105	138	35.7087
AUCAACCUCAUUUAUUUAUCUUAAAAUUAACCA	chr19:41288794-41288995(-)$1	201	65	98	39.1487
CUCCUGUUUCAUCCUUCCCCCUACAUUUCCCCU	chr18:36450551-36450752(+)$1	201	73	106	38.6315
UGUAUCUAACUCUCAUUACUGCAUUAAUUCUAA	chr6:5111020-5111221(+)$1	201	57	90	38.5650
UUUAUUUAUUUCAUCUUGCAAUCUCUAUAAUAA	chr10:12103037-12103238(-)$1	201	6	39	34.8316
CUCUCUCUGUAGUAAUUCACAUCAUUUGCAGCU	chr16:37114978-37115179(-)$1	201	68	101	35.3417
guggggUCCUCUUUUUGUUGUUGUUUUUCCCUG	chr14:22613335-22613536(+)$1	201	59	92	37.8392
AGAAGAUGUAAACUGCUCACCUUAUUCCCUUUC	chr15:30958666-30958867(+)$1	201	151	184	38.9846
ACAUGAUUUUUUUUCCCCCACAUUUCCUUUUCU	chr8:63389593-63389794(-)$1	201	27	60	38.6568
AUUAGUUUUCUUACUCUGUUUUAUCAUUCACUG	chr4:56970802-56971003(-)$1	201	53	86	38.4474
CAAAGGACCAGAAUCGUCAUGCCCUCCCUUUGA	chr13:89749944-89750145(+)$1	201	22	55	34.4469
AUACAGGGCUUAUAAUAAAAAUUUAACACUGUG	chr11:105920293-105920494(+)$1	201	116	149	36.9947
CUCUUUGCUCCCCCACCCCCAUUCUAUCUGCAC	chr10:80484217-80484418(-)$1	201	146	179	34.3791

#DB
((........................)))...)	chr16:65862445-65862646(+)$1	1	73	106	36.2383
((((((...........................	chr17:57219868-57220069(-)$1	1	83	116	39.1209
...((.....................)).....	chr4:128819875-128820076(+)$1	1	8	41	32.3515
.((((.........................)))	chr7:107789455-107789656(+)$1	1	4	37	38.0573
((((((...........................	chr2:121134454-121134655(+)$1	1	76	109	38.6160
(((.((....................)).))))	chr18:67649573-67649774(-)$1	1	141	174	34.3331
(((((.......................)))))	chr1:88439798-88439999(-)$1	1	73	106	37.2475
(((...........................)))	chr9:95357532-95357733(-)$1	1	39	72	38.5364
....((......................))...	chr15:25903137-25903338(+)$1	1	55	88	36.1610
.(((((...........................	chr18:67650028-67650229(-)$1	1	92	125	39.2473
.(((((......................)))))	chrX:162825825-162826026(+)$1	1	89	122	37.9440
(((..........................))).	chr11:54723340-54723541(+)$1	1	80	113	38.2381
((((((...................))))))..	chr5:82170020-82170221(+)$1	1	1	34	31.9894
(((........................))))).	chr18:25636119-25636320(-)$1	1	47	80	36.2950
((((..((..................))..)))	chr11:75439643-75439844(+)$1	1	104	137	32.7304
(((((.....................)))))))	chr12:75399194-75399395(+)$1	1	79	112	35.6494
(((..((...................))..)))	chrX:58437065-58437266(+)$1	1	110	143	33.6656
(((..........................))))	chr8:127434179-127434380(-)$1	1	97	130	38.1959
(((..........................))))	chr11:66025316-66025517(-)$1	1	88	121	38.2817
((((((...........................	chr15:74401810-74402011(+)$1	1	72	105	37.8016
(((((((...................)))))))	chr9:51896540-51896741(+)$1	1	103	136	34.1565
((((.(((..................)))))))	chr18:37680517-37680718(+)$1	1	150	183	32.7811
.(((((((..................)))..))	chr15:84775799-84776000(-)$1	1	76	109	32.4061
.(((((......................)))))	chr6:138311646-138311847(-)$1	1	127	160	36.7621
((((((.....................))).))	chr5:34537967-34538168(-)$1	1	80	113	36.6406
((((((......................)))))	chr12:8758551-8758752(+)$1	1	157	190	37.3934
((((((........................)))	chr1:156239603-156239804(-)$1	1	132	165	36.4214
.(((((...................)))))..)	chr2:156367422-156367623(+)$1	1	62	95	34.0669
..((((.........................))	chr11:49697541-49697742(+)$1	1	73	106	38.3200
((((((.........................).	chr3:100369109-100369310(-)$1	1	76	109	39.0585
.(((((.....................))))))	chr8:26877614-26877815(-)$1	1	80	113	36.9146
)(((((....................)))))..	chr18:6026240-6026441(-)$1	1	107	140	34.3398
((((((.........................))	chr7:51613526-51613727(+)$1	1	72	105	38.8306
.(((((....................)))))))	chr11:41723708-41723909(-)$1	1	162	195	36.0502
((((((.......................))).	chr17:36995197-36995398(+)$1	1	59	92	35.9427
((.(((......................))).)	chr13:83804489-83804690(+)$1	1	70	103	37.8561
((((((....................)))))))	chr6:126588458-126588659(-)$1	1	105	138	35.7087
((.(((...........................	chr19:41288794-41288995(-)$1	1	65	98	39.1487
(.((((...........................	chr18:36450551-36450752(+)$1	1	73	106	38.6315
((((((...........................	chr6:5111020-5111221(+)$1	1	57	90	38.5650
((((((......................)))))	chr10:12103037-12103238(-)$1	1	6	39	34.8316
..........................))))).)	chr16:37114978-37115179(-)$1	1	68	101	35.3417
((((((......................)))))	chr14:22613335-22613536(+)$1	1	59	92	37.8392
((((((...........................	chr15:30958666-30958867(+)$1	1	151	184	38.9846
(.((((...........................	chr8:63389593-63389794(-)$1	1	27	60	38.6568
.(((((.......................))))	chr4:56970802-56971003(-)$1	1	53	86	38.4474
((((((....................)))))).	chr13:89749944-89750145(+)$1	1	22	55	34.4469
((((((......................)))))	chr11:105920293-105920494(+)$1	1	116	149	36.9947
..........................)))))).	chr10:80484217-80484418(-)$1	1	146	179	34.3791

#PSSM
f : 0.16	g : 0.14	c : 0.10	[ : 0.08	e : 0.08	i : 0.06	h : 0.06	! : 0.06	" : 0.04	= : 0.04	^ : 0.04	% : 0.02	d : 0.02	$ : 0.02	: : 0.02	G : 0.02	a : 0.02	
e : 0.24	f : 0.16	g : 0.14	c : 0.08	d : 0.06	i : 0.06	h : 0.06	[ : 0.04	^ : 0.04	% : 0.02	$ : 0.02	! : 0.02	= : 0.02	G : 0.02	
e : 0.24	f : 0.16	d : 0.14	g : 0.10	^ : 0.06	i : 0.06	h : 0.06	c : 0.04	[ : 0.04	% : 0.02	$ : 0.02	= : 0.02	G : 0.02	
e : 0.20	^ : 0.16	d : 0.12	f : 0.12	g : 0.10	c : 0.08	h : 0.06	i : 0.04	b : 0.02	[ : 0.02	$ : 0.02	! : 0.02	= : 0.02	
e : 0.20	^ : 0.16	d : 0.12	f : 0.10	g : 0.08	c : 0.08	b : 0.06	h : 0.06	! : 0.04	i : 0.04	[ : 0.02	= : 0.02	
^ : 0.24	e : 0.18	c : 0.12	g : 0.08	f : 0.08	d : 0.08	b : 0.06	h : 0.06	i : 0.04	! : 0.02	a : 0.02	
^ : 0.89	b : 0.04	c : 0.04	g : 0.02	
^ : 0.93	c : 0.04	b : 0.02	
^ : 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	f : 0.02	e : 0.02	
^ : 0.65	e : 0.10	b : 0.08	c : 0.06	f : 0.06	g : 0.04	
^ : 0.59	e : 0.14	c : 0.08	b : 0.08	f : 0.06	g : 0.04	
^ : 0.40	e : 0.20	c : 0.10	f : 0.10	2 : 0.04	g : 0.04	6 : 0.02	] : 0.02	b : 0.02	i : 0.02	h : 0.02	
^ : 0.30	e : 0.24	f : 0.12	c : 0.08	2 : 0.06	i : 0.04	g : 0.04	3 : 0.02	6 : 0.02	d : 0.02	b : 0.02	h : 0.02	
^ : 0.24	e : 0.22	f : 0.14	c : 0.08	g : 0.06	d : 0.04	i : 0.04	2 : 0.04	h : 0.04	3 : 0.02	6 : 0.02	4 : 0.02	] : 0.02	
^ : 0.18	e : 0.16	f : 0.14	d : 0.08	g : 0.08	c : 0.06	: : 0.04	i : 0.04	h : 0.04	] : 0.04	3 : 0.02	6 : 0.02	4 : 0.02	b : 0.02	2 : 0.02	a : 0.02	
^ : 0.18	g : 0.12	e : 0.12	: : 0.12	d : 0.10	f : 0.10	b : 0.06	] : 0.04	i : 0.04	h : 0.04	6 : 0.02	c : 0.02	4 : 0.02	

#score	1790.619434344415
#seq	49
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_transcript_m1_run2.txt

#BEAR
==========ttttttttttt========	chr19:47809707-47809942(+)$1	235	71	100	21.2895
dd^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:136386344-136386584(-)$1	240	149	178	19.1644
bbeeeeexxxxxxxxxxxxxxxeeeee]b	chr3:95337413-95337648(+)$1	235	150	179	17.3614
:bb[gggggggtttttttttttggggggg	chr4:109125649-109125887(-)$1	238	17	46	18.3459
cca[ccc^^^^^^^^^^^^^^^^^^^^^^	chr13:89135805-89136043(+)$1	238	8	37	20.3451
gg^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr8:114542481-114542716(+)$1	235	146	175	19.4563
:dddd[cccwwwwwwwwwwwwwwcccddd	chr11:6523715-6523950(-)$1	235	173	202	21.1216
=========vvvvvvvvvvvvv=======	chr15:4104015-4104251(+)$1	236	143	172	24.4836
cchhhhhhhhuuuuuuuuuuuuhhhhhhh	chr2:57220188-57220427(+)$1	239	194	223	18.7632
ee::eeeeewwwwwwwwwwwwwweeeee:	chr2:153594688-153594923(+)$1	235	78	107	19.1524
cc[bb[axxxxxxxxxxxxxxxa]bb]cc	chr12:16992617-16992852(+)$1	235	6	35	18.2612
iiiii[bbvvvvvvvvvvvvvbb]iiiii	chr16:38245760-38245995(+)$1	235	77	106	22.4526
iiiiiiiibbtttttttttttbb]iiiii	chr7:149689710-149689945(+)$1	235	114	143	20.5942
=====!!bb^^^^^^^^^^^^^^^^^^^b	chr2:35037198-35037452(-)$1	254	17	46	20.0639
iiiiieeeeeuuuuuuuuuuuueeeee]i	chr5:136384359-136384619(-)$1	260	40	69	21.9466
ggggggg[bbuuuuuuuuuuuubbggggg	chr4:104704625-104704860(-)$1	235	151	180	22.4293
ccffffff^^^^^^^^^^^^^^^^^^^^^	chr16:44160309-44160547(+)$1	238	134	163	19.7193
d"""ccc[bbvvvvvvvvvvvvvbb]ccc	chr5:68012977-68013215(-)$1	238	32	61	22.0650
+++gggggggtttttttttttggggggg0	chr2:104266800-104267037(-)$1	237	136	165	18.0350
ffff!!ccctttttttttttccc22ffff	chr15:4105022-4105266(+)$1	244	208	237	19.1329
gg[ffffffvvvvvvvvvvvvvffffffg	chr12:25727102-25727337(+)$1	235	79	108	22.6193
[ccc!!cccvvvvvvvvvvvvvccc22cc	chrX:99709798-99710042(-)$1	244	154	183	23.6751
gggggg^^^^^^^^^^^^^^^^^^^gggg	chr7:31339759-31340011(+)$1	252	200	229	19.9980
iiiiiiiii^^^^^^^^^^^^^^^^^^ii	chr6:93867623-93867858(-)$1	235	49	78	20.2136
cca[a[a[avvvvvvvvvvvvva]a]a]a	chr4:108702348-108702586(+)$1	238	171	200	24.6894
eeee!!ccctttttttttttccc22eeee	chr3:116445886-116446121(-)$1	235	45	74	19.4242
::gggggggvvvvvvvvvvvvvggggggg	chr5:124951445-124951696(-)$1	251	136	165	21.8796
eee!!cccwwwwwwwwwwwwwwccc]eee	chr4:147247927-147248162(-)$1	235	22	51	23.0285
iiiiiiiiivvvvvvvvvvvvviiiiiii	chr9:107950460-107950695(+)$1	235	41	70	23.7657
eeeee[eeeeettttttttttteeeee]e	chr13:99612929-99613169(-)$1	240	7	36	18.8423
ffffff[bbuuuuuuuuuuuubb]fffff	chr8:107740674-107740909(+)$1	235	138	167	20.7703
cceeeee[bbuuuuuuuuuuuubb]eeee	chr7:35130363-35130625(-)$1	262	178	207	21.4524
ccc[eeeee^^^^^^^^^^^^^^^^^^^^	chr2:76542175-76542425(-)$1	250	179	208	19.8039
ddd!!bb[bbuuuuuuuuuuuubbbb22d	chr19:12842903-12843138(-)$1	235	180	209	20.5626
hhhhddddwwwwwwwwwwwwwwddddccc	chr1:82892197-82892444(+)$1	247	173	202	21.0041
c[gggggggvvvvvvvvvvvvvggggggg	chr5:136386537-136386774(-)$1	237	61	90	23.8607
ggeeeee[bbtttttttttttbb]eeeee	chr5:92481805-92482063(-)$1	258	95	124	19.6320
cc[ffffffuuuuuuuuuuuuffffff]c	chr16:94690321-94690556(+)$1	235	133	162	21.4581
=!!ffffffvvvvvvvvvvvvvffffff=	chr11:109530395-109530652(+)$1	257	140	169	22.7195
ccc[bb^^^^^^^^^^^^^^^^^^^^^bb	chr1:75177799-75178035(-)$1	236	56	85	19.0186
eeeee[bb^^^^^^^^^^^^^^^^^^^^^	chr11:84009578-84009817(+)$1	239	197	226	19.5886
####eeeee^^^^^^^^^^^^^^^^^^^^	chr11:35197248-35197483(+)$1	235	94	123	19.5227
iiiggggggguuuuuuuuuuuuggggggg	chr19:12841729-12841976(-)$1	247	84	113	22.6302
cc^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr9:30957160-30957421(-)$1	261	77	106	19.4769
cc[ggggggguuuuuuuuuuuuggggggg	chr4:104704900-104705153(-)$1	253	215	244	22.6790
gggggg^^^^^^^^^^^^^^^^^^^^^^^	chr15:97965928-97966164(-)$1	236	93	122	20.3527
eeeee!!cccuuuuuuuuuuuuccc22ee	chr11:77653807-77654042(+)$1	235	172	201	22.0233
FFFFddddwwwwwwwwwwwwwwdddd::e	chr16:36035202-36035440(+)$1	238	12	41	17.9702
dd####ccctttttttttttccc4444dd	chr2:76541964-76542206(-)$1	242	61	90	19.9731
iiiiiiiii^^^^^^^^^^^^^^^^^^^^	chr13:21608338-21608573(-)$1	235	3	32	20.3349
b[ggggggguuuuuuuuuuuuggggggg4	chr7:88679712-88679947(-)$1	235	103	132	22.1795
cc"""cccyyyyyyyyyyyyyyyyccc33	chr10:7625625-7625873(-)$1	248	19	48	22.1779
ggg!!ddddvvvvvvvvvvvvvdddd]gg	chr7:133589315-133589553(-)$1	238	89	118	22.7062
:ccc!!cccvvvvvvvvvvvvvccc22cc	chr17:34406174-34406409(+)$1	235	114	143	22.7769
eeee[dddduuuuuuuuuuuudddd]eee	chr2:76544419-76544660(-)$1	241	10	39	20.6043
""ccc[bbvvvvvvvvvvvvvbb]ccc]b	chr2:127124410-127124658(+)$1	248	59	88	21.8244
dd[ggggggguuuuuuuuuuuuggggggg	chr7:119254506-119254741(+)$1	235	66	95	22.3666
e[a!!cccxxxxxxxxxxxxxxxccc22a	chr11:51799963-51800205(-)$1	242	121	150	19.1972
========^^^^^^^^^^^^^^^^^^^^^	chr5:15878304-15878555(+)$1	251	165	194	20.8304
dd!!fffffftttttttttttffffff]d	chr3:97725293-97725538(+)$1	245	37	66	19.3128
eagggggggvvvvvvvvvvvvvggggggg	chr11:51789805-51790053(+)$1	248	206	235	23.6451

#otherMatches

#Seq PSSM
uuaaguauaaaaaaauuaaaauuGUGUUU	chr19:47809707-47809942(+)$1	235	71	100	21.2895
ucucucucucucucucucucucucucucu	chr5:136386344-136386584(-)$1	240	149	178	19.1644
UCCUGUUuuuaauucuucaaucaauagug	chr3:95337413-95337648(+)$1	235	150	179	17.3614
AGGAUACUGCAUCUCUUGUUACUGUAGUG	chr4:109125649-109125887(-)$1	238	17	46	18.3459
cuguggcccuaaaaaguauaaaagucauu	chr13:89135805-89136043(+)$1	238	8	37	20.3451
CAUCUUGCUAUAAAUCUUUGAAAUCUCUU	chr8:114542481-114542716(+)$1	235	146	175	19.4563
UAGCCACUGGUAAUGACUGUAGACAGGGC	chr11:6523715-6523950(-)$1	235	173	202	21.1216
UAUCUUUUACCUUCCUCUGUUUUGAGAGA	chr15:4104015-4104251(+)$1	236	143	172	24.4836
GAUCUCUUGACCUGUUAAUAUUUUGGGAG	chr2:57220188-57220427(+)$1	239	194	223	18.7632
AGAAAGCCUGACCUAGUUGCUUAAGGCUC	chr2:153594688-153594923(+)$1	235	78	107	19.1524
GUGAUCCUAAAAAAAAAUCUGUGUGUGGC	chr12:16992617-16992852(+)$1	235	6	35	18.2612
ACAGUUGUAAAACAUGUAUAAGCUGCUGU	chr16:38245760-38245995(+)$1	235	77	106	22.4526
AAGCAUGGGAAUUUGACGUGCUCAUCAUG	chr7:149689710-149689945(+)$1	235	114	143	20.5942
UUAAAUUUGAUCUUUUCAGCCUUCCUCCC	chr2:35037198-35037452(-)$1	254	17	46	20.0639
ACCAGUGUUAGCUUACUCUUAAUAAUGUC	chr5:136384359-136384619(-)$1	260	40	69	21.9466
UGGUGGGGCCCAUGCAUUUCCAGGUCUGC	chr4:104704625-104704860(-)$1	235	151	180	22.4293
UUAGCAGGUUUUUUUUGUUUUUUCCUUCU	chr16:44160309-44160547(+)$1	238	134	163	19.7193
CGUUUGCUACUAAAAUCUGUGAUGUUGCA	chr5:68012977-68013215(-)$1	238	32	61	22.0650
CUAUGCUACACUAGUUUGCCAUGUAGCAA	chr2:104266800-104267037(-)$1	237	136	165	18.0350
GCUUCUAAGAAUGUCUUAAACUUCAAAGC	chr15:4105022-4105266(+)$1	244	208	237	19.1329
AGCAGUCCCGUUUGGGUGCUUAGGGACUC	chr12:25727102-25727337(+)$1	235	79	108	22.6193
UCUCCUGGUUUUCCUUGUUUCUACCCAGA	chrX:99709798-99710042(-)$1	244	154	183	23.6751
CGCAGGCCUCCUACCGCACUUGUAACCUG	chr7:31339759-31340011(+)$1	252	200	229	19.9980
ucucauuucucuuaaacaacugucuauga	chr6:93867623-93867858(-)$1	235	49	78	20.2136
ugaggguguguguuugugugugagggugu	chr4:108702348-108702586(+)$1	238	171	200	24.6894
AUGAGCACCAUCACCUAAGCGGUAAUCAU	chr3:116445886-116446121(-)$1	235	45	74	19.4242
UGCCAGGCUUGGAACAGUGAAUAGCUUGG	chr5:124951445-124951696(-)$1	251	136	165	21.8796
CUUGGCCAAGGUCAGCAUGUAAUGGAAAG	chr4:147247927-147248162(-)$1	235	22	51	23.0285
UUCCCGGGCCAAGCCCAUACCAGCCCGGG	chr9:107950460-107950695(+)$1	235	41	70	23.7657
GCCCUCUGUGCCCUAAGCAUAUGCACAUG	chr13:99612929-99613169(-)$1	240	7	36	18.8423
GAUGAAGAUGAGUCUUAGAAAAUGUUCAU	chr8:107740674-107740909(+)$1	235	138	167	20.7703
GGAUGGUAGAGAAUUUUGUCAGUCAACUA	chr7:35130363-35130625(-)$1	262	178	207	21.4524
AGCCACAGCaaaauaauaauaauaauaau	chr2:76542175-76542425(-)$1	250	179	208	19.8039
UUCCCUGUGUACUUCAGAAUCAGCCAUUG	chr19:12842903-12843138(-)$1	235	180	209	20.5626
CCAUGUAGAAAAUUUAUUAAAACUACUAG	chr1:82892197-82892444(+)$1	247	173	202	21.0041
CAUUUUUGCCAAAAUACCACUAGUGGAAA	chr5:136386537-136386774(-)$1	237	61	90	23.8607
UUGUGGACACAGAUUUUUGUAGUUUCCAU	chr5:92481805-92482063(-)$1	258	95	124	19.6320
GACAUGUGAACCUUGAAUACAUUACAUUU	chr16:94690321-94690556(+)$1	235	133	162	21.4581
AAUGAUGUAGAACGCCAUAAAAUGCAUUU	chr11:109530395-109530652(+)$1	257	140	169	22.7195
GUGUGCUGCUUGACCACCCCCCCUUCUGU	chr1:75177799-75178035(-)$1	236	56	85	19.0186
gggucugauguaccuccaaacuccugaau	chr11:84009578-84009817(+)$1	239	197	226	19.5886
AAUUUCUUUaaaaaaaaaaaaaaaaaaaa	chr11:35197248-35197483(+)$1	235	94	123	19.5227
AUUAGACCCUAACACAUUUUACAGGGUUU	chr19:12841729-12841976(-)$1	247	84	113	22.6302
CCUGUUuuuguuuguuuguuuauuuguuu	chr9:30957160-30957421(-)$1	261	77	106	19.4769
ACACAGAGCUAUCGUCCCUCUGAGCUCUG	chr4:104704900-104705153(-)$1	253	215	244	22.6790
AAGCAACCAAACCAAAACCAUUUACCUCA	chr15:97965928-97966164(-)$1	236	93	122	20.3527
CUGGCCUGGCCCUUCCCCUGCAGCCCUGC	chr11:77653807-77654042(+)$1	235	172	201	22.0233
CCCUAGGAAGAACAUGCCCACCUCCUGCU	chr16:36035202-36035440(+)$1	238	12	41	17.9702
CUAAUUUGAUGUAGUCCUUUUCAUGCCAG	chr2:76541964-76542206(-)$1	242	61	90	19.9731
AGUUAUUUUGUCAAUAAAACAUGCUUAAA	chr13:21608338-21608573(-)$1	235	3	32	20.3349
CCUCAGCCACCCUCCCCUCCCUGGCUGAA	chr7:88679712-88679947(-)$1	235	103	132	22.1795
UGAAAUAUAAGAAAAAAAUAGGAAAUAAU	chr10:7625625-7625873(-)$1	248	19	48	22.1779
UAAAUCCCCUUCCCGAACUCACGGGGCUU	chr7:133589315-133589553(-)$1	238	89	118	22.7062
CGAUCuguaguaaaccaauguaugcuuau	chr17:34406174-34406409(+)$1	235	114	143	22.7769
AUUUCCAUUUCUUCAAAUAUCAGUGUGAG	chr2:76544419-76544660(-)$1	241	10	39	20.6043
UAGCUGACUGCCUGUGAAUCUGUGAGCAA	chr2:127124410-127124658(+)$1	248	59	88	21.8244
UUCUAGAAUGCUUGUAAAGUCCCGUUUUA	chr7:119254506-119254741(+)$1	235	66	95	22.3666
GCAGAGAAAAAAAGAAAAAGUCCUUCAGU	chr11:51799963-51800205(-)$1	242	121	150	19.1972
AAAUGACAUCAGUCACCACUUCUAAUGCA	chr5:15878304-15878555(+)$1	251	165	194	20.8304
CUGAAAAUGAAAGAUGGCGCCUCGUUUAA	chr3:97725293-97725538(+)$1	245	37	66	19.3128
CCAGCCUCAUUUUACAGCUCACUgaggcu	chr11:51789805-51790053(+)$1	248	206	235	23.6451

#DB
((((((((((...........))))))))	chr19:47809707-47809942(+)$1	1	71	100	21.2895
((...........................	chr5:136386344-136386584(-)$1	1	149	178	19.1644
(((((((...............))))).)	chr3:95337413-95337648(+)$1	1	150	179	17.3614
.((.(((((((...........)))))))	chr4:109125649-109125887(-)$1	1	17	46	18.3459
(((.(((......................	chr13:89135805-89136043(+)$1	1	8	37	20.3451
((...........................	chr8:114542481-114542716(+)$1	1	146	175	19.4563
.((((.(((..............))))))	chr11:6523715-6523950(-)$1	1	173	202	21.1216
(((((((((.............)))))))	chr15:4104015-4104251(+)$1	1	143	172	24.4836
((((((((((............)))))))	chr2:57220188-57220427(+)$1	1	194	223	18.7632
))..(((((..............))))).	chr2:153594688-153594923(+)$1	1	78	107	19.1524
((.((.(...............).)).))	chr12:16992617-16992852(+)$1	1	6	35	18.2612
(((((.((.............)).)))))	chr16:38245760-38245995(+)$1	1	77	106	22.4526
((((((((((...........)).)))))	chr7:149689710-149689945(+)$1	1	114	143	20.5942
(((((..((...................)	chr2:35037198-35037452(-)$1	1	17	46	20.0639
((((((((((............))))).)	chr5:136384359-136384619(-)$1	1	40	69	21.9466
(((((((.((............)))))))	chr4:104704625-104704860(-)$1	1	151	180	22.4293
))((((((.....................	chr16:44160309-44160547(+)$1	1	134	163	19.7193
(...(((.((.............)).)))	chr5:68012977-68013215(-)$1	1	32	61	22.0650
...(((((((...........))))))).	chr2:104266800-104267037(-)$1	1	136	165	18.0350
((((..(((...........)))..))))	chr15:4105022-4105266(+)$1	1	208	237	19.1329
((.((((((.............)))))))	chr12:25727102-25727337(+)$1	1	79	108	22.6193
.(((..(((.............)))..))	chrX:99709798-99710042(-)$1	1	154	183	23.6751
((((((...................))))	chr7:31339759-31340011(+)$1	1	200	229	19.9980
(((((((((..................))	chr6:93867623-93867858(-)$1	1	49	78	20.2136
(((.(.(.(.............).).).)	chr4:108702348-108702586(+)$1	1	171	200	24.6894
((((..(((...........)))..))))	chr3:116445886-116446121(-)$1	1	45	74	19.4242
..(((((((.............)))))))	chr5:124951445-124951696(-)$1	1	136	165	21.8796
(((..(((..............))).)))	chr4:147247927-147248162(-)$1	1	22	51	23.0285
(((((((((.............)))))))	chr9:107950460-107950695(+)$1	1	41	70	23.7657
(((((.(((((...........))))).)	chr13:99612929-99613169(-)$1	1	7	36	18.8423
((((((.((............)).)))))	chr8:107740674-107740909(+)$1	1	138	167	20.7703
))(((((.((............)).))))	chr7:35130363-35130625(-)$1	1	178	207	21.4524
(((.(((((....................	chr2:76542175-76542425(-)$1	1	179	208	19.8039
(((..((.((............))))..)	chr19:12842903-12843138(-)$1	1	180	209	20.5626
))))((((..............))))(((	chr1:82892197-82892444(+)$1	1	173	202	21.0041
(.(((((((.............)))))))	chr5:136386537-136386774(-)$1	1	61	90	23.8607
))(((((.((...........)).)))))	chr5:92481805-92482063(-)$1	1	95	124	19.6320
((.((((((............)))))).)	chr16:94690321-94690556(+)$1	1	133	162	21.4581
(..((((((.............)))))))	chr11:109530395-109530652(+)$1	1	140	169	22.7195
(((.((.....................))	chr1:75177799-75178035(-)$1	1	56	85	19.0186
(((((.((.....................	chr11:84009578-84009817(+)$1	1	197	226	19.5886
....(((((....................	chr11:35197248-35197483(+)$1	1	94	123	19.5227
)))(((((((............)))))))	chr19:12841729-12841976(-)$1	1	84	113	22.6302
((...........................	chr9:30957160-30957421(-)$1	1	77	106	19.4769
((.(((((((............)))))))	chr4:104704900-104705153(-)$1	1	215	244	22.6790
((((((.......................	chr15:97965928-97966164(-)$1	1	93	122	20.3527
(((((..(((............)))..))	chr11:77653807-77654042(+)$1	1	172	201	22.0233
((((((((..............))))..(	chr16:36035202-36035440(+)$1	1	12	41	17.9702
((....(((...........)))....))	chr2:76541964-76542206(-)$1	1	61	90	19.9731
(((((((((....................	chr13:21608338-21608573(-)$1	1	3	32	20.3349
(.(((((((............))))))).	chr7:88679712-88679947(-)$1	1	103	132	22.1795
((...(((................)))..	chr10:7625625-7625873(-)$1	1	19	48	22.1779
(((..((((.............)))).))	chr7:133589315-133589553(-)$1	1	89	118	22.7062
.(((..(((.............)))..))	chr17:34406174-34406409(+)$1	1	114	143	22.7769
((((.((((............)))).)))	chr2:76544419-76544660(-)$1	1	10	39	20.6043
..(((.((.............)).))).)	chr2:127124410-127124658(+)$1	1	59	88	21.8244
((.(((((((............)))))))	chr7:119254506-119254741(+)$1	1	66	95	22.3666
(.(..(((...............)))..)	chr11:51799963-51800205(-)$1	1	121	150	19.1972
((((((((.....................	chr5:15878304-15878555(+)$1	1	165	194	20.8304
((..((((((...........)))))).)	chr3:97725293-97725538(+)$1	1	37	66	19.3128
(((((((((.............)))))))	chr11:51789805-51790053(+)$1	1	206	235	23.6451

#PSSM
c : 0.21	e : 0.14	g : 0.11	i : 0.11	d : 0.09	= : 0.08	: : 0.06	b : 0.03	f : 0.03	+ : 0.01	[ : 0.01	h : 0.01	# : 0.01	F : 0.01	" : 0.01	
c : 0.22	g : 0.11	e : 0.11	i : 0.11	d : 0.09	= : 0.06	[ : 0.04	b : 0.03	" : 0.03	f : 0.03	+ : 0.01	: : 0.01	h : 0.01	! : 0.01	# : 0.01	F : 0.01	a : 0.01	
e : 0.14	g : 0.13	i : 0.11	[ : 0.08	c : 0.08	= : 0.06	^ : 0.04	a : 0.04	f : 0.04	d : 0.03	h : 0.03	" : 0.03	! : 0.03	# : 0.03	b : 0.01	: : 0.01	+ : 0.01	F : 0.01	
g : 0.18	e : 0.13	i : 0.09	f : 0.09	[ : 0.08	! : 0.08	= : 0.06	^ : 0.04	c : 0.04	h : 0.03	" : 0.03	# : 0.03	d : 0.01	: : 0.01	b : 0.01	F : 0.01	
g : 0.19	e : 0.14	! : 0.13	i : 0.09	f : 0.09	= : 0.06	^ : 0.04	c : 0.04	d : 0.04	b : 0.03	h : 0.01	a : 0.01	# : 0.01	" : 0.01	[ : 0.01	
g : 0.19	e : 0.11	[ : 0.11	! : 0.09	f : 0.09	c : 0.08	i : 0.06	d : 0.06	= : 0.04	^ : 0.04	b : 0.03	h : 0.01	# : 0.01	
c : 0.18	g : 0.16	e : 0.13	^ : 0.09	f : 0.08	b : 0.06	i : 0.06	d : 0.06	= : 0.04	a : 0.03	! : 0.03	h : 0.01	[ : 0.01	
c : 0.16	g : 0.14	^ : 0.11	[ : 0.09	e : 0.08	b : 0.08	f : 0.08	i : 0.06	d : 0.06	= : 0.04	x : 0.03	h : 0.01	
^ : 0.16	g : 0.14	b : 0.13	c : 0.11	e : 0.08	f : 0.06	x : 0.04	i : 0.04	w : 0.04	= : 0.03	v : 0.03	d : 0.03	h : 0.01	a : 0.01	y : 0.01	
^ : 0.24	v : 0.21	b : 0.09	g : 0.08	w : 0.08	u : 0.06	x : 0.04	t : 0.04	e : 0.03	= : 0.01	h : 0.01	c : 0.01	y : 0.01	f : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.13	w : 0.08	x : 0.04	g : 0.01	e : 0.01	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.16	w : 0.08	x : 0.04	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.16	w : 0.08	x : 0.04	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.16	w : 0.08	x : 0.04	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.16	w : 0.08	x : 0.04	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.16	w : 0.08	x : 0.04	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.16	w : 0.08	x : 0.04	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.16	w : 0.08	x : 0.04	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.16	w : 0.08	x : 0.04	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.16	w : 0.08	x : 0.04	y : 0.01	
^ : 0.24	v : 0.22	u : 0.21	t : 0.11	w : 0.08	x : 0.04	c : 0.04	y : 0.01	
^ : 0.24	v : 0.19	u : 0.14	w : 0.08	b : 0.08	x : 0.04	c : 0.04	t : 0.03	g : 0.03	f : 0.03	= : 0.01	y : 0.01	d : 0.01	
^ : 0.24	g : 0.14	b : 0.13	c : 0.11	f : 0.06	d : 0.06	e : 0.04	= : 0.03	w : 0.03	a : 0.03	h : 0.01	v : 0.01	i : 0.01	y : 0.01	x : 0.01	
^ : 0.24	g : 0.14	] : 0.11	c : 0.09	e : 0.06	b : 0.06	f : 0.06	d : 0.06	= : 0.03	2 : 0.03	h : 0.01	i : 0.01	4 : 0.01	y : 0.01	
^ : 0.24	g : 0.16	c : 0.13	e : 0.08	f : 0.08	d : 0.06	b : 0.04	i : 0.04	= : 0.03	2 : 0.03	h : 0.01	a : 0.01	] : 0.01	4 : 0.01	
^ : 0.22	g : 0.18	e : 0.11	f : 0.09	c : 0.06	] : 0.06	i : 0.04	2 : 0.04	d : 0.04	= : 0.03	b : 0.03	h : 0.01	4 : 0.01	
^ : 0.22	g : 0.18	e : 0.14	f : 0.09	2 : 0.08	c : 0.06	i : 0.04	= : 0.03	] : 0.03	d : 0.01	h : 0.01	a : 0.01	: : 0.01	4 : 0.01	
^ : 0.19	g : 0.19	] : 0.11	e : 0.11	c : 0.08	i : 0.06	f : 0.06	= : 0.03	d : 0.03	2 : 0.03	h : 0.01	b : 0.01	: : 0.01	3 : 0.01	
^ : 0.18	g : 0.18	e : 0.13	c : 0.09	i : 0.08	b : 0.06	d : 0.06	= : 0.04	f : 0.03	a : 0.03	h : 0.01	: : 0.01	0 : 0.01	4 : 0.01	3 : 0.01	

#score	1274.7770807640145
#seq	61
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_UTR_m3_run2.txt

#BEAR
hhhhhvvvvvvvvvvvvvhhhhhhh	chr8:35893186-35893387(-)$1	201	62	87	20.7788
"""cccuuuuuuuuuuuuccc4444	chr5:102263287-102263488(-)$1	201	154	179	23.6732
eeeyyyyyyyyyyyyyyyyeeeee]	chr2:117097013-117097214(+)$1	201	27	52	22.2023
ffffffvvvvvvvvvvvvvffffff	chr4:25538450-25538651(-)$1	201	25	50	22.0082
b[dddduuuuuuuuuuuuddddbb3	chr7:97594940-97595141(+)$1	201	108	133	22.7627
:fffffftttttttttttffffff:	chr15:100223997-100224198(-)$1	201	157	182	19.9146
e!!ccctttttttttttccc22eee	chr11:78139877-78140078(+)$1	201	75	100	22.2329
e!!bbvvvvvvvvvvvvvbb22eee	chr6:126586833-126587034(-)$1	201	155	180	21.8084
[cccwwwwwwwwwwwwwwccc]ddd	chrX:147418846-147419047(-)$1	201	79	104	21.6837
!!eeeeettttttttttteeeee22	chr5:36227466-36227667(+)$1	201	29	54	22.5253
gggggggtttttttttttggggggg	chrX:162824641-162824842(+)$1	201	13	38	22.5521
[cccwwwwwwwwwwwwwwccc]fff	chr3:107270498-107270699(-)$1	201	34	59	21.9907
ffffffvvvvvvvvvvvvvffffff	chr5:135637287-135637488(+)$1	201	83	108	22.0082
f!!cccuuuuuuuuuuuuccc22ff	chr13:100194390-100194591(-)$1	201	113	138	23.5722
!ddddvvvvvvvvvvvvvdddd333	chr11:97373663-97373864(-)$1	201	17	42	23.1297
ffffffuuuuuuuuuuuuffffff]	chr2:128437583-128437784(-)$1	201	149	174	23.0228
$eeeeeuuuuuuuuuuuueeeee66	chr18:13151333-13151534(+)$1	201	155	180	22.6720
eeeccctttttttttttccc]eeee	chr17:64632287-64632488(-)$1	201	40	65	22.5109
ddyyyyyyyyyyyyyyyydddd333	chr18:64148885-64149086(+)$1	201	141	166	21.6552
"eeeeevvvvvvvvvvvvveeeee2	chr16:66662952-66663153(-)$1	201	45	70	22.8378
eeeeewwwwwwwwwwwwwweeeee:	chr1:66742443-66742644(+)$1	201	88	113	21.1611
##a[ccctttttttttttccc]a55	chr16:92082874-92083075(+)$1	201	116	141	21.3129
ddddddwwwwwwwwwwwwwwdddd:	chr11:97606907-97607108(-)$1	201	40	65	19.8921
ddd[bbuuuuuuuuuuuubb]dddd	chr3:103544404-103544605(-)$1	201	136	161	22.3239
dd[bbwwwwwwwwwwwwwwbb]ddd	chr16:56008746-56008947(+)$1	201	154	179	20.4647
eeeeewwwwwwwwwwwwwweeeee]	chr3:7552252-7552453(+)$1	201	78	103	22.1541
##dddduuuuuuuuuuuudddd333	chr3:126626549-126626750(-)$1	201	86	111	23.6451
d[ddddtttttttttttdddddddd	chr13:41733002-41733203(+)$1	201	155	180	21.5190
iiiiiiuuuuuuuuuuuuiiiiiii	chr18:35023599-35023800(+)$1	201	48	73	23.6887
ffffffvvvvvvvvvvvvvffffff	chr14:78894386-78894587(-)$1	201	11	36	22.0082
hhhhhvvvvvvvvvvvvvhhhhhhh	chrX:106356374-106356575(+)$1	201	167	192	20.7788
ddyyyyyyyyyyyyyyyyddddggg	chr5:108552064-108552265(-)$1	201	48	73	21.4260
ffffwwwwwwwwwwwwwwffffff2	chr7:125263150-125263351(-)$1	201	105	130	21.2242
%dddd[attttttttttta]dddd5	chr12:107076447-107076648(+)$1	201	87	112	21.4416
::dddduuuuuuuuuuuuddddGGG	chr2:130854077-130854278(+)$1	201	140	165	19.6788
c[ddddvvvvvvvvvvvvvdddd44	chr14:119378786-119378987(+)$1	201	137	162	22.6068
fff[avvvvvvvvvvvvva]fffff	chr1:168245616-168245817(+)$1	201	101	126	22.6762
f[dddduuuuuuuuuuuudddd]ff	chr12:75047603-75047804(+)$1	201	155	180	23.3672
ff[ddddtttttttttttdddd]ff	chr4:82450987-82451188(-)$1	201	88	113	22.1707
ggyyyyyyyyyyyyyyyyggggggg	chr15:100873828-100874029(+)$1	201	108	133	21.8726
[eeeeeuuuuuuuuuuuueeeee]c	chr13:19449521-19449722(-)$1	201	106	131	23.7368
[eeeeeuuuuuuuuuuuueeeee]c	chr15:98372795-98372996(-)$1	201	142	167	23.7368
hhhyyyyyyyyyyyyyyyyhhhhhh	chr3:130300990-130301191(+)$1	201	171	196	20.4080
ddd!!bbtttttttttttbbdddd]	chr16:31094083-31094284(-)$1	201	8	33	21.7351
!eeeeettttttttttteeeee333	chr13:98022062-98022263(+)$1	201	118	143	22.5944
fffffwwwwwwwwwwwwwwffffff	chr19:32899712-32899913(+)$1	201	145	170	21.3080
[eeeeeuuuuuuuuuuuueeeeeee	chr1:21388472-21388673(-)$1	201	64	89	23.6203
ffffffuuuuuuuuuuuuffffffG	chrX:158852784-158852985(-)$1	201	65	90	22.3673
ffyyyyyyyyyyyyyyyyffffff]	chr18:69845895-69846096(+)$1	201	87	112	21.4412
eeeeewwwwwwwwwwwwwweeeee:	chr8:71430348-71430549(+)$1	201	0	25	21.1611
gggggggtttttttttttggggggg	chr11:45723978-45724179(+)$1	201	78	103	22.5521
[cccbbyyyyyyyyyyyyyyyybb]	chr3:40594918-40595119(+)$1	201	97	122	19.8595
gggggggtttttttttttggggggg	chr11:106019669-106019870(-)$1	201	119	144	22.5521
gggggvvvvvvvvvvvvvggggggg	chr10:59596116-59596317(+)$1	201	10	35	23.1605
"cccwwwwwwwwwwwwwwccc]eee	chrX:149470910-149471111(-)$1	201	74	99	21.9249
d[eeeeettttttttttteeeee]d	chr5:14861803-14862004(+)$1	201	140	165	22.2938
ggggggtttttttttttggggggg2	chr4:80925263-80925464(-)$1	201	56	81	22.2291
[ccc[bbtttttttttttbb]ccc]	chr1:162151975-162152176(-)$1	201	162	187	22.0935
c!!ddddtttttttttttdddd22c	chr16:32389380-32389581(+)$1	201	13	38	22.0173
ccddddvvvvvvvvvvvvvdddd]c	chr10:112363830-112364031(-)$1	201	138	163	22.4144
ggyyyyyyyyyyyyyyyyggggggg	chr3:138566457-138566658(+)$1	201	162	187	21.8726
ee!!bbtttttttttttbb22eeee	chr9:20158452-20158653(-)$1	201	9	34	21.2838
ee[cccuuuuuuuuuuuuccc22ee	chr7:6659842-6660043(-)$1	201	131	156	23.4353
"bbcccuuuuuuuuuuuuccc22bb	chr17:69638471-69638672(+)$1	201	49	74	22.3463
iiiiiiitttttttttttiiiiiii	chr2:161353828-161354029(-)$1	201	166	191	22.3762
===yyyyyyyyyyyyyyyy======	chr17:28884623-28884824(+)$1	201	105	130	22.1758
gggggguuuuuuuuuuuuggggggg	chr18:36450551-36450752(+)$1	201	6	31	23.7651
ddd[bbtttttttttttbb]dddd3	chr5:84494815-84495016(-)$1	201	103	128	21.5472

#otherMatches

#Seq PSSM
ACAUAAACAGAGGGAAGCUAUGUGA	chr8:35893186-35893387(-)$1	201	62	87	20.7788
UAAACGCUCAAAUACACACGUGAAU	chr5:102263287-102263488(-)$1	201	154	179	23.6732
GACUGUAAACUGGUAUUUUGUUUAG	chr2:117097013-117097214(+)$1	201	27	52	22.2023
UUCAGGCAAACUAAAAUACUCUGAA	chr4:25538450-25538651(-)$1	201	25	50	22.0082
CUCAUGGUCUUGUUUUUACAUGGUA	chr7:97594940-97595141(+)$1	201	108	133	22.7627
CGCUGUGUUUCACUCACCCACAGCU	chr15:100223997-100224198(-)$1	201	157	182	19.9146
UAUCUUUAUCCAGCGCCAAGUCAUC	chr11:78139877-78140078(+)$1	201	75	100	22.2329
CGUACGAAGCAGCCAUAAGUUGGUG	chr6:126586833-126587034(-)$1	201	155	180	21.8084
UGUCCAACUUAAUUCACUGAUCUCA	chrX:147418846-147419047(-)$1	201	79	104	21.6837
AUCUGCUUCCUGCCACUUAGCAGUC	chr5:36227466-36227667(+)$1	201	29	54	22.5253
AACUUGGUCAUUUUAUUCCCAAGUU	chrX:162824641-162824842(+)$1	201	13	38	22.5521
UGUACAGACCUAAACACAUACCAGG	chr3:107270498-107270699(-)$1	201	34	59	21.9907
UUCAGUCCUUGUAAGUUUCACUGGA	chr5:135637287-135637488(+)$1	201	83	108	22.0082
ACAGCAUCUGCCUUCCUUUGUCUUG	chr13:100194390-100194591(-)$1	201	113	138	23.5722
AUUCUUCCAUCUCCUUCUAGAAGCC	chr11:97373663-97373864(-)$1	201	17	42	23.1297
AGUAGGAACUGCAGAAUGCCUACUC	chr2:128437583-128437784(-)$1	201	149	174	23.0228
cuggguacauuguaaCAAACCCAUU	chr18:13151333-13151534(+)$1	201	155	180	22.6720
ACGCUCCCUUCCCACAUGAGAUGUG	chr17:64632287-64632488(-)$1	201	40	65	22.5109
UUUCACUCUCAUUAAAAUAAUGCUC	chr18:64148885-64149086(+)$1	201	141	166	21.6552
CCAUUGCUCUUUUAACAUACAGUGC	chr16:66662952-66663153(-)$1	201	45	70	22.8378
ACAUUAUACAUCUCACAACAAUGUU	chr1:66742443-66742644(+)$1	201	88	113	21.1611
UAUGUUGAAAGAUUUGCACAAGACC	chr16:92082874-92083075(+)$1	201	116	141	21.3129
GCACUGUAAUUCUUAAAACUCAGUU	chr11:97606907-97607108(-)$1	201	40	65	19.8921
UGGUUGCUCAUCCGUCAUCAUCCGC	chr3:103544404-103544605(-)$1	201	136	161	22.3239
GAAACUAAAAUUUGAAAUUGUCUUA	chr16:56008746-56008947(+)$1	201	154	179	20.4647
UGAGAUUUUUCUAUUUCUUUCUCAU	chr3:7552252-7552453(+)$1	201	78	103	22.1541
UAUGCAACUUCCCAUUUCUGCGCAG	chr3:126626549-126626750(-)$1	201	86	111	23.6451
acucuaagccaaugagauagaucug	chr13:41733002-41733203(+)$1	201	155	180	21.5190
GUUCUUCACCUCUAUCCAAAGGACU	chr18:35023599-35023800(+)$1	201	48	73	23.6887
aguguuucucaaccuuccuaacacu	chr14:78894386-78894587(-)$1	201	11	36	22.0082
UUUGAGAAAGUACAAGUAUCAAAGA	chrX:106356374-106356575(+)$1	201	167	192	20.7788
UACCAUAAGACUUAGCACUAGGUAU	chr5:108552064-108552265(-)$1	201	48	73	21.4260
GUUAGUUCUAGUCCAUAAUGGCCUU	chr7:125263150-125263351(-)$1	201	105	130	21.2242
UGAAUCCUUCAUUUCGCUGCAUUCU	chr12:107076447-107076648(+)$1	201	87	112	21.4416
CUCUGGGAAGUUAUCCUACCAGGCC	chr2:130854077-130854278(+)$1	201	140	165	19.6788
gcaggcaagaaaacucacagcuuuu	chr14:119378786-119378987(+)$1	201	137	162	22.6068
CAUGCUAGGACCAAAAGUGGGUGGA	chr1:168245616-168245817(+)$1	201	101	126	22.6762
AAACAUCUUGUUUUUUCUAUGUAUA	chr12:75047603-75047804(+)$1	201	155	180	23.3672
UGUAUGAUUUAAUUUUUUUCAUUUA	chr4:82450987-82451188(-)$1	201	88	113	22.1707
ACCACACCAUCACCAGCAGUUCACA	chr15:100873828-100874029(+)$1	201	108	133	21.8726
UUGUGUUUUUAAACUCAUGCACAUG	chr13:19449521-19449722(-)$1	201	106	131	23.7368
ACAAUAAGAAGAGACAUGUAUUGAC	chr15:98372795-98372996(-)$1	201	142	167	23.7368
CCAUCAUUAAAUGCAGCCUUGGAGG	chr3:130300990-130301191(+)$1	201	171	196	20.4080
AGGCUGCUUGUUCUGACUGCCCUGC	chr16:31094083-31094284(-)$1	201	8	33	21.7351
UUAGGCUAAUUAUACACGUCUGUCU	chr13:98022062-98022263(+)$1	201	118	143	22.5944
UGUGUUACCUUAAACUUUUACAUAU	chr19:32899712-32899913(+)$1	201	145	170	21.3080
UCCUGAAAAACAACUAAAUCAGGAA	chr1:21388472-21388673(-)$1	201	64	89	23.6203
GCCUUUAAUAUGAUAUAGGAAGGCA	chrX:158852784-158852985(-)$1	201	65	90	22.3673
CUACACAAACAUUUCAUAAGUGUUC	chr18:69845895-69846096(+)$1	201	87	112	21.4412
GGAAUAUGUUAGAGAAGUAGUUCCA	chr8:71430348-71430549(+)$1	201	0	25	21.1611
GAUACAACUUUGUUUCCAUUGUAUU	chr11:45723978-45724179(+)$1	201	78	103	22.5521
AUUUCAGAAAAAAAAUCAUGAUUGU	chr3:40594918-40595119(+)$1	201	97	122	19.8595
GGGAGGCCCACAAGCCCAGCUUCCC	chr11:106019669-106019870(-)$1	201	119	144	22.5521
AUUCCUUUCUGCCACCCUGGAAUGG	chr10:59596116-59596317(+)$1	201	10	35	23.1605
UUCAUUUUAUAACACUGUUGACUAA	chrX:149470910-149471111(-)$1	201	74	99	21.9249
UGUUGGUUUAAAUUUAGUACUAAGA	chr5:14861803-14862004(+)$1	201	140	165	22.2938
UGUUUGUUACUCACAGCCAAGCAUC	chr4:80925263-80925464(-)$1	201	56	81	22.2291
CUUACUAUUUUAUAUAUUUGAUAAU	chr1:162151975-162152176(-)$1	201	162	187	22.0935
AUUGGUUUGGGCAGAUGUGACCUUU	chr16:32389380-32389581(+)$1	201	13	38	22.0173
CACAAGUUUCCUUUUUCCUUUUGUU	chr10:112363830-112364031(-)$1	201	138	163	22.4144
UAAAUAAAAAACCAAGCCUAGUAUA	chr3:138566457-138566658(+)$1	201	162	187	21.8726
UGUAGAGAGAGGAAAGAUCACCAGU	chr9:20158452-20158653(-)$1	201	9	34	21.2838
CUAGUGACAAUUCCAGACCACAGAG	chr7:6659842-6660043(-)$1	201	131	156	23.4353
UCAAGUAACCCAUCGACAGCUCAUG	chr17:69638471-69638672(+)$1	201	49	74	22.3463
UGAAGAAACCUGAGCAUCUUCUUCA	chr2:161353828-161354029(-)$1	201	166	191	22.3762
UUUAUAAACAUGAAUCCUCAGGGGU	chr17:28884623-28884824(+)$1	201	105	130	22.1758
GAUGCUCUUUUUGUUUAAAGCAUCU	chr18:36450551-36450752(+)$1	201	6	31	23.7651
CAGCACUGUCUUCCUUUGUACUGAU	chr5:84494815-84495016(-)$1	201	103	128	21.5472

#DB
(((((.............)))))))	chr8:35893186-35893387(-)$1	1	62	87	20.7788
...(((............)))....	chr5:102263287-102263488(-)$1	1	154	179	23.6732
(((................))))).	chr2:117097013-117097214(+)$1	1	27	52	22.2023
((((((.............))))))	chr4:25538450-25538651(-)$1	1	25	50	22.0082
(.((((............)))))).	chr7:97594940-97595141(+)$1	1	108	133	22.7627
.((((((...........)))))).	chr15:100223997-100224198(-)$1	1	157	182	19.9146
(..(((...........)))..)))	chr11:78139877-78140078(+)$1	1	75	100	22.2329
(..((.............))..)))	chr6:126586833-126587034(-)$1	1	155	180	21.8084
.(((..............))).)))	chrX:147418846-147419047(-)$1	1	79	104	21.6837
..(((((...........)))))..	chr5:36227466-36227667(+)$1	1	29	54	22.5253
(((((((...........)))))))	chrX:162824641-162824842(+)$1	1	13	38	22.5521
.(((..............))).)))	chr3:107270498-107270699(-)$1	1	34	59	21.9907
((((((.............))))))	chr5:135637287-135637488(+)$1	1	83	108	22.0082
(..(((............)))..))	chr13:100194390-100194591(-)$1	1	113	138	23.5722
.((((.............))))...	chr11:97373663-97373864(-)$1	1	17	42	23.1297
((((((............)))))).	chr2:128437583-128437784(-)$1	1	149	174	23.0228
.(((((............)))))..	chr18:13151333-13151534(+)$1	1	155	180	22.6720
((((((...........))).))))	chr17:64632287-64632488(-)$1	1	40	65	22.5109
((................))))...	chr18:64148885-64149086(+)$1	1	141	166	21.6552
.(((((.............))))).	chr16:66662952-66663153(-)$1	1	45	70	22.8378
(((((..............))))).	chr1:66742443-66742644(+)$1	1	88	113	21.1611
..(.(((...........))).)..	chr16:92082874-92083075(+)$1	1	116	141	21.3129
))((((..............)))).	chr11:97606907-97607108(-)$1	1	40	65	19.8921
(((.((............)).))))	chr3:103544404-103544605(-)$1	1	136	161	22.3239
((.((..............)).)))	chr16:56008746-56008947(+)$1	1	154	179	20.4647
(((((..............))))).	chr3:7552252-7552453(+)$1	1	78	103	22.1541
..((((............))))...	chr3:126626549-126626750(-)$1	1	86	111	23.6451
(.((((...........))))))))	chr13:41733002-41733203(+)$1	1	155	180	21.5190
((((((............)))))))	chr18:35023599-35023800(+)$1	1	48	73	23.6887
((((((.............))))))	chr14:78894386-78894587(-)$1	1	11	36	22.0082
(((((.............)))))))	chrX:106356374-106356575(+)$1	1	167	192	20.7788
((................)))))))	chr5:108552064-108552265(-)$1	1	48	73	21.4260
((((..............)))))).	chr7:125263150-125263351(-)$1	1	105	130	21.2242
.((((.(...........).)))).	chr12:107076447-107076648(+)$1	1	87	112	21.4416
..((((............)))))))	chr2:130854077-130854278(+)$1	1	140	165	19.6788
(.((((.............))))..	chr14:119378786-119378987(+)$1	1	137	162	22.6068
(((.(.............).)))))	chr1:168245616-168245817(+)$1	1	101	126	22.6762
(.((((............)))).))	chr12:75047603-75047804(+)$1	1	155	180	23.3672
((.((((...........)))).))	chr4:82450987-82451188(-)$1	1	88	113	22.1707
((................)))))))	chr15:100873828-100874029(+)$1	1	108	133	21.8726
.(((((............))))).)	chr13:19449521-19449722(-)$1	1	106	131	23.7368
.(((((............))))).)	chr15:98372795-98372996(-)$1	1	142	167	23.7368
(((................))))))	chr3:130300990-130301191(+)$1	1	171	196	20.4080
(((..((...........)))))).	chr16:31094083-31094284(-)$1	1	8	33	21.7351
.(((((...........)))))...	chr13:98022062-98022263(+)$1	1	118	143	22.5944
(((((..............))))))	chr19:32899712-32899913(+)$1	1	145	170	21.3080
.(((((............)))))))	chr1:21388472-21388673(-)$1	1	64	89	23.6203
((((((............)))))))	chrX:158852784-158852985(-)$1	1	65	90	22.3673
((................)))))).	chr18:69845895-69846096(+)$1	1	87	112	21.4412
(((((..............))))).	chr8:71430348-71430549(+)$1	1	0	25	21.1611
(((((((...........)))))))	chr11:45723978-45724179(+)$1	1	78	103	22.5521
.(((((................)).	chr3:40594918-40595119(+)$1	1	97	122	19.8595
(((((((...........)))))))	chr11:106019669-106019870(-)$1	1	119	144	22.5521
(((((.............)))))))	chr10:59596116-59596317(+)$1	1	10	35	23.1605
.(((..............))).)))	chrX:149470910-149471111(-)$1	1	74	99	21.9249
(.(((((...........))))).)	chr5:14861803-14862004(+)$1	1	140	165	22.2938
((((((...........))))))).	chr4:80925263-80925464(-)$1	1	56	81	22.2291
.(((.((...........)).))).	chr1:162151975-162152176(-)$1	1	162	187	22.0935
(..((((...........))))..)	chr16:32389380-32389581(+)$1	1	13	38	22.0173
((((((.............)))).)	chr10:112363830-112364031(-)$1	1	138	163	22.4144
((................)))))))	chr3:138566457-138566658(+)$1	1	162	187	21.8726
((..((...........))..))))	chr9:20158452-20158653(-)$1	1	9	34	21.2838
((.(((............)))..))	chr7:6659842-6660043(-)$1	1	131	156	23.4353
.(((((............)))..))	chr17:69638471-69638672(+)$1	1	49	74	22.3463
(((((((...........)))))))	chr2:161353828-161354029(-)$1	1	166	191	22.3762
(((................))))))	chr17:28884623-28884824(+)$1	1	105	130	22.1758
((((((............)))))))	chr18:36450551-36450752(+)$1	1	6	31	23.7651
(((.((...........)).)))).	chr5:84494815-84495016(-)$1	1	103	128	21.5472

#PSSM
f : 0.17	e : 0.13	d : 0.13	g : 0.11	[ : 0.10	" : 0.05	h : 0.04	! : 0.04	c : 0.04	: : 0.02	# : 0.02	i : 0.02	b : 0.01	$ : 0.01	% : 0.01	= : 0.01	
e : 0.19	f : 0.16	d : 0.13	g : 0.11	c : 0.08	[ : 0.07	! : 0.07	h : 0.04	# : 0.02	i : 0.02	" : 0.01	: : 0.01	b : 0.01	= : 0.01	
e : 0.19	d : 0.19	f : 0.13	g : 0.08	! : 0.07	c : 0.07	y : 0.07	h : 0.04	[ : 0.04	i : 0.02	" : 0.01	a : 0.01	b : 0.01	= : 0.01	
d : 0.17	c : 0.16	e : 0.16	y : 0.11	f : 0.11	g : 0.08	[ : 0.05	h : 0.02	b : 0.02	i : 0.02	! : 0.02	
d : 0.17	e : 0.16	y : 0.11	c : 0.10	f : 0.10	b : 0.08	g : 0.08	w : 0.05	h : 0.02	i : 0.02	a : 0.01	! : 0.01	[ : 0.01	
d : 0.14	w : 0.13	y : 0.11	e : 0.11	c : 0.10	v : 0.08	f : 0.08	b : 0.08	g : 0.07	i : 0.02	[ : 0.01	
u : 0.25	v : 0.17	w : 0.14	y : 0.13	t : 0.10	g : 0.04	e : 0.02	d : 0.02	b : 0.02	f : 0.01	c : 0.01	a : 0.01	i : 0.01	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
t : 0.29	u : 0.25	v : 0.17	w : 0.14	y : 0.13	
u : 0.25	t : 0.19	v : 0.17	w : 0.14	y : 0.13	c : 0.02	b : 0.02	d : 0.01	e : 0.01	g : 0.01	
c : 0.14	d : 0.14	g : 0.11	e : 0.10	v : 0.08	b : 0.08	w : 0.08	f : 0.07	y : 0.05	h : 0.02	i : 0.02	a : 0.02	
e : 0.17	d : 0.17	c : 0.14	f : 0.13	g : 0.11	b : 0.07	h : 0.04	] : 0.04	i : 0.02	w : 0.01	y : 0.01	2 : 0.01	= : 0.01	
d : 0.23	e : 0.17	f : 0.14	c : 0.11	g : 0.11	h : 0.04	2 : 0.04	] : 0.04	i : 0.02	b : 0.01	y : 0.01	= : 0.01	
d : 0.25	e : 0.20	f : 0.14	g : 0.11	2 : 0.07	] : 0.07	h : 0.04	i : 0.02	4 : 0.01	y : 0.01	c : 0.01	= : 0.01	
e : 0.23	f : 0.16	d : 0.14	g : 0.13	2 : 0.05	3 : 0.05	h : 0.04	b : 0.02	i : 0.02	] : 0.02	4 : 0.01	a : 0.01	G : 0.01	c : 0.01	= : 0.01	
f : 0.20	e : 0.17	g : 0.13	d : 0.11	3 : 0.05	] : 0.05	h : 0.04	b : 0.04	4 : 0.02	2 : 0.02	i : 0.02	6 : 0.01	5 : 0.01	G : 0.01	c : 0.01	= : 0.01	
f : 0.13	g : 0.11	] : 0.10	e : 0.10	3 : 0.08	d : 0.07	: : 0.05	2 : 0.05	c : 0.05	h : 0.04	4 : 0.02	5 : 0.02	i : 0.02	G : 0.02	6 : 0.01	b : 0.01	= : 0.01	

#score	1502.966538908341
#seq	68
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_UTR_m3_run2.txt

#BEAR
eeeeqqqqqqqqeeee	chr2:151919800-151920024(+)$1	224	169	185	13.3521
h[bbqqqqqqqqbb]h	chr8:119413155-119413376(-)$1	221	180	196	11.9515
ddddqqqqqqqqdddd	chr9:108720290-108720511(+)$1	221	130	146	13.9869
ggggqqqqqqqqgggg	chr12:82286101-82286324(+)$1	223	204	220	12.9726
ffffqqqqqqqqffff	chr8:126025856-126026079(+)$1	223	17	33	12.0368
!!bbqqqqqqqqbbee	chr11:78285998-78286221(+)$1	223	20	36	12.6610
ddddqqqqqqqqdddd	chr4:149021588-149021818(+)$1	230	137	153	13.9869
ddddqqqqqqqqdddd	chr10:79979827-79980063(+)$1	236	54	70	13.9869
#cccqqqqqqqqccc4	chr8:73173115-73173340(-)$1	225	33	49	13.5549
ddddqqqqqqqqdddd	chr11:74490115-74490336(-)$1	221	130	146	13.9869
eebbqqqqqqqqbb33	chr8:97876408-97876628(-)$1	220	119	135	12.4916
ee[aqqqqqqqqaeee	chr7:134942912-134943137(+)$1	225	26	42	13.2111
eeeeqqqqqqqqeeee	chr3:151897974-151898190(-)$1	216	99	115	13.3521
iiiiqqqqqqqqiiii	chr11:69672122-69672347(+)$1	225	71	87	12.9739
ddddqqqqqqqqdddd	chr11:95910414-95910652(-)$1	238	137	153	13.9869
"cccqqqqqqqqccc2	chr1:78097956-78098173(+)$1	217	115	131	13.4462
#cccqqqqqqqqccc3	chr17:17665723-17665950(-)$1	227	87	103	13.5854
:cccqqqqqqqqccc:	chr2:157295631-157295847(+)$1	216	14	30	11.9809
eeeeqqqqqqqqeeee	chr15:73617430-73617650(+)$1	220	170	186	13.3521
eebbqqqqqqqqbb]e	chr10:45037626-45037848(+)$1	222	39	55	12.5635
!bbaqqqqqqqqa]bb	chr16:8660515-8660739(+)$1	224	192	208	11.9962
"cccqqqqqqqqccc4	chr10:127564550-127564793(+)$1	243	15	31	13.5833
eeeeqqqqqqqqeeee	chr15:3933732-3933968(-)$1	236	177	193	13.3521
cccaqqqqqqqqa]cc	chr8:89367972-89368195(-)$1	223	113	129	13.1706
ddddqqqqqqqqdddd	chr19:8816531-8816758(+)$1	227	178	194	13.9869
ddddqqqqqqqqdddd	chr2:28542773-28543007(+)$1	234	134	150	13.9869
:cccqqqqqqqqccc:	chr15:27661454-27661707(-)$1	253	40	56	11.9809
ddddqqqqqqqqdddd	chr19:46386703-46386946(-)$1	243	148	164	13.9869
ddddqqqqqqqqdddd	chr12:66231560-66231781(+)$1	221	116	132	13.9869
:cccqqqqqqqqccc:	chr16:19654139-19654362(+)$1	223	149	165	11.9809
ddddqqqqqqqqdddd	chr4:155069591-155069838(+)$1	247	22	38	13.9869
eeeeqqqqqqqqeeee	chr5:34344145-34344363(+)$1	218	66	82	13.3521
eeeeqqqqqqqqeeee	chr7:97066651-97066871(+)$1	220	78	94	13.3521
eeeeqqqqqqqqeeee	chr13:12700818-12701035(-)$1	217	175	191	13.3521
eeeeqqqqqqqqeeee	chr8:72618830-72619051(-)$1	221	79	95	13.3521
:cccqqqqqqqqccc:	chrX:70599619-70599835(+)$1	216	157	173	11.9809
ddddqqqqqqqqdddd	chr14:49631719-49631938(-)$1	219	83	99	13.9869
!cccqqqqqqqqccc2	chr2:166618714-166618937(-)$1	223	72	88	13.5594
:cccqqqqqqqqccc:	chr8:90830296-90830515(-)$1	219	0	16	11.9809
ddddqqqqqqqqdddd	chr19:47338214-47338429(-)$1	215	117	133	13.9869
ddddqqqqqqqqdddd	chrX:9231830-9232056(-)$1	226	100	116	13.9869
ggggqqqqqqqqgggg	chr13:46773143-46773372(+)$1	229	67	83	12.9726
:cccqqqqqqqqccc:	chr19:44469697-44469916(-)$1	219	9	25	11.9809
ddddqqqqqqqqdddd	chr4:130379027-130379249(+)$1	222	75	91	13.9869
d[bbqqqqqqqqbb]d	chr2:28536669-28536892(+)$1	223	153	169	12.6159
ddddqqqqqqqqdddd	chr2:172859053-172859279(+)$1	226	1	17	13.9869
:cccqqqqqqqqccch	chr14:35340734-35340952(+)$1	218	129	145	12.5695
ddddqqqqqqqqdddd	chr6:91706629-91706854(+)$1	225	61	77	13.9869
eeeeqqqqqqqqeeee	chr7:19625821-19626057(+)$1	236	173	189	13.3521
eeeeqqqqqqqqeeee	chr11:7071032-7071257(+)$1	225	60	76	13.3521
ddddqqqqqqqqdddd	chr19:12843525-12843754(-)$1	229	154	170	13.9869
[cccqqqqqqqqccc]	chr2:165701823-165702056(-)$1	233	140	156	13.6527
[cccqqqqqqqqcccc	chr17:24317360-24317583(-)$1	223	193	209	13.6592
ddddqqqqqqqqdddd	chr6:40431349-40431571(+)$1	222	5	21	13.9869
!cccqqqqqqqqccc2	chr10:120832318-120832546(+)$1	228	51	67	13.5594
ffffqqqqqqqqffff	chr2:128920556-128920772(-)$1	216	31	47	12.0368
iiiiqqqqqqqqiiii	chr4:122535718-122535959(+)$1	241	157	173	12.9739
ddddqqqqqqqqdddd	chr17:37629341-37629559(-)$1	218	194	210	13.9869
ggggqqqqqqqqgggg	chr1:138740758-138740981(-)$1	223	4	20	12.9726
ggggqqqqqqqqgggg	chr19:44610459-44610679(+)$1	220	184	200	12.9726
hcccqqqqqqqqcccD	chr16:92083982-92084205(+)$1	223	44	60	12.7159
g[bbqqqqqqqqbb]g	chr18:32390964-32391186(+)$1	222	33	49	12.3305
ddddqqqqqqqqdddd	chr9:59497712-59497933(+)$1	221	69	85	13.9869
d[bbqqqqqqqqbbdd	chr5:149143622-149143841(-)$1	219	92	108	12.8041
eeeeqqqqqqqqeeee	chr17:26110172-26110398(-)$1	226	114	130	13.3521

#otherMatches

#Seq PSSM
UGGAGCCCUCAAUCCA	chr2:151919800-151920024(+)$1	224	169	185	13.3521
uuauggauggaaauua	chr8:119413155-119413376(-)$1	221	180	196	11.9515
GGUCUGAGUCUUGACC	chr9:108720290-108720511(+)$1	221	130	146	13.9869
GUCCCCCGUGUAGGAC	chr12:82286101-82286324(+)$1	223	204	220	12.9726
GAGGACACAUCCCUUC	chr8:126025856-126026079(+)$1	223	17	33	12.0368
ACUGAACUGCACCAGG	chr11:78285998-78286221(+)$1	223	20	36	12.6610
GAUGUACAAAAUCAUU	chr4:149021588-149021818(+)$1	230	137	153	13.9869
UGGUCCUUACCCACCA	chr10:79979827-79980063(+)$1	236	54	70	13.9869
UGGAUGCCACCUUCUC	chr8:73173115-73173340(-)$1	225	33	49	13.5549
AACAAUUCGAACUGUU	chr11:74490115-74490336(-)$1	221	130	146	13.9869
GCACGCCGCAGAGUCU	chr8:97876408-97876628(-)$1	220	119	135	12.4916
CAACAAGAUUCCGUGU	chr7:134942912-134943137(+)$1	225	26	42	13.2111
UUGUCAGCAAAUACAA	chr3:151897974-151898190(-)$1	216	99	115	13.3521
GGUGUGGACUCUCACC	chr11:69672122-69672347(+)$1	225	71	87	12.9739
GUUCCUUUCUUUGAAU	chr11:95910414-95910652(-)$1	238	137	153	13.9869
UACCUCAUUCAUGGUU	chr1:78097956-78098173(+)$1	217	115	131	13.4462
AGUUGCUGUUUGAACC	chr17:17665723-17665950(-)$1	227	87	103	13.5854
AGACUACUUUACGUCC	chr2:157295631-157295847(+)$1	216	14	30	11.9809
CCCAAGUAACUGUGGG	chr15:73617430-73617650(+)$1	220	170	186	13.3521
AGGAAAGAAACAUCAC	chr10:45037626-45037848(+)$1	222	39	55	12.5635
UUGGGAAAAUAGCACG	chr16:8660515-8660739(+)$1	224	192	208	11.9962
UGAGUCUCUAGCCUUU	chr10:127564550-127564793(+)$1	243	15	31	13.5833
GCAUGAUUUGAAAUGC	chr15:3933732-3933968(-)$1	236	177	193	13.3521
GGCCUUCUCAGCGAGC	chr8:89367972-89368195(-)$1	223	113	129	13.1706
UGUCUGGAGAAUGACA	chr19:8816531-8816758(+)$1	227	178	194	13.9869
CAGUGUGUACUGAUUG	chr2:28542773-28543007(+)$1	234	134	150	13.9869
GCAUAAAAUAUAAUGA	chr15:27661454-27661707(-)$1	253	40	56	11.9809
CCCCUCCAUCCUGGGG	chr19:46386703-46386946(-)$1	243	148	164	13.9869
GGGCUGGAAGCUGCCC	chr12:66231560-66231781(+)$1	221	116	132	13.9869
ACUGCAAUAACACAGA	chr16:19654139-19654362(+)$1	223	149	165	11.9809
UGAACCUGAACUUUCA	chr4:155069591-155069838(+)$1	247	22	38	13.9869
GGCUCAACUAUUGGCC	chr5:34344145-34344363(+)$1	218	66	82	13.3521
UAUCAAUCUGCAGAUA	chr7:97066651-97066871(+)$1	220	78	94	13.3521
GAAAUGAAGAUUUUUC	chr13:12700818-12701035(-)$1	217	175	191	13.3521
AUCUCCUGCCUCAGAU	chr8:72618830-72619051(-)$1	221	79	95	13.3521
GAGAUGAACAGUUCUG	chrX:70599619-70599835(+)$1	216	157	173	11.9809
CAUGUUAACGUUCAUG	chr14:49631719-49631938(-)$1	219	83	99	13.9869
AGCUUUCUACCUGGUG	chr2:166618714-166618937(-)$1	223	72	88	13.5594
CGCCCCUUGGCUGGCA	chr8:90830296-90830515(-)$1	219	0	16	11.9809
CCCUUCACAACUAGGG	chr19:47338214-47338429(-)$1	215	117	133	13.9869
AGGUUAUCUAAUAUCU	chrX:9231830-9232056(-)$1	226	100	116	13.9869
UAUUCCUAAACAAGUA	chr13:46773143-46773372(+)$1	229	67	83	12.9726
UGGGUGCCUUAUCUCU	chr19:44469697-44469916(-)$1	219	9	25	11.9809
ACCAAUAAUACAUGGU	chr4:130379027-130379249(+)$1	222	75	91	13.9869
UAAGAUUAGACCCUCA	chr2:28536669-28536892(+)$1	223	153	169	12.6159
GGUGAUCCCUGCCACC	chr2:172859053-172859279(+)$1	226	1	17	13.9869
AAGUAAAGAAGAGCUG	chr14:35340734-35340952(+)$1	218	129	145	12.5695
CUCGUGUUAUUUUGAG	chr6:91706629-91706854(+)$1	225	61	77	13.9869
GGCUCGACUCAUGGCC	chr7:19625821-19626057(+)$1	236	173	189	13.3521
GAGCAAAGCCUAGUUU	chr11:7071032-7071257(+)$1	225	60	76	13.3521
GUUGAAGAAGCACAGC	chr19:12843525-12843754(-)$1	229	154	170	13.9869
GUGUAAUUAGUCACAG	chr2:165701823-165702056(-)$1	233	140	156	13.6527
CAUGCUUGUCCCCAUC	chr17:24317360-24317583(-)$1	223	193	209	13.6592
UGGCAUGGAAGAGCCA	chr6:40431349-40431571(+)$1	222	5	21	13.9869
CACCACUCCUGAGGUC	chr10:120832318-120832546(+)$1	228	51	67	13.5594
AAGGAACUCAACCCUU	chr2:128920556-128920772(-)$1	216	31	47	12.0368
UCAAGAAAAUGAUUGG	chr4:122535718-122535959(+)$1	241	157	173	12.9739
GAUGCAGAAUAAUAUC	chr17:37629341-37629559(-)$1	218	194	210	13.9869
UCCCCAAAACCUGGGA	chr1:138740758-138740981(-)$1	223	4	20	12.9726
AUUGUAUAGAGUCAGU	chr19:44610459-44610679(+)$1	220	184	200	12.9726
GGCUGGUGCAUAAGCA	chr16:92083982-92084205(+)$1	223	44	60	12.7159
GCGUAACUGAUAGCAU	chr18:32390964-32391186(+)$1	222	33	49	12.3305
GAUUCAGAAGGAAAUC	chr9:59497712-59497933(+)$1	221	69	85	13.9869
CUCCUCUCACUUGGGA	chr5:149143622-149143841(-)$1	219	92	108	12.8041
AUGCUUCCAUCCGUGU	chr17:26110172-26110398(-)$1	226	114	130	13.3521

#DB
((((........))))	chr2:151919800-151920024(+)$1	1	169	185	13.3521
(.((........)).)	chr8:119413155-119413376(-)$1	1	180	196	11.9515
((((........))))	chr9:108720290-108720511(+)$1	1	130	146	13.9869
((((........))))	chr12:82286101-82286324(+)$1	1	204	220	12.9726
((((........))))	chr8:126025856-126026079(+)$1	1	17	33	12.0368
..((........))))	chr11:78285998-78286221(+)$1	1	20	36	12.6610
((((........))))	chr4:149021588-149021818(+)$1	1	137	153	13.9869
((((........))))	chr10:79979827-79980063(+)$1	1	54	70	13.9869
.(((........))).	chr8:73173115-73173340(-)$1	1	33	49	13.5549
((((........))))	chr11:74490115-74490336(-)$1	1	130	146	13.9869
((((........))..	chr8:97876408-97876628(-)$1	1	119	135	12.4916
((.(........))))	chr7:134942912-134943137(+)$1	1	26	42	13.2111
((((........))))	chr3:151897974-151898190(-)$1	1	99	115	13.3521
((((........))))	chr11:69672122-69672347(+)$1	1	71	87	12.9739
((((........))))	chr11:95910414-95910652(-)$1	1	137	153	13.9869
.(((........))).	chr1:78097956-78098173(+)$1	1	115	131	13.4462
.(((........))).	chr17:17665723-17665950(-)$1	1	87	103	13.5854
.(((........))).	chr2:157295631-157295847(+)$1	1	14	30	11.9809
((((........))))	chr15:73617430-73617650(+)$1	1	170	186	13.3521
((((........)).)	chr10:45037626-45037848(+)$1	1	39	55	12.5635
.(((........).))	chr16:8660515-8660739(+)$1	1	192	208	11.9962
.(((........))).	chr10:127564550-127564793(+)$1	1	15	31	13.5833
((((........))))	chr15:3933732-3933968(-)$1	1	177	193	13.3521
((((........).))	chr8:89367972-89368195(-)$1	1	113	129	13.1706
((((........))))	chr19:8816531-8816758(+)$1	1	178	194	13.9869
((((........))))	chr2:28542773-28543007(+)$1	1	134	150	13.9869
.(((........))).	chr15:27661454-27661707(-)$1	1	40	56	11.9809
((((........))))	chr19:46386703-46386946(-)$1	1	148	164	13.9869
((((........))))	chr12:66231560-66231781(+)$1	1	116	132	13.9869
.(((........))).	chr16:19654139-19654362(+)$1	1	149	165	11.9809
((((........))))	chr4:155069591-155069838(+)$1	1	22	38	13.9869
((((........))))	chr5:34344145-34344363(+)$1	1	66	82	13.3521
((((........))))	chr7:97066651-97066871(+)$1	1	78	94	13.3521
((((........))))	chr13:12700818-12701035(-)$1	1	175	191	13.3521
((((........))))	chr8:72618830-72619051(-)$1	1	79	95	13.3521
.(((........))).	chrX:70599619-70599835(+)$1	1	157	173	11.9809
((((........))))	chr14:49631719-49631938(-)$1	1	83	99	13.9869
.(((........))).	chr2:166618714-166618937(-)$1	1	72	88	13.5594
.(((........))).	chr8:90830296-90830515(-)$1	1	0	16	11.9809
((((........))))	chr19:47338214-47338429(-)$1	1	117	133	13.9869
((((........))))	chrX:9231830-9232056(-)$1	1	100	116	13.9869
((((........))))	chr13:46773143-46773372(+)$1	1	67	83	12.9726
.(((........))).	chr19:44469697-44469916(-)$1	1	9	25	11.9809
((((........))))	chr4:130379027-130379249(+)$1	1	75	91	13.9869
(.((........)).)	chr2:28536669-28536892(+)$1	1	153	169	12.6159
((((........))))	chr2:172859053-172859279(+)$1	1	1	17	13.9869
.(((........)))(	chr14:35340734-35340952(+)$1	1	129	145	12.5695
((((........))))	chr6:91706629-91706854(+)$1	1	61	77	13.9869
((((........))))	chr7:19625821-19626057(+)$1	1	173	189	13.3521
((((........))))	chr11:7071032-7071257(+)$1	1	60	76	13.3521
((((........))))	chr19:12843525-12843754(-)$1	1	154	170	13.9869
.(((........))).	chr2:165701823-165702056(-)$1	1	140	156	13.6527
.(((........))))	chr17:24317360-24317583(-)$1	1	193	209	13.6592
((((........))))	chr6:40431349-40431571(+)$1	1	5	21	13.9869
.(((........))).	chr10:120832318-120832546(+)$1	1	51	67	13.5594
((((........))))	chr2:128920556-128920772(-)$1	1	31	47	12.0368
((((........))))	chr4:122535718-122535959(+)$1	1	157	173	12.9739
((((........))))	chr17:37629341-37629559(-)$1	1	194	210	13.9869
((((........))))	chr1:138740758-138740981(-)$1	1	4	20	12.9726
((((........))))	chr19:44610459-44610679(+)$1	1	184	200	12.9726
)(((........)))(	chr16:92083982-92084205(+)$1	1	44	60	12.7159
(.((........)).)	chr18:32390964-32391186(+)$1	1	33	49	12.3305
((((........))))	chr9:59497712-59497933(+)$1	1	69	85	13.9869
(.((........))))	chr5:149143622-149143841(-)$1	1	92	108	12.8041
((((........))))	chr17:26110172-26110398(-)$1	1	114	130	13.3521

#PSSM
d : 0.33	e : 0.21	: : 0.10	g : 0.07	! : 0.06	h : 0.03	f : 0.03	# : 0.03	i : 0.03	" : 0.03	[ : 0.03	c : 0.01	
d : 0.30	c : 0.26	e : 0.21	[ : 0.06	g : 0.06	f : 0.03	i : 0.03	! : 0.01	b : 0.01	
d : 0.30	c : 0.26	e : 0.16	b : 0.12	g : 0.06	f : 0.03	i : 0.03	[ : 0.01	
d : 0.30	c : 0.24	e : 0.16	b : 0.10	g : 0.06	a : 0.04	f : 0.03	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 : 0.24	e : 0.16	b : 0.10	g : 0.06	a : 0.04	f : 0.03	i : 0.03	
d : 0.30	c : 0.24	e : 0.18	b : 0.10	g : 0.06	f : 0.03	i : 0.03	] : 0.03	
d : 0.32	c : 0.26	e : 0.20	] : 0.06	g : 0.06	f : 0.03	i : 0.03	3 : 0.01	b : 0.01	
d : 0.33	e : 0.21	: : 0.09	g : 0.07	2 : 0.04	h : 0.03	f : 0.03	4 : 0.03	3 : 0.03	i : 0.03	c : 0.03	b : 0.01	] : 0.01	D : 0.01	

#score	860.0946097554005
#seq	65
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_CDS_m2_run1.txt

#BEAR
d"""ccctttttttttttccc]ddd	chr17:85171367-85171593(-)$1	226	88	113	22.8085
=======vvvvvvvvvvvvv=====	chr11:68862143-68862361(+)$1	218	178	203	24.2282
!!eeeeettttttttttteeeee22	chr8:110078249-110078469(+)$1	220	106	131	23.0656
""cccwwwwwwwwwwwwwwccc===	chr2:154519612-154519837(+)$1	225	58	83	22.6471
!!eeeeeuuuuuuuuuuuueeeee2	chr4:10918369-10918589(-)$1	220	65	90	24.2023
""eeeeettttttttttteeeeegg	chr13:44980017-44980241(+)$1	224	146	171	23.1603
!!ddddwwwwwwwwwwwwwwddddh	chr1:152258966-152259214(+)$1	248	41	66	22.2128
!bb!!bbuuuuuuuuuuuubb22bb	chr18:82806087-82806308(-)$1	221	79	104	21.9452
gggg[ccctttttttttttcccggg	chr16:31133589-31133795(-)$1	206	84	109	23.1491
d####bbtttttttttttbb4444d	chr14:35490384-35490592(+)$1	208	25	50	21.4834
iiiiiiivvvvvvvvvvvvviiiii	chr15:99842227-99842433(+)$1	206	4	29	24.0013
cccyyyyyyyyyyyyyyyycccFFF	chr8:93793989-93794204(-)$1	215	114	139	19.1127
!!eeeeettttttttttteeeee]b	chr4:151359756-151359969(-)$1	213	68	93	23.0167
!!ddddvvvvvvvvvvvvvdddd22	chr1:162990821-162991028(-)$1	207	172	197	23.3951
fff!!bbuuuuuuuuuuuubb22ff	chr2:166760230-166760449(+)$1	219	164	189	22.5415
ffffcccvvvvvvvvvvvvvccc22	chr4:134779344-134779565(-)$1	221	147	172	23.6398
[fffffftttttttttttffffff2	chr1:162654123-162654352(-)$1	229	35	60	22.2685
gggyyyyyyyyyyyyyyyygggggg	chr2:53061881-53062108(+)$1	227	112	137	20.4238
d[eeeeeuuuuuuuuuuuueeeee3	chr19:55817492-55817713(+)$1	221	50	75	23.9764
::ddddvvvvvvvvvvvvvddddFF	chr17:64658880-64659088(-)$1	208	58	83	20.3003
fff[ccctttttttttttcccffff	chr10:40567706-40567917(-)$1	211	29	54	23.0130
!!eeeeeuuuuuuuuuuuueeeee2	chr19:4356734-4356960(-)$1	226	174	199	24.2023
eee[cccuuuuuuuuuuuuccc]ee	chr10:110723181-110723393(+)$1	212	126	151	24.0284
cc[dddduuuuuuuuuuuudddd]c	chr16:13839695-13839913(-)$1	218	163	188	23.6385
hhhhhhhvvvvvvvvvvvvvhhhhh	chr7:96299854-96300078(-)$1	224	71	96	21.7499
hhaa[bbtttttttttttbb]a]a]	chr18:24162652-24162871(+)$1	219	86	111	21.6124
=======uuuuuuuuuuuu======	chr17:79263183-79263418(-)$1	235	137	162	24.3992
:bb[cccuuuuuuuuuuuuccc]bb	chr4:57869797-57870003(+)$1	206	30	55	22.4216
ccc[cccvvvvvvvvvvvvvccccc	chr7:142905380-142905597(-)$1	217	61	86	24.1502
dd[dddduuuuuuuuuuuudddd22	chr10:17731477-17731695(-)$1	218	147	172	23.0884
!!eeeeeyyyyyyyyyyyyyyyyee	chr4:123416295-123416508(-)$1	213	2	27	20.3845
iiiiiiiuuuuuuuuuuuuiiiiii	chr1:45460198-45460408(-)$1	210	164	189	24.1085
Ffffffftttttttttttffffff:	chr10:5242729-5242965(+)$1	236	25	50	20.6848
###ddddtttttttttttdddd333	chr13:69952492-69952712(+)$1	220	141	166	22.8475
[eeeeevvvvvvvvvvvvveeeee]	chr2:130329807-130330045(+)$1	238	81	106	23.5793
[ffffffwwwwwwwwwwwwwwffff	chr18:11880559-11880778(+)$1	219	121	146	21.7437
&&eeeeeuuuuuuuuuuuueeeee8	chr1:13167100-13167312(-)$1	212	71	96	22.3783
hhhhhhhuuuuuuuuuuuuhhhhhh	chr1:164637860-164638079(-)$1	219	137	162	21.6111
ddeeeeevvvvvvvvvvvvveeeee	chr3:14547256-14547487(+)$1	231	114	139	23.2476
dddeeeeettttttttttteeeee]	chr1:66884805-66885026(-)$1	221	177	202	21.9957
$$$$cccvvvvvvvvvvvvvccc66	chr16:38090479-38090725(+)$1	246	64	89	22.5522
fff[cccvvvvvvvvvvvvvccc]f	chr15:79255271-79255497(-)$1	226	157	182	24.0432
eeeeddddtttttttttttdddd]e	chr19:44151741-44151967(-)$1	226	166	191	21.9028
c!!bbwwwwwwwwwwwwwwbb]ccc	chr11:43234632-43234852(-)$1	220	118	143	21.2207
=======uuuuuuuuuuuu======	chr11:77362670-77362903(-)$1	233	178	203	24.3992
b[ddddwwwwwwwwwwwwwwdddd]	chr11:21211056-21211274(+)$1	218	165	190	21.9770
&&eeeeettttttttttteeeeeee	chr15:73094558-73094784(-)$1	226	38	63	21.6430
"ffffffvvvvvvvvvvvvvfffff	chr10:83017421-83017647(+)$1	226	187	212	23.2678
gggggggvvvvvvvvvvvvvggggg	chr9:62221227-62221449(+)$1	222	119	144	23.9047
"ffffffuuuuuuuuuuuuffffff	chr19:3518241-3518453(-)$1	212	157	182	23.3072
ccc[cccvvvvvvvvvvvvvccc22	chr5:96560035-96560244(-)$1	209	57	82	24.0824
:ffffffuuuuuuuuuuuuffffff	chr1:183838359-183838571(-)$1	212	2	27	22.2464
c"""ccctttttttttttccc22cc	chr5:65814695-65814924(-)$1	229	129	154	22.8942
ccc[cccuuuuuuuuuuuuccc]cc	chr16:62802501-62802724(-)$1	223	158	183	24.3641
cc[dddduuuuuuuuuuuuddddcc	chr2:37232321-37232542(-)$1	221	119	144	23.5016
cccyyyyyyyyyyyyyyyycccccc	chr17:78784007-78784224(-)$1	217	8	33	20.4226
effffffuuuuuuuuuuuuffffff	chr15:57772222-57772439(+)$1	217	120	145	22.9992
eeeeddddtttttttttttdddd]e	chr16:18919035-18919260(+)$1	225	71	96	21.9028
a[ddddwwwwwwwwwwwwwwdddda	chr17:84974212-84974426(+)$1	214	144	169	22.0922
$ccccccvvvvvvvvvvvvvccc]c	chr15:77619297-77619533(-)$1	236	11	36	24.0515
iiiiiwwwwwwwwwwwwwwiiiiii	chr11:59582655-59582902(+)$1	247	210	235	22.2646
hhhhhhhvvvvvvvvvvvvvhhhhh	chr2:6329905-6330116(+)$1	211	164	189	21.7499
ffffffbbtttttttttttbb]fff	chr17:36117471-36117680(+)$1	209	103	128	21.2812

#otherMatches

#Seq PSSM
UUAUGAAAACGAAAGACCUUCCGAU	chr17:85171367-85171593(-)$1	226	88	113	22.8085
UCUGCAGGGAGAACUGAAGAUUGCA	chr11:68862143-68862361(+)$1	218	178	203	24.2282
GUCUGGAGCUGUUUUUCAUCCAGGA	chr8:110078249-110078469(+)$1	220	106	131	23.0656
UAUCCACAGCCAAGAAGAAGGAAGA	chr2:154519612-154519837(+)$1	225	58	83	22.6471
UUCUUUUCUUUUUUCCCCUAAAGGU	chr4:10918369-10918589(-)$1	220	65	90	24.2023
CAAAGCAACCACCAACAAUGCUUCA	chr13:44980017-44980241(+)$1	224	146	171	23.1603
UCCCUUGUGUUUAUAUUUUAAAGGA	chr1:152258966-152259214(+)$1	248	41	66	22.2128
CAGACCCUGAGUCAAUACUGGAACU	chr18:82806087-82806308(-)$1	221	79	104	21.9452
GAUGCUGUCCUUCAUGUACGCACAU	chr16:31133589-31133795(-)$1	206	84	109	23.1491
UGUUUCUUCAAAAAAUUUAGCCCAG	chr14:35490384-35490592(+)$1	208	25	50	21.4834
AGAAAUAUAUACCACAAUUUUAUUU	chr15:99842227-99842433(+)$1	206	4	29	24.0013
GCACAGAUUACGAAACAAUUGCAGC	chr8:93793989-93794204(-)$1	215	114	139	19.1127
UAAGCAGCACACAGUCAUCUGCUCG	chr4:151359756-151359969(-)$1	213	68	93	23.0167
CCUGCAUGUUCUGUUUUAUUGUAUA	chr1:162990821-162991028(-)$1	207	172	197	23.3951
UAUUUGAUUUCUGAGUGUUUCCUGU	chr2:166760230-166760449(+)$1	219	164	189	22.5415
UCUGCUUACAUCAAGAACUCAAGAC	chr4:134779344-134779565(-)$1	221	147	172	23.6398
AGCAGAAUUUUAUAUAGUUUCUGCA	chr1:162654123-162654352(-)$1	229	35	60	22.2685
UCCUGUUGCAGCUUUUCUUGGACAG	chr2:53061881-53062108(+)$1	227	112	137	20.4238
ccgccgccccgccAUGUUAGCGGCC	chr19:55817492-55817713(+)$1	221	50	75	23.9764
UUCUUCUAUCCUUUUUUAUGAAGGU	chr17:64658880-64659088(-)$1	208	58	83	20.3003
UUUCAACAUUUUGUUUUAGUUAAAG	chr10:40567706-40567917(-)$1	211	29	54	23.0130
CACACCAGGCUUGAGAAUAUGGUGC	chr19:4356734-4356960(-)$1	226	174	199	24.2023
AGUAAGUACACCAUUUUUAGCUAAC	chr10:110723181-110723393(+)$1	212	126	151	24.0284
CUGACCUCACAUUUAAAAUAGGUAA	chr16:13839695-13839913(-)$1	218	163	188	23.6385
UGUGUCCCCUCCUUACUACAGGGCA	chr7:96299854-96300078(-)$1	224	71	96	21.7499
uggagagaaaccguaucccugugcu	chr18:24162652-24162871(+)$1	219	86	111	21.6124
UCAGAGUAAAGUGGACAAAGCUUUG	chr17:79263183-79263418(-)$1	235	137	162	24.3992
GUGAGGCAAAGCACCCCAAGCCCCA	chr4:57869797-57870003(+)$1	206	30	55	22.4216
GUUCUACCAAUCCAACUCAAGUAAA	chr7:142905380-142905597(-)$1	217	61	86	24.1502
UUGGUAGGAACUCUGAAAGCUGCAA	chr10:17731477-17731695(-)$1	218	147	172	23.0884
AAGAAGGACCAGCCCACCUUUACCC	chr4:123416295-123416508(-)$1	213	2	27	20.3845
UAACAGCCCAAUGUAAUCAGCUGUU	chr1:45460198-45460408(-)$1	210	164	189	24.1085
CAGCAAGUUGCAGUCAUUCUUGCUU	chr10:5242729-5242965(+)$1	236	25	50	20.6848
AGGGCUCUAGCUAAAAACGAGCAAG	chr13:69952492-69952712(+)$1	220	141	166	22.8475
CUGUUAAUUCUUCACACUCUGACAA	chr2:130329807-130330045(+)$1	238	81	106	23.5793
GUGAUGGAUAAACCUCUGGACCUGU	chr18:11880559-11880778(+)$1	219	121	146	21.7437
CGUUGCUGCACAAACCAAGAGCAAA	chr1:13167100-13167312(-)$1	212	71	96	22.3783
AGCAGGCAGCUACUCCCAAGUCUGC	chr1:164637860-164638079(-)$1	219	137	162	21.6111
UUCUCGGACAACAGCACCUACCGGG	chr3:14547256-14547487(+)$1	231	114	139	23.2476
CGCGCAUUCCUAUAGUUAAAGUGCA	chr1:66884805-66885026(-)$1	221	177	202	21.9957
GCACCCUAACAUAAAACAAAAGGAA	chr16:38090479-38090725(+)$1	246	64	89	22.5522
UCUUCCGAAAUCUCUUUCACCGGCA	chr15:79255271-79255497(-)$1	226	157	182	24.0432
AUGGCUGCCCCCUACAUUAGCAGAC	chr19:44151741-44151967(-)$1	226	166	191	21.9028
AGAUCUCACUUCUCCCCUUGAAUGG	chr11:43234632-43234852(-)$1	220	118	143	21.2207
UGGAAAUUAAAACUUUUCUGUUUUC	chr11:77362670-77362903(-)$1	233	178	203	24.3992
CGGAGUAUAACUAAUUCUUAACUUG	chr11:21211056-21211274(+)$1	218	165	190	21.9770
UGCAAGUAAGAAAAUACAGCUUGGA	chr15:73094558-73094784(-)$1	226	38	63	21.6430
CUUUCUGGAAAAAUAGUUAAUAGAA	chr10:83017421-83017647(+)$1	226	187	212	23.2678
UGAAUGCCUACCGAGAAAACGUGUU	chr9:62221227-62221449(+)$1	222	119	144	23.9047
CAGGCUCUUGACAUGUAUUGAGCCU	chr19:3518241-3518453(-)$1	212	157	182	23.3072
GCUCGCAUUCCACCUGAUAUUGCCA	chr5:96560035-96560244(-)$1	209	57	82	24.0824
CUUACAAACUCAUUAUAUAUUGUAA	chr1:183838359-183838571(-)$1	212	2	27	22.2464
CAAAUGGGUACAAAAUUGUCACGGA	chr5:65814695-65814924(-)$1	229	129	154	22.8942
CUCCCCAACCUCCCCCUCCUGGUGA	chr16:62802501-62802724(-)$1	223	158	183	24.3641
AGUGAACAAAUUGAAGUAAGUUCCU	chr2:37232321-37232542(-)$1	221	119	144	23.5016
CUGUGAACAUAAAUUAACUCAGGCC	chr17:78784007-78784224(-)$1	217	8	33	20.4226
GAAAACAAGGAGGUAAGAAUGUUUU	chr15:57772222-57772439(+)$1	217	120	145	22.9992
UGGGAGCUCUACAAAGCCCAGCUGC	chr16:18919035-18919260(+)$1	225	71	96	21.9028
GAGCAGAAACUUCUAAAAACCUGCC	chr17:84974212-84974426(+)$1	214	144	169	22.0922
UGUGGGCUUAAUUAAACCAUGUCUC	chr15:77619297-77619533(-)$1	236	11	36	24.0515
UGCUGGGCUCACUUUUUCAUGGCAG	chr11:59582655-59582902(+)$1	247	210	235	22.2646
GGCUUUGUCCUUCCGUAUUCCAAGG	chr2:6329905-6330116(+)$1	211	164	189	21.7499
GCUGCGCUCCAGUUCCAACAGCCGC	chr17:36117471-36117680(+)$1	209	103	128	21.2812

#DB
(...(((...........))).)))	chr17:85171367-85171593(-)$1	1	88	113	22.8085
(((((((.............)))))	chr11:68862143-68862361(+)$1	1	178	203	24.2282
..(((((...........)))))..	chr8:110078249-110078469(+)$1	1	106	131	23.0656
..(((..............))))))	chr2:154519612-154519837(+)$1	1	58	83	22.6471
..(((((............))))).	chr4:10918369-10918589(-)$1	1	65	90	24.2023
..(((((...........)))))))	chr13:44980017-44980241(+)$1	1	146	171	23.1603
..((((..............)))))	chr1:152258966-152259214(+)$1	1	41	66	22.2128
.((..((............))..))	chr18:82806087-82806308(-)$1	1	79	104	21.9452
((((.(((...........))))))	chr16:31133589-31133795(-)$1	1	84	109	23.1491
(....((...........))....)	chr14:35490384-35490592(+)$1	1	25	50	21.4834
(((((((.............)))))	chr15:99842227-99842433(+)$1	1	4	29	24.0013
(((................))))))	chr8:93793989-93794204(-)$1	1	114	139	19.1127
..(((((...........))))).)	chr4:151359756-151359969(-)$1	1	68	93	23.0167
..((((.............))))..	chr1:162990821-162991028(-)$1	1	172	197	23.3951
(((..((............))..))	chr2:166760230-166760449(+)$1	1	164	189	22.5415
(((((((.............)))..	chr4:134779344-134779565(-)$1	1	147	172	23.6398
.((((((...........)))))).	chr1:162654123-162654352(-)$1	1	35	60	22.2685
(((................))))))	chr2:53061881-53062108(+)$1	1	112	137	20.4238
(.(((((............))))).	chr19:55817492-55817713(+)$1	1	50	75	23.9764
..((((.............))))))	chr17:64658880-64659088(-)$1	1	58	83	20.3003
(((.(((...........)))))))	chr10:40567706-40567917(-)$1	1	29	54	23.0130
..(((((............))))).	chr19:4356734-4356960(-)$1	1	174	199	24.2023
(((.(((............))).))	chr10:110723181-110723393(+)$1	1	126	151	24.0284
((.((((............)))).)	chr16:13839695-13839913(-)$1	1	163	188	23.6385
(((((((.............)))))	chr7:96299854-96300078(-)$1	1	71	96	21.7499
((((.((...........)).).).	chr18:24162652-24162871(+)$1	1	86	111	21.6124
(((((((............))))))	chr17:79263183-79263418(-)$1	1	137	162	24.3992
.((.(((............))).))	chr4:57869797-57870003(+)$1	1	30	55	22.4216
(((.(((.............)))))	chr7:142905380-142905597(-)$1	1	61	86	24.1502
((.((((............))))..	chr10:17731477-17731695(-)$1	1	147	172	23.0884
..(((((................))	chr4:123416295-123416508(-)$1	1	2	27	20.3845
(((((((............))))))	chr1:45460198-45460408(-)$1	1	164	189	24.1085
(((((((...........)))))).	chr10:5242729-5242965(+)$1	1	25	50	20.6848
...((((...........))))...	chr13:69952492-69952712(+)$1	1	141	166	22.8475
.(((((.............))))).	chr2:130329807-130330045(+)$1	1	81	106	23.5793
.((((((..............))))	chr18:11880559-11880778(+)$1	1	121	146	21.7437
..(((((............))))).	chr1:13167100-13167312(-)$1	1	71	96	22.3783
(((((((............))))))	chr1:164637860-164638079(-)$1	1	137	162	21.6111
))(((((.............)))))	chr3:14547256-14547487(+)$1	1	114	139	23.2476
((((((((...........))))).	chr1:66884805-66885026(-)$1	1	177	202	21.9957
....(((.............)))..	chr16:38090479-38090725(+)$1	1	64	89	22.5522
(((.(((.............))).)	chr15:79255271-79255497(-)$1	1	157	182	24.0432
((((((((...........)))).)	chr19:44151741-44151967(-)$1	1	166	191	21.9028
(..((..............)).)))	chr11:43234632-43234852(-)$1	1	118	143	21.2207
(((((((............))))))	chr11:77362670-77362903(-)$1	1	178	203	24.3992
(.((((..............)))).	chr11:21211056-21211274(+)$1	1	165	190	21.9770
..(((((...........)))))))	chr15:73094558-73094784(-)$1	1	38	63	21.6430
.((((((.............)))))	chr10:83017421-83017647(+)$1	1	187	212	23.2678
(((((((.............)))))	chr9:62221227-62221449(+)$1	1	119	144	23.9047
.((((((............))))))	chr19:3518241-3518453(-)$1	1	157	182	23.3072
(((.(((.............)))..	chr5:96560035-96560244(-)$1	1	57	82	24.0824
.((((((............))))))	chr1:183838359-183838571(-)$1	1	2	27	22.2464
(...(((...........)))..))	chr5:65814695-65814924(-)$1	1	129	154	22.8942
(((.(((............))).))	chr16:62802501-62802724(-)$1	1	158	183	24.3641
((.((((............))))))	chr2:37232321-37232542(-)$1	1	119	144	23.5016
(((................)))(((	chr17:78784007-78784224(-)$1	1	8	33	20.4226
(((((((............))))))	chr15:57772222-57772439(+)$1	1	120	145	22.9992
((((((((...........)))).)	chr16:18919035-18919260(+)$1	1	71	96	21.9028
(.((((..............)))))	chr17:84974212-84974426(+)$1	1	144	169	22.0922
.((((((.............))).)	chr15:77619297-77619533(-)$1	1	11	36	24.0515
(((((..............))))))	chr11:59582655-59582902(+)$1	1	210	235	22.2646
(((((((.............)))))	chr2:6329905-6330116(+)$1	1	164	189	21.7499
((((((((...........)).)))	chr17:36117471-36117680(+)$1	1	103	128	21.2812

#PSSM
c : 0.14	! : 0.12	d : 0.09	f : 0.07	" : 0.06	e : 0.06	h : 0.06	= : 0.04	g : 0.04	i : 0.04	[ : 0.04	: : 0.04	& : 0.03	$ : 0.03	F : 0.01	# : 0.01	b : 0.01	a : 0.01	
f : 0.19	! : 0.12	c : 0.12	" : 0.06	e : 0.06	h : 0.06	= : 0.04	g : 0.04	i : 0.04	[ : 0.04	d : 0.04	b : 0.03	# : 0.03	& : 0.03	: : 0.01	$ : 0.01	
e : 0.22	f : 0.19	c : 0.11	d : 0.09	= : 0.04	g : 0.04	i : 0.04	[ : 0.04	h : 0.04	" : 0.03	b : 0.03	# : 0.03	a : 0.01	$ : 0.01	! : 0.01	
e : 0.22	d : 0.14	f : 0.14	[ : 0.11	= : 0.04	i : 0.04	y : 0.04	h : 0.04	" : 0.03	c : 0.03	! : 0.03	g : 0.03	# : 0.01	a : 0.01	$ : 0.01	b : 0.01	
c : 0.20	e : 0.19	d : 0.17	f : 0.12	= : 0.04	i : 0.04	y : 0.04	h : 0.04	! : 0.03	[ : 0.03	# : 0.01	b : 0.01	g : 0.01	
c : 0.20	e : 0.19	d : 0.17	f : 0.12	b : 0.06	= : 0.04	w : 0.04	y : 0.04	h : 0.04	i : 0.03	g : 0.01	
c : 0.20	e : 0.17	f : 0.11	w : 0.09	d : 0.09	b : 0.07	= : 0.04	y : 0.04	v : 0.04	h : 0.04	i : 0.03	g : 0.01	
u : 0.30	v : 0.25	t : 0.19	w : 0.11	y : 0.06	d : 0.03	c : 0.01	e : 0.01	b : 0.01	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	t : 0.26	v : 0.25	w : 0.11	y : 0.06	
u : 0.30	v : 0.25	w : 0.11	t : 0.07	e : 0.06	y : 0.06	c : 0.04	b : 0.03	f : 0.03	d : 0.01	
v : 0.20	c : 0.15	e : 0.15	d : 0.12	b : 0.09	f : 0.07	w : 0.06	= : 0.03	i : 0.03	g : 0.01	y : 0.01	h : 0.01	
c : 0.25	e : 0.17	d : 0.17	f : 0.09	b : 0.06	= : 0.04	i : 0.04	h : 0.04	g : 0.03	4 : 0.01	] : 0.01	y : 0.01	w : 0.01	
c : 0.20	e : 0.17	d : 0.17	f : 0.12	] : 0.04	= : 0.04	2 : 0.04	i : 0.04	h : 0.04	g : 0.03	4 : 0.01	a : 0.01	y : 0.01	
d : 0.17	e : 0.17	f : 0.14	c : 0.12	= : 0.06	] : 0.06	2 : 0.04	g : 0.04	i : 0.04	h : 0.04	4 : 0.01	F : 0.01	y : 0.01	3 : 0.01	
e : 0.15	f : 0.15	] : 0.09	c : 0.09	2 : 0.07	d : 0.06	= : 0.06	g : 0.06	i : 0.04	h : 0.04	b : 0.03	F : 0.03	4 : 0.01	a : 0.01	3 : 0.01	6 : 0.01	
f : 0.14	2 : 0.12	c : 0.12	e : 0.09	= : 0.06	g : 0.06	h : 0.06	] : 0.06	b : 0.04	i : 0.04	d : 0.03	F : 0.03	3 : 0.03	: : 0.01	8 : 0.01	6 : 0.01	a : 0.01	

#score	1428.5373001912756
#seq	63
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_CDS_m3_run1.txt

#BEAR
ddddnnnnndddd	chr7:52381770-52382037(-)$1	267	180	193	11.4241
eeeennnnneeee	chr10:126982548-126982803(-)$1	255	230	243	10.0484
ddddnnnnndddd	chr6:11855916-11856172(-)$1	256	5	18	11.4241
ddddnnnnndddd	chr13:55761939-55762187(+)$1	248	78	91	11.4241
ddddnnnnndddd	chr12:117653829-117654072(+)$1	243	177	190	11.4241
"cccnnnnnccc2	chr7:50711784-50712044(+)$1	260	151	164	9.7326
eeeennnnneeee	chr11:44365126-44365376(+)$1	250	81	94	10.0484
eeeennnnneeee	chr1:66899599-66899836(-)$1	237	70	83	10.0484
ddddnnnnndddd	chr6:88842888-88843146(-)$1	258	37	50	11.4241
[cccnnnnnccc]	chr4:133276401-133276718(-)$1	317	35	48	9.9634
[cccnnnnnccc]	chr4:141050075-141050333(-)$1	258	167	180	9.9634
[cccnnnnnccc]	chr19:20449667-20449923(-)$1	256	181	194	9.9634
ddddnnnnndddd	chr10:79173005-79173269(+)$1	264	98	111	11.4241
ddddnnnnndddd	chr16:4087755-4088022(-)$1	267	156	169	11.4241
ddddnnnnndddd	chrX:9771828-9772063(-)$1	235	180	193	11.4241
ddddnnnnndddd	chr12:73195655-73195904(+)$1	249	209	222	11.4241
eeeennnnneeee	chr8:131239944-131240206(+)$1	262	76	89	10.0484
ccccnnnnncccB	chr12:114383076-114383317(+)$1	241	214	227	8.8770
"cccnnnnnccc4	chr14:121701883-121702123(-)$1	240	177	190	9.9167
eeeennnnneeee	chr12:81285717-81285959(-)$1	242	27	40	10.0484
"cccnnnnnccc]	chr14:121696264-121696526(-)$1	262	147	160	9.9036
ddddnnnnndddd	chr8:93933444-93933724(+)$1	280	5	18	11.4241
ddddnnnnndddd	chr12:103607660-103607923(+)$1	263	242	255	11.4241
ddddnnnnndddd	chr4:63681078-63681340(-)$1	262	152	165	11.4241
[cccnnnnncccd	chr4:43531456-43531704(-)$1	248	108	121	10.2268
ddddnnnnndddd	chr2:84879972-84880234(+)$1	262	140	153	11.4241
'cccnnnnnccc6	chr14:31952038-31952280(+)$1	242	45	58	8.8072
eeeennnnneeee	chr3:87782665-87782920(+)$1	255	20	33	10.0484
ddddnnnnndddd	chr2:152503200-152503481(+)$1	281	194	207	11.4241
!cccnnnnnccc2	chr6:97134714-97134951(-)$1	237	115	128	9.8407
ddddnnnnndddd	chr3:144259683-144259954(+)$1	271	186	199	11.4241
cc[annnnna]cc	chr16:20287869-20288104(-)$1	235	104	117	9.0820
ggggnnnnngggg	chr16:55814122-55814391(-)$1	269	70	83	9.0127
:cccnnnnncccg	chr7:117077068-117077317(-)$1	249	49	62	8.8904
eeeennnnneeee	chr18:78019911-78020183(+)$1	272	1	14	10.0484
ddddnnnnndddd	chr14:31951933-31952206(+)$1	273	225	238	11.4241
ddddnnnnndddd	chr12:111872339-111872574(+)$1	235	116	129	11.4241
ggggnnnnngggg	chr9:22184631-22184892(-)$1	261	33	46	9.0127
[cccnnnnncccd	chr13:15740292-15740545(+)$1	253	47	60	10.2268
#cccnnnnnccc4	chr17:71343762-71344067(-)$1	305	257	270	9.8825
eeeennnnneeee	chr3:87780540-87780788(+)$1	248	62	75	10.0484
eeeennnnneeee	chr15:81539856-81540110(-)$1	254	45	58	10.0484
eeeennnnneeee	chr2:117938703-117938961(+)$1	258	20	33	10.0484
ddddnnnnndddd	chr13:55583954-55584211(-)$1	257	33	46	11.4241
ddddnnnnndddd	chr5:122247142-122247391(+)$1	249	208	221	11.4241
!cccnnnnnccc2	chr15:82012378-82012642(+)$1	264	100	113	9.8407
ddddnnnnndddd	chr7:105053172-105053421(+)$1	249	31	44	11.4241
ddddnnnnndddd	chr7:19678231-19678473(+)$1	242	89	102	11.4241
ddddnnnnndddd	chr7:56827552-56827787(+)$1	235	93	106	11.4241
ddddnnnnndddd	chr8:73119532-73119767(+)$1	235	153	166	11.4241
ddddnnnnndddd	chr17:35138394-35138641(+)$1	247	51	64	11.4241
ddddnnnnndddd	chr13:49298449-49298697(-)$1	248	222	235	11.4241
ddddnnnnndddd	chr11:102057317-102057555(-)$1	238	167	180	11.4241
ddddnnnnndddd	chr6:51417135-51417381(-)$1	246	185	198	11.4241
eeeennnnneeee	chr18:64634662-64634924(-)$1	262	133	146	10.0484
eeeennnnneeee	chr5:121995039-121995275(-)$1	236	44	57	10.0484

#otherMatches

#Seq PSSM
UACCAGAAAGGUA	chr7:52381770-52382037(-)$1	267	180	193	11.4241
GGCCAGAAGGGCC	chr10:126982548-126982803(-)$1	255	230	243	10.0484
AUUUGGACAAGAU	chr6:11855916-11856172(-)$1	256	5	18	11.4241
UCAUGAACUGUGG	chr13:55761939-55762187(+)$1	248	78	91	11.4241
AUGUUAAUUACAU	chr12:117653829-117654072(+)$1	243	177	190	11.4241
AAGCUGCCCGCUG	chr7:50711784-50712044(+)$1	260	151	164	9.7326
CGUGCUCUUCAUG	chr11:44365126-44365376(+)$1	250	81	94	10.0484
CAUCCCCCAGAUG	chr1:66899599-66899836(-)$1	237	70	83	10.0484
UCGAGAGUAUUGA	chr6:88842888-88843146(-)$1	258	37	50	11.4241
CAGUCCCCAACUC	chr4:133276401-133276718(-)$1	317	35	48	9.9634
AGUACGCUCUACA	chr4:141050075-141050333(-)$1	258	167	180	9.9634
UGGAAUCUCUCUU	chr19:20449667-20449923(-)$1	256	181	194	9.9634
CAGAUUGGUUCUG	chr10:79173005-79173269(+)$1	264	98	111	11.4241
GGGCGAGAUGCCU	chr16:4087755-4088022(-)$1	267	156	169	11.4241
GAGAUGUUUUCUC	chrX:9771828-9772063(-)$1	235	180	193	11.4241
UGACGAAAAGUCA	chr12:73195655-73195904(+)$1	249	209	222	11.4241
GUCGCUGAUUGGC	chr8:131239944-131240206(+)$1	262	76	89	10.0484
UGGCCUGUUGCCU	chr12:114383076-114383317(+)$1	241	214	227	8.8770
UAUAUUuuuuguu	chr14:121701883-121702123(-)$1	240	177	190	9.9167
UGCUGCUGGGGCA	chr12:81285717-81285959(-)$1	242	27	40	10.0484
GCCUGAACAAGGA	chr14:121696264-121696526(-)$1	262	147	160	9.9036
UCCAGGCCUUGGA	chr8:93933444-93933724(+)$1	280	5	18	11.4241
AGGUGUACAGCCU	chr12:103607660-103607923(+)$1	263	242	255	11.4241
ACCUGCAGAAGGU	chr4:63681078-63681340(-)$1	262	152	165	11.4241
UGCAGUAAAUGUG	chr4:43531456-43531704(-)$1	248	108	121	10.2268
ACUGGGGGACAGU	chr2:84879972-84880234(+)$1	262	140	153	11.4241
CAGCUGCCUGCUC	chr14:31952038-31952280(+)$1	242	45	58	8.8072
CUCAGACCAUGAG	chr3:87782665-87782920(+)$1	255	20	33	10.0484
GUGUUUUCUGCAU	chr2:152503200-152503481(+)$1	281	194	207	11.4241
GAACUGGCUGUUG	chr6:97134714-97134951(-)$1	237	115	128	9.8407
CACAGACAGUGUG	chr3:144259683-144259954(+)$1	271	186	199	11.4241
CUUCUGCUUGUGG	chr16:20287869-20288104(-)$1	235	104	117	9.0820
GGAAUGACCUUCC	chr16:55814122-55814391(-)$1	269	70	83	9.0127
AUCUGCCAGAGAC	chr7:117077068-117077317(-)$1	249	49	62	8.8904
UGGCAUUAAGUCA	chr18:78019911-78020183(+)$1	272	1	14	10.0484
CUGGAUGGACCAG	chr14:31951933-31952206(+)$1	273	225	238	11.4241
UGCCAAGUGGGCG	chr12:111872339-111872574(+)$1	235	116	129	11.4241
UUUAGGCUGUGAA	chr9:22184631-22184892(-)$1	261	33	46	9.0127
UGUUUCUGUAACA	chr13:15740292-15740545(+)$1	253	47	60	10.2268
CAUGUACCUUAUA	chr17:71343762-71344067(-)$1	305	257	270	9.8825
AACCACUAAGGUU	chr3:87780540-87780788(+)$1	248	62	75	10.0484
ACAGAGCCCCUGU	chr15:81539856-81540110(-)$1	254	45	58	10.0484
GUGUGUUUGACAU	chr2:117938703-117938961(+)$1	258	20	33	10.0484
CUGGUUUCUCCAG	chr13:55583954-55584211(-)$1	257	33	46	11.4241
GAUGUAUCCCGUC	chr5:122247142-122247391(+)$1	249	208	221	11.4241
CUCCCGCCUGGAC	chr15:82012378-82012642(+)$1	264	100	113	9.8407
GUGGGAACUCCAU	chr7:105053172-105053421(+)$1	249	31	44	11.4241
AGGCGCGUUGCCU	chr7:19678231-19678473(+)$1	242	89	102	11.4241
CAUGGGUGACAUG	chr7:56827552-56827787(+)$1	235	93	106	11.4241
CGGAGCGCUUCUG	chr8:73119532-73119767(+)$1	235	153	166	11.4241
AUCGCUGCCCGAU	chr17:35138394-35138641(+)$1	247	51	64	11.4241
CGGGCCUUACCUG	chr13:49298449-49298697(-)$1	248	222	235	11.4241
CUGCUCGCUGCGG	chr11:102057317-102057555(-)$1	238	167	180	11.4241
CACAGACUGUGUG	chr6:51417135-51417381(-)$1	246	185	198	11.4241
GUGGAUCCCCCAU	chr18:64634662-64634924(-)$1	262	133	146	10.0484
GGCUGUGGGAGCC	chr5:121995039-121995275(-)$1	236	44	57	10.0484

#DB
((((.....))))	chr7:52381770-52382037(-)$1	1	180	193	11.4241
((((.....))))	chr10:126982548-126982803(-)$1	1	230	243	10.0484
((((.....))))	chr6:11855916-11856172(-)$1	1	5	18	11.4241
((((.....))))	chr13:55761939-55762187(+)$1	1	78	91	11.4241
((((.....))))	chr12:117653829-117654072(+)$1	1	177	190	11.4241
.(((.....))).	chr7:50711784-50712044(+)$1	1	151	164	9.7326
((((.....))))	chr11:44365126-44365376(+)$1	1	81	94	10.0484
((((.....))))	chr1:66899599-66899836(-)$1	1	70	83	10.0484
((((.....))))	chr6:88842888-88843146(-)$1	1	37	50	11.4241
.(((.....))).	chr4:133276401-133276718(-)$1	1	35	48	9.9634
.(((.....))).	chr4:141050075-141050333(-)$1	1	167	180	9.9634
.(((.....))).	chr19:20449667-20449923(-)$1	1	181	194	9.9634
((((.....))))	chr10:79173005-79173269(+)$1	1	98	111	11.4241
((((.....))))	chr16:4087755-4088022(-)$1	1	156	169	11.4241
((((.....))))	chrX:9771828-9772063(-)$1	1	180	193	11.4241
((((.....))))	chr12:73195655-73195904(+)$1	1	209	222	11.4241
((((.....))))	chr8:131239944-131240206(+)$1	1	76	89	10.0484
)(((.....))))	chr12:114383076-114383317(+)$1	1	214	227	8.8770
.(((.....))).	chr14:121701883-121702123(-)$1	1	177	190	9.9167
((((.....))))	chr12:81285717-81285959(-)$1	1	27	40	10.0484
.(((.....))).	chr14:121696264-121696526(-)$1	1	147	160	9.9036
((((.....))))	chr8:93933444-93933724(+)$1	1	5	18	11.4241
((((.....))))	chr12:103607660-103607923(+)$1	1	242	255	11.4241
((((.....))))	chr4:63681078-63681340(-)$1	1	152	165	11.4241
.(((.....))))	chr4:43531456-43531704(-)$1	1	108	121	10.2268
((((.....))))	chr2:84879972-84880234(+)$1	1	140	153	11.4241
.(((.....))).	chr14:31952038-31952280(+)$1	1	45	58	8.8072
((((.....))))	chr3:87782665-87782920(+)$1	1	20	33	10.0484
((((.....))))	chr2:152503200-152503481(+)$1	1	194	207	11.4241
.(((.....))).	chr6:97134714-97134951(-)$1	1	115	128	9.8407
((((.....))))	chr3:144259683-144259954(+)$1	1	186	199	11.4241
((.(.....).))	chr16:20287869-20288104(-)$1	1	104	117	9.0820
((((.....))))	chr16:55814122-55814391(-)$1	1	70	83	9.0127
.(((.....)))(	chr7:117077068-117077317(-)$1	1	49	62	8.8904
((((.....))))	chr18:78019911-78020183(+)$1	1	1	14	10.0484
((((.....))))	chr14:31951933-31952206(+)$1	1	225	238	11.4241
((((.....))))	chr12:111872339-111872574(+)$1	1	116	129	11.4241
((((.....))))	chr9:22184631-22184892(-)$1	1	33	46	9.0127
.(((.....))))	chr13:15740292-15740545(+)$1	1	47	60	10.2268
.(((.....))).	chr17:71343762-71344067(-)$1	1	257	270	9.8825
((((.....))))	chr3:87780540-87780788(+)$1	1	62	75	10.0484
((((.....))))	chr15:81539856-81540110(-)$1	1	45	58	10.0484
((((.....))))	chr2:117938703-117938961(+)$1	1	20	33	10.0484
((((.....))))	chr13:55583954-55584211(-)$1	1	33	46	11.4241
((((.....))))	chr5:122247142-122247391(+)$1	1	208	221	11.4241
.(((.....))).	chr15:82012378-82012642(+)$1	1	100	113	9.8407
((((.....))))	chr7:105053172-105053421(+)$1	1	31	44	11.4241
((((.....))))	chr7:19678231-19678473(+)$1	1	89	102	11.4241
((((.....))))	chr7:56827552-56827787(+)$1	1	93	106	11.4241
((((.....))))	chr8:73119532-73119767(+)$1	1	153	166	11.4241
((((.....))))	chr17:35138394-35138641(+)$1	1	51	64	11.4241
((((.....))))	chr13:49298449-49298697(-)$1	1	222	235	11.4241
((((.....))))	chr11:102057317-102057555(-)$1	1	167	180	11.4241
((((.....))))	chr6:51417135-51417381(-)$1	1	185	198	11.4241
((((.....))))	chr18:64634662-64634924(-)$1	1	133	146	10.0484
((((.....))))	chr5:121995039-121995275(-)$1	1	44	57	10.0484

#PSSM
d : 0.48	e : 0.21	[ : 0.08	" : 0.05	c : 0.03	! : 0.03	g : 0.03	' : 0.01	: : 0.01	# : 0.01	
d : 0.48	c : 0.26	e : 0.21	g : 0.03	
d : 0.48	c : 0.24	e : 0.21	g : 0.03	[ : 0.01	
d : 0.48	c : 0.24	e : 0.21	g : 0.03	a : 0.01	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
d : 0.48	c : 0.24	e : 0.21	g : 0.03	a : 0.01	
d : 0.48	c : 0.24	e : 0.21	g : 0.03	] : 0.01	
d : 0.48	c : 0.26	e : 0.21	g : 0.03	
d : 0.51	e : 0.21	] : 0.07	2 : 0.05	g : 0.05	4 : 0.03	B : 0.01	6 : 0.01	c : 0.01	

#score	592.1770960756361
#seq	56
#width	13
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_CDS_m3_run2.txt

#BEAR
ccc####cccmmmmccc4444ccc:D	chr2:4805367-4805587(+)$1	220	165	191	11.6386
[bba"""cccmmmmccc333a]bb]f	chr17:35972139-35972359(-)$1	220	189	215	12.8488
"bb####cccmmmmccc333bb333d	chr18:90709382-90709602(+)$1	220	86	112	12.8722
:dddd!!cccmmmmccc22dddd:bb	chr7:25350518-25350738(+)$1	220	93	119	9.5242
fffff!!cccmmmmccc4444fffff	chr9:72465811-72466036(+)$1	225	161	187	13.1258
ee####ddddmmmmdddd22eeeee:	chr15:88656743-88656978(+)$1	235	97	123	9.9132
d[dddd[cccmmmmccc]dddd]ddd	chr17:74945613-74945833(+)$1	220	47	73	10.8129
eee!!cccooooooccc4444eeeee	chr19:5492422-5492643(+)$1	221	159	185	10.5292
:eeeee[cccmmmmccc]eeeee:dd	chr4:139028301-139028533(+)$1	232	167	193	9.3066
ddd"""ddddmmmmdddd4444dddd	chr12:73884712-73884932(+)$1	220	88	114	10.8754
ggggg!!cccmmmmcccggggggg77	chr16:32233054-32233307(-)$1	253	28	54	10.5674
bb!!ccccccmmmmccc]ccc22bb]	chr4:32782330-32782550(+)$1	220	175	201	9.9140
c[ccc[ddddmmmmdddd4444ccc]	chr9:48845847-48846067(+)$1	220	9	35	10.8908
ffffffddddmmmmdddd333fffff	chr17:23949290-23949510(+)$1	220	158	184	10.3680
ccc!!eeeeemmmmeeeee333ccc5	chr9:105550961-105551181(+)$1	220	55	81	8.4363
dddccc!!bbmmmmbb333ccc]ddd	chr1:133727168-133727388(+)$1	220	181	207	10.3189
ggg####cccmmmmccc55555gggg	chrX:155780517-155780746(+)$1	229	78	104	9.9736
ee[bb!!ddddllldddd333bbeee	chrX:148340791-148341011(+)$1	220	56	82	8.6003
fffff"""bbmmmmbb333ffffffD	chr13:23842913-23843133(+)$1	220	190	216	9.9717
==========mmmm============	chr5:31093870-31094092(+)$1	222	151	177	10.8644
ffff!!cccooooooccc333fffff	chr3:82863144-82863367(+)$1	223	42	68	10.2872
"""gggggggmmmmggggggg]a]a2	chr12:111874038-111874258(+)$1	220	128	154	9.0560
==========mmmm==========]d	chr16:93888266-93888487(+)$1	221	152	178	10.8479
==========oooooo==========	chr18:50037762-50037985(+)$1	223	70	96	8.7932
eeee####bbmmmmbb4444eeeee:	chr13:3565788-3566015(-)$1	227	191	217	10.8231
!!dddd!!bbmmmmbb22dddd]ccc	chr4:124779989-124780209(+)$1	220	173	199	9.2723
a[dddd[cccmmmmcccdddd]a]gg	chr4:130256899-130257130(+)$1	231	153	179	10.6569
&&dddd[cccmmmmccc333dddd33	chr10:84091267-84091492(+)$1	225	33	59	11.6373
!ffffff[bbmmmmbb333ffffff2	chr7:29524953-29525173(-)$1	220	101	127	9.6866
ffffff[cccmmmmcccffffffggg	chr15:9124379-9124599(+)$1	220	18	44	10.3663
b[dddd[cccmmmmccc]ddddbb33	chr9:104105401-104105621(-)$1	220	47	73	10.6217
eee[bbacccmmmmccc]a]bb]eee	chr7:107646601-107646821(+)$1	220	164	190	10.6710
ffffa[ddddmmmmdddd]a]fffff	chr14:52818593-52818813(-)$1	220	149	175	9.8597
ffff####ccclllccc333ffffff	chrX:148291927-148292159(+)$1	232	22	48	11.2034
[eeeee!!bbmmmmbb22eeeee]ee	chr17:57392704-57392924(+)$1	220	165	191	9.4795
b####cccooooooccc333bbeeee	chr18:34473942-34474164(+)$1	222	110	136	9.7714
:dddd[ddddmmmmdddd333ddddH	chr19:30249402-30249652(-)$1	250	96	122	9.0413
d$$$$$ddddmmmmdddd4444dddd	chr7:119236608-119236828(+)$1	220	3	29	9.9250
dddd"""cccmmmmcccdddd22ccc	chr16:16886671-16886892(+)$1	221	136	162	10.8014
$$dddd[cccmmmmccc]dddd4444	chr17:29175375-29175595(+)$1	220	190	216	10.7230
"""ddddcccmmmmccc333dddd]e	chr6:17441775-17441995(+)$1	220	8	34	12.1757
eee!!cccooooooccc4444eeeee	chr13:23776344-23776564(+)$1	220	112	138	10.5292
eeeee[ddddllldddd333eeeeeC	chr5:137799021-137799241(+)$1	220	77	103	8.4078
dd$$$$$cccmmmmccc22dddd333	chr7:13510701-13510942(+)$1	241	100	126	11.3917
fff$$$$$ccclllccc4444fffff	chrX:20076549-20076772(+)$1	223	64	90	10.3952
iiiii!!cccmmmmccc333iiiiii	chr16:92079229-92079449(+)$1	220	27	53	13.5051
fffff!!cccmmmmccc22ffffff4	chr3:88713095-88713315(+)$1	220	170	196	12.1481
[eeeee[cccooooooccc]eeeeec	chr2:23041654-23041893(+)$1	239	155	181	8.9804
==========oooooo==========	chr5:106339111-106339331(+)$1	220	68	94	8.7932
[eeeee[cccmmmmccc]eeeee22b	chr2:91446404-91446624(+)$1	220	20	46	10.8245
ffffff[cccmmmmccc]ffffff]d	chr10:36704919-36705139(+)$1	220	77	103	10.9527
!!dddd!!ccclllccc4444dddd2	chr6:127914337-127914557(-)$1	220	24	50	10.4534
eeeee!!cccmmmmccc4444eeeee	chr16:31115993-31116213(-)$1	220	49	75	13.3598
eeee"""cccmmmmccc22eeeeea:	chr14:75709351-75709571(+)$1	220	180	206	11.9174
ffff!!ddddmmmmdddd22ffffff	chrX:7502082-7502302(-)$1	220	151	177	10.3407

#otherMatches

#Seq PSSM
ACUGAAAGGCACAGGCUGCAAAGUGC	chr2:4805367-4805587(+)$1	220	165	191	11.6386
AGUCACCUUCAUUGGAAACAGCACAG	chr17:35972139-35972359(-)$1	220	189	215	12.8488
AGUGAAAUGGAAAACCAGGAACAGAU	chr18:90709382-90709602(+)$1	220	86	112	12.8722
CCCAACCGUGUUCGCAUUUUUGGACC	chr7:25350518-25350738(+)$1	220	93	119	9.5242
CGAUGAACUUACACAAGAUAGCAUUG	chr9:72465811-72466036(+)$1	225	161	187	13.1258
AGCCACCCUCCCGUGAGGAUUUGUGA	chr15:88656743-88656978(+)$1	235	97	123	9.9132
GGAAGGACCUUAAUGGGAUCUUGUUG	chr17:74945613-74945833(+)$1	220	47	73	10.8129
AGAAACGCAAGAAGGCGGUGCUCUUU	chr19:5492422-5492643(+)$1	221	159	185	10.5292
CUAGCGUGCUACAGGGCUUGCUGCGU	chr4:139028301-139028533(+)$1	232	167	193	9.3066
GACGCACACACGGCUGUGAUCGGUUU	chr12:73884712-73884932(+)$1	220	88	114	10.8754
GGGGUUGCCUUUCGAGGACUUCCAAA	chr16:32233054-32233307(-)$1	253	28	54	10.5674
CCCAAAAUCCCCCAGGACUUUAUGGA	chr4:32782330-32782550(+)$1	220	175	201	9.9140
UCUCCCACUUUCUAAGGUACCAGGAA	chr9:48845847-48846067(+)$1	220	9	35	10.8908
UCCCCUUGCUUCAGGGCAUCAAGGGG	chr17:23949290-23949510(+)$1	220	158	184	10.3680
UUACGGAAGGCGUACCUUUGUUUGAU	chr9:105550961-105551181(+)$1	220	55	81	8.4363
AGUCCCGAGCUAACGCCAAGGGAAUU	chr1:133727168-133727388(+)$1	220	181	207	10.3189
GUAAGAGAUGUAUACAUAAAGCUACA	chrX:155780517-155780746(+)$1	229	78	104	9.9736
GAUGGAUGAAGCUCCUUCCAACCUCA	chrX:148340791-148341011(+)$1	220	56	82	8.6003
CUCCGCAAGGGCAACUACUCGGAGCG	chr13:23842913-23843133(+)$1	220	190	216	9.9717
UAGUCUCCUGGGAUUAGGGGGUUAGG	chr5:31093870-31094092(+)$1	222	151	177	10.8644
UUUGAAAAGGCAGUACUUGGAUAAAG	chr3:82863144-82863367(+)$1	223	42	68	10.2872
GUGUGCUUGUAAGUGCAGGCAAUGUG	chr12:111874038-111874258(+)$1	220	128	154	9.0560
UAuguguauauguaugugcacaugua	chr16:93888266-93888487(+)$1	221	152	178	10.8479
ACAUUUGGUUCACUUAGAUUGGAUGU	chr18:50037762-50037985(+)$1	223	70	96	8.7932
AACAACUGUCAUUUGAAUAAUGUUUU	chr13:3565788-3566015(-)$1	227	191	217	10.8231
GAGGACCUAGACGGCUCCGUCCAGGG	chr4:124779989-124780209(+)$1	220	173	199	9.2723
GUGUCCUAGGGAAGCUUGGACUUGUC	chr4:130256899-130257130(+)$1	231	153	179	10.6569
AAGGCCAGAUGUAAAUUGAGGGCCAA	chr10:84091267-84091492(+)$1	225	33	59	11.6373
AGUGCUGCCGAGUCCGCCUCAGCACA	chr7:29524953-29525173(-)$1	220	101	127	9.6866
GAGAAGUAGCUAAUGUUUUUCUUCUU	chr15:9124379-9124599(+)$1	220	18	44	10.3663
CGUUUACGGCAGAUGCCAUGAAGAAA	chr9:104105401-104105621(-)$1	220	47	73	10.6217
CGGGGCCUCUGGAAAGGUGUGUGCUG	chr7:107646601-107646821(+)$1	220	164	190	10.6710
ACAGCAGUAGUAACCUACAGUCUGUG	chr14:52818593-52818813(-)$1	220	149	175	9.8597
AUUUUUAUAGCUCUGUUUUUAAAUUA	chrX:148291927-148292159(+)$1	232	22	48	11.2034
CUGAGGACCCUGGUGGAACCUCACUG	chr17:57392704-57392924(+)$1	220	165	191	9.4795
AGAGGUGCCAAAAAGUAAAGUCCCUG	chr18:34473942-34474164(+)$1	222	110	136	9.7714
CGAUGACUUCUCCCGGAGACACAUCG	chr19:30249402-30249652(-)$1	250	96	122	9.0413
GGAUAAUCGAGAACUUGAACAGCACA	chr7:119236608-119236828(+)$1	220	3	29	9.9250
GGCUCUUUGCGACAGCAGGCCAAUCA	chr16:16886671-16886892(+)$1	221	136	162	10.8014
GCAGGUACUUGAGAGAGCACCUUUUA	chr17:29175375-29175595(+)$1	220	190	216	10.7230
AAAGUCCUCCUGUCGGAAAAGGACCG	chr6:17441775-17441995(+)$1	220	8	34	12.1757
CACCAAGUACACCAGCUCCAAGUGAU	chr13:23776344-23776564(+)$1	220	112	138	10.5292
GCAGCAGGUCACGGGCUGCAGCUGCG	chr5:137799021-137799241(+)$1	220	77	103	8.4078
CUGCCAAGCGCUUCCGCAAAGCACAA	chr7:13510701-13510942(+)$1	241	100	126	11.3917
CAUUUAUCCACAGUGUGUUUUAUGUC	chrX:20076549-20076772(+)$1	223	64	90	10.3952
CCGGUAUUGGAAGUUCAUAGACUGGU	chr16:92079229-92079449(+)$1	220	27	53	13.5051
CUGACCACGGGGACCUGCUGUCAGAA	chr3:88713095-88713315(+)$1	220	170	196	12.1481
GUUUGUGGGCGUAGGAGCCAGCAGGA	chr2:23041654-23041893(+)$1	239	155	181	8.9804
UUGUUUGUAGGUGUUACUGCAGAUGA	chr5:106339111-106339331(+)$1	220	68	94	8.7932
aagacaaaGCUGAAGCUAUGUCUGGC	chr2:91446404-91446624(+)$1	220	20	46	10.8245
UCAUAACUUGCUGCUAAAUUAUGGUU	chr10:36704919-36705139(+)$1	220	77	103	10.9527
CCUCCUUCUCUUCCAGAUCCUGGGAA	chr6:127914337-127914557(-)$1	220	24	50	10.4534
AGCUUCGCCAGGCCUGGAUUAAGGCU	chr16:31115993-31116213(-)$1	220	49	75	13.3598
CAGCCCCAAGGCAUCUUCAGCUGGCA	chr14:75709351-75709571(+)$1	220	180	206	11.9174
GGUGUUGGUAAAAGUGCUCUCACCAU	chrX:7502082-7502302(-)$1	220	151	177	10.3407

#DB
(((....(((....)))....))).)	chr2:4805367-4805587(+)$1	1	165	191	11.6386
.(((...(((....)))...).)).)	chr17:35972139-35972359(-)$1	1	189	215	12.8488
.((....(((....)))...))...)	chr18:90709382-90709602(+)$1	1	86	112	12.8722
.((((..(((....)))..)))).((	chr7:25350518-25350738(+)$1	1	93	119	9.5242
(((((..(((....)))....)))))	chr9:72465811-72466036(+)$1	1	161	187	13.1258
((....((((....))))..))))).	chr15:88656743-88656978(+)$1	1	97	123	9.9132
(.((((.(((....))).)))).)))	chr17:74945613-74945833(+)$1	1	47	73	10.8129
(((..(((......)))....)))))	chr19:5492422-5492643(+)$1	1	159	185	10.5292
.(((((.(((....))).))))).((	chr4:139028301-139028533(+)$1	1	167	193	9.3066
(((...((((....))))....))))	chr12:73884712-73884932(+)$1	1	88	114	10.8754
(((((..(((....))))))))))..	chr16:32233054-32233307(-)$1	1	28	54	10.5674
((..((((((....))).)))..)).	chr4:32782330-32782550(+)$1	1	175	201	9.9140
(.(((.((((....))))....))).	chr9:48845847-48846067(+)$1	1	9	35	10.8908
((((((((((....))))...)))))	chr17:23949290-23949510(+)$1	1	158	184	10.3680
(((..(((((....)))))...))).	chr9:105550961-105551181(+)$1	1	55	81	8.4363
((((((..((....))...))).)))	chr1:133727168-133727388(+)$1	1	181	207	10.3189
(((....(((....))).....))))	chrX:155780517-155780746(+)$1	1	78	104	9.9736
((.((..((((...))))...)))))	chrX:148340791-148341011(+)$1	1	56	82	8.6003
(((((...((....))...)))))))	chr13:23842913-23843133(+)$1	1	190	216	9.9717
((((((((((....)))))))))))(	chr5:31093870-31094092(+)$1	1	151	177	10.8644
((((..(((......)))...)))))	chr3:82863144-82863367(+)$1	1	42	68	10.2872
...(((((((....))))))).).).	chr12:111874038-111874258(+)$1	1	128	154	9.0560
((((((((((....)))))))))).)	chr16:93888266-93888487(+)$1	1	152	178	10.8479
((((((((((......))))))))))	chr18:50037762-50037985(+)$1	1	70	96	8.7932
((((....((....))....))))).	chr13:3565788-3566015(-)$1	1	191	217	10.8231
..((((..((....))..)))).)))	chr4:124779989-124780209(+)$1	1	173	199	9.2723
(.((((.(((....))))))).).))	chr4:130256899-130257130(+)$1	1	153	179	10.6569
..((((.(((....)))...))))..	chr10:84091267-84091492(+)$1	1	33	59	11.6373
.((((((.((....))...)))))).	chr7:29524953-29525173(-)$1	1	101	127	9.6866
((((((.(((....))))))))))))	chr15:9124379-9124599(+)$1	1	18	44	10.3663
(.((((.(((....))).))))))..	chr9:104105401-104105621(-)$1	1	47	73	10.6217
(((.((((((....))).).)).)))	chr7:107646601-107646821(+)$1	1	164	190	10.6710
(((((.((((....)))).).)))))	chr14:52818593-52818813(-)$1	1	149	175	9.8597
((((....(((...)))...))))))	chrX:148291927-148292159(+)$1	1	22	48	11.2034
.(((((..((....))..))))).))	chr17:57392704-57392924(+)$1	1	165	191	9.4795
(....(((......)))...))))))	chr18:34473942-34474164(+)$1	1	110	136	9.7714
.((((.((((....))))...)))))	chr19:30249402-30249652(-)$1	1	96	122	9.0413
(.....((((....))))....))))	chr7:119236608-119236828(+)$1	1	3	29	9.9250
((((...(((....)))))))..)))	chr16:16886671-16886892(+)$1	1	136	162	10.8014
..((((.(((....))).))))....	chr17:29175375-29175595(+)$1	1	190	216	10.7230
...(((((((....)))...)))).)	chr6:17441775-17441995(+)$1	1	8	34	12.1757
(((..(((......)))....)))))	chr13:23776344-23776564(+)$1	1	112	138	10.5292
(((((.((((...))))...))))))	chr5:137799021-137799241(+)$1	1	77	103	8.4078
((.....(((....)))..))))...	chr7:13510701-13510942(+)$1	1	100	126	11.3917
(((.....(((...)))....)))))	chrX:20076549-20076772(+)$1	1	64	90	10.3952
(((((..(((....)))...))))))	chr16:92079229-92079449(+)$1	1	27	53	13.5051
(((((..(((....)))..)))))).	chr3:88713095-88713315(+)$1	1	170	196	12.1481
.(((((.(((......))).))))))	chr2:23041654-23041893(+)$1	1	155	181	8.9804
((((((((((......))))))))))	chr5:106339111-106339331(+)$1	1	68	94	8.7932
.(((((.(((....))).)))))..)	chr2:91446404-91446624(+)$1	1	20	46	10.8245
((((((.(((....))).)))))).)	chr10:36704919-36705139(+)$1	1	77	103	10.9527
..((((..(((...)))....)))).	chr6:127914337-127914557(-)$1	1	24	50	10.4534
(((((..(((....)))....)))))	chr16:31115993-31116213(-)$1	1	49	75	13.3598
((((...(((....)))..)))))).	chr14:75709351-75709571(+)$1	1	180	206	11.9174
((((..((((....))))..))))))	chrX:7502082-7502302(-)$1	1	151	177	10.3407

#PSSM
f : 0.20	e : 0.16	d : 0.10	[ : 0.07	= : 0.07	c : 0.05	" : 0.05	: : 0.05	b : 0.05	! : 0.05	g : 0.03	a : 0.01	& : 0.01	$ : 0.01	i : 0.01	
e : 0.23	f : 0.21	d : 0.10	[ : 0.07	= : 0.07	b : 0.05	c : 0.03	g : 0.03	" : 0.03	! : 0.03	$ : 0.03	& : 0.01	# : 0.01	i : 0.01	
d : 0.21	f : 0.21	e : 0.20	= : 0.07	c : 0.05	b : 0.03	# : 0.03	g : 0.03	" : 0.03	$ : 0.03	! : 0.01	[ : 0.01	i : 0.01	
d : 0.20	f : 0.20	e : 0.14	# : 0.09	! : 0.07	= : 0.07	$ : 0.05	g : 0.03	c : 0.03	a : 0.01	" : 0.01	b : 0.01	[ : 0.01	i : 0.01	
d : 0.18	# : 0.12	f : 0.12	e : 0.10	! : 0.09	" : 0.07	= : 0.07	c : 0.05	$ : 0.05	g : 0.03	b : 0.03	a : 0.01	i : 0.01	
! : 0.16	d : 0.14	# : 0.10	" : 0.09	c : 0.09	e : 0.09	[ : 0.07	f : 0.07	= : 0.07	$ : 0.05	g : 0.01	b : 0.01	
! : 0.20	d : 0.18	[ : 0.18	# : 0.09	c : 0.09	" : 0.07	= : 0.07	$ : 0.03	e : 0.01	g : 0.01	f : 0.01	a : 0.01	
c : 0.54	d : 0.18	! : 0.07	= : 0.07	# : 0.03	e : 0.01	" : 0.01	g : 0.01	[ : 0.01	$ : 0.01	
c : 0.54	d : 0.18	b : 0.10	= : 0.07	o : 0.05	e : 0.01	g : 0.01	
c : 0.52	d : 0.18	b : 0.10	o : 0.07	= : 0.07	e : 0.01	g : 0.01	
m : 0.78	o : 0.12	c : 0.05	d : 0.01	l : 0.01	
m : 0.78	o : 0.12	l : 0.09	
m : 0.78	o : 0.12	l : 0.09	
m : 0.78	o : 0.12	l : 0.07	d : 0.01	
c : 0.56	d : 0.18	b : 0.10	o : 0.07	= : 0.03	e : 0.01	g : 0.01	
c : 0.58	d : 0.18	b : 0.10	o : 0.05	= : 0.03	e : 0.01	g : 0.01	
c : 0.60	d : 0.18	= : 0.07	3 : 0.05	2 : 0.03	e : 0.01	g : 0.01	4 : 0.01	
3 : 0.20	d : 0.20	4 : 0.14	] : 0.14	2 : 0.10	= : 0.07	g : 0.03	c : 0.03	e : 0.01	5 : 0.01	f : 0.01	
3 : 0.27	4 : 0.20	2 : 0.10	d : 0.10	e : 0.07	= : 0.07	g : 0.03	c : 0.03	f : 0.03	5 : 0.01	a : 0.01	] : 0.01	
3 : 0.23	4 : 0.20	d : 0.14	f : 0.09	e : 0.07	= : 0.07	2 : 0.03	g : 0.03	c : 0.03	] : 0.03	5 : 0.01	a : 0.01	
4 : 0.18	d : 0.18	e : 0.14	f : 0.12	3 : 0.09	= : 0.07	b : 0.05	g : 0.03	c : 0.03	a : 0.01	5 : 0.01	] : 0.01	i : 0.01	
f : 0.21	e : 0.20	d : 0.18	b : 0.07	= : 0.07	] : 0.05	4 : 0.05	c : 0.03	2 : 0.03	g : 0.01	3 : 0.01	5 : 0.01	i : 0.01	
f : 0.21	e : 0.21	d : 0.14	] : 0.07	= : 0.07	c : 0.05	b : 0.05	g : 0.03	2 : 0.03	a : 0.03	3 : 0.01	4 : 0.01	i : 0.01	
f : 0.20	e : 0.20	d : 0.14	c : 0.09	= : 0.07	b : 0.05	g : 0.05	] : 0.05	3 : 0.03	: : 0.03	4 : 0.01	i : 0.01	2 : 0.01	
e : 0.20	f : 0.18	d : 0.12	] : 0.07	3 : 0.07	c : 0.07	g : 0.05	= : 0.05	b : 0.03	a : 0.03	: : 0.01	7 : 0.01	4 : 0.01	i : 0.01	2 : 0.01	
f : 0.14	d : 0.14	e : 0.14	: : 0.05	g : 0.05	= : 0.05	2 : 0.05	c : 0.05	3 : 0.05	D : 0.03	b : 0.03	] : 0.03	4 : 0.03	7 : 0.01	5 : 0.01	H : 0.01	C : 0.01	i : 0.01	

#score	579.0541061790914
#seq	55
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_UTR_m3_run1.txt

#BEAR
====$$$$$dddd[ddddnnnnndddd]dddd]=====	chr14:123999020-123999285(-)$1	265	25	63	13.0573
[a[a[a[a[a[a[a[a[annnnna]a]a]a]a]a]a]a	chr2:144300455-144300711(-)$1	256	183	221	14.1864
===========!!ddddoooooodddd22=========	chr13:55698883-55699155(+)$1	272	160	198	19.4262
bb$$$$$==========oooooo==========bbeee	chr4:130378501-130378871(+)$1	370	278	316	15.2000
dbb"""ccc[gggggggooooooggggggg333ccc44	chr9:14160376-14160681(-)$1	305	206	244	15.8198
!ccc[ccc!!bb[ddddoooooodddd]bb]ccc]ccc	chr3:89856727-89856973(+)$1	246	19	57	16.6811
"""===============lll===============33	chr10:7924620-7924918(-)$1	298	53	91	15.7620
===========####cccooooooccc22=========	chr11:62215764-62216055(-)$1	291	145	183	17.7169
ee"""ggggggg!!cccoooooocccgggggggeeeee	chr16:91679071-91679487(+)$1	416	81	119	15.7248
ggggggg[bb!!eeeeeooooooeeeeebb]ggggggg	chr8:91271294-91271707(+)$1	413	348	386	15.3253
ffff"""eeeee!!cccooooooccc22eeeeefffff	chr6:57687955-57688318(+)$1	363	93	131	14.4001
ffffff[ccc!!eeeeeooooooeeeee]ccc]fffff	chr14:49808076-49808440(+)$1	364	26	64	15.1248
!!ggggggg####eeeeennnnneeeee4444gggggg	chr3:102573575-102573831(+)$1	256	54	92	15.2240
Bffffff$$$$$eeeeeooooooeeeee4444ffffff	chr15:96403693-96403972(-)$1	279	34	72	13.9949
ddggggggg####ddddoooooodddd666666ggggg	chr3:144094297-144094585(-)$1	288	53	91	15.3625
===========eeeeeannnnna]eeeee4444=====	chr11:102979254-102979535(+)$1	281	29	67	14.9302
###ggggggg!!eeeeeooooooeeeee666666gggg	chr13:55804541-55804961(+)$1	420	211	249	14.9024
!!ccc!!dddd[eeeeeooooooeeeeeddddccchhh	chr7:108431012-108431268(+)$1	256	12	50	14.3873
a!!ccc[ccc[a!!ddddnnnnndddd]a]ccc]ccc5	chr17:34165456-34165697(-)$1	241	141	179	14.5119
ddd!!ggggggg!!cccooooooccc]ggggggg]ddd	chr11:51604908-51605190(+)$1	282	121	159	15.8924
ddd"""bb"""ffffffooooooffffffbb333dddd	chr2:37425548-37425860(-)$1	312	22	60	13.2025
!==========!!ddddoooooodddd>>>>>>>>>>>	chr10:127764081-127764343(+)$1	262	148	186	16.7725
ddddd[eeeee!!ddddooooooddddeeeee333ddd	chr9:70449732-70450091(-)$1	359	206	244	15.1829
####==========[bboooooobb]==========ee	chr1:23373187-23373542(-)$1	355	215	253	16.4893
ccc[ccc!!ccc[ddddooooooddddccc]cccccc5	chr1:9566497-9566898(+)$1	401	23	61	15.9735
GGdddd####ccc[ddddnnnnndddd22ccc4444dd	chr11:115505349-115505685(-)$1	336	123	161	12.8553
ccc[a!!dddd!!aooooooa22dddd22a]ccc]ccc	chr16:91271517-91271933(+)$1	416	306	344	12.8874
!iiiiiiiiia[cccrrrrrrrrrccc]a]iiiiiiii	chr11:86081744-86082022(-)$1	278	177	215	12.8859
!iiiiiiiii####cccooooooccc4444iiiiiiii	chr14:22615726-22615989(+)$1	263	199	237	18.2426
hhhh[ccc[ccc[ddddoooooodddd]ccc333ccch	chr2:37429674-37430096(-)$1	422	230	268	16.4424
!!ccc[cccdddd[cccooooooccc]dddd4444ccc	chr2:118844189-118844453(-)$1	264	39	77	15.5937
ffffff[a!!dddd[aooooooadddd22a]ffffff]	chr4:108829020-108829310(-)$1	290	34	72	14.3386
dd!!eeeee####eeeeemmmmeeeee333eeeee333	chr9:63494533-63494825(-)$1	292	110	148	12.3738
cc[ffffff[ccc[cccooooooccc]ccc]ffffff]	chr11:55064067-55064407(-)$1	340	148	186	14.5636
============!!ddddmmmmdddd22==========	chr19:59373163-59373593(-)$1	430	134	172	15.2297
ccc!!ccc"""bb!!ddddmmmmdddd22bb]ccc22c	chr8:108459544-108459799(-)$1	255	74	112	12.1794
b[eeeee"""bb[ddddooooooddddbb]eeeee]bb	chr19:44628055-44628327(-)$1	272	205	243	13.8610
cc[ccc==========[ammmma]==========]ccc	chr1:135034932-135035190(+)$1	258	123	161	14.1832
+++ccc!!==========lll==========333ccc>	chr6:38507340-38507648(+)$1	308	78	116	13.3725
$$$ccc"""ccc!!ddddnnnnndddd22ccc333ccc	chr10:116784173-116784645(-)$1	472	277	315	15.5187
bb]cccdddd[bbddddoooooodddd333bb]dddd:	chr9:30273909-30274168(+)$1	259	59	97	13.3049
dddd"""dddd[eeeeeooooooeeeeedddd333ddd	chr14:58161540-58161852(+)$1	312	97	135	14.5009
g"""a[ffffff!!cccooooooccc22ffffff]agg	chr11:94867771-94868102(+)$1	331	237	275	15.1875
eeee!!ccc"""eeeeeooooooeeeee4444ccc22e	chr15:8585562-8585973(-)$1	411	80	118	16.1504
GGccc!!==========nnnnn==========333ccc	chr12:93044407-93044818(-)$1	411	25	63	14.3630
""gggggggbb"""eeeeellleeeee333bb>>>>>>	chr14:15631278-15631659(+)$1	381	287	325	12.2783
d"""ccc!!bb"""ddddnnnnndddd22bb22ccc44	chr13:48974940-48975359(-)$1	419	68	106	14.7224
""bb[eeeee####ddddnnnnndddd333eeeee]bb	chr10:99558936-99559175(+)$1	239	35	73	13.6405
ffffffff!!gggggggooooooggggggg333fffff	chr12:21275727-21276116(+)$1	389	191	229	14.7727
e[bbeeeee!!ccc[cccooooooccc]ccc]eeeee5	chrX:90991609-90991911(+)$1	302	251	289	12.6015
eeeeeiiiiiiiii[cccmmmmccc4444iiiiiiiii	chr18:64435508-64435901(+)$1	393	319	357	12.3152
cc[dddd[eeeee[cccooooooccc]eeeee333ddd	chrX:147084869-147085117(-)$1	248	153	191	14.3735

#otherMatches

#Seq PSSM
GAAGUAGGUUAGGUGGCUAAUAAGGCUUUCUAUUUUCU	chr14:123999020-123999285(-)$1	265	25	63	13.0573
guguguguguguguguguguaugagagagagagagaga	chr2:144300455-144300711(-)$1	256	183	221	14.1864
aaaaaggaagaaaaaCUGUUCGUGGUUACucuuuuuuu	chr13:55698883-55699155(+)$1	272	160	198	19.4262
AGCAGCAGCCCAGGCCUGAUCCUGGGCCUGGGCCUGGG	chr4:130378501-130378871(+)$1	370	278	316	15.2000
UGUAGAGGAAGCAGCAUGAAGCAGUGCUGUGUGUCCAC	chr9:14160376-14160681(-)$1	305	206	244	15.8198
GGGUGGGGAAAUGGGACGGGAAGGUCCGAUGCUUAACU	chr3:89856727-89856973(+)$1	246	19	57	16.6811
GAUGGGUGUUUUUUUUUUUUUAAGGAAAAAAUAUUCUU	chr10:7924620-7924918(-)$1	298	53	91	15.7620
AUUUAUUUUUGAGUAGCAUAUAAUUGCAAUAAGAAUAA	chr11:62215764-62216055(-)$1	291	145	183	17.7169
CUUCAGAGGCCAAGUACAUAUUAGUAUGGCUUCAGUUG	chr16:91679071-91679487(+)$1	416	81	119	15.7248
AGGGGCUCCUAAGUAUGAGACAACAUGCAGUGGUUUCU	chr8:91271294-91271707(+)$1	413	348	386	15.3253
ACUCAUUACAUGAACUCUUAGCUGAGCACAUGUGAGUG	chr6:57687955-57688318(+)$1	363	93	131	14.4001
UUUGCUUUAGAAGGAAGUCCCUUCUUCCCUUACAGUAA	chr14:49808076-49808440(+)$1	364	26	64	15.1248
UAGUGAAGGCCUCGCCUUCCCACAAGGCCUUUCCUUCA	chr3:102573575-102573831(+)$1	256	54	92	15.2240
GGGAUGCCUCACUAUAACAAUAAUUAUGCCAAGCAUUC	chr15:96403693-96403972(-)$1	279	34	72	13.9949
GGCCACUAUUGAUAAACCUUUCUGUUUUAAAAUGUAGU	chr3:144094297-144094585(-)$1	288	53	91	15.3625
CUCUUUCCAAGUUCGGCGACUAGACUGAAAACUUUUGG	chr11:102979254-102979535(+)$1	281	29	67	14.9302
UGAGCUACUCGUGUGCAAUUAUGUGUAUGGAAUGGAGU	chr13:55804541-55804961(+)$1	420	211	249	14.9024
ACGUGGAGAUCACACUGGUGUGACAGUGGAUUUACCUU	chr7:108431012-108431268(+)$1	256	12	50	14.3873
CAGCGUUGUUGCUUUUGGAAAAAUCAAUGGGACCAUGA	chr17:34165456-34165697(-)$1	241	141	179	14.5119
CAGAAUAGGUGUUUUUAGAUUAUUAAUAUAUCUACCUG	chr11:51604908-51605190(+)$1	282	121	159	15.8924
AAGUCUGUUUAAAAUACCCAUUUGUAUUUACUGUUUUC	chr2:37425548-37425860(-)$1	312	22	60	13.2025
UGAAACCGAAAGUACAAACUGUGUUGUCUUUUUUUUUU	chr10:127764081-127764343(+)$1	262	148	186	16.7725
UCAGAUGCUAGUUUACUAAACUCAGUGUUAGCCAUUCU	chr9:70449732-70450091(-)$1	359	206	244	15.1829
UUGAUGUUACAUAUAUAAAUAAAUGAAUGUGUAAUAAA	chr1:23373187-23373542(-)$1	355	215	253	16.4893
UACAUGGAACCCAUGGGCCAUACCCCAGGGGUCAGUAU	chr1:9566497-9566898(+)$1	401	23	61	15.9735
CACACCUGGGCCAUGUGAUUGUUUUAUUUUGGAAUUGG	chr11:115505349-115505685(-)$1	336	123	161	12.8553
UCAUUAACGUUCUCAUUAAAGUAAGCGGAGUUGGGCGA	chr16:91271517-91271933(+)$1	416	306	344	12.8874
AACCUGUUUUGUGUGCAGUUAAUCCAUUCUGAAGCAGG	chr11:86081744-86082022(-)$1	278	177	215	12.8859
ACAGCUUCAAAAAAAAUAUAAAAAUUGUCCUUGAagcu	chr14:22615726-22615989(+)$1	263	199	237	18.2426
AGAAUCAGAGCUGUAGUGGAAUUGCUAAAGCCAGCUGU	chr2:37429674-37430096(-)$1	422	230	268	16.4424
UCGGAUAGAAUGGAUCAGUCAAGUGAGCCAUGUUUUCU	chr2:118844189-118844453(-)$1	264	39	77	15.5937
AACCUUCCACUUCCAGGGUGAGCGGAAAAGAGAGGUUC	chr4:108829020-108829310(-)$1	290	34	72	14.3386
UAUUUAUAGUGUUUUAGAUUUUUCUAACUUUUGUAUCU	chr9:63494533-63494825(-)$1	292	110	148	12.3738
CCACCCACAGAGCUGUUCAGAAAGACUGCUGUGUGGGC	chr11:55064067-55064407(-)$1	340	148	186	14.5636
UUUGCUUUUAUUGUUGUUGCCAAAUGUAAAUGAAAGCA	chr19:59373163-59373593(-)$1	430	134	172	15.2297
AGGAAACUGUGCAGGCCAUGGAGGUGGAAUGAAGUGGC	chr8:108459544-108459799(-)$1	255	74	112	12.1794
CUUGUGUUUUCUCGGGGUGUUUUCCUCAGUGCACAUGG	chr19:44628055-44628327(-)$1	272	205	243	13.8610
ACUAGGGGGUAUUUGGGAGACAUGUCAGAUAUUCACUU	chr1:135034932-135035190(+)$1	258	123	161	14.1832
aaaauagaacagaagauaaauuauuuuuuguguauGUG	chr6:38507340-38507648(+)$1	308	78	116	13.3725
AAAAUAAAAUAGCUUUGGUUUGUCUAAUUUUGCAGUGU	chr10:116784173-116784645(-)$1	472	277	315	15.5187
AGCAGGCUCCAACCUCAAGAUCAUGAGCAUGUGGGAGA	chr9:30273909-30274168(+)$1	259	59	97	13.3049
ACUAUUUUGAAUAGUGGCAGAAACUAUUUUCAUAUUAG	chr14:58161540-58161852(+)$1	312	97	135	14.5009
CCCCUGCACUUCACCCAGGCAGAUGGAGGGGGUGGAGC	chr11:94867771-94868102(+)$1	331	237	275	15.1875
ACAGUUUCGAUAUUACCAAUUUAGGUGGCAAACGAUCC	chr15:8585562-8585973(-)$1	411	80	118	16.1504
AUGUUCUUUGUUUACUAUUUAUUGGUGAACGAUCUGAC	chr12:93044407-93044818(-)$1	411	25	63	14.3630
CGCUUUCUGGCUUUCCUUUCACAAAGGCACGUUCAAAA	chr14:15631278-15631659(+)$1	381	287	325	12.2783
CCAGUAUGUGCCCAUUUGCAAAACAAAAUGCUAAUAAU	chr13:48974940-48975359(-)$1	419	68	106	14.7224
CAACCUGCAGCCUGUCGUUAAUUAUGGUCUCUGCAAGU	chr10:99558936-99559175(+)$1	239	35	73	13.6405
CGGAUUAUUUUCAUUGUCUUAAUGCAGUGAUUUAUAAU	chr12:21275727-21276116(+)$1	389	191	229	14.7727
ACGGGAGUUCUGCCAUGGGAGUUACUAGGGCCAGCUCU	chrX:90991609-90991911(+)$1	302	251	289	12.6015
AGGGAGGAGCCUGAUGCUGCAGAGCCGACUCGGGUUUC	chr18:64435508-64435901(+)$1	393	319	357	12.3152
CUGAGCUUGGCAUGUUAAUGGAAUGGGAUGCUCCUAGC	chrX:147084869-147085117(-)$1	248	153	191	14.3735

#DB
((((.....((((.((((.....)))).)))).)))))	chr14:123999020-123999285(-)$1	1	25	63	13.0573
.(.(.(.(.(.(.(.(.(.....).).).).).).).)	chr2:144300455-144300711(-)$1	1	183	221	14.1864
(((((((((((..((((......))))..)))))))))	chr13:55698883-55699155(+)$1	1	160	198	19.4262
((.....((((((((((......)))))))))))))))	chr4:130378501-130378871(+)$1	1	278	316	15.2000
(((...(((.(((((((......)))))))...)))..	chr9:14160376-14160681(-)$1	1	206	244	15.8198
.(((.(((..((.((((......)))).)).))).)))	chr3:89856727-89856973(+)$1	1	19	57	16.6811
...(((((((((((((((...)))))))))))))))..	chr10:7924620-7924918(-)$1	1	53	91	15.7620
(((((((((((....(((......)))..)))))))))	chr11:62215764-62216055(-)$1	1	145	183	17.7169
((...(((((((..(((......)))))))))))))))	chr16:91679071-91679487(+)$1	1	81	119	15.7248
(((((((.((..(((((......))))))).)))))))	chr8:91271294-91271707(+)$1	1	348	386	15.3253
((((...(((((..(((......)))..))))))))))	chr6:57687955-57688318(+)$1	1	93	131	14.4001
((((((.(((..(((((......))))).))).)))))	chr14:49808076-49808440(+)$1	1	26	64	15.1248
..(((((((....(((((.....)))))....))))))	chr3:102573575-102573831(+)$1	1	54	92	15.2240
(((((((.....(((((......)))))....))))))	chr15:96403693-96403972(-)$1	1	34	72	13.9949
))(((((((....((((......))))......)))))	chr3:144094297-144094585(-)$1	1	53	91	15.3625
(((((((((((((((((.....).)))))....)))))	chr11:102979254-102979535(+)$1	1	29	67	14.9302
...(((((((..(((((......)))))......))))	chr13:55804541-55804961(+)$1	1	211	249	14.9024
..(((..((((.(((((......)))))))))))))))	chr7:108431012-108431268(+)$1	1	12	50	14.3873
(..(((.(((.(..((((.....)))).).))).))).	chr17:34165456-34165697(-)$1	1	141	179	14.5119
(((..(((((((..(((......))).))))))).)))	chr11:51604908-51605190(+)$1	1	121	159	15.8924
(((...((...((((((......))))))))...))))	chr2:37425548-37425860(-)$1	1	22	60	13.2025
.((((((((((..((((......))))...........	chr10:127764081-127764343(+)$1	1	148	186	16.7725
(((((.(((((..((((......)))))))))...)))	chr9:70449732-70450091(-)$1	1	206	244	15.1829
....((((((((((.((......)).))))))))))))	chr1:23373187-23373542(-)$1	1	215	253	16.4893
(((.(((..(((.((((......))))))).)))))).	chr1:9566497-9566898(+)$1	1	23	61	15.9735
((((((....(((.((((.....))))..)))....))	chr11:115505349-115505685(-)$1	1	123	161	12.8553
(((.(..((((..(......)..))))..).))).)))	chr16:91271517-91271933(+)$1	1	306	344	12.8874
.((((((((((.(((.........))).).))))))))	chr11:86081744-86082022(-)$1	1	177	215	12.8859
.(((((((((....(((......)))....))))))))	chr14:22615726-22615989(+)$1	1	199	237	18.2426
((((.(((.(((.((((......)))).)))...))))	chr2:37429674-37430096(-)$1	1	230	268	16.4424
..(((.(((((((.(((......))).))))....)))	chr2:118844189-118844453(-)$1	1	39	77	15.5937
((((((.(..((((.(......)))))..).)))))).	chr4:108829020-108829310(-)$1	1	34	72	14.3386
((..(((((....(((((....)))))...)))))...	chr9:63494533-63494825(-)$1	1	110	148	12.3738
((.((((((.(((.(((......))).))).)))))).	chr11:55064067-55064407(-)$1	1	148	186	14.5636
((((((((((((..((((....))))..))))))))))	chr19:59373163-59373593(-)$1	1	134	172	15.2297
(((..(((...((..((((....))))..)).)))..)	chr8:108459544-108459799(-)$1	1	74	112	12.1794
(.(((((...((.((((......)))))).))))).))	chr19:44628055-44628327(-)$1	1	205	243	13.8610
((.(((((((((((((.(....).)))))))))).)))	chr1:135034932-135035190(+)$1	1	123	161	14.1832
...(((..((((((((((...))))))))))...))).	chr6:38507340-38507648(+)$1	1	78	116	13.3725
...(((...(((..((((.....))))..)))...)))	chr10:116784173-116784645(-)$1	1	277	315	15.5187
)).)))((((.((((((......))))...)).)))).	chr9:30273909-30274168(+)$1	1	59	97	13.3049
((((...((((.(((((......)))))))))...)))	chr14:58161540-58161852(+)$1	1	97	135	14.5009
(...(.((((((..(((......)))..)))))).)))	chr11:94867771-94868102(+)$1	1	237	275	15.1875
((((..(((...(((((......)))))....)))..)	chr15:8585562-8585973(-)$1	1	80	118	16.1504
(((((..((((((((((.....))))))))))...)))	chr12:93044407-93044818(-)$1	1	25	63	14.3630
..(((((((((...(((((...)))))...))......	chr14:15631278-15631659(+)$1	1	287	325	12.2783
(...(((..((...((((.....))))..))..)))..	chr13:48974940-48975359(-)$1	1	68	106	14.7224
..((.(((((....((((.....))))...))))).))	chr10:99558936-99559175(+)$1	1	35	73	13.6405
((((((((..(((((((......)))))))...)))))	chr12:21275727-21276116(+)$1	1	191	229	14.7727
(.(((((((..(((.(((......))).))).))))).	chrX:90991609-90991911(+)$1	1	251	289	12.6015
)))))(((((((((.(((....)))....)))))))))	chr18:64435508-64435901(+)$1	1	319	357	12.3152
((.((((.(((((.(((......))).)))))...)))	chrX:147084869-147085117(-)$1	1	153	191	14.3735

#PSSM
d : 0.15	! : 0.13	c : 0.11	= : 0.09	e : 0.07	f : 0.07	b : 0.05	" : 0.05	g : 0.03	# : 0.03	G : 0.03	[ : 0.01	B : 0.01	a : 0.01	h : 0.01	+ : 0.01	$ : 0.01	
c : 0.13	= : 0.11	d : 0.11	" : 0.09	f : 0.09	! : 0.07	b : 0.05	e : 0.05	# : 0.03	G : 0.03	i : 0.03	[ : 0.03	a : 0.01	g : 0.01	h : 0.01	+ : 0.01	$ : 0.01	
c : 0.13	= : 0.11	f : 0.09	d : 0.09	[ : 0.07	" : 0.07	g : 0.07	b : 0.05	e : 0.05	$ : 0.03	# : 0.03	! : 0.03	i : 0.03	h : 0.01	+ : 0.01	] : 0.01	
c : 0.17	= : 0.13	f : 0.11	" : 0.09	g : 0.09	d : 0.07	! : 0.05	e : 0.05	[ : 0.03	i : 0.03	b : 0.03	a : 0.01	$ : 0.01	# : 0.01	h : 0.01	
c : 0.19	= : 0.13	" : 0.09	g : 0.09	f : 0.09	[ : 0.07	e : 0.07	! : 0.05	d : 0.05	$ : 0.03	a : 0.03	i : 0.03	
c : 0.19	= : 0.13	g : 0.13	f : 0.09	" : 0.07	! : 0.07	e : 0.07	[ : 0.05	i : 0.05	$ : 0.03	d : 0.03	a : 0.01	
= : 0.15	c : 0.15	g : 0.13	e : 0.09	[ : 0.07	f : 0.07	! : 0.07	" : 0.05	i : 0.05	$ : 0.03	d : 0.03	b : 0.01	# : 0.01	
= : 0.19	c : 0.15	g : 0.11	e : 0.09	d : 0.07	! : 0.05	i : 0.05	f : 0.05	$ : 0.03	a : 0.03	[ : 0.03	" : 0.03	b : 0.01	# : 0.01	
= : 0.21	g : 0.11	e : 0.11	c : 0.09	! : 0.09	d : 0.07	" : 0.07	i : 0.05	$ : 0.03	[ : 0.03	f : 0.03	b : 0.01	# : 0.01	
= : 0.21	d : 0.11	c : 0.09	! : 0.07	e : 0.07	# : 0.07	" : 0.07	g : 0.05	b : 0.05	i : 0.05	[ : 0.03	a : 0.01	$ : 0.01	f : 0.01	
= : 0.21	d : 0.11	# : 0.09	c : 0.09	g : 0.07	b : 0.07	! : 0.07	[ : 0.05	e : 0.05	" : 0.05	$ : 0.01	a : 0.01	f : 0.01	i : 0.01	
! : 0.13	= : 0.13	# : 0.11	c : 0.11	g : 0.07	b : 0.07	d : 0.05	e : 0.05	[ : 0.05	" : 0.05	a : 0.03	f : 0.03	$ : 0.01	i : 0.01	
! : 0.21	e : 0.17	= : 0.11	# : 0.11	[ : 0.09	c : 0.07	d : 0.05	g : 0.03	b : 0.03	" : 0.03	f : 0.01	i : 0.01	
d : 0.19	e : 0.19	! : 0.15	= : 0.11	[ : 0.09	# : 0.05	a : 0.03	g : 0.03	c : 0.03	" : 0.03	f : 0.01	i : 0.01	
d : 0.30	e : 0.21	c : 0.17	[ : 0.09	= : 0.09	g : 0.03	# : 0.01	f : 0.01	o : 0.01	! : 0.01	
d : 0.32	c : 0.21	e : 0.21	= : 0.09	a : 0.03	g : 0.03	f : 0.01	b : 0.01	o : 0.01	r : 0.01	
d : 0.32	c : 0.21	e : 0.19	= : 0.07	[ : 0.03	g : 0.03	o : 0.03	a : 0.01	f : 0.01	b : 0.01	r : 0.01	
o : 0.59	d : 0.15	c : 0.05	e : 0.05	a : 0.03	= : 0.03	n : 0.03	r : 0.01	
o : 0.63	n : 0.19	m : 0.07	l : 0.03	r : 0.01	d : 0.01	e : 0.01	
o : 0.63	n : 0.19	m : 0.09	l : 0.05	r : 0.01	
o : 0.61	n : 0.19	m : 0.09	l : 0.05	a : 0.01	r : 0.01	
o : 0.61	n : 0.19	m : 0.09	= : 0.03	2 : 0.01	r : 0.01	l : 0.01	
o : 0.59	n : 0.15	= : 0.05	a : 0.05	e : 0.03	2 : 0.01	r : 0.01	d : 0.01	m : 0.01	c : 0.01	
d : 0.36	e : 0.19	c : 0.17	= : 0.07	g : 0.03	o : 0.03	] : 0.03	a : 0.01	f : 0.01	b : 0.01	r : 0.01	
d : 0.36	c : 0.23	e : 0.21	= : 0.09	g : 0.03	] : 0.01	f : 0.01	b : 0.01	
d : 0.36	c : 0.21	e : 0.21	= : 0.09	g : 0.03	a : 0.01	f : 0.01	] : 0.01	4 : 0.01	
d : 0.34	e : 0.21	= : 0.11	] : 0.09	g : 0.05	c : 0.05	2 : 0.05	4 : 0.03	f : 0.01	
2 : 0.21	e : 0.21	] : 0.11	= : 0.11	g : 0.07	3 : 0.07	c : 0.03	4 : 0.03	a : 0.01	6 : 0.01	f : 0.01	> : 0.01	d : 0.01	b : 0.01	
2 : 0.15	= : 0.13	4 : 0.09	d : 0.07	g : 0.07	e : 0.07	c : 0.07	3 : 0.07	b : 0.05	] : 0.03	6 : 0.03	a : 0.03	f : 0.03	> : 0.01	
= : 0.17	c : 0.13	b : 0.09	4 : 0.09	d : 0.07	g : 0.07	3 : 0.07	a : 0.05	e : 0.05	] : 0.05	6 : 0.03	> : 0.01	f : 0.01	i : 0.01	
= : 0.17	] : 0.13	e : 0.11	c : 0.11	b : 0.09	d : 0.07	4 : 0.07	i : 0.05	3 : 0.03	g : 0.03	6 : 0.03	> : 0.01	f : 0.01	
= : 0.15	c : 0.13	e : 0.11	3 : 0.09	4 : 0.09	d : 0.05	g : 0.05	i : 0.05	f : 0.05	6 : 0.03	] : 0.03	b : 0.03	a : 0.01	> : 0.01	2 : 0.01	
3 : 0.19	= : 0.13	c : 0.13	e : 0.09	] : 0.07	g : 0.07	f : 0.07	4 : 0.05	i : 0.05	6 : 0.03	> : 0.03	2 : 0.01	
= : 0.15	c : 0.15	3 : 0.15	f : 0.13	e : 0.09	g : 0.07	i : 0.05	> : 0.03	4 : 0.03	a : 0.01	b : 0.01	6 : 0.01	] : 0.01	d : 0.01	
c : 0.17	= : 0.13	] : 0.11	f : 0.11	e : 0.09	3 : 0.09	g : 0.07	i : 0.05	d : 0.03	> : 0.03	4 : 0.03	b : 0.01	
c : 0.23	= : 0.13	f : 0.11	d : 0.11	g : 0.07	e : 0.05	i : 0.05	a : 0.03	> : 0.03	2 : 0.03	] : 0.03	h : 0.01	4 : 0.01	3 : 0.01	
c : 0.19	d : 0.13	f : 0.11	= : 0.09	g : 0.09	e : 0.07	i : 0.05	4 : 0.03	3 : 0.03	> : 0.03	2 : 0.03	b : 0.03	] : 0.01	h : 0.01	
c : 0.13	d : 0.11	= : 0.09	g : 0.09	e : 0.07	f : 0.07	5 : 0.05	> : 0.05	i : 0.05	4 : 0.03	3 : 0.03	h : 0.03	] : 0.03	b : 0.03	a : 0.01	: : 0.01	

#score	767.9922141043033
#seq	52
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_CDS_m1_run1.txt

#BEAR
==========[aooooooa]=========	chr10:59190697-59190937(+)$1	240	165	194	14.9861
hhhh!!ccccccooooooccc4444ccc2	chr17:87692075-87692292(+)$1	217	22	51	14.3108
ccc"""ffffffooooooffffff22ccc	chr5:129500604-129500843(-)$1	239	83	112	12.5595
===!!dddd[cccoooooocccdddd444	chr16:34690786-34690994(+)$1	208	111	140	12.3579
::===========nnnnn===========	chr3:66798339-66798575(+)$1	236	21	50	10.1252
ggggg!!bb[bboooooobb]bbgggggg	chr15:79543750-79543961(+)$1	211	78	107	12.2618
ccc"""bb[cccmmmmccc]bb4444ccc	chr9:95940020-95940249(+)$1	229	70	99	9.1823
iiiiiiii[cccrrrrrrrrrccciiiii	chr2:25128759-25128965(+)$1	206	67	96	9.9783
c"""eeeee[bboooooobb]eeeee333	chrX:71542868-71543084(+)$1	216	162	191	12.7511
ffffff[eeeeeooooooeeeee4444ff	chr3:95151848-95152063(-)$1	215	126	155	12.1721
ffccc[bb[cccooooooccc]bb]ccc5	chr2:121901023-121901233(-)$1	210	163	192	13.1115
[bb!!ccc[cccoooooocccccc22bbc	chr12:77072718-77072937(+)$1	219	135	164	13.6996
:iiiiiiiiibboooooobb]iiiiiiii	chr17:71749302-71749524(-)$1	222	44	73	13.0447
====ccceeeeeooooooeeeee]ccc]=	chr7:150706214-150706432(-)$1	218	71	100	13.0460
"dddd!!eeeeeooooooeeeee4444dd	chr8:74207844-74208059(+)$1	215	82	111	12.8626
ccc"""bb[cccnnnnnccc]bbccc333	chr10:29066756-29066977(-)$1	221	126	155	10.5558
hh[a[bb[ddddoooooodddd]bba]hh	chr10:12417745-12418027(-)$1	282	25	54	11.3315
C:eeeee!!cccooooooccc22eeeee:	chr9:121659268-121659478(+)$1	210	169	198	10.6331
bb[bb[bb[cccooooooccc]bb]bb]b	chr1:20810139-20810366(-)$1	227	55	84	12.6668
cc"""dddd[cccnnnnnccc22dddd44	chr16:33104780-33104997(+)$1	217	28	57	9.9255
ceeeee[cccbboooooobb]ccc]eeee	chr2:38489312-38489541(-)$1	229	28	57	12.1358
::dddd"""cccooooooccc]ddddddd	chr3:97924647-97924870(+)$1	223	147	176	11.5216
cc[ccc"""cccbblllbb]ccc333ccc	chr15:36538002-36538213(-)$1	211	20	49	9.5686
e$$$$$ccc[bboooooobbccceeeee]	chr18:6490428-6490655(-)$1	227	129	158	12.0455
a[ffffff[cccoooooocccffffffag	chrX:39600944-39601175(+)$1	231	81	110	12.5289
ddd!!gggggggoooooogggggggdddd	chr2:119598114-119598337(-)$1	223	166	195	12.8688
::==========oooooo==========:	chr1:183060781-183061003(-)$1	222	1	30	12.7463
dddd$$$$$cccooooooccc333dddd2	chr15:99571954-99572181(-)$1	227	13	42	13.4912
[bb!!bb!!cccooooooccc22bb22bb	chr11:21212168-21212394(+)$1	226	26	55	13.0139
:dddd[bb[cccooooooccc]bb]dddd	chr2:103615998-103616225(-)$1	227	63	92	12.3087
eeedddd!!cccooooooccc333dddd]	chr2:91076864-91077087(-)$1	223	87	116	13.9434
bb[eeeee[cccooooooccc]eeeee]b	chr15:99576214-99576433(-)$1	219	145	174	13.0874
cc[ccc[eeeeeooooooeeeee22ccc]	chr1:167320501-167320719(-)$1	218	154	183	12.8368
gggg[a!!ddddoooooodddd22a]ggg	chr15:76735211-76735417(+)$1	206	116	145	12.8814
eeee[bb!!cccooooooccc22bbeeee	chr17:25968032-25968255(-)$1	223	26	55	12.9571
ddddd!!eeeeeooooooeeeee]dddd]	chr19:8895176-8895399(+)$1	223	128	157	12.1523
eee####eeeeeooooooeeeee4444ee	chr4:32825941-32826163(+)$1	222	50	79	13.3973
ddddddd[ddddoooooodddd]dddd33	chr13:55448176-55448402(-)$1	226	166	195	11.5073
=======[eeeeennnnneeeee]=====	chr8:73440886-73441096(+)$1	210	144	173	10.2754
gggg####eeeeennnnneeeee4444gg	chr13:50527514-50527730(+)$1	216	116	145	10.1920
ee:iiiiiiiiiooooooiiiiiiiii::	chr16:29586278-29586513(+)$1	235	137	166	11.1842
ee==========oooooo==========:	chr8:26672638-26672859(+)$1	221	174	203	14.2378
b!!iiiiiiiiiooooooiiiiiiiiibb	chr1:71643813-71644034(-)$1	221	97	126	13.7839
iiiiiiii[ddddnnnnnddddiiiiiii	chr13:73928041-73928264(+)$1	223	55	84	9.9046
hhhhh!!a!!bboooooobb22a4444hh	chr11:70462905-70463134(+)$1	229	184	213	12.6523
""ccc####cccooooooccc4444ccc3	chr17:56744634-56744856(+)$1	222	131	160	15.3551
fffff[ffffffooooooffffff22fff	chrX:23326961-23327182(+)$1	221	50	79	10.8212
d####ccc[cccooooooccc22ccc444	chr15:43339163-43339389(+)$1	226	29	58	14.7602
"""iiiiiiiiiooooooiiiiiiiii]b	chr10:74708301-74708507(+)$1	206	30	59	14.1724
ffff[cccbbbboooooobb]bb]ccc]f	chr7:105414644-105414850(-)$1	206	19	48	11.4016
[bb!!ddddcccooooooccc666666dd	chr7:134167946-134168152(-)$1	206	44	73	11.0837
g$$$$$ccc[cccnnnnncccccc4444g	chr16:22866986-22867202(+)$1	216	37	66	10.3055
iiiiiiii"""bboooooobbiiiiiiii	chr9:117958427-117958645(+)$1	218	187	216	12.1947

#otherMatches

#Seq PSSM
AGAAGUGAGUGUUAUUUCAGGCUUGCUUU	chr10:59190697-59190937(+)$1	240	165	194	14.9861
GGUAGAAGCUCUGGAGUGGGAAUGUGCUA	chr17:87692075-87692292(+)$1	217	22	51	14.3108
UUCCCCCUUUUAAAGAAAUAAAAGAAGAG	chr5:129500604-129500843(-)$1	239	83	112	12.5595
CCGGAUCUCGACCGGGCCAGGUGAGGGCU	chr16:34690786-34690994(+)$1	208	111	140	12.3579
AAAAGUUUAAAAUUUUGUAUUUUGAAUUU	chr3:66798339-66798575(+)$1	236	21	50	10.1252
CCAGGCUGCCGGAAGAUCCCUGUCCUGGU	chr15:79543750-79543961(+)$1	211	78	107	12.2618
UCUACCUAUGAAUCAUUUCCUAAAAAAGA	chr9:95940020-95940249(+)$1	229	70	99	9.1823
GGAGAUGGUCCAGCGCCUCUAUGGUCGUU	chr2:25128759-25128965(+)$1	206	67	96	9.9783
CUUAGACCCUGCCCUGGAGCUGGGUCCCC	chrX:71542868-71543084(+)$1	216	162	191	12.7511
UUCUCAAGAUCUACAUAAAGGUUAGUGUG	chr3:95151848-95152063(-)$1	215	126	155	12.1721
GAUGAAGAUGCUCGUUCCAGCUUCAUCAG	chr2:121901023-121901233(-)$1	210	163	192	13.1115
UGCCCAGGUCUUACAAAGAAGCCUUAGCG	chr12:77072718-77072937(+)$1	219	135	164	13.6996
AACAGCUUUCCCAUUUCAGGUGGAAGUUG	chr17:71749302-71749524(-)$1	222	44	73	13.0447
UGUCUCUCUAAUACAGGAAUUGGAAGGUG	chr7:150706214-150706432(-)$1	218	71	100	13.0460
CCACCUUUCAUUAAGCUGAGUGAUCCUGG	chr8:74207844-74208059(+)$1	215	82	111	12.8626
GAUACCUCCGUUGAAGAAACAGAAUCAGA	chr10:29066756-29066977(-)$1	221	126	155	10.5558
UGAUACUGAUGUCCACUUACAUGGGAGUA	chr10:12417745-12418027(-)$1	282	25	54	11.3315
GAACAUUAUUCCAGAGCAGGAUGAGUGUA	chr9:121659268-121659478(+)$1	210	169	198	10.6331
CCGGCGAUUUCGGAGCUGCGACAUGGCGG	chr1:20810139-20810366(-)$1	227	55	84	12.6668
GCCCGUACUGUGACACACUCAGAAGUAAC	chr16:33104780-33104997(+)$1	217	28	57	9.9255
UUACCUUGUGUCUAUUCUGAUCACCAGGU	chr2:38489312-38489541(-)$1	229	28	57	12.1358
CUAUGUCAACAGUUACACCUGCACAUGCC	chr3:97924647-97924870(+)$1	223	147	176	11.5216
CGAGGCGAUGCUCUACGAGAAGUUCAGCC	chr15:36538002-36538213(-)$1	211	20	49	9.5686
GAAUACGCCUCGAUAAACCGGGCCGUGCC	chr18:6490428-6490655(-)$1	227	129	158	12.0455
GCAUUUGGAUGCCUUAUUGCGCCAGAUCC	chrX:39600944-39601175(+)$1	231	81	110	12.5289
GCUGGAUUUACUCUGAGUGGUGGAUAGCU	chr2:119598114-119598337(-)$1	223	166	195	12.8688
GAUUUUAAAAGACUCUUCUCUUUUGGAAA	chr1:183060781-183061003(-)$1	222	1	30	12.7463
GAGAAAAGGACUAUACAGAGUAGAUCUUG	chr15:99571954-99572181(-)$1	227	13	42	13.4912
UUAUUUUCCuuauuuuauuaauuaauuua	chr11:21212168-21212394(+)$1	226	26	55	13.0139
UUCAUGGCAGAAACACAGUUCAGCAGUGG	chr2:103615998-103616225(-)$1	227	63	92	12.3087
GCUUGAUAUCUCUUCACCGAGUACGUCAU	chr2:91076864-91077087(-)$1	223	87	116	13.9434
GGUUUUAGUUAUGUCAAGAUGCCUGGAUU	chr15:99576214-99576433(-)$1	219	145	174	13.0874
GAGGAAGACCUCGGCCCAGAGGUAAUUUG	chr1:167320501-167320719(-)$1	218	154	183	12.8368
GGGGACAGGGGCAAGCUGGCCCGAGCCUC	chr15:76735211-76735417(+)$1	206	116	145	12.8814
GCUGCUGCUGGUAUGGUGACCCCCACAGC	chr17:25968032-25968255(-)$1	223	26	55	12.9571
UGAGGAACUGGCAGCCAAGCCGGGCUUCA	chr19:8895176-8895399(+)$1	223	128	157	12.1523
GCGGUGAUGCUGAUCCACCAGCAGUUGUG	chr4:32825941-32826163(+)$1	222	50	79	13.3973
GCCGGUCUGGCUGGGAAGGGCCUGACCUU	chr13:55448176-55448402(-)$1	226	166	195	11.5073
CAUCAGGGUGCUGGGCAGUGGCAGCCUGG	chr8:73440886-73441096(+)$1	210	144	173	10.2754
GUCAGAGCUGGUGCUCUUCACCAUACAUG	chr13:50527514-50527730(+)$1	216	116	145	10.1920
CAAAAAAGUGAGUUUACUUUCAUUUUUGC	chr16:29586278-29586513(+)$1	235	137	166	11.1842
UCCUUUCUUGGCUAGUUUGCUGGGAAGGU	chr8:26672638-26672859(+)$1	221	174	203	14.2378
CCAUCUCUUGGACGCCGUUCCAGGAGAGU	chr1:71643813-71644034(-)$1	221	97	126	13.7839
GCGGGAGGCUCGUACUACAUGAUCUCCCG	chr13:73928041-73928264(+)$1	223	55	84	9.9046
UGGUUGAGAUCUGCAAAAAGUGCCAAAAG	chr11:70462905-70463134(+)$1	229	184	213	12.6523
GGGCUAUGGUUCGAACAAGAGAUUGAGUG	chr17:56744634-56744856(+)$1	222	131	160	15.3551
UUUUCUCUUCCUUUCAACAGGAAGCCGAG	chrX:23326961-23327182(+)$1	221	50	79	10.8212
UGCCAGAAAGCGUAAGAUUGCCAUUCGAA	chr15:43339163-43339389(+)$1	226	29	58	14.7602
CAAUGCUUUGGGCUUUUCCCUAGAGCAAA	chr10:74708301-74708507(+)$1	206	30	59	14.1724
UGCUAAAGACCAAAUGAAUGUGUCCUUAA	chr7:105414644-105414850(-)$1	206	19	48	11.4016
ACGAAGGAUCGCCUCCGAGCGCACACAGU	chr7:134167946-134168152(-)$1	206	44	73	11.0837
GGAACCCCUCGUCAGCAGGACAGGAAUAU	chr16:22866986-22867202(+)$1	216	37	66	10.3055
AUUAAAAUAAUUGGUUAAACAAUUUUAAU	chr9:117958427-117958645(+)$1	218	187	216	12.1947

#DB
((((((((((.(......).)))))))))	chr10:59190697-59190937(+)$1	1	165	194	14.9861
((((..((((((......)))....))).	chr17:87692075-87692292(+)$1	1	22	51	14.3108
(((...((((((......))))))..)))	chr5:129500604-129500843(-)$1	1	83	112	12.5595
(((..((((.(((......)))))))...	chr16:34690786-34690994(+)$1	1	111	140	12.3579
..(((((((((((.....)))))))))))	chr3:66798339-66798575(+)$1	1	21	50	10.1252
(((((..((.((......)).))))))))	chr15:79543750-79543961(+)$1	1	78	107	12.2618
(((...((.(((....))).))....)))	chr9:95940020-95940249(+)$1	1	70	99	9.1823
((((((((.(((.........))))))))	chr2:25128759-25128965(+)$1	1	67	96	9.9783
(...(((((.((......)).)))))...	chrX:71542868-71543084(+)$1	1	162	191	12.7511
((((((.(((((......)))))....))	chr3:95151848-95152063(-)$1	1	126	155	12.1721
(((((.((.(((......))).)).))).	chr2:121901023-121901233(-)$1	1	163	192	13.1115
.((..(((.(((......))))))..)))	chr12:77072718-77072937(+)$1	1	135	164	13.6996
.(((((((((((......)).))))))))	chr17:71749302-71749524(-)$1	1	44	73	13.0447
((((((((((((......))))).))).)	chr7:150706214-150706432(-)$1	1	71	100	13.0460
.((((..(((((......)))))....))	chr8:74207844-74208059(+)$1	1	82	111	12.8626
(((...((.(((.....))).)))))...	chr10:29066756-29066977(-)$1	1	126	155	10.5558
((.(.((.((((......)))).))).))	chr10:12417745-12418027(-)$1	1	25	54	11.3315
).(((((..(((......)))..))))).	chr9:121659268-121659478(+)$1	1	169	198	10.6331
((.((.((.(((......))).)).)).)	chr1:20810139-20810366(-)$1	1	55	84	12.6668
((...((((.(((.....)))..))))..	chr16:33104780-33104997(+)$1	1	28	57	9.9255
)(((((.(((((......)).))).))))	chr2:38489312-38489541(-)$1	1	28	57	12.1358
..((((...(((......))).))))(((	chr3:97924647-97924870(+)$1	1	147	176	11.5216
((.(((...(((((...)).)))...)))	chr15:36538002-36538213(-)$1	1	20	49	9.5686
(.....(((.((......)))))))))).	chr18:6490428-6490655(-)$1	1	129	158	12.0455
(.((((((.(((......)))))))))))	chrX:39600944-39601175(+)$1	1	81	110	12.5289
(((..(((((((......)))))))))))	chr2:119598114-119598337(-)$1	1	166	195	12.8688
..((((((((((......)))))))))).	chr1:183060781-183061003(-)$1	1	1	30	12.7463
((((.....(((......)))...)))).	chr15:99571954-99572181(-)$1	1	13	42	13.4912
.((..((..(((......)))..))..))	chr11:21212168-21212394(+)$1	1	26	55	13.0139
.((((.((.(((......))).)).))))	chr2:103615998-103616225(-)$1	1	63	92	12.3087
(((((((..(((......)))...)))).	chr2:91076864-91077087(-)$1	1	87	116	13.9434
((.(((((.(((......))).))))).)	chr15:99576214-99576433(-)$1	1	145	174	13.0874
((.(((.(((((......)))))..))).	chr1:167320501-167320719(-)$1	1	154	183	12.8368
((((.(..((((......))))..).)))	chr15:76735211-76735417(+)$1	1	116	145	12.8814
((((.((..(((......)))..))))))	chr17:25968032-25968255(-)$1	1	26	55	12.9571
(((((..(((((......))))).)))).	chr19:8895176-8895399(+)$1	1	128	157	12.1523
(((....(((((......)))))....))	chr4:32825941-32826163(+)$1	1	50	79	13.3973
(((((((.((((......)))).))))..	chr13:55448176-55448402(-)$1	1	166	195	11.5073
(((((((.(((((.....))))).)))))	chr8:73440886-73441096(+)$1	1	144	173	10.2754
((((....(((((.....)))))....))	chr13:50527514-50527730(+)$1	1	116	145	10.1920
)).(((((((((......)))))))))..	chr16:29586278-29586513(+)$1	1	137	166	11.1842
))((((((((((......)))))))))).	chr8:26672638-26672859(+)$1	1	174	203	14.2378
(..(((((((((......)))))))))))	chr1:71643813-71644034(-)$1	1	97	126	13.7839
((((((((.((((.....)))))))))))	chr13:73928041-73928264(+)$1	1	55	84	9.9046
(((((..(..((......))..)....))	chr11:70462905-70463134(+)$1	1	184	213	12.6523
..(((....(((......)))....))).	chr17:56744634-56744856(+)$1	1	131	160	15.3551
(((((.((((((......))))))..)))	chrX:23326961-23327182(+)$1	1	50	79	10.8212
(....(((.(((......)))..)))...	chr15:43339163-43339389(+)$1	1	29	58	14.7602
...(((((((((......))))))))).)	chr10:74708301-74708507(+)$1	1	30	59	14.1724
((((.(((((((......)).)).))).)	chr7:105414644-105414850(-)$1	1	19	48	11.4016
.((..(((((((......)))......))	chr7:134167946-134168152(-)$1	1	44	73	11.0837
(.....(((.(((.....))))))....)	chr16:22866986-22867202(+)$1	1	37	66	10.3055
((((((((...((......))))))))))	chr9:117958427-117958645(+)$1	1	187	216	12.1947

#PSSM
c : 0.15	e : 0.11	: : 0.09	d : 0.09	= : 0.07	g : 0.07	f : 0.07	h : 0.05	i : 0.05	[ : 0.05	" : 0.05	b : 0.05	C : 0.01	a : 0.01	
c : 0.11	d : 0.11	e : 0.11	b : 0.09	= : 0.07	: : 0.07	i : 0.07	f : 0.07	h : 0.05	g : 0.05	" : 0.05	$ : 0.03	[ : 0.01	! : 0.01	# : 0.01	
= : 0.13	d : 0.13	c : 0.09	[ : 0.09	e : 0.09	i : 0.07	f : 0.07	g : 0.05	" : 0.05	b : 0.05	h : 0.03	$ : 0.03	: : 0.01	! : 0.01	# : 0.01	
i : 0.13	d : 0.13	= : 0.11	" : 0.09	! : 0.09	f : 0.07	c : 0.07	e : 0.07	g : 0.05	h : 0.03	$ : 0.03	# : 0.03	a : 0.01	b : 0.01	
i : 0.13	! : 0.11	d : 0.11	= : 0.09	c : 0.09	" : 0.07	e : 0.07	[ : 0.07	f : 0.05	$ : 0.05	# : 0.05	g : 0.01	b : 0.01	h : 0.01	
i : 0.13	d : 0.11	c : 0.11	= : 0.09	! : 0.09	e : 0.07	[ : 0.07	" : 0.05	b : 0.05	$ : 0.05	# : 0.05	f : 0.03	g : 0.01	a : 0.01	
b : 0.15	c : 0.13	i : 0.13	= : 0.09	d : 0.09	! : 0.09	f : 0.05	e : 0.05	[ : 0.05	# : 0.05	" : 0.03	g : 0.01	$ : 0.01	
e : 0.15	c : 0.13	i : 0.13	b : 0.11	! : 0.09	= : 0.07	f : 0.05	d : 0.05	[ : 0.05	" : 0.03	# : 0.03	g : 0.01	$ : 0.01	a : 0.01	
[ : 0.20	e : 0.16	d : 0.11	! : 0.09	= : 0.07	c : 0.07	i : 0.07	" : 0.05	f : 0.03	b : 0.03	g : 0.01	$ : 0.01	# : 0.01	
c : 0.39	e : 0.15	[ : 0.11	= : 0.07	i : 0.07	d : 0.07	f : 0.03	g : 0.01	! : 0.01	b : 0.01	" : 0.01	
c : 0.43	e : 0.15	b : 0.13	d : 0.07	= : 0.05	i : 0.05	f : 0.03	[ : 0.01	g : 0.01	" : 0.01	
c : 0.43	b : 0.15	e : 0.15	d : 0.07	= : 0.05	i : 0.05	f : 0.03	a : 0.01	g : 0.01	
o : 0.77	c : 0.05	b : 0.03	e : 0.03	= : 0.01	m : 0.01	r : 0.01	n : 0.01	d : 0.01	
o : 0.81	n : 0.13	m : 0.01	r : 0.01	b : 0.01	
o : 0.81	n : 0.13	m : 0.01	r : 0.01	l : 0.01	
o : 0.81	n : 0.13	m : 0.01	r : 0.01	l : 0.01	
o : 0.81	n : 0.13	c : 0.01	r : 0.01	l : 0.01	
o : 0.81	n : 0.11	c : 0.03	r : 0.01	b : 0.01	
c : 0.37	b : 0.15	e : 0.15	d : 0.07	= : 0.05	i : 0.05	f : 0.03	o : 0.03	a : 0.01	r : 0.01	g : 0.01	
c : 0.37	b : 0.15	e : 0.15	d : 0.07	] : 0.05	= : 0.05	i : 0.05	f : 0.03	r : 0.01	g : 0.01	
c : 0.39	e : 0.15	] : 0.11	= : 0.07	d : 0.07	i : 0.05	f : 0.03	b : 0.03	r : 0.01	g : 0.01	2 : 0.01	
e : 0.16	c : 0.13	2 : 0.11	] : 0.09	i : 0.09	= : 0.07	b : 0.07	d : 0.07	f : 0.05	4 : 0.03	3 : 0.03	g : 0.01	6 : 0.01	
e : 0.18	b : 0.11	c : 0.11	i : 0.11	2 : 0.11	= : 0.07	4 : 0.05	f : 0.05	d : 0.03	] : 0.03	3 : 0.03	g : 0.01	a : 0.01	6 : 0.01	
4 : 0.15	c : 0.11	b : 0.11	i : 0.11	= : 0.07	d : 0.07	e : 0.07	] : 0.07	f : 0.05	3 : 0.05	g : 0.03	2 : 0.03	6 : 0.01	
4 : 0.16	d : 0.13	i : 0.13	= : 0.09	2 : 0.07	e : 0.07	] : 0.07	c : 0.07	b : 0.05	g : 0.03	3 : 0.01	f : 0.01	a : 0.01	6 : 0.01	
d : 0.16	c : 0.15	4 : 0.13	i : 0.13	e : 0.11	= : 0.09	2 : 0.07	g : 0.01	a : 0.01	b : 0.01	3 : 0.01	f : 0.01	] : 0.01	6 : 0.01	
c : 0.16	4 : 0.15	d : 0.15	i : 0.13	= : 0.09	e : 0.09	g : 0.03	3 : 0.03	b : 0.03	f : 0.03	] : 0.01	2 : 0.01	6 : 0.01	
d : 0.15	c : 0.13	= : 0.09	] : 0.09	e : 0.09	4 : 0.07	i : 0.07	g : 0.05	3 : 0.05	b : 0.05	f : 0.03	h : 0.03	a : 0.01	: : 0.01	
g : 0.09	d : 0.09	b : 0.09	= : 0.07	c : 0.07	i : 0.07	3 : 0.07	: : 0.07	] : 0.07	4 : 0.05	f : 0.05	e : 0.05	2 : 0.03	h : 0.03	5 : 0.01	

#score	648.8817247536716
#seq	53
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_transcript_m1_run2.txt

#BEAR
cc[bbyyyyyyyyyyyyyyyybb]ccc	chr1:46864681-46864930(-)$1	249	150	177	21.4669
gggcccvvvvvvvvvvvvvccc]gggg	chr1:165845958-165846194(+)$1	236	193	220	24.4928
gggg[ccctttttttttttccc]gggg	chr8:63391717-63391957(-)$1	240	167	194	24.1604
[eeeeewwwwwwwwwwwwwweeeee]e	chr7:103395499-103395736(+)$1	237	158	185	23.1018
!!eeeeeuuuuuuuuuuuueeeeeeee	chr18:82753773-82754078(+)$1	305	192	219	24.3712
##eeeeettttttttttteeeee4444	chr13:78328308-78328543(-)$1	235	94	121	22.8468
ggggggvvvvvvvvvvvvvggggggg:	chr8:114542948-114543210(+)$1	262	232	259	23.5911
eeeeyyyyyyyyyyyyyyyyeeeee22	chr15:37298249-37298509(-)$1	260	170	197	22.5889
##eeeeettttttttttteeeee4444	chr14:46078490-46078735(-)$1	245	176	203	22.8468
gg[cccvvvvvvvvvvvvvccc]gggg	chr10:67558393-67558628(-)$1	235	40	67	24.5656
ggggggguuuuuuuuuuuuggggggg]	chr12:71367074-71367313(-)$1	239	192	219	24.8450
cccccyyyyyyyyyyyyyyyyccc::e	chr8:116895675-116895917(+)$1	242	185	212	20.4327
===yyyyyyyyyyyyyyyy========	chr11:50109114-50109357(-)$1	243	84	111	22.6036
fffffwwwwwwwwwwwwwwffffff]a	chr5:136384869-136385127(-)$1	258	198	225	22.4203
cc[ddddvvvvvvvvvvvvvdddd]cc	chr6:11850322-11850557(-)$1	235	44	71	22.9220
ff[ddddvvvvvvvvvvvvvdddd]ff	chr18:6789009-6789276(+)$1	267	20	47	22.6235
iiiiyyyyyyyyyyyyyyyyiiiiiii	chrX:137009827-137010085(+)$1	258	68	95	23.1446
hhddddwwwwwwwwwwwwwwdddd22h	chr9:64071161-64071396(-)$1	235	184	211	21.2290
eee[cccuuuuuuuuuuuuccceeeee	chr10:106256389-106256638(+)$1	249	28	55	24.5058
d"""cccvvvvvvvvvvvvvccc333d	chr8:87784680-87784930(-)$1	250	53	80	23.4147
iiiiiiiitttttttttttiiiiiiii	chr10:57236016-57236273(-)$1	257	149	176	23.4344
fff[ccctttttttttttccc]fffff	chr11:41945539-41945852(-)$1	313	235	262	23.3459
ggggcccuuuuuuuuuuuuccc]gggg	chr10:114727075-114727322(-)$1	247	86	113	25.0488
eeeee[bbtttttttttttbb]eeeee	chr2:102621818-102622058(+)$1	240	71	98	22.6470
ggggggvvvvvvvvvvvvvggggggg4	chr8:56144782-56145092(+)$1	310	120	147	24.4712
d:eeeeettttttttttteeeeegggg	chr19:55698571-55698820(+)$1	249	44	71	22.0978
[ffffffuuuuuuuuuuuuffffffbb	chr1:155755322-155755563(+)$1	241	63	90	23.4820
cffffffuuuuuuuuuuuuffffff]c	chr13:29999236-29999490(-)$1	254	221	248	24.0998
dddd[bbvvvvvvvvvvvvvbb]dddd	chr1:22411526-22411777(-)$1	251	209	236	21.7547
b[fffffftttttttttttffffff]b	chr6:127639083-127639335(-)$1	252	147	174	22.5890
!!eeeeeuuuuuuuuuuuueeeee]dd	chr4:109059970-109060218(+)$1	248	95	122	24.2490
##eeeeeuuuuuuuuuuuueeeee22f	chr1:52846191-52846426(-)$1	235	131	158	23.8786
ffffffvvvvvvvvvvvvvffffff33	chr12:55172626-55172863(+)$1	237	72	99	23.7824
cc[eeeeettttttttttteeeee]cc	chr2:6463645-6463887(-)$1	242	182	209	23.4282
ddd[ccctttttttttttcccdddd22	chr5:122906744-122907038(-)$1	294	160	187	22.5307
dd:cccvvvvvvvvvvvvvccceeeee	chr2:102624138-102624408(+)$1	270	150	177	22.5712
#ccc[bbtttttttttttbbccceeee	chr1:87804430-87804678(+)$1	248	130	157	22.7504
ff!!bbvvvvvvvvvvvvvbb22ffff	chr4:148554568-148554806(-)$1	238	201	228	22.5611
hhhhyyyyyyyyyyyyyyyyhhhhhhh	chr11:17099396-17099632(+)$1	236	45	72	21.1804
ggggggwwwwwwwwwwwwwwggggggg	chr9:52482140-52482384(-)$1	244	4	31	23.4190
ggg!!bbtttttttttttbb22ggggg	chr1:136645546-136645781(+)$1	235	92	119	22.8160
#eeeeeyyyyyyyyyyyyyyyyeeeee	chr5:68010324-68010596(-)$1	272	164	191	22.1570
===[a[attttttttttta]a======	chr11:77524443-77524703(+)$1	260	137	164	24.3002
eee[ddddtttttttttttddddeeee	chr6:30698403-30698657(-)$1	254	101	128	22.3779
""fffffftttttttttttffffffdd	chrX:8470920-8471173(+)$1	253	131	158	22.5593
ffffffvvvvvvvvvvvvvffffff]b	chr15:31385917-31386158(-)$1	241	117	144	23.4764
cc[eeeeettttttttttteeeeeccc	chr9:79618583-79618902(-)$1	319	228	255	23.3190
d"""cccvvvvvvvvvvvvvccc]ddd	chrX:54486260-54486498(-)$1	238	156	183	22.9576
ccc[cccuuuuuuuuuuuuccc22ccc	chrX:69677955-69678230(-)$1	275	27	54	24.0733
hhhhyyyyyyyyyyyyyyyyhhhhhhh	chr13:38071246-38071486(-)$1	240	74	101	21.1804
ggggggguuuuuuuuuuuuggggggg]	chrX:96661226-96661469(-)$1	243	41	68	24.8450
hhhh[bbuuuuuuuuuuuubb22hhhh	chr2:158211402-158211658(+)$1	256	181	208	22.2033
cc[ddddtttttttttttddddccc]c	chr11:51935829-51936079(+)$1	250	163	190	22.6245
gggggggtttttttttttggggggg::	chr5:17771193-17771449(-)$1	256	200	227	21.7440
ggggggvvvvvvvvvvvvvggggggg>	chr4:152815582-152815817(-)$1	235	43	70	24.3098
eeee[bbuuuuuuuuuuuubb333eee	chr13:9652964-9653199(+)$1	235	140	167	23.5091
!eeeeewwwwwwwwwwwwwweeeee33	chr8:110104207-110104444(-)$1	237	122	149	23.2102
ffffffvvvvvvvvvvvvvffffff22	chr10:74647136-74647376(+)$1	240	171	198	23.4055
:ffffffuuuuuuuuuuuuffffff::	chr2:49627551-49627793(+)$1	242	11	38	21.0581
cgggggggtttttttttttggggggg:	chr4:109125793-109126035(-)$1	242	168	195	22.6977
ff[ayyyyyyyyyyyyyyyya]fffff	chr11:78140021-78140298(+)$1	277	204	231	22.4673
fffeeeeettttttttttteeeee444	chr8:17392841-17393085(-)$1	244	135	162	23.0312
[ddddwwwwwwwwwwwwwwddddeeee	chr17:10404623-10404875(-)$1	252	145	172	21.6532

#otherMatches

#Seq PSSM
GCUUGACUAGCCUAAUUUUAACAUGCU	chr1:46864681-46864930(-)$1	249	150	177	21.4669
CACUCGUCCAGCCACAUCUCGAGGUGA	chr1:165845958-165846194(+)$1	236	193	220	24.4928
UCUUCUUUCAAAAAAAAAAAAAAAAGG	chr8:63391717-63391957(-)$1	240	167	194	24.1604
CUGUUCGAUAAAGUAUGUAGGGACAAU	chr7:103395499-103395736(+)$1	237	158	185	23.1018
UCCUUUGUUUUCUUCCCCCUAAAGAGC	chr18:82753773-82754078(+)$1	305	192	219	24.3712
UCCAAAUAAUUAUAAAAAAUUUGUCCU	chr13:78328308-78328543(-)$1	235	94	121	22.8468
UCCUCUAGGUGGAGUGAAGGGAGGAUG	chr8:114542948-114543210(+)$1	262	232	259	23.5911
AUCAUCUUUUUUUUCCCCUUUGAUUCU	chr15:37298249-37298509(-)$1	260	170	197	22.5889
GGUGGACUUACCAGUAUUGUCCAAUAA	chr14:46078490-46078735(-)$1	245	176	203	22.8468
uguuuguuuguuuguuuUUUAAUUAAA	chr10:67558393-67558628(-)$1	235	40	67	24.5656
CUAUUUGUUCUCCCUCAUUUAAGUAGU	chr12:71367074-71367313(-)$1	239	192	219	24.8450
ACGCUCUCCCCUCUCCCUUAAAGCAAA	chr8:116895675-116895917(+)$1	242	185	212	20.4327
ACGUUCAAGUGCAGUUAUUUGUGGUUA	chr11:50109114-50109357(-)$1	243	84	111	22.6036
UUCUCCUUCCUUUACUGUUGAGAAGUG	chr5:136384869-136385127(-)$1	258	198	225	22.4203
CUGCUGAUAAUGAAGGUCUUUCAGAAG	chr6:11850322-11850557(-)$1	235	44	71	22.9220
GCUUAAUUACUGAAUUACUUGUUAUGU	chr18:6789009-6789276(+)$1	267	20	47	22.6235
AGCUUUUUCCAUCUCACAUUAGCUAUA	chrX:137009827-137010085(+)$1	258	68	95	23.1446
ggagcuggauuacagacaggagcuacc	chr9:64071161-64071396(-)$1	235	184	211	21.2290
GACAGAUGACACCAGCCAAAUCGUCGA	chr10:106256389-106256638(+)$1	249	28	55	24.5058
CCUUAACUCACUUCAUAAUUGUUUAAG	chr8:87784680-87784930(-)$1	250	53	80	23.4147
GGUUAGGCACUAAGAUAAAGUCUAGUC	chr10:57236016-57236273(-)$1	257	149	176	23.4344
UUGCUGAUACCAACUAUUUCAAUAAGU	chr11:41945539-41945852(-)$1	313	235	262	23.3459
GGUGCAAAAAUAUAUACAAUUGUCAUC	chr10:114727075-114727322(-)$1	247	86	113	25.0488
UAUAACUGUCUAAUUUUCUUACUUGUG	chr2:102621818-102622058(+)$1	240	71	98	22.6470
ACAUUGUAUUCUUUUUUCUUGAUGUUC	chr8:56144782-56145092(+)$1	310	120	147	24.4712
AUUUGCCGUUUUUUUAUAGGUAAAGGU	chr19:55698571-55698820(+)$1	249	44	71	22.0978
UGGAAUACCAAGGUCUUUUUAUUCCUC	chr1:155755322-155755563(+)$1	241	63	90	23.4820
UUGAGUUGCUGCUACUAAAAGCUCACA	chr13:29999236-29999490(-)$1	254	221	248	24.0998
CGGCUGCUGCUUCUUUUUCUGUUGCUG	chr1:22411526-22411777(-)$1	251	209	236	21.7547
GUGAUUAGUUUUCCCCAUCCUGAUCCC	chr6:127639083-127639335(-)$1	252	147	174	22.5890
GAGCCAUUUGUGAUGUUUUAUGGUGUU	chr4:109059970-109060218(+)$1	248	95	122	24.2490
AACCCUUCAAUAAAAUACCAAGGGAGG	chr1:52846191-52846426(-)$1	235	131	158	23.8786
AAUGAAAAAAAAAAACCACUUCAUUAC	chr12:55172626-55172863(+)$1	237	72	99	23.7824
AUAAAACUUAAAAAAAUGUAGUUUCAU	chr2:6463645-6463887(-)$1	242	182	209	23.4282
UCAUACUUGUACAAAGAUAGUUGAGCC	chr5:122906744-122907038(-)$1	294	160	187	22.5307
AAGCUGAAGAAAAAAAAAACAGAUACA	chr2:102624138-102624408(+)$1	270	150	177	22.5712
UGGCAUGAGGCUCACAAACAGCCCCCA	chr1:87804430-87804678(+)$1	248	130	157	22.7504
GACCCAGCACAUCUCCAAAUGAUUCUC	chr4:148554568-148554806(-)$1	238	201	228	22.5611
UUUGUCCAUAGUCACAUCUUUAAAAUU	chr11:17099396-17099632(+)$1	236	45	72	21.1804
UACAAAUUUACAAUGGACUUUUUGUAU	chr9:52482140-52482384(-)$1	244	4	31	23.4190
CAUUGAUUAAAAAGCCAUAUAUAUGUU	chr1:136645546-136645781(+)$1	235	92	119	22.8160
CUCACAUUAAAAUAAAACAACUUGUGA	chr5:68010324-68010596(-)$1	272	164	191	22.1570
GCgugucugugugucugugucugugug	chr11:77524443-77524703(+)$1	260	137	164	24.3002
CAUUAUAUGCUUCUAUUUAAUGUGUGA	chr6:30698403-30698657(-)$1	254	101	128	22.3779
GAAGUAGAAAAGCUUGGAGUCUGCUGA	chrX:8470920-8471173(+)$1	253	131	158	22.5593
GUUGUUGUCAAAGAUUUAAAACAGCUG	chr15:31385917-31386158(-)$1	241	117	144	23.4764
UGCUAACCUUUGAAAAUUUGGUUACAG	chr9:79618583-79618902(-)$1	319	228	255	23.3190
ACCCAGUUGCACUUCCCUUUACUAUCA	chrX:54486260-54486498(-)$1	238	156	183	22.9576
UCUGUAGGUAAACUUAUGACUAGAAGA	chrX:69677955-69678230(-)$1	275	27	54	24.0733
uuuuuuuuuuuuuuuuuuuuAAAAAAC	chr13:38071246-38071486(-)$1	240	74	101	21.1804
UUGUCUGAAAUCGUGAUACCAGGUAAC	chrX:96661226-96661469(-)$1	243	41	68	24.8450
aaccaacaccaguuacuaaguaggguu	chr2:158211402-158211658(+)$1	256	181	208	22.2033
UUGUUCUUUGUUACUGUCAGAAAACCU	chr11:51935829-51936079(+)$1	250	163	190	22.6245
GUAAUGUAAAGAAAUUCAGCGUUACCA	chr5:17771193-17771449(-)$1	256	200	227	21.7440
cacugccuccccugccucugcaguguc	chr4:152815582-152815817(-)$1	235	43	70	24.3098
aguguugaccucugaccuccaUCCCAC	chr13:9652964-9653199(+)$1	235	140	167	23.5091
UAUUGUUUACCUUCAAAGAUACAAUUA	chr8:110104207-110104444(-)$1	237	122	149	23.2102
UGGGGCUGCCUCUCUUACCGCCUCACG	chr10:74647136-74647376(+)$1	240	171	198	23.4055
AUCCAGCGUCAGUACAGUAGUUGGAAA	chr2:49627551-49627793(+)$1	242	11	38	21.0581
AUACUGCAUCUCUUGUUACUGUAGUGC	chr4:109125793-109126035(-)$1	242	168	195	22.6977
CUGAGUACAUAGCAAAUAAAUGAGAGC	chr11:78140021-78140298(+)$1	277	204	231	22.4673
GGGUUGUCACACAGAGAAAGACGAGAA	chr8:17392841-17393085(-)$1	244	135	162	23.0312
UGAGAAUAUUAGACUAAGAUCUUACUG	chr17:10404623-10404875(-)$1	252	145	172	21.6532

#DB
((.((................)).)))	chr1:46864681-46864930(-)$1	1	150	177	21.4669
((((((.............))).))))	chr1:165845958-165846194(+)$1	1	193	220	24.4928
((((.(((...........))).))))	chr8:63391717-63391957(-)$1	1	167	194	24.1604
.(((((..............))))).)	chr7:103395499-103395736(+)$1	1	158	185	23.1018
..(((((............))))))))	chr18:82753773-82754078(+)$1	1	192	219	24.3712
..(((((...........)))))....	chr13:78328308-78328543(-)$1	1	94	121	22.8468
((((((.............))))))).	chr8:114542948-114543210(+)$1	1	232	259	23.5911
((((................)))))..	chr15:37298249-37298509(-)$1	1	170	197	22.5889
..(((((...........)))))....	chr14:46078490-46078735(-)$1	1	176	203	22.8468
((.(((.............))).))))	chr10:67558393-67558628(-)$1	1	40	67	24.5656
(((((((............))))))).	chr12:71367074-71367313(-)$1	1	192	219	24.8450
))(((................)))..(	chr8:116895675-116895917(+)$1	1	185	212	20.4327
(((................))))))))	chr11:50109114-50109357(-)$1	1	84	111	22.6036
(((((..............)))))).)	chr5:136384869-136385127(-)$1	1	198	225	22.4203
((.((((.............)))).))	chr6:11850322-11850557(-)$1	1	44	71	22.9220
((.((((.............)))).))	chr18:6789009-6789276(+)$1	1	20	47	22.6235
((((................)))))))	chrX:137009827-137010085(+)$1	1	68	95	23.1446
((((((..............))))..)	chr9:64071161-64071396(-)$1	1	184	211	21.2290
(((.(((............))))))))	chr10:106256389-106256638(+)$1	1	28	55	24.5058
(...(((.............)))...)	chr8:87784680-87784930(-)$1	1	53	80	23.4147
((((((((...........))))))))	chr10:57236016-57236273(-)$1	1	149	176	23.4344
(((.(((...........))).)))))	chr11:41945539-41945852(-)$1	1	235	262	23.3459
(((((((............))).))))	chr10:114727075-114727322(-)$1	1	86	113	25.0488
(((((.((...........)).)))))	chr2:102621818-102622058(+)$1	1	71	98	22.6470
((((((.............))))))).	chr8:56144782-56145092(+)$1	1	120	147	24.4712
).(((((...........)))))((((	chr19:55698571-55698820(+)$1	1	44	71	22.0978
.((((((............))))))))	chr1:155755322-155755563(+)$1	1	63	90	23.4820
(((((((............)))))).)	chr13:29999236-29999490(-)$1	1	221	248	24.0998
((((.((.............)).))))	chr1:22411526-22411777(-)$1	1	209	236	21.7547
(.((((((...........)))))).)	chr6:127639083-127639335(-)$1	1	147	174	22.5890
..(((((............))))).))	chr4:109059970-109060218(+)$1	1	95	122	24.2490
..(((((............)))))..)	chr1:52846191-52846426(-)$1	1	131	158	23.8786
((((((.............))))))..	chr12:55172626-55172863(+)$1	1	72	99	23.7824
((.(((((...........))))).))	chr2:6463645-6463887(-)$1	1	182	209	23.4282
(((.(((...........)))))))..	chr5:122906744-122907038(-)$1	1	160	187	22.5307
)).(((.............)))(((((	chr2:102624138-102624408(+)$1	1	150	177	22.5712
.(((.((...........)))))))))	chr1:87804430-87804678(+)$1	1	130	157	22.7504
((..((.............))..))))	chr4:148554568-148554806(-)$1	1	201	228	22.5611
((((................)))))))	chr11:17099396-17099632(+)$1	1	45	72	21.1804
((((((..............)))))))	chr9:52482140-52482384(-)$1	1	4	31	23.4190
(((..((...........))..)))))	chr1:136645546-136645781(+)$1	1	92	119	22.8160
.(((((................)))))	chr5:68010324-68010596(-)$1	1	164	191	22.1570
(((.(.(...........).)))))))	chr11:77524443-77524703(+)$1	1	137	164	24.3002
(((.((((...........))))))))	chr6:30698403-30698657(-)$1	1	101	128	22.3779
..((((((...........))))))))	chrX:8470920-8471173(+)$1	1	131	158	22.5593
((((((.............)))))).)	chr15:31385917-31386158(-)$1	1	117	144	23.4764
((.(((((...........))))))))	chr9:79618583-79618902(-)$1	1	228	255	23.3190
(...(((.............))).)))	chrX:54486260-54486498(-)$1	1	156	183	22.9576
(((.(((............)))..)))	chrX:69677955-69678230(-)$1	1	27	54	24.0733
((((................)))))))	chr13:38071246-38071486(-)$1	1	74	101	21.1804
(((((((............))))))).	chrX:96661226-96661469(-)$1	1	41	68	24.8450
((((.((............))..))))	chr2:158211402-158211658(+)$1	1	181	208	22.2033
((.((((...........))))))).)	chr11:51935829-51936079(+)$1	1	163	190	22.6245
(((((((...........)))))))..	chr5:17771193-17771449(-)$1	1	200	227	21.7440
((((((.............))))))).	chr4:152815582-152815817(-)$1	1	43	70	24.3098
((((.((............))...)))	chr13:9652964-9653199(+)$1	1	140	167	23.5091
.(((((..............)))))..	chr8:110104207-110104444(-)$1	1	122	149	23.2102
((((((.............))))))..	chr10:74647136-74647376(+)$1	1	171	198	23.4055
.((((((............))))))..	chr2:49627551-49627793(+)$1	1	11	38	21.0581
)(((((((...........))))))).	chr4:109125793-109126035(-)$1	1	168	195	22.6977
((.(................).)))))	chr11:78140021-78140298(+)$1	1	204	231	22.4673
((((((((...........)))))...	chr8:17392841-17393085(-)$1	1	135	162	23.0312
.((((..............))))))))	chr17:10404623-10404875(-)$1	1	145	172	21.6532

#PSSM
g : 0.19	c : 0.14	f : 0.14	d : 0.09	# : 0.07	e : 0.07	h : 0.06	[ : 0.04	! : 0.04	= : 0.03	i : 0.03	b : 0.01	" : 0.01	: : 0.01	
g : 0.20	f : 0.19	c : 0.12	e : 0.12	h : 0.06	d : 0.06	# : 0.04	" : 0.04	! : 0.03	= : 0.03	i : 0.03	: : 0.01	[ : 0.01	
e : 0.22	g : 0.19	f : 0.17	[ : 0.12	d : 0.06	c : 0.04	h : 0.04	= : 0.03	i : 0.03	" : 0.03	: : 0.01	! : 0.01	
e : 0.23	g : 0.15	f : 0.14	d : 0.09	[ : 0.09	c : 0.07	h : 0.04	i : 0.03	" : 0.03	! : 0.03	b : 0.01	y : 0.01	a : 0.01	
e : 0.20	c : 0.17	f : 0.14	g : 0.12	y : 0.09	d : 0.09	[ : 0.07	b : 0.03	i : 0.01	! : 0.01	a : 0.01	
e : 0.19	c : 0.17	y : 0.12	g : 0.12	f : 0.12	b : 0.09	d : 0.07	w : 0.03	[ : 0.03	i : 0.01	
v : 0.15	y : 0.14	e : 0.14	c : 0.12	w : 0.09	b : 0.09	f : 0.07	g : 0.06	d : 0.06	i : 0.01	a : 0.01	
v : 0.23	u : 0.20	t : 0.15	y : 0.14	w : 0.09	e : 0.04	f : 0.03	c : 0.01	i : 0.01	b : 0.01	d : 0.01	g : 0.01	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
t : 0.31	v : 0.23	u : 0.20	y : 0.14	w : 0.09	
v : 0.23	u : 0.20	t : 0.15	y : 0.14	w : 0.09	e : 0.04	c : 0.03	b : 0.03	a : 0.01	d : 0.01	g : 0.01	
c : 0.14	e : 0.14	f : 0.14	y : 0.12	g : 0.11	b : 0.09	v : 0.07	w : 0.06	d : 0.04	= : 0.01	i : 0.01	] : 0.01	
c : 0.19	e : 0.19	f : 0.14	g : 0.12	d : 0.09	b : 0.07	y : 0.04	i : 0.03	h : 0.03	a : 0.03	= : 0.01	2 : 0.01	
e : 0.19	c : 0.17	f : 0.14	g : 0.12	d : 0.11	] : 0.04	2 : 0.04	b : 0.03	= : 0.03	i : 0.03	h : 0.03	y : 0.01	3 : 0.01	
e : 0.25	f : 0.17	g : 0.14	d : 0.09	] : 0.07	c : 0.07	2 : 0.04	= : 0.03	i : 0.03	h : 0.03	b : 0.01	3 : 0.01	
e : 0.25	g : 0.22	f : 0.19	d : 0.07	h : 0.04	] : 0.03	4 : 0.03	c : 0.03	= : 0.03	i : 0.03	3 : 0.03	2 : 0.01	
g : 0.22	e : 0.19	f : 0.19	c : 0.06	] : 0.06	4 : 0.04	d : 0.04	h : 0.04	= : 0.03	i : 0.03	2 : 0.03	: : 0.01	3 : 0.01	
g : 0.20	e : 0.14	] : 0.09	c : 0.07	2 : 0.07	f : 0.06	d : 0.06	4 : 0.04	: : 0.04	3 : 0.04	h : 0.04	= : 0.03	i : 0.03	b : 0.01	
e : 0.17	c : 0.11	g : 0.11	f : 0.07	d : 0.07	4 : 0.06	: : 0.06	h : 0.06	2 : 0.04	b : 0.04	] : 0.03	= : 0.03	i : 0.03	3 : 0.03	a : 0.01	> : 0.01	

#score	1451.4740695120179
#seq	63
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_CDS_m2_run2.txt

#BEAR
dddd[cccooooooccc22d	chrM:14703-14904(+)$1	201	30	50	7.4268
dbb[ddddnnnnndddd]bb	chr7:86596478-86596679(-)$1	201	172	192	11.4570
++++ddddnnnnndddd>>>	chr11:105784325-105784526(+)$1	201	141	161	9.6325
ff"""ddddllldddd333f	chr6:28780126-28780327(-)$1	201	19	39	8.4321
"""eeeeennnnneeeee33	chr9:13586690-13586891(+)$1	201	36	56	11.3816
gggg[a[annnnna]a]ggg	chr15:91180368-91180569(-)$1	201	153	173	9.9308
cc!!ddddoooooodddd44	chr7:124787090-124787291(+)$1	201	111	131	8.8623
::a[ddddnnnnndddd]a:	chr5:29946027-29946228(+)$1	201	105	125	9.8478
$ccc[cccnnnnnccc333c	chr7:118698002-118698203(-)$1	201	51	71	11.8978
"""ccc[annnnna]cccee	chr15:96408933-96409134(-)$1	201	12	32	10.3269
dd[eeeeennnnneeeee]d	chr3:102832956-102833157(+)$1	201	95	115	10.4022
h!!eeeeennnnneeeee88	chr11:94291694-94291895(-)$1	201	104	124	9.9655
d!!ddddoooooodddd22d	chr9:72466852-72467053(+)$1	201	110	130	9.2142
cc!!ddddnnnnndddd22c	chr17:55637456-55637657(+)$1	201	45	65	13.1731
[bb[ddddnnnnndddd22b	chr7:25766685-25766886(-)$1	201	112	132	12.4447
gggg[a[annnnna]a]ggg	chr15:91180367-91180568(-)$1	201	152	172	9.9308
$$$ddddoooooodddd333	chr11:46072124-46072325(-)$1	201	87	107	9.1995
$$$$ddddnnnnndddd333	chr10:12194998-12195199(-)$1	201	118	138	12.7623
bb[eeeeennnnneeeee]b	chr7:51607086-51607287(+)$1	201	93	113	10.5011
ggccccccnnnnnccc]ccc	chr18:35731770-35731971(+)$1	201	49	69	10.6103
d####cccnnnnnccc333d	chr14:94286128-94286329(-)$1	201	77	97	12.2929
ff[eeeeennnnneeeee]f	chr9:66234464-66234665(+)$1	201	131	151	10.2990
bb!!ddddnnnnndddd22b	chr6:137699005-137699206(+)$1	201	44	64	12.8550
eeeeecccnnnnnccc]eee	chr3:108128564-108128765(+)$1	201	65	85	9.9471
####ddddmmmmdddd333b	chr13:63634756-63634957(-)$1	201	94	114	8.3580
c[ccc!!ccclllccc333c	chr3:88876399-88876600(+)$1	201	135	155	7.4790
dbb[ddddnnnnndddd]bb	chr7:86596479-86596680(-)$1	201	173	193	11.4570
ccc[ddddnnnnnddddccc	chr19:29791544-29791745(-)$1	201	21	41	11.8229
cc[bbcccnnnnnccc333b	chr13:54148999-54149200(-)$1	201	123	143	11.6334
cc!!ddddnnnnndddd22c	chr17:55637457-55637658(+)$1	201	44	64	13.1731
eeeeddddnnnnnddddiii	chr2:118616348-118616549(+)$1	201	102	122	11.1485
dd!!ddddnnnnndddd22d	chr6:21167210-21167411(+)$1	201	55	75	12.7561
!ddddddddmmmmdddd22d	chrX:58437286-58437487(+)$1	201	93	113	6.8905
bb[eeeeennnnneeeee]b	chr7:51607060-51607261(+)$1	201	119	139	10.5011
!ddddcccnnnnnccc333d	chr16:11151212-11151413(-)$1	201	113	133	11.7062
gg[ccc[annnnnacccggg	chr2:65601782-65601983(+)$1	201	130	150	10.4844
!!bb[cccnnnnnccc]bbd	chr7:107416551-107416752(+)$1	201	4	24	9.9309
ddddddddnnnnndddd>>>	chr16:37290961-37291162(-)$1	201	72	92	11.1311
ffff[cccnnnnncccffff	chr2:69661781-69661982(+)$1	201	44	64	9.4822
####ddddmmmmdddd333e	chr7:117173239-117173440(+)$1	201	119	139	8.2271
cc[eeeeennnnneeeeecc	chr3:97510871-97511072(-)$1	201	26	46	10.5149
bb[eeeeennnnneeeee]b	chr7:51607115-51607316(+)$1	201	64	84	10.5011
eeee[cccnnnnnccc]eee	chr7:25763829-25764030(-)$1	201	3	23	9.9912
c[ccccccnnnnnccc]ccc	chr5:84494867-84495068(-)$1	201	38	58	10.7833
::bbddddnnnnndddd]bb	chr6:38145475-38145676(-)$1	201	169	189	9.5831
g!!ddddoooooodddd22g	chr13:110744625-110744826(+)$1	201	166	186	9.3318
c####cccnnnnnccc]ccc	chr9:70291300-70291501(-)$1	201	74	94	11.3565
iiiiicccnnnnnccc]iii	chr5:108801267-108801468(+)$1	201	135	155	10.7694
bb"""ddddllldddd333b	chr13:63634757-63634958(-)$1	201	151	171	8.6342
"gggggggnnnnnggggggg	chr11:86516129-86516330(-)$1	201	40	60	9.6185
ccc[ddddnnnnndddd]cc	chr9:108958459-108958660(+)$1	201	58	78	12.1409

#otherMatches

#Seq PSSM
UCCUCUUCCUCCACGAAACA	chrM:14703-14904(+)$1	201	30	50	7.4268
GACGAGGUUCGCUACCUGGU	chr7:86596478-86596679(-)$1	201	172	192	11.4570
UCAAUUCAGCAAAUGGAGAU	chr11:105784325-105784526(+)$1	201	141	161	9.6325
CCUACCUCAAUGUGAGCUCG	chr6:28780126-28780327(-)$1	201	19	39	8.4321
UACUUCUCAUUCAGAGAACU	chr9:13586690-13586891(+)$1	201	36	56	11.3816
ACCUUUGGUAGUUUGGCAGG	chr15:91180368-91180569(-)$1	201	153	173	9.9308
GGUCUUCGAAGAGCUGAGUC	chr7:124787090-124787291(+)$1	201	111	131	8.8623
CUGGAGGAGUUAAUCCUGCU	chr5:29946027-29946228(+)$1	201	105	125	9.8478
AGGGCGGAACCAGUCCUCAC	chr7:118698002-118698203(-)$1	201	51	71	11.8978
CCUGAAGCUCUUUGGUUCAC	chr15:96408933-96409134(-)$1	201	12	32	10.3269
AACUUUCAUCCUUUGGAACU	chr3:102832956-102833157(+)$1	201	95	115	10.4022
CGGCAGUCUUCCUGGCUGAA	chr11:94291694-94291895(-)$1	201	104	124	9.9655
UCACACAGAUGCAUGUGCCA	chr9:72466852-72467053(+)$1	201	110	130	9.2142
AAUUUGAAUUGUUUUUAUUU	chr17:55637456-55637657(+)$1	201	45	65	13.1731
UGGGUACCGACAUGGUAAGC	chr7:25766685-25766886(-)$1	201	112	132	12.4447
ACCUUUGGUAGUUUGGCAGG	chr15:91180367-91180568(-)$1	201	152	172	9.9308
CCCGAGGGCUUUGUUUCACC	chr11:46072124-46072325(-)$1	201	87	107	9.1995
CCUAUUACAUCAAGUAAGUC	chr10:12194998-12195199(-)$1	201	118	138	12.7623
UGACCCCCGUAGUGGGGGCC	chr7:51607086-51607287(+)$1	201	93	113	10.5011
GUACUGCACGCCUUGCUAGU	chr18:35731770-35731971(+)$1	201	49	69	10.6103
ACAAUAGCCCCAAGUUUACU	chr14:94286128-94286329(-)$1	201	77	97	12.2929
UAGCUUUUACUACAGAAGGU	chr9:66234464-66234665(+)$1	201	131	151	10.2990
UGAUUUUAUCUUUUAAAUGC	chr6:137699005-137699206(+)$1	201	44	64	12.8550
UUUGCCAAGAACUUUGUGCA	chr3:108128564-108128765(+)$1	201	65	85	9.9471
AACCCAUAUCACUAUGCAGU	chr13:63634756-63634957(-)$1	201	94	114	8.3580
GUAAGUUACCUUUGGUCuuc	chr3:88876399-88876600(+)$1	201	135	155	7.4790
GACGAGGUUCGCUACCUGGU	chr7:86596479-86596680(-)$1	201	173	193	11.4570
AGACUUUGUCCAUCAAAUCU	chr19:29791544-29791745(-)$1	201	21	41	11.8229
GCACAAGGCAAAACCUACAU	chr13:54148999-54149200(-)$1	201	123	143	11.6334
AAUUUGAAUUGUUUUUAUUU	chr17:55637457-55637658(+)$1	201	44	64	13.1731
CGCCUGCUUUUCCAGCGCCU	chr2:118616348-118616549(+)$1	201	102	122	11.1485
AACUGGGCUUCUUGCUCUUU	chr6:21167210-21167411(+)$1	201	55	75	12.7561
CCAUGUCUUCCCAAAGAUCC	chrX:58437286-58437487(+)$1	201	93	113	6.8905
UGACCCCCGUAGUGGGGGCC	chr7:51607060-51607261(+)$1	201	119	139	10.5011
CUCCUAGGCAUCCCCUCGAA	chr16:11151212-11151413(-)$1	201	113	133	11.7062
UUGCCUACGUUAAGAGGGAA	chr2:65601782-65601983(+)$1	201	130	150	10.4844
UGGCUUAUCUUUAAUAUGCA	chr7:107416551-107416752(+)$1	201	4	24	9.9309
GAAAUACACAUAUUGUAAAU	chr16:37290961-37291162(-)$1	201	72	92	11.1311
UGUUUGUAUUUUUUGCAGCA	chr2:69661781-69661982(+)$1	201	44	64	9.4822
GUAUGUUUAUUGAAAUUUAC	chr7:117173239-117173440(+)$1	201	119	139	8.2271
AACAGUCGACCUCCGAUUUU	chr3:97510871-97511072(-)$1	201	26	46	10.5149
UGACCCCCGUAGUGGGGGCC	chr7:51607115-51607316(+)$1	201	64	84	10.5011
CAGGCCCAGCUGGUGGUUCU	chr7:25763829-25764030(-)$1	201	3	23	9.9912
GAGAGGUUCUCUAGACAUUC	chr5:84494867-84495068(-)$1	201	38	58	10.7833
CAGUCUGGUCCCCUCAGCAC	chr6:38145475-38145676(-)$1	201	169	189	9.5831
UGUACAUACUGUAAUGUUAA	chr13:110744625-110744826(+)$1	201	166	186	9.3318
UUCUCAGAUAUCUUCUCAUG	chr9:70291300-70291501(-)$1	201	74	94	11.3565
GUGUCCUGAAUCACGGAGAC	chr5:108801267-108801468(+)$1	201	135	155	10.7694
CGCACGUGUACUACACCACC	chr13:63634757-63634958(-)$1	201	151	171	8.6342
UGGCUUUGUCUCUUAAGGCU	chr11:86516129-86516330(-)$1	201	40	60	9.6185
UGACCAUCUUUGUGGUGUUU	chr9:108958459-108958660(+)$1	201	58	78	12.1409

#DB
((((.(((......)))..)	chrM:14703-14904(+)$1	1	30	50	7.4268
(((.((((.....)))).))	chr7:86596478-86596679(-)$1	1	172	192	11.4570
....((((.....))))...	chr11:105784325-105784526(+)$1	1	141	161	9.6325
((...((((...))))...)	chr6:28780126-28780327(-)$1	1	19	39	8.4321
...(((((.....)))))..	chr9:13586690-13586891(+)$1	1	36	56	11.3816
((((.(.(.....).).)))	chr15:91180368-91180569(-)$1	1	153	173	9.9308
((..((((......))))..	chr7:124787090-124787291(+)$1	1	111	131	8.8623
..(.((((.....)))).).	chr5:29946027-29946228(+)$1	1	105	125	9.8478
.(((.(((.....)))...)	chr7:118698002-118698203(-)$1	1	51	71	11.8978
...(((.(.....).)))))	chr15:96408933-96409134(-)$1	1	12	32	10.3269
((.(((((.....))))).)	chr3:102832956-102833157(+)$1	1	95	115	10.4022
(..(((((.....)))))..	chr11:94291694-94291895(-)$1	1	104	124	9.9655
(..((((......))))..)	chr9:72466852-72467053(+)$1	1	110	130	9.2142
((..((((.....))))..)	chr17:55637456-55637657(+)$1	1	45	65	13.1731
.((.((((.....))))..)	chr7:25766685-25766886(-)$1	1	112	132	12.4447
((((.(.(.....).).)))	chr15:91180367-91180568(-)$1	1	152	172	9.9308
...((((......))))...	chr11:46072124-46072325(-)$1	1	87	107	9.1995
....((((.....))))...	chr10:12194998-12195199(-)$1	1	118	138	12.7623
((.(((((.....))))).)	chr7:51607086-51607287(+)$1	1	93	113	10.5011
((((((((.....))).)))	chr18:35731770-35731971(+)$1	1	49	69	10.6103
(....(((.....)))...)	chr14:94286128-94286329(-)$1	1	77	97	12.2929
((.(((((.....))))).)	chr9:66234464-66234665(+)$1	1	131	151	10.2990
((..((((.....))))..)	chr6:137699005-137699206(+)$1	1	44	64	12.8550
((((((((.....))).)))	chr3:108128564-108128765(+)$1	1	65	85	9.9471
....((((....))))...)	chr13:63634756-63634957(-)$1	1	94	114	8.3580
(.(((..(((...)))...)	chr3:88876399-88876600(+)$1	1	135	155	7.4790
(((.((((.....)))).))	chr7:86596479-86596680(-)$1	1	173	193	11.4570
(((.((((.....)))))))	chr19:29791544-29791745(-)$1	1	21	41	11.8229
((.(((((.....)))...)	chr13:54148999-54149200(-)$1	1	123	143	11.6334
((..((((.....))))..)	chr17:55637457-55637658(+)$1	1	44	64	13.1731
))))((((.....))))(((	chr2:118616348-118616549(+)$1	1	102	122	11.1485
((..((((.....))))..)	chr6:21167210-21167411(+)$1	1	55	75	12.7561
.((((((((....))))..)	chrX:58437286-58437487(+)$1	1	93	113	6.8905
((.(((((.....))))).)	chr7:51607060-51607261(+)$1	1	119	139	10.5011
.(((((((.....)))...)	chr16:11151212-11151413(-)$1	1	113	133	11.7062
((.(((.(.....)))))))	chr2:65601782-65601983(+)$1	1	130	150	10.4844
..((.(((.....))).)))	chr7:107416551-107416752(+)$1	1	4	24	9.9309
((((((((.....))))...	chr16:37290961-37291162(-)$1	1	72	92	11.1311
((((.(((.....)))))))	chr2:69661781-69661982(+)$1	1	44	64	9.4822
....((((....))))...)	chr7:117173239-117173440(+)$1	1	119	139	8.2271
((.(((((.....)))))))	chr3:97510871-97511072(-)$1	1	26	46	10.5149
((.(((((.....))))).)	chr7:51607115-51607316(+)$1	1	64	84	10.5011
((((.(((.....))).)))	chr7:25763829-25764030(-)$1	1	3	23	9.9912
(.((((((.....))).)))	chr5:84494867-84495068(-)$1	1	38	58	10.7833
..((((((.....)))).))	chr6:38145475-38145676(-)$1	1	169	189	9.5831
(..((((......))))..)	chr13:110744625-110744826(+)$1	1	166	186	9.3318
(....(((.....))).)))	chr9:70291300-70291501(-)$1	1	74	94	11.3565
((((((((.....))).)))	chr5:108801267-108801468(+)$1	1	135	155	10.7694
((...((((...))))...)	chr13:63634757-63634958(-)$1	1	151	171	8.6342
.(((((((.....)))))))	chr11:86516129-86516330(-)$1	1	40	60	9.6185
(((.((((.....)))).))	chr9:108958459-108958660(+)$1	1	58	78	12.1409

#PSSM
c : 0.19	d : 0.15	g : 0.09	b : 0.09	f : 0.05	" : 0.05	$ : 0.05	e : 0.05	! : 0.05	: : 0.03	# : 0.03	+ : 0.01	h : 0.01	[ : 0.01	i : 0.01	
b : 0.15	c : 0.15	d : 0.11	g : 0.09	! : 0.07	# : 0.07	f : 0.05	e : 0.05	" : 0.03	: : 0.03	$ : 0.03	[ : 0.03	+ : 0.01	i : 0.01	
! : 0.15	[ : 0.15	c : 0.11	b : 0.09	d : 0.07	" : 0.07	# : 0.07	g : 0.05	e : 0.05	$ : 0.03	+ : 0.01	a : 0.01	f : 0.01	i : 0.01	
e : 0.21	d : 0.13	[ : 0.11	c : 0.11	! : 0.09	# : 0.07	g : 0.05	b : 0.05	" : 0.03	+ : 0.01	$ : 0.01	f : 0.01	i : 0.01	
d : 0.45	e : 0.17	[ : 0.13	c : 0.09	" : 0.03	# : 0.03	b : 0.01	i : 0.01	g : 0.01	
d : 0.47	c : 0.29	e : 0.15	a : 0.03	! : 0.01	g : 0.01	
d : 0.47	c : 0.25	e : 0.15	[ : 0.07	! : 0.01	g : 0.01	
d : 0.41	c : 0.27	e : 0.15	a : 0.07	o : 0.05	g : 0.01	
n : 0.78	o : 0.09	d : 0.05	m : 0.03	c : 0.01	
n : 0.78	o : 0.09	m : 0.05	l : 0.03	c : 0.01	
n : 0.78	o : 0.09	l : 0.05	m : 0.05	
n : 0.78	o : 0.09	l : 0.05	m : 0.05	
n : 0.78	o : 0.09	d : 0.07	l : 0.01	m : 0.01	
d : 0.45	c : 0.25	e : 0.15	a : 0.07	o : 0.03	g : 0.01	
d : 0.47	c : 0.29	e : 0.15	] : 0.05	g : 0.01	
d : 0.47	c : 0.31	e : 0.15	a : 0.03	g : 0.01	
d : 0.39	3 : 0.17	] : 0.17	e : 0.15	c : 0.05	f : 0.01	g : 0.01	
3 : 0.21	e : 0.19	2 : 0.17	] : 0.09	c : 0.09	g : 0.07	> : 0.03	i : 0.03	d : 0.01	b : 0.01	f : 0.01	
3 : 0.23	2 : 0.17	c : 0.11	] : 0.09	b : 0.07	g : 0.07	e : 0.05	> : 0.03	i : 0.03	4 : 0.01	a : 0.01	8 : 0.01	f : 0.01	
b : 0.21	c : 0.19	d : 0.15	g : 0.09	e : 0.07	f : 0.05	3 : 0.05	> : 0.03	i : 0.03	4 : 0.01	: : 0.01	8 : 0.01	

#score	532.2025025275218
#seq	51
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_UTR_m2_run2.txt

#BEAR
c[ffffffvvvvvvvvvvvvvffffff]	chr12:102277710-102277930(-)$1	220	167	195	24.4963
!!a[ddddvvvvvvvvvvvvvdddd]a]	chr11:17098993-17099213(+)$1	220	87	115	24.8607
ffffffyyyyyyyyyyyyyyyyffffff	chr9:58724750-58724970(-)$1	220	126	154	20.0871
[ggggggguuuuuuuuuuuuggggggg2	chr4:40911989-40912210(+)$1	221	40	68	24.9190
ee!!ddddvvvvvvvvvvvvvddddeee	chr2:173603974-173604194(+)$1	220	190	218	24.4835
hhhhhhhhwwwwwwwwwwwwwwhhhhhh	chr3:107912056-107912297(-)$1	241	48	76	21.6758
f[ffffffwwwwwwwwwwwwwwffffff	chr14:70706011-70706231(-)$1	220	176	204	22.7083
eeffffffuuuuuuuuuuuuffffff::	chr8:72617410-72617630(-)$1	220	56	84	22.0379
d####cccuuuuuuuuuuuuccc4444d	chr4:21751956-21752176(+)$1	220	154	182	24.1154
gggggggwwwwwwwwwwwwwwggggggg	chr6:113230964-113231184(+)$1	220	123	151	24.2220
eee[dddduuuuuuuuuuuudddd]eee	chr14:122558202-122558422(+)$1	220	67	95	24.0147
iiiiiiiivvvvvvvvvvvvviiiiiii	chrX:131124126-131124355(-)$1	229	48	76	25.2797
hhh[eeeeettttttttttteeeee]hh	chr1:153317439-153317659(-)$1	220	157	185	22.7143
!!bb[cccuuuuuuuuuuuuccc]bb33	chr3:58479477-58479704(-)$1	227	137	165	24.1693
###bbccctttttttttttccc]bb333	chr7:91046408-91046628(+)$1	220	130	158	22.2271
bb[ddddvvvvvvvvvvvvvddddbb77	chr9:63489248-63489468(+)$1	220	53	81	22.0634
hhh[dddduuuuuuuuuuuudddd333h	chr3:108229510-108229752(-)$1	242	58	86	23.9434
gggggggwwwwwwwwwwwwwwggggggg	chr11:120649177-120649397(+)$1	220	9	37	24.2220
hh!!dddduuuuuuuuuuuudddd]hhh	chr8:26266984-26267204(-)$1	220	10	38	23.7354
eee[eeeeettttttttttteeeeeeee	chr7:148588717-148588937(+)$1	220	105	133	22.9302
[ccc[ccctttttttttttcccccc]dd	chr18:77391425-77391645(+)$1	220	180	208	23.3873
ee!!eeeeettttttttttteeeee22e	chr3:116210829-116211049(-)$1	220	172	200	22.8870
eee"""ccctttttttttttccc22eee	chr3:90418138-90418358(+)$1	220	89	117	22.8882
:ggggggguuuuuuuuuuuuggggggg:	chr6:72561270-72561510(-)$1	240	210	238	23.1053
dd[fffffftttttttttttffffff22	chr9:7792584-7792804(+)$1	220	106	134	22.3154
ffffff[attttttttttta]fffffff	chr10:85338947-85339178(+)$1	231	6	34	22.8854
eeeee[bbwwwwwwwwwwwwwwbb]eee	chr7:126998469-126998695(-)$1	226	80	108	22.1846
gggggggvvvvvvvvvvvvvggggggg:	chr4:82866418-82866639(-)$1	221	184	212	24.3907
ccc!!cccuuuuuuuuuuuuccc22ccc	chr5:92483013-92483233(-)$1	220	10	38	24.6041
hhhhhhhhvvvvvvvvvvvvvhhhhhhh	chr11:115869796-115870016(-)$1	220	130	158	23.0578
cc[bb[bbtttttttttttbbbb]ccc]	chr12:8757442-8757664(+)$1	222	40	68	21.6306
[bb[dddduuuuuuuuuuuuddddbb]a	chr7:6663643-6663865(-)$1	222	69	97	23.2120
ee[eeeeevvvvvvvvvvvvveeeeeee	chr10:75503577-75503797(+)$1	220	122	150	24.6416
::eeeeevvvvvvvvvvvvveeeeeccc	chr6:122794418-122794652(+)$1	234	108	136	22.3380
ggggg[ccctttttttttttccc]gggg	chr5:92631398-92631618(+)$1	220	179	207	24.2805
"""eeeeeuuuuuuuuuuuueeeee333	chr19:18655306-18655526(-)$1	220	140	168	24.2682
b[ccc[bbuuuuuuuuuuuubb]cccbb	chr19:44379234-44379454(+)$1	220	105	133	22.9364
fffffcccwwwwwwwwwwwwwwccc:II	chr11:49651415-49651637(+)$1	222	168	196	19.5105
f!!eeeeeuuuuuuuuuuuueeeee]ff	chr9:96978920-96979140(-)$1	220	156	184	24.2281
#ddddccctttttttttttccc]ddddd	chr8:14027600-14027820(-)$1	220	47	75	22.4133
:ffffffvvvvvvvvvvvvvffffff::	chr14:55516807-55517042(+)$1	235	192	220	21.3491
a!!ddddwwwwwwwwwwwwwwdddd22a	chr18:68483489-68483709(+)$1	220	114	142	23.0009
========vvvvvvvvvvvvv=======	chr6:67234679-67234899(+)$1	220	21	49	25.2819
gggggggattttttttttta]ggggggg	chr2:167124315-167124551(-)$1	236	79	107	24.2415
fff####bbtttttttttttbb4444ff	chr10:62408295-62408528(+)$1	233	126	154	21.2573
fffffbbwwwwwwwwwwwwwwbb]ffff	chr7:120713495-120713715(+)$1	220	8	36	22.1864
!!ffffffuuuuuuuuuuuuffffffee	chr1:193655680-193655900(+)$1	220	146	174	24.0907
eee[ddddwwwwwwwwwwwwwwddddee	chr7:105002873-105003093(+)$1	220	19	47	22.8132
ddd[bbavvvvvvvvvvvvva]bb]ddd	chr15:7146379-7146599(+)$1	220	21	49	23.2581
hhhhhhhhwwwwwwwwwwwwwwhhhhhh	chr19:41992579-41992799(+)$1	220	26	54	21.6758
cc[eeeeewwwwwwwwwwwwwweeeee]	chr3:51276979-51277199(+)$1	220	18	46	23.3060
:ccccccvvvvvvvvvvvvvccc22ccc	chr11:95911267-95911497(-)$1	230	45	73	23.5700
ddd[eeeeettttttttttteeeee22d	chr5:108510096-108510316(+)$1	220	43	71	22.4489
ddd[cccvvvvvvvvvvvvvccc]dddd	chr9:69855251-69855471(+)$1	220	18	46	24.5140
hhhhhhhhuuuuuuuuuuuuhhhhhhhh	chr12:103632365-103632599(-)$1	234	204	232	22.4146
ffffffwwwwwwwwwwwwwwffffffdd	chr7:152049101-152049321(+)$1	220	135	163	22.1571
ddddcccvvvvvvvvvvvvvccc]dddd	chr1:152208612-152208832(-)$1	220	163	191	24.1376
gggdddd[attttttttttta]dddd]g	chr3:104461324-104461544(+)$1	220	47	75	23.5182
gggggggvvvvvvvvvvvvvggggggg0	chr7:105052093-105052331(+)$1	238	89	117	24.8673
e[eeeee[attttttttttta]eeeeee	chr14:15630159-15630379(+)$1	220	95	123	23.7014
[dddd[ccctttttttttttcccdddd]	chr6:28838705-28838925(+)$1	220	12	40	23.1202
gggggggwwwwwwwwwwwwwwggggggg	chr1:192769872-192770092(+)$1	220	25	53	24.2220

#otherMatches

#Seq PSSM
UGACUUUUGAAUAAUAAAAAGAAAAGUG	chr12:102277710-102277930(-)$1	220	167	195	24.4963
UAGUCACUGUUAUUUUUAUUAAGUGUCC	chr11:17098993-17099213(+)$1	220	87	115	24.8607
GGGCACUAUGGGCCAAAAUUUUGUGUCC	chr9:58724750-58724970(-)$1	220	126	154	20.0871
ACAUUGAUAAGAUAAAAGUGAUUGAUGA	chr4:40911989-40912210(+)$1	221	40	68	24.9190
GUCCAGGCAUCGUCUCCUCAGGCCUACA	chr2:173603974-173604194(+)$1	220	190	218	24.4835
UCUUCUCUUUUUUAGCUAUUACAGGGAG	chr3:107912056-107912297(-)$1	241	48	76	21.6758
GUGAUUCUAAAUGUGUGUACCCAGGAUU	chr14:70706011-70706231(-)$1	220	176	204	22.7083
CUUCGAACGCUACCAACUUAGUUCGAUU	chr8:72617410-72617630(-)$1	220	56	84	22.0379
AGUCCUGUCUCUACCAGUUCACAUCCAU	chr4:21751956-21752176(+)$1	220	154	182	24.1154
AGCAAAACCCCAUUCUGCAAUUUUUGUU	chr6:113230964-113231184(+)$1	220	123	151	24.2220
GGACAGUUGAUUGUAAAUAGGAUUUUCU	chr14:122558202-122558422(+)$1	220	67	95	24.0147
UAAAAGCUGCUUUUCAACAUAGGCUUUU	chrX:131124126-131124355(-)$1	229	48	76	25.2797
UUGCACUUUAGCCUUGAUGAAAAGUACA	chr1:153317439-153317659(-)$1	220	157	185	22.7143
CUCUAUUCUAUUUCCUUCCUGAACAGCU	chr3:58479477-58479704(-)$1	227	137	165	24.1693
UAGGCAGGACCAGAUAGCCCCUCGCAGA	chr7:91046408-91046628(+)$1	220	130	158	22.2271
GGACCUGAAACAUGCUUAGCCAGGCCAG	chr9:63489248-63489468(+)$1	220	53	81	22.0634
CAGAGAGGCCGAGAACCACUCCUCACCC	chr3:108229510-108229752(-)$1	242	58	86	23.9434
CAGUUCCUUCAAGCUGUUCCUGGAGCUG	chr11:120649177-120649397(+)$1	220	9	37	24.2220
cguuugccgaccaugugccaggcacugu	chr8:26266984-26267204(-)$1	220	10	38	23.7354
UUAUGUGAAAUUUUGUCUAAUUCAUUAA	chr7:148588717-148588937(+)$1	220	105	133	22.9302
UUUUGCAACUUAAUAUUUAUUGAAAUGU	chr18:77391425-77391645(+)$1	220	180	208	23.3873
GGGAUCAUGGAAGGGGUGAGUGUGGGAC	chr3:116210829-116211049(-)$1	220	172	200	22.8870
AUGAAGCUCUGAAAUAAAAUGGGACCGU	chr3:90418138-90418358(+)$1	220	89	117	22.8882
CUCCUUGCUGUUUAAGAUGUGCAGGGAA	chr6:72561270-72561510(-)$1	240	210	238	23.1053
UUAGAGUUCAUCUAGAAGUAGAACUUGC	chr9:7792584-7792804(+)$1	220	106	134	22.3154
CCCAAGCCAAAAACUAGAAGACUUGGGG	chr10:85338947-85339178(+)$1	231	6	34	22.8854
CUGUUGUUGAGAAACCAGAGAAAGGAAC	chr7:126998469-126998695(-)$1	226	80	108	22.1846
CUGUUUCUAUUUUUAAUAUUGAGACAGU	chr4:82866418-82866639(-)$1	221	184	212	24.3907
UAGUUUGUGAAAUGAUAAGGGCAUUCUA	chr5:92483013-92483233(-)$1	220	10	38	24.6041
GGGCAUCCUCCUUCUCUAUCUGGGUGCU	chr11:115869796-115870016(-)$1	220	130	158	23.0578
GUGAUAGCUCAGCAUUUACGCAUGAUUG	chr12:8757442-8757664(+)$1	222	40	68	21.6306
GUGUAAGGAAUGUGGAGAAACCUUCAGU	chr7:6663643-6663865(-)$1	222	69	97	23.2120
AGCAGGGUGGCUAGAAUUUAAACCCUCU	chr10:75503577-75503797(+)$1	220	122	150	24.6416
AAGGGAGUAUAAGAAAAAGUUUCCUCCA	chr6:122794418-122794652(+)$1	234	108	136	22.3380
UUUCUCUCUGUUUAAGCUAAAGAUGGAA	chr5:92631398-92631618(+)$1	220	179	207	24.2805
AAAUGGUUAUUAUAACAAUAGACCAAAA	chr19:18655306-18655526(-)$1	220	140	168	24.2682
AUGUGUGGUCCUGGCACCUUCCUCACUC	chr19:44379234-44379454(+)$1	220	105	133	22.9364
UAAAAGUCGAAAUAUUUAUAAUGACGAU	chr11:49651415-49651637(+)$1	222	168	196	19.5105
GUUUUAUGUUAUCUGACACCCAUAAUCA	chr9:96978920-96979140(-)$1	220	156	184	24.2281
UUGAAGACAUUUCUACCACGUUAUUUAU	chr8:14027600-14027820(-)$1	220	47	75	22.4133
aauauuuaaaaaaaaaaaaaaGAUAUAC	chr14:55516807-55517042(+)$1	235	192	220	21.3491
CAGUCCAGUGUAUAGUGUUGAUGGAGAG	chr18:68483489-68483709(+)$1	220	114	142	23.0009
UUAAAAGUAAAACUAAACACAGCUUUUG	chr6:67234679-67234899(+)$1	220	21	49	25.2819
GUCAUUGCUUGAAAAAAAUGACAGUGAC	chr2:167124315-167124551(-)$1	236	79	107	24.2415
AUUGUCAACAAAUGAAGAAAGUCCCAGG	chr10:62408295-62408528(+)$1	233	126	154	21.2573
GAAAACACACUAACCUUUUUAUGAUUUU	chr7:120713495-120713715(+)$1	220	8	36	22.1864
UACCUAAGAAUAGGAUUUGCCUUAGGGA	chr1:193655680-193655900(+)$1	220	146	174	24.0907
aauuacuuuuucuaaaaaauauGAGUGU	chr7:105002873-105003093(+)$1	220	19	47	22.8132
UGUAGUCUUUGACAAAGUAUGAACAGCA	chr15:7146379-7146599(+)$1	220	21	49	23.2581
GCUGUGGUGUGACCAAUGAAAAGCUGCA	chr19:41992579-41992799(+)$1	220	26	54	21.6758
CAUGUUUUUAACUAAUUUAUAUAAAAUC	chr3:51276979-51277199(+)$1	220	18	46	23.3060
AGGUGGCAAGAAGCAAGCAAGCUCAACC	chr11:95911267-95911497(-)$1	230	45	73	23.5700
UUCUUGUGUAUUGCAGAUAAACAUAUUG	chr5:108510096-108510316(+)$1	220	43	71	22.4489
GGGGGCAAUAAUUUUUAGUGUGUACCUA	chr9:69855251-69855471(+)$1	220	18	46	24.5140
AGAAUUAUUUUUAGAAUUAUAUAAUUUU	chr12:103632365-103632599(-)$1	234	204	232	22.4146
GGGAGCAUUCUGCCGUCGCCGCUCCCUC	chr7:152049101-152049321(+)$1	220	135	163	22.1571
GUGAAACUCAGAAACAAACCGUUAUUAC	chr1:152208612-152208832(-)$1	220	163	191	24.1376
GAGCUGAGAUCCCCUGAUGCUGUUAGCC	chr3:104461324-104461544(+)$1	220	47	75	23.5182
GUCAUUCACAGGGACAUCAAGAGUGACA	chr7:105052093-105052331(+)$1	238	89	117	24.8673
AAUAGUAGCUGGCAGCAUUUGGUACUAU	chr14:15630159-15630379(+)$1	220	95	123	23.7014
AUACAUCCGUUCUCAAACUCCGGUGUGC	chr6:28838705-28838925(+)$1	220	12	40	23.1202
GUCUUUCUGUUUAACGAUGGUGAAAGGC	chr1:192769872-192770092(+)$1	220	25	53	24.2220

#DB
(.((((((.............)))))).	chr12:102277710-102277930(-)$1	1	167	195	24.4963
..(.((((.............)))).).	chr11:17098993-17099213(+)$1	1	87	115	24.8607
((((((................))))))	chr9:58724750-58724970(-)$1	1	126	154	20.0871
.(((((((............))))))).	chr4:40911989-40912210(+)$1	1	40	68	24.9190
((..((((.............)))))))	chr2:173603974-173604194(+)$1	1	190	218	24.4835
((((((((..............))))))	chr3:107912056-107912297(-)$1	1	48	76	21.6758
(.((((((..............))))))	chr14:70706011-70706231(-)$1	1	176	204	22.7083
))((((((............))))))..	chr8:72617410-72617630(-)$1	1	56	84	22.0379
(....(((............)))....)	chr4:21751956-21752176(+)$1	1	154	182	24.1154
(((((((..............)))))))	chr6:113230964-113231184(+)$1	1	123	151	24.2220
(((.((((............)))).)))	chr14:122558202-122558422(+)$1	1	67	95	24.0147
((((((((.............)))))))	chrX:131124126-131124355(-)$1	1	48	76	25.2797
(((.(((((...........))))).))	chr1:153317439-153317659(-)$1	1	157	185	22.7143
..((.(((............))).))..	chr3:58479477-58479704(-)$1	1	137	165	24.1693
...(((((...........))).))...	chr7:91046408-91046628(+)$1	1	130	158	22.2271
((.((((.............))))))..	chr9:63489248-63489468(+)$1	1	53	81	22.0634
(((.((((............))))...)	chr3:108229510-108229752(-)$1	1	58	86	23.9434
(((((((..............)))))))	chr11:120649177-120649397(+)$1	1	9	37	24.2220
((..((((............)))).)))	chr8:26266984-26267204(-)$1	1	10	38	23.7354
(((.(((((...........))))))))	chr7:148588717-148588937(+)$1	1	105	133	22.9302
.(((.(((...........)))))).))	chr18:77391425-77391645(+)$1	1	180	208	23.3873
((..(((((...........)))))..)	chr3:116210829-116211049(-)$1	1	172	200	22.8870
(((...(((...........)))..)))	chr3:90418138-90418358(+)$1	1	89	117	22.8882
.(((((((............))))))).	chr6:72561270-72561510(-)$1	1	210	238	23.1053
((.((((((...........))))))..	chr9:7792584-7792804(+)$1	1	106	134	22.3154
((((((.(...........).))))))(	chr10:85338947-85339178(+)$1	1	6	34	22.8854
(((((.((..............)).)))	chr7:126998469-126998695(-)$1	1	80	108	22.1846
(((((((.............))))))).	chr4:82866418-82866639(-)$1	1	184	212	24.3907
(((..(((............)))..)))	chr5:92483013-92483233(-)$1	1	10	38	24.6041
((((((((.............)))))))	chr11:115869796-115870016(-)$1	1	130	158	23.0578
((.((.((...........)))).))).	chr12:8757442-8757664(+)$1	1	40	68	21.6306
.((.((((............)))))).)	chr7:6663643-6663865(-)$1	1	69	97	23.2120
((.(((((.............)))))))	chr10:75503577-75503797(+)$1	1	122	150	24.6416
..(((((.............)))))(((	chr6:122794418-122794652(+)$1	1	108	136	22.3380
(((((.(((...........))).))))	chr5:92631398-92631618(+)$1	1	179	207	24.2805
...(((((............)))))...	chr19:18655306-18655526(-)$1	1	140	168	24.2682
(.(((.((............)).)))))	chr19:44379234-44379454(+)$1	1	105	133	22.9364
)))))(((..............))).))	chr11:49651415-49651637(+)$1	1	168	196	19.5105
(..(((((............))))).))	chr9:96978920-96979140(-)$1	1	156	184	24.2281
.(((((((...........))).)))))	chr8:14027600-14027820(-)$1	1	47	75	22.4133
.((((((.............))))))..	chr14:55516807-55517042(+)$1	1	192	220	21.3491
(..((((..............))))..)	chr18:68483489-68483709(+)$1	1	114	142	23.0009
((((((((.............)))))))	chr6:67234679-67234899(+)$1	1	21	49	25.2819
((((((((...........).)))))))	chr2:167124315-167124551(-)$1	1	79	107	24.2415
(((....((...........))....))	chr10:62408295-62408528(+)$1	1	126	154	21.2573
(((((((..............)).))))	chr7:120713495-120713715(+)$1	1	8	36	22.1864
..((((((............))))))))	chr1:193655680-193655900(+)$1	1	146	174	24.0907
(((.((((..............))))))	chr7:105002873-105003093(+)$1	1	19	47	22.8132
(((.(((.............).)).)))	chr15:7146379-7146599(+)$1	1	21	49	23.2581
((((((((..............))))))	chr19:41992579-41992799(+)$1	1	26	54	21.6758
((.(((((..............))))).	chr3:51276979-51277199(+)$1	1	18	46	23.3060
.((((((.............)))..)))	chr11:95911267-95911497(-)$1	1	45	73	23.5700
(((.(((((...........)))))..)	chr5:108510096-108510316(+)$1	1	43	71	22.4489
(((.(((.............))).))))	chr9:69855251-69855471(+)$1	1	18	46	24.5140
((((((((............))))))))	chr12:103632365-103632599(-)$1	1	204	232	22.4146
((((((..............))))))((	chr7:152049101-152049321(+)$1	1	135	163	22.1571
(((((((.............))).))))	chr1:152208612-152208832(-)$1	1	163	191	24.1376
(((((((.(...........).)))).)	chr3:104461324-104461544(+)$1	1	47	75	23.5182
(((((((.............))))))).	chr7:105052093-105052331(+)$1	1	89	117	24.8673
(.(((((.(...........).))))))	chr14:15630159-15630379(+)$1	1	95	123	23.7014
.((((.(((...........))))))).	chr6:28838705-28838925(+)$1	1	12	40	23.1202
(((((((..............)))))))	chr1:192769872-192770092(+)$1	1	25	53	24.2220

#PSSM
e : 0.16	f : 0.12	g : 0.12	h : 0.11	d : 0.09	c : 0.06	[ : 0.06	: : 0.06	! : 0.04	# : 0.03	b : 0.03	i : 0.01	" : 0.01	a : 0.01	= : 0.01	
g : 0.16	e : 0.14	f : 0.11	h : 0.11	d : 0.11	! : 0.08	c : 0.08	[ : 0.06	# : 0.03	b : 0.03	i : 0.01	: : 0.01	" : 0.01	= : 0.01	
f : 0.17	g : 0.16	e : 0.11	h : 0.09	d : 0.09	! : 0.08	[ : 0.08	c : 0.06	# : 0.03	b : 0.03	a : 0.01	i : 0.01	" : 0.01	= : 0.01	
f : 0.17	[ : 0.16	g : 0.14	e : 0.11	d : 0.09	! : 0.06	h : 0.06	b : 0.04	c : 0.04	# : 0.03	i : 0.01	" : 0.01	= : 0.01	
d : 0.19	f : 0.17	e : 0.17	g : 0.14	h : 0.06	c : 0.06	b : 0.04	# : 0.03	[ : 0.03	i : 0.01	" : 0.01	! : 0.01	= : 0.01	
d : 0.16	c : 0.16	e : 0.16	f : 0.14	g : 0.12	[ : 0.08	h : 0.06	b : 0.03	i : 0.01	" : 0.01	= : 0.01	# : 0.01	
c : 0.20	d : 0.16	e : 0.16	g : 0.12	f : 0.09	h : 0.06	b : 0.06	y : 0.01	i : 0.01	[ : 0.01	= : 0.01	# : 0.01	a : 0.01	w : 0.01	
c : 0.16	v : 0.14	e : 0.12	d : 0.11	w : 0.09	f : 0.08	h : 0.06	b : 0.06	g : 0.03	a : 0.03	[ : 0.03	y : 0.01	i : 0.01	= : 0.01	
v : 0.25	u : 0.24	w : 0.20	t : 0.09	e : 0.06	c : 0.04	a : 0.03	y : 0.01	f : 0.01	b : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
t : 0.27	v : 0.25	u : 0.24	w : 0.20	y : 0.01	
v : 0.25	u : 0.24	w : 0.20	t : 0.17	c : 0.04	a : 0.03	y : 0.01	b : 0.01	
w : 0.19	c : 0.19	v : 0.11	e : 0.11	f : 0.08	d : 0.08	g : 0.06	b : 0.04	a : 0.04	] : 0.03	y : 0.01	h : 0.01	
c : 0.19	d : 0.12	g : 0.12	e : 0.12	f : 0.11	w : 0.11	b : 0.06	] : 0.04	h : 0.03	y : 0.01	i : 0.01	= : 0.01	
c : 0.17	d : 0.16	e : 0.16	f : 0.14	g : 0.12	h : 0.06	b : 0.06	] : 0.04	i : 0.01	= : 0.01	4 : 0.01	
d : 0.19	e : 0.16	f : 0.14	g : 0.12	] : 0.09	h : 0.06	b : 0.04	c : 0.04	2 : 0.04	4 : 0.03	i : 0.01	= : 0.01	
f : 0.16	e : 0.16	d : 0.14	g : 0.14	h : 0.06	] : 0.06	b : 0.06	c : 0.06	2 : 0.04	4 : 0.03	i : 0.01	3 : 0.01	= : 0.01	
f : 0.16	g : 0.14	e : 0.12	d : 0.11	h : 0.08	c : 0.08	] : 0.06	b : 0.04	3 : 0.04	2 : 0.04	4 : 0.03	i : 0.01	: : 0.01	= : 0.01	
e : 0.16	g : 0.14	f : 0.11	d : 0.11	h : 0.09	3 : 0.06	2 : 0.06	c : 0.06	: : 0.03	] : 0.03	a : 0.01	4 : 0.01	i : 0.01	7 : 0.01	b : 0.01	I : 0.01	= : 0.01	
e : 0.16	d : 0.12	h : 0.11	f : 0.09	g : 0.09	] : 0.08	: : 0.06	3 : 0.04	c : 0.04	2 : 0.03	a : 0.03	i : 0.01	7 : 0.01	b : 0.01	I : 0.01	= : 0.01	0 : 0.01	

#score	1441.2061343674832
#seq	62
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_CDS_m3_run1.txt

#BEAR
e[bbqqqqqqqqbb2	chr4:11440317-11440528(+)$1	211	50	65	12.0723
hcccqqqqqqqqccc	chr4:117568094-117568312(-)$1	218	176	191	13.2637
eeeeqqqqqqqqeee	chr1:136355099-136355306(+)$1	207	156	171	13.2615
ffffqqqqqqqqfff	chr1:127999109-127999339(-)$1	230	85	100	12.1293
dd[aqqqqqqqqadd	chr15:102154535-102154743(+)$1	208	100	115	13.4565
:cccqqqqqqqqccc	chr2:165115874-165116095(-)$1	221	30	45	12.5563
ddddqqqqqqqqddd	chr4:32718010-32718219(+)$1	209	67	82	13.9795
eeeeqqqqqqqqeee	chr17:29120945-29121174(-)$1	229	171	186	13.2615
ddddqqqqqqqqddd	chrX:12865822-12866041(+)$1	219	128	143	13.9795
eeeeqqqqqqqqeee	chr5:122199023-122199253(+)$1	230	180	195	13.2615
!cccqqqqqqqqccc	chr19:44369515-44369725(+)$1	210	13	28	13.5464
eeeeqqqqqqqqeee	chr10:128349156-128349379(+)$1	223	4	19	13.2615
eeeeqqqqqqqqeee	chr12:113020131-113020341(+)$1	210	88	103	13.2615
[cccqqqqqqqqccc	chr11:120265475-120265687(-)$1	212	108	123	13.4854
eeeeqqqqqqqqeee	chr2:59749692-59749898(-)$1	206	148	163	13.2615
:cccqqqqqqqqccc	chrM:11342-11571(+)$1	229	106	121	12.5563
ddddqqqqqqqqddd	chr10:22871645-22871878(-)$1	233	184	199	13.9795
h[bbqqqqqqqqbb]	chr9:110453364-110453570(+)$1	206	140	155	12.0276
$cccqqqqqqqqccc	chr18:35731945-35732158(+)$1	213	163	178	13.2079
b[bbqqqqqqqqbb]	chr19:10130912-10131128(+)$1	216	2	17	11.9351
ddddqqqqqqqqddd	chr9:66896760-66896993(-)$1	233	62	77	13.9795
ddddqqqqqqqqddd	chr7:140043023-140043229(-)$1	206	65	80	13.9795
ggggqqqqqqqqggg	chrX:148291947-148292167(+)$1	220	193	208	12.6847
ddddqqqqqqqqddd	chr15:80709345-80709554(+)$1	209	91	106	13.9795
:cccqqqqqqqqccc	chr10:76775094-76775304(-)$1	210	42	57	12.5563
eebbqqqqqqqqbb2	chr9:79510257-79510471(-)$1	214	75	90	12.1336
ddddqqqqqqqqddd	chr11:120473265-120473501(-)$1	236	204	219	13.9795
ddddqqqqqqqqddd	chr1:71645741-71645949(-)$1	208	95	110	13.9795
!cccqqqqqqqqccc	chr1:84779327-84779545(-)$1	218	168	183	13.5464
:cccqqqqqqqqccc	chr1:66903944-66904166(-)$1	222	191	206	12.5563
e[bbqqqqqqqqbb]	chr5:123899865-123900073(+)$1	208	89	104	12.3079
ddddqqqqqqqqddd	chr1:127299966-127300194(-)$1	228	1	16	13.9795
ddddqqqqqqqqddd	chr10:128140931-128141137(-)$1	206	160	175	13.9795
ddddqqqqqqqqddd	chr13:99559290-99559516(-)$1	226	45	60	13.9795
eeeeqqqqqqqqeee	chr18:38100602-38100822(-)$1	220	150	165	13.2615
'cccqqqqqqqqccc	chr2:37496342-37496559(-)$1	217	79	94	12.8799
eeeeqqqqqqqqeee	chr13:58261143-58261365(+)$1	222	143	158	13.2615
ddddqqqqqqqqddd	chr12:87157242-87157458(-)$1	216	39	54	13.9795
a[bbqqqqqqqqbb]	chr11:82697293-82697515(-)$1	222	51	66	12.1972
ddddqqqqqqqqddd	chr4:136097583-136097827(+)$1	244	179	194	13.9795
ddddqqqqqqqqddd	chr4:106872916-106873138(+)$1	222	135	150	13.9795
ccccqqqqqqqqccc	chr13:97432906-97433130(-)$1	224	166	181	13.4453
eeeeqqqqqqqqeee	chr7:73475563-73475782(-)$1	219	115	130	13.2615
ddddqqqqqqqqddd	chr7:63412562-63412770(+)$1	208	13	28	13.9795
ddddqqqqqqqqddd	chr1:193948055-193948295(-)$1	240	133	148	13.9795
ffffqqqqqqqqfff	chr13:49298419-49298629(-)$1	210	92	107	12.1293
d[bbqqqqqqqqbbd	chr10:116804885-116805106(-)$1	221	120	135	12.6044
ffffqqqqqqqqfff	chr13:85366134-85366342(-)$1	208	4	19	12.1293
ddddqqqqqqqqddd	chr12:77046034-77046240(+)$1	206	180	195	13.9795
dd[aqqqqqqqqa]d	chr2:32134512-32134728(-)$1	216	118	133	13.1249
[cccqqqqqqqqccc	chr5:44074299-44074515(+)$1	216	31	46	13.4854
ddddqqqqqqqqddd	chr1:58614047-58614264(-)$1	217	112	127	13.9795
ddddqqqqqqqqddd	chr2:20781257-20781471(-)$1	214	66	81	13.9795
ddddqqqqqqqqddd	chr5:21153040-21153259(+)$1	219	201	216	13.9795
!cccqqqqqqqqccc	chr13:104934198-104934426(-)$1	228	108	123	13.5464
!cccqqqqqqqqccc	chr10:95458129-95458350(+)$1	221	58	73	13.5464
eeeeqqqqqqqqeee	chr7:108546813-108547031(+)$1	218	182	197	13.2615
ddddqqqqqqqqddd	chr4:126764122-126764343(+)$1	221	21	36	13.9795
eeeeqqqqqqqqeee	chr5:117784871-117785079(+)$1	208	2	17	13.2615
"cccqqqqqqqqccc	chr2:25457933-25458172(-)$1	239	7	22	13.4143
eeeeqqqqqqqqeee	chr16:91701223-91701455(-)$1	232	131	146	13.2615
[cccqqqqqqqqccc	chr17:74616281-74616496(-)$1	215	36	51	13.4854
eeeeqqqqqqqqeee	chr2:59143298-59143524(+)$1	226	25	40	13.2615
ddddqqqqqqqqddd	chr10:80172482-80172710(-)$1	228	40	55	13.9795
ddddqqqqqqqqddd	chr1:183891907-183892141(-)$1	234	217	232	13.9795
cc[aqqqqqqqqacc	chr5:130321542-130321758(+)$1	216	111	126	13.0659
!cccqqqqqqqqccc	chr2:31447890-31448103(+)$1	213	144	159	13.5464
ddddqqqqqqqqddd	chr12:11303853-11304076(+)$1	223	170	185	13.9795
ddddqqqqqqqqddd	chr9:44620978-44621198(-)$1	220	88	103	13.9795
!cccqqqqqqqqccc	chr11:107496274-107496501(+)$1	227	33	48	13.5464
c[bbqqqqqqqqbb]	chr3:63794342-63794560(+)$1	218	147	162	12.2093
ffffqqqqqqqqfff	chr19:23288492-23288727(-)$1	235	107	122	12.1293
eeeeqqqqqqqqeee	chr1:60251256-60251478(+)$1	222	102	117	13.2615

#otherMatches

#Seq PSSM
UUUUGAAAUUGAAAU	chr4:11440317-11440528(+)$1	211	50	65	12.0723
GGGUUCCCCUGCAUC	chr4:117568094-117568312(-)$1	218	176	191	13.2637
CACUGCUACCUAAGU	chr1:136355099-136355306(+)$1	207	156	171	13.2615
UUUUUUUUUUAUAGG	chr1:127999109-127999339(-)$1	230	85	100	12.1293
AGACACCCUGAAGCU	chr15:102154535-102154743(+)$1	208	100	115	13.4565
ACAGUACUGCAUCUG	chr2:165115874-165116095(-)$1	221	30	45	12.5563
UUUAGAUUUGUAUGA	chr4:32718010-32718219(+)$1	209	67	82	13.9795
AAGGUCGAUUUCCCU	chr17:29120945-29121174(-)$1	229	171	186	13.2615
GCUGAAAUUGGCCAG	chrX:12865822-12866041(+)$1	219	128	143	13.9795
GUUUAAAGAUACAGA	chr5:122199023-122199253(+)$1	230	180	195	13.2615
UAUGACCCCACCUAU	chr19:44369515-44369725(+)$1	210	13	28	13.5464
AUUCUCAACUCUGAA	chr10:128349156-128349379(+)$1	223	4	19	13.2615
CCGCGCACACGAGCG	chr12:113020131-113020341(+)$1	210	88	103	13.2615
GAGCUUGGCUAUGCU	chr11:120265475-120265687(-)$1	212	108	123	13.4854
UUGCAAGUGAAGGUA	chr2:59749692-59749898(-)$1	206	148	163	13.2615
CCUCACACACACGAG	chrM:11342-11571(+)$1	229	106	121	12.5563
CUAUCUAAUAAUAUG	chr10:22871645-22871878(-)$1	233	184	199	13.9795
UAUGAUCGAAUCCAA	chr9:110453364-110453570(+)$1	206	140	155	12.0276
GCUUAAAAGGAGGAG	chr18:35731945-35732158(+)$1	213	163	178	13.2079
CCUCUUCCCCACGAU	chr19:10130912-10131128(+)$1	216	2	17	11.9351
CAUCAAGAAGAAGAU	chr9:66896760-66896993(-)$1	233	62	77	13.9795
GUUUAUGAGAGAGAA	chr7:140043023-140043229(-)$1	206	65	80	13.9795
GAGGUAUUAUUUUCU	chrX:148291947-148292167(+)$1	220	193	208	12.6847
UGGCCUUGUAUUGCC	chr15:80709345-80709554(+)$1	209	91	106	13.9795
AGACCAGAAAAAGUC	chr10:76775094-76775304(-)$1	210	42	57	12.5563
ACCCAGACCUCAGGA	chr9:79510257-79510471(-)$1	214	75	90	12.1336
UGCUUGCUUCUCAGC	chr11:120473265-120473501(-)$1	236	204	219	13.9795
CUGGAUCCCCUCCCA	chr1:71645741-71645949(-)$1	208	95	110	13.9795
CACAUAUAUUUUUGU	chr1:84779327-84779545(-)$1	218	168	183	13.5464
AGAGUAAGUGCCCUC	chr1:66903944-66904166(-)$1	222	191	206	12.5563
GAUGGGCUUUAACAC	chr5:123899865-123900073(+)$1	208	89	104	12.3079
CUUGACCUAAAACAA	chr1:127299966-127300194(-)$1	228	1	16	13.9795
GUCUGCUCUGAGAGA	chr10:128140931-128141137(-)$1	206	160	175	13.9795
GACUAAAGAAGAAGU	chr13:99559290-99559516(-)$1	226	45	60	13.9795
CCUGACGUAUGACAG	chr18:38100602-38100822(-)$1	220	150	165	13.2615
GCUUGCUGAUUAAAG	chr2:37496342-37496559(-)$1	217	79	94	12.8799
UGUGUUCUUGUCCAC	chr13:58261143-58261365(+)$1	222	143	158	13.2615
AAUGUCCUUUCCCGU	chr12:87157242-87157458(-)$1	216	39	54	13.9795
UGGACAAACUACUUG	chr11:82697293-82697515(-)$1	222	51	66	12.1972
UCUCACAGUGAAGGG	chr4:136097583-136097827(+)$1	244	179	194	13.9795
UUAGGUCUCAGACUG	chr4:106872916-106873138(+)$1	222	135	150	13.9795
UACACUUACAGUUGU	chr13:97432906-97433130(-)$1	224	166	181	13.4453
GAGCCUAUUUCUGCU	chr7:73475563-73475782(-)$1	219	115	130	13.2615
GUUGGUCAUUCACAA	chr7:63412562-63412770(+)$1	208	13	28	13.9795
GGCUCGUAAACUAGC	chr1:193948055-193948295(-)$1	240	133	148	13.9795
CAGCCGCUACCUGCU	chr13:49298419-49298629(-)$1	210	92	107	12.1293
CUGCAAAUAAUGGCG	chr10:116804885-116805106(-)$1	221	120	135	12.6044
GUUGUGUACUUUCAG	chr13:85366134-85366342(-)$1	208	4	19	12.1293
GGAGUGUGCUUUCUC	chr12:77046034-77046240(+)$1	206	180	195	13.9795
UUUGAUCUAAACCUG	chr2:32134512-32134728(-)$1	216	118	133	13.1249
UUACAAAGCCAAGUA	chr5:44074299-44074515(+)$1	216	31	46	13.4854
AGCUCUCUAUAAAGU	chr1:58614047-58614264(-)$1	217	112	127	13.9795
GUGAUAAGCAGUUUA	chr2:20781257-20781471(-)$1	214	66	81	13.9795
cuuugguacugaaaa	chr5:21153040-21153259(+)$1	219	201	216	13.9795
CUGGCUUAAGACUCA	chr13:104934198-104934426(-)$1	228	108	123	13.5464
GCUAUUUUUAAUUAG	chr10:95458129-95458350(+)$1	221	58	73	13.5464
GUCUGAUUGAGAAGA	chr7:108546813-108547031(+)$1	218	182	197	13.2615
UCAGAUGUUUAGUUG	chr4:126764122-126764343(+)$1	221	21	36	13.9795
CUGCAGUGCCGCGCA	chr5:117784871-117785079(+)$1	208	2	17	13.2615
CUUGACAUGGAACAG	chr2:25457933-25458172(-)$1	239	7	22	13.4143
GGGCAAGUGUGAGUC	chr16:91701223-91701455(-)$1	232	131	146	13.2615
AUGAUAUUUGUUUCA	chr17:74616281-74616496(-)$1	215	36	51	13.4854
AUACAUAAUAAAGUG	chr2:59143298-59143524(+)$1	226	25	40	13.2615
ACAGCCAAGUGACUG	chr10:80172482-80172710(-)$1	228	40	55	13.9795
CACAUUCAGAGUUGU	chr1:183891907-183892141(-)$1	234	217	232	13.9795
CGACGAGAUCAUGCG	chr5:130321542-130321758(+)$1	216	111	126	13.0659
UUUAUUAUUUAUUGA	chr2:31447890-31448103(+)$1	213	144	159	13.5464
UUGAGAAGGAUAUCA	chr12:11303853-11304076(+)$1	223	170	185	13.9795
GGCACGAUCAAAUGC	chr9:44620978-44621198(-)$1	220	88	103	13.9795
GUUCUCUUAGAUGAA	chr11:107496274-107496501(+)$1	227	33	48	13.5464
CGUGCUUUGAACCAA	chr3:63794342-63794560(+)$1	218	147	162	12.2093
AGUUGACCGAAGAAC	chr19:23288492-23288727(-)$1	235	107	122	12.1293
UUACCUGAGACUGUG	chr1:60251256-60251478(+)$1	222	102	117	13.2615

#DB
(.((........)).	chr4:11440317-11440528(+)$1	1	50	65	12.0723
((((........)))	chr4:117568094-117568312(-)$1	1	176	191	13.2637
((((........)))	chr1:136355099-136355306(+)$1	1	156	171	13.2615
((((........)))	chr1:127999109-127999339(-)$1	1	85	100	12.1293
((.(........)))	chr15:102154535-102154743(+)$1	1	100	115	13.4565
.(((........)))	chr2:165115874-165116095(-)$1	1	30	45	12.5563
((((........)))	chr4:32718010-32718219(+)$1	1	67	82	13.9795
((((........)))	chr17:29120945-29121174(-)$1	1	171	186	13.2615
((((........)))	chrX:12865822-12866041(+)$1	1	128	143	13.9795
((((........)))	chr5:122199023-122199253(+)$1	1	180	195	13.2615
.(((........)))	chr19:44369515-44369725(+)$1	1	13	28	13.5464
((((........)))	chr10:128349156-128349379(+)$1	1	4	19	13.2615
((((........)))	chr12:113020131-113020341(+)$1	1	88	103	13.2615
.(((........)))	chr11:120265475-120265687(-)$1	1	108	123	13.4854
((((........)))	chr2:59749692-59749898(-)$1	1	148	163	13.2615
.(((........)))	chrM:11342-11571(+)$1	1	106	121	12.5563
((((........)))	chr10:22871645-22871878(-)$1	1	184	199	13.9795
(.((........)).	chr9:110453364-110453570(+)$1	1	140	155	12.0276
.(((........)))	chr18:35731945-35732158(+)$1	1	163	178	13.2079
(.((........)).	chr19:10130912-10131128(+)$1	1	2	17	11.9351
((((........)))	chr9:66896760-66896993(-)$1	1	62	77	13.9795
((((........)))	chr7:140043023-140043229(-)$1	1	65	80	13.9795
((((........)))	chrX:148291947-148292167(+)$1	1	193	208	12.6847
((((........)))	chr15:80709345-80709554(+)$1	1	91	106	13.9795
.(((........)))	chr10:76775094-76775304(-)$1	1	42	57	12.5563
((((........)).	chr9:79510257-79510471(-)$1	1	75	90	12.1336
((((........)))	chr11:120473265-120473501(-)$1	1	204	219	13.9795
((((........)))	chr1:71645741-71645949(-)$1	1	95	110	13.9795
.(((........)))	chr1:84779327-84779545(-)$1	1	168	183	13.5464
.(((........)))	chr1:66903944-66904166(-)$1	1	191	206	12.5563
(.((........)).	chr5:123899865-123900073(+)$1	1	89	104	12.3079
((((........)))	chr1:127299966-127300194(-)$1	1	1	16	13.9795
((((........)))	chr10:128140931-128141137(-)$1	1	160	175	13.9795
((((........)))	chr13:99559290-99559516(-)$1	1	45	60	13.9795
((((........)))	chr18:38100602-38100822(-)$1	1	150	165	13.2615
.(((........)))	chr2:37496342-37496559(-)$1	1	79	94	12.8799
((((........)))	chr13:58261143-58261365(+)$1	1	143	158	13.2615
((((........)))	chr12:87157242-87157458(-)$1	1	39	54	13.9795
(.((........)).	chr11:82697293-82697515(-)$1	1	51	66	12.1972
((((........)))	chr4:136097583-136097827(+)$1	1	179	194	13.9795
((((........)))	chr4:106872916-106873138(+)$1	1	135	150	13.9795
((((........)))	chr13:97432906-97433130(-)$1	1	166	181	13.4453
((((........)))	chr7:73475563-73475782(-)$1	1	115	130	13.2615
((((........)))	chr7:63412562-63412770(+)$1	1	13	28	13.9795
((((........)))	chr1:193948055-193948295(-)$1	1	133	148	13.9795
((((........)))	chr13:49298419-49298629(-)$1	1	92	107	12.1293
(.((........)))	chr10:116804885-116805106(-)$1	1	120	135	12.6044
((((........)))	chr13:85366134-85366342(-)$1	1	4	19	12.1293
((((........)))	chr12:77046034-77046240(+)$1	1	180	195	13.9795
((.(........).)	chr2:32134512-32134728(-)$1	1	118	133	13.1249
.(((........)))	chr5:44074299-44074515(+)$1	1	31	46	13.4854
((((........)))	chr1:58614047-58614264(-)$1	1	112	127	13.9795
((((........)))	chr2:20781257-20781471(-)$1	1	66	81	13.9795
((((........)))	chr5:21153040-21153259(+)$1	1	201	216	13.9795
.(((........)))	chr13:104934198-104934426(-)$1	1	108	123	13.5464
.(((........)))	chr10:95458129-95458350(+)$1	1	58	73	13.5464
((((........)))	chr7:108546813-108547031(+)$1	1	182	197	13.2615
((((........)))	chr4:126764122-126764343(+)$1	1	21	36	13.9795
((((........)))	chr5:117784871-117785079(+)$1	1	2	17	13.2615
.(((........)))	chr2:25457933-25458172(-)$1	1	7	22	13.4143
((((........)))	chr16:91701223-91701455(-)$1	1	131	146	13.2615
.(((........)))	chr17:74616281-74616496(-)$1	1	36	51	13.4854
((((........)))	chr2:59143298-59143524(+)$1	1	25	40	13.2615
((((........)))	chr10:80172482-80172710(-)$1	1	40	55	13.9795
((((........)))	chr1:183891907-183892141(-)$1	1	217	232	13.9795
((.(........)))	chr5:130321542-130321758(+)$1	1	111	126	13.0659
.(((........)))	chr2:31447890-31448103(+)$1	1	144	159	13.5464
((((........)))	chr12:11303853-11304076(+)$1	1	170	185	13.9795
((((........)))	chr9:44620978-44621198(-)$1	1	88	103	13.9795
.(((........)))	chr11:107496274-107496501(+)$1	1	33	48	13.5464
(.((........)).	chr3:63794342-63794560(+)$1	1	147	162	12.2093
((((........)))	chr19:23288492-23288727(-)$1	1	107	122	12.1293
((((........)))	chr1:60251256-60251478(+)$1	1	102	117	13.2615

#PSSM
d : 0.38	e : 0.23	! : 0.08	f : 0.05	: : 0.05	[ : 0.04	c : 0.04	h : 0.02	$ : 0.01	b : 0.01	g : 0.01	' : 0.01	a : 0.01	" : 0.01	
d : 0.36	c : 0.26	e : 0.20	[ : 0.09	f : 0.05	g : 0.01	
d : 0.34	c : 0.24	e : 0.19	b : 0.10	f : 0.05	[ : 0.04	g : 0.01	
d : 0.34	c : 0.24	e : 0.19	b : 0.10	f : 0.05	a : 0.04	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	
d : 0.34	c : 0.24	e : 0.19	b : 0.10	f : 0.05	a : 0.04	g : 0.01	
d : 0.35	c : 0.26	e : 0.19	b : 0.10	f : 0.05	g : 0.01	] : 0.01	
d : 0.38	c : 0.26	e : 0.19	] : 0.06	f : 0.05	2 : 0.02	g : 0.01	

#score	971.6593928341155
#seq	73
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_CDS_m2_run2.txt

#BEAR
eeeeeooooooeeeee333	chr1:193602238-193602475(+)$1	237	21	40	10.5115
cccccooooooccc]cccd	chr8:56140641-56140894(+)$1	253	209	228	12.2938
c[cccooooooccc]ccc:	chr15:27701031-27701272(-)$1	241	118	137	11.6035
gggggooooooggggggg:	chr7:17501488-17501778(-)$1	290	101	120	11.1866
##cccooooooccc333dd	chrX:162824700-162824996(+)$1	296	108	127	12.0843
eecccooooooccc22eee	chr11:90202099-90202341(-)$1	242	218	237	11.6693
ee[bboooooobb]eeeee	chr9:66883791-66884029(-)$1	238	137	156	11.6564
eeeeeooooooeeeee333	chr5:90646461-90646698(-)$1	237	187	206	10.5115
cccbboooooobb22ccc]	chr17:24642176-24642411(+)$1	235	123	142	11.7800
iiiiiooooooiiiiiiii	chr14:37939004-37939242(-)$1	238	4	23	12.2015
cc[bboooooobbccc22f	chrX:143628695-143628930(+)$1	235	136	155	11.4191
hh[bboooooobb]hhhhh	chr11:41960533-41960768(-)$1	235	189	208	11.4101
ggg[aooooooa]gggggg	chr15:31415590-31415861(-)$1	271	104	123	12.0977
fffffooooooffffffdd	chr15:79555743-79555980(-)$1	237	139	158	10.7456
[a[bboooooobba]dddd	chr13:104623795-104624032(-)$1	237	29	48	11.9505
""cccooooooccc4444g	chr6:97128843-97129081(-)$1	238	118	137	11.7618
eeeeeooooooeeeeefff	chr11:72025341-72025578(-)$1	237	28	47	10.2869
gggbboooooobb]ggggg	chr13:74309433-74309675(-)$1	242	8	27	12.2711
!!cccooooooccc22fff	chr8:41532325-41532562(+)$1	237	41	60	11.9623
gggggooooooggggggg2	chr11:100888528-100888792(+)$1	264	106	125	11.9597
a[cccooooooccc]a>>>	chr1:83273913-83274169(-)$1	256	174	193	11.5872
iiiiiooooooiiiiiiii	chr16:90229856-90230093(-)$1	237	108	127	12.2015
gggggoooooogggggggb	chr7:149573591-149573839(-)$1	248	81	100	11.8487
[bb[aooooooa]bba]dd	chr13:100195648-100195890(-)$1	242	95	114	10.3455
hhhhhoooooohhhhhhhh	chr11:87863329-87863588(+)$1	259	136	155	10.7156
!!cccooooooccc22ccc	chr7:20150502-20150751(-)$1	249	26	45	12.1809
cccccooooooccc]ccc]	chr11:78138010-78138267(+)$1	257	150	169	12.3923
ff[bboooooobb]fffff	chr14:104242207-104242444(-)$1	237	78	97	11.5450
d!!bboooooobb22dddd	chr16:17499962-17500197(+)$1	235	86	105	11.4527
ccc[aooooooa]ccc]a]	chrX:10156346-10156601(+)$1	255	102	121	11.7150
ee[bboooooobb]eeeee	chr14:31989531-31989766(-)$1	235	14	33	11.6564
fffffooooooffffff]e	chr13:6602544-6602805(-)$1	261	8	27	10.7896
fffffooooooffffffGG	chrX:12738488-12738723(+)$1	235	120	139	9.6275
""cccooooooccc]dddd	chr11:70483254-70483493(-)$1	239	14	33	12.0589
=====oooooo========	chr2:131762809-131763094(+)$1	285	175	194	12.1050
ff[bboooooobbffffff	chr10:57236816-57237127(-)$1	311	170	189	11.3849
eeeeeooooooeeeee]a4	chr15:58767736-58767981(+)$1	245	184	203	10.4113
[a[bboooooobb]ahhhh	chr11:87794612-87794923(-)$1	311	25	44	11.6929
ddcccooooooccc]dddd	chr11:115667985-115668222(-)$1	237	187	206	11.7139
fff[aooooooa]ffffff	chr6:108491854-108492100(+)$1	246	60	79	11.0369
iiiiiooooooiiiiiiii	chr16:35293974-35294230(+)$1	256	106	125	12.2015
gggggooooooggggggg:	chrX:141894531-141894792(-)$1	261	21	40	11.1866
hhhhhoooooohhhhhhhh	chr5:125546130-125546365(-)$1	235	44	63	10.7156
bbcccooooooccc]bb22	chrX:162824810-162825047(+)$1	237	13	32	10.8074
d[cccooooooccc]dddd	chr11:70483294-70483530(-)$1	236	51	70	12.0640
d[cccooooooccc]dddd	chr10:98477548-98477791(+)$1	243	158	177	12.0640
[a[bboooooobb]aeeee	chr2:181283313-181283550(+)$1	237	203	222	11.8899
hhhhhoooooohhhhhhhh	chr4:126707100-126707361(+)$1	261	20	39	10.7156
dd[bboooooobb]dddd2	chr11:59220569-59220827(-)$1	258	42	61	11.0909
eeeeeooooooeeeeeddd	chr14:65673532-65673769(-)$1	237	201	220	10.3210
e!!bboooooobb22eeee	chr14:76818619-76818854(+)$1	235	115	134	11.6491
hhhhhoooooohhhhhhhh	chr4:126707015-126707250(+)$1	235	105	124	10.7156
fff[aooooooa]ffffff	chr17:34782494-34782729(+)$1	235	45	64	11.0369
fffffooooooffffff]d	chr1:59927210-59927447(+)$1	237	140	159	10.7960
fffbboooooobb333fff	chrX:148317008-148317269(+)$1	261	7	26	11.5820
hhhhhoooooohhhhhhhh	chrX:45721941-45722176(+)$1	235	114	133	10.7156
""cccooooooccc333bb	chr2:6468061-6468303(-)$1	242	56	75	11.7264
gggggooooooggggggg:	chr3:87798024-87798262(-)$1	238	50	69	11.1866
!!cccooooooccc]dddd	chr11:46055717-46055965(-)$1	248	86	105	12.2967

#otherMatches

#Seq PSSM
AGGAGCCUUUCCUCCUCCC	chr1:193602238-193602475(+)$1	237	21	40	10.5115
CUUGCUUGAAUGCAUAGUU	chr8:56140641-56140894(+)$1	253	209	228	12.2938
GUGUCUGUUUUGGCUCAGU	chr15:27701031-27701272(-)$1	241	118	137	11.6035
GAAGCUAACAUGCUUUCGC	chr7:17501488-17501778(-)$1	290	101	120	11.1866
CCGUCUAAUGUGACUAGCA	chrX:162824700-162824996(+)$1	296	108	127	12.0843
AAAUGCAAGAACAUACUUG	chr11:90202099-90202341(-)$1	242	218	237	11.6693
UUGAGGAGGAGUUGGAUCG	chr9:66883791-66884029(-)$1	238	137	156	11.6564
AGGCGCUUCCACGCCUGCC	chr5:90646461-90646698(-)$1	237	187	206	10.5115
CGGGCCGAGUAGCUACCGU	chr17:24642176-24642411(+)$1	235	123	142	11.7800
GGGGGGCCUCUUCUCCUGA	chr14:37939004-37939242(-)$1	238	4	23	12.2015
CUAUGUGUGUUCAGGCAUC	chrX:143628695-143628930(+)$1	235	136	155	11.4191
GGAUUAUUUUGGAGUUAAU	chr11:41960533-41960768(-)$1	235	189	208	11.4101
UAAGGUCUCUUUGUUAGUU	chr15:31415590-31415861(-)$1	271	104	123	12.0977
GGAAGCUCAUCUUUCCCAG	chr15:79555743-79555980(-)$1	237	139	158	10.7456
CGACUAGUGCCAGCAGUCA	chr13:104623795-104624032(-)$1	237	29	48	11.9505
CAGGCCCAGAAGUCCAUCG	chr6:97128843-97129081(-)$1	238	118	137	11.7618
UGCUCCAGUAUGAGCACUU	chr11:72025341-72025578(-)$1	237	28	47	10.2869
GCACUGCGAGGAGAUGCCA	chr13:74309433-74309675(-)$1	242	8	27	12.2711
UACAUAUUACAGUGAUGAU	chr8:41532325-41532562(+)$1	237	41	60	11.9623
UUGGCGAGUGUGCCGAGGG	chr11:100888528-100888792(+)$1	264	106	125	11.9597
AGAGAAAUACAUCUGUGCC	chr1:83273913-83274169(-)$1	256	174	193	11.5872
GGUUUGGAAGAAGAUCUUU	chr16:90229856-90230093(-)$1	237	108	127	12.2015
GCCGGCGACCUCUGGCUUU	chr7:149573591-149573839(-)$1	248	81	100	11.8487
ACGAGUCCUUCCCCGCAUG	chr13:100195648-100195890(-)$1	242	95	114	10.3455
UGUCUUUCUGUAGACAUAU	chr11:87863329-87863588(+)$1	259	136	155	10.7156
CCAACUUCUACGUUUCCCA	chr7:20150502-20150751(-)$1	249	26	45	12.1809
CCGGCUGUACCGCCAGGUC	chr11:78138010-78138267(+)$1	257	150	169	12.3923
CUCGUGUUCGUGCUAGGCA	chr14:104242207-104242444(-)$1	237	78	97	11.5450
CAUGAUUAGCUUCUAGUUU	chr16:17499962-17500197(+)$1	235	86	105	11.4527
GGUGAUCCUGUUGGCCGUU	chrX:10156346-10156601(+)$1	255	102	121	11.7150
GCUAGACCCCACUCGCAGC	chr14:31989531-31989766(-)$1	235	14	33	11.6564
CACUGACAACCCAGUGGGG	chr13:6602544-6602805(-)$1	261	8	27	10.7896
CUGGGAGAAUCCUCAGUUC	chrX:12738488-12738723(+)$1	235	120	139	9.6275
AUCUGCAUCUUCAGCUGUG	chr11:70483254-70483493(-)$1	239	14	33	12.0589
GUUAUCCACCUGUAGCUCU	chr2:131762809-131763094(+)$1	285	175	194	12.1050
AUGUCUGGCAUGAGUCCCA	chr10:57236816-57237127(-)$1	311	170	189	11.3849
CAGAAGAAGAAUUCUGGCA	chr15:58767736-58767981(+)$1	245	184	203	10.4113
AUGGCAAGCAGGCGGCGUU	chr11:87794612-87794923(-)$1	311	25	44	11.6929
GUGGUGAGUGAGCCUGCCU	chr11:115667985-115668222(-)$1	237	187	206	11.7139
UUCCCCAGAAUGAGAGCCA	chr6:108491854-108492100(+)$1	246	60	79	11.0369
GGUGACGCCCAUCAUCAUC	chr16:35293974-35294230(+)$1	256	106	125	12.2015
UUUCACUAACUUGAGGGAU	chrX:141894531-141894792(-)$1	261	21	40	11.1866
UAGGGGAAGCACUCUAUGG	chr5:125546130-125546365(-)$1	235	44	63	10.7156
AGCAGCUCGCUUUGCCUUC	chrX:162824810-162825047(+)$1	237	13	32	10.8074
AUCUGCAUCUUCAGCUGUG	chr11:70483294-70483530(-)$1	236	51	70	12.0640
GUGGUCUUUACACUCUUAU	chr10:98477548-98477791(+)$1	243	158	177	12.0640
UGGAGGCACAGCUGCAGUC	chr2:181283313-181283550(+)$1	237	203	222	11.8899
UCCUAGAGGAAUGGGGCCU	chr4:126707100-126707361(+)$1	261	20	39	10.7156
UGCCAUCCACUUGCCAGAA	chr11:59220569-59220827(-)$1	258	42	61	11.0909
ACUUUUUUGUCAAGGUGUA	chr14:65673532-65673769(-)$1	237	201	220	10.3210
GCAGCCUAGCAGCCCCUGC	chr14:76818619-76818854(+)$1	235	115	134	11.6491
UCCUAGAGGAAUGGGGCCU	chr4:126707015-126707250(+)$1	235	105	124	10.7156
CUUAGACAAACCCAAGCUA	chr17:34782494-34782729(+)$1	235	45	64	11.0369
UGAAAUUAUUUUUUUGCAU	chr1:59927210-59927447(+)$1	237	140	159	10.7960
UUGUCUUAUUUGAAUUUAG	chrX:148317008-148317269(+)$1	261	7	26	11.5820
UCUUUUCAACCAGGGACAG	chrX:45721941-45722176(+)$1	235	114	133	10.7156
AUGACAAUCCAGUCUCUGC	chr2:6468061-6468303(-)$1	242	56	75	11.7264
CUCAGAUGGACUUGAGGCC	chr3:87798024-87798262(-)$1	238	50	69	11.1866
CUGCCCCUUACGGCCGCAU	chr11:46055717-46055965(-)$1	248	86	105	12.2967

#DB
(((((......)))))...	chr1:193602238-193602475(+)$1	1	21	40	10.5115
(((((......))).))))	chr8:56140641-56140894(+)$1	1	209	228	12.2938
(.(((......))).))).	chr15:27701031-27701272(-)$1	1	118	137	11.6035
(((((......))))))).	chr7:17501488-17501778(-)$1	1	101	120	11.1866
..(((......)))...))	chrX:162824700-162824996(+)$1	1	108	127	12.0843
(((((......)))..)))	chr11:90202099-90202341(-)$1	1	218	237	11.6693
((.((......)).)))))	chr9:66883791-66884029(-)$1	1	137	156	11.6564
(((((......)))))...	chr5:90646461-90646698(-)$1	1	187	206	10.5115
(((((......))..))).	chr17:24642176-24642411(+)$1	1	123	142	11.7800
(((((......))))))))	chr14:37939004-37939242(-)$1	1	4	23	12.2015
((.((......)))))..)	chrX:143628695-143628930(+)$1	1	136	155	11.4191
((.((......)).)))))	chr11:41960533-41960768(-)$1	1	189	208	11.4101
(((.(......).))))))	chr15:31415590-31415861(-)$1	1	104	123	12.0977
(((((......))))))((	chr15:79555743-79555980(-)$1	1	139	158	10.7456
.(.((......))).))))	chr13:104623795-104624032(-)$1	1	29	48	11.9505
..(((......)))....)	chr6:97128843-97129081(-)$1	1	118	137	11.7618
(((((......)))))(((	chr11:72025341-72025578(-)$1	1	28	47	10.2869
(((((......)).)))))	chr13:74309433-74309675(-)$1	1	8	27	12.2711
..(((......)))..)))	chr8:41532325-41532562(+)$1	1	41	60	11.9623
(((((......))))))).	chr11:100888528-100888792(+)$1	1	106	125	11.9597
(.(((......))).)...	chr1:83273913-83274169(-)$1	1	174	193	11.5872
(((((......))))))))	chr16:90229856-90230093(-)$1	1	108	127	12.2015
(((((......))))))))	chr7:149573591-149573839(-)$1	1	81	100	11.8487
.((.(......).))).))	chr13:100195648-100195890(-)$1	1	95	114	10.3455
(((((......))))))))	chr11:87863329-87863588(+)$1	1	136	155	10.7156
..(((......)))..)))	chr7:20150502-20150751(-)$1	1	26	45	12.1809
(((((......))).))).	chr11:78138010-78138267(+)$1	1	150	169	12.3923
((.((......)).)))))	chr14:104242207-104242444(-)$1	1	78	97	11.5450
(..((......))..))))	chr16:17499962-17500197(+)$1	1	86	105	11.4527
(((.(......).))).).	chrX:10156346-10156601(+)$1	1	102	121	11.7150
((.((......)).)))))	chr14:31989531-31989766(-)$1	1	14	33	11.6564
(((((......)))))).)	chr13:6602544-6602805(-)$1	1	8	27	10.7896
(((((......))))))))	chrX:12738488-12738723(+)$1	1	120	139	9.6275
..(((......))).))))	chr11:70483254-70483493(-)$1	1	14	33	12.0589
(((((......))))))))	chr2:131762809-131763094(+)$1	1	175	194	12.1050
((.((......))))))))	chr10:57236816-57237127(-)$1	1	170	189	11.3849
(((((......))))).).	chr15:58767736-58767981(+)$1	1	184	203	10.4113
.(.((......)).)))))	chr11:87794612-87794923(-)$1	1	25	44	11.6929
(((((......))).))))	chr11:115667985-115668222(-)$1	1	187	206	11.7139
(((.(......).))))))	chr6:108491854-108492100(+)$1	1	60	79	11.0369
(((((......))))))))	chr16:35293974-35294230(+)$1	1	106	125	12.2015
(((((......))))))).	chrX:141894531-141894792(-)$1	1	21	40	11.1866
(((((......))))))))	chr5:125546130-125546365(-)$1	1	44	63	10.7156
(((((......))).))..	chrX:162824810-162825047(+)$1	1	13	32	10.8074
(.(((......))).))))	chr11:70483294-70483530(-)$1	1	51	70	12.0640
(.(((......))).))))	chr10:98477548-98477791(+)$1	1	158	177	12.0640
.(.((......)).)))))	chr2:181283313-181283550(+)$1	1	203	222	11.8899
(((((......))))))))	chr4:126707100-126707361(+)$1	1	20	39	10.7156
((.((......)).)))).	chr11:59220569-59220827(-)$1	1	42	61	11.0909
(((((......))))))))	chr14:65673532-65673769(-)$1	1	201	220	10.3210
(..((......))..))))	chr14:76818619-76818854(+)$1	1	115	134	11.6491
(((((......))))))))	chr4:126707015-126707250(+)$1	1	105	124	10.7156
(((.(......).))))))	chr17:34782494-34782729(+)$1	1	45	64	11.0369
(((((......)))))).)	chr1:59927210-59927447(+)$1	1	140	159	10.7960
(((((......))...)))	chrX:148317008-148317269(+)$1	1	7	26	11.5820
(((((......))))))))	chrX:45721941-45722176(+)$1	1	114	133	10.7156
..(((......)))...))	chr2:6468061-6468303(-)$1	1	56	75	11.7264
(((((......))))))).	chr3:87798024-87798262(-)$1	1	50	69	11.1866
..(((......))).))))	chr11:46055717-46055965(-)$1	1	86	105	12.2967

#PSSM
e : 0.15	f : 0.15	g : 0.11	c : 0.10	h : 0.10	d : 0.08	[ : 0.06	i : 0.05	" : 0.05	! : 0.05	# : 0.01	a : 0.01	= : 0.01	b : 0.01	
f : 0.15	e : 0.13	g : 0.11	h : 0.10	c : 0.08	! : 0.08	[ : 0.06	i : 0.05	a : 0.05	" : 0.05	b : 0.03	d : 0.03	# : 0.01	= : 0.01	
c : 0.30	[ : 0.16	g : 0.11	f : 0.11	e : 0.08	h : 0.08	i : 0.05	! : 0.03	b : 0.01	= : 0.01	
c : 0.27	b : 0.25	e : 0.08	g : 0.08	[ : 0.08	h : 0.08	f : 0.06	i : 0.05	= : 0.01	
c : 0.27	b : 0.25	e : 0.08	g : 0.08	a : 0.08	h : 0.08	f : 0.06	i : 0.05	= : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
c : 0.27	b : 0.25	e : 0.08	g : 0.08	a : 0.08	h : 0.08	f : 0.06	i : 0.05	= : 0.01	
c : 0.27	b : 0.25	e : 0.08	g : 0.08	] : 0.08	h : 0.08	f : 0.06	i : 0.05	= : 0.01	
c : 0.30	] : 0.13	f : 0.11	g : 0.10	e : 0.08	h : 0.08	2 : 0.05	i : 0.05	a : 0.01	b : 0.01	= : 0.01	3 : 0.01	
] : 0.18	f : 0.13	e : 0.11	g : 0.11	2 : 0.10	h : 0.10	3 : 0.05	i : 0.05	c : 0.03	a : 0.03	4 : 0.01	b : 0.01	= : 0.01	d : 0.01	
e : 0.15	f : 0.13	d : 0.13	g : 0.11	h : 0.11	c : 0.10	3 : 0.05	2 : 0.05	i : 0.05	a : 0.03	4 : 0.01	= : 0.01	b : 0.01	
f : 0.18	d : 0.15	g : 0.11	h : 0.11	c : 0.08	e : 0.08	3 : 0.06	i : 0.05	] : 0.05	2 : 0.01	4 : 0.01	> : 0.01	= : 0.01	b : 0.01	
d : 0.20	g : 0.11	h : 0.11	f : 0.11	c : 0.08	e : 0.08	i : 0.05	3 : 0.03	2 : 0.03	a : 0.03	] : 0.03	4 : 0.01	> : 0.01	G : 0.01	= : 0.01	b : 0.01	
d : 0.22	f : 0.13	h : 0.11	e : 0.10	: : 0.06	] : 0.05	i : 0.05	g : 0.05	2 : 0.05	3 : 0.03	b : 0.03	> : 0.01	c : 0.01	G : 0.01	= : 0.01	4 : 0.01	

#score	674.5895295798479
#seq	59
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_CDS_m1_run2.txt

#BEAR
ee"""cccyyyyyyyyyyyyyyyyccce	chr2:44852502-44852761(-)$1	259	41	69	22.2004
f[bbyyyyyyyyyyyyyyyybbffffff	chr19:4738295-4738608(+)$1	313	28	56	20.7277
ffff[ccctttttttttttccc]fffff	chr5:139494407-139494767(-)$1	360	316	344	23.1698
!bb!!a!!attttttttttta22a22bb	chr12:11332935-11333407(-)$1	472	421	449	23.1264
"ddddcccuuuuuuuuuuuuccc]dddd	chr9:86468046-86468351(+)$1	305	88	116	24.0523
e!!eeeeeuuuuuuuuuuuueeeee22e	chr16:44159558-44159860(+)$1	302	65	93	24.0190
&&&&dddduuuuuuuuuuuudddd4444	chr9:121155845-121156130(-)$1	285	62	90	21.6341
dddd[cccuuuuuuuuuuuuccc22ddd	chr3:86640141-86640395(-)$1	254	0	28	23.6560
$$$bb[ccctttttttttttcccbb555	chr17:27717477-27717945(-)$1	468	83	111	20.7707
dddd[ccctttttttttttcccdddd]f	chr6:91436802-91437048(+)$1	246	84	112	22.9283
d[ffffffuuuuuuuuuuuuffffff]d	chr9:25101160-25101500(+)$1	340	225	253	23.4980
ffffddddwwwwwwwwwwwwwwdddd]f	chr3:116479250-116479561(-)$1	311	59	87	21.5598
dddcccwwwwwwwwwwwwwwccc]dddd	chr5:30652601-30652843(+)$1	242	90	118	21.6538
gggg[cccwwwwwwwwwwwwwwccc444	chr3:126639520-126639791(-)$1	271	116	144	23.1720
ee!!bbwwwwwwwwwwwwwwbb22eeee	chr11:74492855-74493217(-)$1	362	235	263	21.0285
====[cccyyyyyyyyyyyyyyyyccc]	chr17:24858947-24859209(-)$1	262	159	187	22.7857
iiiiiiiiitttttttttttiiiiiiii	chr13:120245813-120246118(+)$1	305	39	67	24.3201
iiiiiiiiitttttttttttiiiiiiii	chr11:54174643-54174923(+)$1	280	32	60	24.3201
[eeeeeyyyyyyyyyyyyyyyyeeeee]	chr2:74359783-74360237(-)$1	454	224	252	22.2073
ddgggggggtttttttttttggggggg:	chr7:82281091-82281443(-)$1	352	55	83	22.6769
%a!!ddddvvvvvvvvvvvvvdddd22a	chr13:55552999-55553300(+)$1	301	216	244	22.7395
!!eeeeewwwwwwwwwwwwwweeeee22	chr11:62140505-62140815(-)$1	310	89	117	22.2580
e####cccuuuuuuuuuuuuccc]eeee	chr16:56165852-56166121(+)$1	269	171	199	24.9545
=========ttttttttttt========	chr3:157687543-157687853(-)$1	310	28	56	24.9680
gggggggwwwwwwwwwwwwwwggggggg	chr4:53549262-53549591(+)$1	329	62	90	22.8385
!ccceeeeettttttttttteeeee333	chr9:45662814-45663141(+)$1	327	260	288	23.9612
eeeee!!auuuuuuuuuuuua22eeeee	chr12:45664862-45665220(+)$1	358	199	227	23.7399
b[ffffffuuuuuuuuuuuuffffff22	chr15:31408006-31408281(-)$1	275	85	113	23.2738
::eeeeevvvvvvvvvvvvveeeeefff	chr4:75889471-75889785(-)$1	314	192	220	21.0097
ffffddddvvvvvvvvvvvvvdddd444	chr13:38138983-38139222(+)$1	239	16	44	23.0369
======yyyyyyyyyyyyyyyy======	chr5:58112926-58113264(+)$1	338	83	111	23.5382
iiiiiiiiitttttttttttiiiiiiii	chr2:124924354-124924698(-)$1	344	32	60	24.3201
e[ffffffuuuuuuuuuuuuffffff]e	chr19:31159235-31159511(-)$1	276	166	194	23.6292
iiiiiiiiitttttttttttiiiiiiii	chr5:15864646-15864921(+)$1	275	94	122	24.3201
a[ffffffwwwwwwwwwwwwwwffffff	chr10:106333286-106333547(+)$1	261	15	43	21.6746
!!ffffffwwwwwwwwwwwwwwffffff	chr19:4728999-4729269(+)$1	270	68	96	21.8507
iiiiiiiiitttttttttttiiiiiiii	chr2:121836217-121836534(+)$1	317	267	295	24.3201
bb"""ccctttttttttttccc]bbccc	chr3:108194593-108195072(-)$1	479	117	145	22.8629
[bb[eeeeettttttttttteeeee22b	chr5:121995069-121995311(-)$1	242	14	42	23.1096
eee"""bbuuuuuuuuuuuubb]eeeee	chr2:62162738-62163174(+)$1	436	323	351	23.7584
hhhhhhhhuuuuuuuuuuuuhhhhhhhh	chr13:41369228-41369669(+)$1	441	186	214	21.7431
ccccccwwwwwwwwwwwwwwccc]ccc3	chr2:26777408-26777676(-)$1	268	150	178	22.4781
iiiiiiiiitttttttttttiiiiiiii	chr3:108194380-108194630(-)$1	250	88	116	24.3201
dggggggguuuuuuuuuuuuggggggg2	chr2:65518791-65519155(+)$1	364	283	311	24.4742
iii"""bbvvvvvvvvvvvvvbb333ii	chr2:26250977-26251347(+)$1	370	226	254	23.6463
fff[ddddwwwwwwwwwwwwwwdddd]f	chr7:67131423-67131866(-)$1	443	48	76	21.8367
ddd"""ccctttttttttttccc]dddd	chr19:47097977-47098443(+)$1	466	124	152	23.7305
ddd!!cccuuuuuuuuuuuuccc]dddd	chr11:6224787-6225145(+)$1	358	16	44	24.4758
fff[cccvvvvvvvvvvvvvccc]ffff	chr19:31158921-31159307(-)$1	386	89	117	23.7303
(((ddddvvvvvvvvvvvvvddddccc3	chrX:39581366-39581612(+)$1	246	100	128	21.1736
[ccc[ddddtttttttttttdddd22cc	chr12:54240281-54240624(+)$1	343	298	326	22.9510
gbb[eeeeettttttttttteeeee>>>	chr3:136550812-136551095(+)$1	283	48	76	22.8384
ggg####attttttttttta4444gggg	chr18:77209330-77209606(+)$1	276	12	40	23.8586
========uuuuuuuuuuuu========	chr1:127290409-127290682(-)$1	273	135	163	25.7139
hhhhhhhhuuuuuuuuuuuuhhhhhhhh	chr10:86164569-86164876(-)$1	307	208	236	21.7431
[bb[eeeeettttttttttteeeee]bb	chr10:40551344-40551725(-)$1	381	60	88	22.9206
bb!!eeeeettttttttttteeeee22b	chr9:106797697-106797994(-)$1	297	122	150	22.9898
###bb[bbuuuuuuuuuuuubb]bb666	chr11:6304900-6305223(+)$1	323	103	131	21.9880
##dddd[bbtttttttttttbb]dddd4	chr6:124399680-124400028(-)$1	348	247	275	22.7602
fffff[bbtttttttttttbbffffffe	chr7:123505554-123505826(-)$1	272	154	182	21.8033

#otherMatches

#Seq PSSM
UGAUUGAGAACCACAGCAUAUCCACUCC	chr2:44852502-44852761(-)$1	259	41	69	22.2004
GCGGGGAGAAGUGGAGAGAGCCCAGAGC	chr19:4738295-4738608(+)$1	313	28	56	20.7277
UUGUGCUUCUUCAAAAACAAAGGGCAAG	chr5:139494407-139494767(-)$1	360	316	344	23.1698
UGCUUGGACUACCUAUAAAUGGACUUGC	chr12:11332935-11333407(-)$1	472	421	449	23.1264
CUAUGGAUUGCGGAAUGAUUAUCACAUG	chr9:86468046-86468351(+)$1	305	88	116	24.0523
UGGCUUUGAGAUUAUCGAGACAAAGAAG	chr16:44159558-44159860(+)$1	302	65	93	24.0190
CUUUUAGGUCUUAACGUUUUCCUGUCUC	chr9:121155845-121156130(-)$1	285	62	90	21.6341
GCGUUUAAUUUUGCUGAUUUUUAUUGCG	chr3:86640141-86640395(-)$1	254	0	28	23.6560
AAAGGUGCUGCAGUGUCACAAGCCCGUG	chr17:27717477-27717945(-)$1	468	83	111	20.7707
UCUGGUGCCCAUUAUCAUUGCACGGACC	chr6:91436802-91437048(+)$1	246	84	112	22.9283
AGGUAAGUAAGAAUUAAUUAACUUACGU	chr9:25101160-25101500(+)$1	340	225	253	23.4980
UGGCGGUUGCUAUGACAUACCAAACUGG	chr3:116479250-116479561(-)$1	311	59	87	21.5598
CUCACCAACCGCAUGAAGAAGGUGGAGG	chr5:30652601-30652843(+)$1	242	90	118	21.6538
UCCUCAUCGAAUGCCUCACCAAGAUCAA	chr3:126639520-126639791(-)$1	271	116	144	23.1720
UGAACACUUUGUUACCUCCUUGGGUAUG	chr11:74492855-74493217(-)$1	362	235	263	21.0285
UCUUCAUUCCACUGCUAAAAAUAAAGUC	chr17:24858947-24859209(-)$1	262	159	187	22.7857
UUUUGUUUGGAAUCAGAGCGCAAGCGAA	chr13:120245813-120246118(+)$1	305	39	67	24.3201
GAGCUUUACUUAGUCUCCGUGUGAAGCU	chr11:54174643-54174923(+)$1	280	32	60	24.3201
AGAUAUACGCUUAAUAUUAUUCAUAUUC	chr2:74359783-74360237(-)$1	454	224	252	22.2073
CCGGGGGGGCCUUUUAGAUUCUCCUCCU	chr7:82281091-82281443(-)$1	352	55	83	22.6769
AGGAGCCCUCUCCCUUCCCCUGGGCCAC	chr13:55552999-55553300(+)$1	301	216	244	22.7395
AGUCAUAUCCCAUCAGAGCCCUAUGAGC	chr11:62140505-62140815(-)$1	310	89	117	22.2580
ACCACAGCAAGAGGAGCCACGCUAUCCU	chr16:56165852-56166121(+)$1	269	171	199	24.9545
UGCUCUUAAUAGUAAUGGAUUUGGGGGC	chr3:157687543-157687853(-)$1	310	28	56	24.9680
AGCAAAGAAAUUAUAUUGGGACUUUGCU	chr4:53549262-53549591(+)$1	329	62	90	22.8385
augaguuuaauccucacaacuaaacuuu	chr9:45662814-45663141(+)$1	327	260	288	23.9612
UGUCGCACGGAAUAAACUAGGGAUGGCA	chr12:45664862-45665220(+)$1	358	199	227	23.7399
CAGCAGGUCAACAAUAACCAGCCUGCAC	chr15:31408006-31408281(-)$1	275	85	113	23.2738
AUGUGGGAGAAAUCAGUGUGUCCACAAG	chr4:75889471-75889785(-)$1	314	192	220	21.0097
cugagccaucuugAUCACUCUUGGUAUA	chr13:38138983-38139222(+)$1	239	16	44	23.0369
GACAGUGAUUCUAAUCAUUUUAAUUGUC	chr5:58112926-58113264(+)$1	338	83	111	23.5382
AAUGGUAUUUACUUUGCUAUAAUGUCAU	chr2:124924354-124924698(-)$1	344	32	60	24.3201
AUGAUCAAAGCUGCUUUUUCUUGAUCUU	chr19:31159235-31159511(-)$1	276	166	194	23.6292
UUUUCUAGAUUGGACGUUUUUUUGGAGA	chr5:15864646-15864921(+)$1	275	94	122	24.3201
ucaaccaucacaAAUAAACACUAUGGUU	chr10:106333286-106333547(+)$1	261	15	43	21.6746
AUGUAGACCAGCCCGACGAGAAGUCUAU	chr19:4728999-4729269(+)$1	270	68	96	21.8507
AUCUUUGGUGCCCAAUAAUAAUCAAGGG	chr2:121836217-121836534(+)$1	317	267	295	24.3201
ACAAAGGCACUUUCCACCCGCCAGUUCC	chr3:108194593-108195072(-)$1	479	117	145	22.8629
AGCUCCGAGCCCUUUGCUUCCUCGGCUG	chr5:121995069-121995311(-)$1	242	14	42	23.1096
GUUACUGCCGUAAGACAUUCGCCAACAC	chr2:62162738-62163174(+)$1	436	323	351	23.7584
aaaaGUGAUAAUAUGUAAAUUUACUUUU	chr13:41369228-41369669(+)$1	441	186	214	21.7431
UACGACUUCUUCCAGACCAUGUCAGUGA	chr2:26777408-26777676(-)$1	268	150	178	22.4781
UCAGACAAAUGCCAUUUUUUUUUGUCUG	chr3:108194380-108194630(-)$1	250	88	116	24.3201
UGUGCACAAUUCUUACCAACUGUGUAUU	chr2:65518791-65519155(+)$1	364	283	311	24.4742
UGAAACUCUGGAAACUUGAAUGAAAGUU	chr2:26250977-26251347(+)$1	370	226	254	23.6463
AAGAAUUACAAAAUGAUUUCACUAAUAU	chr7:67131423-67131866(-)$1	443	48	76	21.8367
GCUACAGAAGAAAGUACCAGUUCAAGCC	chr19:47097977-47098443(+)$1	466	124	152	23.7305
GUGUUGAGGUUUUAAACUAACUCUCACC	chr11:6224787-6225145(+)$1	358	16	44	24.4758
ugcuagcucccugcaucccugcuugcau	chr19:31158921-31159307(-)$1	386	89	117	23.7303
AAUGACAGCUAUUUAAAAUAUGUUGGUU	chrX:39581366-39581612(+)$1	246	100	128	21.1736
CUGUGGAGGGUCCCAGUAUACCUCAAAU	chr12:54240281-54240624(+)$1	343	298	326	22.9510
UCCUGGAGGCUUCCUAACCACCUCUCCU	chr3:136550812-136551095(+)$1	283	48	76	22.8384
AUUCCAGGGAAAUACAAAGCAGCAGAUG	chr18:77209330-77209606(+)$1	276	12	40	23.8586
AGGGAGAUGGAAAUGAGAUAAUCUUUCU	chr1:127290409-127290682(-)$1	273	135	163	25.7139
GAGUUUUUAAACAAAAUGACAGAAGCUC	chr10:86164569-86164876(-)$1	307	208	236	21.7431
GGAAGGAAUUAUACAAAACCAUUCUGUC	chr10:40551344-40551725(-)$1	381	60	88	22.9206
GCCAGCCCUAGAGCAUGAUGAGGGUAUG	chr9:106797697-106797994(-)$1	297	122	150	22.9898
ACUGACCAAUCCUGAUGAACUGCUCUCC	chr11:6304900-6305223(+)$1	323	103	131	21.9880
UUCCAUUCCCUCUCUUUCCCGGCAUGGC	chr6:124399680-124400028(-)$1	348	247	275	22.7602
CUCUGUAGGAGGAAAAGGACUCAGAGAA	chr7:123505554-123505826(-)$1	272	154	182	21.8033

#DB
((...(((................))))	chr2:44852502-44852761(-)$1	1	41	69	22.2004
(.((................))))))))	chr19:4738295-4738608(+)$1	1	28	56	20.7277
((((.(((...........))).)))))	chr5:139494407-139494767(-)$1	1	316	344	23.1698
.((..(..(...........)..)..))	chr12:11332935-11333407(-)$1	1	421	449	23.1264
.(((((((............))).))))	chr9:86468046-86468351(+)$1	1	88	116	24.0523
(..(((((............)))))..)	chr16:44159558-44159860(+)$1	1	65	93	24.0190
....((((............))))....	chr9:121155845-121156130(-)$1	1	62	90	21.6341
((((.(((............)))..)))	chr3:86640141-86640395(-)$1	1	0	28	23.6560
...((.(((...........)))))...	chr17:27717477-27717945(-)$1	1	83	111	20.7707
((((.(((...........))))))).)	chr6:91436802-91437048(+)$1	1	84	112	22.9283
(.((((((............)))))).)	chr9:25101160-25101500(+)$1	1	225	253	23.4980
((((((((..............)))).)	chr3:116479250-116479561(-)$1	1	59	87	21.5598
((((((..............))).))))	chr5:30652601-30652843(+)$1	1	90	118	21.6538
((((.(((..............)))...	chr3:126639520-126639791(-)$1	1	116	144	23.1720
((..((..............))..))))	chr11:74492855-74493217(-)$1	1	235	263	21.0285
((((.(((................))).	chr17:24858947-24859209(-)$1	1	159	187	22.7857
(((((((((...........))))))))	chr13:120245813-120246118(+)$1	1	39	67	24.3201
(((((((((...........))))))))	chr11:54174643-54174923(+)$1	1	32	60	24.3201
.(((((................))))).	chr2:74359783-74360237(-)$1	1	224	252	22.2073
))(((((((...........))))))).	chr7:82281091-82281443(-)$1	1	55	83	22.6769
.(..((((.............))))..)	chr13:55552999-55553300(+)$1	1	216	244	22.7395
..(((((..............)))))..	chr11:62140505-62140815(-)$1	1	89	117	22.2580
(....(((............))).))))	chr16:56165852-56166121(+)$1	1	171	199	24.9545
(((((((((...........))))))))	chr3:157687543-157687853(-)$1	1	28	56	24.9680
(((((((..............)))))))	chr4:53549262-53549591(+)$1	1	62	90	22.8385
.((((((((...........)))))...	chr9:45662814-45663141(+)$1	1	260	288	23.9612
(((((..(............)..)))))	chr12:45664862-45665220(+)$1	1	199	227	23.7399
(.((((((............))))))..	chr15:31408006-31408281(-)$1	1	85	113	23.2738
..(((((.............)))))(((	chr4:75889471-75889785(-)$1	1	192	220	21.0097
((((((((.............))))...	chr13:38138983-38139222(+)$1	1	16	44	23.0369
((((((................))))))	chr5:58112926-58113264(+)$1	1	83	111	23.5382
(((((((((...........))))))))	chr2:124924354-124924698(-)$1	1	32	60	24.3201
(.((((((............)))))).)	chr19:31159235-31159511(-)$1	1	166	194	23.6292
(((((((((...........))))))))	chr5:15864646-15864921(+)$1	1	94	122	24.3201
(.((((((..............))))))	chr10:106333286-106333547(+)$1	1	15	43	21.6746
..((((((..............))))))	chr19:4728999-4729269(+)$1	1	68	96	21.8507
(((((((((...........))))))))	chr2:121836217-121836534(+)$1	1	267	295	24.3201
((...(((...........))).)))))	chr3:108194593-108195072(-)$1	1	117	145	22.8629
.((.(((((...........)))))..)	chr5:121995069-121995311(-)$1	1	14	42	23.1096
(((...((............)).)))))	chr2:62162738-62163174(+)$1	1	323	351	23.7584
((((((((............))))))))	chr13:41369228-41369669(+)$1	1	186	214	21.7431
((((((..............))).))).	chr2:26777408-26777676(-)$1	1	150	178	22.4781
(((((((((...........))))))))	chr3:108194380-108194630(-)$1	1	88	116	24.3201
((((((((............))))))).	chr2:65518791-65519155(+)$1	1	283	311	24.4742
(((...((.............))...))	chr2:26250977-26251347(+)$1	1	226	254	23.6463
(((.((((..............)))).)	chr7:67131423-67131866(-)$1	1	48	76	21.8367
(((...(((...........))).))))	chr19:47097977-47098443(+)$1	1	124	152	23.7305
(((..(((............))).))))	chr11:6224787-6225145(+)$1	1	16	44	24.4758
(((.(((.............))).))))	chr19:31158921-31159307(-)$1	1	89	117	23.7303
...((((.............))))))).	chrX:39581366-39581612(+)$1	1	100	128	21.1736
.(((.((((...........))))..))	chr12:54240281-54240624(+)$1	1	298	326	22.9510
(((.(((((...........)))))...	chr3:136550812-136551095(+)$1	1	48	76	22.8384
(((....(...........)....))))	chr18:77209330-77209606(+)$1	1	12	40	23.8586
((((((((............))))))))	chr1:127290409-127290682(-)$1	1	135	163	25.7139
((((((((............))))))))	chr10:86164569-86164876(-)$1	1	208	236	21.7431
.((.(((((...........))))).))	chr10:40551344-40551725(-)$1	1	60	88	22.9206
((..(((((...........)))))..)	chr9:106797697-106797994(-)$1	1	122	150	22.9898
...((.((............)).))...	chr11:6304900-6305223(+)$1	1	103	131	21.9880
..((((.((...........)).)))).	chr6:124399680-124400028(-)$1	1	247	275	22.7602
(((((.((...........)))))))))	chr7:123505554-123505826(-)$1	1	154	182	21.8033

#PSSM
d : 0.13	e : 0.11	f : 0.11	i : 0.11	! : 0.06	g : 0.06	= : 0.06	[ : 0.06	b : 0.05	h : 0.03	# : 0.03	" : 0.01	& : 0.01	$ : 0.01	% : 0.01	: : 0.01	a : 0.01	c : 0.01	( : 0.01	
d : 0.11	i : 0.11	f : 0.09	b : 0.09	e : 0.08	[ : 0.08	g : 0.06	= : 0.06	! : 0.05	# : 0.05	c : 0.05	h : 0.03	& : 0.01	$ : 0.01	a : 0.01	: : 0.01	( : 0.01	
f : 0.18	d : 0.11	i : 0.11	b : 0.08	g : 0.08	e : 0.08	! : 0.06	= : 0.06	c : 0.05	" : 0.03	# : 0.03	h : 0.03	& : 0.01	$ : 0.01	( : 0.01	
f : 0.15	i : 0.09	" : 0.08	! : 0.08	d : 0.08	e : 0.08	[ : 0.08	c : 0.06	g : 0.06	= : 0.06	b : 0.05	# : 0.03	h : 0.03	& : 0.01	
e : 0.16	d : 0.13	[ : 0.09	f : 0.09	i : 0.09	" : 0.08	b : 0.05	c : 0.05	g : 0.05	= : 0.05	! : 0.03	# : 0.03	h : 0.03	y : 0.01	
c : 0.21	e : 0.15	d : 0.13	i : 0.09	f : 0.08	[ : 0.05	g : 0.05	= : 0.05	" : 0.05	h : 0.03	y : 0.01	a : 0.01	b : 0.01	! : 0.01	# : 0.01	
c : 0.21	e : 0.13	d : 0.11	i : 0.09	f : 0.08	b : 0.06	y : 0.05	w : 0.05	g : 0.05	! : 0.03	= : 0.03	h : 0.03	# : 0.01	[ : 0.01	
c : 0.19	e : 0.09	d : 0.09	i : 0.09	f : 0.08	w : 0.08	b : 0.08	y : 0.05	v : 0.05	g : 0.03	= : 0.03	a : 0.03	h : 0.03	! : 0.01	
u : 0.26	w : 0.16	i : 0.09	v : 0.09	y : 0.08	t : 0.08	e : 0.08	c : 0.03	a : 0.01	g : 0.01	= : 0.01	d : 0.01	b : 0.01	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.38	u : 0.26	w : 0.16	v : 0.09	y : 0.08	
t : 0.30	u : 0.26	w : 0.16	v : 0.09	y : 0.08	c : 0.05	a : 0.01	b : 0.01	
c : 0.19	e : 0.11	w : 0.11	b : 0.09	i : 0.09	y : 0.06	d : 0.05	f : 0.05	v : 0.05	a : 0.03	g : 0.03	= : 0.03	h : 0.03	4 : 0.01	
c : 0.19	e : 0.13	b : 0.09	i : 0.09	d : 0.08	w : 0.08	y : 0.06	f : 0.06	g : 0.05	2 : 0.03	= : 0.03	h : 0.03	4 : 0.01	
c : 0.16	e : 0.15	d : 0.13	f : 0.11	i : 0.09	] : 0.08	2 : 0.05	g : 0.05	= : 0.05	y : 0.03	h : 0.03	b : 0.01	4 : 0.01	
e : 0.18	d : 0.15	f : 0.13	] : 0.11	i : 0.09	b : 0.05	g : 0.05	= : 0.05	y : 0.03	2 : 0.03	h : 0.03	a : 0.01	c : 0.01	3 : 0.01	4 : 0.01	
e : 0.21	d : 0.16	f : 0.15	i : 0.09	c : 0.08	g : 0.06	2 : 0.05	b : 0.05	= : 0.05	h : 0.03	4 : 0.01	3 : 0.01	
f : 0.16	d : 0.15	2 : 0.09	e : 0.09	i : 0.09	c : 0.08	g : 0.06	4 : 0.05	= : 0.05	3 : 0.03	h : 0.03	5 : 0.01	> : 0.01	] : 0.01	6 : 0.01	
f : 0.11	i : 0.11	c : 0.09	d : 0.09	2 : 0.09	] : 0.08	e : 0.08	g : 0.06	4 : 0.05	= : 0.05	b : 0.03	h : 0.03	5 : 0.01	3 : 0.01	> : 0.01	6 : 0.01	
f : 0.15	e : 0.13	i : 0.11	d : 0.09	b : 0.06	4 : 0.06	2 : 0.05	= : 0.05	3 : 0.05	] : 0.03	g : 0.03	c : 0.03	h : 0.03	5 : 0.01	: : 0.01	a : 0.01	> : 0.01	6 : 0.01	

#score	1380.8497512315614
#seq	60
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_CDS_m3_run1.txt

#BEAR
iiiiiiccc[cccnnnnnccc22ccc]iii	chr11:69560639-69560859(-)$1	220	30	60	10.1125
=========!!bbmmmmbb4444=======	chrX:147083983-147084203(-)$1	220	127	157	14.6168
!!dddd[ccc[bbmmmmbb]ccc]dddd22	chr9:95593211-95593436(+)$1	225	63	93	11.5041
==========!!bblllbb22=========	chr17:14039443-14039663(+)$1	220	189	219	11.0883
ccc[ffffffcccmmmmccc]ffffff22c	chr13:100718788-100719016(-)$1	228	138	168	11.2180
eeee"""a[ddddllldddda333eeeee2	chr6:35148845-35149078(+)$1	233	190	220	9.5338
gggggg$$$$$bbmmmmbb4444ggggggg	chr2:166748199-166748419(+)$1	220	118	148	12.9672
ccc[ccc[a!!bbmmmmbb]a]ccc333cc	chr17:56558274-56558494(-)$1	220	139	169	12.9707
fff[a[ddddcccmmmmccc333dddda]f	chrX:72347776-72347997(+)$1	221	28	58	12.8526
:ggggggg!!cccmmmmccc]ggggggg::	chr4:153355324-153355544(+)$1	220	4	34	11.3781
========[ddddmmmmdddd=========	chrX:98744335-98744555(+)$1	220	28	58	13.5469
g[gggggggddddmmmmdddd22ggggggg	chr18:38014108-38014328(-)$1	220	179	209	12.3533
ddd[dddd!!cccmmmmccc22dddddddd	chr10:126604023-126604243(+)$1	220	92	122	12.6448
$$$$iiiiiiiiimmmmiiiiiiiii333d	chr8:123263763-123263983(+)$1	220	99	129	11.9524
eeee[bb"""cccmmmmccc333bb]eeee	chr15:95792461-95792682(+)$1	221	105	135	13.3854
gggggg####cccmmmmccc333ggggggg	chr4:147927090-147927310(+)$1	220	150	180	15.4890
!!bb!!bb[ddddmmmmdddd]bb22bb22	chr6:113514228-113514457(+)$1	229	12	42	10.4822
cc[eeeeebbcccmmmmccc]bb]eeeeec	chr4:56818841-56819080(+)$1	239	15	45	11.1880
fff!!ccc[ddddmmmmdddd]ccc]ffff	chr8:73871439-73871661(+)$1	222	22	52	11.8159
"eeeee!!eeeeemmmmeeeee]eeeee33	chr14:52799068-52799288(-)$1	220	30	60	10.1709
ddd!!dddd[cccmmmmccc]dddd>>>>>	chr5:136208330-136208550(+)$1	220	27	57	11.3059
e[bb[eeeeecccmmmmccc]eeeee]bb]	chr3:153574827-153575070(-)$1	243	10	40	11.0974
[dddd[bb!!cccmmmmccc]bb]ddddee	chr2:5948424-5948644(+)$1	220	40	70	12.3174
"""bb[a####bbmmmmbb4444a]bb333	chr4:62185003-62185223(-)$1	220	75	105	13.3637
dd[ccc####cccmmmmccccccddddbbd	chr11:106853226-106853447(-)$1	221	148	178	12.8054
gggggddddcccammmma]ccc4444dddd	chr6:13021764-13021984(+)$1	220	115	145	11.4448
b!!ccc[a"""bbmmmmbba]ccc]bb333	chr9:21816370-21816590(+)$1	220	103	133	13.2823
gg[dddd"""cccmmmmccc]ddddggggg	chr12:117664176-117664396(+)$1	220	22	52	13.7475
fff[bba"""cccmmmmccc333a]bb]ff	chr17:35972079-35972302(-)$1	223	129	159	13.6313
d[bb[ccc!!cccmmmmccc22ccc]bbdd	chr2:25200953-25201187(+)$1	234	182	212	13.4486
gggggg[a[ddddmmmmdddd]aggggggg	chr17:5290988-5291208(+)$1	220	176	206	12.7999
==========cccmmmmccc4444======	chr12:60093019-60093239(-)$1	220	16	46	15.3084
i!!ccc[ccc[ccclllccc22cccccc55	chr4:11440097-11440329(+)$1	232	75	105	10.1361
####ccc"""cccmmmmccc22ccc22ddd	chr4:34603395-34603615(+)$1	220	169	199	14.4238
iiiiiii!!ddddmmmmdddd]iiiiiiii	chr3:152405348-152405569(+)$1	221	25	55	13.2191
!!dddd[bb!!bbmmmmbb22bb]dddd]e	chr19:36953618-36953868(+)$1	250	200	230	11.2268
""dddd!!eeeeemmmmeeeeedddd]a33	chr16:91912020-91912240(+)$1	220	127	157	10.4991
[a[ccc"""ddddmmmmddddccc]a]fff	chr16:22027974-22028198(+)$1	224	184	214	12.5366
ggggg!!ccccccmmmmccc]ccc]ggggg	chr15:59286894-59287114(+)$1	220	163	193	14.0554
======####ddddllldddd=========	chr8:67197818-67198039(-)$1	221	127	157	11.6101
#ffffff[a!!bbmmmmbb22a]ffffffc	chr18:24172526-24172799(-)$1	273	28	58	11.1648
ccc[dddd"""bbmmmmbb]dddd]ccc]d	chr5:110678341-110678561(+)$1	220	141	171	11.5603
eeee!!ccc[cccmmmmcccccc]eeeee:	chr11:69480924-69481163(-)$1	239	110	140	11.8901
[============mmmm============]	chr15:7116798-7117018(+)$1	220	99	129	13.8404
d!!cccccc[cccmmmmccc22ccc]ccc]	chr9:106353832-106354052(+)$1	220	110	140	14.2694
ee!!ccc!!ddddmmmmdddd]ccc22eee	chrX:71659180-71659400(-)$1	220	36	66	12.1757
g$$$$$ccc[cccmmmmcccccc333gggg	chr5:77711679-77711899(+)$1	220	68	98	12.9238
:dddd[ccc[cccmmmmccc]ccc]ddddD	chr15:51795524-51795744(-)$1	220	41	71	10.9925
!!ddddcccacccmmmmccc22a]ccc]dd	chr1:193650979-193651202(+)$1	223	143	173	13.4346
$$ggggggg[cccmmmmccc333ggggggg	chr7:19590648-19590869(+)$1	221	153	183	14.5964

#otherMatches

#Seq PSSM
GCAGGGCAAGGGAACAGCUCCAAUUGACCC	chr11:69560639-69560859(-)$1	220	30	60	10.1125
ggggauuggagaggaagcuguggcuggUCC	chrX:147083983-147084203(-)$1	220	127	157	14.6168
AUUAGGUCUAAAGCCCACUGUGGCCCUGUG	chr9:95593211-95593436(+)$1	225	63	93	11.5041
GGGUGGGGCCAGGCUGGGCGGGGCUUCAUC	chr17:14039443-14039663(+)$1	220	189	219	11.0883
CACCAGGCUGGUCCUGGGGCUCAGCCUCAG	chr13:100718788-100719016(-)$1	228	138	168	11.2180
UACUGCUGAGUAGAUUCUACCUUAAGUACG	chr6:35148845-35149078(+)$1	233	190	220	9.5338
GCUUUGCCUUUGACUAAUCUAUUCAAGGUA	chr2:166748199-166748419(+)$1	220	118	148	12.9672
CGCGACUGGAGGAGAAAUCACGGGUGAGGC	chr17:56558274-56558494(-)$1	220	139	169	12.9707
GUAUGAUAACCAUAAGGAUGAGAGUUACUU	chrX:72347776-72347997(+)$1	221	28	58	12.8526
CGAGUAAGAAAGCUGCAGUUACUUGCUCAC	chr4:153355324-153355544(+)$1	220	4	34	11.3781
UAGUUUAUCUUUCUGUUGGGAAUAAGCUAU	chrX:98744335-98744555(+)$1	220	28	58	13.5469
UGUUGAGAAGAUGACCAUAUCCUUUCUUGG	chr18:38014108-38014328(-)$1	220	179	209	12.3533
CUGCAGGGUGUGGAGGUUCAGCCCCUCAGG	chr10:126604023-126604243(+)$1	220	92	122	12.6448
AUCAGGAGGUGGAUGCUUCCAUCUUCAAGG	chr8:123263763-123263983(+)$1	220	99	129	11.9524
CUCUGGUGAACAAUAUUUUGGAAAUAAGAG	chr15:95792461-95792682(+)$1	221	105	135	13.3854
GGACAUGAAGCCUGAUGAGGAGAGUGUUCU	chr4:147927090-147927310(+)$1	220	150	180	15.4890
GACUGUGGUACUAAGUGUGGUUCCUGAGGU	chr6:113514228-113514457(+)$1	229	12	42	10.4822
CCUCUUAGAAGUCAUCAGGCAUUGCUAAGG	chr4:56818841-56819080(+)$1	239	15	45	11.1880
GGUCUGUGAGAUUCCACAGUCACACUACCU	chr8:73871439-73871661(+)$1	222	22	52	11.8159
CUCUUUUCUAUCUUAUUAGGUGUGAAGAUA	chr14:52799068-52799288(-)$1	220	30	60	10.1709
UCGAUGCCAAGAAUCCAUUCCUGGCUGCUG	chr5:136208330-136208550(+)$1	220	27	57	11.3059
UGUGUGAGUCUGAGAUGUCACGAUUUCCGG	chr3:153574827-153575070(-)$1	243	10	40	11.0974
UACCUGUGGCCAGUACUUUGACAGAGGUUC	chr2:5948424-5948644(+)$1	220	40	70	12.3174
ACAGCGUACAGGCGggagcagaaaggcaag	chr4:62185003-62185223(-)$1	220	75	105	13.3637
UUCUGGAACAUCUGAACAGACCAAAGCUGU	chr11:106853226-106853447(-)$1	221	148	178	12.8054
UCUCUCAGUUCCCAUAUGUGGAAUUUACUG	chr6:13021764-13021984(+)$1	220	115	145	11.4448
UCAGCUGCACAGGAGGCCCGGAGUAAGUUU	chr9:21816370-21816590(+)$1	220	103	133	13.2823
GUAUUAGCUUGGGAACACUCUCUGAACUUC	chr12:117664176-117664396(+)$1	220	22	52	13.7475
GGCAGUCACCUUCAUUGGAAACAGCACAGC	chr17:35972079-35972302(-)$1	223	129	159	13.6313
cacuugcugcucuuaugagaugagccaggc	chr2:25200953-25201187(+)$1	234	182	212	13.4486
CCUGGCAUGUCUCAACAGGGAGGGCCAGGA	chr17:5290988-5291208(+)$1	220	176	206	12.7999
UCCUGCUACCCAGGGGCCUGGCAUGGUGGU	chr12:60093019-60093239(-)$1	220	16	46	15.3084
AGGGGACGAUGGCUACGAGCAGAUCUCUAG	chr4:11440097-11440329(+)$1	232	75	105	10.1361
UCUUAUCAACAGUUCUUACUCAGAUCUGGG	chr4:34603395-34603615(+)$1	220	169	199	14.4238
GAAUAUGUAAGUGUUUGUACUGUGUGUUUC	chr3:152405348-152405569(+)$1	221	25	55	13.2191
CCGGAGCCACUGCAGAUGCUCUGUCUUCAG	chr19:36953618-36953868(+)$1	250	200	230	11.2268
AAGACCAGGGCUCCAAGGGGCCGGUUACGA	chr16:91912020-91912240(+)$1	220	127	157	10.4991
UCUUAAGACACUGCCCAUAGUUUAUGUGAG	chr16:22027974-22028198(+)$1	224	184	214	12.5366
GGGGCCUGACCUGUGAGCAGUGUCCGCUUC	chr15:59286894-59287114(+)$1	220	163	193	14.0554
UUUCCACCACAUGAACUUCAUUGGGAAUUA	chr8:67197818-67198039(-)$1	221	127	157	11.6101
ccacacuggggagaaaccuuacgagugugu	chr18:24172526-24172799(-)$1	273	28	58	11.1648
ACUGAGAGCUUUCGUGGGACCUCUGAGUCC	chr5:110678341-110678561(+)$1	220	141	171	11.5603
GAGGACUCUUCGAGACAUUGAGACUUUCUA	chr11:69480924-69481163(-)$1	239	110	140	11.8901
AUGCUGAGUGGUAAAGAUACCGUUCAGCAC	chr15:7116798-7117018(+)$1	220	99	129	13.8404
CUGUGGACUACGCCAGUGUGAAGGUACCgu	chr9:106353832-106354052(+)$1	220	110	140	14.2694
AGCUGGCCAGUAUGAUGAUGCAGCCUCCUA	chrX:71659180-71659400(-)$1	220	36	66	12.1757
UGACAACAUGUCUGAGGGGAGUGACGACUC	chr5:77711679-77711899(+)$1	220	68	98	12.9238
AGCUUUUUGGUUCUUAAGAAGCAGCAAGCC	chr15:51795524-51795744(-)$1	220	41	71	10.9925
GACGGCGCUCAGGCGAGCCUUCGAAGCUGC	chr1:193650979-193651202(+)$1	223	143	173	13.4346
CAGCUUCCGAGAGCCUGCUCCUGCGGAGGC	chr7:19590648-19590869(+)$1	221	153	183	14.5964

#DB
(((((((((.(((.....)))..))).)))	chr11:69560639-69560859(-)$1	1	30	60	10.1125
(((((((((..((....))....)))))))	chrX:147083983-147084203(-)$1	1	127	157	14.6168
..((((.(((.((....)).))).))))..	chr9:95593211-95593436(+)$1	1	63	93	11.5041
((((((((((..((...))..)))))))))	chr17:14039443-14039663(+)$1	1	189	219	11.0883
(((.(((((((((....))).))))))..)	chr13:100718788-100719016(-)$1	1	138	168	11.2180
((((...(.((((...)))))...))))).	chr6:35148845-35149078(+)$1	1	190	220	9.5338
((((((.....((....))....)))))))	chr2:166748199-166748419(+)$1	1	118	148	12.9672
(((.(((.(..((....)).).)))...))	chr17:56558274-56558494(-)$1	1	139	169	12.9707
(((.(.(((((((....)))...))))).)	chrX:72347776-72347997(+)$1	1	28	58	12.8526
.(((((((..(((....))).)))))))..	chr4:153355324-153355544(+)$1	1	4	34	11.3781
((((((((.((((....)))))))))))))	chrX:98744335-98744555(+)$1	1	28	58	13.5469
(.(((((((((((....))))..)))))))	chr18:38014108-38014328(-)$1	1	179	209	12.3533
(((.((((..(((....)))..))))))))	chr10:126604023-126604243(+)$1	1	92	122	12.6448
....(((((((((....)))))))))...)	chr8:123263763-123263983(+)$1	1	99	129	11.9524
((((.((...(((....)))...)).))))	chr15:95792461-95792682(+)$1	1	105	135	13.3854
((((((....(((....)))...)))))))	chr4:147927090-147927310(+)$1	1	150	180	15.4890
..((..((.((((....)))).))..))..	chr6:113514228-113514457(+)$1	1	12	42	10.4822
((.((((((((((....))).)).))))))	chr4:56818841-56819080(+)$1	1	15	45	11.1880
(((..(((.((((....)))).))).))))	chr8:73871439-73871661(+)$1	1	22	52	11.8159
.(((((..(((((....))))).)))))..	chr14:52799068-52799288(-)$1	1	30	60	10.1709
(((..((((.(((....))).)))).....	chr5:136208330-136208550(+)$1	1	27	57	11.3059
(.((.((((((((....))).))))).)).	chr3:153574827-153575070(-)$1	1	10	40	11.0974
.((((.((..(((....))).)).))))))	chr2:5948424-5948644(+)$1	1	40	70	12.3174
...((.(....((....))....).))...	chr4:62185003-62185223(-)$1	1	75	105	13.3637
((.(((....(((....)))))))))))))	chr11:106853226-106853447(-)$1	1	148	178	12.8054
(((((((((((((....).)))....))))	chr6:13021764-13021984(+)$1	1	115	145	11.4448
(..(((.(...((....))).))).))...	chr9:21816370-21816590(+)$1	1	103	133	13.2823
((.((((...(((....))).)))))))))	chr12:117664176-117664396(+)$1	1	22	52	13.7475
(((.(((...(((....)))...).)).))	chr17:35972079-35972302(-)$1	1	129	159	13.6313
(.((.(((..(((....)))..))).))))	chr2:25200953-25201187(+)$1	1	182	212	13.4486
((((((.(.((((....)))).))))))))	chr17:5290988-5291208(+)$1	1	176	206	12.7999
(((((((((((((....)))....))))))	chr12:60093019-60093239(-)$1	1	16	46	15.3084
(..(((.(((.(((...)))..))))))..	chr4:11440097-11440329(+)$1	1	75	105	10.1361
....(((...(((....)))..)))..)))	chr4:34603395-34603615(+)$1	1	169	199	14.4238
(((((((..((((....)))).))))))))	chr3:152405348-152405569(+)$1	1	25	55	13.2191
..((((.((..((....))..)).)))).)	chr19:36953618-36953868(+)$1	1	200	230	11.2268
..((((..(((((....))))))))).)..	chr16:91912020-91912240(+)$1	1	127	157	10.4991
.(.(((...((((....))))))).).)))	chr16:22027974-22028198(+)$1	1	184	214	12.5366
(((((..((((((....))).))).)))))	chr15:59286894-59287114(+)$1	1	163	193	14.0554
((((((....((((...)))))))))))))	chr8:67197818-67198039(-)$1	1	127	157	11.6101
.((((((.(..((....))..).)))))))	chr18:24172526-24172799(-)$1	1	28	58	11.1648
(((.((((...((....)).)))).))).)	chr5:110678341-110678561(+)$1	1	141	171	11.5603
((((..(((.(((....)))))).))))).	chr11:69480924-69481163(-)$1	1	110	140	11.8901
.((((((((((((....)))))))))))).	chr15:7116798-7117018(+)$1	1	99	129	13.8404
(..((((((.(((....)))..))).))).	chr9:106353832-106354052(+)$1	1	110	140	14.2694
((..(((..((((....)))).)))..)))	chrX:71659180-71659400(-)$1	1	36	66	12.1757
(.....(((.(((....))))))...))))	chr5:77711679-77711899(+)$1	1	68	98	12.9238
.((((.(((.(((....))).))).))))(	chr15:51795524-51795744(-)$1	1	41	71	10.9925
..(((((((((((....)))..).))).))	chr1:193650979-193651202(+)$1	1	143	173	13.4346
..(((((((.(((....)))...)))))))	chr7:19590648-19590869(+)$1	1	153	183	14.5964

#PSSM
g : 0.16	= : 0.10	e : 0.10	d : 0.10	! : 0.08	c : 0.08	i : 0.06	f : 0.06	" : 0.06	[ : 0.06	: : 0.04	$ : 0.04	# : 0.04	b : 0.02	
! : 0.14	g : 0.14	= : 0.12	e : 0.10	d : 0.10	c : 0.08	f : 0.08	[ : 0.06	$ : 0.06	i : 0.04	" : 0.04	# : 0.02	a : 0.02	
d : 0.16	g : 0.16	= : 0.12	e : 0.08	f : 0.08	[ : 0.08	! : 0.08	c : 0.06	b : 0.06	i : 0.04	$ : 0.04	" : 0.02	# : 0.02	
g : 0.16	d : 0.14	= : 0.12	[ : 0.12	e : 0.10	c : 0.10	b : 0.08	! : 0.06	i : 0.04	$ : 0.04	# : 0.02	f : 0.02	
d : 0.18	g : 0.16	c : 0.16	= : 0.12	! : 0.08	i : 0.06	[ : 0.06	f : 0.04	e : 0.04	b : 0.04	" : 0.02	a : 0.02	$ : 0.02	
c : 0.19	d : 0.18	= : 0.12	g : 0.12	[ : 0.08	i : 0.06	! : 0.06	e : 0.06	f : 0.04	b : 0.04	" : 0.02	$ : 0.02	
c : 0.21	d : 0.12	= : 0.10	[ : 0.10	g : 0.06	b : 0.06	# : 0.06	! : 0.06	f : 0.04	" : 0.04	i : 0.04	e : 0.04	a : 0.04	$ : 0.02	
c : 0.21	= : 0.10	d : 0.10	" : 0.10	# : 0.08	! : 0.08	a : 0.06	g : 0.06	b : 0.06	[ : 0.04	e : 0.04	f : 0.02	$ : 0.02	i : 0.02	
c : 0.18	" : 0.14	! : 0.12	[ : 0.10	= : 0.08	# : 0.08	d : 0.06	e : 0.06	a : 0.04	g : 0.04	b : 0.04	f : 0.02	$ : 0.02	i : 0.02	
d : 0.19	! : 0.16	[ : 0.14	" : 0.12	c : 0.08	# : 0.08	= : 0.06	e : 0.06	f : 0.02	$ : 0.02	i : 0.02	b : 0.02	a : 0.02	
c : 0.50	d : 0.19	! : 0.10	[ : 0.04	e : 0.04	" : 0.04	$ : 0.02	i : 0.02	# : 0.02	= : 0.02	
c : 0.52	d : 0.19	b : 0.18	e : 0.04	! : 0.02	i : 0.02	= : 0.02	
c : 0.50	b : 0.19	d : 0.19	e : 0.04	i : 0.02	a : 0.02	= : 0.02	
m : 0.90	n : 0.02	b : 0.02	l : 0.02	c : 0.02	d : 0.02	
m : 0.90	l : 0.08	n : 0.02	
m : 0.90	l : 0.08	n : 0.02	
m : 0.90	l : 0.06	n : 0.02	d : 0.02	
c : 0.48	b : 0.19	d : 0.19	e : 0.04	n : 0.02	i : 0.02	a : 0.02	= : 0.02	
c : 0.50	b : 0.19	d : 0.19	e : 0.04	i : 0.02	] : 0.02	= : 0.02	
c : 0.52	d : 0.19	4 : 0.06	] : 0.06	2 : 0.06	e : 0.04	i : 0.02	a : 0.02	= : 0.02	
] : 0.19	d : 0.19	2 : 0.18	c : 0.12	3 : 0.10	4 : 0.08	a : 0.04	e : 0.04	i : 0.02	= : 0.02	
c : 0.18	2 : 0.16	3 : 0.12	] : 0.12	4 : 0.08	= : 0.08	b : 0.06	e : 0.06	d : 0.06	f : 0.02	g : 0.02	i : 0.02	a : 0.02	
c : 0.30	3 : 0.12	4 : 0.10	d : 0.10	= : 0.08	b : 0.08	2 : 0.04	i : 0.04	] : 0.04	a : 0.04	f : 0.02	g : 0.02	e : 0.02	
c : 0.23	d : 0.14	] : 0.12	g : 0.12	= : 0.10	f : 0.04	3 : 0.04	i : 0.04	b : 0.04	e : 0.04	a : 0.04	4 : 0.04	
c : 0.18	d : 0.18	] : 0.14	= : 0.12	g : 0.12	e : 0.10	f : 0.04	i : 0.04	b : 0.02	2 : 0.02	4 : 0.02	3 : 0.02	
d : 0.16	g : 0.16	= : 0.12	e : 0.10	c : 0.08	] : 0.08	2 : 0.06	b : 0.06	f : 0.04	3 : 0.04	i : 0.04	> : 0.02	4 : 0.02	a : 0.02	
g : 0.18	d : 0.16	= : 0.12	e : 0.10	b : 0.10	] : 0.08	c : 0.08	f : 0.06	3 : 0.04	2 : 0.04	> : 0.02	i : 0.02	
g : 0.18	d : 0.14	= : 0.12	e : 0.12	3 : 0.08	b : 0.08	f : 0.06	c : 0.06	i : 0.04	a : 0.04	] : 0.04	2 : 0.02	> : 0.02	
g : 0.16	= : 0.12	e : 0.12	d : 0.12	3 : 0.10	f : 0.08	2 : 0.06	] : 0.06	i : 0.04	c : 0.04	b : 0.04	: : 0.02	> : 0.02	5 : 0.02	
g : 0.16	d : 0.16	= : 0.10	c : 0.08	f : 0.08	e : 0.08	3 : 0.08	2 : 0.06	] : 0.06	i : 0.04	: : 0.04	> : 0.02	5 : 0.02	D : 0.02	

#score	620.381634974206
#seq	50
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_UTR_m2_run2.txt

#BEAR
======!!ccc!!ddddpppppppdddd333ccc====	chr11:60967636-60967911(-)$1	275	178	216	12.1578
hhhhhh[ccc[ccccccnnnnnccc22cccccc]hhhh	chr15:78369034-78369329(-)$1	295	22	60	13.6585
gggggg[iiiiiiiii[ammmma22iiiiiiiii]ggg	chr8:23279098-23279376(-)$1	278	222	260	12.2856
============!!cccmmmmccc333===========	chr4:41040007-41040279(-)$1	272	194	232	15.2651
""dddd[ccc"""ddddmmmmdddd22ccc]dddd333	chr14:76510360-76510630(-)$1	270	143	181	13.9686
d"""bbccc$$$$$cccnnnnnccc22ccc]bb]dddd	chr3:22113201-22113477(+)$1	276	30	68	13.9220
ggggggg[ccc####bbnnnnnbb4444cccggggggg	chr8:75094654-75094945(-)$1	291	91	129	14.8695
!!ccc"""bb[ffffffooooooffffffbb333ccc]	chr11:45722917-45723219(+)$1	302	120	158	12.1072
eee[bb[bb####eeeeeooooooeeeee333bb]bb3	chr10:17621670-17621963(-)$1	293	192	230	12.3638
iiiii[ddddcccddddoooooodddd333ccc22ddd	chr16:17158486-17158754(-)$1	268	165	203	15.0430
iiiiii!!bb"""ddddnnnnndddd]bbiiiiiiiii	chr2:169935592-169935870(-)$1	278	73	111	18.1089
=======[dddd[bboooooobbdddd===========	chr5:121203180-121203459(-)$1	279	79	117	13.5869
::ccc[===========nnnnn===========cccff	chr7:4698932-4699219(+)$1	287	65	103	12.6540
a[affffff[a!!eeeeeooooooeeeee]a]ffffff	chr5:137966744-137967196(+)$1	452	296	334	11.7305
!ggggggg!!a[ddddoooooodddd]a22ggggggg2	chr9:123839046-123839326(+)$1	280	212	250	15.8992
hhhhbbccceeeeecccnnnnnccc333eeeee22ccc	chr10:79619905-79620177(+)$1	272	188	226	12.5282
ddd[acccccc!!ddddnnnnndddd22ccc]ccc]a]	chr4:125857692-125857960(-)$1	268	195	233	16.1119
ebb[bb[bb####ddddoooooodddd333bb]bb]bb	chr5:137968399-137968682(+)$1	283	195	233	14.6103
[ggggggg$$$$$ddddooooooddddgggggggdddd	chr13:54685575-54685844(-)$1	269	219	257	15.3824
======[a!!bb[ddddnnnnndddd]bb22a22====	chr3:9434793-9435074(-)$1	281	14	52	15.9497
eeggggggg"""ccc[ccclllcccccc333ggggggg	chr4:10916683-10916972(-)$1	289	99	137	13.6690
iiii[ccc!!a!!cccooooooccc22accciiiiiii	chr2:15000504-15000785(+)$1	281	76	114	16.7125
cc[a"""ccc"""ddddoooooodddd]ccc]a]cccd	chr18:13846911-13847178(-)$1	267	178	216	17.2668
$$$$ccc[bb"""ddddooooooddddbb]ccc333==	chr6:38558726-38559026(+)$1	300	250	288	16.1407
iiiiiiii[ccc[bbddddllldddd]bbccciiiiii	chr1:36161144-36161424(+)$1	280	33	71	13.4979
fff[ffffff"""ddddmmmmdddd22ffffff333ff	chr19:24758574-24758850(-)$1	276	195	233	13.8162
iiiiii!!bb"""ddddnnnnndddd]bbiiiiiiiii	chr2:169935677-169935993(-)$1	316	196	234	18.1089
c$$$$$ccc"""eeeeennnnneeeee333ccc22ccc	chr10:80826473-80826742(+)$1	269	87	125	14.0648
ffffccc[bb!!eeeeeooooooeeeeebbccc]ffff	chr1:156945530-156945807(-)$1	277	156	194	13.0050
ggg!!bb[a!!ccc[ddddllldddd333ccc22a]bb	chr8:119567100-119567369(-)$1	269	99	137	13.3654
ff[bb"""bb####bboooooobb333bb333bbffff	chr12:86411120-86411394(+)$1	274	11	49	14.2011
ggggggdddd[a[ddddnnnnndddd333a]dddd]gg	chr13:48975988-48976352(-)$1	364	128	166	15.9180
d[iiiiiiiii####bbnnnnnbb333iiiiiiiii22	chr2:121278658-121278956(+)$1	298	231	269	14.9255
ffffeeeeeccc[ddddnnnnndddd]ccc333eeeee	chr2:116947323-116947591(+)$1	268	102	140	14.1917
dd"""ggggggg[ddddllldddd]ggggggg333ddd	chr3:68811830-68812103(+)$1	273	39	77	12.9014
gggggg[ccc"""cccooooooccc22cccggggggg]	chr7:150743662-150743930(-)$1	268	161	199	17.4835
c!!ccc[gggggggcccooooooccc]ggggggg]ccc	chr11:53355924-53356193(+)$1	269	86	124	14.8104
b[ccc!!ccc"""accclllccc]a333ccc333ccc]	chr13:38026937-38027208(+)$1	271	71	109	15.5120
bb[eeeeeiiiiiiiiiooooooiiiiiiiii22eeee	chr14:21513175-21513456(+)$1	281	124	162	12.2092
ggggg"""dddd[ddddnnnnndddddddd22gggggg	chr8:74094492-74094837(+)$1	345	267	305	14.7226
dd[bb"""eeeee[cccnnnnnccc333eeeee22bb]	chr2:60266546-60266814(-)$1	268	128	166	12.8885
ffffff!!bb!!ddddoooooodddd333bb]ffffff	chr7:26149541-26149819(+)$1	278	77	115	15.3393
Hiiiiiiiii"""ddddmmmmdddd]iiiiiiiii:ff	chr12:85023298-85023575(+)$1	277	144	182	14.0227
Gdddd[gggggggddddnnnnndddd333gggggggdd	chr5:135421531-135421815(-)$1	284	121	159	14.7793
ff[bb"""ccc!!ddddmmmmdddd22ccc]bb]ffff	chr1:191694539-191694812(+)$1	273	40	78	14.1565
$$ggggggg####cccooooooccc22ggggggg4444	chr2:38583197-38583553(-)$1	356	94	132	16.1625
ddd[a!!dddd!!ddddnnnnndddddddd]a]dddd]	chr3:51277059-51277340(+)$1	281	141	179	14.0707
f"""ffffff!!eeeeennnnneeeee]ffffff4444	chr17:27111012-27111289(+)$1	277	193	231	12.4302
ff[bb[dddd"""cccooooooccc333ddddbbffff	chrX:71482416-71482685(-)$1	269	141	179	14.5643
fffff[dddd!!ddddoooooodddd333dddd22fff	chr3:36467402-36467678(-)$1	276	128	166	14.9556
[iiiiiiiii"""ddddmmmmdddd22iiiiiiiii]a	chr19:7349339-7349782(+)$1	443	70	108	16.2757

#otherMatches

#Seq PSSM
GCAGGGGAUGGAUGUCUUCAGAGCAGACCAACCACUCU	chr11:60967636-60967911(-)$1	275	178	216	12.1578
CCAAGAAACAAGAUAUCUUGGUGAUCAGUCUGUGUCUU	chr15:78369034-78369329(-)$1	295	22	60	13.6585
CAUGUGUACAACUUUAUCGUAGGUCUGAAGUUGUCCGC	chr8:23279098-23279376(-)$1	278	222	260	12.2856
UUUUUUUUUUGAAAUGGACUUCUAGGCUUGGGGAGGGG	chr4:41040007-41040279(-)$1	272	194	232	15.2651
GCACUGCCGCCAGGCUUCAAGGAGCACGCGACAGUUGA	chr14:76510360-76510630(-)$1	270	143	181	13.9686
CACAGCAGCAGAAGCCAGCAUAUGGGGGCUAGCAGCCA	chr3:22113201-22113477(+)$1	276	30	68	13.9220
GUGGGGGUGACCCUUACUGACCGUUACUGUCCCUCCGC	chr8:75094654-75094945(-)$1	291	91	129	14.8695
AUGUCACAGCGUAGUCUGUGGGAGGACUGGCACGGAUG	chr11:45722917-45723219(+)$1	302	120	158	12.1072
GUGUCUGAUGGAGUUCUAAGGUAGUAGGAAGAAUGGGU	chr10:17621670-17621963(-)$1	293	192	230	12.3638
AGCAGAAGCAACAGGUUACUUACAACUCAGUGUAGUGC	chr16:17158486-17158754(-)$1	268	165	203	15.0430
AGGUAACUGUAAAUACCGACGUGGUAAACUUGCUUGAG	chr2:169935592-169935870(-)$1	278	73	111	18.1089
aaaugccuccaugagauccagcuguggggcauuuucuc	chr5:121203180-121203459(-)$1	279	79	117	13.5869
GUGCUAUCCCUGGUGCUACUGGGGUGUCGGGGAGGCUU	chr7:4698932-4699219(+)$1	287	65	103	12.6540
GCGAGCGAGCGAGUGGGGCAGGGUCCCCAGCACUUGUU	chr5:137966744-137967196(+)$1	452	296	334	11.7305
AUUUGUUUUUCUCACCCCUUUUGGUGUGUUGGACAAAG	chr9:123839046-123839326(+)$1	280	212	250	15.8992
UCGCGAGGCGGCCAUCCUCUCUGGACACUGGCCUCGCC	chr10:79619905-79620177(+)$1	272	188	226	12.5282
GGAACUCUGACAAGUCAUCCUCUGACAGGUCAAGACGC	chr4:125857692-125857960(-)$1	268	195	233	16.1119
UGACAGUGUUAGCGUCUGUGAAAAGACAAUAUUCUCUC	chr5:137968399-137968682(+)$1	283	195	233	14.6103
UGAUGUAAAAACCUGCAAUUGUGUGUAUUGUAUCUUCA	chr13:54685575-54685844(-)$1	269	219	257	15.3824
AGGCAGACGACUUCCAUGAGGUGUGGCAGAGGGACUGU	chr3:9434793-9435074(-)$1	281	14	52	15.9497
caggguuccucuguguagcuuugcuuauccuggaacuc	chr4:10916683-10916972(-)$1	289	99	137	13.6690
GAGAUGAGUUCUCAGUUUUUUUACUCUGUUCUUUCAAG	chr2:15000504-15000785(+)$1	281	76	114	16.7125
UGGAUACGGCCCAUAUAUAUAUUUGUAAGCCUUGCAGU	chr18:13846911-13847178(-)$1	267	178	216	17.2668
AGAAACUGCUAUGUUCAGUAUAUUGAGGGGGGUGGGGG	chr6:38558726-38559026(+)$1	300	250	288	16.1407
GGGCAGGGUAGGACCUCUGGGGCAGAUGGCCUCCCUGC	chr1:36161144-36161424(+)$1	280	33	71	13.4979
CUAGUGUCUUGUGAGAAAAGAUUCUgagagacaggaua	chr19:24758574-24758850(-)$1	276	195	233	13.8162
AGGUAACUGUAAAUACCGACGUGGUAAACUUGCUUGAG	chr2:169935677-169935993(-)$1	316	196	234	18.1089
UAUGAAGGACCAGGCAGACACCCUGCCCCCUCCCCAAC	chr10:80826473-80826742(+)$1	269	87	125	14.0648
GCCAUCGUGGCCUUCUGAGCCCCCGGGACCCGAGUGGC	chr1:156945530-156945807(-)$1	277	156	194	13.0050
UUUCAGAUGAUGAGUUUCUCACAGAACCCCUUCCCUUC	chr8:119567100-119567369(-)$1	269	99	137	13.3654
UUCAAUUUUGUUUUGUUUUACCACUUUCAUUUUUAAAC	chr12:86411120-86411394(+)$1	274	11	49	14.2011
GACAGCGCCUGCCGCAGGGAGGCUGCUCUGGAGGCAGC	chr13:48975988-48976352(-)$1	364	128	166	15.9180
UAGGAAGCCUCGUUGCUGUGAAAGAAAGAGGUUUUUAA	chr2:121278658-121278956(+)$1	298	231	269	14.9255
CCUCCAUCUCCUGAUCGGAUCACGGUGAGGGAAAGAUG	chr2:116947323-116947591(+)$1	268	102	140	14.1917
GACCAAAUGGCAGUGGAAAAUCCAAUGUUAUUGAUUCC	chr3:68811830-68812103(+)$1	273	39	77	12.9014
GCAGCCCAGGAGGGGCGCACCUGCCAGCCUGGCUGCUA	chr7:150743662-150743930(-)$1	268	161	199	17.4835
GCCUGGGCUCUGGGCUCCUCACCGAGACUCAGAGGCCA	chr11:53355924-53356193(+)$1	269	86	124	14.8104
CUUCCUUUUCUGACUGCUCUGCAUGAAUGAAUUUGGAU	chr13:38026937-38027208(+)$1	271	71	109	15.5120
CGGUGUUGGGGGUUUGGAGGCAGCUGGGCCCUGGCAAC	chr14:21513175-21513456(+)$1	281	124	162	12.2092
UCUGCAAGACGGCGAGGCGAGACCUCUUGUAAGUAGAU	chr8:74094492-74094837(+)$1	345	267	305	14.7226
AAAGUCCUGCCGGAUGCACAGAGCAGAACUGGCCAGCA	chr2:60266546-60266814(-)$1	268	128	166	12.8885
GGCCCUCUUCCACAGCUACCAUGUUGCCUGAUGGGGCC	chr7:26149541-26149819(+)$1	278	77	115	15.3393
ACUUUCUUAUGACggggaugaccucagugagagagcua	chr12:85023298-85023575(+)$1	277	144	182	14.0227
GCGCAAGCUGGGUCCUGCUGGCCGGGGUAGCUCAGCUG	chr5:135421531-135421815(-)$1	284	121	159	14.7793
CCCUUGUUCUGGCUCAGAAGUCUGAUACAGUGAUGGGU	chr1:191694539-191694812(+)$1	273	40	78	14.1565
UAACUGUCUCUUCCCUUUACCUAGGCAAGAUGGUGAAU	chr2:38583197-38583553(-)$1	356	94	132	16.1625
GUUGGUGAUUGACCAUAGGAAGUAUGCAAUGUGAAUCA	chr3:51277059-51277340(+)$1	281	141	179	14.0707
GGAAGAGGAGCAGGGGUCAGCAGCUCCACUCUUUCAGA	chr17:27111012-27111289(+)$1	277	193	231	12.4302
AUCACAUCCCCAAGAGUCCAUUUUCAGUGGGAGUAUCU	chrX:71482416-71482685(-)$1	269	141	179	14.5643
AAGCUUCAGCUUGUAGGCACGGCUGCUAUGCUGCUAGC	chr3:36467402-36467678(-)$1	276	128	166	14.9556
CUGCAGAGGGCUUGGCCUCUGGGCCUACCCUUUGUGUG	chr19:7349339-7349782(+)$1	443	70	108	16.2757

#DB
((((((..(((..((((.......))))...)))))))	chr11:60967636-60967911(-)$1	1	178	216	12.1578
((((((.(((.((((((.....)))..)))))).))))	chr15:78369034-78369329(-)$1	1	22	60	13.6585
((((((.(((((((((.(....)..))))))))).)))	chr8:23279098-23279376(-)$1	1	222	260	12.2856
((((((((((((..(((....)))...)))))))))))	chr4:41040007-41040279(-)$1	1	194	232	15.2651
..((((.(((...((((....))))..))).))))...	chr14:76510360-76510630(-)$1	1	143	181	13.9686
(...(((((.....(((.....)))..))).)).))))	chr3:22113201-22113477(+)$1	1	30	68	13.9220
(((((((.(((....((.....))....))))))))))	chr8:75094654-75094945(-)$1	1	91	129	14.8695
..(((...((.((((((......))))))))...))).	chr11:45722917-45723219(+)$1	1	120	158	12.1072
(((.((.((....(((((......)))))...)).)).	chr10:17621670-17621963(-)$1	1	192	230	12.3638
(((((.(((((((((((......))))...)))..)))	chr16:17158486-17158754(-)$1	1	165	203	15.0430
((((((..((...((((.....)))).)))))))))))	chr2:169935592-169935870(-)$1	1	73	111	18.1089
(((((((.((((.((......)))))))))))))))))	chr5:121203180-121203459(-)$1	1	79	117	13.5869
..(((.(((((((((((.....))))))))))))))((	chr7:4698932-4699219(+)$1	1	65	103	12.6540
(.(((((((.(..(((((......))))).).))))))	chr5:137966744-137967196(+)$1	1	296	334	11.7305
.(((((((..(.((((......)))).)..))))))).	chr9:123839046-123839326(+)$1	1	212	250	15.8992
))))(((((((((((((.....)))...)))))..)))	chr10:79619905-79620177(+)$1	1	188	226	12.5282
(((.(((((((..((((.....))))..))).))).).	chr4:125857692-125857960(-)$1	1	195	233	16.1119
(((.((.((....((((......))))...)).)).))	chr5:137968399-137968682(+)$1	1	195	233	14.6103
.(((((((.....((((......)))))))))))))))	chr13:54685575-54685844(-)$1	1	219	257	15.3824
((((((.(..((.((((.....)))).))..)..))))	chr3:9434793-9435074(-)$1	1	14	52	15.9497
(((((((((...(((.(((...))))))...)))))))	chr4:10916683-10916972(-)$1	1	99	137	13.6690
((((.(((..(..(((......)))..)))))))))))	chr2:15000504-15000785(+)$1	1	76	114	16.7125
((.(...(((...((((......)))).))).).))))	chr18:13846911-13847178(-)$1	1	178	216	17.2668
....(((.((...((((......)))))).)))...))	chr6:38558726-38559026(+)$1	1	250	288	16.1407
((((((((.(((.((((((...)))).)))))))))))	chr1:36161144-36161424(+)$1	1	33	71	13.4979
(((.((((((...((((....))))..))))))...))	chr19:24758574-24758850(-)$1	1	195	233	13.8162
((((((..((...((((.....)))).)))))))))))	chr2:169935677-169935993(-)$1	1	196	234	18.1089
(.....(((...(((((.....)))))...)))..)))	chr10:80826473-80826742(+)$1	1	87	125	14.0648
(((((((.((..(((((......)))))))))).))))	chr1:156945530-156945807(-)$1	1	156	194	13.0050
(((..((.(..(((.((((...))))...)))..).))	chr8:119567100-119567369(-)$1	1	99	137	13.3654
((.((...((....((......))...))...))))))	chr12:86411120-86411394(+)$1	1	11	49	14.2011
((((((((((.(.((((.....))))...).)))).))	chr13:48975988-48976352(-)$1	1	128	166	15.9180
(.(((((((((....((.....))...)))))))))..	chr2:121278658-121278956(+)$1	1	231	269	14.9255
((((((((((((.((((.....)))).)))...)))))	chr2:116947323-116947591(+)$1	1	102	140	14.1917
((...(((((((.((((...)))).)))))))...)))	chr3:68811830-68812103(+)$1	1	39	77	12.9014
((((((.(((...(((......)))..)))))))))).	chr7:150743662-150743930(-)$1	1	161	199	17.4835
(..(((.((((((((((......))).))))))).)))	chr11:53355924-53356193(+)$1	1	86	124	14.8104
(.(((..(((...((((...))).)...)))...))).	chr13:38026937-38027208(+)$1	1	71	109	15.5120
((.((((((((((((((......)))))))))..))))	chr14:21513175-21513456(+)$1	1	124	162	12.2092
(((((...((((.((((.....))))))))..))))))	chr8:74094492-74094837(+)$1	1	267	305	14.7226
((.((...(((((.(((.....)))...)))))..)).	chr2:60266546-60266814(-)$1	1	128	166	12.8885
((((((..((..((((......))))...)).))))))	chr7:26149541-26149819(+)$1	1	77	115	15.3393
((((((((((...((((....)))).))))))))).((	chr12:85023298-85023575(+)$1	1	144	182	14.0227
(((((.(((((((((((.....))))...)))))))))	chr5:135421531-135421815(-)$1	1	121	159	14.7793
((.((...(((..((((....))))..))).)).))))	chr1:191694539-191694812(+)$1	1	40	78	14.1565
..(((((((....(((......)))..)))))))....	chr2:38583197-38583553(-)$1	1	94	132	16.1625
(((.(..((((..((((.....)))))))).).)))).	chr3:51277059-51277340(+)$1	1	141	179	14.0707
(...((((((..(((((.....))))).))))))....	chr17:27111012-27111289(+)$1	1	193	231	12.4302
((.((.((((...(((......)))...))))))))))	chrX:71482416-71482685(-)$1	1	141	179	14.5643
(((((.((((..((((......))))...))))..)))	chr3:36467402-36467678(-)$1	1	128	166	14.9556
.(((((((((...((((....))))..))))))))).)	chr19:7349339-7349782(+)$1	1	70	108	16.2757

#PSSM
f : 0.17	g : 0.11	d : 0.11	i : 0.09	= : 0.07	e : 0.05	c : 0.05	h : 0.03	! : 0.03	[ : 0.03	$ : 0.03	b : 0.03	" : 0.01	: : 0.01	a : 0.01	H : 0.01	G : 0.01	
g : 0.15	f : 0.15	i : 0.13	d : 0.09	= : 0.07	" : 0.05	[ : 0.05	$ : 0.05	h : 0.03	! : 0.03	e : 0.03	b : 0.03	: : 0.01	c : 0.01	
g : 0.19	i : 0.15	[ : 0.11	f : 0.09	= : 0.07	d : 0.07	" : 0.05	c : 0.05	h : 0.03	$ : 0.03	e : 0.01	a : 0.01	b : 0.01	! : 0.01	
g : 0.17	i : 0.15	[ : 0.09	f : 0.09	= : 0.07	c : 0.07	b : 0.07	" : 0.05	h : 0.03	d : 0.03	$ : 0.03	a : 0.01	! : 0.01	e : 0.01	
g : 0.17	b : 0.15	i : 0.13	c : 0.11	f : 0.09	= : 0.07	d : 0.03	a : 0.03	" : 0.03	e : 0.03	h : 0.01	[ : 0.01	$ : 0.01	! : 0.01	
g : 0.17	" : 0.11	i : 0.11	b : 0.09	[ : 0.09	c : 0.09	= : 0.07	f : 0.07	e : 0.03	! : 0.03	h : 0.01	d : 0.01	$ : 0.01	
[ : 0.15	c : 0.13	g : 0.13	! : 0.11	" : 0.11	d : 0.07	i : 0.07	= : 0.05	f : 0.05	e : 0.03	b : 0.01	
c : 0.19	g : 0.13	i : 0.09	[ : 0.09	" : 0.09	d : 0.09	! : 0.07	f : 0.05	= : 0.03	b : 0.03	e : 0.03	a : 0.01	
c : 0.23	b : 0.17	d : 0.13	i : 0.09	g : 0.09	f : 0.05	! : 0.05	= : 0.03	e : 0.03	$ : 0.01	[ : 0.01	a : 0.01	
c : 0.21	b : 0.13	d : 0.13	i : 0.09	! : 0.07	# : 0.05	g : 0.05	= : 0.03	$ : 0.03	e : 0.03	" : 0.03	f : 0.03	[ : 0.01	
" : 0.25	c : 0.13	! : 0.09	# : 0.07	[ : 0.05	i : 0.05	d : 0.05	a : 0.05	g : 0.05	= : 0.03	$ : 0.03	e : 0.03	b : 0.01	
" : 0.25	! : 0.19	# : 0.11	c : 0.09	g : 0.05	i : 0.03	= : 0.03	$ : 0.03	d : 0.03	e : 0.03	f : 0.01	[ : 0.01	b : 0.01	a : 0.01	
" : 0.21	! : 0.13	[ : 0.13	# : 0.11	e : 0.09	c : 0.07	d : 0.05	i : 0.03	$ : 0.03	g : 0.03	f : 0.01	= : 0.01	
d : 0.47	c : 0.13	e : 0.11	# : 0.05	i : 0.03	b : 0.03	! : 0.01	$ : 0.01	f : 0.01	= : 0.01	g : 0.01	a : 0.01	[ : 0.01	
d : 0.47	c : 0.23	e : 0.09	b : 0.05	i : 0.03	# : 0.03	f : 0.01	= : 0.01	[ : 0.01	
d : 0.50	c : 0.21	e : 0.09	b : 0.05	i : 0.03	f : 0.01	o : 0.01	= : 0.01	[ : 0.01	
d : 0.45	o : 0.17	c : 0.15	e : 0.09	b : 0.03	[ : 0.01	f : 0.01	= : 0.01	i : 0.01	
n : 0.35	o : 0.35	m : 0.11	e : 0.03	d : 0.03	l : 0.03	p : 0.01	a : 0.01	c : 0.01	
o : 0.39	n : 0.35	m : 0.13	d : 0.03	l : 0.03	p : 0.01	c : 0.01	
o : 0.39	n : 0.35	m : 0.13	l : 0.09	p : 0.01	
o : 0.39	n : 0.35	m : 0.13	l : 0.05	p : 0.01	d : 0.01	c : 0.01	
o : 0.37	n : 0.35	d : 0.11	l : 0.05	c : 0.03	p : 0.01	m : 0.01	b : 0.01	
d : 0.39	c : 0.21	o : 0.21	b : 0.07	e : 0.03	p : 0.01	a : 0.01	= : 0.01	
d : 0.50	c : 0.21	b : 0.05	e : 0.05	o : 0.03	p : 0.01	2 : 0.01	f : 0.01	= : 0.01	] : 0.01	i : 0.01	
d : 0.50	c : 0.19	e : 0.09	3 : 0.05	2 : 0.01	4 : 0.01	f : 0.01	= : 0.01	] : 0.01	a : 0.01	i : 0.01	
d : 0.41	2 : 0.17	3 : 0.13	e : 0.09	i : 0.03	c : 0.03	4 : 0.01	f : 0.01	= : 0.01	g : 0.01	] : 0.01	
3 : 0.23	2 : 0.19	d : 0.17	] : 0.13	e : 0.09	i : 0.05	4 : 0.01	f : 0.01	= : 0.01	c : 0.01	g : 0.01	
3 : 0.23	c : 0.13	b : 0.11	i : 0.09	g : 0.07	d : 0.05	= : 0.05	e : 0.05	f : 0.03	a : 0.03	] : 0.03	4 : 0.01	2 : 0.01	
c : 0.21	3 : 0.19	b : 0.13	i : 0.09	e : 0.07	g : 0.07	= : 0.05	f : 0.05	d : 0.05	2 : 0.01	
c : 0.25	3 : 0.13	i : 0.13	g : 0.09	d : 0.07	= : 0.05	b : 0.05	] : 0.03	2 : 0.03	e : 0.03	f : 0.03	a : 0.01	
c : 0.23	i : 0.13	g : 0.13	3 : 0.09	] : 0.09	= : 0.05	b : 0.05	e : 0.03	2 : 0.03	f : 0.03	d : 0.03	a : 0.01	
g : 0.17	c : 0.15	i : 0.15	3 : 0.09	d : 0.07	] : 0.07	= : 0.05	b : 0.05	e : 0.03	a : 0.03	f : 0.03	2 : 0.01	
g : 0.17	i : 0.15	c : 0.13	b : 0.09	3 : 0.07	f : 0.07	= : 0.05	d : 0.05	2 : 0.05	e : 0.03	] : 0.03	a : 0.01	
g : 0.17	i : 0.15	2 : 0.15	] : 0.09	3 : 0.09	b : 0.07	c : 0.05	d : 0.05	f : 0.05	= : 0.03	e : 0.01	
i : 0.13	g : 0.11	f : 0.11	d : 0.09	c : 0.09	2 : 0.09	= : 0.07	] : 0.05	3 : 0.05	e : 0.03	4 : 0.03	h : 0.01	b : 0.01	a : 0.01	
g : 0.13	c : 0.13	f : 0.13	i : 0.11	d : 0.09	= : 0.07	] : 0.07	3 : 0.05	b : 0.03	e : 0.03	4 : 0.03	h : 0.01	: : 0.01	
f : 0.19	g : 0.13	d : 0.11	c : 0.11	= : 0.09	b : 0.07	i : 0.07	e : 0.03	4 : 0.03	h : 0.01	3 : 0.01	a : 0.01	2 : 0.01	] : 0.01	
f : 0.19	d : 0.11	] : 0.11	= : 0.09	g : 0.09	i : 0.07	c : 0.05	3 : 0.03	2 : 0.03	b : 0.03	e : 0.03	4 : 0.03	h : 0.01	a : 0.01	

#score	738.3731440076258
#seq	51
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_UTR_m2_run2.txt

#BEAR
bb"""cccooooooccc333bb	chr16:49911604-49911805(+)$1	201	15	37	12.9599
========oooooo========	chr2:102624838-102625039(+)$1	201	40	62	14.0817
fff[ddddoooooodddd]fff	chr19:44368622-44368823(+)$1	201	170	192	11.1312
:gggggggooooooggggggg:	chr3:72852070-72852271(-)$1	201	175	197	11.4642
b!!eeeeeooooooeeeee22b	chr2:25325143-25325344(-)$1	201	131	153	12.1047
e####cccooooooccc22eee	chr1:157899928-157900129(+)$1	201	155	177	13.1768
d####cccoooooocccddddG	chr1:121555658-121555859(-)$1	201	3	25	12.3664
iii"""bboooooobb]iiiii	chr17:25957905-25958106(+)$1	201	22	44	13.1029
fff!!cccooooooccc]ffff	chr15:9126781-9126982(+)$1	201	153	175	13.1398
cc[eeeeeooooooeeeee]cc	chr1:78702937-78703138(+)$1	201	57	79	12.6109
eeee[cccooooooccceeeee	chr5:138200860-138201061(+)$1	201	8	30	13.2606
ffffff[aooooooaffffff:	chr14:120724246-120724447(+)$1	201	105	127	10.8909
ccca[cccooooooccc]a]cc	chr2:102624532-102624733(+)$1	201	50	72	13.6715
hhheeeeeooooooeeeee]hh	chr16:36035810-36036011(+)$1	201	87	109	11.5935
iiiiiiiiooooooiiiiiiii	chr13:43232300-43232501(+)$1	201	120	142	13.5419
eeeeddddoooooodddd4444	chr3:126624609-126624810(-)$1	201	98	120	11.5825
!!ccc[bboooooobb]ccc44	chr6:115569038-115569239(-)$1	201	138	160	12.6167
dddd[cccooooooccc333dd	chr14:65430470-65430671(-)$1	201	75	97	13.1827
c[ffffffooooooffffffcc	chr17:28883213-28883414(+)$1	201	91	113	11.8648
"""eeeeeooooooeeeee333	chr2:25325106-25325307(-)$1	201	105	127	13.0719
dd[ccc[aooooooa]ccc]dd	chr4:32668176-32668377(+)$1	201	135	157	12.4095
==[eeeeeooooooeeeee]==	chr11:74489934-74490135(-)$1	201	57	79	13.1087
dddd[cccooooooccc22ddd	chr8:125153259-125153460(-)$1	201	139	161	12.4040
c!!eeeeeooooooeeeee]cc	chr11:53291016-53291217(-)$1	201	34	56	12.8318
[gggggggooooooggggggg4	chr1:153666291-153666492(+)$1	201	131	153	13.4522
!!ccc[bboooooobb]ccc22	chr2:31148285-31148486(+)$1	201	173	195	12.3309
[gggggggooooooggggggg]	chr11:119868683-119868884(-)$1	201	113	135	13.4837
cgggggggooooooggggggg:	chr2:102622374-102622575(+)$1	201	75	97	12.4413
[dddd[bboooooobb]dddd]	chr8:73279798-73279999(+)$1	201	48	70	11.5385
gg####bboooooobb333ggg	chrX:162825047-162825248(+)$1	201	7	29	12.9598
:gggggggooooooggggggg:	chr13:21536447-21536648(-)$1	201	103	125	11.4642
iiii[cccooooooccc]iiii	chr8:86464161-86464362(+)$1	201	6	28	14.2476
eeee[cccooooooccc]eeee	chr8:13019494-13019695(+)$1	201	57	79	13.4439
eeee[cccooooooccc4444e	chr3:80491784-80491985(-)$1	201	66	88	13.4532
e####cccooooooccc22eee	chr1:157899929-157900130(+)$1	201	154	176	13.1768
eeee[cccooooooccc]eeee	chr8:13019495-13019696(+)$1	201	56	78	13.4439
"""eeeeeooooooeeeee333	chr2:25325107-25325308(-)$1	201	106	128	13.0719
cgggggggooooooggggggg:	chr2:102622375-102622576(+)$1	201	74	96	12.4413
gggg[cccooooooccc]gggg	chr5:43677679-43677880(+)$1	201	112	134	14.0739
ffff[a[aooooooa]a]ffff	chr6:124997803-124998004(+)$1	201	48	70	12.2193
[dddd[bboooooobb]dddd]	chr8:73279799-73280000(+)$1	201	47	69	11.5385
!!ccc[bboooooobb]ccc44	chr6:115569039-115569240(-)$1	201	139	161	12.6167
eee!!cccooooooccceeeee	chr17:66687050-66687251(-)$1	201	115	137	13.2691
==[eeeeeooooooeeeee]==	chr11:74489933-74490134(-)$1	201	56	78	13.1087
[ccc!!bboooooobb]ccc]d	chr13:74440918-74441119(-)$1	201	125	147	12.5421
e[bb[cccooooooccc]bbee	chr10:63392669-63392870(-)$1	201	4	26	12.4808
========oooooo========	chr13:43232308-43232509(+)$1	201	112	134	14.0817
========oooooo========	chr2:103988340-103988541(-)$1	201	7	29	14.0817
d!!eeeeeooooooeeeee22d	chr6:90332767-90332968(+)$1	201	24	46	12.3153
gggg[cccoooooocccggggg	chr6:126589283-126589484(-)$1	201	27	49	13.9304
bbffffffooooooffffff22	chr2:165609674-165609875(-)$1	201	133	155	11.0548
========oooooo========	chr2:103988339-103988540(-)$1	201	6	28	14.0817

#otherMatches

#Seq PSSM
GUUUUGAAUACAUUUUUUUUGC	chr16:49911604-49911805(+)$1	201	15	37	12.9599
UGAUUUUAGGACCAUGAGAUCA	chr2:102624838-102625039(+)$1	201	40	62	14.0817
AGUCAUAGCACCCUUUGUCGCU	chr19:44368622-44368823(+)$1	201	170	192	11.1312
GGGGAUCGUUGUAUUGAUCCUA	chr3:72852070-72852271(-)$1	201	175	197	11.4642
ACCUGCUCUGCUCUGAGCAAAU	chr2:25325143-25325344(-)$1	201	131	153	12.1047
GCAAUACCUACACCGGUUACCA	chr1:157899928-157900129(+)$1	201	155	177	13.1768
GCACAGUGUCCAUUUACCAGCA	chr1:121555658-121555859(-)$1	201	3	25	12.3664
CCCACAGUCCCCCAACAGGGAG	chr17:25957905-25958106(+)$1	201	22	44	13.1029
ACUCAUGUCUUAAAACAAGGUU	chr15:9126781-9126982(+)$1	201	153	175	13.1398
UUUUGGCAUUGGUUUGCUACAG	chr1:78702937-78703138(+)$1	201	57	79	12.6109
CCUCUCCUCUGCCAAGGGAGGG	chr5:138200860-138201061(+)$1	201	8	30	13.2606
CUUCAAACUUACAUGUUGGAGU	chr14:120724246-120724447(+)$1	201	105	127	10.8909
GCUAUUCCUGUAACGGAUUCAG	chr2:102624532-102624733(+)$1	201	50	72	13.6715
UCUAGUGCUGCUUUGUGCUGAG	chr16:36035810-36036011(+)$1	201	87	109	11.5935
GGAAAGAUGCAGAAAUCUUUCC	chr13:43232300-43232501(+)$1	201	120	142	13.5419
UGAAUACUGUGAGAAGUGAAUU	chr3:126624609-126624810(-)$1	201	98	120	11.5825
AAGCUGUCCACCAAGAAAGCCU	chr6:115569038-115569239(-)$1	201	138	160	12.6167
GUAUCUCCUAUUCUGGAUUAGU	chr14:65430470-65430671(-)$1	201	75	97	13.1827
UAUCUCACUUCACUGUGAGGGG	chr17:28883213-28883414(+)$1	201	91	113	11.8648
UCUGAGCAAAUGGCUGCUCUUC	chr2:25325106-25325307(-)$1	201	105	127	13.0719
AAUAAUCUGCUUGAAUAUUUUU	chr4:32668176-32668377(+)$1	201	135	157	12.4095
GCCUAUCUGUAAGUGGAUAUGU	chr11:74489934-74490135(-)$1	201	57	79	13.1087
CACACUUCCUAAACGAAACUGU	chr8:125153259-125153460(-)$1	201	139	161	12.4040
UUAUCUACCUCAUUGUAGGCAG	chr11:53291016-53291217(-)$1	201	34	56	12.8318
AUAGGUCUCCGUAAAGACCUAC	chr1:153666291-153666492(+)$1	201	131	153	13.4522
UGCCUGCCUCACUUGGGAGGAU	chr2:31148285-31148486(+)$1	201	173	195	12.3309
GUAAAGUAUAUUGUUGCUUUGG	chr11:119868683-119868884(-)$1	201	113	135	13.4837
AAAAUGAUCUAGGAAUCAUUUG	chr2:102622374-102622575(+)$1	201	75	97	12.4413
CAGCGUGGGCAAAACCUCGUUC	chr8:73279798-73279999(+)$1	201	48	70	11.5385
AGCCAAUGAAUUCACAGCUCUG	chrX:162825047-162825248(+)$1	201	7	29	12.9598
AGCUUUAUGUGUGAAUGAAGUG	chr13:21536447-21536648(-)$1	201	103	125	11.4642
GGCGUGUACCUCACUGCCUGCC	chr8:86464161-86464362(+)$1	201	6	28	14.2476
UUUGUGGUACUCUGGCCUCAAA	chr8:13019494-13019695(+)$1	201	57	79	13.4439
GAUGGGGAAAAUGGUCCAUGGU	chr3:80491784-80491985(-)$1	201	66	88	13.4532
GCAAUACCUACACCGGUUACCA	chr1:157899929-157900130(+)$1	201	154	176	13.1768
UUUGUGGUACUCUGGCCUCAAA	chr8:13019495-13019696(+)$1	201	56	78	13.4439
UCUGAGCAAAUGGCUGCUCUUC	chr2:25325107-25325308(-)$1	201	106	128	13.0719
AAAAUGAUCUAGGAAUCAUUUG	chr2:102622375-102622576(+)$1	201	74	96	12.4413
GGUGUUAUGUGUAAAUGUCACC	chr5:43677679-43677880(+)$1	201	112	134	14.0739
UCCACCCCUCUGAUGUGUUGGA	chr6:124997803-124998004(+)$1	201	48	70	12.2193
CAGCGUGGGCAAAACCUCGUUC	chr8:73279799-73280000(+)$1	201	47	69	11.5385
AAGCUGUCCACCAAGAAAGCCU	chr6:115569039-115569240(-)$1	201	139	161	12.6167
UGGUAAACUGAGAUGUUUCGGG	chr17:66687050-66687251(-)$1	201	115	137	13.2691
GCCUAUCUGUAAGUGGAUAUGU	chr11:74489933-74490134(-)$1	201	56	78	13.1087
ACAUAAGCAAUAAAGUGAUGAU	chr13:74440918-74441119(-)$1	201	125	147	12.5421
GGACUUGAGCACAAUCACGUCA	chr10:63392669-63392870(-)$1	201	4	26	12.4808
GGAAAGAUGCAGAAAUCUUUCC	chr13:43232308-43232509(+)$1	201	112	134	14.0817
UCUGUGUUAAAGGCAACACAGG	chr2:103988340-103988541(-)$1	201	7	29	14.0817
guucugugauuuuauacaguuu	chr6:90332767-90332968(+)$1	201	24	46	12.3153
GUUCAUUGCCUUUUUAAGGACG	chr6:126589283-126589484(-)$1	201	27	49	13.9304
UGGGAAGCGUAACUGCUUUUAG	chr2:165609674-165609875(-)$1	201	133	155	11.0548
UCUGUGUUAAAGGCAACACAGG	chr2:103988339-103988540(-)$1	201	6	28	14.0817

#DB
((...(((......)))...))	chr16:49911604-49911805(+)$1	1	15	37	12.9599
((((((((......))))))))	chr2:102624838-102625039(+)$1	1	40	62	14.0817
(((.((((......)))).)))	chr19:44368622-44368823(+)$1	1	170	192	11.1312
.(((((((......))))))).	chr3:72852070-72852271(-)$1	1	175	197	11.4642
(..(((((......)))))..)	chr2:25325143-25325344(-)$1	1	131	153	12.1047
(....(((......)))..)))	chr1:157899928-157900129(+)$1	1	155	177	13.1768
(....(((......)))))))(	chr1:121555658-121555859(-)$1	1	3	25	12.3664
(((...((......)).)))))	chr17:25957905-25958106(+)$1	1	22	44	13.1029
(((..(((......))).))))	chr15:9126781-9126982(+)$1	1	153	175	13.1398
((.(((((......))))).))	chr1:78702937-78703138(+)$1	1	57	79	12.6109
((((.(((......))))))))	chr5:138200860-138201061(+)$1	1	8	30	13.2606
((((((.(......))))))).	chr14:120724246-120724447(+)$1	1	105	127	10.8909
((((.(((......))).).))	chr2:102624532-102624733(+)$1	1	50	72	13.6715
((((((((......))))).))	chr16:36035810-36036011(+)$1	1	87	109	11.5935
((((((((......))))))))	chr13:43232300-43232501(+)$1	1	120	142	13.5419
((((((((......))))....	chr3:126624609-126624810(-)$1	1	98	120	11.5825
..(((.((......)).)))..	chr6:115569038-115569239(-)$1	1	138	160	12.6167
((((.(((......)))...))	chr14:65430470-65430671(-)$1	1	75	97	13.1827
(.((((((......))))))))	chr17:28883213-28883414(+)$1	1	91	113	11.8648
...(((((......)))))...	chr2:25325106-25325307(-)$1	1	105	127	13.0719
((.(((.(......).))).))	chr4:32668176-32668377(+)$1	1	135	157	12.4095
((.(((((......))))).))	chr11:74489934-74490135(-)$1	1	57	79	13.1087
((((.(((......)))..)))	chr8:125153259-125153460(-)$1	1	139	161	12.4040
(..(((((......))))).))	chr11:53291016-53291217(-)$1	1	34	56	12.8318
.(((((((......))))))).	chr1:153666291-153666492(+)$1	1	131	153	13.4522
..(((.((......)).)))..	chr2:31148285-31148486(+)$1	1	173	195	12.3309
.(((((((......))))))).	chr11:119868683-119868884(-)$1	1	113	135	13.4837
)(((((((......))))))).	chr2:102622374-102622575(+)$1	1	75	97	12.4413
.((((.((......)).)))).	chr8:73279798-73279999(+)$1	1	48	70	11.5385
((....((......))...)))	chrX:162825047-162825248(+)$1	1	7	29	12.9598
.(((((((......))))))).	chr13:21536447-21536648(-)$1	1	103	125	11.4642
((((.(((......))).))))	chr8:86464161-86464362(+)$1	1	6	28	14.2476
((((.(((......))).))))	chr8:13019494-13019695(+)$1	1	57	79	13.4439
((((.(((......)))....)	chr3:80491784-80491985(-)$1	1	66	88	13.4532
(....(((......)))..)))	chr1:157899929-157900130(+)$1	1	154	176	13.1768
((((.(((......))).))))	chr8:13019495-13019696(+)$1	1	56	78	13.4439
...(((((......)))))...	chr2:25325107-25325308(-)$1	1	106	128	13.0719
)(((((((......))))))).	chr2:102622375-102622576(+)$1	1	74	96	12.4413
((((.(((......))).))))	chr5:43677679-43677880(+)$1	1	112	134	14.0739
((((.(.(......).).))))	chr6:124997803-124998004(+)$1	1	48	70	12.2193
.((((.((......)).)))).	chr8:73279799-73280000(+)$1	1	47	69	11.5385
..(((.((......)).)))..	chr6:115569039-115569240(-)$1	1	139	161	12.6167
(((..(((......))))))))	chr17:66687050-66687251(-)$1	1	115	137	13.2691
((.(((((......))))).))	chr11:74489933-74490134(-)$1	1	56	78	13.1087
.(((..((......)).))).)	chr13:74440918-74441119(-)$1	1	125	147	12.5421
(.((.(((......))).))))	chr10:63392669-63392870(-)$1	1	4	26	12.4808
((((((((......))))))))	chr13:43232308-43232509(+)$1	1	112	134	14.0817
((((((((......))))))))	chr2:103988340-103988541(-)$1	1	7	29	14.0817
(..(((((......)))))..)	chr6:90332767-90332968(+)$1	1	24	46	12.3153
((((.(((......))))))))	chr6:126589283-126589484(-)$1	1	27	49	13.9304
((((((((......))))))..	chr2:165609674-165609875(-)$1	1	133	155	11.0548
((((((((......))))))))	chr2:103988339-103988540(-)$1	1	6	28	14.0817

#PSSM
e : 0.17	= : 0.11	c : 0.11	d : 0.09	[ : 0.09	f : 0.07	b : 0.05	i : 0.05	! : 0.05	g : 0.05	: : 0.03	" : 0.03	h : 0.01	
g : 0.17	= : 0.11	! : 0.11	e : 0.11	d : 0.09	f : 0.07	# : 0.05	i : 0.05	c : 0.05	b : 0.03	[ : 0.03	" : 0.03	h : 0.01	
g : 0.15	f : 0.11	e : 0.11	c : 0.09	= : 0.07	# : 0.07	[ : 0.07	d : 0.07	" : 0.05	! : 0.05	i : 0.05	h : 0.01	b : 0.01	
e : 0.26	g : 0.15	c : 0.09	= : 0.07	# : 0.07	f : 0.07	d : 0.07	" : 0.03	! : 0.03	i : 0.03	[ : 0.01	a : 0.01	b : 0.01	
[ : 0.23	e : 0.17	g : 0.11	= : 0.07	d : 0.07	# : 0.07	c : 0.07	! : 0.05	f : 0.05	" : 0.03	i : 0.01	
c : 0.34	e : 0.17	g : 0.11	[ : 0.09	= : 0.07	f : 0.05	d : 0.03	" : 0.01	i : 0.01	# : 0.01	a : 0.01	! : 0.01	
c : 0.32	e : 0.17	b : 0.15	g : 0.11	= : 0.07	[ : 0.05	d : 0.03	f : 0.03	i : 0.01	
c : 0.32	e : 0.17	b : 0.15	g : 0.11	= : 0.07	a : 0.05	d : 0.03	f : 0.03	i : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
c : 0.32	e : 0.17	b : 0.15	g : 0.11	= : 0.07	a : 0.05	d : 0.03	f : 0.03	i : 0.01	
c : 0.32	e : 0.17	b : 0.15	g : 0.11	= : 0.07	f : 0.05	d : 0.03	] : 0.03	i : 0.01	
c : 0.34	e : 0.17	] : 0.13	g : 0.11	= : 0.07	f : 0.05	d : 0.03	i : 0.01	3 : 0.01	a : 0.01	
e : 0.21	] : 0.15	g : 0.13	d : 0.09	c : 0.09	= : 0.07	3 : 0.05	2 : 0.05	f : 0.05	i : 0.03	4 : 0.01	
e : 0.24	g : 0.15	f : 0.09	c : 0.09	= : 0.07	3 : 0.05	2 : 0.05	d : 0.05	i : 0.05	4 : 0.03	] : 0.01	a : 0.01	b : 0.01	
g : 0.17	] : 0.13	f : 0.11	e : 0.11	3 : 0.07	= : 0.07	d : 0.07	c : 0.07	i : 0.05	2 : 0.03	4 : 0.03	b : 0.01	
g : 0.17	e : 0.13	= : 0.11	d : 0.11	f : 0.07	2 : 0.07	c : 0.07	4 : 0.07	i : 0.05	3 : 0.03	b : 0.01	h : 0.01	] : 0.01	
e : 0.15	= : 0.11	: : 0.09	d : 0.09	c : 0.07	4 : 0.07	f : 0.05	i : 0.05	] : 0.05	g : 0.05	b : 0.03	3 : 0.03	2 : 0.03	G : 0.01	h : 0.01	

#score	664.5159087480023
#seq	52
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_CDS_m2_run2.txt

#BEAR
ggggg[ffffffmmmmffffffgggggg	chr2:174125804-174126076(+)$1	272	238	266	10.4205
cc!!eeeee[bbmmmmbb22eeeee444	chr7:27949815-27950086(-)$1	271	95	123	10.5377
[ggggggg!!bbmmmmbbggggggg22b	chr12:85733283-85733552(-)$1	269	166	194	11.6185
========!!bbmmmmbb333=======	chr7:28151313-28151603(-)$1	290	4	32	12.1399
$$$eeeee[cccmmmmccc]eeeee777	chr4:33125089-33125364(+)$1	275	206	234	9.0367
bb[ffffff[bbmmmmbb22ffffff]b	chr17:6084525-6084804(+)$1	279	21	49	9.7277
[ggggggg!!ddddllldddd333gggg	chr8:74842841-74843113(+)$1	272	77	105	8.5908
c[dddd"""cccmmmmccc4444dddd]	chr1:36501838-36502111(-)$1	273	94	122	9.3435
:eeeeeffffffmmmmffffff333eee	chr19:8964904-8965185(+)$1	281	166	194	8.5321
:gggggggddddllldddd]gggggggc	chr9:98390942-98391210(+)$1	268	206	234	8.0994
ggggggg!!cccnnnnnccc22gggggg	chr8:63405926-63406223(-)$1	297	192	220	10.1018
=====gggggggooooooggggggg999	chr13:24843895-24844177(-)$1	282	21	49	8.1536
"""ffffff[annnnna]ffffff333e	chr13:69138016-69138287(-)$1	271	211	239	9.0792
bggggggg[ddddlllddddggggggg:	chr11:70466238-70466523(-)$1	285	150	178	8.3375
gggggg[bb[bblllbb]bb]ggggggg	chr2:91803312-91803591(-)$1	279	58	86	8.8459
ggg[bb[a[cccmmmmccc]abbggggg	chr5:75006662-75006928(-)$1	266	144	172	10.4643
b[ffffffcccooooooccc22ffffff	chr11:102978351-102978633(+)$1	282	74	102	8.6176
========[cccmmmmccc]========	chr14:45912564-45912838(-)$1	274	24	52	12.3282
ee!!eeeee[bbmmmmbb]eeeee22ee	chr4:151560200-151560489(+)$1	289	183	211	9.9014
iiiiiii"""ccclllccc22iiiiiii	chr10:79879360-79879636(-)$1	276	185	213	10.8304
fffff####cccmmmmccc333ffffff	chr7:135038927-135039193(-)$1	266	194	222	10.4558
[ggggggg!!bbnnnnnbbgggggggcc	chr5:93697524-93697808(+)$1	284	37	65	9.8118
ca[a!!ffffffnnnnnffffff22a]a	chr3:51288320-51288588(+)$1	268	123	151	8.3600
!!eeeeeeeeeemmmmeeeee22eeeee	chr11:87794777-87795061(-)$1	284	25	53	8.1995
gg[eeeee[cccmmmmccc22eeeee]g	chr7:25670028-25670303(+)$1	275	60	88	11.3709
ccc####ggggggglllggggggg333c	chr19:7273741-7274022(-)$1	281	39	67	8.8633
ccca[ccc[cccmmmmcccccc]a333c	chr1:93275013-93275289(-)$1	276	190	218	11.1963
ggggggg"""bbmmmmbb4444gggggg	chr1:181447940-181448228(-)$1	288	0	28	11.3350
ccc!!bb[a[ammmma]a]bb]ccc22a	chr7:52631886-52632163(-)$1	277	11	39	8.1221
bb[eeeee!!ccclllccc22eeeee]b	chr9:107159263-107159531(-)$1	268	140	168	10.0571
ccc[ffffffaooooooa]ffffff]cc	chr16:36049850-36050132(-)$1	282	48	76	9.1980
iiiiiiii[cccmmmmccciiiiiiiii	chr6:54767244-54767517(+)$1	273	162	190	11.5647
cc!!a[ffffffmmmmffffff]a22cc	chr2:31615419-31615714(+)$1	295	74	102	9.9489
b[ffffff[cccmmmmccc]ffffff]b	chr3:95464619-95464908(+)$1	289	173	201	10.8365
ccc!!dddd[bboooooobb]dddd22c	chr14:70066965-70067244(+)$1	279	182	210	7.7503
#eeeee[ggggggglllggggggg333e	chr19:29086354-29086641(+)$1	287	34	62	9.0214
gggggg[ffffffmmmmffffffggggg	chr2:174125832-174126111(+)$1	279	209	237	9.2835
[a!!eeeee[ccclllccc]eeeeeabb	chr2:34678076-34678352(-)$1	276	19	47	9.9739
[eeeee!!cccnnnnnccc]eeeee]dd	chrX:98514856-98515126(+)$1	270	217	245	8.8069
cceeeeebb[bbmmmmbb]bb333eeee	chr2:156359444-156359715(+)$1	271	214	242	9.0516
eeeee"""ddddmmmmddddeeeee22c	chr8:28383689-28383967(+)$1	278	117	145	8.6851

#otherMatches

#Seq PSSM
UGGGGUGGGCCCUUCGGGGCUCCCCCGG	chr2:174125804-174126076(+)$1	272	238	266	10.4205
GGCUGAGGGAGGAAGUCCAGCCCUCUGC	chr7:27949815-27950086(-)$1	271	95	123	10.5377
UGAGCAGAAAGCCCAGGCUCUGCUCUUG	chr12:85733283-85733552(-)$1	269	166	194	11.6185
GGGGUGGGGGGUGAGGGCAGGUCCAUCU	chr7:28151313-28151603(-)$1	290	4	32	12.1399
CCUGCUAACAGUAAGAGCUCUUGGCUUU	chr4:33125089-33125364(+)$1	275	206	234	9.0367
CAUUGAUGACACGCACGUCUUCGUCAUU	chr17:6084525-6084804(+)$1	279	21	49	9.7277
UGCCUGCCGCGCCUAUAAGGCCUGGGUG	chr8:74842841-74843113(+)$1	272	77	105	8.5908
ACGGGGCCAAGCUUUUGCUCUUUCUCCU	chr1:36501838-36502111(-)$1	273	94	122	9.3435
UGGAAAAAAUAUUAGCAUAUUUCACUUU	chr19:8964904-8965185(+)$1	281	166	194	8.5321
AGACUGGUCCUUGAGGAGGUGCUAGUUU	chr9:98390942-98391210(+)$1	268	206	234	8.0994
UAGGUAAUAGGAUCGAUUCUGUUUGCUU	chr8:63405926-63406223(-)$1	297	192	220	10.1018
GUAGUAGAUUUCCGUUUUGAGGUCUUGA	chr13:24843895-24844177(-)$1	282	21	49	8.1536
CCCGGGACUGGCUCUACGAGUCCUACUA	chr13:69138016-69138287(-)$1	271	211	239	9.0792
GACGGGGAAUUUACAAUGGAUCUUCGUA	chr11:70466238-70466523(-)$1	285	150	178	8.3375
GCUCCGAGCGCGACGCGGGUCCGGAGCC	chr2:91803312-91803591(-)$1	279	58	86	8.8459
GCCCAGACAUCUUUCAAGAAGCUGGCUG	chr5:75006662-75006928(-)$1	266	144	172	10.4643
AAGGGGGCCUGAAGCACCAGCUGCCCCC	chr11:102978351-102978633(+)$1	282	74	102	8.6176
GAGUUCCAGCAGCGCUUUGAUGGGAUUC	chr14:45912564-45912838(-)$1	274	24	52	12.3282
GACGCCUGGCCAGGAGUGUUCGGGGCUC	chr4:151560200-151560489(+)$1	289	183	211	9.9014
AGUGGGGGGGACUUCUGGUAGCCUCAUU	chr10:79879360-79879636(-)$1	276	185	213	10.8304
CGCGCCCGCGAUGAAAAUUACCGCGCGC	chr7:135038927-135039193(-)$1	266	194	222	10.4558
UGGAGGGAUCGCGGCCAGCUCCUUCUGC	chr5:93697524-93697808(+)$1	284	37	65	9.8118
CCACGAUCGGGGUGGACUUCCGAGAGCG	chr3:51288320-51288588(+)$1	268	123	151	8.3600
AUCGUGGGCCGGAAUUUUGGCAGCUAUG	chr11:87794777-87795061(-)$1	284	25	53	8.1995
GUUGACCUGGACCCACGUCAGGGGUUUG	chr7:25670028-25670303(+)$1	275	60	88	11.3709
GCACCUCAGACUACCUUGUGGUCUACCU	chr19:7273741-7274022(-)$1	281	39	67	8.8633
CUGUGGGGUCACAUCUGUGCCUGAUAUC	chr1:93275013-93275289(-)$1	276	190	218	11.1963
AGGUCCUCCUGCGCAUGCUCACAGGACC	chr1:181447940-181448228(-)$1	288	0	28	11.3350
CACAAGCGUGGGGAGCGGGGCAGUGAGC	chr7:52631886-52632163(-)$1	277	11	39	8.1221
UGAGUAGAUUCUGUCUCAGUCUCUAUAC	chr9:107159263-107159531(-)$1	268	140	168	10.0571
UUGAUUUGAGCAUUAAAGUCUCAAGCCA	chr16:36049850-36050132(-)$1	282	48	76	9.1980
gcgggccgcgUCUGGUGAUCGGCUCGCU	chr6:54767244-54767517(+)$1	273	162	190	11.5647
GGAGCGCGGCCUGGCGGGGCUGGGGGCC	chr2:31615419-31615714(+)$1	295	74	102	9.9489
ACAUGCAUCUGUGAAAACAUGUGUAUUU	chr3:95464619-95464908(+)$1	289	173	201	10.8365
GGGAACCAUCUGCGAUGACAAGUGGGAC	chr14:70066965-70067244(+)$1	279	182	210	7.7503
AAGGUUAUUUUGAAGCAUUCAAAAAUGA	chr19:29086354-29086641(+)$1	287	34	62	9.0214
CUGGGGUGGGCCCUUCGGGGCUCCCCCG	chr2:174125832-174126111(+)$1	279	209	237	9.2835
ACAUGCUGCCUGGUCUCUAAGCAGUGGA	chr2:34678076-34678352(-)$1	276	19	47	9.9739
AUUUCACCUGCCUACAGCAAUGAGAAUG	chrX:98514856-98515126(+)$1	270	217	245	8.8069
AUAGCCCACAGCGAGUGCAGUCAGGGGC	chr2:156359444-156359715(+)$1	271	214	242	9.0516
UCUAUGACCGGAAAUUUCUGAUGGAGUG	chr8:28383689-28383967(+)$1	278	117	145	8.6851

#DB
(((((.((((((....))))))))))))	chr2:174125804-174126076(+)$1	1	238	266	10.4205
((..(((((.((....))..)))))...	chr7:27949815-27950086(-)$1	1	95	123	10.5377
.(((((((..((....)))))))))..)	chr12:85733283-85733552(-)$1	1	166	194	11.6185
((((((((..((....))...)))))))	chr7:28151313-28151603(-)$1	1	4	32	12.1399
...(((((.(((....))).)))))...	chr4:33125089-33125364(+)$1	1	206	234	9.0367
((.((((((.((....))..)))))).)	chr17:6084525-6084804(+)$1	1	21	49	9.7277
.(((((((..((((...))))...))))	chr8:74842841-74843113(+)$1	1	77	105	8.5908
(.((((...(((....)))....)))).	chr1:36501838-36502111(-)$1	1	94	122	9.3435
.(((((((((((....))))))...)))	chr19:8964904-8965185(+)$1	1	166	194	8.5321
.(((((((((((...)))).)))))))(	chr9:98390942-98391210(+)$1	1	206	234	8.0994
(((((((..(((.....)))..))))))	chr8:63405926-63406223(-)$1	1	192	220	10.1018
((((((((((((......)))))))...	chr13:24843895-24844177(-)$1	1	21	49	8.1536
...((((((.(.....).))))))...)	chr13:69138016-69138287(-)$1	1	211	239	9.0792
)(((((((.((((...))))))))))).	chr11:70466238-70466523(-)$1	1	150	178	8.3375
((((((.((.((...)).)).)))))))	chr2:91803312-91803591(-)$1	1	58	86	8.8459
(((.((.(.(((....))).))))))))	chr5:75006662-75006928(-)$1	1	144	172	10.4643
(.(((((((((......)))..))))))	chr11:102978351-102978633(+)$1	1	74	102	8.6176
((((((((.(((....))).))))))))	chr14:45912564-45912838(-)$1	1	24	52	12.3282
((..(((((.((....)).)))))..))	chr4:151560200-151560489(+)$1	1	183	211	9.9014
(((((((...(((...)))..)))))))	chr10:79879360-79879636(-)$1	1	185	213	10.8304
(((((....(((....)))...))))))	chr7:135038927-135039193(-)$1	1	194	222	10.4558
.(((((((..((.....)))))))))))	chr5:93697524-93697808(+)$1	1	37	65	9.8118
((.(..((((((.....))))))..).)	chr3:51288320-51288588(+)$1	1	123	151	8.3600
..((((((((((....)))))..)))))	chr11:87794777-87795061(-)$1	1	25	53	8.1995
((.(((((.(((....)))..))))).)	chr7:25670028-25670303(+)$1	1	60	88	11.3709
(((....(((((((...)))))))...)	chr19:7273741-7274022(-)$1	1	39	67	8.8633
((((.(((.(((....)))))).)...)	chr1:93275013-93275289(-)$1	1	190	218	11.1963
(((((((...((....))....))))))	chr1:181447940-181448228(-)$1	1	0	28	11.3350
(((..((.(.(....).).)).)))..)	chr7:52631886-52632163(-)$1	1	11	39	8.1221
((.(((((..(((...)))..))))).)	chr9:107159263-107159531(-)$1	1	140	168	10.0571
(((.(((((((......).)))))).))	chr16:36049850-36050132(-)$1	1	48	76	9.1980
((((((((.(((....))))))))))))	chr6:54767244-54767517(+)$1	1	162	190	11.5647
((..(.((((((....)))))).)..))	chr2:31615419-31615714(+)$1	1	74	102	9.9489
(.((((((.(((....))).)))))).)	chr3:95464619-95464908(+)$1	1	173	201	10.8365
(((..((((.((......)).))))..)	chr14:70066965-70067244(+)$1	1	182	210	7.7503
.(((((.(((((((...)))))))...)	chr19:29086354-29086641(+)$1	1	34	62	9.0214
((((((.((((((....)))))))))))	chr2:174125832-174126111(+)$1	1	209	237	9.2835
.(..(((((.(((...))).))))))))	chr2:34678076-34678352(-)$1	1	19	47	9.9739
.(((((..(((.....))).))))).))	chrX:98514856-98515126(+)$1	1	217	245	8.8069
))(((((((.((....)).))...))))	chr2:156359444-156359715(+)$1	1	214	242	9.0516
(((((...((((....)))))))))..)	chr8:28383689-28383967(+)$1	1	117	145	8.6851

#PSSM
c : 0.24	g : 0.17	[ : 0.12	b : 0.12	= : 0.07	: : 0.04	e : 0.04	i : 0.04	$ : 0.02	" : 0.02	f : 0.02	! : 0.02	# : 0.02	
g : 0.29	c : 0.19	e : 0.12	= : 0.07	[ : 0.07	b : 0.04	i : 0.04	a : 0.04	$ : 0.02	" : 0.02	f : 0.02	! : 0.02	
g : 0.26	e : 0.14	c : 0.12	! : 0.09	[ : 0.09	= : 0.07	f : 0.07	i : 0.04	$ : 0.02	d : 0.02	" : 0.02	
g : 0.24	e : 0.21	! : 0.14	f : 0.12	= : 0.07	[ : 0.04	i : 0.04	a : 0.04	d : 0.02	# : 0.02	
e : 0.29	g : 0.24	f : 0.14	= : 0.07	! : 0.07	i : 0.04	d : 0.02	b : 0.02	# : 0.02	[ : 0.02	a : 0.02	
e : 0.26	g : 0.24	f : 0.12	[ : 0.04	= : 0.04	d : 0.04	b : 0.04	i : 0.04	# : 0.04	! : 0.02	c : 0.02	" : 0.02	
f : 0.21	e : 0.19	g : 0.19	[ : 0.09	= : 0.04	" : 0.04	i : 0.04	# : 0.04	c : 0.02	b : 0.02	d : 0.02	! : 0.02	
f : 0.24	g : 0.19	e : 0.17	" : 0.09	= : 0.04	! : 0.04	b : 0.04	a : 0.02	# : 0.02	c : 0.02	[ : 0.02	i : 0.02	d : 0.02	
f : 0.19	[ : 0.19	! : 0.14	e : 0.09	" : 0.07	d : 0.07	g : 0.07	b : 0.04	c : 0.04	# : 0.02	a : 0.02	
c : 0.29	[ : 0.21	f : 0.14	! : 0.12	d : 0.07	g : 0.07	" : 0.04	e : 0.02	
c : 0.36	b : 0.24	f : 0.12	d : 0.09	g : 0.07	a : 0.07	e : 0.02	
c : 0.31	b : 0.24	f : 0.12	d : 0.09	g : 0.07	n : 0.04	o : 0.04	e : 0.02	m : 0.02	
m : 0.53	n : 0.12	o : 0.09	c : 0.07	d : 0.04	l : 0.04	g : 0.04	f : 0.02	
m : 0.56	l : 0.14	n : 0.12	o : 0.09	g : 0.04	d : 0.02	
m : 0.56	l : 0.21	n : 0.12	o : 0.09	
m : 0.53	l : 0.17	n : 0.12	o : 0.09	d : 0.02	b : 0.02	a : 0.02	
c : 0.31	b : 0.19	o : 0.09	f : 0.07	l : 0.07	d : 0.07	n : 0.07	a : 0.02	e : 0.02	] : 0.02	m : 0.02	
c : 0.36	b : 0.19	f : 0.12	d : 0.09	o : 0.04	] : 0.04	g : 0.04	a : 0.04	e : 0.02	
c : 0.36	f : 0.14	g : 0.09	d : 0.09	] : 0.09	b : 0.07	2 : 0.04	3 : 0.02	e : 0.02	4 : 0.02	
f : 0.17	] : 0.17	2 : 0.12	g : 0.12	b : 0.09	d : 0.07	c : 0.07	3 : 0.04	4 : 0.04	e : 0.04	i : 0.02	
f : 0.21	e : 0.17	g : 0.17	2 : 0.12	3 : 0.04	4 : 0.04	] : 0.04	b : 0.04	d : 0.02	a : 0.02	= : 0.02	c : 0.02	i : 0.02	
f : 0.21	e : 0.19	g : 0.19	3 : 0.07	2 : 0.07	= : 0.04	4 : 0.04	i : 0.04	b : 0.02	c : 0.02	] : 0.02	d : 0.02	
g : 0.26	e : 0.19	f : 0.19	3 : 0.07	= : 0.04	i : 0.04	] : 0.04	4 : 0.02	b : 0.02	2 : 0.02	c : 0.02	d : 0.02	
g : 0.31	e : 0.21	f : 0.14	3 : 0.07	= : 0.04	d : 0.04	i : 0.04	a : 0.04	2 : 0.02	c : 0.02	
g : 0.29	e : 0.21	f : 0.12	3 : 0.12	2 : 0.07	= : 0.04	d : 0.04	i : 0.04	c : 0.02	
g : 0.24	2 : 0.14	e : 0.12	f : 0.09	3 : 0.09	= : 0.04	i : 0.04	a : 0.04	] : 0.04	4 : 0.02	7 : 0.02	d : 0.02	9 : 0.02	
g : 0.21	] : 0.12	2 : 0.09	e : 0.09	3 : 0.09	c : 0.07	= : 0.04	d : 0.04	f : 0.04	i : 0.04	4 : 0.02	7 : 0.02	9 : 0.02	b : 0.02	
g : 0.19	c : 0.19	e : 0.14	b : 0.12	= : 0.04	f : 0.04	i : 0.04	a : 0.04	4 : 0.02	7 : 0.02	] : 0.02	9 : 0.02	: : 0.02	d : 0.02	

#score	396.60142547598787
#seq	41
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_CDS_m2_run1.txt

#BEAR
fffffftttttttttttffffff	chr17:85139875-85140099(-)$1	224	53	76	21.7495
=eeeeettttttttttteeeee4	chr10:21062107-21062322(+)$1	215	76	99	22.9336
fffffvvvvvvvvvvvvvfffff	chr2:44965477-44965704(-)$1	227	179	202	22.1062
[cccwwwwwwwwwwwwwwccc]c	chr13:101435793-101436017(+)$1	224	163	186	21.7542
eeeeewwwwwwwwwwwwwweeee	chr17:37094683-37094890(-)$1	207	167	190	21.5049
e[cccuuuuuuuuuuuuccc]ee	chr15:85189919-85190129(+)$1	210	81	104	23.9265
hhhhhhttttttttttthhhhhh	chr14:99467501-99467712(+)$1	211	33	56	20.5695
[eeeeettttttttttteeeee2	chr15:57723691-57723899(-)$1	208	177	200	22.9546
fffffftttttttttttffffff	chr13:13598569-13598778(+)$1	209	21	44	21.7495
e!!ccctttttttttttccc]ee	chr15:99463058-99463266(-)$1	208	148	171	23.2456
[ddddwwwwwwwwwwwwwwdddd	chr4:133101670-133101956(-)$1	286	225	248	21.3333
:ddddwwwwwwwwwwwwwwdddd	chr12:81297856-81298083(-)$1	227	125	148	20.1613
ceeeeettttttttttteeeee]	chr8:107046478-107046687(-)$1	209	51	74	22.8456
)eeeeettttttttttteeeee8	chr19:38072668-38072885(-)$1	217	146	169	22.0709
[ddddwwwwwwwwwwwwwwdddd	chr1:84757543-84757773(-)$1	230	74	97	21.3333
iiiiiuuuuuuuuuuuuiiiiii	chr13:9692569-9692803(-)$1	234	36	59	23.2071
ggggguuuuuuuuuuuugggggg	chr15:75900848-75901069(-)$1	221	194	217	23.2461
fffffuuuuuuuuuuuuffffff	chr2:180993717-180993938(-)$1	221	43	66	22.4576
"dddduuuuuuuuuuuudddd33	chr3:89539889-89540109(+)$1	220	98	121	23.3331
c[cccuuuuuuuuuuuuccc22c	chr10:28194955-28195161(+)$1	206	119	142	23.5764
#eeeeettttttttttteeeee4	chr3:68825167-68825394(+)$1	227	135	158	22.9780
d[bbwwwwwwwwwwwwwwbb]dd	chr15:35527142-35527364(+)$1	222	68	91	20.0541
""cccwwwwwwwwwwwwwwcccd	chr4:155270143-155270365(+)$1	222	123	146	21.7437
fffffuuuuuuuuuuuuffffff	chrX:12185878-12186109(+)$1	231	54	77	22.4576
!!cccuuuuuuuuuuuuccc22g	chr17:29136858-29137087(-)$1	229	107	130	23.8148
""cccuuuuuuuuuuuuccc333	chr14:21350899-21351142(-)$1	243	83	106	24.0940
e[cccvvvvvvvvvvvvvcccee	chr15:102328834-102329051(+)$1	217	29	52	23.3231
iiiiiuuuuuuuuuuuuiiiiii	chr9:56107659-56107874(-)$1	215	149	172	23.2071
ceeeeettttttttttteeeee3	chr8:124320486-124320698(-)$1	212	133	156	22.9162
eeeeevvvvvvvvvvvvveeeee	chrX:130595487-130595704(+)$1	217	77	100	22.8469
&ddddtttttttttttdddd444	chr15:82968644-82968870(-)$1	226	147	170	20.6605
e[cccwwwwwwwwwwwwwwccc]	chr8:113838864-113839091(-)$1	227	65	88	21.9338
bbddddtttttttttttdddd]b	chr2:32222887-32223102(+)$1	215	147	170	21.5258
g[ddddtttttttttttdddd22	chr8:3514933-3515154(+)$1	221	45	68	22.4776
ff[bbuuuuuuuuuuuubb]fff	chr3:107477841-107478061(-)$1	220	73	96	21.8176
c[cccuuuuuuuuuuuuccc]cc	chr1:20804759-20804980(-)$1	221	113	136	23.9014
gg[ccctttttttttttccc]gg	chr19:10175787-10176000(-)$1	213	42	65	23.2674
!!ddddtttttttttttdddd]e	chr11:23185801-23186031(+)$1	230	88	111	22.7676
eyyyyyyyyyyyyyyyyeeeee]	chr9:37464687-37464913(-)$1	226	143	166	19.4579
!!cccvvvvvvvvvvvvvccc22	chr9:25108979-25109205(+)$1	226	169	192	23.4248
fffffftttttttttttffffff	chr9:66896828-66897061(-)$1	233	0	23	21.7495
!eeeeettttttttttteeeee>	chr3:138531228-138531449(+)$1	221	69	92	22.9114
geeeeettttttttttteeeee>	chr15:4051722-4051944(+)$1	222	175	198	22.7446
:dddduuuuuuuuuuuuddddFF	chr7:35709358-35709570(+)$1	212	3	26	21.1455
iiiiivvvvvvvvvvvvviiiii	chr19:5902327-5902585(-)$1	258	78	101	22.8306
!!cccxxxxxxxxxxxxxxxccc	chr2:118649076-118649296(+)$1	220	76	99	17.1166
hhhhhhttttttttttthhhhhh	chr12:101382270-101382489(-)$1	219	128	151	20.5695
!ddddwwwwwwwwwwwwwwdddd	chr9:107646109-107646335(-)$1	226	33	56	21.3394
gggccctttttttttttccc:::	chrX:97821715-97821935(+)$1	220	86	109	20.2341
hhhhhuuuuuuuuuuuuhhhhhh	chr8:108719186-108719411(+)$1	225	80	103	21.5490

#otherMatches

#Seq PSSM
GAUAAUUUUUUUUCUUCAUUGUC	chr17:85139875-85140099(-)$1	224	53	76	21.7495
CCCUGAAUCAAUUUUCCUUAGGU	chr10:21062107-21062322(+)$1	215	76	99	22.9336
GCCCGAACCAAACUUUUCCGGGC	chr2:44965477-44965704(-)$1	227	179	202	22.1062
AAAGAUCAUAACCCUUAACUUAG	chr13:101435793-101436017(+)$1	224	163	186	21.7542
CCUGGUUUUGCACUCCAUUCCAG	chr17:37094683-37094890(-)$1	207	167	190	21.5049
GCAGCUAAUCACUGAAUGCUUCA	chr15:85189919-85190129(+)$1	210	81	104	23.9265
AUUGCUGAGAAAGAGCGAGCAGU	chr14:99467501-99467712(+)$1	211	33	56	20.5695
CGAAGCCUUCCUCUAUCGCUUCC	chr15:57723691-57723899(-)$1	208	177	200	22.9546
GCUUCCUUCCAGAUCUUGGAAGC	chr13:13598569-13598778(+)$1	209	21	44	21.7495
GGGUCCUAAACACACCUGGAGUC	chr15:99463058-99463266(-)$1	208	148	171	23.2456
GGCGUGCAGGAGGUAAACGACGU	chr4:133101670-133101956(-)$1	286	225	248	21.3333
AGACAGCCCCAUAUAAAAAUGUC	chr12:81297856-81298083(-)$1	227	125	148	20.1613
AUUUUAAAGAAUGAAAAUGGAGC	chr8:107046478-107046687(-)$1	209	51	74	22.8456
CUCCCUGCUAAAUGAAAAGGGAC	chr19:38072668-38072885(-)$1	217	146	169	22.0709
UGCAGAAACACUUCACUUCCUGC	chr1:84757543-84757773(-)$1	230	74	97	21.3333
AAAAUGAAAGGUUUUGGGUUUUG	chr13:9692569-9692803(-)$1	234	36	59	23.2071
GGCCUCAGAGACUCACAAGGCCA	chr15:75900848-75901069(-)$1	221	194	217	23.2461
GAGAUAUUUUUAGUUAGGUCUCA	chr2:180993717-180993938(-)$1	221	43	66	22.4576
GUAUCCACACAGCACCAGGUGAG	chr3:89539889-89540109(+)$1	220	98	121	23.3331
UGACCACAAAUAUCUCAGGUAAG	chr10:28194955-28195161(+)$1	206	119	142	23.5764
GGCUUCAGAAAGAAAAGGAGGUA	chr3:68825167-68825394(+)$1	227	135	158	22.9780
UCCUGAAGACAAAAUGAAAGAAU	chr15:35527142-35527364(+)$1	222	68	91	20.0541
AACUGGACAAGGUAAGAGACAGA	chr4:155270143-155270365(+)$1	222	123	146	21.7437
GUCAUAAUGUUAAAGAAGUGACU	chrX:12185878-12186109(+)$1	231	54	77	22.4576
CGCUCAACAUGAAGAACGAGAAA	chr17:29136858-29137087(-)$1	229	107	130	23.8148
CGGCUGACAUCUGAAGAAGUGUU	chr14:21350899-21351142(-)$1	243	83	106	24.0940
UUGGUGUGAUGAAUUGUAGCUAG	chr15:102328834-102329051(+)$1	217	29	52	23.3231
UUUUCAGUAACAUGGAGGAGGAG	chr9:56107659-56107874(-)$1	215	149	172	23.2071
UGGCCCGGAGCCAUGUGGGGCCU	chr8:124320486-124320698(-)$1	212	133	156	22.9162
CAUGCGGAACUUGAAUGGGCGUG	chrX:130595487-130595704(+)$1	217	77	100	22.8469
AUGCUGAACUCACGAAAGCAGCA	chr15:82968644-82968870(-)$1	226	147	170	20.6605
AUCCUAUUUUUUCCAUGCCAGGC	chr8:113838864-113839091(-)$1	227	65	88	21.9338
ACCACCCCCAAUCGCAAGGUGAG	chr2:32222887-32223102(+)$1	215	147	170	21.5258
ACUGGGUGCCUCUUUUUUCCAUU	chr8:3514933-3515154(+)$1	221	45	68	22.4776
GUGUGAAGAACAUCAAGCAGGCA	chr3:107477841-107478061(-)$1	220	73	96	21.8176
CUGGUGGAUAAAGUGAAGCCUGG	chr1:20804759-20804980(-)$1	221	113	136	23.9014
GAGGCCGUAGCGCACGGGGCAUC	chr19:10175787-10176000(-)$1	213	42	65	23.2674
ACUCCCUAAUCAAGUGUGGGACA	chr11:23185801-23186031(+)$1	230	88	111	22.7676
CAUCCCCUCCGCGCCCCGGAGCU	chr9:37464687-37464913(-)$1	226	143	166	19.4579
AAAAAAAAACACUAAAUAUUUCA	chr9:25108979-25109205(+)$1	226	169	192	23.4248
CCCUGGGAAAGUACAUAUCAGGG	chr9:66896828-66897061(-)$1	233	0	23	21.7495
CUUCUCUUUCAGUUUUUGGGAAU	chr3:138531228-138531449(+)$1	221	69	92	22.9114
UUCUGAAUUACAUUGGGUCAGAA	chr15:4051722-4051944(+)$1	222	175	198	22.7446
UGGUCAUUGGGUAAUGAGGCCCC	chr7:35709358-35709570(+)$1	212	3	26	21.1455
UUCUUUUUCCCUAUAGCCAAGAA	chr19:5902327-5902585(-)$1	258	78	101	22.8306
CAGCUACAAACCGUUUAAUAAGC	chr2:118649076-118649296(+)$1	220	76	99	17.1166
CUAAGAAACAGUGUAUAUCUUGG	chr12:101382270-101382489(-)$1	219	128	151	20.5695
UGACUUUUCAUAUUAAAGUAGUC	chr9:107646109-107646335(-)$1	226	33	56	21.3394
GGUACCAUGAAAGAAGAGGUGAA	chrX:97821715-97821935(+)$1	220	86	109	20.2341
CAUGACACUUAUCUACCUCGUGG	chr8:108719186-108719411(+)$1	225	80	103	21.5490

#DB
((((((...........))))))	chr17:85139875-85140099(-)$1	1	53	76	21.7495
((((((...........))))).	chr10:21062107-21062322(+)$1	1	76	99	22.9336
(((((.............)))))	chr2:44965477-44965704(-)$1	1	179	202	22.1062
.(((..............))).)	chr13:101435793-101436017(+)$1	1	163	186	21.7542
(((((..............))))	chr17:37094683-37094890(-)$1	1	167	190	21.5049
(.(((............))).))	chr15:85189919-85190129(+)$1	1	81	104	23.9265
((((((...........))))))	chr14:99467501-99467712(+)$1	1	33	56	20.5695
.(((((...........))))).	chr15:57723691-57723899(-)$1	1	177	200	22.9546
((((((...........))))))	chr13:13598569-13598778(+)$1	1	21	44	21.7495
(..(((...........))).))	chr15:99463058-99463266(-)$1	1	148	171	23.2456
.((((..............))))	chr4:133101670-133101956(-)$1	1	225	248	21.3333
.((((..............))))	chr12:81297856-81298083(-)$1	1	125	148	20.1613
((((((...........))))).	chr8:107046478-107046687(-)$1	1	51	74	22.8456
.(((((...........))))).	chr19:38072668-38072885(-)$1	1	146	169	22.0709
.((((..............))))	chr1:84757543-84757773(-)$1	1	74	97	21.3333
(((((............))))))	chr13:9692569-9692803(-)$1	1	36	59	23.2071
(((((............))))))	chr15:75900848-75901069(-)$1	1	194	217	23.2461
(((((............))))))	chr2:180993717-180993938(-)$1	1	43	66	22.4576
.((((............))))..	chr3:89539889-89540109(+)$1	1	98	121	23.3331
(.(((............)))..)	chr10:28194955-28195161(+)$1	1	119	142	23.5764
.(((((...........))))).	chr3:68825167-68825394(+)$1	1	135	158	22.9780
(.((..............)).))	chr15:35527142-35527364(+)$1	1	68	91	20.0541
..(((..............))))	chr4:155270143-155270365(+)$1	1	123	146	21.7437
(((((............))))))	chrX:12185878-12186109(+)$1	1	54	77	22.4576
..(((............)))..)	chr17:29136858-29137087(-)$1	1	107	130	23.8148
..(((............)))...	chr14:21350899-21351142(-)$1	1	83	106	24.0940
(.(((.............)))))	chr15:102328834-102329051(+)$1	1	29	52	23.3231
(((((............))))))	chr9:56107659-56107874(-)$1	1	149	172	23.2071
((((((...........))))).	chr8:124320486-124320698(-)$1	1	133	156	22.9162
(((((.............)))))	chrX:130595487-130595704(+)$1	1	77	100	22.8469
.((((...........))))...	chr15:82968644-82968870(-)$1	1	147	170	20.6605
(.(((..............))).	chr8:113838864-113839091(-)$1	1	65	88	21.9338
((((((...........)))).)	chr2:32222887-32223102(+)$1	1	147	170	21.5258
(.((((...........))))..	chr8:3514933-3515154(+)$1	1	45	68	22.4776
((.((............)).)))	chr3:107477841-107478061(-)$1	1	73	96	21.8176
(.(((............))).))	chr1:20804759-20804980(-)$1	1	113	136	23.9014
((.(((...........))).))	chr19:10175787-10176000(-)$1	1	42	65	23.2674
..((((...........)))).)	chr11:23185801-23186031(+)$1	1	88	111	22.7676
(................))))).	chr9:37464687-37464913(-)$1	1	143	166	19.4579
..(((.............)))..	chr9:25108979-25109205(+)$1	1	169	192	23.4248
((((((...........))))))	chr9:66896828-66897061(-)$1	1	0	23	21.7495
.(((((...........))))).	chr3:138531228-138531449(+)$1	1	69	92	22.9114
((((((...........))))).	chr15:4051722-4051944(+)$1	1	175	198	22.7446
.((((............))))((	chr7:35709358-35709570(+)$1	1	3	26	21.1455
(((((.............)))))	chr19:5902327-5902585(-)$1	1	78	101	22.8306
..(((...............)))	chr2:118649076-118649296(+)$1	1	76	99	17.1166
((((((...........))))))	chr12:101382270-101382489(-)$1	1	128	151	20.5695
.((((..............))))	chr9:107646109-107646335(-)$1	1	33	56	21.3394
)))(((...........)))...	chrX:97821715-97821935(+)$1	1	86	109	20.2341
(((((............))))))	chr8:108719186-108719411(+)$1	1	80	103	21.5490

#PSSM
f : 0.14	e : 0.14	! : 0.12	g : 0.10	[ : 0.08	c : 0.08	h : 0.06	i : 0.06	" : 0.06	: : 0.04	= : 0.02	) : 0.02	# : 0.02	d : 0.02	& : 0.02	b : 0.02	
e : 0.19	f : 0.14	[ : 0.14	d : 0.14	! : 0.10	h : 0.06	i : 0.06	g : 0.06	" : 0.04	c : 0.02	b : 0.02	y : 0.02	
c : 0.21	e : 0.19	d : 0.19	f : 0.12	h : 0.06	i : 0.06	g : 0.04	[ : 0.04	! : 0.02	b : 0.02	y : 0.02	
c : 0.27	e : 0.19	d : 0.19	f : 0.12	h : 0.06	i : 0.06	b : 0.04	g : 0.02	y : 0.02	
c : 0.25	e : 0.19	d : 0.19	f : 0.12	h : 0.06	i : 0.06	w : 0.04	g : 0.02	b : 0.02	y : 0.02	
u : 0.27	w : 0.18	e : 0.16	v : 0.10	f : 0.06	c : 0.06	d : 0.06	h : 0.04	t : 0.02	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.40	u : 0.27	w : 0.18	v : 0.10	y : 0.02	x : 0.02	
t : 0.38	u : 0.27	w : 0.18	v : 0.10	d : 0.02	y : 0.02	x : 0.02	
e : 0.18	w : 0.18	c : 0.16	d : 0.12	f : 0.10	v : 0.10	h : 0.06	i : 0.04	g : 0.02	b : 0.02	x : 0.02	
c : 0.21	e : 0.19	w : 0.14	f : 0.12	d : 0.12	h : 0.06	i : 0.06	b : 0.04	g : 0.02	x : 0.02	
c : 0.25	e : 0.21	d : 0.19	f : 0.12	h : 0.06	i : 0.06	g : 0.02	b : 0.02	] : 0.02	x : 0.02	
e : 0.21	d : 0.18	f : 0.14	c : 0.12	] : 0.10	h : 0.06	i : 0.06	2 : 0.04	g : 0.02	3 : 0.02	4 : 0.02	: : 0.02	
e : 0.27	f : 0.14	d : 0.10	2 : 0.08	c : 0.08	] : 0.06	h : 0.06	i : 0.06	g : 0.04	3 : 0.04	4 : 0.02	F : 0.02	: : 0.02	
f : 0.14	e : 0.12	d : 0.12	c : 0.08	4 : 0.06	h : 0.06	2 : 0.06	] : 0.06	i : 0.06	g : 0.06	3 : 0.06	> : 0.04	8 : 0.02	b : 0.02	F : 0.02	: : 0.02	

#score	1106.9210746312012
#seq	50
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_CDS_m3_run1.txt

#BEAR
eeee[ddddqqqqqqqqdddd]eeeee	chr11:84284087-84284293(-)$1	206	149	176	16.7438
ddddd[cccqqqqqqqqccc]dddd44	chr2:130639840-130640046(-)$1	206	110	137	15.9920
dddd[ddddqqqqqqqqdddd]dddd:	chr9:65551058-65551283(-)$1	225	196	223	15.8454
ffff[ddddqqqqqqqqdddd]fffff	chr12:83503972-83504191(+)$1	219	176	203	16.3049
dddd!!cccqqqqqqqqccc22dddd]	chr14:21510646-21510852(+)$1	206	75	102	16.8255
eeeeeddddqqqqqqqqdddd]eeeee	chr12:111867698-111867919(+)$1	221	144	171	16.3818
d"""eeeeeqqqqqqqqeeeee]dddd	chr7:138105488-138105735(+)$1	247	48	75	16.2109
hhh[a[cccqqqqqqqqccc]a]hhhh	chr8:114364219-114364451(-)$1	232	201	228	15.8580
bbgggggggqqqqqqqqggggggg]bb	chr15:79368938-79369170(-)$1	232	61	88	15.0259
ddddeeeeeqqqqqqqqeeeee333dd	chr15:79367841-79368071(-)$1	230	1	28	16.0728
!bb[eeeeeqqqqqqqqeeeeebb22b	chrX:70704095-70704329(-)$1	234	48	75	14.4620
gg####cccqqqqqqqqccc333gggg	chr2:124923658-124923908(-)$1	250	60	87	18.2321
[dddd!!bbqqqqqqqqbb22ddddff	chr4:106019128-106019337(+)$1	209	149	176	14.4881
iiiiiiiiiqqqqqqqqiiiiiiiii5	chr12:80386158-80386379(-)$1	221	172	199	15.5394
[ddddddddqqqqqqqqdddd333ddd	chr9:121657082-121657302(+)$1	220	148	175	17.1537
cc[ffffffqqqqqqqqffffffccc2	chr4:59220653-59220868(+)$1	215	146	173	14.6868
dd"""ddddqqqqqqqqdddd]dddd4	chr1:36929263-36929483(-)$1	220	68	95	17.4860
eee!!ddddqqqqqqqqdddd]eeeee	chr12:103717735-103717955(+)$1	220	5	32	17.1750
e"""eeeeeqqqqqqqqeeeee4444e	chr1:189057739-189057946(+)$1	207	132	159	16.8484
dd"""ddddqqqqqqqqdddd22dddd	chr1:181716838-181717070(-)$1	232	112	139	17.4491
eea!!ddddqqqqqqqqdddd4444a]	chr7:63143147-63143357(+)$1	210	132	159	18.0990
:eeeeecccqqqqqqqqccc333eeee	chr3:130818272-130818478(+)$1	206	71	98	16.0656
gggggg[bbqqqqqqqqbbggggggg:	chr1:89812865-89813082(+)$1	217	148	175	14.6909
b####bbbbqqqqqqqqbb]bb333bb	chr5:66035167-66035392(-)$1	225	122	149	15.0674
iiiiiiiiiqqqqqqqqiiiiiiiii:	chr5:124210249-124210482(+)$1	233	25	52	15.3973
#ccc[a[bbqqqqqqqqbb]a]cccee	chr11:23243497-23243719(+)$1	222	86	113	16.0263
ggggg[cccqqqqqqqqcccggggggg	chrX:65941367-65941585(+)$1	218	10	37	16.7432
e[gggggggqqqqqqqqggggggg]ee	chr5:86458070-86458293(-)$1	223	191	218	15.9875
eeee!!cccqqqqqqqqccc22eeeee	chr8:47294674-47294894(-)$1	220	98	125	16.8133
eee"""cccqqqqqqqqccc333eeee	chr2:120648218-120648438(-)$1	220	183	210	17.8816
c"""eeeeeqqqqqqqqeeeee22ccc	chr15:77638275-77638514(-)$1	239	156	183	16.4808
dddd[ddddqqqqqqqqdddd333ddd	chr5:116438409-116438632(+)$1	223	37	64	17.5210
##a[eeeeeqqqqqqqqeeeeea333d	chr3:121471461-121471677(-)$1	216	140	167	16.4585
ff[a[ddddqqqqqqqqdddda22fff	chr13:49783895-49784101(+)$1	206	60	87	16.7440
!!ccc[cccqqqqqqqqcccccc]ccc	chr10:62732285-62732523(+)$1	238	39	66	16.9216
ccc!!ddddqqqqqqqqdddd333ccc	chr11:93909742-93909962(+)$1	220	82	109	18.3859
dd[eeeeeaqqqqqqqqa]eeeee]dd	chr1:136484464-136484681(+)$1	217	8	35	15.3620
eebb[ddddqqqqqqqqdddd]bb]ee	chr9:67741733-67741949(+)$1	216	12	39	16.1735
ccc[bb[bbqqqqqqqqbb]bb333cc	chr17:33958692-33958898(-)$1	206	109	136	15.2882
fff[a[cccqqqqqqqqccc]a]ffff	chrX:13203259-13203465(-)$1	206	115	142	16.5572
cc####cccqqqqqqqqcccccc]ccc	chr7:4095712-4095939(+)$1	227	200	227	17.4764
c[a!!ddddqqqqqqqqdddd4444a]	chr7:20222730-20222944(-)$1	214	151	178	18.2687
ccc[eeeeeqqqqqqqqeeeee]ccc6	chr7:29092531-29092750(-)$1	219	14	41	15.8396
iiiiiiiiiqqqqqqqqiiiiiiiiic	chr2:166853335-166853553(+)$1	218	75	102	16.2119
[ccc[ddddqqqqqqqqdddd]ccc22	chr9:64013121-64013336(-)$1	215	181	208	16.9803
ccccccabbqqqqqqqqbb]a]ccc]c	chr8:111324251-111324460(+)$1	209	49	76	15.6015
=####ddddqqqqqqqqdddd55555=	chrX:110185423-110185643(-)$1	220	156	183	14.4389
fffff[cccqqqqqqqqccc]ffffff	chrX:65966327-65966563(+)$1	236	94	121	15.6659
[bbffffffqqqqqqqqffffff]bb]	chr11:97032834-97033071(-)$1	237	83	110	13.9309
h"""a[cccqqqqqqqqccca333hhh	chr18:7921319-7921546(+)$1	227	190	217	17.6683
dddffffffqqqqqqqqffffff4444	chr11:106108777-106108999(+)$1	222	112	139	14.8184
$$$$$ddddqqqqqqqqdddd4444ee	chr19:60852571-60852790(-)$1	219	179	206	17.2092
%%%a!!cccqqqqqqqqccc22a4444	chr17:63820718-63820924(-)$1	206	35	62	16.1631
$$$$$ddddqqqqqqqqdddddddd:F	chr15:79567424-79567633(-)$1	209	26	53	14.6659
ff####cccqqqqqqqqccc22fffff	chr12:72261123-72261338(+)$1	215	52	79	16.9209
dddd!!cccqqqqqqqqccc22dddd]	chr19:44369515-44369724(+)$1	209	8	35	16.8255
ggggg!!bbqqqqqqqqbb]ggggggg	chr9:66298611-66298820(+)$1	209	19	46	15.7014
bb[bb!!bbqqqqqqqqbb333bbbb]	chr6:115571746-115571966(-)$1	220	114	141	14.3865

#otherMatches

#Seq PSSM
CAAGCGCUCUGCCUACCGAGUUCUUGG	chr11:84284087-84284293(-)$1	206	149	176	16.7438
CCAUUGCAUGACGGAAAAUGAGGUGAG	chr2:130639840-130640046(-)$1	206	110	137	15.9920
UGCCCCCAGCCCUUCAAUUGGAGGCAG	chr9:65551058-65551283(-)$1	225	196	223	15.8454
GCGCCCACUGGAAAGGAGGUGAGUGCC	chr12:83503972-83504191(+)$1	219	176	203	16.3049
GCUGGAUUGGAUGGAGACAAGACAGUG	chr14:21510646-21510852(+)$1	206	75	102	16.8255
CUUUGACGUGUGGAUUGACGUGCAGAG	chr12:111867698-111867919(+)$1	221	144	171	16.3818
UCGUAUCGGAGGAUGGACUGAUUGUGA	chr7:138105488-138105735(+)$1	247	48	75	16.2109
GGUCCCCGUGGCUGGAAACGAGUGCUU	chr8:114364219-114364451(-)$1	232	201	228	15.8580
AGCUUGCAGAGGAUUUCCUGCGGGACU	chr15:79368938-79369170(-)$1	232	61	88	15.0259
ccaucacacucUUCAGUGUGUGCCUGU	chr15:79367841-79368071(-)$1	230	1	28	16.0728
AACAUGGCGGAGGAGGGUGCCGGUGCC	chrX:70704095-70704329(-)$1	234	48	75	14.4620
ACUUGAAGAAAGGUUAAUUUGCUGUAC	chr2:124923658-124923908(-)$1	250	60	87	18.2321
ACAAUGGUAUGGUAUCUUGAAAUUGAA	chr4:106019128-106019337(+)$1	209	149	176	14.4881
UGGGGCACAUUCAAUGCUGUGCUCCAU	chr12:80386158-80386379(-)$1	221	172	199	15.5394
UCAGAUCUUAGUACAGCGAGACACUCU	chr9:121657082-121657302(+)$1	220	148	175	17.1537
AGAUGGGCUACAUCGUGGGCUUACUUA	chr4:59220653-59220868(+)$1	215	146	173	14.6868
UACCGGGGUAAUUGCAGGCCCAUACGA	chr1:36929263-36929483(-)$1	220	68	95	17.4860
GAAUUCAUGGUUAUAAGUAUGUUUCAA	chr12:103717735-103717955(+)$1	220	5	32	17.1750
UCUUCUAAUGCUAAUAAAUUAGUUACA	chr1:189057739-189057946(+)$1	207	132	159	16.8484
GAUUCGGUUGUAAGUAGGACUUCUCCA	chr1:181716838-181717070(-)$1	232	112	139	17.4491
UCCGAGCUGGCACGCUACAGCAAUAGC	chr7:63143147-63143357(+)$1	210	132	159	18.0990
CGGAGGCCUGUACAACAAGGGACCCUC	chr3:130818272-130818478(+)$1	206	71	98	16.0656
CUCAAUCGGGAAGGAUAUCAUUGAGGA	chr1:89812865-89813082(+)$1	217	148	175	14.6909
AGAAGCCAUAAGGUAAGGUAGGAAGUG	chr5:66035167-66035392(-)$1	225	122	149	15.0674
UUAGUUUAUGUAAACCUGUAGAUUGAU	chr5:124210249-124210482(+)$1	233	25	52	15.3973
AGGAUUGCUUUGAAUAUGGGACUCCUG	chr11:23243497-23243719(+)$1	222	86	113	16.0263
AAAUUCUUAAAUAUCUCUAAAAUUUAA	chrX:65941367-65941585(+)$1	218	10	37	16.7432
UCUUUAAAUAUAACAUAAUUUAAGCAG	chr5:86458070-86458293(-)$1	223	191	218	15.9875
AGAAUCCCCAAGGAGCAGGGCUUUCUC	chr8:47294674-47294894(-)$1	220	98	125	16.8133
CAGAUAUCCUCAGUGUUGGAAUCCUGG	chr2:120648218-120648438(-)$1	220	183	210	17.8816
CACGAGAUGCCACCCCACAUCUACGCC	chr15:77638275-77638514(-)$1	239	156	183	16.4808
AUGUCUUGAAAAACUCCUUAACCCACA	chr5:116438409-116438632(+)$1	223	37	64	17.5210
CAGUGUCCUCUGAACCUGGGACCAAAU	chr3:121471461-121471677(-)$1	216	140	167	16.4585
GCAGAGUACAACAAGCAGUGCCGAGCA	chr13:49783895-49784101(+)$1	206	60	87	16.7440
GAUCCACUUGUUCCACAGAGGGAAUUA	chr10:62732285-62732523(+)$1	238	39	66	16.9216
UGGAAAUUUCAAGAAUUAAGUCAACCA	chr11:93909742-93909962(+)$1	220	82	109	18.3859
UUAAAAUGCUUUUCUUUGACAUUUAGG	chr1:136484464-136484681(+)$1	217	8	35	15.3620
CUCUUUCCUCAUUGGAUAGGAUAGAAG	chr9:67741733-67741949(+)$1	216	12	39	16.1735
UGUCCUACAGAAGUGAGUGCAGCCAAC	chr17:33958692-33958898(-)$1	206	109	136	15.2882
AGUUAGGAGAAUCUGGACUUGUUGCUG	chrX:13203259-13203465(-)$1	206	115	142	16.5572
AGACCCGUCAACUGUGCGACCUGUGGC	chr7:4095712-4095939(+)$1	227	200	227	17.4764
GGAAGUGGGGAAUCUUACCCAAGGCUG	chr7:20222730-20222944(-)$1	214	151	178	18.2687
CCCAGGUGUGUUGACAGACGCCCGGGC	chr7:29092531-29092750(-)$1	219	14	41	15.8396
AUAUUUGUGAACAGCAACACAGAUGUC	chr2:166853335-166853553(+)$1	218	75	102	16.2119
UUGUCGCUAAUUCUUAGUAGCCACAUU	chr9:64013121-64013336(-)$1	215	181	208	16.9803
UGGAAGGCCGUGAUGGGGGACUCUUAC	chr8:111324251-111324460(+)$1	209	49	76	15.6015
AACUUCCGUCCAUCCUCAUGGUUCUGu	chrX:110185423-110185643(-)$1	220	156	183	14.4389
ACGAUCAUUCCCGAACAGAUAAUCGUC	chrX:65966327-65966563(+)$1	236	94	121	15.6659
GUAGUUGUUCGAGACACAACAGCGUGG	chr11:97032834-97033071(-)$1	237	83	110	13.9309
ACCUGCGUGCUCAUUAACACCUACUCU	chr18:7921319-7921546(+)$1	227	190	217	17.6683
AGUGCAGGAAGCUUAAAUUCUGUUCCA	chr11:106108777-106108999(+)$1	222	112	139	14.8184
UUAUAGUUGAGAAGCAGCGACGCCUUG	chr19:60852571-60852790(-)$1	219	179	206	17.2092
GCUGGGCUCAAGAUGCAGAGAACUCAA	chr17:63820718-63820924(-)$1	206	35	62	16.1631
UUAAUGGCCAUUUUUCAGGCCGCCUCU	chr15:79567424-79567633(-)$1	209	26	53	14.6659
AGAUAAAGCAAUCUCCAGUUACCUUGA	chr12:72261123-72261338(+)$1	215	52	79	16.9209
AUCUAUAUGACCCCACCUAUCAGGAUG	chr19:44369515-44369724(+)$1	209	8	35	16.8255
UAUCUGACAGGCAUUCAUGAAGAUGUG	chr9:66298611-66298820(+)$1	209	19	46	15.7014
AGAGACAUGAAAUCCAACAGUAUCCUU	chr6:115571746-115571966(-)$1	220	114	141	14.3865

#DB
((((.((((........)))).)))))	chr11:84284087-84284293(-)$1	1	149	176	16.7438
(((((.(((........))).))))..	chr2:130639840-130640046(-)$1	1	110	137	15.9920
((((.((((........)))).)))).	chr9:65551058-65551283(-)$1	1	196	223	15.8454
((((.((((........)))).)))))	chr12:83503972-83504191(+)$1	1	176	203	16.3049
((((..(((........)))..)))).	chr14:21510646-21510852(+)$1	1	75	102	16.8255
(((((((((........)))).)))))	chr12:111867698-111867919(+)$1	1	144	171	16.3818
(...(((((........))))).))))	chr7:138105488-138105735(+)$1	1	48	75	16.2109
(((.(.(((........))).).))))	chr8:114364219-114364451(-)$1	1	201	228	15.8580
(((((((((........))))))).))	chr15:79368938-79369170(-)$1	1	61	88	15.0259
(((((((((........)))))...))	chr15:79367841-79368071(-)$1	1	1	28	16.0728
.((.(((((........)))))))..)	chrX:70704095-70704329(-)$1	1	48	75	14.4620
((....(((........)))...))))	chr2:124923658-124923908(-)$1	1	60	87	18.2321
.((((..((........))..))))))	chr4:106019128-106019337(+)$1	1	149	176	14.4881
(((((((((........))))))))).	chr12:80386158-80386379(-)$1	1	172	199	15.5394
.((((((((........))))...)))	chr9:121657082-121657302(+)$1	1	148	175	17.1537
((.((((((........))))))))).	chr4:59220653-59220868(+)$1	1	146	173	14.6868
((...((((........)))).)))).	chr1:36929263-36929483(-)$1	1	68	95	17.4860
(((..((((........)))).)))))	chr12:103717735-103717955(+)$1	1	5	32	17.1750
(...(((((........)))))....)	chr1:189057739-189057946(+)$1	1	132	159	16.8484
((...((((........))))..))))	chr1:181716838-181717070(-)$1	1	112	139	17.4491
(((..((((........))))....).	chr7:63143147-63143357(+)$1	1	132	159	18.0990
.((((((((........)))...))))	chr3:130818272-130818478(+)$1	1	71	98	16.0656
((((((.((........))))))))).	chr1:89812865-89813082(+)$1	1	148	175	14.6909
(....((((........)).))...))	chr5:66035167-66035392(-)$1	1	122	149	15.0674
(((((((((........))))))))).	chr5:124210249-124210482(+)$1	1	25	52	15.3973
.(((.(.((........)).).)))))	chr11:23243497-23243719(+)$1	1	86	113	16.0263
(((((.(((........))))))))))	chrX:65941367-65941585(+)$1	1	10	37	16.7432
(.(((((((........))))))).))	chr5:86458070-86458293(-)$1	1	191	218	15.9875
((((..(((........)))..)))))	chr8:47294674-47294894(-)$1	1	98	125	16.8133
(((...(((........)))...))))	chr2:120648218-120648438(-)$1	1	183	210	17.8816
(...(((((........)))))..)))	chr15:77638275-77638514(-)$1	1	156	183	16.4808
((((.((((........))))...)))	chr5:116438409-116438632(+)$1	1	37	64	17.5210
..(.(((((........))))))...)	chr3:121471461-121471677(-)$1	1	140	167	16.4585
((.(.((((........)))))..)))	chr13:49783895-49784101(+)$1	1	60	87	16.7440
..(((.(((........)))))).)))	chr10:62732285-62732523(+)$1	1	39	66	16.9216
(((..((((........))))...)))	chr11:93909742-93909962(+)$1	1	82	109	18.3859
((.((((((........).))))).))	chr1:136484464-136484681(+)$1	1	8	35	15.3620
((((.((((........)))).)).))	chr9:67741733-67741949(+)$1	1	12	39	16.1735
(((.((.((........)).))...))	chr17:33958692-33958898(-)$1	1	109	136	15.2882
(((.(.(((........))).).))))	chrX:13203259-13203465(-)$1	1	115	142	16.5572
((....(((........)))))).)))	chr7:4095712-4095939(+)$1	1	200	227	17.4764
(.(..((((........))))....).	chr7:20222730-20222944(-)$1	1	151	178	18.2687
(((.(((((........))))).))).	chr7:29092531-29092750(-)$1	1	14	41	15.8396
(((((((((........))))))))))	chr2:166853335-166853553(+)$1	1	75	102	16.2119
.(((.((((........)))).)))..	chr9:64013121-64013336(-)$1	1	181	208	16.9803
(((((((((........)).).))).)	chr8:111324251-111324460(+)$1	1	49	76	15.6015
(....((((........)))).....)	chrX:110185423-110185643(-)$1	1	156	183	14.4389
(((((.(((........))).))))))	chrX:65966327-65966563(+)$1	1	94	121	15.6659
.((((((((........)))))).)).	chr11:97032834-97033071(-)$1	1	83	110	13.9309
(...(.(((........))))...)))	chr18:7921319-7921546(+)$1	1	190	217	17.6683
(((((((((........))))))....	chr11:106108777-106108999(+)$1	1	112	139	14.8184
.....((((........))))....))	chr19:60852571-60852790(-)$1	1	179	206	17.2092
...(..(((........)))..)....	chr17:63820718-63820924(-)$1	1	35	62	16.1631
.....((((........)))))))).(	chr15:79567424-79567633(-)$1	1	26	53	14.6659
((....(((........)))..)))))	chr12:72261123-72261338(+)$1	1	52	79	16.9209
((((..(((........)))..)))).	chr19:44369515-44369724(+)$1	1	8	35	16.8255
(((((..((........)).)))))))	chr9:66298611-66298820(+)$1	1	19	46	15.7014
((.((..((........))...)))).	chr6:115571746-115571966(-)$1	1	114	141	14.3865

#PSSM
d : 0.18	e : 0.15	c : 0.13	f : 0.08	g : 0.06	[ : 0.06	b : 0.05	i : 0.05	h : 0.03	! : 0.03	# : 0.03	$ : 0.03	: : 0.01	= : 0.01	% : 0.01	
d : 0.20	e : 0.13	c : 0.13	f : 0.08	" : 0.06	b : 0.06	g : 0.06	i : 0.05	# : 0.05	[ : 0.03	$ : 0.03	h : 0.01	! : 0.01	% : 0.01	
d : 0.15	c : 0.12	e : 0.10	" : 0.10	g : 0.08	# : 0.08	[ : 0.06	f : 0.05	b : 0.05	i : 0.05	a : 0.05	$ : 0.03	h : 0.01	% : 0.01	
d : 0.13	" : 0.12	[ : 0.10	e : 0.08	f : 0.08	g : 0.08	# : 0.08	! : 0.06	c : 0.06	i : 0.05	a : 0.03	b : 0.03	$ : 0.03	
e : 0.17	[ : 0.13	! : 0.13	g : 0.08	# : 0.08	f : 0.06	d : 0.05	a : 0.05	i : 0.05	" : 0.05	c : 0.03	b : 0.03	$ : 0.03	
d : 0.31	e : 0.15	[ : 0.12	! : 0.12	g : 0.05	# : 0.05	i : 0.05	f : 0.05	b : 0.03	a : 0.01	" : 0.01	c : 0.01	
d : 0.31	c : 0.27	e : 0.13	! : 0.05	i : 0.05	f : 0.05	[ : 0.05	g : 0.03	b : 0.01	a : 0.01	
d : 0.31	c : 0.27	e : 0.13	b : 0.13	i : 0.05	f : 0.05	g : 0.03	
d : 0.31	c : 0.27	b : 0.13	e : 0.12	i : 0.05	f : 0.05	g : 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	
d : 0.31	c : 0.27	b : 0.13	e : 0.12	i : 0.05	f : 0.05	g : 0.03	a : 0.01	
d : 0.31	c : 0.27	b : 0.13	e : 0.12	i : 0.05	f : 0.05	g : 0.03	] : 0.01	
d : 0.31	c : 0.27	e : 0.13	] : 0.08	g : 0.05	i : 0.05	f : 0.05	2 : 0.01	3 : 0.01	
d : 0.31	e : 0.13	2 : 0.10	g : 0.08	] : 0.06	3 : 0.06	i : 0.05	f : 0.05	a : 0.05	b : 0.03	c : 0.03	
] : 0.17	e : 0.13	3 : 0.13	2 : 0.10	g : 0.08	f : 0.06	d : 0.05	a : 0.05	i : 0.05	4 : 0.05	b : 0.03	c : 0.03	5 : 0.01	
3 : 0.17	d : 0.12	f : 0.10	e : 0.08	g : 0.08	c : 0.08	] : 0.06	4 : 0.06	b : 0.05	i : 0.05	2 : 0.05	a : 0.03	5 : 0.01	
d : 0.15	3 : 0.13	e : 0.12	g : 0.10	4 : 0.10	c : 0.08	f : 0.06	b : 0.05	i : 0.05	] : 0.05	2 : 0.03	h : 0.01	5 : 0.01	
d : 0.18	c : 0.15	e : 0.10	4 : 0.10	f : 0.08	] : 0.06	3 : 0.06	g : 0.06	i : 0.05	h : 0.03	b : 0.03	2 : 0.01	5 : 0.01	
e : 0.17	d : 0.17	c : 0.12	f : 0.10	4 : 0.06	b : 0.06	g : 0.06	i : 0.05	h : 0.03	2 : 0.03	a : 0.03	3 : 0.01	] : 0.01	5 : 0.01	: : 0.01	
e : 0.18	d : 0.12	c : 0.12	f : 0.10	] : 0.10	4 : 0.06	: : 0.05	b : 0.05	g : 0.05	h : 0.03	2 : 0.03	5 : 0.01	6 : 0.01	= : 0.01	F : 0.01	

#score	942.2225033160662
#seq	58
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_CDS_m3_run1.txt

#BEAR
ceeeeennnnneeeee	chr2:71114420-71114661(-)$1	241	9	25	10.0380
c!!cccnnnnnccc22	chr7:31226612-31226851(-)$1	239	40	56	10.9140
====[annnnna]===	chr2:131762809-131763094(+)$1	285	101	117	10.1865
fff[bbnnnnnbb]ff	chr7:148337524-148337759(+)$1	235	77	93	10.0421
cc[a[annnnna]a]c	chr4:57722929-57723172(+)$1	243	199	215	10.1202
!!ddddnnnnndddd2	chr13:6602544-6602805(-)$1	261	180	196	10.3586
!eeeeennnnneeeee	chr7:65047791-65048042(+)$1	251	151	167	10.1659
:eeeeennnnneeeee	chr7:17501488-17501778(-)$1	290	139	155	9.1461
ffffffnnnnnfffff	chr2:129444097-129444360(+)$1	263	211	227	9.9358
d"""bbnnnnnbb]dd	chr1:59927210-59927447(+)$1	237	197	213	9.8195
"eeeeennnnneeeee	chr13:74168748-74168984(+)$1	236	103	119	10.1511
b[ddddnnnnndddd]	chrX:162824810-162825047(+)$1	237	175	191	10.0570
ffffffnnnnnfffff	chr12:111865180-111865415(+)$1	235	0	16	9.9358
!eeeeennnnneeeee	chr10:76784989-76785224(-)$1	235	95	111	10.1659
$$ddddnnnnnddddd	chr16:17499962-17500197(+)$1	235	188	204	9.6731
!!ddddnnnnndddd2	chr16:35293974-35294230(+)$1	256	165	181	10.3586
[bb[bbnnnnnbb22b	chr5:125546130-125546365(-)$1	235	207	223	9.1862
e!!cccnnnnnccc22	chr1:193602238-193602475(+)$1	237	168	184	10.7416
c[ddddnnnnndddd3	chr10:106256389-106256638(+)$1	249	57	73	10.3884
ccc[bbnnnnnbbccc	chr10:29067362-29067599(-)$1	237	110	126	10.1249
ffffffnnnnnfffff	chr17:34782494-34782729(+)$1	235	167	183	9.9358
bb[cccnnnnnccc]b	chr19:10058959-10059195(+)$1	236	31	47	10.1001
""ddddnnnnndddd3	chrX:148317008-148317269(+)$1	261	229	245	10.4716
:eeeeennnnneeeee	chr11:4964001-4964239(-)$1	238	177	193	9.1461
!eeeeennnnneeeee	chr13:55392432-55392669(+)$1	237	4	20	10.1659
ffffffnnnnnfffff	chr10:126680660-126680895(-)$1	235	185	201	9.9358
c[ddddnnnnnddddc	chr16:35299447-35299697(+)$1	250	220	236	10.1251
bb[cccnnnnncccbb	chr2:25077838-25078075(-)$1	237	94	110	9.6166
eee[bbnnnnnbb]ee	chr10:57236816-57237127(-)$1	311	73	89	10.0415
ee[cccnnnnnccc]e	chr11:90202099-90202341(-)$1	242	91	107	10.6080
ffffffnnnnnfffff	chr12:113025641-113025876(+)$1	235	164	180	9.9358
ffffffnnnnnfffff	chr11:87863329-87863588(+)$1	259	27	43	9.9358
ffffffnnnnnfffff	chr1:135533828-135534091(-)$1	263	139	155	9.9358
gg!!bbnnnnnbb22g	chr11:94853627-94853890(+)$1	263	197	213	10.0432
cc[cccnnnnnccc]c	chr17:82047059-82047320(-)$1	261	82	98	10.7711
!!ddddnnnnndddd]	chr7:137872027-137872262(+)$1	235	175	191	10.3937
c!!cccnnnnnccc22	chr14:60997232-60997490(+)$1	258	153	169	10.9140
ccccccnnnnnccc33	chrX:162824888-162825125(+)$1	237	161	177	10.8814
%%%cccnnnnnccc44	chr2:5950315-5950550(+)$1	235	177	193	9.0439
""ddddnnnnndddd3	chr7:104877404-104877644(-)$1	240	94	110	10.4716
ffffffnnnnnfffff	chr1:174215791-174216026(-)$1	235	142	158	9.9358
eee[bbnnnnnbbeee	chr11:50014060-50014371(-)$1	311	119	135	10.0385
"eeeeennnnneeeee	chr5:131921174-131921409(-)$1	235	91	107	10.1511
ggggbbnnnnnbb]gg	chr2:181283313-181283550(+)$1	237	15	31	10.0827
[ccc[annnnna]ccc	chr10:126699751-126699986(-)$1	235	55	71	10.0929
ccccccnnnnnccc]c	chr9:36557080-36557315(-)$1	235	38	54	10.5966
bbddddnnnnndddd2	chr15:31415590-31415861(-)$1	271	64	80	9.6316
cc!!bbnnnnnbb333	chr16:90229856-90230093(-)$1	237	68	84	10.6703
ddd[bbnnnnnbbddd	chr18:50024647-50024885(+)$1	238	98	114	9.5664
####bbnnnnnbb444	chr15:9104843-9105086(+)$1	243	129	145	10.3234
b!!cccnnnnnccc22	chr9:30959798-30960060(-)$1	262	217	233	10.7275
ggggggnnnnnggggg	chrX:12738488-12738723(+)$1	235	18	34	10.0419
ffffffnnnnnfffff	chr2:9985644-9985896(-)$1	252	22	38	9.9358

#otherMatches

#Seq PSSM
CCCUGACACUCUCAGG	chr2:71114420-71114661(-)$1	241	9	25	10.0380
CCUGACCCCUUGUCUU	chr7:31226612-31226851(-)$1	239	40	56	10.9140
UCUUCCUGAUCGUGGG	chr2:131762809-131763094(+)$1	285	101	117	10.1865
CCCAUUGCCAGAGAGG	chr7:148337524-148337759(+)$1	235	77	93	10.0421
UACCACUAACUGCGAU	chr4:57722929-57723172(+)$1	243	199	215	10.1202
ACUCUAAUUACUAGAA	chr13:6602544-6602805(-)$1	261	180	196	10.3586
CACAGUUCUCCAUUGU	chr7:65047791-65048042(+)$1	251	151	167	10.1659
AGAGUGGACGGCACUC	chr7:17501488-17501778(-)$1	290	139	155	9.1461
GAGCAGGAUCUCUGCU	chr2:129444097-129444360(+)$1	263	211	227	9.9358
UUUAACCUCCUGUCAG	chr1:59927210-59927447(+)$1	237	197	213	9.8195
GGGGGCAAGUAGCCUC	chr13:74168748-74168984(+)$1	236	103	119	10.1511
CAAGAUAUCCAGUCUC	chrX:162824810-162825047(+)$1	237	175	191	10.0570
GGCGGAAGGACUCUGC	chr12:111865180-111865415(+)$1	235	0	16	9.9358
UGUUCUGCCCAAGAAC	chr10:76784989-76785224(-)$1	235	95	111	10.1659
AUUCCAUGCCCUGGGC	chr16:17499962-17500197(+)$1	235	188	204	9.6731
UGGAGUCCACUGCUCG	chr16:35293974-35294230(+)$1	256	165	181	10.3586
UGCCUGGCUCGCAAAG	chr5:125546130-125546365(-)$1	235	207	223	9.1862
AUUUUAGGAAUUGACU	chr1:193602238-193602475(+)$1	237	168	184	10.7416
UGCAAGAAUUGCUUGA	chr10:106256389-106256638(+)$1	249	57	73	10.3884
GGAAGCGAUGUGCUCU	chr10:29067362-29067599(-)$1	237	110	126	10.1249
UGUGGGGGGAACUCAU	chr17:34782494-34782729(+)$1	235	167	183	9.9358
GUGAGGUGUUUCCUGG	chr19:10058959-10059195(+)$1	236	31	47	10.1001
UUAGUGCCCUUCGCUU	chrX:148317008-148317269(+)$1	261	229	245	10.4716
AAGAGUGUGGUGCUCU	chr11:4964001-4964239(-)$1	238	177	193	9.1461
AUGUAAUUUUUUUACA	chr13:55392432-55392669(+)$1	237	4	20	10.1659
GGGCACCGUGAGUGUC	chr10:126680660-126680895(-)$1	235	185	201	9.9358
GACUUCGCUAUGAAGC	chr16:35299447-35299697(+)$1	250	220	236	10.1251
ACACUGGUACACGGGU	chr2:25077838-25078075(-)$1	237	94	110	9.6166
GGGUGAAAAUCUCUUC	chr10:57236816-57237127(-)$1	311	73	89	10.0415
GGCGGCCAAGCGCUCC	chr11:90202099-90202341(-)$1	242	91	107	10.6080
AGGUGUGUGCGACGCU	chr12:113025641-113025876(+)$1	235	164	180	9.9358
GAUAUUAUGUAAAUGU	chr11:87863329-87863588(+)$1	259	27	43	9.9358
GGAUGGUGACUCUAUC	chr1:135533828-135534091(-)$1	263	139	155	9.9358
GUGACGGUCCAUGCAG	chr11:94853627-94853890(+)$1	263	197	213	10.0432
CUACAAAACUAUUGAA	chr17:82047059-82047320(-)$1	261	82	98	10.7711
GGUGGAUAACUUCCAG	chr7:137872027-137872262(+)$1	235	175	191	10.3937
CGACGGACUAGCCGAG	chr14:60997232-60997490(+)$1	258	153	169	10.9140
GUGUCAGCCAAUGAAU	chrX:162824888-162825125(+)$1	237	161	177	10.8814
CACUAGAACUGCUAAG	chr2:5950315-5950550(+)$1	235	177	193	9.0439
CUGCACUUUCCGUGCU	chr7:104877404-104877644(-)$1	240	94	110	10.4716
GCUCAAGUGCAUUGAG	chr1:174215791-174216026(-)$1	235	142	158	9.9358
UGCAUCACGUAGAGCA	chr11:50014060-50014371(-)$1	311	119	135	10.0385
CGCUGCAGUUGGUGGC	chr5:131921174-131921409(-)$1	235	91	107	10.1511
UGGGCCCUUGAGGCCC	chr2:181283313-181283550(+)$1	237	15	31	10.0827
UGCAGCAUCAAGGUGC	chr10:126699751-126699986(-)$1	235	55	71	10.0929
UGGUCUCUGUCAGAUC	chr9:36557080-36557315(-)$1	235	38	54	10.5966
UCCAUUUGAUUGAUGC	chr15:31415590-31415861(-)$1	271	64	80	9.6316
GAUAGCAGGCAGCAGU	chr16:90229856-90230093(-)$1	237	68	84	10.6703
GCAACUCUCCUAGUGC	chr18:50024647-50024885(+)$1	238	98	114	9.5664
GUACCUUCUUUAGCAC	chr15:9104843-9105086(+)$1	243	129	145	10.3234
CAUCUUAGUUCAAGUG	chr9:30959798-30960060(-)$1	262	217	233	10.7275
AAAUGUGGUAGACAUU	chrX:12738488-12738723(+)$1	235	18	34	10.0419
GUCCUCAGAUAGAGGG	chr2:9985644-9985896(-)$1	252	22	38	9.9358

#DB
((((((.....)))))	chr2:71114420-71114661(-)$1	1	9	25	10.0380
(..(((.....)))..	chr7:31226612-31226851(-)$1	1	40	56	10.9140
((((.(.....).)))	chr2:131762809-131763094(+)$1	1	101	117	10.1865
(((.((.....)).))	chr7:148337524-148337759(+)$1	1	77	93	10.0421
((.(.(.....).).)	chr4:57722929-57723172(+)$1	1	199	215	10.1202
..((((.....)))).	chr13:6602544-6602805(-)$1	1	180	196	10.3586
.(((((.....)))))	chr7:65047791-65048042(+)$1	1	151	167	10.1659
.(((((.....)))))	chr7:17501488-17501778(-)$1	1	139	155	9.1461
((((((.....)))))	chr2:129444097-129444360(+)$1	1	211	227	9.9358
(...((.....)).))	chr1:59927210-59927447(+)$1	1	197	213	9.8195
.(((((.....)))))	chr13:74168748-74168984(+)$1	1	103	119	10.1511
(.((((.....)))).	chrX:162824810-162825047(+)$1	1	175	191	10.0570
((((((.....)))))	chr12:111865180-111865415(+)$1	1	0	16	9.9358
.(((((.....)))))	chr10:76784989-76785224(-)$1	1	95	111	10.1659
..((((.....)))))	chr16:17499962-17500197(+)$1	1	188	204	9.6731
..((((.....)))).	chr16:35293974-35294230(+)$1	1	165	181	10.3586
.((.((.....))..)	chr5:125546130-125546365(-)$1	1	207	223	9.1862
(..(((.....)))..	chr1:193602238-193602475(+)$1	1	168	184	10.7416
(.((((.....)))).	chr10:106256389-106256638(+)$1	1	57	73	10.3884
(((.((.....)))))	chr10:29067362-29067599(-)$1	1	110	126	10.1249
((((((.....)))))	chr17:34782494-34782729(+)$1	1	167	183	9.9358
((.(((.....))).)	chr19:10058959-10059195(+)$1	1	31	47	10.1001
..((((.....)))).	chrX:148317008-148317269(+)$1	1	229	245	10.4716
.(((((.....)))))	chr11:4964001-4964239(-)$1	1	177	193	9.1461
.(((((.....)))))	chr13:55392432-55392669(+)$1	1	4	20	10.1659
((((((.....)))))	chr10:126680660-126680895(-)$1	1	185	201	9.9358
(.((((.....)))))	chr16:35299447-35299697(+)$1	1	220	236	10.1251
((.(((.....)))))	chr2:25077838-25078075(-)$1	1	94	110	9.6166
(((.((.....)).))	chr10:57236816-57237127(-)$1	1	73	89	10.0415
((.(((.....))).)	chr11:90202099-90202341(-)$1	1	91	107	10.6080
((((((.....)))))	chr12:113025641-113025876(+)$1	1	164	180	9.9358
((((((.....)))))	chr11:87863329-87863588(+)$1	1	27	43	9.9358
((((((.....)))))	chr1:135533828-135534091(-)$1	1	139	155	9.9358
((..((.....))..)	chr11:94853627-94853890(+)$1	1	197	213	10.0432
((.(((.....))).)	chr17:82047059-82047320(-)$1	1	82	98	10.7711
..((((.....)))).	chr7:137872027-137872262(+)$1	1	175	191	10.3937
(..(((.....)))..	chr14:60997232-60997490(+)$1	1	153	169	10.9140
((((((.....)))..	chrX:162824888-162825125(+)$1	1	161	177	10.8814
...(((.....)))..	chr2:5950315-5950550(+)$1	1	177	193	9.0439
..((((.....)))).	chr7:104877404-104877644(-)$1	1	94	110	10.4716
((((((.....)))))	chr1:174215791-174216026(-)$1	1	142	158	9.9358
(((.((.....)))))	chr11:50014060-50014371(-)$1	1	119	135	10.0385
.(((((.....)))))	chr5:131921174-131921409(-)$1	1	91	107	10.1511
((((((.....)).))	chr2:181283313-181283550(+)$1	1	15	31	10.0827
.(((.(.....).)))	chr10:126699751-126699986(-)$1	1	55	71	10.0929
((((((.....))).)	chr9:36557080-36557315(-)$1	1	38	54	10.5966
((((((.....)))).	chr15:31415590-31415861(-)$1	1	64	80	9.6316
((..((.....))...	chr16:90229856-90230093(-)$1	1	68	84	10.6703
(((.((.....)))))	chr18:50024647-50024885(+)$1	1	98	114	9.5664
....((.....))...	chr15:9104843-9105086(+)$1	1	129	145	10.3234
(..(((.....)))..	chr9:30959798-30960060(-)$1	1	217	233	10.7275
((((((.....)))))	chrX:12738488-12738723(+)$1	1	18	34	10.0419
((((((.....)))))	chr2:9985644-9985896(-)$1	1	22	38	9.9358

#PSSM
c : 0.20	f : 0.18	! : 0.11	b : 0.09	" : 0.07	e : 0.07	g : 0.05	: : 0.03	d : 0.03	[ : 0.03	= : 0.01	$ : 0.01	% : 0.01	# : 0.01	
e : 0.20	f : 0.18	! : 0.13	c : 0.13	b : 0.07	" : 0.05	[ : 0.05	g : 0.05	= : 0.01	$ : 0.01	% : 0.01	d : 0.01	# : 0.01	
d : 0.20	e : 0.18	f : 0.18	! : 0.11	[ : 0.09	c : 0.07	g : 0.03	= : 0.01	" : 0.01	b : 0.01	% : 0.01	# : 0.01	
c : 0.22	d : 0.18	f : 0.16	e : 0.15	[ : 0.11	! : 0.03	g : 0.03	= : 0.01	a : 0.01	" : 0.01	# : 0.01	
c : 0.20	b : 0.20	d : 0.18	f : 0.16	e : 0.15	[ : 0.05	g : 0.01	
c : 0.20	b : 0.20	d : 0.18	f : 0.16	e : 0.15	a : 0.05	g : 0.01	
n : 0.99	
n : 0.99	
n : 0.99	
n : 0.99	
n : 0.99	
c : 0.20	b : 0.20	d : 0.18	f : 0.16	e : 0.15	a : 0.05	g : 0.01	
c : 0.20	b : 0.20	d : 0.18	f : 0.16	e : 0.15	] : 0.05	g : 0.01	
c : 0.24	d : 0.20	e : 0.16	f : 0.16	] : 0.07	2 : 0.03	= : 0.01	a : 0.01	3 : 0.01	4 : 0.01	g : 0.01	
d : 0.22	e : 0.18	f : 0.18	2 : 0.11	] : 0.09	c : 0.03	3 : 0.03	4 : 0.03	g : 0.03	= : 0.01	b : 0.01	
e : 0.20	f : 0.18	2 : 0.13	c : 0.11	3 : 0.09	d : 0.05	b : 0.05	g : 0.05	] : 0.03	4 : 0.03	= : 0.01	

#score	535.7789510881473
#seq	53
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_transcript_m3_run1.txt

#BEAR
bb[a[aqqqqqqqqa]a]b	chrX:103070349-103070568(-)$1	219	93	112	13.6812
ffffffqqqqqqqqfffff	chr17:5941288-5941501(+)$1	213	122	141	13.9357
deeeeeqqqqqqqqeeeee	chr5:91370259-91370473(+)$1	214	145	164	14.3437
:eeeeeqqqqqqqqeeeee	chr9:108468469-108468683(-)$1	214	78	97	13.6489
ggggggqqqqqqqqggggg	chr6:39120047-39120256(-)$1	209	135	154	14.2827
:a[cccqqqqqqqqccc]a	chr5:107412338-107412545(+)$1	207	25	44	13.5277
""ddddqqqqqqqqdddd2	chr2:131113573-131113784(+)$1	211	25	44	13.3546
cc!!bbqqqqqqqqbb22c	chr2:87006943-87007152(-)$1	209	74	93	13.6275
fff[bbqqqqqqqqbbfff	chr1:182904538-182904761(+)$1	223	83	102	13.6602
bb!!bbqqqqqqqqbb22b	chr7:26563364-26563582(-)$1	218	52	71	13.0063
ggggggqqqqqqqqggggg	chr4:108169501-108169740(+)$1	239	64	83	14.2827
ffffffqqqqqqqqfffff	chr3:129724632-129724864(-)$1	232	80	99	13.9357
======qqqqqqqq=====	chr15:75900843-75901070(-)$1	227	160	179	14.5048
d[ddddqqqqqqqqdddd3	chr10:57926461-57926676(+)$1	215	131	150	13.4431
:eeeeeqqqqqqqqeeeee	chr8:124786014-124786222(+)$1	208	4	23	13.6489
cc!!bbqqqqqqqqbb22c	chr15:58253227-58253439(+)$1	212	159	178	13.6275
ceeeeeqqqqqqqqeeeee	chr5:114839000-114839206(+)$1	206	111	130	14.4864
======qqqqqqqq=====	chr16:77069226-77069445(+)$1	219	144	163	14.5048
deeeeeqqqqqqqqeeeee	chr15:66444616-66444835(+)$1	219	18	37	14.3437
eeee[aqqqqqqqqa]eee	chr8:64057635-64057850(-)$1	215	147	166	14.3761
dd[cccqqqqqqqqccc]d	chr12:111855748-111855974(+)$1	226	46	65	14.0547
""ddddqqqqqqqqdddd3	chr10:120984101-120984328(-)$1	227	88	107	13.5863
!!a[bbqqqqqqqqbba22	chr9:53339728-53339957(-)$1	229	157	176	13.6662
deeeeeqqqqqqqqeeeee	chr9:44644646-44644864(-)$1	218	103	122	14.3437
[eeeeeqqqqqqqqeeeee	chr9:24574073-24574294(-)$1	221	34	53	14.5797
dd[cccqqqqqqqqcccdd	chr17:8365712-8365926(+)$1	214	146	165	13.8357
ffffffqqqqqqqqfffff	chr8:27229350-27229569(-)$1	219	23	42	13.9357
:ccc[aqqqqqqqqacccE	chr15:81205201-81205432(-)$1	231	179	198	12.1870
""ddddqqqqqqqqdddd4	chr3:138550013-138550238(+)$1	225	150	169	13.5180
bbddddqqqqqqqqdddd]	chr15:81446353-81446571(+)$1	218	18	37	13.0217
ffffffqqqqqqqqfffff	chr2:124941233-124941461(-)$1	228	68	87	13.9357
####bbqqqqqqqqbb444	chr12:102296874-102297093(-)$1	219	54	73	13.5536
ffffffqqqqqqqqfffff	chr3:89026873-89027105(+)$1	232	90	109	13.9357
b!!cccqqqqqqqqccc]b	chr1:167280940-167281165(-)$1	225	61	80	14.0979
dd!!bbqqqqqqqqbb22d	chr4:81002283-81002493(-)$1	210	76	95	13.2755
b!!cccqqqqqqqqccc22	chr17:56702870-56703097(-)$1	227	116	135	14.0922
:eeeeeqqqqqqqqeeeee	chr19:59050407-59050625(-)$1	218	186	205	13.6489
ggggggqqqqqqqqggggg	chr7:134665012-134665218(+)$1	206	183	202	14.2827
[eeeeeqqqqqqqqeeeee	chr8:72826197-72826412(-)$1	215	13	32	14.5797
eeee[aqqqqqqqqaeeee	chr13:34071408-34071620(+)$1	212	106	125	14.4540
[eeeeeqqqqqqqqeeeee	chr17:24768871-24769078(-)$1	207	22	41	14.5797
ccc[bbqqqqqqqqbbccc	chr9:108382850-108383060(+)$1	210	182	201	13.6008
#eeeeeqqqqqqqqeeeee	chr4:120887347-120887563(-)$1	216	166	185	14.5201
ffffffqqqqqqqqfffff	chr2:83643477-83643686(+)$1	209	15	34	13.9357
====[aqqqqqqqqa]===	chr5:29946027-29946241(+)$1	214	61	80	14.4485
ffffffqqqqqqqqfffff	chr2:48728776-48728998(+)$1	222	200	219	13.9357
ffffffqqqqqqqqfffff	chr11:80207704-80207911(+)$1	207	61	80	13.9357
h[ddddqqqqqqqqdddd3	chr1:36414932-36415162(-)$1	230	52	71	13.3225
ff[a[aqqqqqqqqa]a]f	chr1:55057111-55057334(-)$1	223	30	49	14.2972
cc[cccqqqqqqqqccc]c	chr2:155328396-155328602(-)$1	206	52	71	14.4067
ggggggqqqqqqqqggggg	chr11:106653768-106653986(+)$1	218	112	131	14.2827
eeee[aqqqqqqqqa]eee	chr14:57429390-57429615(-)$1	225	100	119	14.3761
[eeeeeqqqqqqqqeeeee	chr2:34287707-34287935(+)$1	228	10	29	14.5797
""ddddqqqqqqqqdddd5	chr11:54846781-54846989(-)$1	208	86	105	12.6831
ffffffqqqqqqqqfffff	chr18:70612807-70613020(-)$1	213	142	161	13.9357
iiiiiiqqqqqqqqiiiii	chr2:69782363-69782585(+)$1	222	5	24	14.1028
f!!cccqqqqqqqqccc22	chr11:4558190-4558414(+)$1	224	44	63	14.1793
ffffffqqqqqqqqfffff	chr10:75895667-75895884(-)$1	217	45	64	13.9357
dd!!bbqqqqqqqqbb22d	chr17:56204443-56204649(+)$1	206	138	157	13.2755
:eeeeeqqqqqqqqeeeee	chr11:70466529-70466735(-)$1	206	23	42	13.6489
ccc[bbqqqqqqqqbbccc	chr16:45095679-45095904(+)$1	225	20	39	13.6008
!a[cccqqqqqqqqccc33	chr15:81451432-81451677(+)$1	245	201	220	14.6082
!eeeeeqqqqqqqqeeeee	chr16:20560187-20560398(+)$1	211	173	192	14.5848
ggggggqqqqqqqqggggg	chr12:32672694-32672920(-)$1	226	17	36	14.2827

#otherMatches

#Seq PSSM
UCAUGUGAAAAGAAGGAAG	chrX:103070349-103070568(-)$1	219	93	112	13.6812
GGCGGGACCUGGUCCCCGC	chr17:5941288-5941501(+)$1	213	122	141	13.9357
ugcugaaaaaacccuuagc	chr5:91370259-91370473(+)$1	214	145	164	14.3437
UGUCUCCACCCUUAGAGAU	chr9:108468469-108468683(-)$1	214	78	97	13.6489
UAAGAGUAGGGUAUUUCUU	chr6:39120047-39120256(-)$1	209	135	154	14.2827
UGUGCUCCUGAUACGGCUC	chr5:107412338-107412545(+)$1	207	25	44	13.5277
GGGGCCAGGAAGAAGGCCA	chr2:131113573-131113784(+)$1	211	25	44	13.3546
UAUUGGGUAUGGAGCCUUU	chr2:87006943-87007152(-)$1	209	74	93	13.6275
GGGCUGAGGGUAUCCAUCC	chr1:182904538-182904761(+)$1	223	83	102	13.6602
GUCAGCCUUCCCUUGUGUG	chr7:26563364-26563582(-)$1	218	52	71	13.0063
UUUCAGAAUGUUCACUGAG	chr4:108169501-108169740(+)$1	239	64	83	14.2827
gggacugagauaggaguuc	chr3:129724632-129724864(-)$1	232	80	99	13.9357
GAAAUCAUCGUCAAGAUUU	chr15:75900843-75901070(-)$1	227	160	179	14.5048
CUUCAGCACCUUACCUGGC	chr10:57926461-57926676(+)$1	215	131	150	13.4431
GCCAGCCUGGACCAGCUGG	chr8:124786014-124786222(+)$1	208	4	23	13.6489
UUAUCCGACAUCAUGGUCA	chr15:58253227-58253439(+)$1	212	159	178	13.6275
GCUGCUGUGGAUUAAGCAG	chr5:114839000-114839206(+)$1	206	111	130	14.4864
GGUAAAGUCACCCGUUUGC	chr16:77069226-77069445(+)$1	219	144	163	14.5048
GUUCUGCCAACACUCAGAA	chr15:66444616-66444835(+)$1	219	18	37	14.3437
GCUUGGAAGAAGGGUGAAG	chr8:64057635-64057850(-)$1	215	147	166	14.3761
UGCAGCUAUGUUUUGUUCC	chr12:111855748-111855974(+)$1	226	46	65	14.0547
GGGUCUUUAACAAUGGAUG	chr10:120984101-120984328(-)$1	227	88	107	13.5863
CAGACAGAAGAAGAUGCAA	chr9:53339728-53339957(-)$1	229	157	176	13.6662
GUUGUGAACCCUUCCACAA	chr9:44644646-44644864(-)$1	218	103	122	14.3437
AGGAUGUUCCCCACCAUCC	chr9:24574073-24574294(-)$1	221	34	53	14.5797
UCCACCCCAAGUAAGGUGA	chr17:8365712-8365926(+)$1	214	146	165	13.8357
GAGCCGAGCGGCCGCGGCU	chr8:27229350-27229569(-)$1	219	23	42	13.9357
UGAGAGAAGUCCAACCUCG	chr15:81205201-81205432(-)$1	231	179	198	12.1870
uaaacaugaaaaauuguuc	chr3:138550013-138550238(+)$1	225	150	169	13.5180
CAUGUGUUAUUAAUUGCGU	chr15:81446353-81446571(+)$1	218	18	37	13.0217
UAGUUAAAUUUCUAUAGCU	chr2:124941233-124941461(-)$1	228	68	87	13.9357
UAAGUCGACUUGAGGAAAU	chr12:102296874-102297093(-)$1	219	54	73	13.5536
UCAGACACAGACUCGUUUG	chr3:89026873-89027105(+)$1	232	90	109	13.9357
CAGGGACUCUGCUCUCCAG	chr1:167280940-167281165(-)$1	225	61	80	14.0979
CUUACUUUAUUCCUAGAUA	chr4:81002283-81002493(-)$1	210	76	95	13.2755
UGCUGUGGACACAAACAUG	chr17:56702870-56703097(-)$1	227	116	135	14.0922
UGAGAAACAAUAGCUUCUU	chr19:59050407-59050625(-)$1	218	186	205	13.6489
CAUCUGUAUGUUUUCAGGU	chr7:134665012-134665218(+)$1	206	183	202	14.2827
ACGUGACGUAGCAUUCACG	chr8:72826197-72826412(-)$1	215	13	32	14.5797
AUCUUGUGAUAUUUCAGGU	chr13:34071408-34071620(+)$1	212	106	125	14.4540
AGCAGUUCUCUAGUACUGC	chr17:24768871-24769078(-)$1	207	22	41	14.5797
ACUAGGGCUUGUAACCAGU	chr9:108382850-108383060(+)$1	210	182	201	13.6008
GCCGGGAGAAGAGACUCGG	chr4:120887347-120887563(-)$1	216	166	185	14.5201
GGUGCUUCUUAAGUGGCGC	chr2:83643477-83643686(+)$1	209	15	34	13.9357
UUUUAGUUGUAGGUCAGAG	chr5:29946027-29946241(+)$1	214	61	80	14.4485
UACUUGUUCCUACUCAAGU	chr2:48728776-48728998(+)$1	222	200	219	13.9357
AUAAAGGAUCGUUACUUUA	chr11:80207704-80207911(+)$1	207	61	80	13.9357
GCGUAACUCUUGUUUUAUU	chr1:36414932-36415162(-)$1	230	52	71	13.3225
CAUUGCUAAAAUUUGGAUU	chr1:55057111-55057334(-)$1	223	30	49	14.2972
AGCUGCCUCCCAAUGCAUC	chr2:155328396-155328602(-)$1	206	52	71	14.4067
GCCUGUCUCACAUAACAGG	chr11:106653768-106653986(+)$1	218	112	131	14.2827
GUUUGGUGCUACCUCGGAG	chr14:57429390-57429615(-)$1	225	100	119	14.3761
CCUCCGUCAGUGCCUGGAG	chr2:34287707-34287935(+)$1	228	10	29	14.5797
CUGCGUCUGUCCAUACGCC	chr11:54846781-54846989(-)$1	208	86	105	12.6831
GCCAUACGUUAUUCUGUGG	chr18:70612807-70613020(-)$1	213	142	161	13.9357
GUUUACAUGUAGUGGUGAA	chr2:69782363-69782585(+)$1	222	5	24	14.1028
CCAGCACUGUGGUUUGCAA	chr11:4558190-4558414(+)$1	224	44	63	14.1793
GCUGCAAGAAGACCUGCAG	chr10:75895667-75895884(-)$1	217	45	64	13.9357
UCUGAGAACUCUGCCUAUG	chr17:56204443-56204649(+)$1	206	138	157	13.2755
UUGCUUUCCCUAUUAAGCA	chr11:70466529-70466735(-)$1	206	23	42	13.6489
GGUGCUGUUAAAAAAGACU	chr16:45095679-45095904(+)$1	225	20	39	13.6008
ACAUGGGGCAGCAACCAAC	chr15:81451432-81451677(+)$1	245	201	220	14.6082
UGCUCUUCUUCCCUAGGGC	chr16:20560187-20560398(+)$1	211	173	192	14.5848
CCAGCACUCCUUUUUGUUG	chr12:32672694-32672920(-)$1	226	17	36	14.2827

#DB
((.(.(........).).)	chrX:103070349-103070568(-)$1	1	93	112	13.6812
((((((........)))))	chr17:5941288-5941501(+)$1	1	122	141	13.9357
)(((((........)))))	chr5:91370259-91370473(+)$1	1	145	164	14.3437
.(((((........)))))	chr9:108468469-108468683(-)$1	1	78	97	13.6489
((((((........)))))	chr6:39120047-39120256(-)$1	1	135	154	14.2827
.(.(((........))).)	chr5:107412338-107412545(+)$1	1	25	44	13.5277
..((((........)))).	chr2:131113573-131113784(+)$1	1	25	44	13.3546
((..((........))..)	chr2:87006943-87007152(-)$1	1	74	93	13.6275
(((.((........)))))	chr1:182904538-182904761(+)$1	1	83	102	13.6602
((..((........))..)	chr7:26563364-26563582(-)$1	1	52	71	13.0063
((((((........)))))	chr4:108169501-108169740(+)$1	1	64	83	14.2827
((((((........)))))	chr3:129724632-129724864(-)$1	1	80	99	13.9357
((((((........)))))	chr15:75900843-75901070(-)$1	1	160	179	14.5048
(.((((........)))).	chr10:57926461-57926676(+)$1	1	131	150	13.4431
.(((((........)))))	chr8:124786014-124786222(+)$1	1	4	23	13.6489
((..((........))..)	chr15:58253227-58253439(+)$1	1	159	178	13.6275
)(((((........)))))	chr5:114839000-114839206(+)$1	1	111	130	14.4864
((((((........)))))	chr16:77069226-77069445(+)$1	1	144	163	14.5048
((((((........)))))	chr15:66444616-66444835(+)$1	1	18	37	14.3437
((((.(........).)))	chr8:64057635-64057850(-)$1	1	147	166	14.3761
((.(((........))).)	chr12:111855748-111855974(+)$1	1	46	65	14.0547
..((((........)))).	chr10:120984101-120984328(-)$1	1	88	107	13.5863
..(.((........)))..	chr9:53339728-53339957(-)$1	1	157	176	13.6662
)(((((........)))))	chr9:44644646-44644864(-)$1	1	103	122	14.3437
.(((((........)))))	chr9:24574073-24574294(-)$1	1	34	53	14.5797
((.(((........)))))	chr17:8365712-8365926(+)$1	1	146	165	13.8357
((((((........)))))	chr8:27229350-27229569(-)$1	1	23	42	13.9357
.(((.(........)))))	chr15:81205201-81205432(-)$1	1	179	198	12.1870
..((((........)))).	chr3:138550013-138550238(+)$1	1	150	169	13.5180
((((((........)))).	chr15:81446353-81446571(+)$1	1	18	37	13.0217
((((((........)))))	chr2:124941233-124941461(-)$1	1	68	87	13.9357
....((........))...	chr12:102296874-102297093(-)$1	1	54	73	13.5536
((((((........)))))	chr3:89026873-89027105(+)$1	1	90	109	13.9357
(..(((........))).)	chr1:167280940-167281165(-)$1	1	61	80	14.0979
((..((........))..)	chr4:81002283-81002493(-)$1	1	76	95	13.2755
(..(((........)))..	chr17:56702870-56703097(-)$1	1	116	135	14.0922
.(((((........)))))	chr19:59050407-59050625(-)$1	1	186	205	13.6489
((((((........)))))	chr7:134665012-134665218(+)$1	1	183	202	14.2827
.(((((........)))))	chr8:72826197-72826412(-)$1	1	13	32	14.5797
((((.(........)))))	chr13:34071408-34071620(+)$1	1	106	125	14.4540
.(((((........)))))	chr17:24768871-24769078(-)$1	1	22	41	14.5797
(((.((........)))))	chr9:108382850-108383060(+)$1	1	182	201	13.6008
.(((((........)))))	chr4:120887347-120887563(-)$1	1	166	185	14.5201
((((((........)))))	chr2:83643477-83643686(+)$1	1	15	34	13.9357
((((.(........).)))	chr5:29946027-29946241(+)$1	1	61	80	14.4485
((((((........)))))	chr2:48728776-48728998(+)$1	1	200	219	13.9357
((((((........)))))	chr11:80207704-80207911(+)$1	1	61	80	13.9357
(.((((........)))).	chr1:36414932-36415162(-)$1	1	52	71	13.3225
((.(.(........).).)	chr1:55057111-55057334(-)$1	1	30	49	14.2972
((.(((........))).)	chr2:155328396-155328602(-)$1	1	52	71	14.4067
((((((........)))))	chr11:106653768-106653986(+)$1	1	112	131	14.2827
((((.(........).)))	chr14:57429390-57429615(-)$1	1	100	119	14.3761
.(((((........)))))	chr2:34287707-34287935(+)$1	1	10	29	14.5797
..((((........)))).	chr11:54846781-54846989(-)$1	1	86	105	12.6831
((((((........)))))	chr18:70612807-70613020(-)$1	1	142	161	13.9357
((((((........)))))	chr2:69782363-69782585(+)$1	1	5	24	14.1028
(..(((........)))..	chr11:4558190-4558414(+)$1	1	44	63	14.1793
((((((........)))))	chr10:75895667-75895884(-)$1	1	45	64	13.9357
((..((........))..)	chr17:56204443-56204649(+)$1	1	138	157	13.2755
.(((((........)))))	chr11:70466529-70466735(-)$1	1	23	42	13.6489
(((.((........)))))	chr16:45095679-45095904(+)$1	1	20	39	13.6008
.(.(((........)))..	chr15:81451432-81451677(+)$1	1	201	220	14.6082
.(((((........)))))	chr16:20560187-20560398(+)$1	1	173	192	14.5848
((((((........)))))	chr12:32672694-32672920(-)$1	1	17	36	14.2827

#PSSM
f : 0.20	d : 0.12	: : 0.09	c : 0.09	b : 0.07	g : 0.07	" : 0.06	[ : 0.06	= : 0.04	e : 0.04	! : 0.04	# : 0.03	h : 0.01	i : 0.01	
e : 0.26	f : 0.18	c : 0.09	g : 0.07	" : 0.06	d : 0.06	! : 0.06	b : 0.04	= : 0.04	a : 0.03	[ : 0.03	# : 0.01	i : 0.01	
e : 0.26	f : 0.17	! : 0.12	[ : 0.10	d : 0.10	g : 0.07	= : 0.04	c : 0.04	a : 0.01	# : 0.01	i : 0.01	
e : 0.26	f : 0.15	c : 0.14	d : 0.10	g : 0.07	! : 0.07	[ : 0.06	= : 0.04	a : 0.03	# : 0.01	i : 0.01	
e : 0.21	f : 0.15	b : 0.15	c : 0.12	[ : 0.10	d : 0.10	g : 0.07	= : 0.03	i : 0.01	
e : 0.21	f : 0.15	b : 0.15	c : 0.12	a : 0.10	d : 0.10	g : 0.07	= : 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	
e : 0.21	f : 0.15	b : 0.15	c : 0.12	a : 0.10	d : 0.10	g : 0.07	= : 0.03	i : 0.01	
e : 0.23	f : 0.15	b : 0.15	c : 0.14	d : 0.10	] : 0.07	g : 0.07	= : 0.03	i : 0.01	
e : 0.26	f : 0.17	c : 0.17	d : 0.10	g : 0.07	2 : 0.07	a : 0.04	= : 0.04	4 : 0.01	i : 0.01	
e : 0.26	f : 0.17	d : 0.12	2 : 0.12	] : 0.09	g : 0.07	= : 0.04	c : 0.04	4 : 0.01	i : 0.01	3 : 0.01	
e : 0.26	f : 0.18	g : 0.07	c : 0.07	2 : 0.06	3 : 0.06	d : 0.06	b : 0.04	= : 0.04	4 : 0.03	a : 0.01	E : 0.01	] : 0.01	5 : 0.01	i : 0.01	

#score	891.868581034445
#seq	64
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_UTR_m1_run1.txt

#BEAR
:bbggggggg[ddddooooooddddggggggg]	chr10:79811004-79811224(-)$1	220	166	199	12.4350
dddbb[bba"""cccooooooccc333a]bb]b	chr15:34460253-34460475(+)$1	222	46	79	15.2467
bb[ffffff"""a[aooooooa]a]ffffff]b	chr19:4793725-4793959(-)$1	234	83	116	13.4725
d####ccc"""bbrrrrrrrrrbb333ccc444	chr11:116712090-116712324(-)$1	234	77	110	12.4038
b####eeeee[cccbboooooobb333ccc]ee	chr6:119797876-119798095(-)$1	219	20	53	13.8825
h[bb"""dddd[cccoooooocccdddd333bb	chr5:123059197-123059411(-)$1	214	42	75	14.3849
dddd$$$$$ffffffooooooffffff4444dd	chr8:12865237-12865452(+)$1	215	133	166	11.4917
==========!!cccooooooccc=========	chr17:29778077-29778294(+)$1	217	128	161	16.6326
c!!ccc!!ccc[ddddoooooodddd]ccc22c	chr5:116456273-116456499(+)$1	226	181	214	13.7173
bb[a[bb[bb!!cccooooooccc22bb]bb]a	chr9:86396525-86396736(+)$1	211	92	125	14.4572
FFCCCccc####cccooooooccc333ccc:cc	chr4:148681673-148681898(-)$1	225	179	212	12.3949
cc!!dddd[eeeeeooooooeeeee]dddd22c	chr14:60059333-60059545(-)$1	212	150	183	12.5715
f!!============oooooo============	chr11:102888502-102888743(-)$1	241	38	71	15.6430
bb[ccc"""bb[cccoooooocccbb22ccc]b	chrX:156409701-156409909(+)$1	208	159	192	14.6213
cc!!dddd"""ddddoooooodddd]dddd333	chr4:108507172-108507382(+)$1	210	32	65	15.5090
::iiiiiiiii[cccooooooccc22iiiiiii	chr17:24580802-24581024(-)$1	222	40	73	14.3243
ccbb[ccc"""eeeeeooooooeeeee]cccbb	chr5:145945359-145945596(-)$1	237	78	111	12.4501
ccc!!ccc!!cccqqqqqqqqccc22ccc]ccc	chr15:74825250-74825456(-)$1	206	118	151	10.0497
fff!!ddddffffffooooooffffff333ddd	chr2:131124622-131124835(+)$1	213	43	76	11.9705
$$bb[dddd[a[cccooooooccc]a]dddd]b	chr9:118466886-118467105(+)$1	219	97	130	14.8517
:::ggggggg"""bboooooobb4444gggggg	chr14:32004515-32004743(-)$1	228	51	84	12.4234
ggccc[dddd!!cccnnnnnccc4444dddd]c	chr18:90679577-90679815(+)$1	238	76	109	11.7730
DDD==========[aooooooa]==========	chr10:76495919-76496127(+)$1	208	1	34	12.7153
c[ffffff####cccooooooccc333ffffff	chr6:92088907-92089116(+)$1	209	77	110	15.3041
ee"""bb!!a####annnnna4444a22bb333	chr2:29577677-29577907(+)$1	230	146	179	12.2024
ccc####dddd[ddddllldddd22dddd333c	chr17:34133285-34133508(-)$1	223	109	142	10.4231
ggggaeeeee[ddddoooooodddd]eeeee::	chr12:82046420-82046652(+)$1	232	39	72	11.4881
gggg[dddd####bboooooobb333dddd]gg	chr4:108745573-108745787(-)$1	214	39	72	15.0454
ffff[ccc[bb[cccooooooccc]bb4444cc	chr3:96024236-96024459(-)$1	223	134	167	14.9393
bb"""ccc####ddddmmmmdddd333ccc]bb	chr10:5892365-5892577(-)$1	212	144	177	11.6147
cc"""ccc[a!!ccclllccc]a]ccc4444cc	chr5:33206717-33206940(+)$1	223	77	110	11.9309
eeegggggggbbcccooooooccc]bb]ggggg	chr17:26206057-26206272(-)$1	215	29	62	13.4749
ee[a"""eeeeecccooooooccc22eeeee22	chr7:130422827-130423048(-)$1	221	59	92	14.8974
b####ccc!!eeeeeooooooeeeee22ccc]b	chr6:85164426-85164643(-)$1	217	18	51	14.3883
gg"""ccc[ccc[bboooooobbccc]ccc333	chr1:82336975-82337182(+)$1	207	6	39	15.9940
!dddd[dddd[ddddoooooodddd]ddddddd	chr17:6176763-6176994(+)$1	231	50	83	12.4435
ddddeeeeeeeeeeooooooeeeee]eeeee33	chr11:102927252-102927462(+)$1	210	100	133	11.2009
eee[ccc!!bb!!cccnnnnnccc4444bb444	chr19:3898462-3898694(-)$1	232	107	140	11.7405
d!!eeeee"""ddddoooooodddd]eeeee]d	chr6:142959669-142959892(-)$1	223	13	46	14.0883
==[dddddddd[aooooooa]dddd]dddd22=	chr9:44644605-44644813(-)$1	208	128	161	11.5933
eeeeeeeeee[a[bboooooobb]a]eeeee66	chr2:93681972-93682181(-)$1	209	5	38	11.9061
fff$$$$$ccc[cccooooooccc]ccc22fff	chr11:120833714-120833946(-)$1	232	83	116	13.5780
dddd"""dddd!!bboooooobb22dddd333d	chr6:86370235-86370451(+)$1	216	96	129	13.9682
$$$eeeeebb!!cccooooooccc]bb]eeeee	chr19:6352522-6352731(+)$1	209	61	94	13.1953
dd"""ccc!!bbbboooooobb]bb22ccc333	chr2:28535506-28535751(+)$1	245	75	108	13.7296
ffcccccc[a[eeeeeooooooeeeee]a22cc	chr5:143145343-143145562(+)$1	219	144	177	12.1630
!a!!bb!!gggggggoooooogggggggbb22a	chr16:37834208-37834434(+)$1	226	152	185	13.6492
clllccc:ccc[cccooooooccc22ccchhhh	chr2:49101096-49101308(+)$1	212	54	87	12.5048
a[bb[ccc[ccc[bbnnnnnbb]ccc]ccc333	chr15:100238457-100238691(-)$1	234	113	146	10.9831
ggg[ggggggg[cccooooooccc333gggggg	chr18:42734098-42734309(+)$1	211	50	83	16.1870

#otherMatches

#Seq PSSM
GCGGCGGGGAUGAGAUUGGUUUCUUUCCCUGCU	chr10:79811004-79811224(-)$1	220	166	199	12.4350
GGUCAAAGCUCACAGAAAGUCCUGGCUGUCUCU	chr15:34460253-34460475(+)$1	222	46	79	15.2467
UUUUAGCGUUUUGUCAGAACCGUCCGCGCUGCA	chr19:4793725-4793959(-)$1	234	83	116	13.4725
CAUUGGGGGAAAGGACCACAAACUCAGUCCAUC	chr11:116712090-116712324(-)$1	234	77	110	12.4038
cagcagcggcggcCCUGAGGAGAGUAAGGCGGC	chr6:119797876-119798095(-)$1	219	20	53	13.8825
ACUUUAGGAGCACCUUCCGUCAGGGCUUGGUGA	chr5:123059197-123059411(-)$1	214	42	75	14.3849
GGCCUCAUCUUAAGCACUGUGGCUUGAAGCUGG	chr8:12865237-12865452(+)$1	215	133	166	11.4917
CUCUAGGGCGAUGGCGGCUUGGCUUGUUCUAGA	chr17:29778077-29778294(+)$1	217	128	161	16.6326
cccgcccagcccggcccugcuuggccuggccag	chr5:116456273-116456499(+)$1	226	181	214	13.7173
CAAGUGAAUGGAUUUGGAGAAGAAAGCACUCUC	chr9:86396525-86396736(+)$1	211	92	125	14.4572
CUCCCGCCAAUCCUCGAUGCAGAGCUGGGCGGC	chr4:148681673-148681898(-)$1	225	179	212	12.3949
AAAUUAUUUAUCAGUUGAACUUGAUUGGUAUCU	chr14:60059333-60059545(-)$1	212	150	183	12.5715
AUUGUUUGUAGGCGGCAAAAUCUGUCUAUAAAU	chr11:102888502-102888743(-)$1	241	38	71	15.6430
GGUCCCUCAGCACUCGUCCAUGAGGCCUGGGUU	chrX:156409701-156409909(+)$1	208	159	192	14.6213
CCGUCUAACAUCACUUCCUUCAGUGUUUGGCUA	chr4:108507172-108507382(+)$1	210	32	65	15.5090
GAGAGCUGGUCAUUGCUUCACCAGAGGGCCAGC	chr17:24580802-24581024(-)$1	222	40	73	14.3243
GGGUAUGACCGGUAUUACAACAAGUACAUCAAC	chr5:145945359-145945596(-)$1	237	78	111	12.4501
CUGUUGAGUCCAAUAAACCCUUUGUUCUCCCAG	chr15:74825250-74825456(-)$1	206	118	151	10.0497
UUGAAACAGCAGGGGUAGCUUUUCCUGAUCCUG	chr2:131124622-131124835(+)$1	213	43	76	11.9705
AGGAGUCCUGCAUCACACAGCUGAAGAAGGAGU	chr9:118466886-118467105(+)$1	219	97	130	14.8517
CCUUGCAGCUCUAUGCUAUCACAGAACAGCUGC	chr14:32004515-32004743(-)$1	228	51	84	12.4234
AGGCGGGAGCCUGCAUUAUUUGUCUCUGCUCGC	chr18:90679577-90679815(+)$1	238	76	109	11.7730
UUCGGGGCGUGGUCAGUCAGGUAACCACGCCUC	chr10:76495919-76496127(+)$1	208	1	34	12.7153
CCAGGUGACCACUCAGCACGUUGAUCCUCGCCU	chr6:92088907-92089116(+)$1	209	77	110	15.3041
GGAAAGGUAAGAAGCAAGCAGGAAGUGUCCAGG	chr2:29577677-29577907(+)$1	230	146	179	12.2024
GGACUUGGUGACAGACAAUGUCUUCUCAUAUCU	chr17:34133285-34133508(-)$1	223	109	142	10.4231
GCCCCGGAAGUGACGCCAGGACGUCCCUUCCAU	chr12:82046420-82046652(+)$1	232	39	72	11.4881
UGGAUCUGCCUCAGUCUUGACACACAGCAGCUC	chr4:108745573-108745787(-)$1	214	39	72	15.0454
AAGGAGCUAGCUAACGCGCCAGUUUGUGACCAG	chr3:96024236-96024459(-)$1	223	134	167	14.9393
AUAAGGACAUUAAAGUGCGAGCUUCAGGUUGGU	chr10:5892365-5892577(-)$1	212	144	177	11.6147
UCUUUUCCCCAGGACAUUGUUAGUGGACCGCGA	chr5:33206717-33206940(+)$1	223	77	110	11.9309
gcgccccgcgcgcgcccgcccgcgucgccgcgg	chr17:26206057-26206272(-)$1	215	29	62	13.4749
UUGGCGACUGCUGGCUCUGUCGCCUCAGCAGAA	chr7:130422827-130423048(-)$1	221	59	92	14.8974
AACUUGGGUUCCCCACAAGCCUGGGGCUCCUCU	chr6:85164426-85164643(-)$1	217	18	51	14.3883
AGAACGAGAGGGAUCAACACCGGCCUCCUCCUG	chr1:82336975-82337182(+)$1	207	6	39	15.9940
UUCUAAUUUUUCUAGGUUGUGCUGGUGAGAUGG	chr17:6176763-6176994(+)$1	231	50	83	12.4435
ACCUAGCUCGUGAUUGGCAUAUUAUGGAGUUAA	chr11:102927252-102927462(+)$1	210	100	133	11.2009
UGGUGUCUUCCUUGGACCAUAUCCCUUUGGCAU	chr19:3898462-3898694(-)$1	232	107	140	11.7405
GUUGCUUCAUAUUUAAUUGUCUAGAAGAGGCUU	chr6:142959669-142959892(-)$1	223	13	46	14.0883
UCGCCGCUGCAAGUUUUGCCAUGUGUGUGGAAG	chr9:44644605-44644813(-)$1	208	128	161	11.5933
GACAGGGUCUGUAGCAUCCAAGCCAGAGGCCAA	chr2:93681972-93682181(-)$1	209	5	38	11.9061
AGAACAAUCUCGAAGGGAUGACUUGGAGUCUCU	chr11:120833714-120833946(-)$1	232	83	116	13.5780
UUUGUUGGUGACCUCAGUCCAGAAAUCACAACC	chr6:86370235-86370451(+)$1	216	96	129	13.9682
AGGGGAUCCCAGGUUCUGCACAGCAGGUGAUCC	chr19:6352522-6352731(+)$1	209	61	94	13.1953
UGGAAGGUGAGUCUGCAGAAAGAACAAGCCCGA	chr2:28535506-28535751(+)$1	245	75	108	13.7296
CAGGUCUCAGGGGUCUGAGGUUGGACUGUACGA	chr5:143145343-143145562(+)$1	219	144	177	12.1630
UGAACUAGCCCUGCUGGAGGAAGUGGGGGGAGC	chr16:37834208-37834434(+)$1	226	152	185	13.6492
UUAAAGCAUGUGGCCUUUAACGGCGGGCAGUAC	chr2:49101096-49101308(+)$1	212	54	87	12.5048
UCACCGGCUUGCAUCUUGCUGAAGUAUGUCACC	chr15:100238457-100238691(-)$1	234	113	146	10.9831
UUGUGCUUUUUCUCUUAUUUCAGAUCCAAAAAG	chr18:42734098-42734309(+)$1	211	50	83	16.1870

#DB
.(((((((((.((((......))))))))))).	chr10:79811004-79811224(-)$1	1	166	199	12.4350
(((((.(((...(((......)))...).)).)	chr15:34460253-34460475(+)$1	1	46	79	15.2467
((.((((((...(.(......).).)))))).)	chr19:4793725-4793959(-)$1	1	83	116	13.4725
(....(((...((.........))...)))...	chr11:116712090-116712324(-)$1	1	77	110	12.4038
(....(((((.(((((......))...))).))	chr6:119797876-119798095(-)$1	1	20	53	13.8825
(.((...((((.(((......)))))))...))	chr5:123059197-123059411(-)$1	1	42	75	14.3849
((((.....((((((......))))))....))	chr8:12865237-12865452(+)$1	1	133	166	11.4917
((((((((((..(((......))))))))))))	chr17:29778077-29778294(+)$1	1	128	161	16.6326
(..(((..(((.((((......)))).)))..)	chr5:116456273-116456499(+)$1	1	181	214	13.7173
((.(.((.((..(((......)))..)).)).)	chr9:86396525-86396736(+)$1	1	92	125	14.4572
)))))(((....(((......)))...))).((	chr4:148681673-148681898(-)$1	1	179	212	12.3949
((..((((.(((((......))))).))))..)	chr14:60059333-60059545(-)$1	1	150	183	12.5715
(..((((((((((((......))))))))))))	chr11:102888502-102888743(-)$1	1	38	71	15.6430
((.(((...((.(((......)))))..))).)	chrX:156409701-156409909(+)$1	1	159	192	14.6213
((..((((...((((......)))).))))...	chr4:108507172-108507382(+)$1	1	32	65	15.5090
..(((((((((.(((......)))..)))))))	chr17:24580802-24581024(-)$1	1	40	73	14.3243
))((.(((...(((((......))))).)))))	chr5:145945359-145945596(-)$1	1	78	111	12.4501
(((..(((..(((........)))..))).)))	chr15:74825250-74825456(-)$1	1	118	151	10.0497
(((..((((((((((......))))))...)))	chr2:131124622-131124835(+)$1	1	43	76	11.9705
..((.((((.(.(((......))).).)))).)	chr9:118466886-118467105(+)$1	1	97	130	14.8517
...(((((((...((......))....))))))	chr14:32004515-32004743(-)$1	1	51	84	12.4234
))(((.((((..(((.....)))....)))).)	chr18:90679577-90679815(+)$1	1	76	109	11.7730
(((((((((((((.(......).))))))))))	chr10:76495919-76496127(+)$1	1	1	34	12.7153
(.((((((....(((......)))...))))))	chr6:92088907-92089116(+)$1	1	77	110	15.3041
((...((..(....(.....)....)..))...	chr2:29577677-29577907(+)$1	1	146	179	12.2024
(((....((((.((((...))))..))))...)	chr17:34133285-34133508(-)$1	1	109	142	10.4231
)))))(((((.((((......)))).)))))..	chr12:82046420-82046652(+)$1	1	39	72	11.4881
((((.((((....((......))...)))).))	chr4:108745573-108745787(-)$1	1	39	72	15.0454
((((.(((.((.(((......))).))....))	chr3:96024236-96024459(-)$1	1	134	167	14.9393
((...(((....((((....))))...))).))	chr10:5892365-5892577(-)$1	1	144	177	11.6147
((...(((.(..(((...))).).)))....))	chr5:33206717-33206940(+)$1	1	77	110	11.9309
(((((((((((((((......))).)).)))))	chr17:26206057-26206272(-)$1	1	29	62	13.4749
((.(...((((((((......)))..)))))..	chr7:130422827-130423048(-)$1	1	59	92	14.8974
(....(((..(((((......)))))..))).)	chr6:85164426-85164643(-)$1	1	18	51	14.3883
((...(((.(((.((......))))).)))...	chr1:82336975-82337182(+)$1	1	6	39	15.9940
.((((.((((.((((......)))).)))))))	chr17:6176763-6176994(+)$1	1	50	83	12.4435
((((((((((((((......))))).)))))..	chr11:102927252-102927462(+)$1	1	100	133	11.2009
(((.(((..((..(((.....)))....))...	chr19:3898462-3898694(-)$1	1	107	140	11.7405
(..(((((...((((......)))).))))).)	chr6:142959669-142959892(-)$1	1	13	46	14.0883
((.((((((((.(......).)))).))))..)	chr9:44644605-44644813(-)$1	1	128	161	11.5933
((((((((((.(.((......)).).)))))..	chr2:93681972-93682181(-)$1	1	5	38	11.9061
(((.....(((.(((......))).)))..)))	chr11:120833714-120833946(-)$1	1	83	116	13.5780
((((...((((..((......))..))))...)	chr6:86370235-86370451(+)$1	1	96	129	13.9682
...(((((((..(((......))).)).)))))	chr19:6352522-6352731(+)$1	1	61	94	13.1953
((...(((..((((......)).))..)))...	chr2:28535506-28535751(+)$1	1	75	108	13.7296
))((((((.(.(((((......))))).)..))	chr5:143145343-143145562(+)$1	1	144	177	12.1630
.(..((..(((((((......)))))))))..)	chr16:37834208-37834434(+)$1	1	152	185	13.6492
(...))).(((.(((......)))..)))((((	chr2:49101096-49101308(+)$1	1	54	87	12.5048
(.((.(((.(((.((.....)).))).)))...	chr15:100238457-100238691(-)$1	1	113	146	10.9831
(((.(((((((.(((......)))...))))))	chr18:42734098-42734309(+)$1	1	50	83	16.1870

#PSSM
c : 0.18	d : 0.14	b : 0.12	f : 0.10	g : 0.10	e : 0.10	: : 0.06	= : 0.04	$ : 0.04	! : 0.04	h : 0.02	F : 0.02	D : 0.02	a : 0.02	
d : 0.12	c : 0.12	b : 0.10	g : 0.10	e : 0.10	f : 0.08	# : 0.06	[ : 0.06	! : 0.06	= : 0.04	: : 0.04	$ : 0.04	F : 0.02	D : 0.02	a : 0.02	l : 0.02	
! : 0.12	b : 0.10	d : 0.10	[ : 0.10	" : 0.10	c : 0.08	f : 0.08	# : 0.06	g : 0.06	e : 0.06	= : 0.02	C : 0.02	i : 0.02	: : 0.02	D : 0.02	$ : 0.02	l : 0.02	
g : 0.10	b : 0.10	d : 0.10	! : 0.10	" : 0.10	# : 0.08	c : 0.08	f : 0.06	= : 0.06	e : 0.06	a : 0.04	[ : 0.04	C : 0.02	i : 0.02	$ : 0.02	l : 0.02	
" : 0.16	c : 0.12	[ : 0.12	g : 0.08	# : 0.08	d : 0.08	e : 0.08	= : 0.06	b : 0.04	f : 0.04	$ : 0.04	! : 0.04	C : 0.02	i : 0.02	a : 0.02	
c : 0.32	e : 0.12	d : 0.12	g : 0.08	[ : 0.06	" : 0.06	= : 0.06	b : 0.06	f : 0.04	$ : 0.04	i : 0.02	# : 0.02	
c : 0.27	d : 0.16	e : 0.12	g : 0.08	" : 0.08	b : 0.06	= : 0.06	f : 0.04	$ : 0.04	! : 0.04	i : 0.02	# : 0.02	
c : 0.23	d : 0.21	e : 0.14	g : 0.08	! : 0.08	= : 0.06	f : 0.04	$ : 0.04	b : 0.02	[ : 0.02	" : 0.02	i : 0.02	: : 0.02	
d : 0.18	[ : 0.12	g : 0.10	" : 0.10	e : 0.10	! : 0.10	= : 0.06	c : 0.06	# : 0.06	b : 0.04	a : 0.02	f : 0.02	$ : 0.02	i : 0.02	
" : 0.12	e : 0.12	d : 0.12	g : 0.10	c : 0.10	b : 0.10	# : 0.08	= : 0.06	! : 0.06	a : 0.06	f : 0.04	i : 0.02	[ : 0.02	
" : 0.14	[ : 0.12	c : 0.12	! : 0.10	# : 0.10	b : 0.10	d : 0.08	e : 0.08	f : 0.04	= : 0.04	g : 0.04	i : 0.02	a : 0.02	
[ : 0.21	! : 0.14	e : 0.12	d : 0.10	# : 0.10	c : 0.08	" : 0.06	b : 0.06	f : 0.04	= : 0.04	a : 0.02	g : 0.02	
c : 0.40	d : 0.16	e : 0.10	[ : 0.06	a : 0.04	b : 0.04	f : 0.04	= : 0.04	# : 0.04	! : 0.04	" : 0.02	g : 0.02	
c : 0.40	d : 0.16	b : 0.14	e : 0.10	[ : 0.04	f : 0.04	r : 0.02	= : 0.02	q : 0.02	# : 0.02	o : 0.02	g : 0.02	
c : 0.38	d : 0.16	b : 0.14	o : 0.08	a : 0.06	e : 0.06	f : 0.04	r : 0.02	= : 0.02	q : 0.02	g : 0.02	
o : 0.74	d : 0.06	n : 0.06	e : 0.04	r : 0.02	b : 0.02	q : 0.02	l : 0.02	c : 0.02	
o : 0.82	n : 0.08	l : 0.04	r : 0.02	q : 0.02	m : 0.02	
o : 0.82	n : 0.08	l : 0.04	r : 0.02	q : 0.02	m : 0.02	
o : 0.82	n : 0.08	r : 0.02	q : 0.02	l : 0.02	m : 0.02	c : 0.02	
o : 0.80	n : 0.08	r : 0.02	q : 0.02	d : 0.02	m : 0.02	c : 0.02	a : 0.02	
o : 0.74	e : 0.04	c : 0.04	d : 0.04	b : 0.04	r : 0.02	q : 0.02	a : 0.02	n : 0.02	] : 0.02	
c : 0.38	d : 0.16	b : 0.14	o : 0.08	e : 0.06	a : 0.04	f : 0.04	r : 0.02	= : 0.02	4 : 0.02	] : 0.02	g : 0.02	
c : 0.38	d : 0.18	b : 0.14	e : 0.10	] : 0.08	f : 0.04	= : 0.02	4 : 0.02	a : 0.02	g : 0.02	
c : 0.40	d : 0.16	e : 0.10	b : 0.06	4 : 0.06	f : 0.04	= : 0.04	2 : 0.04	] : 0.04	a : 0.02	3 : 0.02	g : 0.02	
d : 0.16	3 : 0.16	2 : 0.14	] : 0.12	e : 0.10	4 : 0.08	= : 0.06	c : 0.06	f : 0.04	b : 0.04	a : 0.02	g : 0.02	
3 : 0.16	] : 0.16	2 : 0.12	d : 0.08	b : 0.08	c : 0.08	f : 0.06	= : 0.06	e : 0.06	4 : 0.06	g : 0.04	a : 0.04	
d : 0.16	3 : 0.14	e : 0.14	] : 0.08	b : 0.08	2 : 0.08	c : 0.08	f : 0.06	= : 0.06	4 : 0.06	g : 0.04	i : 0.02	
c : 0.21	d : 0.19	e : 0.10	g : 0.08	4 : 0.08	] : 0.08	= : 0.06	2 : 0.06	f : 0.04	a : 0.02	b : 0.02	i : 0.02	3 : 0.02	
c : 0.25	d : 0.18	e : 0.12	g : 0.08	4 : 0.06	= : 0.06	b : 0.06	] : 0.04	f : 0.04	3 : 0.04	i : 0.02	2 : 0.02	a : 0.02	
c : 0.21	d : 0.14	e : 0.12	b : 0.10	g : 0.08	3 : 0.08	4 : 0.06	= : 0.06	f : 0.04	2 : 0.04	i : 0.02	] : 0.02	h : 0.02	
3 : 0.16	e : 0.12	4 : 0.10	2 : 0.10	g : 0.08	c : 0.08	d : 0.08	f : 0.06	] : 0.06	= : 0.06	b : 0.04	: : 0.02	i : 0.02	h : 0.02	
] : 0.16	3 : 0.16	g : 0.10	2 : 0.10	c : 0.10	b : 0.06	d : 0.06	= : 0.06	4 : 0.04	e : 0.04	f : 0.04	i : 0.02	: : 0.02	6 : 0.02	h : 0.02	
c : 0.18	b : 0.16	3 : 0.12	d : 0.10	= : 0.08	g : 0.08	4 : 0.04	e : 0.04	a : 0.04	f : 0.04	] : 0.02	i : 0.02	: : 0.02	2 : 0.02	6 : 0.02	h : 0.02	

#score	664.057707141798
#seq	50
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_CDS_m2_run2.txt

#BEAR
fffffvvvvvvvvvvvvvffffffggg	chr6:47527473-47527784(-)$1	311	207	234	21.9689
ccc[cccuuuuuuuuuuuuccc]ccc2	chr8:127998677-127998945(-)$1	268	56	83	24.0802
ffffccctttttttttttccc4444ff	chr13:97863478-97863766(+)$1	288	173	200	24.4635
[a[ddddtttttttttttdddd]a]cc	chr11:87862493-87862796(+)$1	303	151	178	24.7401
dddcccvvvvvvvvvvvvvccc]dddd	chr3:88367054-88367336(+)$1	282	20	47	22.8134
ee[ddddyyyyyyyyyyyyyyyydddd	chr10:42197993-42198284(-)$1	291	158	185	21.1908
e!!ddddtttttttttttdddd22eee	chr10:127520819-127521112(+)$1	293	214	241	23.9535
a[eeeeettttttttttteeeeeaa]d	chr7:134014556-134014927(-)$1	371	18	45	23.6428
:::ddddtttttttttttdddddddd[	chr2:31656762-31657034(+)$1	272	46	73	20.4409
##dddduuuuuuuuuuuudddd333hh	chr2:130440062-130440332(-)$1	270	59	86	23.6070
gg!!bbyyyyyyyyyyyyyyyybb]gg	chr14:52760734-52761006(+)$1	272	133	160	21.6542
bb!!ccctttttttttttccc22bb]e	chr8:87083379-87083647(+)$1	268	192	219	24.1355
gggggggvvvvvvvvvvvvvggggggg	chr13:3587630-3587901(-)$1	271	29	56	23.0004
ee[bbvvvvvvvvvvvvvbb]eeeeec	chr4:148722081-148722350(-)$1	269	12	39	21.2820
"""ddddtttttttttttdddd333cc	chr17:35292431-35292802(-)$1	371	108	135	25.0623
#ffffffuuuuuuuuuuuuffffff44	chr2:162868312-162868598(+)$1	286	94	121	23.3011
a!!ddddtttttttttttdddd22a]a	chr4:131456309-131456587(+)$1	278	245	272	24.4468
f"""ccctttttttttttccc22ffff	chr1:40071247-40071523(+)$1	276	194	221	24.4155
!fffffftttttttttttffffff22b	chr13:23831138-23831414(+)$1	276	199	226	23.4339
b[eeeeettttttttttteeeeebb]e	chr7:36093139-36093409(-)$1	270	68	95	23.0741
gggggggtttttttttttggggggg]f	chr4:153393827-153394134(+)$1	307	164	191	23.8988
dd[a[bbtttttttttttbb]addddh	chr16:87427749-87428016(-)$1	267	119	146	22.3326
iiiiiiivvvvvvvvvvvvviiiiiii	chr13:55170980-55171260(-)$1	280	194	221	22.9571
Gffffffvvvvvvvvvvvvvffffff:	chr13:23838535-23838807(+)$1	272	32	59	20.9833
[bbddddtttttttttttdddd]bb33	chr6:88841553-88841826(-)$1	273	155	182	23.5750
dd[cccvvvvvvvvvvvvvccc22ddd	chr2:164665901-164666177(+)$1	276	181	208	23.2675
[eeeeeuuuuuuuuuuuueeeeedddd	chr15:75805551-75805828(+)$1	277	108	135	22.5718
ccdddduuuuuuuuuuuudddd333cc	chr18:67654717-67654998(-)$1	281	33	60	23.6624
!eeeeeuuuuuuuuuuuueeeeebbcc	chr14:8916313-8916642(+)$1	329	147	174	22.6512
bb!!ccctttttttttttccc22bb]e	chr15:77797661-77797944(-)$1	283	126	153	24.1355
c"""cccuuuuuuuuuuuuccc333cc	chr19:12004339-12004610(+)$1	271	102	129	25.2213
ee[cccvvvvvvvvvvvvvccc]eeee	chr15:90398547-90398819(-)$1	272	87	114	23.5292
b####bbuuuuuuuuuuuubb4444bb	chr2:24646842-24647118(-)$1	276	166	193	22.6581
!fffffftttttttttttffffff333	chr7:148637040-148637308(+)$1	268	6	33	24.0139
!bbyyyyyyyyyyyyyyyybb4444cc	chr4:32781397-32781672(+)$1	275	54	81	21.2690
h!!ddddtttttttttttdddd22hhh	chr19:21872301-21872583(+)$1	282	68	95	23.5915
[ffffffuuuuuuuuuuuuffffffcc	chr5:100962159-100962430(+)$1	271	15	42	23.5100
ffffffuuuuuuuuuuuuffffff22e	chr17:45590931-45591200(-)$1	269	60	87	22.7235
[bbbbwwwwwwwwwwwwwwbb]bb22d	chr3:121346032-121346300(-)$1	268	52	79	20.1848
:fffffftttttttttttffffffbbb	chr1:177829450-177829724(+)$1	274	176	203	21.8347
"""cccvvvvvvvvvvvvvccc333ff	chr2:155683708-155683976(-)$1	268	157	184	24.6132
cc[ddddwwwwwwwwwwwwwwddddcc	chr17:84797482-84797756(-)$1	274	26	53	21.3986
=======ttttttttttt=========	chr14:99467298-99467581(+)$1	283	235	262	24.4765
cc[ddddtttttttttttddddccc33	chr2:26266240-26266514(-)$1	274	209	236	24.0667
[eeeeevvvvvvvvvvvvveeeeeddd	chr7:118218580-118218852(-)$1	272	122	149	22.5425
ee[bbbbvvvvvvvvvvvvvbb]bb]e	chr5:116028834-116029113(+)$1	279	191	218	21.7937
[a[bb[attttttttttta]bb]a]gg	chr5:125366369-125366658(+)$1	289	42	69	24.2670
fffddddyyyyyyyyyyyyyyyydddd	chr1:181725777-181726062(-)$1	285	204	231	21.0107
ggggggyyyyyyyyyyyyyyyyggggg	chr2:25133723-25134051(+)$1	328	90	117	22.1385
###ddddyyyyyyyyyyyyyyyydddd	chr16:34212760-34213031(-)$1	271	23	50	21.5223
!cccccctttttttttttccc]ccc]a	chr17:75142168-75142437(+)$1	269	144	171	24.6099
c"""cccuuuuuuuuuuuuccc22ccc	chr11:80063588-80063857(+)$1	269	120	147	24.6128
fffffvvvvvvvvvvvvvffffff22e	chr7:148633759-148634048(+)$1	289	195	222	21.8435
$bbyyyyyyyyyyyyyyyybbgggggg	chr1:19224039-19224310(+)$1	271	195	222	20.7112
ddd[ccctttttttttttcccdddd::	chr10:79788572-79788842(-)$1	270	35	62	21.6672
ff[ddddvvvvvvvvvvvvvdddd]ff	chr3:65357116-65357387(+)$1	271	25	52	22.7672
ggggg[attttttttttta]ggggggg	chr16:13806538-13806807(+)$1	269	99	126	24.2949
""a[ccctttttttttttccca333ee	chr2:24276886-24277154(-)$1	268	44	71	25.3883
gggggggvvvvvvvvvvvvvggggggg	chr9:102528110-102528383(-)$1	273	107	134	23.0004
fa!!cccuuuuuuuuuuuuccc]a]ff	chr11:78296643-78296913(-)$1	270	171	198	24.6757
!!eeeeeuuuuuuuuuuuueeeeefff	chr16:4496287-4496562(-)$1	275	152	179	23.3336
[ffffffyyyyyyyyyyyyyyyyffff	chr11:53520382-53520658(-)$1	276	104	131	21.2911
:fffffftttttttttttffffffeee	chr7:52094842-52095122(+)$1	280	171	198	22.3782
!!eeeeeuuuuuuuuuuuueeeee22a	chr2:19231570-19231841(+)$1	271	74	101	23.4955
ggggwwwwwwwwwwwwwwggggggg]c	chr11:20124587-20124904(+)$1	317	248	275	20.9583

#otherMatches

#Seq PSSM
AGCUCAAGAGGUUCAGAAGAGCUGAUG	chr6:47527473-47527784(-)$1	311	207	234	21.9689
CAGCACAAAAUUGGGAUCCUGUACUGC	chr8:127998677-127998945(-)$1	268	56	83	24.0802
CCUUUGCUUUGUUUUUUUGUAAAUUGA	chr13:97863478-97863766(+)$1	288	173	200	24.4635
GGAGUUUGUACGGAAAGAAGAUAUGAC	chr11:87862493-87862796(+)$1	303	151	178	24.7401
UCAUCCUCCCAACCUCUUCGGACUGAG	chr3:88367054-88367336(+)$1	282	20	47	22.8134
GCGCGGGUCGUCGCAAUCCCUCCUCCG	chr10:42197993-42198284(-)$1	291	158	185	21.1908
GACGUCCAGUUCGAUGAGGGAUUACCA	chr10:127520819-127521112(+)$1	293	214	241	23.9535
GCAGGCCAGCUACCCAUGGGCCUCCCU	chr7:134014556-134014927(-)$1	371	18	45	23.6428
CAAAGACAAAAUGCACGAGUCUGGCUA	chr2:31656762-31657034(+)$1	272	46	73	20.4409
ACUCUGGUUGCAAUGGGACAGAUAGAU	chr2:130440062-130440332(-)$1	270	59	86	23.6070
UGAAUCACCUCCUGGACUUCAAGAACA	chr14:52760734-52761006(+)$1	272	133	160	21.6542
CAGACACCGACGCAGAAAGUGAGUGGG	chr8:87083379-87083647(+)$1	268	192	219	24.1355
CCUUCCUCAAAGAAAAUAAAGGGAAGG	chr13:3587630-3587901(-)$1	271	29	56	23.0004
GGACCCUGUCUCCUUCCCGGCCUAGCG	chr4:148722081-148722350(-)$1	269	12	39	21.2820
GAACUCAGACCAAGCCAAUGAGGAAUG	chr17:35292431-35292802(-)$1	371	108	135	25.0623
AAAGACUGCACUUCCCCUAGGUCUUCC	chr2:162868312-162868598(+)$1	286	94	121	23.3011
cagccgcagcaaggacaagcggaaggg	chr4:131456309-131456587(+)$1	278	245	272	24.4468
CAAUGUGAACCCCACGAACACUAGGCC	chr1:40071247-40071523(+)$1	276	194	221	24.4155
UGCAGCCAAGAAAAAGUAGGCUGCCUC	chr13:23831138-23831414(+)$1	276	199	226	23.4339
GAUAGCACCUAAAGCAAUUGUUACCAC	chr7:36093139-36093409(-)$1	270	68	95	23.0741
CCUGUAggugugggugugcuguaggug	chr4:153393827-153394134(+)$1	307	164	191	23.8988
AGAUUCCGAUUUCCGAAUGGUGCUGCG	chr16:87427749-87428016(-)$1	267	119	146	22.3326
CUGUGGGUCUCAGGUCUCUUUCUACAG	chr13:55170980-55171260(-)$1	280	194	221	22.9571
UGCUCCUUCAUUUGAAUUUCAGGAGUA	chr13:23838535-23838807(+)$1	272	32	59	20.9833
AGGAGGUGAGUAACCCAGACCUGCCAC	chr6:88841553-88841826(-)$1	273	155	182	23.5750
UGGGCCCUACCUAAAAGAUGGCAGCAA	chr2:164665901-164666177(+)$1	276	181	208	23.2675
CUUCUUCACGCGACAUCAGAGAACUCA	chr15:75805551-75805828(+)$1	277	108	135	22.5718
CCUGAGCUCAUUCUCUCUCUCAUUCGG	chr18:67654717-67654998(-)$1	281	33	60	23.6624
CGUGGCACAGUUCAAACAGCUGCUCGU	chr14:8916313-8916642(+)$1	329	147	174	22.6512
AGGAGGAUGAGACAAGCUUCCAGCUGG	chr15:77797661-77797944(-)$1	283	126	153	24.1355
CAUAUGCUAAUCUAAUGUUGCAGCGGG	chr19:12004339-12004610(+)$1	271	102	129	25.2213
UUUCCUGGCAGAACAAUCAAGGUAGAA	chr15:90398547-90398819(-)$1	272	87	114	23.5292
AUCUAGCCCUAUAUAUCAAGCCUCUUA	chr2:24646842-24647118(-)$1	276	166	193	22.6581
ACUCAAGGUUUAUUGUUGCUUGGGGCU	chr7:148637040-148637308(+)$1	268	6	33	24.0139
UGGCUAAUAUUUUACAGAACCUAUCCA	chr4:32781397-32781672(+)$1	275	54	81	21.2690
UGGGGAUGAUAAAGAUGGAUCCAAGAA	chr19:21872301-21872583(+)$1	282	68	95	23.5915
UGGAUGCAGUUCCACUAUAGUGUCCGG	chr5:100962159-100962430(+)$1	271	15	42	23.5100
AUCCCCAAAUUGACACCAGGGGAUAAU	chr17:45590931-45591200(-)$1	269	60	87	22.7235
acuacuuuaucucuaaaaugUCAGCAA	chr3:121346032-121346300(-)$1	268	52	79	20.1848
AAGUCCUGCCCCGAUUCUGGGACUGCU	chr1:177829450-177829724(+)$1	274	176	203	21.8347
CAUGGCCUCCCCAGCAAAAGCCCACCA	chr2:155683708-155683976(-)$1	268	157	184	24.6132
AGUGUACACGUUUACCUUUUAGUACCU	chr17:84797482-84797756(-)$1	274	26	53	21.3986
UAUUGCUGAGAAAGAGCGAGCAGUGCU	chr14:99467298-99467581(+)$1	283	235	262	24.4765
ACAUGGCAGUAACUCAGAGCCGGUCAU	chr2:26266240-26266514(-)$1	274	209	236	24.0667
ACAGUGGAAAUGCCAACGACGCUGUCA	chr7:118218580-118218852(-)$1	272	122	149	22.5425
ACUGCGCCAUCUCUACCUCCGCUGCUG	chr5:116028834-116029113(+)$1	279	191	218	21.7937
GGAGAGAAGCCCUAUAAAUGUUAUGAG	chr5:125366369-125366658(+)$1	289	42	69	24.2670
UAUGACCUUGGUAUAUCAAGAGUGGUC	chr1:181725777-181726062(-)$1	285	204	231	21.0107
GUCAGGGACAGCAACAUUCAAUCCUGG	chr2:25133723-25134051(+)$1	328	90	117	22.1385
CCUGCUUUACCCACAGCCAUCUUGAGC	chr16:34212760-34213031(-)$1	271	23	50	21.5223
AGAUGUCAGGAGAAAAGAGGCUGUCCC	chr17:75142168-75142437(+)$1	269	144	171	24.6099
GUAACAAGGGAUAAAAAGAUUGACCUG	chr11:80063588-80063857(+)$1	269	120	147	24.6128
GCUGGAUCCAAAUGUCUACCAGCGGCG	chr7:148633759-148634048(+)$1	289	195	222	21.8435
CGCACUUCAGUCUCAUCACGCACGGCU	chr1:19224039-19224310(+)$1	271	195	222	20.7112
AAGAUCUCAACAUCCUAAAGGCUUGGA	chr10:79788572-79788842(-)$1	270	35	62	21.6672
CAAGCACAACUUUGAUCCCCGUGUCUG	chr3:65357116-65357387(+)$1	271	25	52	22.7672
UUUUCUCUUUCUAGCACUGUGAAGACA	chr16:13806538-13806807(+)$1	269	99	126	24.2949
AAGCGCACCACCCACCUCUGCCACAGC	chr2:24276886-24277154(-)$1	268	44	71	25.3883
GGGUUCCUCCUCCUCCCUAUGGGACUC	chr9:102528110-102528383(-)$1	273	107	134	23.0004
GCUCGCAAUUUUGUCCUGGUGCUGUCU	chr11:78296643-78296913(-)$1	270	171	198	24.6757
AAUGGGGUAGGAAUUAAUUCCUCAGGG	chr16:4496287-4496562(-)$1	275	152	179	23.3336
UCCCGGAUCGAAAAGAUGAGCAUUCUG	chr11:53520382-53520658(-)$1	276	104	131	21.2911
GGGGCGCUGCUACUGAACGCGCCUGUG	chr7:52094842-52095122(+)$1	280	171	198	22.3782
GAUCGGGAACCUGCCCCCACCCGAAGA	chr2:19231570-19231841(+)$1	271	74	101	23.4955
AGGCUGCUGCUAAAAUCUGCCUCCGUC	chr11:20124587-20124904(+)$1	317	248	275	20.9583

#DB
(((((.............))))))(((	chr6:47527473-47527784(-)$1	1	207	234	21.9689
(((.(((............))).))).	chr8:127998677-127998945(-)$1	1	56	83	24.0802
(((((((...........)))....))	chr13:97863478-97863766(+)$1	1	173	200	24.4635
.(.((((...........)))).).))	chr11:87862493-87862796(+)$1	1	151	178	24.7401
((((((.............))).))))	chr3:88367054-88367336(+)$1	1	20	47	22.8134
((.((((................))))	chr10:42197993-42198284(-)$1	1	158	185	21.1908
(..((((...........))))..)))	chr10:127520819-127521112(+)$1	1	214	241	23.9535
(.(((((...........))))))).)	chr7:134014556-134014927(-)$1	1	18	45	23.6428
...((((...........))))((((.	chr2:31656762-31657034(+)$1	1	46	73	20.4409
..((((............))))...))	chr2:130440062-130440332(-)$1	1	59	86	23.6070
((..((................)).))	chr14:52760734-52761006(+)$1	1	133	160	21.6542
((..(((...........)))..)).)	chr8:87083379-87083647(+)$1	1	192	219	24.1355
(((((((.............)))))))	chr13:3587630-3587901(-)$1	1	29	56	23.0004
((.((.............)).)))))(	chr4:148722081-148722350(-)$1	1	12	39	21.2820
...((((...........))))...))	chr17:35292431-35292802(-)$1	1	108	135	25.0623
.((((((............))))))..	chr2:162868312-162868598(+)$1	1	94	121	23.3011
(..((((...........))))..).)	chr4:131456309-131456587(+)$1	1	245	272	24.4468
(...(((...........)))..))))	chr1:40071247-40071523(+)$1	1	194	221	24.4155
.((((((...........))))))..)	chr13:23831138-23831414(+)$1	1	199	226	23.4339
(.(((((...........))))))).)	chr7:36093139-36093409(-)$1	1	68	95	23.0741
(((((((...........))))))).)	chr4:153393827-153394134(+)$1	1	164	191	23.8988
((.(.((...........)).)))))(	chr16:87427749-87428016(-)$1	1	119	146	22.3326
(((((((.............)))))))	chr13:55170980-55171260(-)$1	1	194	221	22.9571
(((((((.............)))))).	chr13:23838535-23838807(+)$1	1	32	59	20.9833
.((((((...........)))).))..	chr6:88841553-88841826(-)$1	1	155	182	23.5750
((.(((.............)))..)))	chr2:164665901-164666177(+)$1	1	181	208	23.2675
.(((((............)))))))))	chr15:75805551-75805828(+)$1	1	108	135	22.5718
((((((............))))...))	chr18:67654717-67654998(-)$1	1	33	60	23.6624
.(((((............)))))))))	chr14:8916313-8916642(+)$1	1	147	174	22.6512
((..(((...........)))..)).)	chr15:77797661-77797944(-)$1	1	126	153	24.1355
(...(((............)))...))	chr19:12004339-12004610(+)$1	1	102	129	25.2213
((.(((.............))).))))	chr15:90398547-90398819(-)$1	1	87	114	23.5292
(....((............))....))	chr2:24646842-24647118(-)$1	1	166	193	22.6581
.((((((...........))))))...	chr7:148637040-148637308(+)$1	1	6	33	24.0139
.((................))....))	chr4:32781397-32781672(+)$1	1	54	81	21.2690
(..((((...........))))..)))	chr19:21872301-21872583(+)$1	1	68	95	23.5915
.((((((............))))))))	chr5:100962159-100962430(+)$1	1	15	42	23.5100
((((((............))))))..)	chr17:45590931-45591200(-)$1	1	60	87	22.7235
.((((..............)).))..)	chr3:121346032-121346300(-)$1	1	52	79	20.1848
.((((((...........))))))(((	chr1:177829450-177829724(+)$1	1	176	203	21.8347
...(((.............)))...))	chr2:155683708-155683976(-)$1	1	157	184	24.6132
((.((((..............))))))	chr17:84797482-84797756(-)$1	1	26	53	21.3986
(((((((...........)))))))))	chr14:99467298-99467581(+)$1	1	235	262	24.4765
((.((((...........)))))))..	chr2:26266240-26266514(-)$1	1	209	236	24.0667
.(((((.............))))))))	chr7:118218580-118218852(-)$1	1	122	149	22.5425
((.((((.............)).)).)	chr5:116028834-116029113(+)$1	1	191	218	21.7937
.(.((.(...........).)).).))	chr5:125366369-125366658(+)$1	1	42	69	24.2670
)))((((................))))	chr1:181725777-181726062(-)$1	1	204	231	21.0107
((((((................)))))	chr2:25133723-25134051(+)$1	1	90	117	22.1385
...((((................))))	chr16:34212760-34213031(-)$1	1	23	50	21.5223
.((((((...........))).))).)	chr17:75142168-75142437(+)$1	1	144	171	24.6099
(...(((............)))..)))	chr11:80063588-80063857(+)$1	1	120	147	24.6128
(((((.............))))))..)	chr7:148633759-148634048(+)$1	1	195	222	21.8435
.((................))))))))	chr1:19224039-19224310(+)$1	1	195	222	20.7112
(((.(((...........)))))))..	chr10:79788572-79788842(-)$1	1	35	62	21.6672
((.((((.............)))).))	chr3:65357116-65357387(+)$1	1	25	52	22.7672
(((((.(...........).)))))))	chr16:13806538-13806807(+)$1	1	99	126	24.2949
..(.(((...........))))...))	chr2:24276886-24277154(-)$1	1	44	71	25.3883
(((((((.............)))))))	chr9:102528110-102528383(-)$1	1	107	134	23.0004
((..(((............))).).))	chr11:78296643-78296913(-)$1	1	171	198	24.6757
..(((((............))))))))	chr16:4496287-4496562(-)$1	1	152	179	23.3336
.((((((................))))	chr11:53520382-53520658(-)$1	1	104	131	21.2911
.((((((...........))))))(((	chr7:52094842-52095122(+)$1	1	171	198	22.3782
..(((((............)))))..)	chr2:19231570-19231841(+)$1	1	74	101	23.4955
((((..............))))))).)	chr11:20124587-20124904(+)$1	1	248	275	20.9583

#PSSM
f : 0.12	[ : 0.12	g : 0.10	! : 0.10	c : 0.09	e : 0.07	d : 0.06	b : 0.06	: : 0.04	# : 0.04	" : 0.04	a : 0.03	i : 0.01	G : 0.01	h : 0.01	= : 0.01	$ : 0.01	
f : 0.21	e : 0.10	g : 0.10	b : 0.09	" : 0.09	c : 0.07	! : 0.07	d : 0.06	a : 0.04	# : 0.04	[ : 0.03	: : 0.01	i : 0.01	= : 0.01	
f : 0.20	[ : 0.16	! : 0.10	e : 0.10	g : 0.09	" : 0.07	d : 0.06	b : 0.06	c : 0.03	# : 0.03	: : 0.01	i : 0.01	= : 0.01	a : 0.01	
d : 0.23	f : 0.18	e : 0.10	g : 0.09	c : 0.07	! : 0.06	b : 0.06	[ : 0.04	" : 0.04	y : 0.03	a : 0.01	i : 0.01	# : 0.01	= : 0.01	
c : 0.23	d : 0.23	f : 0.16	e : 0.10	b : 0.07	g : 0.07	y : 0.03	[ : 0.01	i : 0.01	# : 0.01	= : 0.01	w : 0.01	
c : 0.23	d : 0.23	f : 0.13	e : 0.10	b : 0.06	g : 0.06	v : 0.04	y : 0.03	w : 0.03	[ : 0.03	i : 0.01	= : 0.01	
d : 0.20	c : 0.16	v : 0.12	f : 0.12	u : 0.07	e : 0.06	y : 0.06	g : 0.04	b : 0.04	w : 0.03	a : 0.03	i : 0.01	= : 0.01	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
t : 0.40	v : 0.21	u : 0.21	y : 0.12	w : 0.04	
v : 0.16	d : 0.15	u : 0.13	y : 0.12	f : 0.10	c : 0.10	e : 0.06	b : 0.03	g : 0.03	w : 0.03	a : 0.03	= : 0.01	
c : 0.23	d : 0.15	f : 0.13	e : 0.10	y : 0.09	v : 0.09	b : 0.09	g : 0.03	] : 0.03	w : 0.01	= : 0.01	
c : 0.23	d : 0.16	f : 0.15	e : 0.10	y : 0.09	b : 0.09	g : 0.07	] : 0.03	i : 0.01	w : 0.01	= : 0.01	
d : 0.20	f : 0.15	c : 0.12	e : 0.12	y : 0.09	g : 0.09	4 : 0.04	2 : 0.04	a : 0.03	] : 0.03	b : 0.03	i : 0.01	= : 0.01	
f : 0.15	] : 0.12	2 : 0.12	e : 0.12	g : 0.10	3 : 0.09	d : 0.07	y : 0.06	4 : 0.04	b : 0.03	c : 0.03	i : 0.01	= : 0.01	
f : 0.18	d : 0.15	b : 0.12	g : 0.10	3 : 0.09	2 : 0.07	e : 0.07	a : 0.06	c : 0.04	4 : 0.04	i : 0.01	= : 0.01	
d : 0.16	g : 0.12	3 : 0.10	b : 0.10	f : 0.09	] : 0.07	2 : 0.07	c : 0.06	e : 0.06	4 : 0.04	a : 0.03	i : 0.01	h : 0.01	= : 0.01	
c : 0.15	d : 0.13	] : 0.13	g : 0.12	f : 0.12	e : 0.07	2 : 0.07	3 : 0.04	h : 0.03	b : 0.03	4 : 0.01	i : 0.01	= : 0.01	: : 0.01	
c : 0.16	e : 0.15	d : 0.13	g : 0.12	f : 0.12	h : 0.04	a : 0.04	b : 0.04	3 : 0.04	: : 0.03	2 : 0.01	[ : 0.01	4 : 0.01	i : 0.01	= : 0.01	

#score	1496.138520986351
#seq	65
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_UTR_m3_run1.txt

#BEAR
eeeddddpppppppddddD	chr11:50014137-50014377(-)$1	240	90	109	11.6732
ccc[cccpppppppccc]c	chr7:88679264-88679506(-)$1	242	140	159	13.8325
!!eeeeerrrrrrrrreee	chr19:12843558-12843801(-)$1	243	23	42	10.7801
"""ddddpppppppdddd3	chr13:83802224-83802482(+)$1	258	63	82	13.4533
eeeeebbpppppppbb]ee	chr11:94202029-94202276(+)$1	247	114	133	12.2863
hhhhhhhppppppphhhhh	chr3:51321794-51322050(-)$1	256	91	110	11.5435
!bb[cccpppppppccc22	chr4:33107838-33108088(+)$1	250	20	39	13.2845
iii[cccpppppppccc]i	chr3:95701644-95701880(-)$1	236	195	214	14.1617
gggggggrrrrrrrrrggg	chr3:126546663-126546898(+)$1	235	89	108	10.6639
gggg!!apppppppa22gg	chr17:71475852-71476088(+)$1	236	29	48	12.9936
eee[cccpppppppccc]e	chr7:122615150-122615411(-)$1	261	60	79	13.8164
eeeeeeepppppppeeeee	chr13:74308624-74308875(-)$1	251	46	65	13.2914
hhhhhhhppppppphhhhh	chr16:96379067-96379304(+)$1	237	34	53	11.5435
d!!ddddpppppppdddd2	chr4:33107028-33107268(+)$1	240	205	224	13.2388
#ffffffpppppppfffff	chr2:152106642-152106889(+)$1	247	100	119	12.8651
ddd[cccpppppppccc]d	chr17:10401591-10401830(-)$1	239	179	198	13.3687
=======ppppppp=====	chr2:72240598-72240836(+)$1	238	4	23	13.8773
e::ddddpppppppddddF	chr17:87535641-87535878(+)$1	237	210	229	10.5753
[bb[cccpppppppccc]b	chr11:60370509-60370744(+)$1	235	128	147	13.2502
gggg!!apppppppa22gg	chr4:109126604-109126839(-)$1	235	122	141	12.9936
gggggggpppppppggggg	chr16:20692735-20692974(+)$1	239	118	137	13.6691
[ffffffpppppppfffff	chr16:28827388-28827623(-)$1	235	126	145	12.9432
effffffpppppppfffff	chr15:76846166-76846402(-)$1	236	151	170	12.7661
b"""cccpppppppccc33	chr9:123371098-123371348(+)$1	250	134	153	13.8267
gggggggpppppppggggg	chr6:72791604-72791847(-)$1	243	217	236	13.6691
gggggggrrrrrrrrrggg	chr1:36588172-36588416(-)$1	244	120	139	10.6639
==eeeeepppppppeeeee	chr16:38245760-38245995(+)$1	235	210	229	13.6163
=======ppppppp=====	chr4:147247927-147248162(-)$1	235	139	158	13.8773
dddd[bbpppppppbb]dd	chr18:78021350-78021589(+)$1	239	188	207	11.6604
d!!cccrrrrrrrrrccc3	chr19:47333693-47333940(+)$1	247	129	148	10.6843
c[eeeeepppppppeeeee	chr13:68759269-68759508(-)$1	239	113	132	13.6631
:ffffffpppppppfffff	chr9:77505699-77505971(+)$1	272	61	80	11.9136
bb[ddddrrrrrrrrrddd	chr2:180639581-180639817(-)$1	236	200	219	9.8051
effffffpppppppfffff	chr1:134401574-134401813(+)$1	239	181	200	12.7661
[ffffffpppppppfffff	chr18:32391957-32392192(+)$1	235	141	160	12.9432
"""ddddpppppppdddd]	chr17:10401024-10401259(-)$1	235	15	34	13.4308
=======ppppppp=====	chr16:44160392-44160638(+)$1	246	189	208	13.8773
gggggggpppppppggggg	chr16:35303751-35303988(+)$1	237	27	46	13.6691
d[ddddrrrrrrrrrdddd	chrX:71549761-71549996(+)$1	235	10	29	9.8443
b[eeeeerrrrrrrrreee	chr5:136384359-136384619(-)$1	260	78	97	10.4624
cceeeeepppppppeeeee	chr7:119254173-119254453(+)$1	280	81	100	13.4516
hhhhhhhppppppphhhhh	chr11:29642759-29642996(+)$1	237	19	38	11.5435
bb[ddddrrrrrrrrrddd	chr10:39679454-39679689(-)$1	235	29	48	9.8051
hhhddddpppppppdddd]	chr4:119299139-119299385(+)$1	246	116	135	12.7387
cffffffpppppppfffff	chr15:38224969-38225206(-)$1	237	168	187	12.8403
##eeeeepppppppeeeee	chr15:97965928-97966164(-)$1	236	53	72	13.5866
cc[ddddpppppppdddd2	chr11:60013257-60013493(-)$1	236	166	185	13.1566
####cccpppppppccc55	chr3:144352137-144352377(-)$1	240	153	172	12.1403
e"""cccpppppppccc22	chr15:7145780-7146022(+)$1	242	137	156	13.5732
####cccpppppppccc55	chr16:32472416-32472656(+)$1	240	52	71	12.1403
EEeeeeepppppppeeeee	chrX:39460266-39460511(+)$1	245	35	54	11.4266
f[eeeeerrrrrrrrreee	chr2:104266800-104267037(-)$1	237	51	70	10.4886
:eeeeerrrrrrrrreeee	chr5:15878304-15878555(+)$1	251	90	109	9.3089
c!!cccrrrrrrrrrccc]	chr2:155214406-155214651(+)$1	245	161	180	10.7900

#otherMatches

#Seq PSSM
GCUGUGGCCAAGCCCCACC	chr11:50014137-50014377(-)$1	240	90	109	11.6732
ugaaaaggauuagacuuau	chr7:88679264-88679506(-)$1	242	140	159	13.8325
UUUGCACUUUGAACAUGUG	chr19:12843558-12843801(-)$1	243	23	42	10.7801
AUACCUUAAUGGGGAAGGG	chr13:83802224-83802482(+)$1	258	63	82	13.4533
GUUUGCUUAACUUUAGAUA	chr11:94202029-94202276(+)$1	247	114	133	12.2863
UUAGCAUCUUUCCUAUGCU	chr3:51321794-51322050(-)$1	256	91	110	11.5435
agguagcuaaggaugcucu	chr4:33107838-33108088(+)$1	250	20	39	13.2845
GAAUGUUUUUUUGUGGCUU	chr3:95701644-95701880(-)$1	236	195	214	14.1617
UGCGUAGGUAUCCUUGCUA	chr3:126546663-126546898(+)$1	235	89	108	10.6639
GAAGAACACAUUAAGGGUU	chr17:71475852-71476088(+)$1	236	29	48	12.9936
UUGUAUUCUAUGUUAAUUU	chr7:122615150-122615411(-)$1	261	60	79	13.8164
GGCAGUGAAAUGUACACUG	chr13:74308624-74308875(-)$1	251	46	65	13.2914
AGGGAGGGUGUGCGCUUUC	chr16:96379067-96379304(+)$1	237	34	53	11.5435
GUUCUUUUUAAAGCAGAGU	chr4:33107028-33107268(+)$1	240	205	224	13.2388
AUUUCUCAACCAUAGAGAG	chr2:152106642-152106889(+)$1	247	100	119	12.8651
AAGGAUGUAAAAGCCAUGC	chr17:10401591-10401830(-)$1	239	179	198	13.3687
cuUAGGCCAAGCUCGUUUA	chr2:72240598-72240836(+)$1	238	4	23	13.8773
GAAAUGCUACAUUUGUAUG	chr17:87535641-87535878(+)$1	237	210	229	10.5753
CAUUAUCUACCUGUGGUUA	chr11:60370509-60370744(+)$1	235	128	147	13.2502
UGUUGAGGGAAGUAUGUGA	chr4:109126604-109126839(-)$1	235	122	141	12.9936
GCUGGGGGCAUAUGCCCCA	chr16:20692735-20692974(+)$1	239	118	137	13.6691
UGGGGGAACACAUCUCCUC	chr16:28827388-28827623(-)$1	235	126	145	12.9432
AGUGUGGCAUCCACCCACA	chr15:76846166-76846402(-)$1	236	151	170	12.7661
gacagguuaguuuuacccu	chr9:123371098-123371348(+)$1	250	134	153	13.8267
UUUUGAAAUGUAAAUUUAG	chr6:72791604-72791847(-)$1	243	217	236	13.6691
UUGCUUCCUCCGGCCUGAA	chr1:36588172-36588416(-)$1	244	120	139	10.6639
AUUGGGUCAGUCCCACCCA	chr16:38245760-38245995(+)$1	235	210	229	13.6163
UCUUUCUGGGGGGAGGGGG	chr4:147247927-147248162(-)$1	235	139	158	13.8773
UUCAAAGCUGUCCACUAUG	chr18:78021350-78021589(+)$1	239	188	207	11.6604
AGUUGGGAAAAGAAGCCAU	chr19:47333693-47333940(+)$1	247	129	148	10.6843
UGCUCCUAAGCAGAAGGAG	chr13:68759269-68759508(-)$1	239	113	132	13.6631
uguauuagauauuauaaua	chr9:77505699-77505971(+)$1	272	61	80	11.9136
GUCCUCUUUCUUCUCUAGA	chr2:180639581-180639817(-)$1	236	200	219	9.8051
GACCAAUGGUUGUGAUUGG	chr1:134401574-134401813(+)$1	239	181	200	12.7661
CAAAACCUUAUUUUGGUUU	chr18:32391957-32392192(+)$1	235	141	160	12.9432
CAGUCGCCCAGUAUGUGAA	chr17:10401024-10401259(-)$1	235	15	34	13.4308
AAGAUUGUUAUAAUUGAUU	chr16:44160392-44160638(+)$1	246	189	208	13.8773
GGGUGAGAUGAUGACUUAC	chr16:35303751-35303988(+)$1	237	27	46	13.6691
AAAGACUACUUGACUGUCU	chrX:71549761-71549996(+)$1	235	10	29	9.8443
UCAUGGUGAAACUAUAACU	chr5:136384359-136384619(-)$1	260	78	97	10.4624
CAGGUUUGUGAUUAGAGCC	chr7:119254173-119254453(+)$1	280	81	100	13.4516
AUGUUUGCAGUUACCAAAC	chr11:29642759-29642996(+)$1	237	19	38	11.5435
GCACCCCUCCCAGGCUGGG	chr10:39679454-39679689(-)$1	235	29	48	9.8051
GUGUCAGUUUGAUGUUGAC	chr4:119299139-119299385(+)$1	246	116	135	12.7387
AGCUAAAAUUCUUCUUUGG	chr15:38224969-38225206(-)$1	237	168	187	12.8403
CACAUAACAGUGACUUAUG	chr15:97965928-97966164(-)$1	236	53	72	13.5866
AGAUCUGGAAAUUGCAGAG	chr11:60013257-60013493(-)$1	236	166	185	13.1566
CUUUGUCUAUUAUCGAUCC	chr3:144352137-144352377(-)$1	240	153	172	12.1403
AAAAAUGAAAAAAACAUGC	chr15:7145780-7146022(+)$1	242	137	156	13.5732
UUUCUGCUGGGCAUGCGUU	chr16:32472416-32472656(+)$1	240	52	71	12.1403
AGCAAGACCUCUUUUCUUG	chrX:39460266-39460511(+)$1	245	35	54	11.4266
GAUUCAAUGGCUUAGUUUG	chr2:104266800-104267037(-)$1	237	51	70	10.4886
GUAAGUUAAUAUUUUGCUU	chr5:15878304-15878555(+)$1	251	90	109	9.3089
UCCUGACCUAAUUUCUCAA	chr2:155214406-155214651(+)$1	245	161	180	10.7900

#DB
)))((((.......)))))	chr11:50014137-50014377(-)$1	1	90	109	11.6732
(((.(((.......))).)	chr7:88679264-88679506(-)$1	1	140	159	13.8325
..(((((.........)))	chr19:12843558-12843801(-)$1	1	23	42	10.7801
...((((.......)))).	chr13:83802224-83802482(+)$1	1	63	82	13.4533
(((((((.......)).))	chr11:94202029-94202276(+)$1	1	114	133	12.2863
(((((((.......)))))	chr3:51321794-51322050(-)$1	1	91	110	11.5435
.((.(((.......)))..	chr4:33107838-33108088(+)$1	1	20	39	13.2845
(((.(((.......))).)	chr3:95701644-95701880(-)$1	1	195	214	14.1617
(((((((.........)))	chr3:126546663-126546898(+)$1	1	89	108	10.6639
((((..(.......)..))	chr17:71475852-71476088(+)$1	1	29	48	12.9936
(((.(((.......))).)	chr7:122615150-122615411(-)$1	1	60	79	13.8164
))(((((.......)))))	chr13:74308624-74308875(-)$1	1	46	65	13.2914
(((((((.......)))))	chr16:96379067-96379304(+)$1	1	34	53	11.5435
(..((((.......)))).	chr4:33107028-33107268(+)$1	1	205	224	13.2388
.((((((.......)))))	chr2:152106642-152106889(+)$1	1	100	119	12.8651
(((.(((.......))).)	chr17:10401591-10401830(-)$1	1	179	198	13.3687
(((((((.......)))))	chr2:72240598-72240836(+)$1	1	4	23	13.8773
)..((((.......)))))	chr17:87535641-87535878(+)$1	1	210	229	10.5753
.((.(((.......))).)	chr11:60370509-60370744(+)$1	1	128	147	13.2502
((((..(.......)..))	chr4:109126604-109126839(-)$1	1	122	141	12.9936
(((((((.......)))))	chr16:20692735-20692974(+)$1	1	118	137	13.6691
.((((((.......)))))	chr16:28827388-28827623(-)$1	1	126	145	12.9432
)((((((.......)))))	chr15:76846166-76846402(-)$1	1	151	170	12.7661
(...(((.......)))..	chr9:123371098-123371348(+)$1	1	134	153	13.8267
(((((((.......)))))	chr6:72791604-72791847(-)$1	1	217	236	13.6691
(((((((.........)))	chr1:36588172-36588416(-)$1	1	120	139	10.6639
))(((((.......)))))	chr16:38245760-38245995(+)$1	1	210	229	13.6163
(((((((.......)))))	chr4:147247927-147248162(-)$1	1	139	158	13.8773
((((.((.......)).))	chr18:78021350-78021589(+)$1	1	188	207	11.6604
(..(((.........))).	chr19:47333693-47333940(+)$1	1	129	148	10.6843
(.(((((.......)))))	chr13:68759269-68759508(-)$1	1	113	132	13.6631
.((((((.......)))))	chr9:77505699-77505971(+)$1	1	61	80	11.9136
((.((((.........)))	chr2:180639581-180639817(-)$1	1	200	219	9.8051
(((((((.......)))))	chr1:134401574-134401813(+)$1	1	181	200	12.7661
.((((((.......)))))	chr18:32391957-32392192(+)$1	1	141	160	12.9432
...((((.......)))).	chr17:10401024-10401259(-)$1	1	15	34	13.4308
(((((((.......)))))	chr16:44160392-44160638(+)$1	1	189	208	13.8773
(((((((.......)))))	chr16:35303751-35303988(+)$1	1	27	46	13.6691
(.((((.........))))	chrX:71549761-71549996(+)$1	1	10	29	9.8443
(.(((((.........)))	chr5:136384359-136384619(-)$1	1	78	97	10.4624
(((((((.......)))))	chr7:119254173-119254453(+)$1	1	81	100	13.4516
(((((((.......)))))	chr11:29642759-29642996(+)$1	1	19	38	11.5435
((.((((.........)))	chr10:39679454-39679689(-)$1	1	29	48	9.8051
(((((((.......)))).	chr4:119299139-119299385(+)$1	1	116	135	12.7387
)((((((.......)))))	chr15:38224969-38225206(-)$1	1	168	187	12.8403
..(((((.......)))))	chr15:97965928-97966164(-)$1	1	53	72	13.5866
((.((((.......)))).	chr11:60013257-60013493(-)$1	1	166	185	13.1566
....(((.......)))..	chr3:144352137-144352377(-)$1	1	153	172	12.1403
(...(((.......)))..	chr15:7145780-7146022(+)$1	1	137	156	13.5732
....(((.......)))..	chr16:32472416-32472656(+)$1	1	52	71	12.1403
(((((((.......)))))	chrX:39460266-39460511(+)$1	1	35	54	11.4266
(.(((((.........)))	chr2:104266800-104267037(-)$1	1	51	70	10.4886
.(((((.........))))	chr5:15878304-15878555(+)$1	1	90	109	9.3089
(..(((.........))).	chr2:155214406-155214651(+)$1	1	161	180	10.7900

#PSSM
e : 0.14	g : 0.12	c : 0.11	d : 0.09	h : 0.07	# : 0.07	= : 0.07	b : 0.07	[ : 0.05	! : 0.03	" : 0.03	: : 0.03	i : 0.01	E : 0.01	f : 0.01	
g : 0.12	f : 0.12	e : 0.09	! : 0.07	" : 0.07	h : 0.07	b : 0.07	= : 0.07	[ : 0.07	c : 0.05	# : 0.05	d : 0.03	i : 0.01	: : 0.01	E : 0.01	
e : 0.24	g : 0.12	f : 0.12	" : 0.07	h : 0.07	! : 0.05	d : 0.05	= : 0.05	[ : 0.05	b : 0.03	# : 0.03	c : 0.01	i : 0.01	: : 0.01	
d : 0.20	e : 0.20	g : 0.12	f : 0.12	[ : 0.11	h : 0.05	= : 0.05	" : 0.03	c : 0.03	# : 0.03	
c : 0.22	e : 0.20	d : 0.18	f : 0.12	g : 0.09	h : 0.05	= : 0.05	! : 0.03	[ : 0.01	
c : 0.22	d : 0.18	e : 0.18	f : 0.12	g : 0.09	h : 0.05	= : 0.05	b : 0.03	! : 0.03	
c : 0.18	d : 0.16	e : 0.16	f : 0.12	g : 0.09	r : 0.07	h : 0.05	= : 0.05	b : 0.03	a : 0.03	
p : 0.79	r : 0.20	
p : 0.79	r : 0.20	
p : 0.79	r : 0.20	
p : 0.79	r : 0.20	
p : 0.79	r : 0.20	
p : 0.79	r : 0.20	
p : 0.79	r : 0.20	
r : 0.20	c : 0.18	d : 0.12	f : 0.12	e : 0.11	h : 0.05	= : 0.05	g : 0.05	b : 0.03	a : 0.03	
c : 0.22	d : 0.14	r : 0.12	e : 0.12	f : 0.12	h : 0.05	= : 0.05	g : 0.05	b : 0.03	2 : 0.03	
c : 0.22	d : 0.18	e : 0.18	f : 0.12	g : 0.09	h : 0.05	= : 0.05	] : 0.03	2 : 0.03	
d : 0.20	e : 0.20	g : 0.12	f : 0.12	] : 0.09	h : 0.05	= : 0.05	2 : 0.03	c : 0.03	5 : 0.03	3 : 0.01	
e : 0.22	g : 0.12	f : 0.12	d : 0.09	2 : 0.07	3 : 0.05	h : 0.05	= : 0.05	] : 0.05	5 : 0.03	D : 0.01	c : 0.01	i : 0.01	F : 0.01	b : 0.01	

#score	670.2376121586755
#seq	54
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_UTR_m1_run1.txt

#BEAR
ffffffssssssssssffffff]b	chr17:6084525-6084794(+)$1	269	8	32	15.2537
"""ddddssssssssssdddd444	chr3:108706705-108706973(-)$1	268	191	215	15.7197
eeeewwwwwwwwwwwwwweeeee]	chr5:137966884-137967189(+)$1	305	267	291	19.7300
fffffftttttttttttffffff]	chr17:46305894-46306170(+)$1	276	90	114	20.6244
d!!ccctttttttttttccc22dd	chr8:74842835-74843118(+)$1	283	120	144	21.0600
e[bb[auuuuuuuuuuuua]bb]e	chr4:49669033-49669317(+)$1	284	177	201	20.4514
eeee[bbssssssssssbb]eeee	chr19:8907647-8907942(+)$1	295	184	208	15.3435
fffffftttttttttttffffff3	chr10:29066348-29066634(-)$1	286	83	107	20.6495
eeeeeuuuuuuuuuuuueeeee:d	chr11:69813266-69813543(+)$1	277	141	165	19.6778
&eeeeettttttttttteeeee88	chr2:31071139-31071424(+)$1	285	60	84	19.9825
d!!cccssssssssssccc]dddd	chr7:16451277-16451548(-)$1	271	35	59	16.5415
iiiiiitttttttttttiiiiiii	chr4:83921320-83921603(-)$1	283	113	137	21.4406
::ddddtttttttttttddddhhh	chr5:123807806-123808084(+)$1	278	117	141	18.1836
:eeeeettttttttttteeeeeHH	chr19:24758575-24758847(-)$1	272	10	34	18.8821
((dddduuuuuuuuuuuudddd77	chr2:153054809-153055101(-)$1	292	204	228	18.3479
iiiiiivvvvvvvvvvvvviiiii	chr2:30882331-30882614(-)$1	283	135	159	19.8578
iiiiiissssssssssiiiiiiii	chr4:63211331-63211605(+)$1	274	97	121	16.0015
:eeeeettttttttttteeeee::	chr4:151560213-151560493(+)$1	280	149	173	18.4963
cccccuuuuuuuuuuuuccc::::	chr10:80611559-80611834(+)$1	275	172	196	17.0780
eeeewwwwwwwwwwwwwweeeee]	chr2:144232685-144232982(+)$1	297	97	121	19.7300
"""cccuuuuuuuuuuuuccc333	chr6:30079454-30079738(+)$1	284	148	172	21.9627
fffffuuuuuuuuuuuuffffff]	chr12:113887155-113887427(+)$1	272	152	176	20.2496
hh[cccssssssssssccchhhhh	chr10:116509561-116509829(-)$1	268	78	102	15.7286
======ttttttttttt=======	chr5:137967090-137967377(+)$1	287	204	228	21.7460
====xxxxxxxxxxxxxxx=====	chr17:27062059-27062328(+)$1	269	147	171	14.8225
hhhhhhttttttttttthhhhhhh	chr18:75555296-75555568(+)$1	272	56	80	19.1316
hhhhhhuuuuuuuuuuuuhhhhhh	chr1:189057862-189058135(+)$1	273	202	226	19.1885
fffffvvvvvvvvvvvvvffffff	chr16:92085376-92085654(+)$1	278	61	85	19.0100
fffffftttttttttttffffff:	chr15:81535366-81535645(-)$1	279	152	176	19.6233
dd!!bbtttttttttttbb22ddd	chr2:32162879-32163158(+)$1	279	212	236	19.5139
eeeyyyyyyyyyyyyyyyyeeeee	chr16:98170643-98170924(-)$1	281	5	29	18.1405
ee[bbuuuuuuuuuuuubb]eeee	chr15:75831594-75831869(-)$1	275	9	33	20.2588
ggddddvvvvvvvvvvvvvdddd]	chr14:99472889-99473185(+)$1	296	102	126	19.1153
!ffffffssssssssssffffff2	chr3:32240109-32240398(-)$1	289	183	207	15.3648
!!ddddtttttttttttdddd]dd	chr16:91227775-91228057(+)$1	282	85	109	20.8282
[eeeeesssssssssseeeee===	chr11:98015255-98015545(-)$1	290	17	41	16.3731
g!!cccvvvvvvvvvvvvvccc22	chr3:121969343-121969622(+)$1	279	10	34	20.0530
!!eeeeesssssssssseeeee22	chr1:36501804-36502071(-)$1	267	122	146	16.1856
!eeeeeuuuuuuuuuuuueeeee2	chr6:56728722-56729000(-)$1	278	11	35	21.2332
iiiiiiuuuuuuuuuuuuiiiiii	chr6:40353055-40353326(-)$1	271	111	135	21.3767
gg[bbuuuuuuuuuuuubbggggg	chr15:89012665-89012935(-)$1	270	183	207	20.4565
dd[ccctttttttttttcccdddd	chr13:5869145-5869418(+)$1	273	185	209	21.0324
e[acccssssssssssccc]a]ee	chr4:126924747-126925021(+)$1	274	133	157	16.6915
f[ccctttttttttttccc]ffff	chr17:37114860-37115128(-)$1	268	197	221	19.8273
ddduuuuuuuuuuuudddd]bb]e	chr3:145309908-145310184(-)$1	276	129	153	15.4494
[ddddvvvvvvvvvvvvvdddd]a	chr13:73773815-73774087(+)$1	272	188	212	19.4799
"""cccssssssssssccchhhhh	chr2:173526976-173527254(+)$1	278	228	252	16.2182
ggggggvvvvvvvvvvvvvggggg	chr9:60586481-60586749(+)$1	268	28	52	19.7296
!!bbbbtttttttttttbb]bb44	chr3:122242267-122242549(-)$1	282	79	103	20.2456
%%ddddtttttttttttdddd333	chr5:31924774-31925053(+)$1	279	174	198	19.9645
gggggguuuuuuuuuuuugggggg	chr4:33125089-33125363(+)$1	274	126	150	21.2203
####cccssssssssssccc333h	chr2:168780772-168781060(-)$1	288	54	78	16.2285
======ssssssssss========	chr5:93697524-93697801(+)$1	277	166	190	16.4610
"""cccuuuuuuuuuuuuccc333	chr2:32134292-32134583(-)$1	291	158	182	21.9627
eeeeevvvvvvvvvvvvveeeee:	chr5:67078040-67078310(+)$1	270	218	242	19.0054
ccccccssssssssssccc]ccc>	chr5:3692568-3692844(-)$1	276	228	252	16.4587

#otherMatches

#Seq PSSM
UCAUCAUUCAGGACAUUGAUGACA	chr17:6084525-6084794(+)$1	269	8	32	15.2537
UUUUUUCCCCCCAAGUUGAGAUUG	chr3:108706705-108706973(-)$1	268	191	215	15.7197
UCUUUAAUUUUAAACAUUAGGAGA	chr5:137966884-137967189(+)$1	305	267	291	19.7300
CCAUGCUUUUUCAGAUUGUGUGGU	chr17:46305894-46306170(+)$1	276	90	114	20.6244
ACAGCACACACAGUCCCUGCCAUG	chr8:74842835-74843118(+)$1	283	120	144	21.0600
AGGAGUGAAUUUUUGAUAAGUUAU	chr4:49669033-49669317(+)$1	284	177	201	20.4514
ACUCGCUGGUAUUAGAAAGGGAGU	chr19:8907647-8907942(+)$1	295	184	208	15.3435
CAUUAUACUCAUCCUUAGUAGUGC	chr10:29066348-29066634(-)$1	286	83	107	20.6495
AGGUGUCAAUUAGCACUCGCCUCG	chr11:69813266-69813543(+)$1	277	141	165	19.6778
AGGGACUCUUUCUCCUCGUUCCgu	chr2:31071139-31071424(+)$1	285	60	84	19.9825
ccugggcuacauaaaacccuguug	chr7:16451277-16451548(-)$1	271	35	59	16.5415
UUUUCCUUUAUAGUUUUGGGAGAG	chr4:83921320-83921603(-)$1	283	113	137	21.4406
UUGCAUUUAUUUAUUUUGUGUGUG	chr5:123807806-123808084(+)$1	278	117	141	18.1836
UGGGGGGAGGGUAAGUACCCCUUU	chr19:24758575-24758847(-)$1	272	10	34	18.8821
UGUAGAUCUUGUUCCACCUCUAAU	chr2:153054809-153055101(-)$1	292	204	228	18.3479
GGGGGAAGGGAAUGCAGGAUUUCC	chr2:30882331-30882614(-)$1	283	135	159	19.8578
UUUUUAAUUAGUCUAGUAGGAAAA	chr4:63211331-63211605(+)$1	274	97	121	16.0015
GCAGGUAGCCUUUUCGAGCCUGAC	chr4:151560213-151560493(+)$1	280	149	173	18.4963
CCGCCACCCUCCUUCACGGCACUU	chr10:80611559-80611834(+)$1	275	172	196	17.0780
AUUCUCUUCCCAUACAAUGAGUGA	chr2:144232685-144232982(+)$1	297	97	121	19.7300
uuguuguuguuguuguuUUAAAUC	chr6:30079454-30079738(+)$1	284	148	172	21.9627
GUUAUGUUUUAUACCCAGUAACAA	chr12:113887155-113887427(+)$1	272	152	176	20.2496
GUGAGCUGUUAAUAUUGUUGCCAG	chr10:116509561-116509829(-)$1	268	78	102	15.7286
uuuuuUAGaaaaaaaaaaaaagau	chr5:137967090-137967377(+)$1	287	204	228	21.7460
uguuguccuuugccucccaagcag	chr17:27062059-27062328(+)$1	269	147	171	14.8225
UGUAAAUAUAAAGACGUUUUAUAA	chr18:75555296-75555568(+)$1	272	56	80	19.1316
CCUGGGAUGUAGGUUGACCCUGGG	chr1:189057862-189058135(+)$1	273	202	226	19.1885
CAACUGGUUGUAUUUGGGGGUUGC	chr16:92085376-92085654(+)$1	278	61	85	19.0100
GUGUCAUAUUGGUCCUUUGAUACU	chr15:81535366-81535645(-)$1	279	152	176	19.6233
GACAGGGAAAGUGGGUACCAUUCU	chr2:32162879-32163158(+)$1	279	212	236	19.5139
UGGGAUGAAUUAAUACUGGCUAGA	chr16:98170643-98170924(-)$1	281	5	29	18.1405
GACAGCCUCCUCCCAUCCUCUCAU	chr15:75831594-75831869(-)$1	275	9	33	20.2588
GUACUGUGCCUACUUCCCUCAGUA	chr14:99472889-99473185(+)$1	296	102	126	19.1153
AACUGUGUCAAACAACUCACAGUG	chr3:32240109-32240398(-)$1	289	183	207	15.3648
CAUUGUACAAAACGGCCACAACGC	chr16:91227775-91228057(+)$1	282	85	109	20.8282
GUUUCUCUUCAUCACAAGAAGAAG	chr11:98015255-98015545(-)$1	290	17	41	16.3731
CUGGAACAUAAGAUACAAAUUCAU	chr3:121969343-121969622(+)$1	279	10	34	20.0530
GGUCAAGCGGUGGAGUACUUGAAA	chr1:36501804-36502071(-)$1	267	122	146	16.1856
ACUUUAUCCAUCCUGUCUUGAAGA	chr6:56728722-56729000(-)$1	278	11	35	21.2332
GUCCUUGCAGAGGUAAAGAAGGGC	chr6:40353055-40353326(-)$1	271	111	135	21.3767
GGACUCUUUUACCCUCCAGCUUCC	chr15:89012665-89012935(-)$1	270	183	207	20.4565
ACUGGCUGGGGCUGGGUGCCGUCC	chr13:5869145-5869418(+)$1	273	185	209	21.0324
UUCCCUUUACUGGCUCAGGCGUGG	chr4:126924747-126925021(+)$1	274	133	157	16.6915
GUUAACUUUAUUAUUUUUAUCAUU	chr17:37114860-37115128(-)$1	268	197	221	19.8273
UUUGGGGAGGGAGGGGAAAUGUAA	chr3:145309908-145310184(-)$1	276	129	153	15.4494
UCUAUCACAUUUGCUCUCAUGGUC	chr13:73773815-73774087(+)$1	272	188	212	19.4799
CGAUGGGGUACAGAAGCUACCUGG	chr2:173526976-173527254(+)$1	278	228	252	16.2182
GGCAGCUUAGACAGUuccugcugu	chr9:60586481-60586749(+)$1	268	28	52	19.7296
GGGGGGGAUUGUUUGUACCACUGA	chr3:122242267-122242549(-)$1	282	79	103	20.2456
CAGAGACCACAUAUUUAUCUCCCU	chr5:31924774-31925053(+)$1	279	174	198	19.9645
GAUUCCGAUUUUGAUGGAGGAGUU	chr4:33125089-33125363(+)$1	274	126	150	21.2203
CAUCUGCGAAGGAAUGAGCGUCUC	chr2:168780772-168781060(-)$1	288	54	78	16.2285
UUCAGCUUUUCGGAUUGUUGAACU	chr5:93697524-93697801(+)$1	277	166	190	16.4610
GGGUGGGUAUUGUCAAUGUUAAGG	chr2:32134292-32134583(-)$1	291	158	182	21.9627
GCUGUCUUCUUGCGUUCUACAGCC	chr5:67078040-67078310(+)$1	270	218	242	19.0054
UCACAUGAUAACUGCAGUGCUGAC	chr5:3692568-3692844(-)$1	276	228	252	16.4587

#DB
((((((..........)))))).)	chr17:6084525-6084794(+)$1	1	8	32	15.2537
...((((..........))))...	chr3:108706705-108706973(-)$1	1	191	215	15.7197
((((..............))))).	chr5:137966884-137967189(+)$1	1	267	291	19.7300
((((((...........)))))).	chr17:46305894-46306170(+)$1	1	90	114	20.6244
(..(((...........)))..))	chr8:74842835-74843118(+)$1	1	120	144	21.0600
(.((.(............).)).)	chr4:49669033-49669317(+)$1	1	177	201	20.4514
((((.((..........)).))))	chr19:8907647-8907942(+)$1	1	184	208	15.3435
((((((...........)))))).	chr10:29066348-29066634(-)$1	1	83	107	20.6495
(((((............))))).(	chr11:69813266-69813543(+)$1	1	141	165	19.6778
.(((((...........)))))..	chr2:31071139-31071424(+)$1	1	60	84	19.9825
(..(((..........))).))))	chr7:16451277-16451548(-)$1	1	35	59	16.5415
((((((...........)))))))	chr4:83921320-83921603(-)$1	1	113	137	21.4406
..((((...........))))(((	chr5:123807806-123808084(+)$1	1	117	141	18.1836
.(((((...........)))))((	chr19:24758575-24758847(-)$1	1	10	34	18.8821
..((((............))))..	chr2:153054809-153055101(-)$1	1	204	228	18.3479
((((((.............)))))	chr2:30882331-30882614(-)$1	1	135	159	19.8578
((((((..........))))))))	chr4:63211331-63211605(+)$1	1	97	121	16.0015
.(((((...........)))))..	chr4:151560213-151560493(+)$1	1	149	173	18.4963
))(((............)))....	chr10:80611559-80611834(+)$1	1	172	196	17.0780
((((..............))))).	chr2:144232685-144232982(+)$1	1	97	121	19.7300
...(((............)))...	chr6:30079454-30079738(+)$1	1	148	172	21.9627
(((((............)))))).	chr12:113887155-113887427(+)$1	1	152	176	20.2496
((.(((..........))))))))	chr10:116509561-116509829(-)$1	1	78	102	15.7286
((((((...........)))))))	chr5:137967090-137967377(+)$1	1	204	228	21.7460
((((...............)))))	chr17:27062059-27062328(+)$1	1	147	171	14.8225
((((((...........)))))))	chr18:75555296-75555568(+)$1	1	56	80	19.1316
((((((............))))))	chr1:189057862-189058135(+)$1	1	202	226	19.1885
(((((.............))))))	chr16:92085376-92085654(+)$1	1	61	85	19.0100
((((((...........)))))).	chr15:81535366-81535645(-)$1	1	152	176	19.6233
((..((...........))..)))	chr2:32162879-32163158(+)$1	1	212	236	19.5139
(((................)))))	chr16:98170643-98170924(-)$1	1	5	29	18.1405
((.((............)).))))	chr15:75831594-75831869(-)$1	1	9	33	20.2588
((((((.............)))).	chr14:99472889-99473185(+)$1	1	102	126	19.1153
.((((((..........)))))).	chr3:32240109-32240398(-)$1	1	183	207	15.3648
..((((...........)))).))	chr16:91227775-91228057(+)$1	1	85	109	20.8282
.(((((..........))))))))	chr11:98015255-98015545(-)$1	1	17	41	16.3731
(..(((.............)))..	chr3:121969343-121969622(+)$1	1	10	34	20.0530
..(((((..........)))))..	chr1:36501804-36502071(-)$1	1	122	146	16.1856
.(((((............))))).	chr6:56728722-56729000(-)$1	1	11	35	21.2332
((((((............))))))	chr6:40353055-40353326(-)$1	1	111	135	21.3767
((.((............)))))))	chr15:89012665-89012935(-)$1	1	183	207	20.4565
((.(((...........)))))))	chr13:5869145-5869418(+)$1	1	185	209	21.0324
(.((((..........))).).))	chr4:126924747-126925021(+)$1	1	133	157	16.6915
(.(((...........))).))))	chr17:37114860-37115128(-)$1	1	197	221	19.8273
(((............)))).)).)	chr3:145309908-145310184(-)$1	1	129	153	15.4494
.((((.............)))).)	chr13:73773815-73774087(+)$1	1	188	212	19.4799
...(((..........))))))))	chr2:173526976-173527254(+)$1	1	228	252	16.2182
((((((.............)))))	chr9:60586481-60586749(+)$1	1	28	52	19.7296
..((((...........)).))..	chr3:122242267-122242549(-)$1	1	79	103	20.2456
..((((...........))))...	chr5:31924774-31925053(+)$1	1	174	198	19.9645
((((((............))))))	chr4:33125089-33125363(+)$1	1	126	150	21.2203
....(((..........)))...)	chr2:168780772-168781060(-)$1	1	54	78	16.2285
((((((..........))))))))	chr5:93697524-93697801(+)$1	1	166	190	16.4610
...(((............)))...	chr2:32134292-32134583(-)$1	1	158	182	21.9627
(((((.............))))).	chr5:67078040-67078310(+)$1	1	218	242	19.0054
((((((..........))).))).	chr5:3692568-3692844(-)$1	1	228	252	16.4587

#PSSM
e : 0.16	f : 0.12	d : 0.08	g : 0.08	! : 0.08	" : 0.07	i : 0.07	: : 0.05	h : 0.05	= : 0.05	c : 0.03	[ : 0.03	& : 0.01	( : 0.01	% : 0.01	# : 0.01	
e : 0.21	f : 0.12	! : 0.10	" : 0.07	i : 0.07	d : 0.07	g : 0.07	[ : 0.05	h : 0.05	= : 0.05	c : 0.03	: : 0.01	( : 0.01	% : 0.01	# : 0.01	
e : 0.21	f : 0.12	d : 0.12	" : 0.07	! : 0.07	i : 0.07	[ : 0.07	c : 0.05	= : 0.05	b : 0.03	h : 0.03	g : 0.03	a : 0.01	# : 0.01	
c : 0.21	e : 0.19	f : 0.12	d : 0.12	b : 0.07	i : 0.07	= : 0.05	h : 0.03	g : 0.03	! : 0.01	y : 0.01	u : 0.01	# : 0.01	
c : 0.23	e : 0.14	f : 0.12	d : 0.12	i : 0.07	b : 0.07	w : 0.03	[ : 0.03	= : 0.03	h : 0.03	g : 0.03	x : 0.01	y : 0.01	u : 0.01	
c : 0.19	d : 0.10	u : 0.10	e : 0.10	f : 0.08	i : 0.07	b : 0.05	v : 0.05	w : 0.03	= : 0.03	h : 0.03	g : 0.03	a : 0.01	x : 0.01	y : 0.01	t : 0.01	
t : 0.30	u : 0.24	s : 0.16	v : 0.12	w : 0.03	d : 0.01	b : 0.01	x : 0.01	y : 0.01	f : 0.01	e : 0.01	c : 0.01	
t : 0.30	s : 0.24	u : 0.24	v : 0.12	w : 0.03	x : 0.01	y : 0.01	
t : 0.30	s : 0.24	u : 0.24	v : 0.12	w : 0.03	x : 0.01	y : 0.01	
t : 0.30	s : 0.24	u : 0.24	v : 0.12	w : 0.03	x : 0.01	y : 0.01	
t : 0.30	s : 0.24	u : 0.24	v : 0.12	w : 0.03	x : 0.01	y : 0.01	
t : 0.30	s : 0.24	u : 0.24	v : 0.12	w : 0.03	x : 0.01	y : 0.01	
t : 0.30	s : 0.24	u : 0.24	v : 0.12	w : 0.03	x : 0.01	y : 0.01	
t : 0.30	s : 0.24	u : 0.24	v : 0.12	w : 0.03	x : 0.01	y : 0.01	
t : 0.30	s : 0.24	u : 0.24	v : 0.12	w : 0.03	x : 0.01	y : 0.01	
t : 0.30	s : 0.24	u : 0.23	v : 0.12	w : 0.03	x : 0.01	y : 0.01	d : 0.01	
t : 0.28	u : 0.23	v : 0.12	c : 0.10	s : 0.08	w : 0.03	f : 0.01	i : 0.01	x : 0.01	y : 0.01	e : 0.01	d : 0.01	= : 0.01	
c : 0.17	u : 0.14	v : 0.12	f : 0.10	e : 0.10	d : 0.08	b : 0.08	w : 0.03	i : 0.03	= : 0.03	x : 0.01	h : 0.01	y : 0.01	
c : 0.21	e : 0.17	f : 0.12	d : 0.12	b : 0.08	v : 0.07	i : 0.05	= : 0.03	h : 0.03	a : 0.01	x : 0.01	y : 0.01	g : 0.01	
e : 0.19	] : 0.16	f : 0.12	d : 0.12	c : 0.12	i : 0.07	h : 0.07	= : 0.05	g : 0.05	2 : 0.01	
e : 0.23	d : 0.16	f : 0.14	i : 0.07	c : 0.07	h : 0.07	b : 0.05	= : 0.05	g : 0.05	2 : 0.03	: : 0.01	a : 0.01	3 : 0.01	
e : 0.21	f : 0.14	d : 0.10	h : 0.08	i : 0.07	3 : 0.07	= : 0.07	b : 0.05	g : 0.05	] : 0.03	c : 0.03	4 : 0.01	2 : 0.01	: : 0.01	
e : 0.14	f : 0.12	d : 0.10	h : 0.08	] : 0.07	i : 0.07	3 : 0.07	= : 0.07	: : 0.05	g : 0.05	4 : 0.03	2 : 0.03	8 : 0.01	H : 0.01	7 : 0.01	c : 0.01	
d : 0.10	e : 0.10	h : 0.10	] : 0.08	3 : 0.07	i : 0.07	: : 0.07	= : 0.07	2 : 0.07	g : 0.05	4 : 0.03	f : 0.03	b : 0.01	8 : 0.01	H : 0.01	7 : 0.01	a : 0.01	> : 0.01	

#score	1053.3922374554575
#seq	56
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_UTR_m3_run1.txt

#BEAR
eeeeellleeeeed	chr3:88881867-88882364(+)$1	497	145	159	9.3087
eeeeemmmmeeeee	chr19:16459390-16459698(+)$1	308	66	80	11.3206
eeeeemmmmeeeee	chr7:91394755-91395023(-)$1	268	12	26	11.3206
eeeeemmmmeeeee	chr19:45055998-45056450(+)$1	452	1	15	11.3206
[eeeeellleeeee	chr9:96233025-96233524(-)$1	499	443	457	9.3203
eeeeemmmmeeeee	chr8:37631774-37632081(-)$1	307	152	166	11.3206
eeeeemmmmeeeee	chr5:30111583-30111813(+)$1	230	171	185	11.3206
eeeeeooooooeee	chr11:100923607-100924035(+)$1	428	374	388	9.9542
eeeeemmmmeeeee	chr10:85511866-85512260(+)$1	394	127	141	11.3206
eeeeemmmmeeeee	chr4:11892567-11892950(-)$1	383	345	359	11.3206
eeeeemmmmeeeee	chr16:94352252-94352717(-)$1	465	15	29	11.3206
eeeeeooooooeee	chr11:69414603-69414982(-)$1	379	80	94	9.9542
eeeeemmmmeeeee	chr1:174302653-174303057(+)$1	404	117	131	11.3206
eeeeellleeeeed	chr11:74488411-74488677(-)$1	266	98	112	9.3087
eeeeeooooooeee	chr11:109529925-109530411(+)$1	486	328	342	9.9542
eeeeemmmmeeeee	chr2:49628921-49629346(+)$1	425	20	34	11.3206
eeeeeooooooeee	chr5:9480498-9480972(+)$1	474	451	465	9.9542
eeeeemmmmeeeee	chr3:95435709-95436043(+)$1	334	89	103	11.3206
eeeeemmmmeeeee	chr10:59412898-59413232(-)$1	334	60	74	11.3206
eeeeemmmmeeeee	chr18:38623871-38624308(+)$1	437	234	248	11.3206
eeeeemmmmeeeee	chr11:58161056-58161279(+)$1	223	38	52	11.3206
eeeeemmmmeeeee	chr12:53668720-53669026(+)$1	306	282	296	11.3206
eeeeemmmmeeeee	chr13:94971777-94972057(-)$1	280	93	107	11.3206
eeeeemmmmeeeee	chr14:66929622-66929964(+)$1	342	147	161	11.3206
eeeeemmmmeeeee	chr7:106987803-106988125(-)$1	322	169	183	11.3206
eeeeemmmmeeeee	chr4:138932977-138933398(+)$1	421	156	170	11.3206
deeeeellleeeee	chr11:90197972-90198200(-)$1	228	135	149	9.3559
eeeeeooooooeee	chr16:38243648-38243991(+)$1	343	212	226	9.9542
eeeeeooooooeee	chr3:32833153-32833511(+)$1	358	233	247	9.9542
eeeeellleeeeeg	chr2:18138073-18138372(-)$1	299	180	194	9.2861
!eeeeellleeeee	chr3:116251665-116251879(+)$1	214	49	63	9.3314
eeeeemmmmeeeee	chr4:57704361-57704721(+)$1	360	131	145	11.3206
eeeeemmmmeeeee	chr11:77349850-77350160(-)$1	310	284	298	11.3206
eeeeemmmmeeeee	chr2:132131906-132132383(+)$1	477	289	303	11.3206
feeeeellleeeee	chr1:145848021-145848453(-)$1	432	368	382	9.2981
eeeeemmmmeeeee	chr4:134481586-134482049(+)$1	463	107	121	11.3206
!eeeeellleeeee	chr18:61145757-61146147(+)$1	390	344	358	9.3314
eeeeemmmmeeeee	chr5:34347787-34348233(+)$1	446	154	168	11.3206
eeeeemmmmeeeee	chr11:120151442-120151798(+)$1	356	304	318	11.3206
eeeeemmmmeeeee	chr11:45760778-45761015(-)$1	237	70	84	11.3206
eeeeemmmmeeeee	chr12:101447241-101447725(+)$1	484	257	271	11.3206
eeeeemmmmeeeee	chr8:11826827-11827216(+)$1	389	265	279	11.3206
eeeeemmmmeeeee	chr13:38067864-38068122(-)$1	258	101	115	11.3206
eeeeeooooooeee	chr11:62707847-62708300(+)$1	453	156	170	9.9542
eeeeeooooooeee	chr11:77524731-77525182(+)$1	451	92	106	9.9542
eeeeeooooooeee	chr16:11174788-11175123(-)$1	335	244	258	9.9542
eeeeemmmmeeeee	chr11:28287565-28288039(-)$1	474	288	302	11.3206
eeeeemmmmeeeee	chr8:42101421-42101720(-)$1	299	72	86	11.3206
eeeeemmmmeeeee	chr2:35037231-35037544(-)$1	313	83	97	11.3206
eeeeemmmmeeeee	chr14:19101081-19101344(-)$1	263	234	248	11.3206
eeeeemmmmeeeee	chr8:126867654-126867860(+)$1	206	139	153	11.3206
eeeeemmmmeeeee	chr13:55756328-55756766(+)$1	438	350	364	11.3206
eeeeeooooooeee	chr7:148725025-148725497(-)$1	472	186	200	9.9542
eeeeellleeeee]	chr7:91397890-91398127(-)$1	237	30	44	9.1968
eeeeemmmmeeeee	chr3:115647506-115647727(-)$1	221	196	210	11.3206
eeeeeooooooeee	chr1:34934481-34934842(+)$1	361	182	196	9.9542
eeeeeooooooeee	chr14:123319061-123319289(-)$1	228	180	194	9.9542
eeeeeooooooeee	chr2:135907676-135908016(-)$1	340	320	334	9.9542
eeeeeooooooeee	chr16:91014593-91015089(-)$1	496	273	287	9.9542
eeeeemmmmeeeee	chr1:46865934-46866225(-)$1	291	216	230	11.3206
eeeeemmmmeeeee	chr1:166367146-166367642(-)$1	496	112	126	11.3206
eeeeeooooooeee	chr1:78702871-78703163(+)$1	292	126	140	9.9542

#otherMatches

#Seq PSSM
AAAGCUUUGCUUUG	chr3:88881867-88882364(+)$1	497	145	159	9.3087
GCAUGUAUUUAUGU	chr19:16459390-16459698(+)$1	308	66	80	11.3206
UCUUUCCUUAAAGA	chr7:91394755-91395023(-)$1	268	12	26	11.3206
GCGCGCGUUCGCGC	chr19:45055998-45056450(+)$1	452	1	15	11.3206
AUUUAAAACUUGGA	chr9:96233025-96233524(-)$1	499	443	457	9.3203
GUAUUAGUAAAUAU	chr8:37631774-37632081(-)$1	307	152	166	11.3206
CCAGGGUCACUUGG	chr5:30111583-30111813(+)$1	230	171	185	11.3206
GACAGACAGCCCUG	chr11:100923607-100924035(+)$1	428	374	388	9.9542
guguauguguacau	chr10:85511866-85512260(+)$1	394	127	141	11.3206
uuauuuuuUGAUAG	chr4:11892567-11892950(-)$1	383	345	359	11.3206
GGCUUGCCCAGGCU	chr16:94352252-94352717(-)$1	465	15	29	11.3206
CAGCCUUUGGUGGC	chr11:69414603-69414982(-)$1	379	80	94	9.9542
CUUGGAAUGUCAGG	chr1:174302653-174303057(+)$1	404	117	131	11.3206
AGUCAGAUUGGCUG	chr11:74488411-74488677(-)$1	266	98	112	9.3087
CAGUUAACUUAAAU	chr11:109529925-109530411(+)$1	486	328	342	9.9542
AGAUCAUGUGGUUU	chr2:49628921-49629346(+)$1	425	20	34	11.3206
UGUCAGAAUAUUGG	chr5:9480498-9480972(+)$1	474	451	465	9.9542
GCUAGUGAUCUAGU	chr3:95435709-95436043(+)$1	334	89	103	11.3206
GUUAGAAAACUGAC	chr10:59412898-59413232(-)$1	334	60	74	11.3206
UGCAGAAUUCUGUA	chr18:38623871-38624308(+)$1	437	234	248	11.3206
AAACCUGUGGGUUU	chr11:58161056-58161279(+)$1	223	38	52	11.3206
AGUUGUCACCAACU	chr12:53668720-53669026(+)$1	306	282	296	11.3206
UAUGUUUUUGCGUA	chr13:94971777-94972057(-)$1	280	93	107	11.3206
caacuuguuaguug	chr14:66929622-66929964(+)$1	342	147	161	11.3206
GUGCUUAAUAGUAC	chr7:106987803-106988125(-)$1	322	169	183	11.3206
uauaggcuucugug	chr4:138932977-138933398(+)$1	421	156	170	11.3206
GACAGAAAAUCUGU	chr11:90197972-90198200(-)$1	228	135	149	9.3559
AGUGACCGGUUUCA	chr16:38243648-38243991(+)$1	343	212	226	9.9542
AUGGAAAAGGAUUU	chr3:32833153-32833511(+)$1	358	233	247	9.9542
uggcuguaagucac	chr2:18138073-18138372(-)$1	299	180	194	9.2861
UUAAUUGGAGGUUA	chr3:116251665-116251879(+)$1	214	49	63	9.3314
GAUUCUGCAGAGUC	chr4:57704361-57704721(+)$1	360	131	145	11.3206
CUCUUUAGUGAGAG	chr11:77349850-77350160(-)$1	310	284	298	11.3206
AUGAUUUUAGUCAU	chr2:132131906-132132383(+)$1	477	289	303	11.3206
UUUCAGUAACUGGA	chr1:145848021-145848453(-)$1	432	368	382	9.2981
AUCAUGAAUGUGGU	chr4:134481586-134482049(+)$1	463	107	121	11.3206
CAAACGACACGUUU	chr18:61145757-61146147(+)$1	390	344	358	9.3314
CAUAUGACUAUAUG	chr5:34347787-34348233(+)$1	446	154	168	11.3206
UCUGUGACUGCAGA	chr11:120151442-120151798(+)$1	356	304	318	11.3206
GUAUAUGUGUGUAC	chr11:45760778-45761015(-)$1	237	70	84	11.3206
CUCAGCAUCCUGGG	chr12:101447241-101447725(+)$1	484	257	271	11.3206
UUUUAUAUUUAAAA	chr8:11826827-11827216(+)$1	389	265	279	11.3206
GUGCAUCUCUGUAC	chr13:38067864-38068122(-)$1	258	101	115	11.3206
ACAUGUUGGUUUAU	chr11:62707847-62708300(+)$1	453	156	170	9.9542
GUCUUCUAACAAAG	chr11:77524731-77525182(+)$1	451	92	106	9.9542
UUUUCUCUAUUGAA	chr16:11174788-11175123(-)$1	335	244	258	9.9542
GACAGAAUGCUGUU	chr11:28287565-28288039(-)$1	474	288	302	11.3206
CCCUGGCGCCAGGG	chr8:42101421-42101720(-)$1	299	72	86	11.3206
GGCAAGGCUUUGUC	chr2:35037231-35037544(-)$1	313	83	97	11.3206
GGGUUUCAAAACCU	chr14:19101081-19101344(-)$1	263	234	248	11.3206
cucaggaggcugag	chr8:126867654-126867860(+)$1	206	139	153	11.3206
CGGUGUUAGUACUG	chr13:55756328-55756766(+)$1	438	350	364	11.3206
CGGGUGUGAGGGCC	chr7:148725025-148725497(-)$1	472	186	200	9.9542
CUGUCCUUGACGGC	chr7:91397890-91398127(-)$1	237	30	44	9.1968
UGUUUAACGAGGCG	chr3:115647506-115647727(-)$1	221	196	210	11.3206
AGGCUGCAGAGAGC	chr1:34934481-34934842(+)$1	361	182	196	9.9542
UUUUUUCCUAUGAA	chr14:123319061-123319289(-)$1	228	180	194	9.9542
CAUAAGGAGAGUUG	chr2:135907676-135908016(-)$1	340	320	334	9.9542
GGUGAUGACCUUCA	chr16:91014593-91015089(-)$1	496	273	287	9.9542
AAUGGCAUUCCAUU	chr1:46865934-46866225(-)$1	291	216	230	11.3206
ACCAUUUUCAUGGU	chr1:166367146-166367642(-)$1	496	112	126	11.3206
UGGCAUUGGUUUGC	chr1:78702871-78703163(+)$1	292	126	140	9.9542

#DB
(((((...)))))(	chr3:88881867-88882364(+)$1	1	145	159	9.3087
(((((....)))))	chr19:16459390-16459698(+)$1	1	66	80	11.3206
(((((....)))))	chr7:91394755-91395023(-)$1	1	12	26	11.3206
(((((....)))))	chr19:45055998-45056450(+)$1	1	1	15	11.3206
.(((((...)))))	chr9:96233025-96233524(-)$1	1	443	457	9.3203
(((((....)))))	chr8:37631774-37632081(-)$1	1	152	166	11.3206
(((((....)))))	chr5:30111583-30111813(+)$1	1	171	185	11.3206
(((((......)))	chr11:100923607-100924035(+)$1	1	374	388	9.9542
(((((....)))))	chr10:85511866-85512260(+)$1	1	127	141	11.3206
(((((....)))))	chr4:11892567-11892950(-)$1	1	345	359	11.3206
(((((....)))))	chr16:94352252-94352717(-)$1	1	15	29	11.3206
(((((......)))	chr11:69414603-69414982(-)$1	1	80	94	9.9542
(((((....)))))	chr1:174302653-174303057(+)$1	1	117	131	11.3206
(((((...)))))(	chr11:74488411-74488677(-)$1	1	98	112	9.3087
(((((......)))	chr11:109529925-109530411(+)$1	1	328	342	9.9542
(((((....)))))	chr2:49628921-49629346(+)$1	1	20	34	11.3206
(((((......)))	chr5:9480498-9480972(+)$1	1	451	465	9.9542
(((((....)))))	chr3:95435709-95436043(+)$1	1	89	103	11.3206
(((((....)))))	chr10:59412898-59413232(-)$1	1	60	74	11.3206
(((((....)))))	chr18:38623871-38624308(+)$1	1	234	248	11.3206
(((((....)))))	chr11:58161056-58161279(+)$1	1	38	52	11.3206
(((((....)))))	chr12:53668720-53669026(+)$1	1	282	296	11.3206
(((((....)))))	chr13:94971777-94972057(-)$1	1	93	107	11.3206
(((((....)))))	chr14:66929622-66929964(+)$1	1	147	161	11.3206
(((((....)))))	chr7:106987803-106988125(-)$1	1	169	183	11.3206
(((((....)))))	chr4:138932977-138933398(+)$1	1	156	170	11.3206
((((((...)))))	chr11:90197972-90198200(-)$1	1	135	149	9.3559
(((((......)))	chr16:38243648-38243991(+)$1	1	212	226	9.9542
(((((......)))	chr3:32833153-32833511(+)$1	1	233	247	9.9542
(((((...))))))	chr2:18138073-18138372(-)$1	1	180	194	9.2861
.(((((...)))))	chr3:116251665-116251879(+)$1	1	49	63	9.3314
(((((....)))))	chr4:57704361-57704721(+)$1	1	131	145	11.3206
(((((....)))))	chr11:77349850-77350160(-)$1	1	284	298	11.3206
(((((....)))))	chr2:132131906-132132383(+)$1	1	289	303	11.3206
((((((...)))))	chr1:145848021-145848453(-)$1	1	368	382	9.2981
(((((....)))))	chr4:134481586-134482049(+)$1	1	107	121	11.3206
.(((((...)))))	chr18:61145757-61146147(+)$1	1	344	358	9.3314
(((((....)))))	chr5:34347787-34348233(+)$1	1	154	168	11.3206
(((((....)))))	chr11:120151442-120151798(+)$1	1	304	318	11.3206
(((((....)))))	chr11:45760778-45761015(-)$1	1	70	84	11.3206
(((((....)))))	chr12:101447241-101447725(+)$1	1	257	271	11.3206
(((((....)))))	chr8:11826827-11827216(+)$1	1	265	279	11.3206
(((((....)))))	chr13:38067864-38068122(-)$1	1	101	115	11.3206
(((((......)))	chr11:62707847-62708300(+)$1	1	156	170	9.9542
(((((......)))	chr11:77524731-77525182(+)$1	1	92	106	9.9542
(((((......)))	chr16:11174788-11175123(-)$1	1	244	258	9.9542
(((((....)))))	chr11:28287565-28288039(-)$1	1	288	302	11.3206
(((((....)))))	chr8:42101421-42101720(-)$1	1	72	86	11.3206
(((((....)))))	chr2:35037231-35037544(-)$1	1	83	97	11.3206
(((((....)))))	chr14:19101081-19101344(-)$1	1	234	248	11.3206
(((((....)))))	chr8:126867654-126867860(+)$1	1	139	153	11.3206
(((((....)))))	chr13:55756328-55756766(+)$1	1	350	364	11.3206
(((((......)))	chr7:148725025-148725497(-)$1	1	186	200	9.9542
(((((...))))).	chr7:91397890-91398127(-)$1	1	30	44	9.1968
(((((....)))))	chr3:115647506-115647727(-)$1	1	196	210	11.3206
(((((......)))	chr1:34934481-34934842(+)$1	1	182	196	9.9542
(((((......)))	chr14:123319061-123319289(-)$1	1	180	194	9.9542
(((((......)))	chr2:135907676-135908016(-)$1	1	320	334	9.9542
(((((......)))	chr16:91014593-91015089(-)$1	1	273	287	9.9542
(((((....)))))	chr1:46865934-46866225(-)$1	1	216	230	11.3206
(((((....)))))	chr1:166367146-166367642(-)$1	1	112	126	11.3206
(((((......)))	chr1:78702871-78703163(+)$1	1	126	140	9.9542

#PSSM
e : 0.91	! : 0.03	[ : 0.01	d : 0.01	f : 0.01	
e : 0.99	
e : 0.99	
e : 0.99	
e : 0.99	
m : 0.61	o : 0.24	e : 0.08	l : 0.06	
m : 0.61	o : 0.24	l : 0.14	
m : 0.61	o : 0.24	l : 0.14	
m : 0.61	o : 0.24	l : 0.08	e : 0.06	
e : 0.75	o : 0.24	
e : 0.75	o : 0.24	
e : 0.99	
e : 0.99	
e : 0.93	d : 0.03	g : 0.01	] : 0.01	

#score	663.2349111040894
#seq	62
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_UTR_m2_run2.txt

#BEAR
[ddddoooooodddd]	chr16:17045123-17045324(+)$1	201	75	91	10.2930
fffffoooooofffff	chr16:20127523-20127724(+)$1	201	30	46	11.1987
eeeeeooooooeeeee	chr2:157296572-157296773(+)$1	201	24	40	11.8229
gggggooooooggggg	chr11:104189605-104189806(+)$1	201	15	31	11.1798
eeeeeooooooeeeee	chr2:164316181-164316382(+)$1	201	129	145	11.8229
f!!bboooooobb22f	chr2:117106341-117106542(-)$1	201	5	21	9.4124
d[cccooooooccc]d	chr2:102628031-102628232(+)$1	201	128	144	10.6858
fffffoooooofffff	chr1:66742469-66742670(+)$1	201	36	52	11.1987
eeeeeooooooeeeee	chr1:184245876-184246077(-)$1	201	89	105	11.8229
eeeeeooooooeeeee	chrX:35550059-35550260(+)$1	201	24	40	11.8229
eecccooooooccc]e	chr3:80647709-80647910(-)$1	201	72	88	11.2282
=====oooooo=====	chr12:92794869-92795070(-)$1	201	22	38	11.0541
eeeeeooooooeeeee	chr12:73894945-73895146(+)$1	201	73	89	11.8229
fffffoooooofffff	chr1:34935984-34936185(+)$1	201	24	40	11.1987
[ddddooooooddddd	chr8:70236711-70236912(-)$1	201	136	152	10.1495
ccc[aooooooa]ccc	chr13:9667404-9667605(+)$1	201	135	151	10.4531
fffffoooooofffff	chr3:121462693-121462894(-)$1	201	1	17	11.1987
!ddddoooooodddd2	chr3:102806844-102807045(+)$1	201	157	173	9.9441
fffffoooooofffff	chr6:125171772-125171973(+)$1	201	162	178	11.1987
eeeeeooooooeeeee	chrX:92246451-92246652(-)$1	201	117	133	11.8229
fffffoooooofffff	chr7:134949228-134949429(-)$1	201	109	125	11.1987
dddddoooooodddd3	chr7:53129105-53129306(+)$1	201	111	127	10.0568
eeeeeooooooeeeee	chr12:60174357-60174558(+)$1	201	28	44	11.8229
eeeeeooooooeeeee	chr5:33135251-33135452(-)$1	201	182	198	11.8229
fffffoooooofffff	chr2:32271106-32271307(-)$1	201	61	77	11.1987
""cccooooooccc44	chr6:58856161-58856362(-)$1	201	115	131	10.4723
eeeeeooooooeeeee	chr3:135129606-135129807(+)$1	201	70	86	11.8229
fffffoooooofffff	chr7:128787344-128787545(-)$1	201	101	117	11.1987
ee[bboooooobb]ee	chr2:128436759-128436960(-)$1	201	27	43	10.3274
cccccooooooccc]c	chr11:74488608-74488809(-)$1	201	131	147	10.6915
eeeeeooooooeeeee	chr13:69841668-69841869(-)$1	201	66	82	11.8229
iiiiiooooooiiiii	chr11:54176685-54176886(+)$1	201	48	64	10.8063
dddddoooooodddd]	chr10:23908213-23908414(+)$1	201	164	180	10.1125
d!!bboooooobb]dd	chr2:163843755-163843956(+)$1	201	89	105	9.5429
eeeeeooooooeeeee	chr12:82817960-82818161(-)$1	201	32	48	11.8229
fffffoooooofffff	chr1:172129603-172129804(-)$1	201	97	113	11.1987
fffffoooooofffff	chr2:31472124-31472325(+)$1	201	56	72	11.1987
fffffoooooofffff	chr13:6580599-6580800(-)$1	201	125	141	11.1987
e[cccooooooccc]e	chr7:6660011-6660212(-)$1	201	147	163	11.1724
gggggooooooggggg	chr7:104456351-104456552(+)$1	201	86	102	11.1798
dd[bboooooobb]dd	chr15:92170483-92170684(+)$1	201	5	21	9.4600
gggggooooooggggg	chr6:48012979-48013180(-)$1	201	181	197	11.1798
eeeeeooooooeeeee	chr11:87429058-87429259(+)$1	201	104	120	11.8229
[ddddoooooodddd]	chr5:151612500-151612701(+)$1	201	39	55	10.2930
fffffoooooofffff	chr5:89088547-89088748(-)$1	201	180	196	11.1987
gggggooooooggggg	chr5:147547617-147547818(-)$1	201	35	51	11.1798
eeeeeooooooeeeee	chr19:47717433-47717634(+)$1	201	84	100	11.8229
iiiiiooooooiiiii	chr4:41604833-41605034(-)$1	201	49	65	10.8063
[ddddoooooodddd]	chr6:39553747-39553948(-)$1	201	35	51	10.2930
b[cccooooooccc]b	chr2:102630659-102630860(+)$1	201	126	142	10.2340
eeeeeooooooeeeee	chr13:81935733-81935934(+)$1	201	123	139	11.8229
!!cccooooooccccc	chr8:96492965-96493166(+)$1	201	97	113	10.7656
gggggooooooggggg	chr12:47797498-47797699(-)$1	201	95	111	11.1798
gggggooooooggggg	chr1:184245267-184245468(-)$1	201	176	192	11.1798
eeeeeooooooeeeee	chr14:120828530-120828731(+)$1	201	75	91	11.8229
eeeeeooooooeeeee	chr18:33345016-33345217(+)$1	201	183	199	11.8229
gggggooooooggggg	chr7:4097108-4097309(+)$1	201	39	55	11.1798
""cccooooooccc44	chr13:36817685-36817886(-)$1	201	62	78	10.4723
eeeeeooooooeeeee	chr11:29999627-29999828(-)$1	201	28	44	11.8229
ccc[aooooooa]ccc	chr11:68635511-68635712(-)$1	201	165	181	10.4531
fffffoooooofffff	chr12:86682906-86683107(-)$1	201	72	88	11.1987
fffffoooooofffff	chr13:94127427-94127628(+)$1	201	150	166	11.1987
eeeeeooooooeeeee	chr2:106804586-106804787(-)$1	201	5	21	11.8229
eeeeeooooooeeeee	chr15:96405935-96406136(-)$1	201	44	60	11.8229
eee[aooooooa]eee	chr17:24822550-24822751(-)$1	201	121	137	11.3523
f"""aooooooa333f	chr7:107426894-107427095(+)$1	201	170	186	10.2652

#otherMatches

#Seq PSSM
AUAAUUAUAUUGUUAA	chr16:17045123-17045324(+)$1	201	75	91	10.2930
acauGAAUUCCCAUGU	chr16:20127523-20127724(+)$1	201	30	46	11.1987
GGCUGCAGAGACAGUC	chr2:157296572-157296773(+)$1	201	24	40	11.8229
CAGGCUGACCUGCUUG	chr11:104189605-104189806(+)$1	201	15	31	11.1798
CAUUAACUAACUAGUG	chr2:164316181-164316382(+)$1	201	129	145	11.8229
GGAGCAUUUCAGUGAC	chr2:117106341-117106542(-)$1	201	5	21	9.4124
AUCUACAAAGUUAGUU	chr2:102628031-102628232(+)$1	201	128	144	10.6858
AGGGAAUACAGUCUCU	chr1:66742469-66742670(+)$1	201	36	52	11.1987
UGAAAAAAACAUUUCA	chr1:184245876-184246077(-)$1	201	89	105	11.8229
AUGAAACCUUGUUCAU	chrX:35550059-35550260(+)$1	201	24	40	11.8229
aauaauuuuuuuuauu	chr3:80647709-80647910(-)$1	201	72	88	11.2282
CAUAUUACAUCAUAUG	chr12:92794869-92795070(-)$1	201	22	38	11.0541
UCAUAUUUAAUUAUGA	chr12:73894945-73895146(+)$1	201	73	89	11.8229
GCUGGAAGAGGCUGGC	chr1:34935984-34936185(+)$1	201	24	40	11.1987
UCAGGACUGAACCUGG	chr8:70236711-70236912(-)$1	201	136	152	10.1495
GCUGCAGCACAGGGGC	chr13:9667404-9667605(+)$1	201	135	151	10.4531
CCUGAAUUAAAUUGGG	chr3:121462693-121462894(-)$1	201	1	17	11.1987
AACCCAUUCAGGGGUG	chr3:102806844-102807045(+)$1	201	157	173	9.9441
GCAUGAGCAAAUAUGC	chr6:125171772-125171973(+)$1	201	162	178	11.1987
UUGUGGAAGGAUAUAA	chrX:92246451-92246652(-)$1	201	117	133	11.8229
UCUGCCUGACAGUAGA	chr7:134949228-134949429(-)$1	201	109	125	11.1987
CACCUGCAUGAAGGUA	chr7:53129105-53129306(+)$1	201	111	127	10.0568
AAGCAUUUUUCUGUUU	chr12:60174357-60174558(+)$1	201	28	44	11.8229
CUUAAAAACUGUUAAG	chr5:33135251-33135452(-)$1	201	182	198	11.8229
GUGGGCCUGCCCCCAC	chr2:32271106-32271307(-)$1	201	61	77	11.1987
UGCUCUUCUGUGAGAA	chr6:58856161-58856362(-)$1	201	115	131	10.4723
CUUAUGUAGUAAUAAG	chr3:135129606-135129807(+)$1	201	70	86	11.8229
UUCAUCAUCACAUGGA	chr7:128787344-128787545(-)$1	201	101	117	11.1987
UCUUGGUCUAACGUGG	chr2:128436759-128436960(-)$1	201	27	43	10.3274
UGCCUGGGAUAAGGAC	chr11:74488608-74488809(-)$1	201	131	147	10.6915
AUGUUUAUGACAACAU	chr13:69841668-69841869(-)$1	201	66	82	11.8229
GUUAGGUAUGACUAAC	chr11:54176685-54176886(+)$1	201	48	64	10.8063
GCCUGUAUCUUUGGGU	chr10:23908213-23908414(+)$1	201	164	180	10.1125
CCUUGACAUUCCAUGU	chr2:163843755-163843956(+)$1	201	89	105	9.5429
UACAGCAUGCUUUGUA	chr12:82817960-82818161(-)$1	201	32	48	11.8229
UCAUUUCAUGUGAUGA	chr1:172129603-172129804(-)$1	201	97	113	11.1987
UUGAAGCAGUAUUUAA	chr2:31472124-31472325(+)$1	201	56	72	11.1987
CUGGAAUGUUCUCCAG	chr13:6580599-6580800(-)$1	201	125	141	11.1987
ACUCUCAUCACAGACU	chr7:6660011-6660212(-)$1	201	147	163	11.1724
AAAUGUAGAAUCAUUU	chr7:104456351-104456552(+)$1	201	86	102	11.1798
AAAGACCCUCAUCAUU	chr15:92170483-92170684(+)$1	201	5	21	9.4600
AGGGGACACAGCCUCU	chr6:48012979-48013180(-)$1	201	181	197	11.1798
GAAAACAUUUUUUUUC	chr11:87429058-87429259(+)$1	201	104	120	11.8229
UGGUCACUGUAGAUUU	chr5:151612500-151612701(+)$1	201	39	55	10.2930
AAAUAGCUUGUUAUUU	chr5:89088547-89088748(-)$1	201	180	196	11.1987
AAAAAGAAAUGUUUUU	chr5:147547617-147547818(-)$1	201	35	51	11.1798
AUGGAUUUUCUUUCAU	chr19:47717433-47717634(+)$1	201	84	100	11.8229
CUUUCCAUCCAGAGAG	chr4:41604833-41605034(-)$1	201	49	65	10.8063
ACUCCAGUAAGGGAGA	chr6:39553747-39553948(-)$1	201	35	51	10.2930
UGAUGUAGACUCAUGA	chr2:102630659-102630860(+)$1	201	126	142	10.2340
UCAAUGUAGUAGUUGA	chr13:81935733-81935934(+)$1	201	123	139	11.8229
AUUUCAAUAAAGGAGG	chr8:96492965-96493166(+)$1	201	97	113	10.7656
CAUUUCUCAUUGAAUG	chr12:47797498-47797699(-)$1	201	95	111	11.1798
GGUCCCUGUCUGGAUC	chr1:184245267-184245468(-)$1	201	176	192	11.1798
GAUUGUAACUCCAAUC	chr14:120828530-120828731(+)$1	201	75	91	11.8229
AGAGGGCAAUUCCUUU	chr18:33345016-33345217(+)$1	201	183	199	11.8229
UCAGCUCCUCUGCUGG	chr7:4097108-4097309(+)$1	201	39	55	11.1798
UUGUCAUAAGAGAUGC	chr13:36817685-36817886(-)$1	201	62	78	10.4723
AUACAUUAUAUUGUAU	chr11:29999627-29999828(-)$1	201	28	44	11.8229
GUCUGUACCUUCUGAC	chr11:68635511-68635712(-)$1	201	165	181	10.4531
cccauuucuauguggg	chr12:86682906-86683107(-)$1	201	72	88	11.1987
AGAUUAAUUUAAGUUU	chr13:94127427-94127628(+)$1	201	150	166	11.1987
uugcugagggaagcag	chr2:106804586-106804787(-)$1	201	5	21	11.8229
AUCUAUAAAUCUAGGU	chr15:96405935-96406136(-)$1	201	44	60	11.8229
CGCCCCUCUCUGUGUG	chr17:24822550-24822751(-)$1	201	121	137	11.3523
UAUUGGAGACACUUAG	chr7:107426894-107427095(+)$1	201	170	186	10.2652

#DB
.((((......)))).	chr16:17045123-17045324(+)$1	1	75	91	10.2930
(((((......)))))	chr16:20127523-20127724(+)$1	1	30	46	11.1987
(((((......)))))	chr2:157296572-157296773(+)$1	1	24	40	11.8229
(((((......)))))	chr11:104189605-104189806(+)$1	1	15	31	11.1798
(((((......)))))	chr2:164316181-164316382(+)$1	1	129	145	11.8229
(..((......))..)	chr2:117106341-117106542(-)$1	1	5	21	9.4124
(.(((......))).)	chr2:102628031-102628232(+)$1	1	128	144	10.6858
(((((......)))))	chr1:66742469-66742670(+)$1	1	36	52	11.1987
(((((......)))))	chr1:184245876-184246077(-)$1	1	89	105	11.8229
(((((......)))))	chrX:35550059-35550260(+)$1	1	24	40	11.8229
(((((......))).)	chr3:80647709-80647910(-)$1	1	72	88	11.2282
(((((......)))))	chr12:92794869-92795070(-)$1	1	22	38	11.0541
(((((......)))))	chr12:73894945-73895146(+)$1	1	73	89	11.8229
(((((......)))))	chr1:34935984-34936185(+)$1	1	24	40	11.1987
.((((......)))))	chr8:70236711-70236912(-)$1	1	136	152	10.1495
(((.(......).)))	chr13:9667404-9667605(+)$1	1	135	151	10.4531
(((((......)))))	chr3:121462693-121462894(-)$1	1	1	17	11.1987
.((((......)))).	chr3:102806844-102807045(+)$1	1	157	173	9.9441
(((((......)))))	chr6:125171772-125171973(+)$1	1	162	178	11.1987
(((((......)))))	chrX:92246451-92246652(-)$1	1	117	133	11.8229
(((((......)))))	chr7:134949228-134949429(-)$1	1	109	125	11.1987
(((((......)))).	chr7:53129105-53129306(+)$1	1	111	127	10.0568
(((((......)))))	chr12:60174357-60174558(+)$1	1	28	44	11.8229
(((((......)))))	chr5:33135251-33135452(-)$1	1	182	198	11.8229
(((((......)))))	chr2:32271106-32271307(-)$1	1	61	77	11.1987
..(((......)))..	chr6:58856161-58856362(-)$1	1	115	131	10.4723
(((((......)))))	chr3:135129606-135129807(+)$1	1	70	86	11.8229
(((((......)))))	chr7:128787344-128787545(-)$1	1	101	117	11.1987
((.((......)).))	chr2:128436759-128436960(-)$1	1	27	43	10.3274
(((((......))).)	chr11:74488608-74488809(-)$1	1	131	147	10.6915
(((((......)))))	chr13:69841668-69841869(-)$1	1	66	82	11.8229
(((((......)))))	chr11:54176685-54176886(+)$1	1	48	64	10.8063
(((((......)))).	chr10:23908213-23908414(+)$1	1	164	180	10.1125
(..((......)).))	chr2:163843755-163843956(+)$1	1	89	105	9.5429
(((((......)))))	chr12:82817960-82818161(-)$1	1	32	48	11.8229
(((((......)))))	chr1:172129603-172129804(-)$1	1	97	113	11.1987
(((((......)))))	chr2:31472124-31472325(+)$1	1	56	72	11.1987
(((((......)))))	chr13:6580599-6580800(-)$1	1	125	141	11.1987
(.(((......))).)	chr7:6660011-6660212(-)$1	1	147	163	11.1724
(((((......)))))	chr7:104456351-104456552(+)$1	1	86	102	11.1798
((.((......)).))	chr15:92170483-92170684(+)$1	1	5	21	9.4600
(((((......)))))	chr6:48012979-48013180(-)$1	1	181	197	11.1798
(((((......)))))	chr11:87429058-87429259(+)$1	1	104	120	11.8229
.((((......)))).	chr5:151612500-151612701(+)$1	1	39	55	10.2930
(((((......)))))	chr5:89088547-89088748(-)$1	1	180	196	11.1987
(((((......)))))	chr5:147547617-147547818(-)$1	1	35	51	11.1798
(((((......)))))	chr19:47717433-47717634(+)$1	1	84	100	11.8229
(((((......)))))	chr4:41604833-41605034(-)$1	1	49	65	10.8063
.((((......)))).	chr6:39553747-39553948(-)$1	1	35	51	10.2930
(.(((......))).)	chr2:102630659-102630860(+)$1	1	126	142	10.2340
(((((......)))))	chr13:81935733-81935934(+)$1	1	123	139	11.8229
..(((......)))))	chr8:96492965-96493166(+)$1	1	97	113	10.7656
(((((......)))))	chr12:47797498-47797699(-)$1	1	95	111	11.1798
(((((......)))))	chr1:184245267-184245468(-)$1	1	176	192	11.1798
(((((......)))))	chr14:120828530-120828731(+)$1	1	75	91	11.8229
(((((......)))))	chr18:33345016-33345217(+)$1	1	183	199	11.8229
(((((......)))))	chr7:4097108-4097309(+)$1	1	39	55	11.1798
..(((......)))..	chr13:36817685-36817886(-)$1	1	62	78	10.4723
(((((......)))))	chr11:29999627-29999828(-)$1	1	28	44	11.8229
(((.(......).)))	chr11:68635511-68635712(-)$1	1	165	181	10.4531
(((((......)))))	chr12:86682906-86683107(-)$1	1	72	88	11.1987
(((((......)))))	chr13:94127427-94127628(+)$1	1	150	166	11.1987
(((((......)))))	chr2:106804586-106804787(-)$1	1	5	21	11.8229
(((((......)))))	chr15:96405935-96406136(-)$1	1	44	60	11.8229
(((.(......).)))	chr17:24822550-24822751(-)$1	1	121	137	11.3523
(...(......)...)	chr7:107426894-107427095(+)$1	1	170	186	10.2652

#PSSM
e : 0.34	f : 0.24	g : 0.10	d : 0.07	[ : 0.06	c : 0.04	! : 0.03	" : 0.03	i : 0.03	= : 0.01	b : 0.01	
e : 0.33	f : 0.21	d : 0.12	g : 0.10	! : 0.04	[ : 0.04	c : 0.04	" : 0.04	i : 0.03	= : 0.01	
e : 0.30	f : 0.21	c : 0.15	d : 0.10	g : 0.10	! : 0.03	[ : 0.03	i : 0.03	= : 0.01	" : 0.01	
e : 0.28	f : 0.21	c : 0.12	d : 0.10	g : 0.10	b : 0.06	[ : 0.04	i : 0.03	= : 0.01	" : 0.01	
e : 0.28	f : 0.21	c : 0.12	d : 0.10	g : 0.10	b : 0.06	a : 0.06	i : 0.03	= : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
e : 0.28	f : 0.21	c : 0.12	d : 0.10	g : 0.10	b : 0.06	a : 0.06	i : 0.03	= : 0.01	
e : 0.28	f : 0.21	c : 0.12	d : 0.10	g : 0.10	b : 0.06	] : 0.04	i : 0.03	= : 0.01	3 : 0.01	
e : 0.30	f : 0.21	c : 0.15	d : 0.10	g : 0.10	] : 0.04	i : 0.03	2 : 0.01	= : 0.01	3 : 0.01	
e : 0.31	f : 0.21	d : 0.13	g : 0.10	] : 0.07	c : 0.04	4 : 0.03	i : 0.03	2 : 0.01	= : 0.01	3 : 0.01	
e : 0.34	f : 0.24	g : 0.10	] : 0.06	d : 0.06	c : 0.06	4 : 0.03	i : 0.03	= : 0.01	2 : 0.01	3 : 0.01	b : 0.01	

#score	730.4761318484644
#seq	66
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_transcript_m1_run1.txt

#BEAR
iiiiiooooooiiii	chrX:148305940-148306151(+)$1	211	16	31	10.0531
eeeeeooooooeeee	chr5:121599050-121599267(-)$1	217	127	142	10.7865
g[cccooooooccc]	chr18:68018464-68018679(+)$1	215	126	141	10.9933
:ddddoooooodddd	chr6:86369623-86369830(+)$1	207	158	173	11.3737
fddddoooooodddd	chr10:122618692-122618914(-)$1	222	135	150	11.8901
[ddddoooooodddd	chr1:27015925-27016143(-)$1	218	132	147	12.2677
"ddddoooooodddd	chr5:123437638-123437859(-)$1	221	171	186	12.2522
iddddoooooodddd	chr14:52803537-52803770(-)$1	233	107	122	12.0740
"ddddoooooodddd	chr1:95334789-95335015(-)$1	226	46	61	12.2522
!ddddoooooodddd	chr19:29722716-29722940(-)$1	224	197	212	12.3310
!!cccooooooccc2	chr18:34988006-34988216(+)$1	210	117	132	11.0698
d[cccoooooocccd	chr3:55796230-55796453(-)$1	223	62	77	11.0479
ddcccooooooccc]	chr1:15828173-15828396(+)$1	223	19	34	10.9915
:ddddoooooodddd	chr2:50162801-50163024(+)$1	223	48	63	11.3737
[ddddoooooodddd	chr17:25973296-25973520(-)$1	224	11	26	12.2677
eeeeeooooooeeee	chr12:70406701-70406924(+)$1	223	92	107	10.7865
eeeeeooooooeeee	chr19:40677278-40677496(-)$1	218	148	163	10.7865
!ddddoooooodddd	chr5:8448320-8448536(+)$1	216	24	39	12.3310
eeeeeooooooeeee	chr2:126701419-126701642(-)$1	223	87	102	10.7865
eeeeeooooooeeee	chr2:32108325-32108544(+)$1	219	56	71	10.7865
[cccaooooooa]cc	chr17:75758530-75758757(+)$1	227	195	210	10.4770
!ddddoooooodddd	chr9:95767820-95768042(+)$1	222	71	86	12.3310
:ddddoooooodddd	chr5:77023085-77023315(+)$1	230	70	85	11.3737
cddddoooooodddd	chr3:142502140-142502353(-)$1	213	45	60	12.0376
:ddddoooooodddd	chr5:25203983-25204206(-)$1	223	151	166	11.3737
[ddddoooooodddd	chr19:41297528-41297742(-)$1	214	93	108	12.2677
cddddoooooodddd	chr3:121486878-121487104(-)$1	226	177	192	12.0376
d[cccooooooccc]	chr5:50416852-50417072(-)$1	220	130	145	10.8738
##cccooooooccc4	chr4:120831801-120832026(-)$1	225	107	122	10.9699
e[cccooooooccc]	chr7:107503165-107503391(-)$1	226	138	153	10.9923
eddddoooooodddd	chr17:42975560-42975802(-)$1	242	72	87	12.0755
!!cccooooooccc4	chr3:152121424-152121643(+)$1	219	21	36	11.2521
#ddddoooooodddd	chr6:11912570-11912795(+)$1	225	93	108	12.2321
!!cccooooooccc2	chrX:157014750-157014976(+)$1	226	26	41	11.0698
gggggoooooogggg	chr2:121890989-121891210(-)$1	221	61	76	10.0599
ggcccooooooccc4	chr2:74416848-74417067(-)$1	219	61	76	10.8683
:ddddoooooodddd	chr14:46124265-46124493(-)$1	228	211	226	11.3737
$ddddoooooodddd	chr1:40057433-40057653(+)$1	220	102	117	12.0471
:ddddoooooodddd	chr6:108336717-108336937(+)$1	220	27	42	11.3737
[ddddoooooodddd	chr1:71672662-71672895(-)$1	233	151	166	12.2677
d[cccoooooocccd	chrX:74894133-74894366(+)$1	233	72	87	11.0479
!!cccooooooccc4	chr4:126588338-126588570(-)$1	232	209	224	11.2521
:ddddoooooodddd	chr15:32850681-32850894(+)$1	213	166	181	11.3737
c[cccooooooccc]	chr10:104675450-104675686(+)$1	236	213	228	10.9543
[ddddoooooodddd	chr5:23928532-23928750(-)$1	218	101	116	12.2677
cccccoooooocccH	chr1:84790685-84790897(-)$1	212	179	194	9.9210
eeeeeooooooeeee	chr1:34226524-34226742(+)$1	218	116	131	10.7865
!!cccooooooccc]	chr8:26852109-26852320(-)$1	211	89	104	11.2766
##cccooooooccc2	chrX:72766625-72766858(+)$1	233	63	78	10.7876
gggggoooooogggg	chr6:120332902-120333126(+)$1	224	84	99	10.0599
eeeeeooooooeeee	chr8:125422433-125422657(-)$1	224	36	51	10.7865
eeeeeooooooeeee	chr5:104932924-104933150(+)$1	226	185	200	10.7865
ddd[aooooooaddd	chr12:4227826-4228046(+)$1	220	178	193	11.1207
a[cccooooooccc]	chr11:102729220-102729440(-)$1	220	196	211	11.0283
:ddddoooooodddd	chr15:54902884-54903101(-)$1	217	157	172	11.3737
eddddoooooodddd	chr19:4264274-4264489(-)$1	215	30	45	12.0755
gggggoooooogggg	chr10:34117850-34118077(-)$1	227	177	192	10.0599
eeeeeooooooeeee	chr9:21147358-21147582(+)$1	224	116	131	10.7865
eeeeeooooooeeee	chr3:5219235-5219453(-)$1	218	179	194	10.7865
eeeeeooooooeeee	chr1:183085887-183086113(+)$1	226	34	49	10.7865
eeeeeooooooeeee	chr19:53692503-53692728(+)$1	225	120	135	10.7865
Iddddoooooodddd	chr11:98877314-98877520(-)$1	206	141	156	11.0161
gggggoooooogggg	chr8:70487815-70488035(-)$1	220	194	209	10.0599
!ddddoooooodddd	chr3:108514229-108514437(-)$1	208	130	145	12.3310
:ddddoooooodddd	chr15:27777020-27777264(-)$1	244	46	61	11.3737
eee[aooooooa]ee	chr14:33379886-33380103(+)$1	217	158	173	10.2688

#otherMatches

#Seq PSSM
UAAAACUGACCUUUU	chrX:148305940-148306151(+)$1	211	16	31	10.0531
GAGAGCUCAAACUCU	chr5:121599050-121599267(-)$1	217	127	142	10.7865
GUGGUGAUGAAAUCU	chr18:68018464-68018679(+)$1	215	126	141	10.9933
UAACAUCAAACUGUU	chr6:86369623-86369830(+)$1	207	158	173	11.3737
GAGAUCAAAAUGUCU	chr10:122618692-122618914(-)$1	222	135	150	11.8901
gcaggguugggccug	chr1:27015925-27016143(-)$1	218	132	147	12.2677
AUGCUAUGGAAGGCA	chr5:123437638-123437859(-)$1	221	171	186	12.2522
CAUUGUUGUAUCGGU	chr14:52803537-52803770(-)$1	233	107	122	12.0740
CUGGUCUAGUUGCCA	chr1:95334789-95335015(-)$1	226	46	61	12.2522
GCGCAGGAGGAUGCG	chr19:29722716-29722940(-)$1	224	197	212	12.3310
AGCCUUCAGCCAGGA	chr18:34988006-34988216(+)$1	210	117	132	11.0698
ACAGCAGUGACGUUU	chr3:55796230-55796453(-)$1	223	62	77	11.0479
UAAAGUACAAUUUUA	chr1:15828173-15828396(+)$1	223	19	34	10.9915
AGUAAGAACAAUUAC	chr2:50162801-50163024(+)$1	223	48	63	11.3737
UCCUGAGAACACAGG	chr17:25973296-25973520(-)$1	224	11	26	12.2677
UAUCUUAAUCUGGAU	chr12:70406701-70406924(+)$1	223	92	107	10.7865
CCACAAGCUCAUGUG	chr19:40677278-40677496(-)$1	218	148	163	10.7865
UUAAUGUAGAAAUUA	chr5:8448320-8448536(+)$1	216	24	39	12.3310
CCGAGCUGUGACUUG	chr2:126701419-126701642(-)$1	223	87	102	10.7865
GCCUGUGAUUUCAGG	chr2:32108325-32108544(+)$1	219	56	71	10.7865
UCACCAAACAAGAGU	chr17:75758530-75758757(+)$1	227	195	210	10.4770
UGUAAUUAUACUUAC	chr9:95767820-95768042(+)$1	222	71	86	12.3310
AGGAUGAAAAGAUCC	chr5:77023085-77023315(+)$1	230	70	85	11.3737
AUACUCCAAAUAGUG	chr3:142502140-142502353(-)$1	213	45	60	12.0376
AGCCUGUGACAGGGC	chr5:25203983-25204206(-)$1	223	151	166	11.3737
GUCGAAAUCUGUCGG	chr19:41297528-41297742(-)$1	214	93	108	12.2677
UAAGUUCAUCUACUU	chr3:121486878-121487104(-)$1	226	177	192	12.0376
AGUAUUCUCUUGUGG	chr5:50416852-50417072(-)$1	220	130	145	10.8738
CUGCAAGGACGUGUU	chr4:120831801-120832026(-)$1	225	107	122	10.9699
GAGGCCAUUCCGCCC	chr7:107503165-107503391(-)$1	226	138	153	10.9923
AAGUUCUUUUUGACU	chr17:42975560-42975802(-)$1	242	72	87	12.0755
ACAGCAUGAGAGCUC	chr3:152121424-152121643(+)$1	219	21	36	11.2521
UGUGAAGAUCCUCGC	chr6:11912570-11912795(+)$1	225	93	108	12.2321
UAAGGCAAGUAUCUC	chrX:157014750-157014976(+)$1	226	26	41	11.0698
GUUCCCGUGGAGGAA	chr2:121890989-121891210(-)$1	221	61	76	10.0599
UGAUGGGAAGGCAUU	chr2:74416848-74417067(-)$1	219	61	76	10.8683
CGCAGCACAAACUGC	chr14:46124265-46124493(-)$1	228	211	226	11.3737
CGAGCUUUCAUGCUC	chr1:40057433-40057653(+)$1	220	102	117	12.0471
GGGCAUCCUUUUGCC	chr6:108336717-108336937(+)$1	220	27	42	11.3737
UGAUAGUGUGGUGUC	chr1:71672662-71672895(-)$1	233	151	166	12.2677
GCUUUGAAGUGGAAC	chrX:74894133-74894366(+)$1	233	72	87	11.0479
ACGCUGUCGUAAGUC	chr4:126588338-126588570(-)$1	232	209	224	11.2521
ACGCUAGAGCAGGCG	chr15:32850681-32850894(+)$1	213	166	181	11.3737
UGAAUUCAAAUGUUG	chr10:104675450-104675686(+)$1	236	213	228	10.9543
UCUGAAGCGUGUCAG	chr5:23928532-23928750(-)$1	218	101	116	12.2677
UUUCAGCAUAUUGAG	chr1:84790685-84790897(-)$1	212	179	194	9.9210
UCACAAAUAAGUGUG	chr1:34226524-34226742(+)$1	218	116	131	10.7865
CUAAUGAUACAAUUC	chr8:26852109-26852320(-)$1	211	89	104	11.2766
UCCCUCCUCACAGGC	chrX:72766625-72766858(+)$1	233	63	78	10.7876
UUGGGGCUGGACCCA	chr6:120332902-120333126(+)$1	224	84	99	10.0599
UGCAGGCUGGACUGC	chr8:125422433-125422657(-)$1	224	36	51	10.7865
CUGAGGUAUAACUCG	chr5:104932924-104933150(+)$1	226	185	200	10.7865
CCAACAGCCAAGUGG	chr12:4227826-4228046(+)$1	220	178	193	11.1207
UGGGAGAGAAGUCUG	chr11:102729220-102729440(-)$1	220	196	211	11.0283
AGAUCACUCCCGGUC	chr15:54902884-54903101(-)$1	217	157	172	11.3737
GUAAGUCACAUCUUG	chr19:4264274-4264489(-)$1	215	30	45	12.0755
GCCUCCUGGUAGAGG	chr10:34117850-34118077(-)$1	227	177	192	10.0599
UGGUACUGGAUUAUC	chr9:21147358-21147582(+)$1	224	116	131	10.7865
UUAAUACAAAAGUUA	chr3:5219235-5219453(-)$1	218	179	194	10.7865
GUGGCUUGAGUGCCA	chr1:183085887-183086113(+)$1	226	34	49	10.7865
GUUACCAGUAAGUGA	chr19:53692503-53692728(+)$1	225	120	135	10.7865
AAGAUGUCAAAGUCU	chr11:98877314-98877520(-)$1	206	141	156	11.0161
UCCUGUUGGCCCAGG	chr8:70487815-70488035(-)$1	220	194	209	10.0599
ACUGGACUGGCCCAG	chr3:108514229-108514437(-)$1	208	130	145	12.3310
CGCUGCAGGUACAGC	chr15:27777020-27777264(-)$1	244	46	61	11.3737
GCGUCAAGACAGCCG	chr14:33379886-33380103(+)$1	217	158	173	10.2688

#DB
(((((......))))	chrX:148305940-148306151(+)$1	1	16	31	10.0531
(((((......))))	chr5:121599050-121599267(-)$1	1	127	142	10.7865
(.(((......))).	chr18:68018464-68018679(+)$1	1	126	141	10.9933
.((((......))))	chr6:86369623-86369830(+)$1	1	158	173	11.3737
(((((......))))	chr10:122618692-122618914(-)$1	1	135	150	11.8901
.((((......))))	chr1:27015925-27016143(-)$1	1	132	147	12.2677
.((((......))))	chr5:123437638-123437859(-)$1	1	171	186	12.2522
(((((......))))	chr14:52803537-52803770(-)$1	1	107	122	12.0740
.((((......))))	chr1:95334789-95335015(-)$1	1	46	61	12.2522
.((((......))))	chr19:29722716-29722940(-)$1	1	197	212	12.3310
..(((......))).	chr18:34988006-34988216(+)$1	1	117	132	11.0698
(.(((......))))	chr3:55796230-55796453(-)$1	1	62	77	11.0479
(((((......))).	chr1:15828173-15828396(+)$1	1	19	34	10.9915
.((((......))))	chr2:50162801-50163024(+)$1	1	48	63	11.3737
.((((......))))	chr17:25973296-25973520(-)$1	1	11	26	12.2677
(((((......))))	chr12:70406701-70406924(+)$1	1	92	107	10.7865
(((((......))))	chr19:40677278-40677496(-)$1	1	148	163	10.7865
.((((......))))	chr5:8448320-8448536(+)$1	1	24	39	12.3310
(((((......))))	chr2:126701419-126701642(-)$1	1	87	102	10.7865
(((((......))))	chr2:32108325-32108544(+)$1	1	56	71	10.7865
.((((......).))	chr17:75758530-75758757(+)$1	1	195	210	10.4770
.((((......))))	chr9:95767820-95768042(+)$1	1	71	86	12.3310
.((((......))))	chr5:77023085-77023315(+)$1	1	70	85	11.3737
(((((......))))	chr3:142502140-142502353(-)$1	1	45	60	12.0376
.((((......))))	chr5:25203983-25204206(-)$1	1	151	166	11.3737
.((((......))))	chr19:41297528-41297742(-)$1	1	93	108	12.2677
(((((......))))	chr3:121486878-121487104(-)$1	1	177	192	12.0376
(.(((......))).	chr5:50416852-50417072(-)$1	1	130	145	10.8738
..(((......))).	chr4:120831801-120832026(-)$1	1	107	122	10.9699
(.(((......))).	chr7:107503165-107503391(-)$1	1	138	153	10.9923
)((((......))))	chr17:42975560-42975802(-)$1	1	72	87	12.0755
..(((......))).	chr3:152121424-152121643(+)$1	1	21	36	11.2521
.((((......))))	chr6:11912570-11912795(+)$1	1	93	108	12.2321
..(((......))).	chrX:157014750-157014976(+)$1	1	26	41	11.0698
(((((......))))	chr2:121890989-121891210(-)$1	1	61	76	10.0599
(((((......))).	chr2:74416848-74417067(-)$1	1	61	76	10.8683
.((((......))))	chr14:46124265-46124493(-)$1	1	211	226	11.3737
.((((......))))	chr1:40057433-40057653(+)$1	1	102	117	12.0471
.((((......))))	chr6:108336717-108336937(+)$1	1	27	42	11.3737
.((((......))))	chr1:71672662-71672895(-)$1	1	151	166	12.2677
(.(((......))))	chrX:74894133-74894366(+)$1	1	72	87	11.0479
..(((......))).	chr4:126588338-126588570(-)$1	1	209	224	11.2521
.((((......))))	chr15:32850681-32850894(+)$1	1	166	181	11.3737
(.(((......))).	chr10:104675450-104675686(+)$1	1	213	228	10.9543
.((((......))))	chr5:23928532-23928750(-)$1	1	101	116	12.2677
))(((......))))	chr1:84790685-84790897(-)$1	1	179	194	9.9210
(((((......))))	chr1:34226524-34226742(+)$1	1	116	131	10.7865
..(((......))).	chr8:26852109-26852320(-)$1	1	89	104	11.2766
..(((......))).	chrX:72766625-72766858(+)$1	1	63	78	10.7876
(((((......))))	chr6:120332902-120333126(+)$1	1	84	99	10.0599
(((((......))))	chr8:125422433-125422657(-)$1	1	36	51	10.7865
(((((......))))	chr5:104932924-104933150(+)$1	1	185	200	10.7865
(((.(......))))	chr12:4227826-4228046(+)$1	1	178	193	11.1207
(.(((......))).	chr11:102729220-102729440(-)$1	1	196	211	11.0283
.((((......))))	chr15:54902884-54903101(-)$1	1	157	172	11.3737
)((((......))))	chr19:4264274-4264489(-)$1	1	30	45	12.0755
(((((......))))	chr10:34117850-34118077(-)$1	1	177	192	10.0599
(((((......))))	chr9:21147358-21147582(+)$1	1	116	131	10.7865
(((((......))))	chr3:5219235-5219453(-)$1	1	179	194	10.7865
(((((......))))	chr1:183085887-183086113(+)$1	1	34	49	10.7865
(((((......))))	chr19:53692503-53692728(+)$1	1	120	135	10.7865
)((((......))))	chr11:98877314-98877520(-)$1	1	141	156	11.0161
(((((......))))	chr8:70487815-70488035(-)$1	1	194	209	10.0599
.((((......))))	chr3:108514229-108514437(-)$1	1	130	145	12.3310
.((((......))))	chr15:27777020-27777264(-)$1	1	46	61	11.3737
(((.(......).))	chr14:33379886-33380103(+)$1	1	158	173	10.2688

#PSSM
e : 0.24	: : 0.13	! : 0.13	g : 0.09	[ : 0.09	d : 0.07	c : 0.06	# : 0.04	i : 0.03	" : 0.03	f : 0.01	$ : 0.01	a : 0.01	I : 0.01	
d : 0.46	e : 0.19	[ : 0.10	! : 0.07	g : 0.07	c : 0.03	# : 0.03	i : 0.01	
d : 0.45	c : 0.27	e : 0.19	g : 0.06	i : 0.01	
d : 0.43	c : 0.27	e : 0.18	g : 0.06	[ : 0.03	i : 0.01	
d : 0.43	c : 0.25	e : 0.18	g : 0.06	a : 0.04	i : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
d : 0.43	c : 0.25	e : 0.18	g : 0.06	a : 0.04	i : 0.01	
d : 0.45	c : 0.25	e : 0.18	g : 0.06	] : 0.03	i : 0.01	
d : 0.45	c : 0.27	e : 0.19	g : 0.06	i : 0.01	
d : 0.48	e : 0.19	] : 0.10	4 : 0.06	g : 0.06	2 : 0.04	i : 0.01	c : 0.01	H : 0.01	

#score	743.0131414794025
#seq	66
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_CDS_m1_run2.txt

#BEAR
c$$$$$eeeee[ccc[ammmma]ccc22eeeee22ccc4	chr12:8712702-8712926(+)$1	224	48	87	11.6224
####ddddgggggggrrrrrrrrrggggggg]dddd333	chr2:69782275-69782509(+)$1	234	5	44	11.3659
""ccc[bb!!bb!!ddddmmmmdddd22bb]bbccc]ee	chr4:155383894-155384100(+)$1	206	70	109	11.8678
''''''ffffff[ddddoooooodddd22ffffff4444	chr11:90480510-90480731(-)$1	221	87	126	11.9257
"""ggggggg[a[a!!bbnnnnnbb22a]a]ggggggg]	chr1:155325979-155326193(-)$1	214	113	152	12.3482
g[aa"""ccc[cccrrrrrrrrrccc22ccc4444a]a]	chr5:110861830-110862049(-)$1	219	106	145	13.2558
eeedddd[dddd!!cccooooooccc4444dddd22ddd	chr8:35153764-35153980(-)$1	216	58	97	14.2596
###ggggggg!!eeeeeooooooeeeee22ggggggg22	chr5:77423802-77424032(+)$1	230	184	223	14.3777
dd[bbccc[dddd[cccooooooccc]dddd22ccc777	chr16:45825015-45825229(-)$1	214	33	72	13.6811
a[a[bbccc[ccc!!cccmmmmccc333ccc]ccc]bb]	chr3:94837517-94837740(-)$1	223	61	100	13.2893
f[ccchhhhhhhh[cccooooooccc22hhhhhhhh>>>	chr1:58471348-58471573(-)$1	225	20	59	14.8503
""ddddbbffffffcccooooooccc22ffffff66666	chr11:105207977-105208206(+)$1	229	77	116	13.6941
!!gggggggbb"""ccclllccc22bb]ggggggg4444	chr11:85048100-85048317(-)$1	217	13	52	12.2515
!ccc[bb[a[dddd[aooooooa]dddd]a]bb]ccc22	chr1:60400145-60400365(+)$1	220	61	100	13.1890
b"""dddd[dddd[ccclllccc]dddd333dddd333b	chr4:155235746-155235955(+)$1	209	135	174	10.9400
cc"""ccc[eeeee!!bbnnnnnbb333eeeee]ccc22	chr2:118248071-118248278(+)$1	207	132	171	11.5171
iieeeee[ccc[eeeeeooooooeeeee]ccceeeee66	chr7:13511857-13512077(+)$1	220	162	201	12.1353
ahhhhhhhhccc[bboooooobbccc333hhhhhhhh33	chr7:141973938-141974157(+)$1	219	51	90	11.9338
e[ffffff!!bb[ddddoooooodddd]bb22ffffff3	chr10:24630511-24630718(+)$1	207	20	59	13.6142
a[dddd####a[ffffffooooooffffffadddd]a33	chr15:73173497-73173717(-)$1	220	64	103	11.9910
eeee"""eeeee!!cccooooooccc]eeeee22eeeee	chr12:52901821-52902042(-)$1	221	122	161	14.5345
eeeeedddd[bb!!cccnnnnnccc333bb22dddd]ee	chr10:127000723-127000947(-)$1	224	2	41	11.8466
$$$eeeeecccbb"""bboooooobb333bb]ccc]eee	chr19:44151652-44151858(-)$1	206	85	124	12.9553
:iiiiiiiii[bbddddoooooodddd4444bb]iiiii	chr14:87490822-87491041(-)$1	219	35	74	13.2759
ffff"""bb$$$$$cccnnnnnccc333bb333ffffff	chr2:158632581-158632826(+)$1	245	94	133	11.5623
[ggggggg!!bb[acccooooooccc4444a]bb22ggg	chr14:122025037-122025250(-)$1	213	21	60	16.2954
cc[a[a[ggggggg[cccmmmmcccggggggg]aa]ccc	chr2:61602819-61603028(+)$1	209	87	126	12.0585
:::ccc!!eeeeeddddoooooodddd22eeeee333cc	chr1:164635015-164635239(-)$1	224	162	201	11.7394
$$$dddd[ccc"""cccooooooccc4444ccc22dddd	chr1:52246192-52246454(-)$1	262	110	149	15.8790
ff&&&&&&&ccc!!cccooooooccc22ccc333fffff	chr2:146852960-146853182(+)$1	222	177	216	13.1354
iiiiiiiii[ccc[aooooooa]ccc]iiiiiiiii:::	chr11:85891265-85891471(-)$1	206	148	187	12.1127
cc]accc"""bb!!cccooooooccc22bb333ccc:::	chr11:95866790-95867011(-)$1	221	19	58	15.0884
gg####ccc[gggggggoooooogggggggcccgggggg	chr7:125292302-125292516(-)$1	214	130	169	14.7945
ggggg!!a!!bb!!cccooooooccc22bb]a22ggggg	chrX:103070778-103070990(-)$1	212	29	68	17.6529
ccccc!!ccc!!ddddoooooodddd22ccc]ccc]ccc	chr3:121160025-121160247(+)$1	222	72	111	14.9843
##eeeeeffffff[cccoooooocccffffff8888888	chr13:53449448-53449671(-)$1	223	11	50	12.4842
::ggggggg[eeeee[aooooooaeeeeegggggggeee	chr17:46703011-46703239(-)$1	228	129	168	11.7853
$$$$hhhhhhhh!!cccooooooccc22hhhhhhhha22	chr10:80993978-80994191(-)$1	213	16	55	15.5409
$$$a[ggggggg!!cccooooooccc22ggggggg]a22	chr9:22164771-22164987(-)$1	216	126	165	18.5676
"""a[ggggggg[bboooooobbggggggg]abb]ccc]	chr5:104888865-104889101(+)$1	236	31	70	12.4453
"ccc[ccc[bb!!ddddllldddd4444bb]cccccc33	chr5:122022638-122022857(-)$1	219	120	159	12.5605
ccdddd####ddddcccooooooccc22dddd22dddd]	chr10:74707792-74708002(+)$1	210	113	152	14.9088
"""eeeeeccc!!ddddlllddddccc22eeeee333cc	chr8:98276407-98276625(-)$1	218	112	151	12.1127
+++++ffffff"""cccooooooccc333ffffffbbgg	chr9:70291370-70291583(-)$1	213	113	152	13.1155
:ccc[ccc!!ccc[a[cccmmmmccc]a]ccc333ccc]	chr11:61961039-61961250(+)$1	211	66	105	12.3441
hhhhhhh####bb[cccooooooccc]bb333hhhhhhh	chr14:87437183-87437412(-)$1	229	148	187	13.0463
feeeee[cccbb!!cccooooooccc22bb333ccceee	chr2:29862063-29862271(+)$1	208	129	168	16.5812
ddffffff"""a!!ccclllccc22a333ffffff4444	chr10:127126217-127126425(+)$1	208	65	104	12.3231
eeeeedddd!!bb[cccoooooocccbb22dddd00000	chr3:85408316-85408522(+)$1	206	44	83	11.9661
:ccc[iiiiiiiii[cccmmmmccc]iiiiiiiii]ccc	chr5:108002764-108002982(-)$1	218	161	200	11.3148
eee$$$$$eeeee!!bboooooobb22eeeee333eeee	chr19:41313078-41313297(-)$1	219	7	46	12.1855
hhhh!!ccc!!gggggggooooooggggggg333ccc22	chr10:12459180-12459428(-)$1	248	140	179	13.7496
iiii!!bb!!ddddddddmmmmdddd22dddd22bb333	chr15:11916118-11916355(-)$1	237	60	99	11.2593
=========ccc[ddddoooooodddd]ccc22======	chr10:39526544-39526768(+)$1	224	59	98	15.4069

#otherMatches

#Seq PSSM
AAAAAGUUUUGGGAACCUGAUGAUUCAACAAAAGAUGGA	chr12:8712702-8712926(+)$1	224	48	87	11.6224
GAUUCUAAGAUGUGUAAUAAUAUAAUACAUUGUUAGUGA	chr2:69782275-69782509(+)$1	234	5	44	11.3659
ACCACCUGGAGCCCGAGGAGAUCCUCAAGUACAGUGAGU	chr4:155383894-155384100(+)$1	206	70	109	11.8678
UAUAUUUUAUCCUAGGGAUCCUGCCUUUCGGGUGAUUAC	chr11:90480510-90480731(-)$1	221	87	126	11.9257
CUAUGGCUCUCCUGGACCUACUUGGGACCGAGGAGCCAA	chr1:155325979-155326193(-)$1	214	113	152	12.3482
GUCCCUUUGCAGCCCUCCAAACAGGUGAGCAUUCUGUGC	chr5:110861830-110862049(-)$1	219	106	145	13.2558
gcguguguguCUUUCUGUCCUUUCAGCCCCAGACUCUAC	chr8:35153764-35153980(-)$1	216	58	97	14.2596
CUUGGAUUUCAUGCAGACAUUUUUCUGUUAGAAAUUUCA	chr5:77423802-77424032(+)$1	230	184	223	14.3777
UCCUCGUGUGGCUCGGAAGAUGCUCCUGGCCUCCACCUC	chr16:45825015-45825229(-)$1	214	33	72	13.6811
UGACGCCCUACUGAAGAUGACCAUCAACCAGCAGGAGUU	chr3:94837517-94837740(-)$1	223	61	100	13.2893
GACUGAUUAUGUGUACUUUCUCCAGUUUUGCAUAGUAAU	chr1:58471348-58471573(-)$1	225	20	59	14.8503
CACAGCCCCUCAGCCCACUUCACUGGCCGCUGGGAUGAU	chr11:105207977-105208206(+)$1	229	77	116	13.6941
CCGUGGAGCUCGAGUGGAUCCCGGAGACGCUCUACAACA	chr11:85048100-85048317(-)$1	217	13	52	12.2515
CGCGCGGGCGGGCGAGAGGAAGCAUGCUGGACUUCGCCA	chr1:60400145-60400365(+)$1	220	61	100	13.1890
UCACAACAAGAUUUGGCUCUGCCUGGUUCAGUGUUCCUG	chr4:155235746-155235955(+)$1	209	135	174	10.9400
UGCCAGCUGACUUCCAAGACUUCCUGAAGAAGUGAGUGA	chr2:118248071-118248278(+)$1	207	132	171	11.5171
CUUUGGAACAACUAUACCUUCCUGUGUGCUUGUCUAAUC	chr7:13511857-13512077(+)$1	220	162	201	12.1353
UAGGAUGCAGGUACAGUUCAGUGACCUCUUGUGUCUUUG	chr7:141973938-141974157(+)$1	219	51	90	11.9338
CCCGAUAGAUUGGCGUGGCAUUUUAUGACAUGCUGUUGA	chr10:24630511-24630718(+)$1	207	20	59	13.6142
AGUAUUAAAGGUCUUUCAUUAUUUUGAAAGCAGUAGUGA	chr15:73173497-73173717(-)$1	220	64	103	11.9910
UAUUAAACUGGGCCUCUGCGUUUGGAACUCAGGAAAUGG	chr12:52901821-52902042(-)$1	221	122	161	14.5345
AGGGGAGCCAGUCAUGCCCUUAGCACCUACCAGGCUGCC	chr10:127000723-127000947(-)$1	224	2	41	11.8466
GAACAUCCUCUGACAUGUGUGGUAACUCCUCAAGAUGGG	chr19:44151652-44151858(-)$1	206	85	124	12.9553
CAUGAGGAAAUAUUAACUUGUGUGUUAUUUUAUUUUUCU	chr14:87490822-87491041(-)$1	219	35	74	13.2759
CUGGACAGCGGAAGGACGAGUGGUCGGAGUGACCCAGCC	chr2:158632581-158632826(+)$1	245	94	133	11.5623
UCCCAUUUCCCCCCCCAGCAUUAUGGUCCAGAGGUUAAG	chr14:122025037-122025250(-)$1	213	21	60	16.2954
CCCGAGAUGGUUGUUGGUUGGUAUCACAGUCACCCUGGC	chr2:61602819-61603028(+)$1	209	87	126	12.0585
CAUGAGCAGUUUAUGCCUAUACCGGCAGAUAAACGACCU	chr1:164635015-164635239(-)$1	224	162	201	11.7394
AACGUCAUGGGCAUGAUGUGUUGGUCUCCUCCUCUUGAC	chr1:52246192-52246454(-)$1	262	110	149	15.8790
UAUAAUGAAUAUAACCCAggucagggguguagcuuaauc	chr2:146852960-146853182(+)$1	222	177	216	13.1354
UGUGGUUUUGUCUGUGCCCAAGGAGAGGAAGUCACAUUU	chr11:85891265-85891471(-)$1	206	148	187	12.1127
GCUCGGCCUUGCCUGGAACCGUGUCCUUGCCCCGCCACC	chr11:95866790-95867011(-)$1	221	19	58	15.0884
AUGAACUAGAUAGUCUGAUCGAGCAGACUACUGAUGGAG	chr7:125292302-125292516(-)$1	214	130	169	14.7945
UCCAUAGCAGGAGGUUCCAUUGAGAAAGUCAGGAGUGGA	chrX:103070778-103070990(-)$1	212	29	68	17.6529
CAACAAAGUUGCUUCCCAGAAAGGAAUGAGCGUGUAUGG	chr3:121160025-121160247(+)$1	222	72	111	14.9843
CUUCCUUGCAGGGACAGUGCGGCCUGCUUUGCUAUCCAG	chr13:53449448-53449671(-)$1	223	11	50	12.4842
AGUGUUCACUCAUGGAGAGAUGCCCCAUGGUGGACAGGC	chr17:46703011-46703239(-)$1	228	129	168	11.7853
GAGGUCAGAGCGCAGGAAGUGGAUCCAUUGCUUUGAGAA	chr10:80993978-80994191(-)$1	213	16	55	15.5409
AAAUGCAGGUAUGCUCUGGCAUAGGAAGAUAUUUGGGAC	chr9:22164771-22164987(-)$1	216	126	165	18.5676
AAGCGUGGAGCCGCGACAACCCGGGCUUUGAGGCAGAGG	chr5:104888865-104889101(+)$1	236	31	70	12.4453
AGUCUCGGGUGGUGGGGAACCCCUUCGACAGCCGGACGG	chr5:122022638-122022857(-)$1	219	120	159	12.5605
CCGGCUAAACCAGAGCAAAAAACUGCCCUCUGUAAGUCA	chr10:74707792-74708002(+)$1	210	113	152	14.9088
CUUACAUGGCAUUGGGUCUGGCCCUGCGAUAUGUUCUUG	chr8:98276407-98276625(-)$1	218	112	151	12.1127
CUCAAGUGGAUUACGUGAUUCCGCAUCCUGUCCAUGCUU	chr9:70291370-70291583(-)$1	213	113	152	13.1155
CCAGAAGCCCCCUGAGUGGAAUCCCAGUGAGGACUGCUC	chr11:61961039-61961250(+)$1	211	66	105	12.3441
AGGUAACUUAUCUCUGGACAUCACCGUAGCAUGUUACUU	chr14:87437183-87437412(-)$1	229	148	187	13.0463
AAGAAGUGGUGACCAGCUAUCCUGCUUAUCCUUGCUCUU	chr2:29862063-29862271(+)$1	208	129	168	16.5812
UCGGGUAAAUAGUUCCAAGUUGGUCCGAGUUACCCAGGU	chr10:127126217-127126425(+)$1	208	65	104	12.3231
ACUGUAUCUAUCUAGGGAAGAAACCCAGUCAGGUGACCA	chr3:85408316-85408522(+)$1	206	44	83	11.9661
AUGGCCUCUGUCAGUGUUGUAAGGCCUUGAUAGAGUUCA	chr5:108002764-108002982(-)$1	218	161	200	11.3148
AGAUGUGUUCAGACCGUCAAGUCACCCUCUGAUCUUCUC	chr19:41313078-41313297(-)$1	219	7	46	12.1855
CAGCUACCAGAUAGCGCUAGAGGAAGUGCUGACGUGGCU	chr10:12459180-12459428(-)$1	248	140	179	13.7496
GUUCGGGACUUCAAAGGAAAAAUUCUAAUUGAUAUUAGA	chr15:11916118-11916355(-)$1	237	60	99	11.2593
AUGUUUUGUUAUAAAAAGUUAUGUUUUAAUGAAGCAGAA	chr10:39526544-39526768(+)$1	224	59	98	15.4069

#DB
(.....(((((.(((.(....).)))..)))))..))).	chr12:8712702-8712926(+)$1	1	48	87	11.6224
....(((((((((((.........))))))).))))...	chr2:69782275-69782509(+)$1	1	5	44	11.3659
..(((.((..((..((((....))))..)).))))).))	chr4:155383894-155384100(+)$1	1	70	109	11.8678
......((((((.((((......))))..))))))....	chr11:90480510-90480731(-)$1	1	87	126	11.9257
...(((((((.(.(..((.....))..).).))))))).	chr1:155325979-155326193(-)$1	1	113	152	12.3482
(.((...(((.(((.........)))..)))....).).	chr5:110861830-110862049(-)$1	1	106	145	13.2558
)))((((.((((..(((......)))....))))..)))	chr8:35153764-35153980(-)$1	1	58	97	14.2596
...(((((((..(((((......)))))..)))))))..	chr5:77423802-77424032(+)$1	1	184	223	14.3777
((.(((((.((((.(((......))).))))..)))...	chr16:45825015-45825229(-)$1	1	33	72	13.6811
(.(.(((((.(((..(((....)))...))).))).)).	chr3:94837517-94837740(-)$1	1	61	100	13.2893
(.(((((((((((.(((......)))..))))))))...	chr1:58471348-58471573(-)$1	1	20	59	14.8503
..(((((((((((((((......)))..)))))).....	chr11:105207977-105208206(+)$1	1	77	116	13.6941
..(((((((((...(((...)))..)).)))))))....	chr11:85048100-85048317(-)$1	1	13	52	12.2515
.(((.((.(.((((.(......).)))).).)).)))..	chr1:60400145-60400365(+)$1	1	61	100	13.1890
(...((((.((((.(((...))).))))...))))...)	chr4:155235746-155235955(+)$1	1	135	174	10.9400
((...(((.(((((..((.....))...))))).)))..	chr2:118248071-118248278(+)$1	1	132	171	11.5171
(((((((.(((.(((((......))))).))))))))..	chr7:13511857-13512077(+)$1	1	162	201	12.1353
((((((((((((.((......)))))...))))))))..	chr7:141973938-141974157(+)$1	1	51	90	11.9338
(.((((((..((.((((......)))).))..)))))).	chr10:24630511-24630718(+)$1	1	20	59	13.6142
(.((((....(.((((((......))))))))))).)..	chr15:73173497-73173717(-)$1	1	64	103	11.9910
((((...(((((..(((......))).)))))..)))))	chr12:52901821-52902042(-)$1	1	122	161	14.5345
(((((((((.((..(((.....)))...))..)))).))	chr10:127000723-127000947(-)$1	1	2	41	11.8466
...((((((((((...((......))...)).))).)))	chr19:44151652-44151858(-)$1	1	85	124	12.9553
.(((((((((.((((((......))))....)).)))))	chr14:87490822-87491041(-)$1	1	35	74	13.2759
((((...((.....(((.....)))...))...))))))	chr2:158632581-158632826(+)$1	1	94	133	11.5623
.(((((((..((.((((......)))....).))..)))	chr14:122025037-122025250(-)$1	1	21	60	16.2954
((.(.(.(((((((.(((....)))))))))).)).)))	chr2:61602819-61603028(+)$1	1	87	126	12.0585
...(((..(((((((((......))))..)))))...))	chr1:164635015-164635239(-)$1	1	162	201	11.7394
...((((.(((...(((......)))....)))..))))	chr1:52246192-52246454(-)$1	1	110	149	15.8790
((.......(((..(((......)))..)))...)))))	chr2:146852960-146853182(+)$1	1	177	216	13.1354
(((((((((.(((.(......).))).)))))))))...	chr11:85891265-85891471(-)$1	1	148	187	12.1127
)).)(((...((..(((......)))..))...)))...	chr11:95866790-95867011(-)$1	1	19	58	15.0884
((....(((.(((((((......))))))))))))))))	chr7:125292302-125292516(-)$1	1	130	169	14.7945
(((((..(..((..(((......)))..)).)..)))))	chrX:103070778-103070990(-)$1	1	29	68	17.6529
(((((..(((..((((......))))..))).))).)))	chr3:121160025-121160247(+)$1	1	72	111	14.9843
..(((((((((((.(((......))))))))).......	chr13:53449448-53449671(-)$1	1	11	50	12.4842
..(((((((.(((((.(......)))))))))))))(((	chr17:46703011-46703239(-)$1	1	129	168	11.7853
....((((((((..(((......)))..)))))))))..	chr10:80993978-80994191(-)$1	1	16	55	15.5409
...(.(((((((..(((......)))..))))))).)..	chr9:22164771-22164987(-)$1	1	126	165	18.5676
...(.(((((((.((......))))))))).))).))).	chr5:104888865-104889101(+)$1	1	31	70	12.4453
.(((.(((.((..((((...))))....)).))))))..	chr5:122022638-122022857(-)$1	1	120	159	12.5605
((((((....(((((((......)))..))))..)))).	chr10:74707792-74708002(+)$1	1	113	152	14.9088
...((((((((..((((...)))))))..)))))...))	chr8:98276407-98276625(-)$1	1	112	151	12.1127
.....((((((...(((......)))...))))))))))	chr9:70291370-70291583(-)$1	1	113	152	13.1155
.(((.(((..(((.(.(((....))).).)))...))).	chr11:61961039-61961250(+)$1	1	66	105	12.3441
(((((((....((.(((......))).))...)))))))	chr14:87437183-87437412(-)$1	1	148	187	13.0463
)(((((.(((((..(((......)))..))...))))))	chr2:29862063-29862271(+)$1	1	129	168	16.5812
((((((((...(..(((...)))..)...))))))....	chr10:127126217-127126425(+)$1	1	65	104	12.3231
(((((((((..((.(((......)))))..)))).....	chr3:85408316-85408522(+)$1	1	44	83	11.9661
.(((.(((((((((.(((....))).))))))))).)))	chr5:108002764-108002982(-)$1	1	161	200	11.3148
(((.....(((((..((......))..)))))...))))	chr19:41313078-41313297(-)$1	1	7	46	12.1855
((((..(((..(((((((......)))))))...)))..	chr10:12459180-12459428(-)$1	1	140	179	13.7496
((((..((..((((((((....))))..))))..))...	chr15:11916118-11916355(-)$1	1	60	99	11.2593
((((((((((((.((((......)))).)))..))))))	chr10:39526544-39526768(+)$1	1	59	98	15.4069

#PSSM
c : 0.11	" : 0.11	e : 0.11	: : 0.09	f : 0.07	$ : 0.07	# : 0.05	g : 0.05	a : 0.05	i : 0.05	d : 0.03	! : 0.03	h : 0.03	' : 0.01	b : 0.01	[ : 0.01	+ : 0.01	= : 0.01	
c : 0.16	" : 0.11	e : 0.11	$ : 0.09	[ : 0.09	i : 0.07	# : 0.05	h : 0.05	g : 0.05	d : 0.03	f : 0.03	: : 0.03	' : 0.01	! : 0.01	+ : 0.01	= : 0.01	
e : 0.14	c : 0.12	$ : 0.09	" : 0.09	g : 0.07	# : 0.05	d : 0.05	h : 0.05	f : 0.05	i : 0.05	a : 0.03	[ : 0.03	' : 0.01	: : 0.01	& : 0.01	] : 0.01	+ : 0.01	= : 0.01	
c : 0.14	e : 0.14	g : 0.11	a : 0.09	d : 0.09	$ : 0.05	h : 0.05	f : 0.05	i : 0.05	# : 0.03	" : 0.03	' : 0.01	b : 0.01	[ : 0.01	& : 0.01	+ : 0.01	= : 0.01	
d : 0.12	[ : 0.12	e : 0.12	g : 0.11	c : 0.09	" : 0.07	h : 0.05	$ : 0.03	b : 0.03	f : 0.03	i : 0.03	! : 0.03	' : 0.01	& : 0.01	# : 0.01	+ : 0.01	= : 0.01	
d : 0.16	g : 0.12	c : 0.11	e : 0.09	h : 0.07	! : 0.07	" : 0.05	f : 0.05	i : 0.05	$ : 0.03	b : 0.03	[ : 0.01	' : 0.01	a : 0.01	& : 0.01	# : 0.01	= : 0.01	
c : 0.14	g : 0.12	d : 0.11	e : 0.09	b : 0.07	f : 0.07	h : 0.07	" : 0.05	i : 0.05	! : 0.05	# : 0.03	[ : 0.03	& : 0.01	$ : 0.01	= : 0.01	
c : 0.18	g : 0.14	f : 0.09	e : 0.07	d : 0.07	b : 0.07	[ : 0.07	h : 0.05	# : 0.05	i : 0.05	! : 0.01	& : 0.01	" : 0.01	a : 0.01	$ : 0.01	= : 0.01	
c : 0.18	g : 0.14	! : 0.11	e : 0.07	f : 0.07	[ : 0.07	d : 0.05	h : 0.05	# : 0.05	i : 0.05	" : 0.03	a : 0.01	b : 0.01	& : 0.01	= : 0.01	
c : 0.18	! : 0.14	g : 0.11	[ : 0.11	e : 0.09	f : 0.07	d : 0.05	# : 0.05	h : 0.03	b : 0.03	i : 0.03	" : 0.03	$ : 0.01	
c : 0.18	b : 0.16	e : 0.11	d : 0.11	g : 0.09	f : 0.07	! : 0.07	[ : 0.05	h : 0.03	a : 0.01	$ : 0.01	# : 0.01	" : 0.01	i : 0.01	
b : 0.20	c : 0.12	g : 0.11	d : 0.11	e : 0.09	! : 0.07	[ : 0.05	f : 0.05	" : 0.05	a : 0.03	h : 0.03	$ : 0.01	i : 0.01	
! : 0.24	[ : 0.12	e : 0.11	d : 0.11	c : 0.09	g : 0.07	b : 0.07	f : 0.05	" : 0.05	h : 0.01	$ : 0.01	i : 0.01	
! : 0.24	d : 0.20	[ : 0.14	g : 0.07	e : 0.07	" : 0.07	c : 0.03	a : 0.03	f : 0.03	b : 0.03	$ : 0.01	i : 0.01	
c : 0.44	d : 0.18	! : 0.07	g : 0.05	e : 0.05	[ : 0.05	b : 0.03	a : 0.03	r : 0.01	f : 0.01	" : 0.01	
c : 0.48	d : 0.18	[ : 0.05	o : 0.05	r : 0.03	! : 0.03	e : 0.03	g : 0.03	a : 0.01	f : 0.01	" : 0.01	b : 0.01	
c : 0.49	d : 0.16	o : 0.09	b : 0.07	a : 0.03	r : 0.03	e : 0.03	g : 0.03	f : 0.01	
o : 0.61	l : 0.09	c : 0.07	b : 0.05	r : 0.03	d : 0.03	n : 0.03	m : 0.01	f : 0.01	g : 0.01	
o : 0.66	m : 0.11	l : 0.09	n : 0.07	r : 0.03	c : 0.01	
o : 0.66	m : 0.12	l : 0.09	n : 0.07	r : 0.03	
o : 0.66	m : 0.12	n : 0.07	c : 0.05	r : 0.03	d : 0.03	
o : 0.61	m : 0.11	n : 0.07	c : 0.05	a : 0.03	r : 0.03	b : 0.03	d : 0.03	
o : 0.57	c : 0.14	d : 0.09	] : 0.03	r : 0.03	n : 0.03	b : 0.03	a : 0.01	m : 0.01	
c : 0.51	d : 0.18	b : 0.05	o : 0.05	e : 0.03	2 : 0.03	] : 0.03	g : 0.03	r : 0.01	a : 0.01	
c : 0.53	d : 0.18	g : 0.07	b : 0.07	e : 0.05	2 : 0.03	f : 0.01	4 : 0.01	
c : 0.44	d : 0.18	g : 0.09	3 : 0.07	e : 0.05	2 : 0.03	b : 0.03	f : 0.01	4 : 0.01	a : 0.01	] : 0.01	
2 : 0.29	3 : 0.14	d : 0.12	g : 0.09	] : 0.09	4 : 0.07	e : 0.05	b : 0.03	f : 0.03	c : 0.01	i : 0.01	
2 : 0.31	3 : 0.14	g : 0.09	4 : 0.09	e : 0.09	d : 0.05	] : 0.05	a : 0.03	f : 0.03	i : 0.03	b : 0.03	
b : 0.16	g : 0.12	e : 0.09	2 : 0.09	c : 0.09	3 : 0.09	] : 0.07	4 : 0.07	d : 0.05	f : 0.05	h : 0.03	i : 0.03	
b : 0.16	g : 0.14	c : 0.12	e : 0.11	f : 0.11	4 : 0.07	d : 0.05	h : 0.05	a : 0.03	2 : 0.03	3 : 0.03	i : 0.03	
c : 0.16	g : 0.12	e : 0.11	] : 0.11	f : 0.09	d : 0.09	3 : 0.09	h : 0.05	2 : 0.03	a : 0.03	i : 0.03	b : 0.01	4 : 0.01	
e : 0.11	g : 0.11	d : 0.11	3 : 0.11	] : 0.09	f : 0.09	c : 0.09	2 : 0.07	b : 0.05	h : 0.05	i : 0.03	a : 0.03	4 : 0.01	
3 : 0.12	d : 0.11	2 : 0.11	c : 0.11	e : 0.09	b : 0.09	f : 0.09	g : 0.09	h : 0.07	i : 0.03	4 : 0.01	] : 0.01	8 : 0.01	
c : 0.14	2 : 0.11	d : 0.11	f : 0.11	g : 0.11	h : 0.07	3 : 0.07	] : 0.05	e : 0.05	b : 0.03	i : 0.03	4 : 0.01	a : 0.01	8 : 0.01	= : 0.01	
c : 0.20	g : 0.12	f : 0.11	d : 0.09	2 : 0.07	h : 0.07	3 : 0.07	i : 0.05	e : 0.03	4 : 0.01	6 : 0.01	a : 0.01	8 : 0.01	] : 0.01	0 : 0.01	b : 0.01	= : 0.01	
c : 0.20	] : 0.12	g : 0.09	d : 0.07	h : 0.07	4 : 0.05	3 : 0.05	e : 0.05	f : 0.05	2 : 0.03	i : 0.03	b : 0.03	a : 0.01	6 : 0.01	8 : 0.01	0 : 0.01	= : 0.01	
c : 0.18	e : 0.11	3 : 0.09	g : 0.09	] : 0.05	4 : 0.05	d : 0.05	f : 0.05	a : 0.05	b : 0.03	h : 0.03	: : 0.03	7 : 0.01	> : 0.01	6 : 0.01	i : 0.01	8 : 0.01	0 : 0.01	= : 0.01	
c : 0.14	e : 0.12	3 : 0.11	2 : 0.11	g : 0.09	4 : 0.05	d : 0.05	f : 0.05	6 : 0.03	: : 0.03	a : 0.01	7 : 0.01	b : 0.01	> : 0.01	i : 0.01	8 : 0.01	h : 0.01	0 : 0.01	= : 0.01	
e : 0.12	3 : 0.11	] : 0.11	2 : 0.11	c : 0.09	4 : 0.07	g : 0.07	d : 0.03	6 : 0.03	f : 0.03	: : 0.03	7 : 0.01	> : 0.01	b : 0.01	i : 0.01	8 : 0.01	h : 0.01	0 : 0.01	= : 0.01	

#score	715.7254188075126
#seq	54
#width	39
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_transcript_m2_run1.txt

#BEAR
iiiii!!eeeee!!cccooooooccceeeee]iiiiii	chr2:155214089-155214332(+)$1	243	4	42	16.1871
ffffff!!dddd[ccc[ccclllccc333ccc333ddd	chr5:115252491-115252726(+)$1	235	48	86	12.6263
eccc"""eeeee####cccmmmmccc22eeeeeccc]e	chr1:153210533-153210769(+)$1	236	178	216	12.1719
""bbdddd[bb!!ddddoooooodddd333bb]dddd]	chr3:141965381-141965616(-)$1	235	167	205	13.6634
####ffffff[ccccccammmma]ccc]ccc]ffffff	chr15:76910055-76910291(-)$1	236	24	62	11.6261
gggg[ccc[ddddrrrrrrrrrdddd333ccc]ggggg	chr19:43574327-43574562(-)$1	235	41	79	12.0240
ee$$$$$===========nnnnn===========22ee	chr5:32320229-32320464(+)$1	235	121	159	12.6402
bb[ccc[ccc[a!!cccnnnnnccc22a]ccc22ccc]	chr8:46911742-46911988(+)$1	246	44	82	13.1603
b[iiiiiiiii[ccc[aooooooaccc>>>>>>>>>>>	chr17:33884446-33884681(-)$1	235	53	91	13.6030
========!!eeeee[cccmmmmccc]eeeee22====	chr16:64857934-64858194(+)$1	260	93	131	12.7560
gggggffffff[eeeeeooooooeeeee333ffffff0	chr9:70625984-70626219(+)$1	235	52	90	12.8648
==####dddd!!ddddoooooodddd22dddd333===	chr17:85463643-85463882(-)$1	239	140	178	15.7431
"ggggggg"""eeeee!!aooooooa22eeeee333gg	chr12:73090945-73091181(+)$1	236	93	131	14.3562
========"""a[ddddoooooodddda22========	chr19:5099357-5099592(-)$1	235	7	45	17.1728
""iiiiiiiii"""ddddmmmmdddd22iiiiiiiii3	chr4:107904863-107905105(-)$1	242	198	236	14.9736
gggg"""eeeee[ddddooooooddddeeeee4444gg	chr9:96233096-96233334(-)$1	238	72	110	15.4698
iiii!!dddd####cccooooooccc22dddd]iiiii	chr4:104704712-104704996(-)$1	284	178	216	17.3645
ddd==========!!cccnnnnnccc]==========:	chr18:34505052-34505287(-)$1	235	169	207	13.9305
ccc"""ccc[ccc[cccooooooccc]ccc]ccc4444	chr1:166367534-166367783(-)$1	249	205	243	17.0184
ciiiiiiiii[a[cccpppppppccc]a333iiiiiii	chr18:35750845-35751081(+)$1	236	135	173	11.8494
dddd"""bb[gggggggoooooogggggggbb22dddd	chr4:8534154-8534411(+)$1	257	168	206	12.7647
gg####ccc"""eeeeeooooooeeeeeccc333gggg	chr11:29642544-29642783(+)$1	239	57	95	15.5341
fff!!==========ssssssssss==========333	chr2:134420523-134420770(-)$1	247	180	218	12.0632
$$$ffffff!!cccrrrrrrrrrccc22ffffff333b	chr6:125076626-125076862(+)$1	236	160	198	11.7452
&ggggggg!!ccc[ccclllccc]cccggggggg22ee	chr1:99717957-99718198(-)$1	241	54	92	11.9484
ggggg[dddd####ddddllldddd333dddd22gggg	chr10:82203496-82203737(+)$1	241	10	48	13.3320
eeee[ccc[bb[a[cccooooooccc]a]bbccc]eee	chr1:43180304-43180550(-)$1	246	164	202	14.9862
gggggg####eeeeeooooooeeeee22gggggggccc	chr8:98238288-98238548(+)$1	260	172	210	13.0098
a[ccc[eeeee[a[cccmmmmccc]a]eeeee333ccc	chr8:23678766-23679001(+)$1	235	45	83	12.3689
###ffffff"""a!!ddddllldddd22a]ffffff55	chr10:42254586-42254830(+)$1	244	195	233	11.4089
iiiggggggg####ddddmmmmdddd]ggggggg22ii	chr2:120334730-120334965(-)$1	235	136	174	13.6160
:ccc"""bb[gggggggooooooggggggg]bb22ccc	chr13:94204139-94204375(-)$1	236	158	196	13.1993
ddd"""ccc[ccc[cccooooooccc]ccc]ccc4444	chr11:94887931-94888172(-)$1	241	188	226	16.5611
ccc[ffffff"""eeeeeooooooeeeeeffffff]cc	chr4:82870373-82870608(-)$1	235	123	161	12.7748
eeeee[ccc[cccddddoooooodddd22ccc]cccee	chr8:127942175-127942418(-)$1	243	35	73	15.0026
eeeee[cccdddd[cccooooooccc22dddd]ccc]e	chr1:60389515-60389763(+)$1	248	16	54	15.2483
!ccc[a!!ffffff!!cccmmmmccc22ffffff333a	chr11:50014073-50014323(-)$1	250	168	206	12.2962
ffffff!!eeeeeddddoooooodddd]eeeee]ffff	chr8:46912753-46912988(+)$1	235	50	88	13.4619
[ccc!!==========bboooooobb22==========	chr1:34933815-34934074(+)$1	259	86	124	16.0014
ddddccc[bb####cccooooooccc4444bb]ccc::	chr11:87897636-87897884(+)$1	248	52	90	13.6311
fff!!==========[aooooooa]==========666	chr13:94615440-94615675(+)$1	235	140	178	15.3902
ddd[bb!!gggggggcccnnnnnccc]ggggggg333b	chr6:39542613-39542851(+)$1	238	131	169	12.8456
g[eeeee[a"""a[cccrrrrrrrrrccca]a]eeeee	chr8:34893345-34893581(-)$1	236	81	119	11.4747
c:iiiiiiiii!!ddddoooooodddd22iiiiiiiii	chr2:121373570-121373818(-)$1	248	23	61	16.0600
c[ccc[a[ccc"""cccmmmmccc]ccc]a]ccc]ccc	chrX:71674370-71674605(-)$1	235	37	75	12.8646
==========####cccooooooccc22==========	chr11:62215867-62216106(-)$1	239	197	235	19.4652
c]cccccc[bb!!ddddoooooodddd]bb]ccchhhh	chr14:55565114-55565368(-)$1	254	117	155	13.5100
"""bb[ggggggg[ccclllccc]ggggggg22bb333	chr2:31923305-31923540(-)$1	235	117	155	11.7014
ffffff[dddd"""cccnnnnnccc333dddd]fffff	chr11:87793793-87794058(-)$1	265	225	263	12.4614
eeee[bb[ccc!!ddddooooooddddccc]bb]eeee	chr3:103545044-103545290(-)$1	246	15	53	13.9348
"""gggggggddddddddllldddd333dddd4444gg	chr8:124121256-124121494(+)$1	238	111	149	13.0067
=======!!ccc[eeeeemmmmeeeee]ccc]======	chr15:58649129-58649364(-)$1	235	95	133	12.8612
b!!dddd[ccc!!ddddoooooodddd]ccc]dddd22	chr1:183835465-183835707(-)$1	242	188	226	13.9495
ccc[bb"""ccc"""bboooooobb333ccc]bb]ccc	chr19:56006291-56006549(+)$1	258	59	97	14.4908

#otherMatches

#Seq PSSM
AACCCCAGGUUUCAGGUCUCAGAGCCAAGCCAGGGUUG	chr2:155214089-155214332(+)$1	243	4	42	16.1871
AUAGUCUUUUCCUCCAAGGCAGGGUCAUGUGGUCUGGA	chr5:115252491-115252726(+)$1	235	48	86	12.6263
UAUUUUACUUUUUGAAGGUUGAUACUGUAAAAGAAUAA	chr1:153210533-153210769(+)$1	236	178	216	12.1719
GCUCCUGUUCUUACAAAGAUAUAUUUGACCAGUACAGA	chr3:141965381-141965616(-)$1	235	167	205	13.6634
UUCCGGGGACUGACGCGCUUUAGUCGCUGUCUGUCCCC	chr15:76910055-76910291(-)$1	236	24	62	11.6261
GGUGUUGGCUGGGGCAUUAAAACUCAUCAUCGCCACCC	chr19:43574327-43574562(-)$1	235	41	79	12.0240
UGGGUAGGAAAGCAAGCAGAGUAUGUUUGCUUUUUACA	chr5:32320229-32320464(+)$1	235	121	159	12.6402
CGAGUGUGAUUUUUUGUUGAGUGCAUUACAUCUUCACA	chr8:46911742-46911988(+)$1	246	44	82	13.1603
CUGCCAGAGCCUGUGACUGCCCUGCACUUUCUuuuucu	chr17:33884446-33884681(-)$1	235	53	91	13.6030
UAGGGGCAGAGUGCAUUCUGUUAGGGUUGUAUCAUGUC	chr16:64857934-64858194(+)$1	260	93	131	12.7560
UCAGAUCAGGUGGAAUUACUCAAAAUUUAAAGCCUGAA	chr9:70625984-70626219(+)$1	235	52	90	12.8648
GGGGCAGGAGAACAGGAGAACGCCUGGCCUCCCAAUCA	chr17:85463643-85463882(-)$1	239	140	178	15.7431
UGUACAUAGAAGUCUUAAGUGUUGUCCGGGGACCUAUG	chr12:73090945-73091181(+)$1	236	93	131	14.3562
CCUCAGAGCCUGACAGGGCCAGACCUGCUUCUCUGGGG	chr19:5099357-5099592(-)$1	235	7	45	17.1728
CCUUGGUACGUGCUGAUGAAAACAUUUAAUGUGCCAAA	chr4:107904863-107905105(-)$1	242	198	236	14.9736
AGCAUUUAAAUUAGGUGAAUGUGCACCGAUUUUUGUUG	chr9:96233096-96233334(-)$1	238	72	110	15.4698
CGAGGCAUUUCAAAGGUACACUAACCAAAAGUACUUGG	chr4:104704712-104704996(-)$1	284	178	216	17.3645
GCUGCAGUGAAAUAAACUCCAAAAGUAAUUUUGCUGCA	chr18:34505052-34505287(-)$1	235	169	207	13.9305
UUCUCUGGAGGCAUCAUGCGCUGGUGCUGCGUCCUUAU	chr1:166367534-166367783(-)$1	249	205	243	17.0184
AUGUAUAAUCUGUGUUUACUUGUAACUCUCUGGUUAUA	chr18:35750845-35751081(+)$1	236	135	173	11.8494
GGCUGUGUGUGUGUUAACCUGUUUUAAUGCCAAAAGCU	chr4:8534154-8534411(+)$1	257	168	206	12.7647
UGACCUCUGAGUCAUUGGUUAUACAGUGUAGUCCCAAG	chr11:29642544-29642783(+)$1	239	57	95	15.5341
CAGUAUAUUAUAAAAUGGUGUGUUUUUUUGUAAUAGUU	chr2:134420523-134420770(-)$1	247	180	218	12.0632
UAGAAGCAGUAACAAUGAAAUUAUGUGUUUGUUUAUGA	chr6:125076626-125076862(+)$1	236	160	198	11.7452
UCUUCCAUGGUAGCGCUCAAAGCCCUAAUGGAAGUUUA	chr1:99717957-99718198(-)$1	241	54	92	11.9484
AAAGGGUCCUGUCCAAGCAGUGUUUACAAGGAGGCCUU	chr10:82203496-82203737(+)$1	241	10	48	13.3320
CUGUCCUGACUGUGGAAAGGAUAUUUGAAGGCGGCACA	chr1:43180304-43180550(-)$1	246	164	202	14.9862
UUCAGUUCACUCACGUGCUUCCGUGAAUACUGAAUGUG	chr8:98238288-98238548(+)$1	260	172	210	13.0098
GUGCCCGUGGCUGGACUCUUCAGUGCUGCUAUCAUGGC	chr8:23678766-23679001(+)$1	235	45	83	12.3689
CCCGCUGUGUCCGUGUGCACACUGUAGCCCCACAGCCC	chr10:42254586-42254830(+)$1	244	195	233	11.4089
AUCAUUGGGAGUACCCAUCUUAGUGGAUCUUAGUGGGA	chr2:120334730-120334965(-)$1	235	136	174	13.6160
CCCAGUUUACAGUACAUUGUAGUGUGUGCUUUAUAUGG	chr13:94204139-94204375(-)$1	236	158	196	13.1993
CUCUACUCUGGAUGGUAUGAAGUUGCAAUUGGGAACUU	chr11:94887931-94888172(-)$1	241	188	226	16.5611
GAAUCAUCUUUUAAAAUCUGUUGUGAUUUAAGAUGUUU	chr4:82870373-82870608(-)$1	235	123	161	12.7748
CUGCGCGCGUAGUUUGCUUUCUUGUAGUUGCUCUGCUG	chr8:127942175-127942418(-)$1	243	35	73	15.0026
AGGAGUCAGGAUUAGUAAAACACUGCAAAAUCACUGUC	chr1:60389515-60389763(+)$1	248	16	54	15.2483
AUAGGAAAGUGCAUGAGGAGAGUUUUGAAUGUGCAUAU	chr11:50014073-50014323(-)$1	250	168	206	12.2962
UAUCUUCACAGAUCACAAGUAAAUGUGAAUCUGAAAGA	chr8:46912753-46912988(+)$1	235	50	88	13.4619
CAUUUUCUGUGCAUAGCUUCUGUUAGUCCUGUGUGCAG	chr1:34933815-34934074(+)$1	259	86	124	16.0014
GUAUGCAUACUUUAUUCACUUAAGAAGCUUGUCUGCAA	chr11:87897636-87897884(+)$1	248	52	90	13.6311
UUCCAUUGUGUAGCUgcucauuuggagcugcacagcau	chr13:94615440-94615675(+)$1	235	140	178	15.3902
CUUGAACAGGCAGCGCUGCCAUCCGGACGCUGUCACCU	chr6:39542613-39542851(+)$1	238	131	169	12.8456
AUCACAAUCUUUGUAUCUUUGUUUUUGAUCUGCUUGUG	chr8:34893345-34893581(-)$1	236	81	119	11.4747
CCUUUUGUUUGUUUUUGUUUUUUCAAAUCUGAGCAGAG	chr2:121373570-121373818(-)$1	248	23	61	16.0600
AAGGCGUGGCUAUGCUGCUAACGGAAGUGGGGUCAUCC	chrX:71674370-71674605(-)$1	235	37	75	12.8646
UUUAUUUUUGAGUAGCAUAUAAUUGCAAUAAGAAUAAA	chr11:62215867-62216106(-)$1	239	197	235	19.4652
GAGGAGCUGCGGGCUGUGGUGGAGCAGACGGAGCGGUC	chr14:55565114-55565368(-)$1	254	117	155	13.5100
UUGAGCUGCUUGAGGGACACUCCGUUAAGCGUACUAAC	chr2:31923305-31923540(-)$1	235	117	155	11.7014
GUGGCUGUCUGUUCCCUGGGAAAGGUUUUGGAAGGUCA	chr11:87793793-87794058(-)$1	265	225	263	12.4614
AUCAUUAUAUUAAGCUGUGCGUUCAGCAGUCUGUUGGU	chr3:103545044-103545290(-)$1	246	15	53	13.9348
GUUGUCAAGUGGUAGACUGCAAGUCCAAUGCUCCAGAC	chr8:124121256-124121494(+)$1	238	111	149	13.0067
uuuuucacucucuaggugucagcauuuugggcugggaa	chr15:58649129-58649364(-)$1	235	95	133	12.8612
CAUAAAGGAUGGAACAAACGGAGUUGUAUGUGCUUUCA	chr1:183835465-183835707(-)$1	242	188	226	13.9495
CGCCUCCUCGUCCUCCAUGCCCCUGCUUGAUUGAAGUG	chr19:56006291-56006549(+)$1	258	59	97	14.4908

#DB
(((((..(((((..(((......)))))))).))))))	chr2:155214089-155214332(+)$1	1	4	42	16.1871
((((((..((((.(((.(((...)))...)))...)))	chr5:115252491-115252726(+)$1	1	48	86	12.6263
((((...(((((....(((....)))..)))))))).)	chr1:153210533-153210769(+)$1	1	178	216	12.1719
..((((((.((..((((......))))...)).)))).	chr3:141965381-141965616(-)$1	1	167	205	13.6634
....((((((.(((((((....).))).))).))))))	chr15:76910055-76910291(-)$1	1	24	62	11.6261
((((.(((.((((.........))))...))).)))))	chr19:43574327-43574562(-)$1	1	41	79	12.0240
((.....(((((((((((.....)))))))))))..))	chr5:32320229-32320464(+)$1	1	121	159	12.6402
((.(((.(((.(..(((.....)))..).)))..))).	chr8:46911742-46911988(+)$1	1	44	82	13.1603
(.(((((((((.(((.(......))))...........	chr17:33884446-33884681(-)$1	1	53	91	13.6030
((((((((..(((((.(((....))).)))))..))))	chr16:64857934-64858194(+)$1	1	93	131	12.7560
(((((((((((.(((((......)))))...)))))).	chr9:70625984-70626219(+)$1	1	52	90	12.8648
((....((((..((((......))))..))))...)))	chr17:85463643-85463882(-)$1	1	140	178	15.7431
.(((((((...(((((..(......)..)))))...))	chr12:73090945-73091181(+)$1	1	93	131	14.3562
((((((((...(.((((......)))))..))))))))	chr19:5099357-5099592(-)$1	1	7	45	17.1728
..(((((((((...((((....))))..))))))))).	chr4:107904863-107905105(-)$1	1	198	236	14.9736
((((...(((((.((((......)))))))))....))	chr9:96233096-96233334(-)$1	1	72	110	15.4698
((((..((((....(((......)))..)))).)))))	chr4:104704712-104704996(-)$1	1	178	216	17.3645
)))((((((((((..(((.....))).)))))))))).	chr18:34505052-34505287(-)$1	1	169	207	13.9305
(((...(((.(((.(((......))).))).)))....	chr1:166367534-166367783(-)$1	1	205	243	17.0184
((((((((((.(.(((.......))).)...)))))))	chr18:35750845-35751081(+)$1	1	135	173	11.8494
((((...((.(((((((......)))))))))..))))	chr4:8534154-8534411(+)$1	1	168	206	12.7647
((....(((...(((((......))))))))...))))	chr11:29642544-29642783(+)$1	1	57	95	15.5341
(((..((((((((((..........))))))))))...	chr2:134420523-134420770(-)$1	1	180	218	12.0632
...((((((..(((.........)))..))))))...)	chr6:125076626-125076862(+)$1	1	160	198	11.7452
.(((((((..(((.(((...))).))))))))))..))	chr1:99717957-99718198(-)$1	1	54	92	11.9484
(((((.((((....((((...))))...))))..))))	chr10:82203496-82203737(+)$1	1	10	48	13.3320
((((.(((.((.(.(((......))).).))))).)))	chr1:43180304-43180550(-)$1	1	164	202	14.9862
((((((....(((((......)))))..)))))))(((	chr8:98238288-98238548(+)$1	1	172	210	13.0098
(.(((.(((((.(.(((....))).).)))))...)))	chr8:23678766-23679001(+)$1	1	45	83	12.3689
...((((((...(..((((...))))..).))))))..	chr10:42254586-42254830(+)$1	1	195	233	11.4089
((((((((((....((((....)))).)))))))..))	chr2:120334730-120334965(-)$1	1	136	174	13.6160
.(((...((.(((((((......))))))).))..)))	chr13:94204139-94204375(-)$1	1	158	196	13.1993
(((...(((.(((.(((......))).))).)))....	chr11:94887931-94888172(-)$1	1	188	226	16.5611
(((.((((((...(((((......))))))))))).))	chr4:82870373-82870608(-)$1	1	123	161	12.7748
(((((.(((.(((((((......))))..))).)))))	chr8:127942175-127942418(-)$1	1	35	73	15.0026
(((((.(((((((.(((......)))..)))).))).)	chr1:60389515-60389763(+)$1	1	16	54	15.2483
.(((.(..((((((..(((....)))..))))))...)	chr11:50014073-50014323(-)$1	1	168	206	12.2962
((((((..(((((((((......)))).))))).))))	chr8:46912753-46912988(+)$1	1	50	88	13.4619
.(((..((((((((((((......))..))))))))))	chr1:34933815-34934074(+)$1	1	86	124	16.0014
))))(((.((....(((......)))....)).)))..	chr11:87897636-87897884(+)$1	1	52	90	13.6311
(((..((((((((((.(......).))))))))))...	chr13:94615440-94615675(+)$1	1	140	178	15.3902
(((.((..((((((((((.....))).)))))))...)	chr6:39542613-39542851(+)$1	1	131	169	12.8456
(.(((((.(...(.(((.........)))).).)))))	chr8:34893345-34893581(-)$1	1	81	119	11.4747
).(((((((((..((((......))))..)))))))))	chr2:121373570-121373818(-)$1	1	23	61	16.0600
(.(((.(.(((...(((....))).))).).))).)))	chrX:71674370-71674605(-)$1	1	37	75	12.8646
((((((((((....(((......)))..))))))))))	chr11:62215867-62216106(-)$1	1	197	235	19.4652
).)))(((.((..((((......)))).)).)))((((	chr14:55565114-55565368(-)$1	1	117	155	13.5100
...((.(((((((.(((...))).)))))))..))...	chr2:31923305-31923540(-)$1	1	117	155	11.7014
((((((.((((...(((.....)))...)))).)))))	chr11:87793793-87794058(-)$1	1	225	263	12.4614
((((.((.(((..((((......))))))).)).))))	chr3:103545044-103545290(-)$1	1	15	53	13.9348
...(((((((((((((((...))))...))))....))	chr8:124121256-124121494(+)$1	1	111	149	13.0067
(((((((..(((.(((((....))))).))).))))))	chr15:58649129-58649364(-)$1	1	95	133	12.8612
(..((((.(((..((((......)))).))).))))..	chr1:183835465-183835707(-)$1	1	188	226	13.9495
(((.((...(((...((......))...))).)).)))	chr19:56006291-56006549(+)$1	1	59	97	14.4908

#PSSM
g : 0.12	c : 0.12	e : 0.11	f : 0.09	" : 0.09	= : 0.09	d : 0.09	i : 0.05	b : 0.05	# : 0.03	$ : 0.01	& : 0.01	a : 0.01	: : 0.01	! : 0.01	[ : 0.01	
g : 0.14	c : 0.12	f : 0.09	e : 0.09	= : 0.09	d : 0.09	i : 0.07	" : 0.07	[ : 0.07	# : 0.03	b : 0.01	$ : 0.01	: : 0.01	] : 0.01	! : 0.01	
c : 0.18	i : 0.12	g : 0.12	f : 0.09	d : 0.09	e : 0.09	# : 0.07	= : 0.07	$ : 0.03	" : 0.03	b : 0.01	[ : 0.01	! : 0.01	
g : 0.16	c : 0.14	i : 0.11	f : 0.09	= : 0.09	e : 0.09	# : 0.05	d : 0.05	[ : 0.05	b : 0.03	" : 0.03	! : 0.03	$ : 0.01	
f : 0.12	g : 0.12	" : 0.11	i : 0.09	c : 0.09	= : 0.09	[ : 0.07	! : 0.07	e : 0.05	b : 0.05	d : 0.03	# : 0.03	$ : 0.01	
f : 0.14	= : 0.12	" : 0.11	[ : 0.11	c : 0.09	g : 0.09	i : 0.07	! : 0.05	b : 0.05	d : 0.03	# : 0.03	$ : 0.01	a : 0.01	e : 0.01	
c : 0.16	= : 0.14	! : 0.09	" : 0.09	d : 0.09	f : 0.09	g : 0.09	i : 0.07	[ : 0.03	e : 0.03	$ : 0.01	# : 0.01	a : 0.01	b : 0.01	
c : 0.16	= : 0.14	! : 0.09	d : 0.09	f : 0.09	g : 0.09	[ : 0.09	e : 0.07	i : 0.07	b : 0.03	# : 0.01	" : 0.01	
c : 0.16	f : 0.11	= : 0.11	e : 0.09	d : 0.09	[ : 0.07	i : 0.07	g : 0.07	! : 0.05	" : 0.05	b : 0.05	# : 0.01	a : 0.01	
d : 0.12	= : 0.11	c : 0.11	e : 0.09	" : 0.09	[ : 0.09	b : 0.07	f : 0.07	i : 0.07	g : 0.07	! : 0.05	# : 0.01	
c : 0.16	e : 0.12	" : 0.11	d : 0.09	= : 0.09	# : 0.09	g : 0.07	b : 0.05	[ : 0.05	i : 0.05	f : 0.03	! : 0.03	
c : 0.14	e : 0.12	" : 0.12	! : 0.11	= : 0.09	# : 0.09	d : 0.07	[ : 0.07	g : 0.07	a : 0.05	f : 0.01	
! : 0.12	c : 0.12	# : 0.11	e : 0.11	[ : 0.09	= : 0.09	" : 0.09	d : 0.07	g : 0.07	a : 0.07	f : 0.01	
d : 0.20	[ : 0.14	e : 0.12	# : 0.11	c : 0.09	! : 0.07	= : 0.07	" : 0.07	g : 0.05	r : 0.01	f : 0.01	
c : 0.35	d : 0.25	e : 0.12	= : 0.07	! : 0.05	g : 0.05	r : 0.03	# : 0.01	" : 0.01	
c : 0.37	d : 0.27	e : 0.09	[ : 0.05	r : 0.03	= : 0.03	g : 0.03	# : 0.01	s : 0.01	o : 0.01	! : 0.01	b : 0.01	
c : 0.38	d : 0.25	e : 0.07	r : 0.03	a : 0.03	o : 0.03	g : 0.03	b : 0.03	[ : 0.01	= : 0.01	! : 0.01	p : 0.01	s : 0.01	
o : 0.48	c : 0.11	d : 0.09	r : 0.05	n : 0.03	l : 0.03	m : 0.03	e : 0.03	a : 0.01	= : 0.01	! : 0.01	p : 0.01	s : 0.01	b : 0.01	
o : 0.51	m : 0.11	n : 0.09	c : 0.07	l : 0.07	r : 0.05	a : 0.01	p : 0.01	s : 0.01	d : 0.01	
o : 0.53	m : 0.16	n : 0.09	l : 0.09	r : 0.05	c : 0.01	p : 0.01	s : 0.01	
o : 0.53	m : 0.16	n : 0.09	l : 0.07	r : 0.05	c : 0.03	p : 0.01	s : 0.01	
o : 0.51	m : 0.12	n : 0.09	c : 0.07	r : 0.05	l : 0.03	d : 0.03	p : 0.01	s : 0.01	e : 0.01	
o : 0.49	d : 0.12	c : 0.11	m : 0.05	n : 0.05	r : 0.03	e : 0.03	l : 0.01	a : 0.01	p : 0.01	s : 0.01	
c : 0.37	d : 0.29	e : 0.07	] : 0.05	o : 0.05	a : 0.03	g : 0.03	= : 0.01	s : 0.01	r : 0.01	b : 0.01	
c : 0.38	d : 0.29	e : 0.09	g : 0.05	] : 0.05	b : 0.03	= : 0.01	o : 0.01	s : 0.01	r : 0.01	
c : 0.37	d : 0.25	e : 0.09	3 : 0.07	= : 0.05	g : 0.05	a : 0.03	2 : 0.01	b : 0.01	r : 0.01	
2 : 0.24	d : 0.16	] : 0.16	3 : 0.11	e : 0.09	c : 0.09	= : 0.05	g : 0.05	4 : 0.01	
2 : 0.25	e : 0.12	3 : 0.12	g : 0.11	] : 0.09	c : 0.09	= : 0.07	a : 0.07	> : 0.01	4 : 0.01	
c : 0.16	e : 0.14	g : 0.12	= : 0.11	d : 0.11	3 : 0.09	] : 0.05	2 : 0.05	f : 0.03	> : 0.01	i : 0.01	a : 0.01	4 : 0.01	b : 0.01	
c : 0.22	e : 0.12	g : 0.12	= : 0.11	d : 0.11	3 : 0.05	f : 0.05	i : 0.03	b : 0.03	a : 0.03	> : 0.01	2 : 0.01	] : 0.01	4 : 0.01	
c : 0.16	e : 0.12	= : 0.12	] : 0.12	d : 0.11	g : 0.09	b : 0.07	f : 0.07	3 : 0.03	i : 0.03	> : 0.01	
c : 0.16	= : 0.12	e : 0.11	d : 0.11	] : 0.09	b : 0.09	f : 0.09	g : 0.07	i : 0.05	> : 0.01	3 : 0.01	a : 0.01	2 : 0.01	
] : 0.14	= : 0.14	f : 0.11	2 : 0.09	c : 0.09	i : 0.07	3 : 0.07	g : 0.07	e : 0.05	b : 0.05	4 : 0.03	> : 0.01	d : 0.01	
c : 0.16	= : 0.14	f : 0.12	i : 0.09	3 : 0.09	g : 0.09	2 : 0.09	d : 0.03	4 : 0.03	] : 0.03	b : 0.03	> : 0.01	e : 0.01	
= : 0.14	3 : 0.12	f : 0.11	i : 0.09	c : 0.09	g : 0.07	2 : 0.07	4 : 0.07	d : 0.05	] : 0.05	e : 0.03	> : 0.01	h : 0.01	b : 0.01	
c : 0.18	= : 0.12	3 : 0.11	i : 0.09	f : 0.09	d : 0.07	4 : 0.07	g : 0.05	2 : 0.05	e : 0.05	> : 0.01	] : 0.01	6 : 0.01	h : 0.01	
c : 0.12	= : 0.12	i : 0.11	g : 0.11	e : 0.11	3 : 0.09	f : 0.07	d : 0.05	] : 0.03	4 : 0.03	> : 0.01	5 : 0.01	: : 0.01	6 : 0.01	h : 0.01	2 : 0.01	
e : 0.14	g : 0.11	= : 0.11	c : 0.11	i : 0.09	f : 0.05	3 : 0.05	d : 0.03	] : 0.03	: : 0.03	4 : 0.03	b : 0.03	> : 0.01	0 : 0.01	5 : 0.01	a : 0.01	6 : 0.01	h : 0.01	2 : 0.01	

#score	746.1744868912555
#seq	54
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_UTR_m3_run1.txt

#BEAR
ffffffqqqqqqqqffffff	chr11:54683637-54683857(+)$1	220	140	160	13.6470
cc[cccqqqqqqqqccc333	chr15:99843069-99843289(+)$1	220	140	160	15.7514
""ddddqqqqqqqqddddcc	chr5:135096993-135097215(-)$1	222	12	32	15.3201
ggggggqqqqqqqqgggggg	chr19:29091893-29092114(+)$1	221	102	122	14.0907
dddcccqqqqqqqqccc333	chr13:23662847-23663105(-)$1	258	121	141	15.5041
!!ddddqqqqqqqqdddd22	chr4:25544108-25544328(-)$1	220	132	152	15.9285
ggg[bbqqqqqqqqbb333g	chr18:46892766-46892986(-)$1	220	111	131	13.5096
!!ddddqqqqqqqqdddd99	chr1:34248936-34249170(+)$1	234	173	193	14.5452
dddd[aqqqqqqqqa]dddd	chr7:75882485-75882705(-)$1	220	80	100	13.7558
ffffffqqqqqqqqffffff	chr9:54759012-54759232(+)$1	220	184	204	13.6470
a!!cccqqqqqqqqccc22a	chr1:188544883-188545103(-)$1	220	51	71	15.3895
!!bb[aqqqqqqqqa]bb22	chr3:95566309-95566529(-)$1	220	155	175	13.8521
ddacccqqqqqqqqccc]a]	chr16:20561011-20561231(+)$1	220	166	186	14.7014
beeeeeqqqqqqqqeeeee2	chr1:4887261-4887481(+)$1	220	121	141	13.9170
ffffffqqqqqqqqffffff	chr18:42499541-42499761(+)$1	220	111	131	13.6470
###cccqqqqqqqqccc666	chr10:110933012-110933232(+)$1	220	132	152	14.3978
ggggggqqqqqqqqgggggg	chrX:65969489-65969709(+)$1	220	178	198	14.0907
[eeeeeqqqqqqqqeeeeeb	chr6:29325189-29325425(+)$1	236	9	29	13.7746
ee[cccqqqqqqqqccc]ee	chr11:106110631-106110869(-)$1	238	65	85	14.5238
ffffffqqqqqqqqffffff	chr8:124405329-124405557(-)$1	228	148	168	13.6470
ff[cccqqqqqqqqccc]ff	chr15:98349679-98349899(-)$1	220	111	131	14.7987
""ddddqqqqqqqqdddd33	chr8:129458703-129458927(-)$1	224	90	110	16.1974
"""cccqqqqqqqqccc444	chr19:61167859-61168079(+)$1	220	168	188	15.7866
ggggggqqqqqqqqgggggg	chr7:17021612-17021832(+)$1	220	89	109	14.0907
bb[cccqqqqqqqqccc333	chr14:22664687-22664907(+)$1	220	142	162	15.3485
Feeeeeqqqqqqqqeeeee:	chr12:114310580-114310801(+)$1	221	22	42	12.6776
''ddddqqqqqqqqddddah	chr3:122241808-122242042(-)$1	234	116	136	13.7982
[ccc[aqqqqqqqqa]ccc]	chr13:101549430-101549650(-)$1	220	71	91	14.5145
ffffffqqqqqqqqffffff	chr17:29104655-29104875(+)$1	220	88	108	13.6470
c!!cccqqqqqqqqccc22c	chr12:39593714-39593953(+)$1	239	188	208	15.3218
b[ddddqqqqqqqqdddd]b	chr17:88049906-88050142(+)$1	236	96	116	14.9312
ddddbbqqqqqqqqbb]ddd	chr2:128678061-128678281(+)$1	220	93	113	12.6505
ffffffqqqqqqqqffffff	chr2:135798627-135798867(+)$1	240	62	82	13.6470
"""cccqqqqqqqqcccfff	chr1:129840275-129840504(+)$1	229	22	42	15.1387
d[ddddqqqqqqqqdddddd	chr5:33370310-33370530(+)$1	220	3	23	14.6317
!!ddddqqqqqqqqdddd22	chr11:6256164-6256384(+)$1	220	83	103	15.9285
""ddddqqqqqqqqdddd33	chr5:28740349-28740569(+)$1	220	123	143	16.1974
ffffffqqqqqqqqffffff	chr7:6659425-6659645(-)$1	220	171	191	13.6470
"""cccqqqqqqqqccc444	chr4:45389131-45389351(+)$1	220	34	54	15.7866
$$ddddqqqqqqqqdddd55	chr13:74459801-74460050(-)$1	249	158	178	13.9644
b[ddddqqqqqqqqdddd22	chr4:22330606-22330826(+)$1	220	51	71	15.4880
c[ddddqqqqqqqqdddd]c	chr8:3154273-3154493(-)$1	220	121	141	15.3569
!eeeeeqqqqqqqqeeeee2	chr6:28366669-28366889(-)$1	220	10	30	14.3258
dddcccqqqqqqqqccc22d	chr9:71332501-71332721(-)$1	220	76	96	14.6183
eeeeeeqqqqqqqqeeeee:	chr7:148048791-148049012(+)$1	221	41	61	12.9447
bb[cccqqqqqqqqcccbb2	chr16:17038353-17038590(+)$1	237	21	41	14.0314
!!ddddqqqqqqqqdddd22	chr10:62436708-62436928(+)$1	220	23	43	15.9285
ffffffqqqqqqqqffffff	chr6:148128043-148128264(-)$1	221	158	178	13.6470
F:ddddqqqqqqqqdddd:d	chr3:116376403-116376625(-)$1	222	94	114	12.5835
[eeeeeqqqqqqqqeeeee]	chr5:110600429-110600649(+)$1	220	44	64	14.2428
ffffffqqqqqqqqffffff	chr8:72542795-72543015(-)$1	220	100	120	13.6470
c[ddddqqqqqqqqdddd]c	chr10:98729672-98729892(+)$1	220	54	74	15.3569
fffcccqqqqqqqqccc22f	chr10:43232781-43233001(+)$1	220	135	155	14.8407
!ccc[aqqqqqqqqa]ccc4	chr1:137198224-137198460(-)$1	236	52	72	14.5880
###cccqqqqqqqqccchhh	chr18:42498821-42499041(+)$1	220	99	119	14.3746
ccddddqqqqqqqqdddd]c	chr2:32562968-32563188(-)$1	220	25	45	15.0967
eeddddqqqqqqqqdddd22	chr17:28199309-28199529(+)$1	220	143	163	15.2554
""ddddqqqqqqqqdddd22	chr5:110683963-110684183(+)$1	220	68	88	15.9058
ccddddqqqqqqqqdddd33	chr11:102661135-102661386(-)$1	251	197	217	15.6889

#otherMatches

#Seq PSSM
GCAGACGGGGGACAGUCUGU	chr11:54683637-54683857(+)$1	220	140	160	13.6470
CUUGAGUAGAUUUUCUUUGU	chr15:99843069-99843289(+)$1	220	140	160	15.7514
UUGCUAUAUCUAUCUAGUGC	chr5:135096993-135097215(-)$1	222	12	32	15.3201
AAAAGUCUUUUUGUGCUUUU	chr19:29091893-29092114(+)$1	221	102	122	14.0907
UGCGUCAAUGUCUGGACGUG	chr13:23662847-23663105(-)$1	258	121	141	15.5041
UUGUUUUAGCUGUUGAACUU	chr4:25544108-25544328(-)$1	220	132	152	15.9285
ggucucacuauguagaucug	chr18:46892766-46892986(-)$1	220	111	131	13.5096
GUGGAGGAAAGUAUCUCCGA	chr1:34248936-34249170(+)$1	234	173	193	14.5452
GGAUUGUUCACAUUCCAUCU	chr7:75882485-75882705(-)$1	220	80	100	13.7558
AAAAUAAUCUGUCAUAUUUU	chr9:54759012-54759232(+)$1	220	184	204	13.6470
GGAUCCUUUGCUGUGGACAC	chr1:188544883-188545103(-)$1	220	51	71	15.3895
UUCAUCCUGUUCUUGCUGUU	chr3:95566309-95566529(-)$1	220	155	175	13.8521
AGCCCCUGCUGCUUGGGAGU	chr16:20561011-20561231(+)$1	220	166	186	14.7014
CCAGCUGAAAUGUAGGCUGU	chr1:4887261-4887481(+)$1	220	121	141	13.9170
AUUAGGUCCCACCUUCUGAU	chr18:42499541-42499761(+)$1	220	111	131	13.6470
UUGAGGACGGCCGCCCUGUA	chr10:110933012-110933232(+)$1	220	132	152	14.3978
AGAAGAAAUAACUAUCUUUU	chrX:65969489-65969709(+)$1	220	178	198	14.0907
UCUUGAAAAAUCAAUCAAGU	chr6:29325189-29325425(+)$1	236	9	29	13.7746
UCGGAUGAAGAAGGAUCAGA	chr11:106110631-106110869(-)$1	238	65	85	14.5238
UGUCAUUCCUGUUUGUGAUG	chr8:124405329-124405557(-)$1	228	148	168	13.6470
UGAUCAUCUCUCCCUGAACA	chr15:98349679-98349899(-)$1	220	111	131	14.7987
AGGGCAAAUUAUGCUGUCAU	chr8:129458703-129458927(-)$1	224	90	110	16.1974
ACCGUUCCCCCAAUAACAAA	chr19:61167859-61168079(+)$1	220	168	188	15.7866
UAUCUGUAGAGUACCGGAUA	chr7:17021612-17021832(+)$1	220	89	109	14.0907
AAAGAUUUUUUUUUGUUAUA	chr14:22664687-22664907(+)$1	220	142	162	15.3485
GCUGGACAGGAUCAUCCAGG	chr12:114310580-114310801(+)$1	221	22	42	12.6776
UAAAGCUGGUGUUUGCUUCC	chr3:122241808-122242042(-)$1	234	116	136	13.7982
CAUAGGAUACCUACCGUGUU	chr13:101549430-101549650(-)$1	220	71	91	14.5145
CCGUCCUCCACCCUGGGCGG	chr17:29104655-29104875(+)$1	220	88	108	13.6470
GUUUGGUUUAUUGUCCAUCC	chr12:39593714-39593953(+)$1	239	188	208	15.3218
GAUCGUAAAAUUAGACGAAC	chr17:88049906-88050142(+)$1	236	96	116	14.9312
CCAAAGAUACCAGGCUGUUG	chr2:128678061-128678281(+)$1	220	93	113	12.6505
UACGUGGAAGUCGAUAUGUA	chr2:135798627-135798867(+)$1	240	62	82	13.6470
AAACCCAUAGAUACGGGCUG	chr1:129840275-129840504(+)$1	229	22	42	15.1387
UUAUAAACUGUUUCUUGUGA	chr5:33370310-33370530(+)$1	220	3	23	14.6317
UGUGGGAAACUUACCCCAGC	chr11:6256164-6256384(+)$1	220	83	103	15.9285
AGUUUUAGAUUCAGGAAAGA	chr5:28740349-28740569(+)$1	220	123	143	16.1974
AUUGUGUAACCCUUUACAAU	chr7:6659425-6659645(-)$1	220	171	191	13.6470
CACAAUUAAAAACUAUUAUA	chr4:45389131-45389351(+)$1	220	34	54	15.7866
gcaccaucauucucugguca	chr13:74459801-74460050(-)$1	249	158	178	13.9644
CAUGGAUUAUUGUUUCCACA	chr4:22330606-22330826(+)$1	220	51	71	15.4880
UUGAAACACAUAUUUUUCUG	chr8:3154273-3154493(-)$1	220	121	141	15.3569
AAUGUUUGGCCAUUAAUAUA	chr6:28366669-28366889(-)$1	220	10	30	14.3258
CCUGUUUGUUAUAUAACCAA	chr9:71332501-71332721(-)$1	220	76	96	14.6183
CGCUGCCACCCACUGCAGUA	chr7:148048791-148049012(+)$1	221	41	61	12.9447
UGCGACUGGUAAAUGUUCAU	chr16:17038353-17038590(+)$1	237	21	41	14.0314
UUUUAAAAAAUAAAUUGAUC	chr10:62436708-62436928(+)$1	220	23	43	15.9285
CUGUCUACCUCCUGAGAUAG	chr6:148128043-148128264(-)$1	221	158	178	13.6470
UAACUGGAUUCUCACAGUGG	chr3:116376403-116376625(-)$1	222	94	114	12.5835
CUGUAGCACAAAUACUAUAA	chr5:110600429-110600649(+)$1	220	44	64	14.2428
GGACCUGAAUGAGAGGGUUC	chr8:72542795-72543015(-)$1	220	100	120	13.6470
AUGUAGUUUUGACUCUGCCU	chr10:98729672-98729892(+)$1	220	54	74	15.3569
UGCUGUAGAGGGACACAUUG	chr10:43232781-43233001(+)$1	220	135	155	14.8407
AGGUGGGACAUCAGCGGCCA	chr1:137198224-137198460(-)$1	236	52	72	14.5880
UUUGAAAUAAGUGAUUCAGU	chr18:42498821-42499041(+)$1	220	99	119	14.3746
CGCCAGCUCUUCCUCUGGAU	chr2:32562968-32563188(-)$1	220	25	45	15.0967
UUGUAAGAAAAAUGUUAUUU	chr17:28199309-28199529(+)$1	220	143	163	15.2554
CCCUGACUCAGACUUCAGUA	chr5:110683963-110684183(+)$1	220	68	88	15.9058
UGUUGGCUCAUGAUCCAAAC	chr11:102661135-102661386(-)$1	251	197	217	15.6889

#DB
((((((........))))))	chr11:54683637-54683857(+)$1	1	140	160	13.6470
((.(((........)))...	chr15:99843069-99843289(+)$1	1	140	160	15.7514
..((((........))))))	chr5:135096993-135097215(-)$1	1	12	32	15.3201
((((((........))))))	chr19:29091893-29092114(+)$1	1	102	122	14.0907
((((((........)))...	chr13:23662847-23663105(-)$1	1	121	141	15.5041
..((((........))))..	chr4:25544108-25544328(-)$1	1	132	152	15.9285
(((.((........))...)	chr18:46892766-46892986(-)$1	1	111	131	13.5096
..((((........))))..	chr1:34248936-34249170(+)$1	1	173	193	14.5452
((((.(........).))))	chr7:75882485-75882705(-)$1	1	80	100	13.7558
((((((........))))))	chr9:54759012-54759232(+)$1	1	184	204	13.6470
(..(((........)))..)	chr1:188544883-188545103(-)$1	1	51	71	15.3895
..((.(........).))..	chr3:95566309-95566529(-)$1	1	155	175	13.8521
((((((........))).).	chr16:20561011-20561231(+)$1	1	166	186	14.7014
((((((........))))).	chr1:4887261-4887481(+)$1	1	121	141	13.9170
((((((........))))))	chr18:42499541-42499761(+)$1	1	111	131	13.6470
...(((........)))...	chr10:110933012-110933232(+)$1	1	132	152	14.3978
((((((........))))))	chrX:65969489-65969709(+)$1	1	178	198	14.0907
.(((((........))))))	chr6:29325189-29325425(+)$1	1	9	29	13.7746
((.(((........))).))	chr11:106110631-106110869(-)$1	1	65	85	14.5238
((((((........))))))	chr8:124405329-124405557(-)$1	1	148	168	13.6470
((.(((........))).))	chr15:98349679-98349899(-)$1	1	111	131	14.7987
..((((........))))..	chr8:129458703-129458927(-)$1	1	90	110	16.1974
...(((........)))...	chr19:61167859-61168079(+)$1	1	168	188	15.7866
((((((........))))))	chr7:17021612-17021832(+)$1	1	89	109	14.0907
((.(((........)))...	chr14:22664687-22664907(+)$1	1	142	162	15.3485
((((((........))))).	chr12:114310580-114310801(+)$1	1	22	42	12.6776
..((((........))))))	chr3:122241808-122242042(-)$1	1	116	136	13.7982
.(((.(........).))).	chr13:101549430-101549650(-)$1	1	71	91	14.5145
((((((........))))))	chr17:29104655-29104875(+)$1	1	88	108	13.6470
(..(((........)))..)	chr12:39593714-39593953(+)$1	1	188	208	15.3218
(.((((........)))).)	chr17:88049906-88050142(+)$1	1	96	116	14.9312
((((((........)).)))	chr2:128678061-128678281(+)$1	1	93	113	12.6505
((((((........))))))	chr2:135798627-135798867(+)$1	1	62	82	13.6470
...(((........))))))	chr1:129840275-129840504(+)$1	1	22	42	15.1387
(.((((........))))))	chr5:33370310-33370530(+)$1	1	3	23	14.6317
..((((........))))..	chr11:6256164-6256384(+)$1	1	83	103	15.9285
..((((........))))..	chr5:28740349-28740569(+)$1	1	123	143	16.1974
((((((........))))))	chr7:6659425-6659645(-)$1	1	171	191	13.6470
...(((........)))...	chr4:45389131-45389351(+)$1	1	34	54	15.7866
..((((........))))..	chr13:74459801-74460050(-)$1	1	158	178	13.9644
(.((((........))))..	chr4:22330606-22330826(+)$1	1	51	71	15.4880
(.((((........)))).)	chr8:3154273-3154493(-)$1	1	121	141	15.3569
.(((((........))))).	chr6:28366669-28366889(-)$1	1	10	30	14.3258
((((((........)))..)	chr9:71332501-71332721(-)$1	1	76	96	14.6183
)(((((........))))).	chr7:148048791-148049012(+)$1	1	41	61	12.9447
((.(((........))))).	chr16:17038353-17038590(+)$1	1	21	41	14.0314
..((((........))))..	chr10:62436708-62436928(+)$1	1	23	43	15.9285
((((((........))))))	chr6:148128043-148128264(-)$1	1	158	178	13.6470
(.((((........)))).(	chr3:116376403-116376625(-)$1	1	94	114	12.5835
.(((((........))))).	chr5:110600429-110600649(+)$1	1	44	64	14.2428
((((((........))))))	chr8:72542795-72543015(-)$1	1	100	120	13.6470
(.((((........)))).)	chr10:98729672-98729892(+)$1	1	54	74	15.3569
((((((........)))..)	chr10:43232781-43233001(+)$1	1	135	155	14.8407
.(((.(........).))).	chr1:137198224-137198460(-)$1	1	52	72	14.5880
...(((........))))))	chr18:42498821-42499041(+)$1	1	99	119	14.3746
((((((........)))).)	chr2:32562968-32563188(-)$1	1	25	45	15.0967
((((((........))))..	chr17:28199309-28199529(+)$1	1	143	163	15.2554
..((((........))))..	chr5:110683963-110684183(+)$1	1	68	88	15.9058
((((((........))))..	chr11:102661135-102661386(-)$1	1	197	217	15.6889

#PSSM
f : 0.18	" : 0.11	! : 0.11	c : 0.10	d : 0.10	b : 0.08	g : 0.06	[ : 0.05	e : 0.05	# : 0.03	F : 0.03	a : 0.01	' : 0.01	$ : 0.01	
f : 0.18	e : 0.13	" : 0.11	! : 0.11	c : 0.08	d : 0.08	[ : 0.08	g : 0.06	# : 0.03	b : 0.03	' : 0.01	$ : 0.01	: : 0.01	
d : 0.38	f : 0.16	e : 0.10	[ : 0.08	g : 0.06	" : 0.05	! : 0.03	# : 0.03	c : 0.03	b : 0.01	a : 0.01	
d : 0.35	c : 0.30	f : 0.15	e : 0.10	g : 0.05	[ : 0.01	b : 0.01	
d : 0.32	c : 0.27	f : 0.15	e : 0.10	[ : 0.06	g : 0.05	b : 0.03	
d : 0.32	c : 0.27	f : 0.15	e : 0.10	a : 0.06	g : 0.05	b : 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 : 0.32	c : 0.27	f : 0.15	e : 0.10	a : 0.06	g : 0.05	b : 0.03	
d : 0.32	c : 0.27	f : 0.15	e : 0.10	] : 0.06	g : 0.05	b : 0.03	
d : 0.33	c : 0.30	f : 0.15	e : 0.10	g : 0.05	3 : 0.01	b : 0.01	] : 0.01	
d : 0.35	f : 0.16	e : 0.10	3 : 0.06	2 : 0.06	g : 0.05	] : 0.05	b : 0.03	4 : 0.03	c : 0.03	6 : 0.01	h : 0.01	
f : 0.18	2 : 0.18	3 : 0.11	e : 0.11	] : 0.06	c : 0.05	g : 0.05	d : 0.05	a : 0.03	4 : 0.03	9 : 0.01	6 : 0.01	5 : 0.01	b : 0.01	: : 0.01	h : 0.01	
f : 0.20	2 : 0.16	3 : 0.10	c : 0.08	d : 0.08	g : 0.06	] : 0.05	4 : 0.05	b : 0.03	: : 0.03	h : 0.03	9 : 0.01	a : 0.01	6 : 0.01	e : 0.01	5 : 0.01	

#score	858.2680689524885
#seq	59
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_CDS_m3_run1.txt

#BEAR
:bb!!ffffffqqqqqqqqffffff]	chr15:31522041-31522321(-)$1	280	48	74	13.9619
dddd"""ddddqqqqqqqqdddd22d	chr17:83623476-83623763(+)$1	287	12	38	16.7762
!!dddd[ddddqqqqqqqqddddddd	chr19:5770175-5770443(-)$1	268	68	94	16.4529
!ccc[ffffffqqqqqqqqffffffc	chr11:55302469-55302760(+)$1	291	180	206	15.1825
ddd]eeeeebbqqqqqqqqbbeeeee	chr17:88386043-88386321(+)$1	278	157	183	14.5576
eeee[a[a[bbqqqqqqqqbb22a]a	chr14:121691148-121691419(-)$1	271	63	89	14.6891
[aiiiiiiiiiqqqqqqqqiiiiiii	chr5:42210565-42210839(-)$1	274	41	67	16.2782
gg!!a!!ddddqqqqqqqqdddd333	chr2:62339207-62339477(-)$1	270	234	260	17.5153
!!bb[ffffffqqqqqqqqffffffb	chr1:163171669-163172027(-)$1	358	83	109	14.5362
fffffffff[aqqqqqqqqa]fffff	chr8:44736206-44736475(-)$1	269	13	39	14.3963
eeeee[cccbbqqqqqqqqbb]ccc]	chr15:96265234-96265516(-)$1	282	245	271	14.7387
eeeee[eeeeeqqqqqqqqeeeee]e	chr17:64245297-64245565(+)$1	268	218	244	16.3955
!bb[gggggggqqqqqqqqggggggg	chr8:87198822-87199109(-)$1	287	159	185	16.0314
""iiiiiiiiiqqqqqqqqiiiiiii	chr14:47938973-47939339(+)$1	366	167	193	16.3673
e[bb!!eeeeeqqqqqqqqeeeee22	chr5:114582066-114582344(+)$1	278	241	267	16.2517
:ccc[ffffffqqqqqqqqffffffc	chr11:72951022-72951290(-)$1	268	230	256	14.2634
ddd[ccc[cccqqqqqqqqccc]ccc	chr8:82163810-82164082(+)$1	272	15	41	16.0145
fff####ddddqqqqqqqqddddfff	chr5:138609190-138609502(-)$1	312	104	130	16.2876
####ccc[cccqqqqqqqqccc22cc	chr4:123188092-123188372(-)$1	280	93	119	15.9728
dd::gggggggqqqqqqqqggggggg	chr4:116299856-116300129(-)$1	273	177	203	14.1562
##dddd"""bbqqqqqqqqbb22ddd	chr1:9535866-9536144(+)$1	278	191	217	14.1366
"eeeeeeeeeeqqqqqqqqeeeee88	chr17:51921864-51922132(-)$1	268	65	91	15.3648
b[a!!ddddbbqqqqqqqqbb]dddd	chr19:60839820-60840127(-)$1	307	48	74	14.7399
a[dddd[ddddqqqqqqqqdddd]dd	chr10:90559026-90559310(+)$1	284	115	141	16.5811
ggggg!!a!!aqqqqqqqqa22a22g	chr18:75528598-75528869(+)$1	271	63	89	15.5197
$$dddd!!cccqqqqqqqqccc]ddd	chr2:84283302-84283574(-)$1	272	164	190	15.7059
ffffff!!cccqqqqqqqqccc333f	chr15:77798484-77798771(-)$1	287	109	135	16.1792
g!!bb[bbcccqqqqqqqqccc333b	chr11:98189225-98189495(-)$1	270	204	230	15.4089
eeee"""ddddqqqqqqqqdddd444	chrX:136384131-136384403(-)$1	272	191	217	16.9249
:::ccc[ddddqqqqqqqqdddd]cc	chr11:87794725-87795066(-)$1	341	288	314	14.3513
ggggggeeeeeqqqqqqqqeeeee22	chr9:108701514-108701781(+)$1	267	56	82	16.2800
[dddd[eeeeeqqqqqqqqeeeee]d	chr8:97437118-97437386(-)$1	268	235	261	16.6148
dddd"""ddddqqqqqqqqdddd333	chr2:154519585-154519863(+)$1	278	0	26	17.3083
ffffffeeeeeqqqqqqqqeeeee]f	chr14:32515061-32515366(-)$1	305	90	116	15.8134
ddddgggggggqqqqqqqqggggggg	chr13:74877226-74877496(-)$1	270	220	246	15.9952
:gggggggcccqqqqqqqqccc333g	chr16:90245531-90245808(-)$1	277	74	100	15.9188
hdddd!!ddddqqqqqqqqdddd]dd	chr6:71363116-71363392(-)$1	276	147	173	16.5100
dbb[gggggggqqqqqqqqggggggg	chr5:140919140-140919421(+)$1	281	15	41	15.7872
!bbbb!!ddddqqqqqqqqdddd22b	chr7:116871284-116871551(-)$1	267	195	221	16.0380
""dddd!!cccqqqqqqqqcccdddd	chr15:85762627-85762895(-)$1	268	151	177	16.1993
"dddd[eeeeeqqqqqqqqeeeee]d	chr8:89375415-89375690(-)$1	275	149	175	16.6641
::eeeee[cccqqqqqqqqccceeee	chr19:5985471-5985739(-)$1	268	53	79	14.3263
eeeegggggggqqqqqqqqggggggg	chr4:135888291-135888583(+)$1	292	23	49	15.9538
ddiiiiiiiiiqqqqqqqqiiiiiii	chr4:11249003-11249282(-)$1	279	171	197	16.0683
cc!!eeeee[aqqqqqqqqa]eeeee	chr8:114526344-114526615(-)$1	271	171	197	15.8849
:ccc"""ddddqqqqqqqqddddccc	chr2:120339260-120339533(-)$1	273	100	126	16.2062
bccc!!eeeeeqqqqqqqqeeeeecc	chr4:154909396-154909687(+)$1	291	131	157	16.6692
ddiiiiiiiiiqqqqqqqqiiiiiii	chr4:117941927-117942226(-)$1	299	168	194	16.0683
::iiiiiiiiiqqqqqqqqiiiiiii	chr16:87486565-87486840(-)$1	275	47	73	14.5875
eeeee[eeeeeqqqqqqqqeeeee22	chr16:94913623-94913907(+)$1	284	186	212	16.2263
e:dddd[ddddqqqqqqqqdddd]dd	chr10:128061493-128061783(-)$1	290	16	42	15.5757
b[eeeee[cccqqqqqqqqccceeee	chr15:79117458-79117733(-)$1	275	120	146	15.8039
%cccccc[cccqqqqqqqqcccccc2	chr13:68714079-68714377(-)$1	298	216	242	15.4660
ffffff[ddddqqqqqqqqdddd]ff	chr4:82493456-82493728(-)$1	272	229	255	16.1075
"ccc!!eeeeeqqqqqqqqeeeee22	chr14:32016366-32016646(-)$1	280	84	110	16.8760
eee####ddddqqqqqqqqdddd444	chr2:90853336-90853670(+)$1	334	129	155	16.8443
"""ccc[ddddqqqqqqqqdddd]cc	chr2:29770728-29771012(+)$1	284	148	174	16.9984
ddd"""eeeeeqqqqqqqqeeeee]d	chr2:73111926-73112196(+)$1	270	122	148	16.7237
ccc"""eeeeeqqqqqqqqeeeeecc	chr12:33533433-33533733(+)$1	300	231	257	16.7801
fffccc[ddddqqqqqqqqdddd]cc	chr16:93870840-93871115(+)$1	275	133	159	16.5664
cc!!gggggggqqqqqqqqggggggg	chr8:93743939-93744212(-)$1	273	182	208	16.2953
fff[bbeeeeeqqqqqqqqeeeee]b	chr8:74844537-74844831(+)$1	294	255	281	15.5200
fffff!!ddddqqqqqqqqddddfff	chr5:21307023-21307298(+)$1	275	172	198	16.1926
ccc[bb!!cccqqqqqqqqccc22bb	chr11:61348645-61348915(-)$1	270	116	142	15.2758
dd[a[dddd[aqqqqqqqqa]dddd]	chr11:85005241-85005530(-)$1	289	151	177	15.5369
ccdddd[ddddqqqqqqqqdddd]dd	chr10:127522380-127522662(+)$1	282	236	262	16.5057

#otherMatches

#Seq PSSM
AGCUGUUGGGUUGGCUAUUGCCCAGU	chr15:31522041-31522321(-)$1	280	48	74	13.9619
AAGAAAAUUACCCAGAUCUGUAAACU	chr17:83623476-83623763(+)$1	287	12	38	16.7762
AUGGCCGCUGUGUUUGUGGACAGGGC	chr19:5770175-5770443(-)$1	268	68	94	16.4529
CAGGCUCUGCGGAGGUUCAUGCAGAC	chr11:55302469-55302760(+)$1	291	180	206	15.1825
CUUAUUAAUGCUGAAGAACGCAGGGA	chr17:88386043-88386321(+)$1	278	157	183	14.5576
UCUUGUGUGCAUUUCCAGCUGAAAGA	chr14:121691148-121691419(-)$1	271	63	89	14.6891
GCUCCUGUGCCACAGCAAAGGCACGG	chr5:42210565-42210839(-)$1	274	41	67	16.2782
UGAACCAAUGCAAGUACUAGCGUGUA	chr2:62339207-62339477(-)$1	270	234	260	17.5153
GAAGAGGAAGCCAAACAAUGUUUCCC	chr1:163171669-163172027(-)$1	358	83	109	14.5362
AGGGAUAUUGCUAUAAAAUGGAAUGU	chr8:44736206-44736475(-)$1	269	13	39	14.3963
AUGGCUCACCUUUAGGUUUAGUGUGU	chr15:96265234-96265516(-)$1	282	245	271	14.7387
UUUAUGGCUCUGAGAAUAAAGAGUGA	chr17:64245297-64245565(+)$1	268	218	244	16.3955
GGCACGCGGCACAAGGUCUUGCUGCG	chr8:87198822-87199109(-)$1	287	159	185	16.0314
CAUGUGUAUGCACGAGAAAGCAUAUA	chr14:47938973-47939339(+)$1	366	167	193	16.3673
UAGAGAGGAAUCUAACAGUGUUUCAG	chr5:114582066-114582344(+)$1	278	241	267	16.2517
AAUCGUGUUGUGAAAGAAGACAGCAG	chr11:72951022-72951290(-)$1	268	230	256	14.2634
CCCGACGGCGUGGACCAGGGCGGCGU	chr8:82163810-82164082(+)$1	272	15	41	16.0145
CUUACUCUCAGAAACUUACCUGGAAG	chr5:138609190-138609502(-)$1	312	104	130	16.2876
AGAAUUGCUGCUGCAGAUUGCAAACA	chr4:123188092-123188372(-)$1	280	93	119	15.9728
UGGUUUCCGCUGACAAGUAAGCGGGA	chr4:116299856-116300129(-)$1	273	177	203	14.1562
GACACUAAAGAAUGGCUGAUCGAGGU	chr1:9535866-9536144(+)$1	278	191	217	14.1366
AGCCUUUGGAGCAGCAAGUUUCCACA	chr17:51921864-51922132(-)$1	268	65	91	15.3648
CAAGACCAUCAGAAGAACGUGAAUgg	chr19:60839820-60840127(-)$1	307	48	74	14.7399
UGUUCAACAUGGAGGACGACAUGCUG	chr10:90559026-90559310(+)$1	284	115	141	16.5811
CGCCcggcggcgaggacgaggaggag	chr18:75528598-75528869(+)$1	271	63	89	15.5197
CUGAGUUCCGUCUACAUUCACGUACU	chr2:84283302-84283574(-)$1	272	164	190	15.7059
GUCCCUCACAGGUUGCAGACUGGACA	chr15:77798484-77798771(-)$1	287	109	135	16.1792
CAAGCUGCGGCGACAGAAGGCCAACG	chr11:98189225-98189495(-)$1	270	204	230	15.4089
ACUUUGAGUAUACCAAAGAAUACCGG	chrX:136384131-136384403(-)$1	272	191	217	16.9249
AAAAACCAAACUCCUUUCUGUUUAGU	chr11:87794725-87795066(-)$1	341	288	314	14.3513
AGCCAUAAGUUAGAAGAAGAAUUUGA	chr9:108701514-108701781(+)$1	267	56	82	16.2800
GCGCCGUGAGCGCCAGGAGGCUCAGG	chr8:97437118-97437386(-)$1	268	235	261	16.6148
uguacacguacacguacacguacaca	chr2:154519585-154519863(+)$1	278	0	26	17.3083
UUGGUGGCGAGCAGGAGUACUUGUAC	chr14:32515061-32515366(-)$1	305	90	116	15.8134
UGGAUGACAGUCAGCAUUCAUUGUUA	chr13:74877226-74877496(-)$1	270	220	246	15.9952
UGGGAUGUUGAACUUGGUGUCACUUA	chr16:90245531-90245808(-)$1	277	74	100	15.9188
GAGUAAGUUACUCUUUCUUGUAGGUG	chr6:71363116-71363392(-)$1	276	147	173	16.5100
CCUGUGGGCCAGUGUCGUGUGGCCUG	chr5:140919140-140919421(+)$1	281	15	41	15.7872
GGCCGGCCUUCAUCCGCAAGAGGAAC	chr7:116871284-116871551(-)$1	267	195	221	16.0380
AGUCAUGACCUUGGACUAUGGGAUGG	chr15:85762627-85762895(-)$1	268	151	177	16.1993
UGCUUCUCAUGAUGACAGGUAUGAAG	chr8:89375415-89375690(-)$1	275	149	175	16.6641
UAGUGGGACCUGGUGUGUGAGGCCCG	chr19:5985471-5985739(-)$1	268	53	79	14.3263
GGUUUGGUGGACGUUAUUCUCUAUCA	chr4:135888291-135888583(+)$1	292	23	49	15.9538
GGCGGGCUCGGGAGAGGGGCCGGGCC	chr4:11249003-11249282(-)$1	279	171	197	16.0683
AGGGGGUCAAGUUACAAGUCAUGGCC	chr8:114526344-114526615(-)$1	271	171	197	15.8849
CUGCUUAAGUCCCAUGAUCGACUGCA	chr2:120339260-120339533(-)$1	273	100	126	16.2062
GGCAUCUGGCAAAGAUUUAUGCCAUG	chr4:154909396-154909687(+)$1	291	131	157	16.6692
CUGGGCAGGCUUUAGAGUUGGCCUGC	chr4:117941927-117942226(-)$1	299	168	194	16.0683
UACUACAAGGAUCAUUUUUUUUUUGU	chr16:87486565-87486840(-)$1	275	47	73	14.5875
UACAUUGAAACUUGAGUUUGUUUCUU	chr16:94913623-94913907(+)$1	284	186	212	16.2263
AUGCUGGGGUUAAGUAGGCAACCGCA	chr10:128061493-128061783(-)$1	290	16	42	15.5757
UGCACAGAUCCAGAUGGGCGGGCUGU	chr15:79117458-79117733(-)$1	275	120	146	15.8039
GCAUCAGAUGCCCCCUUGAGCACUGC	chr13:68714079-68714377(-)$1	298	216	242	15.4660
UGUCCUCUUUCCUCACUAUGAAGAAG	chr4:82493456-82493728(-)$1	272	229	255	16.1075
CUUCCACCCAAAAAGAUAAUUGGGAA	chr14:32016366-32016646(-)$1	280	84	110	16.8760
AUGAAGAGGCUUAAAGUGCAGCUCAA	chr2:90853336-90853670(+)$1	334	129	155	16.8443
GGGCUUGAGGGGUGUGGUACCCUGAG	chr2:29770728-29771012(+)$1	284	148	174	16.9984
CGCUCCGCCCGUCGCUACUCGGGCCG	chr2:73111926-73112196(+)$1	270	122	148	16.7237
ACAAAUUAGGAAAAGGGAGUCUUGUG	chr12:33533433-33533733(+)$1	300	231	257	16.7801
ACAUGGGUGUGAGGAACGGCACAGCC	chr16:93870840-93871115(+)$1	275	133	159	16.5664
GAAAGCUCAAGGAUGAGAUUUUGAGU	chr8:93743939-93744212(-)$1	273	182	208	16.2953
CCUUGCACAUGAAGCGACACAUGUAG	chr8:74844537-74844831(+)$1	294	255	281	15.5200
GUGAAUUUGUCAAAAUAACGGCAUUU	chr5:21307023-21307298(+)$1	275	172	198	16.1926
GCCAUGAGCAGAGAGGUUGCUGAGCA	chr11:61348645-61348915(-)$1	270	116	142	15.2758
CUACAGUGGACUAGAAUAUGAUUACC	chr11:85005241-85005530(-)$1	289	151	177	15.5369
GGCAAUGAUUUAUACCAUGAAAUGAU	chr10:127522380-127522662(+)$1	282	236	262	16.5057

#DB
.((..((((((........)))))).	chr15:31522041-31522321(-)$1	1	48	74	13.9619
((((...((((........))))..)	chr17:83623476-83623763(+)$1	1	12	38	16.7762
..((((.((((........)))))))	chr19:5770175-5770443(-)$1	1	68	94	16.4529
.(((.((((((........)))))))	chr11:55302469-55302760(+)$1	1	180	206	15.1825
))).)))))((........))(((((	chr17:88386043-88386321(+)$1	1	157	183	14.5576
((((.(.(.((........))..).)	chr14:121691148-121691419(-)$1	1	63	89	14.6891
.((((((((((........)))))))	chr5:42210565-42210839(-)$1	1	41	67	16.2782
((..(..((((........))))...	chr2:62339207-62339477(-)$1	1	234	260	17.5153
..((.((((((........)))))))	chr1:163171669-163172027(-)$1	1	83	109	14.5362
)))((((((.(........).)))))	chr8:44736206-44736475(-)$1	1	13	39	14.3963
(((((.(((((........)).))).	chr15:96265234-96265516(-)$1	1	245	271	14.7387
(((((.(((((........))))).)	chr17:64245297-64245565(+)$1	1	218	244	16.3955
.((.(((((((........)))))))	chr8:87198822-87199109(-)$1	1	159	185	16.0314
..(((((((((........)))))))	chr14:47938973-47939339(+)$1	1	167	193	16.3673
(.((..(((((........)))))..	chr5:114582066-114582344(+)$1	1	241	267	16.2517
.(((.((((((........)))))))	chr11:72951022-72951290(-)$1	1	230	256	14.2634
(((.(((.(((........))).)))	chr8:82163810-82164082(+)$1	1	15	41	16.0145
(((....((((........)))))))	chr5:138609190-138609502(-)$1	1	104	130	16.2876
....(((.(((........)))..))	chr4:123188092-123188372(-)$1	1	93	119	15.9728
))..(((((((........)))))))	chr4:116299856-116300129(-)$1	1	177	203	14.1562
..((((...((........))..)))	chr1:9535866-9536144(+)$1	1	191	217	14.1366
.((((((((((........)))))..	chr17:51921864-51922132(-)$1	1	65	91	15.3648
(.(..((((((........)).))))	chr19:60839820-60840127(-)$1	1	48	74	14.7399
(.((((.((((........)))).))	chr10:90559026-90559310(+)$1	1	115	141	16.5811
(((((..(..(........)..)..)	chr18:75528598-75528869(+)$1	1	63	89	15.5197
..((((..(((........))).)))	chr2:84283302-84283574(-)$1	1	164	190	15.7059
((((((..(((........)))...)	chr15:77798484-77798771(-)$1	1	109	135	16.1792
(..((.(((((........)))...)	chr11:98189225-98189495(-)$1	1	204	230	15.4089
((((...((((........))))...	chrX:136384131-136384403(-)$1	1	191	217	16.9249
...(((.((((........)))).))	chr11:87794725-87795066(-)$1	1	288	314	14.3513
(((((((((((........)))))..	chr9:108701514-108701781(+)$1	1	56	82	16.2800
.((((.(((((........))))).)	chr8:97437118-97437386(-)$1	1	235	261	16.6148
((((...((((........))))...	chr2:154519585-154519863(+)$1	1	0	26	17.3083
(((((((((((........))))).)	chr14:32515061-32515366(-)$1	1	90	116	15.8134
))))(((((((........)))))))	chr13:74877226-74877496(-)$1	1	220	246	15.9952
.((((((((((........)))...)	chr16:90245531-90245808(-)$1	1	74	100	15.9188
(((((..((((........)))).))	chr6:71363116-71363392(-)$1	1	147	173	16.5100
)((.(((((((........)))))))	chr5:140919140-140919421(+)$1	1	15	41	15.7872
.((((..((((........))))..)	chr7:116871284-116871551(-)$1	1	195	221	16.0380
..((((..(((........)))))))	chr15:85762627-85762895(-)$1	1	151	177	16.1993
.((((.(((((........))))).)	chr8:89375415-89375690(-)$1	1	149	175	16.6641
..(((((.(((........)))))))	chr19:5985471-5985739(-)$1	1	53	79	14.3263
(((((((((((........)))))))	chr4:135888291-135888583(+)$1	1	23	49	15.9538
(((((((((((........)))))))	chr4:11249003-11249282(-)$1	1	171	197	16.0683
((..(((((.(........).)))))	chr8:114526344-114526615(-)$1	1	171	197	15.8849
.(((...((((........)))))))	chr2:120339260-120339533(-)$1	1	100	126	16.2062
((((..(((((........)))))))	chr4:154909396-154909687(+)$1	1	131	157	16.6692
))(((((((((........)))))))	chr4:117941927-117942226(-)$1	1	168	194	16.0683
..(((((((((........)))))))	chr16:87486565-87486840(-)$1	1	47	73	14.5875
(((((.(((((........)))))..	chr16:94913623-94913907(+)$1	1	186	212	16.2263
).((((.((((........)))).))	chr10:128061493-128061783(-)$1	1	16	42	15.5757
(.(((((.(((........)))))))	chr15:79117458-79117733(-)$1	1	120	146	15.8039
.((((((.(((........)))))).	chr13:68714079-68714377(-)$1	1	216	242	15.4660
((((((.((((........)))).))	chr4:82493456-82493728(-)$1	1	229	255	16.1075
.(((..(((((........)))))..	chr14:32016366-32016646(-)$1	1	84	110	16.8760
(((....((((........))))...	chr2:90853336-90853670(+)$1	1	129	155	16.8443
...(((.((((........)))).))	chr2:29770728-29771012(+)$1	1	148	174	16.9984
(((...(((((........))))).)	chr2:73111926-73112196(+)$1	1	122	148	16.7237
(((...(((((........)))))))	chr12:33533433-33533733(+)$1	1	231	257	16.7801
((((((.((((........)))).))	chr16:93870840-93871115(+)$1	1	133	159	16.5664
((..(((((((........)))))))	chr8:93743939-93744212(-)$1	1	182	208	16.2953
(((.(((((((........))))).)	chr8:74844537-74844831(+)$1	1	255	281	15.5200
(((((..((((........)))))))	chr5:21307023-21307298(+)$1	1	172	198	16.1926
(((.((..(((........)))..))	chr11:61348645-61348915(-)$1	1	116	142	15.2758
((.(.((((.(........).)))).	chr11:85005241-85005530(-)$1	1	151	177	15.5369
))((((.((((........)))).))	chr10:127522380-127522662(+)$1	1	236	262	16.5057

#PSSM
d : 0.16	e : 0.13	f : 0.12	: : 0.10	" : 0.09	! : 0.07	c : 0.07	g : 0.06	b : 0.04	[ : 0.03	# : 0.03	a : 0.01	$ : 0.01	h : 0.01	% : 0.01	
d : 0.19	c : 0.16	e : 0.12	f : 0.12	b : 0.06	g : 0.06	[ : 0.06	: : 0.06	! : 0.04	" : 0.04	# : 0.03	a : 0.01	$ : 0.01	
d : 0.24	e : 0.15	c : 0.12	f : 0.12	b : 0.09	i : 0.07	! : 0.06	g : 0.04	: : 0.03	# : 0.01	a : 0.01	" : 0.01	[ : 0.01	
d : 0.19	c : 0.13	e : 0.13	! : 0.07	i : 0.07	f : 0.07	[ : 0.07	b : 0.06	# : 0.04	g : 0.04	" : 0.03	] : 0.01	: : 0.01	a : 0.01	
d : 0.15	g : 0.13	e : 0.12	" : 0.09	c : 0.09	! : 0.07	[ : 0.07	i : 0.07	f : 0.07	b : 0.06	# : 0.03	a : 0.01	
d : 0.13	f : 0.12	! : 0.12	g : 0.12	" : 0.09	[ : 0.09	c : 0.09	e : 0.07	i : 0.07	# : 0.03	b : 0.03	a : 0.01	
e : 0.25	[ : 0.13	! : 0.13	g : 0.10	f : 0.07	" : 0.07	i : 0.07	c : 0.06	# : 0.03	d : 0.03	b : 0.01	
d : 0.30	e : 0.22	g : 0.10	f : 0.07	i : 0.07	[ : 0.07	! : 0.06	a : 0.03	c : 0.01	" : 0.01	b : 0.01	
d : 0.30	e : 0.22	c : 0.18	g : 0.09	f : 0.07	i : 0.07	[ : 0.01	" : 0.01	! : 0.01	
d : 0.27	e : 0.19	c : 0.16	g : 0.09	b : 0.07	i : 0.07	f : 0.06	[ : 0.04	! : 0.01	
d : 0.27	e : 0.19	c : 0.16	g : 0.09	b : 0.07	i : 0.07	f : 0.06	a : 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	
d : 0.27	e : 0.19	c : 0.16	g : 0.09	b : 0.07	i : 0.07	f : 0.06	a : 0.06	
d : 0.27	e : 0.19	c : 0.16	g : 0.09	b : 0.07	i : 0.07	f : 0.06	] : 0.04	2 : 0.01	
d : 0.28	e : 0.22	c : 0.16	g : 0.09	f : 0.07	i : 0.07	2 : 0.04	] : 0.03	
d : 0.31	e : 0.25	g : 0.09	f : 0.07	i : 0.07	2 : 0.06	3 : 0.04	c : 0.03	] : 0.03	a : 0.01	
e : 0.25	] : 0.12	f : 0.10	d : 0.09	g : 0.09	2 : 0.07	i : 0.07	3 : 0.07	c : 0.06	4 : 0.03	a : 0.01	
d : 0.15	c : 0.15	f : 0.12	2 : 0.10	] : 0.10	g : 0.09	i : 0.07	3 : 0.07	e : 0.06	4 : 0.03	8 : 0.01	b : 0.01	
d : 0.19	c : 0.15	g : 0.12	f : 0.09	e : 0.07	i : 0.07	b : 0.07	2 : 0.07	] : 0.04	3 : 0.03	4 : 0.03	a : 0.01	8 : 0.01	

#score	1045.9294109991374
#seq	66
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_UTR_m3_run2.txt

#BEAR
dddd####ddddmmmmdddd4444dd	chr2:36107254-36107469(+)$1	215	132	158	11.5283
ggggggg[ddddmmmmddddgggggg	chr3:146645980-146646204(-)$1	224	79	105	11.0956
#dddd"""ddddmmmmdddddddd44	chr5:111214607-111214834(-)$1	227	47	73	10.7419
cccdddd!!cccmmmmcccdddd]cc	chr2:155643141-155643372(+)$1	231	18	44	10.6390
eeeee"""ddddmmmmdddd22eeee	chr8:73033645-73033872(-)$1	227	63	89	11.1105
!ffffff!!cccmmmmccc22fffff	chr11:50013973-50014221(-)$1	248	73	99	10.7056
cc[ffffffcccmmmmccc333ffff	chr6:50243406-50243627(-)$1	221	9	35	10.5509
ggggggg!!cccmmmmccc]gggggg	chr2:25098522-25098751(+)$1	229	184	210	11.8074
ddd!!bb[ddddmmmmddddbb22dd	chr11:17098834-17099052(+)$1	218	113	139	9.6780
cc[dddd[ddddmmmmdddd333ddd	chr10:126324278-126324500(-)$1	222	93	119	10.7970
)iiiiiiiii[ammmmaiiiiiiiii	chr19:9186717-9186938(-)$1	221	59	85	9.8662
fff!!a!!ddddllldddd22a333f	chr12:15798721-15798966(-)$1	245	153	179	9.8504
deeeee!!ddddmmmmdddd]eeeee	chr8:86459350-86459570(+)$1	220	147	173	10.7428
$bb!!gggggggmmmmggggggg]bb	chr11:120668684-120668901(-)$1	217	131	157	9.0347
dddd[gggggggmmmmggggggg333	chr17:46786919-46787144(+)$1	225	167	193	10.3430
dd[bb"""ddddmmmmdddd4444bb	chr18:37170433-37170675(+)$1	242	38	64	11.0442
$$$$$ddddcccmmmmccc]dddd33	chr3:36347785-36348007(+)$1	222	39	65	9.4276
dddbb####ddddllldddd333bb2	chr7:134947403-134947629(-)$1	226	144	170	8.3149
hhhhhh!!ddddmmmmdddd4444hh	chr17:25380242-25380460(+)$1	218	59	85	10.3337
ccccc"""cccnnnnncccccc]ccc	chr12:103802897-103803126(+)$1	229	160	186	8.0949
b!!a[cccddddmmmmdddd]ccc22	chr15:80762153-80762376(+)$1	223	63	89	10.8119
ggggggg!!cccmmmmccc]gggggg	chr2:32271048-32271292(-)$1	244	121	147	11.8074
hhh"""ffffffmmmmffffff4444	chr7:119260114-119260330(-)$1	216	79	105	8.9744
eeeeebb[ddddmmmmdddd]bb]ee	chr9:107950500-107950730(+)$1	230	123	149	10.0672
hhh####eeeeemmmmeeeee4444h	chr8:24216408-24216630(+)$1	222	137	163	9.5977
"ccc$$$$$ccclllccc4444ccc3	chr7:29093108-29093338(-)$1	230	60	86	9.1122
dd####bb[cccmmmmcccbb4444d	chr6:60347210-60347433(+)$1	223	167	193	10.4961
eeee"""eeeeemmmmeeeee333ee	chr18:20844760-20844987(-)$1	227	81	107	10.2176
eebb!!ccc[bbmmmmbb]ccc22bb	chr10:95004223-95004458(+)$1	235	30	56	8.8036
ggg[bb!!ddddmmmmdddd]bb]gg	chr15:10499054-10499275(-)$1	221	81	107	10.7858
fffff[ccccccmmmmccc]ccc22f	chr1:74443112-74443365(+)$1	253	184	210	10.6900
ffffff!!ddddmmmmddddffffff	chr4:42963224-42963441(+)$1	217	42	68	10.1584
:ffffff[ddddmmmmdddd]fffff	chr6:102113455-102113678(-)$1	223	191	217	9.2328
fccc[gggggggmmmmggggggg]cc	chr13:110846098-110846323(-)$1	225	136	162	10.1216
dddd####ddddllldddd22dddd2	chr11:97258671-97258901(+)$1	230	190	216	8.4357
eeeee[ccc[bbmmmmbb]ccc]eee	chr9:79662735-79662958(+)$1	223	10	36	9.4390
a[ddddccc[bbmmmmbbccc]dddd	chr2:31939028-31939265(-)$1	237	190	216	8.7208
dd[eeeeea[bbmmmmbb]a]eeeee	chr8:46743938-46744159(+)$1	221	37	63	8.7572
a[ggggggg[bbmmmmbb22gggggg	chr2:157386934-157387152(-)$1	218	56	82	9.5584
[eeeee[eeeeemmmmeeeeeeeeee	chr7:56862344-56862573(+)$1	229	166	192	8.6435
eeeee####cccmmmmccc666666e	chr8:126894049-126894284(-)$1	235	109	135	9.5243
ffff[ccc[cccmmmmccc]ccc22f	chr3:9283629-9283847(+)$1	218	108	134	11.0664
fffeeeee[cccmmmmccceeeee66	chr16:4615692-4615925(+)$1	233	17	43	9.1307
:ggggggg[cccmmmmccc]gggggg	chr16:16927224-16927444(+)$1	220	4	30	10.5040
ffffdddd[cccmmmmccc]ddddee	chr18:10567288-10567517(-)$1	229	144	170	9.6561
[ccc[ccc[ccclllccc]cccccc]	chr3:144799794-144800012(-)$1	218	180	206	9.0321
eeee[aa!!cccmmmmccc22a]a]e	chr11:69756448-69756670(+)$1	222	47	73	11.9523
a####bb[ddddmmmmddddbb4444	chr5:145317211-145317449(+)$1	238	163	189	10.4602
iiiiiii"""bbmmmmbb333iiiii	chr2:126568302-126568524(-)$1	222	113	139	10.8774
ccc"""ffffffmmmmffffffccc]	chr3:126865071-126865296(-)$1	225	124	150	9.0559
$$ccc!!a[cccmmmmccc]a22ccc	chr10:80329994-80330217(+)$1	223	22	48	10.9761
!eeeee"""cccmmmmccceeeee22	chr11:3549462-3549681(+)$1	219	33	59	10.9182
cc!!ccc"""bblllbbccc]ccc]g	chr2:153229592-153229818(+)$1	226	86	112	8.6707
=============lll==========	chr10:80614137-80614357(+)$1	220	61	87	9.1896
:===========mmmm==========	chr1:58959388-58959623(-)$1	235	184	210	10.2184
fcccccc!!bbmmmmbbccc]ccc]f	chr3:152448808-152449033(+)$1	225	152	178	8.6606
eeebb"""ddddmmmmdddd22bbHH	chr8:97848721-97848943(+)$1	222	159	185	9.0106
gggggccc!!bbmmmmbb333ccc]g	chr11:69592496-69592731(+)$1	235	98	124	10.7039
b:cccccc[cccmmmmccc22ccc]c	chr10:79493694-79493916(-)$1	222	164	190	10.0515
ee"""ddddcccmmmmccc]dddd44	chr8:109580089-109580307(+)$1	218	136	162	10.4113

#otherMatches

#Seq PSSM
CCUCAAUUUUCUUCCUAGAAUUUGGA	chr2:36107254-36107469(+)$1	215	132	158	11.5283
AAAGCAAUGUGAGGAAUCAUUUGCUU	chr3:146645980-146646204(-)$1	224	79	105	11.0956
AAGGGUAUGGUCUUCUGGCCCCCUGU	chr5:111214607-111214834(-)$1	227	47	73	10.7419
CUCUGCCAAACCCAACGGUGGUAUGA	chr2:155643141-155643372(+)$1	231	18	44	10.6390
AGGGCAUAGUUGAGUCCAGCCGGCCC	chr8:73033645-73033872(-)$1	227	63	89	11.1105
AGUGCAUGAGGAGAGUUUUGAAUGUG	chr11:50013973-50014221(-)$1	248	73	99	10.7056
AGUGCAAGCCAGUUUUUUGUUUGCUU	chr6:50243406-50243627(-)$1	221	9	35	10.5509
UGGUCCUCACCAGGCCUGGCAGGACC	chr2:25098522-25098751(+)$1	229	184	210	11.8074
GACUGUGUCUUAUUGCUGAGCAGCGU	chr11:17098834-17099052(+)$1	218	113	139	9.6780
ACGGCAGAAAGGAACUCCUUAAACUG	chr10:126324278-126324500(-)$1	222	93	119	10.7970
CAGCCCCAGUUGUCCUCAUUGGGGCU	chr19:9186717-9186938(-)$1	221	59	85	9.8662
CUUCCCCACUGAUAAUCAGGAGACCA	chr12:15798721-15798966(-)$1	245	153	179	9.8504
CUCAAGCCUGACUCUAGUCGCCUUGA	chr8:86459350-86459570(+)$1	220	147	173	10.7428
AGAUUUCUGGGAAAGUUUCUAGACUC	chr11:120668684-120668901(-)$1	217	131	157	9.0347
UACUACCUUUUCACUUGGGAGGGCGC	chr17:46786919-46787144(+)$1	225	167	193	10.3430
UCAGCGAAGAGAGACAUUUUGGAGGC	chr18:37170433-37170675(+)$1	242	38	64	11.0442
AAACACAAACCUACACAGGAUUUGGA	chr3:36347785-36348007(+)$1	222	39	65	9.4276
CCCCUGAACCCCAUCCUGGGCCGAGU	chr7:134947403-134947629(-)$1	226	144	170	8.3149
GUGGGGGCGCCCACUAGGGUCAAGUC	chr17:25380242-25380460(+)$1	218	59	85	10.3337
GUCAGCACAGAUUCCUUCUCUGAACA	chr12:103802897-103803126(+)$1	229	160	186	8.0949
GUUCUGGUUUGUUCCUGCAACACCUU	chr15:80762153-80762376(+)$1	223	63	89	10.8119
GCUGCAGCAUCCAUGCGGACCUGUGG	chr2:32271048-32271292(-)$1	244	121	147	11.8074
UUAUAUAUUUAAAAAGUUAGGUUAAU	chr7:119260114-119260330(-)$1	216	79	105	8.9744
GUGGGCCGUGCAGUGGUGUGGGGAUU	chr9:107950500-107950730(+)$1	230	123	149	10.0672
GUUCCAGUGGCAGACGUGCUGAUCAA	chr8:24216408-24216630(+)$1	222	137	163	9.5977
CGAGCCCACCAGUCCCUGCCUUCUCC	chr7:29093108-29093338(-)$1	230	60	86	9.1122
AUCAAGGCUCCUAUUUAGGGCAUACA	chr6:60347210-60347433(+)$1	223	167	193	10.4961
UGAGACAGGGCUCUUUGGCCCCUCCU	chr18:20844760-20844987(-)$1	227	81	107	10.2176
GGCCUGUUACCUUCAUAGAUAAGUGG	chr10:95004223-95004458(+)$1	235	30	56	8.8036
CCAUCUGAGGCCACGUGGCUGAGUUG	chr15:10499054-10499275(-)$1	221	81	107	10.7858
CCUCCUCCAUGGCCCCCCGCUGGCUG	chr1:74443112-74443365(+)$1	253	184	210	10.6900
UGGGGAUUGGGCUUGGGUCCUCCCCA	chr4:42963224-42963441(+)$1	217	42	68	10.1584
UAUAGUUUUCUUUUACAAGAUGGCUA	chr6:102113455-102113678(-)$1	223	191	217	9.2328
UUCACCUUUUCUCCUCAGAAAAGUUG	chr13:110846098-110846323(-)$1	225	136	162	10.1216
GGGUCCCUGGAGUCGCUCCCUGCCCC	chr11:97258671-97258901(+)$1	230	190	216	8.4357
UAAUUCUGAUUCUAGUGGUUCAAAGU	chr9:79662735-79662958(+)$1	223	10	36	9.4390
GGAGCCCUGCGCGGCAGUCAGCGGCU	chr2:31939028-31939265(-)$1	237	190	216	8.7208
CCUCCCCCCCCCCCAUGGAGUGGGGG	chr8:46743938-46744159(+)$1	221	37	63	8.7572
GGAGCUUUUCCAACUGUGCUGAGAGC	chr2:157386934-157387152(-)$1	218	56	82	9.5584
AUGGAAAUUUUAAACGUAAGAUUCCA	chr7:56862344-56862573(+)$1	229	166	192	8.6435
GUUCAGACCAGGCAAGCUUACAAAAU	chr8:126894049-126894284(-)$1	235	109	135	9.5243
CUUCAGGAAGUUGAUAAAUCUCUAAG	chr3:9283629-9283847(+)$1	218	108	134	11.0664
UAGACCAGGCUCAGAAGGGCUGGUUA	chr16:4615692-4615925(+)$1	233	17	43	9.1307
UGGAGUCUUGUGCUUUCACUGGACUC	chr16:16927224-16927444(+)$1	220	4	30	10.5040
UUGUUCCAUUUUCAUAAAAUUGGAAA	chr18:10567288-10567517(-)$1	229	144	170	9.6561
ACCUUCAUAAUACAAUAUCAUGAGGA	chr3:144799794-144800012(-)$1	218	180	206	9.0321
UGGGAGGAAAGCACUCGCUCACACAC	chr11:69756448-69756670(+)$1	222	47	73	11.9523
CUAAUGCAGGCUGUGUGGCCGCCCUU	chr5:145317211-145317449(+)$1	238	163	189	10.4602
UGCAUUCAGCUCUCCUGACACGGAUG	chr2:126568302-126568524(-)$1	222	113	139	10.8774
GGCUCCGGUCUGAAGACAGACUGUCU	chr3:126865071-126865296(-)$1	225	124	150	9.0559
CUGGCUCUGGGUGGUUGCUGAAUGCC	chr10:80329994-80330217(+)$1	223	22	48	10.9761
AGUUCCAAUUCCACGGGGAGGGACAA	chr11:3549462-3549681(+)$1	219	33	59	10.9182
GCUCAGAAAAGCGCUGCUCUUGUAUG	chr2:153229592-153229818(+)$1	226	86	112	8.6707
CCUGAGGGUGCUCGGUGGGUGCCCUU	chr10:80614137-80614357(+)$1	220	61	87	9.1896
aGAAAAGUUAGUUGUAACUAACUUUU	chr1:58959388-58959623(-)$1	235	184	210	10.2184
gacuuggaugcacuugccuacagucc	chr3:152448808-152449033(+)$1	225	152	178	8.6606
GGUUGGAGAUGACAUUUCAUGACAGU	chr8:97848721-97848943(+)$1	222	159	185	9.0106
GAGGGGAUGGGGACUGCCAAAGUCAC	chr11:69592496-69592731(+)$1	235	98	124	10.7039
UGAUCUGCCCUCCUCGGAGCCGCAUG	chr10:79493694-79493916(-)$1	222	164	190	10.0515
GAAGAGCCGGUGGAUGCGCUCGGUGC	chr8:109580089-109580307(+)$1	218	136	162	10.4113

#DB
((((....((((....))))....))	chr2:36107254-36107469(+)$1	1	132	158	11.5283
(((((((.((((....))))))))))	chr3:146645980-146646204(-)$1	1	79	105	11.0956
.((((...((((....))))))))..	chr5:111214607-111214834(-)$1	1	47	73	10.7419
(((((((..(((....))))))).))	chr2:155643141-155643372(+)$1	1	18	44	10.6390
(((((...((((....))))..))))	chr8:73033645-73033872(-)$1	1	63	89	11.1105
.((((((..(((....)))..)))))	chr11:50013973-50014221(-)$1	1	73	99	10.7056
((.(((((((((....)))...))))	chr6:50243406-50243627(-)$1	1	9	35	10.5509
(((((((..(((....))).))))))	chr2:25098522-25098751(+)$1	1	184	210	11.8074
(((..((.((((....))))))..))	chr11:17098834-17099052(+)$1	1	113	139	9.6780
((.((((.((((....))))...)))	chr10:126324278-126324500(-)$1	1	93	119	10.7970
.(((((((((.(....))))))))))	chr19:9186717-9186938(-)$1	1	59	85	9.8662
(((..(..((((...))))..)...)	chr12:15798721-15798966(-)$1	1	153	179	9.8504
)(((((..((((....)))).)))))	chr8:86459350-86459570(+)$1	1	147	173	10.7428
.((..(((((((....))))))).))	chr11:120668684-120668901(-)$1	1	131	157	9.0347
((((.(((((((....)))))))...	chr17:46786919-46787144(+)$1	1	167	193	10.3430
((.((...((((....))))....))	chr18:37170433-37170675(+)$1	1	38	64	11.0442
.....(((((((....))).))))..	chr3:36347785-36348007(+)$1	1	39	65	9.4276
(((((....((((...))))...)).	chr7:134947403-134947629(-)$1	1	144	170	8.3149
((((((..((((....))))....))	chr17:25380242-25380460(+)$1	1	59	85	10.3337
(((((...(((.....)))))).)))	chr12:103802897-103803126(+)$1	1	160	186	8.0949
(..(.(((((((....)))).)))..	chr15:80762153-80762376(+)$1	1	63	89	10.8119
(((((((..(((....))).))))))	chr2:32271048-32271292(-)$1	1	121	147	11.8074
(((...((((((....))))))....	chr7:119260114-119260330(-)$1	1	79	105	8.9744
(((((((.((((....)))).)).))	chr9:107950500-107950730(+)$1	1	123	149	10.0672
(((....(((((....)))))....)	chr8:24216408-24216630(+)$1	1	137	163	9.5977
.(((.....(((...)))....))).	chr7:29093108-29093338(-)$1	1	60	86	9.1122
((....((.(((....)))))....)	chr6:60347210-60347433(+)$1	1	167	193	10.4961
((((...(((((....)))))...))	chr18:20844760-20844987(-)$1	1	81	107	10.2176
((((..(((.((....)).)))..))	chr10:95004223-95004458(+)$1	1	30	56	8.8036
(((.((..((((....)))).)).))	chr15:10499054-10499275(-)$1	1	81	107	10.7858
(((((.((((((....))).)))..)	chr1:74443112-74443365(+)$1	1	184	210	10.6900
((((((..((((....))))))))))	chr4:42963224-42963441(+)$1	1	42	68	10.1584
.((((((.((((....)))).)))))	chr6:102113455-102113678(-)$1	1	191	217	9.2328
((((.(((((((....))))))).))	chr13:110846098-110846323(-)$1	1	136	162	10.1216
((((....((((...))))..)))).	chr11:97258671-97258901(+)$1	1	190	216	8.4357
(((((.(((.((....)).))).)))	chr9:79662735-79662958(+)$1	1	10	36	9.4390
(.(((((((.((....))))).))))	chr2:31939028-31939265(-)$1	1	190	216	8.7208
((.((((((.((....)).).)))))	chr8:46743938-46744159(+)$1	1	37	63	8.7572
(.(((((((.((....))..))))))	chr2:157386934-157387152(-)$1	1	56	82	9.5584
.(((((.(((((....))))))))))	chr7:56862344-56862573(+)$1	1	166	192	8.6435
(((((....(((....)))......)	chr8:126894049-126894284(-)$1	1	109	135	9.5243
((((.(((.(((....))).)))..)	chr3:9283629-9283847(+)$1	1	108	134	11.0664
((((((((.(((....))))))))..	chr16:4615692-4615925(+)$1	1	17	43	9.1307
.(((((((.(((....))).))))))	chr16:16927224-16927444(+)$1	1	4	30	10.5040
))))((((.(((....))).))))((	chr18:10567288-10567517(-)$1	1	144	170	9.6561
.(((.(((.(((...))).)))))).	chr3:144799794-144800012(-)$1	1	180	206	9.0321
((((.((..(((....)))..).).)	chr11:69756448-69756670(+)$1	1	47	73	11.9523
(....((.((((....))))))....	chr5:145317211-145317449(+)$1	1	163	189	10.4602
(((((((...((....))...)))))	chr2:126568302-126568524(-)$1	1	113	139	10.8774
(((...((((((....))))))))).	chr3:126865071-126865296(-)$1	1	124	150	9.0559
..(((..(.(((....))).)..)))	chr10:80329994-80330217(+)$1	1	22	48	10.9761
.(((((...(((....))))))))..	chr11:3549462-3549681(+)$1	1	33	59	10.9182
((..(((...((...))))).))).)	chr2:153229592-153229818(+)$1	1	86	112	8.6707
(((((((((((((...))))))))))	chr10:80614137-80614357(+)$1	1	61	87	9.1896
.(((((((((((....))))))))))	chr1:58959388-58959623(-)$1	1	184	210	10.2184
(((((((..((....))))).))).)	chr3:152448808-152449033(+)$1	1	152	178	8.6606
)))((...((((....))))..))))	chr8:97848721-97848943(+)$1	1	159	185	9.0106
((((((((..((....))...))).)	chr11:69592496-69592731(+)$1	1	98	124	10.7039
).((((((.(((....)))..))).)	chr10:79493694-79493916(-)$1	1	164	190	10.0515
((...(((((((....))).))))..	chr8:109580089-109580307(+)$1	1	136	162	10.4113

#PSSM
d : 0.15	e : 0.15	f : 0.13	c : 0.09	g : 0.08	$ : 0.05	h : 0.05	: : 0.05	a : 0.05	! : 0.03	b : 0.03	[ : 0.03	# : 0.01	) : 0.01	" : 0.01	i : 0.01	= : 0.01	
e : 0.19	c : 0.16	d : 0.15	f : 0.13	g : 0.09	h : 0.05	i : 0.03	$ : 0.03	[ : 0.03	= : 0.03	b : 0.01	! : 0.01	# : 0.01	: : 0.01	
e : 0.16	c : 0.15	f : 0.13	d : 0.11	g : 0.11	[ : 0.06	h : 0.05	i : 0.03	b : 0.03	! : 0.03	# : 0.03	= : 0.03	$ : 0.01	" : 0.01	
e : 0.18	d : 0.11	f : 0.11	c : 0.11	g : 0.09	! : 0.06	b : 0.06	" : 0.05	# : 0.05	i : 0.03	= : 0.03	$ : 0.01	h : 0.01	a : 0.01	[ : 0.01	
e : 0.15	g : 0.09	[ : 0.09	# : 0.08	d : 0.08	f : 0.08	c : 0.08	! : 0.06	b : 0.06	" : 0.06	i : 0.03	$ : 0.03	= : 0.03	h : 0.01	
g : 0.13	" : 0.13	c : 0.11	# : 0.09	d : 0.09	e : 0.08	f : 0.06	b : 0.06	i : 0.03	a : 0.03	! : 0.03	[ : 0.03	= : 0.03	h : 0.01	$ : 0.01	
c : 0.18	g : 0.13	" : 0.11	! : 0.09	# : 0.08	d : 0.08	f : 0.08	b : 0.06	i : 0.03	e : 0.03	= : 0.03	$ : 0.01	[ : 0.01	a : 0.01	
! : 0.18	c : 0.15	" : 0.13	[ : 0.09	g : 0.08	e : 0.08	# : 0.06	f : 0.05	d : 0.05	= : 0.03	i : 0.01	$ : 0.01	b : 0.01	a : 0.01	
d : 0.33	[ : 0.13	! : 0.11	c : 0.08	g : 0.06	f : 0.05	e : 0.05	" : 0.05	# : 0.03	= : 0.03	i : 0.01	$ : 0.01	a : 0.01	
c : 0.35	d : 0.31	[ : 0.08	g : 0.05	e : 0.05	f : 0.03	" : 0.03	= : 0.03	i : 0.01	b : 0.01	! : 0.01	
c : 0.35	d : 0.31	b : 0.15	g : 0.05	e : 0.05	f : 0.03	= : 0.03	[ : 0.01	
c : 0.33	d : 0.31	b : 0.13	g : 0.05	e : 0.05	f : 0.03	= : 0.03	a : 0.01	n : 0.01	m : 0.01	
m : 0.86	l : 0.08	d : 0.01	n : 0.01	= : 0.01	
m : 0.86	l : 0.11	n : 0.01	
m : 0.86	l : 0.11	n : 0.01	
m : 0.85	d : 0.03	l : 0.03	c : 0.03	b : 0.03	n : 0.01	
c : 0.35	d : 0.31	b : 0.15	g : 0.05	e : 0.05	f : 0.03	= : 0.03	a : 0.01	
c : 0.38	d : 0.31	b : 0.11	g : 0.05	e : 0.05	f : 0.03	= : 0.03	i : 0.01	
c : 0.36	d : 0.31	] : 0.06	g : 0.05	e : 0.05	f : 0.03	3 : 0.03	= : 0.03	i : 0.01	4 : 0.01	2 : 0.01	
d : 0.30	] : 0.15	c : 0.11	2 : 0.09	e : 0.08	3 : 0.05	g : 0.05	f : 0.03	= : 0.03	i : 0.01	4 : 0.01	b : 0.01	a : 0.01	6 : 0.01	
g : 0.13	] : 0.13	2 : 0.11	c : 0.11	d : 0.08	3 : 0.08	e : 0.08	4 : 0.06	b : 0.05	f : 0.05	= : 0.03	i : 0.01	6 : 0.01	a : 0.01	
c : 0.18	g : 0.13	4 : 0.09	d : 0.09	f : 0.08	e : 0.08	3 : 0.06	b : 0.06	2 : 0.05	i : 0.03	a : 0.03	= : 0.03	] : 0.01	6 : 0.01	
c : 0.16	g : 0.13	4 : 0.11	d : 0.11	e : 0.09	f : 0.06	3 : 0.06	2 : 0.05	] : 0.05	b : 0.05	i : 0.03	= : 0.03	6 : 0.01	
c : 0.16	4 : 0.11	d : 0.11	e : 0.11	g : 0.08	] : 0.08	f : 0.06	2 : 0.06	3 : 0.05	i : 0.03	b : 0.03	= : 0.03	6 : 0.01	a : 0.01	
e : 0.13	c : 0.11	g : 0.09	4 : 0.09	d : 0.08	] : 0.08	f : 0.06	b : 0.06	2 : 0.06	3 : 0.05	i : 0.03	6 : 0.03	= : 0.03	h : 0.01	H : 0.01	
e : 0.16	g : 0.13	f : 0.13	d : 0.08	c : 0.08	4 : 0.06	2 : 0.06	b : 0.05	3 : 0.05	i : 0.03	h : 0.03	] : 0.03	= : 0.03	6 : 0.01	H : 0.01	

#score	600.2113496155254
#seq	60
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_CDS_m2_run2.txt

#BEAR
dddd[bbqqqqqqqqbbdddd	chr6:111445780-111446114(+)$1	334	234	255	13.2904
gggggggqqqqqqqqgggggg	chr3:33712932-33713313(+)$1	381	71	92	15.6557
ggeeeeeqqqqqqqqeeeee:	chr5:8144073-8144460(-)$1	387	35	56	13.4543
gggggggqqqqqqqqgggggg	chr6:73213895-73214266(+)$1	371	138	159	15.6557
g[ccc[aqqqqqqqqaccc22	chrX:12733486-12733774(+)$1	288	199	220	14.9448
fffbb[aqqqqqqqqa]bb]f	chr16:28372732-28373173(-)$1	441	367	388	13.5507
ffff!!aqqqqqqqqa22fff	chr8:96677724-96678057(+)$1	333	2	23	14.1691
####cccqqqqqqqqccceee	chr11:53093804-53094141(-)$1	337	245	266	14.8082
c[eeeeeqqqqqqqqeeeee]	chr6:72269087-72269490(-)$1	403	159	180	14.5060
ee[ddddqqqqqqqqdddd22	chrX:133365526-133365801(+)$1	275	198	219	13.5287
fff[cccqqqqqqqqccc]ff	chr5:68039676-68039899(-)$1	223	128	149	15.2656
&&eeeeeqqqqqqqqeeeee4	chr15:95071752-95072172(-)$1	420	253	274	12.7833
c[eeeeeqqqqqqqqeeeee]	chr5:133017569-133017874(-)$1	305	260	281	14.5060
[ffffffqqqqqqqqffffff	chr17:47067317-47067664(-)$1	347	85	106	14.2396
ccc!!bbqqqqqqqqbb22cc	chr2:148700823-148701129(-)$1	306	76	97	14.1763
a[eeeeeqqqqqqqqeeeeea	chr13:8852697-8852984(-)$1	287	78	99	14.3763
:ffffffqqqqqqqqffffff	chr8:40130698-40131025(+)$1	327	29	50	13.2412
gggggggqqqqqqqqgggggg	chr11:109522564-109522950(+)$1	386	156	177	15.6557
gggddddqqqqqqqqdddd]g	chr9:80148341-80148630(+)$1	289	169	190	14.4306
cc[bb[aqqqqqqqqabbccc	chr3:33708169-33708451(+)$1	282	119	140	14.1263
gg!!cccqqqqqqqqccc]gg	chr3:40583180-40583659(+)$1	479	302	323	15.8600
ccc[cccqqqqqqqqccc]cc	chr5:145653792-145654141(-)$1	349	133	154	15.6062
[ccccccqqqqqqqqccc]cc	chr11:69418680-69419127(-)$1	447	116	137	15.4192
ccc[cccqqqqqqqqccc]cc	chr8:13370985-13371453(+)$1	468	355	376	15.6062
!ffffffqqqqqqqqffffff	chr2:5812064-5812507(-)$1	443	212	233	14.2558
gggggggqqqqqqqqgggggg	chr17:33806746-33807199(-)$1	453	325	346	15.6557
a[eeeeeqqqqqqqqeeeee]	chr6:36693312-36693583(-)$1	271	102	123	14.4563
gggggggqqqqqqqqgggggg	chr4:134481586-134482049(+)$1	463	56	77	15.6557
iiiiiiiqqqqqqqqiiiiii	chr10:127029065-127029552(-)$1	487	67	88	15.4398
ddd[cccqqqqqqqqccc]dd	chr1:182878911-182879275(+)$1	364	40	61	14.7417
gggggggqqqqqqqqgggggg	chr6:145812638-145813010(-)$1	372	104	125	15.6557
hhhhhhhqqqqqqqqhhhhhh	chr5:90651026-90651450(-)$1	424	308	329	13.9456
$$$ddddqqqqqqqqddddcc	chr4:117225471-117225810(+)$1	339	81	102	13.2825
gggggggqqqqqqqqgggggg	chr11:121323012-121323332(+)$1	320	176	197	15.6557
b[a[cccqqqqqqqqccc]ab	chr13:97425745-97426051(-)$1	306	97	118	15.0062
=======qqqqqqqq======	chr18:36957489-36957940(+)$1	451	26	47	15.3807
ffff[bbqqqqqqqqbb]fff	chr18:40367294-40367581(-)$1	287	110	131	13.9571
gggggggqqqqqqqqgggggg	chr6:110653200-110653642(+)$1	442	245	266	15.6557
'ffffffqqqqqqqqffffff	chr17:17976503-17976850(+)$1	347	220	241	13.5429
cc[ddddqqqqqqqqdddd]c	chr2:30163075-30163479(+)$1	404	201	222	14.3122
hhhhh[aqqqqqqqqahhhhh	chr4:11892567-11892950(-)$1	383	130	151	14.4139
bb!!cccqqqqqqqqccc22b	chr4:24825713-24826196(+)$1	483	231	252	14.3597
eee[cccqqqqqqqqccceee	chr4:58831798-58832237(-)$1	439	135	156	15.0528
hhaddddqqqqqqqqdddd]a	chr4:87800488-87800910(+)$1	422	272	293	13.8446
cc[ddddqqqqqqqqddddcc	chr1:181675201-181675689(-)$1	488	441	462	14.2562
eee!!bbqqqqqqqqbb22ee	chr17:34740314-34740611(-)$1	297	239	260	13.7444
hhhh!!aqqqqqqqqa22hhh	chr9:59525866-59526083(+)$1	217	82	103	14.0712
gggggggqqqqqqqqgggggg	chr5:151599159-151599372(+)$1	213	19	40	15.6557
hhhhh[aqqqqqqqqa]hhhh	chr12:107050482-107050834(+)$1	352	238	259	14.4284
dddd[bbqqqqqqqqbbdddd	chr8:75216954-75217272(+)$1	318	179	200	13.2904
ddd[cccqqqqqqqqcccddd	chr16:18077703-18077995(-)$1	292	7	28	14.5365
eeee[bbqqqqqqqqbb]eee	chr11:100879794-100880019(+)$1	225	27	48	13.9459
gggggggqqqqqqqqgggggg	chr11:121103761-121103997(+)$1	236	131	152	15.6557
ddd[a[aqqqqqqqqa]a]dd	chr5:68238185-68238514(-)$1	329	215	236	14.3878
!ffffffqqqqqqqqffffff	chr1:166368154-166368590(-)$1	436	71	92	14.2558
ggggg[aqqqqqqqqaggggg	chr12:68321761-68322236(-)$1	475	95	116	15.7658
iiii[bbqqqqqqqqbb]iii	chr15:100225326-100225762(-)$1	436	359	380	14.7364
e[ccc[aqqqqqqqqa]ccce	chr17:86568130-86568477(+)$1	347	286	307	14.9841
hhhhhhhqqqqqqqqhhhhhh	chrX:12192836-12193290(+)$1	454	344	365	13.9456
ggeeeeeqqqqqqqqeeeee3	chr18:65363477-65363768(+)$1	291	218	239	14.4612
eee[cccqqqqqqqqccceee	chr10:98431342-98431688(+)$1	346	214	235	15.0528
:ffffffqqqqqqqqffffff	chr10:83073831-83074266(-)$1	435	308	329	13.2412
cc!!cccqqqqqqqqccc22c	chr2:102621550-102622048(+)$1	498	34	55	15.2013
####cccqqqqqqqqccc22b	chr9:72860606-72860915(+)$1	309	35	56	14.3360
cccddddqqqqqqqqdddd]c	chr11:92961241-92961729(+)$1	488	310	331	14.2102
iiiiiiiqqqqqqqqiiiiii	chr5:51944889-51945222(-)$1	333	22	43	15.4398
Bffffffqqqqqqqqffffff	chr11:88702491-88702906(-)$1	415	198	219	13.2488
hhhhhhhqqqqqqqqhhhhhh	chr1:160432378-160432585(+)$1	207	26	47	13.9456
gggggggqqqqqqqqgggggg	chr12:71373350-71373847(-)$1	497	207	228	15.6557
f!!ddddqqqqqqqqddddff	chr9:66692859-66693241(-)$1	382	288	309	14.0466
ccc[cccqqqqqqqqccc]cc	chr8:63401766-63402065(-)$1	299	93	114	15.6062
bbeeeeeqqqqqqqqeeeee]	chr2:164824421-164824905(+)$1	484	441	462	13.8523
:ccc[bbqqqqqqqqbb]ccc	chr1:78702871-78703163(+)$1	292	0	21	13.3838

#otherMatches

#Seq PSSM
UUUACUCUUGACUUUGAUGAA	chr6:111445780-111446114(+)$1	334	234	255	13.2904
GCUGCAGGCGGCUUGCUGUAG	chr3:33712932-33713313(+)$1	381	71	92	15.6557
AUUCCUUCUUUACCUGGGGAA	chr5:8144073-8144460(-)$1	387	35	56	13.4543
GAAGUCAGAAGGCUAUGGCUU	chr6:73213895-73214266(+)$1	371	138	159	15.6557
AAGAUACAUAUCAGAGAUUGC	chrX:12733486-12733774(+)$1	288	199	220	14.9448
CAACUUCUAGAUAAUGCAGUU	chr16:28372732-28373173(-)$1	441	367	388	13.5507
GAUGGAGACAGAUGCCGACAU	chr8:96677724-96678057(+)$1	333	2	23	14.1691
AACAUGUUAAAAAUUACAAGC	chr11:53093804-53094141(-)$1	337	245	266	14.8082
AGACUGGCGUGUGUAUCGGUG	chr6:72269087-72269490(-)$1	403	159	180	14.5060
CACUGGUACAGAAAAGCUAAU	chrX:133365526-133365801(+)$1	275	198	219	13.5287
GGACAUGGGUAAGAACAUCUC	chr5:68039676-68039899(-)$1	223	128	149	15.2656
AUGUGCCCUGUGUCUGGUGCU	chr15:95071752-95072172(-)$1	420	253	274	12.7833
GGGCCGGGUUAGGAACCGGUG	chr5:133017569-133017874(-)$1	305	260	281	14.5060
guguguguguguguguAUACA	chr17:47067317-47067664(-)$1	347	85	106	14.2396
GCGACCCCAAAACAAGGCCCG	chr2:148700823-148701129(-)$1	306	76	97	14.1763
GCACUGGCUCUGGAACCAGUC	chr13:8852697-8852984(-)$1	287	78	99	14.3763
CCAAGAGAGCUGAUACUUUUG	chr8:40130698-40131025(+)$1	327	29	50	13.2412
uguguauuuguguaugugcac	chr11:109522564-109522950(+)$1	386	156	177	15.6557
AGUACGUAUGAAUGCAUGUAG	chr9:80148341-80148630(+)$1	289	169	190	14.4306
ACAUGAGCAAAGAUACCAGUU	chr3:33708169-33708451(+)$1	282	119	140	14.1263
UGCUGCUCCCUCCUCAGCUCA	chr3:40583180-40583659(+)$1	479	302	323	15.8600
GGCCUCUUUAUAAUUGGAUGC	chr5:145653792-145654141(-)$1	349	133	154	15.6062
GCAGCAGCUGUAUAUCUGACU	chr11:69418680-69419127(-)$1	447	116	137	15.4192
UGUGUCUGCAGGUAGAGAGGC	chr8:13370985-13371453(+)$1	468	355	376	15.6062
AGGUUUUGAUUAGUAAGAAUU	chr2:5812064-5812507(-)$1	443	212	233	14.2558
GGGGCUUGCAAACAGGAGUCC	chr17:33806746-33807199(-)$1	453	325	346	15.6557
UGACUGUGGAGAAUGGCAGUG	chr6:36693312-36693583(-)$1	271	102	123	14.4563
CUGUGCUCAGCAUACAGUAUA	chr4:134481586-134482049(+)$1	463	56	77	15.6557
uaugcauguguaucugugugu	chr10:127029065-127029552(-)$1	487	67	88	15.4398
CCUGGUGUUUUCCAUCAUAAG	chr1:182878911-182879275(+)$1	364	40	61	14.7417
GGGGAGCUGAGCAGCGCUUCC	chr6:145812638-145813010(-)$1	372	104	125	15.6557
GUUUUAUGUAUUGGAAUGGAA	chr5:90651026-90651450(-)$1	424	308	329	13.9456
AAAUGUGUGUCUGUCCACAGC	chr4:117225471-117225810(+)$1	339	81	102	13.2825
UACAUACUGgugugugugugu	chr11:121323012-121323332(+)$1	320	176	197	15.6557
GCUGUGAGAAUGUGAUCGGAU	chr13:97425745-97426051(-)$1	306	97	118	15.0062
UCUUCCUUAUCCUUCAGGAGG	chr18:36957489-36957940(+)$1	451	26	47	15.3807
UUAGGAAUGUUUUGUUUGUUA	chr18:40367294-40367581(-)$1	287	110	131	13.9571
AGAACCACAAUGCCAUGGUUC	chr6:110653200-110653642(+)$1	442	245	266	15.6557
guuuuguuuuuuguuacaggg	chr17:17976503-17976850(+)$1	347	220	241	13.5429
AUGAACUGUCUAUGGAGUUGG	chr2:30163075-30163479(+)$1	404	201	222	14.3122
UGUCGGCUCCGUGUUGUGAUG	chr4:11892567-11892950(-)$1	383	130	151	14.4139
uguguguAGAGGGGAGCAGUC	chr4:24825713-24826196(+)$1	483	231	252	14.3597
CAGCUGGCCAGAGAACCAUUG	chr4:58831798-58832237(-)$1	439	135	156	15.0528
ACCUGUGGGAAuguguacaug	chr4:87800488-87800910(+)$1	422	272	293	13.8446
GGUCAGUCCAUGCUCAUUGCC	chr1:181675201-181675689(-)$1	488	441	462	14.2562
GCGAGCGGGGCGGGGCGAGCG	chr17:34740314-34740611(-)$1	297	239	260	13.7444
UCUUCCCUGUGCUGUGUAAGG	chr9:59525866-59526083(+)$1	217	82	103	14.0712
UGAAGAUUAUACAAUGUCUUC	chr5:151599159-151599372(+)$1	213	19	40	15.6557
UUCUUGAUUAUGUAUUGGAGA	chr12:107050482-107050834(+)$1	352	238	259	14.4284
GGGUAGGGAAcagcaccacuu	chr8:75216954-75217272(+)$1	318	179	200	13.2904
CUGUGCUCUCAGACUGGCCAG	chr16:18077703-18077995(-)$1	292	7	28	14.5365
ACACAGAAUGUAGACUCAGUG	chr11:100879794-100880019(+)$1	225	27	48	13.9459
GAGGAAGGUGUCCAGCUUUCU	chr11:121103761-121103997(+)$1	236	131	152	15.6557
ugugugugGCCGGGAAGAGAC	chr5:68238185-68238514(-)$1	329	215	236	14.3878
CCGUGGACACUGAAAUCCGCG	chr1:166368154-166368590(-)$1	436	71	92	14.2558
CGGGCACCUCGACUCGGCCCG	chr12:68321761-68322236(-)$1	475	95	116	15.7658
uugccuaaaacucacuaugua	chr15:100225326-100225762(-)$1	436	359	380	14.7364
AGCUGAAGAGACAUAUACAGU	chr17:86568130-86568477(+)$1	347	286	307	14.9841
UUGAAUUGUGAUAUAGAUUCA	chrX:12192836-12193290(+)$1	454	344	365	13.9456
agggacagaagucaguguccu	chr18:65363477-65363768(+)$1	291	218	239	14.4612
GACAUGGCCAACAACUCAGUU	chr10:98431342-98431688(+)$1	346	214	235	15.0528
AAUGUCCUCCAUAGUGGAUAU	chr10:83073831-83074266(-)$1	435	308	329	13.2412
CCUGUAAGUUGGAUGUUGAUG	chr2:102621550-102622048(+)$1	498	34	55	15.2013
AAACCAAAACCAGAAUUGCAG	chr9:72860606-72860915(+)$1	309	35	56	14.3360
UGGGAGGUGCUUUUUCUUCUU	chr11:92961241-92961729(+)$1	488	310	331	14.2102
GCUGGGUGAGUGACAGCCCAG	chr5:51944889-51945222(-)$1	333	22	43	15.4398
CCCCAGAAUUGUAAAUUUGGG	chr11:88702491-88702906(-)$1	415	198	219	13.2488
UUCGGGAGACACCCAUCCUGG	chr1:160432378-160432585(+)$1	207	26	47	13.9456
uguaugugugugugugcgugc	chr12:71373350-71373847(-)$1	497	207	228	15.6557
CAGUAUUAGUGGUUCAGUGGC	chr9:66692859-66693241(-)$1	382	288	309	14.0466
AAUGACUGUGUCUCUGGUGGU	chr8:63401766-63402065(-)$1	299	93	114	15.6062
CUCUGAGUGCAAUAUUUCAGU	chr2:164824421-164824905(+)$1	484	441	462	13.8523
UGAGCCCUGACCCAUGGACUC	chr1:78702871-78703163(+)$1	292	0	21	13.3838

#DB
((((.((........))))))	chr6:111445780-111446114(+)$1	1	234	255	13.2904
(((((((........))))))	chr3:33712932-33713313(+)$1	1	71	92	15.6557
))(((((........))))).	chr5:8144073-8144460(-)$1	1	35	56	13.4543
(((((((........))))))	chr6:73213895-73214266(+)$1	1	138	159	15.6557
(.(((.(........))))..	chrX:12733486-12733774(+)$1	1	199	220	14.9448
(((((.(........).)).)	chr16:28372732-28373173(-)$1	1	367	388	13.5507
((((..(........)..)))	chr8:96677724-96678057(+)$1	1	2	23	14.1691
....(((........))))))	chr11:53093804-53094141(-)$1	1	245	266	14.8082
(.(((((........))))).	chr6:72269087-72269490(-)$1	1	159	180	14.5060
((.((((........))))..	chrX:133365526-133365801(+)$1	1	198	219	13.5287
(((.(((........))).))	chr5:68039676-68039899(-)$1	1	128	149	15.2656
..(((((........))))).	chr15:95071752-95072172(-)$1	1	253	274	12.7833
(.(((((........))))).	chr5:133017569-133017874(-)$1	1	260	281	14.5060
.((((((........))))))	chr17:47067317-47067664(-)$1	1	85	106	14.2396
(((..((........))..))	chr2:148700823-148701129(-)$1	1	76	97	14.1763
(.(((((........))))))	chr13:8852697-8852984(-)$1	1	78	99	14.3763
.((((((........))))))	chr8:40130698-40131025(+)$1	1	29	50	13.2412
(((((((........))))))	chr11:109522564-109522950(+)$1	1	156	177	15.6557
(((((((........)))).)	chr9:80148341-80148630(+)$1	1	169	190	14.4306
((.((.(........))))))	chr3:33708169-33708451(+)$1	1	119	140	14.1263
((..(((........))).))	chr3:40583180-40583659(+)$1	1	302	323	15.8600
(((.(((........))).))	chr5:145653792-145654141(-)$1	1	133	154	15.6062
.((((((........))).))	chr11:69418680-69419127(-)$1	1	116	137	15.4192
(((.(((........))).))	chr8:13370985-13371453(+)$1	1	355	376	15.6062
.((((((........))))))	chr2:5812064-5812507(-)$1	1	212	233	14.2558
(((((((........))))))	chr17:33806746-33807199(-)$1	1	325	346	15.6557
(.(((((........))))).	chr6:36693312-36693583(-)$1	1	102	123	14.4563
(((((((........))))))	chr4:134481586-134482049(+)$1	1	56	77	15.6557
(((((((........))))))	chr10:127029065-127029552(-)$1	1	67	88	15.4398
(((.(((........))).))	chr1:182878911-182879275(+)$1	1	40	61	14.7417
(((((((........))))))	chr6:145812638-145813010(-)$1	1	104	125	15.6557
(((((((........))))))	chr5:90651026-90651450(-)$1	1	308	329	13.9456
...((((........))))))	chr4:117225471-117225810(+)$1	1	81	102	13.2825
(((((((........))))))	chr11:121323012-121323332(+)$1	1	176	197	15.6557
(.(.(((........))).))	chr13:97425745-97426051(-)$1	1	97	118	15.0062
(((((((........))))))	chr18:36957489-36957940(+)$1	1	26	47	15.3807
((((.((........)).)))	chr18:40367294-40367581(-)$1	1	110	131	13.9571
(((((((........))))))	chr6:110653200-110653642(+)$1	1	245	266	15.6557
.((((((........))))))	chr17:17976503-17976850(+)$1	1	220	241	13.5429
((.((((........)))).)	chr2:30163075-30163479(+)$1	1	201	222	14.3122
(((((.(........))))))	chr4:11892567-11892950(-)$1	1	130	151	14.4139
((..(((........)))..)	chr4:24825713-24826196(+)$1	1	231	252	14.3597
(((.(((........))))))	chr4:58831798-58832237(-)$1	1	135	156	15.0528
(((((((........)))).)	chr4:87800488-87800910(+)$1	1	272	293	13.8446
((.((((........))))))	chr1:181675201-181675689(-)$1	1	441	462	14.2562
(((..((........))..))	chr17:34740314-34740611(-)$1	1	239	260	13.7444
((((..(........)..)))	chr9:59525866-59526083(+)$1	1	82	103	14.0712
(((((((........))))))	chr5:151599159-151599372(+)$1	1	19	40	15.6557
(((((.(........).))))	chr12:107050482-107050834(+)$1	1	238	259	14.4284
((((.((........))))))	chr8:75216954-75217272(+)$1	1	179	200	13.2904
(((.(((........))))))	chr16:18077703-18077995(-)$1	1	7	28	14.5365
((((.((........)).)))	chr11:100879794-100880019(+)$1	1	27	48	13.9459
(((((((........))))))	chr11:121103761-121103997(+)$1	1	131	152	15.6557
(((.(.(........).).))	chr5:68238185-68238514(-)$1	1	215	236	14.3878
.((((((........))))))	chr1:166368154-166368590(-)$1	1	71	92	14.2558
(((((.(........))))))	chr12:68321761-68322236(-)$1	1	95	116	15.7658
((((.((........)).)))	chr15:100225326-100225762(-)$1	1	359	380	14.7364
(.(((.(........).))))	chr17:86568130-86568477(+)$1	1	286	307	14.9841
(((((((........))))))	chrX:12192836-12193290(+)$1	1	344	365	13.9456
(((((((........))))).	chr18:65363477-65363768(+)$1	1	218	239	14.4612
(((.(((........))))))	chr10:98431342-98431688(+)$1	1	214	235	15.0528
.((((((........))))))	chr10:83073831-83074266(-)$1	1	308	329	13.2412
((..(((........)))..)	chr2:102621550-102622048(+)$1	1	34	55	15.2013
....(((........)))..)	chr9:72860606-72860915(+)$1	1	35	56	14.3360
(((((((........)))).)	chr11:92961241-92961729(+)$1	1	310	331	14.2102
(((((((........))))))	chr5:51944889-51945222(-)$1	1	22	43	15.4398
(((((((........))))))	chr11:88702491-88702906(-)$1	1	198	219	13.2488
(((((((........))))))	chr1:160432378-160432585(+)$1	1	26	47	13.9456
(((((((........))))))	chr12:71373350-71373847(-)$1	1	207	228	15.6557
(..((((........))))))	chr9:66692859-66693241(-)$1	1	288	309	14.0466
(((.(((........))).))	chr8:63401766-63402065(-)$1	1	93	114	15.6062
(((((((........))))).	chr2:164824421-164824905(+)$1	1	441	462	13.8523
.(((.((........)).)))	chr1:78702871-78703163(+)$1	1	0	21	13.3838

#PSSM
g : 0.23	c : 0.15	h : 0.09	e : 0.08	d : 0.06	f : 0.06	: : 0.04	i : 0.04	b : 0.04	# : 0.02	[ : 0.02	a : 0.02	! : 0.02	& : 0.01	$ : 0.01	= : 0.01	' : 0.01	B : 0.01	
g : 0.21	f : 0.15	c : 0.15	[ : 0.09	h : 0.09	d : 0.06	e : 0.06	i : 0.04	# : 0.02	b : 0.02	& : 0.01	$ : 0.01	= : 0.01	! : 0.01	
g : 0.17	e : 0.16	f : 0.15	c : 0.12	h : 0.08	d : 0.06	[ : 0.05	! : 0.05	i : 0.04	# : 0.02	a : 0.02	$ : 0.01	= : 0.01	
g : 0.16	d : 0.13	[ : 0.13	e : 0.12	f : 0.12	h : 0.08	! : 0.06	c : 0.05	i : 0.04	b : 0.02	# : 0.02	= : 0.01	
c : 0.23	g : 0.16	e : 0.10	d : 0.10	f : 0.09	[ : 0.08	h : 0.06	! : 0.05	b : 0.02	i : 0.02	= : 0.01	a : 0.01	
c : 0.20	g : 0.15	b : 0.10	e : 0.10	[ : 0.10	d : 0.10	f : 0.09	h : 0.04	! : 0.02	i : 0.02	= : 0.01	
c : 0.20	g : 0.15	a : 0.13	b : 0.10	e : 0.10	d : 0.10	f : 0.09	h : 0.04	i : 0.02	= : 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 : 0.20	g : 0.15	a : 0.13	b : 0.10	e : 0.10	d : 0.10	f : 0.09	h : 0.04	i : 0.02	= : 0.01	
c : 0.21	g : 0.16	b : 0.12	e : 0.10	d : 0.10	f : 0.09	] : 0.05	h : 0.05	2 : 0.02	i : 0.02	= : 0.01	
c : 0.23	g : 0.16	d : 0.13	e : 0.10	f : 0.09	h : 0.06	2 : 0.05	] : 0.05	b : 0.02	i : 0.02	= : 0.01	a : 0.01	
g : 0.16	e : 0.16	d : 0.15	f : 0.12	] : 0.12	h : 0.08	2 : 0.06	c : 0.05	i : 0.04	b : 0.01	= : 0.01	
g : 0.17	e : 0.17	f : 0.15	c : 0.13	h : 0.08	d : 0.06	2 : 0.06	] : 0.06	i : 0.04	a : 0.01	= : 0.01	
g : 0.19	f : 0.16	c : 0.16	e : 0.08	h : 0.08	d : 0.06	] : 0.05	i : 0.04	b : 0.04	2 : 0.02	a : 0.02	: : 0.01	4 : 0.01	= : 0.01	3 : 0.01	

#score	1062.4714677096017
#seq	73
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_CDS_m3_run1.txt

#BEAR
FfffffflllffffffJ	chr5:123244349-123244627(-)$1	278	126	143	9.2839
cfffffflllffffff:	chr12:85733283-85733551(-)$1	268	216	233	10.1292
ggggggglllggggggg	chr6:51413984-51414275(-)$1	291	89	106	7.3139
:fffffflllffffffe	chr19:4792248-4792540(-)$1	292	148	165	9.8164
:fffffflllffffff:	chr2:31615425-31615714(+)$1	289	171	188	9.2448
dfffffflllffffff]	chr7:117008949-117009223(-)$1	274	147	164	10.8594
ffffooooooffffff]	chr11:120481937-120482225(-)$1	288	191	208	8.5221
fffff[annnnna]fff	chr13:69138020-69138287(-)$1	267	215	232	7.3877
bffffffmmmmffffff	chr9:65194460-65194740(+)$1	280	145	162	8.8197
ffffffmmmmffffff:	chr9:108701514-108701781(+)$1	267	104	121	8.6561
""eeeeellleeeee33	chr11:70466234-70466555(-)$1	321	144	161	6.0573
fffffnnnnnffffff]	chr3:95464619-95464902(+)$1	283	19	36	8.8640
[ffffffmmmmffffff	chr2:174125804-174126076(+)$1	272	243	260	9.1720
[bb[ccclllccc]bb]	chr1:181447930-181448215(-)$1	285	240	257	6.5633
ggggggglllggggggg	chr19:7273750-7274023(-)$1	273	47	64	7.3139
=======lll=======	chr8:23489738-23490016(-)$1	278	6	23	6.7510
fffffnnnnnffffff]	chr8:74842835-74843118(+)$1	283	33	50	8.8640
"ffffffmmmmffffff	chr14:64225928-64226213(+)$1	285	37	54	9.0577
:fffffflllffffffD	chr11:102978353-102978633(+)$1	280	258	275	8.8017
=ffffffmmmmffffff	chr5:122096592-122096861(-)$1	269	183	200	9.0292
ffffffmmmmffffff:	chr3:96066811-96067101(-)$1	290	224	241	8.6561
ffffffnnnnnffffff	chr2:121205212-121205496(-)$1	284	192	209	9.0155
ffffccclllccc]fff	chr19:5384494-5384777(-)$1	283	173	190	9.4121
fffffffmmmmffffff	chr1:184398226-184398498(-)$1	272	141	158	9.1690
eee[ccclllccc]eee	chr2:34678076-34678352(-)$1	276	25	42	6.8095
ffffccclllccc]fff	chrX:98514856-98515126(+)$1	270	32	49	9.4121
ffffffoooooofffff	chr9:66219966-66220240(+)$1	274	138	155	8.8089
ffffffmmmmffffff]	chr11:87794792-87795066(-)$1	274	235	252	9.5936
Cfffffflllffffff:	chr3:146444016-146444284(-)$1	268	68	85	9.0253
ffffffnnnnnffffff	chr8:86770442-86770710(-)$1	268	32	49	9.0155
ffffffammmma]ffff	chr18:60859088-60859368(-)$1	280	241	258	8.3303
[fffffflllffffff2	chr4:135883045-135883340(+)$1	295	73	90	10.9503
:fffffflllffffffF	chr19:29086354-29086632(+)$1	278	178	195	9.7460
ffffccclllccc]fff	chr19:5384549-5384817(-)$1	268	213	230	9.4121
fffcccmmmmccc]fff	chr7:27949815-27950086(-)$1	271	163	180	7.3908
!fffffflllffffff7	chr19:8964904-8965185(+)$1	281	222	239	10.5405
ee!!ccclllccc22ee	chr9:107159264-107159531(-)$1	267	146	163	5.6846
eee[ccclllccc]eee	chr13:55651491-55651760(-)$1	269	249	266	6.8095
ffffffmmmmffffffe	chr2:40774602-40774870(-)$1	268	189	206	9.2277
!ffffffnnnnnfffff	chr3:51288320-51288589(+)$1	269	128	145	8.3632
!!eeeeellleeeee]a	chr8:63406007-63406293(-)$1	286	142	159	6.0511
fffffnnnnnffffff3	chr7:28151330-28151601(-)$1	271	99	116	8.7782
ffffffmmmmffffff:	chr3:102703878-102704148(-)$1	270	122	139	8.6561
ffffffmmmmffffff]	chr1:93275018-93275289(-)$1	271	62	79	9.5936
[fffffflllffffff]	chr4:151560213-151560493(+)$1	280	128	145	11.2459
ffffffoooooofffff	chr16:36049855-36050132(-)$1	277	134	151	8.8089
!fffffflllffffff2	chr15:76028312-76028598(-)$1	286	241	258	10.8872
""eeeeellleeeee33	chr9:53773691-53773975(-)$1	284	91	108	6.0573
ffffff4444ffffff]	chr3:154259844-154260111(-)$1	267	244	261	8.7558

#otherMatches

#Seq PSSM
GGGCUGUUUUGCGGCUG	chr5:123244349-123244627(-)$1	278	126	143	9.2839
UGGAUAACGCUUGUCUG	chr12:85733283-85733551(-)$1	268	216	233	10.1292
AUGAUUUUGGAAAUUAU	chr6:51413984-51414275(-)$1	291	89	106	7.3139
UCACUCUUUUGGAGUGC	chr19:4792248-4792540(-)$1	292	148	165	9.8164
AGAAGGGGCUCUCUUCG	chr2:31615425-31615714(+)$1	289	171	188	9.2448
CCUCGGGAAGCCCGGGC	chr7:117008949-117009223(-)$1	274	147	164	10.8594
CUCUGAACUGGGAGGCA	chr11:120481937-120482225(-)$1	288	191	208	8.5221
GGACUGGCUCUACGAGU	chr13:69138020-69138287(-)$1	267	215	232	7.3877
GAGCGGCUGCAGCCGCU	chr9:65194460-65194740(+)$1	280	145	162	8.8197
UUAUACUACAGUGUAGA	chr9:108701514-108701781(+)$1	267	104	121	8.6561
GCCAGAAAUGUUCUGUG	chr11:70466234-70466555(-)$1	321	144	161	6.0573
GUGGAGUUCUUCCACGU	chr3:95464619-95464902(+)$1	283	19	36	8.8640
UGGGCCCUUCGGGGCUC	chr2:174125804-174126076(+)$1	272	243	260	9.1720
GGCUUACACUGUGUGCA	chr1:181447930-181448215(-)$1	285	240	257	6.5633
AGACUACCUUGUGGUCU	chr19:7273750-7274023(-)$1	273	47	64	7.3139
GCUUCUGAGACAGAAGU	chr8:23489738-23490016(-)$1	278	6	23	6.7510
GUCCCCAUCCGGGACGC	chr8:74842835-74843118(+)$1	283	33	50	8.8640
ACCCCCAAUGAUGGGGG	chr14:64225928-64226213(+)$1	285	37	54	9.0577
AGCAGGAGGCUCCUGCC	chr11:102978353-102978633(+)$1	280	258	275	8.8017
CUGCAGUAAGGACUGCA	chr5:122096592-122096861(-)$1	269	183	200	9.0292
GGCCCUUUUUAGGGCCA	chr3:96066811-96067101(-)$1	290	224	241	8.6561
UCAUGAUUUCCUCGUGA	chr2:121205212-121205496(-)$1	284	192	209	9.0155
GCAGUGUAGGGCAGUUG	chr19:5384494-5384777(-)$1	283	173	190	9.4121
UUUUCAGUACUCUGAAG	chr1:184398226-184398498(-)$1	272	141	158	9.1690
UGCCUGGUCUCUAAGCA	chr2:34678076-34678352(-)$1	276	25	42	6.8095
UUCGUGAUCAUUACCGG	chrX:98514856-98515126(+)$1	270	32	49	9.4121
CGAACUGGUCUAAGUUU	chr9:66219966-66220240(+)$1	274	138	155	8.8089
CUGUGCUACUGCAUGGA	chr11:87794792-87795066(-)$1	274	235	252	9.5936
CGCCUGUUUCACAGGCA	chr3:146444016-146444284(-)$1	268	68	85	9.0253
CUGUUCACAGAGAACAG	chr8:86770442-86770710(-)$1	268	32	49	9.0155
CAUGCCCUUCUGUGGCA	chr18:60859088-60859368(-)$1	280	241	258	8.3303
AUGUUGGAUUCUAAUAG	chr4:135883045-135883340(+)$1	295	73	90	10.9503
CCUUACCACAGGUAAGC	chr19:29086354-29086632(+)$1	278	178	195	9.7460
GCAGUGUAGGGCAGUUG	chr19:5384549-5384817(-)$1	268	213	230	9.4121
CGGUACUAUGGUAUCUG	chr7:27949815-27950086(-)$1	271	163	180	7.3908
GACCUCCCCUGGAGGUG	chr19:8964904-8965185(+)$1	281	222	239	10.5405
GAUUCUGUCUCAGUCUC	chr9:107159264-107159531(-)$1	267	146	163	5.6846
AUUGCCAUACUGGGAGU	chr13:55651491-55651760(-)$1	269	249	266	6.8095
CAGCUCUGAUGAGUUGG	chr2:40774602-40774870(-)$1	268	189	206	9.2277
AUCGGGGUGGACUUCCG	chr3:51288320-51288589(+)$1	269	128	145	8.3632
UCGCUGUGGAGCAGCUU	chr8:63406007-63406293(-)$1	286	142	159	6.0511
CAGCUGGACAAGCUGGG	chr7:28151330-28151601(-)$1	271	99	116	8.7782
CAAGUUGAGAAGCUUGC	chr3:102703878-102704148(-)$1	270	122	139	8.6561
UUUCUGCUUUCAGGGAC	chr1:93275018-93275289(-)$1	271	62	79	9.5936
GCGCCUCUGGGAGGUGG	chr4:151560213-151560493(+)$1	280	128	145	11.2459
GAUUUUGAGAAGAAGAU	chr16:36049855-36050132(-)$1	277	134	151	8.8089
UUGCUUGGCCCAGGUAC	chr15:76028312-76028598(-)$1	286	241	258	10.8872
ACACUCCACUGGAGUCU	chr9:53773691-53773975(-)$1	284	91	108	6.0573
GAGUUUUUCACCACCAG	chr3:154259844-154260111(-)$1	267	244	261	8.7558

#DB
)((((((...)))))))	chr5:123244349-123244627(-)$1	1	126	143	9.2839
)((((((...)))))).	chr12:85733283-85733551(-)$1	1	216	233	10.1292
(((((((...)))))))	chr6:51413984-51414275(-)$1	1	89	106	7.3139
.((((((...))))))(	chr19:4792248-4792540(-)$1	1	148	165	9.8164
.((((((...)))))).	chr2:31615425-31615714(+)$1	1	171	188	9.2448
(((((((...)))))).	chr7:117008949-117009223(-)$1	1	147	164	10.8594
((((......)))))).	chr11:120481937-120482225(-)$1	1	191	208	8.5221
(((((.(.....).)))	chr13:69138020-69138287(-)$1	1	215	232	7.3877
)((((((....))))))	chr9:65194460-65194740(+)$1	1	145	162	8.8197
((((((....)))))).	chr9:108701514-108701781(+)$1	1	104	121	8.6561
..(((((...)))))..	chr11:70466234-70466555(-)$1	1	144	161	6.0573
(((((.....)))))).	chr3:95464619-95464902(+)$1	1	19	36	8.8640
.((((((....))))))	chr2:174125804-174126076(+)$1	1	243	260	9.1720
.((.(((...))).)).	chr1:181447930-181448215(-)$1	1	240	257	6.5633
(((((((...)))))))	chr19:7273750-7274023(-)$1	1	47	64	7.3139
(((((((...)))))))	chr8:23489738-23490016(-)$1	1	6	23	6.7510
(((((.....)))))).	chr8:74842835-74843118(+)$1	1	33	50	8.8640
.((((((....))))))	chr14:64225928-64226213(+)$1	1	37	54	9.0577
.((((((...)))))))	chr11:102978353-102978633(+)$1	1	258	275	8.8017
)((((((....))))))	chr5:122096592-122096861(-)$1	1	183	200	9.0292
((((((....)))))).	chr3:96066811-96067101(-)$1	1	224	241	8.6561
((((((.....))))))	chr2:121205212-121205496(-)$1	1	192	209	9.0155
(((((((...))).)))	chr19:5384494-5384777(-)$1	1	173	190	9.4121
)((((((....))))))	chr1:184398226-184398498(-)$1	1	141	158	9.1690
(((.(((...))).)))	chr2:34678076-34678352(-)$1	1	25	42	6.8095
(((((((...))).)))	chrX:98514856-98515126(+)$1	1	32	49	9.4121
((((((......)))))	chr9:66219966-66220240(+)$1	1	138	155	8.8089
((((((....)))))).	chr11:87794792-87795066(-)$1	1	235	252	9.5936
)((((((...)))))).	chr3:146444016-146444284(-)$1	1	68	85	9.0253
((((((.....))))))	chr8:86770442-86770710(-)$1	1	32	49	9.0155
(((((((....).))))	chr18:60859088-60859368(-)$1	1	241	258	8.3303
.((((((...)))))).	chr4:135883045-135883340(+)$1	1	73	90	10.9503
.((((((...)))))))	chr19:29086354-29086632(+)$1	1	178	195	9.7460
(((((((...))).)))	chr19:5384549-5384817(-)$1	1	213	230	9.4121
((((((....))).)))	chr7:27949815-27950086(-)$1	1	163	180	7.3908
.((((((...)))))).	chr19:8964904-8965185(+)$1	1	222	239	10.5405
((..(((...)))..))	chr9:107159264-107159531(-)$1	1	146	163	5.6846
(((.(((...))).)))	chr13:55651491-55651760(-)$1	1	249	266	6.8095
((((((....))))))(	chr2:40774602-40774870(-)$1	1	189	206	9.2277
.((((((.....)))))	chr3:51288320-51288589(+)$1	1	128	145	8.3632
..(((((...))))).)	chr8:63406007-63406293(-)$1	1	142	159	6.0511
(((((.....)))))).	chr7:28151330-28151601(-)$1	1	99	116	8.7782
((((((....)))))).	chr3:102703878-102704148(-)$1	1	122	139	8.6561
((((((....)))))).	chr1:93275018-93275289(-)$1	1	62	79	9.5936
.((((((...)))))).	chr4:151560213-151560493(+)$1	1	128	145	11.2459
((((((......)))))	chr16:36049855-36050132(-)$1	1	134	151	8.8089
.((((((...)))))).	chr15:76028312-76028598(-)$1	1	241	258	10.8872
..(((((...)))))..	chr9:53773691-53773975(-)$1	1	91	108	6.0573
))))))....)))))).	chr3:154259844-154260111(-)$1	1	244	261	8.7558

#PSSM
f : 0.44	: : 0.08	[ : 0.08	! : 0.08	" : 0.06	e : 0.06	g : 0.04	= : 0.04	F : 0.02	c : 0.02	d : 0.02	b : 0.02	C : 0.02	
f : 0.79	e : 0.06	g : 0.04	" : 0.04	b : 0.02	= : 0.02	! : 0.02	
f : 0.79	e : 0.10	g : 0.04	b : 0.02	= : 0.02	! : 0.02	
f : 0.77	e : 0.06	[ : 0.06	g : 0.04	= : 0.02	c : 0.02	! : 0.02	
f : 0.69	c : 0.16	e : 0.06	g : 0.04	o : 0.02	= : 0.02	
f : 0.61	c : 0.16	e : 0.06	n : 0.06	g : 0.04	o : 0.02	[ : 0.02	= : 0.02	
f : 0.36	m : 0.14	c : 0.14	n : 0.10	o : 0.06	e : 0.06	g : 0.04	a : 0.04	= : 0.02	4 : 0.02	
l : 0.51	m : 0.26	n : 0.14	o : 0.06	4 : 0.02	
l : 0.51	m : 0.26	n : 0.14	o : 0.06	4 : 0.02	
l : 0.51	m : 0.26	n : 0.14	o : 0.06	4 : 0.02	
f : 0.46	c : 0.16	m : 0.12	n : 0.08	e : 0.06	g : 0.04	o : 0.04	= : 0.02	
f : 0.61	c : 0.16	e : 0.06	g : 0.04	n : 0.04	o : 0.04	= : 0.02	a : 0.02	
f : 0.67	c : 0.16	e : 0.06	g : 0.04	a : 0.02	= : 0.02	] : 0.02	
f : 0.69	] : 0.16	e : 0.06	g : 0.04	= : 0.02	2 : 0.02	
f : 0.79	e : 0.10	g : 0.04	b : 0.02	= : 0.02	2 : 0.02	
f : 0.79	e : 0.06	g : 0.04	3 : 0.04	b : 0.02	= : 0.02	] : 0.02	
f : 0.32	] : 0.18	: : 0.12	e : 0.10	3 : 0.06	g : 0.04	2 : 0.04	J : 0.02	= : 0.02	D : 0.02	F : 0.02	7 : 0.02	a : 0.02	

#score	424.7169836129206
#seq	49
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_transcript_m2_run1.txt

#BEAR
:eeeeewwwwwwwwwwwwwweeeee:	chr1:133920198-133920417(+)$1	219	14	40	21.0063
ggggggguuuuuuuuuuuuggggggg	chr2:71114727-71114940(-)$1	213	53	79	24.2737
ffffffwwwwwwwwwwwwwwffffff	chr18:11880559-11880778(+)$1	219	122	148	22.5846
eeeeeeeettttttttttteeeee]e	chr11:29363483-29363709(+)$1	226	194	220	21.6982
f[cccxxxxxxxxxxxxxxxcccfff	chr14:28959012-28959240(+)$1	228	29	55	19.6814
###ddddvvvvvvvvvvvvvdddd22	chr15:81725535-81725769(+)$1	234	203	229	22.2858
&eeeeewwwwwwwwwwwwwweeeee8	chr2:132359729-132359957(-)$1	228	139	165	21.7080
:ffffffuuuuuuuuuuuuffffffF	chr8:131246230-131246454(+)$1	224	7	33	22.2861
::eeeeeuuuuuuuuuuuueeeee:e	chr5:20402043-20402249(-)$1	206	85	111	20.6285
ee!!cccvvvvvvvvvvvvvccc22e	chr4:86437186-86437411(+)$1	225	57	83	22.8954
ebbddddvvvvvvvvvvvvvdddd]b	chr16:36831501-36831737(+)$1	236	84	110	22.0491
=======vvvvvvvvvvvvv======	chrX:138087883-138088100(+)$1	217	156	182	23.7233
ccc[bbuuuuuuuuuuuubb]ccc:b	chr11:84850005-84850231(-)$1	226	139	165	20.9758
c[ddddyyyyyyyyyyyyyyyydddd	chr9:123028271-123028492(+)$1	221	134	160	21.9375
$$$dddduuuuuuuuuuuudddd888	chr1:95317835-95318050(-)$1	215	63	89	21.4847
g[eeeeeyyyyyyyyyyyyyyyyeee	chr6:67222093-67222311(+)$1	218	166	192	21.4551
dddd!!awwwwwwwwwwwwwwa22dd	chr16:33457488-33457697(+)$1	209	65	91	21.3009
iiiiyyyyyyyyyyyyyyyyiiiiii	chr2:166854705-166854918(+)$1	213	42	68	22.9926
ccc[cccattttttttttta]ccccc	chr4:154889650-154889870(+)$1	220	7	33	23.2870
c[cccyyyyyyyyyyyyyyyyccc]c	chr4:11990836-11991054(-)$1	218	109	135	23.4931
!!bbddddtttttttttttdddd]bb	chr1:10072231-10072457(+)$1	226	99	125	20.8447
gggggggvvvvvvvvvvvvvgggggg	chr12:13367682-13367902(+)$1	220	15	41	23.6335
====yyyyyyyyyyyyyyyy======	chr5:135912217-135912456(-)$1	239	38	64	23.1407
ffffffwwwwwwwwwwwwwwffffff	chr5:121587371-121587602(-)$1	231	150	176	22.5846
iiiiiiwwwwwwwwwwwwwwiiiiii	chr1:181325643-181325864(-)$1	221	179	205	23.4080
ffffffvvvvvvvvvvvvvffffffc	chr18:12295096-12295316(+)$1	220	128	154	22.5566
dd!!cccwwwwwwwwwwwwwwccc]d	chr11:3558594-3558816(+)$1	222	52	78	22.6148
=!!bbyyyyyyyyyyyyyyyybb444	chr12:100112627-100112858(-)$1	231	84	110	21.9033
c!!cccuuuuuuuuuuuucccccc]b	chr9:14366454-14366679(-)$1	225	87	113	23.0914
ccc[cccvvvvvvvvvvvvvccc]cc	chr5:136572441-136572662(+)$1	221	114	140	23.5071
ggggggguuuuuuuuuuuuggggggg	chr2:30179026-30179237(+)$1	211	151	177	24.2737
hhhh[ccctttttttttttccc]hhh	chr7:135850495-135850736(-)$1	241	36	62	21.2516
##eeeeeuuuuuuuuuuuueeeeecc	chr18:6490428-6490655(-)$1	227	186	212	23.5948
bbcccyyyyyyyyyyyyyyyyccc]b	chr4:84742587-84742822(+)$1	235	81	107	22.6501
hhhhhhhuuuuuuuuuuuuhhhhhhh	chr2:121095890-121096130(-)$1	240	152	178	21.1704
ggggggguuuuuuuuuuuuggggggg	chr16:4914428-4914645(+)$1	217	37	63	24.2737
[ffffffuuuuuuuuuuuuffffff]	chr1:55057818-55058029(-)$1	211	138	164	23.5365
[fffffftttttttttttffffff]c	chr14:49797644-49797860(+)$1	216	69	95	22.0418
c[ccc[auuuuuuuuuuuua]ccc]c	chr8:75263258-75263470(+)$1	212	66	92	25.0584
eeeeewwwwwwwwwwwwwweeeee]c	chr9:7169471-7169696(-)$1	225	180	206	22.2115
:dddd[auuuuuuuuuuuua]dddd:	chr4:15913673-15913889(+)$1	216	140	166	22.0231
"""dddduuuuuuuuuuuudddd]gg	chr1:136304132-136304359(+)$1	227	153	179	23.6012
%ffffffuuuuuuuuuuuuffffff4	chr11:78036213-78036433(-)$1	220	158	184	22.9023
bddddbbuuuuuuuuuuuubb4444d	chr10:95504639-95504854(+)$1	215	111	137	22.2295
ff"""bbtttttttttttbb333fff	chr10:7422609-7422815(+)$1	206	32	58	21.1419
""cccyyyyyyyyyyyyyyyyccc]c	chr16:20540493-20540715(+)$1	222	30	56	23.4107
:gggggggtttttttttttggggggg	chr9:110451929-110452145(+)$1	216	94	120	21.5079
ee[dddduuuuuuuuuuuudddd]ee	chr2:80399149-80399372(-)$1	223	171	197	23.1048
:ffffffuuuuuuuuuuuuffffff:	chr12:16968391-16968609(+)$1	218	84	110	21.8183
eeeyyyyyyyyyyyyyyyyeeeee]f	chr19:53702452-53702670(+)$1	218	78	104	21.4420
ggggggguuuuuuuuuuuuggggggg	chr4:58866205-58866426(-)$1	221	29	55	24.2737
c[eeeeettttttttttteeeeeccc	chr1:33685140-33685367(-)$1	227	59	85	22.0142
:ffffffuuuuuuuuuuuuffffff:	chr15:80086548-80086773(+)$1	225	136	162	21.8183
[ddddavvvvvvvvvvvvva]dddd]	chr7:87487997-87488217(+)$1	220	69	95	22.6141
ggggggxxxxxxxxxxxxxxxggggg	chr5:138052537-138052743(-)$1	206	65	91	20.0049
ffffffwwwwwwwwwwwwwwffffff	chr5:135916024-135916241(-)$1	217	92	118	22.5846
gggdddduuuuuuuuuuuudddd333	chr18:35073692-35073910(-)$1	218	148	174	23.7125
ccddddwwwwwwwwwwwwwwdddd]c	chr10:126989780-126990005(-)$1	225	56	82	22.7230
gggggbbtttttttttttbb]ggggg	chr8:109890855-109891076(+)$1	221	73	99	22.2678
iiiiiiivvvvvvvvvvvvviiiiii	chr4:148636739-148636966(-)$1	227	82	108	23.4915
gggggggvvvvvvvvvvvvvgggggg	chrX:90841446-90841663(-)$1	217	63	89	23.6335

#otherMatches

#Seq PSSM
CCUGCAGAAGACAUAACCAGUGCAGU	chr1:133920198-133920417(+)$1	219	14	40	21.0063
AGGAGGAUUAAAUGUGGCUUUCUCCU	chr2:71114727-71114940(-)$1	213	53	79	24.2737
UGAUGGAUAAACCUCUGGACCUGUCA	chr18:11880559-11880778(+)$1	219	122	148	22.5846
AAGGGCUUGGAGCUCAUGAGAGCCUC	chr11:29363483-29363709(+)$1	226	194	220	21.6982
uuguccccauauuuccuUUAGACAGG	chr14:28959012-28959240(+)$1	228	29	55	19.6814
AUGGCUAUGCUACAGUUCAUUAGCAG	chr15:81725535-81725769(+)$1	234	203	229	22.2858
AUAUGAUAGGUAUUUGUUUUUCAUAA	chr2:132359729-132359957(-)$1	228	139	165	21.7080
UGUUACACUUUUUGUUUUAUGUGACU	chr8:131246230-131246454(+)$1	224	7	33	22.2861
CAGCUCUAAGAAUCAAGGAAGAGCCU	chr5:20402043-20402249(-)$1	206	85	111	20.6285
AGCUCCUUGCUGAUGAAUCUGGGUCC	chr4:86437186-86437411(+)$1	225	57	83	22.8954
AGGUGGUAGAAAAAAAUGAAGCCAGC	chr16:36831501-36831737(+)$1	236	84	110	22.0491
UCAUAGUCAAAUCUGCUCCUGCUGUG	chrX:138087883-138088100(+)$1	217	156	182	23.7233
GCUAUCUUCUCUUCCUUCGACAGCAG	chr11:84850005-84850231(-)$1	226	139	165	20.9758
GAAGCUGGAGAAACCGAAUGAAGGCU	chr9:123028271-123028492(+)$1	221	134	160	21.9375
UUUCUGUACCAAUCUUCAAACAGUUU	chr1:95317835-95318050(-)$1	215	63	89	21.4847
UCAGUGAAACCAAAACUGCUAACUUA	chr6:67222093-67222311(+)$1	218	166	192	21.4551
ccacagcuguaucaagaaccugaagu	chr16:33457488-33457697(+)$1	209	65	91	21.3009
AGCUUACUAACCAUCUCUUUGGCUCU	chr2:166854705-166854918(+)$1	213	42	68	22.9926
GUGUGCUCUUUCCUAAAAUGUAGCUA	chr4:154889650-154889870(+)$1	220	7	33	23.2870
CUUCAGCAGCCCUGUAUUUUAUGAUG	chr4:11990836-11991054(-)$1	218	109	135	23.4931
CAGGAGGUGAAGAUCGAGAACUUACC	chr1:10072231-10072457(+)$1	226	99	125	20.8447
GGAGGCUUUUACCUUGACUUAGUCUC	chr12:13367682-13367902(+)$1	220	15	41	23.6335
CGGGACAUAGUGACACCAAGCCUGUU	chr5:135912217-135912456(-)$1	239	38	64	23.1407
CUGCACCCCAACGCCACCCUGUGCAG	chr5:121587371-121587602(-)$1	231	150	176	22.5846
UCAACAGCCCUUGCUUCUUGUGUUGA	chr1:181325643-181325864(-)$1	221	179	205	23.4080
CUGGAGAAAACAUUGACACUUCCAGU	chr18:12295096-12295316(+)$1	220	128	154	22.5566
UGUUGACUCUUAAAAUUUAUUGUUUC	chr11:3558594-3558816(+)$1	222	52	78	22.6148
UUAACUUUUAAACCAAUUACUGUGAU	chr12:100112627-100112858(-)$1	231	84	110	21.9033
AUCGGAGGCACAUCGAGAUCCUGGAC	chr9:14366454-14366679(-)$1	225	87	113	23.0914
GCUGGAAUGAGACAUUUGAUUUUGAG	chr5:136572441-136572662(+)$1	221	114	140	23.5071
GGAGCAGCUCCCCUGUUACCUGCUCC	chr2:30179026-30179237(+)$1	211	151	177	24.2737
GUGUUCUUUCCCUUCUCCCAGGUAUA	chr7:135850495-135850736(-)$1	241	36	62	21.2516
GAGGAGUCGGUACGUGUUAACUCCCC	chr18:6490428-6490655(-)$1	227	186	212	23.5948
CUCACUAAACAGUCAUCAAAUGUGAA	chr4:84742587-84742822(+)$1	235	81	107	22.6501
AUCUGAAAGAAAAGAAAGCUUCAGGU	chr2:121095890-121096130(-)$1	240	152	178	21.1704
CAGUGUCCCUGCCCAACCUGAUGCUG	chr16:4914428-4914645(+)$1	217	37	63	24.2737
GUGGAAGGCCGAGAGAUUAUUUCUAA	chr1:55057818-55058029(-)$1	211	138	164	23.5365
GUUUAUUUUCAAGGCCAUGGUAGGGG	chr14:49797644-49797860(+)$1	216	69	95	22.0418
CUGGAACACAACAAGAAACGCUCUCG	chr8:75263258-75263470(+)$1	212	66	92	25.0584
CCCAGAAACUCUUGACAAACUGGGCA	chr9:7169471-7169696(-)$1	225	180	206	22.2115
AGGUGUCUUUAUUAACUGUGUCGCCA	chr4:15913673-15913889(+)$1	216	140	166	22.0231
UAUCUGUCCUUUCCUUCCUACAGUCU	chr1:136304132-136304359(+)$1	227	153	179	23.6012
AGAGGUAAUGCUGACUCCCUACCUCA	chr11:78036213-78036433(-)$1	220	158	184	22.9023
CGAGUGCUCAACCAAAAAUGCCUUAA	chr10:95504639-95504854(+)$1	215	111	137	22.2295
GCCCUGCAAAGAUGAACAGCCUAGCU	chr10:7422609-7422815(+)$1	206	32	58	21.1419
CCCAAACUCCUUUCCUUCCUAUUGAU	chr16:20540493-20540715(+)$1	222	30	56	23.4107
AAGCUGAGAACGCUGAACCUUCAGCU	chr9:110451929-110452145(+)$1	216	94	120	21.5079
ccagaggcccagcucuacuccucggg	chr2:80399149-80399372(-)$1	223	171	197	23.1048
AGUUUAGAACAAGAAGAAGCUGAACA	chr12:16968391-16968609(+)$1	218	84	110	21.8183
CUAAUUCAUUAGUUACUUGUGGAGAG	chr19:53702452-53702670(+)$1	218	78	104	21.4420
UUUAGAuuuauuuuuucucauuuaaa	chr4:58866205-58866426(-)$1	221	29	55	24.2737
GUGCCACUUAAGGACAUCGUGGCCAU	chr1:33685140-33685367(-)$1	227	59	85	22.0142
CUUCGAGUUAAGCACAUUCCUCGAAU	chr15:80086548-80086773(+)$1	225	136	162	21.8183
CCGCUCACAAACACCGACAGCAGCGA	chr7:87487997-87488217(+)$1	220	69	95	22.6141
AGUCCCCACGCCCACACACCCGGGGC	chr5:138052537-138052743(-)$1	206	65	91	20.0049
GCGGCUCAUUCAGAUCCCCCAGCUGC	chr5:135916024-135916241(-)$1	217	92	118	22.5846
UUAGCAGACGAGUUUGGAACUGCAUC	chr18:35073692-35073910(-)$1	218	148	174	23.7125
GCCAAGACAUCCCACACAUCUUUGCG	chr10:126989780-126990005(-)$1	225	56	82	22.7230
UGUGGCUUUUUAUUUUUUAGACUACA	chr8:109890855-109891076(+)$1	221	73	99	22.2678
GGCAACUCCCGAACUGCAAUGGUUGC	chr4:148636739-148636966(-)$1	227	82	108	23.4915
UUUUCCCUUCUUCUCUUCAUGGGAGA	chrX:90841446-90841663(-)$1	217	63	89	23.6335

#DB
.(((((..............))))).	chr1:133920198-133920417(+)$1	1	14	40	21.0063
(((((((............)))))))	chr2:71114727-71114940(-)$1	1	53	79	24.2737
((((((..............))))))	chr18:11880559-11880778(+)$1	1	122	148	22.5846
((((((((...........))))).)	chr11:29363483-29363709(+)$1	1	194	220	21.6982
(.(((...............))))))	chr14:28959012-28959240(+)$1	1	29	55	19.6814
...((((.............))))..	chr15:81725535-81725769(+)$1	1	203	229	22.2858
.(((((..............))))).	chr2:132359729-132359957(-)$1	1	139	165	21.7080
.((((((............))))))(	chr8:131246230-131246454(+)$1	1	7	33	22.2861
..(((((............))))).(	chr5:20402043-20402249(-)$1	1	85	111	20.6285
((..(((.............)))..)	chr4:86437186-86437411(+)$1	1	57	83	22.8954
)((((((.............)))).)	chr16:36831501-36831737(+)$1	1	84	110	22.0491
(((((((.............))))))	chrX:138087883-138088100(+)$1	1	156	182	23.7233
(((.((............)).))).(	chr11:84850005-84850231(-)$1	1	139	165	20.9758
(.((((................))))	chr9:123028271-123028492(+)$1	1	134	160	21.9375
...((((............))))...	chr1:95317835-95318050(-)$1	1	63	89	21.4847
(.(((((................)))	chr6:67222093-67222311(+)$1	1	166	192	21.4551
((((..(..............)..))	chr16:33457488-33457697(+)$1	1	65	91	21.3009
((((................))))))	chr2:166854705-166854918(+)$1	1	42	68	22.9926
(((.((((...........).)))))	chr4:154889650-154889870(+)$1	1	7	33	23.2870
(.(((................))).)	chr4:11990836-11991054(-)$1	1	109	135	23.4931
..((((((...........)))).))	chr1:10072231-10072457(+)$1	1	99	125	20.8447
(((((((.............))))))	chr12:13367682-13367902(+)$1	1	15	41	23.6335
((((................))))))	chr5:135912217-135912456(-)$1	1	38	64	23.1407
((((((..............))))))	chr5:121587371-121587602(-)$1	1	150	176	22.5846
((((((..............))))))	chr1:181325643-181325864(-)$1	1	179	205	23.4080
((((((.............)))))))	chr18:12295096-12295316(+)$1	1	128	154	22.5566
((..(((..............))).)	chr11:3558594-3558816(+)$1	1	52	78	22.6148
(..((................))...	chr12:100112627-100112858(-)$1	1	84	110	21.9033
(..(((............)))))).)	chr9:14366454-14366679(-)$1	1	87	113	23.0914
(((.(((.............))).))	chr5:136572441-136572662(+)$1	1	114	140	23.5071
(((((((............)))))))	chr2:30179026-30179237(+)$1	1	151	177	24.2737
((((.(((...........))).)))	chr7:135850495-135850736(-)$1	1	36	62	21.2516
..(((((............)))))))	chr18:6490428-6490655(-)$1	1	186	212	23.5948
(((((................))).)	chr4:84742587-84742822(+)$1	1	81	107	22.6501
(((((((............)))))))	chr2:121095890-121096130(-)$1	1	152	178	21.1704
(((((((............)))))))	chr16:4914428-4914645(+)$1	1	37	63	24.2737
.((((((............)))))).	chr1:55057818-55058029(-)$1	1	138	164	23.5365
.((((((...........)))))).)	chr14:49797644-49797860(+)$1	1	69	95	22.0418
(.(((.(............).))).)	chr8:75263258-75263470(+)$1	1	66	92	25.0584
(((((..............))))).)	chr9:7169471-7169696(-)$1	1	180	206	22.2115
.((((.(............).)))).	chr4:15913673-15913889(+)$1	1	140	166	22.0231
...((((............)))).))	chr1:136304132-136304359(+)$1	1	153	179	23.6012
.((((((............)))))).	chr11:78036213-78036433(-)$1	1	158	184	22.9023
)((((((............))....)	chr10:95504639-95504854(+)$1	1	111	137	22.2295
((...((...........))...)))	chr10:7422609-7422815(+)$1	1	32	58	21.1419
..(((................))).)	chr16:20540493-20540715(+)$1	1	30	56	23.4107
.(((((((...........)))))))	chr9:110451929-110452145(+)$1	1	94	120	21.5079
((.((((............)))).))	chr2:80399149-80399372(-)$1	1	171	197	23.1048
.((((((............)))))).	chr12:16968391-16968609(+)$1	1	84	110	21.8183
(((................))))).)	chr19:53702452-53702670(+)$1	1	78	104	21.4420
(((((((............)))))))	chr4:58866205-58866426(-)$1	1	29	55	24.2737
(.(((((...........))))))))	chr1:33685140-33685367(-)$1	1	59	85	22.0142
.((((((............)))))).	chr15:80086548-80086773(+)$1	1	136	162	21.8183
.(((((.............).)))).	chr7:87487997-87488217(+)$1	1	69	95	22.6141
((((((...............)))))	chr5:138052537-138052743(-)$1	1	65	91	20.0049
((((((..............))))))	chr5:135916024-135916241(-)$1	1	92	118	22.5846
(((((((............))))...	chr18:35073692-35073910(-)$1	1	148	174	23.7125
((((((..............)))).)	chr10:126989780-126990005(-)$1	1	56	82	22.7230
(((((((...........)).)))))	chr8:109890855-109891076(+)$1	1	73	99	22.2678
(((((((.............))))))	chr4:148636739-148636966(-)$1	1	82	108	23.4915
(((((((.............))))))	chrX:90841446-90841663(-)$1	1	63	89	23.6335

#PSSM
g : 0.16	c : 0.14	: : 0.11	f : 0.09	e : 0.09	= : 0.04	i : 0.04	[ : 0.04	# : 0.03	d : 0.03	h : 0.03	b : 0.03	" : 0.03	& : 0.01	$ : 0.01	! : 0.01	% : 0.01	
f : 0.18	g : 0.16	e : 0.11	[ : 0.09	d : 0.08	c : 0.06	i : 0.04	! : 0.04	# : 0.03	b : 0.03	= : 0.03	h : 0.03	" : 0.03	: : 0.01	$ : 0.01	
g : 0.16	f : 0.16	e : 0.14	c : 0.13	d : 0.09	! : 0.06	i : 0.04	b : 0.03	= : 0.03	h : 0.03	" : 0.03	# : 0.01	$ : 0.01	[ : 0.01	
d : 0.19	f : 0.16	g : 0.14	e : 0.13	c : 0.09	[ : 0.04	i : 0.04	! : 0.03	= : 0.03	b : 0.03	h : 0.03	" : 0.01	y : 0.01	
d : 0.19	f : 0.16	c : 0.16	g : 0.14	e : 0.13	y : 0.04	b : 0.03	i : 0.03	= : 0.01	! : 0.01	[ : 0.01	h : 0.01	" : 0.01	
f : 0.16	d : 0.14	g : 0.13	e : 0.11	y : 0.11	c : 0.09	b : 0.06	i : 0.03	[ : 0.03	x : 0.01	= : 0.01	! : 0.01	h : 0.01	w : 0.01	a : 0.01	
w : 0.13	y : 0.13	g : 0.11	d : 0.11	f : 0.09	e : 0.08	c : 0.08	a : 0.04	b : 0.04	x : 0.03	u : 0.03	v : 0.03	= : 0.01	h : 0.01	i : 0.01	
u : 0.34	w : 0.16	v : 0.16	y : 0.14	t : 0.06	x : 0.03	e : 0.01	a : 0.01	d : 0.01	c : 0.01	g : 0.01	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.34	w : 0.16	v : 0.16	t : 0.14	y : 0.14	x : 0.03	
u : 0.31	w : 0.16	v : 0.16	y : 0.14	t : 0.08	b : 0.04	x : 0.03	c : 0.01	f : 0.01	e : 0.01	
w : 0.14	v : 0.13	y : 0.13	f : 0.11	e : 0.09	g : 0.08	d : 0.08	b : 0.06	a : 0.06	x : 0.03	c : 0.03	h : 0.01	
f : 0.16	e : 0.13	d : 0.13	g : 0.11	] : 0.09	y : 0.09	c : 0.08	i : 0.04	= : 0.03	w : 0.03	h : 0.01	b : 0.01	3 : 0.01	x : 0.01	
c : 0.19	f : 0.16	d : 0.16	g : 0.14	e : 0.13	i : 0.04	= : 0.03	y : 0.03	a : 0.01	b : 0.01	h : 0.01	4 : 0.01	3 : 0.01	
c : 0.18	d : 0.18	f : 0.16	g : 0.14	e : 0.13	i : 0.04	= : 0.03	y : 0.01	2 : 0.01	b : 0.01	] : 0.01	h : 0.01	4 : 0.01	3 : 0.01	
f : 0.19	g : 0.14	c : 0.14	e : 0.13	d : 0.09	] : 0.06	i : 0.04	2 : 0.03	= : 0.03	4 : 0.03	h : 0.03	8 : 0.01	3 : 0.01	
] : 0.19	f : 0.18	g : 0.16	e : 0.06	d : 0.06	c : 0.06	i : 0.04	2 : 0.03	: : 0.03	= : 0.03	4 : 0.03	h : 0.03	8 : 0.01	b : 0.01	3 : 0.01	
c : 0.18	g : 0.16	f : 0.09	e : 0.08	b : 0.08	: : 0.06	d : 0.06	i : 0.04	8 : 0.03	= : 0.03	4 : 0.03	h : 0.03	] : 0.03	2 : 0.01	F : 0.01	3 : 0.01	

#score	1371.4171821020623
#seq	61
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_CDS_m1_run2.txt

#BEAR
$$$$$ccc[cccooooooccc22ccc333e	chr11:49637152-49637372(+)$1	220	160	190	16.1016
&eeeee[ccc[bboooooobb]ccc]eeee	chr1:141319699-141319919(+)$1	220	91	121	12.7178
ee!!bb[ccc[bboooooobb]ccc22bb2	chr3:122637270-122637490(-)$1	220	175	205	12.1987
b!!iiiiiiiiiooooooiiiiiiiii333	chr13:113283688-113283911(+)$1	223	60	90	15.5994
eee[ccc!!cccooooooccc]ccceeeee	chr17:23953009-23953232(+)$1	223	141	171	16.3965
bb[ccc[ccc[bboooooobb]ccc]ccc]	chr19:11017631-11017857(-)$1	226	9	39	13.7002
ddd!!dddd!!aooooooa22dddd]dddd	chr7:5044372-5044596(+)$1	224	132	162	12.4579
::==========oooooo==========:c	chr11:6239765-6239987(+)$1	222	17	47	13.0911
biiiiiiiii[aooooooaiiiiiiiiiee	chr11:68786648-68786868(-)$1	220	131	161	14.9858
========[cccooooooccc=========	chr10:80571584-80571804(+)$1	220	180	210	16.8169
[ffffff[ddddoooooodddd22ffffff	chr3:51247759-51247983(+)$1	224	117	147	12.9839
dddd[ddddcccooooooccc]dddd]ddd	chr3:36451554-36451774(+)$1	220	3	33	13.8770
cc[iiiiiiiiiooooooiiiiiiiii]cc	chr3:95131114-95131334(-)$1	220	40	70	15.3275
f!!ccc"""cccooooooccc22ccc333f	chr5:139702676-139702917(+)$1	241	203	233	17.6762
b[ffffff[cccooooooccc333ffffff	chr11:54374740-54374978(+)$1	238	161	191	15.7800
hhhhhhhh[cccooooooccc]hhhhhhhh	chr8:114292518-114292740(-)$1	222	96	126	12.9035
[ccceeeee[bboooooobb]eeeee]ccc	chr10:83045903-83046123(+)$1	220	86	116	13.2077
dd[ccc"""cccooooooccc]ccc]dddd	chr10:5991033-5991253(-)$1	220	73	103	16.8300
ggggg!!a[cccooooooccca]ggggggg	chr6:70794670-70794901(+)$1	231	41	71	16.3185
%%%ccc"""cccooooooccc333ccc666	chr7:109575107-109575352(+)$1	245	132	162	15.1316
[eeeeebb!!bboooooobb22bb]eeeee	chr4:12022400-12022620(+)$1	220	123	153	13.2068
###dddd[ddddoooooodddd]dddd22g	chr4:15925134-15925354(-)$1	220	108	138	12.7902
+ffffff!!cccooooooccc22ffffff>	chr4:6129418-6129640(+)$1	222	156	186	15.2160
eee[ccc!!cccooooooccc]ccceeeee	chr17:23953105-23953325(+)$1	220	45	75	16.3965
b[==========oooooo==========bb	chr9:48818250-48818470(+)$1	220	130	160	15.2968
cccc[ccc[cccooooooccc]ccc22ccc	chr9:61262522-61262742(+)$1	220	127	157	16.1782
ggggggg!!cccooooooccc22ggggggg	chr4:32843245-32843465(+)$1	220	57	87	16.8137
cggggggg[cccoooooocccggggggg::	chr4:115824574-115824806(+)$1	232	163	193	14.2803
fffff####cccooooooccc333ffffff	chr2:32161019-32161239(+)$1	220	29	59	16.5134
ceeeee[eeeeeooooooeeeeeeeeee44	chr17:17515431-17515651(+)$1	220	76	106	12.4273
$$$$$bb!!cccooooooccc22bb333cc	chr5:138221140-138221360(+)$1	220	60	90	15.4499
cc[dddd!!cccooooooccc]ddddcccD	chr12:40763146-40763366(-)$1	220	38	68	14.7153
ggggg[a[acccooooooccc]a]a]gggg	chr5:21308868-21309090(+)$1	222	14	44	16.4415
cc[ccca####cccmmmmccc333a]ccc]	chr2:144369510-144369730(-)$1	220	158	188	11.5052
ffffff[ccc[aooooooacccffffffbb	chr3:122484406-122484628(+)$1	222	14	44	13.8099
ffff$$$$$cccooooooccc4444fffff	chr19:5685574-5685794(-)$1	220	65	95	15.1309
$$$$$gggggggooooooggggggg]eeee	chr5:25330900-25331120(+)$1	220	59	89	13.7992
ccc[bb####bboooooobb333bb]ccc]	chr19:9021125-9021345(+)$1	220	82	112	15.2678
ee[cccffffffooooooffffff]ccc33	chr8:109188057-109188277(+)$1	220	154	184	13.0019
ffffff"""cccooooooccc4444fffff	chr1:177812983-177813203(+)$1	220	100	130	16.2169
$$$ccc"""ddddoooooodddd333ccc5	chr10:90559201-90559422(+)$1	221	77	107	12.7623
"""ccc"""cccnnnnnccc333ccc333e	chr7:100066202-100066422(+)$1	220	173	203	13.0573
[cccdddd!!bboooooobb333dddd666	chr1:152278266-152278486(+)$1	220	107	137	13.5859
dd!!cccddddoooooodddd]ccc]dddd	chr11:23184976-23185196(+)$1	220	89	119	12.3701
###eeeee!!bboooooobb22eeeeeddd	chr16:91641463-91641683(-)$1	220	84	114	13.9185
e!!ggggggg[aooooooa]ggggggg444	chr3:95699267-95699487(+)$1	220	152	182	15.0495
+dddd####cccooooooccc333dddd]b	chr17:28465676-28465896(+)$1	220	77	107	15.4276
ffff[dddd[bboooooobb]dddd]ffff	chr19:46587719-46587941(+)$1	222	40	70	12.9469
eeeeeccc!!bboooooobb22ccc]eeee	chr13:13600937-13601157(+)$1	220	12	42	14.7338
ggggg!!eeeeeooooooeeeee4444ggg	chr5:24770784-24771008(+)$1	224	180	210	13.2204
eeeee"""ddddooooooddddeeeee]bb	chr18:25297427-25297649(-)$1	222	55	85	12.8853

#otherMatches

#Seq PSSM
AAUUUUGAGACCAACACAGGUAAUCACCAU	chr11:49637152-49637372(+)$1	220	160	190	16.1016
GACUCUUCGGAAGAAAAUGCUGCUGUGGAG	chr1:141319699-141319919(+)$1	220	91	121	12.7178
GAGAGUCGACAGUAACGAAACAGUCUCGCC	chr3:122637270-122637490(-)$1	220	175	205	12.1987
UGUUAAGAUAAAAAGCACUUUGUUUUAUGA	chr13:113283688-113283911(+)$1	223	60	90	15.5994
CGACGACGAUCUCGAAGUAGAAGUCUUGUG	chr17:23953009-23953232(+)$1	223	141	171	16.3965
CCGUCUCCUUUUCCUCAAAGAUAAGCAGAG	chr19:11017631-11017857(-)$1	226	9	39	13.7002
AGCGGGGAGGAGGAGUUGCAGCUCCAGCUG	chr7:5044372-5044596(+)$1	224	132	162	12.4579
UAGGGGUAGGGUGGAGCAGCUUUGCCCUGG	chr11:6239765-6239987(+)$1	222	17	47	13.0911
GGGCUGUGCACGUGCUAUCUGUGCAGCCUC	chr11:68786648-68786868(-)$1	220	131	161	14.9858
GAUcggggucuuacugugaagcccuggucc	chr10:80571584-80571804(+)$1	220	180	210	16.8169
UUUAAAAAUAUAUAGCAUUGUAACUUUUAA	chr3:51247759-51247983(+)$1	224	117	147	12.9839
GGUGUGCGGACUUGUCUCGGUGCCGUUCAU	chr3:36451554-36451774(+)$1	220	3	33	13.8770
AGUGUCAGUGAAGGUGGAUUUGCUGACUCU	chr3:95131114-95131334(-)$1	220	40	70	15.3275
AGCUCAUUCUUUUCUCGUAAAUCUGACUAU	chr5:139702676-139702917(+)$1	241	203	233	17.6762
AUGCUGAAUUGCUUUUUUGUAUGCUUCAGU	chr11:54374740-54374978(+)$1	238	161	191	15.7800
CAGUUUGAAAUUGAGCGAGAUCUCAGGCUG	chr8:114292518-114292740(-)$1	222	96	126	12.9035
AUCUCUUUAGUAUCCUUUUGAUAGAGCAGA	chr10:83045903-83046123(+)$1	220	86	116	13.2077
CUGUCUGAGUACGAUGCGGUAGAGAGAGAG	chr10:5991033-5991253(-)$1	220	73	103	16.8300
GGCCGCUGAUGGAgcgcgccacccggcccg	chr6:70794670-70794901(+)$1	231	41	71	16.3185
CACGCUUUUUGGUACCUUCCAUGUGGCCCA	chr7:109575107-109575352(+)$1	245	132	162	15.1316
UCCUGACCUAAAGUUUAAUUGUGGUUCAGG	chr4:12022400-12022620(+)$1	220	123	153	13.2068
CCUUUGGUUGGAGAUAAUUUCGUUCGAUUC	chr4:15925134-15925354(-)$1	220	108	138	12.7902
GAAGACAAAACUAAGGUCAGUACUGUCUUA	chr4:6129418-6129640(+)$1	222	156	186	15.2160
CGACGACGAUCUCGAAGUAGAAGUCUUGUG	chr17:23953105-23953325(+)$1	220	45	75	16.3965
GAUUGGCUGGAGGAUGCGUUCCAGCUAGCU	chr9:48818250-48818470(+)$1	220	130	160	15.2968
CUCAAGUUCGCCUAUUGUGGUAAGCCCUGA	chr9:61262522-61262742(+)$1	220	127	157	16.1782
AGCAUAGACGAAGCAGUGUUCACCUGUGCU	chr4:32843245-32843465(+)$1	220	57	87	16.8137
GUGCUGGAUGUGGAAGUAUACUCCAGUAGA	chr4:115824574-115824806(+)$1	232	163	193	14.2803
CGUGUGCAGCUGAAAGAGCAGAAGGCACGU	chr2:32161019-32161239(+)$1	220	29	59	16.5134
UUCUAGACAGGUAGUUGAAUCUGUUGGAAA	chr17:17515431-17515651(+)$1	220	76	106	12.4273
CCCUUCAGAAGAUACCUUUCUCAUGCAUCG	chr5:138221140-138221360(+)$1	220	60	90	15.4499
GAAUGGACUGUCAGACCAGACUUCCAUCCU	chr12:40763146-40763366(-)$1	220	38	68	14.7153
CUCAGGGGCUCGGUUUGACGAUGGCGCUGG	chr5:21308868-21309090(+)$1	222	14	44	16.4415
GAGUUCCAUGAACUGAUUAGUGUGGUGAAG	chr2:144369510-144369730(-)$1	220	158	188	11.5052
agagCCUGUGUGUAUUUUCCAUGGCUUUGU	chr3:122484406-122484628(+)$1	222	14	44	13.8099
UGACACACUUCGUUCCUUUGACACAGUCAU	chr19:5685574-5685794(-)$1	220	65	95	15.1309
GGCAAGUUGGUGAACGCACACUAACGGGGA	chr5:25330900-25331120(+)$1	220	59	89	13.7992
CCGGCAGAUUGAUCAGUUUCUCGUGGUGGC	chr19:9021125-9021345(+)$1	220	82	112	15.2678
GUGUGUGACUGUGAAGGGACGGUCAACAAC	chr8:109188057-109188277(+)$1	220	154	184	13.0019
CCUGUCAACGUGAAGAAGUACAAAGGACAG	chr1:177812983-177813203(+)$1	220	100	130	16.2169
GACUUCAUAGCAUAUUCAAGUGCACGGGAA	chr10:90559201-90559422(+)$1	221	77	107	12.7623
UUUUUGUUUGUUUGUUUGAUUUUUAACCUU	chr7:100066202-100066422(+)$1	220	173	203	13.0573
AGGACCUCCAGGAUAAAACCACAGAGGAGC	chr1:152278266-152278486(+)$1	220	107	137	13.5859
UGGAGUCCAGGAUAUGGCUUGUGACACAUU	chr11:23184976-23185196(+)$1	220	89	119	12.3701
CGAUGCUUUGGCCCCACAGCACAAGCAGCU	chr16:91641463-91641683(-)$1	220	84	114	13.9185
UAUUUUGGCUGAUGCACUUGGGCCAGGUGU	chr3:95699267-95699487(+)$1	220	152	182	15.0495
AGCAGCAAAGUCUCACGCGACACCCUGUAC	chr17:28465676-28465896(+)$1	220	77	107	15.4276
CAGGAGGCCAAGAAGCUGCUGGGCUCCCUG	chr19:46587719-46587941(+)$1	222	40	70	12.9469
GUGAACAAUGACCAACUUGUAUUUGCUUCA	chr13:13600937-13601157(+)$1	220	12	42	14.7338
GGAACCUGGGCUUUAUCUAGUCCUGAUGUU	chr5:24770784-24771008(+)$1	224	180	210	13.2204
UCACAGAAGAGUCCGACAACUUUGUGAACA	chr18:25297427-25297649(-)$1	222	55	85	12.8853

#DB
.....(((.(((......)))..)))...)	chr11:49637152-49637372(+)$1	1	160	190	16.1016
.(((((.(((.((......)).))).))))	chr1:141319699-141319919(+)$1	1	91	121	12.7178
((..((.(((.((......)).)))..)).	chr3:122637270-122637490(-)$1	1	175	205	12.1987
(..(((((((((......)))))))))...	chr13:113283688-113283911(+)$1	1	60	90	15.5994
(((.(((..(((......))).))))))))	chr17:23953009-23953232(+)$1	1	141	171	16.3965
((.(((.(((.((......)).))).))).	chr19:11017631-11017857(-)$1	1	9	39	13.7002
(((..((((..(......)..)))).))))	chr7:5044372-5044596(+)$1	1	132	162	12.4579
..((((((((((......)))))))))).(	chr11:6239765-6239987(+)$1	1	17	47	13.0911
)(((((((((.(......))))))))))((	chr11:68786648-68786868(-)$1	1	131	161	14.9858
((((((((.(((......))))))))))))	chr10:80571584-80571804(+)$1	1	180	210	16.8169
.((((((.((((......))))..))))))	chr3:51247759-51247983(+)$1	1	117	147	12.9839
((((.(((((((......))).)))).)))	chr3:36451554-36451774(+)$1	1	3	33	13.8770
((.(((((((((......))))))))).))	chr3:95131114-95131334(-)$1	1	40	70	15.3275
(..(((...(((......)))..)))...)	chr5:139702676-139702917(+)$1	1	203	233	17.6762
(.((((((.(((......)))...))))))	chr11:54374740-54374978(+)$1	1	161	191	15.7800
((((((((.(((......))).))))))))	chr8:114292518-114292740(-)$1	1	96	126	12.9035
.((((((((.((......)).))))).)))	chr10:83045903-83046123(+)$1	1	86	116	13.2077
((.(((...(((......))).))).))))	chr10:5991033-5991253(-)$1	1	73	103	16.8300
(((((..(.(((......)))).)))))))	chr6:70794670-70794901(+)$1	1	41	71	16.3185
...(((...(((......)))...)))...	chr7:109575107-109575352(+)$1	1	132	162	15.1316
.(((((((..((......))..)).)))))	chr4:12022400-12022620(+)$1	1	123	153	13.2068
...((((.((((......)))).))))..)	chr4:15925134-15925354(-)$1	1	108	138	12.7902
.((((((..(((......)))..)))))).	chr4:6129418-6129640(+)$1	1	156	186	15.2160
(((.(((..(((......))).))))))))	chr17:23953105-23953325(+)$1	1	45	75	16.3965
(.((((((((((......))))))))))))	chr9:48818250-48818470(+)$1	1	130	160	15.2968
)(((.(((.(((......))).)))..)))	chr9:61262522-61262742(+)$1	1	127	157	16.1782
(((((((..(((......)))..)))))))	chr4:32843245-32843465(+)$1	1	57	87	16.8137
)(((((((.(((......))))))))))..	chr4:115824574-115824806(+)$1	1	163	193	14.2803
(((((....(((......)))...))))))	chr2:32161019-32161239(+)$1	1	29	59	16.5134
((((((.(((((......))))))))))..	chr17:17515431-17515651(+)$1	1	76	106	12.4273
.....((..(((......)))..))...))	chr5:138221140-138221360(+)$1	1	60	90	15.4499
((.((((..(((......))).))))))))	chr12:40763146-40763366(-)$1	1	38	68	14.7153
(((((.(.((((......))).).).))))	chr5:21308868-21309090(+)$1	1	14	44	16.4415
((.((((....(((....)))...).))).	chr2:144369510-144369730(-)$1	1	158	188	11.5052
((((((.(((.(......))))))))))((	chr3:122484406-122484628(+)$1	1	14	44	13.8099
((((.....(((......)))....)))))	chr19:5685574-5685794(-)$1	1	65	95	15.1309
.....(((((((......))))))).))))	chr5:25330900-25331120(+)$1	1	59	89	13.7992
(((.((....((......))...)).))).	chr19:9021125-9021345(+)$1	1	82	112	15.2678
((.(((((((((......)))))).)))..	chr8:109188057-109188277(+)$1	1	154	184	13.0019
((((((...(((......)))....)))))	chr1:177812983-177813203(+)$1	1	100	130	16.2169
...(((...((((......))))...))).	chr10:90559201-90559422(+)$1	1	77	107	12.7623
...(((...(((.....)))...)))...)	chr7:100066202-100066422(+)$1	1	173	203	13.0573
.(((((((..((......))...))))...	chr1:152278266-152278486(+)$1	1	107	137	13.5859
((..(((((((......)))).))).))))	chr11:23184976-23185196(+)$1	1	89	119	12.3701
...(((((..((......))..))))))))	chr16:91641463-91641683(-)$1	1	84	114	13.9185
(..(((((((.(......).)))))))...	chr3:95699267-95699487(+)$1	1	152	182	15.0495
.((((....(((......)))...)))).)	chr17:28465676-28465896(+)$1	1	77	107	15.4276
((((.((((.((......)).)))).))))	chr19:46587719-46587941(+)$1	1	40	70	12.9469
((((((((..((......))..))).))))	chr13:13600937-13601157(+)$1	1	12	42	14.7338
(((((..(((((......)))))....)))	chr5:24770784-24771008(+)$1	1	180	210	13.2204
(((((...((((......))))))))).))	chr18:25297427-25297649(-)$1	1	55	85	12.8853

#PSSM
e : 0.13	c : 0.13	f : 0.11	b : 0.09	$ : 0.07	d : 0.07	[ : 0.07	g : 0.07	# : 0.03	+ : 0.03	& : 0.01	: : 0.01	= : 0.01	h : 0.01	% : 0.01	" : 0.01	
e : 0.17	f : 0.13	c : 0.13	d : 0.09	g : 0.09	$ : 0.07	! : 0.05	[ : 0.03	# : 0.03	b : 0.01	: : 0.01	i : 0.01	= : 0.01	h : 0.01	% : 0.01	" : 0.01	
f : 0.15	e : 0.13	[ : 0.11	! : 0.09	g : 0.09	$ : 0.07	c : 0.07	d : 0.05	= : 0.05	# : 0.03	i : 0.01	h : 0.01	% : 0.01	" : 0.01	
c : 0.21	f : 0.15	e : 0.11	g : 0.11	d : 0.07	$ : 0.05	! : 0.05	i : 0.05	[ : 0.05	= : 0.05	h : 0.01	
c : 0.21	e : 0.13	f : 0.11	g : 0.11	$ : 0.07	d : 0.07	i : 0.05	= : 0.05	[ : 0.05	b : 0.03	! : 0.01	h : 0.01	
c : 0.27	d : 0.11	e : 0.09	f : 0.09	g : 0.07	b : 0.05	i : 0.05	= : 0.05	! : 0.03	# : 0.03	h : 0.01	[ : 0.01	$ : 0.01	" : 0.01	
" : 0.13	c : 0.11	d : 0.11	[ : 0.09	f : 0.07	g : 0.07	i : 0.05	= : 0.05	# : 0.05	e : 0.03	! : 0.03	b : 0.03	a : 0.03	h : 0.01	$ : 0.01	
c : 0.13	" : 0.13	! : 0.11	d : 0.09	e : 0.07	# : 0.07	i : 0.05	= : 0.05	[ : 0.05	g : 0.05	f : 0.03	h : 0.01	a : 0.01	b : 0.01	$ : 0.01	
! : 0.19	[ : 0.13	d : 0.13	" : 0.11	c : 0.07	# : 0.07	i : 0.05	e : 0.05	= : 0.03	g : 0.03	a : 0.01	$ : 0.01	f : 0.01	
c : 0.52	! : 0.09	d : 0.09	i : 0.05	= : 0.03	[ : 0.03	e : 0.03	# : 0.03	g : 0.03	f : 0.01	
c : 0.45	b : 0.13	[ : 0.11	d : 0.09	i : 0.03	= : 0.03	e : 0.03	! : 0.01	# : 0.01	g : 0.01	f : 0.01	
c : 0.47	b : 0.19	a : 0.07	d : 0.07	i : 0.03	= : 0.03	e : 0.03	g : 0.01	f : 0.01	o : 0.01	
o : 0.88	b : 0.05	c : 0.01	d : 0.01	n : 0.01	
o : 0.96	c : 0.01	n : 0.01	
o : 0.96	m : 0.01	n : 0.01	
o : 0.96	m : 0.01	n : 0.01	
o : 0.96	m : 0.01	n : 0.01	
o : 0.94	m : 0.01	c : 0.01	d : 0.01	
c : 0.47	b : 0.13	o : 0.07	a : 0.07	d : 0.07	i : 0.03	= : 0.03	e : 0.03	g : 0.01	f : 0.01	
c : 0.49	b : 0.19	d : 0.09	i : 0.05	= : 0.03	e : 0.03	2 : 0.01	g : 0.01	f : 0.01	] : 0.01	
c : 0.47	d : 0.09	2 : 0.07	b : 0.05	i : 0.05	3 : 0.05	= : 0.03	] : 0.03	e : 0.03	g : 0.03	f : 0.01	
] : 0.23	2 : 0.15	3 : 0.15	d : 0.11	i : 0.05	= : 0.05	e : 0.05	g : 0.05	4 : 0.03	a : 0.01	c : 0.01	f : 0.01	
c : 0.17	3 : 0.15	2 : 0.11	d : 0.09	e : 0.09	i : 0.05	= : 0.05	g : 0.05	] : 0.03	f : 0.03	4 : 0.03	h : 0.01	b : 0.01	a : 0.01	
c : 0.23	d : 0.11	3 : 0.11	g : 0.09	e : 0.07	i : 0.05	= : 0.05	b : 0.05	f : 0.05	4 : 0.05	2 : 0.01	h : 0.01	] : 0.01	
c : 0.25	d : 0.13	f : 0.09	g : 0.09	e : 0.07	i : 0.05	= : 0.05	4 : 0.05	] : 0.03	b : 0.03	a : 0.03	h : 0.01	3 : 0.01	
] : 0.21	e : 0.13	f : 0.13	c : 0.09	d : 0.09	g : 0.07	i : 0.05	= : 0.05	2 : 0.03	3 : 0.03	h : 0.01	4 : 0.01	
e : 0.17	f : 0.15	c : 0.13	d : 0.11	g : 0.09	3 : 0.07	i : 0.05	= : 0.05	2 : 0.03	] : 0.03	h : 0.01	4 : 0.01	
c : 0.15	f : 0.15	e : 0.13	d : 0.11	3 : 0.09	g : 0.09	= : 0.05	] : 0.03	6 : 0.03	b : 0.01	i : 0.01	h : 0.01	2 : 0.01	4 : 0.01	
c : 0.17	e : 0.13	f : 0.13	3 : 0.09	d : 0.09	b : 0.07	g : 0.07	: : 0.03	6 : 0.03	4 : 0.03	= : 0.01	h : 0.01	2 : 0.01	] : 0.01	
e : 0.17	f : 0.13	d : 0.09	c : 0.09	g : 0.09	b : 0.07	] : 0.05	3 : 0.03	6 : 0.03	4 : 0.03	2 : 0.01	= : 0.01	h : 0.01	> : 0.01	: : 0.01	D : 0.01	5 : 0.01	

#score	738.519111717171
#seq	51
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_CDS_m2_run2.txt

#BEAR
$$$$eeeeesssssssssseeeee22hhh	chr2:174125804-174126076(+)$1	272	26	55	14.2831
eeeeexxxxxxxxxxxxxxxeeeee:eee	chr19:4792248-4792540(-)$1	292	14	43	14.7571
==========ssssssssss=========	chr5:122096592-122096861(-)$1	269	154	183	15.2148
d"""ddddssssssssssdddd4444ddd	chr3:108706705-108706973(-)$1	268	190	219	14.6917
i!!eeeeeuuuuuuuuuuuueeeee22ii	chr6:56728722-56729000(-)$1	278	9	38	20.5253
ccc[bb!!bbtttttttttttbb22bb]c	chr6:22240953-22241221(+)$1	268	215	244	17.9528
:ggggggguuuuuuuuuuuuggggggg::	chr4:33125089-33125363(+)$1	274	124	153	17.3780
cdddd!!ccctttttttttttccc22ddd	chr8:74842835-74843118(+)$1	283	116	145	19.0135
ggggggg[cccrrrrrrrrrcccgggggg	chr17:6084525-6084794(+)$1	269	163	192	12.5464
hhhh!!ccctttttttttttccc22hhhh	chr4:45372561-45372833(+)$1	272	31	60	19.2344
ccc!!bb[bbrrrrrrrrrbb]bb22ccc	chr5:108863239-108863508(-)$1	269	144	173	11.8958
#gggggggwwwwwwwwwwwwwwggggggg	chr16:36049855-36050132(-)$1	277	15	44	20.2233
gg!!bbyyyyyyyyyyyyyyyybb]gggg	chr14:52760734-52761005(+)$1	271	133	162	19.0919
eee!!cccuuuuuuuuuuuuccc22eeee	chr14:45912565-45912837(-)$1	272	241	270	21.3605
ccc[ddddrrrrrrrrrddddccc22fff	chr5:123244349-123244627(-)$1	278	80	109	12.1648
ffff!!bbuuuuuuuuuuuubb22fffff	chr2:32092881-32093158(+)$1	277	234	263	19.1673
fffff[bb[arrrrrrrrra]bb333fff	chr4:155331122-155331424(+)$1	302	57	86	12.6773
ggggdddduuuuuuuuuuuudddd:::::	chr3:102703878-102704148(-)$1	270	61	90	16.3029
d[ffffffvvvvvvvvvvvvvffffffdd	chr2:156606174-156606446(+)$1	272	200	229	17.9345
dddccc[ddddrrrrrrrrrdddd22ccc	chr7:25670028-25670303(+)$1	275	184	213	12.0616
[dddd[bbxxxxxxxxxxxxxxxbb]ddd	chr2:153142656-153142935(+)$1	279	6	35	15.7725
d^^^^^^^^^^^^^^^^^^^dddd]eeee	chr17:35292437-35292710(-)$1	273	108	137	13.1964
===[bbcccssssssssssccc4444bb]	chr14:70066969-70067240(+)$1	271	38	67	15.4481
c[a[ddddvvvvvvvvvvvvvdddd]a]c	chr13:73773815-73774087(+)$1	272	185	214	20.1571
e"""dddduuuuuuuuuuuuddddeeeee	chr8:28383691-28383967(+)$1	276	171	200	20.7768
iii[dddd[bbssssssssssbb]dddd7	chr2:34678076-34678352(-)$1	276	160	189	12.9908
hhhhhhbbvvvvvvvvvvvvvbb]hhhhh	chr19:5384549-5384817(-)$1	268	86	115	17.3154
ggg[dddduuuuuuuuuuuudddd22ggg	chr19:46681074-46681349(+)$1	275	135	164	22.1526
!!ffffffyyyyyyyyyyyyyyyyfffff	chr10:126721767-126722035(-)$1	268	165	194	17.7867
e[addddvvvvvvvvvvvvvdddd]a22e	chr13:81930942-81931210(+)$1	268	57	86	19.0017
eee[ddddxxxxxxxxxxxxxxxdddd]e	chr6:51413984-51414275(-)$1	291	50	79	16.6225
[ddddxxxxxxxxxxxxxxxdddd22eee	chr8:95850590-95850858(-)$1	268	199	228	16.8417
bb!!eeeeesssssssssseeeee22bbF	chr1:36501804-36502071(-)$1	267	120	149	14.3982
fffff[ccctttttttttttccc]fffff	chr17:37114860-37115128(-)$1	268	193	222	19.0103
ddd"""ccctttttttttttccc333ddd	chr9:64825922-64826205(+)$1	283	182	211	20.4924
==========ssssssssss=========	chr5:93697524-93697801(+)$1	277	162	191	15.2148

#otherMatches

#Seq PSSM
GAAACCCUGUUAGAAGUUCCAGGGAGGGA	chr2:174125804-174126076(+)$1	272	26	55	14.2831
GGGCCAAGUUUGAGGAGUACGGCCCAGUC	chr19:4792248-4792540(-)$1	292	14	43	14.7571
GGGAAGGUUUCCUGUCUCUAGAACUUUCU	chr5:122096592-122096861(-)$1	269	154	183	15.2148
CUUUUUUCCCCCCAAGUUGAGAUUGUGCA	chr3:108706705-108706973(-)$1	268	190	219	14.6917
AAACUUUAUCCAUCCUGUCUUGAAGAAUC	chr6:56728722-56729000(-)$1	278	9	38	20.5253
GCCAUGAAUCUACACAACAACGAAGCGGG	chr6:22240953-22241221(+)$1	268	215	244	17.9528
CAGAUUCCGAUUUUGAUGGAGGAGUUUAC	chr4:33125089-33125363(+)$1	274	124	153	17.3780
GGCCACAGCACACACAGUCCCUGCCAUGG	chr8:74842835-74843118(+)$1	283	116	145	19.0135
AGACACUUGAGAGAGGCCAGCUCAGUGUC	chr17:6084525-6084794(+)$1	269	163	192	12.5464
GAGAUUAAAUGAACCAGUUUUUUUUUUUC	chr4:45372561-45372833(+)$1	272	31	60	19.2344
AGGUCUCUCCACUCAUCAAGGUGAAUCCU	chr5:108863239-108863508(-)$1	269	144	173	11.8958
CUGAAAGAUACAAAUAGCAUUUUUUUUCA	chr16:36049855-36050132(-)$1	277	15	44	20.2233
UGAAUCACCUCCUGGACUUCAAGAACAGC	chr14:52760734-52761005(+)$1	271	133	162	19.0919
AUACAUUAUAACAUAGAUAUUAACAUAUA	chr14:45912565-45912837(-)$1	272	241	270	21.3605
ACUCGGCAGAACUGGCAUGCCAGUGAGUC	chr5:123244349-123244627(-)$1	278	80	109	12.1648
GAGAGACAUUCUGGGUUUCUUGGAUCUCU	chr2:32092881-32093158(+)$1	277	234	263	19.1673
UUUCUCUCAGGAAAUUAAACAGAAACAGA	chr4:155331122-155331424(+)$1	302	57	86	12.6773
UGUCACACUUUUUUUCUAUUGUGUUUAGG	chr3:102703878-102704148(-)$1	270	61	90	16.3029
CUCAGGUCAGUGUACACGGGAGACCUGGG	chr2:156606174-156606446(+)$1	272	200	229	17.9345
CCUUCCUCAAAAAGUAAGUGUUUGUUGGA	chr7:25670028-25670303(+)$1	275	184	213	12.0616
AUGCAAUCUUUGUUAUCACUAUUGAAUGC	chr2:153142656-153142935(+)$1	279	6	35	15.7725
CAGCACUUAUGACCUCUAAAGCUGUGGGG	chr17:35292437-35292710(-)$1	273	108	137	13.1964
UGGGGCCCUGACAGCUCGAAGGAUACGUG	chr14:70066969-70067240(+)$1	271	38	67	15.4481
CUGUCUAUCACAUUUGCUCUCAUGGUCUG	chr13:73773815-73774087(+)$1	272	185	214	20.1571
CCAAAGGACCUGCCAGCCAUUCCUGGGGU	chr8:28383691-28383967(+)$1	276	171	200	20.7768
GCUAUUUUGAGGAUGAAGCAACUGGAGGA	chr2:34678076-34678352(-)$1	276	160	189	12.9908
CUCCUCAGGAAAAUAAAGACACUGGGGGA	chr19:5384549-5384817(-)$1	268	86	115	17.3154
GAGAAGUCAGAAGACAGUGGGACUGGUUC	chr19:46681074-46681349(+)$1	275	135	164	22.1526
UUGGGAGACCUGCCCCCCCUAUUAUUUCC	chr10:126721767-126722035(-)$1	268	165	194	17.7867
AAGCAUUUAAACUAUUUGACGAUGACGAU	chr13:81930942-81931210(+)$1	268	57	86	19.0017
CCAAUUCUUUUACAGGAAAUUAUGGAAGU	chr6:51413984-51414275(-)$1	291	50	79	16.6225
AAGUAUCACUCUCAAACAACUAUUGAACC	chr8:95850590-95850858(-)$1	268	199	228	16.8417
CGGGUCAAGCGGUGGAGUACUUGAAACGG	chr1:36501804-36502071(-)$1	267	120	149	14.3982
GGAUGUUAACUUUAUUAUUUUUAUCAUUU	chr17:37114860-37115128(-)$1	268	193	222	19.0103
UGUAUUGCUGACCCAGAGAGAGCUACACA	chr9:64825922-64826205(+)$1	283	182	211	20.4924
GGGGUUCAGCUUUUCGGAUUGUUGAACUU	chr5:93697524-93697801(+)$1	277	162	191	15.2148

#DB
....(((((..........)))))..)))	chr2:174125804-174126076(+)$1	1	26	55	14.2831
(((((...............))))).(((	chr19:4792248-4792540(-)$1	1	14	43	14.7571
((((((((((..........)))))))))	chr5:122096592-122096861(-)$1	1	154	183	15.2148
(...((((..........))))....)))	chr3:108706705-108706973(-)$1	1	190	219	14.6917
(..(((((............)))))..))	chr6:56728722-56729000(-)$1	1	9	38	20.5253
(((.((..((...........))..)).)	chr6:22240953-22241221(+)$1	1	215	244	17.9528
.(((((((............)))))))..	chr4:33125089-33125363(+)$1	1	124	153	17.3780
)((((..(((...........)))..)))	chr8:74842835-74843118(+)$1	1	116	145	19.0135
(((((((.(((.........)))))))))	chr17:6084525-6084794(+)$1	1	163	192	12.5464
((((..(((...........)))..))))	chr4:45372561-45372833(+)$1	1	31	60	19.2344
(((..((.((.........)).))..)))	chr5:108863239-108863508(-)$1	1	144	173	11.8958
.(((((((..............)))))))	chr16:36049855-36050132(-)$1	1	15	44	20.2233
((..((................)).))))	chr14:52760734-52761005(+)$1	1	133	162	19.0919
(((..(((............)))..))))	chr14:45912565-45912837(-)$1	1	241	270	21.3605
(((.((((.........)))))))..)))	chr5:123244349-123244627(-)$1	1	80	109	12.1648
((((..((............))..)))))	chr2:32092881-32093158(+)$1	1	234	263	19.1673
(((((.((.(.........).))...)))	chr4:155331122-155331424(+)$1	1	57	86	12.6773
))))((((............)))).....	chr3:102703878-102704148(-)$1	1	61	90	16.3029
(.((((((.............))))))))	chr2:156606174-156606446(+)$1	1	200	229	17.9345
((((((.((((.........))))..)))	chr7:25670028-25670303(+)$1	1	184	213	12.0616
.((((.((...............)).)))	chr2:153142656-153142935(+)$1	1	6	35	15.7725
(...................)))).))))	chr17:35292437-35292710(-)$1	1	108	137	13.1964
(((.(((((..........)))....)).	chr14:70066969-70067240(+)$1	1	38	67	15.4481
(.(.((((.............)))).).)	chr13:73773815-73774087(+)$1	1	185	214	20.1571
(...((((............)))))))))	chr8:28383691-28383967(+)$1	1	171	200	20.7768
(((.((((.((..........)).)))).	chr2:34678076-34678352(-)$1	1	160	189	12.9908
((((((((.............)).)))))	chr19:5384549-5384817(-)$1	1	86	115	17.3154
(((.((((............))))..)))	chr19:46681074-46681349(+)$1	1	135	164	22.1526
..((((((................)))))	chr10:126721767-126722035(-)$1	1	165	194	17.7867
(.(((((.............)))).)..)	chr13:81930942-81931210(+)$1	1	57	86	19.0017
(((.((((...............)))).)	chr6:51413984-51414275(-)$1	1	50	79	16.6225
.((((...............))))..)))	chr8:95850590-95850858(-)$1	1	199	228	16.8417
((..(((((..........)))))..)))	chr1:36501804-36502071(-)$1	1	120	149	14.3982
(((((.(((...........))).)))))	chr17:37114860-37115128(-)$1	1	193	222	19.0103
(((...(((...........)))...)))	chr9:64825922-64826205(+)$1	1	182	211	20.4924
((((((((((..........)))))))))	chr5:93697524-93697801(+)$1	1	162	191	15.2148

#PSSM
e : 0.13	d : 0.13	c : 0.13	g : 0.11	= : 0.08	f : 0.08	i : 0.05	h : 0.05	[ : 0.05	$ : 0.02	: : 0.02	# : 0.02	! : 0.02	b : 0.02	
g : 0.16	d : 0.13	e : 0.08	= : 0.08	c : 0.08	f : 0.08	[ : 0.08	" : 0.05	! : 0.05	h : 0.05	$ : 0.02	^ : 0.02	i : 0.02	b : 0.02	
g : 0.13	d : 0.13	f : 0.13	e : 0.08	= : 0.08	! : 0.08	c : 0.08	" : 0.05	h : 0.05	a : 0.05	$ : 0.02	^ : 0.02	i : 0.02	
[ : 0.19	f : 0.13	g : 0.11	d : 0.11	! : 0.11	" : 0.08	e : 0.05	= : 0.05	h : 0.05	$ : 0.02	c : 0.02	^ : 0.02	
d : 0.33	e : 0.11	! : 0.11	f : 0.11	b : 0.08	g : 0.08	= : 0.05	c : 0.02	^ : 0.02	h : 0.02	" : 0.02	
d : 0.25	b : 0.11	e : 0.08	g : 0.08	! : 0.08	[ : 0.08	x : 0.05	= : 0.05	c : 0.05	f : 0.05	^ : 0.02	h : 0.02	" : 0.02	
d : 0.25	c : 0.13	b : 0.13	e : 0.08	g : 0.08	x : 0.05	= : 0.05	! : 0.05	f : 0.05	y : 0.02	[ : 0.02	^ : 0.02	
d : 0.25	c : 0.16	b : 0.11	e : 0.08	x : 0.05	= : 0.05	g : 0.05	[ : 0.05	f : 0.05	! : 0.02	y : 0.02	^ : 0.02	v : 0.02	
u : 0.19	c : 0.16	x : 0.11	v : 0.11	e : 0.05	= : 0.05	b : 0.05	y : 0.05	[ : 0.05	s : 0.02	w : 0.02	r : 0.02	d : 0.02	^ : 0.02	
u : 0.19	s : 0.11	x : 0.11	v : 0.11	b : 0.08	t : 0.08	= : 0.05	c : 0.05	y : 0.05	w : 0.02	r : 0.02	a : 0.02	d : 0.02	^ : 0.02	
u : 0.19	s : 0.16	t : 0.13	x : 0.11	v : 0.11	r : 0.08	y : 0.05	c : 0.02	w : 0.02	d : 0.02	^ : 0.02	b : 0.02	
s : 0.19	u : 0.19	t : 0.13	r : 0.13	x : 0.11	v : 0.11	y : 0.05	w : 0.02	^ : 0.02	
s : 0.19	u : 0.19	t : 0.13	r : 0.13	x : 0.11	v : 0.11	y : 0.05	w : 0.02	^ : 0.02	
s : 0.19	u : 0.19	t : 0.13	r : 0.13	x : 0.11	v : 0.11	y : 0.05	w : 0.02	^ : 0.02	
s : 0.19	u : 0.19	t : 0.13	r : 0.13	x : 0.11	v : 0.11	y : 0.05	w : 0.02	^ : 0.02	
s : 0.19	u : 0.19	t : 0.13	r : 0.13	x : 0.11	v : 0.11	y : 0.05	w : 0.02	^ : 0.02	
s : 0.19	u : 0.19	t : 0.13	r : 0.13	x : 0.11	v : 0.11	y : 0.05	w : 0.02	^ : 0.02	
s : 0.19	u : 0.19	t : 0.13	x : 0.11	r : 0.11	v : 0.11	y : 0.05	w : 0.02	d : 0.02	^ : 0.02	
u : 0.19	s : 0.16	t : 0.13	x : 0.11	r : 0.11	v : 0.11	d : 0.05	y : 0.05	w : 0.02	^ : 0.02	
u : 0.19	t : 0.13	x : 0.11	v : 0.11	s : 0.08	e : 0.05	d : 0.05	r : 0.05	y : 0.05	b : 0.02	w : 0.02	a : 0.02	^ : 0.02	c : 0.02	
d : 0.25	c : 0.16	e : 0.11	v : 0.08	= : 0.05	t : 0.05	b : 0.05	y : 0.05	x : 0.05	g : 0.02	w : 0.02	] : 0.02	s : 0.02	
d : 0.25	c : 0.22	b : 0.13	e : 0.11	= : 0.05	y : 0.05	x : 0.05	g : 0.02	] : 0.02	w : 0.02	f : 0.02	
d : 0.22	c : 0.19	b : 0.16	e : 0.11	= : 0.05	4 : 0.05	g : 0.05	x : 0.05	2 : 0.02	f : 0.02	y : 0.02	
d : 0.25	e : 0.11	2 : 0.11	g : 0.08	b : 0.08	] : 0.08	= : 0.05	4 : 0.05	c : 0.05	3 : 0.05	f : 0.02	y : 0.02	
2 : 0.30	f : 0.11	e : 0.08	g : 0.08	] : 0.08	d : 0.08	= : 0.05	4 : 0.05	3 : 0.05	: : 0.02	b : 0.02	h : 0.02	
2 : 0.25	g : 0.11	f : 0.11	e : 0.08	: : 0.05	= : 0.05	4 : 0.05	h : 0.05	3 : 0.05	] : 0.05	d : 0.05	b : 0.02	a : 0.02	
d : 0.16	f : 0.16	e : 0.13	g : 0.13	h : 0.08	b : 0.08	= : 0.05	2 : 0.05	c : 0.05	: : 0.02	a : 0.02	
d : 0.16	e : 0.13	f : 0.13	g : 0.11	h : 0.08	] : 0.08	= : 0.05	: : 0.05	c : 0.05	b : 0.05	i : 0.02	2 : 0.02	
e : 0.19	d : 0.13	f : 0.13	c : 0.11	g : 0.11	h : 0.08	= : 0.05	: : 0.05	i : 0.02	] : 0.02	7 : 0.02	F : 0.02	

#score	605.6568329268307
#seq	36
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_CDS_m1_run1.txt

#BEAR
ee[a[gggggggssssssssssggggggg	chr4:131358759-131359037(-)$1	278	151	180	13.5013
++ffffffwwwwwwwwwwwwwwffffffc	chrX:147007026-147007294(-)$1	268	46	75	13.2787
geeeee[bb!!cccqqqqqqqqccc]bb]	chr10:79879360-79879636(-)$1	276	149	178	8.2303
eee[addddvvvvvvvvvvvvvdddd]a2	chr13:81930934-81931204(+)$1	270	63	92	15.1287
:===========ssssssssss=======	chr5:93697524-93697808(+)$1	284	160	189	13.7431
eeeeeccc^^^^^^^^^^^^^^^^^^^^^	chr1:184398226-184398498(-)$1	272	174	203	11.2792
!!ffffff[cccssssssssssccc333f	chr6:51413984-51414268(-)$1	284	239	268	15.3816
ddddccc[ddddrrrrrrrrrdddd22cc	chr7:25670028-25670303(+)$1	275	183	212	10.9352
ccc####bb[cccrrrrrrrrrccc]bb3	chr18:24743678-24743948(-)$1	270	72	101	12.0695
$$$ccc[cccuuuuuuuuuuuucccccc5	chr4:151560200-151560489(+)$1	289	245	274	16.0434
c[a[bb!!ccctttttttttttccc22bb	chr4:45372561-45372833(+)$1	272	104	133	16.4830
dggggggg[cccrrrrrrrrrcccggggg	chr17:6084525-6084804(+)$1	279	162	191	11.5768
fff[ffffff"""cccooooooccc333f	chr14:45912564-45912838(-)$1	274	149	178	8.3578
eee[a!!ddddddddoooooodddd4444	chr13:69138016-69138287(-)$1	271	148	177	8.8236
ddddd"""ddddssssssssssdddd444	chr3:108706698-108706973(-)$1	275	186	215	14.6667
]gggggggdddduuuuuuuuuuuudddd:	chr3:102703879-102704149(-)$1	270	58	87	14.4300
======[bbcccssssssssssccc4444	chr14:70066965-70067244(+)$1	279	39	68	16.4013
eeee"""dddduuuuuuuuuuuuddddee	chr8:28383689-28383967(+)$1	278	170	199	16.1787
""ccc!!bb[bbrrrrrrrrrbb]bb22c	chr5:108863235-108863508(-)$1	273	142	171	10.5940
ffffff[a!!eeeeeooooooeeeee]a]	chr5:137966809-137967086(+)$1	277	234	263	7.3099
[bb[bb[bb[eeeeeooooooeeeee333	chr7:135038927-135039193(-)$1	266	28	57	7.6629
e!!eeeeedddd^^^^^^^^^^^^^^^^^	chr17:35292431-35292717(-)$1	286	104	133	11.1964
[ccc[a[ddddvvvvvvvvvvvvvdddd]	chr13:73773790-73774082(+)$1	292	207	236	16.1499
gggggg[dddduuuuuuuuuuuudddd22	chr19:46681119-46681390(+)$1	271	87	116	16.8751
ccdddd!!ccctttttttttttccc22dd	chr8:74842841-74843113(+)$1	272	109	138	16.5633
::dddd[ddddssssssssssdddddddd	chr11:70466238-70466523(-)$1	285	75	104	11.2872
ffffffff[ccctttttttttttccc]ff	chr17:37114860-37115135(-)$1	275	197	226	15.1600
iiiiiiiii!!cccqqqqqqqqccciiii	chr8:63405926-63406223(-)$1	297	228	257	8.6634
cc[dddd!!ccc[aooooooa]ccc]ddd	chr3:51288320-51288588(+)$1	268	59	88	8.0465
hh$$$$$eeeeesssssssssseeeee22	chr2:174125804-174126076(+)$1	272	23	52	12.4823
iiiii!!eeeeeuuuuuuuuuuuueeeee	chr6:56728726-56729000(-)$1	274	5	34	15.4296
eee!!a[bba[cccqqqqqqqqccc]a]b	chr7:27949815-27950086(-)$1	271	22	51	8.7099
:::ggggggguuuuuuuuuuuuggggggg	chr4:33125089-33125364(+)$1	275	122	151	12.9184
iiii[dddd[bbssssssssssbb]dddd	chr2:34678076-34678352(-)$1	276	159	188	12.7595
!dddd"""ccctttttttttttccc333d	chr9:64825922-64826205(+)$1	283	180	209	17.5624
!a!!bb[ffffffcccooooooccc22ff	chr11:102978351-102978633(+)$1	282	69	98	7.7476
###ccc[ddddrrrrrrrrrddddccc22	chr5:123244330-123244627(-)$1	297	77	106	11.2534
$$$cccyyyyyyyyyyyyyyyyccc4444	chr2:153142650-153142935(+)$1	285	150	179	14.9868
ggggg!!bbyyyyyyyyyyyyyyyybb]g	chr14:52760735-52761006(+)$1	271	129	158	14.5254
[ccc[eeeee"""cccooooooccc4444	chr11:120481895-120482204(-)$1	309	35	64	9.0762
[eeeee[ddddxxxxxxxxxxxxxxxddd	chr8:95850590-95850858(-)$1	268	193	222	13.9354

#otherMatches

#Seq PSSM
UCUCACUGAGAUAACCACCAACAUCUCAG	chr4:131358759-131359037(-)$1	278	151	180	13.5013
UUCAUUCCCUUUCCCUUUCCCAGGAAUGC	chrX:147007026-147007294(-)$1	268	46	75	13.2787
GCACUGGCCUCGGUGAGCAGGGGCCUGGG	chr10:79879360-79879636(-)$1	276	149	178	8.2303
GAAAGCAUUUAAACUAUUUGACGAUGACG	chr13:81930934-81931204(+)$1	270	63	92	15.1287
AAGGGGUUCAGCUUUUCGGAUUGUUGAAC	chr5:93697524-93697808(+)$1	284	160	189	13.7431
GUCUAGUGGAAGAAAACAGCCAAUGACUA	chr1:184398226-184398498(-)$1	272	174	203	11.2792
CUGCAUCUCAGAAAGCGAGGAAUCUAAUA	chr6:51413984-51414268(-)$1	284	239	268	15.3816
GCCUUCCUCAAAAAGUAAGUGUUUGUUGG	chr7:25670028-25670303(+)$1	275	183	212	10.9352
GUGCCCAGGGGCUGCAAGAACAAGUGCCA	chr18:24743678-24743948(-)$1	270	72	101	12.0695
GAACCAGAGCAGAUCACCAAAAGCUUGGA	chr4:151560200-151560489(+)$1	289	245	274	16.0434
UGAUGAUACCACAAUAGCACUAUGGGAUC	chr4:45372561-45372833(+)$1	272	104	133	16.4830
CAGACACUUGAGAGAGGCCAGCUCAGUGU	chr17:6084525-6084804(+)$1	279	162	191	11.5768
UCCAGAUUUUCAGCUCUUCACUGGGAAUA	chr14:45912564-45912838(-)$1	274	149	178	8.3578
UGCGGGACCGCGCCGAggcggcggcagca	chr13:69138016-69138287(-)$1	271	148	177	8.8236
UCUGCUUUUUUCCCCCCAAGUUGAGAUUG	chr3:108706698-108706973(-)$1	275	186	215	14.6667
UGACUGUCACACUUUUUUUCUAUUGUGUU	chr3:102703879-102704149(-)$1	270	58	87	14.4300
GAGUGGGGCCCUGACAGCUCGAAGGAUAC	chr14:70066965-70067244(+)$1	279	39	68	16.4013
CCCCCAAAGGACCUGCCAGCCAUUCCUGG	chr8:28383689-28383967(+)$1	278	170	199	16.1787
UCAGGUCUCUCCACUCAUCAAGGUGAAUC	chr5:108863235-108863508(-)$1	273	142	171	10.5940
AGCGAGCGAGUGGGGCAGGGUCCCCAGCA	chr5:137966809-137967086(+)$1	277	234	263	7.3099
CGUGGUGACAGCAGGCCCCGCCCUGCCCC	chr7:135038927-135039193(-)$1	266	28	57	7.6629
GACUCCCCCAGCAGCACUUAUGACCUCUA	chr17:35292431-35292717(-)$1	286	104	133	11.1964
CUCCUGUCUAUCACAUUUGCUCUCAUGGU	chr13:73773790-73774082(+)$1	292	207	236	16.1499
CUUGAGAAGUCAGAAGACAGUGGGACUGG	chr19:46681119-46681390(+)$1	271	87	116	16.8751
GGGCCACAGCACACACAGUCCCUGCCAUG	chr8:74842841-74843113(+)$1	272	109	138	16.5633
CGGUCAAGUUUUUUCGUCAAUGGGCUGAC	chr11:70466238-70466523(-)$1	285	75	104	11.2872
GAAGGAUGUUAACUUUAUUAUUUUUAUCA	chr17:37114860-37115135(-)$1	275	197	226	15.1600
GCUGUUGGCAAUCUGAGAAAAAAGAGCCA	chr8:63405926-63406223(-)$1	297	228	257	8.6634
AACGUGGGCAAGACGUGCCUGACUUACCG	chr3:51288320-51288588(+)$1	268	59	88	8.0465
CCGGAAACCCUGUUAGAAGUUCCAGGGAG	chr2:174125804-174126076(+)$1	272	23	52	12.4823
GGGGAAACUUUAUCCAUCCUGUCUUGAAG	chr6:56728726-56729000(-)$1	274	5	34	15.4296
UGUGACAGCGGUGCcagcaacagcagcag	chr7:27949815-27950086(-)$1	271	22	51	8.7099
CCCAGAUUCCGAUUUUGAUGGAGGAGUUU	chr4:33125089-33125364(+)$1	275	122	151	12.9184
GGCUAUUUUGAGGAUGAAGCAACUGGAGG	chr2:34678076-34678352(-)$1	276	159	188	12.7595
UUUGUAUUGCUGACCCAGAGAGAGCUACA	chr9:64825922-64826205(+)$1	283	180	209	17.5624
GGGAGAAGGGGGCCUGAAGCACCAGCUGC	chr11:102978351-102978633(+)$1	282	69	98	7.7476
GUAACUCGGCAGAACUGGCAUGCCAGUGA	chr5:123244330-123244627(-)$1	297	77	106	11.2534
UGAAGGAAGCCACCAAGAUCAACCUGUCC	chr2:153142650-153142935(+)$1	285	150	179	14.9868
GGCUGAAUCACCUCCUGGACUUCAAGAAC	chr14:52760735-52761006(+)$1	271	129	158	14.5254
AGUAUGUACGAGUGUUUGAUGUGACUGAG	chr11:120481895-120482204(-)$1	309	35	64	9.0762
UAAGGUAAGUAUCACUCUCAAACAACUAU	chr8:95850590-95850858(-)$1	268	193	222	13.9354

#DB
((.(.(((((((..........)))))))	chr4:131358759-131359037(-)$1	1	151	180	13.5013
..((((((..............)))))))	chrX:147007026-147007294(-)$1	1	46	75	13.2787
)(((((.((..(((........))).)).	chr10:79879360-79879636(-)$1	1	149	178	8.2303
(((.(((((.............)))).).	chr13:81930934-81931204(+)$1	1	63	92	15.1287
.(((((((((((..........)))))))	chr5:93697524-93697808(+)$1	1	160	189	13.7431
((((((((.....................	chr1:184398226-184398498(-)$1	1	174	203	11.2792
..((((((.(((..........)))...)	chr6:51413984-51414268(-)$1	1	239	268	15.3816
(((((((.((((.........))))..))	chr7:25670028-25670303(+)$1	1	183	212	10.9352
(((....((.(((.........))).)).	chr18:24743678-24743948(-)$1	1	72	101	12.0695
...(((.(((............)))))).	chr4:151560200-151560489(+)$1	1	245	274	16.0434
(.(.((..(((...........)))..))	chr4:45372561-45372833(+)$1	1	104	133	16.4830
((((((((.(((.........))))))))	chr17:6084525-6084804(+)$1	1	162	191	11.5768
(((.((((((...(((......)))...)	chr14:45912564-45912838(-)$1	1	149	178	8.3578
(((.(..((((((((......))))....	chr13:69138016-69138287(-)$1	1	148	177	8.8236
(((((...((((..........))))...	chr3:108706698-108706973(-)$1	1	186	215	14.6667
.)))))))((((............)))).	chr3:102703879-102704149(-)$1	1	58	87	14.4300
((((((.(((((..........)))....	chr14:70066965-70067244(+)$1	1	39	68	16.4013
((((...((((............))))))	chr8:28383689-28383967(+)$1	1	170	199	16.1787
..(((..((.((.........)).))..)	chr5:108863235-108863508(-)$1	1	142	171	10.5940
((((((.(..(((((......))))).).	chr5:137966809-137967086(+)$1	1	234	263	7.3099
.((.((.((.(((((......)))))...	chr7:135038927-135039193(-)$1	1	28	57	7.6629
(..(((((((((.................	chr17:35292431-35292717(-)$1	1	104	133	11.1964
.(((.(.((((.............)))).	chr13:73773790-73774082(+)$1	1	207	236	16.1499
((((((.((((............))))..	chr19:46681119-46681390(+)$1	1	87	116	16.8751
))((((..(((...........)))..))	chr8:74842841-74843113(+)$1	1	109	138	16.5633
..((((.((((..........))))))))	chr11:70466238-70466523(-)$1	1	75	104	11.2872
((((((((.(((...........))).))	chr17:37114860-37115135(-)$1	1	197	226	15.1600
(((((((((..(((........)))))))	chr8:63405926-63406223(-)$1	1	228	257	8.6634
((.((((..(((.(......).))).)))	chr3:51288320-51288588(+)$1	1	59	88	8.0465
((.....(((((..........)))))..	chr2:174125804-174126076(+)$1	1	23	52	12.4823
(((((..(((((............)))))	chr6:56728726-56729000(-)$1	1	5	34	15.4296
(((..(.(((.(((........))).).)	chr7:27949815-27950086(-)$1	1	22	51	8.7099
...(((((((............)))))))	chr4:33125089-33125364(+)$1	1	122	151	12.9184
((((.((((.((..........)).))))	chr2:34678076-34678352(-)$1	1	159	188	12.7595
.((((...(((...........)))...)	chr9:64825922-64826205(+)$1	1	180	209	17.5624
.(..((.(((((((((......)))..))	chr11:102978351-102978633(+)$1	1	69	98	7.7476
...(((.((((.........)))))))..	chr5:123244330-123244627(-)$1	1	77	106	11.2534
...(((................)))....	chr2:153142650-153142935(+)$1	1	150	179	14.9868
(((((..((................)).)	chr14:52760735-52761006(+)$1	1	129	158	14.5254
.(((.(((((...(((......)))....	chr11:120481895-120482204(-)$1	1	35	64	9.0762
.(((((.((((...............)))	chr8:95850590-95850858(-)$1	1	193	222	13.9354

#PSSM
e : 0.17	c : 0.09	[ : 0.09	g : 0.07	: : 0.07	! : 0.07	d : 0.07	f : 0.07	i : 0.07	$ : 0.04	+ : 0.02	] : 0.02	= : 0.02	" : 0.02	h : 0.02	# : 0.02	
e : 0.19	c : 0.12	g : 0.09	d : 0.07	f : 0.07	i : 0.07	= : 0.04	! : 0.04	$ : 0.04	: : 0.04	+ : 0.02	[ : 0.02	" : 0.02	b : 0.02	h : 0.02	a : 0.02	# : 0.02	
e : 0.17	f : 0.12	d : 0.12	c : 0.09	g : 0.09	$ : 0.07	i : 0.07	[ : 0.04	= : 0.04	! : 0.04	a : 0.02	b : 0.02	: : 0.02	# : 0.02	
d : 0.14	c : 0.14	e : 0.12	[ : 0.12	g : 0.12	f : 0.09	i : 0.07	= : 0.04	! : 0.04	a : 0.02	# : 0.02	$ : 0.02	
f : 0.12	c : 0.12	g : 0.12	d : 0.12	[ : 0.09	e : 0.09	b : 0.07	a : 0.04	= : 0.04	i : 0.04	# : 0.02	" : 0.02	$ : 0.02	! : 0.02	
g : 0.12	f : 0.12	d : 0.12	c : 0.12	e : 0.09	! : 0.09	b : 0.07	" : 0.07	= : 0.04	a : 0.04	# : 0.02	i : 0.02	$ : 0.02	
[ : 0.29	! : 0.14	g : 0.09	f : 0.09	d : 0.07	" : 0.07	c : 0.04	e : 0.04	= : 0.02	# : 0.02	i : 0.02	$ : 0.02	y : 0.02	
d : 0.21	b : 0.17	f : 0.12	g : 0.09	e : 0.09	! : 0.07	c : 0.04	" : 0.04	= : 0.02	[ : 0.02	a : 0.02	i : 0.02	y : 0.02	
d : 0.31	b : 0.17	c : 0.09	[ : 0.07	e : 0.07	g : 0.04	f : 0.04	! : 0.04	w : 0.02	= : 0.02	^ : 0.02	i : 0.02	y : 0.02	
d : 0.26	c : 0.21	[ : 0.09	! : 0.07	e : 0.07	g : 0.04	f : 0.04	y : 0.04	w : 0.02	v : 0.02	= : 0.02	^ : 0.02	a : 0.02	
d : 0.26	c : 0.21	e : 0.09	! : 0.04	u : 0.04	" : 0.04	b : 0.04	y : 0.04	g : 0.02	w : 0.02	v : 0.02	= : 0.02	^ : 0.02	[ : 0.02	f : 0.02	
c : 0.21	d : 0.12	u : 0.09	e : 0.09	t : 0.07	v : 0.04	" : 0.04	b : 0.04	y : 0.04	g : 0.02	w : 0.02	= : 0.02	^ : 0.02	s : 0.02	f : 0.02	r : 0.02	x : 0.02	
s : 0.19	u : 0.14	c : 0.09	r : 0.09	t : 0.09	v : 0.04	^ : 0.04	" : 0.04	e : 0.04	y : 0.04	w : 0.02	d : 0.02	[ : 0.02	f : 0.02	x : 0.02	
s : 0.19	c : 0.14	u : 0.14	r : 0.12	t : 0.09	v : 0.04	^ : 0.04	e : 0.04	y : 0.04	w : 0.02	d : 0.02	a : 0.02	x : 0.02	
s : 0.19	u : 0.14	r : 0.12	t : 0.09	q : 0.07	c : 0.07	v : 0.04	^ : 0.04	e : 0.04	y : 0.04	w : 0.02	d : 0.02	o : 0.02	x : 0.02	
s : 0.19	u : 0.14	r : 0.12	t : 0.09	o : 0.09	q : 0.07	c : 0.07	v : 0.04	^ : 0.04	y : 0.04	w : 0.02	x : 0.02	
s : 0.19	o : 0.17	u : 0.14	r : 0.12	t : 0.09	q : 0.07	v : 0.04	^ : 0.04	y : 0.04	w : 0.02	x : 0.02	
s : 0.19	o : 0.17	u : 0.14	r : 0.12	t : 0.09	q : 0.07	v : 0.04	^ : 0.04	y : 0.04	w : 0.02	x : 0.02	
s : 0.19	o : 0.17	u : 0.14	r : 0.12	t : 0.09	q : 0.07	v : 0.04	^ : 0.04	y : 0.04	w : 0.02	x : 0.02	
s : 0.19	o : 0.17	u : 0.14	r : 0.12	t : 0.09	q : 0.07	v : 0.04	^ : 0.04	y : 0.04	w : 0.02	x : 0.02	
s : 0.19	u : 0.14	o : 0.14	r : 0.09	t : 0.09	q : 0.07	v : 0.04	^ : 0.04	y : 0.04	w : 0.02	a : 0.02	d : 0.02	x : 0.02	
s : 0.17	u : 0.14	d : 0.09	t : 0.09	q : 0.07	o : 0.07	v : 0.04	^ : 0.04	e : 0.04	y : 0.04	w : 0.02	r : 0.02	c : 0.02	b : 0.02	] : 0.02	x : 0.02	
c : 0.39	d : 0.14	u : 0.09	e : 0.07	g : 0.04	^ : 0.04	b : 0.04	f : 0.02	= : 0.02	v : 0.02	t : 0.02	y : 0.02	x : 0.02	
c : 0.41	d : 0.19	e : 0.07	g : 0.04	^ : 0.04	u : 0.04	f : 0.02	= : 0.02	] : 0.02	v : 0.02	b : 0.02	y : 0.02	x : 0.02	
c : 0.41	d : 0.21	e : 0.09	g : 0.07	^ : 0.04	f : 0.02	= : 0.02	b : 0.02	] : 0.02	y : 0.02	x : 0.02	
d : 0.19	] : 0.09	2 : 0.09	4 : 0.09	e : 0.09	g : 0.07	3 : 0.07	c : 0.07	^ : 0.04	b : 0.04	f : 0.02	= : 0.02	i : 0.02	x : 0.02	
d : 0.19	2 : 0.12	4 : 0.12	3 : 0.09	g : 0.07	b : 0.07	] : 0.07	^ : 0.04	c : 0.04	e : 0.04	f : 0.02	= : 0.02	i : 0.02	a : 0.02	
d : 0.17	4 : 0.12	3 : 0.09	2 : 0.09	g : 0.07	f : 0.07	b : 0.07	a : 0.04	^ : 0.04	c : 0.04	e : 0.04	] : 0.04	= : 0.02	i : 0.02	
d : 0.14	4 : 0.12	g : 0.09	2 : 0.09	f : 0.09	c : 0.07	] : 0.07	^ : 0.04	3 : 0.04	b : 0.04	e : 0.04	= : 0.02	5 : 0.02	: : 0.02	i : 0.02	

#score	517.4067277475662
#seq	41
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_CDS_m2_run1.txt

#BEAR
cbb[bbnnnnnbb]bb7	chr9:98390942-98391210(+)$1	268	80	97	8.8535
ffffffnnnnnffffff	chr9:65194529-65194809(+)$1	280	129	146	11.4418
ffffffnnnnnffffff	chr14:103482193-103482469(-)$1	276	78	95	11.4418
cc[cccnnnnnccc]cc	chr3:96066825-96067098(-)$1	273	174	191	11.6856
Fddddannnnna]dddd	chr2:32092890-32093158(+)$1	268	206	223	9.7408
ffffffnnnnnffffff	chr3:95464614-95464908(+)$1	294	23	40	11.4418
dddd[annnnna]dddd	chr11:87794777-87795061(-)$1	284	118	135	10.0405
eee[bbnnnnnbbeeee	chr5:138223490-138223786(-)$1	296	25	42	10.1937
ddd!!annnnna22ddd	chr5:123244330-123244627(-)$1	297	221	238	9.8200
ccc[bbnnnnnbb]ccc	chr14:64225930-64226213(+)$1	283	6	23	10.6303
ggggggnnnnngggggg	chr8:74844691-74844960(+)$1	269	74	91	11.0367
!!ddddnnnnndddddd	chr11:97574608-97574878(+)$1	270	239	256	9.2928
e!!cccnnnnnccc]ee	chrX:98514856-98515126(+)$1	270	222	239	11.5065
f!!cccnnnnnccc22f	chr7:117008957-117009223(-)$1	266	233	250	11.3509
dd[cccnnnnnccc]dd	chr7:25670028-25670303(+)$1	275	137	154	11.3099
ffff[annnnna]ffff	chr13:69138016-69138287(-)$1	271	216	233	11.4204
ggggggnnnnngggggg	chr7:28151313-28151603(-)$1	290	265	282	11.0367
eeecccnnnnnccc:FF	chr2:34678076-34678352(-)$1	276	210	227	9.6419
ffffffnnnnnffffff	chr8:74842841-74843113(+)$1	272	26	43	11.4418
cc!!bbnnnnnbb22cc	chr17:35292433-35292717(-)$1	284	33	50	10.4845
gggcccnnnnnccc]gg	chr5:122096593-122096864(-)$1	271	136	153	11.6836
fffcccnnnnnccceee	chr4:135883045-135883347(+)$1	302	32	49	11.3964
cc[cccnnnnnccc]cc	chr7:135038924-135039193(-)$1	269	141	158	11.6856
ddddbbnnnnnbb]ddd	chr6:22240953-22241221(+)$1	268	129	146	9.9138
ffffffnnnnnffffff	chr2:121205209-121205478(-)$1	269	174	191	11.4418
ffffffnnnnnffffff	chr8:86770433-86770706(-)$1	273	28	45	11.4418
ffffffnnnnnffffff	chr2:40774602-40774881(-)$1	279	151	168	11.4418
f!!cccnnnnnccc22f	chr19:29086354-29086641(+)$1	287	242	259	11.3509
ggggggnnnnngggggg	chr18:60859085-60859370(-)$1	285	171	188	11.0367

#otherMatches

#Seq PSSM
ACCAUCAUGACGAAGGA	chr9:98390942-98391210(+)$1	268	80	97	8.8535
GCUGGAGAGGGUCCGGC	chr9:65194529-65194809(+)$1	280	129	146	11.4418
UGGGCAUGACCUGCCCG	chr14:103482193-103482469(-)$1	276	78	95	11.4418
GGAGGCUAGACGCCGCC	chr3:96066825-96067098(-)$1	273	174	191	11.6856
CUUGCCGUACAGUGCAA	chr2:32092890-32093158(+)$1	268	206	223	9.7408
UGUGGAGUUCUUCCACG	chr3:95464614-95464908(+)$1	294	23	40	11.4418
UCGGGCUAGGUGGCCGA	chr11:87794777-87795061(-)$1	284	118	135	10.0405
CUGUGGAGAACCCCAGG	chr5:138223490-138223786(-)$1	296	25	42	10.1937
CUGUACAACACGGUCAG	chr5:123244330-123244627(-)$1	297	221	238	9.8200
GGCGCCGUGGAGGGGCU	chr14:64225930-64226213(+)$1	283	6	23	10.6303
GGGCCUUCUCCAGGUCC	chr8:74844691-74844960(+)$1	269	74	91	11.0367
UGUCCCCAUCAGGGAGA	chr11:97574608-97574878(+)$1	270	239	256	9.2928
ACCUGCCUACAGCAAUG	chrX:98514856-98515126(+)$1	270	222	239	11.5065
CAACGGGCCGUCCGAGG	chr7:117008957-117009223(-)$1	266	233	250	11.3509
UACUGUAAAAGACGUUA	chr7:25670028-25670303(+)$1	275	137	154	11.3099
GACUGGCUCUACGAGUC	chr13:69138016-69138287(-)$1	271	216	233	11.4204
UGAGCAUGCUUUGCUCA	chr7:28151313-28151603(-)$1	290	265	282	11.0367
UUCGUUAAUUGGACAUA	chr2:34678076-34678352(-)$1	276	210	227	9.6419
CGUCCCCAUCCGGGACG	chr8:74842841-74843113(+)$1	272	26	43	11.4418
CAAGCCAAUGAGGAAUG	chr17:35292433-35292717(-)$1	284	33	50	10.4845
UGGGGACCCACUCCACC	chr5:122096593-122096864(-)$1	271	136	153	11.6836
AGACAGGAAGUCUGACU	chr4:135883045-135883347(+)$1	302	32	49	11.3964
UGUGCCUCGCUGGCUUA	chr7:135038924-135039193(-)$1	269	141	158	11.6856
AUGUCCAGUACGGCAUG	chr6:22240953-22241221(+)$1	268	129	146	9.9138
UCAUGAUUUCCUCGUGA	chr2:121205209-121205478(-)$1	269	174	191	11.4418
CUGUUCACAGAGAACAG	chr8:86770433-86770706(-)$1	273	28	45	11.4418
GCUGUGUUCCUCAUGGC	chr2:40774602-40774881(-)$1	279	151	168	11.4418
CUUUAGGACCACUGUUG	chr19:29086354-29086641(+)$1	287	242	259	11.3509
UUCAGAUCUUUUCUGAG	chr18:60859085-60859370(-)$1	285	171	188	11.0367

#DB
(((.((.....)).)).	chr9:98390942-98391210(+)$1	1	80	97	8.8535
((((((.....))))))	chr9:65194529-65194809(+)$1	1	129	146	11.4418
((((((.....))))))	chr14:103482193-103482469(-)$1	1	78	95	11.4418
((.(((.....))).))	chr3:96066825-96067098(-)$1	1	174	191	11.6856
((((((.....).))))	chr2:32092890-32093158(+)$1	1	206	223	9.7408
((((((.....))))))	chr3:95464614-95464908(+)$1	1	23	40	11.4418
((((.(.....).))))	chr11:87794777-87795061(-)$1	1	118	135	10.0405
(((.((.....))))))	chr5:138223490-138223786(-)$1	1	25	42	10.1937
(((..(.....)..)))	chr5:123244330-123244627(-)$1	1	221	238	9.8200
(((.((.....)).)))	chr14:64225930-64226213(+)$1	1	6	23	10.6303
((((((.....))))))	chr8:74844691-74844960(+)$1	1	74	91	11.0367
..((((.....))))))	chr11:97574608-97574878(+)$1	1	239	256	9.2928
(..(((.....))).))	chrX:98514856-98515126(+)$1	1	222	239	11.5065
(..(((.....)))..)	chr7:117008957-117009223(-)$1	1	233	250	11.3509
((.(((.....))).))	chr7:25670028-25670303(+)$1	1	137	154	11.3099
((((.(.....).))))	chr13:69138016-69138287(-)$1	1	216	233	11.4204
((((((.....))))))	chr7:28151313-28151603(-)$1	1	265	282	11.0367
)))(((.....))).))	chr2:34678076-34678352(-)$1	1	210	227	9.6419
((((((.....))))))	chr8:74842841-74843113(+)$1	1	26	43	11.4418
((..((.....))..))	chr17:35292433-35292717(-)$1	1	33	50	10.4845
((((((.....))).))	chr5:122096593-122096864(-)$1	1	136	153	11.6836
)))(((.....)))(((	chr4:135883045-135883347(+)$1	1	32	49	11.3964
((.(((.....))).))	chr7:135038924-135039193(-)$1	1	141	158	11.6856
((((((.....)).)))	chr6:22240953-22241221(+)$1	1	129	146	9.9138
((((((.....))))))	chr2:121205209-121205478(-)$1	1	174	191	11.4418
((((((.....))))))	chr8:86770433-86770706(-)$1	1	28	45	11.4418
((((((.....))))))	chr2:40774602-40774881(-)$1	1	151	168	11.4418
(..(((.....)))..)	chr19:29086354-29086641(+)$1	1	242	259	11.3509
((((((.....))))))	chr18:60859085-60859370(-)$1	1	171	188	11.0367

#PSSM
f : 0.37	c : 0.17	d : 0.13	g : 0.13	e : 0.10	F : 0.03	! : 0.03	
f : 0.31	d : 0.17	c : 0.13	g : 0.13	! : 0.13	e : 0.06	b : 0.03	
f : 0.31	d : 0.17	g : 0.13	! : 0.13	[ : 0.10	e : 0.06	b : 0.03	c : 0.03	
c : 0.31	f : 0.27	d : 0.13	[ : 0.10	g : 0.10	! : 0.06	
c : 0.31	f : 0.24	b : 0.17	g : 0.10	d : 0.06	[ : 0.06	! : 0.03	
c : 0.31	f : 0.24	b : 0.17	a : 0.13	g : 0.10	d : 0.03	
n : 0.99	
n : 0.99	
n : 0.99	
n : 0.99	
n : 0.99	
c : 0.31	f : 0.24	b : 0.17	a : 0.13	g : 0.10	d : 0.03	
c : 0.31	f : 0.24	b : 0.17	] : 0.10	g : 0.10	2 : 0.03	d : 0.03	
c : 0.31	f : 0.27	] : 0.10	d : 0.10	g : 0.10	2 : 0.06	e : 0.03	
f : 0.27	] : 0.17	d : 0.17	g : 0.10	2 : 0.10	e : 0.06	b : 0.03	c : 0.03	: : 0.03	
f : 0.27	d : 0.20	c : 0.13	g : 0.13	e : 0.10	2 : 0.06	b : 0.03	F : 0.03	
f : 0.34	d : 0.20	c : 0.13	g : 0.13	e : 0.10	7 : 0.03	F : 0.03	

#score	315.20621664237234
#seq	29
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_CDS_m1_run2.txt

#BEAR
fffyyyyyyyyyyyyyyyyfffff	chr14:21585278-21585515(-)$1	237	97	121	19.7125
fff[ccctttttttttttccc22f	chr10:127747416-127747658(+)$1	242	146	170	22.3200
deeeeewwwwwwwwwwwwwweeee	chr9:44509617-44509877(-)$1	260	28	52	21.6344
hhhhhhhuuuuuuuuuuuuhhhhh	chr8:113573540-113573777(+)$1	237	43	67	21.9675
bb[dddduuuuuuuuuuuudddd]	chr4:128900082-128900324(-)$1	242	94	118	22.4141
[eeeeevvvvvvvvvvvvveeeee	chr4:40800329-40800571(-)$1	242	143	167	23.1634
Cffffffuuuuuuuuuuuufffff	chr7:29962094-29962334(-)$1	240	28	52	21.8567
cccddddvvvvvvvvvvvvvdddd	chr10:79872863-79873108(-)$1	245	27	51	22.2512
gggggwwwwwwwwwwwwwwggggg	chr2:128454220-128454495(-)$1	275	191	215	22.3881
iiiiiivvvvvvvvvvvvviiiii	chr12:109749955-109750216(+)$1	261	174	198	23.9037
d[eeeeevvvvvvvvvvvvveeee	chr7:134343171-134343409(-)$1	238	194	218	22.8353
:ffffffuuuuuuuuuuuufffff	chr9:57104155-57104410(-)$1	255	49	73	22.0522
:fffffftttttttttttffffff	chr1:92973414-92973656(+)$1	242	0	24	20.9777
fffff[bbtttttttttttbb]ff	chr2:84903915-84904159(+)$1	244	14	38	21.4898
ff"""bbtttttttttttbb333f	chrX:11635510-11635771(-)$1	261	12	36	21.6084
""eeeeettttttttttteeeee3	chr10:79325130-79325368(+)$1	238	16	40	22.0959
fffffffuuuuuuuuuuuufffff	chr9:24255007-24255248(-)$1	241	154	178	22.8958
####ccctttttttttttccc333	chr10:116491832-116492089(-)$1	257	157	181	22.4942
b[a[ddddtttttttttttdddda	chr9:56943205-56943461(+)$1	256	223	247	21.4758
"ddddyyyyyyyyyyyyyyyyddd	chr3:141975231-141975486(-)$1	255	57	81	19.7668
iiiiiiiuuuuuuuuuuuuiiiii	chr9:113571307-113571553(-)$1	246	155	179	24.0465
hhhhh[attttttttttta]hhhh	chrX:12283405-12283667(-)$1	262	11	35	22.1476
eeee!!attttttttttta22eee	chr10:45073608-45073849(+)$1	241	53	77	22.5001
gggggggtttttttttttgggggg	chr15:9051180-9051431(-)$1	251	17	41	22.8600
eee[cccuuuuuuuuuuuuccc]e	chr4:154534591-154534871(-)$1	280	91	115	23.7642
hhhhhhhuuuuuuuuuuuuhhhhh	chr15:84120811-84121073(+)$1	262	205	229	21.9675
b[ddddwwwwwwwwwwwwwwdddd	chr3:88985782-88986036(+)$1	254	133	157	21.1082
gggggggtttttttttttgggggg	chr13:55771472-55771731(+)$1	259	140	164	22.8600
d[ddddvvvvvvvvvvvvvdddd]	chr1:71683733-71683995(-)$1	262	204	228	22.5955
========ttttttttttt=====	chr8:131239944-131240206(+)$1	262	166	190	22.7302
eeeeeeewwwwwwwwwwwwwweee	chr11:40501078-40501315(-)$1	237	132	156	21.0995
iiiii[awwwwwwwwwwwwwwa]i	chr17:25931883-25932133(-)$1	250	123	147	22.0266
dbb[bbvvvvvvvvvvvvvbb333	chr16:85015385-85015647(-)$1	262	82	106	22.0741
gggggwwwwwwwwwwwwwwggggg	chr8:64028579-64028829(-)$1	250	92	116	22.3881
[ccc[bbvvvvvvvvvvvvvbb]c	chr8:129904254-129904517(+)$1	263	38	62	22.5969
f[fffffftttttttttttfffff	chr1:174029753-174029988(+)$1	235	14	38	21.7595
e!!dddduuuuuuuuuuuudddd2	chr3:88290675-88290958(-)$1	283	28	52	22.6130
[fffffftttttttttttffffff	chr16:92606070-92606327(-)$1	257	162	186	22.0106
gggggggtttttttttttgggggg	chr7:63179204-63179451(+)$1	247	50	74	22.8600
hhhhhhhuuuuuuuuuuuuhhhhh	chr4:118966212-118966452(-)$1	240	20	44	21.9675
%eeeeevvvvvvvvvvvvveeeee	chr17:29469537-29469814(-)$1	277	47	71	22.4394
ccceeeeettttttttttteeeee	chr17:35972113-35972424(-)$1	311	17	41	21.8710
ca!!cccyyyyyyyyyyyyyyyyc	chr1:164627685-164627947(-)$1	262	153	177	19.8441
iii[cccbbtttttttttttbb]c	chr6:86698759-86698994(-)$1	235	55	79	19.9122
iiiiiiiuuuuuuuuuuuuiiiii	chr7:149573551-149573861(-)$1	310	37	61	24.0465
e[bb[bbuuuuuuuuuuuubb]bb	chr9:113566110-113566370(-)$1	260	125	149	21.9225
!ccc[bbuuuuuuuuuuuubb]cc	chr12:53619063-53619311(+)$1	248	120	144	23.0564
gggggwwwwwwwwwwwwwwggggg	chr14:55054914-55055169(+)$1	255	216	240	22.3881
dddd[bbtttttttttttbb]ddd	chr11:52201852-52202111(+)$1	259	58	82	21.2381
ii[cccvvvvvvvvvvvvvccc]i	chr15:78757067-78757339(+)$1	272	51	75	23.8030
$$$ddddtttttttttttdddd]d	chr17:35972558-35972812(-)$1	254	169	193	20.9858
gggggwwwwwwwwwwwwwwggggg	chr9:58337580-58337815(+)$1	235	68	92	22.3881
gggggwwwwwwwwwwwwwwggggg	chr14:31992921-31993158(-)$1	237	188	212	22.3881
$$eeeeeuuuuuuuuuuuueeeee	chr17:35286888-35287126(-)$1	238	17	41	22.7654
eeeecccuuuuuuuuuuuucccee	chr5:23316612-23316862(+)$1	250	174	198	23.5407
cca[bbwwwwwwwwwwwwwwbb]a	chr8:86457718-86457957(+)$1	239	36	60	21.2054
ddfffffftttttttttttfffff	chr15:25654888-25655135(+)$1	247	52	76	21.4055
bb!!ddddtttttttttttddddb	chr11:77629212-77629465(+)$1	253	15	39	20.9435
ggggggvvvvvvvvvvvvvggggg	chr2:84455146-84455387(-)$1	241	110	134	23.9202
eeee[avvvvvvvvvvvvva]eee	chr15:37948923-37949174(-)$1	251	1	25	23.3435

#otherMatches

#Seq PSSM
UUAACCACAUCCACCAGCAUGACA	chr14:21585278-21585515(-)$1	237	97	121	19.7125
CUCCCAGGUUGUACCUCACUGCUG	chr10:127747416-127747658(+)$1	242	146	170	22.3200
UCUGUGCUCUUCCCCUCCCCCACG	chr9:44509617-44509877(-)$1	260	28	52	21.6344
CUCUGCCCUCUGCAGCCCCGGCGG	chr8:113573540-113573777(+)$1	237	43	67	21.9675
CAAGAGCUCGAACCAAGCUGCUCC	chr4:128900082-128900324(-)$1	242	94	118	22.4141
GCUCGGUAAGACCCAGGAUCUGAG	chr4:40800329-40800571(-)$1	242	143	167	23.1634
GGUUAGCUCCCCAGUACCUGUUAA	chr7:29962094-29962334(-)$1	240	28	52	21.8567
GCCCCUCUCUGACCCCACCUGAGG	chr10:79872863-79873108(-)$1	245	27	51	22.2512
UGGAGAGAUGAACUAUGGCUUCCA	chr2:128454220-128454495(-)$1	275	191	215	22.3881
uucucaaagucuguaaguaugaga	chr12:109749955-109750216(+)$1	261	174	198	23.9037
AGGCUAGGAUUUGUUACUUACUGG	chr7:134343171-134343409(-)$1	238	194	218	22.8353
CGAGUGGAACUACGGCCCACCACU	chr9:57104155-57104410(-)$1	255	49	73	22.0522
GCCUCCCUGAGUGUGUGUGGGGGG	chr1:92973414-92973656(+)$1	242	0	24	20.9777
CCCCAAGUGAAGUUAGGGAAUGUG	chr2:84903915-84904159(+)$1	244	14	38	21.4898
GGAACGCUUCCUCUACCUGCCACC	chrX:11635510-11635771(-)$1	261	12	36	21.6084
GGUUAGGAGACCAGACAGCUUAAA	chr10:79325130-79325368(+)$1	238	16	40	22.0959
GGGGACACAUUguuacuccuguuc	chr9:24255007-24255248(-)$1	241	154	178	22.8958
GUAAGCUAUGAAGAGAGAGGUGAA	chr10:116491832-116492089(-)$1	257	157	181	22.4942
GUGUACACAAGUUACAACAGUGUC	chr9:56943205-56943461(+)$1	256	223	247	21.4758
UGGCCUACAAUAAAGCACCACGGC	chr3:141975231-141975486(-)$1	255	57	81	19.7668
AAAAAUAUACAGGUAAAUUUGUUU	chr9:113571307-113571553(-)$1	246	155	179	24.0465
UAAGAUCUUUCACACUGUGUUUUU	chrX:12283405-12283667(-)$1	262	11	35	22.1476
UUAUAGGAAAAGACAUUACAAAUA	chr10:45073608-45073849(+)$1	241	53	77	22.5001
GUGCUUUGACUUCACUGAAAAGCA	chr15:9051180-9051431(-)$1	251	17	41	22.8600
CAGCGCCUUUCUGCUUUCCGGCCC	chr4:154534591-154534871(-)$1	280	91	115	23.7642
GUUAAGAACCAAUGCAUCCUCUUG	chr15:84120811-84121073(+)$1	262	205	229	21.9675
CCCUGCUCUUCACCGGCAUCGCAG	chr3:88985782-88986036(+)$1	254	133	157	21.1082
AAGUUUGAUGAAACAGAACAGGCU	chr13:55771472-55771731(+)$1	259	140	164	22.8600
UGCCAGUCUAUGCUACUAUUUGGA	chr1:71683733-71683995(-)$1	262	204	228	22.5955
UAUUGUUUUACCCAAUGAUGGACA	chr8:131239944-131240206(+)$1	262	166	190	22.7302
UUUCGAAGAGCAAGACCAAAAUUC	chr11:40501078-40501315(-)$1	237	132	156	21.0995
GGGCUGUGCUCCCCGCUUCCAAGA	chr17:25931883-25932133(-)$1	250	123	147	22.0266
CGGAGCAGAAAGACAGACAGCACA	chr16:85015385-85015647(-)$1	262	82	106	22.0741
GGCUGCCCACGCCAACCUCCAGCC	chr8:64028579-64028829(-)$1	250	92	116	22.3881
ACAAAGCAUUGUGUCCUUGGGCCU	chr8:129904254-129904517(+)$1	263	38	62	22.5969
GUAGAAGACCCACUUUUUCUCUUU	chr1:174029753-174029988(+)$1	235	14	38	21.7595
ACAGCCAUCACCUCUCCUUUGGCA	chr3:88290675-88290958(-)$1	283	28	52	22.6130
AGGCCGGGCCCUUCCAGACCGGCU	chr16:92606070-92606327(-)$1	257	162	186	22.0106
GUUCUUCCACCACCAGCUGAAGGA	chr7:63179204-63179451(+)$1	247	50	74	22.8600
GUUGUUGUGCUUUGUUUUCCAGCA	chr4:118966212-118966452(-)$1	240	20	44	21.9675
GCAGGGUUCCCUCCAGCACCCCUG	chr17:29469537-29469814(-)$1	277	47	71	22.4394
UGUGCCUGAACUUACCCAGCAGGU	chr17:35972113-35972424(-)$1	311	17	41	21.8710
cccagacccagacccaCAAACCAG	chr1:164627685-164627947(-)$1	262	153	177	19.8441
AGACGAGGUGAAAUUCCUAAGCAU	chr6:86698759-86698994(-)$1	235	55	79	19.9122
ACCCGUUGAGGGCCAAACAAGCGG	chr7:149573551-149573861(-)$1	310	37	61	24.0465
CAUGCAGCAGCGCCUCCAACUCCA	chr9:113566110-113566370(-)$1	260	125	149	21.9225
UGCAGCCUUUAAACCACAUGGGUG	chr12:53619063-53619311(+)$1	248	120	144	23.0564
GCAGCAUCCCUCCCCGUUAGUUGU	chr14:55054914-55055169(+)$1	255	216	240	22.3881
ACCUCUGUCUCAACUCCCCACAGG	chr11:52201852-52202111(+)$1	259	58	82	21.2381
UGAUCCAGUUAAAAAGGUCGGAGC	chr15:78757067-78757339(+)$1	272	51	75	23.8030
CUCUACGACAUCUGCUUCCGUACC	chr17:35972558-35972812(-)$1	254	169	193	20.9858
AGGGCAUCUCUUACCCUUAGUCCU	chr9:58337580-58337815(+)$1	235	68	92	22.3881
CUGCAGACCGAGCAGACAGUGUAG	chr14:31992921-31993158(-)$1	237	188	212	22.3881
AUGGCCUUCCUGUUCUAAUGGGCU	chr17:35286888-35287126(-)$1	238	17	41	22.7654
AUGUGGAUGAAAUGAAGGUUCCAG	chr5:23316612-23316862(+)$1	250	174	198	23.5407
CUGUCCAUCACUAUAUAACAGGCC	chr8:86457718-86457957(+)$1	239	36	60	21.2054
CUCCUCACAGAACCGAGUAGUGAG	chr15:25654888-25655135(+)$1	247	52	76	21.4055
UGACUUCCAAUCUAUAUCAGGAAC	chr11:77629212-77629465(+)$1	253	15	39	20.9435
GUCAGUGCUUACCAACACUGCUGG	chr2:84455146-84455387(-)$1	241	110	134	23.9202
AGUUGAGAGAAUGUGGUGAUGGAC	chr15:37948923-37949174(-)$1	251	1	25	23.3435

#DB
(((................)))))	chr14:21585278-21585515(-)$1	1	97	121	19.7125
(((.(((...........)))..)	chr10:127747416-127747658(+)$1	1	146	170	22.3200
((((((..............))))	chr9:44509617-44509877(-)$1	1	28	52	21.6344
(((((((............)))))	chr8:113573540-113573777(+)$1	1	43	67	21.9675
((.((((............)))).	chr4:128900082-128900324(-)$1	1	94	118	22.4141
.(((((.............)))))	chr4:40800329-40800571(-)$1	1	143	167	23.1634
(((((((............)))))	chr7:29962094-29962334(-)$1	1	28	52	21.8567
)))((((.............))))	chr10:79872863-79873108(-)$1	1	27	51	22.2512
(((((..............)))))	chr2:128454220-128454495(-)$1	1	191	215	22.3881
((((((.............)))))	chr12:109749955-109750216(+)$1	1	174	198	23.9037
(.(((((.............))))	chr7:134343171-134343409(-)$1	1	194	218	22.8353
.((((((............)))))	chr9:57104155-57104410(-)$1	1	49	73	22.0522
.((((((...........))))))	chr1:92973414-92973656(+)$1	1	0	24	20.9777
(((((.((...........)).))	chr2:84903915-84904159(+)$1	1	14	38	21.4898
((...((...........))...)	chrX:11635510-11635771(-)$1	1	12	36	21.6084
..(((((...........))))).	chr10:79325130-79325368(+)$1	1	16	40	22.0959
)((((((............)))))	chr9:24255007-24255248(-)$1	1	154	178	22.8958
....(((...........)))...	chr10:116491832-116492089(-)$1	1	157	181	22.4942
(.(.((((...........)))))	chr9:56943205-56943461(+)$1	1	223	247	21.4758
.((((................)))	chr3:141975231-141975486(-)$1	1	57	81	19.7668
(((((((............)))))	chr9:113571307-113571553(-)$1	1	155	179	24.0465
(((((.(...........).))))	chrX:12283405-12283667(-)$1	1	11	35	22.1476
((((..(...........)..)))	chr10:45073608-45073849(+)$1	1	53	77	22.5001
(((((((...........))))))	chr15:9051180-9051431(-)$1	1	17	41	22.8600
(((.(((............))).)	chr4:154534591-154534871(-)$1	1	91	115	23.7642
(((((((............)))))	chr15:84120811-84121073(+)$1	1	205	229	21.9675
(.((((..............))))	chr3:88985782-88986036(+)$1	1	133	157	21.1082
(((((((...........))))))	chr13:55771472-55771731(+)$1	1	140	164	22.8600
(.((((.............)))).	chr1:71683733-71683995(-)$1	1	204	228	22.5955
((((((((...........)))))	chr8:131239944-131240206(+)$1	1	166	190	22.7302
))(((((..............)))	chr11:40501078-40501315(-)$1	1	132	156	21.0995
(((((.(..............).)	chr17:25931883-25932133(-)$1	1	123	147	22.0266
)((.((.............))...	chr16:85015385-85015647(-)$1	1	82	106	22.0741
(((((..............)))))	chr8:64028579-64028829(-)$1	1	92	116	22.3881
.(((.((.............)).)	chr8:129904254-129904517(+)$1	1	38	62	22.5969
(.((((((...........)))))	chr1:174029753-174029988(+)$1	1	14	38	21.7595
(..((((............)))).	chr3:88290675-88290958(-)$1	1	28	52	22.6130
.((((((...........))))))	chr16:92606070-92606327(-)$1	1	162	186	22.0106
(((((((...........))))))	chr7:63179204-63179451(+)$1	1	50	74	22.8600
(((((((............)))))	chr4:118966212-118966452(-)$1	1	20	44	21.9675
.(((((.............)))))	chr17:29469537-29469814(-)$1	1	47	71	22.4394
((((((((...........)))))	chr17:35972113-35972424(-)$1	1	17	41	21.8710
((..(((................)	chr1:164627685-164627947(-)$1	1	153	177	19.8441
(((.(((((...........)).)	chr6:86698759-86698994(-)$1	1	55	79	19.9122
(((((((............)))))	chr7:149573551-149573861(-)$1	1	37	61	24.0465
(.((.((............)).))	chr9:113566110-113566370(-)$1	1	125	149	21.9225
.(((.((............)).))	chr12:53619063-53619311(+)$1	1	120	144	23.0564
(((((..............)))))	chr14:55054914-55055169(+)$1	1	216	240	22.3881
((((.((...........)).)))	chr11:52201852-52202111(+)$1	1	58	82	21.2381
((.(((.............))).)	chr15:78757067-78757339(+)$1	1	51	75	23.8030
...((((...........)))).)	chr17:35972558-35972812(-)$1	1	169	193	20.9858
(((((..............)))))	chr9:58337580-58337815(+)$1	1	68	92	22.3881
(((((..............)))))	chr14:31992921-31993158(-)$1	1	188	212	22.3881
..(((((............)))))	chr17:35286888-35287126(-)$1	1	17	41	22.7654
))))(((............)))((	chr5:23316612-23316862(+)$1	1	174	198	23.5407
(((.((..............)).)	chr8:86457718-86457957(+)$1	1	36	60	21.2054
((((((((...........)))))	chr15:25654888-25655135(+)$1	1	52	76	21.4055
((..((((...........)))))	chr11:77629212-77629465(+)$1	1	15	39	20.9435
((((((.............)))))	chr2:84455146-84455387(-)$1	1	110	134	23.9202
((((.(.............).)))	chr15:37948923-37949174(-)$1	1	1	25	23.3435

#PSSM
g : 0.15	e : 0.11	f : 0.09	d : 0.09	i : 0.09	h : 0.06	b : 0.06	c : 0.06	[ : 0.05	: : 0.03	" : 0.03	$ : 0.03	C : 0.01	# : 0.01	= : 0.01	% : 0.01	! : 0.01	
f : 0.15	g : 0.15	e : 0.13	i : 0.09	[ : 0.09	c : 0.08	h : 0.06	b : 0.05	d : 0.05	$ : 0.03	" : 0.01	# : 0.01	= : 0.01	! : 0.01	a : 0.01	
e : 0.18	f : 0.16	g : 0.15	i : 0.08	h : 0.06	c : 0.06	d : 0.06	! : 0.05	[ : 0.03	a : 0.03	b : 0.03	" : 0.01	# : 0.01	= : 0.01	$ : 0.01	
e : 0.18	g : 0.15	d : 0.13	f : 0.13	[ : 0.09	h : 0.06	i : 0.06	c : 0.05	! : 0.03	y : 0.01	" : 0.01	# : 0.01	= : 0.01	b : 0.01	
d : 0.15	g : 0.15	e : 0.13	f : 0.13	c : 0.11	[ : 0.08	h : 0.06	i : 0.06	b : 0.03	y : 0.01	" : 0.01	! : 0.01	= : 0.01	
e : 0.13	d : 0.13	c : 0.11	f : 0.11	b : 0.11	w : 0.08	g : 0.06	h : 0.05	i : 0.05	[ : 0.05	y : 0.03	! : 0.01	= : 0.01	a : 0.01	
w : 0.13	v : 0.13	f : 0.11	c : 0.09	d : 0.09	b : 0.09	e : 0.08	h : 0.05	a : 0.05	g : 0.05	y : 0.03	i : 0.03	= : 0.01	
u : 0.24	t : 0.21	v : 0.18	w : 0.16	y : 0.05	b : 0.03	d : 0.03	f : 0.03	= : 0.01	e : 0.01	
t : 0.33	u : 0.24	v : 0.18	w : 0.16	y : 0.05	b : 0.01	
t : 0.35	u : 0.24	v : 0.18	w : 0.16	y : 0.05	
t : 0.35	u : 0.24	v : 0.18	w : 0.16	y : 0.05	
t : 0.35	u : 0.24	v : 0.18	w : 0.16	y : 0.05	
t : 0.35	u : 0.24	v : 0.18	w : 0.16	y : 0.05	
t : 0.35	u : 0.24	v : 0.18	w : 0.16	y : 0.05	
t : 0.35	u : 0.24	v : 0.18	w : 0.16	y : 0.05	
t : 0.35	u : 0.24	v : 0.18	w : 0.16	y : 0.05	
t : 0.35	u : 0.24	v : 0.18	w : 0.16	y : 0.05	
t : 0.35	u : 0.24	v : 0.18	w : 0.16	y : 0.05	
u : 0.24	v : 0.18	w : 0.16	t : 0.13	y : 0.05	g : 0.05	c : 0.03	f : 0.03	b : 0.03	a : 0.03	e : 0.01	d : 0.01	
g : 0.15	f : 0.13	d : 0.09	b : 0.09	c : 0.08	w : 0.08	e : 0.08	h : 0.05	v : 0.05	i : 0.05	y : 0.03	] : 0.01	2 : 0.01	= : 0.01	t : 0.01	a : 0.01	
g : 0.15	f : 0.13	d : 0.13	e : 0.11	b : 0.11	c : 0.08	h : 0.06	i : 0.05	y : 0.03	w : 0.03	] : 0.03	3 : 0.01	2 : 0.01	= : 0.01	
e : 0.16	d : 0.16	g : 0.15	f : 0.13	h : 0.06	i : 0.05	] : 0.05	3 : 0.05	c : 0.05	b : 0.05	2 : 0.01	= : 0.01	a : 0.01	y : 0.01	
e : 0.18	f : 0.15	d : 0.15	g : 0.15	] : 0.11	h : 0.06	i : 0.05	3 : 0.05	2 : 0.01	= : 0.01	y : 0.01	b : 0.01	c : 0.01	
f : 0.18	e : 0.18	g : 0.15	d : 0.08	i : 0.08	h : 0.06	c : 0.06	3 : 0.05	] : 0.03	a : 0.03	b : 0.03	= : 0.01	2 : 0.01	

#score	1330.6896069925606
#seq	60
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_CDS_m2_run1.txt

#BEAR
"""bb####gggggggnnnnngggggggbb333c	chrX:54043686-54043909(+)$1	223	78	112	11.9313
ffffff####a!!cccnnnnnccc22a]ffffff	chr15:73412421-73412641(-)$1	220	70	104	14.5115
eeffffffa####ccclllccc333a]ffffff]	chr3:145606721-145606960(+)$1	239	147	181	11.3779
ddd[ggggggg!!cccnnnnncccggggggg]dd	chr12:21302452-21302672(+)$1	220	38	72	12.3896
e[ffffff####ddddoooooodddd4444ffff	chr15:83407339-83407559(-)$1	220	75	109	13.5037
[bb[ccc[dddd!!cccnnnnnccc]dddd]ccc	chr5:32789863-32790083(+)$1	220	91	125	10.7447
dffffff!!gggggggooooooggggggg22fff	chr7:105457754-105457974(-)$1	220	80	114	10.7487
::a[dddd####ddddnnnnndddd4444dddd]	chr9:103238306-103238533(+)$1	227	125	159	12.2362
ggg[ccc[a####cccnnnnnccc22accc]ggg	chr1:93213605-93213832(+)$1	227	113	147	16.2150
[ddddccc"""ddddccclllccc]ddddccc44	chr6:125142271-125142492(+)$1	221	157	191	11.3080
[bb[eeeeeccc"""ccclllccc22ccc333ee	chr19:10682270-10682490(+)$1	220	96	130	10.9956
=====[ccc####eeeeellleeeeeccc]====	chr7:87361732-87361952(+)$1	220	46	80	11.5321
eeeee[bb"""ddddoooooodddd333bb]eee	chr4:151343864-151344084(+)$1	220	114	148	12.8366
d[a[bb[ccc"""cccmmmmccc]ccc]bb]add	chr18:57534094-57534314(+)$1	220	136	170	10.8140
ggggg[ddddbb[cccnnnnncccbb]ddddggg	chr8:63378918-63379138(+)$1	220	114	148	10.9674
Hccc[eeeee"""cccnnnnnccceeeee]ccc:	chr13:41103378-41103615(+)$1	237	118	152	10.7914
cc[ccc!!ccc!!cccnnnnnccc]ccc22ccc2	chr11:102148573-102148793(+)$1	220	53	87	13.5208
ggggggg[a"""addddmmmmdddd]a333a]gg	chr18:44572119-44572339(+)$1	220	141	175	12.9514
iiii####bb!!cccooooooccc22bbiiiiii	chr6:71822773-71822995(+)$1	222	122	156	13.8064
b[eeeee[bb!!ddddnnnnndddd22bb4444e	chr11:78134717-78134937(+)$1	220	137	171	12.6471
hhhccc"""cccddddnnnnndddd]ccc333cc	chr11:57926488-57926710(+)$1	222	171	205	13.5031
ccc[ccc"""ffffffnnnnnffffff]ccc]cc	chr6:113070742-113070962(+)$1	220	35	69	11.5731
eee!!a####bb!!bbnnnnnbb22bb333a22e	chr1:182503688-182503917(+)$1	229	33	67	12.1211
!!ffffffdddd[cccooooooccc]dddd]fff	chr12:103227913-103228155(+)$1	242	61	95	11.0604
d"""dddd####ddddnnnnndddddddddddd]	chr8:42407269-42407496(+)$1	227	16	50	12.6720
ddffffff"""bb[cccmmmmccc]bb4444fff	chr9:44442133-44442354(+)$1	221	144	178	11.2964
a[ggggggg"""cccooooooccc666666gggg	chr3:30929916-30930150(+)$1	234	37	71	12.3787
iiii[bb"""bb[ddddllldddd]bb]bb]iii	chr18:6220720-6220940(-)$1	220	32	66	11.4055
gggdddd[ccc[ddddnnnnndddd]cccdddd:	chr3:88124429-88124662(+)$1	233	117	151	10.9209
d[ffffff####ddddmmmmdddd333ffffff]	chr5:110667035-110667256(+)$1	221	82	116	11.8947
======="""bb!!a!!bblllbb22a]bb333=	chr6:126771950-126772188(-)$1	238	101	135	10.6170
eeee[cccbb[a[cccmmmmccc]a]bb4444cc	chrX:54041217-54041457(+)$1	240	110	144	10.7824
:eeeeea"""bb[cccnnnnnccc]bb333a]ee	chr18:56899415-56899636(+)$1	221	124	158	12.8863
[bbdddd[bb####cccmmmmccc333bb]dddd	chr2:34627997-34628217(+)$1	220	84	118	10.7774
e$$$$$ccc####ccclllccc4444ccc4444e	chr1:38922709-38922929(-)$1	220	154	188	12.6078
iiii####bb!!ddddmmmmdddd22bb4444ii	chr14:102318535-102318755(+)$1	220	155	189	11.9589
ffff[a[bb!!ccc[annnnna]cccbb]a]fff	chr8:46110087-46110307(+)$1	220	18	52	11.8403
ddccc[ccc!!ddddoooooodddd>>>>>>>>>	chr1:6229991-6230211(+)$1	220	155	189	11.5912
ff"""bb####eeeeennnnneeeee4444bb33	chr18:12307194-12307414(+)$1	220	164	198	12.4707
bb####gggggggcccooooooccc]ggggggg5	chr6:94558966-94559186(-)$1	220	163	197	11.1000
ggggg[ccc[ccc[bbnnnnnbbcccccc22ggg	chr9:72584452-72584672(+)$1	220	56	90	11.5442
$$$$$bb"""ccc"""aooooooa333ccc]bb4	chr11:74713637-74713860(+)$1	223	52	86	11.6493
ccc"""ccc!!ddddoooooodddd22ccc]ccc	chr1:82339260-82339480(+)$1	220	97	131	13.6536
cc!!bb[a####ddddoooooodddda]bb22cc	chr13:74476929-74477149(-)$1	220	46	80	13.5147
cc[dddd####ddddoooooodddd333dddd22	chr6:11912650-11912870(+)$1	220	3	37	13.2140
:ccc"""ccc!!cccooooooccc22ccc22ccc	chr17:46546560-46546782(+)$1	222	109	143	13.4051
DD:dddd####bbcccooooooccc]bb333ddd	chr14:56195520-56195740(+)$1	220	55	89	10.5650
gg!!ccc!!cccrrrrrrrrrccc333ccc0000	chr15:83057935-83058157(-)$1	222	162	196	9.7454
dd"""dddd"""aaooooooa]a333dddd333d	chr2:156571559-156571779(+)$1	220	132	166	12.5755
fffbbbb"""bb[cccnnnnncccbb]bb]bb]f	chr1:36125455-36125676(+)$1	221	172	206	11.4836
========####ddddmmmmdddd22========	chr1:44034012-44034232(+)$1	220	34	68	13.3457
ggggggg$$$$$cccoooooocccggggggg]bb	chr19:9080210-9080430(+)$1	220	113	147	12.8903
[ccc!!ccc[eeeeeooooooeeeee]ccc22cc	chr11:79921891-79922114(+)$1	223	52	86	11.0119
c[bbccc[ccc!!ddddmmmmdddd4444ccc]c	chr10:119645803-119646025(+)$1	222	3	37	10.9543
::ffffff####cccooooooccc22ffffffdd	chr11:107050356-107050576(-)$1	220	5	39	11.9279
=======ccc[bb[cccmmmmccc]bbccc]===	chr4:117265598-117265818(+)$1	220	55	89	11.0682
fff!!a[dddd[cccooooooccc22dddd]a22	chr18:3430997-3431222(+)$1	225	79	113	11.9471
====$$$$$ccc[cccnnnnnccc]ccc======	chr14:55236652-55236872(-)$1	220	104	138	13.6460
+++++dddd####cccnnnnnccc4444dddddd	chr3:100727130-100727350(+)$1	220	65	99	10.8915
bbffffff####ddddnnnnnddddffffff]bb	chr6:71902923-71903147(+)$1	224	170	204	12.2281

#otherMatches

#Seq PSSM
GCGUGGAUUGCUACAAGAACUUUGUGGCCAAGAA	chrX:54043686-54043909(+)$1	223	78	112	11.9313
UUCCCUUGCAGUAUGUCCACCACAGUCCGGGGAA	chr15:73412421-73412641(-)$1	220	70	104	14.5115
AGUGUUUGCUUUUGUGCGUUACUAUGACAGACAU	chr3:145606721-145606960(+)$1	239	147	181	11.3779
GUUCUUUGUGUUCACAGCUUUUGUAUACAGGUGA	chr12:21302452-21302672(+)$1	220	38	72	12.3896
UAUCAGGAAAGCGGGUGAUGCAGCCCCAAAUCCU	chr15:83407339-83407559(-)$1	220	75	109	13.5037
CGGAUAUGAAUUUUUUGCUAAACGACAGUUGGUA	chr5:32789863-32790083(+)$1	220	91	125	10.7447
GAGAACUAUGUGGUGACCUUGUUCGUCGCUGAGU	chr7:105457754-105457974(-)$1	220	80	114	10.7487
UAUGGGCACAAAUGACAAAGAGUCACCUCUGUUG	chr9:103238306-103238533(+)$1	227	125	159	12.2362
CUGGAGGUGAGAGGGCGAAAGGCCAGCCCUGCAG	chr1:93213605-93213832(+)$1	227	113	147	16.2150
GGCAUGCCGAAGCUUCUCUCUGGGUAAGUGGCUU	chr6:125142271-125142492(+)$1	221	157	191	11.3080
GACAUCAUUACAAGAGCCCAUGGCAAUGUCCAGG	chr19:10682270-10682490(+)$1	220	96	130	10.9956
GAUGCUGUCCCCGAGGUUCCUGGCCUGACUGUGU	chr7:87361732-87361952(+)$1	220	46	80	11.5321
GCCAUCCUCUCUGGAAGUCUCUCCACCCAGAAUG	chr4:151343864-151344084(+)$1	220	114	148	12.8366
GUGGCUGCUGUCCGAGAUGCCUUCCAGGAGGUCU	chr18:57534094-57534314(+)$1	220	136	170	10.8140
UAGGGUCGCACGUGUUCAUCCGACUGUUGUGCUC	chr8:63378918-63379138(+)$1	220	114	148	10.9674
AGCUCACAGGUGAGGCCACAUGCUCCUGUUGGCA	chr13:41103378-41103615(+)$1	237	118	152	10.7914
ACCCAGUCAGCAGCCAGGCCAUGGAGCUCUCUGA	chr11:102148573-102148793(+)$1	220	53	87	13.5208
AGCAGCAGAAUCCCUUGGUGGUAAGAGUUGUGUG	chr18:44572119-44572339(+)$1	220	141	175	12.9514
GGGAUUGAGCAGGCUGUUCAGAGUGAGCUCCCUU	chr6:71822773-71822995(+)$1	222	122	156	13.8064
UAGAUCCCAGCUGCCAGCUGAUGGCUACUAACUG	chr11:78134717-78134937(+)$1	220	137	171	12.6471
CUUAUGACAUCGGGAGUGGUUCUCUGUGACAACG	chr11:57926488-57926710(+)$1	222	171	205	13.5031
UGUCUGCAAAGGAGAAGAGAAUUUUCUAGUAAAC	chr6:113070742-113070962(+)$1	220	35	69	11.5731
GGGCAGGAUUGUGGCCUGCAUGGAGACUAACGAC	chr1:182503688-182503917(+)$1	229	33	67	12.1211
UGUCAUUUUUCUCCCUUGUAUUAGGUAGAAUGGA	chr12:103227913-103228155(+)$1	242	61	95	11.0604
UUUAAUGAAUUGGCUUUCUUUAAGCUCAUGCAAG	chr8:42407269-42407496(+)$1	227	16	50	12.6720
GUAAGUAAGAAUGGGGGUAGCCUCGCAGACAUUG	chr9:44442133-44442354(+)$1	221	144	178	11.2964
ugagggccagcacgccuggcuGUGAUAAAGUGGU	chr3:30929916-30930150(+)$1	234	37	71	12.3787
CAGUGAUAAACCAGCUGCUGCAGUCGGAAUGGCU	chr18:6220720-6220940(-)$1	220	32	66	11.4055
GCCCAGGCGUUAGAGGUCAUCCCUCGGACCUUGA	chr3:88124429-88124662(+)$1	233	117	151	10.9209
CGUUGUUGACCUGUAUCUUAAUACUCCUGACAAA	chr5:110667035-110667256(+)$1	221	82	116	11.8947
CUGUCUUCUGAGAUCGAGGAAACCAAGCCUGCCA	chr6:126771950-126772188(-)$1	238	101	135	10.6170
CCAUAAGCGCUGAUGCCAAGGUAACUGUUGUUGC	chrX:54041217-54041457(+)$1	240	110	144	10.7824
GCGCCGCAUGCUGUCUGACAGAGAGAGAGAGAUG	chr18:56899415-56899636(+)$1	221	124	158	12.8863
CGGUGUGUUCAAGAACGGCCGCGUGGAGAUCAUA	chr2:34627997-34628217(+)$1	220	84	118	10.7774
CAGGCAUGAGAUAGCCCCAGGCAUUAUUAGAAAG	chr1:38922709-38922929(-)$1	220	154	188	12.6078
gggcagaggcagaagcuaaggcuugggcggaggc	chr14:102318535-102318755(+)$1	220	155	189	11.9589
CGUGCGGGCAACUGACUCCCUGACGGGCGCUCAC	chr8:46110087-46110307(+)$1	220	18	52	11.8403
AGAGAAAGCUGAGAUGAAAAGAUCUACUGAACUG	chr1:6229991-6230211(+)$1	220	155	189	11.5912
UUAAAACAACCCUUAAUGAGUUUAAGAAUCGUGA	chr18:12307194-12307414(+)$1	220	164	198	12.4707
UCACCUGGCUUAAGGGAGGUCGCCCAUUGAGCCU	chr6:94558966-94559186(-)$1	220	163	197	11.1000
GCUUGUGUAAUGAAGAUCACCUCUCAUACUUCAA	chr9:72584452-72584672(+)$1	220	56	90	11.5442
AAGAAACAAAUAGAUGCCCGAAAGAAGCUAAGUA	chr11:74713637-74713860(+)$1	223	52	86	11.6493
GUCAACAUUUUGGGCUUUCCUGUCCCUAAUAGAU	chr1:82339260-82339480(+)$1	220	97	131	13.6536
GACACUGUGAAAGGCUCCGACUGGCUGGGGGAUC	chr13:74476929-74477149(-)$1	220	46	80	13.5147
GUGUAGCUUUUGUGAAGAUCCUCGCUUUGCUAGA	chr6:11912650-11912870(+)$1	220	3	37	13.2140
GAGUGAGGCUAAGCAAGACACUGUAAAGCGAACU	chr17:46546560-46546782(+)$1	222	109	143	13.4051
CUCUGGAACUUCCUGCUGCUCUGCACGGUCAUCU	chr14:56195520-56195740(+)$1	220	55	89	10.5650
UGCUGGCCCAGCUACAUGCCCGCUAUUGCCCUAC	chr15:83057935-83058157(-)$1	222	162	196	9.7454
GGACAGUCAAGACCACAAGAGCGAAGUGACGAGC	chr2:156571559-156571779(+)$1	220	132	166	12.5755
GGGCGCGCCCGGUGGCCGCGUGCCCCCCGACGAC	chr1:36125455-36125676(+)$1	221	172	206	11.4836
UUUAGAAGUUACCGUGUGUUCAUGUUCUUCUGAG	chr1:44034012-44034232(+)$1	220	34	68	13.3457
UUGAGGUUCAUGGCCCAGACUGGCACCUUAAGAU	chr19:9080210-9080430(+)$1	220	113	147	12.8903
UAGAUUCAGUGUAUAACUUAGUAUGCUCUGUUUU	chr11:79921891-79922114(+)$1	223	52	86	11.0119
GUCUGGCGGCCAUCCCGGAAGUGGGUGAAGGCGG	chr10:119645803-119646025(+)$1	222	3	37	10.9543
AUGGCAACCCUGGAAGAAGAAUUCACGUUGUCUA	chr11:107050356-107050576(-)$1	220	5	39	11.9279
UCUGUUCUUGUGCGCUUUCCAGAGGGUCGAUGAG	chr4:117265598-117265818(+)$1	220	55	89	11.0682
CUUGAUGUGAAAAUGAUUAACCAUGAUUCAGAAA	chr18:3430997-3431222(+)$1	225	79	113	11.9471
CUCGGAGGUGGUGCAGAUCUGCUGGACUUGGGUC	chr14:55236652-55236872(-)$1	220	104	138	13.6460
UGCUGCUGGAGAACCUGCGUGGGGAAGGCCAGGG	chr3:100727130-100727350(+)$1	220	65	99	10.8915
GCUCAGCCAGUUUGCCGGAGGGGUGGGCUGAUGU	chr6:71902923-71903147(+)$1	224	170	204	12.2281

#DB
...((....(((((((.....)))))))))...)	chrX:54043686-54043909(+)$1	1	78	112	11.9313
((((((....(..(((.....)))..).))))))	chr15:73412421-73412641(-)$1	1	70	104	14.5115
(((((((((....(((...)))...).)))))).	chr3:145606721-145606960(+)$1	1	147	181	11.3779
(((.(((((((..(((.....)))))))))).))	chr12:21302452-21302672(+)$1	1	38	72	12.3896
(.((((((....((((......))))....))))	chr15:83407339-83407559(-)$1	1	75	109	13.5037
.((.(((.((((..(((.....))).)))).)))	chr5:32789863-32790083(+)$1	1	91	125	10.7447
)((((((..(((((((......)))))))..)))	chr7:105457754-105457974(-)$1	1	80	114	10.7487
..(.((((....((((.....))))....)))).	chr9:103238306-103238533(+)$1	1	125	159	12.2362
(((.(((.(....(((.....)))..)))).)))	chr1:93213605-93213832(+)$1	1	113	147	16.2150
.(((((((...(((((((...))).)))))))..	chr6:125142271-125142492(+)$1	1	157	191	11.3080
.((.((((((((...(((...)))..)))...))	chr19:10682270-10682490(+)$1	1	96	130	10.9956
(((((.(((....(((((...)))))))).))))	chr7:87361732-87361952(+)$1	1	46	80	11.5321
(((((.((...((((......))))...)).)))	chr4:151343864-151344084(+)$1	1	114	148	12.8366
(.(.((.(((...(((....))).))).)).)))	chr18:57534094-57534314(+)$1	1	136	170	10.8140
(((((.((((((.(((.....))))).)))))))	chr8:63378918-63379138(+)$1	1	114	148	10.9674
((((.(((((...(((.....)))))))).))).	chr13:41103378-41103615(+)$1	1	118	152	10.7914
((.(((..(((..(((.....))).)))..))).	chr11:102148573-102148793(+)$1	1	53	87	13.5208
(((((((.(...(((((....)))).)...).))	chr18:44572119-44572339(+)$1	1	141	175	12.9514
((((....((..(((......)))..))))))))	chr6:71822773-71822995(+)$1	1	122	156	13.8064
(.(((((.((..((((.....))))..))....)	chr11:78134717-78134937(+)$1	1	137	171	12.6471
((((((...(((((((.....)))).)))...))	chr11:57926488-57926710(+)$1	1	171	205	13.5031
(((.(((...((((((.....)))))).))).))	chr6:113070742-113070962(+)$1	1	35	69	11.5731
(((..(....((..((.....))..))...)..)	chr1:182503688-182503917(+)$1	1	33	67	12.1211
..((((((((((.(((......))).)))).)))	chr12:103227913-103228155(+)$1	1	61	95	11.0604
(...((((....((((.....)))))))))))).	chr8:42407269-42407496(+)$1	1	16	50	12.6720
))((((((...((.(((....))).))....)))	chr9:44442133-44442354(+)$1	1	144	178	11.2964
(.(((((((...(((......)))......))))	chr3:30929916-30930150(+)$1	1	37	71	12.3787
((((.((...((.((((...)))).)).)).)))	chr18:6220720-6220940(-)$1	1	32	66	11.4055
)))((((.(((.((((.....)))).))))))).	chr3:88124429-88124662(+)$1	1	117	151	10.9209
(.((((((....((((....))))...)))))).	chr5:110667035-110667256(+)$1	1	82	116	11.8947
(((((((...((..(..((...))..).))...)	chr6:126771950-126772188(-)$1	1	101	135	10.6170
((((.(((((.(.(((....))).).))....))	chrX:54041217-54041457(+)$1	1	110	144	10.7824
.((((((...((.(((.....))).))...).))	chr18:56899415-56899636(+)$1	1	124	158	12.8863
.((((((.((....(((....)))...)).))))	chr2:34627997-34628217(+)$1	1	84	118	10.7774
(.....(((....(((...)))....)))....)	chr1:38922709-38922929(-)$1	1	154	188	12.6078
((((....((..((((....))))..))....))	chr14:102318535-102318755(+)$1	1	155	189	11.9589
((((.(.((..(((.(.....).))))).).)))	chr8:46110087-46110307(+)$1	1	18	52	11.8403
(((((.(((..((((......)))).........	chr1:6229991-6230211(+)$1	1	155	189	11.5912
((...((....(((((.....)))))....))..	chr18:12307194-12307414(+)$1	1	164	198	12.4707
((....((((((((((......))).))))))).	chr6:94558966-94559186(-)$1	1	163	197	11.1000
(((((.(((.(((.((.....))))))))..)))	chr9:72584452-72584672(+)$1	1	56	90	11.5442
.....((...(((...(......)...))).)).	chr11:74713637-74713860(+)$1	1	52	86	11.6493
(((...(((..((((......))))..))).)))	chr1:82339260-82339480(+)$1	1	97	131	13.6536
((..((.(....((((......))))).))..))	chr13:74476929-74477149(-)$1	1	46	80	13.5147
((.((((....((((......))))...))))..	chr6:11912650-11912870(+)$1	1	3	37	13.2140
.(((...(((..(((......)))..)))..)))	chr17:46546560-46546782(+)$1	1	109	143	13.4051
((.((((....(((((......))).))...)))	chr14:56195520-56195740(+)$1	1	55	89	10.5650
((..(((..(((.........)))...)))....	chr15:83057935-83058157(-)$1	1	162	196	9.7454
((...((((...((......).)...))))...)	chr2:156571559-156571779(+)$1	1	132	166	12.5755
(((((((...((.(((.....))))).)).)).)	chr1:36125455-36125676(+)$1	1	172	206	11.4836
((((((((....((((....))))..))))))))	chr1:44034012-44034232(+)$1	1	34	68	13.3457
(((((((.....(((......)))))))))).))	chr19:9080210-9080430(+)$1	1	113	147	12.8903
.(((..(((.(((((......))))).)))..))	chr11:79921891-79922114(+)$1	1	52	86	11.0119
(.(((((.(((..((((....))))....))).)	chr10:119645803-119646025(+)$1	1	3	37	10.9543
..((((((....(((......)))..))))))((	chr11:107050356-107050576(-)$1	1	5	39	11.9279
((((((((((.((.(((....))).))))).)))	chr4:117265598-117265818(+)$1	1	55	89	11.0682
(((..(.((((.(((......)))..)))).)..	chr18:3430997-3431222(+)$1	1	79	113	11.9471
((((.....(((.(((.....))).)))))))))	chr14:55236652-55236872(-)$1	1	104	138	13.6460
.....((((....(((.....)))....))))))	chr3:100727130-100727350(+)$1	1	65	99	10.8915
((((((((....((((.....)))))))))).))	chr6:71902923-71903147(+)$1	1	170	204	12.2281

#PSSM
d : 0.13	g : 0.11	e : 0.09	c : 0.09	f : 0.08	[ : 0.08	= : 0.08	: : 0.06	i : 0.05	b : 0.05	" : 0.01	H : 0.01	h : 0.01	! : 0.01	a : 0.01	$ : 0.01	D : 0.01	+ : 0.01	
c : 0.13	g : 0.11	f : 0.09	[ : 0.09	e : 0.08	d : 0.08	b : 0.08	= : 0.08	i : 0.05	" : 0.03	: : 0.03	$ : 0.03	h : 0.01	! : 0.01	D : 0.01	+ : 0.01	
f : 0.19	g : 0.11	c : 0.09	= : 0.08	e : 0.08	" : 0.06	b : 0.06	i : 0.05	d : 0.03	a : 0.03	[ : 0.03	$ : 0.03	! : 0.03	h : 0.01	# : 0.01	: : 0.01	+ : 0.01	
f : 0.16	[ : 0.11	c : 0.09	d : 0.08	= : 0.08	g : 0.08	e : 0.06	! : 0.06	" : 0.06	b : 0.05	i : 0.05	$ : 0.03	# : 0.01	+ : 0.01	
f : 0.15	c : 0.13	d : 0.11	g : 0.09	b : 0.06	e : 0.06	= : 0.06	[ : 0.06	" : 0.06	# : 0.05	! : 0.05	$ : 0.05	+ : 0.01	
f : 0.15	c : 0.15	d : 0.13	b : 0.09	[ : 0.08	# : 0.06	g : 0.06	e : 0.06	a : 0.05	= : 0.05	$ : 0.03	" : 0.03	! : 0.01	
c : 0.21	d : 0.15	f : 0.13	# : 0.08	g : 0.08	b : 0.08	[ : 0.06	e : 0.05	= : 0.05	" : 0.03	! : 0.01	a : 0.01	$ : 0.01	
c : 0.18	# : 0.13	f : 0.11	[ : 0.11	" : 0.11	d : 0.09	g : 0.05	! : 0.05	e : 0.03	b : 0.03	$ : 0.03	a : 0.01	= : 0.01	
# : 0.23	c : 0.19	" : 0.16	d : 0.09	b : 0.09	a : 0.05	g : 0.05	! : 0.03	e : 0.03	$ : 0.03	
# : 0.30	" : 0.19	c : 0.16	b : 0.08	g : 0.06	d : 0.06	! : 0.05	[ : 0.03	e : 0.01	$ : 0.01	
# : 0.28	c : 0.15	" : 0.13	! : 0.11	b : 0.09	g : 0.06	d : 0.05	[ : 0.03	a : 0.01	f : 0.01	$ : 0.01	e : 0.01	
# : 0.23	b : 0.15	! : 0.13	d : 0.11	c : 0.11	" : 0.08	g : 0.05	[ : 0.03	e : 0.03	f : 0.01	a : 0.01	$ : 0.01	
d : 0.26	c : 0.15	! : 0.11	[ : 0.11	# : 0.09	g : 0.05	" : 0.05	b : 0.05	a : 0.03	e : 0.03	f : 0.01	r : 0.01	
c : 0.39	d : 0.31	! : 0.05	e : 0.05	[ : 0.05	g : 0.03	" : 0.03	f : 0.01	# : 0.01	r : 0.01	a : 0.01	
c : 0.44	d : 0.31	e : 0.05	g : 0.03	" : 0.03	b : 0.03	f : 0.01	a : 0.01	[ : 0.01	r : 0.01	o : 0.01	
c : 0.38	d : 0.23	o : 0.19	g : 0.03	e : 0.03	b : 0.03	f : 0.01	! : 0.01	a : 0.01	" : 0.01	r : 0.01	
n : 0.36	o : 0.30	c : 0.09	m : 0.08	d : 0.05	l : 0.03	e : 0.01	! : 0.01	a : 0.01	r : 0.01	
n : 0.38	o : 0.31	m : 0.16	l : 0.05	c : 0.03	e : 0.01	b : 0.01	r : 0.01	
n : 0.38	o : 0.31	m : 0.16	l : 0.09	b : 0.01	r : 0.01	
n : 0.38	o : 0.31	m : 0.16	l : 0.08	c : 0.03	r : 0.01	
n : 0.38	o : 0.30	m : 0.08	c : 0.06	l : 0.06	d : 0.06	r : 0.01	a : 0.01	
c : 0.43	d : 0.26	o : 0.11	e : 0.05	b : 0.03	g : 0.01	n : 0.01	f : 0.01	l : 0.01	a : 0.01	] : 0.01	
c : 0.46	d : 0.30	e : 0.05	b : 0.05	g : 0.03	3 : 0.01	f : 0.01	4 : 0.01	] : 0.01	o : 0.01	a : 0.01	
c : 0.46	d : 0.30	e : 0.05	g : 0.03	3 : 0.03	] : 0.03	f : 0.01	2 : 0.01	b : 0.01	4 : 0.01	a : 0.01	
d : 0.23	2 : 0.18	c : 0.11	] : 0.11	3 : 0.09	g : 0.06	e : 0.06	b : 0.03	4 : 0.03	f : 0.01	6 : 0.01	a : 0.01	
2 : 0.19	] : 0.13	3 : 0.11	b : 0.11	c : 0.08	g : 0.06	d : 0.06	4 : 0.06	e : 0.06	f : 0.03	a : 0.01	6 : 0.01	> : 0.01	
c : 0.16	b : 0.16	d : 0.09	3 : 0.09	g : 0.08	a : 0.08	4 : 0.08	] : 0.06	f : 0.05	2 : 0.03	e : 0.01	6 : 0.01	> : 0.01	= : 0.01	
c : 0.24	b : 0.13	d : 0.11	] : 0.09	4 : 0.09	g : 0.08	3 : 0.08	f : 0.06	e : 0.01	6 : 0.01	> : 0.01	= : 0.01	
c : 0.23	b : 0.15	d : 0.15	4 : 0.11	f : 0.08	g : 0.06	3 : 0.06	= : 0.03	e : 0.01	2 : 0.01	i : 0.01	6 : 0.01	] : 0.01	> : 0.01	
d : 0.16	c : 0.15	4 : 0.11	b : 0.09	3 : 0.09	f : 0.08	2 : 0.06	] : 0.06	g : 0.05	= : 0.03	i : 0.01	6 : 0.01	a : 0.01	> : 0.01	
] : 0.18	d : 0.11	3 : 0.09	f : 0.09	2 : 0.08	c : 0.08	4 : 0.08	g : 0.06	= : 0.05	a : 0.05	b : 0.03	i : 0.01	> : 0.01	0 : 0.01	
f : 0.15	c : 0.11	d : 0.11	] : 0.09	3 : 0.08	g : 0.08	= : 0.06	4 : 0.06	2 : 0.05	b : 0.05	a : 0.03	i : 0.03	e : 0.01	> : 0.01	0 : 0.01	
c : 0.16	d : 0.15	f : 0.13	g : 0.09	3 : 0.06	= : 0.06	4 : 0.05	e : 0.05	i : 0.05	2 : 0.05	b : 0.05	] : 0.03	> : 0.01	0 : 0.01	
c : 0.16	f : 0.11	d : 0.11	e : 0.09	g : 0.08	= : 0.08	] : 0.06	2 : 0.05	i : 0.05	4 : 0.03	: : 0.03	b : 0.03	> : 0.01	3 : 0.01	5 : 0.01	0 : 0.01	

#score	722.5513168562635
#seq	60
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_CDS_m3_run1.txt

#BEAR
gddddqqqqqqqqdddd:	chr5:122696466-122696737(-)$1	271	93	111	14.4268
eeeeeqqqqqqqqeeeee	chr10:128244012-128244299(+)$1	287	34	52	13.8486
eeeeeqqqqqqqqeeeee	chr18:76446389-76446666(+)$1	277	45	63	13.8486
:ddddqqqqqqqqdddd:	chr13:21903541-21903824(+)$1	283	193	211	13.7227
#ddddqqqqqqqqdddd4	chr17:56565724-56565994(-)$1	270	127	145	15.3552
dddddqqqqqqqqddddD	chr10:127527031-127527307(+)$1	276	97	115	13.9647
eeeeeqqqqqqqqeeeee	chr6:67221105-67221457(+)$1	352	97	115	13.8486
!!cccqqqqqqqqccc22	chr19:45587836-45588106(+)$1	270	237	255	14.5701
eeeeeqqqqqqqqeeeee	chrX:101281250-101281519(-)$1	269	163	181	13.8486
!!a[aqqqqqqqqa]a22	chr2:91776782-91777058(-)$1	276	39	57	13.6865
e[cccqqqqqqqqcccee	chr12:72316949-72317221(+)$1	272	237	255	14.2730
=====qqqqqqqq=====	chr7:52381456-52381729(-)$1	273	243	261	13.6362
c[cccqqqqqqqqccc]c	chr7:30977396-30977676(-)$1	280	203	221	14.3045
b[cccqqqqqqqqccc]b	chr1:187220969-187221241(+)$1	272	102	120	13.9287
a[cccqqqqqqqqccc]a	chr16:17284424-17284704(-)$1	280	114	132	14.5414
[ddddqqqqqqqqdddd2	chr11:4694291-4694568(-)$1	277	56	74	15.3085
=====qqqqqqqq=====	chr11:5604563-5604832(-)$1	269	24	42	13.6362
cccbbqqqqqqqqbb]cc	chr7:52118763-52119040(-)$1	277	23	41	12.5531
d[cccqqqqqqqqccc]d	chr2:20702442-20702720(+)$1	278	110	128	14.1006
cccccqqqqqqqqccc]c	chr14:32075268-32075538(-)$1	270	78	96	14.1278
:ddddqqqqqqqqdddd:	chr1:55139797-55140072(-)$1	275	165	183	13.7227
cc[bbqqqqqqqqbbccc	chr17:56323132-56323402(-)$1	270	175	193	12.6034
eeeeeqqqqqqqqeeeee	chr8:12947996-12948331(+)$1	335	81	99	13.8486
[ddddqqqqqqqqdddd2	chr6:129401596-129401865(-)$1	269	62	80	15.3085
$ddddqqqqqqqqdddd5	chr4:46472868-46473142(+)$1	274	38	56	14.5100
a"""aqqqqqqqqa333a	chr2:53009569-53009852(-)$1	283	33	51	13.3543
[ddddqqqqqqqqdddd]	chr2:166435200-166435469(-)$1	269	162	180	15.3388
a[cccqqqqqqqqccc]a	chr9:108485040-108485308(-)$1	268	128	146	14.5414
!!cccqqqqqqqqccc22	chr17:45708683-45708966(-)$1	283	16	34	14.5701
eeeeeqqqqqqqqeeeee	chr16:8695056-8695337(-)$1	281	244	262	13.8486
[ddddqqqqqqqqdddde	chr15:98350666-98350938(-)$1	272	140	158	15.1507
[a[bbqqqqqqqqbb]a]	chr4:138452539-138452807(-)$1	268	179	197	12.7496
c[cccqqqqqqqqccc]c	chr4:137298988-137299270(-)$1	282	213	231	14.3045
#ddddqqqqqqqqdddd]	chr19:60849703-60849972(-)$1	269	108	126	15.3307
gggggqqqqqqqqggggg	chr9:94437813-94438081(-)$1	268	49	67	13.2458
:ddddqqqqqqqqdddd:	chr5:116181088-116181365(-)$1	277	214	232	13.7227
ddd[aqqqqqqqqa]ddd	chr13:77245126-77245400(-)$1	274	160	178	13.8234
b[cccqqqqqqqqccc]b	chr5:4082995-4083264(-)$1	269	53	71	13.9287
[ddddqqqqqqqqdddd2	chr11:68843060-68843328(+)$1	268	82	100	15.3085
ee[bbqqqqqqqqbbeee	chr6:47490548-47490817(-)$1	269	213	231	12.7735
!ddddqqqqqqqqdddd2	chr4:132383952-132384240(-)$1	288	124	142	15.3688
:ddddqqqqqqqqddddD	chr7:140206322-140206619(-)$1	297	212	230	13.3822
[ddddqqqqqqqqdddda	chr8:93534532-93534803(+)$1	271	101	119	15.2886
a[cccqqqqqqqqccc]a	chr9:44041765-44042048(-)$1	283	88	106	14.5414
""cccqqqqqqqqccc33	chr12:109356282-109356574(-)$1	292	167	185	14.6911
eee[aqqqqqqqqa]eee	chr11:97686039-97686316(+)$1	277	58	76	13.5537
eeeeeqqqqqqqqeeeee	chr9:30876493-30876778(+)$1	285	183	201	13.8486
$ddddqqqqqqqqdddd>	chr10:86154255-86154580(-)$1	325	139	157	15.0267
eddddqqqqqqqqddddC	chr2:34631160-34631449(+)$1	289	267	285	14.1347
!ddddqqqqqqqqdddd]	chr1:172810584-172810852(-)$1	268	13	31	15.3990
eeeeeqqqqqqqqeeeee	chr14:57390422-57390712(-)$1	290	196	214	13.8486
"ddddqqqqqqqqdddd3	chr5:114815670-114815939(-)$1	269	60	78	15.4723
eeeeeqqqqqqqqeeeee	chr5:144024897-144025185(-)$1	288	13	31	13.8486
gggggqqqqqqqqggggg	chrX:12868276-12868559(+)$1	283	184	202	13.2458
!ddddqqqqqqqqdddd7	chr1:71675776-71676062(-)$1	286	158	176	14.9356
d[cccqqqqqqqqccc22	chr15:99611223-99611577(-)$1	354	295	313	14.1687
""cccqqqqqqqqccc22	chr5:135693175-135693443(+)$1	268	138	156	14.4104
:ddddqqqqqqqqdddd:	chr2:165884632-165884906(+)$1	274	36	54	13.7227
:ddddqqqqqqqqdddd:	chr8:26939165-26939461(-)$1	296	5	23	13.7227
##cccqqqqqqqqccc22	chr17:83850194-83850462(+)$1	268	92	110	14.3369
gggggqqqqqqqqggggg	chr6:148754801-148755081(-)$1	280	247	265	13.2458
[ddddqqqqqqqqdddd]	chr8:73054738-73055013(+)$1	275	4	22	15.3388
hddddqqqqqqqqdddd:	chr4:137192728-137193018(+)$1	290	148	166	14.2131
c[cccqqqqqqqqccccc	chr19:7432582-7432875(-)$1	293	160	178	14.1665
"ddddqqqqqqqqdddd]	chr16:20692334-20692663(+)$1	329	27	45	15.3568
eeeeeqqqqqqqqeeeee	chr1:182827661-182827940(+)$1	279	179	197	13.8486
eeebbqqqqqqqqbb]ee	chr5:67365700-67365971(+)$1	271	112	130	12.7206
bddddqqqqqqqqdddd4	chr9:70526857-70527145(+)$1	288	107	125	14.9682
!!cccqqqqqqqqccc44	chr17:84831403-84831691(-)$1	288	185	203	14.7281
:ddddqqqqqqqqddddc	chr3:96067066-96067359(-)$1	293	214	232	14.2589
eeeeeqqqqqqqqeeeee	chr10:90615877-90616157(-)$1	280	214	232	13.8486
eeeeeqqqqqqqqeeeee	chr15:102188999-102189267(-)$1	268	57	75	13.8486
:ddddqqqqqqqqdddd:	chr8:107783742-107784014(-)$1	272	140	158	13.7227

#otherMatches

#Seq PSSM
GCCUGUGAAUAUCUGGGA	chr5:122696466-122696737(-)$1	271	93	111	14.4268
GUAUUGGUGGGAGAGUAU	chr10:128244012-128244299(+)$1	287	34	52	13.8486
CCAUGCUUUGCAUCAUGG	chr18:76446389-76446666(+)$1	277	45	63	13.8486
AGGGCAUCACGAAGCCCG	chr13:21903541-21903824(+)$1	283	193	211	13.7227
ACCAUGAAAGGCGAUGGC	chr17:56565724-56565994(-)$1	270	127	145	15.3552
AAGCCGUGGCAAAGGCUG	chr10:127527031-127527307(+)$1	276	97	115	13.9647
GUUGGAAGAAGACCCGAU	chr6:67221105-67221457(+)$1	352	97	115	13.8486
AGCAGUCUGAAGCCUGGC	chr19:45587836-45588106(+)$1	270	237	255	14.5701
GGAACCUCAAACAGUUCC	chrX:101281250-101281519(-)$1	269	163	181	13.8486
AGCGGGUAACUAAUGGGA	chr2:91776782-91777058(-)$1	276	39	57	13.6865
CCAAAACAAGAAAUUUGU	chr12:72316949-72317221(+)$1	272	237	255	14.2730
UGGUGAGGACGGACACUG	chr7:52381456-52381729(-)$1	273	243	261	13.6362
CCGGAAGUUCCCAUCCCG	chr7:30977396-30977676(-)$1	280	203	221	14.3045
UAUGAGCACUUGAUCACA	chr1:187220969-187221241(+)$1	272	102	120	13.9287
UGGCCAAGUUUAAGGUGA	chr16:17284424-17284704(-)$1	280	114	132	14.5414
UUGGGAACCAUGACCUAU	chr11:4694291-4694568(-)$1	277	56	74	15.3085
GCCUGUUCCAUGUCAGGU	chr11:5604563-5604832(-)$1	269	24	42	13.6362
UCGGCCUCAUCCCGCACG	chr7:52118763-52119040(-)$1	277	23	41	12.5531
CUCUGCCUCCCCACAGUG	chr2:20702442-20702720(+)$1	278	110	128	14.1006
GAUGUGGCUGAGAAUAUU	chr14:32075268-32075538(-)$1	270	78	96	14.1278
AGUAUGGGAUUUGAUACG	chr1:55139797-55140072(-)$1	275	165	183	13.7227
ACCGUGCCAUUUGACGUG	chr17:56323132-56323402(-)$1	270	175	193	12.6034
GGUCAUUGGAUCCUGACC	chr8:12947996-12948331(+)$1	335	81	99	13.8486
AUCUGAGGGUAGACAGGC	chr6:129401596-129401865(-)$1	269	62	80	15.3085
guuguuuucuguuacagu	chr4:46472868-46473142(+)$1	274	38	56	14.5100
GAAACAUACUAUAGACAU	chr2:53009569-53009852(-)$1	283	33	51	13.3543
GCAAGAAGGUGAACUUGA	chr2:166435200-166435469(-)$1	269	162	180	15.3388
AUGGUGAGCGCAAACCUU	chr9:108485040-108485308(-)$1	268	128	146	14.5414
GUUGGAUACUUUCCCAGA	chr17:45708683-45708966(-)$1	283	16	34	14.5701
CUUCCGGUAAGAAGGAAG	chr16:8695056-8695337(-)$1	281	244	262	13.8486
CUUCGCUAACUCUUGAAG	chr15:98350666-98350938(-)$1	272	140	158	15.1507
GCGGCGAggagggguggg	chr4:138452539-138452807(-)$1	268	179	197	12.7496
AUCCCUCGAGGCUGGGCU	chr4:137298988-137299270(-)$1	282	213	231	14.3045
UGUUGAUGCUUUCCAACU	chr19:60849703-60849972(-)$1	269	108	126	15.3307
UGAAGAACGUGUACUUCG	chr9:94437813-94438081(-)$1	268	49	67	13.2458
GAGCUGACGGACAAGCUA	chr5:116181088-116181365(-)$1	277	214	232	13.7227
UCAGGUAAAAUUUUGUGA	chr13:77245126-77245400(-)$1	274	160	178	13.8234
AAUGGAUAUUUUCCCACU	chr5:4082995-4083264(-)$1	269	53	71	13.9287
UGUGUAAUAUUUAAUAUU	chr11:68843060-68843328(+)$1	268	82	100	15.3085
agacuuacucuguagcug	chr6:47490548-47490817(-)$1	269	213	231	12.7735
GCGGAUGGAGGGCUCUGG	chr4:132383952-132384240(-)$1	288	124	142	15.3688
GGGGGUAAAACUGUCCCG	chr7:140206322-140206619(-)$1	297	212	230	13.3822
AGACCCUGUGACCGGUCC	chr8:93534532-93534803(+)$1	271	101	119	15.2886
CGUGAAGAAGAGCUCGGG	chr9:44041765-44042048(-)$1	283	88	106	14.5414
CUGAGUGCAUAUUCUCCU	chr12:109356282-109356574(-)$1	292	167	185	14.6911
GCAAGCUCAUCUUCAUGU	chr11:97686039-97686316(+)$1	277	58	76	13.5537
uuuaauuuaauuuuuaaa	chr9:30876493-30876778(+)$1	285	183	201	13.8486
acucagagcaggaugagg	chr10:86154255-86154580(-)$1	325	139	157	15.0267
CUUCUGAAGAUAAAGAAA	chr2:34631160-34631449(+)$1	289	267	285	14.1347
CUUGCUUAUCAUUGCAGA	chr1:172810584-172810852(-)$1	268	13	31	15.3990
GUCCAGUUAAAUAUGGAC	chr14:57390422-57390712(-)$1	290	196	214	13.8486
ACAGGUUGAGUUCCCUGA	chr5:114815670-114815939(-)$1	269	60	78	15.4723
ACCUAAUUUCAAAUGGGU	chr5:144024897-144025185(-)$1	288	13	31	13.8486
AAGUUCAAUACAUAACUU	chrX:12868276-12868559(+)$1	283	184	202	13.2458
AACCACAGUACCUUGGUA	chr1:71675776-71676062(-)$1	286	158	176	14.9356
GAUCUGGACCUGAAGAAG	chr15:99611223-99611577(-)$1	354	295	313	14.1687
GGACCAGGAGUUAGGUGG	chr5:135693175-135693443(+)$1	268	138	156	14.4104
AACAGAAAUGUUCCUGUG	chr2:165884632-165884906(+)$1	274	36	54	13.7227
CGGGCAUAAUCCAGCCUA	chr8:26939165-26939461(-)$1	296	5	23	13.7227
AAAACCAAAAUUCGUUCA	chr17:83850194-83850462(+)$1	268	92	110	14.3369
UCuuuuuuuuuuuaaaga	chr6:148754801-148755081(-)$1	280	247	265	13.2458
AUGGCACUGGAUGGCCAC	chr8:73054738-73055013(+)$1	275	4	22	15.3388
GGCUGGCCCACUGCAGCA	chr4:137192728-137193018(+)$1	290	148	166	14.2131
GAGGAGGUAGUUAUCCCC	chr19:7432582-7432875(-)$1	293	160	178	14.1665
UGGUGAAGGAAGACGCCU	chr16:20692334-20692663(+)$1	329	27	45	15.3568
GAGGCAGGACCAGGCCUC	chr1:182827661-182827940(+)$1	279	179	197	13.8486
CCUCUGAGAAAGAAGAAG	chr5:67365700-67365971(+)$1	271	112	130	12.7206
GAUCGAUGCACCGCGGUU	chr9:70526857-70527145(+)$1	288	107	125	14.9682
AAAGUGACCUUUGGCUGU	chr17:84831403-84831691(-)$1	288	185	203	14.7281
AGGGUAUCACCAAGCCCG	chr3:96067066-96067359(-)$1	293	214	232	14.2589
CUGUUUUCAAACUAACAG	chr10:90615877-90616157(-)$1	280	214	232	13.8486
AGGGCCCCAGCAUGUCCU	chr15:102188999-102189267(-)$1	268	57	75	13.8486
CUCUGACGUACUGCAGAU	chr8:107783742-107784014(-)$1	272	140	158	13.7227

#DB
)((((........)))).	chr5:122696466-122696737(-)$1	1	93	111	14.4268
(((((........)))))	chr10:128244012-128244299(+)$1	1	34	52	13.8486
(((((........)))))	chr18:76446389-76446666(+)$1	1	45	63	13.8486
.((((........)))).	chr13:21903541-21903824(+)$1	1	193	211	13.7227
.((((........)))).	chr17:56565724-56565994(-)$1	1	127	145	15.3552
)((((........))))(	chr10:127527031-127527307(+)$1	1	97	115	13.9647
(((((........)))))	chr6:67221105-67221457(+)$1	1	97	115	13.8486
..(((........)))..	chr19:45587836-45588106(+)$1	1	237	255	14.5701
(((((........)))))	chrX:101281250-101281519(-)$1	1	163	181	13.8486
..(.(........).)..	chr2:91776782-91777058(-)$1	1	39	57	13.6865
(.(((........)))))	chr12:72316949-72317221(+)$1	1	237	255	14.2730
(((((........)))))	chr7:52381456-52381729(-)$1	1	243	261	13.6362
(.(((........))).)	chr7:30977396-30977676(-)$1	1	203	221	14.3045
(.(((........))).)	chr1:187220969-187221241(+)$1	1	102	120	13.9287
(.(((........))).)	chr16:17284424-17284704(-)$1	1	114	132	14.5414
.((((........)))).	chr11:4694291-4694568(-)$1	1	56	74	15.3085
(((((........)))))	chr11:5604563-5604832(-)$1	1	24	42	13.6362
(((((........)).))	chr7:52118763-52119040(-)$1	1	23	41	12.5531
(.(((........))).)	chr2:20702442-20702720(+)$1	1	110	128	14.1006
(((((........))).)	chr14:32075268-32075538(-)$1	1	78	96	14.1278
.((((........)))).	chr1:55139797-55140072(-)$1	1	165	183	13.7227
((.((........)))))	chr17:56323132-56323402(-)$1	1	175	193	12.6034
(((((........)))))	chr8:12947996-12948331(+)$1	1	81	99	13.8486
.((((........)))).	chr6:129401596-129401865(-)$1	1	62	80	15.3085
.((((........)))).	chr4:46472868-46473142(+)$1	1	38	56	14.5100
(...(........)...)	chr2:53009569-53009852(-)$1	1	33	51	13.3543
.((((........)))).	chr2:166435200-166435469(-)$1	1	162	180	15.3388
(.(((........))).)	chr9:108485040-108485308(-)$1	1	128	146	14.5414
..(((........)))..	chr17:45708683-45708966(-)$1	1	16	34	14.5701
(((((........)))))	chr16:8695056-8695337(-)$1	1	244	262	13.8486
.((((........)))))	chr15:98350666-98350938(-)$1	1	140	158	15.1507
.(.((........)).).	chr4:138452539-138452807(-)$1	1	179	197	12.7496
(.(((........))).)	chr4:137298988-137299270(-)$1	1	213	231	14.3045
.((((........)))).	chr19:60849703-60849972(-)$1	1	108	126	15.3307
(((((........)))))	chr9:94437813-94438081(-)$1	1	49	67	13.2458
.((((........)))).	chr5:116181088-116181365(-)$1	1	214	232	13.7227
(((.(........).)))	chr13:77245126-77245400(-)$1	1	160	178	13.8234
(.(((........))).)	chr5:4082995-4083264(-)$1	1	53	71	13.9287
.((((........)))).	chr11:68843060-68843328(+)$1	1	82	100	15.3085
((.((........)))))	chr6:47490548-47490817(-)$1	1	213	231	12.7735
.((((........)))).	chr4:132383952-132384240(-)$1	1	124	142	15.3688
.((((........)))))	chr7:140206322-140206619(-)$1	1	212	230	13.3822
.((((........)))))	chr8:93534532-93534803(+)$1	1	101	119	15.2886
(.(((........))).)	chr9:44041765-44042048(-)$1	1	88	106	14.5414
..(((........)))..	chr12:109356282-109356574(-)$1	1	167	185	14.6911
(((.(........).)))	chr11:97686039-97686316(+)$1	1	58	76	13.5537
(((((........)))))	chr9:30876493-30876778(+)$1	1	183	201	13.8486
.((((........)))).	chr10:86154255-86154580(-)$1	1	139	157	15.0267
)((((........)))))	chr2:34631160-34631449(+)$1	1	267	285	14.1347
.((((........)))).	chr1:172810584-172810852(-)$1	1	13	31	15.3990
(((((........)))))	chr14:57390422-57390712(-)$1	1	196	214	13.8486
.((((........)))).	chr5:114815670-114815939(-)$1	1	60	78	15.4723
(((((........)))))	chr5:144024897-144025185(-)$1	1	13	31	13.8486
(((((........)))))	chrX:12868276-12868559(+)$1	1	184	202	13.2458
.((((........)))).	chr1:71675776-71676062(-)$1	1	158	176	14.9356
(.(((........)))..	chr15:99611223-99611577(-)$1	1	295	313	14.1687
..(((........)))..	chr5:135693175-135693443(+)$1	1	138	156	14.4104
.((((........)))).	chr2:165884632-165884906(+)$1	1	36	54	13.7227
.((((........)))).	chr8:26939165-26939461(-)$1	1	5	23	13.7227
..(((........)))..	chr17:83850194-83850462(+)$1	1	92	110	14.3369
(((((........)))))	chr6:148754801-148755081(-)$1	1	247	265	13.2458
.((((........)))).	chr8:73054738-73055013(+)$1	1	4	22	15.3388
)((((........)))).	chr4:137192728-137193018(+)$1	1	148	166	14.2131
(.(((........)))))	chr19:7432582-7432875(-)$1	1	160	178	14.1665
.((((........)))).	chr16:20692334-20692663(+)$1	1	27	45	15.3568
(((((........)))))	chr1:182827661-182827940(+)$1	1	179	197	13.8486
(((((........)).))	chr5:67365700-67365971(+)$1	1	112	130	12.7206
(((((........)))).	chr9:70526857-70527145(+)$1	1	107	125	14.9682
..(((........)))..	chr17:84831403-84831691(-)$1	1	185	203	14.7281
.((((........))))(	chr3:96067066-96067359(-)$1	1	214	232	14.2589
(((((........)))))	chr10:90615877-90616157(-)$1	1	214	232	13.8486
(((((........)))))	chr15:102188999-102189267(-)$1	1	57	75	13.8486
.((((........)))).	chr8:107783742-107784014(-)$1	1	140	158	13.7227

#PSSM
e : 0.23	: : 0.10	[ : 0.10	! : 0.09	c : 0.08	g : 0.05	d : 0.05	a : 0.05	" : 0.05	# : 0.04	b : 0.04	= : 0.02	$ : 0.02	h : 0.01	
d : 0.41	e : 0.20	[ : 0.15	! : 0.05	c : 0.04	" : 0.04	g : 0.04	= : 0.02	a : 0.01	# : 0.01	
d : 0.41	c : 0.26	e : 0.19	[ : 0.04	g : 0.04	= : 0.02	a : 0.01	" : 0.01	
d : 0.39	c : 0.24	e : 0.16	b : 0.06	[ : 0.04	g : 0.04	= : 0.02	" : 0.01	
d : 0.39	c : 0.24	e : 0.16	b : 0.06	a : 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 : 0.39	c : 0.24	e : 0.16	b : 0.06	a : 0.05	g : 0.04	= : 0.02	
d : 0.39	c : 0.24	e : 0.16	b : 0.06	] : 0.04	g : 0.04	= : 0.02	3 : 0.01	
d : 0.41	c : 0.26	e : 0.19	] : 0.04	g : 0.04	= : 0.02	a : 0.01	3 : 0.01	
d : 0.41	e : 0.21	] : 0.12	2 : 0.08	c : 0.04	g : 0.04	= : 0.02	3 : 0.02	a : 0.01	4 : 0.01	
e : 0.23	2 : 0.13	: : 0.10	c : 0.09	] : 0.08	a : 0.06	4 : 0.04	g : 0.04	D : 0.02	= : 0.02	b : 0.02	d : 0.02	3 : 0.02	5 : 0.01	> : 0.01	C : 0.01	7 : 0.01	

#score	1034.730586572018
#seq	73
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_CDS_m3_run2.txt

#BEAR
cccqqqqqqqqccc:	chr14:32002864-32003105(-)$1	241	48	63	12.8783
fffqqqqqqqqffff	chr17:26394865-26395096(+)$1	231	170	185	12.1532
eeeqqqqqqqqeeee	chr9:112060196-112060438(-)$1	242	91	106	12.7324
===qqqqqqqq====	chr9:44756834-44757095(-)$1	261	36	51	12.9549
dddqqqqqqqqdddd	chr4:53715474-53715717(+)$1	243	103	118	13.3681
dddqqqqqqqqdddd	chr3:126657790-126658046(-)$1	256	5	20	13.3681
hbbqqqqqqqqbb]h	chr5:143665451-143665723(-)$1	272	208	223	12.1344
eeeqqqqqqqqeeee	chr19:44377469-44377702(+)$1	233	6	21	12.7324
cccqqqqqqqqccc:	chr8:96543418-96543688(-)$1	270	170	185	12.8783
===qqqqqqqq====	chr3:136540509-136540752(+)$1	243	51	66	12.9549
eeeqqqqqqqqeeee	chr13:100195674-100195909(-)$1	235	170	185	12.7324
cccqqqqqqqqccc:	chr3:141975336-141975572(-)$1	236	112	127	12.8783
!bbqqqqqqqqbb22	chr8:90304909-90305140(-)$1	231	155	170	12.0433
hhhqqqqqqqqhhhh	chr8:56135416-56135665(+)$1	249	54	69	12.1271
cccqqqqqqqqccc]	chr9:20890587-20890827(-)$1	240	13	28	13.6915
dddqqqqqqqqdddd	chr15:54681446-54681682(-)$1	236	69	84	13.3681
cccqqqqqqqqccc:	chr8:19693688-19693928(+)$1	240	168	183	12.8783
eeeqqqqqqqqeeee	chr18:20828451-20828687(+)$1	236	190	205	12.7324
cccqqqqqqqqccc:	chr1:162880995-162881230(+)$1	235	102	117	12.8783
eeeqqqqqqqqeeee	chrY:349719-349951(+)$1	232	45	60	12.7324
cccqqqqqqqqccc:	chr13:65397952-65398195(+)$1	243	180	195	12.8783
dddqqqqqqqqdddd	chr11:19964717-19964956(-)$1	239	212	227	13.3681
cccqqqqqqqqccc:	chr5:68042729-68042960(-)$1	231	7	22	12.8783
cccqqqqqqqqccc]	chr4:4694975-4695214(-)$1	239	110	125	13.6915
dddqqqqqqqqdddd	chr3:148521597-148521837(-)$1	240	81	96	13.3681
cccqqqqqqqqcccc	chr9:25097036-25097275(+)$1	239	102	117	13.6252
cccqqqqqqqqccc]	chr14:78912638-78912905(-)$1	267	50	65	13.6915
cccqqqqqqqqccc]	chr4:155552958-155553195(-)$1	237	123	138	13.6915
dddqqqqqqqqdddd	chr9:3021160-3021417(+)$1	257	120	135	13.3681
cccqqqqqqqqccc:	chr16:30355831-30356062(-)$1	231	206	221	12.8783
fffqqqqqqqqffff	chr7:135837988-135838257(+)$1	269	229	244	12.1532
dddqqqqqqqqdddd	chr5:21523725-21523966(-)$1	241	41	56	13.3681
!bbqqqqqqqqbb22	chr13:21841932-21842194(-)$1	262	228	243	12.0433
bbbqqqqqqqqbb]b	chr8:108199913-108200153(+)$1	240	210	225	11.9172
dddqqqqqqqqdddd	chr3:65186805-65187037(-)$1	232	92	107	13.3681
eeeqqqqqqqqeeee	chr6:38145447-38145705(-)$1	258	240	255	12.7324
cccqqqqqqqqccc]	chr5:143666040-143666324(-)$1	284	111	126	13.6915
!!aqqqqqqqqa22a	chr9:49314953-49315222(-)$1	269	95	110	12.3141
ebbqqqqqqqqbb]e	chr9:64564469-64564788(-)$1	319	82	97	12.4046
cccqqqqqqqqcccc	chr10:80833985-80834216(-)$1	231	158	173	13.6252
cccqqqqqqqqccc]	chr5:93611914-93612163(-)$1	249	97	112	13.6915
gggqqqqqqqqgggg	chr18:24740810-24741041(-)$1	231	147	162	12.8437
dddqqqqqqqqdddd	chr11:6368452-6368684(-)$1	232	182	197	13.3681
cccqqqqqqqqcccc	chr15:28365883-28366114(+)$1	231	25	40	13.6252
ddaqqqqqqqqa]dd	chr2:44844101-44844333(-)$1	232	44	59	13.0548
dddqqqqqqqqdddd	chr14:31984429-31984694(-)$1	265	201	216	13.3681
dddqqqqqqqqdddd	chr12:62940733-62940964(+)$1	231	191	206	13.3681
hhhqqqqqqqqhhhh	chrX:158216921-158217176(+)$1	255	158	173	12.1271
gggqqqqqqqqgggg	chr13:98016545-98016793(+)$1	248	90	105	12.8437
dddqqqqqqqqdddd	chr2:52984994-52985225(+)$1	231	40	55	13.3681
cccqqqqqqqqccca	chr11:6368491-6368792(-)$1	301	278	293	13.6390
dddqqqqqqqqdddd	chrX:103033526-103033763(-)$1	237	198	213	13.3681
fffqqqqqqqqffff	chr18:78020972-78021226(+)$1	254	50	65	12.1532
dddqqqqqqqqdddd	chr5:67677275-67677509(+)$1	234	129	144	13.3681
"bbqqqqqqqqbb]a	chr17:27717674-27717919(-)$1	245	219	234	12.3253
eeeqqqqqqqqeeee	chr5:122909463-122909720(-)$1	257	220	235	12.7324
cccqqqqqqqqccc2	chr5:115548045-115548303(+)$1	258	157	172	13.4799
i[aqqqqqqqqaiii	chr6:141511571-141511837(+)$1	266	164	179	12.8810
hhhqqqqqqqqhhhh	chrM:12153-12430(+)$1	277	30	45	12.1271
cccqqqqqqqqccc:	chrM:7237-7495(+)$1	258	154	169	12.8783
dddqqqqqqqqdddd	chr5:77287443-77287679(+)$1	236	180	195	13.3681
cccqqqqqqqqccc4	chr14:71316794-71317025(+)$1	231	193	208	13.5937
ebbqqqqqqqqbb]e	chr1:164621183-164621441(-)$1	258	202	217	12.4046
dddqqqqqqqqdddd	chr17:56577312-56577552(-)$1	240	163	178	13.3681
dddqqqqqqqqdddd	chr16:16484211-16484443(-)$1	232	209	224	13.3681
dddqqqqqqqqdddd	chr2:122512614-122512845(-)$1	231	6	21	13.3681
fffqqqqqqqqffff	chr14:7269194-7269429(-)$1	235	42	57	12.1532
cccqqqqqqqqccc2	chr10:101944837-101945069(-)$1	232	135	150	13.4799
dddqqqqqqqqdddd	chrM:9802-10062(+)$1	260	102	117	13.3681
fffqqqqqqqqffff	chr8:36003674-36003936(-)$1	262	161	176	12.1532
"bbqqqqqqqqbb]b	chr19:59069462-59069693(-)$1	231	189	204	12.0881
[bbqqqqqqqqbb]c	chr16:35704748-35704988(-)$1	240	87	102	12.4043
dddqqqqqqqqdddd	chr5:38550069-38550326(-)$1	257	13	28	13.3681
c[aqqqqqqqqaccc	chr7:129221921-129222153(+)$1	232	68	83	13.2233
eeeqqqqqqqqeeee	chr5:89093039-89093270(-)$1	231	46	61	12.7324
eeeqqqqqqqqeeee	chr12:103632671-103632925(-)$1	254	31	46	12.7324

#otherMatches

#Seq PSSM
GGCUUCAAGAUGCCA	chr14:32002864-32003105(-)$1	241	48	63	12.8783
GAUGUUUGUAAGUUA	chr17:26394865-26395096(+)$1	231	170	185	12.1532
GAAAGCAAUACUUCC	chr9:112060196-112060438(-)$1	242	91	106	12.7324
GAUGUAACUGAAUUU	chr9:44756834-44757095(-)$1	261	36	51	12.9549
AGACUUCUAAAUCUC	chr4:53715474-53715717(+)$1	243	103	118	13.3681
CUGUCUUCUCUUAGG	chr3:126657790-126658046(-)$1	256	5	20	13.3681
GAGUCCGGCCCCUCC	chr5:143665451-143665723(-)$1	272	208	223	12.1344
UGCUUCUAUUUGCAG	chr19:44377469-44377702(+)$1	233	6	21	12.7324
ACUGUAGAACAAGUU	chr8:96543418-96543688(-)$1	270	170	185	12.8783
GGAGAGUAAAUUCUU	chr3:136540509-136540752(+)$1	243	51	66	12.9549
CAGGAUUUGAACUGU	chr13:100195674-100195909(-)$1	235	170	185	12.7324
GCUGUAUCCAAAGUC	chr3:141975336-141975572(-)$1	236	112	127	12.8783
CCGAACAGCCACGAG	chr8:90304909-90305140(-)$1	231	155	170	12.0433
CAUACCUCUUCAUGU	chr8:56135416-56135665(+)$1	249	54	69	12.1271
GGGCAGCUGACCCCU	chr9:20890587-20890827(-)$1	240	13	28	13.6915
ACUUUGAAAGUGGUU	chr15:54681446-54681682(-)$1	236	69	84	13.3681
CUAGAACAUGAUAGC	chr8:19693688-19693928(+)$1	240	168	183	12.8783
AUUUUGUUUUUAGUC	chr18:20828451-20828687(+)$1	236	190	205	12.7324
CAGAAAACCUCCUGC	chr1:162880995-162881230(+)$1	235	102	117	12.8783
AGAGUGUGUAAUCUU	chrY:349719-349951(+)$1	232	45	60	12.7324
GCUAUAAAGAAGGCA	chr13:65397952-65398195(+)$1	243	180	195	12.8783
ACCAAGAAAAGGGUG	chr11:19964717-19964956(-)$1	239	212	227	13.3681
UCCUCCUUUUUGGAC	chr5:68042729-68042960(-)$1	231	7	22	12.8783
CACUCUUGGAUGUGC	chr4:4694975-4695214(-)$1	239	110	125	13.6915
GGAACAAUAACUUCA	chr3:148521597-148521837(-)$1	240	81	96	13.3681
GACUCAUUUUUGUUU	chr9:25097036-25097275(+)$1	239	102	117	13.6252
UGUUUACAAACACAG	chr14:78912638-78912905(-)$1	267	50	65	13.6915
GUGAACCCACGUACA	chr4:155552958-155553195(-)$1	237	123	138	13.6915
cacguuuuuaaguga	chr9:3021160-3021417(+)$1	257	120	135	13.3681
CUAUAUUCCAUUAGA	chr16:30355831-30356062(-)$1	231	206	221	12.8783
UGGAAGUGAACUUGG	chr7:135837988-135838257(+)$1	269	229	244	12.1532
AGGAAUUUACAUCUG	chr5:21523725-21523966(-)$1	241	41	56	13.3681
CUCAUGACCAAGAAU	chr13:21841932-21842194(-)$1	262	228	243	12.0433
UCUUCAGUUACAGAA	chr8:108199913-108200153(+)$1	240	210	225	11.9172
UUCUUUAUACUGAAG	chr3:65186805-65187037(-)$1	232	92	107	13.3681
AGCACCUACCAGCUC	chr6:38145447-38145705(-)$1	258	240	255	12.7324
UGAGAGGGAAAUCGU	chr5:143666040-143666324(-)$1	284	111	126	13.6915
GACUUAAAAAUGGAC	chr9:49314953-49315222(-)$1	269	95	110	12.3141
CCGCCCACCACUGAG	chr9:64564469-64564788(-)$1	319	82	97	12.4046
CAGAAAAUCACCUGC	chr10:80833985-80834216(-)$1	231	158	173	13.6252
UUUAUCAAGGCAAGA	chr5:93611914-93612163(-)$1	249	97	112	13.6915
AUUAUGCAGAAAAUG	chr18:24740810-24741041(-)$1	231	147	162	12.8437
UAGGAAUCUCACUGC	chr11:6368452-6368684(-)$1	232	182	197	13.3681
AUAUAUUUUUUUAUA	chr15:28365883-28366114(+)$1	231	25	40	13.6252
ugcggagaagggacg	chr2:44844101-44844333(-)$1	232	44	59	13.0548
GCCUCUGAAGUGGCA	chr14:31984429-31984694(-)$1	265	201	216	13.3681
GUGAGCUUGCACACC	chr12:62940733-62940964(+)$1	231	191	206	13.3681
AGCUUUAAAACGUUU	chrX:158216921-158217176(+)$1	255	158	173	12.1271
CAGCAUAACCACUGU	chr13:98016545-98016793(+)$1	248	90	105	12.8437
uGUAUUUCCCAGCAA	chr2:52984994-52985225(+)$1	231	40	55	13.3681
UACUUUGUAUUGUAG	chr11:6368491-6368792(-)$1	301	278	293	13.6390
UCCACAGUAACGGAG	chrX:103033526-103033763(-)$1	237	198	213	13.3681
UUUCUAUUUCCAAAC	chr18:78020972-78021226(+)$1	254	50	65	12.1532
AGAAGACUAUGUCUC	chr5:67677275-67677509(+)$1	234	129	144	13.3681
AGCAGACUGAAGCAU	chr17:27717674-27717919(-)$1	245	219	234	12.3253
ACUGAUCAGCGGGUG	chr5:122909463-122909720(-)$1	257	220	235	12.7324
GGUGUCUUUGUGCUU	chr5:115548045-115548303(+)$1	258	157	172	13.4799
GUGUCAAGUCUCCUC	chr6:141511571-141511837(+)$1	266	164	179	12.8810
GAAUUAUAUCUUUCC	chrM:12153-12430(+)$1	277	30	45	12.1271
ACCUAAAACCUGGUG	chrM:7237-7495(+)$1	258	154	169	12.8783
ACAGGAGACAGUGUG	chr5:77287443-77287679(+)$1	236	180	195	13.3681
UUGAUUUCUUCCAAC	chr14:71316794-71317025(+)$1	231	193	208	13.5937
UAGGAACCUAACUCA	chr1:164621183-164621441(-)$1	258	202	217	12.4046
GGCUCACCCAUGCCC	chr17:56577312-56577552(-)$1	240	163	178	13.3681
UGGGGUGAACACCAU	chr16:16484211-16484443(-)$1	232	209	224	13.3681
ACAUCUGUCUCUGUU	chr2:122512614-122512845(-)$1	231	6	21	13.3681
GCUGGAGGAGGAGCA	chr14:7269194-7269429(-)$1	235	42	57	12.1532
GAUUACCUGAUAUCU	chr10:101944837-101945069(-)$1	232	135	150	13.4799
UAGCCUUCUCACUAU	chrM:9802-10062(+)$1	260	102	117	13.3681
UAAAGGGAAAAUUGA	chr8:36003674-36003936(-)$1	262	161	176	12.1532
AGCCUCUCCAAGCCC	chr19:59069462-59069693(-)$1	231	189	204	12.0881
CACCUUUUUAAGUAA	chr16:35704748-35704988(-)$1	240	87	102	12.4043
GGCCACGGCUCGCCC	chr5:38550069-38550326(-)$1	257	13	28	13.3681
CUCUUACUACUGGGU	chr7:129221921-129222153(+)$1	232	68	83	13.2233
UUGUUCUUCCUCAGA	chr5:89093039-89093270(-)$1	231	46	61	12.7324
AUGACUCCCCCCAUG	chr12:103632671-103632925(-)$1	254	31	46	12.7324

#DB
(((........))).	chr14:32002864-32003105(-)$1	1	48	63	12.8783
(((........))))	chr17:26394865-26395096(+)$1	1	170	185	12.1532
(((........))))	chr9:112060196-112060438(-)$1	1	91	106	12.7324
(((........))))	chr9:44756834-44757095(-)$1	1	36	51	12.9549
(((........))))	chr4:53715474-53715717(+)$1	1	103	118	13.3681
(((........))))	chr3:126657790-126658046(-)$1	1	5	20	13.3681
(((........)).)	chr5:143665451-143665723(-)$1	1	208	223	12.1344
(((........))))	chr19:44377469-44377702(+)$1	1	6	21	12.7324
(((........))).	chr8:96543418-96543688(-)$1	1	170	185	12.8783
(((........))))	chr3:136540509-136540752(+)$1	1	51	66	12.9549
(((........))))	chr13:100195674-100195909(-)$1	1	170	185	12.7324
(((........))).	chr3:141975336-141975572(-)$1	1	112	127	12.8783
.((........))..	chr8:90304909-90305140(-)$1	1	155	170	12.0433
(((........))))	chr8:56135416-56135665(+)$1	1	54	69	12.1271
(((........))).	chr9:20890587-20890827(-)$1	1	13	28	13.6915
(((........))))	chr15:54681446-54681682(-)$1	1	69	84	13.3681
(((........))).	chr8:19693688-19693928(+)$1	1	168	183	12.8783
(((........))))	chr18:20828451-20828687(+)$1	1	190	205	12.7324
(((........))).	chr1:162880995-162881230(+)$1	1	102	117	12.8783
(((........))))	chrY:349719-349951(+)$1	1	45	60	12.7324
(((........))).	chr13:65397952-65398195(+)$1	1	180	195	12.8783
(((........))))	chr11:19964717-19964956(-)$1	1	212	227	13.3681
(((........))).	chr5:68042729-68042960(-)$1	1	7	22	12.8783
(((........))).	chr4:4694975-4695214(-)$1	1	110	125	13.6915
(((........))))	chr3:148521597-148521837(-)$1	1	81	96	13.3681
(((........))))	chr9:25097036-25097275(+)$1	1	102	117	13.6252
(((........))).	chr14:78912638-78912905(-)$1	1	50	65	13.6915
(((........))).	chr4:155552958-155553195(-)$1	1	123	138	13.6915
(((........))))	chr9:3021160-3021417(+)$1	1	120	135	13.3681
(((........))).	chr16:30355831-30356062(-)$1	1	206	221	12.8783
(((........))))	chr7:135837988-135838257(+)$1	1	229	244	12.1532
(((........))))	chr5:21523725-21523966(-)$1	1	41	56	13.3681
.((........))..	chr13:21841932-21842194(-)$1	1	228	243	12.0433
(((........)).)	chr8:108199913-108200153(+)$1	1	210	225	11.9172
(((........))))	chr3:65186805-65187037(-)$1	1	92	107	13.3681
(((........))))	chr6:38145447-38145705(-)$1	1	240	255	12.7324
(((........))).	chr5:143666040-143666324(-)$1	1	111	126	13.6915
..(........)..)	chr9:49314953-49315222(-)$1	1	95	110	12.3141
(((........)).)	chr9:64564469-64564788(-)$1	1	82	97	12.4046
(((........)))(	chr10:80833985-80834216(-)$1	1	158	173	13.6252
(((........))).	chr5:93611914-93612163(-)$1	1	97	112	13.6915
(((........))))	chr18:24740810-24741041(-)$1	1	147	162	12.8437
(((........))))	chr11:6368452-6368684(-)$1	1	182	197	13.3681
(((........))))	chr15:28365883-28366114(+)$1	1	25	40	13.6252
(((........).))	chr2:44844101-44844333(-)$1	1	44	59	13.0548
(((........))))	chr14:31984429-31984694(-)$1	1	201	216	13.3681
(((........))))	chr12:62940733-62940964(+)$1	1	191	206	13.3681
(((........))))	chrX:158216921-158217176(+)$1	1	158	173	12.1271
(((........))))	chr13:98016545-98016793(+)$1	1	90	105	12.8437
(((........))))	chr2:52984994-52985225(+)$1	1	40	55	13.3681
(((........))))	chr11:6368491-6368792(-)$1	1	278	293	13.6390
(((........))))	chrX:103033526-103033763(-)$1	1	198	213	13.3681
(((........))))	chr18:78020972-78021226(+)$1	1	50	65	12.1532
(((........))))	chr5:67677275-67677509(+)$1	1	129	144	13.3681
.((........)).)	chr17:27717674-27717919(-)$1	1	219	234	12.3253
(((........))))	chr5:122909463-122909720(-)$1	1	220	235	12.7324
(((........))).	chr5:115548045-115548303(+)$1	1	157	172	13.4799
(.(........))))	chr6:141511571-141511837(+)$1	1	164	179	12.8810
(((........))))	chrM:12153-12430(+)$1	1	30	45	12.1271
(((........))).	chrM:7237-7495(+)$1	1	154	169	12.8783
(((........))))	chr5:77287443-77287679(+)$1	1	180	195	13.3681
(((........))).	chr14:71316794-71317025(+)$1	1	193	208	13.5937
(((........)).)	chr1:164621183-164621441(-)$1	1	202	217	12.4046
(((........))))	chr17:56577312-56577552(-)$1	1	163	178	13.3681
(((........))))	chr16:16484211-16484443(-)$1	1	209	224	13.3681
(((........))))	chr2:122512614-122512845(-)$1	1	6	21	13.3681
(((........))))	chr14:7269194-7269429(-)$1	1	42	57	12.1532
(((........))).	chr10:101944837-101945069(-)$1	1	135	150	13.4799
(((........))))	chrM:9802-10062(+)$1	1	102	117	13.3681
(((........))))	chr8:36003674-36003936(-)$1	1	161	176	12.1532
.((........)).)	chr19:59069462-59069693(-)$1	1	189	204	12.0881
.((........)).)	chr16:35704748-35704988(-)$1	1	87	102	12.4043
(((........))))	chr5:38550069-38550326(-)$1	1	13	28	13.3681
(.(........))))	chr7:129221921-129222153(+)$1	1	68	83	13.2233
(((........))))	chr5:89093039-89093270(-)$1	1	46	61	12.7324
(((........))))	chr12:103632671-103632925(-)$1	1	31	46	12.7324

#PSSM
c : 0.30	d : 0.27	e : 0.14	f : 0.06	h : 0.05	! : 0.03	= : 0.02	g : 0.02	" : 0.02	b : 0.01	i : 0.01	[ : 0.01	
c : 0.28	d : 0.27	e : 0.11	b : 0.11	f : 0.06	h : 0.03	= : 0.02	g : 0.02	[ : 0.02	! : 0.01	
c : 0.28	d : 0.26	e : 0.11	b : 0.11	f : 0.06	a : 0.05	h : 0.03	= : 0.02	g : 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	
c : 0.28	d : 0.26	e : 0.11	b : 0.11	f : 0.06	a : 0.05	h : 0.03	= : 0.02	g : 0.02	
c : 0.30	d : 0.26	e : 0.11	b : 0.11	f : 0.06	h : 0.03	= : 0.02	g : 0.02	2 : 0.01	] : 0.01	i : 0.01	
c : 0.30	d : 0.27	e : 0.11	] : 0.09	f : 0.06	2 : 0.03	h : 0.03	= : 0.02	g : 0.02	i : 0.01	
d : 0.27	e : 0.14	: : 0.11	] : 0.07	f : 0.06	c : 0.06	h : 0.05	2 : 0.05	a : 0.03	= : 0.02	b : 0.02	g : 0.02	i : 0.01	4 : 0.01	

#score	985.0621631943554
#seq	76
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_UTR_m3_run2.txt

#BEAR
""eeeee[cccmmmmccc]eeeee33	chr17:66687051-66687252(-)$1	201	43	69	12.1229
##eeeee!!bbmmmmbb22eeeee44	chr18:32394530-32394731(+)$1	201	116	142	10.2405
!!bb[bb[cccmmmmccc]bb]bb33	chr2:124491683-124491884(+)$1	201	151	177	11.3606
d!!dddd"""ammmma333dddd333	chr19:10059339-10059540(+)$1	201	74	100	10.8093
eeeee"""cccmmmmccc22eeeee:	chr8:125153259-125153460(-)$1	201	1	27	10.8951
ffff####cccmmmmccc4444ffff	chrX:162826124-162826325(+)$1	201	150	176	11.6185
eeee####cccmmmmccc22eeeee]	chr6:90332759-90332960(+)$1	201	86	112	11.9993
g####ccccccmmmmccc]ccc]ggg	chr9:51895472-51895673(+)$1	201	162	188	12.3314
ggggccc[cccmmmmcccccc]gggg	chr6:35461666-35461867(-)$1	201	27	53	11.6301
ccc####ddddmmmmdddd4444ccc	chr3:55804393-55804594(-)$1	201	62	88	11.6326
ggggbb[ddddmmmmdddd22bb]gg	chr18:34478294-34478495(+)$1	201	153	179	9.7991
[dddd[cccbbmmmmbb22ccc]ddd	chr10:63392669-63392870(-)$1	201	70	96	9.7654
ccc[bb[ddddmmmmdddd]bb]ccc	chr2:140485071-140485272(-)$1	201	124	150	10.4845
cc"""bbddddmmmmdddd333bb44	chr8:34527695-34527896(+)$1	201	131	157	11.1639
eeeeccc[cccmmmmccc]ccc]eee	chr8:113659249-113659450(+)$1	201	164	190	11.7446
ccc[ddddcccmmmmccc22ddddcc	chr9:32070989-32071190(+)$1	201	119	145	11.2660
b[bb[a[ddddmmmmdddd]a]bb]b	chr3:55791875-55792076(-)$1	201	140	166	9.8974
===========mmmm===========	chr2:146050380-146050581(+)$1	201	111	137	11.9132
===========mmmm===========	chr4:75587224-75587425(-)$1	201	148	174	11.9132
f[bb[a[ddddmmmmddddabb]fff	chr6:124997802-124998003(+)$1	201	151	177	10.0071
""dddd[ddddmmmmdddddddd333	chr14:65430470-65430671(-)$1	201	125	151	10.6071
c[ccc[eeeeellleeeee333ccc]	chr1:138525843-138526044(+)$1	201	55	81	8.3082
iiiiddddcccmmmmccc]dddd>>>	chr10:127830932-127831133(+)$1	201	7	33	10.5686
cc[ccc!!cccmmmmccc]ccc]ccc	chr7:6659158-6659359(-)$1	201	129	155	12.6170
ccc"""cccccclllccc]ccc22cc	chr8:42003248-42003449(+)$1	201	96	122	9.5984
""bb[bb[cccmmmmccc]bb]bbff	chr15:92171051-92171252(+)$1	201	10	36	10.5504
[ccc[bbddddmmmmdddd4444bb]	chr7:53685479-53685680(+)$1	201	69	95	10.6377
iiiiiiiddddmmmmdddd]iiiiii	chr6:113697619-113697820(-)$1	201	125	151	11.0344
:eeeee!!cccmmmmccc22eeeee:	chr2:103988354-103988555(-)$1	201	88	114	9.9281
c[cccbb[cccmmmmccc]bb]ccc]	chr8:11199543-11199744(-)$1	201	129	155	11.6231
&&iiiiiiiiimmmmiiiiiiiiigg	chr10:80861742-80861943(-)$1	201	27	53	9.7828
cc[eeeeecccmmmmccc22eeeeec	chr2:124491255-124491456(+)$1	201	5	31	11.3936
!!ccc"""cccmmmmccc333cccff	chr9:75066129-75066330(+)$1	201	91	117	12.9046
cc!!bb[ddddmmmmddddbb22ccc	chr9:96583733-96583934(-)$1	201	27	53	10.1659
ccc[bb[ddddmmmmdddd]bb]ccc	chr2:140485070-140485271(-)$1	201	123	149	10.4845
[dddd[eeeeemmmmeeeee]dddd3	chr9:103083662-103083863(+)$1	201	27	53	9.5300
!!a"""eeeeemmmmeeeee333a22	chr6:141481094-141481295(+)$1	201	33	59	11.1713
""eeeee[cccmmmmccc]eeeee33	chr17:66687052-66687253(-)$1	201	44	70	12.1229
:ccc[ccccccmmmmccc22ccc]cc	chr1:171673408-171673609(-)$1	201	3	29	11.1759
b!!iiiiiiiiillliiiiiiiii22	chr9:77830863-77831064(+)$1	201	48	74	8.6503
cc[a!!eeeeemmmmeeeee]a]ccc	chr2:102628947-102629148(+)$1	201	26	52	10.6408
cc"""ccc[aammmma]a]ccc333c	chr1:172123558-172123759(-)$1	201	149	175	11.7365
d!!dddd"""ammmma333dddd333	chr19:10059338-10059539(+)$1	201	75	101	10.8093
ggggggg!!bbmmmmbb333gggggg	chr17:45678883-45679084(-)$1	201	50	76	10.9031
ffccc[eeeeemmmmeeeee]ccc33	chrX:133613777-133613978(+)$1	201	26	52	10.3789
ffccc[eeeeemmmmeeeee]ccc77	chr3:108194427-108194628(-)$1	201	10	36	9.0433
eee[ccc!!bbmmmmbbccceeeee4	chr7:116879709-116879910(-)$1	201	59	85	10.1710
:eeeee!!cccmmmmccc22eeeee:	chr2:103988355-103988556(-)$1	201	89	115	9.9281
ee"""ggggggglllggggggg333e	chr3:45224086-45224287(+)$1	201	29	55	8.2575
dd"""ccc[bbmmmmbbccc22dddd	chr12:15799978-15800179(-)$1	201	73	99	9.4109
[dddd[cccbbmmmmbb22ccc]ddd	chr10:63392670-63392871(-)$1	201	71	97	9.7654
ffff[a!!cccmmmmccc22a22fff	chr2:33263737-33263938(-)$1	201	124	150	11.6596
eeee!!eeeeemmmmeeeee333eee	chr13:94174675-94174876(+)$1	201	35	61	10.3074
eeeeccc[cccmmmmccc]ccc]eee	chr8:113659250-113659451(+)$1	201	163	189	11.7446
===========mmmm===========	chr4:75587213-75587414(-)$1	201	137	163	11.9132

#otherMatches

#Seq PSSM
AAAGGAAAGAUGUAGAUCCUUUCUCA	chr17:66687051-66687252(-)$1	201	43	69	12.1229
UUAAUGUCUGACAUCUCUUAUAUUUC	chr18:32394530-32394731(+)$1	201	116	142	10.2405
CAUCGUGUUCGGCUCUGAUCAGGAAU	chr2:124491683-124491884(+)$1	201	151	177	11.3606
ACACGGUGAUGAGAGCUAAGCUGACU	chr19:10059339-10059540(+)$1	201	74	100	10.8093
UAGGGCUCCGUCCAUGCGUUCCCUAC	chr8:125153259-125153460(-)$1	201	1	27	10.8951
AACUAUGUAUAUUCAUGUUAAGAGUU	chrX:162826124-162826325(+)$1	201	150	176	11.6185
GAAAUAUUCACCUUUGUGCUUUUCAC	chr6:90332759-90332960(+)$1	201	86	112	11.9993
AUCAUGGCCUUCACUGAGUGCUUUUG	chr9:51895472-51895673(+)$1	201	162	188	12.3314
AGCCCUAGCUGUGAGCAGUAGUGGCU	chr6:35461666-35461867(-)$1	201	27	53	11.6301
CAACAGCAAUGAAAACAUUAUAUUUG	chr3:55804393-55804594(-)$1	201	62	88	11.6326
AAGCCAAGUAUAUUUGUACAGUGUGU	chr18:34478294-34478495(+)$1	201	153	179	9.7991
CUGAGCAGCGCCCAGGCUUGCUACUC	chr10:63392669-63392870(-)$1	201	70	96	9.7654
CGCUGUGUUGAACAAUCAGGACUGCG	chr2:140485071-140485272(-)$1	201	124	150	10.4845
GGCUUGAAACUCAAAAGUUCCCUCCC	chr8:34527695-34527896(+)$1	201	131	157	11.1639
GAGCGAUUGUGUGGACACUGUCUGCU	chr8:113659249-113659450(+)$1	201	164	190	11.7446
CCUCGUGUGUGACCUCACAAACACAG	chr9:32070989-32071190(+)$1	201	119	145	11.2660
AGGAUGUUGAUAUCAAUCGCCUUCGU	chr3:55791875-55792076(-)$1	201	140	166	9.8974
UUUAGGAAAGAAUCGUUUUUUCUAGA	chr2:146050380-146050581(+)$1	201	111	137	11.9132
AGAAUGAAAGGCGUGCUUUUUAUUUU	chr4:75587224-75587425(-)$1	201	148	174	11.9132
CGGAUGUGAGAACCGUUUCCUCGGGG	chr6:124997802-124998003(+)$1	201	151	177	10.0071
UUAAAAUGUAGUAUACUGCUUUUUUG	chr14:65430470-65430671(-)$1	201	125	151	10.6071
UAUUGUACAGGGAUCUUGUCAUCAAA	chr1:138525843-138526044(+)$1	201	55	81	8.3082
GGCUGAGGAGGGCCGCCUCCCUCUCU	chr10:127830932-127831133(+)$1	201	7	33	10.5686
CGCUAGAUCACAGUAGUGCCUAAUGA	chr7:6659158-6659359(-)$1	201	129	155	12.6170
GCUAAAUAACCAAACUGGAUUAAAAG	chr8:42003248-42003449(+)$1	201	96	122	9.5984
UAUGCAGGUUUGGAAAAAGCUACAGA	chr15:92171051-92171252(+)$1	201	10	36	10.5504
CUCUAGCCAGGUUCCUCUGCACAGCC	chr7:53685479-53685680(+)$1	201	69	95	10.6377
UCUUUGGCUAUUUGUGUGGUUUAAGG	chr6:113697619-113697820(-)$1	201	125	151	11.0344
AUGAUUGCUUUAAAAAAAAAAAUCAC	chr2:103988354-103988555(-)$1	201	88	114	9.9281
GGCCUCUGUUUGCUGAAGGAGAAGGA	chr8:11199543-11199744(-)$1	201	129	155	11.6231
Aauauauauauaaauauauauauaua	chr10:80861742-80861943(-)$1	201	27	53	9.7828
CCAUUUCUUUCGUUUGAAGCAGAAGG	chr2:124491255-124491456(+)$1	201	5	31	11.3936
UAGCAGCUUUGGAGCCAAUCAUGUUG	chr9:75066129-75066330(+)$1	201	91	117	12.9046
GUCCGUUGUAUAUAUGUACACCCACA	chr9:96583733-96583934(-)$1	201	27	53	10.1659
CGCUGUGUUGAACAAUCAGGACUGCG	chr2:140485070-140485271(-)$1	201	123	149	10.4845
CUCUCUCUCUAGGAGUAGGGUGGGAC	chr9:103083662-103083863(+)$1	201	27	53	9.5300
UAGUCUGGUUAUGUGUAACUUUUCGU	chr6:141481094-141481295(+)$1	201	33	59	11.1713
AAAGGAAAGAUGUAGAUCCUUUCUCA	chr17:66687052-66687253(-)$1	201	44	70	12.1229
AUUUUCCCAAGUCUCCUUAAGGGUGA	chr1:171673408-171673609(-)$1	201	3	29	11.1759
UGCUGAAUUGUGGUUCACAAUUUAAA	chr9:77830863-77831064(+)$1	201	48	74	8.6503
CUGUAUCCCUGGGGGCGGGGCAGAGC	chr2:102628947-102629148(+)$1	201	26	52	10.6408
UGAUAGCUUCCUGAUGUGUGGUGGAU	chr1:172123558-172123759(-)$1	201	149	175	11.7365
ACACGGUGAUGAGAGCUAAGCUGACU	chr19:10059338-10059539(+)$1	201	75	101	10.8093
AGGCCUGGCUCGGGAGAAGACAGGCC	chr17:45678883-45679084(-)$1	201	50	76	10.9031
GGUAAGUUAGACAUUUCUGAAUUAAG	chrX:133613777-133613978(+)$1	201	26	52	10.3789
CAUGGUGGCCCUGAGGGGCCCCCAGC	chr3:108194427-108194628(-)$1	201	10	36	9.0433
CAGCGUGCUGGCCUCCCCACUUGACU	chr7:116879709-116879910(-)$1	201	59	85	10.1710
AUGAUUGCUUUAAAAAAAAAAAUCAC	chr2:103988355-103988556(-)$1	201	89	115	9.9281
UUCUUCUUUCUUUAAAAGAAAGUGAA	chr3:45224086-45224287(+)$1	201	29	55	8.2575
UUGCAGAUCUCGAUAGAAUCCAAACU	chr12:15799978-15800179(-)$1	201	73	99	9.4109
CUGAGCAGCGCCCAGGCUUGCUACUC	chr10:63392670-63392871(-)$1	201	71	97	9.7654
GUUAAGAAUGAAUUCUCAAGCCAUAA	chr2:33263737-33263938(-)$1	201	124	150	11.6596
UAGUGUAUCUAUAUUUAGAUCAAACU	chr13:94174675-94174876(+)$1	201	35	61	10.3074
GAGCGAUUGUGUGGACACUGUCUGCU	chr8:113659250-113659451(+)$1	201	163	189	11.7446
AGAAUGAAAGGCGUGCUUUUUAUUUU	chr4:75587213-75587414(-)$1	201	137	163	11.9132

#DB
..(((((.(((....))).)))))..	chr17:66687051-66687252(-)$1	1	43	69	12.1229
..(((((..((....))..)))))..	chr18:32394530-32394731(+)$1	1	116	142	10.2405
..((.((.(((....))).)).))..	chr2:124491683-124491884(+)$1	1	151	177	11.3606
(..((((...(....)...))))...	chr19:10059339-10059540(+)$1	1	74	100	10.8093
(((((...(((....)))..))))).	chr8:125153259-125153460(-)$1	1	1	27	10.8951
((((....(((....)))....))))	chrX:162826124-162826325(+)$1	1	150	176	11.6185
((((....(((....)))..))))).	chr6:90332759-90332960(+)$1	1	86	112	11.9993
(....((((((....))).))).)))	chr9:51895472-51895673(+)$1	1	162	188	12.3314
(((((((.(((....)))))).))))	chr6:35461666-35461867(-)$1	1	27	53	11.6301
(((....((((....))))....)))	chr3:55804393-55804594(-)$1	1	62	88	11.6326
((((((.((((....))))..)).))	chr18:34478294-34478495(+)$1	1	153	179	9.7991
.((((.(((((....))..))).)))	chr10:63392669-63392870(-)$1	1	70	96	9.7654
(((.((.((((....)))).)).)))	chr2:140485071-140485272(-)$1	1	124	150	10.4845
((...((((((....))))...))..	chr8:34527695-34527896(+)$1	1	131	157	11.1639
(((((((.(((....))).))).)))	chr8:113659249-113659450(+)$1	1	164	190	11.7446
(((.(((((((....)))..))))))	chr9:32070989-32071190(+)$1	1	119	145	11.2660
(.((.(.((((....)))).).)).)	chr3:55791875-55792076(-)$1	1	140	166	9.8974
(((((((((((....)))))))))))	chr2:146050380-146050581(+)$1	1	111	137	11.9132
(((((((((((....)))))))))))	chr4:75587224-75587425(-)$1	1	148	174	11.9132
(.((.(.((((....))))))).)))	chr6:124997802-124998003(+)$1	1	151	177	10.0071
..((((.((((....))))))))...	chr14:65430470-65430671(-)$1	1	125	151	10.6071
(.(((.(((((...)))))...))).	chr1:138525843-138526044(+)$1	1	55	81	8.3082
(((((((((((....))).))))...	chr10:127830932-127831133(+)$1	1	7	33	10.5686
((.(((..(((....))).))).)))	chr7:6659158-6659359(-)$1	1	129	155	12.6170
(((...((((((...))).)))..))	chr8:42003248-42003449(+)$1	1	96	122	9.5984
..((.((.(((....))).)).))))	chr15:92171051-92171252(+)$1	1	10	36	10.5504
.(((.((((((....))))....)).	chr7:53685479-53685680(+)$1	1	69	95	10.6377
(((((((((((....)))).))))))	chr6:113697619-113697820(-)$1	1	125	151	11.0344
.(((((..(((....)))..))))).	chr2:103988354-103988555(-)$1	1	88	114	9.9281
(.(((((.(((....))).)).))).	chr8:11199543-11199744(-)$1	1	129	155	11.6231
..(((((((((....)))))))))))	chr10:80861742-80861943(-)$1	1	27	53	9.7828
((.((((((((....)))..))))))	chr2:124491255-124491456(+)$1	1	5	31	11.3936
..(((...(((....)))...)))))	chr9:75066129-75066330(+)$1	1	91	117	12.9046
((..((.((((....))))))..)))	chr9:96583733-96583934(-)$1	1	27	53	10.1659
(((.((.((((....)))).)).)))	chr2:140485070-140485271(-)$1	1	123	149	10.4845
.((((.(((((....))))).)))).	chr9:103083662-103083863(+)$1	1	27	53	9.5300
..(...(((((....)))))...)..	chr6:141481094-141481295(+)$1	1	33	59	11.1713
..(((((.(((....))).)))))..	chr17:66687052-66687253(-)$1	1	44	70	12.1229
.(((.((((((....)))..))).))	chr1:171673408-171673609(-)$1	1	3	29	11.1759
(..(((((((((...)))))))))..	chr9:77830863-77831064(+)$1	1	48	74	8.6503
((.(..(((((....))))).).)))	chr2:102628947-102629148(+)$1	1	26	52	10.6408
((...(((.((....).).)))...)	chr1:172123558-172123759(-)$1	1	149	175	11.7365
(..((((...(....)...))))...	chr19:10059338-10059539(+)$1	1	75	101	10.8093
(((((((..((....))...))))))	chr17:45678883-45679084(-)$1	1	50	76	10.9031
(((((.(((((....))))).)))..	chrX:133613777-133613978(+)$1	1	26	52	10.3789
(((((.(((((....))))).)))..	chr3:108194427-108194628(-)$1	1	10	36	9.0433
(((.(((..((....)))))))))).	chr7:116879709-116879910(-)$1	1	59	85	10.1710
.(((((..(((....)))..))))).	chr2:103988355-103988556(-)$1	1	89	115	9.9281
((...(((((((...)))))))...)	chr3:45224086-45224287(+)$1	1	29	55	8.2575
((...(((.((....)))))..))))	chr12:15799978-15800179(-)$1	1	73	99	9.4109
.((((.(((((....))..))).)))	chr10:63392670-63392871(-)$1	1	71	97	9.7654
((((.(..(((....)))..)..)))	chr2:33263737-33263938(-)$1	1	124	150	11.6596
((((..(((((....)))))...)))	chr13:94174675-94174876(+)$1	1	35	61	10.3074
(((((((.(((....))).))).)))	chr8:113659250-113659451(+)$1	1	163	189	11.7446
(((((((((((....)))))))))))	chr4:75587213-75587414(-)$1	1	137	163	11.9132

#PSSM
c : 0.23	e : 0.12	f : 0.09	" : 0.07	g : 0.07	[ : 0.07	! : 0.05	d : 0.05	= : 0.05	: : 0.05	b : 0.03	i : 0.03	# : 0.01	& : 0.01	
c : 0.23	e : 0.16	! : 0.10	" : 0.07	f : 0.07	d : 0.07	[ : 0.07	g : 0.05	= : 0.05	# : 0.03	i : 0.03	& : 0.01	
c : 0.21	e : 0.20	b : 0.07	! : 0.07	d : 0.07	" : 0.07	g : 0.05	= : 0.05	i : 0.05	[ : 0.05	f : 0.03	# : 0.01	a : 0.01	
e : 0.20	c : 0.14	d : 0.10	" : 0.10	b : 0.07	[ : 0.07	i : 0.07	g : 0.05	= : 0.05	f : 0.03	# : 0.03	! : 0.01	a : 0.01	
c : 0.18	d : 0.14	e : 0.12	[ : 0.12	" : 0.10	# : 0.07	b : 0.07	= : 0.05	i : 0.05	! : 0.03	g : 0.01	
b : 0.16	c : 0.16	e : 0.10	[ : 0.10	d : 0.09	" : 0.07	# : 0.05	a : 0.05	= : 0.05	i : 0.05	! : 0.03	g : 0.03	
e : 0.20	c : 0.20	[ : 0.12	b : 0.09	d : 0.07	! : 0.07	# : 0.05	= : 0.05	i : 0.05	" : 0.03	g : 0.03	
d : 0.23	[ : 0.14	e : 0.14	! : 0.12	c : 0.12	" : 0.07	= : 0.05	# : 0.03	i : 0.03	g : 0.01	
c : 0.43	d : 0.20	e : 0.12	! : 0.05	= : 0.05	" : 0.03	i : 0.03	[ : 0.03	g : 0.01	
c : 0.40	d : 0.20	e : 0.12	b : 0.10	= : 0.05	" : 0.03	i : 0.03	a : 0.01	g : 0.01	
c : 0.40	d : 0.20	e : 0.12	b : 0.10	a : 0.05	= : 0.05	i : 0.03	g : 0.01	
m : 0.92	l : 0.01	c : 0.01	i : 0.01	g : 0.01	
m : 0.92	l : 0.07	
m : 0.92	l : 0.07	
m : 0.92	l : 0.05	e : 0.01	
c : 0.40	d : 0.20	e : 0.12	b : 0.10	a : 0.05	= : 0.05	i : 0.03	g : 0.01	
c : 0.40	d : 0.20	e : 0.12	b : 0.10	= : 0.05	3 : 0.03	i : 0.03	] : 0.01	g : 0.01	
c : 0.43	d : 0.20	e : 0.12	2 : 0.05	3 : 0.05	= : 0.05	i : 0.03	a : 0.01	g : 0.01	
] : 0.21	2 : 0.20	d : 0.20	e : 0.12	3 : 0.07	c : 0.05	= : 0.05	i : 0.03	4 : 0.01	g : 0.01	
c : 0.20	e : 0.16	2 : 0.16	b : 0.07	d : 0.07	] : 0.07	3 : 0.07	4 : 0.05	= : 0.05	i : 0.03	a : 0.01	g : 0.01	
c : 0.18	e : 0.16	b : 0.12	d : 0.09	3 : 0.09	] : 0.07	4 : 0.05	= : 0.05	i : 0.05	2 : 0.03	a : 0.03	g : 0.03	
c : 0.21	e : 0.16	d : 0.10	] : 0.09	b : 0.07	3 : 0.07	4 : 0.05	= : 0.05	i : 0.05	2 : 0.05	g : 0.03	a : 0.01	
] : 0.18	e : 0.16	d : 0.12	c : 0.10	b : 0.09	3 : 0.07	= : 0.05	2 : 0.05	i : 0.05	g : 0.03	4 : 0.03	f : 0.01	
e : 0.21	c : 0.20	b : 0.09	3 : 0.09	d : 0.09	f : 0.05	g : 0.05	= : 0.05	i : 0.05	] : 0.03	> : 0.01	2 : 0.01	a : 0.01	
c : 0.20	3 : 0.16	e : 0.16	f : 0.09	g : 0.09	d : 0.07	= : 0.05	4 : 0.03	2 : 0.03	] : 0.01	> : 0.01	b : 0.01	i : 0.01	7 : 0.01	
c : 0.20	3 : 0.14	f : 0.09	g : 0.09	] : 0.07	e : 0.07	4 : 0.05	: : 0.05	d : 0.05	= : 0.05	2 : 0.03	b : 0.01	> : 0.01	i : 0.01	7 : 0.01	

#score	592.1217913961345
#seq	55
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_CDS_m3_run2.txt

#BEAR
JJJJJ______EEEEE:::	chr7:133603008-133603243(-)$1	235	129	148	8.9316
EEE}CCCZZZFFFFFFYYF	chr17:34406174-34406409(+)$1	235	156	175	11.3021
EEYYBB?????DDDDEEEE	chr11:67062033-67062294(+)$1	261	118	137	9.6843
FFFZZZBB~~~~FFFFFF:	chr14:60248649-60248884(+)$1	235	194	213	11.1916
FFFFFZZZBB}EEEEEZZZ	chr11:50014137-50014377(-)$1	240	169	188	10.6127
::DDDD?????EEEEEBBB	chr11:6523715-6523950(-)$1	235	203	222	8.3967
GGGGG}A~~~~IIIIIIII	chr15:102797233-102797477(+)$1	244	175	194	8.3121
DDYYA}BB}EEEEEEEEEE	chr2:76561979-76562240(-)$1	261	239	258	10.5341
CCC}CCCZZZA}HHHHHHH	chr19:6389709-6389944(+)$1	235	199	218	9.0460
ff::BB}BBYYEEEEEZZZ	chr7:134356893-134357130(+)$1	237	115	134	8.0766
FFFFFF?????EEEEE:::	chr2:76723096-76723358(-)$1	262	243	262	8.8977
HHYYCCC}EEEEE}FFFFF	chr11:30008996-30009231(-)$1	235	212	231	9.8460
}A}CCCBB}CCCDDDD}DD	chr2:76594261-76594496(-)$1	235	209	228	8.7587
GGG}DDDD}BB}EEEEEBB	chr10:77670618-77670856(-)$1	238	173	192	9.3118
EEE}DDDD~~~~FFFFFFd	chr13:12380759-12380997(-)$1	238	147	166	9.8948
FFFFFBB}A}FFFFFF}DD	chr9:72510245-72510480(+)$1	235	200	219	10.4232
}BB}BBZZZBB}FFFFFFY	chr5:29761756-29761991(+)$1	235	164	183	11.2716
CCYYCCCZZZCCCJJJJJJ	chr4:43535508-43535762(-)$1	254	211	230	9.1380
GEEEEEACCCYYFFFFFF:	chr1:36879850-36880085(-)$1	235	216	235	9.0349
DDDDYYBBZZZEEEEE:::	chr2:35151973-35152210(+)$1	237	115	134	9.3188
FFFFFF~~~~FFFFFF}A:	chr10:19329021-19329256(+)$1	235	216	235	10.9821
FFF}CCC~~~~EEEEE}DD	chr4:129522281-129522528(+)$1	247	197	216	12.9999
:BBYYBB~~~~IIIIIIII	chr11:67067428-67067680(+)$1	252	229	248	9.8191
CCYYCCC}AYYCCCBBJJJ	chr11:67065960-67066209(+)$1	249	133	152	8.9528
FFFFFDDDDYYEEEEECCC	chr6:29411059-29411294(+)$1	235	213	232	9.4182
CBB}CCCYYDDDDBBZZZD	chr7:52399799-52400034(-)$1	235	211	230	7.9549

#otherMatches

#Seq PSSM
GGGGACAUCGUGGAGGUGG	chr7:133603008-133603243(-)$1	235	129	148	8.9316
acaaauaaacgagacucag	chr17:34406174-34406409(+)$1	235	156	175	11.3021
GACAAGAACAAGGACCCCC	chr11:67062033-67062294(+)$1	261	118	137	9.6843
UACCCCACCAAGGGCAGUA	chr14:60248649-60248884(+)$1	235	194	213	11.1916
CUUGGCAUUCUUGUAGAAU	chr11:50014137-50014377(-)$1	240	169	188	10.6127
UUGGGCAUUUGGGUUGGGG	chr11:6523715-6523950(-)$1	235	203	222	8.3967
UGCGGGGUGAUGAGGGGCU	chr15:102797233-102797477(+)$1	244	175	194	8.3121
CUCCAGUGUUUUCCUUUUA	chr2:76561979-76562240(-)$1	261	239	258	10.5341
UCCAUUCGGAGAUCCUCAA	chr19:6389709-6389944(+)$1	235	199	218	9.0460
CUGACCAUGUUUGGGGAAA	chr7:134356893-134357130(+)$1	237	115	134	8.0766
GGAUUGCUUGCCAUCCUUU	chr2:76723096-76723358(-)$1	262	243	262	8.8977
UCAUGGUCUGGAAUGUGAA	chr11:30008996-30009231(-)$1	235	212	231	9.8460
UGGUCAUCAGAAGUGUCUU	chr2:76594261-76594496(-)$1	235	209	228	8.7587
AGGAAGCAGCUAGCAGAGU	chr10:77670618-77670856(-)$1	238	173	192	9.3118
CACGAGGCCUUUGAGAGCG	chr13:12380759-12380997(-)$1	238	147	166	9.8948
GGGGUUCAUCGUGGCGAGG	chr9:72510245-72510480(+)$1	235	200	219	10.4232
UGUACGAAAGCAGCGAGGA	chr5:29761756-29761991(+)$1	235	164	183	11.2716
CCGACGUGAGUGUGGGCCC	chr4:43535508-43535762(-)$1	254	211	230	9.1380
UUAGUGCUCAAAUGGGAAA	chr1:36879850-36880085(-)$1	235	216	235	9.0349
UGGCCAGAAACAGGUAAUU	chr2:35151973-35152210(+)$1	237	115	134	9.3188
UCACCGCCUAUCACUCCCG	chr10:19329021-19329256(+)$1	235	216	235	10.9821
CAACUCAAAUUUUUACCUU	chr4:129522281-129522528(+)$1	247	197	216	12.9999
AGCAAAGCAUGAGAGGUCU	chr11:67067428-67067680(+)$1	252	229	248	9.8191
UGGACUUAGAAAGAGCCAA	chr11:67065960-67066209(+)$1	249	133	152	8.9528
UGUGCCACACCCCUCUGCA	chr6:29411059-29411294(+)$1	235	213	232	9.4182
CUCAGUGAACCAGGCACAA	chr7:52399799-52400034(-)$1	235	211	230	7.9549

#DB
)))))......)))))...	chr7:133603008-133603243(-)$1	1	129	148	8.9316
))).)))...))))))..)	chr17:34406174-34406409(+)$1	1	156	175	11.3021
))..)).....))))((((	chr11:67062033-67062294(+)$1	1	118	137	9.6843
)))...))....)))))).	chr14:60248649-60248884(+)$1	1	194	213	11.1916
)))))...)).)))))...	chr11:50014137-50014377(-)$1	1	169	188	10.6127
..)))).....))))))))	chr11:6523715-6523950(-)$1	1	203	222	8.3967
))))).)....))))))))	chr15:102797233-102797477(+)$1	1	175	194	8.3121
))..).)).))))))))))	chr2:76561979-76562240(-)$1	1	239	258	10.5341
))).)))...).)))))))	chr19:6389709-6389944(+)$1	1	199	218	9.0460
))..)).))..)))))...	chr7:134356893-134357130(+)$1	1	115	134	8.0766
)))))).....)))))...	chr2:76723096-76723358(-)$1	1	243	262	8.8977
))..))).))))).)))))	chr11:30008996-30009231(-)$1	1	212	231	9.8460
.).))))).))))))).))	chr2:76594261-76594496(-)$1	1	209	228	8.7587
))).)))).)).)))))))	chr10:77670618-77670856(-)$1	1	173	192	9.3118
))).))))....))))))(	chr13:12380759-12380997(-)$1	1	147	166	9.8948
))))))).).)))))).))	chr9:72510245-72510480(+)$1	1	200	219	10.4232
.)).))...)).)))))).	chr5:29761756-29761991(+)$1	1	164	183	11.2716
))..)))...)))))))))	chr4:43535508-43535762(-)$1	1	211	230	9.1380
))))))))))..)))))).	chr1:36879850-36880085(-)$1	1	216	235	9.0349
))))..))...)))))...	chr2:35151973-35152210(+)$1	1	115	134	9.3188
))))))....)))))).).	chr10:19329021-19329256(+)$1	1	216	235	10.9821
))).)))....))))).))	chr4:129522281-129522528(+)$1	1	197	216	12.9999
.))..))....))))))))	chr11:67067428-67067680(+)$1	1	229	248	9.8191
))..))).)..))))))))	chr11:67065960-67066209(+)$1	1	133	152	8.9528
)))))))))..))))))))	chr6:29411059-29411294(+)$1	1	213	232	9.4182
))).)))..))))))...)	chr7:52399799-52400034(-)$1	1	211	230	7.9549

#PSSM
F : 0.26	C : 0.15	E : 0.11	G : 0.11	: : 0.07	D : 0.07	} : 0.07	J : 0.03	f : 0.03	H : 0.03	
F : 0.26	E : 0.15	C : 0.11	B : 0.11	G : 0.07	D : 0.07	J : 0.03	: : 0.03	f : 0.03	H : 0.03	A : 0.03	
F : 0.26	Y : 0.19	E : 0.11	B : 0.11	D : 0.07	G : 0.07	J : 0.03	C : 0.03	: : 0.03	} : 0.03	
} : 0.26	Y : 0.23	F : 0.19	D : 0.07	J : 0.03	Z : 0.03	G : 0.03	: : 0.03	C : 0.03	E : 0.03	
C : 0.30	F : 0.19	B : 0.11	D : 0.11	Y : 0.07	J : 0.03	Z : 0.03	G : 0.03	A : 0.03	E : 0.03	
C : 0.30	B : 0.19	D : 0.15	Z : 0.07	} : 0.07	F : 0.07	_ : 0.03	E : 0.03	Y : 0.03	
C : 0.26	B : 0.23	? : 0.11	D : 0.11	Z : 0.07	A : 0.07	_ : 0.03	} : 0.03	~ : 0.03	
Z : 0.19	B : 0.19	~ : 0.15	? : 0.11	} : 0.11	D : 0.11	_ : 0.03	C : 0.03	Y : 0.03	
~ : 0.23	Z : 0.19	? : 0.11	} : 0.11	B : 0.07	A : 0.07	_ : 0.03	E : 0.03	C : 0.03	D : 0.03	Y : 0.03	
~ : 0.23	Z : 0.15	? : 0.11	B : 0.11	Y : 0.11	E : 0.07	C : 0.07	_ : 0.03	} : 0.03	D : 0.03	
~ : 0.19	Y : 0.15	F : 0.11	? : 0.11	E : 0.07	C : 0.07	B : 0.07	_ : 0.03	} : 0.03	A : 0.03	Z : 0.03	D : 0.03	
E : 0.38	F : 0.11	} : 0.11	C : 0.11	D : 0.07	~ : 0.07	I : 0.07	Y : 0.03	
E : 0.42	F : 0.26	D : 0.11	I : 0.07	C : 0.07	H : 0.03	
E : 0.38	F : 0.26	D : 0.07	I : 0.07	H : 0.03	} : 0.03	J : 0.03	C : 0.03	B : 0.03	
E : 0.38	F : 0.30	D : 0.07	I : 0.07	B : 0.07	H : 0.03	J : 0.03	
E : 0.42	F : 0.30	I : 0.07	H : 0.03	D : 0.03	J : 0.03	B : 0.03	Z : 0.03	
F : 0.19	} : 0.15	: : 0.11	E : 0.11	Z : 0.11	I : 0.07	J : 0.07	Y : 0.03	B : 0.03	H : 0.03	C : 0.03	
F : 0.19	: : 0.11	Z : 0.11	D : 0.11	E : 0.07	B : 0.07	I : 0.07	J : 0.07	Y : 0.03	H : 0.03	A : 0.03	C : 0.03	
: : 0.23	D : 0.15	F : 0.07	E : 0.07	Z : 0.07	B : 0.07	I : 0.07	J : 0.07	H : 0.03	d : 0.03	Y : 0.03	C : 0.03	

#score	252.11168559877694
#seq	26
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_UTR_m1_run2.txt

#BEAR
eeeeettttttttttteeeee:ee	chr17:32909155-32909524(-)$1	369	229	253	21.2266
eeeeewwwwwwwwwwwwwweeeee	chr2:52289433-52289763(-)$1	330	255	279	22.2713
fffffuuuuuuuuuuuuffffff:	chr18:15549686-15550030(-)$1	344	279	303	22.4154
[ddddvvvvvvvvvvvvvddddff	chr5:115177321-115177680(-)$1	359	329	353	22.6269
fffffftttttttttttffffff:	chr3:60430627-60431021(+)$1	394	346	370	21.3671
fdddduuuuuuuuuuuudddd]ff	chr2:29927081-29927353(+)$1	272	207	231	22.9683
"dddduuuuuuuuuuuudddd444	chr9:95358692-95359015(-)$1	323	31	55	22.5624
ceeeeettttttttttteeeeedd	chr1:66743526-66743897(+)$1	371	237	261	22.6569
fffffuuuuuuuuuuuuffffff:	chr11:16183399-16183666(+)$1	267	90	114	22.4154
eeeeevvvvvvvvvvvvveeeee4	chr15:30958467-30958814(+)$1	347	150	174	23.6889
fffffftttttttttttffffffc	chr2:163879632-163879908(-)$1	276	126	150	22.2379
eyyyyyyyyyyyyyyyyeeeee]d	chr4:106873338-106873607(+)$1	269	110	134	20.2988
ffyyyyyyyyyyyyyyyyffffff	chrX:71611253-71611525(-)$1	272	102	126	20.5315
hhhhhhttttttttttthhhhhhh	chrX:101476024-101476291(-)$1	267	63	87	20.3956
ggggggtttttttttttggggggg	chr1:107177419-107177860(-)$1	441	70	94	23.2182
eeeeeuuuuuuuuuuuueeeeeii	chr13:98022609-98023090(+)$1	481	68	92	24.1891
fffffftttttttttttffffffG	chr3:31017485-31017953(+)$1	468	438	462	21.8133
gggggyyyyyyyyyyyyyyyyggg	chr11:110130823-110131065(-)$1	242	145	169	21.1687
eddddwwwwwwwwwwwwwwdddd2	chr17:33883970-33884273(-)$1	303	258	282	21.1075
dddwwwwwwwwwwwwwwdddd]ee	chr15:11773602-11773857(-)$1	255	169	193	20.5892
gggggvvvvvvvvvvvvvgggggg	chr2:72240647-72240912(+)$1	265	172	196	24.0692
gggbbuuuuuuuuuuuubb]gggg	chr3:151897179-151897537(+)$1	358	78	102	23.0668
eeeeeyyyyyyyyyyyyyyyyeee	chr4:57909336-57909673(+)$1	337	213	237	20.7752
eeeeevvvvvvvvvvvvveeeee2	chr8:46424183-46424452(-)$1	269	112	136	23.6363
fffffwwwwwwwwwwwwwwfffff	chr13:102451115-102451412(-)$1	297	171	195	21.6023
ggggguuuuuuuuuuuuggggggg	chr6:21678745-21679124(+)$1	379	302	326	24.3489
ggggggtttttttttttggggggg	chr11:97544492-97544816(+)$1	324	165	189	23.2182
:dddduuuuuuuuuuuudddd:cc	chr11:62972833-62973132(+)$1	299	184	208	20.7728
eyyyyyyyyyyyyyyyyeeeee33	chr5:67446659-67446933(+)$1	274	99	123	20.4131
[eeeeettttttttttteeeeecc	chr8:83223740-83224038(-)$1	298	126	150	23.0253
gggggvvvvvvvvvvvvvgggggg	chr6:85894429-85894742(-)$1	313	228	252	24.0692
iiiiivvvvvvvvvvvvviiiiii	chr5:103337863-103338166(-)$1	303	113	137	23.8130
fffffuuuuuuuuuuuuffffffd	chr3:88391940-88392186(+)$1	246	115	139	23.1645
eeeeewwwwwwwwwwwwwweeeee	chr18:64432028-64432425(+)$1	397	340	364	22.2713
ggggguuuuuuuuuuuuggggggg	chr9:57809968-57810271(+)$1	303	131	155	24.3489
d[cccvvvvvvvvvvvvvccc]dd	chr15:79619078-79619549(-)$1	471	21	45	22.9148
beeeeettttttttttteeeee]b	chr19:46590739-46590999(+)$1	260	9	33	22.5248
gggggvvvvvvvvvvvvvgggggg	chr3:117023559-117024055(-)$1	496	308	332	24.0692
iiiiiitttttttttttiiiiiii	chr3:108194380-108194630(-)$1	250	91	115	22.8886
hhhhhvvvvvvvvvvvvvhhhhhh	chr2:52284320-52284738(-)$1	418	125	149	21.7188
!ddddwwwwwwwwwwwwwwdddd2	chr4:4693496-4693779(-)$1	283	30	54	21.1050
!eeeeettttttttttteeeee]d	chr12:72420711-72421129(+)$1	418	67	91	22.9695
fffffvvvvvvvvvvvvvffffff	chr1:79791459-79791719(-)$1	260	190	214	22.9494
##cccuuuuuuuuuuuuccc333h	chr1:88427073-88427337(+)$1	264	216	240	22.9829
dyyyyyyyyyyyyyyyyddddggg	chr7:89030283-89030629(-)$1	346	285	309	19.8902
g[cccvvvvvvvvvvvvvccc333	chr8:107741180-107741530(+)$1	350	61	85	23.4062
hhhhhhttttttttttthhhhhhh	chr14:78892441-78892727(-)$1	286	135	159	20.3956
fffffuuuuuuuuuuuuffffff2	chr18:80315264-80315571(+)$1	307	23	47	23.1674
ddddyyyyyyyyyyyyyyyydddd	chr14:27734839-27735169(-)$1	330	266	290	19.9228
=====uuuuuuuuuuuu=======	chr4:83102342-83102675(-)$1	333	303	327	24.1837
Hddddtttttttttttddddccc[	chr2:5219734-5220057(-)$1	323	255	279	20.5607
iiiiiuuuuuuuuuuuuiiiiiii	chr5:4806276-4806764(-)$1	488	31	55	24.1321
eeeeeuuuuuuuuuuuueeeee::	chr15:82121785-82122131(+)$1	346	205	229	22.0778
e[cccuuuuuuuuuuuuccceeee	chr14:52506538-52506830(+)$1	292	84	108	23.7505
eeeeevvvvvvvvvvvvveeeee0	chr4:134453786-134454036(-)$1	250	113	137	23.3457
ggggggtttttttttttggggggg	chr4:4694064-4694366(-)$1	302	219	243	23.2182
ggggguuuuuuuuuuuuggggggg	chr4:109877400-109877726(-)$1	326	53	77	24.3489
eeewwwwwwwwwwwwwweeeee]b	chr6:108771428-108771877(+)$1	449	158	182	21.4376
eeeeevvvvvvvvvvvvveeeee:	chr15:75900599-75900878(-)$1	279	227	251	22.8843
ggggguuuuuuuuuuuuggggggg	chr18:46893848-46894128(-)$1	280	226	250	24.3489
=====vvvvvvvvvvvvv======	chr17:56077871-56078247(-)$1	376	331	355	23.8089
ggggguuuuuuuuuuuuggggggg	chr2:119793273-119793560(+)$1	287	196	220	24.3489
gg[bbwwwwwwwwwwwwwwbb]gg	chr4:33138964-33139438(+)$1	474	245	269	21.1949

#otherMatches

#Seq PSSM
cuguuauucccccuaagacagagu	chr17:32909155-32909524(-)$1	369	229	253	21.2266
CCAGCUGUGGAAUUUAUUUGCUGG	chr2:52289433-52289763(-)$1	330	255	279	22.2713
GGAUUUAAAAUACCAAUAAUCUCC	chr18:15549686-15550030(-)$1	344	279	303	22.4154
ucuuuuguuaucuauuguaaagcu	chr5:115177321-115177680(-)$1	359	329	353	22.6269
CUUCAGUGUUAUUGUUUCUGGAGC	chr3:60430627-60431021(+)$1	394	346	370	21.3671
UUACAAUAAAAUCAGUGUGUACAC	chr2:29927081-29927353(+)$1	272	207	231	22.9683
CAUUCUUUAAUAUUCUUGAGUACU	chr9:95358692-95359015(-)$1	323	31	55	22.5624
AGGAGACAAACAAACCUUCUCUGU	chr1:66743526-66743897(+)$1	371	237	261	22.6569
AUUCCCUCUUACAGUAUGGAAUGG	chr11:16183399-16183666(+)$1	267	90	114	22.4154
CCGCUCUUCUCACCAUCUAGUGGC	chr15:30958467-30958814(+)$1	347	150	174	23.6889
ACCCAGAUAUGCACAGACUGGGUG	chr2:163879632-163879908(-)$1	276	126	150	22.2379
UAAUAACCGAAACCUUAGGGUGUG	chr4:106873338-106873607(+)$1	269	110	134	20.2988
UUGUAAAAUUAACACUAAAGAUGC	chrX:71611253-71611525(-)$1	272	102	126	20.5315
UAAUUAUAGUUUGUUUUUAAUUAU	chrX:101476024-101476291(-)$1	267	63	87	20.3956
GAAGGUAUUAAAAGAAAACUUUCA	chr1:107177419-107177860(-)$1	441	70	94	23.2182
GGUUCUUCUUAUUUUGUGAGCCGG	chr13:98022609-98023090(+)$1	481	68	92	24.1891
UUCUCAUUACAGACUCUUGGGAAG	chr3:31017485-31017953(+)$1	468	438	462	21.8133
AAUGUAUUUUUAAUAUUGUUAACA	chr11:110130823-110131065(-)$1	242	145	169	21.1687
CCUCAUCCCAAACUCUCUCUGAGC	chr17:33883970-33884273(-)$1	303	258	282	21.1075
GCAGCCACCACAAAUGAUGCAUAG	chr15:11773602-11773857(-)$1	255	169	193	20.5892
UAACCCUUUCACUCAGUUGGUUAA	chr2:72240647-72240912(+)$1	265	172	196	24.0692
UACCUGUUAAGAUCUUAAGUGUAG	chr3:151897179-151897537(+)$1	358	78	102	23.0668
UUCAGUUACAAAAACAAUUUCCUG	chr4:57909336-57909673(+)$1	337	213	237	20.7752
UGCACACAGAUAGUAUUAGUGCAU	chr8:46424183-46424452(-)$1	269	112	136	23.6363
GGGCAGUUAAGAAGCACAAUGCCU	chr13:102451115-102451412(-)$1	297	171	195	21.6023
AAAUGAAUUAAUCCAAACAUUUUC	chr6:21678745-21679124(+)$1	379	302	326	24.3489
UUUCUAACUGCUAUUACUAGAAAG	chr11:97544492-97544816(+)$1	324	165	189	23.2182
AGAUGCAUCAAAAUAAACAUCAGA	chr11:62972833-62973132(+)$1	299	184	208	20.7728
UGAUAAGUUUCAGCCAGACACGAA	chr5:67446659-67446933(+)$1	274	99	123	20.4131
GUUCUCCAUUUUUCUAAGGGAAUG	chr8:83223740-83224038(-)$1	298	126	150	23.0253
UGUAUAAACAUAAUAAAAAUACAA	chr6:85894429-85894742(-)$1	313	228	252	24.0692
GCAGGGUGCCUACCUUUGCCUGCU	chr5:103337863-103338166(-)$1	303	113	137	23.8130
GGCCUGGAAGUUGGAGAGGGCCUC	chr3:88391940-88392186(+)$1	246	115	139	23.1645
ACUCUCUCAGAAAAAAAAAAGAGU	chr18:64432028-64432425(+)$1	397	340	364	22.2713
CUGGGAUAGGAUCAGAGUCCAGGG	chr9:57809968-57810271(+)$1	303	131	155	24.3489
CCAGCCCCUACCCUAACAGCUAGG	chr15:79619078-79619549(-)$1	471	21	45	22.9148
CUUUGGCAUCUUCAAACCCAAGUG	chr19:46590739-46590999(+)$1	260	9	33	22.5248
CUUAGUUUAUUAAGUUUUCUGAGG	chr3:117023559-117024055(-)$1	496	308	332	24.0692
GACAAAUGCCAUUUUUUUUUGUCU	chr3:108194380-108194630(-)$1	250	91	115	22.8886
UAAAACAUAUGAACUUUAUUUUGU	chr2:52284320-52284738(-)$1	418	125	149	21.7188
CCCACUCAGUUGACAGAAUGUGGU	chr4:4693496-4693779(-)$1	283	30	54	21.1050
ACCGGACCGCUGACUUAUCUGGAA	chr12:72420711-72421129(+)$1	418	67	91	22.9695
AGAGACUCCCUCCCCACAUCUUUC	chr1:79791459-79791719(-)$1	260	190	214	22.9494
CUGGUUUUUCUGUGUGUACUUUGU	chr1:88427073-88427337(+)$1	264	216	240	22.9829
UGUCAUACCAAAAUAAAGCAAGGA	chr7:89030283-89030629(-)$1	346	285	309	19.8902
GUCUUAUAAUUCAUAAACAAGUAC	chr8:107741180-107741530(+)$1	350	61	85	23.4062
CGCCUGCUCUGCACACACAGGCGC	chr14:78892441-78892727(-)$1	286	135	159	20.3956
GGGAUUAAAAGCCAACUGUUCCAU	chr18:80315264-80315571(+)$1	307	23	47	23.1674
CCCAGUUGUGUUCAUGUCCAUGGG	chr14:27734839-27735169(-)$1	330	266	290	19.9228
CAGCUAGAUAGCCACCAGGUUGUU	chr4:83102342-83102675(-)$1	333	303	327	24.1837
CUGUAUAUAAGAAUCUUGCAAAGC	chr2:5219734-5220057(-)$1	323	255	279	20.5607
AGGAUUAAGUUGUCAUCAUUCUGG	chr5:4806276-4806764(-)$1	488	31	55	24.1321
ACCCUUGUGUCUAUGUUGGGGUCA	chr15:82121785-82122131(+)$1	346	205	229	22.0778
CGCAAAACUACCUACCAUUGGCAG	chr14:52506538-52506830(+)$1	292	84	108	23.7505
AACAAAAAAACAAAAGAGUUGUUG	chr4:134453786-134454036(-)$1	250	113	137	23.3457
AAAGGGGCCAUUGUUCAUCCUUUC	chr4:4694064-4694366(-)$1	302	219	243	23.2182
GCCCGUGCUGAUAAAAUUGGGCUG	chr4:109877400-109877726(-)$1	326	53	77	24.3489
AGAACUCCUGUCGUUCCUCUGAAG	chr6:108771428-108771877(+)$1	449	158	182	21.4376
CUGUAGUGUACAUAAAGAUGCAGA	chr15:75900599-75900878(-)$1	279	227	251	22.8843
GUGUGCCAUUACUCCCACACACUC	chr18:46893848-46894128(-)$1	280	226	250	24.3489
GAAGAUUAGUAGAACCAUUCUUCA	chr17:56077871-56078247(-)$1	376	331	355	23.8089
ACUAAUUAAAGCAGAAUUUGGUGU	chr2:119793273-119793560(+)$1	287	196	220	24.3489
UGAGCCAACCGAACCUUCUGUACG	chr4:33138964-33139438(+)$1	474	245	269	21.1949

#DB
(((((...........))))).((	chr17:32909155-32909524(-)$1	1	229	253	21.2266
(((((..............)))))	chr2:52289433-52289763(-)$1	1	255	279	22.2713
(((((............)))))).	chr18:15549686-15550030(-)$1	1	279	303	22.4154
.((((.............))))))	chr5:115177321-115177680(-)$1	1	329	353	22.6269
((((((...........)))))).	chr3:60430627-60431021(+)$1	1	346	370	21.3671
(((((............)))).))	chr2:29927081-29927353(+)$1	1	207	231	22.9683
.((((............))))...	chr9:95358692-95359015(-)$1	1	31	55	22.5624
)(((((...........)))))((	chr1:66743526-66743897(+)$1	1	237	261	22.6569
(((((............)))))).	chr11:16183399-16183666(+)$1	1	90	114	22.4154
(((((.............))))).	chr15:30958467-30958814(+)$1	1	150	174	23.6889
((((((...........)))))))	chr2:163879632-163879908(-)$1	1	126	150	22.2379
(................))))).)	chr4:106873338-106873607(+)$1	1	110	134	20.2988
((................))))))	chrX:71611253-71611525(-)$1	1	102	126	20.5315
((((((...........)))))))	chrX:101476024-101476291(-)$1	1	63	87	20.3956
((((((...........)))))))	chr1:107177419-107177860(-)$1	1	70	94	23.2182
(((((............)))))((	chr13:98022609-98023090(+)$1	1	68	92	24.1891
((((((...........)))))))	chr3:31017485-31017953(+)$1	1	438	462	21.8133
(((((................)))	chr11:110130823-110131065(-)$1	1	145	169	21.1687
(((((..............)))).	chr17:33883970-33884273(-)$1	1	258	282	21.1075
(((..............)))).))	chr15:11773602-11773857(-)$1	1	169	193	20.5892
(((((.............))))))	chr2:72240647-72240912(+)$1	1	172	196	24.0692
(((((............)).))))	chr3:151897179-151897537(+)$1	1	78	102	23.0668
(((((................)))	chr4:57909336-57909673(+)$1	1	213	237	20.7752
(((((.............))))).	chr8:46424183-46424452(-)$1	1	112	136	23.6363
(((((..............)))))	chr13:102451115-102451412(-)$1	1	171	195	21.6023
(((((............)))))))	chr6:21678745-21679124(+)$1	1	302	326	24.3489
((((((...........)))))))	chr11:97544492-97544816(+)$1	1	165	189	23.2182
.((((............)))).((	chr11:62972833-62973132(+)$1	1	184	208	20.7728
(................)))))..	chr5:67446659-67446933(+)$1	1	99	123	20.4131
.(((((...........)))))))	chr8:83223740-83224038(-)$1	1	126	150	23.0253
(((((.............))))))	chr6:85894429-85894742(-)$1	1	228	252	24.0692
(((((.............))))))	chr5:103337863-103338166(-)$1	1	113	137	23.8130
(((((............)))))))	chr3:88391940-88392186(+)$1	1	115	139	23.1645
(((((..............)))))	chr18:64432028-64432425(+)$1	1	340	364	22.2713
(((((............)))))))	chr9:57809968-57810271(+)$1	1	131	155	24.3489
(.(((.............))).))	chr15:79619078-79619549(-)$1	1	21	45	22.9148
((((((...........))))).)	chr19:46590739-46590999(+)$1	1	9	33	22.5248
(((((.............))))))	chr3:117023559-117024055(-)$1	1	308	332	24.0692
((((((...........)))))))	chr3:108194380-108194630(-)$1	1	91	115	22.8886
(((((.............))))))	chr2:52284320-52284738(-)$1	1	125	149	21.7188
.((((..............)))).	chr4:4693496-4693779(-)$1	1	30	54	21.1050
.(((((...........))))).)	chr12:72420711-72421129(+)$1	1	67	91	22.9695
(((((.............))))))	chr1:79791459-79791719(-)$1	1	190	214	22.9494
..(((............)))...)	chr1:88427073-88427337(+)$1	1	216	240	22.9829
(................)))))))	chr7:89030283-89030629(-)$1	1	285	309	19.8902
(.(((.............)))...	chr8:107741180-107741530(+)$1	1	61	85	23.4062
((((((...........)))))))	chr14:78892441-78892727(-)$1	1	135	159	20.3956
(((((............)))))).	chr18:80315264-80315571(+)$1	1	23	47	23.1674
((((................))))	chr14:27734839-27735169(-)$1	1	266	290	19.9228
(((((............)))))))	chr4:83102342-83102675(-)$1	1	303	327	24.1837
)((((...........))))(((.	chr2:5219734-5220057(-)$1	1	255	279	20.5607
(((((............)))))))	chr5:4806276-4806764(-)$1	1	31	55	24.1321
(((((............)))))..	chr15:82121785-82122131(+)$1	1	205	229	22.0778
(.(((............)))))))	chr14:52506538-52506830(+)$1	1	84	108	23.7505
(((((.............))))).	chr4:134453786-134454036(-)$1	1	113	137	23.3457
((((((...........)))))))	chr4:4694064-4694366(-)$1	1	219	243	23.2182
(((((............)))))))	chr4:109877400-109877726(-)$1	1	53	77	24.3489
(((..............))))).)	chr6:108771428-108771877(+)$1	1	158	182	21.4376
(((((.............))))).	chr15:75900599-75900878(-)$1	1	227	251	22.8843
(((((............)))))))	chr18:46893848-46894128(-)$1	1	226	250	24.3489
(((((.............))))))	chr17:56077871-56078247(-)$1	1	331	355	23.8089
(((((............)))))))	chr2:119793273-119793560(+)$1	1	196	220	24.3489
((.((..............)).))	chr4:33138964-33139438(+)$1	1	245	269	21.1949

#PSSM
e : 0.23	g : 0.23	f : 0.17	d : 0.06	h : 0.04	i : 0.04	[ : 0.03	! : 0.03	= : 0.03	" : 0.01	c : 0.01	: : 0.01	b : 0.01	# : 0.01	H : 0.01	
e : 0.23	g : 0.22	f : 0.15	d : 0.14	y : 0.04	h : 0.04	i : 0.04	[ : 0.04	= : 0.03	# : 0.01	
e : 0.23	g : 0.20	f : 0.14	d : 0.14	y : 0.06	c : 0.06	h : 0.04	i : 0.04	= : 0.03	[ : 0.01	
e : 0.22	g : 0.19	f : 0.14	d : 0.12	y : 0.06	c : 0.06	h : 0.04	i : 0.04	w : 0.03	b : 0.03	= : 0.03	
e : 0.22	g : 0.19	f : 0.14	d : 0.11	y : 0.07	c : 0.06	h : 0.04	i : 0.04	w : 0.03	b : 0.03	= : 0.03	
u : 0.30	v : 0.22	w : 0.12	y : 0.11	e : 0.06	f : 0.04	g : 0.04	t : 0.03	h : 0.03	i : 0.01	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	t : 0.23	v : 0.22	w : 0.12	y : 0.11	
u : 0.30	v : 0.22	t : 0.20	w : 0.12	y : 0.11	e : 0.01	d : 0.01	
v : 0.22	e : 0.15	g : 0.12	f : 0.11	w : 0.09	d : 0.09	y : 0.06	h : 0.03	i : 0.03	c : 0.03	b : 0.01	= : 0.01	
e : 0.22	g : 0.17	f : 0.14	d : 0.11	w : 0.09	c : 0.06	h : 0.04	y : 0.04	i : 0.04	= : 0.03	b : 0.01	
e : 0.25	g : 0.17	f : 0.15	d : 0.14	c : 0.06	h : 0.04	y : 0.04	i : 0.04	= : 0.03	] : 0.01	b : 0.01	
e : 0.26	g : 0.19	f : 0.15	d : 0.14	h : 0.04	i : 0.04	c : 0.04	y : 0.03	= : 0.03	3 : 0.01	b : 0.01	
e : 0.26	g : 0.22	f : 0.15	d : 0.06	] : 0.06	h : 0.04	i : 0.04	: : 0.03	3 : 0.03	= : 0.03	4 : 0.01	c : 0.01	
g : 0.23	f : 0.19	e : 0.15	d : 0.07	] : 0.06	i : 0.06	h : 0.04	c : 0.04	3 : 0.04	= : 0.03	4 : 0.01	: : 0.01	
g : 0.23	e : 0.09	d : 0.09	: : 0.07	f : 0.07	h : 0.06	i : 0.06	2 : 0.06	c : 0.04	4 : 0.03	3 : 0.03	b : 0.03	= : 0.03	G : 0.01	[ : 0.01	0 : 0.01	

#score	1416.8935926246756
#seq	63
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_transcript_m2_run2.txt

#BEAR
[ddddqqqqqqqqdddd	chr13:68759076-68759277(-)$1	201	97	114	13.6360
cc[bbqqqqqqqqbbcc	chr1:162152453-162152662(-)$1	209	118	135	13.4243
hhcccqqqqqqqqccc]	chr2:42029104-42029317(-)$1	213	187	204	13.7328
$ddddqqqqqqqqdddd	chrX:158850973-158851186(-)$1	213	75	92	13.3983
$$cccqqqqqqqqccc2	chr2:112993197-112993426(-)$1	229	133	150	13.4945
gggggqqqqqqqqgggg	chr11:41945636-41945837(-)$1	201	94	111	13.5806
b[abbqqqqqqqqbb]a	chr1:22422260-22422462(-)$1	202	52	69	13.1091
cc[bbqqqqqqqqbb]c	chr10:75723192-75723398(-)$1	206	53	70	13.3854
d[cccqqqqqqqqccc]	chr1:193897786-193898001(-)$1	215	163	180	13.9677
""cccqqqqqqqqccc2	chr9:15716473-15716688(-)$1	215	140	157	13.9559
cc[bbqqqqqqqqbbcc	chr16:43627392-43627592(+)$1	200	23	40	13.4243
eeeeeqqqqqqqqeeee	chr3:157674303-157674512(-)$1	209	42	59	13.4801
gggggqqqqqqqqgggg	chr9:70439871-70440080(-)$1	209	67	84	13.5806
eecccqqqqqqqqccc]	chr7:53172000-53172217(-)$1	217	158	175	14.0394
hhhhhqqqqqqqqhhhh	chr1:164343556-164343775(-)$1	219	186	203	12.6697
###bbqqqqqqqqbb44	chr2:136607009-136607209(+)$1	200	91	108	13.1997
!bbbbqqqqqqqqbb]b	chr2:145803701-145803918(+)$1	217	74	91	12.5657
eeeeaqqqqqqqqa]ee	chr5:14252957-14253163(+)$1	206	173	190	13.5725
eeeeeqqqqqqqqeeee	chr3:107425119-107425344(-)$1	225	106	123	13.4801
$ddddqqqqqqqqdddd	chr2:42453217-42453433(-)$1	216	142	159	13.3983
ee[bbqqqqqqqqbb]e	chr18:83166391-83166626(+)$1	235	201	218	13.5120
"ddddqqqqqqqqdddd	chr2:62888378-62888608(-)$1	230	153	170	13.6139
FFcccqqqqqqqqccc:	chr6:37897323-37897542(+)$1	219	164	181	11.9339
eeeeeqqqqqqqqeeee	chr11:118040536-118040745(-)$1	209	37	54	13.4801
dd[bbqqqqqqqqbb]d	chr15:26275813-26276036(+)$1	223	103	120	13.3247
eeeeeqqqqqqqqeeee	chr6:65064729-65064937(+)$1	208	150	167	13.4801
cddddqqqqqqqqdddd	chr7:134160999-134161205(-)$1	206	49	66	13.4970
hhhhhqqqqqqqqhhhh	chr5:122906645-122906848(-)$1	203	53	70	12.6697
iiiiiqqqqqqqqiiii	chr2:38042756-38042978(-)$1	222	174	191	13.7097
!!cccqqqqqqqqccc2	chr14:48325669-48325881(+)$1	212	66	83	14.1582
!!cccqqqqqqqqccc2	chr15:39703029-39703243(+)$1	214	114	131	14.1582
c[cccqqqqqqqqccc]	chr9:74905111-74905316(+)$1	205	124	141	14.0883
!ddddqqqqqqqqdddd	chr2:41123523-41123745(-)$1	222	174	191	13.6939
eeeeeqqqqqqqqeeee	chr9:66691571-66691774(-)$1	203	122	139	13.4801
eeeeeqqqqqqqqeeee	chrX:39031213-39031414(+)$1	201	66	83	13.4801
ee[bbqqqqqqqqbbee	chr2:121131484-121131684(+)$1	200	113	130	13.4958
eeeeeqqqqqqqqeeee	chr2:4376560-4376775(+)$1	215	196	213	13.4801
ccc[aqqqqqqqqa]cc	chr13:38015469-38015702(+)$1	233	55	72	13.5592
:ddddqqqqqqqqdddd	chr15:40887050-40887258(+)$1	208	170	187	12.6175
iiiiiqqqqqqqqiiii	chr13:100191418-100191620(-)$1	202	65	82	13.7097
gggggqqqqqqqqgggg	chr11:35228791-35229015(+)$1	224	104	121	13.5806
a[cccqqqqqqqqccc]	chr5:122384420-122384655(-)$1	235	114	131	14.1028
:ddddqqqqqqqqdddd	chr2:79675530-79675740(+)$1	210	174	191	12.6175
"""bbqqqqqqqqbb]b	chr15:80799115-80799336(-)$1	221	40	57	13.0833
[ddddqqqqqqqqdddd	chr19:28084949-28085171(-)$1	222	50	67	13.6360
:ddddqqqqqqqqdddd	chr19:28001379-28001615(-)$1	236	116	133	12.6175
gggggqqqqqqqqgggg	chr8:105157571-105157772(-)$1	201	52	69	13.5806
:ddddqqqqqqqqdddd	chr9:54452171-54452379(+)$1	208	58	75	12.6175
=====qqqqqqqq====	chr16:17045195-17045401(+)$1	206	64	81	13.7914
eecccqqqqqqqqccc]	chr6:124761054-124761263(-)$1	209	123	140	14.0394
eeeeeqqqqqqqqeeee	chr2:166928761-166928985(+)$1	224	49	66	13.4801
dddbbqqqqqqqqbb22	chr10:70717945-70718171(+)$1	226	55	72	12.9397
!ddddqqqqqqqqdddd	chr17:73591453-73591662(+)$1	209	30	47	13.6939
"""bbqqqqqqqqbb33	chr4:129693944-129694163(+)$1	219	33	50	13.4499
eeeeeqqqqqqqqeeee	chr9:108958464-108958665(+)$1	201	163	180	13.4801
f!!bbqqqqqqqqbb22	chr5:67078156-67078362(+)$1	206	77	94	13.0945
eeeeeqqqqqqqqeeee	chr12:38079352-38079579(+)$1	227	156	173	13.4801
ccc[aqqqqqqqqa]cc	chr15:100069304-100069505(+)$1	201	132	149	13.5592
ddd[aqqqqqqqqa]dd	chr18:15220175-15220396(-)$1	221	154	171	13.3876
eeeeeqqqqqqqqeeee	chr5:122886127-122886342(+)$1	215	150	167	13.4801
hhh[aqqqqqqqqahhh	chr5:4805788-4805992(-)$1	204	69	86	13.0177
!!cccqqqqqqqqccc2	chr13:110195288-110195499(+)$1	211	3	20	14.1582
##cccqqqqqqqqcccd	chr17:85471279-85471484(-)$1	205	81	98	13.9484
hhhhhqqqqqqqqhhhh	chr11:57143123-57143333(+)$1	210	38	55	12.6697
fffffqqqqqqqqffff	chr13:23832085-23832302(+)$1	217	118	135	12.2832
eeeeeqqqqqqqqeeee	chr2:132133871-132134071(+)$1	200	1	18	13.4801
b[cccqqqqqqqqccc]	chr4:153531662-153531867(-)$1	205	75	92	13.8456
[ddddqqqqqqqqdddd	chr14:40088153-40088374(-)$1	221	175	192	13.6360
ii[bbqqqqqqqqbb]i	chr5:25271999-25272218(+)$1	219	179	196	13.5266
gggggqqqqqqqqgggg	chr2:119240722-119240942(-)$1	220	65	82	13.5806
ccc[aqqqqqqqqaccc	chr5:14678185-14678398(+)$1	213	165	182	13.7388

#otherMatches

#Seq PSSM
CCCGUCACUCAACAUGG	chr13:68759076-68759277(-)$1	201	97	114	13.6360
UGUGUGUUUUGAGACCA	chr1:162152453-162152662(-)$1	209	118	135	13.4243
AAAUAAAAGUCACUGUA	chr2:42029104-42029317(-)$1	213	187	204	13.7328
UCAUAAAUAUUUCUGUG	chrX:158850973-158851186(-)$1	213	75	92	13.3983
GCCAUAAUUUUAAAUGA	chr2:112993197-112993426(-)$1	229	133	150	13.4945
UAGAUCAGUUGCUAUCU	chr11:41945636-41945837(-)$1	201	94	111	13.5806
AGGGUUUAAAAUUGCAU	chr1:22422260-22422462(-)$1	202	52	69	13.1091
GGGUGUAGGCGAUCAGU	chr10:75723192-75723398(-)$1	206	53	70	13.3854
CUGGCCCCUGGCUGCCU	chr1:193897786-193898001(-)$1	215	163	180	13.9677
GAUGGAAAAUUAGCCAA	chr9:15716473-15716688(-)$1	215	140	157	13.9559
GAAUCUGCCAUAUGAUC	chr16:43627392-43627592(+)$1	200	23	40	13.4243
GGCUAAAUUUUUGUGGC	chr3:157674303-157674512(-)$1	209	42	59	13.4801
AAAGAUUACAUUUUUUU	chr9:70439871-70440080(-)$1	209	67	84	13.5806
UUGCCACGGAGGAGGCG	chr7:53172000-53172217(-)$1	217	158	175	14.0394
AAUUUAUGCUAUCAAAU	chr1:164343556-164343775(-)$1	219	186	203	12.6697
UCUGGCUCUCUUUCUUU	chr2:136607009-136607209(+)$1	200	91	108	13.1997
accccagucccgaggag	chr2:145803701-145803918(+)$1	217	74	91	12.5657
UUUUCAUAAUCAAGAAA	chr5:14252957-14253163(+)$1	206	173	190	13.5725
UCUUUUUAAAAUUAGAG	chr3:107425119-107425344(-)$1	225	106	123	13.4801
UGAGUUGUAGAUUGCUC	chr2:42453217-42453433(-)$1	216	142	159	13.3983
GCCGUGUGAGAGAGCAG	chr18:83166391-83166626(+)$1	235	201	218	13.5120
UGUGCACUAAAAAGCAC	chr2:62888378-62888608(-)$1	230	153	170	13.6139
UUCUAGUUAUGUGUAGU	chr6:37897323-37897542(+)$1	219	164	181	11.9339
GCCCUGCAGGGGAGGGG	chr11:118040536-118040745(-)$1	209	37	54	13.4801
GCUUUGCUUCAUAAAUG	chr15:26275813-26276036(+)$1	223	103	120	13.3247
GGUGGCAUUCCAUCCAC	chr6:65064729-65064937(+)$1	208	150	167	13.4801
GGGAAAACUAAAAUUCC	chr7:134160999-134161205(-)$1	206	49	66	13.4970
UUUUUAAAAGAAAAAAA	chr5:122906645-122906848(-)$1	203	53	70	12.6697
gguucugugaaucgaac	chr2:38042756-38042978(-)$1	222	174	191	13.7097
UUUAUUUCUUAGUAUAC	chr14:48325669-48325881(+)$1	212	66	83	14.1582
UAGUAUAAUAAGUUACA	chr15:39703029-39703243(+)$1	214	114	131	14.1582
CUCAUUCUGCAGUGUGU	chr9:74905111-74905316(+)$1	205	124	141	14.0883
UACAAUGUGUAUUUUGU	chr2:41123523-41123745(-)$1	222	174	191	13.6939
GGCUUACUGUGGGAAGC	chr9:66691571-66691774(-)$1	203	122	139	13.4801
UGAAACUGUGAUUUUUC	chrX:39031213-39031414(+)$1	201	66	83	13.4801
GCCUGCUCCCCCUCAGC	chr2:121131484-121131684(+)$1	200	113	130	13.4958
GACAUACUCUCUAAUGU	chr2:4376560-4376775(+)$1	215	196	213	13.4801
CGUGCAAGAAAAGGGAU	chr13:38015469-38015702(+)$1	233	55	72	13.5592
ugucauuguuauuUGAU	chr15:40887050-40887258(+)$1	208	170	187	12.6175
AAGUAAUAUGUAGUGCU	chr13:100191418-100191620(-)$1	202	65	82	13.7097
UUGAAUGUUUUGUUUUA	chr11:35228791-35229015(+)$1	224	104	121	13.5806
UGGAGGUUAGCAGCUUG	chr5:122384420-122384655(-)$1	235	114	131	14.1028
GGCUUACACAUUAAAGU	chr2:79675530-79675740(+)$1	210	174	191	12.6175
ucugccugccucugccu	chr15:80799115-80799336(-)$1	221	40	57	13.0833
AGGGGCUCGCUUUCUCC	chr19:28084949-28085171(-)$1	222	50	67	13.6360
UGUAGUGGCGUAUCUAC	chr19:28001379-28001615(-)$1	236	116	133	12.6175
UAUGUACAAUACAAUGU	chr8:105157571-105157772(-)$1	201	52	69	13.5806
AGCUGUCUUCCCUUAGC	chr9:54452171-54452379(+)$1	208	58	75	12.6175
UUAUUUUGACAUCAAUG	chr16:17045195-17045401(+)$1	206	64	81	13.7914
CACCGCCCUAUUAUGGU	chr6:124761054-124761263(-)$1	209	123	140	14.0394
CUUGUUUUAAAGUGCGA	chr2:166928761-166928985(+)$1	224	49	66	13.4801
CAUUCAACCCACAGAAU	chr10:70717945-70718171(+)$1	226	55	72	12.9397
CUACACGUUUAACUGUA	chr17:73591453-73591662(+)$1	209	30	47	13.6939
UUUGCUACUGUCUGCCC	chr4:129693944-129694163(+)$1	219	33	50	13.4499
UUGGUUCACCCAUGCCG	chr9:108958464-108958665(+)$1	201	163	180	13.4801
UGCAGCUUUAGCACUUA	chr5:67078156-67078362(+)$1	206	77	94	13.0945
CCUGAUUUUUCUCUCAG	chr12:38079352-38079579(+)$1	227	156	173	13.4801
cagcuuuccuguuaccu	chr15:100069304-100069505(+)$1	201	132	149	13.5592
UCCGGUACCAGUUCGGG	chr18:15220175-15220396(-)$1	221	154	171	13.3876
CCUUGUAUGAUGUUGAG	chr5:122886127-122886342(+)$1	215	150	167	13.4801
GCAACUUUUUCAUGUGU	chr5:4805788-4805992(-)$1	204	69	86	13.0177
UUAGGUCAUGAUUCCUC	chr13:110195288-110195499(+)$1	211	3	20	14.1582
CAAAGAACUGCCCCUUU	chr17:85471279-85471484(-)$1	205	81	98	13.9484
CGGUGUGACCCACCACU	chr11:57143123-57143333(+)$1	210	38	55	12.6697
UGCUUCUAAUAAAAAGC	chr13:23832085-23832302(+)$1	217	118	135	12.2832
GUGcacacacgcaugua	chr2:132133871-132134071(+)$1	200	1	18	13.4801
CCAGCCACACACAGCUU	chr4:153531662-153531867(-)$1	205	75	92	13.8456
ACAGUCCCUGAAAACUG	chr14:40088153-40088374(-)$1	221	175	192	13.6360
agcaauuuuucuuuuuc	chr5:25271999-25272218(+)$1	219	179	196	13.5266
UUUAAAAAAAUCAUUAA	chr2:119240722-119240942(-)$1	220	65	82	13.5806
GCAACUAAAAUAUGUGC	chr5:14678185-14678398(+)$1	213	165	182	13.7388

#DB
.((((........))))	chr13:68759076-68759277(-)$1	1	97	114	13.6360
((.((........))))	chr1:162152453-162152662(-)$1	1	118	135	13.4243
(((((........))).	chr2:42029104-42029317(-)$1	1	187	204	13.7328
.((((........))))	chrX:158850973-158851186(-)$1	1	75	92	13.3983
..(((........))).	chr2:112993197-112993426(-)$1	1	133	150	13.4945
(((((........))))	chr11:41945636-41945837(-)$1	1	94	111	13.5806
(.(((........)).)	chr1:22422260-22422462(-)$1	1	52	69	13.1091
((.((........)).)	chr10:75723192-75723398(-)$1	1	53	70	13.3854
(.(((........))).	chr1:193897786-193898001(-)$1	1	163	180	13.9677
..(((........))).	chr9:15716473-15716688(-)$1	1	140	157	13.9559
((.((........))))	chr16:43627392-43627592(+)$1	1	23	40	13.4243
(((((........))))	chr3:157674303-157674512(-)$1	1	42	59	13.4801
(((((........))))	chr9:70439871-70440080(-)$1	1	67	84	13.5806
(((((........))).	chr7:53172000-53172217(-)$1	1	158	175	14.0394
(((((........))))	chr1:164343556-164343775(-)$1	1	186	203	12.6697
...((........))..	chr2:136607009-136607209(+)$1	1	91	108	13.1997
.((((........)).)	chr2:145803701-145803918(+)$1	1	74	91	12.5657
(((((........).))	chr5:14252957-14253163(+)$1	1	173	190	13.5725
(((((........))))	chr3:107425119-107425344(-)$1	1	106	123	13.4801
.((((........))))	chr2:42453217-42453433(-)$1	1	142	159	13.3983
((.((........)).)	chr18:83166391-83166626(+)$1	1	201	218	13.5120
.((((........))))	chr2:62888378-62888608(-)$1	1	153	170	13.6139
))(((........))).	chr6:37897323-37897542(+)$1	1	164	181	11.9339
(((((........))))	chr11:118040536-118040745(-)$1	1	37	54	13.4801
((.((........)).)	chr15:26275813-26276036(+)$1	1	103	120	13.3247
(((((........))))	chr6:65064729-65064937(+)$1	1	150	167	13.4801
)((((........))))	chr7:134160999-134161205(-)$1	1	49	66	13.4970
(((((........))))	chr5:122906645-122906848(-)$1	1	53	70	12.6697
(((((........))))	chr2:38042756-38042978(-)$1	1	174	191	13.7097
..(((........))).	chr14:48325669-48325881(+)$1	1	66	83	14.1582
..(((........))).	chr15:39703029-39703243(+)$1	1	114	131	14.1582
(.(((........))).	chr9:74905111-74905316(+)$1	1	124	141	14.0883
.((((........))))	chr2:41123523-41123745(-)$1	1	174	191	13.6939
(((((........))))	chr9:66691571-66691774(-)$1	1	122	139	13.4801
(((((........))))	chrX:39031213-39031414(+)$1	1	66	83	13.4801
((.((........))))	chr2:121131484-121131684(+)$1	1	113	130	13.4958
(((((........))))	chr2:4376560-4376775(+)$1	1	196	213	13.4801
(((.(........).))	chr13:38015469-38015702(+)$1	1	55	72	13.5592
.((((........))))	chr15:40887050-40887258(+)$1	1	170	187	12.6175
(((((........))))	chr13:100191418-100191620(-)$1	1	65	82	13.7097
(((((........))))	chr11:35228791-35229015(+)$1	1	104	121	13.5806
(.(((........))).	chr5:122384420-122384655(-)$1	1	114	131	14.1028
.((((........))))	chr2:79675530-79675740(+)$1	1	174	191	12.6175
...((........)).)	chr15:80799115-80799336(-)$1	1	40	57	13.0833
.((((........))))	chr19:28084949-28085171(-)$1	1	50	67	13.6360
.((((........))))	chr19:28001379-28001615(-)$1	1	116	133	12.6175
(((((........))))	chr8:105157571-105157772(-)$1	1	52	69	13.5806
.((((........))))	chr9:54452171-54452379(+)$1	1	58	75	12.6175
(((((........))))	chr16:17045195-17045401(+)$1	1	64	81	13.7914
(((((........))).	chr6:124761054-124761263(-)$1	1	123	140	14.0394
(((((........))))	chr2:166928761-166928985(+)$1	1	49	66	13.4801
(((((........))..	chr10:70717945-70718171(+)$1	1	55	72	12.9397
.((((........))))	chr17:73591453-73591662(+)$1	1	30	47	13.6939
...((........))..	chr4:129693944-129694163(+)$1	1	33	50	13.4499
(((((........))))	chr9:108958464-108958665(+)$1	1	163	180	13.4801
(..((........))..	chr5:67078156-67078362(+)$1	1	77	94	13.0945
(((((........))))	chr12:38079352-38079579(+)$1	1	156	173	13.4801
(((.(........).))	chr15:100069304-100069505(+)$1	1	132	149	13.5592
(((.(........).))	chr18:15220175-15220396(-)$1	1	154	171	13.3876
(((((........))))	chr5:122886127-122886342(+)$1	1	150	167	13.4801
(((.(........))))	chr5:4805788-4805992(-)$1	1	69	86	13.0177
..(((........))).	chr13:110195288-110195499(+)$1	1	3	20	14.1582
..(((........))))	chr17:85471279-85471484(-)$1	1	81	98	13.9484
(((((........))))	chr11:57143123-57143333(+)$1	1	38	55	12.6697
(((((........))))	chr13:23832085-23832302(+)$1	1	118	135	12.2832
(((((........))))	chr2:132133871-132134071(+)$1	1	1	18	13.4801
(.(((........))).	chr4:153531662-153531867(-)$1	1	75	92	13.8456
.((((........))))	chr14:40088153-40088374(-)$1	1	175	192	13.6360
((.((........)).)	chr5:25271999-25272218(+)$1	1	179	196	13.5266
(((((........))))	chr2:119240722-119240942(-)$1	1	65	82	13.5806
(((.(........))))	chr5:14678185-14678398(+)$1	1	165	182	13.7388

#PSSM
e : 0.23	c : 0.11	! : 0.08	h : 0.07	g : 0.07	d : 0.05	" : 0.05	: : 0.05	[ : 0.04	$ : 0.04	i : 0.04	b : 0.02	# : 0.02	f : 0.02	F : 0.01	a : 0.01	= : 0.01	
e : 0.23	d : 0.22	c : 0.08	h : 0.07	g : 0.07	[ : 0.07	! : 0.05	" : 0.04	i : 0.04	# : 0.02	$ : 0.01	b : 0.01	F : 0.01	= : 0.01	f : 0.01	
c : 0.23	d : 0.21	e : 0.18	[ : 0.09	g : 0.07	h : 0.05	i : 0.02	" : 0.02	a : 0.01	# : 0.01	b : 0.01	= : 0.01	! : 0.01	f : 0.01	
b : 0.19	c : 0.19	d : 0.18	e : 0.18	g : 0.07	[ : 0.07	h : 0.04	i : 0.02	= : 0.01	f : 0.01	
b : 0.19	c : 0.19	d : 0.18	e : 0.16	a : 0.08	g : 0.07	h : 0.04	i : 0.02	= : 0.01	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	
b : 0.19	c : 0.19	d : 0.18	e : 0.16	a : 0.08	g : 0.07	h : 0.04	i : 0.02	= : 0.01	f : 0.01	
c : 0.21	b : 0.19	d : 0.18	e : 0.16	g : 0.07	h : 0.05	] : 0.05	i : 0.02	= : 0.01	f : 0.01	
c : 0.26	d : 0.19	e : 0.19	] : 0.09	g : 0.07	h : 0.05	i : 0.02	2 : 0.02	4 : 0.01	= : 0.01	3 : 0.01	f : 0.01	
d : 0.22	e : 0.21	] : 0.09	2 : 0.09	c : 0.08	g : 0.07	h : 0.05	i : 0.04	b : 0.02	a : 0.01	4 : 0.01	: : 0.01	= : 0.01	3 : 0.01	f : 0.01	

#score	953.8371131267429
#seq	71
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_CDS_m1_run1.txt

#BEAR
gggggg^^^^^^^^^^^^^^^^^^^gg	chr4:95669064-95669265(+)$1	201	10	37	18.9296
hffffffvvvvvvvvvvvvvffffffh	chr17:85468282-85468483(-)$1	201	154	181	22.0302
c[cccccctttttttttttccc]ccc]	chr2:104311843-104312044(-)$1	201	82	109	20.7671
fffccc^^^^^^^^^^^^^^^^^^^^^	chr11:21228861-21229062(-)$1	201	79	106	19.5675
gg[ddddvvvvvvvvvvvvvdddd]gg	chr12:112782664-112782865(+)$1	201	41	68	21.7934
ffffffyyyyyyyyyyyyyyyyfffff	chr17:21088241-21088442(+)$1	201	63	90	22.6454
ddd[dddduuuuuuuuuuuuddddddd	chr10:29067207-29067408(-)$1	201	170	197	20.4396
==!!bbwwwwwwwwwwwwwwbb22===	chr2:163454797-163454998(-)$1	201	120	147	22.4440
gggggggvvvvvvvvvvvvvggggggg	chr18:49857946-49858147(-)$1	201	160	187	22.2058
ffffff^^^^^^^^^^^^^^^^^^^^^	chr6:113792199-113792400(-)$1	201	96	123	19.4866
dddd^^^^^^^^^^^^^^^^^^^^^^^	chr4:107533664-107533865(+)$1	201	145	172	18.0649
ffffffwwwwwwwwwwwwwwffffff2	chr3:126657841-126658042(-)$1	201	110	137	23.8983
c[cccccctttttttttttccc]ccc]	chr2:104311844-104312045(-)$1	201	83	110	20.7671
ffffffwwwwwwwwwwwwwwffffff2	chr3:126657842-126658043(-)$1	201	111	138	23.8983
ii"""cccuuuuuuuuuuuuccc4444	chr18:20823889-20824090(+)$1	201	22	49	23.6989
ggggggvvvvvvvvvvvvvggggggg]	chr9:78385927-78386128(-)$1	201	11	38	21.7374
dd!!dddduuuuuuuuuuuudddd22d	chr4:123189286-123189487(-)$1	201	89	116	21.0218
fffccc^^^^^^^^^^^^^^^^^^^^^	chr11:21228862-21229063(-)$1	201	80	107	19.5675
ii"""cccuuuuuuuuuuuuccc4444	chr18:20823883-20824084(+)$1	201	28	55	23.6989
dddeeeeeuuuuuuuuuuuueeeee::	chr6:124997802-124998003(+)$1	201	74	101	19.5025
ff[ccc^^^^^^^^^^^^^^^^^^^^^	chr1:196633637-196633838(+)$1	201	6	33	19.6903
ee"""ddddtttttttttttdddd333	chr3:57262844-57263045(-)$1	201	154	181	19.3400
ddd[dddduuuuuuuuuuuuddddddd	chr10:29067206-29067407(-)$1	201	169	196	20.4396
ffff[auuuuuuuuuuuua]ffffff2	chr11:97317730-97317931(+)$1	201	53	80	21.8091
ggggggguuuuuuuuuuuuggggggg:	chr2:60071964-60072165(+)$1	201	5	32	20.9588
"""cccwwwwwwwwwwwwwwccc333b	chr19:46339196-46339397(+)$1	201	75	102	23.9910
ffffffwwwwwwwwwwwwwwffffff4	chr1:16993931-16994132(-)$1	201	95	122	24.0441
ffffffwwwwwwwwwwwwwwffffff2	chr3:126657840-126658041(-)$1	201	109	136	23.8983
ffeeeeevvvvvvvvvvvvveeeee::	chr12:88653588-88653789(-)$1	201	147	174	20.2884
ggggg[bbtttttttttttbb]ggggg	chr9:77640840-77641041(+)$1	201	107	134	19.2803
ff[ccc^^^^^^^^^^^^^^^^^^^^^	chr1:196633638-196633839(+)$1	201	5	32	19.6903
a[eeeeeuuuuuuuuuuuueeeee]a]	chr18:15556547-15556748(-)$1	201	19	46	21.6388
ccceeeeeuuuuuuuuuuuueeeee]c	chr16:33727470-33727671(+)$1	201	7	34	21.5967
dd!!dddduuuuuuuuuuuudddd]dd	chr11:80291681-80291882(+)$1	201	41	68	21.0549
ffffffbbuuuuuuuuuuuubb]ffff	chr13:55576519-55576720(-)$1	201	127	154	22.1284
:ffffffvvvvvvvvvvvvvffffff:	chr13:100204670-100204871(-)$1	201	76	103	20.8838
fffffxxxxxxxxxxxxxxxffffff]	chr16:41955272-41955473(+)$1	201	169	196	20.9354
ddd[cccvvvvvvvvvvvvvccc]ddd	chr1:175274479-175274680(-)$1	201	54	81	21.8281
e!!ccc[bbtttttttttttbbccc55	chr11:42300679-42300880(+)$1	201	71	98	18.4642
a[bbbbwwwwwwwwwwwwwwbb]bb]a	chr3:95738674-95738875(+)$1	201	105	132	21.6621
hhhh[cccuuuuuuuuuuuuccchhhh	chr10:57247502-57247703(-)$1	201	30	57	20.4808
ffff[auuuuuuuuuuuua]ffffff2	chr11:97317729-97317930(+)$1	201	54	81	21.8091
ffffffyyyyyyyyyyyyyyyyfffff	chr17:21088240-21088441(+)$1	201	64	91	22.6454
ffffffbbuuuuuuuuuuuubb]ffff	chr13:55576518-55576719(-)$1	201	126	153	22.1284
fffffxxxxxxxxxxxxxxxffffff]	chr16:41955271-41955472(+)$1	201	170	197	20.9354
"""cccwwwwwwwwwwwwwwccc333b	chr19:46339198-46339399(+)$1	201	73	100	23.9910
cc[cccxxxxxxxxxxxxxxxccc333	chr10:56108278-56108479(+)$1	201	40	67	21.9892
ffffff^^^^^^^^^^^^^^^^^^^^^	chr10:66682856-66683057(+)$1	201	137	164	19.4866
ggggggguuuuuuuuuuuuggggggg:	chr2:60071962-60072163(+)$1	201	7	34	20.9588
cc[cccxxxxxxxxxxxxxxxccc]cc	chr2:49403880-49404081(+)$1	201	149	176	21.1988
:eeeeewwwwwwwwwwwwwweeeeecc	chr2:107136219-107136420(+)$1	201	99	126	21.3851
fffffxxxxxxxxxxxxxxxffffff2	chr3:108194427-108194628(-)$1	201	138	165	20.8795
ii"""cccuuuuuuuuuuuuccc4444	chr18:20823886-20824087(+)$1	201	25	52	23.6989
cc[cccxxxxxxxxxxxxxxxccc333	chr10:56108279-56108480(+)$1	201	39	66	21.9892
$$ddddvvvvvvvvvvvvvdddd4444	chrM:3488-3689(+)$1	201	55	82	20.9033
##cccyyyyyyyyyyyyyyyyccc333	chr11:56825449-56825650(+)$1	201	157	184	23.0340
ffffffxxxxxxxxxxxxxxxffffff	chr11:107073685-107073886(-)$1	201	10	37	20.8839
ii"""cccuuuuuuuuuuuuccc4444	chr18:20823884-20824085(+)$1	201	27	54	23.6989
iiiiii^^^^^^^^^^^^^^^^^^^^^	chr5:24878526-24878727(-)$1	201	46	73	19.1055

#otherMatches

#Seq PSSM
UAUAGUGUGAAGACAAAGGAUAGAAAC	chr4:95669064-95669265(+)$1	201	10	37	18.9296
UCUCAGCCGAGCCUAACAACGCUGAGC	chr17:85468282-85468483(-)$1	201	154	181	22.0302
AAACUCAGUCAAGUGCCUUUUGUAGUG	chr2:104311843-104312044(-)$1	201	82	109	20.7671
UGCUUGUGAUGUCAAACCUCUAUAGCC	chr11:21228861-21229062(-)$1	201	79	106	19.5675
UGGAAAUAAUCUAGUCCUGCAUUUGUA	chr12:112782664-112782865(+)$1	201	41	68	21.7934
AGCUUCGUCUCAAUAGUAUCAAGAAGC	chr17:21088241-21088442(+)$1	201	63	90	22.6454
AUGGUUCAAUAUAGGAGAAAUGAACAU	chr10:29067207-29067408(-)$1	201	170	197	20.4396
AUGACCAAUGAACCUGGUAAGGGAAUG	chr2:163454797-163454998(-)$1	201	120	147	22.4440
UUAGCACGUCUGUCCCUGUGGUGCUAG	chr18:49857946-49858147(-)$1	201	160	187	22.2058
CGACUUUUACUCCAAAAACCAAAGAAA	chr6:113792199-113792400(-)$1	201	96	123	19.4866
CUGGGACAACCAUCCACGACCCUACCU	chr4:107533664-107533865(+)$1	201	145	172	18.0649
CAAAGAAAAUAGACUUCCUCUCUUUGU	chr3:126657841-126658042(-)$1	201	110	137	23.8983
AAACUCAGUCAAGUGCCUUUUGUAGUG	chr2:104311844-104312045(-)$1	201	83	110	20.7671
CAAAGAAAAUAGACUUCCUCUCUUUGU	chr3:126657842-126658043(-)$1	201	111	138	23.8983
UCACACAGAUCCACAAGCUCCUGACAG	chr18:20823889-20824090(+)$1	201	22	49	23.6989
UCCCUGUCCAGAACACUAUUAGGGAAU	chr9:78385927-78386128(-)$1	201	11	38	21.7374
CAGAUGGCAAGAAUACCAAAGCCGAGU	chr4:123189286-123189487(-)$1	201	89	116	21.0218
UGCUUGUGAUGUCAAACCUCUAUAGCC	chr11:21228862-21229063(-)$1	201	80	107	19.5675
UCACACAGAUCCACAAGCUCCUGACAG	chr18:20823883-20824084(+)$1	201	28	55	23.6989
GCCUGUGGAUCCCAACGAACCCACAUA	chr6:124997802-124998003(+)$1	201	74	101	19.5025
CUCUGGCACCCACUAACUAUUUCAUUG	chr1:196633637-196633838(+)$1	201	6	33	19.6903
AGUCUGCUCUGAACAAAAGCGAGCCCU	chr3:57262844-57263045(-)$1	201	154	181	19.3400
AUGGUUCAAUAUAGGAGAAAUGAACAU	chr10:29067206-29067407(-)$1	201	169	196	20.4396
GGCACCUCUGAAGAUGCUGAUGCCCCC	chr11:97317730-97317931(+)$1	201	53	80	21.8091
GUUCCUUCUUCAUAUUCACAGGGAGCA	chr2:60071964-60072165(+)$1	201	5	32	20.9588
UACAUCAAAAAGCUCAUGGAGAUCAUC	chr19:46339196-46339397(+)$1	201	75	102	23.9910
CUUGCUAUACCAAAGAAUCCAGCAAGC	chr1:16993931-16994132(-)$1	201	95	122	24.0441
CAAAGAAAAUAGACUUCCUCUCUUUGU	chr3:126657840-126658041(-)$1	201	109	136	23.8983
UACCUUUGAUCAAUACUAAAAGAGGUU	chr12:88653588-88653789(-)$1	201	147	174	20.2884
AUUUGGAAGUGCAACCAAAUUGCAGAU	chr9:77640840-77641041(+)$1	201	107	134	19.2803
CUCUGGCACCCACUAACUAUUUCAUUG	chr1:196633638-196633839(+)$1	201	5	32	19.6903
GGUGGAGUUAAUAAUCACUUUCCAGUU	chr18:15556547-15556748(-)$1	201	19	46	21.6388
CCUCUGACCACUUCAACCACGUCAGCA	chr16:33727470-33727671(+)$1	201	7	34	21.5967
GCAAUGAGAUCUCCUACCCGCUCAAGC	chr11:80291681-80291882(+)$1	201	41	68	21.0549
UGCCAGCCUCAUUGAUCUAUGGCCUGG	chr13:55576519-55576720(-)$1	201	127	154	22.1284
GAAGUAGACAUCCCGAUUUCCUACUUA	chr13:100204670-100204871(-)$1	201	76	103	20.8838
CCUGGAGACACCUUACACCACUAGGUA	chr16:41955272-41955473(+)$1	201	169	196	20.9354
UCCAGGGGACCAAACACGAAUCCAGGA	chr1:175274479-175274680(-)$1	201	54	81	21.8281
UUACAAUGUAAUUCCUUUAAACUUGAC	chr11:42300679-42300880(+)$1	201	71	98	18.4642
AGUGGAAACAAAAUAAAAGAUCUCAGU	chr3:95738674-95738875(+)$1	201	105	132	21.6621
AGACGAUUUUAAACUAUGCUGAUGUUU	chr10:57247502-57247703(-)$1	201	30	57	20.4808
GGCACCUCUGAAGAUGCUGAUGCCCCC	chr11:97317729-97317930(+)$1	201	54	81	21.8091
AGCUUCGUCUCAAUAGUAUCAAGAAGC	chr17:21088240-21088441(+)$1	201	64	91	22.6454
UGCCAGCCUCAUUGAUCUAUGGCCUGG	chr13:55576518-55576719(-)$1	201	126	153	22.1284
CCUGGAGACACCUUACACCACUAGGUA	chr16:41955271-41955472(+)$1	201	170	197	20.9354
UACAUCAAAAAGCUCAUGGAGAUCAUC	chr19:46339198-46339399(+)$1	201	73	100	23.9910
GCCGGAAGCACCAUCUCCAACUCCCAC	chr10:56108278-56108479(+)$1	201	40	67	21.9892
ACUAGUCAAACUCCAUUACCUACCAUU	chr10:66682856-66683057(+)$1	201	137	164	19.4866
GUUCCUUCUUCAUAUUCACAGGGAGCA	chr2:60071962-60072163(+)$1	201	7	34	20.9588
AGUUGGCCACACUACUACAAACCACUU	chr2:49403880-49404081(+)$1	201	149	176	21.1988
UUGCCUUACUUCAUCACUCUGGGCACU	chr2:107136219-107136420(+)$1	201	99	126	21.3851
UUCUAUUUUUAACCCCUUCCUGGAAUU	chr3:108194427-108194628(-)$1	201	138	165	20.8795
UCACACAGAUCCACAAGCUCCUGACAG	chr18:20823886-20824087(+)$1	201	25	52	23.6989
GCCGGAAGCACCAUCUCCAACUCCCAC	chr10:56108279-56108480(+)$1	201	39	66	21.9892
UACUAUCAUCAACAUUCCUAUGGAUCC	chrM:3488-3689(+)$1	201	55	82	20.9033
UAUCCAGAUAGGUGAGUGAGAGGGGCA	chr11:56825449-56825650(+)$1	201	157	184	23.0340
GCAUCGCCCUACUGCCUUCCUCGGUGC	chr11:107073685-107073886(-)$1	201	10	37	20.8839
UCACACAGAUCCACAAGCUCCUGACAG	chr18:20823884-20824085(+)$1	201	27	54	23.6989
UGCCAACAACAUACAUCUCAGUCACUC	chr5:24878526-24878727(-)$1	201	46	73	19.1055

#DB
((((((...................))	chr4:95669064-95669265(+)$1	1	10	37	18.9296
)((((((.............))))))(	chr17:85468282-85468483(-)$1	1	154	181	22.0302
(.((((((...........))).))).	chr2:104311843-104312044(-)$1	1	82	109	20.7671
((((((.....................	chr11:21228861-21229062(-)$1	1	79	106	19.5675
((.((((.............)))).))	chr12:112782664-112782865(+)$1	1	41	68	21.7934
((((((................)))))	chr17:21088241-21088442(+)$1	1	63	90	22.6454
(((.((((............)))))))	chr10:29067207-29067408(-)$1	1	170	197	20.4396
((..((..............))..)))	chr2:163454797-163454998(-)$1	1	120	147	22.4440
(((((((.............)))))))	chr18:49857946-49858147(-)$1	1	160	187	22.2058
((((((.....................	chr6:113792199-113792400(-)$1	1	96	123	19.4866
((((.......................	chr4:107533664-107533865(+)$1	1	145	172	18.0649
((((((..............)))))).	chr3:126657841-126658042(-)$1	1	110	137	23.8983
(.((((((...........))).))).	chr2:104311844-104312045(-)$1	1	83	110	20.7671
((((((..............)))))).	chr3:126657842-126658043(-)$1	1	111	138	23.8983
((...(((............)))....	chr18:20823889-20824090(+)$1	1	22	49	23.6989
((((((.............))))))).	chr9:78385927-78386128(-)$1	1	11	38	21.7374
((..((((............))))..)	chr4:123189286-123189487(-)$1	1	89	116	21.0218
((((((.....................	chr11:21228862-21229063(-)$1	1	80	107	19.5675
((...(((............)))....	chr18:20823883-20824084(+)$1	1	28	55	23.6989
)))(((((............)))))..	chr6:124997802-124998003(+)$1	1	74	101	19.5025
((.(((.....................	chr1:196633637-196633838(+)$1	1	6	33	19.6903
((...((((...........))))...	chr3:57262844-57263045(-)$1	1	154	181	19.3400
(((.((((............)))))))	chr10:29067206-29067407(-)$1	1	169	196	20.4396
((((.(............).)))))).	chr11:97317730-97317931(+)$1	1	53	80	21.8091
(((((((............))))))).	chr2:60071964-60072165(+)$1	1	5	32	20.9588
...(((..............)))...)	chr19:46339196-46339397(+)$1	1	75	102	23.9910
((((((..............)))))).	chr1:16993931-16994132(-)$1	1	95	122	24.0441
((((((..............)))))).	chr3:126657840-126658041(-)$1	1	109	136	23.8983
))(((((.............)))))..	chr12:88653588-88653789(-)$1	1	147	174	20.2884
(((((.((...........)).)))))	chr9:77640840-77641041(+)$1	1	107	134	19.2803
((.(((.....................	chr1:196633638-196633839(+)$1	1	5	32	19.6903
(.(((((............))))).).	chr18:15556547-15556748(-)$1	1	19	46	21.6388
((((((((............))))).)	chr16:33727470-33727671(+)$1	1	7	34	21.5967
((..((((............)))).))	chr11:80291681-80291882(+)$1	1	41	68	21.0549
((((((((............)).))))	chr13:55576519-55576720(-)$1	1	127	154	22.1284
.((((((.............)))))).	chr13:100204670-100204871(-)$1	1	76	103	20.8838
(((((...............)))))).	chr16:41955272-41955473(+)$1	1	169	196	20.9354
(((.(((.............))).)))	chr1:175274479-175274680(-)$1	1	54	81	21.8281
(..(((.((...........)))))..	chr11:42300679-42300880(+)$1	1	71	98	18.4642
(.((((..............)).)).)	chr3:95738674-95738875(+)$1	1	105	132	21.6621
((((.(((............)))))))	chr10:57247502-57247703(-)$1	1	30	57	20.4808
((((.(............).)))))).	chr11:97317729-97317930(+)$1	1	54	81	21.8091
((((((................)))))	chr17:21088240-21088441(+)$1	1	64	91	22.6454
((((((((............)).))))	chr13:55576518-55576719(-)$1	1	126	153	22.1284
(((((...............)))))).	chr16:41955271-41955472(+)$1	1	170	197	20.9354
...(((..............)))...)	chr19:46339198-46339399(+)$1	1	73	100	23.9910
((.(((...............)))...	chr10:56108278-56108479(+)$1	1	40	67	21.9892
((((((.....................	chr10:66682856-66683057(+)$1	1	137	164	19.4866
(((((((............))))))).	chr2:60071962-60072163(+)$1	1	7	34	20.9588
((.(((...............))).))	chr2:49403880-49404081(+)$1	1	149	176	21.1988
.(((((..............)))))((	chr2:107136219-107136420(+)$1	1	99	126	21.3851
(((((...............)))))).	chr3:108194427-108194628(-)$1	1	138	165	20.8795
((...(((............)))....	chr18:20823886-20824087(+)$1	1	25	52	23.6989
((.(((...............)))...	chr10:56108279-56108480(+)$1	1	39	66	21.9892
..((((.............))))....	chrM:3488-3689(+)$1	1	55	82	20.9033
..(((................)))...	chr11:56825449-56825650(+)$1	1	157	184	23.0340
((((((...............))))))	chr11:107073685-107073886(-)$1	1	10	37	20.8839
((...(((............)))....	chr18:20823884-20824085(+)$1	1	27	54	23.6989
((((((.....................	chr5:24878526-24878727(-)$1	1	46	73	19.1055

#PSSM
f : 0.35	g : 0.11	d : 0.11	c : 0.10	i : 0.08	h : 0.03	e : 0.03	" : 0.03	a : 0.03	: : 0.03	= : 0.01	$ : 0.01	# : 0.01	
f : 0.38	g : 0.11	d : 0.11	i : 0.08	[ : 0.06	c : 0.06	e : 0.03	" : 0.03	= : 0.01	! : 0.01	h : 0.01	$ : 0.01	# : 0.01	
f : 0.33	" : 0.11	g : 0.10	[ : 0.10	d : 0.10	c : 0.06	! : 0.06	e : 0.05	b : 0.01	h : 0.01	i : 0.01	
f : 0.30	c : 0.22	g : 0.10	" : 0.08	e : 0.08	d : 0.05	[ : 0.05	! : 0.05	b : 0.01	h : 0.01	i : 0.01	
f : 0.27	c : 0.23	g : 0.10	d : 0.10	" : 0.08	e : 0.08	[ : 0.05	b : 0.03	^ : 0.01	i : 0.01	
c : 0.30	f : 0.22	d : 0.11	g : 0.08	e : 0.08	x : 0.05	b : 0.03	a : 0.03	^ : 0.01	[ : 0.01	y : 0.01	i : 0.01	
^ : 0.15	w : 0.15	c : 0.13	x : 0.11	d : 0.10	e : 0.06	y : 0.05	g : 0.05	b : 0.05	f : 0.03	v : 0.03	u : 0.03	[ : 0.01	
^ : 0.15	w : 0.15	v : 0.13	c : 0.11	x : 0.11	d : 0.08	u : 0.08	b : 0.06	y : 0.05	e : 0.03	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.05	y : 0.05	d : 0.01	b : 0.01	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	
u : 0.30	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	
u : 0.27	^ : 0.15	w : 0.15	v : 0.13	x : 0.11	t : 0.08	y : 0.05	a : 0.03	
u : 0.22	^ : 0.15	w : 0.15	x : 0.11	v : 0.10	y : 0.05	g : 0.05	c : 0.03	t : 0.03	] : 0.03	b : 0.01	e : 0.01	d : 0.01	
f : 0.18	c : 0.16	^ : 0.15	d : 0.11	b : 0.10	e : 0.08	g : 0.06	x : 0.06	y : 0.05	
c : 0.23	f : 0.20	^ : 0.15	d : 0.11	b : 0.08	e : 0.08	g : 0.06	y : 0.03	] : 0.01	
f : 0.23	c : 0.22	^ : 0.15	d : 0.11	] : 0.08	g : 0.08	e : 0.08	2 : 0.01	
f : 0.27	^ : 0.15	c : 0.11	d : 0.10	g : 0.08	4 : 0.08	e : 0.08	3 : 0.03	2 : 0.01	] : 0.01	b : 0.01	h : 0.01	
f : 0.27	^ : 0.15	3 : 0.10	g : 0.08	4 : 0.08	] : 0.06	e : 0.06	c : 0.05	d : 0.05	= : 0.01	2 : 0.01	b : 0.01	h : 0.01	
f : 0.27	^ : 0.13	g : 0.11	3 : 0.10	4 : 0.08	c : 0.06	d : 0.06	: : 0.03	] : 0.03	= : 0.01	2 : 0.01	a : 0.01	5 : 0.01	h : 0.01	
^ : 0.13	] : 0.10	2 : 0.10	4 : 0.10	f : 0.08	d : 0.08	: : 0.08	g : 0.06	3 : 0.06	c : 0.05	h : 0.03	b : 0.03	= : 0.01	5 : 0.01	a : 0.01	

#score	1260.9919414932326
#seq	59
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_CDS_m1_run2.txt

#BEAR
===="""bb####ccclllccc22bb333==========:	chr5:140895564-140895849(+)$1	285	37	77	13.5603
[ccc!!eeeee[ddddooooooddddeeeeeccc]dddd]	chr2:180646301-180646569(-)$1	268	131	171	13.7105
ee"""dddd"""ddddoooooodddddddd4444eeeee]	chr13:99043616-99043931(+)$1	315	129	169	15.3758
==[ccc[bb!!a[ddddoooooodddd]a22bbccc====	chr14:99712283-99712565(+)$1	282	26	66	15.8902
!ggggggg!!dddd[aooooooa]ddddggggggg]ccc:	chr10:122452029-122452299(-)$1	270	4	44	14.8863
iiiiiii"""bb"""aooooooa333bb22iiiiiiiii]	chr6:85416542-85416842(+)$1	300	152	192	17.7435
cc"""ccc!!dddd!!aooooooa22dddd22ccc22ccc	chr10:75207952-75208236(-)$1	284	153	193	14.6823
========"""bb[bboooooobb]bb333==========	chr1:39958237-39958520(+)$1	283	199	239	18.6500
&ffffffdddda[cccooooooccc]a333dddd333fff	chr2:174167206-174167482(+)$1	276	110	150	15.4898
$$==========[a!!ammmma22a]==========333g	chr4:116957903-116958181(-)$1	278	231	271	14.8772
eee:ccc[bb[a!!bboooooobb22a]bbccc:a[====	chr4:151597090-151597385(+)$1	295	122	162	13.3244
###ccc[ddddeeeeeooooooeeeee]dddd]cccbbgg	chr14:65357258-65357547(+)$1	289	49	89	13.7622
[a[bb!!a!!ffffffooooooffffff22a4444bb]a]	chr15:10416295-10416563(+)$1	268	152	192	15.5036
[dddd!!dddd"""bboooooobb4444dddd]dddd]gg	chr11:96214252-96214520(+)$1	268	49	89	14.6002
###ggggggg"""cccmmmmccc333ggggggg4444ccc	chr2:160795786-160796075(-)$1	289	231	271	13.5681
ffffff[bb!!eeeeeooooooeeeee22bb]ffffffbb	chr13:85428342-85428610(-)$1	268	186	226	12.7786
======[bbcccssssssssssccc4444bb]========	chr14:70066965-70067244(+)$1	279	39	79	11.8046
eeee[dddd!!cccbboooooobb]ccc333dddd]eeee	chr2:156002946-156003217(-)$1	271	188	228	15.1739
=========!!ddddoooooodddd88888888=======	chr16:37511332-37511621(-)$1	289	194	234	14.3068
[a!!ccc[dddd!!bboooooobb22dddd]ccc22a]bb	chr13:76249094-76249378(+)$1	284	126	166	14.6846
dd[eeeee!!bb[bb[aooooooa]bb]bb22eeeee333	chr15:77605464-77605743(-)$1	279	166	206	13.9164
[ggggggg!!ffffffooooooffffffggggggg]dddd	chr7:148599791-148600059(-)$1	268	202	242	14.3675
a!!a[dddda"""cccnnnnnccc333a]dddd]a22a22	chr6:142316853-142317130(-)$1	277	94	134	12.9452
gggggg"""ccc[ddddnnnnndddd333cccggggggg]	chr14:104865907-104866176(-)$1	269	166	206	13.4276
!!ccc[bba"""bbbboooooobb]bb4444a]bb]ccc2	chr4:98404125-98404408(+)$1	283	73	113	15.9095
::ggggggggggggggooooooggggggg333ggggggg:	chr7:3658229-3658604(+)$1	375	206	246	13.7436
gggggg[ccc"""cccooooooccc22cccggggggg]cc	chr7:150743662-150743930(-)$1	268	161	201	16.9705
=========!!ccc[bblllbb]ccc22==========::	chr2:180999660-180999954(-)$1	294	69	109	12.5207
b[a[eeeee[aeeeeeooooooeeeee4444a]eeeee22	chr12:74209655-74209931(-)$1	276	57	97	14.4472
$$bb[ccc[gggggggooooooggggggg22ccc]bbeee	chr7:6661651-6661928(-)$1	277	216	256	14.6796
da[dddd"""ffffffooooooffffff333ddddaffff	chr18:85150543-85150823(+)$1	280	114	154	14.3314
!bb[==========[cccmmmmccc]==========]bb]	chr1:75525657-75525930(+)$1	273	182	222	13.2639
i!!bb[iiiiiiiiibboooooobb]iiiiiiiii]bb22	chr17:57121284-57121553(-)$1	269	119	159	14.7088
!ccc"""accc!!ddddmmmmdddd]ccc]a333ccc22b	chr13:38074831-38075100(-)$1	269	48	88	12.6462
ccbbeeeeebb[ddddooooooddddbb333eeeee]bb2	chr18:42388238-42388508(-)$1	270	149	189	13.2442
rrrreeeeegggggggoooooogggggggcccddddffff	chr13:115780236-115780511(-)$1	275	106	146	12.1800
ggg!!a[a####ddddrrrrrrrrrdddd4444a]a22gg	chr3:94573756-94574039(-)$1	283	20	60	12.7177
gggggggggggg[ddddmmmmdddd]ggggggg333gggg	chr1:95197961-95198238(-)$1	277	206	246	12.3450
[ccc[dddd[a[bb[aooooooa]bba]dddd]ccc333f	chr13:100195671-100195942(-)$1	271	136	176	15.2979
=======[accc!!ddddllldddd4444ccc]a]=====	chr1:74486437-74486717(-)$1	280	218	258	14.2958
###ccc$$$$$a!!bboooooobb22accc22eeeee666	chrX:148462255-148462526(+)$1	271	96	136	14.6318
=========!!a[cccooooooccc]a]===========a	chr14:56445096-56445373(+)$1	277	108	148	19.9587
ccbb"""bb!!a[bboooooobb333a22bb4444bb22c	chr5:125549229-125549517(-)$1	288	187	227	14.8707
"""cccccc[bb[cccmmmmcccbbccc4444ccc333bb	chr11:68577688-68577965(+)$1	277	108	148	13.1265
eeee!!cccgggggggooooooggggggg]ccc4444eee	chr7:72017488-72017763(-)$1	275	89	129	15.1357
ccc[bb"""gggggggooooooggggggg333bb]ccc]b	chr5:36828835-36829107(+)$1	272	181	221	15.5831
=======####dddd[bblllbbdddd333==========	chr4:84152292-84152573(-)$1	281	107	147	14.5160
[ccc[ccc!!bb[ddddooooooddddbb]ccc]ccc333	chr14:69863190-69863472(-)$1	282	100	140	15.5127
ii####ccc####bbqqqqqqqqbb333ccc22iiiiiii	chr7:133643550-133643828(-)$1	278	8	48	11.9350
"""ffffff[ccccccooooooccc333ccc55555ffff	chr6:134418590-134418860(-)$1	270	176	216	13.1206
cc[dddd"""bb[bbbboooooobb333bb]bb]dddd]c	chr7:13620905-13621174(-)$1	269	69	109	13.7671
"""dddd[bb[a[cccooooooccca]bbdddd]ccc::c	chr10:80850008-80850296(+)$1	288	37	77	13.4940
e[bb[ggggggg[cccooooooccc]gggggggbbeeeee	chr2:90844843-90845120(+)$1	277	93	133	15.1940
eeffffff"""a[cccammmma]ccc]a4444ffffff]e	chr8:113568741-113569025(+)$1	284	173	213	13.0059

#otherMatches

#Seq PSSM
CGGGAAGGCAGAGGCCGUUGGCGAGCAGGCCCGGGGGCAC	chr5:140895564-140895849(+)$1	285	37	77	13.5603
GUGGGUUCAGUUGUCAACAGUGUGGCACUGACUGGUGUCC	chr2:180646301-180646569(-)$1	268	131	171	13.7105
UUUUGACUUUGCACAGGGCUUACUGUAAGUGUGUGGGAGG	chr13:99043616-99043931(+)$1	315	129	169	15.3758
UGUGGGCUGUGCCGCUGGUCUUGCAGCAGACCACCUCACC	chr14:99712283-99712565(+)$1	282	26	66	15.8902
UAAUAAAACUGUUACAUAUUUUUAUAACUUUUAUUUUCUA	chr10:122452029-122452299(-)$1	270	4	44	14.8863
GACCCAAAUUGGAGGAGAGAGGUGAGCCUAUUGGGUCUUC	chr6:85416542-85416842(+)$1	300	152	192	17.7435
GAAAGUGGAGAGACAGCAAAGCGGAGGUCUGCCCGGGUCC	chr10:75207952-75208236(-)$1	284	153	193	14.6823
UUGUUCCCCGUGGCGUGGAGAAACUUCUUAGGGGACGAGG	chr1:39958237-39958520(+)$1	283	199	239	18.6500
GUGGCCGCCAUGAGCAACCUGGUGCCCCCUGUGGAGCUGG	chr2:174167206-174167482(+)$1	276	110	150	15.4898
UCUGGUGACCAGGUCACUUCUGGUAGCUGGUCAUCAUUUC	chr4:116957903-116958181(-)$1	278	231	271	14.8772
GGUAUGUGCCCCUGUCAUUGAAGAAUGUGGACAAGGUCCU	chr4:151597090-151597385(+)$1	295	122	162	13.3244
GUGCUGGGAAUCACCACUUCUCUGGUGUGUUUGCAGGAGC	chr14:65357258-65357547(+)$1	289	49	89	13.7622
GUGCAAGCAAAUGCCUUUAUUCAGGUAUGGGGGAGUGAAG	chr15:10416295-10416563(+)$1	268	152	192	15.5036
CGCAGACUGCGCACGGCCUACACCAACACGCAACUGCUGG	chr11:96214252-96214520(+)$1	268	49	89	14.6002
CCAGUUUGUAGUUACUGUGAAGUUUAUAUAAAUCAAUGCU	chr2:160795786-160796075(-)$1	289	231	271	13.5681
CGGCAGCGUGCCGGGUCAAGUUACCCGCGGCCCUGCCGGU	chr13:85428342-85428610(-)$1	268	186	226	12.7786
GAGUGGGGCCCUGACAGCUCGAAGGAUACGUGUCACUUCU	chr14:70066965-70067244(+)$1	279	39	79	11.8046
GAAAUCUAUUCUUGUGGUUAAGCAUCAAACUAUGGUUUUC	chr2:156002946-156003217(-)$1	271	188	228	15.1739
CAGGUGCUUAAGGGCCUUCCCGCCCGUGUAAGAAAGCACC	chr16:37511332-37511621(-)$1	289	194	234	14.3068
AGAAAGCUGCUGAACUAGAGCCAGAACAGCUGCUCGCCUG	chr13:76249094-76249378(+)$1	284	126	166	14.6846
CCAGGGUGGAGGAGGAGGAGGAGCGCUGCCAGUACCUGCA	chr15:77605464-77605743(-)$1	279	166	206	13.9164
CUGACUCUGGGCAAACGUUUGUGUUUGUGGAGUUGAGAUU	chr7:148599791-148600059(-)$1	268	202	242	14.3675
GGACAUUGUCAAGCUAAUUAAUGGACGGUACAAAGGACAA	chr6:142316853-142317130(-)$1	277	94	134	12.9452
GUGUCCCAGGGCAAGAGCCACCCUUUCAAGCCGGACGCCA	chr14:104865907-104866176(-)$1	269	166	206	13.4276
AGGGUGAGCGAACAGGAAGAUGCCGUGGAGGGACUGACCA	chr4:98404125-98404408(+)$1	283	73	113	15.9095
ACUUGGCUGAACUGGAGGAUUGUCUAGUUUUCCAGCUGAA	chr7:3658229-3658604(+)$1	375	206	246	13.7436
GCAGCCCAGGAGGGGCGCACCUGCCAGCCUGGCUGCUAUG	chr7:150743662-150743930(-)$1	268	161	201	16.9705
UAGGAAAUGCUUUGGAAAGUUUGUAACUCAUUUUCUGUUU	chr2:180999660-180999954(-)$1	294	69	109	12.5207
UGUGUCAUUCCCAGGGCUGAUACCCUGCACUGAAGUGAAA	chr12:74209655-74209931(-)$1	276	57	97	14.4472
AGGCCUCAGUUUCUGAAGAGCAUCAGAAAGAUGACGCUGG	chr7:6661651-6661928(-)$1	277	216	256	14.6796
GGAGUGUGCGCAGACCUAGGGUGGUUUGAAAAUACCGAUG	chr18:85150543-85150823(+)$1	280	114	154	14.3314
agAGGCCUGUGACCGUAGAGCUUUGGGGUCAUGGGUGUCG	chr1:75525657-75525930(+)$1	273	182	222	13.2639
UGGUGGCCGAGUUCUACAAUACGGUGAGGGCUUGGGCAGG	chr17:57121284-57121553(-)$1	269	119	159	14.7088
UAAACAUGCAGCUUAUUUGUAAAUGUCUGACUUCUUUCUA	chr13:38074831-38075100(-)$1	269	48	88	12.6462
GCAGGGGGGUGACCUGAAUGGGCAGGCGGAGUCUCCACUG	chr18:42388238-42388508(-)$1	270	149	189	13.2442
UUCACAGCGCAUUCCCUCAGGUGGGGAUGGGAAGACGCUG	chr13:115780236-115780511(-)$1	275	106	146	12.1800
GGAGACACAAGAGGAAAAUGACGAAUUCCGAAGGCGCAUC	chr3:94573756-94574039(-)$1	283	20	60	12.7177
GCACUGGGGUGUCAGAGGUCAUUCUCAUAUUCUCGAAGUG	chr1:95197961-95198238(-)$1	277	206	246	12.3450
GGUCAUGCAAGACGAGUCCUUCCCCGCAUGCAAGAUAGAA	chr13:100195671-100195942(-)$1	271	136	176	15.2979
AGCCACUCGCACUCUGCUCCCGGCACUCUGUGACUGGUGG	chr1:74486437-74486717(-)$1	280	218	258	14.2958
AAACAUUAUAAGAAACGUAAAGGUGACAUGGAUGAGCUGG	chrX:148462255-148462526(+)$1	271	96	136	14.6318
GUGCUGGGGGUGGUCGUGUUCUUGAGUGUCCCAGCAUCCG	chr14:56445096-56445373(+)$1	277	108	148	19.9587
gcggagaacgagaaggaAGAACUCAGCAAGUAAGGCCUGG	chr5:125549229-125549517(-)$1	288	187	227	14.8707
CUCACGCCCAGGAUCAAGGUUGGCCGGGAUUACGUACAGA	chr11:68577688-68577965(+)$1	277	108	148	13.1265
CUUCCCUGUCGGCCCCGACCGUGGGGCCGCGCACUCAGAA	chr7:72017488-72017763(-)$1	275	89	129	15.1357
CAAAAGAUCAGGGAAGCCAAAACUUUCCUCCCCUCUUGAC	chr5:36828835-36829107(+)$1	272	181	221	15.5831
ACCUGGAGGAACCAGACCAGAGGCUGGAAGUCCAGGUUUG	chr4:84152292-84152573(-)$1	281	107	147	14.5160
AGUCAGCCUUCAGUUGUAUCCGGACAGUGUGGCGGACCGA	chr14:69863190-69863472(-)$1	282	100	140	15.5127
AAGGAUGAGAAGUGGGCCCAUCACCUGACUCUGUUGCUCC	chr7:133643550-133643828(-)$1	278	8	48	11.9350
CAUUGUGGUAAACCCCGAGAAAGGGUAUGUUCCAAAGCCA	chr6:134418590-134418860(-)$1	270	176	216	13.1206
AGGAGCCGAACCCUGAGGACCCACUGAACAAGGAGGCUGC	chr7:13620905-13621174(-)$1	269	69	109	13.7671
AGGCCACAUGUGCAGGACCCUACCUCUCAGUGGACCCAGC	chr10:80850008-80850296(+)$1	288	37	77	13.4940
AGCAGCAGAUGCAGCAGAUCAGUGCAGCGUCUGUGUGGGG	chr2:90844843-90845120(+)$1	277	93	133	15.1940
AGGAGUGACUCGUAAGCACCUGUCUUCCCUUCUCACUCUC	chr8:113568741-113569025(+)$1	284	173	213	13.0059

#DB
((((...((....(((...)))..))...)))))))))).	chr5:140895564-140895849(+)$1	1	37	77	13.5603
.(((..(((((.((((......)))))))))))).)))).	chr2:180646301-180646569(-)$1	1	131	171	13.7105
((...((((...((((......))))))))....))))).	chr13:99043616-99043931(+)$1	1	129	169	15.3758
((.(((.((..(.((((......)))).)..)))))))))	chr14:99712283-99712565(+)$1	1	26	66	15.8902
.(((((((..((((.(......).))))))))))).))).	chr10:122452029-122452299(-)$1	1	4	44	14.8863
(((((((...((...(......)...))..))))))))).	chr6:85416542-85416842(+)$1	1	152	192	17.7435
((...(((..((((..(......)..))))..)))..)))	chr10:75207952-75208236(-)$1	1	153	193	14.6823
((((((((...((.((......)).))...))))))))))	chr1:39958237-39958520(+)$1	1	199	239	18.6500
.(((((((((((.(((......))).)...))))...)))	chr2:174167206-174167482(+)$1	1	110	150	15.4898
..((((((((((.(..(....)..).))))))))))...)	chr4:116957903-116958181(-)$1	1	231	271	14.8772
))).(((.((.(..((......))..).))))).(.((((	chr4:151597090-151597385(+)$1	1	122	162	13.3244
...(((.(((((((((......))))).)))).)))))))	chr14:65357258-65357547(+)$1	1	49	89	13.7622
.(.((..(..((((((......))))))..)....)).).	chr15:10416295-10416563(+)$1	1	152	192	15.5036
.((((..((((...((......))....)))).)))).))	chr11:96214252-96214520(+)$1	1	49	89	14.6002
...(((((((...(((....)))...)))))))....)))	chr2:160795786-160796075(-)$1	1	231	271	13.5681
((((((.((..(((((......)))))..)).))))))))	chr13:85428342-85428610(-)$1	1	186	226	12.7786
((((((.(((((..........)))....)).))))))))	chr14:70066965-70067244(+)$1	1	39	79	11.8046
((((.((((..(((((......)).)))...)))).))))	chr2:156002946-156003217(-)$1	1	188	228	15.1739
(((((((((..((((......))))........)))))))	chr16:37511332-37511621(-)$1	1	194	234	14.3068
.(..(((.((((..((......))..)))).)))..).))	chr13:76249094-76249378(+)$1	1	126	166	14.6846
((.(((((..((.((.(......).)).))..)))))...	chr15:77605464-77605743(-)$1	1	166	206	13.9164
.(((((((..((((((......))))))))))))).))))	chr7:148599791-148600059(-)$1	1	202	242	14.3675
(..(.(((((...(((.....)))...).)))).)..)..	chr6:142316853-142317130(-)$1	1	94	134	12.9452
((((((...(((.((((.....))))...)))))))))).	chr14:104865907-104866176(-)$1	1	166	206	13.4276
..(((.(((...((((......)).))....).)).))).	chr4:98404125-98404408(+)$1	1	73	113	15.9095
..((((((((((((((......)))))))...))))))).	chr7:3658229-3658604(+)$1	1	206	246	13.7436
((((((.(((...(((......)))..)))))))))).))	chr7:150743662-150743930(-)$1	1	161	201	16.9705
(((((((((..(((.((...)).)))..))))))))))..	chr2:180999660-180999954(-)$1	1	69	109	12.5207
(.(.(((((.((((((......)))))....).)))))..	chr12:74209655-74209931(-)$1	1	57	97	14.4472
..((.(((.(((((((......)))))))..))).)))))	chr7:6661651-6661928(-)$1	1	216	256	14.6796
)(.((((...((((((......))))))...)))))((((	chr18:85150543-85150823(+)$1	1	114	154	14.3314
.((.((((((((((.(((....))).)))))))))).)).	chr1:75525657-75525930(+)$1	1	182	222	13.2639
(..((.(((((((((((......)).))))))))).))..	chr17:57121284-57121553(-)$1	1	119	159	14.7088
.(((...((((..((((....)))).))).)...)))..)	chr13:38074831-38075100(-)$1	1	48	88	12.6462
(((((((((((.((((......))))))...))))).)).	chr18:42388238-42388508(-)$1	1	149	189	13.2442
....)))))(((((((......)))))))(((((((((((	chr13:115780236-115780511(-)$1	1	106	146	12.1800
(((..(.(....((((.........))))....).)..))	chr3:94573756-94574039(-)$1	1	20	60	12.7177
((((((((((((.((((....)))).)))))))...))))	chr1:95197961-95198238(-)$1	1	206	246	12.3450
.(((.((((.(.((.(......).))).)))).)))...)	chr13:100195671-100195942(-)$1	1	136	176	15.2979
(((((((.((((..((((...))))....))).).)))))	chr1:74486437-74486717(-)$1	1	218	258	14.2958
...(((.....(..((......))..))))..)))))...	chrX:148462255-148462526(+)$1	1	96	136	14.6318
(((((((((..(.(((......))).).))))))))))))	chr14:56445096-56445373(+)$1	1	108	148	19.9587
((((...((..(.((......))...)..))....))..)	chr5:125549229-125549517(-)$1	1	187	227	14.8707
...((((((.((.(((....))))))))....)))...))	chr11:68577688-68577965(+)$1	1	108	148	13.1265
((((..((((((((((......))))))).)))....)))	chr7:72017488-72017763(-)$1	1	89	129	15.1357
(((.((...(((((((......)))))))...)).))).)	chr5:36828835-36829107(+)$1	1	181	221	15.5831
(((((((....((((.((...))))))...))))))))))	chr4:84152292-84152573(-)$1	1	107	147	14.5160
.(((.(((..((.((((......)))))).))).)))...	chr14:69863190-69863472(-)$1	1	100	140	15.5127
((....(((....((........))...)))..)))))))	chr7:133643550-133643828(-)$1	1	8	48	11.9350
...((((((.((((((......)))...))).....))))	chr6:134418590-134418860(-)$1	1	176	216	13.1206
((.((((...((.((((......))...)).)).)))).)	chr7:13620905-13621174(-)$1	1	69	109	13.7671
...((((.((.(.(((......)))).)))))).)))..(	chr10:80850008-80850296(+)$1	1	37	77	13.4940
(.((.(((((((.(((......))).))))))))))))))	chr2:90844843-90845120(+)$1	1	93	133	15.1940
((((((((...(.((((....).))).)....)))))).)	chr8:113568741-113569025(+)$1	1	173	213	13.0059

#PSSM
= : 0.16	[ : 0.12	e : 0.11	c : 0.09	! : 0.07	g : 0.07	i : 0.05	# : 0.05	" : 0.05	$ : 0.03	d : 0.03	& : 0.01	f : 0.01	a : 0.01	: : 0.01	b : 0.01	r : 0.01	
= : 0.16	c : 0.16	g : 0.11	e : 0.09	# : 0.05	a : 0.05	! : 0.05	" : 0.05	i : 0.03	f : 0.03	$ : 0.03	d : 0.03	[ : 0.03	: : 0.01	b : 0.01	r : 0.01	
= : 0.16	g : 0.12	c : 0.11	" : 0.09	[ : 0.09	b : 0.09	# : 0.07	f : 0.05	e : 0.05	! : 0.05	i : 0.01	d : 0.01	a : 0.01	r : 0.01	
= : 0.16	c : 0.16	g : 0.12	b : 0.11	f : 0.07	d : 0.07	e : 0.05	[ : 0.05	" : 0.03	! : 0.03	i : 0.01	: : 0.01	a : 0.01	r : 0.01	# : 0.01	
= : 0.16	c : 0.12	g : 0.12	[ : 0.11	" : 0.09	f : 0.07	d : 0.07	e : 0.07	! : 0.05	b : 0.05	i : 0.01	# : 0.01	
c : 0.16	= : 0.16	g : 0.14	d : 0.12	! : 0.07	f : 0.07	e : 0.07	" : 0.05	[ : 0.03	i : 0.01	a : 0.01	b : 0.01	# : 0.01	
c : 0.14	= : 0.14	d : 0.12	[ : 0.11	g : 0.11	" : 0.09	e : 0.09	f : 0.05	i : 0.03	! : 0.03	b : 0.01	$ : 0.01	
d : 0.12	c : 0.12	b : 0.11	g : 0.11	= : 0.11	e : 0.09	" : 0.09	[ : 0.07	a : 0.05	f : 0.03	i : 0.01	$ : 0.01	# : 0.01	
d : 0.14	b : 0.12	" : 0.12	! : 0.11	= : 0.09	c : 0.09	e : 0.07	g : 0.07	a : 0.03	# : 0.03	[ : 0.01	i : 0.01	$ : 0.01	f : 0.01	
! : 0.24	g : 0.14	" : 0.12	c : 0.09	# : 0.07	d : 0.07	[ : 0.07	b : 0.05	= : 0.03	e : 0.01	a : 0.01	i : 0.01	$ : 0.01	
" : 0.12	! : 0.12	g : 0.12	d : 0.11	b : 0.11	c : 0.09	# : 0.07	f : 0.05	= : 0.03	[ : 0.03	a : 0.03	e : 0.01	i : 0.01	$ : 0.01	
a : 0.14	g : 0.12	" : 0.11	b : 0.11	c : 0.11	d : 0.09	# : 0.05	[ : 0.05	e : 0.05	f : 0.05	= : 0.03	i : 0.01	! : 0.01	
[ : 0.25	d : 0.14	" : 0.09	! : 0.09	g : 0.09	b : 0.05	e : 0.05	f : 0.05	c : 0.05	# : 0.03	s : 0.01	= : 0.01	i : 0.01	
c : 0.24	d : 0.24	b : 0.11	g : 0.09	! : 0.07	e : 0.05	f : 0.05	" : 0.03	[ : 0.01	a : 0.01	s : 0.01	= : 0.01	i : 0.01	
d : 0.22	c : 0.20	b : 0.20	g : 0.09	[ : 0.07	e : 0.05	f : 0.05	! : 0.03	" : 0.01	s : 0.01	i : 0.01	
c : 0.22	d : 0.18	b : 0.18	g : 0.09	a : 0.05	e : 0.05	f : 0.05	! : 0.03	o : 0.03	[ : 0.03	s : 0.01	q : 0.01	
o : 0.59	d : 0.11	a : 0.07	b : 0.07	m : 0.03	l : 0.01	s : 0.01	n : 0.01	c : 0.01	r : 0.01	q : 0.01	
o : 0.70	m : 0.11	l : 0.03	n : 0.03	s : 0.01	c : 0.01	r : 0.01	d : 0.01	b : 0.01	q : 0.01	
o : 0.70	m : 0.12	l : 0.07	n : 0.03	s : 0.01	r : 0.01	q : 0.01	
o : 0.70	m : 0.12	l : 0.05	n : 0.03	c : 0.01	s : 0.01	r : 0.01	q : 0.01	
o : 0.70	m : 0.09	c : 0.05	n : 0.03	l : 0.03	s : 0.01	b : 0.01	r : 0.01	q : 0.01	
o : 0.66	c : 0.07	d : 0.07	b : 0.05	a : 0.03	s : 0.01	n : 0.01	m : 0.01	r : 0.01	q : 0.01	
c : 0.20	b : 0.16	d : 0.14	o : 0.11	g : 0.09	a : 0.05	e : 0.05	f : 0.05	2 : 0.03	] : 0.03	r : 0.01	q : 0.01	
d : 0.20	b : 0.20	c : 0.20	g : 0.09	3 : 0.05	e : 0.05	f : 0.05	2 : 0.03	] : 0.03	a : 0.03	r : 0.01	
d : 0.22	c : 0.18	b : 0.11	g : 0.09	3 : 0.07	2 : 0.07	] : 0.07	e : 0.05	f : 0.05	a : 0.01	4 : 0.01	r : 0.01	
d : 0.16	] : 0.14	3 : 0.12	b : 0.09	2 : 0.09	g : 0.09	c : 0.07	e : 0.05	f : 0.05	4 : 0.05	8 : 0.01	a : 0.01	
d : 0.14	g : 0.14	3 : 0.11	a : 0.11	b : 0.09	e : 0.07	f : 0.05	4 : 0.05	c : 0.05	= : 0.03	2 : 0.03	] : 0.03	8 : 0.01	i : 0.01	
3 : 0.14	g : 0.14	] : 0.11	d : 0.09	4 : 0.09	c : 0.09	b : 0.07	f : 0.05	2 : 0.05	= : 0.03	a : 0.03	e : 0.01	8 : 0.01	i : 0.01	
g : 0.18	3 : 0.14	d : 0.12	4 : 0.11	b : 0.09	c : 0.09	2 : 0.07	= : 0.07	e : 0.01	a : 0.01	8 : 0.01	] : 0.01	i : 0.01	
d : 0.14	3 : 0.14	c : 0.12	b : 0.11	= : 0.09	g : 0.09	4 : 0.09	2 : 0.07	] : 0.05	e : 0.01	8 : 0.01	i : 0.01	
c : 0.14	= : 0.12	4 : 0.11	g : 0.11	d : 0.11	2 : 0.09	3 : 0.09	b : 0.05	i : 0.03	a : 0.03	] : 0.03	e : 0.01	8 : 0.01	
c : 0.16	d : 0.14	= : 0.12	4 : 0.11	g : 0.11	2 : 0.07	3 : 0.05	b : 0.03	i : 0.03	] : 0.03	a : 0.03	8 : 0.01	e : 0.01	5 : 0.01	
= : 0.14	c : 0.14	g : 0.14	d : 0.11	] : 0.11	4 : 0.07	b : 0.05	e : 0.05	i : 0.03	f : 0.03	8 : 0.01	3 : 0.01	2 : 0.01	5 : 0.01	
= : 0.16	c : 0.14	4 : 0.09	g : 0.09	d : 0.09	e : 0.07	] : 0.07	i : 0.05	b : 0.05	f : 0.03	3 : 0.03	a : 0.03	: : 0.01	5 : 0.01	
= : 0.16	c : 0.14	] : 0.09	e : 0.09	g : 0.09	d : 0.09	4 : 0.07	i : 0.05	3 : 0.03	a : 0.03	f : 0.03	b : 0.03	2 : 0.01	5 : 0.01	
= : 0.18	c : 0.12	e : 0.11	] : 0.09	d : 0.07	2 : 0.05	3 : 0.05	b : 0.05	g : 0.05	i : 0.03	4 : 0.03	f : 0.03	a : 0.03	[ : 0.01	5 : 0.01	
= : 0.18	e : 0.11	c : 0.11	b : 0.09	f : 0.09	d : 0.07	3 : 0.07	g : 0.07	2 : 0.05	i : 0.03	4 : 0.03	] : 0.03	a : 0.01	
= : 0.18	e : 0.11	f : 0.11	c : 0.09	3 : 0.09	b : 0.07	] : 0.07	d : 0.05	g : 0.05	2 : 0.05	i : 0.03	a : 0.01	6 : 0.01	: : 0.01	
= : 0.16	g : 0.11	e : 0.09	c : 0.09	b : 0.09	2 : 0.09	f : 0.07	3 : 0.07	] : 0.05	d : 0.03	i : 0.03	: : 0.03	a : 0.01	6 : 0.01	
= : 0.12	] : 0.11	c : 0.11	f : 0.09	g : 0.09	b : 0.09	e : 0.09	2 : 0.09	: : 0.07	3 : 0.03	d : 0.01	6 : 0.01	a : 0.01	i : 0.01	

#score	776.1860720038311
#seq	54
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_CDS_m2_run2.txt

#BEAR
cccqqqqqqqqcccI	chr13:100205071-100205280(-)$1	209	103	118	12.5802
eeeqqqqqqqqeeee	chr4:94236341-94236545(-)$1	204	117	132	12.5689
dddqqqqqqqqdddd	chr12:8943424-8943641(+)$1	217	174	189	13.1867
eeeqqqqqqqqeeee	chr9:40610849-40611059(+)$1	210	43	58	12.5689
bbaqqqqqqqqa]bb	chr2:80388900-80389116(-)$1	216	80	95	11.9099
!bbqqqqqqqqbb22	chr11:120569892-120570099(+)$1	207	104	119	12.6271
hhaqqqqqqqqa]hh	chr15:36408977-36409190(-)$1	213	185	200	12.2573
!bbqqqqqqqqbb33	chr7:3637294-3637512(-)$1	218	73	88	12.9943
dddqqqqqqqqdddd	chr7:17546503-17546710(+)$1	207	165	180	13.1867
cccqqqqqqqqccc]	chr7:107647288-107647488(+)$1	200	70	85	14.0113
cccqqqqqqqqccc4	chr7:31307938-31308139(-)$1	201	49	64	13.9804
dddqqqqqqqqdddd	chr12:112865977-112866201(+)$1	224	44	59	13.1867
dddqqqqqqqqdddd	chr9:13425868-13426071(+)$1	203	172	187	13.1867
fffqqqqqqqqffff	chr14:18859174-18859389(+)$1	215	135	150	12.0763
dddqqqqqqqqdddd	chr7:30162961-30163190(-)$1	229	10	25	13.1867
cccqqqqqqqqccc]	chr7:52381780-52381983(-)$1	203	167	182	14.0113
eeeqqqqqqqqeeee	chr9:108958464-108958665(+)$1	201	165	180	12.5689
cccqqqqqqqqccc3	chr14:71096362-71096583(-)$1	221	69	84	14.0557
eeeqqqqqqqqeeee	chr7:25766741-25766941(-)$1	200	37	52	12.5689
cccqqqqqqqqccc:	chr5:3847365-3847583(+)$1	218	17	32	13.1925
dddqqqqqqqqdddd	chr6:100754529-100754744(+)$1	215	14	29	13.1867
eeeqqqqqqqqeeee	chr2:102596159-102596362(+)$1	203	30	45	12.5689
bbbqqqqqqqqbb22	chr10:57242880-57243082(-)$1	202	111	126	12.3043
eeeqqqqqqqqeeee	chrX:132280683-132280895(+)$1	212	18	33	12.5689
iiiqqqqqqqqiiii	chr4:41068446-41068659(-)$1	213	142	157	12.8121
cccqqqqqqqqccc]	chr17:81788150-81788352(-)$1	202	93	108	14.0113
dddqqqqqqqqdddd	chr9:61762112-61762333(-)$1	221	89	104	13.1867
cccqqqqqqqqccc:	chr2:180821409-180821611(-)$1	202	125	140	13.1925
cccqqqqqqqqcccc	chr12:34051911-34052114(+)$1	203	92	107	13.8304
cccqqqqqqqqccc]	chr11:31830082-31830290(+)$1	208	58	73	14.0113
cccqqqqqqqqccce	chr11:66913343-66913562(+)$1	219	71	86	13.8309
dddqqqqqqqqdddd	chr8:72847004-72847227(+)$1	223	126	141	13.1867
!bbqqqqqqqqbb44	chr3:54703255-54703460(-)$1	205	108	123	12.8878
dddqqqqqqqqdddd	chr17:87226862-87227071(+)$1	209	65	80	13.1867
eeeqqqqqqqqeeee	chr8:125916966-125917166(+)$1	200	15	30	12.5689
fffqqqqqqqqffff	chr14:55527021-55527222(+)$1	201	161	176	12.0763
eeeqqqqqqqqeeee	chr11:75356739-75356963(+)$1	224	42	57	12.5689
cccqqqqqqqqccc7	chr17:45705101-45705310(-)$1	209	105	120	13.4656
!bbqqqqqqqqbb]e	chr12:53618886-53619091(+)$1	205	8	23	12.7147
cccqqqqqqqqccc]	chr2:20793242-20793446(+)$1	204	104	119	14.0113
cccqqqqqqqqccc:	chr2:121259210-121259417(+)$1	207	65	80	13.1925
c[aqqqqqqqqaccc	chr5:14678185-14678398(+)$1	213	167	182	13.2875
[bbqqqqqqqqbb22	chr14:22602843-22603045(+)$1	202	112	127	12.5975
cccqqqqqqqqccc]	chr15:98427531-98427759(-)$1	228	92	107	14.0113
cccqqqqqqqqccc2	chr11:109528873-109529073(+)$1	200	175	190	13.9241
cccqqqqqqqqccc2	chr9:113820494-113820696(+)$1	202	57	72	13.9241
eeeqqqqqqqqeeee	chr4:133276481-133276682(-)$1	201	144	159	12.5689
[bbqqqqqqqqbb]d	chr15:77746094-77746327(-)$1	233	60	75	12.7143
cccqqqqqqqqccc]	chr12:25608984-25609195(-)$1	211	62	77	14.0113
dddqqqqqqqqdddd	chrX:55287496-55287731(+)$1	235	181	196	13.1867
gggqqqqqqqqgggg	chr13:8885112-8885332(+)$1	220	198	213	12.7403
cccqqqqqqqqcccb	chr5:143665395-143665598(-)$1	203	162	177	13.5878
cccqqqqqqqqccc2	chrX:148315107-148315308(+)$1	201	63	78	13.9241
cccqqqqqqqqccc:	chr9:28804002-28804231(-)$1	229	173	188	13.1925
cccqqqqqqqqccc2	chr18:64661359-64661568(-)$1	209	78	93	13.9241
cccqqqqqqqqccc]	chr2:91015754-91015958(-)$1	204	63	78	14.0113
dddqqqqqqqqdddd	chr15:76683570-76683788(-)$1	218	178	193	13.1867
cccqqqqqqqqccc:	chr5:131950837-131951042(-)$1	205	84	99	13.1925
cccqqqqqqqqccc:	chr3:94970860-94971077(-)$1	217	200	215	13.1925
!bbqqqqqqqqbb22	chr4:135107868-135108084(-)$1	216	171	186	12.6271
dddqqqqqqqqdddd	chr1:75471489-75471691(-)$1	202	58	73	13.1867
[bbqqqqqqqqbb]c	chr12:8992445-8992669(+)$1	224	107	122	12.6845
[bbqqqqqqqqbb]a	chr1:164628098-164628303(+)$1	205	108	123	12.7269
cccqqqqqqqqccc3	chr1:174242589-174242799(+)$1	210	22	37	14.0557
hbbqqqqqqqqbba!	chr15:101947159-101947365(-)$1	206	111	126	12.2709
dddqqqqqqqqdddd	chr5:143535406-143535610(-)$1	204	116	131	13.1867
"bbqqqqqqqqbb]c	chr2:28085035-28085254(+)$1	219	72	87	12.5976
dddqqqqqqqqdddd	chr7:52084501-52084712(+)$1	211	40	55	13.1867
dddqqqqqqqqdddd	chr18:50054596-50054802(+)$1	206	166	181	13.1867
cccqqqqqqqqccc3	chr10:17813589-17813790(+)$1	201	141	156	14.0557
dddqqqqqqqqdddd	chr6:124696336-124696540(-)$1	204	136	151	13.1867
cccqqqqqqqqccc:	chr7:20281563-20281764(-)$1	201	118	133	13.1925

#otherMatches

#Seq PSSM
GCUGGAAGAGGAGCG	chr13:100205071-100205280(-)$1	209	103	118	12.5802
CUUUGUUAGUCAGGC	chr4:94236341-94236545(-)$1	204	117	132	12.5689
CAGGUUAACUACUGU	chr12:8943424-8943641(+)$1	217	174	189	13.1867
UGGAACUAUUGCUGG	chr9:40610849-40611059(+)$1	210	43	58	12.5689
GUCUCAUCAGUGCAC	chr2:80388900-80389116(-)$1	216	80	95	11.9099
UGCACUUUGGAGCUG	chr11:120569892-120570099(+)$1	207	104	119	12.6271
CUGGGGAGAGGCAAG	chr15:36408977-36409190(-)$1	213	185	200	12.2573
CUCUUCUACAUGAUC	chr7:3637294-3637512(-)$1	218	73	88	12.9943
GUGAGCUUGGGCACU	chr7:17546503-17546710(+)$1	207	165	180	13.1867
ACCACAGCGCAGGUC	chr7:107647288-107647488(+)$1	200	70	85	14.0113
ACCGCUCCACAGGUC	chr7:31307938-31308139(-)$1	201	49	64	13.9804
UCAGCAAAUCAUGAA	chr12:112865977-112866201(+)$1	224	44	59	13.1867
GCAAAAGAUCAUGCU	chr9:13425868-13426071(+)$1	203	172	187	13.1867
CUCUUCUGUCUGGGU	chr14:18859174-18859389(+)$1	215	135	150	12.0763
ucccaagugcuggag	chr7:30162961-30163190(-)$1	229	10	25	13.1867
GCCUCAAGACUGGCA	chr7:52381780-52381983(-)$1	203	167	182	14.0113
GGUUCACCCAUGCCG	chr9:108958464-108958665(+)$1	201	165	180	12.5689
AAGAAUCUGAACUUG	chr14:71096362-71096583(-)$1	221	69	84	14.0557
UUUGACAACCUGAAG	chr7:25766741-25766941(-)$1	200	37	52	12.5689
cuguaaucauucagu	chr5:3847365-3847583(+)$1	218	17	32	13.1925
GUACUACCCUCUGCA	chr6:100754529-100754744(+)$1	215	14	29	13.1867
GGGCAUCUUUCUCCC	chr2:102596159-102596362(+)$1	203	30	45	12.5689
UGCUAUUCUUUGUCU	chr10:57242880-57243082(-)$1	202	111	126	12.3043
UUUAAAAAACCAAAU	chrX:132280683-132280895(+)$1	212	18	33	12.5689
CCUGGUACCGAGGGC	chr4:41068446-41068659(-)$1	213	142	157	12.8121
ACAGUUCAAAGUGUC	chr17:81788150-81788352(-)$1	202	93	108	14.0113
GUCUACAGCAUGGCU	chr9:61762112-61762333(-)$1	221	89	104	13.1867
UAGUAUUUCUUCUGU	chr2:180821409-180821611(-)$1	202	125	140	13.1925
UGCUCUCAGACGCAG	chr12:34051911-34052114(+)$1	203	92	107	13.8304
GUUUUCUAAUCAACA	chr11:31830082-31830290(+)$1	208	58	73	14.0113
CUGACCUCACGCAGC	chr11:66913343-66913562(+)$1	219	71	86	13.8309
AACAUCUAUUGGUUC	chr8:72847004-72847227(+)$1	223	126	141	13.1867
UGCUGAUCAUUGCUC	chr3:54703255-54703460(-)$1	205	108	123	12.8878
CUCAUGCCAGAGAGC	chr17:87226862-87227071(+)$1	209	65	80	13.1867
CAGCAUUUCCUCUGU	chr8:125916966-125917166(+)$1	200	15	30	12.5689
GAGGACAGGUAUUCU	chr14:55527021-55527222(+)$1	201	161	176	12.0763
GGCUCCUUCCUGCUC	chr11:75356739-75356963(+)$1	224	42	57	12.5689
AUCUACCGCAUGAUU	chr17:45705101-45705310(-)$1	209	105	120	13.4656
AAGAAACAUGCCUCA	chr12:53618886-53619091(+)$1	205	8	23	12.7147
GCAGGAAUAUGUGCA	chr2:20793242-20793446(+)$1	204	104	119	14.0113
UCCUUGAUGCUGGAC	chr2:121259210-121259417(+)$1	207	65	80	13.1925
AACUAAAAUAUGUGC	chr5:14678185-14678398(+)$1	213	167	182	13.2875
UGCUUUACCAUGUUU	chr14:22602843-22603045(+)$1	202	112	127	12.5975
CGGGAUUUAUGCCGC	chr15:98427531-98427759(-)$1	228	92	107	14.0113
CCAUUUUUCAUUGGG	chr11:109528873-109529073(+)$1	200	175	190	13.9241
GCCUCCGUAUUGGCU	chr9:113820494-113820696(+)$1	202	57	72	13.9241
CUGCAUAUCCUCAGC	chr4:133276481-133276682(-)$1	201	144	159	12.5689
GCUAGCCAUCAAGAA	chr15:77746094-77746327(-)$1	233	60	75	12.7143
AUAAUCAAAGAUAUA	chr12:25608984-25609195(-)$1	211	62	77	14.0113
CAGCCACAACCCUGG	chrX:55287496-55287731(+)$1	235	181	196	13.1867
CUGAGGUGAUGCGGU	chr13:8885112-8885332(+)$1	220	198	213	12.7403
CAAAACCUAACUUGC	chr5:143665395-143665598(-)$1	203	162	177	13.5878
GCUAGAUCAACAGCU	chrX:148315107-148315308(+)$1	201	63	78	13.9241
UGCAAAAUGAAGCAA	chr9:28804002-28804231(-)$1	229	173	188	13.1925
AUUAAUGAACCAAUC	chr18:64661359-64661568(-)$1	209	78	93	13.9241
CCAUACAUCAUUGGA	chr2:91015754-91015958(-)$1	204	63	78	14.0113
acuaucagaaaaguc	chr15:76683570-76683788(-)$1	218	178	193	13.1867
CUGCCCAACCACAGC	chr5:131950837-131951042(-)$1	205	84	99	13.1925
UCCUACCAGAUGGAA	chr3:94970860-94971077(-)$1	217	200	215	13.1925
UCAGUAAACAGUGGA	chr4:135107868-135108084(-)$1	216	171	186	12.6271
GCUGUCGCCAGAGCG	chr1:75471489-75471691(-)$1	202	58	73	13.1867
GCUUUGACAAUGGGA	chr12:8992445-8992669(+)$1	224	107	122	12.6845
Gggaacuggagcugg	chr1:164628098-164628303(+)$1	205	108	123	12.7269
GGCCCCCCAGAGCCC	chr1:174242589-174242799(+)$1	210	22	37	14.0557
UGUGCCAGUUGACGU	chr15:101947159-101947365(-)$1	206	111	126	12.2709
CAGCCCACCACCUGC	chr5:143535406-143535610(-)$1	204	116	131	13.1867
AUCCCCUUCCAGAAC	chr2:28085035-28085254(+)$1	219	72	87	12.5976
GCUACACAGCCAGCU	chr7:52084501-52084712(+)$1	211	40	55	13.1867
AUGAUAUUCUACAUG	chr18:50054596-50054802(+)$1	206	166	181	13.1867
GCAUUUUUGUUUGCU	chr10:17813589-17813790(+)$1	201	141	156	14.0557
CCCCAUCCCCAGGGU	chr6:124696336-124696540(-)$1	204	136	151	13.1867
CUUGCUUAAUAAAGA	chr7:20281563-20281764(-)$1	201	118	133	13.1925

#DB
(((........))))	chr13:100205071-100205280(-)$1	1	103	118	12.5802
(((........))))	chr4:94236341-94236545(-)$1	1	117	132	12.5689
(((........))))	chr12:8943424-8943641(+)$1	1	174	189	13.1867
(((........))))	chr9:40610849-40611059(+)$1	1	43	58	12.5689
(((........).))	chr2:80388900-80389116(-)$1	1	80	95	11.9099
.((........))..	chr11:120569892-120570099(+)$1	1	104	119	12.6271
(((........).))	chr15:36408977-36409190(-)$1	1	185	200	12.2573
.((........))..	chr7:3637294-3637512(-)$1	1	73	88	12.9943
(((........))))	chr7:17546503-17546710(+)$1	1	165	180	13.1867
(((........))).	chr7:107647288-107647488(+)$1	1	70	85	14.0113
(((........))).	chr7:31307938-31308139(-)$1	1	49	64	13.9804
(((........))))	chr12:112865977-112866201(+)$1	1	44	59	13.1867
(((........))))	chr9:13425868-13426071(+)$1	1	172	187	13.1867
(((........))))	chr14:18859174-18859389(+)$1	1	135	150	12.0763
(((........))))	chr7:30162961-30163190(-)$1	1	10	25	13.1867
(((........))).	chr7:52381780-52381983(-)$1	1	167	182	14.0113
(((........))))	chr9:108958464-108958665(+)$1	1	165	180	12.5689
(((........))).	chr14:71096362-71096583(-)$1	1	69	84	14.0557
(((........))))	chr7:25766741-25766941(-)$1	1	37	52	12.5689
(((........))).	chr5:3847365-3847583(+)$1	1	17	32	13.1925
(((........))))	chr6:100754529-100754744(+)$1	1	14	29	13.1867
(((........))))	chr2:102596159-102596362(+)$1	1	30	45	12.5689
(((........))..	chr10:57242880-57243082(-)$1	1	111	126	12.3043
(((........))))	chrX:132280683-132280895(+)$1	1	18	33	12.5689
(((........))))	chr4:41068446-41068659(-)$1	1	142	157	12.8121
(((........))).	chr17:81788150-81788352(-)$1	1	93	108	14.0113
(((........))))	chr9:61762112-61762333(-)$1	1	89	104	13.1867
(((........))).	chr2:180821409-180821611(-)$1	1	125	140	13.1925
(((........))))	chr12:34051911-34052114(+)$1	1	92	107	13.8304
(((........))).	chr11:31830082-31830290(+)$1	1	58	73	14.0113
(((........))))	chr11:66913343-66913562(+)$1	1	71	86	13.8309
(((........))))	chr8:72847004-72847227(+)$1	1	126	141	13.1867
.((........))..	chr3:54703255-54703460(-)$1	1	108	123	12.8878
(((........))))	chr17:87226862-87227071(+)$1	1	65	80	13.1867
(((........))))	chr8:125916966-125917166(+)$1	1	15	30	12.5689
(((........))))	chr14:55527021-55527222(+)$1	1	161	176	12.0763
(((........))))	chr11:75356739-75356963(+)$1	1	42	57	12.5689
(((........))).	chr17:45705101-45705310(-)$1	1	105	120	13.4656
.((........)).)	chr12:53618886-53619091(+)$1	1	8	23	12.7147
(((........))).	chr2:20793242-20793446(+)$1	1	104	119	14.0113
(((........))).	chr2:121259210-121259417(+)$1	1	65	80	13.1925
(.(........))))	chr5:14678185-14678398(+)$1	1	167	182	13.2875
.((........))..	chr14:22602843-22603045(+)$1	1	112	127	12.5975
(((........))).	chr15:98427531-98427759(-)$1	1	92	107	14.0113
(((........))).	chr11:109528873-109529073(+)$1	1	175	190	13.9241
(((........))).	chr9:113820494-113820696(+)$1	1	57	72	13.9241
(((........))))	chr4:133276481-133276682(-)$1	1	144	159	12.5689
.((........)).)	chr15:77746094-77746327(-)$1	1	60	75	12.7143
(((........))).	chr12:25608984-25609195(-)$1	1	62	77	14.0113
(((........))))	chrX:55287496-55287731(+)$1	1	181	196	13.1867
(((........))))	chr13:8885112-8885332(+)$1	1	198	213	12.7403
(((........))))	chr5:143665395-143665598(-)$1	1	162	177	13.5878
(((........))).	chrX:148315107-148315308(+)$1	1	63	78	13.9241
(((........))).	chr9:28804002-28804231(-)$1	1	173	188	13.1925
(((........))).	chr18:64661359-64661568(-)$1	1	78	93	13.9241
(((........))).	chr2:91015754-91015958(-)$1	1	63	78	14.0113
(((........))))	chr15:76683570-76683788(-)$1	1	178	193	13.1867
(((........))).	chr5:131950837-131951042(-)$1	1	84	99	13.1925
(((........))).	chr3:94970860-94971077(-)$1	1	200	215	13.1925
.((........))..	chr4:135107868-135108084(-)$1	1	171	186	12.6271
(((........))))	chr1:75471489-75471691(-)$1	1	58	73	13.1867
.((........)).)	chr12:8992445-8992669(+)$1	1	107	122	12.6845
.((........)).)	chr1:164628098-164628303(+)$1	1	108	123	12.7269
(((........))).	chr1:174242589-174242799(+)$1	1	22	37	14.0557
)((........))(.	chr15:101947159-101947365(-)$1	1	111	126	12.2709
(((........))))	chr5:143535406-143535610(-)$1	1	116	131	13.1867
.((........)).)	chr2:28085035-28085254(+)$1	1	72	87	12.5976
(((........))))	chr7:52084501-52084712(+)$1	1	40	55	13.1867
(((........))))	chr18:50054596-50054802(+)$1	1	166	181	13.1867
(((........))).	chr10:17813589-17813790(+)$1	1	141	156	14.0557
(((........))))	chr6:124696336-124696540(-)$1	1	136	151	13.1867
(((........))).	chr7:20281563-20281764(-)$1	1	118	133	13.1925

#PSSM
c : 0.40	d : 0.22	e : 0.12	! : 0.06	[ : 0.05	b : 0.02	h : 0.02	f : 0.02	i : 0.01	g : 0.01	" : 0.01	
c : 0.38	d : 0.22	b : 0.18	e : 0.12	f : 0.02	h : 0.01	i : 0.01	[ : 0.01	g : 0.01	
c : 0.38	d : 0.22	b : 0.16	e : 0.12	a : 0.04	f : 0.02	i : 0.01	g : 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 : 0.38	d : 0.22	b : 0.16	e : 0.12	a : 0.04	f : 0.02	i : 0.01	g : 0.01	
c : 0.40	d : 0.22	b : 0.16	e : 0.12	] : 0.02	f : 0.02	i : 0.01	g : 0.01	
c : 0.40	d : 0.22	e : 0.12	] : 0.06	2 : 0.05	f : 0.02	b : 0.01	h : 0.01	3 : 0.01	i : 0.01	4 : 0.01	g : 0.01	a : 0.01	
d : 0.23	e : 0.15	2 : 0.11	] : 0.11	: : 0.09	3 : 0.05	c : 0.05	b : 0.02	4 : 0.02	f : 0.02	I : 0.01	h : 0.01	i : 0.01	7 : 0.01	g : 0.01	a : 0.01	! : 0.01	

#score	946.5944588975196
#seq	72
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_CDS_m1_run2.txt

#BEAR
eeeee####==========lll==========4444e	chr9:58488395-58488825(+)$1	430	375	412	16.4921
"ggggggg$$$$$ggggggglllgggggggggggggg	chr2:24513769-24514130(-)$1	361	265	302	13.0317
=========dddd"""ddddllldddd333dddd444	chr5:122906860-122907274(-)$1	414	37	74	13.1790
eeiiiiiiiii!!arrrrrrrrra22iiiiiiiii44	chr9:24286327-24286556(-)$1	229	116	153	15.9976
Giiiiiiiii"""ddddooooooddddiiiiiiiii:	chr8:26941573-26941858(-)$1	285	13	50	16.0190
ffff[bb[ccc####cccooooooccc333cccbbff	chr9:40153367-40153855(-)$1	488	330	367	13.0892
cc]ccciiiiiiiii[cccmmmmccc]iiiiiiiiiD	chr2:5812064-5812507(-)$1	443	384	421	15.0530
!!iiiiiiiii$$$$$bbmmmmbb333iiiiiiiii2	chr17:69633228-69633612(+)$1	384	18	55	15.2592
ddd[============lll============]dddd:	chr17:23960569-23960868(+)$1	299	1	38	14.2001
"""bb!!ggggggg[cccooooooccc]ggggggg22	chr11:121323012-121323332(+)$1	320	270	307	15.6612
[==========[aeeeeemmmmeeeee22a]======	chr17:66321492-66321809(-)$1	317	176	213	15.2745
bbb!!iiiiiiiii[a[bblllbb]a]iiiiiiiii5	chr6:71460053-71460389(+)$1	336	18	55	15.4409
bb[ccc[ggggggg[cccnnnnnccc333gggggggc	chr6:124713638-124713981(-)$1	343	203	240	14.7714
ii$$$$$===========oooooo===========77	chr2:164817903-164818295(+)$1	392	200	237	18.3796
ggggggg####ccccccooooooccc]cccggggggg	chr13:104676280-104676638(-)$1	358	160	197	15.1579
bbccc[===========oooooo===========]cc	chr8:75216954-75217272(+)$1	318	122	159	19.5181
hhhh=============oooooo=============8	chr7:71879400-71879781(+)$1	381	219	256	19.8079
=====[============qqqqqqqq===========	chr6:73213895-73214266(+)$1	371	217	254	17.4166
$$$$$==========[apppppppa]==========d	chr10:127521992-127522358(+)$1	366	287	324	15.0349
a[a[a[a[a[a[a[a[arrrrrrrrra]a]a]a]a]a	chr11:75451604-75452086(+)$1	482	287	324	13.8258
ggggggg[a!!gggggggnnnnnggggggg22agggg	chr4:134481586-134482049(+)$1	463	240	277	13.6933
cc"""==========[aqqqqqqqqa==========5	chr2:90403875-90404326(-)$1	451	94	131	16.1206
[===========[ccc[bbmmmmbb22ccc=======	chr6:143015401-143015813(-)$1	412	120	157	16.5204
ggg[ccc[ccc[ccc[cccmmmmccc]ccc333ccc2	chr7:38781417-38781808(-)$1	391	251	288	13.0031
!iiiiiiiii[iiiiiiiiillliiiiiiiii]iiii	chr4:24825713-24826196(+)$1	483	307	344	17.9763
!==========="""cccmmmmccc4444========	chr3:152020918-152021299(+)$1	381	310	347	18.5180
ee[==========[a[bbnnnnnbb22a]========	chr19:44377492-44377905(+)$1	413	177	214	17.3310
bccc[aggggggg!!ddddmmmmdddd]ggggggg]a	chr19:45871213-45871631(-)$1	418	360	397	12.9771
bb::::============oooooo============B	chr3:126713492-126713921(-)$1	429	248	285	14.8705
=============!!cccpppppppccc4444=====	chr1:182878911-182879275(+)$1	364	151	188	14.8465
iiii####==========oooooo==========22i	chr4:126289475-126289913(+)$1	438	149	186	19.6277
====================333bb22iiiiiiiii]	chr1:184812994-184813414(+)$1	420	214	251	16.5718
ggggggg[bb[gggggggooooooggggggg22bb]g	chr5:122910047-122910436(-)$1	389	97	134	14.1583
""==========!!ddddllldddd]==========8	chr13:120167362-120167857(-)$1	495	22	59	17.6269
=========[ccc[a[ddddllldddd22a]ccc===	chr17:28123143-28123488(+)$1	345	50	87	14.8416
[iiiiiiiii"""ggggggglllggggggg333iiii	chr10:57236685-57237120(-)$1	435	205	242	16.2175
iiiiii"""eeeeerrrrrrrrreeeee4444iiiii	chr5:133017569-133017874(-)$1	305	20	57	12.8026
c!!ggggggg!!a[ddddllldddd]a22ggggggg4	chr10:58813201-58813560(+)$1	359	243	280	13.4626
fff####iiiiiiiii[aooooooa]iiiiiiiii22	chr6:72269087-72269490(-)$1	403	282	319	17.7399
[=================nnnnn==============	chr11:79329730-79330113(+)$1	383	273	310	20.4672
bb================mmmm===============	chr17:24777491-24777817(-)$1	326	107	144	19.5151
:::=============oooooo=============:E	chr16:85080007-85080458(-)$1	451	1	38	14.9398
:==========[ffffffnnnnnffffff]=======	chr11:69418680-69419127(-)$1	447	405	442	15.0447
:==========[cccrrrrrrrrrccc]=========	chr16:18077703-18077995(-)$1	292	212	249	17.2156
bb[cccggggggg"""cccmmmmccc333ggggggg2	chr1:162125525-162125777(+)$1	252	28	65	14.4190
b[==========vvvvvvvvvvvvv==========]b	chr7:129777307-129777773(+)$1	466	397	434	15.9344
""===========[cccooooooccc22=========	chr17:70871444-70871905(+)$1	461	158	195	20.3551
[=================qqqqqqqq===========	chr12:54248764-54249104(+)$1	340	45	82	17.5344
edddd[ccc[ccc[cccooooooccc]ccc333ccc]	chr3:126728352-126728841(-)$1	489	307	344	13.7197
eeeee:==========[bbmmmmbb]==========E	chr7:3656230-3656530(+)$1	300	127	164	14.2857
==================nnnnn==============	chr6:113753666-113754141(-)$1	475	190	227	20.4294
bb"""ggggggg[ddddooooooddddggggggg444	chr14:103581576-103581789(-)$1	213	38	75	14.7861

#otherMatches

#Seq PSSM
CAGCAUUGACUGUGUACAAGAUUUGUACACAGCUUUU	chr9:58488395-58488825(+)$1	430	375	412	16.4921
UCCCCAGUGUCAUGGUGUCCCACGGAUGCUGCUGGGG	chr2:24513769-24514130(-)$1	361	265	302	13.0317
UUUGUGCUGCUCAUUAUGCCCCUGGUGGUCUGGGUCU	chr5:122906860-122907274(-)$1	414	37	74	13.1790
UGAAUGACAAGCUGACUGAAUACCCCCUUGUUAUUAA	chr9:24286327-24286556(-)$1	229	116	153	15.9976
UUUACUAGGAUAUUUCUUCUUCUAGGAUCUUAGUAAU	chr8:26941573-26941858(-)$1	285	13	50	16.0190
ACUGCACUCUGCUGCGCUCCUAAUGGCUUCCAGGUUA	chr9:40153367-40153855(-)$1	488	330	367	13.0892
gcgucagauucccuggaauuggaguugcagggaguug	chr2:5812064-5812507(-)$1	443	384	421	15.0530
AGCUGAUGGAUGGCUCGGAGAUCCUCAGUCUGUUAGA	chr17:69633228-69633612(+)$1	384	18	55	15.2592
UGCCCUGUCCACUGGGGUACUCGGUGGAUGGUGUGCG	chr17:23960569-23960868(+)$1	299	1	38	14.2001
cuuugaucaguagugaguuucuauauuaacuacugug	chr11:121323012-121323332(+)$1	320	270	307	15.6612
GGUACGCAUGCGUGGCAGUUGUCUGUUGUGGGUAUGC	chr17:66321492-66321809(-)$1	317	176	213	15.2745
AGGAAGAACAAGUCACUGUGAUACUGAGGCUUGUUCA	chr6:71460053-71460389(+)$1	336	18	55	15.4409
GCACUCUACCAGGACUUUGUCCGGAACUAUCCUGGUG	chr6:124713638-124713981(-)$1	343	203	240	14.7714
gugugugugugugcgugcgugcaugcaugcgugCGAG	chr2:164817903-164818295(+)$1	392	200	237	18.3796
GUUGGAAAAGUUGUUGUUAUAUUAUAUGCAUUCUGAU	chr13:104676280-104676638(-)$1	358	160	197	15.1579
gagugggugcauguguguguauuuauguaugcaugCA	chr8:75216954-75217272(+)$1	318	122	159	19.5181
ugugugugugugCAUCGGUGGGUUGGUGCAUGCAUGU	chr7:71879400-71879781(+)$1	381	219	256	19.8079
caugugcgugcucggguguuugugugugcucgggugu	chr6:73213895-73214266(+)$1	371	217	254	17.4166
UUUGGUCCGUGUUUUCCAAAUACAGUAAAGCAUGGAG	chr10:127521992-127522358(+)$1	366	287	324	15.0349
agagagagaguguguguguguaugugagagagagugu	chr11:75451604-75452086(+)$1	482	287	324	13.8258
UUGGGCUAGGGACUGUUUGUGUAAGGCAGUGACAGCU	chr4:134481586-134482049(+)$1	463	240	277	13.6933
augaaugagguucugcguuuaaucuccagaaccucaa	chr2:90403875-90404326(-)$1	451	94	131	16.1206
GUGCUUGUUCCUUACGUGCUGCUGUCCUGUAGGAAUG	chr6:143015401-143015813(-)$1	412	120	157	16.5204
GAGAGCAGCAACAGAAGUUUGAUGAUCUCUAUUUUGA	chr7:38781417-38781808(-)$1	391	251	288	13.0031
ggguauacuuaggguauacuuaggguauacuuagggu	chr4:24825713-24826196(+)$1	483	307	344	17.9763
aauuuuauacauauuaauaacaauuuuugauguauaa	chr3:152020918-152021299(+)$1	381	310	347	18.5180
GGAAGCUGCAAGAGCGGCUGAGUGUGGGGUCUUGCAG	chr19:44377492-44377905(+)$1	413	177	214	17.3310
GUAUGUCACCUGUAUGCCUUAACAGGUGACAGGUGUA	chr19:45871213-45871631(-)$1	418	360	397	12.9771
gugugugugugcgcgcgcgcgagugcguguguaugcg	chr3:126713492-126713921(-)$1	429	248	285	14.8705
CAUAUCUGUGCAUCCUUCUGAGUGUGAAUAUUGUGCA	chr1:182878911-182879275(+)$1	364	151	188	14.8465
CACAAGUGUGUGUGCACAAGUGUGUGUGUGCACAAGU	chr4:126289475-126289913(+)$1	438	149	186	19.6277
UAuguauguauaugcaugucuguggggauaagugugu	chr1:184812994-184813414(+)$1	420	214	251	16.5718
UGGCUGUUUUUGUAUUUUCUUGGUAAAGUAUUUGACA	chr5:122910047-122910436(-)$1	389	97	134	14.1583
augggaauuuuguucuuguuccaagccaaaauuccuu	chr13:120167362-120167857(-)$1	495	22	59	17.6269
CAGACGGAGAUGGGCAGUGCUUUGCAUGAGGCUGCUU	chr17:28123143-28123488(+)$1	345	50	87	14.8416
GUAACAGUAUUCCCAAUUUUUGUAAAGUUGUAUGUGC	chr10:57236685-57237120(-)$1	435	205	242	16.2175
UUCCUCGCGGCGGGAGGGAAAAGCCCGUGCAGGAGGA	chr5:133017569-133017874(-)$1	305	20	57	12.8026
UAUUGUAGUCUCUGUGGUAAAAUCAGAAUGACUGCAC	chr10:58813201-58813560(+)$1	359	243	280	13.4626
AAACCAACCAGCAGGGGGCUUGAACGCCUUGUUGGGU	chr6:72269087-72269490(-)$1	403	282	319	17.7399
UGGUGUUGCUUGUUCAGGAGUGAUUUGGGCAGGUGAU	chr11:79329730-79330113(+)$1	383	273	310	20.4672
gugugcgugcgugcgugcgugcgugcgugugcgugug	chr17:24777491-24777817(-)$1	326	107	144	19.5151
UUCUAGCUGUGGUUCGAUUGUCCGGGCUGUGGCUGUG	chr16:85080007-85080458(-)$1	451	1	38	14.9398
CGGCGAUGCCUUUGGGGCGCAGGGUCCCGCGGGCGUC	chr11:69418680-69419127(-)$1	447	405	442	15.0447
AAGGGGUUAGGUGCUGAGCAUUAGGGUCCCUAGCCCC	chr16:18077703-18077995(-)$1	292	212	249	17.2156
CUAUCUGCUUUCCCGUCCUGGCUAGGUUAGGAGAGCC	chr1:162125525-162125777(+)$1	252	28	65	14.4190
CUUCAGUAUUUGUAAUUUUUAAAGUCAGAUGCUGAUG	chr7:129777307-129777773(+)$1	466	397	434	15.9344
GUUUGGGUAUAAACAACUCUUUUGUUACUUUGUAUCU	chr17:70871444-70871905(+)$1	461	158	195	20.3551
AAGCUCGGGGCUGGCCUGACCCACCCUGGGCUGGUCU	chr12:54248764-54249104(+)$1	340	45	82	17.5344
CCAAAGUGGGAGUCGAUGUCGCUGUCUGCUGAGCCAG	chr3:126728352-126728841(-)$1	489	307	344	13.7197
CGUCUGUUUGAAGGUGUGUAUGAGCCUAUUUUCGAAG	chr7:3656230-3656530(+)$1	300	127	164	14.2857
ugugugugugcaugcaugggguguguguguguaugug	chr6:113753666-113754141(-)$1	475	190	227	20.4294
CUUACAGGAAGGCAAGCUCCUUUGCUUUCUUCUUCCC	chr14:103581576-103581789(-)$1	213	38	75	14.7861

#DB
(((((....((((((((((...))))))))))....)	chr9:58488395-58488825(+)$1	1	375	412	16.4921
.(((((((.....(((((((...))))))))))))))	chr2:24513769-24514130(-)$1	1	265	302	13.0317
(((((((((((((...((((...))))...))))...	chr5:122906860-122907274(-)$1	1	37	74	13.1790
(((((((((((..(.........)..)))))))))..	chr9:24286327-24286556(-)$1	1	116	153	15.9976
((((((((((...((((......))))))))))))).	chr8:26941573-26941858(-)$1	1	13	50	16.0190
((((.((.(((....(((......)))...)))))))	chr9:40153367-40153855(-)$1	1	330	367	13.0892
)).)))(((((((((.(((....))).))))))))))	chr2:5812064-5812507(-)$1	1	384	421	15.0530
..(((((((((.....((....))...))))))))).	chr17:69633228-69633612(+)$1	1	18	55	15.2592
(((.((((((((((((...)))))))))))).)))).	chr17:23960569-23960868(+)$1	1	1	38	14.2001
...((..(((((((.(((......))).)))))))..	chr11:121323012-121323332(+)$1	1	270	307	15.6612
.((((((((((.((((((....)))))..).))))))	chr17:66321492-66321809(-)$1	1	176	213	15.2745
(((..(((((((((.(.((...)).).))))))))).	chr6:71460053-71460389(+)$1	1	18	55	15.4409
((.(((.(((((((.(((.....)))...))))))))	chr6:124713638-124713981(-)$1	1	203	240	14.7714
((.....(((((((((((......)))))))))))..	chr2:164817903-164818295(+)$1	1	200	237	18.3796
(((((((....((((((......))).))))))))))	chr13:104676280-104676638(-)$1	1	160	197	15.1579
(((((.(((((((((((......))))))))))).))	chr8:75216954-75217272(+)$1	1	122	159	19.5181
(((((((((((((((((......))))))))))))).	chr7:71879400-71879781(+)$1	1	219	256	19.8079
(((((.((((((((((((........)))))))))))	chr6:73213895-73214266(+)$1	1	217	254	17.4166
.....((((((((((.(.......).)))))))))))	chr10:127521992-127522358(+)$1	1	287	324	15.0349
(.(.(.(.(.(.(.(.(.........).).).).).)	chr11:75451604-75452086(+)$1	1	287	324	13.8258
(((((((.(..(((((((.....)))))))..)))))	chr4:134481586-134482049(+)$1	1	240	277	13.6933
((...((((((((((.(........))))))))))).	chr2:90403875-90404326(-)$1	1	94	131	16.1206
.(((((((((((.(((.((....))..))))))))))	chr6:143015401-143015813(-)$1	1	120	157	16.5204
(((.(((.(((.(((.(((....))).)))...))).	chr7:38781417-38781808(-)$1	1	251	288	13.0031
.(((((((((.(((((((((...))))))))).))))	chr4:24825713-24826196(+)$1	1	307	344	17.9763
.(((((((((((...(((....)))....))))))))	chr3:152020918-152021299(+)$1	1	310	347	18.5180
((.((((((((((.(.((.....))..).))))))))	chr19:44377492-44377905(+)$1	1	177	214	17.3310
((((.((((((((..((((....)))).))))))).)	chr19:45871213-45871631(-)$1	1	360	397	12.9771
))....((((((((((((......)))))))))))))	chr3:126713492-126713921(-)$1	1	248	285	14.8705
(((((((((((((..(((.......)))....)))))	chr1:182878911-182879275(+)$1	1	151	188	14.8465
((((....((((((((((......))))))))))..)	chr4:126289475-126289913(+)$1	1	149	186	19.6277
))))))))))))))))))))...))..))))))))).	chr1:184812994-184813414(+)$1	1	214	251	16.5718
(((((((.((.(((((((......)))))))..)).)	chr5:122910047-122910436(-)$1	1	97	134	14.1583
..((((((((((..((((...)))).)))))))))).	chr13:120167362-120167857(-)$1	1	22	59	17.6269
(((((((((.(((.(.((((...))))..).))))))	chr17:28123143-28123488(+)$1	1	50	87	14.8416
.(((((((((...(((((((...)))))))...))))	chr10:57236685-57237120(-)$1	1	205	242	16.2175
((((((...(((((.........)))))....)))))	chr5:133017569-133017874(-)$1	1	20	57	12.8026
(..(((((((..(.((((...)))).)..))))))).	chr10:58813201-58813560(+)$1	1	243	280	13.4626
(((....(((((((((.(......).)))))))))..	chr6:72269087-72269490(-)$1	1	282	319	17.7399
.(((((((((((((((((.....))))))))))))))	chr11:79329730-79330113(+)$1	1	273	310	20.4672
))((((((((((((((((....)))))))))))))))	chr17:24777491-24777817(-)$1	1	107	144	19.5151
...(((((((((((((......))))))))))))).(	chr16:85080007-85080458(-)$1	1	1	38	14.9398
.((((((((((.((((((.....)))))).)))))))	chr11:69418680-69419127(-)$1	1	405	442	15.0447
.((((((((((.(((.........))).)))))))))	chr16:18077703-18077995(-)$1	1	212	249	17.2156
((.((((((((((...(((....)))...))))))).	chr1:162125525-162125777(+)$1	1	28	65	14.4190
(.((((((((((.............)))))))))).)	chr7:129777307-129777773(+)$1	1	397	434	15.9344
..(((((((((((.(((......)))..)))))))))	chr17:70871444-70871905(+)$1	1	158	195	20.3551
.(((((((((((((((((........)))))))))))	chr12:54248764-54249104(+)$1	1	45	82	17.5344
(((((.(((.(((.(((......))).)))...))).	chr3:126728352-126728841(-)$1	1	307	344	13.7197
))))).((((((((((.((....)).)))))))))))	chr7:3656230-3656530(+)$1	1	127	164	14.2857
((((((((((((((((((.....))))))))))))))	chr6:113753666-113754141(-)$1	1	190	227	20.4294
((...(((((((.((((......)))))))))))...	chr14:103581576-103581789(-)$1	1	38	75	14.7861

#PSSM
b : 0.17	= : 0.11	e : 0.09	[ : 0.09	" : 0.07	g : 0.07	c : 0.05	! : 0.05	i : 0.05	: : 0.05	f : 0.03	G : 0.01	d : 0.01	h : 0.01	$ : 0.01	a : 0.01	
= : 0.24	b : 0.13	i : 0.11	g : 0.09	e : 0.07	c : 0.05	" : 0.05	f : 0.03	! : 0.03	d : 0.03	[ : 0.03	h : 0.01	$ : 0.01	: : 0.01	
= : 0.32	i : 0.13	g : 0.09	" : 0.05	[ : 0.05	e : 0.03	f : 0.03	d : 0.03	$ : 0.03	c : 0.03	: : 0.03	] : 0.01	b : 0.01	h : 0.01	a : 0.01	! : 0.01	
= : 0.36	i : 0.13	g : 0.09	c : 0.09	[ : 0.05	e : 0.03	$ : 0.03	" : 0.03	f : 0.01	b : 0.01	! : 0.01	h : 0.01	: : 0.01	# : 0.01	d : 0.01	
= : 0.40	i : 0.11	g : 0.09	c : 0.09	e : 0.03	[ : 0.03	$ : 0.03	" : 0.03	# : 0.03	b : 0.01	! : 0.01	a : 0.01	: : 0.01	d : 0.01	
= : 0.42	i : 0.13	g : 0.11	c : 0.07	[ : 0.07	# : 0.05	: : 0.03	b : 0.01	! : 0.01	$ : 0.01	a : 0.01	
= : 0.49	g : 0.15	i : 0.13	# : 0.05	c : 0.03	b : 0.01	! : 0.01	[ : 0.01	$ : 0.01	a : 0.01	" : 0.01	
= : 0.51	i : 0.15	g : 0.13	[ : 0.09	# : 0.05	" : 0.01	c : 0.01	
= : 0.53	i : 0.15	g : 0.11	c : 0.05	# : 0.03	a : 0.03	$ : 0.01	b : 0.01	" : 0.01	
= : 0.51	i : 0.15	g : 0.11	[ : 0.05	c : 0.03	$ : 0.01	d : 0.01	# : 0.01	! : 0.01	b : 0.01	e : 0.01	
= : 0.51	i : 0.09	g : 0.09	c : 0.07	" : 0.03	! : 0.03	[ : 0.03	$ : 0.01	d : 0.01	# : 0.01	a : 0.01	e : 0.01	
= : 0.46	g : 0.13	[ : 0.09	i : 0.07	c : 0.05	$ : 0.03	! : 0.03	" : 0.03	d : 0.01	# : 0.01	e : 0.01	
= : 0.38	g : 0.11	c : 0.09	i : 0.07	" : 0.05	a : 0.05	$ : 0.03	! : 0.03	[ : 0.03	d : 0.01	# : 0.01	e : 0.01	f : 0.01	v : 0.01	
= : 0.32	g : 0.11	[ : 0.11	i : 0.07	c : 0.07	" : 0.05	! : 0.05	d : 0.03	e : 0.03	a : 0.01	# : 0.01	$ : 0.01	f : 0.01	v : 0.01	
= : 0.32	c : 0.11	g : 0.07	d : 0.07	" : 0.05	i : 0.05	[ : 0.05	a : 0.05	r : 0.03	! : 0.03	# : 0.01	$ : 0.01	e : 0.01	f : 0.01	v : 0.01	
= : 0.28	c : 0.17	[ : 0.13	d : 0.09	g : 0.07	r : 0.05	" : 0.03	i : 0.03	$ : 0.01	e : 0.01	a : 0.01	f : 0.01	v : 0.01	
= : 0.23	c : 0.21	d : 0.13	g : 0.07	[ : 0.07	r : 0.05	a : 0.05	b : 0.03	l : 0.01	e : 0.01	i : 0.01	o : 0.01	f : 0.01	v : 0.01	
= : 0.19	o : 0.15	c : 0.15	d : 0.09	b : 0.09	g : 0.07	r : 0.07	l : 0.01	e : 0.01	p : 0.01	q : 0.01	i : 0.01	a : 0.01	f : 0.01	v : 0.01	
o : 0.28	n : 0.11	r : 0.07	m : 0.07	d : 0.05	c : 0.05	l : 0.05	b : 0.05	q : 0.05	= : 0.03	g : 0.03	p : 0.03	i : 0.01	v : 0.01	
o : 0.28	m : 0.19	n : 0.11	l : 0.07	r : 0.07	q : 0.05	g : 0.03	d : 0.03	= : 0.03	p : 0.03	i : 0.01	v : 0.01	
o : 0.28	m : 0.19	l : 0.17	n : 0.11	r : 0.07	q : 0.05	p : 0.03	= : 0.01	3 : 0.01	v : 0.01	
o : 0.28	m : 0.19	l : 0.13	n : 0.11	r : 0.07	q : 0.05	p : 0.03	d : 0.03	= : 0.01	3 : 0.01	v : 0.01	
o : 0.26	m : 0.11	n : 0.11	l : 0.09	= : 0.07	r : 0.07	q : 0.05	b : 0.03	p : 0.03	d : 0.03	e : 0.01	c : 0.01	3 : 0.01	v : 0.01	
= : 0.15	c : 0.15	d : 0.13	o : 0.13	b : 0.11	g : 0.05	q : 0.05	e : 0.03	p : 0.03	r : 0.03	a : 0.01	i : 0.01	f : 0.01	v : 0.01	
= : 0.21	c : 0.21	d : 0.13	g : 0.07	b : 0.07	q : 0.05	e : 0.03	a : 0.03	2 : 0.01	3 : 0.01	] : 0.01	r : 0.01	i : 0.01	p : 0.01	f : 0.01	v : 0.01	
= : 0.23	c : 0.21	d : 0.09	] : 0.09	g : 0.07	2 : 0.07	e : 0.03	a : 0.03	q : 0.03	3 : 0.01	r : 0.01	i : 0.01	4 : 0.01	f : 0.01	
= : 0.34	d : 0.09	] : 0.09	g : 0.07	c : 0.07	2 : 0.07	i : 0.05	3 : 0.05	e : 0.03	a : 0.03	4 : 0.01	f : 0.01	
= : 0.34	i : 0.15	g : 0.09	c : 0.09	3 : 0.07	] : 0.07	2 : 0.07	4 : 0.01	a : 0.01	e : 0.01	f : 0.01	
= : 0.38	i : 0.15	g : 0.13	3 : 0.07	c : 0.07	2 : 0.05	4 : 0.05	a : 0.01	] : 0.01	f : 0.01	
= : 0.42	g : 0.19	i : 0.15	c : 0.07	3 : 0.03	a : 0.03	] : 0.03	4 : 0.03	
= : 0.46	g : 0.17	i : 0.15	3 : 0.05	] : 0.03	4 : 0.03	d : 0.01	c : 0.01	a : 0.01	2 : 0.01	
= : 0.46	g : 0.15	i : 0.15	3 : 0.05	c : 0.03	] : 0.03	2 : 0.03	4 : 0.03	d : 0.01	
= : 0.46	g : 0.15	i : 0.15	3 : 0.05	d : 0.03	c : 0.03	a : 0.03	4 : 0.01	] : 0.01	2 : 0.01	
= : 0.46	i : 0.19	g : 0.17	c : 0.05	d : 0.03	b : 0.03	4 : 0.01	] : 0.01	
= : 0.44	i : 0.19	g : 0.15	4 : 0.05	b : 0.03	c : 0.03	d : 0.01	] : 0.01	a : 0.01	2 : 0.01	
= : 0.38	i : 0.15	g : 0.11	4 : 0.07	] : 0.07	2 : 0.05	c : 0.05	f : 0.01	d : 0.01	7 : 0.01	: : 0.01	
= : 0.26	2 : 0.09	g : 0.07	4 : 0.07	i : 0.07	: : 0.03	5 : 0.03	c : 0.03	8 : 0.03	a : 0.03	] : 0.03	E : 0.03	e : 0.01	f : 0.01	D : 0.01	7 : 0.01	d : 0.01	B : 0.01	b : 0.01	

#score	830.1643523016556
#seq	52
#width	37
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_UTR_m2_run2.txt

#BEAR
eeeffffffooooooffffff22ee	chr10:7926903-7927128(+)$1	225	174	199	10.9073
!!gggggggooooooggggggg22d	chr12:32170791-32171018(-)$1	227	169	194	12.6176
"iiiiiiiiinnnnniiiiiiiii3	chr1:159066620-159066837(-)$1	217	170	195	9.6674
g"""eeeeeooooooeeeee]gggg	chr17:34253058-34253282(-)$1	224	118	143	12.2868
iiiiiiiiiooooooiiiiiiiiiH	chr2:180821340-180821577(-)$1	237	175	200	13.3012
"""bb[cccoooooocccbb22eee	chr12:3248971-3249192(-)$1	221	95	120	12.2961
==========lll==========:d	chr7:127987162-127987384(-)$1	222	100	125	9.7222
eeeeee[bboooooobb22eeeee2	chr18:47406517-47406752(-)$1	235	23	48	11.9888
ggggggcccooooooccc]gggggg	chr18:10181497-10181725(-)$1	228	123	148	13.6169
eeeeeeeeeooooooeeeee22eee	chr4:15213355-15213573(+)$1	218	21	46	10.9958
dddd[ddddoooooodddd]dddd3	chr6:118103379-118103600(-)$1	221	52	77	10.9250
fffff[bbaooooooa]bb]fffff	chr5:135886946-135887175(-)$1	229	37	62	11.1921
bb!!eeeeeooooooeeeee]bbff	chr11:86520113-86520333(-)$1	220	92	117	10.6874
ee[ccccccooooooccc]ccc]ee	chr2:126894763-126894985(+)$1	222	78	103	13.1580
!!==========lll==========	chr17:56273088-56273324(-)$1	236	88	113	11.1902
dd[ccc[bboooooobb22ccc]dd	chr15:21516522-21516764(+)$1	242	187	212	12.5554
===========mmmm==========	chr17:27162272-27162505(-)$1	233	148	173	10.5010
""dddd[bboooooobb22dddd44	chr11:93807549-93807769(+)$1	220	87	112	11.6999
=========ammmma]=========	chr5:77301132-77301361(+)$1	229	102	127	10.3365
dddd[ddddoooooodddddddd]c	chr7:52965737-52965966(-)$1	229	157	182	10.7302
f[eeeee[aooooooaeeeee]fff	chr10:41627344-41627560(+)$1	216	179	204	11.6574
===========mmmm==========	chr9:59237726-59237953(-)$1	227	12	37	10.5010
ffff!!cccooooooccc]ffffff	chr5:108535982-108536230(+)$1	248	195	220	12.8830
ccc####bboooooobb4444ccc]	chr11:120486475-120486692(-)$1	217	51	76	13.2866
h!!ccc[bboooooobb]ccc333h	chr8:72784742-72784972(+)$1	230	154	179	13.0426
a!!dddd[aooooooa]dddd22a]	chr11:105920063-105920292(+)$1	229	73	98	11.5519
gg####cccooooooccc22ggggg	chr12:47800418-47800638(-)$1	220	87	112	13.7503
iiiiiiiiiooooooiiiiiiiii]	chr16:3862040-3862306(-)$1	266	210	235	14.0683
======rrrrrrrrr==========	chr13:40811659-40811884(-)$1	225	191	216	9.7046
fffff!!bboooooobb22ffffff	chr11:50625786-50626024(-)$1	238	16	41	12.3470
=========oooooo==========	chr10:120361576-120361826(-)$1	250	85	110	14.9642
gggg"""bboooooobb22gggggg	chr17:27173217-27173444(+)$1	227	90	115	13.6319
e!!bb[cccooooooccc]bb22ee	chr4:90918756-90918989(-)$1	233	136	161	12.6692
dd[bb[cccooooooccc]bb]ddd	chr14:31932464-31932689(+)$1	225	29	54	12.1293
c####ddddoooooodddd4444cc	chr3:133129134-133129359(-)$1	225	147	172	12.3037
cc!!a!!bboooooobb22a]ccc2	chr18:44577980-44578208(+)$1	228	50	75	13.2977
fffff[cccooooooccc]ffffff	chr11:94269599-94269821(-)$1	222	44	69	12.5929
eeeee!!bboooooobb22eeeeef	chr11:78336812-78337060(-)$1	248	96	121	12.3621
fffff!!bboooooobb]ffffff:	chr4:87486911-87487142(-)$1	231	171	196	11.3194
$$$$$ddddooooooddddeeeee3	chr15:6746292-6746510(-)$1	218	161	186	10.9439
dd[ffffffooooooffffff333d	chr12:3501278-3501503(+)$1	225	120	145	11.4214
============lll==========	chr16:44085737-44085953(-)$1	216	146	171	11.1861
eee!!a[bboooooobb]a22eeee	chr11:78288300-78288530(-)$1	230	50	75	12.7277
=========oooooo==========	chr4:106758609-106758831(+)$1	222	171	196	14.9642
fffffddddoooooodddd22ffff	chr5:34974487-34974710(+)$1	223	105	130	10.9830
ee[bb[cccooooooccc]bb22ee	chr3:89587511-89587736(+)$1	225	90	115	12.4397
d$$$$$cccoooooocccdddd]hh	chr12:8977930-8978145(+)$1	215	102	127	11.5019
gggg[a[bboooooobb]a22gggg	chr17:21982497-21982719(-)$1	222	149	174	13.2965
f####ddddoooooodddd333fff	chr4:45047329-45047552(-)$1	223	147	172	12.5063
c!!ccc[bboooooobbccc]ccc5	chr6:34749747-34749962(+)$1	215	64	89	12.3669
iiiiiiibboooooobb333iiiii	chr11:6007396-6007629(-)$1	233	146	171	14.3056
ffff!!cccoooooocccffffff:	chr2:32643414-32643648(-)$1	234	5	30	11.6050
ddd"""cccooooooccc4444ddd	chr10:60562430-60562649(-)$1	219	91	116	12.9267
ddd"""cccooooooccc333dddd	chr4:154635621-154635844(-)$1	223	169	194	13.0526
b[cccddddoooooodddd]ccc]b	chr11:75390127-75390355(+)$1	228	8	33	11.3159
eee[eeeeeooooooeeeee]eeee	chr14:47940919-47941147(+)$1	228	133	158	11.3910
#iiiiiiiiillliiiiiiiii333	chr10:121024613-121024835(-)$1	222	43	68	9.6411
===========mmmm==========	chr18:35023432-35023648(+)$1	216	102	127	10.5010
hhhh!!cccooooooccc]hhhhhh	chr5:138619056-138619285(+)$1	229	41	66	11.6149

#otherMatches

#Seq PSSM
UUUUAAUGCACUCGAGCAUUAAUGA	chr10:7926903-7927128(+)$1	225	174	199	10.9073
UUAGGAUAUUAUCGUAUAUCCUUUG	chr12:32170791-32171018(-)$1	227	169	194	12.6176
AUGAGAGAGAAUAAAUUUCUUUCAG	chr1:159066620-159066837(-)$1	217	170	195	9.6674
CAACUGUUACAUUUAUAACAAGGUA	chr17:34253058-34253282(-)$1	224	118	143	12.2868
uauacacaugugugaauguguauag	chr2:180821340-180821577(-)$1	237	175	200	13.3012
CUUGAUAUUUAAACUGAUUCCUGCC	chr12:3248971-3249192(-)$1	221	95	120	12.2961
CUGGGGUCCACUCUGGACCUCGGCU	chr7:127987162-127987384(-)$1	222	100	125	9.7222
AUAUGCUGGCUGCUACCUUGCAUAA	chr18:47406517-47406752(-)$1	235	23	48	11.9888
CGCCGGAGCGACCGGGCUGCUGGCG	chr18:10181497-10181725(-)$1	228	123	148	13.6169
UGUGUGGCAGAUGAGUGCCAUUCAC	chr4:15213355-15213573(+)$1	218	21	46	10.9958
CAUGUGUGGGGUCUGCCAUUCAUGA	chr6:118103379-118103600(-)$1	221	52	77	10.9250
GACAGAAGCAUCACCGUCUACUGUC	chr5:135886946-135887175(-)$1	229	37	62	11.1921
GCCAUUGAUUCUUACAUCAAAGCAG	chr11:86520113-86520333(-)$1	220	92	117	10.6874
AGUGUUGGCUGACGUGCUAAGCUCU	chr2:126894763-126894985(+)$1	222	78	103	13.1580
CUGAUGUUAGCCUGGGGCUGAUAUU	chr17:56273088-56273324(-)$1	236	88	113	11.1902
UCUCUACGUCAAGAAGCAAUAGUGA	chr15:21516522-21516764(+)$1	242	187	212	12.5554
GGACUUGGGGUUCACAUCCCAGGUC	chr17:27162272-27162505(-)$1	233	148	173	10.5010
UUUUAGUAGUUUAAUCUUUUUAACC	chr11:93807549-93807769(+)$1	220	87	112	11.6999
UUAUUCUGUCUACCGUACAGGAUGA	chr5:77301132-77301361(+)$1	229	102	127	10.3365
CUUGAGGGGCAGGUUCCCCCAGGUG	chr7:52965737-52965966(-)$1	229	157	182	10.7302
UAAGUUCACACAUGCGGAAUUGAGU	chr10:41627344-41627560(+)$1	216	179	204	11.6574
UAAUAAAAUAAACUUUUAUUUUGUU	chr9:59237726-59237953(-)$1	227	12	37	10.5010
AAAUCAGAGGAGAGACUUAAUUUUU	chr5:108535982-108536230(+)$1	248	195	220	12.8830
GGACUUGGAGAGCAAUCAGUCUCCU	chr11:120486475-120486692(-)$1	217	51	76	13.2866
guguaugugagugagcagguguguu	chr8:72784742-72784972(+)$1	230	154	179	13.0426
CUGUCAGUGACUUUCCCCUGAGUGU	chr11:105920063-105920292(+)$1	229	73	98	11.5519
GCCAAAGCACUGUCAUGUAUGUCUU	chr12:47800418-47800638(-)$1	220	87	112	13.7503
UACAGAUUUUGCUUUAAAUCUGUAA	chr16:3862040-3862306(-)$1	266	210	235	14.0683
CUUAGAAAUCCAAGGUUUGGGUAAG	chr13:40811659-40811884(-)$1	225	191	216	9.7046
cucaggaggugcucucccacugagc	chr11:50625786-50626024(-)$1	238	16	41	12.3470
UACAUAUGUAGCUGCACAUAUGUAC	chr10:120361576-120361826(-)$1	250	85	110	14.9642
UUAGUUUGGCAUUCACCUCCUGGGC	chr17:27173217-27173444(+)$1	227	90	115	13.6319
UUCCUAAAGAAAUCCCUUCAGAUAG	chr4:90918756-90918989(-)$1	233	136	161	12.6692
AAGUUGACAAUGAAAUGUGAAGUUG	chr14:31932464-31932689(+)$1	225	29	54	12.1293
AAAGUAGCUACAGAAAGCUUAAGUG	chr3:133129134-133129359(-)$1	225	147	172	12.3037
GCAGAGAGCAUGGAAGCAAUAGCUG	chr18:44577980-44578208(+)$1	228	50	75	13.2977
auauauauacauacauaucuauaua	chr11:94269599-94269821(-)$1	222	44	69	12.5929
UGAGGCCACCAAUCUGUUUUCUCAG	chr11:78336812-78337060(-)$1	248	96	121	12.3621
UUCCUAAGAUGGCCUUCAAGGAACC	chr4:87486911-87487142(-)$1	231	171	196	11.3194
UCAGAAGGCUCUCCUGCCUCACUGU	chr15:6746292-6746510(-)$1	218	161	186	10.9439
UCAUGCUGGGUUUUGCUGGCAGAAG	chr12:3501278-3501503(+)$1	225	120	145	11.4214
UAGUGCGUCUUUAGUAAGGAUGUGU	chr16:44085737-44085953(-)$1	216	146	171	11.1861
GGGCCGCCCCUCUCAGGACUCCUCU	chr11:78288300-78288530(-)$1	230	50	75	12.7277
UGAAUAUUAGAGAAAUGGUGUUCAC	chr4:106758609-106758831(+)$1	222	171	196	14.9642
CUGCUGCAGUUGGGCCUGCAGAGCA	chr5:34974487-34974710(+)$1	223	105	130	10.9830
GUUCACCAGUCCUACUUGAUGCUGC	chr3:89587511-89587736(+)$1	225	90	115	12.4397
AAAUUUUGAAUUCUAUCAUUUUGUU	chr12:8977930-8978145(+)$1	215	102	127	11.5019
GCAGGGGGGUGUUUUCCGCAGCUGC	chr17:21982497-21982719(-)$1	222	149	174	13.2965
UCACUGUCCUACACUGGGCCAUAUC	chr4:45047329-45047552(-)$1	223	147	172	12.5063
CGAUGUUCCUUAGCUGGACGGGAUU	chr6:34749747-34749962(+)$1	215	64	89	12.3669
GGGUGCUGCAUUCAAGCCUGGGUAC	chr11:6007396-6007629(-)$1	233	146	171	14.3056
AAUAAUUUCUCAAAUGGAUAUUUAA	chr2:32643414-32643648(-)$1	234	5	30	11.6050
UACGACAGCAUUUUAGCUUCAGGUA	chr10:60562430-60562649(-)$1	219	91	116	12.9267
UAAUACUCCAGAUUAGGAAAUUUAA	chr4:154635621-154635844(-)$1	223	169	194	13.0526
GAGUCAUUCUUCCAUGGAUAGAUCC	chr11:75390127-75390355(+)$1	228	8	33	11.3159
UCUGGGUUCAGGAAAGAAUCAAGAA	chr14:47940919-47941147(+)$1	228	133	158	11.3910
AUCUCAUUUGUUACAGGUGAGAAGA	chr10:121024613-121024835(-)$1	222	43	68	9.6411
GUCCUUCUACUCACGAGUAGAAGGA	chr18:35023432-35023648(+)$1	216	102	127	10.5010
GGGUAAGUAAGACACUGCCAUCCUG	chr5:138619056-138619285(+)$1	229	41	66	11.6149

#DB
(((((((((......))))))..))	chr10:7926903-7927128(+)$1	1	174	199	10.9073
..(((((((......)))))))..)	chr12:32170791-32171018(-)$1	1	169	194	12.6176
.(((((((((.....))))))))).	chr1:159066620-159066837(-)$1	1	170	195	9.6674
(...(((((......))))).))))	chr17:34253058-34253282(-)$1	1	118	143	12.2868
(((((((((......))))))))))	chr2:180821340-180821577(-)$1	1	175	200	13.3012
...((.(((......)))))..)))	chr12:3248971-3249192(-)$1	1	95	120	12.2961
((((((((((...)))))))))).(	chr7:127987162-127987384(-)$1	1	100	125	9.7222
((((((.((......))..))))).	chr18:47406517-47406752(-)$1	1	23	48	11.9888
(((((((((......))).))))))	chr18:10181497-10181725(-)$1	1	123	148	13.6169
(((((((((......)))))..)))	chr4:15213355-15213573(+)$1	1	21	46	10.9958
((((.((((......)))).)))).	chr6:118103379-118103600(-)$1	1	52	77	10.9250
(((((.(((......).)).)))))	chr5:135886946-135887175(-)$1	1	37	62	11.1921
((..(((((......))))).))((	chr11:86520113-86520333(-)$1	1	92	117	10.6874
((.((((((......))).))).))	chr2:126894763-126894985(+)$1	1	78	103	13.1580
..((((((((((...))))))))))	chr17:56273088-56273324(-)$1	1	88	113	11.1902
((.(((.((......))..))).))	chr15:21516522-21516764(+)$1	1	187	212	12.5554
(((((((((((....))))))))))	chr17:27162272-27162505(-)$1	1	148	173	10.5010
..((((.((......))..))))..	chr11:93807549-93807769(+)$1	1	87	112	11.6999
((((((((((....).)))))))))	chr5:77301132-77301361(+)$1	1	102	127	10.3365
((((.((((......)))))))).)	chr7:52965737-52965966(-)$1	1	157	182	10.7302
(.(((((.(......)))))).)))	chr10:41627344-41627560(+)$1	1	179	204	11.6574
(((((((((((....))))))))))	chr9:59237726-59237953(-)$1	1	12	37	10.5010
((((..(((......))).))))))	chr5:108535982-108536230(+)$1	1	195	220	12.8830
(((....((......))....))).	chr11:120486475-120486692(-)$1	1	51	76	13.2866
(..(((.((......)).)))...)	chr8:72784742-72784972(+)$1	1	154	179	13.0426
(..((((.(......).))))..).	chr11:105920063-105920292(+)$1	1	73	98	11.5519
((....(((......)))..)))))	chr12:47800418-47800638(-)$1	1	87	112	13.7503
(((((((((......))))))))).	chr16:3862040-3862306(-)$1	1	210	235	14.0683
((((((.........))))))))))	chr13:40811659-40811884(-)$1	1	191	216	9.7046
(((((..((......))..))))))	chr11:50625786-50626024(-)$1	1	16	41	12.3470
(((((((((......))))))))))	chr10:120361576-120361826(-)$1	1	85	110	14.9642
((((...((......))..))))))	chr17:27173217-27173444(+)$1	1	90	115	13.6319
(..((.(((......))).))..))	chr4:90918756-90918989(-)$1	1	136	161	12.6692
((.((.(((......))).)).)))	chr14:31932464-31932689(+)$1	1	29	54	12.1293
(....((((......))))....))	chr3:133129134-133129359(-)$1	1	147	172	12.3037
((..(..((......))..).))).	chr18:44577980-44578208(+)$1	1	50	75	13.2977
(((((.(((......))).))))))	chr11:94269599-94269821(-)$1	1	44	69	12.5929
(((((..((......))..))))))	chr11:78336812-78337060(-)$1	1	96	121	12.3621
(((((..((......)).)))))).	chr4:87486911-87487142(-)$1	1	171	196	11.3194
.....((((......))))))))).	chr15:6746292-6746510(-)$1	1	161	186	10.9439
((.((((((......))))))...)	chr12:3501278-3501503(+)$1	1	120	145	11.4214
((((((((((((...))))))))))	chr16:44085737-44085953(-)$1	1	146	171	11.1861
(((..(.((......)).)..))))	chr11:78288300-78288530(-)$1	1	50	75	12.7277
(((((((((......))))))))))	chr4:106758609-106758831(+)$1	1	171	196	14.9642
(((((((((......))))..))))	chr5:34974487-34974710(+)$1	1	105	130	10.9830
((.((.(((......))).))..))	chr3:89587511-89587736(+)$1	1	90	115	12.4397
(.....(((......))))))).))	chr12:8977930-8978145(+)$1	1	102	127	11.5019
((((.(.((......)).)..))))	chr17:21982497-21982719(-)$1	1	149	174	13.2965
(....((((......))))...)))	chr4:45047329-45047552(-)$1	1	147	172	12.5063
(..(((.((......))))).))).	chr6:34749747-34749962(+)$1	1	64	89	12.3669
(((((((((......))...)))))	chr11:6007396-6007629(-)$1	1	146	171	14.3056
((((..(((......))))))))).	chr2:32643414-32643648(-)$1	1	5	30	11.6050
(((...(((......)))....)))	chr10:60562430-60562649(-)$1	1	91	116	12.9267
(((...(((......)))...))))	chr4:154635621-154635844(-)$1	1	169	194	13.0526
(.(((((((......)))).))).)	chr11:75390127-75390355(+)$1	1	8	33	11.3159
(((.(((((......))))).))))	chr14:47940919-47941147(+)$1	1	133	158	11.3910
.(((((((((...)))))))))...	chr10:121024613-121024835(-)$1	1	43	68	9.6411
(((((((((((....))))))))))	chr18:35023432-35023648(+)$1	1	102	127	10.5010
((((..(((......))).))))))	chr5:138619056-138619285(+)$1	1	41	66	11.6149

#PSSM
e : 0.15	= : 0.15	f : 0.15	d : 0.13	g : 0.08	c : 0.06	" : 0.05	i : 0.05	! : 0.03	b : 0.03	h : 0.03	a : 0.01	$ : 0.01	# : 0.01	
= : 0.15	e : 0.13	d : 0.11	f : 0.11	! : 0.10	i : 0.08	g : 0.06	" : 0.05	[ : 0.03	c : 0.03	# : 0.03	$ : 0.03	b : 0.01	h : 0.01	
= : 0.16	e : 0.11	f : 0.11	! : 0.10	i : 0.08	d : 0.08	[ : 0.08	g : 0.06	# : 0.05	" : 0.03	c : 0.03	$ : 0.03	h : 0.01	
= : 0.16	f : 0.15	i : 0.08	c : 0.08	g : 0.06	b : 0.06	e : 0.06	d : 0.06	# : 0.06	" : 0.05	! : 0.05	$ : 0.03	[ : 0.01	h : 0.01	
= : 0.16	f : 0.11	e : 0.11	i : 0.08	c : 0.08	b : 0.06	! : 0.06	# : 0.06	[ : 0.05	" : 0.05	g : 0.03	d : 0.03	$ : 0.03	a : 0.01	
= : 0.16	d : 0.15	! : 0.11	e : 0.10	[ : 0.10	i : 0.08	c : 0.06	" : 0.05	f : 0.03	g : 0.03	# : 0.03	a : 0.03	$ : 0.01	
c : 0.23	= : 0.15	d : 0.13	[ : 0.11	i : 0.08	e : 0.08	! : 0.06	f : 0.03	g : 0.01	b : 0.01	# : 0.01	r : 0.01	" : 0.01	
b : 0.25	c : 0.23	= : 0.15	d : 0.11	i : 0.06	e : 0.06	f : 0.03	[ : 0.03	g : 0.01	r : 0.01	
c : 0.23	b : 0.23	= : 0.15	d : 0.11	i : 0.06	e : 0.06	a : 0.05	f : 0.03	g : 0.01	r : 0.01	
o : 0.83	= : 0.10	i : 0.03	a : 0.01	r : 0.01	
o : 0.83	= : 0.08	l : 0.03	n : 0.01	m : 0.01	r : 0.01	
o : 0.83	m : 0.06	l : 0.03	= : 0.03	n : 0.01	r : 0.01	
o : 0.83	l : 0.06	m : 0.06	n : 0.01	r : 0.01	
o : 0.83	m : 0.06	l : 0.03	n : 0.01	= : 0.01	r : 0.01	i : 0.01	
o : 0.83	m : 0.05	l : 0.03	n : 0.01	= : 0.01	a : 0.01	r : 0.01	i : 0.01	
c : 0.23	b : 0.23	= : 0.15	d : 0.11	i : 0.06	e : 0.06	a : 0.05	f : 0.03	g : 0.01	] : 0.01	
c : 0.23	b : 0.23	= : 0.16	d : 0.11	e : 0.08	i : 0.06	f : 0.03	] : 0.03	g : 0.01	
c : 0.25	= : 0.16	d : 0.13	2 : 0.11	e : 0.08	i : 0.06	] : 0.06	f : 0.03	g : 0.01	b : 0.01	4 : 0.01	3 : 0.01	
= : 0.16	d : 0.15	2 : 0.13	] : 0.13	e : 0.08	f : 0.06	i : 0.06	b : 0.03	4 : 0.03	c : 0.03	a : 0.03	3 : 0.03	g : 0.01	
= : 0.16	e : 0.13	f : 0.11	i : 0.06	b : 0.06	c : 0.06	d : 0.06	2 : 0.06	g : 0.05	] : 0.05	4 : 0.05	3 : 0.05	a : 0.01	h : 0.01	
= : 0.16	f : 0.13	i : 0.08	] : 0.08	2 : 0.08	d : 0.08	g : 0.06	e : 0.06	c : 0.06	4 : 0.05	b : 0.05	3 : 0.03	h : 0.01	
= : 0.16	f : 0.11	2 : 0.10	g : 0.10	c : 0.10	i : 0.08	e : 0.08	d : 0.08	3 : 0.05	] : 0.03	4 : 0.03	b : 0.01	h : 0.01	
= : 0.16	f : 0.15	e : 0.11	d : 0.10	2 : 0.08	g : 0.08	i : 0.06	c : 0.06	] : 0.05	3 : 0.05	b : 0.01	4 : 0.01	h : 0.01	
e : 0.18	f : 0.16	= : 0.15	g : 0.08	d : 0.08	i : 0.06	c : 0.06	3 : 0.05	] : 0.03	h : 0.03	2 : 0.01	: : 0.01	4 : 0.01	a : 0.01	
f : 0.15	= : 0.15	e : 0.13	d : 0.11	g : 0.08	3 : 0.06	] : 0.05	h : 0.05	2 : 0.03	c : 0.03	: : 0.03	H : 0.01	4 : 0.01	5 : 0.01	i : 0.01	b : 0.01	

#score	709.1331632515827
#seq	59
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_UTR_m1_run1.txt

#BEAR
ffffbb[bbuuuuuuuuuuuubb]bb]ffff	chr13:100195453-100195707(-)$1	254	59	90	22.9732
a!!cccxxxxxxxxxxxxxxxccc22a]eee	chr11:51799897-51800143(-)$1	246	61	92	19.8597
g[gggggggyyyyyyyyyyyyyyyygggggg	chr1:66488858-66489099(+)$1	241	143	174	24.1056
=====[a[attttttttttta]a========	chr11:77524382-77524622(+)$1	240	196	227	26.2343
=======wwwwwwwwwwwwww==========	chr1:175265869-175266113(-)$1	244	89	120	25.7590
iiiiiiiiixxxxxxxxxxxxxxxiiiiiii	chr15:98568195-98568451(-)$1	256	4	35	21.0714
ffbb[ddddvvvvvvvvvvvvvdddd]bb]f	chr18:25636494-25636747(-)$1	253	167	198	23.1349
eeeee[cccvvvvvvvvvvvvvccceeeee2	chr14:34192179-34192416(-)$1	237	190	221	24.4994
eeeeeeeewwwwwwwwwwwwwweeeee]eee	chr13:34994550-34994812(+)$1	262	2	33	23.7035
gggg!!cccuuuuuuuuuuuuccc22ggggg	chr11:105916222-105916468(+)$1	246	93	124	26.6804
=======wwwwwwwwwwwwww==========	chrX:78340150-78340389(+)$1	239	125	156	25.7590
!!gggggggtttttttttttggggggg22gg	chr1:58583961-58584200(-)$1	239	107	138	24.0244
iiiiiiiiiwwwwwwwwwwwwwwiiiiiiii	chr10:110733431-110733666(+)$1	235	156	187	25.3173
ggggggcccuuuuuuuuuuuuccc4444ggg	chr16:44085816-44086071(-)$1	255	181	212	27.0007
[ccc[dddduuuuuuuuuuuudddd333ccc	chr18:34478851-34479088(+)$1	237	62	93	25.8035
eeeee!!bbyyyyyyyyyyyyyyyybb]eee	chr6:71341915-71342171(-)$1	256	144	175	22.3020
ggggg[cccuuuuuuuuuuuuccc]gggggg	chr11:109530312-109530563(+)$1	251	77	108	26.8980
iiiiiiiiiyyyyyyyyyyyyyyyyiiiiii	chrX:137009737-137009977(+)$1	240	153	184	24.4032
f####eeeeettttttttttteeeee]ffff	chr2:122510412-122510649(-)$1	237	163	194	22.8983
eeee"""ccctttttttttttccc333eeee	chr19:59371866-59372114(-)$1	248	148	179	24.6378
"""fffffftttttttttttffffff4444d	chr12:39358640-39358903(+)$1	263	55	86	22.3510
:gggggggvvvvvvvvvvvvvggggggg:gg	chr5:122903787-122904080(-)$1	293	107	138	23.4537
ggggg[ddddtttttttttttdddd]ggggg	chr5:32794483-32794768(+)$1	285	148	179	24.4701
ddddbbyyyyyyyyyyyyyyyybb]dddd33	chr15:30958338-30958591(+)$1	253	8	39	21.7330
[ccceeeeeuuuuuuuuuuuueeeee]ccc2	chr5:122906402-122906659(-)$1	257	55	86	24.8239
$ccc[dddduuuuuuuuuuuudddd]ccc33	chr18:34481615-34481852(+)$1	237	80	111	24.9920
HHHffffffuuuuuuuuuuuuffffffdddd	chr9:72595391-72595637(+)$1	246	40	71	21.5255
iiiiiiiiiuuuuuuuuuuuuiiiiiiiii:	chr11:42443035-42443275(+)$1	240	150	181	25.5664
addddyyyyyyyyyyyyyyyydddd]a333d	chr11:90139073-90139323(+)$1	250	215	246	22.6079
dddd[cccvvvvvvvvvvvvvcccddddggg	chr16:17044950-17045193(+)$1	243	20	51	24.1589
e"""eeeeettttttttttteeeee4444ee	chr1:38852135-38852371(-)$1	236	87	118	23.4580
ccc!!ddddvvvvvvvvvvvvvdddd22ccc	chr15:58615289-58615539(-)$1	250	76	107	24.2953
========^^^^^^^^^^^^^^^^^^^^===	chr2:70438879-70439132(+)$1	253	189	220	18.1267
iiiiiiiiiwwwwwwwwwwwwwwiiiiiiii	chr3:89238790-89239031(+)$1	241	38	69	25.3173
eeeeeyyyyyyyyyyyyyyyyeeeee22eee	chr19:58870931-58871176(-)$1	245	111	142	22.7070
eee[eeeeeuuuuuuuuuuuueeeee22eee	chr5:14863241-14863485(+)$1	244	134	165	24.8759
:ggggggg[attttttttttta]ggggggg:	chr16:84954981-84955283(-)$1	302	137	168	23.1140
:eeeeeddddtttttttttttdddd]eeeee	chr5:23011882-23012127(-)$1	245	198	229	22.1043
ddd[ddddvvvvvvvvvvvvvdddd]dddd]	chr10:80169675-80169910(-)$1	235	18	49	23.2995
ffffff[ccctttttttttttccc]ffffff	chr5:139494237-139494472(-)$1	235	19	50	23.2621
=========vvvvvvvvvvvvv=========	chr11:41945233-41945477(-)$1	244	177	208	26.6605
ddd[bbyyyyyyyyyyyyyyyybb]dddddd	chr5:113672263-113672498(-)$1	235	9	40	21.6617
:gggggggvvvvvvvvvvvvvggggggg:gg	chr1:33855577-33855826(-)$1	249	8	39	23.4537
eeggggggguuuuuuuuuuuuggggggg::=	chr4:40680719-40680957(+)$1	238	56	87	23.8428
###cccxxxxxxxxxxxxxxxccc4444hhh	chr2:73450408-73450703(-)$1	295	200	231	19.7141
=======[attttttttttta]=========	chr9:107998481-107998718(-)$1	237	140	171	26.2470
eeee"""bbvvvvvvvvvvvvvbb4444eee	chr5:65986221-65986472(+)$1	251	126	157	24.3015
=====[a[attttttttttta]a========	chr11:77524443-77524703(+)$1	260	135	166	26.2343
)))))dddduuuuuuuuuuuudddd>>>>>>	chr11:41945344-41945595(-)$1	251	139	170	21.0299
fffff[cccuuuuuuuuuuuuccc333ffff	chr6:125171712-125171970(+)$1	258	134	165	25.9012
cc[eeeeevvvvvvvvvvvvveeeee]cccc	chr2:37229678-37229920(-)$1	242	132	163	24.2085
gggg!!cccuuuuuuuuuuuuccc333gggg	chr10:98487879-98488126(+)$1	247	70	101	27.3918
eee!!cccwwwwwwwwwwwwwwccc333eee	chr10:94254917-94255155(-)$1	238	163	194	25.3056
gggggddddvvvvvvvvvvvvvdddd]gggg	chr2:35035992-35036228(-)$1	236	198	229	25.1280
ggggg[cccvvvvvvvvvvvvvccc]ggggg	chr10:67558393-67558628(-)$1	235	37	68	26.1413
c[ggggggguuuuuuuuuuuuggggggg]cc	chr5:34343833-34344118(+)$1	285	236	267	25.9084
bbgggggggwwwwwwwwwwwwwwggggggg]	chr11:41946367-41946629(-)$1	262	82	113	24.2287

#otherMatches

#Seq PSSM
uaccugccagaugcuauacuaugucauggug	chr13:100195453-100195707(-)$1	254	59	90	22.9732
AGAGAAAAAAAGAAAAAGUCCUUCAGUUUAG	chr11:51799897-51800143(-)$1	246	61	92	19.8597
GGGGGUUCUUUCUUCUGAUAAUUCUAGAGCC	chr1:66488858-66489099(+)$1	241	143	174	24.1056
GCGCgugucugugugucugugucugugugug	chr11:77524382-77524622(+)$1	240	196	227	26.2343
uuguguaaguguguguaaguaugcauggaug	chr1:175265869-175266113(-)$1	244	89	120	25.7590
UGCUGCUCCAGACACAUCCAGCAGGGAGCAG	chr15:98568195-98568451(-)$1	256	4	35	21.0714
AAAACUCAGAAUCAGAAAAACACUGAAUUAU	chr18:25636494-25636747(-)$1	253	167	198	23.1349
GUGAGUAGAAUACCCAGCACCGUCUCUCACC	chr14:34192179-34192416(-)$1	237	190	221	24.4994
UUCUUUACCUUUUAUUUCUUUUGUAAAUGAA	chr13:34994550-34994812(+)$1	262	2	33	23.7035
CCAGGCCAGUUACCCCGCUGUCUGUGUUGGA	chr11:105916222-105916468(+)$1	246	93	124	26.6804
GGCAUAUGCUGCAAACUUCCAAUAUGCUUAU	chrX:78340150-78340389(+)$1	239	125	156	25.7590
aaaaaAAAAAAAAAAAAAGGUUUUUUUCAUC	chr1:58583961-58584200(-)$1	239	107	138	24.0244
UCUUAUUAAUAAGAUUAACAUAUUUAGUGAG	chr10:110733431-110733666(+)$1	235	156	187	25.3173
UGAAGAGGCUACAGAAACAAUGCCCAGAUUU	chr16:44085816-44086071(-)$1	255	181	212	27.0007
AAGUAGGUAGAAUUUUUGCUAUGCUGUAACU	chr18:34478851-34479088(+)$1	237	62	93	25.8035
CUGUGAACCUGUAUAUUAUUCAAAUGGCUAC	chr6:71341915-71342171(-)$1	256	144	175	22.3020
AACUUCCAUAAUCUAUAUUAAAUGAGGGUUU	chr11:109530312-109530563(+)$1	251	77	108	26.8980
AGUAUAGCUUUUUCCAUCUCACAUUAGCUAU	chrX:137009737-137009977(+)$1	240	153	184	24.4032
UAUAAAAAUUAGCCCUCAACAGAUUUCAGAA	chr2:122510412-122510649(-)$1	237	163	194	22.8983
AAGCUUUAGUUCUAAGAAUCUACUCAUGCUU	chr19:59371866-59372114(-)$1	248	148	179	24.6378
UUUAUCAGUUCUAUUUUUCUAUUGAUUCUUU	chr12:39358640-39358903(+)$1	263	55	86	22.3510
AUGUCAUAGCCUCUCUAACUGUAUGAUAAUU	chr5:122903787-122904080(-)$1	293	107	138	23.4537
AAUAAUUUCUGUAUGUGAUCAAGAGUUUAUU	chr5:32794483-32794768(+)$1	285	148	179	24.4701
CAGUGUUAAAAGAAAAUAAAUUACAAUUGAU	chr15:30958338-30958591(+)$1	253	8	39	21.7330
CCAGCCUGCUCGGCUUCUUCUGUAGGUCUGA	chr5:122906402-122906659(-)$1	257	55	86	24.8239
CGACUGUAUGUUCUGUGUAUAAUGCUGUUCU	chr18:34481615-34481852(+)$1	237	80	111	24.9920
CUGCGACAUACUUAGUACCACAUGUCGCUAC	chr9:72595391-72595637(+)$1	246	40	71	21.5255
UGUAUAGUUUUUUUUUCUUUUGAUUAUACAA	chr11:42443035-42443275(+)$1	240	150	181	25.5664
CGCCAUAAAUAAAACAUUGAUUGGCAGGUUG	chr11:90139073-90139323(+)$1	250	215	246	22.6079
GCUGUGGAGUUGAUGGUGUUAUCCCAGUGCG	chr16:17044950-17045193(+)$1	243	20	51	24.1589
ACACAGUGGUCCUCUGCUCUCCACUCCCAUA	chr1:38852135-38852371(-)$1	236	87	118	23.4580
GGAAGGAGCCAAAAUAUCCCAUGCUUAAUCC	chr15:58615289-58615539(-)$1	250	76	107	24.2953
UAUGUACAGUUAUAUAUACCUCUCUCUAUGU	chr2:70438879-70439132(+)$1	253	189	220	18.1267
ACACGAGGCAGCCCCUCUACUUAGCUUUGUG	chr3:89238790-89239031(+)$1	241	38	69	25.3173
CUUGCCUCCUAUGUUGCUUAAGCGAGCUGAU	chr19:58870931-58871176(-)$1	245	111	142	22.7070
CAGAUAUAUCUUAAUAACUUAAUGUAAACUG	chr5:14863241-14863485(+)$1	244	134	165	24.8759
AACGUGGGCGUCUAGCUGCUUCUCCUACGUA	chr16:84954981-84955283(-)$1	302	137	168	23.1140
AAGAGACAGAAUCAACAUACCUUUGCUCUCU	chr5:23011882-23012127(-)$1	245	198	229	22.1043
UCUACAGACAUUCUGGCUUCCUUUGAGGACA	chr10:80169675-80169910(-)$1	235	18	49	23.2995
UCUUGUGCUUCUUCAAAAACAAAGGGCAAGA	chr5:139494237-139494472(-)$1	235	19	50	23.2621
UCAUGGUCUAAUCACAUUUAUAAGACCAUGA	chr11:41945233-41945477(-)$1	244	177	208	26.6605
CACAAGAAUUCCCUCUGCCUCCCUCGUGCCU	chr5:113672263-113672498(-)$1	235	9	40	21.6617
GAUGUGAUUUUUUUUGUAGUUAUUAUAUAUA	chr1:33855577-33855826(-)$1	249	8	39	23.4537
CUCCAACGUAACUGCAAUUUAAUGUUGGUAG	chr4:40680719-40680957(+)$1	238	56	87	23.8428
AAUGCACCACACAACAUUUUCUGUUAAAUUA	chr2:73450408-73450703(-)$1	295	200	231	19.7141
CCCUCUCUCUCCUUCUCUCUGUGAGGGGGGA	chr9:107998481-107998718(-)$1	237	140	171	26.2470
AAAUAAAGCUAAUUAAACGUCUGUGUAAAUU	chr5:65986221-65986472(+)$1	251	126	157	24.3015
GCGCgugucugugugucugugucugugugug	chr11:77524443-77524703(+)$1	260	135	166	26.2343
UAAAAGAGGUCCAUUAAUAUUCCUUAUAAAA	chr11:41945344-41945595(-)$1	251	139	170	21.0299
GGGUGUUAGUCCUUCUACUUUCUAUCUCACC	chr6:125171712-125171970(+)$1	258	134	165	25.9012
UAGCGUUUGCACUGACUAACAAGAUGGUAUU	chr2:37229678-37229920(-)$1	242	132	163	24.2085
UGGUUAUGCUUAAAUAUGAAUGUAAUUACCA	chr10:98487879-98488126(+)$1	247	70	101	27.3918
UAAAAGAUACAUUUUACAUUUCAUCAAAUUG	chr10:94254917-94255155(-)$1	238	163	194	25.3056
UGUAGAGUGAUCCAUUUGCUUACACUGUUGC	chr2:35035992-35036228(-)$1	236	198	229	25.1280
guuuguuuguuuguuuguuuUUUAAUUAAAC	chr10:67558393-67558628(-)$1	235	37	68	26.1413
CAUUGUGGACCAUCUGAACUAUCCACAAAGC	chr5:34343833-34344118(+)$1	285	236	267	25.9084
ACCUAUGUCUUUAUUGCACAAAUGAUAUAGU	chr11:41946367-41946629(-)$1	262	82	113	24.2287

#DB
((((((.((............)).)).))))	chr13:100195453-100195707(-)$1	1	59	90	22.9732
(..(((...............)))..).)))	chr11:51799897-51800143(-)$1	1	61	92	19.8597
(.(((((((................))))))	chr1:66488858-66489099(+)$1	1	143	174	24.1056
(((((.(.(...........).)))))))))	chr11:77524382-77524622(+)$1	1	196	227	26.2343
(((((((..............))))))))))	chr1:175265869-175266113(-)$1	1	89	120	25.7590
(((((((((...............)))))))	chr15:98568195-98568451(-)$1	1	4	35	21.0714
((((.((((.............)))).)).)	chr18:25636494-25636747(-)$1	1	167	198	23.1349
(((((.(((.............)))))))).	chr14:34192179-34192416(-)$1	1	190	221	24.4994
((((((((..............))))).)))	chr13:34994550-34994812(+)$1	1	2	33	23.7035
((((..(((............)))..)))))	chr11:105916222-105916468(+)$1	1	93	124	26.6804
(((((((..............))))))))))	chrX:78340150-78340389(+)$1	1	125	156	25.7590
..(((((((...........)))))))..))	chr1:58583961-58584200(-)$1	1	107	138	24.0244
(((((((((..............))))))))	chr10:110733431-110733666(+)$1	1	156	187	25.3173
(((((((((............)))....)))	chr16:44085816-44086071(-)$1	1	181	212	27.0007
.(((.((((............))))...)))	chr18:34478851-34479088(+)$1	1	62	93	25.8035
(((((..((................)).)))	chr6:71341915-71342171(-)$1	1	144	175	22.3020
(((((.(((............))).))))))	chr11:109530312-109530563(+)$1	1	77	108	26.8980
(((((((((................))))))	chrX:137009737-137009977(+)$1	1	153	184	24.4032
(....(((((...........))))).))))	chr2:122510412-122510649(-)$1	1	163	194	22.8983
((((...(((...........)))...))))	chr19:59371866-59372114(-)$1	1	148	179	24.6378
...((((((...........))))))....)	chr12:39358640-39358903(+)$1	1	55	86	22.3510
.(((((((.............))))))).((	chr5:122903787-122904080(-)$1	1	107	138	23.4537
(((((.((((...........)))).)))))	chr5:32794483-32794768(+)$1	1	148	179	24.4701
((((((................)).))))..	chr15:30958338-30958591(+)$1	1	8	39	21.7330
.((((((((............))))).))).	chr5:122906402-122906659(-)$1	1	55	86	24.8239
.(((.((((............)))).)))..	chr18:34481615-34481852(+)$1	1	80	111	24.9920
(((((((((............))))))((((	chr9:72595391-72595637(+)$1	1	40	71	21.5255
(((((((((............))))))))).	chr11:42443035-42443275(+)$1	1	150	181	25.5664
(((((................)))).)...)	chr11:90139073-90139323(+)$1	1	215	246	22.6079
((((.(((.............))))))))))	chr16:17044950-17045193(+)$1	1	20	51	24.1589
(...(((((...........)))))....))	chr1:38852135-38852371(-)$1	1	87	118	23.4580
(((..((((.............))))..)))	chr15:58615289-58615539(-)$1	1	76	107	24.2953
((((((((....................)))	chr2:70438879-70439132(+)$1	1	189	220	18.1267
(((((((((..............))))))))	chr3:89238790-89239031(+)$1	1	38	69	25.3173
(((((................)))))..)))	chr19:58870931-58871176(-)$1	1	111	142	22.7070
(((.(((((............)))))..)))	chr5:14863241-14863485(+)$1	1	134	165	24.8759
.(((((((.(...........).))))))).	chr16:84954981-84955283(-)$1	1	137	168	23.1140
.(((((((((...........)))).)))))	chr5:23011882-23012127(-)$1	1	198	229	22.1043
(((.((((.............)))).)))).	chr10:80169675-80169910(-)$1	1	18	49	23.2995
((((((.(((...........))).))))))	chr5:139494237-139494472(-)$1	1	19	50	23.2621
(((((((((.............)))))))))	chr11:41945233-41945477(-)$1	1	177	208	26.6605
(((.((................)).))))))	chr5:113672263-113672498(-)$1	1	9	40	21.6617
.(((((((.............))))))).((	chr1:33855577-33855826(-)$1	1	8	39	23.4537
))(((((((............)))))))..(	chr4:40680719-40680957(+)$1	1	56	87	23.8428
...(((...............)))....)))	chr2:73450408-73450703(-)$1	1	200	231	19.7141
(((((((.(...........).)))))))))	chr9:107998481-107998718(-)$1	1	140	171	26.2470
((((...((.............))....)))	chr5:65986221-65986472(+)$1	1	126	157	24.3015
(((((.(.(...........).)))))))))	chr11:77524443-77524703(+)$1	1	135	166	26.2343
.....((((............))))......	chr11:41945344-41945595(-)$1	1	139	170	21.0299
(((((.(((............)))...))))	chr6:125171712-125171970(+)$1	1	134	165	25.9012
((.(((((.............))))).))))	chr2:37229678-37229920(-)$1	1	132	163	24.2085
((((..(((............)))...))))	chr10:98487879-98488126(+)$1	1	70	101	27.3918
(((..(((..............)))...)))	chr10:94254917-94255155(-)$1	1	163	194	25.3056
(((((((((.............)))).))))	chr2:35035992-35036228(-)$1	1	198	229	25.1280
(((((.(((.............))).)))))	chr10:67558393-67558628(-)$1	1	37	68	26.1413
(.(((((((............))))))).))	chr5:34343833-34344118(+)$1	1	236	267	25.9084
(((((((((..............))))))).	chr11:41946367-41946629(-)$1	1	82	113	24.2287

#PSSM
e : 0.17	g : 0.14	= : 0.12	f : 0.08	i : 0.08	: : 0.07	d : 0.07	c : 0.05	a : 0.03	[ : 0.03	! : 0.01	" : 0.01	$ : 0.01	H : 0.01	# : 0.01	) : 0.01	b : 0.01	
e : 0.17	g : 0.17	= : 0.12	i : 0.08	c : 0.08	d : 0.08	f : 0.07	! : 0.03	[ : 0.03	# : 0.03	" : 0.03	H : 0.01	) : 0.01	b : 0.01	
g : 0.26	e : 0.15	= : 0.12	i : 0.08	d : 0.08	c : 0.07	f : 0.05	# : 0.03	" : 0.03	! : 0.01	b : 0.01	H : 0.01	) : 0.01	[ : 0.01	
g : 0.26	e : 0.14	= : 0.12	f : 0.08	c : 0.08	i : 0.08	d : 0.05	[ : 0.05	! : 0.03	b : 0.01	# : 0.01	" : 0.01	) : 0.01	
g : 0.22	e : 0.15	= : 0.12	i : 0.08	[ : 0.07	! : 0.07	f : 0.07	b : 0.05	c : 0.03	" : 0.03	d : 0.03	# : 0.01	) : 0.01	
g : 0.15	[ : 0.12	d : 0.12	e : 0.12	= : 0.08	i : 0.08	c : 0.07	b : 0.05	! : 0.05	f : 0.05	" : 0.03	y : 0.03	
d : 0.15	c : 0.15	g : 0.14	e : 0.10	= : 0.08	i : 0.08	y : 0.07	[ : 0.03	x : 0.03	a : 0.03	" : 0.03	f : 0.03	! : 0.01	
c : 0.19	d : 0.15	g : 0.14	e : 0.10	i : 0.08	y : 0.07	b : 0.05	[ : 0.05	x : 0.03	w : 0.03	f : 0.03	= : 0.03	
c : 0.15	d : 0.14	g : 0.08	i : 0.08	v : 0.08	w : 0.07	e : 0.07	y : 0.07	b : 0.05	a : 0.05	x : 0.03	f : 0.03	^ : 0.01	[ : 0.01	= : 0.01	
u : 0.26	v : 0.21	y : 0.12	w : 0.12	t : 0.10	x : 0.05	c : 0.03	d : 0.03	e : 0.01	^ : 0.01	a : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	t : 0.21	v : 0.21	y : 0.12	w : 0.12	x : 0.05	^ : 0.01	
u : 0.26	v : 0.21	y : 0.12	w : 0.12	t : 0.10	x : 0.05	a : 0.05	g : 0.01	f : 0.01	e : 0.01	^ : 0.01	
c : 0.17	v : 0.12	d : 0.12	e : 0.10	y : 0.08	w : 0.08	g : 0.08	] : 0.05	= : 0.03	f : 0.03	b : 0.01	x : 0.01	i : 0.01	^ : 0.01	a : 0.01	
c : 0.22	d : 0.17	e : 0.12	g : 0.08	b : 0.07	= : 0.07	y : 0.05	w : 0.05	a : 0.03	f : 0.03	x : 0.01	i : 0.01	^ : 0.01	] : 0.01	
c : 0.22	d : 0.17	e : 0.12	g : 0.12	= : 0.10	y : 0.05	i : 0.05	b : 0.05	f : 0.03	] : 0.01	x : 0.01	^ : 0.01	
d : 0.19	e : 0.12	g : 0.12	= : 0.10	i : 0.07	] : 0.07	y : 0.05	c : 0.05	4 : 0.05	3 : 0.05	2 : 0.03	f : 0.03	b : 0.01	^ : 0.01	
g : 0.15	e : 0.12	= : 0.10	d : 0.10	] : 0.10	i : 0.08	3 : 0.08	4 : 0.07	f : 0.05	b : 0.03	2 : 0.03	^ : 0.01	> : 0.01	
g : 0.21	] : 0.10	= : 0.10	i : 0.08	4 : 0.08	3 : 0.08	d : 0.07	e : 0.05	2 : 0.05	a : 0.03	f : 0.03	b : 0.01	c : 0.01	^ : 0.01	> : 0.01	
g : 0.22	= : 0.10	i : 0.08	4 : 0.08	d : 0.08	f : 0.07	2 : 0.07	] : 0.05	e : 0.05	3 : 0.05	c : 0.05	b : 0.01	^ : 0.01	> : 0.01	
g : 0.19	e : 0.17	= : 0.12	i : 0.08	c : 0.08	f : 0.07	d : 0.07	: : 0.05	4 : 0.03	b : 0.01	2 : 0.01	3 : 0.01	h : 0.01	> : 0.01	] : 0.01	
g : 0.24	e : 0.19	= : 0.12	i : 0.08	c : 0.08	f : 0.07	3 : 0.05	d : 0.05	] : 0.01	4 : 0.01	: : 0.01	h : 0.01	> : 0.01	
g : 0.21	e : 0.17	= : 0.14	f : 0.08	i : 0.07	c : 0.07	d : 0.07	2 : 0.03	3 : 0.03	: : 0.03	] : 0.03	h : 0.01	> : 0.01	

#score	1370.6697841266516
#seq	57
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_CDS_m2_run1.txt

#BEAR
dcccqqqqqqqqccc]	chr8:71425001-71425238(+)$1	237	130	146	13.7032
:cccqqqqqqqqccc:	chr1:89088986-89089221(+)$1	235	169	185	12.0148
ggggqqqqqqqqgggg	chr2:164824339-164824574(+)$1	235	152	168	12.6858
Ecccqqqqqqqqcccc	chr10:127478579-127478814(+)$1	235	9	25	12.7698
!cccrrrrrrrrrccc	chr11:109528792-109529029(+)$1	237	154	170	7.9277
[cccqqqqqqqqccc]	chr2:154519610-154519845(+)$1	235	148	164	13.8435
:cccqqqqqqqqcccF	chr11:21457365-21457606(-)$1	241	96	112	12.3579
ggggqqqqqqqqgggg	chr16:58732621-58732862(+)$1	241	219	235	12.6858
#cccwwwwwwwwwwww	chr2:113875924-113876162(-)$1	238	10	26	8.6091
a!!aqqqqqqqqa22a	chr4:126425743-126425995(-)$1	252	196	212	12.4082
ddddqqqqqqqqdddd	chr2:76723068-76723305(-)$1	237	190	206	12.5300
ggggqqqqqqqqgggg	chr15:100228029-100228266(-)$1	237	91	107	12.6858
ddddqqqqqqqqdddd	chr5:122941662-122941901(-)$1	239	190	206	12.5300
ddbbqqqqqqqqbb22	chr5:122915945-122916192(-)$1	247	124	140	11.7459
ddddwwwwwwwwwwww	chr2:76648356-76648591(-)$1	235	95	111	8.1928
eeeeqqqqqqqqeeee	chr14:37935173-37935433(-)$1	260	198	214	11.9390
[cccqqqqqqqqccc]	chr2:163842323-163842558(+)$1	235	131	147	13.8435
cc[aqqqqqqqqa]cc	chr14:21598358-21598594(-)$1	236	57	73	13.0472
gg[aqqqqqqqqa]gg	chr14:55570985-55571225(-)$1	240	114	130	12.8111
ddddqqqqqqqqdddd	chr14:55565114-55565368(-)$1	254	27	43	12.5300
ddddqqqqqqqqdddd	chr5:23633758-23634000(+)$1	242	16	32	12.5300
ffffqqqqqqqqffff	chr2:156795708-156795945(-)$1	237	210	226	11.8964
[cccqqqqqqqqccc]	chr11:54792867-54793114(-)$1	247	51	67	13.8435
[cccqqqqqqqqccc]	chr3:95292215-95292460(+)$1	245	108	124	13.8435
ddddqqqqqqqqdddd	chr10:81028331-81028570(+)$1	239	85	101	12.5300
:cccqqqqqqqqccc:	chr8:23678766-23679001(+)$1	235	209	225	12.0148
ffffqqqqqqqqffff	chr5:122907217-122907452(-)$1	235	199	215	11.8964
!!bbqqqqqqqqbb22	chr1:137742034-137742281(+)$1	247	96	112	11.8588
eeeeqqqqqqqqeeee	chrX:12738490-12738727(+)$1	237	170	186	11.9390

#otherMatches

#Seq PSSM
UGGAUAAGCGACUCCU	chr8:71425001-71425238(+)$1	237	130	146	13.7032
CCUGCCCCAUCUCAGU	chr1:89088986-89089221(+)$1	235	169	185	12.0148
AGCCCCUCUCAAGGCU	chr2:164824339-164824574(+)$1	235	152	168	12.6858
AGACCCUAUUAUGUCA	chr10:127478579-127478814(+)$1	235	9	25	12.7698
AUGCUUCACUCACGCA	chr11:109528792-109529029(+)$1	237	154	170	7.9277
GCUGGGCCCAGACGGA	chr2:154519610-154519845(+)$1	235	148	164	13.8435
ACCUGACAGCAAAGGA	chr11:21457365-21457606(-)$1	241	96	112	12.3579
GAACCUCUGAACGUUC	chr16:58732621-58732862(+)$1	241	219	235	12.6858
AGCCCCGCUGAACCCC	chr2:113875924-113876162(-)$1	238	10	26	8.6091
UGACAUUUCGCAGCAG	chr4:126425743-126425995(-)$1	252	196	212	12.4082
GGAUUGCUUGCCAUCC	chr2:76723068-76723305(-)$1	237	190	206	12.5300
GUCCAGGAGCUAGGGC	chr15:100228029-100228266(-)$1	237	91	107	12.6858
UGCAAUCGUGGGUGUG	chr5:122941662-122941901(-)$1	239	190	206	12.5300
UUGGAGAAGCUACCGA	chr5:122915945-122916192(-)$1	247	124	140	11.7459
AGCCCAAAACAUUCCG	chr2:76648356-76648591(-)$1	235	95	111	8.1928
GGUUUAGAAGAUAGCC	chr14:37935173-37935433(-)$1	260	198	214	11.9390
GAACUAAUGUCUGUUG	chr2:163842323-163842558(+)$1	235	131	147	13.8435
CCAGGGCUACAACAGG	chr14:21598358-21598594(-)$1	236	57	73	13.0472
AGCUGCAGAAGAAACU	chr14:55570985-55571225(-)$1	240	114	130	12.8111
CAGCUGGAUGAUGCUG	chr14:55565114-55565368(-)$1	254	27	43	12.5300
UUAAUAUUCCCUUUAA	chr5:23633758-23634000(+)$1	242	16	32	12.5300
UGGUUUUCUUGUGCUA	chr2:156795708-156795945(-)$1	237	210	226	11.8964
AUGAUUACUUUCUCAC	chr11:54792867-54793114(-)$1	247	51	67	13.8435
AUCUAAGACCCGAGAA	chr3:95292215-95292460(+)$1	245	108	124	13.8435
UGACGGAGAGAAGUCG	chr10:81028331-81028570(+)$1	239	85	101	12.5300
CGCCUUCCAGAUGGCU	chr8:23678766-23679001(+)$1	235	209	225	12.0148
UGGCAUUUCCUGGCCG	chr5:122907217-122907452(-)$1	235	199	215	11.8964
GAGCAAGAGGAGGCAG	chr1:137742034-137742281(+)$1	247	96	112	11.8588
GUUAAGAAAUCAUAAC	chrX:12738490-12738727(+)$1	237	170	186	11.9390

#DB
((((........))).	chr8:71425001-71425238(+)$1	1	130	146	13.7032
.(((........))).	chr1:89088986-89089221(+)$1	1	169	185	12.0148
((((........))))	chr2:164824339-164824574(+)$1	1	152	168	12.6858
((((........)))(	chr10:127478579-127478814(+)$1	1	9	25	12.7698
.(((.........)))	chr11:109528792-109529029(+)$1	1	154	170	7.9277
.(((........))).	chr2:154519610-154519845(+)$1	1	148	164	13.8435
.(((........))))	chr11:21457365-21457606(-)$1	1	96	112	12.3579
((((........))))	chr16:58732621-58732862(+)$1	1	219	235	12.6858
.(((............	chr2:113875924-113876162(-)$1	1	10	26	8.6091
(..(........)..)	chr4:126425743-126425995(-)$1	1	196	212	12.4082
((((........))))	chr2:76723068-76723305(-)$1	1	190	206	12.5300
((((........))))	chr15:100228029-100228266(-)$1	1	91	107	12.6858
((((........))))	chr5:122941662-122941901(-)$1	1	190	206	12.5300
((((........))..	chr5:122915945-122916192(-)$1	1	124	140	11.7459
((((............	chr2:76648356-76648591(-)$1	1	95	111	8.1928
((((........))))	chr14:37935173-37935433(-)$1	1	198	214	11.9390
.(((........))).	chr2:163842323-163842558(+)$1	1	131	147	13.8435
((.(........).))	chr14:21598358-21598594(-)$1	1	57	73	13.0472
((.(........).))	chr14:55570985-55571225(-)$1	1	114	130	12.8111
((((........))))	chr14:55565114-55565368(-)$1	1	27	43	12.5300
((((........))))	chr5:23633758-23634000(+)$1	1	16	32	12.5300
((((........))))	chr2:156795708-156795945(-)$1	1	210	226	11.8964
.(((........))).	chr11:54792867-54793114(-)$1	1	51	67	13.8435
.(((........))).	chr3:95292215-95292460(+)$1	1	108	124	13.8435
((((........))))	chr10:81028331-81028570(+)$1	1	85	101	12.5300
.(((........))).	chr8:23678766-23679001(+)$1	1	209	225	12.0148
((((........))))	chr5:122907217-122907452(-)$1	1	199	215	11.8964
..((........))..	chr1:137742034-137742281(+)$1	1	96	112	11.8588
((((........))))	chrX:12738490-12738727(+)$1	1	170	186	11.9390

#PSSM
d : 0.27	g : 0.13	[ : 0.13	: : 0.10	! : 0.06	e : 0.06	f : 0.06	E : 0.03	# : 0.03	a : 0.03	c : 0.03	
c : 0.41	d : 0.24	g : 0.13	! : 0.06	e : 0.06	f : 0.06	
c : 0.37	d : 0.20	g : 0.10	b : 0.06	e : 0.06	[ : 0.06	f : 0.06	! : 0.03	
c : 0.37	d : 0.20	g : 0.10	a : 0.10	b : 0.06	e : 0.06	f : 0.06	
q : 0.89	w : 0.06	r : 0.03	
q : 0.89	w : 0.06	r : 0.03	
q : 0.89	w : 0.06	r : 0.03	
q : 0.89	w : 0.06	r : 0.03	
q : 0.89	w : 0.06	r : 0.03	
q : 0.89	w : 0.06	r : 0.03	
q : 0.89	w : 0.06	r : 0.03	
q : 0.89	w : 0.06	r : 0.03	
c : 0.31	d : 0.17	g : 0.10	a : 0.10	w : 0.06	b : 0.06	e : 0.06	f : 0.06	r : 0.03	
c : 0.34	d : 0.17	g : 0.10	w : 0.06	b : 0.06	e : 0.06	] : 0.06	f : 0.06	2 : 0.03	
c : 0.37	d : 0.17	g : 0.13	2 : 0.10	w : 0.06	e : 0.06	f : 0.06	
] : 0.17	d : 0.17	g : 0.13	c : 0.10	: : 0.06	w : 0.06	2 : 0.06	e : 0.06	f : 0.06	F : 0.03	a : 0.03	

#score	353.2151143648723
#seq	29
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_CDS_m2_run2.txt

#BEAR
gggggggtttttttttttggggggg::	chr9:21479490-21479710(+)$1	220	77	104	21.9001
ffffffuuuuuuuuuuuuffffff444	chr10:39582438-39582678(+)$1	240	172	199	23.4661
##dddduuuuuuuuuuuudddd333cc	chr13:44918665-44918885(+)$1	220	160	187	24.5263
ccc[ccctttttttttttccc]ccc::	chr19:21900535-21900756(+)$1	221	83	110	22.0846
""dddduuuuuuuuuuuudddd22ggg	chr19:60897018-60897238(+)$1	220	160	187	24.1129
afffffftttttttttttffffff333	chr18:24172635-24172855(-)$1	220	16	43	22.8573
ggggggvvvvvvvvvvvvvgggggggf	chr17:68159103-68159348(+)$1	245	25	52	24.7395
c[ddddtttttttttttdddd]cccgg	chr8:90674039-90674264(+)$1	225	40	67	22.8491
!!eeeeettttttttttteeeee22bb	chr10:79281969-79282189(+)$1	220	91	118	22.5683
a!!cccuuuuuuuuuuuuccc22a]bb	chr14:31772291-31772511(+)$1	220	42	69	24.6066
gggggggtttttttttttggggggg]g	chr5:73691831-73692066(+)$1	235	129	156	23.7217
ee[cccwwwwwwwwwwwwwwccc]eee	chr17:72155911-72156180(+)$1	269	200	227	22.9007
bb[cccuuuuuuuuuuuucccbb]ddd	chr16:87487854-87488074(-)$1	220	66	93	23.4410
ggggggwwwwwwwwwwwwwwggggggg	chr9:120482824-120483044(+)$1	220	94	121	23.3373
!!cccvvvvvvvvvvvvvccc22a22g	chr14:30783149-30783369(+)$1	220	153	180	24.3068
eeeeeattttttttttta]eeeee22e	chrX:12671074-12671316(+)$1	242	97	124	22.6579
======uuuuuuuuuuuu=========	chr13:73921949-73922169(+)$1	220	85	112	25.1029
a[ddddtttttttttttdddda]ffff	chr8:108765975-108766198(+)$1	223	67	94	22.6050
ee[ddddtttttttttttddddeeeee	chr14:76513876-76514096(+)$1	220	152	179	22.6032
ggggccctttttttttttccc::dddd	chr2:121260529-121260749(+)$1	220	74	101	21.5185
ggggggtttttttttttggggggg]ee	chr6:3542355-3542575(+)$1	220	13	40	23.2307
eeecccyyyyyyyyyyyyyyyyccc::	chr19:45076065-45076285(+)$1	220	15	42	19.0330
beeeeeuuuuuuuuuuuueeeee22bb	chr4:123028163-123028392(-)$1	229	88	115	22.9972
##dddduuuuuuuuuuuudddd]bb22	chr8:124530918-124531138(+)$1	220	78	105	23.2876
=======ttttttttttt=========	chr1:82337136-82337356(+)$1	220	162	189	24.0253
ggggggwwwwwwwwwwwwwwggggggg	chr12:111903890-111904112(+)$1	222	73	100	23.3373
[eeeeevvvvvvvvvvvvveeeee]ee	chr6:91469460-91469684(+)$1	224	83	110	23.9294
$cccyyyyyyyyyyyyyyyyccc333f	chr14:121316513-121316733(+)$1	220	113	140	21.3914
ggggggtttttttttttggggggg]ee	chr11:30715478-30715698(+)$1	220	170	197	23.2307
hhhhhhuuuuuuuuuuuuhhhhhhhhF	chr17:46398422-46398642(-)$1	220	154	181	21.7121
ccccccvvvvvvvvvvvvvccc]ccc]	chr4:138953254-138953474(+)$1	220	159	186	24.7480
'fffffftttttttttttffffff666	chr4:46160220-46160452(+)$1	232	127	154	20.7606
deeeeevvvvvvvvvvvvveeeee]dd	chr7:107778266-107778495(+)$1	229	131	158	23.4839
###bbvvvvvvvvvvvvvbb333gggg	chr2:155922456-155922676(-)$1	220	96	123	23.3050
&bb[ccctttttttttttccc]bb777	chr7:6661551-6661773(-)$1	222	151	178	20.6934
!ddddwwwwwwwwwwwwwwddddffff	chr12:71561238-71561458(+)$1	220	108	135	21.9638
cccddddtttttttttttdddd22ccc	chr11:86503392-86503612(+)$1	220	62	89	22.7918
gggggguuuuuuuuuuuuggggggg::	chr8:36532264-36532489(-)$1	225	26	53	23.0243
ffffffwwwwwwwwwwwwwwffffff2	chr11:105114514-105114734(+)$1	220	64	91	21.6462
fffffftttttttttttffffff]a]e	chr10:66702080-66702303(+)$1	223	155	182	22.1175
hcccbbuuuuuuuuuuuubb]ccc444	chr19:5963715-5963935(-)$1	220	169	196	23.3131
:eeeeeuuuuuuuuuuuueeeeeeeee	chr9:60718483-60718705(+)$1	222	2	29	22.4984
a[ddddbbtttttttttttbb]dddd]	chr9:118466128-118466348(+)$1	220	124	151	20.3397
fffbbwwwwwwwwwwwwwwbb]fffff	chr11:76759645-76759865(+)$1	220	89	116	21.2802
ffffffuuuuuuuuuuuuffffffeee	chr13:13788771-13788991(+)$1	220	112	139	23.1714
d[dddduuuuuuuuuuuudddd]dddd	chr18:45005296-45005516(+)$1	220	143	170	23.5374
%%cccvvvvvvvvvvvvvccc]=====	chr11:23180318-23180541(+)$1	223	131	158	23.5911
a!!cccuuuuuuuuuuuuccc22a]cc	chr12:66109520-66109746(+)$1	226	91	118	24.9822
e!!cccvvvvvvvvvvvvvccc]eeee	chr4:126781540-126781760(+)$1	220	162	189	24.7067
c!!cccwwwwwwwwwwwwwwccc22cc	chr1:71619450-71619670(+)$1	220	29	56	23.2073
[cccwwwwwwwwwwwwwwccc333ddd	chr4:41326700-41326921(+)$1	221	162	189	22.5125
gggggguuuuuuuuuuuuggggggg]b	chr2:121126656-121126876(+)$1	220	174	201	24.6495
[ddddvvvvvvvvvvvvvddddhhhhh	chr15:80079766-80079987(+)$1	221	72	99	22.7164
======wwwwwwwwwwwwww=======	chr16:15752729-15752949(+)$1	220	19	46	23.5776
iiiiiiwwwwwwwwwwwwwwiiiiiii	chr3:107134778-107135011(-)$1	233	172	199	23.3305
eeee[bbtttttttttttbbeeeee]b	chr7:29603441-29603661(+)$1	220	45	72	21.9547
::ddddtttttttttttddddiiiiii	chr15:58775322-58775549(-)$1	227	130	157	20.9930
hhhhhhvvvvvvvvvvvvvhhhhhhhh	chr17:15862244-15862465(+)$1	221	99	126	22.1621
======vvvvvvvvvvvvv========	chr13:36338137-36338357(+)$1	220	110	137	25.0978
dd[ddddtttttttttttdddd]dddd	chr5:92890963-92891183(-)$1	220	124	151	22.3393
ff[cccvvvvvvvvvvvvvccc333ff	chr2:29004064-29004298(+)$1	234	178	205	24.9034

#otherMatches

#Seq PSSM
CUGAGUAUUUCAUUUUCCUGCUCAGUA	chr9:21479490-21479710(+)$1	220	77	104	21.9001
AGAGACUCUUGCCCUGCUGUCUCUAAG	chr10:39582438-39582678(+)$1	240	172	199	23.4661
GAAUGCACAGAAAAGGCAGCAUGGGGA	chr13:44918665-44918885(+)$1	220	160	187	24.5263
GUGGCCAAAACAAGUACAUGGGCACAG	chr19:21900535-21900756(+)$1	221	83	110	22.0846
CUGCCAGAGUGAAGAAAAUGGCUCUUU	chr19:60897018-60897238(+)$1	220	160	187	24.1129
cccuacaaaugccuugaaugugggaaa	chr18:24172635-24172855(-)$1	220	16	43	22.8573
UUGACAGAGGUUUAUGAAGUGUUAACC	chr17:68159103-68159348(+)$1	245	25	52	24.7395
GGUAUGAAUACUGGCAACAUGGUCAUU	chr8:90674039-90674264(+)$1	225	40	67	22.8491
GGUUAUCAGAACGUGGAAGAUGAAGCA	chr10:79281969-79282189(+)$1	220	91	118	22.5683
CAAUGCCAAAAGUUUACAGCACAGAGC	chr14:31772291-31772511(+)$1	220	42	69	24.6066
GUGUUCACAUUCACACUUUGGAUAUCU	chr5:73691831-73692066(+)$1	235	129	156	23.7217
UGGGGGGGAAAGUUUCAACACCCGUGG	chr17:72155911-72156180(+)$1	269	200	227	22.9007
AACACCAAGACUGUGACAGGUUUGAAA	chr16:87487854-87488074(-)$1	220	66	93	23.4410
GAAGGCAAAGAAAAUGGUAAGUCUUCA	chr9:120482824-120483044(+)$1	220	94	121	23.3373
GUAAGUAUAAAAGCAuuucuuuaauug	chr14:30783149-30783369(+)$1	220	153	180	24.3068
GCAGACAAAAUUGCAAAGAUCUGCCCU	chrX:12671074-12671316(+)$1	242	97	124	22.6579
GAGGGGAAGAACAUGGCACUUUUUGAG	chr13:73921949-73922169(+)$1	220	85	112	25.1029
GACCUGUGUGUGACUGUCAGGCUCACU	chr8:108765975-108766198(+)$1	223	67	94	22.6050
UGGCUUUAAAAAUCAAGAAAAGUAUGA	chr14:76513876-76514096(+)$1	220	152	179	22.6032
GUGGCCACUGUAAGAAUCUGGAACCCA	chr2:121260529-121260749(+)$1	220	74	101	21.5185
GUCUGACCUCUUUACUAUUAGACUUGC	chr6:3542355-3542575(+)$1	220	13	40	23.2307
GACGAGGUCGAAGACGAAAAUACUCAU	chr19:45076065-45076285(+)$1	220	15	42	19.0330
CCUCUGACUUUGACCUUCUAGAGACGC	chr4:123028163-123028392(-)$1	229	88	115	22.9972
CAGGGCCACCUCCACAUUGCCCAGGUG	chr8:124530918-124531138(+)$1	220	78	105	23.2876
CACCUUCUCCCUGCUUACGGGGGUGGU	chr1:82337136-82337356(+)$1	220	162	189	24.0253
AGCUGCAGAACAUCUCACAAGCAGCUG	chr12:111903890-111904112(+)$1	222	73	100	23.3373
CUUAUGAUCAACAUUUAAAUAUGAUCC	chr6:91469460-91469684(+)$1	224	83	110	23.9294
AAGCCAUCAGAAACACAACCGCUGCCG	chr14:121316513-121316733(+)$1	220	113	140	21.3914
UUAGGCUUAUCUUCUACGUUUAGUACA	chr11:30715478-30715698(+)$1	220	170	197	23.2307
CCUCAGCUACCAGACGCACUGAGGCCU	chr17:46398422-46398642(-)$1	220	154	181	21.7121
GCAAGCUCCAUUUCUGAAUGCUGUGCU	chr4:138953254-138953474(+)$1	220	159	186	24.7480
AUGAUUCGUCAACUUAAAGAAUCACUA	chr4:46160220-46160452(+)$1	232	127	154	20.7606
GCUUGAUUCCUAGCUACAUUCGAGACU	chr7:107778266-107778495(+)$1	229	131	158	23.4839
CAUCCAAUAACUAAGAAAGGUAUGCUU	chr2:155922456-155922676(-)$1	220	96	123	23.3050
AUGACCUCACAAGCCACCAGGACACCC	chr7:6661551-6661773(-)$1	222	151	178	20.6934
AGCACUUUUUCAACUCUCUGUGUACAU	chr12:71561238-71561458(+)$1	220	108	135	21.9638
UCACCCAUGCAAAAACCUUGGGACUGA	chr11:86503392-86503612(+)$1	220	62	89	22.7918
cCGAGUUCUUAAUUACUUACUUGGUUC	chr8:36532264-36532489(-)$1	225	26	53	23.0243
CUGAAAUCGCCACCAUUGUUUUUCAGG	chr11:105114514-105114734(+)$1	220	64	91	21.6462
AAGGGCUUCAUGCCAGUGUCCUUACCG	chr10:66702080-66702303(+)$1	223	155	182	22.1175
GGUCCCGACUAAACAACAGGUGACAUU	chr19:5963715-5963935(-)$1	220	169	196	23.3131
AAGCAGGAAGCAGAGAGACUGCUGGCG	chr9:60718483-60718705(+)$1	222	2	29	22.4984
GGUGGCGCGAUUGAAAGAGGCGGUCAG	chr9:118466128-118466348(+)$1	220	124	151	20.3397
UUCCCACAGGACUAAAUUCGGAGAAGG	chr11:76759645-76759865(+)$1	220	89	116	21.2802
UUCAGAUAUUAUUGACAUUUUGAGAAC	chr13:13788771-13788991(+)$1	220	112	139	23.1714
UGACUUAUUGGAUGAUGGAGGUGAUGC	chr18:45005296-45005516(+)$1	220	143	170	23.5374
AUGAGGAACAAUUUGAAACUCUGUUUA	chr11:23180318-23180541(+)$1	223	131	158	23.5911
AAUUUCAUCUGGAACAAAGGAUAUGGC	chr12:66109520-66109746(+)$1	226	91	118	24.9822
UCAUGAUCAGUUUUUAUUUUCAAAACC	chr4:126781540-126781760(+)$1	220	162	189	24.7067
AGAUGGACCAGUCCUACAAACCAGAUG	chr1:71619450-71619670(+)$1	220	29	56	23.2073
UGUGUACAGAAGAAUCAUCACCUCCAG	chr4:41326700-41326921(+)$1	221	162	189	22.5125
CCCUGCAGAUGCCUCCGAGCAGGGACG	chr2:121126656-121126876(+)$1	220	174	201	24.6495
CACCAUCAUGAAUGUCCCUGGUUUCUU	chr15:80079766-80079987(+)$1	221	72	99	22.7164
GAGGAGGAAAAUUAUUACAUUUUUUUG	chr16:15752729-15752949(+)$1	220	19	46	23.5776
AUGAUCUCAGAAGGGCUUUUGAUCGUU	chr3:107134778-107135011(-)$1	233	172	199	23.3305
UGGCAGUAACCCCAACAAACGCCAGCG	chr7:29603441-29603661(+)$1	220	45	72	21.9547
AAGACACCAGUGAUCCCUGUCAAAACC	chr15:58775322-58775549(-)$1	227	130	157	20.9930
CUCUGACUCAGGAAGUCAAUCAGAGUC	chr17:15862244-15862465(+)$1	221	99	126	22.1621
GGUGGAUUGCUACUUCCCCUUCACCCA	chr13:36338137-36338357(+)$1	220	110	137	25.0978
AUCUGCUGUCACCAAUAAGGCAUAUGU	chr5:92890963-92891183(-)$1	220	124	151	22.3393
UAAGUAUUCUUUAAUUCUUUGCCCCUA	chr2:29004064-29004298(+)$1	234	178	205	24.9034

#DB
(((((((...........)))))))..	chr9:21479490-21479710(+)$1	1	77	104	21.9001
((((((............))))))...	chr10:39582438-39582678(+)$1	1	172	199	23.4661
..((((............))))...))	chr13:44918665-44918885(+)$1	1	160	187	24.5263
(((.(((...........))).)))..	chr19:21900535-21900756(+)$1	1	83	110	22.0846
..((((............))))..)))	chr19:60897018-60897238(+)$1	1	160	187	24.1129
(((((((...........))))))...	chr18:24172635-24172855(-)$1	1	16	43	22.8573
((((((.............))))))))	chr17:68159103-68159348(+)$1	1	25	52	24.7395
(.((((...........)))).)))))	chr8:90674039-90674264(+)$1	1	40	67	22.8491
..(((((...........)))))..))	chr10:79281969-79282189(+)$1	1	91	118	22.5683
(..(((............)))..).))	chr14:31772291-31772511(+)$1	1	42	69	24.6066
(((((((...........))))))).)	chr5:73691831-73692066(+)$1	1	129	156	23.7217
((.(((..............))).)))	chr17:72155911-72156180(+)$1	1	200	227	22.9007
((.(((............))))).)))	chr16:87487854-87488074(-)$1	1	66	93	23.4410
((((((..............)))))))	chr9:120482824-120483044(+)$1	1	94	121	23.3373
..(((.............)))..)..)	chr14:30783149-30783369(+)$1	1	153	180	24.3068
((((((...........).)))))..)	chrX:12671074-12671316(+)$1	1	97	124	22.6579
((((((............)))))))))	chr13:73921949-73922169(+)$1	1	85	112	25.1029
(.((((...........))))).))))	chr8:108765975-108766198(+)$1	1	67	94	22.6050
((.((((...........)))))))))	chr14:76513876-76514096(+)$1	1	152	179	22.6032
))))(((...........)))..((((	chr2:121260529-121260749(+)$1	1	74	101	21.5185
((((((...........))))))).))	chr6:3542355-3542575(+)$1	1	13	40	23.2307
)))(((................)))..	chr19:45076065-45076285(+)$1	1	15	42	19.0330
((((((............)))))..))	chr4:123028163-123028392(-)$1	1	88	115	22.9972
..((((............)))).))..	chr8:124530918-124531138(+)$1	1	78	105	23.2876
(((((((...........)))))))))	chr1:82337136-82337356(+)$1	1	162	189	24.0253
((((((..............)))))))	chr12:111903890-111904112(+)$1	1	73	100	23.3373
.(((((.............))))).))	chr6:91469460-91469684(+)$1	1	83	110	23.9294
.(((................)))...)	chr14:121316513-121316733(+)$1	1	113	140	21.3914
((((((...........))))))).))	chr11:30715478-30715698(+)$1	1	170	197	23.2307
((((((............)))))))))	chr17:46398422-46398642(-)$1	1	154	181	21.7121
((((((.............))).))).	chr4:138953254-138953474(+)$1	1	159	186	24.7480
.((((((...........))))))...	chr4:46160220-46160452(+)$1	1	127	154	20.7606
((((((.............))))).))	chr7:107778266-107778495(+)$1	1	131	158	23.4839
...((.............))...))))	chr2:155922456-155922676(-)$1	1	96	123	23.3050
.((.(((...........))).))...	chr7:6661551-6661773(-)$1	1	151	178	20.6934
.((((..............))))))))	chr12:71561238-71561458(+)$1	1	108	135	21.9638
(((((((...........))))..)))	chr11:86503392-86503612(+)$1	1	62	89	22.7918
((((((............)))))))..	chr8:36532264-36532489(-)$1	1	26	53	23.0243
((((((..............)))))).	chr11:105114514-105114734(+)$1	1	64	91	21.6462
((((((...........)))))).).)	chr10:66702080-66702303(+)$1	1	155	182	22.1175
((((((............)).)))...	chr19:5963715-5963935(-)$1	1	169	196	23.3131
.(((((............)))))((((	chr9:60718483-60718705(+)$1	1	2	29	22.4984
(.((((((...........)).)))).	chr9:118466128-118466348(+)$1	1	124	151	20.3397
(((((..............)).)))))	chr11:76759645-76759865(+)$1	1	89	116	21.2802
((((((............)))))))))	chr13:13788771-13788991(+)$1	1	112	139	23.1714
(.((((............)))).))))	chr18:45005296-45005516(+)$1	1	143	170	23.5374
..(((.............))).)))))	chr11:23180318-23180541(+)$1	1	131	158	23.5911
(..(((............)))..).))	chr12:66109520-66109746(+)$1	1	91	118	24.9822
(..(((.............))).))))	chr4:126781540-126781760(+)$1	1	162	189	24.7067
(..(((..............)))..))	chr1:71619450-71619670(+)$1	1	29	56	23.2073
.(((..............)))...)))	chr4:41326700-41326921(+)$1	1	162	189	22.5125
((((((............))))))).)	chr2:121126656-121126876(+)$1	1	174	201	24.6495
.((((.............)))))))))	chr15:80079766-80079987(+)$1	1	72	99	22.7164
((((((..............)))))))	chr16:15752729-15752949(+)$1	1	19	46	23.5776
((((((..............)))))))	chr3:107134778-107135011(-)$1	1	172	199	23.3305
((((.((...........))))))).)	chr7:29603441-29603661(+)$1	1	45	72	21.9547
..((((...........))))((((((	chr15:58775322-58775549(-)$1	1	130	157	20.9930
((((((.............))))))))	chr17:15862244-15862465(+)$1	1	99	126	22.1621
((((((.............))))))))	chr13:36338137-36338357(+)$1	1	110	137	25.0978
((.((((...........)))).))))	chr5:92890963-92891183(-)$1	1	124	151	22.3393
((.(((.............)))...))	chr2:29004064-29004298(+)$1	1	178	205	24.9034

#PSSM
g : 0.16	f : 0.09	e : 0.09	c : 0.08	a : 0.08	= : 0.06	# : 0.04	! : 0.04	[ : 0.04	h : 0.04	d : 0.04	b : 0.03	: : 0.03	" : 0.01	$ : 0.01	' : 0.01	& : 0.01	% : 0.01	i : 0.01	
g : 0.16	e : 0.14	f : 0.13	c : 0.09	! : 0.09	[ : 0.06	= : 0.06	# : 0.04	d : 0.04	b : 0.03	h : 0.03	" : 0.01	% : 0.01	i : 0.01	: : 0.01	
g : 0.16	d : 0.16	c : 0.13	e : 0.13	f : 0.11	[ : 0.08	! : 0.06	= : 0.06	h : 0.03	# : 0.01	b : 0.01	i : 0.01	
c : 0.22	d : 0.21	g : 0.16	e : 0.11	f : 0.09	= : 0.06	[ : 0.03	h : 0.03	b : 0.03	i : 0.01	
c : 0.22	d : 0.21	g : 0.14	f : 0.09	e : 0.09	= : 0.06	b : 0.04	h : 0.03	y : 0.01	w : 0.01	i : 0.01	[ : 0.01	
c : 0.19	d : 0.18	g : 0.14	f : 0.09	e : 0.08	v : 0.06	= : 0.06	w : 0.04	h : 0.03	b : 0.03	a : 0.01	y : 0.01	i : 0.01	
u : 0.26	v : 0.19	w : 0.16	t : 0.11	c : 0.04	d : 0.04	g : 0.03	f : 0.03	y : 0.03	b : 0.03	e : 0.01	= : 0.01	
t : 0.32	u : 0.26	v : 0.19	w : 0.16	y : 0.03	b : 0.01	
t : 0.34	u : 0.26	v : 0.19	w : 0.16	y : 0.03	
t : 0.34	u : 0.26	v : 0.19	w : 0.16	y : 0.03	
t : 0.34	u : 0.26	v : 0.19	w : 0.16	y : 0.03	
t : 0.34	u : 0.26	v : 0.19	w : 0.16	y : 0.03	
t : 0.34	u : 0.26	v : 0.19	w : 0.16	y : 0.03	
t : 0.34	u : 0.26	v : 0.19	w : 0.16	y : 0.03	
t : 0.34	u : 0.26	v : 0.19	w : 0.16	y : 0.03	
t : 0.34	u : 0.26	v : 0.19	w : 0.16	y : 0.03	
t : 0.34	u : 0.26	v : 0.19	w : 0.16	y : 0.03	
u : 0.26	t : 0.22	v : 0.19	w : 0.16	d : 0.04	g : 0.03	y : 0.03	a : 0.01	f : 0.01	
d : 0.18	c : 0.14	w : 0.14	v : 0.13	g : 0.09	f : 0.08	e : 0.04	b : 0.04	= : 0.03	y : 0.03	] : 0.01	h : 0.01	t : 0.01	
d : 0.19	c : 0.19	g : 0.11	w : 0.11	e : 0.09	f : 0.08	b : 0.08	= : 0.04	y : 0.03	h : 0.03	
c : 0.24	d : 0.19	g : 0.14	e : 0.11	f : 0.09	= : 0.06	h : 0.03	b : 0.03	y : 0.01	3 : 0.01	] : 0.01	i : 0.01	
g : 0.14	d : 0.14	e : 0.11	c : 0.11	f : 0.09	] : 0.09	= : 0.06	2 : 0.04	h : 0.03	3 : 0.03	i : 0.03	b : 0.01	a : 0.01	: : 0.01	y : 0.01	
g : 0.14	e : 0.13	f : 0.11	c : 0.11	] : 0.09	2 : 0.08	= : 0.08	3 : 0.06	h : 0.04	b : 0.03	d : 0.03	i : 0.03	: : 0.01	
g : 0.16	f : 0.13	e : 0.11	c : 0.08	2 : 0.08	= : 0.08	3 : 0.06	d : 0.06	a : 0.04	] : 0.04	h : 0.04	b : 0.03	i : 0.03	
g : 0.14	] : 0.09	e : 0.09	d : 0.09	c : 0.08	2 : 0.08	= : 0.08	3 : 0.06	f : 0.06	h : 0.04	4 : 0.03	i : 0.03	b : 0.01	6 : 0.01	7 : 0.01	a : 0.01	
e : 0.13	d : 0.11	g : 0.09	c : 0.08	= : 0.08	f : 0.08	: : 0.06	] : 0.06	b : 0.04	2 : 0.04	h : 0.04	4 : 0.03	3 : 0.03	i : 0.03	6 : 0.01	7 : 0.01	
e : 0.16	g : 0.11	f : 0.09	d : 0.09	b : 0.08	= : 0.08	: : 0.06	c : 0.06	4 : 0.03	2 : 0.03	] : 0.03	h : 0.03	i : 0.03	3 : 0.01	F : 0.01	6 : 0.01	7 : 0.01	

#score	1401.4828093899343
#seq	61
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_transcript_m2_run2.txt

#BEAR
dddccc"""cccoooooocccccc]dddd2	chr6:108772639-108772889(+)$1	250	155	185	13.6379
gggggg!!ddddoooooodddd22gggggg	chr16:17046878-17047138(+)$1	260	140	170	13.7222
cdddd!!eeeeeooooooeeeeedddd]cc	chr14:65673532-65673769(-)$1	237	194	224	12.0895
[hhhhhhhhcccooooooccc22hhhhhhh	chr2:174171813-174172084(+)$1	271	145	175	11.8486
::eeeee!!cccooooooccc4444eeeee	chr1:174215791-174216026(-)$1	235	200	230	12.4828
gggggg"""cccmmmmccc333ggggggge	chr15:31412540-31412775(-)$1	235	65	95	10.1080
:iiiiiiiii[aooooooaiiiiiiiii::	chr11:106641590-106641828(-)$1	238	181	211	12.4953
bggggggg"""bboooooobb333gggggg	chr15:78500420-78500657(-)$1	237	119	149	12.6073
!eeeee!!cccrrrrrrrrrccc]eeeee2	chr6:35459715-35459959(-)$1	244	180	210	10.4514
#eeeee!!ddddoooooodddd22eeeee4	chr11:41960533-41960768(-)$1	235	66	96	13.0928
cccdddd!!cccooooooccc333ddddcc	chr16:7411239-7411495(+)$1	256	51	81	13.9001
+ccc!!ccccccooooooccc]ccc]ccch	chr12:21396205-21396445(-)$1	240	131	161	13.4971
a[a[bb[eeeeeooooooeeeee]bb]a]a	chr17:90992261-90992524(-)$1	263	15	45	11.9351
ee[iiiiiiiiiooooooiiiiiiiii]ee	chr10:116785268-116785504(-)$1	236	33	63	14.8087
eeeedddd!!bboooooobb22dddd22ee	chr16:7412006-7412266(+)$1	260	159	189	11.3691
bb[iiiiiiiiiooooooiiiiiiiii]bb	chr1:166367412-166367682(-)$1	270	197	227	13.9212
!dddd!!eeeeeooooooeeeeedddd]dd	chr6:124909261-124909515(-)$1	254	64	94	12.0731
ddccc[bb[cccooooooccc]bb]ccc]d	chr5:73705123-73705367(+)$1	244	97	127	13.1321
iiiiiii"""bboooooobb4444iiiiii	chr5:148274170-148274405(+)$1	235	43	73	14.9489
iiiiiiiicccnnnnnccc]iiiiiiiii3	chr2:134420264-134420541(-)$1	277	62	92	10.1837
dd[===========mmmm===========]	chr1:34200801-34201038(+)$1	237	125	155	11.0474
============ppppppp===========	chr4:137797665-137797900(+)$1	235	87	117	10.2336
!dddd[ffffffooooooffffff]dddd2	chr16:37887247-37887484(+)$1	237	97	127	11.8965
cc####ccccccooooooccc]ccc333cc	chr18:61147502-61147742(+)$1	240	128	158	14.1203
==========[aooooooa]==========	chr10:4516095-4516348(+)$1	253	133	163	16.2878
!eeeee[bb[bboooooobb]bb]eeeee3	chrX:10173074-10173327(+)$1	253	119	149	12.4621
gggg[eeeeerrrrrrrrreeeee333ggg	chr9:71904886-71905139(-)$1	253	111	141	9.6328
4eeeeeffffffooooooffffffeeeeel	chrX:56315652-56315887(-)$1	235	115	145	11.4697
ggggggg[bb[aooooooa]bb]ggggggg	chr10:82203481-82203732(+)$1	251	186	216	13.5923
iiii$$$$$cccooooooccc4444iiiii	chr16:17047321-17047576(+)$1	255	25	55	14.4668
fffff[eeeeeooooooeeeee333fffff	chr2:136606810-136607074(+)$1	264	87	117	11.1331
gggeeeee[cccooooooccc]eeeee333	chr8:47886692-47886927(+)$1	235	122	152	14.2452
!bb[ccc[ddddoooooodddd]cccbb22	chr19:44380207-44380487(+)$1	280	227	257	11.9680
eeeee[ffffffooooooffffff]eeeee	chr12:16992280-16992535(+)$1	255	217	247	12.3792
ggg[bbccccccooooooccc22ccc]bb]	chr5:108174394-108174647(-)$1	253	70	100	13.2508
ffffa[ffffffooooooffffff]a4444	chr13:38070622-38070872(-)$1	250	115	145	12.2406
c[ccc####cccooooooccc333cccccc	chr7:26013303-26013538(-)$1	235	48	78	14.8733
c[cccccc[cccmmmmccc]ccc333ccc]	chr7:138056465-138056711(+)$1	246	70	100	9.3669
!eeeee[bb!!aooooooa333bb]eeeee	chr6:115226335-115226607(+)$1	272	230	260	13.3850
===!!ccc[cccooooooccc]ccc22===	chrX:141894531-141894792(-)$1	261	191	221	14.8009
eeee[bb[ddddooooooddddbb]eeeee	chr9:107998481-107998718(-)$1	237	180	210	12.0334
"""cccccccccooooooccc]ccc>>>>>	chr11:74488555-74488832(-)$1	277	147	177	12.8780
a[ggggggg[bboooooobb]ggggggg]a	chr19:21468794-21469035(-)$1	241	100	130	13.8475
eeiiiiiiiiirrrrrrrrriiiiiiiii5	chr9:49509849-49510087(-)$1	238	168	198	10.6720
===========qqqqqqqq===========	chr9:62641359-62641604(-)$1	245	203	233	10.7085
=========ddddllldddd]=========	chr5:104508405-104508686(-)$1	281	206	236	10.7780
iiiiiii[ddddooooooddddiiiiiiii	chr16:45141387-45141623(-)$1	236	202	232	14.4702
##dddd!!ddddoooooodddd]dddd]dd	chr6:114197708-114197947(+)$1	239	192	222	12.2268
&&==========oooooo==========77	chr9:46030826-46031085(+)$1	259	191	221	13.4530
[ffffffeeeeeooooooeeeee22fffff	chr5:122906744-122907038(-)$1	294	102	132	11.5396
===========qqqqqqqq===========	chr2:102630145-102630383(+)$1	238	92	122	10.7085
==="""a[cccrrrrrrrrrccc]a333==	chr19:58179070-58179308(+)$1	238	29	59	11.1295
fffff[dddd[aooooooa]ddddffffff	chr9:40014099-40014334(+)$1	235	120	150	11.8338
eeee[dddd[bboooooobb]ddddeeeee	chr2:148522575-148522837(-)$1	262	108	138	11.8726
[ffffff####aooooooa4444ffffffh	chr10:48819694-48819932(-)$1	238	80	110	12.9667
ddd[eeeee[bboooooobb]eeeee]ddd	chr10:115962195-115962436(-)$1	241	70	100	11.8596

#otherMatches

#Seq PSSM
GGUUGACUUGUAAAUUGAUACUCAUGCCGA	chr6:108772639-108772889(+)$1	250	155	185	13.6379
GUUUGGAAUAUGAUACCCUAUAACCCAGAU	chr16:17046878-17047138(+)$1	260	140	170	13.7222
UGUAUCAACUUUUUUGUCAAGGUGUACGGC	chr14:65673532-65673769(-)$1	237	194	224	12.0895
AGUUGGUCACCCACCAUAGGGCAUGAUCAA	chr2:174171813-174172084(+)$1	271	145	175	11.8486
AAGGUGGCAGAAAUCCCCUUCAACUCCACC	chr1:174215791-174216026(-)$1	235	200	230	12.4828
GAGUAUCUAUCAUACUUGAAAUAUAUUCAC	chr15:31412540-31412775(-)$1	235	65	95	10.1080
CGUAGAGGCCUCUUACCUGGGUUUUUGCAC	chr11:106641590-106641828(-)$1	238	181	211	12.4953
CGGGGGUGGGGAGACUUGACUGAACACCUC	chr15:78500420-78500657(-)$1	237	119	149	12.6073
UAACAUCUCAGAAAAAAACCCUGCAUGUUC	chr6:35459715-35459959(-)$1	244	180	210	10.4514
GGACCAGAGAGCCAGCCCGUUCAGUGGUUG	chr11:41960533-41960768(-)$1	235	66	96	13.0928
UCUGCCCCAUCCUUUUUCGGAGCAGGGCCA	chr16:7411239-7411495(+)$1	256	51	81	13.9001
GAGUUGGACCACUAUAUUGUGUGUUUGCUA	chr12:21396205-21396445(-)$1	240	131	161	13.4971
cugugcugugugaguguguaugcuguucug	chr17:90992261-90992524(-)$1	263	15	45	11.9351
UUAACAUUGGGCUGUAUUGUUCAGUGUGAA	chr10:116785268-116785504(-)$1	236	33	63	14.8087
AACUGUACUUUCCCCUACGAUCGUAUGUAG	chr16:7412006-7412266(+)$1	260	159	189	11.3691
UUUUAUUUUUUUCUGCAAGAAAAAGUGUAA	chr1:166367412-166367682(-)$1	270	197	227	13.9212
GGCCAGUGCAGGUCAUGUUCUGUUGGUACC	chr6:124909261-124909515(-)$1	254	64	94	12.0731
GCUAAUGCGUUUUAAUGUAAAGGUCUUAUG	chr5:73705123-73705367(+)$1	244	97	127	13.1321
GACAGUGUUCAGCUACCACUAUCUUACUGU	chr5:148274170-148274405(+)$1	235	43	73	14.9489
UGAAAUGAGAAAUCAGUUCAUCAUUUCAAG	chr2:134420264-134420541(-)$1	277	62	92	10.1837
gcucaguggugguggugaugcugcugcugu	chr1:34200801-34201038(+)$1	237	125	155	11.0474
UUUCUUCCCAUGUGAGCAUUGUGGGAAGGA	chr4:137797665-137797900(+)$1	235	87	117	10.2336
CUCAGUAAUGUGUGGUUUUAUAUUUCUGAC	chr16:37887247-37887484(+)$1	237	97	127	11.8965
UAAAUAGCUACAAAUUUAUGUGAGUCCGUG	chr18:61147502-61147742(+)$1	240	128	158	14.1203
UUUGGAACCUGUGUACAAGGAGGUUCCAAA	chr10:4516095-4516348(+)$1	253	133	163	16.2878
UGCCGAUGGUAAUUAUCUUUUCUUUUGGCU	chrX:10173074-10173327(+)$1	253	119	149	12.4621
CAGCUGUAGUUUUGGCUUUGCUAUGGUGCU	chr9:71904886-71905139(-)$1	253	111	141	9.6328
GUGGCUUCUUGUGUAAAGACAGGAACUGUG	chrX:56315652-56315887(-)$1	235	115	145	11.4697
UAGCUUCCAUGAUGUGUCUGAUAGAAGCUA	chr10:82203481-82203732(+)$1	251	186	216	13.5923
GUUUUUUCAUUAUAUUGUUAAACUUGAACA	chr16:17047321-17047576(+)$1	255	25	55	14.4668
CUCUCCUCCAAAUGUUGUUGGACAAGAGAG	chr2:136606810-136607074(+)$1	264	87	117	11.1331
GCUGGAGCAGAUAGCAGAAUUGGUUUCCAU	chr8:47886692-47886927(+)$1	235	122	152	14.2452
UGGAUCUGCAGGAUUGCCUCUGGGGACCUC	chr19:44380207-44380487(+)$1	280	227	257	11.9680
UUACCUUAGAUGUGUUUUUAUUUAUGGUAA	chr12:16992280-16992535(+)$1	255	217	247	12.3792
CCAAAGAGAUUGUUUUAUCAACUUCUACUC	chr5:108174394-108174647(-)$1	253	70	100	13.2508
AGAUAGAAUUUUAAGAAAAAAAUUGUCACG	chr13:38070622-38070872(-)$1	250	115	145	12.2406
UUGUUAUAAUUUUUUCUUAAAGAAAACGUC	chr7:26013303-26013538(-)$1	235	48	78	14.8733
GUGAUUAUCAGGAUCUCCUAAUAUUUAUCU	chr7:138056465-138056711(+)$1	246	70	100	9.3669
GUUAUAUCUGUCUUCAGUGUUAAGUUGUAA	chr6:115226335-115226607(+)$1	272	230	260	13.3850
GGAAGAGAAUGUGAUGAGACACUUUGCUCU	chrX:141894531-141894792(-)$1	261	191	221	14.8009
ACAAAGUCAAACAAACAAGUUUACAUUGUA	chr9:107998481-107998718(-)$1	237	180	210	12.0334
UGUGCCUUGCCUGGGAUAAGGACAAUGAUA	chr11:74488555-74488832(-)$1	277	147	177	12.8780
AGGCAUAAAUAGUUGUGUUUUUUUGUGUGU	chr19:21468794-21469035(-)$1	241	100	130	13.8475
GUACAUGUGCAAUACAUUuaugcaugugug	chr9:49509849-49510087(-)$1	238	168	198	10.6720
UUGUGUAAAUUGUCACAUAAAUUUGCAUGA	chr9:62641359-62641604(-)$1	245	203	233	10.7085
CAUAUGUAGCAAAACAUUUGUUUGCAUGUG	chr5:104508405-104508686(-)$1	281	206	236	10.7780
UUCUGAAAGUCAAGUCUCUGGCUUUAGGAU	chr16:45141387-45141623(-)$1	236	202	232	14.4702
CAGUGAUAGUGGGCAUAUCCACCUCACCAA	chr6:114197708-114197947(+)$1	239	192	222	12.2268
UUGUGUGCACACGUAUGAGUGUGUACAUGC	chr9:46030826-46031085(+)$1	259	191	221	13.4530
AUUUUAUGCAGAUAUUUUUUUGUAGAUGAA	chr5:122906744-122907038(-)$1	294	102	132	11.5396
GCCUGCUCUGCUUGCCUGUGUGGAGUAGGU	chr2:102630145-102630383(+)$1	238	92	122	10.7085
GUGCCUCCGGCCUUUGCUUUGCCAGCCUCA	chr19:58179070-58179308(+)$1	238	29	59	11.1295
GUGCUGUUAGUGUCUUUCCUCUAGAGUGCU	chr9:40014099-40014334(+)$1	235	120	150	11.8338
AAUAAGUUUGUAAUUCAGUAGAAACUGUUU	chr2:148522575-148522837(-)$1	262	108	138	11.8726
GUUUUUUUUUUCUGUUUUGUUUUAAAAAAU	chr10:48819694-48819932(-)$1	238	80	110	12.9667
ACACGCAUUUGCUGCCUCGCUAGUGUCUGU	chr10:115962195-115962436(-)$1	241	70	100	11.8596

#DB
((((((...(((......)))))).)))).	chr6:108772639-108772889(+)$1	1	155	185	13.6379
((((((..((((......))))..))))))	chr16:17046878-17047138(+)$1	1	140	170	13.7222
(((((..(((((......))))))))).))	chr14:65673532-65673769(-)$1	1	194	224	12.0895
.(((((((((((......)))..)))))))	chr2:174171813-174172084(+)$1	1	145	175	11.8486
..(((((..(((......)))....)))))	chr1:174215791-174216026(-)$1	1	200	230	12.4828
((((((...(((....)))...)))))))(	chr15:31412540-31412775(-)$1	1	65	95	10.1080
.(((((((((.(......))))))))))..	chr11:106641590-106641828(-)$1	1	181	211	12.4953
)(((((((...((......))...))))))	chr15:78500420-78500657(-)$1	1	119	149	12.6073
.(((((..(((.........))).))))).	chr6:35459715-35459959(-)$1	1	180	210	10.4514
.(((((..((((......))))..))))).	chr11:41960533-41960768(-)$1	1	66	96	13.0928
)))((((..(((......)))...))))((	chr16:7411239-7411495(+)$1	1	51	81	13.9001
.(((..((((((......))).))).))))	chr12:21396205-21396445(-)$1	1	131	161	13.4971
(.(.((.(((((......))))).)).).)	chr17:90992261-90992524(-)$1	1	15	45	11.9351
((.(((((((((......))))))))).))	chr10:116785268-116785504(-)$1	1	33	63	14.8087
((((((((..((......))..))))..))	chr16:7412006-7412266(+)$1	1	159	189	11.3691
((.(((((((((......))))))))).))	chr1:166367412-166367682(-)$1	1	197	227	13.9212
.((((..(((((......))))))))).))	chr6:124909261-124909515(-)$1	1	64	94	12.0731
(((((.((.(((......))).)).))).)	chr5:73705123-73705367(+)$1	1	97	127	13.1321
(((((((...((......))....))))))	chr5:148274170-148274405(+)$1	1	43	73	14.9489
(((((((((((.....))).))))))))).	chr2:134420264-134420541(-)$1	1	62	92	10.1837
((.(((((((((((....))))))))))).	chr1:34200801-34201038(+)$1	1	125	155	11.0474
((((((((((((.......)))))))))))	chr4:137797665-137797900(+)$1	1	87	117	10.2336
.((((.((((((......)))))).)))).	chr16:37887247-37887484(+)$1	1	97	127	11.8965
((....((((((......))).)))...))	chr18:61147502-61147742(+)$1	1	128	158	14.1203
((((((((((.(......).))))))))))	chr10:4516095-4516348(+)$1	1	133	163	16.2878
.(((((.((.((......)).)).))))).	chrX:10173074-10173327(+)$1	1	119	149	12.4621
((((.(((((.........)))))...)))	chr9:71904886-71905139(-)$1	1	111	141	9.6328
.)))))((((((......))))))(((((.	chrX:56315652-56315887(-)$1	1	115	145	11.4697
(((((((.((.(......).)).)))))))	chr10:82203481-82203732(+)$1	1	186	216	13.5923
((((.....(((......)))....)))))	chr16:17047321-17047576(+)$1	1	25	55	14.4668
(((((.(((((......)))))...)))))	chr2:136606810-136607074(+)$1	1	87	117	11.1331
((((((((.(((......))).)))))...	chr8:47886692-47886927(+)$1	1	122	152	14.2452
.((.(((.((((......)))).)))))..	chr19:44380207-44380487(+)$1	1	227	257	11.9680
(((((.((((((......)))))).)))))	chr12:16992280-16992535(+)$1	1	217	247	12.3792
(((.((((((((......)))..))).)).	chr5:108174394-108174647(-)$1	1	70	100	13.2508
(((((.((((((......)))))).)....	chr13:38070622-38070872(-)$1	1	115	145	12.2406
(.(((....(((......)))...))))))	chr7:26013303-26013538(-)$1	1	48	78	14.8733
(.((((((.(((....))).)))...))).	chr7:138056465-138056711(+)$1	1	70	100	9.3669
.(((((.((..(......)...)).)))))	chr6:115226335-115226607(+)$1	1	230	260	13.3850
(((..(((.(((......))).)))..)))	chrX:141894531-141894792(-)$1	1	191	221	14.8009
((((.((.((((......)))))).)))))	chr9:107998481-107998718(-)$1	1	180	210	12.0334
...(((((((((......))).))).....	chr11:74488555-74488832(-)$1	1	147	177	12.8780
(.(((((((.((......)).))))))).)	chr19:21468794-21469035(-)$1	1	100	130	13.8475
(((((((((((.........))))))))).	chr9:49509849-49510087(-)$1	1	168	198	10.6720
(((((((((((........)))))))))))	chr9:62641359-62641604(-)$1	1	203	233	10.7085
(((((((((((((...)))).)))))))))	chr5:104508405-104508686(-)$1	1	206	236	10.7780
(((((((.((((......))))))))))))	chr16:45141387-45141623(-)$1	1	202	232	14.4702
..((((..((((......)))).)))).))	chr6:114197708-114197947(+)$1	1	192	222	12.2268
..((((((((((......))))))))))..	chr9:46030826-46031085(+)$1	1	191	221	13.4530
.(((((((((((......)))))..)))))	chr5:122906744-122907038(-)$1	1	102	132	11.5396
(((((((((((........)))))))))))	chr2:102630145-102630383(+)$1	1	92	122	10.7085
(((...(.(((.........))).)...))	chr19:58179070-58179308(+)$1	1	29	59	11.1295
(((((.((((.(......).))))))))))	chr9:40014099-40014334(+)$1	1	120	150	11.8338
((((.((((.((......)).)))))))))	chr2:148522575-148522837(-)$1	1	108	138	11.8726
.((((((....(......)....)))))))	chr10:48819694-48819932(-)$1	1	80	110	12.9667
(((.(((((.((......)).))))).)))	chr10:115962195-115962436(-)$1	1	70	100	11.8596

#PSSM
= : 0.12	g : 0.10	! : 0.10	e : 0.10	c : 0.08	d : 0.07	i : 0.07	[ : 0.05	f : 0.05	: : 0.03	b : 0.03	# : 0.03	a : 0.03	+ : 0.01	4 : 0.01	" : 0.01	& : 0.01	
e : 0.19	d : 0.12	g : 0.12	= : 0.12	i : 0.08	f : 0.08	[ : 0.07	c : 0.05	b : 0.03	h : 0.01	: : 0.01	" : 0.01	# : 0.01	& : 0.01	
e : 0.17	g : 0.14	= : 0.14	d : 0.10	i : 0.10	c : 0.08	f : 0.08	[ : 0.05	h : 0.01	a : 0.01	# : 0.01	b : 0.01	" : 0.01	
e : 0.19	i : 0.14	= : 0.12	c : 0.10	g : 0.10	d : 0.08	f : 0.08	[ : 0.07	h : 0.01	# : 0.01	! : 0.01	" : 0.01	
e : 0.16	i : 0.12	= : 0.12	c : 0.10	d : 0.10	g : 0.08	f : 0.07	[ : 0.05	! : 0.03	b : 0.03	h : 0.01	# : 0.01	$ : 0.01	a : 0.01	" : 0.01	
e : 0.16	i : 0.12	= : 0.12	[ : 0.10	c : 0.08	g : 0.08	d : 0.07	! : 0.05	b : 0.05	# : 0.03	f : 0.03	h : 0.01	$ : 0.01	" : 0.01	
i : 0.12	c : 0.12	= : 0.12	! : 0.10	f : 0.10	e : 0.08	d : 0.07	g : 0.05	[ : 0.05	" : 0.03	b : 0.03	h : 0.01	$ : 0.01	# : 0.01	a : 0.01	
e : 0.14	= : 0.12	! : 0.10	c : 0.10	i : 0.08	[ : 0.08	f : 0.07	" : 0.05	d : 0.05	b : 0.05	g : 0.03	# : 0.03	h : 0.01	$ : 0.01	
d : 0.14	e : 0.12	c : 0.12	= : 0.12	" : 0.07	i : 0.07	[ : 0.07	f : 0.07	! : 0.05	b : 0.05	# : 0.03	h : 0.01	$ : 0.01	g : 0.01	
c : 0.32	d : 0.14	e : 0.10	= : 0.10	i : 0.07	f : 0.07	[ : 0.07	" : 0.03	! : 0.03	b : 0.01	# : 0.01	
c : 0.32	d : 0.12	b : 0.10	e : 0.08	= : 0.08	[ : 0.07	f : 0.07	i : 0.05	" : 0.01	r : 0.01	! : 0.01	# : 0.01	
c : 0.26	d : 0.12	b : 0.12	a : 0.10	e : 0.07	r : 0.07	f : 0.07	= : 0.05	i : 0.03	q : 0.03	n : 0.01	o : 0.01	
o : 0.76	r : 0.07	m : 0.03	q : 0.03	b : 0.01	n : 0.01	= : 0.01	p : 0.01	d : 0.01	
o : 0.78	r : 0.07	m : 0.03	q : 0.03	n : 0.01	= : 0.01	p : 0.01	l : 0.01	
o : 0.78	r : 0.07	m : 0.05	q : 0.03	n : 0.01	p : 0.01	l : 0.01	
o : 0.78	r : 0.07	m : 0.05	q : 0.03	n : 0.01	p : 0.01	l : 0.01	
o : 0.78	r : 0.07	c : 0.05	q : 0.03	m : 0.01	p : 0.01	d : 0.01	
o : 0.76	r : 0.07	c : 0.05	q : 0.03	m : 0.01	p : 0.01	e : 0.01	d : 0.01	
c : 0.28	d : 0.12	a : 0.10	b : 0.10	e : 0.08	r : 0.07	f : 0.07	i : 0.03	= : 0.03	q : 0.03	o : 0.01	p : 0.01	
c : 0.23	d : 0.12	b : 0.12	e : 0.10	] : 0.08	= : 0.08	f : 0.07	i : 0.05	r : 0.05	3 : 0.03	4 : 0.01	
c : 0.28	d : 0.12	e : 0.10	= : 0.10	i : 0.08	] : 0.08	f : 0.07	3 : 0.03	b : 0.03	4 : 0.03	2 : 0.01	
d : 0.14	e : 0.12	= : 0.12	] : 0.10	3 : 0.08	i : 0.08	c : 0.07	4 : 0.07	f : 0.07	2 : 0.05	b : 0.03	g : 0.01	
c : 0.14	e : 0.12	= : 0.12	i : 0.10	2 : 0.07	4 : 0.07	3 : 0.07	b : 0.07	f : 0.07	d : 0.05	] : 0.05	g : 0.03	
c : 0.12	= : 0.12	d : 0.10	i : 0.10	3 : 0.08	f : 0.08	] : 0.07	2 : 0.05	4 : 0.05	g : 0.05	b : 0.05	e : 0.05	h : 0.01	
] : 0.12	i : 0.12	c : 0.12	= : 0.12	d : 0.10	e : 0.10	g : 0.08	3 : 0.05	4 : 0.03	f : 0.03	h : 0.01	b : 0.01	2 : 0.01	a : 0.01	
e : 0.19	i : 0.14	d : 0.12	= : 0.12	g : 0.08	c : 0.07	3 : 0.07	f : 0.07	h : 0.01	] : 0.01	b : 0.01	a : 0.01	2 : 0.01	> : 0.01	
e : 0.17	i : 0.14	= : 0.12	d : 0.10	g : 0.08	c : 0.07	f : 0.07	] : 0.05	3 : 0.05	2 : 0.03	h : 0.01	b : 0.01	4 : 0.01	> : 0.01	
e : 0.16	= : 0.14	g : 0.10	i : 0.10	] : 0.08	d : 0.07	c : 0.07	f : 0.07	3 : 0.05	b : 0.03	h : 0.01	a : 0.01	2 : 0.01	4 : 0.01	> : 0.01	
e : 0.19	= : 0.14	c : 0.10	d : 0.08	g : 0.08	i : 0.08	f : 0.07	] : 0.05	b : 0.03	h : 0.01	: : 0.01	3 : 0.01	2 : 0.01	4 : 0.01	> : 0.01	7 : 0.01	
e : 0.14	= : 0.12	2 : 0.07	g : 0.07	c : 0.07	d : 0.07	h : 0.05	i : 0.05	3 : 0.05	] : 0.05	f : 0.05	4 : 0.03	a : 0.03	: : 0.01	b : 0.01	l : 0.01	> : 0.01	5 : 0.01	7 : 0.01	

#score	698.138039141348
#seq	56
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_UTR_m3_run2.txt

#BEAR
===========mmmm==========	chr5:114838681-114838901(+)$1	220	147	172	12.0419
:==========mmmm==========	chr15:76911213-76911433(-)$1	220	2	27	11.0637
ccc!!ffffffmmmmffffff333c	chr7:30891023-30891250(+)$1	227	17	42	9.5835
dffffff[cccmmmmccc]ffffff	chr2:153442985-153443232(-)$1	247	73	98	10.4882
ggg####ddddmmmmdddd22gggg	chr11:87864063-87864283(+)$1	220	97	122	10.8541
cc[dddd[cccmmmmcccddddccc	chr3:30515823-30516048(+)$1	225	131	156	10.1659
ggggg!!ddddmmmmdddd]ggggg	chr5:23469366-23469587(-)$1	221	143	168	11.0413
[dddd[a[cccmmmmccc]adddd]	chr5:115593571-115593791(-)$1	220	45	70	10.8403
iiiiiiii[bbmmmmbb]iiiiiii	chr14:21839673-21839893(+)$1	220	137	162	11.4207
!dddd"""cccmmmmcccddddccc	chrX:93362328-93362548(+)$1	220	101	126	10.6620
bb[dddd!!bbmmmmbb333dddd2	chr3:104258314-104258534(-)$1	220	71	96	9.3578
"""ccc"""bbmmmmbbccc333dd	chr15:10376709-10376943(-)$1	234	40	65	10.7582
ggg####ddddmmmmdddd333ggg	chr1:180179679-180179907(+)$1	228	116	141	11.3473
ee[eeeee[bbmmmmbb]eeeee]e	chr13:18079624-18079844(-)$1	220	142	167	9.7678
fffff[eeeeemmmmeeeeefffff	chr9:105546444-105546664(+)$1	220	163	188	9.5028
hhhhhhh[cccmmmmccc]hhhhhh	chr8:42426753-42426974(-)$1	221	16	41	9.2754
cc####eeeeemmmmeeeee4444c	chr7:146060068-146060288(+)$1	220	113	138	10.1879
"eeeeea[cccmmmmccc333a]ee	chr2:6362667-6362901(+)$1	234	25	50	11.6514
ffff!!eeeeemmmmeeeee4444f	chr16:31254514-31254754(-)$1	240	65	90	10.1685
ffffffeeeeemmmmeeeee333ff	chr3:65184457-65184677(-)$1	220	77	102	9.8882
deeeee!!cccmmmmccc22eeeee	chr4:118992943-118993181(-)$1	238	77	102	10.7285
cc[eeeeecccmmmmccc]eeeee]	chr19:53454056-53454276(-)$1	220	190	215	10.8235
ggggggg!!bbmmmmbb]ggggggg	chr4:116944641-116944861(-)$1	220	166	191	11.3188
:iiiiiiiiiooooooiiiiiiiii	chr2:71227235-71227455(+)$1	220	186	211	7.6396
ffbbccc[cccmmmmccc]ccc]bb	chr16:20509030-20509250(+)$1	220	163	188	10.0328
dd"""bb[cccmmmmccc]bb333d	chr13:100195621-100195841(-)$1	220	140	165	10.2687
&&gggggggbbmmmmbb]ggggggg	chr14:56290543-56290777(-)$1	234	174	199	9.5790
eeeee"""cccmmmmccc333eeee	chr16:20692653-20692874(+)$1	221	61	86	11.8198
"dddd"""cccmmmmccc333dddd	chr13:101387291-101387511(-)$1	220	166	191	11.4015
[eeeeeeeeeemmmmeeeee]eeee	chr4:86257481-86257704(-)$1	223	45	70	9.4767
:ccc!!a[cccmmmmccc]a22ccc	chr6:119303686-119303910(-)$1	224	81	106	11.0646
hhhhhh!!cccmmmmccc333hhhh	chr4:132102475-132102695(+)$1	220	68	93	10.6520
ffff!!a[cccmmmmccc]a22fff	chrX:53838967-53839215(-)$1	248	17	42	11.6857
dddd"""ddddmmmmdddd22dddd	chr13:75844866-75845086(+)$1	220	60	85	9.5517
ffff"""ddddmmmmdddd]fffff	chr12:25301432-25301652(+)$1	220	19	44	10.2048
[ccc"""ddddmmmmdddd]cccgg	chr1:65205326-65205547(-)$1	221	70	95	10.8422
#eeeee[ddddmmmmdddd]eeeee	chr2:17992669-17992906(+)$1	237	104	129	9.5319
ggggggg!!bbmmmmbb333ggggg	chr11:97745256-97745477(-)$1	221	173	198	11.7712
iiiiiiii[ccclllccciiiiiii	chr18:61747016-61747236(+)$1	220	98	123	9.4552
cggggggg[ccclllcccggggggg	chr5:135636935-135637155(+)$1	220	91	116	9.1352
fffff####bbmmmmbb4444ffff	chr1:179379281-179379501(+)$1	220	45	70	10.6483
====a[eeeeemmmmeeeeeaffff	chr4:71861009-71861229(-)$1	220	140	165	10.1042
[==========mmmm==========	chr14:22613786-22614009(+)$1	223	147	172	12.1033
========cccmmmmccc22=====	chr15:81625799-81626019(+)$1	220	94	119	12.3129
biiiiiiiiiooooooiiiiiiiii	chr4:134064505-134064725(+)$1	220	130	155	8.3771
a[aa[ffffffmmmmffffff]a]a	chr4:151356950-151357170(-)$1	220	119	144	8.9984
ffffff[a[bbmmmmbb333a]fff	chr6:92138480-92138700(-)$1	220	143	168	10.6695
c$$$$$eeeeemmmmeeeee4444c	chr19:43574326-43574546(-)$1	220	108	133	9.0512
ccc[ggggggglllgggggggccc3	chr11:98781939-98782159(+)$1	220	124	149	8.1268
ee!!gggggggmmmmggggggg333	chr2:79510808-79511028(+)$1	220	70	95	10.7935
dddccca[cccmmmmccc]a]ccc2	chr17:13117038-13117286(+)$1	248	100	125	11.0758
ccc[eeeeebbmmmmbb]eeeeecc	chr19:4012506-4012726(-)$1	220	88	113	9.9530
ffffff[a[bbmmmmbb]a]fffff	chr5:140227365-140227585(-)$1	220	159	184	10.0580
gggggg!!cccmmmmccc]gggggg	chr3:104460400-104460635(+)$1	235	152	177	12.3075
!!ccc!!ddddmmmmdddd22ccc]	chr1:179693827-179694047(-)$1	220	13	38	10.7229
ffccc[bb[bbmmmmbb]bb]ccc3	chrX:69066393-69066619(+)$1	226	81	106	9.5040
b[a[gggggggmmmmggggggg]a]	chr16:16312337-16312560(-)$1	223	103	128	10.5902
ddd"""eeeeemmmmeeeee]dddd	chr11:95331788-95332020(+)$1	232	135	160	9.4508

#otherMatches

#Seq PSSM
GCUCUGCAGGGCGAGCUCUGCAGAG	chr5:114838681-114838901(+)$1	220	147	172	12.0419
GGCUGUGCUUUCUUUGAGGCACAGC	chr15:76911213-76911433(-)$1	220	2	27	11.0637
CCUUAAAAUACAAAGGUAUUUAAUA	chr7:30891023-30891250(+)$1	227	17	42	9.5835
gauuuauuuauuauuauacauaagu	chr2:153442985-153443232(-)$1	247	73	98	10.4882
UUAGGUGGGUAGUAAUACCAGUAAA	chr11:87864063-87864283(+)$1	220	97	122	10.8541
CCGCACCGCACUGUUGUGGGUGGGU	chr3:30515823-30516048(+)$1	225	131	156	10.1659
GGGUCAGUGGGGAGGCCUGGGACUC	chr5:23469366-23469587(-)$1	221	143	168	11.0413
GCAUCCAGGCAGUCAUGUGUGAUGG	chr5:115593571-115593791(-)$1	220	45	70	10.8403
AUGCUGGUCGCUGGAGCAACCAGUA	chr14:21839673-21839893(+)$1	220	137	162	11.4207
UUUAGUAUGUCAGAUGACCUAGGAU	chrX:93362328-93362548(+)$1	220	101	126	10.6620
CUGUAUUGGGGACAUCUGAAAAUGG	chr3:104258314-104258534(-)$1	220	71	96	9.3578
ACUGGUCAUGCAAGAGCACCUUCAG	chr15:10376709-10376943(-)$1	234	40	65	10.7582
GGGAGAACUUUGUAUGAAGCUGCCC	chr1:180179679-180179907(+)$1	228	116	141	11.3473
gcuggcuugccccagggagaguuug	chr13:18079624-18079844(-)$1	220	142	167	9.7678
GUCUGUAGAGAGUUAUUUCUCAGAC	chr9:105546444-105546664(+)$1	220	163	188	9.5028
GGCUGGUGAGCACACGUUGGCCAGC	chr8:42426753-42426974(-)$1	221	16	41	9.2754
GAACAAGAGGUCAGUGCUUCACAGU	chr7:146060068-146060288(+)$1	220	113	138	10.1879
AGUCCUCCUGGGUAUCCAUAUGCAG	chr2:6362667-6362901(+)$1	234	25	50	11.6514
GACUUAUGUACCAGAGUACACACCA	chr16:31254514-31254754(-)$1	240	65	90	10.1685
GUUUCUGUGGUCUGUGCUACUUAGG	chr3:65184457-65184677(-)$1	220	77	102	9.8882
GGGUUUCUACUUCCGGGUCAAAGCC	chr4:118992943-118993181(-)$1	238	77	102	10.7285
GAGUUUGUAAUUUUUAUUAACGAGA	chr19:53454056-53454276(-)$1	220	190	215	10.8235
UGCUUCCAGGAUGGUUUGGGAAGCA	chr4:116944641-116944861(-)$1	220	166	191	11.3188
GAGGCGGCCGUGACAGUGGCCGCCU	chr2:71227235-71227455(+)$1	220	186	211	7.6396
AUUAUUGGAACGGAAGUUGCAACUA	chr16:20509030-20509250(+)$1	220	163	188	10.0328
AAACUACCUUUUCUAAAACGUCcau	chr13:100195621-100195841(-)$1	220	140	165	10.2687
UCGGUGCAGGGUUGGCCGCUGCGCC	chr14:56290543-56290777(-)$1	234	174	199	9.5790
UCUCUCCUCCCCCCAGGGCACAGAG	chr16:20692653-20692874(+)$1	221	61	86	11.8198
AAUGUGAAGGAGUAAUCCAGAAUAU	chr13:101387291-101387511(-)$1	220	166	191	11.4015
CGCUGGGCUUGGAUCCGAGCUCCAG	chr4:86257481-86257704(-)$1	223	45	70	9.4767
AGUGUCCAUCCGGAAGGAAGCUCAC	chr6:119303686-119303910(-)$1	224	81	106	11.0646
GUUUUUAGGUUAAAGAGCGAAAAAA	chr4:132102475-132102695(+)$1	220	68	93	10.6520
CGACUAAGUCAGAUUUGGGUGUGUU	chrX:53838967-53839215(-)$1	248	17	42	11.6857
GGGCGGCCCGCAGCUGUGGAAGCCC	chr13:75844866-75845086(+)$1	220	60	85	9.5517
AUGUCUGauauaaauauauaauaua	chr12:25301432-25301652(+)$1	220	19	44	10.2048
AGACCACUGGAGAAUUCCAAGUCUA	chr1:65205326-65205547(-)$1	221	70	95	10.8422
ACCUACUGGACCGUGGUUUUGUAGG	chr2:17992669-17992906(+)$1	237	104	129	9.5319
GGUGGGACGAGACGACUAAAUCCCA	chr11:97745256-97745477(-)$1	221	173	198	11.7712
AGCAGACGAUUGGAGCAGCGUUUGU	chr18:61747016-61747236(+)$1	220	98	123	9.4552
cacugucccguaguauauggauagu	chr5:135636935-135637155(+)$1	220	91	116	9.1352
AAACUUUGUGUGGCAACUUCUGGUU	chr1:179379281-179379501(+)$1	220	45	70	10.6483
CGCGGAGGAUAGAGCUAUCCCGGAA	chr4:71861009-71861229(-)$1	220	140	165	10.1042
GCUCAUUUCUCACCUGAGAGAUGAG	chr14:22613786-22614009(+)$1	223	147	172	12.1033
AUAUAUGUCGCCCCUGUGAUGCAUA	chr15:81625799-81626019(+)$1	220	94	119	12.3129
GGGGGCUAAAGGCAAGUUUGGUCCC	chr4:134064505-134064725(+)$1	220	130	155	8.3771
UGCUGCGACAGGCAGUUGUCGGGUG	chr4:151356950-151357170(-)$1	220	119	144	8.9984
UUCUGUGGAGUAUUAGCAGGUGAUG	chr6:92138480-92138700(-)$1	220	143	168	10.6695
UGGUCUGGAACAUUAGUUUUUUUAA	chr19:43574326-43574546(-)$1	220	108	133	9.0512
AGGACUCCUGGAGUCCAGGGGCCUU	chr11:98781939-98782159(+)$1	220	124	149	8.1268
CAUUGUAGAUUAAAGAGUCUAUUGU	chr2:79510808-79511028(+)$1	220	70	95	10.7935
UUGGUCCAUGGGAAACCACGAGACA	chr17:13117038-13117286(+)$1	248	100	125	11.0758
CCGUCUGGCUCCCGCGAUGCUAGCG	chr19:4012506-4012726(-)$1	220	88	113	9.9530
UGUCCAAGACACACCUGCCCUGGAC	chr5:140227365-140227585(-)$1	220	159	184	10.0580
gguucuuagguuugaacccagggcc	chr3:104460400-104460635(+)$1	235	152	177	12.3075
CAGUUAAUGCAAUUUUGCACAAAUA	chr1:179693827-179694047(-)$1	220	13	38	10.7229
CAUUUGCAAAUGAAAAUGUGGAAAA	chrX:69066393-69066619(+)$1	226	81	106	9.5040
AGGGAAAGGGGAAGCUUCCUUUGUG	chr16:16312337-16312560(-)$1	223	103	128	10.5902
CACCUCCGGCAGAAAUGUCGAGUGG	chr11:95331788-95332020(+)$1	232	135	160	9.4508

#DB
(((((((((((....))))))))))	chr5:114838681-114838901(+)$1	1	147	172	12.0419
.((((((((((....))))))))))	chr15:76911213-76911433(-)$1	1	2	27	11.0637
(((..((((((....))))))...)	chr7:30891023-30891250(+)$1	1	17	42	9.5835
)((((((.(((....))).))))))	chr2:153442985-153443232(-)$1	1	73	98	10.4882
(((....((((....))))..))))	chr11:87864063-87864283(+)$1	1	97	122	10.8541
((.((((.(((....))))))))))	chr3:30515823-30516048(+)$1	1	131	156	10.1659
(((((..((((....)))).)))))	chr5:23469366-23469587(-)$1	1	143	168	11.0413
.((((.(.(((....))).))))).	chr5:115593571-115593791(-)$1	1	45	70	10.8403
((((((((.((....)).)))))))	chr14:21839673-21839893(+)$1	1	137	162	11.4207
.((((...(((....))))))))))	chrX:93362328-93362548(+)$1	1	101	126	10.6620
((.((((..((....))...)))).	chr3:104258314-104258534(-)$1	1	71	96	9.3578
...(((...((....)))))...))	chr15:10376709-10376943(-)$1	1	40	65	10.7582
(((....((((....))))...)))	chr1:180179679-180179907(+)$1	1	116	141	11.3473
((.(((((.((....)).))))).)	chr13:18079624-18079844(-)$1	1	142	167	9.7678
(((((.(((((....))))))))))	chr9:105546444-105546664(+)$1	1	163	188	9.5028
(((((((.(((....))).))))))	chr8:42426753-42426974(-)$1	1	16	41	9.2754
((....(((((....)))))....)	chr7:146060068-146060288(+)$1	1	113	138	10.1879
.((((((.(((....)))...).))	chr2:6362667-6362901(+)$1	1	25	50	11.6514
((((..(((((....)))))....)	chr16:31254514-31254754(-)$1	1	65	90	10.1685
(((((((((((....)))))...))	chr3:65184457-65184677(-)$1	1	77	102	9.8882
((((((..(((....)))..)))))	chr4:118992943-118993181(-)$1	1	77	102	10.7285
((.((((((((....))).))))).	chr19:53454056-53454276(-)$1	1	190	215	10.8235
(((((((..((....)).)))))))	chr4:116944641-116944861(-)$1	1	166	191	11.3188
.(((((((((......)))))))))	chr2:71227235-71227455(+)$1	1	186	211	7.6396
(((((((.(((....))).))).))	chr16:20509030-20509250(+)$1	1	163	188	10.0328
((...((.(((....))).))...)	chr13:100195621-100195841(-)$1	1	140	165	10.2687
..(((((((((....)).)))))))	chr14:56290543-56290777(-)$1	1	174	199	9.5790
(((((...(((....)))...))))	chr16:20692653-20692874(+)$1	1	61	86	11.8198
.((((...(((....)))...))))	chr13:101387291-101387511(-)$1	1	166	191	11.4015
.((((((((((....))))).))))	chr4:86257481-86257704(-)$1	1	45	70	9.4767
.(((..(.(((....))).)..)))	chr6:119303686-119303910(-)$1	1	81	106	11.0646
((((((..(((....)))...))))	chr4:132102475-132102695(+)$1	1	68	93	10.6520
((((..(.(((....))).)..)))	chrX:53838967-53839215(-)$1	1	17	42	11.6857
((((...((((....))))..))))	chr13:75844866-75845086(+)$1	1	60	85	9.5517
((((...((((....)))).)))))	chr12:25301432-25301652(+)$1	1	19	44	10.2048
.(((...((((....)))).)))))	chr1:65205326-65205547(-)$1	1	70	95	10.8422
.(((((.((((....)))).)))))	chr2:17992669-17992906(+)$1	1	104	129	9.5319
(((((((..((....))...)))))	chr11:97745256-97745477(-)$1	1	173	198	11.7712
((((((((.(((...))))))))))	chr18:61747016-61747236(+)$1	1	98	123	9.4552
)(((((((.(((...))))))))))	chr5:135636935-135637155(+)$1	1	91	116	9.1352
(((((....((....))....))))	chr1:179379281-179379501(+)$1	1	45	70	10.6483
))))(.(((((....))))))((((	chr4:71861009-71861229(-)$1	1	140	165	10.1042
.((((((((((....))))))))))	chr14:22613786-22614009(+)$1	1	147	172	12.1033
(((((((((((....)))..)))))	chr15:81625799-81626019(+)$1	1	94	119	12.3129
)(((((((((......)))))))))	chr4:134064505-134064725(+)$1	1	130	155	8.3771
(.((.((((((....)))))).).)	chr4:151356950-151357170(-)$1	1	119	144	8.9984
((((((.(.((....))...).)))	chr6:92138480-92138700(-)$1	1	143	168	10.6695
(.....(((((....)))))....)	chr19:43574326-43574546(-)$1	1	108	133	9.0512
(((.(((((((...)))))))))).	chr11:98781939-98782159(+)$1	1	124	149	8.1268
((..(((((((....)))))))...	chr2:79510808-79511028(+)$1	1	70	95	10.7935
(((((((.(((....))).).))).	chr17:13117038-13117286(+)$1	1	100	125	11.0758
(((.(((((((....)).)))))))	chr19:4012506-4012726(-)$1	1	88	113	9.9530
((((((.(.((....)).).)))))	chr5:140227365-140227585(-)$1	1	159	184	10.0580
((((((..(((....))).))))))	chr3:104460400-104460635(+)$1	1	152	177	12.3075
..(((..((((....))))..))).	chr1:179693827-179694047(-)$1	1	13	38	10.7229
(((((.((.((....)).)).))).	chrX:69066393-69066619(+)$1	1	81	106	9.5040
(.(.(((((((....))))))).).	chr16:16312337-16312560(-)$1	1	103	128	10.5902
(((...(((((....))))).))))	chr11:95331788-95332020(+)$1	1	135	160	9.4508

#PSSM
f : 0.17	c : 0.13	d : 0.10	g : 0.10	[ : 0.06	= : 0.05	: : 0.05	b : 0.05	" : 0.05	e : 0.05	i : 0.03	! : 0.03	h : 0.03	& : 0.01	# : 0.01	a : 0.01	
f : 0.18	c : 0.13	g : 0.12	d : 0.12	e : 0.12	= : 0.08	i : 0.06	h : 0.03	[ : 0.03	b : 0.01	" : 0.01	& : 0.01	$ : 0.01	! : 0.01	
f : 0.15	g : 0.13	c : 0.12	d : 0.10	= : 0.08	e : 0.08	[ : 0.06	i : 0.06	" : 0.03	h : 0.03	a : 0.03	# : 0.01	b : 0.01	$ : 0.01	! : 0.01	
f : 0.15	e : 0.12	d : 0.10	g : 0.10	c : 0.10	= : 0.08	i : 0.06	# : 0.05	[ : 0.05	! : 0.03	h : 0.03	" : 0.03	b : 0.01	a : 0.01	$ : 0.01	
g : 0.15	e : 0.13	f : 0.10	d : 0.08	c : 0.08	" : 0.08	= : 0.06	! : 0.06	i : 0.06	# : 0.05	h : 0.03	a : 0.01	[ : 0.01	$ : 0.01	
g : 0.13	" : 0.12	e : 0.12	f : 0.10	! : 0.08	= : 0.06	# : 0.06	[ : 0.06	i : 0.06	c : 0.05	d : 0.03	h : 0.03	b : 0.01	$ : 0.01	
e : 0.18	" : 0.12	g : 0.12	! : 0.08	a : 0.08	= : 0.06	i : 0.06	f : 0.05	# : 0.05	[ : 0.05	d : 0.03	b : 0.03	h : 0.01	c : 0.01	
e : 0.18	[ : 0.17	d : 0.13	! : 0.10	g : 0.08	= : 0.06	i : 0.06	" : 0.06	f : 0.03	a : 0.03	# : 0.01	b : 0.01	
c : 0.31	e : 0.15	d : 0.13	[ : 0.12	g : 0.06	= : 0.05	! : 0.05	f : 0.03	i : 0.03	" : 0.01	# : 0.01	
c : 0.34	b : 0.20	d : 0.13	e : 0.13	= : 0.05	g : 0.05	f : 0.03	i : 0.03	
c : 0.34	b : 0.20	d : 0.13	e : 0.13	= : 0.05	g : 0.05	f : 0.03	o : 0.03	
m : 0.91	o : 0.03	c : 0.03	l : 0.01	
m : 0.91	l : 0.05	o : 0.03	
m : 0.91	l : 0.05	o : 0.03	
m : 0.91	o : 0.03	l : 0.03	g : 0.01	
c : 0.34	b : 0.20	d : 0.13	e : 0.13	= : 0.05	g : 0.05	f : 0.03	o : 0.03	
c : 0.34	b : 0.20	d : 0.13	e : 0.13	= : 0.05	g : 0.05	f : 0.03	i : 0.03	
c : 0.36	d : 0.13	e : 0.13	] : 0.12	= : 0.05	3 : 0.05	g : 0.05	f : 0.03	i : 0.03	4 : 0.01	
] : 0.17	d : 0.17	e : 0.17	3 : 0.12	g : 0.10	i : 0.06	= : 0.05	f : 0.03	2 : 0.03	c : 0.01	4 : 0.01	a : 0.01	b : 0.01	
e : 0.18	3 : 0.13	g : 0.12	2 : 0.08	] : 0.08	a : 0.06	i : 0.06	= : 0.05	f : 0.05	d : 0.03	c : 0.03	b : 0.03	h : 0.01	4 : 0.01	
g : 0.15	3 : 0.12	f : 0.10	2 : 0.08	e : 0.08	= : 0.06	d : 0.06	i : 0.06	4 : 0.06	] : 0.06	c : 0.03	a : 0.03	h : 0.01	b : 0.01	
g : 0.15	d : 0.12	e : 0.12	f : 0.10	c : 0.10	3 : 0.08	= : 0.06	i : 0.06	4 : 0.05	h : 0.03	2 : 0.03	] : 0.03	a : 0.01	
f : 0.13	g : 0.13	c : 0.13	e : 0.12	3 : 0.08	d : 0.08	= : 0.06	i : 0.06	4 : 0.05	] : 0.05	h : 0.03	a : 0.01	
f : 0.15	g : 0.15	c : 0.13	d : 0.10	e : 0.10	= : 0.06	i : 0.06	3 : 0.05	4 : 0.05	] : 0.03	h : 0.03	b : 0.01	a : 0.01	
f : 0.17	g : 0.15	c : 0.12	e : 0.10	d : 0.08	= : 0.06	] : 0.06	i : 0.06	3 : 0.05	2 : 0.03	h : 0.03	b : 0.01	a : 0.01	

#score	601.9007684026606
#seq	58
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_CDS_m2_run2.txt

#BEAR
$$$$bb!!ddddoooooodddd22bb22gg	chr10:74709204-74709442(+)$1	238	158	188	15.2353
eeeee!!dddd[aooooooa]ddddeeeee	chr2:163453498-163453751(-)$1	253	51	81	12.4026
fffff"""ddddooooooddddffffff]f	chr10:58920498-58920729(-)$1	231	55	85	14.6098
g!!eeeee[cccooooooccc]eeeeeggg	chr9:16835099-16835348(+)$1	249	155	185	14.6466
c!!ggggggg[aooooooa]gggggggccc	chr6:127095971-127096231(-)$1	260	157	187	15.0041
ff[accc[ddddoooooodddd22ccc]a]	chr4:41137640-41137883(+)$1	243	119	149	16.3644
dd[ccc[eeeeeooooooeeeee]cccddd	chr11:77364330-77364574(-)$1	244	64	94	14.0010
gg!!ccc[bb[aooooooa]bbccc22ggg	chr3:8560238-8560544(+)$1	306	151	181	13.9553
$ggggggg"""aooooooa333ggggggg2	chr6:115799641-115799877(-)$1	236	56	86	14.2984
eeee[bb!!cccooooooccc4444bb]ee	chr12:3908102-3908363(+)$1	261	192	222	14.5870
iiiiii!!ddddoooooodddd]iiiiiii	chr13:81833400-81833631(-)$1	231	127	157	16.4991
hh!!a!!eeeeeooooooeeeee22a4444	chr11:120432727-120432980(-)$1	253	45	75	14.7139
============lll============fff	chr19:41306757-41306996(-)$1	239	16	46	10.7627
bb!!eeeee[bboooooobbeeeee]bb]c	chr1:93826535-93826766(-)$1	231	102	132	12.8667
ffff[ccc!!bboooooobb22ccc]ffff	chr1:154976179-154976427(-)$1	248	131	161	12.4063
hhh!!ccc!!bboooooobb333ccc22hh	chr1:59927202-59927489(+)$1	287	23	53	13.5008
========[cccooooooccc]========	chr4:49668539-49668775(+)$1	236	193	223	15.8777
::::ccc[ddddoooooodddd333cccff	chr17:6229323-6229570(+)$1	247	22	52	12.7150
ff[ccc!!ddddoooooodddd]ccc]fff	chr8:63374242-63374498(+)$1	256	200	230	16.1147
eeeee"""ddddoooooodddd22eeeee:	chr1:56947923-56948206(-)$1	283	111	141	14.5585
c"""bb!!ddddoooooodddd333bb333	chr10:39374090-39374321(-)$1	231	116	146	17.1868
dddd[gggggggooooooggggggg]dddd	chr13:113504301-113504532(+)$1	231	27	57	12.7705
""==========oooooo==========]c	chr10:79224832-79225063(-)$1	231	150	180	15.8350
cc!!eeeeecccooooooccc]eeeee22c	chr14:67426590-67426886(-)$1	296	150	180	14.6950
b!!eeeeeddddoooooodddd]eeeee22	chr9:45780976-45781211(-)$1	235	65	95	15.0339
h"""ddddddddoooooodddd]dddd]hh	chr13:95612575-95612869(+)$1	294	235	265	14.5750
cc[ccc[eeeeeooooooeeeee333ccc2	chr2:6467998-6468236(-)$1	238	15	45	15.1354
b[ccc!!eeeeerrrrrrrrreeeee333c	chr19:10059172-10059428(+)$1	256	135	165	9.7371
bb[ccc[ccc[aooooooa]ccccccbbcc	chr6:135683371-135683607(-)$1	236	25	55	14.1798
ccc!!cccddddoooooodddd22ccc22c	chr5:143666936-143667210(-)$1	274	138	168	16.0714
%%%ccc!!bb[aooooooa]bb22ccc444	chr11:75565352-75565588(+)$1	236	49	79	13.3567
eee!!gggggggooooooggggggg333ee	chr18:16791454-16791686(-)$1	232	11	41	14.2970
####ccc[bb[aooooooa]bb]cccccc]	chr15:76924817-76925071(-)$1	254	157	187	14.6927
ggggggg[ddddoooooodddd22gggggg	chr6:134456278-134456518(-)$1	240	120	150	16.1031
!bb!!bb[ddddoooooodddd]bbbb22e	chr14:73574191-73574422(+)$1	231	7	37	14.3945
&&ccc"""ddddoooooodddd333ccc77	chr2:98507083-98507435(-)$1	352	226	256	14.6916
eeee[bb!!cccooooooccc]bb]eeeee	chr6:141511571-141511837(+)$1	266	52	82	13.4963
c!!bb"""ddddoooooodddd]bb]ccc]	chr11:75309812-75310054(+)$1	242	182	212	15.8191
!!dddd[eeeeeooooooeeeeedddd]hh	chr6:24904587-24904823(-)$1	236	17	47	13.2492
eeeee####cccooooooccc333eeeee:	chr12:101444518-101444782(+)$1	264	56	86	14.1716
ccc[bb"""cccooooooccc4444bb]cc	chr17:26394865-26395096(+)$1	231	82	112	15.3374
:gggggggddddoooooodddd4444gggg	chr10:57247376-57247607(-)$1	231	120	150	15.0857
f!!cccbb[cccooooooccc]bb]ccc]f	chr3:88985012-88985244(+)$1	232	181	211	14.2376
ccc[eeeee[bboooooobb]eeeee]ccc	chr17:35032463-35032716(+)$1	253	97	127	13.0271

#otherMatches

#Seq PSSM
ACAAGGAAAAGGCGGAGACUUUGGCCAGUA	chr10:74709204-74709442(+)$1	238	158	188	15.2353
UGCCUAUGCUCCGCCGUCACAGAGUGGGCA	chr2:163453498-163453751(-)$1	253	51	81	12.4026
CUGAGUCAAAGAGUUUAAUCUUCUUGGUCA	chr10:58920498-58920729(-)$1	231	55	85	14.6098
CCAAGUUCAUCAAUUAUGUGAAGAAUUGUU	chr9:16835099-16835348(+)$1	249	155	185	14.6466
CAUGCGCAGACCUUCAUCGCUCUGUGCGCU	chr6:127095971-127096231(-)$1	260	157	187	15.0041
AUGACGACUUGUaugacgacgacauugaug	chr4:41137640-41137883(+)$1	243	119	149	16.3644
CUAUAUAGGCUAAAGUGAUGGCCAAUGAGG	chr11:77364330-77364574(-)$1	244	64	94	14.0010
UGCGAUAUCAGUAUGGGAAGUGUAUGACAU	chr3:8560238-8560544(+)$1	306	151	181	13.9553
UAAUUGGAAUUCUGAAAUGUGGUCCAGUUC	chr6:115799641-115799877(-)$1	236	56	86	14.2984
UCGGAGGCAGAGUCUCCUCUCCCACCCCCC	chr12:3908102-3908363(+)$1	261	192	222	14.5870
AAAACAUUUAUAUUUUAUUGUAUUGUUUUU	chr13:81833400-81833631(-)$1	231	127	157	16.4991
CACAGAAGAGUCUGACCUGGCUCAGCAGUA	chr11:120432727-120432980(-)$1	253	45	75	14.7139
CGUCUCUUUUCUUUCAGGAAGGAGAUGGAU	chr19:41306757-41306996(-)$1	239	16	46	10.7627
GGUUGUGUUUCUUUCCUCAGAACAUUCCUU	chr1:93826535-93826766(-)$1	231	102	132	12.8667
UUCAUUCUAGAGUUUGAUCUGCAGGUUGAA	chr1:154976179-154976427(-)$1	248	131	161	12.4063
GUGACAGGGCAGUCCAUUCUAAAUCUAGCA	chr1:59927202-59927489(+)$1	287	23	53	13.5008
UUUCACGUUUUCUGCUUUGAGUGUGUGAAG	chr4:49668539-49668775(+)$1	236	193	223	15.8777
ACCAGCCUGCUGCAUCUCCAGCCUCGGCAG	chr17:6229323-6229570(+)$1	247	22	52	12.7150
UUCAGGUAAAGGCUCUUCUCUUCUCUAAAA	chr8:63374242-63374498(+)$1	256	200	230	16.1147
CAUUGUAAAUAGCACAUACUAUGCCAAUGU	chr1:56947923-56948206(-)$1	283	111	141	14.5585
CAGGUCGGCACAUGCUCCUGUGGAAGAGAG	chr10:39374090-39374321(-)$1	231	116	146	17.1868
GUUUCUGUCUUUUCUCCUAGAGAUAAGAGC	chr13:113504301-113504532(+)$1	231	27	57	12.7705
UCGGUACGGGGCCCGGCAGCCCCGUGCCCG	chr10:79224832-79225063(-)$1	231	150	180	15.8350
CUGACUUUGUGUACAAACGCAUCAAAGCAA	chr14:67426590-67426886(-)$1	296	150	180	14.6950
UCAUUGUUGUCUGGGUAGGGACAAACAACC	chr9:45780976-45781211(-)$1	235	65	95	15.0339
UUUCUUUGCAUAACUUAAUGUGUCAAAUAA	chr13:95612575-95612869(+)$1	294	235	265	14.5750
GCAAUCCAGGCUAUGAACGGCUUUCAGAUC	chr2:6467998-6468236(-)$1	238	15	45	15.1354
AGGUGAAAUCCAUUAAAGAACUGGGUGACC	chr19:10059172-10059428(+)$1	256	135	165	9.7371
GGCAGCACCAGCUCCAUUGAUGGGCUCUAU	chr6:135683371-135683607(-)$1	236	25	55	14.1798
CCCCAUUGAACAUGGCAUUGUUACCAACUG	chr5:143666936-143667210(-)$1	274	138	168	16.0714
GAAAGUAGCAGGGAUGGACGUGGAGCUGAC	chr11:75565352-75565588(+)$1	236	49	79	13.3567
GUUAUCUUUUUGUCUUUUUAGAAAGUGCAA	chr18:16791454-16791686(-)$1	232	11	41	14.2970
UUACCAGGACGGAUUUUACGGUGCUGACCU	chr15:76924817-76925071(-)$1	254	157	187	14.6927
UCUGUCUUUAUAGGUACAUGUAUUGGACAG	chr6:134456278-134456518(-)$1	240	120	150	16.1031
CCUGACGACCACCUCACUGUGGCCGAGUCU	chr14:73574191-73574422(+)$1	231	7	37	14.3945
caugauuuucaguuuucuuugauuuucagu	chr2:98507083-98507435(-)$1	352	226	256	14.6916
GAAAGAUAAUGGAUGUUCCCAAAUGUUUCU	chr6:141511571-141511837(+)$1	266	52	82	13.4963
GCCGUACCAGCUAUGAAGAGUUCACCCACA	chr11:75309812-75310054(+)$1	242	182	212	15.8191
UCUGGGACUUCGAAUGUGCGGGGCCUGUUC	chr6:24904587-24904823(-)$1	236	17	47	13.2492
AGAUACUGAAAUGUUAUGAUUAUUUGUCUU	chr12:101444518-101444782(+)$1	264	56	86	14.1716
AGACCUGUUUUUUGAAUUAGAUGUAAGAUU	chr17:26394865-26395096(+)$1	231	82	112	15.3374
AAGAACAACUGAAUAAGGUCAGGCUUUUGU	chr10:57247376-57247607(-)$1	231	120	150	15.0857
UUCAGGUGUGUGAGCUACCAUUCGUCCUCA	chr3:88985012-88985244(+)$1	232	181	211	14.2376
UUCAUUGAGCCCAAAAUAGGCCUUAAAGAA	chr17:35032463-35032716(+)$1	253	97	127	13.0271

#DB
....((..((((......))))..))..))	chr10:74709204-74709442(+)$1	1	158	188	15.2353
(((((..((((.(......).)))))))))	chr2:163453498-163453751(-)$1	1	51	81	12.4026
(((((...((((......)))))))))).)	chr10:58920498-58920729(-)$1	1	55	85	14.6098
(..(((((.(((......))).))))))))	chr9:16835099-16835348(+)$1	1	155	185	14.6466
(..(((((((.(......).))))))))))	chr6:127095971-127096231(-)$1	1	157	187	15.0041
((.((((.((((......))))..))).).	chr4:41137640-41137883(+)$1	1	119	149	16.3644
((.(((.(((((......))))).))))))	chr11:77364330-77364574(-)$1	1	64	94	14.0010
((..(((.((.(......).)))))..)))	chr3:8560238-8560544(+)$1	1	151	181	13.9553
.(((((((...(......)...))))))).	chr6:115799641-115799877(-)$1	1	56	86	14.2984
((((.((..(((......)))....)).))	chr12:3908102-3908363(+)$1	1	192	222	14.5870
((((((..((((......)))).)))))))	chr13:81833400-81833631(-)$1	1	127	157	16.4991
((..(..(((((......)))))..)....	chr11:120432727-120432980(-)$1	1	45	75	14.7139
((((((((((((...))))))))))))(((	chr19:41306757-41306996(-)$1	1	16	46	10.7627
((..(((((.((......))))))).)).)	chr1:93826535-93826766(-)$1	1	102	132	12.8667
((((.(((..((......))..))).))))	chr1:154976179-154976427(-)$1	1	131	161	12.4063
(((..(((..((......))...)))..))	chr1:59927202-59927489(+)$1	1	23	53	13.5008
((((((((.(((......))).))))))))	chr4:49668539-49668775(+)$1	1	193	223	15.8777
....(((.((((......))))...)))((	chr17:6229323-6229570(+)$1	1	22	52	12.7150
((.(((..((((......)))).))).)))	chr8:63374242-63374498(+)$1	1	200	230	16.1147
(((((...((((......))))..))))).	chr1:56947923-56948206(-)$1	1	111	141	14.5585
(...((..((((......))))...))...	chr10:39374090-39374321(-)$1	1	116	146	17.1868
((((.(((((((......))))))).))))	chr13:113504301-113504532(+)$1	1	27	57	12.7705
..((((((((((......)))))))))).)	chr10:79224832-79225063(-)$1	1	150	180	15.8350
((..((((((((......))).)))))..)	chr14:67426590-67426886(-)$1	1	150	180	14.6950
(..(((((((((......)))).)))))..	chr9:45780976-45781211(-)$1	1	65	95	15.0339
(...((((((((......)))).)))).))	chr13:95612575-95612869(+)$1	1	235	265	14.5750
((.(((.(((((......)))))...))).	chr2:6467998-6468236(-)$1	1	15	45	15.1354
(.(((..(((((.........)))))...)	chr19:10059172-10059428(+)$1	1	135	165	9.7371
((.(((.(((.(......).))))))))))	chr6:135683371-135683607(-)$1	1	25	55	14.1798
(((..(((((((......))))..)))..)	chr5:143666936-143667210(-)$1	1	138	168	16.0714
...(((..((.(......).))..)))...	chr11:75565352-75565588(+)$1	1	49	79	13.3567
(((..(((((((......)))))))...))	chr18:16791454-16791686(-)$1	1	11	41	14.2970
....(((.((.(......).)).)))))).	chr15:76924817-76925071(-)$1	1	157	187	14.6927
(((((((.((((......))))..))))))	chr6:134456278-134456518(-)$1	1	120	150	16.1031
.((..((.((((......)))).))))..)	chr14:73574191-73574422(+)$1	1	7	37	14.3945
..(((...((((......))))...)))..	chr2:98507083-98507435(-)$1	1	226	256	14.6916
((((.((..(((......))).)).)))))	chr6:141511571-141511837(+)$1	1	52	82	13.4963
(..((...((((......)))).)).))).	chr11:75309812-75310054(+)$1	1	182	212	15.8191
..((((.(((((......))))))))).))	chr6:24904587-24904823(-)$1	1	17	47	13.2492
(((((....(((......)))...))))).	chr12:101444518-101444782(+)$1	1	56	86	14.1716
(((.((...(((......)))....)).))	chr17:26394865-26395096(+)$1	1	82	112	15.3374
.(((((((((((......))))....))))	chr10:57247376-57247607(-)$1	1	120	150	15.0857
(..(((((.(((......))).)).))).)	chr3:88985012-88985244(+)$1	1	181	211	14.2376
(((.(((((.((......)).))))).)))	chr17:35032463-35032716(+)$1	1	97	127	13.0271

#PSSM
c : 0.18	e : 0.13	f : 0.11	b : 0.09	g : 0.06	h : 0.06	$ : 0.04	d : 0.04	= : 0.04	: : 0.04	! : 0.04	i : 0.02	" : 0.02	% : 0.02	# : 0.02	& : 0.02	
e : 0.13	! : 0.13	c : 0.11	f : 0.09	g : 0.09	b : 0.06	" : 0.06	d : 0.04	h : 0.04	= : 0.04	$ : 0.02	i : 0.02	: : 0.02	[ : 0.02	% : 0.02	# : 0.02	& : 0.02	
! : 0.20	e : 0.13	[ : 0.11	c : 0.11	g : 0.06	= : 0.06	f : 0.04	" : 0.04	d : 0.04	$ : 0.02	i : 0.02	h : 0.02	: : 0.02	% : 0.02	# : 0.02	b : 0.02	
c : 0.18	! : 0.18	e : 0.15	g : 0.09	= : 0.06	f : 0.04	" : 0.04	d : 0.04	[ : 0.04	$ : 0.02	a : 0.02	i : 0.02	: : 0.02	# : 0.02	b : 0.02	
c : 0.27	e : 0.18	b : 0.09	g : 0.09	[ : 0.09	! : 0.09	= : 0.06	d : 0.04	f : 0.02	i : 0.02	a : 0.02	
c : 0.29	b : 0.13	g : 0.13	e : 0.11	" : 0.09	! : 0.06	= : 0.06	d : 0.04	i : 0.02	# : 0.02	
! : 0.18	c : 0.15	g : 0.13	" : 0.11	e : 0.11	[ : 0.09	b : 0.09	= : 0.06	d : 0.02	# : 0.02	
e : 0.22	! : 0.15	[ : 0.13	" : 0.11	g : 0.11	c : 0.09	= : 0.06	d : 0.04	# : 0.02	b : 0.02	
d : 0.38	e : 0.18	! : 0.09	[ : 0.06	g : 0.06	b : 0.06	" : 0.04	= : 0.04	c : 0.02	# : 0.02	
d : 0.38	c : 0.20	e : 0.11	g : 0.06	b : 0.06	= : 0.04	[ : 0.04	! : 0.04	" : 0.02	
d : 0.38	c : 0.18	[ : 0.11	e : 0.11	b : 0.09	= : 0.04	g : 0.04	" : 0.02	
d : 0.36	c : 0.18	a : 0.13	e : 0.11	b : 0.09	= : 0.04	g : 0.04	[ : 0.02	
o : 0.93	a : 0.02	l : 0.02	r : 0.02	
o : 0.95	l : 0.02	r : 0.02	
o : 0.95	l : 0.02	r : 0.02	
o : 0.95	= : 0.02	r : 0.02	
o : 0.95	= : 0.02	r : 0.02	
o : 0.95	= : 0.02	r : 0.02	
d : 0.36	c : 0.18	a : 0.13	e : 0.09	b : 0.09	= : 0.04	g : 0.04	o : 0.02	r : 0.02	
d : 0.36	c : 0.18	] : 0.11	e : 0.09	b : 0.09	= : 0.04	g : 0.04	a : 0.02	3 : 0.02	r : 0.02	
d : 0.36	c : 0.20	e : 0.11	g : 0.06	b : 0.06	] : 0.04	3 : 0.04	= : 0.04	2 : 0.02	r : 0.02	
d : 0.38	e : 0.15	] : 0.11	g : 0.06	b : 0.06	3 : 0.06	4 : 0.04	= : 0.04	2 : 0.02	c : 0.02	
e : 0.20	] : 0.15	2 : 0.13	3 : 0.11	g : 0.09	c : 0.06	4 : 0.06	= : 0.06	b : 0.04	d : 0.02	f : 0.02	
2 : 0.15	e : 0.13	c : 0.13	3 : 0.11	g : 0.09	b : 0.09	d : 0.06	4 : 0.06	= : 0.06	f : 0.02	] : 0.02	i : 0.02	
c : 0.22	e : 0.18	g : 0.11	3 : 0.09	b : 0.06	d : 0.06	4 : 0.06	= : 0.06	] : 0.04	f : 0.02	i : 0.02	2 : 0.02	
c : 0.25	e : 0.20	b : 0.11	] : 0.09	g : 0.06	= : 0.06	d : 0.04	3 : 0.04	f : 0.02	2 : 0.02	i : 0.02	a : 0.02	4 : 0.02	
c : 0.22	e : 0.15	b : 0.13	g : 0.09	2 : 0.06	= : 0.06	d : 0.06	f : 0.04	] : 0.04	3 : 0.04	i : 0.02	4 : 0.02	
c : 0.18	2 : 0.11	e : 0.11	g : 0.11	] : 0.11	f : 0.09	3 : 0.06	d : 0.04	4 : 0.04	b : 0.04	= : 0.04	i : 0.02	
c : 0.15	g : 0.13	e : 0.13	] : 0.09	f : 0.09	2 : 0.09	h : 0.06	d : 0.04	4 : 0.04	3 : 0.04	a : 0.02	i : 0.02	= : 0.02	7 : 0.02	
c : 0.20	f : 0.13	g : 0.11	e : 0.11	] : 0.06	2 : 0.06	h : 0.06	d : 0.04	4 : 0.04	: : 0.04	i : 0.02	= : 0.02	3 : 0.02	7 : 0.02	

#score	632.301699460091
#seq	44
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_CDS_m1_run2.txt

#BEAR
ddd[cccooooooccc]dddd	chr2:76594261-76594496(-)$1	235	133	154	12.8864
dd"""cccmmmmccc4444dd	chr7:74904121-74904374(-)$1	253	198	219	8.3709
ccc[cccoooooocccccc]c	chr2:76561979-76562240(-)$1	261	162	183	12.7330
$$$$cccooooooccc55555	chr4:43527519-43527758(-)$1	239	50	71	9.6542
bb!!cccnnnnnccc333bb]	chr17:25969080-25969315(-)$1	235	38	59	8.1595
gggggggoooooogggggggF	chr2:76565493-76565731(-)$1	238	1	22	10.4522
"""ddddoooooodddddddd	chr10:19329021-19329256(+)$1	235	33	54	10.9279
eee!!bboooooobb333eee	chr4:129523617-129523873(+)$1	256	28	49	11.7956
ddcccbboooooobb]ccc44	chr19:9078779-9079016(+)$1	237	146	167	11.4751
ccc[a[aooooooa]a]ccc]	chr7:52399799-52400034(-)$1	235	170	191	12.2440
cc[ddddoooooodddd]ccc	chr9:72510245-72510480(+)$1	235	85	106	10.9627
%%%%cccooooooccc66666	chr2:76689541-76689776(-)$1	235	44	65	9.4877
ccc[cccooooooccc]ccc:	chr4:43535508-43535762(-)$1	254	110	131	12.3695
$$$$$bboooooobb22dddd	chr2:67350602-67350837(+)$1	235	137	158	10.8340
eeee[bboooooobb]eeeee	chr14:60248649-60248884(+)$1	235	10	31	10.1884
dd!!ccc[aooooooa]cccd	chr2:76606134-76606371(-)$1	237	161	182	10.5521
ddd[cccooooooccc]dddd	chr6:29411059-29411294(+)$1	235	130	151	12.8864
ee!!cccooooooccc4444e	chr1:174215791-174216027(-)$1	236	206	227	13.5212
ebb[cccoooooocccbb333	chr7:133592024-133592270(-)$1	246	69	90	11.7892
gggggggooooooggggggg]	chr5:29761756-29761991(+)$1	235	202	223	11.0414
cc"""cccmmmmccc333ccc	chr14:60898841-60899085(+)$1	244	123	144	8.5015
ddd[cccoooooocccdddd3	chr10:77670618-77670856(-)$1	238	210	231	12.6954
gggggggooooooggggggg]	chr11:30014728-30014963(-)$1	235	50	71	11.0414
fffff[aooooooa]ffffff	chr11:67067428-67067680(+)$1	252	190	211	9.5068
d!!ddddoooooodddddddd	chr11:6523715-6523950(-)$1	235	63	84	11.0479
dddddddooooooddddeeee	chr4:129522281-129522528(+)$1	247	127	148	10.2892

#otherMatches

#Seq PSSM
ACCCCAAGUGAAAUUGUGGUU	chr2:76594261-76594496(-)$1	235	133	154	12.8864
GGGAGCGCAACGGCGGGAGCU	chr7:74904121-74904374(-)$1	253	198	219	8.3709
GGCUCUGAAUCUACAGGCCCU	chr2:76561979-76562240(-)$1	261	162	183	12.7330
GAACGUGGAGAUACACCAGAC	chr4:43527519-43527758(-)$1	239	50	71	9.6542
GCAUUGACCAGAUCAUUGGCU	chr17:25969080-25969315(-)$1	235	38	59	8.1595
UUAUUAAGCCAAAUUAAUAAA	chr2:76565493-76565731(-)$1	238	1	22	10.4522
CCCUGUCCACAGUGACAGCUC	chr10:19329021-19329256(+)$1	235	33	54	10.9279
UUAAAACCUAAAAGUCUCUGA	chr4:129523617-129523873(+)$1	256	28	49	11.7956
UUUCUGUACCAAAGCUAGAUA	chr19:9078779-9079016(+)$1	237	146	167	11.4751
GGCAGUCAGGACAGUCAGCCA	chr7:52399799-52400034(-)$1	235	170	191	12.2440
CCGCUGCAGCCUAGUAGGGGC	chr9:72510245-72510480(+)$1	235	85	106	10.9627
GAAGACUAUGAGGAGUAUAAA	chr2:76689541-76689776(-)$1	235	44	65	9.4877
CCUCCAGAAGAAGCUGAAGGG	chr4:43535508-43535762(-)$1	254	110	131	12.3695
AACCAGCAAUCAAGCAGCAAG	chr2:67350602-67350837(+)$1	235	137	158	10.8340
GGCUCAUCCUCUCGUCAGUCC	chr14:60248649-60248884(+)$1	235	10	31	10.1884
AGAUGGGUGUCGGUCCUCCCC	chr2:76606134-76606371(-)$1	237	161	182	10.5521
UCAAGGUCAAUGUGCCCUGAA	chr6:29411059-29411294(+)$1	235	130	151	12.8864
GGCAGAAAUCCCCUUCAACUC	chr1:174215791-174216027(-)$1	236	206	227	13.5212
CCGUGCCUACACUGGCCGUGA	chr7:133592024-133592270(-)$1	246	69	90	11.7892
GAGACUGGACAGACAGUCUUG	chr5:29761756-29761991(+)$1	235	202	223	11.0414
ACUUCUGGAUGCCCACUUGUG	chr14:60898841-60899085(+)$1	244	123	144	8.5015
AAAUGGAAAAGUAUCCUUUGA	chr10:77670618-77670856(-)$1	238	210	231	12.6954
AGCUGCAGGAGGAUGCAGCUC	chr11:30014728-30014963(-)$1	235	50	71	11.0414
ACAGAGUCAGGUCAGUCUGUG	chr11:67067428-67067680(+)$1	252	190	211	9.5068
CCAAAGGAAAAGGCCUUGCUU	chr11:6523715-6523950(-)$1	235	63	84	11.0479
CAGUGCAUUGUGUUGCAGGAU	chr4:129522281-129522528(+)$1	247	127	148	10.2892

#DB
(((.(((......))).))))	chr2:76594261-76594496(-)$1	1	133	154	12.8864
((...(((....)))....))	chr7:74904121-74904374(-)$1	1	198	219	8.3709
(((.(((......)))))).)	chr2:76561979-76562240(-)$1	1	162	183	12.7330
....(((......))).....	chr4:43527519-43527758(-)$1	1	50	71	9.6542
((..(((.....)))...)).	chr17:25969080-25969315(-)$1	1	38	59	8.1595
(((((((......)))))))(	chr2:76565493-76565731(-)$1	1	1	22	10.4522
...((((......))))))))	chr10:19329021-19329256(+)$1	1	33	54	10.9279
(((..((......))...)))	chr4:129523617-129523873(+)$1	1	28	49	11.7956
(((((((......)).)))..	chr19:9078779-9079016(+)$1	1	146	167	11.4751
(((.(.(......).).))).	chr7:52399799-52400034(-)$1	1	170	191	12.2440
((.((((......)))).)))	chr9:72510245-72510480(+)$1	1	85	106	10.9627
....(((......))).....	chr2:76689541-76689776(-)$1	1	44	65	9.4877
(((.(((......))).))).	chr4:43535508-43535762(-)$1	1	110	131	12.3695
.....((......))..))))	chr2:67350602-67350837(+)$1	1	137	158	10.8340
((((.((......)).)))))	chr14:60248649-60248884(+)$1	1	10	31	10.1884
((..(((.(......).))))	chr2:76606134-76606371(-)$1	1	161	182	10.5521
(((.(((......))).))))	chr6:29411059-29411294(+)$1	1	130	151	12.8864
((..(((......)))....)	chr1:174215791-174216027(-)$1	1	206	227	13.5212
(((.(((......)))))...	chr7:133592024-133592270(-)$1	1	69	90	11.7892
(((((((......))))))).	chr5:29761756-29761991(+)$1	1	202	223	11.0414
((...(((....)))...)))	chr14:60898841-60899085(+)$1	1	123	144	8.5015
(((.(((......))))))).	chr10:77670618-77670856(-)$1	1	210	231	12.6954
(((((((......))))))).	chr11:30014728-30014963(-)$1	1	50	71	11.0414
(((((.(......).))))))	chr11:67067428-67067680(+)$1	1	190	211	9.5068
(..((((......))))))))	chr11:6523715-6523950(-)$1	1	63	84	11.0479
)))((((......))))((((	chr4:129522281-129522528(+)$1	1	127	148	10.2892

#PSSM
d : 0.30	c : 0.19	e : 0.15	g : 0.11	$ : 0.07	b : 0.03	" : 0.03	% : 0.03	f : 0.03	
d : 0.26	c : 0.19	g : 0.11	e : 0.11	$ : 0.07	b : 0.07	" : 0.03	% : 0.03	f : 0.03	! : 0.03	
d : 0.15	c : 0.15	! : 0.15	" : 0.11	g : 0.11	$ : 0.07	e : 0.07	[ : 0.03	% : 0.03	b : 0.03	f : 0.03	
[ : 0.26	! : 0.15	d : 0.15	g : 0.11	" : 0.07	$ : 0.07	c : 0.03	% : 0.03	e : 0.03	f : 0.03	
c : 0.46	d : 0.15	g : 0.11	" : 0.07	! : 0.03	a : 0.03	$ : 0.03	[ : 0.03	f : 0.03	
c : 0.49	d : 0.15	b : 0.15	g : 0.11	[ : 0.07	
c : 0.49	d : 0.15	b : 0.15	g : 0.11	a : 0.07	
o : 0.84	c : 0.07	n : 0.03	[ : 0.03	
o : 0.84	m : 0.07	n : 0.03	a : 0.03	
o : 0.88	m : 0.07	n : 0.03	
o : 0.88	m : 0.07	n : 0.03	
o : 0.88	m : 0.07	n : 0.03	
o : 0.88	c : 0.11	
c : 0.46	d : 0.15	b : 0.15	g : 0.11	a : 0.07	o : 0.03	
c : 0.46	d : 0.15	b : 0.15	g : 0.11	] : 0.07	o : 0.03	
c : 0.34	d : 0.15	3 : 0.11	g : 0.11	] : 0.07	a : 0.07	4 : 0.03	2 : 0.03	f : 0.03	
] : 0.19	d : 0.19	3 : 0.11	g : 0.11	4 : 0.07	c : 0.07	5 : 0.03	6 : 0.03	2 : 0.03	e : 0.03	b : 0.03	f : 0.03	
d : 0.23	c : 0.19	3 : 0.11	g : 0.11	4 : 0.07	e : 0.07	5 : 0.03	] : 0.03	6 : 0.03	b : 0.03	f : 0.03	
c : 0.26	d : 0.23	g : 0.11	e : 0.11	4 : 0.07	5 : 0.03	b : 0.03	6 : 0.03	3 : 0.03	f : 0.03	
d : 0.26	c : 0.19	g : 0.11	e : 0.11	4 : 0.07	] : 0.03	5 : 0.03	b : 0.03	6 : 0.03	3 : 0.03	f : 0.03	
d : 0.26	] : 0.15	e : 0.15	c : 0.11	3 : 0.07	5 : 0.03	F : 0.03	4 : 0.03	6 : 0.03	: : 0.03	f : 0.03	

#score	285.41477014039987
#seq	26
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_transcript_m3_run1.txt

#BEAR
========!!cccmmmmccc=========	chr4:126707188-126707402(+)$1	214	114	143	13.2857
c[eeeee"""cccnnnnnccc333eeeee	chr9:108700299-108700520(+)$1	221	50	79	12.0415
gggg[eeeeecccmmmmccc]eeeee22g	chr19:56007445-56007664(+)$1	219	175	204	10.5116
c[ggggggg[cccmmmmcccgggggggcc	chrX:98407382-98407601(-)$1	219	37	66	11.7847
a####dddd[cccmmmmccc22dddd444	chr3:83964924-83965127(-)$1	203	119	148	12.1807
Ebb[dddd!!cccmmmmccc22dddd]bb	chr9:75485109-75485312(+)$1	203	135	164	10.3353
ggggg$$$$$bboooooobb333gggggg	chr11:105790194-105790405(-)$1	211	47	76	12.4933
gg!!ccc!!cccooooooccc4444ccc3	chr3:115813401-115813617(-)$1	216	175	204	13.9425
ggggg[ccc!!ccclllccc22cccgggg	chr5:112902391-112902600(-)$1	209	31	60	11.3760
::bbccc"""bboooooobb333ccc]bb	chr14:65431505-65431715(-)$1	210	172	201	10.8998
fff$$$$$cccooooooccc4444fffff	chr5:125497922-125498128(-)$1	206	119	148	10.7391
:a!!dddd[cccooooooccc]dddd22a	chr15:5168034-5168239(+)$1	205	80	109	11.1556
####ccc"""cccmmmmccc333ccc444	chr6:143011352-143011569(-)$1	217	101	130	15.2136
$$$$eeeee[cccmmmmccc333eeeee6	chr16:17841953-17842156(-)$1	203	148	177	11.9255
ggggggg"""bboooooobb333gggggg	chr2:25915283-25915483(+)$1	200	7	36	13.6642
hhhhh$$$$$cccmmmmccc4444hhhhh	chr4:109125114-109125320(-)$1	206	48	77	10.4693
ddeeeee"""bboooooobb22eeeee33	chr2:158209429-158209635(+)$1	206	59	88	11.9562
iiiiiiii!!cccmmmmccc]iiiiiiii	chr10:7435732-7435940(+)$1	208	43	72	12.8734
cc[dddd[a[bbaooooooa]bb]a]ddd	chr17:25053679-25053898(-)$1	219	103	132	9.8942
iiiiiiii!!cccnnnnnccciiiiiiii	chr2:91005298-91005500(-)$1	202	132	161	11.3187
ccccc[bb!!cccmmmmccc22bb]ccc]	chr15:79947115-79947316(+)$1	201	128	157	11.5555
c"""eeeee!!bbmmmmbb]eeeee333c	chr16:8704883-8705088(-)$1	205	85	114	10.0045
::ggggggg[cccmmmmccc22ggggggg	chr2:163843018-163843221(+)$1	203	145	174	10.7142
$$$$ccc"""ddddmmmmdddd]ccc333	chr3:95749332-95749534(+)$1	202	25	54	10.2432
$$$eeeee!!cccnnnnnccc]eeeee22	chr16:17574289-17574498(-)$1	209	135	164	10.3208
ff!!ccc"""aooooooa333ccc22fff	chr16:26715485-26715706(+)$1	221	151	180	12.0861
e$$$$$gggggggmmmmggggggg333ee	chr8:129688971-129689205(+)$1	234	147	176	9.4368
Dffffff"""cccmmmmccc333ffffff	chr11:115292440-115292646(-)$1	206	3	32	11.7758
d####ccc!!cccmmmmccc22ccc22dd	chr12:74007029-74007255(-)$1	226	174	203	13.1164
###ccc$$$$$bbmmmmbb4444cccggg	chr12:106006436-106006636(-)$1	200	81	110	11.3457
eee!!ccc!!bboooooobb333ccc22e	chr18:46946326-46946526(+)$1	200	109	138	12.8822
hhhhhha[a[cccmmmmccc]a]a]hhhh	chr18:35023824-35024028(+)$1	204	15	44	10.2771
d!!eeeee!!cccmmmmccceeeee22dd	chr2:120335228-120335446(-)$1	218	150	179	11.1812
[a!!ccc"""cccooooooccc666666c	chr2:121131484-121131684(+)$1	200	155	184	10.7894
ddddddd!!ddddmmmmdddd333dddd8	chr9:27858132-27858334(+)$1	202	55	84	9.1923
##ggggggg[cccmmmmcccggggggg]c	chr16:64858258-64858466(+)$1	208	60	89	11.9523
ggggg####ddddmmmmdddd4444gggg	chr5:138594067-138594291(-)$1	224	73	102	10.7023
ggggggg"""cccooooooccc4444ggg	chr18:83166391-83166626(+)$1	235	63	92	12.9933
b!!bb[ccc[bboooooobb]ccc]bb22	chr2:164823976-164824177(+)$1	201	85	114	10.2804
$$$==========nnnnn==========h	chr11:68904207-68904408(+)$1	201	89	118	10.0568
f[dddd[ccccccmmmmccc]cccdddd]	chr2:17641147-17641369(-)$1	222	168	197	10.5134
bb[dddd!!cccooooooccc22dddd]b	chr8:34512532-34512749(+)$1	217	132	161	11.7753
c"""cccddddoooooodddd]ccc333c	chrX:153882680-153882885(-)$1	205	168	197	10.7943
c!!dddd!!cccooooooccc22dddd22	chr1:62845042-62845257(+)$1	215	117	146	12.6334
c[dddd####bboooooobb4444dddd]	chr15:100046405-100046622(+)$1	217	112	141	12.1237
dd!!ccc"""aooooooa22ccc22dddd	chr13:89461147-89461348(+)$1	201	89	118	10.5875
eeccc[ddddcccmmmmccc22dddd]cc	chr2:52256008-52256208(-)$1	200	86	115	10.4836
b[eeeee!!cccnnnnnccc22eeeeebb	chr8:107741713-107741922(-)$1	209	170	199	10.1622
""eeeee"""ddddllldddd333eeeee	chr11:51082964-51083169(+)$1	205	6	35	10.4136
:ggggggg[cccooooooccc]ggggggg	chr11:69638636-69638840(-)$1	204	145	174	11.5500
eee[iiiiiiiiimmmmiiiiiiiii]ee	chr11:101054057-101054262(-)$1	205	23	52	10.0117
dd!!ccc!!cccooooooccc22ccc333	chr12:107075231-107075450(+)$1	219	158	187	13.9115
="""eeeee!!bbnnnnnbb333eeeee=	chr3:83964381-83964596(-)$1	215	9	38	10.6174
:ffffff!!cccnnnnnccc4444fffff	chr18:51477229-51477458(+)$1	229	133	162	9.6066
"ffffff[a[bboooooobb]a]ffffff	chr11:65501888-65502095(-)$1	207	46	75	10.3472
[a$$$$$ccccccmmmmccc]ccc4444a	chr3:138588882-138589089(-)$1	207	147	176	11.1608
ddd"""gggggggmmmmggggggg333dd	chrX:102993234-102993438(+)$1	204	118	147	9.3846
======="""cccmmmmccc=========	chr17:25101205-25101420(-)$1	215	86	115	13.6825
e####ccccccooooooccc]ccceeeee	chr2:58437882-58438087(+)$1	205	14	43	11.6354
ff"""bb[cccooooooccc]bbffffff	chr5:136384373-136384574(-)$1	201	172	201	10.0178

#otherMatches

#Seq PSSM
GAUGUUAGCAGUUUAUUGACCUGAUAUUU	chr4:126707188-126707402(+)$1	214	114	143	13.2857
UGCUUUCCCUUGUUGAGUGCAUUAGAGAG	chr9:108700299-108700520(+)$1	221	50	79	12.0415
AUGUGUUUGGUAGCAGACUGUCCAGAAAG	chr19:56007445-56007664(+)$1	219	175	204	10.5116
CUAGCUGCUGAGCCCAUGCUGGUAGCUGA	chrX:98407382-98407601(-)$1	219	37	66	11.7847
CAAAAACACUUUCUAAUGAACUGUGUGGU	chr3:83964924-83965127(-)$1	203	119	148	12.1807
CGGCAUGAUAGCAAAACUGUAUUUAUUCU	chr9:75485109-75485312(+)$1	203	135	164	10.3353
GUUUGAUAUAUCAGGAUAGAGAACAAACA	chr11:105790194-105790405(-)$1	211	47	76	12.4933
CUGACUGUUGUAACUUAAUGCUUCUUAGA	chr3:115813401-115813617(-)$1	216	175	204	13.9425
CUCUGCGGUGUGAGCUUCUCCGACCCGGA	chr5:112902391-112902600(-)$1	209	31	60	11.3760
AAGCCUUGUUGCAUAUGAGCCAAAAGUGC	chr14:65431505-65431715(-)$1	210	172	201	10.8998
UCUCCAAAGGCCACCCAGCCCACAAGACU	chr5:125497922-125498128(-)$1	206	119	148	10.7391
UGUUGUGCUAAUGUUCUAAUUUGUGCUUC	chr15:5168034-5168239(+)$1	205	80	109	11.1556
UGAUCUGCCUUACAACUGUGCUUCAGCUG	chr6:143011352-143011569(-)$1	217	101	130	15.2136
UACCUCUGCAUGGCUCCCCAGGAGUAGAC	chr16:17841953-17842156(-)$1	203	148	177	11.9255
UAAAUGUUUACAGUAUAAUGAAUGCAUUU	chr2:25915283-25915483(+)$1	200	7	36	13.6642
CUUGGAAAUACUGAAAUUAGACUAUCAGG	chr4:109125114-109125320(-)$1	206	48	77	10.4693
guguggcaaauguuuguucaaagccauug	chr2:158209429-158209635(+)$1	206	59	88	11.9562
UCUGAUUUAAUAAUAUGUUAGAAAUUAGA	chr10:7435732-7435940(+)$1	208	43	72	12.8734
UCUUUUCUGUCGCUACUAUGUUGUCUGAA	chr17:25053679-25053898(-)$1	219	103	132	9.8942
GGUUGCAGAUAGAAACAAUCUUUGUAGCU	chr2:91005298-91005500(-)$1	202	132	161	11.3187
UACUCGUUACUCGAGUUUGAUGAAGGGGU	chr15:79947115-79947316(+)$1	201	128	157	11.5555
GUUUCAUUGCUGCUCUCGCUCAGUGUCUC	chr16:8704883-8705088(-)$1	205	85	114	10.0045
AUUAGCAGCGUGUGAAAACAGGGCUGUUA	chr2:163843018-163843221(+)$1	203	145	174	10.7142
UCUUAGAAAAGAAUUCUCAUUCAUCUUCC	chr3:95749332-95749534(+)$1	202	25	54	10.2432
GAAAUAUGACUCCUUUUCGGACCAUAUAC	chr16:17574289-17574498(-)$1	209	135	164	10.3208
UUCUGUGUCUGUUGAAUCUACCACCUAAG	chr16:26715485-26715706(+)$1	221	151	180	12.0861
gcauaauauuagcaacuguuaguaagcca	chr8:129688971-129689205(+)$1	234	147	176	9.4368
GGACGAUGAUGCUGAAGAGCUAGAUUGUC	chr11:115292440-115292646(-)$1	206	3	32	11.7758
CUAUUAAUUUUAUGAAAAUAUUAUUUUGA	chr12:74007029-74007255(-)$1	226	174	203	13.1164
CACCUCUGUCUGUAUCUGCUUCUGAGGGG	chr12:106006436-106006636(-)$1	200	81	110	11.3457
GCUUUGGAUUCAUAGAUUUGUUUUCCUUA	chr18:46946326-46946526(+)$1	200	109	138	12.8822
GUUUUCCUUGGGGUAUUCUUGAUGUGAAG	chr18:35023824-35024028(+)$1	204	15	44	10.2771
CGACGGGAAACACAGUAGUGUCCUGAAGU	chr2:120335228-120335446(-)$1	218	150	179	11.1812
CGCACCCUGUGGCUCUCUUGCCUUCUCUG	chr2:121131484-121131684(+)$1	200	155	184	10.7894
AGCUUCAAAGUAGAUGCCUAUAUAUGAAA	chr9:27858132-27858334(+)$1	202	55	84	9.1923
AUAUAGUGGUAGUUGAUGCUUUACUAUUG	chr16:64858258-64858466(+)$1	208	60	89	11.9523
UUUGAUCUCUUGCUUCUGCAGUCCUUCAA	chr5:138594067-138594291(-)$1	224	73	102	10.7023
UCCAGGAGAAUCAUUGGCUUGAGCAGUCU	chr18:83166391-83166626(+)$1	235	63	92	12.9933
GCGCUUCUCUGACCUUUUUCUGAGUAGAA	chr2:164823976-164824177(+)$1	201	85	114	10.2804
CCCUGUAAAUAGCCAGCUGuuauuuauac	chr11:68904207-68904408(+)$1	201	89	118	10.0568
UGUAUGUCUGAGUGUAUACUAUAGUAUGG	chr2:17641147-17641369(-)$1	222	168	197	10.5134
CCAUGGUUCAAGAAGUUCCUUUCACUAAG	chr8:34512532-34512749(+)$1	217	132	161	11.7753
auguagcccagucuaaccuggagcuuauu	chrX:153882680-153882885(-)$1	205	168	197	10.7943
CAUCUCUCAUAGCAUUAUCUAAAAGGGCA	chr1:62845042-62845257(+)$1	215	117	146	12.6334
UUGUUUGUAAAGCUUAUACUCCCAGAAUU	chr15:100046405-100046622(+)$1	217	112	141	12.1237
GGUACAUUUUCUGUCUUGCCAUGGUCCUU	chr13:89461147-89461348(+)$1	201	89	118	10.5875
UGAAUCAUCUGCAUAGUUGCUUGGAUCAU	chr2:52256008-52256208(-)$1	200	86	115	10.4836
UCAUUUUAAAUACAGAUUAUGAAAAAUAU	chr8:107741713-107741922(-)$1	209	170	199	10.1622
AUGCAUUUGAAGCCUCUGGCUGGCGGUGC	chr11:51082964-51083169(+)$1	205	6	35	10.4136
UUGGGAGGUCUGCCUCCCUAGCCCUCCCA	chr11:69638636-69638840(-)$1	204	145	174	11.5500
GUGCCAGUGCUGUGGUGGCAGCACUGUCA	chr11:101054057-101054262(-)$1	205	23	52	10.0117
CAUCCGGAUCGCGCCUCUGUGUGCUGCAU	chr12:107075231-107075450(+)$1	219	158	187	13.9115
UGAAUUGAAAUGCUGACUGCCUGUUUAAA	chr3:83964381-83964596(-)$1	215	9	38	10.6174
UCCAUCUAAAUCUCUCUGGUAAUGAGAUG	chr18:51477229-51477458(+)$1	229	133	162	9.6066
GUGCAGGGAUAUUGCCUUAUUUGUCUGUA	chr11:65501888-65502095(-)$1	207	46	75	10.3472
UGGAUAAGUGGACUAAUGUUGCAUAAUAC	chr3:138588882-138589089(-)$1	207	147	176	11.1608
CAACAUUUUAAAUCGUCAUUUAAGCCAUU	chrX:102993234-102993438(+)$1	204	118	147	9.3846
GGGAGGCCAUAGCCACUGCUGCUUUCUUU	chr17:25101205-25101420(-)$1	215	86	115	13.6825
ccuuuaccuccaccuccggaugguggauc	chr2:58437882-58438087(+)$1	205	14	43	11.6354
GUUUCGCUAAGGAAUUAUUUCGCACACGG	chr5:136384373-136384574(-)$1	201	172	201	10.0178

#DB
((((((((..(((....))))))))))))	chr4:126707188-126707402(+)$1	1	114	143	13.2857
(.(((((...(((.....)))...)))))	chr9:108700299-108700520(+)$1	1	50	79	12.0415
((((.((((((((....))).)))))..)	chr19:56007445-56007664(+)$1	1	175	204	10.5116
(.(((((((.(((....))))))))))))	chrX:98407382-98407601(-)$1	1	37	66	11.7847
(....((((.(((....)))..))))...	chr3:83964924-83965127(-)$1	1	119	148	12.1807
(((.((((..(((....)))..)))).))	chr9:75485109-75485312(+)$1	1	135	164	10.3353
(((((.....((......))...))))))	chr11:105790194-105790405(-)$1	1	47	76	12.4933
((..(((..(((......)))....))).	chr3:115813401-115813617(-)$1	1	175	204	13.9425
(((((.(((..(((...)))..)))))))	chr5:112902391-112902600(-)$1	1	31	60	11.3760
..(((((...((......))...))).))	chr14:65431505-65431715(-)$1	1	172	201	10.8998
(((.....(((......)))....)))))	chr5:125497922-125498128(-)$1	1	119	148	10.7391
.(..((((.(((......))).))))..)	chr15:5168034-5168239(+)$1	1	80	109	11.1556
....(((...(((....)))...)))...	chr6:143011352-143011569(-)$1	1	101	130	15.2136
....(((((.(((....)))...))))).	chr16:17841953-17842156(-)$1	1	148	177	11.9255
(((((((...((......))...))))))	chr2:25915283-25915483(+)$1	1	7	36	13.6642
(((((.....(((....)))....)))))	chr4:109125114-109125320(-)$1	1	48	77	10.4693
(((((((...((......))..)))))..	chr2:158209429-158209635(+)$1	1	59	88	11.9562
((((((((..(((....))).))))))))	chr10:7435732-7435940(+)$1	1	43	72	12.8734
((.((((.(.(((......).)).).)))	chr17:25053679-25053898(-)$1	1	103	132	9.8942
((((((((..(((.....)))))))))))	chr2:91005298-91005500(-)$1	1	132	161	11.3187
(((((.((..(((....)))..)).))).	chr15:79947115-79947316(+)$1	1	128	157	11.5555
(...(((((..((....)).)))))...)	chr16:8704883-8705088(-)$1	1	85	114	10.0045
..(((((((.(((....)))..)))))))	chr2:163843018-163843221(+)$1	1	145	174	10.7142
....(((...((((....)))).)))...	chr3:95749332-95749534(+)$1	1	25	54	10.2432
...(((((..(((.....))).)))))..	chr16:17574289-17574498(-)$1	1	135	164	10.3208
((..(((...(......)...)))..)))	chr16:26715485-26715706(+)$1	1	151	180	12.0861
(.....(((((((....)))))))...))	chr8:129688971-129689205(+)$1	1	147	176	9.4368
(((((((...(((....)))...))))))	chr11:115292440-115292646(-)$1	1	3	32	11.7758
(....(((..(((....)))..)))..))	chr12:74007029-74007255(-)$1	1	174	203	13.1164
...(((.....((....))....))))))	chr12:106006436-106006636(-)$1	1	81	110	11.3457
(((..(((..((......))...)))..)	chr18:46946326-46946526(+)$1	1	109	138	12.8822
(((((((.(.(((....))).).).))))	chr18:35023824-35024028(+)$1	1	15	44	10.2771
(..(((((..(((....))))))))..))	chr2:120335228-120335446(-)$1	1	150	179	11.1812
.(..(((...(((......)))......)	chr2:121131484-121131684(+)$1	1	155	184	10.7894
(((((((..((((....))))...)))).	chr9:27858132-27858334(+)$1	1	55	84	9.1923
..(((((((.(((....)))))))))).)	chr16:64858258-64858466(+)$1	1	60	89	11.9523
(((((....((((....))))....))))	chr5:138594067-138594291(-)$1	1	73	102	10.7023
(((((((...(((......)))....)))	chr18:83166391-83166626(+)$1	1	63	92	12.9933
(..((.(((.((......)).))).))..	chr2:164823976-164824177(+)$1	1	85	114	10.2804
...((((((((((.....)))))))))))	chr11:68904207-68904408(+)$1	1	89	118	10.0568
(.((((.((((((....))).))))))).	chr2:17641147-17641369(-)$1	1	168	197	10.5134
((.((((..(((......)))..)))).)	chr8:34512532-34512749(+)$1	1	132	161	11.7753
(...(((((((......)))).)))...)	chrX:153882680-153882885(-)$1	1	168	197	10.7943
(..((((..(((......)))..))))..	chr1:62845042-62845257(+)$1	1	117	146	12.6334
(.((((....((......))....)))).	chr15:100046405-100046622(+)$1	1	112	141	12.1237
((..(((...(......)..)))..))))	chr13:89461147-89461348(+)$1	1	89	118	10.5875
))(((.(((((((....)))..)))).))	chr2:52256008-52256208(-)$1	1	86	115	10.4836
(.(((((..(((.....)))..)))))))	chr8:107741713-107741922(-)$1	1	170	199	10.1622
..(((((...((((...))))...)))))	chr11:51082964-51083169(+)$1	1	6	35	10.4136
.(((((((.(((......))).)))))))	chr11:69638636-69638840(-)$1	1	145	174	11.5500
(((.(((((((((....))))))))).))	chr11:101054057-101054262(-)$1	1	23	52	10.0117
((..(((..(((......)))..)))...	chr12:107075231-107075450(+)$1	1	158	187	13.9115
(...(((((..((.....))...))))))	chr3:83964381-83964596(-)$1	1	9	38	10.6174
.((((((..(((.....)))....)))))	chr18:51477229-51477458(+)$1	1	133	162	9.6066
.((((((.(.((......)).).))))))	chr11:65501888-65502095(-)$1	1	46	75	10.3472
.(.....((((((....))).)))....)	chr3:138588882-138589089(-)$1	1	147	176	11.1608
(((...(((((((....)))))))...))	chrX:102993234-102993438(+)$1	1	118	147	9.3846
(((((((...(((....))))))))))))	chr17:25101205-25101420(-)$1	1	86	115	13.6825
(....((((((......))).))))))))	chr2:58437882-58438087(+)$1	1	14	43	11.6354
((...((.(((......))).))))))))	chr5:136384373-136384574(-)$1	1	172	201	10.0178

#PSSM
c : 0.13	g : 0.11	d : 0.11	: : 0.08	e : 0.08	f : 0.06	$ : 0.06	= : 0.05	# : 0.05	b : 0.05	h : 0.03	i : 0.03	[ : 0.03	" : 0.03	a : 0.01	E : 0.01	D : 0.01	
g : 0.13	# : 0.09	f : 0.09	[ : 0.08	$ : 0.08	d : 0.08	" : 0.06	a : 0.05	e : 0.05	! : 0.05	= : 0.03	b : 0.03	: : 0.03	h : 0.03	i : 0.03	c : 0.03	
g : 0.16	! : 0.15	e : 0.09	$ : 0.09	# : 0.08	f : 0.06	" : 0.06	d : 0.06	= : 0.03	b : 0.03	h : 0.03	i : 0.03	[ : 0.03	c : 0.03	
g : 0.16	! : 0.11	e : 0.09	d : 0.09	$ : 0.08	" : 0.08	# : 0.06	= : 0.05	c : 0.05	f : 0.05	[ : 0.03	b : 0.03	h : 0.03	i : 0.03	
c : 0.19	e : 0.15	g : 0.15	d : 0.13	= : 0.05	# : 0.05	$ : 0.05	i : 0.05	f : 0.05	h : 0.03	" : 0.03	[ : 0.01	! : 0.01	b : 0.01	
c : 0.21	e : 0.16	d : 0.15	g : 0.09	$ : 0.08	[ : 0.06	= : 0.05	i : 0.05	f : 0.05	h : 0.01	# : 0.01	" : 0.01	b : 0.01	
c : 0.23	e : 0.16	g : 0.13	d : 0.13	$ : 0.08	= : 0.05	i : 0.05	f : 0.05	b : 0.03	# : 0.03	a : 0.01	[ : 0.01	
" : 0.21	! : 0.11	c : 0.11	e : 0.09	g : 0.09	d : 0.08	$ : 0.06	[ : 0.06	i : 0.05	= : 0.03	# : 0.03	b : 0.01	
! : 0.26	" : 0.21	c : 0.11	g : 0.08	e : 0.06	d : 0.05	$ : 0.05	a : 0.05	[ : 0.03	# : 0.03	= : 0.01	i : 0.01	
" : 0.21	c : 0.21	! : 0.19	[ : 0.15	d : 0.06	$ : 0.05	g : 0.03	e : 0.01	= : 0.01	# : 0.01	i : 0.01	
c : 0.60	b : 0.15	d : 0.08	! : 0.05	a : 0.03	g : 0.03	$ : 0.01	= : 0.01	i : 0.01	
c : 0.56	b : 0.19	o : 0.09	d : 0.06	g : 0.03	= : 0.01	i : 0.01	
c : 0.43	o : 0.33	d : 0.06	b : 0.05	g : 0.03	n : 0.03	a : 0.01	= : 0.01	i : 0.01	
m : 0.44	o : 0.38	n : 0.11	d : 0.03	c : 0.01	
m : 0.46	o : 0.38	n : 0.11	l : 0.03	
m : 0.46	o : 0.38	n : 0.11	l : 0.03	
m : 0.46	o : 0.38	n : 0.11	l : 0.03	
c : 0.43	o : 0.28	n : 0.08	d : 0.06	b : 0.03	a : 0.03	g : 0.03	m : 0.01	i : 0.01	
c : 0.58	b : 0.18	d : 0.08	o : 0.05	g : 0.03	3 : 0.01	= : 0.01	2 : 0.01	i : 0.01	
c : 0.61	b : 0.15	d : 0.08	g : 0.03	a : 0.01	] : 0.01	3 : 0.01	4 : 0.01	= : 0.01	2 : 0.01	i : 0.01	
c : 0.19	] : 0.16	2 : 0.15	3 : 0.15	4 : 0.08	d : 0.08	g : 0.06	= : 0.05	e : 0.03	i : 0.01	
2 : 0.19	3 : 0.18	c : 0.13	4 : 0.11	g : 0.06	] : 0.06	= : 0.05	e : 0.05	i : 0.05	b : 0.03	a : 0.03	d : 0.01	
3 : 0.18	c : 0.15	4 : 0.13	e : 0.09	g : 0.09	d : 0.06	= : 0.05	i : 0.05	b : 0.05	] : 0.05	2 : 0.05	6 : 0.01	
c : 0.23	e : 0.13	g : 0.13	4 : 0.11	d : 0.09	= : 0.05	3 : 0.05	i : 0.05	f : 0.05	] : 0.01	b : 0.01	a : 0.01	6 : 0.01	2 : 0.01	
e : 0.18	d : 0.15	c : 0.15	g : 0.09	f : 0.08	4 : 0.06	= : 0.05	i : 0.05	] : 0.05	2 : 0.03	3 : 0.03	h : 0.01	a : 0.01	6 : 0.01	
d : 0.16	e : 0.15	g : 0.13	c : 0.13	f : 0.08	3 : 0.06	= : 0.05	i : 0.05	2 : 0.05	h : 0.03	4 : 0.03	] : 0.01	6 : 0.01	b : 0.01	
g : 0.16	e : 0.13	d : 0.11	f : 0.09	3 : 0.09	2 : 0.08	] : 0.06	= : 0.05	4 : 0.05	c : 0.03	h : 0.03	i : 0.03	6 : 0.01	b : 0.01	
g : 0.13	d : 0.13	e : 0.11	2 : 0.09	f : 0.09	3 : 0.08	c : 0.06	= : 0.05	4 : 0.05	b : 0.05	h : 0.03	i : 0.03	] : 0.03	6 : 0.01	
g : 0.15	e : 0.09	c : 0.09	f : 0.09	d : 0.08	b : 0.06	3 : 0.06	= : 0.05	h : 0.05	] : 0.05	2 : 0.05	4 : 0.03	a : 0.03	i : 0.03	6 : 0.01	8 : 0.01	

#score	680.3824625379837
#seq	60
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_UTR_m2_run1.txt

#BEAR
fffffvvvvvvvvvvvvvffffff33	chr10:6080049-6080270(-)$1	221	45	71	23.1265
[cccvvvvvvvvvvvvvccc]agggg	chr9:63987687-63987897(-)$1	210	49	75	23.6242
cc[bbvvvvvvvvvvvvvbb]ccc]d	chr4:91042928-91043144(-)$1	216	138	164	23.2487
fffffuuuuuuuuuuuuffffff22b	chr17:26389831-26390039(+)$1	208	147	173	22.3377
gg[bbtttttttttttbb]ggggggg	chr17:29176690-29176925(+)$1	235	191	217	21.9382
eeeeeuuuuuuuuuuuueeeee]bb2	chr15:77592131-77592338(-)$1	207	172	198	23.6978
ggyyyyyyyyyyyyyyyyggggggg]	chr19:60890578-60890798(+)$1	220	36	62	20.6620
""cccuuuuuuuuuuuuccc4444dd	chr2:74522397-74522614(+)$1	217	165	191	23.2141
eeeeeuuuuuuuuuuuueeeee::::	chr16:91677579-91677807(+)$1	228	25	51	20.8745
ffffvvvvvvvvvvvvvffffffbb[	chr19:46718784-46719007(+)$1	223	156	182	22.3712
hhhbbwwwwwwwwwwwwwwbb]hhhh	chr10:79221389-79221596(-)$1	207	161	187	20.3809
b[bbwwwwwwwwwwwwwwbbbb]ccc	chr6:116212474-116212682(+)$1	208	126	152	21.3012
ggggggtttttttttttggggggg55	chr12:66163920-66164138(+)$1	218	150	176	20.8938
:dddduuuuuuuuuuuudddd:::hh	chr16:17111206-17111413(-)$1	207	15	41	19.1299
hhhbbuuuuuuuuuuuubb]hhhhhh	chr5:13399331-13399559(+)$1	228	70	96	21.7220
cc[bbuuuuuuuuuuuubb22ccc33	chr9:123429403-123429617(+)$1	214	55	81	22.8388
eeeevvvvvvvvvvvvveeeee22dd	chr16:91793769-91793996(+)$1	227	114	140	23.4532
ddd[bbtttttttttttbb]dddd::	chr8:109894234-109894452(+)$1	218	71	97	20.4316
eeeeeuuuuuuuuuuuueeeee333e	chr14:46276808-46277014(-)$1	206	20	46	24.1297
ggggggtttttttttttggggggg]f	chr3:89197323-89197547(-)$1	224	169	195	22.1993
eeeeeuuuuuuuuuuuueeeee::::	chrX:148461176-148461402(+)$1	226	11	37	20.8745
ee[ccctttttttttttccc]eeeee	chr1:87593467-87593696(+)$1	229	79	105	22.4045
ddddwwwwwwwwwwwwwwdddd]===	chr9:80117842-80118065(+)$1	223	177	203	22.8498
e[cccvvvvvvvvvvvvvccc]eeee	chr14:32000153-32000388(-)$1	235	113	139	23.7589
bddddvvvvvvvvvvvvvdddd]bbc	chr12:85462152-85462378(+)$1	226	15	41	23.3993
iiiiivvvvvvvvvvvvviiiiiiii	chr2:121332249-121332470(-)$1	221	48	74	24.1522
eeeewwwwwwwwwwwwwweeeee::g	chr6:38078173-38078392(-)$1	219	49	75	21.4813
ffddddtttttttttttdddd]ffff	chr11:100338006-100338213(-)$1	207	53	79	21.4091
eeewwwwwwwwwwwwwweeeee]ddd	chr5:124765565-124765787(-)$1	222	10	36	22.1773
cccbbtttttttttttbb]ccc333f	chr2:29589033-29589245(+)$1	212	29	55	21.8818
[eeeeettttttttttteeeee]bb:	chr15:78760469-78760694(+)$1	225	199	225	21.8739
=====uuuuuuuuuuuu=========	chr4:123060473-123060679(-)$1	206	14	40	24.2369
ffffwwwwwwwwwwwwwwffffff::	chr2:174170884-174171112(+)$1	228	29	55	20.5790
=====uuuuuuuuuuuu=========	chr17:14041401-14041614(+)$1	213	183	209	24.2369
ggggguuuuuuuuuuuuggggggg::	chr1:58960041-58960258(-)$1	217	190	216	22.3671
eeeeeuuuuuuuuuuuueeeee]ccc	chr10:107599161-107599403(+)$1	242	117	143	24.1165
eeeeevvvvvvvvvvvvveeeeeFFF	chr1:34254000-34254209(+)$1	209	179	205	22.8418
eeeeeuuuuuuuuuuuueeeee:ddd	chr15:79316109-79316326(-)$1	217	56	82	22.6979
[dddduuuuuuuuuuuudddd]ccc:	chr5:31215834-31216044(+)$1	210	149	175	22.7729
ffffftttttttttttffffff22aD	chr9:107642921-107643130(-)$1	209	138	164	20.3875
b!!bbvvvvvvvvvvvvvbb22bb22	chr13:120239445-120239668(+)$1	223	117	143	21.9824
ddddavvvvvvvvvvvvva]dddd::	chr8:82208559-82208775(-)$1	216	13	39	22.2822
ddddwwwwwwwwwwwwwwdddd]ccc	chr7:74413105-74413323(-)$1	218	14	40	22.8042
eeeeettttttttttteeeeecccnn	chr15:100445968-100446187(+)$1	219	85	111	20.9453
feeeeettttttttttteeeee]fff	chr9:45677207-45677430(-)$1	223	149	175	22.2453
=====uuuuuuuuuuuu=========	chr9:53341926-53342144(-)$1	218	175	201	24.2369
ddddyyyyyyyyyyyyyyyydddd:e	chr11:100831800-100832013(-)$1	213	57	83	19.2553
ffffftttttttttttffffff]bb2	chr10:36854649-36854865(-)$1	216	183	209	21.2216
hhh[bbtttttttttttbbhhhhhhh	chr2:181303851-181304071(-)$1	220	137	163	20.4346
[dddduuuuuuuuuuuudddd]eeee	chr1:173998276-173998488(-)$1	212	52	78	23.0691
eeeewwwwwwwwwwwwwweeeeeddd	chr16:10283178-10283404(-)$1	226	123	149	22.6139
iyyyyyyyyyyyyyyyyiiiiiiiii	chr15:77591181-77591390(-)$1	209	147	173	19.8933
ddddwwwwwwwwwwwwwwdddd:ddd	chr3:107471124-107471353(-)$1	229	54	80	21.3856
ggcccvvvvvvvvvvvvvccc]gggg	chr17:56553329-56553545(-)$1	216	115	141	24.1685
e[cccuuuuuuuuuuuuccc333eee	chr1:153738330-153738550(-)$1	220	59	85	23.7427
ccc[bbtttttttttttbb]ccc:GG	chr8:12842874-12843097(+)$1	223	178	204	20.3094
ddd[bbtttttttttttbb]dddd::	chr13:55315326-55315547(+)$1	221	18	44	20.4316
i[cccvvvvvvvvvvvvvccc22iii	chr17:33805837-33806063(-)$1	226	134	160	23.9628
!ddddvvvvvvvvvvvvvdddd22ee	chr7:105365195-105365405(-)$1	210	117	143	23.3609
=====vvvvvvvvvvvvv========	chr4:144780368-144780594(-)$1	226	18	44	24.4107
ddddwwwwwwwwwwwwwwdddd333c	chr11:80283225-80283452(+)$1	227	122	148	22.9057
d[cccvvvvvvvvvvvvvcccdddd]	chr14:32004515-32004743(-)$1	228	108	134	23.5999

#otherMatches

#Seq PSSM
UUUUUUUUUUUUUCUUUUAAGGAGUU	chr10:6080049-6080270(-)$1	221	45	71	23.1265
UGGCUCGUUGUCUUUCUGCUUGCAGA	chr9:63987687-63987897(-)$1	210	49	75	23.6242
GUAGCGACCUACUAAAAAGCAACACG	chr4:91042928-91043144(-)$1	216	138	164	23.2487
UCCGCCCAGGCGCAGAUGCGGGCCCU	chr17:26389831-26390039(+)$1	208	147	173	22.3377
CUGCUGGUUAAAAAUAAGGAGUAAGC	chr17:29176690-29176925(+)$1	235	191	217	21.9382
CUUUGAGAAUCUGAUACCAAAGAGUC	chr15:77592131-77592338(-)$1	207	172	198	23.6978
AAACAAACUUCUCCACCCUUUCGUCU	chr19:60890578-60890798(+)$1	220	36	62	20.6620
CUUUCUUUCCCUUCAGUGAACACAGA	chr2:74522397-74522614(+)$1	217	165	191	23.2141
AGGUAUAAUAGUAAAUUUGCCUUUUU	chr16:91677579-91677807(+)$1	228	25	51	20.8745
CUGGUGUAAGUCCUUGUCCAGGGGGU	chr19:46718784-46719007(+)$1	223	156	182	22.3712
CGGGCCCAGCACCCAACCAGCGCCGG	chr10:79221389-79221596(-)$1	207	161	187	20.3809
UCACUUCCUUUACCCAAUGUAGCUGA	chr6:116212474-116212682(+)$1	208	126	152	21.3012
cggaccugaggacagcuggucugcaC	chr12:66163920-66164138(+)$1	218	150	176	20.8938
CCUGGAAACCACAAUUCCCAGAAUGC	chr16:17111206-17111413(-)$1	207	15	41	19.1299
UGUCAUCUCUCCCUGCUUGUGCACAG	chr5:13399331-13399559(+)$1	228	70	96	21.7220
AUAGUUUUCACCAAAUCACAGAUCAA	chr9:123429403-123429617(+)$1	214	55	81	22.8388
UGGAUCAAGUGGAAUUUUCCAUAGCC	chr16:91793769-91793996(+)$1	227	114	140	23.4532
CUGUCUUUUCAGAUUGUAGUCAGCUU	chr8:109894234-109894452(+)$1	218	71	97	20.4316
GAUGGAGGAGCUGGUGACCAUCGAGC	chr14:46276808-46277014(-)$1	206	20	46	24.1297
UGGGCGGAGGGAGGGGGUGCCUGGGG	chr3:89197323-89197547(-)$1	224	169	195	22.1993
CUCgaagaacaaggaaauugagaagg	chrX:148461176-148461402(+)$1	226	11	37	20.8745
CGGUUCUAGAAUAAAGUGAAAUGUGU	chr1:87593467-87593696(+)$1	229	79	105	22.4045
UCUUUUUUGCCUGUAUUUAAGAUAAA	chr9:80117842-80118065(+)$1	223	177	203	22.8498
UGUGGACCUACGAGACAACCGGAUUG	chr14:32000153-32000388(-)$1	235	113	139	23.7589
GGCUGAAUCAACAAAUCCCAGCACUG	chr12:85462152-85462378(+)$1	226	15	41	23.3993
CUGGUUCCUCUACCCCCUACCGGAAG	chr2:121332249-121332470(-)$1	221	48	74	24.1522
CAGUACAGAACUUCCACAGCUGAUCA	chr6:38078173-38078392(-)$1	219	49	75	21.4813
UAAGAUUUUAAGAUACUAUCUGUAGG	chr11:100338006-100338213(-)$1	207	53	79	21.4091
CAGUGAGAGAAAUGAGUCUGUUGUCA	chr5:124765565-124765787(-)$1	222	10	36	22.1773
GGCCUGCCUUUUACCAAGUGCCCUUG	chr2:29589033-29589245(+)$1	212	29	55	21.8818
GGGGCCCCGCCCAACCUGGUCCAUCU	chr15:78760469-78760694(+)$1	225	199	225	21.8739
CUAUUAAGGAGGAGACAGAUGGUCUG	chr4:123060473-123060679(-)$1	206	14	40	24.2369
GCGCCGCAAGUGGAUCCAGUGCUUCA	chr2:174170884-174171112(+)$1	228	29	55	20.5790
UGAAUAUCUAAUUAAUAAUUCAAUUU	chr17:14041401-14041614(+)$1	213	183	209	24.2369
UAGAAAACUAAACCAAAUUCUAUUGA	chr1:58960041-58960258(-)$1	217	190	216	22.3671
CGAGCGUCUCCUCCCCGGCUCGCGGC	chr10:107599161-107599403(+)$1	242	117	143	24.1165
GUACCAGUCCAAGCAAGAGGUACACC	chr1:34254000-34254209(+)$1	209	179	205	22.8418
CCUGUCCCUUGUCCCCCACAGGCCCU	chr15:79316109-79316326(-)$1	217	56	82	22.6979
CCCUCAGAAGUACAGAAGAGGAGAGC	chr5:31215834-31216044(+)$1	210	149	175	22.7729
UGGUUGUCAACACCAAAGCCACCACU	chr9:107642921-107643130(-)$1	209	138	164	20.3875
CCAUGCAACUUCAACAUACAGAGAAG	chr13:120239445-120239668(+)$1	223	117	143	21.9824
ACUGCCCCCUUCUAAAAAGCCAGUCA	chr8:82208559-82208775(-)$1	216	13	39	22.2822
UGAAUUUUCCAAUUGUAUUUCAGACG	chr7:74413105-74413323(-)$1	218	14	40	22.8042
GUCACGUGACACGGAAGUGACUCCGA	chr15:100445968-100446187(+)$1	219	85	111	20.9453
UGCCUCCACCACCCUCAGAGGUAAGA	chr9:45677207-45677430(-)$1	223	149	175	22.2453
GUAAUAUAGUAUUUGAAGUUGUUUUU	chr9:53341926-53342144(-)$1	218	175	201	24.2369
GGGCAACUCGCAGAUUCCCCGCCCCA	chr11:100831800-100832013(-)$1	213	57	83	19.2553
UGUUCUAAUUUUCUGUGAGCACACUA	chr10:36854649-36854865(-)$1	216	183	209	21.2216
UUGAGUUUAAAAAUGUUACCGAAAUA	chr2:181303851-181304071(-)$1	220	137	163	20.4346
AGCAUUUUCUUUUUUCUAUGUCCCGA	chr1:173998276-173998488(-)$1	212	52	78	23.0691
ggauacucuuucaaaacaaucccuca	chr16:10283178-10283404(-)$1	226	123	149	22.6139
uucuuuuuuuuuuuuuuAAAGGAAAA	chr15:77591181-77591390(-)$1	209	147	173	19.8933
AGUGUCUCUUUCUCCAACCACUCUCC	chr3:107471124-107471353(-)$1	229	54	80	21.3856
AGUGCAUAAGACCAAGGAGCAGUUUG	chr17:56553329-56553545(-)$1	216	115	141	24.1685
CUGCUAAACCCCACCUCAGCCCUGUU	chr1:153738330-153738550(-)$1	220	59	85	23.7427
GGGUCAGAUAGCACAUAUGUCCCGUG	chr8:12842874-12843097(+)$1	223	178	204	20.3094
UCCCAGCCCCCACCUCACUAGGAGAC	chr13:55315326-55315547(+)$1	221	18	44	20.4316
GUGAGCUCUUUUUUUUCCUUCuuuuu	chr17:33805837-33806063(-)$1	226	134	160	23.9628
UCAAGAACCCCCCAAAGACUUGUACA	chr7:105365195-105365405(-)$1	210	117	143	23.3609
UUUAUAGAUUCAGAGACCAUGAGAGA	chr4:144780368-144780594(-)$1	226	18	44	24.4107
CAGCACACAUUUGGCCAAGCUGUACG	chr11:80283225-80283452(+)$1	227	122	148	22.9057
GUGGUGAUGCCAAGACUGACCUUGGA	chr14:32004515-32004743(-)$1	228	108	134	23.5999

#DB
(((((.............))))))..	chr10:6080049-6080270(-)$1	1	45	71	23.1265
.(((.............))).)))))	chr9:63987687-63987897(-)$1	1	49	75	23.6242
((.((.............)).))).)	chr4:91042928-91043144(-)$1	1	138	164	23.2487
(((((............))))))..)	chr17:26389831-26390039(+)$1	1	147	173	22.3377
((.((...........)).)))))))	chr17:29176690-29176925(+)$1	1	191	217	21.9382
(((((............))))).)).	chr15:77592131-77592338(-)$1	1	172	198	23.6978
((................))))))).	chr19:60890578-60890798(+)$1	1	36	62	20.6620
..(((............)))....))	chr2:74522397-74522614(+)$1	1	165	191	23.2141
(((((............)))))....	chr16:91677579-91677807(+)$1	1	25	51	20.8745
((((.............))))))((.	chr19:46718784-46719007(+)$1	1	156	182	22.3712
(((((..............)).))))	chr10:79221389-79221596(-)$1	1	161	187	20.3809
(.((..............)))).)))	chr6:116212474-116212682(+)$1	1	126	152	21.3012
((((((...........)))))))..	chr12:66163920-66164138(+)$1	1	150	176	20.8938
.((((............))))...((	chr16:17111206-17111413(-)$1	1	15	41	19.1299
(((((............)).))))))	chr5:13399331-13399559(+)$1	1	70	96	21.7220
((.((............))..)))..	chr9:123429403-123429617(+)$1	1	55	81	22.8388
((((.............)))))..))	chr16:91793769-91793996(+)$1	1	114	140	23.4532
(((.((...........)).))))..	chr8:109894234-109894452(+)$1	1	71	97	20.4316
(((((............)))))...)	chr14:46276808-46277014(-)$1	1	20	46	24.1297
((((((...........))))))).)	chr3:89197323-89197547(-)$1	1	169	195	22.1993
(((((............)))))....	chrX:148461176-148461402(+)$1	1	11	37	20.8745
((.(((...........))).)))))	chr1:87593467-87593696(+)$1	1	79	105	22.4045
((((..............)))).)))	chr9:80117842-80118065(+)$1	1	177	203	22.8498
(.(((.............))).))))	chr14:32000153-32000388(-)$1	1	113	139	23.7589
(((((.............)))).))(	chr12:85462152-85462378(+)$1	1	15	41	23.3993
(((((.............))))))))	chr2:121332249-121332470(-)$1	1	48	74	24.1522
((((..............)))))..(	chr6:38078173-38078392(-)$1	1	49	75	21.4813
((((((...........)))).))))	chr11:100338006-100338213(-)$1	1	53	79	21.4091
(((..............))))).)))	chr5:124765565-124765787(-)$1	1	10	36	22.1773
(((((...........)).)))...)	chr2:29589033-29589245(+)$1	1	29	55	21.8818
.(((((...........))))).)).	chr15:78760469-78760694(+)$1	1	199	225	21.8739
(((((............)))))))))	chr4:123060473-123060679(-)$1	1	14	40	24.2369
((((..............))))))..	chr2:174170884-174171112(+)$1	1	29	55	20.5790
(((((............)))))))))	chr17:14041401-14041614(+)$1	1	183	209	24.2369
(((((............)))))))..	chr1:58960041-58960258(-)$1	1	190	216	22.3671
(((((............))))).)))	chr10:107599161-107599403(+)$1	1	117	143	24.1165
(((((.............))))))))	chr1:34254000-34254209(+)$1	1	179	205	22.8418
(((((............))))).(((	chr15:79316109-79316326(-)$1	1	56	82	22.6979
.((((............)))).))).	chr5:31215834-31216044(+)$1	1	149	175	22.7729
(((((...........))))))..))	chr9:107642921-107643130(-)$1	1	138	164	20.3875
(..((.............))..))..	chr13:120239445-120239668(+)$1	1	117	143	21.9824
(((((.............).))))..	chr8:82208559-82208775(-)$1	1	13	39	22.2822
((((..............)))).)))	chr7:74413105-74413323(-)$1	1	14	40	22.8042
(((((...........)))))(((..	chr15:100445968-100446187(+)$1	1	85	111	20.9453
((((((...........))))).)))	chr9:45677207-45677430(-)$1	1	149	175	22.2453
(((((............)))))))))	chr9:53341926-53342144(-)$1	1	175	201	24.2369
((((................)))).(	chr11:100831800-100832013(-)$1	1	57	83	19.2553
(((((...........)))))).)).	chr10:36854649-36854865(-)$1	1	183	209	21.2216
(((.((...........)))))))))	chr2:181303851-181304071(-)$1	1	137	163	20.4346
.((((............)))).))))	chr1:173998276-173998488(-)$1	1	52	78	23.0691
((((..............)))))(((	chr16:10283178-10283404(-)$1	1	123	149	22.6139
(................)))))))))	chr15:77591181-77591390(-)$1	1	147	173	19.8933
((((..............)))).(((	chr3:107471124-107471353(-)$1	1	54	80	21.3856
(((((.............))).))))	chr17:56553329-56553545(-)$1	1	115	141	24.1685
(.(((............)))...)))	chr1:153738330-153738550(-)$1	1	59	85	23.7427
(((.((...........)).))).))	chr8:12842874-12843097(+)$1	1	178	204	20.3094
(((.((...........)).))))..	chr13:55315326-55315547(+)$1	1	18	44	20.4316
(.(((.............)))..)))	chr17:33805837-33806063(-)$1	1	134	160	23.9628
.((((.............))))..))	chr7:105365195-105365405(-)$1	1	117	143	23.3609
(((((.............))))))))	chr4:144780368-144780594(-)$1	1	18	44	24.4107
((((..............))))...)	chr11:80283225-80283452(+)$1	1	122	148	22.9057
(.(((.............))))))).	chr14:32004515-32004743(-)$1	1	108	134	23.5999

#PSSM
e : 0.24	d : 0.14	f : 0.12	g : 0.09	[ : 0.06	c : 0.06	= : 0.06	h : 0.04	b : 0.04	i : 0.04	" : 0.01	: : 0.01	! : 0.01	
e : 0.24	d : 0.20	f : 0.11	g : 0.09	c : 0.08	[ : 0.08	= : 0.06	h : 0.04	" : 0.01	i : 0.01	! : 0.01	y : 0.01	
e : 0.22	d : 0.22	c : 0.14	f : 0.09	[ : 0.06	= : 0.06	h : 0.04	g : 0.04	y : 0.03	b : 0.01	i : 0.01	! : 0.01	
e : 0.20	d : 0.19	c : 0.12	b : 0.12	f : 0.09	[ : 0.06	= : 0.06	g : 0.04	y : 0.03	i : 0.01	w : 0.01	
b : 0.17	e : 0.16	w : 0.14	c : 0.11	d : 0.09	f : 0.06	= : 0.06	v : 0.04	y : 0.04	g : 0.04	i : 0.01	a : 0.01	
u : 0.29	v : 0.25	w : 0.16	t : 0.08	b : 0.06	y : 0.04	g : 0.03	e : 0.03	c : 0.01	d : 0.01	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	t : 0.24	w : 0.16	y : 0.04	
u : 0.29	v : 0.25	w : 0.16	t : 0.16	y : 0.04	b : 0.03	f : 0.03	e : 0.01	
v : 0.20	e : 0.17	w : 0.14	b : 0.12	c : 0.06	f : 0.06	d : 0.06	g : 0.04	= : 0.04	y : 0.03	i : 0.01	
e : 0.22	d : 0.16	b : 0.14	c : 0.12	f : 0.09	g : 0.06	= : 0.06	] : 0.03	i : 0.03	w : 0.01	a : 0.01	y : 0.01	
e : 0.22	d : 0.16	c : 0.14	f : 0.09	g : 0.08	] : 0.08	b : 0.06	= : 0.06	i : 0.03	2 : 0.01	y : 0.01	h : 0.01	
e : 0.22	d : 0.22	f : 0.09	c : 0.09	g : 0.08	= : 0.06	] : 0.04	b : 0.03	h : 0.03	2 : 0.03	i : 0.03	4 : 0.01	3 : 0.01	
e : 0.22	d : 0.17	f : 0.09	] : 0.09	c : 0.08	g : 0.08	= : 0.06	h : 0.03	i : 0.03	2 : 0.03	a : 0.01	4 : 0.01	b : 0.01	: : 0.01	3 : 0.01	
] : 0.16	g : 0.11	e : 0.09	f : 0.08	c : 0.08	: : 0.08	d : 0.08	2 : 0.06	3 : 0.06	= : 0.06	h : 0.04	i : 0.03	4 : 0.01	b : 0.01	
d : 0.14	g : 0.11	c : 0.11	b : 0.09	: : 0.08	= : 0.08	f : 0.06	2 : 0.06	e : 0.06	h : 0.04	3 : 0.04	i : 0.04	4 : 0.01	F : 0.01	
: : 0.14	d : 0.11	3 : 0.08	b : 0.08	e : 0.08	= : 0.08	g : 0.06	h : 0.06	c : 0.06	i : 0.04	] : 0.03	2 : 0.03	f : 0.03	5 : 0.01	F : 0.01	a : 0.01	n : 0.01	G : 0.01	
: : 0.14	d : 0.11	e : 0.11	c : 0.08	= : 0.08	g : 0.06	h : 0.06	f : 0.06	2 : 0.04	i : 0.04	3 : 0.03	] : 0.03	b : 0.01	[ : 0.01	5 : 0.01	F : 0.01	D : 0.01	n : 0.01	G : 0.01	

#score	1381.339547675569
#seq	62
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_UTR_m2_run1.txt

#BEAR
==========!!cccooooooccc]=========	chr19:23063579-23064008(+)$1	429	283	317	21.9995
ggggg[iiiiiiiiiooooooiiiiiiiii]ggg	chr19:32197198-32197618(-)$1	420	139	173	19.9970
==============oooooo==============	chr1:175265736-175266225(-)$1	489	151	185	22.0137
b[ccc==========oooooo==========22c	chr15:82121279-82121772(+)$1	493	268	302	21.1929
""ggggggg[eeeeeooooooeeeee]ggggggg	chr4:132633072-132633451(+)$1	379	275	309	15.5507
cc[eeeee####cccooooooccc333eeeee]c	chr5:37357519-37358017(-)$1	498	414	448	16.2387
ccc[============mmmm============]c	chr13:94972773-94973269(-)$1	496	146	180	18.4614
dddd===========mmmm===========]ddd	chr9:121648136-121648590(+)$1	454	401	435	16.5085
eeeee"""gggggggooooooggggggg333eee	chr17:24215134-24215535(-)$1	401	144	178	16.4127
[dddd"""ccc[cccooooooccc]cccdddd]a	chr5:73713687-73713987(-)$1	300	53	87	15.8567
cc!!eeeee"""cccooooooccc]eeeee4444	chr15:54670434-54670855(-)$1	421	267	301	16.8323
!!=============oooooo=============	chr4:32669165-32669627(+)$1	462	253	287	23.2407
D==========[ccclllccc==========:gg	chr10:98487875-98488211(+)$1	336	39	73	15.6284
d]a============oooooo============:	chr15:50490408-50490764(-)$1	356	222	256	21.0670
dddd[ccc"""ddddoooooodddd4444ccc]d	chr11:77349850-77350160(-)$1	310	48	82	14.7264
dd[bb[a[ccc[cccoooooocccccc]a22bb2	chr8:126358819-126359141(+)$1	322	62	96	15.3108
eeeeebb[gggggggooooooggggggg]bb444	chr19:50223818-50224063(-)$1	245	104	138	15.4580
======%%%%%%cccooooooccc==========	chr5:30594582-30594919(+)$1	337	41	75	16.8086
hbb[============lll============]bb	chr16:44222971-44223358(+)$1	387	192	226	17.8069
ii"""===========nnnnn===========]i	chr8:89366383-89366805(-)$1	422	312	346	19.3261
ccc$$$$$gggggggoooooogggggggccc:dd	chr14:66484603-66484938(+)$1	335	29	63	14.5464
!!==========cccnnnnnccc4444=======	chr13:45016380-45016698(+)$1	318	66	100	17.9493
[============rrrrrrrrr============	chr2:102141262-102141759(-)$1	497	361	395	18.1706
cccbb[==========nnnnn==========]bb	chr5:52928173-52928629(-)$1	456	283	317	17.2196
[==============mmmm==============]	chr4:43045497-43045902(-)$1	405	124	158	19.1508
[==========ddddnnnnndddd]=========	chr5:145497211-145497704(-)$1	493	116	150	16.6036
!!ggggggg"""cccooooooccc4444gggggg	chr5:8144073-8144460(-)$1	387	177	211	18.5340
::::===========oooooo===========cc	chr10:62207252-62207550(-)$1	298	23	57	18.1401
==============aooooooa]===========	chr10:56109409-56109885(+)$1	476	46	80	22.4905
[bb!!==========oooooo==========333	chr4:126289741-126290063(+)$1	322	34	68	22.2330
ee$$$$$===========lll===========55	chr15:99845108-99845358(+)$1	250	67	101	15.7848
===============mmmm===============	chr13:94972114-94972452(-)$1	338	151	185	19.1355
a[=============oooooo=============	chr5:8622690-8622956(-)$1	266	95	129	22.9723
==============oooooo==============	chr14:59854210-59854569(+)$1	359	197	231	22.0137
FFiiiiiiiii[cccooooooccc]iiiiiiiii	chr14:67421766-67422081(-)$1	315	91	125	19.1768
eeee[==========oooooo==========]ee	chr16:91014890-91015267(-)$1	377	287	321	21.1265
eee[eeeee"""cccooooooccceeeee22eee	chr15:38418103-38418397(-)$1	294	18	52	15.1079
h$$$$$==========nnnnn==========hhh	chr11:68904164-68904572(+)$1	408	129	163	16.6889
[ccc!!dddd[ddddooooooddddddddccc]e	chr9:108959137-108959432(+)$1	295	176	210	13.8394
========"""bb[aooooooa]bb333======	chr4:117810045-117810531(-)$1	486	187	221	19.2374
$$ffffff####cccooooooccc4444ffffff	chr3:143851434-143851892(-)$1	458	369	403	15.1131
f"""cccdddd[cccooooooccc]dddd]ccc4	chr18:84266423-84266735(+)$1	312	137	171	15.7607
===========[cccooooooccc==========	chr3:152482178-152482665(-)$1	487	255	289	22.2344
####iiiiiiiii[aooooooa]iiiiiiiii22	chr6:72269087-72269490(-)$1	403	285	319	19.9688
i!!============oooooo============2	chr2:26871722-26872000(+)$1	278	118	152	22.8695
!!ccc==========oooooo==========333	chr4:122624038-122624336(-)$1	298	160	194	22.5194
e[ccc!!dddd[cccooooooccc]dddd22ccc	chr5:142937345-142937582(+)$1	237	68	102	15.5041
[accc[dddd!!cccooooooccc]dddd22ccc	chr16:31251932-31252375(-)$1	443	239	273	15.7745
dd::=============mmmm=============	chr5:113672190-113672536(-)$1	346	170	204	16.1127
gg"""eeeee[ddddooooooddddeeeee4444	chr9:96233025-96233524(-)$1	499	264	298	14.5179
!!ccc[ccc[ccc[aooooooaccc]ccc]ccc2	chr1:168322803-168323179(+)$1	376	325	359	16.5979

#otherMatches

#Seq PSSM
AUGUGACCAUUUUGUAUUUGAACACAUGGUUAUA	chr19:23063579-23064008(+)$1	429	283	317	21.9995
GUGUGCACAUGCACAAgugugugugcguguucau	chr19:32197198-32197618(-)$1	420	139	173	19.9970
GUACAuguguguauguguguguguguacguguau	chr1:175265736-175266225(-)$1	489	151	185	22.0137
guguguguaugcauguguguguauguaugcgugu	chr15:82121279-82121772(+)$1	493	268	302	21.1929
UGGUCCCGUGGUGUGCAAAUUCGCAUGGUGGGGC	chr4:132633072-132633451(+)$1	379	275	309	15.5507
CCCAGUGGUCACGUCCUGCCUGGCUUCCUACUUG	chr5:37357519-37358017(-)$1	498	414	448	16.2387
AGUAUUCAUAUAGUAAAGUUUUACUGUAUGAAAA	chr13:94972773-94973269(-)$1	496	146	180	18.4614
UCAACUUGAGACAAGUUAUCUUGUCUCAAGCUUG	chr9:121648136-121648590(+)$1	454	401	435	16.5085
CUGUGGUUCCUGCCUUACAGCAGGCAGGUUGUAU	chr17:24215134-24215535(-)$1	401	144	178	16.4127
GGAAGUUUGGUCCUCCCUUUUGAGAACCCUUUGC	chr5:73713687-73713987(-)$1	300	53	87	15.8567
CGUGUAGUCCUGUUCUGUAUUGAAAGACUGAUUU	chr15:54670434-54670855(-)$1	421	267	301	16.8323
CAUUUUUUAAAACCUGCCUCUGGGUUUUgagaga	chr4:32669165-32669627(+)$1	462	253	287	23.2407
AGAAAGGGAAAUGUUCUCAGCUUUCUUUUUUAUU	chr10:98487875-98488211(+)$1	336	39	73	15.6284
AguguguaugugugcguguguguaugugugCAUU	chr15:50490408-50490764(-)$1	356	222	256	21.0670
UCAGAAGUCUCUAGCUUUAGUGCUAAAAUACUAC	chr11:77349850-77350160(-)$1	310	48	82	14.7264
CACUCAGUGAGCUUUCUUUUUAAACUCCCAGGAA	chr8:126358819-126359141(+)$1	322	62	96	15.3108
AAGGUGGACUUACUUACAGCAAAGUAAGGCUUAC	chr19:50223818-50224063(-)$1	245	104	138	15.4580
AAUAAUUCCUUUCACUAUAUUGUGGUUAUUUUAU	chr5:30594582-30594919(+)$1	337	41	75	16.8086
UGUGUAUUUAUCAUGUUGCACAUGGUAAAUGGAU	chr16:44222971-44223358(+)$1	387	192	226	17.8069
GGUCCAGUGUGGUUGACAGGCUCAGCUGUAUUUC	chr8:89366383-89366805(-)$1	422	312	346	19.3261
GGAAUACGUCACCUGAGAUCACAGGUGAUCCAAG	chr14:66484603-66484938(+)$1	335	29	63	14.5464
AAGAUGGAGAAAAGCCUUACGUUUCCGUUUCUUC	chr13:45016380-45016698(+)$1	318	66	100	17.9493
uguguguguAAAUGAGAAUGAGAUUUGUACACAC	chr2:102141262-102141759(-)$1	497	361	395	18.1706
UCAUGUGUGUUUGAUGUUAUCCGUUGAGCGCUCA	chr5:52928173-52928629(-)$1	456	283	317	17.2196
guguguguguguACAGCUGUGUGCGUGCAUACAA	chr4:43045497-43045902(-)$1	405	124	158	19.1508
CCCCCCCGCCUGCUUGCUGGAAGCUGGGUGGGGG	chr5:145497211-145497704(-)$1	493	116	150	16.6036
CGGAGCGGGGCAGCUUAUAUUGGUGGGAUUUGCU	chr5:8144073-8144460(-)$1	387	177	211	18.5340
ACGGCUCAGGUGUAUGACACAGUGCACUUGGGGA	chr10:62207252-62207550(-)$1	298	23	57	18.1401
UUUGUGGUGUGGGCCAACGUGGUGUUUACAUUAU	chr10:56109409-56109885(+)$1	476	46	80	22.4905
guaaggcauguguguuuauguaugcauguguggc	chr4:126289741-126290063(+)$1	322	34	68	22.2330
UAAUGAAUGUGAAUGUGUAAUAUAUAUUUGCAGU	chr15:99845108-99845358(+)$1	250	67	101	15.7848
AUUCAGAGUAUGACUUUGGAGUUGUGUUUUGAGU	chr13:94972114-94972452(-)$1	338	151	185	19.1355
CUCgugcgugcgugugagugagcgcguguguaug	chr5:8622690-8622956(-)$1	266	95	129	22.9723
GAAAGGAUGAAAGUUUACAUGCUUUUGUUCUUUU	chr14:59854210-59854569(+)$1	359	197	231	22.0137
AACUGCAGUGACUUGAUGCUCUAAAUCAUUGUAG	chr14:67421766-67422081(-)$1	315	91	125	19.1768
ugugugugugugugugugugugcauguAUAUUUA	chr16:91014890-91015267(-)$1	377	287	321	21.1265
CAAAACUUAAAGGGUGGCACAACUUGAGUCCUUG	chr15:38418103-38418397(-)$1	294	18	52	15.1079
gCCCCCUGUAAAUAGCCAGCUGuuauuuauacau	chr11:68904164-68904572(+)$1	408	129	163	16.6889
UGUCUAGACAUGUGGCUUCCUCUGCUGUUGACCA	chr9:108959137-108959432(+)$1	295	176	210	13.8394
ugugcuugagaaugugugugugggugugCAAGUA	chr4:117810045-117810531(-)$1	486	187	221	19.2374
aaaaacuuaaaagaaaaaauauuCAACAGAGUUU	chr3:143851434-143851892(-)$1	458	369	403	15.1131
GUAAUAAAAUAAUCUAAUCAAAGACUAUUAUUAA	chr18:84266423-84266735(+)$1	312	137	171	15.7607
uguauauauguguguguaugugcaaugugugugu	chr3:152482178-152482665(-)$1	487	255	289	22.2344
CCAACCAGCAGGGGGCUUGAACGCCUUGUUGGGU	chr6:72269087-72269490(-)$1	403	285	319	19.9688
CAAGUGUGUGUACACAUGCACGUGUACAUGCAUG	chr2:26871722-26872000(+)$1	278	118	152	22.8695
AUGACUAUGUAUAUAGUGAUGUGUGUAUGUAUGU	chr4:122624038-122624336(-)$1	298	160	194	22.5194
AUGAUAAUUCUGUAAAAGUAAUUGGGGGAGGGUC	chr5:142937345-142937582(+)$1	237	68	102	15.5041
UCCAUGGCAUGAAGUCUGUCUGCUGgugugugug	chr16:31251932-31252375(-)$1	443	239	273	15.7745
GGCAUGGGCGGGAGGGGGGUAUUCCUCCUGCCCA	chr5:113672190-113672536(-)$1	346	170	204	16.1127
CAUUUAAAUUAGGUGAAUGUGCACCGAUUUUUGU	chr9:96233025-96233524(-)$1	499	264	298	14.5179
UAGGUGACAUCGUACAAUAAAGAUGCUGUGGCCG	chr1:168322803-168323179(+)$1	376	325	359	16.5979

#DB
((((((((((..(((......))).)))))))))	chr19:23063579-23064008(+)$1	1	283	317	21.9995
(((((.(((((((((......))))))))).)))	chr19:32197198-32197618(-)$1	1	139	173	19.9970
((((((((((((((......))))))))))))))	chr1:175265736-175266225(-)$1	1	151	185	22.0137
(.(((((((((((((......))))))))))..)	chr15:82121279-82121772(+)$1	1	268	302	21.1929
..(((((((.(((((......))))).)))))))	chr4:132633072-132633451(+)$1	1	275	309	15.5507
((.(((((....(((......)))...))))).)	chr5:37357519-37358017(-)$1	1	414	448	16.2387
(((.((((((((((((....)))))))))))).)	chr13:94972773-94973269(-)$1	1	146	180	18.4614
(((((((((((((((....))))))))))).)))	chr9:121648136-121648590(+)$1	1	401	435	16.5085
(((((...(((((((......)))))))...)))	chr17:24215134-24215535(-)$1	1	144	178	16.4127
.((((...(((.(((......))).))))))).)	chr5:73713687-73713987(-)$1	1	53	87	15.8567
((..(((((...(((......))).)))))....	chr15:54670434-54670855(-)$1	1	267	301	16.8323
..(((((((((((((......)))))))))))))	chr4:32669165-32669627(+)$1	1	253	287	23.2407
(((((((((((.(((...))))))))))))).((	chr10:98487875-98488211(+)$1	1	39	73	15.6284
).)((((((((((((......)))))))))))).	chr15:50490408-50490764(-)$1	1	222	256	21.0670
((((.(((...((((......))))....))).)	chr11:77349850-77350160(-)$1	1	48	82	14.7264
((.((.(.(((.(((......)))))).)..)).	chr8:126358819-126359141(+)$1	1	62	96	15.3108
(((((((.(((((((......))))))).))...	chr19:50223818-50224063(-)$1	1	104	138	15.4580
((((((......(((......)))))))))))))	chr5:30594582-30594919(+)$1	1	41	75	16.8086
)((.((((((((((((...)))))))))))).))	chr16:44222971-44223358(+)$1	1	192	226	17.8069
((...(((((((((((.....))))))))))).)	chr8:89366383-89366805(-)$1	1	312	346	19.3261
(((.....(((((((......)))))))))).((	chr14:66484603-66484938(+)$1	1	29	63	14.5464
..(((((((((((((.....)))....)))))))	chr13:45016380-45016698(+)$1	1	66	100	17.9493
.((((((((((((.........))))))))))))	chr2:102141262-102141759(-)$1	1	361	395	18.1706
(((((.((((((((((.....)))))))))).))	chr5:52928173-52928629(-)$1	1	283	317	17.2196
.((((((((((((((....)))))))))))))).	chr4:43045497-43045902(-)$1	1	124	158	19.1508
.((((((((((((((.....)))).)))))))))	chr5:145497211-145497704(-)$1	1	116	150	16.6036
..(((((((...(((......)))....))))))	chr5:8144073-8144460(-)$1	1	177	211	18.5340
....(((((((((((......)))))))))))((	chr10:62207252-62207550(-)$1	1	23	57	18.1401
(((((((((((((((......).)))))))))))	chr10:56109409-56109885(+)$1	1	46	80	22.4905
.((..((((((((((......))))))))))...	chr4:126289741-126290063(+)$1	1	34	68	22.2330
((.....(((((((((((...)))))))))))..	chr15:99845108-99845358(+)$1	1	67	101	15.7848
(((((((((((((((....)))))))))))))))	chr13:94972114-94972452(-)$1	1	151	185	19.1355
(.(((((((((((((......)))))))))))))	chr5:8622690-8622956(-)$1	1	95	129	22.9723
((((((((((((((......))))))))))))))	chr14:59854210-59854569(+)$1	1	197	231	22.0137
(((((((((((.(((......))).)))))))))	chr14:67421766-67422081(-)$1	1	91	125	19.1768
((((.((((((((((......)))))))))).))	chr16:91014890-91015267(-)$1	1	287	321	21.1265
(((.(((((...(((......))))))))..)))	chr15:38418103-38418397(-)$1	1	18	52	15.1079
(.....((((((((((.....)))))))))))))	chr11:68904164-68904572(+)$1	1	129	163	16.6889
.(((..((((.((((......))))))))))).)	chr9:108959137-108959432(+)$1	1	176	210	13.8394
((((((((...((.(......).))...))))))	chr4:117810045-117810531(-)$1	1	187	221	19.2374
..((((((....(((......)))....))))))	chr3:143851434-143851892(-)$1	1	369	403	15.1131
(...(((((((.(((......))).)))).))).	chr18:84266423-84266735(+)$1	1	137	171	15.7607
(((((((((((.(((......)))))))))))))	chr3:152482178-152482665(-)$1	1	255	289	22.2344
....(((((((((.(......).)))))))))..	chr6:72269087-72269490(-)$1	1	285	319	19.9688
(..((((((((((((......)))))))))))).	chr2:26871722-26872000(+)$1	1	118	152	22.8695
..(((((((((((((......))))))))))...	chr4:122624038-122624336(-)$1	1	160	194	22.5194
(.(((..((((.(((......))).))))..)))	chr5:142937345-142937582(+)$1	1	68	102	15.5041
.((((.((((..(((......))).))))..)))	chr16:31251932-31252375(-)$1	1	239	273	15.7745
))..(((((((((((((....)))))))))))))	chr5:113672190-113672536(-)$1	1	170	204	16.1127
((...(((((.((((......)))))))))....	chr9:96233025-96233524(-)$1	1	264	298	14.5179
..(((.(((.(((.(......)))).))).))).	chr1:168322803-168323179(+)$1	1	325	359	16.5979

#PSSM
= : 0.15	[ : 0.13	e : 0.11	c : 0.09	d : 0.09	! : 0.09	g : 0.03	h : 0.03	i : 0.03	b : 0.01	" : 0.01	D : 0.01	: : 0.01	a : 0.01	F : 0.01	$ : 0.01	f : 0.01	# : 0.01	
= : 0.23	c : 0.11	! : 0.11	d : 0.09	e : 0.09	[ : 0.05	g : 0.03	" : 0.03	b : 0.03	$ : 0.03	] : 0.01	i : 0.01	: : 0.01	F : 0.01	# : 0.01	a : 0.01	
= : 0.29	c : 0.17	e : 0.07	g : 0.05	d : 0.05	" : 0.05	[ : 0.03	! : 0.03	b : 0.03	: : 0.03	$ : 0.03	a : 0.01	i : 0.01	f : 0.01	# : 0.01	
= : 0.33	c : 0.11	e : 0.07	g : 0.05	[ : 0.05	d : 0.05	" : 0.05	$ : 0.05	! : 0.03	b : 0.03	: : 0.03	i : 0.01	f : 0.01	# : 0.01	
= : 0.43	c : 0.11	e : 0.09	g : 0.05	$ : 0.05	[ : 0.03	b : 0.03	" : 0.03	! : 0.03	i : 0.03	d : 0.01	f : 0.01	
= : 0.52	[ : 0.09	e : 0.07	$ : 0.05	g : 0.03	" : 0.03	c : 0.03	i : 0.03	! : 0.03	b : 0.01	f : 0.01	
= : 0.54	e : 0.07	i : 0.05	c : 0.05	g : 0.03	" : 0.03	$ : 0.03	d : 0.03	a : 0.01	b : 0.01	% : 0.01	f : 0.01	! : 0.01	
= : 0.56	e : 0.07	d : 0.07	i : 0.05	g : 0.03	" : 0.03	c : 0.03	[ : 0.03	% : 0.01	$ : 0.01	f : 0.01	
= : 0.54	g : 0.09	d : 0.07	i : 0.05	c : 0.05	e : 0.05	# : 0.03	" : 0.03	% : 0.01	
= : 0.54	" : 0.09	d : 0.07	i : 0.05	g : 0.05	[ : 0.03	# : 0.03	c : 0.03	% : 0.01	e : 0.01	
= : 0.52	" : 0.09	i : 0.05	g : 0.05	c : 0.05	! : 0.03	# : 0.03	[ : 0.03	d : 0.03	e : 0.01	% : 0.01	
= : 0.47	[ : 0.13	d : 0.07	g : 0.05	" : 0.05	! : 0.03	i : 0.03	# : 0.03	e : 0.01	% : 0.01	b : 0.01	c : 0.01	
= : 0.45	c : 0.33	d : 0.07	g : 0.05	i : 0.03	e : 0.01	b : 0.01	
= : 0.43	c : 0.31	d : 0.07	g : 0.05	[ : 0.05	i : 0.01	e : 0.01	r : 0.01	
= : 0.37	c : 0.31	d : 0.07	a : 0.07	g : 0.05	o : 0.03	i : 0.01	e : 0.01	r : 0.01	
o : 0.72	= : 0.13	m : 0.05	n : 0.03	l : 0.01	r : 0.01	
o : 0.72	n : 0.09	m : 0.07	l : 0.03	= : 0.03	r : 0.01	
o : 0.72	m : 0.09	n : 0.09	l : 0.03	r : 0.01	= : 0.01	
o : 0.72	m : 0.09	n : 0.09	l : 0.03	c : 0.01	r : 0.01	
o : 0.72	n : 0.09	= : 0.07	m : 0.03	c : 0.01	r : 0.01	l : 0.01	
o : 0.68	= : 0.13	n : 0.05	c : 0.03	r : 0.01	d : 0.01	l : 0.01	m : 0.01	
= : 0.43	c : 0.29	d : 0.07	a : 0.07	g : 0.05	i : 0.01	e : 0.01	r : 0.01	
= : 0.45	c : 0.31	d : 0.07	g : 0.05	] : 0.05	i : 0.01	e : 0.01	
= : 0.47	c : 0.29	d : 0.07	g : 0.05	i : 0.03	e : 0.01	4 : 0.01	b : 0.01	
= : 0.50	] : 0.15	g : 0.05	d : 0.05	4 : 0.05	i : 0.03	e : 0.03	c : 0.03	3 : 0.01	b : 0.01	
= : 0.54	e : 0.07	4 : 0.07	d : 0.07	i : 0.05	g : 0.05	3 : 0.03	c : 0.03	] : 0.01	
= : 0.54	4 : 0.07	d : 0.07	i : 0.05	g : 0.05	c : 0.05	e : 0.05	3 : 0.03	] : 0.01	
= : 0.56	g : 0.07	e : 0.07	d : 0.07	i : 0.05	4 : 0.05	c : 0.03	] : 0.01	3 : 0.01	
= : 0.58	d : 0.09	e : 0.07	i : 0.05	g : 0.03	c : 0.03	3 : 0.01	4 : 0.01	a : 0.01	] : 0.01	f : 0.01	
= : 0.58	2 : 0.07	i : 0.05	e : 0.05	c : 0.05	g : 0.03	] : 0.03	3 : 0.01	d : 0.01	b : 0.01	f : 0.01	
= : 0.56	c : 0.09	2 : 0.07	] : 0.03	g : 0.03	4 : 0.03	i : 0.03	e : 0.01	3 : 0.01	d : 0.01	b : 0.01	f : 0.01	
= : 0.41	c : 0.11	g : 0.05	e : 0.05	4 : 0.05	] : 0.05	d : 0.03	: : 0.03	3 : 0.03	i : 0.03	2 : 0.01	b : 0.01	h : 0.01	f : 0.01	
= : 0.33	] : 0.11	c : 0.09	g : 0.07	e : 0.05	4 : 0.05	b : 0.05	2 : 0.03	d : 0.03	3 : 0.03	5 : 0.01	i : 0.01	h : 0.01	f : 0.01	
= : 0.27	c : 0.11	g : 0.07	e : 0.07	4 : 0.07	2 : 0.07	d : 0.05	b : 0.03	i : 0.03	3 : 0.03	a : 0.01	: : 0.01	] : 0.01	5 : 0.01	h : 0.01	f : 0.01	

#score	927.5335366793506
#seq	51
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_UTR_m1_run2.txt

#BEAR
ffff[ccctttttttttttccc]fff	chr7:88314965-88315257(+)$1	292	236	262	22.9484
:ffffffuuuuuuuuuuuuffffffH	chr7:97592413-97592717(+)$1	304	69	95	21.7770
b[eeeeeuuuuuuuuuuuueeeeebb	chr5:111086972-111087242(+)$1	270	209	235	24.0303
gggggggxxxxxxxxxxxxxxxgggg	chr4:135420035-135420303(+)$1	268	193	219	19.4040
=====[bbtttttttttttbb333==	chr10:80616204-80616486(-)$1	282	189	215	22.7730
gggggggtttttttttttggggggg:	chr2:106802838-106803115(-)$1	277	64	90	22.4078
c[cccccctttttttttttccc]ccc	chr11:50108631-50108915(-)$1	284	176	202	23.2163
ff[cccvvvvvvvvvvvvvccc]fff	chr12:8712675-8712967(+)$1	292	199	225	23.6271
eee[cccuuuuuuuuuuuuccc]eee	chr15:75877939-75878222(-)$1	283	136	162	24.5486
hhhhhhhwwwwwwwwwwwwwwhhhhh	chr2:173526804-173527105(+)$1	301	141	167	21.8271
c[eeeeeuuuuuuuuuuuueeeeecc	chr6:36796208-36796479(-)$1	271	237	263	24.7469
ffffffvvvvvvvvvvvvvffffff]	chr5:124819112-124819387(-)$1	275	44	70	22.8383
gggggggyyyyyyyyyyyyyyyyggg	chr15:25926975-25927264(+)$1	289	141	167	22.6990
hhhhhhhuuuuuuuuuuuuhhhhhhh	chr9:58066553-58066849(-)$1	296	214	240	22.4587
ddd[ddddtttttttttttdddd]dd	chr5:64301047-64301328(-)$1	281	22	48	21.4582
iiiiiiiuuuuuuuuuuuuiiiiiii	chrX:71188443-71188742(-)$1	299	64	90	25.2556
ddeeeeevvvvvvvvvvvvveeeee:	chr7:87385396-87385668(+)$1	272	162	188	23.2092
fffff[awwwwwwwwwwwwwwa]fff	chr18:68423943-68424215(-)$1	272	105	131	22.8151
hhhhhhhyyyyyyyyyyyyyyyyhhh	chr5:124822672-124822950(-)$1	278	168	194	20.9179
ee!!cccvvvvvvvvvvvvvccc]ee	chr11:30779726-30779995(+)$1	269	62	88	24.2230
=======uuuuuuuuuuuu=======	chr1:120574996-120575275(+)$1	279	8	34	25.4230
[ffffffuuuuuuuuuuuuffffffc	chr2:165610251-165610519(-)$1	268	132	158	23.5285
!!eeeeevvvvvvvvvvvvveeeee2	chr11:76071349-76071637(-)$1	288	163	189	24.5659
+eeeeevvvvvvvvvvvvveeeee22	chr10:127568434-127568707(-)$1	273	108	134	22.7045
gggggggtttttttttttggggggg:	chr17:24185422-24185696(-)$1	274	17	43	22.4078
gggggggtttttttttttgggggggf	chr17:88122725-88123129(+)$1	404	303	329	23.2425
"""cccvvvvvvvvvvvvvccc333f	chr2:155683708-155683976(-)$1	268	157	183	23.6327
cceeeeevvvvvvvvvvvvveeeee:	chr10:127568556-127568827(-)$1	271	227	253	23.5236
e!!ddddvvvvvvvvvvvvvdddd22	chr7:16912295-16912645(-)$1	350	226	252	23.1367
####bbvvvvvvvvvvvvvbb4444f	chr4:9502339-9502629(-)$1	290	14	40	21.9370
=======uuuuuuuuuuuu=======	chr13:8889812-8890083(+)$1	271	3	29	25.4230
"""eeeeettttttttttteeeeeee	chr1:11587796-11588069(+)$1	273	14	40	23.0837
g[eeeeevvvvvvvvvvvvveeeeeg	chr2:31828547-31828817(+)$1	270	58	84	24.8651
e!!dddduuuuuuuuuuuudddd]ee	chr3:7553536-7553818(+)$1	282	29	55	23.7499
!!eeeeeyyyyyyyyyyyyyyyyeee	chr10:95006920-95007194(+)$1	274	101	127	22.3667
eeeeccctttttttttttccc4444e	chr2:101540929-101541207(+)$1	278	1	27	22.6137
""eeeeevvvvvvvvvvvvveeeee]	chr18:24050068-24050343(+)$1	275	104	130	24.5841
gggggggyyyyyyyyyyyyyyyyggg	chr10:127183094-127183373(+)$1	279	103	129	22.6990
gggggggwwwwwwwwwwwwwwggggg	chr5:115573835-115574103(-)$1	268	11	37	24.0230
iiiiiivvvvvvvvvvvvviiiiiii	chr10:80169722-80169993(-)$1	271	4	30	24.4680
iiiiiiiyyyyyyyyyyyyyyyyiii	chr3:97475435-97475708(+)$1	273	176	202	22.7210
feeeeevvvvvvvvvvvvveeeee]f	chr5:111049866-111050135(+)$1	269	207	233	23.7742
dddd[bbvvvvvvvvvvvvvbbdddd	chr2:128677625-128677943(+)$1	318	219	245	21.9446
ggggggguuuuuuuuuuuuggggggg	chr7:97595897-97596318(+)$1	421	101	127	25.1236
ffeeeeeuuuuuuuuuuuueeeee]f	chr3:103159358-103159659(+)$1	301	182	208	24.5368
eee[cccvvvvvvvvvvvvvccc]ee	chr13:101545622-101545897(-)$1	275	151	177	24.2281
iiiiiiiitttttttttttiiiiiii	chr7:149267469-149267748(-)$1	279	92	118	23.5681
=======wwwwwwwwwwwwww=====	chr14:78894799-78895080(-)$1	281	217	243	24.1788
e[bb[awwwwwwwwwwwwwwabb]ee	chr17:17975286-17975558(+)$1	272	101	127	21.9745
ggggggguuuuuuuuuuuuggggggg	chr1:63190223-63190519(-)$1	296	224	250	25.1236
c[eeeeeuuuuuuuuuuuueeeeecc	chr8:109895578-109895893(+)$1	315	154	180	24.7469
gggggggwwwwwwwwwwwwwwggggg	chr4:116273624-116273900(-)$1	276	47	73	24.0230
hh[dddduuuuuuuuuuuudddd]hh	chr16:17047034-17047387(+)$1	353	289	315	23.2865
ggggggguuuuuuuuuuuuggggggg	chr3:14610988-14611278(-)$1	290	238	264	25.1236
b[eeeeeuuuuuuuuuuuueeeee]b	chr15:76913025-76913293(-)$1	268	19	45	24.4111
eeeeee[attttttttttta]eeeee	chr13:55698704-55698991(+)$1	287	136	162	23.6914
iiiiiiiuuuuuuuuuuuuiiiiiii	chr6:108772164-108772437(+)$1	273	150	176	25.2556
gggggggwwwwwwwwwwwwwwggggg	chr4:136448338-136448605(-)$1	267	76	102	24.0230
[bb[cccuuuuuuuuuuuuccc]bb]	chr11:101861277-101861545(-)$1	268	15	41	23.5082
fffddddwwwwwwwwwwwwwwdddd2	chr16:20331399-20331670(-)$1	271	229	255	22.0272
fbbeeeeettttttttttteeeee]b	chr13:41054610-41054885(+)$1	275	81	107	22.3498
ff[ddddyyyyyyyyyyyyyyyyddd	chr2:146049849-146050127(+)$1	278	41	67	21.1011
fffffffuuuuuuuuuuuuffffff:	chr6:32801528-32801800(-)$1	272	210	236	22.5100

#otherMatches

#Seq PSSM
agggaagccaucucugcaugcugucc	chr7:88314965-88315257(+)$1	292	236	262	22.9484
AGCCGCGGGAAGAGGACGACGCGGCG	chr7:97592413-97592717(+)$1	304	69	95	21.7770
GUAUUCAGAAAAAAAUAAAUGGAUCA	chr5:111086972-111087242(+)$1	270	209	235	24.0303
GAUGUUGGUUGACCAUAAUUUGCAAC	chr4:135420035-135420303(+)$1	268	193	219	19.4040
CUCCCCGGCUGCCUCCUUACCUUCGG	chr10:80616204-80616486(-)$1	282	189	215	22.7730
ccaggcUGCUAAAUUUAAAGUUUGGG	chr2:106802838-106803115(-)$1	277	64	90	22.4078
GCUGGCCCACACCUUUCUAGGGUCCA	chr11:50108631-50108915(-)$1	284	176	202	23.2163
UAUGAAUAAAUUCAAAAUUUUUUUAA	chr12:8712675-8712967(+)$1	292	199	225	23.6271
AGGAGCUGAGGACUUUGGAAGCAUCU	chr15:75877939-75878222(-)$1	283	136	162	24.5486
UUCAUGGAUAUAAGGGAAAAGCUGUG	chr2:173526804-173527105(+)$1	301	141	167	21.8271
AAGGCUUGACCCAAGAACAAAGCCUC	chr6:36796208-36796479(-)$1	271	237	263	24.7469
AAACUAGUCACCCUGUUCAUAGUUUU	chr5:124819112-124819387(-)$1	275	44	70	22.8383
CGAAUGGUUCCUUUGCUGCUACUUCA	chr15:25926975-25927264(+)$1	289	141	167	22.6990
UGACCUUAUGGCCAUCUUGGAGGUCA	chr9:58066553-58066849(-)$1	296	214	240	22.4587
CCAUUGGUGUGAUGCAUUAACUACUG	chr5:64301047-64301328(-)$1	281	22	48	21.4582
GUGAUGUCCACCUUAAUCAGCAUCAC	chrX:71188443-71188742(-)$1	299	64	90	25.2556
ACAGAUACAUCCAGCUACCUUGUCUU	chr7:87385396-87385668(+)$1	272	162	188	23.2092
UAAAUGUUUAUUCUUUAUCCUGGAUU	chr18:68423943-68424215(-)$1	272	105	131	22.8151
GAUGCAACUUUUAUCCUCAUUCCUUG	chr5:124822672-124822950(-)$1	278	168	194	20.9179
GUUUGGCCUCAUUAGUCUUCGCUCAC	chr11:30779726-30779995(+)$1	269	62	88	24.2230
UCUAGUUAGAGAUGCUAUGGACUAGG	chr1:120574996-120575275(+)$1	279	8	34	25.4230
UGGCGUUACGAAUGCAGCCAGCGCCC	chr2:165610251-165610519(-)$1	268	132	158	23.5285
uaacaguucauagaacgcuuacugug	chr11:76071349-76071637(-)$1	288	163	189	24.5659
CCUCCAGUAGACAAAGCAAUGGAGAU	chr10:127568434-127568707(-)$1	273	108	134	22.7045
GGUGUUUAUACUCUUUAGAAAUGCCU	chr17:24185422-24185696(-)$1	274	17	43	22.4078
UAUAAAUAAAAUCAUGUAGUUUGUAC	chr17:88122725-88123129(+)$1	404	303	329	23.2425
CAUGGCCUCCCCAGCAAAAGCCCACC	chr2:155683708-155683976(-)$1	268	157	183	23.6327
ACCUCCAGUAGACAAAGCAAUGGAGA	chr10:127568556-127568827(-)$1	271	227	253	23.5236
AUAAAGUGUCUUUCUCUUAAACUUGC	chr7:16912295-16912645(-)$1	350	226	252	23.1367
GUAUGUAAUCUGUUUCAAAACUCUGG	chr4:9502339-9502629(-)$1	290	14	40	21.9370
AAAUGGUGGGAUAACUUAAACCAUUU	chr13:8889812-8890083(+)$1	271	3	29	25.4230
UAUGCUAUUACAGUCAAAUAUAGUGG	chr1:11587796-11588069(+)$1	273	14	40	23.0837
GACCUCUGCAGAGCACAGAAAGAGGC	chr2:31828547-31828817(+)$1	270	58	84	24.8651
UUUGCACAAUUAGUUUCGAGUGUUGU	chr3:7553536-7553818(+)$1	282	29	55	23.7499
AUGCCUGGGCUGAAAAGAAACAACAG	chr10:95006920-95007194(+)$1	274	101	127	22.3667
GGAUGGAUGCUUCCCAAUUCCCAGAA	chr2:101540929-101541207(+)$1	278	1	27	22.6137
UUUCCUGUUAUUUUCUUUCUCAGGGU	chr18:24050068-24050343(+)$1	275	104	130	24.5841
GAGUUCAUCCCCACCCCCACCCUUGG	chr10:127183094-127183373(+)$1	279	103	129	22.6990
AGAGUACUUGAGAGAAAGGAUGUGCU	chr5:115573835-115574103(-)$1	268	11	37	24.0230
AGCAGUCAGUGCUUCCCCAGCUGUUC	chr10:80169722-80169993(-)$1	271	4	30	24.4680
AUUGUUGUAUCUACACUUCCUGUUAA	chr3:97475435-97475708(+)$1	273	176	202	22.7210
AGGUGCAUCCUCACACCAAGCACCGU	chr5:111049866-111050135(+)$1	269	207	233	23.7742
CACGUGCUGCUGCUACUUCUGCUGUG	chr2:128677625-128677943(+)$1	318	219	245	21.9446
UUAUCGUAUACUUUAAAAAAUGGUAA	chr7:97595897-97596318(+)$1	421	101	127	25.1236
GCCUUUUCAUACUGCACUUAAAAGAG	chr3:103159358-103159659(+)$1	301	182	208	24.5368
GCCGCGGGAGAGGUCUGAGGCCGGGG	chr13:101545622-101545897(-)$1	275	151	177	24.2281
AGUAAAUAUUUCGAUUUUUUAUUUAU	chr7:149267469-149267748(-)$1	279	92	118	23.5681
AUAAACUUUAACCUUCCCACUAGUUU	chr14:78894799-78895080(-)$1	281	217	243	24.1788
UAGGCGAACUACUUACCAACCCCCAG	chr17:17975286-17975558(+)$1	272	101	127	21.9745
AUACUAUGCUUAUCCGAAAAUGGUAU	chr1:63190223-63190519(-)$1	296	224	250	25.1236
UAUAUGAUGUGUUACGUUCUCAUAGU	chr8:109895578-109895893(+)$1	315	154	180	24.7469
UCCUGGGAAAACUGGUAGAAACCUGG	chr4:116273624-116273900(-)$1	276	47	73	24.0230
AAGAUUUUAUUAAGAAUUUAAAUGUU	chr16:17047034-17047387(+)$1	353	289	315	23.2865
ACCUUGCGGCCACCCCUUAGCAGGGU	chr3:14610988-14611278(-)$1	290	238	264	25.1236
GUCACUGCAUCCAGCUUCACAGUGUC	chr15:76913025-76913293(-)$1	268	19	45	24.4111
GGGGUUGCAGUGCACAAAAGGGGCCC	chr13:55698704-55698991(+)$1	287	136	162	23.6914
AGUUUUUUUUUUUUUUCUCAAAAGCU	chr6:108772164-108772437(+)$1	273	150	176	25.2556
GGAGGGAGAAUUCAGUACCAGUUCCU	chr4:136448338-136448605(-)$1	267	76	102	24.0230
UGUUUCAGCUUUAUAAAUAUGACACU	chr11:101861277-101861545(-)$1	268	15	41	23.5082
GUUUGCUAAAUACCUUAUAAAAGCAA	chr16:20331399-20331670(-)$1	271	229	255	22.0272
UCCCACAGGAAAGGUGCUACUGUGUG	chr13:41054610-41054885(+)$1	275	81	107	22.3498
CUUGCUAGUAUUCGCUGUGUUCAUGG	chr2:146049849-146050127(+)$1	278	41	67	21.1011
UCUAUUAUAUAAGCCCUUUUAGUAGC	chr6:32801528-32801800(-)$1	272	210	236	22.5100

#DB
((((.(((...........))).)))	chr7:88314965-88315257(+)$1	1	236	262	22.9484
.((((((............))))))(	chr7:97592413-97592717(+)$1	1	69	95	21.7770
(.(((((............)))))))	chr5:111086972-111087242(+)$1	1	209	235	24.0303
(((((((...............))))	chr4:135420035-135420303(+)$1	1	193	219	19.4040
(((((.((...........))...))	chr10:80616204-80616486(-)$1	1	189	215	22.7730
(((((((...........))))))).	chr2:106802838-106803115(-)$1	1	64	90	22.4078
(.((((((...........))).)))	chr11:50108631-50108915(-)$1	1	176	202	23.2163
((.(((.............))).)))	chr12:8712675-8712967(+)$1	1	199	225	23.6271
(((.(((............))).)))	chr15:75877939-75878222(-)$1	1	136	162	24.5486
(((((((..............)))))	chr2:173526804-173527105(+)$1	1	141	167	21.8271
(.(((((............)))))))	chr6:36796208-36796479(-)$1	1	237	263	24.7469
((((((.............)))))).	chr5:124819112-124819387(-)$1	1	44	70	22.8383
(((((((................)))	chr15:25926975-25927264(+)$1	1	141	167	22.6990
(((((((............)))))))	chr9:58066553-58066849(-)$1	1	214	240	22.4587
(((.((((...........)))).))	chr5:64301047-64301328(-)$1	1	22	48	21.4582
(((((((............)))))))	chrX:71188443-71188742(-)$1	1	64	90	25.2556
))(((((.............))))).	chr7:87385396-87385668(+)$1	1	162	188	23.2092
(((((.(..............).)))	chr18:68423943-68424215(-)$1	1	105	131	22.8151
(((((((................)))	chr5:124822672-124822950(-)$1	1	168	194	20.9179
((..(((.............))).))	chr11:30779726-30779995(+)$1	1	62	88	24.2230
(((((((............)))))))	chr1:120574996-120575275(+)$1	1	8	34	25.4230
.((((((............)))))))	chr2:165610251-165610519(-)$1	1	132	158	23.5285
..(((((.............))))).	chr11:76071349-76071637(-)$1	1	163	189	24.5659
.(((((.............)))))..	chr10:127568434-127568707(-)$1	1	108	134	22.7045
(((((((...........))))))).	chr17:24185422-24185696(-)$1	1	17	43	22.4078
(((((((...........)))))))(	chr17:88122725-88123129(+)$1	1	303	329	23.2425
...(((.............)))...)	chr2:155683708-155683976(-)$1	1	157	183	23.6327
))(((((.............))))).	chr10:127568556-127568827(-)$1	1	227	253	23.5236
(..((((.............))))..	chr7:16912295-16912645(-)$1	1	226	252	23.1367
....((.............))....)	chr4:9502339-9502629(-)$1	1	14	40	21.9370
(((((((............)))))))	chr13:8889812-8890083(+)$1	1	3	29	25.4230
...(((((...........)))))))	chr1:11587796-11588069(+)$1	1	14	40	23.0837
(.(((((.............))))))	chr2:31828547-31828817(+)$1	1	58	84	24.8651
(..((((............)))).))	chr3:7553536-7553818(+)$1	1	29	55	23.7499
..(((((................)))	chr10:95006920-95007194(+)$1	1	101	127	22.3667
(((((((...........)))....)	chr2:101540929-101541207(+)$1	1	1	27	22.6137
..(((((.............))))).	chr18:24050068-24050343(+)$1	1	104	130	24.5841
(((((((................)))	chr10:127183094-127183373(+)$1	1	103	129	22.6990
(((((((..............)))))	chr5:115573835-115574103(-)$1	1	11	37	24.0230
((((((.............)))))))	chr10:80169722-80169993(-)$1	1	4	30	24.4680
(((((((................)))	chr3:97475435-97475708(+)$1	1	176	202	22.7210
((((((.............))))).)	chr5:111049866-111050135(+)$1	1	207	233	23.7742
((((.((.............))))))	chr2:128677625-128677943(+)$1	1	219	245	21.9446
(((((((............)))))))	chr7:97595897-97596318(+)$1	1	101	127	25.1236
(((((((............))))).)	chr3:103159358-103159659(+)$1	1	182	208	24.5368
(((.(((.............))).))	chr13:101545622-101545897(-)$1	1	151	177	24.2281
((((((((...........)))))))	chr7:149267469-149267748(-)$1	1	92	118	23.5681
(((((((..............)))))	chr14:78894799-78895080(-)$1	1	217	243	24.1788
(.((.(..............))).))	chr17:17975286-17975558(+)$1	1	101	127	21.9745
(((((((............)))))))	chr1:63190223-63190519(-)$1	1	224	250	25.1236
(.(((((............)))))))	chr8:109895578-109895893(+)$1	1	154	180	24.7469
(((((((..............)))))	chr4:116273624-116273900(-)$1	1	47	73	24.0230
((.((((............)))).))	chr16:17047034-17047387(+)$1	1	289	315	23.2865
(((((((............)))))))	chr3:14610988-14611278(-)$1	1	238	264	25.1236
(.(((((............))))).)	chr15:76913025-76913293(-)$1	1	19	45	24.4111
)(((((.(...........).)))))	chr13:55698704-55698991(+)$1	1	136	162	23.6914
(((((((............)))))))	chr6:108772164-108772437(+)$1	1	150	176	25.2556
(((((((..............)))))	chr4:136448338-136448605(-)$1	1	76	102	24.0230
.((.(((............))).)).	chr11:101861277-101861545(-)$1	1	15	41	23.5082
(((((((..............)))).	chr16:20331399-20331670(-)$1	1	229	255	22.0272
)(((((((...........))))).)	chr13:41054610-41054885(+)$1	1	81	107	22.3498
((.((((................)))	chr2:146049849-146050127(+)$1	1	41	67	21.1011
)((((((............)))))).	chr6:32801528-32801800(-)$1	1	210	236	22.5100

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

#score	1472.39385489261
#seq	63
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_CDS_m1_run2.txt

#BEAR
!!dddduuuuuuuuuuuudddd33	chrX:140311710-140311966(-)$1	256	129	153	23.4174
iii[bbtttttttttttbb]iiii	chr4:108297531-108297762(+)$1	231	93	117	21.7964
:eeeeeuuuuuuuuuuuueeeeec	chr1:157128099-157128330(-)$1	231	85	109	23.1423
####bbvvvvvvvvvvvvvbb444	chr9:46100130-46100361(+)$1	231	184	208	22.0407
cc[cccuuuuuuuuuuuuccc]cc	chr14:73574191-73574422(+)$1	231	118	142	23.6569
ccc[ccctttttttttttccc333	chr9:97345995-97346254(-)$1	259	55	79	22.7366
ddddwwwwwwwwwwwwwwdddd22	chr13:100199225-100199472(-)$1	247	196	220	20.5374
fff[bbvvvvvvvvvvvvvbb]ff	chrM:7742-7992(+)$1	250	186	210	22.1972
ceeeeevvvvvvvvvvvvveeeee	chr14:27741764-27742004(-)$1	240	30	54	23.7432
iiiiiiuuuuuuuuuuuuiiiiii	chr14:17231391-17231651(+)$1	260	23	47	23.8390
ddd[ccctttttttttttccc]dd	chr13:99629618-99629880(-)$1	262	121	145	22.1592
!eeeeeuuuuuuuuuuuueeeee]	chr6:88456664-88456900(-)$1	236	162	186	24.3459
eeeebbuuuuuuuuuuuubb]eee	chr12:99673338-99673583(-)$1	245	27	51	23.0281
Deeeeeuuuuuuuuuuuueeeee:	chr11:23321146-23321408(+)$1	262	220	244	22.2388
!eeeeeyyyyyyyyyyyyyyyyee	chrX:101278512-101278757(-)$1	245	205	229	21.4052
[bb[bbvvvvvvvvvvvvvbbbb]	chr14:67434167-67434403(-)$1	236	60	84	21.4871
f!!cccvvvvvvvvvvvvvccc55	chr8:82223156-82223387(-)$1	231	31	55	21.7846
eeeeewwwwwwwwwwwwwweeeee	chr7:117192390-117192630(+)$1	240	33	57	22.4317
fffffftttttttttttffffff:	chr15:9112154-9112385(+)$1	231	159	183	20.6347
eeeeevvvvvvvvvvvvveeeeec	chr4:49668539-49668775(+)$1	236	71	95	23.1909
!eeeeeyyyyyyyyyyyyyyyyee	chrX:101278454-101278709(-)$1	255	157	181	21.4052
[eeeeeuuuuuuuuuuuueeeee]	chr13:100201046-100201309(-)$1	263	197	221	24.3335
iiiiiivvvvvvvvvvvvviiiii	chr6:36665422-36665813(-)$1	391	231	255	23.5273
ddd[bbyyyyyyyyyyyyyyyybb	chr15:98571690-98571930(-)$1	240	171	195	19.8769
:eeeeettttttttttteeeee::	chr4:123045090-123045343(-)$1	253	60	84	19.9045
%%%cccuuuuuuuuuuuuccc444	chr3:148521597-148521837(-)$1	240	193	217	21.4275
eeeeewwwwwwwwwwwwwweeeee	chr6:29324391-29324622(+)$1	231	65	89	22.4317
ddddyyyyyyyyyyyyyyyydddd	chr6:148131538-148131814(-)$1	276	245	269	20.1173
:eeeeeuuuuuuuuuuuueeeeeF	chr17:57161124-57161385(-)$1	261	92	116	22.7974
d!!cccuuuuuuuuuuuuccc22d	chr13:46796904-46797135(-)$1	231	144	168	23.2518
!!ddddyyyyyyyyyyyyyyyydd	chr9:115155120-115155382(-)$1	262	52	76	20.5589
gg!!bbvvvvvvvvvvvvvbb22g	chr10:36717110-36717342(+)$1	232	65	89	22.4093
eedddduuuuuuuuuuuudddd33	chr17:82047770-82048013(-)$1	243	41	65	23.2458
fffffftttttttttttffffffE	chr9:108474652-108474925(-)$1	273	63	87	20.4594
!fffffftttttttttttffffff	chr7:66560114-66560383(-)$1	269	146	170	21.6263
ggggggvvvvvvvvvvvvvggggg	chr4:4694720-4694969(-)$1	249	107	131	23.5051
ee[cccvvvvvvvvvvvvvcccee	chr6:4574077-4574312(+)$1	235	192	216	23.3671
gggggguuuuuuuuuuuugggggg	chr17:32336071-32336310(-)$1	239	103	127	23.7641
fffffftttttttttttffffff:	chr4:147991599-147991856(-)$1	257	71	95	20.6347
!!dddduuuuuuuuuuuudddd]e	chr12:103632671-103632925(-)$1	254	177	201	23.2101
=======ttttttttttt======	chr18:63111822-63112081(+)$1	259	29	53	22.5757
eeeeewwwwwwwwwwwwwweeeee	chr11:69219075-69219309(-)$1	234	210	234	22.4317
ceeeeeuuuuuuuuuuuueeeee:	chr11:98018627-98018859(-)$1	232	51	75	23.3307
ii[cccuuuuuuuuuuuuccc]ii	chr7:99723183-99723414(+)$1	231	45	69	23.8954
ffffffuuuuuuuuuuuuffffff	chr15:92076389-92076648(+)$1	259	87	111	22.6542
gggggguuuuuuuuuuuugggggg	chr6:136557348-136557611(+)$1	263	206	230	23.7641
[eeeeeuuuuuuuuuuuueeeeee	chr10:114658487-114658745(-)$1	258	89	113	24.1844
ddddwwwwwwwwwwwwwwdddd33	chr18:43493536-43493786(-)$1	250	74	98	20.9770
[fffffftttttttttttffffff	chr18:10000519-10000752(-)$1	233	65	89	21.6139
c!!ddddtttttttttttdddd33	chr15:12095852-12096109(+)$1	257	202	226	22.0805
======vvvvvvvvvvvvv=====	chr7:72468833-72469072(-)$1	239	38	62	23.5893
hhhhhhyyyyyyyyyyyyyyyyhh	chr6:36691299-36691531(-)$1	232	2	26	19.7207
eeeeevvvvvvvvvvvvveeeee:	chr2:98507083-98507435(-)$1	352	282	306	22.4297
:eeeeeuuuuuuuuuuuueeeee:	chr8:11207090-11207357(-)$1	267	217	241	22.3810
hhhhhhuuuuuuuuuuuuhhhhhh	chr3:103581357-103581598(-)$1	241	155	179	21.5796
ffffffuuuuuuuuuuuuffffff	chr1:38112034-38112265(-)$1	231	177	201	22.6542
cceeeeettttttttttteeeee4	chr11:75309812-75310054(+)$1	242	105	129	22.7172
ggggggvvvvvvvvvvvvvggggg	chr4:34758902-34759141(-)$1	239	86	110	23.5051
hhhhhhuuuuuuuuuuuuhhhhhh	chr3:126647772-126648004(-)$1	232	86	110	21.5796
hhhhhhvvvvvvvvvvvvvhhhhh	chr18:16791454-16791686(-)$1	232	74	98	21.5444
ggggggwwwwwwwwwwwwwwgggg	chr5:136673563-136673820(-)$1	257	204	228	22.2066
ggggg[attttttttttta]gggg	chr6:41577332-41577563(+)$1	231	85	109	23.1022
ddddddtttttttttttdddd]dd	chr1:56947923-56948206(-)$1	283	78	102	21.2664

#otherMatches

#Seq PSSM
UUGUGGUCCUGAAAAAUUCCGCUA	chrX:140311710-140311966(-)$1	256	129	153	23.4174
GGGCCCUAAUGUGCCUUGGAUUCU	chr4:108297531-108297762(+)$1	231	93	117	21.7964
UGCAUGGGACUGAUCAUACAUGUU	chr1:157128099-157128330(-)$1	231	85	109	23.1423
GAGAACAAGAAUAAGAAAGGUGAG	chr9:46100130-46100361(+)$1	231	184	208	22.0407
CUUCUCAAAAUUAGGUAAGAGUGG	chr14:73574191-73574422(+)$1	231	118	142	23.6569
GAGAGGCCAUUAGUCCCAGCCAAC	chr9:97345995-97346254(-)$1	259	55	79	22.7366
GACCACCACCACUCCUGAGGUCAA	chr13:100199225-100199472(-)$1	247	196	220	20.5374
GAACGAAAAUCUAUUUGCCUCAUU	chrM:7742-7992(+)$1	250	186	210	22.1972
UGUGCUGCAAAAAUAGAAAAGUAC	chr14:27741764-27742004(-)$1	240	30	54	23.7432
UUGUAUAGAUUAUGGAAAAUGCAG	chr14:17231391-17231651(+)$1	260	23	47	23.8390
UAUCCUCGAUAGCAACAAGAGAGU	chr13:99629618-99629880(-)$1	262	121	145	22.1592
AGAUGUAAGUCUAAGUCCACAUCC	chr6:88456664-88456900(-)$1	236	162	186	24.3459
GUUGAGAUCCAUGACAAGCUGCAA	chr12:99673338-99673583(-)$1	245	27	51	23.0281
GUAUGCUUUAAAAUAUAUGCAUGA	chr11:23321146-23321408(+)$1	262	220	244	22.2388
CACAUUUUCCAGAAAGACAUUUGA	chrX:101278512-101278757(-)$1	245	205	229	21.4052
CUGCGGCCUUUGUCACCUCCCCAC	chr14:67434167-67434403(-)$1	236	60	84	21.4871
CUUGCUUUUUUUUUUCCUUAGUUU	chr8:82223156-82223387(-)$1	231	31	55	21.7846
AAGCCCCUAAUCACAACAUGGCUU	chr7:117192390-117192630(+)$1	240	33	57	22.4317
GUUGAUGAAGGAAAAGAAUUAAUC	chr15:9112154-9112385(+)$1	231	159	183	20.6347
UGAGGUUUAUUUAUAGUUCCUCAG	chr4:49668539-49668775(+)$1	236	71	95	23.1909
CACAUUUUCCAGAAAGACAUUUGA	chrX:101278454-101278709(-)$1	255	157	181	21.4052
UAGUCCCUCUGAUAUCCAGGACUC	chr13:100201046-100201309(-)$1	263	197	221	24.3335
AAAACAAAGAGAAAAGAAAUGUUU	chr6:36665422-36665813(-)$1	391	231	255	23.5273
CCAAGGUAUGACAGACAGAGCUCC	chr15:98571690-98571930(-)$1	240	171	195	19.8769
UAGUUGAAAGAAUUUGCCAACUUU	chr4:123045090-123045343(-)$1	253	60	84	19.9045
AAAGGAUUUUAGAAUUUUUCCCAA	chr3:148521597-148521837(-)$1	240	193	217	21.4275
AGGCCACAGAUUUCGGGGAGGCCU	chr6:29324391-29324622(+)$1	231	65	89	22.4317
AGGUUAACAUUCAUUUCUUUGCCU	chr6:148131538-148131814(-)$1	276	245	269	20.1173
UCCUGUCUCUCCCUCUCUGCAGGC	chr17:57161124-57161385(-)$1	261	92	116	22.7974
UCAGCCAUUACCAAACAAGGUAUA	chr13:46796904-46797135(-)$1	231	144	168	23.2518
GAGAUUGGAAAUAAAGACAUUAAA	chr9:115155120-115155382(-)$1	262	52	76	20.5589
UUGUUUUUUCAUUGUUUUUAAUAG	chr10:36717110-36717342(+)$1	232	65	89	22.4093
AUUCUGAAGGAACUUAAGCAGAAG	chr17:82047770-82048013(-)$1	243	41	65	23.2458
GCGCAUCCUCAUUUCCCGUGUGCU	chr9:108474652-108474925(-)$1	273	63	87	20.4594
UUUGCUUGAAUAUUCCGGAAGUAA	chr7:66560114-66560383(-)$1	269	146	170	21.6263
UCAGGACAUUAGUAAGCAUUCCUG	chr4:4694720-4694969(-)$1	249	107	131	23.5051
GAAUAUUAUCAAUACUCCUGUGUC	chr6:4574077-4574312(+)$1	235	192	216	23.3671
CGUGAGGCUCCCUCUCCGCUUAUG	chr17:32336071-32336310(-)$1	239	103	127	23.7641
AGCACUUCAUUGAAAGUAGUGCUG	chr4:147991599-147991856(-)$1	257	71	95	20.6347
CACUGGAAUAUGAACCAACCAGAG	chr12:103632671-103632925(-)$1	254	177	201	23.2101
GCAGGGAGGACAGCUGGGUCCCUG	chr18:63111822-63112081(+)$1	259	29	53	22.5757
UCCUGCCACCAAAAUACCUCAGGA	chr11:69219075-69219309(-)$1	234	210	234	22.4317
CUUUCAAACUAAUAAUAAUGAAAA	chr11:98018627-98018859(-)$1	232	51	75	23.3307
UUAAAAAUACUAAUUUUCUUUAAA	chr7:99723183-99723414(+)$1	231	45	69	23.8954
AUCUUCAACAUCCAGCUAGAAGAU	chr15:92076389-92076648(+)$1	259	87	111	22.6542
UUUUUUGUCAAAGGAAAAAAAAAA	chr6:136557348-136557611(+)$1	263	206	230	23.7641
GCAUAUGGCUUAAUACAAGUAUGU	chr10:114658487-114658745(-)$1	258	89	113	24.1844
CCUGAUAUCCACUCCUUCCAGGAA	chr18:43493536-43493786(-)$1	250	74	98	20.9770
GAGUUAUAUGUAGUUUGAAUAAUU	chr18:10000519-10000752(-)$1	233	65	89	21.6139
UUAAACAUUCUACUUUACUGUUAA	chr15:12095852-12096109(+)$1	257	202	226	22.0805
UAUAUUCCUAAAACCAACUAGuau	chr7:72468833-72469072(-)$1	239	38	62	23.5893
AUACAACCUCUUAAUAUCAAAAUU	chr6:36691299-36691531(-)$1	232	2	26	19.7207
guggacauuucuaaauuuuccacc	chr2:98507083-98507435(-)$1	352	282	306	22.4297
AUGGCAUCCUUUUCUAUUUGCUAC	chr8:11207090-11207357(-)$1	267	217	241	22.3810
CACAAGAAUCAUACCUGCCUUGUG	chr3:103581357-103581598(-)$1	241	155	179	21.5796
CUCCUCUAUCUAAUUCCUGAGGAG	chr1:38112034-38112265(-)$1	231	177	201	22.6542
UGUGUCUGUGUACAGUAAAGACAA	chr11:75309812-75310054(+)$1	242	105	129	22.7172
GAGAAUCUUCCAAUACCAAAUUCU	chr4:34758902-34759141(-)$1	239	86	110	23.5051
GCUGAUGAAUCAUUAGCAGUCAGC	chr3:126647772-126648004(-)$1	232	86	110	21.5796
GAAGGCAAUCCCACUUAUGGCCUU	chr18:16791454-16791686(-)$1	232	74	98	21.5444
UUUUUGUuuuguuuuuuuuuuaaa	chr5:136673563-136673820(-)$1	257	204	228	22.2066
AGCCUCCAGGUUAUCAUAGAGGGC	chr6:41577332-41577563(+)$1	231	85	109	23.1022
AUCUCUCCCUUCUUUUCAGAGUAU	chr1:56947923-56948206(-)$1	283	78	102	21.2664

#DB
..((((............))))..	chrX:140311710-140311966(-)$1	1	129	153	23.4174
(((.((...........)).))))	chr4:108297531-108297762(+)$1	1	93	117	21.7964
.(((((............)))))(	chr1:157128099-157128330(-)$1	1	85	109	23.1423
....((.............))...	chr9:46100130-46100361(+)$1	1	184	208	22.0407
((.(((............))).))	chr14:73574191-73574422(+)$1	1	118	142	23.6569
(((.(((...........)))...	chr9:97345995-97346254(-)$1	1	55	79	22.7366
((((..............))))..	chr13:100199225-100199472(-)$1	1	196	220	20.5374
(((.((.............)).))	chrM:7742-7992(+)$1	1	186	210	22.1972
)(((((.............)))))	chr14:27741764-27742004(-)$1	1	30	54	23.7432
((((((............))))))	chr14:17231391-17231651(+)$1	1	23	47	23.8390
(((.(((...........))).))	chr13:99629618-99629880(-)$1	1	121	145	22.1592
.(((((............))))).	chr6:88456664-88456900(-)$1	1	162	186	24.3459
((((((............)).)))	chr12:99673338-99673583(-)$1	1	27	51	23.0281
)(((((............))))).	chr11:23321146-23321408(+)$1	1	220	244	22.2388
.(((((................))	chrX:101278512-101278757(-)$1	1	205	229	21.4052
.((.((.............)))).	chr14:67434167-67434403(-)$1	1	60	84	21.4871
(..(((.............)))..	chr8:82223156-82223387(-)$1	1	31	55	21.7846
(((((..............)))))	chr7:117192390-117192630(+)$1	1	33	57	22.4317
((((((...........)))))).	chr15:9112154-9112385(+)$1	1	159	183	20.6347
(((((.............))))))	chr4:49668539-49668775(+)$1	1	71	95	23.1909
.(((((................))	chrX:101278454-101278709(-)$1	1	157	181	21.4052
.(((((............))))).	chr13:100201046-100201309(-)$1	1	197	221	24.3335
((((((.............)))))	chr6:36665422-36665813(-)$1	1	231	255	23.5273
(((.((................))	chr15:98571690-98571930(-)$1	1	171	195	19.8769
.(((((...........)))))..	chr4:123045090-123045343(-)$1	1	60	84	19.9045
...(((............)))...	chr3:148521597-148521837(-)$1	1	193	217	21.4275
(((((..............)))))	chr6:29324391-29324622(+)$1	1	65	89	22.4317
((((................))))	chr6:148131538-148131814(-)$1	1	245	269	20.1173
.(((((............)))))(	chr17:57161124-57161385(-)$1	1	92	116	22.7974
(..(((............)))..)	chr13:46796904-46797135(-)$1	1	144	168	23.2518
..((((................))	chr9:115155120-115155382(-)$1	1	52	76	20.5589
((..((.............))..)	chr10:36717110-36717342(+)$1	1	65	89	22.4093
((((((............))))..	chr17:82047770-82048013(-)$1	1	41	65	23.2458
((((((...........))))))(	chr9:108474652-108474925(-)$1	1	63	87	20.4594
.((((((...........))))))	chr7:66560114-66560383(-)$1	1	146	170	21.6263
((((((.............)))))	chr4:4694720-4694969(-)$1	1	107	131	23.5051
((.(((.............)))))	chr6:4574077-4574312(+)$1	1	192	216	23.3671
((((((............))))))	chr17:32336071-32336310(-)$1	1	103	127	23.7641
((((((...........)))))).	chr4:147991599-147991856(-)$1	1	71	95	20.6347
..((((............)))).)	chr12:103632671-103632925(-)$1	1	177	201	23.2101
(((((((...........))))))	chr18:63111822-63112081(+)$1	1	29	53	22.5757
(((((..............)))))	chr11:69219075-69219309(-)$1	1	210	234	22.4317
)(((((............))))).	chr11:98018627-98018859(-)$1	1	51	75	23.3307
((.(((............))).))	chr7:99723183-99723414(+)$1	1	45	69	23.8954
((((((............))))))	chr15:92076389-92076648(+)$1	1	87	111	22.6542
((((((............))))))	chr6:136557348-136557611(+)$1	1	206	230	23.7641
.(((((............))))))	chr10:114658487-114658745(-)$1	1	89	113	24.1844
((((..............))))..	chr18:43493536-43493786(-)$1	1	74	98	20.9770
.((((((...........))))))	chr18:10000519-10000752(-)$1	1	65	89	21.6139
(..((((...........))))..	chr15:12095852-12096109(+)$1	1	202	226	22.0805
((((((.............)))))	chr7:72468833-72469072(-)$1	1	38	62	23.5893
((((((................))	chr6:36691299-36691531(-)$1	1	2	26	19.7207
(((((.............))))).	chr2:98507083-98507435(-)$1	1	282	306	22.4297
.(((((............))))).	chr8:11207090-11207357(-)$1	1	217	241	22.3810
((((((............))))))	chr3:103581357-103581598(-)$1	1	155	179	21.5796
((((((............))))))	chr1:38112034-38112265(-)$1	1	177	201	22.6542
(((((((...........))))).	chr11:75309812-75310054(+)$1	1	105	129	22.7172
((((((.............)))))	chr4:34758902-34759141(-)$1	1	86	110	23.5051
((((((............))))))	chr3:126647772-126648004(-)$1	1	86	110	21.5796
((((((.............)))))	chr18:16791454-16791686(-)$1	1	74	98	21.5444
((((((..............))))	chr5:136673563-136673820(-)$1	1	204	228	22.2066
(((((.(...........).))))	chr6:41577332-41577563(+)$1	1	85	109	23.1022
((((((...........)))).))	chr1:56947923-56948206(-)$1	1	78	102	21.2664

#PSSM
e : 0.12	! : 0.11	d : 0.11	f : 0.11	g : 0.11	c : 0.09	i : 0.06	: : 0.06	[ : 0.06	h : 0.06	= : 0.03	# : 0.01	D : 0.01	% : 0.01	
e : 0.31	f : 0.12	g : 0.11	! : 0.09	d : 0.09	i : 0.06	h : 0.06	c : 0.04	= : 0.03	# : 0.01	b : 0.01	% : 0.01	
e : 0.30	d : 0.15	f : 0.12	g : 0.09	! : 0.06	h : 0.06	i : 0.04	[ : 0.04	= : 0.03	# : 0.01	c : 0.01	b : 0.01	% : 0.01	
e : 0.30	d : 0.14	f : 0.11	[ : 0.09	c : 0.09	g : 0.09	h : 0.06	i : 0.03	= : 0.03	# : 0.01	! : 0.01	
e : 0.28	c : 0.12	b : 0.11	f : 0.11	d : 0.09	g : 0.09	h : 0.06	w : 0.03	i : 0.03	= : 0.03	y : 0.01	
e : 0.20	c : 0.12	b : 0.11	f : 0.11	d : 0.09	w : 0.07	g : 0.07	h : 0.06	i : 0.03	v : 0.03	= : 0.03	y : 0.01	[ : 0.01	
u : 0.36	v : 0.22	t : 0.09	w : 0.09	y : 0.09	c : 0.03	f : 0.03	= : 0.01	d : 0.01	e : 0.01	a : 0.01	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	t : 0.22	v : 0.22	w : 0.09	y : 0.09	
u : 0.36	v : 0.22	t : 0.12	w : 0.09	y : 0.09	f : 0.04	b : 0.01	e : 0.01	d : 0.01	
e : 0.19	v : 0.19	d : 0.11	f : 0.11	c : 0.09	y : 0.09	w : 0.06	b : 0.03	g : 0.03	h : 0.03	i : 0.01	= : 0.01	a : 0.01	
e : 0.25	c : 0.12	d : 0.11	f : 0.11	y : 0.09	b : 0.07	g : 0.06	h : 0.04	] : 0.03	i : 0.03	= : 0.03	w : 0.01	
e : 0.25	d : 0.12	c : 0.12	f : 0.11	g : 0.09	y : 0.07	b : 0.06	i : 0.04	h : 0.04	= : 0.03	] : 0.01	
e : 0.26	d : 0.11	f : 0.11	g : 0.09	] : 0.07	y : 0.07	i : 0.04	h : 0.04	4 : 0.03	c : 0.03	2 : 0.03	= : 0.03	3 : 0.01	b : 0.01	
e : 0.30	f : 0.12	g : 0.09	3 : 0.07	i : 0.06	d : 0.06	h : 0.06	2 : 0.04	4 : 0.03	b : 0.03	= : 0.03	c : 0.01	5 : 0.01	: : 0.01	] : 0.01	
e : 0.15	: : 0.11	g : 0.11	3 : 0.07	f : 0.07	d : 0.07	i : 0.06	h : 0.06	c : 0.04	4 : 0.04	] : 0.04	= : 0.03	2 : 0.01	5 : 0.01	b : 0.01	F : 0.01	E : 0.01	

#score	1407.4540874291256
#seq	63
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_UTR_m3_run1.txt

#BEAR
eeeee[ddddmmmmdddd333eeeee	chrX:133370696-133370935(+)$1	239	173	199	12.8170
fffff[ddddmmmmdddd22ffffff	chr13:110851792-110852038(-)$1	246	179	205	12.2027
dddd"""cccmmmmccc333dddd44	chr11:51799777-51800012(-)$1	235	10	36	11.4105
biiiiiiiiimmmmiiiiiiiii===	chr7:129771692-129771938(+)$1	246	141	167	11.3378
iii####ddddllldddd22iiiiii	chr2:90856084-90856323(+)$1	239	188	214	11.8987
ee[bb[ddddmmmmdddd]bbeeeee	chr10:20799470-20799713(+)$1	243	16	42	11.2938
==========mmmm============	chrX:67597794-67598053(-)$1	259	202	228	12.5554
bb!!a[ddddmmmmdddda22bb333	chr14:35157790-35158046(+)$1	256	175	201	11.6800
lleeeeecccmmmmccc=========	chr4:150433731-150433967(-)$1	236	97	123	10.5066
=======[bbmmmmbb333=======	chr2:104268029-104268282(-)$1	253	218	244	12.0105
iii[bb[ddddllldddd]bb]iiii	chr8:91275365-91275606(+)$1	241	60	86	9.5288
c!!cccddddmmmmdddd]ccc4444	chr13:110847795-110848040(-)$1	245	158	184	11.9409
e[ccc!!cccmmmmccc22ccc333e	chr7:58924688-58924934(+)$1	246	199	225	11.9224
gg"""ddddnnnnndddd]ggggggg	chr18:61144869-61145184(+)$1	315	145	171	9.3637
ggggggddddmmmmdddd]ggggggg	chr15:98000145-98000402(+)$1	257	185	211	12.9284
==========mmmm==========>>	chr2:49628039-49628283(+)$1	244	88	114	11.9252
!!ddddddddmmmmdddd22dddd]g	chr12:85717554-85717790(-)$1	236	161	187	11.6230
==========mmmm===========:	chr14:73762119-73762423(-)$1	304	111	137	11.4679
d[a!!eeeeemmmmeeeee22adddd	chr10:69487551-69487788(+)$1	237	201	227	9.8316
[ccc####bbmmmmbb333ccc]eee	chr6:58855494-58855767(-)$1	273	85	111	10.5104
ee$$$$$cccmmmmccc4444eeeee	chr1:13130196-13130450(-)$1	254	164	190	10.7249
fffff!!ddddllldddd22ffffff	chr4:109060040-109060297(+)$1	257	214	240	9.9955
a[agggggggmmmmggggggg]a]a]	chr15:98570061-98570299(-)$1	238	9	35	10.1865
ffff!!ddddmmmmdddd22ffffff	chr17:88390678-88390933(-)$1	255	15	41	12.7643
====!!ddddmmmmdddd>>>>>>>>	chr1:155756600-155756860(+)$1	260	27	53	11.6981
ggggggddddllldddd22ggggggg	chr5:68009416-68009700(-)$1	284	82	108	10.6747
!eeeee[cccmmmmccc22eeeee]e	chr1:186720782-186721020(-)$1	238	53	79	10.7788
gggggg[abbmmmmbb]a]ggggggg	chr6:113695732-113695973(-)$1	241	8	34	10.5454
eeee!!ddddmmmmddddeeeee22d	chr10:70021207-70021480(-)$1	273	171	197	11.4183
dddd!!ddddmmmmdddd333dddd]	chrX:149044783-149045051(-)$1	268	136	162	12.5301
iiiiii[cccmmmmccc]iiiiiiii	chr8:124124022-124124257(-)$1	235	21	47	12.1611
[ccc!!ddddmmmmddddccc]gggg	chr11:40493045-40493294(-)$1	249	207	233	12.5818
iiii"""cccnnnnnccc]iiiiiii	chr5:14863032-14863277(+)$1	245	82	108	9.4375
fff####cccmmmmccc22ffffff:	chr7:13616124-13616359(+)$1	235	208	234	10.3320
d[bb!!ddddmmmmdddd22bb]ddd	chr1:84366775-84367081(-)$1	306	279	305	12.2102
eeeee[ddddmmmmdddd22eeeeee	chr16:84954651-84954892(-)$1	241	36	62	12.4524
ffff!!a[bbmmmmbb]a22ffffff	chr5:23012981-23013218(-)$1	237	19	45	10.2183
gggggg[ccclllccc333ggggggg	chr15:82121507-82121747(+)$1	240	108	134	10.0647
iiii[eeeeemmmmeeeeeiiiiiii	chr8:97197811-97198067(+)$1	256	82	108	11.0775
ggggg[ddddmmmmdddd333ggggg	chrX:162824427-162824682(+)$1	255	8	34	13.9843
eeee[eeeeemmmmeeeee22eeeee	chr15:31385917-31386158(-)$1	241	206	232	9.8922
[iiiiiiiiimmmmiiiiiiiii22c	chr14:67422478-67422739(-)$1	261	157	183	11.0631
==========mmmm============	chr11:90139604-90139846(+)$1	242	45	71	12.5554
==========mmmm============	chr10:116507931-116508166(-)$1	235	174	200	12.5554
ccc"""ddddmmmmdddd22ccc:::	chr10:117252445-117252689(-)$1	244	163	189	10.2502
hhh"""ddddmmmmdddd4444hhhh	chrX:93914205-93914455(+)$1	250	87	113	11.9164
gggggg[cccmmmmcccgggggggdd	chr9:25115814-25116074(+)$1	260	119	145	11.2069
$$bb!!ddddmmmmdddd22bb4444	chr2:117107351-117107596(-)$1	245	63	89	12.0127
ffff!!ddddllldddd22ffffffi	chr6:13034877-13035125(+)$1	248	151	177	9.9495
""eeeeecccmmmmccc]eeeeeeee	chr3:7443158-7443406(+)$1	248	42	68	9.8328
d####eeeeemmmmeeeee4444ddd	chr1:155755842-155756095(+)$1	253	67	93	9.6783
ggggg[ddddmmmmdddd22gggggg	chr6:115224399-115224701(+)$1	302	27	53	13.7846

#otherMatches

#Seq PSSM
GGGGAUGCCUGAGAAGGUGACUCCCC	chrX:133370696-133370935(+)$1	239	173	199	12.8170
AUAUGUGGCAAACUUGCUCUUAUAUU	chr13:110851792-110852038(-)$1	246	179	205	12.2027
UGUGAACUAAGUUAUUGCUGCAUAAA	chr11:51799777-51800012(-)$1	235	10	36	11.4105
Cuaaaaauaaauuuuuauuuuuauuu	chr7:129771692-129771938(+)$1	246	141	167	11.3378
ACAAGAGUGCCCAGGGCGUAUGUGGA	chr2:90856084-90856323(+)$1	239	188	214	11.8987
GGCUGGACUGACAACAGUACACCAAA	chr10:20799470-20799713(+)$1	243	16	42	11.2938
guguguguauguguauauauacauau	chrX:67597794-67598053(-)$1	259	202	228	12.5554
CAGACAUUAUUUAUAUAAGGAUGAAC	chr14:35157790-35158046(+)$1	256	175	201	11.6800
GCCCAACGGGGGGUCCCUGAGACUUG	chr4:150433731-150433967(-)$1	236	97	123	10.5066
ACAUUUGAGUGUAAACCUCCAAAUGU	chr2:104268029-104268282(-)$1	253	218	244	12.0105
GGAUUUAUAUUGGAGAUACAACUCCC	chr8:91275365-91275606(+)$1	241	60	86	9.5288
UCUGAAUGUGUGUCCACAGUUCUGCC	chr13:110847795-110848040(-)$1	245	158	184	11.9409
ACCAUGAGAUUCCCAUCAAGUGCAAU	chr7:58924688-58924934(+)$1	246	199	225	11.9224
GGCUCUACCGCCCAGGUGCCCCACUC	chr18:61144869-61145184(+)$1	315	145	171	9.3637
GGGCUUCAGACCCGUCUGCAAGCCCC	chr15:98000145-98000402(+)$1	257	185	211	12.9284
AUGUGUGUGCUUAUGCACAUGCGUGU	chr2:49628039-49628283(+)$1	244	88	114	11.9252
CUUAGAGCUGUCCUCAGUAuuuuauu	chr12:85717554-85717790(-)$1	236	161	187	11.6230
GAUUUUAGACAAAUGUUUGGAAUUUA	chr14:73762119-73762423(-)$1	304	111	137	11.4679
GUGGGUAUUUAAAAAAAUGGACUGAC	chr10:69487551-69487788(+)$1	237	201	227	9.8316
UCUGUAAAGCAUGUGUAUCCAGUGUU	chr6:58855494-58855767(-)$1	273	85	111	10.5104
UAAAAUCCAUUUAAGUGUUCAUGCAA	chr1:13130196-13130450(-)$1	254	164	190	10.7249
UAAAAAUGUGUACUAUAUCAUUUUGC	chr4:109060040-109060297(+)$1	257	214	240	9.9955
CGCCUGUAUAUAUGUGUAUAGAGAGA	chr15:98570061-98570299(-)$1	238	9	35	10.1865
AUGAUUUUAAUGCUUUAAUCUCAUGU	chr17:88390678-88390933(-)$1	255	15	41	12.7643
UGCCCUUCAGUUUUCUGGUUGUUUGU	chr1:155756600-155756860(+)$1	260	27	53	11.6981
GCGCUGCAUGCUGCGUGGAUAGUGUC	chr5:68009416-68009700(-)$1	284	82	108	10.6747
GGUGGAGGGGAUGUCCUGGUCCACAG	chr1:186720782-186721020(-)$1	238	53	79	10.7788
GAGGCCUGACAUUAGUGCUGGCUUCC	chr6:113695732-113695973(-)$1	241	8	34	10.5454
UUCGAUUAAACAAAUUUAUGAAGGCC	chr10:70021207-70021480(-)$1	273	171	197	11.4183
UAUGUAGUGCUCUAGCAUGCUUGUAA	chrX:149044783-149045051(-)$1	268	136	162	12.5301
UUCUGUUUUGUGGUCAGUAUAGGGAA	chr8:124124022-124124257(-)$1	235	21	47	12.1611
UUAUUUUUGCAACUGUAAGUAUGGUU	chr11:40493045-40493294(-)$1	249	207	233	12.5818
CCAAUAAAACAUGAAGUUCUUGGAGA	chr5:14863032-14863277(+)$1	245	82	108	9.4375
ACAAAAUGGUUUUUACUUCUGUGGAU	chr7:13616124-13616359(+)$1	235	208	234	10.3320
UGCACUGUUCUGUUGAACUCUGAGGA	chr1:84366775-84367081(-)$1	306	279	305	12.2102
UCAUCAUAAGCACUUUUACGGGUGGG	chr16:84954651-84954892(-)$1	241	36	62	12.4524
UCCUGUGCACCAUGGUCCUGGGGAAG	chr5:23012981-23013218(-)$1	237	19	45	10.2183
GAAAGUCCUUUGUAAGUCUGCUUUCU	chr15:82121507-82121747(+)$1	240	108	134	10.0647
CGAGGUGUGCUUGUGCAUGCUUGUGU	chr8:97197811-97198067(+)$1	256	82	108	11.0775
UAAAUAUAUACUUCUAUAGUCAUUUA	chrX:162824427-162824682(+)$1	255	8	34	13.9843
GACAGUAUACAUGUGUAUGUAUGUCU	chr15:31385917-31386158(-)$1	241	206	232	9.8922
GUGUUUACAGGUCCCUGUAAGCAGUG	chr14:67422478-67422739(-)$1	261	157	183	11.0631
GUUGCUGGGGAUGUCUUCAGUAGUCA	chr11:90139604-90139846(+)$1	242	45	71	12.5554
UGUAUGuauaaauauauauauauaua	chr10:116507931-116508166(-)$1	235	174	200	12.5554
GGAGAGUACAAUAAUGUAAAUCCUAA	chr10:117252445-117252689(-)$1	244	163	189	10.2502
UCCUUUUGGCUUCAGCUGUUUUGGGG	chrX:93914205-93914455(+)$1	250	87	113	11.9164
GAAAUGCAUUUGUAGAUCAUUUCUAG	chr9:25115814-25116074(+)$1	260	119	145	11.2069
ACACACAGCUAAAUAGCUAAGUCAAA	chr2:117107351-117107596(-)$1	245	63	89	12.0127
GUACAAUAUUGUAAAUAAAGUGCAUG	chr6:13034877-13035125(+)$1	248	151	177	9.9495
AUUUUACUAAUAAUUUGUGUGAAUUG	chr3:7443158-7443406(+)$1	248	42	68	9.8328
AGAGUAGuauuuuuauauuuaaaugu	chr1:155755842-155756095(+)$1	253	67	93	9.6783
GGCAGAUGCUCCGCAGUACACUGCUG	chr6:115224399-115224701(+)$1	302	27	53	13.7846

#DB
(((((.((((....))))...)))))	chrX:133370696-133370935(+)$1	1	173	199	12.8170
(((((.((((....))))..))))))	chr13:110851792-110852038(-)$1	1	179	205	12.2027
((((...(((....)))...))))..	chr11:51799777-51800012(-)$1	1	10	36	11.4105
)(((((((((....)))))))))(((	chr7:129771692-129771938(+)$1	1	141	167	11.3378
(((....((((...))))..))))))	chr2:90856084-90856323(+)$1	1	188	214	11.8987
((.((.((((....)))).)))))))	chr10:20799470-20799713(+)$1	1	16	42	11.2938
((((((((((....))))))))))))	chrX:67597794-67598053(-)$1	1	202	228	12.5554
((..(.((((....)))))..))...	chr14:35157790-35158046(+)$1	1	175	201	11.6800
..)))))(((....)))(((((((((	chr4:150433731-150433967(-)$1	1	97	123	10.5066
(((((((.((....))...)))))))	chr2:104268029-104268282(-)$1	1	218	244	12.0105
(((.((.((((...)))).)).))))	chr8:91275365-91275606(+)$1	1	60	86	9.5288
(..(((((((....)))).)))....	chr13:110847795-110848040(-)$1	1	158	184	11.9409
(.(((..(((....)))..)))...)	chr7:58924688-58924934(+)$1	1	199	225	11.9224
((...((((.....)))).)))))))	chr18:61144869-61145184(+)$1	1	145	171	9.3637
((((((((((....)))).)))))))	chr15:98000145-98000402(+)$1	1	185	211	12.9284
((((((((((....))))))))))..	chr2:49628039-49628283(+)$1	1	88	114	11.9252
..((((((((....))))..)))).)	chr12:85717554-85717790(-)$1	1	161	187	11.6230
((((((((((....))))))))))).	chr14:73762119-73762423(-)$1	1	111	137	11.4679
(.(..(((((....)))))..)))))	chr10:69487551-69487788(+)$1	1	201	227	9.8316
.(((....((....))...))).)))	chr6:58855494-58855767(-)$1	1	85	111	10.5104
((.....(((....)))....)))))	chr1:13130196-13130450(-)$1	1	164	190	10.7249
(((((..((((...))))..))))))	chr4:109060040-109060297(+)$1	1	214	240	9.9955
(.((((((((....))))))).).).	chr15:98570061-98570299(-)$1	1	9	35	10.1865
((((..((((....))))..))))))	chr17:88390678-88390933(-)$1	1	15	41	12.7643
((((..((((....))))........	chr1:155756600-155756860(+)$1	1	27	53	11.6981
((((((((((...))))..)))))))	chr5:68009416-68009700(-)$1	1	82	108	10.6747
.(((((.(((....)))..))))).)	chr1:186720782-186721020(-)$1	1	53	79	10.7788
((((((.(((....)).).)))))))	chr6:113695732-113695973(-)$1	1	8	34	10.5454
((((..((((....)))))))))..)	chr10:70021207-70021480(-)$1	1	171	197	11.4183
((((..((((....))))...)))).	chrX:149044783-149045051(-)$1	1	136	162	12.5301
((((((.(((....))).))))))))	chr8:124124022-124124257(-)$1	1	21	47	12.1611
.(((..((((....))))))).))))	chr11:40493045-40493294(-)$1	1	207	233	12.5818
((((...(((.....))).)))))))	chr5:14863032-14863277(+)$1	1	82	108	9.4375
(((....(((....)))..)))))).	chr7:13616124-13616359(+)$1	1	208	234	10.3320
(.((..((((....))))..)).)))	chr1:84366775-84367081(-)$1	1	279	305	12.2102
(((((.((((....))))..))))))	chr16:84954651-84954892(-)$1	1	36	62	12.4524
((((..(.((....)).)..))))))	chr5:23012981-23013218(-)$1	1	19	45	10.2183
((((((.(((...)))...)))))))	chr15:82121507-82121747(+)$1	1	108	134	10.0647
((((.(((((....))))))))))))	chr8:97197811-97198067(+)$1	1	82	108	11.0775
(((((.((((....))))...)))))	chrX:162824427-162824682(+)$1	1	8	34	13.9843
((((.(((((....)))))..)))))	chr15:31385917-31386158(-)$1	1	206	232	9.8922
.(((((((((....)))))))))..)	chr14:67422478-67422739(-)$1	1	157	183	11.0631
((((((((((....))))))))))))	chr11:90139604-90139846(+)$1	1	45	71	12.5554
((((((((((....))))))))))))	chr10:116507931-116508166(-)$1	1	174	200	12.5554
(((...((((....))))..)))...	chr10:117252445-117252689(-)$1	1	163	189	10.2502
(((...((((....))))....))))	chrX:93914205-93914455(+)$1	1	87	113	11.9164
((((((.(((....))))))))))((	chr9:25115814-25116074(+)$1	1	119	145	11.2069
..((..((((....))))..))....	chr2:117107351-117107596(-)$1	1	63	89	12.0127
((((..((((...))))..))))))(	chr6:13034877-13035125(+)$1	1	151	177	9.9495
..((((((((....))).))))))))	chr3:7443158-7443406(+)$1	1	42	68	9.8328
(....(((((....)))))....)))	chr1:155755842-155756095(+)$1	1	67	93	9.6783
(((((.((((....))))..))))))	chr6:115224399-115224701(+)$1	1	27	53	13.7846

#PSSM
g : 0.15	e : 0.13	= : 0.13	f : 0.11	d : 0.09	i : 0.09	[ : 0.05	b : 0.03	c : 0.03	! : 0.03	l : 0.01	a : 0.01	h : 0.01	$ : 0.01	" : 0.01	
g : 0.15	e : 0.13	i : 0.13	= : 0.13	f : 0.11	[ : 0.07	c : 0.05	d : 0.03	! : 0.03	b : 0.01	l : 0.01	h : 0.01	$ : 0.01	" : 0.01	# : 0.01	
e : 0.13	i : 0.13	= : 0.13	g : 0.13	f : 0.11	c : 0.07	d : 0.05	! : 0.03	a : 0.03	b : 0.03	[ : 0.01	" : 0.01	$ : 0.01	h : 0.01	# : 0.01	
g : 0.15	e : 0.13	= : 0.13	f : 0.09	i : 0.09	c : 0.07	d : 0.05	# : 0.05	b : 0.05	" : 0.05	! : 0.03	[ : 0.01	$ : 0.01	
! : 0.19	g : 0.15	= : 0.11	e : 0.09	" : 0.09	# : 0.07	i : 0.05	f : 0.03	b : 0.03	c : 0.03	[ : 0.03	a : 0.01	d : 0.01	$ : 0.01	
! : 0.21	[ : 0.13	e : 0.13	= : 0.11	g : 0.11	" : 0.07	i : 0.05	# : 0.05	d : 0.03	b : 0.01	c : 0.01	$ : 0.01	
d : 0.42	= : 0.11	e : 0.11	[ : 0.11	# : 0.05	" : 0.03	i : 0.03	! : 0.03	$ : 0.01	g : 0.01	a : 0.01	
d : 0.48	c : 0.21	= : 0.09	e : 0.07	i : 0.03	[ : 0.03	# : 0.01	g : 0.01	a : 0.01	
d : 0.48	c : 0.21	= : 0.09	b : 0.07	e : 0.07	i : 0.03	g : 0.01	
d : 0.46	c : 0.21	= : 0.09	b : 0.07	e : 0.07	i : 0.03	n : 0.01	g : 0.01	
m : 0.84	d : 0.05	l : 0.05	n : 0.03	
m : 0.84	l : 0.11	n : 0.03	
m : 0.84	l : 0.11	n : 0.03	
m : 0.84	l : 0.05	n : 0.03	d : 0.03	c : 0.01	
d : 0.48	c : 0.19	= : 0.09	b : 0.07	e : 0.07	i : 0.03	g : 0.01	n : 0.01	
d : 0.48	c : 0.21	= : 0.09	b : 0.07	e : 0.07	i : 0.03	g : 0.01	
d : 0.48	c : 0.19	= : 0.09	e : 0.07	3 : 0.05	i : 0.03	] : 0.03	g : 0.01	
d : 0.44	= : 0.11	2 : 0.09	3 : 0.07	e : 0.07	i : 0.03	g : 0.03	a : 0.03	] : 0.03	4 : 0.01	c : 0.01	
2 : 0.30	3 : 0.13	] : 0.13	= : 0.11	e : 0.11	i : 0.05	4 : 0.03	g : 0.03	a : 0.01	> : 0.01	c : 0.01	
2 : 0.26	= : 0.13	g : 0.13	i : 0.09	3 : 0.07	c : 0.07	4 : 0.05	e : 0.05	b : 0.03	f : 0.03	> : 0.01	
g : 0.15	= : 0.13	f : 0.11	i : 0.11	c : 0.09	b : 0.07	e : 0.07	3 : 0.05	2 : 0.05	4 : 0.05	d : 0.03	> : 0.01	
e : 0.15	g : 0.15	= : 0.13	f : 0.11	i : 0.11	c : 0.07	d : 0.05	b : 0.05	] : 0.05	4 : 0.03	a : 0.01	> : 0.01	
g : 0.17	e : 0.15	i : 0.13	= : 0.13	f : 0.11	d : 0.07	4 : 0.05	] : 0.03	b : 0.01	3 : 0.01	a : 0.01	> : 0.01	c : 0.01	h : 0.01	
g : 0.17	e : 0.15	= : 0.15	f : 0.11	d : 0.11	i : 0.09	3 : 0.03	4 : 0.03	2 : 0.03	] : 0.01	> : 0.01	: : 0.01	h : 0.01	
g : 0.15	e : 0.13	= : 0.13	f : 0.11	i : 0.09	d : 0.09	4 : 0.05	3 : 0.03	> : 0.03	] : 0.03	2 : 0.03	a : 0.01	: : 0.01	h : 0.01	
e : 0.17	g : 0.17	= : 0.11	i : 0.11	d : 0.09	f : 0.07	4 : 0.05	: : 0.05	> : 0.03	] : 0.03	3 : 0.01	c : 0.01	h : 0.01	

#score	589.2915071843908
#seq	52
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_CDS_m1_run1.txt

#BEAR
b[ddddtttttttttttdddd]b	chr1:75212527-75212747(-)$1	220	17	40	22.2540
ddddwwwwwwwwwwwwwwdddd]	chr9:46084820-46085053(+)$1	233	87	110	20.9876
fffffftttttttttttffffff	chr11:75282000-75282220(+)$1	220	155	178	22.5499
eeeeeattttttttttta]eeee	chr5:65796509-65796729(+)$1	220	2	25	22.9328
hhhh[auuuuuuuuuuuuahhhh	chr2:128827836-128828056(+)$1	220	122	145	21.5756
eeeeeuuuuuuuuuuuueeeee]	chr5:107977988-107978208(-)$1	220	56	79	22.5351
fffffftttttttttttffffff	chr2:29794637-29794857(+)$1	220	47	70	22.5499
fffffftttttttttttffffff	chr12:112907748-112907968(-)$1	220	68	91	22.5499
!!ddddtttttttttttdddd22	chr16:22383622-22383844(-)$1	222	146	169	22.3875
ggggggtttttttttttgggggg	chr2:71684148-71684379(+)$1	231	200	223	22.9894
b[cccuuuuuuuuuuuuccc]bb	chr11:50196446-50196666(+)$1	220	119	142	22.6585
gggggguuuuuuuuuuuuggggg	chr8:73891456-73891676(+)$1	220	180	203	22.9297
gggggwwwwwwwwwwwwwwgggg	chr11:102057051-102057271(-)$1	220	170	193	21.4732
!!dddduuuuuuuuuuuuddddd	chr15:3997434-3997654(+)$1	220	10	33	22.2325
:cccvvvvvvvvvvvvvccc:FF	chr12:72294263-72294483(+)$1	220	162	185	19.8065
gggccctttttttttttccc]gg	chr4:138926762-138926982(+)$1	220	103	126	23.6318
fffffftttttttttttffffff	chr7:6661332-6661552(-)$1	220	55	78	22.5499
ggggggtttttttttttgggggg	chr4:147519959-147520180(-)$1	221	187	210	22.9894
bbdddduuuuuuuuuuuudddd]	chr11:106103013-106103233(+)$1	220	151	174	21.8279
ggggggvvvvvvvvvvvvvgggg	chr5:147111211-147111432(+)$1	221	35	58	22.0607
gggggguuuuuuuuuuuuggggg	chr18:31955640-31955868(+)$1	228	29	52	22.9297
!!ddddtttttttttttdddd22	chr4:102812635-102812855(+)$1	220	26	49	22.3875
eeeewwwwwwwwwwwwwweeeee	chr7:63439688-63439910(+)$1	222	185	208	21.2635
""bb[attttttttttta]bb33	chr12:111855738-111855958(+)$1	220	131	154	22.2217
eee[bbtttttttttttbbeeee	chr11:76024519-76024750(-)$1	231	104	127	21.9528
ddddvvvvvvvvvvvvvdddd]c	chr13:35998061-35998281(-)$1	220	191	214	21.8898
====wwwwwwwwwwwwww=====	chr5:125193383-125193603(+)$1	220	115	138	21.8599
ccc[bbuuuuuuuuuuuubb]cc	chr4:32782241-32782461(+)$1	220	132	155	21.9868
hhhwwwwwwwwwwwwwwhhhhhh	chr10:57942089-57942309(+)$1	220	53	76	19.2236
iiiivvvvvvvvvvvvviiiiii	chr2:149943001-149943226(-)$1	225	106	129	22.3845
ffyyyyyyyyyyyyyyyyfffff	chr15:5126479-5126699(+)$1	220	97	120	20.5594
deeeeeuuuuuuuuuuuueeeee	chrX:46059474-46059695(+)$1	221	187	210	22.1638
ee[ccctttttttttttccc]ee	chr10:85420277-85420497(-)$1	220	75	98	23.2567
cccwwwwwwwwwwwwwwccc]bb	chr3:157203923-157204155(+)$1	232	95	118	20.5873
[dddduuuuuuuuuuuudddd]b	chrX:137008334-137008563(+)$1	229	144	167	22.3229
gggggwwwwwwwwwwwwwwgggg	chrX:161433711-161433931(+)$1	220	179	202	21.4732
====bbuuuuuuuuuuuubb]==	chr9:110451253-110451473(+)$1	220	105	128	22.3067
eeeevvvvvvvvvvvvveeeee]	chr11:79842656-79842876(+)$1	220	167	190	22.1137
!!ddddtttttttttttdddd]f	chr18:42728045-42728265(+)$1	220	97	120	22.8271
c[dddduuuuuuuuuuuuddddc	chr8:109192249-109192469(+)$1	220	43	66	22.3548
ccc[auuuuuuuuuuuua]cccg	chr4:140864518-140864739(+)$1	221	38	61	23.1390
fffffvvvvvvvvvvvvvfffff	chr2:119073674-119073895(+)$1	221	123	146	22.5183
[cccvvvvvvvvvvvvvccc]cc	chr19:55352471-55352693(+)$1	222	80	103	22.7567
ffddddtttttttttttdddd]f	chr2:121728753-121728973(+)$1	220	148	171	22.5976
d!!ccctttttttttttccc333	chr1:162885091-162885311(+)$1	220	48	71	23.4234
======ttttttttttt======	chr3:132323442-132323662(-)$1	220	58	81	23.0975
cyyyyyyyyyyyyyyyyccc333	chr9:121658350-121658570(+)$1	220	92	115	20.2107
aa[ccctttttttttttccc]a]	chr5:33369671-33369891(+)$1	220	109	132	23.3306
byyyyyyyyyyyyyyyybb4444	chr12:85009013-85009233(+)$1	220	63	86	18.9325
eeeeevvvvvvvvvvvvveeeee	chr9:110610910-110611130(+)$1	220	121	144	22.3519
!!ddddtttttttttttdddd]f	chr1:34339292-34339512(+)$1	220	131	154	22.8271
fffffvvvvvvvvvvvvvfffff	chr6:85571907-85572140(+)$1	233	55	78	22.5183
ddddwwwwwwwwwwwwwwdddd:	chr12:8735575-8735795(+)$1	220	113	136	19.8948
fffffftttttttttttffffff	chr7:108546777-108546999(+)$1	222	11	34	22.5499
##cccuuuuuuuuuuuuccc22e	chr8:125944405-125944625(+)$1	220	189	212	22.7554
fffffuuuuuuuuuuuuffffff	chr11:60678467-60678689(-)$1	222	93	116	22.6137
fffffftttttttttttffffff	chr1:6235465-6235685(+)$1	220	193	216	22.5499
:eeeeeuuuuuuuuuuuueeeee	chr4:108707246-108707466(+)$1	220	136	159	21.3099
cc[cccwwwwwwwwwwwwwwccc	chr16:72970361-72970581(+)$1	220	60	83	20.3256
fffffftttttttttttffffff	chr1:75526776-75526996(+)$1	220	158	181	22.5499
hhhhhuuuuuuuuuuuuhhhhhh	chr3:134931954-134932174(+)$1	220	163	186	20.8038
"""ccctttttttttttccc333	chr14:21512873-21513093(+)$1	220	51	74	23.2800
ffyyyyyyyyyyyyyyyyfffff	chr6:83878842-83879062(+)$1	220	123	146	20.5594
eeeewwwwwwwwwwwwwweeeee	chr10:4544337-4544560(+)$1	223	70	93	21.2635

#otherMatches

#Seq PSSM
UAUGCACCAGUCAUUUCUGCAGA	chr1:75212527-75212747(-)$1	220	17	40	22.2540
CCACCAACUGUGAGAAUUGUGGG	chr9:46084820-46085053(+)$1	233	87	110	20.9876
AAGGCUGAAUCGGGAAAGGCCUU	chr11:75282000-75282220(+)$1	220	155	178	22.5499
AGAAUCAAAAUCACUAAGAAUUC	chr5:65796509-65796729(+)$1	220	2	25	22.9328
GGGCACGAGUCAUUAAAGGGCCU	chr2:128827836-128828056(+)$1	220	122	145	21.5756
GUUCUGGCUCGAGUAGAAGAACU	chr5:107977988-107978208(-)$1	220	56	79	22.5351
GAGAGGAAGGUGCGAGCCCUCUC	chr2:29794637-29794857(+)$1	220	47	70	22.5499
CCGCCUGGGCUUCUCGGAGGUGG	chr12:112907748-112907968(-)$1	220	68	91	22.5499
CCGGACAAUCAGCGCCCGUUCCU	chr16:22383622-22383844(-)$1	222	146	169	22.3875
GGCCACUUCUCUACACCGUGGCU	chr2:71684148-71684379(+)$1	231	200	223	22.9894
ACGUGUUCAACUAAAUUCACUUG	chr11:50196446-50196666(+)$1	220	119	142	22.6585
CAGCAGACUAACUUUUUCCUGCU	chr8:73891456-73891676(+)$1	220	180	203	22.9297
UGUUUAUUUUUUCUAUUAAAAAC	chr11:102057051-102057271(-)$1	220	170	193	21.4732
UUCCCUUCCUCUCCUUUUAGGGU	chr15:3997434-3997654(+)$1	220	10	33	22.2325
AGGAAAAAUAUUAAAUAUCCAAC	chr12:72294263-72294483(+)$1	220	162	185	19.8065
GUGACAGAGAGCACGGAUGUCCA	chr4:138926762-138926982(+)$1	220	103	126	23.6318
CUAUAUGAAUGUCCAAAAUGUGG	chr7:6661332-6661552(-)$1	220	55	78	22.5499
UUGCCCUAUACAACCUUGGGCAA	chr4:147519959-147520180(-)$1	221	187	210	22.9894
ACCCCAGCCUUUAUUUUAUGGGU	chr11:106103013-106103233(+)$1	220	151	174	21.8279
UUUUCUGUUUAACCAAUUGAGAA	chr5:147111211-147111432(+)$1	221	35	58	22.0607
GCCAAGUCACUUACAUUUCUUGG	chr18:31955640-31955868(+)$1	228	29	52	22.9297
CCAGUGGCCCACAACAGCAUUUU	chr4:102812635-102812855(+)$1	220	26	49	22.3875
UGCUUUUAAAUAAUAUAUAGCAA	chr7:63439688-63439910(+)$1	222	185	208	21.2635
AACCCCAAGACAUGAAAGUGGCC	chr12:111855738-111855958(+)$1	220	131	154	22.2217
GCUUCCUUUGGACGGUUGGAGCC	chr11:76024519-76024750(-)$1	231	104	127	21.9528
CACUAUCAUAAUUACAGGGUGAG	chr13:35998061-35998281(-)$1	220	191	214	21.8898
GCUGUUCUCUGUGUACACCGGCC	chr5:125193383-125193603(+)$1	220	115	138	21.8599
UAGAUGAAUUAAAUUUGGCACCU	chr4:32782241-32782461(+)$1	220	132	155	21.9868
GUCAACGUCUUCUCUUAGACAUU	chr10:57942089-57942309(+)$1	220	53	76	19.2236
uggacgucacaguucucuccaaa	chr2:149943001-149943226(-)$1	225	106	129	22.3845
AAAGAAGUGUGUGAGAAGUUCGA	chr15:5126479-5126699(+)$1	220	97	120	20.5594
UGAGGCUUCGCUUUUUUUGCCUC	chrX:46059474-46059695(+)$1	221	187	210	22.1638
UUCUUGGACAAGAUCAAUAAAAA	chr10:85420277-85420497(-)$1	220	75	98	23.2567
UUUGGACGUAAAAAGAAAAAAUA	chr3:157203923-157204155(+)$1	232	95	118	20.5873
UGAUUGAUCCAAAACCAAAUUUC	chrX:137008334-137008563(+)$1	229	144	167	22.3229
AUGCCCCGAAUUUUAUGAAGGUA	chrX:161433711-161433931(+)$1	220	179	202	21.4732
UGAGGAAAACAAACAAUCUCAUU	chr9:110451253-110451473(+)$1	220	105	128	22.3067
AUGGCUGAGAGAAAAAACCAUUA	chr11:79842656-79842876(+)$1	220	167	190	22.1137
GAGAACGGGAAAGAGAAGUUCAG	chr18:42728045-42728265(+)$1	220	97	120	22.8271
CUCUUCCUUUUAGAACCUGAAGG	chr8:109192249-109192469(+)$1	220	43	66	22.3548
GGCACCAACUUCCAGAAGCGCCA	chr4:140864518-140864739(+)$1	221	38	61	23.1390
GCUGGUAUUACAACCCAUUCAGU	chr2:119073674-119073895(+)$1	221	123	146	22.5183
CCCUUACUCUCUCUCCUAGGUGU	chr19:55352471-55352693(+)$1	222	80	103	22.7567
AAGUAUUUAAAUAAUGUAUGCUU	chr2:121728753-121728973(+)$1	220	148	171	22.5976
UCCGGGAAAGCCCUAUACCCAUU	chr1:162885091-162885311(+)$1	220	48	71	23.4234
CCCUUUGAGGUGAAGGGGAAGGG	chr3:132323442-132323662(-)$1	220	58	81	23.0975
CCAGAGAAGGAGAAGCAGGGAAA	chr9:121658350-121658570(+)$1	220	92	115	20.2107
GCGAGACAACCUCACCCUCUGGA	chr5:33369671-33369891(+)$1	220	109	132	23.3306
GGgaaagagagagagaacgagaa	chr12:85009013-85009233(+)$1	220	63	86	18.9325
ACAUGAAUCCUUUUCCCCCAUGU	chr9:110610910-110611130(+)$1	220	121	144	22.3519
AAGUCUGUGGAAAGGUAGGAUGU	chr1:34339292-34339512(+)$1	220	131	154	22.8271
AAAAAGUAAAACCUGUUAUUUUU	chr6:85571907-85572140(+)$1	233	55	78	22.5183
CUGCAAAUAGUCUUACAGGCAGC	chr12:8735575-8735795(+)$1	220	113	136	19.8948
CUCUGUCUAACUUCUCCACAGAG	chr7:108546777-108546999(+)$1	222	11	34	22.5499
AGAGUGUGAGAAUUGUGACUGCC	chr8:125944405-125944625(+)$1	220	189	212	22.7554
ACAUCUCCCUGCCCGCUGGUGUG	chr11:60678467-60678689(-)$1	222	93	116	22.6137
UUCCUGGUUUCUUUGUACAGGGA	chr1:6235465-6235685(+)$1	220	193	216	22.5499
AAACCCGAAGUCACGCCAGGGUU	chr4:108707246-108707466(+)$1	220	136	159	21.3099
CCGGCCUCCCCCAGUCAUUCGGC	chr16:72970361-72970581(+)$1	220	60	83	20.3256
GUGGCCUUGGCCUCUCUGGCCAC	chr1:75526776-75526996(+)$1	220	158	181	22.5499
cugggucacccgcuaaccccagc	chr3:134931954-134932174(+)$1	220	163	186	20.8038
UGGUGGAAGACAAGAGCCUAAGU	chr14:21512873-21513093(+)$1	220	51	74	23.2800
CCAAGAUUUUACCCAGCAGGGAG	chr6:83878842-83879062(+)$1	220	123	146	20.5594
AGCAUCCCAACAAAACCUUGCUG	chr10:4544337-4544560(+)$1	223	70	93	21.2635

#DB
(.((((...........)))).)	chr1:75212527-75212747(-)$1	1	17	40	22.2540
((((..............)))).	chr9:46084820-46085053(+)$1	1	87	110	20.9876
((((((...........))))))	chr11:75282000-75282220(+)$1	1	155	178	22.5499
((((((...........).))))	chr5:65796509-65796729(+)$1	1	2	25	22.9328
((((.(............)))))	chr2:128827836-128828056(+)$1	1	122	145	21.5756
(((((............))))).	chr5:107977988-107978208(-)$1	1	56	79	22.5351
((((((...........))))))	chr2:29794637-29794857(+)$1	1	47	70	22.5499
((((((...........))))))	chr12:112907748-112907968(-)$1	1	68	91	22.5499
..((((...........))))..	chr16:22383622-22383844(-)$1	1	146	169	22.3875
((((((...........))))))	chr2:71684148-71684379(+)$1	1	200	223	22.9894
(.(((............))).))	chr11:50196446-50196666(+)$1	1	119	142	22.6585
((((((............)))))	chr8:73891456-73891676(+)$1	1	180	203	22.9297
(((((..............))))	chr11:102057051-102057271(-)$1	1	170	193	21.4732
..((((............)))))	chr15:3997434-3997654(+)$1	1	10	33	22.2325
.(((.............))).))	chr12:72294263-72294483(+)$1	1	162	185	19.8065
((((((...........))).))	chr4:138926762-138926982(+)$1	1	103	126	23.6318
((((((...........))))))	chr7:6661332-6661552(-)$1	1	55	78	22.5499
((((((...........))))))	chr4:147519959-147520180(-)$1	1	187	210	22.9894
((((((............)))).	chr11:106103013-106103233(+)$1	1	151	174	21.8279
((((((.............))))	chr5:147111211-147111432(+)$1	1	35	58	22.0607
((((((............)))))	chr18:31955640-31955868(+)$1	1	29	52	22.9297
..((((...........))))..	chr4:102812635-102812855(+)$1	1	26	49	22.3875
((((..............)))))	chr7:63439688-63439910(+)$1	1	185	208	21.2635
..((.(...........).))..	chr12:111855738-111855958(+)$1	1	131	154	22.2217
(((.((...........))))))	chr11:76024519-76024750(-)$1	1	104	127	21.9528
((((.............)))).)	chr13:35998061-35998281(-)$1	1	191	214	21.8898
((((..............)))))	chr5:125193383-125193603(+)$1	1	115	138	21.8599
(((.((............)).))	chr4:32782241-32782461(+)$1	1	132	155	21.9868
(((..............))))))	chr10:57942089-57942309(+)$1	1	53	76	19.2236
((((.............))))))	chr2:149943001-149943226(-)$1	1	106	129	22.3845
((................)))))	chr15:5126479-5126699(+)$1	1	97	120	20.5594
)(((((............)))))	chrX:46059474-46059695(+)$1	1	187	210	22.1638
((.(((...........))).))	chr10:85420277-85420497(-)$1	1	75	98	23.2567
(((..............))).))	chr3:157203923-157204155(+)$1	1	95	118	20.5873
.((((............)))).)	chrX:137008334-137008563(+)$1	1	144	167	22.3229
(((((..............))))	chrX:161433711-161433931(+)$1	1	179	202	21.4732
((((((............)).))	chr9:110451253-110451473(+)$1	1	105	128	22.3067
((((.............))))).	chr11:79842656-79842876(+)$1	1	167	190	22.1137
..((((...........)))).)	chr18:42728045-42728265(+)$1	1	97	120	22.8271
(.((((............)))))	chr8:109192249-109192469(+)$1	1	43	66	22.3548
(((.(............).))))	chr4:140864518-140864739(+)$1	1	38	61	23.1390
(((((.............)))))	chr2:119073674-119073895(+)$1	1	123	146	22.5183
.(((.............))).))	chr19:55352471-55352693(+)$1	1	80	103	22.7567
((((((...........)))).)	chr2:121728753-121728973(+)$1	1	148	171	22.5976
(..(((...........)))...	chr1:162885091-162885311(+)$1	1	48	71	23.4234
((((((...........))))))	chr3:132323442-132323662(-)$1	1	58	81	23.0975
(................)))...	chr9:121658350-121658570(+)$1	1	92	115	20.2107
((.(((...........))).).	chr5:33369671-33369891(+)$1	1	109	132	23.3306
(................))....	chr12:85009013-85009233(+)$1	1	63	86	18.9325
(((((.............)))))	chr9:110610910-110611130(+)$1	1	121	144	22.3519
..((((...........)))).)	chr1:34339292-34339512(+)$1	1	131	154	22.8271
(((((.............)))))	chr6:85571907-85572140(+)$1	1	55	78	22.5183
((((..............)))).	chr12:8735575-8735795(+)$1	1	113	136	19.8948
((((((...........))))))	chr7:108546777-108546999(+)$1	1	11	34	22.5499
..(((............)))..)	chr8:125944405-125944625(+)$1	1	189	212	22.7554
(((((............))))))	chr11:60678467-60678689(-)$1	1	93	116	22.6137
((((((...........))))))	chr1:6235465-6235685(+)$1	1	193	216	22.5499
.(((((............)))))	chr4:108707246-108707466(+)$1	1	136	159	21.3099
((.(((..............)))	chr16:72970361-72970581(+)$1	1	60	83	20.3256
((((((...........))))))	chr1:75526776-75526996(+)$1	1	158	181	22.5499
(((((............))))))	chr3:134931954-134932174(+)$1	1	163	186	20.8038
...(((...........)))...	chr14:21512873-21513093(+)$1	1	51	74	23.2800
((................)))))	chr6:83878842-83879062(+)$1	1	123	146	20.5594
((((..............)))))	chr10:4544337-4544560(+)$1	1	70	93	21.2635

#PSSM
f : 0.20	e : 0.12	g : 0.12	c : 0.09	d : 0.07	! : 0.07	b : 0.06	h : 0.04	= : 0.04	: : 0.03	" : 0.03	[ : 0.03	i : 0.01	a : 0.01	# : 0.01	
f : 0.20	e : 0.15	g : 0.12	! : 0.09	c : 0.09	d : 0.06	[ : 0.04	h : 0.04	= : 0.04	" : 0.03	y : 0.03	b : 0.01	i : 0.01	a : 0.01	# : 0.01	
d : 0.20	f : 0.15	e : 0.14	g : 0.12	c : 0.10	y : 0.06	h : 0.04	= : 0.04	[ : 0.04	b : 0.01	i : 0.01	! : 0.01	" : 0.01	
d : 0.20	f : 0.15	c : 0.15	e : 0.12	g : 0.10	y : 0.06	[ : 0.04	= : 0.04	h : 0.03	w : 0.03	b : 0.01	i : 0.01	
d : 0.15	f : 0.15	c : 0.12	w : 0.10	g : 0.10	e : 0.07	v : 0.07	y : 0.06	b : 0.04	[ : 0.03	a : 0.01	= : 0.01	h : 0.01	
d : 0.14	w : 0.14	v : 0.12	f : 0.10	u : 0.10	c : 0.09	g : 0.07	y : 0.06	a : 0.04	b : 0.04	e : 0.03	= : 0.01	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
t : 0.37	u : 0.26	w : 0.15	v : 0.14	y : 0.06	
c : 0.17	u : 0.15	d : 0.12	w : 0.12	f : 0.12	v : 0.06	a : 0.04	e : 0.03	g : 0.03	b : 0.03	h : 0.03	y : 0.03	i : 0.01	= : 0.01	
d : 0.20	f : 0.18	c : 0.17	e : 0.10	g : 0.06	b : 0.06	] : 0.04	w : 0.04	= : 0.03	h : 0.03	a : 0.01	v : 0.01	i : 0.01	
d : 0.20	f : 0.18	c : 0.18	e : 0.14	g : 0.10	h : 0.04	b : 0.04	= : 0.03	i : 0.01	4 : 0.01	w : 0.01	
d : 0.20	f : 0.18	e : 0.14	] : 0.12	g : 0.10	h : 0.04	3 : 0.04	= : 0.03	c : 0.03	: : 0.01	b : 0.01	i : 0.01	4 : 0.01	2 : 0.01	
f : 0.18	e : 0.15	g : 0.12	] : 0.09	d : 0.07	3 : 0.06	c : 0.06	h : 0.04	2 : 0.04	= : 0.04	b : 0.03	F : 0.01	i : 0.01	a : 0.01	4 : 0.01	
f : 0.23	e : 0.14	g : 0.14	] : 0.07	c : 0.07	b : 0.06	3 : 0.06	h : 0.04	= : 0.04	2 : 0.03	d : 0.01	F : 0.01	i : 0.01	4 : 0.01	: : 0.01	

#score	1411.699921461933
#seq	64
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_UTR_m3_run1.txt

#BEAR
fffff[cccpppppppccc22f	chr11:85125737-85126018(+)$1	281	44	66	14.9403
eeeee[cccpppppppccc]ee	chr2:13140584-13140859(-)$1	275	14	36	15.2000
=======rrrrrrrrr======	chr11:101151069-101151348(-)$1	279	128	150	11.9037
"eeeee[bbpppppppbb]eee	chr11:40493341-40493615(-)$1	274	141	163	13.6549
""gggggggpppppppgggggg	chr2:173606899-173607167(+)$1	268	205	227	15.4438
fff"""cccpppppppccc333	chr19:7349339-7349782(+)$1	443	286	308	15.2027
hhhhhh!!apppppppa22hhh	chr11:102167112-102167406(-)$1	294	194	216	12.9183
f[ffffffapppppppa]ffff	chr5:130321590-130321869(+)$1	279	151	173	14.1772
=========ppppppp======	chr6:42230887-42231165(+)$1	278	68	90	15.7728
"dddd[cccrrrrrrrrrcccd	chr18:82724541-82724817(+)$1	276	148	170	10.5395
iiiiiiiiipppppppiiiiii	chr16:98014244-98014518(-)$1	274	209	231	15.5522
ee!!eeeeepppppppeeeee]	chr19:41992629-41992926(+)$1	297	26	48	14.0050
gggggggrrrrrrrrrgggggg	chr5:109000300-109000571(-)$1	271	147	169	11.6276
iiiiiiiiipppppppiiiiii	chr2:30007361-30007628(+)$1	267	92	114	15.5522
eeeeeddddpppppppdddd]e	chr15:84818020-84818289(-)$1	269	74	96	13.5014
c!!ffffffpppppppffffff	chr11:70839635-70839920(+)$1	285	15	37	14.4098
iiiiiddddpppppppdddd]i	chr15:84145097-84145375(+)$1	278	11	33	14.2454
chhhhhhhhppppppphhhhhh	chr18:34931400-34931674(+)$1	274	182	204	13.0942
ffffffcccpppppppccc333	chr8:86463326-86463605(+)$1	279	145	167	15.0406
eeeee[cccpppppppccc]ee	chr2:157901685-157901969(+)$1	284	76	98	15.2000
[dddd!!bbpppppppbb22dd	chr7:20283425-20283716(-)$1	291	247	269	13.1233
c[gggggggpppppppgggggg	chr3:79263142-79263499(-)$1	357	26	48	15.5196
eeee[ddddpppppppddddee	chr1:158578551-158578904(+)$1	353	83	105	13.5283
=========ppppppp======	chr4:94610744-94611021(-)$1	277	4	26	15.7728
g!!bb[cccpppppppccc]bb	chr3:31017840-31018202(+)$1	362	196	218	14.8836
::ccc[cccpppppppccc]cc	chr11:6006184-6006481(-)$1	297	3	25	13.7862
e"""cccbbpppppppbb]ccc	chr1:64778800-64779081(-)$1	281	207	229	14.1495
ccbb[ddddpppppppdddd]b	chr13:55418339-55418626(+)$1	287	189	211	13.3820
ff:ffffffpppppppffffff	chr4:41141983-41142315(-)$1	332	290	312	13.0054
ca[ffffffpppppppffffff	chr2:26763272-26763540(-)$1	268	94	116	14.3026
c[gggggggpppppppgggggg	chrX:102994208-102994518(-)$1	310	214	236	15.5196
"""ddddbbpppppppbb]ddd	chr3:88165751-88166031(+)$1	280	146	168	13.1170
ff[bb[cccpppppppccc]bb	chr7:52214680-52214986(-)$1	306	211	233	14.5914
ee[ccc[bbpppppppbb]ccc	chr7:126859512-126859787(-)$1	275	169	191	14.0821
eeee!!cccrrrrrrrrrccce	chr14:48151278-48151549(+)$1	271	211	233	11.0862
fff[eeeeepppppppeeeeef	chr1:33829730-33830005(-)$1	275	35	57	13.8014
d[bb[ddddpppppppdddd]b	chr1:20793158-20793606(-)$1	448	52	74	13.3902
c:gggggggpppppppgggggg	chr7:106627112-106627407(-)$1	295	200	222	14.5013
[a[ccccccpppppppccc]cc	chr17:87535174-87535449(+)$1	275	210	232	15.5899
bhhhhhhhhppppppphhhhhh	chr7:104055478-104055754(+)$1	276	190	212	12.8729
ddd[a[cccpppppppccc]a3	chr8:13377465-13377767(+)$1	302	32	54	15.1717
hbb[eeeeepppppppeeeee]	chr4:133163261-133163544(-)$1	283	197	219	13.4387
fff"""cccpppppppccc333	chr19:7498500-7498881(+)$1	381	172	194	15.2027
::gggggggpppppppgggggg	chr13:48975241-48975557(-)$1	316	31	53	13.5596
::bb!!cccpppppppccc22b	chr11:94505766-94506036(+)$1	270	46	68	12.8905
EEgggggggpppppppgggggg	chr14:58161754-58162047(+)$1	293	208	230	13.4988
bbbbeeeeepppppppeeeee]	chr1:193655668-193655943(+)$1	275	214	236	13.1309
d!!ffffffpppppppffffff	chr1:174064779-174065072(+)$1	293	142	164	14.2633
eeee!!cccpppppppccc22e	chr11:72254765-72255057(+)$1	292	113	135	14.9790
""a[eeeeepppppppeeeeea	chr7:52237030-52237313(-)$1	283	60	82	14.0019
ggg[ccc[arrrrrrrrra]cc	chr19:18792500-18792769(+)$1	269	214	236	11.2797
""ccc!!bbpppppppbb22cc	chr11:104192167-104192450(+)$1	283	57	79	14.0980
fff!!ddddpppppppdddd]f	chr9:48850407-48850684(+)$1	277	18	40	13.8131
dd:ffffffpppppppffffff	chr2:90854906-90855190(+)$1	284	64	86	12.8886
iiiiiiiiipppppppiiiiii	chr17:71200620-71200913(-)$1	293	18	40	15.5522
iiiiiiirrrrrrrrriiiiii	chr3:90195311-90195579(-)$1	268	187	209	11.7371
EEgggggggpppppppgggggg	chr10:80571568-80571849(+)$1	281	28	50	13.4988
[ccccccrrrrrrrrrccc]cc	chr5:4754685-4754957(-)$1	272	155	177	11.4770
gggg!!bbrrrrrrrrrbb]gg	chr1:136244389-136244659(-)$1	270	225	247	10.8687
dddffffffpppppppffffff	chr12:103807140-103807408(-)$1	268	17	39	13.7219

#otherMatches

#Seq PSSM
UUUCUACACGGGCUAGGUGAAA	chr11:85125737-85126018(+)$1	281	44	66	14.9403
GAACUGGGCUUACACUGUCAGG	chr2:13140584-13140859(-)$1	275	14	36	15.2000
CUGGGGGUUUGCGGUUUUUCUG	chr11:101151069-101151348(-)$1	279	128	150	11.9037
UCAAGAAUAAAGGAAAUAGUUU	chr11:40493341-40493615(-)$1	274	141	163	13.6549
UACUGAGAAUGAAUGCUUCUCA	chr2:173606899-173607167(+)$1	268	205	227	15.4438
CAAAAGUUUGGAGAAAGAAGGG	chr19:7349339-7349782(+)$1	443	286	308	15.2027
GCAUAGAAugugugugaggcug	chr11:102167112-102167406(-)$1	294	194	216	12.9183
UGUCCAAGCUUCAAGUGAUUUG	chr5:130321590-130321869(+)$1	279	151	173	14.1772
UCAUCUGUCAUGAAGGGACAGA	chr6:42230887-42231165(+)$1	278	68	90	15.7728
UUCAUGACAAAAAAAAAAUGUG	chr18:82724541-82724817(+)$1	276	148	170	10.5395
CUCUUGGCAGAUGGCAUGCUGG	chr16:98014244-98014518(-)$1	274	209	231	15.5522
UGUCCUGCACUCUUCCUGCAGU	chr19:41992629-41992926(+)$1	297	26	48	14.0050
ACCCACUCAAAUUGAAGGUGGG	chr5:109000300-109000571(-)$1	271	147	169	11.6276
GAGCUCCUGCAGCUCCCGGGAG	chr2:30007361-30007628(+)$1	267	92	114	15.5522
CGCCGGGCAGGGCCUGUGCCUC	chr15:84818020-84818289(-)$1	269	74	96	13.5014
Cgggcugaggacauagcucagu	chr11:70839635-70839920(+)$1	285	15	37	14.4098
CUGUGCUGCCUUCCUCGCAGAC	chr15:84145097-84145375(+)$1	278	11	33	14.2454
UUUUCUGAUCUUACAAGUCAGA	chr18:34931400-34931674(+)$1	274	182	204	13.0942
CUGGGCCUUAUACCACGAGAAA	chr8:86463326-86463605(+)$1	279	145	167	15.0406
UCCUUGCUCCCAUGCAGAGAGA	chr2:157901685-157901969(+)$1	284	76	98	15.2000
AUCUCUUCUGCUGGUGGGUUGA	chr7:20283425-20283716(-)$1	291	247	269	13.1233
UGCCUAGUGGCUCUUACAUUGG	chr3:79263142-79263499(-)$1	357	26	48	15.5196
AGUUAUUCACCUGUUUUGAGAG	chr1:158578551-158578904(+)$1	353	83	105	13.5283
uggauuaaaauauuccuuuaau	chr4:94610744-94611021(-)$1	277	4	26	15.7728
UAACAAACAGUGUGUGUGUGUG	chr3:31017840-31018202(+)$1	362	196	218	14.8836
CUGUGUUGACUCAUCUUCAUUA	chr11:6006184-6006481(-)$1	297	3	25	13.7862
CAUAUCUGUACUGAUAACAAGA	chr1:64778800-64779081(-)$1	281	207	229	14.1495
UGGCCGCAGGGAUUUACUGCUG	chr13:55418339-55418626(+)$1	287	189	211	13.3820
GUACUUGUAAAUGUGAUACAAG	chr4:41141983-41142315(-)$1	332	290	312	13.0054
CCUUCCCUUCAAUGAAGAGGGA	chr2:26763272-26763540(-)$1	268	94	116	14.3026
UUAAGAGAAUUUUUUUUUCUUU	chrX:102994208-102994518(-)$1	310	214	236	15.5196
AGCCCUGGUAGGCUGAGCACAG	chr3:88165751-88166031(+)$1	280	146	168	13.1170
CACCUGGUAAUAAAGAUGUGAG	chr7:52214680-52214986(-)$1	306	211	233	14.5914
ccaggaaagaaagcuacuaucc	chr7:126859512-126859787(-)$1	275	169	191	14.0821
CAGUAUUGUAUAUUAUGAACAG	chr14:48151278-48151549(+)$1	271	211	233	11.0862
GAUAUCUUUUAGACUUGAGGAA	chr1:33829730-33830005(-)$1	275	35	57	13.8014
AUCGUCUUCCUUAUCUGAAGUU	chr1:20793158-20793606(-)$1	448	52	74	13.3902
AGGUGCUUGGACAUAGUAAGCA	chr7:106627112-106627407(-)$1	295	200	222	14.5013
UCCACUGGUUGACGAUGCCAAG	chr17:87535174-87535449(+)$1	275	210	232	15.5899
UUGGGAGCUCUGGUUAGGCUCC	chr7:104055478-104055754(+)$1	276	190	212	12.8729
UAAUGCAGAGCCUCUAUCUACC	chr8:13377465-13377767(+)$1	302	32	54	15.1717
UGCUUUGAGUGUAGGCCUCAGU	chr4:133163261-133163544(-)$1	283	197	219	13.4387
CUUAUUUAUUAUGCGUGUAUCA	chr19:7498500-7498881(+)$1	381	172	194	15.2027
AGUUCAAUGGAGAUUACGUUGA	chr13:48975241-48975557(-)$1	316	31	53	13.5596
AACCUAGAAACUUGACUUCAUG	chr11:94505766-94506036(+)$1	270	46	68	12.8905
UUAACUUUAUAAAGAUUAAAGU	chr14:58161754-58162047(+)$1	293	208	230	13.4988
CUGUCCUGCAUCCUAGGCAGGC	chr1:193655668-193655943(+)$1	275	214	236	13.1309
CACUUAGCCAUGGUCGGGUUGG	chr1:174064779-174065072(+)$1	293	142	164	14.2633
GCUCAGCAUGGCGGAGAUGAAG	chr11:72254765-72255057(+)$1	292	113	135	14.9790
AGGAUGAGGUGCGCACCCUCAC	chr7:52237030-52237313(-)$1	283	60	82	14.0019
CACCGAUUCUUUAUCCCUGUGU	chr19:18792500-18792769(+)$1	269	214	236	11.2797
GUGGUUUCUUCAUCAUGGUUAC	chr11:104192167-104192450(+)$1	283	57	79	14.0980
UGUGAAUUUGUAUAAAAAAUAA	chr9:48850407-48850684(+)$1	277	18	40	13.8131
GGAAGCUUAAACCUCAUAAGUU	chr2:90854906-90855190(+)$1	284	64	86	12.8886
UCUUCUCUGGGGUGGACAGAGG	chr17:71200620-71200913(-)$1	293	18	40	15.5522
UUUUGCUUUUUCUUUUGGCAAA	chr3:90195311-90195579(-)$1	268	187	209	11.7371
AGCUCAAGGACGACGACUUUGA	chr10:80571568-80571849(+)$1	281	28	50	13.4988
CUGACUUUUUAUGGAUGAGCUC	chr5:4754685-4754957(-)$1	272	155	177	11.4770
AUCAAGAGGAAAACCAACUAUG	chr1:136244389-136244659(-)$1	270	225	247	10.8687
GUCCCUCUUUUCAGGUGAGAGG	chr12:103807140-103807408(-)$1	268	17	39	13.7219

#DB
(((((.(((.......)))..)	chr11:85125737-85126018(+)$1	1	44	66	14.9403
(((((.(((.......))).))	chr2:13140584-13140859(-)$1	1	14	36	15.2000
(((((((.........))))))	chr11:101151069-101151348(-)$1	1	128	150	11.9037
.(((((.((.......)).)))	chr11:40493341-40493615(-)$1	1	141	163	13.6549
..(((((((.......))))))	chr2:173606899-173607167(+)$1	1	205	227	15.4438
(((...(((.......)))...	chr19:7349339-7349782(+)$1	1	286	308	15.2027
((((((..(.......)..)))	chr11:102167112-102167406(-)$1	1	194	216	12.9183
(.(((((((.......).))))	chr5:130321590-130321869(+)$1	1	151	173	14.1772
(((((((((.......))))))	chr6:42230887-42231165(+)$1	1	68	90	15.7728
.((((.(((.........))))	chr18:82724541-82724817(+)$1	1	148	170	10.5395
(((((((((.......))))))	chr16:98014244-98014518(-)$1	1	209	231	15.5522
((..(((((.......))))).	chr19:41992629-41992926(+)$1	1	26	48	14.0050
(((((((.........))))))	chr5:109000300-109000571(-)$1	1	147	169	11.6276
(((((((((.......))))))	chr2:30007361-30007628(+)$1	1	92	114	15.5522
(((((((((.......)))).)	chr15:84818020-84818289(-)$1	1	74	96	13.5014
(..((((((.......))))))	chr11:70839635-70839920(+)$1	1	15	37	14.4098
(((((((((.......)))).)	chr15:84145097-84145375(+)$1	1	11	33	14.2454
(((((((((.......))))))	chr18:34931400-34931674(+)$1	1	182	204	13.0942
(((((((((.......)))...	chr8:86463326-86463605(+)$1	1	145	167	15.0406
(((((.(((.......))).))	chr2:157901685-157901969(+)$1	1	76	98	15.2000
.((((..((.......))..))	chr7:20283425-20283716(-)$1	1	247	269	13.1233
(.(((((((.......))))))	chr3:79263142-79263499(-)$1	1	26	48	15.5196
((((.((((.......))))))	chr1:158578551-158578904(+)$1	1	83	105	13.5283
(((((((((.......))))))	chr4:94610744-94611021(-)$1	1	4	26	15.7728
(..((.(((.......))).))	chr3:31017840-31018202(+)$1	1	196	218	14.8836
..(((.(((.......))).))	chr11:6006184-6006481(-)$1	1	3	25	13.7862
(...(((((.......)).)))	chr1:64778800-64779081(-)$1	1	207	229	14.1495
))((.((((.......)))).)	chr13:55418339-55418626(+)$1	1	189	211	13.3820
)).((((((.......))))))	chr4:41141983-41142315(-)$1	1	290	312	13.0054
)(.((((((.......))))))	chr2:26763272-26763540(-)$1	1	94	116	14.3026
(.(((((((.......))))))	chrX:102994208-102994518(-)$1	1	214	236	15.5196
...((((((.......)).)))	chr3:88165751-88166031(+)$1	1	146	168	13.1170
((.((.(((.......))).))	chr7:52214680-52214986(-)$1	1	211	233	14.5914
((.(((.((.......)).)))	chr7:126859512-126859787(-)$1	1	169	191	14.0821
((((..(((.........))))	chr14:48151278-48151549(+)$1	1	211	233	11.0862
(((.(((((.......))))))	chr1:33829730-33830005(-)$1	1	35	57	13.8014
(.((.((((.......)))).)	chr1:20793158-20793606(-)$1	1	52	74	13.3902
).(((((((.......))))))	chr7:106627112-106627407(-)$1	1	200	222	14.5013
.(.((((((.......))).))	chr17:87535174-87535449(+)$1	1	210	232	15.5899
(((((((((.......))))))	chr7:104055478-104055754(+)$1	1	190	212	12.8729
(((.(.(((.......))).).	chr8:13377465-13377767(+)$1	1	32	54	15.1717
(((.(((((.......))))).	chr4:133163261-133163544(-)$1	1	197	219	13.4387
(((...(((.......)))...	chr19:7498500-7498881(+)$1	1	172	194	15.2027
..(((((((.......))))))	chr13:48975241-48975557(-)$1	1	31	53	13.5596
..((..(((.......)))..)	chr11:94505766-94506036(+)$1	1	46	68	12.8905
(((((((((.......))))))	chr14:58161754-58162047(+)$1	1	208	230	13.4988
))(((((((.......))))).	chr1:193655668-193655943(+)$1	1	214	236	13.1309
(..((((((.......))))))	chr1:174064779-174065072(+)$1	1	142	164	14.2633
((((..(((.......)))..)	chr11:72254765-72255057(+)$1	1	113	135	14.9790
..(.(((((.......))))))	chr7:52237030-52237313(-)$1	1	60	82	14.0019
(((.(((.(.........).))	chr19:18792500-18792769(+)$1	1	214	236	11.2797
..(((..((.......))..))	chr11:104192167-104192450(+)$1	1	57	79	14.0980
(((..((((.......)))).)	chr9:48850407-48850684(+)$1	1	18	40	13.8131
)).((((((.......))))))	chr2:90854906-90855190(+)$1	1	64	86	12.8886
(((((((((.......))))))	chr17:71200620-71200913(-)$1	1	18	40	15.5522
(((((((.........))))))	chr3:90195311-90195579(-)$1	1	187	209	11.7371
(((((((((.......))))))	chr10:80571568-80571849(+)$1	1	28	50	13.4988
.((((((.........))).))	chr5:4754685-4754957(-)$1	1	155	177	11.4770
((((..((.........)).))	chr1:136244389-136244659(-)$1	1	225	247	10.8687
(((((((((.......))))))	chr12:103807140-103807408(-)$1	1	17	39	13.7219

#PSSM
f : 0.15	e : 0.15	c : 0.11	" : 0.09	i : 0.08	d : 0.08	g : 0.06	= : 0.05	[ : 0.05	: : 0.05	h : 0.03	b : 0.03	E : 0.03	
e : 0.15	f : 0.13	" : 0.08	d : 0.08	i : 0.08	[ : 0.06	: : 0.06	= : 0.05	h : 0.05	g : 0.05	! : 0.05	c : 0.03	a : 0.03	b : 0.03	E : 0.03	
g : 0.16	f : 0.11	e : 0.11	i : 0.08	b : 0.08	d : 0.06	! : 0.06	[ : 0.06	= : 0.05	h : 0.05	c : 0.05	" : 0.03	: : 0.03	a : 0.01	
f : 0.15	g : 0.15	e : 0.11	b : 0.09	i : 0.08	c : 0.08	[ : 0.08	= : 0.05	" : 0.05	h : 0.05	d : 0.05	! : 0.03	
f : 0.15	e : 0.15	g : 0.13	c : 0.11	i : 0.08	! : 0.08	= : 0.05	h : 0.05	d : 0.05	[ : 0.05	" : 0.03	b : 0.03	a : 0.01	
[ : 0.13	g : 0.13	f : 0.13	d : 0.11	e : 0.09	! : 0.09	c : 0.08	i : 0.06	= : 0.05	h : 0.05	" : 0.03	
c : 0.30	g : 0.13	f : 0.11	d : 0.11	e : 0.08	i : 0.06	= : 0.05	! : 0.05	[ : 0.03	h : 0.03	b : 0.01	
c : 0.24	b : 0.11	g : 0.11	f : 0.11	d : 0.09	e : 0.08	r : 0.06	i : 0.05	= : 0.03	h : 0.03	! : 0.01	[ : 0.01	
c : 0.24	g : 0.11	b : 0.09	d : 0.09	f : 0.09	r : 0.08	e : 0.08	a : 0.05	i : 0.05	= : 0.03	h : 0.03	
p : 0.86	r : 0.13	
p : 0.86	r : 0.13	
p : 0.86	r : 0.13	
p : 0.86	r : 0.13	
p : 0.86	r : 0.13	
p : 0.86	r : 0.13	
p : 0.86	r : 0.13	
c : 0.23	g : 0.13	b : 0.09	d : 0.09	f : 0.09	e : 0.08	r : 0.06	i : 0.06	= : 0.05	a : 0.03	h : 0.03	
c : 0.23	g : 0.13	b : 0.11	d : 0.09	f : 0.09	e : 0.08	i : 0.06	= : 0.05	r : 0.05	h : 0.03	2 : 0.01	] : 0.01	
c : 0.26	g : 0.13	f : 0.11	d : 0.09	e : 0.08	] : 0.06	i : 0.06	= : 0.05	2 : 0.05	h : 0.03	a : 0.01	b : 0.01	
] : 0.16	g : 0.13	f : 0.11	d : 0.11	e : 0.09	2 : 0.08	c : 0.06	i : 0.06	= : 0.05	3 : 0.05	h : 0.05	
e : 0.15	g : 0.15	c : 0.15	f : 0.11	] : 0.08	i : 0.06	2 : 0.05	= : 0.05	3 : 0.05	h : 0.05	d : 0.03	b : 0.03	a : 0.01	
f : 0.16	g : 0.15	e : 0.11	c : 0.11	i : 0.08	b : 0.08	3 : 0.06	= : 0.05	h : 0.05	d : 0.05	] : 0.05	a : 0.01	

#score	831.0624045455908
#seq	60
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_UTR_m2_run2.txt

#BEAR
:gggggggcccbboooooobb]ccc]ggggg	chr3:34550683-34550905(+)$1	222	81	112	12.2746
=======$$$$$ammmma4444=========	chr4:49525458-49525722(-)$1	264	19	50	12.5997
ddd[gggggggbboooooobb]gggggggdd	chr7:137537312-137537532(-)$1	220	73	104	12.7021
ddd!!ccc!!cccooooooccc333ccc22d	chr5:8453730-8453950(+)$1	220	51	82	14.5392
=======!!ddddoooooodddd]=======	chr4:47426337-47426557(+)$1	220	129	160	15.6139
$$$a[dddd[cccooooooccc]dddd]a66	chr13:24999671-24999891(-)$1	220	151	182	11.7131
=========!!apppppppa22=========	chr1:87791123-87791343(+)$1	220	28	59	11.3723
fff[ccc"""cccrrrrrrrrrcccccc]ff	chr8:123179808-123180028(-)$1	220	138	169	11.6396
==========ccclllccc]==========2	chr3:135128308-135128538(+)$1	230	86	117	13.3863
occciiiiiiiiiooooooiiiiiiiii:::	chr6:72382842-72383062(-)$1	220	171	202	11.2087
ggggggg####cccmmmmccc333ggggggg	chr8:12868183-12868403(+)$1	220	177	208	12.2264
####eeeee[cccooooooccc]eeeee444	chr16:91505903-91506123(+)$1	220	74	105	13.3559
ggggggg"""cccooooooccc22ggggggg	chr16:4040024-4040244(-)$1	220	115	146	15.7748
eeeeee$$$$$bboooooobb4444eeeeec	chr16:36932590-36932810(+)$1	220	96	127	11.6756
cc[dddd####ccclllccc333dddd]ccc	chr16:37835595-37835817(+)$1	222	87	118	10.5308
ggggg[gggggggoooooogggggggggggg	chr8:34729665-34729885(+)$1	220	48	79	13.8997
gggggg"""ddddoooooodddd333ggggg	chr18:34478854-34479076(+)$1	222	32	63	14.3072
dd!!==========nnnnn==========22	chr6:85893848-85894069(-)$1	221	173	204	12.5988
=============ppppppp===========	chr1:166193781-166194001(+)$1	220	58	89	12.0451
======####ddddmmmmdddd22=======	chr6:149258755-149258975(+)$1	220	125	156	12.0178
=============rrrrrrrrr=========	chr11:79847209-79847430(+)$1	221	13	44	13.9641
ccc[bb[ffffffooooooffffff]bb]cc	chr1:120195050-120195270(-)$1	220	24	55	10.5742
=============ppppppp===========	chr4:41661976-41662198(-)$1	222	124	155	12.0451
=========[cccmmmmccc]==========	chr4:102837353-102837573(+)$1	220	186	217	13.3749
eeee[bb"""cccoooooocccbb]eeeee]	chr6:120314524-120314744(+)$1	220	156	187	12.9984
=========[cccssssssssssccc=====	chr18:44579555-44579775(+)$1	220	143	174	11.5268
iiiiiiiii[cccooooooccciiiiiiiii	chr5:24092689-24092916(+)$1	227	0	31	16.2921
dddd####a[cccrrrrrrrrrccc]a4444	chr6:129492120-129492340(+)$1	220	154	185	11.2964
ccc"""gggggggooooooggggggg22ccc	chr2:168057488-168057708(+)$1	220	81	112	12.9529
b[bb[eeeee[bboooooobb333eeeee]b	chr14:119380188-119380429(+)$1	241	168	199	11.2263
e!!ffffff!!bboooooobb4444ffffff	chr2:131108276-131108496(+)$1	220	14	45	12.2105
#ggggggg!!ddddnnnnndddd]ggggggg	chr19:32894944-32895165(+)$1	221	21	52	11.0494
============qqqqqqqq===========	chr9:109795640-109795860(+)$1	220	188	219	12.1348
ddd!!ccc!!cccooooooccc]cccdddd]	chr11:102264595-102264815(-)$1	220	114	145	13.9436
"""ccc[a!!cccooooooccc]accc]fff	chr13:67807256-67807492(-)$1	236	152	183	14.8253
iiiiiii[a[a[bbmmmmbba]a]iiiiiii	chr3:108186694-108186914(+)$1	220	95	126	10.9156
ccc[ccc"""cccooooooccc333ccc]cc	chr10:5990964-5991184(-)$1	220	3	34	15.7210
ddd[dddd!!cccooooooccc22dddd333	chr10:74773716-74773936(+)$1	220	18	49	13.4212
=========[bbqqqqqqqqbb]========	chr12:73091916-73092149(+)$1	233	20	51	11.2447
=========!!ddddllldddd=========	chr17:34165636-34165856(-)$1	220	32	63	12.9017
a[ggggggg!!ccclllccc]ggggggg]a]	chr7:29959371-29959591(-)$1	220	93	124	11.9367
bffffff"""cccnnnnnccc333ffffff]	chr2:26875490-26875710(+)$1	220	161	192	10.9024
ffff!!ccc[cccoooooocccccc22ffff	chr2:103605972-103606192(-)$1	220	36	67	12.9220
!!ggggggg[ccclllcccggggggg]bb22	chr5:108777200-108777439(+)$1	239	45	76	10.6872
e[ccc[ccc[ccclllccc]ccc]ccc]eee	chr18:56912265-56912495(+)$1	230	177	208	10.4421
dddd####eeeeeooooooeeeee]dddd]b	chr7:120049603-120049836(+)$1	233	26	57	10.6455
d!!dddd[eeeeeooooooeeeee333dddd	chr18:65783023-65783243(+)$1	220	135	166	10.8299
===[a####ddddoooooodddd22a]====	chr5:116096511-116096738(+)$1	227	142	173	14.2013
!!dddd"""ddddoooooodddddddd]bb4	chr7:134166240-134166489(-)$1	249	206	237	11.7628
iiiiccciiiiiiiiillliiiiiiiii333	chr12:81209035-81209263(-)$1	228	30	61	11.6194
dffffff!!ddddoooooodddd4444ffff	chr7:36560082-36560302(-)$1	220	136	167	11.9018
$$$$ggggggg[aooooooa]gggggggccc	chr5:30597404-30597650(+)$1	246	19	50	13.0266
####ccc!!acccrrrrrrrrrccc]a22cc	chr9:20944147-20944367(-)$1	220	150	181	11.3903

#otherMatches

#Seq PSSM
GAUAAACAUGGCAAUCAAAUGUCCAUUGUUU	chr3:34550683-34550905(+)$1	222	81	112	12.2746
UAGAUGUCUGAAGGAAACGUGAACAUCUGGU	chr4:49525458-49525722(-)$1	264	19	50	12.5997
AAGAGCACAUUCCAUCCCAGGAAAUGUGCCU	chr7:137537312-137537532(-)$1	220	73	104	12.7021
CAGGGACAUUGUGUUCCCUCACUCCUGUUAC	chr5:8453730-8453950(+)$1	220	51	82	14.5392
GGUAGGGGGUGCCCCUACUGGUAGCCCUGCU	chr4:47426337-47426557(+)$1	220	129	160	15.6139
UUUUGUGAUGUGAUGACCUUCAAAUUGGAUC	chr13:24999671-24999891(-)$1	220	151	182	11.7131
GGUGCCUGCGGCGCAGCAAGAAGCAGGCAUU	chr1:87791123-87791343(+)$1	220	28	59	11.3723
UUUUAAACAUUCCAAAAAACUAGGAUUUUGA	chr8:123179808-123180028(-)$1	220	138	169	11.6396
UAACUGCUUUUAGAAACUGUAAAGUAGUUAC	chr3:135128308-135128538(+)$1	230	86	117	13.3863
GUGCCUUUCAGGAUCUAUUUUUUGGAGGUUU	chr6:72382842-72383062(-)$1	220	171	202	11.2087
GUUGGAAGUAUUAUGAAAGUGUGAUUCUAAU	chr8:12868183-12868403(+)$1	220	177	208	12.2264
AGGAGCUGGCGUUGUUUAAGAUCUCAGUGUG	chr16:91505903-91506123(+)$1	220	74	105	13.3559
ACACUGACAGCCAAGACACUGGAUUUAGUGU	chr16:4040024-4040244(-)$1	220	115	146	15.7748
AGAACUGACAAUGGACAGACAGCAAGGUUCG	chr16:36932590-36932810(+)$1	220	96	127	11.6756
CAAGACAAUUUGGCUCUGCCUAGUGUUCUGU	chr16:37835595-37835817(+)$1	222	87	118	10.5308
uuaaaauauauauauauacauauauauuuaa	chr8:34729665-34729885(+)$1	220	48	79	13.8997
UAUUUUAACUGAACUAGAUUUUAUCAAAAGU	chr18:34478854-34479076(+)$1	222	32	63	14.3072
UUUCUACAGUGUACUUUGUGUACACUGUGCU	chr6:85893848-85894069(-)$1	221	173	204	12.5988
UUCUUGGAUUGCUUAUGAGCAGUAAUUUAAG	chr1:166193781-166194001(+)$1	220	58	89	12.0451
GGUAAAAUUGUAUUUACAGGUAAGUUUGCCU	chr6:149258755-149258975(+)$1	220	125	156	12.0178
GAAGAUGUAGGUGUAGAAUUAUUGCUUAUGU	chr11:79847209-79847430(+)$1	221	13	44	13.9641
UUUCAGAUGCAAUGAACAAAUUGCACUUAAA	chr1:120195050-120195270(-)$1	220	24	55	10.5742
GCUCUGAGGUCAGGGUCAGGUUGACCUUAGA	chr4:41661976-41662198(-)$1	222	124	155	12.0451
GAGUUCUUGAAACUGUUGUUACAGGAACUUU	chr4:102837353-102837573(+)$1	220	186	217	13.3749
CCGAGUGCCCGGUCUUUGAGCCCAGUUGGGA	chr6:120314524-120314744(+)$1	220	156	187	12.9984
GUUUGAGAGGUGAGACUUUAAAAUCGCUUUU	chr18:44579555-44579775(+)$1	220	143	174	11.5268
GGCAGGACCUGAGAACCCGCUCGGUCCUGCU	chr5:24092689-24092916(+)$1	227	0	31	16.2921
CAGCUUCAGGUUCUGGUACUUUGAAGUCAAU	chr6:129492120-129492340(+)$1	220	154	185	11.2964
UUCGAGCUUUACAAAAUAAUGUAGGGAAGAG	chr2:168057488-168057708(+)$1	220	81	112	12.9529
CGACCUGCCUUACAGAUACGUCCUGGGUAAG	chr14:119380188-119380429(+)$1	241	168	199	11.2263
GUUUUAAAAAUACUACAUUGUUUGCUUUUAA	chr2:131108276-131108496(+)$1	220	14	45	12.2105
GUUUGCAGUUGGCUAAGGAAGUUUCUGCAGG	chr19:32894944-32895165(+)$1	221	21	52	11.0494
GUAAAUUUUGAAGUCAAAGGUUCAGAGUUUA	chr9:109795640-109795860(+)$1	220	188	219	12.1348
GGAUCAGGAGACUGAGCCAAGUGCCUUCCCU	chr11:102264595-102264815(-)$1	220	114	145	13.9436
caaugguggagcuagagaaaguacccaagga	chr13:67807256-67807492(-)$1	236	152	183	14.8253
UUCCUGCGUAGACUGUGAAGCGAGGUGGGGA	chr3:108186694-108186914(+)$1	220	95	126	10.9156
UCUGUCUGAGUACGAUGCGGUAGAGAGAGAG	chr10:5990964-5991184(-)$1	220	3	34	15.7210
GCUCCGGGAUACACUUGUUUGUCACCUGCAA	chr10:74773716-74773936(+)$1	220	18	49	13.4212
UGAAGUGAUCGCUGUUACGUGUUGUCAUUUU	chr12:73091916-73092149(+)$1	233	20	51	11.2447
GCAUCUCCACUGCAGUCACUGUUGGAGGUGC	chr17:34165636-34165856(-)$1	220	32	63	12.9017
AUUUGGGAGUUUGCGAAGCGUUUCCCAGUUG	chr7:29959371-29959591(-)$1	220	93	124	11.9367
CUGUUUCACUGGCACAUGGCUCCAGGGACAU	chr2:26875490-26875710(+)$1	220	161	192	10.9024
UGACUUACAUGGGGAUUGGUCCUGUUUGUCA	chr2:103605972-103606192(-)$1	220	36	67	12.9220
CCAUUUUAAAUACUAUGUAUUAAAAUUUCCC	chr5:108777200-108777439(+)$1	239	45	76	10.6872
CCUUUUUGACACUGAAAGUUUUGUAAAAGAA	chr18:56912265-56912495(+)$1	230	177	208	10.4421
GCGACUUCAUGGCUUCUCUGUUGUCUCGUGU	chr7:120049603-120049836(+)$1	233	26	57	10.6455
CAGCAGGACUUCGACAAACUGAAGGCACUUG	chr18:65783023-65783243(+)$1	220	135	166	10.8299
UAGGCGCUCUCCCUUCCAUGGGAAAGGCUGG	chr5:116096511-116096738(+)$1	227	142	173	14.2013
CAGAGGACAGCAGCAGCCACUGCCCUCACCU	chr7:134166240-134166489(-)$1	249	206	237	11.7628
UUGGuuauuuuauuuuaaaaaaaugaaaaau	chr12:81209035-81209263(-)$1	228	30	61	11.6194
CGAGGCCAACCUGGAUUAGCAGGACUGGGCC	chr7:36560082-36560302(-)$1	220	136	167	11.9018
UAUUGUGAUUUCCCUUUCAGAAAAUCAUUCU	chr5:30597404-30597650(+)$1	246	19	50	13.0266
CCCUAGCUCCCAACUUCUUCACUUGUGCUGC	chr9:20944147-20944367(-)$1	220	150	181	11.3903

#DB
.((((((((((((......)).))).)))))	chr3:34550683-34550905(+)$1	1	81	112	12.2746
(((((((.....(....)....)))))))))	chr4:49525458-49525722(-)$1	1	19	50	12.5997
(((.(((((((((......)).)))))))))	chr7:137537312-137537532(-)$1	1	73	104	12.7021
(((..(((..(((......)))...)))..)	chr5:8453730-8453950(+)$1	1	51	82	14.5392
(((((((..((((......)))).)))))))	chr4:47426337-47426557(+)$1	1	129	160	15.6139
...(.((((.(((......))).)))).)..	chr13:24999671-24999891(-)$1	1	151	182	11.7131
(((((((((..(.......)..)))))))))	chr1:87791123-87791343(+)$1	1	28	59	11.3723
(((.(((...(((.........)))))).))	chr8:123179808-123180028(-)$1	1	138	169	11.6396
(((((((((((((...))).)))))))))).	chr3:135128308-135128538(+)$1	1	86	117	13.3863
.)))(((((((((......)))))))))...	chr6:72382842-72383062(-)$1	1	171	202	11.2087
(((((((....(((....)))...)))))))	chr8:12868183-12868403(+)$1	1	177	208	12.2264
....(((((.(((......))).)))))...	chr16:91505903-91506123(+)$1	1	74	105	13.3559
(((((((...(((......)))..)))))))	chr16:4040024-4040244(-)$1	1	115	146	15.7748
)(((((.....((......))....)))))(	chr16:36932590-36932810(+)$1	1	96	127	11.6756
((.((((....(((...)))...)))).)))	chr16:37835595-37835817(+)$1	1	87	118	10.5308
(((((.(((((((......))))))))))))	chr8:34729665-34729885(+)$1	1	48	79	13.8997
((((((...((((......))))...)))))	chr18:34478854-34479076(+)$1	1	32	63	14.3072
((..((((((((((.....))))))))))..	chr6:85893848-85894069(-)$1	1	173	204	12.5988
(((((((((((((.......)))))))))))	chr1:166193781-166194001(+)$1	1	58	89	12.0451
((((((....((((....))))..)))))))	chr6:149258755-149258975(+)$1	1	125	156	12.0178
(((((((((((((.........)))))))))	chr11:79847209-79847430(+)$1	1	13	44	13.9641
(((.((.((((((......)))))).)).))	chr1:120195050-120195270(-)$1	1	24	55	10.5742
(((((((((((((.......)))))))))))	chr4:41661976-41662198(-)$1	1	124	155	12.0451
(((((((((.(((....))).))))))))))	chr4:102837353-102837573(+)$1	1	186	217	13.3749
((((.((...(((......))))).))))).	chr6:120314524-120314744(+)$1	1	156	187	12.9984
(((((((((.(((..........))))))))	chr18:44579555-44579775(+)$1	1	143	174	11.5268
(((((((((.(((......))))))))))))	chr5:24092689-24092916(+)$1	1	0	31	16.2921
((((....(.(((.........))).)....	chr6:129492120-129492340(+)$1	1	154	185	11.2964
(((...(((((((......)))))))..)))	chr2:168057488-168057708(+)$1	1	81	112	12.9529
(.((.(((((.((......))...))))).)	chr14:119380188-119380429(+)$1	1	168	199	11.2263
(..((((((..((......))....))))))	chr2:131108276-131108496(+)$1	1	14	45	12.2105
.(((((((..((((.....)))).)))))))	chr19:32894944-32895165(+)$1	1	21	52	11.0494
((((((((((((........)))))))))))	chr9:109795640-109795860(+)$1	1	188	219	12.1348
(((..(((..(((......))).))))))).	chr11:102264595-102264815(-)$1	1	114	145	13.9436
...(((.(..(((......))).)))).)))	chr13:67807256-67807492(-)$1	1	152	183	14.8253
(((((((.(.(.((....))).).)))))))	chr3:108186694-108186914(+)$1	1	95	126	10.9156
(((.(((...(((......)))...))).))	chr10:5990964-5991184(-)$1	1	3	34	15.7210
(((.((((..(((......)))..))))...	chr10:74773716-74773936(+)$1	1	18	49	13.4212
(((((((((.((........)).))))))))	chr12:73091916-73092149(+)$1	1	20	51	11.2447
(((((((((..((((...)))))))))))))	chr17:34165636-34165856(-)$1	1	32	63	12.9017
(.(((((((..(((...))).))))))).).	chr7:29959371-29959591(-)$1	1	93	124	11.9367
(((((((...(((.....)))...)))))).	chr2:26875490-26875710(+)$1	1	161	192	10.9024
((((..(((.(((......))))))..))))	chr2:103605972-103606192(-)$1	1	36	67	12.9220
..(((((((.(((...)))))))))).))..	chr5:108777200-108777439(+)$1	1	45	76	10.6872
(.(((.(((.(((...))).))).))).)))	chr18:56912265-56912495(+)$1	1	177	208	10.4421
((((....(((((......))))).)))).)	chr7:120049603-120049836(+)$1	1	26	57	10.6455
(..((((.(((((......)))))...))))	chr18:65783023-65783243(+)$1	1	135	166	10.8299
(((.(....((((......))))..).))))	chr5:116096511-116096738(+)$1	1	142	173	14.2013
..((((...((((......)))))))).)).	chr7:134166240-134166489(-)$1	1	206	237	11.7628
((((((((((((((((...)))))))))...	chr12:81209035-81209263(-)$1	1	30	61	11.6194
(((((((..((((......))))....))))	chr7:36560082-36560302(-)$1	1	136	167	11.9018
....(((((((.(......).))))))))))	chr5:30597404-30597650(+)$1	1	19	50	13.0266
....(((..((((.........))).)..))	chr9:20944147-20944367(-)$1	1	150	181	11.3903

#PSSM
= : 0.26	d : 0.16	g : 0.07	e : 0.07	c : 0.07	# : 0.05	i : 0.05	$ : 0.03	f : 0.03	b : 0.03	! : 0.03	: : 0.01	o : 0.01	" : 0.01	a : 0.01	
= : 0.26	d : 0.13	g : 0.11	c : 0.09	f : 0.07	! : 0.07	i : 0.05	[ : 0.05	$ : 0.03	# : 0.03	e : 0.03	" : 0.01	
= : 0.26	g : 0.15	d : 0.13	c : 0.09	f : 0.07	! : 0.05	i : 0.05	$ : 0.03	# : 0.03	e : 0.03	[ : 0.01	b : 0.01	" : 0.01	
= : 0.24	g : 0.15	[ : 0.11	d : 0.09	f : 0.07	! : 0.05	c : 0.05	i : 0.05	# : 0.03	e : 0.03	a : 0.01	" : 0.01	b : 0.01	$ : 0.01	
= : 0.26	g : 0.18	c : 0.11	d : 0.07	! : 0.05	[ : 0.05	i : 0.05	f : 0.05	e : 0.03	# : 0.03	b : 0.01	" : 0.01	a : 0.01	
= : 0.26	g : 0.16	c : 0.13	d : 0.09	i : 0.05	e : 0.05	# : 0.05	f : 0.05	[ : 0.03	b : 0.03	" : 0.01	! : 0.01	
= : 0.24	g : 0.18	c : 0.15	d : 0.07	# : 0.07	i : 0.05	f : 0.05	e : 0.03	" : 0.03	[ : 0.03	$ : 0.01	b : 0.01	
= : 0.20	g : 0.15	" : 0.13	# : 0.11	c : 0.07	! : 0.05	i : 0.05	$ : 0.03	d : 0.03	e : 0.03	f : 0.03	[ : 0.03	a : 0.01	
= : 0.20	! : 0.15	" : 0.13	g : 0.11	# : 0.07	e : 0.07	c : 0.05	i : 0.05	$ : 0.03	f : 0.03	a : 0.03	d : 0.01	
[ : 0.20	! : 0.16	= : 0.11	d : 0.09	" : 0.09	g : 0.07	# : 0.05	e : 0.05	$ : 0.03	i : 0.03	c : 0.01	f : 0.01	a : 0.01	
c : 0.39	d : 0.13	= : 0.09	g : 0.07	! : 0.07	$ : 0.03	i : 0.03	# : 0.03	e : 0.03	f : 0.01	[ : 0.01	a : 0.01	b : 0.01	
c : 0.43	d : 0.15	b : 0.11	= : 0.09	i : 0.03	g : 0.03	[ : 0.03	e : 0.03	$ : 0.01	a : 0.01	f : 0.01	
c : 0.43	d : 0.15	b : 0.11	= : 0.07	a : 0.03	i : 0.03	g : 0.03	q : 0.03	e : 0.03	p : 0.01	f : 0.01	
o : 0.52	r : 0.07	p : 0.05	l : 0.05	c : 0.05	d : 0.05	m : 0.03	q : 0.03	= : 0.01	s : 0.01	b : 0.01	n : 0.01	i : 0.01	
o : 0.52	m : 0.09	l : 0.09	r : 0.07	p : 0.05	n : 0.05	q : 0.03	s : 0.01	d : 0.01	i : 0.01	
o : 0.52	l : 0.11	m : 0.09	r : 0.07	p : 0.05	n : 0.05	q : 0.03	s : 0.01	i : 0.01	
o : 0.52	m : 0.09	r : 0.07	l : 0.07	p : 0.05	c : 0.05	n : 0.05	q : 0.03	s : 0.01	
o : 0.52	c : 0.11	r : 0.07	p : 0.05	m : 0.05	n : 0.05	q : 0.03	l : 0.03	a : 0.01	s : 0.01	
o : 0.52	c : 0.15	r : 0.07	p : 0.05	n : 0.03	d : 0.03	q : 0.03	4 : 0.01	s : 0.01	b : 0.01	l : 0.01	
c : 0.30	d : 0.15	b : 0.11	r : 0.07	g : 0.05	a : 0.03	] : 0.03	i : 0.03	p : 0.03	q : 0.03	e : 0.03	4 : 0.01	= : 0.01	f : 0.01	s : 0.01	
c : 0.26	d : 0.15	b : 0.11	= : 0.09	r : 0.07	g : 0.05	] : 0.05	i : 0.03	e : 0.03	4 : 0.01	2 : 0.01	3 : 0.01	f : 0.01	s : 0.01	a : 0.01	
c : 0.22	d : 0.15	= : 0.11	g : 0.09	r : 0.07	3 : 0.07	] : 0.05	4 : 0.05	i : 0.03	e : 0.03	2 : 0.01	f : 0.01	s : 0.01	b : 0.01	
= : 0.18	c : 0.11	g : 0.11	3 : 0.11	d : 0.11	] : 0.09	i : 0.05	2 : 0.05	4 : 0.03	e : 0.03	f : 0.01	b : 0.01	s : 0.01	a : 0.01	
= : 0.20	c : 0.13	g : 0.11	3 : 0.11	] : 0.07	2 : 0.07	d : 0.05	i : 0.05	e : 0.05	4 : 0.05	f : 0.01	b : 0.01	a : 0.01	
= : 0.24	c : 0.16	g : 0.16	3 : 0.07	d : 0.07	i : 0.07	4 : 0.05	e : 0.03	f : 0.03	] : 0.03	2 : 0.01	
= : 0.24	g : 0.16	c : 0.13	d : 0.09	] : 0.07	i : 0.07	e : 0.07	3 : 0.03	f : 0.03	2 : 0.01	a : 0.01	4 : 0.01	
= : 0.26	g : 0.16	d : 0.11	c : 0.09	i : 0.07	e : 0.07	a : 0.03	2 : 0.03	f : 0.03	] : 0.03	b : 0.01	3 : 0.01	4 : 0.01	
= : 0.28	g : 0.16	] : 0.09	i : 0.07	e : 0.07	f : 0.07	d : 0.07	c : 0.05	b : 0.03	2 : 0.03	4 : 0.01	
= : 0.28	g : 0.13	f : 0.09	] : 0.07	e : 0.07	c : 0.05	d : 0.05	2 : 0.03	4 : 0.03	i : 0.03	3 : 0.03	b : 0.03	a : 0.01	: : 0.01	
= : 0.26	g : 0.11	f : 0.11	c : 0.11	d : 0.05	2 : 0.05	e : 0.05	4 : 0.03	i : 0.03	] : 0.03	3 : 0.03	6 : 0.01	: : 0.01	a : 0.01	b : 0.01	
= : 0.24	c : 0.13	g : 0.11	f : 0.09	] : 0.07	d : 0.05	2 : 0.05	4 : 0.05	i : 0.03	b : 0.03	3 : 0.03	6 : 0.01	: : 0.01	e : 0.01	

#score	662.3712158714561
#seq	53
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_transcript_m1_run2.txt

#BEAR
eeee[bbuuuuuuuuuuuubbeeee	chr8:42426368-42426582(+)$1	214	60	85	23.4356
=====yyyyyyyyyyyyyyyy====	chr14:39641307-39641523(-)$1	216	100	125	24.0384
!eeeeexxxxxxxxxxxxxxxeeee	chr5:65558809-65559012(-)$1	203	7	32	19.9157
gddddyyyyyyyyyyyyyyyydddd	chr9:57380015-57380223(+)$1	208	21	46	22.8218
eeee[bbvvvvvvvvvvvvvbb22e	chr8:46911604-46911819(+)$1	215	32	57	22.5078
d:eeeeevvvvvvvvvvvvveeeee	chr2:25432157-25432362(-)$1	205	155	180	22.2127
hhhhhyyyyyyyyyyyyyyyyhhhh	chr13:17853924-17854147(-)$1	223	158	183	22.0503
"""ddddtttttttttttdddd333	chr8:113334379-113334605(-)$1	226	184	209	21.7586
iiiiiiiuuuuuuuuuuuuiiiiii	chr16:94369392-94369625(-)$1	233	10	35	24.0798
eeeee[auuuuuuuuuuuua]eeee	chrX:159377598-159377821(+)$1	223	115	140	24.0662
========ttttttttttt======	chr1:81333225-81333439(+)$1	214	161	186	22.8634
dd[bbbbwwwwwwwwwwwwwwbb22	chr1:13555061-13555264(-)$1	203	158	183	20.7935
gggggyyyyyyyyyyyyyyyygggg	chr2:32644734-32644934(-)$1	200	73	98	23.8105
ddd[cccuuuuuuuuuuuuccc444	chr3:97011187-97011391(-)$1	204	123	148	23.3684
deeeeewwwwwwwwwwwwwweeeee	chr4:109877511-109877715(+)$1	204	138	163	22.6790
ddddddddtttttttttttdddd]d	chr18:35414005-35414219(+)$1	214	66	91	21.3236
)))ddddvvvvvvvvvvvvvdddd0	chr6:112669881-112670084(-)$1	203	48	73	20.7500
h[eeeeevvvvvvvvvvvvveeeee	chr7:25807936-25808151(-)$1	215	116	141	23.3664
""eeeeevvvvvvvvvvvvveeeee	chr9:36686079-36686288(+)$1	209	76	101	23.5033
gggggggvvvvvvvvvvvvvggggg	chr19:28058962-28059178(-)$1	216	11	36	23.4755
gggdddduuuuuuuuuuuudddd]g	chr15:38418724-38418936(-)$1	212	18	43	23.6318
[ffffffuuuuuuuuuuuuffffff	chr1:155755334-155755536(+)$1	202	51	76	22.6871
ggggggguuuuuuuuuuuugggggg	chr2:28325676-28325878(+)$1	202	82	107	23.8198
hhhhhhhwwwwwwwwwwwwwwhhhh	chr8:98238439-98238640(-)$1	201	58	83	20.7775
dddd[bbvvvvvvvvvvvvvbb22d	chr14:65353371-65353578(+)$1	207	120	145	22.0334
cccc[bbtttttttttttbb]ccc]	chr9:64985501-64985701(+)$1	200	14	39	21.4023
====[bbvvvvvvvvvvvvvbb]==	chr17:84219928-84220128(+)$1	200	117	142	23.3431
fffffyyyyyyyyyyyyyyyyffff	chr3:9433999-9434209(-)$1	210	37	62	22.7979
iiiiiyyyyyyyyyyyyyyyyiiii	chr13:77382676-77382911(+)$1	235	59	84	23.8585
gggggggwwwwwwwwwwwwwwgggg	chr9:55983793-55983999(-)$1	206	39	64	22.9431
fffffyyyyyyyyyyyyyyyyffff	chr12:103979879-103980090(-)$1	211	102	127	22.7979
fffffyyyyyyyyyyyyyyyyffff	chr1:121805243-121805477(-)$1	234	113	138	22.7979
c!!eeeeettttttttttteeeee]	chr7:88414270-88414487(+)$1	217	170	195	22.3940
%%eeeeeuuuuuuuuuuuueeeee6	chr14:77956303-77956527(+)$1	224	26	51	22.0348
:ccc[bbuuuuuuuuuuuubb]ccc	chr4:41061567-41061775(-)$1	208	63	88	21.9779
[ddddyyyyyyyyyyyyyyyydddd	chr4:120640883-120641083(-)$1	200	120	145	22.8810
ddd[cccvvvvvvvvvvvvvccc]d	chr8:74874381-74874604(-)$1	223	108	133	22.8765
[a!!ddddtttttttttttdddd22	chr2:136607532-136607733(+)$1	201	28	53	21.7211
""eeeeeuuuuuuuuuuuueeeee3	chr4:119036393-119036620(-)$1	227	44	69	23.9382
bb[a[ccctttttttttttcccabb	chr10:111901470-111901681(+)$1	211	161	186	21.3245
gggg[bbwwwwwwwwwwwwwwbb]g	chr4:33139085-33139287(+)$1	202	122	147	22.4062
iiiiiiivvvvvvvvvvvvviiiii	chr6:108805665-108805895(+)$1	230	134	159	23.6621
!!eeeeeuuuuuuuuuuuueeeee2	chr9:107715148-107715373(-)$1	225	48	73	23.8865
]bbdddduuuuuuuuuuuudddd::	chr11:6008016-6008223(-)$1	207	73	98	20.3283
g[eeeeevvvvvvvvvvvvveeeee	chr12:73313191-73313391(-)$1	200	64	89	23.6099
b[ddddwwwwwwwwwwwwwwdddd]	chr8:97646619-97646837(-)$1	218	82	107	22.0805
=====yyyyyyyyyyyyyyyy====	chr13:81035079-81035288(+)$1	209	30	55	24.0384
ff[dddduuuuuuuuuuuudddd22	chr13:100192217-100192422(-)$1	205	113	138	23.0083
[ffffffuuuuuuuuuuuuffffff	chr11:115446193-115446407(-)$1	214	132	157	22.6871
ggg[cccuuuuuuuuuuuuccc]gg	chr5:33557125-33557345(-)$1	220	81	106	24.2337
gg"""ccctttttttttttccc]gg	chr3:83964725-83964926(-)$1	201	70	95	22.5652
:eeeeewwwwwwwwwwwwwweeeee	chr3:115415192-115415394(-)$1	202	111	136	21.8772
Geeeeewwwwwwwwwwwwwweeeee	chr2:117107534-117107739(-)$1	205	118	143	22.3970
ffff[ccctttttttttttccc]ff	chr7:105060004-105060204(+)$1	200	119	144	22.3160
!!eeeeevvvvvvvvvvvvveeeee	chr11:78140055-78140257(-)$1	202	144	169	23.6549
ggggggguuuuuuuuuuuugggggg	chr1:133924306-133924514(+)$1	208	58	83	23.8198
fffffyyyyyyyyyyyyyyyyffff	chr17:66844582-66844807(-)$1	225	35	60	22.7979
Ieeeeevvvvvvvvvvvvveeeeed	chr3:60431252-60431453(+)$1	201	11	36	21.4080
===[cccuuuuuuuuuuuuccc]==	chr17:66001028-66001230(-)$1	202	163	188	24.3584
gggg[ccctttttttttttccc22g	chrX:97697189-97697405(+)$1	216	86	111	22.7124
ffffffwwwwwwwwwwwwwwfffff	chr10:69448889-69449091(+)$1	202	37	62	21.7388
iiiiiiiwwwwwwwwwwwwwwiiii	chr5:115573942-115574174(-)$1	232	82	107	23.0960
iiiiiiiwwwwwwwwwwwwwwiiii	chr15:98635547-98635750(-)$1	203	43	68	23.0960
###ddddtttttttttttdddd22f	chr7:138486835-138487035(-)$1	200	76	101	21.2117
#ddddyyyyyyyyyyyyyyyydddd	chr15:82123659-82123865(+)$1	206	52	77	22.7752

#otherMatches

#Seq PSSM
UGAUUGCCCAUUAAAAUAAGUAUCA	chr8:42426368-42426582(+)$1	214	60	85	23.4356
GCUUGCUUGCCUGUCUCUUCUUAAG	chr14:39641307-39641523(-)$1	216	100	125	24.0384
AAAAGGACAAAACCAAAUAAACCUU	chr5:65558809-65559012(-)$1	203	7	32	19.9157
AGCACUUUACUGGCUAAUUCUGUGC	chr9:57380015-57380223(+)$1	208	21	46	22.8218
GCAGUUCAUUUUCUUUUCACGAGUU	chr8:46911604-46911819(+)$1	215	32	57	22.5078
GCUCUCCCCAAGCCAGUCAAGGAGA	chr2:25432157-25432362(-)$1	205	155	180	22.2127
aggaguuuauuuuuuuacauuuucc	chr13:17853924-17854147(-)$1	223	158	183	22.0503
CCUGAAUAUAUAAAACUAGUUUUUA	chr8:113334379-113334605(-)$1	226	184	209	21.7586
GAAGUUGGCAUGCUGGAAACAGCUU	chr16:94369392-94369625(-)$1	233	10	35	24.0798
CGUGCUCUCUCUCUCCCAUGCGUAU	chrX:159377598-159377821(+)$1	223	115	140	24.0662
UUCCAUAUAUUCUUUGUUGAUGUGG	chr1:81333225-81333439(+)$1	214	161	186	22.8634
CACCAGCUAAAAAAUGUCCGUGCCA	chr1:13555061-13555264(-)$1	203	158	183	20.7935
UAUGUAUCCCACAGUAAGUUCACAU	chr2:32644734-32644934(-)$1	200	73	98	23.8105
UCUAGCACACCUUAUCCCAUGCCUC	chr3:97011187-97011391(-)$1	204	123	148	23.3684
CAGCCCAAUUUUAUCAGCACGGGCU	chr4:109877511-109877715(+)$1	204	138	163	22.6790
AUUAUGACGCAUGGCUACAGUUACU	chr18:35414005-35414219(+)$1	214	66	91	21.3236
UCUGACUCCUGCCUGUUUUUAGUCC	chr6:112669881-112670084(-)$1	203	48	73	20.7500
CUGUCAGCUGUGUCUUGUUCCUGGC	chr7:25807936-25808151(-)$1	215	116	141	23.3664
UGUCCAACCUAACCUCAUCUUUGGA	chr9:36686079-36686288(+)$1	209	76	101	23.5033
CACACAAACACCUGUGAUUAUUGUG	chr19:28058962-28059178(-)$1	216	11	36	23.4755
CUUAGUAAUUCUUCCUUCGUACUAA	chr15:38418724-38418936(-)$1	212	18	43	23.6318
UGGAAUACCAAGGUCUUUUUAUUCC	chr1:155755334-155755536(+)$1	202	51	76	22.6871
AGACUUGAACAUAGCUAGCCAAGuu	chr2:28325676-28325878(+)$1	202	82	107	23.8198
auauCUUAAGAACACAGCAAAAAGA	chr8:98238439-98238640(-)$1	201	58	83	20.7775
gaucugcuuucucucucucugucug	chr14:65353371-65353578(+)$1	207	120	145	22.0334
GGAUGCCUUAAGUUCUUUGGAGUCU	chr9:64985501-64985701(+)$1	200	14	39	21.4023
CAGUAAGCCACCUUUUCUUCCUCAC	chr17:84219928-84220128(+)$1	200	117	142	23.3431
GUAAUCUUAAAUACAAUAAUAAUUA	chr3:9433999-9434209(-)$1	210	37	62	22.7979
aggucccauuugucaauucuugauc	chr13:77382676-77382911(+)$1	235	59	84	23.8585
GUCUUUGUUCAUCUUCAAAAUCAGA	chr9:55983793-55983999(-)$1	206	39	64	22.9431
GCUUCUAAAUAUCAUUUUCUUGGAG	chr12:103979879-103980090(-)$1	211	102	127	22.7979
GCUGACAACACUCUACAUCCCUCAG	chr1:121805243-121805477(-)$1	234	113	138	22.7979
AUAAGGCUUCGUUUGAUAUGGCCUC	chr7:88414270-88414487(+)$1	217	170	195	22.3940
GUGCACAAAUUUCGUUUAAUGUGUU	chr14:77956303-77956527(+)$1	224	26	51	22.0348
AGCCUGAUCCACAUCCCCUUCUGGC	chr4:41061567-41061775(-)$1	208	63	88	21.9779
UAUGUGUAAAUUCCUUAAUAAAUAU	chr4:120640883-120641083(-)$1	200	120	145	22.8810
GCUUCuguguauccuugagucagug	chr8:74874381-74874604(-)$1	223	108	133	22.8765
ACAAAGCAACAACUACGCAUGCUCA	chr2:136607532-136607733(+)$1	201	28	53	21.7211
ccaaaacuauuauugucuuguuuuu	chr4:119036393-119036620(-)$1	227	44	69	23.9382
GAAGCAGCAAUUCACCAUAGUUCUC	chr10:111901470-111901681(+)$1	211	161	186	21.3245
CAUGAGCCAACCGAACCUUCUGUAC	chr4:33139085-33139287(+)$1	202	122	147	22.4062
UGAUGUUGUUAAGCACAAUGGAUAU	chr6:108805665-108805895(+)$1	230	134	159	23.6621
uugagcaucucuacagcccUGCUUU	chr9:107715148-107715373(-)$1	225	48	73	23.8865
AGCCAUUUUUUUCUUUCAUGAUGAA	chr11:6008016-6008223(-)$1	207	73	98	20.3283
CAAGCACUAAAGUAUAGAGUGUGUU	chr12:73313191-73313391(-)$1	200	64	89	23.6099
cugcugucuucaaucuccuucagcu	chr8:97646619-97646837(-)$1	218	82	107	22.0805
UUUGAGAAACAAAGUGCAAUAUUAA	chr13:81035079-81035288(+)$1	209	30	55	24.0384
UAGGAGCUUUCUAAUACUCGUUUUA	chr13:100192217-100192422(-)$1	205	113	138	23.0083
GCUCCCCAUAAGCCUUUCAGGGGAG	chr11:115446193-115446407(-)$1	214	132	157	22.6871
GUCAUCCUGGGGACUGUGUGGAGGA	chr5:33557125-33557345(-)$1	220	81	106	24.2337
AACACAGCCUUAACCUCAUGCUUUU	chr3:83964725-83964926(-)$1	201	70	95	22.5652
CGUGCUCCCGCUCUACCACAAGCAC	chr3:115415192-115415394(-)$1	202	111	136	21.8772
CAGGCCAACUUAUAGCUCUAGGUCU	chr2:117107534-117107739(-)$1	205	118	143	22.3970
AUUUGAAAACCAUAACAGCUUUGAA	chr7:105060004-105060204(+)$1	200	119	144	22.3160
UGGUGGAGACAGGAAAAAGGUCCAC	chr11:78140055-78140257(-)$1	202	144	169	23.6549
UUCCCGUUAAUUCUUUCUCAUGGGG	chr1:133924306-133924514(+)$1	208	58	83	23.8198
GGAGAGAAGAAAGAUGUAAUAUUUC	chr17:66844582-66844807(-)$1	225	35	60	22.7979
GAGACACAAUAACAAAAAAUGUUUG	chr3:60431252-60431453(+)$1	201	11	36	21.4080
UGAGUGUCCUUUCCUCAUUACAGUC	chr17:66001028-66001230(-)$1	202	163	188	24.3584
AGCAUGGCAUUUCGACUUGGCUUCU	chrX:97697189-97697405(+)$1	216	86	111	22.7124
CGGCUCCAAUCACAGUGCCCGGGCC	chr10:69448889-69449091(+)$1	202	37	62	21.7388
AGAGUACUUGAGAGAAAGGAUGUGC	chr5:115573942-115574174(-)$1	232	82	107	23.0960
GCGAUGCCCCUCUUUGUUCUCGUGU	chr15:98635547-98635750(-)$1	203	43	68	23.0960
UCCGUGCUUGUUUGCAUUGCGCUUG	chr7:138486835-138487035(-)$1	200	76	101	21.2117
CCAGCCACCCCCUGCCCCACUGCUG	chr15:82123659-82123865(+)$1	206	52	77	22.7752

#DB
((((.((............))))))	chr8:42426368-42426582(+)$1	1	60	85	23.4356
(((((................))))	chr14:39641307-39641523(-)$1	1	100	125	24.0384
.(((((...............))))	chr5:65558809-65559012(-)$1	1	7	32	19.9157
)((((................))))	chr9:57380015-57380223(+)$1	1	21	46	22.8218
((((.((.............))..)	chr8:46911604-46911819(+)$1	1	32	57	22.5078
).(((((.............)))))	chr2:25432157-25432362(-)$1	1	155	180	22.2127
(((((................))))	chr13:17853924-17854147(-)$1	1	158	183	22.0503
...((((...........))))...	chr8:113334379-113334605(-)$1	1	184	209	21.7586
(((((((............))))))	chr16:94369392-94369625(-)$1	1	10	35	24.0798
(((((.(............).))))	chrX:159377598-159377821(+)$1	1	115	140	24.0662
((((((((...........))))))	chr1:81333225-81333439(+)$1	1	161	186	22.8634
((.((((..............))..	chr1:13555061-13555264(-)$1	1	158	183	20.7935
(((((................))))	chr2:32644734-32644934(-)$1	1	73	98	23.8105
(((.(((............)))...	chr3:97011187-97011391(-)$1	1	123	148	23.3684
)(((((..............)))))	chr4:109877511-109877715(+)$1	1	138	163	22.6790
((((((((...........)))).)	chr18:35414005-35414219(+)$1	1	66	91	21.3236
...((((.............)))).	chr6:112669881-112670084(-)$1	1	48	73	20.7500
(.(((((.............)))))	chr7:25807936-25808151(-)$1	1	116	141	23.3664
..(((((.............)))))	chr9:36686079-36686288(+)$1	1	76	101	23.5033
(((((((.............)))))	chr19:28058962-28059178(-)$1	1	11	36	23.4755
(((((((............)))).)	chr15:38418724-38418936(-)$1	1	18	43	23.6318
.((((((............))))))	chr1:155755334-155755536(+)$1	1	51	76	22.6871
(((((((............))))))	chr2:28325676-28325878(+)$1	1	82	107	23.8198
(((((((..............))))	chr8:98238439-98238640(-)$1	1	58	83	20.7775
((((.((.............))..)	chr14:65353371-65353578(+)$1	1	120	145	22.0334
((((.((...........)).))).	chr9:64985501-64985701(+)$1	1	14	39	21.4023
((((.((.............)).))	chr17:84219928-84220128(+)$1	1	117	142	23.3431
(((((................))))	chr3:9433999-9434209(-)$1	1	37	62	22.7979
(((((................))))	chr13:77382676-77382911(+)$1	1	59	84	23.8585
(((((((..............))))	chr9:55983793-55983999(-)$1	1	39	64	22.9431
(((((................))))	chr12:103979879-103980090(-)$1	1	102	127	22.7979
(((((................))))	chr1:121805243-121805477(-)$1	1	113	138	22.7979
(..(((((...........))))).	chr7:88414270-88414487(+)$1	1	170	195	22.3940
..(((((............))))).	chr14:77956303-77956527(+)$1	1	26	51	22.0348
.(((.((............)).)))	chr4:41061567-41061775(-)$1	1	63	88	21.9779
.((((................))))	chr4:120640883-120641083(-)$1	1	120	145	22.8810
(((.(((.............))).)	chr8:74874381-74874604(-)$1	1	108	133	22.8765
.(..((((...........))))..	chr2:136607532-136607733(+)$1	1	28	53	21.7211
..(((((............))))).	chr4:119036393-119036620(-)$1	1	44	69	23.9382
((.(.(((...........))))))	chr10:111901470-111901681(+)$1	1	161	186	21.3245
((((.((..............)).)	chr4:33139085-33139287(+)$1	1	122	147	22.4062
(((((((.............)))))	chr6:108805665-108805895(+)$1	1	134	159	23.6621
..(((((............))))).	chr9:107715148-107715373(-)$1	1	48	73	23.8865
.))((((............))))..	chr11:6008016-6008223(-)$1	1	73	98	20.3283
(.(((((.............)))))	chr12:73313191-73313391(-)$1	1	64	89	23.6099
(.((((..............)))).	chr8:97646619-97646837(-)$1	1	82	107	22.0805
(((((................))))	chr13:81035079-81035288(+)$1	1	30	55	24.0384
((.((((............))))..	chr13:100192217-100192422(-)$1	1	113	138	23.0083
.((((((............))))))	chr11:115446193-115446407(-)$1	1	132	157	22.6871
(((.(((............))).))	chr5:33557125-33557345(-)$1	1	81	106	24.2337
((...(((...........))).))	chr3:83964725-83964926(-)$1	1	70	95	22.5652
.(((((..............)))))	chr3:115415192-115415394(-)$1	1	111	136	21.8772
((((((..............)))))	chr2:117107534-117107739(-)$1	1	118	143	22.3970
((((.(((...........))).))	chr7:105060004-105060204(+)$1	1	119	144	22.3160
..(((((.............)))))	chr11:78140055-78140257(-)$1	1	144	169	23.6549
(((((((............))))))	chr1:133924306-133924514(+)$1	1	58	83	23.8198
(((((................))))	chr17:66844582-66844807(-)$1	1	35	60	22.7979
((((((.............)))))(	chr3:60431252-60431453(+)$1	1	11	36	21.4080
(((.(((............))).))	chr17:66001028-66001230(-)$1	1	163	188	24.3584
((((.(((...........)))..)	chrX:97697189-97697405(+)$1	1	86	111	22.7124
((((((..............)))))	chr10:69448889-69449091(+)$1	1	37	62	21.7388
(((((((..............))))	chr5:115573942-115574174(-)$1	1	82	107	23.0960
(((((((..............))))	chr15:98635547-98635750(-)$1	1	43	68	23.0960
...((((...........))))..)	chr7:138486835-138487035(-)$1	1	76	101	21.2117
.((((................))))	chr15:82123659-82123865(+)$1	1	52	77	22.7752

#PSSM
g : 0.18	d : 0.10	f : 0.10	= : 0.07	i : 0.07	[ : 0.06	e : 0.04	! : 0.04	h : 0.04	" : 0.04	c : 0.03	: : 0.03	b : 0.03	# : 0.03	) : 0.01	% : 0.01	] : 0.01	G : 0.01	I : 0.01	
g : 0.15	f : 0.13	e : 0.12	d : 0.12	= : 0.07	i : 0.07	" : 0.04	[ : 0.04	! : 0.04	h : 0.03	c : 0.03	b : 0.03	: : 0.01	) : 0.01	% : 0.01	a : 0.01	# : 0.01	
e : 0.24	g : 0.13	d : 0.12	f : 0.12	= : 0.07	i : 0.07	[ : 0.04	h : 0.03	" : 0.03	c : 0.03	! : 0.03	) : 0.01	b : 0.01	# : 0.01	
e : 0.26	d : 0.18	f : 0.12	g : 0.10	i : 0.07	= : 0.06	[ : 0.06	h : 0.03	c : 0.03	b : 0.01	! : 0.01	a : 0.01	" : 0.01	
e : 0.23	d : 0.18	[ : 0.15	f : 0.10	i : 0.07	g : 0.07	c : 0.06	= : 0.04	h : 0.03	b : 0.01	" : 0.01	
e : 0.21	y : 0.18	d : 0.13	b : 0.12	c : 0.12	i : 0.06	g : 0.06	f : 0.04	[ : 0.01	= : 0.01	h : 0.01	
y : 0.18	e : 0.13	b : 0.12	d : 0.12	c : 0.12	w : 0.07	i : 0.06	g : 0.06	f : 0.03	x : 0.01	a : 0.01	= : 0.01	h : 0.01	v : 0.01	
u : 0.26	v : 0.20	y : 0.18	w : 0.16	c : 0.06	t : 0.04	d : 0.03	x : 0.01	= : 0.01	e : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	t : 0.16	w : 0.16	x : 0.01	
u : 0.26	v : 0.20	y : 0.18	w : 0.16	t : 0.12	d : 0.03	x : 0.01	b : 0.01	
y : 0.18	v : 0.18	w : 0.16	d : 0.10	c : 0.10	e : 0.07	b : 0.04	f : 0.03	g : 0.03	x : 0.01	i : 0.01	a : 0.01	= : 0.01	
e : 0.20	y : 0.18	d : 0.13	c : 0.12	w : 0.09	b : 0.07	g : 0.04	f : 0.04	i : 0.03	] : 0.03	x : 0.01	= : 0.01	
e : 0.24	d : 0.18	c : 0.13	f : 0.10	b : 0.07	i : 0.07	g : 0.07	= : 0.04	h : 0.03	] : 0.01	
e : 0.24	d : 0.15	f : 0.10	i : 0.07	g : 0.07	] : 0.07	2 : 0.06	= : 0.04	c : 0.04	h : 0.03	b : 0.03	3 : 0.01	4 : 0.01	a : 0.01	
e : 0.24	f : 0.12	2 : 0.10	g : 0.10	= : 0.07	d : 0.07	i : 0.07	] : 0.06	h : 0.03	c : 0.03	3 : 0.01	4 : 0.01	b : 0.01	: : 0.01	
e : 0.18	g : 0.15	f : 0.13	d : 0.10	= : 0.07	i : 0.07	2 : 0.06	] : 0.04	h : 0.03	3 : 0.03	4 : 0.01	0 : 0.01	6 : 0.01	c : 0.01	b : 0.01	: : 0.01	

#score	1474.6274467016767
#seq	65
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_CDS_m1_run2.txt

#BEAR
"dddd[bbpppppppbb]dddda	chr7:135038924-135039193(-)$1	269	99	122	11.6910
ccc[ddddrrrrrrrrrddddcc	chr5:123244330-123244627(-)$1	297	80	103	10.8498
!!bb[bbrrrrrrrrrbb]bb22	chr5:108863240-108863508(-)$1	268	147	170	10.5418
bb!!cccqqqqqqqqccc]bb33	chr9:107159265-107159531(-)$1	266	50	73	7.6698
:ccc[cccpppppppccc]ccc:	chr19:5384494-5384771(-)$1	277	0	23	12.7609
[ccc!!cccooooooccc]ccc2	chr11:97574608-97574878(+)$1	270	61	84	7.4916
ccffffffpppppppffffff]c	chr3:96066825-96067098(-)$1	273	114	137	12.3321
ccc[ddddrrrrrrrrrdddd22	chr7:25670028-25670303(+)$1	275	187	210	11.2135
""ffffffpppppppffffffdd	chr16:36049850-36050132(-)$1	282	216	239	12.2715
nnccccccpppppppccc:dddd	chr8:23489736-23490016(-)$1	280	59	82	11.2570
%%%%ddddpppppppdddddddd	chr8:86770433-86770706(-)$1	273	150	173	10.1452
fff[bb[arrrrrrrrra]bb33	chr4:155331129-155331405(+)$1	276	52	75	11.0519
ffff[cccssssssssssccc33	chr6:51413975-51414275(-)$1	300	250	273	7.5896
$$$$$cccpppppppccc333cc	chr9:66220026-66220300(+)$1	274	217	240	13.9300
""ffffffpppppppffffff33	chr3:95464614-95464908(+)$1	294	130	153	13.3584
dd[eeeeepppppppeeeee]dd	chr19:7273742-7274025(-)$1	283	135	158	11.1358
fff!!cccpppppppccc22fff	chr3:154259844-154260110(-)$1	266	41	64	12.9259
b[ccc[cccooooooccc]ccc]	chr7:28151313-28151603(-)$1	290	131	154	7.2755
b!!bb[bbpppppppbb]bb22b	chr2:32092890-32093158(+)$1	268	131	154	11.3275
ddddddddrrrrrrrrrdddd::	chr7:52631892-52632163(-)$1	271	155	178	8.3574
:eeeeerrrrrrrrreeeeeccc	chr6:22240953-22241221(+)$1	268	68	91	8.8146
ddffffffpppppppffffff22	chr1:184398225-184398498(-)$1	273	85	108	12.2657
hhh!!cccrrrrrrrrrccc333	chr16:91227498-91227771(+)$1	273	104	127	11.9358
"""eeeeepppppppeeeee333	chr14:45912564-45912838(-)$1	274	78	101	13.0409
ddd!!cccpppppppccc]dddd	chr4:45372561-45372833(+)$1	272	148	171	13.3830
bb[cccrrrrrrrrrccc]bb33	chr18:24743679-24743949(-)$1	270	80	103	11.7225
e####cccpppppppccc88888	chr8:74844691-74844960(+)$1	269	188	211	12.4506
:ccc[abbpppppppbb]a]ccc	chr18:60859085-60859370(-)$1	285	114	137	11.8405
fffffcccpppppppccc333ff	chr6:56728726-56729000(-)$1	274	209	232	13.1442
%%%%%cccpppppppccc4444g	chr11:102978337-102978633(+)$1	296	154	177	12.0097
b[ccc[bbpppppppbb333ccc	chr9:97269861-97270130(-)$1	269	162	185	12.9156
ccc[ddddrrrrrrrrrdddd]c	chr5:138223490-138223786(-)$1	296	83	106	10.9768

#otherMatches

#Seq PSSM
UGGGCACCACCUGGAGGAGCCCU	chr7:135038924-135039193(-)$1	269	99	122	11.6910
ACUCGGCAGAACUGGCAUGCCAG	chr5:123244330-123244627(-)$1	297	80	103	10.8498
UCUCUCCACUCAUCAAGGUGAAU	chr5:108863240-108863508(-)$1	268	147	170	10.5418
CCUUCUAGCAAUCCAUGGUGGUC	chr9:107159265-107159531(-)$1	266	50	73	7.6698
GGCUGGGAGAACACAUCUGGGUU	chr19:5384494-5384771(-)$1	277	0	23	12.7609
CAGUAGACGUGACUCUGUGACUU	chr11:97574608-97574878(+)$1	270	61	84	7.4916
GUCACCGCUAUGGAUGUGGUGUA	chr3:96066825-96067098(-)$1	273	114	137	12.3321
UCCUCAAAAAGUAAGUGUUUGUU	chr7:25670028-25670303(+)$1	275	187	210	11.2135
GCUGGGCCUGUAUUCGGCCUGCA	chr16:36049850-36050132(-)$1	282	216	239	12.2715
UACCACCUAAAACAAAGGACCAC	chr8:23489736-23490016(-)$1	280	59	82	11.2570
GACGUGGUAAUGAAGGCCAGCUC	chr8:86770433-86770706(-)$1	273	150	173	10.1452
UCUCUCAGGAAAUUAAACAGAAA	chr4:155331129-155331405(+)$1	276	52	75	11.0519
AUCUCAGAAAGCGAGGAAUCUAA	chr6:51413975-51414275(-)$1	300	250	273	7.5896
CAAAUGAAAGCAAGAUUCCUCCU	chr9:66220026-66220300(+)$1	274	217	240	13.9300
AGCCUUGUGAGUGCAAUAGGGGA	chr3:95464614-95464908(+)$1	294	130	153	13.3584
GCCGGACUGUUAAGGAGUUCUGC	chr19:7273742-7274025(-)$1	283	135	158	11.1358
UGGCGGCAAUAUGGCUGCGCCCA	chr3:154259844-154260110(-)$1	266	41	64	12.9259
GAGGUGUCGGAGAAGUGGGACCG	chr7:28151313-28151603(-)$1	290	131	154	7.2755
GGGCUGUGGUGUAAGUAGAGAUC	chr2:32092890-32093158(+)$1	268	131	154	11.3275
GCCCCAGAGAAUGGAUAUCUGAU	chr7:52631892-52632163(-)$1	271	155	178	8.3574
ACCACCUUGCAGAAUGGUGGCUC	chr6:22240953-22241221(+)$1	268	68	91	8.8146
CAACGCUCCCUGAAUGAGUGUUU	chr1:184398225-184398498(-)$1	273	85	108	12.2657
CCGACGCCAAGUGAGCCGGCCAG	chr16:91227498-91227771(+)$1	273	104	127	11.9358
CUGAGGAACUUGUACUUCCUGUA	chr14:45912564-45912838(-)$1	274	78	101	13.0409
CCAAAGUAUGCACUUUACAUGGU	chr4:45372561-45372833(+)$1	272	148	171	13.3830
GGGGCUGCAAGAACAAGUGCCAU	chr18:24743679-24743949(-)$1	270	80	103	11.7225
CCCUUGCAAACAGACUGCUAUUU	chr8:74844691-74844960(+)$1	269	188	211	12.4506
CCUGGACCAACCUGAGGCUGCAG	chr18:60859085-60859370(-)$1	285	114	137	11.8405
UAAAAAUCUAUCUUUGAUACAUU	chr6:56728726-56729000(-)$1	274	209	232	13.1442
AGAAGGGCGAGAAGGGCCAGAAU	chr11:102978337-102978633(+)$1	296	154	177	12.0097
UUACCAUCACAUUCAGAAAGGGU	chr9:97269861-97270130(-)$1	269	162	185	12.9156
GUCCUGUGUACUUGUUCCACAAG	chr5:138223490-138223786(-)$1	296	83	106	10.9768

#DB
.((((.((.......)).)))))	chr7:135038924-135039193(-)$1	1	99	122	11.6910
(((.((((.........))))))	chr5:123244330-123244627(-)$1	1	80	103	10.8498
..((.((.........)).))..	chr5:108863240-108863508(-)$1	1	147	170	10.5418
((..(((........))).))..	chr9:107159265-107159531(-)$1	1	50	73	7.6698
.(((.(((.......))).))).	chr19:5384494-5384771(-)$1	1	0	23	12.7609
.(((..(((......))).))).	chr11:97574608-97574878(+)$1	1	61	84	7.4916
((((((((.......)))))).)	chr3:96066825-96067098(-)$1	1	114	137	12.3321
(((.((((.........))))..	chr7:25670028-25670303(+)$1	1	187	210	11.2135
..((((((.......))))))))	chr16:36049850-36050132(-)$1	1	216	239	12.2715
..)))(((.......))).((((	chr8:23489736-23490016(-)$1	1	59	82	11.2570
....((((.......))))))))	chr8:86770433-86770706(-)$1	1	150	173	10.1452
(((.((.(.........).))..	chr4:155331129-155331405(+)$1	1	52	75	11.0519
((((.(((..........)))..	chr6:51413975-51414275(-)$1	1	250	273	7.5896
.....(((.......)))...))	chr9:66220026-66220300(+)$1	1	217	240	13.9300
..((((((.......))))))..	chr3:95464614-95464908(+)$1	1	130	153	13.3584
((.(((((.......))))).))	chr19:7273742-7274025(-)$1	1	135	158	11.1358
(((..(((.......)))..)))	chr3:154259844-154260110(-)$1	1	41	64	12.9259
(.(((.(((......))).))).	chr7:28151313-28151603(-)$1	1	131	154	7.2755
(..((.((.......)).))..)	chr2:32092890-32093158(+)$1	1	131	154	11.3275
))))((((.........))))..	chr7:52631892-52632163(-)$1	1	155	178	8.3574
.(((((.........)))))(((	chr6:22240953-22241221(+)$1	1	68	91	8.8146
((((((((.......))))))..	chr1:184398225-184398498(-)$1	1	85	108	12.2657
(((..(((.........)))...	chr16:91227498-91227771(+)$1	1	104	127	11.9358
...(((((.......)))))...	chr14:45912564-45912838(-)$1	1	78	101	13.0409
(((..(((.......))).))))	chr4:45372561-45372833(+)$1	1	148	171	13.3830
((.(((.........))).))..	chr18:24743679-24743949(-)$1	1	80	103	11.7225
(....(((.......))).....	chr8:74844691-74844960(+)$1	1	188	211	12.4506
.(((.(((.......)).).)))	chr18:60859085-60859370(-)$1	1	114	137	11.8405
((((((((.......)))...))	chr6:56728726-56729000(-)$1	1	209	232	13.1442
.....(((.......)))....)	chr11:102978337-102978633(+)$1	1	154	177	12.0097
(.(((.((.......))...)))	chr9:97269861-97270130(-)$1	1	162	185	12.9156
(((.((((.........)))).)	chr5:138223490-138223786(-)$1	1	83	106	10.9768

#PSSM
b : 0.15	" : 0.12	c : 0.12	f : 0.12	d : 0.12	: : 0.09	% : 0.06	! : 0.03	[ : 0.03	n : 0.03	$ : 0.03	h : 0.03	e : 0.03	
c : 0.21	d : 0.15	f : 0.12	" : 0.09	! : 0.06	b : 0.06	% : 0.06	[ : 0.06	n : 0.03	$ : 0.03	e : 0.03	h : 0.03	# : 0.03	
c : 0.28	f : 0.25	d : 0.09	! : 0.06	% : 0.06	[ : 0.06	b : 0.03	$ : 0.03	e : 0.03	h : 0.03	" : 0.03	# : 0.03	
c : 0.21	f : 0.18	[ : 0.12	! : 0.12	e : 0.09	d : 0.06	b : 0.06	% : 0.06	$ : 0.03	# : 0.03	
d : 0.18	c : 0.15	f : 0.15	[ : 0.12	! : 0.12	e : 0.09	b : 0.06	$ : 0.03	# : 0.03	% : 0.03	
c : 0.37	d : 0.15	[ : 0.12	f : 0.12	e : 0.09	b : 0.06	! : 0.03	a : 0.03	
c : 0.40	b : 0.15	d : 0.15	f : 0.12	e : 0.06	r : 0.06	[ : 0.03	
c : 0.37	d : 0.15	b : 0.12	f : 0.12	r : 0.09	e : 0.06	q : 0.03	a : 0.03	
p : 0.59	r : 0.28	c : 0.06	q : 0.03	s : 0.03	
p : 0.59	r : 0.28	o : 0.06	q : 0.03	s : 0.03	
p : 0.59	r : 0.28	o : 0.06	q : 0.03	s : 0.03	
p : 0.59	r : 0.28	o : 0.06	q : 0.03	s : 0.03	
p : 0.59	r : 0.28	o : 0.06	q : 0.03	s : 0.03	
p : 0.59	r : 0.28	o : 0.06	q : 0.03	s : 0.03	
p : 0.59	r : 0.28	o : 0.06	q : 0.03	s : 0.03	
c : 0.37	r : 0.21	b : 0.12	f : 0.12	e : 0.09	d : 0.03	s : 0.03	
c : 0.37	r : 0.18	b : 0.15	f : 0.12	e : 0.09	d : 0.03	s : 0.03	
c : 0.40	d : 0.15	f : 0.12	] : 0.09	e : 0.09	b : 0.03	a : 0.03	s : 0.03	3 : 0.03	
] : 0.25	d : 0.18	f : 0.12	3 : 0.09	e : 0.09	c : 0.06	: : 0.03	2 : 0.03	b : 0.03	8 : 0.03	a : 0.03	4 : 0.03	
d : 0.25	b : 0.15	c : 0.15	f : 0.12	3 : 0.09	e : 0.09	2 : 0.03	8 : 0.03	] : 0.03	4 : 0.03	
d : 0.25	c : 0.21	f : 0.15	b : 0.12	3 : 0.12	] : 0.03	2 : 0.03	8 : 0.03	4 : 0.03	
c : 0.25	3 : 0.21	d : 0.18	2 : 0.12	] : 0.06	f : 0.06	: : 0.03	8 : 0.03	4 : 0.03	
c : 0.21	3 : 0.21	d : 0.15	2 : 0.12	: : 0.06	f : 0.06	a : 0.03	] : 0.03	b : 0.03	8 : 0.03	g : 0.03	

#score	359.6776179011907
#seq	32
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_CDS_m1_run2.txt

#BEAR
eeeeevvvvvvvvvvvvveeeee	chr1:178686355-178686556(-)$1	201	119	142	20.2654
fffffxxxxxxxxxxxxxxxfff	chr16:37094510-37094711(-)$1	201	58	81	20.1477
e[ccc^^^^^^^^^^^^^^^^^^	chr12:86275471-86275672(-)$1	201	81	104	20.0900
eee^^^^^^^^^^^^^^^^^^^e	chrX:70925756-70925957(+)$1	201	84	107	19.9181
$$cccuuuuuuuuuuuuccc444	chr3:26032131-26032332(-)$1	201	21	44	19.7156
!!eeeeeuuuuuuuuuuuueeee	chr1:34284737-34284938(+)$1	201	43	66	20.2959
d[cccwwwwwwwwwwwwwwcccd	chr17:23952389-23952590(+)$1	201	25	48	22.4749
cccccwwwwwwwwwwwwwwcccD	chr1:84790282-84790483(-)$1	201	143	166	21.3113
^^^^^^^^^^^^^^^^^^^dddd	chr16:33726705-33726906(+)$1	201	68	91	19.2280
ccc^^^^^^^^^^^^^^^^^^cc	chr1:183852313-183852514(-)$1	201	144	167	19.9120
%%dddduuuuuuuuuuuudddd6	chr19:41330650-41330851(-)$1	201	82	105	18.0810
eeeeewwwwwwwwwwwwwweeee	chr5:150561969-150562170(+)$1	201	89	112	22.0049
:eeeeeuuuuuuuuuuuueeeee	chr8:108632384-108632585(+)$1	201	136	159	19.0798
"""bbwwwwwwwwwwwwwwbb44	chr17:55637457-55637658(+)$1	201	145	168	21.2747
d[a^^^^^^^^^^^^^^^^^^^^	chr15:4043974-4044175(+)$1	201	9	32	20.0551
iiiiiiiuuuuuuuuuuuuiiii	chr1:164637898-164638099(-)$1	201	157	180	18.9246
[ddddxxxxxxxxxxxxxxxddd	chr10:126935966-126936167(+)$1	201	110	133	20.3066
d^^^^^^^^^^^^^^^^^^dddd	chr10:120362398-120362599(-)$1	201	57	80	19.1845
fffffxxxxxxxxxxxxxxxfff	chr8:97948472-97948673(-)$1	201	122	145	20.1477
eeeeewwwwwwwwwwwwwweeee	chr8:23176224-23176425(+)$1	201	76	99	22.0049
fffffyyyyyyyyyyyyyyyyff	chr8:96490727-96490928(+)$1	201	15	38	20.5413
ffffffuuuuuuuuuuuufffff	chr3:108198902-108199103(-)$1	201	11	34	19.1109
::cccwwwwwwwwwwwwwwccc:	chr3:87860546-87860747(-)$1	201	86	109	19.5465
ggggggguuuuuuuuuuuugggg	chr11:55123815-55124016(-)$1	201	115	138	19.1801
c[cccvvvvvvvvvvvvvccc22	chr15:37939336-37939537(-)$1	201	12	35	20.4438
ee^^^^^^^^^^^^^^^^^^^^^	chr2:28085031-28085232(+)$1	201	86	109	19.9039
[dddd^^^^^^^^^^^^^^^^^^	chr12:54240669-54240870(+)$1	201	87	110	19.4245
!!cccxxxxxxxxxxxxxxxccc	chr5:89628699-89628900(+)$1	201	167	190	21.3002
d!!cccuuuuuuuuuuuuccc22	chr17:80251933-80252134(-)$1	201	52	75	20.1384
!dddd^^^^^^^^^^^^^^^^^^	chr9:54294249-54294450(-)$1	201	40	63	19.4515
a[cccwwwwwwwwwwwwwwccc]	chr15:59162365-59162566(+)$1	201	50	73	22.5670
eeeeewwwwwwwwwwwwwweeee	chr13:90237876-90238077(+)$1	201	148	171	22.0049
d[cccxxxxxxxxxxxxxxxccc	chrX:158279460-158279661(-)$1	201	122	145	21.1218
f!!bb^^^^^^^^^^^^^^^^^^	chrX:58437088-58437289(+)$1	201	89	112	19.3946
eeeeewwwwwwwwwwwwwweeee	chr17:66668741-66668942(-)$1	201	151	174	22.0049
d[cccxxxxxxxxxxxxxxxccc	chr11:107465334-107465535(+)$1	201	82	105	21.1218
e[bb^^^^^^^^^^^^^^^^^^^	chr6:126592609-126592810(-)$1	201	79	102	19.5625
ffffffvvvvvvvvvvvvvffff	chr7:6660130-6660331(-)$1	201	132	155	19.8527
fffffwwwwwwwwwwwwwwffff	chr5:37359192-37359393(-)$1	201	91	114	21.3554
ddddxxxxxxxxxxxxxxxdddd	chr9:16180737-16180938(-)$1	201	50	73	19.9287
!!cccxxxxxxxxxxxxxxxccc	chr2:121736484-121736685(+)$1	201	121	144	21.3002
eeeeexxxxxxxxxxxxxxxeee	chr8:87125194-87125395(+)$1	201	88	111	20.6350
[ddddwwwwwwwwwwwwwwdddd	chr3:136544364-136544565(+)$1	201	154	177	21.5849
^^^^^^^^^^^^^^^^^^^^ccc	chr1:134834667-134834868(+)$1	201	75	98	19.8631
eee^^^^^^^^^^^^^^^^^^^e	chrX:20224905-20225106(+)$1	201	83	106	19.9181
ddddyyyyyyyyyyyyyyyyddd	chr6:38145475-38145676(-)$1	201	71	94	20.5899
!!cccwwwwwwwwwwwwwwccc3	chr10:66682776-66682977(+)$1	201	91	114	22.7461
iiiiiiiuuuuuuuuuuuuiiii	chr14:125075702-125075903(-)$1	201	88	111	18.9246
^^^^^^^^^^^^^^^^^^^dddd	chr5:34808443-34808644(+)$1	201	88	111	19.2280
b[eeeeeuuuuuuuuuuuueeee	chr5:84494875-84495076(-)$1	201	25	48	19.9317
ffffffvvvvvvvvvvvvvffff	chr11:94323115-94323316(-)$1	201	93	116	19.8527
ffffffvvvvvvvvvvvvvffff	chr11:70808632-70808833(-)$1	201	92	115	19.8527
ccccccvvvvvvvvvvvvvccc]	chr4:134392212-134392413(-)$1	201	120	143	20.9673
eeeeewwwwwwwwwwwwwweeee	chr12:32394224-32394425(-)$1	201	80	103	22.0049
ffcccwwwwwwwwwwwwwwccc2	chr2:117113512-117113713(-)$1	201	124	147	22.0533
ffffffvvvvvvvvvvvvvffff	chr7:6256519-6256720(+)$1	201	60	83	19.8527
ee^^^^^^^^^^^^^^^^^^^^^	chr2:28085030-28085231(+)$1	201	87	110	19.9039
^^^^^^^^^^^^^^^^^^^dddd	chr16:29586079-29586280(+)$1	201	70	93	19.2280
d[dddduuuuuuuuuuuuddddd	chr5:23002174-23002375(+)$1	201	112	135	19.5658
[ddddyyyyyyyyyyyyyyyydd	chr6:118601923-118602124(-)$1	201	81	104	20.6621
:eeeeeuuuuuuuuuuuueeeee	chr7:51607060-51607261(+)$1	201	0	23	19.0798
iiiiiiiuuuuuuuuuuuuiiii	chr7:25779537-25779738(-)$1	201	166	189	18.9246
^^^^^^^^^^^^^^^^^^^^ccc	chr1:134834648-134834849(+)$1	201	94	117	19.8631
f[cccwwwwwwwwwwwwwwcccf	chr18:7918374-7918575(+)$1	201	150	173	22.4718
c^^^^^^^^^^^^^^^^^^^ccc	chr10:40655936-40656137(+)$1	201	119	142	19.8897
c[eeeeeuuuuuuuuuuuueeee	chr1:37434365-37434566(+)$1	201	8	31	20.1876

#otherMatches

#Seq PSSM
AGUUCCAACAUCCCCAUAGAACU	chr1:178686355-178686556(-)$1	201	119	142	20.2654
CUUUCACUUUCAGCUUCACAGAA	chr16:37094510-37094711(-)$1	201	58	81	20.1477
GCUUCCAUGCCUGCAUUUCAUAU	chr12:86275471-86275672(-)$1	201	81	104	20.0900
CAGGGCAUCUUCAUCUUCAACAU	chrX:70925756-70925957(+)$1	201	84	107	19.9181
GUAUGUCCCCAGAAUAUCAUUGA	chr3:26032131-26032332(-)$1	201	21	44	19.7156
CAGAAAGACUUUGGCAAAACUUU	chr1:34284737-34284938(+)$1	201	43	66	20.2959
UUCUUCUUCACCCACAUCUAAGA	chr17:23952389-23952590(+)$1	201	25	48	22.4749
AGGGUGAAACAAGGAAAAGACCA	chr1:84790282-84790483(-)$1	201	143	166	21.3113
CUCAACCCUCACCGUCACAACCC	chr16:33726705-33726906(+)$1	201	68	91	19.2280
GUCCUCUCAACAAAAACUCUCGA	chr1:183852313-183852514(-)$1	201	144	167	19.9120
AAGAAACAUAUAAAUACUUUUCA	chr19:41330650-41330851(-)$1	201	82	105	18.0810
CCAGUAUCAUUUCACAAACACUG	chr5:150561969-150562170(+)$1	201	89	112	22.0049
AGCACAUUCACCUCAUUCUGUGC	chr8:108632384-108632585(+)$1	201	136	159	19.0798
UUUACAUUCUUCACCCCAAGUUC	chr17:55637457-55637658(+)$1	201	145	168	21.2747
GUGUUCCCCUUAACUGACGUCUU	chr15:4043974-4044175(+)$1	201	9	32	20.0551
AGCAGGCAGCUACUCCCAAGUCU	chr1:164637898-164638099(-)$1	201	157	180	18.9246
CCCAAUCUCCCUCCCCUCUUUUG	chr10:126935966-126936167(+)$1	201	110	133	20.3066
CAACACUCCCUUGAAGCCAGCAA	chr10:120362398-120362599(-)$1	201	57	80	19.1845
UCCCUGGUGCUAGAGAUUGAAGG	chr8:97948472-97948673(-)$1	201	122	145	20.1477
AAUGUGGAAUUUAAAAUAAACAU	chr8:23176224-23176425(+)$1	201	76	99	22.0049
CUUGUUCCUCUAUAUCUUCCUAC	chr8:96490727-96490928(+)$1	201	15	38	20.5413
UGGGUGCCCUCCCCAUAUUACCC	chr3:108198902-108199103(-)$1	201	11	34	19.1109
ACCAGACUUACUCAUCUCACUGA	chr3:87860546-87860747(-)$1	201	86	109	19.5465
AGGAGUGAUAUCUCUCAAACGCU	chr11:55123815-55124016(-)$1	201	115	138	19.1801
UUACGAGAAAUGAUGAGACGUUC	chr15:37939336-37939537(-)$1	201	12	35	20.4438
AGAACAAAUACUCUCACAUCUCC	chr2:28085031-28085232(+)$1	201	86	109	19.9039
AGAUUCUUCAUUUUCAUCCACAA	chr12:54240669-54240870(+)$1	201	87	110	19.4245
UUGCCUCCUACAGUAUCCUUGGU	chr5:89628699-89628900(+)$1	201	167	190	21.3002
CUCGCACCCCUGCCACACUGUUU	chr17:80251933-80252134(-)$1	201	52	75	20.1384
CCUGUAAAACACACAAAAGCUUC	chr9:54294249-54294450(-)$1	201	40	63	19.4515
GCGUGUUCUAUCCUAUUUCCACU	chr15:59162365-59162566(+)$1	201	50	73	22.5670
GUGCUUAUAUCCGAUCCCUGGCA	chr13:90237876-90238077(+)$1	201	148	171	22.0049
UGCUGAAUCAACACACUAUGCAG	chrX:158279460-158279661(-)$1	201	122	145	21.1218
AAUCAACGUCUUCCCCAAAAUCC	chrX:58437088-58437289(+)$1	201	89	112	19.3946
GUGCUUAUAUCCGAUUCCUGGCA	chr17:66668741-66668942(-)$1	201	151	174	22.0049
ACGCUCAUCGUCCUCAUUUCAGU	chr11:107465334-107465535(+)$1	201	82	105	21.1218
AACAUCUUCACAGACCCUUUCUU	chr6:126592609-126592810(-)$1	201	79	102	19.5625
AAGAAGAGCAAAGCCAAACCUUC	chr7:6660130-6660331(-)$1	201	132	155	19.8527
GUUGGCCACUUCAUCAUCCUCAA	chr5:37359192-37359393(-)$1	201	91	114	21.3554
CAUCUCUGCUAUUGAUAUUGAUG	chr9:16180737-16180938(-)$1	201	50	73	19.9287
CAGCCUCUCUCACCAAACAUGGC	chr2:121736484-121736685(+)$1	201	121	144	21.3002
CUCAGAAUAACUUCAUCAACCUG	chr8:87125194-87125395(+)$1	201	88	111	20.6350
UGCUGGAGCGUCUACCUAACAGU	chr3:136544364-136544565(+)$1	201	154	177	21.5849
UUUCUUUCAUCCAUCCUCGCGCC	chr1:134834667-134834868(+)$1	201	75	98	19.8631
CAGUCAUACACCAUCAUAUCACC	chrX:20224905-20225106(+)$1	201	83	106	19.9181
GUCAUCCCCAGCACCCAUUUUGA	chr6:38145475-38145676(-)$1	201	71	94	20.5899
AAUCACAUUUCACCUUUUUUGAG	chr10:66682776-66682977(+)$1	201	91	114	22.7461
UUCUUUGGAACAUUUUCAGCAAA	chr14:125075702-125075903(-)$1	201	88	111	18.9246
GAAACCUCAUCUCACUCCCCUUC	chr5:34808443-34808644(+)$1	201	88	111	19.2280
CCUUCAUGUAAUACCAAUAGUGA	chr5:84494875-84495076(-)$1	201	25	48	19.9317
UCAUUCUUCUCAUCAUCGUGAGU	chr11:94323115-94323316(-)$1	201	93	116	19.8527
AGUGAUCAUUUCAACCAACAUCG	chr11:70808632-70808833(-)$1	201	92	115	19.8527
AUGGCUUUUUUUCGCUGCUAGCA	chr4:134392212-134392413(-)$1	201	120	143	20.9673
UGAAGUAAAUUUUUUCAGUCUUC	chr12:32394224-32394425(-)$1	201	80	103	22.0049
CCCACCUUCUGUGACAACUGUGC	chr2:117113512-117113713(-)$1	201	124	147	22.0533
UUAUGAUACAUAGAAGAAUUCAU	chr7:6256519-6256720(+)$1	201	60	83	19.8527
AGAACAAAUACUCUCACAUCUCC	chr2:28085030-28085231(+)$1	201	87	110	19.9039
AACGUACCGCUCCAAAAACUCCA	chr16:29586079-29586280(+)$1	201	70	93	19.2280
UCAGGAAAGAUCCAGGAGUCCUA	chr5:23002174-23002375(+)$1	201	112	135	19.5658
AUGAAUAUACUCAACAUGCUUUU	chr6:118601923-118602124(-)$1	201	81	104	20.6621
CCGGCCCCCUCCUCUUCCGGCCG	chr7:51607060-51607261(+)$1	201	0	23	19.0798
CCACAGAGGAUCAGUCAGGUCUG	chr7:25779537-25779738(-)$1	201	166	189	18.9246
UUUCUUUCAUCCAUCCUCGCGCC	chr1:134834648-134834849(+)$1	201	94	117	19.8631
UACAGUCCCUAUGAAACCUUUGA	chr18:7918374-7918575(+)$1	201	150	173	22.4718
CCUCAACUCCUCCCCCACCAGUC	chr10:40655936-40656137(+)$1	201	119	142	19.8897
GUGGCUUGGAUGACUUGGAGAGC	chr1:37434365-37434566(+)$1	201	8	31	20.1876

#DB
(((((.............)))))	chr1:178686355-178686556(-)$1	1	119	142	20.2654
(((((...............)))	chr16:37094510-37094711(-)$1	1	58	81	20.1477
(.(((..................	chr12:86275471-86275672(-)$1	1	81	104	20.0900
(((...................)	chrX:70925756-70925957(+)$1	1	84	107	19.9181
..(((............)))...	chr3:26032131-26032332(-)$1	1	21	44	19.7156
..(((((............))))	chr1:34284737-34284938(+)$1	1	43	66	20.2959
(.(((..............))))	chr17:23952389-23952590(+)$1	1	25	48	22.4749
))(((..............))))	chr1:84790282-84790483(-)$1	1	143	166	21.3113
...................))))	chr16:33726705-33726906(+)$1	1	68	91	19.2280
(((..................))	chr1:183852313-183852514(-)$1	1	144	167	19.9120
..((((............)))).	chr19:41330650-41330851(-)$1	1	82	105	18.0810
(((((..............))))	chr5:150561969-150562170(+)$1	1	89	112	22.0049
.(((((............)))))	chr8:108632384-108632585(+)$1	1	136	159	19.0798
...((..............))..	chr17:55637457-55637658(+)$1	1	145	168	21.2747
(.(....................	chr15:4043974-4044175(+)$1	1	9	32	20.0551
(((((((............))))	chr1:164637898-164638099(-)$1	1	157	180	18.9246
.((((...............)))	chr10:126935966-126936167(+)$1	1	110	133	20.3066
(..................))))	chr10:120362398-120362599(-)$1	1	57	80	19.1845
(((((...............)))	chr8:97948472-97948673(-)$1	1	122	145	20.1477
(((((..............))))	chr8:23176224-23176425(+)$1	1	76	99	22.0049
(((((................))	chr8:96490727-96490928(+)$1	1	15	38	20.5413
((((((............)))))	chr3:108198902-108199103(-)$1	1	11	34	19.1109
..(((..............))).	chr3:87860546-87860747(-)$1	1	86	109	19.5465
(((((((............))))	chr11:55123815-55124016(-)$1	1	115	138	19.1801
(.(((.............)))..	chr15:37939336-37939537(-)$1	1	12	35	20.4438
((.....................	chr2:28085031-28085232(+)$1	1	86	109	19.9039
.((((..................	chr12:54240669-54240870(+)$1	1	87	110	19.4245
..(((...............)))	chr5:89628699-89628900(+)$1	1	167	190	21.3002
(..(((............)))..	chr17:80251933-80252134(-)$1	1	52	75	20.1384
.((((..................	chr9:54294249-54294450(-)$1	1	40	63	19.4515
(.(((..............))).	chr15:59162365-59162566(+)$1	1	50	73	22.5670
(((((..............))))	chr13:90237876-90238077(+)$1	1	148	171	22.0049
(.(((...............)))	chrX:158279460-158279661(-)$1	1	122	145	21.1218
(..((..................	chrX:58437088-58437289(+)$1	1	89	112	19.3946
(((((..............))))	chr17:66668741-66668942(-)$1	1	151	174	22.0049
(.(((...............)))	chr11:107465334-107465535(+)$1	1	82	105	21.1218
(.((...................	chr6:126592609-126592810(-)$1	1	79	102	19.5625
((((((.............))))	chr7:6660130-6660331(-)$1	1	132	155	19.8527
(((((..............))))	chr5:37359192-37359393(-)$1	1	91	114	21.3554
((((...............))))	chr9:16180737-16180938(-)$1	1	50	73	19.9287
..(((...............)))	chr2:121736484-121736685(+)$1	1	121	144	21.3002
(((((...............)))	chr8:87125194-87125395(+)$1	1	88	111	20.6350
.((((..............))))	chr3:136544364-136544565(+)$1	1	154	177	21.5849
....................)))	chr1:134834667-134834868(+)$1	1	75	98	19.8631
(((...................)	chrX:20224905-20225106(+)$1	1	83	106	19.9181
((((................)))	chr6:38145475-38145676(-)$1	1	71	94	20.5899
..(((..............))).	chr10:66682776-66682977(+)$1	1	91	114	22.7461
(((((((............))))	chr14:125075702-125075903(-)$1	1	88	111	18.9246
...................))))	chr5:34808443-34808644(+)$1	1	88	111	19.2280
(.(((((............))))	chr5:84494875-84495076(-)$1	1	25	48	19.9317
((((((.............))))	chr11:94323115-94323316(-)$1	1	93	116	19.8527
((((((.............))))	chr11:70808632-70808833(-)$1	1	92	115	19.8527
((((((.............))).	chr4:134392212-134392413(-)$1	1	120	143	20.9673
(((((..............))))	chr12:32394224-32394425(-)$1	1	80	103	22.0049
(((((..............))).	chr2:117113512-117113713(-)$1	1	124	147	22.0533
((((((.............))))	chr7:6256519-6256720(+)$1	1	60	83	19.8527
((.....................	chr2:28085030-28085231(+)$1	1	87	110	19.9039
...................))))	chr16:29586079-29586280(+)$1	1	70	93	19.2280
(.((((............)))))	chr5:23002174-23002375(+)$1	1	112	135	19.5658
.((((................))	chr6:118601923-118602124(-)$1	1	81	104	20.6621
.(((((............)))))	chr7:51607060-51607261(+)$1	1	0	23	19.0798
(((((((............))))	chr7:25779537-25779738(-)$1	1	166	189	18.9246
....................)))	chr1:134834648-134834849(+)$1	1	94	117	19.8631
(.(((..............))))	chr18:7918374-7918575(+)$1	1	150	173	22.4718
(...................)))	chr10:40655936-40656137(+)$1	1	119	142	19.8897
(.(((((............))))	chr1:37434365-37434566(+)$1	1	8	31	20.1876

#PSSM
e : 0.19	f : 0.18	d : 0.13	c : 0.09	! : 0.07	^ : 0.07	[ : 0.06	: : 0.04	i : 0.04	$ : 0.01	% : 0.01	" : 0.01	g : 0.01	a : 0.01	b : 0.01	
e : 0.19	[ : 0.18	f : 0.15	^ : 0.10	d : 0.10	! : 0.09	c : 0.04	i : 0.04	$ : 0.01	% : 0.01	" : 0.01	: : 0.01	g : 0.01	
c : 0.24	e : 0.21	f : 0.13	^ : 0.13	d : 0.13	i : 0.04	! : 0.03	" : 0.01	a : 0.01	g : 0.01	b : 0.01	
c : 0.24	^ : 0.19	e : 0.18	f : 0.13	d : 0.13	b : 0.04	i : 0.04	g : 0.01	
c : 0.24	^ : 0.21	e : 0.18	f : 0.13	d : 0.10	i : 0.04	b : 0.03	g : 0.01	x : 0.01	y : 0.01	
^ : 0.27	w : 0.22	x : 0.13	e : 0.07	f : 0.07	i : 0.04	y : 0.04	v : 0.03	d : 0.03	c : 0.03	u : 0.01	g : 0.01	
^ : 0.27	w : 0.22	x : 0.13	v : 0.10	u : 0.10	e : 0.04	i : 0.04	y : 0.04	g : 0.01	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.21	x : 0.13	v : 0.10	y : 0.04	
^ : 0.27	w : 0.22	u : 0.19	x : 0.13	v : 0.10	y : 0.04	c : 0.01	
^ : 0.27	w : 0.22	x : 0.13	u : 0.10	v : 0.07	e : 0.04	c : 0.04	y : 0.04	d : 0.03	f : 0.01	
^ : 0.21	e : 0.16	c : 0.16	x : 0.12	d : 0.12	f : 0.09	i : 0.04	y : 0.04	b : 0.01	g : 0.01	
c : 0.25	e : 0.18	^ : 0.16	d : 0.15	f : 0.12	i : 0.04	y : 0.03	4 : 0.01	b : 0.01	g : 0.01	
c : 0.24	e : 0.18	d : 0.16	^ : 0.15	f : 0.13	i : 0.04	4 : 0.03	2 : 0.03	g : 0.01	
e : 0.21	d : 0.16	f : 0.15	^ : 0.12	c : 0.12	i : 0.04	2 : 0.04	4 : 0.03	] : 0.03	D : 0.01	6 : 0.01	: : 0.01	g : 0.01	3 : 0.01	

#score	1341.4634083522049
#seq	66
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_UTR_m3_run2.txt

#BEAR
ccc[bbqqqqqqqqbbccc	chr16:23359737-23360015(+)$1	278	192	211	13.1826
b!!cccqqqqqqqqcccbb	chr2:180757431-180757703(-)$1	272	117	136	13.3944
ddd!!aqqqqqqqqa22dd	chr5:142936364-142936643(+)$1	279	34	53	12.6739
bb[cccqqqqqqqqccc]b	chr11:85125725-85125995(+)$1	270	208	227	13.4352
fffcccqqqqqqqqccc]f	chr10:110934017-110934347(+)$1	330	305	324	14.3202
hh[cccqqqqqqqqccc]h	chr19:44380182-44380455(+)$1	273	29	48	13.6200
b[ddddqqqqqqqqdddd]	chr15:12199451-12199730(+)$1	279	189	208	13.3358
:eeeeeqqqqqqqqeeeee	chr10:126935638-126935912(+)$1	274	110	129	14.4063
Geeeeeqqqqqqqqeeeee	chr17:13166022-13166299(-)$1	277	104	123	14.9105
:eeeeeqqqqqqqqeeeee	chr2:30302781-30303158(+)$1	377	324	343	14.4063
ggggggqqqqqqqqggggg	chr6:66968952-66969235(+)$1	283	61	80	14.4498
ffffffqqqqqqqqfffff	chr4:55094491-55094766(+)$1	275	89	108	14.5136
##ddddqqqqqqqqdddd2	chr16:4544895-4545201(-)$1	306	191	210	13.0725
[eeeeeqqqqqqqqeeeee	chr10:36715583-36715860(+)$1	277	113	132	15.3441
"eeeeeqqqqqqqqeeeee	chr11:51818333-51818604(+)$1	271	8	27	15.2705
!eeeeeqqqqqqqqeeeee	chr2:30960656-30960930(-)$1	274	100	119	15.3234
ffffffqqqqqqqqfffff	chr19:44377491-44377856(+)$1	365	271	290	14.5136
eee[bbqqqqqqqqbb]ee	chr15:99842523-99842814(+)$1	291	38	57	13.7682
"eeeeeqqqqqqqqeeeee	chr3:89539174-89539454(+)$1	280	188	207	15.2705
!eeeeeqqqqqqqqeeeee	chr4:46484842-46485149(+)$1	307	98	117	15.3234
ffffffqqqqqqqqfffff	chr9:96440736-96441025(-)$1	289	18	37	14.5136
ffffffqqqqqqqqfffff	chr17:34748100-34748374(+)$1	274	165	184	14.5136
ee[cccqqqqqqqqcccee	chr11:33062820-33063102(-)$1	282	132	151	14.5747
ffffffqqqqqqqqfffff	chr11:93820476-93820747(-)$1	271	159	178	14.5136
ffffbbqqqqqqqqbb]ff	chr1:88243714-88243999(-)$1	285	259	278	13.5488
ffffffqqqqqqqqfffff	chr9:30881658-30881942(+)$1	284	215	234	14.5136
!!ddddqqqqqqqqdddd4	chr17:56155995-56156265(+)$1	270	9	28	13.4717
iiiiiiqqqqqqqqiiiii	chr5:141091024-141091300(+)$1	276	138	157	13.9921
ffffffqqqqqqqqfffff	chr8:69414100-69414377(+)$1	277	83	102	14.5136
ffffffqqqqqqqqfffff	chr10:116786171-116786441(-)$1	270	176	195	14.5136
cc[cccqqqqqqqqccccc	chrX:7451799-7452072(+)$1	273	8	27	14.1257
gcccbbqqqqqqqqbb]cc	chr11:97545300-97545746(+)$1	446	248	267	13.1840
:eeeeeqqqqqqqqeeeee	chr18:82725021-82725303(+)$1	282	153	172	14.4063
:ccc[aqqqqqqqqa]ccc	chr15:93074665-93074951(-)$1	286	117	136	13.0373
[eeeeeqqqqqqqqeeeee	chrX:71556526-71556811(+)$1	285	223	242	15.3441
[eeeeeqqqqqqqqeeeee	chr3:152124138-152124407(+)$1	269	196	215	15.3441
gccc[aqqqqqqqqa]ccc	chr6:51539299-51539573(+)$1	274	201	220	13.8814
ffffffqqqqqqqqfffff	chr19:44650109-44650403(+)$1	294	247	266	14.5136
ggggggqqqqqqqqggggg	chr2:75766370-75766653(+)$1	283	138	157	14.4498
ceeeeeqqqqqqqqeeeee	chr13:56842942-56843221(+)$1	279	84	103	15.2019
eeeeeaqqqqqqqqa]eee	chr15:79746833-79747120(-)$1	287	125	144	14.7512
ffddddqqqqqqqqddddd	chr16:17139735-17140007(-)$1	272	146	165	13.3631
ffffffqqqqqqqqfffff	chr9:114420766-114421041(-)$1	275	103	122	14.5136
ggggggqqqqqqqqggggg	chr10:79593821-79594089(-)$1	268	148	167	14.4498
:eeeeeqqqqqqqqeeeee	chr1:82892603-82892879(+)$1	276	174	193	14.4063
ee[cccqqqqqqqqccc]e	chr11:87793125-87793420(-)$1	295	65	84	14.4265
b[ddddqqqqqqqqdddd]	chr9:58724120-58724412(-)$1	292	43	62	13.3358
c!!cccqqqqqqqqccc22	chr1:154686190-154686479(-)$1	289	8	27	13.6598
&eeeeeqqqqqqqqeeeee	chr6:128380710-128380990(-)$1	280	208	227	14.7029
gggg[aqqqqqqqqa]ggg	chr7:106627131-106627426(-)$1	295	186	205	14.2581
ggggggqqqqqqqqggggg	chr5:25196839-25197116(-)$1	277	10	29	14.4498
ffffffqqqqqqqqfffff	chr11:97021757-97022109(-)$1	352	304	323	14.5136
"""cccqqqqqqqqccc33	chrX:71475920-71476197(-)$1	277	229	248	13.9367
ggggggqqqqqqqqggggg	chr2:165896047-165896322(+)$1	275	233	252	14.4498
ee[cccqqqqqqqqcccee	chr11:53074854-53075134(-)$1	280	202	221	14.5747
ffffffqqqqqqqqfffff	chr1:194933630-194933914(-)$1	284	60	79	14.5136
eeeeeeqqqqqqqqeeeee	chr3:152448376-152448722(+)$1	346	163	182	15.1095
cc!!bbqqqqqqqqbbccc	chr13:24895116-24895390(+)$1	274	191	210	13.2418
geeeeeqqqqqqqqeeeee	chr17:25404914-25405205(-)$1	291	20	39	15.2505
iii[bbqqqqqqqqbb]ii	chr10:74997990-74998267(+)$1	277	244	263	13.3170
ffffffqqqqqqqqfffff	chr4:11099983-11100255(+)$1	272	91	110	14.5136
e[ddddqqqqqqqqdddd]	chr14:47430808-47431084(-)$1	276	70	89	13.3915
[eeeeeqqqqqqqqeeeee	chr6:124998952-124999240(+)$1	288	123	142	15.3441
[eeeeeqqqqqqqqeeeee	chr3:95466290-95466558(+)$1	268	171	190	15.3441
####bbqqqqqqqqbb444	chr11:87864985-87865263(+)$1	278	157	176	12.6334
:eeeeeqqqqqqqqeeeee	chr13:108838962-108839232(+)$1	270	231	250	14.4063
ggggggqqqqqqqqggggg	chr8:109899716-109899990(+)$1	274	154	173	14.4498
Deeeeeqqqqqqqqeeeee	chr3:95960992-95961262(+)$1	270	14	33	14.1089
ffffffqqqqqqqqfffff	chr15:102265438-102265721(+)$1	283	211	230	14.5136
:eeeeeqqqqqqqqeeeee	chr9:30876493-30876778(+)$1	285	182	201	14.4063
[eeeeeqqqqqqqqeeeee	chr11:40493238-40493518(-)$1	280	136	155	15.3441

#otherMatches

#Seq PSSM
CUGUGGAUAGAGUGCCCAG	chr16:23359737-23360015(+)$1	278	192	211	13.1826
CAUUGUGACAUGGAACAGG	chr2:180757431-180757703(-)$1	272	117	136	13.3944
CUGGGCACGAGGCAGGACA	chr5:142936364-142936643(+)$1	279	34	53	12.6739
CUCGAUGUAAGUCAAUUUA	chr11:85125725-85125995(+)$1	270	208	227	13.4352
UGAUAUUCAGCAUUAUAUU	chr10:110934017-110934347(+)$1	330	305	324	14.3202
AUAAGAGACUAAGAUCUGA	chr19:44380182-44380455(+)$1	273	29	48	13.6200
GCUGUCCAUGCAGAGGCAC	chr15:12199451-12199730(+)$1	279	189	208	13.3358
GAGCUAGCUCUCAAUAGCU	chr10:126935638-126935912(+)$1	274	110	129	14.4063
GUUCAUGUAUACAAAUGAA	chr17:13166022-13166299(-)$1	277	104	123	14.9105
ACUGAGAAGCACAACUCAG	chr2:30302781-30303158(+)$1	377	324	343	14.4063
GGAGUUGUUUAUAAAAUUU	chr6:66968952-66969235(+)$1	283	61	80	14.4498
AAUUUAGAAUUUGGUAGGU	chr4:55094491-55094766(+)$1	275	89	108	14.5136
CUCAGUUGGGGUUUGCUGC	chr16:4544895-4545201(-)$1	306	191	210	13.0725
CUCUCACUAGGUAAUGAGG	chr10:36715583-36715860(+)$1	277	113	132	15.3441
CUAAGCAUUAUAGAGCUUG	chr11:51818333-51818604(+)$1	271	8	27	15.2705
UCUUGAGAAAUACAUCAAG	chr2:30960656-30960930(-)$1	274	100	119	15.3234
AGUAUUGCCACCCAGAUGC	chr19:44377491-44377856(+)$1	365	271	290	14.5136
GUAAUGGGAAAGAGCAAUA	chr15:99842523-99842814(+)$1	291	38	57	13.7682
CCUGGAGUUGUGAAUCCAG	chr3:89539174-89539454(+)$1	280	188	207	15.2705
GUUUGUUUUUCACUGCAGA	chr4:46484842-46485149(+)$1	307	98	117	15.3234
cuccgcuccugagugcggg	chr9:96440736-96441025(-)$1	289	18	37	14.5136
GAGCUACUAUGGGCUGGCU	chr17:34748100-34748374(+)$1	274	165	184	14.5136
UCGAUGGAUAUGGACAUGA	chr11:33062820-33063102(-)$1	282	132	151	14.5747
GCAGUGUUACGUGCCACUG	chr11:93820476-93820747(-)$1	271	159	178	14.5136
uuauugagagccaccaugu	chr1:88243714-88243999(-)$1	285	259	278	13.5488
AUGCUUAUAUAUGAAGGUA	chr9:30881658-30881942(+)$1	284	215	234	14.5136
GUGCUCAAGCAGGGGAGCU	chr17:56155995-56156265(+)$1	270	9	28	13.4717
GAGGGUCUUAUUUUAUCUU	chr5:141091024-141091300(+)$1	276	138	157	13.9921
CUAGUGCAAAAAUUCAUUA	chr8:69414100-69414377(+)$1	277	83	102	14.5136
UGGUUAUAUAUAUUUGGCC	chr10:116786171-116786441(-)$1	270	176	195	14.5136
ACAUUCAGACAAAGGAAGU	chrX:7451799-7452072(+)$1	273	8	27	14.1257
CACCCUAAGUGAGAAGAGG	chr11:97545300-97545746(+)$1	446	248	267	13.1840
UGCUGUACCUAAUGACGGC	chr18:82725021-82725303(+)$1	282	153	172	14.4063
ACCUGUAUGAGAAAGGAGG	chr15:93074665-93074951(-)$1	286	117	136	13.0373
CCCAACUCUUAGGUGUUGG	chrX:71556526-71556811(+)$1	285	223	242	15.3441
GUCGUGUUUUGCCUCAUGA	chr3:152124138-152124407(+)$1	269	196	215	15.3441
GUAUCCUGUAUCAUGUGUA	chr6:51539299-51539573(+)$1	274	201	220	13.8814
CGGUGGUCAGCUUCUCACC	chr19:44650109-44650403(+)$1	294	247	266	14.5136
AGUGGGAAUGGGAACUUGC	chr2:75766370-75766653(+)$1	283	138	157	14.4498
CCUCUUCCUCAGCAAAGAG	chr13:56842942-56843221(+)$1	279	84	103	15.2019
AGUCCCUGGAGAUUGUGGA	chr15:79746833-79747120(-)$1	287	125	144	14.7512
AAGCUGAGUUGUCACAGCA	chr16:17139735-17140007(-)$1	272	146	165	13.3631
GCUAAGAAACUCGAUUUAG	chr9:114420766-114421041(-)$1	275	103	122	14.5136
GCCGUGCAUGGGUACACGG	chr10:79593821-79594089(-)$1	268	148	167	14.4498
AUACUUGUGUAAAAAGGUA	chr1:82892603-82892879(+)$1	276	174	193	14.4063
GGCAGGAGAAUGCCCCUUC	chr11:87793125-87793420(-)$1	295	65	84	14.4265
UGAAUGAAAUGUAACAUUG	chr9:58724120-58724412(-)$1	292	43	62	13.3358
GGAGCAGUUGUUAAUGCAG	chr1:154686190-154686479(-)$1	289	8	27	13.6598
CGCUGCCCACCUCUGCAGC	chr6:128380710-128380990(-)$1	280	208	227	14.7029
AGCAGUUUGGUUUUGGUGC	chr7:106627131-106627426(-)$1	295	186	205	14.2581
UAGAUGCCUUGGAACAUCU	chr5:25196839-25197116(-)$1	277	10	29	14.4498
AGCAGUUGACAAGUGCUGU	chr11:97021757-97022109(-)$1	352	304	323	14.5136
GGACGUGGUGGAGAAUGAG	chrX:71475920-71476197(-)$1	277	229	248	13.9367
GGAAUGGUGAACCACAUUC	chr2:165896047-165896322(+)$1	275	233	252	14.4498
GAUGAAGUGCACUGUUCUC	chr11:53074854-53075134(-)$1	280	202	221	14.5747
CGUGCUGUAUUCCAAGUAU	chr1:194933630-194933914(-)$1	284	60	79	14.5136
UCAUAUGUUUUUAAAUAUG	chr3:152448376-152448722(+)$1	346	163	182	15.1095
GAAAGAAAAAAGAAUCUCU	chr13:24895116-24895390(+)$1	274	191	210	13.2418
GUUAGCAUAUAUCAGCUGA	chr17:25404914-25405205(-)$1	291	20	39	15.2505
uuuguuuuguuuuUGAGGA	chr10:74997990-74998267(+)$1	277	244	263	13.3170
ACAGAACAUUAACUUUCUG	chr4:11099983-11100255(+)$1	272	91	110	14.5136
GGUUCAUUUGGGACUGAAG	chr14:47430808-47431084(-)$1	276	70	89	13.3915
GCAUCCUCUGGAUUGGAUG	chr6:124998952-124999240(+)$1	288	123	142	15.3441
AUAGGGAAGAAGUGCCCUG	chr3:95466290-95466558(+)$1	268	171	190	15.3441
AGAGCAUAAUAAACUGAGU	chr11:87864985-87865263(+)$1	278	157	176	12.6334
ACAUGAGAAAUUAAUCAUG	chr13:108838962-108839232(+)$1	270	231	250	14.4063
UGCUAGCAAGAGGAUUAGC	chr8:109899716-109899990(+)$1	274	154	173	14.4498
UGGCUUCUUUUGUUAAGCC	chr3:95960992-95961262(+)$1	270	14	33	14.1089
UAGUUUGGUUUAGAAGACU	chr15:102265438-102265721(+)$1	283	211	230	14.5136
auuuaauuuaauuuuuaaa	chr9:30876493-30876778(+)$1	285	182	201	14.4063
GGACCGGCUGAGAGCGGUC	chr11:40493238-40493518(-)$1	280	136	155	15.3441

#DB
(((.((........)))))	chr16:23359737-23360015(+)$1	1	192	211	13.1826
(..(((........)))))	chr2:180757431-180757703(-)$1	1	117	136	13.3944
(((..(........)..))	chr5:142936364-142936643(+)$1	1	34	53	12.6739
((.(((........))).)	chr11:85125725-85125995(+)$1	1	208	227	13.4352
((((((........))).)	chr10:110934017-110934347(+)$1	1	305	324	14.3202
((.(((........))).)	chr19:44380182-44380455(+)$1	1	29	48	13.6200
(.((((........)))).	chr15:12199451-12199730(+)$1	1	189	208	13.3358
.(((((........)))))	chr10:126935638-126935912(+)$1	1	110	129	14.4063
((((((........)))))	chr17:13166022-13166299(-)$1	1	104	123	14.9105
.(((((........)))))	chr2:30302781-30303158(+)$1	1	324	343	14.4063
((((((........)))))	chr6:66968952-66969235(+)$1	1	61	80	14.4498
((((((........)))))	chr4:55094491-55094766(+)$1	1	89	108	14.5136
..((((........)))).	chr16:4544895-4545201(-)$1	1	191	210	13.0725
.(((((........)))))	chr10:36715583-36715860(+)$1	1	113	132	15.3441
.(((((........)))))	chr11:51818333-51818604(+)$1	1	8	27	15.2705
.(((((........)))))	chr2:30960656-30960930(-)$1	1	100	119	15.3234
((((((........)))))	chr19:44377491-44377856(+)$1	1	271	290	14.5136
(((.((........)).))	chr15:99842523-99842814(+)$1	1	38	57	13.7682
.(((((........)))))	chr3:89539174-89539454(+)$1	1	188	207	15.2705
.(((((........)))))	chr4:46484842-46485149(+)$1	1	98	117	15.3234
((((((........)))))	chr9:96440736-96441025(-)$1	1	18	37	14.5136
((((((........)))))	chr17:34748100-34748374(+)$1	1	165	184	14.5136
((.(((........)))))	chr11:33062820-33063102(-)$1	1	132	151	14.5747
((((((........)))))	chr11:93820476-93820747(-)$1	1	159	178	14.5136
((((((........)).))	chr1:88243714-88243999(-)$1	1	259	278	13.5488
((((((........)))))	chr9:30881658-30881942(+)$1	1	215	234	14.5136
..((((........)))).	chr17:56155995-56156265(+)$1	1	9	28	13.4717
((((((........)))))	chr5:141091024-141091300(+)$1	1	138	157	13.9921
((((((........)))))	chr8:69414100-69414377(+)$1	1	83	102	14.5136
((((((........)))))	chr10:116786171-116786441(-)$1	1	176	195	14.5136
((.(((........)))))	chrX:7451799-7452072(+)$1	1	8	27	14.1257
((((((........)).))	chr11:97545300-97545746(+)$1	1	248	267	13.1840
.(((((........)))))	chr18:82725021-82725303(+)$1	1	153	172	14.4063
.(((.(........).)))	chr15:93074665-93074951(-)$1	1	117	136	13.0373
.(((((........)))))	chrX:71556526-71556811(+)$1	1	223	242	15.3441
.(((((........)))))	chr3:152124138-152124407(+)$1	1	196	215	15.3441
)(((.(........).)))	chr6:51539299-51539573(+)$1	1	201	220	13.8814
((((((........)))))	chr19:44650109-44650403(+)$1	1	247	266	14.5136
((((((........)))))	chr2:75766370-75766653(+)$1	1	138	157	14.4498
((((((........)))))	chr13:56842942-56843221(+)$1	1	84	103	15.2019
((((((........).)))	chr15:79746833-79747120(-)$1	1	125	144	14.7512
))((((........))))(	chr16:17139735-17140007(-)$1	1	146	165	13.3631
((((((........)))))	chr9:114420766-114421041(-)$1	1	103	122	14.5136
((((((........)))))	chr10:79593821-79594089(-)$1	1	148	167	14.4498
.(((((........)))))	chr1:82892603-82892879(+)$1	1	174	193	14.4063
((.(((........))).)	chr11:87793125-87793420(-)$1	1	65	84	14.4265
(.((((........)))).	chr9:58724120-58724412(-)$1	1	43	62	13.3358
(..(((........)))..	chr1:154686190-154686479(-)$1	1	8	27	13.6598
.(((((........)))))	chr6:128380710-128380990(-)$1	1	208	227	14.7029
((((.(........).)))	chr7:106627131-106627426(-)$1	1	186	205	14.2581
((((((........)))))	chr5:25196839-25197116(-)$1	1	10	29	14.4498
((((((........)))))	chr11:97021757-97022109(-)$1	1	304	323	14.5136
...(((........)))..	chrX:71475920-71476197(-)$1	1	229	248	13.9367
((((((........)))))	chr2:165896047-165896322(+)$1	1	233	252	14.4498
((.(((........)))))	chr11:53074854-53075134(-)$1	1	202	221	14.5747
((((((........)))))	chr1:194933630-194933914(-)$1	1	60	79	14.5136
)(((((........)))))	chr3:152448376-152448722(+)$1	1	163	182	15.1095
((..((........)))))	chr13:24895116-24895390(+)$1	1	191	210	13.2418
((((((........)))))	chr17:25404914-25405205(-)$1	1	20	39	15.2505
(((.((........)).))	chr10:74997990-74998267(+)$1	1	244	263	13.3170
((((((........)))))	chr4:11099983-11100255(+)$1	1	91	110	14.5136
(.((((........)))).	chr14:47430808-47431084(-)$1	1	70	89	13.3915
.(((((........)))))	chr6:124998952-124999240(+)$1	1	123	142	15.3441
.(((((........)))))	chr3:95466290-95466558(+)$1	1	171	190	15.3441
....((........))...	chr11:87864985-87865263(+)$1	1	157	176	12.6334
.(((((........)))))	chr13:108838962-108839232(+)$1	1	231	250	14.4063
((((((........)))))	chr8:109899716-109899990(+)$1	1	154	173	14.4498
((((((........)))))	chr3:95960992-95961262(+)$1	1	14	33	14.1089
((((((........)))))	chr15:102265438-102265721(+)$1	1	211	230	14.5136
.(((((........)))))	chr9:30876493-30876778(+)$1	1	182	201	14.4063
.(((((........)))))	chr11:40493238-40493518(-)$1	1	136	155	15.3441

#PSSM
f : 0.23	g : 0.14	: : 0.09	e : 0.09	[ : 0.08	c : 0.07	b : 0.05	" : 0.04	! : 0.04	# : 0.02	i : 0.02	d : 0.01	h : 0.01	G : 0.01	& : 0.01	D : 0.01	
e : 0.38	f : 0.23	g : 0.09	c : 0.08	! : 0.04	[ : 0.04	# : 0.02	i : 0.02	d : 0.01	b : 0.01	h : 0.01	" : 0.01	
e : 0.33	f : 0.22	d : 0.09	g : 0.09	[ : 0.08	c : 0.05	! : 0.04	i : 0.02	" : 0.01	# : 0.01	
e : 0.32	f : 0.21	c : 0.18	g : 0.09	d : 0.08	[ : 0.04	! : 0.02	i : 0.01	# : 0.01	
e : 0.32	f : 0.19	c : 0.14	b : 0.09	d : 0.08	g : 0.08	[ : 0.04	! : 0.01	i : 0.01	
e : 0.30	f : 0.19	c : 0.14	b : 0.09	d : 0.08	g : 0.08	a : 0.07	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 : 0.30	f : 0.19	c : 0.14	b : 0.09	d : 0.08	g : 0.08	a : 0.07	i : 0.01	
e : 0.30	f : 0.19	c : 0.14	b : 0.09	d : 0.08	g : 0.08	] : 0.05	2 : 0.01	i : 0.01	
e : 0.32	c : 0.19	f : 0.19	g : 0.09	d : 0.08	] : 0.05	2 : 0.01	i : 0.01	4 : 0.01	
e : 0.36	f : 0.21	d : 0.09	g : 0.09	c : 0.08	] : 0.05	i : 0.02	b : 0.01	2 : 0.01	3 : 0.01	4 : 0.01	
e : 0.38	f : 0.22	g : 0.09	c : 0.08	] : 0.04	b : 0.02	d : 0.02	2 : 0.02	4 : 0.02	i : 0.02	h : 0.01	3 : 0.01	

#score	1014.3753415070847
#seq	71
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_UTR_m1_run2.txt

#BEAR
cc[eeeeettttttttttteeeee]c	chr2:6463668-6463872(-)$1	204	167	193	22.7181
[bbddddwwwwwwwwwwwwwwdddd]	chr3:124025217-124025421(+)$1	204	148	174	21.6993
""eeeeevvvvvvvvvvvvveeeee2	chr9:36686079-36686288(+)$1	209	76	102	23.8784
h!!ddddvvvvvvvvvvvvvdddd22	chr6:51411844-51412058(-)$1	214	81	107	22.7774
bbeeeeevvvvvvvvvvvvveeeee]	chr15:79654544-79654745(-)$1	201	61	87	23.1057
c!!cccyyyyyyyyyyyyyyyyccc]	chr11:87794087-87794292(-)$1	205	69	95	23.2512
[ddddyyyyyyyyyyyyyyyydddd]	chr7:3330566-3330767(+)$1	201	94	120	22.1705
!!fffffftttttttttttffffff2	chr6:72559863-72560067(-)$1	204	48	74	21.9998
!!eeeeevvvvvvvvvvvvveeeee]	chr16:7411453-7411654(+)$1	201	143	169	24.0720
iiiiiiiuuuuuuuuuuuuiiiiiii	chr2:29037770-29037973(+)$1	203	62	88	23.8385
####cccxxxxxxxxxxxxxxxccc4	chr11:35602575-35602779(+)$1	204	25	51	18.5500
!bb[cccuuuuuuuuuuuucccbb22	chr5:31783781-31783989(+)$1	208	80	106	22.9284
d[ddddwwwwwwwwwwwwwwdddd]d	chr4:136878317-136878518(+)$1	201	45	71	21.6819
fffffbbtttttttttttbbgggggg	chr19:41288869-41289075(-)$1	206	88	114	21.3676
b[ccc[bbtttttttttttbbccc]b	chr13:46744812-46745014(+)$1	202	53	79	21.4787
ggg[ddddtttttttttttdddd]gg	chr5:32794508-32794715(+)$1	207	125	151	22.2497
c"""ddddtttttttttttdddd333	chr8:113334379-113334605(-)$1	226	183	209	22.6432
dd!!ddddtttttttttttdddd]dd	chr5:8067802-8068008(-)$1	206	35	61	21.4280
gggggggxxxxxxxxxxxxxxxgggg	chr14:29289154-29289358(+)$1	204	1	27	18.4096
""cccbbuuuuuuuuuuuubb]ccc]	chrX:72355559-72355763(-)$1	204	65	91	23.5057
e!!ddddvvvvvvvvvvvvvddddee	chr10:111900717-111900918(+)$1	201	98	124	22.7794
:fffffftttttttttttffffffcc	chr1:157898831-157899034(+)$1	203	66	92	20.3026
"""ddddvvvvvvvvvvvvvdddd22	chr11:103684118-103684319(-)$1	201	53	79	23.0985
ggggggguuuuuuuuuuuuggggggg	chr2:28325676-28325878(+)$1	202	82	108	23.7094
ii[ddddtttttttttttddddiiii	chr11:77525542-77525748(+)$1	206	87	113	22.0562
""eeeeettttttttttteeeee]ff	chr19:55143564-55143787(-)$1	223	11	37	22.7918
gggggggxxxxxxxxxxxxxxxgggg	chr1:162152453-162152662(-)$1	209	166	192	18.4096
[ffffffvvvvvvvvvvvvvffffff	chr2:181285017-181285217(+)$1	200	117	143	22.3547
eeee[ccctttttttttttccc]eee	chr18:24049759-24049969(+)$1	210	108	134	22.2369
:gggggggtttttttttttggggggg	chr11:105920205-105920410(-)$1	205	101	127	21.3245
gggggggvvvvvvvvvvvvvgggggg	chr8:27139827-27140044(+)$1	217	67	93	23.1760
""eeeeettttttttttteeeeeccc	chr17:43225303-43225514(+)$1	211	172	198	22.7743
g[eeeeevvvvvvvvvvvvveeeee]	chr12:73313191-73313391(-)$1	200	64	90	23.8354
:bb[cccvvvvvvvvvvvvvccc]bb	chr7:58118380-58118582(+)$1	202	5	31	21.1806
!!eeeeeyyyyyyyyyyyyyyyyeee	chr3:87728904-87729122(-)$1	218	45	71	22.9802
[eeeeeyyyyyyyyyyyyyyyyeeee	chrX:159216528-159216745(+)$1	217	126	152	22.9320
!!eeeeeyyyyyyyyyyyyyyyyeee	chr19:56672112-56672321(+)$1	209	99	125	22.9802
g####bbuuuuuuuuuuuubb333gg	chr3:131306147-131306355(+)$1	208	35	61	23.1581
cccyyyyyyyyyyyyyyyyccc4444	chr12:79785154-79785356(-)$1	202	128	154	21.0377
!ffffffwwwwwwwwwwwwwwfffff	chr10:107937261-107937461(-)$1	200	113	139	21.8325
eeeeyyyyyyyyyyyyyyyyeeeee]	chr17:23957887-23958090(+)$1	203	21	47	22.3087
d"""ccctttttttttttccc]dddd	chr12:56969426-56969635(+)$1	209	34	60	21.9738
c[eeeeevvvvvvvvvvvvveeeeec	chr5:102339864-102340067(-)$1	203	20	46	23.5545
e[bb[bbtttttttttttbb]bb333	chr2:33586484-33586686(-)$1	202	138	164	20.9965
$$$$ccctttttttttttccc4444c	chr9:121648834-121649046(+)$1	212	129	155	21.8150
hhhhhhwwwwwwwwwwwwwwhhhhhh	chr6:38553764-38553983(+)$1	219	40	66	19.7926
b!!eeeeettttttttttteeeee22	chr1:137647620-137647821(+)$1	201	123	149	22.8027
ffff[bbvvvvvvvvvvvvvbb333f	chr15:54670557-54670758(-)$1	201	13	39	22.0152
)ffffffuuuuuuuuuuuuffffff>	chr16:43628403-43628606(+)$1	203	106	132	22.1866
ggggggguuuuuuuuuuuuggggggg	chrX:34428082-34428285(+)$1	203	73	99	23.7094
ffffffwwwwwwwwwwwwwwffffff	chr2:31148520-31148721(+)$1	201	122	148	21.3917
cc[eeeeettttttttttteeeeecc	chr9:79618487-79618687(-)$1	200	13	39	22.6098
eeeeeyyyyyyyyyyyyyyyyeeeee	chr12:111929429-111929636(+)$1	207	168	194	22.5175
""cccxxxxxxxxxxxxxxxccc333	chr17:78777199-78777414(-)$1	215	118	144	18.8293
========ttttttttttt=======	chr5:136384722-136384923(-)$1	201	121	147	22.8625
=======wwwwwwwwwwwwww=====	chr16:43621435-43621643(+)$1	208	149	175	22.9241
ffffffyyyyyyyyyyyyyyyyffff	chr10:53626445-53626651(-)$1	206	56	82	22.0667
::eeeeeuuuuuuuuuuuueeeee::	chr15:11913713-11913914(+)$1	201	162	188	20.1840
=======uuuuuuuuuuuu=======	chr16:52206650-52206855(+)$1	205	43	69	24.2698

#otherMatches

#Seq PSSM
AUAAAACUUAAAAAAAUGUAGUUUCA	chr2:6463668-6463872(-)$1	204	167	193	22.7181
GUGGUGGGAAUUAAGAUUAAACCACU	chr3:124025217-124025421(+)$1	204	148	174	21.6993
UGUCCAACCUAACCUCAUCUUUGGAG	chr9:36686079-36686288(+)$1	209	76	102	23.8784
GCCAAGUGAUCAUUAAUAAAGCUUUU	chr6:51411844-51412058(-)$1	214	81	107	22.7774
UCUCUUUUCUCUCACAUUUUAAAGAU	chr15:79654544-79654745(-)$1	201	61	87	23.1057
CCUGACUUCCCCUUUACAUUCUGUCU	chr11:87794087-87794292(-)$1	205	69	95	23.2512
AGGUGUCCCCAGUGCUCCCUCCGCCA	chr7:3330566-3330767(+)$1	201	94	120	22.1705
UUAGGCUGUCCCCUUCUUCCAGCCUU	chr6:72559863-72560067(-)$1	204	48	74	21.9998
AAACUUUAAAAAGAAAAAAAAAAGUG	chr16:7411453-7411654(+)$1	201	143	169	24.0720
UCUAAAAAUUACUUGUGCAUUUUGGG	chr2:29037770-29037973(+)$1	203	62	88	23.8385
CUAUGUUGUCUUUUCCCACCCAAGCU	chr11:35602575-35602779(+)$1	204	25	51	18.5500
AAAUAGCUUUAUCAUGUGUGCUUUGU	chr5:31783781-31783989(+)$1	208	80	106	22.9284
UGGUUUUAUUCCUUUGUUUUAAAUGA	chr4:136878317-136878518(+)$1	201	45	71	21.6819
uaaaaGCUAUUCAAUUCUGCAUGGAA	chr19:41288869-41289075(-)$1	206	88	114	21.3676
AUACAGUCUUCAUAUCACUGAUGUUU	chr13:46744812-46745014(+)$1	202	53	79	21.4787
UAAUUUCUGUAUGUGAUCAAGAGUUU	chr5:32794508-32794715(+)$1	207	125	151	22.2497
UCCUGAAUAUAUAAAACUAGUUUUUA	chr8:113334379-113334605(-)$1	226	183	209	22.6432
GGAUGUAUGCCACUUAAGAAUACCCC	chr5:8067802-8068008(-)$1	206	35	61	21.4280
GGACAGCUAGCUCCCGUCUCCUGUUG	chr14:29289154-29289358(+)$1	204	1	27	18.4096
AAUGCCAAAAUCAAACAGCUGUGCAA	chrX:72355559-72355763(-)$1	204	65	91	23.5057
UACUUGCUUCAAACCAUCCUGCAAAU	chr10:111900717-111900918(+)$1	201	98	124	22.7794
AAGUUGCUAAAGGAAACUGUAACUGG	chr1:157898831-157899034(+)$1	203	66	92	20.3026
GAAGGUCAACUUCUACAUGAGACCAA	chr11:103684118-103684319(-)$1	201	53	79	23.0985
AGACUUGAACAUAGCUAGCCAAGuuu	chr2:28325676-28325878(+)$1	202	82	108	23.7094
AUGUCCAUUUUGCUUGCCUGGAAUUU	chr11:77525542-77525748(+)$1	206	87	113	22.0562
AAUGAGCGCUGCUCCCCAGCUUGCGC	chr19:55143564-55143787(-)$1	223	11	37	22.7918
UUUGUGGACUUCUAAAUACCACCCAC	chr1:162152453-162152662(-)$1	209	166	192	18.4096
CCUGUCACUAUCAAUGCCUCUGGCAG	chr2:181285017-181285217(+)$1	200	117	143	22.3547
UUUGCGAGUCUAACCUCCUCUCAUAA	chr18:24049759-24049969(+)$1	210	108	134	22.2369
AAAGCUUUAGAACAGAAGGAAAGUUU	chr11:105920205-105920410(-)$1	205	101	127	21.3245
CAUCUACAUAAAAUAUCUGGGUAGGU	chr8:27139827-27140044(+)$1	217	67	93	23.1760
GUAACUCUAUUCGACUUUGAGUUGUC	chr17:43225303-43225514(+)$1	211	172	198	22.7743
CAAGCACUAAAGUAUAGAGUGUGUUA	chr12:73313191-73313391(-)$1	200	64	90	23.8354
GGGCUGAUUUCUUUUUCUUUUUAACC	chr7:58118380-58118582(+)$1	202	5	31	21.1806
CUGCCUGGCCAUGAACUACCCUACAG	chr3:87728904-87729122(-)$1	218	45	71	22.9802
CGAGGAUAACUUUUACACUUUUUCCU	chrX:159216528-159216745(+)$1	217	126	152	22.9320
AAGCUUUGCUGUUAUUUGUUUUAAAA	chr19:56672112-56672321(+)$1	209	99	125	22.9802
GUUUCCCUCCGCGUGCAUUGGUUUUG	chr3:131306147-131306355(+)$1	208	35	61	23.1581
AGAUGAGAAAAACACAAGUUCUGCAG	chr12:79785154-79785356(-)$1	202	128	154	21.0377
AAUGUAUUGUAUCACACCGUUGUAUA	chr10:107937261-107937461(-)$1	200	113	139	21.8325
CAGGCUCCAACCCCCGCAAACCUGGU	chr17:23957887-23958090(+)$1	203	21	47	22.3087
CAUCGCGUUUAUUUGCCUCGCAGGUC	chr12:56969426-56969635(+)$1	209	34	60	21.9738
CUCCACCUGACAUUCUCCUUGGUGGG	chr5:102339864-102340067(-)$1	203	20	46	23.5545
GCACAGUUCCCUAUCCCCACCGUCCC	chr2:33586484-33586686(-)$1	202	138	164	20.9965
CAUUAGAUUUUCUUCGUUUCUUCCCA	chr9:121648834-121649046(+)$1	212	129	155	21.8150
UUUGUuuuccaauauguauuaacaaa	chr6:38553764-38553983(+)$1	219	40	66	19.7926
GCGGUCCAUUCCCAAGCCUUGGACAC	chr1:137647620-137647821(+)$1	201	123	149	22.8027
GUUUUUCUCCUUUAAUUCUUGAUGUA	chr15:54670557-54670758(-)$1	201	13	39	22.0152
AGUGUGUCUCUUGCCCCCAACGCAUC	chr16:43628403-43628606(+)$1	203	106	132	22.1866
AUGUUAAGUAAAUCUGGAAUUAGCGU	chrX:34428082-34428285(+)$1	203	73	99	23.7094
UUGGAAUCCAUAACACUUUUUUUCAA	chr2:31148520-31148721(+)$1	201	122	148	21.3917
UGCUAACCUUUGAAAAUUUGGUUACA	chr9:79618487-79618687(-)$1	200	13	39	22.6098
CUAUAGUAUCACAGUAUCACAUGUAG	chr12:111929429-111929636(+)$1	207	168	194	22.5175
GCAACACUAAUCAUGAACACGUUUUU	chr17:78777199-78777414(-)$1	215	118	144	18.8293
ACAUUUAUUACCUUACACUGUAGGUG	chr5:136384722-136384923(-)$1	201	121	147	22.8625
UGUUCCUGUACCACCGAGAGAGGGAG	chr16:43621435-43621643(+)$1	208	149	175	22.9241
GGGUGAUUAUGUUCAUGUUUCCUCAC	chr10:53626445-53626651(-)$1	206	56	82	22.0667
AAUCCAAAUAUACAACAGCUUGGAAA	chr15:11913713-11913914(+)$1	201	162	188	20.1840
GUAUGAAUACAAGUUUUUUUUUAUAC	chr16:52206650-52206855(+)$1	205	43	69	24.2698

#DB
((.(((((...........))))).)	chr2:6463668-6463872(-)$1	1	167	193	22.7181
.((((((..............)))).	chr3:124025217-124025421(+)$1	1	148	174	21.6993
..(((((.............))))).	chr9:36686079-36686288(+)$1	1	76	102	23.8784
(..((((.............))))..	chr6:51411844-51412058(-)$1	1	81	107	22.7774
(((((((.............))))).	chr15:79654544-79654745(-)$1	1	61	87	23.1057
(..(((................))).	chr11:87794087-87794292(-)$1	1	69	95	23.2512
.((((................)))).	chr7:3330566-3330767(+)$1	1	94	120	22.1705
..((((((...........)))))).	chr6:72559863-72560067(-)$1	1	48	74	21.9998
..(((((.............))))).	chr16:7411453-7411654(+)$1	1	143	169	24.0720
(((((((............)))))))	chr2:29037770-29037973(+)$1	1	62	88	23.8385
....(((...............))).	chr11:35602575-35602779(+)$1	1	25	51	18.5500
.((.(((............)))))..	chr5:31783781-31783989(+)$1	1	80	106	22.9284
(.((((..............)))).)	chr4:136878317-136878518(+)$1	1	45	71	21.6819
)))))((...........))((((((	chr19:41288869-41289075(-)$1	1	88	114	21.3676
(.(((.((...........))))).)	chr13:46744812-46745014(+)$1	1	53	79	21.4787
(((.((((...........)))).))	chr5:32794508-32794715(+)$1	1	125	151	22.2497
(...((((...........))))...	chr8:113334379-113334605(-)$1	1	183	209	22.6432
((..((((...........)))).))	chr5:8067802-8068008(-)$1	1	35	61	21.4280
(((((((...............))))	chr14:29289154-29289358(+)$1	1	1	27	18.4096
..(((((............)).))).	chrX:72355559-72355763(-)$1	1	65	91	23.5057
(..((((.............))))))	chr10:111900717-111900918(+)$1	1	98	124	22.7794
.((((((...........))))))((	chr1:157898831-157899034(+)$1	1	66	92	20.3026
...((((.............))))..	chr11:103684118-103684319(-)$1	1	53	79	23.0985
(((((((............)))))))	chr2:28325676-28325878(+)$1	1	82	108	23.7094
((.((((...........))))))))	chr11:77525542-77525748(+)$1	1	87	113	22.0562
..(((((...........))))).))	chr19:55143564-55143787(-)$1	1	11	37	22.7918
(((((((...............))))	chr1:162152453-162152662(-)$1	1	166	192	18.4096
.((((((.............))))))	chr2:181285017-181285217(+)$1	1	117	143	22.3547
((((.(((...........))).)))	chr18:24049759-24049969(+)$1	1	108	134	22.2369
.(((((((...........)))))))	chr11:105920205-105920410(-)$1	1	101	127	21.3245
(((((((.............))))))	chr8:27139827-27140044(+)$1	1	67	93	23.1760
..(((((...........))))))))	chr17:43225303-43225514(+)$1	1	172	198	22.7743
(.(((((.............))))).	chr12:73313191-73313391(-)$1	1	64	90	23.8354
.((.(((.............))).))	chr7:58118380-58118582(+)$1	1	5	31	21.1806
..(((((................)))	chr3:87728904-87729122(-)$1	1	45	71	22.9802
.(((((................))))	chrX:159216528-159216745(+)$1	1	126	152	22.9320
..(((((................)))	chr19:56672112-56672321(+)$1	1	99	125	22.9802
(....((............))...))	chr3:131306147-131306355(+)$1	1	35	61	23.1581
(((................)))....	chr12:79785154-79785356(-)$1	1	128	154	21.0377
.((((((..............)))))	chr10:107937261-107937461(-)$1	1	113	139	21.8325
((((................))))).	chr17:23957887-23958090(+)$1	1	21	47	22.3087
(...(((...........))).))))	chr12:56969426-56969635(+)$1	1	34	60	21.9738
(.(((((.............))))))	chr5:102339864-102340067(-)$1	1	20	46	23.5545
(.((.((...........)).))...	chr2:33586484-33586686(-)$1	1	138	164	20.9965
....(((...........)))....)	chr9:121648834-121649046(+)$1	1	129	155	21.8150
((((((..............))))))	chr6:38553764-38553983(+)$1	1	40	66	19.7926
(..(((((...........)))))..	chr1:137647620-137647821(+)$1	1	123	149	22.8027
((((.((.............))...)	chr15:54670557-54670758(-)$1	1	13	39	22.0152
.((((((............)))))).	chr16:43628403-43628606(+)$1	1	106	132	22.1866
(((((((............)))))))	chrX:34428082-34428285(+)$1	1	73	99	23.7094
((((((..............))))))	chr2:31148520-31148721(+)$1	1	122	148	21.3917
((.(((((...........)))))))	chr9:79618487-79618687(-)$1	1	13	39	22.6098
(((((................)))))	chr12:111929429-111929636(+)$1	1	168	194	22.5175
..(((...............)))...	chr17:78777199-78777414(-)$1	1	118	144	18.8293
((((((((...........)))))))	chr5:136384722-136384923(-)$1	1	121	147	22.8625
(((((((..............)))))	chr16:43621435-43621643(+)$1	1	149	175	22.9241
((((((................))))	chr10:53626445-53626651(-)$1	1	56	82	22.0667
..(((((............)))))..	chr15:11913713-11913914(+)$1	1	162	188	20.1840
(((((((............)))))))	chr16:52206650-52206855(+)$1	1	43	69	24.2698

#PSSM
g : 0.13	c : 0.10	" : 0.10	! : 0.10	e : 0.08	[ : 0.06	f : 0.06	: : 0.06	b : 0.05	d : 0.05	= : 0.05	h : 0.03	i : 0.03	# : 0.01	$ : 0.01	) : 0.01	
" : 0.13	! : 0.13	f : 0.13	g : 0.11	[ : 0.08	b : 0.06	e : 0.06	c : 0.05	= : 0.05	d : 0.03	i : 0.03	# : 0.03	$ : 0.01	h : 0.01	: : 0.01	
e : 0.23	f : 0.15	g : 0.11	! : 0.08	b : 0.06	c : 0.06	[ : 0.05	" : 0.05	= : 0.05	d : 0.03	# : 0.03	i : 0.01	$ : 0.01	h : 0.01	
e : 0.28	f : 0.15	d : 0.11	g : 0.10	c : 0.06	[ : 0.05	= : 0.05	# : 0.03	" : 0.03	i : 0.01	! : 0.01	y : 0.01	b : 0.01	$ : 0.01	h : 0.01	
e : 0.25	d : 0.16	c : 0.15	f : 0.13	g : 0.10	[ : 0.05	= : 0.05	y : 0.03	i : 0.01	# : 0.01	h : 0.01	
e : 0.23	d : 0.15	c : 0.11	f : 0.11	g : 0.10	b : 0.08	y : 0.06	= : 0.05	i : 0.01	[ : 0.01	h : 0.01	x : 0.01	
e : 0.22	d : 0.13	y : 0.11	c : 0.10	b : 0.10	g : 0.10	f : 0.08	w : 0.05	= : 0.05	i : 0.01	x : 0.01	
v : 0.20	y : 0.15	u : 0.15	t : 0.13	w : 0.10	x : 0.06	e : 0.05	d : 0.05	f : 0.01	b : 0.01	c : 0.01	g : 0.01	= : 0.01	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
t : 0.32	v : 0.20	y : 0.15	u : 0.15	w : 0.10	x : 0.06	
v : 0.20	t : 0.18	y : 0.15	u : 0.15	w : 0.10	x : 0.06	b : 0.03	e : 0.03	c : 0.03	f : 0.01	d : 0.01	
v : 0.20	y : 0.13	e : 0.10	w : 0.10	c : 0.08	b : 0.08	x : 0.06	d : 0.06	f : 0.05	g : 0.05	= : 0.03	i : 0.01	
e : 0.20	d : 0.13	y : 0.11	c : 0.11	f : 0.08	g : 0.08	b : 0.06	w : 0.05	x : 0.05	= : 0.03	i : 0.01	] : 0.01	h : 0.01	
e : 0.22	d : 0.16	f : 0.10	c : 0.10	y : 0.08	g : 0.08	x : 0.05	= : 0.05	] : 0.03	b : 0.03	i : 0.01	3 : 0.01	4 : 0.01	h : 0.01	
e : 0.23	d : 0.16	f : 0.11	g : 0.11	c : 0.10	= : 0.05	i : 0.03	b : 0.03	y : 0.03	3 : 0.03	4 : 0.03	] : 0.01	h : 0.01	
e : 0.25	d : 0.11	f : 0.11	g : 0.11	c : 0.08	3 : 0.08	] : 0.06	= : 0.05	i : 0.03	4 : 0.03	b : 0.01	h : 0.01	
e : 0.20	g : 0.15	f : 0.11	c : 0.10	d : 0.06	2 : 0.06	3 : 0.06	] : 0.05	= : 0.05	i : 0.03	4 : 0.03	b : 0.01	h : 0.01	: : 0.01	
g : 0.15	] : 0.13	c : 0.10	2 : 0.10	e : 0.10	f : 0.10	d : 0.05	3 : 0.05	= : 0.05	i : 0.03	4 : 0.03	b : 0.03	h : 0.01	> : 0.01	: : 0.01	

#score	1307.5175320144692
#seq	59
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_CDS_m3_run1.txt

#BEAR
bb[ccc[bb!!cccmmmmccc]bb]ccc]bb	chr8:27204017-27204239(+)$1	222	50	81	13.2175
cc####ccc####bblllbb333ccc4444c	chr10:126620292-126620514(+)$1	222	154	185	12.1109
dddd[dddd!!cccmmmmccc]dddd]dddd	chr13:67646130-67646349(+)$1	219	33	64	14.1859
ffffffccc!!cccmmmmccc22ccc]ffff	chr16:11997154-11997374(+)$1	220	34	65	14.9708
fffffeeeee[cccmmmmccceeeee22fff	chr14:21220346-21220564(-)$1	218	97	128	11.8636
eeeeccc"""ddddmmmmdddd333ccc]ee	chr16:57147822-57148042(+)$1	220	96	127	12.2790
ggg[eeeee!!cccmmmmccc22eeeee]gg	chr3:116209649-116209871(+)$1	222	154	185	15.4869
dddd[a[ccc[cccmmmmcccccc]a]dddd	chr15:95260242-95260467(-)$1	225	114	145	14.0996
hhhheeeee!!cccmmmmccc22eeeee]hh	chr7:151596905-151597139(+)$1	234	167	198	14.1767
a"""==========mmmm==========a]=	chr15:10469645-10469863(+)$1	218	113	144	12.6413
dddd[ccc"""cccmmmmcccccc]dddd::	chr7:134177543-134177767(-)$1	224	62	93	12.8750
dddd!!bb"""cccmmmmccc333bb22ddd	chr11:59999567-59999787(+)$1	220	104	135	15.1980
::ccc[ccc!!cccmmmmccc22ccc]ccc:	chrX:66798202-66798431(+)$1	229	149	180	13.4668
ffffff[ccccccmmmmccc333ccc]ffff	chr16:4875432-4875653(+)$1	221	188	219	12.2236
eeeeebbccc[cccmmmmccc]ccc::eeee	chr9:107947011-107947228(+)$1	217	110	141	11.8521
[bb[bb!!ccccccmmmmccc]cccbb]bb]	chr18:53379966-53380185(+)$1	219	102	133	12.2851
a[bb[a[ddddcccmmmmccc4444dddd]a	chr8:96561207-96561431(+)$1	224	120	151	13.6905
ggggggg[ccc[ccclllccc]cccgggggg	chr15:95071929-95072155(-)$1	226	152	183	11.5264
ddd===========mmmm===========44	chr7:30313732-30313953(+)$1	221	10	41	12.6167
ddd[eeeee!!cccmmmmccc333eeeeedd	chrX:152008193-152008412(-)$1	219	99	130	15.8250
dd!!ccc[ccccccmmmmccc]ccc]ccc22	chr8:77745721-77745943(+)$1	222	63	94	13.9272
ccc"""dddd!!ccclllccc22dddd]ccc	chr10:107072430-107072652(+)$1	222	113	144	12.6216
ee"""eeeee!!bbmmmmbb22eeeee4444	chr1:187107739-187107963(-)$1	224	99	130	11.7922
e!!ffffff"""bbmmmmbb333ffffff22	chr17:85465486-85465723(-)$1	237	52	83	11.7500
dd[eeeee!!cccnnnnnccc22eeeeeddd	chr3:19574150-19574365(-)$1	215	170	201	11.4538
##eeeee####cccmmmmccc666666eeee	chr16:52270732-52270953(-)$1	221	80	111	12.3461
]ccceeeee!!cccmmmmccc22eeeee:::	chr17:8340388-8340611(-)$1	223	77	108	12.4893
"""ccc"""a[cccmmmmccc]a333ccc44	chr11:70266491-70266718(+)$1	227	161	192	15.3347
ddddadddd!!cccmmmmccc4444dddd]a	chr17:24130794-24131015(+)$1	221	58	89	15.0732
iiiiiiii####ccclllccc4444iiiiii	chr8:12948025-12948246(+)$1	221	83	114	13.4416
!eeeee[ccc!!ccclllccc22ccc333ee	chr6:97303075-97303292(-)$1	217	57	88	13.8975
a$$$$$eeeeecccmmmmccc]eeeee22ad	chr14:31730320-31730541(-)$1	221	51	82	11.9219
[bb[ccc####cccmmmmccccccbb]a]a]	chr2:84563718-84563951(-)$1	233	41	72	14.0071
eee!!ccc"""ccclllccc333ccc22eee	chr10:115663090-115663311(+)$1	221	187	218	14.3469
ccccccccc!!cccmmmmccc22ccc]ccc]	chr10:75934172-75934392(+)$1	220	57	88	16.1753
dd!!dddd"""ccclllccc333dddddddd	chr6:121806311-121806532(-)$1	221	40	71	13.7897
ffffff[ccc[cccmmmmccc22ccc4444f	chr3:129336136-129336360(+)$1	224	110	141	15.2627
eeeeee[ccc[cccmmmmccc22ccceeeee	chr11:70985594-70985815(-)$1	221	122	153	15.3020
d!!dddd####cccmmmmccc22dddddddd	chr6:39525064-39525294(+)$1	230	86	117	15.3214
c"""ccccccddddmmmmdddd]ccc]cccc	chr7:134548321-134548542(+)$1	221	186	217	11.5374
bbdddd[ccccccmmmmccc333ccc]dddd	chr6:48487693-48487909(+)$1	216	122	153	12.5908
"dddd####a[cccmmmmccc]a22ddddcc	chr11:109511658-109511879(+)$1	221	122	153	14.0617
[eeeee!!bb[cccmmmmccc]bb22eeeee	chr4:126413133-126413355(+)$1	222	73	104	12.7395
ffffeeeee!!ccclllccc333eeeee]ff	chr2:164949121-164949343(+)$1	222	141	172	12.9478
::ccc!!ddddcccmmmmccc333dddd22c	chr2:104098475-104098701(-)$1	226	34	65	12.5112
dd"""ccc"""cccmmmmccc333ccc5555	chr10:58546241-58546461(-)$1	220	32	63	14.1437
ggdddd!!ccccccmmmmccc4444ccc444	chr9:108014149-108014379(-)$1	230	136	167	14.9408
ccceeeee"""cccmmmmccc22eeeee]cc	chr4:147967942-147968169(+)$1	227	50	81	15.8891
ddd[==========mmmm==========]dd	chr17:71743969-71744192(-)$1	223	147	178	12.6461
cc"""dddd!!cccmmmmcccdddd333ccc	chr1:73966187-73966409(-)$1	222	174	205	14.0303
[dddd[bb"""cccmmmmccc4444bb22dd	chr11:86509014-86509237(-)$1	223	43	74	14.5858
gggggg[a!!ddddllldddd22a]gggggg	chr14:61828482-61828699(+)$1	217	63	94	10.5467

#otherMatches

#Seq PSSM
AACUAUAAUUUGAAACUAUUCUAUAAUAUUU	chr8:27204017-27204239(+)$1	222	50	81	13.2175
UCAAUGGGUGACUGUAAUGCUGGGCCAAGGG	chr10:126620292-126620514(+)$1	222	154	185	12.1109
UUACAAUAUACCAUCUCAAUGCAUAUAGUAA	chr13:67646130-67646349(+)$1	219	33	64	14.1859
GACCACAUGGAGAGAGACCUUAACAUCGUGG	chr16:11997154-11997374(+)$1	220	34	65	14.9708
CAGUUUGUGCACAGAGUGCUGGCACAUGAGC	chr14:21220346-21220564(-)$1	218	97	128	11.8636
AUGCUACAACUUAUGUUCAUAAAGGGUAUGU	chr16:57147822-57148042(+)$1	220	96	127	12.2790
GUAAAGGUUAUCUCUGUUGAGCCGAUUUCUG	chr3:116209649-116209871(+)$1	222	154	185	15.4869
CGGCCCCUGCGUAUGUGGAUGGCAAGUGCUG	chr15:95260242-95260467(-)$1	225	114	145	14.0996
CGGGCAGCUUCAGUUCCCGCUCUGGCUGACC	chr7:151596905-151597139(+)$1	234	167	198	14.1767
GCAUGUUUCUUGGCCUGAGCUGGGAGGCCUG	chr15:10469645-10469863(+)$1	218	113	144	12.6413
GCCCAUCCUAAGGCACUUGCUGGAAGGGCAG	chr7:134177543-134177767(-)$1	224	62	93	12.8750
CCCCUAUAGCCAGCAGCCGCUUAGUACUGGG	chr11:59999567-59999787(+)$1	220	104	135	15.1980
AACCUCUCCUUUGGAUCACUAUUGGAUGGGA	chrX:66798202-66798431(+)$1	229	149	180	13.4668
CCACAGGGGCGGCUGCGGCUGGUGUUGCUGU	chr16:4875432-4875653(+)$1	221	188	219	12.2236
GUACCCGGCAGCAUGGCGAUGAUGCUUCAGC	chr9:107947011-107947228(+)$1	217	110	141	11.8521
UUGCCUAGCCUUACCCCUGUGAAGGAGACAU	chr18:53379966-53380185(+)$1	219	102	133	12.2851
CACCGUUCAGCCAUGGUAAUGGGGUGCUGUA	chr8:96561207-96561431(+)$1	224	120	151	13.6905
AUGGGAUGUUUGCGCCAGGCGGAGAAUCCUG	chr15:95071929-95072155(-)$1	226	152	183	11.5264
GUUGGGGAGGUCUAUGUAUGGACCUUCCCUC	chr7:30313732-30313953(+)$1	221	10	41	12.6167
CAGCUGUGCCUUCAAAUCUGACCUGUACACU	chrX:152008193-152008412(-)$1	219	99	130	15.8250
CUGUGCCGCCAGGUCCCUGCCAUGGAGGCUG	chr8:77745721-77745943(+)$1	222	63	94	13.9272
CCACACAUGCAAUAUUCUGUACAGCAUCUGG	chr10:107072430-107072652(+)$1	222	113	144	12.6216
CCAUGGCUUCCACGGCAUCGAUGAGGUGUAA	chr1:187107739-187107963(-)$1	224	99	130	11.7922
AUACACAGGUCUGGCUUUCUCUUUCUGUGAC	chr17:85465486-85465723(-)$1	237	52	83	11.7500
agaggaaAGAGCAGUUGGUGUCAUUUCCCUU	chr3:19574150-19574365(-)$1	215	170	201	11.4538
UUAAUGGCAGGUAUUAUAGUAAAAUUAUCAU	chr16:52270732-52270953(-)$1	221	80	111	12.3461
CGCUCCCGGGCUGGAUCUCCGUGCUGGGCUG	chr17:8340388-8340611(-)$1	223	77	108	12.4893
ACUGUCAAAUGGCUCUAAAGCGAGUAGACUA	chr11:70266491-70266718(+)$1	227	161	192	15.3347
CACCCCUUGAACGAUCCUUUGCACCCAGGAG	chr17:24130794-24131015(+)$1	221	58	89	15.0732
ACAGCAUGACUUUGAGCCUCAUCUCCGUGCU	chr8:12948025-12948246(+)$1	221	83	114	13.4416
UAAAUACAUAUUGAUCAUGUCUUUAUUUUUA	chr6:97303075-97303292(-)$1	217	57	88	13.8975
GACUCUGGCCCUGGAGAACCAUGGGCUUGCC	chr14:31730320-31730541(-)$1	221	51	82	11.9219
UGGUAGAGAUAUGGUGCACCAUCUCCUGAGU	chr2:84563718-84563951(-)$1	233	41	72	14.0071
GGCCGUCUCAACCCCCCGGGAGAAGGUAGCC	chr10:115663090-115663311(+)$1	221	187	218	14.3469
GGGGGCGUGUCUUCUUUAGAGCUCACAGCCA	chr10:75934172-75934392(+)$1	220	57	88	16.1753
GAACCACCAUCUCAGUGUGAAAAGGUGUCAG	chr6:121806311-121806532(-)$1	221	40	71	13.7897
CUGGUCUUCAACUGGAUGCAGCAUGACAACG	chr3:129336136-129336360(+)$1	224	110	141	15.2627
CCUCAGUGCUCAGUGCCUGCUCCAGCCUGAG	chr11:70985594-70985815(-)$1	221	122	153	15.3020
UCAGGCUCCCUGGCAUCUGCCUAAGUCAGAU	chr6:39525064-39525294(+)$1	230	86	117	15.3214
UGAAGGGGGUCACACCACUGUGUACCACCCG	chr7:134548321-134548542(+)$1	221	186	217	11.5374
GCUGGGCCCUGGUUCGUGCCCAAAGGACCCA	chr6:48487693-48487909(+)$1	216	122	153	12.5908
CACCGAAUCGUCCCACGUGGGUCUGCGGUAG	chr11:109511658-109511879(+)$1	221	122	153	14.0617
ACCAUGGCGGAGUAUGUGUGCACCAACAUGG	chr4:126413133-126413355(+)$1	222	73	104	12.7395
GUGUAGCGAGCUCCGGGGGAUUGUCGUUCAC	chr2:164949121-164949343(+)$1	222	141	172	12.9478
AGGGACAGACAAUCUACAGAUACAUGUCACU	chr2:104098475-104098701(-)$1	226	34	65	12.5112
GACCAGCCCAUAGCAUGAGCUCUAGGCCAUA	chr10:58546241-58546461(-)$1	220	32	63	14.1437
ACCACCCAGCCUGCCUCGGUACUGCGGCCCA	chr9:108014149-108014379(-)$1	230	136	167	14.9408
AAGGAGAUGAGGCACUUCUGCAAAUCUCUCU	chr4:147967942-147968169(+)$1	227	50	81	15.8891
AGGCAAAUUGUUUACUUGUAAACAAUUUACU	chr17:71743969-71744192(-)$1	223	147	178	12.6461
AAGCCGAGGUAGGAGAUAUCCCCUCAUGUUG	chr1:73966187-73966409(-)$1	222	174	205	14.0303
AGGUCAGCCCCAGCUGAUGCUAACAGCAGGA	chr11:86509014-86509237(-)$1	223	43	74	14.5858
GUUUCAACUUGGUUUAUAACUGUGAUGAAAC	chr14:61828482-61828699(+)$1	217	63	94	10.5467

#DB
((.(((.((..(((....))).)).))).))	chr8:27204017-27204239(+)$1	1	50	81	13.2175
((....(((....((...))...)))....)	chr10:126620292-126620514(+)$1	1	154	185	12.1109
((((.((((..(((....))).)))).))))	chr13:67646130-67646349(+)$1	1	33	64	14.1859
(((((((((..(((....)))..))).))))	chr16:11997154-11997374(+)$1	1	34	65	14.9708
((((((((((.(((....))))))))..)))	chr14:21220346-21220564(-)$1	1	97	128	11.8636
(((((((...((((....))))...))).))	chr16:57147822-57148042(+)$1	1	96	127	12.2790
(((.(((((..(((....)))..))))).))	chr3:116209649-116209871(+)$1	1	154	185	15.4869
((((.(.(((.(((....)))))).).))))	chr15:95260242-95260467(-)$1	1	114	145	14.0996
(((((((((..(((....)))..))))).))	chr7:151596905-151597139(+)$1	1	167	198	14.1767
(...((((((((((....))))))))))).)	chr15:10469645-10469863(+)$1	1	113	144	12.6413
((((.(((...(((....)))))).))))..	chr7:134177543-134177767(-)$1	1	62	93	12.8750
((((..((...(((....)))...))..)))	chr11:59999567-59999787(+)$1	1	104	135	15.1980
..(((.(((..(((....)))..))).))).	chrX:66798202-66798431(+)$1	1	149	180	13.4668
((((((.((((((....)))...))).))))	chr16:4875432-4875653(+)$1	1	188	219	12.2236
)))))))(((.(((....))).)))..((((	chr9:107947011-107947228(+)$1	1	110	141	11.8521
.((.((..((((((....))).))))).)).	chr18:53379966-53380185(+)$1	1	102	133	12.2851
(.((.(.(((((((....)))....)))).)	chr8:96561207-96561431(+)$1	1	120	151	13.6905
(((((((.(((.(((...))).)))))))))	chr15:95071929-95072155(-)$1	1	152	183	11.5264
((((((((((((((....)))))))))))..	chr7:30313732-30313953(+)$1	1	10	41	12.6167
(((.(((((..(((....)))...)))))))	chrX:152008193-152008412(-)$1	1	99	130	15.8250
((..(((.((((((....))).))).)))..	chr8:77745721-77745943(+)$1	1	63	94	13.9272
(((...((((..(((...)))..)))).)))	chr10:107072430-107072652(+)$1	1	113	144	12.6216
((...(((((..((....))..)))))....	chr1:187107739-187107963(-)$1	1	99	130	11.7922
(..((((((...((....))...))))))..	chr17:85465486-85465723(-)$1	1	52	83	11.7500
((.(((((..(((.....)))..))))))))	chr3:19574150-19574365(-)$1	1	170	201	11.4538
..(((((....(((....)))......))))	chr16:52270732-52270953(-)$1	1	80	111	12.3461
.)))(((((..(((....)))..)))))...	chr17:8340388-8340611(-)$1	1	77	108	12.4893
...(((...(.(((....))).)...)))..	chr11:70266491-70266718(+)$1	1	161	192	15.3347
(((((((((..(((....)))....)))).)	chr17:24130794-24131015(+)$1	1	58	89	15.0732
((((((((....(((...)))....))))))	chr8:12948025-12948246(+)$1	1	83	114	13.4416
.(((((.(((..(((...)))..)))...))	chr6:97303075-97303292(-)$1	1	57	88	13.8975
(.....((((((((....))).)))))..))	chr14:31730320-31730541(-)$1	1	51	82	11.9219
.((.(((....(((....)))))))).).).	chr2:84563718-84563951(-)$1	1	41	72	14.0071
(((..(((...(((...)))...)))..)))	chr10:115663090-115663311(+)$1	1	187	218	14.3469
(((((((((..(((....)))..))).))).	chr10:75934172-75934392(+)$1	1	57	88	16.1753
((..((((...(((...)))...))))))))	chr6:121806311-121806532(-)$1	1	40	71	13.7897
((((((.(((.(((....)))..)))....)	chr3:129336136-129336360(+)$1	1	110	141	15.2627
((((((.(((.(((....)))..))))))))	chr11:70985594-70985815(-)$1	1	122	153	15.3020
(..((((....(((....)))..))))))))	chr6:39525064-39525294(+)$1	1	86	117	15.3214
(...((((((((((....)))).))).))))	chr7:134548321-134548542(+)$1	1	186	217	11.5374
((((((.((((((....)))...))).))))	chr6:48487693-48487909(+)$1	1	122	153	12.5908
.((((....(.(((....))).)..))))))	chr11:109511658-109511879(+)$1	1	122	153	14.0617
.(((((..((.(((....))).))..)))))	chr4:126413133-126413355(+)$1	1	73	104	12.7395
(((((((((..(((...)))...))))).))	chr2:164949121-164949343(+)$1	1	141	172	12.9478
..(((..(((((((....)))...))))..)	chr2:104098475-104098701(-)$1	1	34	65	12.5112
((...(((...(((....)))...)))....	chr10:58546241-58546461(-)$1	1	32	63	14.1437
((((((..((((((....)))....)))...	chr9:108014149-108014379(-)$1	1	136	167	14.9408
((((((((...(((....)))..))))).))	chr4:147967942-147968169(+)$1	1	50	81	15.8891
(((.((((((((((....)))))))))).))	chr17:71743969-71744192(-)$1	1	147	178	12.6461
((...((((..(((....)))))))...)))	chr1:73966187-73966409(-)$1	1	174	205	14.0303
.((((.((...(((....)))....))..))	chr11:86509014-86509237(-)$1	1	43	74	14.5858
((((((.(..((((...))))..).))))))	chr14:61828482-61828699(+)$1	1	63	94	10.5467

#PSSM
d : 0.24	c : 0.11	e : 0.11	f : 0.09	g : 0.07	[ : 0.07	a : 0.05	b : 0.03	: : 0.03	" : 0.03	h : 0.01	# : 0.01	] : 0.01	i : 0.01	! : 0.01	
d : 0.26	e : 0.13	c : 0.11	f : 0.09	b : 0.07	g : 0.07	" : 0.05	: : 0.03	! : 0.03	h : 0.01	[ : 0.01	# : 0.01	i : 0.01	$ : 0.01	
d : 0.23	e : 0.13	" : 0.11	c : 0.11	f : 0.09	! : 0.07	g : 0.05	b : 0.05	[ : 0.03	# : 0.01	h : 0.01	i : 0.01	$ : 0.01	
d : 0.19	e : 0.15	c : 0.11	f : 0.11	" : 0.11	[ : 0.09	! : 0.05	g : 0.03	# : 0.01	h : 0.01	b : 0.01	= : 0.01	i : 0.01	$ : 0.01	
e : 0.23	c : 0.17	d : 0.11	f : 0.09	[ : 0.07	" : 0.07	= : 0.05	! : 0.03	g : 0.03	# : 0.01	b : 0.01	a : 0.01	i : 0.01	$ : 0.01	
e : 0.24	c : 0.19	d : 0.13	f : 0.07	= : 0.05	# : 0.03	a : 0.03	! : 0.03	[ : 0.03	b : 0.03	g : 0.03	" : 0.01	i : 0.01	$ : 0.01	
c : 0.21	e : 0.21	[ : 0.17	d : 0.11	! : 0.07	= : 0.05	b : 0.05	g : 0.01	f : 0.01	" : 0.01	i : 0.01	# : 0.01	
c : 0.28	e : 0.19	d : 0.13	# : 0.07	b : 0.05	= : 0.05	! : 0.05	" : 0.03	[ : 0.03	f : 0.01	i : 0.01	a : 0.01	
c : 0.30	" : 0.17	e : 0.15	d : 0.11	# : 0.09	= : 0.05	b : 0.03	! : 0.03	f : 0.01	
! : 0.26	c : 0.23	" : 0.17	# : 0.09	e : 0.05	= : 0.05	d : 0.05	a : 0.03	b : 0.01	
! : 0.28	[ : 0.15	" : 0.15	c : 0.13	# : 0.09	d : 0.09	= : 0.05	e : 0.01	
c : 0.75	d : 0.05	= : 0.05	! : 0.05	# : 0.03	[ : 0.01	" : 0.01	
c : 0.82	d : 0.05	= : 0.05	b : 0.03	# : 0.01	
c : 0.76	b : 0.05	d : 0.05	= : 0.05	m : 0.03	n : 0.01	
m : 0.80	c : 0.07	l : 0.07	b : 0.01	n : 0.01	
m : 0.80	l : 0.17	n : 0.01	
m : 0.80	l : 0.17	n : 0.01	
m : 0.76	l : 0.09	c : 0.09	n : 0.01	d : 0.01	
c : 0.82	b : 0.05	d : 0.05	= : 0.05	
c : 0.82	b : 0.05	d : 0.05	= : 0.05	
c : 0.73	3 : 0.13	d : 0.05	= : 0.05	2 : 0.01	
2 : 0.28	3 : 0.21	] : 0.19	4 : 0.09	d : 0.05	c : 0.05	= : 0.05	e : 0.01	6 : 0.01	
2 : 0.26	3 : 0.23	c : 0.13	4 : 0.09	e : 0.05	= : 0.05	b : 0.03	d : 0.03	a : 0.03	6 : 0.01	] : 0.01	
c : 0.34	e : 0.17	3 : 0.11	d : 0.09	4 : 0.09	= : 0.05	b : 0.03	f : 0.01	6 : 0.01	2 : 0.01	a : 0.01	
c : 0.30	e : 0.19	d : 0.11	4 : 0.09	] : 0.07	= : 0.05	3 : 0.03	b : 0.03	2 : 0.03	f : 0.01	6 : 0.01	
c : 0.28	e : 0.19	d : 0.17	b : 0.07	= : 0.05	g : 0.03	3 : 0.03	a : 0.01	: : 0.01	] : 0.01	f : 0.01	6 : 0.01	i : 0.01	2 : 0.01	
e : 0.21	] : 0.17	d : 0.15	c : 0.11	2 : 0.05	= : 0.05	4 : 0.03	b : 0.03	g : 0.03	3 : 0.03	: : 0.01	f : 0.01	6 : 0.01	i : 0.01	
e : 0.21	d : 0.19	c : 0.15	2 : 0.09	4 : 0.05	f : 0.05	= : 0.05	] : 0.03	g : 0.03	3 : 0.03	i : 0.01	a : 0.01	5 : 0.01	
d : 0.21	] : 0.15	c : 0.13	e : 0.11	4 : 0.07	f : 0.07	2 : 0.05	g : 0.03	a : 0.01	b : 0.01	= : 0.01	: : 0.01	i : 0.01	3 : 0.01	5 : 0.01	
d : 0.19	e : 0.13	c : 0.13	4 : 0.11	f : 0.07	g : 0.05	] : 0.05	2 : 0.05	b : 0.03	: : 0.03	a : 0.03	h : 0.01	i : 0.01	5 : 0.01	
d : 0.21	c : 0.13	e : 0.13	f : 0.09	4 : 0.07	g : 0.05	: : 0.05	] : 0.05	a : 0.03	2 : 0.03	b : 0.01	h : 0.01	= : 0.01	i : 0.01	5 : 0.01	

#score	700.0192163558518
#seq	52
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_CDS_m3_run1.txt

#BEAR
Eiiiiiiiiiooooooiiiiiiiii:	chr6:56728726-56729000(-)$1	274	163	189	8.2088
ggggggg!!ddddllldddd333ggg	chr8:74842841-74843113(+)$1	272	78	104	9.3369
::ffffff[bboooooobb]ffffff	chr16:91227498-91227771(+)$1	273	191	217	8.3044
:gggggggddddllldddd]gggggg	chr9:98390942-98391210(+)$1	268	206	232	8.6733
:ffffffcccooooooccc22fffff	chr11:102978337-102978633(+)$1	296	89	115	9.3799
fffff####cccmmmmccc333ffff	chr7:135038924-135039193(-)$1	269	194	220	10.7260
:eeeee!!bboooooobb22eeeeeg	chr5:122096593-122096864(-)$1	271	107	133	8.3900
ccca[ccc[cccmmmmcccccc]a33	chr1:93275013-93275289(-)$1	276	190	216	10.1434
##ccc[ffffffmmmmffffff]ccc	chr14:103482193-103482469(-)$1	276	176	202	9.3010
========[cccmmmmccc]======	chr14:45912564-45912838(-)$1	274	24	50	11.9706
[a!!eeeee[ccclllccc]eeeeea	chr2:34678076-34678352(-)$1	276	19	45	9.5459
========!!bbmmmmbb333=====	chr7:28151313-28151603(-)$1	290	4	30	11.0634
[eeeee[a[bboooooobb]aeeeee	chr11:97574608-97574878(+)$1	270	133	159	9.5666
a[cccbb[ddddmmmmdddd]bb]cc	chr13:69138016-69138287(-)$1	271	60	86	7.9391
:eeeeeffffffmmmmffffff333e	chr19:8964904-8965185(+)$1	281	166	192	8.3931
c"""ffffffccclllccc]ffffff	chrX:98514856-98515126(+)$1	270	26	52	9.9724
eeeeeeecccooooooccc]eeeee2	chr7:117008957-117009223(-)$1	266	87	113	9.5053
!!eeeee####ammmma4444eeeee	chr2:40774602-40774881(-)$1	279	59	85	10.3695
ccggggggg[bbmmmmbbggggggg]	chr19:5384494-5384771(-)$1	277	202	228	9.7003
!ccc!!bb[a[ammmma]a]bb]ccc	chr7:52631892-52632163(-)$1	271	10	36	9.7789
ggggg[ffffffmmmmffffffgggg	chr2:174125804-174126079(+)$1	275	238	264	9.5906
gggggg"""ccclllccc4444gggg	chr9:66220026-66220300(+)$1	274	28	54	10.6099
=============lll==========	chr2:121205209-121205478(-)$1	269	95	121	10.5759
:ccc[ffffffaooooooa]ffffff	chr16:36049850-36050132(-)$1	282	47	73	9.3080
!ccc!!a[ddddmmmmdddda22ccc	chr9:108701514-108701781(+)$1	267	162	188	8.6323
b[ffffff[cccmmmmccc]ffffff	chr3:95464614-95464908(+)$1	294	178	204	11.2499
b[eeeee!!ccclllccc22eeeee]	chr9:107159265-107159531(-)$1	266	141	167	9.9231

#otherMatches

#Seq PSSM
AUAUCCUUUGCUAAACCAGAGGAUAA	chr6:56728726-56729000(-)$1	274	163	189	8.2088
GCCUGCCGCGCCUAUAAGGCCUGGGU	chr8:74842841-74843113(+)$1	272	78	104	9.3369
GGGGCUCUGUUGCAAGAAGGGGAGCU	chr16:91227498-91227771(+)$1	273	191	217	8.3044
AGACUGGUCCUUGAGGAGGUGCUAGU	chr9:98390942-98391210(+)$1	268	206	232	8.6733
AGGGGGCCUGAAGCACCAGCUGCCCC	chr11:102978337-102978633(+)$1	296	89	115	9.3799
CGCGCCCGCGAUGAAAAUUACCGCGC	chr7:135038924-135039193(-)$1	269	194	220	10.7260
UGCCUUGGAGAAGUACCUGAAGGGCU	chr5:122096593-122096864(-)$1	271	107	133	8.3900
CUGUGGGGUCACAUCUGUGCCUGAUA	chr1:93275013-93275289(-)$1	276	190	216	10.1434
AAUUUGUCAGCUAUUGGGCUGGGGGA	chr14:103482193-103482469(-)$1	276	176	202	9.3010
GAGUUCCAGCAGCGCUUUGAUGGGAU	chr14:45912564-45912838(-)$1	274	24	50	11.9706
ACAUGCUGCCUGGUCUCUAAGCAGUG	chr2:34678076-34678352(-)$1	276	19	45	9.5459
GGGGUGGGGGGUGAGGGCAGGUCCAU	chr7:28151313-28151603(-)$1	290	4	30	11.0634
CCCGGAUGGACUAACCUGUGCUCUGG	chr11:97574608-97574878(+)$1	270	133	159	9.5666
GAGCGGCGCUGCCCGGGCAGGGCGCG	chr13:69138016-69138287(-)$1	271	60	86	7.9391
UGGAAAAAAUAUUAGCAUAUUUCACU	chr19:8964904-8965185(+)$1	281	166	192	8.3931
CAAGGGUUCGUGAUCAUUACCGGGCC	chrX:98514856-98515126(+)$1	270	26	52	9.9724
GCCGCAGGCUCUACGCGGCUCUGCGC	chr7:117008957-117009223(-)$1	266	87	113	9.5053
UAUUGCUAUAUGAUCUCUAACAGCAA	chr2:40774602-40774881(-)$1	279	59	85	10.3695
AGGGGCAUGUGGGUUCUCCAUGUUCA	chr19:5384494-5384771(-)$1	277	202	228	9.7003
GCACAAGCGUGGGGAGCGGGGCAGUG	chr7:52631892-52632163(-)$1	271	10	36	9.7789
UGGGGUGGGCCCUUCGGGGCUCCCCC	chr2:174125804-174126079(+)$1	275	238	264	9.5906
UCAGUGAACGCCCCCGGUCAAGCACU	chr9:66220026-66220300(+)$1	274	28	54	10.6099
CUUCAUCCUUCCAGCUUGGGAGGAUG	chr2:121205209-121205478(-)$1	269	95	121	10.5759
CUUGAUUUGAGCAUUAAAGUCUCAAG	chr16:36049850-36050132(-)$1	282	47	73	9.3080
CUUGGAGCAUGAAAUGUCAUCAACAA	chr9:108701514-108701781(+)$1	267	162	188	8.6323
ACAUGCAUCUGUGAAAACAUGUGUAU	chr3:95464614-95464908(+)$1	294	178	204	11.2499
GAGUAGAUUCUGUCUCAGUCUCUAUA	chr9:107159265-107159531(-)$1	266	141	167	9.9231

#DB
((((((((((......))))))))).	chr6:56728726-56729000(-)$1	1	163	189	8.2088
(((((((..((((...))))...)))	chr8:74842841-74843113(+)$1	1	78	104	9.3369
..((((((.((......)).))))))	chr16:91227498-91227771(+)$1	1	191	217	8.3044
.(((((((((((...)))).))))))	chr9:98390942-98391210(+)$1	1	206	232	8.6733
.(((((((((......)))..)))))	chr11:102978337-102978633(+)$1	1	89	115	9.3799
(((((....(((....)))...))))	chr7:135038924-135039193(-)$1	1	194	220	10.7260
.(((((..((......))..)))))(	chr5:122096593-122096864(-)$1	1	107	133	8.3900
((((.(((.(((....)))))).)..	chr1:93275013-93275289(-)$1	1	190	216	10.1434
..(((.((((((....)))))).)))	chr14:103482193-103482469(-)$1	1	176	202	9.3010
((((((((.(((....))).))))))	chr14:45912564-45912838(-)$1	1	24	50	11.9706
.(..(((((.(((...))).))))))	chr2:34678076-34678352(-)$1	1	19	45	9.5459
((((((((..((....))...)))))	chr7:28151313-28151603(-)$1	1	4	30	11.0634
.(((((.(.((......)).))))))	chr11:97574608-97574878(+)$1	1	133	159	9.5666
(.(((((.((((....)))).)).))	chr13:69138016-69138287(-)$1	1	60	86	7.9391
.(((((((((((....))))))...)	chr19:8964904-8965185(+)$1	1	166	192	8.3931
(...(((((((((...))).))))))	chrX:98514856-98515126(+)$1	1	26	52	9.9724
((((((((((......))).))))).	chr7:117008957-117009223(-)$1	1	87	113	9.5053
..(((((....(....)....)))))	chr2:40774602-40774881(-)$1	1	59	85	10.3695
(((((((((.((....))))))))).	chr19:5384494-5384771(-)$1	1	202	228	9.7003
.(((..((.(.(....).).)).)))	chr7:52631892-52632163(-)$1	1	10	36	9.7789
(((((.((((((....))))))))))	chr2:174125804-174126079(+)$1	1	238	264	9.5906
((((((...(((...)))....))))	chr9:66220026-66220300(+)$1	1	28	54	10.6099
(((((((((((((...))))))))))	chr2:121205209-121205478(-)$1	1	95	121	10.5759
.(((.(((((((......).))))))	chr16:36049850-36050132(-)$1	1	47	73	9.3080
.(((..(.((((....)))))..)))	chr9:108701514-108701781(+)$1	1	162	188	8.6323
(.((((((.(((....))).))))))	chr3:95464614-95464908(+)$1	1	178	204	11.2499
(.(((((..(((...)))..))))).	chr9:107159265-107159531(-)$1	1	141	167	9.9231

#PSSM
: : 0.22	g : 0.11	c : 0.11	= : 0.11	! : 0.11	[ : 0.07	b : 0.07	E : 0.03	f : 0.03	# : 0.03	a : 0.03	e : 0.03	
c : 0.18	g : 0.14	e : 0.14	= : 0.11	[ : 0.11	f : 0.07	i : 0.03	: : 0.03	# : 0.03	a : 0.03	" : 0.03	! : 0.03	
e : 0.22	c : 0.22	g : 0.18	f : 0.14	= : 0.11	i : 0.03	! : 0.03	" : 0.03	
e : 0.22	g : 0.18	c : 0.18	f : 0.14	= : 0.11	i : 0.03	a : 0.03	! : 0.03	" : 0.03	
e : 0.25	g : 0.18	f : 0.18	= : 0.11	[ : 0.07	c : 0.07	! : 0.07	i : 0.03	
e : 0.25	f : 0.18	g : 0.14	= : 0.11	[ : 0.07	! : 0.07	i : 0.03	# : 0.03	c : 0.03	b : 0.03	
f : 0.29	e : 0.14	g : 0.11	= : 0.11	b : 0.07	i : 0.03	# : 0.03	! : 0.03	c : 0.03	[ : 0.03	" : 0.03	a : 0.03	
f : 0.25	! : 0.11	c : 0.11	= : 0.11	g : 0.07	# : 0.07	[ : 0.07	i : 0.03	e : 0.03	a : 0.03	b : 0.03	" : 0.03	
[ : 0.22	f : 0.18	! : 0.11	d : 0.11	c : 0.07	# : 0.07	i : 0.03	b : 0.03	e : 0.03	g : 0.03	" : 0.03	= : 0.03	
c : 0.29	f : 0.18	d : 0.14	b : 0.11	[ : 0.07	i : 0.03	! : 0.03	# : 0.03	a : 0.03	= : 0.03	
c : 0.29	o : 0.14	d : 0.14	b : 0.14	f : 0.14	# : 0.03	[ : 0.03	= : 0.03	
c : 0.29	o : 0.22	d : 0.14	f : 0.11	a : 0.11	b : 0.07	= : 0.03	
m : 0.48	o : 0.25	l : 0.11	c : 0.07	d : 0.03	= : 0.03	
m : 0.48	o : 0.25	l : 0.25	
m : 0.48	o : 0.25	l : 0.25	
m : 0.48	o : 0.25	l : 0.14	c : 0.07	d : 0.03	
c : 0.37	d : 0.14	o : 0.11	b : 0.11	f : 0.11	a : 0.07	i : 0.03	= : 0.03	
c : 0.37	b : 0.18	d : 0.14	f : 0.11	i : 0.03	4 : 0.03	] : 0.03	= : 0.03	o : 0.03	
c : 0.29	d : 0.14	f : 0.11	b : 0.07	2 : 0.07	4 : 0.07	a : 0.07	i : 0.03	3 : 0.03	g : 0.03	= : 0.03	
] : 0.37	d : 0.11	2 : 0.11	f : 0.11	3 : 0.07	4 : 0.07	i : 0.03	c : 0.03	g : 0.03	= : 0.03	
f : 0.25	e : 0.14	3 : 0.11	g : 0.07	= : 0.07	a : 0.07	4 : 0.07	i : 0.03	2 : 0.03	c : 0.03	] : 0.03	b : 0.03	
f : 0.29	e : 0.22	= : 0.11	3 : 0.07	g : 0.07	b : 0.07	i : 0.03	c : 0.03	4 : 0.03	2 : 0.03	
f : 0.22	e : 0.22	g : 0.14	] : 0.11	= : 0.11	3 : 0.07	i : 0.03	b : 0.03	2 : 0.03	
f : 0.22	e : 0.22	g : 0.18	c : 0.11	= : 0.11	i : 0.03	a : 0.03	] : 0.03	3 : 0.03	
f : 0.22	e : 0.22	g : 0.18	c : 0.14	= : 0.11	3 : 0.07	i : 0.03	
f : 0.22	g : 0.18	c : 0.14	= : 0.11	e : 0.11	] : 0.07	: : 0.03	3 : 0.03	a : 0.03	2 : 0.03	

#score	260.1598242667703
#seq	27
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_UTR_m2_run1.txt

#BEAR
eeeeeqqqqqqqqeeeee	chr14:27475776-27476062(+)$1	286	84	102	15.3770
eeeeeqqqqqqqqeeeee	chr15:10266498-10266766(+)$1	268	76	94	15.3770
eeeeeqqqqqqqqeeeee	chr11:105787847-105788093(+)$1	246	30	48	15.3770
"ddddqqqqqqqqdddd4	chr3:145555977-145556249(+)$1	272	154	172	13.6202
[ddddqqqqqqqqdddd]	chr2:125565155-125565414(-)$1	259	31	49	13.9466
eeeeeqqqqqqqqeeeee	chr2:65861377-65861849(+)$1	472	268	286	15.3770
eeeeeqqqqqqqqeeeee	chr16:57169036-57169384(-)$1	348	278	296	15.3770
c[cccqqqqqqqqccccc	chr1:136243437-136243806(-)$1	369	261	279	13.8905
eeeeeqqqqqqqqeeeee	chr2:49405618-49406044(+)$1	426	152	170	15.3770
eeeeeqqqqqqqqeeeee	chr5:135657461-135657766(+)$1	305	53	71	15.3770
[ddddqqqqqqqqdddd]	chr19:10525539-10525873(+)$1	334	185	203	13.9466
gggggqqqqqqqqggggg	chrX:92245447-92245823(-)$1	376	185	203	14.3580
eeeeeqqqqqqqqeeeee	chr5:92483475-92483841(-)$1	366	206	224	15.3770
!!cccqqqqqqqqcccee	chr1:24819919-24820219(+)$1	300	55	73	14.4173
h[cccqqqqqqqqccc33	chr2:66109958-66110257(-)$1	299	244	262	13.9313
eeeeeqqqqqqqqeeeee	chr13:41371668-41372046(+)$1	378	115	133	15.3770
eeeeeqqqqqqqqeeeee	chr1:167145371-167145653(-)$1	282	230	248	15.3770
c[cccqqqqqqqqccc]c	chr3:31101673-31101960(-)$1	287	172	190	13.9667
gggggqqqqqqqqggggg	chr11:77994701-77994962(-)$1	261	196	214	14.3580
eeeeeqqqqqqqqeeeee	chr2:181284796-181285243(+)$1	447	70	88	15.3770
eeeeeqqqqqqqqeeeee	chr1:23884444-23884739(-)$1	295	129	147	15.3770
eeeeeqqqqqqqqeeeee	chrX:154270707-154271079(-)$1	372	351	369	15.3770
iiiiiqqqqqqqqiiiii	chr2:121759787-121760067(+)$1	280	137	155	14.0289
fffffqqqqqqqqfffff	chr7:71031287-71031599(-)$1	312	125	143	13.9874
fffffqqqqqqqqfffff	chr18:34505411-34505834(-)$1	423	372	390	13.9874
fffffqqqqqqqqfffff	chr2:104266860-104267256(-)$1	396	130	148	13.9874
eeeeeqqqqqqqqeeeee	chr18:82725818-82726204(+)$1	386	345	363	15.3770
[ddddqqqqqqqqdddd]	chr3:27140725-27141010(+)$1	285	228	246	13.9466
eeeeeqqqqqqqqeeeee	chr2:163842310-163842661(+)$1	351	166	184	15.3770
eecccqqqqqqqqccc]e	chr11:50048389-50048708(+)$1	319	107	125	14.5041
eeeeeqqqqqqqqeeeee	chr2:155215215-155215684(+)$1	469	2	20	15.3770
gggggqqqqqqqqggggg	chr4:25544657-25544957(-)$1	300	184	202	14.3580
dddddqqqqqqqqdddd]	chr8:74864797-74865145(-)$1	348	304	322	13.7397
ccc[aqqqqqqqqa]ccc	chr11:100208541-100208836(-)$1	295	13	31	13.5418
ffcccqqqqqqqqccc]f	chr6:120389930-120390207(+)$1	277	209	227	14.0599
ddd[aqqqqqqqqa]ddd	chr1:167259626-167260086(-)$1	460	409	427	13.4483
iiiiiqqqqqqqqiiiii	chr11:54683767-54684108(+)$1	341	59	77	14.0289
eeebbqqqqqqqqbb]ee	chr7:148615779-148616067(-)$1	288	24	42	13.4953
eeeeeqqqqqqqqeeeee	chr4:24935845-24936196(+)$1	351	278	296	15.3770
fffffqqqqqqqqfffff	chr4:94715962-94716345(-)$1	383	65	83	13.9874
[ddddqqqqqqqqdddd]	chr6:134874456-134874731(+)$1	275	70	88	13.9466
=====qqqqqqqq=====	chr5:14862582-14862993(+)$1	411	22	40	14.2126
!ddddqqqqqqqqdddd3	chr10:23907979-23908353(+)$1	374	300	318	13.8679
fffffqqqqqqqqfffff	chr17:33783079-33783493(-)$1	414	241	259	13.9874
eeeeeqqqqqqqqeeeee	chrX:99710825-99711109(-)$1	284	95	113	15.3770
gggggqqqqqqqqggggg	chr3:27142554-27142931(+)$1	377	70	88	14.3580
d[cccqqqqqqqqccc22	chr3:83577963-83578277(+)$1	314	54	72	13.5893
eeeeeqqqqqqqqeeeee	chr13:113296760-113297152(+)$1	392	210	228	15.3770
!!cccqqqqqqqqccc22	chr1:33854442-33854750(-)$1	308	46	64	13.7209
fffffqqqqqqqqfffff	chr13:49478960-49479268(+)$1	308	100	118	13.9874
eeeeeqqqqqqqqeeeee	chr6:30404848-30405257(+)$1	409	22	40	15.3770
fffffqqqqqqqqfffff	chr12:3402806-3403123(+)$1	317	73	91	13.9874
!!cccqqqqqqqqccc22	chr6:148937703-148937975(-)$1	272	207	225	13.7209
eeeeeqqqqqqqqeeeee	chr3:138567207-138567493(+)$1	286	257	275	15.3770
eeeeeqqqqqqqqeeeee	chr13:78328164-78328458(-)$1	294	180	198	15.3770
eeeeaqqqqqqqqa]eee	chr9:28728136-28728616(+)$1	480	31	49	14.8294
gggggqqqqqqqqggggg	chr5:145869373-145869723(+)$1	350	330	348	14.3580
fffffqqqqqqqqfffff	chr7:89030283-89030629(-)$1	346	118	136	13.9874
eeeeeqqqqqqqqeeeee	chr4:15211829-15212221(+)$1	392	0	18	15.3770
h[cccqqqqqqqqccchh	chr3:88992869-88993169(+)$1	300	246	264	13.6070
fffffqqqqqqqqfffff	chr5:125316109-125316423(-)$1	314	80	98	13.9874
iiiiiqqqqqqqqiiiii	chr1:94756298-94756583(+)$1	285	66	84	14.0289
cccccqqqqqqqqccc]c	chr7:137907916-137908176(+)$1	260	101	119	13.8517
gggggqqqqqqqqggggg	chr11:68634880-68635237(-)$1	357	266	284	14.3580
eeeeeqqqqqqqqeeeee	chr15:11913014-11913346(-)$1	332	239	257	15.3770
ddd[aqqqqqqqqadddd	chr11:68559558-68559921(+)$1	363	143	161	13.4812
ee[bbqqqqqqqqbb]ee	chr3:90161840-90162161(+)$1	321	34	52	13.3093
gggggqqqqqqqqggggg	chr17:80248412-80248687(-)$1	275	14	32	14.3580
!ddddqqqqqqqqdddd2	chr18:64659216-64659508(-)$1	292	138	156	13.6846
fffffqqqqqqqqfffff	chr14:45968272-45968582(+)$1	310	44	62	13.9874
eeeeeqqqqqqqqeeeee	chr19:55142438-55142697(-)$1	259	138	156	15.3770
gggggqqqqqqqqggggg	chr11:117883072-117883396(+)$1	324	287	305	14.3580
[ddddqqqqqqqqdddd2	chr1:33855339-33855727(-)$1	388	120	138	13.7208
fffffqqqqqqqqfffff	chr2:180417206-180417473(-)$1	267	188	206	13.9874
fffffqqqqqqqqfffff	chr15:100873138-100873523(+)$1	385	56	74	13.9874
bddddqqqqqqqqdddd]	chr10:114726769-114727038(-)$1	269	241	259	13.5009

#otherMatches

#Seq PSSM
AAAUGUAGCAUUCCAUUU	chr14:27475776-27476062(+)$1	286	84	102	15.3770
GACAGUUAAAUCUUUGUC	chr15:10266498-10266766(+)$1	268	76	94	15.3770
UUUUUAAACACAAGAAAA	chr11:105787847-105788093(+)$1	246	30	48	15.3770
CAUAUUUCACAACAUAUC	chr3:145555977-145556249(+)$1	272	154	172	13.6202
UCUGUAAGAUCAAACAGU	chr2:125565155-125565414(-)$1	259	31	49	13.9466
CCAGACGAUUGCAUCUGG	chr2:65861377-65861849(+)$1	472	268	286	15.3770
CUCGACACCCUCUUUGAG	chr16:57169036-57169384(-)$1	348	278	296	15.3770
GUGGCUUUUCUCUGCCCU	chr1:136243437-136243806(-)$1	369	261	279	13.8905
UUGCACUUGAAUUUGCAA	chr2:49405618-49406044(+)$1	426	152	170	15.3770
AGUACCUGCCCCAGUACU	chr5:135657461-135657766(+)$1	305	53	71	15.3770
CCCUCCAGCACCAGAGGC	chr19:10525539-10525873(+)$1	334	185	203	13.9466
UAGCCCUUUCUAUGGCUA	chrX:92245447-92245823(-)$1	376	185	203	14.3580
AACAGGAUUCAUAUUGUU	chr5:92483475-92483841(-)$1	366	206	224	15.3770
UUGGCUAAACAAUGUCUC	chr1:24819919-24820219(+)$1	300	55	73	14.4173
UUAGCCAUCUUCAGCUCU	chr2:66109958-66110257(-)$1	299	244	262	13.9313
ACUGUGUGUGUUAAUAGU	chr13:41371668-41372046(+)$1	378	115	133	15.3770
UACAAAAUUAAUCUUGUA	chr1:167145371-167145653(-)$1	282	230	248	15.3770
GUCAGAAACAAAACUGUC	chr3:31101673-31101960(-)$1	287	172	190	13.9667
GGUUGUGAGCAUCUAACU	chr11:77994701-77994962(-)$1	261	196	214	14.3580
UCCAGGUCAAAAGCUGGA	chr2:181284796-181285243(+)$1	447	70	88	15.3770
UAAAGCAAGACUACUUUA	chr1:23884444-23884739(-)$1	295	129	147	15.3770
AUUUCUCACAAAUGAAAU	chrX:154270707-154271079(-)$1	372	351	369	15.3770
UGCAUGGUUGACAGUGUA	chr2:121759787-121760067(+)$1	280	137	155	14.0289
AAGGCCAUGUUCCGUCUU	chr7:71031287-71031599(-)$1	312	125	143	13.9874
AAUAUGAUAUUAAAUAUU	chr18:34505411-34505834(-)$1	423	372	390	13.9874
GGGUAUUUAAUGUUACUC	chr2:104266860-104267256(-)$1	396	130	148	13.9874
GGUUGUUUAACACUGGCC	chr18:82725818-82726204(+)$1	386	345	363	15.3770
UGGUUUCCCAAAUGACUC	chr3:27140725-27141010(+)$1	285	228	246	13.9466
GUGAUCUGUUUGUGUCAC	chr2:163842310-163842661(+)$1	351	166	184	15.3770
UACACUACUUUAUGUGCU	chr11:50048389-50048708(+)$1	319	107	125	14.5041
ACCUAUAACGUCUUAGGU	chr2:155215215-155215684(+)$1	469	2	20	15.3770
AAGCAUUUGAUGUUGCUU	chr4:25544657-25544957(-)$1	300	184	202	14.3580
CCCCACCAGUGAUUGGGA	chr8:74864797-74865145(-)$1	348	304	322	13.7397
GUCUCUGUGUCCUGUGGC	chr11:100208541-100208836(-)$1	295	13	31	13.5418
GACUGGCAGAUAACAGCU	chr6:120389930-120390207(+)$1	277	209	227	14.0599
UUGUUGCUUUCUAAUUAA	chr1:167259626-167260086(-)$1	460	409	427	13.4483
GUCGGCAGAUGAACUGGC	chr11:54683767-54684108(+)$1	341	59	77	14.0289
GCCAGUUUAGCGUCUGGG	chr7:148615779-148616067(-)$1	288	24	42	13.4953
CAGAGUCAAAUCCCUCUG	chr4:24935845-24936196(+)$1	351	278	296	15.3770
UUCUGAAAAUUUCCAGAA	chr4:94715962-94716345(-)$1	383	65	83	13.9874
GUAGCACAUAAACGUUAG	chr6:134874456-134874731(+)$1	275	70	88	13.9466
CGUGUUUAUAACUAUAUG	chr5:14862582-14862993(+)$1	411	22	40	14.2126
AAAGAUUCCAGUCUCUUA	chr10:23907979-23908353(+)$1	374	300	318	13.8679
CAAUUUUUUUUGUAGUUG	chr17:33783079-33783493(-)$1	414	241	259	13.9874
GUAAGUUGGUUUUCUUAU	chrX:99710825-99711109(-)$1	284	95	113	15.3770
CUUUCCAUUCUAUGAAGG	chr3:27142554-27142931(+)$1	377	70	88	14.3580
CAGUCUAUAAAUUGACGA	chr3:83577963-83578277(+)$1	314	54	72	13.5893
UACCUUGUACCUUAGGUA	chr13:113296760-113297152(+)$1	392	210	228	15.3770
CACUUAAAUUUUAAAGGA	chr1:33854442-33854750(-)$1	308	46	64	13.7209
CCCUGGACACUCACAGGG	chr13:49478960-49479268(+)$1	308	100	118	13.9874
AAAGGUCAGCCUCCCUUU	chr6:30404848-30405257(+)$1	409	22	40	15.3770
GACUGAUACCCCCCAGUC	chr12:3402806-3403123(+)$1	317	73	91	13.9874
ccucccaagugcuggaau	chr6:148937703-148937975(-)$1	272	207	225	13.7209
UCCUUAAAACACAAAGGG	chr3:138567207-138567493(+)$1	286	257	275	15.3770
AAAUUGAAGUGAAAAUUU	chr13:78328164-78328458(-)$1	294	180	198	15.3770
UGGGCUAAAAAAUGUCCC	chr9:28728136-28728616(+)$1	480	31	49	14.8294
GGAUCAGGCCCUAGAUCU	chr5:145869373-145869723(+)$1	350	330	348	14.3580
GAUGAAGUUAGAGUCAUC	chr7:89030283-89030629(-)$1	346	118	136	13.9874
GGCAGUAAAACCUUUGCC	chr4:15211829-15212221(+)$1	392	0	18	15.3770
aguuauuuaaccuuaauu	chr3:88992869-88993169(+)$1	300	246	264	13.6070
CCGGCAGUCCCGCGCUGG	chr5:125316109-125316423(-)$1	314	80	98	13.9874
AAGGCUGCUUACCGCuuu	chr1:94756298-94756583(+)$1	285	66	84	14.0289
UUUGCAUUUUCUAGUAUA	chr7:137907916-137908176(+)$1	260	101	119	13.8517
UGGAAACAAUAAAUUUCA	chr11:68634880-68635237(-)$1	357	266	284	14.3580
CAGUUUUAGAGUUGACUG	chr15:11913014-11913346(-)$1	332	239	257	15.3770
GUGACACUGAAGCGCAUG	chr11:68559558-68559921(+)$1	363	143	161	13.4812
ACAUGAUCCCUCCCAGGU	chr3:90161840-90162161(+)$1	321	34	52	13.3093
UUUGUAGUUUAUGGCAAA	chr17:80248412-80248687(-)$1	275	14	32	14.3580
GCCGUGUGUUCUAAUGGG	chr18:64659216-64659508(-)$1	292	138	156	13.6846
GUCAGGAAAGUGGCUGAC	chr14:45968272-45968582(+)$1	310	44	62	13.9874
CUGCACAGUUGAAUGCAG	chr19:55142438-55142697(-)$1	259	138	156	15.3770
GGCUCAGAUACCAGGGCC	chr11:117883072-117883396(+)$1	324	287	305	14.3580
UUGUUUUCUUUAUAACAC	chr1:33855339-33855727(-)$1	388	120	138	13.7208
UUGUUAGCCUUUCAGCAA	chr2:180417206-180417473(-)$1	267	188	206	13.9874
CUCUCCCAGCUCAGAGAG	chr15:100873138-100873523(+)$1	385	56	74	13.9874
GGGCUCCUGUAGUAGCCA	chr10:114726769-114727038(-)$1	269	241	259	13.5009

#DB
(((((........)))))	chr14:27475776-27476062(+)$1	1	84	102	15.3770
(((((........)))))	chr15:10266498-10266766(+)$1	1	76	94	15.3770
(((((........)))))	chr11:105787847-105788093(+)$1	1	30	48	15.3770
.((((........)))).	chr3:145555977-145556249(+)$1	1	154	172	13.6202
.((((........)))).	chr2:125565155-125565414(-)$1	1	31	49	13.9466
(((((........)))))	chr2:65861377-65861849(+)$1	1	268	286	15.3770
(((((........)))))	chr16:57169036-57169384(-)$1	1	278	296	15.3770
(.(((........)))))	chr1:136243437-136243806(-)$1	1	261	279	13.8905
(((((........)))))	chr2:49405618-49406044(+)$1	1	152	170	15.3770
(((((........)))))	chr5:135657461-135657766(+)$1	1	53	71	15.3770
.((((........)))).	chr19:10525539-10525873(+)$1	1	185	203	13.9466
(((((........)))))	chrX:92245447-92245823(-)$1	1	185	203	14.3580
(((((........)))))	chr5:92483475-92483841(-)$1	1	206	224	15.3770
..(((........)))))	chr1:24819919-24820219(+)$1	1	55	73	14.4173
(.(((........)))..	chr2:66109958-66110257(-)$1	1	244	262	13.9313
(((((........)))))	chr13:41371668-41372046(+)$1	1	115	133	15.3770
(((((........)))))	chr1:167145371-167145653(-)$1	1	230	248	15.3770
(.(((........))).)	chr3:31101673-31101960(-)$1	1	172	190	13.9667
(((((........)))))	chr11:77994701-77994962(-)$1	1	196	214	14.3580
(((((........)))))	chr2:181284796-181285243(+)$1	1	70	88	15.3770
(((((........)))))	chr1:23884444-23884739(-)$1	1	129	147	15.3770
(((((........)))))	chrX:154270707-154271079(-)$1	1	351	369	15.3770
(((((........)))))	chr2:121759787-121760067(+)$1	1	137	155	14.0289
(((((........)))))	chr7:71031287-71031599(-)$1	1	125	143	13.9874
(((((........)))))	chr18:34505411-34505834(-)$1	1	372	390	13.9874
(((((........)))))	chr2:104266860-104267256(-)$1	1	130	148	13.9874
(((((........)))))	chr18:82725818-82726204(+)$1	1	345	363	15.3770
.((((........)))).	chr3:27140725-27141010(+)$1	1	228	246	13.9466
(((((........)))))	chr2:163842310-163842661(+)$1	1	166	184	15.3770
(((((........))).)	chr11:50048389-50048708(+)$1	1	107	125	14.5041
(((((........)))))	chr2:155215215-155215684(+)$1	1	2	20	15.3770
(((((........)))))	chr4:25544657-25544957(-)$1	1	184	202	14.3580
(((((........)))).	chr8:74864797-74865145(-)$1	1	304	322	13.7397
(((.(........).)))	chr11:100208541-100208836(-)$1	1	13	31	13.5418
(((((........))).)	chr6:120389930-120390207(+)$1	1	209	227	14.0599
(((.(........).)))	chr1:167259626-167260086(-)$1	1	409	427	13.4483
(((((........)))))	chr11:54683767-54684108(+)$1	1	59	77	14.0289
(((((........)).))	chr7:148615779-148616067(-)$1	1	24	42	13.4953
(((((........)))))	chr4:24935845-24936196(+)$1	1	278	296	15.3770
(((((........)))))	chr4:94715962-94716345(-)$1	1	65	83	13.9874
.((((........)))).	chr6:134874456-134874731(+)$1	1	70	88	13.9466
(((((........)))))	chr5:14862582-14862993(+)$1	1	22	40	14.2126
.((((........)))).	chr10:23907979-23908353(+)$1	1	300	318	13.8679
(((((........)))))	chr17:33783079-33783493(-)$1	1	241	259	13.9874
(((((........)))))	chrX:99710825-99711109(-)$1	1	95	113	15.3770
(((((........)))))	chr3:27142554-27142931(+)$1	1	70	88	14.3580
(.(((........)))..	chr3:83577963-83578277(+)$1	1	54	72	13.5893
(((((........)))))	chr13:113296760-113297152(+)$1	1	210	228	15.3770
..(((........)))..	chr1:33854442-33854750(-)$1	1	46	64	13.7209
(((((........)))))	chr13:49478960-49479268(+)$1	1	100	118	13.9874
(((((........)))))	chr6:30404848-30405257(+)$1	1	22	40	15.3770
(((((........)))))	chr12:3402806-3403123(+)$1	1	73	91	13.9874
..(((........)))..	chr6:148937703-148937975(-)$1	1	207	225	13.7209
(((((........)))))	chr3:138567207-138567493(+)$1	1	257	275	15.3770
(((((........)))))	chr13:78328164-78328458(-)$1	1	180	198	15.3770
(((((........).)))	chr9:28728136-28728616(+)$1	1	31	49	14.8294
(((((........)))))	chr5:145869373-145869723(+)$1	1	330	348	14.3580
(((((........)))))	chr7:89030283-89030629(-)$1	1	118	136	13.9874
(((((........)))))	chr4:15211829-15212221(+)$1	1	0	18	15.3770
(.(((........)))))	chr3:88992869-88993169(+)$1	1	246	264	13.6070
(((((........)))))	chr5:125316109-125316423(-)$1	1	80	98	13.9874
(((((........)))))	chr1:94756298-94756583(+)$1	1	66	84	14.0289
(((((........))).)	chr7:137907916-137908176(+)$1	1	101	119	13.8517
(((((........)))))	chr11:68634880-68635237(-)$1	1	266	284	14.3580
(((((........)))))	chr15:11913014-11913346(-)$1	1	239	257	15.3770
(((.(........)))))	chr11:68559558-68559921(+)$1	1	143	161	13.4812
((.((........)).))	chr3:90161840-90162161(+)$1	1	34	52	13.3093
(((((........)))))	chr17:80248412-80248687(-)$1	1	14	32	14.3580
.((((........)))).	chr18:64659216-64659508(-)$1	1	138	156	13.6846
(((((........)))))	chr14:45968272-45968582(+)$1	1	44	62	13.9874
(((((........)))))	chr19:55142438-55142697(-)$1	1	138	156	15.3770
(((((........)))))	chr11:117883072-117883396(+)$1	1	287	305	14.3580
.((((........)))).	chr1:33855339-33855727(-)$1	1	120	138	13.7208
(((((........)))))	chr2:180417206-180417473(-)$1	1	188	206	13.9874
(((((........)))))	chr15:100873138-100873523(+)$1	1	56	74	13.9874
(((((........)))).	chr10:114726769-114727038(-)$1	1	241	259	13.5009

#PSSM
e : 0.38	f : 0.17	g : 0.10	[ : 0.06	! : 0.06	c : 0.05	d : 0.05	i : 0.03	h : 0.02	" : 0.01	= : 0.01	b : 0.01	
e : 0.38	f : 0.17	d : 0.15	g : 0.10	[ : 0.06	! : 0.03	i : 0.03	c : 0.02	= : 0.01	
e : 0.35	d : 0.15	c : 0.15	f : 0.15	g : 0.10	i : 0.03	= : 0.01	[ : 0.01	
e : 0.34	f : 0.15	c : 0.14	d : 0.13	g : 0.10	i : 0.03	[ : 0.03	b : 0.02	= : 0.01	
e : 0.32	f : 0.15	c : 0.14	d : 0.13	g : 0.10	a : 0.05	i : 0.03	b : 0.02	= : 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 : 0.32	f : 0.15	c : 0.14	d : 0.13	g : 0.10	a : 0.05	i : 0.03	b : 0.02	= : 0.01	
e : 0.32	f : 0.15	d : 0.14	c : 0.14	g : 0.10	i : 0.03	] : 0.03	b : 0.02	= : 0.01	
e : 0.34	d : 0.15	c : 0.15	f : 0.15	g : 0.10	i : 0.03	] : 0.02	= : 0.01	
e : 0.38	d : 0.15	f : 0.15	g : 0.10	] : 0.05	i : 0.03	2 : 0.03	c : 0.02	3 : 0.01	= : 0.01	h : 0.01	
e : 0.39	f : 0.17	g : 0.10	] : 0.07	2 : 0.06	c : 0.05	i : 0.03	3 : 0.02	d : 0.02	4 : 0.01	= : 0.01	h : 0.01	

#score	1096.7276329381853
#seq	76
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_UTR_m2_run2.txt

#BEAR
ddd[eeeeeuuuuuuuuuuuueeeee]ddd	chr6:124998417-124998693(+)$1	276	207	237	24.3204
a[bbeeeeeuuuuuuuuuuuueeeee22bb	chr7:26013509-26013782(-)$1	273	148	178	23.8008
ggggggyyyyyyyyyyyyyyyyggggggg]	chr2:18127902-18128184(-)$1	282	104	134	24.1740
hhhhhyyyyyyyyyyyyyyyyhhhhhhhh2	chr19:6376876-6377157(+)$1	281	232	262	20.8155
:dddd[cccuuuuuuuuuuuuccc]dddd:	chr6:11957466-11957743(+)$1	277	106	136	22.5848
gggg[ddddwwwwwwwwwwwwwwddddggg	chr14:55133546-55133818(-)$1	272	56	86	23.0970
iiiiiiiwwwwwwwwwwwwwwiiiiiiiii	chr2:152106630-152106912(+)$1	282	29	59	24.6329
a$$$$$cccuuuuuuuuuuuuccc4444a]	chr11:6374791-6375078(-)$1	287	47	77	23.8731
:gggggggwwwwwwwwwwwwwwggggggg:	chr4:116273619-116273895(-)$1	276	41	71	22.8131
EEggggggguuuuuuuuuuuuggggggg:d	chr4:56890694-56890996(-)$1	302	31	61	22.2788
=========wwwwwwwwwwwwww=======	chr7:52488648-52488937(+)$1	289	223	253	25.0947
ggccc[ddddwwwwwwwwwwwwwwdddd22	chr12:107043028-107043308(+)$1	280	111	141	20.9612
eeeeeeeeevvvvvvvvvvvvveeeee22e	chr3:105768919-105769200(+)$1	281	40	70	23.6183
=========ttttttttttt==========	chr8:87359322-87359598(-)$1	276	204	234	24.5050
$$eeeeeyyyyyyyyyyyyyyyyeeeee44	chr10:81028703-81028981(+)$1	278	169	199	23.1134
ddd[bbcccvvvvvvvvvvvvvccc]bb]d	chr8:125986012-125986288(+)$1	276	59	89	23.1295
cc[eeeeevvvvvvvvvvvvveeeee]ccc	chr2:172860016-172860295(+)$1	279	58	88	24.0845
ggggfffffftttttttttttffffff333	chr17:34248922-34249283(-)$1	361	218	248	23.1119
=========wwwwwwwwwwwwww=======	chr8:112252016-112252299(-)$1	283	147	177	25.0947
iiiiiiiiiyyyyyyyyyyyyyyyyiiiii	chrX:147905367-147905638(+)$1	271	56	86	23.6774
d"""fffffftttttttttttffffff333	chr19:44646212-44646488(+)$1	276	208	238	23.0360
d!!ddddbbuuuuuuuuuuuubb]dddd]d	chrX:147005997-147006272(-)$1	275	199	229	23.5841
e[bbddddvvvvvvvvvvvvvdddd]bb]e	chr8:97466808-97467081(+)$1	273	63	93	22.2763
ddd!!cccvvvvvvvvvvvvvccc]dddd]	chr17:53646542-53646813(+)$1	271	178	208	23.6741
[ffffff[attttttttttta]ffffff33	chr12:53668692-53668979(+)$1	287	191	221	23.1539
eee!!ddddtttttttttttdddd]eeeee	chr15:80764970-80765260(+)$1	290	153	183	21.8115
=========uuuuuuuuuuuu=========	chr6:73226547-73226823(+)$1	276	150	180	26.5721
##ccc[cccxxxxxxxxxxxxxxxccc]cc	chr11:104189831-104190161(+)$1	330	115	145	20.0640
i"""eeeeewwwwwwwwwwwwwweeeee]i	chr6:117874977-117875253(+)$1	276	197	227	24.0726
b[ffffffwwwwwwwwwwwwwwffffff]b	chr4:128897084-128897384(-)$1	300	168	198	23.0785
eeeeeee[bbtttttttttttbbeeeee]e	chr13:94964296-94964569(+)$1	273	167	197	22.3987
ii!!eeeeeuuuuuuuuuuuueeeee22ii	chr6:56728731-56729000(-)$1	269	8	38	25.2792
b[gggggggvvvvvvvvvvvvvggggggg]	chr1:64780405-64780725(-)$1	320	78	108	24.8860
iiiiiiiwwwwwwwwwwwwwwiiiiiiiii	chr11:97543068-97543397(+)$1	329	141	171	24.6329
hhhhhyyyyyyyyyyyyyyyyhhhhhhhh2	chr19:17296084-17296389(+)$1	305	211	241	20.8155
cccffffffvvvvvvvvvvvvvffffff]c	chr8:109536846-109537118(+)$1	272	75	105	23.5591
ffff[bbyyyyyyyyyyyyyyyybb]ffff	chr6:140602585-140602859(+)$1	274	201	231	21.5220
e!!ffffffuuuuuuuuuuuuffffffeee	chr1:193655668-193655995(+)$1	327	157	187	24.0594
ee[bb[cccuuuuuuuuuuuuccc]bbeee	chr2:181317688-181317988(-)$1	300	152	182	23.9260
c[eeeeexxxxxxxxxxxxxxxeeeeeccc	chr4:147986523-147986821(-)$1	298	250	280	20.5327
iiiii[ccctttttttttttccciiiiiii	chr11:102152044-102152330(-)$1	286	191	221	24.6744
b"""eeeeeuuuuuuuuuuuueeeee]bbf	chr3:135070976-135071258(-)$1	282	105	135	24.3482
d!!ffffffuuuuuuuuuuuuffffff444	chr4:149993691-149994033(+)$1	342	42	72	24.5270
hhhhhhyyyyyyyyyyyyyyyyhhhhhhhh	chr4:118951463-118951731(-)$1	268	23	53	21.6603
b[cccddddwwwwwwwwwwwwwwdddd]cc	chr2:131072952-131073235(+)$1	283	249	279	22.7280
hhhhhhhhwwwwwwwwwwwwwwhhhhhhhh	chr16:27439564-27439840(+)$1	276	72	102	21.7374
cc####ddddtttttttttttdddd4444c	chr3:95435494-95435793(+)$1	299	174	204	22.0655
:bb[eeeeevvvvvvvvvvvvveeeee22b	chr10:127180686-127180969(+)$1	283	38	68	22.6457
dddgggggggtttttttttttggggggg::	chr6:30079493-30079764(+)$1	271	54	84	21.3025
iiiiiiiwwwwwwwwwwwwwwiiiiiiiii	chr1:133921978-133922403(+)$1	425	33	63	24.6329
dd[eeeeewwwwwwwwwwwwwweeeee333	chr4:129276074-129276352(-)$1	278	234	264	24.2771
fff[aeeeeettttttttttteeeee]a]f	chr10:60563131-60563453(-)$1	322	249	279	22.8270
========yyyyyyyyyyyyyyyy======	chr2:38922794-38923074(-)$1	280	182	212	24.7769
:::ccccccuuuuuuuuuuuuccc]ccc::	chr11:97023014-97023309(-)$1	295	186	216	20.4129
:dddd[cccuuuuuuuuuuuuccc]dddd:	chr2:3375577-3375848(-)$1	271	6	36	22.5848
gggggg[bbuuuuuuuuuuuubb]gggggg	chr2:84510058-84510335(-)$1	277	127	157	24.8672
ddddfffffftttttttttttffffff22d	chr15:96245044-96245315(-)$1	271	73	103	21.6741
cc[a[cccxxxxxxxxxxxxxxxccc]a]c	chr11:74491038-74491317(-)$1	279	161	191	20.9997
=========ttttttttttt==========	chr6:134665732-134666024(-)$1	292	161	191	24.5050
iiiiiiiiwwwwwwwwwwwwwwiiiiiiii	chr1:192831874-192832144(-)$1	270	37	67	25.1997
iiiiiiiiiuuuuuuuuuuuuiiiiiiiii	chr10:86311534-86311805(-)$1	271	136	166	26.2383

#otherMatches

#Seq PSSM
GCUCUCCUCCCGCCUCUCCCAGAGGGAAGU	chr6:124998417-124998693(+)$1	276	207	237	24.3204
GUGAGGACCUUCUACCCCCUUGGUCCCCUC	chr7:26013509-26013782(-)$1	273	148	178	23.8008
AUCCCUAACACUUAUUUAACUGGGGGGUGG	chr2:18127902-18128184(-)$1	282	104	134	24.1740
AGAAAUUUCUCUGGGCCUUUUUUUCUGUGU	chr19:6376876-6377157(+)$1	281	232	262	20.8155
UGCUUCUCUGUUAUGAAAUAAAGAAAGGUG	chr6:11957466-11957743(+)$1	277	106	136	22.5848
UGAAACAGGGUUUUAACAGGGUACCUGUUC	chr14:55133546-55133818(-)$1	272	56	86	23.0970
AUCUUGGCUUUAGUAACUUUAUCAAGGUGG	chr2:152106630-152106912(+)$1	282	29	59	24.6329
UAUGCAGAUGAAAUGAAAGAGAUCCAGGAG	chr11:6374791-6375078(-)$1	287	47	77	23.8731
AUCCUGGGAAAACUGGUAGAAACCUGGGAA	chr4:116273619-116273895(-)$1	276	41	71	22.8131
CAGGGAAGAGGUUUUACGGAAUUUUCCUAG	chr4:56890694-56890996(-)$1	302	31	61	22.2788
UGGGGUGGGACUUCUUAAUCUCCCCCACCC	chr7:52488648-52488937(+)$1	289	223	253	25.0947
CUCCCACAAUCUGUAAUUGAAAAUGUUGGA	chr12:107043028-107043308(+)$1	280	111	141	20.9612
AUUUGGUUUGUAUAGUUUGAGAAGACCUAA	chr3:105768919-105769200(+)$1	281	40	70	23.6183
uauauauauauauauauaacauauauauau	chr8:87359322-87359598(-)$1	276	204	234	24.5050
UCCCCUCUUCCCCAAAUAAACGUGAGGGUU	chr10:81028703-81028981(+)$1	278	169	199	23.1134
UGAGAGUUGUCAUCGUCAUCCUUAAUCUGU	chr8:125986012-125986288(+)$1	276	59	89	23.1295
GGGUCCCUCCACACCUACCUCAGGGAGCCA	chr2:172860016-172860295(+)$1	279	58	88	24.0845
GGCCUGGGGAUUUUAGUCACCUCUCCAGUU	chr17:34248922-34249283(-)$1	361	218	248	23.1119
AGUUUGGCUGCAAUAGCUCCUCAAGUUGGG	chr8:112252016-112252299(-)$1	283	147	177	25.0947
CUGUUCAGAACAACAAAUACUUCACUUUGA	chrX:147905367-147905638(+)$1	271	56	86	23.6774
UCCUGUCCCUGUGCUGCAAUGAGGGAUUCU	chr19:44646212-44646488(+)$1	276	208	238	23.0360
AAAGGUCACGUCUUUGUUUCAGUAGACCAU	chrX:147005997-147006272(-)$1	275	199	229	23.5841
UAGUUGGGUAGAUUCUCAGGUCCCAUGCCA	chr8:97466808-97467081(+)$1	273	63	93	22.2763
GUACUUGCAAUUGUAACAUAAGUAUUACAA	chr17:53646542-53646813(+)$1	271	178	208	23.6741
UUCAUCUUCUAAGUAAAUUUGUGGAUGAUU	chr12:53668692-53668979(+)$1	287	191	221	23.1539
UGGAAGGGCUUUACUAGUGUGCCUACCAAA	chr15:80764970-80765260(+)$1	290	153	183	21.8115
UUUGAAGGACACAACAAGAAAUUCUUUAAA	chr6:73226547-73226823(+)$1	276	150	180	26.5721
UGGCAGCAAUGAGAGAUUUGAGACUUGGUG	chr11:104189831-104190161(+)$1	330	115	145	20.0640
UUCUCAUGCAAACUUUUCUUCUAGCAUGUA	chr6:117874977-117875253(+)$1	276	197	227	24.0726
GGAGGACAAUCAAAGUAAGCACUGUUCUGC	chr4:128897084-128897384(-)$1	300	168	198	23.0785
GCCUUUGUCAAACAUGUAUUCUGUAAAGUG	chr13:94964296-94964569(+)$1	273	167	197	22.3987
GAAACUUUAUCCAUCCUGUCUUGAAGAAUC	chr6:56728731-56729000(-)$1	269	8	38	25.2792
UCGUGUCUUGAAUAAGUUAGAGGAGGCAUU	chr1:64780405-64780725(-)$1	320	78	108	24.8860
UGGUUGGACCUACCACAUAAACCAAUCAGC	chr11:97543068-97543397(+)$1	329	141	171	24.6329
GUUGAAAACAAAAAUUACCACUUAACUGUC	chr19:17296084-17296389(+)$1	305	211	241	20.8155
AGCAGAGCUAUAGCAGUAAGAGAGCUCUGG	chr8:109536846-109537118(+)$1	272	75	105	23.5591
AAGCAGUGUAAAUAGUUUGAGUAACAGCUU	chr6:140602585-140602859(+)$1	274	201	231	21.5220
UUACCUAAGAAUAGGAUUUGCCUUAGGGAA	chr1:193655668-193655995(+)$1	327	157	187	24.0594
CAACUGUGGAAGGGAAGGGGGCCAAAGUGC	chr2:181317688-181317988(-)$1	300	152	182	23.9260
AACUUGAAUAUGUAUCAAGAUCUCAAGUGC	chr4:147986523-147986821(-)$1	298	250	280	20.5327
CAGGAAGGGGCCCAGCCUCACCCUCCUGGG	chr11:102152044-102152330(-)$1	286	191	221	24.6744
AAAAGCCUUGUugugugugugaggguguga	chr3:135070976-135071258(-)$1	282	105	135	24.3482
CUAAAACACAUCUGCAUAAUAGUGUUUGUU	chr4:149993691-149994033(+)$1	342	42	72	24.5270
UCGGUAUCGCCGAAACUUCAAUUACCGACG	chr4:118951463-118951731(-)$1	268	23	53	21.6603
UGGUCUCCAUUCUCUCCCUAUACUGGAUGA	chr2:131072952-131073235(+)$1	283	249	279	22.7280
agaggguggguaugugggggagcacccucu	chr16:27439564-27439840(+)$1	276	72	102	21.7374
GUUUAUGACUGAUAAAAAAGAAGUUUCCUA	chr3:95435494-95435793(+)$1	299	174	204	22.0655
AAGAGGCUGAGAAGAACCCGGACAGCUGAC	chr10:127180686-127180969(+)$1	283	38	68	22.6457
CAGGAGGCAAUAUUUUUGGGUUUGCCUUGA	chr6:30079493-30079764(+)$1	271	54	84	21.3025
UAAUAUUGUGUAAACUAAGUAAGUAUUGAU	chr1:133921978-133922403(+)$1	425	33	63	24.6329
UACUCCCAGCUACUUCAUCCUGUGGGAAAC	chr4:129276074-129276352(-)$1	278	234	264	24.2771
CUCAGGUGGGUGUCUGUCUGUCCCACGCAG	chr10:60563131-60563453(-)$1	322	249	279	22.8270
UUAGCUUUAUUCAAAGUAUCACUAAAAGUU	chr2:38922794-38923074(-)$1	280	182	212	24.7769
UACAGUUGUUACAAAGAAAAUGCAGACUUC	chr11:97023014-97023309(-)$1	295	186	216	20.4129
ACAAAAACUAACAAUUGAAAAAGUAUUUGG	chr2:3375577-3375848(-)$1	271	6	36	22.5848
GAGGUGGUUGAAGAAUUGAAGAAGUACCUU	chr2:84510058-84510335(-)$1	277	127	157	24.8672
CCGGGGUCUACAGAAAAAACCUAGGCUGAC	chr15:96245044-96245315(-)$1	271	73	103	21.6741
GUUCUUCCUCCCUUUUUUCCUCUGGAUGCA	chr11:74491038-74491317(-)$1	279	161	191	20.9997
GCUGACAGUCAUACACUACAGCUGUCAGUC	chr6:134665732-134666024(-)$1	292	161	191	24.5050
GUCAGUUGUUUUUUUCAGGUACCAGUUGAU	chr1:192831874-192832144(-)$1	270	37	67	25.1997
AUUCCUGGUGCCUACACUUUAGCCAGGAGU	chr10:86311534-86311805(-)$1	271	136	166	26.2383

#DB
(((.(((((............))))).)))	chr6:124998417-124998693(+)$1	1	207	237	24.3204
(.(((((((............)))))..))	chr7:26013509-26013782(-)$1	1	148	178	23.8008
((((((................))))))).	chr2:18127902-18128184(-)$1	1	104	134	24.1740
(((((................)))))))).	chr19:6376876-6377157(+)$1	1	232	262	20.8155
.((((.(((............))).)))).	chr6:11957466-11957743(+)$1	1	106	136	22.5848
((((.((((..............)))))))	chr14:55133546-55133818(-)$1	1	56	86	23.0970
(((((((..............)))))))))	chr2:152106630-152106912(+)$1	1	29	59	24.6329
(.....(((............)))....).	chr11:6374791-6375078(-)$1	1	47	77	23.8731
.(((((((..............))))))).	chr4:116273619-116273895(-)$1	1	41	71	22.8131
(((((((((............))))))).(	chr4:56890694-56890996(-)$1	1	31	61	22.2788
(((((((((..............)))))))	chr7:52488648-52488937(+)$1	1	223	253	25.0947
(((((.((((..............))))..	chr12:107043028-107043308(+)$1	1	111	141	20.9612
(((((((((.............)))))..)	chr3:105768919-105769200(+)$1	1	40	70	23.6183
(((((((((...........))))))))))	chr8:87359322-87359598(-)$1	1	204	234	24.5050
..(((((................)))))..	chr10:81028703-81028981(+)$1	1	169	199	23.1134
(((.(((((.............))).)).)	chr8:125986012-125986288(+)$1	1	59	89	23.1295
((.(((((.............))))).)))	chr2:172860016-172860295(+)$1	1	58	88	24.0845
((((((((((...........))))))...	chr17:34248922-34249283(-)$1	1	218	248	23.1119
(((((((((..............)))))))	chr8:112252016-112252299(-)$1	1	147	177	25.0947
(((((((((................)))))	chrX:147905367-147905638(+)$1	1	56	86	23.6774
(...((((((...........))))))...	chr19:44646212-44646488(+)$1	1	208	238	23.0360
(..((((((............)).)))).)	chrX:147005997-147006272(-)$1	1	199	229	23.5841
(.((((((.............)))).)).)	chr8:97466808-97467081(+)$1	1	63	93	22.2763
(((..(((.............))).)))).	chr17:53646542-53646813(+)$1	1	178	208	23.6741
.((((((.(...........).))))))..	chr12:53668692-53668979(+)$1	1	191	221	23.1539
(((..((((...........)))).)))))	chr15:80764970-80765260(+)$1	1	153	183	21.8115
(((((((((............)))))))))	chr6:73226547-73226823(+)$1	1	150	180	26.5721
..(((.(((...............))).))	chr11:104189831-104190161(+)$1	1	115	145	20.0640
(...(((((..............))))).)	chr6:117874977-117875253(+)$1	1	197	227	24.0726
(.((((((..............)))))).)	chr4:128897084-128897384(-)$1	1	168	198	23.0785
(((((((.((...........))))))).)	chr13:94964296-94964569(+)$1	1	167	197	22.3987
((..(((((............)))))..))	chr6:56728731-56729000(-)$1	1	8	38	25.2792
(.(((((((.............))))))).	chr1:64780405-64780725(-)$1	1	78	108	24.8860
(((((((..............)))))))))	chr11:97543068-97543397(+)$1	1	141	171	24.6329
(((((................)))))))).	chr19:17296084-17296389(+)$1	1	211	241	20.8155
(((((((((.............)))))).)	chr8:109536846-109537118(+)$1	1	75	105	23.5591
((((.((................)).))))	chr6:140602585-140602859(+)$1	1	201	231	21.5220
(..((((((............)))))))))	chr1:193655668-193655995(+)$1	1	157	187	24.0594
((.((.(((............))).)))))	chr2:181317688-181317988(-)$1	1	152	182	23.9260
(.(((((...............))))))))	chr4:147986523-147986821(-)$1	1	250	280	20.5327
(((((.(((...........))))))))))	chr11:102152044-102152330(-)$1	1	191	221	24.6744
(...(((((............))))).)))	chr3:135070976-135071258(-)$1	1	105	135	24.3482
(..((((((............))))))...	chr4:149993691-149994033(+)$1	1	42	72	24.5270
((((((................))))))))	chr4:118951463-118951731(-)$1	1	23	53	21.6603
(.(((((((..............)))).))	chr2:131072952-131073235(+)$1	1	249	279	22.7280
((((((((..............))))))))	chr16:27439564-27439840(+)$1	1	72	102	21.7374
((....((((...........))))....)	chr3:95435494-95435793(+)$1	1	174	204	22.0655
.((.(((((.............)))))..)	chr10:127180686-127180969(+)$1	1	38	68	22.6457
)))(((((((...........)))))))..	chr6:30079493-30079764(+)$1	1	54	84	21.3025
(((((((..............)))))))))	chr1:133921978-133922403(+)$1	1	33	63	24.6329
((.(((((..............)))))...	chr4:129276074-129276352(-)$1	1	234	264	24.2771
(((.((((((...........))))).).)	chr10:60563131-60563453(-)$1	1	249	279	22.8270
((((((((................))))))	chr2:38922794-38923074(-)$1	1	182	212	24.7769
...((((((............))).)))..	chr11:97023014-97023309(-)$1	1	186	216	20.4129
.((((.(((............))).)))).	chr2:3375577-3375848(-)$1	1	6	36	22.5848
((((((.((............)).))))))	chr2:84510058-84510335(-)$1	1	127	157	24.8672
((((((((((...........))))))..)	chr15:96245044-96245315(-)$1	1	73	103	21.6741
((.(.(((...............))).).)	chr11:74491038-74491317(-)$1	1	161	191	20.9997
(((((((((...........))))))))))	chr6:134665732-134666024(-)$1	1	161	191	24.5050
((((((((..............))))))))	chr1:192831874-192832144(-)$1	1	37	67	25.1997
(((((((((............)))))))))	chr10:86311534-86311805(-)$1	1	136	166	26.2383

#PSSM
d : 0.14	i : 0.14	= : 0.09	e : 0.09	g : 0.08	: : 0.08	c : 0.08	h : 0.06	b : 0.06	a : 0.03	f : 0.03	E : 0.01	$ : 0.01	[ : 0.01	# : 0.01	
d : 0.13	i : 0.13	[ : 0.09	g : 0.09	= : 0.09	h : 0.06	e : 0.06	c : 0.06	" : 0.04	! : 0.04	f : 0.04	$ : 0.03	E : 0.01	# : 0.01	b : 0.01	: : 0.01	
d : 0.11	g : 0.11	i : 0.11	= : 0.09	e : 0.08	h : 0.06	c : 0.06	[ : 0.06	! : 0.06	f : 0.06	b : 0.04	" : 0.04	$ : 0.01	# : 0.01	: : 0.01	
g : 0.13	i : 0.11	= : 0.09	e : 0.09	f : 0.09	[ : 0.06	h : 0.06	d : 0.06	c : 0.06	b : 0.04	" : 0.04	! : 0.04	$ : 0.01	# : 0.01	a : 0.01	
e : 0.19	f : 0.13	i : 0.11	g : 0.09	= : 0.09	h : 0.06	d : 0.06	c : 0.06	[ : 0.04	b : 0.03	! : 0.03	$ : 0.01	# : 0.01	a : 0.01	
e : 0.21	f : 0.13	g : 0.09	[ : 0.09	i : 0.09	= : 0.09	d : 0.08	c : 0.04	y : 0.03	b : 0.03	h : 0.03	$ : 0.01	# : 0.01	
e : 0.21	c : 0.16	f : 0.13	d : 0.11	i : 0.09	= : 0.09	y : 0.06	g : 0.06	b : 0.01	h : 0.01	[ : 0.01	
e : 0.16	c : 0.16	f : 0.11	y : 0.09	d : 0.09	= : 0.09	g : 0.06	w : 0.04	i : 0.04	b : 0.03	[ : 0.03	x : 0.01	h : 0.01	
e : 0.13	c : 0.13	w : 0.13	y : 0.11	f : 0.09	d : 0.08	= : 0.08	g : 0.04	v : 0.04	b : 0.04	i : 0.03	x : 0.03	a : 0.01	
u : 0.26	w : 0.21	y : 0.13	v : 0.13	t : 0.08	f : 0.04	x : 0.04	d : 0.03	b : 0.01	g : 0.01	e : 0.01	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	t : 0.19	y : 0.13	v : 0.13	x : 0.04	
u : 0.26	w : 0.22	y : 0.13	v : 0.13	t : 0.11	x : 0.04	= : 0.03	a : 0.01	d : 0.01	c : 0.01	
w : 0.18	c : 0.11	e : 0.09	y : 0.09	v : 0.08	f : 0.08	i : 0.06	= : 0.04	b : 0.04	d : 0.04	x : 0.04	h : 0.03	g : 0.03	] : 0.01	
e : 0.16	c : 0.13	f : 0.13	w : 0.09	g : 0.08	i : 0.08	h : 0.06	y : 0.06	= : 0.04	b : 0.04	d : 0.04	x : 0.03	
e : 0.21	c : 0.13	f : 0.13	i : 0.09	g : 0.08	d : 0.08	= : 0.08	h : 0.06	y : 0.03	] : 0.03	w : 0.01	x : 0.01	b : 0.01	
e : 0.21	f : 0.13	g : 0.09	] : 0.09	d : 0.09	i : 0.09	= : 0.09	h : 0.06	c : 0.04	4 : 0.01	y : 0.01	b : 0.01	
e : 0.22	f : 0.13	d : 0.11	i : 0.11	g : 0.09	= : 0.09	h : 0.06	] : 0.04	c : 0.04	4 : 0.03	b : 0.01	
f : 0.14	e : 0.13	d : 0.11	i : 0.11	g : 0.09	= : 0.09	] : 0.08	h : 0.06	b : 0.04	2 : 0.03	4 : 0.03	c : 0.03	
g : 0.11	i : 0.11	d : 0.09	= : 0.09	e : 0.09	2 : 0.08	h : 0.06	f : 0.06	4 : 0.04	b : 0.04	c : 0.04	3 : 0.04	] : 0.03	a : 0.03	
] : 0.14	i : 0.13	= : 0.09	g : 0.08	d : 0.06	h : 0.06	2 : 0.06	c : 0.06	3 : 0.06	: : 0.04	4 : 0.04	e : 0.04	b : 0.03	a : 0.01	f : 0.01	
i : 0.14	c : 0.11	= : 0.09	e : 0.09	d : 0.08	: : 0.08	] : 0.06	3 : 0.06	b : 0.04	2 : 0.04	f : 0.04	g : 0.03	4 : 0.03	h : 0.03	

#score	1420.403311816282
#seq	61
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_UTR_m1_run1.txt

#BEAR
ggcccuuuuuuuuuuuuccc]gg	chr10:114727177-114727442(-)$1	265	208	231	22.8904
ffbbvvvvvvvvvvvvvbb]fff	chr3:115413835-115414079(-)$1	244	74	97	20.2979
eeeewwwwwwwwwwwwwweeeee	chr19:44469747-44470068(-)$1	321	161	184	21.2957
[eeeeettttttttttteeeee2	chr11:62158174-62158452(-)$1	278	69	92	23.5060
ggggggtttttttttttgggggg	chr19:44471909-44472184(-)$1	275	38	61	23.2104
ggggggvvvvvvvvvvvvvgggg	chr5:138081407-138081646(+)$1	239	203	226	22.6436
iiiiiiuuuuuuuuuuuuiiiii	chr4:149995208-149995459(+)$1	251	4	27	23.0662
a[ddddtttttttttttdddd]a	chr1:193736890-193737155(+)$1	265	33	56	22.7634
eeeeevvvvvvvvvvvvveeeee	chr3:54607973-54608237(-)$1	264	99	122	22.9328
:ddddwwwwwwwwwwwwwwdddd	chr3:107471073-107471321(-)$1	248	21	44	19.9449
[ddddvvvvvvvvvvvvvdddd]	chr11:94812945-94813207(+)$1	262	74	97	22.5777
eeeeevvvvvvvvvvvvveeeee	chr16:20608487-20608723(-)$1	236	203	226	22.9328
bbcccuuuuuuuuuuuuccc333	chr2:119411091-119411450(+)$1	359	34	57	22.3387
ddcccuuuuuuuuuuuuccc]dd	chr1:175264356-175264680(-)$1	324	182	205	22.3322
cccyyyyyyyyyyyyyyyyccc]	chr14:76102228-76102466(-)$1	238	72	95	20.8619
fffffftttttttttttffffff	chr9:58500345-58500765(+)$1	420	9	32	22.1869
ggggggtttttttttttgggggg	chr1:162153093-162153344(-)$1	251	149	172	23.2104
fffyyyyyyyyyyyyyyyyffff	chr4:97779678-97779986(+)$1	308	49	72	20.3145
fffffftttttttttttffffff	chr9:64983539-64983851(+)$1	312	251	274	22.1869
dd[ccctttttttttttccc333	chr9:75421703-75421954(-)$1	251	115	138	23.4309
b!!awwwwwwwwwwwwwwa22bb	chr8:125418528-125418768(-)$1	240	48	71	19.7805
:ddddvvvvvvvvvvvvvdddd:	chr18:15548410-15548819(-)$1	409	137	160	20.6414
fffffftttttttttttffffff	chr18:38000045-38000310(+)$1	265	96	119	22.1869
ggggggtttttttttttgggggg	chrX:141883147-141883412(-)$1	265	188	211	23.2104
!eeeeettttttttttteeeeea	chr17:90435851-90436116(-)$1	265	26	49	23.5013
dddcccuuuuuuuuuuuuccc33	chr17:46685741-46685996(-)$1	255	103	126	23.2348
::dddduuuuuuuuuuuudddd:	chr11:78382259-78382511(-)$1	252	104	127	19.8835
!!ddddtttttttttttdddd22	chr2:49629383-49629665(+)$1	282	228	251	22.7176
iiiiiivvvvvvvvvvvvviiii	chr4:86629006-86629273(-)$1	267	52	75	22.4951
deeeeeuuuuuuuuuuuueeeee	chr13:100204615-100204882(-)$1	267	218	241	23.2209
hhhhhhttttttttttthhhhhh	chr19:40921213-40921471(+)$1	258	208	231	20.9855
dddyyyyyyyyyyyyyyyydddd	chr15:37897557-37897836(-)$1	279	50	73	20.2879
ggggggtttttttttttgggggg	chr16:43862569-43862848(-)$1	279	123	146	23.2104
[eeeeettttttttttteeeee]	chr6:23446712-23446974(-)$1	262	80	103	23.7104
[eeeeettttttttttteeeeed	chr4:128789488-128789745(-)$1	257	35	58	23.3930
!!ddddtttttttttttddddee	chrX:133370970-133371234(+)$1	264	86	109	22.9426
ggggguuuuuuuuuuuugggggg	chr4:137212080-137212324(+)$1	244	35	58	22.6493
iiiccctttttttttttccc]ii	chr13:89749712-89749977(+)$1	265	94	117	23.5129
:eeeeettttttttttteeeee:	chr2:71181893-71182158(-)$1	265	214	237	21.7741
ccccccvvvvvvvvvvvvvccc]	chr9:98902239-98902507(+)$1	268	34	57	22.6804
fffyyyyyyyyyyyyyyyyffff	chr9:51895360-51895695(+)$1	335	3	26	20.3145
b[cccwwwwwwwwwwwwwwccc]	chr9:115996713-115996957(-)$1	244	117	140	21.3934
:eeeeettttttttttteeeeeF	chr18:36664979-36665227(-)$1	248	16	39	22.2182
g!!cccvvvvvvvvvvvvvccc]	chr9:36540109-36540386(-)$1	277	200	223	22.9604
ee[ccctttttttttttccceee	chr9:118950705-118950950(+)$1	245	216	239	23.5966
ddd[avvvvvvvvvvvvva]ddd	chr2:70439775-70440064(+)$1	289	102	125	22.1840
ceeeeettttttttttteeeee:	chr2:153594020-153594277(+)$1	257	172	195	22.6156
======vvvvvvvvvvvvv====	chr9:106056370-106056595(+)$1	225	117	140	22.6129
fffffwwwwwwwwwwwwwwffff	chr1:37496161-37496448(-)$1	287	106	129	20.5883
fffffftttttttttttffffff	chr15:27661376-27661611(-)$1	235	185	208	22.1869
ee[cccuuuuuuuuuuuuccc33	chr1:64644225-64644477(+)$1	252	207	230	23.4964
f!!cccuuuuuuuuuuuuccc22	chr4:109878572-109878824(-)$1	252	147	170	23.1639
gggyyyyyyyyyyyyyyyygggg	chr1:66488972-66489232(+)$1	260	35	58	21.0296
f!!cccuuuuuuuuuuuuccc22	chr13:100194425-100194737(-)$1	312	259	282	23.1639
ddd[bbtttttttttttbb]ddd	chr8:123197821-123198128(+)$1	307	120	143	21.6224
hhhhhhuuuuuuuuuuuuhhhhh	chr13:90244128-90244388(+)$1	260	9	32	21.1796
[eeeeeuuuuuuuuuuuueeeee	chr11:106643733-106644035(-)$1	302	142	165	23.4369
""ddddtttttttttttdddd]e	chr10:79457310-79457597(+)$1	287	180	203	22.6419
:ddddvvvvvvvvvvvvvdddd:	chr6:102114987-102115278(-)$1	291	143	166	20.6414
ggggggtttttttttttgggggg	chr14:19038170-19038452(-)$1	282	47	70	23.2104
geeeeettttttttttteeeee:	chr11:88157887-88158158(-)$1	271	160	183	22.6689
:eeeeeuuuuuuuuuuuueeeee	chr10:7344142-7344393(+)$1	251	212	235	22.4887
$eeeeeuuuuuuuuuuuueeeee	chr11:61591098-61591336(-)$1	238	186	209	23.1248
e!!ccctttttttttttccc22e	chr5:67447115-67447371(+)$1	256	54	77	23.0876
e!!cccvvvvvvvvvvvvvccc4	chr5:40005231-40005490(-)$1	259	19	42	22.6896
deeeeettttttttttteeeee]	chr3:80491906-80492171(-)$1	265	13	36	23.4944

#otherMatches

#Seq PSSM
UGCAAAAAUAUAUACAAUUGUCA	chr10:114727177-114727442(-)$1	265	208	231	22.8904
UAACAAAGAAUAACGAAGUCUAC	chr3:115413835-115414079(-)$1	244	74	97	20.2979
UGGGUGCCUUAUCUCUUUCCUAA	chr19:44469747-44470068(-)$1	321	161	184	21.2957
AAGAGCCACAGCGGAAAGCUUUG	chr11:62158174-62158452(-)$1	278	69	92	23.5060
UUAAAUAAUAACAAUAAAUUUGA	chr19:44471909-44472184(-)$1	275	38	61	23.2104
UCCCCCUACCAGCUGCUAUGGGG	chr5:138081407-138081646(+)$1	239	203	226	22.6436
UCAUGCUCCCAGAACCAUGCAUG	chr4:149995208-149995459(+)$1	251	4	27	23.0662
GGGCUCAUCUUGAACUCGAGUGC	chr1:193736890-193737155(+)$1	265	33	56	22.7634
UAAAUAUUGAAUUUUUGCAUUUA	chr3:54607973-54608237(-)$1	264	99	122	22.9328
CAGUGUCUCUUUCUCCAACCACU	chr3:107471073-107471321(-)$1	248	21	44	19.9449
CCCCAAAAGCCAAAAAUAUGGGA	chr11:94812945-94813207(+)$1	262	74	97	22.5777
ACAUUUCCAUAUCUUCCCAAUGU	chr16:20608487-20608723(-)$1	236	203	226	22.9328
GUCAGUACCAUCUUCCCCUGUUA	chr2:119411091-119411450(+)$1	359	34	57	22.3387
GAUGCCAAACCAAUGAAGCAUUC	chr1:175264356-175264680(-)$1	324	182	205	22.3322
UUUGAUUUGUUUGUUUCUGAAAA	chr14:76102228-76102466(-)$1	238	72	95	20.8619
UGUAAAUUCUGAAAUCUUUUGCA	chr9:58500345-58500765(+)$1	420	9	32	22.1869
AAAUAUUUUUUUCAAUUAUAUUU	chr1:162153093-162153344(-)$1	251	149	172	23.2104
AGUAACUAAUUUUUAUAUAGCUA	chr4:97779678-97779986(+)$1	308	49	72	20.3145
GCAGCCUACCACAGCAUGGCUGU	chr9:64983539-64983851(+)$1	312	251	274	22.1869
AAAUCCUCUUCUCCACCGGACCA	chr9:75421703-75421954(-)$1	251	115	138	23.4309
CAGCAAAGCAGAGAGGGAGAGGG	chr8:125418528-125418768(-)$1	240	48	71	19.7805
AGAGAGCCAAACAGACAAUCUUA	chr18:15548410-15548819(-)$1	409	137	160	20.6414
GGCAGGCUUAUCCAUCUCCUGCC	chr18:38000045-38000310(+)$1	265	96	119	22.1869
UGUCUCUGCCCUUCAUUGAGGCA	chrX:141883147-141883412(-)$1	265	188	211	23.2104
CGUUCUAAAAGACGGUGAGGACC	chr17:90435851-90436116(-)$1	265	26	49	23.5013
CCCUCUCACUCCAGCCAAAGAAA	chr17:46685741-46685996(-)$1	255	103	126	23.2348
UACUACUGAAGAUGUAAUGUAGC	chr11:78382259-78382511(-)$1	252	104	127	19.8835
UUUCCUAGAAUAGCUAAAGGAUC	chr2:49629383-49629665(+)$1	282	228	251	22.7176
GAUGGCAAACUGUACAUAGGCUG	chr4:86629006-86629273(-)$1	267	52	75	22.4951
ACUGGAGAAACUCAAACAUCUAG	chr13:100204615-100204882(-)$1	267	218	241	23.2209
CAGGACGAAUGCAGUGGGUCCUG	chr19:40921213-40921471(+)$1	258	208	231	20.9855
CAGAACAACAUAAUUUACACUGU	chr15:37897557-37897836(-)$1	279	50	73	20.2879
AUGUUCAUAUGUCCCAGGAAUAU	chr16:43862569-43862848(-)$1	279	123	146	23.2104
GUGUUAUACCCAACUUCUAAUAG	chr6:23446712-23446974(-)$1	262	80	103	23.7104
CUGCUGCAGUGUGAUCCCAGCAG	chr4:128789488-128789745(-)$1	257	35	58	23.3930
UAGGAGUCAAAUACAUUCUCUUU	chrX:133370970-133371234(+)$1	264	86	109	22.9426
UGUUUGGGCAUUAAAGAAAACGU	chr4:137212080-137212324(+)$1	244	35	58	22.6493
UUAACUUUUGAAUACUUAGUAUA	chr13:89749712-89749977(+)$1	265	94	117	23.5129
AAGGACUUUCUAUAAAUGUUCUG	chr2:71181893-71182158(-)$1	265	214	237	21.7741
AUGGUCAAGAAAAAACAAGGACU	chr9:98902239-98902507(+)$1	268	34	57	22.6804
UUCUAAGAAAAUUAUUGAUGAAG	chr9:51895360-51895695(+)$1	335	3	26	20.3145
UAGAUCAAAUAAAUCCAAAGUCC	chr9:115996713-115996957(-)$1	244	117	140	21.3934
CCCUGGAGCAGAAUAUCCCAGGG	chr18:36664979-36665227(-)$1	248	16	39	22.2182
UAGGUCCCCAAAUGAACCAGAUA	chr9:36540109-36540386(-)$1	277	200	223	22.9604
UUUGGCCCCCAGCCACCGCCAAG	chr9:118950705-118950950(+)$1	245	216	239	23.5966
CUAGAUCUCCUGUAAUUUUGUAG	chr2:70439775-70440064(+)$1	289	102	125	22.1840
CCCCAAAUUCCAUUUUAUUGGGA	chr2:153594020-153594277(+)$1	257	172	195	22.6156
AUGUGAUUCUAUUGCUCGCUCAU	chr9:106056370-106056595(+)$1	225	117	140	22.6129
UUCAAGUUUGCUGCUAUAAUUGA	chr1:37496161-37496448(-)$1	287	106	129	20.5883
UACAGUCAGAUGAAAAUACUGUA	chr15:27661376-27661611(-)$1	235	185	208	22.1869
GUUGACUGCCAAAUUAAUGUUUU	chr1:64644225-64644477(+)$1	252	207	230	23.4964
CGUUGUUGAAUAUAAUAUACAUA	chr4:109878572-109878824(-)$1	252	147	170	23.1639
UCUUUCUUCUGAUAAUUCUAGAG	chr1:66488972-66489232(+)$1	260	35	58	21.0296
ACAGCAUCUGCCUUCCUUUGUCU	chr13:100194425-100194737(-)$1	312	259	282	23.1639
AAGGCCAACCCCAUUCAGGGCUU	chr8:123197821-123198128(+)$1	307	120	143	21.6224
UGUCUCUGAACAUGGAAUGAGAU	chr13:90244128-90244388(+)$1	260	9	32	21.1796
UCUUUACACCUAAUAACAUAAAG	chr11:106643733-106644035(-)$1	302	142	165	23.4369
cugccucagcuuccuaagggcug	chr10:79457310-79457597(+)$1	287	180	203	22.6419
AUGCCUUAAUAUUUGCUUGGUAA	chr6:102114987-102115278(-)$1	291	143	166	20.6414
UUCACAAUAUUUUAAACUGUGAA	chr14:19038170-19038452(-)$1	282	47	70	23.2104
UGCUGUAAUAUAAGACAACAGCU	chr11:88157887-88158158(-)$1	271	160	183	22.6689
AAUCCAAAAGGUGAUGUCUGGGU	chr10:7344142-7344393(+)$1	251	212	235	22.4887
AUACAAAACUACUACAUAUUGUA	chr11:61591098-61591336(-)$1	238	186	209	23.1248
CCUUAGAAAACGCAAAGCUGUUG	chr5:67447115-67447371(+)$1	256	54	77	23.0876
ACAGUAUUAGAUUCACAGUUGCC	chr5:40005231-40005490(-)$1	259	19	42	22.6896
ACUUGACAUCAACUGCAUCAAGA	chr3:80491906-80492171(-)$1	265	13	36	23.4944

#DB
(((((............))).))	chr10:114727177-114727442(-)$1	1	208	231	22.8904
((((.............)).)))	chr3:115413835-115414079(-)$1	1	74	97	20.2979
((((..............)))))	chr19:44469747-44470068(-)$1	1	161	184	21.2957
.(((((...........))))).	chr11:62158174-62158452(-)$1	1	69	92	23.5060
((((((...........))))))	chr19:44471909-44472184(-)$1	1	38	61	23.2104
((((((.............))))	chr5:138081407-138081646(+)$1	1	203	226	22.6436
((((((............)))))	chr4:149995208-149995459(+)$1	1	4	27	23.0662
(.((((...........)))).)	chr1:193736890-193737155(+)$1	1	33	56	22.7634
(((((.............)))))	chr3:54607973-54608237(-)$1	1	99	122	22.9328
.((((..............))))	chr3:107471073-107471321(-)$1	1	21	44	19.9449
.((((.............)))).	chr11:94812945-94813207(+)$1	1	74	97	22.5777
(((((.............)))))	chr16:20608487-20608723(-)$1	1	203	226	22.9328
(((((............)))...	chr2:119411091-119411450(+)$1	1	34	57	22.3387
(((((............))).))	chr1:175264356-175264680(-)$1	1	182	205	22.3322
(((................))).	chr14:76102228-76102466(-)$1	1	72	95	20.8619
((((((...........))))))	chr9:58500345-58500765(+)$1	1	9	32	22.1869
((((((...........))))))	chr1:162153093-162153344(-)$1	1	149	172	23.2104
(((................))))	chr4:97779678-97779986(+)$1	1	49	72	20.3145
((((((...........))))))	chr9:64983539-64983851(+)$1	1	251	274	22.1869
((.(((...........)))...	chr9:75421703-75421954(-)$1	1	115	138	23.4309
(..(..............)..))	chr8:125418528-125418768(-)$1	1	48	71	19.7805
.((((.............)))).	chr18:15548410-15548819(-)$1	1	137	160	20.6414
((((((...........))))))	chr18:38000045-38000310(+)$1	1	96	119	22.1869
((((((...........))))))	chrX:141883147-141883412(-)$1	1	188	211	23.2104
.(((((...........))))))	chr17:90435851-90436116(-)$1	1	26	49	23.5013
((((((............)))..	chr17:46685741-46685996(-)$1	1	103	126	23.2348
..((((............)))).	chr11:78382259-78382511(-)$1	1	104	127	19.8835
..((((...........))))..	chr2:49629383-49629665(+)$1	1	228	251	22.7176
((((((.............))))	chr4:86629006-86629273(-)$1	1	52	75	22.4951
)(((((............)))))	chr13:100204615-100204882(-)$1	1	218	241	23.2209
((((((...........))))))	chr19:40921213-40921471(+)$1	1	208	231	20.9855
(((................))))	chr15:37897557-37897836(-)$1	1	50	73	20.2879
((((((...........))))))	chr16:43862569-43862848(-)$1	1	123	146	23.2104
.(((((...........))))).	chr6:23446712-23446974(-)$1	1	80	103	23.7104
.(((((...........))))))	chr4:128789488-128789745(-)$1	1	35	58	23.3930
..((((...........))))))	chrX:133370970-133371234(+)$1	1	86	109	22.9426
(((((............))))))	chr4:137212080-137212324(+)$1	1	35	58	22.6493
((((((...........))).))	chr13:89749712-89749977(+)$1	1	94	117	23.5129
.(((((...........))))).	chr2:71181893-71182158(-)$1	1	214	237	21.7741
((((((.............))).	chr9:98902239-98902507(+)$1	1	34	57	22.6804
(((................))))	chr9:51895360-51895695(+)$1	1	3	26	20.3145
(.(((..............))).	chr9:115996713-115996957(-)$1	1	117	140	21.3934
.(((((...........)))))(	chr18:36664979-36665227(-)$1	1	16	39	22.2182
(..(((.............))).	chr9:36540109-36540386(-)$1	1	200	223	22.9604
((.(((...........))))))	chr9:118950705-118950950(+)$1	1	216	239	23.5966
(((.(.............).)))	chr2:70439775-70440064(+)$1	1	102	125	22.1840
)(((((...........))))).	chr2:153594020-153594277(+)$1	1	172	195	22.6156
((((((.............))))	chr9:106056370-106056595(+)$1	1	117	140	22.6129
(((((..............))))	chr1:37496161-37496448(-)$1	1	106	129	20.5883
((((((...........))))))	chr15:27661376-27661611(-)$1	1	185	208	22.1869
((.(((............)))..	chr1:64644225-64644477(+)$1	1	207	230	23.4964
(..(((............)))..	chr4:109878572-109878824(-)$1	1	147	170	23.1639
(((................))))	chr1:66488972-66489232(+)$1	1	35	58	21.0296
(..(((............)))..	chr13:100194425-100194737(-)$1	1	259	282	23.1639
(((.((...........)).)))	chr8:123197821-123198128(+)$1	1	120	143	21.6224
((((((............)))))	chr13:90244128-90244388(+)$1	1	9	32	21.1796
.(((((............)))))	chr11:106643733-106644035(-)$1	1	142	165	23.4369
..((((...........)))).)	chr10:79457310-79457597(+)$1	1	180	203	22.6419
.((((.............)))).	chr6:102114987-102115278(-)$1	1	143	166	20.6414
((((((...........))))))	chr14:19038170-19038452(-)$1	1	47	70	23.2104
)(((((...........))))).	chr11:88157887-88158158(-)$1	1	160	183	22.6689
.(((((............)))))	chr10:7344142-7344393(+)$1	1	212	235	22.4887
.(((((............)))))	chr11:61591098-61591336(-)$1	1	186	209	23.1248
(..(((...........)))..)	chr5:67447115-67447371(+)$1	1	54	77	23.0876
(..(((.............))).	chr5:40005231-40005490(-)$1	1	19	42	22.6896
((((((...........))))).	chr3:80491906-80492171(-)$1	1	13	36	23.4944

#PSSM
g : 0.16	f : 0.15	d : 0.12	e : 0.10	: : 0.10	[ : 0.07	i : 0.04	b : 0.04	c : 0.04	! : 0.04	h : 0.03	a : 0.01	= : 0.01	" : 0.01	$ : 0.01	
e : 0.27	d : 0.15	g : 0.13	f : 0.12	! : 0.12	i : 0.04	[ : 0.03	c : 0.03	h : 0.03	b : 0.01	: : 0.01	= : 0.01	" : 0.01	
e : 0.24	d : 0.19	g : 0.12	f : 0.10	c : 0.09	! : 0.09	i : 0.04	[ : 0.04	h : 0.03	b : 0.01	= : 0.01	
e : 0.24	c : 0.22	d : 0.13	g : 0.10	y : 0.07	f : 0.07	i : 0.03	h : 0.03	[ : 0.03	b : 0.01	a : 0.01	= : 0.01	
c : 0.22	e : 0.22	d : 0.13	g : 0.10	y : 0.07	f : 0.07	w : 0.03	i : 0.03	h : 0.03	v : 0.01	a : 0.01	= : 0.01	b : 0.01	
e : 0.19	c : 0.16	v : 0.10	g : 0.09	w : 0.07	d : 0.07	y : 0.07	u : 0.06	f : 0.06	i : 0.03	h : 0.03	= : 0.01	b : 0.01	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
t : 0.42	u : 0.22	v : 0.19	w : 0.07	y : 0.07	
v : 0.18	u : 0.16	e : 0.13	c : 0.10	g : 0.09	w : 0.07	y : 0.07	d : 0.06	f : 0.06	b : 0.03	h : 0.01	
e : 0.24	c : 0.16	d : 0.12	g : 0.09	v : 0.09	y : 0.07	f : 0.06	w : 0.04	b : 0.03	a : 0.03	h : 0.03	i : 0.01	
c : 0.24	e : 0.24	d : 0.15	g : 0.12	f : 0.10	] : 0.04	i : 0.03	h : 0.03	2 : 0.01	= : 0.01	
e : 0.25	d : 0.18	c : 0.13	f : 0.12	g : 0.12	] : 0.04	i : 0.03	3 : 0.03	2 : 0.03	h : 0.03	= : 0.01	
e : 0.27	g : 0.13	d : 0.13	f : 0.12	c : 0.07	3 : 0.06	2 : 0.06	i : 0.04	] : 0.03	h : 0.03	b : 0.01	= : 0.01	
e : 0.16	g : 0.13	f : 0.12	] : 0.10	d : 0.09	: : 0.09	2 : 0.06	3 : 0.06	i : 0.04	a : 0.03	h : 0.03	b : 0.01	F : 0.01	= : 0.01	4 : 0.01	

#score	1472.7573619206
#seq	66
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_UTR_m3_run2.txt

#BEAR
eeeeeqqqqqqqqeeeee8	chr15:3933607-3933871(-)$1	264	79	98	14.2001
ccc[aqqqqqqqqacccff	chr18:66141408-66141656(-)$1	248	64	83	14.2456
gggggqqqqqqqqgggggg	chr1:164527958-164528225(+)$1	267	154	173	14.3811
!ddddqqqqqqqqdddd22	chr9:25115310-25115561(+)$1	251	89	108	13.4320
eddddqqqqqqqqdddd22	chr2:153594020-153594277(+)$1	257	6	25	13.4487
fffffqqqqqqqqffffff	chr2:112106406-112106674(+)$1	268	54	73	14.9197
#ddddqqqqqqqqdddd33	chr10:77903205-77903465(-)$1	260	233	252	13.7137
fffffqqqqqqqqffffff	chr14:58221305-58221563(-)$1	258	25	44	14.9197
fffffqqqqqqqqffffff	chr2:37283914-37284154(-)$1	240	143	162	14.9197
c[cccqqqqqqqqccc]cc	chr1:130083278-130083540(+)$1	262	135	154	14.8346
gggggqqqqqqqqgggggg	chr16:20331477-20331724(-)$1	247	105	124	14.3811
eeeeeqqqqqqqqeeeee:	chr10:67558271-67558536(-)$1	265	245	264	13.7198
"ddddqqqqqqqqdddd22	chr4:149021553-149021806(+)$1	253	171	190	13.3434
e[cccqqqqqqqqccceee	chr11:106642296-106642571(-)$1	275	193	212	15.0939
e[cccqqqqqqqqccc]ee	chr4:126540886-126541151(-)$1	265	90	109	15.1587
fffffqqqqqqqqffffff	chr11:77348129-77348364(-)$1	235	54	73	14.9197
!ddddqqqqqqqqdddd22	chr2:119598162-119598407(-)$1	245	34	53	13.4320
fffffqqqqqqqqffffff	chr8:48265561-48265933(-)$1	372	8	27	14.9197
"bb[aqqqqqqqqabb333	chr12:86682745-86683001(-)$1	256	18	37	13.1136
eeeeeqqqqqqqqeeeee:	chr17:10406748-10407069(-)$1	321	203	222	13.7198
c[cccqqqqqqqqccc]cc	chr14:61585030-61585284(-)$1	254	177	196	14.8346
d[cccqqqqqqqqcccddd	chr1:175265224-175265479(-)$1	255	182	201	14.1908
[ddddqqqqqqqqdddd]b	chr12:4839965-4840285(-)$1	320	121	140	13.4983
eeeeeqqqqqqqqeeeee:	chr5:107536897-107537202(-)$1	305	17	36	13.7198
fffffqqqqqqqqffffff	chr2:30119173-30119428(+)$1	255	9	28	14.9197
eeeeeqqqqqqqqeeeee:	chr9:44960651-44960901(+)$1	250	65	84	13.7198
eeeeeqqqqqqqqeeeee]	chr2:153592668-153592925(+)$1	257	98	117	14.6668
f[cccqqqqqqqqccc]ff	chr2:163843748-163844018(+)$1	270	232	251	15.2081
c[cccqqqqqqqqccc]cc	chr2:124492650-124492915(+)$1	265	209	228	14.8346
!ddddqqqqqqqqdddd]h	chr3:89904320-89904571(+)$1	251	197	216	13.4117
fffffqqqqqqqqffffff	chr3:109487907-109488147(+)$1	240	139	158	14.9197
c[cccqqqqqqqqccc]cc	chr7:54333858-54334099(-)$1	241	61	80	14.8346
fffffqqqqqqqqffffff	chr3:84300622-84300979(-)$1	357	293	312	14.9197
"""bbqqqqqqqqbb]fff	chr2:6468112-6468359(-)$1	247	139	158	13.2251
eeeeeqqqqqqqqeeeee:	chr17:69639139-69639406(+)$1	267	39	58	13.7198
fffffqqqqqqqqffffff	chr14:58316006-58316265(-)$1	259	212	231	14.9197
eeeeeqqqqqqqqeeeeee	chr10:77060892-77061140(+)$1	248	98	117	14.5278
eee[aqqqqqqqqa]eeee	chr8:34527589-34527920(+)$1	331	299	318	14.2939
e[cccqqqqqqqqccc]ee	chr6:148940603-148940857(-)$1	254	46	65	15.1587
e[cccqqqqqqqqccc]ee	chr17:87397867-87398149(+)$1	282	239	258	15.1587
e[cccqqqqqqqqccc]ee	chr8:127432579-127432841(-)$1	262	160	179	15.1587
=====qqqqqqqq======	chr18:82723822-82724163(+)$1	341	35	54	14.2264
""cccqqqqqqqqccc333	chr6:113698440-113698705(-)$1	265	202	221	14.8286
!!cccqqqqqqqqccc333	chr18:39646741-39646994(-)$1	253	33	52	15.0302
eeeeeqqqqqqqqeeeee]	chr4:138854406-138854714(-)$1	308	216	235	14.6668
fffffqqqqqqqqffffff	chr9:77831023-77831285(+)$1	262	23	42	14.9197
!ddddqqqqqqqqdddd22	chr1:176539332-176539586(+)$1	254	117	136	13.4320
ffffaqqqqqqqqa]ffff	chr10:118296436-118296685(-)$1	249	11	30	14.5538
eeeeeqqqqqqqqeeeeeb	chr1:108668257-108668497(-)$1	240	133	152	14.3330
ee[bbqqqqqqqqbb]eee	chr5:120984102-120984417(-)$1	315	260	279	13.4264
[ddddqqqqqqqqdddd]c	chr5:110688249-110688524(-)$1	275	181	200	13.7017
fffffqqqqqqqqffffff	chr10:77061218-77061567(+)$1	349	268	287	14.9197
fffffqqqqqqqqffffff	chr2:84442342-84442623(-)$1	281	48	67	14.9197
!!cccqqqqqqqqccceee	chr10:20798929-20799196(+)$1	267	211	230	14.9696
fffffqqqqqqqqffffff	chr8:24559526-24559799(+)$1	273	20	39	14.9197
e[cccqqqqqqqqccceee	chr8:107991359-107991685(-)$1	326	192	211	15.0939
eeeeeqqqqqqqqeeeee]	chr14:45905444-45905737(-)$1	293	25	44	14.6668
###bbqqqqqqqqbb4444	chr6:145168134-145168370(-)$1	236	129	148	12.7904
fffffqqqqqqqqffffff	chr7:26028492-26028807(-)$1	315	93	112	14.9197
fffffqqqqqqqqffffff	chr3:82344081-82344330(-)$1	249	220	239	14.9197
gggggqqqqqqqqgggggg	chr1:66488794-66489047(+)$1	253	65	84	14.3811
eeeeeqqqqqqqqeeeee:	chr1:163919306-163919558(-)$1	252	3	22	13.7198
eeeeeqqqqqqqqeeeee:	chr3:8663940-8664191(-)$1	251	198	217	13.7198
fffffqqqqqqqqffffff	chr1:34220419-34220699(+)$1	280	180	199	14.9197
i[cccqqqqqqqqccciii	chr9:44211856-44212102(-)$1	246	127	146	14.7668
fffffqqqqqqqqffffff	chr16:8621367-8621677(+)$1	310	54	73	14.9197
eecccqqqqqqqqccc]ee	chr8:4285746-4285988(-)$1	242	47	66	14.9853
fffffqqqqqqqqffffff	chr1:74902983-74903293(+)$1	310	104	123	14.9197
e[cccqqqqqqqqccc]ee	chr16:8699131-8699382(-)$1	251	105	124	15.1587
gggggqqqqqqqqgggggg	chr2:117107253-117107506(-)$1	253	47	66	14.3811

#otherMatches

#Seq PSSM
GGCAUGAUUUGAAAUGCCA	chr15:3933607-3933871(-)$1	264	79	98	14.2001
AGAACUCCUUCAUGUCUGU	chr18:66141408-66141656(-)$1	248	64	83	14.2456
AGGGUCUGAGUUUAUCUUG	chr1:164527958-164528225(+)$1	267	154	173	14.3811
UAAUGCAAGAAAACAUUUU	chr9:25115310-25115561(+)$1	251	89	108	13.4320
AAUGUUAUGUAGUGCAUGC	chr2:153594020-153594277(+)$1	257	6	25	13.4487
ACCUGAUACACAACAGGUG	chr2:112106406-112106674(+)$1	268	54	73	14.9197
GGACCUUUCUGUUGGUCAC	chr10:77903205-77903465(-)$1	260	233	252	13.7137
UUAAGUGUUCAUUUUUAAU	chr14:58221305-58221563(-)$1	258	25	44	14.9197
GAGAUUCUACAUUGUCUCA	chr2:37283914-37284154(-)$1	240	143	162	14.9197
GCCUGGUCCUCCACAGCCA	chr1:130083278-130083540(+)$1	262	135	154	14.8346
UUUUUGUACUGUAAAGAGA	chr16:20331477-20331724(-)$1	247	105	124	14.3811
GGAGGAUGCUGCCCCUCUU	chr10:67558271-67558536(-)$1	265	245	264	13.7198
CGAUGUACAAAAUCAUUUU	chr4:149021553-149021806(+)$1	253	171	190	13.3434
GUAGGUUCCUAGUCCUCGA	chr11:106642296-106642571(-)$1	275	193	212	15.0939
UUGUAUAAAAUUCUACCAU	chr4:126540886-126541151(-)$1	265	90	109	15.1587
AUUUCCAUAUCUAGAGAUG	chr11:77348129-77348364(-)$1	235	54	73	14.9197
AUGGAGACCAUAGUUCAAG	chr2:119598162-119598407(-)$1	245	34	53	13.4320
GCAGGUGUCUUUCUCUGCG	chr8:48265561-48265933(-)$1	372	8	27	14.9197
UCCUCUAUCAAAUGGGUUG	chr12:86682745-86683001(-)$1	256	18	37	13.1136
UACUGCAAAGCAACAGUAA	chr17:10406748-10407069(-)$1	321	203	222	13.7198
GACUGACUGUAGGCGGCCU	chr14:61585030-61585284(-)$1	254	177	196	14.8346
CUCUUAUAGCAGCAAGGGA	chr1:175265224-175265479(-)$1	255	182	201	14.1908
CCUUACCUGCACUUAAGCC	chr12:4839965-4840285(-)$1	320	121	140	13.4983
CGAUGCAUAGAUACAUUGA	chr5:107536897-107537202(-)$1	305	17	36	13.7198
GCGUCGUGUCAUGGAUGUA	chr2:30119173-30119428(+)$1	255	9	28	14.9197
CUGUCAGCUUAUAGGCAGC	chr9:44960651-44960901(+)$1	250	65	84	13.7198
CUUUUCAUAAGCAAAAAGU	chr2:153592668-153592925(+)$1	257	98	117	14.6668
GAACAAAAAAAAAUGUGCA	chr2:163843748-163844018(+)$1	270	232	251	15.2081
CUUGGGACAGUGACCAUGG	chr2:124492650-124492915(+)$1	265	209	228	14.8346
uaaauuuuauauuauuuuG	chr3:89904320-89904571(+)$1	251	197	216	13.4117
AUUGUGUUUUAGAACAAUU	chr3:109487907-109488147(+)$1	240	139	158	14.9197
CCUGGUCCCUACCCCAAGC	chr7:54333858-54334099(-)$1	241	61	80	14.8346
UGGAUAACAUUUGAUUCAU	chr3:84300622-84300979(-)$1	357	293	312	14.9197
CAAUCCAGGCUAUGAACGG	chr2:6468112-6468359(-)$1	247	139	158	13.2251
UACAGAAUUUCCACUGUAA	chr17:69639139-69639406(+)$1	267	39	58	13.7198
GUGGUCAAACUCUACUACU	chr14:58316006-58316265(-)$1	259	212	231	14.9197
UAGGCUCCCUCAUGCCUAA	chr10:77060892-77061140(+)$1	248	98	117	14.5278
AAUUUGUCUCAAAAUAUUC	chr8:34527589-34527920(+)$1	331	299	318	14.2939
UUAGGCACCGAUACCUUGU	chr6:148940603-148940857(-)$1	254	46	65	15.1587
AGUCUACUGGACAAGAGUG	chr17:87397867-87398149(+)$1	282	239	258	15.1587
AAAGCUUUAUGACGCUGUU	chr8:127432579-127432841(-)$1	262	160	179	15.1587
UCCCGAGAUGCCCCGGGAA	chr18:82723822-82724163(+)$1	341	35	54	14.2264
CAUGGACCCGCCGCCACCC	chr6:113698440-113698705(-)$1	265	202	221	14.8286
UAAUCGGAUCAGAGAUAAU	chr18:39646741-39646994(-)$1	253	33	52	15.0302
GGGACCCAGGGUUGUCCCU	chr4:138854406-138854714(-)$1	308	216	235	14.6668
GCAGGGCCCAGAGCUUGUU	chr9:77831023-77831285(+)$1	262	23	42	14.9197
UGGGAAUACCUCCUCCCCC	chr1:176539332-176539586(+)$1	254	117	136	13.4320
GGCACAGAUGACAGAUGCC	chr10:118296436-118296685(-)$1	249	11	30	14.5538
GUCUUUUAUAGCCAAGAUU	chr1:108668257-108668497(-)$1	240	133	152	14.3330
UGCAGCCUUUGAUUUCCAG	chr5:120984102-120984417(-)$1	315	260	279	13.4264
uguauauacuaccauaccu	chr5:110688249-110688524(-)$1	275	181	200	13.7017
CUUUGUUUUGUCCCAAGGG	chr10:77061218-77061567(+)$1	349	268	287	14.9197
GGAAGUGUGAGUUCUUCCC	chr2:84442342-84442623(-)$1	281	48	67	14.9197
CUGCUGCUGGAAAAGCCAA	chr10:20798929-20799196(+)$1	267	211	230	14.9696
UGUUUGCUUUUUAAAACAU	chr8:24559526-24559799(+)$1	273	20	39	14.9197
AUGGCUGACUCUUGCCUGC	chr8:107991359-107991685(-)$1	326	192	211	15.0939
UGUUCACUGAGGAGGACGG	chr14:45905444-45905737(-)$1	293	25	44	14.6668
AGAUGAUCUGAGACAGUUA	chr6:145168134-145168370(-)$1	236	129	148	12.7904
AUUUUAUAAACCAAAAAUU	chr7:26028492-26028807(-)$1	315	93	112	14.9197
GUUUUAUUUCUGGAAAACU	chr3:82344081-82344330(-)$1	249	220	239	14.9197
AAAGGUUUUUUUUUUUUUU	chr1:66488794-66489047(+)$1	253	65	84	14.3811
CAUGCUAACUUACGCAUGC	chr1:163919306-163919558(-)$1	252	3	22	13.7198
GCAAAGCAUUAUAUUUGCA	chr3:8663940-8664191(-)$1	251	198	217	13.7198
GUAUAUGAAUUUUUGUGCU	chr1:34220419-34220699(+)$1	280	180	199	14.9197
GUGAUGGUGACAGAUCCUG	chr9:44211856-44212102(-)$1	246	127	146	14.7668
UAGAUCUGUACCUAUCUAU	chr16:8621367-8621677(+)$1	310	54	73	14.9197
GAGCAACAGAACAUGCAUU	chr8:4285746-4285988(-)$1	242	47	66	14.9853
UGGGCAUCUCAAAGUCCAC	chr1:74902983-74903293(+)$1	310	104	123	14.9197
CAAAUGCCUAUAUGUUAGU	chr16:8699131-8699382(-)$1	251	105	124	15.1587
AAGAAUCUGUGACUUUUUA	chr2:117107253-117107506(-)$1	253	47	66	14.3811

#DB
(((((........))))).	chr15:3933607-3933871(-)$1	1	79	98	14.2001
(((.(........))))))	chr18:66141408-66141656(-)$1	1	64	83	14.2456
(((((........))))))	chr1:164527958-164528225(+)$1	1	154	173	14.3811
.((((........))))..	chr9:25115310-25115561(+)$1	1	89	108	13.4320
(((((........))))..	chr2:153594020-153594277(+)$1	1	6	25	13.4487
(((((........))))))	chr2:112106406-112106674(+)$1	1	54	73	14.9197
.((((........))))..	chr10:77903205-77903465(-)$1	1	233	252	13.7137
(((((........))))))	chr14:58221305-58221563(-)$1	1	25	44	14.9197
(((((........))))))	chr2:37283914-37284154(-)$1	1	143	162	14.9197
(.(((........))).))	chr1:130083278-130083540(+)$1	1	135	154	14.8346
(((((........))))))	chr16:20331477-20331724(-)$1	1	105	124	14.3811
(((((........))))).	chr10:67558271-67558536(-)$1	1	245	264	13.7198
.((((........))))..	chr4:149021553-149021806(+)$1	1	171	190	13.3434
(.(((........))))))	chr11:106642296-106642571(-)$1	1	193	212	15.0939
(.(((........))).))	chr4:126540886-126541151(-)$1	1	90	109	15.1587
(((((........))))))	chr11:77348129-77348364(-)$1	1	54	73	14.9197
.((((........))))..	chr2:119598162-119598407(-)$1	1	34	53	13.4320
(((((........))))))	chr8:48265561-48265933(-)$1	1	8	27	14.9197
.((.(........)))...	chr12:86682745-86683001(-)$1	1	18	37	13.1136
(((((........))))).	chr17:10406748-10407069(-)$1	1	203	222	13.7198
(.(((........))).))	chr14:61585030-61585284(-)$1	1	177	196	14.8346
(.(((........))))))	chr1:175265224-175265479(-)$1	1	182	201	14.1908
.((((........)))).)	chr12:4839965-4840285(-)$1	1	121	140	13.4983
(((((........))))).	chr5:107536897-107537202(-)$1	1	17	36	13.7198
(((((........))))))	chr2:30119173-30119428(+)$1	1	9	28	14.9197
(((((........))))).	chr9:44960651-44960901(+)$1	1	65	84	13.7198
(((((........))))).	chr2:153592668-153592925(+)$1	1	98	117	14.6668
(.(((........))).))	chr2:163843748-163844018(+)$1	1	232	251	15.2081
(.(((........))).))	chr2:124492650-124492915(+)$1	1	209	228	14.8346
.((((........)))).)	chr3:89904320-89904571(+)$1	1	197	216	13.4117
(((((........))))))	chr3:109487907-109488147(+)$1	1	139	158	14.9197
(.(((........))).))	chr7:54333858-54334099(-)$1	1	61	80	14.8346
(((((........))))))	chr3:84300622-84300979(-)$1	1	293	312	14.9197
...((........)).)))	chr2:6468112-6468359(-)$1	1	139	158	13.2251
(((((........))))).	chr17:69639139-69639406(+)$1	1	39	58	13.7198
(((((........))))))	chr14:58316006-58316265(-)$1	1	212	231	14.9197
(((((........))))))	chr10:77060892-77061140(+)$1	1	98	117	14.5278
(((.(........).))))	chr8:34527589-34527920(+)$1	1	299	318	14.2939
(.(((........))).))	chr6:148940603-148940857(-)$1	1	46	65	15.1587
(.(((........))).))	chr17:87397867-87398149(+)$1	1	239	258	15.1587
(.(((........))).))	chr8:127432579-127432841(-)$1	1	160	179	15.1587
(((((........))))))	chr18:82723822-82724163(+)$1	1	35	54	14.2264
..(((........)))...	chr6:113698440-113698705(-)$1	1	202	221	14.8286
..(((........)))...	chr18:39646741-39646994(-)$1	1	33	52	15.0302
(((((........))))).	chr4:138854406-138854714(-)$1	1	216	235	14.6668
(((((........))))))	chr9:77831023-77831285(+)$1	1	23	42	14.9197
.((((........))))..	chr1:176539332-176539586(+)$1	1	117	136	13.4320
(((((........).))))	chr10:118296436-118296685(-)$1	1	11	30	14.5538
(((((........))))))	chr1:108668257-108668497(-)$1	1	133	152	14.3330
((.((........)).)))	chr5:120984102-120984417(-)$1	1	260	279	13.4264
.((((........)))).)	chr5:110688249-110688524(-)$1	1	181	200	13.7017
(((((........))))))	chr10:77061218-77061567(+)$1	1	268	287	14.9197
(((((........))))))	chr2:84442342-84442623(-)$1	1	48	67	14.9197
..(((........))))))	chr10:20798929-20799196(+)$1	1	211	230	14.9696
(((((........))))))	chr8:24559526-24559799(+)$1	1	20	39	14.9197
(.(((........))))))	chr8:107991359-107991685(-)$1	1	192	211	15.0939
(((((........))))).	chr14:45905444-45905737(-)$1	1	25	44	14.6668
...((........))....	chr6:145168134-145168370(-)$1	1	129	148	12.7904
(((((........))))))	chr7:26028492-26028807(-)$1	1	93	112	14.9197
(((((........))))))	chr3:82344081-82344330(-)$1	1	220	239	14.9197
(((((........))))))	chr1:66488794-66489047(+)$1	1	65	84	14.3811
(((((........))))).	chr1:163919306-163919558(-)$1	1	3	22	13.7198
(((((........))))).	chr3:8663940-8664191(-)$1	1	198	217	13.7198
(((((........))))))	chr1:34220419-34220699(+)$1	1	180	199	14.9197
(.(((........))))))	chr9:44211856-44212102(-)$1	1	127	146	14.7668
(((((........))))))	chr16:8621367-8621677(+)$1	1	54	73	14.9197
(((((........))).))	chr8:4285746-4285988(-)$1	1	47	66	14.9853
(((((........))))))	chr1:74902983-74903293(+)$1	1	104	123	14.9197
(.(((........))).))	chr16:8699131-8699382(-)$1	1	105	124	15.1587
(((((........))))))	chr2:117107253-117107506(-)$1	1	47	66	14.3811

#PSSM
e : 0.34	f : 0.28	! : 0.08	c : 0.07	g : 0.05	" : 0.05	# : 0.02	[ : 0.02	d : 0.01	= : 0.01	i : 0.01	
f : 0.27	e : 0.22	[ : 0.20	d : 0.12	g : 0.05	" : 0.02	! : 0.02	c : 0.01	b : 0.01	= : 0.01	# : 0.01	
c : 0.27	f : 0.27	e : 0.20	d : 0.12	g : 0.05	b : 0.01	" : 0.01	= : 0.01	[ : 0.01	# : 0.01	
f : 0.27	c : 0.25	e : 0.18	d : 0.12	g : 0.05	[ : 0.04	b : 0.04	= : 0.01	
f : 0.25	c : 0.25	e : 0.18	d : 0.12	a : 0.05	g : 0.05	b : 0.04	= : 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	
f : 0.25	c : 0.25	e : 0.18	d : 0.12	a : 0.05	g : 0.05	b : 0.04	= : 0.01	
c : 0.27	f : 0.25	e : 0.18	d : 0.12	g : 0.05	b : 0.05	] : 0.02	= : 0.01	
c : 0.27	f : 0.27	e : 0.20	d : 0.12	g : 0.05	] : 0.02	b : 0.01	= : 0.01	4 : 0.01	
f : 0.28	e : 0.25	] : 0.15	d : 0.14	g : 0.05	3 : 0.04	c : 0.01	= : 0.01	4 : 0.01	i : 0.01	
e : 0.34	f : 0.31	2 : 0.07	g : 0.05	3 : 0.05	c : 0.05	] : 0.04	d : 0.01	= : 0.01	4 : 0.01	i : 0.01	
f : 0.31	e : 0.17	: : 0.10	2 : 0.07	c : 0.07	g : 0.05	3 : 0.05	] : 0.04	b : 0.02	8 : 0.01	d : 0.01	h : 0.01	= : 0.01	4 : 0.01	i : 0.01	

#score	1009.7703070383087
#seq	70
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_CDS_m3_run1.txt

#BEAR
(ddddqqqqqqqqdddd7	chr9:71331219-71331420(-)$1	201	83	101	13.4338
eeeeeqqqqqqqqeeeee	chr11:31001017-31001218(+)$1	201	76	94	13.1466
eeeeeqqqqqqqqeeeee	chr6:23638699-23638900(-)$1	201	12	30	13.1466
cccccqqqqqqqqccc22	chr10:17444021-17444222(+)$1	201	81	99	14.0742
eeeeeqqqqqqqqeeeee	chr10:66682776-66682977(+)$1	201	151	169	13.1466
cc[bbqqqqqqqqbb]cc	chr4:118808324-118808525(+)$1	201	84	102	13.5704
eeeeeqqqqqqqqeeeee	chr2:132130873-132131074(+)$1	201	125	143	13.1466
ccc[aqqqqqqqqa]ccc	chr4:144671527-144671728(-)$1	201	133	151	13.8165
c[cccqqqqqqqqccc]c	chr2:25099279-25099480(+)$1	201	106	124	14.3161
:ddddqqqqqqqqdddd:	chr6:28780126-28780327(-)$1	201	172	190	12.9508
eee[aqqqqqqqqa]eee	chr15:59194706-59194907(-)$1	201	10	28	13.4345
gddddqqqqqqqqdddd]	chr9:101003604-101003805(+)$1	201	10	28	14.3973
ee[bbqqqqqqqqbbeee	chr9:32066852-32067053(+)$1	201	145	163	13.4023
c[cccqqqqqqqqccc]c	chr3:115415601-115415802(-)$1	201	176	194	14.3161
ccc[aqqqqqqqqa]ccc	chr4:144671526-144671727(-)$1	201	132	150	13.8165
$$cccqqqqqqqqccccc	chrX:155899959-155900160(+)$1	201	176	194	13.9814
ee[bbqqqqqqqqbb]ee	chr2:83719203-83719404(+)$1	201	16	34	13.4170
+ddddqqqqqqqqdddd=	chr14:30932205-30932406(-)$1	201	172	190	13.8983
bb[bbqqqqqqqqbb]bb	chr13:9876408-9876609(-)$1	201	64	82	12.5759
!!cccqqqqqqqqccc22	chr14:70861508-70861709(+)$1	201	174	192	14.3956
[ddddqqqqqqqqdddd]	chr3:88785128-88785329(+)$1	201	156	174	14.5346
fff[aqqqqqqqqa]fff	chr2:128907728-128907929(+)$1	201	147	165	12.6833
d[cccqqqqqqqqccc]d	chr10:20045110-20045311(+)$1	201	146	164	14.0187
cc[bbqqqqqqqqbb]cc	chr2:80370320-80370521(-)$1	201	30	48	13.5704
""cccqqqqqqqqccccc	chr5:14713807-14714008(+)$1	201	77	95	14.3701
##cccqqqqqqqqccc33	chr13:90237876-90238077(+)$1	201	97	115	14.5713
ee[bbqqqqqqqqbbeee	chr11:76233180-76233381(-)$1	201	164	182	13.4023
(ddddqqqqqqqqdddd7	chr9:71331220-71331421(-)$1	201	84	102	13.4338
[ddddqqqqqqqqdddd]	chr14:33022729-33022930(+)$1	201	172	190	14.5346
!!cccqqqqqqqqccc22	chr2:91510892-91511093(+)$1	201	161	179	14.3956
!ddddqqqqqqqqdddd4	chr12:8275223-8275424(+)$1	201	105	123	14.6442
c[cccqqqqqqqqccc]c	chr2:25099274-25099475(+)$1	201	111	129	14.3161
"ddddqqqqqqqqdddd6	chr10:89112690-89112891(-)$1	201	155	173	14.1396
bddddqqqqqqqqdddd]	chr13:92123032-92123233(-)$1	201	122	140	14.2782
!!cccqqqqqqqqccc22	chr8:113262156-113262357(+)$1	201	97	115	14.3956
dd[bbqqqqqqqqbb]dd	chr13:68873487-68873688(-)$1	201	22	40	13.4466
[ddddqqqqqqqqdddde	chr14:94286626-94286827(-)$1	201	116	134	14.3269
[bb[aqqqqqqqqa]bb]	chr16:90939063-90939264(-)$1	201	35	53	12.6232
eeeeeqqqqqqqqeeeee	chr7:118698002-118698203(-)$1	201	133	151	13.1466
cc[bbqqqqqqqqbb]cc	chr2:80370321-80370522(-)$1	201	31	49	13.5704
bb[bbqqqqqqqqbb]bb	chr6:137699004-137699205(+)$1	201	175	193	12.5759
:ddddqqqqqqqqdddd:	chr18:50031212-50031413(+)$1	201	78	96	12.9508
e[cccqqqqqqqqcccee	chr5:34787350-34787551(+)$1	201	126	144	14.1499
!!cccqqqqqqqqccccc	chr12:34051822-34052023(+)$1	201	179	197	14.5284
b[cccqqqqqqqqccc]b	chr17:35972345-35972546(-)$1	201	52	70	13.9120
iii[aqqqqqqqqa]iii	chr3:126640667-126640868(-)$1	201	69	87	13.5251
!!cccqqqqqqqqccc22	chr9:44627181-44627382(-)$1	201	94	112	14.3956
:ddddqqqqqqqqdddd:	chr12:71048391-71048592(+)$1	201	154	172	12.9508
eeeeeqqqqqqqqeeeee	chr11:68904057-68904258(+)$1	201	126	144	13.1466
:ddddqqqqqqqqddddc	chr8:96490752-96490953(+)$1	201	135	153	13.6170
:ddddqqqqqqqqdddd:	chr17:44217689-44217890(+)$1	201	163	181	12.9508
:ddddqqqqqqqqddddA	chr8:96490727-96490928(+)$1	201	160	178	12.8958
gggggqqqqqqqqggggg	chr18:37980412-37980613(+)$1	201	100	118	13.2613
cccccqqqqqqqqccc::	chr12:54240669-54240870(+)$1	201	177	195	12.6373
:ddddqqqqqqqqddddA	chr8:96490728-96490929(+)$1	201	159	177	12.8958
=====qqqqqqqq=====	chr2:37345224-37345425(+)$1	201	127	145	13.7331
cc!!aqqqqqqqqa22cc	chr13:51245888-51246089(+)$1	201	99	117	13.2158
!!cccqqqqqqqqccc22	chr1:75182271-75182472(-)$1	201	146	164	14.3956
eddddqqqqqqqqdddd]	chr5:114491780-114491981(-)$1	201	63	81	14.3631
bb[bbqqqqqqqqbbbb]	chr7:149541800-149542001(-)$1	201	43	61	12.6257
"ddddqqqqqqqqdddd5	chr12:54243581-54243782(+)$1	201	128	146	13.8768
eeeeeqqqqqqqqeeeee	chr5:102250442-102250643(+)$1	201	171	189	13.1466
g!!bbqqqqqqqqbbggg	chr7:134703487-134703688(+)$1	201	160	178	13.5434
!ddddqqqqqqqqdddd2	chr15:6723801-6724002(+)$1	201	148	166	14.4994
!ddddqqqqqqqqddddb	chr12:101611701-101611902(-)$1	201	170	188	14.2627
bddddqqqqqqqqdddd]	chr15:54429881-54430082(+)$1	201	143	161	14.2782
ee[bbqqqqqqqqbb]ee	chr2:83719204-83719405(+)$1	201	15	33	13.4170
c[cccqqqqqqqqccc]c	chr7:66531203-66531404(-)$1	201	33	51	14.3161
dddbbqqqqqqqqbb]dd	chr4:25547582-25547783(-)$1	201	144	162	13.4339
gggggqqqqqqqqggggg	chrX:70925756-70925957(+)$1	201	5	23	13.2613
cc[bbqqqqqqqqbbccc	chr2:160775241-160775442(-)$1	201	9	27	13.6606
""cccqqqqqqqqccc33	chr5:67070868-67071069(+)$1	201	162	180	14.6172

#otherMatches

#Seq PSSM
AGGGACCUACACAUCUCA	chr9:71331219-71331420(-)$1	201	83	101	13.4338
CAGAGCACCUUCACUCUG	chr11:31001017-31001218(+)$1	201	76	94	13.1466
GCAGACGAAGCCUUCUGC	chr6:23638699-23638900(-)$1	201	12	30	13.1466
AAGCUCAACAACCAGUAU	chr10:17444021-17444222(+)$1	201	81	99	14.0742
ACCUGUUUAAACCCAGGU	chr10:66682776-66682977(+)$1	201	151	169	13.1466
GGUCCUAUUCCAUGGUUC	chr4:118808324-118808525(+)$1	201	84	102	13.5704
CAUCUGCCUUGGAAGAUG	chr2:132130873-132131074(+)$1	201	125	143	13.1466
GCUCGGGGACAGGUAAGC	chr4:144671527-144671728(-)$1	201	133	151	13.8165
CCCACCUGCCACCGUGAG	chr2:25099279-25099480(+)$1	201	106	124	14.3161
CCACCUCUACCACGGUGC	chr6:28780126-28780327(-)$1	201	172	190	12.9508
CUGCCUACCCGCUGCCGG	chr15:59194706-59194907(-)$1	201	10	28	13.4345
GCUGUCCUAAUUUGCAGC	chr9:101003604-101003805(+)$1	201	10	28	14.3973
CACACCACAAUAAGUUGG	chr9:32066852-32067053(+)$1	201	145	163	13.4023
CCAUGUACUAUUUCAUAG	chr3:115415601-115415802(-)$1	201	176	194	14.3161
GCUCGGGGACAGGUAAGC	chr4:144671526-144671727(-)$1	201	132	150	13.8165
UAUCUUAUUCCCCAGACC	chrX:155899959-155900160(+)$1	201	176	194	13.9814
UAUAGAUUGUAAACUUUA	chr2:83719203-83719404(+)$1	201	16	34	13.4170
UGACUUUCUCUGUGGUUG	chr14:30932205-30932406(-)$1	201	172	190	13.8983
GGCGCAAACAGCAGUACC	chr13:9876408-9876609(-)$1	201	64	82	12.5759
GACCUGAACAAGAAGGAG	chr14:70861508-70861709(+)$1	201	174	192	14.3956
AAAUGGCAGAUUACAUUA	chr3:88785128-88785329(+)$1	201	156	174	14.5346
GAAGGGAAUGAAAUGUUC	chr2:128907728-128907929(+)$1	201	147	165	12.6833
CAUUAAAAGGCAAUAGAG	chr10:20045110-20045311(+)$1	201	146	164	14.0187
ACUGCUGUUAUUUGUUGU	chr2:80370320-80370521(-)$1	201	30	48	13.5704
UUGACCCUAAAAUGUCUA	chr5:14713807-14714008(+)$1	201	77	95	14.3701
UUUUCAAUUUUCAGAGUC	chr13:90237876-90238077(+)$1	201	97	115	14.5713
GGAGGCCCCACCUCCCCU	chr11:76233180-76233381(-)$1	201	164	182	13.4023
AGGGACCUACACAUCUCA	chr9:71331220-71331421(-)$1	201	84	102	13.4338
UGAUGCAGUUUUACAUUU	chr14:33022729-33022930(+)$1	201	172	190	14.5346
CUGAGCUCACCACCUCCA	chr2:91510892-91511093(+)$1	201	161	179	14.3956
AUCCAAAAGCUCAUGGGA	chr12:8275223-8275424(+)$1	201	105	123	14.6442
CCCACCUGCCACCGUGAG	chr2:25099274-25099475(+)$1	201	111	129	14.3161
AUUGAAAACAACCUCAAC	chr10:89112690-89112891(-)$1	201	155	173	14.1396
GCUGGCAAAGCUCUCAGA	chr13:92123032-92123233(-)$1	201	122	140	14.2782
CAAAUCAUCUACCAUUCC	chr8:113262156-113262357(+)$1	201	97	115	14.3956
CUUUACAACAUAAUAUAG	chr13:68873487-68873688(-)$1	201	22	40	13.4466
UGUAUGACAACCAGUAUC	chr14:94286626-94286827(-)$1	201	116	134	14.3269
UGACCCAUUUGAAGAUCU	chr16:90939063-90939264(-)$1	201	35	53	12.6232
ACUUUGAGAUAGAAGAGU	chr7:118698002-118698203(-)$1	201	133	151	13.1466
ACUGCUGUUAUUUGUUGU	chr2:80370321-80370522(-)$1	201	31	49	13.5704
GCAGAGACAAGCAUCCGC	chr6:137699004-137699205(+)$1	201	175	193	12.5759
AGAGAAGAUUCUAUCUCC	chr18:50031212-50031413(+)$1	201	78	96	12.9508
AUGUACCCUUGCAUACUG	chr5:34787350-34787551(+)$1	201	126	144	14.1499
CAUGCUCUCAGACGCAGC	chr12:34051822-34052023(+)$1	201	179	197	14.5284
CAUGGUGCCAUUCCCACG	chr17:35972345-35972546(-)$1	201	52	70	13.9120
UUGUUGUUCUAGAAUUAG	chr3:126640667-126640868(-)$1	201	69	87	13.5251
CCUUCAUCUCACCGAACU	chr9:44627181-44627382(-)$1	201	94	112	14.3956
ACCCAAACUUUGAUGGGA	chr12:71048391-71048592(+)$1	201	154	172	12.9508
GCCCUGCCUAAGAAGGGC	chr11:68904057-68904258(+)$1	201	126	144	13.1466
AGGUGGUAUUCGACGCCG	chr8:96490752-96490953(+)$1	201	135	153	13.6170
AACCAUUACACUUUGGUC	chr17:44217689-44217890(+)$1	201	163	181	12.9508
AGGUGGUAUUCGACGCCG	chr8:96490727-96490928(+)$1	201	160	178	12.8958
UCAGAUCAAGCCUUCUGA	chr18:37980412-37980613(+)$1	201	100	118	13.2613
GAGCCAGAAUUCAGGCAG	chr12:54240669-54240870(+)$1	201	177	195	12.6373
AGGUGGUAUUCGACGCCG	chr8:96490728-96490929(+)$1	201	159	177	12.8958
AGGUAGUACAGAAUAUUU	chr2:37345224-37345425(+)$1	201	127	145	13.7331
CUCACUUUGUUUUGGAAG	chr13:51245888-51246089(+)$1	201	99	117	13.2158
UUCCGCAACUUUACGGUC	chr1:75182271-75182472(-)$1	201	146	164	14.3956
GUCUUGAAACAGGAAGAC	chr5:114491780-114491981(-)$1	201	63	81	14.3631
GGCUGUUUAACAUCACCA	chr7:149541800-149542001(-)$1	201	43	61	12.6257
AGGUAGAAUGUAAUGCCC	chr12:54243581-54243782(+)$1	201	128	146	13.8768
GAGCUCACAGACCAGCUC	chr5:102250442-102250643(+)$1	201	171	189	13.1466
CCCAGCCAGCACCCUGUC	chr7:134703487-134703688(+)$1	201	160	178	13.5434
UCAGAAAGAUAUAUUUGU	chr15:6723801-6724002(+)$1	201	148	166	14.4994
CUUCCCUUACUCCGGAAU	chr12:101611701-101611902(-)$1	201	170	188	14.2627
AGCGGCCACCUCCCUGCA	chr15:54429881-54430082(+)$1	201	143	161	14.2782
UAUAGAUUGUAAACUUUA	chr2:83719204-83719405(+)$1	201	15	33	13.4170
CAGCAGCAGAACAUGCAG	chr7:66531203-66531404(-)$1	201	33	51	14.3161
GAUUCACCAUAGAGACAU	chr4:25547582-25547783(-)$1	201	144	162	13.4339
GGUCUGCAUGGUAAGGCU	chrX:70925756-70925957(+)$1	201	5	23	13.2613
CUCUGGUAGACGACAAGC	chr2:160775241-160775442(-)$1	201	9	27	13.6606
AACCAAGACAAGCUGGAA	chr5:67070868-67071069(+)$1	201	162	180	14.6172

#DB
.((((........)))).	chr9:71331219-71331420(-)$1	1	83	101	13.4338
(((((........)))))	chr11:31001017-31001218(+)$1	1	76	94	13.1466
(((((........)))))	chr6:23638699-23638900(-)$1	1	12	30	13.1466
(((((........)))..	chr10:17444021-17444222(+)$1	1	81	99	14.0742
(((((........)))))	chr10:66682776-66682977(+)$1	1	151	169	13.1466
((.((........)).))	chr4:118808324-118808525(+)$1	1	84	102	13.5704
(((((........)))))	chr2:132130873-132131074(+)$1	1	125	143	13.1466
(((.(........).)))	chr4:144671527-144671728(-)$1	1	133	151	13.8165
(.(((........))).)	chr2:25099279-25099480(+)$1	1	106	124	14.3161
.((((........)))).	chr6:28780126-28780327(-)$1	1	172	190	12.9508
(((.(........).)))	chr15:59194706-59194907(-)$1	1	10	28	13.4345
(((((........)))).	chr9:101003604-101003805(+)$1	1	10	28	14.3973
((.((........)))))	chr9:32066852-32067053(+)$1	1	145	163	13.4023
(.(((........))).)	chr3:115415601-115415802(-)$1	1	176	194	14.3161
(((.(........).)))	chr4:144671526-144671727(-)$1	1	132	150	13.8165
..(((........)))))	chrX:155899959-155900160(+)$1	1	176	194	13.9814
((.((........)).))	chr2:83719203-83719404(+)$1	1	16	34	13.4170
.((((........)))))	chr14:30932205-30932406(-)$1	1	172	190	13.8983
((.((........)).))	chr13:9876408-9876609(-)$1	1	64	82	12.5759
..(((........)))..	chr14:70861508-70861709(+)$1	1	174	192	14.3956
.((((........)))).	chr3:88785128-88785329(+)$1	1	156	174	14.5346
(((.(........).)))	chr2:128907728-128907929(+)$1	1	147	165	12.6833
(.(((........))).)	chr10:20045110-20045311(+)$1	1	146	164	14.0187
((.((........)).))	chr2:80370320-80370521(-)$1	1	30	48	13.5704
..(((........)))))	chr5:14713807-14714008(+)$1	1	77	95	14.3701
..(((........)))..	chr13:90237876-90238077(+)$1	1	97	115	14.5713
((.((........)))))	chr11:76233180-76233381(-)$1	1	164	182	13.4023
.((((........)))).	chr9:71331220-71331421(-)$1	1	84	102	13.4338
.((((........)))).	chr14:33022729-33022930(+)$1	1	172	190	14.5346
..(((........)))..	chr2:91510892-91511093(+)$1	1	161	179	14.3956
.((((........)))).	chr12:8275223-8275424(+)$1	1	105	123	14.6442
(.(((........))).)	chr2:25099274-25099475(+)$1	1	111	129	14.3161
.((((........)))).	chr10:89112690-89112891(-)$1	1	155	173	14.1396
(((((........)))).	chr13:92123032-92123233(-)$1	1	122	140	14.2782
..(((........)))..	chr8:113262156-113262357(+)$1	1	97	115	14.3956
((.((........)).))	chr13:68873487-68873688(-)$1	1	22	40	13.4466
.((((........)))))	chr14:94286626-94286827(-)$1	1	116	134	14.3269
.((.(........).)).	chr16:90939063-90939264(-)$1	1	35	53	12.6232
(((((........)))))	chr7:118698002-118698203(-)$1	1	133	151	13.1466
((.((........)).))	chr2:80370321-80370522(-)$1	1	31	49	13.5704
((.((........)).))	chr6:137699004-137699205(+)$1	1	175	193	12.5759
.((((........)))).	chr18:50031212-50031413(+)$1	1	78	96	12.9508
(.(((........)))))	chr5:34787350-34787551(+)$1	1	126	144	14.1499
..(((........)))))	chr12:34051822-34052023(+)$1	1	179	197	14.5284
(.(((........))).)	chr17:35972345-35972546(-)$1	1	52	70	13.9120
(((.(........).)))	chr3:126640667-126640868(-)$1	1	69	87	13.5251
..(((........)))..	chr9:44627181-44627382(-)$1	1	94	112	14.3956
.((((........)))).	chr12:71048391-71048592(+)$1	1	154	172	12.9508
(((((........)))))	chr11:68904057-68904258(+)$1	1	126	144	13.1466
.((((........))))(	chr8:96490752-96490953(+)$1	1	135	153	13.6170
.((((........)))).	chr17:44217689-44217890(+)$1	1	163	181	12.9508
.((((........)))))	chr8:96490727-96490928(+)$1	1	160	178	12.8958
(((((........)))))	chr18:37980412-37980613(+)$1	1	100	118	13.2613
))(((........)))..	chr12:54240669-54240870(+)$1	1	177	195	12.6373
.((((........)))))	chr8:96490728-96490929(+)$1	1	159	177	12.8958
(((((........)))))	chr2:37345224-37345425(+)$1	1	127	145	13.7331
((..(........)..))	chr13:51245888-51246089(+)$1	1	99	117	13.2158
..(((........)))..	chr1:75182271-75182472(-)$1	1	146	164	14.3956
(((((........)))).	chr5:114491780-114491981(-)$1	1	63	81	14.3631
((.((........)))).	chr7:149541800-149542001(-)$1	1	43	61	12.6257
.((((........)))).	chr12:54243581-54243782(+)$1	1	128	146	13.8768
(((((........)))))	chr5:102250442-102250643(+)$1	1	171	189	13.1466
(..((........)))))	chr7:134703487-134703688(+)$1	1	160	178	13.5434
.((((........)))).	chr15:6723801-6724002(+)$1	1	148	166	14.4994
.((((........)))))	chr12:101611701-101611902(-)$1	1	170	188	14.2627
(((((........)))).	chr15:54429881-54430082(+)$1	1	143	161	14.2782
((.((........)).))	chr2:83719204-83719405(+)$1	1	15	33	13.4170
(.(((........))).)	chr7:66531203-66531404(-)$1	1	33	51	14.3161
(((((........)).))	chr4:25547582-25547783(-)$1	1	144	162	13.4339
(((((........)))))	chrX:70925756-70925957(+)$1	1	5	23	13.2613
((.((........)))))	chr2:160775241-160775442(-)$1	1	9	27	13.6606
..(((........)))..	chr5:67070868-67071069(+)$1	1	162	180	14.6172

#PSSM
e : 0.19	c : 0.18	! : 0.12	: : 0.09	b : 0.08	g : 0.05	[ : 0.05	" : 0.05	d : 0.04	( : 0.02	$ : 0.01	+ : 0.01	f : 0.01	# : 0.01	i : 0.01	= : 0.01	
d : 0.33	e : 0.16	c : 0.12	[ : 0.09	! : 0.09	b : 0.05	" : 0.02	g : 0.02	$ : 0.01	f : 0.01	# : 0.01	i : 0.01	= : 0.01	
d : 0.31	c : 0.29	[ : 0.16	e : 0.11	g : 0.02	! : 0.02	f : 0.01	b : 0.01	i : 0.01	= : 0.01	
d : 0.30	c : 0.26	b : 0.19	e : 0.09	[ : 0.08	g : 0.02	= : 0.01	! : 0.01	
d : 0.30	c : 0.26	b : 0.19	e : 0.09	a : 0.09	g : 0.02	= : 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 : 0.30	c : 0.26	b : 0.19	e : 0.09	a : 0.09	g : 0.02	= : 0.01	
d : 0.30	c : 0.26	b : 0.19	e : 0.09	] : 0.08	g : 0.02	= : 0.01	2 : 0.01	
d : 0.30	c : 0.30	e : 0.13	] : 0.12	g : 0.04	b : 0.02	f : 0.01	i : 0.01	= : 0.01	2 : 0.01	
d : 0.33	e : 0.18	c : 0.13	2 : 0.08	] : 0.08	b : 0.05	g : 0.04	3 : 0.02	f : 0.01	i : 0.01	: : 0.01	= : 0.01	
c : 0.20	e : 0.19	] : 0.11	2 : 0.09	: : 0.06	b : 0.05	d : 0.04	g : 0.04	7 : 0.02	= : 0.02	3 : 0.02	A : 0.02	f : 0.01	4 : 0.01	6 : 0.01	i : 0.01	5 : 0.01	

#score	985.8284803045525
#seq	72
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_UTR_m1_run1.txt

#BEAR
DDeeeeevvvvvvvvvvvvveeeee:	chr19:28085472-28085697(-)$1	225	3	29	20.2794
ccc!!cccuuuuuuuuuuuuccc]cc	chr1:34364623-34364833(+)$1	210	103	129	24.3866
ddd[ddddxxxxxxxxxxxxxxxddd	chr3:121693140-121693366(+)$1	226	151	177	18.3133
ccceeeeettttttttttteeeee::	chr5:124186278-124186496(-)$1	218	167	193	20.8105
fff[cccvvvvvvvvvvvvvccc]ff	chr12:27130301-27130522(-)$1	221	127	153	22.8685
#dddd[bbtttttttttttbb]dddd	chr11:53383977-53384201(+)$1	224	67	93	20.8203
dddd[cccuuuuuuuuuuuucccddd	chr11:86539769-86539992(-)$1	223	84	110	23.8154
ee[ayyyyyyyyyyyyyyyya]eeee	chr6:148153222-148153465(-)$1	243	169	195	20.7032
d[aeeeeeuuuuuuuuuuuueeeee]	chr1:136514223-136514447(+)$1	224	139	165	24.0700
2ddddcccvvvvvvvvvvvvvccc::	chr7:137307400-137307624(-)$1	224	183	209	21.3612
eeee[cccuuuuuuuuuuuuccceee	chr12:8755525-8755742(+)$1	217	20	46	24.1143
cc$$$$$bbuuuuuuuuuuuubb22c	chr17:86567965-86568189(+)$1	224	130	156	20.4859
cccceeeeettttttttttteeeee]	chr6:84793994-84794213(-)$1	219	170	196	22.5692
h!!ddddvvvvvvvvvvvvvdddd22	chr6:51411822-51412052(-)$1	230	75	101	23.2232
bb[ddddvvvvvvvvvvvvvddddbb	chr11:29363710-29363937(+)$1	227	148	174	22.2243
:gggggggtttttttttttggggggg	chr8:12636855-12637065(-)$1	210	6	32	20.4465
ff[ddddwwwwwwwwwwwwwwdddd]	chr1:188545064-188545278(-)$1	214	150	176	22.7837
fffffcccvvvvvvvvvvvvvccc]f	chr16:33961577-33961793(-)$1	216	72	98	23.1758
ee[eeeeeyyyyyyyyyyyyyyyyee	chr15:25742665-25742883(+)$1	218	128	154	21.7993
eeee!!bbuuuuuuuuuuuubbeeee	chr15:6388760-6388977(+)$1	217	82	108	22.8910
!!a[ddddtttttttttttdddd]a2	chr3:55806665-55806913(-)$1	248	29	55	22.6392
iii[cccxxxxxxxxxxxxxxxccc]	chrX:148468144-148468375(+)$1	231	7	33	18.8633
hhhhhhhhuuuuuuuuuuuuhhhhhh	chr11:106124326-106124536(+)$1	210	101	127	20.7776
cc!!dddduuuuuuuuuuuudddd22	chr8:98312591-98312813(-)$1	222	79	105	24.5745
ddffffffwwwwwwwwwwwwwwffff	chr4:69942301-69942512(-)$1	211	182	208	21.1341
fffffddddtttttttttttdddd]f	chr2:121728702-121728942(+)$1	240	196	222	22.3450
d!!eeeeeuuuuuuuuuuuueeeee]	chr13:101255921-101256151(-)$1	230	157	183	24.3285
ea!!bbyyyyyyyyyyyyyyyybb22	chr2:91550415-91550632(-)$1	217	9	35	20.8885
========uuuuuuuuuuuu======	chr3:85932166-85932379(+)$1	213	93	119	23.7603
ddddd[bbvvvvvvvvvvvvvbb]dd	chr5:138187183-138187400(+)$1	217	20	46	21.9148
ff"""cccvvvvvvvvvvvvvccc33	chr14:55261357-55261572(-)$1	215	145	171	23.8929
####dddduuuuuuuuuuuudddd22	chr14:56181713-56181937(+)$1	224	121	147	24.1603
eeeeeddddtttttttttttdddd]e	chr10:79711797-79712018(+)$1	221	189	215	22.8255
eeeeeddddtttttttttttdddd]e	chr16:18919035-18919260(+)$1	225	70	96	22.8255
dddd[ddddtttttttttttdddd]d	chr1:157888016-157888239(+)$1	223	53	79	22.6560
ee!!dddduuuuuuuuuuuudddd]e	chr6:86363738-86363948(+)$1	210	3	29	24.5934
d####cccvvvvvvvvvvvvvccc66	chr19:5422795-5423021(-)$1	226	33	59	22.8665
ffffff[awwwwwwwwwwwwwwa]ff	chr4:147418506-147418714(+)$1	208	82	108	21.6157
ccc"""ccctttttttttttccc333	chr13:96372892-96373117(-)$1	225	186	212	23.1142
cc[bbcccuuuuuuuuuuuuccc]bb	chr10:80170533-80170753(-)$1	220	81	107	23.3002
ccc:dddduuuuuuuuuuuudddd::	chr11:32139816-32140035(-)$1	219	127	153	21.6836
iiiiiiiiwwwwwwwwwwwwwwiiii	chr10:42941434-42941654(+)$1	220	20	46	22.2815
ccc:cccvvvvvvvvvvvvvccc:::	chrX:148463718-148463943(+)$1	225	157	183	19.8344
dddd[ddddtttttttttttdddd]d	chr5:100819704-100819917(-)$1	213	8	34	22.6560
i!!eeeeeuuuuuuuuuuuueeeeei	chrX:110156937-110157178(-)$1	241	125	151	24.1378
###eeeeeyyyyyyyyyyyyyyyyee	chr4:114641798-114642013(-)$1	215	130	156	21.6935
f####ddddtttttttttttdddd]f	chrX:45896201-45896424(-)$1	223	49	75	22.9210
dd[eeeeewwwwwwwwwwwwwweeee	chr17:71813113-71813336(-)$1	223	7	33	22.7876
!!ffffffyyyyyyyyyyyyyyyyff	chr6:6508329-6508547(-)$1	218	164	190	20.7150
iiiiicccuuuuuuuuuuuuccc]ii	chr17:33801452-33801671(-)$1	219	113	139	24.1546
gggggggyyyyyyyyyyyyyyyyggg	chr4:49668741-49668959(+)$1	218	75	101	21.6777
(((eeeeeuuuuuuuuuuuueeeeef	chr17:32390017-32390238(-)$1	221	189	215	21.9113
cc:eeeeevvvvvvvvvvvvveeeee	chr8:131246283-131246492(+)$1	209	137	163	22.4864
cc[a[cccuuuuuuuuuuuuccc]a]	chr5:129491165-129491380(-)$1	215	1	27	24.7305
!eeeeebbwwwwwwwwwwwwwwbb]e	chr10:4522619-4522834(+)$1	215	111	137	21.7111
2bbeeeeettttttttttteeeee::	chr13:55755321-55755540(+)$1	219	159	185	19.7601
ddd[ddddvvvvvvvvvvvvvdddd]	chr14:122532416-122532641(+)$1	225	145	171	23.6158
fff[cccwwwwwwwwwwwwwwccc]f	chr11:79061801-79062029(-)$1	228	30	56	22.6955

#otherMatches

#Seq PSSM
GCGAGUGucucccucucccucgcucc	chr19:28085472-28085697(-)$1	225	3	29	20.2794
GGUAAGUCCACAUUCUCUCUGACAAC	chr1:34364623-34364833(+)$1	210	103	129	24.3866
UUAUUGAACAUUCUGUGAUUUCUUUC	chr3:121693140-121693366(+)$1	226	151	177	18.3133
CCUGauuuuuuuuuuuuuuaaaucau	chr5:124186278-124186496(-)$1	218	167	193	20.8105
CCAAGUCUAUUCUGGAUGUUGGCGUG	chr12:27130301-27130522(-)$1	221	127	153	22.8685
AGUCGGAGAAGCCGGAAAGCUGCGAU	chr11:53383977-53384201(+)$1	224	67	93	20.8203
ccaauguccuacaaaauccugacuug	chr11:86539769-86539992(-)$1	223	84	110	23.8154
UAACUAACUUUUUUCUUCUUGAUACC	chr6:148153222-148153465(-)$1	243	169	195	20.7032
AUGUCAGCUUUGAAUUUGAUGUUGAG	chr1:136514223-136514447(+)$1	224	139	165	24.0700
AGCACCAGGAACCUACUUACACUGAG	chr7:137307400-137307624(-)$1	224	183	209	21.3612
AUAUGUGCCUUUAAUUUUUAGCAAUG	chr12:8755525-8755742(+)$1	217	20	46	24.1143
CCACCAAGCAAAAGACCAACAGCCCG	chr17:86567965-86568189(+)$1	224	130	156	20.4859
CGGUCCAUACCACCAAGCUUUAUGGU	chr6:84793994-84794213(-)$1	219	170	196	22.5692
GCCAAGUGAUCAUUAAUAAAGCUUUU	chr6:51411822-51412052(-)$1	230	75	101	23.2232
GCCUAGAGGAACUGAAAAUAUCUAGC	chr11:29363710-29363937(+)$1	227	148	174	22.2243
UACAACGCCUCUCAAUUAUGUGUUGU	chr8:12636855-12637065(-)$1	210	6	32	20.4465
GAAAUUUAACCUGUUUUUCUAAAAUA	chr1:188545064-188545278(-)$1	214	150	176	22.7837
GAGUUCUUAAUAUUUGAAGACAGGAA	chr16:33961577-33961793(-)$1	216	72	98	23.1758
AAAGAAACAUUUUUUUUGGACUCGGU	chr15:25742665-25742883(+)$1	218	128	154	21.7993
ACAGCCAGAAACAUGUUGACCUCUGU	chr15:6388760-6388977(+)$1	217	82	108	22.8910
CUCCGCCUUCCCUUUGUUUAGGCUGU	chr3:55806665-55806913(-)$1	248	29	55	22.6392
AUACAGAUUUUUAUCUUGCCCUUCUU	chrX:148468144-148468375(+)$1	231	7	33	18.8633
UGAUAAACACUACAACUCCAGUUUGU	chr11:106124326-106124536(+)$1	210	101	127	20.7776
AGCCUAAUUACAAAGAAAGCAUUAAC	chr8:98312591-98312813(-)$1	222	79	105	24.5745
GAAGACACGGUGGAGCUGAAGAGUGU	chr4:69942301-69942512(-)$1	211	182	208	21.1341
ACUAAGUAUUUAAAUAAUGUAUGCUU	chr2:121728702-121728942(+)$1	240	196	222	22.3450
GACUUUGCUUAUCUAACUCUGUAAAA	chr13:101255921-101256151(-)$1	230	157	183	24.3285
GAAGGGGAAGCUCUGAGAAAAACCAG	chr2:91550415-91550632(-)$1	217	9	35	20.8885
GUGAAGAUUCUGAGCAACCUAUCUUU	chr3:85932166-85932379(+)$1	213	93	119	23.7603
GGGUUGUCAACAGCCCAGAAAGAGAG	chr5:138187183-138187400(+)$1	217	20	46	21.9148
ACACGUCCCCUCAUAUCAAAUGGAGC	chr14:55261357-55261572(-)$1	215	145	171	23.8929
GGAGAUCGAUAUAACCCACCCGGUAA	chr14:56181713-56181937(+)$1	224	121	147	24.1603
ACUUUUUCAUUCCCUAAUACUGAAUA	chr10:79711797-79712018(+)$1	221	189	215	22.8255
AUGGGAGCUCUACAAAGCCCAGCUGC	chr16:18919035-18919260(+)$1	225	70	96	22.8255
AGGAACGGCCUAGUGGUACCGCUGAU	chr1:157888016-157888239(+)$1	223	53	79	22.6560
augcuuagcCAUAAAUAAAUCUAAAA	chr6:86363738-86363948(+)$1	210	3	29	24.5934
CCUUUGCCACCAGCACCCCCCGGCCC	chr19:5422795-5423021(-)$1	226	33	59	22.8665
GCUUCAGCUAUGCCACAGACCUGGUG	chr4:147418506-147418714(+)$1	208	82	108	21.6157
AGCACCAGGUACAUCACACCCCUUCG	chr13:96372892-96373117(-)$1	225	186	212	23.1142
CCUGCUGGAGGAAAUGAAGACCACGU	chr10:80170533-80170753(-)$1	220	81	107	23.3002
GAGUGAGCUUCCCAUUGACUGCUCCC	chr11:32139816-32140035(-)$1	219	127	153	21.6836
UUGGAAUCGCCGUCUCCUGUUAGAUU	chr10:42941434-42941654(+)$1	220	20	46	22.2815
AGUAGCCGCCAGCAGCGAAAGGCAGA	chrX:148463718-148463943(+)$1	225	157	183	19.8344
UAGAGUUACUAGUUUAAAAUGUAGGU	chr5:100819704-100819917(-)$1	213	8	34	22.6560
GUGGAUGUGCAUCAGACAUAACAUUC	chrX:110156937-110157178(-)$1	241	125	151	24.1378
AAAGUACAUUAAAGAAGGAAAGAUUG	chr4:114641798-114642013(-)$1	215	130	156	21.6935
UUUCAUGAAGGCAGUUACAAUUCACA	chrX:45896201-45896424(-)$1	223	49	75	22.9210
AUUCAGAAUAAAUUCAUUGUAUUUCU	chr17:71813113-71813336(-)$1	223	7	33	22.7876
ACGGGAUACUUUAAAGAACAUGUUUA	chr6:6508329-6508547(-)$1	218	164	190	20.7150
UGUUUGAUAGACCGAUGCACGUCAAG	chr17:33801452-33801671(-)$1	219	113	139	24.1546
GCCAAUGAUUUCCAUCGCAUCUACAU	chr4:49668741-49668959(+)$1	218	75	101	21.6777
CAUUGGGUCUAAGAAAAUCAGCUCAC	chr17:32390017-32390238(-)$1	221	189	215	21.9113
GUGUGUGUAGGAAGAGAGAUAAUACA	chr8:131246283-131246492(+)$1	209	137	163	22.4864
CAGAGUUCCUAAGAAACCAUGAAGUG	chr5:129491165-129491380(-)$1	215	1	27	24.7305
UCCUAGAGUGUUUGUAUAUUUUCUGC	chr10:4522619-4522834(+)$1	215	111	137	21.7111
UGCCCAUGUUUAGACACAUCAUGGAU	chr13:55755321-55755540(+)$1	219	159	185	19.7601
AAGGCUGAAGACAAACAAAAGUUAGA	chr14:122532416-122532641(+)$1	225	145	171	23.6158
UCGUUGCGUUAAUAUAGAAUGGCAUC	chr11:79061801-79062029(-)$1	228	30	56	22.6955

#DB
(((((((.............))))).	chr19:28085472-28085697(-)$1	1	3	29	20.2794
(((..(((............))).))	chr1:34364623-34364833(+)$1	1	103	129	24.3866
(((.((((...............)))	chr3:121693140-121693366(+)$1	1	151	177	18.3133
)))(((((...........)))))..	chr5:124186278-124186496(-)$1	1	167	193	20.8105
(((.(((.............))).))	chr12:27130301-27130522(-)$1	1	127	153	22.8685
.((((.((...........)).))))	chr11:53383977-53384201(+)$1	1	67	93	20.8203
((((.(((............))))))	chr11:86539769-86539992(-)$1	1	84	110	23.8154
((.(................).))))	chr6:148153222-148153465(-)$1	1	169	195	20.7032
(.((((((............))))).	chr1:136514223-136514447(+)$1	1	139	165	24.0700
.))))(((.............)))..	chr7:137307400-137307624(-)$1	1	183	209	21.3612
((((.(((............))))))	chr12:8755525-8755742(+)$1	1	20	46	24.1143
((.....((............))..)	chr17:86567965-86568189(+)$1	1	130	156	20.4859
)((((((((...........))))).	chr6:84793994-84794213(-)$1	1	170	196	22.5692
(..((((.............))))..	chr6:51411822-51412052(-)$1	1	75	101	23.2232
((.((((.............))))))	chr11:29363710-29363937(+)$1	1	148	174	22.2243
.(((((((...........)))))))	chr8:12636855-12637065(-)$1	1	6	32	20.4465
((.((((..............)))).	chr1:188545064-188545278(-)$1	1	150	176	22.7837
((((((((.............))).)	chr16:33961577-33961793(-)$1	1	72	98	23.1758
((.(((((................))	chr15:25742665-25742883(+)$1	1	128	154	21.7993
((((..((............))))))	chr15:6388760-6388977(+)$1	1	82	108	22.8910
..(.((((...........)))).).	chr3:55806665-55806913(-)$1	1	29	55	22.6392
(((.(((...............))).	chrX:148468144-148468375(+)$1	1	7	33	18.8633
((((((((............))))))	chr11:106124326-106124536(+)$1	1	101	127	20.7776
((..((((............))))..	chr8:98312591-98312813(-)$1	1	79	105	24.5745
))((((((..............))))	chr4:69942301-69942512(-)$1	1	182	208	21.1341
(((((((((...........)))).)	chr2:121728702-121728942(+)$1	1	196	222	22.3450
(..(((((............))))).	chr13:101255921-101256151(-)$1	1	157	183	24.3285
((..((................))..	chr2:91550415-91550632(-)$1	1	9	35	20.8885
((((((((............))))))	chr3:85932166-85932379(+)$1	1	93	119	23.7603
(((((.((.............)).))	chr5:138187183-138187400(+)$1	1	20	46	21.9148
((...(((.............)))..	chr14:55261357-55261572(-)$1	1	145	171	23.8929
....((((............))))..	chr14:56181713-56181937(+)$1	1	121	147	24.1603
(((((((((...........)))).)	chr10:79711797-79712018(+)$1	1	189	215	22.8255
(((((((((...........)))).)	chr16:18919035-18919260(+)$1	1	70	96	22.8255
((((.((((...........)))).)	chr1:157888016-157888239(+)$1	1	53	79	22.6560
((..((((............)))).)	chr6:86363738-86363948(+)$1	1	3	29	24.5934
(....(((.............)))..	chr19:5422795-5423021(-)$1	1	33	59	22.8665
((((((.(..............).))	chr4:147418506-147418714(+)$1	1	82	108	21.6157
(((...(((...........)))...	chr13:96372892-96373117(-)$1	1	186	212	23.1142
((.(((((............))).))	chr10:80170533-80170753(-)$1	1	81	107	23.3002
))).((((............))))..	chr11:32139816-32140035(-)$1	1	127	153	21.6836
((((((((..............))))	chr10:42941434-42941654(+)$1	1	20	46	22.2815
))).(((.............)))...	chrX:148463718-148463943(+)$1	1	157	183	19.8344
((((.((((...........)))).)	chr5:100819704-100819917(-)$1	1	8	34	22.6560
(..(((((............))))))	chrX:110156937-110157178(-)$1	1	125	151	24.1378
...(((((................))	chr4:114641798-114642013(-)$1	1	130	156	21.6935
(....((((...........)))).)	chrX:45896201-45896424(-)$1	1	49	75	22.9210
((.(((((..............))))	chr17:71813113-71813336(-)$1	1	7	33	22.7876
..((((((................))	chr6:6508329-6508547(-)$1	1	164	190	20.7150
((((((((............))).))	chr17:33801452-33801671(-)$1	1	113	139	24.1546
(((((((................)))	chr4:49668741-49668959(+)$1	1	75	101	21.6777
...(((((............))))))	chr17:32390017-32390238(-)$1	1	189	215	21.9113
)).(((((.............)))))	chr8:131246283-131246492(+)$1	1	137	163	22.4864
((.(.(((............))).).	chr5:129491165-129491380(-)$1	1	1	27	24.7305
.(((((((..............)).)	chr10:4522619-4522834(+)$1	1	111	137	21.7111
.))(((((...........)))))..	chr13:55755321-55755540(+)$1	1	159	185	19.7601
(((.((((.............)))).	chr14:122532416-122532641(+)$1	1	145	171	23.6158
(((.(((..............))).)	chr11:79061801-79062029(-)$1	1	30	56	22.6955

#PSSM
c : 0.18	d : 0.18	f : 0.13	e : 0.13	i : 0.06	# : 0.05	! : 0.05	2 : 0.03	h : 0.03	D : 0.01	b : 0.01	: : 0.01	= : 0.01	g : 0.01	( : 0.01	
c : 0.18	d : 0.17	e : 0.13	f : 0.12	! : 0.08	# : 0.06	i : 0.05	b : 0.03	g : 0.03	D : 0.01	[ : 0.01	h : 0.01	a : 0.01	= : 0.01	( : 0.01	
d : 0.13	f : 0.12	[ : 0.12	e : 0.10	c : 0.10	! : 0.10	# : 0.06	i : 0.05	a : 0.03	g : 0.03	$ : 0.01	h : 0.01	= : 0.01	" : 0.01	( : 0.01	: : 0.01	b : 0.01	
e : 0.27	d : 0.15	[ : 0.10	f : 0.08	! : 0.06	# : 0.05	a : 0.03	g : 0.03	" : 0.03	: : 0.03	i : 0.03	$ : 0.01	c : 0.01	h : 0.01	= : 0.01	b : 0.01	
e : 0.25	d : 0.22	[ : 0.08	f : 0.08	c : 0.06	! : 0.03	g : 0.03	b : 0.03	" : 0.03	# : 0.03	i : 0.03	y : 0.01	$ : 0.01	h : 0.01	= : 0.01	
d : 0.27	c : 0.24	e : 0.22	f : 0.05	[ : 0.03	g : 0.03	y : 0.01	$ : 0.01	! : 0.01	h : 0.01	b : 0.01	= : 0.01	" : 0.01	i : 0.01	
d : 0.27	c : 0.25	e : 0.20	b : 0.06	y : 0.03	g : 0.03	f : 0.03	$ : 0.01	h : 0.01	= : 0.01	[ : 0.01	i : 0.01	
d : 0.22	c : 0.18	e : 0.18	v : 0.08	b : 0.08	y : 0.05	w : 0.03	f : 0.03	g : 0.01	x : 0.01	h : 0.01	= : 0.01	a : 0.01	i : 0.01	
u : 0.29	v : 0.20	w : 0.12	y : 0.10	d : 0.10	t : 0.08	x : 0.03	b : 0.01	e : 0.01	c : 0.01	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	t : 0.22	v : 0.20	w : 0.12	y : 0.10	x : 0.03	
u : 0.31	v : 0.20	t : 0.13	w : 0.12	y : 0.10	x : 0.03	e : 0.03	b : 0.01	g : 0.01	d : 0.01	
d : 0.22	c : 0.15	e : 0.13	v : 0.12	w : 0.12	y : 0.08	x : 0.03	b : 0.03	a : 0.01	u : 0.01	g : 0.01	h : 0.01	= : 0.01	
d : 0.25	c : 0.24	e : 0.15	y : 0.08	w : 0.08	b : 0.05	x : 0.03	] : 0.03	g : 0.01	h : 0.01	= : 0.01	
d : 0.27	c : 0.25	e : 0.20	b : 0.06	y : 0.06	x : 0.01	g : 0.01	h : 0.01	f : 0.01	= : 0.01	a : 0.01	i : 0.01	
d : 0.29	e : 0.22	] : 0.13	c : 0.10	y : 0.05	g : 0.03	b : 0.03	2 : 0.01	h : 0.01	f : 0.01	= : 0.01	3 : 0.01	i : 0.01	: : 0.01	
e : 0.22	] : 0.17	d : 0.10	: : 0.08	2 : 0.08	f : 0.06	c : 0.03	b : 0.03	g : 0.03	a : 0.03	3 : 0.03	i : 0.03	h : 0.01	= : 0.01	6 : 0.01	
e : 0.18	f : 0.15	] : 0.12	: : 0.10	d : 0.10	2 : 0.08	i : 0.05	c : 0.03	b : 0.03	g : 0.03	3 : 0.03	h : 0.01	= : 0.01	6 : 0.01	

#score	1295.6738190716735
#seq	58
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_CDS_m2_run2.txt

#BEAR
a$$$$$cccooooooccc]a]ad	chr5:110582085-110582343(+)$1	258	95	118	13.0902
fff"""cccooooooccc22fff	chr12:56848002-56848247(-)$1	245	24	47	12.9115
!ddddbbbboooooobb]bb]dd	chr16:17573581-17573823(-)$1	242	130	153	11.0752
d!!ccccccooooooccc]ccc]	chr4:149127834-149128099(-)$1	265	171	194	13.8192
[bb!!ddddoooooodddd]bb]	chr8:113337471-113337724(-)$1	253	168	191	11.3014
eeeee[cccooooooccc]eeee	chr6:38449086-38449323(+)$1	237	3	26	12.8984
iiiiiii[aooooooa]iiiiii	chr3:40574383-40574667(+)$1	284	136	159	13.6027
ffffffcccoooooocccfffff	chr4:43428926-43429180(+)$1	254	217	240	12.1915
fff[ccc[aooooooa]ccc]ff	chr1:140429273-140429509(-)$1	236	192	215	12.7148
c!!ffffffooooooffffff22	chr14:21822300-21822542(+)$1	242	88	111	12.1033
ii!!eeeeeooooooeeeee22i	chr2:65509568-65509817(+)$1	249	106	129	12.6460
==[bb[cccooooooccc]bb]=	chr8:70244683-70244938(-)$1	255	67	90	13.6168
$$$$eeeeeooooooeeeeeddd	chr4:94353416-94353689(+)$1	273	200	223	11.1825
[ccc!!cccooooooccc4444c	chr15:31401324-31401584(-)$1	260	192	215	14.2149
gggggg[bboooooobbgggggg	chr14:28313473-28313749(-)$1	276	28	51	13.2440
:bbccc[bboooooobb]ccc]b	chr10:70022383-70022621(-)$1	238	209	232	11.6052
####eeeeeooooooeeeee22b	chr7:108656489-108656744(+)$1	255	182	205	12.2162
"""ffffffooooooffffff]d	chr10:5313453-5313712(+)$1	259	95	118	12.2603
bbgggggggooooooggggggg2	chr11:49493421-49493699(-)$1	278	89	112	12.6191
gggggg[bboooooobbgggggg	chr6:39573538-39573782(-)$1	244	18	41	13.2440
dd"""ddddoooooodddd333d	chr2:138109159-138109401(+)$1	242	32	55	12.5599
bdddd[cccoooooocccdddd:	chr8:126908010-126908271(-)$1	261	36	59	11.5544
======[bboooooobb333===	chr9:86489672-86489907(-)$1	235	182	205	14.2689
b[gggggggooooooggggggg]	chr10:80005028-80005284(-)$1	256	42	65	13.0924
ggggg!!bboooooobb4444gg	chr6:71379014-71379250(-)$1	236	131	154	13.7249
cccdddd[aooooooadddd333	chr13:104553861-104554110(-)$1	249	71	94	12.5743
iiiiiiiiiooooooiiiiiiii	chr11:79845243-79845491(+)$1	248	140	163	13.5834
bb"""ddddoooooodddd333b	chr1:87981688-87981939(+)$1	251	9	32	12.5213
ggggg[cccaooooooa]ccc]g	chr16:95053859-95054108(-)$1	249	191	214	12.6725
bb[bb[cccooooooccc]bb]b	chr10:104807418-104807680(-)$1	262	57	80	12.8473
ggg[ccc[aooooooa]cccggg	chr11:29607640-29607912(+)$1	272	21	44	13.4061
eeeee[cccooooooccc]eeee	chr9:15723512-15723773(-)$1	261	10	33	12.8984
gggggggggooooooggggggg:	chr19:6294413-6294672(+)$1	259	102	125	12.2303
hhh[cccbboooooobb]ccc22	chr11:106646651-106646913(-)$1	262	113	136	12.6038
eeeeeeeeeooooooeeeee]ee	chr1:172896591-172896838(-)$1	247	35	58	11.3889
gg[ccc[bboooooobb]ccc]g	chr16:85079983-85080234(-)$1	251	6	29	13.4747
dddd"""bboooooobb333ddd	chr12:66058530-66058776(-)$1	246	150	173	12.5098
"""dddd[aooooooa]dddd]g	chr11:78385779-78386030(-)$1	251	130	153	12.6000
dddd!!cccooooooccc]dddd	chr10:7644395-7644669(-)$1	274	140	163	12.8687
#ccc"""bboooooobb4444cc	chr15:95455279-95455545(-)$1	266	95	118	13.3213
gggg!!cccooooooccc4444g	chr5:150433858-150434121(-)$1	263	163	186	14.4276
=========oooooo========	chr11:30732467-30732707(+)$1	240	211	234	14.2599
eee"""cccooooooccc4444e	chr2:37454633-37454877(-)$1	244	89	112	13.8117
bb!!eeeeeooooooeeeee22b	chr2:28324888-28325166(+)$1	278	204	227	11.9807
=========oooooo========	chr8:87805662-87805917(-)$1	255	135	158	14.2599
cccffffffooooooffffff]c	chr9:82769689-82769943(-)$1	254	226	249	11.8953
c[ddddcccooooooccc]dddd	chr18:34472365-34472785(+)$1	420	58	81	12.6856
!!ccc!!bboooooobb22ccc]	chr16:4939475-4939733(+)$1	258	81	104	13.1081
iiiiiiiiiooooooiiiiiiii	chr1:4883429-4883674(+)$1	245	52	75	13.5834
c!!bb[cccooooooccc]bb22	chr9:122184526-122184785(-)$1	259	151	174	13.2447
b"""eeeeeooooooeeeee]bb	chr9:40124380-40124650(-)$1	270	112	135	11.9288

#otherMatches

#Seq PSSM
AAUAAAAUCACUCAAGAUAUGCU	chr5:110582085-110582343(+)$1	258	95	118	13.0902
UUCUUCUUGAACCUGCAAAUGAA	chr12:56848002-56848247(-)$1	245	24	47	12.9115
UGAGCUACCUGACCUGGCUACGC	chr16:17573581-17573823(-)$1	242	130	153	11.0752
UUCUCUCAGCUGGCUCUGCAGGU	chr4:149127834-149128099(-)$1	265	171	194	13.8192
GGCUGGGGCAGACAAGUUUGGCA	chr8:113337471-113337724(-)$1	253	168	191	11.3014
GCUGGGACUUACACUGGUGUUAG	chr6:38449086-38449323(+)$1	237	3	26	12.8984
AUUUUAUACUAAUUUGCAUGAAG	chr3:40574383-40574667(+)$1	284	136	159	13.6027
GCCCAGUACGAUUAAGUGAGGGC	chr4:43428926-43429180(+)$1	254	217	240	12.1915
AAAGGUAAGUUUGUUCAUGCAUU	chr1:140429273-140429509(-)$1	236	192	215	12.7148
AAGAUUGCAGAAUUAUGUGAUGA	chr14:21822300-21822542(+)$1	242	88	111	12.1033
AUAAAGGGAAAGCAAUCUCUCGG	chr2:65509568-65509817(+)$1	249	106	129	12.6460
UCUUUGUGUCCAUGUGCAGGAUG	chr8:70244683-70244938(-)$1	255	67	90	13.6168
CACAUGCUCAGGUAAGAGCACUU	chr4:94353416-94353689(+)$1	273	200	223	11.1825
GUUAAAGAGUGGUCCCUCAUGGU	chr15:31401324-31401584(-)$1	260	192	215	14.2149
GAAAAUAGUAGAUUGACAUUUUC	chr14:28313473-28313749(-)$1	276	28	51	13.2440
AGGGAAGCCACCCCAGGAUUCAC	chr10:70022383-70022621(-)$1	238	209	232	11.6052
AAUGAUGAGGUCCCACUCAUGCG	chr7:108656489-108656744(+)$1	255	182	205	12.2162
CAAACUUCUCCUGAAGGAGGUCA	chr10:5313453-5313712(+)$1	259	95	118	12.2603
GGCUAAUGCUCAUAUGCAUUGGG	chr11:49493421-49493699(-)$1	278	89	112	12.6191
UUUCAGUCUUUAUUCAGCUGAAA	chr6:39573538-39573782(-)$1	244	18	41	13.2440
AGAUACAUCUAUUGUGAUGAAAU	chr2:138109159-138109401(+)$1	242	32	55	12.5599
CGCUUCGAGAAAAUCCUCAAGUA	chr8:126908010-126908271(-)$1	261	36	59	11.5544
GCUUUGAGUAAUCCGACCAGCAA	chr9:86489672-86489907(-)$1	235	182	205	14.2689
CAUGUCUGCCCUGUAGUGGACGG	chr10:80005028-80005284(-)$1	256	42	65	13.0924
GUUCUGACACAGUGCUGCAAAAG	chr6:71379014-71379250(-)$1	236	131	154	13.7249
CCAACCAUGACAAGCCUGGUACC	chr13:104553861-104554110(-)$1	249	71	94	12.5743
CUGUUUGUAGAAAAUUAUGGACA	chr11:79845243-79845491(+)$1	248	140	163	13.5834
GCAAUGUAUGUAUAAAUACUUGG	chr1:87981688-87981939(+)$1	251	9	32	12.5213
UGGAAGCCACAGGUAAGAUGGGU	chr16:95053859-95054108(-)$1	249	191	214	12.6725
CCCUGAGCUUUGAUUGGUCCAUG	chr10:104807418-104807680(-)$1	262	57	80	12.8473
UGGUGCUUCUGUAGCGCAGCCCA	chr11:29607640-29607912(+)$1	272	21	44	13.4061
AAGGCUGAAUGUUGUUUCUGCUU	chr9:15723512-15723773(-)$1	261	10	33	12.8984
AAGCUCUUCGAGGCAGAGGAGCA	chr19:6294413-6294672(+)$1	259	102	125	12.2303
GGCUGCUGAAUAUUGUCGAGCUU	chr11:106646651-106646913(-)$1	262	113	136	12.6038
GGUGUUUCUGGAAGGGGAAACCA	chr1:172896591-172896838(-)$1	247	35	58	11.3889
CUGCGGCAUCGACAAGUUCCGAG	chr16:85079983-85080234(-)$1	251	6	29	13.4747
ACUCUGUGACAUCAUUCUUCGAG	chr12:66058530-66058776(-)$1	246	150	173	12.5098
CACCCCUACCUAGAUGAAGGGCG	chr11:78385779-78386030(-)$1	251	130	153	12.6000
AAUUCCCAGAAGUGCCUGAAGUU	chr10:7644395-7644669(-)$1	274	140	163	12.8687
AGGUGAAGAUUUGGUUCCAGAAC	chr15:95455279-95455545(-)$1	266	95	118	13.3213
AGUAGGGCCCAGCCAGGCAGUGU	chr5:150433858-150434121(-)$1	263	163	186	14.4276
AAUAGUUCUGAUUUGAGGAUUAU	chr11:30732467-30732707(+)$1	240	211	234	14.2599
CUGUCCCUUUUAGGUAAGAACUC	chr2:37454633-37454877(-)$1	244	89	112	13.8117
GUUCUCUCACUUAAUUGAGACUA	chr2:28324888-28325166(+)$1	278	204	227	11.9807
GGAUGCUCUGGCUCAGGAGUAUC	chr8:87805662-87805917(-)$1	255	135	158	14.2599
GUGUAGCUGUAGAUCCAGUUGUC	chr9:82769689-82769943(-)$1	254	226	249	11.8953
UACCACCGAGUUCCAUUGUGUGG	chr18:34472365-34472785(+)$1	420	58	81	12.6856
UCUGUACGCACGGCAGCUGACAU	chr16:4939475-4939733(+)$1	258	81	104	13.1081
GCCAUUUUUGCCAUAGGAAAUGG	chr1:4883429-4883674(+)$1	245	52	75	13.5834
AUGGAGGUUAGUGGAAACGUUAC	chr9:122184526-122184785(-)$1	259	151	174	13.2447
UCCAAAGAGACAUUCUUCUUCAG	chr9:40124380-40124650(-)$1	270	112	135	11.9288

#DB
(.....(((......))).).))	chr5:110582085-110582343(+)$1	1	95	118	13.0902
(((...(((......)))..)))	chr12:56848002-56848247(-)$1	1	24	47	12.9115
.((((((((......)).)).))	chr16:17573581-17573823(-)$1	1	130	153	11.0752
(..((((((......))).))).	chr4:149127834-149128099(-)$1	1	171	194	13.8192
.((..((((......)))).)).	chr8:113337471-113337724(-)$1	1	168	191	11.3014
(((((.(((......))).))))	chr6:38449086-38449323(+)$1	1	3	26	12.8984
(((((((.(......).))))))	chr3:40574383-40574667(+)$1	1	136	159	13.6027
))))))(((......)))(((((	chr4:43428926-43429180(+)$1	1	217	240	12.1915
(((.(((.(......).))).))	chr1:140429273-140429509(-)$1	1	192	215	12.7148
(..((((((......))))))..	chr14:21822300-21822542(+)$1	1	88	111	12.1033
((..(((((......)))))..)	chr2:65509568-65509817(+)$1	1	106	129	12.6460
((.((.(((......))).)).)	chr8:70244683-70244938(-)$1	1	67	90	13.6168
....(((((......))))))))	chr4:94353416-94353689(+)$1	1	200	223	11.1825
.(((..(((......)))....)	chr15:31401324-31401584(-)$1	1	192	215	14.2149
((((((.((......))))))))	chr14:28313473-28313749(-)$1	1	28	51	13.2440
.(((((.((......)).))).)	chr10:70022383-70022621(-)$1	1	209	232	11.6052
....(((((......)))))..)	chr7:108656489-108656744(+)$1	1	182	205	12.2162
...((((((......)))))).)	chr10:5313453-5313712(+)$1	1	95	118	12.2603
(((((((((......))))))).	chr11:49493421-49493699(-)$1	1	89	112	12.6191
((((((.((......))))))))	chr6:39573538-39573782(-)$1	1	18	41	13.2440
((...((((......))))...)	chr2:138109159-138109401(+)$1	1	32	55	12.5599
)((((.(((......))))))).	chr8:126908010-126908271(-)$1	1	36	59	11.5544
((((((.((......))...)))	chr9:86489672-86489907(-)$1	1	182	205	14.2689
(.(((((((......))))))).	chr10:80005028-80005284(-)$1	1	42	65	13.0924
(((((..((......))....))	chr6:71379014-71379250(-)$1	1	131	154	13.7249
(((((((.(......)))))...	chr13:104553861-104554110(-)$1	1	71	94	12.5743
(((((((((......))))))))	chr11:79845243-79845491(+)$1	1	140	163	13.5834
((...((((......))))...)	chr1:87981688-87981939(+)$1	1	9	32	12.5213
(((((.((((......).))).)	chr16:95053859-95054108(-)$1	1	191	214	12.6725
((.((.(((......))).)).)	chr10:104807418-104807680(-)$1	1	57	80	12.8473
(((.(((.(......).))))))	chr11:29607640-29607912(+)$1	1	21	44	13.4061
(((((.(((......))).))))	chr9:15723512-15723773(-)$1	1	10	33	12.8984
))(((((((......))))))).	chr19:6294413-6294672(+)$1	1	102	125	12.2303
(((.(((((......)).)))..	chr11:106646651-106646913(-)$1	1	113	136	12.6038
(((((((((......))))).))	chr1:172896591-172896838(-)$1	1	35	58	11.3889
((.(((.((......)).))).)	chr16:85079983-85080234(-)$1	1	6	29	13.4747
((((...((......))...)))	chr12:66058530-66058776(-)$1	1	150	173	12.5098
...((((.(......).)))).)	chr11:78385779-78386030(-)$1	1	130	153	12.6000
((((..(((......))).))))	chr10:7644395-7644669(-)$1	1	140	163	12.8687
.(((...((......))....))	chr15:95455279-95455545(-)$1	1	95	118	13.3213
((((..(((......)))....)	chr5:150433858-150434121(-)$1	1	163	186	14.4276
(((((((((......))))))))	chr11:30732467-30732707(+)$1	1	211	234	14.2599
(((...(((......)))....)	chr2:37454633-37454877(-)$1	1	89	112	13.8117
((..(((((......)))))..)	chr2:28324888-28325166(+)$1	1	204	227	11.9807
(((((((((......))))))))	chr8:87805662-87805917(-)$1	1	135	158	14.2599
(((((((((......)))))).)	chr9:82769689-82769943(-)$1	1	226	249	11.8953
(.(((((((......))).))))	chr18:34472365-34472785(+)$1	1	58	81	12.6856
..(((..((......))..))).	chr16:4939475-4939733(+)$1	1	81	104	13.1081
(((((((((......))))))))	chr1:4883429-4883674(+)$1	1	52	75	13.5834
(..((.(((......))).))..	chr9:122184526-122184785(-)$1	1	151	174	13.2447
(...(((((......))))).))	chr9:40124380-40124650(-)$1	1	112	135	11.9288

#PSSM
g : 0.15	b : 0.13	c : 0.09	d : 0.07	e : 0.07	i : 0.07	= : 0.07	f : 0.05	! : 0.03	[ : 0.03	# : 0.03	" : 0.03	a : 0.01	$ : 0.01	: : 0.01	h : 0.01	
g : 0.15	b : 0.11	d : 0.09	! : 0.07	e : 0.07	i : 0.07	= : 0.07	c : 0.07	f : 0.05	" : 0.05	$ : 0.03	[ : 0.03	# : 0.01	h : 0.01	
g : 0.17	d : 0.09	! : 0.09	c : 0.09	" : 0.09	e : 0.07	f : 0.05	i : 0.05	[ : 0.05	= : 0.05	$ : 0.03	b : 0.03	# : 0.01	h : 0.01	
g : 0.15	d : 0.13	c : 0.11	" : 0.09	f : 0.07	! : 0.05	e : 0.05	i : 0.05	[ : 0.05	b : 0.05	= : 0.05	$ : 0.03	# : 0.01	
e : 0.15	c : 0.13	g : 0.13	" : 0.11	d : 0.09	! : 0.07	f : 0.07	i : 0.05	b : 0.05	= : 0.05	$ : 0.01	
[ : 0.13	c : 0.11	d : 0.11	e : 0.11	! : 0.09	g : 0.09	" : 0.07	f : 0.07	i : 0.05	= : 0.05	$ : 0.01	b : 0.01	
c : 0.37	e : 0.11	d : 0.09	[ : 0.09	i : 0.05	f : 0.05	g : 0.05	! : 0.03	" : 0.03	= : 0.03	b : 0.01	
c : 0.31	b : 0.21	e : 0.11	[ : 0.09	d : 0.05	f : 0.05	g : 0.05	i : 0.03	= : 0.03	
c : 0.31	b : 0.21	e : 0.11	a : 0.09	d : 0.05	f : 0.05	g : 0.05	i : 0.03	= : 0.03	
o : 0.98	a : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
c : 0.29	b : 0.21	e : 0.11	a : 0.09	d : 0.05	f : 0.05	g : 0.05	i : 0.03	= : 0.03	o : 0.01	
c : 0.29	b : 0.21	e : 0.11	d : 0.07	] : 0.07	f : 0.05	g : 0.05	i : 0.03	= : 0.03	a : 0.01	
c : 0.33	e : 0.11	] : 0.09	d : 0.09	g : 0.09	i : 0.05	f : 0.05	3 : 0.03	4 : 0.03	= : 0.03	2 : 0.01	
] : 0.17	d : 0.11	c : 0.11	e : 0.11	4 : 0.09	g : 0.09	f : 0.07	i : 0.05	2 : 0.03	3 : 0.03	= : 0.03	b : 0.01	
c : 0.15	e : 0.15	4 : 0.09	g : 0.09	d : 0.09	b : 0.07	f : 0.07	3 : 0.07	i : 0.05	= : 0.03	a : 0.01	2 : 0.01	] : 0.01	
c : 0.11	d : 0.11	g : 0.11	] : 0.09	f : 0.09	4 : 0.09	b : 0.07	i : 0.05	2 : 0.05	3 : 0.05	= : 0.05	e : 0.03	
] : 0.15	g : 0.13	d : 0.11	2 : 0.11	f : 0.05	c : 0.05	e : 0.05	i : 0.05	4 : 0.05	3 : 0.05	= : 0.05	b : 0.03	a : 0.01	
d : 0.15	g : 0.15	b : 0.11	] : 0.07	e : 0.07	i : 0.07	2 : 0.07	= : 0.07	f : 0.05	c : 0.05	: : 0.03	3 : 0.01	

#score	654.4467632845318
#seq	51
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_UTR_m1_run2.txt

#BEAR
!bb[eeeeettttttttttteeeeeb	chr3:107271560-107272022(-)$1	462	87	113	22.3304
cc[eeeeeuuuuuuuuuuuueeeee2	chr2:173923727-173924185(+)$1	458	407	433	24.6309
a####cccwwwwwwwwwwwwwwccc2	chr3:55274457-55274796(+)$1	339	12	38	22.2896
fff[a[bbvvvvvvvvvvvvvbb]a]	chr14:14936799-14937085(+)$1	286	128	154	21.7380
"ggggggguuuuuuuuuuuugggggg	chr17:43224907-43225264(+)$1	357	250	276	23.8063
cc[eeeeettttttttttteeeee]c	chr4:150004457-150004862(-)$1	405	12	38	22.9502
cc[eeeeettttttttttteeeeecc	chr9:79618443-79618879(-)$1	436	205	231	22.8546
!a[eeeeeuuuuuuuuuuuueeeee]	chr4:154931703-154932048(+)$1	345	262	288	25.2058
====[a[bbtttttttttttbb]a]=	chr4:138931681-138932030(+)$1	349	313	339	21.5853
bbeeeeevvvvvvvvvvvvveeeee]	chr11:90200938-90201372(-)$1	434	24	50	23.4648
========wwwwwwwwwwwwww====	chr3:151847504-151847964(-)$1	460	162	188	22.2925
========yyyyyyyyyyyyyyyy==	chr9:108000430-108000921(-)$1	491	168	194	21.3107
fffffcccvvvvvvvvvvvvvccc]f	chr4:40959962-40960185(+)$1	223	42	68	22.4890
hhhhhhhawwwwwwwwwwwwwwa]hh	chr11:75518300-75518583(+)$1	283	18	44	20.0154
ggggggxxxxxxxxxxxxxxxggggg	chr4:86629080-86629405(-)$1	325	161	187	18.4563
###eeeeeuuuuuuuuuuuueeeee2	chr4:11892567-11892950(-)$1	383	186	212	25.1461
eee[dddduuuuuuuuuuuuddddee	chr11:97362677-97363137(+)$1	460	223	249	23.0817
[ddddccctttttttttttccc]ddd	chr6:86938144-86938640(+)$1	496	185	211	21.8036
e[fffffftttttttttttffffff]	chr18:64149114-64149397(+)$1	283	190	216	21.8070
dd[eeeeewwwwwwwwwwwwwweeee	chr3:95998835-95999324(+)$1	489	416	442	22.2071
[ffffffvvvvvvvvvvvvvffffff	chr9:57443737-57444087(+)$1	350	192	218	22.5143
!dddd[ccctttttttttttccc]dd	chr1:169019755-169020242(+)$1	487	330	356	22.1064
ffff!!ccctttttttttttccc22f	chr13:54482367-54482866(+)$1	499	99	125	21.6469
[ggggggguuuuuuuuuuuugggggg	chr4:131780572-131780871(-)$1	299	118	144	23.7238
####dddduuuuuuuuuuuuddddgg	chr1:89841672-89841920(-)$1	248	185	211	23.9141
ggggg[ccctttttttttttcccggg	chr2:10360114-10360496(+)$1	382	13	39	22.5614
"""eeeeettttttttttteeeee33	chr5:67748025-67748248(+)$1	223	161	187	23.8765
eeeeexxxxxxxxxxxxxxxeeeeed	chr12:30219888-30220172(+)$1	284	85	111	18.1646
"""bbyyyyyyyyyyyyyyyybb333	chr16:35002206-35002544(+)$1	338	265	291	21.8613
###ddddyyyyyyyyyyyyyyyyddd	chr1:174428714-174429055(+)$1	341	252	278	21.9003
bb[ddddvvvvvvvvvvvvvdddd]b	chr16:4764336-4764708(-)$1	372	300	326	22.2258
%%%ccc[auuuuuuuuuuuua]ccc4	chr5:73704809-73705125(+)$1	316	253	279	22.7319
F:eeeeevvvvvvvvvvvvveeeee:	chr5:102358243-102358546(-)$1	303	237	263	21.3730
c[fffffftttttttttttffffff]	chr17:33783166-33783649(-)$1	483	261	287	21.9012
eeeeeeeeettttttttttteeeee:	chr3:143851434-143851892(-)$1	458	265	291	21.7424
####ddddtttttttttttdddd444	chr9:32563966-32564282(+)$1	316	282	308	22.4880
ffffyyyyyyyyyyyyyyyyffffff	chr5:107535768-107536194(-)$1	426	284	310	20.7584
hhhh[cccuuuuuuuuuuuuccc]hh	chr1:82232670-82232997(-)$1	327	170	196	22.4865
ccc[dddduuuuuuuuuuuudddd]c	chr10:56109142-56109601(+)$1	459	173	199	23.3183
b!!cccwwwwwwwwwwwwwwcccbb]	chr9:42221886-42222132(-)$1	246	201	227	22.0464
###ddddvvvvvvvvvvvvvdddd55	chr18:39534985-39535328(+)$1	343	38	64	21.9999
""cccyyyyyyyyyyyyyyyyccc44	chr10:117251660-117252105(-)$1	445	401	427	22.6530
""ffffffuuuuuuuuuuuuffffff	chr2:160595423-160595695(-)$1	272	120	146	23.5997
:ffffffvvvvvvvvvvvvvffffff	chr4:128986838-128987097(-)$1	259	153	179	21.4229
"""eeeeeuuuuuuuuuuuueeeee]	chr3:135070923-135071369(-)$1	446	217	243	25.3661
!eeeeewwwwwwwwwwwwwweeeeef	chr9:82763621-82764018(-)$1	397	164	190	22.9255
gggg[cccattttttttttta]ccc]	chr5:151299703-151300129(+)$1	426	253	279	23.0909
:ddddyyyyyyyyyyyyyyyydddd:	chr8:71430462-71430779(+)$1	317	9	35	19.7002
##eeeeevvvvvvvvvvvvveeeee3	chr6:143153653-143154051(+)$1	398	77	103	24.4109
gg[fffffftttttttttttffffff	chr1:94914236-94914538(-)$1	302	223	249	21.7195
!!ddddwwwwwwwwwwwwwwdddd44	chr3:146101860-146102223(+)$1	363	295	321	22.5343
!!eeeeevvvvvvvvvvvvveeeee4	chr15:30958285-30958776(+)$1	491	330	356	24.2916
dd[eeeeettttttttttteeeeedd	chr16:31252884-31253303(-)$1	419	17	43	22.3587
$$$cccyyyyyyyyyyyyyyyyccc>	chr7:17501203-17501515(-)$1	312	240	266	21.9912
bb!!cccxxxxxxxxxxxxxxxccc2	chrX:162825513-162825886(+)$1	373	228	254	18.4017
##ffffffvvvvvvvvvvvvvfffff	chr6:142959900-142960246(-)$1	346	196	222	22.6751
fffffffftttttttttttffffff2	chr10:101853696-101854026(+)$1	330	116	142	21.3573
iiiiiiiiuuuuuuuuuuuuiiiiii	chr14:60919273-60919696(+)$1	423	106	132	23.4916
ddd[eeeeettttttttttteeeee]	chr11:106641675-106642066(-)$1	391	148	174	22.6201
eeeee[bbuuuuuuuuuuuubb22ee	chr2:130534772-130535000(-)$1	228	81	107	22.1098
[dddd[cccuuuuuuuuuuuuccc22	chr10:93433897-93434236(-)$1	339	257	283	22.2917
eee[cccxxxxxxxxxxxxxxxccc]	chr1:34872607-34873035(-)$1	428	262	288	18.5405
&&&ddddvvvvvvvvvvvvvdddd88	chr11:102166880-102167311(-)$1	431	346	372	20.8094
[eeeeewwwwwwwwwwwwwweeeee]	chr5:90651026-90651450(-)$1	424	370	396	23.2230

#otherMatches

#Seq PSSM
AGCUAGGGCUGUUUGCUUAUGCCUUG	chr3:107271560-107272022(-)$1	462	87	113	22.3304
CCACCCCACCACUUCAGAAUUGGGGA	chr2:173923727-173924185(+)$1	458	407	433	24.6309
GAUAUGUCAAAUUCAUUAUAGCGAUU	chr3:55274457-55274796(+)$1	339	12	38	22.2896
CCAGUCGCUGGUUGUUUGAAUGCAGG	chr14:14936799-14937085(+)$1	286	128	154	21.7380
UGGAAAAUGCCCACCACUAAAUUUUU	chr17:43224907-43225264(+)$1	357	250	276	23.8063
UACCUUCCUUACUACCUUUGGAGGCU	chr4:150004457-150004862(-)$1	405	12	38	22.9502
UGCUAACCUUUGAAAAUUUGGUUACA	chr9:79618443-79618879(-)$1	436	205	231	22.8546
AGUUCAUUUGCAUUUAAAUCAGUGAU	chr4:154931703-154932048(+)$1	345	262	288	25.2058
GUGAGAACUAAUUUUAACCAAGCUGU	chr4:138931681-138932030(+)$1	349	313	339	21.5853
ACCAUUCCUUAUAGAACACAGAGUGU	chr11:90200938-90201372(-)$1	434	24	50	23.4648
uguguguguguguguguguguguacg	chr3:151847504-151847964(-)$1	460	162	188	22.2925
cgugugugugugugugugugugugua	chr9:108000430-108000921(-)$1	491	168	194	21.3107
agcugcacugucuagccuccugugau	chr4:40959962-40960185(+)$1	223	42	68	22.4890
AAUUUACCUUCUUAGUUGUCUUGUGU	chr11:75518300-75518583(+)$1	283	18	44	20.0154
UGUCUGUACAUAACUGGAAUUCGGAU	chr4:86629080-86629405(-)$1	325	161	187	18.4563
AUUGGUAGGUAUUCACAUAACUACCU	chr4:11892567-11892950(-)$1	383	186	212	25.1461
uauguguguguguguguAGUCACAGU	chr11:97362677-97363137(+)$1	460	223	249	23.0817
UGUACCCAUAUAGCAGUCCUGGAGUG	chr6:86938144-86938640(+)$1	496	185	211	21.8036
AAAAUGUCUCGUCUCCUACGACAUUC	chr18:64149114-64149397(+)$1	283	190	216	21.8070
UGUGUGAAUGUGCGACCCUUCUUUCA	chr3:95998835-95999324(+)$1	489	416	442	22.2071
CUGCCCUUAACCGCCUCCUUAGGGCA	chr9:57443737-57444087(+)$1	350	192	218	22.5143
CUUCAUACAGAAUGGUGUAAUGUCUG	chr1:169019755-169020242(+)$1	487	330	356	22.1064
CUGUGACUUGUGGAGAAAUGGAGAGA	chr13:54482367-54482866(+)$1	499	99	125	21.6469
AGCAUGCAAgugugugugugugugug	chr4:131780572-131780871(-)$1	299	118	144	23.7238
UUAAAGAAAAAAAUAAAACAUUCUUA	chr1:89841672-89841920(-)$1	248	185	211	23.9141
GUUACCACUGACUGUAUUAAAGUGUG	chr2:10360114-10360496(+)$1	382	13	39	22.5614
AACUGAAGCCAAAUUACAAUUUUAAA	chr5:67748025-67748248(+)$1	223	161	187	23.8765
CGCGCCGAUAGAGAGAAGAUGUGCGG	chr12:30219888-30220172(+)$1	284	85	111	18.1646
UAGCUCACAAUUUUUAAAUAAAGGAU	chr16:35002206-35002544(+)$1	338	265	291	21.8613
UUUUUUAAAAAACAGGUGAAUAAUAA	chr1:174428714-174429055(+)$1	341	252	278	21.9003
gggcaucagaucucacuacagauggc	chr16:4764336-4764708(-)$1	372	300	326	22.2258
GGGAGGGGGGAGCAAGCACACGCCUA	chr5:73704809-73705125(+)$1	316	253	279	22.7319
UAUUUCUUCCCCUUGAAUCUAGAAAA	chr5:102358243-102358546(-)$1	303	237	263	21.3730
UUGUUAACCAUUUUAAUUUGUUGGCU	chr17:33783166-33783649(-)$1	483	261	287	21.9012
UAUGUAGAAAUCCCCCCUACUUCUAA	chr3:143851434-143851892(-)$1	458	265	291	21.7424
CUUCACCCUUCUCCAUAUUGGGUUCC	chr9:32563966-32564282(+)$1	316	282	308	22.4880
AAACUUUUUUUUUUUAUCCUGUUUGU	chr5:107535768-107536194(-)$1	426	284	310	20.7584
UUACAGAGAGCACAUAAAAACUUAGU	chr1:82232670-82232997(-)$1	327	170	196	22.4865
ACAAUCGCUUCUGUCUAUGUGUGGGU	chr10:56109142-56109601(+)$1	459	173	199	23.3183
CACUCUUAUUUUUGAACUUUGGAGCC	chr9:42221886-42222132(-)$1	246	201	227	22.0464
ACAUGCAUACCUACCAUUCUUGCGGC	chr18:39534985-39535328(+)$1	343	38	64	21.9999
GUGGCCAAAUGUAAACUAAAAGCCUU	chr10:117251660-117252105(-)$1	445	401	427	22.6530
CAGAGAACAGAAGCCUGAACGUUCUC	chr2:160595423-160595695(-)$1	272	120	146	23.5997
CUAGUUUGUGUUUGUUUUUAAGAUUA	chr4:128986838-128987097(-)$1	259	153	179	21.4229
AAAGCCUUGUugugugugugagggug	chr3:135070923-135071369(-)$1	446	217	243	25.3661
AAUGUCAUUUUUAAACUUCAGACAUA	chr9:82763621-82764018(-)$1	397	164	190	22.9255
UCUGCAUGCAUCCCUUAAUAGCCAUU	chr5:151299703-151300129(+)$1	426	253	279	23.0909
AACAAUAAAAAUAUGUAUAAUUUGUC	chr8:71430462-71430779(+)$1	317	9	35	19.7002
UUCUUUCCUCCUUAAAAUCCGAGAGU	chr6:143153653-143154051(+)$1	398	77	103	24.4109
GGAGGAUCAGGUGAGGGGUAUGAUCC	chr1:94914236-94914538(-)$1	302	223	249	21.7195
UACUGUAGAUUUUUAACAAAGCAGGU	chr3:146101860-146102223(+)$1	363	295	321	22.5343
AUCCGCUCUUCUCACCAUCUAGUGGC	chr15:30958285-30958776(+)$1	491	330	356	24.2916
AAUGUCUUUCUUUUUUUAUGGGACUU	chr16:31252884-31253303(-)$1	419	17	43	22.3587
CCAUGCUCACAAGAACCAACCUGCAA	chr7:17501203-17501515(-)$1	312	240	266	21.9912
UGUCAGCUCUGCCUUAAUAUUUGCUU	chrX:162825513-162825886(+)$1	373	228	254	18.4017
CUGGAUGGGUAGUGUGUUAGACCAUC	chr6:142959900-142960246(-)$1	346	196	222	22.6751
UUCCUGGAAAACAAUCAAAUUCAGGU	chr10:101853696-101854026(+)$1	330	116	142	21.3573
UGACUGUAGUGUAAGAAAUGUAUAGU	chr14:60919273-60919696(+)$1	423	106	132	23.4916
UGAGUGGUUUUCAAUGGCAUGGCUAG	chr11:106641675-106642066(-)$1	391	148	174	22.6201
GCCUACCAGAGAUGAAUGAAUGAAUG	chr2:130534772-130535000(-)$1	228	81	107	22.1098
UGAAUUGUAUGUUACAUUUUUUAUUU	chr10:93433897-93434236(-)$1	339	257	283	22.2917
GGGGUGAGCUUUGUAUCUUUUGUCAG	chr1:34872607-34873035(-)$1	428	262	288	18.5405
CUAGCAGGAACAAACCAAGGCUGCCC	chr11:102166880-102167311(-)$1	431	346	372	20.8094
agcugaaucguccuccuaucucagcc	chr5:90651026-90651450(-)$1	424	370	396	23.2230

#DB
.((.(((((...........))))))	chr3:107271560-107272022(-)$1	1	87	113	22.3304
((.(((((............))))).	chr2:173923727-173924185(+)$1	1	407	433	24.6309
(....(((..............))).	chr3:55274457-55274796(+)$1	1	12	38	22.2896
(((.(.((.............)).).	chr14:14936799-14937085(+)$1	1	128	154	21.7380
.(((((((............))))))	chr17:43224907-43225264(+)$1	1	250	276	23.8063
((.(((((...........))))).)	chr4:150004457-150004862(-)$1	1	12	38	22.9502
((.(((((...........)))))))	chr9:79618443-79618879(-)$1	1	205	231	22.8546
.(.(((((............))))).	chr4:154931703-154932048(+)$1	1	262	288	25.2058
((((.(.((...........)).).)	chr4:138931681-138932030(+)$1	1	313	339	21.5853
(((((((.............))))).	chr11:90200938-90201372(-)$1	1	24	50	23.4648
((((((((..............))))	chr3:151847504-151847964(-)$1	1	162	188	22.2925
((((((((................))	chr9:108000430-108000921(-)$1	1	168	194	21.3107
((((((((.............))).)	chr4:40959962-40960185(+)$1	1	42	68	22.4890
((((((((..............).))	chr11:75518300-75518583(+)$1	1	18	44	20.0154
((((((...............)))))	chr4:86629080-86629405(-)$1	1	161	187	18.4563
...(((((............))))).	chr4:11892567-11892950(-)$1	1	186	212	25.1461
(((.((((............))))))	chr11:97362677-97363137(+)$1	1	223	249	23.0817
.(((((((...........))).)))	chr6:86938144-86938640(+)$1	1	185	211	21.8036
(.((((((...........)))))).	chr18:64149114-64149397(+)$1	1	190	216	21.8070
((.(((((..............))))	chr3:95998835-95999324(+)$1	1	416	442	22.2071
.((((((.............))))))	chr9:57443737-57444087(+)$1	1	192	218	22.5143
.((((.(((...........))).))	chr1:169019755-169020242(+)$1	1	330	356	22.1064
((((..(((...........)))..)	chr13:54482367-54482866(+)$1	1	99	125	21.6469
.(((((((............))))))	chr4:131780572-131780871(-)$1	1	118	144	23.7238
....((((............))))))	chr1:89841672-89841920(-)$1	1	185	211	23.9141
(((((.(((...........))))))	chr2:10360114-10360496(+)$1	1	13	39	22.5614
...(((((...........)))))..	chr5:67748025-67748248(+)$1	1	161	187	23.8765
(((((...............)))))(	chr12:30219888-30220172(+)$1	1	85	111	18.1646
...((................))...	chr16:35002206-35002544(+)$1	1	265	291	21.8613
...((((................)))	chr1:174428714-174429055(+)$1	1	252	278	21.9003
((.((((.............)))).)	chr16:4764336-4764708(-)$1	1	300	326	22.2258
...(((.(............).))).	chr5:73704809-73705125(+)$1	1	253	279	22.7319
).(((((.............))))).	chr5:102358243-102358546(-)$1	1	237	263	21.3730
(.((((((...........)))))).	chr17:33783166-33783649(-)$1	1	261	287	21.9012
))))(((((...........))))).	chr3:143851434-143851892(-)$1	1	265	291	21.7424
....((((...........))))...	chr9:32563966-32564282(+)$1	1	282	308	22.4880
((((................))))))	chr5:107535768-107536194(-)$1	1	284	310	20.7584
((((.(((............))).))	chr1:82232670-82232997(-)$1	1	170	196	22.4865
(((.((((............)))).)	chr10:56109142-56109601(+)$1	1	173	199	23.3183
(..(((..............))))).	chr9:42221886-42222132(-)$1	1	201	227	22.0464
...((((.............))))..	chr18:39534985-39535328(+)$1	1	38	64	21.9999
..(((................)))..	chr10:117251660-117252105(-)$1	1	401	427	22.6530
..((((((............))))))	chr2:160595423-160595695(-)$1	1	120	146	23.5997
.((((((.............))))))	chr4:128986838-128987097(-)$1	1	153	179	21.4229
...(((((............))))).	chr3:135070923-135071369(-)$1	1	217	243	25.3661
.(((((..............))))))	chr9:82763621-82764018(-)$1	1	164	190	22.9255
((((.((((...........).))).	chr5:151299703-151300129(+)$1	1	253	279	23.0909
.((((................)))).	chr8:71430462-71430779(+)$1	1	9	35	19.7002
..(((((.............))))).	chr6:143153653-143154051(+)$1	1	77	103	24.4109
((.((((((...........))))))	chr1:94914236-94914538(-)$1	1	223	249	21.7195
..((((..............))))..	chr3:146101860-146102223(+)$1	1	295	321	22.5343
..(((((.............))))).	chr15:30958285-30958776(+)$1	1	330	356	24.2916
((.(((((...........)))))))	chr16:31252884-31253303(-)$1	1	17	43	22.3587
...(((................))).	chr7:17501203-17501515(-)$1	1	240	266	21.9912
((..(((...............))).	chrX:162825513-162825886(+)$1	1	228	254	18.4017
..((((((.............)))))	chr6:142959900-142960246(-)$1	1	196	222	22.6751
((((((((...........)))))).	chr10:101853696-101854026(+)$1	1	116	142	21.3573
((((((((............))))))	chr14:60919273-60919696(+)$1	1	106	132	23.4916
(((.(((((...........))))).	chr11:106641675-106642066(-)$1	1	148	174	22.6201
(((((.((............))..))	chr2:130534772-130535000(-)$1	1	81	107	22.1098
.((((.(((............)))..	chr10:93433897-93434236(-)$1	1	257	283	22.2917
(((.(((...............))).	chr1:34872607-34873035(-)$1	1	262	288	18.5405
...((((.............))))..	chr11:102166880-102167311(-)$1	1	346	372	20.8094
.(((((..............))))).	chr5:90651026-90651450(-)$1	1	370	396	23.2230

#PSSM
# : 0.10	! : 0.09	" : 0.09	e : 0.09	c : 0.07	f : 0.07	[ : 0.07	b : 0.06	g : 0.06	= : 0.04	d : 0.04	h : 0.03	: : 0.03	a : 0.01	% : 0.01	F : 0.01	$ : 0.01	i : 0.01	& : 0.01	
# : 0.12	f : 0.10	e : 0.10	d : 0.10	g : 0.09	" : 0.07	b : 0.06	c : 0.06	= : 0.04	! : 0.04	h : 0.03	[ : 0.03	a : 0.01	% : 0.01	: : 0.01	$ : 0.01	i : 0.01	& : 0.01	
f : 0.17	e : 0.17	[ : 0.12	# : 0.09	d : 0.09	g : 0.07	= : 0.04	" : 0.04	h : 0.03	c : 0.03	! : 0.03	b : 0.01	% : 0.01	$ : 0.01	i : 0.01	& : 0.01	
e : 0.28	f : 0.17	d : 0.14	[ : 0.09	g : 0.07	c : 0.06	# : 0.04	= : 0.04	h : 0.03	b : 0.01	! : 0.01	i : 0.01	
e : 0.31	d : 0.20	f : 0.14	c : 0.09	g : 0.06	[ : 0.04	= : 0.03	# : 0.01	a : 0.01	h : 0.01	! : 0.01	b : 0.01	y : 0.01	i : 0.01	
e : 0.28	c : 0.15	d : 0.14	f : 0.12	[ : 0.07	y : 0.06	g : 0.04	= : 0.03	a : 0.01	h : 0.01	! : 0.01	x : 0.01	i : 0.01	
e : 0.25	c : 0.17	d : 0.12	f : 0.12	y : 0.07	w : 0.06	b : 0.03	g : 0.03	[ : 0.03	= : 0.03	x : 0.03	h : 0.01	i : 0.01	
e : 0.18	c : 0.14	v : 0.14	f : 0.09	y : 0.09	x : 0.06	d : 0.06	w : 0.06	b : 0.04	g : 0.03	= : 0.03	a : 0.03	i : 0.01	
u : 0.21	v : 0.18	t : 0.14	w : 0.12	y : 0.10	x : 0.06	c : 0.06	e : 0.04	b : 0.01	a : 0.01	f : 0.01	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
t : 0.28	u : 0.23	v : 0.18	w : 0.12	y : 0.10	x : 0.06	
u : 0.23	v : 0.18	t : 0.14	w : 0.12	y : 0.10	e : 0.06	x : 0.06	f : 0.04	c : 0.01	d : 0.01	
e : 0.28	d : 0.12	f : 0.12	y : 0.09	c : 0.09	w : 0.06	v : 0.04	x : 0.04	g : 0.03	b : 0.03	a : 0.03	i : 0.01	u : 0.01	
e : 0.28	c : 0.14	d : 0.14	f : 0.14	w : 0.06	b : 0.06	g : 0.04	y : 0.04	] : 0.03	x : 0.03	i : 0.01	
e : 0.29	c : 0.21	d : 0.14	f : 0.14	g : 0.04	b : 0.03	] : 0.03	y : 0.03	= : 0.01	a : 0.01	i : 0.01	2 : 0.01	
e : 0.29	d : 0.15	c : 0.14	f : 0.14	] : 0.06	g : 0.06	2 : 0.03	a : 0.01	= : 0.01	y : 0.01	3 : 0.01	4 : 0.01	b : 0.01	i : 0.01	
e : 0.26	f : 0.14	c : 0.10	g : 0.07	] : 0.07	d : 0.07	4 : 0.04	= : 0.03	h : 0.03	2 : 0.03	3 : 0.03	a : 0.01	b : 0.01	5 : 0.01	i : 0.01	8 : 0.01	
] : 0.17	f : 0.14	2 : 0.09	g : 0.07	d : 0.07	4 : 0.07	c : 0.04	= : 0.04	e : 0.04	3 : 0.04	: : 0.04	b : 0.03	h : 0.03	5 : 0.01	> : 0.01	i : 0.01	8 : 0.01	

#score	1426.3943525360503
#seq	64
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_CDS_m1_run2.txt

#BEAR
bbddddvvvvvvvvvvvvvddd	chr10:40655947-40656176(+)$1	229	74	96	22.7087
bb[cccuuuuuuuuuuuuccc]	chr7:35982781-35983000(+)$1	219	48	70	22.7095
cccccwwwwwwwwwwwwwwccc	chr7:130313489-130313707(+)$1	218	76	98	22.2426
cc[cccwwwwwwwwwwwwwwcc	chr14:28296934-28297172(-)$1	238	177	199	22.5551
gggg[avvvvvvvvvvvvva]g	chr11:99146204-99146428(+)$1	224	81	103	23.5016
ffffffwwwwwwwwwwwwwwff	chr7:53048777-53049007(+)$1	230	129	151	21.5790
ccccccuuuuuuuuuuuuccc]	chr10:57698921-57699141(+)$1	220	18	40	22.8914
%eeeeevvvvvvvvvvvvveee	chr9:26895614-26895842(+)$1	228	136	158	22.8653
========ttttttttttt===	chr4:147920502-147920722(+)$1	220	149	171	21.1266
!bb[ccctttttttttttccc]	chr1:10199615-10199839(-)$1	224	174	196	22.1099
$$a[bbuuuuuuuuuuuubb]a	chr9:123738417-123738638(+)$1	221	84	106	21.2135
gggggguuuuuuuuuuuugggg	chr16:36824656-36824876(-)$1	220	126	148	22.4177
c[fffffftttttttttttfff	chr11:101027785-101028011(-)$1	226	50	72	20.5092
dd[dddduuuuuuuuuuuuddd	chr10:29067189-29067408(-)$1	219	171	193	21.6962
ggggggvvvvvvvvvvvvvggg	chr1:182524104-182524336(+)$1	232	47	69	23.6597
!eeeeevvvvvvvvvvvvveee	chr7:37554401-37554639(+)$1	238	140	162	23.4433
%eeeeevvvvvvvvvvvvveee	chr2:80464331-80464555(+)$1	224	32	54	22.8653
======vvvvvvvvvvvvv===	chr12:80366653-80366880(-)$1	227	27	49	23.7054
ggggggwwwwwwwwwwwwwwgg	chr6:126827150-126827365(+)$1	215	96	118	22.3810
c[ddddvvvvvvvvvvvvvddd	chrX:66978126-66978355(+)$1	229	10	32	23.0716
:eeeeettttttttttteeeee	chr6:103591906-103592130(+)$1	224	5	27	19.8963
"""cccvvvvvvvvvvvvvccc	chr11:75385892-75386115(+)$1	223	175	197	23.9760
hhhccctttttttttttccccc	chr9:72179028-72179243(+)$1	215	84	106	20.9373
hffffffuuuuuuuuuuuufff	chr7:130314176-130314397(+)$1	221	30	52	21.6510
:ffffffuuuuuuuuuuuufff	chr1:63631875-63632116(+)$1	241	162	184	21.1736
""eeeeeuuuuuuuuuuuueee	chr10:39251735-39251955(+)$1	220	171	193	22.4034
:eeeeevvvvvvvvvvvvveee	chr13:59912800-59913023(-)$1	223	121	143	22.6047
d"""bbtttttttttttbb333	chr17:34069574-34069791(+)$1	217	127	149	19.7214
gggggggtttttttttttgggg	chr11:80291743-80291963(+)$1	220	150	172	21.5568
hhhhhhhuuuuuuuuuuuuhhh	chr14:67447532-67447756(-)$1	224	197	219	20.7802
[ffffffuuuuuuuuuuuufff	chr7:112902963-112903213(-)$1	250	43	65	21.9560
gggggguuuuuuuuuuuugggg	chr19:47209844-47210067(-)$1	223	101	123	22.4177
hhhhhhvvvvvvvvvvvvvhhh	chr11:107533876-107534096(+)$1	220	142	164	22.1195
ff"""ccctttttttttttccc	chr13:54836593-54836814(-)$1	221	124	146	21.0900
fff[ccctttttttttttccc]	chr4:108185611-108185839(+)$1	228	35	57	22.0960
====ddddtttttttttttddd	chr5:92386840-92387067(-)$1	227	56	78	20.6957
b[cccyyyyyyyyyyyyyyyyc	chr8:9988072-9988306(+)$1	234	103	125	20.1206
::ddddvvvvvvvvvvvvvddd	chr15:8288433-8288654(+)$1	221	37	59	21.3219
:eeeeeuuuuuuuuuuuueeee	chr11:96213245-96213492(+)$1	247	160	182	21.4415
======vvvvvvvvvvvvv===	chr15:30704806-30705047(+)$1	241	151	173	23.7054
eeddddvvvvvvvvvvvvvddd	chr6:124654491-124654715(-)$1	224	73	95	22.7396
ccc[ccctttttttttttccc]	chrX:58437509-58437735(+)$1	226	52	74	22.3818
bcccyyyyyyyyyyyyyyyycc	chr10:126723088-126723334(-)$1	246	95	117	19.9007
HHddddvvvvvvvvvvvvvddd	chr5:73697718-73697942(+)$1	224	94	116	21.8807
b!!cccuuuuuuuuuuuuccc]	chr19:10281600-10281832(+)$1	232	162	184	22.9831
i"""bbvvvvvvvvvvvvvbb5	chr8:47292789-47293022(-)$1	233	88	110	21.5603
!eeeeeyyyyyyyyyyyyyyyy	chr7:56708721-56708951(+)$1	230	112	134	20.0270
hhhhhhvvvvvvvvvvvvvhhh	chr10:79616979-79617201(+)$1	222	76	98	22.1195
eee[ccctttttttttttccc]	chr18:46748110-46748333(-)$1	223	59	81	22.1523
:eeeeeuuuuuuuuuuuueeee	chr7:126620754-126620973(+)$1	219	1	23	21.4415
ddd[cccuuuuuuuuuuuuccc	chr9:54756535-54756753(-)$1	218	93	115	22.6413
::::cccuuuuuuuuuuuuccc	chr7:66527293-66527524(-)$1	231	131	153	19.2443
ffffffwwwwwwwwwwwwwwff	chr11:60981714-60981954(-)$1	240	84	106	21.5790
gg!!cccuuuuuuuuuuuuccc	chr18:35108671-35108897(-)$1	226	150	172	23.1977
beeeeeuuuuuuuuuuuueeee	chr19:45841805-45842025(-)$1	220	22	44	22.0590
ffffffwwwwwwwwwwwwwwff	chr8:74147307-74147541(+)$1	234	59	81	21.5790
ggggggyyyyyyyyyyyyyyyy	chr17:35261118-35261349(+)$1	231	149	171	20.1344
!!ddddyyyyyyyyyyyyyyyy	chr13:69877512-69877740(-)$1	228	79	101	19.9107
[bbdddduuuuuuuuuuuuddd	chr13:14146489-14146727(-)$1	238	193	215	21.6697
:eeeeettttttttttteeeee	chr7:111055157-111055381(+)$1	224	187	209	19.8963
hhhhhhvvvvvvvvvvvvvhhh	chr4:151686157-151686374(-)$1	217	83	105	22.1195
$$$cccvvvvvvvvvvvvvccc	chr16:11087780-11088019(-)$1	239	120	142	23.3637
CCCcccvvvvvvvvvvvvvccc	chr11:43518120-43518364(+)$1	244	181	203	20.6279
##eeeeeuuuuuuuuuuuueee	chr4:55542814-55543052(-)$1	238	21	43	22.3501
$bb[cccuuuuuuuuuuuuccc	chr15:100447306-100447539(+)$1	233	96	118	22.6463
ffffffwwwwwwwwwwwwwwff	chr5:82123484-82123723(+)$1	239	116	138	21.5790

#otherMatches

#Seq PSSM
GCCUUGUCCACUUCUUCACUAA	chr10:40655947-40656176(+)$1	229	74	96	22.7087
GCUGAGACCCACCAAUGCCUUC	chr7:35982781-35983000(+)$1	219	48	70	22.7095
GGCCAGUAUUAGAAAACAAUGG	chr7:130313489-130313707(+)$1	218	76	98	22.2426
AGGUAUGCACUCUUCACCAAGU	chr14:28296934-28297172(-)$1	238	177	199	22.5551
GCUCCGAAUCCACCCCUUACUG	chr11:99146204-99146428(+)$1	224	81	103	23.5016
GCGUGCUUCCGGUCAUCAGCGC	chr7:53048777-53049007(+)$1	230	129	151	21.5790
UGGGCCUGCCCCUCCUGUGGCG	chr10:57698921-57699141(+)$1	220	18	40	22.8914
AUGGACCUCUGAAGAUAAUGUC	chr9:26895614-26895842(+)$1	228	136	158	22.8653
CGGCAGGAUAUAUGCUCCUUUU	chr4:147920502-147920722(+)$1	220	149	171	21.1266
ACUGUUGAUCAUAUAAACCAAG	chr1:10199615-10199839(-)$1	224	174	196	22.1099
CUGUGCUAUUGUUUACCUGUUC	chr9:123738417-123738638(+)$1	221	84	106	21.2135
UAUAGAAGUAAGUAGUUCUCUA	chr16:36824656-36824876(-)$1	220	126	148	22.4177
ACCCUUACGAGAGGAGGCAGUG	chr11:101027785-101028011(-)$1	226	50	72	20.5092
UGGUUCAAUAUAGGAGAAAUGA	chr10:29067189-29067408(-)$1	219	171	193	21.6962
UGUCUGUCCCCUUCCCUUCCAG	chr1:182524104-182524336(+)$1	232	47	69	23.6597
UGCAGCCAAAAUCAUCCCUGCU	chr7:37554401-37554639(+)$1	238	140	162	23.4433
GGUGACUCAUAUUCUCAAUGUU	chr2:80464331-80464555(+)$1	224	32	54	22.8653
AUGGACAUACUCUAGAUGCGUU	chr12:80366653-80366880(-)$1	227	27	49	23.7054
CAGGCUUCCUUAAUAUCUGUGG	chr6:126827150-126827365(+)$1	215	96	118	22.3810
UAUAUCCUUAUAAAUAACAGAU	chrX:66978126-66978355(+)$1	229	10	32	23.0716
AGAAAGUAUUAGAGACCCUUUC	chr6:103591906-103592130(+)$1	224	5	27	19.8963
CCCUGGAUCCUGCCCUUCACCA	chr11:75385892-75386115(+)$1	223	175	197	23.9760
GUUCACGAGUGUAUUGAGUGUU	chr9:72179028-72179243(+)$1	215	84	106	20.9373
UCACCAUGGGGAAGUGGAAAUG	chr7:130314176-130314397(+)$1	221	30	52	21.6510
CGCCGCAUGUCUUCUUCUCUGU	chr1:63631875-63632116(+)$1	241	162	184	21.1736
GAUCAUGAAGAAGCUGAAGCAU	chr10:39251735-39251955(+)$1	220	171	193	22.4034
UUGUUCAAGAAUGUUUAAAGAA	chr13:59912800-59913023(-)$1	223	121	143	22.6047
ACCUUGACCUUUGACCCCACAC	chr17:34069574-34069791(+)$1	217	127	149	19.7214
AGGAGGACAAGAAGCGACUCCU	chr11:80291743-80291963(+)$1	220	150	172	21.5568
UGCAGGGCCUCUCCUCCACCCC	chr14:67447532-67447756(-)$1	224	197	219	20.7802
UGGAGGUAGUAGCAAGAGGGCC	chr7:112902963-112903213(-)$1	250	43	65	21.9560
CUGGGGAUAAAGGCUUCCCCCC	chr19:47209844-47210067(-)$1	223	101	123	22.4177
UUAAUGACAGCAGCAGAGACAU	chr11:107533876-107534096(+)$1	220	142	164	22.1195
UCCUUACUGUCCAUGUCCAAGU	chr13:54836593-54836814(-)$1	221	124	146	21.0900
AGUAAGAAACCAGUGAAGUCUG	chr4:108185611-108185839(+)$1	228	35	57	22.0960
GACAAGCUUUAUACCUGCCGGC	chr5:92386840-92387067(-)$1	227	56	78	20.6957
AUGCCUUCUCUCUUCAUCUCUG	chr8:9988072-9988306(+)$1	234	103	125	20.1206
AAAGGAAUAAGUAAAAAAAUCC	chr15:8288433-8288654(+)$1	221	37	59	21.3219
CUGGAUGAAAGAGAAGAAAUCC	chr11:96213245-96213492(+)$1	247	160	182	21.4415
GUUUUGGAGACAAUAAAAUUAA	chr15:30704806-30705047(+)$1	241	151	173	23.7054
UCAGCAACUAUCCACUCUCUGC	chr6:124654491-124654715(-)$1	224	73	95	22.7396
AAGUCUUCCUGAAAAUCCAAGU	chrX:58437509-58437735(+)$1	226	52	74	22.3818
UCAGACUCUCCUCUCUUCCACU	chr10:126723088-126723334(-)$1	246	95	117	19.9007
UCAGGCACUAUACUCAAAAGCC	chr5:73697718-73697942(+)$1	224	94	116	21.8807
GUUGGCAUCUACGUAUAAGUCU	chr19:10281600-10281832(+)$1	232	162	184	22.9831
GAUUGCAAAAGAUGAAGGAGCC	chr8:47292789-47293022(-)$1	233	88	110	21.5603
ACAACCAUCCCAACACAGCCAC	chr7:56708721-56708951(+)$1	230	112	134	20.0270
AUUUGCCAAUCUCCCACCAGCA	chr10:79616979-79617201(+)$1	222	76	98	22.1195
GCUCCGGGAAGCUCAAGGCCGA	chr18:46748110-46748333(-)$1	223	59	81	22.1523
CGUCAGACGAAAACCAUCCUGA	chr7:126620754-126620973(+)$1	219	1	23	21.4415
CCAAGGAAUCUGCAUUUUCUCC	chr9:54756535-54756753(-)$1	218	93	115	22.6413
UGCAGGCCUCAUUUCCACAGCC	chr7:66527293-66527524(-)$1	231	131	153	19.2443
UGCGGCAUCCACCUGAACCGGC	chr11:60981714-60981954(-)$1	240	84	106	21.5790
GGUUGAGGCUCAUGGAAAACUC	chr18:35108671-35108897(-)$1	226	150	172	23.1977
CUGUUCUACCUUCCUUACGAGC	chr19:45841805-45842025(-)$1	220	22	44	22.0590
CCUAUGUCUCUGCUAUCUCCCA	chr8:74147307-74147541(+)$1	234	59	81	21.5790
CCCCAGCCCUCCAACCUUCCCC	chr17:35261118-35261349(+)$1	231	149	171	20.1344
CAUGAAGGAGACCAACACAGAG	chr13:69877512-69877740(-)$1	228	79	101	19.9107
UGCGGUGAAGCUUUUCACACGC	chr13:14146489-14146727(-)$1	238	193	215	21.6697
CUAAGGUAUACCACCAUCCUUA	chr7:111055157-111055381(+)$1	224	187	209	19.8963
CCUCAUCAAGGCGGAGAUCAUG	chr4:151686157-151686374(-)$1	217	83	105	22.1195
CCAAACAAGCCCUCAUGAAGUU	chr16:11087780-11088019(-)$1	239	120	142	23.3637
CGCCGCCUCGGAAAAUUAAGCG	chr11:43518120-43518364(+)$1	244	181	203	20.6279
CAGGACUACCCCUACACUGAGU	chr4:55542814-55543052(-)$1	238	21	43	22.3501
CAGACCUUACAUCUUCCUCAGG	chr15:100447306-100447539(+)$1	233	96	118	22.6463
CUGUAACCACCUCACCAACUUU	chr5:82123484-82123723(+)$1	239	116	138	21.5790

#DB
((((((.............)))	chr10:40655947-40656176(+)$1	1	74	96	22.7087
((.(((............))).	chr7:35982781-35983000(+)$1	1	48	70	22.7095
))(((..............)))	chr7:130313489-130313707(+)$1	1	76	98	22.2426
((.(((..............))	chr14:28296934-28297172(-)$1	1	177	199	22.5551
((((.(.............).)	chr11:99146204-99146428(+)$1	1	81	103	23.5016
((((((..............))	chr7:53048777-53049007(+)$1	1	129	151	21.5790
((((((............))).	chr10:57698921-57699141(+)$1	1	18	40	22.8914
.(((((.............)))	chr9:26895614-26895842(+)$1	1	136	158	22.8653
((((((((...........)))	chr4:147920502-147920722(+)$1	1	149	171	21.1266
.((.(((...........))).	chr1:10199615-10199839(-)$1	1	174	196	22.1099
..(.((............)).)	chr9:123738417-123738638(+)$1	1	84	106	21.2135
((((((............))))	chr16:36824656-36824876(-)$1	1	126	148	22.4177
(.((((((...........)))	chr11:101027785-101028011(-)$1	1	50	72	20.5092
((.((((............)))	chr10:29067189-29067408(-)$1	1	171	193	21.6962
((((((.............)))	chr1:182524104-182524336(+)$1	1	47	69	23.6597
.(((((.............)))	chr7:37554401-37554639(+)$1	1	140	162	23.4433
.(((((.............)))	chr2:80464331-80464555(+)$1	1	32	54	22.8653
((((((.............)))	chr12:80366653-80366880(-)$1	1	27	49	23.7054
((((((..............))	chr6:126827150-126827365(+)$1	1	96	118	22.3810
(.((((.............)))	chrX:66978126-66978355(+)$1	1	10	32	23.0716
.(((((...........)))))	chr6:103591906-103592130(+)$1	1	5	27	19.8963
...(((.............)))	chr11:75385892-75386115(+)$1	1	175	197	23.9760
)))(((...........)))((	chr9:72179028-72179243(+)$1	1	84	106	20.9373
(((((((............)))	chr7:130314176-130314397(+)$1	1	30	52	21.6510
.((((((............)))	chr1:63631875-63632116(+)$1	1	162	184	21.1736
..(((((............)))	chr10:39251735-39251955(+)$1	1	171	193	22.4034
.(((((.............)))	chr13:59912800-59913023(-)$1	1	121	143	22.6047
(...((...........))...	chr17:34069574-34069791(+)$1	1	127	149	19.7214
(((((((...........))))	chr11:80291743-80291963(+)$1	1	150	172	21.5568
(((((((............)))	chr14:67447532-67447756(-)$1	1	197	219	20.7802
.((((((............)))	chr7:112902963-112903213(-)$1	1	43	65	21.9560
((((((............))))	chr19:47209844-47210067(-)$1	1	101	123	22.4177
((((((.............)))	chr11:107533876-107534096(+)$1	1	142	164	22.1195
((...(((...........)))	chr13:54836593-54836814(-)$1	1	124	146	21.0900
(((.(((...........))).	chr4:108185611-108185839(+)$1	1	35	57	22.0960
((((((((...........)))	chr5:92386840-92387067(-)$1	1	56	78	20.6957
(.(((................)	chr8:9988072-9988306(+)$1	1	103	125	20.1206
..((((.............)))	chr15:8288433-8288654(+)$1	1	37	59	21.3219
.(((((............))))	chr11:96213245-96213492(+)$1	1	160	182	21.4415
((((((.............)))	chr15:30704806-30705047(+)$1	1	151	173	23.7054
))((((.............)))	chr6:124654491-124654715(-)$1	1	73	95	22.7396
(((.(((...........))).	chrX:58437509-58437735(+)$1	1	52	74	22.3818
((((................))	chr10:126723088-126723334(-)$1	1	95	117	19.9007
((((((.............)))	chr5:73697718-73697942(+)$1	1	94	116	21.8807
(..(((............))).	chr19:10281600-10281832(+)$1	1	162	184	22.9831
(...((.............)).	chr8:47292789-47293022(-)$1	1	88	110	21.5603
.(((((................	chr7:56708721-56708951(+)$1	1	112	134	20.0270
((((((.............)))	chr10:79616979-79617201(+)$1	1	76	98	22.1195
(((.(((...........))).	chr18:46748110-46748333(-)$1	1	59	81	22.1523
.(((((............))))	chr7:126620754-126620973(+)$1	1	1	23	21.4415
(((.(((............)))	chr9:54756535-54756753(-)$1	1	93	115	22.6413
....(((............)))	chr7:66527293-66527524(-)$1	1	131	153	19.2443
((((((..............))	chr11:60981714-60981954(-)$1	1	84	106	21.5790
((..(((............)))	chr18:35108671-35108897(-)$1	1	150	172	23.1977
((((((............))))	chr19:45841805-45842025(-)$1	1	22	44	22.0590
((((((..............))	chr8:74147307-74147541(+)$1	1	59	81	21.5790
((((((................	chr17:35261118-35261349(+)$1	1	149	171	20.1344
..((((................	chr13:69877512-69877740(-)$1	1	79	101	19.9107
.((((((............)))	chr13:14146489-14146727(-)$1	1	193	215	21.6697
.(((((...........)))))	chr7:111055157-111055381(+)$1	1	187	209	19.8963
((((((.............)))	chr4:151686157-151686374(-)$1	1	83	105	22.1195
...(((.............)))	chr16:11087780-11088019(-)$1	1	120	142	23.3637
)))(((.............)))	chr11:43518120-43518364(+)$1	1	181	203	20.6279
..(((((............)))	chr4:55542814-55543052(-)$1	1	21	43	22.3501
.((.(((............)))	chr15:100447306-100447539(+)$1	1	96	118	22.6463
((((((..............))	chr5:82123484-82123723(+)$1	1	116	138	21.5790

#PSSM
g : 0.12	: : 0.12	b : 0.09	c : 0.09	f : 0.09	h : 0.09	= : 0.06	! : 0.06	$ : 0.04	d : 0.04	% : 0.03	" : 0.03	[ : 0.03	e : 0.03	H : 0.01	i : 0.01	C : 0.01	# : 0.01	
e : 0.18	f : 0.13	g : 0.12	b : 0.07	c : 0.07	h : 0.07	= : 0.06	" : 0.06	[ : 0.04	$ : 0.03	d : 0.03	: : 0.03	! : 0.03	H : 0.01	C : 0.01	# : 0.01	
e : 0.19	f : 0.13	d : 0.10	g : 0.10	c : 0.07	h : 0.07	= : 0.06	" : 0.06	[ : 0.04	b : 0.04	! : 0.03	a : 0.01	: : 0.01	$ : 0.01	C : 0.01	
e : 0.18	c : 0.16	d : 0.12	f : 0.12	g : 0.10	[ : 0.10	= : 0.06	h : 0.06	" : 0.04	: : 0.01	! : 0.01	
c : 0.27	e : 0.18	d : 0.13	f : 0.12	g : 0.09	h : 0.06	= : 0.04	b : 0.04	[ : 0.01	" : 0.01	y : 0.01	
c : 0.25	e : 0.18	d : 0.13	f : 0.12	g : 0.09	h : 0.06	= : 0.04	b : 0.04	y : 0.03	w : 0.01	a : 0.01	
v : 0.30	u : 0.13	c : 0.13	w : 0.10	y : 0.07	f : 0.06	t : 0.06	d : 0.04	e : 0.03	= : 0.01	g : 0.01	h : 0.01	
u : 0.31	v : 0.30	t : 0.13	w : 0.10	y : 0.07	= : 0.01	f : 0.01	c : 0.01	d : 0.01	
u : 0.31	v : 0.30	t : 0.19	w : 0.10	y : 0.07	
u : 0.31	v : 0.30	t : 0.19	w : 0.10	y : 0.07	
u : 0.31	v : 0.30	t : 0.19	w : 0.10	y : 0.07	
u : 0.31	v : 0.30	t : 0.19	w : 0.10	y : 0.07	
u : 0.31	v : 0.30	t : 0.19	w : 0.10	y : 0.07	
u : 0.31	v : 0.30	t : 0.19	w : 0.10	y : 0.07	
u : 0.31	v : 0.30	t : 0.19	w : 0.10	y : 0.07	
u : 0.31	v : 0.30	t : 0.19	w : 0.10	y : 0.07	
u : 0.31	v : 0.30	t : 0.19	w : 0.10	y : 0.07	
u : 0.31	v : 0.30	t : 0.13	w : 0.10	y : 0.07	e : 0.03	c : 0.01	b : 0.01	
v : 0.30	u : 0.18	c : 0.12	w : 0.10	e : 0.07	y : 0.07	t : 0.06	g : 0.04	b : 0.03	
c : 0.25	e : 0.16	d : 0.12	w : 0.09	y : 0.07	g : 0.06	f : 0.06	h : 0.06	= : 0.04	b : 0.03	a : 0.01	3 : 0.01	
c : 0.28	e : 0.16	d : 0.12	f : 0.12	g : 0.07	h : 0.06	y : 0.06	= : 0.04	] : 0.03	3 : 0.01	b : 0.01	
c : 0.19	e : 0.16	d : 0.12	f : 0.12	] : 0.10	g : 0.09	h : 0.06	= : 0.04	y : 0.04	a : 0.01	3 : 0.01	5 : 0.01	

#score	1442.7056643927692
#seq	66
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_CDS_m2_run2.txt

#BEAR
[ccc!!ccc"""cccnnnnnccc]ccc22ccc]d	chr14:99439582-99439893(-)$1	311	177	211	13.6631
:eeeeeccc[ddddoooooodddd]ccc]eeeee	chr11:86508933-86509260(-)$1	327	190	224	12.3761
[ccc[ccc"""cccnnnnnccc]ccc]cccccc4	chr10:122475428-122475713(-)$1	285	57	91	13.7641
a[eeeee[bb!!bboooooobb22bb]eeeee]a	chr18:82723822-82724244(+)$1	422	143	177	13.2061
::dddddddd[cccooooooccc333dddd]ddd	chr13:99043635-99043956(+)$1	321	93	127	13.0742
[bb[ccc!!ccc[aooooooa]ccc22ccc]bbc	chr13:93866636-93867016(-)$1	380	290	324	13.8073
####eeeee[ddddnnnnndddd333eeeeeggg	chr4:125862205-125862455(-)$1	250	54	88	12.2339
gggggg[bb[ddddoooooodddd]bb]gggggg	chr3:126474481-126474957(+)$1	476	58	92	13.7462
dddggggggg!!cccnnnnnccc]gggggggccc	chr1:34208944-34209263(+)$1	319	210	244	12.6700
$$$$ccc####cccnnnnnccc4444ccc333dd	chrX:50911825-50912166(+)$1	341	118	152	14.6450
c"""eeeee"""cccmmmmccc4444eeeee22c	chr10:66484413-66484742(-)$1	329	26	60	12.4525
cccc[==========lll==========ccc]cc	chr5:123318072-123318377(+)$1	305	26	60	13.0940
ccc"""ccc!!cccooooooccc4444ccc4444	chr3:108194200-108194527(-)$1	327	264	298	17.8113
[gggggggccc[cccnnnnnccc]ccc333gggg	chr4:75889471-75889785(-)$1	314	48	82	13.1587
$$$$dddd"""cccooooooccc333dddd5555	chr4:120561932-120562205(+)$1	273	140	174	14.0822
cceeeee[a"""bboooooobb333a]eeeee33	chr5:135499342-135499584(+)$1	242	101	135	15.7931
ggggg[dddd[aooooooadddd333ggggggg:	chr6:86625372-86625669(-)$1	297	83	117	12.6322
!!ffffff"""abboooooobb]a333ffffff]	chr18:12914476-12914865(-)$1	389	60	94	15.0183
hdddddddd!!cccooooooccc22dddd66666	chr8:125603240-125603534(+)$1	294	67	101	12.4939
[dddd[ccc"""bboooooobb333cccddddbb	chr6:17892715-17892981(+)$1	266	91	125	14.7832
ggccc[bb"""cccooooooccc22bb]ccc::H	chr5:8120945-8121224(-)$1	279	69	103	13.7320
===========!!cccmmmmccc22=========	chr12:60173619-60174051(+)$1	432	343	377	13.1058
b!!cccccc!!cccooooooccc]ccc]ccc22b	chr19:9001214-9001495(+)$1	281	71	105	16.7035
dd[ccc[gggggggooooooggggggg]ccc22d	chr6:87793839-87794252(-)$1	413	34	68	13.8768
eeee[ccc"""cccooooooccc333ccceeeee	chr2:49597357-49597650(+)$1	293	199	233	16.8833
$$$$$ffffffcccooooooccc333ffffff44	chr2:25322688-25322974(-)$1	286	94	128	14.8622
a[ffffff####bboooooobb333ffffff]a8	chr19:46605730-46605971(-)$1	241	95	129	14.6639
ggggggg####ddddmmmmdddd4444ggggggg	chr16:16318428-16318734(-)$1	306	129	163	12.3420
""eeeee[bb[cccoooooocccbbeeeee]===	chr4:137797433-137797725(+)$1	292	234	268	14.2692
diiiiiiiiiddddnnnnndddd333iiiiiiii	chr11:98218266-98218735(+)$1	469	58	92	13.3416
####ccc"""cccrrrrrrrrrccc]ccc4444c	chr4:134901005-134901347(-)$1	342	179	213	12.3551
!iiiiiiiii[cccooooooccciiiiiiiiidd	chr12:54248754-54249154(+)$1	400	55	89	16.6096
[iiiiiiiii[cccooooooccc333iiiiiiii	chr14:22612268-22612653(+)$1	385	71	105	18.2923
b[gggggggbbcccooooooccc666666bb22g	chr9:89899591-89899842(+)$1	251	153	187	12.4251
ggggggg"""ddddooooooddddggggggg]dd	chr5:8117579-8117860(-)$1	281	33	67	14.6591
!!ccc"""a[ddddnnnnndddd]a333ccc22d	chr8:98395700-98395975(-)$1	275	237	271	13.1018
::ccc[cccbbcccooooooccc]bb]ccc]ccc	chr17:65929882-65930150(-)$1	268	232	266	13.3124
a!!eeeee[a"""bbnnnnnbb333a]eeeee22	chr6:108382514-108382783(+)$1	269	203	237	12.3534
ccc[==========oooooo==========]ccc	chr16:30332280-30332575(-)$1	295	52	86	16.1043
"eeeee$$$$$cccooooooccceeeee333a22	chr17:15944363-15944648(-)$1	285	198	232	14.3247
bb[ccc"""eeeeeooooooeeeeeccc]bb333	chr8:127088048-127088346(-)$1	298	17	51	12.6480
ccc[gggggggcccooooooccc]ggggggg]cc	chr1:22278577-22279037(-)$1	460	376	410	15.9411
gggg"""bb[ddddoooooodddd]bb4444ggg	chr11:104169077-104169352(+)$1	275	155	189	13.5800
hhhhhh$$$$$cccooooooccc4444hhhhhhh	chr10:40551344-40551725(-)$1	381	258	292	14.0768
$$$$$dddd[ddddoooooodddd22dddd4444	chr1:137049266-137049547(+)$1	281	220	254	13.2782
e[cccbbccc[bboooooobb]ccc]bb4444cc	chr9:59240966-59241279(-)$1	313	164	198	11.8920
==="""ccc####bbnnnnnbb4444ccc333==	chr7:26100770-26101024(+)$1	254	85	119	14.1491
"""iiiiiiiii[annnnnaiiiiiiiii333dd	chr13:30632673-30632931(-)$1	258	4	38	13.4489
::============oooooo============gg	chr14:31926848-31927301(+)$1	453	165	199	14.6073
gggg!!ccc!!ddddlllddddccc22ggggggg	chr1:16450164-16450514(-)$1	350	298	332	11.6361
===============lll================	chrX:154372252-154372679(-)$1	427	349	383	13.6742
!!hhhhhhhh[cccooooooccchhhhhhhh22c	chr11:77635997-77636292(+)$1	295	153	187	13.2433
iiiiii[ccc!!bboooooobb22ccc]iiiiii	chr4:75603029-75603349(-)$1	320	153	187	15.4490
ff"""a[a"""cccooooooccc]aaffffff]f	chr19:4289567-4289829(-)$1	262	84	118	15.9230
f::ccc!!ccccccooooooccc22ccc22ccc:	chr10:20679687-20679950(+)$1	263	177	211	12.6577
b!!ddddgggggggooooooggggggg]dddd]b	chr9:54264395-54264709(-)$1	314	171	205	12.8760
!iiiiiiiii####bbmmmmbb4444iiiiiiii	chr2:129453578-129453827(+)$1	249	123	157	12.0038
##ccc!!ccc[ddddmmmmdddd333ccc22ccc	chr11:48619417-48619691(+)$1	274	223	257	12.2443

#otherMatches

#Seq PSSM
GUUUGUGAUAAAUAGAAAUACUACAUCUAGAAGU	chr14:99439582-99439893(-)$1	311	177	211	13.6631
UGAGAUGGAAGCUGAUCCUGUAGUCUCCUAUUUU	chr11:86508933-86509260(-)$1	327	190	224	12.3761
UCUUUUCUCCAAACAUCAAGUUCAGACAAGGCUC	chr10:122475428-122475713(-)$1	285	57	91	13.7641
GAUGUGAUGGCAUCACAGAAGAGACCCUCACAGC	chr18:82723822-82724244(+)$1	422	143	177	13.2061
UACUCUUGUAUUCACUCUUUUGACUUUGCACAGG	chr13:99043635-99043956(+)$1	321	93	127	13.0742
AGCCCAUAGUCCACAGAGAGGAGGAGCAUGUGCC	chr13:93866636-93867016(-)$1	380	290	324	13.8073
UAAAAUUUAAUUCAGUAAAUGGAAGCUAAAUAAG	chr4:125862205-125862455(-)$1	250	54	88	12.2339
CUCCUUGAGCAAUGUGUUUCUAUUACUGAAGGAG	chr3:126474481-126474957(+)$1	476	58	92	13.7462
UGAAGGUGAGUUGUCUUCUUGACUCUUACCUGUG	chr1:34208944-34209263(+)$1	319	210	244	12.6700
UGCAAGCUUCUGCCCAUAAGGCCUGCGCUGAUGC	chrX:50911825-50912166(+)$1	341	118	152	14.6450
UGUAGAAUAAAUGUAAGCAUACUAAAUAUUUGAA	chr10:66484413-66484742(-)$1	329	26	60	12.4525
UGCAUGGAUGCGGUCAUUGACUGUGUCCUGCUGG	chr5:123318072-123318377(+)$1	305	26	60	13.0940
AGCCCUGGAUUUGGGGCCUACCAUCCUUCCUCUC	chr3:108194200-108194527(-)$1	327	264	298	17.8113
UAGACGAUUGUAACAACACCUGUGACAGCUAUUG	chr4:75889471-75889785(-)$1	314	48	82	13.1587
GAGGGGCCCCAAGGCAAGGUCCUGCAGGUCAGUG	chr4:120561932-120562205(+)$1	273	140	174	14.0822
CGGGAGCAUGAAGGACCGAACCCAGGAGCUCCGC	chr5:135499342-135499584(+)$1	242	101	135	15.7931
UUUUUAUCAUAGGCAGUACAUGAAUCGAAAAGGC	chr6:86625372-86625669(-)$1	297	83	117	12.6322
AAGGUCCUAACCCCUACAGUGGAGCACAGGACUG	chr18:12914476-12914865(-)$1	389	60	94	15.0183
GCACAGAAUCAGCUUAAGAUGGCACGUUUCACCA	chr8:125603240-125603534(+)$1	294	67	101	12.4939
CUUCUGUGCCAACCUCUCAUGGACCGCAAGAAAG	chr6:17892715-17892981(+)$1	266	91	125	14.7832
UGGUUACCUCCUGUGCACAAACAUUGGCAACAUC	chr5:8120945-8121224(-)$1	279	69	103	13.7320
GCAUAAUUUUGUAAGAGUUAUUUAUCAAAAUUAU	chr12:60173619-60174051(+)$1	432	343	377	13.1058
CGGCAGGGCCAGGGCUCAGACCCAGCCAUUGAGG	chr19:9001214-9001495(+)$1	281	71	105	16.7035
UGAUUUGAGAACGGUGUUAUUUGUUCUGAGAAGC	chr6:87793839-87794252(-)$1	413	34	68	13.8768
UGAGAUCCGGGAGUGAGUUGGCUGGGGGGCUCAU	chr2:49597357-49597650(+)$1	293	199	233	16.8833
CUUCUUUCUUGGCAGAUAAGUGCAUUCAAGAGUA	chr2:25322688-25322974(-)$1	286	94	128	14.8622
GAUGGCAUGAACUGGGUCUGCAAGAAUGUCAACG	chr19:46605730-46605971(-)$1	241	95	129	14.6639
UGUUAAAUUGCAUGUUUUAACAUAUCUUUUAACA	chr16:16318428-16318734(-)$1	306	129	163	12.3420
AAAGGGUAUCAUGAUUGAAUUCAGAAUCUUACUU	chr4:137797433-137797725(+)$1	292	234	268	14.2692
GUCCUCUUUAUUUGUCUUUCAGAGCCUGGAGAGG	chr11:98218266-98218735(+)$1	469	58	92	13.3416
AAUUACUUGUAGAAAUCUUGACUCUUAGUUUUGU	chr4:134901005-134901347(-)$1	342	179	213	12.3551
AAGCUCGGGGCUGGCCUGACCCACCCUGGGCUGG	chr12:54248754-54249154(+)$1	400	55	89	16.6096
UAGGAGAGCGAGGAUUUGGUUCCCUAUGUUUUCU	chr14:22612268-22612653(+)$1	385	71	105	18.2923
GCAGGAUGUCCAUCUCAUUUGAUCACCAAGGCAA	chr9:89899591-89899842(+)$1	251	153	187	12.4251
UUAGUUUUAAACUCAGAUGAGAGUGAAUUAACGG	chr5:8117579-8117860(-)$1	281	33	67	14.6591
AACCCACACGUGGAUUCGCUCCAGGGAGGGGGAG	chr8:98395700-98395975(-)$1	275	237	271	13.1018
CCCGCGGUGACCAAUUUUUUUUGUGUGUACAGCG	chr17:65929882-65930150(-)$1	268	232	266	13.3124
GGAGCUGAUGACUGGAUCUCCCCCCCCUCAGCCA	chr6:108382514-108382783(+)$1	269	203	237	12.3534
CCCCUUGGGAAUAUGCUGCUGUGUUCUUAAUGGG	chr16:30332280-30332575(-)$1	295	52	86	16.1043
UGCAUUGAUGAUGGACAAGGCCAGGUGUCUGCUA	chr17:15944363-15944648(-)$1	285	198	232	14.3247
CUGCGCCCAGCUGGAGAACCCCAGUGUGGAGACA	chr8:127088048-127088346(-)$1	298	17	51	12.6480
AUCUUGUUGGAAGAACUUGAUCUGUCCAGCAUGG	chr1:22278577-22279037(-)$1	460	376	410	15.9411
GCAAAAUCUGAGAGAGGUAACUCUGGGUCCAUUG	chr11:104169077-104169352(+)$1	275	155	189	13.5800
AAAAGAUCCUAUUUUUGAAUAAAGCAUUCUUUUU	chr10:40551344-40551725(-)$1	381	258	292	14.0768
CUGAUGCAGAACCACACACAUGGUCCCUGUUAAU	chr1:137049266-137049547(+)$1	281	220	254	13.2782
UACAUUGAGGACUGAGACUGGCCCUGCAUAAAAU	chr9:59240966-59241279(-)$1	313	164	198	11.8920
UUCUCCGCGUCCCCUCCCUCAGCCCCUGCCCCGA	chr7:26100770-26101024(+)$1	254	85	119	14.1491
UUUUAAAUGGAGAGGCAAACCUCUGUUUGUGCGC	chr13:30632673-30632931(-)$1	258	4	38	13.4489
AAAUUUGUUGUGUCCUUCAAGGCAUGAUGGGUGG	chr14:31926848-31927301(+)$1	453	165	199	14.6073
ccuaggaucaucaguacugcuggguaauagguuu	chr1:16450164-16450514(-)$1	350	298	332	11.6361
auauauaauauauaugucauauauauuauauaua	chrX:154372252-154372679(-)$1	427	349	383	13.6742
CCUUUGCCUUACAGAAGCUGCUGAAGGUAAAAAA	chr11:77635997-77636292(+)$1	295	153	187	13.2433
AUGUAACUUUAAUGAGAGCCCAGAGGAAUUACAU	chr4:75603029-75603349(-)$1	320	153	187	15.4490
GUCCAGACACAGCCCCUUCCGGCAGCACAAGACC	chr19:4289567-4289829(-)$1	262	84	118	15.9230
UGCCCACUAAGCCUGAGUCAAGGUACUUCAUGGA	chr10:20679687-20679950(+)$1	263	177	211	12.6577
CGAUCCAUCUUGAUGAUUUAGUUAAGGUUGGAAG	chr9:54264395-54264709(-)$1	314	171	205	12.8760
ACGCCAGGGAAAUAACCCAGGUACAGUCUUUGGU	chr2:129453578-129453827(+)$1	249	123	157	12.0038
GAGCAGACCACUGGUGUUUACUAUCCUGGCAUGU	chr11:48619417-48619691(+)$1	274	223	257	12.2443

#DB
.(((..(((...(((.....))).)))..))).)	chr14:99439582-99439893(-)$1	1	177	211	13.6631
.((((((((.((((......)))).))).)))))	chr11:86508933-86509260(-)$1	1	190	224	12.3761
.(((.(((...(((.....))).))).)))))).	chr10:122475428-122475713(-)$1	1	57	91	13.7641
(.(((((.((..((......))..)).))))).)	chr18:82723822-82724244(+)$1	1	143	177	13.2061
..((((((((.(((......)))...)))).)))	chr13:99043635-99043956(+)$1	1	93	127	13.0742
.((.(((..(((.(......).)))..))).)))	chr13:93866636-93867016(-)$1	1	290	324	13.8073
....(((((.((((.....))))...))))))))	chr4:125862205-125862455(-)$1	1	54	88	12.2339
((((((.((.((((......)))).)).))))))	chr3:126474481-126474957(+)$1	1	58	92	13.7462
)))(((((((..(((.....))).)))))))(((	chr1:34208944-34209263(+)$1	1	210	244	12.6700
....(((....(((.....)))....)))...))	chrX:50911825-50912166(+)$1	1	118	152	14.6450
(...(((((...(((....)))....)))))..)	chr10:66484413-66484742(-)$1	1	26	60	12.4525
((((.((((((((((...))))))))))))).))	chr5:123318072-123318377(+)$1	1	26	60	13.0940
(((...(((..(((......)))....)))....	chr3:108194200-108194527(-)$1	1	264	298	17.8113
.((((((((((.(((.....))).)))...))))	chr4:75889471-75889785(-)$1	1	48	82	13.1587
....((((...(((......)))...))))....	chr4:120561932-120562205(+)$1	1	140	174	14.0822
(((((((.(...((......))...).)))))..	chr5:135499342-135499584(+)$1	1	101	135	15.7931
(((((.((((.(......)))))...))))))).	chr6:86625372-86625669(-)$1	1	83	117	12.6322
..((((((...(((......)).)...)))))).	chr18:12914476-12914865(-)$1	1	60	94	15.0183
(((((((((..(((......)))..)))).....	chr8:125603240-125603534(+)$1	1	67	101	12.4939
.((((.(((...((......))...)))))))))	chr6:17892715-17892981(+)$1	1	91	125	14.7832
))(((.((...(((......)))..)).)))..)	chr5:8120945-8121224(-)$1	1	69	103	13.7320
(((((((((((..(((....)))..)))))))))	chr12:60173619-60174051(+)$1	1	343	377	13.1058
(..((((((..(((......))).))).)))..)	chr19:9001214-9001495(+)$1	1	71	105	16.7035
((.(((.(((((((......))))))).)))..)	chr6:87793839-87794252(-)$1	1	34	68	13.8768
((((.(((...(((......)))...))))))))	chr2:49597357-49597650(+)$1	1	199	233	16.8833
.....(((((((((......)))...))))))..	chr2:25322688-25322974(-)$1	1	94	128	14.8622
(.((((((....((......))...)))))).).	chr19:46605730-46605971(-)$1	1	95	129	14.6639
(((((((....((((....))))....)))))))	chr16:16318428-16318734(-)$1	1	129	163	12.3420
..(((((.((.(((......)))))))))).)))	chr4:137797433-137797725(+)$1	1	234	268	14.2692
)(((((((((((((.....))))...))))))))	chr11:98218266-98218735(+)$1	1	58	92	13.3416
....(((...(((.........))).)))....)	chr4:134901005-134901347(-)$1	1	179	213	12.3551
.(((((((((.(((......))))))))))))))	chr12:54248754-54249154(+)$1	1	55	89	16.6096
.(((((((((.(((......)))...))))))))	chr14:22612268-22612653(+)$1	1	71	105	18.2923
(.((((((((((((......)))......))..)	chr9:89899591-89899842(+)$1	1	153	187	12.4251
(((((((...((((......))))))))))).))	chr5:8117579-8117860(-)$1	1	33	67	14.6591
..(((...(.((((.....)))).)...)))..)	chr8:98395700-98395975(-)$1	1	237	271	13.1018
..(((.((((((((......))).)).))).)))	chr17:65929882-65930150(-)$1	1	232	266	13.3124
(..(((((.(...((.....))...).)))))..	chr6:108382514-108382783(+)$1	1	203	237	12.3534
(((.((((((((((......)))))))))).)))	chr16:30332280-30332575(-)$1	1	52	86	16.1043
.(((((.....(((......))))))))...)..	chr17:15944363-15944648(-)$1	1	198	232	14.3247
((.(((...(((((......)))))))).))...	chr8:127088048-127088346(-)$1	1	17	51	12.6480
(((.((((((((((......))).))))))).))	chr1:22278577-22279037(-)$1	1	376	410	15.9411
((((...((.((((......)))).))....)))	chr11:104169077-104169352(+)$1	1	155	189	13.5800
((((((.....(((......)))....)))))))	chr10:40551344-40551725(-)$1	1	258	292	14.0768
.....((((.((((......))))..))))....	chr1:137049266-137049547(+)$1	1	220	254	13.2782
(.((((((((.((......)).))).))....))	chr9:59240966-59241279(-)$1	1	164	198	11.8920
(((...(((....((.....))....)))...))	chr7:26100770-26101024(+)$1	1	85	119	14.1491
...(((((((((.(.....))))))))))...))	chr13:30632673-30632931(-)$1	1	4	38	13.4489
..((((((((((((......))))))))))))((	chr14:31926848-31927301(+)$1	1	165	199	14.6073
((((..(((..((((...)))))))..)))))))	chr1:16450164-16450514(-)$1	1	298	332	11.6361
(((((((((((((((...))))))))))))))))	chrX:154372252-154372679(-)$1	1	349	383	13.6742
..((((((((.(((......)))))))))))..)	chr11:77635997-77636292(+)$1	1	153	187	13.2433
((((((.(((..((......))..))).))))))	chr4:75603029-75603349(-)$1	1	153	187	15.4490
((...(.(...(((......))).)))))))).)	chr19:4289567-4289829(-)$1	1	84	118	15.9230
)..(((..((((((......)))..)))..))).	chr10:20679687-20679950(+)$1	1	177	211	12.6577
(..(((((((((((......))))))).)))).)	chr9:54264395-54264709(-)$1	1	171	205	12.8760
.(((((((((....((....))....))))))))	chr2:129453578-129453827(+)$1	1	123	157	12.0038
..(((..(((.((((....))))...)))..)))	chr11:48619417-48619691(+)$1	1	223	257	12.2443

#PSSM
g : 0.12	[ : 0.10	c : 0.10	! : 0.08	: : 0.06	$ : 0.06	b : 0.06	a : 0.05	# : 0.05	d : 0.05	= : 0.05	" : 0.05	h : 0.03	e : 0.03	f : 0.03	i : 0.01	
g : 0.13	c : 0.12	! : 0.10	i : 0.08	[ : 0.06	: : 0.06	d : 0.06	$ : 0.06	e : 0.05	# : 0.05	" : 0.05	= : 0.05	b : 0.03	h : 0.01	f : 0.01	
c : 0.18	g : 0.13	e : 0.10	i : 0.08	d : 0.06	$ : 0.06	= : 0.06	" : 0.05	! : 0.05	# : 0.03	f : 0.03	[ : 0.03	h : 0.03	b : 0.01	: : 0.01	
c : 0.20	g : 0.15	e : 0.12	i : 0.10	d : 0.06	$ : 0.06	" : 0.06	[ : 0.05	= : 0.05	# : 0.03	f : 0.03	h : 0.03	
c : 0.20	e : 0.13	g : 0.13	i : 0.10	d : 0.08	" : 0.06	= : 0.06	[ : 0.05	! : 0.03	f : 0.03	$ : 0.03	h : 0.03	
c : 0.15	e : 0.13	g : 0.12	i : 0.10	d : 0.08	= : 0.08	" : 0.06	[ : 0.06	! : 0.05	f : 0.05	h : 0.03	b : 0.01	a : 0.01	
c : 0.22	e : 0.10	d : 0.10	g : 0.10	= : 0.08	i : 0.08	[ : 0.06	f : 0.05	" : 0.05	b : 0.03	$ : 0.03	! : 0.03	h : 0.01	
c : 0.22	g : 0.10	d : 0.08	= : 0.08	i : 0.08	" : 0.06	[ : 0.05	e : 0.05	b : 0.05	f : 0.05	! : 0.03	# : 0.03	$ : 0.03	h : 0.01	a : 0.01	
c : 0.22	" : 0.15	g : 0.08	= : 0.08	i : 0.08	b : 0.06	d : 0.06	# : 0.05	e : 0.03	a : 0.03	$ : 0.03	! : 0.01	f : 0.01	[ : 0.01	h : 0.01	
" : 0.20	[ : 0.10	c : 0.10	= : 0.08	i : 0.08	b : 0.06	g : 0.06	# : 0.06	! : 0.06	d : 0.03	$ : 0.03	f : 0.01	a : 0.01	e : 0.01	h : 0.01	
" : 0.18	d : 0.13	[ : 0.13	! : 0.12	# : 0.08	= : 0.08	c : 0.06	g : 0.05	b : 0.03	$ : 0.03	f : 0.01	e : 0.01	i : 0.01	
c : 0.39	d : 0.18	" : 0.08	! : 0.06	= : 0.06	# : 0.05	a : 0.03	g : 0.03	[ : 0.01	e : 0.01	b : 0.01	i : 0.01	
c : 0.44	d : 0.18	b : 0.12	= : 0.06	[ : 0.03	g : 0.03	# : 0.03	o : 0.01	! : 0.01	" : 0.01	e : 0.01	
c : 0.44	d : 0.18	b : 0.13	= : 0.06	a : 0.03	o : 0.03	g : 0.03	r : 0.01	e : 0.01	# : 0.01	
o : 0.65	n : 0.10	c : 0.08	d : 0.05	b : 0.05	= : 0.03	r : 0.01	
o : 0.65	n : 0.18	m : 0.05	l : 0.05	c : 0.01	r : 0.01	b : 0.01	
o : 0.65	n : 0.18	m : 0.08	l : 0.05	r : 0.01	
o : 0.65	n : 0.18	m : 0.08	l : 0.05	r : 0.01	
o : 0.63	n : 0.18	m : 0.08	= : 0.03	a : 0.01	r : 0.01	d : 0.01	
o : 0.62	d : 0.12	n : 0.08	c : 0.05	= : 0.03	m : 0.03	r : 0.01	b : 0.01	a : 0.01	
c : 0.44	d : 0.20	b : 0.17	= : 0.06	g : 0.03	a : 0.01	r : 0.01	e : 0.01	i : 0.01	
c : 0.44	d : 0.20	b : 0.15	= : 0.06	] : 0.03	g : 0.03	r : 0.01	e : 0.01	i : 0.01	
c : 0.46	d : 0.18	4 : 0.06	= : 0.06	3 : 0.06	] : 0.03	2 : 0.03	g : 0.03	e : 0.01	i : 0.01	
3 : 0.22	] : 0.13	4 : 0.12	2 : 0.10	d : 0.08	c : 0.08	= : 0.06	g : 0.03	i : 0.03	e : 0.03	a : 0.01	b : 0.01	6 : 0.01	h : 0.01	
3 : 0.24	c : 0.15	4 : 0.12	g : 0.08	2 : 0.08	= : 0.06	] : 0.05	b : 0.05	i : 0.03	a : 0.03	e : 0.03	6 : 0.01	h : 0.01	
3 : 0.18	c : 0.15	4 : 0.12	b : 0.08	g : 0.08	= : 0.08	2 : 0.05	a : 0.05	e : 0.03	] : 0.03	i : 0.03	d : 0.01	f : 0.01	6 : 0.01	h : 0.01	
c : 0.22	g : 0.10	] : 0.08	= : 0.08	i : 0.08	d : 0.06	e : 0.06	b : 0.06	4 : 0.05	f : 0.05	2 : 0.03	3 : 0.03	6 : 0.01	h : 0.01	
c : 0.22	e : 0.12	] : 0.10	g : 0.10	= : 0.08	i : 0.08	d : 0.06	f : 0.06	3 : 0.03	h : 0.03	2 : 0.01	6 : 0.01	4 : 0.01	b : 0.01	
c : 0.24	g : 0.12	e : 0.10	d : 0.10	i : 0.10	f : 0.06	= : 0.06	2 : 0.03	] : 0.03	3 : 0.03	4 : 0.03	h : 0.03	6 : 0.01	
c : 0.17	e : 0.13	g : 0.12	d : 0.08	3 : 0.08	i : 0.08	f : 0.06	= : 0.06	4 : 0.05	b : 0.03	h : 0.03	2 : 0.03	6 : 0.01	
c : 0.13	g : 0.13	e : 0.12	] : 0.08	4 : 0.08	i : 0.08	3 : 0.06	f : 0.06	= : 0.05	d : 0.03	b : 0.03	h : 0.03	5 : 0.01	6 : 0.01	2 : 0.01	
c : 0.12	g : 0.12	2 : 0.10	e : 0.08	i : 0.08	3 : 0.06	] : 0.06	4 : 0.06	= : 0.06	d : 0.05	f : 0.05	b : 0.01	5 : 0.01	6 : 0.01	: : 0.01	a : 0.01	h : 0.01	
c : 0.15	g : 0.13	2 : 0.13	d : 0.08	] : 0.06	4 : 0.06	= : 0.06	i : 0.06	e : 0.03	b : 0.03	3 : 0.03	5 : 0.01	f : 0.01	6 : 0.01	: : 0.01	a : 0.01	h : 0.01	
c : 0.18	d : 0.13	g : 0.13	4 : 0.06	= : 0.06	i : 0.06	b : 0.05	e : 0.03	3 : 0.03	: : 0.03	2 : 0.03	a : 0.01	5 : 0.01	] : 0.01	6 : 0.01	H : 0.01	8 : 0.01	h : 0.01	f : 0.01	

#score	805.155468074197
#seq	58
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_UTR_m2_run1.txt

#BEAR
ffffffwwwwwwwwwwwwwwffffff]a]	chr5:136384701-136384948(-)$1	247	18	47	21.3311
&&ffffffuuuuuuuuuuuuffffffhhh	chr2:179769256-179769476(+)$1	220	20	49	21.8640
$eeeeewwwwwwwwwwwwwweeeee22ii	chr11:105118110-105118352(+)$1	242	206	235	20.8292
eeee[acccuuuuuuuuuuuuccc]a]ee	chr2:180452940-180453160(+)$1	220	83	112	24.2155
::ggggggguuuuuuuuuuuuggggggg:	chr1:193733570-193733790(+)$1	220	51	80	22.0562
cc!!ddddvvvvvvvvvvvvvdddd4444	chr3:151897060-151897281(+)$1	221	73	102	23.7233
gg!!eeeeewwwwwwwwwwwwwweeeeeg	chr12:60060450-60060685(-)$1	235	186	215	21.7515
""bb[ddddtttttttttttddddbbiii	chr8:23679413-23679635(+)$1	222	105	134	23.0707
e:gggggggtttttttttttggggggg::	chr18:90712235-90712469(+)$1	234	178	207	21.7837
=====[a[attttttttttta]a======	chr11:77524425-77524646(+)$1	221	153	182	25.5299
ddddeeeeettttttttttteeeee333d	chr1:60133716-60133936(-)$1	220	22	51	23.3980
"dddd[cccvvvvvvvvvvvvvcccdddd	chr4:116372062-116372282(+)$1	220	175	204	22.9177
##gggggggtttttttttttggggggg>>	chr1:4836631-4836851(+)$1	220	137	166	24.3071
b[a[dddduuuuuuuuuuuudddda]bbg	chr12:81781348-81781568(+)$1	220	64	93	22.9618
iiiiiiiivvvvvvvvvvvvviiiiiiii	chr11:70754920-70755140(+)$1	220	163	192	24.5791
bbccc[bbwwwwwwwwwwwwwwbb]ccc]	chr3:145606749-145606970(+)$1	221	0	29	21.7553
ibb[eeeeettttttttttteeeee]bb8	chr1:65205800-65206029(-)$1	229	167	196	23.0581
%%gggggggtttttttttttggggggg77	chr19:41289253-41289480(-)$1	227	42	71	22.5619
"bb"""cccvvvvvvvvvvvvvccc5555	chr6:143154598-143154818(+)$1	220	156	185	20.9811
&&eeeeevvvvvvvvvvvvveeeee4444	chr9:95357753-95357985(-)$1	232	55	84	21.9922
fffff[bbwwwwwwwwwwwwwwbb]ffff	chr12:52475333-52475553(+)$1	220	85	114	21.6902
d"""eeeeeuuuuuuuuuuuueeeee333	chr2:29813979-29814207(+)$1	228	177	206	24.2479
dddd[ddddtttttttttttdddd]dddd	chr13:29999785-30000005(-)$1	220	85	114	22.6337
!!bb!!cccvvvvvvvvvvvvvccc22bb	chr15:99843543-99843763(+)$1	220	173	202	23.3701
c[ffffffvvvvvvvvvvvvvffffff]c	chr8:81033260-81033480(+)$1	220	76	105	23.7523
eeefffffftttttttttttffffff444	chrX:68670494-68670719(+)$1	225	102	131	23.6687
gggffffffwwwwwwwwwwwwwwffffff	chr8:106750903-106751123(-)$1	220	102	131	21.7212
ffffffbbwwwwwwwwwwwwwwbb]ffff	chr16:27450927-27451147(+)$1	220	29	58	21.5006
fffffyyyyyyyyyyyyyyyyffffff33	chr10:77890212-77890432(+)$1	220	172	201	21.6292
cc[fffffftttttttttttffffffccc	chr2:29699245-29699466(+)$1	221	56	85	23.6843
iiiiiyyyyyyyyyyyyyyyyiiiiiiii	chr12:92797616-92797836(-)$1	220	118	147	22.2556
=========wwwwwwwwwwwwww======	chr18:14784758-14784978(-)$1	220	149	178	23.3325
:bb!!ddddtttttttttttdddd]bb::	chr3:32238170-32238407(-)$1	237	70	99	20.6583
ggggg[ccctttttttttttccc]ggggg	chr8:63391749-63391983(-)$1	234	192	221	24.8411
[bbfffffftttttttttttffffff]bb	chr2:119474919-119475142(+)$1	223	111	140	23.3403
iiiiiiiiitttttttttttiiiiiiiii	chr5:100982773-100983017(-)$1	244	105	134	24.5576
iiiiiiiivvvvvvvvvvvvviiiiiiii	chr18:61747158-61747378(+)$1	220	162	191	24.5791
ccc[eeeeettttttttttteeeee]ccc	chr7:133635577-133635798(-)$1	221	89	118	23.9277
ddddd[cccwwwwwwwwwwwwwwcccddd	chr4:11098864-11099088(+)$1	224	143	172	21.2064
[bb!!ddddtttttttttttdddd22bb]	chr7:71353178-71353398(+)$1	220	138	167	23.0083
[ddddddddtttttttttttdddd]dddd	chr16:13537957-13538178(-)$1	221	151	180	22.6246
ffffffcccwwwwwwwwwwwwwwccc]ff	chr17:29771531-29771751(+)$1	220	110	139	21.9723
ccc[bb[bbtttttttttttbbbb]ccc]	chr12:8757444-8757664(+)$1	220	37	66	22.6102
fff!!dddduuuuuuuuuuuudddd]fff	chr11:53229899-53230119(+)$1	220	161	190	23.5137
hh[a[ddddtttttttttttdddd]a]hh	chr11:100337684-100337904(-)$1	220	136	165	23.1173
iiiiiiiiiwwwwwwwwwwwwwwiiiiii	chr15:58287976-58288196(+)$1	220	77	106	22.7966
=========ttttttttttt=========	chr19:47809692-47809923(+)$1	231	87	116	25.2990
d[eeeeeyyyyyyyyyyyyyyyyeeeeed	chrX:70331833-70332073(-)$1	240	115	144	21.3516
gggg!!ccctttttttttttccc]ggggg	chr4:118109571-118109791(-)$1	220	110	139	24.8089
ee[bb[bbyyyyyyyyyyyyyyyybb]bb	chr12:34122929-34123149(+)$1	220	84	113	20.2186
ccc[ddddwwwwwwwwwwwwwwdddd]cc	chr9:50571846-50572066(-)$1	220	66	95	22.1854
:ggggggguuuuuuuuuuuugggggggBB	chr1:162901221-162901441(+)$1	220	2	31	21.6780
c[gggggggtttttttttttggggggg]c	chr3:26996880-26997100(-)$1	220	56	85	24.5456
eeeffffffuuuuuuuuuuuuffffff]e	chr16:96214626-96214847(-)$1	221	15	44	23.5145
eeeeeyyyyyyyyyyyyyyyyeeeee444	chr11:87793846-87794066(-)$1	220	19	48	21.4342

#otherMatches

#Seq PSSM
CUUCUCCUUCCUUUACUGUUGAGAAGUGU	chr5:136384701-136384948(-)$1	247	18	47	21.3311
AGGCAAAGGCUCAAUCCUCACUUUGUAAC	chr2:179769256-179769476(+)$1	220	20	49	21.8640
UUCAAUAUUGAGAACUGUGAGUUGAUAUC	chr11:105118110-105118352(+)$1	242	206	235	20.8292
GGCAGACAGACAUGAACAUUACUGAUGUG	chr2:180452940-180453160(+)$1	220	83	112	24.2155
AUCAUCUUUGUGAGUCUUGAAAAAGAUGU	chr1:193733570-193733790(+)$1	220	51	80	22.0562
AGCUCAUUGUGGAUGUUUUGAAAUGUUUU	chr3:151897060-151897281(+)$1	221	73	102	23.7233
AUUGGAUUUAUUUUAUGGCUUAAGAAUUA	chr12:60060450-60060685(-)$1	235	186	215	21.7515
GUGCCAGUGUUGCAUCUUCCCAUUGCUUG	chr8:23679413-23679635(+)$1	222	105	134	23.0707
UAAGACUUAAAUAACAGGACUGAGUUUGC	chr18:90712235-90712469(+)$1	234	178	207	21.7837
GCGCgugucugugugucugugucugugug	chr11:77524425-77524646(+)$1	221	153	182	25.5299
CAGAGCAUUAAAACAAUGUAGAUGUUAAU	chr1:60133716-60133936(-)$1	220	22	51	23.3980
UGUGUACCAUUUACCUGCCUGUUGGAUAC	chr4:116372062-116372282(+)$1	220	175	204	22.9177
UUUUUCACAGUUUCUAUCAAUGUGAAAUA	chr1:4836631-4836851(+)$1	220	137	166	24.3071
UUGUCUACAGCACACUCUUAGUAGCCAGA	chr12:81781348-81781568(+)$1	220	64	93	22.9618
CUGGCUGCAGGCUACCCGAGAGCAGCCAG	chr11:70754920-70755140(+)$1	220	163	192	24.5791
CCCUCUUCAAGAUGAUGACAAAGAUGAGC	chr3:145606749-145606970(+)$1	221	0	29	21.7553
AUUGCCACCUUAAUGAAUGUGGUGGGGAA	chr1:65205800-65206029(-)$1	229	167	196	23.0581
UUGUGGAUGGCUUCAAGUAACAUCUAUUU	chr19:41289253-41289480(-)$1	227	42	71	22.5619
AACGUUGGCAUUUAUUUAUUUAGCCUCUC	chr6:143154598-143154818(+)$1	220	156	185	20.9811
AUAUGGCAAUCCUUCUUUCAGCCGUUUUC	chr9:95357753-95357985(-)$1	232	55	84	21.9922
CAAUAGACACCUUUUAUUUCAAGUGUGUU	chr12:52475333-52475553(+)$1	220	85	114	21.6902
AAUAAGGCUUUUAUAGUUCACAGCCUCUG	chr2:29813979-29814207(+)$1	228	177	206	24.2479
GUAUGUUUGGGAAGAAAAAACAAAGGUGC	chr13:29999785-30000005(-)$1	220	85	114	22.6337
cugugcgggcauaaaucuccaacccuggc	chr15:99843543-99843763(+)$1	220	173	202	23.3701
GAGUGGCAAUUUGACUUGCUCUGCUGCAU	chr8:81033260-81033480(+)$1	220	76	105	23.7523
CAAUGGAGUGUUGUCCUCUAACUCUGGUA	chrX:68670494-68670719(+)$1	225	102	131	23.6687
GUGCAUCUGGAAAAGACUGGACACAGAUG	chr8:106750903-106751123(-)$1	220	102	131	21.7212
GGGCAAGCUUAAUUAUGUAACUGUGUUGC	chr16:27450927-27451147(+)$1	220	29	58	21.5006
UUUAAUUUUUUUCCCCUUUGUUUGAAAAA	chr10:77890212-77890432(+)$1	220	172	201	21.6292
GGCUGGCCUCCCCCCCACAUAGGCCACCA	chr2:29699245-29699466(+)$1	221	56	85	23.6843
AUUUUAAUUCACUUGUAUAAGAAAAUUUA	chr12:92797616-92797836(-)$1	220	118	147	22.2556
CUUGUGCUUUAACUUUCUUAACUGGGCAC	chr18:14784758-14784978(-)$1	220	149	178	23.3325
CCCUCCUGUAUAUACAGAAAACAGUGGAC	chr3:32238170-32238407(-)$1	237	70	99	20.6583
UUCUUCUUUCAAAAAAAAAAAAAAAAGGA	chr8:63391749-63391983(-)$1	234	192	221	24.8411
AGAAUCUUAGCAUGAGAAAAUAAGAUAUC	chr2:119474919-119475142(+)$1	223	111	140	23.3403
AAUUAGAGAACGGUGAAAUCUUUCUAGUU	chr5:100982773-100983017(-)$1	244	105	134	24.5576
UUUCUAUUGCAUUUUUUUUCAAGUGGAAA	chr18:61747158-61747378(+)$1	220	162	191	24.5791
CAGCUCCCCUUCCACCCCCCGGGGAACUG	chr7:133635577-133635798(-)$1	221	89	118	23.9277
GGGUCAUAUGUUGGUAACUUGAAAUAGAC	chr4:11098864-11099088(+)$1	224	143	172	21.2064
AAAUACUGCGACGAAGGAGGGUAGGUUUG	chr7:71353178-71353398(+)$1	220	138	167	23.0083
UGACUGAUGCACAUCCCCUCCAUCUGGUC	chr16:13537957-13538178(-)$1	221	151	180	22.6246
GUUCUCAGCCACAUGAACGACUUGCUGGA	chr17:29771531-29771751(+)$1	220	110	139	21.9723
AGUGAUAGCUCAGCAUUUACGCAUGAUUG	chr12:8757444-8757664(+)$1	220	37	66	22.6102
CCUCAUCAAUGAUGUAUGCUUUUGACAGG	chr11:53229899-53230119(+)$1	220	161	190	23.5137
UCUGCAUCUGUAACCCACAAAGAUUCUGG	chr11:100337684-100337904(-)$1	220	136	165	23.1173
GAUCAGGGCUCUUAAUCUCAUUUGCUUUG	chr15:58287976-58288196(+)$1	220	77	106	22.7966
uaaguauaaaaaaauuaaaauuGUGUUUA	chr19:47809692-47809923(+)$1	231	87	116	25.2990
ACGUGGCUUGAAUCAGUGGAAAUGCCAUU	chrX:70331833-70332073(-)$1	240	115	144	21.3516
CUGGACGCACCCAUCCCCAAUGCCCCGGU	chr4:118109571-118109791(-)$1	220	110	139	24.8089
AUGGGACAUUCACAAAUAAAUACUUGAUU	chr12:34122929-34123149(+)$1	220	84	113	20.2186
CUCCUGCUGUGUAUAUGAUCCAAGCGUGA	chr9:50571846-50572066(-)$1	220	66	95	22.1854
UAGGCUCAGUCUGUUUUCCGUGAGUCUCU	chr1:162901221-162901441(+)$1	220	2	31	21.6780
AAAUACUAUUGUGUAUUUGUAUAGUAUCU	chr3:26996880-26997100(-)$1	220	56	85	24.5456
UGCUGAAUUUUAACUGGGUCUGAUUUAUG	chr16:96214626-96214847(-)$1	221	15	44	23.5145
UACGUUUGUGUUUGUCUGUGUGCGUGUGU	chr11:87793846-87794066(-)$1	220	19	48	21.4342

#DB
((((((..............)))))).).	chr5:136384701-136384948(-)$1	1	18	47	21.3311
..((((((............)))))))))	chr2:179769256-179769476(+)$1	1	20	49	21.8640
.(((((..............)))))..))	chr11:105118110-105118352(+)$1	1	206	235	20.8292
((((.((((............))).).))	chr2:180452940-180453160(+)$1	1	83	112	24.2155
..(((((((............))))))).	chr1:193733570-193733790(+)$1	1	51	80	22.0562
((..((((.............))))....	chr3:151897060-151897281(+)$1	1	73	102	23.7233
((..(((((..............))))))	chr12:60060450-60060685(-)$1	1	186	215	21.7515
..((.((((...........)))))))))	chr8:23679413-23679635(+)$1	1	105	134	23.0707
).(((((((...........)))))))..	chr18:90712235-90712469(+)$1	1	178	207	21.7837
(((((.(.(...........).)))))))	chr11:77524425-77524646(+)$1	1	153	182	25.5299
(((((((((...........)))))...)	chr1:60133716-60133936(-)$1	1	22	51	23.3980
.((((.(((.............)))))))	chr4:116372062-116372282(+)$1	1	175	204	22.9177
..(((((((...........)))))))..	chr1:4836631-4836851(+)$1	1	137	166	24.3071
(.(.((((............))))).)))	chr12:81781348-81781568(+)$1	1	64	93	22.9618
((((((((.............))))))))	chr11:70754920-70755140(+)$1	1	163	192	24.5791
(((((.((..............)).))).	chr3:145606749-145606970(+)$1	1	0	29	21.7553
(((.(((((...........))))).)).	chr1:65205800-65206029(-)$1	1	167	196	23.0581
..(((((((...........)))))))..	chr19:41289253-41289480(-)$1	1	42	71	22.5619
.((...(((.............)))....	chr6:143154598-143154818(+)$1	1	156	185	20.9811
..(((((.............)))))....	chr9:95357753-95357985(-)$1	1	55	84	21.9922
(((((.((..............)).))))	chr12:52475333-52475553(+)$1	1	85	114	21.6902
(...(((((............)))))...	chr2:29813979-29814207(+)$1	1	177	206	24.2479
((((.((((...........)))).))))	chr13:29999785-30000005(-)$1	1	85	114	22.6337
..((..(((.............)))..))	chr15:99843543-99843763(+)$1	1	173	202	23.3701
(.((((((.............)))))).)	chr8:81033260-81033480(+)$1	1	76	105	23.7523
(((((((((...........))))))...	chrX:68670494-68670719(+)$1	1	102	131	23.6687
)))((((((..............))))))	chr8:106750903-106751123(-)$1	1	102	131	21.7212
((((((((..............)).))))	chr16:27450927-27451147(+)$1	1	29	58	21.5006
(((((................))))))..	chr10:77890212-77890432(+)$1	1	172	201	21.6292
((.((((((...........)))))))))	chr2:29699245-29699466(+)$1	1	56	85	23.6843
(((((................))))))))	chr12:92797616-92797836(-)$1	1	118	147	22.2556
(((((((((..............))))))	chr18:14784758-14784978(-)$1	1	149	178	23.3325
.((..((((...........)))).))..	chr3:32238170-32238407(-)$1	1	70	99	20.6583
(((((.(((...........))).)))))	chr8:63391749-63391983(-)$1	1	192	221	24.8411
.((((((((...........)))))).))	chr2:119474919-119475142(+)$1	1	111	140	23.3403
(((((((((...........)))))))))	chr5:100982773-100983017(-)$1	1	105	134	24.5576
((((((((.............))))))))	chr18:61747158-61747378(+)$1	1	162	191	24.5791
(((.(((((...........))))).)))	chr7:133635577-133635798(-)$1	1	89	118	23.9277
)((((.(((..............))))))	chr4:11098864-11099088(+)$1	1	143	172	21.2064
.((..((((...........))))..)).	chr7:71353178-71353398(+)$1	1	138	167	23.0083
.((((((((...........)))).))))	chr16:13537957-13538178(-)$1	1	151	180	22.6246
(((((((((..............))).))	chr17:29771531-29771751(+)$1	1	110	139	21.9723
(((.((.((...........)))).))).	chr12:8757444-8757664(+)$1	1	37	66	22.6102
(((..((((............)))).)))	chr11:53229899-53230119(+)$1	1	161	190	23.5137
((.(.((((...........)))).).))	chr11:100337684-100337904(-)$1	1	136	165	23.1173
(((((((((..............))))))	chr15:58287976-58288196(+)$1	1	77	106	22.7966
(((((((((...........)))))))))	chr19:47809692-47809923(+)$1	1	87	116	25.2990
(.(((((................))))))	chrX:70331833-70332073(-)$1	1	115	144	21.3516
((((..(((...........))).)))))	chr4:118109571-118109791(-)$1	1	110	139	24.8089
((.((.((................)).))	chr12:34122929-34123149(+)$1	1	84	113	20.2186
(((.((((..............)))).))	chr9:50571846-50572066(-)$1	1	66	95	22.1854
.(((((((............)))))))((	chr1:162901221-162901441(+)$1	1	2	31	21.6780
(.(((((((...........))))))).)	chr3:26996880-26997100(-)$1	1	56	85	24.5456
(((((((((............)))))).)	chr16:96214626-96214847(-)$1	1	15	44	23.5145
(((((................)))))...	chr11:87793846-87794066(-)$1	1	19	48	21.4342

#PSSM
c : 0.12	f : 0.10	e : 0.10	i : 0.10	d : 0.09	g : 0.07	: : 0.05	" : 0.05	= : 0.05	[ : 0.05	& : 0.03	b : 0.03	$ : 0.01	# : 0.01	% : 0.01	! : 0.01	h : 0.01	
f : 0.10	e : 0.10	b : 0.10	c : 0.09	g : 0.09	d : 0.09	i : 0.09	[ : 0.07	= : 0.05	& : 0.03	: : 0.03	" : 0.03	# : 0.01	% : 0.01	! : 0.01	h : 0.01	
g : 0.16	f : 0.14	e : 0.12	b : 0.12	d : 0.09	i : 0.09	c : 0.07	= : 0.05	[ : 0.05	! : 0.03	a : 0.01	" : 0.01	
f : 0.21	g : 0.14	e : 0.09	! : 0.09	d : 0.09	[ : 0.09	i : 0.09	b : 0.05	= : 0.05	" : 0.03	c : 0.01	a : 0.01	
f : 0.21	e : 0.16	g : 0.12	d : 0.10	i : 0.09	! : 0.09	[ : 0.07	= : 0.05	b : 0.03	c : 0.01	" : 0.01	
f : 0.18	d : 0.18	e : 0.14	[ : 0.12	g : 0.10	i : 0.07	y : 0.05	! : 0.03	= : 0.03	a : 0.01	" : 0.01	b : 0.01	
d : 0.18	c : 0.14	f : 0.12	e : 0.12	g : 0.10	i : 0.07	b : 0.07	y : 0.05	w : 0.03	= : 0.03	a : 0.01	[ : 0.01	
d : 0.18	c : 0.14	f : 0.12	g : 0.10	e : 0.09	b : 0.09	i : 0.07	y : 0.07	w : 0.03	= : 0.03	[ : 0.01	v : 0.01	
c : 0.14	d : 0.12	w : 0.10	g : 0.09	v : 0.09	e : 0.09	f : 0.09	y : 0.09	u : 0.05	= : 0.03	i : 0.03	a : 0.01	b : 0.01	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
t : 0.40	w : 0.21	u : 0.14	v : 0.14	y : 0.09	
w : 0.18	v : 0.12	d : 0.12	f : 0.09	e : 0.09	u : 0.09	g : 0.09	y : 0.09	c : 0.03	a : 0.01	i : 0.01	b : 0.01	= : 0.01	
w : 0.18	d : 0.16	f : 0.14	e : 0.12	g : 0.10	i : 0.07	c : 0.05	v : 0.05	y : 0.03	] : 0.01	b : 0.01	= : 0.01	
d : 0.18	f : 0.14	e : 0.12	c : 0.10	g : 0.10	w : 0.10	i : 0.07	b : 0.07	y : 0.03	a : 0.01	= : 0.01	
d : 0.18	f : 0.16	e : 0.16	c : 0.10	g : 0.10	i : 0.09	b : 0.07	= : 0.05	] : 0.03	y : 0.01	
f : 0.16	e : 0.16	] : 0.16	g : 0.14	c : 0.09	i : 0.09	d : 0.05	= : 0.05	b : 0.03	a : 0.01	2 : 0.01	
f : 0.20	g : 0.14	i : 0.09	e : 0.07	d : 0.07	] : 0.07	c : 0.07	2 : 0.05	b : 0.05	= : 0.05	a : 0.03	4 : 0.03	3 : 0.01	5 : 0.01	
g : 0.14	] : 0.12	f : 0.12	i : 0.10	4 : 0.07	d : 0.07	b : 0.07	c : 0.07	= : 0.05	2 : 0.03	e : 0.03	3 : 0.03	h : 0.01	5 : 0.01	
i : 0.12	b : 0.10	c : 0.09	f : 0.09	4 : 0.07	d : 0.07	e : 0.05	g : 0.05	= : 0.05	3 : 0.05	] : 0.05	h : 0.03	: : 0.03	a : 0.01	> : 0.01	7 : 0.01	5 : 0.01	B : 0.01	
i : 0.12	d : 0.10	f : 0.09	c : 0.09	] : 0.07	4 : 0.07	g : 0.07	: : 0.05	= : 0.05	b : 0.05	h : 0.03	e : 0.03	3 : 0.03	> : 0.01	8 : 0.01	7 : 0.01	5 : 0.01	B : 0.01	

#score	1255.9460376002992
#seq	55
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_transcript_m2_run2.txt

#BEAR
ffff[auuuuuuuuuuuuaffffff	chr13:58188463-58188664(-)$1	201	77	102	23.2503
gggggggtttttttttttggggggg	chr4:77696029-77696230(-)$1	201	125	150	22.6470
iiiiiivvvvvvvvvvvvviiiiii	chr13:32905897-32906098(+)$1	201	83	108	24.2021
$eeeeeuuuuuuuuuuuueeeee66	chr18:13151333-13151534(+)$1	201	155	180	23.0634
ff[a[auuuuuuuuuuuua]a]fff	chr13:59235138-59235339(+)$1	201	49	74	23.4380
[cccyyyyyyyyyyyyyyyyccc]=	chr7:103421307-103421508(+)$1	201	88	113	21.0271
dd[bbyyyyyyyyyyyyyyyybb]d	chrX:153985942-153986143(-)$1	201	42	67	19.5259
::dddduuuuuuuuuuuuddddeee	chr16:94662096-94662297(+)$1	201	89	114	21.4653
hhhhhhvvvvvvvvvvvvvhhhhhh	chr19:32899916-32900117(+)$1	201	11	36	22.4361
ffffffvvvvvvvvvvvvvffffff	chr4:110343616-110343817(+)$1	201	88	113	23.1972
ddd[bbtttttttttttbb]dddd3	chr5:84494815-84495016(-)$1	201	103	128	21.2264
FFFcccuuuuuuuuuuuucccdddd	chr6:32419648-32419849(-)$1	201	13	38	22.5946
cc[cccuuuuuuuuuuuuccc]ccc	chr13:18841462-18841663(+)$1	201	50	75	23.9872
eeeeeevvvvvvvvvvvvveeeee:	chr16:67601856-67602057(-)$1	201	109	134	23.7657
[ddddyyyyyyyyyyyyyyyydddd	chr3:30717892-30718093(+)$1	201	3	28	20.6030
gggggggtttttttttttggggggg	chrX:143448542-143448743(+)$1	201	25	50	22.6470
fffffftttttttttttffffff]b	chr1:58583108-58583309(-)$1	201	11	36	21.5064
iiiiiiitttttttttttiiiiiii	chr14:19649297-19649498(-)$1	201	127	152	22.4771
dddcccuuuuuuuuuuuuccc]ddd	chr12:90808461-90808662(+)$1	201	61	86	23.7235
ffffffuuuuuuuuuuuuffffff:	chr8:96492731-96492932(+)$1	201	130	155	21.9687
c[ddddtttttttttttdddd]ccc	chr9:55906554-55906755(+)$1	201	160	185	21.9478
ffffffvvvvvvvvvvvvvffffff	chr2:29856703-29856904(+)$1	201	119	144	23.1972
Feeeeettttttttttteeeeeeee	chr4:141317792-141317993(-)$1	201	39	64	22.4739
!ddddwwwwwwwwwwwwwwdddd]e	chr13:74459705-74459906(-)$1	201	130	155	22.9267
ddd[ccctttttttttttcccdddd	chr9:45666982-45667183(+)$1	201	141	166	22.6578
dd[ddddtttttttttttddddddd	chr2:103988491-103988692(-)$1	201	90	115	22.0541
eeeeevvvvvvvvvvvvveeeee33	chr1:58647734-58647935(+)$1	201	77	102	24.2540
[bb[bbtttttttttttbbbb]ddd	chr15:99328883-99329084(-)$1	201	104	129	20.4530
[eeeeevvvvvvvvvvvvveeeeee	chr3:151842891-151843092(-)$1	201	71	96	24.8099
ggggggvvvvvvvvvvvvvgggggg	chr3:95434177-95434378(+)$1	201	91	116	24.3619
:eeeeeuuuuuuuuuuuueeeee::	chr9:10209205-10209406(-)$1	201	111	136	21.5612
eeeeevvvvvvvvvvvvveeeee::	chr1:178686355-178686556(-)$1	201	119	144	22.4309
hhhhhhwwwwwwwwwwwwwwhhhhh	chr6:126588255-126588456(-)$1	201	170	195	21.0148
Eeeeeevvvvvvvvvvvvveeeee:	chr4:56973510-56973711(-)$1	201	175	200	22.8811
eeeeevvvvvvvvvvvvveeeee]c	chr4:104023054-104023255(+)$1	201	45	70	24.4578
:ddddyyyyyyyyyyyyyyyydddd	chr11:118657267-118657468(-)$1	201	91	116	19.4795
eeeeevvvvvvvvvvvvveeeee]c	chr6:80061489-80061690(+)$1	201	9	34	24.4578
"eeeeeuuuuuuuuuuuueeeee22	chr9:68685905-68686106(+)$1	201	113	138	23.9760
ee[cccuuuuuuuuuuuuccc]eee	chr7:65053135-65053336(+)$1	201	166	191	24.1903
gggggguuuuuuuuuuuuggggggg	chr4:36664008-36664209(-)$1	201	15	40	23.9142
eeecccvvvvvvvvvvvvvccc]ee	chr12:45502637-45502838(+)$1	201	113	138	24.3821
c[eeeeettttttttttteeeee]c	chr10:70718463-70718664(-)$1	201	31	56	23.2634
[eeeeeuuuuuuuuuuuueeeee]c	chr15:98372794-98372995(-)$1	201	141	166	24.7115
[cccwwwwwwwwwwwwwwccccccf	chr10:77801932-77802133(-)$1	201	131	156	22.0847
hhhhhhvvvvvvvvvvvvvhhhhhh	chr7:63231792-63231993(-)$1	201	125	150	22.4361
[eeeeeuuuuuuuuuuuueeeee]d	chr9:68531223-68531424(+)$1	201	76	101	24.6458
"eeeeeuuuuuuuuuuuueeeee]i	chr4:77162678-77162879(-)$1	201	29	54	24.5276
eeeeevvvvvvvvvvvvveeeeeee	chr14:16231577-16231778(-)$1	201	59	84	24.1707
cc[cccvvvvvvvvvvvvvccc22c	chr3:109652933-109653134(-)$1	201	77	102	23.9923
gggggggtttttttttttggggggg	chr10:90612024-90612225(-)$1	201	38	63	22.6470
ffffffvvvvvvvvvvvvvffffff	chr2:24686211-24686412(-)$1	201	132	157	23.1972
eeeddddtttttttttttdddd]ee	chr1:133832012-133832213(+)$1	201	35	60	22.3288
""cccvvvvvvvvvvvvvccc]eee	chr2:77730631-77730832(-)$1	201	51	76	23.8197
cc[cccvvvvvvvvvvvvvcccccc	chr17:71167758-71167959(+)$1	201	70	95	24.2782
dd[cccuuuuuuuuuuuucccdddd	chr16:93718667-93718868(+)$1	201	87	112	23.7965
[ddddwwwwwwwwwwwwwwdddd]e	chr8:16996630-16996831(-)$1	201	89	114	22.9667
ddd[bbwwwwwwwwwwwwwwbb]dd	chr16:56008835-56009036(+)$1	201	64	89	21.1777
ggggggvvvvvvvvvvvvvgggggg	chr10:59596116-59596317(+)$1	201	9	34	24.3619
deeeeevvvvvvvvvvvvveeeee:	chr2:14998438-14998639(+)$1	201	114	139	23.7057
gggggggtttttttttttggggggg	chr7:65081162-65081363(+)$1	201	91	116	22.6470
[adddduuuuuuuuuuuudddd]a]	chr6:8544122-8544323(+)$1	201	58	83	23.3698
""cccwwwwwwwwwwwwwwccc22c	chr16:52202469-52202670(+)$1	201	85	110	22.4584
d[ddddvvvvvvvvvvvvvdddd]d	chr11:17099884-17100085(+)$1	201	13	38	23.9364
[cccyyyyyyyyyyyyyyyyccc]b	chr10:118963288-118963489(+)$1	201	110	135	20.8173

#otherMatches

#Seq PSSM
UGUCACUCCUAUAUCCAUGGACAUA	chr13:58188463-58188664(-)$1	201	77	102	23.2503
UGGUAAUUUUAAGUCUCUGUUACUA	chr4:77696029-77696230(-)$1	201	125	150	22.6470
UUUCUUUUAAUUCAUCUUCAAGAAA	chr13:32905897-32906098(+)$1	201	83	108	24.2021
cuggguacauuguaaCAAACCCAUU	chr18:13151333-13151534(+)$1	201	155	180	23.0634
UACAGUGUUUAAAAAAAAAGUUUGU	chr13:59235138-59235339(+)$1	201	49	74	23.4380
UCUAUGCCCAUUUCAUCCUCUAGCC	chr7:103421307-103421508(+)$1	201	88	113	21.0271
UAAGGUUUUUAUUUUAAUCAUCCAU	chrX:153985942-153986143(-)$1	201	42	67	19.5259
ACCUCAUUCUGUCAUUCCUGAGAGA	chr16:94662096-94662297(+)$1	201	89	114	21.4653
UUAAAAUAAAGCUGCAUAUUUUUAA	chr19:32899916-32900117(+)$1	201	11	36	22.4361
ACAUUUACCAUUUCAUCUAAAAUGU	chr4:110343616-110343817(+)$1	201	88	113	23.1972
CAGCACUGUCUUCCUUUGUACUGAU	chr5:84494815-84495016(-)$1	201	103	128	21.2264
UGUGGGUUGACUUAAUUUCCCGUGC	chr6:32419648-32419849(-)$1	201	13	38	22.5946
uaaucuauucaguccauaagaaugu	chr13:18841462-18841663(+)$1	201	50	75	23.9872
UUUGUUUCCACAAGAUAAUGACAAC	chr16:67601856-67602057(-)$1	201	109	134	23.7657
AGCUGGGGGACUAAAUAAGUACAGC	chr3:30717892-30718093(+)$1	201	3	28	20.6030
GUAUUUUCAUUAUCAUUUAGAAUAC	chrX:143448542-143448743(+)$1	201	25	50	22.6470
GCAGGGCCAUAAUCAAACCUUGUCU	chr1:58583108-58583309(-)$1	201	11	36	21.5064
GUAAUUCCUCUAUAAUCAGAAUUGC	chr14:19649297-19649498(-)$1	201	127	152	22.4771
AUGCUGCCAUCUACUACCCAGACGU	chr12:90808461-90808662(+)$1	201	61	86	23.7235
AAGAACAAAAAAAAUAAAGUUUUUA	chr8:96492731-96492932(+)$1	201	130	155	21.9687
UUUUUGUUUUAUUUUUCCAGAUAAA	chr9:55906554-55906755(+)$1	201	160	185	21.9478
GGGAGAAUCUCAGAACUGCUCUCCC	chr2:29856703-29856904(+)$1	201	119	144	23.1972
AACUCUGUAGUUUUCAAAGAGUCUU	chr4:141317792-141317993(-)$1	201	39	64	22.4739
guucaugcccugacuuccuugaaau	chr13:74459705-74459906(-)$1	201	130	155	22.9267
CAUCACCAUCCUUCCUCAGGUAUGU	chr9:45666982-45667183(+)$1	201	141	166	22.6578
CCAUUUUCAUAAAUCACCAGAAGGG	chr2:103988491-103988692(-)$1	201	90	115	22.0541
AAUGUAUCUCUUUUCAAAACAUUUC	chr1:58647734-58647935(+)$1	201	77	102	24.2540
AGAAGCAAAGCCAAGUAGCUCCGGA	chr15:99328883-99329084(-)$1	201	104	129	20.4530
GUUCUUUUUUUUUUUUAGUAAGAAU	chr3:151842891-151843092(-)$1	201	71	96	24.8099
UCUCAUGCUGUCAUCCUUAAUGAGA	chr3:95434177-95434378(+)$1	201	91	116	24.3619
cccuugcccccaucuccauaaggaa	chr9:10209205-10209406(-)$1	201	111	136	21.5612
AGUUCCAACAUCCCCAUAGAACUUA	chr1:178686355-178686556(-)$1	201	119	144	22.4309
GAGAGACCAAAGAUAUUAAUUUUCU	chr6:126588255-126588456(-)$1	201	170	195	21.0148
GCUAGCCACUGAUAGACCUGCUGGA	chr4:56973510-56973711(-)$1	201	175	200	22.8811
ccugccucucaucucacugcaggag	chr4:104023054-104023255(+)$1	201	45	70	24.4578
CUGCCAUCUUCUCAUCCAUCCGGCA	chr11:118657267-118657468(-)$1	201	91	116	19.4795
CAAGGUCUUCUGAAGCCUCUUUGCA	chr6:80061489-80061690(+)$1	201	9	34	24.4578
AUCAGCUAACUAAGACUUGCUGGAU	chr9:68685905-68686106(+)$1	201	113	138	23.9760
uguuccccauucuaaguuggauuga	chr7:65053135-65053336(+)$1	201	166	191	24.1903
UGGGAAGCUUGCAUUCUAUUCCCAG	chr4:36664008-36664209(-)$1	201	15	40	23.9142
CUGGCAUCUCCUUUUUAACUGCUUA	chr12:45502637-45502838(+)$1	201	113	138	24.3821
UAUGUCUACAGAUACAACAGGCACG	chr10:70718463-70718664(-)$1	201	31	56	23.2634
ACAAUAAGAAGAGACAUGUAUUGAC	chr15:98372794-98372995(-)$1	201	141	166	24.7115
accacauuuaaauuuuuaugggguu	chr10:77801932-77802133(-)$1	201	131	156	22.0847
UUUCUUUCUGAUAAAACUUAAGAAA	chr7:63231792-63231993(-)$1	201	125	150	22.4361
ugaguucucauuaucucaagcucuc	chr9:68531223-68531424(+)$1	201	76	101	24.6458
UGAAAAAAAACAAAAGGAUUUUCUG	chr4:77162678-77162879(-)$1	201	29	54	24.5276
ACUAACCUCCAUUCAUACUUAGUAG	chr14:16231577-16231778(-)$1	201	59	84	24.1707
GACUGUAUCUGCUCACUCCACAUCU	chr3:109652933-109653134(-)$1	201	77	102	23.9923
UGUUUUUAAUAACUGUAGAAAAACA	chr10:90612024-90612225(-)$1	201	38	63	22.6470
ACAUAUUACAAAAUGAACUGUGUGU	chr2:24686211-24686412(-)$1	201	132	157	23.1972
AUUUGUAAAUAAGAGCUCUACAUAG	chr1:133832012-133832213(+)$1	201	35	60	22.3288
UUUUCUAUCCUCAACCUUGAAUGUG	chr2:77730631-77730832(-)$1	201	51	76	23.8197
UGUAGGUCACUCACAUCCUCCUCAG	chr17:71167758-71167959(+)$1	201	70	95	24.2782
ugucuggcucauuucacacagcauu	chr16:93718667-93718868(+)$1	201	87	112	23.7965
uguguccaccaucucaccuacauug	chr8:16996630-16996831(-)$1	201	89	114	22.9667
UGAAACUAAAAUUUGAAAUUGUCUU	chr16:56008835-56009036(+)$1	201	64	89	21.1777
CAUUCCUUUCUGCCACCCUGGAAUG	chr10:59596116-59596317(+)$1	201	9	34	24.3619
UGUGAUAGUACAAUUUUAAGUUACU	chr2:14998438-14998639(+)$1	201	114	139	23.7057
GUUUCUACUGUUCACUUUUGGAAAC	chr7:65081162-65081363(+)$1	201	91	116	22.6470
GCGUGUGACGAAAUUUAAAUGCAGG	chr6:8544122-8544323(+)$1	201	58	83	23.3698
ACUGACUUCCUCAUUUCACUCACCU	chr16:52202469-52202670(+)$1	201	85	110	22.4584
UAAUCUGCAUAAUUUAAAAAGAUGA	chr11:17099884-17100085(+)$1	201	13	38	23.9364
ucuguguuuuauuucauuuucaguc	chr10:118963288-118963489(+)$1	201	110	135	20.8173

#DB
((((.(............)))))))	chr13:58188463-58188664(-)$1	1	77	102	23.2503
(((((((...........)))))))	chr4:77696029-77696230(-)$1	1	125	150	22.6470
((((((.............))))))	chr13:32905897-32906098(+)$1	1	83	108	24.2021
.(((((............)))))..	chr18:13151333-13151534(+)$1	1	155	180	23.0634
((.(.(............).).)))	chr13:59235138-59235339(+)$1	1	49	74	23.4380
.(((................))).)	chr7:103421307-103421508(+)$1	1	88	113	21.0271
((.((................)).)	chrX:153985942-153986143(-)$1	1	42	67	19.5259
..((((............))))(((	chr16:94662096-94662297(+)$1	1	89	114	21.4653
((((((.............))))))	chr19:32899916-32900117(+)$1	1	11	36	22.4361
((((((.............))))))	chr4:110343616-110343817(+)$1	1	88	113	23.1972
(((.((...........)).)))).	chr5:84494815-84495016(-)$1	1	103	128	21.2264
((((((............)))((((	chr6:32419648-32419849(-)$1	1	13	38	22.5946
((.(((............))).)))	chr13:18841462-18841663(+)$1	1	50	75	23.9872
)(((((.............))))).	chr16:67601856-67602057(-)$1	1	109	134	23.7657
.((((................))))	chr3:30717892-30718093(+)$1	1	3	28	20.6030
(((((((...........)))))))	chrX:143448542-143448743(+)$1	1	25	50	22.6470
((((((...........)))))).)	chr1:58583108-58583309(-)$1	1	11	36	21.5064
(((((((...........)))))))	chr14:19649297-19649498(-)$1	1	127	152	22.4771
((((((............))).)))	chr12:90808461-90808662(+)$1	1	61	86	23.7235
((((((............)))))).	chr8:96492731-96492932(+)$1	1	130	155	21.9687
(.((((...........)))).)))	chr9:55906554-55906755(+)$1	1	160	185	21.9478
((((((.............))))))	chr2:29856703-29856904(+)$1	1	119	144	23.1972
((((((...........)))))(((	chr4:141317792-141317993(-)$1	1	39	64	22.4739
.((((..............)))).)	chr13:74459705-74459906(-)$1	1	130	155	22.9267
(((.(((...........)))))))	chr9:45666982-45667183(+)$1	1	141	166	22.6578
((.((((...........)))))))	chr2:103988491-103988692(-)$1	1	90	115	22.0541
(((((.............)))))..	chr1:58647734-58647935(+)$1	1	77	102	24.2540
.((.((...........)))).)))	chr15:99328883-99329084(-)$1	1	104	129	20.4530
.(((((.............))))))	chr3:151842891-151843092(-)$1	1	71	96	24.8099
((((((.............))))))	chr3:95434177-95434378(+)$1	1	91	116	24.3619
.(((((............)))))..	chr9:10209205-10209406(-)$1	1	111	136	21.5612
(((((.............)))))..	chr1:178686355-178686556(-)$1	1	119	144	22.4309
((((((..............)))))	chr6:126588255-126588456(-)$1	1	170	195	21.0148
)(((((.............))))).	chr4:56973510-56973711(-)$1	1	175	200	22.8811
(((((.............))))).)	chr4:104023054-104023255(+)$1	1	45	70	24.4578
.((((................))))	chr11:118657267-118657468(-)$1	1	91	116	19.4795
(((((.............))))).)	chr6:80061489-80061690(+)$1	1	9	34	24.4578
.(((((............)))))..	chr9:68685905-68686106(+)$1	1	113	138	23.9760
((.(((............))).)))	chr7:65053135-65053336(+)$1	1	166	191	24.1903
((((((............)))))))	chr4:36664008-36664209(-)$1	1	15	40	23.9142
((((((.............))).))	chr12:45502637-45502838(+)$1	1	113	138	24.3821
(.(((((...........))))).)	chr10:70718463-70718664(-)$1	1	31	56	23.2634
.(((((............))))).)	chr15:98372794-98372995(-)$1	1	141	166	24.7115
.(((..............)))))))	chr10:77801932-77802133(-)$1	1	131	156	22.0847
((((((.............))))))	chr7:63231792-63231993(-)$1	1	125	150	22.4361
.(((((............))))).)	chr9:68531223-68531424(+)$1	1	76	101	24.6458
.(((((............))))).)	chr4:77162678-77162879(-)$1	1	29	54	24.5276
(((((.............)))))((	chr14:16231577-16231778(-)$1	1	59	84	24.1707
((.(((.............)))..)	chr3:109652933-109653134(-)$1	1	77	102	23.9923
(((((((...........)))))))	chr10:90612024-90612225(-)$1	1	38	63	22.6470
((((((.............))))))	chr2:24686211-24686412(-)$1	1	132	157	23.1972
(((((((...........)))).))	chr1:133832012-133832213(+)$1	1	35	60	22.3288
..(((.............))).)))	chr2:77730631-77730832(-)$1	1	51	76	23.8197
((.(((.............))))))	chr17:71167758-71167959(+)$1	1	70	95	24.2782
((.(((............)))))))	chr16:93718667-93718868(+)$1	1	87	112	23.7965
.((((..............)))).)	chr8:16996630-16996831(-)$1	1	89	114	22.9667
(((.((..............)).))	chr16:56008835-56009036(+)$1	1	64	89	21.1777
((((((.............))))))	chr10:59596116-59596317(+)$1	1	9	34	24.3619
)(((((.............))))).	chr2:14998438-14998639(+)$1	1	114	139	23.7057
(((((((...........)))))))	chr7:65081162-65081363(+)$1	1	91	116	22.6470
.(((((............)))).).	chr6:8544122-8544323(+)$1	1	58	83	23.3698
..(((..............)))..)	chr16:52202469-52202670(+)$1	1	85	110	22.4584
(.((((.............)))).)	chr11:17099884-17100085(+)$1	1	13	38	23.9364
.(((................))).)	chr10:118963288-118963489(+)$1	1	110	135	20.8173

#PSSM
[ : 0.15	d : 0.14	e : 0.14	f : 0.10	g : 0.10	c : 0.07	" : 0.06	: : 0.04	h : 0.04	i : 0.03	F : 0.03	$ : 0.01	! : 0.01	E : 0.01	
e : 0.29	d : 0.17	f : 0.10	g : 0.10	c : 0.09	h : 0.04	[ : 0.04	i : 0.03	" : 0.03	: : 0.01	F : 0.01	b : 0.01	a : 0.01	
e : 0.29	d : 0.18	[ : 0.12	g : 0.10	f : 0.09	c : 0.07	h : 0.04	i : 0.03	F : 0.01	b : 0.01	
e : 0.26	c : 0.20	d : 0.15	g : 0.10	f : 0.09	[ : 0.06	h : 0.04	i : 0.03	a : 0.01	b : 0.01	
e : 0.26	c : 0.17	d : 0.15	g : 0.10	f : 0.07	b : 0.06	h : 0.04	[ : 0.03	i : 0.03	y : 0.03	w : 0.01	
e : 0.18	c : 0.14	g : 0.10	d : 0.09	v : 0.09	y : 0.07	f : 0.07	w : 0.06	h : 0.04	b : 0.04	a : 0.03	i : 0.03	
v : 0.34	u : 0.26	w : 0.09	y : 0.07	t : 0.07	g : 0.06	d : 0.03	i : 0.01	c : 0.01	e : 0.01	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.21	w : 0.09	y : 0.07	
v : 0.34	u : 0.26	t : 0.14	w : 0.09	y : 0.07	b : 0.03	f : 0.01	d : 0.01	e : 0.01	
v : 0.25	e : 0.20	c : 0.12	g : 0.07	y : 0.07	d : 0.07	w : 0.07	a : 0.03	b : 0.03	f : 0.03	i : 0.01	
e : 0.26	c : 0.18	d : 0.12	g : 0.10	f : 0.09	y : 0.07	i : 0.03	] : 0.03	h : 0.03	w : 0.03	b : 0.01	
e : 0.26	c : 0.21	d : 0.14	g : 0.10	f : 0.09	y : 0.04	h : 0.04	i : 0.03	b : 0.03	a : 0.01	
e : 0.26	d : 0.20	g : 0.10	] : 0.10	c : 0.10	f : 0.09	h : 0.04	i : 0.03	b : 0.03	
e : 0.31	d : 0.18	f : 0.10	g : 0.10	c : 0.09	] : 0.06	h : 0.04	i : 0.03	2 : 0.03	b : 0.01	
] : 0.20	e : 0.17	d : 0.15	g : 0.10	f : 0.09	c : 0.06	h : 0.04	2 : 0.04	i : 0.03	: : 0.03	6 : 0.01	3 : 0.01	a : 0.01	
d : 0.18	e : 0.15	c : 0.14	g : 0.10	f : 0.09	: : 0.09	i : 0.04	h : 0.04	3 : 0.03	b : 0.03	6 : 0.01	= : 0.01	2 : 0.01	] : 0.01	

#score	1465.9775636255135
#seq	64
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_UTR_m2_run2.txt

#BEAR
=========[bb[bboooooobb]bb]==========:	chr16:11088235-11088527(-)$1	292	11	49	17.1622
===========!!bboooooobb22===========GG	chr10:5326096-5326360(+)$1	264	6	44	17.7711
ff[eeeee####cccooooooccc22eeeee]ffffff	chr11:53944947-53945207(+)$1	260	158	196	14.7853
=========="""bboooooobb]============22	chr5:89668398-89668709(+)$1	311	159	197	19.4423
$$$==========[aooooooa]==========22ddd	chr11:53230594-53230867(+)$1	273	45	83	17.4477
"ffffff####ddddoooooodddd333ffffff333c	chr1:174202203-174202459(-)$1	256	184	222	15.4480
::==========[bbnnnnnbb]==========eeeee	chr4:101139374-101139633(+)$1	259	7	45	12.6478
ggg[ffffff"""bboooooobb333ffffff22gggg	chr4:150242726-150243008(+)$1	282	190	228	15.9982
gggg[eeeee"""bboooooobb333eeeee22ggggg	chr19:7500379-7500638(-)$1	259	13	51	16.4598
ccc[===========lll===========]cccggggg	chr15:74553983-74554237(+)$1	254	50	88	14.4821
!!ggggggg####ccclllccc4444ggggggg22a22	chr5:37186513-37186770(-)$1	257	56	94	13.3239
ddd[eeeee####cccmmmmccc333eeeee]dddd]b	chr8:87784589-87784840(-)$1	251	184	222	11.3227
Edddd[eeeee[cccooooooccc4444eeeee]dddd	chr3:80491659-80491930(-)$1	271	4	42	13.8405
eee[eeeee[cccbboooooobb]ccc]eeeee]eeee	chr11:7106478-7106713(-)$1	235	13	51	15.5377
dddd"""==========mmmm==========4444ddd	chr10:60895293-60895559(-)$1	266	178	216	13.2167
cc[ccc[ccc[cccooooooccc]ccc22ccc]ccc]d	chr6:149505939-149506218(+)$1	279	176	214	14.5171
$$$ccc!!eeeeebboooooobb333eeeee4444ccc	chr1:95404935-95405243(+)$1	308	177	215	15.8524
hdddd[eeeeeddddoooooodddd22eeeee]dddd]	chr11:106125055-106125314(-)$1	259	177	215	12.8234
dddd[dddd[bb[bboooooobb]bb]dddd333dddd	chr10:92711136-92711375(+)$1	239	184	222	14.0194
ee[a!!ccc####bbmmmmbb333ccc22a]eeeee33	chr2:120832905-120833172(+)$1	267	84	122	12.0808
[eeeee[bb!!a[bboooooobb]a22bb]eeeee]bb	chr15:103029823-103030085(-)$1	262	156	194	14.7673
a[iiiiiiiii[cccqqqqqqqqccc]iiiiiiiii]a	chr12:101446087-101446358(+)$1	271	173	211	11.4537
e[a!!ffffffddddoooooodddd]ffffff22a]ee	chr13:67573569-67573809(-)$1	240	28	66	13.4999
:===============lll===============:eee	chr6:51412824-51413092(-)$1	268	179	217	13.5305
fffff[a[ccc[cccoooooocccccc]a]ffffff>>	chr3:115648895-115649198(-)$1	303	178	216	14.8317
####ffffff[ccc[aooooooa]ccc333ffffff22	chr18:20832128-20832457(+)$1	329	156	194	14.8249
ddd"""ggggggg[aooooooa]gggggggdddd]ccc	chr17:87230519-87230783(+)$1	264	115	153	14.7429
####ccc"""eeeeeooooooeeeeeccc333gggggg	chr11:29642570-29642829(+)$1	259	33	71	14.5069
ee!!ggggggg!!bbnnnnnbb22ggggggg22eeeee	chr6:24902975-24903222(-)$1	247	67	105	12.1415
"""bb!!bb[bb[bboooooobb]bb]bb22bb4444=	chr11:120422361-120422606(-)$1	245	28	66	14.4739
d[===========ssssssssss===========dddd	chr8:60004599-60004919(-)$1	320	278	316	12.2751
c[bb!!bbbbcccbboooooobb]ccc333bb]bb22b	chr8:13174551-13174858(+)$1	307	147	185	14.1425
cc[a!!a[ddddcccnnnnnccc]dddd]a333a]ccc	chr4:123163477-123163715(-)$1	238	110	148	11.8070
fffff[accc[ddddoooooodddd22ccc]a]fffff	chr4:41137699-41137962(+)$1	263	57	95	13.6706
dddd####cccddddoooooodddd]ccc]dddd333c	chr9:4419733-4420004(-)$1	271	213	251	14.0811
!a"""bb[bb"""bbmmmmbbbb]bb333a333eeeee	chr13:85355115-85355375(-)$1	260	28	66	12.4118
!!iiiiiiiiiddddmmmmdddd22iiiiiiiii4444	chr16:35697942-35698209(-)$1	267	12	50	12.7304
========a[eeeeellleeeee]a]===========2	chr1:179379365-179379654(+)$1	289	160	198	12.8566
dddd"""eeeee[bboooooobb22eeeeedddddddd	chr7:148615765-148616064(-)$1	299	225	263	13.8816
[a[dddd####ddddoooooodddd]dddd]a]fffff	chr1:63095497-63095759(-)$1	262	31	69	13.8107
===========[cccbbmmmmbb]ccc]==========	chr6:114265612-114265871(+)$1	259	182	220	13.7823
$$$$===========mmmm===========ffffffii	chr15:80768661-80768938(+)$1	277	178	216	13.5745
:ffffff!!bb[cccooooooccc]bb22ffffffddd	chr11:29999961-30000324(-)$1	363	63	101	12.8187
f[ggggggg"""cccooooooccc55555ggggggg]f	chr10:107937075-107937333(-)$1	258	13	51	12.9979
c!!===========mmmm===========22ccc]a22	chr11:117623847-117624113(+)$1	266	215	253	13.1955
"""ffffff!!ddddoooooodddd4444ffffff444	chr2:131881224-131881488(-)$1	264	21	59	15.3034
ffffff!!dddd!!aooooooa22ddddffffff]a]e	chr7:86506156-86506446(+)$1	290	231	269	13.6244
b####ddddccc[bboooooobb]ccc22ddddbb]dd	chr11:69639011-69639274(-)$1	263	139	177	14.2230
!!bbiiiiiiiii[aooooooaiiiiiiiii]bb]ccc	chr13:44969618-44969921(+)$1	303	208	246	16.2077
[eeeeeeeeeeddddoooooodddd333eeeee]eeee	chr2:138112775-138113030(+)$1	255	183	221	14.2162
[eeeee"""ffffffooooooffffffeeeeebb333a	chrX:101736334-101736574(-)$1	240	154	192	13.0791
eee[bb"""bb[cccoooooocccbb]bbeeeee]bb]	chr3:117024044-117024281(-)$1	237	85	123	13.3545

#otherMatches

#Seq PSSM
GGCAGCAUCCCCCUGCUGUAACACGGUGGUGCUGCCAC	chr16:11088235-11088527(-)$1	292	11	49	17.1622
UCUUUGGGGCAUGAUGCUUUGAUGUUGCUUUAGAGGCA	chr10:5326096-5326360(+)$1	264	6	44	17.7711
UUCUAUUUGUUGUGGCUUUAACCAAAAAAUAAAAAUGU	chr11:53944947-53945207(+)$1	260	158	196	14.7853
UUUUAUGAAGCUUUCUAUUGUGACUUUUAUGGAAUUAA	chr5:89668398-89668709(+)$1	311	159	197	19.4423
UUGGUACCUGAUUUAGUGUAAUCAAUUGGGUAUAAUGC	chr11:53230594-53230867(+)$1	273	45	83	17.4477
AGUGCUGACCAAUAGCGUAUACUGUACCCAGCGCCAUC	chr1:174202203-174202459(-)$1	256	184	222	15.4480
CAGUGUUGGCUUAAGUUUCCCUGGAGCUGGCACGUCAG	chr4:101139374-101139633(+)$1	259	7	45	12.6478
GAUUUAUUCAUUUUGUUGCAUUAUUUUGAAUAUUGUCU	chr4:150242726-150243008(+)$1	282	190	228	15.9982
UUUCUUUGUUGCUGCUGCUGUGUUAAAAUAAUUGGAAA	chr19:7500379-7500638(-)$1	259	13	51	16.4598
CAGCCAGUCCGUUCCAUGGGAAUGGGCUGCCUGGGGUG	chr15:74553983-74554237(+)$1	254	50	88	14.4821
GAGCUGUGUUAAUUCUCGAAGACUCCAUGCAGCAAUGG	chr5:37186513-37186770(-)$1	257	56	94	13.3239
UCUGGUCCUAUGUGAGAUUACUUUAGAGGACAGGAGUA	chr8:87784589-87784840(-)$1	251	184	222	11.3227
GGGAAGUGAUGGGGAAAAUGGUCCAUGGUAUCAGUUCC	chr3:80491659-80491930(-)$1	271	4	42	13.8405
UCCAGCCUCUCAAAAUAAAGUUUGUUGUGAGGUGGGGC	chr11:7106478-7106713(-)$1	235	13	51	15.5377
AAUAUCAGUCUCUCCUUAUCAGAGGAGAGACCUUUUAU	chr10:60895293-60895559(-)$1	266	178	216	13.2167
AGGACAAAUUACUUGAAGGAAAGAAAUGGUGUGCUUAU	chr6:149505939-149506218(+)$1	279	176	214	14.5171
UAUGCUAUGCUGUGGAGAGAACCAAAGCAGCUAUGAGC	chr1:95404935-95405243(+)$1	308	177	215	15.8524
CAGCCCCCUGCAGGCAGGCAGGCCUGAGUAGGAGGCUG	chr11:106125055-106125314(-)$1	259	177	215	12.8234
UGAGAGGCUGCUCGCGUCACAGCCGGAAGCCAUACUCA	chr10:92711136-92711375(+)$1	239	184	222	14.0194
AGGAAGCAGUCACUCCUUGGACAUCUGAAUGUUGGAAA	chr2:120832905-120833172(+)$1	267	84	122	12.0808
UAUUGGUUCUCCUGUAAUAUAACUGAUGAUCUGAUUCC	chr15:103029823-103030085(-)$1	262	156	194	14.7673
GGAGCUUUGGCUUCCAAGUUCGGGGGUGUCGGAGCUGC	chr12:101446087-101446358(+)$1	271	173	211	11.4537
AAGUAUGAAGAAUGUCUCCUUGCGUCUCUUUACCCCUG	chr13:67573569-67573809(-)$1	240	28	66	13.4999
CUUUUUUAAGAUUUUUCUCAAAAGUUUUGAAAAGCUAU	chr6:51412824-51413092(-)$1	268	179	217	13.5305
GCAUAGAAAUGUACCAUCAAAGGUCAUGUGUAUGUUUU	chr3:115648895-115649198(-)$1	303	178	216	14.8317
CCCAUUUGUACCAAAACAGUGUUCUUGCUCUAUAAACC	chr18:20832128-20832457(+)$1	329	156	194	14.8249
AAAAAUACAUAGUUGUUGUACCUGCUAUGUUUUACCGU	chr17:87230519-87230783(+)$1	264	115	153	14.7429
ACCUCUGAGUCAUUGGUUAUACAGUGUAGUCCCAAGCA	chr11:29642570-29642829(+)$1	259	33	71	14.5069
AUGAUGGCCAACUAAUUCUUUUCAUUGGCCAAAAUUUA	chr6:24902975-24903222(-)$1	247	67	105	12.1415
CCAGGACCUCGACCUAGAAGAAGCUUUAGAGCCAGACA	chr11:120422361-120422606(-)$1	245	28	66	14.4739
CCUUUAACUCGGUUUCCUGAACCGCCGAGUUAAAGCAU	chr8:60004599-60004919(-)$1	320	278	316	12.2751
UUACUAUGCACAAAGGAAUAACUAUUGAAAUGACGGUG	chr8:13174551-13174858(+)$1	307	147	185	14.1425
CAGUGAUGCUCUCCGGCGGUUGGAAGAGGAAGAGGUGA	chr4:123163477-123163715(-)$1	238	110	148	11.8070
UUUAUGACGACUUGUaugacgacgacauugaugaugaa	chr4:41137699-41137962(+)$1	263	57	95	13.6706
ACAGUUAAUAGAGGUCAAAGAACCUGCUACCUGUGUCU	chr9:4419733-4420004(-)$1	271	213	251	14.0811
AGGAACUAUGAAAUCAACUGACAAGGAAACGCAUUCUA	chr13:85355115-85355375(-)$1	260	28	66	12.4118
AAUGCAGAGUAGCUUAUGCAGGUGAUGCUUUGCAGAUG	chr16:35697942-35698209(-)$1	267	12	50	12.7304
GGUGUCAAAGAACUUGACAGGUUGUGUUGAUGCUCUUA	chr1:179379365-179379654(+)$1	289	160	198	12.8566
ACUACCUGGGGCUCCAGUCUGGGCUGCCCCUAGUUCAC	chr7:148615765-148616064(-)$1	299	225	263	13.8816
AGUGAUGUACCACAACCCAGCUUGUUUAUCUCAGUUUU	chr1:63095497-63095759(-)$1	262	31	69	13.8107
UGGUCAUGGACCGGGGCUUCGGCAUUUUGUUCAUGGCC	chr6:114265612-114265871(+)$1	259	182	220	13.7823
CCUUGUGUCUGUGCAGGGCUGCACAGGCAUGAUUGUAU	chr15:80768661-80768938(+)$1	277	178	216	13.5745
CAGAUUUUUUUAAUGAAAUUAUAUAGAUUAGAUCUCAG	chr11:29999961-30000324(-)$1	363	63	101	12.8187
CCAGUAUGCUAAAGAUUUAUUUCUAGUUUGUGUAUUUG	chr10:107937075-107937333(-)$1	258	13	51	12.9979
UUAAAGAUGAUCAAUGUUUUGAUUGUUUUACAAGGAAG	chr11:117623847-117624113(+)$1	266	215	253	13.1955
GCCGUCAGCGAGCGAAGCCUCUCGUGUCGGCUGAUAAA	chr2:131881224-131881488(-)$1	264	21	59	15.3034
CAAGUGCUCCACUUCUGGAACGUUGUGGUACUUGAGUC	chr7:86506156-86506446(+)$1	290	231	269	13.6244
CCUUUGCCGCCCUCUAUUACAAGCGGGACCGGCGCCAG	chr11:69639011-69639274(-)$1	263	139	177	14.2230
CUUGGAGGACACAUGGCACCACUGUGUUCUCACAUCUU	chr13:44969618-44969921(+)$1	303	208	246	16.2077
UUCAGGACACUGCAUCCAACCGUGCAUCAGUGUGCUUG	chr2:138112775-138113030(+)$1	255	183	221	14.2162
UCACAGUUCGGGUGUUCCAUUGCACCCCUGUGCAGAUC	chrX:101736334-101736574(-)$1	240	154	192	13.0791
CAGUGACUUUGUGUUAGAAUAGACCAUUCUUGGCUUCC	chr3:117024044-117024281(-)$1	237	85	123	13.3545

#DB
(((((((((.((.((......)).)).)))))))))).	chr16:11088235-11088527(-)$1	1	11	49	17.1622
(((((((((((..((......))..)))))))))))((	chr10:5326096-5326360(+)$1	1	6	44	17.7711
((.(((((....(((......)))..))))).))))))	chr11:53944947-53945207(+)$1	1	158	196	14.7853
((((((((((...((......)).))))))))))))..	chr5:89668398-89668709(+)$1	1	159	197	19.4423
...((((((((((.(......).))))))))))..)))	chr11:53230594-53230867(+)$1	1	45	83	17.4477
.((((((....((((......))))...))))))...)	chr1:174202203-174202459(-)$1	1	184	222	15.4480
..((((((((((.((.....)).))))))))))(((((	chr4:101139374-101139633(+)$1	1	7	45	12.6478
(((.((((((...((......))...))))))..))))	chr4:150242726-150243008(+)$1	1	190	228	15.9982
((((.(((((...((......))...)))))..)))))	chr19:7500379-7500638(-)$1	1	13	51	16.4598
(((.(((((((((((...))))))))))).))))))))	chr15:74553983-74554237(+)$1	1	50	88	14.4821
..(((((((....(((...)))....)))))))..)..	chr5:37186513-37186770(-)$1	1	56	94	13.3239
(((.(((((....(((....)))...))))).)))).)	chr8:87784589-87784840(-)$1	1	184	222	11.3227
(((((.(((((.(((......)))....))))).))))	chr3:80491659-80491930(-)$1	1	4	42	13.8405
(((.(((((.(((((......)).))).))))).))))	chr11:7106478-7106713(-)$1	1	13	51	15.5377
((((...((((((((((....))))))))))....)))	chr10:60895293-60895559(-)$1	1	178	216	13.2167
((.(((.(((.(((......))).)))..))).))).)	chr6:149505939-149506218(+)$1	1	176	214	14.5171
...(((..(((((((......))...)))))....)))	chr1:95404935-95405243(+)$1	1	177	215	15.8524
(((((.(((((((((......))))..))))).)))).	chr11:106125055-106125314(-)$1	1	177	215	12.8234
((((.((((.((.((......)).)).))))...))))	chr10:92711136-92711375(+)$1	1	184	222	14.0194
((.(..(((....((....))...)))..).)))))..	chr2:120832905-120833172(+)$1	1	84	122	12.0808
.(((((.((..(.((......)).)..)).))))).))	chr15:103029823-103030085(-)$1	1	156	194	14.7673
(.(((((((((.(((........))).))))))))).)	chr12:101446087-101446358(+)$1	1	173	211	11.4537
(.(..((((((((((......)))).))))))..).))	chr13:67573569-67573809(-)$1	1	28	66	13.4999
.(((((((((((((((...))))))))))))))).(((	chr6:51412824-51413092(-)$1	1	179	217	13.5305
(((((.(.(((.(((......)))))).).))))))..	chr3:115648895-115649198(-)$1	1	178	216	14.8317
....((((((.(((.(......).)))...))))))..	chr18:20832128-20832457(+)$1	1	156	194	14.8249
(((...(((((((.(......).))))))))))).)))	chr17:87230519-87230783(+)$1	1	115	153	14.7429
....(((...(((((......))))))))...))))))	chr11:29642570-29642829(+)$1	1	33	71	14.5069
((..(((((((..((.....))..)))))))..)))))	chr6:24902975-24903222(-)$1	1	67	105	12.1415
...((..((.((.((......)).)).))..))....)	chr11:120422361-120422606(-)$1	1	28	66	14.4739
(.(((((((((((..........)))))))))))))))	chr8:60004599-60004919(-)$1	1	278	316	12.2751
(.((..(((((((((......)).)))...)).))..)	chr8:13174551-13174858(+)$1	1	147	185	14.1425
((.(..(.(((((((.....))).)))).)...).)))	chr4:123163477-123163715(-)$1	1	110	148	11.8070
(((((.((((.((((......))))..))).).)))))	chr4:41137699-41137962(+)$1	1	57	95	13.6706
((((....(((((((......)))).))).))))...)	chr9:4419733-4420004(-)$1	1	213	251	14.0811
.(...((.((...((....)))).))...)...)))))	chr13:85355115-85355375(-)$1	1	28	66	12.4118
..(((((((((((((....))))..)))))))))....	chr16:35697942-35698209(-)$1	1	12	50	12.7304
(((((((((.(((((...))))).).))))))))))).	chr1:179379365-179379654(+)$1	1	160	198	12.8566
((((...(((((.((......))..)))))))))))))	chr7:148615765-148616064(-)$1	1	225	263	13.8816
.(.((((....((((......)))).)))).).)))))	chr1:63095497-63095759(-)$1	1	31	69	13.8107
(((((((((((.(((((....)).))).))))))))))	chr6:114265612-114265871(+)$1	1	182	220	13.7823
....(((((((((((....)))))))))))))))))((	chr15:80768661-80768938(+)$1	1	178	216	13.5745
.((((((..((.(((......))).))..))))))(((	chr11:29999961-30000324(-)$1	1	63	101	12.8187
(.(((((((...(((......))).....))))))).)	chr10:107937075-107937333(-)$1	1	13	51	12.9979
(..(((((((((((....)))))))))))..))).)..	chr11:117623847-117624113(+)$1	1	215	253	13.1955
...((((((..((((......))))....))))))...	chr2:131881224-131881488(-)$1	1	21	59	15.3034
((((((..((((..(......)..)))))))))).).)	chr7:86506156-86506446(+)$1	1	231	269	13.6244
(....(((((((.((......)).)))..)))))).))	chr11:69639011-69639274(-)$1	1	139	177	14.2230
..(((((((((((.(......)))))))))).)).)))	chr13:44969618-44969921(+)$1	1	208	246	16.2077
.((((((((((((((......))))...))))).))))	chr2:138112775-138113030(+)$1	1	183	221	14.2162
.(((((...((((((......)))))))))))))...)	chrX:101736334-101736574(-)$1	1	154	192	13.0791
(((.((...((.(((......))))).))))))).)).	chr3:117024044-117024281(-)$1	1	85	123	13.3545

#PSSM
d : 0.13	= : 0.09	f : 0.09	c : 0.09	e : 0.09	! : 0.07	[ : 0.07	$ : 0.05	" : 0.05	: : 0.05	g : 0.03	# : 0.03	E : 0.01	h : 0.01	a : 0.01	b : 0.01	
d : 0.15	e : 0.13	= : 0.11	f : 0.11	[ : 0.09	! : 0.07	$ : 0.05	c : 0.05	# : 0.05	g : 0.03	" : 0.03	a : 0.03	: : 0.01	
= : 0.15	d : 0.15	[ : 0.09	f : 0.09	e : 0.09	g : 0.07	$ : 0.05	# : 0.05	" : 0.05	i : 0.03	! : 0.03	b : 0.03	c : 0.01	a : 0.01	
= : 0.19	d : 0.13	f : 0.11	[ : 0.09	e : 0.07	g : 0.05	# : 0.05	b : 0.05	c : 0.03	a : 0.03	i : 0.03	! : 0.03	" : 0.03	$ : 0.01	
= : 0.23	f : 0.15	e : 0.11	" : 0.07	! : 0.07	g : 0.05	d : 0.05	c : 0.05	i : 0.05	[ : 0.03	b : 0.03	# : 0.03	
= : 0.23	e : 0.13	f : 0.13	[ : 0.07	! : 0.07	g : 0.05	" : 0.05	c : 0.05	d : 0.05	i : 0.05	b : 0.03	# : 0.01	
= : 0.23	e : 0.13	f : 0.11	g : 0.07	" : 0.07	! : 0.05	d : 0.05	i : 0.05	a : 0.05	[ : 0.03	c : 0.03	b : 0.03	# : 0.01	
= : 0.24	e : 0.15	f : 0.07	g : 0.07	# : 0.05	c : 0.05	! : 0.05	b : 0.05	i : 0.05	[ : 0.05	" : 0.05	d : 0.03	
= : 0.23	e : 0.15	c : 0.09	f : 0.07	g : 0.07	d : 0.07	b : 0.07	# : 0.05	i : 0.05	" : 0.05	a : 0.01	! : 0.01	
= : 0.21	# : 0.11	e : 0.11	[ : 0.09	c : 0.09	f : 0.07	b : 0.07	i : 0.05	! : 0.03	g : 0.03	" : 0.03	d : 0.03	
= : 0.19	e : 0.13	# : 0.11	b : 0.09	" : 0.09	c : 0.09	[ : 0.05	i : 0.05	! : 0.03	f : 0.03	g : 0.03	d : 0.03	
d : 0.21	= : 0.15	[ : 0.11	" : 0.09	c : 0.09	# : 0.07	e : 0.07	b : 0.05	! : 0.03	a : 0.01	g : 0.01	i : 0.01	f : 0.01	
c : 0.24	d : 0.17	[ : 0.13	= : 0.13	" : 0.07	! : 0.05	# : 0.05	e : 0.05	g : 0.01	i : 0.01	f : 0.01	
b : 0.32	c : 0.24	d : 0.17	= : 0.09	[ : 0.05	e : 0.03	s : 0.01	! : 0.01	f : 0.01	
b : 0.32	c : 0.21	d : 0.17	a : 0.07	= : 0.07	e : 0.03	o : 0.01	[ : 0.01	s : 0.01	m : 0.01	f : 0.01	
o : 0.65	m : 0.09	n : 0.05	l : 0.03	c : 0.03	= : 0.03	q : 0.01	a : 0.01	s : 0.01	b : 0.01	
o : 0.67	m : 0.11	l : 0.07	n : 0.05	= : 0.01	q : 0.01	s : 0.01	b : 0.01	
o : 0.67	m : 0.15	l : 0.07	n : 0.05	q : 0.01	s : 0.01	
o : 0.67	m : 0.13	n : 0.05	= : 0.03	l : 0.03	q : 0.01	s : 0.01	e : 0.01	
o : 0.67	= : 0.07	n : 0.05	m : 0.05	b : 0.03	c : 0.01	q : 0.01	s : 0.01	d : 0.01	e : 0.01	
o : 0.65	b : 0.07	= : 0.07	c : 0.07	m : 0.03	q : 0.01	s : 0.01	d : 0.01	e : 0.01	
b : 0.32	c : 0.19	d : 0.17	= : 0.09	a : 0.07	e : 0.03	3 : 0.01	q : 0.01	o : 0.01	s : 0.01	f : 0.01	
b : 0.28	c : 0.17	d : 0.17	= : 0.09	] : 0.05	e : 0.03	2 : 0.03	4 : 0.01	3 : 0.01	q : 0.01	a : 0.01	s : 0.01	i : 0.01	f : 0.01	
] : 0.26	= : 0.15	d : 0.15	c : 0.13	2 : 0.09	3 : 0.09	4 : 0.01	g : 0.01	e : 0.01	i : 0.01	f : 0.01	
d : 0.19	= : 0.17	c : 0.17	b : 0.09	2 : 0.07	3 : 0.07	4 : 0.03	a : 0.03	g : 0.03	e : 0.01	] : 0.01	5 : 0.01	i : 0.01	f : 0.01	
= : 0.19	c : 0.17	b : 0.11	3 : 0.11	2 : 0.07	] : 0.07	4 : 0.05	g : 0.03	e : 0.03	d : 0.03	i : 0.03	5 : 0.01	f : 0.01	
= : 0.21	c : 0.19	] : 0.09	e : 0.09	3 : 0.05	f : 0.05	g : 0.05	2 : 0.05	d : 0.05	4 : 0.03	i : 0.03	b : 0.01	5 : 0.01	
= : 0.23	e : 0.13	3 : 0.09	2 : 0.07	d : 0.07	g : 0.05	] : 0.05	b : 0.05	i : 0.05	c : 0.05	f : 0.03	4 : 0.03	5 : 0.01	
= : 0.24	e : 0.19	f : 0.07	2 : 0.07	g : 0.05	b : 0.05	i : 0.05	3 : 0.05	c : 0.05	d : 0.03	a : 0.01	] : 0.01	5 : 0.01	4 : 0.01	
= : 0.21	e : 0.21	f : 0.11	] : 0.07	g : 0.07	d : 0.05	a : 0.05	i : 0.05	3 : 0.05	c : 0.03	2 : 0.03	
e : 0.21	= : 0.19	f : 0.17	d : 0.09	g : 0.05	] : 0.05	i : 0.05	3 : 0.05	c : 0.03	2 : 0.03	b : 0.01	
= : 0.17	f : 0.17	e : 0.15	3 : 0.07	d : 0.07	] : 0.05	c : 0.05	2 : 0.03	g : 0.03	4 : 0.03	i : 0.03	b : 0.03	a : 0.03	
= : 0.17	f : 0.15	e : 0.11	d : 0.09	] : 0.09	2 : 0.07	g : 0.05	3 : 0.05	b : 0.05	c : 0.03	4 : 0.03	i : 0.03	
f : 0.19	= : 0.13	e : 0.11	d : 0.09	2 : 0.07	g : 0.07	b : 0.07	] : 0.05	4 : 0.05	c : 0.03	i : 0.03	3 : 0.01	a : 0.01	
f : 0.15	e : 0.13	d : 0.11	] : 0.11	= : 0.09	g : 0.09	4 : 0.07	3 : 0.05	2 : 0.03	b : 0.03	c : 0.01	i : 0.01	a : 0.01	: : 0.01	
d : 0.17	e : 0.13	f : 0.11	= : 0.09	g : 0.09	c : 0.09	3 : 0.05	a : 0.05	] : 0.05	4 : 0.05	i : 0.01	2 : 0.01	b : 0.01	
d : 0.17	e : 0.13	2 : 0.09	] : 0.09	3 : 0.07	g : 0.07	c : 0.07	= : 0.05	f : 0.05	4 : 0.05	b : 0.03	G : 0.01	> : 0.01	i : 0.01	
d : 0.17	e : 0.15	c : 0.11	2 : 0.09	f : 0.07	g : 0.07	b : 0.05	] : 0.03	a : 0.03	= : 0.03	4 : 0.03	: : 0.01	G : 0.01	3 : 0.01	> : 0.01	i : 0.01	

#score	734.9997492698884
#seq	52
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_UTR_m1_run2.txt

#BEAR
gggg####ddddoooooodddd4444ggggg	chr1:52242107-52242367(-)$1	260	172	203	17.0319
d!!eeeee[cccooooooccceeeee]dddd	chr11:77342751-77342988(-)$1	237	96	127	14.2729
eeeeee!!ddddoooooodddd4444eeeee	chr3:8560526-8560790(+)$1	264	66	97	16.5390
dddd!!eeeeeooooooeeeee22dddd::c	chr4:21764215-21764461(+)$1	246	92	123	12.0693
ccceeeee[cccooooooccc333eeeeeee	chr17:37210062-37210309(+)$1	247	59	90	15.0860
ffffff[eeeeeooooooeeeeeffffffdd	chr10:57235490-57235747(-)$1	257	210	241	12.8251
iiiiccc[ddddnnnnndddd]ccc4444ii	chr2:104268201-104268453(-)$1	252	9	40	10.8381
c[ccc[eeeeeooooooeeeee]ccc]cccd	chr16:7410797-7411034(+)$1	237	182	213	13.7638
dddda!!ddddddddllldddd22dddd22a	chrX:10172774-10173058(+)$1	284	212	243	10.8913
##dddd[eeeeeooooooeeeee]dddd22a	chr12:11332635-11332919(-)$1	284	205	236	14.0796
ffeeeee[ddddoooooodddd]eeeeeccc	chr15:12114338-12114590(+)$1	252	137	168	15.4994
gggg!!ccc[aooooooa]ccc22ggggggg	chr4:138013083-138013383(+)$1	300	255	286	14.1922
gg[ccc!!ddddoooooodddd22ccc]ggg	chr12:30605470-30605720(+)$1	250	55	86	16.9357
d[dddd"""cccooooooccc4444dddd]d	chr4:136877788-136878075(-)$1	287	33	64	15.3131
[dddd"""ddddoooooodddddddd]ccc]	chr1:99718162-99718399(-)$1	237	88	119	15.9294
e"""cccccccccooooooccc]ccc>>>>>	chr11:74488555-74488832(-)$1	277	146	177	12.0018
eeeeegggggggooooooggggggg4444ee	chr5:65986736-65986975(+)$1	239	69	100	13.4732
[ddddbb[ddddoooooodddd]bb]ddddb	chr13:57527829-57528069(-)$1	240	128	159	14.4689
eeeee$$$$$bboooooobb4444eeeee]a	chr11:90200168-90200404(-)$1	236	121	152	12.8536
hh####eeeeeooooooeeeee333hhhhhh	chr3:115952641-115952877(-)$1	236	49	80	13.0771
dddd[eeeeecccooooooccc22eeeeedd	chr1:155541635-155541875(+)$1	240	22	53	13.4345
d[ccc"""ddddooooooddddccc]dddd]	chr9:62642657-62642895(-)$1	238	150	181	16.1688
eee[bbbb!!cccooooooccc22bb]bb]e	chr7:11073285-11073520(-)$1	235	2	33	11.8947
eee[eeeeeddddmmmmdddd333eeeee]e	chr1:58583961-58584200(-)$1	239	38	69	10.6726
!!a!!dddd[aooooooa]dddd22a]a22=	chr11:105919934-105920189(+)$1	255	200	231	13.5993
eeeeea[eeeeeooooooeeeee]a333eee	chr7:129771692-129771938(+)$1	246	106	137	14.7361
bccc[gggggggooooooggggggg]ccc]b	chr1:135198146-135198383(+)$1	237	191	222	13.4528
cc!!ccc[ddddoooooodddd]ccc]ccc2	chrX:67598089-67598347(-)$1	258	32	63	16.0884
ggggg"""ddddooooooddddggggggg]b	chr11:32646160-32646395(+)$1	235	77	108	16.3888
hhhhhhhhddddoooooodddd333hhhhhh	chr13:110851434-110851737(-)$1	303	203	234	14.4963
ddd####eeeeeooooooeeeeedddddddd	chr1:194672302-194672562(-)$1	260	43	74	13.9181
:cccbb!!ddddoooooodddd22bb]ccc:	chr11:77524382-77524622(+)$1	240	156	187	14.2496
gggggeeeee[aooooooa]eeeee]ggggg	chr2:73450531-73450829(-)$1	298	97	128	13.8459
###ffffffcccooooooccc4444ffffff	chr10:4516256-4516502(+)$1	246	169	200	13.1876
b[iiiiiiiiiooooooiiiiiiiii]bbee	chr1:166367304-166367599(-)$1	295	115	146	12.4825
=ddddccc[cccooooooccc]ccc333ddd	chr13:94130198-94130438(+)$1	240	174	205	13.9716
fffff"""ddddooooooddddffffff>>>	chr9:64034271-64034530(-)$1	259	158	189	14.5719
dddda!!eeeeeooooooeeeee22a]dddd	chr6:35459165-35459407(-)$1	242	209	240	14.9014
e[eeeee[ddddoooooodddd22eeeee]e	chr15:93330112-93330354(-)$1	242	22	53	16.6441
iiiii"""ddddoooooodddd22iiiiiii	chr2:49627830-49628089(+)$1	259	113	144	17.4507
hhhhh"""ddddoooooodddd4444hhhhh	chr10:41905723-41905958(-)$1	235	174	205	15.7523
:ccc[a!!ddddoooooodddd22accc:::	chr13:110847795-110848040(-)$1	245	32	63	13.4403
=========[bboooooobb]==========	chr11:87033367-87033638(+)$1	271	226	257	13.6763
###iiiiiiiiiooooooiiiiiiiii>>>>	chr10:117252107-117252342(-)$1	235	78	109	13.3957
c[eeeee!!cccooooooccc]eeeee]ccc	chr12:75047608-75047865(+)$1	257	214	245	14.5122
fggggggg[cccooooooccc]ggggggg44	chr2:134420759-134421076(-)$1	317	11	42	14.3628
[dddd"""ddddoooooodddd22dddd333	chr8:70218764-70219027(-)$1	263	131	162	17.0447

#otherMatches

#Seq PSSM
UAUUUAAUAAUGUAUCUUUAUUUUCCAGUAU	chr1:52242107-52242367(-)$1	260	172	203	17.0319
GCUUAUUGUACAGUAUAUUGUCAGUAUUCUU	chr11:77342751-77342988(-)$1	237	96	127	14.2729
AGUUAUUUCAUGAUCUUACAUGUCCUGUAAC	chr3:8560526-8560790(+)$1	264	66	97	16.5390
AUUCUGAUGAUGUGCCAAUUAUGUGAAUGCU	chr4:21764215-21764461(+)$1	246	92	123	12.0693
CUGGGAAACAGAUGGUUUUCUUUCUUUCCAU	chr17:37210062-37210309(+)$1	247	59	90	15.0860
CCACAGGCCUUUUUUUCCAAAGGUUGUGGCC	chr10:57235490-57235747(-)$1	257	210	241	12.8251
UAGGUGAUUAACUAGUUGUUAUUUAGCUUUC	chr2:104268201-104268453(-)$1	252	9	40	10.8381
UAAUUUUUAUGGAAUUACAUGAUAAUCAUAU	chr16:7410797-7411034(+)$1	237	182	213	13.7638
CACAGUGUAGCCAGGCCCCCUGCAGCUAGUC	chrX:10172774-10173058(+)$1	284	212	243	10.8913
CCCCCACGGUAAUGUAACUUAUUAUGGGCUG	chr12:11332635-11332919(-)$1	284	205	236	14.0796
CAUUUGUCUAUCUAGUGUGAUAUAUAAAGGU	chr15:12114338-12114590(+)$1	252	137	168	15.4994
ACCUCUGUAGAUACUGUUGUACUUGGGUCAU	chr4:138013083-138013383(+)$1	300	255	286	14.1922
UUUUGUACGUUUUCAUAUAAGCUGACAUAGU	chr12:30605470-30605720(+)$1	250	55	86	16.9357
CACUAUGAAAAGGGUUGGCUUGCUAGUAGAG	chr4:136877788-136878075(-)$1	287	33	64	15.3131
AAGUUCUGUGCAUUUGAUUGUAAACUGUACU	chr1:99718162-99718399(-)$1	237	88	119	15.9294
CUGUGCCUUGCCUGGGAUAAGGACAAUGAUA	chr11:74488555-74488832(-)$1	277	146	177	12.0018
GCUGAGGAACAGUGUCCCUUGUUCCACUUUU	chr5:65986736-65986975(+)$1	239	69	100	13.4732
AUGAGGAUGGCUUCACAUGGCUUUCUCUCAG	chr13:57527829-57528069(-)$1	240	128	159	14.4689
GACGACUCCUGCUCCAACGCUUUCUUGUUUC	chr11:90200168-90200404(-)$1	236	121	152	12.8536
AGCAAAGACAGCUUGCUUUGUUGCACUCUUG	chr3:115952641-115952877(-)$1	236	49	80	13.0771
CUUCCUUGGUUGUAGCCAGACAAGGCCAAGA	chr1:155541635-155541875(+)$1	240	22	53	13.4345
AAAUUCAAGUUGAAGGAACAACAGUGUCUGC	chr9:62642657-62642895(-)$1	238	150	181	16.1688
UAGUGAAAUGCAGUCAACUCUGAUUUAUCCU	chr7:11073285-11073520(-)$1	235	2	33	11.8947
cuggccuggucuacagauggaguucuaggac	chr1:58583961-58584200(-)$1	239	38	69	10.6726
CUCUGUCAGUGACUUUCCCCUGAGUGUGAAU	chr11:105919934-105920189(+)$1	255	200	231	13.5993
UGUUCUGGAAGCAGUUGAGCUUUGAAAAGAA	chr7:129771692-129771938(+)$1	246	106	137	14.7361
CCUUGCCUUUUUGAUCCAAAGAAGGGGAGAG	chr1:135198146-135198383(+)$1	237	191	222	13.4528
UUUCAAUAAUUUCAUUAAAAAUGAUUCAGUG	chrX:67598089-67598347(-)$1	258	32	63	16.0884
AAGUGAGUUCUGCACAGUCGGACAUUUCUGU	chr11:32646160-32646395(+)$1	235	77	108	16.3888
AGUUUUGCCUUUGUCUAAAAAGAAAGUGGGA	chr13:110851434-110851737(-)$1	303	203	234	14.4963
UUGGAUUUUGUAGUUUUGUACAACAGAUAAA	chr1:194672302-194672562(-)$1	260	43	74	13.9181
UUACCAUCCUGUUGUGCUGCAGCUUGUGUAU	chr11:77524382-77524622(+)$1	240	156	187	14.2496
CCAGAGUAAACUGUCAUGACUUUGCUUUUGG	chr2:73450531-73450829(-)$1	298	97	128	13.8459
UUCUGUUUAAGUCACAGAGCUAUAAUAAACA	chr10:4516256-4516502(+)$1	246	169	200	13.1876
UUUAUUUUUUUCUGCAAGAAAAAGUGUAAUG	chr1:166367304-166367599(-)$1	295	115	146	12.4825
GGCUUGUGUGUUUGCAACAACUCAUUAAAGG	chr13:94130198-94130438(+)$1	240	174	205	13.9716
CACAGCAUGUGCCAAAUUGUACUUGUGUCAU	chr9:64034271-64034530(-)$1	259	158	189	14.5719
UCCACAAUGUCAUUCCCUUGACACAGUUGGG	chr6:35459165-35459407(-)$1	242	209	240	14.9014
CGGUGCAAAUAUUAAUGUAUAUACUGUACAG	chr15:93330112-93330354(-)$1	242	22	53	16.6441
AUUUGUUUUCAUGAAUUUGUGGUUUAGAUAG	chr2:49627830-49628089(+)$1	259	113	144	17.4507
GGAUAUUUUAAGUGUCGUCUUGUGUUUGUUU	chr10:41905723-41905958(-)$1	235	174	205	15.7523
CCAGCUAACCCAUCUGUCUGGGGAACUGACU	chr13:110847795-110848040(-)$1	245	32	63	13.4403
gcaugugugugcgcauguguuuacgcaugua	chr11:87033367-87033638(+)$1	271	226	257	13.6763
GUAUAAUGUCUUAGAUUAAAGACGUUGCCUU	chr10:117252107-117252342(-)$1	235	78	109	13.3957
UCUAACACUAACUGUACUGUUUUGUUAUAUC	chr12:75047608-75047865(+)$1	257	214	245	14.5122
UGGAGCUUUUGCUGGUGUGUACAGGUUUUCU	chr2:134420759-134421076(-)$1	317	11	42	14.3628
AACAGUUAACAUGUCUAAAUGUGUUUGUCCA	chr8:70218764-70219027(-)$1	263	131	162	17.0447

#DB
((((....((((......))))....)))))	chr1:52242107-52242367(-)$1	1	172	203	17.0319
(..(((((.(((......)))))))).))))	chr11:77342751-77342988(-)$1	1	96	127	14.2729
)(((((..((((......))))....)))))	chr3:8560526-8560790(+)$1	1	66	97	16.5390
((((..(((((......)))))..))))..(	chr4:21764215-21764461(+)$1	1	92	123	12.0693
)))(((((.(((......)))...)))))((	chr17:37210062-37210309(+)$1	1	59	90	15.0860
((((((.(((((......)))))))))))((	chr10:57235490-57235747(-)$1	1	210	241	12.8251
(((((((.((((.....)))).)))....))	chr2:104268201-104268453(-)$1	1	9	40	10.8381
(.(((.(((((......))))).))).))))	chr16:7410797-7411034(+)$1	1	182	213	13.7638
))))(..((((((((...))))..))))..)	chrX:10172774-10173058(+)$1	1	212	243	10.8913
..((((.(((((......))))).))))..)	chr12:11332635-11332919(-)$1	1	205	236	14.0796
))(((((.((((......)))).)))))(((	chr15:12114338-12114590(+)$1	1	137	168	15.4994
((((..(((.(......).)))..)))))))	chr4:138013083-138013383(+)$1	1	255	286	14.1922
((.(((..((((......))))..))).)))	chr12:30605470-30605720(+)$1	1	55	86	16.9357
(.((((...(((......)))....)))).)	chr4:136877788-136878075(-)$1	1	33	64	15.3131
.((((...((((......)))))))).))).	chr1:99718162-99718399(-)$1	1	88	119	15.9294
(...(((((((((......))).))).....	chr11:74488555-74488832(-)$1	1	146	177	12.0018
((((((((((((......)))))))....))	chr5:65986736-65986975(+)$1	1	69	100	13.4732
.((((((.((((......)))).)).)))))	chr13:57527829-57528069(-)$1	1	128	159	14.4689
(((((.....((......))....))))).)	chr11:90200168-90200404(-)$1	1	121	152	12.8536
((....(((((......)))))...))))))	chr3:115952641-115952877(-)$1	1	49	80	13.0771
((((.((((((((......)))..)))))))	chr1:155541635-155541875(+)$1	1	22	53	13.4345
(.(((...((((......))))))).)))).	chr9:62642657-62642895(-)$1	1	150	181	16.1688
(((.((((..(((......)))..)).)).)	chr7:11073285-11073520(-)$1	1	2	33	11.8947
(((.(((((((((....))))...))))).)	chr1:58583961-58584200(-)$1	1	38	69	10.6726
..(..((((.(......).))))..).)..)	chr11:105919934-105920189(+)$1	1	200	231	13.5993
((((((.(((((......))))).)...)))	chr7:129771692-129771938(+)$1	1	106	137	14.7361
((((.(((((((......))))))).))).)	chr1:135198146-135198383(+)$1	1	191	222	13.4528
((..(((.((((......)))).))).))).	chrX:67598089-67598347(-)$1	1	32	63	16.0884
(((((...((((......))))))))))).)	chr11:32646160-32646395(+)$1	1	77	108	16.3888
((((((((((((......))))...))))))	chr13:110851434-110851737(-)$1	1	203	234	14.4963
(((....(((((......)))))))))))))	chr1:194672302-194672562(-)$1	1	43	74	13.9181
.(((((..((((......))))..)).))).	chr11:77524382-77524622(+)$1	1	156	187	14.2496
((((((((((.(......).))))).)))))	chr2:73450531-73450829(-)$1	1	97	128	13.8459
...(((((((((......)))....))))))	chr10:4516256-4516502(+)$1	1	169	200	13.1876
(.(((((((((......))))))))).))))	chr1:166367304-166367599(-)$1	1	115	146	12.4825
((((((((.(((......))).)))...)))	chr13:94130198-94130438(+)$1	1	174	205	13.9716
(((((...((((......))))))))))...	chr9:64034271-64034530(-)$1	1	158	189	14.5719
(((((..(((((......)))))..).))))	chr6:35459165-35459407(-)$1	1	209	240	14.9014
(.(((((.((((......))))..))))).)	chr15:93330112-93330354(-)$1	1	22	53	16.6441
(((((...((((......))))..)))))))	chr2:49627830-49628089(+)$1	1	113	144	17.4507
(((((...((((......))))....)))))	chr10:41905723-41905958(-)$1	1	174	205	15.7523
.(((.(..((((......))))..))))...	chr13:110847795-110848040(-)$1	1	32	63	13.4403
(((((((((.((......)).))))))))))	chr11:87033367-87033638(+)$1	1	226	257	13.6763
...(((((((((......)))))))))....	chr10:117252107-117252342(-)$1	1	78	109	13.3957
(.(((((..(((......))).))))).)))	chr12:75047608-75047865(+)$1	1	214	245	14.5122
((((((((.(((......))).)))))))..	chr2:134420759-134421076(-)$1	1	11	42	14.3628
.((((...((((......))))..))))...	chr8:70218764-70219027(-)$1	1	131	162	17.0447

#PSSM
d : 0.17	e : 0.17	g : 0.10	c : 0.08	f : 0.08	# : 0.06	[ : 0.06	h : 0.06	i : 0.04	b : 0.04	: : 0.04	= : 0.04	! : 0.02	
d : 0.19	g : 0.12	e : 0.12	[ : 0.12	c : 0.10	f : 0.06	# : 0.06	h : 0.06	! : 0.04	i : 0.04	" : 0.02	= : 0.02	
d : 0.23	e : 0.19	c : 0.12	g : 0.10	i : 0.06	# : 0.06	! : 0.04	f : 0.04	h : 0.04	[ : 0.02	" : 0.02	a : 0.02	= : 0.02	
d : 0.21	e : 0.19	c : 0.12	g : 0.10	i : 0.08	f : 0.06	# : 0.04	[ : 0.04	! : 0.04	h : 0.04	" : 0.02	= : 0.02	
e : 0.21	c : 0.12	d : 0.12	# : 0.06	! : 0.06	f : 0.06	[ : 0.06	g : 0.06	i : 0.06	a : 0.04	b : 0.04	h : 0.04	= : 0.02	
e : 0.19	" : 0.14	c : 0.10	! : 0.08	# : 0.06	d : 0.06	g : 0.06	b : 0.06	f : 0.04	a : 0.04	i : 0.04	[ : 0.02	$ : 0.02	h : 0.02	= : 0.02	
e : 0.23	" : 0.17	! : 0.12	c : 0.10	[ : 0.06	g : 0.06	# : 0.04	b : 0.04	i : 0.04	$ : 0.02	d : 0.02	h : 0.02	f : 0.02	= : 0.02	
e : 0.27	" : 0.17	! : 0.10	[ : 0.10	c : 0.06	g : 0.06	d : 0.04	i : 0.04	# : 0.02	$ : 0.02	b : 0.02	h : 0.02	f : 0.02	= : 0.02	
d : 0.42	e : 0.23	[ : 0.08	c : 0.04	g : 0.04	! : 0.04	i : 0.04	" : 0.02	$ : 0.02	f : 0.02	= : 0.02	
d : 0.42	e : 0.21	c : 0.17	[ : 0.06	g : 0.04	i : 0.04	$ : 0.02	! : 0.02	
d : 0.42	c : 0.21	e : 0.17	a : 0.04	g : 0.04	b : 0.04	i : 0.04	[ : 0.02	
d : 0.42	c : 0.21	o : 0.12	e : 0.10	g : 0.04	b : 0.04	a : 0.02	i : 0.02	
o : 0.87	c : 0.06	d : 0.04	n : 0.02	
o : 0.93	n : 0.02	d : 0.02	m : 0.02	
o : 0.93	n : 0.02	d : 0.02	m : 0.02	
o : 0.93	n : 0.02	l : 0.02	m : 0.02	
o : 0.93	n : 0.02	l : 0.02	m : 0.02	
o : 0.80	e : 0.06	d : 0.04	a : 0.04	l : 0.02	i : 0.02	
d : 0.42	e : 0.17	c : 0.14	o : 0.06	] : 0.04	g : 0.04	b : 0.04	i : 0.04	a : 0.02	
d : 0.44	c : 0.23	e : 0.17	g : 0.04	b : 0.04	i : 0.04	] : 0.02	
d : 0.44	c : 0.23	e : 0.19	g : 0.04	i : 0.04	4 : 0.02	] : 0.02	
d : 0.40	e : 0.21	] : 0.08	c : 0.08	4 : 0.06	3 : 0.04	g : 0.04	i : 0.04	= : 0.02	
2 : 0.23	e : 0.17	4 : 0.12	] : 0.10	3 : 0.08	g : 0.08	c : 0.06	d : 0.04	i : 0.04	f : 0.02	= : 0.02	
2 : 0.27	4 : 0.12	c : 0.12	e : 0.08	3 : 0.08	g : 0.08	f : 0.04	] : 0.04	d : 0.04	i : 0.04	b : 0.02	= : 0.02	
e : 0.19	c : 0.14	d : 0.12	4 : 0.10	g : 0.10	b : 0.06	i : 0.06	f : 0.04	3 : 0.04	2 : 0.04	a : 0.04	= : 0.02	
e : 0.17	d : 0.14	4 : 0.10	c : 0.10	] : 0.08	f : 0.06	g : 0.06	i : 0.06	h : 0.04	b : 0.04	a : 0.04	3 : 0.04	= : 0.02	
] : 0.19	e : 0.17	d : 0.17	g : 0.10	f : 0.06	c : 0.06	h : 0.06	4 : 0.04	3 : 0.04	i : 0.04	> : 0.02	= : 0.02	
d : 0.21	e : 0.14	c : 0.12	g : 0.10	f : 0.06	h : 0.06	4 : 0.04	] : 0.04	> : 0.04	b : 0.04	3 : 0.04	a : 0.02	i : 0.02	= : 0.02	
d : 0.14	e : 0.14	c : 0.14	g : 0.12	2 : 0.06	> : 0.06	h : 0.06	: : 0.04	f : 0.04	4 : 0.04	b : 0.04	i : 0.02	= : 0.02	3 : 0.02	
d : 0.17	] : 0.14	c : 0.12	e : 0.10	g : 0.08	2 : 0.06	> : 0.06	h : 0.06	: : 0.04	i : 0.04	f : 0.02	= : 0.02	4 : 0.02	3 : 0.02	
d : 0.17	e : 0.17	g : 0.08	c : 0.06	a : 0.06	> : 0.06	b : 0.06	h : 0.06	i : 0.04	] : 0.04	= : 0.04	: : 0.04	2 : 0.02	f : 0.02	4 : 0.02	3 : 0.02	

#score	669.4837148928023
#seq	47
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_CDS_m2_run2.txt

#BEAR
gg[cccuuuuuuuuuuuuccc]ggg	chr9:65194667-65194955(+)$1	288	24	49	24.1432
[ddddvvvvvvvvvvvvvdddd]cc	chr10:126503945-126504279(+)$1	334	298	323	23.0143
!cccyyyyyyyyyyyyyyyyccc22	chr13:65282830-65283104(-)$1	274	10	35	21.7237
fffffvvvvvvvvvvvvvffffff]	chr13:54723073-54723350(+)$1	277	138	163	23.4103
ffffffuuuuuuuuuuuuffffffC	chr15:80086670-80086962(+)$1	292	15	40	22.2853
[eeeeettttttttttteeeee]dd	chr9:21192094-21192373(+)$1	279	242	267	23.2622
c[accctttttttttttccc]a]cc	chr5:115597962-115598253(-)$1	291	192	217	23.4374
!eeeeeuuuuuuuuuuuueeeee22	chr4:10918345-10918617(-)$1	272	94	119	24.0125
eeeeyyyyyyyyyyyyyyyyeeeee	chr10:127522057-127522370(+)$1	313	58	83	21.3658
[eeeeettttttttttteeeee]cc	chr1:190811280-190811581(-)$1	301	268	293	23.6321
eeeeeuuuuuuuuuuuueeeeeggg	chr3:33712897-33713295(+)$1	398	84	109	23.2888
cccccctttttttttttccc]ccc3	chr9:79991507-79991782(+)$1	275	63	88	23.7435
fffffftttttttttttffffff::	chr17:74945525-74945796(+)$1	271	0	25	21.3424
b[cccuuuuuuuuuuuuccc]bbee	chr17:24292797-24293086(-)$1	289	46	71	22.3319
b[bb[attttttttttta]bb]bb]	chr2:166845025-166845307(+)$1	282	97	122	22.3716
eee[bbtttttttttttbb]eeeee	chr6:92766383-92766653(-)$1	270	106	131	22.2830
hhhhhvvvvvvvvvvvvvhhhhhhh	chr1:158572624-158572908(+)$1	284	92	117	21.2437
dd[cccuuuuuuuuuuuuccc]ddd	chr6:125084486-125084777(+)$1	291	108	133	23.1459
hhcccwwwwwwwwwwwwwwccc444	chr5:110689288-110689563(-)$1	275	41	66	22.0974
:eeeeeuuuuuuuuuuuueeeee::	chr4:133308324-133308608(-)$1	284	229	254	21.0481
gggg[attttttttttta]gggggg	chr3:95127896-95128180(-)$1	284	93	118	24.0997
fffffftttttttttttffffff]e	chr5:33369193-33369512(+)$1	319	189	214	23.0368
$dddduuuuuuuuuuuuddddccc]	chr7:29965176-29965444(-)$1	268	122	147	22.5017
ii[bbwwwwwwwwwwwwwwbbiiii	chr2:162908893-162909169(+)$1	276	236	261	21.4198
$$cccvvvvvvvvvvvvvccc22cc	chr9:44197395-44197665(+)$1	270	71	96	22.6058
======ttttttttttt========	chr15:82958160-82958444(-)$1	284	158	183	23.8665
ccc[bbtttttttttttbb]ccc==	chr19:16056004-16056312(-)$1	308	216	241	22.5203
eeeeewwwwwwwwwwwwwweeeee2	chr17:24361728-24362019(-)$1	291	241	266	22.2730
iiiiiitttttttttttiiiiiiii	chr13:24895116-24895390(+)$1	274	241	266	23.3194
[ddddwwwwwwwwwwwwwwdddd22	chr13:23836822-23837098(-)$1	276	210	235	21.7024
ggggggtttttttttttggggggg2	chr15:51796402-51796684(-)$1	282	79	104	23.5716
ddyyyyyyyyyyyyyyyyddddccc	chr2:33309486-33309782(-)$1	296	225	250	20.3954
gggggwwwwwwwwwwwwwwgggggg	chr2:34629449-34629736(+)$1	287	9	34	22.4563
b[cccvvvvvvvvvvvvvccc]bb2	chr4:116414240-116414519(+)$1	279	112	137	23.2403
!eeeeeuuuuuuuuuuuueeeee22	chr15:77754760-77755033(-)$1	273	40	65	24.0125
:dddduuuuuuuuuuuudddd:ccc	chr6:29369914-29370194(+)$1	280	38	63	20.5188
heeeeettttttttttteeeeeccc	chr6:93651147-93651441(-)$1	294	129	154	23.3185
======ttttttttttt========	chr2:130101606-130101876(+)$1	270	82	107	23.8665
cc[bbwwwwwwwwwwwwwwbb]ccc	chr9:57267920-57268202(-)$1	282	236	261	21.2911
fffffftttttttttttffffff]c	chr7:13511813-13512093(+)$1	280	28	53	23.1530
[eeeeeuuuuuuuuuuuueeeee]d	chr8:26281624-26281893(-)$1	269	95	120	23.8544
c[cccvvvvvvvvvvvvvccc]ccc	chr4:133236648-133236917(-)$1	269	110	135	23.8102
fffffwwwwwwwwwwwwwwffffff	chr1:71660350-71660628(-)$1	278	80	105	21.8213
gggggggtttttttttttggggggg	chr9:78424810-78425093(-)$1	283	257	282	22.1269
ffffffuuuuuuuuuuuuffffff]	chr11:120441488-120441769(-)$1	281	85	110	23.5295
gggggvvvvvvvvvvvvvggggggg	chr2:157294103-157294378(+)$1	275	23	48	23.7627
ffffffuuuuuuuuuuuuffffff2	chr17:27244062-27244330(+)$1	268	44	69	23.5120
fa[cccuuuuuuuuuuuuccc]a]f	chr13:64253801-64254089(-)$1	288	35	60	23.7298
eeeeyyyyyyyyyyyyyyyyeeeee	chr17:75940512-75940790(-)$1	278	121	146	21.3658
hhddddvvvvvvvvvvvvvdddd55	chr11:101861827-101862095(-)$1	268	13	38	20.6964
!!ddddtttttttttttdddd333e	chr6:128385690-128385961(-)$1	271	158	183	22.9619
fffffftttttttttttffffff22	chr9:83736690-83736972(+)$1	282	195	220	23.1726
b[ddddtttttttttttdddd]bb4	chr4:109634364-109634633(+)$1	269	179	204	22.3641
======uuuuuuuuuuuu=======	chr2:129636580-129636852(+)$1	272	5	30	24.2208
eeeeevvvvvvvvvvvvveeeee66	chr17:34063318-34063589(+)$1	271	97	122	22.8973
ffffffuuuuuuuuuuuuffffff3	chr11:69611984-69612252(-)$1	268	180	205	23.6692
dddddvvvvvvvvvvvvvdddd333	chr17:27060007-27060292(+)$1	285	25	50	23.1680
======ttttttttttt========	chr15:25709999-25710280(+)$1	281	65	90	23.8665
ffffyyyyyyyyyyyyyyyyfffff	chr18:37975096-37975365(+)$1	269	202	227	21.2643
$eeeeettttttttttteeeee666	chrX:71485642-71485922(-)$1	280	92	117	22.0844
!eeeeeuuuuuuuuuuuueeeee22	chr13:34289584-34289852(-)$1	268	196	221	24.0125

#otherMatches

#Seq PSSM
UCGUGAGAGGGCCCGGGAUCGGGAG	chr9:65194667-65194955(+)$1	288	24	49	24.1432
CCCCUAGCUCUACACUAAAGGGCAG	chr10:126503945-126504279(+)$1	334	298	323	23.0143
GAGUGAGCAUAAUCUAAAUAACUAA	chr13:65282830-65283104(-)$1	274	10	35	21.7237
CUGAGGAGCAGGAUCUAACUCAGGA	chr13:54723073-54723350(+)$1	277	138	163	23.4103
UUCGAGUUAAGCACAUUCCUCGAAU	chr15:80086670-80086962(+)$1	292	15	40	22.2853
CUUAGAUAUUUGAAUUCUCUAAAAU	chr9:21192094-21192373(+)$1	279	242	267	23.2622
CAGACCAACAAGAACAGGGUGCAGU	chr5:115597962-115598253(-)$1	291	192	217	23.4374
UCUUUUCUUUUUUCCCCUAAAGGUU	chr4:10918345-10918617(-)$1	272	94	119	24.0125
GUUCUGACCCUUUCCUCCCUGAACC	chr10:127522057-127522370(+)$1	313	58	83	21.3658
CGUGAGUACGUAGACAUCUCGCUGU	chr1:190811280-190811581(-)$1	301	268	293	23.6321
UGUCAUAAUAGAAAUAUUGGCAGCU	chr3:33712897-33713295(+)$1	398	84	109	23.2888
CAGAGUAAAGACAAGAAGCUGCUGA	chr9:79991507-79991782(+)$1	275	63	88	23.7435
AGGAUUGUUGGUUUUAAAAUCUUAA	chr17:74945525-74945796(+)$1	271	0	25	21.3424
UCGACGACACUCUCCAUGUCCAGGC	chr17:24292797-24293086(-)$1	289	46	71	22.3319
CCAGCGGGCAGCCACUACACUAGAU	chr2:166845025-166845307(+)$1	282	97	122	22.3716
UCCUACAGCAGACCAGAGUCGGAGC	chr6:92766383-92766653(-)$1	270	106	131	22.2830
UGAGCAAACUGGAACUUAGCUUACA	chr1:158572624-158572908(+)$1	284	92	117	21.2437
CAGCACCAAUUCAAAACAGUGAUGG	chr6:125084486-125084777(+)$1	291	108	133	23.1459
UUGCCUGAACAAAGCAGCUGGCUAU	chr5:110689288-110689563(-)$1	275	41	66	22.0974
ACAGCCGAGCGGGGAGGGGGCUGGG	chr4:133308324-133308608(-)$1	284	229	254	21.0481
ACUUGGGACUACAACUACGAAGUGG	chr3:95127896-95128180(-)$1	284	93	118	24.0997
GAGACAGUUUGCAAUGAUGUCUUGG	chr5:33369193-33369512(+)$1	319	189	214	23.0368
UGUGGAGAAGAACUGGGCCGCCUGA	chr7:29965176-29965444(-)$1	268	122	147	22.5017
CAGCCCCUCAAACUACUUAGGUGGC	chr2:162908893-162909169(+)$1	276	236	261	21.4198
CGGCCCAAAGACAAGAAUGGCACCC	chr9:44197395-44197665(+)$1	270	71	96	22.6058
CAGGGCAGAGGAGGGUGGCUCUGUU	chr15:82958160-82958444(-)$1	284	158	183	23.8665
ACCUGCAACAUUUGAAAGCUGGUUU	chr19:16056004-16056312(-)$1	308	216	241	22.5203
CUGAGGAAAGUAUCGAACACUCGGG	chr17:24361728-24362019(-)$1	291	241	266	22.2730
GCCUUUGUGUUCAAGGAGAAGGUAA	chr13:24895116-24895390(+)$1	274	241	266	23.3194
AUACUUCUGAUUUUUACUUAGUACC	chr13:23836822-23837098(-)$1	276	210	235	21.7024
UUCUGGUGGCCAUUUAUUCAGGAUG	chr15:51796402-51796684(-)$1	282	79	104	23.5716
UGGGGAUAAAAGAAGAGGCGUCCCA	chr2:33309486-33309782(-)$1	296	225	250	20.3954
UAUGGGACUCAGAGCUCUACCAUAU	chr2:34629449-34629736(+)$1	287	9	34	22.4563
CGUCUGGAAGAAUUUGAAGGAGGUG	chr4:116414240-116414519(+)$1	279	112	137	23.2403
GACCUUGCCAUUGAAUAUGAGGUAG	chr15:77754760-77755033(-)$1	273	40	65	24.0125
AGCAGCCCCACCCUACCCUGCCUCC	chr6:29369914-29370194(+)$1	280	38	63	20.5188
UUCUGGGUGGAAAUGAACCAGGGGA	chr6:93651147-93651441(-)$1	294	129	154	23.3185
UUAAAGUCCCAUCUUCUUUUUAGGA	chr2:130101606-130101876(+)$1	270	82	107	23.8665
AGUGAUUCCUGGUGUCUGUUCUCUC	chr9:57267920-57268202(-)$1	282	236	261	21.2911
AGGUGGGUCAGGGCAUACCACUUGG	chr7:13511813-13512093(+)$1	280	28	53	23.1530
AGGCAUAGAAAAGGAGACAUGCCAG	chr8:26281624-26281893(-)$1	269	95	120	23.8544
CCAGGACCCCUUCUCAACCCUAGGC	chr4:133236648-133236917(-)$1	269	110	135	23.8102
GUGGACCCCGCUAAACUCUUCCACC	chr1:71660350-71660628(-)$1	278	80	105	21.8213
GUAAAACUUUGCGUUCUUGUUUUAC	chr9:78424810-78425093(-)$1	283	257	282	22.1269
UGGCAGAACAGGAACCCACUGCUGA	chr11:120441488-120441769(-)$1	281	85	110	23.5295
UGGCCUUUGAGCAGCCCUGGCCAGG	chr2:157294103-157294378(+)$1	275	23	48	23.7627
CCUAGGAGAGAGGUGGUGCCUGGGG	chr17:27244062-27244330(+)$1	268	44	69	23.5120
gcgggcggcgUCGUUUCAGCCGGAC	chr13:64253801-64254089(-)$1	288	35	60	23.7298
CUCCAAAAAAAGCUCAAGAAGGAGG	chr17:75940512-75940790(-)$1	278	121	146	21.3658
AGCACCCCCCAGACCACAUGGUGUC	chr11:101861827-101862095(-)$1	268	13	38	20.6964
AAGCCAGAAUAUGCCUAUGGCGCAG	chr6:128385690-128385961(-)$1	271	158	183	22.9619
UACUUUAAAGGAAAAAAAAAGUAUG	chr9:83736690-83736972(+)$1	282	195	220	23.1726
GAUGGGCUCCUCACCAACCCACCUA	chr4:109634364-109634633(+)$1	269	179	204	22.3641
GACUUCUACAUGGCUCCCGAAGUCU	chr2:129636580-129636852(+)$1	272	5	30	24.2208
GUCUGCUUUUCUCCUCCUCGGACUC	chr17:34063318-34063589(+)$1	271	97	122	22.8973
CUGGAGGGUGGGUAUGGGCUCCAGA	chr11:69611984-69612252(-)$1	268	180	205	23.6692
UGGGGACAGAGCGGAACACCCUGGA	chr17:27060007-27060292(+)$1	285	25	50	23.1680
GAUUGGUGUCAAGGUUGUUGAUUUU	chr15:25709999-25710280(+)$1	281	65	90	23.8665
UCCCAGAGGAGUCACAGGAAGGGAC	chr18:37975096-37975365(+)$1	269	202	227	21.2643
GUGAAGGAAACAGCCGACUUCAAGG	chrX:71485642-71485922(-)$1	280	92	117	22.0844
AUGGGUAGAUCUGGACAGACCCACC	chr13:34289584-34289852(-)$1	268	196	221	24.0125

#DB
((.(((............))).)))	chr9:65194667-65194955(+)$1	1	24	49	24.1432
.((((.............)))).))	chr10:126503945-126504279(+)$1	1	298	323	23.0143
.(((................)))..	chr13:65282830-65283104(-)$1	1	10	35	21.7237
(((((.............)))))).	chr13:54723073-54723350(+)$1	1	138	163	23.4103
((((((............))))))(	chr15:80086670-80086962(+)$1	1	15	40	22.2853
.(((((...........))))).))	chr9:21192094-21192373(+)$1	1	242	267	23.2622
(.((((...........))).).))	chr5:115597962-115598253(-)$1	1	192	217	23.4374
.(((((............)))))..	chr4:10918345-10918617(-)$1	1	94	119	24.0125
((((................)))))	chr10:127522057-127522370(+)$1	1	58	83	21.3658
.(((((...........))))).))	chr1:190811280-190811581(-)$1	1	268	293	23.6321
(((((............)))))(((	chr3:33712897-33713295(+)$1	1	84	109	23.2888
((((((...........))).))).	chr9:79991507-79991782(+)$1	1	63	88	23.7435
((((((...........))))))..	chr17:74945525-74945796(+)$1	1	0	25	21.3424
(.(((............))).))))	chr17:24292797-24293086(-)$1	1	46	71	22.3319
(.((.(...........).)).)).	chr2:166845025-166845307(+)$1	1	97	122	22.3716
(((.((...........)).)))))	chr6:92766383-92766653(-)$1	1	106	131	22.2830
(((((.............)))))))	chr1:158572624-158572908(+)$1	1	92	117	21.2437
((.(((............))).)))	chr6:125084486-125084777(+)$1	1	108	133	23.1459
(((((..............)))...	chr5:110689288-110689563(-)$1	1	41	66	22.0974
.(((((............)))))..	chr4:133308324-133308608(-)$1	1	229	254	21.0481
((((.(...........).))))))	chr3:95127896-95128180(-)$1	1	93	118	24.0997
((((((...........)))))).)	chr5:33369193-33369512(+)$1	1	189	214	23.0368
.((((............))))))).	chr7:29965176-29965444(-)$1	1	122	147	22.5017
((.((..............))))))	chr2:162908893-162909169(+)$1	1	236	261	21.4198
..(((.............)))..))	chr9:44197395-44197665(+)$1	1	71	96	22.6058
((((((...........))))))))	chr15:82958160-82958444(-)$1	1	158	183	23.8665
(((.((...........)).)))((	chr19:16056004-16056312(-)$1	1	216	241	22.5203
(((((..............))))).	chr17:24361728-24362019(-)$1	1	241	266	22.2730
((((((...........))))))))	chr13:24895116-24895390(+)$1	1	241	266	23.3194
.((((..............))))..	chr13:23836822-23837098(-)$1	1	210	235	21.7024
((((((...........))))))).	chr15:51796402-51796684(-)$1	1	79	104	23.5716
((................)))))))	chr2:33309486-33309782(-)$1	1	225	250	20.3954
(((((..............))))))	chr2:34629449-34629736(+)$1	1	9	34	22.4563
(.(((.............))).)).	chr4:116414240-116414519(+)$1	1	112	137	23.2403
.(((((............)))))..	chr15:77754760-77755033(-)$1	1	40	65	24.0125
.((((............)))).(((	chr6:29369914-29370194(+)$1	1	38	63	20.5188
)(((((...........)))))(((	chr6:93651147-93651441(-)$1	1	129	154	23.3185
((((((...........))))))))	chr2:130101606-130101876(+)$1	1	82	107	23.8665
((.((..............)).)))	chr9:57267920-57268202(-)$1	1	236	261	21.2911
((((((...........)))))).)	chr7:13511813-13512093(+)$1	1	28	53	23.1530
.(((((............))))).)	chr8:26281624-26281893(-)$1	1	95	120	23.8544
(.(((.............))).)))	chr4:133236648-133236917(-)$1	1	110	135	23.8102
(((((..............))))))	chr1:71660350-71660628(-)$1	1	80	105	21.8213
(((((((...........)))))))	chr9:78424810-78425093(-)$1	1	257	282	22.1269
((((((............)))))).	chr11:120441488-120441769(-)$1	1	85	110	23.5295
(((((.............)))))))	chr2:157294103-157294378(+)$1	1	23	48	23.7627
((((((............)))))).	chr17:27244062-27244330(+)$1	1	44	69	23.5120
((.(((............))).).)	chr13:64253801-64254089(-)$1	1	35	60	23.7298
((((................)))))	chr17:75940512-75940790(-)$1	1	121	146	21.3658
((((((.............))))..	chr11:101861827-101862095(-)$1	1	13	38	20.6964
..((((...........))))...)	chr6:128385690-128385961(-)$1	1	158	183	22.9619
((((((...........))))))..	chr9:83736690-83736972(+)$1	1	195	220	23.1726
(.((((...........)))).)).	chr4:109634364-109634633(+)$1	1	179	204	22.3641
((((((............)))))))	chr2:129636580-129636852(+)$1	1	5	30	24.2208
(((((.............)))))..	chr17:34063318-34063589(+)$1	1	97	122	22.8973
((((((............)))))).	chr11:69611984-69612252(-)$1	1	180	205	23.6692
(((((.............))))...	chr17:27060007-27060292(+)$1	1	25	50	23.1680
((((((...........))))))))	chr15:25709999-25710280(+)$1	1	65	90	23.8665
((((................)))))	chr18:37975096-37975365(+)$1	1	202	227	21.2643
.(((((...........)))))...	chrX:71485642-71485922(-)$1	1	92	117	22.0844
.(((((............)))))..	chr13:34289584-34289852(-)$1	1	196	221	24.0125

#PSSM
f : 0.19	g : 0.09	e : 0.09	[ : 0.08	! : 0.08	c : 0.08	b : 0.06	h : 0.06	= : 0.06	d : 0.04	$ : 0.04	: : 0.03	i : 0.03	
e : 0.24	f : 0.18	d : 0.11	g : 0.09	[ : 0.09	c : 0.06	= : 0.06	h : 0.04	i : 0.03	$ : 0.01	a : 0.01	! : 0.01	
e : 0.24	f : 0.18	d : 0.13	c : 0.13	[ : 0.08	g : 0.08	= : 0.06	a : 0.01	b : 0.01	h : 0.01	i : 0.01	y : 0.01	
e : 0.22	c : 0.18	f : 0.18	d : 0.13	g : 0.08	= : 0.06	b : 0.04	[ : 0.03	h : 0.01	i : 0.01	y : 0.01	
e : 0.19	c : 0.16	f : 0.16	d : 0.13	y : 0.08	b : 0.06	= : 0.06	g : 0.06	[ : 0.03	h : 0.01	i : 0.01	
v : 0.14	e : 0.14	f : 0.13	w : 0.11	c : 0.08	y : 0.08	u : 0.06	= : 0.06	d : 0.04	a : 0.03	b : 0.03	g : 0.03	i : 0.01	
t : 0.34	u : 0.27	v : 0.16	w : 0.11	y : 0.08	g : 0.01	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
t : 0.36	u : 0.27	v : 0.16	w : 0.11	y : 0.08	
u : 0.21	v : 0.16	w : 0.11	y : 0.08	e : 0.08	f : 0.06	d : 0.06	c : 0.04	= : 0.04	a : 0.03	b : 0.03	i : 0.01	g : 0.01	t : 0.01	
e : 0.18	c : 0.14	f : 0.14	d : 0.11	w : 0.11	y : 0.06	= : 0.06	g : 0.04	] : 0.03	b : 0.03	h : 0.01	i : 0.01	v : 0.01	
e : 0.19	c : 0.16	f : 0.16	d : 0.14	g : 0.08	y : 0.06	= : 0.06	b : 0.04	] : 0.03	h : 0.01	i : 0.01	
e : 0.24	f : 0.18	c : 0.14	d : 0.14	g : 0.08	= : 0.06	] : 0.04	b : 0.04	h : 0.01	i : 0.01	
e : 0.24	f : 0.18	] : 0.13	d : 0.08	c : 0.08	g : 0.08	= : 0.06	i : 0.03	a : 0.01	b : 0.01	h : 0.01	2 : 0.01	: : 0.01	3 : 0.01	
f : 0.18	e : 0.16	c : 0.14	g : 0.11	] : 0.06	b : 0.06	= : 0.06	d : 0.04	i : 0.03	3 : 0.03	h : 0.01	4 : 0.01	2 : 0.01	a : 0.01	6 : 0.01	
c : 0.18	g : 0.11	f : 0.11	2 : 0.09	e : 0.08	= : 0.08	] : 0.06	b : 0.04	d : 0.03	: : 0.03	i : 0.03	3 : 0.03	6 : 0.03	h : 0.01	4 : 0.01	5 : 0.01	
c : 0.16	2 : 0.16	g : 0.09	e : 0.09	= : 0.08	] : 0.06	d : 0.04	3 : 0.04	f : 0.04	: : 0.03	4 : 0.03	i : 0.03	6 : 0.03	C : 0.01	h : 0.01	5 : 0.01	

#score	1388.245879320034
#seq	61
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_CDS_m2_run2.txt

#BEAR
=======[bb[gggggggmmmmggggggg]bb=======	chr13:55463699-55463946(-)$1	247	37	76	12.2085
ggggccc####gggggggmmmmggggggg]ccc]ggggg	chr5:29923509-29923771(+)$1	262	179	218	13.3842
!!ccc$$$$$ccc[cccmmmmccc]ccc4444ccc333b	chr11:69159027-69159271(-)$1	244	107	146	15.3323
eee[ccc!!a"""ddddoooooodddd22a22ccc]eee	chr19:3356244-3356482(+)$1	238	67	106	15.9723
!ffffff####eeeeeooooooeeeee333ffffff22b	chr6:29306556-29306792(+)$1	236	190	229	14.8290
eeeeccc!!gggggggooooooggggggg333ccc]eee	chr15:9054762-9055035(-)$1	273	46	85	18.8723
::eeeee"""ccc[cccnnnnnccc22ccc4444eeeee	chr16:56697532-56697787(-)$1	255	95	134	12.6152
=$$$$$bb[ccc!!bboooooobb22ccc]bb=======	chr18:52684679-52684931(-)$1	252	69	108	14.8432
[iiiiiiiii"""cccooooooccc22iiiiiiiii]a8	chr16:32902393-32902648(+)$1	255	150	189	15.9015
iiiii[ccc[ccc[bboooooobb]ccc]ccciiiiiii	chrX:20249891-20250146(+)$1	255	23	62	15.5984
eeeee####gggggggooooooggggggg4444eeeee]	chr15:53175858-53176099(-)$1	241	174	213	18.5622
eeee[ccc!!ccccccooooooccc22ccc22ccceeee	chr14:55515836-55516073(+)$1	237	2	41	17.0599
cc[bbeeeeebb[cccooooooccc]bb333eeeee]bb	chr11:69171103-69171342(-)$1	239	73	112	14.7318
d[ccc####eeeee[ccclllccceeeee333ccc]ddd	chr3:107469994-107470241(-)$1	247	39	78	14.7621
bb[bb"""ccc!!cccooooooccc]ccc333bbbb]ff	chr10:80643049-80643305(+)$1	256	112	151	17.3884
dd####a!!gggggggooooooggggggg22a22dddd]	chr1:71695678-71695939(-)$1	261	49	88	16.8225
!!ccc####cccddddoooooodddd]ccc333ccc22c	chr11:86096614-86096851(-)$1	237	185	224	17.6763
c"""a[a####ccc[bboooooobbccc4444a]a]ccc	chr5:31553304-31553542(+)$1	238	27	66	18.0805
iiii[ccc[gggggggmmmmggggggg]ccc]iiiiiii	chr1:140998417-140998654(+)$1	237	179	218	12.1668
e!!eeeee####ddddoooooodddd4444eeeeeeeee	chr9:120860651-120860926(+)$1	275	21	60	15.3892
d$$$$$dddd!!ccc[aooooooa]ccc22dddddddd4	chr15:43097652-43097896(-)$1	244	95	134	13.5349
eeeeeebbdddd!!bboooooobb]dddd]bb333eeee	chr2:121259670-121259916(+)$1	246	92	131	13.2530
f[eeeee!!ccceeeeennnnneeeee4444ccceeeee	chr11:3154535-3154788(-)$1	253	178	217	13.0402
bbdddd"""ccc[cccooooooccc22ccc4444dddd:	chrX:12733273-12733511(+)$1	238	37	76	16.2310
d!!dddd####ccc[bbnnnnnbb]ccc22dddd22ddd	chr2:164827436-164827687(-)$1	251	164	203	12.0905
===####eeeee[cccooooooccceeeee333======	chr16:14391375-14391633(+)$1	258	134	173	17.1708
fbb!!cccccc!!cccmmmmccc333ccc4444ccc22b	chr11:101425973-101426212(+)$1	239	118	157	13.0598
hhhhhhhddddcccddddoooooodddd4444ccc]ddd	chr11:117863623-117863887(+)$1	264	193	232	12.7307
eeeeebb####ggggggglllggggggg4444bb]eeee	chr6:124767254-124767493(-)$1	239	129	168	14.6858
#ddddbb!!ccc[cccooooooccc]ccc4444bb]ddd	chrX:70933946-70934190(-)$1	244	190	229	17.6865
eee[bbffffff[ccccccooooooccc4444ccc]fff	chr3:88288446-88288738(-)$1	292	19	58	13.0320
c[ccc$$$$$ffffffooooooffffff22cccccc]ee	chr1:137296608-137296853(-)$1	245	128	167	15.5708
d!!bb[eeeeea[ddddoooooodddd]a333eeeee33	chr8:90870715-90870952(-)$1	237	103	142	15.1491
eecccbb"""eeeee[aooooooa]eeeee333bb]ccc	chr19:56006090-56006399(+)$1	309	79	118	16.0885
bb==============oooooo==============333	chr15:76002413-76002712(-)$1	299	62	101	17.3050
ccc[bb!!gggggggaooooooa]gggggggbb]ccc66	chr3:131305946-131306191(+)$1	245	176	215	14.2767
dd[a!!bb[gggggggooooooggggggg333bb22a]d	chr11:106125945-106126183(-)$1	238	92	131	17.3959
cc"""ccc####bb[cccmmmmccc]bb4444ccc333c	chr19:34316134-34316397(-)$1	263	159	198	14.5075
b[ffffff[bb[ddddoooooodddd]bb22ffffff]b	chr11:79756744-79756985(-)$1	241	119	158	12.6868
e####ccciiiiiiiiillliiiiiiiii]ccc333eee	chr13:60277297-60277576(-)$1	279	49	88	13.6926
gg"""bb!!eeeeeccclllccc]eeeee333bb333gg	chr4:108701293-108701539(+)$1	246	56	95	14.0639
eeeee"""bb!!ddddoooooodddd22bb333eeeeeb	chrX:71482189-71482444(-)$1	255	190	229	15.2775
cc[ddddddddcccbboooooobb]ccc4444dddd]dd	chr19:9078755-9079013(+)$1	258	161	200	15.2598
cc[ccc[==========mmmm==========]ccc]ccc	chr17:79360407-79360664(-)$1	257	193	232	14.0919
"""ccc"""ccc"""aooooooa333ccc55555ccc33	chr4:126698843-126699101(+)$1	258	110	149	15.7643
hhhhhhh"""ffffffooooooffffff4444hhhhhhh	chr2:131129057-131129298(-)$1	241	23	62	14.9515
bb!!bb####ffffffooooooffffff4444bb22bb3	chr7:26013756-26014020(-)$1	264	55	94	16.3073
c[eeeeebb!!eeeeeooooooeeeee22bb]eeeeecc	chr2:91341475-91341712(+)$1	237	77	116	13.3267

#otherMatches

#Seq PSSM
GGGUCAGCGGUGCCCAGGGAGGCCUGGGCUUCCUGGCCC	chr13:55463699-55463946(-)$1	247	37	76	12.2085
AUUUCAAAUAAAGAGGUUGAUGAGCCUCUGUUGCAGGUA	chr5:29923509-29923771(+)$1	262	179	218	13.3842
CCUUCUCUCUCUGUGGCCCGGGCCCCAGUUCUGAACCAG	chr11:69159027-69159271(-)$1	244	107	146	15.3323
CACAGUGGCCGCAUGUCAAGCCAGACGAAGAACAUCGUG	chr19:3356244-3356482(+)$1	238	67	106	15.9723
UGAGAAACACUAAAAACCUUUCUUUUUUUUUUUCUUUUC	chr6:29306556-29306792(+)$1	236	190	229	14.8290
CUUACGAAAUGAAGCACCCCUCUGUUUUAGGCUCGAUGA	chr15:9054762-9055035(-)$1	273	46	85	18.8723
ACAGAAGACCGCUCCGGAACACCUGACAGCAUUGCUUCU	chr16:56697532-56697787(-)$1	255	95	134	12.6152
UAUGACCUGCUUGAUGCCAACACACAGAGGAGAGUGGCU	chr18:52684679-52684931(-)$1	252	69	108	14.8432
AUUCUUGACAAAAAGAGAACAGUCUGAUGUUAAGAAAGU	chr16:32902393-32902648(+)$1	255	150	189	15.9015
UUGUGUCUCUCCUUGGCUGUUUCUUAGGUGGGUGCAGGG	chrX:20249891-20250146(+)$1	255	23	62	15.5984
GCCCUGGGCCCUGGAUACCUGAGUCCAGGUGGGAGGGUG	chr15:53175858-53176099(-)$1	241	174	213	18.5622
CCUUAGAUGAGUCCCUGUUCAGAGGAAGACAAAUCAAGG	chr14:55515836-55516073(+)$1	237	2	41	17.0599
GAUGAGAUGGGGCUGGGCAAGACCAUCCAAACCAUCGUC	chr11:69171103-69171342(-)$1	239	73	112	14.7318
CUAGUUUUAUUUUAUGUCCUUGACUAAGAAAUGCUUGGU	chr3:107469994-107470241(-)$1	247	39	78	14.7621
CCACUAGGUCUUGGCUUAUUGUGGUUGGAGAGGGGGAAC	chr10:80643049-80643305(+)$1	256	112	151	17.3884
AUGAAGGGGGUCAGUCCUACAAGAUUGGCGACAAGUGGA	chr1:71695678-71695939(-)$1	261	49	88	16.8225
GAAUGUUAUUAGAUGUCCACAAACAUACUGUUUCAUAGU	chr11:86096614-86096851(-)$1	237	185	224	17.6763
GCCUGUGUUCUGGGUGCCUCCCUGCCCCCCCUCUCUCAG	chr5:31553304-31553542(+)$1	238	27	66	18.0805
GAGUGGCUCGGGCCUUUCUGAGGGCUCAGGCGGCUUUGU	chr1:140998417-140998654(+)$1	237	179	218	12.1668
GCAUGGCUAACAAAGGCUCUCCUCUUCCCAGGUCACCAG	chr9:120860651-120860926(+)$1	275	21	60	15.3892
CAGCAACAGAUAGAAAUGCUUUAAGUUCGCUCUGGGGAA	chr15:43097652-43097896(-)$1	244	95	134	13.5349
UGAUGGCAACUUGAAGAGAUACCUGAAGUCUGAACCCAU	chr2:121259670-121259916(+)$1	246	92	131	13.2530
GAGCAUUCUGGCUGAAUAUAAGAUUCAUAAUGCUGAUGU	chr11:3154535-3154788(-)$1	253	178	217	13.0402
CCCAGAAAGUCAGCUGAUACAACAGAAUGAGCAGUCUGA	chrX:12733273-12733511(+)$1	238	37	76	16.2310
CAAAAUCCUCAGCCUCUUCAAUAGUGGCGCGGUUGCGGC	chr2:164827436-164827687(-)$1	251	164	203	12.0905
AGCCCAACACUGCUGGGCAUCACCAUGGUGAGUGUUGGC	chr16:14391375-14391633(+)$1	258	134	173	17.1708
GAGAGUCUUGGGAUCAGACAUGAAGACCACAGAGGAGCC	chr11:101425973-101426212(+)$1	239	118	157	13.0598
AAGGUGUACCUCUUUGACAACAACGUCAUCCUGAGUGGG	chr11:117863623-117863887(+)$1	264	193	232	12.7307
GGGACCUAAAGUCCGGGAUGGUCCUGGAAGUGAGUGUCC	chr6:124767254-124767493(-)$1	239	129	168	14.6858
AAGUGAGGAUGGCUGUCCUAUUACACCCAGAAGCUCCAC	chrX:70933946-70934190(-)$1	244	190	229	17.6865
GGCCGCGCCUCCUCCCACUCAUCCCAGUCUCAGGGUGGA	chr3:88288446-88288738(-)$1	292	19	58	13.0320
UAUGUCCCCUGAACUGAUUCAGCAGUUCCUACAGGCAAC	chr1:137296608-137296853(-)$1	245	128	167	15.5708
UGCUGGCAGCGCGAGAGGGAAGACUCUGGAGAUGCUGAA	chr8:90870715-90870952(-)$1	237	103	142	15.1491
CAAGGCCUCUGCCCUCUGUCCCAAUGGGGCUCUGGACCU	chr19:56006090-56006399(+)$1	309	79	118	16.0885
GCCUCAGGGCCUUCAGCCUCUCUUGGGGGCCCUGAGUCU	chr15:76002413-76002712(-)$1	299	62	101	17.3050
CAGCCACCGACAGCCCUUCUCUGCGGUUGUCUGACUGGA	chr3:131305946-131306191(+)$1	245	176	215	14.2767
CUGCUAUGACAUUGAUGUAGAGGUUGAUGACCCACUGAA	chr11:106125945-106126183(-)$1	238	92	131	17.3959
GUCUACCUUCCAGCAGAUGUGGAUCAGCAAACAGGAAUA	chr19:34316134-34316397(-)$1	263	159	198	14.5075
UGGCAGAGGCUGGGACCGAAUUGUUCAAGGACUCUGUAA	chr11:79756744-79756985(-)$1	241	119	158	12.6868
GCGUGUGCGAUGGGCUGGAGCGGCCCAUCUGCGAAUCGG	chr13:60277297-60277576(-)$1	279	49	88	13.6926
uuauaGGAAAUGCUGAGACACUCAAGCAUGAACCAAAGA	chr4:108701293-108701539(+)$1	246	56	95	14.0639
CAGGUGCAGCGGUACCCUGCAAGGUAGAGCCAGGCCUGG	chrX:71482189-71482444(-)$1	255	190	229	15.2775
AUGUGGACAUUUCUGUACCAAAGCUAGAUAUUAGUGCUC	chr19:9078755-9079013(+)$1	258	161	200	15.2598
AGUUUGGCAUUGUUUAUGGAGGUAAGCAAUGACAGCCUG	chr17:79360407-79360664(-)$1	257	193	232	14.0919
UCCGCCGCAGGAAUCCAAGCCCGUCGUCCCCCAAGGCCC	chr4:126698843-126699101(+)$1	258	110	149	15.7643
UGUGCAACAUGCCGGUGCUGCAGCUGGCCCAAUUGCACA	chr2:131129057-131129298(-)$1	241	23	62	14.9515
CCUCUCCUUCCUUCAGCUUUAACUGAAGCUCAGACUGGC	chr7:26013756-26014020(-)$1	264	55	94	16.3073
GUGUGAAUAAUGGUGGCUGUACUCACCUCUGCUUUGCCC	chr2:91341475-91341712(+)$1	237	77	116	13.3267

#DB
(((((((.((.(((((((....))))))).)))))))))	chr13:55463699-55463946(-)$1	1	37	76	12.2085
(((((((....(((((((....))))))).))).)))))	chr5:29923509-29923771(+)$1	1	179	218	13.3842
..(((.....(((.(((....))).)))....)))...)	chr11:69159027-69159271(-)$1	1	107	146	15.3323
(((.(((..(...((((......))))..)..))).)))	chr19:3356244-3356482(+)$1	1	67	106	15.9723
.((((((....(((((......)))))...))))))..)	chr6:29306556-29306792(+)$1	1	190	229	14.8290
(((((((..(((((((......)))))))...))).)))	chr15:9054762-9055035(-)$1	1	46	85	18.8723
..(((((...(((.(((.....)))..)))....)))))	chr16:56697532-56697787(-)$1	1	95	134	12.6152
(.....((.(((..((......))..))).)))))))))	chr18:52684679-52684931(-)$1	1	69	108	14.8432
.(((((((((...(((......)))..))))))))).).	chr16:32902393-32902648(+)$1	1	150	189	15.9015
(((((.(((.(((.((......)).))).))))))))))	chrX:20249891-20250146(+)$1	1	23	62	15.5984
(((((....(((((((......)))))))....))))).	chr15:53175858-53176099(-)$1	1	174	213	18.5622
((((.(((..((((((......)))..)))..)))))))	chr14:55515836-55516073(+)$1	1	2	41	17.0599
((.(((((((((.(((......))).))...))))).))	chr11:69171103-69171342(-)$1	1	73	112	14.7318
(.(((....(((((.(((...))))))))...))).)))	chr3:107469994-107470241(-)$1	1	39	78	14.7621
((.((...(((..(((......))).)))...)))).))	chr10:80643049-80643305(+)$1	1	112	151	17.3884
((....(..(((((((......)))))))..)..)))).	chr1:71695678-71695939(-)$1	1	49	88	16.8225
..(((....(((((((......)))).)))...)))..)	chr11:86096614-86096851(-)$1	1	185	224	17.6763
(...(.(....(((.((......)))))....).).)))	chr5:31553304-31553542(+)$1	1	27	66	18.0805
((((.(((.(((((((....))))))).))).)))))))	chr1:140998417-140998654(+)$1	1	179	218	12.1668
(..(((((....((((......))))....)))))))))	chr9:120860651-120860926(+)$1	1	21	60	15.3892
(.....((((..(((.(......).)))..)))))))).	chr15:43097652-43097896(-)$1	1	95	134	13.5349
((((((((((((..((......)).)))).))...))))	chr2:121259670-121259916(+)$1	1	92	131	13.2530
(.(((((..((((((((.....)))))....))))))))	chr11:3154535-3154788(-)$1	1	178	217	13.0402
))((((...(((.(((......)))..)))....)))).	chrX:12733273-12733511(+)$1	1	37	76	16.2310
(..((((....(((.((.....)).)))..))))..)))	chr2:164827436-164827687(-)$1	1	164	203	12.0905
(((....(((((.(((......))))))))...))))))	chr16:14391375-14391633(+)$1	1	134	173	17.1708
(((..((((((..(((....)))...)))....)))..)	chr11:101425973-101426212(+)$1	1	118	157	13.0598
((((((((((((((((((......))))....))).)))	chr11:117863623-117863887(+)$1	1	193	232	12.7307
(((((((....(((((((...)))))))....)).))))	chr6:124767254-124767493(-)$1	1	129	168	14.6858
.((((((..(((.(((......))).)))....)).)))	chrX:70933946-70934190(-)$1	1	190	229	17.6865
(((.((((((((.((((((......)))....))).)))	chr3:88288446-88288738(-)$1	1	19	58	13.0320
(.(((.....((((((......))))))..)))))).))	chr1:137296608-137296853(-)$1	1	128	167	15.5708
(..((.((((((.((((......)))).)...)))))..	chr8:90870715-90870952(-)$1	1	103	142	15.1491
(((((((...(((((.(......).)))))...)).)))	chr19:56006090-56006399(+)$1	1	79	118	16.0885
((((((((((((((((......))))))))))))))...	chr15:76002413-76002712(-)$1	1	62	101	17.3050
(((.((..((((((((......).))))))))).)))..	chr3:131305946-131306191(+)$1	1	176	215	14.2767
((.(..((.(((((((......)))))))...))..).)	chr11:106125945-106126183(-)$1	1	92	131	17.3959
((...(((....((.(((....))).))....)))...)	chr19:34316134-34316397(-)$1	1	159	198	14.5075
(.((((((.((.((((......)))).))..)))))).)	chr11:79756744-79756985(-)$1	1	119	158	12.6868
(....((((((((((((...))))))))).)))...)))	chr13:60277297-60277576(-)$1	1	49	88	13.6926
((...((..((((((((...))).)))))...))...))	chr4:108701293-108701539(+)$1	1	56	95	14.0639
(((((...((..((((......))))..))...))))))	chrX:71482189-71482444(-)$1	1	190	229	15.2775
((.(((((((((((((......)).)))....)))).))	chr19:9078755-9079013(+)$1	1	161	200	15.2598
((.(((.((((((((((....)))))))))).))).)))	chr17:79360407-79360664(-)$1	1	193	232	14.0919
...(((...(((...(......)...))).....)))..	chr4:126698843-126699101(+)$1	1	110	149	15.7643
(((((((...((((((......))))))....)))))))	chr2:131129057-131129298(-)$1	1	23	62	14.9515
((..((....((((((......))))))....))..)).	chr7:26013756-26014020(-)$1	1	55	94	16.3073
(.(((((((..(((((......)))))..)).)))))))	chr2:91341475-91341712(+)$1	1	77	116	13.3267

#PSSM
e : 0.22	c : 0.16	d : 0.12	b : 0.10	= : 0.06	! : 0.06	g : 0.04	i : 0.04	f : 0.04	h : 0.04	: : 0.02	[ : 0.02	# : 0.02	" : 0.02	
e : 0.18	! : 0.10	c : 0.10	[ : 0.10	b : 0.10	i : 0.06	d : 0.06	= : 0.04	g : 0.04	$ : 0.04	" : 0.04	h : 0.04	f : 0.02	: : 0.02	# : 0.02	
e : 0.22	c : 0.12	[ : 0.10	" : 0.08	! : 0.08	= : 0.06	i : 0.06	f : 0.04	$ : 0.04	# : 0.04	d : 0.04	h : 0.04	g : 0.02	b : 0.02	
e : 0.20	c : 0.14	d : 0.08	[ : 0.06	i : 0.06	b : 0.06	# : 0.06	" : 0.06	= : 0.04	f : 0.04	$ : 0.04	! : 0.04	h : 0.04	g : 0.02	a : 0.02	
c : 0.20	e : 0.16	b : 0.12	d : 0.08	# : 0.06	= : 0.04	f : 0.04	$ : 0.04	i : 0.04	[ : 0.04	! : 0.04	h : 0.04	" : 0.04	a : 0.02	
c : 0.20	b : 0.14	e : 0.12	# : 0.10	$ : 0.08	[ : 0.06	d : 0.06	= : 0.04	f : 0.04	" : 0.04	h : 0.04	i : 0.02	! : 0.02	
c : 0.18	b : 0.14	e : 0.12	# : 0.10	" : 0.08	f : 0.06	d : 0.06	= : 0.04	$ : 0.04	a : 0.04	h : 0.04	i : 0.02	! : 0.02	[ : 0.02	
# : 0.18	! : 0.14	" : 0.14	c : 0.12	b : 0.08	e : 0.08	d : 0.06	$ : 0.04	f : 0.04	= : 0.04	[ : 0.02	i : 0.02	
# : 0.22	! : 0.14	" : 0.10	[ : 0.08	d : 0.08	b : 0.06	c : 0.06	e : 0.06	$ : 0.04	i : 0.04	= : 0.04	f : 0.02	g : 0.02	
# : 0.16	c : 0.16	g : 0.12	e : 0.10	d : 0.08	b : 0.06	" : 0.06	$ : 0.04	i : 0.04	! : 0.04	= : 0.04	a : 0.02	[ : 0.02	f : 0.02	
c : 0.25	# : 0.14	g : 0.12	e : 0.10	f : 0.08	! : 0.06	d : 0.06	" : 0.04	b : 0.04	= : 0.04	[ : 0.02	i : 0.02	
c : 0.29	g : 0.18	e : 0.12	! : 0.08	f : 0.08	" : 0.04	# : 0.04	= : 0.04	b : 0.02	d : 0.02	a : 0.02	[ : 0.02	i : 0.02	
g : 0.18	c : 0.18	e : 0.12	[ : 0.12	! : 0.08	d : 0.08	" : 0.06	f : 0.06	= : 0.04	b : 0.02	i : 0.02	
c : 0.29	g : 0.18	d : 0.12	e : 0.12	[ : 0.06	f : 0.06	! : 0.04	= : 0.04	b : 0.02	i : 0.02	" : 0.02	
c : 0.27	g : 0.18	d : 0.14	e : 0.08	b : 0.08	[ : 0.08	f : 0.06	= : 0.04	i : 0.02	" : 0.02	
c : 0.29	g : 0.16	d : 0.14	b : 0.12	e : 0.06	f : 0.06	[ : 0.04	= : 0.04	a : 0.04	i : 0.02	
o : 0.56	c : 0.12	g : 0.06	d : 0.06	b : 0.04	m : 0.04	a : 0.04	e : 0.02	i : 0.02	= : 0.02	
o : 0.66	m : 0.08	g : 0.06	n : 0.06	c : 0.06	l : 0.04	d : 0.02	
o : 0.68	m : 0.14	l : 0.08	n : 0.06	c : 0.02	
o : 0.70	m : 0.14	l : 0.08	n : 0.06	
o : 0.70	m : 0.10	n : 0.06	l : 0.04	c : 0.04	g : 0.02	i : 0.02	
o : 0.70	c : 0.08	m : 0.06	n : 0.06	g : 0.04	i : 0.02	= : 0.02	
c : 0.27	g : 0.16	o : 0.14	b : 0.10	d : 0.08	e : 0.06	f : 0.06	= : 0.04	a : 0.04	i : 0.02	
c : 0.22	g : 0.16	d : 0.12	b : 0.12	e : 0.06	f : 0.06	a : 0.04	3 : 0.04	o : 0.04	= : 0.04	] : 0.04	i : 0.02	
g : 0.18	c : 0.18	] : 0.14	d : 0.14	e : 0.10	f : 0.06	3 : 0.04	= : 0.04	2 : 0.02	b : 0.02	o : 0.02	i : 0.02	
g : 0.18	d : 0.16	c : 0.14	e : 0.14	2 : 0.10	] : 0.08	f : 0.06	3 : 0.04	= : 0.04	i : 0.02	
c : 0.25	g : 0.18	e : 0.14	2 : 0.10	d : 0.08	f : 0.06	b : 0.04	] : 0.04	= : 0.04	4 : 0.02	i : 0.02	
c : 0.33	g : 0.16	e : 0.08	2 : 0.06	b : 0.06	f : 0.06	i : 0.04	] : 0.04	4 : 0.04	d : 0.04	= : 0.04	3 : 0.02	
4 : 0.22	c : 0.20	g : 0.14	2 : 0.10	e : 0.08	3 : 0.04	i : 0.04	= : 0.04	b : 0.04	] : 0.02	d : 0.02	a : 0.02	
4 : 0.29	3 : 0.16	c : 0.12	] : 0.10	2 : 0.10	e : 0.04	= : 0.04	b : 0.04	a : 0.02	i : 0.02	g : 0.02	5 : 0.02	
4 : 0.31	3 : 0.22	c : 0.10	b : 0.08	2 : 0.08	d : 0.04	= : 0.04	f : 0.02	i : 0.02	e : 0.02	g : 0.02	5 : 0.02	
4 : 0.29	3 : 0.20	c : 0.10	b : 0.08	] : 0.06	2 : 0.04	f : 0.04	e : 0.04	d : 0.04	i : 0.02	a : 0.02	= : 0.02	5 : 0.02	
c : 0.27	b : 0.12	4 : 0.10	3 : 0.10	e : 0.08	= : 0.06	i : 0.06	d : 0.06	f : 0.04	2 : 0.02	a : 0.02	5 : 0.02	h : 0.02	
c : 0.27	b : 0.14	e : 0.12	= : 0.08	] : 0.06	i : 0.06	d : 0.06	f : 0.04	4 : 0.04	3 : 0.04	2 : 0.02	5 : 0.02	h : 0.02	
c : 0.29	e : 0.16	= : 0.08	d : 0.08	i : 0.06	b : 0.06	3 : 0.06	2 : 0.06	f : 0.04	g : 0.02	a : 0.02	] : 0.02	h : 0.02	
e : 0.22	] : 0.18	c : 0.10	= : 0.08	3 : 0.08	d : 0.08	i : 0.06	2 : 0.06	f : 0.04	g : 0.02	b : 0.02	h : 0.02	
e : 0.27	d : 0.14	] : 0.10	c : 0.10	3 : 0.08	= : 0.06	2 : 0.06	i : 0.04	f : 0.04	g : 0.02	a : 0.02	h : 0.02	b : 0.02	
e : 0.25	d : 0.16	3 : 0.10	c : 0.08	= : 0.06	2 : 0.06	g : 0.04	i : 0.04	b : 0.04	f : 0.04	] : 0.04	a : 0.02	6 : 0.02	h : 0.02	
e : 0.20	b : 0.12	d : 0.12	c : 0.12	3 : 0.08	= : 0.06	g : 0.04	i : 0.04	] : 0.04	f : 0.04	8 : 0.02	4 : 0.02	: : 0.02	6 : 0.02	h : 0.02	

#score	724.4298098339478
#seq	48
#width	39
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_UTR_m2_run2.txt

#BEAR
bb"""iiiiiiiiiooooooiiiiiiiii4444b	chr19:5456362-5456644(-)$1	282	0	34	14.8426
c[iiiiiiiiixxxxxxxxxxxxxxxiiiiiiii	chr6:30079454-30079738(+)$1	284	220	254	10.9433
dd"""iiiiiiiiiooooooiiiiiiiii4444d	chr19:5456442-5456715(-)$1	273	71	105	15.1034
e"""==========qqqqqqqq==========ee	chr4:99324902-99325179(+)$1	277	235	269	11.2672
!!ccc[a[a[a[bboooooobb]aa]a]ccc]bb	chr15:75900547-75900820(-)$1	273	207	241	13.8148
gggggggccc!!annnnna22ccc333ggggggg	chr5:3692568-3692844(-)$1	276	1	35	11.4045
dddd[ccc!!ddddoooooodddd333ccc22dd	chr16:91227775-91228057(+)$1	282	17	51	14.0293
$$$$eeeee!!cccnnnnnccceeeeeggggggg	chr11:105142917-105143213(+)$1	296	109	143	11.2471
!!ccc"""cccrrrrrrrrrccc333ccc333ff	chr17:34791783-34792075(+)$1	292	176	210	12.6458
c:hhhhhhhhacccooooooccc]a4444hhhhh	chr6:56728722-56729000(-)$1	278	109	143	12.2251
d[aeeeee[eeeeeooooooeeeee]eeeee]a2	chr1:36501804-36502071(-)$1	267	81	115	12.7493
==========="""ccclllccc22=========	chr16:36750514-36750783(-)$1	269	135	169	13.0334
ggggggg!!cccqqqqqqqqccc333gggggggb	chr7:24891396-24891687(+)$1	291	90	124	11.2431
f[bb[eeeee[cccooooooccc]eeeee]bbff	chr11:69813266-69813543(+)$1	277	174	208	13.5817
=====!!dddd[bboooooobb]dddd22=====	chr4:83921320-83921603(-)$1	283	14	48	13.6220
iiiiiiiii[ddddooooooddddiiiiiiiii:	chr19:8907647-8907942(+)$1	295	47	81	15.0309
$$$iiiiiiiii!!aooooooa22iiiiiiiii2	chr4:137798696-137798973(+)$1	277	98	132	14.1400
ccc"""hhhhhhhhoooooohhhhhhhh333ccc	chr11:53590388-53590670(+)$1	282	177	211	12.3528
cc[ggggggg!!ddddllldddd333gggggggc	chr8:74842835-74843118(+)$1	283	81	115	11.8598
ff!!eeeee!!cccooooooccc22eeeeeffff	chr12:113887155-113887427(+)$1	272	76	110	14.5355
rrra]eeeeeddddoooooodddd==========	chr3:133126987-133127277(-)$1	290	175	209	13.4085
ccc"""ccc[ddddoooooodddd22ccc333cc	chr15:79655890-79656177(-)$1	287	226	260	15.2902
hh"""bb####cccooooooccc22bb]hhhhhh	chr2:152654216-152654493(-)$1	277	116	150	14.1193
#ffffff!!eeeeeooooooeeeee22ffffff4	chr8:123178705-123178986(-)$1	281	210	244	12.3231
iiiiii[ccc!!bboooooobb]ccciiiiiiii	chr5:137966884-137967189(+)$1	305	81	115	15.0240
$$$$$bb"""ddddoooooodddd333bb4444e	chr3:96066811-96067101(-)$1	290	58	92	14.0154
=======!!ffffffnnnnnffffff========	chr3:145309908-145310184(-)$1	276	181	215	11.2791
iiiiiiii"""cccpppppppccc]iiiiiiiii	chr15:79655086-79655360(-)$1	274	140	174	11.7887
"""a[bbeeeee[aooooooaeeeee]bb]a333	chr2:14999759-15000046(+)$1	287	143	177	13.4458
fffff"""bbddddoooooodddd4444bb333f	chr1:64840465-64840739(-)$1	274	86	120	13.2243
d[eeeee####ddddooooooddddeeeeedddd	chr8:74844691-74844960(+)$1	269	148	182	11.7079
gggggggddddcccooooooccc]dddd22gggg	chr10:116510428-116510732(-)$1	304	250	284	14.1626
$iiiiiiiii[cccmmmmccciiiiiiiiiccc]	chr6:54767279-54767565(+)$1	286	125	159	11.7704
ccc####gggggggooooooggggggg4444ccc	chr17:6084525-6084794(+)$1	269	103	137	14.1044
cc####dddd[cccooooooccc]ddddcccHHH	chr18:24443319-24443593(+)$1	274	229	263	12.4273
cffffff####cccnnnnnccc]ffffff]ccc]	chr10:86297943-86298211(+)$1	268	60	94	10.7820
ggggg!!ccc[cccmmmmcccccc22ggggggg:	chr17:37209978-37210255(+)$1	277	125	159	10.6374
eeeedddd!!ddddoooooodddd]dddd]eeee	chr15:101926291-101926563(+)$1	272	214	248	12.5468
"ggggggg####bbnnnnnbb4444ggggggg44	chr5:108863239-108863508(-)$1	269	63	97	11.5154
iii[cccccc[cccoooooocccccc22ccc22i	chr5:123807806-123808084(+)$1	278	198	232	14.9178
iiiii[ccc!!cccooooooccc]ccc22iiiii	chr11:97574603-97574878(+)$1	275	61	95	16.4039
cccdddd"""cccrrrrrrrrrccc]dddd]ccc	chr5:141098323-141098600(-)$1	277	49	83	10.7442
""ccc[bb[eeeeeooooooeeeeebb]ccc444	chr6:140599338-140599620(+)$1	282	231	265	13.0695
[ffffff####cccooooooccc4444ffffff]	chr7:30106095-30106365(-)$1	270	156	190	14.9944
c[ddddccc!!cccooooooccc22ccc22dddd	chr1:62843122-62843399(+)$1	277	199	233	14.1341
eee[eeeee[cccrrrrrrrrrccc]eeeee333	chr6:124863939-124864222(-)$1	283	68	102	11.0103
!!ddddbb[eeeeeooooooeeeeebb]dddd>>	chr11:117828728-117829006(-)$1	278	170	204	11.1110
=======####cccooooooccc333========	chr15:44595258-44595531(-)$1	273	154	188	18.6929
eeee[eeeee[cccooooooccc]eeeeeeeeee	chr3:105771255-105771551(+)$1	296	253	287	13.6410
===========ccclllccc22===========g	chr15:79656061-79656335(-)$1	274	130	164	12.6107
ee[a!!ddddddddoooooodddd4444dddda]	chr13:69138020-69138287(-)$1	267	149	183	13.4185
iiiiiiii!!cccqqqqqqqqccc22iiiiiiii	chr17:37114860-37115128(-)$1	268	70	104	12.1780

#otherMatches

#Seq PSSM
CCUUGCUCUUGCUGGCAGAGCAGCAGGGGAAAUG	chr19:5456362-5456644(-)$1	282	0	34	14.8426
auaggguugcauuaucaguauuacuuuguaacuc	chr6:30079454-30079738(+)$1	284	220	254	10.9433
CCUUGCUCUUGCUGGCAGAGCAGCAGGGGAAAUG	chr19:5456442-5456715(-)$1	273	71	105	15.1034
GCUUUGAACUUUCAUAUUUUUUUGAAGGUUCACU	chr4:99324902-99325179(+)$1	277	235	269	11.2672
AAGUCCCUGUGUCUGAAAUUGGUCCUGUGACCCA	chr15:75900547-75900820(-)$1	273	207	241	13.8148
GGCAGUGGGCAGGGGGGACAGGCCAGAUGCUGCC	chr5:3692568-3692844(-)$1	276	1	35	11.4045
GGAGAGAUGCGUUCGUUCCAGAACCUGGUUGACU	chr16:91227775-91228057(+)$1	282	17	51	14.0293
GAAAAGCUGGUAGCACAAGGCUCGGCUGGGGAUG	chr11:105142917-105143213(+)$1	296	109	143	11.2471
GUGUGUGCGUAUCuuuuuuuuauuauuauuaaau	chr17:34791783-34792075(+)$1	292	176	210	12.6458
UUGCACUUCCGCCUGUAUAGGGGACUUGAGGGAG	chr6:56728722-56729000(-)$1	278	109	143	12.2251
UUCUGUUGGGGUCUGGGCCGGGGCCGCGGCAUGU	chr1:36501804-36502071(-)$1	267	81	115	12.7493
CUUGGGAAUAUUAGGACUAUGUCAUGUGUUCCUA	chr16:36750514-36750783(-)$1	269	135	169	13.0334
ACUGAAUGUUAGAUCAAAUACUGCAAGUUUAGUG	chr7:24891396-24891687(+)$1	291	90	124	11.2431
CUGUUGGCCGGCUGCUCAGACAGACGGCCUGCGU	chr11:69813266-69813543(+)$1	277	174	208	13.5817
GUACAUAUGUGUGCCUCUGUGUCUACACUUGUGC	chr4:83921320-83921603(-)$1	283	14	48	13.6220
CUCUUUCCAAGGCUGCAGUGGGCCUGGGAGGAGA	chr19:8907647-8907942(+)$1	295	47	81	15.0309
AUAUCCUCUGGCCCCUUACAUGCUGCCAGAGGAG	chr4:137798696-137798973(+)$1	277	98	132	14.1400
CUGAUCAGAGGUGUACACUAACAUUUCUCCCCAG	chr11:53590388-53590670(+)$1	282	177	211	12.3528
UGUGCCUGCCGCGCCUAUAAGGCCUGGGUGGGCC	chr8:74842835-74843118(+)$1	283	81	115	11.8598
CUAUGUUUGAAGCCUGAGGUGGCCACAGACAGCA	chr12:113887155-113887427(+)$1	272	76	110	14.5355
CACCUCUGUCCAUUAGAUCAAGUGGGAGGCAGAU	chr3:133126987-133127277(-)$1	290	175	209	13.4085
AGAUGCGAGCCUGCCAAUGAGCAGCCCUCUUCUC	chr15:79655890-79656177(-)$1	287	226	260	15.2902
agacuguaugugggugugaguccuggcccuguca	chr2:152654216-152654493(-)$1	277	116	150	14.1193
AGUCUGUACGGCCAGCAGGAUGGCCCAGCAGAUG	chr8:123178705-123178986(-)$1	281	210	244	12.3231
CUCGGGUGGUGGCAGCAGCAUGGACCCUUGGGUC	chr5:137966884-137967189(+)$1	305	81	115	15.0240
UCCUGGAGAACGUCAUCCGCGACGCAGUCACCUA	chr3:96066811-96067101(-)$1	290	58	92	14.0154
UUUUAUAUCAGUGAAGAGaauuuauuuauaaaau	chr3:145309908-145310184(-)$1	276	181	215	11.2791
GAACCCAGCCUGGUCAGUUCUACCCUUGGGUUCC	chr15:79655086-79655360(-)$1	274	140	174	11.7887
GGAUGGGAACUGAGAAAAUACCAGUUACUGAAAG	chr2:14999759-15000046(+)$1	287	143	177	13.4458
UUCAGUCCGCGUAACUACUCUUGCUUUUGUAUCC	chr1:64840465-64840739(-)$1	274	86	120	13.2243
CAUGCGCGACUGUGGCAGGUUCCACGCGCGGGGC	chr8:74844691-74844960(+)$1	269	148	182	11.7079
CCAGUCAGCACCUCUGUCUUGAGUGUGCUGUGAU	chr10:116510428-116510732(-)$1	304	250	284	14.1626
uggcgggccgcgUCUGGUGAUCGGCUCGCUCCCG	chr6:54767279-54767565(+)$1	286	125	159	11.7704
GCCUUUUCUCUUACCCAGAAGUGAGAGCGCUGGU	chr17:6084525-6084794(+)$1	269	103	137	14.1044
UGCGACUGCAAAGUAGCGAGACUGUGCACACUGA	chr18:24443319-24443593(+)$1	274	229	263	12.4273
gggcuggccuuggacucaauccuccggccucagc	chr10:86297943-86298211(+)$1	268	60	94	10.7820
AUCUGGGUCUUCAGUACUCUGGGAAACAGAUGGU	chr17:37209978-37210255(+)$1	277	125	159	10.6374
CAUUUCUGGAUGAGGAAGCACUUAACAGGUAGUG	chr15:101926291-101926563(+)$1	272	214	248	12.5468
GGAGGCGGCUUUCAUUCUCUGUCUUCCGCCUCAG	chr5:108863239-108863508(-)$1	269	63	97	11.5154
aguagguuccagggaucgaacucggaucaucaag	chr5:123807806-123808084(+)$1	278	198	232	14.9178
AGAGACAGUAGACGUGACUCUGUGACUUUUCUCU	chr11:97574603-97574878(+)$1	275	61	95	16.4039
CUUUCCUCUCGGUUUCAUUCUCACCCAGGACAAG	chr5:141098323-141098600(-)$1	277	49	83	10.7442
CAGUGGAACAGCUUCUGAAAAGGCUUUGCAUGCU	chr6:140599338-140599620(+)$1	282	231	265	13.0695
GCCACAGUCUGUGGAUUUCCCCAAACCCUGUGGG	chr7:30106095-30106365(-)$1	270	156	190	14.9944
UCUCCAGGUACCUAGACAAAUAGAGACCAUUGGG	chr1:62843122-62843399(+)$1	277	199	233	14.1341
AGGUGGGGCGGGAACACACAAAUCCAGCCCCCUU	chr6:124863939-124864222(-)$1	283	68	102	11.0103
CGGUCGGUCGCCUCUCCUCCGAGGCACAUGGCAC	chr11:117828728-117829006(-)$1	278	170	204	11.1110
UGUGAUGUUCAGAGAAAAAccuuagguaucaugc	chr15:44595258-44595531(-)$1	273	154	188	18.6929
AAGGACAGGUAGUGCAUUUACAUGGCCUGCUUUG	chr3:105771255-105771551(+)$1	296	253	287	13.6410
GACAGCGGUAGUGGGACCCAACUUACUGUUGUUG	chr15:79656061-79656335(-)$1	274	130	164	12.6107
GCGGGACCGCGCCGAggcggcggcagcagcggcg	chr13:69138020-69138287(-)$1	267	149	183	13.4185
GUUCCAGGUCUGUCUGCAACCAUACCCCUGGAAU	chr17:37114860-37115128(-)$1	268	70	104	12.1780

#DB
((...(((((((((......)))))))))....)	chr19:5456362-5456644(-)$1	1	0	34	14.8426
(.(((((((((...............))))))))	chr6:30079454-30079738(+)$1	1	220	254	10.9433
((...(((((((((......)))))))))....)	chr19:5456442-5456715(-)$1	1	71	105	15.1034
(...((((((((((........))))))))))))	chr4:99324902-99325179(+)$1	1	235	269	11.2672
..(((.(.(.(.((......)).)).).))).))	chr15:75900547-75900820(-)$1	1	207	241	13.8148
((((((((((..(.....)..)))...)))))))	chr5:3692568-3692844(-)$1	1	1	35	11.4045
((((.(((..((((......))))...)))..))	chr16:91227775-91228057(+)$1	1	17	51	14.0293
....(((((..(((.....)))))))))))))))	chr11:105142917-105143213(+)$1	1	109	143	11.2471
..(((...(((.........)))...)))...))	chr17:34791783-34792075(+)$1	1	176	210	12.6458
).((((((((((((......))).)....)))))	chr6:56728722-56729000(-)$1	1	109	143	12.2251
(.((((((.(((((......))))).))))).).	chr1:36501804-36502071(-)$1	1	81	115	12.7493
(((((((((((...(((...)))..)))))))))	chr16:36750514-36750783(-)$1	1	135	169	13.0334
(((((((..(((........)))...)))))))(	chr7:24891396-24891687(+)$1	1	90	124	11.2431
(.((.(((((.(((......))).))))).))))	chr11:69813266-69813543(+)$1	1	174	208	13.5817
(((((..((((.((......)).))))..)))))	chr4:83921320-83921603(-)$1	1	14	48	13.6220
(((((((((.((((......))))))))))))).	chr19:8907647-8907942(+)$1	1	47	81	15.0309
...(((((((((..(......)..))))))))).	chr4:137798696-137798973(+)$1	1	98	132	14.1400
(((...((((((((......))))))))...)))	chr11:53590388-53590670(+)$1	1	177	211	12.3528
((.(((((((..((((...))))...))))))))	chr8:74842835-74843118(+)$1	1	81	115	11.8598
((..(((((..(((......)))..)))))))))	chr12:113887155-113887427(+)$1	1	76	110	14.5355
...).)))))((((......))))((((((((((	chr3:133126987-133127277(-)$1	1	175	209	13.4085
(((...(((.((((......))))..)))...))	chr15:79655890-79656177(-)$1	1	226	260	15.2902
((...((....(((......)))..)).))))))	chr2:152654216-152654493(-)$1	1	116	150	14.1193
.((((((..(((((......)))))..)))))).	chr8:123178705-123178986(-)$1	1	210	244	12.3231
((((((.(((..((......)).)))))))))))	chr5:137966884-137967189(+)$1	1	81	115	15.0240
.....((...((((......))))...))....)	chr3:96066811-96067101(-)$1	1	58	92	14.0154
(((((((..((((((.....))))))))))))))	chr3:145309908-145310184(-)$1	1	181	215	11.2791
((((((((...(((.......))).)))))))))	chr15:79655086-79655360(-)$1	1	140	174	11.7887
...(.(((((((.(......)))))).)).)...	chr2:14999759-15000046(+)$1	1	143	177	13.4458
(((((...((((((......))))....))...)	chr1:64840465-64840739(-)$1	1	86	120	13.2243
(.(((((....((((......)))))))))))))	chr8:74844691-74844960(+)$1	1	148	182	11.7079
((((((((((((((......))).))))..))))	chr10:116510428-116510732(-)$1	1	250	284	14.1626
.(((((((((.(((....))))))))))))))).	chr6:54767279-54767565(+)$1	1	125	159	11.7704
(((....(((((((......)))))))....)))	chr17:6084525-6084794(+)$1	1	103	137	14.1044
((....((((.(((......))).))))))))))	chr18:24443319-24443593(+)$1	1	229	263	12.4273
(((((((....(((.....))).)))))).))).	chr10:86297943-86298211(+)$1	1	60	94	10.7820
(((((..(((.(((....))))))..))))))).	chr17:37209978-37210255(+)$1	1	125	159	10.6374
((((((((..((((......)))).)))).))))	chr15:101926291-101926563(+)$1	1	214	248	12.5468
.(((((((....((.....))....)))))))..	chr5:108863239-108863508(-)$1	1	63	97	11.5154
(((.((((((.(((......))))))..)))..)	chr5:123807806-123808084(+)$1	1	198	232	14.9178
(((((.(((..(((......))).)))..)))))	chr11:97574603-97574878(+)$1	1	61	95	16.4039
(((((((...(((.........))).)))).)))	chr5:141098323-141098600(-)$1	1	49	83	10.7442
..(((.((.(((((......))))))).)))...	chr6:140599338-140599620(+)$1	1	231	265	13.0695
.((((((....(((......)))....)))))).	chr7:30106095-30106365(-)$1	1	156	190	14.9944
(.(((((((..(((......)))..)))..))))	chr1:62843122-62843399(+)$1	1	199	233	14.1341
(((.(((((.(((.........))).)))))...	chr6:124863939-124864222(-)$1	1	68	102	11.0103
..((((((.(((((......))))))).))))..	chr11:117828728-117829006(-)$1	1	170	204	11.1110
(((((((....(((......)))...))))))))	chr15:44595258-44595531(-)$1	1	154	188	18.6929
((((.(((((.(((......))).))))))))))	chr3:105771255-105771551(+)$1	1	253	287	13.6410
((((((((((((((...)))..)))))))))))(	chr15:79656061-79656335(-)$1	1	130	164	12.6107
((.(..((((((((......))))....))))).	chr13:69138020-69138287(-)$1	1	149	183	13.4185
((((((((..(((........)))..))))))))	chr17:37114860-37115128(-)$1	1	70	104	12.1780

#PSSM
c : 0.19	i : 0.11	e : 0.09	= : 0.09	d : 0.07	g : 0.07	$ : 0.07	! : 0.05	f : 0.05	" : 0.05	b : 0.01	r : 0.01	h : 0.01	# : 0.01	[ : 0.01	
i : 0.13	c : 0.11	[ : 0.09	g : 0.09	= : 0.09	f : 0.09	e : 0.07	" : 0.05	! : 0.05	$ : 0.05	d : 0.03	b : 0.01	: : 0.01	r : 0.01	h : 0.01	
i : 0.15	c : 0.13	" : 0.09	g : 0.09	= : 0.09	f : 0.07	e : 0.07	d : 0.05	$ : 0.05	[ : 0.03	h : 0.01	a : 0.01	b : 0.01	! : 0.01	r : 0.01	# : 0.01	
i : 0.15	" : 0.11	g : 0.11	= : 0.09	d : 0.07	e : 0.07	f : 0.07	c : 0.05	a : 0.05	$ : 0.03	# : 0.03	[ : 0.03	h : 0.01	b : 0.01	! : 0.01	
i : 0.15	= : 0.11	g : 0.11	" : 0.09	e : 0.09	c : 0.07	[ : 0.07	f : 0.07	d : 0.07	# : 0.03	h : 0.01	] : 0.01	$ : 0.01	! : 0.01	
i : 0.17	e : 0.15	= : 0.09	g : 0.09	" : 0.07	d : 0.07	[ : 0.05	! : 0.05	b : 0.05	f : 0.05	c : 0.03	# : 0.03	h : 0.01	
i : 0.15	e : 0.15	= : 0.09	g : 0.09	c : 0.09	b : 0.09	d : 0.07	f : 0.05	" : 0.03	h : 0.03	! : 0.03	a : 0.01	[ : 0.01	# : 0.01	
i : 0.15	c : 0.15	e : 0.15	d : 0.09	# : 0.09	" : 0.07	= : 0.05	! : 0.05	g : 0.05	h : 0.03	b : 0.03	[ : 0.01	
c : 0.15	e : 0.13	i : 0.11	! : 0.11	# : 0.11	d : 0.07	= : 0.05	[ : 0.05	" : 0.05	h : 0.03	g : 0.03	a : 0.01	b : 0.01	
e : 0.15	! : 0.13	c : 0.11	# : 0.11	i : 0.09	[ : 0.07	d : 0.07	= : 0.05	" : 0.05	h : 0.03	g : 0.03	f : 0.01	b : 0.01	
d : 0.19	! : 0.13	[ : 0.11	# : 0.11	c : 0.09	e : 0.09	i : 0.07	= : 0.05	a : 0.03	h : 0.01	f : 0.01	" : 0.01	g : 0.01	
c : 0.42	d : 0.17	e : 0.09	i : 0.05	! : 0.05	[ : 0.03	x : 0.01	= : 0.01	r : 0.01	" : 0.01	h : 0.01	f : 0.01	g : 0.01	# : 0.01	
c : 0.40	d : 0.19	b : 0.07	e : 0.07	i : 0.03	x : 0.01	= : 0.01	a : 0.01	r : 0.01	" : 0.01	q : 0.01	! : 0.01	h : 0.01	f : 0.01	[ : 0.01	g : 0.01	
c : 0.34	d : 0.19	b : 0.07	e : 0.07	r : 0.05	i : 0.03	q : 0.03	x : 0.01	= : 0.01	n : 0.01	" : 0.01	! : 0.01	h : 0.01	f : 0.01	a : 0.01	g : 0.01	
o : 0.61	n : 0.07	q : 0.05	r : 0.05	d : 0.03	m : 0.03	x : 0.01	c : 0.01	a : 0.01	f : 0.01	p : 0.01	l : 0.01	
o : 0.65	n : 0.09	q : 0.05	r : 0.05	m : 0.03	x : 0.01	c : 0.01	d : 0.01	p : 0.01	l : 0.01	
o : 0.65	n : 0.09	q : 0.05	r : 0.05	l : 0.03	m : 0.03	x : 0.01	c : 0.01	p : 0.01	
o : 0.65	n : 0.09	q : 0.05	r : 0.05	l : 0.03	m : 0.03	x : 0.01	p : 0.01	c : 0.01	
o : 0.65	n : 0.07	q : 0.05	r : 0.05	c : 0.05	l : 0.03	x : 0.01	a : 0.01	p : 0.01	
o : 0.65	c : 0.09	q : 0.05	r : 0.05	x : 0.01	2 : 0.01	l : 0.01	d : 0.01	n : 0.01	p : 0.01	b : 0.01	
c : 0.36	d : 0.17	b : 0.07	e : 0.07	i : 0.03	q : 0.03	2 : 0.03	o : 0.03	r : 0.03	x : 0.01	h : 0.01	f : 0.01	p : 0.01	a : 0.01	g : 0.01	
c : 0.40	d : 0.19	e : 0.09	i : 0.05	b : 0.05	r : 0.03	x : 0.01	q : 0.01	a : 0.01	h : 0.01	f : 0.01	g : 0.01	4 : 0.01	2 : 0.01	
c : 0.40	d : 0.19	e : 0.11	] : 0.07	i : 0.05	= : 0.03	x : 0.01	2 : 0.01	h : 0.01	f : 0.01	g : 0.01	4 : 0.01	
d : 0.19	c : 0.15	e : 0.11	] : 0.11	2 : 0.09	3 : 0.07	i : 0.05	= : 0.03	f : 0.03	4 : 0.03	x : 0.01	a : 0.01	h : 0.01	g : 0.01	
e : 0.15	3 : 0.13	2 : 0.13	i : 0.09	c : 0.09	d : 0.07	4 : 0.07	= : 0.05	a : 0.03	f : 0.03	] : 0.03	x : 0.01	h : 0.01	g : 0.01	
3 : 0.13	i : 0.11	e : 0.11	= : 0.07	] : 0.07	4 : 0.07	d : 0.07	2 : 0.07	c : 0.07	b : 0.05	f : 0.03	g : 0.03	x : 0.01	h : 0.01	
i : 0.17	e : 0.13	= : 0.11	g : 0.09	d : 0.09	c : 0.07	4 : 0.07	3 : 0.05	b : 0.05	2 : 0.03	a : 0.01	h : 0.01	] : 0.01	f : 0.01	
i : 0.17	= : 0.11	g : 0.11	e : 0.11	] : 0.07	c : 0.07	4 : 0.07	d : 0.07	2 : 0.05	f : 0.05	b : 0.03	h : 0.01	
i : 0.17	c : 0.13	= : 0.11	g : 0.11	e : 0.11	2 : 0.07	d : 0.07	f : 0.05	b : 0.05	4 : 0.03	3 : 0.01	h : 0.01	
i : 0.15	= : 0.13	g : 0.11	c : 0.09	e : 0.09	4 : 0.07	] : 0.07	3 : 0.05	d : 0.05	h : 0.03	f : 0.03	2 : 0.03	b : 0.01	
i : 0.13	= : 0.13	g : 0.13	c : 0.11	4 : 0.07	3 : 0.07	e : 0.07	d : 0.07	f : 0.05	h : 0.03	2 : 0.01	b : 0.01	a : 0.01	] : 0.01	
i : 0.13	= : 0.13	g : 0.13	3 : 0.09	c : 0.09	4 : 0.07	d : 0.07	f : 0.05	] : 0.03	2 : 0.03	h : 0.03	e : 0.03	b : 0.01	H : 0.01	
i : 0.13	g : 0.11	= : 0.11	c : 0.11	4 : 0.09	f : 0.09	e : 0.05	d : 0.05	3 : 0.05	h : 0.03	a : 0.03	b : 0.01	H : 0.01	2 : 0.01	> : 0.01	
i : 0.11	= : 0.09	c : 0.09	d : 0.07	e : 0.07	g : 0.07	f : 0.07	] : 0.07	b : 0.05	4 : 0.05	h : 0.03	2 : 0.03	: : 0.03	3 : 0.03	H : 0.01	> : 0.01	

#score	680.1729359728585
#seq	52
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_transcript_m3_run2.txt

#BEAR
cccccqqqqqqqqccc]	chr16:15624614-15624876(-)$1	262	97	114	13.5254
hhhhhqqqqqqqqhhhh	chr7:87896413-87896668(-)$1	255	123	140	12.1064
hhhhhqqqqqqqqhhhh	chr5:122906673-122906935(-)$1	262	140	157	12.1064
:ddddqqqqqqqqdddd	chr11:78127861-78128120(+)$1	259	185	202	13.3994
d!!bbqqqqqqqqbb22	chr17:71339039-71339277(-)$1	238	105	122	11.8202
=====qqqqqqqq====	chr2:93536477-93536731(-)$1	254	158	175	13.5482
[ddddqqqqqqqqdddd	chrX:136287326-136287570(+)$1	244	204	221	14.3952
eeeeeqqqqqqqqeeee	chr16:22253273-22253540(-)$1	267	121	138	13.9250
:ddddqqqqqqqqdddd	chr15:79193423-79193661(-)$1	238	169	186	13.3994
[ddddqqqqqqqqdddd	chrX:70933946-70934190(-)$1	244	158	175	14.3952
fffffqqqqqqqqffff	chr11:50013943-50014255(-)$1	312	90	107	12.6371
eeeeeqqqqqqqqeeee	chr12:114058501-114058773(-)$1	272	15	32	13.9250
!ddddqqqqqqqqdddd	chr2:117948950-117949206(+)$1	256	198	215	14.3748
hhhhhqqqqqqqqhhhh	chr3:136481682-136481917(+)$1	235	103	120	12.1064
eeeeeqqqqqqqqeeee	chr9:44732087-44732348(-)$1	261	147	164	13.9250
ddd[aqqqqqqqqa]dd	chr6:51411881-51412141(-)$1	260	224	241	13.6552
c[cccqqqqqqqqcccc	chr10:128358464-128358705(-)$1	241	89	106	13.5482
eeeeeqqqqqqqqeeee	chr6:4707128-4707378(+)$1	250	217	234	13.9250
cddddqqqqqqqqdddd	chr5:54023943-54024186(+)$1	243	221	238	14.2523
=====qqqqqqqq====	chr10:128378559-128378803(+)$1	244	57	74	13.5482
####aqqqqqqqqa333	chr2:130335813-130336110(+)$1	297	181	198	12.5942
&ddddqqqqqqqqdddd	chr9:118474724-118474960(+)$1	236	46	63	13.7297
g[cccqqqqqqqqcccg	chr9:54484054-54484292(-)$1	238	184	201	13.6108
iiiiiqqqqqqqqiiii	chr14:12808906-12809161(+)$1	255	33	50	13.4598
eeebbqqqqqqqqbb]e	chr5:65949653-65949913(+)$1	260	53	70	12.6604
:ddddqqqqqqqqdddd	chr9:77608895-77609136(+)$1	241	66	83	13.3994
gggggqqqqqqqqgggg	chr10:60793405-60793642(-)$1	237	90	107	13.4016
!ddddqqqqqqqqdddd	chr19:57141349-57141587(-)$1	238	91	108	14.3748
d[cccqqqqqqqqccc]	chr11:115560286-115560540(-)$1	254	3	20	13.4704
[ddddqqqqqqqqdddd	chr5:100391188-100391427(-)$1	239	202	219	14.3952
eeeeeqqqqqqqqeeee	chr11:77635356-77635618(+)$1	262	146	163	13.9250
eeeeeqqqqqqqqeeee	chr15:98570173-98570480(-)$1	307	48	65	13.9250
bbcccqqqqqqqqccc]	chr11:3555006-3555241(+)$1	235	183	200	13.0359
cc[bbqqqqqqqqbb]c	chr19:9088504-9088758(+)$1	254	183	200	12.3450
ddd[aqqqqqqqqa]dd	chr18:50038263-50038521(+)$1	258	8	25	13.6552
eeeeeqqqqqqqqeeee	chr6:86814142-86814377(+)$1	235	204	221	13.9250
[ddddqqqqqqqqdddd	chr11:32162017-32162257(-)$1	240	139	156	14.3952
fffffqqqqqqqqffff	chr16:72765928-72766186(+)$1	258	168	185	12.6371
bddddqqqqqqqqdddd	chr15:25732960-25733220(+)$1	260	149	166	14.0652
fffffqqqqqqqqffff	chr1:137744961-137745200(+)$1	239	184	201	12.6371
fffffqqqqqqqqffff	chr9:72595590-72595885(+)$1	295	215	232	12.6371
fffffqqqqqqqqffff	chr1:158358280-158358533(-)$1	253	101	118	12.6371
[ddddqqqqqqqqdddd	chr15:53142184-53142451(-)$1	267	86	103	14.3952
:ddddqqqqqqqqdddd	chr4:141132603-141132842(-)$1	239	7	24	13.3994
fffffqqqqqqqqffff	chr1:58814143-58814402(+)$1	259	22	39	12.6371
eeeeeqqqqqqqqeeee	chr11:75231336-75231578(-)$1	242	82	99	13.9250
fddddqqqqqqqqdddd	chr5:38939670-38939941(-)$1	271	169	186	14.2234
eeeeeqqqqqqqqeeee	chr12:92797502-92797740(-)$1	238	142	159	13.9250
'ddddqqqqqqqqdddd	chr13:74464182-74464443(-)$1	261	68	85	13.7638
#ddddqqqqqqqqdddd	chr3:69389794-69390041(-)$1	247	210	227	14.2733
ff!!aqqqqqqqqa22f	chr12:71085464-71085699(-)$1	235	89	106	12.5987
eeeeeqqqqqqqqeeee	chr14:8657379-8657647(+)$1	268	37	54	13.9250
:ddddqqqqqqqqdddd	chr10:127566504-127566755(-)$1	251	25	42	13.3994
f[cccqqqqqqqqccc]	chr10:59459175-59459421(-)$1	246	187	204	13.5490
=====qqqqqqqq====	chr1:157127661-157127897(-)$1	236	168	185	13.5482
eeeeeqqqqqqqqeeee	chr19:45489370-45489615(+)$1	245	187	204	13.9250

#otherMatches

#Seq PSSM
CCUGCUCUGAGCUGCAU	chr16:15624614-15624876(-)$1	262	97	114	13.5254
GUCUGUCUGUCUUUGGA	chr7:87896413-87896668(-)$1	255	123	140	12.1064
UUUUUAAAAGAAAAAAA	chr5:122906673-122906935(-)$1	262	140	157	12.1064
UUCAGUAAUUUGUCUGG	chr11:78127861-78128120(+)$1	259	185	202	13.3994
UAGCUGGGAAAGAGGAA	chr17:71339039-71339277(-)$1	238	105	122	11.8202
UUUGCAGAGCCAAGCGA	chr2:93536477-93536731(-)$1	254	158	175	13.5482
GGACUUAUUUAGCAGUU	chrX:136287326-136287570(+)$1	244	204	221	14.3952
UCCCCCUCUUGAUGGGG	chr16:22253273-22253540(-)$1	267	121	138	13.9250
UAGCUUCCUUCACAGCU	chr15:79193423-79193661(-)$1	238	169	186	13.3994
AAGCUAAAAGAUGAGCU	chrX:70933946-70934190(-)$1	244	158	175	14.3952
UUUUCAGGCAAUAGGAA	chr11:50013943-50014255(-)$1	312	90	107	12.6371
GUGCAGUCCUACGUGUG	chr12:114058501-114058773(-)$1	272	15	32	13.9250
CUGGGACACCAACCCCA	chr2:117948950-117949206(+)$1	256	198	215	14.3748
GUGAGGAUCAGAGCUUG	chr3:136481682-136481917(+)$1	235	103	120	12.1064
CUCUUAUUUGAAAAAGA	chr9:44732087-44732348(-)$1	261	147	164	13.9250
UAGGUAAAAGUUAGGCU	chr6:51411881-51412141(-)$1	260	224	241	13.6552
GAGUCUCCUUACUGACC	chr10:128358464-128358705(-)$1	241	89	106	13.5482
CAGUUUUCGUCUUGACU	chr6:4707128-4707378(+)$1	250	217	234	13.9250
acaagcaccucuacuug	chr5:54023943-54024186(+)$1	243	221	238	14.2523
GCCAACAGCUACCUUGG	chr10:128378559-128378803(+)$1	244	57	74	13.5482
UCUUCUGCCCACUGUCU	chr2:130335813-130336110(+)$1	297	181	198	12.5942
AGCACCAAGGACAGUGU	chr9:118474724-118474960(+)$1	236	46	63	13.7297
CUGUGGGAGAAGAUACG	chr9:54484054-54484292(-)$1	238	184	201	13.6108
AGAACCUUGUUUUGuuu	chr14:12808906-12809161(+)$1	255	33	50	13.4598
uggaucacuucaaauac	chr5:65949653-65949913(+)$1	260	53	70	12.6604
UGCAGUUUUAUUUCUGU	chr9:77608895-77609136(+)$1	241	66	83	13.3994
UCCUGGGGUACAGCGGG	chr10:60793405-60793642(-)$1	237	90	107	13.4016
UGUUAUUACAGCUUGAC	chr19:57141349-57141587(-)$1	238	91	108	14.3748
GCCAUCGCCAAAUAUGA	chr11:115560286-115560540(-)$1	254	3	20	13.4704
AGCGGGAACUUCAUUGC	chr5:100391188-100391427(-)$1	239	202	219	14.3952
UGCUGGCUCUGGACAGC	chr11:77635356-77635618(+)$1	262	146	163	13.9250
GGCACUGGUUGCUGUGC	chr15:98570173-98570480(-)$1	307	48	65	13.9250
gccucugccuucugagu	chr11:3555006-3555241(+)$1	235	183	200	13.0359
GCCCCAAAUUUAAGGUG	chr19:9088504-9088758(+)$1	254	183	200	12.3450
ACUCGAUCCAUGACCAG	chr18:50038263-50038521(+)$1	258	8	25	13.6552
augguggcucacaacca	chr6:86814142-86814377(+)$1	235	204	221	13.9250
cuauguccacuuuuaua	chr11:32162017-32162257(-)$1	240	139	156	14.3952
UCAGCUUUCCUUUGCUG	chr16:72765928-72766186(+)$1	258	168	185	12.6371
GCCUCUUCCCUAUGGGG	chr15:25732960-25733220(+)$1	260	149	166	14.0652
ACAAGAGAAACCACUUG	chr1:137744961-137745200(+)$1	239	184	201	12.6371
GAGUUCCAUGUAUGACU	chr9:72595590-72595885(+)$1	295	215	232	12.6371
ACAGCCAUUUCACGUUG	chr1:158358280-158358533(-)$1	253	101	118	12.6371
UGAAUUUCUUUUUAUUC	chr15:53142184-53142451(-)$1	267	86	103	14.3952
ucugcauuugaaggcag	chr4:141132603-141132842(-)$1	239	7	24	13.3994
ucuuuaaaaaaaaaaag	chr1:58814143-58814402(+)$1	259	22	39	12.6371
CCGGGAUGCAGGCCCUG	chr11:75231336-75231578(-)$1	242	82	99	13.9250
CUCCAUUUCUUUCUGGA	chr5:38939670-38939941(-)$1	271	169	186	14.2234
GAUUUAAAGAAAAGGAU	chr12:92797502-92797740(-)$1	238	142	159	13.9250
AGUAUGUCUCCAGAUGC	chr13:74464182-74464443(-)$1	261	68	85	13.7638
gacugcaauagaacagu	chr3:69389794-69390041(-)$1	247	210	227	14.2733
CCAACAAUUCCCAGACG	chr12:71085464-71085699(-)$1	235	89	106	12.5987
CAGAACCUGAUUUUUCU	chr14:8657379-8657647(+)$1	268	37	54	13.9250
GAAGUUAAUUUAUACUU	chr10:127566504-127566755(-)$1	251	25	42	13.3994
UGUUCACCUACCCGAAA	chr10:59459175-59459421(-)$1	246	187	204	13.5490
UCUGUCAGUUUCUAUGG	chr1:157127661-157127897(-)$1	236	168	185	13.5482
AAGUUUUUCAUCUAACU	chr19:45489370-45489615(+)$1	245	187	204	13.9250

#DB
(((((........))).	chr16:15624614-15624876(-)$1	1	97	114	13.5254
(((((........))))	chr7:87896413-87896668(-)$1	1	123	140	12.1064
(((((........))))	chr5:122906673-122906935(-)$1	1	140	157	12.1064
.((((........))))	chr11:78127861-78128120(+)$1	1	185	202	13.3994
(..((........))..	chr17:71339039-71339277(-)$1	1	105	122	11.8202
(((((........))))	chr2:93536477-93536731(-)$1	1	158	175	13.5482
.((((........))))	chrX:136287326-136287570(+)$1	1	204	221	14.3952
(((((........))))	chr16:22253273-22253540(-)$1	1	121	138	13.9250
.((((........))))	chr15:79193423-79193661(-)$1	1	169	186	13.3994
.((((........))))	chrX:70933946-70934190(-)$1	1	158	175	14.3952
(((((........))))	chr11:50013943-50014255(-)$1	1	90	107	12.6371
(((((........))))	chr12:114058501-114058773(-)$1	1	15	32	13.9250
.((((........))))	chr2:117948950-117949206(+)$1	1	198	215	14.3748
(((((........))))	chr3:136481682-136481917(+)$1	1	103	120	12.1064
(((((........))))	chr9:44732087-44732348(-)$1	1	147	164	13.9250
(((.(........).))	chr6:51411881-51412141(-)$1	1	224	241	13.6552
(.(((........))))	chr10:128358464-128358705(-)$1	1	89	106	13.5482
(((((........))))	chr6:4707128-4707378(+)$1	1	217	234	13.9250
(((((........))))	chr5:54023943-54024186(+)$1	1	221	238	14.2523
(((((........))))	chr10:128378559-128378803(+)$1	1	57	74	13.5482
....(........)...	chr2:130335813-130336110(+)$1	1	181	198	12.5942
.((((........))))	chr9:118474724-118474960(+)$1	1	46	63	13.7297
(.(((........))))	chr9:54484054-54484292(-)$1	1	184	201	13.6108
(((((........))))	chr14:12808906-12809161(+)$1	1	33	50	13.4598
(((((........)).)	chr5:65949653-65949913(+)$1	1	53	70	12.6604
.((((........))))	chr9:77608895-77609136(+)$1	1	66	83	13.3994
(((((........))))	chr10:60793405-60793642(-)$1	1	90	107	13.4016
.((((........))))	chr19:57141349-57141587(-)$1	1	91	108	14.3748
(.(((........))).	chr11:115560286-115560540(-)$1	1	3	20	13.4704
.((((........))))	chr5:100391188-100391427(-)$1	1	202	219	14.3952
(((((........))))	chr11:77635356-77635618(+)$1	1	146	163	13.9250
(((((........))))	chr15:98570173-98570480(-)$1	1	48	65	13.9250
(((((........))).	chr11:3555006-3555241(+)$1	1	183	200	13.0359
((.((........)).)	chr19:9088504-9088758(+)$1	1	183	200	12.3450
(((.(........).))	chr18:50038263-50038521(+)$1	1	8	25	13.6552
(((((........))))	chr6:86814142-86814377(+)$1	1	204	221	13.9250
.((((........))))	chr11:32162017-32162257(-)$1	1	139	156	14.3952
(((((........))))	chr16:72765928-72766186(+)$1	1	168	185	12.6371
(((((........))))	chr15:25732960-25733220(+)$1	1	149	166	14.0652
(((((........))))	chr1:137744961-137745200(+)$1	1	184	201	12.6371
(((((........))))	chr9:72595590-72595885(+)$1	1	215	232	12.6371
(((((........))))	chr1:158358280-158358533(-)$1	1	101	118	12.6371
.((((........))))	chr15:53142184-53142451(-)$1	1	86	103	14.3952
.((((........))))	chr4:141132603-141132842(-)$1	1	7	24	13.3994
(((((........))))	chr1:58814143-58814402(+)$1	1	22	39	12.6371
(((((........))))	chr11:75231336-75231578(-)$1	1	82	99	13.9250
)((((........))))	chr5:38939670-38939941(-)$1	1	169	186	14.2234
(((((........))))	chr12:92797502-92797740(-)$1	1	142	159	13.9250
.((((........))))	chr13:74464182-74464443(-)$1	1	68	85	13.7638
.((((........))))	chr3:69389794-69390041(-)$1	1	210	227	14.2733
((..(........)..)	chr12:71085464-71085699(-)$1	1	89	106	12.5987
(((((........))))	chr14:8657379-8657647(+)$1	1	37	54	13.9250
.((((........))))	chr10:127566504-127566755(-)$1	1	25	42	13.3994
(.(((........))).	chr10:59459175-59459421(-)$1	1	187	204	13.5490
(((((........))))	chr1:157127661-157127897(-)$1	1	168	185	13.5482
(((((........))))	chr19:45489370-45489615(+)$1	1	187	204	13.9250

#PSSM
e : 0.21	f : 0.16	: : 0.08	[ : 0.08	c : 0.07	d : 0.07	h : 0.05	= : 0.05	! : 0.03	# : 0.03	g : 0.03	b : 0.03	& : 0.01	i : 0.01	' : 0.01	
d : 0.35	e : 0.21	f : 0.12	[ : 0.07	h : 0.05	= : 0.05	c : 0.03	! : 0.01	# : 0.01	i : 0.01	g : 0.01	b : 0.01	
d : 0.35	e : 0.21	c : 0.10	f : 0.10	h : 0.05	= : 0.05	! : 0.03	# : 0.01	i : 0.01	g : 0.01	[ : 0.01	
d : 0.32	e : 0.19	c : 0.10	f : 0.10	h : 0.05	b : 0.05	= : 0.05	[ : 0.03	# : 0.01	i : 0.01	g : 0.01	! : 0.01	
d : 0.32	e : 0.19	c : 0.10	f : 0.10	a : 0.07	h : 0.05	b : 0.05	= : 0.05	i : 0.01	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	
d : 0.32	e : 0.19	c : 0.10	f : 0.10	a : 0.07	h : 0.05	b : 0.05	= : 0.05	i : 0.01	g : 0.01	
d : 0.32	e : 0.19	c : 0.10	f : 0.10	h : 0.05	b : 0.05	= : 0.05	] : 0.03	3 : 0.01	i : 0.01	g : 0.01	2 : 0.01	
d : 0.35	e : 0.19	c : 0.10	f : 0.10	h : 0.05	= : 0.05	2 : 0.03	] : 0.03	3 : 0.01	i : 0.01	g : 0.01	
d : 0.35	e : 0.21	f : 0.12	] : 0.07	h : 0.05	= : 0.05	c : 0.03	g : 0.03	2 : 0.01	3 : 0.01	i : 0.01	

#score	754.924127674781
#seq	56
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_CDS_m1_run1.txt

#BEAR
eeccc[a[eeeee[bbnnnnnbbeeeee]a]ccc22ee	chr4:46172478-46172698(+)$1	220	81	119	12.3267
eee[a!!iiiiiiiiiooooooiiiiiiiii8888888	chr5:46087620-46087840(+)$1	220	169	207	11.5283
cccffffff####cccnnnnncccffffff22cccccc	chr2:70527239-70527459(+)$1	220	63	101	13.8121
[ddddccc[ccc!!bboooooobb4444cccccc]ddd	chr6:113265359-113265580(+)$1	221	171	209	14.5379
iii"""eeeee[cccooooooccceeeee333iiiiii	chr10:127645540-127645761(+)$1	221	30	68	14.7018
$$$$$ggggggg!!bbnnnnnbb]gggggggeeeeedd	chr7:148402921-148403141(+)$1	220	108	146	12.4251
==========ccc[bblllbb]ccc333==========	chr5:110738057-110738277(+)$1	220	88	126	12.8733
!dddd!!iiiiiiiiiooooooiiiiiiiii22dddd2	chr5:144638407-144638631(+)$1	224	167	205	13.3350
hhhhhhhhdddd[cccnnnnnccc]dddd333hhhhhh	chr19:8954855-8955075(-)$1	220	162	200	12.2525
dddd!!ffffff!!bboooooobbffffffdddd]ccc	chr17:83809369-83809612(+)$1	243	24	62	12.2469
ddda:ccccccccc[bbnnnnnbb]ccc]ccc]cccee	chr1:162142684-162142909(-)$1	225	79	117	11.5213
fffff"""bb!!cccooooooccc22bb4444ffffff	chr5:30582666-30582886(+)$1	220	46	84	13.3112
$$$$$ggggggg[cccmmmmccc333ggggggg333ff	chr7:19590642-19590869(+)$1	227	156	194	12.4734
dd"""ccca!!ccc[bbaooooooa]bbccc22a]ccc	chr3:134914386-134914606(+)$1	220	44	82	12.1364
ee####ccc!!eeeeeooooooeeeee22ccc22eeee	chr1:136456895-136457115(+)$1	220	179	217	12.1375
[bb[dddd####ddddoooooodddd333dddd]bbbb	chrX:20450486-20450706(+)$1	220	66	104	11.8129
cc!!ccc"""dddd[bboooooobbdddd]ccc22ccc	chr11:79927601-79927821(+)$1	220	89	127	11.8332
ggggggg####ccc[ammmma]cccggggggg]fffff	chr17:33956692-33956912(+)$1	220	108	146	11.7854
c!!cccffffff!!bbnnnnnbb22ffffff22ccccc	chr2:90843874-90844094(+)$1	220	3	41	12.6098
ccc[dddd[ccc[cccnnnnnccc]ccc22dddd]ccc	chr19:41986466-41986686(+)$1	220	14	52	14.6567
!!a[ccceeeee[cccooooooccc22eeeee]ccca2	chr8:24522544-24522764(+)$1	220	73	111	13.9399
bb!!ffffff"""cccmmmmccc333ffffff333bb]	chr9:62225260-62225480(+)$1	220	157	195	12.0648
ddd####bb[ccc[bboooooobb]ccc333bb4444d	chr7:13896264-13896484(+)$1	220	70	108	14.2711
bbeeeee[ccc"""bbnnnnnbb4444ccc]eeeee]b	chr5:135694043-135694263(+)$1	220	100	138	13.1463
eeeee####bb[cccooooooccc]bb4444eeeee33	chr16:91858374-91858594(+)$1	220	71	109	13.3711
dddd"""bb[ccc[bbnnnnnbb]ccc]bb333dddd4	chr16:5238644-5238865(+)$1	221	139	177	12.5707
eee[ggggggga[cccnnnnnccc]a]ggggggg333e	chr9:123451371-123451591(+)$1	220	123	161	15.4429
ggg[a[dddd"""cccmmmmcccdddda]ggggggg]b	chr11:120650661-120650881(-)$1	220	23	61	11.7197
bbffffff!!ccccccnnnnnccc333ccc22ffffff	chr11:74759581-74759801(+)$1	220	17	55	14.0363
###ccc[ccc"""cccmmmmccc4444ccc]ccc4444	chr12:104646372-104646595(-)$1	223	149	187	13.8179
ddd!!ccc[dddd[bboooooobb]dddd]ccc333dd	chr7:86589210-86589430(+)$1	220	11	49	13.9642
ccc[iiiiiiiiicccnnnnnccc]iiiiiiiii]ccc	chr1:173934713-173934934(-)$1	221	135	173	15.7415
fbb!!ffffff!!cccooooooccc22ffffff22bb]	chr1:60328991-60329212(+)$1	221	122	160	13.2027
iiiii"""ccc!!ddddllldddd]ccc333iiiiiii	chr1:187100920-187101141(+)$1	221	18	56	13.1003
cc!!eeeee!!ccc[annnnna]ccc]eeeee]ccc22	chr15:76005253-76005473(-)$1	220	162	200	13.2735
#bb!!===========mmmm===========bb22bb]	chr6:71835412-71835632(-)$1	220	73	111	11.6561
fff####ccc"""ddddllldddd333ccc333fffff	chr1:34348534-34348774(+)$1	240	86	124	12.8856
eccc!!ccc[a[ddddnnnnndddda]ccc333ccc]e	chr18:37926248-37926468(+)$1	220	40	78	14.1359
a[bb!!dddd!!cccooooooccc]dddd22bb]a333	chr14:21512880-21513100(+)$1	220	116	154	13.8605
bb!!bb"""bb!!bboooooobb22bb333bbbbdddd	chr13:55315209-55315429(+)$1	220	110	148	11.2944
%%hhhhhhhh"""cccnnnnnccc333hhhhhhhh444	chr6:108764880-108765100(+)$1	220	96	134	12.1615
ccc[dddd"""ccc[aooooooa]cccddddccc]ddd	chr2:181114748-181114968(+)$1	220	153	191	13.6287
hhbbdddd[ccc[cccnnnnnccc]ccc22dddd]bb:	chr6:122663274-122663495(+)$1	221	181	219	12.2201
###bbccc[a[ddddoooooodddd]a]ccc]bb22bb	chr11:88843213-88843464(+)$1	251	65	103	11.6507
:bbggggggg!!ddddoooooodddd]ggggggg]bbb	chr6:92133768-92133988(-)$1	220	40	78	12.0082
eeeedddd[bb!!cccnnnnnccc333bb22dddd]ee	chr10:127000735-127000955(-)$1	220	11	49	13.5329
!ffffff!!a"""cccooooooccc333a22ffffff2	chr1:173268367-173268589(+)$1	222	82	120	14.8469
eeeee####ccc!!bboooooobb333ccc333eeeee	chr3:113916084-113916304(+)$1	220	41	79	15.1908
dd:eeeeeccc[cccooooooccc22ccc333eeeee:	chr2:24808693-24808915(+)$1	222	144	182	12.3044
hhhhhccc[bb[ccc[aooooooa]ccc]bbccc22hh	chr13:73932535-73932755(+)$1	220	140	178	11.9762
b[ccc####bb!!cccnnnnnccc333bb4444ccc33	chr14:48326006-48326226(+)$1	220	158	196	15.7177
fffffcccccceeeeennnnneeeee333ccc]ccc]f	chrX:71488150-71488371(-)$1	221	131	169	11.9407
c[a[ccc[bb[ccc[annnnna]cccbb]ccc]a22cc	chr9:113682734-113682970(+)$1	236	120	158	13.8208
###ggggggg"""cccnnnnnccc]ggggggg4444dd	chr10:25223901-25224125(+)$1	224	68	106	15.7247
cc"""eeeee"""cccnnnnnccceeeeeccc]bbccc	chr2:101524722-101524942(+)$1	220	63	101	14.1364
"ccc[cccdddd!!ccclllccc22dddd22ccc]ccc	chr6:125070385-125070606(+)$1	221	16	54	12.3434
dd!!dddd!!gggggggoooooogggggggdddd]ddd	chr18:6216844-6217064(-)$1	220	109	147	11.5757
iiii!!a[dddd[cccnnnnncccdddd]a]iiiiiii	chr2:164596716-164596936(+)$1	220	100	138	14.4043
========[a[eeeeeooooooeeeee]a=========	chr19:21354925-21355188(+)$1	263	194	232	13.5378
gggggggeeeee!!bbnnnnnbb22eeeee22gggggg	chr2:130358747-130358967(+)$1	220	17	55	12.8100
ggggggg!!dddd[bboooooobb]dddd333gggggg	chrX:10161077-10161297(+)$1	220	11	49	14.2740

#otherMatches

#Seq PSSM
GCGUCUGGACACGAUGAGUACCACGUGUGUUGACAGGU	chr4:46172478-46172698(+)$1	220	81	119	12.3267
UGUGCAUUGACUGCACCUUGAAGUGCAGUUGUUUUCGC	chr5:46087620-46087840(+)$1	220	169	207	11.5283
ACCUCCCUGCUCCGCACAUCAUGCCAGGGGUCGGUUUG	chr2:70527239-70527459(+)$1	220	63	101	13.8121
AUCCCGCCACACAGGUACACAGGCAACAGUGGGCAGGG	chr6:113265359-113265580(+)$1	221	171	209	14.5379
UGGCCCCACUUCAGAACGCUAUCUAAGUGAUUCCAGAC	chr10:127645540-127645761(+)$1	221	30	68	14.7018
CGGACAGGGCCUAGCCUGUCUGGAAGGCCCUCCUCAGA	chr7:148402921-148403141(+)$1	220	108	146	12.4251
AGAGGGGUCUCCUGUCACUGAGAGGUAAAGACCUCUUU	chr5:110738057-110738277(+)$1	220	88	126	12.8733
CUUGACCUGUGUUUAUUAUGCUGUAAAUGUAUUUCAAU	chr5:144638407-144638631(+)$1	224	167	205	13.3350
UCUUGGUGCUCCGGACAUGGAGUCGGGAGAUACACCAG	chr19:8954855-8955075(-)$1	220	162	200	12.2525
UGACGUUCAAGACCGCCUCUCAGCUCUUGAGUCACGAG	chr17:83809369-83809612(+)$1	243	24	62	12.2469
CAGCUCCGGCCUCGGGUCUGACGCGCGACGGCAUGGCU	chr1:162142684-162142909(-)$1	225	79	117	11.5213
GUUUACUUUGUUGUGACUGUGUACUCCAUCUUUGGACG	chr5:30582666-30582886(+)$1	220	46	84	13.3112
CCGCAGCUUCCGAGAGCCUGCUCCUGCGGAGGCCCUGC	chr7:19590642-19590869(+)$1	227	156	194	12.4734
GCAGAUGCCAGUGAAGCCAAGAAGGAGCUCAAGGAGCA	chr3:134914386-134914606(+)$1	220	44	82	12.1364
CCCAUAGCCGAGCAGACUGGGAUCUGUAAGGUGCGGCC	chr1:136456895-136457115(+)$1	220	179	217	12.1375
ACUCUGAGCCCUGCUCAGCAAAGAGCUUUCUCAAAGAC	chrX:20450486-20450706(+)$1	220	66	104	11.8129
GGUAGGCAAAUCCUGUCUCAGCUGAAGGAAGCUACCCA	chr11:79927601-79927821(+)$1	220	89	127	11.8332
GGGUUCUUCGAGGGGUGAAAAGCCUGGGGCCUGAGCUG	chr17:33956692-33956912(+)$1	220	108	146	11.7854
UAAGAUGGUAUCCCACAAUAAGUUAGAUAUUCAGUCAG	chr2:90843874-90844094(+)$1	220	3	41	12.6098
GGCUGCGAAGAGAAUCUCGGCGAUCCUCAGUUGCUGCU	chr19:41986466-41986686(+)$1	220	14	52	14.6567
GUCUGGACCGGCCCAUCUACCCGUGUCGCUGGCUCUGC	chr8:24522544-24522764(+)$1	220	73	111	13.9399
ACUAAGGAAUGAACCUGUUUGGGGAAAUUCCUAUUGUG	chr9:62225260-62225480(+)$1	220	157	195	12.0648
CCUACUACUAUCCUCUCUCACAGGUGGACAAAGAAAAA	chr7:13896264-13896484(+)$1	220	70	108	14.2711
UCCAGGAGAGAGAAACAAAAGGUAAAAUUUGUCCUGAG	chr5:135694043-135694263(+)$1	220	100	138	13.1463
UUCUCCAGAGUUUAUUGCCAUGUACACAUACGAGAGUU	chr16:91858374-91858594(+)$1	220	71	109	13.3711
ACCAAUGCUAUGCGGGAGGACCUGGCAGAGAACUGGUG	chr16:5238644-5238865(+)$1	221	139	177	12.5707
UUGUGAUGAUGGAGCAGAUGAUGUACUCAUCAUUGACC	chr9:123451371-123451591(+)$1	220	123	161	15.4429
UUAAGACCAAAUUAGAGAAGUCUUUGGCCUGGAAAGGG	chr11:120650661-120650881(-)$1	220	23	61	11.7197
GGGGAUGACACUACUCGCCUGGAGAUUUGGAUUCAUCC	chr11:74759581-74759801(+)$1	220	17	55	14.0363
ACAGCCAGGUUCAAGCACGAGUUAACUGCCCGGUCAAU	chr12:104646372-104646595(-)$1	223	149	187	13.8179
UGGAAGCAAUGCUCGGUACUGCCCCAGCAAUGUGGGCC	chr7:86589210-86589430(+)$1	220	11	49	13.9642
UGAGGAAUUUGUGGAUCCCAAGUCACAUAAGUUCGUCA	chr1:173934713-173934934(-)$1	221	135	173	15.7415
AGCUUCCUGUUUUUAUGAACAGAUGUUGACAGGCUGCU	chr1:60328991-60329212(+)$1	221	122	160	13.2027
GAAAGUCAGGCAGUGGCCAUGCUGAGCCCUCCUUUCUG	chr1:187100920-187101141(+)$1	221	18	56	13.1003
CGCCGCCUCACUGCCGAAGACCUGUACGAGGCCCGGAU	chr15:76005253-76005473(-)$1	220	162	200	13.2735
UCAGUUUGAUUUGUUCACUGGAACAAAUUGAUGUCACC	chr6:71835412-71835632(-)$1	220	73	111	11.6561
UUCCCUUUCAGACCUUCAUGGAAGAAAUGACCAGAAAA	chr1:34348534-34348774(+)$1	240	86	124	12.8856
CCCGAAUGCUCACUUCUCACUGGAGGUGCAGAACGGAG	chr18:37926248-37926468(+)$1	220	40	78	14.1359
GGCAGCUACUGAGCUAAAGCAAGUGGGUAAAUGGCAUA	chr14:21512880-21513100(+)$1	220	116	154	13.8605
GGAAGCAAUGAAAAGACAGCCCUCCUCCCAGCCCCCAC	chr13:55315209-55315429(+)$1	220	110	148	11.2944
GAUCUGGGACAUAGGCGGACAGCCCCGGUUCCGGAGCA	chr6:108764880-108765100(+)$1	220	96	134	12.1615
CUGAGGCAGUAUGGGCUCCAGUGGCUAUGCCCAGAGGA	chr2:181114748-181114968(+)$1	220	153	191	13.6287
UGCCAGUGAUUUGGAGGUGAAUUUGGAAGCCACUAGGG	chr6:122663274-122663495(+)$1	221	181	219	12.2201
GUACGCCUGUCCCCACCAGUUUGGGAAGAGGAUGGGGG	chr11:88843213-88843464(+)$1	251	65	103	11.6507
UCCCGAUCCGCCGUACGCUGCAGUACCUGGGUCGCGGG	chr6:92133768-92133988(-)$1	220	40	78	12.0082
GGGGAGCCAGUCAUGCCCUUAGCACCUACCAGGCUGCC	chr10:127000735-127000955(-)$1	220	11	49	13.5329
GCGGGCCUAAAGAGGCGGGCAAGCCAGGUGUGGCCCGA	chr1:173268367-173268589(+)$1	222	82	120	14.8469
UUUCCAACAGGUAAGAAUUUCAUCGUGGCCAAAGGAGA	chr3:113916084-113916304(+)$1	220	41	79	15.1908
CUGCAGCUGGUACCAUGGGGCUGGCGACCCAAAGCUGA	chr2:24808693-24808915(+)$1	222	144	182	12.3044
CACCAUGCUAGUUGGCAUCUACUUCCCGUCUGUAACUG	chr13:73932535-73932755(+)$1	220	140	178	11.9762
UGCGCACAGGUGAGACGCUCAGUCAGAACACAAGCGAA	chr14:48326006-48326226(+)$1	220	158	196	15.7177
GGCUAAGACUGUCUGGUCAACCUAGAAGGUAGCUCUAU	chrX:71488150-71488371(-)$1	221	131	169	11.9407
CUGAGGAUUGAUUUGUGUAAAAGAGACAUUCCCCCUGC	chr9:113682734-113682970(+)$1	236	120	158	13.8208
ACAAUUUCUGAUGCCUCACAAAGGACAGAAAUCUCCAC	chr10:25223901-25224125(+)$1	224	68	106	15.7247
GAACCUCUCCAGCUCCUUCAUGGAGGAGAUCCAGGGCU	chr2:101524722-101524942(+)$1	220	63	101	14.1364
AGGUGUGUGUGGCCGGCCCCGCCCCCCACCCACGGGCC	chr6:125070385-125070606(+)$1	221	16	54	12.3434
UUUCAUCUAGCUUCUGGCAUCAACCAGAAGGGAUCAAG	chr18:6216844-6217064(-)$1	220	109	147	11.5757
GCCUUCCCUGAGUCAGACAACCUGUUCAAGUGGGUGGG	chr2:164596716-164596936(+)$1	220	100	138	14.4043
CAUUAAAGAGCAGAUGCAUGGCCAUUUUCCUUUGAUGU	chr19:21354925-21355188(+)$1	263	194	232	13.5378
AAACAAGAUUGGAUCUAGUGAAGUGUUAAuugcuuguu	chr2:130358747-130358967(+)$1	220	17	55	12.8100
GUCCUGGGAGACUGAGAGGAACCUGAGUCAGAUUAGGA	chrX:10161077-10161297(+)$1	220	11	49	14.2740

#DB
(((((.(.(((((.((.....))))))).).)))..))	chr4:46172478-46172698(+)$1	1	81	119	12.3267
(((.(..(((((((((......))))))))).......	chr5:46087620-46087840(+)$1	1	169	207	11.5283
(((((((((....(((.....)))))))))..))))))	chr2:70527239-70527459(+)$1	1	63	101	13.8121
.(((((((.(((..((......))....)))))).)))	chr6:113265359-113265580(+)$1	1	171	209	14.5379
(((...(((((.(((......))))))))...))))))	chr10:127645540-127645761(+)$1	1	30	68	14.7018
.....(((((((..((.....)).))))))))))))))	chr7:148402921-148403141(+)$1	1	108	146	12.4251
(((((((((((((.((...)).)))...))))))))))	chr5:110738057-110738277(+)$1	1	88	126	12.8733
.((((..(((((((((......)))))))))..)))).	chr5:144638407-144638631(+)$1	1	167	205	13.3350
((((((((((((.(((.....))).))))...))))))	chr19:8954855-8955075(-)$1	1	162	200	12.2525
((((..((((((..((......)))))))))))).)))	chr17:83809369-83809612(+)$1	1	24	62	12.2469
)))).(((((((((.((.....)).))).))).)))((	chr1:162142684-162142909(-)$1	1	79	117	11.5213
(((((...((..(((......)))..))....))))))	chr5:30582666-30582886(+)$1	1	46	84	13.3112
.....(((((((.(((....)))...)))))))...))	chr7:19590642-19590869(+)$1	1	156	194	12.4734
((...((((..(((.(((......).)))))..).)))	chr3:134914386-134914606(+)$1	1	44	82	12.1364
((....(((..(((((......)))))..)))..))))	chr1:136456895-136457115(+)$1	1	179	217	12.1375
.((.((((....((((......))))...)))).))))	chrX:20450486-20450706(+)$1	1	66	104	11.8129
((..(((...((((.((......)))))).)))..)))	chr11:79927601-79927821(+)$1	1	89	127	11.8332
(((((((....(((.(....).)))))))))).)))))	chr17:33956692-33956912(+)$1	1	108	146	11.7854
(..(((((((((..((.....))..))))))..)))))	chr2:90843874-90844094(+)$1	1	3	41	12.6098
(((.((((.(((.(((.....))).)))..)))).)))	chr19:41986466-41986686(+)$1	1	14	52	14.6567
..(.((((((((.(((......)))..))))).)))).	chr8:24522544-24522764(+)$1	1	73	111	13.9399
((..((((((...(((....)))...))))))...)).	chr9:62225260-62225480(+)$1	1	157	195	12.0648
(((....((.(((.((......)).)))...))....)	chr7:13896264-13896484(+)$1	1	70	108	14.2711
(((((((.(((...((.....))....))).))))).)	chr5:135694043-135694263(+)$1	1	100	138	13.1463
(((((....((.(((......))).))....)))))..	chr16:91858374-91858594(+)$1	1	71	109	13.3711
((((...((.(((.((.....)).))).))...)))).	chr16:5238644-5238865(+)$1	1	139	177	12.5707
(((.((((((((.(((.....))).).)))))))...)	chr9:123451371-123451591(+)$1	1	123	161	15.4429
(((.(.((((...(((....)))))))).))))))).)	chr11:120650661-120650881(-)$1	1	23	61	11.7197
((((((((..((((((.....)))...)))..))))))	chr11:74759581-74759801(+)$1	1	17	55	14.0363
...(((.(((...(((....)))....))).)))....	chr12:104646372-104646595(-)$1	1	149	187	13.8179
(((..(((.((((.((......)).)))).)))...))	chr7:86589210-86589430(+)$1	1	11	49	13.9642
(((.((((((((((((.....))).))))))))).)))	chr1:173934713-173934934(-)$1	1	135	173	15.7415
(((..((((((..(((......)))..))))))..)).	chr1:60328991-60329212(+)$1	1	122	160	13.2027
(((((...(((..((((...)))).)))...)))))))	chr1:187100920-187101141(+)$1	1	18	56	13.1003
((..(((((..(((.(.....).))).))))).)))..	chr15:76005253-76005473(-)$1	1	162	200	13.2735
.((..(((((((((((....)))))))))))))..)).	chr6:71835412-71835632(-)$1	1	73	111	11.6561
(((....(((...((((...))))...)))...)))))	chr1:34348534-34348774(+)$1	1	86	124	12.8856
((((..(((.(.((((.....))))).)))...))).)	chr18:37926248-37926468(+)$1	1	40	78	14.1359
(.((..((((..(((......))).))))..)).)...	chr14:21512880-21513100(+)$1	1	116	154	13.8605
((..((...((..((......))..))...))))))))	chr13:55315209-55315429(+)$1	1	110	148	11.2944
..((((((((...(((.....)))...))))))))...	chr6:108764880-108765100(+)$1	1	96	134	12.1615
(((.((((...(((.(......).)))))))))).)))	chr2:181114748-181114968(+)$1	1	153	191	13.6287
))((((((.(((.(((.....))).)))..)))).)).	chr6:122663274-122663495(+)$1	1	181	219	12.2201
...(((((.(.((((......)))).).))).))..))	chr11:88843213-88843464(+)$1	1	65	103	11.6507
.(((((((((..((((......)))).))))))).))(	chr6:92133768-92133988(-)$1	1	40	78	12.0082
((((((((.((..(((.....)))...))..)))).))	chr10:127000735-127000955(-)$1	1	11	49	13.5329
.((((((..(...(((......)))...)..)))))).	chr1:173268367-173268589(+)$1	1	82	120	14.8469
(((((....(((..((......))...)))...)))))	chr3:113916084-113916304(+)$1	1	41	79	15.1908
)).((((((((.(((......)))..)))...))))).	chr2:24808693-24808915(+)$1	1	144	182	12.3044
((((((((.((.(((.(......).))).)))))..))	chr13:73932535-73932755(+)$1	1	140	178	11.9762
(.(((....((..(((.....)))...))....)))..	chr14:48326006-48326226(+)$1	1	158	196	15.7177
((((((((((((((((.....)))))...))).))).)	chrX:71488150-71488371(-)$1	1	131	169	11.9407
(.(.(((.((.(((.(.....).))))).))).)..))	chr9:113682734-113682970(+)$1	1	120	158	13.8208
...(((((((...(((.....))).)))))))....))	chr10:25223901-25224125(+)$1	1	68	106	15.7247
((...(((((...(((.....))))))))))).)))))	chr2:101524722-101524942(+)$1	1	63	101	14.1364
.(((.(((((((..(((...)))..))))..))).)))	chr6:125070385-125070606(+)$1	1	16	54	12.3434
((..((((..(((((((......))))))))))).)))	chr18:6216844-6217064(-)$1	1	109	147	11.5757
((((..(.((((.(((.....))))))).).)))))))	chr2:164596716-164596936(+)$1	1	100	138	14.4043
((((((((.(.(((((......))))).))))))))))	chr19:21354925-21355188(+)$1	1	194	232	13.5378
((((((((((((..((.....))..)))))..))))))	chr2:130358747-130358967(+)$1	1	17	55	12.8100
(((((((..((((.((......)).))))...))))))	chrX:10161077-10161297(+)$1	1	11	49	14.2740

#PSSM
c : 0.14	e : 0.13	d : 0.13	b : 0.08	f : 0.06	g : 0.06	# : 0.06	i : 0.04	! : 0.04	h : 0.04	[ : 0.03	$ : 0.03	= : 0.03	a : 0.01	% : 0.01	: : 0.01	" : 0.01	
d : 0.16	c : 0.14	b : 0.13	e : 0.11	f : 0.06	g : 0.06	i : 0.04	h : 0.04	# : 0.04	[ : 0.04	$ : 0.03	= : 0.03	! : 0.03	% : 0.01	
c : 0.13	d : 0.11	e : 0.09	b : 0.09	! : 0.09	f : 0.08	# : 0.06	g : 0.06	i : 0.04	h : 0.04	$ : 0.03	= : 0.03	" : 0.03	a : 0.03	: : 0.01	
[ : 0.14	! : 0.13	c : 0.09	f : 0.08	g : 0.08	e : 0.08	d : 0.06	" : 0.04	h : 0.04	# : 0.04	b : 0.04	$ : 0.03	= : 0.03	i : 0.03	a : 0.01	
d : 0.13	c : 0.11	! : 0.11	f : 0.09	g : 0.09	e : 0.08	" : 0.06	h : 0.04	# : 0.04	a : 0.03	$ : 0.03	= : 0.03	i : 0.03	b : 0.03	: : 0.01	[ : 0.01	
c : 0.21	g : 0.13	! : 0.09	# : 0.09	d : 0.09	f : 0.08	" : 0.06	e : 0.06	= : 0.04	[ : 0.03	h : 0.03	i : 0.01	b : 0.01	
c : 0.21	g : 0.13	d : 0.13	f : 0.11	e : 0.08	# : 0.08	" : 0.06	= : 0.04	a : 0.03	! : 0.03	h : 0.03	[ : 0.01	i : 0.01	
c : 0.19	d : 0.13	f : 0.09	e : 0.09	g : 0.08	[ : 0.06	" : 0.06	# : 0.06	i : 0.04	= : 0.04	h : 0.03	b : 0.03	! : 0.03	
c : 0.14	[ : 0.13	e : 0.09	f : 0.08	g : 0.08	d : 0.08	# : 0.08	b : 0.06	! : 0.06	i : 0.04	" : 0.04	= : 0.03	a : 0.01	h : 0.01	
c : 0.18	d : 0.11	b : 0.11	e : 0.08	g : 0.08	! : 0.08	f : 0.06	i : 0.04	# : 0.04	[ : 0.04	a : 0.04	= : 0.03	" : 0.03	h : 0.01	
c : 0.21	" : 0.14	d : 0.09	! : 0.09	b : 0.08	e : 0.06	g : 0.06	i : 0.04	# : 0.04	f : 0.04	[ : 0.04	= : 0.01	a : 0.01	
c : 0.22	" : 0.14	! : 0.13	d : 0.11	e : 0.09	[ : 0.08	i : 0.04	g : 0.04	# : 0.03	f : 0.03	a : 0.01	= : 0.01	
c : 0.26	! : 0.19	" : 0.14	[ : 0.11	d : 0.11	e : 0.06	i : 0.04	# : 0.01	= : 0.01	g : 0.01	
c : 0.52	! : 0.11	d : 0.11	[ : 0.09	e : 0.04	i : 0.03	" : 0.01	= : 0.01	b : 0.01	g : 0.01	
c : 0.44	b : 0.22	[ : 0.11	d : 0.09	e : 0.04	i : 0.03	= : 0.01	g : 0.01	
c : 0.34	b : 0.26	o : 0.11	d : 0.08	a : 0.06	e : 0.04	i : 0.03	= : 0.01	[ : 0.01	g : 0.01	
n : 0.37	o : 0.37	m : 0.09	b : 0.04	d : 0.03	l : 0.01	a : 0.01	c : 0.01	g : 0.01	
o : 0.42	n : 0.39	m : 0.09	l : 0.06	a : 0.01	
o : 0.44	n : 0.39	m : 0.09	l : 0.06	
o : 0.44	n : 0.39	m : 0.09	l : 0.04	b : 0.01	
o : 0.44	n : 0.39	c : 0.08	d : 0.03	b : 0.01	a : 0.01	= : 0.01	
c : 0.37	o : 0.32	b : 0.11	d : 0.06	] : 0.03	a : 0.03	n : 0.01	= : 0.01	e : 0.01	
c : 0.45	b : 0.22	d : 0.09	o : 0.06	e : 0.04	i : 0.03	] : 0.03	= : 0.01	a : 0.01	
c : 0.40	b : 0.13	d : 0.11	e : 0.06	2 : 0.06	] : 0.04	i : 0.03	3 : 0.03	4 : 0.03	o : 0.01	= : 0.01	a : 0.01	g : 0.01	
] : 0.22	c : 0.14	3 : 0.13	e : 0.09	2 : 0.09	d : 0.09	4 : 0.04	i : 0.03	f : 0.03	g : 0.03	a : 0.01	b : 0.01	= : 0.01	
3 : 0.16	d : 0.16	c : 0.16	e : 0.11	g : 0.06	2 : 0.06	i : 0.04	f : 0.04	4 : 0.04	] : 0.03	b : 0.03	a : 0.03	= : 0.01	
3 : 0.16	c : 0.14	d : 0.13	e : 0.09	g : 0.08	b : 0.08	f : 0.06	] : 0.06	i : 0.04	4 : 0.04	2 : 0.03	= : 0.01	a : 0.01	
c : 0.21	d : 0.13	g : 0.11	e : 0.09	f : 0.08	3 : 0.08	b : 0.08	i : 0.04	] : 0.04	4 : 0.03	2 : 0.01	a : 0.01	= : 0.01	h : 0.01	
c : 0.16	g : 0.11	d : 0.11	] : 0.09	f : 0.08	e : 0.08	3 : 0.08	i : 0.04	2 : 0.04	b : 0.04	= : 0.03	4 : 0.03	a : 0.03	h : 0.01	
c : 0.22	g : 0.13	3 : 0.11	2 : 0.09	f : 0.08	i : 0.04	= : 0.04	4 : 0.04	e : 0.04	a : 0.03	d : 0.03	] : 0.03	b : 0.03	h : 0.01	
c : 0.16	3 : 0.16	2 : 0.11	g : 0.11	d : 0.09	] : 0.06	i : 0.04	= : 0.04	4 : 0.04	f : 0.04	e : 0.03	b : 0.03	h : 0.01	
c : 0.21	3 : 0.13	2 : 0.09	d : 0.09	g : 0.09	e : 0.08	b : 0.06	f : 0.04	i : 0.04	= : 0.03	4 : 0.03	8 : 0.01	h : 0.01	] : 0.01	
c : 0.14	] : 0.11	d : 0.09	g : 0.09	3 : 0.08	b : 0.08	i : 0.06	e : 0.06	2 : 0.06	f : 0.06	= : 0.03	h : 0.03	4 : 0.03	8 : 0.01	
c : 0.22	d : 0.11	e : 0.08	f : 0.08	g : 0.08	i : 0.06	2 : 0.06	3 : 0.04	b : 0.04	= : 0.03	h : 0.03	a : 0.03	] : 0.03	4 : 0.03	8 : 0.01	
] : 0.16	c : 0.13	2 : 0.11	e : 0.09	f : 0.08	d : 0.06	3 : 0.06	i : 0.04	4 : 0.04	g : 0.04	= : 0.03	h : 0.03	b : 0.03	8 : 0.01	a : 0.01	
c : 0.24	d : 0.09	e : 0.09	b : 0.09	f : 0.08	2 : 0.06	3 : 0.06	4 : 0.06	i : 0.04	g : 0.04	= : 0.03	8 : 0.01	h : 0.01	] : 0.01	
c : 0.16	d : 0.14	b : 0.11	e : 0.09	f : 0.09	] : 0.06	3 : 0.06	i : 0.04	4 : 0.04	= : 0.03	h : 0.03	g : 0.03	8 : 0.01	a : 0.01	2 : 0.01	
c : 0.16	d : 0.13	e : 0.11	f : 0.09	b : 0.08	2 : 0.06	i : 0.04	] : 0.04	3 : 0.04	4 : 0.04	= : 0.03	h : 0.03	: : 0.03	g : 0.03	8 : 0.01	

#score	801.6218182532413
#seq	61
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_CDS_m1_run1.txt

#BEAR
b!!bbcccooooooccc]bb]bb	chr13:55651491-55651760(-)$1	269	170	193	11.7945
:eeeee[aooooooa]eeeee:b	chr18:36908130-36908401(+)$1	271	159	182	9.3801
bb[eeeeeooooooeeeee333b	chr7:135038927-135039193(-)$1	266	35	58	11.2002
dddeeeeeooooooeeeee]ddd	chr15:76028312-76028598(-)$1	286	198	221	9.9298
#gggggggooooooggggggg44	chr17:6084525-6084794(+)$1	269	109	132	11.6501
[ccc[cccoooooocccccc]cc	chr5:122096592-122096861(-)$1	269	88	111	12.6571
cc[ffffffooooooffffff]c	chr17:32498259-32498531(-)$1	272	240	263	9.8618
cc[ddddoooooodddd]ccc]a	chr14:64225928-64226213(+)$1	285	252	275	10.0846
fffffcccooooooccc22ffff	chr11:102978353-102978633(+)$1	280	75	98	11.9715
=gggggggooooooggggggg99	chr13:24843895-24844178(-)$1	283	26	49	10.4984
ffff[cccoooooocccffffff	chr6:22240953-22241221(+)$1	268	162	185	12.0309
eeeeecccooooooccc]eeeee	chr7:117008949-117009223(-)$1	274	89	112	12.2067
eeeeecccooooooccc]eeeee	chr2:40774602-40774870(-)$1	268	75	98	12.2067
bb[eeeeeooooooeeeeebb]d	chr11:117828728-117829006(-)$1	278	176	199	10.2634
ffff[cccooooooccc4444ff	chr9:107159264-107159531(-)$1	267	240	263	12.7322
[eeeee[aooooooa]eeeee]b	chr19:5384549-5384817(-)$1	268	125	148	11.3849
fffff[cccnnnnnccc]fffff	chr8:63406007-63406293(-)$1	286	206	229	8.1072
cc"""cccoooooocccccc]ee	chr19:7273750-7274023(-)$1	273	80	103	12.6084
ff!!ccc[ccclllccc]ccc]f	chr5:92391556-92391827(-)$1	271	5	28	8.4065
!ccc[a[bboooooobb]a]ccc	chr6:54767279-54767565(+)$1	286	55	78	10.4591
ccc!!cccooooooccc]ccc22	chr11:97574603-97574878(+)$1	275	67	90	12.8882
iiiiii[aooooooa]iiiiiii	chr4:131358759-131359027(-)$1	268	181	204	11.7225
gbb[bbbboooooobb333bbbb	chr3:146444016-146444284(-)$1	268	92	115	10.1005
ffff!!cccnnnnnccc22ffff	chr19:29086354-29086632(+)$1	278	239	262	8.1330
ee"""cccooooooccc333eee	chr9:37297061-37297336(+)$1	275	181	204	13.1323
===========lll=========	chr2:121205212-121205496(-)$1	284	115	138	8.6631
dd[bbcccooooooccc22bb33	chr2:156606174-156606446(+)$1	272	81	104	11.7874
!dddd[bboooooobb]dddd22	chr14:70066969-70067240(+)$1	271	182	205	9.7879
dddd[cccoooooocccdddd]b	chr5:93697524-93697801(+)$1	277	82	105	11.6624
b!!eeeeeooooooeeeee22bb	chr9:108701514-108701781(+)$1	267	227	250	10.4290
==========lll==========	chr8:23489738-23490016(-)$1	278	3	26	8.7203
b[cccrrrrrrrrrccc]bb333	chr18:24743677-24743947(-)$1	270	79	102	7.6917
ddddddddoooooodddd4444d	chr13:69138020-69138287(-)$1	267	155	178	10.3660
b"""ddddoooooodddd333bb	chr3:96066811-96067101(-)$1	290	64	87	11.0309
f!!ccc[bboooooobb]ccc55	chr3:108706705-108706973(-)$1	268	114	137	9.1918
[ccc[cccooooooccc]ccc]b	chr7:28151330-28151601(-)$1	271	130	153	13.3267
b[ffffffooooooffffff]bb	chr19:4792248-4792540(-)$1	292	104	127	10.5350
:bb[cccbboooooobb]ccc]b	chr2:91803321-91803605(-)$1	284	195	218	9.3148
dd"""cccooooooccc333ddd	chr2:163884396-163884667(-)$1	271	131	154	12.7612
!bb####ccclllccc333bb33	chr13:81930942-81931210(+)$1	268	104	127	7.7556
####ddddooooooddddeeeee	chr8:74844691-74844960(+)$1	269	155	178	10.4104
ff"""cccooooooccc333fff	chr14:45912565-45912837(-)$1	272	156	179	13.1837
hh####bboooooobb333hhhh	chr4:135883045-135883340(+)$1	295	108	131	10.4678
ee[eeeeeooooooeeeee]eee	chr1:36501804-36502071(-)$1	267	87	110	10.6659
!ccc[aooooooa]ccc]ddddc	chr3:51288320-51288589(+)$1	269	67	90	9.5306
b[ffffffooooooffffff]bb	chr11:120481937-120482225(-)$1	288	187	210	10.5350
ffffff[aooooooa]ffffff:	chr5:75006662-75006928(-)$1	266	102	125	10.1451
eeee!!cccnnnnnccc]eeeee	chrX:98514856-98515126(+)$1	270	219	242	8.3242
!!ccc[bboooooobb4444ccc	chr2:153142656-153142935(+)$1	279	142	165	11.5689
[ccc[cccmmmmcccccc]a333	chr1:93275018-93275289(-)$1	271	194	217	7.8457
hhhhacccooooooccc]a4444	chr6:56728722-56729000(-)$1	278	115	138	12.3696
eeeee[bboooooobb]eeeee:	chr2:156359397-156359677(+)$1	280	30	53	9.7840

#otherMatches

#Seq PSSM
AAUGCGGUGAGUGAGCCUGCCUG	chr13:55651491-55651760(-)$1	269	170	193	11.7945
GAUGGUGUGAACAAAGACUAUGA	chr18:36908130-36908401(+)$1	271	159	182	9.3801
ACAGCAGGCCCCGCCCUGCCCCG	chr7:135038927-135039193(-)$1	266	35	58	11.2002
GCCGCUCAGGUUGGUGGGCAGGC	chr15:76028312-76028598(-)$1	286	198	221	9.9298
UCUCUUACCCAGAAGUGAGAGCG	chr17:6084525-6084794(+)$1	269	109	132	11.6501
UGGCGAUUCCACAAGAUGCCUUG	chr5:122096592-122096861(-)$1	269	88	111	12.6571
GUCAGUGCUAGUUGAGGCACUCA	chr17:32498259-32498531(-)$1	272	240	263	9.8618
CUGGGCUAGGUUGAGCCGGGGGU	chr14:64225928-64226213(+)$1	285	252	275	10.0846
GGGGCCUGAAGCACCAGCUGCCC	chr11:102978353-102978633(+)$1	280	75	98	11.9715
UAGAUUUCCGUUUUGAGGUCUUG	chr13:24843895-24844178(-)$1	283	26	49	10.4984
UUCUAGAUCUUCCCAUCAGAAAC	chr6:22240953-22241221(+)$1	268	162	185	12.0309
CGCAGGCUCUACGCGGCUCUGCG	chr7:117008949-117009223(-)$1	274	89	112	12.2067
UUUCUAUGUUUAUUCAUAAGAAA	chr2:40774602-40774870(-)$1	268	75	98	12.2067
GUCGCCUCUCCUCCGAGGCACAU	chr11:117828728-117829006(-)$1	278	176	199	10.2634
AGUGAUCCAGCCAAGGAAUACCA	chr9:107159264-107159531(-)$1	267	240	263	12.7322
UGGCUGGAUGAUACUGCAGCCUG	chr19:5384549-5384817(-)$1	268	125	148	11.3849
UGGGGCUGACUGCAUCACUCCCG	chr8:63406007-63406293(-)$1	286	206	229	8.1072
CUCAGGCUACCUACAGCGGGAGA	chr19:7273750-7274023(-)$1	273	80	103	12.6084
UUAAGGCGUGGCUUCCAAGCUGG	chr5:92391556-92391827(-)$1	271	5	28	8.4065
ACUCAGUGCACAGCAGCCCAGAG	chr6:54767279-54767565(+)$1	286	55	78	10.4591
AGUAGACGUGACUCUGUGACUUU	chr11:97574603-97574878(+)$1	275	67	90	12.8882
UGGGAUGCGGCCCAGAAUCCCAG	chr4:131358759-131359027(-)$1	268	181	204	11.7225
GGCACCGCACAAGAGCACAGGGC	chr3:146444016-146444284(-)$1	268	92	115	10.1005
GUUCUUUAGGACCACUGUUGAAU	chr19:29086354-29086632(+)$1	278	239	262	8.1330
UCAUCGCUGUAUGGGGCAACGAG	chr9:37297061-37297336(+)$1	275	181	204	13.1323
UCAUCCUUCCAGCUUGGGAGGAU	chr2:121205212-121205496(-)$1	284	115	138	8.6631
AACGAGGCGCCAGGGCCCAUCAA	chr2:156606174-156606446(+)$1	272	81	104	11.7874
ACCAUCUGCGAUGACAAGUGGGA	chr14:70066969-70067240(+)$1	271	182	205	9.7879
CCGGAUUAUAUUCUUAACCGGCC	chr5:93697524-93697801(+)$1	277	82	105	11.6624
CAGUACAGUAUCCUUUGUAAAGG	chr9:108701514-108701781(+)$1	267	227	250	10.4290
ACGGCUUCUGAGACAGAAGUUGU	chr8:23489738-23490016(-)$1	278	3	26	8.7203
GGGCUGCAAGAACAAGUGCCAUU	chr18:24743677-24743947(-)$1	270	79	102	7.6917
CCGCGCCGAggcggcggcagcag	chr13:69138020-69138287(-)$1	267	155	178	10.3660
AGAACGUCAUCCGCGACGCAGUC	chr3:96066811-96067101(-)$1	290	64	87	11.0309
AAAGCAAAGAUGAGACUGUGUGA	chr3:108706705-108706973(-)$1	268	114	137	9.1918
AGGUGUCGGAGAAGUGGGACCGU	chr7:28151330-28151601(-)$1	271	130	153	13.3267
UGGAGGCCAUCAGGGGCCUCGAC	chr19:4792248-4792540(-)$1	292	104	127	10.5350
AGCGUGGGUAUCCAAGCGCCAGG	chr2:91803321-91803605(-)$1	284	195	218	9.3148
GGAUGUGGAGAGAGCCAAAGCUC	chr2:163884396-163884667(-)$1	271	131	154	12.7612
AGGAAUUUACGGCGUGUUGCCAG	chr13:81930942-81931210(+)$1	268	104	127	7.7556
GACUGUGGCAGGUUCCACGCGCG	chr8:74844691-74844960(+)$1	269	155	178	10.4104
UUCAGCUCUUCACUGGGAAUAAA	chr14:45912565-45912837(-)$1	272	156	179	13.1837
UUCGUAGGUAAAAUCCCAAGAGA	chr4:135883045-135883340(+)$1	295	108	131	10.4678
UGGGGUCUGGGCCGGGGCCGCGG	chr1:36501804-36502071(-)$1	267	87	110	10.6659
CAAGACGUGCCUGACUUACCGCU	chr3:51288320-51288589(+)$1	269	67	90	9.5306
CAGCCUCUGAACUGGGAGGCAGC	chr11:120481937-120482225(-)$1	288	187	210	10.5350
GACGCGUCCAUCUCGUCGUGUCC	chr5:75006662-75006928(-)$1	266	102	125	10.1451
UUCACCUGCCUACAGCAAUGAGA	chrX:98514856-98515126(+)$1	270	219	242	8.3242
ACUGAAGGAAGCCACCAAGAUCA	chr2:153142656-153142935(+)$1	279	142	165	11.5689
GGGGUCACAUCUGUGCCUGAUAU	chr1:93275018-93275289(-)$1	271	194	217	7.8457
UUCCGCCUGUAUAGGGGACUUGA	chr6:56728722-56729000(-)$1	278	115	138	12.3696
GUGAUGAUAACCACAUGGUCACA	chr2:156359397-156359677(+)$1	280	30	53	9.7840

#DB
(..(((((......))).)).))	chr13:55651491-55651760(-)$1	1	170	193	11.7945
.(((((.(......).))))).(	chr18:36908130-36908401(+)$1	1	159	182	9.3801
((.(((((......)))))...)	chr7:135038927-135039193(-)$1	1	35	58	11.2002
((((((((......))))).)))	chr15:76028312-76028598(-)$1	1	198	221	9.9298
.(((((((......)))))))..	chr17:6084525-6084794(+)$1	1	109	132	11.6501
.(((.(((......)))))).))	chr5:122096592-122096861(-)$1	1	88	111	12.6571
((.((((((......)))))).)	chr17:32498259-32498531(-)$1	1	240	263	9.8618
((.((((......)))).))).)	chr14:64225928-64226213(+)$1	1	252	275	10.0846
((((((((......)))..))))	chr11:102978353-102978633(+)$1	1	75	98	11.9715
((((((((......)))))))..	chr13:24843895-24844178(-)$1	1	26	49	10.4984
((((.(((......)))))))))	chr6:22240953-22241221(+)$1	1	162	185	12.0309
((((((((......))).)))))	chr7:117008949-117009223(-)$1	1	89	112	12.2067
((((((((......))).)))))	chr2:40774602-40774870(-)$1	1	75	98	12.2067
((.(((((......))))))).)	chr11:117828728-117829006(-)$1	1	176	199	10.2634
((((.(((......)))....))	chr9:107159264-107159531(-)$1	1	240	263	12.7322
.(((((.(......).))))).)	chr19:5384549-5384817(-)$1	1	125	148	11.3849
(((((.(((.....))).)))))	chr8:63406007-63406293(-)$1	1	206	229	8.1072
((...(((......)))))).))	chr19:7273750-7274023(-)$1	1	80	103	12.6084
((..(((.(((...))).))).)	chr5:92391556-92391827(-)$1	1	5	28	8.4065
.(((.(.((......)).).)))	chr6:54767279-54767565(+)$1	1	55	78	10.4591
(((..(((......))).)))..	chr11:97574603-97574878(+)$1	1	67	90	12.8882
((((((.(......).)))))))	chr4:131358759-131359027(-)$1	1	181	204	11.7225
(((.((((......))...))))	chr3:146444016-146444284(-)$1	1	92	115	10.1005
((((..(((.....)))..))))	chr19:29086354-29086632(+)$1	1	239	262	8.1330
((...(((......)))...)))	chr9:37297061-37297336(+)$1	1	181	204	13.1323
(((((((((((...)))))))))	chr2:121205212-121205496(-)$1	1	115	138	8.6631
((.(((((......)))..))..	chr2:156606174-156606446(+)$1	1	81	104	11.7874
.((((.((......)).))))..	chr14:70066969-70067240(+)$1	1	182	205	9.7879
((((.(((......))))))).)	chr5:93697524-93697801(+)$1	1	82	105	11.6624
(..(((((......)))))..))	chr9:108701514-108701781(+)$1	1	227	250	10.4290
((((((((((...))))))))))	chr8:23489738-23490016(-)$1	1	3	26	8.7203
(.(((.........))).))...	chr18:24743677-24743947(-)$1	1	79	102	7.6917
((((((((......))))....)	chr13:69138020-69138287(-)$1	1	155	178	10.3660
(...((((......))))...))	chr3:96066811-96067101(-)$1	1	64	87	11.0309
(..(((.((......)).)))..	chr3:108706705-108706973(-)$1	1	114	137	9.1918
.(((.(((......))).))).)	chr7:28151330-28151601(-)$1	1	130	153	13.3267
(.((((((......)))))).))	chr19:4792248-4792540(-)$1	1	104	127	10.5350
.((.(((((......)).))).)	chr2:91803321-91803605(-)$1	1	195	218	9.3148
((...(((......)))...)))	chr2:163884396-163884667(-)$1	1	131	154	12.7612
.((....(((...)))...))..	chr13:81930942-81931210(+)$1	1	104	127	7.7556
....((((......)))))))))	chr8:74844691-74844960(+)$1	1	155	178	10.4104
((...(((......)))...)))	chr14:45912565-45912837(-)$1	1	156	179	13.1837
((....((......))...))))	chr4:135883045-135883340(+)$1	1	108	131	10.4678
((.(((((......))))).)))	chr1:36501804-36502071(-)$1	1	87	110	10.6659
.(((.(......).))).)))))	chr3:51288320-51288589(+)$1	1	67	90	9.5306
(.((((((......)))))).))	chr11:120481937-120482225(-)$1	1	187	210	10.5350
((((((.(......).)))))).	chr5:75006662-75006928(-)$1	1	102	125	10.1451
((((..(((.....))).)))))	chrX:98514856-98515126(+)$1	1	219	242	8.3242
..(((.((......))....)))	chr2:153142656-153142935(+)$1	1	142	165	11.5689
.(((.(((....)))))).)...	chr1:93275018-93275289(-)$1	1	194	217	7.8457
((((((((......))).)....	chr6:56728722-56729000(-)$1	1	115	138	12.3696
(((((.((......)).))))).	chr2:156359397-156359677(+)$1	1	30	53	9.7840

#PSSM
f : 0.17	b : 0.15	e : 0.11	d : 0.09	! : 0.09	[ : 0.07	c : 0.07	= : 0.05	: : 0.03	# : 0.03	h : 0.03	i : 0.01	g : 0.01	
c : 0.17	e : 0.15	f : 0.15	d : 0.11	b : 0.09	! : 0.07	[ : 0.05	g : 0.03	= : 0.03	h : 0.03	i : 0.01	" : 0.01	# : 0.01	
c : 0.15	f : 0.15	e : 0.11	[ : 0.11	" : 0.09	! : 0.07	d : 0.07	b : 0.05	g : 0.03	= : 0.03	# : 0.03	i : 0.01	h : 0.01	
e : 0.21	f : 0.17	c : 0.15	" : 0.09	d : 0.07	# : 0.05	b : 0.03	g : 0.03	! : 0.03	[ : 0.03	= : 0.03	i : 0.01	h : 0.01	
e : 0.19	[ : 0.15	f : 0.11	d : 0.09	c : 0.09	" : 0.07	b : 0.05	! : 0.05	g : 0.03	= : 0.03	# : 0.03	i : 0.01	a : 0.01	
c : 0.38	e : 0.13	f : 0.07	d : 0.07	[ : 0.07	g : 0.03	a : 0.03	! : 0.03	= : 0.03	# : 0.03	i : 0.01	b : 0.01	r : 0.01	
c : 0.42	[ : 0.11	e : 0.09	b : 0.09	d : 0.07	f : 0.05	g : 0.03	= : 0.03	r : 0.01	# : 0.01	o : 0.01	
c : 0.40	b : 0.15	e : 0.09	a : 0.07	f : 0.05	d : 0.05	g : 0.03	o : 0.03	= : 0.03	[ : 0.01	r : 0.01	
o : 0.75	c : 0.09	b : 0.05	= : 0.03	f : 0.01	r : 0.01	m : 0.01	
o : 0.82	n : 0.05	c : 0.03	= : 0.03	r : 0.01	m : 0.01	
o : 0.82	n : 0.05	l : 0.03	c : 0.01	= : 0.01	r : 0.01	m : 0.01	
o : 0.82	l : 0.07	n : 0.05	r : 0.01	m : 0.01	
o : 0.80	l : 0.07	n : 0.05	r : 0.01	a : 0.01	c : 0.01	
o : 0.78	n : 0.05	l : 0.03	c : 0.03	d : 0.01	= : 0.01	r : 0.01	] : 0.01	
c : 0.46	e : 0.09	b : 0.09	a : 0.07	o : 0.07	d : 0.07	g : 0.03	= : 0.03	f : 0.03	
c : 0.46	b : 0.15	e : 0.09	] : 0.07	d : 0.07	f : 0.05	g : 0.03	= : 0.03	
c : 0.44	e : 0.13	f : 0.07	d : 0.07	b : 0.05	3 : 0.05	g : 0.03	= : 0.03	] : 0.03	i : 0.01	4 : 0.01	
] : 0.28	e : 0.15	3 : 0.11	f : 0.09	d : 0.09	c : 0.05	2 : 0.05	g : 0.03	4 : 0.03	= : 0.03	i : 0.01	
e : 0.23	c : 0.15	3 : 0.13	f : 0.11	2 : 0.05	4 : 0.05	d : 0.05	b : 0.03	g : 0.03	a : 0.03	= : 0.03	i : 0.01	] : 0.01	
c : 0.15	f : 0.15	e : 0.13	b : 0.11	3 : 0.09	4 : 0.07	] : 0.05	d : 0.05	g : 0.03	= : 0.03	i : 0.01	2 : 0.01	h : 0.01	a : 0.01	
e : 0.17	c : 0.15	f : 0.13	] : 0.09	d : 0.09	3 : 0.07	b : 0.07	4 : 0.05	g : 0.03	= : 0.03	i : 0.01	2 : 0.01	h : 0.01	
] : 0.15	e : 0.15	f : 0.13	b : 0.11	3 : 0.09	d : 0.05	4 : 0.05	c : 0.05	2 : 0.03	= : 0.03	: : 0.01	9 : 0.01	i : 0.01	5 : 0.01	h : 0.01	
b : 0.23	f : 0.13	e : 0.13	c : 0.09	d : 0.07	3 : 0.07	4 : 0.03	2 : 0.03	= : 0.03	: : 0.03	a : 0.01	9 : 0.01	i : 0.01	5 : 0.01	h : 0.01	

#score	553.2675908257986
#seq	52
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_UTR_m1_run2.txt

#BEAR
gggg"""dddd[ddddllldddd]dddd22gggggg	chr16:84862133-84862371(+)$1	238	22	58	11.6658
b[eeeee[ccc[cccnnnnnccc]ccc]eeeee]bb	chr17:25033940-25034160(+)$1	220	131	167	13.0129
dddd!!ggggggg[annnnna]ggggggg22dddd:	chr3:38350544-38350764(-)$1	220	91	127	11.5778
eee[===========mmmm===========eeeeef	chr4:26251611-26251831(-)$1	220	98	134	12.7574
f####ccc[ffffffooooooffffff]ccc333ff	chr14:58421000-58421220(+)$1	220	49	85	11.3398
eeee[cccdddd[cccmmmmccc22dddd]ccceee	chr7:96289557-96289777(-)$1	220	137	173	11.4712
a[ccc!!ccc"""cccmmmmccc]ccc22ccca22c	chr15:98568109-98568329(-)$1	220	170	206	13.0820
gggggggggg[fffffflllffffff4444gggggg	chr4:33108097-33108317(+)$1	220	169	205	11.2345
c[ccc[dddd####ccclllccc4444dddd]ccc]	chr4:132925692-132925916(+)$1	224	122	158	12.3836
gggggg[a[a!!cccnnnnnccc4444a]a]ggggg	chr1:95263641-95263903(+)$1	262	10	46	16.5117
hhhhhhh"""a!!bbnnnnnbb22ahhhhhhhh333	chr18:77873293-77873513(-)$1	220	49	85	12.6291
&eeeeeiiiiiiiiinnnnniiiiiiiii333eeee	chr1:145454883-145455103(-)$1	220	128	164	12.9544
==========!!cccnnnnnccc22==========]	chr10:79323602-79323822(+)$1	220	128	164	17.8899
!bb!!eeeee[cccooooooccc22eeeee22bb22	chr15:99843713-99843933(+)$1	220	88	124	12.2388
hhhhh[dddd!!cccnnnnncccdddd22hhhhhhh	chr6:38555878-38556098(+)$1	220	71	107	12.2903
cc!!ggggggg[cccooooooccc]ggggggg22cc	chr1:138166286-138166506(-)$1	220	57	93	14.1711
ccc[ccc[a[ccc[ammmmaccc]a]ccc22ccc44	chr15:34213240-34213473(+)$1	233	66	102	12.7354
eee!!dddd!!ddddoooooodddddddd22eeeee	chr11:30097719-30097940(-)$1	221	139	175	11.5862
e[ggggggg####cccmmmmccc4444ggggggg22	chr3:33712344-33712583(+)$1	239	125	161	14.2261
e[==========!!aooooooa333==========]	chr1:34255263-34255483(+)$1	220	84	120	16.9787
c[dddd[bb!!cccooooooccc333bb]dddd]cc	chr12:93045320-93045540(-)$1	220	136	172	13.4712
[ccc[ccc[ffffffnnnnnffffff]ccc]ccc]a	chr8:88242356-88242576(-)$1	220	108	144	12.0051
ggggggccc$$$$$bbmmmmbb333ccc]ggggggg	chr9:67743830-67744057(+)$1	227	117	153	12.9984
e[eeeee[cccddddmmmmdddd333ccc]eeeee]	chr10:52040223-52040452(+)$1	229	96	132	11.6089
f!!eeeee[a!!cccnnnnnccc22a22eeeee444	chr11:32645286-32645514(+)$1	228	32	68	14.3228
c[hhhhhhhh"""bbnnnnnbb333hhhhhhhhccc	chr19:41992762-41992982(+)$1	220	171	207	12.8821
d[ccc"""gggggggnnnnnggggggg]ccc]dddd	chr11:60245831-60246052(+)$1	221	155	191	12.8205
ggg"""dddd!!cccnnnnnccc]dddd22gggggg	chr11:21049949-21050187(+)$1	238	106	142	14.9623
Fccc"""ccc!!ddddlllddddccc4444cccccc	chr11:100181313-100181556(+)$1	243	110	146	11.6161
gggggg!!gggggggooooooggggggg]ggggggg	chr11:117828420-117828647(-)$1	227	182	218	14.2253
================mmmm================	chr9:43950517-43950759(+)$1	242	171	207	14.3428
g[a[ccc!!ddddoooooodddd22cccaggggggg	chr1:95716921-95717157(+)$1	236	104	140	13.1738
=====$$$$$eeeeeooooooeeeee333=======	chr14:45968511-45968731(+)$1	220	154	190	12.6698
i!!a!!ccc"""cccnnnnnccc333ccc]a22iii	chr6:91707458-91707678(+)$1	220	118	154	17.0176
eeeee"""ccc[bboooooobbccceeeee]ggggg	chr12:117608727-117608953(+)$1	226	168	204	12.3926
iii"""ccc"""bboooooobb333ccc]iiiiiii	chr18:73799596-73799816(-)$1	220	108	144	16.3319
h"""cccbb!!ddddnnnnndddd22bb333ccc33	chr8:26876050-26876270(-)$1	220	160	196	13.3841
[bbffffff"""cccoooooocccffffff]bb]ee	chr10:18252177-18252403(+)$1	226	161	197	11.7077
[bb[ccc"""ccccccmmmmccc]cccccc]bb]a]	chr9:109984936-109985178(+)$1	242	96	132	12.1416
eee!!ffffff!!bboooooobb22ffffff]eeee	chr16:13702590-13702824(+)$1	234	102	138	11.9666
"""==========!!aooooooa22==========4	chr11:62327187-62327407(+)$1	220	65	101	15.3847
%hhhhhhhh!!cccooooooccc22hhhhhhhheee	chr9:43615395-43615616(+)$1	221	15	51	12.4265
gggg"""ccc[ddddmmmmdddd22ccc22gggggg	chr1:120731731-120731951(-)$1	220	127	163	13.1957
e[a[ccc####cccooooooccc22cccaeeeee22	chr8:86462404-86462625(+)$1	221	93	129	15.1258
iiiiiiiii!!eeeeeooooooeeeeeiiiiiiiii	chr14:65673025-65673253(-)$1	228	82	118	12.8351
[dddd!!ccc[ddddnnnnndddd]ccc333dddd]	chr3:41418323-41418557(+)$1	234	188	224	13.1836
dd[a[ccc####ddddllldddd22cccadddd333	chr5:30593499-30593737(+)$1	238	177	213	12.7365
eeeee[iiiiiiiiinnnnniiiiiiiii22eeeee	chr5:130718562-130718782(+)$1	220	9	45	13.6083
===========[cccnnnnnccc22===========	chrX:7701436-7701656(-)$1	220	25	61	17.4714
iiiiiiii[fffffflllffffff22iiiiiiiii]	chr6:72561432-72561652(-)$1	220	133	169	11.7813
iiiiiiii[a"""cccmmmmccc333a]iiiiiiii	chr6:127913056-127913276(-)$1	220	147	183	15.6431
ggggggg[gggggggnnnnnggggggg22ggggggg	chr11:54331251-54331472(+)$1	221	1	37	14.0404
eee"""bb$$$$$bbnnnnnbb4444bb4444eeee	chr4:82447125-82447345(-)$1	220	65	101	12.5571
gggg!!ccc$$$$$annnnna4444ccc22gggggg	chr1:63641381-63641601(+)$1	220	70	106	15.5021

#otherMatches

#Seq PSSM
UUCUUUCAGUUCAUUUCCCAAAUUGGCUUUAGAAGA	chr16:84862133-84862371(+)$1	238	22	58	11.6658
AUGGAGGUUGGCAAGUAAGUCUUACCAUCUUCCCUG	chr17:25033940-25034160(+)$1	220	131	167	13.0129
AGUCAGUGCCUGGGGGCACGUGUCAGGCAGAGACUC	chr3:38350544-38350764(-)$1	220	91	127	11.5778
GUGUGUAAAGUGGAAAAUGUUUUAUUUUAUUAUAUG	chr4:26251611-26251831(-)$1	220	98	134	12.7574
GUUGGAUGUACUUUGGUAUAUUAAAGUCCAUAUGUU	chr14:58421000-58421220(+)$1	220	49	85	11.3398
AUGUCUCAGUGUUCACAGGAGUGUUACACUUGAAUA	chr7:96289557-96289777(-)$1	220	137	173	11.4712
GUAGACUGUACAUGUUUAAUAACUUGCCUUCUCUAU	chr15:98568109-98568329(-)$1	220	170	206	13.0820
GGCAGGAACACUCCUGUGACAUAGGGCCCAUGUUCC	chr4:33108097-33108317(+)$1	220	169	205	11.2345
GCUGCUGGCUCACUGCGAGCCGCCUCCAGCCUGCGC	chr4:132925692-132925916(+)$1	224	122	158	12.3836
cugagggaagaggaugaaaaguuaaagcaugccuua	chr1:95263641-95263903(+)$1	262	10	46	16.5117
UUAUCAGUCAGGACCUCAUUGGCACCUGGUAGGGCA	chr18:77873293-77873513(-)$1	220	49	85	12.6291
AAAGUGAUAUAUUUCUAUCUGGAAUAUGUUUCCACU	chr1:145454883-145455103(-)$1	220	128	164	12.9544
GUGCUCUGCUUAUACAUGGAGUAGUGGUGGGGUGCU	chr10:79323602-79323822(+)$1	220	128	164	17.8899
acuaguuucugucuaaagaaagaaaaGGAAAAGGAA	chr15:99843713-99843933(+)$1	220	88	124	12.2388
ucaggaggcuugucauaaauugaggccagcuugggc	chr6:38555878-38556098(+)$1	220	71	107	12.2903
CAAAGGGCUACAUUUUGAUUUGAAAGUAGCUUCCUG	chr1:138166286-138166506(-)$1	220	57	93	14.1711
GAGUGGAGUGUGGUGAGUUCCCAGAGUCUUUCUCAA	chr15:34213240-34213473(+)$1	233	66	102	12.7354
GGCCGCUGUCGCCGGCCUACACCGGGCAGGUGCCUU	chr11:30097719-30097940(-)$1	221	139	175	11.5862
AAAGAUGGUGAGAUUGUUUGCAAAAUAGCCAUUUGC	chr3:33712344-33712583(+)$1	239	125	161	14.2261
CAUGUGUGUUUUAAGGAAUUACAGAGAGAUAUGCAA	chr1:34255263-34255483(+)$1	220	84	120	16.9787
CUGAAGAUAUAUAUAGAUAGAUAGAUUAACUUCUGA	chr12:93045320-93045540(-)$1	220	136	172	13.4712
AAGGACGUGUAAAUAAAAACUAUUUAAAUGACCUGU	chr8:88242356-88242576(-)$1	220	108	144	12.0051
AAGCCUUCUUACCUGAUAAUUCCACAGACAGGUUUU	chr9:67743830-67744057(+)$1	227	117	153	12.9984
GAUUGCUAGCAAUGGUGGCCCAUUUAUGCAAGCAAA	chr10:52040223-52040452(+)$1	229	96	132	11.6089
GGUUGCUGUGCUGGCCUAGAGCCUCCUUCAGUAUUC	chr11:32645286-32645514(+)$1	228	32	68	14.3228
AUCAGUGGGAUAAACUCCUUGUACCUCUUGCUGUGU	chr19:41992762-41992982(+)$1	220	171	207	12.8821
GAGAUGGCAGGCCUGAACCCCGGGCCUUGUCCCCAG	chr11:60245831-60246052(+)$1	221	155	191	12.8205
UUGUUUUGAAAAUUAUCAUUUGGGUUCACUCAGGAA	chr11:21049949-21050187(+)$1	238	106	142	14.9623
AGGAAAAGGAAUCGUAUCGUAUGUCCGCUAUCCAGA	chr11:100181313-100181556(+)$1	243	110	146	11.6161
GUUUGCGCUUUGAUUUGGUUUGAUCAAGAGCAGGCA	chr11:117828420-117828647(-)$1	227	182	218	14.2253
GUGUGUGUGuauacauauauguguguauauauauau	chr9:43950517-43950759(+)$1	242	171	207	14.3428
uugcuggagcuaggcaaugcugggaccacagauggc	chr1:95716921-95717157(+)$1	236	104	140	13.1738
GAGCAUUUCUUAUGACUUAUUUUAUAUUUUGUUUUC	chr14:45968511-45968731(+)$1	220	154	190	12.6698
CAGGUCCAGGGCAUUGUCUAAGUAAACUGUCAAGCC	chr6:91707458-91707678(+)$1	220	118	154	17.0176
CAGUGGUGUAGUGAUGUGUUUCCUGUGCUGUGUGGA	chr12:117608727-117608953(+)$1	226	168	204	12.3926
GUGCUUGAAGAUCAGAAAGAUGCAGUUCUUGCUGAG	chr18:73799596-73799816(-)$1	220	108	144	16.3319
UUAUGCUCUAAGAGGAGAAACCUUAAAGCUUAGCUG	chr8:26876050-26876270(-)$1	220	160	196	13.3841
CGGGGAGGCCUUGGUGCAGCUGCCGccuccuccucc	chr10:18252177-18252403(+)$1	226	161	197	11.7077
GGUGUAGUUUGCAGGCUGAAGCCAUGUCUAAAUGAG	chr9:109984936-109985178(+)$1	242	96	132	12.1416
agcacuaggaaaacaggcagguggauuuuugaguuc	chr16:13702590-13702824(+)$1	234	102	138	11.9666
CUUGGGUUUUUAUUUGUGUCCCCUUAUGAGAACUUU	chr11:62327187-62327407(+)$1	220	65	101	15.3847
GAUUCCCCUGGUCCUGACCUGGAGGGGGGGAGUGGU	chr9:43615395-43615616(+)$1	221	15	51	12.4265
GAGAAAGGCGCAUCCCCCGGGAUAUUGUAGUCUCCU	chr1:120731731-120731951(-)$1	220	127	163	13.1957
CUGUGCCAGGGGUCAGUGAGGACGAGGCCGGUGGAC	chr8:86462404-86462625(+)$1	221	93	129	15.1258
UUUUUAAAUUCAGUAACAGCUAUUAUUAUUUAAAGA	chr14:65673025-65673253(-)$1	228	82	118	12.8351
GCAGGGACAGAGCAGAGCUGCUGCACUGAGAUUUGG	chr3:41418323-41418557(+)$1	234	188	224	13.1836
CUUGUGGAAUUGUGGACUUUCUAACUCCCAGCUUAC	chr5:30593499-30593737(+)$1	238	177	213	12.7365
UUAGAUGGAAAACAAUACUUUUGUUUUUUCUUCUAA	chr5:130718562-130718782(+)$1	220	9	45	13.6083
CUUUCCUUAUUCCCUGAGUGAGGAAGGUGAGGAAGG	chrX:7701436-7701656(-)$1	220	25	61	17.4714
UUUGAUGGGAUUUUUUAAAAAAAUGAUCAUUGAACA	chr6:72561432-72561652(-)$1	220	133	169	11.7813
GCAUUGGGGAGAAGACCCUUGUUAGAUGCCCAGUGC	chr6:127913056-127913276(-)$1	220	147	183	15.6431
UGAAAAGAGUUUUGGCCUGUUUAAAAUAAUUUUUCA	chr11:54331251-54331472(+)$1	221	1	37	14.0404
CUGUUUGAUCUCCACUUAAUGUUCUUUCUCCUUAGC	chr4:82447125-82447345(-)$1	220	65	101	12.5571
GCUGUACCCCUUUACUGAAUGGCAUGGGCUCAGCUU	chr1:63641381-63641601(+)$1	220	70	106	15.5021

#DB
((((...((((.((((...)))).))))..))))))	chr16:84862133-84862371(+)$1	1	22	58	11.6658
(.(((((.(((.(((.....))).))).))))).))	chr17:25033940-25034160(+)$1	1	131	167	13.0129
((((..(((((((.(.....).)))))))..)))).	chr3:38350544-38350764(-)$1	1	91	127	11.5778
(((.(((((((((((....))))))))))))))))(	chr4:26251611-26251831(-)$1	1	98	134	12.7574
(....(((.((((((......)))))).)))...))	chr14:58421000-58421220(+)$1	1	49	85	11.3398
((((.(((((((.(((....)))..)))).))))))	chr7:96289557-96289777(-)$1	1	137	173	11.4712
(.(((..(((...(((....))).)))..))))..)	chr15:98568109-98568329(-)$1	1	170	206	13.0820
)))(((((((.((((((...))))))....))))))	chr4:33108097-33108317(+)$1	1	169	205	11.2345
(.(((.((((....(((...)))....)))).))).	chr4:132925692-132925916(+)$1	1	122	158	12.3836
((((((.(.(..(((.....)))....).).)))))	chr1:95263641-95263903(+)$1	1	10	46	16.5117
(((((((...(..((.....))..)))))))))...	chr18:77873293-77873513(-)$1	1	49	85	12.6291
.((((((((((((((.....)))))))))...))))	chr1:145454883-145455103(-)$1	1	128	164	12.9544
((((((((((..(((.....)))..)))))))))).	chr10:79323602-79323822(+)$1	1	128	164	17.8899
.((..(((((.(((......)))..)))))..))..	chr15:99843713-99843933(+)$1	1	88	124	12.2388
(((((.((((..(((.....)))))))..)))))))	chr6:38555878-38556098(+)$1	1	71	107	12.2903
((..(((((((.(((......))).)))))))..))	chr1:138166286-138166506(-)$1	1	57	93	14.1711
(((.(((.(.(((.(....)))).).)))..)))..	chr15:34213240-34213473(+)$1	1	66	102	12.7354
(((..((((..((((......))))))))..)))))	chr11:30097719-30097940(-)$1	1	139	175	11.5862
(.(((((((....(((....)))....)))))))..	chr3:33712344-33712583(+)$1	1	125	161	14.2261
(.((((((((((..(......)...)))))))))).	chr1:34255263-34255483(+)$1	1	84	120	16.9787
(.((((.((..(((......)))...)).)))).))	chr12:93045320-93045540(-)$1	1	136	172	13.4712
.(((.(((.((((((.....)))))).))).))).)	chr8:88242356-88242576(-)$1	1	108	144	12.0051
(((((((((.....((....))...))).)))))))	chr9:67743830-67744057(+)$1	1	117	153	12.9984
(.(((((.(((((((....))))...))).))))).	chr10:52040223-52040452(+)$1	1	96	132	11.6089
(..(((((.(..(((.....)))..)..)))))...	chr11:32645286-32645514(+)$1	1	32	68	14.3228
(.((((((((...((.....))...)))))))))))	chr19:41992762-41992982(+)$1	1	171	207	12.8821
(.(((...(((((((.....))))))).))).))))	chr11:60245831-60246052(+)$1	1	155	191	12.8205
(((...((((..(((.....))).))))..))))))	chr11:21049949-21050187(+)$1	1	106	142	14.9623
((((...(((..((((...)))))))....)))(((	chr11:100181313-100181556(+)$1	1	110	146	11.6161
((((((..(((((((......))))))).)))))))	chr11:117828420-117828647(-)$1	1	182	218	14.2253
((((((((((((((((....))))))))))))))))	chr9:43950517-43950759(+)$1	1	171	207	14.3428
(.(.(((..((((......))))..)))))))))))	chr1:95716921-95717157(+)$1	1	104	140	13.1738
(((((.....(((((......)))))...)))))))	chr14:45968511-45968731(+)$1	1	154	190	12.6698
(..(..(((...(((.....)))...))).)..)))	chr6:91707458-91707678(+)$1	1	118	154	17.0176
(((((...(((.((......)))))))))).)))))	chr12:117608727-117608953(+)$1	1	168	204	12.3926
(((...(((...((......))...))).)))))))	chr18:73799596-73799816(-)$1	1	108	144	16.3319
(...(((((..((((.....))))..))...)))..	chr8:26876050-26876270(-)$1	1	160	196	13.3841
.((((((((...(((......))))))))).)).))	chr10:18252177-18252403(+)$1	1	161	197	11.7077
.((.(((...((((((....))).)))))).)).).	chr9:109984936-109985178(+)$1	1	96	132	12.1416
(((..((((((..((......))..)))))).))))	chr16:13702590-13702824(+)$1	1	102	138	11.9666
...((((((((((..(......)..)))))))))).	chr11:62327187-62327407(+)$1	1	65	101	15.3847
.((((((((..(((......)))..)))))))))))	chr9:43615395-43615616(+)$1	1	15	51	12.4265
((((...(((.((((....))))..)))..))))))	chr1:120731731-120731951(-)$1	1	127	163	13.1957
(.(.(((....(((......)))..)))))))))..	chr8:86462404-86462625(+)$1	1	93	129	15.1258
(((((((((..(((((......))))))))))))))	chr14:65673025-65673253(-)$1	1	82	118	12.8351
.((((..(((.((((.....)))).)))...)))).	chr3:41418323-41418557(+)$1	1	188	224	13.1836
((.(.(((....((((...))))..))))))))...	chr5:30593499-30593737(+)$1	1	177	213	12.7365
(((((.(((((((((.....)))))))))..)))))	chr5:130718562-130718782(+)$1	1	9	45	13.6083
(((((((((((.(((.....)))..)))))))))))	chrX:7701436-7701656(-)$1	1	25	61	17.4714
((((((((.((((((...))))))..))))))))).	chr6:72561432-72561652(-)$1	1	133	169	11.7813
((((((((.(...(((....)))...).))))))))	chr6:127913056-127913276(-)$1	1	147	183	15.6431
(((((((.(((((((.....)))))))..)))))))	chr11:54331251-54331472(+)$1	1	1	37	14.0404
(((...((.....((.....))....))....))))	chr4:82447125-82447345(-)$1	1	65	101	12.5571
((((..(((.....(.....)....)))..))))))	chr1:63641381-63641601(+)$1	1	70	106	15.5021

#PSSM
e : 0.20	g : 0.18	c : 0.09	i : 0.09	= : 0.07	[ : 0.07	d : 0.05	h : 0.05	f : 0.03	b : 0.01	a : 0.01	& : 0.01	! : 0.01	F : 0.01	" : 0.01	% : 0.01	
[ : 0.20	g : 0.16	e : 0.14	= : 0.07	c : 0.07	i : 0.07	d : 0.05	h : 0.05	b : 0.05	! : 0.03	" : 0.03	# : 0.01	
g : 0.18	e : 0.18	c : 0.11	= : 0.09	h : 0.07	i : 0.07	d : 0.05	b : 0.05	! : 0.05	a : 0.03	" : 0.03	# : 0.01	[ : 0.01	
g : 0.16	e : 0.12	= : 0.11	[ : 0.09	c : 0.09	h : 0.07	! : 0.07	" : 0.07	d : 0.05	i : 0.05	a : 0.03	# : 0.01	f : 0.01	
c : 0.14	= : 0.12	g : 0.12	" : 0.11	e : 0.11	! : 0.11	h : 0.07	[ : 0.05	i : 0.05	d : 0.03	# : 0.01	f : 0.01	
c : 0.16	" : 0.14	g : 0.12	= : 0.11	e : 0.09	! : 0.09	[ : 0.05	h : 0.05	i : 0.05	d : 0.03	f : 0.03	$ : 0.01	
c : 0.24	= : 0.11	" : 0.09	g : 0.09	i : 0.09	e : 0.07	d : 0.07	! : 0.05	h : 0.05	[ : 0.03	f : 0.03	$ : 0.01	b : 0.01	
c : 0.22	= : 0.11	d : 0.09	i : 0.09	[ : 0.07	g : 0.07	" : 0.07	b : 0.05	e : 0.03	h : 0.03	! : 0.03	f : 0.03	a : 0.01	$ : 0.01	# : 0.01	
c : 0.20	g : 0.12	d : 0.11	= : 0.11	[ : 0.11	i : 0.05	" : 0.03	b : 0.03	h : 0.03	$ : 0.03	f : 0.03	# : 0.03	e : 0.01	a : 0.01	! : 0.01	
c : 0.12	d : 0.11	g : 0.11	= : 0.11	" : 0.09	! : 0.09	f : 0.07	$ : 0.07	a : 0.05	# : 0.05	i : 0.03	e : 0.01	[ : 0.01	h : 0.01	
! : 0.20	" : 0.11	c : 0.09	g : 0.09	= : 0.09	f : 0.07	[ : 0.07	# : 0.07	d : 0.05	$ : 0.05	i : 0.03	a : 0.01	e : 0.01	
! : 0.14	d : 0.12	" : 0.11	c : 0.11	[ : 0.09	g : 0.07	= : 0.07	f : 0.07	# : 0.05	$ : 0.05	i : 0.03	e : 0.03	
c : 0.29	d : 0.16	g : 0.07	f : 0.07	= : 0.05	" : 0.05	! : 0.05	$ : 0.05	# : 0.03	i : 0.03	e : 0.03	b : 0.03	[ : 0.01	
c : 0.35	d : 0.14	b : 0.11	f : 0.07	g : 0.05	[ : 0.03	= : 0.03	i : 0.03	! : 0.03	$ : 0.03	e : 0.03	# : 0.01	o : 0.01	
c : 0.29	d : 0.14	o : 0.12	b : 0.09	a : 0.07	f : 0.07	g : 0.05	= : 0.03	i : 0.03	e : 0.03	! : 0.01	
n : 0.37	o : 0.27	c : 0.11	m : 0.07	d : 0.05	f : 0.01	b : 0.01	= : 0.01	a : 0.01	e : 0.01	l : 0.01	
n : 0.37	o : 0.31	m : 0.20	l : 0.07	f : 0.01	c : 0.01	
n : 0.37	o : 0.31	m : 0.20	l : 0.11	
n : 0.37	o : 0.31	m : 0.20	l : 0.09	f : 0.01	
n : 0.37	o : 0.29	m : 0.12	d : 0.11	l : 0.03	= : 0.01	a : 0.01	f : 0.01	
c : 0.35	o : 0.18	d : 0.14	b : 0.11	f : 0.05	a : 0.03	= : 0.03	i : 0.03	g : 0.03	
c : 0.38	d : 0.16	b : 0.12	f : 0.07	g : 0.05	= : 0.03	i : 0.03	o : 0.03	] : 0.01	a : 0.01	e : 0.01	4 : 0.01	
c : 0.40	d : 0.16	g : 0.07	f : 0.07	3 : 0.07	= : 0.03	i : 0.03	e : 0.03	4 : 0.03	2 : 0.01	b : 0.01	a : 0.01	
2 : 0.24	3 : 0.14	] : 0.11	4 : 0.09	g : 0.07	f : 0.07	d : 0.07	c : 0.07	= : 0.03	i : 0.03	e : 0.03	
2 : 0.25	3 : 0.14	c : 0.09	4 : 0.09	d : 0.07	g : 0.07	f : 0.07	= : 0.03	a : 0.03	i : 0.03	] : 0.03	e : 0.03	
c : 0.22	= : 0.11	d : 0.09	g : 0.09	f : 0.09	4 : 0.07	e : 0.07	3 : 0.07	h : 0.05	i : 0.03	2 : 0.03	] : 0.01	a : 0.01	
c : 0.25	= : 0.11	d : 0.09	g : 0.09	4 : 0.09	f : 0.05	h : 0.05	i : 0.05	e : 0.05	b : 0.05	] : 0.01	2 : 0.01	3 : 0.01	a : 0.01	
c : 0.24	= : 0.11	d : 0.09	] : 0.07	g : 0.07	2 : 0.07	i : 0.07	h : 0.05	b : 0.05	4 : 0.03	e : 0.03	f : 0.03	a : 0.01	3 : 0.01	
2 : 0.12	c : 0.12	= : 0.11	] : 0.09	i : 0.09	e : 0.07	g : 0.05	d : 0.05	4 : 0.05	h : 0.05	a : 0.05	3 : 0.05	f : 0.03	
2 : 0.14	= : 0.12	g : 0.11	e : 0.09	c : 0.09	h : 0.07	i : 0.07	] : 0.05	4 : 0.05	d : 0.05	3 : 0.05	f : 0.03	a : 0.01	
g : 0.20	= : 0.11	e : 0.09	2 : 0.09	c : 0.09	] : 0.09	h : 0.07	i : 0.07	d : 0.05	3 : 0.05	a : 0.01	f : 0.01	4 : 0.01	
g : 0.24	e : 0.12	c : 0.11	= : 0.11	d : 0.07	h : 0.07	i : 0.07	] : 0.05	3 : 0.03	2 : 0.03	b : 0.03	4 : 0.01	
g : 0.22	e : 0.18	c : 0.11	= : 0.11	d : 0.09	h : 0.07	i : 0.07	b : 0.05	2 : 0.03	3 : 0.01	a : 0.01	
g : 0.22	e : 0.18	c : 0.11	= : 0.11	i : 0.09	] : 0.07	d : 0.05	3 : 0.05	2 : 0.03	b : 0.01	h : 0.01	4 : 0.01	
g : 0.20	e : 0.18	= : 0.11	c : 0.09	i : 0.09	2 : 0.07	d : 0.05	3 : 0.05	4 : 0.03	b : 0.01	f : 0.01	h : 0.01	] : 0.01	a : 0.01	
g : 0.20	e : 0.14	] : 0.12	c : 0.09	i : 0.07	3 : 0.05	2 : 0.05	4 : 0.05	= : 0.05	f : 0.03	b : 0.01	: : 0.01	h : 0.01	a : 0.01	d : 0.01	

#score	724.272086920752
#seq	54
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_UTR_m2_run1.txt

#BEAR
==========[a[cccooooooccc]a============9	chr14:120829600-120829835(+)$1	235	113	153	19.0029
"iiiiiiiii"""ddddmmmmdddd22iiiiiiiii333d	chr4:107904863-107905105(-)$1	242	199	239	16.8742
cciiiiiiiii[eeeeellleeeee22iiiiiiiii4444	chr11:68666423-68666666(-)$1	243	44	84	15.1518
fffff!!eeeeeddddoooooodddd]eeeee]ffffff]	chr8:46912753-46912988(+)$1	235	51	91	13.6242
[ggggggg!!bb[ddddmmmmdddd]bb22gggggggddd	chr5:122903599-122903846(-)$1	247	95	135	13.8147
eeeeggggggg!!ddddmmmmdddd333gggggggfffff	chr19:24757738-24757973(-)$1	235	64	104	14.3020
$$dddd[ccc[ddddoooooodddd]ccc]dddd4444ff	chr2:22796897-22797132(-)$1	235	176	216	14.1211
f[cccaccc!!ggggggglllggggggg22ccc]a]ccc]	chr11:109529767-109530009(+)$1	242	135	175	12.5704
!!ccc[a[ccc[ddddoooooodddd4444ccc]a]ccc3	chr8:4524695-4524930(+)$1	235	71	111	17.5226
ggggggg!!ccc[ccclllccc]cccggggggg22eeeee	chr1:99717957-99718198(-)$1	241	55	95	12.1411
ffff!!gggggggddddmmmmdddd4444ggggggg333f	chr9:96218337-96218572(+)$1	235	151	191	14.8440
ggggffffff[eeeeeooooooeeeee333ffffff0000	chr9:70625984-70626219(+)$1	235	53	93	13.2234
"""bb[ccc####cccmmmmccc4444cccbb333bb]cc	chr8:112254772-112255023(-)$1	251	195	235	12.8427
[============rrrrrrrrr============]cccgg	chr11:40492882-40493117(-)$1	235	154	194	14.8865
[ccc[eeeee[a[cccmmmmccc]a]eeeee333ccc]a3	chr8:23678766-23679001(+)$1	235	46	86	12.7582
cc!!==========bboooooobb22==========]ccc	chr1:34933815-34934074(+)$1	259	88	128	17.4558
iiiiiiiii[bb[ddddmmmmdddd]bb22iiiiiiiii3	chr4:15844545-15844787(-)$1	242	87	127	15.2159
ccc[ccciiiiiiiiillliiiiiiiii333ccc]ccchh	chr4:57909670-57909907(+)$1	237	104	144	12.9711
"bbdddd[bb!!ddddoooooodddd333bb]dddd]bb3	chr3:141965381-141965616(-)$1	235	168	208	14.4377
[a[ccc[bb!!eeeeeooooooeeeee]bb]ccc]aeeee	chr3:60812561-60812821(+)$1	260	111	151	14.3728
=====ccc[eeeeebboooooobb22eeeee22ccc333=	chr7:146765008-146765298(+)$1	290	162	202	14.6385
[iiiiiiiii[ccc[aooooooaccc>>>>>>>>>>>>>>	chr17:33884446-33884681(-)$1	235	54	94	14.1017
[ggggggg!!bb[ddddmmmmdddd]bb22gggggggddd	chr5:122903658-122903893(-)$1	235	142	182	13.8147
gggggg[ccc[ddddrrrrrrrrrdddd333ccc]ggggg	chr19:43574327-43574562(-)$1	235	39	79	12.9258
cc"""ccc[ccc[cccooooooccc]ccc]ccc4444ccc	chr1:166367534-166367783(-)$1	249	206	246	17.0345
eee"""ccc!!eeeeeooooooeeeee22ccc]eeeeeff	chr13:74460049-74460289(-)$1	240	63	103	15.1027
iiiiii"""bb!!ddddmmmmdddd22bb333iiiiiiii	chr11:109529368-109529612(+)$1	244	168	208	15.2681
===========eeeeennnnneeeee22===========7	chr19:57111016-57111251(-)$1	235	13	53	15.3159
:ccc[ggggggg[bb[aooooooa]bb]ggggggg]ccc:	chr10:82203496-82203737(+)$1	241	166	206	12.5048
fff!!==========ssssssssss==========333ff	chr2:134420523-134420770(-)$1	247	180	220	12.5903
&ccc!!ccc####cccooooooccc55555ccc22ccc44	chr9:48463289-48463524(-)$1	235	147	187	13.6212
==####dddd!!ddddoooooodddd22dddd333=====	chr17:85463643-85463882(-)$1	239	140	180	17.3037
:iiiiiiiii!!ddddoooooodddd22iiiiiiiii:EE	chr2:121373570-121373818(-)$1	248	24	64	14.5926
dd"""ccc[ccc[cccooooooccc]ccc]ccc4444ddd	chr11:94887931-94888172(-)$1	241	189	229	16.2036
ggggggg####eeeeeooooooeeeee22gggggggccc[	chr8:98238288-98238548(+)$1	260	171	211	16.1946
[bb"""ccc"""ddddnnnnndddd333ccc]bb]eeeee	chr18:34506258-34506494(-)$1	236	133	173	14.2733
========"""ccc!!ccclllccc]ccc]==========	chr18:78021134-78021386(+)$1	252	92	132	15.3914
dddiiiiiiiii[ddddmmmmdddd]iiiiiiiii]dddd	chr19:37097078-37097315(-)$1	237	194	234	14.5166
iiiiii"""bb!!ddddmmmmdddd22bb333iiiiiiii	chr11:109529413-109529649(+)$1	236	123	163	15.2681
ddd"""ccc!!eeeeeooooooeeeee22ccc333dddd]	chr14:76907381-76907616(+)$1	235	65	105	15.9936
ccc!!eeeee"""a[annnnna]a333eeeee22ccc333	chr13:29999430-29999670(-)$1	240	17	57	13.3422
===dddd!!gggggggooooooggggggg22dddd22===	chr6:71342077-71342314(-)$1	237	69	109	14.0084
bb!!ggggggg!!eeeeellleeeeeggggggg22bb333	chr7:134861138-134861380(+)$1	242	156	196	13.0991
========####dddd[bbmmmmbb]dddd333=======	chr11:50108806-50109049(-)$1	243	69	109	13.0346
=======dddd"""bboooooobb4444dddd]=======	chr2:163450342-163450596(-)$1	254	121	161	16.2214
ccc[eeeee####cccooooooccc333eeeee]cccccc	chr2:132134563-132134798(+)$1	235	122	162	16.3407
i$$$$$ggggggg[bboooooobb]gggggggiiiiiiii	chr7:35130774-35131009(-)$1	235	193	233	14.7240
dddd"""ccc####bboooooobb4444ccc]ddddbbgg	chr18:68427442-68427680(-)$1	238	44	84	14.3427
[==========!!eeeeemmmmeeeee]==========]c	chr12:71568417-71568671(+)$1	254	199	239	15.6679
!!dddd[ccc!!ddddoooooodddd]ccc]dddd22bb3	chr1:183835465-183835707(-)$1	242	189	229	15.0381
ggg"""eeeee[ddddooooooddddeeeee4444ggggg	chr9:96233096-96233334(-)$1	238	73	113	15.9211

#otherMatches

#Seq PSSM
AAGUAUUUUGACUUUUGAGAUUGAAUGUAAAAUAUUUUAA	chr14:120829600-120829835(+)$1	235	113	153	19.0029
CUUGGUACGUGCUGAUGAAAACAUUUAAUGUGCCAAAUUG	chr4:107904863-107905105(-)$1	242	199	239	16.8742
GCCUCCGACACCCAGGGAGCCCCUGACGUGUCGGGGAGGA	chr11:68666423-68666666(-)$1	243	44	84	15.1518
AUCUUCACAGAUCACAAGUAAAUGUGAAUCUGAAAGAUAG	chr8:46912753-46912988(+)$1	235	51	91	13.6242
AUUAUUGUAACUUAUUUAAUGAAGUCAGAAGCAGUAGACA	chr5:122903599-122903846(-)$1	247	95	135	13.8147
GUCGGCGCCUUAAGGAAAGAUUUCCAGCAAGGUGUUUGUU	chr19:24757738-24757973(-)$1	235	64	104	14.3020
UAAAUUUUUAUGUAUUGAAAUAUACUUAACAAUUCAAGAU	chr2:22796897-22797132(-)$1	235	176	216	14.1211
GUGACCGUGUUGUGGUCUGAAAGGCCACCCCGCUGAGUCC	chr11:109529767-109530009(+)$1	242	135	175	12.5704
aagcagggcccaguuucaaaacaaacaaUGGGGGUGUGUG	chr8:4524695-4524930(+)$1	235	71	111	17.5226
CUUCCAUGGUAGCGCUCAAAGCCCUAAUGGAAGUUUAGCU	chr1:99717957-99718198(-)$1	241	55	95	12.1411
UUGCAUUUGUGUUUAGUGAAAACUAGAGAAACACAAUAAG	chr9:96218337-96218572(+)$1	235	151	191	14.8440
CAGAUCAGGUGGAAUUACUCAAAAUUUAAAGCCUGAAAAU	chr9:70625984-70626219(+)$1	235	53	93	13.2234
AUUCCGCUAUAAGGCUUUUUAGCAUUUUAGGGCCAGgaga	chr8:112254772-112255023(-)$1	251	195	235	12.8427
CGUGUGUGuauuuuuuuaauauaaauacauauauauGUCU	chr11:40492882-40493117(-)$1	235	154	194	14.8865
UGCCCGUGGCUGGACUCUUCAGUGCUGCUAUCAUGGCUCU	chr8:23678766-23679001(+)$1	235	46	86	12.7582
UUUUCUGUGCAUAGCUUCUGUUAGUCCUGUGUGCAGUAAU	chr1:34933815-34934074(+)$1	259	88	128	17.4558
AUGAAUAGAUCUAUGCAAGAAUGUAGAGUUUCUGUUUGUU	chr4:15844545-15844787(-)$1	242	87	127	15.2159
UGCUUUGGUUUUAUAGUGUCUGUGAGGCAUUCGAUGCAAC	chr4:57909670-57909907(+)$1	237	104	144	12.9711
CUCCUGUUCUUACAAAGAUAUAUUUGACCAGUACAGAGAA	chr3:141965381-141965616(-)$1	235	168	208	14.4377
AUGUCCUGUAAAAGCACAGUAUUGUUUGGCUGGAGGGAGC	chr3:60812561-60812821(+)$1	260	111	151	14.3728
UGUGUGUAAACCUGGCAGAAAAGCGACGGGUGAUGCUGGG	chr7:146765008-146765298(+)$1	290	162	202	14.6385
UGCCAGAGCCUGUGACUGCCCUGCACUUUCUuuuucuuuu	chr17:33884446-33884681(-)$1	235	54	94	14.1017
AUUAUUGUAACUUAUUUAAUGAAGUCAGAAGCAGUAGACA	chr5:122903658-122903893(-)$1	235	142	182	13.8147
UGGGUGUUGGCUGGGGCAUUAAAACUCAUCAUCGCCACCC	chr19:43574327-43574562(-)$1	235	39	79	12.9258
UCUCUGGAGGCAUCAUGCGCUGGUGCUGCGUCCUUAUGAA	chr1:166367534-166367783(-)$1	249	206	246	17.0345
AAUUUUCUUCCGCUGUCUAGCUGCAGCACAAGUAUUGUUU	chr13:74460049-74460289(-)$1	240	63	103	15.1027
GUCUAUCCCUGCCUUUAAGUUUGAAAUCAUUUGUAGAUGG	chr11:109529368-109529612(+)$1	244	168	208	15.2681
CCGUCUCCCUCAGCUCUGCCUGGGCUCCGAGGGAGAUGGA	chr19:57111016-57111251(-)$1	235	13	53	15.3159
UUGUGUAGCUUCCAUGAUGUGUCUGAUAGAAGCUAAACAU	chr10:82203496-82203737(+)$1	241	166	206	12.5048
CAGUAUAUUAUAAAAUGGUGUGUUUUUUUGUAAUAGUUUU	chr2:134420523-134420770(-)$1	247	180	220	12.5903
AAAGCUACCUCUUCUGUUUGUCCAGUCUUUGGUUCCUUCU	chr9:48463289-48463524(-)$1	235	147	187	13.6212
GGGGCAGGAGAACAGGAGAACGCCUGGCCUCCCAAUCAGU	chr17:85463643-85463882(-)$1	239	140	180	17.3037
CUUUUGUUUGUUUUUGUUUUUUCAAAUCUGAGCAGAGAGU	chr2:121373570-121373818(-)$1	248	24	64	14.5926
UCUACUCUGGAUGGUAUGAAGUUGCAAUUGGGAACUUGAG	chr11:94887931-94888172(-)$1	241	189	229	16.2036
GUUCAGUUCACUCACGUGCUUCCGUGAAUACUGAAUGUGA	chr8:98238288-98238548(+)$1	260	171	211	16.1946
GCAUAUACAUAUAUAUGGAAAAUGUUAUUGUUUGGCUAGA	chr18:34506258-34506494(-)$1	236	133	173	14.2733
ACAUGAAUAAAAGUUCCAUACUGUGUGCUAGUUUGUGUGG	chr18:78021134-78021386(+)$1	252	92	132	15.3914
AUGAUAUUUUCUAAGUAAGUUUAUUCAGaaaauauauauu	chr19:37097078-37097315(-)$1	237	194	234	14.5166
GUCUAUCCCUGCCUUUAAGUUUGAAAUCAUUUGUAGAUGG	chr11:109529413-109529649(+)$1	236	123	163	15.2681
AUUUCCCAGUAGGGGUUUCUGCACCUCACCUGUAUAGUCG	chr14:76907381-76907616(+)$1	235	65	105	15.9936
UGCUUCUGGCUUUGUGUAAUUCUCUUUGCCAGCUGCAUCG	chr13:29999430-29999670(-)$1	240	17	57	13.3422
GUUAUGCAUGUGUAUAGAAGUGUGUGCACCAGCAUCAAAC	chr6:71342077-71342314(-)$1	237	69	109	14.0084
ggauggccuggaacuugcuauguaggccaggcuggccucc	chr7:134861138-134861380(+)$1	242	156	196	13.0991
GGAGGUCUGACAGCUCGGGUCCUCUGGAGCACAAGGCUUU	chr11:50108806-50109049(-)$1	243	69	109	13.0346
GAGUGUGUGAAAGUCAAAGGCAUGUCAGUUUAUUACAUUU	chr2:163450342-163450596(-)$1	254	121	161	16.2214
GAGAGGAGGCUAAUUGUUGGUUCAGACUCCUCCGCUUGGG	chr2:132134563-132134798(+)$1	235	122	162	16.3407
UUCAUUUCAAAGCUACACUGCAGUUGCUUUGGGGCAGGAA	chr7:35130774-35131009(-)$1	235	193	233	14.7240
GGUUCACUGUUUAACUGCAUCAAGCUUUGCAAGACCGCUG	chr18:68427442-68427680(-)$1	238	44	84	14.3427
GUUGAAGAGAAGUUUGAUUUCUGUUAGUUUCUUUUCAGAG	chr12:71568417-71568671(+)$1	254	199	239	15.6679
AUAAAGGAUGGAACAAACGGAGUUGUAUGUGCUUUCAGAG	chr1:183835465-183835707(-)$1	242	189	229	15.0381
GCAUUUAAAUUAGGUGAAUGUGCACCGAUUUUUGUUGUUG	chr9:96233096-96233334(-)$1	238	73	113	15.9211

#DB
((((((((((.(.(((......))).))))))))))))).	chr14:120829600-120829835(+)$1	1	113	153	19.0029
.(((((((((...((((....))))..)))))))))...)	chr4:107904863-107905105(-)$1	1	199	239	16.8742
(((((((((((.(((((...)))))..)))))))))....	chr11:68666423-68666666(-)$1	1	44	84	15.1518
(((((..(((((((((......)))).))))).)))))).	chr8:46912753-46912988(+)$1	1	51	91	13.6242
.(((((((..((.((((....)))).))..))))))))))	chr5:122903599-122903846(-)$1	1	95	135	13.8147
))))(((((((..((((....))))...)))))))(((((	chr19:24757738-24757973(-)$1	1	64	104	14.3020
..((((.(((.((((......)))).))).))))....))	chr2:22796897-22797132(-)$1	1	176	216	14.1211
(.(((((((..(((((((...)))))))..))).).))).	chr11:109529767-109530009(+)$1	1	135	175	12.5704
..(((.(.(((.((((......))))....))).).))).	chr8:4524695-4524930(+)$1	1	71	111	17.5226
(((((((..(((.(((...))).))))))))))..)))))	chr1:99717957-99718198(-)$1	1	55	95	12.1411
((((..(((((((((((....))))....)))))))...)	chr9:96218337-96218572(+)$1	1	151	191	14.8440
((((((((((.(((((......)))))...))))))....	chr9:70625984-70626219(+)$1	1	53	93	13.2234
...((.(((....(((....)))....)))))...)).))	chr8:112254772-112255023(-)$1	1	195	235	12.8427
.((((((((((((.........)))))))))))).)))))	chr11:40492882-40493117(-)$1	1	154	194	14.8865
.(((.(((((.(.(((....))).).)))))...))).).	chr8:23678766-23679001(+)$1	1	46	86	12.7582
((..((((((((((((......))..)))))))))).)))	chr1:34933815-34934074(+)$1	1	88	128	17.4558
(((((((((.((.((((....)))).))..))))))))).	chr4:15844545-15844787(-)$1	1	87	127	15.2159
(((.((((((((((((...)))))))))...))).)))((	chr4:57909670-57909907(+)$1	1	104	144	12.9711
.((((((.((..((((......))))...)).)))).)).	chr3:141965381-141965616(-)$1	1	168	208	14.4377
.(.(((.((..(((((......))))).)).))).)))))	chr3:60812561-60812821(+)$1	1	111	151	14.3728
((((((((.(((((((......))..)))))..)))...)	chr7:146765008-146765298(+)$1	1	162	202	14.6385
.(((((((((.(((.(......))))..............	chr17:33884446-33884681(-)$1	1	54	94	14.1017
.(((((((..((.((((....)))).))..))))))))))	chr5:122903658-122903893(-)$1	1	142	182	13.8147
((((((.(((.((((.........))))...))).)))))	chr19:43574327-43574562(-)$1	1	39	79	12.9258
((...(((.(((.(((......))).))).)))....)))	chr1:166367534-166367783(-)$1	1	206	246	17.0345
(((...(((..(((((......)))))..))).)))))))	chr13:74460049-74460289(-)$1	1	63	103	15.1027
((((((...((..((((....))))..))...))))))))	chr11:109529368-109529612(+)$1	1	168	208	15.2681
((((((((((((((((.....)))))..))))))))))).	chr19:57111016-57111251(-)$1	1	13	53	15.3159
.(((.(((((((.((.(......).)).))))))).))).	chr10:82203496-82203737(+)$1	1	166	206	12.5048
(((..((((((((((..........))))))))))...))	chr2:134420523-134420770(-)$1	1	180	220	12.5903
.(((..(((....(((......))).....)))..)))..	chr9:48463289-48463524(-)$1	1	147	187	13.6212
((....((((..((((......))))..))))...)))))	chr17:85463643-85463882(-)$1	1	140	180	17.3037
.(((((((((..((((......))))..))))))))).((	chr2:121373570-121373818(-)$1	1	24	64	14.5926
((...(((.(((.(((......))).))).)))....)))	chr11:94887931-94888172(-)$1	1	189	229	16.2036
(((((((....(((((......)))))..)))))))(((.	chr8:98238288-98238548(+)$1	1	171	211	16.1946
.((...(((...((((.....))))...))).)).)))))	chr18:34506258-34506494(-)$1	1	133	173	14.2733
((((((((...(((..(((...))).))).))))))))))	chr18:78021134-78021386(+)$1	1	92	132	15.3914
((((((((((((.((((....)))).))))))))).))))	chr19:37097078-37097315(-)$1	1	194	234	14.5166
((((((...((..((((....))))..))...))))))))	chr11:109529413-109529649(+)$1	1	123	163	15.2681
(((...(((..(((((......)))))..)))...)))).	chr14:76907381-76907616(+)$1	1	65	105	15.9936
(((..(((((...(.(.....).)...)))))..)))...	chr13:29999430-29999670(-)$1	1	17	57	13.3422
(((((((..(((((((......)))))))..))))..)))	chr6:71342077-71342314(-)$1	1	69	109	14.0084
((..(((((((..(((((...))))))))))))..))...	chr7:134861138-134861380(+)$1	1	156	196	13.0991
((((((((....((((.((....)).))))...)))))))	chr11:50108806-50109049(-)$1	1	69	109	13.0346
(((((((((((...((......))....)))).)))))))	chr2:163450342-163450596(-)$1	1	121	161	16.2214
(((.(((((....(((......)))...))))).)))(((	chr2:132134563-132134798(+)$1	1	122	162	16.3407
(.....(((((((.((......)).)))))))))))))))	chr7:35130774-35131009(-)$1	1	193	233	14.7240
((((...(((....((......))....))).))))))))	chr18:68427442-68427680(-)$1	1	44	84	14.3427
.((((((((((..(((((....))))).)))))))))).)	chr12:71568417-71568671(+)$1	1	199	239	15.6679
..((((.(((..((((......)))).))).))))..)).	chr1:183835465-183835707(-)$1	1	189	229	15.0381
(((...(((((.((((......)))))))))....)))))	chr9:96233096-96233334(-)$1	1	73	113	15.9211

#PSSM
= : 0.15	[ : 0.15	c : 0.11	g : 0.09	f : 0.07	i : 0.07	d : 0.07	" : 0.05	e : 0.03	! : 0.03	: : 0.03	$ : 0.01	& : 0.01	b : 0.01	
= : 0.19	c : 0.17	g : 0.13	i : 0.11	d : 0.07	f : 0.05	b : 0.05	e : 0.03	$ : 0.03	! : 0.03	[ : 0.01	" : 0.01	a : 0.01	
= : 0.17	c : 0.15	i : 0.13	g : 0.13	d : 0.09	f : 0.05	" : 0.05	e : 0.03	! : 0.03	b : 0.03	[ : 0.01	# : 0.01	$ : 0.01	
= : 0.15	i : 0.15	g : 0.11	c : 0.11	" : 0.11	d : 0.09	! : 0.07	f : 0.03	[ : 0.03	e : 0.01	b : 0.01	# : 0.01	$ : 0.01	
= : 0.17	i : 0.15	g : 0.13	" : 0.13	d : 0.07	c : 0.07	! : 0.07	f : 0.03	[ : 0.03	b : 0.01	# : 0.01	e : 0.01	$ : 0.01	
= : 0.17	i : 0.15	g : 0.15	c : 0.09	" : 0.09	d : 0.07	! : 0.05	e : 0.05	[ : 0.03	a : 0.01	f : 0.01	# : 0.01	$ : 0.01	
c : 0.19	= : 0.17	g : 0.17	i : 0.11	[ : 0.07	e : 0.07	d : 0.05	" : 0.05	! : 0.01	a : 0.01	f : 0.01	
c : 0.25	= : 0.15	i : 0.13	g : 0.13	e : 0.09	[ : 0.03	! : 0.03	" : 0.03	d : 0.03	f : 0.01	b : 0.01	# : 0.01	
c : 0.21	i : 0.13	= : 0.11	e : 0.09	g : 0.09	! : 0.07	[ : 0.05	" : 0.05	b : 0.03	d : 0.03	# : 0.03	f : 0.01	
c : 0.15	= : 0.11	i : 0.11	! : 0.11	g : 0.11	e : 0.09	# : 0.09	b : 0.05	d : 0.03	" : 0.03	f : 0.01	[ : 0.01	
! : 0.15	[ : 0.11	g : 0.11	# : 0.11	b : 0.09	= : 0.09	" : 0.07	c : 0.07	i : 0.05	e : 0.05	d : 0.01	
! : 0.17	e : 0.15	g : 0.09	c : 0.09	# : 0.09	" : 0.07	[ : 0.05	b : 0.05	= : 0.05	a : 0.03	d : 0.03	i : 0.03	
d : 0.21	[ : 0.19	e : 0.15	! : 0.09	g : 0.07	# : 0.07	" : 0.05	= : 0.05	c : 0.03	i : 0.01	
d : 0.39	c : 0.19	e : 0.19	g : 0.03	= : 0.03	r : 0.01	i : 0.01	b : 0.01	a : 0.01	" : 0.01	[ : 0.01	# : 0.01	
d : 0.39	e : 0.17	c : 0.15	b : 0.11	g : 0.03	[ : 0.03	r : 0.01	i : 0.01	= : 0.01	! : 0.01	
d : 0.35	e : 0.17	c : 0.15	b : 0.09	g : 0.03	r : 0.03	a : 0.03	o : 0.01	i : 0.01	[ : 0.01	s : 0.01	! : 0.01	
o : 0.49	d : 0.17	e : 0.05	n : 0.05	l : 0.03	m : 0.03	r : 0.03	g : 0.01	a : 0.01	s : 0.01	c : 0.01	[ : 0.01	
o : 0.50	m : 0.21	l : 0.05	n : 0.05	r : 0.03	e : 0.03	g : 0.01	s : 0.01	c : 0.01	b : 0.01	
o : 0.50	m : 0.23	l : 0.09	n : 0.05	r : 0.03	s : 0.01	c : 0.01	b : 0.01	
o : 0.50	m : 0.25	l : 0.07	n : 0.05	r : 0.03	c : 0.01	i : 0.01	s : 0.01	
o : 0.50	m : 0.21	l : 0.05	c : 0.05	n : 0.05	r : 0.03	e : 0.01	i : 0.01	s : 0.01	
o : 0.49	d : 0.21	e : 0.05	c : 0.05	r : 0.03	m : 0.03	g : 0.01	i : 0.01	s : 0.01	l : 0.01	a : 0.01	
d : 0.35	e : 0.17	c : 0.15	b : 0.09	g : 0.03	] : 0.03	= : 0.01	i : 0.01	a : 0.01	r : 0.01	o : 0.01	s : 0.01	m : 0.01	
d : 0.35	e : 0.17	c : 0.15	b : 0.11	g : 0.03	a : 0.03	4 : 0.01	= : 0.01	] : 0.01	i : 0.01	r : 0.01	s : 0.01	
d : 0.37	e : 0.17	c : 0.15	4 : 0.05	g : 0.03	2 : 0.03	] : 0.03	= : 0.01	a : 0.01	i : 0.01	s : 0.01	3 : 0.01	b : 0.01	
] : 0.21	d : 0.15	e : 0.15	2 : 0.11	3 : 0.07	4 : 0.07	g : 0.05	c : 0.03	= : 0.03	i : 0.01	b : 0.01	5 : 0.01	
e : 0.17	2 : 0.13	3 : 0.09	g : 0.09	4 : 0.09	b : 0.07	c : 0.07	= : 0.05	] : 0.03	i : 0.03	d : 0.03	a : 0.01	> : 0.01	5 : 0.01	
c : 0.11	2 : 0.11	e : 0.09	b : 0.09	3 : 0.09	g : 0.09	= : 0.07	i : 0.07	4 : 0.07	] : 0.05	d : 0.03	> : 0.01	5 : 0.01	
c : 0.15	2 : 0.13	= : 0.11	e : 0.11	g : 0.11	i : 0.07	3 : 0.07	b : 0.05	d : 0.05	4 : 0.03	> : 0.01	5 : 0.01	
g : 0.13	= : 0.11	e : 0.11	c : 0.11	2 : 0.09	3 : 0.09	i : 0.07	] : 0.07	d : 0.05	b : 0.03	4 : 0.01	> : 0.01	5 : 0.01	
g : 0.17	c : 0.17	= : 0.13	e : 0.11	i : 0.09	3 : 0.09	d : 0.05	b : 0.03	] : 0.03	f : 0.01	> : 0.01	2 : 0.01	
c : 0.19	g : 0.17	= : 0.13	i : 0.09	d : 0.09	3 : 0.07	e : 0.05	] : 0.05	f : 0.01	b : 0.01	2 : 0.01	> : 0.01	4 : 0.01	
i : 0.15	g : 0.15	c : 0.15	= : 0.13	d : 0.09	3 : 0.09	] : 0.05	2 : 0.03	f : 0.01	> : 0.01	b : 0.01	e : 0.01	4 : 0.01	
= : 0.17	i : 0.15	g : 0.11	d : 0.09	2 : 0.07	3 : 0.07	c : 0.07	] : 0.05	4 : 0.05	f : 0.03	> : 0.01	e : 0.01	b : 0.01	
= : 0.15	i : 0.15	g : 0.11	] : 0.09	4 : 0.07	c : 0.07	d : 0.07	2 : 0.05	3 : 0.05	f : 0.03	a : 0.03	> : 0.01	e : 0.01	
= : 0.15	i : 0.13	c : 0.13	g : 0.11	] : 0.07	f : 0.05	4 : 0.05	e : 0.05	d : 0.05	b : 0.03	2 : 0.03	a : 0.01	> : 0.01	3 : 0.01	
c : 0.19	= : 0.13	i : 0.09	3 : 0.07	4 : 0.07	g : 0.07	e : 0.07	b : 0.05	f : 0.03	] : 0.03	d : 0.03	2 : 0.03	0 : 0.01	> : 0.01	
c : 0.19	= : 0.15	3 : 0.11	d : 0.09	e : 0.07	i : 0.07	b : 0.05	4 : 0.03	f : 0.03	] : 0.03	g : 0.03	0 : 0.01	> : 0.01	: : 0.01	
c : 0.15	= : 0.13	3 : 0.09	f : 0.09	d : 0.09	g : 0.07	i : 0.07	e : 0.05	4 : 0.03	b : 0.03	0 : 0.01	a : 0.01	h : 0.01	> : 0.01	E : 0.01	] : 0.01	
3 : 0.13	= : 0.11	d : 0.09	f : 0.09	c : 0.09	g : 0.07	] : 0.05	e : 0.05	i : 0.05	4 : 0.03	9 : 0.01	0 : 0.01	h : 0.01	> : 0.01	7 : 0.01	: : 0.01	E : 0.01	[ : 0.01	

#score	750.531547734381
#seq	51
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_CDS_m3_run1.txt

#BEAR
ccddddqqqqqqqqdddd]cc	chr4:108391009-108391334(-)$1	325	294	315	14.2321
"""cccqqqqqqqqccc333e	chr5:67070800-67071054(+)$1	254	229	250	15.7898
fff[bbqqqqqqqqbb]ffff	chr8:28234245-28234510(-)$1	265	41	62	14.6217
ddd[bbqqqqqqqqbb]dddd	chr9:108474602-108474925(-)$1	323	40	61	14.4638
b"""bbqqqqqqqqbb]bbcc	chr9:106792391-106792658(-)$1	267	176	197	14.1688
ffffffqqqqqqqqffffff3	chr7:125918737-125918979(+)$1	242	53	74	14.0768
ddd[bbqqqqqqqqbbdddd]	chr5:23345492-23345749(-)$1	257	92	113	14.4413
ggggggqqqqqqqqggggggg	chr2:168473083-168473340(-)$1	257	25	46	15.5111
hh[cccqqqqqqqqccchhhh	chr4:151737453-151737691(+)$1	238	158	179	14.8504
ffffffqqqqqqqqffffff]	chrX:35966303-35966712(+)$1	409	39	60	14.0569
hhhcccqqqqqqqqccc]hhh	chr10:57920286-57920579(+)$1	293	155	176	14.8699
c!!cccqqqqqqqqccc22cc	chr4:98120889-98121222(+)$1	333	22	43	15.7520
bb!!bbqqqqqqqqbb22bb2	chr17:56037466-56037794(+)$1	328	267	288	13.6571
dddd[aqqqqqqqqa]ddddh	chr1:80263466-80263912(-)$1	446	67	88	14.0620
======qqqqqqqq=======	chr16:96746895-96747169(+)$1	274	83	104	15.6115
[ccc[aqqqqqqqqa]ccc]a	chr2:65518791-65519155(+)$1	364	201	222	15.2144
cc[cccqqqqqqqqccc]ccc	chr18:37979735-37980009(+)$1	274	90	111	15.8547
a[ddddqqqqqqqqdddd]a]	chr7:51609859-51610116(+)$1	257	151	172	14.1568
[ccc[aqqqqqqqqa]ccc]e	chr7:31226551-31226895(-)$1	344	64	85	15.1851
ffffffqqqqqqqqffffff]	chr11:76270069-76270378(-)$1	309	250	271	14.0569
ffffffqqqqqqqqffffffF	chr3:55340258-55340631(+)$1	373	176	197	13.5676
iiiiiiqqqqqqqqiiiiiii	chr2:90705252-90705674(+)$1	422	72	93	15.3422
ggggggqqqqqqqqggggggg	chr8:13483591-13483839(-)$1	248	205	226	15.5111
ggggggqqqqqqqqggggggg	chr7:63188272-63188598(-)$1	326	167	188	15.5111
ggggggqqqqqqqqggggggg	chr17:23957747-23958244(+)$1	497	444	465	15.5111
dddcccqqqqqqqqccc]ddd	chr10:127875333-127875627(+)$1	294	85	106	15.0018
eee[bbqqqqqqqqbbeeeee	chr13:41369228-41369669(+)$1	441	374	395	14.5516
c!!cccqqqqqqqqccc22cc	chr4:106250691-106250984(+)$1	293	8	29	15.7520
"a[cccqqqqqqqqccca333	chr18:7921461-7921713(+)$1	252	51	72	15.7923
ddd[bbqqqqqqqqbbdddd2	chr6:113724094-113724531(-)$1	437	203	224	14.2332
ggggggqqqqqqqqggggggg	chr8:74179472-74179739(-)$1	267	30	51	15.5111
[eeeeeqqqqqqqqeeeee]c	chr2:59773150-59773575(-)$1	425	127	148	14.3418
ggggggqqqqqqqqggggggg	chr8:125823915-125824147(-)$1	232	1	22	15.5111
ggggggqqqqqqqqggggggg	chr5:3847358-3847603(+)$1	245	139	160	15.5111
d[a!!aqqqqqqqqa22a]dd	chr17:46434288-46434557(+)$1	269	88	109	14.5520
iii[bbqqqqqqqqbb]iiii	chr6:39360046-39360313(-)$1	267	97	118	15.4724
gg[cccqqqqqqqqccc333g	chr2:80192907-80193261(+)$1	354	5	26	16.1297
dd[cccqqqqqqqqccc]ddd	chr15:64599320-64599695(-)$1	375	260	281	15.2155
"""cccqqqqqqqqccc22cc	chr2:91439268-91439523(+)$1	255	197	218	15.5406
eeeebbqqqqqqqqbb]eeee	chr4:149018873-149019190(+)$1	317	256	277	14.4825
ddd[bbqqqqqqqqbb]dddd	chr3:55340453-55340846(+)$1	393	189	210	14.4638
eeecccqqqqqqqqccc]eee	chr6:113723240-113723591(-)$1	351	240	261	15.2047
ccccccqqqqqqqqccc]ccc	chr2:120256228-120256468(+)$1	240	210	231	15.6965
gg!!bbqqqqqqqqbbggggg	chr8:72230920-72231206(-)$1	286	243	264	15.6045
c[ddddqqqqqqqqddddccc	chr8:98237078-98237543(+)$1	465	94	115	14.2687
ccc[bbqqqqqqqqbb22ccc	chr8:26275933-26276196(-)$1	263	150	171	15.0494
c!!cccqqqqqqqqccc22cc	chr5:115548020-115548487(+)$1	467	179	200	15.7520
ggggggqqqqqqqqggggggg	chr10:57940368-57940631(+)$1	263	45	66	15.5111
""ddddqqqqqqqqddddeee	chr4:85025169-85025425(+)$1	256	19	40	13.8942
[a[cccqqqqqqqqccc]a]f	chrX:92246405-92246796(-)$1	391	60	81	15.7491
gggggaqqqqqqqqa]ggggg	chr8:128384642-128385024(-)$1	382	265	286	15.5435
Fcccbbqqqqqqqqbb]ccc:	chr13:93866466-93866777(-)$1	311	289	310	13.6553
ggggggqqqqqqqqggggggg	chr10:90579505-90579829(-)$1	324	166	187	15.5111
"eeeeeqqqqqqqqeeeee33	chr17:78780867-78781117(-)$1	250	97	118	14.2920
dd[cccqqqqqqqqccc22dd	chr12:104655387-104655691(-)$1	304	116	137	15.1089
!!a!!aqqqqqqqqa22a22a	chr13:99124549-99124777(+)$1	228	103	124	14.6590
ccc!!aqqqqqqqqa22ccce	chr2:9980437-9980742(-)$1	305	192	213	14.7009
!eeeeeqqqqqqqqeeeee33	chr2:140029175-140029503(+)$1	328	173	194	14.3715
#eeeeeqqqqqqqqeeeee44	chr11:6224787-6225145(+)$1	358	297	318	14.0149
ggggbbqqqqqqqqbb]gggg	chr2:102617487-102617874(+)$1	387	86	107	15.4899
[eeeeeqqqqqqqqeeeee]a	chr4:9557767-9558115(-)$1	348	213	234	14.2600
ccccccqqqqqqqqccc333c	chr7:99568934-99569342(+)$1	408	203	224	15.8476
c[ddddqqqqqqqqdddd]cc	chr6:124811218-124811494(-)$1	276	175	196	14.3461
[eeeeeqqqqqqqqeeeee]f	chr15:6746058-6746305(+)$1	247	125	146	14.2219
ggggggqqqqqqqqggggggg	chr9:55993191-55993451(-)$1	260	185	206	15.5111
f[a[bbqqqqqqqqbb]afff	chr19:47694185-47694437(+)$1	252	8	29	14.9332
dddcccqqqqqqqqccc]ddd	chr6:115755421-115755711(-)$1	290	246	267	15.0018
fffcccqqqqqqqqccc]fff	chr4:33333264-33333530(-)$1	266	224	245	15.1487

#otherMatches

#Seq PSSM
AGAGCAAGUCAGAAUGCUAUU	chr4:108391009-108391334(-)$1	325	294	315	14.2321
CAACCAAGACAAGCUGGAAUU	chr5:67070800-67071054(+)$1	254	229	250	15.7898
AUAGUGAAAUAGAGCAGUAUU	chr8:28234245-28234510(-)$1	265	41	62	14.6217
GUUCCUGAAAGAAAAGCAGCC	chr9:108474602-108474925(-)$1	323	40	61	14.4638
ACUCGGACCCUGUGCCUUCUA	chr9:106792391-106792658(-)$1	267	176	197	14.1688
UCCUCUCUCCCACAGGGGGAU	chr7:125918737-125918979(+)$1	242	53	74	14.0768
AAAUGUUUUAGCCUACUUUGG	chr5:23345492-23345749(-)$1	257	92	113	14.4413
UGUGAGCCGUCCCUCUCACAU	chr2:168473083-168473340(-)$1	257	25	46	15.5111
GCACCUGCCGGGUGAGGGCUG	chr4:151737453-151737691(+)$1	238	158	179	14.8504
AUGAAUGCAUAAAAAUUCAUA	chrX:35966303-35966712(+)$1	409	39	60	14.0569
UUCUCUGCUUUUGAAGAUGGG	chr10:57920286-57920579(+)$1	293	155	176	14.8699
GCUUGCUAGAAGUCGCACACA	chr4:98120889-98121222(+)$1	333	22	43	15.7520
uacuggagagaaacccuauaa	chr17:56037466-56037794(+)$1	328	267	288	13.6571
GGCUCGAUUCUUACCAAGUCC	chr1:80263466-80263912(-)$1	446	67	88	14.0620
GUUUGUUUUUUACUACAGAUG	chr16:96746895-96747169(+)$1	274	83	104	15.6115
GCAUGUGCAUGAAAAGAUGGG	chr2:65518791-65519155(+)$1	364	201	222	15.2144
UGUGAGCUUUUAUACUCUCAG	chr18:37979735-37980009(+)$1	274	90	111	15.8547
AGAGGUGAGCAGAGGCCUGUG	chr7:51609859-51610116(+)$1	257	151	172	14.1568
GAGGGAAAGUGACCUGCCUGC	chr7:31226551-31226895(-)$1	344	64	85	15.1851
UUCCGGAUACACAAUCGGAAU	chr11:76270069-76270378(-)$1	309	250	271	14.0569
AUUUGUCAUGAUCAAUAAAUG	chr3:55340258-55340631(+)$1	373	176	197	13.5676
UUCUUUUCUUUUCCAGGGAAA	chr2:90705252-90705674(+)$1	422	72	93	15.3422
GUAGCCAGGGGUAAGGCUGCU	chr8:13483591-13483839(-)$1	248	205	226	15.5111
CUUUUCGAAAAGAUGAAAAGG	chr7:63188272-63188598(-)$1	326	167	188	15.5111
AGCGGGCUCCUUCCCCUGCUU	chr17:23957747-23958244(+)$1	497	444	465	15.5111
CACAUGGGGGACGACAUGGUG	chr10:127875333-127875627(+)$1	294	85	106	15.0018
UCCCUCCUUUAUAUGAGGACU	chr13:41369228-41369669(+)$1	441	374	395	14.5516
AAACGCAUUAGACAGCGGCUG	chr4:106250691-106250984(+)$1	293	8	29	15.7520
UGCGUGCUCAUUAACACCUAC	chr18:7921461-7921713(+)$1	252	51	72	15.7923
UGCCAGAGGAGAAGCUGUAUA	chr6:113724094-113724531(-)$1	437	203	224	14.2332
GCACCUCUAGUGAUGGGUGUA	chr8:74179472-74179739(-)$1	267	30	51	15.5111
GGGGUAUUUGUCAUUGUCUGC	chr2:59773150-59773575(-)$1	425	127	148	14.3418
UUUUGAAGUCCGAAUCAAAGU	chr8:125823915-125824147(-)$1	232	1	22	15.5111
aaauauauauauaaauauuuu	chr5:3847358-3847603(+)$1	245	139	160	15.5111
GGUGACAGGAGGAAGGUGGCA	chr17:46434288-46434557(+)$1	269	88	109	14.5520
GAUACUUUAUGCAUGGGGUUU	chr6:39360046-39360313(-)$1	267	97	118	15.4724
UUGUGAUAUUCUCUUCAGUAA	chr2:80192907-80193261(+)$1	354	5	26	16.1297
UAAGUUGAGAAGAGAGCAUAU	chr15:64599320-64599695(-)$1	375	260	281	15.2155
CACAGAAUAUAAACUCUAAUG	chr2:91439268-91439523(+)$1	255	197	218	15.5406
CCUGGGUGUGGUCUUCACAGG	chr4:149018873-149019190(+)$1	317	256	277	14.4825
GCCCCCUUAUGAGUGGUGGUU	chr3:55340453-55340846(+)$1	393	189	210	14.4638
CAGCAGCCCUGAGCCUGACUG	chr6:113723240-113723591(-)$1	351	240	261	15.2047
CUCGUGGAGAUCAACACAGAG	chr2:120256228-120256468(+)$1	240	210	231	15.6965
uaccggagagaagcccuauga	chr8:72230920-72231206(-)$1	286	243	264	15.6045
CACUCAGACAGCAGUGAGGGG	chr8:98237078-98237543(+)$1	465	94	115	14.2687
CUGACCAUGGAGAAGGAGCAG	chr8:26275933-26276196(-)$1	263	150	171	15.0494
GCCGGUGUCUUUGUGCUUUCU	chr5:115548020-115548487(+)$1	467	179	200	15.7520
UUUGCAACAAUGACUGCAAAU	chr10:57940368-57940631(+)$1	263	45	66	15.5111
GACUUUGAUUAUAAGAAGAAG	chr4:85025169-85025425(+)$1	256	19	40	13.8942
CUGUCACUUUCCACUGAGAAG	chrX:92246405-92246796(-)$1	391	60	81	15.7491
UGUGUCUGUAUCUUGAAUACA	chr8:128384642-128385024(-)$1	382	265	286	15.5435
UCUAGAAGAAGAGAUCAUAGA	chr13:93866466-93866777(-)$1	311	289	310	13.6553
GAAAGUGCAAAGGAACUUUUA	chr10:90579505-90579829(-)$1	324	166	187	15.5111
UUGGCAGUCCUGCAUGCCAUG	chr17:78780867-78781117(-)$1	250	97	118	14.2920
UCCUGGAUGUCAUGCCGCUGA	chr12:104655387-104655691(-)$1	304	116	137	15.1089
gacgacgaggaggaggaggac	chr13:99124549-99124777(+)$1	228	103	124	14.6590
UGAGUGUUUCUGUUCUAUUAC	chr2:9980437-9980742(-)$1	305	192	213	14.7009
AAAUAAUAAAUACUUUGUUCA	chr2:140029175-140029503(+)$1	328	173	194	14.3715
GUUAUUAACCAACAAGUAGAG	chr11:6224787-6225145(+)$1	358	297	318	14.0149
UCAUCUUUAGGGAUAGAAUGA	chr2:102617487-102617874(+)$1	387	86	107	15.4899
GGGGUUCAGGGAAAGACCUGU	chr4:9557767-9558115(-)$1	348	213	234	14.2600
GCAGAACACGUCUCUUCUAAU	chr7:99568934-99569342(+)$1	408	203	224	15.8476
AACGCCAAGAAGCAGGCGCUG	chr6:124811218-124811494(-)$1	276	175	196	14.3461
UGUUGGCAAUUCCACCAAUUC	chr15:6746058-6746305(+)$1	247	125	146	14.2219
CAGGGGUGGUUUGUCUCUUGA	chr9:55993191-55993451(-)$1	260	185	206	15.5111
AAGAACAGAACAAAGUACUUC	chr19:47694185-47694437(+)$1	252	8	29	14.9332
GCAGGGUUCAGAAUCCCAUGC	chr6:115755421-115755711(-)$1	290	246	267	15.0018
UGCUUCCUCCGAUCGAAUGCA	chr4:33333264-33333530(-)$1	266	224	245	15.1487

#DB
((((((........)))).))	chr4:108391009-108391334(-)$1	1	294	315	14.2321
...(((........)))...)	chr5:67070800-67071054(+)$1	1	229	250	15.7898
(((.((........)).))))	chr8:28234245-28234510(-)$1	1	41	62	14.6217
(((.((........)).))))	chr9:108474602-108474925(-)$1	1	40	61	14.4638
(...((........)).))))	chr9:106792391-106792658(-)$1	1	176	197	14.1688
((((((........)))))).	chr7:125918737-125918979(+)$1	1	53	74	14.0768
(((.((........)))))).	chr5:23345492-23345749(-)$1	1	92	113	14.4413
((((((........)))))))	chr2:168473083-168473340(-)$1	1	25	46	15.5111
((.(((........)))))))	chr4:151737453-151737691(+)$1	1	158	179	14.8504
((((((........)))))).	chrX:35966303-35966712(+)$1	1	39	60	14.0569
((((((........))).)))	chr10:57920286-57920579(+)$1	1	155	176	14.8699
(..(((........)))..))	chr4:98120889-98121222(+)$1	1	22	43	15.7520
((..((........))..)).	chr17:56037466-56037794(+)$1	1	267	288	13.6571
((((.(........).)))))	chr1:80263466-80263912(-)$1	1	67	88	14.0620
((((((........)))))))	chr16:96746895-96747169(+)$1	1	83	104	15.6115
.(((.(........).))).)	chr2:65518791-65519155(+)$1	1	201	222	15.2144
((.(((........))).)))	chr18:37979735-37980009(+)$1	1	90	111	15.8547
(.((((........)))).).	chr7:51609859-51610116(+)$1	1	151	172	14.1568
.(((.(........).))).)	chr7:31226551-31226895(-)$1	1	64	85	15.1851
((((((........)))))).	chr11:76270069-76270378(-)$1	1	250	271	14.0569
((((((........))))))(	chr3:55340258-55340631(+)$1	1	176	197	13.5676
((((((........)))))))	chr2:90705252-90705674(+)$1	1	72	93	15.3422
((((((........)))))))	chr8:13483591-13483839(-)$1	1	205	226	15.5111
((((((........)))))))	chr7:63188272-63188598(-)$1	1	167	188	15.5111
((((((........)))))))	chr17:23957747-23958244(+)$1	1	444	465	15.5111
((((((........))).)))	chr10:127875333-127875627(+)$1	1	85	106	15.0018
(((.((........)))))))	chr13:41369228-41369669(+)$1	1	374	395	14.5516
(..(((........)))..))	chr4:106250691-106250984(+)$1	1	8	29	15.7520
.(.(((........))))...	chr18:7921461-7921713(+)$1	1	51	72	15.7923
(((.((........)))))).	chr6:113724094-113724531(-)$1	1	203	224	14.2332
((((((........)))))))	chr8:74179472-74179739(-)$1	1	30	51	15.5111
.(((((........))))).)	chr2:59773150-59773575(-)$1	1	127	148	14.3418
((((((........)))))))	chr8:125823915-125824147(-)$1	1	1	22	15.5111
((((((........)))))))	chr5:3847358-3847603(+)$1	1	139	160	15.5111
(.(..(........)..).))	chr17:46434288-46434557(+)$1	1	88	109	14.5520
(((.((........)).))))	chr6:39360046-39360313(-)$1	1	97	118	15.4724
((.(((........)))...)	chr2:80192907-80193261(+)$1	1	5	26	16.1297
((.(((........))).)))	chr15:64599320-64599695(-)$1	1	260	281	15.2155
...(((........)))..))	chr2:91439268-91439523(+)$1	1	197	218	15.5406
((((((........)).))))	chr4:149018873-149019190(+)$1	1	256	277	14.4825
(((.((........)).))))	chr3:55340453-55340846(+)$1	1	189	210	14.4638
((((((........))).)))	chr6:113723240-113723591(-)$1	1	240	261	15.2047
((((((........))).)))	chr2:120256228-120256468(+)$1	1	210	231	15.6965
((..((........)))))))	chr8:72230920-72231206(-)$1	1	243	264	15.6045
(.((((........)))))))	chr8:98237078-98237543(+)$1	1	94	115	14.2687
(((.((........))..)))	chr8:26275933-26276196(-)$1	1	150	171	15.0494
(..(((........)))..))	chr5:115548020-115548487(+)$1	1	179	200	15.7520
((((((........)))))))	chr10:57940368-57940631(+)$1	1	45	66	15.5111
..((((........)))))))	chr4:85025169-85025425(+)$1	1	19	40	13.8942
.(.(((........))).).)	chrX:92246405-92246796(-)$1	1	60	81	15.7491
((((((........).)))))	chr8:128384642-128385024(-)$1	1	265	286	15.5435
)(((((........)).))).	chr13:93866466-93866777(-)$1	1	289	310	13.6553
((((((........)))))))	chr10:90579505-90579829(-)$1	1	166	187	15.5111
.(((((........)))))..	chr17:78780867-78781117(-)$1	1	97	118	14.2920
((.(((........)))..))	chr12:104655387-104655691(-)$1	1	116	137	15.1089
..(..(........)..)..)	chr13:99124549-99124777(+)$1	1	103	124	14.6590
(((..(........)..))))	chr2:9980437-9980742(-)$1	1	192	213	14.7009
.(((((........)))))..	chr2:140029175-140029503(+)$1	1	173	194	14.3715
.(((((........)))))..	chr11:6224787-6225145(+)$1	1	297	318	14.0149
((((((........)).))))	chr2:102617487-102617874(+)$1	1	86	107	15.4899
.(((((........))))).)	chr4:9557767-9558115(-)$1	1	213	234	14.2600
((((((........)))...)	chr7:99568934-99569342(+)$1	1	203	224	15.8476
(.((((........)))).))	chr6:124811218-124811494(-)$1	1	175	196	14.3461
.(((((........))))).)	chr15:6746058-6746305(+)$1	1	125	146	14.2219
((((((........)))))))	chr9:55993191-55993451(-)$1	1	185	206	15.5111
(.(.((........)).))))	chr19:47694185-47694437(+)$1	1	8	29	14.9332
((((((........))).)))	chr6:115755421-115755711(-)$1	1	246	267	15.0018
((((((........))).)))	chr4:33333264-33333530(-)$1	1	224	245	15.1487

#PSSM
g : 0.20	c : 0.16	d : 0.14	f : 0.10	[ : 0.08	" : 0.07	e : 0.04	b : 0.02	h : 0.02	i : 0.02	! : 0.02	= : 0.01	a : 0.01	F : 0.01	# : 0.01	
g : 0.20	c : 0.13	d : 0.13	e : 0.13	f : 0.08	[ : 0.07	" : 0.05	! : 0.05	h : 0.02	i : 0.02	a : 0.02	b : 0.01	= : 0.01	
d : 0.17	g : 0.17	e : 0.13	[ : 0.10	c : 0.10	f : 0.08	! : 0.07	" : 0.04	a : 0.04	i : 0.02	h : 0.01	= : 0.01	
c : 0.32	g : 0.17	[ : 0.13	e : 0.10	d : 0.08	! : 0.07	f : 0.05	" : 0.01	= : 0.01	i : 0.01	
c : 0.27	b : 0.22	g : 0.16	e : 0.08	d : 0.07	f : 0.05	[ : 0.04	! : 0.04	= : 0.01	i : 0.01	
c : 0.27	b : 0.22	g : 0.14	a : 0.10	e : 0.08	d : 0.07	f : 0.05	= : 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 : 0.27	b : 0.22	g : 0.14	a : 0.10	e : 0.08	d : 0.07	f : 0.05	= : 0.01	i : 0.01	
c : 0.27	b : 0.22	g : 0.14	e : 0.08	d : 0.07	f : 0.05	] : 0.05	2 : 0.04	= : 0.01	i : 0.01	
c : 0.30	g : 0.17	] : 0.13	d : 0.11	e : 0.10	2 : 0.07	f : 0.05	= : 0.01	i : 0.01	
g : 0.19	d : 0.14	] : 0.13	e : 0.11	2 : 0.10	f : 0.07	c : 0.05	a : 0.05	3 : 0.04	i : 0.02	b : 0.01	h : 0.01	= : 0.01	
g : 0.19	e : 0.14	d : 0.11	c : 0.11	f : 0.10	2 : 0.08	] : 0.05	3 : 0.05	b : 0.02	h : 0.02	i : 0.02	= : 0.01	a : 0.01	
c : 0.19	g : 0.19	d : 0.14	f : 0.10	3 : 0.08	] : 0.08	e : 0.05	h : 0.02	i : 0.02	b : 0.01	= : 0.01	a : 0.01	2 : 0.01	4 : 0.01	
g : 0.20	c : 0.19	e : 0.10	d : 0.10	f : 0.07	3 : 0.05	] : 0.05	h : 0.04	a : 0.04	2 : 0.02	i : 0.02	= : 0.01	F : 0.01	: : 0.01	4 : 0.01	

#score	1015.4896905580315
#seq	68
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_transcript_m1_run1.txt

#BEAR
[gggggggyyyyyyyyyyyyyyyyggggggg]	chr1:66488941-66489253(+)$1	312	61	93	24.1091
fffff[dddduuuuuuuuuuuudddd]fffff	chr12:75047608-75047865(+)$1	257	146	178	24.6074
d[eeeee[bbuuuuuuuuuuuubb333eeeee	chr13:9652964-9653199(+)$1	235	137	169	24.7942
####eeeeevvvvvvvvvvvvveeeee]gggg	chr5:8075068-8075331(-)$1	263	98	130	25.0314
eee[ffffffvvvvvvvvvvvvvffffff333	chr12:55172626-55172863(+)$1	237	68	100	25.2282
:eeeeecccwwwwwwwwwwwwwwccc]eeeee	chr16:11134462-11134700(-)$1	238	54	86	23.8092
eeeee[cccvvvvvvvvvvvvvccceeeee22	chr14:34192044-34192281(-)$1	237	55	87	24.6807
fffffcccxxxxxxxxxxxxxxxccc]fffff	chr11:97252214-97252452(+)$1	238	65	97	19.6498
ffff[fffffftttttttttttffffff22ff	chrX:102318827-102319101(+)$1	274	35	67	23.6012
gggggg[cccuuuuuuuuuuuuccc]gggggg	chr11:109530312-109530563(+)$1	251	76	108	26.6374
&eeeeeyyyyyyyyyyyyyyyyeeeee22ddd	chr2:6465623-6465886(-)$1	263	156	188	21.2766
::gggggggvvvvvvvvvvvvvggggggg:gg	chr5:122903787-122904080(-)$1	293	106	138	22.6968
dddd[fffffftttttttttttffffffdddd	chr18:36957772-36958009(+)$1	237	106	138	23.1230
ffff"""ddddtttttttttttdddd333fff	chr4:83102600-83102843(-)$1	243	32	64	23.5112
h!!ccc[cccuuuuuuuuuuuuccc22ccc33	chrX:69677955-69678230(-)$1	275	24	56	25.9359
d"""eeeeewwwwwwwwwwwwwweeeee22dd	chr1:152209721-152209959(-)$1	238	12	44	23.9017
:gggggggavvvvvvvvvvvvva]ggggggg:	chr3:156289319-156289567(+)$1	248	48	80	23.8413
eee[ccc[bbtttttttttttbbccc]eeeee	chr6:30404880-30405127(+)$1	247	116	148	23.5438
"""ggggggguuuuuuuuuuuuggggggg444	chr17:43225044-43225279(+)$1	235	111	143	26.1312
==========xxxxxxxxxxxxxxx=======	chr11:4382365-4382603(-)$1	238	33	65	20.1665
ffff!!dddduuuuuuuuuuuuddddffffff	chr15:36407574-36407829(-)$1	255	221	253	24.5792
eeee[eeeeewwwwwwwwwwwwwweeeee]ee	chr7:103395499-103395736(+)$1	237	154	186	23.8526
eeeeeeeeeettttttttttteeeee]eeeee	chr15:93115153-93115388(-)$1	235	38	70	23.4585
!!bbddddccctttttttttttccc]dddd]b	chr15:76910785-76911023(-)$1	238	186	218	22.8454
[ffffff[ccctttttttttttcccffffff2	chr12:85717554-85717790(-)$1	236	66	98	24.5043
:iiiiiiiiiuuuuuuuuuuuuiiiiiiiii:	chr6:108772233-108772495(+)$1	262	78	110	24.1681
c[ccceeeeeuuuuuuuuuuuueeeee]ccc2	chr5:122906460-122906727(-)$1	267	122	154	25.2725
$$$$$cccwwwwwwwwwwwwwwccc22fffff	chr4:150433959-150434227(-)$1	268	191	223	23.4952
%gggggggyyyyyyyyyyyyyyyyggggggg]	chr2:32644740-32645028(-)$1	288	164	196	23.6094
:ddddfffffftttttttttttffffff]ddd	chr9:58500334-58500635(+)$1	301	15	47	22.3945
ee"""eeeeevvvvvvvvvvvvveeeee333e	chr2:25915222-25915471(-)$1	249	35	67	25.2158
eee!!eeeeeuuuuuuuuuuuueeeeeeeeee	chr18:82753773-82754078(+)$1	305	189	221	25.3818
==========uuuuuuuuuuuu==========	chr5:122906986-122907245(-)$1	259	215	247	26.4586
hhhgggggggtttttttttttggggggg333h	chrX:154260176-154260432(-)$1	256	212	244	23.4212
ddd!!ccc[attttttttttta]ccc22dddd	chr15:99330398-99330651(-)$1	253	104	136	23.9644
c[ffffffxxxxxxxxxxxxxxxffffff]cc	chr15:37298357-37298603(-)$1	246	158	190	19.6977
iiiiifffffftttttttttttffffffdddd	chrX:102992876-102993111(-)$1	235	136	168	23.7488
iiii####bbuuuuuuuuuuuubb4444iiii	chr6:144948021-144948268(-)$1	247	176	208	24.9035
:gggggggwwwwwwwwwwwwwwggggggg:ff	chr8:70219262-70219497(-)$1	235	17	49	22.8317
c[ccceeeeeuuuuuuuuuuuueeeee]ccc]	chr15:80655862-80656097(+)$1	235	176	208	25.4601
:ffffffcccuuuuuuuuuuuuccc22fffff	chr9:18117323-18117558(+)$1	235	170	202	24.9323
bb[a!!eeeeettttttttttteeeeea]bb]	chr17:90435982-90436223(-)$1	241	128	160	23.2713
ff[a"""ccctttttttttttccc4444a]ff	chr5:67679172-67679423(+)$1	251	109	141	24.2899
ccc"""eeeeettttttttttteeeeeccc]b	chr17:43225407-43225655(+)$1	248	64	96	23.8906
ccc[ffffffvvvvvvvvvvvvvffffff]cc	chr2:181285043-181285280(+)$1	237	88	120	25.0533
"iiiiiiiiixxxxxxxxxxxxxxxiiiiiii	chr10:20799470-20799713(+)$1	243	115	147	19.7099
dd!!ffffffvvvvvvvvvvvvvffffff000	chr5:14794013-14794274(+)$1	261	38	70	23.6042
iii####cccuuuuuuuuuuuuccc4444iii	chrX:39458697-39458980(+)$1	283	76	108	26.2480
fff$$$$$ccctttttttttttccc333ffff	chr18:33596650-33596921(-)$1	271	111	143	23.8509
ccc[bbcccwwwwwwwwwwwwwwccc]bb]cc	chr4:59233332-59233585(+)$1	253	43	75	23.8906
ggggggg[ccctttttttttttccc]gggggg	chr8:63391717-63391957(-)$1	240	164	196	25.3673
(a[gggggggvvvvvvvvvvvvvggggggg]a	chr2:52288175-52288413(-)$1	238	180	212	25.0027
ccc[ddddwwwwwwwwwwwwwwdddd]ccc]e	chrX:149935458-149935705(+)$1	247	93	125	23.3215
eeeee!!cccvvvvvvvvvvvvvccc22eeee	chr11:19963965-19964203(-)$1	238	69	101	25.0394
bdddd[cccyyyyyyyyyyyyyyyyccc]ddd	chrX:162824265-162824526(+)$1	261	228	260	22.1426
$$$gggggggtttttttttttggggggg22gg	chr5:15876630-15876866(+)$1	236	131	163	23.3795
deeeee!!bbvvvvvvvvvvvvvbb22eeeee	chr5:151612526-151612769(+)$1	243	47	79	23.6777
ddd[ffffffuuuuuuuuuuuuffffff]ddd	chr11:35599911-35600172(+)$1	261	207	239	24.9646
e####bbddddtttttttttttdddd]bb333	chr2:163842490-163842728(+)$1	238	8	40	22.7845
HHHHffffffuuuuuuuuuuuuffffffdddd	chr9:72595391-72595637(+)$1	246	39	71	22.4249
""ccc!!cccvvvvvvvvvvvvvccc22ccc2	chr13:54860178-54860450(-)$1	272	7	39	25.3041

#otherMatches

#Seq PSSM
GGGGUUCUUUCUUCUGAUAAUUCUAGAGCCUG	chr1:66488941-66489253(+)$1	312	61	93	24.1091
UAGUAAACAUCUUGUUUUUUCUAUGUAUACUG	chr12:75047608-75047865(+)$1	257	146	178	24.6074
gagaguguugaccucugaccuccaUCCCACUC	chr13:9652964-9653199(+)$1	235	137	169	24.7942
ACAGAUCCACAUGCUUCUCUUCUGGGUACCUU	chr5:8075068-8075331(-)$1	263	98	130	25.0314
ACAAAAUGAAAAAAAAAAACCACUUCAUUACC	chr12:55172626-55172863(+)$1	237	68	100	25.2282
GGUGGCGGCAGCGACGGUAUAAAGCCGGCCAC	chr16:11134462-11134700(-)$1	238	54	86	23.8092
GUGAGUAGAAUACCCAGCACCGUCUCUCACCC	chr14:34192044-34192281(-)$1	237	55	87	24.6807
GAACUGUUUCUGUUUUUUCCUCUAACUAguuu	chr11:97252214-97252452(+)$1	238	65	97	19.6498
GUAUCUUGAAAAGUUUCCAUUGUUUUAGUAAU	chrX:102318827-102319101(+)$1	274	35	67	23.6012
AAACUUCCAUAAUCUAUAUUAAAUGAGGGUUU	chr11:109530312-109530563(+)$1	251	76	108	26.6374
GUGGACUAUUAGAUGUGUUUGUGUUCAGCAAA	chr2:6465623-6465886(-)$1	263	156	188	21.2766
AAUGUCAUAGCCUCUCUAACUGUAUGAUAAUU	chr5:122903787-122904080(-)$1	293	106	138	22.6968
GGAGUCACAGAACCUCUGCCCAUCUGUGUUCC	chr18:36957772-36958009(+)$1	237	106	138	23.1230
AGUAGUUGGGGGAAAAGAAAAACCCUUUAUAU	chr4:83102600-83102843(-)$1	243	32	64	23.5112
GUGUCUGUAGGUAAACUUAUGACUAGAAGAGU	chrX:69677955-69678230(-)$1	275	24	56	25.9359
UCCCUGAUCAUCCAGAAAUCACGGAUCAACAG	chr1:152209721-152209959(-)$1	238	12	44	23.9017
UUUGUCAGCUUUCACCUCUCCUGUCUGACAGC	chr3:156289319-156289567(+)$1	248	48	80	23.8413
GUGGACGUCCUUUUGCAGUCUGGUGUGCAUGC	chr6:30404880-30405127(+)$1	247	116	148	23.5438
GUUGGAAAAUGCCCACCACUAAAUUUUUUUUU	chr17:43225044-43225279(+)$1	235	111	143	26.1312
AAAGAAAAAUAUCCCAGUUGUCUUAAUUUUUU	chr11:4382365-4382603(-)$1	238	33	65	20.1665
AUUCAAGUUCAAAGCAUGUUCAGGACGAGUGC	chr15:36407574-36407829(-)$1	255	221	253	24.5792
AUAGCUGUUCGAUAAAGUAUGUAGGGACAAUU	chr7:103395499-103395736(+)$1	237	154	186	23.8526
UUAAUGCACCUGCUGGUACUUGGUGUGAUUAA	chr15:93115153-93115388(-)$1	235	38	70	23.4585
CAUCAGCCAGGCAGUUGCCAUCCCUGGGCUAG	chr15:76910785-76911023(-)$1	238	186	218	22.8454
GCUUCCCAUCUAUAAUUGAGAAAGAGGGGGGA	chr12:85717554-85717790(-)$1	236	66	98	24.5043
UGAAGUUUUUUUUUUUUUUCUCAAAAGCUUUC	chr6:108772233-108772495(+)$1	262	78	110	24.1681
CCCAGCCUGCUCGGCUUCUUCUGUAGGUCUGA	chr5:122906460-122906727(-)$1	267	122	154	25.2725
UUCAUGAUAAAAUUAAUAGCUAAUCUUAUUCU	chr4:150433959-150434227(-)$1	268	191	223	23.4952
CUGUAUGUAUCCCACAGUAAGUUCACAUGCAA	chr2:32644740-32645028(-)$1	288	164	196	23.6094
AAUCAUGUAAAUUCUGAAAUCUUUUGCACUGA	chr9:58500334-58500635(+)$1	301	15	47	22.3945
UGCAUGCGUUACUAAUACAAACAAAUGUGAUC	chr2:25915222-25915471(-)$1	249	35	67	25.2158
GCUUCCUUUGUUUUCUUCCCCCUAAAGAGCUU	chr18:82753773-82754078(+)$1	305	189	221	25.3818
UUGUUUUGCUUUUUCUGACUCCAGUGGGACAA	chr5:122906986-122907245(-)$1	259	215	247	26.4586
GGAGGGAUAGAUCCUCCUUUACUAUUCUAUAU	chrX:154260176-154260432(-)$1	256	212	244	23.4212
AGAAUGUCCCUUCCCUGUCCUGUGACCCUCUC	chr15:99330398-99330651(-)$1	253	104	136	23.9644
CUUUUGCCCCUUGCUUCUUUCAUGGUGGAUGU	chr15:37298357-37298603(-)$1	246	158	190	19.6977
UAAAUGACAUAAGUGACCAAAAUGUGUUGUGC	chrX:102992876-102993111(-)$1	235	136	168	23.7488
UUGUCCGCACUGCCCUUUUUACGUAACUAUAA	chr6:144948021-144948268(-)$1	247	176	208	24.9035
UAGAUAUUCUUUAUUCUCCUUAAAUAUUUCCU	chr8:70219262-70219497(-)$1	235	17	49	22.8317
GUGUCAGAGUAAGCAAGUUGAAACUUUGGGCC	chr15:80655862-80656097(+)$1	235	176	208	25.4601
UUUGUGCCUCUAUCUUCCUUUCGAGUUGCAUA	chr9:18117323-18117558(+)$1	235	170	202	24.9323
UGGGACGUUCUAAAAGACGGUGAGGACCGCAC	chr17:90435982-90436223(-)$1	241	128	160	23.2713
acucuuucauuugugucGUGUGUGCGCUGUGU	chr5:67679172-67679423(+)$1	251	109	141	24.2899
GACUGUAACUCUAUUCGACUUUGAGUUGUCUU	chr17:43225407-43225655(+)$1	248	64	96	23.8906
CCACCUGUCACUAUCAAUGCCUCUGGCAGCUG	chr2:181285043-181285280(+)$1	237	88	120	25.0533
UAUAGUUUAGUCUGAAUAUUUGUUUUUAAAUU	chr10:20799470-20799713(+)$1	243	115	147	19.7099
GCAUGGCAGCUUAAUGUUCAUCUGUUGCCUUC	chr5:14794013-14794274(+)$1	261	38	70	23.6042
aguuaaguguaaaauacaaauggcaaaacacu	chrX:39458697-39458980(+)$1	283	76	108	26.2480
CAUUUGUGGCAUUAUGUAGAAUUGCAGUGUGC	chr18:33596650-33596921(-)$1	271	111	143	23.8509
GGUAUCUGCUCUUUAAUUUAUUUGCAUGGCAC	chr4:59233332-59233585(+)$1	253	43	75	23.8906
UUUUCUUCUUUCAAAAAAAAAAAAAAAAGGAA	chr8:63391717-63391957(-)$1	240	164	196	25.3673
UUGACAAGCUACCAUCUGAUACAGGCUUGUGA	chr2:52288175-52288413(-)$1	238	180	212	25.0027
AUUGUACAUCUAGAAGUAUUACUGUAGAAUCU	chrX:149935458-149935705(+)$1	247	93	125	23.3215
GUUUGGGCUAGAGUUUUAUGUGAUGGAACAAA	chr11:19963965-19964203(-)$1	238	69	101	25.0394
CUUUGGGGGGAUUUUUUUUUUUUUACCCACAG	chrX:162824265-162824526(+)$1	261	228	260	22.1426
CUGUUGCACGGUUGGAGAGUACGUGUAAAAGG	chr5:15876630-15876866(+)$1	236	131	163	23.3795
AUGAGCCUGUAAUUUUACAACCCGCCUGUUCA	chr5:151612526-151612769(+)$1	243	47	79	23.6777
UAUGGGAAAUGGACCUAUAUUAAUUUCUGAUA	chr11:35599911-35600172(+)$1	261	207	239	24.9646
UAUCCUCCACAUUAUGUCCCUUUGUGCGAUAA	chr2:163842490-163842728(+)$1	238	8	40	22.7845
ACUGCGACAUACUUAGUACCACAUGUCGCUAC	chr9:72595391-72595637(+)$1	246	39	71	22.4249
CCCAAUUCGACCCCUAAAAuguuuuguuuugu	chr13:54860178-54860450(-)$1	272	7	39	25.3041

#DB
.(((((((................))))))).	chr1:66488941-66489253(+)$1	1	61	93	24.1091
(((((.((((............)))).)))))	chr12:75047608-75047865(+)$1	1	146	178	24.6074
(.(((((.((............))...)))))	chr13:9652964-9653199(+)$1	1	137	169	24.7942
....(((((.............))))).))))	chr5:8075068-8075331(-)$1	1	98	130	25.0314
(((.((((((.............))))))...	chr12:55172626-55172863(+)$1	1	68	100	25.2282
.((((((((..............))).)))))	chr16:11134462-11134700(-)$1	1	54	86	23.8092
(((((.(((.............))))))))..	chr14:34192044-34192281(-)$1	1	55	87	24.6807
((((((((...............))).)))))	chr11:97252214-97252452(+)$1	1	65	97	19.6498
((((.((((((...........))))))..))	chrX:102318827-102319101(+)$1	1	35	67	23.6012
((((((.(((............))).))))))	chr11:109530312-109530563(+)$1	1	76	108	26.6374
.(((((................)))))..)))	chr2:6465623-6465886(-)$1	1	156	188	21.2766
..(((((((.............))))))).((	chr5:122903787-122904080(-)$1	1	106	138	22.6968
((((.((((((...........))))))))))	chr18:36957772-36958009(+)$1	1	106	138	23.1230
((((...((((...........))))...)))	chr4:83102600-83102843(-)$1	1	32	64	23.5112
(..(((.(((............)))..)))..	chrX:69677955-69678230(-)$1	1	24	56	25.9359
(...(((((..............)))))..))	chr1:152209721-152209959(-)$1	1	12	44	23.9017
.((((((((.............).))))))).	chr3:156289319-156289567(+)$1	1	48	80	23.8413
(((.(((.((...........))))).)))))	chr6:30404880-30405127(+)$1	1	116	148	23.5438
...(((((((............)))))))...	chr17:43225044-43225279(+)$1	1	111	143	26.1312
((((((((((...............)))))))	chr11:4382365-4382603(-)$1	1	33	65	20.1665
((((..((((............))))))))))	chr15:36407574-36407829(-)$1	1	221	253	24.5792
((((.(((((..............))))).))	chr7:103395499-103395736(+)$1	1	154	186	23.8526
((((((((((...........))))).)))))	chr15:93115153-93115388(-)$1	1	38	70	23.4585
..(((((((((...........))).)))).)	chr15:76910785-76911023(-)$1	1	186	218	22.8454
.((((((.(((...........))))))))).	chr12:85717554-85717790(-)$1	1	66	98	24.5043
.(((((((((............))))))))).	chr6:108772233-108772495(+)$1	1	78	110	24.1681
(.((((((((............))))).))).	chr5:122906460-122906727(-)$1	1	122	154	25.2725
.....(((..............)))..)))))	chr4:150433959-150434227(-)$1	1	191	223	23.4952
.(((((((................))))))).	chr2:32644740-32645028(-)$1	1	164	196	23.6094
.((((((((((...........)))))).)))	chr9:58500334-58500635(+)$1	1	15	47	22.3945
((...(((((.............)))))...)	chr2:25915222-25915471(-)$1	1	35	67	25.2158
(((..(((((............))))))))))	chr18:82753773-82754078(+)$1	1	189	221	25.3818
((((((((((............))))))))))	chr5:122906986-122907245(-)$1	1	215	247	26.4586
((((((((((...........)))))))...)	chrX:154260176-154260432(-)$1	1	212	244	23.4212
(((..(((.(...........).)))..))))	chr15:99330398-99330651(-)$1	1	104	136	23.9644
(.((((((...............)))))).))	chr15:37298357-37298603(-)$1	1	158	190	19.6977
)))))((((((...........))))))((((	chrX:102992876-102993111(-)$1	1	136	168	23.7488
((((....((............))....))))	chr6:144948021-144948268(-)$1	1	176	208	24.9035
.(((((((..............))))))).((	chr8:70219262-70219497(-)$1	1	17	49	22.8317
(.((((((((............))))).))).	chr15:80655862-80656097(+)$1	1	176	208	25.4601
.(((((((((............)))..)))))	chr9:18117323-18117558(+)$1	1	170	202	24.9323
((.(..(((((...........)))))).)).	chr17:90435982-90436223(-)$1	1	128	160	23.2713
((.(...(((...........)))....).))	chr5:67679172-67679423(+)$1	1	109	141	24.2899
(((...(((((...........)))))))).)	chr17:43225407-43225655(+)$1	1	64	96	23.8906
(((.((((((.............)))))).))	chr2:181285043-181285280(+)$1	1	88	120	25.0533
.(((((((((...............)))))))	chr10:20799470-20799713(+)$1	1	115	147	19.7099
((..((((((.............))))))...	chr5:14794013-14794274(+)$1	1	38	70	23.6042
(((....(((............)))....)))	chrX:39458697-39458980(+)$1	1	76	108	26.2480
(((.....(((...........)))...))))	chr18:33596650-33596921(-)$1	1	111	143	23.8509
(((.(((((..............))).)).))	chr4:59233332-59233585(+)$1	1	43	75	23.8906
(((((((.(((...........))).))))))	chr8:63391717-63391957(-)$1	1	164	196	25.3673
.(.(((((((.............))))))).)	chr2:52288175-52288413(-)$1	1	180	212	25.0027
(((.((((..............)))).))).)	chrX:149935458-149935705(+)$1	1	93	125	23.3215
(((((..(((.............)))..))))	chr11:19963965-19964203(-)$1	1	69	101	25.0394
)((((.(((................))).)))	chrX:162824265-162824526(+)$1	1	228	260	22.1426
...(((((((...........)))))))..))	chr5:15876630-15876866(+)$1	1	131	163	23.3795
((((((..((.............))..)))))	chr5:151612526-151612769(+)$1	1	47	79	23.6777
(((.((((((............)))))).)))	chr11:35599911-35600172(+)$1	1	207	239	24.9646
(....((((((...........)))).))...	chr2:163842490-163842728(+)$1	1	8	40	22.7845
((((((((((............))))))((((	chr9:72595391-72595637(+)$1	1	39	71	22.4249
..(((..(((.............)))..))).	chr13:54860178-54860450(-)$1	1	7	39	25.3041

#PSSM
e : 0.14	f : 0.11	d : 0.11	: : 0.11	c : 0.11	" : 0.04	i : 0.04	[ : 0.03	g : 0.03	h : 0.03	= : 0.03	$ : 0.03	b : 0.03	# : 0.01	& : 0.01	! : 0.01	% : 0.01	( : 0.01	H : 0.01	
e : 0.18	f : 0.14	g : 0.09	d : 0.09	i : 0.08	[ : 0.06	c : 0.06	" : 0.04	# : 0.03	! : 0.03	= : 0.03	$ : 0.03	: : 0.01	h : 0.01	b : 0.01	a : 0.01	H : 0.01	
e : 0.18	f : 0.14	g : 0.11	c : 0.11	d : 0.08	i : 0.08	" : 0.04	[ : 0.04	# : 0.03	! : 0.03	= : 0.03	$ : 0.03	b : 0.01	h : 0.01	H : 0.01	
g : 0.18	f : 0.13	e : 0.13	[ : 0.09	c : 0.06	i : 0.06	# : 0.04	d : 0.04	" : 0.04	! : 0.04	= : 0.03	$ : 0.03	a : 0.03	b : 0.01	H : 0.01	
g : 0.18	f : 0.16	e : 0.14	c : 0.08	" : 0.06	! : 0.06	d : 0.06	[ : 0.04	i : 0.04	# : 0.04	= : 0.03	$ : 0.03	b : 0.01	
e : 0.19	f : 0.19	g : 0.18	c : 0.08	! : 0.06	[ : 0.04	" : 0.04	= : 0.03	d : 0.03	i : 0.03	# : 0.03	b : 0.03	$ : 0.01	
f : 0.19	e : 0.18	g : 0.16	c : 0.13	d : 0.06	! : 0.04	[ : 0.03	" : 0.03	= : 0.03	i : 0.03	# : 0.03	y : 0.01	$ : 0.01	b : 0.01	
c : 0.22	e : 0.16	f : 0.16	g : 0.14	d : 0.09	[ : 0.06	= : 0.03	i : 0.03	y : 0.01	# : 0.01	$ : 0.01	! : 0.01	
c : 0.24	e : 0.16	f : 0.14	g : 0.08	d : 0.06	b : 0.06	y : 0.04	w : 0.04	x : 0.03	= : 0.03	i : 0.03	a : 0.01	[ : 0.01	
c : 0.18	f : 0.14	e : 0.13	w : 0.09	y : 0.06	d : 0.06	b : 0.06	v : 0.06	g : 0.06	x : 0.03	= : 0.03	i : 0.03	a : 0.01	
u : 0.26	v : 0.19	w : 0.11	t : 0.09	y : 0.06	x : 0.06	f : 0.06	c : 0.06	d : 0.03	e : 0.03	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
t : 0.29	u : 0.26	v : 0.19	w : 0.11	y : 0.06	x : 0.06	
u : 0.26	v : 0.19	t : 0.19	w : 0.11	y : 0.06	x : 0.06	g : 0.03	b : 0.01	e : 0.01	a : 0.01	c : 0.01	
c : 0.18	e : 0.13	v : 0.13	f : 0.09	d : 0.08	g : 0.08	w : 0.06	x : 0.06	y : 0.04	b : 0.04	a : 0.01	i : 0.01	= : 0.01	] : 0.01	
c : 0.29	e : 0.16	f : 0.16	g : 0.09	d : 0.08	y : 0.04	b : 0.04	x : 0.03	] : 0.01	w : 0.01	i : 0.01	= : 0.01	
c : 0.27	e : 0.18	f : 0.16	g : 0.14	d : 0.08	x : 0.03	4 : 0.03	3 : 0.01	i : 0.01	= : 0.01	y : 0.01	b : 0.01	
e : 0.19	f : 0.18	g : 0.14	c : 0.13	d : 0.08	2 : 0.06	] : 0.04	4 : 0.04	3 : 0.03	= : 0.03	i : 0.03	
f : 0.19	g : 0.18	e : 0.18	] : 0.13	2 : 0.11	3 : 0.04	4 : 0.04	= : 0.03	i : 0.03	d : 0.01	c : 0.01	
f : 0.26	g : 0.18	e : 0.16	2 : 0.06	c : 0.06	] : 0.04	4 : 0.04	3 : 0.03	= : 0.03	i : 0.03	b : 0.03	d : 0.01	a : 0.01	
f : 0.18	g : 0.16	e : 0.14	c : 0.09	d : 0.08	2 : 0.06	] : 0.06	3 : 0.04	i : 0.04	= : 0.03	b : 0.03	a : 0.01	4 : 0.01	
d : 0.14	f : 0.13	e : 0.13	g : 0.11	c : 0.09	] : 0.08	3 : 0.06	i : 0.06	2 : 0.04	: : 0.03	= : 0.03	4 : 0.01	b : 0.01	0 : 0.01	
f : 0.18	d : 0.14	g : 0.13	e : 0.13	c : 0.09	3 : 0.08	] : 0.06	i : 0.06	= : 0.03	2 : 0.01	4 : 0.01	b : 0.01	0 : 0.01	
f : 0.16	e : 0.16	d : 0.14	g : 0.08	] : 0.06	2 : 0.06	3 : 0.04	c : 0.04	i : 0.04	: : 0.03	= : 0.03	b : 0.03	4 : 0.01	h : 0.01	0 : 0.01	a : 0.01	

#score	1457.69274261061
#seq	61
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_UTR_m2_run1.txt

#BEAR
eee[attttttttttta]eeee	chr8:123178705-123178982(-)$1	277	146	168	18.9761
hh[cccssssssssssccchhh	chr10:116509619-116509901(-)$1	282	150	172	13.1381
eeeeettttttttttteeeee8	chr2:31071139-31071424(+)$1	285	61	83	18.3449
ffffftttttttttttffffff	chr17:46305889-46306171(+)$1	282	96	118	17.6056
b[bbwwwwwwwwwwwwwwbb]b	chr8:125096552-125096860(+)$1	308	39	61	16.9053
eeeeeuuuuuuuuuuuueeeee	chr6:56728726-56729000(-)$1	274	12	34	19.0793
hhhhuuuuuuuuuuuuhhhhhh	chr1:189057919-189058218(+)$1	299	147	169	16.8058
cc[ddddrrrrrrrrrdddd]c	chr5:138223490-138223786(-)$1	296	84	106	11.0108
eeeeesssssssssseeeee::	chr17:34791868-34792151(+)$1	283	7	29	11.6001
cccccuuuuuuuuuuuuccc::	chr10:80611569-80611846(+)$1	277	162	184	17.7803
Bddddyyyyyyyyyyyyyyyyd	chr11:97574608-97574878(+)$1	270	7	29	15.3083
eeee[bbrrrrrrrrrbbeeee	chr15:79655896-79656195(-)$1	299	183	205	10.4883
eeeeebbrrrrrrrrrbb4444	chr1:62843167-62843435(+)$1	268	94	116	10.6725
fffffuuuuuuuuuuuufffff	chr12:113887155-113887428(+)$1	273	152	174	18.0410
ffffftttttttttttffffff	chr15:81535417-81535702(-)$1	285	210	232	17.6056
iiiiixxxxxxxxxxxxxxxii	chr17:27062050-27062328(+)$1	278	155	177	14.5264
eeeddddrrrrrrrrrdddd:e	chr16:98014687-98014959(-)$1	272	35	57	9.9385
:ddddtttttttttttddddhh	chr5:123807810-123808084(+)$1	274	114	136	17.3750
eeccc^^^^^^^^^^^^^^^^^	chr1:184398225-184398498(-)$1	273	177	199	11.3446
!ddddtttttttttttdddd]d	chr16:91227771-91228058(+)$1	287	90	112	18.9964
ffffftttttttttttffffff	chr15:81535368-81535654(-)$1	286	162	184	17.6056
##cccssssssssssccc333h	chr2:168780770-168781049(-)$1	279	45	67	13.4595
iiiiitttttttttttiiiiii	chr4:83921329-83921604(-)$1	275	115	137	18.3815
ddd[awwwwwwwwwwwwwwa]d	chr13:5869145-5869421(+)$1	276	153	175	18.2394
eeee[arrrrrrrrra]eeeee	chr3:133126987-133127268(-)$1	281	154	176	11.4659
dddduuuuuuuuuuuudddd77	chr2:153054827-153055101(-)$1	274	206	228	17.5277
bb[auuuuuuuuuuuua]bb]e	chr4:49669033-49669321(+)$1	288	179	201	17.9431
ddwwwwwwwwwwwwwwdddd]c	chr15:75831591-75831876(-)$1	285	221	243	17.2278
ccc[cccrrrrrrrrrccc]cc	chr11:69813257-69813539(+)$1	282	44	66	11.2711
ddddwwwwwwwwwwwwwwdddd	chr2:157383278-157383551(-)$1	273	186	208	17.8340
hh!!cccrrrrrrrrrccc333	chr16:91227498-91227771(+)$1	273	105	127	11.4722
!!ccctttttttttttccc22d	chr8:74842841-74843113(+)$1	272	115	137	19.0478
ccxxxxxxxxxxxxxxxccc22	chr6:124863939-124864209(-)$1	270	151	173	14.6433
""cccuuuuuuuuuuuuccc33	chr2:32134292-32134577(-)$1	285	153	175	19.6079
[ddddyyyyyyyyyyyyyyyyd	chr15:81678793-81679086(-)$1	293	44	66	16.3426
cc[bbrrrrrrrrrbb]ccc22	chr18:24443321-24443593(+)$1	272	160	182	10.0235
ddd[bbssssssssssbb]ddd	chr2:34678076-34678352(-)$1	276	165	187	12.4465
fccccccssssssssssccc]c	chr5:3692542-3692817(-)$1	275	200	222	13.1609
gg[bbuuuuuuuuuuuubbggg	chr15:89012665-89012935(-)$1	270	183	205	18.2691
eeeeettttttttttteeeee:	chr15:44595248-44595531(-)$1	283	209	231	17.8790
ffffvvvvvvvvvvvvvfffff	chr11:79507176-79507447(+)$1	271	34	56	17.4069
&ddddssssssssssddddeee	chr14:71003926-71004195(-)$1	269	84	106	12.4540
eeeeewwwwwwwwwwwwwweee	chr2:144232685-144232977(+)$1	292	96	118	18.1281
eeeeettttttttttteeeeeH	chr19:24758574-24758848(-)$1	274	12	34	18.0555
hhhhhttttttttttthhhhhh	chr18:75555294-75555568(+)$1	274	59	81	16.7579
eeeeewwwwwwwwwwwwwweee	chr7:107985018-107985335(+)$1	317	16	38	18.1281
cc[ddddrrrrrrrrrdddd22	chr7:25670028-25670303(+)$1	275	188	210	10.8100
!cccvvvvvvvvvvvvvccc22	chr3:121969333-121969624(+)$1	291	22	44	18.7875
&ddddcccrrrrrrrrrccc]d	chr11:29642123-29642419(+)$1	296	130	152	9.9430
iiiiitttttttttttiiiiii	chr11:68923178-68923496(+)$1	318	242	264	18.3815
iddddtttttttttttdddd22	chr5:137968786-137969068(+)$1	282	12	34	18.7988
c[cccuuuuuuuuuuuuccc]c	chr7:134911688-134911984(+)$1	296	159	181	19.7140

#otherMatches

#Seq PSSM
CAGCCUAAGUGUGUGUGCCUGG	chr8:123178705-123178982(-)$1	277	146	168	18.9761
GUGAGCUGUUAAUAUUGUUGCC	chr10:116509619-116509901(-)$1	282	150	172	13.1381
GGGACUCUUUCUCCUCGUUCCg	chr2:31071139-31071424(+)$1	285	61	83	18.3449
CAUGCUUUUUCAGAUUGUGUGG	chr17:46305889-46306171(+)$1	282	96	118	17.6056
ACGCACUUACGCCUUUAAGCCU	chr8:125096552-125096860(+)$1	308	39	61	16.9053
CUUUAUCCAUCCUGUCUUGAAG	chr6:56728726-56729000(-)$1	274	12	34	19.0793
UGGGAUGUAGGUUGACCCUGGG	chr1:189057919-189058218(+)$1	299	147	169	16.8058
UCCUGUGUACUUGUUCCACAAG	chr5:138223490-138223786(-)$1	296	84	106	11.0108
CUCCUUUAUCUGUUUGGGAGUC	chr17:34791868-34792151(+)$1	283	7	29	11.6001
CCGCCACCCUCCUUCACGGCAC	chr10:80611569-80611846(+)$1	277	162	184	17.7803
CCAGCAGCCUUUCCCUUCACAG	chr11:97574608-97574878(+)$1	270	7	29	15.3083
CGGCUGACGGGUAAAAUCGCUG	chr15:79655896-79656195(-)$1	299	183	205	10.4883
UUGGAGCUUUUUUGUUGCCUUA	chr1:62843167-62843435(+)$1	268	94	116	10.6725
GUUAUGUUUUAUACCCAGUAAC	chr12:113887155-113887428(+)$1	273	152	174	18.0410
UGUCAUAUUGGUCCUUUGAUAC	chr15:81535417-81535702(-)$1	285	210	232	17.6056
uuguuguccuuugccucccaag	chr17:27062050-27062328(+)$1	278	155	177	14.5264
GGUGGUUAUGUCUGAAAACCAA	chr16:98014687-98014959(-)$1	272	35	57	9.9385
UGCAUUUAUUUAUUUUGUGUGU	chr5:123807810-123808084(+)$1	274	114	136	17.3750
UAGUGGAAGAAAACAGCCAAUG	chr1:184398225-184398498(-)$1	273	177	199	11.3446
AUUGUACAAAACGGCCACAACG	chr16:91227771-91228058(+)$1	287	90	112	18.9964
UGUCAUAUUGGUCCUUUGAUAC	chr15:81535368-81535654(-)$1	286	162	184	17.6056
UCUGCGAAGGAAUGAGCGUCUC	chr2:168780770-168781049(-)$1	279	45	67	13.4595
UUUCCUUUAUAGUUUUGGGAGA	chr4:83921329-83921604(-)$1	275	115	137	18.3815
GUCUCACUUAUGAAACACAGCG	chr13:5869145-5869421(+)$1	276	153	175	18.2394
GCAGUGACAUCCCACCUCUGUC	chr3:133126987-133127268(-)$1	281	154	176	11.4659
UAGAUCUUGUUCCACCUCUAAU	chr2:153054827-153055101(-)$1	274	206	228	17.5277
GAGUGAAUUUUUGAUAAGUUAU	chr4:49669033-49669321(+)$1	288	179	201	17.9431
GCUCCCCACCCUCCCCGCCUCA	chr15:75831591-75831876(-)$1	285	221	243	17.2278
UACUUUCUUUUACACCGGAUGU	chr11:69813257-69813539(+)$1	282	44	66	11.2711
CCCCUUGCUCAUUGAUUUGGGG	chr2:157383278-157383551(-)$1	273	186	208	17.8340
CGACGCCAAGUGAGCCGGCCAG	chr16:91227498-91227771(+)$1	273	105	127	11.4722
CAGCACACACAGUCCCUGCCAU	chr8:74842841-74843113(+)$1	272	115	137	19.0478
CUCAUUUCCAUCUCUCCAGACA	chr6:124863939-124864209(-)$1	270	151	173	14.6433
GGUGGGUAUUGUCAAUGUUAAG	chr2:32134292-32134577(-)$1	285	153	175	19.6079
UCACCCAGGAGCAAAACAGAAG	chr15:81678793-81679086(-)$1	293	44	66	16.3426
CUCAGCCAUUAAAACUCAGACU	chr18:24443321-24443593(+)$1	272	160	182	10.0235
UUUGAGGAUGAAGCAACUGGAG	chr2:34678076-34678352(-)$1	276	165	187	12.4465
UUCACAUGAUAACUGCAGUGCU	chr5:3692542-3692817(-)$1	275	200	222	13.1609
GGACUCUUUUACCCUCCAGCUU	chr15:89012665-89012935(-)$1	270	183	205	18.2691
auuggcccagagcucaccaauu	chr15:44595248-44595531(-)$1	283	209	231	17.8790
GGGUUUGCAGGACUGAUACCCU	chr11:79507176-79507447(+)$1	271	34	56	17.4069
UGCCUGUCCACCCAAAGGCUCC	chr14:71003926-71004195(-)$1	269	84	106	12.4540
CAUUCUCUUCCCAUACAAUGAG	chr2:144232685-144232977(+)$1	292	96	118	18.1281
GGGGGGAGGGUAAGUACCCCUU	chr19:24758574-24758848(-)$1	274	12	34	18.0555
GUAAAUAUAAAGACGUUUUAUA	chr18:75555294-75555568(+)$1	274	59	81	16.7579
GACCAAGAACAAACCCACCUGG	chr7:107985018-107985335(+)$1	317	16	38	18.1281
CCUCAAAAAGUAAGUGUUUGUU	chr7:25670028-25670303(+)$1	275	188	210	10.8100
GGAACAUAAGAUACAAAUUCAU	chr3:121969333-121969624(+)$1	291	22	44	18.7875
AGGCACUUGGUGAAUAAAGGAU	chr11:29642123-29642419(+)$1	296	130	152	9.9430
AUUUUUUUUUUAAUACAAAAUG	chr11:68923178-68923496(+)$1	318	242	264	18.3815
GAGGGCACUUGUCUCUUCCUAC	chr5:137968786-137969068(+)$1	282	12	34	18.7988
UGUGGGGAGGGCAGAAAUCAGA	chr7:134911688-134911984(+)$1	296	159	181	19.7140

#DB
(((.(...........).))))	chr8:123178705-123178982(-)$1	1	146	168	18.9761
((.(((..........))))))	chr10:116509619-116509901(-)$1	1	150	172	13.1381
(((((...........))))).	chr2:31071139-31071424(+)$1	1	61	83	18.3449
(((((...........))))))	chr17:46305889-46306171(+)$1	1	96	118	17.6056
(.((..............)).)	chr8:125096552-125096860(+)$1	1	39	61	16.9053
(((((............)))))	chr6:56728726-56729000(-)$1	1	12	34	19.0793
((((............))))))	chr1:189057919-189058218(+)$1	1	147	169	16.8058
((.((((.........)))).)	chr5:138223490-138223786(-)$1	1	84	106	11.0108
(((((..........)))))..	chr17:34791868-34792151(+)$1	1	7	29	11.6001
))(((............)))..	chr10:80611569-80611846(+)$1	1	162	184	17.7803
(((((................)	chr11:97574608-97574878(+)$1	1	7	29	15.3083
((((.((.........))))))	chr15:79655896-79656195(-)$1	1	183	205	10.4883
(((((((.........))....	chr1:62843167-62843435(+)$1	1	94	116	10.6725
(((((............)))))	chr12:113887155-113887428(+)$1	1	152	174	18.0410
(((((...........))))))	chr15:81535417-81535702(-)$1	1	210	232	17.6056
(((((...............))	chr17:27062050-27062328(+)$1	1	155	177	14.5264
)))((((.........)))).(	chr16:98014687-98014959(-)$1	1	35	57	9.9385
.((((...........))))((	chr5:123807810-123808084(+)$1	1	114	136	17.3750
(((((.................	chr1:184398225-184398498(-)$1	1	177	199	11.3446
.((((...........)))).)	chr16:91227771-91228058(+)$1	1	90	112	18.9964
(((((...........))))))	chr15:81535368-81535654(-)$1	1	162	184	17.6056
..(((..........)))...)	chr2:168780770-168781049(-)$1	1	45	67	13.4595
(((((...........))))))	chr4:83921329-83921604(-)$1	1	115	137	18.3815
(((.(..............).)	chr13:5869145-5869421(+)$1	1	153	175	18.2394
((((.(.........).)))))	chr3:133126987-133127268(-)$1	1	154	176	11.4659
((((............))))..	chr2:153054827-153055101(-)$1	1	206	228	17.5277
((.(............).)).)	chr4:49669033-49669321(+)$1	1	179	201	17.9431
((..............)))).)	chr15:75831591-75831876(-)$1	1	221	243	17.2278
(((.(((.........))).))	chr11:69813257-69813539(+)$1	1	44	66	11.2711
((((..............))))	chr2:157383278-157383551(-)$1	1	186	208	17.8340
((..(((.........)))...	chr16:91227498-91227771(+)$1	1	105	127	11.4722
..(((...........)))..)	chr8:74842841-74843113(+)$1	1	115	137	19.0478
((...............)))..	chr6:124863939-124864209(-)$1	1	151	173	14.6433
..(((............)))..	chr2:32134292-32134577(-)$1	1	153	175	19.6079
.((((................)	chr15:81678793-81679086(-)$1	1	44	66	16.3426
((.((.........)).)))..	chr18:24443321-24443593(+)$1	1	160	182	10.0235
(((.((..........)).)))	chr2:34678076-34678352(-)$1	1	165	187	12.4465
(((((((..........))).)	chr5:3692542-3692817(-)$1	1	200	222	13.1609
((.((............)))))	chr15:89012665-89012935(-)$1	1	183	205	18.2691
(((((...........))))).	chr15:44595248-44595531(-)$1	1	209	231	17.8790
((((.............)))))	chr11:79507176-79507447(+)$1	1	34	56	17.4069
.((((..........)))))))	chr14:71003926-71004195(-)$1	1	84	106	12.4540
(((((..............)))	chr2:144232685-144232977(+)$1	1	96	118	18.1281
(((((...........)))))(	chr19:24758574-24758848(-)$1	1	12	34	18.0555
(((((...........))))))	chr18:75555294-75555568(+)$1	1	59	81	16.7579
(((((..............)))	chr7:107985018-107985335(+)$1	1	16	38	18.1281
((.((((.........))))..	chr7:25670028-25670303(+)$1	1	188	210	10.8100
.(((.............)))..	chr3:121969333-121969624(+)$1	1	22	44	18.7875
.(((((((.........))).)	chr11:29642123-29642419(+)$1	1	130	152	9.9430
(((((...........))))))	chr11:68923178-68923496(+)$1	1	242	264	18.3815
(((((...........))))..	chr5:137968786-137969068(+)$1	1	12	34	18.7988
(.(((............))).)	chr7:134911688-134911984(+)$1	1	159	181	19.7140

#PSSM
e : 0.24	c : 0.13	f : 0.11	d : 0.09	h : 0.07	i : 0.07	! : 0.05	b : 0.03	& : 0.03	B : 0.01	: : 0.01	# : 0.01	" : 0.01	[ : 0.01	g : 0.01	
e : 0.24	d : 0.23	c : 0.15	f : 0.09	h : 0.07	i : 0.05	[ : 0.03	# : 0.01	b : 0.01	! : 0.01	" : 0.01	g : 0.01	
e : 0.23	d : 0.21	c : 0.17	[ : 0.11	f : 0.09	i : 0.05	h : 0.03	b : 0.01	w : 0.01	! : 0.01	x : 0.01	
d : 0.23	e : 0.19	c : 0.17	f : 0.09	[ : 0.07	b : 0.05	i : 0.05	h : 0.03	a : 0.01	w : 0.01	! : 0.01	x : 0.01	
c : 0.19	d : 0.19	e : 0.15	f : 0.07	w : 0.05	u : 0.05	i : 0.05	b : 0.05	a : 0.03	[ : 0.03	v : 0.03	x : 0.01	h : 0.01	
t : 0.26	u : 0.17	w : 0.11	c : 0.09	d : 0.05	s : 0.05	b : 0.05	y : 0.03	x : 0.03	v : 0.03	^ : 0.01	a : 0.01	r : 0.01	
t : 0.26	u : 0.17	w : 0.11	s : 0.09	c : 0.07	d : 0.05	y : 0.03	b : 0.03	x : 0.03	r : 0.03	v : 0.03	^ : 0.01	
t : 0.26	u : 0.17	r : 0.17	s : 0.11	w : 0.11	y : 0.03	x : 0.03	v : 0.03	^ : 0.01	c : 0.01	
t : 0.26	r : 0.19	u : 0.17	s : 0.11	w : 0.11	y : 0.03	x : 0.03	v : 0.03	^ : 0.01	
t : 0.26	r : 0.19	u : 0.17	s : 0.11	w : 0.11	y : 0.03	x : 0.03	v : 0.03	^ : 0.01	
t : 0.26	r : 0.19	u : 0.17	s : 0.11	w : 0.11	y : 0.03	x : 0.03	v : 0.03	^ : 0.01	
t : 0.26	r : 0.19	u : 0.17	s : 0.11	w : 0.11	y : 0.03	x : 0.03	v : 0.03	^ : 0.01	
t : 0.26	r : 0.19	u : 0.17	s : 0.11	w : 0.11	y : 0.03	x : 0.03	v : 0.03	^ : 0.01	
t : 0.26	r : 0.19	u : 0.17	s : 0.11	w : 0.11	y : 0.03	x : 0.03	v : 0.03	^ : 0.01	
t : 0.26	u : 0.17	r : 0.17	s : 0.11	w : 0.11	y : 0.03	x : 0.03	v : 0.03	^ : 0.01	b : 0.01	
t : 0.26	u : 0.17	r : 0.15	w : 0.11	s : 0.05	y : 0.03	x : 0.03	v : 0.03	e : 0.01	^ : 0.01	c : 0.01	a : 0.01	b : 0.01	d : 0.01	
d : 0.17	u : 0.11	c : 0.09	w : 0.09	e : 0.07	f : 0.05	b : 0.05	a : 0.03	h : 0.03	y : 0.03	x : 0.03	i : 0.03	] : 0.03	v : 0.03	^ : 0.01	s : 0.01	r : 0.01	
c : 0.24	d : 0.17	e : 0.11	f : 0.09	w : 0.09	b : 0.07	] : 0.03	h : 0.03	y : 0.03	i : 0.03	x : 0.01	^ : 0.01	
c : 0.23	d : 0.19	e : 0.15	f : 0.09	b : 0.05	w : 0.05	h : 0.03	y : 0.03	i : 0.03	4 : 0.01	x : 0.01	^ : 0.01	3 : 0.01	] : 0.01	
e : 0.21	d : 0.19	c : 0.15	f : 0.09	h : 0.05	b : 0.03	y : 0.03	3 : 0.03	i : 0.03	4 : 0.01	x : 0.01	^ : 0.01	a : 0.01	] : 0.01	2 : 0.01	g : 0.01	
e : 0.19	] : 0.17	2 : 0.11	f : 0.09	h : 0.07	: : 0.05	i : 0.05	3 : 0.05	y : 0.03	d : 0.03	4 : 0.01	^ : 0.01	7 : 0.01	c : 0.01	g : 0.01	
e : 0.17	d : 0.15	h : 0.09	f : 0.09	c : 0.09	2 : 0.09	: : 0.05	i : 0.05	3 : 0.03	8 : 0.01	b : 0.01	4 : 0.01	^ : 0.01	7 : 0.01	g : 0.01	H : 0.01	

#score	816.7591026138517
#seq	52
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_CDS_m2_run2.txt

#BEAR
f"""bboooooobb333fff	chr15:96414691-96414926(-)$1	235	116	136	11.3804
"""cccooooooccc4444g	chr6:97128843-97129081(-)$1	238	117	137	12.0847
eee[bboooooobb]eeeee	chr14:31989531-31989766(-)$1	235	13	33	11.0303
iiiiiiooooooiiiiiiii	chr14:37939004-37939242(-)$1	238	3	23	12.2406
bb[cccoooooocccbbccc	chr7:129777075-129777383(+)$1	308	233	253	11.3889
eeecccooooooccc22eee	chr11:90202099-90202341(-)$1	242	217	237	11.5193
!bbcccooooooccc]bb22	chrX:162824810-162825047(+)$1	237	12	32	11.1614
ffffffooooooffffffdd	chr7:106603330-106603565(+)$1	235	113	133	11.2079
ccddddoooooodddd]ccc	chr10:126675733-126675988(-)$1	255	141	161	10.6751
ccccccooooooccc]cccd	chr8:56140641-56140894(+)$1	253	208	228	12.5851
dd[cccooooooccc]dddd	chr10:98477548-98477791(+)$1	243	157	177	11.8286
iiiiiiooooooiiiiiiii	chr16:35293974-35294230(+)$1	256	105	125	12.2406
dddcccooooooccc]dddd	chr11:115667985-115668222(-)$1	237	186	206	11.5619
ffffffooooooffffff::	chr7:20150502-20150751(-)$1	249	141	161	9.7077
c[ddddooooooddddcccd	chr13:55392432-55392669(+)$1	237	76	96	10.7478
ccc[bboooooobb]ccc55	chr11:68620525-68620761(+)$1	236	110	130	10.1532
[ccc[aooooooa]ccc]a]	chrX:10156346-10156601(+)$1	255	101	121	12.0945
fff[bboooooobb]fffff	chr14:104242207-104242444(-)$1	237	77	97	11.3588
ffff[aooooooa]ffffff	chr6:108491854-108492100(+)$1	246	59	79	11.4162
ccccccooooooccc]ccc]	chr11:78138010-78138267(+)$1	257	149	169	12.6728
"""cccooooooccc333bb	chr2:6468061-6468303(-)$1	242	55	75	12.1141
fff[bboooooobbffffff	chr10:57236816-57237127(-)$1	311	169	189	11.2988
ffffffooooooffffffdd	chr15:79555743-79555980(-)$1	237	138	158	11.2079
ggg!!aooooooa22ggggg	chr11:41946818-41947090(-)$1	272	176	196	11.5891
ggggggooooooggggggg2	chr11:100888528-100888792(+)$1	264	105	125	12.0299
"""cccooooooccc]dddd	chr11:70483254-70483493(-)$1	239	13	33	12.0311
e!!cccooooooccc4444e	chr1:174215791-174216026(-)$1	235	206	226	12.1159
hhhhhhoooooohhhhhhhh	chr5:125546130-125546365(-)$1	235	43	63	10.1977
hhhhhhoooooohhhhhhhh	chr4:126707100-126707361(+)$1	261	19	39	10.1977
ccc[bboooooobbccc22f	chrX:143628695-143628930(+)$1	235	135	155	11.2891
d[a[bboooooobba]dddd	chr13:104623795-104624032(-)$1	237	28	48	11.2633
a[bb[aooooooa]bba]dd	chr13:100195648-100195890(-)$1	242	94	114	10.6408
ffffffooooooffffff]e	chr13:6602544-6602805(-)$1	261	7	27	11.3067
hhhhhhoooooohhhhhhhh	chrX:45721941-45722176(+)$1	235	113	133	10.1977
hhhhhhoooooohhhhhhhh	chr11:87863329-87863588(+)$1	259	135	155	10.1977
hhh[bboooooobb]hhhhh	chr11:41960533-41960768(-)$1	235	188	208	10.6197
dd[cccooooooccc]dddd	chr11:70483294-70483530(-)$1	236	50	70	11.8286
gggg[aooooooa]gggggg	chr15:31415590-31415861(-)$1	271	103	123	12.2073
###cccooooooccc333dd	chrX:162824700-162824996(+)$1	296	107	127	12.2257
ee[cccooooooccc]eeee	chr11:55208949-55209192(-)$1	243	37	57	12.1406
ffffffooooooffffff::	chr3:146395453-146395688(-)$1	235	214	234	9.7077
ggggggooooooggggggg:	chrX:141894531-141894792(-)$1	261	20	40	11.4202
##ddddoooooodddda]bb	chr13:74476965-74477204(-)$1	239	111	131	10.1323
deeeeeooooooeeeeefff	chr11:72025341-72025578(-)$1	237	27	47	10.1968
%eeeeeooooooeeeee333	chr1:193602238-193602475(+)$1	237	20	40	9.9676
bbddddoooooodddd22bb	chr9:36557080-36557315(-)$1	235	113	133	9.3656
eee[bboooooobb]eeeee	chr9:66883791-66884029(-)$1	238	136	156	11.0303
a[ddddooooooddddaeee	chr11:86602657-86602898(-)$1	241	73	93	10.4008
cc[cccooooooccc]ccc:	chr15:27701031-27701272(-)$1	241	117	137	11.9853
ffffffooooooffffffGG	chrX:12738488-12738723(+)$1	235	119	139	10.2849
ccccccooooooccc]cccc	chrX:69679876-69680119(-)$1	243	99	119	12.6337
ffffbboooooobb333fff	chrX:148317008-148317269(+)$1	261	6	26	11.4013
======oooooo========	chr2:131762809-131763094(+)$1	285	174	194	12.2451
iiiiiiooooooiiiiiiii	chr16:90229856-90230093(-)$1	237	107	127	12.2406
ffffffooooooffffff]d	chr1:59927210-59927447(+)$1	237	139	159	11.3086
ggggggoooooogggggggb	chr7:149573591-149573839(-)$1	248	80	100	12.0168
ggggggooooooggggggg:	chr7:17501488-17501778(-)$1	290	100	120	11.4202
b[bb[aooooooa]bb]bb2	chr11:109528789-109529095(+)$1	306	14	34	9.9605
ffffffooooooffffff::	chr2:34631511-34631748(+)$1	237	118	138	9.7077
ggggbboooooobb]ggggg	chr13:74309433-74309675(-)$1	242	7	27	11.9365
ccccccooooooccc]ccc:	chr11:87794612-87794923(-)$1	311	215	235	11.8737
#eeeeeooooooeeeee333	chr5:90646461-90646698(-)$1	237	186	206	10.6301

#otherMatches

#Seq PSSM
UCCUGACGGCCAUCUUUGGG	chr15:96414691-96414926(-)$1	235	116	136	11.3804
CCAGGCCCAGAAGUCCAUCG	chr6:97128843-97129081(-)$1	238	117	137	12.0847
UGCUAGACCCCACUCGCAGC	chr14:31989531-31989766(-)$1	235	13	33	11.0303
AGGGGGGCCUCUUCUCCUGA	chr14:37939004-37939242(-)$1	238	3	23	12.2406
UGUGGAACUGACUCCCACUG	chr7:129777075-129777383(+)$1	308	233	253	11.3889
CAAAUGCAAGAACAUACUUG	chr11:90202099-90202341(-)$1	242	217	237	11.5193
UAGCAGCUCGCUUUGCCUUC	chrX:162824810-162825047(+)$1	237	12	32	11.1614
AGUGUGAACCUGUACACUGU	chr7:106603330-106603565(+)$1	235	113	133	11.2079
ACCUGAGUGAGUUCAGUGUC	chr10:126675733-126675988(-)$1	255	141	161	10.6751
ACUUGCUUGAAUGCAUAGUU	chr8:56140641-56140894(+)$1	253	208	228	12.5851
AGUGGUCUUUACACUCUUAU	chr10:98477548-98477791(+)$1	243	157	177	11.8286
UGGUGACGCCCAUCAUCAUC	chr16:35293974-35294230(+)$1	256	105	125	12.2406
GGUGGUGAGUGAGCCUGCCU	chr11:115667985-115668222(-)$1	237	186	206	11.5619
CUGUGGGCAUUGCCACAGUA	chr7:20150502-20150751(-)$1	249	141	161	9.7077
GUCCGCUGUCCUGUGGCAUA	chr13:55392432-55392669(+)$1	237	76	96	10.7478
CUCGAGGCAGAGCUGGAGGA	chr11:68620525-68620761(+)$1	236	110	130	10.1532
GGGUGAUCCUGUUGGCCGUU	chrX:10156346-10156601(+)$1	255	101	121	12.0945
CCUCGUGUUCGUGCUAGGCA	chr14:104242207-104242444(-)$1	237	77	97	11.3588
GUUCCCCAGAAUGAGAGCCA	chr6:108491854-108492100(+)$1	246	59	79	11.4162
GCCGGCUGUACCGCCAGGUC	chr11:78138010-78138267(+)$1	257	149	169	12.6728
UAUGACAAUCCAGUCUCUGC	chr2:6468061-6468303(-)$1	242	55	75	12.1141
GAUGUCUGGCAUGAGUCCCA	chr10:57236816-57237127(-)$1	311	169	189	11.2988
GGGAAGCUCAUCUUUCCCAG	chr15:79555743-79555980(-)$1	237	138	158	11.2079
UGAUUCCUAUCUGCUUUACU	chr11:41946818-41947090(-)$1	272	176	196	11.5891
UUUGGCGAGUGUGCCGAGGG	chr11:100888528-100888792(+)$1	264	105	125	12.0299
UAUCUGCAUCUUCAGCUGUG	chr11:70483254-70483493(-)$1	239	13	33	12.0311
GCAGAAAUCCCCUUCAACUC	chr1:174215791-174216026(-)$1	235	206	226	12.1159
GUAGGGGAAGCACUCUAUGG	chr5:125546130-125546365(-)$1	235	43	63	10.1977
GUCCUAGAGGAAUGGGGCCU	chr4:126707100-126707361(+)$1	261	19	39	10.1977
GCUAUGUGUGUUCAGGCAUC	chrX:143628695-143628930(+)$1	235	135	155	11.2891
CCGACUAGUGCCAGCAGUCA	chr13:104623795-104624032(-)$1	237	28	48	11.2633
GACGAGUCCUUCCCCGCAUG	chr13:100195648-100195890(-)$1	242	94	114	10.6408
CCACUGACAACCCAGUGGGG	chr13:6602544-6602805(-)$1	261	7	27	11.3067
GUCUUUUCAACCAGGGACAG	chrX:45721941-45722176(+)$1	235	113	133	10.1977
GUGUCUUUCUGUAGACAUAU	chr11:87863329-87863588(+)$1	259	135	155	10.1977
UGGAUUAUUUUGGAGUUAAU	chr11:41960533-41960768(-)$1	235	188	208	10.6197
UAUCUGCAUCUUCAGCUGUG	chr11:70483294-70483530(-)$1	236	50	70	11.8286
UUAAGGUCUCUUUGUUAGUU	chr15:31415590-31415861(-)$1	271	103	123	12.2073
UCCGUCUAAUGUGACUAGCA	chrX:162824700-162824996(+)$1	296	107	127	12.2257
GUAGAGCCUUAUUUUAACCA	chr11:55208949-55209192(-)$1	243	37	57	12.1406
GUUGGAGCGGGUUCCAAUCC	chr3:146395453-146395688(-)$1	235	214	234	9.7077
CUUUCACUAACUUGAGGGAU	chrX:141894531-141894792(-)$1	261	20	40	11.4202
AAGGCUCCGACUGGCUGGGG	chr13:74476965-74477204(-)$1	239	111	131	10.1323
CUGCUCCAGUAUGAGCACUU	chr11:72025341-72025578(-)$1	237	27	47	10.1968
CAGGAGCCUUUCCUCCUCCC	chr1:193602238-193602475(+)$1	237	20	40	9.9676
CCGGAGUGUUAUCUCCCUGG	chr9:36557080-36557315(-)$1	235	113	133	9.3656
GUUGAGGAGGAGUUGGAUCG	chr9:66883791-66884029(-)$1	238	136	156	11.0303
GUGCGGGCAGGACCGCCUCA	chr11:86602657-86602898(-)$1	241	73	93	10.4008
UGUGUCUGUUUUGGCUCAGU	chr15:27701031-27701272(-)$1	241	117	137	11.9853
GCUGGGAGAAUCCUCAGUUC	chrX:12738488-12738723(+)$1	235	119	139	10.2849
UCAGCUAUCAAGGGCAUGAU	chrX:69679876-69680119(-)$1	243	99	119	12.6337
UUUGUCUUAUUUGAAUUUAG	chrX:148317008-148317269(+)$1	261	6	26	11.4013
GGUUAUCCACCUGUAGCUCU	chr2:131762809-131763094(+)$1	285	174	194	12.2451
AGGUUUGGAAGAAGAUCUUU	chr16:90229856-90230093(-)$1	237	107	127	12.2406
GUGAAAUUAUUUUUUUGCAU	chr1:59927210-59927447(+)$1	237	139	159	11.3086
AGCCGGCGACCUCUGGCUUU	chr7:149573591-149573839(-)$1	248	80	100	12.0168
GGAAGCUAACAUGCUUUCGC	chr7:17501488-17501778(-)$1	290	100	120	11.4202
UGAAGUGCGUUAAGUUGGAC	chr11:109528789-109529095(+)$1	306	14	34	9.9605
GUAGGUGCACUGAUCUGCUA	chr2:34631511-34631748(+)$1	237	118	138	9.7077
GGCACUGCGAGGAGAUGCCA	chr13:74309433-74309675(-)$1	242	7	27	11.9365
ACAUUAUUUUUUUGGUUGUA	chr11:87794612-87794923(-)$1	311	215	235	11.8737
GAGGCGCUUCCACGCCUGCC	chr5:90646461-90646698(-)$1	237	186	206	10.6301

#DB
(...((......))...)))	chr15:96414691-96414926(-)$1	1	116	136	11.3804
...(((......)))....)	chr6:97128843-97129081(-)$1	1	117	137	12.0847
(((.((......)).)))))	chr14:31989531-31989766(-)$1	1	13	33	11.0303
((((((......))))))))	chr14:37939004-37939242(-)$1	1	3	23	12.2406
((.(((......))))))))	chr7:129777075-129777383(+)$1	1	233	253	11.3889
((((((......)))..)))	chr11:90202099-90202341(-)$1	1	217	237	11.5193
.(((((......))).))..	chrX:162824810-162825047(+)$1	1	12	32	11.1614
((((((......))))))((	chr7:106603330-106603565(+)$1	1	113	133	11.2079
((((((......)))).)))	chr10:126675733-126675988(-)$1	1	141	161	10.6751
((((((......))).))))	chr8:56140641-56140894(+)$1	1	208	228	12.5851
((.(((......))).))))	chr10:98477548-98477791(+)$1	1	157	177	11.8286
((((((......))))))))	chr16:35293974-35294230(+)$1	1	105	125	12.2406
((((((......))).))))	chr11:115667985-115668222(-)$1	1	186	206	11.5619
((((((......))))))..	chr7:20150502-20150751(-)$1	1	141	161	9.7077
(.((((......)))))))(	chr13:55392432-55392669(+)$1	1	76	96	10.7478
(((.((......)).)))..	chr11:68620525-68620761(+)$1	1	110	130	10.1532
.(((.(......).))).).	chrX:10156346-10156601(+)$1	1	101	121	12.0945
(((.((......)).)))))	chr14:104242207-104242444(-)$1	1	77	97	11.3588
((((.(......).))))))	chr6:108491854-108492100(+)$1	1	59	79	11.4162
((((((......))).))).	chr11:78138010-78138267(+)$1	1	149	169	12.6728
...(((......)))...))	chr2:6468061-6468303(-)$1	1	55	75	12.1141
(((.((......))))))))	chr10:57236816-57237127(-)$1	1	169	189	11.2988
((((((......))))))((	chr15:79555743-79555980(-)$1	1	138	158	11.2079
(((..(......)..)))))	chr11:41946818-41947090(-)$1	1	176	196	11.5891
((((((......))))))).	chr11:100888528-100888792(+)$1	1	105	125	12.0299
...(((......))).))))	chr11:70483254-70483493(-)$1	1	13	33	12.0311
(..(((......)))....)	chr1:174215791-174216026(-)$1	1	206	226	12.1159
((((((......))))))))	chr5:125546130-125546365(-)$1	1	43	63	10.1977
((((((......))))))))	chr4:126707100-126707361(+)$1	1	19	39	10.1977
(((.((......)))))..)	chrX:143628695-143628930(+)$1	1	135	155	11.2891
(.(.((......))).))))	chr13:104623795-104624032(-)$1	1	28	48	11.2633
(.((.(......).))).))	chr13:100195648-100195890(-)$1	1	94	114	10.6408
((((((......)))))).)	chr13:6602544-6602805(-)$1	1	7	27	11.3067
((((((......))))))))	chrX:45721941-45722176(+)$1	1	113	133	10.1977
((((((......))))))))	chr11:87863329-87863588(+)$1	1	135	155	10.1977
(((.((......)).)))))	chr11:41960533-41960768(-)$1	1	188	208	10.6197
((.(((......))).))))	chr11:70483294-70483530(-)$1	1	50	70	11.8286
((((.(......).))))))	chr15:31415590-31415861(-)$1	1	103	123	12.2073
...(((......)))...))	chrX:162824700-162824996(+)$1	1	107	127	12.2257
((.(((......))).))))	chr11:55208949-55209192(-)$1	1	37	57	12.1406
((((((......))))))..	chr3:146395453-146395688(-)$1	1	214	234	9.7077
((((((......))))))).	chrX:141894531-141894792(-)$1	1	20	40	11.4202
..((((......))))).))	chr13:74476965-74477204(-)$1	1	111	131	10.1323
)(((((......)))))(((	chr11:72025341-72025578(-)$1	1	27	47	10.1968
.(((((......)))))...	chr1:193602238-193602475(+)$1	1	20	40	9.9676
((((((......))))..))	chr9:36557080-36557315(-)$1	1	113	133	9.3656
(((.((......)).)))))	chr9:66883791-66884029(-)$1	1	136	156	11.0303
(.((((......)))))(((	chr11:86602657-86602898(-)$1	1	73	93	10.4008
((.(((......))).))).	chr15:27701031-27701272(-)$1	1	117	137	11.9853
((((((......))))))))	chrX:12738488-12738723(+)$1	1	119	139	10.2849
((((((......))).))))	chrX:69679876-69680119(-)$1	1	99	119	12.6337
((((((......))...)))	chrX:148317008-148317269(+)$1	1	6	26	11.4013
((((((......))))))))	chr2:131762809-131763094(+)$1	1	174	194	12.2451
((((((......))))))))	chr16:90229856-90230093(-)$1	1	107	127	12.2406
((((((......)))))).)	chr1:59927210-59927447(+)$1	1	139	159	11.3086
((((((......))))))))	chr7:149573591-149573839(-)$1	1	80	100	12.0168
((((((......))))))).	chr7:17501488-17501778(-)$1	1	100	120	11.4202
(.((.(......).)).)).	chr11:109528789-109529095(+)$1	1	14	34	9.9605
((((((......))))))..	chr2:34631511-34631748(+)$1	1	118	138	9.7077
((((((......)).)))))	chr13:74309433-74309675(-)$1	1	7	27	11.9365
((((((......))).))).	chr11:87794612-87794923(-)$1	1	215	235	11.8737
.(((((......)))))...	chr5:90646461-90646698(-)$1	1	186	206	10.6301

#PSSM
f : 0.20	c : 0.14	g : 0.11	e : 0.08	d : 0.08	h : 0.08	" : 0.04	i : 0.04	b : 0.04	# : 0.04	a : 0.03	! : 0.01	[ : 0.01	% : 0.01	= : 0.01	
f : 0.19	c : 0.14	e : 0.11	g : 0.11	[ : 0.08	h : 0.08	" : 0.06	i : 0.04	b : 0.04	d : 0.04	# : 0.03	! : 0.01	= : 0.01	
f : 0.19	c : 0.11	g : 0.11	e : 0.09	d : 0.09	[ : 0.08	h : 0.08	" : 0.06	i : 0.04	b : 0.04	! : 0.01	a : 0.01	# : 0.01	= : 0.01	
c : 0.29	f : 0.16	[ : 0.12	g : 0.09	d : 0.08	h : 0.06	i : 0.04	e : 0.04	b : 0.03	" : 0.01	! : 0.01	= : 0.01	
c : 0.27	b : 0.17	f : 0.12	d : 0.08	[ : 0.08	g : 0.06	h : 0.06	i : 0.04	e : 0.04	! : 0.01	= : 0.01	
c : 0.27	b : 0.17	f : 0.12	a : 0.09	d : 0.08	g : 0.06	h : 0.06	i : 0.04	e : 0.04	= : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
c : 0.27	b : 0.17	f : 0.12	a : 0.09	d : 0.08	g : 0.06	h : 0.06	i : 0.04	e : 0.04	= : 0.01	
c : 0.27	b : 0.17	f : 0.12	d : 0.08	] : 0.08	g : 0.06	h : 0.06	i : 0.04	e : 0.04	2 : 0.01	= : 0.01	
c : 0.30	f : 0.16	] : 0.09	d : 0.08	g : 0.08	h : 0.06	i : 0.04	e : 0.04	3 : 0.03	b : 0.03	2 : 0.01	a : 0.01	= : 0.01	
] : 0.19	f : 0.17	g : 0.11	e : 0.08	d : 0.08	h : 0.08	3 : 0.06	i : 0.04	b : 0.04	c : 0.04	4 : 0.03	2 : 0.01	= : 0.01	
f : 0.17	c : 0.14	g : 0.11	e : 0.09	d : 0.08	h : 0.08	3 : 0.06	i : 0.04	a : 0.04	4 : 0.03	b : 0.03	2 : 0.03	] : 0.03	= : 0.01	
f : 0.22	c : 0.14	g : 0.11	e : 0.08	d : 0.08	h : 0.08	3 : 0.06	i : 0.04	] : 0.04	4 : 0.03	b : 0.03	2 : 0.03	= : 0.01	
d : 0.14	c : 0.12	g : 0.11	f : 0.09	e : 0.08	h : 0.08	b : 0.06	i : 0.04	: : 0.04	4 : 0.03	2 : 0.03	] : 0.03	3 : 0.03	5 : 0.01	a : 0.01	G : 0.01	= : 0.01	
d : 0.19	f : 0.11	e : 0.11	: : 0.11	h : 0.08	g : 0.06	b : 0.06	i : 0.04	c : 0.04	2 : 0.04	] : 0.03	3 : 0.03	5 : 0.01	G : 0.01	= : 0.01	

#score	697.6251153035932
#seq	62
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_UTR_m3_run1.txt

#BEAR
ddddddd!!a!!aooooooa22a22dddd333	chr8:26270075-26270319(-)$1	244	77	109	13.6779
[ddddccc!!cccooooooccc4444ccc]dd	chr5:98313645-98313928(-)$1	283	57	89	15.6893
ggggggg[eeeeeooooooeeeee]ggggggg	chr6:65064493-65064746(+)$1	253	186	218	14.4779
ff:dddd!!ddddoooooodddd]ddddeeee	chr11:72581581-72581830(+)$1	249	61	93	13.1233
hh[bb!!ccc!!ccclllccc333ccc4444b	chr11:6255969-6256276(+)$1	307	116	148	10.4762
adddd!!ccccccooooooccc666666ccc2	chr17:26833974-26834234(+)$1	260	62	94	12.7548
cccc!!ccc!!cccnnnnnccc22ccc333cc	chr16:17429178-17429420(+)$1	242	105	137	11.9741
!cccccc!!ddddoooooodddd333ccc]cc	chr16:15624614-15624876(-)$1	262	163	195	16.4156
hhh[ccc"""a[aooooooa]a333ccc]hhh	chr13:29045139-29045383(-)$1	244	109	141	15.2146
ggggggg[ccc[aooooooa]ccc]ggggggg	chr1:94755369-94755649(+)$1	280	176	208	15.3475
dddd[ccc[ddddooooooddddccc]dddd:	chr16:87484106-87484350(-)$1	244	212	244	13.5891
ffffff"""ddddoooooodddd]ffffffee	chr11:53357290-53357582(+)$1	292	109	141	14.1347
"""cccbb!!ccc[aooooooa]ccc22bb22	chr5:114813497-114813742(-)$1	245	164	196	11.6062
eggggggg[ddddoooooodddd]ggggggg:	chr18:35413953-35414234(+)$1	281	189	221	14.7890
cc[gggggggcccooooooccc]ggggggg]c	chr11:53355998-53356241(+)$1	243	16	48	15.7364
cc[ccc"""eeeeeooooooeeeeecccccce	chr8:97346562-97346807(-)$1	245	147	179	12.9106
!eeeee[addddoooooodddd]a]eeeee]b	chr10:80078350-80078599(+)$1	249	16	48	12.7662
=======!!ddddoooooodddd]========	chr16:24983817-24984102(+)$1	285	36	68	16.6203
hhhhhhcccddddoooooodddd4444ccc]h	chr17:34056514-34056758(+)$1	244	99	131	14.4497
++++ggggggg[aooooooa]ggggggg]iii	chr2:121257956-121258217(+)$1	261	197	229	11.9376
ddd[ccc[eeeeeooooooeeeee]cccdddd	chr7:6659898-6660159(-)$1	261	212	244	13.2887
dddd!!ddddcccooooooccc]dddddddd]	chr13:91841444-91841692(+)$1	248	49	81	13.5403
##bb!!gggggggooooooggggggg22bb22	chr9:49312146-49312384(-)$1	238	85	117	12.8948
c!!ccc!!cccddddllldddd]ccc22ccc3	chr17:24732708-24732950(+)$1	242	100	132	10.8749
eeeee!!a!!cccooooooccc22a4444eee	chr16:8635408-8635660(-)$1	252	13	45	15.7385
eeeee[dddd[bboooooobb]dddd]eeeee	chr17:27889382-27889620(-)$1	238	60	92	12.0867
[bbgggggggcccooooooccc88888888gg	chr18:52677937-52678208(-)$1	271	152	184	12.0649
cc[dddd[cccbboooooobb]ccc]dddd]c	chrX:131338661-131338903(-)$1	242	182	214	13.0264
fccc####bb[bboooooobbbb4444ccc]f	chr17:56326431-56326671(-)$1	240	30	62	13.1371
==============nnnnn=============	chr4:53579243-53579552(+)$1	309	136	168	11.8447
ffffffa[eeeeeooooooeeeee]a]fffff	chr2:179896889-179897147(+)$1	258	176	208	12.8859
!!ffffff!!cccooooooccc22ffffffbb	chr2:103900239-103900532(+)$1	293	118	150	14.0688
ggggdddd[a[bboooooobba]dddd]gggg	chr12:113032839-113033086(+)$1	247	138	170	13.4687
dddd[bb####bboooooobb333bb]dddd]	chr19:46451963-46452202(-)$1	239	38	70	13.1395
ggg"""ccc[cccnnnnncccccc]ggggggg	chr15:77591627-77591923(-)$1	296	239	271	11.3227
ggggg[a!!ddddoooooodddd22a]ggggg	chr6:83290169-83290418(+)$1	249	53	85	16.4666
cc[eeeee[ccc!!aooooooa22ccc333ee	chr3:66777290-66777538(-)$1	248	134	166	12.6836
e::bb[ddddcccooooooccc333dddd]bb	chr5:136385328-136385586(-)$1	258	69	101	12.1654
[ggggggg[addddmmmmdddd]a]ggggggg	chr11:6248586-6248824(+)$1	238	178	210	10.9913
eeee[ccc[ddddoooooodddd]ccc]eeee	chr1:155755448-155755706(+)$1	258	124	156	15.0032
&============lll============333d	chr4:57723874-57724119(+)$1	245	167	199	10.8850
bggggggg[abboooooobb]a]ggggggg]b	chr12:114312271-114312537(+)$1	266	139	171	12.7022
gggg[bb!!ddddoooooodddd]bb]ggggg	chr13:100192842-100193104(-)$1	262	187	219	15.3006
eeeee:gggggggoooooogggggggeeeee[	chr16:10960882-10961166(-)$1	284	150	182	12.1738
!!ccc[gggggggooooooggggggg333ccc	chr9:66877260-66877571(-)$1	311	199	231	14.9331
ggggg$$$$$cccooooooccc333ggggggg	chr10:39584279-39584535(+)$1	256	142	174	16.0428
iii:::ccc[cccooooooccc22cccccc[d	chr19:12540951-12541200(-)$1	249	84	116	12.3403
+a[bb[a[ddddoooooodddd]a]bbadddd	chr17:73290642-73290885(+)$1	243	72	104	12.0789
ccdddd[aeeeeeooooooeeeee]a]dddd4	chr5:34973760-34974046(+)$1	286	197	229	13.0129
ff"""ccc!!cccooooooccc22ccc]ffff	chr11:76592620-76592868(-)$1	248	127	159	15.4428
======"""ddddoooooodddd4444=====	chr8:131256668-131256967(+)$1	299	131	163	16.6716
###ggggggg[cccnnnnnccc]ggggggg]b	chr15:96517808-96518072(-)$1	264	139	171	11.1455
ggg!!bb!!ddddoooooodddd22bb22ggg	chr7:3629758-3629999(-)$1	241	159	191	14.9433

#otherMatches

#Seq PSSM
GCUGGGAAAGACCGACUGAGAGCCGUCCCGUG	chr8:26270075-26270319(-)$1	244	77	109	13.6779
UUGUGGCACUGCUCCAAGAAGCCUUAUGCACA	chr5:98313645-98313928(-)$1	283	57	89	15.6893
auauauaGUGUCUUUCACUGGAUAAUGUGUGU	chr6:65064493-65064746(+)$1	253	186	218	14.4779
UUAAGCUAAGCUGUAUUUUUAGUGAGCUGCCC	chr11:72581581-72581830(+)$1	249	61	93	13.1233
UCAUCUUGCUAGGGCCAAGCUGAGAGCUCAUG	chr11:6255969-6256276(+)$1	307	116	148	10.4762
CUCUGCCUCAGCUCCCGCCAGCUCUUAAUGAU	chr17:26833974-26834234(+)$1	260	62	94	12.7548
CCAAAAGGCCCAGAGACUAUCUUAGCUAGCUU	chr16:17429178-17429420(+)$1	242	105	137	11.9741
UGAAAGGCAGUAUUCCACUAUAUAAACCUCUU	chr16:15624614-15624876(-)$1	262	163	195	16.4156
AAGGGACUUAGGCGCUAGAGACGAUGUCGCUU	chr13:29045139-29045383(-)$1	244	109	141	15.2146
AUGGGCCACAGAUGUCAGAAAUUGAGGCCCAU	chr1:94755369-94755649(+)$1	280	176	208	15.3475
AAUAAAUGUGUUACUGUUAUGGCCGUCUGUUU	chr16:87484106-87484350(-)$1	244	212	244	13.5891
GUGUGGUCUCCCCUUGUUUGGGGCUCAUACUG	chr11:53357290-53357582(+)$1	292	109	141	14.1347
CACGCCGCCUUCUGGUCUUUUCGAGAUCGCCU	chr5:114813497-114813742(-)$1	245	164	196	11.6062
CGUGUGUUGUGAUGCUGUAAUCAGAACAUGCU	chr18:35413953-35414234(+)$1	281	189	221	14.7890
GGGCUCUGGGCUCCUCACCGAGACUCAGAGGC	chr11:53355998-53356241(+)$1	243	16	48	15.7364
GGACUUCCUCAGGAUGUAGUUCUUGGAGCCAU	chr8:97346562-97346807(-)$1	245	147	179	12.9106
CCUCUACCCCAUCGUGUCAUGGAGAUGGAGUC	chr10:80078350-80078599(+)$1	249	16	48	12.7662
AGGUUGGCUAGUAUGGCUUUAUUUCCGACCUU	chr16:24983817-24984102(+)$1	285	36	68	16.6203
UAGGAGAGAUCGUAGCACCAUGAAGCCUCUGC	chr17:34056514-34056758(+)$1	244	99	131	14.4497
AACCUGUGUUUUCUUUUGUGCAGACACGUUUA	chr2:121257956-121258217(+)$1	261	197	229	11.9376
UCCAUUUCAUCUAAGUAACUAGAUUGAGGGAA	chr7:6659898-6660159(-)$1	261	212	244	13.2887
GCCCUGUCUGCUCUGUCCUGGGUCAGAGGGCU	chr13:91841444-91841692(+)$1	248	49	81	13.5403
CUUUGGCUUUGUUGAAUGAAGCAGAGAAGAUU	chr9:49312146-49312384(-)$1	238	85	117	12.8948
UCAGGUUCAGCGGGCUGCGCCCAGCUCUACCC	chr17:24732708-24732950(+)$1	242	100	132	10.8749
gaacuggugacacaggcagguggagaaaaagu	chr16:8635408-8635660(-)$1	252	13	45	15.7385
GCCCGGGUGCGUGGGUGCACAGGUGCGUGGGU	chr17:27889382-27889620(-)$1	238	60	92	12.0867
AGAGCUAACAUGCCCUGCAGCAUAUUUUACUG	chr18:52677937-52678208(-)$1	271	152	184	12.0649
AUGUGUACCAUCAAUAAAGUGUAUGUUGCAAA	chrX:131338661-131338903(-)$1	242	182	214	13.0264
GAGGAGAAGUCGCCAUUGAGCACACAACCUCC	chr17:56326431-56326671(-)$1	240	30	62	13.1371
CCCUCGAGUGUGAGUGUGCUUUAUGUUUGGGG	chr4:53579243-53579552(+)$1	309	136	168	11.8447
AGUGUGCAUGUUUCAGUCCAGGCAAGUUACAU	chr2:179896889-179897147(+)$1	258	176	208	12.8859
UAGGCGCUACAUGACACUACAUUAGGCGUUGG	chr2:103900239-103900532(+)$1	293	118	150	14.0688
GGACACACUGACGUAGAUUUGCUGUGUAGUCU	chr12:113032839-113033086(+)$1	247	138	170	13.4687
UGGCUUCUCCUACGUCCUGGUUUCGAUGCCAU	chr19:46451963-46452202(-)$1	239	38	70	13.1395
ACUCUAGAAAGGCCAACAGCCUUCCGGUGGCU	chr15:77591627-77591923(-)$1	296	239	271	11.3227
GAAGCUUGGAUCUAAAGACAGAUAAAUGUUUC	chr6:83290169-83290418(+)$1	249	53	85	16.4666
UGCGCUGGACCCGGGAUCCCACGAGGGCCACC	chr3:66777290-66777538(-)$1	248	134	166	12.6836
CAUUGAAGGAAGCUCUGCUGCUAUGUCCUACA	chr5:136385328-136385586(-)$1	258	69	101	12.1654
AUCCAUGUGCGGCUGAGUGGCCAGGAUGUGGA	chr11:6248586-6248824(+)$1	238	178	210	10.9913
UAGGCAUAGCUGUCACAAAGCGGGUGUACUUA	chr1:155755448-155755706(+)$1	258	124	156	15.0032
AACAGUCUUUCUGACAUAGGGGGGCUGUCAUA	chr4:57723874-57724119(+)$1	245	167	199	10.8850
AGCGCGCUGUGACUGAUUUCUAGAGUGUGUAU	chr12:114312271-114312537(+)$1	266	139	171	12.7022
CCUCAGUGAUGGCCACGGAGCCGAGCCGAGGA	chr13:100192842-100193104(-)$1	262	187	219	15.3006
UGCAGAGGUAGUAGACAAUUGCUACCAGAAGU	chr16:10960882-10961166(-)$1	284	150	182	12.1738
CACCUUUUGUUGGCUUUCUUCAAUAACCUAGG	chr9:66877260-66877571(-)$1	311	199	231	14.9331
CGCUCUGAGCCUCGAGUUGGAGAACGAGUGCC	chr10:39584279-39584535(+)$1	256	142	174	16.0428
AUACUUCAGUCAAAAGUACUUGUCCUGGCAUC	chr19:12540951-12541200(-)$1	249	84	116	12.3403
CGUGUUGUGGUGUCUUCUCAUCCCUACCCCAG	chr17:73290642-73290885(+)$1	243	72	104	12.0789
CCAUGGUCUGAGAAAACACUCUCAUGUCCAUC	chr5:34973760-34974046(+)$1	286	197	229	13.0129
GGUUUGGUCCCUGCUCUCUCAGAAGCUUCUUG	chr11:76592620-76592868(-)$1	248	127	159	15.4428
AUCUUUUAAUGUGUCUGUUUGCAAUAUGGGGG	chr8:131256668-131256967(+)$1	299	131	163	16.6716
GAGGCCAACAUGCCUCUGUGGCCUGUUGGCAG	chr15:96517808-96518072(-)$1	264	139	171	11.1455
UGACCUUUUCAGACCUUCCUCUGCUAACAUCA	chr7:3629758-3629999(-)$1	241	159	191	14.9433

#DB
(((((((..(..(......)..)..))))...	chr8:26270075-26270319(-)$1	1	77	109	13.6779
.(((((((..(((......)))....))).))	chr5:98313645-98313928(-)$1	1	57	89	15.6893
(((((((.(((((......))))).)))))))	chr6:65064493-65064746(+)$1	1	186	218	14.4779
)).((((..((((......)))).))))((((	chr11:72581581-72581830(+)$1	1	61	93	13.1233
((.((..(((..(((...)))...)))....)	chr11:6255969-6256276(+)$1	1	116	148	10.4762
(((((..((((((......)))......))).	chr17:26833974-26834234(+)$1	1	62	94	12.7548
((((..(((..(((.....)))..)))...))	chr16:17429178-17429420(+)$1	1	105	137	11.9741
.((((((..((((......))))...))).))	chr16:15624614-15624876(-)$1	1	163	195	16.4156
(((.(((...(.(......).)...))).)))	chr13:29045139-29045383(-)$1	1	109	141	15.2146
(((((((.(((.(......).))).)))))))	chr1:94755369-94755649(+)$1	1	176	208	15.3475
((((.(((.((((......))))))).)))).	chr16:87484106-87484350(-)$1	1	212	244	13.5891
((((((...((((......)))).))))))((	chr11:53357290-53357582(+)$1	1	109	141	14.1347
...(((((..(((.(......).)))..))..	chr5:114813497-114813742(-)$1	1	164	196	11.6062
)(((((((.((((......)))).))))))).	chr18:35413953-35414234(+)$1	1	189	221	14.7890
((.((((((((((......))).))))))).)	chr11:53355998-53356241(+)$1	1	16	48	15.7364
((.(((...(((((......))))))))))))	chr8:97346562-97346807(-)$1	1	147	179	12.9106
.(((((.(((((......)))).).))))).)	chr10:80078350-80078599(+)$1	1	16	48	12.7662
(((((((..((((......)))).))))))))	chr16:24983817-24984102(+)$1	1	36	68	16.6203
(((((((((((((......))))....))).)	chr17:34056514-34056758(+)$1	1	99	131	14.4497
....(((((((.(......).))))))).)))	chr2:121257956-121258217(+)$1	1	197	229	11.9376
(((.(((.(((((......))))).)))))))	chr7:6659898-6660159(-)$1	1	212	244	13.2887
((((..(((((((......))).)))))))).	chr13:91841444-91841692(+)$1	1	49	81	13.5403
..((..(((((((......)))))))..))..	chr9:49312146-49312384(-)$1	1	85	117	12.8948
(..(((..(((((((...)))).)))..))).	chr17:24732708-24732950(+)$1	1	100	132	10.8749
(((((..(..(((......)))..)....)))	chr16:8635408-8635660(-)$1	1	13	45	15.7385
(((((.((((.((......)).)))).)))))	chr17:27889382-27889620(-)$1	1	60	92	12.0867
.((((((((((((......)))........))	chr18:52677937-52678208(-)$1	1	152	184	12.0649
((.((((.(((((......)).))).)))).)	chrX:131338661-131338903(-)$1	1	182	214	13.0264
((((....((.((......))))....))).)	chr17:56326431-56326671(-)$1	1	30	62	13.1371
((((((((((((((.....)))))))))))))	chr4:53579243-53579552(+)$1	1	136	168	11.8447
(((((((.(((((......))))).).)))))	chr2:179896889-179897147(+)$1	1	176	208	12.8859
..((((((..(((......)))..))))))))	chr2:103900239-103900532(+)$1	1	118	150	14.0688
((((((((.(.((......))).)))).))))	chr12:113032839-113033086(+)$1	1	138	170	13.4687
((((.((....((......))...)).)))).	chr19:46451963-46452202(-)$1	1	38	70	13.1395
(((...(((.(((.....)))))).)))))))	chr15:77591627-77591923(-)$1	1	239	271	11.3227
(((((.(..((((......))))..).)))))	chr6:83290169-83290418(+)$1	1	53	85	16.4666
((.(((((.(((..(......)..)))...))	chr3:66777290-66777538(-)$1	1	134	166	12.6836
)..((.(((((((......)))...)))).))	chr5:136385328-136385586(-)$1	1	69	101	12.1654
.(((((((.(((((....)))).).)))))))	chr11:6248586-6248824(+)$1	1	178	210	10.9913
((((.(((.((((......)))).))).))))	chr1:155755448-155755706(+)$1	1	124	156	15.0032
.((((((((((((...))))))))))))...)	chr4:57723874-57724119(+)$1	1	167	199	10.8850
((((((((.(((......)).).))))))).)	chr12:114312271-114312537(+)$1	1	139	171	12.7022
((((.((..((((......)))).)).)))))	chr13:100192842-100193104(-)$1	1	187	219	15.3006
))))).(((((((......)))))))(((((.	chr16:10960882-10961166(-)$1	1	150	182	12.1738
..(((.(((((((......)))))))...)))	chr9:66877260-66877571(-)$1	1	199	231	14.9331
(((((.....(((......)))...)))))))	chr10:39584279-39584535(+)$1	1	142	174	16.0428
)))...(((.(((......)))..)))(((.(	chr19:12540951-12541200(-)$1	1	84	116	12.3403
.(.((.(.((((......)))).).)))))))	chr17:73290642-73290885(+)$1	1	72	104	12.0789
((((((.((((((......))))).).)))).	chr5:34973760-34974046(+)$1	1	197	229	13.0129
((...(((..(((......)))..))).))))	chr11:76592620-76592868(-)$1	1	127	159	15.4428
((((((...((((......))))....)))))	chr8:131256668-131256967(+)$1	1	131	163	16.6716
...(((((((.(((.....))).))))))).)	chr15:96517808-96518072(-)$1	1	139	171	11.1455
(((..((..((((......))))..))..)))	chr7:3629758-3629999(-)$1	1	159	191	14.9433

#PSSM
g : 0.15	c : 0.13	e : 0.11	d : 0.09	f : 0.09	! : 0.07	[ : 0.05	h : 0.05	= : 0.05	+ : 0.03	# : 0.03	a : 0.01	" : 0.01	& : 0.01	b : 0.01	i : 0.01	
g : 0.20	c : 0.15	d : 0.13	e : 0.09	f : 0.07	= : 0.07	h : 0.05	! : 0.05	# : 0.03	" : 0.01	+ : 0.01	b : 0.01	: : 0.01	i : 0.01	a : 0.01	
g : 0.20	d : 0.15	[ : 0.11	e : 0.09	c : 0.07	= : 0.07	f : 0.05	: : 0.03	h : 0.03	" : 0.03	b : 0.03	+ : 0.01	! : 0.01	i : 0.01	# : 0.01	
g : 0.22	d : 0.16	c : 0.13	e : 0.11	b : 0.07	= : 0.07	f : 0.05	[ : 0.03	" : 0.03	h : 0.01	+ : 0.01	: : 0.01	! : 0.01	
g : 0.20	d : 0.13	c : 0.13	e : 0.09	! : 0.07	[ : 0.07	= : 0.07	b : 0.05	f : 0.05	" : 0.03	h : 0.01	# : 0.01	: : 0.01	
c : 0.18	g : 0.16	! : 0.11	d : 0.09	[ : 0.09	= : 0.07	f : 0.05	b : 0.05	e : 0.03	: : 0.03	h : 0.01	# : 0.01	" : 0.01	$ : 0.01	
g : 0.22	c : 0.20	d : 0.13	! : 0.07	b : 0.07	" : 0.05	= : 0.05	a : 0.05	[ : 0.03	# : 0.01	f : 0.01	e : 0.01	$ : 0.01	
c : 0.18	g : 0.18	! : 0.15	[ : 0.11	" : 0.07	d : 0.07	a : 0.05	# : 0.03	= : 0.03	b : 0.01	f : 0.01	e : 0.01	$ : 0.01	
! : 0.22	c : 0.16	[ : 0.13	g : 0.13	d : 0.09	e : 0.07	" : 0.07	= : 0.03	b : 0.01	# : 0.01	$ : 0.01	
d : 0.32	g : 0.13	! : 0.11	c : 0.11	e : 0.09	a : 0.07	= : 0.03	[ : 0.03	" : 0.01	b : 0.01	# : 0.01	$ : 0.01	
c : 0.32	d : 0.28	e : 0.09	g : 0.07	[ : 0.07	! : 0.05	= : 0.03	a : 0.01	# : 0.01	b : 0.01	
c : 0.30	d : 0.30	b : 0.11	e : 0.09	[ : 0.05	g : 0.05	! : 0.03	= : 0.03	
c : 0.30	d : 0.26	e : 0.09	b : 0.09	a : 0.07	o : 0.05	g : 0.05	= : 0.03	! : 0.01	
o : 0.79	c : 0.05	d : 0.03	[ : 0.01	e : 0.01	= : 0.01	n : 0.01	! : 0.01	l : 0.01	
o : 0.81	n : 0.07	a : 0.03	c : 0.01	d : 0.01	m : 0.01	l : 0.01	
o : 0.84	n : 0.07	l : 0.05	m : 0.01	
o : 0.84	n : 0.07	l : 0.03	m : 0.01	= : 0.01	
o : 0.84	n : 0.07	l : 0.03	m : 0.01	= : 0.01	
o : 0.79	d : 0.07	n : 0.05	c : 0.03	= : 0.01	b : 0.01	
d : 0.30	c : 0.28	b : 0.11	a : 0.07	e : 0.07	o : 0.05	g : 0.05	= : 0.03	
d : 0.30	c : 0.28	e : 0.09	b : 0.09	] : 0.07	g : 0.05	o : 0.03	= : 0.03	2 : 0.01	
d : 0.30	c : 0.28	e : 0.09	a : 0.09	g : 0.07	3 : 0.03	] : 0.03	= : 0.03	2 : 0.01	b : 0.01	
d : 0.24	] : 0.18	2 : 0.11	e : 0.09	3 : 0.09	g : 0.07	c : 0.05	= : 0.03	a : 0.01	4 : 0.01	6 : 0.01	8 : 0.01	b : 0.01	
2 : 0.16	g : 0.13	] : 0.11	3 : 0.11	c : 0.11	e : 0.09	4 : 0.07	a : 0.05	d : 0.05	= : 0.03	6 : 0.01	8 : 0.01	
c : 0.18	] : 0.16	g : 0.15	4 : 0.07	d : 0.07	3 : 0.07	2 : 0.05	= : 0.05	f : 0.03	b : 0.03	6 : 0.01	e : 0.01	a : 0.01	8 : 0.01	
g : 0.24	c : 0.22	d : 0.11	4 : 0.09	b : 0.07	= : 0.05	a : 0.05	f : 0.03	6 : 0.01	3 : 0.01	e : 0.01	8 : 0.01	] : 0.01	
c : 0.20	g : 0.18	] : 0.13	d : 0.11	4 : 0.07	2 : 0.05	= : 0.05	f : 0.03	e : 0.03	b : 0.03	6 : 0.01	8 : 0.01	3 : 0.01	
g : 0.22	d : 0.15	c : 0.15	2 : 0.07	= : 0.07	3 : 0.05	f : 0.05	e : 0.05	] : 0.05	4 : 0.03	6 : 0.01	8 : 0.01	a : 0.01	
g : 0.22	d : 0.16	c : 0.15	e : 0.09	3 : 0.07	f : 0.07	= : 0.05	4 : 0.03	] : 0.03	b : 0.03	8 : 0.01	2 : 0.01	
g : 0.24	c : 0.13	d : 0.13	e : 0.11	3 : 0.07	f : 0.07	] : 0.05	= : 0.05	b : 0.03	4 : 0.01	h : 0.01	i : 0.01	8 : 0.01	
g : 0.20	d : 0.13	e : 0.13	] : 0.13	c : 0.11	= : 0.05	3 : 0.03	2 : 0.03	f : 0.03	b : 0.03	4 : 0.01	h : 0.01	i : 0.01	[ : 0.01	
g : 0.18	e : 0.13	b : 0.11	d : 0.09	c : 0.09	2 : 0.05	= : 0.05	f : 0.05	3 : 0.03	h : 0.03	: : 0.03	] : 0.03	i : 0.01	[ : 0.01	4 : 0.01	

#score	716.0589121901922
#seq	53
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_UTR_m2_run1.txt

#BEAR
d[eeeee[ccc"""cccmmmmccc]ccc]eeeee]dd	chr7:19631157-19631363(+)$1	206	120	157	10.7200
dddd!!bb####cccooooooccc22bb4444dddd:	chr1:108686498-108686725(-)$1	227	62	99	13.9193
=====a"""ddddddddllldddd]dddd333a]===	chr2:155798991-155799211(+)$1	220	83	120	11.4512
hhhhhhccc"""cccooooooccc333ccc]hhhhhh	chr5:53253093-53253316(+)$1	223	95	132	14.3330
eee[ggggggg[ddddmmmmdddd333ggggggg333	chr5:121329169-121329379(-)$1	210	90	127	12.1269
ggggggg####ddddoooooodddd4444ggggggg:	chr4:83102258-83102471(-)$1	213	55	92	14.8733
g[bb[ccc$$$$$bboooooobb4444ccc]bb22gg	chr1:74708253-74708459(+)$1	206	67	104	13.7052
!bb!!bb!!bb!!bboooooobb22bb22bb22bb22	chr3:84351830-84352052(-)$1	222	44	81	13.5166
ee####eeeee[cccooooooccceeeee4444eeee	chr3:36938105-36938322(+)$1	217	119	156	14.3119
:eeeee[dddd[cccoooooocccdddd22eeeee::	chr11:102338174-102338390(-)$1	216	151	188	11.8730
!bb[bb[ccc!!ddddoooooodddd22ccc]bb333	chr11:51499004-51499225(-)$1	221	8	45	13.8994
b[bbggggggg[cccooooooccc333ggggggg]bb	chr9:51895212-51895425(+)$1	213	38	75	15.6925
=========="""cccmmmmccc333==========]	chr7:74461726-74461946(-)$1	220	10	47	13.9951
"""============oooooo============333e	chr2:131113177-131113391(+)$1	214	136	173	16.2324
cc[acccccc[aaddddllldddd]a]a]ccc]ccc]	chr11:3255803-3256014(-)$1	211	167	204	11.7164
b[eeeee!!dddd[ccclllccc]dddd22eeeee33	chr8:75876260-75876503(-)$1	243	107	144	10.5786
dd####eeeee!!bboooooobb333eeeee]ddddb	chr10:90623230-90623452(-)$1	222	113	150	14.0330
!ccc!!ccc[a!!ddddmmmmdddd22a]cccccc33	chr15:99158444-99158663(-)$1	219	69	106	11.8518
bb[============nnnnn============bb]cc	chr1:183133090-183133302(-)$1	212	129	166	11.7376
cc[bb[a[dddd[aooooooa]dddd]a]bb]ccc22	chr1:60400145-60400354(+)$1	209	63	100	13.3525
cccdddd[ddddddddaooooooa]dddd]dddd22d	chr3:33976787-33977006(+)$1	219	76	113	10.6865
ffffffeeeee!!bboooooobb22eeeee]ffffff	chr18:24430019-24430238(+)$1	219	91	128	12.6626
dd[ffffff[a!!bboooooobb22affffffddddc	chr15:96518490-96518699(-)$1	209	63	100	12.9983
bbgggggggccc[bboooooobb]ccc22ggggggg5	chr5:30389706-30389928(-)$1	222	26	63	13.9056
ddd[bb!!bb"""bboooooobb22bb22bbdddd22	chr11:29412369-29412589(+)$1	220	34	71	13.5337
%%%eeeee"""ddddoooooodddd333eeeee6666	chr5:111185444-111185661(-)$1	217	48	85	11.3497
eeee[bb[a[eeeeeooooooeeeee]a]bb]eeeee	chr10:75745216-75745426(-)$1	210	79	116	12.6961
gggggggbb[eeeeeooooooeeeee333bb::ffff	chr9:107460238-107460458(+)$1	220	34	71	11.3095
eee[ggggggg!!cccmmmmccc22gggggggeeeee	chr1:36206881-36207106(-)$1	225	33	70	11.2222
:ccc[eeeee"""bboooooobb333eeeee22ccc:	chr15:44451334-44451540(+)$1	206	110	147	12.9978
ccc[ggggggg!!cccnnnnnccc]ggggggg]ccc8	chr11:116029001-116029207(-)$1	206	15	52	12.3588
gggggg!!a[dddd[ammmma]dddda22ggggggg3	chr19:5055626-5055848(+)$1	222	59	96	11.7769
&&&&&&&ccc!!cccooooooccc22ccc>>>>>>>>	chr15:99150375-99150581(-)$1	206	22	59	11.3558
ggggggccc"""cccmmmmccc333ccc>>>>>>>>>	chr1:34267919-34268148(+)$1	229	102	139	10.9969
ccc[ccc!!ffffffooooooffffff22ccc22ccc	chr3:151896469-151896686(+)$1	217	108	145	12.8907
$$bb[dddd[a[cccooooooccc]a]dddd]bb22e	chr9:118466931-118467164(+)$1	233	52	89	14.4812
dd:bb[dddd!!cccooooooccc4444dddd]bbbb	chr4:144746190-144746431(-)$1	241	56	93	13.3073
eeeee!!dddd!!cccnnnnncccdddd]eeeee]dd	chr6:34548507-34548740(+)$1	233	155	192	10.7477
ffffffdddd!!cccooooooccc]dddd]ffffff]	chr12:88782180-88782400(-)$1	220	167	204	14.3230
d####ccc[a[ddddoooooodddda]cccdddd22d	chr6:51511924-51512136(+)$1	212	127	164	14.2375
e::bb[cccccccccooooooccc]ccc]ccc]bbdd	chr12:79962995-79963214(+)$1	219	129	166	12.7047
ccc!!a!!ccc[ccclllccc]ccc22a22ccc]fff	chr4:3502001-3502210(+)$1	209	60	97	11.6586
bbb[dddd####cccoooooocccddddbb]bb]a22	chrX:161418049-161418275(-)$1	226	81	118	13.8441
[bb"""iiiiiiiiiooooooiiiiiiiii22bb]ee	chrX:148305940-148306151(+)$1	211	6	43	13.8775
ggggg!!cccddddoooooodddd]ccc22ggggggg	chr9:118469856-118470070(+)$1	214	108	145	14.0946
dooooooddddddddooooooddddccc[ddddffff	chr8:131249824-131250039(+)$1	215	94	131	10.7396
b[dddd!!a[eeeeeooooooeeeee]a333ddddbb	chr4:151164441-151164665(-)$1	224	104	141	13.0059
ffffff!!a[a[cccooooooccc]a]a22ffffff5	chr4:134301333-134301542(-)$1	209	135	172	15.4565
:eeeee"""a[ddddoooooodddd]a4444eeeee:	chr19:10614147-10614376(+)$1	229	69	106	12.7967
ggggg####ffffffooooooffffff333ggggggg	chr13:104968281-104968494(-)$1	213	27	64	13.8363
bb!!bb[eeeee[aooooooaeeeee]bb22bb333g	chr16:45093761-45093980(+)$1	219	133	170	11.7471
bb####bb[bb[cccooooooccc]bbbbbb]=====	chr9:74885632-74885850(+)$1	218	86	123	13.9707
ccc[ccc[ccc[cccoooooocccccc]ccc22cccc	chr1:58770307-58770521(+)$1	214	138	175	15.4741
ggg!!dddd"""ddddmmmmdddd22ddddggggggg	chr9:66377998-66378217(-)$1	219	59	96	10.8604
"ffffff[ccc!!ccclllccc4444ccc]ffffff8	chr1:36241176-36241397(-)$1	221	88	125	11.1416
iiii[a[dddd!!bb[aooooooa]bb22dddd]a]i	chr9:36533335-36533568(-)$1	233	133	170	12.6074
=========[bb[bboooooobb]bb]==========	chr16:11088305-11088520(-)$1	215	4	41	14.5350
c!!bb"""bb!!cccooooooccc]bb22bb22cccd	chr17:46401778-46402006(-)$1	228	161	198	15.0673

#otherMatches

#Seq PSSM
CUUCUUGACCUCAGCUCUCACGAGAAGGACAGGGUGA	chr7:19631157-19631363(+)$1	206	120	157	10.7200
GAUGAAGCACAAGGUGAUAAAGCCAAGCAAAGUAUCA	chr1:108686498-108686725(-)$1	227	62	99	13.9193
UUAGGCAGAACAGUCCAUUGUGGAGCUGUCAGGUUCU	chr2:155798991-155799211(+)$1	220	83	120	11.4512
AUGUAAUUGGAAGAUCGAUGAAUCAAGCAAUUUGCAU	chr5:53253093-53253316(+)$1	223	95	132	14.3330
UCACUGUCUAUGCCUGGGAACAGGGGAAUGGAUGUAA	chr5:121329169-121329379(-)$1	210	90	127	12.1269
GCUACGUUAGCUUGCCUCUUUGUAAUAAUGCGUAGUC	chr4:83102258-83102471(-)$1	213	55	92	14.8733
UGUGGGACAGAAAGCGGCAGAGCGUGGGUCGCGUGGC	chr1:74708253-74708459(+)$1	206	67	104	13.7052
uuauuuauuuauuuauuuauuuauuuauuuauuuauu	chr3:84351830-84352052(-)$1	222	44	81	13.5166
UCCAUUGAAGGAGUGAGCCAGCACCUUUCUCCCGAAU	chr3:36938105-36938322(+)$1	217	119	156	14.3119
AGGAGGGGAGGAUUGGUUCAACAGCUUUAUUCUCUGG	chr11:102338174-102338390(-)$1	216	151	188	11.8730
UCUCCUAUUCGAUCGAGUGCAUUCGAAAGAAAAGUUC	chr11:51499004-51499225(-)$1	221	8	45	13.8994
UUUCCUUAAGUGCAGUCAUCUCUGAUAGCUUGAGUGA	chr9:51895212-51895425(+)$1	213	38	75	15.6925
UUUGUAUAGCAUUUAAUGAUUUACAAGUUGUACAGAA	chr7:74461726-74461946(-)$1	220	10	47	13.9951
GAAUGUGUGCCCUUAAUGAAGUAAGGGCACAUGAGAU	chr2:131113177-131113391(+)$1	214	136	173	16.2324
UGGGACCCCUGUCCGUACUCUGCGAGUAGAGGAGGUA	chr11:3255803-3256014(-)$1	211	167	204	11.7164
UGUACCUCUGCCUGGAUGUAGUCAAGGCCAAGGUAAG	chr8:75876260-75876503(-)$1	243	107	144	10.5786
GUCCAUGUCUACCACUACCAUGUUCUUAGGCUGCACA	chr10:90623230-90623452(-)$1	222	113	150	14.0330
CAGUACUCUCCCUGGCCGCAGGGCCCUGAAGAACUCC	chr15:99158444-99158663(-)$1	219	69	106	11.8518
GCAUCCAUGUCCUUAGUGGGUAAGGAUGUGGGGUUCU	chr1:183133090-183133302(-)$1	212	129	166	11.7376
CGCGGGCGGGCGAGAGGAAGCAUGCUGGACUUCGCCA	chr1:60400145-60400354(+)$1	209	63	100	13.3525
CUAGAUUUGCUGUCUACUAAAGUGAUGGAGCAGUGUG	chr3:33976787-33977006(+)$1	219	76	113	10.6865
GAAAUAGUGACAUGCUCCCAUGUUGGUCAUGUGUUUC	chr18:24430019-24430238(+)$1	219	91	128	12.6626
GGCAUCCUGAGAGGUGCCAUGACAACCAGGAUCCUGU	chr15:96518490-96518699(-)$1	209	63	100	12.9983
UGUGGUGAAUGGGGAACUGUCUUGCCAGCUUUACCAG	chr5:30389706-30389928(-)$1	222	26	63	13.9056
agaagcaaugaaggcacaaaagcaacacagcucuuuc	chr11:29412369-29412589(+)$1	220	34	71	13.5337
UCCAUCUGCACCCCAAUCCCCUGGGUACCAGAUACAG	chr5:111185444-111185661(-)$1	217	48	85	11.3497
CUGCACGAUGACCGGAUUGUCUUGGUGGCUGAGCAGC	chr10:75745216-75745426(-)$1	210	79	116	12.6961
AGCAUCUGCAUGUUCUAUCACGAACACGGGCACGUGA	chr9:107460238-107460458(+)$1	220	34	71	11.3095
CAUUCAGUUGGGUUCAUUGUUGACAUCAAUUGAUGGU	chr1:36206881-36207106(-)$1	225	33	70	11.2222
GUGCAGUGGGUAUGAUUUUUUUUUUUUCCGCCAGCAA	chr15:44451334-44451540(+)$1	206	110	147	12.9978
AUGCCUUCAUGGAGUUGGUUGAAUAUGUGAAGACGUG	chr11:116029001-116029207(-)$1	206	15	52	12.3588
UCUUCUCAGACAUAGCAUCUGGUGUGCAAAGAAGGGA	chr19:5055626-5055848(+)$1	222	59	96	11.7769
CCCCACUGGGAUGACCCCUCUGUCUGCCCUUUACUUA	chr15:99150375-99150581(-)$1	206	22	59	11.3558
GAUCUGUCCAAGUGUGUGAACGAACGGAAUGAAAAGC	chr1:34267919-34268148(+)$1	229	102	139	10.9969
UCCAGCCAGUAUAGAACUAGCUCUGUAGGGGUGAGGA	chr3:151896469-151896686(+)$1	217	108	145	12.8907
AGGAGUCCUGCAUCACACAGCUGAAGAAGGAGUUAGC	chr9:118466931-118467164(+)$1	233	52	89	14.4812
UGAGAAGUUCAAUGUUCACCUACAGUUAGAACGUCGG	chr4:144746190-144746431(-)$1	241	56	93	13.3073
GAGGUAAGAGACAAAGUCUUUCUUUCUCCGCCUUCAG	chr6:34548507-34548740(+)$1	233	155	192	10.7477
gcugggguuaaaggugugugugccaugacacccggcu	chr12:88782180-88782400(-)$1	220	167	204	14.3230
CAGCAGAAAGAGGUAAGAUGCUACCCAUUCGUUUAUG	chr6:51511924-51512136(+)$1	212	127	164	14.2375
CACGGCGUGGGACCCUACUUCGGGAUUCACACAUCCA	chr12:79962995-79963214(+)$1	219	129	166	12.7047
GCGUCCCCAGGCGCGUUCCGCUCCUCUGCCCGCGCGA	chr4:3502001-3502210(+)$1	209	60	97	11.6586
GCGACGGGUACAACCACAAUAGGUUCCGCGACUGUGA	chrX:161418049-161418275(-)$1	226	81	118	13.8441
CCUGAUGAAGUAAAACUGACCUUUUACUUCCAAGUGU	chrX:148305940-148306151(+)$1	211	6	43	13.8775
CCAGGAGAUACGAGGAGAUACUCGAUGUACCUUGGUU	chr9:118469856-118470070(+)$1	214	108	145	14.0946
GACUGUCCUACUGGUCCCGACAUCAUCCCAAUUGUAG	chr8:131249824-131250039(+)$1	215	94	131	10.7396
CGUGGUGAAGggccaggaccauggcuguggagccagg	chr4:151164441-151164665(-)$1	224	104	141	13.0059
GCUGCCAAUGCUGCUGUGUGAAGCUGGAAAGGCAGUU	chr4:134301333-134301542(-)$1	209	135	172	15.4565
GACUGUCUUCAUGGCAUAGAGGCCAAGUCAUACAGUG	chr19:10614147-10614376(+)$1	229	69	106	12.7967
UUAGUGGUUGAGGCAAGUGUGUGCUUCUGAGCUAAGG	chr13:104968281-104968494(-)$1	213	27	64	13.8363
CAAACCUGAAGUAGCCCUGACAUUUCUGGGAUGGAAU	chr16:45093761-45093980(+)$1	219	133	170	11.7471
GCACCAUGUCCGCGGAAGUCCCCGAGGCAGCGUCUGC	chr9:74885632-74885850(+)$1	218	86	123	13.9707
CCAGCGAAGACAGGCGACAAAGCCGUUGUUGAGUGGG	chr1:58770307-58770521(+)$1	214	138	175	15.4741
CCUUUUGGAUCAUCUACACUUAGAACUUCAGGGUGGC	chr9:66377998-66378217(-)$1	219	59	96	10.8604
AGAGACAGUGAAAGUGGAGCACGUGGUCAGUGUCUUG	chr1:36241176-36241397(-)$1	221	88	125	11.1416
UUUUGUGGAAGACUGGGAUUUGGUGCAAACUUUGGGA	chr9:36533335-36533568(-)$1	233	133	170	12.6074
GGCAGCAUCCCCCUGCUGUAACACGGUGGUGCUGCCA	chr16:11088305-11088520(-)$1	215	4	41	14.5350
CCAGCGAACAGACGGUAUGUCCCGAUGAGGCCUGCAU	chr17:46401778-46402006(-)$1	228	161	198	15.0673

#DB
(.(((((.(((...(((....))).))).))))).))	chr7:19631157-19631363(+)$1	1	120	157	10.7200
((((..((....(((......)))..))....)))).	chr1:108686498-108686725(-)$1	1	62	99	13.9193
((((((...((((((((...)))).))))...).)))	chr2:155798991-155799211(+)$1	1	83	120	11.4512
(((((((((...(((......)))...))).))))))	chr5:53253093-53253316(+)$1	1	95	132	14.3330
(((.(((((((.((((....))))...)))))))...	chr5:121329169-121329379(-)$1	1	90	127	12.1269
(((((((....((((......))))....))))))).	chr4:83102258-83102471(-)$1	1	55	92	14.8733
(.((.(((.....((......))....))).))..))	chr1:74708253-74708459(+)$1	1	67	104	13.7052
.((..((..((..((......))..))..))..))..	chr3:84351830-84352052(-)$1	1	44	81	13.5166
((....(((((.(((......))))))))....))))	chr3:36938105-36938322(+)$1	1	119	156	14.3119
.(((((.((((.(((......)))))))..)))))..	chr11:102338174-102338390(-)$1	1	151	188	11.8730
.((.((.(((..((((......))))..))).))...	chr11:51499004-51499225(-)$1	1	8	45	13.8994
(.(((((((((.(((......)))...))))))).))	chr9:51895212-51895425(+)$1	1	38	75	15.6925
((((((((((...(((....)))...)))))))))).	chr7:74461726-74461946(-)$1	1	10	47	13.9951
...((((((((((((......))))))))))))...)	chr2:131113177-131113391(+)$1	1	136	173	16.2324
((.(((((((.((((((...)))).).).))).))).	chr11:3255803-3256014(-)$1	1	167	204	11.7164
(.(((((..((((.(((...))).))))..)))))..	chr8:75876260-75876503(-)$1	1	107	144	10.5786
((....(((((..((......))...))))).)))))	chr10:90623230-90623452(-)$1	1	113	150	14.0330
.(((..(((.(..((((....))))..).))))))..	chr15:99158444-99158663(-)$1	1	69	106	11.8518
((.((((((((((((.....)))))))))))))).))	chr1:183133090-183133302(-)$1	1	129	166	11.7376
((.((.(.((((.(......).)))).).)).)))..	chr1:60400145-60400354(+)$1	1	63	100	13.3525
)))((((.(((((((((......).)))).))))..)	chr3:33976787-33977006(+)$1	1	76	113	10.6865
(((((((((((..((......))..))))).))))))	chr18:24430019-24430238(+)$1	1	91	128	12.6626
((.((((((.(..((......))..))))))))))))	chr15:96518490-96518699(-)$1	1	63	100	12.9983
((((((((((((.((......)).)))..))))))).	chr5:30389706-30389928(-)$1	1	26	63	13.9056
(((.((..((...((......))..))..))))))..	chr11:29412369-29412589(+)$1	1	34	71	13.5337
...(((((...((((......))))...)))))....	chr5:111185444-111185661(-)$1	1	48	85	11.3497
((((.((.(.(((((......))))).).)).)))))	chr10:75745216-75745426(-)$1	1	79	116	12.6961
)))))))((.(((((......)))))...))..((((	chr9:107460238-107460458(+)$1	1	34	71	11.3095
(((.(((((((..(((....)))..))))))))))))	chr1:36206881-36207106(-)$1	1	33	70	11.2222
.(((.(((((...((......))...)))))..))).	chr15:44451334-44451540(+)$1	1	110	147	12.9978
(((.(((((((..(((.....))).))))))).))).	chr11:116029001-116029207(-)$1	1	15	52	12.3588
((((((..(.((((.(....).)))))..))))))).	chr19:5055626-5055848(+)$1	1	59	96	11.7769
.......(((..(((......)))..)))........	chr15:99150375-99150581(-)$1	1	22	59	11.3558
(((((((((...(((....)))...))).........	chr1:34267919-34268148(+)$1	1	102	139	10.9969
(((.(((..((((((......))))))..)))..)))	chr3:151896469-151896686(+)$1	1	108	145	12.8907
..((.((((.(.(((......))).).)))).))..)	chr9:118466931-118467164(+)$1	1	52	89	14.4812
)).((.((((..(((......)))....)))).))((	chr4:144746190-144746431(-)$1	1	56	93	13.3073
(((((..((((..(((.....))))))).))))).))	chr6:34548507-34548740(+)$1	1	155	192	10.7477
((((((((((..(((......))).)))).)))))).	chr12:88782180-88782400(-)$1	1	167	204	14.3230
(....(((.(.((((......))))).)))))))..)	chr6:51511924-51512136(+)$1	1	127	164	14.2375
)..((.(((((((((......))).))).))).))((	chr12:79962995-79963214(+)$1	1	129	166	12.7047
(((..(..(((.(((...))).)))..)..))).)))	chr4:3502001-3502210(+)$1	1	60	97	11.6586
(((.((((....(((......))))))))).)).)..	chrX:161418049-161418275(-)$1	1	81	118	13.8441
.((...(((((((((......)))))))))..)).))	chrX:148305940-148306151(+)$1	1	6	43	13.8775
(((((..(((((((......)))).)))..)))))))	chr9:118469856-118470070(+)$1	1	108	145	14.0946
(......))))((((......))))(((.((((((((	chr8:131249824-131250039(+)$1	1	94	131	10.7396
(.((((..(.(((((......))))).)...))))))	chr4:151164441-151164665(-)$1	1	104	141	13.0059
((((((..(.(.(((......))).).)..)))))).	chr4:134301333-134301542(-)$1	1	135	172	15.4565
.(((((...(.((((......)))).)....))))).	chr19:10614147-10614376(+)$1	1	69	106	12.7967
(((((....((((((......))))))...)))))))	chr13:104968281-104968494(-)$1	1	27	64	13.8363
((..((.(((((.(......)))))).))..))...)	chr16:45093761-45093980(+)$1	1	133	170	11.7471
((....((.((.(((......))).)))))).)))))	chr9:74885632-74885850(+)$1	1	86	123	13.9707
(((.(((.(((.(((......)))))).)))..))))	chr1:58770307-58770521(+)$1	1	138	175	15.4741
(((..((((...((((....))))..)))))))))))	chr9:66377998-66378217(-)$1	1	59	96	10.8604
.((((((.(((..(((...)))....))).)))))).	chr1:36241176-36241397(-)$1	1	88	125	11.1416
((((.(.((((..((.(......).))..)))).).)	chr9:36533335-36533568(-)$1	1	133	170	12.6074
(((((((((.((.((......)).)).))))))))))	chr16:11088305-11088520(-)$1	1	4	41	14.5350
(..((...((..(((......))).))..))..))))	chr17:46401778-46402006(-)$1	1	161	198	15.0673

#PSSM
d : 0.13	g : 0.13	b : 0.13	c : 0.13	e : 0.10	= : 0.05	! : 0.05	: : 0.05	f : 0.05	" : 0.03	h : 0.01	% : 0.01	& : 0.01	$ : 0.01	[ : 0.01	i : 0.01	
c : 0.15	b : 0.13	e : 0.12	g : 0.12	[ : 0.08	d : 0.08	f : 0.06	= : 0.05	h : 0.01	" : 0.01	% : 0.01	& : 0.01	$ : 0.01	# : 0.01	: : 0.01	o : 0.01	i : 0.01	! : 0.01	
e : 0.13	g : 0.13	b : 0.12	c : 0.12	# : 0.06	[ : 0.06	f : 0.06	d : 0.05	= : 0.05	: : 0.03	! : 0.03	h : 0.01	" : 0.01	% : 0.01	& : 0.01	o : 0.01	i : 0.01	
[ : 0.13	e : 0.12	g : 0.12	b : 0.12	= : 0.08	f : 0.08	! : 0.06	# : 0.06	d : 0.05	c : 0.03	h : 0.01	a : 0.01	& : 0.01	" : 0.01	o : 0.01	i : 0.01	
g : 0.18	b : 0.12	e : 0.10	! : 0.08	= : 0.08	[ : 0.08	f : 0.08	# : 0.06	c : 0.05	d : 0.05	h : 0.01	& : 0.01	" : 0.01	o : 0.01	
g : 0.15	e : 0.10	c : 0.08	b : 0.08	d : 0.08	f : 0.08	! : 0.06	# : 0.06	= : 0.06	a : 0.05	[ : 0.05	" : 0.03	h : 0.01	& : 0.01	o : 0.01	
c : 0.15	e : 0.12	g : 0.12	! : 0.12	d : 0.10	b : 0.06	[ : 0.06	= : 0.06	" : 0.05	f : 0.03	a : 0.01	& : 0.01	i : 0.01	o : 0.01	# : 0.01	
c : 0.17	d : 0.15	! : 0.13	[ : 0.10	e : 0.10	g : 0.08	= : 0.06	b : 0.05	" : 0.05	# : 0.03	f : 0.01	i : 0.01	
c : 0.20	d : 0.17	g : 0.08	e : 0.08	# : 0.06	= : 0.06	a : 0.06	" : 0.05	! : 0.05	b : 0.05	[ : 0.03	$ : 0.01	f : 0.01	i : 0.01	
c : 0.17	d : 0.17	[ : 0.15	e : 0.08	" : 0.06	g : 0.06	b : 0.06	# : 0.05	= : 0.05	f : 0.03	a : 0.03	$ : 0.01	i : 0.01	
d : 0.17	" : 0.12	e : 0.12	c : 0.10	! : 0.08	g : 0.06	a : 0.06	# : 0.05	b : 0.05	[ : 0.05	= : 0.03	f : 0.03	$ : 0.01	i : 0.01	
! : 0.25	d : 0.18	[ : 0.15	" : 0.12	e : 0.06	# : 0.03	= : 0.03	c : 0.03	f : 0.03	$ : 0.01	a : 0.01	i : 0.01	b : 0.01	
c : 0.29	d : 0.22	! : 0.17	" : 0.06	[ : 0.06	e : 0.05	= : 0.03	f : 0.03	$ : 0.01	a : 0.01	i : 0.01	
c : 0.37	d : 0.24	b : 0.17	e : 0.05	= : 0.03	a : 0.03	f : 0.03	" : 0.01	[ : 0.01	i : 0.01	
c : 0.41	d : 0.20	b : 0.17	o : 0.05	e : 0.05	= : 0.03	f : 0.03	[ : 0.01	i : 0.01	
o : 0.67	c : 0.12	d : 0.12	n : 0.01	a : 0.01	m : 0.01	l : 0.01	[ : 0.01	
o : 0.68	m : 0.10	d : 0.05	n : 0.05	c : 0.03	a : 0.03	l : 0.03	
o : 0.72	m : 0.13	l : 0.08	n : 0.05	
o : 0.72	m : 0.13	l : 0.06	n : 0.05	c : 0.01	
o : 0.72	m : 0.12	l : 0.05	n : 0.05	c : 0.05	
o : 0.67	c : 0.10	d : 0.08	a : 0.05	m : 0.03	n : 0.03	= : 0.01	
c : 0.39	d : 0.18	b : 0.15	e : 0.06	o : 0.05	] : 0.05	= : 0.03	f : 0.03	i : 0.01	
c : 0.37	d : 0.24	b : 0.15	e : 0.06	= : 0.03	o : 0.03	f : 0.03	3 : 0.01	i : 0.01	4 : 0.01	
c : 0.32	d : 0.24	2 : 0.08	3 : 0.06	e : 0.06	] : 0.05	4 : 0.03	= : 0.03	a : 0.03	f : 0.03	i : 0.01	
] : 0.22	d : 0.22	2 : 0.13	3 : 0.12	e : 0.08	4 : 0.05	c : 0.05	= : 0.03	f : 0.03	i : 0.01	b : 0.01	
d : 0.17	c : 0.12	3 : 0.12	b : 0.10	e : 0.10	2 : 0.08	a : 0.08	4 : 0.06	= : 0.03	g : 0.03	f : 0.03	i : 0.01	] : 0.01	
c : 0.15	] : 0.15	d : 0.13	b : 0.10	3 : 0.08	e : 0.06	4 : 0.05	2 : 0.05	= : 0.05	f : 0.05	g : 0.03	a : 0.03	i : 0.01	
c : 0.17	d : 0.15	2 : 0.13	a : 0.12	g : 0.06	e : 0.06	= : 0.06	b : 0.05	4 : 0.05	3 : 0.05	f : 0.01	i : 0.01	] : 0.01	
2 : 0.20	] : 0.12	c : 0.12	d : 0.10	e : 0.08	g : 0.06	= : 0.06	4 : 0.05	3 : 0.05	b : 0.05	f : 0.01	> : 0.01	i : 0.01	[ : 0.01	
c : 0.15	b : 0.13	g : 0.12	e : 0.10	2 : 0.10	d : 0.08	= : 0.06	4 : 0.05	3 : 0.05	] : 0.05	> : 0.03	f : 0.01	i : 0.01	
g : 0.17	e : 0.12	b : 0.12	c : 0.12	d : 0.10	] : 0.06	= : 0.06	f : 0.06	4 : 0.05	3 : 0.03	> : 0.03	2 : 0.03	
g : 0.17	d : 0.12	e : 0.10	] : 0.10	2 : 0.08	c : 0.08	f : 0.08	= : 0.06	b : 0.05	4 : 0.03	> : 0.03	3 : 0.01	h : 0.01	: : 0.01	
d : 0.15	e : 0.13	g : 0.13	b : 0.12	2 : 0.08	= : 0.06	] : 0.06	f : 0.06	c : 0.05	> : 0.03	a : 0.01	h : 0.01	4 : 0.01	: : 0.01	
e : 0.13	g : 0.13	d : 0.12	b : 0.12	c : 0.12	f : 0.10	] : 0.06	= : 0.05	2 : 0.03	3 : 0.03	> : 0.03	h : 0.01	6 : 0.01	
c : 0.13	f : 0.12	g : 0.10	e : 0.10	] : 0.08	d : 0.08	= : 0.06	3 : 0.06	2 : 0.06	b : 0.05	> : 0.03	a : 0.03	h : 0.01	6 : 0.01	
g : 0.12	2 : 0.12	c : 0.12	f : 0.12	d : 0.10	3 : 0.10	e : 0.08	= : 0.06	b : 0.05	> : 0.03	h : 0.01	: : 0.01	6 : 0.01	] : 0.01	
d : 0.10	e : 0.10	: : 0.08	3 : 0.08	g : 0.08	2 : 0.06	b : 0.06	c : 0.06	f : 0.06	= : 0.05	] : 0.05	5 : 0.03	8 : 0.03	> : 0.03	h : 0.01	6 : 0.01	i : 0.01	

#score	751.1785598414903
#seq	58
#width	37
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_CDS_m3_run2.txt

#BEAR
eeeeeqqqqqqqqeeeee:	chr19:4726530-4726776(+)$1	246	207	226	13.0189
!!cccqqqqqqqqcccccc	chr14:65673532-65673769(-)$1	237	12	31	14.0049
fffffqqqqqqqqffffff	chr18:50024647-50024885(+)$1	238	9	28	12.5010
eeeeeqqqqqqqqeeeeee	chrX:162824888-162825125(+)$1	237	119	138	13.7369
d[cccqqqqqqqqcccddd	chr15:3987046-3987281(+)$1	235	75	94	13.7654
eeeeeqqqqqqqqeeeeea	chr15:96414691-96414926(-)$1	235	71	90	13.7478
:ddddqqqqqqqqdddd::	chr6:4706066-4706310(+)$1	244	76	95	11.5057
iii[aqqqqqqqqa]iiii	chr19:10058959-10059195(+)$1	236	54	73	13.5437
ee[bbqqqqqqqqbb]eee	chr2:25077838-25078075(-)$1	237	21	40	13.6862
gggggqqqqqqqqgggggg	chr14:76818619-76818854(+)$1	235	195	214	13.3657
eee[aqqqqqqqqa]eeee	chrX:133369561-133369797(+)$1	236	83	102	13.9115
c!!bbqqqqqqqqbb22cc	chr10:34018422-34018682(+)$1	260	16	35	13.2926
fff[aqqqqqqqqa]ffff	chr2:34631511-34631748(+)$1	237	174	193	12.9345
=====qqqqqqqq======	chr11:86602657-86602898(-)$1	241	107	126	13.7105
eecccqqqqqqqqccc]ee	chr9:30959798-30960060(-)$1	262	86	105	13.9755
dd[bbqqqqqqqqbbdddd	chr11:5774281-5774520(-)$1	239	112	131	13.4508
fffffqqqqqqqqffffff	chr11:100888528-100888792(+)$1	264	22	41	12.5010
c!!bbqqqqqqqqbb22cc	chr13:74168748-74168984(+)$1	236	154	173	13.2926
[ddddqqqqqqqqddddcc	chr11:68620525-68620761(+)$1	236	210	229	13.7955
dd[bbqqqqqqqqbb]ddd	chr19:10058659-10058899(+)$1	240	150	169	13.4402
:eeeeeqqqqqqqqeeeee	chr13:100195648-100195890(-)$1	242	148	167	10.9433
:eeeeeqqqqqqqqeeeee	chrX:162824700-162824996(+)$1	296	2	21	10.9433
e[cccqqqqqqqqccc]ee	chr10:53063680-53063917(+)$1	237	215	234	13.9693
:ddddqqqqqqqqdddd::	chr9:95945897-95946132(+)$1	235	1	20	11.5057
ddd[aqqqqqqqqa]dddd	chr5:29619320-29619555(-)$1	235	116	135	13.6354
""cccqqqqqqqqccc22g	chr6:4591853-4592090(+)$1	237	194	213	13.6703
:ddddqqqqqqqqdddd:f	chr10:57236816-57237127(-)$1	311	148	167	12.1465
eeeeeqqqqqqqqeeeee:	chr10:126699751-126699986(-)$1	235	112	131	13.0189
"ddddqqqqqqqqdddd33	chr15:27701031-27701272(-)$1	241	35	54	13.9531
:ddddqqqqqqqqddddCC	chr19:7289793-7290030(-)$1	237	110	129	11.2207
bb[bbqqqqqqqqbb]bbc	chr3:19968893-19969128(+)$1	235	121	140	12.5128
eeeeeqqqqqqqqeeeee]	chr19:47331845-47332080(+)$1	235	159	178	13.7968
bb[bbqqqqqqqqbb]bb]	chr2:181041364-181041632(-)$1	268	55	74	12.5176
[a[bbqqqqqqqqbb]a]a	chr11:78138010-78138267(+)$1	257	190	209	13.4454
###bbqqqqqqqqbb4444	chr2:129444097-129444360(+)$1	263	89	108	13.3460
eeeeeqqqqqqqqeeeee:	chrX:12738488-12738723(+)$1	235	171	190	13.0189
#ddddqqqqqqqqdddd33	chr7:118217767-118218002(-)$1	235	134	153	13.9343
:eeeeeqqqqqqqqeeeee	chr15:79555743-79555980(-)$1	237	2	21	10.9433
dddddqqqqqqqqdddd]d	chr6:97128843-97129081(-)$1	238	11	30	13.6080
ddd[aqqqqqqqqadddd]	chr5:72015103-72015349(-)$1	246	16	35	13.8349
eee[aqqqqqqqqa]eeee	chr7:104877404-104877644(-)$1	240	195	214	13.9115
cccccqqqqqqqqcccggg	chr11:109528789-109529095(+)$1	306	257	276	13.7433
gggggqqqqqqqqgggggg	chr10:76784989-76785224(-)$1	235	201	220	13.3657
##cccqqqqqqqqccc333	chr10:126680660-126680895(-)$1	235	72	91	14.0506
"""bbqqqqqqqqbb333b	chr11:118355369-118355606(-)$1	237	116	135	13.3640
eeeeeqqqqqqqqeeeeee	chrX:162824810-162825047(+)$1	237	197	216	13.7369
"ddddqqqqqqqqdddd55	chrX:141894531-141894792(-)$1	261	64	83	12.3303
dddddqqqqqqqqdddd22	chr4:57722929-57723172(+)$1	243	65	84	13.3743
b[cccqqqqqqqqccc]bb	chrX:45721941-45722176(+)$1	235	42	61	13.3589
:ddddqqqqqqqqddddee	chr5:104513928-104514170(-)$1	242	124	143	13.0841
gggggqqqqqqqqgggggg	chr11:41960533-41960768(-)$1	235	144	163	13.3657
gg!!aqqqqqqqqa22ggg	chr3:146395453-146395688(-)$1	235	136	155	13.2094
dd[bbqqqqqqqqbb]ddd	chr5:137736972-137737209(-)$1	237	130	149	13.4402
fffffqqqqqqqqffffff	chr11:41946818-41947090(-)$1	272	150	169	12.5010
c[cccqqqqqqqqccc]cc	chr8:96491846-96492107(+)$1	261	94	113	13.9843
:ddddqqqqqqqqddddCC	chr10:126675733-126675988(-)$1	255	171	190	11.2207
cccccqqqqqqqqccc22c	chr5:131921174-131921409(-)$1	235	56	75	13.6243
fffffqqqqqqqqffffff	chr11:50014060-50014371(-)$1	311	139	158	12.5010
eeeeeqqqqqqqqeeeee]	chr6:36693305-36693540(-)$1	235	31	50	13.7968
dd[bbqqqqqqqqbbdddd	chr11:49502571-49502808(-)$1	237	32	51	13.4508
cccccqqqqqqqqccc]cc	chr11:94853627-94853890(+)$1	263	62	81	13.8780
!!cccqqqqqqqqccc22c	chr8:56140641-56140894(+)$1	253	160	179	13.8602
:eeeeeqqqqqqqqeeeee	chr1:83273913-83274169(-)$1	256	50	69	10.9433

#otherMatches

#Seq PSSM
GGCAAAUUCGUGGUUGCCA	chr19:4726530-4726776(+)$1	246	207	226	13.0189
AGCAGACAUGGCACUGGCU	chr14:65673532-65673769(-)$1	237	12	31	14.0049
ACUGAUUUCCAUUUUAGUG	chr18:50024647-50024885(+)$1	238	9	28	12.5010
AAGAACAACUCAAUUCUUA	chrX:162824888-162825125(+)$1	237	119	138	13.7369
UAUAGGAGCUUUACUGAAG	chr15:3987046-3987281(+)$1	235	75	94	13.7654
AGAUGGUUUCCAACAUCUC	chr15:96414691-96414926(-)$1	235	71	90	13.7478
cugcaucaccaucugcauc	chr6:4706066-4706310(+)$1	244	76	95	11.5057
UGAUUGGUAGAUGACUUGA	chr19:10058959-10059195(+)$1	236	54	73	13.5437
GCACCGCUAUUCAGGAGCU	chr2:25077838-25078075(-)$1	237	21	40	13.6862
AGGUAAGAUCACGUGCUUC	chr14:76818619-76818854(+)$1	235	195	214	13.3657
UGACCUUCCACCUGUUUAU	chrX:133369561-133369797(+)$1	236	83	102	13.9115
CUACAAUACUAUCUGAUGG	chr10:34018422-34018682(+)$1	260	16	35	13.2926
UCGUUGGGAGAAAAUUGAG	chr2:34631511-34631748(+)$1	237	174	193	12.9345
GAUUUACAGUAAAGAGUUU	chr11:86602657-86602898(-)$1	241	107	126	13.7105
AGGUCAUUGACGAGACUCU	chr9:30959798-30960060(-)$1	262	86	105	13.9755
CUGCGAAAGAUGACGGGAG	chr11:5774281-5774520(-)$1	239	112	131	13.4508
GAGUUCCCAACCUGACUCU	chr11:100888528-100888792(+)$1	264	22	41	12.5010
ACAGGACUUACACCCAUUG	chr13:74168748-74168984(+)$1	236	154	173	13.2926
AGGCUGCGAACAAAGCCCG	chr11:68620525-68620761(+)$1	236	210	229	13.7955
AUAUAAAGGUAAGUAGAUC	chr19:10058659-10058899(+)$1	240	150	169	13.4402
CCACAGGAUUUGAACUGUG	chr13:100195648-100195890(-)$1	242	148	167	10.9433
UCUUCAACCUACUAUGAAG	chrX:162824700-162824996(+)$1	296	2	21	10.9433
GAAGCAACGCACCGCUGCC	chr10:53063680-53063917(+)$1	237	215	234	13.9693
CCAUAGCAUGCCAUAUGAA	chr9:95945897-95946132(+)$1	235	1	20	11.5057
GUUGCUGAUUCUUGGGAUG	chr5:29619320-29619555(-)$1	235	116	135	13.6354
UGGCAUGUACGAUUGCAUU	chr6:4591853-4592090(+)$1	237	194	213	13.6703
AUCGGGAUUUUGACUGAAU	chr10:57236816-57237127(-)$1	311	148	167	12.1465
GGGGACAAGUUCAUCCCCA	chr10:126699751-126699986(-)$1	235	112	131	13.0189
UAUUAUCUUGAACUAAUUU	chr15:27701031-27701272(-)$1	241	35	54	13.9531
UGGGUCCUGUCACACCUGG	chr19:7289793-7290030(-)$1	237	110	129	11.2207
UGAUCGCACGAGAGAACAG	chr3:19968893-19969128(+)$1	235	121	140	12.5128
GUGGACACAGUCAUCUACA	chr19:47331845-47332080(+)$1	235	159	178	13.7968
CGCCCUUACCCUUGGCCGC	chr2:181041364-181041632(-)$1	268	55	74	12.5176
GUGAAAAAGUGCAUUGGGG	chr11:78138010-78138267(+)$1	257	190	209	13.4454
CCUCAGAUAAUAAUGCUAC	chr2:129444097-129444360(+)$1	263	89	108	13.3460
GGUUAAGAAAUCAUAACCA	chrX:12738488-12738723(+)$1	235	171	190	13.0189
CAUCUUAAUGACCAGGUAA	chr7:118217767-118218002(-)$1	235	134	153	13.9343
GCCACAUACCAAGUUGUGG	chr15:79555743-79555980(-)$1	237	2	21	10.9433
gggccgccgcugaggccgc	chr6:97128843-97129081(-)$1	238	11	30	13.6080
AUGACCACCCUAAGCAUCA	chr5:72015103-72015349(-)$1	246	16	35	13.8349
GUUAUGGCUUUUAAAAACC	chr7:104877404-104877644(-)$1	240	195	214	13.9115
CACCAUUUUUCAUUGGGAG	chr11:109528789-109529095(+)$1	306	257	276	13.7433
UCUGUGGAGGUAAACGGGC	chr10:76784989-76785224(-)$1	235	201	220	13.3657
UUCCUUCUCUGACAGGUCA	chr10:126680660-126680895(-)$1	235	72	91	14.0506
ACAGCAACCUACAGCAUCG	chr11:118355369-118355606(-)$1	237	116	135	13.3640
AAGAACAACUCAAUUCUUA	chrX:162824810-162825047(+)$1	237	197	216	13.7369
AGGGCAACUCCCAGCCCAC	chrX:141894531-141894792(-)$1	261	64	83	12.3303
UGGCCACAGACCCGGCCCC	chr4:57722929-57723172(+)$1	243	65	84	13.3743
ccagccuccUUCAGUUUGA	chrX:45721941-45722176(+)$1	235	42	61	13.3589
GCUUUGGAAUUAAAGAGGG	chr5:104513928-104514170(-)$1	242	124	143	13.0841
CAGUUGACUCUGGAAUUGU	chr11:41960533-41960768(-)$1	235	144	163	13.3657
GGGAGGAGAAAGAUAGCCU	chr3:146395453-146395688(-)$1	235	136	155	13.2094
GAUGAUGUUGACUUCUUUU	chr5:137736972-137737209(-)$1	237	130	149	13.4402
AGAAUUGCUUUCUGUUCUC	chr11:41946818-41947090(-)$1	272	150	169	12.5010
UGGACUCUUUGCUGUUGAU	chr8:96491846-96492107(+)$1	261	94	113	13.9843
ACGGCGAGAUUAAGCUGGU	chr10:126675733-126675988(-)$1	255	171	190	11.2207
GAGCCUUUUAACCGGCCGU	chr5:131921174-131921409(-)$1	235	56	75	13.6243
GGCUUCUAUAGAUAGGCCC	chr11:50014060-50014371(-)$1	311	139	158	12.5010
UCUUUGCAGAAAAAAAGGU	chr6:36693305-36693540(-)$1	235	31	50	13.7968
UCCUGUAUUCCUUCAGACA	chr11:49502571-49502808(-)$1	237	32	51	13.4508
CCCCCACAGCACCGGGUGG	chr11:94853627-94853890(+)$1	263	62	81	13.8780
CUUCACAGCUCAAUGAUUG	chr8:56140641-56140894(+)$1	253	160	179	13.8602
AUCAUACACUAAAUUAUGA	chr1:83273913-83274169(-)$1	256	50	69	10.9433

#DB
(((((........))))).	chr19:4726530-4726776(+)$1	1	207	226	13.0189
..(((........))))))	chr14:65673532-65673769(-)$1	1	12	31	14.0049
(((((........))))))	chr18:50024647-50024885(+)$1	1	9	28	12.5010
(((((........)))))(	chrX:162824888-162825125(+)$1	1	119	138	13.7369
(.(((........))))))	chr15:3987046-3987281(+)$1	1	75	94	13.7654
(((((........))))))	chr15:96414691-96414926(-)$1	1	71	90	13.7478
.((((........))))..	chr6:4706066-4706310(+)$1	1	76	95	11.5057
(((.(........).))))	chr19:10058959-10059195(+)$1	1	54	73	13.5437
((.((........)).)))	chr2:25077838-25078075(-)$1	1	21	40	13.6862
(((((........))))))	chr14:76818619-76818854(+)$1	1	195	214	13.3657
(((.(........).))))	chrX:133369561-133369797(+)$1	1	83	102	13.9115
(..((........))..))	chr10:34018422-34018682(+)$1	1	16	35	13.2926
(((.(........).))))	chr2:34631511-34631748(+)$1	1	174	193	12.9345
(((((........))))))	chr11:86602657-86602898(-)$1	1	107	126	13.7105
(((((........))).))	chr9:30959798-30960060(-)$1	1	86	105	13.9755
((.((........))))))	chr11:5774281-5774520(-)$1	1	112	131	13.4508
(((((........))))))	chr11:100888528-100888792(+)$1	1	22	41	12.5010
(..((........))..))	chr13:74168748-74168984(+)$1	1	154	173	13.2926
.((((........))))))	chr11:68620525-68620761(+)$1	1	210	229	13.7955
((.((........)).)))	chr19:10058659-10058899(+)$1	1	150	169	13.4402
.(((((........)))))	chr13:100195648-100195890(-)$1	1	148	167	10.9433
.(((((........)))))	chrX:162824700-162824996(+)$1	1	2	21	10.9433
(.(((........))).))	chr10:53063680-53063917(+)$1	1	215	234	13.9693
.((((........))))..	chr9:95945897-95946132(+)$1	1	1	20	11.5057
(((.(........).))))	chr5:29619320-29619555(-)$1	1	116	135	13.6354
..(((........)))..)	chr6:4591853-4592090(+)$1	1	194	213	13.6703
.((((........)))).(	chr10:57236816-57237127(-)$1	1	148	167	12.1465
(((((........))))).	chr10:126699751-126699986(-)$1	1	112	131	13.0189
.((((........))))..	chr15:27701031-27701272(-)$1	1	35	54	13.9531
.((((........))))))	chr19:7289793-7290030(-)$1	1	110	129	11.2207
((.((........)).))(	chr3:19968893-19969128(+)$1	1	121	140	12.5128
(((((........))))).	chr19:47331845-47332080(+)$1	1	159	178	13.7968
((.((........)).)).	chr2:181041364-181041632(-)$1	1	55	74	12.5176
.(.((........)).).)	chr11:78138010-78138267(+)$1	1	190	209	13.4454
...((........))....	chr2:129444097-129444360(+)$1	1	89	108	13.3460
(((((........))))).	chrX:12738488-12738723(+)$1	1	171	190	13.0189
.((((........))))..	chr7:118217767-118218002(-)$1	1	134	153	13.9343
.(((((........)))))	chr15:79555743-79555980(-)$1	1	2	21	10.9433
(((((........)))).)	chr6:97128843-97129081(-)$1	1	11	30	13.6080
(((.(........))))).	chr5:72015103-72015349(-)$1	1	16	35	13.8349
(((.(........).))))	chr7:104877404-104877644(-)$1	1	195	214	13.9115
))(((........)))(((	chr11:109528789-109529095(+)$1	1	257	276	13.7433
(((((........))))))	chr10:76784989-76785224(-)$1	1	201	220	13.3657
..(((........)))...	chr10:126680660-126680895(-)$1	1	72	91	14.0506
...((........))...)	chr11:118355369-118355606(-)$1	1	116	135	13.3640
(((((........)))))(	chrX:162824810-162825047(+)$1	1	197	216	13.7369
.((((........))))..	chrX:141894531-141894792(-)$1	1	64	83	12.3303
(((((........))))..	chr4:57722929-57723172(+)$1	1	65	84	13.3743
(.(((........))).))	chrX:45721941-45722176(+)$1	1	42	61	13.3589
.((((........))))((	chr5:104513928-104514170(-)$1	1	124	143	13.0841
(((((........))))))	chr11:41960533-41960768(-)$1	1	144	163	13.3657
((..(........)..)))	chr3:146395453-146395688(-)$1	1	136	155	13.2094
((.((........)).)))	chr5:137736972-137737209(-)$1	1	130	149	13.4402
(((((........))))))	chr11:41946818-41947090(-)$1	1	150	169	12.5010
(.(((........))).))	chr8:96491846-96492107(+)$1	1	94	113	13.9843
.((((........))))))	chr10:126675733-126675988(-)$1	1	171	190	11.2207
(((((........)))..)	chr5:131921174-131921409(-)$1	1	56	75	13.6243
(((((........))))))	chr11:50014060-50014371(-)$1	1	139	158	12.5010
(((((........))))).	chr6:36693305-36693540(-)$1	1	31	50	13.7968
((.((........))))))	chr11:49502571-49502808(-)$1	1	32	51	13.4508
(((((........))).))	chr11:94853627-94853890(+)$1	1	62	81	13.8780
..(((........)))..)	chr8:56140641-56140894(+)$1	1	160	179	13.8602
.(((((........)))))	chr1:83273913-83274169(-)$1	1	50	69	10.9433

#PSSM
e : 0.20	: : 0.15	d : 0.14	c : 0.09	f : 0.07	g : 0.06	" : 0.06	b : 0.04	# : 0.04	! : 0.03	[ : 0.03	i : 0.01	= : 0.01	
d : 0.28	e : 0.25	f : 0.07	! : 0.06	[ : 0.06	g : 0.06	c : 0.04	" : 0.03	b : 0.03	# : 0.03	i : 0.01	= : 0.01	a : 0.01	
e : 0.22	d : 0.22	c : 0.19	[ : 0.12	f : 0.07	g : 0.04	! : 0.04	i : 0.01	= : 0.01	# : 0.01	" : 0.01	
e : 0.19	c : 0.19	d : 0.19	b : 0.19	[ : 0.09	f : 0.06	g : 0.04	= : 0.01	! : 0.01	
e : 0.19	c : 0.19	d : 0.19	b : 0.19	a : 0.11	f : 0.06	g : 0.04	= : 0.01	
q : 0.93	e : 0.06	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.19	d : 0.19	b : 0.19	e : 0.12	a : 0.11	f : 0.06	q : 0.06	g : 0.04	= : 0.01	
d : 0.20	e : 0.19	c : 0.19	b : 0.19	] : 0.07	f : 0.06	g : 0.04	= : 0.01	2 : 0.01	
d : 0.25	e : 0.22	c : 0.19	] : 0.09	f : 0.07	g : 0.04	2 : 0.04	i : 0.01	= : 0.01	4 : 0.01	3 : 0.01	
d : 0.30	e : 0.23	f : 0.07	g : 0.07	2 : 0.07	] : 0.07	b : 0.03	3 : 0.03	c : 0.01	i : 0.01	= : 0.01	a : 0.01	4 : 0.01	
e : 0.28	d : 0.11	c : 0.09	f : 0.07	g : 0.07	2 : 0.06	3 : 0.06	: : 0.04	b : 0.04	C : 0.03	] : 0.03	i : 0.01	= : 0.01	4 : 0.01	5 : 0.01	
e : 0.19	c : 0.14	d : 0.11	f : 0.09	g : 0.09	: : 0.07	] : 0.06	3 : 0.04	a : 0.03	C : 0.03	b : 0.03	i : 0.01	= : 0.01	4 : 0.01	5 : 0.01	2 : 0.01	

#score	827.2443656660079
#seq	63
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_CDS_m3_run2.txt

#BEAR
gggggggnnnnnggggggg	chr1:58476928-58477273(-)$1	345	304	323	11.6348
eeeee[annnnna]eeeee	chr2:121174016-121174334(-)$1	318	242	261	10.5646
ddd[cccnnnnnccc]ddd	chr11:92961241-92961729(+)$1	488	160	179	11.4255
!!bb[bbnnnnnbb]bbee	chr2:115888705-115889133(-)$1	428	359	378	10.9737
fff[cccnnnnncccffff	chr17:66321492-66321809(-)$1	317	262	281	11.3649
=======nnnnn=======	chrX:12192836-12193290(+)$1	454	147	166	11.8095
dddd[bbnnnnnbb]dddd	chr17:33806746-33807199(-)$1	453	396	415	11.6474
dd[a[bbnnnnnbb]a]dd	chr18:61086560-61086783(+)$1	223	133	152	11.8077
!!cccbbnnnnnbb]ccc2	chr18:36957489-36957940(+)$1	451	93	112	11.9997
dddd[bbnnnnnbb]dddd	chr17:75040679-75041079(+)$1	400	347	366	11.6474
dddd[bbnnnnnbb]dddd	chr4:117225471-117225810(+)$1	339	304	323	11.6474
gggg[bbnnnnnbbggggg	chr3:90058866-90059346(+)$1	480	307	326	12.1375
dd"""bbnnnnnbb22ddd	chr5:122906860-122907274(-)$1	414	382	401	11.0681
gggggggnnnnnggggggg	chr15:82967737-82968034(-)$1	297	189	208	11.6348
ddd[cccnnnnncccdddd	chr12:68322051-68322546(-)$1	495	438	457	11.3861
iiiiiiinnnnniiiiiii	chr2:11401497-11401837(-)$1	340	185	204	11.3852
ddd[cccnnnnncccdddd	chr13:38071453-38071754(-)$1	301	162	181	11.3861
dddd[bbnnnnnbb]dddd	chr4:134029029-134029351(+)$1	322	273	292	11.6474
cceeeeennnnneeeee33	chr11:103774433-103774794(-)$1	361	295	314	10.2643
ffff[bbnnnnnbb]ffff	chr17:10406115-10406612(-)$1	497	300	319	11.7232
e[eeeeennnnneeeee]e	chr13:9694301-9694673(-)$1	372	215	234	10.0436
"bb[cccnnnnnccc]bb3	chr9:53400103-53400486(-)$1	383	287	306	10.7321
dd!!cccnnnnnccc22dd	chr1:166368154-166368590(-)$1	436	370	389	11.0610
effffffnnnnnffffffF	chr5:148354363-148354769(+)$1	406	197	216	10.6766
cffffffnnnnnffffff:	chr4:101296290-101296695(+)$1	405	152	171	10.2771
fff!!bbnnnnnbb22fff	chr17:35272358-35272734(+)$1	376	184	203	11.1757
ee!!cccnnnnnccceeee	chr3:84771346-84771693(+)$1	347	267	286	11.4164
cc[ddddnnnnnddddccc	chr10:59761746-59761997(+)$1	251	2	21	10.1182
!!bb[bbnnnnnbb]bb22	chr17:17976503-17976850(+)$1	347	99	118	10.7344
cc!!cccnnnnnccc22cc	chr7:31408366-31408578(-)$1	212	94	113	11.1228
#ffffffnnnnnffffff5	chr9:118482006-118482369(+)$1	363	209	228	10.5581
ddd[cccnnnnncccdddd	chr9:72860606-72860915(+)$1	309	166	185	11.3861
=======nnnnn=======	chr10:128393667-128394158(+)$1	491	76	95	11.8095
"ffffffnnnnnffffff4	chr3:101387700-101388008(-)$1	308	254	273	11.3313
gggggggnnnnnggggggg	chr5:115886085-115886343(+)$1	258	159	178	11.6348
[ccc[bbnnnnnbb]ccc]	chr11:50199217-50199454(+)$1	237	70	89	12.1613
'ffffffnnnnnffffff5	chr3:33712932-33713313(+)$1	381	255	274	9.9597
#ffffffnnnnnffffff3	chr11:100879794-100880019(+)$1	225	159	178	11.3763
ccc[cccnnnnnccc]ccc	chr7:71879400-71879781(+)$1	381	51	70	11.6441
eeeee[annnnna]eeeee	chrX:12680443-12680746(+)$1	303	49	68	10.5646
"ddddbbnnnnnbb]dddd	chr3:89812042-89812351(-)$1	309	186	205	11.3864
:ccc[bbnnnnnbb]ccc:	chr12:100036914-100037312(-)$1	398	97	116	10.1824
gggggggnnnnnggggggg	chrX:34144707-34145186(+)$1	479	459	478	11.6348
gggggggnnnnnggggggg	chr7:104854114-104854439(+)$1	325	243	262	11.6348
gggggggnnnnnggggggg	chr2:167332502-167332848(+)$1	346	292	311	11.6348
eeeeebbnnnnnbb]eeee	chr14:73768027-73768310(-)$1	283	75	94	11.3725
gggggggnnnnnggggggg	chr7:16725526-16726008(+)$1	482	373	392	11.6348
dd[ddddnnnnndddd]dd	chr1:63603899-63604110(+)$1	211	176	195	9.9811
+ffffffnnnnnffffff>	chr10:31670723-31670965(-)$1	242	65	84	10.4250
ddd[cccnnnnncccdddd	chr9:107463758-107464071(+)$1	313	152	171	11.3861
dffffffnnnnnffffff]	chr8:47292623-47293054(-)$1	431	143	162	11.2258
gggggggnnnnnggggggg	chr2:32279048-32279470(-)$1	422	385	404	11.6348
c!!ddddnnnnnddddccc	chr6:113441918-113442267(+)$1	349	13	32	10.1293
dd[ddddnnnnnddddddd	chr7:31226029-31226240(-)$1	211	166	185	9.9867
eeee[bbnnnnnbb]eeee	chr1:181675201-181675689(-)$1	488	242	261	11.6618
c"""cccnnnnncccccc]	chrX:162817849-162818181(+)$1	332	69	88	11.4768
""ccc[annnnna]ccc22	chr15:95071752-95072172(-)$1	420	296	315	10.8556
!ffffffnnnnnffffff3	chr6:113687873-113688205(-)$1	332	140	159	11.4699
gggggbbnnnnnbb]gggg	chr1:172810686-172811097(-)$1	411	43	62	12.1709
b[ccc[annnnna]ccc33	chr5:45190627-45190944(-)$1	317	59	78	11.0452
"ffffffnnnnnffffff3	chr12:15816293-15816638(-)$1	345	58	77	11.4129

#otherMatches

#Seq PSSM
AAGAUGUAUAGAAUAUUUU	chr1:58476928-58477273(-)$1	345	304	323	11.6348
CUUUAGUACUCAAGUAAAG	chr2:121174016-121174334(-)$1	318	242	261	10.5646
CUGGCCGGCUGUCGGGUGG	chr11:92961241-92961729(+)$1	488	160	179	11.4255
UGAGGAGACAGACUGCUUG	chr2:115888705-115889133(-)$1	428	359	378	10.9737
ucccagacuaguucuggac	chr17:66321492-66321809(-)$1	317	262	281	11.3649
GAUUCGAAUAGAUUGAAUU	chrX:12192836-12193290(+)$1	454	147	166	11.8095
CCCAAUUUGGAUAACUGGG	chr17:33806746-33807199(-)$1	453	396	415	11.6474
ACUCUCAGUGAAugugugu	chr18:61086560-61086783(+)$1	223	133	152	11.8077
GAGAGCCGAGGAGGACUUG	chr18:36957489-36957940(+)$1	451	93	112	11.9997
CCAUAUCAGUUGGAGAUGG	chr17:75040679-75041079(+)$1	400	347	366	11.6474
UAGUGAAACAAAUUGGCUA	chr4:117225471-117225810(+)$1	339	304	323	11.6474
GGGAUGUGCUGAACUCUCU	chr3:90058866-90059346(+)$1	480	307	326	12.1375
GUUCUGUUUAAUACUCAUA	chr5:122906860-122907274(-)$1	414	382	401	11.0681
CUUGACGAGAUCUGUUAGG	chr15:82967737-82968034(-)$1	297	189	208	11.6348
GCGCGCCUUGCUGGCCGCU	chr12:68322051-68322546(-)$1	495	438	457	11.3861
UGAGAACAUACCGUUCUCA	chr2:11401497-11401837(-)$1	340	185	204	11.3852
CAGUGCAGCCUGUGCUUGC	chr13:38071453-38071754(-)$1	301	162	181	11.3861
GACUGAGGCUGACUAAGUU	chr4:134029029-134029351(+)$1	322	273	292	11.6474
CUGAUUGAUAUACAAUCUC	chr11:103774433-103774794(-)$1	361	295	314	10.2643
UGCAAUUUAACUAGGUGCG	chr17:10406115-10406612(-)$1	497	300	319	11.7232
AUGAUAGGUUGUUUAUCUU	chr13:9694301-9694673(-)$1	372	215	234	10.0436
CGGGAUGGAGAGCAUGUCC	chr9:53400103-53400486(-)$1	383	287	306	10.7321
CUACUGUAAAUGACAAAAG	chr1:166368154-166368590(-)$1	436	370	389	11.0610
GAAGAUUAGAUGAAUCUUG	chr5:148354363-148354769(+)$1	406	197	216	10.6766
GGUUGUCCACAAGACAACA	chr4:101296290-101296695(+)$1	405	152	171	10.2771
GGGGGCGGUCAGCGAGCCC	chr17:35272358-35272734(+)$1	376	184	203	11.1757
UUGAUCCCAACAGGAAAGG	chr3:84771346-84771693(+)$1	347	267	286	11.4164
GGAGCUUUACACGAGCCCU	chr10:59761746-59761997(+)$1	251	2	21	10.1182
gucugguuuauugcgagug	chr17:17976503-17976850(+)$1	347	99	118	10.7344
GUGUGUGAGUGGUACCGGC	chr7:31408366-31408578(-)$1	212	94	113	11.1228
AUGGGCAGAUUGUGUUCAC	chr9:118482006-118482369(+)$1	363	209	228	10.5581
CCCAUUCCACCAGAAGGGU	chr9:72860606-72860915(+)$1	309	166	185	11.3861
CUCGGCCAUGGAGGCUGGG	chr10:128393667-128394158(+)$1	491	76	95	11.8095
GGGGGUAGGCAUUAUCUCA	chr3:101387700-101388008(-)$1	308	254	273	11.3313
CGCUUGAGUGUUUCAGGUG	chr5:115886085-115886343(+)$1	258	159	178	11.6348
GAGCAGUGAACAGCAGCUA	chr11:50199217-50199454(+)$1	237	70	89	12.1613
UCUGAAAGAAUAUUUCAGU	chr3:33712932-33713313(+)$1	381	255	274	9.9597
UCCGUAUGUGCAAUGUGGU	chr11:100879794-100880019(+)$1	225	159	178	11.3763
AGUUGGAGUUCUUCCUAUU	chr7:71879400-71879781(+)$1	381	51	70	11.6441
GAGAUGGGCUAACGAUCUC	chrX:12680443-12680746(+)$1	303	49	68	10.5646
UGACCCUUGCUUAGUGGUC	chr3:89812042-89812351(-)$1	309	186	205	11.3864
CGAGCUCUCUUUGAACUUU	chr12:100036914-100037312(-)$1	398	97	116	10.1824
UUUUCCUGAGAGAGGGAAA	chrX:34144707-34145186(+)$1	479	459	478	11.6348
GGCCCUGAGCUCCAGGGCU	chr7:104854114-104854439(+)$1	325	243	262	11.6348
UGCAUGCCUGCUGUGUGUG	chr2:167332502-167332848(+)$1	346	292	311	11.6348
GGACCCGGGUGACGUGGUU	chr14:73768027-73768310(-)$1	283	75	94	11.3725
GUUUGCCUGGAUGGCGGAC	chr7:16725526-16726008(+)$1	482	373	392	11.6348
CAUUGUAUCUUUUAUAUUG	chr1:63603899-63604110(+)$1	211	176	195	9.9811
CUUCUAGUGUUUCUGGAAU	chr10:31670723-31670965(-)$1	242	65	84	10.4250
GCAGUGCAAAGAGCGUGCC	chr9:107463758-107464071(+)$1	313	152	171	11.3861
ACGCUUUCUUCAAAGGUGC	chr8:47292623-47293054(-)$1	431	143	162	11.2258
AAUCUCUAGAUAGGAGAUU	chr2:32279048-32279470(-)$1	422	385	404	11.6348
CGCUGCAAAAAGUGCAGCC	chr6:113441918-113442267(+)$1	349	13	32	10.1293
GGUAGGAcuccuuccuccu	chr7:31226029-31226240(-)$1	211	166	185	9.9867
GUGUGUAAUGAAUGGACGC	chr1:181675201-181675689(-)$1	488	242	261	11.6618
GUUCGUGUUCCUCACCUAU	chrX:162817849-162818181(+)$1	332	69	88	11.4768
AGUAAGAGUGAAUGUUGAA	chr15:95071752-95072172(-)$1	420	296	315	10.8556
AGAAGCAAUUGGUGCUUUA	chr6:113687873-113688205(-)$1	332	140	159	11.4699
AGAGGCUAAGUGAGUCCUC	chr1:172810686-172811097(-)$1	411	43	62	12.1709
CUCAgccugccugccugcc	chr5:45190627-45190944(-)$1	317	59	78	11.0452
CUGUGGCCCAUUGCCACGA	chr12:15816293-15816638(-)$1	345	58	77	11.4129

#DB
(((((((.....)))))))	chr1:58476928-58477273(-)$1	1	304	323	11.6348
(((((.(.....).)))))	chr2:121174016-121174334(-)$1	1	242	261	10.5646
(((.(((.....))).)))	chr11:92961241-92961729(+)$1	1	160	179	11.4255
..((.((.....)).))))	chr2:115888705-115889133(-)$1	1	359	378	10.9737
(((.(((.....)))))))	chr17:66321492-66321809(-)$1	1	262	281	11.3649
(((((((.....)))))))	chrX:12192836-12193290(+)$1	1	147	166	11.8095
((((.((.....)).))))	chr17:33806746-33807199(-)$1	1	396	415	11.6474
((.(.((.....)).).))	chr18:61086560-61086783(+)$1	1	133	152	11.8077
..(((((.....)).))).	chr18:36957489-36957940(+)$1	1	93	112	11.9997
((((.((.....)).))))	chr17:75040679-75041079(+)$1	1	347	366	11.6474
((((.((.....)).))))	chr4:117225471-117225810(+)$1	1	304	323	11.6474
((((.((.....)))))))	chr3:90058866-90059346(+)$1	1	307	326	12.1375
((...((.....))..)))	chr5:122906860-122907274(-)$1	1	382	401	11.0681
(((((((.....)))))))	chr15:82967737-82968034(-)$1	1	189	208	11.6348
(((.(((.....)))))))	chr12:68322051-68322546(-)$1	1	438	457	11.3861
(((((((.....)))))))	chr2:11401497-11401837(-)$1	1	185	204	11.3852
(((.(((.....)))))))	chr13:38071453-38071754(-)$1	1	162	181	11.3861
((((.((.....)).))))	chr4:134029029-134029351(+)$1	1	273	292	11.6474
(((((((.....)))))..	chr11:103774433-103774794(-)$1	1	295	314	10.2643
((((.((.....)).))))	chr17:10406115-10406612(-)$1	1	300	319	11.7232
(.(((((.....))))).)	chr13:9694301-9694673(-)$1	1	215	234	10.0436
.((.(((.....))).)).	chr9:53400103-53400486(-)$1	1	287	306	10.7321
((..(((.....)))..))	chr1:166368154-166368590(-)$1	1	370	389	11.0610
)((((((.....)))))))	chr5:148354363-148354769(+)$1	1	197	216	10.6766
)((((((.....)))))).	chr4:101296290-101296695(+)$1	1	152	171	10.2771
(((..((.....))..)))	chr17:35272358-35272734(+)$1	1	184	203	11.1757
((..(((.....)))))))	chr3:84771346-84771693(+)$1	1	267	286	11.4164
((.((((.....)))))))	chr10:59761746-59761997(+)$1	1	2	21	10.1182
..((.((.....)).))..	chr17:17976503-17976850(+)$1	1	99	118	10.7344
((..(((.....)))..))	chr7:31408366-31408578(-)$1	1	94	113	11.1228
.((((((.....)))))).	chr9:118482006-118482369(+)$1	1	209	228	10.5581
(((.(((.....)))))))	chr9:72860606-72860915(+)$1	1	166	185	11.3861
(((((((.....)))))))	chr10:128393667-128394158(+)$1	1	76	95	11.8095
.((((((.....)))))).	chr3:101387700-101388008(-)$1	1	254	273	11.3313
(((((((.....)))))))	chr5:115886085-115886343(+)$1	1	159	178	11.6348
.(((.((.....)).))).	chr11:50199217-50199454(+)$1	1	70	89	12.1613
.((((((.....)))))).	chr3:33712932-33713313(+)$1	1	255	274	9.9597
.((((((.....)))))).	chr11:100879794-100880019(+)$1	1	159	178	11.3763
(((.(((.....))).)))	chr7:71879400-71879781(+)$1	1	51	70	11.6441
(((((.(.....).)))))	chrX:12680443-12680746(+)$1	1	49	68	10.5646
.((((((.....)).))))	chr3:89812042-89812351(-)$1	1	186	205	11.3864
.(((.((.....)).))).	chr12:100036914-100037312(-)$1	1	97	116	10.1824
(((((((.....)))))))	chrX:34144707-34145186(+)$1	1	459	478	11.6348
(((((((.....)))))))	chr7:104854114-104854439(+)$1	1	243	262	11.6348
(((((((.....)))))))	chr2:167332502-167332848(+)$1	1	292	311	11.6348
(((((((.....)).))))	chr14:73768027-73768310(-)$1	1	75	94	11.3725
(((((((.....)))))))	chr7:16725526-16726008(+)$1	1	373	392	11.6348
((.((((.....)))).))	chr1:63603899-63604110(+)$1	1	176	195	9.9811
.((((((.....)))))).	chr10:31670723-31670965(-)$1	1	65	84	10.4250
(((.(((.....)))))))	chr9:107463758-107464071(+)$1	1	152	171	11.3861
(((((((.....)))))).	chr8:47292623-47293054(-)$1	1	143	162	11.2258
(((((((.....)))))))	chr2:32279048-32279470(-)$1	1	385	404	11.6348
(..((((.....)))))))	chr6:113441918-113442267(+)$1	1	13	32	10.1293
((.((((.....)))))))	chr7:31226029-31226240(-)$1	1	166	185	9.9867
((((.((.....)).))))	chr1:181675201-181675689(-)$1	1	242	261	11.6618
(...(((.....)))))).	chrX:162817849-162818181(+)$1	1	69	88	11.4768
..(((.(.....).)))..	chr15:95071752-95072172(-)$1	1	296	315	10.8556
.((((((.....)))))).	chr6:113687873-113688205(-)$1	1	140	159	11.4699
(((((((.....)).))))	chr1:172810686-172811097(-)$1	1	43	62	12.1709
(.(((.(.....).)))..	chr5:45190627-45190944(-)$1	1	59	78	11.0452
.((((((.....)))))).	chr12:15816293-15816638(-)$1	1	58	77	11.4129

#PSSM
d : 0.24	g : 0.16	e : 0.11	c : 0.11	" : 0.08	! : 0.06	f : 0.04	= : 0.03	# : 0.03	i : 0.01	[ : 0.01	' : 0.01	: : 0.01	+ : 0.01	b : 0.01	
d : 0.24	f : 0.21	g : 0.16	c : 0.09	e : 0.08	! : 0.06	= : 0.03	[ : 0.03	" : 0.03	i : 0.01	b : 0.01	
f : 0.21	g : 0.16	d : 0.16	e : 0.09	c : 0.09	[ : 0.06	! : 0.06	b : 0.04	= : 0.03	" : 0.03	i : 0.01	
f : 0.18	g : 0.16	d : 0.14	[ : 0.13	e : 0.09	c : 0.08	! : 0.06	b : 0.03	= : 0.03	" : 0.03	a : 0.01	i : 0.01	
c : 0.24	[ : 0.19	f : 0.16	g : 0.14	e : 0.08	d : 0.08	= : 0.03	" : 0.01	i : 0.01	! : 0.01	
b : 0.29	c : 0.19	f : 0.16	g : 0.13	[ : 0.06	d : 0.06	= : 0.03	e : 0.03	i : 0.01	
b : 0.29	c : 0.19	f : 0.16	g : 0.13	a : 0.06	d : 0.06	= : 0.03	e : 0.03	i : 0.01	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
b : 0.29	c : 0.19	f : 0.16	g : 0.13	a : 0.06	d : 0.06	= : 0.03	e : 0.03	i : 0.01	
b : 0.29	c : 0.19	f : 0.16	g : 0.13	] : 0.06	d : 0.06	= : 0.03	e : 0.03	i : 0.01	
] : 0.24	c : 0.22	f : 0.16	g : 0.14	e : 0.06	d : 0.06	= : 0.03	2 : 0.03	i : 0.01	
d : 0.21	f : 0.19	g : 0.16	e : 0.11	c : 0.09	2 : 0.06	] : 0.04	b : 0.03	= : 0.03	a : 0.01	i : 0.01	
f : 0.21	d : 0.19	g : 0.16	c : 0.14	e : 0.11	b : 0.04	= : 0.03	] : 0.03	2 : 0.03	i : 0.01	
d : 0.24	f : 0.21	g : 0.16	c : 0.13	e : 0.09	= : 0.03	3 : 0.03	2 : 0.03	i : 0.01	] : 0.01	b : 0.01	
d : 0.24	g : 0.16	e : 0.11	3 : 0.09	c : 0.06	f : 0.04	2 : 0.04	] : 0.04	= : 0.03	: : 0.03	5 : 0.03	i : 0.01	F : 0.01	4 : 0.01	> : 0.01	

#score	683.2839279968985
#seq	61
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_UTR_m3_run1.txt

#BEAR
iiiiiiiooooooiiiiii	chr16:98170643-98170924(-)$1	281	122	141	7.4976
gggggggmmmmggggggg9	chr4:140669579-140669861(-)$1	282	217	236	9.9162
gggggggoooooogggggg	chr16:98014687-98014959(-)$1	272	69	88	7.8453
fff!!bbmmmmbbffffff	chr18:34930992-34931266(+)$1	274	131	150	7.8698
ffff!!ammmma22fffff	chr7:24891396-24891687(+)$1	291	169	188	8.1723
gggggggmmmmggggggg4	chr15:80761852-80762143(+)$1	291	254	273	10.6054
fff[cccmmmmccc22fff	chr17:32498259-32498531(-)$1	272	93	112	8.4344
cggggggglllgggggggc	chr11:114729900-114730186(+)$1	286	46	65	7.9389
f[eeeeemmmmeeeee]ff	chr6:140599401-140599683(+)$1	282	90	109	8.9688
gggggggmmmmggggggg]	chr7:25670028-25670303(+)$1	275	161	180	10.7081
dffffffmmmmffffff]d	chr6:136757209-136757498(+)$1	289	182	201	8.6393
gggggggmmmmggggggg3	chr7:151775188-151775456(-)$1	268	30	49	10.7318
iiiiiiimmmmiiiiiiii	chr2:32162879-32163158(+)$1	279	142	161	10.2298
c[eeeeemmmmeeeeeccc	chr9:90098128-90098412(-)$1	284	19	38	8.9998
effffffmmmmffffff33	chr19:8964904-8965185(+)$1	281	171	190	9.0250
iiiiiiimmmmiiiiiiii	chr4:133831673-133831946(-)$1	273	17	36	10.2298
[ffffffmmmmffffff]d	chr10:76508552-76508827(+)$1	275	19	38	9.0201
gggggggmmmmggggggg]	chr7:30106095-30106365(-)$1	270	97	116	10.7081
=======mmmm========	chr4:99324902-99325179(+)$1	277	194	213	10.4203
gggggggmmmmggggggg:	chr1:62843122-62843399(+)$1	277	160	179	9.7459
[a[ddddmmmmddddaccc	chr6:140543075-140543349(+)$1	274	143	162	7.4119
d[eeeeemmmmeeeee]dd	chr11:68923114-68923385(+)$1	271	15	34	8.5875
=======mmmm========	chr9:30881664-30881966(+)$1	302	180	199	10.4203
gggggggmmmmggggggg:	chr11:117828673-117828941(-)$1	268	36	55	9.7459
a[eeeeemmmmeeeee]a]	chr17:6084525-6084794(+)$1	269	242	261	9.0802
f[eeeeemmmmeeeee]ff	chr6:140599338-140599620(+)$1	282	153	172	8.9688
eeee!!ammmma22eeeee	chr14:99472889-99473185(+)$1	296	178	197	7.6686
gggggggmmmmgggggggg	chr5:123809705-123809975(+)$1	270	85	104	10.6102
c[cccbbmmmmbb]ccccc	chr15:80761597-80761877(+)$1	280	205	224	7.8317
c[eeeeemmmmeeeeeccc	chr2:144232685-144232982(+)$1	297	135	154	8.9998
!ffffffmmmmffffff22	chr2:157383309-157383584(-)$1	275	117	136	8.8098
iiiiiiimmmmiiiiiiii	chr2:32134292-32134583(-)$1	291	191	210	10.2298
gggggggmmmmggggggg:	chr11:117828728-117829006(-)$1	278	101	120	9.7459
c[eeeeemmmmeeeee]cc	chr2:14999759-15000046(+)$1	287	57	76	9.1582
iiiiiiimmmmiiiiiiii	chr2:31071139-31071424(+)$1	285	159	178	10.2298
[ggggggglllggggggg]	chr3:122242267-122242549(-)$1	282	144	163	8.2394
gggggggoooooogggggg	chr15:81678793-81679067(-)$1	274	183	202	7.8453
g"""cccmmmmccc22ggg	chr16:92084365-92084642(+)$1	277	147	166	8.6647
hh!!cccmmmmccchhhhh	chr3:108163830-108164132(+)$1	302	12	31	8.3188
[ffffffmmmmffffff]c	chr15:102261453-102261755(+)$1	302	108	127	9.1919
[bb[cccmmmmcccbb]dd	chr4:63211331-63211605(+)$1	274	237	256	7.7030
[ffffffmmmmffffff22	chr9:60586481-60586749(+)$1	268	101	120	8.8824
gggggggmmmmggggggg2	chr4:135560383-135560657(-)$1	274	198	217	10.5052
!!eeeeemmmmeeeee22c	chr19:5456362-5456644(-)$1	282	243	262	8.6512
eee[cccmmmmccc]eeee	chr4:33125089-33125363(+)$1	274	211	230	8.4972
ccc[cccmmmmccc]cccG	chr14:71003925-71004204(-)$1	279	43	62	8.3692

#otherMatches

#Seq PSSM
CUGAGUAGUGGGAUGCUUG	chr16:98170643-98170924(-)$1	281	122	141	7.4976
UUUGUAGUUGUCUAUAAAU	chr4:140669579-140669861(-)$1	282	217	236	9.9162
UACAGAGGUUCAGCUCUGU	chr16:98014687-98014959(-)$1	272	69	88	7.8453
GGAAGGCAGUUGCUCCUUU	chr18:34930992-34931266(+)$1	274	131	150	7.8698
GCUUCUCUGUUGCAAAGCU	chr7:24891396-24891687(+)$1	291	169	188	8.1723
GUUGGGUAUAAACCUAGCU	chr15:80761852-80762143(+)$1	291	254	273	10.6054
CCCAGUCUGAGGAUGAGGG	chr17:32498259-32498531(-)$1	272	93	112	8.4344
CAAGAUCUCUCAGGUCUUU	chr11:114729900-114730186(+)$1	286	46	65	7.9389
GAAUAUAUUAAUAUAUACU	chr6:140599401-140599683(+)$1	282	90	109	8.9688
GGAGUUCGUCAGAGCUCUG	chr7:25670028-25670303(+)$1	275	161	180	10.7081
AGGCCACCUGUGUGGCCAU	chr6:136757209-136757498(+)$1	289	182	201	8.6393
CUUCUGGGAGCUCAGAAGU	chr7:151775188-151775456(-)$1	268	30	49	10.7318
GCAGUUGGGGCUAACUGCC	chr2:32162879-32163158(+)$1	279	142	161	10.2298
GACAGUGGUCUUACUGCUA	chr9:90098128-90098412(-)$1	284	19	38	8.9998
AAAAUAUUAGCAUAUUUCA	chr19:8964904-8965185(+)$1	281	171	190	9.0250
ACAGGGAUUUGUCUUUGUu	chr4:133831673-133831946(-)$1	273	17	36	10.2298
UUGGUUUCCCUGGGCCAUA	chr10:76508552-76508827(+)$1	275	19	38	9.0201
auauauauauauauauauu	chr7:30106095-30106365(-)$1	270	97	116	10.7081
UAUUUUUUUAAGAAAAUAA	chr4:99324902-99325179(+)$1	277	194	213	10.4203
AUCUAGCUCUGGCUGGGUU	chr1:62843122-62843399(+)$1	277	160	179	9.7459
AGAGUUAGGAAUGACCAGU	chr6:140543075-140543349(+)$1	274	143	162	7.4119
AAGCUGCUGAAGUGGUCUG	chr11:68923114-68923385(+)$1	271	15	34	8.5875
AUUUUGUUUAUACAAAAUG	chr9:30881664-30881966(+)$1	302	180	199	10.4203
AUUCGGGAGUUCCUGGAUC	chr11:117828673-117828941(-)$1	268	36	55	9.7459
CAUUCAUUCAGAUGAAAGC	chr17:6084525-6084794(+)$1	269	242	261	9.0802
GAAUAUAUUAAUAUAUACU	chr6:140599338-140599620(+)$1	282	153	172	8.9688
uaaauuauguuuuuuuuaa	chr14:99472889-99473185(+)$1	296	178	197	7.6686
UCUGGGUCCUGGCCUGGGG	chr5:123809705-123809975(+)$1	270	85	104	10.6102
AUGAAGUGCCGACAUUCUG	chr15:80761597-80761877(+)$1	280	205	224	7.8317
CUAAgcugaagaguuugag	chr2:144232685-144232982(+)$1	297	135	154	8.9998
UGGCACUGAUCGGUGCUUC	chr2:157383309-157383584(-)$1	275	117	136	8.8098
AUACUUGUGAGUAGGUGUG	chr2:32134292-32134583(-)$1	291	191	210	10.2298
AUUCGGGAGUUCCUGGAUC	chr11:117828728-117829006(-)$1	278	101	120	9.7459
GUGUUGUAAAUAUAACUCA	chr2:14999759-15000046(+)$1	287	57	76	9.1582
UGGGGCAUUAGUGCUUUGU	chr2:31071139-31071424(+)$1	285	159	178	10.2298
GAGAAUGUGAAACGUUCUG	chr3:122242267-122242549(-)$1	282	144	163	8.2394
UUUUUUCUCUAGCGAAGGA	chr15:81678793-81679067(-)$1	274	183	202	7.8453
GGAACGGAGCUCUGCGCUG	chr16:92084365-92084642(+)$1	277	147	166	8.6647
auaaacuguauaguguaca	chr3:108163830-108164132(+)$1	302	12	31	8.3188
GAGGCAUUAAUGUGCUUGG	chr15:102261453-102261755(+)$1	302	108	127	9.1919
CCUUAGAGUACUCUAGCCU	chr4:63211331-63211605(+)$1	274	237	256	7.7030
aagaaauaaaaguuucuag	chr9:60586481-60586749(+)$1	268	101	120	8.8824
AGGGUGGAUGGUCACCCUG	chr4:135560383-135560657(-)$1	274	198	217	10.5052
ACGGUGGUAGACCACUAAC	chr19:5456362-5456644(-)$1	282	243	262	8.6512
UAACAGUAAGAGCUCUUGG	chr4:33125089-33125363(+)$1	274	211	230	8.4972
AGGUCGGUCUGCUGUCCUG	chr14:71003925-71004204(-)$1	279	43	62	8.3692

#DB
(((((((......))))))	chr16:98170643-98170924(-)$1	1	122	141	7.4976
(((((((....))))))).	chr4:140669579-140669861(-)$1	1	217	236	9.9162
(((((((......))))))	chr16:98014687-98014959(-)$1	1	69	88	7.8453
(((..((....))))))))	chr18:34930992-34931266(+)$1	1	131	150	7.8698
((((..(....)..)))))	chr7:24891396-24891687(+)$1	1	169	188	8.1723
(((((((....))))))).	chr15:80761852-80762143(+)$1	1	254	273	10.6054
(((.(((....)))..)))	chr17:32498259-32498531(-)$1	1	93	112	8.4344
)(((((((...)))))))(	chr11:114729900-114730186(+)$1	1	46	65	7.9389
(.(((((....))))).))	chr6:140599401-140599683(+)$1	1	90	109	8.9688
(((((((....))))))).	chr7:25670028-25670303(+)$1	1	161	180	10.7081
(((((((....)))))).)	chr6:136757209-136757498(+)$1	1	182	201	8.6393
(((((((....))))))).	chr7:151775188-151775456(-)$1	1	30	49	10.7318
(((((((....))))))))	chr2:32162879-32163158(+)$1	1	142	161	10.2298
(.(((((....))))))))	chr9:90098128-90098412(-)$1	1	19	38	8.9998
(((((((....))))))..	chr19:8964904-8965185(+)$1	1	171	190	9.0250
(((((((....))))))))	chr4:133831673-133831946(-)$1	1	17	36	10.2298
.((((((....)))))).)	chr10:76508552-76508827(+)$1	1	19	38	9.0201
(((((((....))))))).	chr7:30106095-30106365(-)$1	1	97	116	10.7081
(((((((....))))))))	chr4:99324902-99325179(+)$1	1	194	213	10.4203
(((((((....))))))).	chr1:62843122-62843399(+)$1	1	160	179	9.7459
.(.((((....))))))))	chr6:140543075-140543349(+)$1	1	143	162	7.4119
(.(((((....))))).))	chr11:68923114-68923385(+)$1	1	15	34	8.5875
(((((((....))))))))	chr9:30881664-30881966(+)$1	1	180	199	10.4203
(((((((....))))))).	chr11:117828673-117828941(-)$1	1	36	55	9.7459
(.(((((....))))).).	chr17:6084525-6084794(+)$1	1	242	261	9.0802
(.(((((....))))).))	chr6:140599338-140599620(+)$1	1	153	172	8.9688
((((..(....)..)))))	chr14:99472889-99473185(+)$1	1	178	197	7.6686
(((((((....)))))))(	chr5:123809705-123809975(+)$1	1	85	104	10.6102
(.(((((....)).)))))	chr15:80761597-80761877(+)$1	1	205	224	7.8317
(.(((((....))))))))	chr2:144232685-144232982(+)$1	1	135	154	8.9998
.((((((....))))))..	chr2:157383309-157383584(-)$1	1	117	136	8.8098
(((((((....))))))))	chr2:32134292-32134583(-)$1	1	191	210	10.2298
(((((((....))))))).	chr11:117828728-117829006(-)$1	1	101	120	9.7459
(.(((((....))))).))	chr2:14999759-15000046(+)$1	1	57	76	9.1582
(((((((....))))))))	chr2:31071139-31071424(+)$1	1	159	178	10.2298
.(((((((...))))))).	chr3:122242267-122242549(-)$1	1	144	163	8.2394
(((((((......))))))	chr15:81678793-81679067(-)$1	1	183	202	7.8453
(...(((....)))..)))	chr16:92084365-92084642(+)$1	1	147	166	8.6647
((..(((....))))))))	chr3:108163830-108164132(+)$1	1	12	31	8.3188
.((((((....)))))).)	chr15:102261453-102261755(+)$1	1	108	127	9.1919
.((.(((....))))).))	chr4:63211331-63211605(+)$1	1	237	256	7.7030
.((((((....))))))..	chr9:60586481-60586749(+)$1	1	101	120	8.8824
(((((((....))))))).	chr4:135560383-135560657(-)$1	1	198	217	10.5052
..(((((....)))))..)	chr19:5456362-5456644(-)$1	1	243	262	8.6512
(((.(((....))).))))	chr4:33125089-33125363(+)$1	1	211	230	8.4972
(((.(((....))).)))(	chr14:71003925-71004204(-)$1	1	43	62	8.3692

#PSSM
g : 0.28	c : 0.13	[ : 0.13	i : 0.10	f : 0.10	e : 0.06	d : 0.04	= : 0.04	! : 0.04	a : 0.02	h : 0.02	
g : 0.30	f : 0.19	[ : 0.17	i : 0.10	= : 0.04	e : 0.04	a : 0.02	" : 0.02	h : 0.02	b : 0.02	! : 0.02	c : 0.02	
g : 0.30	e : 0.21	f : 0.19	i : 0.10	= : 0.04	c : 0.04	[ : 0.02	" : 0.02	! : 0.02	b : 0.02	
g : 0.30	e : 0.19	f : 0.15	i : 0.10	[ : 0.08	! : 0.04	= : 0.04	d : 0.02	c : 0.02	" : 0.02	
g : 0.30	e : 0.17	c : 0.15	f : 0.13	i : 0.10	! : 0.06	= : 0.04	d : 0.02	
g : 0.30	e : 0.17	c : 0.13	f : 0.13	i : 0.10	b : 0.04	! : 0.04	= : 0.04	d : 0.02	
g : 0.30	e : 0.17	c : 0.13	f : 0.13	i : 0.10	b : 0.04	a : 0.04	= : 0.04	d : 0.02	
m : 0.89	o : 0.06	g : 0.04	
m : 0.89	o : 0.06	l : 0.04	
m : 0.89	o : 0.06	l : 0.04	
m : 0.89	o : 0.06	l : 0.04	
g : 0.26	e : 0.17	c : 0.13	f : 0.13	i : 0.08	o : 0.06	b : 0.04	a : 0.04	= : 0.04	d : 0.02	
g : 0.26	e : 0.17	c : 0.13	f : 0.13	i : 0.08	o : 0.06	b : 0.04	2 : 0.04	= : 0.04	d : 0.02	
g : 0.30	e : 0.17	f : 0.15	c : 0.13	i : 0.10	2 : 0.04	= : 0.04	d : 0.02	] : 0.02	
g : 0.30	e : 0.19	f : 0.17	i : 0.10	2 : 0.04	= : 0.04	] : 0.04	d : 0.02	c : 0.02	h : 0.02	b : 0.02	
g : 0.30	e : 0.21	f : 0.17	i : 0.10	2 : 0.04	= : 0.04	c : 0.04	a : 0.02	h : 0.02	b : 0.02	
g : 0.32	f : 0.19	] : 0.13	i : 0.10	c : 0.10	= : 0.04	e : 0.04	h : 0.02	2 : 0.02	
g : 0.32	c : 0.13	i : 0.10	f : 0.10	] : 0.06	2 : 0.06	= : 0.04	d : 0.04	e : 0.04	3 : 0.02	a : 0.02	h : 0.02	
c : 0.17	i : 0.10	f : 0.10	g : 0.08	] : 0.08	d : 0.08	: : 0.06	2 : 0.06	3 : 0.04	= : 0.04	e : 0.04	9 : 0.02	4 : 0.02	h : 0.02	G : 0.02	

#score	418.0757338804304
#seq	46
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_UTR_m3_run2.txt

#BEAR
FFffffffqqqqqqqqffffffccc	chr11:120242232-120242467(-)$1	235	63	88	13.5405
fff[bbbbqqqqqqqqbb]bb]fff	chr11:87793048-87793296(-)$1	248	49	74	12.9669
b[ffffffqqqqqqqqffffff]bb	chr16:17044965-17045200(+)$1	235	187	212	14.0272
ffff[cccqqqqqqqqccc]fffff	chr3:135069805-135070052(-)$1	247	189	214	14.7914
hhhhhhhhqqqqqqqqhhhhhhhh3	chr2:120142924-120143159(-)$1	235	67	92	12.4978
&&&eeeeeqqqqqqqqeeeee22ee	chrX:35772881-35773116(-)$1	235	162	187	12.8967
[dddd[bbqqqqqqqqbb22ddddc	chr6:124885829-124886072(+)$1	243	195	220	13.1161
ggg[ddddrrrrrrrrrdddd]ggg	chr9:72595393-72595632(+)$1	239	147	172	9.1593
eeeeddddqqqqqqqqdddd]eeee	chr1:16667513-16667749(+)$1	236	150	175	13.4841
c[ffffffqqqqqqqqffffff22c	chr3:7444770-7445008(+)$1	238	190	215	14.3048
$ccc!!bbqqqqqqqqbb22ccc44	chr1:183835465-183835707(-)$1	242	23	48	14.1354
dddeeeeeqqqqqqqqeeeee]ddd	chr3:32832774-32833009(+)$1	235	126	151	14.1619
ffff[cccqqqqqqqqcccffffff	chr11:74490419-74490654(-)$1	235	199	224	14.7154
!!ffffffqqqqqqqqffffff444	chr4:137798854-137799096(+)$1	242	203	228	14.8986
gg!!ddddqqqqqqqqdddd66666	chr10:81028331-81028570(+)$1	239	81	106	12.6035
fgggggggqqqqqqqqggggggg44	chrX:39150455-39150694(-)$1	239	175	200	15.4773
###eeeeeqqqqqqqqeeeee333b	chr5:136384853-136385106(-)$1	253	100	125	15.1534
:gggggggqqqqqqqqggggggg::	chr2:155214089-155214332(+)$1	243	60	85	12.8486
hhhhhhhhqqqqqqqqhhhhhhhh4	chr5:122906679-122906924(-)$1	245	126	151	12.4741
eeffffffqqqqqqqqffffff000	chr11:53231320-53231556(+)$1	236	164	189	13.2766
========ssssssssss=======	chr12:111820777-111821023(+)$1	246	203	228	9.1667
iiiiiiiiqqqqqqqqiiiiiiiii	chr1:179380299-179380534(+)$1	235	167	192	15.1975
a!!eeeeerrrrrrrrreeeee22a	chr16:96377526-96377769(+)$1	243	34	59	9.3106
fffffcccqqqqqqqqccc]fffff	chr19:57107966-57108210(-)$1	244	140	165	14.5987
========qqqqqqqq=========	chr2:104269211-104269455(-)$1	244	152	177	15.6344
gggggg[aqqqqqqqqa22gggggg	chr17:73290639-73290902(+)$1	263	191	216	14.6531
!gggggggqqqqqqqqggggggg22	chr10:42254586-42254830(+)$1	244	121	146	15.2320
f!!eeeeeqqqqqqqqeeeee]fff	chr1:120194993-120195256(-)$1	263	181	206	14.9676
!!ccc[bbqqqqqqqqbb]ccc444	chr10:17444910-17445145(+)$1	235	180	205	14.8507
ffff[cccqqqqqqqqcccffffff	chr11:74490259-74490505(-)$1	246	50	75	14.7154
[ccc[cccqqqqqqqqcccccca:C	chr8:109895182-109895417(+)$1	235	113	138	13.4329
b[a[ddddqqqqqqqqddddabb]g	chr16:37834384-37834622(+)$1	238	180	205	13.6158
e[ddddbbqqqqqqqqbb]ddddee	chr18:61747162-61747398(+)$1	236	114	139	13.2882
bb[eeeeeqqqqqqqqeeeee]bb:	chr5:136384536-136384800(-)$1	264	3	28	13.5234
:gggggggqqqqqqqqgggggggee	chr5:108708170-108708410(+)$1	240	109	134	14.3201
b[ccccccqqqqqqqqccc333ccc	chr1:23375775-23376023(-)$1	248	14	39	15.3620
cc[ccc[aqqqqqqqqa]cccccc]	chr8:13939586-13939827(+)$1	241	128	153	14.8937
eea[ddddqqqqqqqqdddd]a]ee	chr2:134423693-134423928(-)$1	235	10	35	13.9183
$$$cccbbqqqqqqqqbb]cccccc	chr7:146764317-146764554(+)$1	237	28	53	14.0013
cc!!ddddqqqqqqqqdddd333cc	chr15:103028081-103028333(-)$1	252	154	179	14.7951
[dddd[bbqqqqqqqqbbdddd]cc	chr11:86508268-86508512(-)$1	244	194	219	13.6443
eeeeeeeeqqqqqqqqeeeee4444	chr11:87897636-87897884(+)$1	248	108	133	14.8070
gggg[cccssssssssssccc]ggg	chr19:57110532-57110769(-)$1	237	104	129	9.1483
dd"""cccqqqqqqqqccc333ddd	chr2:179769162-179769397(+)$1	235	120	145	14.6760
ddda!!bbqqqqqqqqbb22a]ddd	chr15:97965006-97965244(-)$1	238	83	108	13.3263
[gggggggrrrrrrrrrggggggg]	chr9:3478532-3478767(+)$1	235	157	182	10.1087
cc[eeeeeqqqqqqqqeeeee22cc	chr2:155214586-155214823(+)$1	237	21	46	14.8815
gggeeeeeqqqqqqqqeeeee]ggg	chr16:33500989-33501236(+)$1	247	131	156	15.1538
%%%eeeeeqqqqqqqqeeeee22gg	chr12:8944977-8945224(+)$1	247	107	132	12.9848
bb"""cccqqqqqqqqccc333bb]	chr4:42970629-42970867(+)$1	238	161	186	14.5936
!ccc[cccrrrrrrrrrccc]ccc2	chr2:51780224-51780459(-)$1	235	203	228	9.7246
:gggggggqqqqqqqqggggggg::	chr15:12280154-12280391(+)$1	237	211	236	12.8486
========qqqqqqqq=========	chr8:98238195-98238439(+)$1	244	145	170	15.6344
bb[eeeeeqqqqqqqqeeeee]bb>	chr2:72240601-72240839(+)$1	238	166	191	14.2592
eee!!cccrrrrrrrrrccceeeee	chr11:109528792-109529029(+)$1	237	150	175	9.0248
d[ffffffqqqqqqqqffffffddd	chr5:122906038-122906273(-)$1	235	120	145	13.9756
[ddddcccqqqqqqqqccc]dddd]	chr8:71425001-71425238(+)$1	237	126	151	14.3045

#otherMatches

#Seq PSSM
AGGGCUGGUAGUGUCUCUGGCUAGG	chr11:120242232-120242467(-)$1	235	63	88	13.5405
CAAACCGUUAUUGGGUACAGGAUUG	chr11:87793048-87793296(-)$1	248	49	74	12.9669
UUGUAUUCCAUGAAGAGAAUGCUAC	chr16:17044965-17045200(+)$1	235	187	212	14.0272
uuggaucccuggaacuggaauuaac	chr3:135069805-135070052(-)$1	247	189	214	14.7914
UUUUCUACUAAGAUGUGUAGGAGAA	chr2:120142924-120143159(-)$1	235	67	92	12.4978
UAUAGACAAUACACACUGUCUUUGU	chrX:35772881-35773116(-)$1	235	162	187	12.8967
UGGACUAGUUCCAAUUCUUUGUCCC	chr6:124885829-124886072(+)$1	243	195	220	13.1161
UAGUCACUUAAGUCACUAGUGUUUA	chr9:72595393-72595632(+)$1	239	147	172	9.1593
gugaggcccuagaauuggccuucau	chr1:16667513-16667749(+)$1	236	150	175	13.4841
GCUUUCUGCUCUAUAACAGAAAAUC	chr3:7444770-7445008(+)$1	238	190	215	14.3048
GUUUUCCAUAAUCCAUUGCUAAAAU	chr1:183835465-183835707(-)$1	242	23	48	14.1354
CUGUGUCGUUUGACAUUGACGCCAG	chr3:32832774-32833009(+)$1	235	126	151	14.1619
AAGCACUGUCCUACUUUAGGCUUCU	chr11:74490419-74490654(-)$1	235	199	224	14.7154
AAAAGCUGCUGAACUACAGCUUAGU	chr4:137798854-137799096(+)$1	242	203	228	14.8986
AGGAUGACGGAGAGAAGUCGGAUUA	chr10:81028331-81028570(+)$1	239	81	106	12.6035
GGGUUUUGGCUUCUUAUAAAAUUUU	chrX:39150455-39150694(-)$1	239	175	200	15.4773
UUUGCUGUGUUCUAGAACAGUCAUG	chr5:136384853-136385106(-)$1	253	100	125	15.1534
CGAGGGUAAAAGUAGCUGCCCUCUU	chr2:155214089-155214332(+)$1	243	60	85	12.8486
UGGUUUUUAAAAGAAAAAAAACUAA	chr5:122906679-122906924(-)$1	245	126	151	12.4741
AUGUCCAGCACAUACCUUGGACUCC	chr11:53231320-53231556(+)$1	236	164	189	13.2766
UUUGUACAAAAUGUCCUAUGUACAG	chr12:111820777-111821023(+)$1	246	203	228	9.1667
GGUCAAAUGUAUGUUAAUUUGGCUG	chr1:179380299-179380534(+)$1	235	167	192	15.1975
GGGAAGGCCAGCUACAAGUCUUUAC	chr16:96377526-96377769(+)$1	243	34	59	9.3106
GGACAGGGAAGGAGCACCCAUGUCC	chr19:57107966-57108210(-)$1	244	140	165	14.5987
UGCUUUUUCCUUAUUAAGAGGGCAG	chr2:104269211-104269455(-)$1	244	152	177	15.6344
GUGGCUUCUUCCUUUUGCUGGUCAC	chr17:73290639-73290902(+)$1	263	191	216	14.6531
UUGUCUUGGCAGUUGACAAGACAUU	chr10:42254586-42254830(+)$1	244	121	146	15.2320
AACUCUUCUUCUCUAUGGAGAAUCA	chr1:120194993-120195256(-)$1	263	181	206	14.9676
UCGAGUACAGACUUAAGUUUUCAAA	chr10:17444910-17445145(+)$1	235	180	205	14.8507
AAGCACUGUCCUACUUUAGGCUUCU	chr11:74490259-74490505(-)$1	246	50	75	14.7154
UCCUCUGUUUGUAACUGCAAGGCUG	chr8:109895182-109895417(+)$1	235	113	138	13.4329
AUGAUGCAGACACUUAUGUACUUCA	chr16:37834384-37834622(+)$1	238	180	205	13.6158
GUCCUUGUGAAUAUUAACUGAGGUA	chr18:61747162-61747398(+)$1	236	114	139	13.2882
UAUUACCUUACACUGUAGGUGUUAU	chr5:136384536-136384800(-)$1	264	3	28	13.5234
UUUGUUACUGUUUUGUGUAACAGUG	chr5:108708170-108708410(+)$1	240	109	134	14.3201
CCUGUACCAGUGUCCAGGUGUAACA	chr1:23375775-23376023(-)$1	248	14	39	15.3620
UGGUGUGAGUAUUCUGUGACACAAG	chr8:13939586-13939827(+)$1	241	128	153	14.8937
AGCAUCCUUAAAGUGCAGGAAGUCU	chr2:134423693-134423928(-)$1	235	10	35	13.9183
CAAGCCUCACCUGCUAGACGGCCGG	chr7:146764317-146764554(+)$1	237	28	53	14.0013
UAGAGGCAAUAUCAAAUGCUGGAUA	chr15:103028081-103028333(-)$1	252	154	179	14.7951
UAACCCUCCCUUCCCUGAGGUUUGU	chr11:86508268-86508512(-)$1	244	194	219	13.6443
UCUUCUUUGGGGAGGGAGAGAGUUG	chr11:87897636-87897884(+)$1	248	108	133	14.8070
AGCAGAUCUGUGAGUCUCGAUGUGC	chr19:57110532-57110769(-)$1	237	104	129	9.1483
AGGCUCAAUCCUCACUUUGUAACUU	chr2:179769162-179769397(+)$1	235	120	145	14.6760
CAGCUAACUCAAAAACGUGUGCCUG	chr15:97965006-97965244(-)$1	238	83	108	13.3263
GUUCUCAACAUUUGAUCUUGAGAAA	chr9:3478532-3478767(+)$1	235	157	182	10.1087
CUCCAAUUUCUCAUCUGGUUGCAAG	chr2:155214586-155214823(+)$1	237	21	46	14.8815
UGUAUGUAAGCAAUAAUACAUAGCA	chr16:33500989-33501236(+)$1	247	131	156	15.1538
UUUGAUAGAAAGUACACUGUCUUGU	chr12:8944977-8945224(+)$1	247	107	132	12.9848
CCUUUGGCUUCCUCCUGUUUCUGGA	chr4:42970629-42970867(+)$1	238	161	186	14.5936
agcauuguaaguugaaaacacugug	chr2:51780224-51780459(-)$1	235	203	228	9.7246
UUUAUGAGCUAUGCCCCUCAUGAUA	chr15:12280154-12280391(+)$1	237	211	236	12.8486
GGUGUUCUGAGGCAAGAGGACACCC	chr8:98238195-98238439(+)$1	244	145	170	15.6344
UGGGCUUUUUCUUUUUAAAGCGCAU	chr2:72240601-72240839(+)$1	238	166	191	14.2592
GUCCAUGCUUCACUCACGCAGACUG	chr11:109528792-109529029(+)$1	237	150	175	9.0248
CGUUGUAUGUAGGUUGGUGUAAGGG	chr5:122906038-122906273(-)$1	235	120	145	13.9756
UAAGUGGAUAAGCGACUCCUACUUC	chr8:71425001-71425238(+)$1	237	126	151	14.3045

#DB
((((((((........))))))(((	chr11:120242232-120242467(-)$1	1	63	88	13.5405
(((.((((........)).)).)))	chr11:87793048-87793296(-)$1	1	49	74	12.9669
(.((((((........)))))).))	chr16:17044965-17045200(+)$1	1	187	212	14.0272
((((.(((........))).)))))	chr3:135069805-135070052(-)$1	1	189	214	14.7914
((((((((........)))))))).	chr2:120142924-120143159(-)$1	1	67	92	12.4978
...(((((........)))))..))	chrX:35772881-35773116(-)$1	1	162	187	12.8967
.((((.((........))..)))))	chr6:124885829-124886072(+)$1	1	195	220	13.1161
(((.((((.........)))).)))	chr9:72595393-72595632(+)$1	1	147	172	9.1593
((((((((........)))).))))	chr1:16667513-16667749(+)$1	1	150	175	13.4841
(.((((((........))))))..)	chr3:7444770-7445008(+)$1	1	190	215	14.3048
.(((..((........))..)))..	chr1:183835465-183835707(-)$1	1	23	48	14.1354
((((((((........))))).)))	chr3:32832774-32833009(+)$1	1	126	151	14.1619
((((.(((........)))))))))	chr11:74490419-74490654(-)$1	1	199	224	14.7154
..((((((........))))))...	chr4:137798854-137799096(+)$1	1	203	228	14.8986
((..((((........)))).....	chr10:81028331-81028570(+)$1	1	81	106	12.6035
((((((((........)))))))..	chrX:39150455-39150694(-)$1	1	175	200	15.4773
...(((((........)))))...)	chr5:136384853-136385106(-)$1	1	100	125	15.1534
.(((((((........)))))))..	chr2:155214089-155214332(+)$1	1	60	85	12.8486
((((((((........)))))))).	chr5:122906679-122906924(-)$1	1	126	151	12.4741
((((((((........))))))...	chr11:53231320-53231556(+)$1	1	164	189	13.2766
((((((((..........)))))))	chr12:111820777-111821023(+)$1	1	203	228	9.1667
((((((((........)))))))))	chr1:179380299-179380534(+)$1	1	167	192	15.1975
(..(((((.........)))))..)	chr16:96377526-96377769(+)$1	1	34	59	9.3106
((((((((........))).)))))	chr19:57107966-57108210(-)$1	1	140	165	14.5987
((((((((........)))))))))	chr2:104269211-104269455(-)$1	1	152	177	15.6344
((((((.(........)..))))))	chr17:73290639-73290902(+)$1	1	191	216	14.6531
.(((((((........)))))))..	chr10:42254586-42254830(+)$1	1	121	146	15.2320
(..(((((........))))).)))	chr1:120194993-120195256(-)$1	1	181	206	14.9676
..(((.((........)).)))...	chr10:17444910-17445145(+)$1	1	180	205	14.8507
((((.(((........)))))))))	chr11:74490259-74490505(-)$1	1	50	75	14.7154
.(((.(((........))))))).)	chr8:109895182-109895417(+)$1	1	113	138	13.4329
(.(.((((........))))))).)	chr16:37834384-37834622(+)$1	1	180	205	13.6158
(.((((((........)).))))))	chr18:61747162-61747398(+)$1	1	114	139	13.2882
((.(((((........))))).)).	chr5:136384536-136384800(-)$1	1	3	28	13.5234
.(((((((........)))))))((	chr5:108708170-108708410(+)$1	1	109	134	14.3201
(.((((((........)))...)))	chr1:23375775-23376023(-)$1	1	14	39	15.3620
((.(((.(........).)))))).	chr8:13939586-13939827(+)$1	1	128	153	14.8937
(((.((((........)))).).))	chr2:134423693-134423928(-)$1	1	10	35	13.9183
...(((((........)).))))))	chr7:146764317-146764554(+)$1	1	28	53	14.0013
((..((((........))))...))	chr15:103028081-103028333(-)$1	1	154	179	14.7951
.((((.((........)))))).))	chr11:86508268-86508512(-)$1	1	194	219	13.6443
((((((((........)))))....	chr11:87897636-87897884(+)$1	1	108	133	14.8070
((((.(((..........))).)))	chr19:57110532-57110769(-)$1	1	104	129	9.1483
((...(((........)))...)))	chr2:179769162-179769397(+)$1	1	120	145	14.6760
((((..((........))..).)))	chr15:97965006-97965244(-)$1	1	83	108	13.3263
.(((((((.........))))))).	chr9:3478532-3478767(+)$1	1	157	182	10.1087
((.(((((........)))))..))	chr2:155214586-155214823(+)$1	1	21	46	14.8815
((((((((........))))).)))	chr16:33500989-33501236(+)$1	1	131	156	15.1538
...(((((........)))))..))	chr12:8944977-8945224(+)$1	1	107	132	12.9848
((...(((........)))...)).	chr4:42970629-42970867(+)$1	1	161	186	14.5936
.(((.(((.........))).))).	chr2:51780224-51780459(-)$1	1	203	228	9.7246
.(((((((........)))))))..	chr15:12280154-12280391(+)$1	1	211	236	12.8486
((((((((........)))))))))	chr8:98238195-98238439(+)$1	1	145	170	15.6344
((.(((((........))))).)).	chr2:72240601-72240839(+)$1	1	166	191	14.2592
(((..(((.........))))))))	chr11:109528792-109529029(+)$1	1	150	175	9.0248
(.((((((........)))))))))	chr5:122906038-122906273(-)$1	1	120	145	13.9756
.(((((((........))).)))).	chr8:71425001-71425238(+)$1	1	126	151	14.3045

#PSSM
f : 0.12	b : 0.10	e : 0.10	[ : 0.08	g : 0.08	c : 0.07	d : 0.07	! : 0.07	: : 0.05	= : 0.05	h : 0.03	$ : 0.03	F : 0.01	& : 0.01	# : 0.01	i : 0.01	a : 0.01	% : 0.01	
g : 0.19	[ : 0.10	d : 0.10	c : 0.10	f : 0.08	e : 0.08	! : 0.07	= : 0.05	b : 0.05	h : 0.03	F : 0.01	& : 0.01	# : 0.01	i : 0.01	$ : 0.01	% : 0.01	
f : 0.19	g : 0.17	d : 0.10	c : 0.08	! : 0.07	[ : 0.07	e : 0.05	= : 0.05	h : 0.03	a : 0.03	" : 0.03	& : 0.01	# : 0.01	i : 0.01	$ : 0.01	% : 0.01	
e : 0.21	f : 0.17	g : 0.14	c : 0.12	[ : 0.07	d : 0.07	! : 0.05	= : 0.05	h : 0.03	" : 0.03	i : 0.01	a : 0.01	
e : 0.19	d : 0.17	f : 0.12	g : 0.12	[ : 0.10	c : 0.07	! : 0.05	= : 0.05	h : 0.03	" : 0.03	b : 0.01	i : 0.01	
c : 0.24	e : 0.19	d : 0.12	g : 0.12	f : 0.10	[ : 0.05	= : 0.05	h : 0.03	! : 0.03	b : 0.01	i : 0.01	
c : 0.21	e : 0.19	b : 0.14	f : 0.10	d : 0.10	g : 0.10	= : 0.05	h : 0.03	[ : 0.03	i : 0.01	
c : 0.21	e : 0.19	b : 0.14	f : 0.10	d : 0.10	g : 0.10	= : 0.05	h : 0.03	a : 0.03	i : 0.01	
q : 0.87	r : 0.08	s : 0.03	
q : 0.87	r : 0.08	s : 0.03	
q : 0.87	r : 0.08	s : 0.03	
q : 0.87	r : 0.08	s : 0.03	
q : 0.87	r : 0.08	s : 0.03	
q : 0.87	r : 0.08	s : 0.03	
q : 0.87	r : 0.08	s : 0.03	
q : 0.87	r : 0.08	s : 0.03	
e : 0.17	c : 0.15	b : 0.14	f : 0.10	r : 0.08	d : 0.08	g : 0.08	h : 0.03	s : 0.03	= : 0.03	a : 0.03	i : 0.01	
c : 0.19	e : 0.19	b : 0.14	f : 0.10	d : 0.10	g : 0.10	h : 0.03	s : 0.03	= : 0.03	i : 0.01	2 : 0.01	] : 0.01	
c : 0.22	e : 0.19	d : 0.12	f : 0.10	g : 0.10	] : 0.07	2 : 0.07	= : 0.05	h : 0.03	i : 0.01	
e : 0.19	f : 0.14	d : 0.14	g : 0.12	c : 0.12	] : 0.05	2 : 0.05	= : 0.05	3 : 0.05	h : 0.03	b : 0.01	i : 0.01	
e : 0.21	f : 0.17	g : 0.12	c : 0.10	d : 0.08	3 : 0.07	] : 0.05	= : 0.05	h : 0.03	a : 0.03	b : 0.01	6 : 0.01	i : 0.01	
f : 0.17	] : 0.15	g : 0.12	c : 0.10	3 : 0.08	d : 0.07	2 : 0.05	e : 0.05	= : 0.05	h : 0.03	6 : 0.01	i : 0.01	b : 0.01	a : 0.01	4 : 0.01	
g : 0.17	d : 0.12	c : 0.10	f : 0.10	2 : 0.08	b : 0.07	] : 0.05	4 : 0.05	= : 0.05	h : 0.03	e : 0.03	3 : 0.03	6 : 0.01	0 : 0.01	i : 0.01	a : 0.01	
c : 0.14	f : 0.10	e : 0.10	d : 0.10	g : 0.10	4 : 0.08	b : 0.07	2 : 0.05	: : 0.05	= : 0.05	h : 0.03	6 : 0.01	3 : 0.01	0 : 0.01	i : 0.01	] : 0.01	
c : 0.14	f : 0.10	e : 0.10	g : 0.10	4 : 0.10	d : 0.07	] : 0.07	: : 0.05	= : 0.05	b : 0.03	2 : 0.03	3 : 0.01	6 : 0.01	0 : 0.01	i : 0.01	a : 0.01	C : 0.01	> : 0.01	

#score	773.1058730854553
#seq	57
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_UTR_m2_run2.txt

#BEAR
[ccc####cccooooooccc]ccc]ccc	chr7:80571870-80572093(-)$1	223	14	42	17.1553
####bb!!cccooooooccc22bb22==	chrX:93913773-93913996(-)$1	223	169	197	16.3175
cccccc[ddddoooooodddd]ccc22c	chr11:99699245-99699467(+)$1	222	104	132	14.5093
=========[aooooooa]=========	chr10:4516149-4516378(+)$1	229	80	108	14.9212
[dddd!!ddddoooooodddd333dddd	chr4:101484771-101484993(-)$1	222	37	65	14.8160
::ccc"""cccooooooccc333ccc::	chr13:21609165-21609390(-)$1	225	9	37	14.6291
f!!ccc!!cccooooooccc]ccc22ff	chr10:79416694-79416913(+)$1	219	166	194	16.4043
ggggggg[a[aooooooa]a]ggggggg	chr3:103817292-103817514(-)$1	222	152	180	14.6758
eeee[bb[cccooooooccc]bb333ee	chr11:78870993-78871215(+)$1	222	67	95	14.8894
ffffff[ddddoooooodddd]ffffff	chr11:62182740-62182979(-)$1	239	8	36	12.7565
!ccc####cccooooooccc4444ccc3	chr11:75080848-75081070(+)$1	222	89	117	17.7511
#ffffff[cccoooooocccffffff]a	chr1:171905622-171905845(+)$1	223	188	216	14.2615
eeeee"""cccooooooccc333eeeee	chr4:19538116-19538335(-)$1	219	59	87	16.9541
ggggggg:cccoooooocccggggggg!	chr2:121033680-121033902(-)$1	222	34	62	14.3168
####bb!!cccooooooccc22bb333b	chr10:45037626-45037848(+)$1	222	109	137	16.5205
FFFccc!!cccooooooccc22ccc::e	chr5:141097152-141097377(-)$1	225	117	145	13.9253
$$$bb[a[cccooooooccc333a]bb4	chr5:93601446-93601665(+)$1	219	21	49	16.1119
ccdddd!!cccooooooccc]dddd]cc	chr6:120392783-120392998(-)$1	215	7	35	16.0503
ccc[ddddcccooooooccc333dddd]	chr12:85936282-85936504(+)$1	222	129	157	16.0025
!bbbb!!ddddoooooodddd22bb]bb	chr8:109899903-109900122(+)$1	219	163	191	13.3605
$$$$gggggggooooooggggggg====	chr11:119134307-119134527(+)$1	220	48	76	13.3628
!ddddccc[aooooooa]ccc]dddd44	chrX:71279102-71279327(-)$1	225	146	174	13.0030
::ccc"""cccooooooccc4444ccc:	chr8:112747840-112748072(+)$1	232	201	229	14.9765
idddd!!acccooooooccc]a22dddd	chr15:34213642-34213866(+)$1	224	118	146	15.6536
fffff"""cccooooooccc333fffff	chr2:136907148-136907369(-)$1	221	133	161	16.7040
c!!ddddccc!!aooooooa22ccc333	chr10:20118773-20118994(-)$1	221	159	187	12.7104
!ccc[bb[cccooooooccc4444bbcc	chrX:11705288-11705507(+)$1	219	61	89	16.0061
ccc:ccc[cccooooooccc]cccGGGG	chr2:69588565-69588799(+)$1	234	203	231	12.9441
%a[gggggggooooooggggggg]a333	chrX:101702203-101702425(-)$1	222	142	170	12.2162
!ccc####cccooooooccc22ccc333	chr17:26390424-26390642(-)$1	218	26	54	18.2355
[dddd"""cccoooooocccdddd]ddd	chr10:39966553-39966777(-)$1	224	44	72	15.7427
c!!ddddddddoooooodddd]dddd22	chr4:73362586-73362804(+)$1	218	150	178	13.1710
gga[ccc[cccoooooocccccc333a]	chr9:30879230-30879452(-)$1	222	67	95	16.1760
hhhhhhh[cccooooooccc22hhhhhh	chr13:74494735-74494957(-)$1	222	97	125	14.0445
c[eeeee[cccooooooccc]eeeee33	chr2:181118008-181118227(+)$1	219	173	201	15.4037
:eeeee!!cccooooooccc22eeeee:	chr11:96216613-96216846(+)$1	233	141	169	14.5088
:dddd"""cccooooooccc333ddddg	chr6:13036305-13036520(-)$1	215	100	128	16.6133
===[ccc[cccooooooccc]ccc333=	chr5:65989453-65989675(+)$1	222	30	58	16.8313
Deeeee"""bboooooobb333eeeeeF	chr2:153055527-153055750(-)$1	223	190	218	12.5965
cceeeee[cccooooooccc]eeeeehh	chr15:81416813-81417037(+)$1	224	137	165	14.6957
gggg"""bb[aooooooa]bb333gggg	chr14:56244695-56244917(-)$1	222	57	85	14.5580
===========oooooo===========	chr2:167340810-167341030(+)$1	220	149	177	15.0881
dgggggggabboooooobb]a]gggggg	chr3:94294928-94295159(+)$1	231	201	229	13.1555
"ccc[ccc[aooooooaccc22ccc]bb	chr8:86193992-86194212(-)$1	220	84	112	14.4816
dddd"""ddddoooooodddddddd]cc	chr3:87558017-87558238(-)$1	221	12	40	13.8589
===========oooooo===========	chr11:118164068-118164307(-)$1	239	135	163	15.0881
fff####ddddoooooodddd333ffff	chr4:45047306-45047525(-)$1	219	118	146	14.3969
!!bb"""ddddoooooodddd]bb22a]	chr6:48451046-48451265(-)$1	219	83	111	14.2315
!dddd!!ddddoooooodddd22ddddd	chr11:45958303-45958533(+)$1	230	184	212	14.3472
:dddd"""cccoooooocccddddiiii	chr1:167795860-167796081(-)$1	221	140	168	15.3190
hhhhhhh[cccooooooccc22hhhhhh	chr7:34894906-34895135(-)$1	229	3	31	14.0445

#otherMatches

#Seq PSSM
ACCACUGUGUCCUCUCUGACUUGGCCAG	chr7:80571870-80572093(-)$1	223	14	42	17.1553
AAAAACAAUAAGAAAUAUUACAGUgaaa	chrX:93913773-93913996(-)$1	223	169	197	16.3175
GAGAUGGGUUUCCAAAUGAAUGUAUGGC	chr11:99699245-99699467(+)$1	222	104	132	14.5093
UUGGAACCUGUGUACAAGGAGGUUCCAA	chr10:4516149-4516378(+)$1	229	80	108	14.9212
UGAAUUAGAUUCAUGGAGGUUGGUAUUC	chr4:101484771-101484993(-)$1	222	37	65	14.8160
AAUGAGUUAUCAAAGGCGAUUUAUCACA	chr13:21609165-21609390(-)$1	225	9	37	14.6291
ACUCAGCAGCCCUUCUUGGUCCUGUCUG	chr10:79416694-79416913(+)$1	219	166	194	16.4043
CUUAGCAAUGUGGCCUUGGAAUGCUGAG	chr3:103817292-103817514(-)$1	222	152	180	14.6758
CUCUAGCAGAUCACCACAUUAGCAUGGG	chr11:78870993-78871215(+)$1	222	67	95	14.8894
AAUAAAAAUAACUUAUUUUAUCUUUAUU	chr11:62182740-62182979(-)$1	239	8	36	12.7565
UGGCAGUGGGAAAAAAAUCUAGUGGCCU	chr11:75080848-75081070(+)$1	222	89	117	17.7511
UUUCAUUUGUAAAGGAAUACAGUGAACU	chr1:171905622-171905845(+)$1	223	188	216	14.2615
UAUCAGUAGACACAGAAGUCGUGUGAUA	chr4:19538116-19538335(-)$1	219	59	87	16.9541
UAGAGAAACAGUUGUCUCUGGUCCGUUG	chr2:121033680-121033902(-)$1	222	34	62	14.3168
UCACCCCUAACAGAACAGUUCCGGAAUU	chr10:45037626-45037848(+)$1	222	109	137	16.5205
GGGAGUGAGCAGUCCAGUGCCAGCUGCC	chr5:141097152-141097377(-)$1	225	117	145	13.9253
ACUGUGACCAGUUCCAUCUGCUAUGACU	chr5:93601446-93601665(+)$1	219	21	49	16.1119
ggcugucuuagaacacacuauauagacc	chr6:120392783-120392998(-)$1	215	7	35	16.0503
UGGGCCCAGGACUUCUCUCUAGGUGGGG	chr12:85936282-85936504(+)$1	222	129	157	16.0025
UCAUAUUAAUAAAGUUCUGUUUUUACUG	chr8:109899903-109900122(+)$1	219	163	191	13.3605
UCCACCCUGAGUGGCCCCUUAGGGUCAG	chr11:119134307-119134527(+)$1	220	48	76	13.3628
UGGCCUGCCAGAGUCGUUGCAUGGCCCA	chrX:71279102-71279327(-)$1	225	146	174	13.0030
AAUGUAACCCAGAAUGAUGGCUAAACAA	chr8:112747840-112748072(+)$1	232	201	229	14.9765
UUGGUUACCUGCACCAACAGAGCCACCA	chr15:34213642-34213866(+)$1	224	118	146	15.6536
aauuuugaaaaguaauauuuauuaaauu	chr2:136907148-136907369(-)$1	221	133	161	16.7040
AGUAACUGAAUUAUUUACUUUUUUCUAU	chr10:20118773-20118994(-)$1	221	159	187	12.7104
AGCGAGCAAGGCACAGACCUGAGAGCCG	chrX:11705288-11705507(+)$1	219	61	89	16.0061
UGGAAACAAGCUUAACUGUUGGUUGCAG	chr2:69588565-69588799(+)$1	234	203	231	12.9441
ACGGCUUAGCAGACAAGUUaagcggaca	chrX:101702203-101702425(-)$1	222	142	170	12.2162
UGCCGAGAGGUGACUAAACCGAGGCUAA	chr17:26390424-26390642(-)$1	218	26	54	18.2355
GGGGGCGAGUCUCCCGUGACCUCCGACG	chr10:39966553-39966777(-)$1	224	44	72	15.7427
GCAGAUGCCAUGAGACUGUGGCCAUCCU	chr4:73362586-73362804(+)$1	218	150	178	13.1710
UACCCUUGUUGGCCUUACAAAAGAUAGC	chr9:30879230-30879452(-)$1	222	67	95	16.1760
GUAUUUUUUUCCCCUUAGAACUAAAAUA	chr13:74494735-74494957(-)$1	222	97	125	14.0445
CAUCCUGUCUUUAACAUGAGUUAGGAAG	chr2:181118008-181118227(+)$1	219	173	201	15.4037
UCAUGAAUUAAAUAAUCUUAUGUCAUGU	chr11:96216613-96216846(+)$1	233	141	169	14.5088
ACUUGAUUUUCGUUGAAGAGUUGCAGGC	chr6:13036305-13036520(-)$1	215	100	128	16.6133
UAGCGGGUGAUGUUGGUGUCUCCUUACC	chr5:65989453-65989675(+)$1	222	30	58	16.8313
ACUAGGGUUUCAGGACAGACUACCUAGG	chr2:153055527-153055750(-)$1	223	190	218	12.5965
GAGCUCCGGAGCCCACCCUUAGGAGCGG	chr15:81416813-81417037(+)$1	224	137	165	14.6957
UGCUGCUCCUGACGUUCCUGGCCAAGCA	chr14:56244695-56244917(-)$1	222	57	85	14.5580
CUGACAUUCUUGCUCUGAAGAGUGUUGG	chr2:167340810-167341030(+)$1	220	149	177	15.0881
UGCCCCAGGCCUUGAUUGGACUCUGGGG	chr3:94294928-94295159(+)$1	231	201	229	13.1555
GGCCCCUCACAGCUGCGGAGCAGGCAGC	chr8:86193992-86194212(-)$1	220	84	112	14.4816
CUGGUUGGAUGGGUGAGUAUUCCAGGCU	chr3:87558017-87558238(-)$1	221	12	40	13.8589
CCAGGCUGAGCAGCACGGCUCGGUUUGG	chr11:118164068-118164307(-)$1	239	135	163	15.0881
GGUCACUGUCCUACACUGGGCCAUAUCC	chr4:45047306-45047525(-)$1	219	118	146	14.3969
AACUGGACACUGAAGGAAGUGGGGAGCG	chr6:48451046-48451265(-)$1	219	83	111	14.2315
UCCUGGCUAUAGUAUUGUAUACACAGGG	chr11:45958303-45958533(+)$1	230	184	212	14.3472
AGGGAACUGGCACCUUGGCCUCCCAAAA	chr1:167795860-167796081(-)$1	221	140	168	15.3190
GUGACUGAGCUCUGAGAAGCAGCGGUCA	chr7:34894906-34895135(-)$1	229	3	31	14.0445

#DB
.(((....(((......))).))).)))	chr7:80571870-80572093(-)$1	1	14	42	17.1553
....((..(((......)))..))..))	chrX:93913773-93913996(-)$1	1	169	197	16.3175
((((((.((((......)))).)))..)	chr11:99699245-99699467(+)$1	1	104	132	14.5093
(((((((((.(......).)))))))))	chr10:4516149-4516378(+)$1	1	80	108	14.9212
.((((..((((......))))...))))	chr4:101484771-101484993(-)$1	1	37	65	14.8160
..(((...(((......)))...)))..	chr13:21609165-21609390(-)$1	1	9	37	14.6291
(..(((..(((......))).)))..))	chr10:79416694-79416913(+)$1	1	166	194	16.4043
(((((((.(.(......).).)))))))	chr3:103817292-103817514(-)$1	1	152	180	14.6758
((((.((.(((......))).))...))	chr11:78870993-78871215(+)$1	1	67	95	14.8894
((((((.((((......)))).))))))	chr11:62182740-62182979(-)$1	1	8	36	12.7565
.(((....(((......)))....))).	chr11:75080848-75081070(+)$1	1	89	117	17.7511
.((((((.(((......))))))))).)	chr1:171905622-171905845(+)$1	1	188	216	14.2615
(((((...(((......)))...)))))	chr4:19538116-19538335(-)$1	1	59	87	16.9541
))))))).(((......)))(((((((.	chr2:121033680-121033902(-)$1	1	34	62	14.3168
....((..(((......)))..))...)	chr10:45037626-45037848(+)$1	1	109	137	16.5205
((((((..(((......)))..)))..(	chr5:141097152-141097377(-)$1	1	117	145	13.9253
...((.(.(((......)))...).)).	chr5:93601446-93601665(+)$1	1	21	49	16.1119
((((((..(((......))).)))).))	chr6:120392783-120392998(-)$1	1	7	35	16.0503
(((.(((((((......)))...)))).	chr12:85936282-85936504(+)$1	1	129	157	16.0025
.((((..((((......))))..)).))	chr8:109899903-109900122(+)$1	1	163	191	13.3605
....(((((((......)))))))))))	chr11:119134307-119134527(+)$1	1	48	76	13.3628
.(((((((.(......).))).))))..	chrX:71279102-71279327(-)$1	1	146	174	13.0030
..(((...(((......)))....))).	chr8:112747840-112748072(+)$1	1	201	229	14.9765
(((((..((((......))).)..))))	chr15:34213642-34213866(+)$1	1	118	146	15.6536
(((((...(((......)))...)))))	chr2:136907148-136907369(-)$1	1	133	161	16.7040
(..(((((((..(......)..)))...	chr10:20118773-20118994(-)$1	1	159	187	12.7104
.(((.((.(((......)))....))))	chrX:11705288-11705507(+)$1	1	61	89	16.0061
))).(((.(((......))).)))))))	chr2:69588565-69588799(+)$1	1	203	231	12.9441
.(.(((((((......))))))).)...	chrX:101702203-101702425(-)$1	1	142	170	12.2162
.(((....(((......)))..)))...	chr17:26390424-26390642(-)$1	1	26	54	18.2355
.((((...(((......))))))).)))	chr10:39966553-39966777(-)$1	1	44	72	15.7427
(..((((((((......)))).))))..	chr4:73362586-73362804(+)$1	1	150	178	13.1710
(((.(((.(((......))))))...).	chr9:30879230-30879452(-)$1	1	67	95	16.1760
(((((((.(((......)))..))))))	chr13:74494735-74494957(-)$1	1	97	125	14.0445
(.(((((.(((......))).)))))..	chr2:181118008-181118227(+)$1	1	173	201	15.4037
.(((((..(((......)))..))))).	chr11:96216613-96216846(+)$1	1	141	169	14.5088
.((((...(((......)))...))))(	chr6:13036305-13036520(-)$1	1	100	128	16.6133
(((.(((.(((......))).)))...)	chr5:65989453-65989675(+)$1	1	30	58	16.8313
)(((((...((......))...))))))	chr2:153055527-153055750(-)$1	1	190	218	12.5965
))(((((.(((......))).)))))((	chr15:81416813-81417037(+)$1	1	137	165	14.6957
((((...((.(......).))...))))	chr14:56244695-56244917(-)$1	1	57	85	14.5580
(((((((((((......)))))))))))	chr2:167340810-167341030(+)$1	1	149	177	15.0881
)((((((((((......)).).))))))	chr3:94294928-94295159(+)$1	1	201	229	13.1555
.(((.(((.(......))))..))).))	chr8:86193992-86194212(-)$1	1	84	112	14.4816
((((...((((......)))))))).))	chr3:87558017-87558238(-)$1	1	12	40	13.8589
(((((((((((......)))))))))))	chr11:118164068-118164307(-)$1	1	135	163	15.0881
(((....((((......))))...))))	chr4:45047306-45047525(-)$1	1	118	146	14.3969
..((...((((......)))).))..).	chr6:48451046-48451265(-)$1	1	83	111	14.2315
.((((..((((......))))..)))))	chr11:45958303-45958533(+)$1	1	184	212	14.3472
.((((...(((......)))))))((((	chr1:167795860-167796081(-)$1	1	140	168	15.3190
(((((((.(((......)))..))))))	chr7:34894906-34895135(-)$1	1	3	31	14.0445

#PSSM
c : 0.15	! : 0.13	: : 0.09	= : 0.07	f : 0.07	g : 0.07	[ : 0.05	# : 0.05	e : 0.03	$ : 0.03	h : 0.03	d : 0.03	F : 0.01	i : 0.01	% : 0.01	D : 0.01	" : 0.01	
c : 0.19	d : 0.15	g : 0.09	= : 0.07	! : 0.07	e : 0.07	f : 0.07	# : 0.03	: : 0.03	$ : 0.03	h : 0.03	F : 0.01	b : 0.01	a : 0.01	[ : 0.01	
c : 0.19	d : 0.17	e : 0.11	= : 0.07	g : 0.07	f : 0.07	! : 0.05	# : 0.03	$ : 0.03	b : 0.03	h : 0.03	F : 0.01	[ : 0.01	a : 0.01	
d : 0.21	c : 0.19	e : 0.11	g : 0.09	# : 0.05	= : 0.05	f : 0.05	b : 0.05	[ : 0.05	h : 0.03	$ : 0.01	: : 0.01	
d : 0.21	c : 0.15	g : 0.09	e : 0.09	# : 0.07	b : 0.07	= : 0.05	[ : 0.05	f : 0.05	" : 0.05	h : 0.03	
" : 0.19	c : 0.15	g : 0.09	# : 0.07	b : 0.07	! : 0.07	d : 0.07	e : 0.07	= : 0.05	f : 0.03	h : 0.03	[ : 0.01	
" : 0.21	! : 0.19	g : 0.09	c : 0.09	# : 0.07	= : 0.05	d : 0.05	[ : 0.03	b : 0.03	h : 0.03	e : 0.03	f : 0.01	a : 0.01	
[ : 0.23	d : 0.19	" : 0.15	! : 0.11	# : 0.05	= : 0.05	g : 0.05	c : 0.05	: : 0.01	a : 0.01	b : 0.01	
c : 0.60	d : 0.17	= : 0.05	a : 0.03	g : 0.03	[ : 0.03	" : 0.01	b : 0.01	
c : 0.60	d : 0.17	[ : 0.05	g : 0.03	a : 0.03	b : 0.03	= : 0.03	
c : 0.58	d : 0.17	a : 0.05	o : 0.05	b : 0.03	= : 0.03	g : 0.01	! : 0.01	
o : 0.98	! : 0.01	
o : 0.98	a : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 0.94	a : 0.03	g : 0.01	
c : 0.60	d : 0.17	a : 0.05	g : 0.03	b : 0.03	= : 0.03	] : 0.01	o : 0.01	
c : 0.62	d : 0.17	] : 0.05	g : 0.03	b : 0.03	= : 0.03	o : 0.01	
c : 0.62	d : 0.17	= : 0.05	a : 0.03	g : 0.03	3 : 0.01	b : 0.01	] : 0.01	
d : 0.21	] : 0.19	2 : 0.17	3 : 0.13	= : 0.05	4 : 0.05	g : 0.05	c : 0.03	f : 0.01	b : 0.01	a : 0.01	
2 : 0.21	3 : 0.19	] : 0.11	c : 0.09	g : 0.07	d : 0.07	= : 0.05	4 : 0.05	e : 0.03	b : 0.01	f : 0.01	a : 0.01	
c : 0.19	3 : 0.17	d : 0.11	g : 0.09	b : 0.07	e : 0.07	= : 0.05	4 : 0.05	2 : 0.05	f : 0.03	h : 0.03	
c : 0.19	d : 0.17	3 : 0.09	e : 0.09	b : 0.07	g : 0.07	= : 0.05	f : 0.05	4 : 0.05	h : 0.03	a : 0.01	2 : 0.01	] : 0.01	
d : 0.17	c : 0.15	e : 0.09	= : 0.07	g : 0.07	3 : 0.07	f : 0.07	] : 0.05	2 : 0.05	b : 0.03	h : 0.03	G : 0.01	a : 0.01	i : 0.01	
d : 0.15	3 : 0.13	e : 0.09	c : 0.07	2 : 0.07	= : 0.07	g : 0.07	f : 0.07	] : 0.07	b : 0.03	h : 0.03	: : 0.01	G : 0.01	i : 0.01	
c : 0.11	d : 0.11	3 : 0.11	= : 0.09	f : 0.07	g : 0.07	e : 0.07	b : 0.05	h : 0.05	2 : 0.03	: : 0.03	a : 0.03	] : 0.01	4 : 0.01	G : 0.01	i : 0.01	
= : 0.11	c : 0.09	3 : 0.09	d : 0.07	f : 0.07	g : 0.07	: : 0.05	e : 0.05	b : 0.05	] : 0.05	h : 0.05	4 : 0.03	a : 0.01	! : 0.01	G : 0.01	2 : 0.01	F : 0.01	i : 0.01	

#score	760.4962692085161
#seq	51
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_transcript_m2_run1.txt

#BEAR
b[===========mmmm===========	chr11:78139798-78140058(+)$1	260	220	248	10.7482
[ffffff!!cccooooooccc22fffff	chr11:69844425-69844660(+)$1	235	175	203	13.3017
ggggffffff[aooooooa]ffffff88	chr11:60371591-60371839(+)$1	248	140	168	11.7843
::==========oooooo==========	chr4:154932290-154932578(+)$1	288	257	285	13.9614
ffffff!!ddddoooooodddd4444ff	chr15:79618422-79618682(-)$1	260	59	87	12.4612
ccc[bb[eeeeeooooooeeeee]bb]c	chr14:63761672-63761934(+)$1	262	203	231	12.4324
ffff"""bb[bboooooobbbb22ffff	chr2:109740223-109740462(+)$1	239	195	223	12.2974
dd===========nnnnn==========	chr17:71070171-71070415(+)$1	244	175	203	11.0726
ddd!!cccddddoooooodddd]ccc33	chr8:9547168-9547421(-)$1	253	144	172	12.8415
dd==========oooooo==========	chr2:104269558-104269795(-)$1	237	28	56	15.5236
!dddd!!eeeeeooooooeeeeedddd2	chr7:105060692-105060952(+)$1	260	126	154	12.3696
dddd!!eeeeeooooooeeeee22dddd	chr4:21764215-21764461(+)$1	246	92	120	10.7371
[dddd"""ddddoooooodddddddd]c	chr1:99718162-99718399(-)$1	237	88	116	12.4047
dddda!!eeeeeooooooeeeee22a]d	chr6:35458991-35459226(-)$1	235	28	56	12.6397
=====$$$$$bboooooobb22======	chr3:45224704-45224947(+)$1	243	30	58	13.6941
bb[bbgggggggooooooggggggg333	chr16:96289147-96289385(-)$1	238	27	55	13.6812
c"""dddd!!bboooooobb22dddd44	chr8:73282076-73282333(+)$1	257	108	136	12.8169
ffff!!bb[cccooooooccc]bbffff	chr19:7501194-7501478(-)$1	284	136	164	12.8917
b[eeeee!!cccooooooccc]eeeee]	chr10:115981798-115982060(-)$1	262	86	114	13.2828
=============mmmm===========	chr15:54433142-54433381(+)$1	239	119	147	10.8935
==========[bbmmmmbb=========	chr2:148520371-148520608(-)$1	237	149	177	9.7131
:bb!!ccc[cccooooooccc]ccc22b	chr12:45699869-45700108(+)$1	239	123	151	12.4828
ffffff[eeeeeooooooeeeee333ff	chr2:136606810-136607074(+)$1	264	86	114	12.8339
d####dddd[bboooooobb]ddddddd	chr16:17152997-17153239(-)$1	242	18	46	12.2551
cddddbb"""bboooooobb]bb]dddd	chr2:131763802-131764064(+)$1	262	184	212	12.1390
a[ggggggg[bboooooobb]ggggggg	chr19:21468794-21469035(-)$1	241	100	128	14.5387
"ggggggg[cccooooooccc]gggggg	chr11:105916324-105916572(+)$1	248	116	144	14.7083
ccc[a[ffffffooooooffffff]a]c	chr16:94690461-94690700(+)$1	239	154	182	13.1366
eee[a[ffffffooooooffffffa]ee	chr6:24563982-24564219(-)$1	237	91	119	12.5058
::ggggggg[bboooooobb]ggggggg	chrX:156560065-156560305(-)$1	240	88	116	12.7851
ggggg!!ccc[aooooooa]ccc22ggg	chr4:138013083-138013383(+)$1	300	254	282	13.7715
eeeedddd!!bboooooobb22dddd33	chr4:97780058-97780298(+)$1	240	93	121	12.7264
:ffffff!!cccooooooccc22fffff	chr18:6789859-6790095(+)$1	236	205	233	12.4699
[dddd!!eeeeeooooooeeeee]dddd	chr14:9129129-9129385(-)$1	256	197	225	12.6258
iiiiiii"""bboooooobb4444iiii	chr5:148274170-148274405(+)$1	235	43	71	14.5124
BB:iiiiiiiiiooooooiiiiiiiii:	chr12:45307050-45307286(-)$1	236	15	43	11.0107
ccc!!dddd[bboooooobb]ddddccc	chr7:107789216-107789457(+)$1	241	36	64	13.1544
ccc[agggggggooooooggggggg]a]	chr19:60604468-60604707(-)$1	239	158	186	14.4829
dddd[gggggggooooooggggggg]dd	chr4:57729155-57729390(+)$1	235	8	36	13.7817
$eeeee[eeeeeooooooeeeee]eeee	chr3:88883066-88883304(+)$1	238	93	121	12.1133
ffffa[ffffffooooooffffff]a44	chr13:38070622-38070872(-)$1	250	115	143	12.6816
iiiiii!!ddddoooooodddd22iiii	chr18:9995406-9995644(-)$1	238	202	230	13.4342
dddd[gggggggooooooggggggg]dd	chr11:74490264-74490516(-)$1	252	151	179	13.7817
fbb!!gggggggooooooggggggg]bb	chr11:41725164-41725415(-)$1	251	184	212	13.4592
eee[dddd[a[aooooooa]addddeee	chrX:96661644-96661902(-)$1	258	2	30	12.3572
iiiiiiiii!!annnnna22iiiiiiii	chr6:125171782-125172028(+)$1	246	11	39	9.8230
fffffgggggggooooooggggggg333	chr5:122905949-122906267(-)$1	318	256	284	14.2165
:ggggggg!!bboooooobb]ggggggg	chr5:67677922-67678238(+)$1	316	131	159	13.8675
ffff[ddddcccooooooccc]dddd]f	chrX:159227189-159227442(-)$1	253	29	57	13.0673
hhhhh"""ddddoooooodddd4444hh	chr10:41905723-41905958(-)$1	235	174	202	11.5810
ffffffff[cccooooooccc]ffffff	chr2:136607056-136607366(+)$1	310	207	235	13.1361
::ccc[bb[cccooooooccc]bb]ccc	chrX:91974163-91974412(+)$1	249	37	65	11.4049
ggg[bbccccccooooooccc22ccc]b	chr5:108174394-108174647(-)$1	253	70	98	13.1742
ggdddd[bb[bboooooobbbb]dddd]	chr6:115224767-115225019(+)$1	252	163	191	12.0922

#otherMatches

#Seq PSSM
GGAUGGGAGGGUAGAGAUGCCCUCCCAU	chr11:78139798-78140058(+)$1	260	220	248	10.7482
AGCAUCCUGUUUGUCAAUGAAGUGGAUG	chr11:69844425-69844660(+)$1	235	175	203	13.3017
GUGAGGGCCUUGUGCAUUCUAGGCCUUG	chr11:60371591-60371839(+)$1	248	140	168	11.7843
UUAUUUGUGUAUGAAACAAUGUACAAAU	chr4:154932290-154932578(+)$1	288	257	285	13.9614
GACGUGACGCAGGAGAGGCUGCAGCCCA	chr15:79618422-79618682(-)$1	260	59	87	12.4612
CUGGAAAAAAAAACUUGCUUUUUGUUGU	chr14:63761672-63761934(+)$1	262	203	231	12.4324
UUUUUAAGAUCAUCUUCCUGUUGUAAAA	chr2:109740223-109740462(+)$1	239	195	223	12.2974
CGGGGGUGUGUGUUCAAUGCAUGCAUCU	chr17:71070171-71070415(+)$1	244	175	203	11.0726
GUCUUAGCUCAUUUGAAUGUGAUGCUUU	chr8:9547168-9547421(-)$1	253	144	172	12.8415
AUGGGAGCAAAAGUCCAGUUUUGCUCCU	chr2:104269558-104269795(-)$1	237	28	56	15.5236
AUGCUCAGAGGUCCUACUGCCUCAGCAG	chr7:105060692-105060952(+)$1	260	126	154	12.3696
AUUCUGAUGAUGUGCCAAUUAUGUGAAU	chr4:21764215-21764461(+)$1	246	92	120	10.7371
AAGUUCUGUGCAUUUGAUUGUAAACUGU	chr1:99718162-99718399(-)$1	237	88	116	12.4047
UCCACAAUGUCAUUCCCUUGACACAGUU	chr6:35458991-35459226(-)$1	235	28	56	12.6397
UUUGUCUUAUACUUUCAUGUCAACAAGG	chr3:45224704-45224947(+)$1	243	30	58	13.6941
CCUGCUUGGUUUCCUGCCAGACCAGCCU	chr16:96289147-96289385(-)$1	238	27	55	13.6812
GUUUUUGUAAACCAUCCCGUCCACAGUU	chr8:73282076-73282333(+)$1	257	108	136	12.8169
UUUGCAGUGCUUUAGCCUGAGGACCAAA	chr19:7501194-7501478(-)$1	284	136	164	12.8917
GGAUAAAACUCAAAAUGAUGACUUUAUG	chr10:115981798-115982060(-)$1	262	86	114	13.2828
UAUGCAUGAAUAUAUAAAUAUUUAUGUA	chr15:54433142-54433381(+)$1	239	119	147	10.8935
UUGucucagcacuugggaggcugaggca	chr2:148520371-148520608(-)$1	237	149	177	9.7131
GUGUUGCUGUAGUGUUCUCUAGAGCUUC	chr12:45699869-45700108(+)$1	239	123	151	12.4828
GCUCUCCUCCAAAUGUUGUUGGACAAGA	chr2:136606810-136607074(+)$1	264	86	114	12.8339
GGAACAGGGUGGCUUUUCCCUCCCUCUG	chr16:17152997-17153239(-)$1	242	18	46	12.2551
UUGGGCUUUCAGCGUGCACUCAGUUCCG	chr2:131763802-131764064(+)$1	262	184	212	12.1390
AGGCAUAAAUAGUUGUGUUUUUUUGUGU	chr19:21468794-21469035(-)$1	241	100	128	14.5387
UUGUUUGUCAGCUGUUGUGUUCAUAAAC	chr11:105916324-105916572(+)$1	248	116	144	14.7083
UUCUGAGACAUUGUCUGUGGUGUCCCUG	chr16:94690461-94690700(+)$1	239	154	182	13.1366
CACUGUGGGUGGCACUAUUUAUUCCUGU	chr6:24563982-24564219(-)$1	237	91	119	12.5058
UAAUGAUGUAUCGCAACAGAAAUGUCAU	chrX:156560065-156560305(-)$1	240	88	116	12.7851
GACCUCUGUAGAUACUGUUGUACUUGGG	chr4:138013083-138013383(+)$1	300	254	282	13.7715
CGCAGACAGGCGUAGUCUUGAGUGUCCU	chr4:97780058-97780298(+)$1	240	93	121	12.7264
AUACAUUCUGUAUAUUUUUAUUAAAUGU	chr18:6789859-6790095(+)$1	236	205	233	12.4699
AUGGAGAGACCUCAAGGCAGGUCAUCCA	chr14:9129129-9129385(-)$1	256	197	225	12.6258
GACAGUGUUCAGCUACCACUAUCUUACU	chr5:148274170-148274405(+)$1	235	43	71	14.5124
UGAAUGAUUUUGUUUGAUCAAAAUCAUA	chr12:45307050-45307286(-)$1	236	15	43	11.0107
GCAAUAUGUAUUUCCCUUGAAACAUUGC	chr7:107789216-107789457(+)$1	241	36	64	13.1544
AUAUCUUUGCUUAAAACCAAGCAGAUGU	chr19:60604468-60604707(-)$1	239	158	186	14.4829
GCUGCAGGUUGGACAUGCCUGAUCUAUA	chr4:57729155-57729390(+)$1	235	8	36	13.7817
CAUAUCUAAAUAGAUGAUUGUUUUGAUG	chr3:88883066-88883304(+)$1	238	93	121	12.1133
AGAUAGAAUUUUAAGAAAAAAAUUGUCA	chr13:38070622-38070872(-)$1	250	115	143	12.6816
AAGAGGGAUUAACAACUUUUGACAUUUC	chr18:9995406-9995644(-)$1	238	202	230	13.4342
GUAGAAUUUGAUCUUCCCAUUGAGUGUU	chr11:74490264-74490516(-)$1	252	151	179	13.7817
AACUCAUGUUAUCAUCAUAUAGCAUUGU	chr11:41725164-41725415(-)$1	251	184	212	13.4592
CCAAGGCUCGUCGUAACAGUCAGCCUGG	chrX:96661644-96661902(-)$1	258	2	30	12.3572
CCUGGGUUUCUGUCCAUCUAAGGCUUAG	chr6:125171782-125172028(+)$1	246	11	39	9.8230
ACUGAUGAACGUUUGCGCAUGUUCAAGG	chr5:122905949-122906267(-)$1	318	256	284	14.2165
AAAAAUGGAUUGCCUGUACACCUAUUUU	chr5:67677922-67678238(+)$1	316	131	159	13.8675
ACAUUAUUUGUAUUUAAUUGCUAAGUCA	chrX:159227189-159227442(-)$1	253	29	57	13.0673
GGAUAUUUUAAGUGUCGUCUUGUGUUUG	chr10:41905723-41905958(-)$1	235	174	202	11.5810
UACACAGUAUUGUUCUUGUAAAACUGUG	chr2:136607056-136607366(+)$1	310	207	235	13.1361
CUCCAAUUGUGAGAAAAAUCAGAAGUGG	chrX:91974163-91974412(+)$1	249	37	65	11.4049
CCAAAGAGAUUGUUUUAUCAACUUCUAC	chr5:108174394-108174647(-)$1	253	70	98	13.1742
GCUACAGUCUGGUGCAGUUCGAGUGUGU	chr6:115224767-115225019(+)$1	252	163	191	12.0922

#DB
(.(((((((((((....)))))))))))	chr11:78139798-78140058(+)$1	1	220	248	10.7482
.((((((..(((......)))..)))))	chr11:69844425-69844660(+)$1	1	175	203	13.3017
((((((((((.(......).))))))..	chr11:60371591-60371839(+)$1	1	140	168	11.7843
..((((((((((......))))))))))	chr4:154932290-154932578(+)$1	1	257	285	13.9614
((((((..((((......))))....))	chr15:79618422-79618682(-)$1	1	59	87	12.4612
(((.((.(((((......))))).)).)	chr14:63761672-63761934(+)$1	1	203	231	12.4324
((((...((.((......))))..))))	chr2:109740223-109740462(+)$1	1	195	223	12.2974
))(((((((((((.....))))))))))	chr17:71070171-71070415(+)$1	1	175	203	11.0726
(((..(((((((......)))).)))..	chr8:9547168-9547421(-)$1	1	144	172	12.8415
((((((((((((......))))))))))	chr2:104269558-104269795(-)$1	1	28	56	15.5236
.((((..(((((......))))))))).	chr7:105060692-105060952(+)$1	1	126	154	12.3696
((((..(((((......)))))..))))	chr4:21764215-21764461(+)$1	1	92	120	10.7371
.((((...((((......)))))))).)	chr1:99718162-99718399(-)$1	1	88	116	12.4047
(((((..(((((......)))))..).)	chr6:35458991-35459226(-)$1	1	28	56	12.6397
(((((.....((......))..))))))	chr3:45224704-45224947(+)$1	1	30	58	13.6941
((.(((((((((......)))))))...	chr16:96289147-96289385(-)$1	1	27	55	13.6812
(...((((..((......))..))))..	chr8:73282076-73282333(+)$1	1	108	136	12.8169
((((..((.(((......))).))))))	chr19:7501194-7501478(-)$1	1	136	164	12.8917
(.(((((..(((......))).))))).	chr10:115981798-115982060(-)$1	1	86	114	13.2828
(((((((((((((....)))))))))))	chr15:54433142-54433381(+)$1	1	119	147	10.8935
((((((((((.((....)))))))))))	chr2:148520371-148520608(-)$1	1	149	177	9.7131
.((..(((.(((......))).)))..)	chr12:45699869-45700108(+)$1	1	123	151	12.4828
((((((.(((((......)))))...))	chr2:136606810-136607074(+)$1	1	86	114	12.8339
(....((((.((......)).)))))))	chr16:17152997-17153239(-)$1	1	18	46	12.2551
(((((((...((......)).)).))))	chr2:131763802-131764064(+)$1	1	184	212	12.1390
(.(((((((.((......)).)))))))	chr19:21468794-21469035(-)$1	1	100	128	14.5387
.(((((((.(((......))).))))))	chr11:105916324-105916572(+)$1	1	116	144	14.7083
(((.(.((((((......)))))).).)	chr16:94690461-94690700(+)$1	1	154	182	13.1366
(((.(.((((((......))))))).))	chr6:24563982-24564219(-)$1	1	91	119	12.5058
..(((((((.((......)).)))))))	chrX:156560065-156560305(-)$1	1	88	116	12.7851
(((((..(((.(......).)))..)))	chr4:138013083-138013383(+)$1	1	254	282	13.7715
((((((((..((......))..))))..	chr4:97780058-97780298(+)$1	1	93	121	12.7264
.((((((..(((......)))..)))))	chr18:6789859-6790095(+)$1	1	205	233	12.4699
.((((..(((((......))))).))))	chr14:9129129-9129385(-)$1	1	197	225	12.6258
(((((((...((......))....))))	chr5:148274170-148274405(+)$1	1	43	71	14.5124
((.(((((((((......))))))))).	chr12:45307050-45307286(-)$1	1	15	43	11.0107
(((..((((.((......)).)))))))	chr7:107789216-107789457(+)$1	1	36	64	13.1544
(((.((((((((......))))))).).	chr19:60604468-60604707(-)$1	1	158	186	14.4829
((((.(((((((......))))))).))	chr4:57729155-57729390(+)$1	1	8	36	13.7817
.(((((.(((((......))))).))))	chr3:88883066-88883304(+)$1	1	93	121	12.1133
(((((.((((((......)))))).)..	chr13:38070622-38070872(-)$1	1	115	143	12.6816
((((((..((((......))))..))))	chr18:9995406-9995644(-)$1	1	202	230	13.4342
((((.(((((((......))))))).))	chr11:74490264-74490516(-)$1	1	151	179	13.7817
(((..(((((((......))))))).))	chr11:41725164-41725415(-)$1	1	184	212	13.4592
(((.((((.(.(......).))))))))	chrX:96661644-96661902(-)$1	1	2	30	12.3572
(((((((((..(.....)..))))))))	chr6:125171782-125172028(+)$1	1	11	39	9.8230
((((((((((((......)))))))...	chr5:122905949-122906267(-)$1	1	256	284	14.2165
.(((((((..((......)).)))))))	chr5:67677922-67678238(+)$1	1	131	159	13.8675
((((.(((((((......))).)))).)	chrX:159227189-159227442(-)$1	1	29	57	13.0673
(((((...((((......))))....))	chr10:41905723-41905958(-)$1	1	174	202	11.5810
))((((((.(((......))).))))))	chr2:136607056-136607366(+)$1	1	207	235	13.1361
..(((.((.(((......))).)).)))	chrX:91974163-91974412(+)$1	1	37	65	11.4049
(((.((((((((......)))..))).)	chr5:108174394-108174647(-)$1	1	70	98	13.1742
((((((.((.((......)))).)))).	chr6:115224767-115225019(+)$1	1	163	191	12.0922

#PSSM
f : 0.16	d : 0.14	: : 0.11	c : 0.11	g : 0.07	b : 0.05	[ : 0.05	= : 0.05	e : 0.05	i : 0.05	! : 0.01	a : 0.01	" : 0.01	B : 0.01	$ : 0.01	h : 0.01	
d : 0.20	f : 0.18	g : 0.11	c : 0.07	e : 0.07	[ : 0.05	: : 0.05	= : 0.05	b : 0.05	i : 0.05	" : 0.01	# : 0.01	B : 0.01	h : 0.01	
f : 0.18	d : 0.18	= : 0.12	g : 0.12	c : 0.09	e : 0.09	i : 0.05	b : 0.03	[ : 0.01	" : 0.01	# : 0.01	: : 0.01	h : 0.01	
f : 0.18	d : 0.16	= : 0.12	g : 0.11	[ : 0.11	! : 0.07	i : 0.07	e : 0.05	b : 0.01	" : 0.01	# : 0.01	h : 0.01	c : 0.01	
d : 0.14	= : 0.12	f : 0.12	! : 0.11	a : 0.09	g : 0.09	i : 0.07	b : 0.05	[ : 0.05	e : 0.03	" : 0.01	# : 0.01	h : 0.01	c : 0.01	
g : 0.18	d : 0.12	= : 0.11	f : 0.11	! : 0.11	[ : 0.07	i : 0.07	b : 0.05	" : 0.05	c : 0.03	e : 0.03	$ : 0.01	
g : 0.18	f : 0.12	= : 0.11	! : 0.11	d : 0.11	[ : 0.07	" : 0.05	c : 0.05	b : 0.05	i : 0.05	e : 0.03	$ : 0.01	
g : 0.18	e : 0.12	= : 0.11	d : 0.11	! : 0.09	f : 0.09	b : 0.07	c : 0.07	" : 0.07	i : 0.03	$ : 0.01	
d : 0.14	g : 0.14	e : 0.12	= : 0.11	! : 0.11	[ : 0.11	f : 0.07	b : 0.03	" : 0.03	c : 0.03	i : 0.03	$ : 0.01	
c : 0.20	e : 0.12	= : 0.11	[ : 0.11	g : 0.11	d : 0.09	f : 0.07	! : 0.07	" : 0.03	$ : 0.01	i : 0.01	a : 0.01	
b : 0.22	c : 0.18	e : 0.12	g : 0.11	= : 0.09	d : 0.09	[ : 0.07	f : 0.05	i : 0.01	! : 0.01	
b : 0.24	c : 0.18	e : 0.11	g : 0.11	= : 0.09	d : 0.09	a : 0.07	f : 0.05	o : 0.01	i : 0.01	
o : 0.90	= : 0.05	b : 0.01	n : 0.01	
o : 0.90	m : 0.05	n : 0.03	
o : 0.90	m : 0.05	n : 0.03	
o : 0.90	m : 0.05	n : 0.03	
o : 0.90	m : 0.05	n : 0.03	
o : 0.88	= : 0.03	n : 0.01	e : 0.01	b : 0.01	a : 0.01	
b : 0.24	c : 0.18	e : 0.12	g : 0.11	= : 0.09	d : 0.09	a : 0.05	f : 0.05	i : 0.01	2 : 0.01	
b : 0.22	c : 0.18	e : 0.12	= : 0.11	g : 0.11	d : 0.09	] : 0.05	f : 0.05	i : 0.01	2 : 0.01	
c : 0.20	e : 0.12	= : 0.11	g : 0.11	] : 0.11	d : 0.09	f : 0.07	2 : 0.05	b : 0.03	i : 0.03	4 : 0.01	a : 0.01	
g : 0.16	d : 0.14	e : 0.12	] : 0.12	= : 0.11	2 : 0.11	f : 0.07	b : 0.05	i : 0.03	c : 0.01	4 : 0.01	
g : 0.18	= : 0.12	e : 0.12	d : 0.12	2 : 0.11	f : 0.09	4 : 0.05	b : 0.05	] : 0.03	c : 0.03	i : 0.03	
g : 0.18	d : 0.16	= : 0.12	f : 0.12	2 : 0.09	] : 0.07	4 : 0.05	c : 0.05	b : 0.03	i : 0.03	e : 0.01	3 : 0.01	
d : 0.22	g : 0.18	= : 0.12	f : 0.11	i : 0.07	c : 0.05	] : 0.05	4 : 0.03	2 : 0.03	e : 0.03	b : 0.01	3 : 0.01	a : 0.01	
d : 0.18	= : 0.12	f : 0.11	g : 0.09	] : 0.09	c : 0.07	i : 0.07	a : 0.05	3 : 0.05	e : 0.05	4 : 0.03	b : 0.01	2 : 0.01	
d : 0.14	= : 0.12	f : 0.12	] : 0.11	g : 0.09	3 : 0.07	e : 0.07	i : 0.07	4 : 0.03	c : 0.03	8 : 0.01	2 : 0.01	a : 0.01	b : 0.01	h : 0.01	
f : 0.14	= : 0.12	d : 0.12	c : 0.09	g : 0.09	3 : 0.07	] : 0.05	b : 0.05	e : 0.05	i : 0.05	4 : 0.03	8 : 0.01	2 : 0.01	: : 0.01	h : 0.01	

#score	687.6622402060142
#seq	54
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_transcript_m2_run1.txt

#BEAR
GGG:dddd"""ccc[cccnnnnnccc]ccc333ddd	chr4:126706308-126706556(+)$1	248	130	166	12.5443
d[eeeeeggggggg"""ccclllccc333ggggggg	chr11:60013257-60013493(-)$1	236	81	117	12.1200
###ggggggg####ddddmmmmdddd333ggggggg	chr16:38245760-38245995(+)$1	235	148	184	11.9082
ffggggggg####ddddoooooodddd4444ggggg	chr11:29642384-29642629(+)$1	245	124	160	14.1214
b!!bb[ccc"""ffffffnnnnnffffff333ccc]	chr1:36588172-36588416(-)$1	244	24	60	13.8612
eeedddd==========[aooooooa]=========	chr3:102832811-102833065(+)$1	254	102	138	14.6110
dddd"""dddd"""ddddoooooodddddddd333d	chr10:19329021-19329256(+)$1	235	22	58	13.5567
[dddd"""ccc[ffffffooooooffffff]ccc33	chr2:130101955-130102202(+)$1	247	94	130	13.8722
g[ccc"""dddd"""cccmmmmccc4444dddd444	chr7:74904121-74904374(-)$1	253	188	224	12.4677
gggggg!!ccc"""cccooooooccc]ccc22gggg	chr12:112776564-112776799(+)$1	235	130	166	16.2810
dd!!ggggggg[ccc[bbnnnnnbbcccggggggg]	chr13:12380759-12380997(-)$1	238	62	98	12.9806
:ggggggg"""bb[cccooooooccc]bbggggggg	chr5:136384359-136384619(-)$1	260	211	247	14.5055
hhh"""ccc[ccc"""bbnnnnnbb333cccccc]h	chr15:31385712-31385954(-)$1	242	59	95	13.2181
dddd[ccc"""a!!ddddnnnnndddd22a22ccc]	chr2:76689541-76689776(-)$1	235	123	159	13.5791
[a[a[dddd[dddd[a[annnnna]a]dddd]dddd	chr9:66107240-66107497(+)$1	257	103	139	12.8066
ddd==========!!cccnnnnnccc]=========	chr18:34505052-34505293(-)$1	241	175	211	16.2050
""ccc[ccc[ccc[a[bbnnnnnbb]accc>>>>>>	chr11:75578686-75578922(+)$1	236	161	197	12.3824
$$ccc"""==========nnnnn==========333	chr3:144352137-144352377(-)$1	240	42	78	16.0585
cccdddd!!iiiiiiiiiooooooiiiiiiiiiddd	chr4:104704977-104705228(-)$1	251	78	114	14.5415
"dddd[ccc[bb!!cccooooooccc22bb4444cc	chr13:59037387-59037622(+)$1	235	19	55	14.8778
eeeee"""===========mmmm===========66	chr9:107950750-107950985(+)$1	235	87	123	12.1435
===========[eeeeeooooooeeeee333=====	chr7:122617910-122618153(-)$1	243	41	77	15.1118
:ccc!!dddd!!ffffffooooooffffff22dddd	chr7:122797650-122797885(-)$1	235	85	121	12.2288
========="""ccc!!ccclllccc]ccc]=====	chr18:78021176-78021422(+)$1	246	49	85	14.6330
fffff[dddd!!eeeeeooooooeeeee333dddd]	chr10:120220470-120220730(-)$1	260	75	111	12.8054
bb"""ggggggg"""cccnnnnnccc]ggggggg33	chr2:76594261-76594496(-)$1	235	46	82	15.2326
ccc[dddd"""bb[cccooooooccc]bb]dddd]c	chr15:93115081-93115316(-)$1	235	27	63	14.8025
dddd!!ddddccc[ddddoooooodddd]ccc]ddd	chr19:12843558-12843801(-)$1	243	158	194	12.9937
gg####ccc"""eeeeeooooooeeeeeccc333gg	chr11:29642544-29642783(+)$1	239	57	93	14.7869
iiiiii####ccc[cccooooooccc]ccciiiiii	chr2:14998809-14999056(+)$1	247	82	118	16.4750
cc]ddddccc[gggggggnnnnnggggggg22ccce	chr4:94716681-94716936(-)$1	255	157	193	12.9687
c===========!!cccooooooccc]=========	chrX:99710689-99710958(-)$1	269	117	153	17.5111
b!!bbdddd"""eeeeeooooooeeeeedddd]bb3	chr17:87398130-87398377(+)$1	247	128	164	12.7700
cc[bb!!gggggggcccooooooccc22ggggggg2	chr6:67235597-67235832(+)$1	235	14	50	15.0252
$$$ddddccc!!ffffffooooooffffff333ccc	chr7:139905158-139905393(-)$1	235	139	175	13.5736
ccccc!!a"""ccc[cccnnnnnccc]ccc333a22	chr2:152106642-152106889(+)$1	247	155	191	16.2533
==="""iiiiiiiiirrrrrrrrriiiiiiiii]==	chr10:110603284-110603536(+)$1	252	140	176	12.5107
a[ccc[iiiiiiiiicccnnnnnccc]iiiiiiiii	chr4:98042275-98042510(-)$1	235	145	181	15.8580
""ccc[eeeee"""ddddnnnnndddd]eeeee]cc	chr1:36587649-36587884(-)$1	235	15	51	12.4748
b"""ccc!!dddd[cccoooooocccdddd22ccc2	chr9:50307974-50308209(+)$1	235	54	90	14.9320
[eeeeecccccc[bbcccooooooccc]bb]ccc33	chr7:119254506-119254741(+)$1	235	140	176	13.7233
iiiiiiii[ddddccc[annnnna]ccc22dddd33	chr2:180639581-180639817(-)$1	236	85	121	13.3958
c[dddd[ccc[ffffffooooooffffffccc22dd	chr11:77530551-77530786(+)$1	235	56	92	12.7288
a[a[dddd[dddd[a[aooooooa]a]dddd]dddd	chr9:66106735-66107035(+)$1	300	235	271	13.7622
b[ccc!!ccc[bb[bb[aooooooa]bb]bb]ccc]	chr14:35374752-35374991(-)$1	239	156	192	13.2474
fccc"""dddd####cccmmmmccc333dddd]ccc	chr11:60370509-60370744(+)$1	235	54	90	12.1662
e!!ccc[eeeee[acccooooooccc]a]eeeee]c	chr5:115595369-115595620(-)$1	251	69	105	14.1861
!!eeeee"""ddddddddoooooodddd]dddd333	chr11:40499480-40499715(-)$1	235	81	117	13.4002
ee"""ccc!!dddd[cccnnnnncccddddccceee	chr9:123371098-123371348(+)$1	250	170	206	13.0872
gaddddccc!!dddd[ccclllccc333dddd]ccc	chr16:36035202-36035440(+)$1	238	155	191	12.1887
"""dddd####gggggggnnnnngggggggdddd33	chr19:53447618-53447853(+)$1	235	178	214	14.3045

#otherMatches

#Seq PSSM
CUGUGGCAAAAUAAGUUUUUGAUGAAGUUACUGUGC	chr4:126706308-126706556(+)$1	248	130	166	12.5443
UUCCCUUGAGGACCUUUGUCAUUGGCUGUGGUCUUC	chr11:60013257-60013493(-)$1	236	81	117	12.1200
UUAACUUCCAUCUUAUUAGUAAUGGUCGUUGGGAGU	chr16:38245760-38245995(+)$1	235	148	184	11.9082
GUUAGAUUGCCAAUAUAAGUAAAUAUAGACAUAAUC	chr11:29642384-29642629(+)$1	245	124	160	14.1214
GAUGACUGGCACCUGUGGAUCACCCACGGCCACCAU	chr1:36588172-36588416(-)$1	244	24	60	13.8612
UCUUCAGUGCUGUACUGUGAGAUUGCCCGGUGCAGC	chr3:102832811-102833065(+)$1	254	102	138	14.6110
CUGUGAAGAGCCCCUGUCCACAGUGACAGCUCCAGA	chr10:19329021-19329256(+)$1	235	22	58	13.5567
GUACACCUCAGCCUAGGCCACUGUGCCUGGUCUGUA	chr2:130101955-130102202(+)$1	247	94	130	13.8722
AUGCCGAGCUGGGAGCGCAACGGCGGGAGCUAGAGG	chr7:74904121-74904374(-)$1	253	188	224	12.4677
CAGCGCCUCUUCCUCCCAGUCCCGGGCGAGCCGCGU	chr12:112776564-112776799(+)$1	235	130	166	16.2810
CCCCUUUGCAGGCAAAGAACAGAUCUUGCUGCAGAA	chr13:12380759-12380997(-)$1	238	62	98	12.9806
CUCCGUGUUUCGCUAAGGAAUUAUUUCGCACACGGA	chr5:136384359-136384619(-)$1	260	211	247	14.5055
UUUGUAAUCAUGACAAUCCUAUAGAACCUUAGAUGG	chr15:31385712-31385954(-)$1	242	59	95	13.2181
GUGAGGUGGAGCACUAUGAAGAGCAUGAGGAAUACG	chr2:76689541-76689776(-)$1	235	123	159	13.5791
GUGUGUACAGUGUAGAGAACAGAUGUGUAUAGUGUA	chr9:66107240-66107497(+)$1	257	103	139	12.8066
GCUGCAGUGAAAUAAACUCCAAAAGUAAUUUUGCUG	chr18:34505052-34505293(-)$1	241	175	211	16.2050
AUGGAAGCCUGCAUGCGUGUUCAAcucuguuccucc	chr11:75578686-75578922(+)$1	236	161	197	12.3824
AGCAGGACCCGGUGCUUCCAGCAGGAGUGCUGGUUA	chr3:144352137-144352377(-)$1	240	42	78	16.0585
CCAGGGUGAAGUCUCAUACCUAAAUGUGAGACUGCC	chr4:104704977-104705228(-)$1	251	78	114	14.5415
UUGAAACUCACUUCAUCUUGUUUGGUCUAGACUAGA	chr13:59037387-59037622(+)$1	235	19	55	14.8778
CUGGGGAAAUUUCCUUUGCUUCUGUGGAGGAAAUGU	chr9:107950750-107950985(+)$1	235	87	123	12.1435
AAAGGCAAACAUUUAGCACAGUAGUUAAUUUUGUUU	chr7:122617910-122618153(-)$1	243	41	77	15.1118
GUUGCAUCUCUUUUCUAACUGUAUUUAGGAUUGAGA	chr7:122797650-122797885(-)$1	235	85	121	12.2288
CACAUGAAUAAAAGUUCCAUACUGUGUGCUAGUUUG	chr18:78021176-78021422(+)$1	246	49	85	14.6330
GUGUUGUGUUAGAUUGCUAGGCUGCGAUAACGAUGG	chr10:120220470-120220730(-)$1	260	75	111	12.8054
CUGAGCCUUCAGUACUCCACAAAGGAUCUGAAGGAG	chr2:76594261-76594496(-)$1	235	46	82	15.2326
GUAUGAAUCUUUGCCAAUGUUUUUUGACAUGUUUUU	chr15:93115081-93115316(-)$1	235	27	63	14.8025
UGGGAUCCUUCCUACAAGAGGUACUUUGAAGGCAAG	chr19:12843558-12843801(-)$1	243	158	194	12.9937
UGACCUCUGAGUCAUUGGUUAUACAGUGUAGUCCCA	chr11:29642544-29642783(+)$1	239	57	93	14.7869
GACUUAGCAUAGACAGUUCUUUUGCUUUCUUAGGUU	chr2:14998809-14999056(+)$1	247	82	118	16.4750
GGCGCGCCUGGCUUUGGCGUGGAGCCAGAGAGCAGC	chr4:94716681-94716936(-)$1	255	157	193	12.9687
CUUCUUCACUCAAAGGCUGCUUUGCUCUGAGUGGGG	chrX:99710689-99710958(-)$1	269	117	153	17.5111
GAAGAAACUGUAUAGUUAACAUGAGCUAAGUUGUCA	chr17:87398130-87398377(+)$1	247	128	164	12.7700
AGAUUGUAGCAUAUGCUCCCUUAAGUCAGUAUGCUU	chr6:67235597-67235832(+)$1	235	14	50	15.0252
CCUGGGCGGCAGUACUCCAAACCCGGGGUGGGGGUU	chr7:139905158-139905393(-)$1	235	139	175	13.5736
GCCACUUGCAGUGACUAUUUAUUGUACUCGAUUCUU	chr2:152106642-152106889(+)$1	247	155	191	16.2533
UUUGCAGUGAGAUUAUUAAAAUGCUGGUUUUAUAAA	chr10:110603284-110603536(+)$1	252	140	176	12.5107
agagcccacucacugugcaggaagcaguagugagug	chr4:98042275-98042510(-)$1	235	145	181	15.8580
GGCUGAGGGGCAUGUCAGCAGGACUGAGGCCCCACA	chr1:36587649-36587884(-)$1	235	15	51	12.4748
CUAAGAGACAACUGAGUAAUAACACUAGUUUCCUCC	chr9:50307974-50308209(+)$1	235	54	90	14.9320
AUCUGCCCAUCUAUGGAAUAAAGUUUCUCGGGGGCC	chr7:119254506-119254741(+)$1	235	140	176	13.7233
CUUGCCACCGUCUGCCACUGCAUGAGGUUUGGGCUC	chr2:180639581-180639817(-)$1	236	85	121	13.3958
UUGCAUGUUCUAAGUAGUUUCACUUACUUGAAGUGU	chr11:77530551-77530786(+)$1	235	56	92	12.7288
UGUGUAUAGUGUAGAGAGCAGGGUGUGUACAGUGUA	chr9:66106735-66107035(+)$1	300	235	271	13.7622
CACUCCUGCUCUCUGCCCACCCCAGAGCUGACAGCU	chr14:35374752-35374991(-)$1	239	156	192	13.2474
UGUGCUUGUAAAUCUCUGUAGUUAGUUGUUGCCCAC	chr11:60370509-60370744(+)$1	235	54	90	12.1662
UUUGGGUUAAAGGGGCUGGGUGGGGCACGCUUUAUU	chr5:115595369-115595620(-)$1	251	69	105	14.1861
agacaUGGGGGCUUACUGCUUUUAUAGUCAAGUGGA	chr11:40499480-40499715(-)$1	235	81	117	13.4002
gccaugguaauccugcucaguacgagaggaaccgca	chr9:123371098-123371348(+)$1	250	170	206	13.0872
AGAACUGCAAAUGAGUUCAAUGUGACUUCUCGGUGC	chr16:36035202-36035440(+)$1	238	155	191	12.1887
UUAAUGUCAGAGCUAUCUUCCGUGGAUAGCACGUCU	chr19:53447618-53447853(+)$1	235	178	214	14.3045

#DB
(((.((((...(((.(((.....))).)))...)))	chr4:126706308-126706556(+)$1	1	130	166	12.5443
(.((((((((((((...(((...)))...)))))))	chr11:60013257-60013493(-)$1	1	81	117	12.1200
...(((((((....((((....))))...)))))))	chr16:38245760-38245995(+)$1	1	148	184	11.9082
(((((((((....((((......))))....)))))	chr11:29642384-29642629(+)$1	1	124	160	14.1214
(..((.(((...((((((.....))))))...))).	chr1:36588172-36588416(-)$1	1	24	60	13.8612
)))))))((((((((((.(......).)))))))))	chr3:102832811-102833065(+)$1	1	102	138	14.6110
((((...((((...((((......))))))))...)	chr10:19329021-19329256(+)$1	1	22	58	13.5567
.((((...(((.((((((......)))))).)))..	chr2:130101955-130102202(+)$1	1	94	130	13.8722
(.(((...((((...(((....)))....))))...	chr7:74904121-74904374(-)$1	1	188	224	12.4677
((((((..(((...(((......))).)))..))))	chr12:112776564-112776799(+)$1	1	130	166	16.2810
((..(((((((.(((.((.....)))))))))))).	chr13:12380759-12380997(-)$1	1	62	98	12.9806
.(((((((...((.(((......))).)))))))))	chr5:136384359-136384619(-)$1	1	211	247	14.5055
(((...(((.(((...((.....))...)))))).)	chr15:31385712-31385954(-)$1	1	59	95	13.2181
((((.(((...(..((((.....))))..)..))).	chr2:76689541-76689776(-)$1	1	123	159	13.5791
.(.(.((((.((((.(.(.....).).)))).))))	chr9:66107240-66107497(+)$1	1	103	139	12.8066
)))((((((((((..(((.....))).)))))))))	chr18:34505052-34505293(-)$1	1	175	211	16.2050
..(((.(((.(((.(.((.....)).))))......	chr11:75578686-75578922(+)$1	1	161	197	12.3824
..(((...((((((((((.....))))))))))...	chr3:144352137-144352377(-)$1	1	42	78	16.0585
)))((((..(((((((((......))))))))))))	chr4:104704977-104705228(-)$1	1	78	114	14.5415
.((((.(((.((..(((......)))..))....))	chr13:59037387-59037622(+)$1	1	19	55	14.8778
(((((...(((((((((((....)))))))))))..	chr9:107950750-107950985(+)$1	1	87	123	12.1435
(((((((((((.(((((......)))))...)))))	chr7:122617910-122618153(-)$1	1	41	77	15.1118
.(((..((((..((((((......))))))..))))	chr7:122797650-122797885(-)$1	1	85	121	12.2288
(((((((((...(((..(((...))).))).)))))	chr18:78021176-78021422(+)$1	1	49	85	14.6330
(((((.((((..(((((......)))))...)))).	chr10:120220470-120220730(-)$1	1	75	111	12.8054
((...(((((((...(((.....))).)))))))..	chr2:76594261-76594496(-)$1	1	46	82	15.2326
(((.((((...((.(((......))).)).)))).)	chr15:93115081-93115316(-)$1	1	27	63	14.8025
((((..(((((((.((((......)))).))).)))	chr19:12843558-12843801(-)$1	1	158	194	12.9937
((....(((...(((((......))))))))...))	chr11:29642544-29642783(+)$1	1	57	93	14.7869
((((((....(((.(((......))).)))))))))	chr2:14998809-14999056(+)$1	1	82	118	16.4750
)).))))(((.(((((((.....)))))))..)))(	chr4:94716681-94716936(-)$1	1	157	193	12.9687
)(((((((((((..(((......))).)))))))))	chrX:99710689-99710958(-)$1	1	117	153	17.5111
(..((((((...(((((......))))))))).)).	chr17:87398130-87398377(+)$1	1	128	164	12.7700
((.((..((((((((((......)))..))))))).	chr6:67235597-67235832(+)$1	1	14	50	15.0252
...(((((((..((((((......))))))...)))	chr7:139905158-139905393(-)$1	1	139	175	13.5736
(((((..(...(((.(((.....))).)))...)..	chr2:152106642-152106889(+)$1	1	155	191	16.2533
(((...(((((((((.........))))))))).))	chr10:110603284-110603536(+)$1	1	140	176	12.5107
(.(((.((((((((((((.....))).)))))))))	chr4:98042275-98042510(-)$1	1	145	181	15.8580
..(((.(((((...((((.....)))).))))).))	chr1:36587649-36587884(-)$1	1	15	51	12.4748
(...(((..((((.(((......)))))))..))).	chr9:50307974-50308209(+)$1	1	54	90	14.9320
.(((((((((((.(((((......))).)).)))..	chr7:119254506-119254741(+)$1	1	140	176	13.7233
((((((((.(((((((.(.....).)))..))))..	chr2:180639581-180639817(-)$1	1	85	121	13.3958
(.((((.(((.((((((......)))))))))..))	chr11:77530551-77530786(+)$1	1	56	92	12.7288
(.(.((((.((((.(.(......).).)))).))))	chr9:66106735-66107035(+)$1	1	235	271	13.7622
(.(((..(((.((.((.(......).)).)).))).	chr14:35374752-35374991(-)$1	1	156	192	13.2474
)(((...((((....(((....)))...)))).)))	chr11:60370509-60370744(+)$1	1	54	90	12.1662
(..(((.(((((.((((......))).).))))).)	chr5:115595369-115595620(-)$1	1	69	105	14.1861
..(((((...((((((((......)))).))))...	chr11:40499480-40499715(-)$1	1	81	117	13.4002
((...(((..((((.(((.....)))))))))))))	chr9:123371098-123371348(+)$1	1	170	206	13.0872
(((((((((..((((.(((...)))...)))).)))	chr16:36035202-36035440(+)$1	1	155	191	12.1887
...((((....(((((((.....)))))))))))..	chr19:53447618-53447853(+)$1	1	178	214	14.3045

#PSSM
c : 0.13	d : 0.11	b : 0.09	e : 0.07	g : 0.07	" : 0.07	f : 0.05	[ : 0.05	= : 0.05	: : 0.03	$ : 0.03	i : 0.03	a : 0.03	G : 0.01	# : 0.01	h : 0.01	! : 0.01	
d : 0.13	c : 0.13	[ : 0.11	! : 0.07	e : 0.07	" : 0.07	= : 0.07	g : 0.05	f : 0.03	a : 0.03	$ : 0.03	i : 0.03	G : 0.01	# : 0.01	h : 0.01	b : 0.01	
c : 0.21	d : 0.15	e : 0.09	! : 0.07	= : 0.07	" : 0.07	g : 0.05	# : 0.03	[ : 0.03	i : 0.03	G : 0.01	h : 0.01	f : 0.01	] : 0.01	$ : 0.01	a : 0.01	
d : 0.23	c : 0.19	" : 0.09	e : 0.07	g : 0.07	= : 0.07	b : 0.05	[ : 0.03	i : 0.03	: : 0.01	! : 0.01	a : 0.01	f : 0.01	# : 0.01	
d : 0.23	c : 0.17	" : 0.11	g : 0.09	e : 0.07	= : 0.07	b : 0.05	[ : 0.03	! : 0.03	i : 0.03	f : 0.01	# : 0.01	
d : 0.23	" : 0.15	g : 0.11	[ : 0.11	! : 0.09	c : 0.07	= : 0.07	e : 0.05	i : 0.03	# : 0.01	
d : 0.25	c : 0.19	" : 0.11	g : 0.09	! : 0.07	= : 0.07	e : 0.05	i : 0.05	[ : 0.03	# : 0.01	
c : 0.25	d : 0.19	g : 0.13	= : 0.09	" : 0.09	! : 0.05	i : 0.05	# : 0.03	e : 0.03	a : 0.01	
c : 0.25	d : 0.15	= : 0.13	" : 0.11	g : 0.11	! : 0.05	# : 0.03	i : 0.03	e : 0.03	[ : 0.03	
" : 0.19	d : 0.17	c : 0.13	= : 0.11	g : 0.09	[ : 0.07	# : 0.05	i : 0.05	e : 0.03	! : 0.03	
" : 0.17	d : 0.17	c : 0.13	= : 0.11	g : 0.07	! : 0.07	# : 0.05	i : 0.05	[ : 0.05	e : 0.03	b : 0.01	
d : 0.15	c : 0.13	" : 0.13	g : 0.09	= : 0.09	b : 0.07	# : 0.05	[ : 0.05	i : 0.05	! : 0.05	a : 0.01	f : 0.01	e : 0.01	
c : 0.15	d : 0.13	f : 0.09	" : 0.09	g : 0.07	= : 0.07	e : 0.07	# : 0.05	b : 0.05	! : 0.05	i : 0.05	[ : 0.03	
[ : 0.15	" : 0.11	c : 0.09	d : 0.09	f : 0.09	g : 0.07	! : 0.07	e : 0.07	= : 0.05	i : 0.05	# : 0.03	b : 0.01	a : 0.01	
c : 0.23	d : 0.15	f : 0.09	[ : 0.07	" : 0.07	e : 0.07	= : 0.05	i : 0.05	a : 0.03	g : 0.03	b : 0.03	! : 0.01	# : 0.01	
c : 0.37	d : 0.13	f : 0.09	[ : 0.07	e : 0.07	= : 0.05	" : 0.03	g : 0.03	a : 0.01	i : 0.01	! : 0.01	r : 0.01	b : 0.01	
c : 0.37	d : 0.13	f : 0.09	e : 0.07	= : 0.05	b : 0.05	[ : 0.05	g : 0.03	" : 0.01	i : 0.01	! : 0.01	r : 0.01	a : 0.01	
o : 0.31	c : 0.23	d : 0.11	f : 0.07	b : 0.05	a : 0.05	= : 0.03	g : 0.03	[ : 0.01	i : 0.01	r : 0.01	
o : 0.49	n : 0.33	c : 0.05	m : 0.05	a : 0.01	= : 0.01	r : 0.01	
o : 0.50	n : 0.33	m : 0.07	c : 0.03	r : 0.01	l : 0.01	
o : 0.50	n : 0.33	m : 0.07	l : 0.05	r : 0.01	
o : 0.50	n : 0.33	m : 0.07	l : 0.05	r : 0.01	
o : 0.50	n : 0.33	c : 0.05	l : 0.03	d : 0.01	m : 0.01	r : 0.01	
c : 0.39	o : 0.19	d : 0.07	e : 0.07	b : 0.05	a : 0.05	f : 0.03	= : 0.03	g : 0.03	r : 0.01	
c : 0.41	d : 0.13	f : 0.09	e : 0.07	b : 0.05	] : 0.05	= : 0.03	i : 0.03	g : 0.03	o : 0.01	a : 0.01	
c : 0.39	d : 0.13	f : 0.09	e : 0.07	a : 0.05	3 : 0.05	] : 0.03	= : 0.03	i : 0.03	g : 0.03	4 : 0.01	
] : 0.29	d : 0.15	3 : 0.09	f : 0.09	e : 0.07	c : 0.05	= : 0.03	i : 0.03	2 : 0.03	g : 0.03	4 : 0.01	a : 0.01	b : 0.01	
c : 0.15	d : 0.13	3 : 0.09	f : 0.09	= : 0.09	e : 0.07	b : 0.05	2 : 0.05	i : 0.05	g : 0.05	4 : 0.03	] : 0.03	a : 0.01	
c : 0.15	d : 0.15	f : 0.09	= : 0.09	g : 0.09	3 : 0.07	b : 0.07	] : 0.07	i : 0.05	4 : 0.03	2 : 0.03	e : 0.01	
c : 0.19	d : 0.19	g : 0.15	= : 0.09	3 : 0.05	f : 0.05	i : 0.05	b : 0.05	e : 0.03	4 : 0.01	a : 0.01	] : 0.01	2 : 0.01	
d : 0.21	3 : 0.11	g : 0.11	= : 0.09	2 : 0.09	c : 0.09	i : 0.07	] : 0.05	4 : 0.03	e : 0.03	> : 0.01	b : 0.01	
d : 0.19	g : 0.13	= : 0.13	c : 0.11	3 : 0.09	2 : 0.09	i : 0.07	] : 0.05	e : 0.03	> : 0.01	4 : 0.01	
c : 0.17	d : 0.17	g : 0.15	= : 0.13	3 : 0.09	i : 0.07	] : 0.07	e : 0.03	> : 0.01	4 : 0.01	2 : 0.01	
c : 0.21	d : 0.19	g : 0.15	= : 0.11	3 : 0.07	4 : 0.03	i : 0.03	] : 0.03	e : 0.03	> : 0.01	b : 0.01	a : 0.01	2 : 0.01	
c : 0.19	d : 0.15	g : 0.15	3 : 0.15	= : 0.11	] : 0.05	i : 0.03	4 : 0.01	> : 0.01	6 : 0.01	b : 0.01	2 : 0.01	e : 0.01	
d : 0.15	3 : 0.15	c : 0.13	g : 0.11	= : 0.11	] : 0.09	2 : 0.05	i : 0.03	e : 0.03	4 : 0.01	h : 0.01	> : 0.01	6 : 0.01	

#score	707.7826008441787
#seq	51
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_UTR_m1_run2.txt

#BEAR
!!cccvvvvvvvvvvvvvccc22	chr10:45089358-45089596(+)$1	238	121	144	22.3622
=======ttttttttttt=====	chr10:62207228-62207468(-)$1	240	201	224	22.9192
[ccc[bbtttttttttttbb]cc	chr1:158360392-158360630(-)$1	238	41	64	22.3253
!eeeeeuuuuuuuuuuuueeeee	chr17:15907795-15908044(+)$1	249	96	119	23.6506
iiiiwwwwwwwwwwwwwwiiiii	chr7:126117230-126117479(-)$1	249	203	226	20.9385
::eeeeettttttttttteeeee	chr10:44878256-44878513(+)$1	257	75	98	20.9933
#eeeeettttttttttteeeeeh	chr7:135689962-135690201(+)$1	239	134	157	22.0992
ffffwwwwwwwwwwwwwwfffff	chr5:38918829-38919076(-)$1	247	223	246	20.2829
!!dddduuuuuuuuuuuudddd2	chr13:58278919-58279154(-)$1	235	2	25	22.9630
!fffffftttttttttttfffff	chr19:5134411-5134658(-)$1	247	60	83	22.0711
iiyyyyyyyyyyyyyyyyiiiii	chr15:77591067-77591325(-)$1	258	81	104	20.3015
fffffftttttttttttffffff	chr17:56850982-56851227(+)$1	245	150	173	21.1038
======yyyyyyyyyyyyyyyy=	chr12:106170088-106170323(-)$1	235	141	164	20.3793
ddd[bbvvvvvvvvvvvvvbb]d	chr6:115790697-115790955(-)$1	258	111	134	21.3891
dd!!ccctttttttttttccc]d	chr11:20125515-20125768(+)$1	253	9	32	22.4682
FFeeeeettttttttttteeeee	chr15:32850626-32850896(+)$1	270	161	184	22.1188
gggggggtttttttttttggggg	chr11:95135994-95136251(-)$1	257	207	230	22.5418
:eeeeeuuuuuuuuuuuueeeee	chr11:22735085-22735323(-)$1	238	73	96	22.5336
[ddddwwwwwwwwwwwwwwdddd	chr14:66929913-66930197(+)$1	284	182	205	21.1895
ddd[ccctttttttttttccc22	chr6:108616049-108616373(+)$1	324	237	260	22.2232
!ddddyyyyyyyyyyyyyyyydd	chr4:107479847-107480086(+)$1	239	70	93	20.6330
gggggguuuuuuuuuuuuggggg	chr19:59373221-59373507(-)$1	286	222	245	23.2285
!eeeeeuuuuuuuuuuuueeeee	chr7:134943315-134943558(+)$1	243	129	152	23.6506
dd!!ccctttttttttttccc22	chr19:44380274-44380547(+)$1	273	82	105	22.2325
ffffffuuuuuuuuuuuufffff	chr2:52548332-52548583(-)$1	251	157	180	22.3882
======uuuuuuuuuuuu=====	chr3:65186475-65186712(-)$1	237	205	228	23.5436
[cccyyyyyyyyyyyyyyyyccc	chr6:101100244-101100495(-)$1	251	93	116	20.9239
ee[cccuuuuuuuuuuuuccc]e	chr4:41138393-41138638(+)$1	245	139	162	23.0985
gggggguuuuuuuuuuuuggggg	chrX:132704575-132704848(-)$1	273	73	96	23.2285
::eeeeettttttttttteeeee	chr9:88356433-88356669(-)$1	236	38	61	20.9933
cddddvvvvvvvvvvvvvdddd]	chr2:71100857-71101104(+)$1	247	140	163	22.2098
ffffwwwwwwwwwwwwwwfffff	chr5:102264572-102264808(-)$1	236	169	192	20.2829
EEeeeeettttttttttteeeee	chrX:35773347-35773583(-)$1	236	199	222	21.0230
dd!!ccctttttttttttccc22	chr19:44380145-44380468(+)$1	323	211	234	22.2325
ffffffuuuuuuuuuuuufffff	chr4:126114950-126115196(-)$1	246	8	31	22.3882
::eeeeettttttttttteeeee	chr11:105790106-105790367(+)$1	261	10	33	20.9933
!!ddddtttttttttttddddbb	chr1:78703063-78703324(+)$1	261	48	71	21.1762
ffffffuuuuuuuuuuuufffff	chr3:60332837-60333117(+)$1	280	71	94	22.3882
ffffffvvvvvvvvvvvvvffff	chr6:142351584-142351834(+)$1	250	28	51	21.8112
ecccbbuuuuuuuuuuuubb]cc	chr4:141370498-141370743(+)$1	245	54	77	22.2826
[eeeeettttttttttteeeee]	chr15:3932198-3932474(-)$1	276	164	187	22.5019
[ccc!!attttttttttta22cc	chr15:103129634-103129931(+)$1	297	44	67	22.7065
[ddddvvvvvvvvvvvvvdddd]	chr3:88882313-88882549(+)$1	236	198	221	22.5116
ggddddvvvvvvvvvvvvvdddd	chr19:11017372-11017617(-)$1	245	185	208	22.2595
eeddddvvvvvvvvvvvvvdddd	chr19:56005960-56006259(+)$1	299	244	267	22.1070
[eeeeevvvvvvvvvvvvveeee	chr11:32645105-32645344(+)$1	239	188	211	23.0552
ffyyyyyyyyyyyyyyyyfffff	chr12:86473813-86474053(+)$1	240	89	112	19.8139
ggg!!bbtttttttttttbb]gg	chr1:158578178-158578433(+)$1	255	21	44	22.3579
[eeeeettttttttttteeeee]	chr5:21992291-21992574(-)$1	283	30	53	22.5019
dddd[bbtttttttttttbb]dd	chr2:180708641-180708899(+)$1	258	106	129	21.8264
fffffbbtttttttttttbb]ff	chr1:94756612-94756859(+)$1	247	129	152	21.6745
""ddddtttttttttttdddd33	chr8:113334372-113334622(-)$1	250	202	225	21.6801
eeeeewwwwwwwwwwwwwweeee	chr15:78760406-78760712(+)$1	306	213	236	21.3932
ggggggvvvvvvvvvvvvvgggg	chr15:79550608-79550854(+)$1	246	51	74	22.6274
=======ttttttttttt=====	chr3:97725790-97726043(+)$1	253	112	135	22.9192
:eeeeeuuuuuuuuuuuueeeee	chr9:56343958-56344219(+)$1	261	118	141	22.5336
[eeeeevvvvvvvvvvvvveeee	chr2:37229672-37229967(-)$1	295	181	204	23.0552
!ddddwwwwwwwwwwwwwwdddd	chr13:38593037-38593294(-)$1	257	185	208	21.1584
hhhhhhuuuuuuuuuuuuhhhhh	chr4:151764803-151765076(-)$1	273	227	250	20.8895
[ddddwwwwwwwwwwwwwwdddd	chr2:119411119-119411358(+)$1	239	107	130	21.1895
gggggggtttttttttttggggg	chr2:104266733-104267003(-)$1	270	105	128	22.5418
!!bbyyyyyyyyyyyyyyyybb2	chr14:49631804-49632068(-)$1	264	116	139	19.6368
ee!!bbtttttttttttbb22ee	chr19:7500939-7501176(-)$1	237	93	116	20.8235
eeeeeeuuuuuuuuuuuueeeee	chr10:90626794-90627044(-)$1	250	192	215	23.3287
ggggggwwwwwwwwwwwwwwggg	chr4:147991047-147991310(-)$1	263	150	173	21.0049
[ddddvvvvvvvvvvvvvddddd	chr15:27523118-27523368(+)$1	250	185	208	22.3594
''dddduuuuuuuuuuuudddd9	chr18:80932138-80932373(-)$1	235	35	58	20.8969
fbb!!bbtttttttttttbb333	chr5:135657397-135657646(+)$1	249	75	98	21.5835
::eeeeettttttttttteeeee	chr8:74676581-74676817(+)$1	236	184	207	20.9933
======vvvvvvvvvvvvv====	chr15:35861701-35861936(-)$1	235	29	52	22.8573
ccccccuuuuuuuuuuuuccc]c	chr7:6658952-6659253(-)$1	301	71	94	23.0682
[ccc[bbtttttttttttbb]cc	chr9:7932098-7932341(-)$1	243	182	205	22.3253
cccddddtttttttttttdddd]	chr2:155919784-155920021(-)$1	237	210	233	22.2088

#otherMatches

#Seq PSSM
CUGACAUAACAUUAAAAAGUUUA	chr10:45089358-45089596(+)$1	238	121	144	22.3622
CUUUGUUAUAGUUUCCCCAAUAA	chr10:62207228-62207468(-)$1	240	201	224	22.9192
CCUUCCACUGUAUUUUUCUGAAA	chr1:158360392-158360630(-)$1	238	41	64	22.3253
AUUAUUGUAAAUGGAUUAAAUGA	chr17:15907795-15908044(+)$1	249	96	119	23.6506
CUUUAAUGCAAAUUUUUAAAAGG	chr7:126117230-126117479(-)$1	249	203	226	20.9385
AAUGGGAUUUCCAGUUCCUCCCA	chr10:44878256-44878513(+)$1	257	75	98	20.9933
CUAACCCUAACCCCUCUGGUUGU	chr7:135689962-135690201(+)$1	239	134	157	22.0992
UUGCACAUGAGAAAUAAAGCAAG	chr5:38918829-38919076(-)$1	247	223	246	20.2829
GAUUCUGUGCUGUUAUAAAGGAA	chr13:58278919-58279154(-)$1	235	2	25	22.9630
UUUCUGGAAAUGAAAAACCUGGA	chr19:5134411-5134658(-)$1	247	60	83	22.0711
uuucuuuuuuuuuuuuuuAAAGG	chr15:77591067-77591325(-)$1	258	81	104	20.3015
ACAUUUAUGUAAGAUUGAAAUGU	chr17:56850982-56851227(+)$1	245	150	173	21.1038
UACAGAAUUUUUAUAUGCCAUGU	chr12:106170088-106170323(-)$1	235	141	164	20.3793
aggaccucugCUUGCUUCUGGCC	chr6:115790697-115790955(-)$1	258	111	134	21.3891
AUUCUACUCAGCAGCCACGUGUG	chr11:20125515-20125768(+)$1	253	9	32	22.4682
GGGUUGGGAGUACAGAAGCCAAC	chr15:32850626-32850896(+)$1	270	161	184	22.1188
UAAGUCCAUUCCCUUUCGGGACU	chr11:95135994-95136251(-)$1	257	207	230	22.5418
AUUAUCACGUAUUCCUUAGAUAA	chr11:22735085-22735323(-)$1	238	73	96	22.5336
gagcaucuuuccucauguuugcu	chr14:66929913-66930197(+)$1	284	182	205	21.1895
UGUAGGCUAUUUCCUCUUGCCCA	chr6:108616049-108616373(+)$1	324	237	260	22.2232
UGCCUUCUGCUUCUCACCUCCAG	chr4:107479847-107480086(+)$1	239	70	93	20.6330
UGCAUUGAAUAGAGAAUAAGUGC	chr19:59373221-59373507(-)$1	286	222	245	23.2285
UGGAACCCUGCCUCAUCUGUUCC	chr7:134943315-134943558(+)$1	243	129	152	23.6506
ucCGUGGAUUCCUUAAAACCAGA	chr19:44380274-44380547(+)$1	273	82	105	22.2325
CUAAAUUAUAAAAGCUUUAUUUA	chr2:52548332-52548583(-)$1	251	157	180	22.3882
UUAUUUGuuuuuuuauuaaagua	chr3:65186475-65186712(-)$1	237	205	228	23.5436
AUAGUCUAAAUUUGCCACUCCUG	chr6:101100244-101100495(-)$1	251	93	116	20.9239
UCAGUGACACCAUCCCAACAUGG	chr4:41138393-41138638(+)$1	245	139	162	23.0985
UUUAAUAAGUGGGAGUUAAUUAA	chrX:132704575-132704848(-)$1	273	73	96	23.2285
AGGCUAUGGAAGAAAUGAAUGGU	chr9:88356433-88356669(-)$1	236	38	61	20.9933
UGUCAUUUUUAAUACAGCUGACA	chr2:71100857-71101104(+)$1	247	140	163	22.2098
UUUUUUUUUUUAAUCCUCAAAGA	chr5:102264572-102264808(-)$1	236	169	192	20.2829
GCCUGAAAACCUUACUAGUUCAG	chrX:35773347-35773583(-)$1	236	199	222	21.0230
ucCGUGGAUUCCUUAAAACCAGA	chr19:44380145-44380468(+)$1	323	211	234	22.2325
CAUUUGCUUCUGUUUACACAAAU	chr4:126114950-126115196(-)$1	246	8	31	22.3882
UCUGUCUCCUCCAACCCAAGACG	chr11:105790106-105790367(+)$1	261	10	33	20.9933
ACGUCACCAUUUUUAACUGACAG	chr1:78703063-78703324(+)$1	261	48	71	21.1762
CCUUCUGCCAGGAAAUCAAGGAG	chr3:60332837-60333117(+)$1	280	71	94	22.3882
AUCCUACCUCAAUAGCUCAUGGG	chr6:142351584-142351834(+)$1	250	28	51	21.8112
UGGGACUUCCUUGAAAAUGUGCC	chr4:141370498-141370743(+)$1	245	54	77	22.2826
CUGGGGCCCCUUUAUAACUCCAU	chr15:3932198-3932474(-)$1	276	164	187	22.5019
GAGGAACAGUGAUUUAAAGGCCC	chr15:103129634-103129931(+)$1	297	44	67	22.7065
AUUAAAGAAAAAAAGAAAUUAAG	chr3:88882313-88882549(+)$1	236	198	221	22.5116
augcacaccuuuuauccccgugc	chr19:11017372-11017617(-)$1	245	185	208	22.2595
ACCUGCCACCUGCCGCUCUGCAG	chr19:56005960-56006259(+)$1	299	244	267	22.1070
GUGGAGAUUGUCACACCUACUCC	chr11:32645105-32645344(+)$1	239	188	211	23.0552
GACUCUUAUCUUCUGCUAUCUUG	chr12:86473813-86474053(+)$1	240	89	112	19.8139
CUUCAGAGAUUUGUACCAUCAAA	chr1:158578178-158578433(+)$1	255	21	44	22.3579
CACUAUUUUAAAAGAUCAUAGUU	chr5:21992291-21992574(-)$1	283	30	53	22.5019
UCUGUGUUUAUCUUCAGUGCUCA	chr2:180708641-180708899(+)$1	258	106	129	21.8264
UCCUUGUAUGAAUUAAAGGCUGG	chr1:94756612-94756859(+)$1	247	129	152	21.6745
CUGAAUAUAUAAAACUAGUUUUU	chr8:113334372-113334622(-)$1	250	202	225	21.6801
CCCAUAAUCCAGCCCUUUCAUGG	chr15:78760406-78760712(+)$1	306	213	236	21.3932
CAGCCCGAUUUUCCAUGGGGGGU	chr15:79550608-79550854(+)$1	246	51	74	22.6274
uguuuuguuuuguuuuguugaga	chr3:97725790-97726043(+)$1	253	112	135	22.9192
UGCUGUUUCUCUCUGUAUGCAGU	chr9:56343958-56344219(+)$1	261	118	141	22.5336
GCGUUUGCACUGACUAACAAGAU	chr2:37229672-37229967(-)$1	295	181	204	23.0552
UGCCUGAGUUUUGGGAAGGAGGC	chr13:38593037-38593294(-)$1	257	185	208	21.1584
UUCUGAUCUCUCCUUUCCUCAGA	chr4:151764803-151765076(-)$1	273	227	250	20.8895
CAUGCUGCCUUCCAUCCCUGCAU	chr2:119411119-119411358(+)$1	239	107	130	21.1895
UGCUACACUAGUUUGCCAUGUAG	chr2:104266733-104267003(-)$1	270	105	128	22.5418
UUGUUAAUUAUUAUUUCCAUGCU	chr14:49631804-49632068(-)$1	264	116	139	19.6368
UGAUAGAUACAACAGAACUUACA	chr19:7500939-7501176(-)$1	237	93	116	20.8235
CUCUGCAGAAAACACAAGGCAGA	chr10:90626794-90627044(-)$1	250	192	215	23.3287
CUUUGCAGGAGAACUUGGAAGCA	chr4:147991047-147991310(-)$1	263	150	173	21.0049
CAGACUUUUCCUGUUCAUGUUUG	chr15:27523118-27523368(+)$1	250	185	208	22.3594
UAUCUGUAAAACCAUACUCAGAA	chr18:80932138-80932373(-)$1	235	35	58	20.8969
CUCCUGCAGAAAACCCCAGCCAU	chr5:135657397-135657646(+)$1	249	75	98	21.5835
UCUCAGUUAACAUCUCACACUGA	chr8:74676581-74676817(+)$1	236	184	207	20.9933
UGGUAGUAAUAAAGAUUGUUUAU	chr15:35861701-35861936(-)$1	235	29	52	22.8573
GCUCUUACAUUGUAAAUAAGGAA	chr7:6658952-6659253(-)$1	301	71	94	23.0682
CUGACUCUCACUAAAUUUGAAUC	chr9:7932098-7932341(-)$1	243	182	205	22.3253
GGCUCUUUUUCUAAAUUUAAGAU	chr2:155919784-155920021(-)$1	237	210	233	22.2088

#DB
..(((.............)))..	chr10:45089358-45089596(+)$1	1	121	144	22.3622
(((((((...........)))))	chr10:62207228-62207468(-)$1	1	201	224	22.9192
.(((.((...........)).))	chr1:158360392-158360630(-)$1	1	41	64	22.3253
.(((((............)))))	chr17:15907795-15908044(+)$1	1	96	119	23.6506
((((..............)))))	chr7:126117230-126117479(-)$1	1	203	226	20.9385
..(((((...........)))))	chr10:44878256-44878513(+)$1	1	75	98	20.9933
.(((((...........))))))	chr7:135689962-135690201(+)$1	1	134	157	22.0992
((((..............)))))	chr5:38918829-38919076(-)$1	1	223	246	20.2829
..((((............)))).	chr13:58278919-58279154(-)$1	1	2	25	22.9630
.((((((...........)))))	chr19:5134411-5134658(-)$1	1	60	83	22.0711
((................)))))	chr15:77591067-77591325(-)$1	1	81	104	20.3015
((((((...........))))))	chr17:56850982-56851227(+)$1	1	150	173	21.1038
((((((................)	chr12:106170088-106170323(-)$1	1	141	164	20.3793
(((.((.............)).)	chr6:115790697-115790955(-)$1	1	111	134	21.3891
((..(((...........))).)	chr11:20125515-20125768(+)$1	1	9	32	22.4682
(((((((...........)))))	chr15:32850626-32850896(+)$1	1	161	184	22.1188
(((((((...........)))))	chr11:95135994-95136251(-)$1	1	207	230	22.5418
.(((((............)))))	chr11:22735085-22735323(-)$1	1	73	96	22.5336
.((((..............))))	chr14:66929913-66930197(+)$1	1	182	205	21.1895
(((.(((...........)))..	chr6:108616049-108616373(+)$1	1	237	260	22.2232
.((((................))	chr4:107479847-107480086(+)$1	1	70	93	20.6330
((((((............)))))	chr19:59373221-59373507(-)$1	1	222	245	23.2285
.(((((............)))))	chr7:134943315-134943558(+)$1	1	129	152	23.6506
((..(((...........)))..	chr19:44380274-44380547(+)$1	1	82	105	22.2325
((((((............)))))	chr2:52548332-52548583(-)$1	1	157	180	22.3882
((((((............)))))	chr3:65186475-65186712(-)$1	1	205	228	23.5436
.(((................)))	chr6:101100244-101100495(-)$1	1	93	116	20.9239
((.(((............))).)	chr4:41138393-41138638(+)$1	1	139	162	23.0985
((((((............)))))	chrX:132704575-132704848(-)$1	1	73	96	23.2285
..(((((...........)))))	chr9:88356433-88356669(-)$1	1	38	61	20.9933
(((((.............)))).	chr2:71100857-71101104(+)$1	1	140	163	22.2098
((((..............)))))	chr5:102264572-102264808(-)$1	1	169	192	20.2829
))(((((...........)))))	chrX:35773347-35773583(-)$1	1	199	222	21.0230
((..(((...........)))..	chr19:44380145-44380468(+)$1	1	211	234	22.2325
((((((............)))))	chr4:126114950-126115196(-)$1	1	8	31	22.3882
..(((((...........)))))	chr11:105790106-105790367(+)$1	1	10	33	20.9933
..((((...........))))))	chr1:78703063-78703324(+)$1	1	48	71	21.1762
((((((............)))))	chr3:60332837-60333117(+)$1	1	71	94	22.3882
((((((.............))))	chr6:142351584-142351834(+)$1	1	28	51	21.8112
)(((((............)).))	chr4:141370498-141370743(+)$1	1	54	77	22.2826
.(((((...........))))).	chr15:3932198-3932474(-)$1	1	164	187	22.5019
.(((..(...........)..))	chr15:103129634-103129931(+)$1	1	44	67	22.7065
.((((.............)))).	chr3:88882313-88882549(+)$1	1	198	221	22.5116
))((((.............))))	chr19:11017372-11017617(-)$1	1	185	208	22.2595
((((((.............))))	chr19:56005960-56006259(+)$1	1	244	267	22.1070
.(((((.............))))	chr11:32645105-32645344(+)$1	1	188	211	23.0552
((................)))))	chr12:86473813-86474053(+)$1	1	89	112	19.8139
(((..((...........)).))	chr1:158578178-158578433(+)$1	1	21	44	22.3579
.(((((...........))))).	chr5:21992291-21992574(-)$1	1	30	53	22.5019
((((.((...........)).))	chr2:180708641-180708899(+)$1	1	106	129	21.8264
(((((((...........)).))	chr1:94756612-94756859(+)$1	1	129	152	21.6745
..((((...........))))..	chr8:113334372-113334622(-)$1	1	202	225	21.6801
(((((..............))))	chr15:78760406-78760712(+)$1	1	213	236	21.3932
((((((.............))))	chr15:79550608-79550854(+)$1	1	51	74	22.6274
(((((((...........)))))	chr3:97725790-97726043(+)$1	1	112	135	22.9192
.(((((............)))))	chr9:56343958-56344219(+)$1	1	118	141	22.5336
.(((((.............))))	chr2:37229672-37229967(-)$1	1	181	204	23.0552
.((((..............))))	chr13:38593037-38593294(-)$1	1	185	208	21.1584
((((((............)))))	chr4:151764803-151765076(-)$1	1	227	250	20.8895
.((((..............))))	chr2:119411119-119411358(+)$1	1	107	130	21.1895
(((((((...........)))))	chr2:104266733-104267003(-)$1	1	105	128	22.5418
..((................)).	chr14:49631804-49632068(-)$1	1	116	139	19.6368
((..((...........))..))	chr19:7500939-7501176(-)$1	1	93	116	20.8235
((((((............)))))	chr10:90626794-90627044(-)$1	1	192	215	23.3287
((((((..............)))	chr4:147991047-147991310(-)$1	1	150	173	21.0049
.((((.............)))))	chr15:27523118-27523368(+)$1	1	185	208	22.3594
..((((............)))).	chr18:80932138-80932373(-)$1	1	35	58	20.8969
(((..((...........))...	chr5:135657397-135657646(+)$1	1	75	98	21.5835
..(((((...........)))))	chr8:74676581-74676817(+)$1	1	184	207	20.9933
((((((.............))))	chr15:35861701-35861936(-)$1	1	29	52	22.8573
((((((............))).)	chr7:6658952-6659253(-)$1	1	71	94	23.0682
.(((.((...........)).))	chr9:7932098-7932341(-)$1	1	182	205	22.3253
(((((((...........)))).	chr2:155919784-155920021(-)$1	1	210	233	22.2088

#PSSM
[ : 0.16	f : 0.13	! : 0.12	g : 0.10	: : 0.08	d : 0.08	e : 0.08	= : 0.06	c : 0.04	i : 0.02	# : 0.01	F : 0.01	E : 0.01	" : 0.01	h : 0.01	' : 0.01	
e : 0.19	d : 0.17	f : 0.13	g : 0.10	c : 0.09	= : 0.06	! : 0.05	: : 0.05	i : 0.02	F : 0.01	E : 0.01	" : 0.01	h : 0.01	' : 0.01	b : 0.01	
e : 0.23	d : 0.21	f : 0.12	c : 0.10	g : 0.09	= : 0.06	! : 0.05	y : 0.02	b : 0.02	i : 0.01	[ : 0.01	h : 0.01	
e : 0.23	d : 0.20	f : 0.12	c : 0.10	! : 0.08	g : 0.08	= : 0.06	y : 0.02	[ : 0.02	i : 0.01	h : 0.01	b : 0.01	
e : 0.23	d : 0.19	c : 0.09	f : 0.09	g : 0.08	= : 0.06	y : 0.05	[ : 0.04	w : 0.04	b : 0.04	! : 0.04	h : 0.01	
e : 0.21	b : 0.12	w : 0.09	d : 0.09	f : 0.08	c : 0.08	g : 0.08	= : 0.06	y : 0.06	v : 0.05	! : 0.01	h : 0.01	
u : 0.23	v : 0.16	w : 0.10	t : 0.09	b : 0.08	e : 0.08	y : 0.08	c : 0.05	= : 0.02	g : 0.02	f : 0.01	a : 0.01	d : 0.01	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.41	u : 0.23	v : 0.16	w : 0.10	y : 0.08	
t : 0.31	u : 0.23	v : 0.16	w : 0.10	y : 0.08	e : 0.04	d : 0.02	f : 0.01	b : 0.01	
e : 0.19	b : 0.10	f : 0.10	d : 0.10	v : 0.10	c : 0.09	w : 0.06	y : 0.05	g : 0.05	= : 0.04	i : 0.02	a : 0.01	h : 0.01	
e : 0.23	d : 0.17	f : 0.12	b : 0.10	c : 0.09	g : 0.06	= : 0.05	y : 0.05	i : 0.02	2 : 0.02	h : 0.01	w : 0.01	
e : 0.23	d : 0.17	f : 0.12	c : 0.10	] : 0.08	g : 0.08	= : 0.05	i : 0.02	y : 0.02	b : 0.02	2 : 0.02	h : 0.01	3 : 0.01	
e : 0.24	d : 0.17	f : 0.13	g : 0.09	c : 0.06	2 : 0.05	= : 0.05	] : 0.05	i : 0.02	b : 0.02	3 : 0.02	y : 0.01	h : 0.01	
e : 0.21	f : 0.13	d : 0.13	g : 0.09	2 : 0.08	c : 0.08	= : 0.06	] : 0.06	i : 0.02	h : 0.02	3 : 0.02	b : 0.01	9 : 0.01	

#score	1601.957210919071
#seq	73
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_UTR_m2_run1.txt

#BEAR
bbgggggggffffffmmmmffffff333ggggggg]	chr15:27396439-27396677(+)$1	238	87	123	11.4287
gg!!gggggggeeeeellleeeee4444gggggggg	chr5:136384359-136384619(-)$1	260	111	147	11.4490
==========!!cccnnnnnccc]==========::	chr18:34505052-34505293(-)$1	241	178	214	13.0562
=======333eeeee4444ccc]==========333	chr11:51799963-51800205(-)$1	242	165	201	11.1919
eee[ccc$$$$$bboooooobbccc]eeeee333bb	chr11:51789805-51790053(+)$1	248	81	117	11.1049
eeeggggggg"""ccclllccc333ggggggg22ee	chr11:60013257-60013493(-)$1	236	85	121	14.3141
dddd[bbccc!!cccmmmmccc22ccc333bb]ddd	chr19:21346951-21347187(+)$1	236	27	63	12.8016
b!!eeeeebb[ddddmmmmdddd]bb]eeeee333b	chr9:107950460-107950695(+)$1	235	160	196	10.8095
hgggggggeeeeebbmmmmbb333eeeee22ggggg	chr2:174155522-174155762(+)$1	240	113	149	11.7733
iiii####ccc[cccooooooccc]ccciiiiiiii	chr2:14998809-14999056(+)$1	247	84	120	13.1577
ggggggg####ddddmmmmdddd333ggggggg444	chr16:38245760-38245995(+)$1	235	151	187	13.9495
hh!!eeeee####bbmmmmbb333eeeee333hhhh	chr3:120905483-120905743(-)$1	260	176	212	12.6590
c"""dddd####cccmmmmccc333dddd]ccc:::	chr11:60370509-60370744(+)$1	235	57	93	12.5705
d"""ffffff[ddddmmmmdddd]ffffff333ddd	chr12:55960170-55960414(-)$1	244	95	131	11.7742
####ccc!!ggggggglllggggggg22ccc>>>>>	chr7:122617910-122618153(-)$1	243	143	179	11.4500
f"""ffffff!!cccmmmmccc22ffffff333fff	chr7:138588944-138589179(+)$1	235	95	131	14.1164
dddd"""ccc[ddddmmmmddddccc]dddd22ccc	chr2:32489706-32489967(+)$1	261	126	162	10.9239
b"""ccc[ccc[cccooooooccccccccc]bbeee	chr17:10401591-10401830(-)$1	239	101	137	12.6109
ccdddd[ccc!!cccmmmmccc22ccc]dddd]ccc	chr4:33107838-33108088(+)$1	250	115	151	13.7261
eeeee[eeeee[cccnnnnnccc]eeeee333eeee	chr14:21479143-21479380(-)$1	237	110	146	10.5951
:iiiiiiiii[bboooooobb]iiiiiiiiicccdd	chr13:23831413-23831656(+)$1	243	68	104	10.9913
ggg!!eeeee!!cccmmmmccc]eeeeeggggggg2	chr13:55445984-55446219(-)$1	235	142	178	13.6324
eeeccc[eeeeecccmmmmccc]eeeee]ccc]eee	chr5:36944678-36944920(-)$1	242	43	79	11.8828
"""ccc[ccc"""bbnnnnnbb333cccccc]hhhh	chr15:31385712-31385954(-)$1	242	62	98	12.4898
cccc[bb$$$$$cccmmmmccc333bb]ccc]ccc]	chr1:133921657-133921904(+)$1	247	204	240	13.8586
ee!!dddd!!cccooooooccc22dddd4444eeee	chrX:99709798-99710042(-)$1	244	207	243	11.7808
:ccc!!dddd!!cccmmmmccc333ddddccc:ccc	chr10:82203477-82203715(+)$1	238	153	189	12.3616
####ccc"""eeeeeooooooeeeeeccc333gggg	chr11:29642590-29642878(+)$1	288	13	49	12.2699
ee[iiiiiiiiicccmmmmccc333iiiiiiiii]e	chr16:7412188-7412449(+)$1	261	153	189	15.3370
"""dddd[ccc[cccmmmmccc22ccc]dddd22ee	chr3:102832811-102833065(+)$1	254	54	90	13.7387
==========!!bb!!ammmma22bb22========	chr2:72241690-72241976(+)$1	286	204	240	12.1620
"""ccc[bb[a!!bbmmmmbb22a]bb]ccchhhhh	chr7:25321336-25321574(+)$1	238	87	123	11.5572
d!!dddd[ccc[bboooooobb]ccc]dddd22ddd	chr4:33107028-33107268(+)$1	240	93	129	11.1242
gg!!ccc"""cccooooooccc]ccc22gggggggd	chr12:112776564-112776799(+)$1	235	134	170	13.6782
ee!!ccc"""eeeeennnnneeeee333ccc]eeee	chr16:94690321-94690556(+)$1	235	6	42	10.7977
ggggggg!!bb!!bbmmmmbb]bb22ggggggg]cc	chr7:52665530-52665765(+)$1	235	107	143	12.0543
"""============oooooo============333	chr7:99792676-99792911(-)$1	235	70	106	14.7139
b[ccc[dddd!!ddddllldddd]dddd]ccc]bb]	chr8:24259437-24259677(+)$1	240	132	168	10.4254
bb!!gggggggcccooooooccc22ggggggg22bb	chr6:67235597-67235832(+)$1	235	17	53	13.0594
!bbggggggg"""bbmmmmbb333ggggggg333bb	chr17:27716430-27716665(-)$1	235	94	130	14.2425
:ggggggg[a!!cccmmmmccc22a]gggggggHHH	chr13:97408636-97408876(+)$1	240	160	196	12.5159
ggg[ccc!!a!!cccmmmmccc333a22cccggggg	chr13:59037387-59037622(+)$1	235	71	107	16.2261
#a[ggggggg"""ccclllccc333gggggggafff	chr4:42970622-42970863(+)$1	241	54	90	14.5589
ccc[ccc!!ccccccnnnnnccc4444ccc22cccc	chr15:103023875-103024111(-)$1	236	7	43	12.6587
dbbdddd[a"""cccmmmmccc333adddd]bb22d	chr17:33855430-33855665(-)$1	235	52	88	13.1017
fff"""gggggggooooooggggggg22ffffffee	chr12:33660678-33660920(+)$1	242	74	110	10.3443
cc"""==========nnnnn==========333ccc	chr3:144352137-144352377(-)$1	240	45	81	13.6968
ccc[ccc!!ffffffmmmmffffff22ccc]ccc77	chr7:88679712-88679947(-)$1	235	20	56	10.4877
========####ddddllldddd]==========::	chr13:83802497-83802751(+)$1	254	4	40	12.2967
ccc[ffffff"""bbmmmmbb22ffffff]ccc333	chr3:69357854-69358091(+)$1	237	98	134	12.1753
$ccc[ccc"""ddddmmmmddddccc22ccc333cc	chr17:10406395-10406643(-)$1	248	163	199	13.1727
ccc"""dddd!!cccmmmmccc22dddd333ccc00	chr2:180882414-180882658(-)$1	244	19	55	13.1558
BBgggggggbb[cccmmmmccc]bb22ggggggg:d	chr2:121137360-121137598(-)$1	238	35	71	10.7004
!!cccbb[bb[a[bbmmmmbb]a]bb]bb]ccc444	chr11:100643827-100644078(-)$1	251	110	146	11.1280
c[dddd"""bb[cccooooooccc]bb]dddd]ccc	chr15:93115081-93115316(-)$1	235	29	65	11.3551
[ggggggg####ddddlllddddggggggg]dddd]	chr11:75578686-75578922(+)$1	236	60	96	11.7822
ddddffffff[cccoooooocccffffffggggggg	chr4:15210745-15211006(+)$1	261	170	206	10.9807
===========[cccmmmmccc]===========ee	chr3:60431536-60431776(+)$1	240	143	179	15.7654
gg!!dddd!!eeeeennnnneeeee22dddd333gg	chr15:7145780-7146022(+)$1	242	27	63	10.1962

#otherMatches

#Seq PSSM
CUUUCUCCCCGGCAGAUCUUUGUUGUGUGGGAGGGC	chr15:27396439-27396677(+)$1	238	87	123	11.4287
GAACGCGCGGACGUUCUCAGAACGCGCCUCUGUGCU	chr5:136384359-136384619(-)$1	260	111	147	11.4490
GCAGUGAAAUAAACUCCAAAAGUAAUUUUGCUGCAU	chr18:34505052-34505293(-)$1	241	178	214	13.0562
GCUUGUGUAUCUUGAUUAAUGUACUUUUUAUUGCAU	chr11:51799963-51800205(-)$1	242	165	201	11.1919
AGCUGUGUCACUGGAGCACCCCCACUGCUGGGCUCA	chr11:51789805-51790053(+)$1	248	81	117	11.1049
CUUGAGGACCUUUGUCAUUGGCUGUGGUCUUCCAGA	chr11:60013257-60013493(-)$1	236	85	121	14.3141
GGAGCGGCGCUAGCCCCGCGGCCUGCGGUUCUUCUC	chr19:21346951-21347187(+)$1	236	27	63	12.8016
GCUGUGGGCCGUGCAGUGGUGUGGGGAUUCAUUCUC	chr9:107950460-107950695(+)$1	235	160	196	10.8095
CCUGCUCUGCUCCGCCUCGGCCCCGGAGCGAGGGGC	chr2:174155522-174155762(+)$1	240	113	149	11.7733
CUUAGCAUAGACAGUUCUUUUGCUUUCUUAGGUUUG	chr2:14998809-14999056(+)$1	247	84	120	13.1577
ACUUCCAUCUUAUUAGUAAUGGUCGUUGGGAGUCUU	chr16:38245760-38245995(+)$1	235	151	187	13.9495
UUAUGGAAUUUUUGUGUAGAUUAUAUUCUUAAAAGU	chr3:120905483-120905743(-)$1	260	176	212	12.6590
GCUUGUAAAUCUCUGUAGUUAGUUGUUGCCCACAGA	chr11:60370509-60370744(+)$1	235	57	93	12.5705
UGUGGCUUUUUGGUAAGGCUGCUUAGAAGCAUGAGA	chr12:55960170-55960414(-)$1	244	95	131	11.7742
GAAACUUGAUUUUGCUUAUAGUAAGAAAAAGAAAAA	chr7:122617910-122618153(-)$1	243	143	179	11.4500
AAAGUAUUUUGGUGCUUUUGCAAAAGGAUAAUGUUU	chr7:138588944-138589179(+)$1	235	95	131	14.1164
cagguguguguguggaccuccaccacuccugguuuu	chr2:32489706-32489967(+)$1	261	126	162	10.9239
UACAUGCAUUAUGUGUCACAUUACUGGGCAAACUGU	chr17:10401591-10401830(-)$1	239	101	137	12.6109
cagugcugagaacuggacccagagcuuugugcaugu	chr4:33107838-33108088(+)$1	250	115	151	13.7261
GCAUUUGUGUUUCUCUCUGUGGGCAGCACUUUAGUG	chr14:21479143-21479380(-)$1	237	110	146	10.5951
CGGUGGGAUGGGUGGGGUUGCGUGUCCCACCUAGAC	chr13:23831413-23831656(+)$1	243	68	104	10.9913
CCGUACCAGACUGUCAGAUGGCCUCUGGCGGUGCUU	chr13:55445984-55446219(-)$1	235	142	178	13.6324
UCCCCUGCAGUGGGUCAGGGCCUUGCUGAAGGAGGA	chr5:36944678-36944920(-)$1	242	43	79	11.8828
GUAAUCAUGACAAUCCUAUAGAACCUUAGAUGGAAA	chr15:31385712-31385954(-)$1	242	62	98	12.4898
GUUCCCAGGAUGUGCAAUAGUAGUGUGAGAAGUAGU	chr1:133921657-133921904(+)$1	247	204	240	13.8586
CAAAUGUUAAGGGUUUUCUCCCAGAACAGUAAUGGG	chrX:99709798-99710042(-)$1	244	207	243	11.7808
UUGAACUUACCUCAUUAUUAUGUUUGUAAUCAUUGU	chr10:82203477-82203715(+)$1	238	153	189	12.3616
ACCUCUGAGUCAUUGGUUAUACAGUGUAGUCCCAAG	chr11:29642590-29642878(+)$1	288	13	49	12.2699
UAUUUAUUUGGAAUGUUUUCAUUUAUCUAAAUAACU	chr16:7412188-7412449(+)$1	261	153	189	15.3370
CAACAGCUUUGAAAGAGCACUUCCCAACGCUGCUAG	chr3:102832811-102833065(+)$1	254	54	90	13.7387
ACUAGGUAUAGCUACUAUUGUUUCUAAGUAUGUUUG	chr2:72241690-72241976(+)$1	286	204	240	12.1620
aagcuaUGCGCCUGUUCCCACUAGAGUCUAGACGGG	chr7:25321336-25321574(+)$1	238	87	123	11.5572
UAACUAUGUGUGUGCUUUUAUAGAUAGGUAGGGAAC	chr4:33107028-33107268(+)$1	240	93	129	11.1242
GCCUCUUCCUCCCAGUCCCGGGCGAGCCGCGUUGGG	chr12:112776564-112776799(+)$1	235	134	170	13.6782
GUUCUGUUUGACUUUUGUGUAAAGUAAUGCAUGCAA	chr16:94690321-94690556(+)$1	235	6	42	10.7977
AUUCUGUGAGCUCUGGAGUCAUGCAGACAGGAUGUG	chr7:52665530-52665765(+)$1	235	107	143	12.0543
AAUGAAAUUGUAUGUGUACAAAUGUACAAUUUUCAC	chr7:99792676-99792911(-)$1	235	70	106	14.7139
GUCCCAUCUCAAAGUUCUCGGCUGGGGAAGGGCCUG	chr8:24259437-24259677(+)$1	240	132	168	10.4254
UUGUAGCAUAUGCUCCCUUAAGUCAGUAUGCUUAAA	chr6:67235597-67235832(+)$1	235	17	53	13.0594
CGGUUGGUAUUUUAUAGAGGUUUUGUGCCGAACUCC	chr17:27716430-27716665(-)$1	235	94	130	14.2425
UACAUCACCAGUUAACAUUUUAUAUUGUGAUGUUUA	chr13:97408636-97408876(+)$1	240	160	196	12.5159
UCCGCUGAAGGGGGACGAUUCCAUACAACAGGGAGC	chr13:59037387-59037622(+)$1	235	71	107	16.2261
UGCAGUGGCUGGAGAGAGACUUGAGAGCUACUCGGA	chr4:42970622-42970863(+)$1	241	54	90	14.5589
AGCCAUCAGUAUGUCCUUAAGAUGUUUGUAAAGAUG	chr15:103023875-103024111(-)$1	236	7	43	12.6587
UGCCCGGACGCAGGUGCUCGCCGGAGCCGGAGCAAG	chr17:33855430-33855665(-)$1	235	52	88	13.1017
UUUAAGAUGUAAAUGUAUUUUUACAUGAAAGUUUGA	chr12:33660678-33660920(+)$1	242	74	110	10.3443
AGGACCCGGUGCUUCCAGCAGGAGUGCUGGUUACUG	chr3:144352137-144352377(-)$1	240	45	81	13.6968
GAUCUGCAAUGGCAUUUCAAUGCCAAAGCAUGUCAC	chr7:88679712-88679947(-)$1	235	20	56	10.4877
GUUGUGACCCUUUGCAAAAUGUAUGUUACAAUAGAU	chr13:83802497-83802751(+)$1	254	4	40	12.2967
AUUGCUGUCUGCACUGGAGAGGAAGGCAGGAGUCCU	chr3:69357854-69358091(+)$1	237	98	134	12.1753
AAUGAAUGCAAUAUUGAUAGAUACAUGACAUACUAC	chr17:10406395-10406643(-)$1	248	163	199	13.1727
Gcgcccccagccccgcccccggcacuggccccgccc	chr2:180882414-180882658(-)$1	244	19	55	13.1558
GCUGGCUCAGAAGGCCCCUGCCAUCAGUGAGCUAUC	chr2:121137360-121137598(-)$1	238	35	71	10.7004
UUGUCUCCGCCUGUCUUCUGAGAUGUAGAUGACUGU	chr11:100643827-100644078(-)$1	251	110	146	11.1280
AUGAAUCUUUGCCAAUGUUUUUUGACAUGUUUUUAC	chr15:93115081-93115316(-)$1	235	29	65	11.3551
GUGUUGCUGAAAAGCAUGGUGCUGGUAACAGUUCAA	chr11:75578686-75578922(+)$1	236	60	96	11.7822
AAGGGUGAACUGUUUUGUUUAAUGUUCACUUGCUUG	chr4:15210745-15211006(+)$1	261	170	206	10.9807
CUCUGUUCAGCAGUUCUAAAAUCGCUGAGUAGGGGC	chr3:60431536-60431776(+)$1	240	143	179	15.7654
AAUUUGCUUAAGUUAAAUUCUAACUGUGGCAUACUU	chr15:7145780-7146022(+)$1	242	27	63	10.1962

#DB
(((((((((((((((....))))))...))))))).	chr15:27396439-27396677(+)$1	1	87	123	11.4287
((..((((((((((((...)))))....))))))))	chr5:136384359-136384619(-)$1	1	111	147	11.4490
((((((((((..(((.....))).))))))))))..	chr18:34505052-34505293(-)$1	1	178	214	13.0562
)))))))...)))))....))).))))))))))...	chr11:51799963-51800205(-)$1	1	165	201	11.1919
(((.(((.....((......))))).)))))...))	chr11:51789805-51790053(+)$1	1	81	117	11.1049
((((((((((...(((...)))...)))))))..))	chr11:60013257-60013493(-)$1	1	85	121	14.3141
((((.(((((..(((....)))..)))...)).)))	chr19:21346951-21347187(+)$1	1	27	63	12.8016
(..(((((((.((((....)))).)).)))))...)	chr9:107950460-107950695(+)$1	1	160	196	10.8095
(((((((((((((((....))...)))))..)))))	chr2:174155522-174155762(+)$1	1	113	149	11.7733
((((....(((.(((......))).)))))))))))	chr2:14998809-14999056(+)$1	1	84	120	13.1577
(((((((....((((....))))...)))))))...	chr16:38245760-38245995(+)$1	1	151	187	13.9495
((..(((((....((....))...)))))...))))	chr3:120905483-120905743(-)$1	1	176	212	12.6590
(...((((....(((....)))...)))).)))...	chr11:60370509-60370744(+)$1	1	57	93	12.5705
(...((((((.((((....)))).))))))...)))	chr12:55960170-55960414(-)$1	1	95	131	11.7742
....(((..(((((((...)))))))..))).....	chr7:122617910-122618153(-)$1	1	143	179	11.4500
(...((((((..(((....)))..))))))...)))	chr7:138588944-138589179(+)$1	1	95	131	14.1164
((((...(((.((((....))))))).))))..)))	chr2:32489706-32489967(+)$1	1	126	162	10.9239
(...(((.(((.(((......))))))))).)))))	chr17:10401591-10401830(-)$1	1	101	137	12.6109
((((((.(((..(((....)))..))).)))).)))	chr4:33107838-33108088(+)$1	1	115	151	13.7261
(((((.(((((.(((.....))).)))))...))))	chr14:21479143-21479380(-)$1	1	110	146	10.5951
.(((((((((.((......)).)))))))))(((((	chr13:23831413-23831656(+)$1	1	68	104	10.9913
(((..(((((..(((....))).)))))))))))).	chr13:55445984-55446219(-)$1	1	142	178	13.6324
((((((.((((((((....))).))))).))).)))	chr5:36944678-36944920(-)$1	1	43	79	11.8828
...(((.(((...((.....))...)))))).))))	chr15:31385712-31385954(-)$1	1	62	98	12.4898
((((.((.....(((....)))...)).))).))).	chr1:133921657-133921904(+)$1	1	204	240	13.8586
((..((((..(((......)))..))))....))))	chrX:99709798-99710042(-)$1	1	207	243	11.7808
.(((..((((..(((....)))...))))))).(((	chr10:82203477-82203715(+)$1	1	153	189	12.3616
....(((...(((((......))))))))...))))	chr11:29642590-29642878(+)$1	1	13	49	12.2699
((.((((((((((((....)))...))))))))).)	chr16:7412188-7412449(+)$1	1	153	189	15.3370
...((((.(((.(((....)))..))).))))..))	chr3:102832811-102833065(+)$1	1	54	90	13.7387
((((((((((..((..(....)..))..))))))))	chr2:72241690-72241976(+)$1	1	204	240	12.1620
...(((.((.(..((....))..).)).))))))))	chr7:25321336-25321574(+)$1	1	87	123	11.5572
(..((((.(((.((......)).))).))))..)))	chr4:33107028-33107268(+)$1	1	93	129	11.1242
((..(((...(((......))).)))..)))))))(	chr12:112776564-112776799(+)$1	1	134	170	13.6782
((..(((...(((((.....)))))...))).))))	chr16:94690321-94690556(+)$1	1	6	42	10.7977
(((((((..((..((....)).))..))))))).))	chr7:52665530-52665765(+)$1	1	107	143	12.0543
...((((((((((((......))))))))))))...	chr7:99792676-99792911(-)$1	1	70	106	14.7139
(.(((.((((..((((...)))).)))).))).)).	chr8:24259437-24259677(+)$1	1	132	168	10.4254
((..((((((((((......)))..)))))))..))	chr6:67235597-67235832(+)$1	1	17	53	13.0594
.(((((((((...((....))...)))))))...))	chr17:27716430-27716665(-)$1	1	94	130	14.2425
.(((((((.(..(((....)))..).))))))))))	chr13:97408636-97408876(+)$1	1	160	196	12.5159
(((.(((..(..(((....)))...)..))))))))	chr13:59037387-59037622(+)$1	1	71	107	16.2261
.(.(((((((...(((...)))...)))))))))))	chr4:42970622-42970863(+)$1	1	54	90	14.5589
(((.(((..((((((.....)))....)))..))))	chr15:103023875-103024111(-)$1	1	7	43	12.6587
(((((((.(...(((....)))...))))).))..)	chr17:33855430-33855665(-)$1	1	52	88	13.1017
(((...(((((((......)))))))..))))))))	chr12:33660678-33660920(+)$1	1	74	110	10.3443
((...((((((((((.....))))))))))...)))	chr3:144352137-144352377(-)$1	1	45	81	13.6968
(((.(((..((((((....))))))..))).)))..	chr7:88679712-88679947(-)$1	1	20	56	10.4877
((((((((....((((...)))).))))))))))..	chr13:83802497-83802751(+)$1	1	4	40	12.2967
(((.((((((...((....))..)))))).)))...	chr3:69357854-69358091(+)$1	1	98	134	12.1753
.(((.(((...((((....)))))))..)))...))	chr17:10406395-10406643(-)$1	1	163	199	13.1727
(((...((((..(((....)))..))))...)))..	chr2:180882414-180882658(-)$1	1	19	55	13.1558
(((((((((((.(((....))).))..))))))).(	chr2:121137360-121137598(-)$1	1	35	71	10.7004
..(((((.((.(.((....)).).)).)).)))...	chr11:100643827-100644078(-)$1	1	110	146	11.1280
(.((((...((.(((......))).)).)))).)))	chr15:93115081-93115316(-)$1	1	29	65	11.3551
.(((((((....((((...))))))))))).)))).	chr11:75578686-75578922(+)$1	1	60	96	11.7822
))))((((((.(((......)))))))))(((((((	chr4:15210745-15211006(+)$1	1	170	206	10.9807
(((((((((((.(((....))).)))))))))))((	chr3:60431536-60431776(+)$1	1	143	179	15.7654
((..((((..(((((.....)))))..))))...))	chr15:7145780-7146022(+)$1	1	27	63	10.1962

#PSSM
c : 0.15	g : 0.11	e : 0.11	d : 0.10	b : 0.08	= : 0.08	" : 0.06	# : 0.05	: : 0.05	h : 0.03	f : 0.03	! : 0.03	i : 0.01	$ : 0.01	B : 0.01	[ : 0.01	
g : 0.16	c : 0.15	" : 0.13	e : 0.11	= : 0.08	b : 0.06	d : 0.05	! : 0.05	i : 0.03	# : 0.03	[ : 0.03	h : 0.01	a : 0.01	f : 0.01	B : 0.01	
g : 0.15	! : 0.15	" : 0.15	c : 0.15	= : 0.08	d : 0.08	e : 0.06	i : 0.03	# : 0.03	[ : 0.03	b : 0.03	f : 0.01	
g : 0.16	! : 0.13	d : 0.13	c : 0.13	" : 0.11	= : 0.10	[ : 0.08	i : 0.05	e : 0.03	# : 0.03	
c : 0.23	g : 0.20	d : 0.13	= : 0.10	f : 0.06	" : 0.06	[ : 0.05	e : 0.05	i : 0.03	! : 0.03	# : 0.01	
c : 0.22	g : 0.20	d : 0.13	= : 0.11	f : 0.06	b : 0.05	e : 0.05	" : 0.05	[ : 0.03	i : 0.03	# : 0.01	! : 0.01	
g : 0.22	c : 0.16	d : 0.15	= : 0.11	e : 0.06	f : 0.06	[ : 0.06	b : 0.05	" : 0.03	i : 0.03	# : 0.01	
g : 0.18	= : 0.10	d : 0.10	c : 0.08	e : 0.08	! : 0.08	[ : 0.08	f : 0.06	" : 0.06	$ : 0.03	# : 0.03	i : 0.03	3 : 0.01	b : 0.01	
g : 0.13	c : 0.13	! : 0.11	= : 0.08	e : 0.08	" : 0.08	# : 0.06	f : 0.06	b : 0.05	d : 0.05	$ : 0.03	i : 0.03	3 : 0.01	[ : 0.01	a : 0.01	
c : 0.15	g : 0.11	f : 0.10	= : 0.08	b : 0.08	# : 0.08	" : 0.08	e : 0.06	d : 0.05	$ : 0.03	i : 0.03	! : 0.03	a : 0.03	3 : 0.01	[ : 0.01	
! : 0.18	e : 0.11	" : 0.11	c : 0.11	[ : 0.10	# : 0.08	g : 0.06	b : 0.05	= : 0.05	f : 0.03	$ : 0.03	i : 0.01	a : 0.01	
! : 0.22	[ : 0.13	e : 0.11	" : 0.10	d : 0.08	c : 0.08	# : 0.06	f : 0.03	$ : 0.03	g : 0.03	= : 0.03	b : 0.01	i : 0.01	a : 0.01	
c : 0.44	d : 0.13	e : 0.10	" : 0.08	b : 0.06	f : 0.03	g : 0.03	! : 0.03	= : 0.03	# : 0.01	[ : 0.01	
c : 0.44	b : 0.18	d : 0.13	e : 0.08	o : 0.06	f : 0.03	= : 0.03	g : 0.01	
c : 0.40	o : 0.13	d : 0.13	b : 0.13	e : 0.08	f : 0.03	= : 0.03	g : 0.01	! : 0.01	
m : 0.50	o : 0.22	n : 0.11	d : 0.05	c : 0.03	e : 0.01	4 : 0.01	g : 0.01	! : 0.01	
m : 0.50	o : 0.22	l : 0.11	n : 0.11	4 : 0.01	a : 0.01	
m : 0.52	o : 0.22	l : 0.11	n : 0.11	4 : 0.01	
m : 0.52	o : 0.22	l : 0.11	n : 0.11	4 : 0.01	
c : 0.35	o : 0.15	d : 0.13	b : 0.13	n : 0.11	f : 0.03	g : 0.03	e : 0.01	m : 0.01	
c : 0.44	b : 0.18	d : 0.13	o : 0.08	e : 0.05	f : 0.03	g : 0.03	m : 0.01	= : 0.01	
c : 0.49	d : 0.13	e : 0.06	b : 0.05	3 : 0.05	] : 0.05	f : 0.03	g : 0.03	2 : 0.03	= : 0.03	a : 0.01	
3 : 0.20	2 : 0.16	c : 0.15	d : 0.13	] : 0.11	e : 0.06	f : 0.03	g : 0.03	= : 0.03	i : 0.01	b : 0.01	a : 0.01	
3 : 0.22	2 : 0.15	c : 0.13	] : 0.11	e : 0.10	f : 0.06	= : 0.06	g : 0.05	b : 0.03	i : 0.01	a : 0.01	4 : 0.01	
3 : 0.16	c : 0.15	e : 0.13	f : 0.10	= : 0.10	b : 0.06	g : 0.06	] : 0.05	d : 0.05	4 : 0.03	2 : 0.03	i : 0.01	a : 0.01	
c : 0.16	g : 0.11	= : 0.10	b : 0.10	e : 0.10	d : 0.08	f : 0.06	2 : 0.06	3 : 0.05	4 : 0.03	] : 0.03	i : 0.03	a : 0.03	
2 : 0.15	g : 0.13	c : 0.11	= : 0.10	e : 0.10	d : 0.10	] : 0.06	f : 0.06	b : 0.05	3 : 0.03	4 : 0.03	i : 0.03	
g : 0.15	d : 0.15	e : 0.11	= : 0.10	c : 0.10	2 : 0.10	] : 0.08	f : 0.06	3 : 0.05	i : 0.03	4 : 0.01	b : 0.01	
g : 0.22	c : 0.18	d : 0.15	= : 0.11	e : 0.08	f : 0.08	i : 0.05	3 : 0.03	] : 0.03	4 : 0.01	b : 0.01	
g : 0.23	c : 0.22	= : 0.11	d : 0.11	3 : 0.08	i : 0.05	] : 0.05	f : 0.05	e : 0.03	2 : 0.01	4 : 0.01	
g : 0.22	c : 0.22	3 : 0.11	= : 0.10	d : 0.10	] : 0.06	i : 0.05	e : 0.03	2 : 0.03	b : 0.01	4 : 0.01	f : 0.01	
g : 0.23	3 : 0.16	c : 0.15	= : 0.10	d : 0.06	b : 0.05	2 : 0.05	] : 0.05	i : 0.03	e : 0.01	> : 0.01	4 : 0.01	h : 0.01	f : 0.01	
g : 0.20	3 : 0.13	c : 0.13	= : 0.10	2 : 0.08	] : 0.08	h : 0.05	e : 0.05	i : 0.03	b : 0.03	> : 0.01	: : 0.01	a : 0.01	f : 0.01	d : 0.01	
c : 0.16	g : 0.15	3 : 0.13	e : 0.08	= : 0.06	2 : 0.06	d : 0.06	h : 0.05	f : 0.05	i : 0.03	4 : 0.03	: : 0.01	> : 0.01	] : 0.01	b : 0.01	H : 0.01	
g : 0.15	e : 0.15	c : 0.15	d : 0.08	: : 0.06	3 : 0.06	b : 0.06	h : 0.05	4 : 0.03	f : 0.03	i : 0.01	> : 0.01	] : 0.01	= : 0.01	H : 0.01	2 : 0.01	7 : 0.01	0 : 0.01	
e : 0.16	c : 0.13	d : 0.11	g : 0.10	] : 0.06	b : 0.06	: : 0.05	3 : 0.05	h : 0.05	4 : 0.03	f : 0.03	i : 0.01	> : 0.01	2 : 0.01	= : 0.01	H : 0.01	7 : 0.01	0 : 0.01	

#score	733.9213858285591
#seq	59
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_CDS_m1_run1.txt

#BEAR
ggggggguuuuuuuuuuuuggggg	chr2:65518961-65519243(+)$1	282	114	138	22.6962
eeeeeyyyyyyyyyyyyyyyyeee	chr5:72033396-72033648(-)$1	252	59	83	22.0142
ffffffvvvvvvvvvvvvvfffff	chr14:31880765-31881051(+)$1	286	152	176	22.4938
cc!!bbvvvvvvvvvvvvvbb]cc	chr4:148555533-148555793(-)$1	260	215	239	22.7737
gggeeeeettttttttttteeeee	chr5:90673282-90673555(-)$1	273	167	191	21.5424
ccceeeeettttttttttteeeee	chr17:35972171-35972442(-)$1	271	35	59	21.3924
ffbb[ccctttttttttttccc]b	chr7:130458067-130458305(-)$1	238	146	170	20.8114
ddddyyyyyyyyyyyyyyyydddd	chr4:149021385-149021630(+)$1	245	159	183	21.0801
ggggggwwwwwwwwwwwwwwgggg	chr12:112871731-112871994(+)$1	263	41	65	21.9821
ffffffvvvvvvvvvvvvvfffff	chr4:82029410-82029661(-)$1	251	46	70	22.4938
eeeeeyyyyyyyyyyyyyyyyeee	chr11:80291493-80291784(+)$1	291	242	266	22.0142
eeeeeavvvvvvvvvvvvva]eee	chr7:26096356-26096599(+)$1	243	170	194	23.6110
a[ddddtttttttttttddddagg	chr12:99953151-99953409(-)$1	258	102	126	21.1461
b"""bbuuuuuuuuuuuubb]bb]	chr10:108020816-108021073(-)$1	257	56	80	21.0991
b[dddduuuuuuuuuuuudddd]b	chr9:108399156-108399391(+)$1	235	23	47	22.1206
:eeeeeuuuuuuuuuuuueeeee:	chr9:61908669-61908929(-)$1	260	0	24	20.7799
ddddccctttttttttttccc]dd	chr4:88056428-88056684(+)$1	256	217	241	22.2163
!!ddddtttttttttttdddd]dd	chr4:61853200-61853455(-)$1	255	172	196	21.1578
gggggggtttttttttttgggggg	chr12:66166648-66166893(-)$1	245	191	215	21.8744
eeeeeyyyyyyyyyyyyyyyyeee	chr10:127547719-127548056(+)$1	337	279	303	22.0142
!!ddddvvvvvvvvvvvvvdddd2	chr13:45006442-45006751(+)$1	309	270	294	22.7736
ffffffwwwwwwwwwwwwwwffff	chr10:78529857-78530135(-)$1	278	33	57	21.3322
===!!bbuuuuuuuuuuuubb333	chr13:23713571-23713918(-)$1	347	189	213	22.3912
ffffffuuuuuuuuuuuuffffff	chr15:72957284-72957553(-)$1	269	151	175	21.8939
:fffffftttttttttttffffff	chr1:84721158-84721408(-)$1	250	22	46	20.3592
ffff[auuuuuuuuuuuua]ffff	chr4:75717787-75718033(-)$1	246	181	205	22.6292
ggggggguuuuuuuuuuuuggggg	chr6:148130078-148130347(-)$1	269	237	261	22.6962
e[ddddwwwwwwwwwwwwwwdddd	chr19:29662105-29662342(+)$1	237	183	207	21.7819
e[ddddvvvvvvvvvvvvvdddde	chr17:13132731-13132980(-)$1	249	128	152	23.1800
ggggggyyyyyyyyyyyyyyyygg	chr14:18859118-18859370(+)$1	252	118	142	21.3592
$$$ccctttttttttttccc4444	chr4:101279133-101279400(+)$1	267	152	176	20.3954
ddddbbwwwwwwwwwwwwwwbb]d	chr11:68657240-68657519(-)$1	279	125	149	21.0446
h"""ccctttttttttttccc333	chr18:35373359-35373642(-)$1	283	141	165	21.9408
ffffffyyyyyyyyyyyyyyyyff	chr4:81973564-81973836(-)$1	272	123	147	20.8192
e[ddddtttttttttttdddd]ee	chr1:133252057-133252295(-)$1	238	183	207	21.4595
:bb[ccctttttttttttccc]bb	chr7:118215994-118216317(-)$1	323	180	204	20.3990
ddddddvvvvvvvvvvvvvddddG	chr9:30984486-30984735(-)$1	249	209	233	22.2309
!eeeeevvvvvvvvvvvvveeeee	chr6:17871891-17872127(+)$1	236	35	59	23.3813
====bbvvvvvvvvvvvvvbb]==	chr6:71460202-71460447(+)$1	245	137	161	22.9561
eeeeewwwwwwwwwwwwwweeeee	chr10:7639638-7639894(-)$1	256	144	168	22.0963
eccc[awwwwwwwwwwwwwwaccc	chr11:50125003-50125270(-)$1	267	218	242	21.7643
dddd[bbtttttttttttbb]ddd	chr11:65509701-65509956(-)$1	255	11	35	21.2736
hh!!bbvvvvvvvvvvvvvbb]hh	chr1:38398477-38398716(-)$1	239	93	117	22.1261
:ddddwwwwwwwwwwwwwwddddF	chr1:130093473-130093737(+)$1	264	60	84	20.3151
eeeeeyyyyyyyyyyyyyyyyeee	chr2:74359968-74360297(-)$1	329	285	309	22.0142
c[ddddtttttttttttdddd]cc	chr16:17018280-17018548(+)$1	268	72	96	21.2002
ddddcccuuuuuuuuuuuuccc]d	chr1:196623811-196624058(+)$1	247	86	110	22.7553
ddd[bbvvvvvvvvvvvvvbb]dd	chr1:59924725-59925115(+)$1	390	85	109	22.5857
hhheeeeettttttttttteeeee	chr8:72544229-72544467(-)$1	238	188	212	20.9002
gggggggtttttttttttgggggg	chr19:10517216-10517465(+)$1	249	192	216	21.8744
f!!bbwwwwwwwwwwwwwwbb]ff	chrX:137213046-137213296(+)$1	250	66	90	21.3058
beeeeevvvvvvvvvvvvveeeee	chr7:130336330-130336634(+)$1	304	137	161	23.1686
eee[bbvvvvvvvvvvvvvbbeee	chr11:61359898-61360151(-)$1	253	35	59	23.0365
::ddddvvvvvvvvvvvvvdddde	chr17:12464745-12465001(-)$1	256	126	150	21.0881
eeeeeccctttttttttttccc]e	chr6:17615204-17615487(+)$1	283	169	193	22.0817
"""cccuuuuuuuuuuuucccccc	chr6:58834983-58835247(+)$1	264	119	143	22.5762
eeeeeccctttttttttttccc]e	chr14:28725938-28726258(+)$1	320	39	63	22.0817
gggggggtttttttttttgggggg	chr9:49352655-49352921(-)$1	266	135	159	21.8744
eeeeewwwwwwwwwwwwwweeeee	chr8:125944717-125944989(+)$1	272	124	148	22.0963
CCeeeeeuuuuuuuuuuuueeeee	chr11:97397632-97397884(-)$1	252	226	250	20.5795
iiiiiiiitttttttttttiiiii	chr7:147258437-147258688(-)$1	251	128	152	21.0324
fffff[attttttttttta]ffff	chr15:63763055-63763331(-)$1	276	243	267	22.2216
f[bbyyyyyyyyyyyyyyyybbff	chr6:124696250-124696510(-)$1	260	160	184	20.4893

#otherMatches

#Seq PSSM
GUGCACAAUUCUUACCAACUGUGU	chr2:65518961-65519243(+)$1	282	114	138	22.6962
ACCUAUUUACUUCAUACUUACUAG	chr5:72033396-72033648(-)$1	252	59	83	22.0142
CAAGAGCUCAUCCAUAACCUUUUU	chr14:31880765-31881051(+)$1	286	152	176	22.4938
UUUUGCUUCAUUUCCUCAUGCuga	chr4:148555533-148555793(-)$1	260	215	239	22.7737
CCUCAGCACCUACCACCACUGCUG	chr5:90673282-90673555(-)$1	273	167	191	21.5424
UGUGCCUGAACUUACCCAGCAGGU	chr17:35972171-35972442(-)$1	271	35	59	21.3924
CGGUAAGCACCUUCCCUUGGCUGA	chr7:130458067-130458305(-)$1	238	146	170	20.8114
gauggggaggaagaggaagaCAUC	chr4:149021385-149021630(+)$1	245	159	183	21.0801
CAGAAUAAAAUAUGAACUGCAUUC	chr12:112871731-112871994(+)$1	263	41	65	21.9821
UUCUUUCAUAACAAAUUAAAAAGA	chr4:82029410-82029661(-)$1	251	46	70	22.4938
CUACCCGCUCAAGCCCUUCCUGGU	chr11:80291493-80291784(+)$1	291	242	266	22.0142
CGAGCCUCCUGCCUGCUAUGUGCU	chr7:26096356-26096599(+)$1	243	170	194	23.6110
CUGGAGCCUACCGUCUACUUCGGC	chr12:99953151-99953409(-)$1	258	102	126	21.1461
CUCCGCUACGUCCCUACUGCCGGC	chr10:108020816-108021073(-)$1	257	56	80	21.0991
CAGGUCUCCAUCACUUUUGACCCG	chr9:108399156-108399391(+)$1	235	23	47	22.1206
AGUAGUGUUCAAGGAUAAACUACa	chr9:61908669-61908929(-)$1	260	0	24	20.7799
CAGAAGCUUUUUAGGACUGCUAUC	chr4:88056428-88056684(+)$1	256	217	241	22.2163
AAACGGAAAUCACACUGCCGUACU	chr4:61853200-61853455(-)$1	255	172	196	21.1578
GUAUAUAGUUUUUCUAAAUAUGUG	chr12:66166648-66166893(-)$1	245	191	215	21.8744
CCCCUUCUUUCUCAGUUCCCUGGG	chr10:127547719-127548056(+)$1	337	279	303	22.0142
GAGGGCAGUGAUAAAUAGGGCCUG	chr13:45006442-45006751(+)$1	309	270	294	22.7736
aucaucagaaaacgcauacagaug	chr10:78529857-78530135(-)$1	278	33	57	21.3322
AAACCGCAGCCAAGAAAAAGUAAA	chr13:23713571-23713918(-)$1	347	189	213	22.3912
UUUACCAAAGAAAUCAAAGGUAAA	chr15:72957284-72957553(-)$1	269	151	175	21.8939
UUCGGAGUUUAAAUCCACCUCUGA	chr1:84721158-84721408(-)$1	250	22	46	20.3592
AUGAGGUAACUGUGUCUUUGUUGU	chr4:75717787-75718033(-)$1	246	181	205	22.6292
AAAUAUGAGAACCCGGAAACAUAU	chr6:148130078-148130347(-)$1	269	237	261	22.6962
ACGUCAGUGAGUACAGAGAAUGGC	chr19:29662105-29662342(+)$1	237	183	207	21.7819
CACCGUGCCUGUCCACGAAAUGGG	chr17:13132731-13132980(-)$1	249	128	152	23.1800
CAUCACACCAGCAAUUACCAGAGU	chr14:18859118-18859370(+)$1	252	118	142	21.3592
CCCCAAAAAUGUCUGUGUUGUCCA	chr4:101279133-101279400(+)$1	267	152	176	20.3954
CAGGCUGAACAAAGAAAUAGAGAC	chr11:68657240-68657519(-)$1	279	125	149	21.0446
AUCUGCAAAAUUUGGACCUGUCUU	chr18:35373359-35373642(-)$1	283	141	165	21.9408
UAUCCUCCUCACCUGAAUCCUCAG	chr4:81973564-81973836(-)$1	272	123	147	20.8192
CCAUGACCUGUCUGAUAUUAUUGA	chr1:133252057-133252295(-)$1	238	183	207	21.4595
CACUGCGAAAAUUCAUUCCGCUGU	chr7:118215994-118216317(-)$1	323	180	204	20.3990
AUGUGAUAAAAAUGAGUUCUCGCU	chr9:30984486-30984735(-)$1	249	209	233	22.2309
UCAGUGUUGAAUUCAUAAUCACUG	chr6:17871891-17872127(+)$1	236	35	59	23.3813
CGACACUGUUGCCCUGUUUGUCGU	chr6:71460202-71460447(+)$1	245	137	161	22.9561
UUGGACUACUUAUCCUGCAUCCAA	chr10:7639638-7639894(-)$1	256	144	168	22.0963
gcugucuuugaacucacuauguag	chr11:50125003-50125270(-)$1	267	218	242	21.7643
GCUGAGGUUUUGUCUCUUCCCCAG	chr11:65509701-65509956(-)$1	255	11	35	21.2736
UUCUGCUAUUCAAGCUCCUGCCAA	chr1:38398477-38398716(-)$1	239	93	117	22.1261
GUGGCUUACAAUUAUAGAUGCCAG	chr1:130093473-130093737(+)$1	264	60	84	20.3151
GAUAUACGCUUAAUAUUAUUCAUA	chr2:74359968-74360297(-)$1	329	285	309	22.0142
UUUGACCUUAACCUCCUGUCACAC	chr16:17018280-17018548(+)$1	268	72	96	21.2002
UCAGGGUCGCCUAGAAUAUGCCAC	chr1:196623811-196624058(+)$1	247	86	110	22.7553
GCUCAGAUCUAUCCUCUCCCUAAG	chr1:59924725-59925115(+)$1	390	85	109	22.5857
CUGACAUCAUACAAGCAGCGGUGU	chr8:72544229-72544467(-)$1	238	188	212	20.9002
GUCCAUCCCUCUGAACAAGGUGGA	chr19:10517216-10517465(+)$1	249	192	216	21.8744
UGCCUGGACCACGAGAAUGAGAAG	chrX:137213046-137213296(+)$1	250	66	90	21.3058
GCAUAGGUAUAGACGUAAACUGUG	chr7:130336330-130336634(+)$1	304	137	161	23.1686
CUGACCUGACCUACAAUGUGGUAG	chr11:61359898-61360151(-)$1	253	35	59	23.0365
UAAGCCUUACCUCAGUCUCGGCUG	chr17:12464745-12465001(-)$1	256	126	150	21.0881
CUAAGAUCGACUGGAACAAGAUCC	chr6:17615204-17615487(+)$1	283	169	193	22.0817
CCAAGCUAAGACCAAGAUGCUGCA	chr6:58834983-58835247(+)$1	264	119	143	22.5762
GAUUGUCUUCUUCUUUUACAGAUU	chr14:28725938-28726258(+)$1	320	39	63	22.0817
UGGCAUUUCAAGUGGUAUGAUGCC	chr9:49352655-49352921(-)$1	266	135	159	21.8744
GAAGCCCUCUACGACAUCUGCUUC	chr8:125944717-125944989(+)$1	272	124	148	22.0963
AGGCUCGCAAUGUCUUCUACGAGC	chr11:97397632-97397884(-)$1	252	226	250	20.5795
CUGCAGACCAGCCAAAGAAGUUUG	chr7:147258437-147258688(-)$1	251	128	152	21.0324
UCAAAUCUCCUUAUUCUUGCUUUG	chr15:63763055-63763331(-)$1	276	243	267	22.2216
CACCACCCUCCUUCAGAACAGGGA	chr6:124696250-124696510(-)$1	260	160	184	20.4893

#DB
(((((((............)))))	chr2:65518961-65519243(+)$1	1	114	138	22.6962
(((((................)))	chr5:72033396-72033648(-)$1	1	59	83	22.0142
((((((.............)))))	chr14:31880765-31881051(+)$1	1	152	176	22.4938
((..((.............)).))	chr4:148555533-148555793(-)$1	1	215	239	22.7737
)))(((((...........)))))	chr5:90673282-90673555(-)$1	1	167	191	21.5424
((((((((...........)))))	chr17:35972171-35972442(-)$1	1	35	59	21.3924
((((.(((...........))).)	chr7:130458067-130458305(-)$1	1	146	170	20.8114
((((................))))	chr4:149021385-149021630(+)$1	1	159	183	21.0801
((((((..............))))	chr12:112871731-112871994(+)$1	1	41	65	21.9821
((((((.............)))))	chr4:82029410-82029661(-)$1	1	46	70	22.4938
(((((................)))	chr11:80291493-80291784(+)$1	1	242	266	22.0142
((((((.............).)))	chr7:26096356-26096599(+)$1	1	170	194	23.6110
(.((((...........)))))))	chr12:99953151-99953409(-)$1	1	102	126	21.1461
(...((............)).)).	chr10:108020816-108021073(-)$1	1	56	80	21.0991
(.((((............)))).)	chr9:108399156-108399391(+)$1	1	23	47	22.1206
.(((((............))))).	chr9:61908669-61908929(-)$1	1	0	24	20.7799
(((((((...........))).))	chr4:88056428-88056684(+)$1	1	217	241	22.2163
..((((...........)))).))	chr4:61853200-61853455(-)$1	1	172	196	21.1578
(((((((...........))))))	chr12:66166648-66166893(-)$1	1	191	215	21.8744
(((((................)))	chr10:127547719-127548056(+)$1	1	279	303	22.0142
..((((.............)))).	chr13:45006442-45006751(+)$1	1	270	294	22.7736
((((((..............))))	chr10:78529857-78530135(-)$1	1	33	57	21.3322
(((..((............))...	chr13:23713571-23713918(-)$1	1	189	213	22.3912
((((((............))))))	chr15:72957284-72957553(-)$1	1	151	175	21.8939
.((((((...........))))))	chr1:84721158-84721408(-)$1	1	22	46	20.3592
((((.(............).))))	chr4:75717787-75718033(-)$1	1	181	205	22.6292
(((((((............)))))	chr6:148130078-148130347(-)$1	1	237	261	22.6962
(.((((..............))))	chr19:29662105-29662342(+)$1	1	183	207	21.7819
(.((((.............)))))	chr17:13132731-13132980(-)$1	1	128	152	23.1800
((((((................))	chr14:18859118-18859370(+)$1	1	118	142	21.3592
...(((...........)))....	chr4:101279133-101279400(+)$1	1	152	176	20.3954
((((((..............)).)	chr11:68657240-68657519(-)$1	1	125	149	21.0446
(...(((...........)))...	chr18:35373359-35373642(-)$1	1	141	165	21.9408
((((((................))	chr4:81973564-81973836(-)$1	1	123	147	20.8192
(.((((...........)))).))	chr1:133252057-133252295(-)$1	1	183	207	21.4595
.((.(((...........))).))	chr7:118215994-118216317(-)$1	1	180	204	20.3990
))((((.............)))))	chr9:30984486-30984735(-)$1	1	209	233	22.2309
.(((((.............)))))	chr6:17871891-17872127(+)$1	1	35	59	23.3813
((((((.............)).))	chr6:71460202-71460447(+)$1	1	137	161	22.9561
(((((..............)))))	chr10:7639638-7639894(-)$1	1	144	168	22.0963
((((.(..............))))	chr11:50125003-50125270(-)$1	1	218	242	21.7643
((((.((...........)).)))	chr11:65509701-65509956(-)$1	1	11	35	21.2736
((..((.............)).))	chr1:38398477-38398716(-)$1	1	93	117	22.1261
.((((..............))))(	chr1:130093473-130093737(+)$1	1	60	84	20.3151
(((((................)))	chr2:74359968-74360297(-)$1	1	285	309	22.0142
(.((((...........)))).))	chr16:17018280-17018548(+)$1	1	72	96	21.2002
(((((((............))).)	chr1:196623811-196624058(+)$1	1	86	110	22.7553
(((.((.............)).))	chr1:59924725-59925115(+)$1	1	85	109	22.5857
((((((((...........)))))	chr8:72544229-72544467(-)$1	1	188	212	20.9002
(((((((...........))))))	chr19:10517216-10517465(+)$1	1	192	216	21.8744
(..((..............)).))	chrX:137213046-137213296(+)$1	1	66	90	21.3058
((((((.............)))))	chr7:130336330-130336634(+)$1	1	137	161	23.1686
(((.((.............)))))	chr11:61359898-61360151(-)$1	1	35	59	23.0365
..((((.............))))(	chr17:12464745-12465001(-)$1	1	126	150	21.0881
((((((((...........))).)	chr6:17615204-17615487(+)$1	1	169	193	22.0817
...(((............))))))	chr6:58834983-58835247(+)$1	1	119	143	22.5762
((((((((...........))).)	chr14:28725938-28726258(+)$1	1	39	63	22.0817
(((((((...........))))))	chr9:49352655-49352921(-)$1	1	135	159	21.8744
(((((..............)))))	chr8:125944717-125944989(+)$1	1	124	148	22.0963
))(((((............)))))	chr11:97397632-97397884(-)$1	1	226	250	20.5795
((((((((...........)))))	chr7:147258437-147258688(-)$1	1	128	152	21.0324
(((((.(...........).))))	chr15:63763055-63763331(-)$1	1	243	267	22.2216
(.((................))))	chr6:124696250-124696510(-)$1	1	160	184	20.4893

#PSSM
e : 0.22	f : 0.15	g : 0.12	d : 0.11	: : 0.07	c : 0.04	b : 0.04	! : 0.04	h : 0.04	= : 0.03	a : 0.01	$ : 0.01	" : 0.01	C : 0.01	i : 0.01	
e : 0.20	f : 0.14	g : 0.12	d : 0.12	[ : 0.11	c : 0.04	" : 0.04	! : 0.04	= : 0.03	h : 0.03	$ : 0.01	b : 0.01	: : 0.01	C : 0.01	i : 0.01	
d : 0.26	e : 0.22	g : 0.12	f : 0.12	! : 0.04	b : 0.04	" : 0.04	c : 0.03	= : 0.03	$ : 0.01	h : 0.01	i : 0.01	
e : 0.25	d : 0.25	f : 0.12	g : 0.11	! : 0.04	b : 0.04	c : 0.04	[ : 0.04	" : 0.03	= : 0.01	i : 0.01	
e : 0.25	d : 0.17	b : 0.12	g : 0.11	f : 0.11	c : 0.09	[ : 0.06	y : 0.03	! : 0.01	i : 0.01	
d : 0.15	b : 0.14	c : 0.14	g : 0.11	e : 0.11	y : 0.09	f : 0.09	w : 0.06	a : 0.04	i : 0.01	[ : 0.01	
v : 0.22	w : 0.14	y : 0.12	c : 0.11	u : 0.09	g : 0.07	t : 0.07	e : 0.06	b : 0.03	f : 0.01	i : 0.01	a : 0.01	
v : 0.22	t : 0.22	u : 0.17	w : 0.14	y : 0.12	e : 0.04	c : 0.04	i : 0.01	
t : 0.33	v : 0.22	u : 0.17	w : 0.14	y : 0.12	
t : 0.33	v : 0.22	u : 0.17	w : 0.14	y : 0.12	
t : 0.33	v : 0.22	u : 0.17	w : 0.14	y : 0.12	
t : 0.33	v : 0.22	u : 0.17	w : 0.14	y : 0.12	
t : 0.33	v : 0.22	u : 0.17	w : 0.14	y : 0.12	
t : 0.33	v : 0.22	u : 0.17	w : 0.14	y : 0.12	
t : 0.33	v : 0.22	u : 0.17	w : 0.14	y : 0.12	
t : 0.33	v : 0.22	u : 0.17	w : 0.14	y : 0.12	
t : 0.33	v : 0.22	u : 0.17	w : 0.14	y : 0.12	
t : 0.25	v : 0.22	u : 0.17	w : 0.14	y : 0.12	d : 0.06	c : 0.01	
v : 0.22	w : 0.14	y : 0.12	t : 0.11	u : 0.07	d : 0.07	c : 0.07	g : 0.04	b : 0.03	f : 0.03	a : 0.03	e : 0.01	
d : 0.15	b : 0.14	e : 0.14	c : 0.14	y : 0.12	g : 0.07	w : 0.07	f : 0.06	] : 0.03	a : 0.01	i : 0.01	
d : 0.19	b : 0.14	e : 0.14	c : 0.12	f : 0.11	g : 0.09	y : 0.09	] : 0.04	4 : 0.01	a : 0.01	i : 0.01	
e : 0.23	] : 0.15	d : 0.14	f : 0.11	g : 0.09	c : 0.09	b : 0.04	3 : 0.03	y : 0.03	a : 0.01	4 : 0.01	i : 0.01	
e : 0.25	d : 0.17	f : 0.15	g : 0.12	] : 0.09	c : 0.06	b : 0.03	3 : 0.03	4 : 0.01	= : 0.01	h : 0.01	i : 0.01	
e : 0.30	f : 0.15	g : 0.12	d : 0.12	c : 0.06	b : 0.04	3 : 0.03	] : 0.01	: : 0.01	2 : 0.01	4 : 0.01	G : 0.01	= : 0.01	h : 0.01	F : 0.01	i : 0.01	

#score	1374.8781786810066
#seq	63
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_UTR_m2_run1.txt

#BEAR
ffff####cccccclllccc333ccc	chrX:92835609-92835874(-)$1	265	175	201	11.1504
gg!!ccc!!bboooooobb22ccc]g	chr13:3564606-3564873(+)$1	267	180	206	12.6995
eeeee####cccmmmmccc22eeeee	chr5:15880040-15880294(+)$1	254	2	28	9.6646
eeeee"""cccmmmmccc333eeeee	chr13:83803423-83803723(+)$1	300	58	84	9.8215
effffff[cccooooooccc]fffff	chr2:30119069-30119301(+)$1	232	190	216	12.7565
eeeee[eeeeeooooooeeeee]eee	chr17:5343294-5343543(+)$1	249	125	151	11.7853
ddiiiiiiiiiooooooiiiiiiiii	chr7:63188098-63188362(-)$1	264	67	93	12.9957
iiiii"""cccooooooccc55555i	chr14:65672838-65673100(-)$1	262	227	253	12.1628
===========oooooo=========	chr9:51923358-51923591(-)$1	233	160	186	14.2752
eeee[bb!!bboooooobb22bb]ee	chr1:171672138-171672402(-)$1	264	91	117	11.8300
[ccc####cccooooooccc333ccc	chr1:157127198-157127484(-)$1	286	99	125	15.8574
==============lll=========	chr11:77525592-77525832(+)$1	240	160	186	10.7280
eee####dddd[aooooooa]dddd]	chr7:117037221-117037469(-)$1	248	179	205	11.1229
ffffff[ddddoooooodddd]ffff	chr11:69730390-69730640(-)$1	250	89	115	12.1178
eeee[a!!cccnnnnnccc22a]eee	chr7:59249053-59249293(-)$1	240	26	52	10.4577
eeeee"""cccooooooccc333eee	chr16:66661922-66662201(-)$1	279	227	253	15.8633
========[bboooooobb]======	chr2:131878316-131878547(-)$1	231	199	225	13.5522
[ffffff[cccooooooccc]fffff	chrX:101477493-101477747(-)$1	254	51	77	12.8408
====="""cccooooooccc22====	chr5:148446857-148447102(-)$1	245	48	74	16.1427
""ccc"""cccnnnnnccc4444ccc	chr9:44444896-44445128(+)$1	232	10	36	11.2180
===========oooooo=========	chr1:153210516-153210776(+)$1	260	130	156	14.2752
dddd[a[ddddoooooodddd]a]dd	chr8:63390878-63391130(-)$1	252	1	27	12.6331
eeee####ddddooooooddddeeee	chr13:74496847-74497099(+)$1	252	214	240	12.5263
[ccc"""ddddooooooddddccc]h	chr2:118930091-118930322(-)$1	231	162	188	13.6345
====####cccooooooccc333===	chr5:84487283-84487539(-)$1	256	139	165	16.5996
""eeeee[cccooooooccceeeeeh	chr10:96083558-96083799(+)$1	241	115	141	12.6844
gggg!!ccc[bboooooobb]cccgg	chr11:78337016-78337256(-)$1	240	207	233	11.4789
ggggg"""cccooooooccc]ggggg	chr1:13129324-13129560(-)$1	236	143	169	15.2137
!!ccc"""ddddmmmmdddd333ccc	chr9:49323182-49323431(-)$1	249	157	183	10.3998
dddd"""ddddoooooodddd333dd	chr3:9434129-9434379(-)$1	250	79	105	13.8586
(dddd!!ddddoooooodddd22ddd	chr3:50176095-50176369(-)$1	274	60	86	11.9860
hhhhhhh!!bboooooobb333hhhh	chr7:11072520-11072752(-)$1	232	127	153	10.9313
[dddd[eeeeeooooooeeeee4444	chr4:34035528-34035792(+)$1	264	169	195	11.5987
"eeeee[ddddoooooodddd>>>>>	chr18:64435205-64435476(+)$1	271	166	192	11.7315
g[a[bb"""bboooooobb333bb]a	chr11:95629281-95629530(+)$1	249	141	167	12.9518
ddd[a[eeeeeooooooeeeee]a]d	chr16:89788639-89788893(-)$1	254	60	86	11.4753
eeeedddd!!aooooooa22dddd]e	chr19:27837440-27837682(-)$1	242	149	175	11.0503
ffff####cccooooooccc4444ff	chr15:36929092-36929374(-)$1	282	17	43	15.1931
CCeeeee[cccooooooccc22eeee	chr5:108930829-108931072(+)$1	243	186	212	11.0504
eeeee"""cccooooooccc333eee	chr12:60059713-60059958(-)$1	245	82	108	15.8633
eee####ddddoooooodddd4444e	chr13:41369314-41369580(+)$1	266	19	45	14.2428
b!!==========lll==========	chr11:104195071-104195313(-)$1	242	1	27	10.3118
&ffffff[cccooooooccc]fffff	chr1:167803360-167803615(-)$1	255	189	215	12.0854
=====[ccc[bboooooobb]ccc]=	chr6:7813808-7814039(+)$1	231	36	62	11.7458
fff####ddddoooooodddd4444f	chr13:23445732-23445997(-)$1	265	90	116	13.8686
e[dddd[ddddoooooodddd]dddd	chr13:34994462-34994712(+)$1	250	150	176	12.0008
e============lll==========	chr15:12113982-12114225(+)$1	243	14	40	10.7676
ggggggg!!cccnnnnnccc]ggggg	chr6:122405641-122405971(-)$1	330	149	175	9.9996
===ccceeeeeooooooeeeee4444	chr17:35970965-35971215(-)$1	250	93	119	11.7940
::ccc"""cccooooooccc22ccc:	chr3:100366205-100366461(-)$1	256	80	106	11.8418
dd[dddd!!bboooooobb22dddd]	chr11:106642348-106642753(-)$1	405	170	196	11.2062
iiii"""ddddoooooodddd22iii	chr2:49627833-49628122(+)$1	289	111	137	14.3460
gggggg[ddddoooooodddd]gggg	chr11:87864515-87864755(+)$1	240	211	237	13.2214
iiiii####cccmmmmccciiiiiii	chr7:149190003-149190234(+)$1	231	196	222	10.3006
Hffffff[cccoooooocccffffff	chr4:125391203-125391523(+)$1	320	132	158	11.6027

#otherMatches

#Seq PSSM
GGUUUAAGACCAGCUGUGCUUUGGGU	chrX:92835609-92835874(-)$1	265	175	201	11.1504
UUAUGUCAAGUAUCACAGCAGGGCCA	chr13:3564606-3564873(+)$1	267	180	206	12.6995
UCGUGUUUUAGGGAUUCUUUUCAUGA	chr5:15880040-15880294(+)$1	254	2	28	9.6646
GUCAGCAAACUAUUGGGUCAACUGAC	chr13:83803423-83803723(+)$1	300	58	84	9.8215
GGUCUGACUUGUAGACUCAGUUCAGA	chr2:30119069-30119301(+)$1	232	190	216	12.7565
CUUUGGGAAGUGAAUUGACUUUAUAA	chr17:5343294-5343543(+)$1	249	125	151	11.7853
AUCUUUUUAAGGACAUGUUUGAAAAG	chr7:63188098-63188362(-)$1	264	67	93	12.9957
CGGUCCCCCCCGUCCCAGGGACACUG	chr14:65672838-65673100(-)$1	262	227	253	12.1628
GUGAUCUCCUUCUCGGCAGGGAGGUU	chr9:51923358-51923591(-)$1	233	160	186	14.2752
GUUUUUAUUAUUGUAUUGUUUUAUAA	chr1:171672138-171672402(-)$1	264	91	117	11.8300
UAAACCAAAGUUUUAUUGCUAAAUUU	chr1:157127198-157127484(-)$1	286	99	125	15.8574
GAAAAUUCUAGUUUCCUGAAUUGGGA	chr11:77525592-77525832(+)$1	240	160	186	10.7280
CACUGGUCACUGGCUUUCAUGGGUGU	chr7:117037221-117037469(-)$1	248	179	205	11.1229
CUUUUUAAUUCAAUUUGGAAUCAGAA	chr11:69730390-69730640(-)$1	250	89	115	12.1178
UCCCCGCCAUUAUAAAAGUUUCUGGG	chr7:59249053-59249293(-)$1	240	26	52	10.4577
UCUGUGAGGUACAAACUUAUGAAACA	chr16:66661922-66662201(-)$1	279	227	253	15.8633
UAAGUAUUUUAAAACUAUGUAAUAUU	chr2:131878316-131878547(-)$1	231	199	225	13.5522
UUUGAUUUGUAAAUUAGUAUUAGUUA	chrX:101477493-101477747(-)$1	254	51	77	12.8408
AGAGGCCUUAGGCAAUUCUGUUUUUC	chr5:148446857-148447102(-)$1	245	48	74	16.1427
CUGUCUAAAGUUCUCCACUAGCUGAC	chr9:44444896-44445128(+)$1	232	10	36	11.2180
UUUUUGUGUUUGGAACGGAAUGCAAA	chr1:153210516-153210776(+)$1	260	130	156	14.2752
AAUCUCCCAGCUUGUGUGCUGUGUGG	chr8:63390878-63391130(-)$1	252	1	27	12.6331
AGUAGUACUUUGGCAAAGCAAAUACU	chr13:74496847-74497099(+)$1	252	214	240	12.5263
gcugaucuggaacucacucuguagac	chr2:118930091-118930322(-)$1	231	162	188	13.6345
GCAGGAACUGACUUACAUCGAAAUug	chr5:84487283-84487539(-)$1	256	139	165	16.5996
GUGUCUUUGACUUUGCUGUCAAGACU	chr10:96083558-96083799(+)$1	241	115	141	12.6844
GGAACUAAGAUGACAAUCCAACUUUU	chr11:78337016-78337256(-)$1	240	207	233	11.4789
CAUCACUUUGUUCAUCUGCAUUGAUG	chr1:13129324-13129560(-)$1	236	143	169	15.2137
CUUUGCAUUAUUAAAGGAUAUAACAG	chr9:49323182-49323431(-)$1	249	157	183	10.3998
AGGAAUCAAAACGGGAAUUUUAUCUC	chr3:9434129-9434379(-)$1	250	79	105	13.8586
UUUCUCCUUAUUUCUUUAUAGACAGA	chr3:50176095-50176369(-)$1	274	60	86	11.9860
gugaaaauucauguuacuguccuuuu	chr7:11072520-11072752(-)$1	232	127	153	10.9313
AUUGAUGUAAUUUAAUUGUUAUUUAU	chr4:34035528-34035792(+)$1	264	169	195	11.5987
UCGUUCUGGGUCUUUAAGCCCCUCUU	chr18:64435205-64435476(+)$1	271	166	192	11.7315
AGAGAUUUUGAUGCUGUUCCGCAUGU	chr11:95629281-95629530(+)$1	249	141	167	12.9518
AGGGUGGUCGUCUCUGUACGAUGAGC	chr16:89788639-89788893(-)$1	254	60	86	11.4753
UAAAAGAAAUGUUUGGUCUCUUCUAU	chr19:27837440-27837682(-)$1	242	149	175	11.0503
ACAAUGUUGCUGACUAGAGUUUUCUU	chr15:36929092-36929374(-)$1	282	17	43	15.1931
CAAGGGUUUAUGCGUAAAUAUUACCU	chr5:108930829-108931072(+)$1	243	186	212	11.0504
UUGUUAUUAUACUCAACUAUCUAAAU	chr12:60059713-60059958(-)$1	245	82	108	15.8633
gcacaugccauagcuuaaugggcgau	chr13:41369314-41369580(+)$1	266	19	45	14.2428
GAGGGGGAAAGGAAUUUUCUUUUUCU	chr11:104195071-104195313(-)$1	242	1	27	10.3118
UUGAUUUUAGCUAGUUUGUUUAAGUC	chr1:167803360-167803615(-)$1	255	189	215	12.0854
aaaauuauuuguuuuauuauuaauua	chr6:7813808-7814039(+)$1	231	36	62	11.7458
CAGUGAAUUUAGCUCAGUAAAGAAUC	chr13:23445732-23445997(-)$1	265	90	116	13.8686
GUUGUCUAUUGCAUAAACAGUUGACA	chr13:34994462-34994712(+)$1	250	150	176	12.0008
UUCAUGGAAGAACCAAGUUUUUCUAU	chr15:12113982-12114225(+)$1	243	14	40	10.7676
UUGUAAAGAGGAAAACAUCCAUUUAC	chr6:122405641-122405971(-)$1	330	149	175	9.9996
GUGCGGCAAGGUCUUGGUCUUGGUCU	chr17:35970965-35971215(-)$1	250	93	119	11.7940
CUGGGUUAACUAAAUACAGUAUCCCU	chr3:100366205-100366461(-)$1	256	80	106	11.8418
UUUUCCUUAAGAGUGAACUACAGGAC	chr11:106642348-106642753(-)$1	405	170	196	11.2062
UUUGUUUUCAUGAAUUUGUGGUUUAG	chr2:49627833-49628122(+)$1	289	111	137	14.3460
GAUGCACGAUGGAAUUGUGUUUUGCA	chr11:87864515-87864755(+)$1	240	211	237	13.2214
ACAGGAUAUCCAGAAGUGGCUUGUGU	chr7:149190003-149190234(+)$1	231	196	222	10.3006
CACUGUGAUAUAUCAAAGUGCACAGU	chr4:125391203-125391523(+)$1	320	132	158	11.6027

#DB
((((....((((((...)))...)))	chrX:92835609-92835874(-)$1	1	175	201	11.1504
((..(((..((......))..))).)	chr13:3564606-3564873(+)$1	1	180	206	12.6995
(((((....(((....)))..)))))	chr5:15880040-15880294(+)$1	1	2	28	9.6646
(((((...(((....)))...)))))	chr13:83803423-83803723(+)$1	1	58	84	9.8215
)((((((.(((......))).)))))	chr2:30119069-30119301(+)$1	1	190	216	12.7565
(((((.(((((......))))).)))	chr17:5343294-5343543(+)$1	1	125	151	11.7853
))(((((((((......)))))))))	chr7:63188098-63188362(-)$1	1	67	93	12.9957
(((((...(((......))).....)	chr14:65672838-65673100(-)$1	1	227	253	12.1628
(((((((((((......)))))))))	chr9:51923358-51923591(-)$1	1	160	186	14.2752
((((.((..((......))..)).))	chr1:171672138-171672402(-)$1	1	91	117	11.8300
.(((....(((......)))...)))	chr1:157127198-157127484(-)$1	1	99	125	15.8574
((((((((((((((...)))))))))	chr11:77525592-77525832(+)$1	1	160	186	10.7280
(((....((((.(......).)))).	chr7:117037221-117037469(-)$1	1	179	205	11.1229
((((((.((((......)))).))))	chr11:69730390-69730640(-)$1	1	89	115	12.1178
((((.(..(((.....)))..).)))	chr7:59249053-59249293(-)$1	1	26	52	10.4577
(((((...(((......)))...)))	chr16:66661922-66662201(-)$1	1	227	253	15.8633
((((((((.((......)).))))))	chr2:131878316-131878547(-)$1	1	199	225	13.5522
.((((((.(((......))).)))))	chrX:101477493-101477747(-)$1	1	51	77	12.8408
(((((...(((......)))..))))	chr5:148446857-148447102(-)$1	1	48	74	16.1427
..(((...(((.....)))....)))	chr9:44444896-44445128(+)$1	1	10	36	11.2180
(((((((((((......)))))))))	chr1:153210516-153210776(+)$1	1	130	156	14.2752
((((.(.((((......)))).).))	chr8:63390878-63391130(-)$1	1	1	27	12.6331
((((....((((......))))))))	chr13:74496847-74497099(+)$1	1	214	240	12.5263
.(((...((((......))))))).)	chr2:118930091-118930322(-)$1	1	162	188	13.6345
((((....(((......)))...)))	chr5:84487283-84487539(-)$1	1	139	165	16.5996
..(((((.(((......)))))))))	chr10:96083558-96083799(+)$1	1	115	141	12.6844
((((..(((.((......)).)))))	chr11:78337016-78337256(-)$1	1	207	233	11.4789
(((((...(((......))).)))))	chr1:13129324-13129560(-)$1	1	143	169	15.2137
..(((...((((....))))...)))	chr9:49323182-49323431(-)$1	1	157	183	10.3998
((((...((((......))))...))	chr3:9434129-9434379(-)$1	1	79	105	13.8586
.((((..((((......))))..)))	chr3:50176095-50176369(-)$1	1	60	86	11.9860
(((((((..((......))...))))	chr7:11072520-11072752(-)$1	1	127	153	10.9313
.((((.(((((......)))))....	chr4:34035528-34035792(+)$1	1	169	195	11.5987
.(((((.((((......)))).....	chr18:64435205-64435476(+)$1	1	166	192	11.7315
(.(.((...((......))...)).)	chr11:95629281-95629530(+)$1	1	141	167	12.9518
(((.(.(((((......))))).).)	chr16:89788639-89788893(-)$1	1	60	86	11.4753
((((((((..(......)..)))).)	chr19:27837440-27837682(-)$1	1	149	175	11.0503
((((....(((......)))....))	chr15:36929092-36929374(-)$1	1	17	43	15.1931
))(((((.(((......)))..))))	chr5:108930829-108931072(+)$1	1	186	212	11.0504
(((((...(((......)))...)))	chr12:60059713-60059958(-)$1	1	82	108	15.8633
(((....((((......))))....)	chr13:41369314-41369580(+)$1	1	19	45	14.2428
(..((((((((((...))))))))))	chr11:104195071-104195313(-)$1	1	1	27	10.3118
.((((((.(((......))).)))))	chr1:167803360-167803615(-)$1	1	189	215	12.0854
(((((.(((.((......)).))).)	chr6:7813808-7814039(+)$1	1	36	62	11.7458
(((....((((......))))....)	chr13:23445732-23445997(-)$1	1	90	116	13.8686
(.((((.((((......)))).))))	chr13:34994462-34994712(+)$1	1	150	176	12.0008
(((((((((((((...))))))))))	chr15:12113982-12114225(+)$1	1	14	40	10.7676
(((((((..(((.....))).)))))	chr6:122405641-122405971(-)$1	1	149	175	9.9996
(((((((((((......)))))....	chr17:35970965-35971215(-)$1	1	93	119	11.7940
..(((...(((......)))..))).	chr3:100366205-100366461(-)$1	1	80	106	11.8418
((.((((..((......))..)))).	chr11:106642348-106642753(-)$1	1	170	196	11.2062
((((...((((......))))..)))	chr2:49627833-49628122(+)$1	1	111	137	14.3460
((((((.((((......)))).))))	chr11:87864515-87864755(+)$1	1	211	237	13.2214
(((((....(((....))))))))))	chr7:149190003-149190234(+)$1	1	196	222	10.3006
(((((((.(((......)))))))))	chr4:125391203-125391523(+)$1	1	132	158	11.6027

#PSSM
e : 0.25	= : 0.14	g : 0.10	d : 0.09	f : 0.07	[ : 0.07	i : 0.05	" : 0.05	! : 0.01	( : 0.01	h : 0.01	C : 0.01	b : 0.01	& : 0.01	: : 0.01	H : 0.01	
e : 0.21	= : 0.16	f : 0.14	d : 0.12	g : 0.09	i : 0.05	c : 0.03	" : 0.03	! : 0.03	[ : 0.03	h : 0.01	C : 0.01	: : 0.01	
e : 0.25	= : 0.16	f : 0.14	d : 0.10	c : 0.09	i : 0.07	g : 0.07	! : 0.03	h : 0.01	a : 0.01	[ : 0.01	
e : 0.21	= : 0.16	f : 0.12	c : 0.10	d : 0.10	i : 0.07	g : 0.07	# : 0.05	[ : 0.03	! : 0.01	h : 0.01	
# : 0.14	e : 0.14	= : 0.14	c : 0.09	f : 0.09	d : 0.09	i : 0.05	[ : 0.05	" : 0.05	g : 0.05	! : 0.01	h : 0.01	b : 0.01	a : 0.01	
" : 0.21	# : 0.18	= : 0.10	f : 0.09	[ : 0.07	e : 0.05	d : 0.05	c : 0.03	b : 0.03	a : 0.03	! : 0.03	g : 0.03	i : 0.01	h : 0.01	
" : 0.23	# : 0.18	e : 0.10	= : 0.10	[ : 0.09	f : 0.07	c : 0.05	! : 0.03	d : 0.03	i : 0.01	b : 0.01	h : 0.01	g : 0.01	
d : 0.23	" : 0.18	# : 0.12	! : 0.10	[ : 0.10	= : 0.10	e : 0.07	c : 0.03	i : 0.01	
c : 0.38	d : 0.25	! : 0.10	= : 0.09	e : 0.07	# : 0.03	i : 0.01	[ : 0.01	" : 0.01	
c : 0.40	d : 0.25	b : 0.10	= : 0.09	e : 0.07	[ : 0.03	i : 0.01	! : 0.01	
c : 0.40	d : 0.25	b : 0.14	= : 0.09	e : 0.07	i : 0.01	a : 0.01	
o : 0.72	c : 0.07	= : 0.05	n : 0.03	d : 0.03	b : 0.03	m : 0.01	[ : 0.01	
o : 0.78	m : 0.07	= : 0.05	n : 0.05	c : 0.01	a : 0.01	
o : 0.80	m : 0.07	n : 0.05	l : 0.03	c : 0.01	= : 0.01	
o : 0.80	l : 0.07	m : 0.07	n : 0.05	
o : 0.80	l : 0.07	m : 0.05	n : 0.05	c : 0.01	
o : 0.80	c : 0.09	l : 0.03	= : 0.03	d : 0.01	n : 0.01	
c : 0.40	d : 0.21	b : 0.10	= : 0.09	e : 0.07	o : 0.07	i : 0.01	a : 0.01	
c : 0.38	d : 0.23	b : 0.14	= : 0.09	e : 0.07	3 : 0.01	i : 0.01	o : 0.01	2 : 0.01	
c : 0.30	d : 0.23	2 : 0.10	= : 0.09	e : 0.07	3 : 0.05	i : 0.03	b : 0.03	a : 0.01	] : 0.01	4 : 0.01	
d : 0.23	3 : 0.16	2 : 0.14	] : 0.14	= : 0.10	e : 0.09	i : 0.03	4 : 0.03	5 : 0.01	f : 0.01	
3 : 0.16	e : 0.12	= : 0.10	2 : 0.09	c : 0.07	f : 0.07	d : 0.07	] : 0.07	4 : 0.07	i : 0.03	g : 0.03	5 : 0.01	b : 0.01	a : 0.01	> : 0.01	
3 : 0.12	= : 0.12	4 : 0.10	c : 0.09	e : 0.09	f : 0.09	d : 0.07	] : 0.05	g : 0.05	i : 0.03	b : 0.03	2 : 0.03	5 : 0.01	a : 0.01	h : 0.01	> : 0.01	
c : 0.16	e : 0.16	= : 0.14	f : 0.09	d : 0.09	4 : 0.09	i : 0.05	g : 0.05	] : 0.03	5 : 0.01	3 : 0.01	h : 0.01	> : 0.01	b : 0.01	a : 0.01	
e : 0.18	= : 0.14	] : 0.10	f : 0.10	d : 0.10	c : 0.09	g : 0.07	4 : 0.07	i : 0.05	5 : 0.01	h : 0.01	> : 0.01	
e : 0.20	= : 0.16	f : 0.12	g : 0.09	d : 0.09	c : 0.07	i : 0.07	h : 0.05	] : 0.03	4 : 0.03	> : 0.01	a : 0.01	: : 0.01	

#score	685.5162251429002
#seq	55
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_CDS_m1_run1.txt

#BEAR
bb[aooooooa]bbfff	chr10:102866868-102867085(+)$1	217	87	104	10.1232
cccaooooooa]ccc]e	chr4:140558333-140558555(+)$1	222	191	208	11.7433
bb[aooooooa]bb]cc	chr7:88622732-88622949(-)$1	217	53	70	10.6835
hhhhoooooohhhhhhh	chr1:181615783-181616007(+)$1	224	57	74	10.1961
ggggooooooggggggg	chr17:26255765-26255988(+)$1	223	149	166	10.9114
h[bboooooobb]hhhh	chr11:70250061-70250286(-)$1	225	79	96	11.3128
iiiiooooooiiiiiii	chr17:25029885-25030106(-)$1	221	202	219	11.3397
ffffooooooffffff]	chr15:4893578-4893795(-)$1	217	77	94	9.5828
[cccooooooccc]ccc	chr7:147174076-147174297(+)$1	221	194	211	11.9568
hhhhoooooohhhhhhh	chr5:23325207-23325435(+)$1	228	101	118	10.1961
bb[aooooooa]bb444	chr3:108194364-108194594(-)$1	230	160	177	10.4134
dcccooooooccc]ddd	chr1:164605729-164605969(-)$1	240	86	103	11.1701
hhhhoooooohhhhhhh	chr17:24322252-24322476(-)$1	224	188	205	10.1961
[cccoooooocccccc:	chr18:42738100-42738325(+)$1	225	8	25	10.9415
b[bboooooobb]bb]a	chr2:129298258-129298475(+)$1	217	73	90	11.0437
!cccooooooccc]bb]	chr5:68165868-68166089(-)$1	221	72	89	11.3727
c[bboooooobb]ccch	chr7:114217688-114217910(-)$1	222	158	175	11.8787
====oooooo=======	chr5:35249734-35249956(+)$1	222	162	179	11.3885
ccbboooooobb]ccce	chr2:25296327-25296559(+)$1	232	170	187	11.9316
bb[aooooooa]bb22f	chr8:96561207-96561431(+)$1	224	174	191	10.0701
ddbboooooobb]dddd	chr15:76444819-76445041(+)$1	222	57	74	10.9750
[cccooooooccc]ccc	chr15:94192889-94193111(-)$1	222	37	54	11.9568
!cccooooooccc]ccc	chr4:115982067-115982289(+)$1	222	143	160	11.9883
""bboooooobb22fff	chr4:59607249-59607467(+)$1	218	168	185	11.0025
gg[aooooooa]ggggg	chr9:110474439-110474654(-)$1	215	194	211	11.4975
ddddoooooodddd22f	chr9:54251732-54251953(-)$1	221	66	83	9.5714
ddddoooooodddd]ee	chr6:86933747-86933973(+)$1	226	27	44	9.9048
ddddoooooodddd]ee	chr1:160784882-160785101(+)$1	219	38	55	9.9048
ccbboooooobb]ccc]	chr12:4639733-4639957(+)$1	224	67	84	12.0561
c[bboooooobb22ccc	chr14:100422229-100422461(-)$1	232	165	182	11.5659
[cccooooooccc]ccc	chr2:69505135-69505356(-)$1	221	12	29	11.9568
[cccooooooccc]ggg	chr18:37107144-37107371(+)$1	227	185	202	11.8199
!cccooooooccc22cc	chr7:13513599-13513818(+)$1	219	16	33	11.5846
bcccooooooccc]bb:	chr9:62619051-62619267(+)$1	216	20	37	10.0408
ee[aooooooa]eeeee	chr19:5384605-5384829(+)$1	224	69	86	10.4640
hhhhoooooohhhhhhh	chr6:93695497-93695712(-)$1	215	65	82	10.1961
""bboooooobb333dd	chr4:57869417-57869640(+)$1	223	190	207	11.7467
cc[aooooooa]ccc]e	chr8:11541879-11542100(+)$1	221	62	79	11.7287
ggggooooooggggggg	chr7:52780027-52780253(-)$1	226	3	20	10.9114
"cccoooooocccffff	chr17:24709590-24709817(+)$1	227	179	196	11.1183
c[bboooooobb]ccc4	chr9:54731680-54731896(-)$1	216	94	111	11.9371
a[bboooooobb]a]dd	chr11:58886716-58886937(+)$1	221	132	149	11.6386
"cccooooooccc333b	chr10:80700056-80700273(-)$1	217	198	215	11.6582
bcccooooooccc]bb3	chr11:102264892-102265112(-)$1	220	134	151	10.9593
[cccoooooocccdddd	chr16:20123074-20123304(+)$1	230	44	61	11.2075
##bboooooobb4444d	chr12:104384467-104384691(-)$1	224	203	220	11.4341
!!bboooooobb]ccc9	chr3:109467206-109467427(+)$1	221	110	127	11.4238
ddddooooooddddggg	chr5:144180464-144180704(+)$1	240	41	58	10.0384
"cccooooooccc333h	chr16:38482583-38482807(+)$1	224	89	106	11.8051
ee[aooooooa]eeeee	chr7:109952652-109952873(+)$1	221	35	52	10.4640
ccbboooooobb]ccc]	chr11:30029481-30029700(-)$1	219	158	175	12.0561
c[bboooooobb]cccC	chr11:70324059-70324275(+)$1	216	191	208	10.9065
ddddoooooodddd]a]	chr19:4916620-4916835(-)$1	215	179	196	10.1185
hhhhoooooohhhhhhh	chr2:128943664-128943884(-)$1	220	198	215	10.1961
ddbboooooobb]dddd	chr6:18373828-18374051(-)$1	223	115	132	10.9750
$$bboooooobb4444e	chr17:74985308-74985533(+)$1	225	96	113	11.0706
cc[aooooooaccc333	chr2:130901609-130901830(-)$1	221	171	188	11.9763
ddddoooooodddd]dd	chr8:40134451-40134672(+)$1	221	193	210	9.8897
##bboooooobbiiiii	chr15:99567911-99568140(-)$1	229	53	70	11.7670
ii[aooooooaiiiiii	chr8:42295673-42295893(+)$1	220	74	91	11.8202
cc[aooooooa]ccc::	chr8:86488873-86489090(-)$1	217	37	54	9.8889
c[bboooooobb]ccc4	chr2:120359431-120359651(+)$1	220	41	58	11.9371

#otherMatches

#Seq PSSM
CAGCAACUCAGGUGUUC	chr10:102866868-102867085(+)$1	217	87	104	10.1232
CCUCCCACCCGCAGGAA	chr4:140558333-140558555(+)$1	222	191	208	11.7433
GCCCAUCAUAGUGCCCA	chr7:88622732-88622949(-)$1	217	53	70	10.6835
GCUACUCCCAUAGCCAU	chr1:181615783-181616007(+)$1	224	57	74	10.1961
UUUUGGUGGAGAGACUG	chr17:26255765-26255988(+)$1	223	149	166	10.9114
UGUAGGCGGGUGGGGGG	chr11:70250061-70250286(-)$1	225	79	96	11.3128
UGGGUGUCAUUUCAGGC	chr17:25029885-25030106(-)$1	221	202	219	11.3397
CCAGCAUGAACUGGAAA	chr15:4893578-4893795(-)$1	217	77	94	9.5828
GUCCUACCCUGGAGGCC	chr7:147174076-147174297(+)$1	221	194	211	11.9568
UUAAAUGAAGUUGGGGU	chr5:23325207-23325435(+)$1	228	101	118	10.1961
GGUCCCCAUUGUCCCCC	chr3:108194364-108194594(-)$1	230	160	177	10.4134
ACUGGCCAGUCAGAUGC	chr1:164605729-164605969(-)$1	240	86	103	11.1701
AUUGCCAAGACAGUGUC	chr17:24322252-24322476(-)$1	224	188	205	10.1961
AUGGGAGCCACCACCUU	chr18:42738100-42738325(+)$1	225	8	25	10.9415
CACAAUGCCCUGAGGAC	chr2:129298258-129298475(+)$1	217	73	90	11.0437
AGUCCAAACCGACAUCU	chr5:68165868-68166089(-)$1	221	72	89	11.3727
UGAUGAUUGGGUAAUGC	chr7:114217688-114217910(-)$1	222	158	175	11.8787
UGAGGGUGUACUUGCCU	chr5:35249734-35249956(+)$1	222	162	179	11.3885
CUGGCACCUCCCAAGGU	chr2:25296327-25296559(+)$1	232	170	187	11.9316
UGGGGAGGAUCGCAGCC	chr8:96561207-96561431(+)$1	224	174	191	10.0701
CCCAAUAACCUGAGGCU	chr15:76444819-76445041(+)$1	222	57	74	10.9750
AUCUUUUAUUAGGCGAC	chr15:94192889-94193111(-)$1	222	37	54	11.9568
UGGACCACCAUCCUCCA	chr4:115982067-115982289(+)$1	222	143	160	11.9883
AAUGUUUUCUCAGAGAA	chr4:59607249-59607467(+)$1	218	168	185	11.0025
AGUGUGUGUUCUUUCAU	chr9:110474439-110474654(-)$1	215	194	211	11.4975
GAUUGUAAAAGAUUACA	chr9:54251732-54251953(-)$1	221	66	83	9.5714
CGUUGCCUGGAAUGCUG	chr6:86933747-86933973(+)$1	226	27	44	9.9048
GGGGCUUCUUCCCCUCC	chr1:160784882-160785101(+)$1	219	38	55	9.9048
UGCACCUCACUGACAUG	chr12:4639733-4639957(+)$1	224	67	84	12.0561
UAGAUCACUUUCAGACA	chr14:100422229-100422461(-)$1	232	165	182	11.5659
AUCUUUAAAUAGAGGUC	chr2:69505135-69505356(-)$1	221	12	29	11.9568
GCUGGUGGAGCGGAGGG	chr18:37107144-37107371(+)$1	227	185	202	11.8199
UCUGCCCACACAGCCCG	chr7:13513599-13513818(+)$1	219	16	33	11.5846
CCUGAAAAGCCAGAGCA	chr9:62619051-62619267(+)$1	216	20	37	10.0408
UGCAGUAUCAUCCAGCC	chr19:5384605-5384829(+)$1	224	69	86	10.4640
CCAAUGGGAUUUGGCUU	chr6:93695497-93695712(-)$1	215	65	82	10.1961
AGUCAACAUGGAAGAGA	chr4:57869417-57869640(+)$1	223	190	207	11.7467
AUGAAAGCAAUGAUCUG	chr8:11541879-11542100(+)$1	221	62	79	11.7287
UGGAGGGUGGUCCAGCU	chr7:52780027-52780253(-)$1	226	3	20	10.9114
CUGUCCUAAUACAGAGC	chr17:24709590-24709817(+)$1	227	179	196	11.1183
CCUCGACAUGGAAGCUU	chr9:54731680-54731896(-)$1	216	94	111	11.9371
GCUCCUCCGUGAACCGG	chr11:58886716-58886937(+)$1	221	132	149	11.6386
GGGUGGGUUAGCUGAGU	chr10:80700056-80700273(-)$1	217	198	215	11.6582
GGCUGAAUCUGGCACCA	chr11:102264892-102265112(-)$1	220	134	151	10.9593
AGUGUCCUACCACGGCU	chr16:20123074-20123304(+)$1	230	44	61	11.2075
AAAGUCAACUCUCAAGG	chr12:104384467-104384691(-)$1	224	203	220	11.4341
AGCUGGACAGAGGGGUA	chr3:109467206-109467427(+)$1	221	110	127	11.4238
UCCAUCUACCUGGAGUC	chr5:144180464-144180704(+)$1	240	41	58	10.0384
CAUCACAACCGAUUCUU	chr16:38482583-38482807(+)$1	224	89	106	11.8051
CCCCAGAAGAGAGGAAG	chr7:109952652-109952873(+)$1	221	35	52	10.4640
GCGUCCCACAGCAGCCA	chr11:30029481-30029700(-)$1	219	158	175	12.0561
GGAGGUAGGACUGCUUG	chr11:70324059-70324275(+)$1	216	191	208	10.9065
CUGGAAAGGACCAGUCC	chr19:4916620-4916835(-)$1	215	179	196	10.1185
GGAAUUCUUUUUUCUCU	chr2:128943664-128943884(-)$1	220	198	215	10.1961
UGCUGCUGGAGGACAGA	chr6:18373828-18374051(-)$1	223	115	132	10.9750
CAGACCUUUAUCAAAUC	chr17:74985308-74985533(+)$1	225	96	113	11.0706
UGACCCUCCAGCGCAGC	chr2:130901609-130901830(-)$1	221	171	188	11.9763
UUACUUCAGUGUGAAAA	chr8:40134451-40134672(+)$1	221	193	210	9.8897
UAGGUGCUCUCCCAGGA	chr15:99567911-99568140(-)$1	229	53	70	11.7670
GUACUGAGAUGACAGUC	chr8:42295673-42295893(+)$1	220	74	91	11.8202
UUACUUACCUGAAAGAC	chr8:86488873-86489090(-)$1	217	37	54	9.8889
UGUGUCGGCUUAGAUCU	chr2:120359431-120359651(+)$1	220	41	58	11.9371

#DB
((.(......).)))))	chr10:102866868-102867085(+)$1	1	87	104	10.1232
((((......).))).)	chr4:140558333-140558555(+)$1	1	191	208	11.7433
((.(......).)).))	chr7:88622732-88622949(-)$1	1	53	70	10.6835
((((......)))))))	chr1:181615783-181616007(+)$1	1	57	74	10.1961
((((......)))))))	chr17:26255765-26255988(+)$1	1	149	166	10.9114
(.((......)).))))	chr11:70250061-70250286(-)$1	1	79	96	11.3128
((((......)))))))	chr17:25029885-25030106(-)$1	1	202	219	11.3397
((((......)))))).	chr15:4893578-4893795(-)$1	1	77	94	9.5828
.(((......))).)))	chr7:147174076-147174297(+)$1	1	194	211	11.9568
((((......)))))))	chr5:23325207-23325435(+)$1	1	101	118	10.1961
((.(......).))...	chr3:108194364-108194594(-)$1	1	160	177	10.4134
((((......))).)))	chr1:164605729-164605969(-)$1	1	86	103	11.1701
((((......)))))))	chr17:24322252-24322476(-)$1	1	188	205	10.1961
.(((......)))))).	chr18:42738100-42738325(+)$1	1	8	25	10.9415
(.((......)).)).)	chr2:129298258-129298475(+)$1	1	73	90	11.0437
.(((......))).)).	chr5:68165868-68166089(-)$1	1	72	89	11.3727
(.((......)).))))	chr7:114217688-114217910(-)$1	1	158	175	11.8787
((((......)))))))	chr5:35249734-35249956(+)$1	1	162	179	11.3885
((((......)).))))	chr2:25296327-25296559(+)$1	1	170	187	11.9316
((.(......).))..)	chr8:96561207-96561431(+)$1	1	174	191	10.0701
((((......)).))))	chr15:76444819-76445041(+)$1	1	57	74	10.9750
.(((......))).)))	chr15:94192889-94193111(-)$1	1	37	54	11.9568
.(((......))).)))	chr4:115982067-115982289(+)$1	1	143	160	11.9883
..((......))..)))	chr4:59607249-59607467(+)$1	1	168	185	11.0025
((.(......).)))))	chr9:110474439-110474654(-)$1	1	194	211	11.4975
((((......))))..)	chr9:54251732-54251953(-)$1	1	66	83	9.5714
((((......)))).))	chr6:86933747-86933973(+)$1	1	27	44	9.9048
((((......)))).))	chr1:160784882-160785101(+)$1	1	38	55	9.9048
((((......)).))).	chr12:4639733-4639957(+)$1	1	67	84	12.0561
(.((......))..)))	chr14:100422229-100422461(-)$1	1	165	182	11.5659
.(((......))).)))	chr2:69505135-69505356(-)$1	1	12	29	11.9568
.(((......))).)))	chr18:37107144-37107371(+)$1	1	185	202	11.8199
.(((......)))..))	chr7:13513599-13513818(+)$1	1	16	33	11.5846
((((......))).)).	chr9:62619051-62619267(+)$1	1	20	37	10.0408
((.(......).)))))	chr19:5384605-5384829(+)$1	1	69	86	10.4640
((((......)))))))	chr6:93695497-93695712(-)$1	1	65	82	10.1961
..((......))...))	chr4:57869417-57869640(+)$1	1	190	207	11.7467
((.(......).))).)	chr8:11541879-11542100(+)$1	1	62	79	11.7287
((((......)))))))	chr7:52780027-52780253(-)$1	1	3	20	10.9114
.(((......)))))))	chr17:24709590-24709817(+)$1	1	179	196	11.1183
(.((......)).))).	chr9:54731680-54731896(-)$1	1	94	111	11.9371
(.((......)).).))	chr11:58886716-58886937(+)$1	1	132	149	11.6386
.(((......)))...)	chr10:80700056-80700273(-)$1	1	198	215	11.6582
((((......))).)).	chr11:102264892-102265112(-)$1	1	134	151	10.9593
.(((......)))))))	chr16:20123074-20123304(+)$1	1	44	61	11.2075
..((......))....)	chr12:104384467-104384691(-)$1	1	203	220	11.4341
..((......)).))).	chr3:109467206-109467427(+)$1	1	110	127	11.4238
((((......)))))))	chr5:144180464-144180704(+)$1	1	41	58	10.0384
.(((......)))...)	chr16:38482583-38482807(+)$1	1	89	106	11.8051
((.(......).)))))	chr7:109952652-109952873(+)$1	1	35	52	10.4640
((((......)).))).	chr11:30029481-30029700(-)$1	1	158	175	12.0561
(.((......)).))))	chr11:70324059-70324275(+)$1	1	191	208	10.9065
((((......)))).).	chr19:4916620-4916835(-)$1	1	179	196	10.1185
((((......)))))))	chr2:128943664-128943884(-)$1	1	198	215	10.1961
((((......)).))))	chr6:18373828-18374051(-)$1	1	115	132	10.9750
..((......))....)	chr17:74985308-74985533(+)$1	1	96	113	11.0706
((.(......))))...	chr2:130901609-130901830(-)$1	1	171	188	11.9763
((((......)))).))	chr8:40134451-40134672(+)$1	1	193	210	9.8897
..((......)))))))	chr15:99567911-99568140(-)$1	1	53	70	11.7670
((.(......)))))))	chr8:42295673-42295893(+)$1	1	74	91	11.8202
((.(......).)))..	chr8:86488873-86489090(-)$1	1	37	54	9.8889
(.((......)).))).	chr2:120359431-120359651(+)$1	1	41	58	11.9371

#PSSM
c : 0.19	d : 0.14	b : 0.11	h : 0.09	[ : 0.09	" : 0.08	! : 0.06	g : 0.04	i : 0.03	e : 0.03	# : 0.03	f : 0.01	= : 0.01	a : 0.01	$ : 0.01	
c : 0.35	[ : 0.12	d : 0.12	h : 0.08	b : 0.06	g : 0.04	i : 0.03	" : 0.03	e : 0.03	# : 0.03	f : 0.01	= : 0.01	! : 0.01	$ : 0.01	
b : 0.30	c : 0.25	[ : 0.17	d : 0.09	h : 0.08	g : 0.03	i : 0.01	f : 0.01	= : 0.01	
b : 0.30	c : 0.24	a : 0.19	d : 0.09	h : 0.08	g : 0.03	i : 0.01	f : 0.01	= : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
b : 0.30	c : 0.24	a : 0.19	d : 0.09	h : 0.08	g : 0.03	i : 0.01	f : 0.01	= : 0.01	
b : 0.30	c : 0.25	] : 0.16	d : 0.09	h : 0.08	g : 0.03	i : 0.03	f : 0.01	= : 0.01	
c : 0.30	] : 0.20	d : 0.09	h : 0.08	b : 0.06	g : 0.04	i : 0.04	2 : 0.03	e : 0.03	4 : 0.03	f : 0.01	= : 0.01	3 : 0.01	
c : 0.20	] : 0.14	d : 0.14	h : 0.09	b : 0.08	g : 0.04	i : 0.04	2 : 0.04	3 : 0.04	f : 0.03	e : 0.03	4 : 0.03	= : 0.01	a : 0.01	
c : 0.27	] : 0.09	h : 0.09	g : 0.08	f : 0.06	d : 0.06	b : 0.06	3 : 0.06	i : 0.04	4 : 0.04	2 : 0.04	e : 0.03	= : 0.01	
c : 0.25	d : 0.11	h : 0.09	g : 0.08	f : 0.06	e : 0.06	] : 0.04	i : 0.04	4 : 0.04	b : 0.04	3 : 0.04	2 : 0.03	= : 0.01	a : 0.01	: : 0.01	
e : 0.12	h : 0.12	d : 0.12	c : 0.11	f : 0.08	g : 0.08	] : 0.08	i : 0.04	4 : 0.04	: : 0.04	3 : 0.03	a : 0.01	= : 0.01	b : 0.01	9 : 0.01	C : 0.01	

#score	685.613528488563
#seq	62
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_UTR_m1_run1.txt

#BEAR
::eeeeevvvvvvvvvvvvveeeee	chr14:67487155-67487356(-)$1	201	90	115	21.3731
!ddddxxxxxxxxxxxxxxxdddd]	chr18:85049069-85049270(+)$1	201	66	91	18.7184
iii"""bbtttttttttttbb333i	chr6:71760519-71760720(+)$1	201	167	192	20.4757
ddeeeeeuuuuuuuuuuuueeeee:	chr6:124997802-124998003(+)$1	201	75	100	22.5302
$eeeeewwwwwwwwwwwwwweeeee	chr1:166368304-166368505(-)$1	201	143	168	23.5749
!!ddddvvvvvvvvvvvvvdddd]d	chr5:104542378-104542579(-)$1	201	91	116	22.2572
ffffffvvvvvvvvvvvvvffffff	chr17:45678883-45679084(-)$1	201	146	171	22.1075
$eeeeewwwwwwwwwwwwwweeeee	chr1:166368228-166368429(-)$1	201	67	92	23.5749
dd!!ccctttttttttttccc22dd	chr19:44380200-44380401(+)$1	201	156	181	20.7568
[bb[cccuuuuuuuuuuuuccc]bb	chr9:58724981-58725182(-)$1	201	31	56	22.6200
!eeeeevvvvvvvvvvvvveeeee]	chr15:88901158-88901359(+)$1	201	151	176	23.7915
$eeeeewwwwwwwwwwwwwweeeee	chr1:166368303-166368504(-)$1	201	142	167	23.5749
gggggwwwwwwwwwwwwwwgggggg	chr1:157694756-157694957(-)$1	201	119	144	22.3848
eeeee[bbtttttttttttbb]eee	chr2:102621783-102621984(+)$1	201	106	131	21.3024
:ffffffuuuuuuuuuuuuffffff	chr8:11448449-11448650(+)$1	201	61	86	21.8519
ggggggguuuuuuuuuuuugggggg	chr7:118215758-118215959(-)$1	201	168	193	23.2772
eeeee[bbtttttttttttbb]eee	chr2:102621774-102621975(+)$1	201	115	140	21.3024
#eeeeeyyyyyyyyyyyyyyyyeee	chr4:148550625-148550826(-)$1	201	65	90	21.8349
ff"""bbtttttttttttbb333ff	chr6:71760520-71760721(+)$1	201	167	192	20.0925
eeeebbvvvvvvvvvvvvvbb]eee	chr12:99672769-99672970(-)$1	201	131	156	22.5259
gg!!ccctttttttttttccc22gg	chr15:80763847-80764048(+)$1	201	29	54	21.3376
##eeeeeuuuuuuuuuuuueeeeeb	chr2:33263737-33263938(-)$1	201	32	57	23.5265
eeeeyyyyyyyyyyyyyyyyeeeee	chr7:73317372-73317573(+)$1	201	160	185	21.1233
[ffffffuuuuuuuuuuuuffffff	chr1:172123560-172123761(-)$1	201	110	135	23.0057
hhhhhhhuuuuuuuuuuuuhhhhhh	chr11:7078335-7078536(+)$1	201	19	44	20.7666
!ffffffwwwwwwwwwwwwwwffff	chr10:107937284-107937485(-)$1	201	137	162	22.3704
"ccc[bbvvvvvvvvvvvvvbb]cc	chr5:68013051-68013252(-)$1	201	72	97	22.1151
hhhhhwwwwwwwwwwwwwwhhhhhh	chr7:110974999-110975200(-)$1	201	137	162	20.3190
$$$ddddwwwwwwwwwwwwwwdddd	chr13:24999535-24999736(-)$1	201	72	97	21.2001
ddeeeeeuuuuuuuuuuuueeeee:	chr6:124997803-124998004(+)$1	201	74	99	22.5302
eeeddddyyyyyyyyyyyyyyyydd	chr12:60059950-60060151(-)$1	201	99	124	19.8527
EEddddvvvvvvvvvvvvvddddff	chr13:43232300-43232501(+)$1	201	38	63	19.9597
[bbddddxxxxxxxxxxxxxxxddd	chr14:65871755-65871956(-)$1	201	130	155	17.8856
ggggggguuuuuuuuuuuugggggg	chrX:154260064-154260265(-)$1	201	3	28	23.2772
!ffffffxxxxxxxxxxxxxxxfff	chr9:75066129-75066330(+)$1	201	10	35	18.7368
ffffffwwwwwwwwwwwwwwfffff	chr4:61958516-61958717(+)$1	201	87	112	22.2543
!eeeeevvvvvvvvvvvvveeeee]	chr15:88901157-88901358(+)$1	201	152	177	23.7915
cc[dddduuuuuuuuuuuudddd33	chr18:34478807-34479008(+)$1	201	108	133	22.4823
hhfffffftttttttttttffffff	chr1:121555657-121555858(-)$1	201	65	90	20.1608
ggggggguuuuuuuuuuuugggggg	chr4:81940722-81940923(-)$1	201	160	185	23.2772
::eeeeevvvvvvvvvvvvveeeee	chr8:93576347-93576548(+)$1	201	159	184	21.3731
[ffffffxxxxxxxxxxxxxxxfff	chr10:112364596-112364797(-)$1	201	161	186	18.6868
ee[bbwwwwwwwwwwwwwwbb]eee	chr11:57873542-57873743(+)$1	201	146	171	21.7984
!cccxxxxxxxxxxxxxxxccc22c	chr11:109528870-109529071(+)$1	201	143	168	18.2172
#ffffffuuuuuuuuuuuuffffff	chr1:20927320-20927521(+)$1	201	136	161	22.9550
ddddcccwwwwwwwwwwwwwwccc]	chr16:94690241-94690442(+)$1	201	153	178	22.0647
iiii[bbxxxxxxxxxxxxxxxbb]	chr13:100193753-100193954(-)$1	201	62	87	17.9205
hhhhhhvvvvvvvvvvvvvhhhhhh	chr4:75587213-75587414(-)$1	201	35	60	20.5637
$eeeeewwwwwwwwwwwwwweeeee	chr1:166368246-166368447(-)$1	201	85	110	23.5749
gggddddwwwwwwwwwwwwwwdddd	chr9:15545938-15546139(+)$1	201	160	185	21.9721
#eeeeeyyyyyyyyyyyyyyyyeee	chr4:148550624-148550825(-)$1	201	64	89	21.8349
ee!!ccctttttttttttccceeee	chr1:194330836-194331037(+)$1	201	83	108	21.8569
beeeeevvvvvvvvvvvvveeeee]	chr10:72137458-72137659(+)$1	201	33	58	23.2036
ggg[cccwwwwwwwwwwwwwwccc]	chr9:32070989-32071190(+)$1	201	40	65	22.6807
gg"""bbvvvvvvvvvvvvvbb333	chrX:133371564-133371765(+)$1	201	143	168	21.6907
####ccctttttttttttcccdddd	chr10:107936045-107936246(-)$1	201	48	73	20.9627
[dddd[bbtttttttttttbbdddd	chr11:119400218-119400419(-)$1	201	51	76	20.4745
[ffffffuuuuuuuuuuuuffffff	chr1:172123558-172123759(-)$1	201	108	133	23.0057
ggggggguuuuuuuuuuuugggggg	chr7:118215720-118215921(-)$1	201	130	155	23.2772
eeeeeeeuuuuuuuuuuuueeeee:	chr7:118215630-118215831(-)$1	201	40	65	22.7748
$ccccccuuuuuuuuuuuuccc]cc	chr7:6659020-6659221(-)$1	201	38	63	23.3617
hhhhhwwwwwwwwwwwwwwhhhhhh	chr7:110974998-110975199(-)$1	201	136	161	20.3190

#otherMatches

#Seq PSSM
UCCGGCUAUCUUUGCUUUAAAGCUG	chr14:67487155-67487356(-)$1	201	90	115	21.3731
CUUUGUACUCUUCAACUUUUCAAAU	chr18:85049069-85049270(+)$1	201	66	91	18.7184
AUUUUUCUUUUAAAAAAAUAGUGUA	chr6:71760519-71760720(+)$1	201	167	192	20.4757
CCUGUGGAUCCCAACGAACCCACAU	chr6:124997802-124998003(+)$1	201	75	100	22.5302
AAAGAUACACAAACCUACUAGUCUU	chr1:166368304-166368505(-)$1	201	143	168	23.5749
UUGUCAAACUUUUACCUCCUGGCUG	chr5:104542378-104542579(-)$1	201	91	116	22.2572
CACACUGAUGGAUAAUAAAAGUGUG	chr17:45678883-45679084(-)$1	201	146	171	22.1075
AAAGAUACACAAACCUACUAGUCUU	chr1:166368228-166368429(-)$1	201	67	92	23.5749
ucCGUGGAUUCCUUAAAACCAGAGA	chr19:44380200-44380401(+)$1	201	156	181	20.7568
AUGAGCUGACCAAAGAGAUGGCCCA	chr9:58724981-58725182(-)$1	201	31	56	22.6200
AUAUCAAUAAAUACUAUUCUGAUAA	chr15:88901158-88901359(+)$1	201	151	176	23.7915
AAAGAUACACAAACCUACUAGUCUU	chr1:166368303-166368504(-)$1	201	142	167	23.5749
ACUUCCCAUCUCUCCCGCAGAAGUC	chr1:157694756-157694957(-)$1	201	119	144	22.3848
UAUAACUGUCUAAUUUUCUUACUUG	chr2:102621783-102621984(+)$1	201	106	131	21.3024
ugcgccaccacacccagcuUGGUGC	chr8:11448449-11448650(+)$1	201	61	86	21.8519
GUUACAGAAAAAUUCUUAACUGUAA	chr7:118215758-118215959(-)$1	201	168	193	23.2772
UAUAACUGUCUAAUUUUCUUACUUG	chr2:102621774-102621975(+)$1	201	115	140	21.3024
CAUGCUAUAACAGAAUCCAUGAAGC	chr4:148550625-148550826(-)$1	201	65	90	21.8349
UUUUUCUUUUAAAAAAAUAGUGUAA	chr6:71760520-71760721(+)$1	201	167	192	20.0925
CUCUGCCAAAAUGAACCAAGCAAGA	chr12:99672769-99672970(-)$1	201	131	156	22.5259
UCAAACUUUAAGCUUCCCAGUGGGA	chr15:80763847-80764048(+)$1	201	29	54	21.3376
UUGAGUUUUAAAUGAUCAUGAUUCC	chr2:33263737-33263938(-)$1	201	32	57	23.5265
UACCUGAUGAACAAAACUUUGGUAU	chr7:73317372-73317573(+)$1	201	160	185	21.1233
UUGAGUUUCAUUGUAAACUGACUCG	chr1:172123560-172123761(-)$1	201	110	135	23.0057
UGAAUAAUUUGUCCUAUUUUUAUUU	chr11:7078335-7078536(+)$1	201	19	44	20.7666
AAUGUAUUGUAUCACACCGUUGUAU	chr10:107937284-107937485(-)$1	201	137	162	22.3704
UUGCUACUAAAAUCUGUGAUGUUGC	chr5:68013051-68013252(-)$1	201	72	97	22.1151
GCAUUUAUUUCACUGCAAUGAUGUU	chr7:110974999-110975200(-)$1	201	137	162	20.3190
CCCCUGUGCAGCUACUUCAAAACAG	chr13:24999535-24999736(-)$1	201	72	97	21.2001
CCUGUGGAUCCCAACGAACCCACAU	chr6:124997803-124998004(+)$1	201	74	99	22.5302
CUUUUACCUUUUAAAGUUUACUUGU	chr12:60059950-60060151(-)$1	201	99	124	19.8527
AAAUGUGGUGGGGAUUUUAACAUGG	chr13:43232300-43232501(+)$1	201	38	63	19.9597
UCUUCUGAACCAUUAUGACCAACAG	chr14:65871755-65871956(-)$1	201	130	155	17.8856
UGUGGCUGCAUAAUAUACAAGUCAC	chrX:154260064-154260265(-)$1	201	3	28	23.2772
GCAUACAAAAUACAAUCCCAUAUGU	chr9:75066129-75066330(+)$1	201	10	35	18.7368
UGUUCUCACCUUUUUGCCUUGGAAC	chr4:61958516-61958717(+)$1	201	87	112	22.2543
AUAUCAAUAAAUACUAUUCUGAUAA	chr15:88901157-88901358(+)$1	201	152	177	23.7915
GUAGGUAGAAUUUUUGCUAUGCUGU	chr18:34478807-34479008(+)$1	201	108	133	22.4823
UAAUGAUGUAACUUAUAUUUAUCAU	chr1:121555657-121555858(-)$1	201	65	90	20.1608
AAAAAAGAAAUAAUGUAUGCuuuuu	chr4:81940722-81940923(-)$1	201	160	185	23.2772
UCAGGGGUUUUUAAACACAUCCUCU	chr8:93576347-93576548(+)$1	201	159	184	21.3731
CAUGUCUUGAAUUACAUACUGCGGA	chr10:112364596-112364797(-)$1	201	161	186	18.6868
UGUUGUCUUUCCAUCUUAUUACCAC	chr11:57873542-57873743(+)$1	201	146	171	21.7984
UCUUGUCUCUUUAUACUAAAAGUUG	chr11:109528870-109529071(+)$1	201	143	168	18.2172
GGGAAUGUCUAAACUCUUUUAUUUU	chr1:20927320-20927521(+)$1	201	136	161	22.9550
GUAUUAGAAACUAUUCAAAAACUAG	chr16:94690241-94690442(+)$1	201	153	178	22.0647
UCUCAACUUCUAUGUUGACCAUGUA	chr13:100193753-100193954(-)$1	201	62	87	17.9205
UUGGAUGCAUAGACUGAAAAUUCAA	chr4:75587213-75587414(-)$1	201	35	60	20.5637
AAAGAUACACAAACCUACUAGUCUU	chr1:166368246-166368447(-)$1	201	85	110	23.5749
UGCGACUCCUUUUUUUUUUUCAGUC	chr9:15545938-15546139(+)$1	201	160	185	21.9721
CAUGCUAUAACAGAAUCCAUGAAGC	chr4:148550624-148550825(-)$1	201	64	89	21.8349
AACCUCAAAAAAAAAAAAUGAUUGU	chr1:194330836-194331037(+)$1	201	83	108	21.8569
cacggcACUUAACAUUUCAGUUGUA	chr10:72137458-72137659(+)$1	201	33	58	23.2036
CCCACAUGUUUCUCUAAUUCUGUGG	chr9:32070989-32071190(+)$1	201	40	65	22.6807
AUCUUGAUUAGUUUCAUAUUUCCCA	chrX:133371564-133371765(+)$1	201	143	168	21.6907
AAAUGGCACUAUUAUGAAGCCACUA	chr10:107936045-107936246(-)$1	201	48	73	20.9627
CAUUGAGGAGAAACAAAAGCCCAAU	chr11:119400218-119400419(-)$1	201	51	76	20.4745
UUGAGUUUCAUUGUAAACUGACUCG	chr1:172123558-172123759(-)$1	201	108	133	23.0057
GUUACAGAAAAAUUCUUAACUGUAA	chr7:118215720-118215921(-)$1	201	130	155	23.2772
GUUACAGAAAAAUUCUUAACUGUAA	chr7:118215630-118215831(-)$1	201	40	65	22.7748
GGCUCUUACAUUGUAAAUAAGGAAG	chr7:6659020-6659221(-)$1	201	38	63	23.3617
GCAUUUAUUUCACUGCAAUGAUGUU	chr7:110974998-110975199(-)$1	201	136	161	20.3190

#DB
..(((((.............)))))	chr14:67487155-67487356(-)$1	1	90	115	21.3731
.((((...............)))).	chr18:85049069-85049270(+)$1	1	66	91	18.7184
(((...((...........))...)	chr6:71760519-71760720(+)$1	1	167	192	20.4757
))(((((............))))).	chr6:124997802-124998003(+)$1	1	75	100	22.5302
.(((((..............)))))	chr1:166368304-166368505(-)$1	1	143	168	23.5749
..((((.............)))).)	chr5:104542378-104542579(-)$1	1	91	116	22.2572
((((((.............))))))	chr17:45678883-45679084(-)$1	1	146	171	22.1075
.(((((..............)))))	chr1:166368228-166368429(-)$1	1	67	92	23.5749
((..(((...........)))..))	chr19:44380200-44380401(+)$1	1	156	181	20.7568
.((.(((............))).))	chr9:58724981-58725182(-)$1	1	31	56	22.6200
.(((((.............))))).	chr15:88901158-88901359(+)$1	1	151	176	23.7915
.(((((..............)))))	chr1:166368303-166368504(-)$1	1	142	167	23.5749
(((((..............))))))	chr1:157694756-157694957(-)$1	1	119	144	22.3848
(((((.((...........)).)))	chr2:102621783-102621984(+)$1	1	106	131	21.3024
.((((((............))))))	chr8:11448449-11448650(+)$1	1	61	86	21.8519
(((((((............))))))	chr7:118215758-118215959(-)$1	1	168	193	23.2772
(((((.((...........)).)))	chr2:102621774-102621975(+)$1	1	115	140	21.3024
.(((((................)))	chr4:148550625-148550826(-)$1	1	65	90	21.8349
((...((...........))...))	chr6:71760520-71760721(+)$1	1	167	192	20.0925
((((((.............)).)))	chr12:99672769-99672970(-)$1	1	131	156	22.5259
((..(((...........)))..))	chr15:80763847-80764048(+)$1	1	29	54	21.3376
..(((((............))))))	chr2:33263737-33263938(-)$1	1	32	57	23.5265
((((................)))))	chr7:73317372-73317573(+)$1	1	160	185	21.1233
.((((((............))))))	chr1:172123560-172123761(-)$1	1	110	135	23.0057
(((((((............))))))	chr11:7078335-7078536(+)$1	1	19	44	20.7666
.((((((..............))))	chr10:107937284-107937485(-)$1	1	137	162	22.3704
.(((.((.............)).))	chr5:68013051-68013252(-)$1	1	72	97	22.1151
(((((..............))))))	chr7:110974999-110975200(-)$1	1	137	162	20.3190
...((((..............))))	chr13:24999535-24999736(-)$1	1	72	97	21.2001
))(((((............))))).	chr6:124997803-124998004(+)$1	1	74	99	22.5302
(((((((................))	chr12:60059950-60060151(-)$1	1	99	124	19.8527
((((((.............))))((	chr13:43232300-43232501(+)$1	1	38	63	19.9597
.((((((...............)))	chr14:65871755-65871956(-)$1	1	130	155	17.8856
(((((((............))))))	chrX:154260064-154260265(-)$1	1	3	28	23.2772
.((((((...............)))	chr9:75066129-75066330(+)$1	1	10	35	18.7368
((((((..............)))))	chr4:61958516-61958717(+)$1	1	87	112	22.2543
.(((((.............))))).	chr15:88901157-88901358(+)$1	1	152	177	23.7915
((.((((............))))..	chr18:34478807-34479008(+)$1	1	108	133	22.4823
))((((((...........))))))	chr1:121555657-121555858(-)$1	1	65	90	20.1608
(((((((............))))))	chr4:81940722-81940923(-)$1	1	160	185	23.2772
..(((((.............)))))	chr8:93576347-93576548(+)$1	1	159	184	21.3731
.((((((...............)))	chr10:112364596-112364797(-)$1	1	161	186	18.6868
((.((..............)).)))	chr11:57873542-57873743(+)$1	1	146	171	21.7984
.(((...............)))..)	chr11:109528870-109529071(+)$1	1	143	168	18.2172
.((((((............))))))	chr1:20927320-20927521(+)$1	1	136	161	22.9550
(((((((..............))).	chr16:94690241-94690442(+)$1	1	153	178	22.0647
((((.((...............)).	chr13:100193753-100193954(-)$1	1	62	87	17.9205
((((((.............))))))	chr4:75587213-75587414(-)$1	1	35	60	20.5637
.(((((..............)))))	chr1:166368246-166368447(-)$1	1	85	110	23.5749
)))((((..............))))	chr9:15545938-15546139(+)$1	1	160	185	21.9721
.(((((................)))	chr4:148550624-148550825(-)$1	1	64	89	21.8349
((..(((...........)))))))	chr1:194330836-194331037(+)$1	1	83	108	21.8569
((((((.............))))).	chr10:72137458-72137659(+)$1	1	33	58	23.2036
(((.(((..............))).	chr9:32070989-32071190(+)$1	1	40	65	22.6807
((...((.............))...	chrX:133371564-133371765(+)$1	1	143	168	21.6907
....(((...........)))))))	chr10:107936045-107936246(-)$1	1	48	73	20.9627
.((((.((...........))))))	chr11:119400218-119400419(-)$1	1	51	76	20.4745
.((((((............))))))	chr1:172123558-172123759(-)$1	1	108	133	23.0057
(((((((............))))))	chr7:118215720-118215921(-)$1	1	130	155	23.2772
))(((((............))))).	chr7:118215630-118215831(-)$1	1	40	65	22.7748
.((((((............))).))	chr7:6659020-6659221(-)$1	1	38	63	23.3617
(((((..............))))))	chr7:110974998-110975199(-)$1	1	136	161	20.3190

#PSSM
g : 0.14	e : 0.12	! : 0.11	$ : 0.09	[ : 0.09	# : 0.08	h : 0.08	d : 0.06	: : 0.04	f : 0.04	i : 0.03	" : 0.01	E : 0.01	c : 0.01	b : 0.01	
e : 0.27	f : 0.16	g : 0.14	d : 0.09	h : 0.08	c : 0.06	: : 0.03	i : 0.03	b : 0.03	# : 0.03	! : 0.01	$ : 0.01	E : 0.01	
e : 0.32	f : 0.16	g : 0.11	d : 0.08	h : 0.06	! : 0.04	c : 0.04	i : 0.03	b : 0.03	" : 0.03	[ : 0.03	$ : 0.01	# : 0.01	
e : 0.30	d : 0.16	f : 0.16	g : 0.08	h : 0.06	" : 0.04	! : 0.04	c : 0.04	[ : 0.03	b : 0.01	i : 0.01	# : 0.01	
e : 0.27	f : 0.16	d : 0.14	c : 0.12	g : 0.08	h : 0.06	" : 0.04	b : 0.03	[ : 0.03	y : 0.01	x : 0.01	
e : 0.24	f : 0.16	c : 0.12	d : 0.11	b : 0.08	w : 0.06	g : 0.06	[ : 0.04	x : 0.03	h : 0.03	" : 0.01	y : 0.01	
w : 0.14	b : 0.12	v : 0.12	c : 0.12	f : 0.12	e : 0.09	d : 0.08	g : 0.06	y : 0.04	x : 0.03	h : 0.01	
u : 0.25	w : 0.22	v : 0.19	x : 0.09	t : 0.08	b : 0.06	y : 0.06	f : 0.01	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	t : 0.16	x : 0.09	y : 0.06	
u : 0.25	w : 0.22	v : 0.19	x : 0.09	t : 0.08	c : 0.06	y : 0.06	b : 0.01	
w : 0.16	b : 0.11	e : 0.11	c : 0.11	f : 0.09	x : 0.08	g : 0.08	v : 0.06	y : 0.06	h : 0.06	d : 0.04	
e : 0.22	b : 0.12	f : 0.11	c : 0.11	g : 0.08	w : 0.08	d : 0.06	h : 0.06	x : 0.06	y : 0.04	3 : 0.01	
e : 0.24	d : 0.12	f : 0.12	c : 0.08	g : 0.08	] : 0.06	h : 0.06	x : 0.06	y : 0.04	3 : 0.03	2 : 0.03	b : 0.03	
e : 0.33	f : 0.16	d : 0.14	g : 0.08	h : 0.06	3 : 0.04	2 : 0.04	] : 0.04	c : 0.03	y : 0.01	b : 0.01	
e : 0.33	f : 0.19	d : 0.12	g : 0.09	h : 0.06	c : 0.06	3 : 0.04	b : 0.03	] : 0.01	2 : 0.01	
e : 0.22	f : 0.19	d : 0.12	] : 0.11	g : 0.09	h : 0.06	: : 0.04	c : 0.04	b : 0.03	3 : 0.03	i : 0.01	

#score	1344.4720897303444
#seq	62
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_UTR_m3_run1.txt

#BEAR
:::ccc[a!!a[bbmmmmbb]a22a]cc	chr10:127707596-127707825(+)$1	229	129	157	11.4139
bbbb[bbdddd[bbmmmmbb]dddd]bb	chr10:5170564-5170800(+)$1	236	129	157	10.8498
ccc$$$$$ccc[bbmmmmbb]ccc22cc	chr7:140158214-140158434(+)$1	220	7	35	12.5862
[iiiiiiiii!!bbmmmmbb666666ii	chr1:36500308-36500543(-)$1	235	108	136	11.9653
b[cccccc####bbmmmmbb4444ccc]	chr17:28736375-28736609(-)$1	234	176	204	14.3843
!bb"""ccc[ddddmmmmdddd]ccc33	chr2:154718333-154718550(-)$1	217	101	129	9.9616
C==========ccclllccc333=====	chr7:149562935-149563158(-)$1	223	147	175	10.6080
==========[cccmmmmccc]======	chr19:6353877-6354087(+)$1	210	10	38	13.7082
cccffffff!!cccmmmmcccffffff]	chr12:87172823-87173033(+)$1	210	53	81	10.7546
dd$$$$$ccc!!bbmmmmbb]ccc333d	chr15:81688391-81688602(-)$1	211	116	144	13.3253
eeee"""gggggggmmmmggggggg333	chr16:29625551-29625777(+)$1	226	154	182	11.3995
iiii[bb####cccmmmmccc22bb]ii	chr16:18825009-18825236(+)$1	227	90	118	12.4785
eeee:ddddbb[bbmmmmbb333bb]dd	chr8:131209678-131209891(+)$1	213	88	116	11.4582
cccffffff"""bbmmmmbb]ffffff2	chrX:139268699-139268926(+)$1	227	192	220	12.3060
[a[ffffff"""bbmmmmbb4444ffff	chr3:29908612-29908839(-)$1	227	68	96	13.3377
bb[bb[a!!bb[bbmmmmbb]bb22a]b	chr5:151476389-151476621(+)$1	232	56	84	12.0637
dddd"""bb"""bbmmmmbb]bb]dddd	chr13:43398776-43398987(-)$1	211	77	105	12.8545
a[iiiiiiiii[bbmmmmbb]iiiiiii	chr2:58299304-58299540(-)$1	236	182	210	14.1028
::==========[ammmma]========	chrX:105985057-105985275(-)$1	218	31	59	11.0610
==========[ccclllccc]=======	chr19:32588735-32588966(+)$1	231	149	177	11.2383
cbb[ddddbb[cccmmmmccc]bb4444	chrX:148298330-148298555(+)$1	225	107	135	11.0160
ffff!!bb!!a!!ammmma22a22bb22	chr2:167469444-167469658(-)$1	214	70	98	10.3137
:ccc[ccc"""cccmmmmccc333ccc]	chr6:32999275-32999514(-)$1	239	156	184	12.7883
cc!!dddd####bbmmmmbb4444dddd	chrX:98742268-98742487(+)$1	219	45	73	13.6391
ddd[ccc[bb[cccmmmmccc]bb22cc	chr2:152673722-152673931(+)$1	209	47	75	11.1664
eeeee[dddd!!bbmmmmbb]dddd]ee	chr8:4327709-4327943(+)$1	234	125	153	12.4304
eeeee[bb[bb[bbmmmmbb]bb]bb]e	chr6:24614778-24615003(-)$1	225	39	67	11.8663
ee::==========mmmm==========	chr2:157903443-157903663(+)$1	220	68	96	10.8706
=========bb[bbmmmmbb]bb]====	chr2:61549811-61550020(+)$1	209	167	195	14.0194
=====[dddd[cccmmmmccc22dddd]	chr1:169238802-169239051(+)$1	249	39	67	11.9269
####eeeeecccbbmmmmbb]ccc>>>>	chr16:57156231-57156443(+)$1	212	92	120	11.6909
"dddda[bb[cccammmma]cccbb]a]	chr5:8063631-8063847(+)$1	216	58	86	10.3051
d[ccc!!dddd[bbmmmmbbdddd]ccc	chr2:27390472-27390690(+)$1	218	158	186	11.8008
===[bb####bbbbmmmmbb]bb4444b	chr4:40633618-40633837(-)$1	219	145	173	12.8280
cdddd[dddd[cccmmmmccc22dddd2	chr11:96667841-96668072(+)$1	231	105	133	10.7464
:=============mmmm==========	chr10:58799709-58799926(+)$1	217	6	34	12.4160
h####iiiiiiiiimmmmiiiiiiiii6	chr13:77240180-77240408(-)$1	228	45	73	11.1397
ooooobbccc[cccmmmmccc333ccce	chr17:45570288-45570507(-)$1	219	120	148	11.2586
d"""dddd[a[cccmmmmcccadddddd	chr7:119254174-119254382(+)$1	208	148	176	11.0927
ffffff$$$$$cccmmmmccc333ffff	chr1:78474681-78474913(-)$1	232	140	168	11.2340
b[a[cccdddd[bbmmmmbb22dddd]c	chr17:56558240-56558498(-)$1	258	78	106	12.1315
eeeeggggggg[bbmmmmbb]ggggggg	chrX:71484351-71484573(-)$1	222	95	123	12.9575
d"""cccccc[cccmmmmccc22ccc]c	chr11:84214307-84214535(+)$1	228	133	161	12.4027
dd"""ccc"""cccmmmmccc]ccc]dd	chrX:98736103-98736324(+)$1	221	117	145	12.8569
eeee"""dddd[bbmmmmbb]dddd]ee	chr1:34224411-34224634(+)$1	223	127	155	12.4576
eeeee"""ccc[bbmmmmbbccc]eeee	chr16:91672298-91672513(+)$1	215	137	165	12.6218
eeee[ccc"""cccmmmmccc22ccc]e	chr9:83003863-83004096(-)$1	233	180	208	12.7449
b!!bb[ccc!!cccmmmmccc333ccc]	chr8:13369361-13369590(+)$1	229	121	149	13.0394
===========[bbmmmmbb]=======	chr13:76325004-76325223(+)$1	219	18	46	15.1736
========####bbmmmmbb>>>>>>>>	chr5:25004247-25004471(-)$1	224	178	206	13.4168
cc:dddd[ccc[bbmmmmbb]ccc]ddd	chr1:177811201-177811426(+)$1	225	58	86	11.4496
!!dddd!!bb!!bbmmmmbb]bb333dd	chr11:105945813-105946027(+)$1	214	110	138	13.1657
eeee####a!!cccmmmmccc22a22ee	chr2:59052708-59052921(+)$1	213	95	123	12.4426
bbffffff####bbmmmmbb22ffffff	chr3:87516895-87517103(+)$1	208	43	71	12.1069
eeeeebb!!cccbbmmmmbb]ccc22bb	chr17:24612635-24612842(-)$1	207	105	133	12.0562
:eeeeeagggggggmmmmggggggg]a]	chr19:6341380-6341603(+)$1	223	189	217	9.7031
[a[ffffffa[cccmmmmccc]a]ffff	chr5:148537185-148537418(-)$1	233	46	74	11.2280

#otherMatches

#Seq PSSM
GAAGUUGCAGCGAGAGCACUGGAAGGAG	chr10:127707596-127707825(+)$1	229	129	157	11.4139
CUGGUGGCCGAGUCUCAGGAGUCGGACC	chr10:5170564-5170800(+)$1	236	129	157	10.8498
GCAUACAAGUCAUCGGGAGGAGACAUUG	chr7:140158214-140158434(+)$1	220	7	35	12.5862
UUCGCUAUGGAACCUGAUGGGCAACGCC	chr1:36500308-36500543(-)$1	235	108	136	11.9653
GAGCCCUGGACAGCAAAGGUACCACAGC	chr17:28736375-28736609(-)$1	234	176	204	14.3843
ACUACAGCCAUGUCCGGGGACGAGGUGA	chr2:154718333-154718550(-)$1	217	101	129	9.9616
ACAUCUCUUCUGGUGGGGCCUGUGGAAG	chr7:149562935-149563158(-)$1	223	147	175	10.6080
GGUAGAGGAGUUGAGCCCUCACCUUCUC	chr19:6353877-6354087(+)$1	210	10	38	13.7082
GCAGGAGAAUUCCAGUUUUGGUUUUCCA	chr12:87172823-87173033(+)$1	210	53	81	10.7546
CCCUCUCUACCCUCAAACGACGUAAAAG	chr15:81688391-81688602(-)$1	211	116	144	13.3253
UAUCAAAgaguuggugauuuggcuuaga	chr16:29625551-29625777(+)$1	226	154	182	11.3995
UGGAGACCAAACCUGACAAGGCUGUAUC	chr16:18825009-18825236(+)$1	227	90	118	12.4785
GCCGAGGUCCGCCGACACCGACCCGAGA	chr8:131209678-131209891(+)$1	213	88	116	11.4582
UCUGCUGGAUUUGCUCCGGCUUCCAGCC	chrX:139268699-139268926(+)$1	227	192	220	12.3060
CCAGAUGUAGGAAGCUGGCUCAAGUACA	chr3:29908612-29908839(-)$1	227	68	96	13.3377
cggcggcggcggcggcggcggcgagggc	chr5:151476389-151476621(+)$1	232	56	84	12.0637
CUGGAGAUCCCGGCAGCAGCAGAACCGG	chr13:43398776-43398987(-)$1	211	77	105	12.8545
UGCUGAUGUUUACAAGGAUGCGAACAUU	chr2:58299304-58299540(-)$1	236	182	210	14.1028
UUUCAAAUUAUUGCUUCAGGAAUAAUUU	chrX:105985057-105985275(-)$1	218	31	59	11.0610
GGGUGGUUGUGUUUGCAGGAGGUAGCca	chr19:32588735-32588966(+)$1	231	149	177	11.2383
GAGUGCUGUUGAUGAGCUCAUGAGACAC	chrX:148298330-148298555(+)$1	225	107	135	11.0160
CAUGAAAUGGGCACAGAAGAUCAAGUAG	chr2:167469444-167469658(-)$1	214	70	98	10.3137
UCCAGCGUUUAUGGUGCUUCAGGUAUGG	chr6:32999275-32999514(-)$1	239	156	184	12.7883
GGAUGAUGAUAAACCUUGGUACUCCAUU	chrX:98742268-98742487(+)$1	219	45	73	13.6391
GUUGAGUCCUGACGCGGUCGUGAGUCGC	chr2:152673722-152673931(+)$1	209	47	75	11.1664
GCAGAAGGAAAAUCAAGUGGGUUCCAUC	chr8:4327709-4327943(+)$1	234	125	153	12.4304
GCGgcugccgccgccgccgcugccgccg	chr6:24614778-24615003(-)$1	225	39	67	11.8663
GACUGAGUACUCUGGAGACAGGGUGCUC	chr2:157903443-157903663(+)$1	220	68	96	10.8706
GAGGCGGGCCUGGGACGUCCGGGAGCCU	chr2:61549811-61550020(+)$1	209	167	195	14.0194
GGGUCGGCGCCCCGGAAGCGGAAGUGUA	chr1:169238802-169239051(+)$1	249	39	67	11.9269
UAUAAAGAAACUCCUGGUGGCAGUACAG	chr16:57156231-57156443(+)$1	212	92	120	11.6909
AGCGGGAAGAUCACGUUUGAUGACUACA	chr5:8063631-8063847(+)$1	216	58	86	10.3051
GUGAGUUCAGCUCCUCAUGGGUUGUUUU	chr2:27390472-27390690(+)$1	218	158	186	11.8008
GUGAGCUCUUGAAGCUGCCUCUCCGUUG	chr4:40633618-40633837(-)$1	219	145	173	12.8280
CUGACCUGGUCCCUGCCAAGGAAGCCAA	chr11:96667841-96668072(+)$1	231	105	133	10.7464
GUUAUGAAUUAGUUGUUAAAUUGAUUUG	chr10:58799709-58799926(+)$1	217	6	34	12.4160
AUUAAAUACUGUUUUUUAGAGCAGUAUG	chr13:77240180-77240408(-)$1	228	45	73	11.1397
AAGAUGCCCCGGAUUAUGAUCAAAGGGG	chr17:45570288-45570507(-)$1	219	120	148	11.2586
GCCGGCCGGCAUGUAAAUACAGCGGUCC	chr7:119254174-119254382(+)$1	208	148	176	11.0927
GAAGAGGUAAUGAGUAGGCUCUGACUCU	chr1:78474681-78474913(-)$1	232	140	168	11.2340
UGAGACCUUUGGGGACUUCUGGCGGAUG	chr17:56558240-56558498(-)$1	258	78	106	12.1315
UUUCUUGGGGAGGUGUCAGCAUCCCCAA	chrX:71484351-71484573(-)$1	222	95	123	12.9575
UACCUGCCACAGAAACCAUUCAAGUGAG	chr11:84214307-84214535(+)$1	228	133	161	12.4027
GCACAGUCAGAAUCUAAGGAUGGACAGC	chrX:98736103-98736324(+)$1	221	117	145	12.8569
UAGUCAAUGAAAUCGACAGAAUUCGAGC	chr1:34224411-34224634(+)$1	223	127	155	12.4576
CACCAUUUAGGUCCUGGUGGCCUCUGGU	chr16:91672298-91672513(+)$1	215	137	165	12.6218
UGCUAAUUUUUUAGGACUCUAUUAGUCA	chr9:83003863-83004096(-)$1	233	180	208	12.7449
GCAGCAUCCAACACUAUUGUGGUAGGAA	chr8:13369361-13369590(+)$1	229	121	149	13.0394
CCAACGUCUGUAUGAUUUCACACAGGUG	chr13:76325004-76325223(+)$1	219	18	46	15.1736
GCCCCGAGCCCCGCAGCCGCAGACAAAA	chr5:25004247-25004471(-)$1	224	178	206	13.4168
CAGGUUUGAGGAGCCACGGCGCCUGGAA	chr1:177811201-177811426(+)$1	225	58	86	11.4496
GGAGAACAGUGGCCGGUCGGAGCGUCUU	chr11:105945813-105946027(+)$1	214	110	138	13.1657
UCUCCACUGGCCCAGGCAUGGAACCCGA	chr2:59052708-59052921(+)$1	213	95	123	12.4426
GCCUGCGAAACAGUGAGGACCCUCGCAG	chr3:87516895-87517103(+)$1	208	43	71	12.1069
GGUAUAGUGACGCCAAGAGGAUGUAUCU	chr17:24612635-24612842(-)$1	207	105	133	12.0562
CGGGGGCAGAGAGUUAACAUUUUCUAGA	chr19:6341380-6341603(+)$1	223	189	217	9.7031
CGGCUGCGCCGUCGGCCUCGGAGAGCGC	chr5:148537185-148537418(-)$1	233	46	74	11.2280

#DB
...(((.(..(.((....)).)..).))	chr10:127707596-127707825(+)$1	1	129	157	11.4139
))((.((((((.((....)).)))).))	chr10:5170564-5170800(+)$1	1	129	157	10.8498
(((.....(((.((....)).)))..))	chr7:140158214-140158434(+)$1	1	7	35	12.5862
.(((((((((..((....))......))	chr1:36500308-36500543(-)$1	1	108	136	11.9653
(.((((((....((....))....))).	chr17:28736375-28736609(-)$1	1	176	204	14.3843
.((...(((.((((....)))).)))..	chr2:154718333-154718550(-)$1	1	101	129	9.9616
((((((((((((((...)))...)))))	chr7:149562935-149563158(-)$1	1	147	175	10.6080
((((((((((.(((....))).))))))	chr19:6353877-6354087(+)$1	1	10	38	13.7082
(((((((((..(((....))))))))).	chr12:87172823-87173033(+)$1	1	53	81	10.7546
((.....(((..((....)).)))...)	chr15:81688391-81688602(-)$1	1	116	144	13.3253
((((...(((((((....)))))))...	chr16:29625551-29625777(+)$1	1	154	182	11.3995
((((.((....(((....)))..)).))	chr16:18825009-18825236(+)$1	1	90	118	12.4785
)))).((((((.((....))...)).))	chr8:131209678-131209891(+)$1	1	88	116	11.4582
(((((((((...((....)).)))))).	chrX:139268699-139268926(+)$1	1	192	220	12.3060
.(.((((((...((....))....))))	chr3:29908612-29908839(-)$1	1	68	96	13.3377
((.((.(..((.((....)).))..).)	chr5:151476389-151476621(+)$1	1	56	84	12.0637
((((...((...((....)).)).))))	chr13:43398776-43398987(-)$1	1	77	105	12.8545
(.(((((((((.((....)).)))))))	chr2:58299304-58299540(-)$1	1	182	210	14.1028
..((((((((((.(....).))))))))	chrX:105985057-105985275(-)$1	1	31	59	11.0610
((((((((((.(((...))).)))))))	chr19:32588735-32588966(+)$1	1	149	177	11.2383
(((.((((((.(((....))).))....	chrX:148298330-148298555(+)$1	1	107	135	11.0160
((((..((..(..(....)..)..))..	chr2:167469444-167469658(-)$1	1	70	98	10.3137
.(((.(((...(((....)))...))).	chr6:32999275-32999514(-)$1	1	156	184	12.7883
((..((((....((....))....))))	chrX:98742268-98742487(+)$1	1	45	73	13.6391
(((.(((.((.(((....))).))..))	chr2:152673722-152673931(+)$1	1	47	75	11.1664
(((((.((((..((....)).)))).))	chr8:4327709-4327943(+)$1	1	125	153	12.4304
(((((.((.((.((....)).)).)).)	chr6:24614778-24615003(-)$1	1	39	67	11.8663
))..((((((((((....))))))))))	chr2:157903443-157903663(+)$1	1	68	96	10.8706
(((((((((((.((....)).)).))))	chr2:61549811-61550020(+)$1	1	167	195	14.0194
(((((.((((.(((....)))..)))).	chr1:169238802-169239051(+)$1	1	39	67	11.9269
....((((((((((....)).)))....	chr16:57156231-57156443(+)$1	1	92	120	11.6909
.(((((.((.((((....).))))).).	chr5:8063631-8063847(+)$1	1	58	86	10.3051
(.(((..((((.((....)))))).)))	chr2:27390472-27390690(+)$1	1	158	186	11.8008
(((.((....((((....)).))....)	chr4:40633618-40633837(-)$1	1	145	173	12.8280
(((((.((((.(((....)))..)))).	chr11:96667841-96668072(+)$1	1	105	133	10.7464
.(((((((((((((....))))))))))	chr10:58799709-58799926(+)$1	1	6	34	12.4160
(....(((((((((....))))))))).	chr13:77240180-77240408(-)$1	1	45	73	11.1397
.....))(((.(((....)))...)))(	chr17:45570288-45570507(-)$1	1	120	148	11.2586
(...((((.(.(((....))))))))))	chr7:119254174-119254382(+)$1	1	148	176	11.0927
((((((.....(((....)))...))))	chr1:78474681-78474913(-)$1	1	140	168	11.2340
(.(.(((((((.((....))..)))).)	chr17:56558240-56558498(-)$1	1	78	106	12.1315
))))(((((((.((....)).)))))))	chrX:71484351-71484573(-)$1	1	95	123	12.9575
(...((((((.(((....)))..))).)	chr11:84214307-84214535(+)$1	1	133	161	12.4027
((...(((...(((....))).))).))	chrX:98736103-98736324(+)$1	1	117	145	12.8569
((((...((((.((....)).)))).))	chr1:34224411-34224634(+)$1	1	127	155	12.4576
(((((...(((.((....))))).))))	chr16:91672298-91672513(+)$1	1	137	165	12.6218
((((.(((...(((....)))..))).)	chr9:83003863-83004096(-)$1	1	180	208	12.7449
(..((.(((..(((....)))...))).	chr8:13369361-13369590(+)$1	1	121	149	13.0394
(((((((((((.((....)).)))))))	chr13:76325004-76325223(+)$1	1	18	46	15.1736
((((((((....((....))........	chr5:25004247-25004471(-)$1	1	178	206	13.4168
)).((((.(((.((....)).))).)))	chr1:177811201-177811426(+)$1	1	58	86	11.4496
..((((..((..((....)).))...))	chr11:105945813-105946027(+)$1	1	110	138	13.1657
((((....(..(((....)))..)..))	chr2:59052708-59052921(+)$1	1	95	123	12.4426
((((((((....((....))..))))))	chr3:87516895-87517103(+)$1	1	43	71	12.1069
(((((((..(((((....)).)))..))	chr17:24612635-24612842(-)$1	1	105	133	12.0562
.(((((((((((((....))))))).).	chr19:6341380-6341603(+)$1	1	189	217	9.7031
.(.(((((((.(((....))).).))))	chr5:148537185-148537418(-)$1	1	46	74	11.2280

#PSSM
e : 0.19	c : 0.12	= : 0.12	d : 0.12	b : 0.10	: : 0.08	[ : 0.05	! : 0.03	f : 0.03	C : 0.01	i : 0.01	a : 0.01	# : 0.01	" : 0.01	h : 0.01	o : 0.01	
e : 0.21	= : 0.15	c : 0.10	d : 0.10	b : 0.08	[ : 0.07	: : 0.03	i : 0.03	a : 0.03	f : 0.03	# : 0.03	" : 0.03	! : 0.03	o : 0.01	
e : 0.19	= : 0.17	c : 0.10	d : 0.08	: : 0.05	b : 0.05	i : 0.05	[ : 0.05	f : 0.05	" : 0.05	! : 0.03	# : 0.03	$ : 0.01	o : 0.01	a : 0.01	
e : 0.19	= : 0.15	f : 0.12	d : 0.08	c : 0.07	" : 0.07	[ : 0.07	b : 0.05	i : 0.05	$ : 0.03	# : 0.03	! : 0.01	: : 0.01	o : 0.01	
= : 0.17	d : 0.12	c : 0.10	f : 0.10	e : 0.10	" : 0.08	[ : 0.07	b : 0.05	$ : 0.03	i : 0.03	# : 0.03	: : 0.01	! : 0.01	o : 0.01	g : 0.01	
= : 0.15	c : 0.14	f : 0.10	d : 0.10	[ : 0.10	b : 0.08	" : 0.08	i : 0.05	$ : 0.03	! : 0.03	e : 0.03	a : 0.01	g : 0.01	# : 0.01	
c : 0.15	= : 0.15	d : 0.14	b : 0.10	f : 0.08	" : 0.07	$ : 0.05	i : 0.05	[ : 0.03	a : 0.03	! : 0.03	# : 0.03	e : 0.01	g : 0.01	
d : 0.19	c : 0.15	= : 0.15	f : 0.08	b : 0.07	i : 0.05	g : 0.05	# : 0.05	! : 0.05	$ : 0.03	[ : 0.03	a : 0.01	e : 0.01	" : 0.01	
d : 0.14	c : 0.14	= : 0.14	# : 0.10	b : 0.08	! : 0.07	f : 0.07	i : 0.05	g : 0.05	" : 0.05	[ : 0.03	e : 0.01	$ : 0.01	a : 0.01	
c : 0.14	d : 0.12	= : 0.12	b : 0.12	# : 0.10	" : 0.10	! : 0.08	i : 0.05	g : 0.05	[ : 0.03	a : 0.03	$ : 0.01	
[ : 0.17	! : 0.12	c : 0.10	" : 0.10	d : 0.08	# : 0.08	= : 0.08	b : 0.08	g : 0.05	a : 0.03	i : 0.03	$ : 0.01	
c : 0.38	[ : 0.26	! : 0.08	# : 0.07	" : 0.05	= : 0.05	g : 0.03	d : 0.01	b : 0.01	i : 0.01	
b : 0.50	c : 0.35	g : 0.03	= : 0.03	d : 0.01	[ : 0.01	! : 0.01	i : 0.01	
b : 0.50	c : 0.33	a : 0.05	g : 0.03	= : 0.03	d : 0.01	i : 0.01	
m : 0.96	l : 0.03	
m : 0.96	l : 0.03	
m : 0.96	l : 0.03	
m : 0.96	c : 0.03	
b : 0.50	c : 0.33	a : 0.05	g : 0.03	= : 0.03	d : 0.01	i : 0.01	
b : 0.50	c : 0.33	g : 0.03	] : 0.03	= : 0.03	d : 0.01	2 : 0.01	i : 0.01	
] : 0.35	c : 0.33	4 : 0.05	= : 0.05	2 : 0.05	d : 0.03	3 : 0.03	g : 0.03	6 : 0.01	i : 0.01	> : 0.01	
2 : 0.14	c : 0.12	3 : 0.10	b : 0.10	d : 0.08	] : 0.08	= : 0.08	a : 0.05	4 : 0.05	g : 0.05	f : 0.03	i : 0.03	6 : 0.01	> : 0.01	
2 : 0.14	c : 0.14	b : 0.14	d : 0.10	3 : 0.10	= : 0.10	4 : 0.05	f : 0.05	g : 0.05	i : 0.03	6 : 0.01	] : 0.01	> : 0.01	a : 0.01	
c : 0.15	d : 0.14	= : 0.12	b : 0.08	] : 0.08	3 : 0.08	4 : 0.07	2 : 0.05	f : 0.05	g : 0.05	i : 0.03	6 : 0.01	> : 0.01	a : 0.01	
d : 0.15	c : 0.14	= : 0.14	f : 0.10	2 : 0.08	b : 0.08	g : 0.05	3 : 0.03	i : 0.03	4 : 0.03	> : 0.03	] : 0.03	a : 0.01	6 : 0.01	e : 0.01	
] : 0.15	c : 0.14	= : 0.14	d : 0.12	f : 0.10	2 : 0.07	3 : 0.05	i : 0.03	4 : 0.03	b : 0.03	> : 0.03	6 : 0.01	a : 0.01	g : 0.01	e : 0.01	
d : 0.15	c : 0.14	= : 0.14	f : 0.10	] : 0.08	i : 0.07	e : 0.07	3 : 0.05	b : 0.03	4 : 0.03	> : 0.03	a : 0.03	2 : 0.01	g : 0.01	
= : 0.14	d : 0.14	] : 0.12	e : 0.12	c : 0.10	b : 0.07	f : 0.07	i : 0.05	2 : 0.05	3 : 0.03	> : 0.03	4 : 0.01	6 : 0.01	g : 0.01	

#score	688.3639390145522
#seq	57
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_UTR_m1_run1.txt

#BEAR
ccyyyyyyyyyyyyyyyyccc]fff	chr7:30811020-30811240(+)$1	220	135	160	20.9575
gggggvvvvvvvvvvvvvggggggg	chrX:130425520-130425755(-)$1	235	89	114	23.4631
c[dddduuuuuuuuuuuudddd]cc	chr9:53381163-53381386(-)$1	223	48	73	23.6666
bbcccvvvvvvvvvvvvvccc]bb]	chr19:46669193-46669415(-)$1	222	161	186	23.2944
:cccccctttttttttttccc]ccc	chr8:73292129-73292351(-)$1	222	60	85	22.7063
eeecccuuuuuuuuuuuuccc22ee	chr6:56051171-56051394(+)$1	223	15	40	23.9574
cc[cccuuuuuuuuuuuucccccc:	chr9:75531492-75531724(-)$1	232	15	40	23.7180
iiiiiiuuuuuuuuuuuuiiiiiii	chr15:76546822-76547041(-)$1	219	24	49	23.8601
ffffffuuuuuuuuuuuuffffff4	chr4:148939302-148939521(+)$1	219	74	99	22.9943
:eeeeeuuuuuuuuuuuueeeee::	chr2:143768409-143768635(+)$1	226	8	33	20.8501
d[dddduuuuuuuuuuuudddd]dd	chr10:21412591-21412810(-)$1	219	157	182	23.1986
f[ddddtttttttttttddddffff	chr19:10059329-10059571(+)$1	242	214	239	21.9817
iiiiiiuuuuuuuuuuuuiiiiiii	chr15:7146589-7146812(+)$1	223	181	206	23.8601
ccddddtttttttttttdddd]ccc	chr12:33660775-33660997(+)$1	222	54	79	22.3179
bb[bbwwwwwwwwwwwwwwbb]bbe	chr5:116859011-116859231(+)$1	220	163	188	21.0611
:ddddvvvvvvvvvvvvvddddGGG	chr11:75833443-75833666(-)$1	223	133	158	20.6288
bbeeeeettttttttttteeeee]b	chr2:75513693-75513909(+)$1	216	56	81	21.6333
!cccwwwwwwwwwwwwwwccc22dd	chr4:117605008-117605227(-)$1	219	181	206	21.9169
bb[cccvvvvvvvvvvvvvcccbb:	chr9:69605427-69605648(-)$1	221	67	92	22.3422
gggcccuuuuuuuuuuuuccc]ggg	chr8:72411585-72411807(-)$1	222	125	150	24.8096
hddddvvvvvvvvvvvvvdddd]hh	chr4:116359819-116360035(-)$1	216	102	127	22.2920
gggggggtttttttttttggggggg	chr2:181319295-181319520(-)$1	225	3	28	22.5897
:eeeeevvvvvvvvvvvvveeeee:	chr8:74152054-74152297(-)$1	243	2	27	21.2233
[eeeeevvvvvvvvvvvvveeeeeb	chr1:168236956-168237177(+)$1	221	33	58	22.6344
""ddddtttttttttttdddd333f	chr4:120731783-120732020(-)$1	237	145	170	22.2187
ee[cccuuuuuuuuuuuuccc]eee	chr17:32491327-32491562(-)$1	235	40	65	24.4817
ddddwwwwwwwwwwwwwwdddd]ff	chr15:89294025-89294242(+)$1	217	25	50	21.4025
bbdddduuuuuuuuuuuudddd22b	chr11:106147762-106147981(+)$1	219	115	140	22.6308
ff!!ccctttttttttttccc]fff	chr7:134335357-134335578(+)$1	221	50	75	23.4343
[cccwwwwwwwwwwwwwwccc]ccc	chr7:53450655-53450874(+)$1	219	74	99	22.5609
e!!bbwwwwwwwwwwwwwwbb22ee	chr2:84978650-84978872(+)$1	222	6	31	21.2335
ff[bbvvvvvvvvvvvvvbbfffff	chr17:35032247-35032474(+)$1	227	53	78	22.3015
gggggvvvvvvvvvvvvvggggggg	chr19:6400730-6400952(+)$1	222	112	137	23.4631
eee[ccctttttttttttccc]eee	chr17:3151241-3151467(+)$1	226	102	127	23.1374
""eeeeettttttttttteeeeebb	chr14:35340734-35340952(+)$1	218	71	96	21.7474
ffffffuuuuuuuuuuuuffffff]	chr4:21788011-21788231(-)$1	220	113	138	23.0490
dd[cccuuuuuuuuuuuuccc]ddd	chr4:129380986-129381217(-)$1	231	62	87	24.0427
ee[cccuuuuuuuuuuuuccceeee	chr19:40625431-40625653(-)$1	222	187	212	24.1965
!fffffftttttttttttffffff4	chr19:5134512-5134736(-)$1	224	138	163	21.8737
gggggvvvvvvvvvvvvvggggggg	chr6:121329472-121329695(-)$1	223	172	197	23.4631
fffcccyyyyyyyyyyyyyyyyccc	chr13:9685514-9685747(-)$1	233	136	161	21.0282
ffffffwwwwwwwwwwwwwwfffff	chr12:29122637-29122852(+)$1	215	90	115	21.4172
d"""ccctttttttttttccc6666	chr19:24753797-24754015(-)$1	218	143	168	21.1672
ffffffvvvvvvvvvvvvvffffff	chr7:31092392-31092623(+)$1	231	85	110	22.4939
gggggvvvvvvvvvvvvvggggggg	chr9:44754250-44754470(-)$1	220	45	70	23.4631
!!ddddyyyyyyyyyyyyyyyyddd	chr4:118933630-118933854(-)$1	224	50	75	20.4672
eeeeewwwwwwwwwwwwwweeeee5	chr17:15082542-15082772(+)$1	230	193	218	21.1654
bb[cccuuuuuuuuuuuuccc]bb:	chr6:64617400-64617650(+)$1	250	155	180	23.3754
d[ddddyyyyyyyyyyyyyyyyddd	chr11:44818733-44818963(+)$1	230	61	86	20.3021
======uuuuuuuuuuuu=======	chr3:40598814-40599038(+)$1	224	55	80	24.1821
c[dddduuuuuuuuuuuudddd]cc	chr5:124570087-124570308(+)$1	221	22	47	23.6666
:eeeeevvvvvvvvvvvvveeeee:	chr12:42178653-42178884(-)$1	231	9	34	21.2233
gggggggtttttttttttggggggg	chr2:113836170-113836397(-)$1	227	51	76	22.5897
bb!!bbuuuuuuuuuuuubb22bb]	chr17:9200978-9201199(-)$1	221	56	81	22.0555
gggggggtttttttttttggggggg	chr16:46447976-46448215(-)$1	239	80	105	22.5897
iiiiiyyyyyyyyyyyyyyyyiiii	chr10:7625809-7626024(-)$1	215	143	168	21.3901
:eeeeeuuuuuuuuuuuueeeee::	chr2:69672510-69672734(+)$1	224	92	117	20.8501
+++cccuuuuuuuuuuuuccc7777	chr14:72938354-72938574(+)$1	220	42	67	20.2594
ccddddtttttttttttdddd333c	chr11:69470559-69470785(-)$1	226	21	46	22.3360
ffffffwwwwwwwwwwwwwwfffff	chr11:90138768-90139003(+)$1	235	200	225	21.4172
hh[cccuuuuuuuuuuuuccc]hhh	chr11:87040424-87040644(-)$1	220	125	150	23.8506
ee[cccyyyyyyyyyyyyyyyyccc	chr10:79597819-79598059(-)$1	240	153	178	21.2483

#otherMatches

#Seq PSSM
GCAUCUAAAGUCACGUCGGUUAGUU	chr7:30811020-30811240(+)$1	220	135	160	20.9575
UGUAUCCUUGAUUAAUAAAUAUAAA	chrX:130425520-130425755(-)$1	235	89	114	23.4631
AGUAUAAAACUUCAGAAAUAUAGUU	chr9:53381163-53381386(-)$1	223	48	73	23.6666
CCCUUAUUAAAGUAGACAAAGAGGA	chr19:46669193-46669415(-)$1	222	161	186	23.2944
UGCCGAGAAUCUUCCCCACUCUGGC	chr8:73292129-73292351(-)$1	222	60	85	22.7063
GUAACAGAAAAAAAAAAAUGUCCUA	chr6:56051171-56051394(+)$1	223	15	40	23.9574
GCAUCCUCCUUCCAGCCCGGAGCAA	chr9:75531492-75531724(-)$1	232	15	40	23.7180
UCUUCUAACUUGUCAUCAGGGGGAG	chr15:76546822-76547041(-)$1	219	24	49	23.8601
GGCAGCUCCAGCCUCUCUGCUGCCC	chr4:148939302-148939521(+)$1	219	74	99	22.9943
UGUGUACAACACCUAAUAUACACUA	chr2:143768409-143768635(+)$1	226	8	33	20.8501
CUCCAGGAAACCCAAACACUGGUGA	chr10:21412591-21412810(-)$1	219	157	182	23.1986
AAUUUGUACCAUUUCUUCAAAUAAA	chr19:10059329-10059571(+)$1	242	214	239	21.9817
UUUACAAGACACACAUACUGUGAAC	chr15:7146589-7146812(+)$1	223	181	206	23.8601
AACAAUAAUUUAACUAAGUUGCUUC	chr12:33660775-33660997(+)$1	222	54	79	22.3179
GGAGAAAUCUAUUACUACAUCAUCC	chr5:116859011-116859231(+)$1	220	163	188	21.0611
CCAAGCUCCUCAGUAAAACUUGGCU	chr11:75833443-75833666(-)$1	223	133	158	20.6288
UGAGAACAGUAUAAAUAAGUUCUGU	chr2:75513693-75513909(+)$1	216	56	81	21.6333
AUCCCUUUAAAGCCAACAGGACAGC	chr4:117605008-117605227(-)$1	219	181	206	21.9169
GGUGUCUACAUUAAAUUAUGACCUA	chr9:69605427-69605648(-)$1	221	67	92	22.3422
CUGCCUCUUUUGUGUACCAGGCCAG	chr8:72411585-72411807(-)$1	222	125	150	24.8096
UAGCUCAAUCAGAACACAGGCUCAC	chr4:116359819-116360035(-)$1	216	102	127	22.2920
GCAGGGCCUACCCAUCAUGCCCUGC	chr2:181319295-181319520(-)$1	225	3	28	22.5897
UGGCUGUGUGUGUGUUUUCUAGCCC	chr8:74152054-74152297(-)$1	243	2	27	21.2233
AUAUUUCUAAGUUUUUAAAAAAUAA	chr1:168236956-168237177(+)$1	221	33	58	22.6344
AAGUGAGACAUUAAAAAUUGCCAAU	chr4:120731783-120732020(-)$1	237	145	170	22.2187
GAUCUGCCCUAGCCCCCUCAGUUCC	chr17:32491327-32491562(-)$1	235	40	65	24.4817
UAUGUCUCUUUGUUUUUUCAUAUGG	chr15:89294025-89294242(+)$1	217	25	50	21.4025
ACAGCCACCAACCCACUAGGCUCCG	chr11:106147762-106147981(+)$1	219	115	140	22.6308
caguuccgaaccuaagcaggguugg	chr7:134335357-134335578(+)$1	221	50	75	23.4343
GUCAGUCUUGUUUAUUAGUGAGUUC	chr7:53450655-53450874(+)$1	219	74	99	22.5609
UUAGUGAAUCCUACCAAUAACCCAG	chr2:84978650-84978872(+)$1	222	6	31	21.2335
CCGACAGCCUCAAAUUCCGUGGCCA	chr17:35032247-35032474(+)$1	227	53	78	22.3015
AGUCCCCACUGAUGACCAGGAUUAU	chr19:6400730-6400952(+)$1	222	112	137	23.4631
CAGCCAGCACUCUUCAAUCUGACUG	chr17:3151241-3151467(+)$1	226	102	127	23.1374
CUGGACAAACCUCUGAGCUGUCCCA	chr14:35340734-35340952(+)$1	218	71	96	21.7474
UUCACUGGAAGUGCAAUAGGUGAAC	chr4:21788011-21788231(-)$1	220	113	138	23.0490
GAGUCUUUAGUCCCACAUGGAGUCC	chr4:129380986-129381217(-)$1	231	62	87	24.0427
ACUCCAUUUUGGCCUUCUUGGGUGU	chr19:40625431-40625653(-)$1	222	187	212	24.1965
UUUCUGGAAAUGAAAAACCUGGAGU	chr19:5134512-5134736(-)$1	224	138	163	21.8737
UAGGGACAUCUGGACACCUCCUAGG	chr6:121329472-121329695(-)$1	223	172	197	23.4631
UGCGGAUUUUUUCUUAAAUAUUUCC	chr13:9685514-9685747(-)$1	233	136	161	21.0282
GCAGAUGAAUACUAAAAUAAAUCUG	chr12:29122637-29122852(+)$1	215	90	115	21.4172
CCAUUCCCUCAUUGUCAUGGAUUCA	chr19:24753797-24754015(-)$1	218	143	168	21.1672
GUCCUGGAAGCAUGAAUUACAGGAC	chr7:31092392-31092623(+)$1	231	85	110	22.4939
CGGAUGCCUUCUUUCUGAAUCUGGG	chr9:44754250-44754470(-)$1	220	45	70	23.4631
UAGAUUCCUUCCACCCUCUGCAGAU	chr4:118933630-118933854(-)$1	224	50	75	20.4672
UGCAACUAAGUUCUUCAAAUUGCAC	chr17:15082542-15082772(+)$1	230	193	218	21.1654
GUCCUGUCUUUUUAAAAUCAGUGCC	chr6:64617400-64617650(+)$1	250	155	180	23.3754
UUCUGCGCCUUAAAGCUUAUCAGUG	chr11:44818733-44818963(+)$1	230	61	86	20.3021
GUAAUAAACCAGGAUGAAUAUUGCA	chr3:40598814-40599038(+)$1	224	55	80	24.1821
GAGUCGACAUUAAACGAACGGCAUU	chr5:124570087-124570308(+)$1	221	22	47	23.6666
CCUCCUCUAAUCAACCUCUGGGAGU	chr12:42178653-42178884(-)$1	231	9	34	21.2233
CUGGAGGAUAUUUCUCCCCCUUCAG	chr2:113836170-113836397(-)$1	227	51	76	22.5897
CAUGUCAACACUUAAACAGAAUUGA	chr17:9200978-9201199(-)$1	221	56	81	22.0555
UAUAAUCUCAAGUAUAAUGAUUGUG	chr16:46447976-46448215(-)$1	239	80	105	22.5897
UGCUUGGAAUGGGGCUAAGGGAAGU	chr10:7625809-7626024(-)$1	215	143	168	21.3901
AAGAGGGAACCUUCUCUACCUCUAC	chr2:69672510-69672734(+)$1	224	92	117	20.8501
AUGCCCAUUCUAUUAUAAGGGAAAU	chr14:72938354-72938574(+)$1	220	42	67	20.2594
GCCCAGGUCCUCUUCUACUGGAACG	chr11:69470559-69470785(-)$1	226	21	46	22.3360
UUUUGAUACCAUCCACUUUUUCAGA	chr11:90138768-90139003(+)$1	235	200	225	21.4172
UUUUGAGUUGAGUUGUAAUCAUAAG	chr11:87040424-87040644(-)$1	220	125	150	23.8506
AGAUCAGCCCCUCAACCUCCAGUGA	chr10:79597819-79598059(-)$1	240	153	178	21.2483

#DB
((................))).)))	chr7:30811020-30811240(+)$1	1	135	160	20.9575
(((((.............)))))))	chrX:130425520-130425755(-)$1	1	89	114	23.4631
(.((((............)))).))	chr9:53381163-53381386(-)$1	1	48	73	23.6666
(((((.............))).)).	chr19:46669193-46669415(-)$1	1	161	186	23.2944
.((((((...........))).)))	chr8:73292129-73292351(-)$1	1	60	85	22.7063
((((((............)))..))	chr6:56051171-56051394(+)$1	1	15	40	23.9574
((.(((............)))))).	chr9:75531492-75531724(-)$1	1	15	40	23.7180
((((((............)))))))	chr15:76546822-76547041(-)$1	1	24	49	23.8601
((((((............)))))).	chr4:148939302-148939521(+)$1	1	74	99	22.9943
.(((((............)))))..	chr2:143768409-143768635(+)$1	1	8	33	20.8501
(.((((............)))).))	chr10:21412591-21412810(-)$1	1	157	182	23.1986
(.((((...........))))))))	chr19:10059329-10059571(+)$1	1	214	239	21.9817
((((((............)))))))	chr15:7146589-7146812(+)$1	1	181	206	23.8601
((((((...........)))).)))	chr12:33660775-33660997(+)$1	1	54	79	22.3179
((.((..............)).)))	chr5:116859011-116859231(+)$1	1	163	188	21.0611
.((((.............))))(((	chr11:75833443-75833666(-)$1	1	133	158	20.6288
(((((((...........))))).)	chr2:75513693-75513909(+)$1	1	56	81	21.6333
.(((..............)))..))	chr4:117605008-117605227(-)$1	1	181	206	21.9169
((.(((.............))))).	chr9:69605427-69605648(-)$1	1	67	92	22.3422
((((((............))).)))	chr8:72411585-72411807(-)$1	1	125	150	24.8096
(((((.............)))).))	chr4:116359819-116360035(-)$1	1	102	127	22.2920
(((((((...........)))))))	chr2:181319295-181319520(-)$1	1	3	28	22.5897
.(((((.............))))).	chr8:74152054-74152297(-)$1	1	2	27	21.2233
.(((((.............))))))	chr1:168236956-168237177(+)$1	1	33	58	22.6344
..((((...........))))...)	chr4:120731783-120732020(-)$1	1	145	170	22.2187
((.(((............))).)))	chr17:32491327-32491562(-)$1	1	40	65	24.4817
((((..............)))).))	chr15:89294025-89294242(+)$1	1	25	50	21.4025
((((((............))))..)	chr11:106147762-106147981(+)$1	1	115	140	22.6308
((..(((...........))).)))	chr7:134335357-134335578(+)$1	1	50	75	23.4343
.(((..............))).)))	chr7:53450655-53450874(+)$1	1	74	99	22.5609
(..((..............))..))	chr2:84978650-84978872(+)$1	1	6	31	21.2335
((.((.............)))))))	chr17:35032247-35032474(+)$1	1	53	78	22.3015
(((((.............)))))))	chr19:6400730-6400952(+)$1	1	112	137	23.4631
(((.(((...........))).)))	chr17:3151241-3151467(+)$1	1	102	127	23.1374
..(((((...........)))))))	chr14:35340734-35340952(+)$1	1	71	96	21.7474
((((((............)))))).	chr4:21788011-21788231(-)$1	1	113	138	23.0490
((.(((............))).)))	chr4:129380986-129381217(-)$1	1	62	87	24.0427
((.(((............)))))))	chr19:40625431-40625653(-)$1	1	187	212	24.1965
.((((((...........)))))).	chr19:5134512-5134736(-)$1	1	138	163	21.8737
(((((.............)))))))	chr6:121329472-121329695(-)$1	1	172	197	23.4631
)))(((................)))	chr13:9685514-9685747(-)$1	1	136	161	21.0282
((((((..............)))))	chr12:29122637-29122852(+)$1	1	90	115	21.4172
(...(((...........)))....	chr19:24753797-24754015(-)$1	1	143	168	21.1672
((((((.............))))))	chr7:31092392-31092623(+)$1	1	85	110	22.4939
(((((.............)))))))	chr9:44754250-44754470(-)$1	1	45	70	23.4631
..((((................)))	chr4:118933630-118933854(-)$1	1	50	75	20.4672
(((((..............))))).	chr17:15082542-15082772(+)$1	1	193	218	21.1654
((.(((............))).)).	chr6:64617400-64617650(+)$1	1	155	180	23.3754
(.((((................)))	chr11:44818733-44818963(+)$1	1	61	86	20.3021
((((((............)))))))	chr3:40598814-40599038(+)$1	1	55	80	24.1821
(.((((............)))).))	chr5:124570087-124570308(+)$1	1	22	47	23.6666
.(((((.............))))).	chr12:42178653-42178884(-)$1	1	9	34	21.2233
(((((((...........)))))))	chr2:113836170-113836397(-)$1	1	51	76	22.5897
((..((............))..)).	chr17:9200978-9201199(-)$1	1	56	81	22.0555
(((((((...........)))))))	chr16:46447976-46448215(-)$1	1	80	105	22.5897
(((((................))))	chr10:7625809-7626024(-)$1	1	143	168	21.3901
.(((((............)))))..	chr2:69672510-69672734(+)$1	1	92	117	20.8501
...(((............)))....	chr14:72938354-72938574(+)$1	1	42	67	20.2594
((((((...........))))...)	chr11:69470559-69470785(-)$1	1	21	46	22.3360
((((((..............)))))	chr11:90138768-90139003(+)$1	1	200	225	21.4172
((.(((............))).)))	chr11:87040424-87040644(-)$1	1	125	150	23.8506
((.(((................)))	chr10:79597819-79598059(-)$1	1	153	178	21.2483

#PSSM
f : 0.14	g : 0.12	b : 0.11	e : 0.11	c : 0.09	: : 0.09	d : 0.08	i : 0.04	! : 0.04	h : 0.03	[ : 0.03	" : 0.03	= : 0.01	+ : 0.01	
e : 0.17	f : 0.14	g : 0.12	c : 0.11	b : 0.11	[ : 0.08	d : 0.06	i : 0.04	" : 0.04	! : 0.03	= : 0.01	+ : 0.01	h : 0.01	
d : 0.20	e : 0.16	[ : 0.16	g : 0.12	f : 0.11	c : 0.06	i : 0.04	! : 0.04	y : 0.01	" : 0.01	= : 0.01	+ : 0.01	
c : 0.25	d : 0.20	e : 0.12	g : 0.11	f : 0.09	i : 0.04	b : 0.04	! : 0.03	y : 0.01	[ : 0.01	" : 0.01	= : 0.01	
c : 0.27	d : 0.19	e : 0.12	g : 0.11	f : 0.09	b : 0.06	i : 0.04	w : 0.04	y : 0.01	= : 0.01	
c : 0.25	d : 0.16	v : 0.12	e : 0.11	f : 0.09	w : 0.09	g : 0.04	y : 0.03	i : 0.03	= : 0.01	b : 0.01	
u : 0.33	v : 0.20	w : 0.12	y : 0.09	c : 0.06	t : 0.06	g : 0.04	e : 0.03	f : 0.01	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	t : 0.22	v : 0.20	w : 0.12	y : 0.09	
u : 0.33	v : 0.20	t : 0.16	w : 0.12	y : 0.09	d : 0.06	
c : 0.27	d : 0.17	g : 0.11	w : 0.08	v : 0.08	y : 0.08	e : 0.06	f : 0.04	i : 0.03	b : 0.03	= : 0.01	
c : 0.29	d : 0.17	e : 0.12	g : 0.11	y : 0.08	f : 0.06	b : 0.06	i : 0.03	w : 0.03	= : 0.01	
c : 0.29	d : 0.17	e : 0.12	g : 0.11	f : 0.11	y : 0.08	i : 0.03	b : 0.03	= : 0.01	2 : 0.01	
] : 0.20	e : 0.14	f : 0.12	g : 0.11	d : 0.11	2 : 0.06	y : 0.06	i : 0.04	c : 0.03	3 : 0.03	6 : 0.01	= : 0.01	7 : 0.01	
e : 0.17	f : 0.16	g : 0.12	c : 0.09	] : 0.08	b : 0.08	2 : 0.06	i : 0.04	d : 0.04	3 : 0.03	G : 0.01	6 : 0.01	= : 0.01	7 : 0.01	h : 0.01	
f : 0.17	e : 0.14	g : 0.12	c : 0.12	b : 0.09	d : 0.08	i : 0.04	: : 0.03	h : 0.03	3 : 0.03	G : 0.01	] : 0.01	2 : 0.01	6 : 0.01	= : 0.01	7 : 0.01	
f : 0.14	g : 0.12	c : 0.12	: : 0.11	e : 0.09	d : 0.08	b : 0.06	] : 0.04	i : 0.04	4 : 0.03	h : 0.03	G : 0.01	6 : 0.01	5 : 0.01	= : 0.01	7 : 0.01	

#score	1389.735514649768
#seq	62
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_UTR_m1_run1.txt

#BEAR
ggggguuuuuuuuuuuugggggg	chr6:13034868-13035117(+)$1	249	30	53	23.3700
!dddduuuuuuuuuuuudddd22	chr4:134772502-134772737(-)$1	235	48	71	22.9830
:cccwwwwwwwwwwwwwwccc::	chr8:23678766-23679001(+)$1	235	176	199	19.2154
ddddvvvvvvvvvvvvvdddd::	chr15:4104924-4105174(+)$1	250	187	210	20.5512
fffffuuuuuuuuuuuuffffff	chr14:76907113-76907357(+)$1	244	22	45	22.2002
hhhhhvvvvvvvvvvvvvhhhhh	chr17:44174023-44174259(+)$1	236	69	92	21.5089
ggggguuuuuuuuuuuugggggg	chr12:71568417-71568671(+)$1	254	84	107	23.3700
!dddduuuuuuuuuuuudddd22	chr3:7444770-7445008(+)$1	238	126	149	22.9830
cccccctttttttttttccc]cc	chr11:50108692-50108928(-)$1	236	191	214	22.7228
[ddddtttttttttttdddd]a4	chr6:72561602-72561837(-)$1	235	184	207	21.8603
fffffuuuuuuuuuuuuffffff	chr11:88156714-88156953(-)$1	239	211	234	22.2002
[cccwwwwwwwwwwwwwwccc]b	chr5:33590727-33590969(-)$1	242	128	151	21.9602
ddddwwwwwwwwwwwwwwdddd:	chr11:115940745-115940980(-)$1	235	50	73	20.6799
gggggvvvvvvvvvvvvvggggg	chr11:6255709-6255944(+)$1	235	148	171	23.2274
[cccvvvvvvvvvvvvvccc]bb	chr18:20190016-20190254(-)$1	238	191	214	22.5302
ggggguuuuuuuuuuuugggggg	chr7:118215763-118216008(-)$1	245	219	242	23.3700
c[cccuuuuuuuuuuuuccc]cc	chr15:97622441-97622677(+)$1	236	132	155	23.7762
[ddddtttttttttttdddd]a2	chr11:19964296-19964533(-)$1	237	131	154	21.7578
e!!bbyyyyyyyyyyyyyyyybb	chr18:31941014-31941249(+)$1	235	118	141	20.0880
g[ddddtttttttttttdddd]g	chr5:32794615-32794875(+)$1	260	20	43	22.3215
f[cccvvvvvvvvvvvvvcccff	chr9:42772398-42772633(-)$1	235	184	207	23.2015
fffffftttttttttttffffff	chr6:35458992-35459232(-)$1	240	97	120	21.1188
eebbwwwwwwwwwwwwwwbb]ee	chr2:155214089-155214332(+)$1	243	196	219	20.7449
gggggvvvvvvvvvvvvvggggg	chr5:122903804-122904044(-)$1	240	74	97	23.2274
eeeeeuuuuuuuuuuuueeeee]	chr5:136384536-136384800(-)$1	264	226	249	22.7339
ggggggtttttttttttgggggg	chr18:34505313-34505548(-)$1	235	128	151	22.1980
geeeeettttttttttteeeee6	chr11:74197647-74197893(-)$1	246	153	176	21.3482
:dddduuuuuuuuuuuudddd:g	chr2:109739556-109739796(+)$1	240	132	155	21.2239
==[a[attttttttttta]a===	chr11:77524469-77524712(+)$1	243	112	135	22.9061
iiiiiitttttttttttiiiiii	chr14:37691621-37691860(-)$1	239	157	180	22.1041
fffffwwwwwwwwwwwwwwffff	chr5:136384853-136385106(-)$1	253	177	200	20.8769
cddddyyyyyyyyyyyyyyyydd	chr15:103028081-103028333(-)$1	252	198	221	20.4161
ddddyyyyyyyyyyyyyyyyddd	chr4:14841122-14841357(+)$1	235	193	216	20.5207
hhh[avvvvvvvvvvvvva]hhh	chr14:21851608-21851851(+)$1	243	42	65	22.1968
!eeeeettttttttttteeeee4	chr8:46911742-46911988(+)$1	246	160	183	21.7898
[dddduuuuuuuuuuuudddd]e	chrX:102993034-102993276(-)$1	242	10	33	23.1886
a[cccvvvvvvvvvvvvvccca]	chr3:103544754-103544989(-)$1	235	194	217	23.4356
gggbbuuuuuuuuuuuubb]ggg	chr3:103545044-103545290(-)$1	246	95	118	22.9325
f[cccvvvvvvvvvvvvvcccff	chr16:17044965-17045200(+)$1	235	8	31	23.2015
cccbbvvvvvvvvvvvvvbb]cc	chr13:21605280-21605515(-)$1	235	164	187	22.4958
fffffuuuuuuuuuuuuffffff	chr8:42077305-42077542(-)$1	237	3	26	22.2002
hhhhhvvvvvvvvvvvvvhhhhh	chr15:36407463-36407701(-)$1	238	155	178	21.5089
dddd[attttttttttta]dddd	chr19:5099357-5099592(-)$1	235	212	235	22.3562
!!cccyyyyyyyyyyyyyyyycc	chr16:57152881-57153132(+)$1	251	168	191	21.1716
ffyyyyyyyyyyyyyyyyfffff	chr2:104269211-104269455(-)$1	244	86	109	19.9196
eeeeeuuuuuuuuuuuueeeee:	chr6:67235593-67235829(+)$1	236	69	92	21.8073
ggg[bbtttttttttttbb]ggg	chr2:155973180-155973415(-)$1	235	97	120	22.0103
eeeeettttttttttteeeee>>	chr9:55906171-55906406(+)$1	235	57	80	20.9267
c!!bbuuuuuuuuuuuubb22cc	chr10:42254586-42254830(+)$1	244	86	109	22.4836
##ddddtttttttttttdddd22	chr1:129839793-129840031(+)$1	238	31	54	21.6931
"ddddvvvvvvvvvvvvvdddd4	chr15:7146700-7146935(+)$1	235	169	192	22.8474
####bbtttttttttttbb4444	chr16:96377526-96377769(+)$1	243	167	190	21.2285
!!cccwwwwwwwwwwwwwwccc]	chr4:97780418-97780653(+)$1	235	188	211	22.2503
ddddwwwwwwwwwwwwwwddddf	chr2:72245089-72245325(+)$1	236	16	39	21.4607
cccwwwwwwwwwwwwwwccc===	chr2:154519610-154519845(+)$1	235	62	85	21.3541
eee[bbtttttttttttbbeeee	chr9:120869129-120869380(+)$1	251	64	87	21.4345
gggggvvvvvvvvvvvvvggggg	chr18:78021187-78021422(+)$1	235	55	78	23.2274
=====uuuuuuuuuuuu======	chr13:74459848-74460091(-)$1	243	22	45	23.5777
eeeeeyyyyyyyyyyyyyyyyee	chr11:87793883-87794158(-)$1	275	111	134	20.2954
hdddduuuuuuuuuuuudddd::	chr2:155214408-155214646(+)$1	238	134	157	21.2788
c!!bbuuuuuuuuuuuubb22cc	chr16:28827388-28827623(-)$1	235	82	105	22.4836
d[ccctttttttttttcccdddd	chr5:122906679-122906924(-)$1	245	48	71	21.8971

#otherMatches

#Seq PSSM
GGUUGCAUAAUAUUUACCAACCA	chr6:13034868-13035117(+)$1	249	30	53	23.3700
AGAACUUGAGGUGCUAUGUUCCA	chr4:134772502-134772737(-)$1	235	48	71	22.9830
UUGCUUUCCCUGACACAUGCACA	chr8:23678766-23679001(+)$1	235	176	199	19.2154
GUACAAGGCCCAGGAGAGUACGU	chr15:4104924-4105174(+)$1	250	187	210	20.5512
UUUGUGUAUGUAGUGUAACGAAU	chr14:76907113-76907357(+)$1	244	22	45	22.2002
GAUAACAUGCAUCUCCUCUUAUC	chr17:44174023-44174259(+)$1	236	69	92	21.5089
UAGGCCUCUCCUUUAUAGUUUAA	chr12:71568417-71568671(+)$1	254	84	107	23.3700
GCUUAACUUUUUUAAACUAAGAA	chr3:7444770-7445008(+)$1	238	126	149	22.9830
UGGCCCACACCUUUCUAGGGUCC	chr11:50108692-50108928(-)$1	236	191	214	22.7228
GCUGCAAACCAAACUAGCAGGUU	chr6:72561602-72561837(-)$1	235	184	207	21.8603
UUUCUAUUUACAAAUUAGGAAAG	chr11:88156714-88156953(-)$1	239	211	234	22.2002
GUCAACAAAAAGAAAACCUGAGG	chr5:33590727-33590969(-)$1	242	128	151	21.9602
CUUUUUUUUUUUUUCUCUAGAGC	chr11:115940745-115940980(-)$1	235	50	73	20.6799
GCCUGUGCCGACUUCUCUCAGGC	chr11:6255709-6255944(+)$1	235	148	171	23.2274
AAACUUCUUUAUAAUGUGUUCUG	chr18:20190016-20190254(-)$1	238	191	214	22.5302
UACAGAAAAAUUCUUAACUGUAA	chr7:118215763-118216008(-)$1	245	219	242	23.3700
AAAGGCAGGAGCUAGCACCUCUC	chr15:97622441-97622677(+)$1	236	132	155	23.7762
UAGGCUUCCAAUUUUUGCUUUCU	chr11:19964296-19964533(-)$1	237	131	154	21.7578
UAGCCUGCUGAGGAAUGGAAUGG	chr18:31941014-31941249(+)$1	235	118	141	20.0880
AUUUCUGUAUGUGAUCAAGAGUU	chr5:32794615-32794875(+)$1	260	20	43	22.3215
GUGCUCUUGUUCCCGUCUGGCUG	chr9:42772398-42772633(-)$1	235	184	207	23.2015
GAAUGCUAACUAAUACUGUGUUU	chr6:35458992-35459232(-)$1	240	97	120	21.1188
GCAGAUCAAAAUUUUACACUAGC	chr2:155214089-155214332(+)$1	243	196	219	20.7449
UCAUAGCCUCUCUAACUGUAUGA	chr5:122903804-122904044(-)$1	240	74	97	23.2274
UGUUAGCUUACUCUUAAUAAUGU	chr5:136384536-136384800(-)$1	264	226	249	22.7339
UGGCCCUAGCGUAAUAUGGGUCA	chr18:34505313-34505548(-)$1	235	128	151	22.1980
UUCUGGGCCAGCAGCAACCAGGU	chr11:74197647-74197893(-)$1	246	153	176	21.3482
AAUUCUAAUUAAUAUAUGGAUGA	chr2:109739556-109739796(+)$1	240	132	155	21.2239
Cgugucugugugucugugucugu	chr11:77524469-77524712(+)$1	243	112	135	22.9061
UGUGUAUUUAGGAAGUCUAUGCA	chr14:37691621-37691860(-)$1	239	157	180	22.1041
UUCUCCUUCCUUUACUGUUGAGA	chr5:136384853-136385106(-)$1	253	177	200	20.8769
UAACUUGAUGAAAUGAAGGAUGG	chr15:103028081-103028333(-)$1	252	198	221	20.4161
CAGUUGUUCCAUUACUUGUUGCU	chr4:14841122-14841357(+)$1	235	193	216	20.5207
GGGUGUUAUCCUGCCCAUCCUCC	chr14:21851608-21851851(+)$1	243	42	65	22.1968
UUGGUCAACUGUUACGAGACUAU	chr8:46911742-46911988(+)$1	246	160	183	21.7898
UGAUAUUGUAUCUGUUUUGUCCC	chrX:102993034-102993276(-)$1	242	10	33	23.1886
CAUAGUUUUACAUUCAUUCUGGC	chr3:103544754-103544989(-)$1	235	194	217	23.4356
UACCGUUUAUGUCAUUCUGUGUG	chr3:103545044-103545290(-)$1	246	95	118	22.9325
GUGGAGUUGAUGGUGUUAUCCCA	chr16:17044965-17045200(+)$1	235	8	31	23.2015
CAGCAUCUUCCCUUAUUCUGUCU	chr13:21605280-21605515(-)$1	235	164	187	22.4958
CCACUGGAAUGGAACAGAGUGGC	chr8:42077305-42077542(-)$1	237	3	26	22.2002
AAUAUAUGUAAUAUGUAAAUAUU	chr15:36407463-36407701(-)$1	238	155	178	21.5089
CCAGUGUGUAUUUAAGUCCCUGG	chr19:5099357-5099592(-)$1	235	212	235	22.3562
GUGCAACAAAAGCUUAGAACCUG	chr16:57152881-57153132(+)$1	251	168	191	21.1716
CUUUCCUUUCCUUUCAGUAGAGU	chr2:104269211-104269455(-)$1	244	86	109	19.9196
UUACUUCUUAUUUUAAUAGUAAU	chr6:67235593-67235829(+)$1	236	69	92	21.8073
UUUUCAAUUAAUGUCUCUGUAAA	chr2:155973180-155973415(-)$1	235	97	120	22.0103
UUGUGCCAUAUGACCACACAGUC	chr9:55906171-55906406(+)$1	235	57	80	20.9267
GUACACUAACACUCACCUGCUCC	chr10:42254586-42254830(+)$1	244	86	109	22.4836
GGGAUGGUAUUUAAUGACAUCAU	chr1:129839793-129840031(+)$1	238	31	54	21.6931
UCUAGGUCUCUGUAAAUGCUAGC	chr15:7146700-7146935(+)$1	235	169	192	22.8474
GUCAGGAUUUUCUACACCCGCCA	chr16:96377526-96377769(+)$1	243	167	190	21.2285
AAGAAAAAAAAAAGACAACUUCC	chr4:97780418-97780653(+)$1	235	188	211	22.2503
GUGGAUAAUUAUUUCAAACUACA	chr2:72245089-72245325(+)$1	236	16	39	21.4607
UCCACAGCCAAGAAGAAGGAAGA	chr2:154519610-154519845(+)$1	235	62	85	21.3541
GCUUGCUUUUAUUUUUUGCAGUA	chr9:120869129-120869380(+)$1	251	64	87	21.4345
CAUACUGUGUGCUAGUUUGUGUG	chr18:78021187-78021422(+)$1	235	55	78	23.2274
UGUCCAUGUUUAUUUGAGGGCGU	chr13:74459848-74460091(-)$1	243	22	45	23.5777
UACGUUUGUGUUUGUCUGUGUGC	chr11:87793883-87794158(-)$1	275	111	134	20.2954
UGGCUCAAAUUUCAGAAGGCCUC	chr2:155214408-155214646(+)$1	238	134	157	21.2788
GCUUGCUUUCUGUCCCACACCCA	chr16:28827388-28827623(-)$1	235	82	105	22.4836
AUACUUGUACAAAGAUAGUUGAG	chr5:122906679-122906924(-)$1	245	48	71	21.8971

#DB
(((((............))))))	chr6:13034868-13035117(+)$1	1	30	53	23.3700
.((((............))))..	chr4:134772502-134772737(-)$1	1	48	71	22.9830
.(((..............)))..	chr8:23678766-23679001(+)$1	1	176	199	19.2154
((((.............))))..	chr15:4104924-4105174(+)$1	1	187	210	20.5512
(((((............))))))	chr14:76907113-76907357(+)$1	1	22	45	22.2002
(((((.............)))))	chr17:44174023-44174259(+)$1	1	69	92	21.5089
(((((............))))))	chr12:71568417-71568671(+)$1	1	84	107	23.3700
.((((............))))..	chr3:7444770-7445008(+)$1	1	126	149	22.9830
((((((...........))).))	chr11:50108692-50108928(-)$1	1	191	214	22.7228
.((((...........)))).).	chr6:72561602-72561837(-)$1	1	184	207	21.8603
(((((............))))))	chr11:88156714-88156953(-)$1	1	211	234	22.2002
.(((..............))).)	chr5:33590727-33590969(-)$1	1	128	151	21.9602
((((..............)))).	chr11:115940745-115940980(-)$1	1	50	73	20.6799
(((((.............)))))	chr11:6255709-6255944(+)$1	1	148	171	23.2274
.(((.............))).))	chr18:20190016-20190254(-)$1	1	191	214	22.5302
(((((............))))))	chr7:118215763-118216008(-)$1	1	219	242	23.3700
(.(((............))).))	chr15:97622441-97622677(+)$1	1	132	155	23.7762
.((((...........)))).).	chr11:19964296-19964533(-)$1	1	131	154	21.7578
(..((................))	chr18:31941014-31941249(+)$1	1	118	141	20.0880
(.((((...........)))).)	chr5:32794615-32794875(+)$1	1	20	43	22.3215
(.(((.............)))))	chr9:42772398-42772633(-)$1	1	184	207	23.2015
((((((...........))))))	chr6:35458992-35459232(-)$1	1	97	120	21.1188
((((..............)).))	chr2:155214089-155214332(+)$1	1	196	219	20.7449
(((((.............)))))	chr5:122903804-122904044(-)$1	1	74	97	23.2274
(((((............))))).	chr5:136384536-136384800(-)$1	1	226	249	22.7339
((((((...........))))))	chr18:34505313-34505548(-)$1	1	128	151	22.1980
((((((...........))))).	chr11:74197647-74197893(-)$1	1	153	176	21.3482
.((((............)))).(	chr2:109739556-109739796(+)$1	1	132	155	21.2239
((.(.(...........).))))	chr11:77524469-77524712(+)$1	1	112	135	22.9061
((((((...........))))))	chr14:37691621-37691860(-)$1	1	157	180	22.1041
(((((..............))))	chr5:136384853-136385106(-)$1	1	177	200	20.8769
(((((................))	chr15:103028081-103028333(-)$1	1	198	221	20.4161
((((................)))	chr4:14841122-14841357(+)$1	1	193	216	20.5207
(((.(.............).)))	chr14:21851608-21851851(+)$1	1	42	65	22.1968
.(((((...........))))).	chr8:46911742-46911988(+)$1	1	160	183	21.7898
.((((............)))).)	chrX:102993034-102993276(-)$1	1	10	33	23.1886
(.(((.............)))).	chr3:103544754-103544989(-)$1	1	194	217	23.4356
(((((............)).)))	chr3:103545044-103545290(-)$1	1	95	118	22.9325
(.(((.............)))))	chr16:17044965-17045200(+)$1	1	8	31	23.2015
(((((.............)).))	chr13:21605280-21605515(-)$1	1	164	187	22.4958
(((((............))))))	chr8:42077305-42077542(-)$1	1	3	26	22.2002
(((((.............)))))	chr15:36407463-36407701(-)$1	1	155	178	21.5089
((((.(...........).))))	chr19:5099357-5099592(-)$1	1	212	235	22.3562
..(((................))	chr16:57152881-57153132(+)$1	1	168	191	21.1716
((................)))))	chr2:104269211-104269455(-)$1	1	86	109	19.9196
(((((............))))).	chr6:67235593-67235829(+)$1	1	69	92	21.8073
(((.((...........)).)))	chr2:155973180-155973415(-)$1	1	97	120	22.0103
(((((...........)))))..	chr9:55906171-55906406(+)$1	1	57	80	20.9267
(..((............))..))	chr10:42254586-42254830(+)$1	1	86	109	22.4836
..((((...........))))..	chr1:129839793-129840031(+)$1	1	31	54	21.6931
.((((.............)))).	chr15:7146700-7146935(+)$1	1	169	192	22.8474
....((...........))....	chr16:96377526-96377769(+)$1	1	167	190	21.2285
..(((..............))).	chr4:97780418-97780653(+)$1	1	188	211	22.2503
((((..............))))(	chr2:72245089-72245325(+)$1	1	16	39	21.4607
(((..............))))))	chr2:154519610-154519845(+)$1	1	62	85	21.3541
(((.((...........))))))	chr9:120869129-120869380(+)$1	1	64	87	21.4345
(((((.............)))))	chr18:78021187-78021422(+)$1	1	55	78	23.2274
(((((............))))))	chr13:74459848-74460091(-)$1	1	22	45	23.5777
(((((................))	chr11:87793883-87794158(-)$1	1	111	134	20.2954
)((((............))))..	chr2:155214408-155214646(+)$1	1	134	157	21.2788
(..((............))..))	chr16:28827388-28827623(-)$1	1	82	105	22.4836
(.(((...........)))))))	chr5:122906679-122906924(-)$1	1	48	71	21.8971

#PSSM
g : 0.17	f : 0.12	c : 0.11	e : 0.11	d : 0.09	! : 0.08	[ : 0.08	h : 0.06	: : 0.03	= : 0.03	# : 0.03	i : 0.01	a : 0.01	" : 0.01	
d : 0.22	g : 0.14	e : 0.12	c : 0.09	f : 0.09	[ : 0.09	! : 0.08	h : 0.04	= : 0.03	# : 0.03	i : 0.01	
d : 0.25	c : 0.20	g : 0.14	e : 0.11	f : 0.08	h : 0.04	! : 0.04	b : 0.01	[ : 0.01	i : 0.01	y : 0.01	# : 0.01	= : 0.01	
d : 0.25	c : 0.17	g : 0.11	b : 0.09	e : 0.09	f : 0.08	[ : 0.04	h : 0.03	a : 0.01	i : 0.01	y : 0.01	# : 0.01	w : 0.01	= : 0.01	
d : 0.17	c : 0.12	b : 0.12	g : 0.11	w : 0.09	e : 0.09	f : 0.08	v : 0.03	h : 0.03	[ : 0.03	y : 0.03	i : 0.01	a : 0.01	= : 0.01	
u : 0.29	v : 0.20	w : 0.12	y : 0.09	t : 0.06	b : 0.04	d : 0.03	e : 0.03	a : 0.03	c : 0.01	f : 0.01	g : 0.01	i : 0.01	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	t : 0.27	v : 0.20	w : 0.12	y : 0.09	
u : 0.29	v : 0.20	t : 0.20	w : 0.12	y : 0.09	d : 0.03	e : 0.01	c : 0.01	
v : 0.17	d : 0.16	w : 0.11	y : 0.09	b : 0.09	c : 0.08	e : 0.08	g : 0.06	f : 0.06	a : 0.03	i : 0.01	= : 0.01	
d : 0.20	c : 0.16	b : 0.12	g : 0.11	f : 0.08	y : 0.08	e : 0.08	h : 0.03	] : 0.03	w : 0.03	i : 0.01	a : 0.01	= : 0.01	
d : 0.24	c : 0.16	g : 0.11	f : 0.09	e : 0.09	y : 0.08	] : 0.04	h : 0.03	b : 0.03	2 : 0.03	a : 0.01	i : 0.01	4 : 0.01	= : 0.01	
d : 0.22	g : 0.14	] : 0.11	c : 0.09	f : 0.09	e : 0.09	y : 0.06	h : 0.04	= : 0.04	2 : 0.03	i : 0.01	4 : 0.01	
g : 0.14	f : 0.12	c : 0.11	d : 0.11	e : 0.11	: : 0.06	2 : 0.04	h : 0.04	a : 0.04	] : 0.04	= : 0.04	b : 0.03	i : 0.01	> : 0.01	4 : 0.01	
g : 0.17	f : 0.14	c : 0.09	: : 0.08	2 : 0.06	4 : 0.06	e : 0.06	d : 0.06	h : 0.04	b : 0.04	] : 0.04	= : 0.04	6 : 0.01	i : 0.01	> : 0.01	

#score	1363.9537481220837
#seq	62
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_transcript_m3_run1.txt

#BEAR
eeeooooooeeeee	chr15:31388225-31388481(-)$1	256	150	164	9.2017
eeeemmmmeeeee2	chr12:30607230-30607516(+)$1	286	230	244	9.9912
eeeooooooeeeee	chr9:18117323-18117558(+)$1	235	50	64	9.2017
eeeooooooeeeee	chr9:109907249-109907502(+)$1	253	91	105	9.2017
eeeooooooeeeee	chr1:165847023-165847271(+)$1	248	34	48	9.2017
eeeeellleeeee:	chr15:79555743-79555980(-)$1	237	180	194	9.8821
eeeeellleeeee:	chr5:124570009-124570271(-)$1	262	100	114	9.8821
eeeooooooeeeee	chr13:110844350-110844643(-)$1	293	199	213	9.2017
eeeemmmmeeeee:	chr3:107271774-107272028(-)$1	254	181	195	9.6682
eeeeellleeeee:	chr11:69155749-69155994(+)$1	245	99	113	9.8821
eeeemmmmeeeee:	chr3:100366810-100367049(-)$1	239	167	181	9.6682
eeeemmmmeeeee:	chr18:34504500-34504770(-)$1	270	12	26	9.6682
eeeemmmmeeeee]	chr2:18764715-18764956(-)$1	241	133	147	10.1251
eeeemmmmeeeee:	chr9:110140606-110140860(+)$1	254	141	155	9.6682
eeeeellleeeee:	chr11:105916222-105916468(+)$1	246	145	159	9.8821
eeeooooooeeeee	chr2:49628039-49628283(+)$1	244	27	41	9.2017
eeeeellleeeee:	chr10:34018682-34018956(+)$1	274	222	236	9.8821
eeeeellleeeee3	chr10:119335971-119336206(+)$1	235	92	106	10.3821
eeeooooooeeeee	chr7:7235377-7235612(-)$1	235	143	157	9.2017
eeeemmmmeeeee3	chrX:96661226-96661469(-)$1	243	133	147	10.1682
eeeemmmmeeeee4	chr19:58870931-58871176(-)$1	245	202	216	10.1047
eeeeellleeeee2	chr18:61145875-61146177(+)$1	302	227	241	10.2051
eeeooooooeeeee	chr1:186696369-186696617(-)$1	248	95	109	9.2017
eeeeellleeeee:	chr11:119400282-119400539(-)$1	257	42	56	9.8821
eeeemmmmeeeee:	chr3:8560526-8560790(+)$1	264	19	33	9.6682
eeeeellleeeee:	chr6:86937455-86937718(+)$1	263	228	242	9.8821
eeeemmmmeeeee2	chr12:11332842-11333088(-)$1	246	166	180	9.9912
eeeemmmmeeeee4	chr17:37210548-37210814(+)$1	266	113	127	10.1047
eeeemmmmeeeee:	chr5:65863869-65864104(-)$1	235	18	32	9.6682
eeeemmmmeeeee]	chr10:57236016-57236273(-)$1	257	58	72	10.1251
eeeemmmmeeeeeh	chr19:20717399-20717640(+)$1	241	117	131	9.4372
eeeeellleeeeeb	chr19:32899039-32899283(+)$1	244	117	131	9.9764
eeeooooooeeeee	chr8:124124022-124124257(-)$1	235	103	117	9.2017
eeeeellleeeee]	chr6:108500443-108500706(+)$1	263	192	206	10.3390
eeeooooooeeeee	chr6:115224767-115225019(+)$1	252	59	73	9.2017
eeeeellleeeee:	chr7:91398354-91398593(-)$1	239	94	108	9.8821
eeeemmmmeeeee:	chr7:66561836-66562082(+)$1	246	155	169	9.6682
eeeemmmmeeeeed	chr12:8758937-8759200(+)$1	263	188	202	9.7516
eeeemmmmeeeee5	chr2:135298384-135298643(+)$1	259	192	206	9.6590
eeeemmmmeeeee3	chr14:120829821-120830077(+)$1	256	97	111	10.1682
eeeemmmmeeeeeD	chr17:87397467-87397705(+)$1	238	1	15	9.1451
eeeooooooeeeee	chr11:41945344-41945595(-)$1	251	37	51	9.2017
eeeooooooeeeee	chr15:74554052-74554296(+)$1	244	178	192	9.2017
eeeeellleeeee]	chr9:113885607-113885863(+)$1	256	107	121	10.3390
eeeemmmmeeeeee	chr18:64432505-64432751(+)$1	246	164	178	9.8666
eeeemmmmeeeee:	chr4:86630781-86631037(-)$1	256	21	35	9.6682
eeeemmmmeeeee]	chr17:87832784-87833026(-)$1	242	30	44	10.1251
eeeeellleeeeee	chr11:106118590-106118825(+)$1	235	25	39	10.0805
eeeemmmmeeeee:	chr15:53047161-53047398(-)$1	237	37	51	9.6682
eeeeellleeeee2	chr7:106603330-106603565(+)$1	235	94	108	10.2051
eeeeellleeeee4	chr11:90139073-90139323(+)$1	250	62	76	10.3186
eeeooooooeeeee	chr19:41287280-41287515(-)$1	235	132	146	9.2017
eeeeellleeeee3	chr16:29652402-29652664(+)$1	262	115	129	10.3821
eeeeellleeeeeE	chr12:83097836-83098082(+)$1	246	73	87	9.5053
eeeeellleeeee4	chrX:69217246-69217525(+)$1	279	157	171	10.3186
eeeemmmmeeeee:	chr3:19968893-19969128(+)$1	235	106	120	9.6682
eeeooooooeeeee	chr8:71636369-71636642(+)$1	273	51	65	9.2017
eeeeellleeeee0	chrX:67596350-67596618(-)$1	268	47	61	9.9962

#otherMatches

#Seq PSSM
GUAAUAUUGUAUAG	chr15:31388225-31388481(-)$1	256	150	164	9.2017
CCAUACACAUGGUC	chr12:30607230-30607516(+)$1	286	230	244	9.9912
GAAAUGGAAUUCUU	chr9:18117323-18117558(+)$1	235	50	64	9.2017
uuUUAAAAUGAGAC	chr9:109907249-109907502(+)$1	253	91	105	9.2017
GACAAUACAGUCCA	chr1:165847023-165847271(+)$1	248	34	48	9.2017
GGUGCCCAGCACCC	chr15:79555743-79555980(-)$1	237	180	194	9.8821
UCCUAUUCUGGGGU	chr5:124570009-124570271(-)$1	262	100	114	9.8821
UUAUUUUUUUGAAG	chr13:110844350-110844643(-)$1	293	199	213	9.2017
UUGCUUCUGUGAGU	chr3:107271774-107272028(-)$1	254	181	195	9.6682
CAUUUGUAAAAUGU	chr11:69155749-69155994(+)$1	245	99	113	9.8821
GCUUUCACAAGUAC	chr3:100366810-100367049(-)$1	239	167	181	9.6682
CCUGUCCUCAGGUG	chr18:34504500-34504770(-)$1	270	12	26	9.6682
UGAGAGUACUUAGU	chr2:18764715-18764956(-)$1	241	133	147	10.1251
CUUUGUCUAAGGCU	chr9:110140606-110140860(+)$1	254	141	155	9.6682
CAGCCCAGGGCUGG	chr11:105916222-105916468(+)$1	246	145	159	9.8821
CCUGGAGUAAGGGG	chr2:49628039-49628283(+)$1	244	27	41	9.2017
UUCUUACCAAGAAC	chr10:34018682-34018956(+)$1	274	222	236	9.8821
AAGUACCGUAUUUG	chr10:119335971-119336206(+)$1	235	92	106	10.3821
GCACUUGACUGUAU	chr7:7235377-7235612(-)$1	235	143	157	9.2017
UAGUUUUCACUAGA	chrX:96661226-96661469(-)$1	243	133	147	10.1682
UUUGGACCCAGAGA	chr19:58870931-58871176(-)$1	245	202	216	10.1047
AAACGACACGUUUU	chr18:61145875-61146177(+)$1	302	227	241	10.2051
CUCGUGACAGAGUG	chr1:186696369-186696617(-)$1	248	95	109	9.2017
CGAGCGUGGCUCGA	chr11:119400282-119400539(-)$1	257	42	56	9.8821
GUAAAUAUUUACAU	chr3:8560526-8560790(+)$1	264	19	33	9.6682
CGUCUCCCAGAUGC	chr6:86937455-86937718(+)$1	263	228	242	9.8821
CAUUUGCUAAUGAA	chr12:11332842-11333088(-)$1	246	166	180	9.9912
AUGGUUGUCUAUGU	chr17:37210548-37210814(+)$1	266	113	127	10.1047
GUAAUCACUUGCAC	chr5:65863869-65864104(-)$1	235	18	32	9.6682
UUUUGCAAAAGAUA	chr10:57236016-57236273(-)$1	257	58	72	10.1251
GCAUAGUCGUGUUU	chr19:20717399-20717640(+)$1	241	117	131	9.4372
GUUGCUCUGUAACA	chr19:32899039-32899283(+)$1	244	117	131	9.9764
ACGUUACCUUGUGG	chr8:124124022-124124257(-)$1	235	103	117	9.2017
CAGCAUAUUGCUGA	chr6:108500443-108500706(+)$1	263	192	206	10.3390
CUGCAUGACUAGGG	chr6:115224767-115225019(+)$1	252	59	73	9.2017
GAGGGUCCCCCUCA	chr7:91398354-91398593(-)$1	239	94	108	9.8821
UGACUAUAGUCAUC	chr7:66561836-66562082(+)$1	246	155	169	9.6682
UAGAAAAAUCUGAC	chr12:8758937-8759200(+)$1	263	188	202	9.7516
CUAUUGACAUGGCU	chr2:135298384-135298643(+)$1	259	192	206	9.6590
UGUAAUCUUGCAUA	chr14:120829821-120830077(+)$1	256	97	111	10.1682
GCAGAGCACUGCUG	chr17:87397467-87397705(+)$1	238	1	15	9.1451
CAUGAAAGAAUGUA	chr11:41945344-41945595(-)$1	251	37	51	9.2017
UGCCCAGAUGCACA	chr15:74554052-74554296(+)$1	244	178	192	9.2017
UAGCUGCUGGCUGU	chr9:113885607-113885863(+)$1	256	107	121	10.3390
GUGUGCCUAUACAU	chr18:64432505-64432751(+)$1	246	164	178	9.8666
AGACUAUUGUCUUA	chr4:86630781-86631037(-)$1	256	21	35	9.6682
ACUGUGGACAGUCA	chr17:87832784-87833026(-)$1	242	30	44	10.1251
AGAUUGAUAAUCUC	chr11:106118590-106118825(+)$1	235	25	39	10.0805
UAGAUUUUUCUGAA	chr15:53047161-53047398(-)$1	237	37	51	9.6682
CUAUGCAUCGUGGA	chr7:106603330-106603565(+)$1	235	94	108	10.2051
UGCCACUUUGGUGC	chr11:90139073-90139323(+)$1	250	62	76	10.3186
CAUGUCAAAAUGUU	chr19:41287280-41287515(-)$1	235	132	146	9.2017
GUUCAGUUUGAAUA	chr16:29652402-29652664(+)$1	262	115	129	10.3821
CACGGCUCCCGUGU	chr12:83097836-83098082(+)$1	246	73	87	9.5053
UCUGUAAAGCAGAC	chrX:69217246-69217525(+)$1	279	157	171	10.3186
AAGCUCUAGCUUGG	chr3:19968893-19969128(+)$1	235	106	120	9.6682
CAGAGCACCCUGAG	chr8:71636369-71636642(+)$1	273	51	65	9.2017
UGCUAUGAUAGCAU	chrX:67596350-67596618(-)$1	268	47	61	9.9962

#DB
(((......)))))	chr15:31388225-31388481(-)$1	1	150	164	9.2017
((((....))))).	chr12:30607230-30607516(+)$1	1	230	244	9.9912
(((......)))))	chr9:18117323-18117558(+)$1	1	50	64	9.2017
(((......)))))	chr9:109907249-109907502(+)$1	1	91	105	9.2017
(((......)))))	chr1:165847023-165847271(+)$1	1	34	48	9.2017
(((((...))))).	chr15:79555743-79555980(-)$1	1	180	194	9.8821
(((((...))))).	chr5:124570009-124570271(-)$1	1	100	114	9.8821
(((......)))))	chr13:110844350-110844643(-)$1	1	199	213	9.2017
((((....))))).	chr3:107271774-107272028(-)$1	1	181	195	9.6682
(((((...))))).	chr11:69155749-69155994(+)$1	1	99	113	9.8821
((((....))))).	chr3:100366810-100367049(-)$1	1	167	181	9.6682
((((....))))).	chr18:34504500-34504770(-)$1	1	12	26	9.6682
((((....))))).	chr2:18764715-18764956(-)$1	1	133	147	10.1251
((((....))))).	chr9:110140606-110140860(+)$1	1	141	155	9.6682
(((((...))))).	chr11:105916222-105916468(+)$1	1	145	159	9.8821
(((......)))))	chr2:49628039-49628283(+)$1	1	27	41	9.2017
(((((...))))).	chr10:34018682-34018956(+)$1	1	222	236	9.8821
(((((...))))).	chr10:119335971-119336206(+)$1	1	92	106	10.3821
(((......)))))	chr7:7235377-7235612(-)$1	1	143	157	9.2017
((((....))))).	chrX:96661226-96661469(-)$1	1	133	147	10.1682
((((....))))).	chr19:58870931-58871176(-)$1	1	202	216	10.1047
(((((...))))).	chr18:61145875-61146177(+)$1	1	227	241	10.2051
(((......)))))	chr1:186696369-186696617(-)$1	1	95	109	9.2017
(((((...))))).	chr11:119400282-119400539(-)$1	1	42	56	9.8821
((((....))))).	chr3:8560526-8560790(+)$1	1	19	33	9.6682
(((((...))))).	chr6:86937455-86937718(+)$1	1	228	242	9.8821
((((....))))).	chr12:11332842-11333088(-)$1	1	166	180	9.9912
((((....))))).	chr17:37210548-37210814(+)$1	1	113	127	10.1047
((((....))))).	chr5:65863869-65864104(-)$1	1	18	32	9.6682
((((....))))).	chr10:57236016-57236273(-)$1	1	58	72	10.1251
((((....))))))	chr19:20717399-20717640(+)$1	1	117	131	9.4372
(((((...))))))	chr19:32899039-32899283(+)$1	1	117	131	9.9764
(((......)))))	chr8:124124022-124124257(-)$1	1	103	117	9.2017
(((((...))))).	chr6:108500443-108500706(+)$1	1	192	206	10.3390
(((......)))))	chr6:115224767-115225019(+)$1	1	59	73	9.2017
(((((...))))).	chr7:91398354-91398593(-)$1	1	94	108	9.8821
((((....))))).	chr7:66561836-66562082(+)$1	1	155	169	9.6682
((((....)))))(	chr12:8758937-8759200(+)$1	1	188	202	9.7516
((((....))))).	chr2:135298384-135298643(+)$1	1	192	206	9.6590
((((....))))).	chr14:120829821-120830077(+)$1	1	97	111	10.1682
((((....)))))(	chr17:87397467-87397705(+)$1	1	1	15	9.1451
(((......)))))	chr11:41945344-41945595(-)$1	1	37	51	9.2017
(((......)))))	chr15:74554052-74554296(+)$1	1	178	192	9.2017
(((((...))))).	chr9:113885607-113885863(+)$1	1	107	121	10.3390
((((....)))))(	chr18:64432505-64432751(+)$1	1	164	178	9.8666
((((....))))).	chr4:86630781-86631037(-)$1	1	21	35	9.6682
((((....))))).	chr17:87832784-87833026(-)$1	1	30	44	10.1251
(((((...))))))	chr11:106118590-106118825(+)$1	1	25	39	10.0805
((((....))))).	chr15:53047161-53047398(-)$1	1	37	51	9.6682
(((((...))))).	chr7:106603330-106603565(+)$1	1	94	108	10.2051
(((((...))))).	chr11:90139073-90139323(+)$1	1	62	76	10.3186
(((......)))))	chr19:41287280-41287515(-)$1	1	132	146	9.2017
(((((...))))).	chr16:29652402-29652664(+)$1	1	115	129	10.3821
(((((...))))))	chr12:83097836-83098082(+)$1	1	73	87	9.5053
(((((...))))).	chrX:69217246-69217525(+)$1	1	157	171	10.3186
((((....))))).	chr3:19968893-19969128(+)$1	1	106	120	9.6682
(((......)))))	chr8:71636369-71636642(+)$1	1	51	65	9.2017
(((((...))))).	chrX:67596350-67596618(-)$1	1	47	61	9.9962

#PSSM
e : 1.00	
e : 1.00	
e : 1.00	
e : 0.75	o : 0.24	
m : 0.41	e : 0.34	o : 0.24	
m : 0.41	l : 0.34	o : 0.24	
m : 0.41	l : 0.34	o : 0.24	
m : 0.41	l : 0.34	o : 0.24	
e : 0.75	o : 0.24	
e : 1.00	
e : 1.00	
e : 1.00	
e : 1.00	
: : 0.31	e : 0.27	] : 0.08	2 : 0.06	3 : 0.06	4 : 0.06	h : 0.01	b : 0.01	d : 0.01	5 : 0.01	D : 0.01	E : 0.01	0 : 0.01	

#score	565.3773761508812
#seq	58
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_UTR_m1_run2.txt

#BEAR
dddd!!ccc[cccooooooccc]cccdddd]hh	chr2:121283287-121283508(+)$1	221	93	126	15.4354
dddd!!gggggggooooooggggggg22dddd:	chr7:107475465-107475685(-)$1	220	16	49	14.6482
a[a[ccc!!ddddooooooddddccc]a]a]bb	chr6:127443582-127443802(+)$1	220	63	96	15.2144
eeeee!!dddd[aooooooadddd22eeeeedd	chr1:162129692-162129912(+)$1	220	122	155	13.4848
eee!!ccc[ddddoooooodddd22ccc22eee	chr15:76371488-76371708(+)$1	220	17	50	14.2328
ff==========[annnnna]==========22	chr13:104608834-104609057(-)$1	223	93	126	12.1668
dd####gggggggooooooggggggg333dddd	chr9:114421416-114421636(-)$1	220	186	219	15.9991
!!ggggggg!!bboooooobb]ggggggg]ccc	chr11:6305989-6306209(+)$1	220	4	37	16.0552
e[ggggggg!!bboooooobb22ggggggg]ee	chr12:52476151-52476371(+)$1	220	4	37	15.5896
##ggggggg[ccclllcccggggggg22ggggg	chr13:53428296-53428516(-)$1	220	134	167	11.5299
ccc"""a!!ddddoooooodddd22a333ccc:	chr6:88454094-88454314(-)$1	220	169	202	15.5519
eee!!ccc!!ccc[aooooooa]ccc22ccc33	chr13:100185018-100185238(+)$1	220	114	147	14.3850
:ggggggg!!bboooooobb333gggggggeee	chr13:73457381-73457601(-)$1	220	17	50	13.1702
eeccc[ccc!!bboooooobb22ccc22ccc33	chr11:77350311-77350546(-)$1	235	113	146	15.5073
iiiiiii####cccmmmmccc22iiiiiiiiid	chr1:122009792-122010012(-)$1	220	39	72	11.1376
::ggggggg[cccooooooccc]ggggggg:::	chr18:49857378-49857601(-)$1	223	187	220	12.9194
Feeeee[ccccccooooooccc]ccc]eeeeeh	chr2:106539373-106539593(+)$1	220	108	141	14.9381
a[cccdddd[cccoooooocccdddd22ccca3	chr2:156133225-156133453(+)$1	228	120	153	15.3539
fffffeeeeecccooooooccc]eeeee]ffff	chr4:130066858-130067078(+)$1	220	50	83	14.2071
g"""eeeee[cccooooooccc22eeeee22gg	chr6:29326332-29326552(+)$1	220	54	87	15.5374
ddd[bb####cccooooooccc22bb22dddd2	chr18:64676022-64676242(-)$1	220	59	92	15.1409
dd!!dddd!!cccooooooccc]dddd]dddd5	chr8:40134382-40134603(+)$1	221	71	104	14.8082
:ffffff!!ddddoooooodddd333ffffff:	chr5:124452402-124452632(+)$1	230	157	190	12.6417
d"""iiiiiiiiiooooooiiiiiiiiidddd:	chr2:26447124-26447344(+)$1	220	187	220	15.4707
=======####bboooooobb333=========	chr2:155673382-155673602(-)$1	220	67	100	17.0984
c[eeeee"""cccnnnnnccc4444eeeeeccc	chr11:100898043-100898263(+)$1	220	86	119	11.0328
ee####bb[ddddoooooodddd]bbeeeee33	chr7:105363244-105363464(-)$1	220	90	123	14.3870
[bbgggggggcccooooooccc]ggggggg333	chr16:21995330-21995562(-)$1	232	121	154	16.8728
#bb[bb"""ddddoooooodddd]bb]bb22dd	chr3:85931837-85932057(+)$1	220	174	207	12.9062
dddd[bb!!ddddooooooddddbb]ddddfff	chr11:103845907-103846127(+)$1	220	99	132	12.8303
c!!ccc[ffffffooooooffffff333ccc22	chr11:86903404-86903624(-)$1	220	116	149	14.6040
ggggggg"""cccooooooccc22ggggggg::	chr8:123102476-123102708(+)$1	232	8	41	15.5775
=========[cccooooooccc]==========	chr2:38583142-38583366(-)$1	224	176	209	18.4249
###ffffff[cccooooooccc22ffffff444	chr3:35792581-35792801(-)$1	220	125	158	15.2683
fff!!a!!eeeeeooooooeeeee22a4444ff	chr2:148517892-148518114(+)$1	222	23	56	13.9879
ggggg[eeeeebboooooobb]eeeee]ggggg	chr1:136514333-136514553(+)$1	220	92	125	14.4029
bb]a]eeeeecccooooooccc:ccc[ccc"""	chr11:8332305-8332525(-)$1	220	150	183	12.3112
=============oooooo=============:	chr11:32645021-32645241(+)$1	220	64	97	16.8561
!!ccc[a[eeeeeooooooeeeeea]ccciiii	chrX:101476686-101476909(-)$1	223	113	146	14.5774
dddd!!ccc[cccooooooccc]ccc22dddd3	chr9:35312362-35312596(+)$1	234	130	163	16.4892
cc$$$$$ffffffooooooffffffccc]ccc:	chr17:43804399-43804619(+)$1	220	165	198	12.7573
####iiiiiiiiiooooooiiiiiiiii88888	chr19:10270997-10271225(+)$1	228	170	203	14.1720
ccc[a[ccc[cccoooooocccccc333a]ccc	chr1:34249418-34249638(+)$1	220	1	34	17.1560
D==========bboooooobb]==========:	chr5:38918773-38918993(-)$1	220	34	67	15.4381
========!!cccooooooccc]==========	chr10:61570996-61571228(-)$1	232	123	156	18.5458
gggg"""ffffffooooooffffff]ggggggg	chr6:119797803-119798023(-)$1	220	73	106	14.5666
cc####gggggggooooooggggggg4444ccc	chr12:103808111-103808350(-)$1	239	136	169	16.2263
eeeee[a[eeeeeooooooeeeee]a]eeeee:	chr16:89788720-89788947(-)$1	227	112	145	13.2846
!!bb[ccc[ddddoooooodddd]ccc]bb]cc	chr10:62044684-62044918(-)$1	234	43	76	14.4762
bb!!eeeee[cccooooooccc]eeeee333bb	chr17:6236461-6236681(+)$1	220	97	130	15.4603
iiii"""ccc[bboooooobbccc333iiiiii	chr5:122624794-122625014(+)$1	220	23	56	16.0357
[eeeee[dddd[aooooooa]dddd]eeeee]c	chr11:88157333-88157553(-)$1	220	92	125	13.6335

#otherMatches

#Seq PSSM
GGCUAUGUCCGUCAUUGGAGACAGACGGUCCAG	chr2:121283287-121283508(+)$1	221	93	126	15.4354
ACAAAGCCACAGGCUAAAUCCUGUGGAAUUGUU	chr7:107475465-107475685(-)$1	220	16	49	14.6482
GUUGUAGUUGAGGUUGUUUCCUUCUAGACCUGU	chr6:127443582-127443802(+)$1	220	63	96	15.2144
AGGGUCUAGUAUGUUUAGUCUACUUAACCCUGA	chr1:162129692-162129912(+)$1	220	122	155	13.4848
UACCGAGUAUUUCGCAGCGGAAAGGACUGUGUG	chr15:76371488-76371708(+)$1	220	17	50	14.2328
AUGAAUAUAGUAGAAGAGAUGUGCUGUAUUUUG	chr13:104608834-104609057(-)$1	223	93	126	12.1668
CUCUUCCCUCCUGAAGGCCUAGGAGGCACAGGA	chr9:114421416-114421636(-)$1	220	186	219	15.9991
AAAGCGCCUGGGCCUGCAAGCAGGGUGCUGGCC	chr11:6305989-6306209(+)$1	220	4	37	16.0552
CCUAUGACUUUGCUUUAGUGUUUAGUCAUAAGA	chr12:52476151-52476371(+)$1	220	4	37	15.5896
GACAUGUGCCACGGAUCGUGUGCAUGGAAGGCC	chr13:53428296-53428516(-)$1	220	134	167	11.5299
CUGGGUCCACCACACCUCAGUGGAAGUAGCAGA	chr6:88454094-88454314(-)$1	220	169	202	15.5519
CUGGGUGCAGACUGGGAAUAUCGGGUGAGCGUG	chr13:100185018-100185238(+)$1	220	114	147	14.3850
ACCUGAUUUUCAAUGUGCUGUCUAAUUGGGAUU	chr13:73457381-73457601(-)$1	220	17	50	13.1702
GAUGCCAUAUUUGAACUGCCAUCUAUUAGCAUA	chr11:77350311-77350546(-)$1	235	113	146	15.5073
UAAUGUAGAUGAUAUGGCUGUGAUACAUUAGGG	chr1:122009792-122010012(-)$1	220	39	72	11.1376
UAAGUGACACAGAGGGCAGUUUAUGUCAUUAAG	chr18:49857378-49857601(-)$1	223	187	220	12.9194
AGAGGUUGGCUGAAACCCAUCAUGCCCGCUUCC	chr2:106539373-106539593(+)$1	220	108	141	14.9381
GACAGGGCUCUCUUGAUCUGGAAGCCAACUGCA	chr2:156133225-156133453(+)$1	228	120	153	15.3539
AUGGUGUCUGGGCUGACCUGCCUCAGAUGACCA	chr4:130066858-130067078(+)$1	220	50	83	14.2071
UCUGCUAGGAUGGCAUCUUCUGGACCUGGGUGC	chr6:29326332-29326552(+)$1	220	54	87	15.5374
UGAUGCAACGCCUCAGUCAAGGAAGCCUUCAGU	chr18:64676022-64676242(-)$1	220	59	92	15.1409
UACUCAGGCACCAUUGCUUUGGCCCUGUUAGUG	chr8:40134382-40134603(+)$1	221	71	104	14.8082
GACCUGUGACCCUUGAGCCAGGGAGAGCAGGUA	chr5:124452402-124452632(+)$1	230	157	190	12.6417
CAAAUCAUGGGACGGUUGAGUUUUAUGGGGAAG	chr2:26447124-26447344(+)$1	220	187	220	15.4707
ggcaggcagagcuacacagagaaagccugucuu	chr2:155673382-155673602(-)$1	220	67	100	17.0984
GCUUCCAGAACAUAGUAGAUGCUUAUGGGAUCG	chr11:100898043-100898263(+)$1	220	86	119	11.0328
GCUGUAGAGUUUUUGUUUUAGGAGUUGCCUUGA	chr7:105363244-105363464(-)$1	220	90	123	14.3870
ugcugaggcuauguuuuuucaucaguuucaugu	chr16:21995330-21995562(-)$1	232	121	154	16.8728
UUGGCAUAUGAUUGCACUUGAUUUUGGCAUUUA	chr3:85931837-85932057(+)$1	220	174	207	12.9062
GUUAAUGUAGGAGAUGAUGUUCCCAGUGGCCCC	chr11:103845907-103846127(+)$1	220	99	132	12.8303
UAUUUCCAGAAAUCCCAUUAUUUCUAUUGAAUG	chr11:86903404-86903624(-)$1	220	116	149	14.6040
UAAGGGAUAUCCGAGGUGACGGUUUCCCUUGCA	chr8:123102476-123102708(+)$1	232	8	41	15.5775
AUAUAUUUAUUUCACGACAGAGUUGAAUGUAUG	chr2:38583142-38583366(-)$1	224	176	209	18.4249
UUUCAGAUUGAUUGAUUCAGAUAUGAUUUGUUU	chr3:35792581-35792801(-)$1	220	125	158	15.2683
gcugagaacccuugAACUAGAGGGGACCAGAAG	chr2:148517892-148518114(+)$1	222	23	56	13.9879
AGGCCCGCUGGCUGGAAGAGGUUCAGCAGGCUU	chr1:136514333-136514553(+)$1	220	92	125	14.4029
UGGGGGUGGGGGGAGAGGGCCUAAUUAGAAAUC	chr11:8332305-8332525(-)$1	220	150	183	12.3112
GGCUAUAUUACCUCUGCACAGGUGAUAUAGCUA	chr11:32645021-32645241(+)$1	220	64	97	16.8561
GAAGAUGAUGGGGUUCAUUUCUCACCUCUCuuu	chrX:101476686-101476909(-)$1	223	113	146	14.5774
GACUCAGAAAGAAAAUUAAUUCCUUCAUGGUCC	chr9:35312362-35312596(+)$1	234	130	163	16.4892
UUAUGGAGUUAUUCUCACCAAUAGCAAUCGCCG	chr17:43804399-43804619(+)$1	220	165	198	12.7573
CACCUCUGCUAUUGUAGAAAGUGGCAGAAUAUC	chr19:10270997-10271225(+)$1	228	170	203	14.1720
GAAGUAUCUUGAAAAGCAGUUUAGACAAAGUUC	chr1:34249418-34249638(+)$1	220	1	34	17.1560
CCCCUUCCUGCCUGCUCUGGGAGUAGGGAGGGC	chr5:38918773-38918993(-)$1	220	34	67	15.4381
uggccuggaacucaccauggagaccaggucggc	chr10:61570996-61571228(-)$1	232	123	156	18.5458
GCUCCCGGCCCUGGCUGGGCAGGGCAGAGCGCC	chr6:119797803-119798023(-)$1	220	73	106	14.5666
CUGAUUUUCUGAUGUUAUGAUCGGAAUGAAGGG	chr12:103808111-103808350(-)$1	239	136	169	16.2263
AAAGGGUGGUCGUCUCUGUACGAUGAGCCUUUA	chr16:89788720-89788947(-)$1	227	112	145	13.2846
CCAUGGAUCUGCCUAUCUUGGUGUGUCGAUCUU	chr10:62044684-62044918(-)$1	234	43	76	14.4762
AGCUUGGAUAUAGAGUGUACUGCAUUUACUUCU	chr17:6236461-6236681(+)$1	220	97	130	15.4603
GGCCAGGGCAUCGAGGCUGCGUGCACAGGCCGC	chr5:122624794-122625014(+)$1	220	23	56	16.0357
UAAGGACGGCCGUGUUUUGAGGGUCUUCCUUUC	chr11:88157333-88157553(-)$1	220	92	125	13.6335

#DB
((((..(((.(((......))).))))))).))	chr2:121283287-121283508(+)$1	1	93	126	15.4354
((((..(((((((......)))))))..)))).	chr7:107475465-107475685(-)$1	1	16	49	14.6482
(.(.(((..((((......))))))).).).))	chr6:127443582-127443802(+)$1	1	63	96	15.2144
(((((..((((.(......)))))..)))))((	chr1:162129692-162129912(+)$1	1	122	155	13.4848
(((..(((.((((......))))..)))..)))	chr15:76371488-76371708(+)$1	1	17	50	14.2328
((((((((((((.(.....).))))))))))..	chr13:104608834-104609057(-)$1	1	93	126	12.1668
((....(((((((......)))))))...))))	chr9:114421416-114421636(-)$1	1	186	219	15.9991
..(((((((..((......)).))))))).)))	chr11:6305989-6306209(+)$1	1	4	37	16.0552
(.(((((((..((......))..))))))).))	chr12:52476151-52476371(+)$1	1	4	37	15.5896
..(((((((.(((...))))))))))..)))))	chr13:53428296-53428516(-)$1	1	134	167	11.5299
(((...(..((((......))))..)...))).	chr6:88454094-88454314(-)$1	1	169	202	15.5519
(((..(((..(((.(......).)))..)))..	chr13:100185018-100185238(+)$1	1	114	147	14.3850
.(((((((..((......))...)))))))(((	chr13:73457381-73457601(-)$1	1	17	50	13.1702
(((((.(((..((......))..)))..)))..	chr11:77350311-77350546(-)$1	1	113	146	15.5073
(((((((....(((....)))..))))))))))	chr1:122009792-122010012(-)$1	1	39	72	11.1376
..(((((((.(((......))).)))))))...	chr18:49857378-49857601(-)$1	1	187	220	12.9194
((((((.((((((......))).))).)))))(	chr2:106539373-106539593(+)$1	1	108	141	14.9381
(.(((((((.(((......)))))))..)))).	chr2:156133225-156133453(+)$1	1	120	153	15.3539
(((((((((((((......))).))))).))))	chr4:130066858-130067078(+)$1	1	50	83	14.2071
(...(((((.(((......)))..)))))..))	chr6:29326332-29326552(+)$1	1	54	87	15.5374
(((.((....(((......)))..))..)))).	chr18:64676022-64676242(-)$1	1	59	92	15.1409
((..((((..(((......))).)))).)))).	chr8:40134382-40134603(+)$1	1	71	104	14.8082
.((((((..((((......))))...)))))).	chr5:124452402-124452632(+)$1	1	157	190	12.6417
(...(((((((((......))))))))))))).	chr2:26447124-26447344(+)$1	1	187	220	15.4707
(((((((....((......))...)))))))))	chr2:155673382-155673602(-)$1	1	67	100	17.0984
(.(((((...(((.....)))....))))))))	chr11:100898043-100898263(+)$1	1	86	119	11.0328
((....((.((((......)))).)))))))..	chr7:105363244-105363464(-)$1	1	90	123	14.3870
.((((((((((((......))).)))))))...	chr16:21995330-21995562(-)$1	1	121	154	16.8728
.((.((...((((......)))).)).))..))	chr3:85931837-85932057(+)$1	1	174	207	12.9062
((((.((..((((......)))))).)))))))	chr11:103845907-103846127(+)$1	1	99	132	12.8303
(..(((.((((((......))))))...)))..	chr11:86903404-86903624(-)$1	1	116	149	14.6040
(((((((...(((......)))..)))))))..	chr8:123102476-123102708(+)$1	1	8	41	15.5775
(((((((((.(((......))).))))))))))	chr2:38583142-38583366(-)$1	1	176	209	18.4249
...((((((.(((......)))..))))))...	chr3:35792581-35792801(-)$1	1	125	158	15.2683
(((..(..(((((......)))))..)....))	chr2:148517892-148518114(+)$1	1	23	56	13.9879
(((((.(((((((......)).))))).)))))	chr1:136514333-136514553(+)$1	1	92	125	14.4029
)).).)))))(((......))).(((.(((...	chr11:8332305-8332525(-)$1	1	150	183	12.3112
(((((((((((((......))))))))))))).	chr11:32645021-32645241(+)$1	1	64	97	16.8561
..(((.(.(((((......)))))).)))))))	chrX:101476686-101476909(-)$1	1	113	146	14.5774
((((..(((.(((......))).)))..)))).	chr9:35312362-35312596(+)$1	1	130	163	16.4892
((.....((((((......))))))))).))).	chr17:43804399-43804619(+)$1	1	165	198	12.7573
....(((((((((......))))))))).....	chr19:10270997-10271225(+)$1	1	170	203	14.1720
(((.(.(((.(((......))))))...).)))	chr1:34249418-34249638(+)$1	1	1	34	17.1560
(((((((((((((......)).)))))))))).	chr5:38918773-38918993(-)$1	1	34	67	15.4381
((((((((..(((......))).))))))))))	chr10:61570996-61571228(-)$1	1	123	156	18.5458
((((...((((((......)))))).)))))))	chr6:119797803-119798023(-)$1	1	73	106	14.5666
((....(((((((......)))))))....)))	chr12:103808111-103808350(-)$1	1	136	169	16.2263
(((((.(.(((((......))))).).))))).	chr16:89788720-89788947(-)$1	1	112	145	13.2846
..((.(((.((((......)))).))).)).))	chr10:62044684-62044918(-)$1	1	43	76	14.4762
((..(((((.(((......))).)))))...))	chr17:6236461-6236681(+)$1	1	97	130	15.4603
((((...(((.((......)))))...))))))	chr5:122624794-122625014(+)$1	1	23	56	16.0357
.(((((.((((.(......).)))).))))).)	chr11:88157333-88157553(-)$1	1	92	125	13.6335

#PSSM
d : 0.15	e : 0.13	c : 0.11	# : 0.07	g : 0.07	= : 0.07	f : 0.05	! : 0.05	: : 0.05	a : 0.03	i : 0.03	[ : 0.03	b : 0.03	F : 0.01	D : 0.01	
e : 0.15	d : 0.13	= : 0.09	[ : 0.07	f : 0.07	! : 0.07	c : 0.07	g : 0.07	b : 0.07	# : 0.05	i : 0.03	" : 0.03	: : 0.01	
g : 0.15	e : 0.13	= : 0.11	d : 0.09	# : 0.09	c : 0.09	f : 0.05	! : 0.05	b : 0.05	i : 0.03	" : 0.03	a : 0.01	] : 0.01	$ : 0.01	
g : 0.17	= : 0.11	e : 0.09	! : 0.09	d : 0.07	[ : 0.07	# : 0.07	c : 0.07	" : 0.05	f : 0.05	i : 0.03	a : 0.01	$ : 0.01	b : 0.01	
g : 0.15	e : 0.13	! : 0.11	= : 0.11	c : 0.09	# : 0.05	" : 0.05	i : 0.05	f : 0.05	b : 0.03	[ : 0.03	d : 0.01	] : 0.01	$ : 0.01	a : 0.01	
g : 0.13	e : 0.13	= : 0.11	c : 0.09	[ : 0.09	! : 0.07	# : 0.05	" : 0.05	i : 0.05	b : 0.05	d : 0.03	f : 0.03	a : 0.01	$ : 0.01	
g : 0.19	c : 0.15	= : 0.11	e : 0.11	a : 0.05	i : 0.05	[ : 0.05	" : 0.05	! : 0.03	d : 0.03	f : 0.03	b : 0.03	# : 0.01	$ : 0.01	
c : 0.17	g : 0.17	! : 0.09	= : 0.09	e : 0.09	d : 0.07	f : 0.07	# : 0.05	" : 0.05	i : 0.03	[ : 0.03	b : 0.01	
g : 0.15	! : 0.15	e : 0.15	c : 0.11	= : 0.07	f : 0.07	d : 0.05	[ : 0.05	# : 0.05	" : 0.05	i : 0.03	
[ : 0.19	d : 0.19	! : 0.13	e : 0.11	g : 0.07	= : 0.05	# : 0.05	f : 0.05	c : 0.03	i : 0.03	" : 0.03	
c : 0.38	d : 0.19	e : 0.07	g : 0.05	= : 0.05	! : 0.05	f : 0.05	# : 0.03	i : 0.03	b : 0.01	[ : 0.01	
c : 0.40	d : 0.15	b : 0.15	g : 0.05	f : 0.05	e : 0.05	[ : 0.03	= : 0.03	i : 0.03	
c : 0.40	d : 0.15	b : 0.13	g : 0.05	f : 0.05	e : 0.05	a : 0.03	i : 0.03	[ : 0.01	o : 0.01	= : 0.01	
o : 0.90	a : 0.01	l : 0.01	[ : 0.01	c : 0.01	n : 0.01	
o : 0.90	n : 0.03	l : 0.01	a : 0.01	m : 0.01	
o : 0.92	n : 0.03	l : 0.01	m : 0.01	
o : 0.92	n : 0.03	c : 0.01	m : 0.01	
o : 0.92	n : 0.03	c : 0.01	m : 0.01	
o : 0.90	c : 0.05	n : 0.01	b : 0.01	
c : 0.36	d : 0.15	b : 0.15	g : 0.07	a : 0.05	f : 0.05	e : 0.05	i : 0.03	o : 0.01	= : 0.01	
c : 0.36	d : 0.17	b : 0.13	g : 0.07	f : 0.05	e : 0.05	] : 0.03	i : 0.03	o : 0.01	3 : 0.01	= : 0.01	
c : 0.34	d : 0.19	g : 0.07	] : 0.05	2 : 0.05	f : 0.05	e : 0.05	= : 0.03	3 : 0.03	i : 0.03	a : 0.01	4 : 0.01	
] : 0.21	d : 0.21	2 : 0.13	g : 0.09	e : 0.07	= : 0.05	f : 0.05	3 : 0.03	i : 0.03	c : 0.03	4 : 0.01	: : 0.01	
c : 0.17	g : 0.17	2 : 0.11	e : 0.11	= : 0.09	d : 0.07	i : 0.05	] : 0.05	f : 0.05	3 : 0.03	4 : 0.01	b : 0.01	
g : 0.19	c : 0.17	= : 0.11	2 : 0.07	e : 0.07	b : 0.07	f : 0.07	i : 0.05	d : 0.05	3 : 0.03	4 : 0.01	a : 0.01	] : 0.01	
c : 0.19	g : 0.19	= : 0.11	e : 0.09	3 : 0.07	] : 0.07	i : 0.05	b : 0.05	2 : 0.03	a : 0.03	d : 0.03	f : 0.01	
e : 0.15	2 : 0.13	g : 0.13	= : 0.11	3 : 0.09	] : 0.07	c : 0.07	d : 0.05	i : 0.05	f : 0.03	a : 0.01	[ : 0.01	4 : 0.01	
e : 0.17	2 : 0.13	g : 0.13	= : 0.11	c : 0.07	3 : 0.07	i : 0.07	] : 0.05	d : 0.03	f : 0.03	4 : 0.03	a : 0.01	b : 0.01	
g : 0.17	d : 0.13	e : 0.13	= : 0.11	c : 0.11	] : 0.05	3 : 0.05	i : 0.03	f : 0.03	b : 0.03	4 : 0.03	2 : 0.01	8 : 0.01	a : 0.01	
d : 0.15	g : 0.15	c : 0.13	e : 0.11	= : 0.11	2 : 0.05	i : 0.05	f : 0.05	] : 0.03	4 : 0.03	a : 0.01	8 : 0.01	b : 0.01	3 : 0.01	
c : 0.19	e : 0.13	d : 0.11	= : 0.11	] : 0.07	g : 0.07	i : 0.05	f : 0.05	2 : 0.03	3 : 0.03	4 : 0.03	: : 0.01	" : 0.01	8 : 0.01	
d : 0.15	c : 0.13	e : 0.09	= : 0.09	g : 0.07	3 : 0.07	f : 0.07	i : 0.05	b : 0.03	2 : 0.03	: : 0.03	h : 0.01	a : 0.01	4 : 0.01	" : 0.01	8 : 0.01	] : 0.01	
: : 0.19	c : 0.11	3 : 0.11	d : 0.07	g : 0.07	e : 0.05	2 : 0.05	f : 0.05	= : 0.05	h : 0.03	b : 0.03	i : 0.03	5 : 0.01	4 : 0.01	" : 0.01	8 : 0.01	

#score	764.5076989284197
#seq	52
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_UTR_m2_run1.txt

#BEAR
hhhhhhhqqqqqqqqhhhhhhh	chr1:45432382-45432652(-)$1	270	32	54	13.6126
dddd[bbqqqqqqqqbb22ddd	chr15:76912491-76912744(-)$1	253	14	36	13.9269
cccddddqqqqqqqqdddd]cc	chr1:94755595-94755860(+)$1	265	179	201	14.6310
!!eeeeeqqqqqqqqeeeee22	chr9:35314119-35314355(+)$1	236	33	55	14.3646
dd!!cccqqqqqqqqcccdddd	chr13:56839388-56839640(+)$1	252	126	148	15.0945
gggggggqqqqqqqqggggggg	chr10:57886674-57886974(+)$1	300	91	113	15.0877
hhhhhhhqqqqqqqqhhhhhhh	chr3:57261336-57261574(-)$1	238	112	134	13.6126
:ccc[bbqqqqqqqqbbccccc	chr3:53281764-53282025(+)$1	261	17	39	13.8608
c!!ddddqqqqqqqqddddccc	chr7:17081402-17081644(-)$1	242	182	204	14.8453
!ccc[bbqqqqqqqqbbccc]d	chr11:52221354-52221593(+)$1	239	147	169	15.0003
$ffffffqqqqqqqqfffffff	chr7:30971958-30972213(-)$1	255	208	230	13.1610
ff[ddddqqqqqqqqdddd]ff	chr4:40152063-40152305(-)$1	242	78	100	14.2780
gggggggqqqqqqqqggggggg	chr15:83130917-83131157(-)$1	240	49	71	15.0877
b[eeeeeqqqqqqqqeeeeebb	chr2:32164610-32164855(-)$1	245	46	68	13.7900
ddd[cccqqqqqqqqcccdddd	chr17:10401475-10401757(-)$1	282	254	276	14.7701
c[eeeeeqqqqqqqqeeeee]c	chr18:56912511-56912824(+)$1	313	242	264	14.6307
ee[ddddqqqqqqqqdddd]ee	chr1:182919669-182919904(-)$1	235	12	34	14.4036
[ffffffqqqqqqqqffffff]	chr6:146566971-146567230(-)$1	259	110	132	13.7006
e"""cccqqqqqqqqccc22ee	chr1:74443121-74443384(+)$1	263	33	55	14.8402
hhhhhhhqqqqqqqqhhhhhhh	chrX:71481000-71481240(-)$1	240	114	136	13.6126
e[cccbbqqqqqqqqbb]ccc]	chr11:97699644-97699882(+)$1	238	162	184	14.7902
dddd[bbqqqqqqqqbb]dddd	chr13:99612127-99612402(-)$1	275	5	27	14.2224
bb"""bbqqqqqqqqbb22bb3	chr3:14871614-14871873(+)$1	259	116	138	13.5876
iiiiiiiqqqqqqqqiiiiiii	chr11:69730583-69730847(-)$1	264	173	195	15.3889
bb[ddddqqqqqqqqddddbbe	chr4:141240550-141240797(-)$1	247	160	182	13.7529
hhhhh[aqqqqqqqqahhhhhh	chr4:53634965-53635223(+)$1	258	147	169	13.9966
ee!!cccqqqqqqqqccceeee	chr4:154530031-154530304(-)$1	273	250	272	15.1575
dd!!cccqqqqqqqqccc22dd	chr13:38592617-38592864(-)$1	247	205	227	14.9524
iiiiiiiqqqqqqqqiiiiiii	chr18:60717226-60717485(+)$1	259	207	229	15.3889
====[bbqqqqqqqqbb]====	chr14:63761578-63761892(+)$1	314	167	189	15.2658
g[eeeeeqqqqqqqqeeeee22	chr3:88285229-88285544(-)$1	315	269	291	14.3225
bb[ddddqqqqqqqqdddd]bb	chr3:107544784-107545052(-)$1	268	112	134	13.8862
[ccccccqqqqqqqqccc]ccc	chr5:34694815-34695070(+)$1	255	119	141	15.4236
hhhhhhhqqqqqqqqhhhhhhh	chr11:109530585-109530838(+)$1	253	77	99	13.6126
=!!bb[aqqqqqqqqa]bb===	chr11:75227304-75227576(-)$1	272	77	99	14.1721
=======qqqqqqqq=======	chr4:63156558-63156814(-)$1	256	70	92	15.4793
ddddcccqqqqqqqqccc]ddd	chr10:95010579-95010840(-)$1	261	216	238	14.7274
bbeeeeeqqqqqqqqeeeee22	chr10:79324224-79324479(+)$1	255	34	56	13.7991
c"""cccqqqqqqqqccc4444	chr5:141098860-141099157(-)$1	297	100	122	15.2883
hheeeeeqqqqqqqqeeeee44	chr14:70580317-70580578(-)$1	261	76	98	14.2449
[dddd[aqqqqqqqqa]dddd]	chr7:108021156-108021395(-)$1	239	196	218	14.5358
[ffffffqqqqqqqqffffff]	chr17:75936402-75936640(-)$1	238	139	161	13.7006
!ccc[bbqqqqqqqqbbccc22	chr11:102264486-102264728(-)$1	242	158	180	14.7535
bb[ddddqqqqqqqqddddbb:	chr2:153593215-153593465(+)$1	250	139	161	12.8710
ii!!cccqqqqqqqqccc4444	chr12:81268832-81269071(-)$1	239	68	90	15.6415
c[a[cccqqqqqqqqccc]a]c	chr9:123500698-123500950(+)$1	252	98	120	15.5963
[aeeeeeqqqqqqqqeeeee]a	chr5:115119460-115119704(-)$1	244	214	236	14.5158
dd!!cccqqqqqqqqcccdddd	chr11:86526020-86526275(-)$1	255	71	93	15.0945
iii[cccqqqqqqqqccc22ii	chr18:36917108-36917358(+)$1	250	76	98	15.4180
ddbb[bbqqqqqqqqbb]bb]d	chr17:69638592-69638904(+)$1	312	156	178	13.4816
ffff[bbqqqqqqqqbb22fff	chr15:103028669-103028951(-)$1	282	206	228	13.6809
iiicccaqqqqqqqqa]ccc::	chr14:68351378-68351639(+)$1	261	25	47	13.3812
"""ddddqqqqqqqqddddeee	chr2:164716634-164716878(+)$1	244	210	232	14.4445
cccddddqqqqqqqqdddd]cc	chr13:100195383-100195625(-)$1	242	162	184	14.6310
bb[ddddqqqqqqqqdddd22b	chr13:98021123-98021385(+)$1	262	210	232	13.8781
=======qqqqqqqq=======	chr17:71343637-71343960(-)$1	323	275	297	15.4793
[ffffffqqqqqqqqffffff4	chr14:21851864-21852117(+)$1	253	94	116	13.6536
eeee!!aqqqqqqqqa22eeee	chr3:88548580-88548821(-)$1	241	140	162	14.0388
!ddddbbqqqqqqqqbb]dddd	chr17:21093638-21093879(+)$1	241	123	145	14.2668
hhhhh[aqqqqqqqqa]hhhhh	chr10:82657762-82658016(+)$1	254	152	174	13.9883
gggggggqqqqqqqqggggggg	chr5:32459220-32459473(+)$1	253	154	176	15.0877
fffff[aqqqqqqqqa]fffff	chr5:93603216-93603477(+)$1	261	182	204	13.7103
c[eeeeeqqqqqqqqeeeee]c	chr5:141096454-141096697(-)$1	243	56	78	14.6307
d[eeeeeqqqqqqqqeeeee]d	chr2:104267590-104267827(-)$1	237	63	85	14.4333
ccc[cccqqqqqqqqccc]ccc	chr2:153054171-153054409(-)$1	238	142	164	15.4397
bb"""bbqqqqqqqqbbbb333	chr1:72908443-72908690(-)$1	247	90	112	13.9385
gggggggqqqqqqqqggggggg	chr19:9093115-9093368(+)$1	253	174	196	15.0877
$$$ddddqqqqqqqqdddd22e	chrX:156561336-156561597(-)$1	261	225	247	13.6035
gggg[bbqqqqqqqqbbggggg	chrX:159216497-159216807(+)$1	310	52	74	15.0336
ccbbcccqqqqqqqqccc6666	chr11:95136292-95136534(-)$1	242	87	109	12.6415
eee!!bbqqqqqqqqbb22eee	chr1:158360119-158360365(-)$1	246	131	153	14.1609
ddddcccqqqqqqqqccc]ddd	chr11:100576886-100577129(-)$1	243	220	242	14.7274

#otherMatches

#Seq PSSM
UGAAUACGUUGCUUAGUAUUUA	chr1:45432382-45432652(-)$1	270	32	54	13.6126
GCAAUUGACACAUACCAUCUUG	chr15:76912491-76912744(-)$1	253	14	36	13.9269
UUCUCUAGUAUGACGUAGGUGA	chr1:94755595-94755860(+)$1	265	179	201	14.6310
gauauauaaauauaaauauaaa	chr9:35314119-35314355(+)$1	236	33	55	14.3646
AGUUAGUUACUAUGUGCUCUGU	chr13:56839388-56839640(+)$1	252	126	148	15.0945
AAAGCACUCAUUCCCGUGCUUU	chr10:57886674-57886974(+)$1	300	91	113	15.0877
UUUUUAAUUUUUAUUUUGAAAG	chr3:57261336-57261574(-)$1	238	112	134	13.6126
AGUGAGACAUUUGCUUCCACGU	chr3:53281764-53282025(+)$1	261	17	39	13.8608
GUUGCAGUUGGUCCCCUGCCCU	chr7:17081402-17081644(-)$1	242	182	204	14.8453
UCUGGCAAAAGAGACUGCAGUU	chr11:52221354-52221593(+)$1	239	147	169	15.0003
CGGACUCUGAGUGCUGAGUCCA	chr7:30971958-30972213(-)$1	255	208	230	13.1610
UUAAAAUGACAUAUAAUUUAAA	chr4:40152063-40152305(-)$1	242	78	100	14.2780
UGCCAGGCUGUCCAACCUGGUA	chr15:83130917-83131157(-)$1	240	49	71	15.0877
GUGUGGCAAGAGAGGGCCACCA	chr2:32164610-32164855(-)$1	245	46	68	13.7900
AAAUGUAGCAUUUUAUACUUUC	chr17:10401475-10401757(-)$1	282	254	276	14.7701
CAAUAUAUGAACUUUUGUAUGG	chr18:56912511-56912824(+)$1	313	242	264	14.6307
CAUGGCUUUAGCAGCAGCCCUG	chr1:182919669-182919904(-)$1	235	12	34	14.4036
UUAUGUGCCCGUGCACACAUAC	chr6:146566971-146567230(-)$1	259	110	132	13.7006
UUUAGGUGCCUCUAAACCCCAG	chr1:74443121-74443384(+)$1	263	33	55	14.8402
GUGAUGGCACACACACCAUUAC	chrX:71481000-71481240(-)$1	240	114	136	13.6126
AAGUGACCCUGUGAAGUCCGCC	chr11:97699644-97699882(+)$1	238	162	184	14.7902
GCUAGACUCAAGGGUGUGUGGU	chr13:99612127-99612402(-)$1	275	5	27	14.2224
UCCCUACUCCAAGCUGUCCGAC	chr3:14871614-14871873(+)$1	259	116	138	13.5876
UCCCUUGGCCAGGAAUGAGGGA	chr11:69730583-69730847(-)$1	264	173	195	15.3889
CUCGGGAAUUGCAGCUCCCAGA	chr4:141240550-141240797(-)$1	247	160	182	13.7529
UACAGAGAUAACUGCCCUGUAG	chr4:53634965-53635223(+)$1	258	147	169	13.9966
CUCCGCUCUAGUCCUAGCAGGG	chr4:154530031-154530304(-)$1	273	250	272	15.1575
AUCUCUCUAAUGAUUGAGCAGU	chr13:38592617-38592864(-)$1	247	205	227	14.9524
AGAUAGAAAAUAGUCUUUGUUU	chr18:60717226-60717485(+)$1	259	207	229	15.3889
GCUUUGUGUACCUCAACCAAGU	chr14:63761578-63761892(+)$1	314	167	189	15.2658
AAUGAUGGAGGGCAAUGUCAAG	chr3:88285229-88285544(-)$1	315	269	291	14.3225
GAGCUAUGAAUGAGAAUGGGUC	chr3:107544784-107545052(-)$1	268	112	134	13.8862
AUGUCUGCUCAAGCAUAGUAUA	chr5:34694815-34695070(+)$1	255	119	141	15.4236
UAGACUUUUCAAGAUAAGUCUA	chr11:109530585-109530838(+)$1	253	77	99	13.6126
UUUGGACGAGGACAGGACCGUG	chr11:75227304-75227576(-)$1	272	77	99	14.1721
GGCUGCGCCCCCCACUGCGGCC	chr4:63156558-63156814(-)$1	256	70	92	15.4793
UACUCAUUCUAAAUUAUGUAGU	chr10:95010579-95010840(-)$1	261	216	238	14.7274
ACAGGCACCACUCCUUGCCUCA	chr10:79324224-79324479(+)$1	255	34	56	13.7991
UUCAUGCUGCCCCUUGCACUCU	chr5:141098860-141099157(-)$1	297	100	122	15.2883
GAAGGCCCAAUGACAGGCCUUG	chr14:70580317-70580578(-)$1	261	76	98	14.2449
GGUUAGCAUUUCCAAGGUGACG	chr7:108021156-108021395(-)$1	239	196	218	14.5358
AAGCUGUGAAAGAAAGUGGCUG	chr17:75936402-75936640(-)$1	238	139	161	13.7006
UGAUCGCCCUUUUUUGUAUCCC	chr11:102264486-102264728(-)$1	242	158	180	14.7535
GCCUGAGGCGAAGAGCUCAGCU	chr2:153593215-153593465(+)$1	250	139	161	12.8710
UCCACCAGUCUUAAAUGGAAAA	chr12:81268832-81269071(-)$1	239	68	90	15.6415
AUUGUGGGAAAUACACUAGACU	chr9:123500698-123500950(+)$1	252	98	120	15.5963
GCCCAAUGAGGAACAAUUGGUG	chr5:115119460-115119704(-)$1	244	214	236	14.5158
CAAAACUAACAGAUCAGUUGCC	chr11:86526020-86526275(-)$1	255	71	93	15.0945
AAAUGUUUAUUGUAUAACUCUU	chr18:36917108-36917358(+)$1	250	76	98	15.4180
UUCUCCUCAACCACAAGCAGUA	chr17:69638592-69638904(+)$1	312	156	178	13.4816
UCUUUCUUCUUGUAUAGUUGAG	chr15:103028669-103028951(-)$1	282	206	228	13.6809
AAUUCCCAACCACCAGAGGAUC	chr14:68351378-68351639(+)$1	261	25	47	13.3812
AUUUGUAAAAGGAAAUACAGAA	chr2:164716634-164716878(+)$1	244	210	232	14.4445
CUAGGUAUUGGCAUUUAUCAUa	chr13:100195383-100195625(-)$1	242	162	184	14.6310
AAGUGUCGGGACAGAGACAGAU	chr13:98021123-98021385(+)$1	262	210	232	13.8781
GAAAGUUAUCCACUCAAUUUUU	chr17:71343637-71343960(-)$1	323	275	297	15.4793
ucuugaacuuauggauucaagu	chr14:21851864-21852117(+)$1	253	94	116	13.6536
GUGGACCUUGUUAAUGCGCCAC	chr3:88548580-88548821(-)$1	241	140	162	14.0388
CAAUGUCAAGAGUGAGAUCAUU	chr17:21093638-21093879(+)$1	241	123	145	14.2668
uacauacacacaugggcaugua	chr10:82657762-82658016(+)$1	254	152	174	13.9883
UAGGAUAAUGAUCUCUAUUUUG	chr5:32459220-32459473(+)$1	253	154	176	15.0877
CACAUCGUACUGUCUCUGUGUG	chr5:93603216-93603477(+)$1	261	182	204	13.7103
UGGGGAACUUUAUUUUUCUUGG	chr5:141096454-141096697(-)$1	243	56	78	14.6307
GCAUUUUAUAUAAUAGAAAUAU	chr2:104267590-104267827(-)$1	237	63	85	14.4333
GAUAUUAUCCUAAGUUGAAAUC	chr2:153054171-153054409(-)$1	238	142	164	15.4397
gGACUCCACAACCAAGGCUGAA	chr1:72908443-72908690(-)$1	247	90	112	13.9385
GGAGCAAGGUCUUAAUUGCUCU	chr19:9093115-9093368(+)$1	253	174	196	15.0877
CAGCCACCAGGAAUUGUGGAGG	chrX:156561336-156561597(-)$1	261	225	247	13.6035
AAGAACGGACAUCAUUGUUUUA	chrX:159216497-159216807(+)$1	310	52	74	15.0336
CCCAUGCUUUCCUUUGUAUUUA	chr11:95136292-95136534(-)$1	242	87	109	12.6415
gugucccaagugcuaggaucac	chr1:158360119-158360365(-)$1	246	131	153	14.1609
GGCUGCUCUUCCCUCAGCUGGC	chr11:100576886-100577129(-)$1	243	220	242	14.7274

#DB
(((((((........)))))))	chr1:45432382-45432652(-)$1	1	32	54	13.6126
((((.((........))..)))	chr15:76912491-76912744(-)$1	1	14	36	13.9269
(((((((........)))).))	chr1:94755595-94755860(+)$1	1	179	201	14.6310
..(((((........)))))..	chr9:35314119-35314355(+)$1	1	33	55	14.3646
((..(((........)))))))	chr13:56839388-56839640(+)$1	1	126	148	15.0945
(((((((........)))))))	chr10:57886674-57886974(+)$1	1	91	113	15.0877
(((((((........)))))))	chr3:57261336-57261574(-)$1	1	112	134	13.6126
.(((.((........)))))((	chr3:53281764-53282025(+)$1	1	17	39	13.8608
(..((((........)))))))	chr7:17081402-17081644(-)$1	1	182	204	14.8453
.(((.((........))))).)	chr11:52221354-52221593(+)$1	1	147	169	15.0003
.((((((........)))))))	chr7:30971958-30972213(-)$1	1	208	230	13.1610
((.((((........)))).))	chr4:40152063-40152305(-)$1	1	78	100	14.2780
(((((((........)))))))	chr15:83130917-83131157(-)$1	1	49	71	15.0877
(.(((((........)))))))	chr2:32164610-32164855(-)$1	1	46	68	13.7900
(((.(((........)))))))	chr17:10401475-10401757(-)$1	1	254	276	14.7701
(.(((((........))))).)	chr18:56912511-56912824(+)$1	1	242	264	14.6307
((.((((........)))).))	chr1:182919669-182919904(-)$1	1	12	34	14.4036
.((((((........)))))).	chr6:146566971-146567230(-)$1	1	110	132	13.7006
(...(((........)))..))	chr1:74443121-74443384(+)$1	1	33	55	14.8402
(((((((........)))))))	chrX:71481000-71481240(-)$1	1	114	136	13.6126
(.(((((........)).))).	chr11:97699644-97699882(+)$1	1	162	184	14.7902
((((.((........)).))))	chr13:99612127-99612402(-)$1	1	5	27	14.2224
((...((........))..)).	chr3:14871614-14871873(+)$1	1	116	138	13.5876
(((((((........)))))))	chr11:69730583-69730847(-)$1	1	173	195	15.3889
((.((((........)))))))	chr4:141240550-141240797(-)$1	1	160	182	13.7529
(((((.(........)))))))	chr4:53634965-53635223(+)$1	1	147	169	13.9966
((..(((........)))))))	chr4:154530031-154530304(-)$1	1	250	272	15.1575
((..(((........)))..))	chr13:38592617-38592864(-)$1	1	205	227	14.9524
(((((((........)))))))	chr18:60717226-60717485(+)$1	1	207	229	15.3889
((((.((........)).))))	chr14:63761578-63761892(+)$1	1	167	189	15.2658
(.(((((........)))))..	chr3:88285229-88285544(-)$1	1	269	291	14.3225
((.((((........)))).))	chr3:107544784-107545052(-)$1	1	112	134	13.8862
.((((((........))).)))	chr5:34694815-34695070(+)$1	1	119	141	15.4236
(((((((........)))))))	chr11:109530585-109530838(+)$1	1	77	99	13.6126
(..((.(........).)))))	chr11:75227304-75227576(-)$1	1	77	99	14.1721
(((((((........)))))))	chr4:63156558-63156814(-)$1	1	70	92	15.4793
(((((((........))).)))	chr10:95010579-95010840(-)$1	1	216	238	14.7274
(((((((........)))))..	chr10:79324224-79324479(+)$1	1	34	56	13.7991
(...(((........)))....	chr5:141098860-141099157(-)$1	1	100	122	15.2883
(((((((........)))))..	chr14:70580317-70580578(-)$1	1	76	98	14.2449
.((((.(........).)))).	chr7:108021156-108021395(-)$1	1	196	218	14.5358
.((((((........)))))).	chr17:75936402-75936640(-)$1	1	139	161	13.7006
.(((.((........)))))..	chr11:102264486-102264728(-)$1	1	158	180	14.7535
((.((((........)))))).	chr2:153593215-153593465(+)$1	1	139	161	12.8710
((..(((........)))....	chr12:81268832-81269071(-)$1	1	68	90	15.6415
(.(.(((........))).).)	chr9:123500698-123500950(+)$1	1	98	120	15.5963
.((((((........))))).)	chr5:115119460-115119704(-)$1	1	214	236	14.5158
((..(((........)))))))	chr11:86526020-86526275(-)$1	1	71	93	15.0945
(((.(((........)))..))	chr18:36917108-36917358(+)$1	1	76	98	15.4180
((((.((........)).)).)	chr17:69638592-69638904(+)$1	1	156	178	13.4816
((((.((........))..)))	chr15:103028669-103028951(-)$1	1	206	228	13.6809
)))((((........).)))..	chr14:68351378-68351639(+)$1	1	25	47	13.3812
...((((........)))))))	chr2:164716634-164716878(+)$1	1	210	232	14.4445
(((((((........)))).))	chr13:100195383-100195625(-)$1	1	162	184	14.6310
((.((((........))))..)	chr13:98021123-98021385(+)$1	1	210	232	13.8781
(((((((........)))))))	chr17:71343637-71343960(-)$1	1	275	297	15.4793
.((((((........)))))).	chr14:21851864-21852117(+)$1	1	94	116	13.6536
((((..(........)..))))	chr3:88548580-88548821(-)$1	1	140	162	14.0388
.((((((........)).))))	chr17:21093638-21093879(+)$1	1	123	145	14.2668
(((((.(........).)))))	chr10:82657762-82658016(+)$1	1	152	174	13.9883
(((((((........)))))))	chr5:32459220-32459473(+)$1	1	154	176	15.0877
(((((.(........).)))))	chr5:93603216-93603477(+)$1	1	182	204	13.7103
(.(((((........))))).)	chr5:141096454-141096697(-)$1	1	56	78	14.6307
(.(((((........))))).)	chr2:104267590-104267827(-)$1	1	63	85	14.4333
(((.(((........))).)))	chr2:153054171-153054409(-)$1	1	142	164	15.4397
((...((........))))...	chr1:72908443-72908690(-)$1	1	90	112	13.9385
(((((((........)))))))	chr19:9093115-9093368(+)$1	1	174	196	15.0877
...((((........))))..)	chrX:156561336-156561597(-)$1	1	225	247	13.6035
((((.((........)))))))	chrX:159216497-159216807(+)$1	1	52	74	15.0336
(((((((........)))....	chr11:95136292-95136534(-)$1	1	87	109	12.6415
(((..((........))..)))	chr1:158360119-158360365(-)$1	1	131	153	14.1609
(((((((........))).)))	chr11:100576886-100577129(-)$1	1	220	242	14.7274

#PSSM
d : 0.13	c : 0.12	b : 0.11	h : 0.09	g : 0.08	e : 0.08	[ : 0.08	i : 0.06	! : 0.05	= : 0.05	f : 0.04	$ : 0.02	: : 0.01	" : 0.01	
d : 0.15	c : 0.11	h : 0.09	f : 0.09	[ : 0.09	b : 0.09	g : 0.06	i : 0.06	e : 0.05	! : 0.04	" : 0.04	= : 0.04	a : 0.01	$ : 0.01	
e : 0.15	c : 0.11	d : 0.09	! : 0.09	h : 0.08	f : 0.08	[ : 0.08	g : 0.06	" : 0.06	i : 0.05	= : 0.04	b : 0.02	a : 0.01	$ : 0.01	
d : 0.23	e : 0.13	h : 0.08	! : 0.08	c : 0.08	f : 0.08	g : 0.06	[ : 0.05	" : 0.05	= : 0.04	b : 0.04	i : 0.02	
c : 0.23	d : 0.18	[ : 0.12	e : 0.12	h : 0.08	f : 0.06	g : 0.05	" : 0.02	i : 0.02	= : 0.02	! : 0.02	b : 0.01	
c : 0.22	b : 0.19	d : 0.15	e : 0.12	[ : 0.06	h : 0.05	g : 0.05	f : 0.05	i : 0.02	= : 0.02	! : 0.01	
c : 0.20	b : 0.19	d : 0.15	e : 0.12	a : 0.09	h : 0.05	g : 0.05	f : 0.05	i : 0.02	= : 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 : 0.20	b : 0.19	d : 0.15	e : 0.12	a : 0.09	h : 0.05	g : 0.05	f : 0.05	i : 0.02	= : 0.02	
c : 0.20	b : 0.19	d : 0.15	e : 0.12	h : 0.06	] : 0.06	g : 0.05	f : 0.05	i : 0.02	= : 0.02	2 : 0.01	
c : 0.26	d : 0.16	e : 0.12	h : 0.08	2 : 0.06	g : 0.06	f : 0.06	] : 0.06	i : 0.02	b : 0.02	= : 0.02	
d : 0.23	e : 0.15	2 : 0.09	h : 0.08	g : 0.06	c : 0.06	f : 0.06	] : 0.06	= : 0.04	b : 0.04	i : 0.02	4 : 0.02	6 : 0.01	
e : 0.18	d : 0.12	c : 0.11	h : 0.08	f : 0.08	] : 0.06	g : 0.06	2 : 0.06	b : 0.05	= : 0.05	i : 0.02	4 : 0.02	a : 0.01	3 : 0.01	6 : 0.01	
d : 0.13	c : 0.09	] : 0.09	f : 0.09	h : 0.08	2 : 0.08	e : 0.08	g : 0.06	b : 0.06	= : 0.05	i : 0.04	4 : 0.04	: : 0.01	3 : 0.01	6 : 0.01	
d : 0.16	c : 0.12	e : 0.11	h : 0.08	g : 0.06	2 : 0.05	f : 0.05	] : 0.05	= : 0.05	4 : 0.05	b : 0.04	i : 0.04	3 : 0.02	: : 0.02	a : 0.01	6 : 0.01	

#score	1037.3192547732222
#seq	72
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_transcript_m3_run1.txt

#BEAR
ggggg[ddddllldddd]ggg	chr14:37688954-37689189(-)$1	235	66	87	9.4179
dddd[ddddmmmmdddddddd	chr11:49502571-49502808(-)$1	237	146	167	11.9877
=========mmmm========	chr1:166367495-166367803(-)$1	308	159	180	9.0143
iii[eeeeemmmmeeeeeiii	chr8:97197811-97198067(+)$1	256	83	104	9.5530
!!bb[ddddmmmmdddd]bb2	chr10:56110018-56110270(+)$1	252	178	199	12.1624
eea!!ddddllldddd333a]	chrX:10173441-10173689(+)$1	248	114	135	10.6686
eee!!ddddmmmmdddd]eee	chr4:149994270-149994518(+)$1	248	195	216	13.2710
eeeeeddddmmmmdddd333e	chr15:37297668-37297906(-)$1	238	147	168	13.2167
ddd!!ddddmmmmdddd]ddd	chr5:90646461-90646698(-)$1	237	74	95	13.3222
ddd!!ddddmmmmdddd5555	chr14:37934193-37934437(-)$1	244	98	119	11.0885
=========mmmm========	chr1:166367605-166367872(-)$1	267	228	249	9.0143
ccc!!ddddmmmmdddd22cc	chr11:50108319-50108564(-)$1	245	209	230	13.7968
eee!!ddddmmmmdddd]eee	chr14:124813378-124813628(-)$1	250	138	159	13.2710
ee"""ddddmmmmdddd5555	chr19:10523731-10523966(+)$1	235	122	143	11.1672
eee[eeeeemmmmeeeee22e	chr16:36035171-36035406(+)$1	235	115	136	9.6805
c[bb[ddddmmmmdddd22bb	chr19:44381122-44381370(+)$1	248	164	185	12.4689
c[bb[ddddmmmmdddd333b	chr2:5215541-5215779(-)$1	238	153	174	13.3851
:ccc[ddddmmmmdddd]ccc	chr15:27523728-27523972(+)$1	244	70	91	12.3723
##bb[ddddmmmmdddd]bb4	chr2:173059269-173059507(-)$1	238	18	39	12.2043
ddd"""cccmmmmccc4444d	chr11:4667755-4668009(-)$1	254	197	218	10.1450
dddd[ddddmmmmdddd]ddd	chr17:85463636-85463892(-)$1	256	105	126	12.8179
cc!!eeeeemmmmeeeee22c	chr11:42445141-42445381(+)$1	240	156	177	10.0396
b]cccddddmmmmddddgggg	chr11:41725286-41725547(-)$1	261	147	168	11.4559
cc!!eeeeemmmmeeeeeccc	chr6:35459165-35459407(-)$1	242	70	91	9.8151
b!!a[ddddmmmmdddd]a]b	chr15:37986467-37986724(-)$1	257	121	142	13.2145
ccc!!ddddmmmmdddd]ccc	chr2:130540453-130540688(-)$1	235	207	228	13.7317
======ddddllldddd]===	chr5:104508405-104508686(-)$1	281	209	230	10.2339
EEcccddddmmmmdddd]ccc	chr10:107935762-107936048(-)$1	286	232	253	10.8543
fffffddddmmmmdddd]fff	chrX:69217655-69217917(+)$1	262	153	174	11.4489
ccc!!ddddmmmmdddd22cc	chr2:138112642-138112881(+)$1	239	208	229	13.7968
ddddeeeeemmmmeeeee333	chr1:66488941-66489253(+)$1	312	96	117	9.8972
!!cccddddmmmmdddd]ccc	chr13:110847795-110848040(-)$1	245	159	180	12.8465
ddd!!ddddmmmmdddd22dd	chr10:70718207-70718465(-)$1	258	60	81	13.5170
eeea!!cccmmmmccc22a]e	chr2:174154883-174155120(+)$1	237	96	117	9.4487
cc"""ddddmmmmdddd22cc	chr10:117252445-117252689(-)$1	244	164	185	13.8210
e"""eeeeemmmmeeeee]ee	chr2:103900825-103901060(+)$1	235	134	155	9.6897
eeeeaddddmmmmdddd]a]e	chr2:104269558-104269795(-)$1	237	118	139	12.7709
dddd[ddddmmmmdddd]ddd	chr19:7500920-7501169(-)$1	249	40	61	12.8179
b####ddddmmmmdddd6666	chr15:23207405-23207640(+)$1	235	199	220	11.6809
!!cccddddmmmmdddd]ccc	chr2:94192195-94192445(-)$1	250	177	198	12.8465
dddd[ddddmmmmdddd]ddd	chrX:48358269-48358532(-)$1	263	55	76	12.8179
eee!!ddddmmmmdddd333e	chr11:118163443-118163694(-)$1	251	140	161	14.2766
cc"""ddddmmmmdddd333c	chr14:37722401-37722636(-)$1	235	10	31	14.4472
====[ddddmmmmdddd]===	chr11:17098607-17098842(+)$1	235	10	31	13.7255
====eeeeemmmmeeeee333	chr13:94204257-94204515(-)$1	258	120	141	10.3328
eeee[ddddmmmmdddd333e	chr10:82212795-82213038(-)$1	243	46	67	13.7692
dd"""ddddmmmmdddddddd	chr10:36854607-36854858(-)$1	251	135	156	12.5623

#otherMatches

#Seq PSSM
AUGUUAGGGAACUUUCUAAGC	chr14:37688954-37689189(-)$1	235	66	87	9.4179
GAAGAUUCAGUAUUGGACUUU	chr11:49502571-49502808(-)$1	237	146	167	11.9877
CUGUCACUGUGGCUAGUGAUG	chr1:166367495-166367803(-)$1	308	159	180	9.0143
GAGGUGUGCUUGUGCAUGCUU	chr8:97197811-97198067(+)$1	256	83	104	9.5530
CAAUAAAAUUUUAAUUUAGUA	chr10:56110018-56110270(+)$1	252	178	199	12.1624
GACGUUGAGGACCUCAUCAGA	chrX:10173441-10173689(+)$1	248	114	135	10.6686
GGAUUCAGUGUUGACUGUUCC	chr4:149994270-149994518(+)$1	248	195	216	13.2710
UUACUACAGAAGACUGUUUUA	chr15:37297668-37297906(-)$1	238	147	168	13.2167
CGUCUCGUUUUCAAAUGUAUG	chr5:90646461-90646698(-)$1	237	74	95	13.3222
CUUUGUGGCUUAUGCUAAGAU	chr14:37934193-37934437(-)$1	244	98	119	11.0885
CUGUCACUGUGGCUAGUGAUG	chr1:166367605-166367872(-)$1	267	228	249	9.0143
GUGCUAGAGGAGCCUCUCCCA	chr11:50108319-50108564(-)$1	245	209	230	13.7968
gguggguggggaaccauagcc	chr14:124813378-124813628(-)$1	250	138	159	13.2710
ACUUUGUAGGCACCUACUCAC	chr19:10523731-10523966(+)$1	235	122	143	11.1672
UACUGUGUUCACUGACAUUUG	chr16:36035171-36035406(+)$1	235	115	136	9.6805
CCGAAAGUAUUUCUACUCAUC	chr19:44381122-44381370(+)$1	248	164	185	12.4689
UGGCUGCCAAGUCUGGUUUUG	chr2:5215541-5215779(-)$1	238	153	174	13.3851
AUCUAGCAUCCUAAUGCCAGG	chr15:27523728-27523972(+)$1	244	70	91	12.3723
GAAGUGUCAGGUAUGAUUCUG	chr2:173059269-173059507(-)$1	238	18	39	12.2043
CCACUCCCCAACUGGGCUUCU	chr11:4667755-4668009(-)$1	254	197	218	10.1450
CAUCAUGCUCCUCAGUAGGAU	chr17:85463636-85463892(-)$1	256	105	126	12.8179
CCUUAAGUAGCUUUACUUUUG	chr11:42445141-42445381(+)$1	240	156	177	10.0396
UAUCUGUGAAGAAUCACAAUA	chr11:41725286-41725547(-)$1	261	147	168	11.4559
CAAUUGCAGUGUUUUGCAUGC	chr6:35459165-35459407(-)$1	242	70	91	9.8151
AUUGGACUUGAGUAAGUGCUU	chr15:37986467-37986724(-)$1	257	121	142	13.2145
CCUAAGCUGUCCACAGUGAGG	chr2:130540453-130540688(-)$1	235	207	228	13.7317
AUGUAGCAAAACAUUUGUUUG	chr5:104508405-104508686(-)$1	281	209	230	10.2339
UCGCCCACUUGAUAGUGCGGC	chr10:107935762-107936048(-)$1	286	232	253	10.8543
AAUGGAUUAAUUUUGGUACCA	chrX:69217655-69217917(+)$1	262	153	174	11.4489
AAUCAUAUCUUAAGAUAGUAU	chr2:138112642-138112881(+)$1	239	208	229	13.7968
CCAUAGAAAGGUAUUUCUUCA	chr1:66488941-66489253(+)$1	312	96	117	9.8972
CUGAAUGUGUGUCCACAGUUC	chr13:110847795-110848040(-)$1	245	159	180	12.8465
GGAAACUCUGCUGAGAGCAUU	chr10:70718207-70718465(-)$1	258	60	81	13.5170
caccaccaUUGCUGUGUAGUG	chr2:174154883-174155120(+)$1	237	96	117	9.4487
GAGAGUACAAUAAUGUAAAUC	chr10:117252445-117252689(-)$1	244	164	185	13.8210
UCUUCAUGAUGUCUCAUGUAG	chr2:103900825-103901060(+)$1	235	134	155	9.6897
CUGUGUCUAGACUUAGAGCAA	chr2:104269558-104269795(-)$1	237	118	139	12.7709
UCCAGAACUUUUAGGUUGUGG	chr19:7500920-7501169(-)$1	249	40	61	12.8179
ACAAUGGUUUAAAAACUUACA	chr15:23207405-23207640(+)$1	235	199	220	11.6809
agugugguguacauaccugca	chr2:94192195-94192445(-)$1	250	177	198	12.8465
UUGAUCUAUAAUAAUAGCUCA	chrX:48358269-48358532(-)$1	263	55	76	12.8179
AAAAUGCUUCCAAAAGCCUCU	chr11:118163443-118163694(-)$1	251	140	161	14.2766
CAAUGUGUGAAUACACAAAGU	chr14:37722401-37722636(-)$1	235	10	31	14.4472
uauacauauguaaauauuuau	chr11:17098607-17098842(+)$1	235	10	31	13.7255
UUUAUUCUGUGUAUAGAACUU	chr13:94204257-94204515(-)$1	258	120	141	10.3328
UUUCAUGAAUGAUUUUAAAAG	chr10:82212795-82213038(-)$1	243	46	67	13.7692
AACGUUGCUUACAAGCAUUGC	chr10:36854607-36854858(-)$1	251	135	156	12.5623

#DB
(((((.((((...)))).)))	chr14:37688954-37689189(-)$1	1	66	87	9.4179
((((.((((....))))))))	chr11:49502571-49502808(-)$1	1	146	167	11.9877
(((((((((....))))))))	chr1:166367495-166367803(-)$1	1	159	180	9.0143
(((.(((((....))))))))	chr8:97197811-97198067(+)$1	1	83	104	9.5530
..((.((((....)))).)).	chr10:56110018-56110270(+)$1	1	178	199	12.1624
(((..((((...))))...).	chrX:10173441-10173689(+)$1	1	114	135	10.6686
(((..((((....)))).)))	chr4:149994270-149994518(+)$1	1	195	216	13.2710
(((((((((....))))...)	chr15:37297668-37297906(-)$1	1	147	168	13.2167
(((..((((....)))).)))	chr5:90646461-90646698(-)$1	1	74	95	13.3222
(((..((((....))))....	chr14:37934193-37934437(-)$1	1	98	119	11.0885
(((((((((....))))))))	chr1:166367605-166367872(-)$1	1	228	249	9.0143
(((..((((....))))..))	chr11:50108319-50108564(-)$1	1	209	230	13.7968
(((..((((....)))).)))	chr14:124813378-124813628(-)$1	1	138	159	13.2710
((...((((....))))....	chr19:10523731-10523966(+)$1	1	122	143	11.1672
(((.(((((....)))))..)	chr16:36035171-36035406(+)$1	1	115	136	9.6805
(.((.((((....))))..))	chr19:44381122-44381370(+)$1	1	164	185	12.4689
(.((.((((....))))...)	chr2:5215541-5215779(-)$1	1	153	174	13.3851
.(((.((((....)))).)))	chr15:27523728-27523972(+)$1	1	70	91	12.3723
..((.((((....)))).)).	chr2:173059269-173059507(-)$1	1	18	39	12.2043
(((...(((....)))....)	chr11:4667755-4668009(-)$1	1	197	218	10.1450
((((.((((....)))).)))	chr17:85463636-85463892(-)$1	1	105	126	12.8179
((..(((((....)))))..)	chr11:42445141-42445381(+)$1	1	156	177	10.0396
).)))((((....))))((((	chr11:41725286-41725547(-)$1	1	147	168	11.4559
((..(((((....))))))))	chr6:35459165-35459407(-)$1	1	70	91	9.8151
(..(.((((....)))).).)	chr15:37986467-37986724(-)$1	1	121	142	13.2145
(((..((((....)))).)))	chr2:130540453-130540688(-)$1	1	207	228	13.7317
((((((((((...)))).)))	chr5:104508405-104508686(-)$1	1	209	230	10.2339
))(((((((....)))).)))	chr10:107935762-107936048(-)$1	1	232	253	10.8543
(((((((((....)))).)))	chrX:69217655-69217917(+)$1	1	153	174	11.4489
(((..((((....))))..))	chr2:138112642-138112881(+)$1	1	208	229	13.7968
(((((((((....)))))...	chr1:66488941-66489253(+)$1	1	96	117	9.8972
..(((((((....)))).)))	chr13:110847795-110848040(-)$1	1	159	180	12.8465
(((..((((....))))..))	chr10:70718207-70718465(-)$1	1	60	81	13.5170
((((..(((....)))..).)	chr2:174154883-174155120(+)$1	1	96	117	9.4487
((...((((....))))..))	chr10:117252445-117252689(-)$1	1	164	185	13.8210
(...(((((....))))).))	chr2:103900825-103901060(+)$1	1	134	155	9.6897
(((((((((....)))).).)	chr2:104269558-104269795(-)$1	1	118	139	12.7709
((((.((((....)))).)))	chr19:7500920-7501169(-)$1	1	40	61	12.8179
(....((((....))))....	chr15:23207405-23207640(+)$1	1	199	220	11.6809
..(((((((....)))).)))	chr2:94192195-94192445(-)$1	1	177	198	12.8465
((((.((((....)))).)))	chrX:48358269-48358532(-)$1	1	55	76	12.8179
(((..((((....))))...)	chr11:118163443-118163694(-)$1	1	140	161	14.2766
((...((((....))))...)	chr14:37722401-37722636(-)$1	1	10	31	14.4472
((((.((((....)))).)))	chr11:17098607-17098842(+)$1	1	10	31	13.7255
(((((((((....)))))...	chr13:94204257-94204515(-)$1	1	120	141	10.3328
((((.((((....))))...)	chr10:82212795-82213038(-)$1	1	46	67	13.7692
((...((((....))))))))	chr10:36854607-36854858(-)$1	1	135	156	12.5623

#PSSM
e : 0.23	d : 0.21	c : 0.19	= : 0.10	! : 0.06	b : 0.06	g : 0.02	i : 0.02	: : 0.02	# : 0.02	E : 0.02	f : 0.02	
d : 0.21	e : 0.21	c : 0.17	= : 0.10	! : 0.08	[ : 0.04	# : 0.04	g : 0.02	i : 0.02	] : 0.02	E : 0.02	f : 0.02	" : 0.02	
d : 0.19	e : 0.17	c : 0.17	= : 0.10	" : 0.10	b : 0.08	! : 0.06	g : 0.02	i : 0.02	a : 0.02	f : 0.02	# : 0.02	
! : 0.25	" : 0.12	d : 0.10	= : 0.10	c : 0.10	b : 0.08	e : 0.06	[ : 0.04	a : 0.04	g : 0.02	f : 0.02	# : 0.02	
[ : 0.25	! : 0.23	e : 0.17	" : 0.10	c : 0.08	= : 0.06	g : 0.02	f : 0.02	a : 0.02	# : 0.02	
d : 0.72	e : 0.14	= : 0.06	[ : 0.02	" : 0.02	! : 0.02	
d : 0.76	e : 0.14	= : 0.04	c : 0.04	
d : 0.76	e : 0.14	= : 0.04	c : 0.04	
d : 0.76	e : 0.14	= : 0.04	c : 0.04	
m : 0.93	d : 0.04	l : 0.02	
m : 0.93	l : 0.06	
m : 0.93	l : 0.06	
m : 0.93	l : 0.04	d : 0.02	
d : 0.76	e : 0.14	= : 0.04	c : 0.04	
d : 0.76	e : 0.14	= : 0.04	c : 0.04	
d : 0.76	e : 0.14	= : 0.04	c : 0.04	
d : 0.74	e : 0.14	= : 0.04	3 : 0.02	4 : 0.02	2 : 0.02	
] : 0.40	e : 0.14	3 : 0.12	2 : 0.12	d : 0.04	= : 0.04	5 : 0.04	4 : 0.02	g : 0.02	6 : 0.02	
3 : 0.17	2 : 0.14	d : 0.12	c : 0.12	= : 0.08	a : 0.06	g : 0.04	b : 0.04	e : 0.04	5 : 0.04	i : 0.02	4 : 0.02	f : 0.02	] : 0.02	6 : 0.02	
c : 0.19	d : 0.14	3 : 0.14	= : 0.08	b : 0.06	e : 0.06	] : 0.06	g : 0.04	5 : 0.04	2 : 0.04	i : 0.02	a : 0.02	4 : 0.02	f : 0.02	6 : 0.02	
c : 0.23	e : 0.19	d : 0.17	= : 0.08	b : 0.06	g : 0.04	5 : 0.04	3 : 0.04	i : 0.02	2 : 0.02	] : 0.02	4 : 0.02	f : 0.02	6 : 0.02	

#score	559.8867295643298
#seq	47
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_CDS_m1_run2.txt

#BEAR
ccc[cccssssssssssccccc	chr2:6468061-6468303(-)$1	242	164	186	12.8036
"cccvvvvvvvvvvvvvccc88	chr4:126707015-126707250(+)$1	235	165	187	19.3922
!!ccc^^^^^^^^^^^^^^^^^	chr12:21315974-21316209(+)$1	235	168	190	17.5998
ccc[cccssssssssssccc]c	chr11:78335201-78335436(+)$1	235	51	73	12.8292
[ddddyyyyyyyyyyyyyyyyd	chr19:47331845-47332080(+)$1	235	57	79	20.1699
eeeeettttttttttteeeee:	chr1:59927210-59927447(+)$1	237	94	116	16.4066
[dddduuuuuuuuuuuudddd=	chr11:115667985-115668222(-)$1	237	46	68	20.3233
cccwwwwwwwwwwwwwwccc]e	chr16:11134462-11134700(-)$1	238	60	82	19.1473
::ccctttttttttttccc:ee	chr13:78336959-78337194(-)$1	235	25	47	15.2616
[ccc^^^^^^^^^^^^^^^^^^	chr14:31989531-31989766(-)$1	235	92	114	17.4340
ggggg^^^^^^^^^^^^^^^^^	chr7:118217767-118218002(-)$1	235	56	78	16.9413
======ttttttttttt=====	chr2:181041364-181041632(-)$1	268	188	210	16.9663
fdddduuuuuuuuuuuudddd]	chr15:31418450-31418687(-)$1	237	63	85	20.0558
eeeeettttttttttteeeee]	chr7:137872027-137872262(+)$1	235	69	91	17.0463
gg[cccsssssssssscccggg	chr12:73675052-73675287(+)$1	235	106	128	12.7160
fffffuuuuuuuuuuuufffff	chr7:20150502-20150751(-)$1	249	163	185	18.3802
!cccxxxxxxxxxxxxxxxccc	chr11:109528789-109529095(+)$1	306	224	246	17.4010
!!ccc^^^^^^^^^^^^^^^^^	chr11:70483294-70483530(-)$1	236	86	108	17.5998
cddddwwwwwwwwwwwwwwddd	chr15:83666718-83666956(+)$1	238	71	93	20.0878
dddwwwwwwwwwwwwwwdddd:	chr7:148337524-148337759(+)$1	235	140	162	18.2795
ggggguuuuuuuuuuuuggggg	chr11:86602657-86602898(-)$1	241	170	192	19.3098
gggggyyyyyyyyyyyyyyyyg	chr11:31917577-31917812(+)$1	235	105	127	19.6184
:dddduuuuuuuuuuuudddd:	chr3:146395453-146395688(-)$1	235	60	82	18.6495
ddddvvvvvvvvvvvvvdddd:	chr11:72025341-72025578(-)$1	237	178	200	18.4631
ccccc^^^^^^^^^^^^^^^^^	chr10:126680660-126680895(-)$1	235	123	145	17.3261
dddwwwwwwwwwwwwwwddddb	chr15:99351509-99351763(-)$1	254	41	63	18.6724
!ccc^^^^^^^^^^^^^^^^^^	chr11:55208949-55209192(-)$1	243	159	181	17.4617
eeeevvvvvvvvvvvvveeeee	chr10:53063680-53063917(+)$1	237	74	96	18.4484
!dddduuuuuuuuuuuudddd2	chr9:95945897-95946132(+)$1	235	113	135	20.3274
fffff^^^^^^^^^^^^^^^^^	chr6:4706066-4706310(+)$1	244	181	203	16.3508
g[ccctttttttttttccc]gg	chr8:63391717-63391957(-)$1	240	170	192	17.8279
ffffftttttttttttffffff	chr8:46095312-46095551(+)$1	239	146	168	15.8632
hhhhh^^^^^^^^^^^^^^^^^	chr16:14153931-14154176(-)$1	245	42	64	16.1667
!!ccc^^^^^^^^^^^^^^^^^	chr11:70483254-70483493(-)$1	239	49	71	17.5998
:ddddtttttttttttddddCC	chr5:90646461-90646698(-)$1	237	214	236	14.9152
hhhhhvvvvvvvvvvvvvhhhh	chr19:10058659-10058899(+)$1	240	64	86	17.1321
[dddd^^^^^^^^^^^^^^^^^	chr5:72015103-72015349(-)$1	246	133	155	17.5330
[dddd[axxxxxxxxxxxxxxx	chr7:65047791-65048042(+)$1	251	40	62	16.1579
'ddddtttttttttttdddd99	chr18:46664687-46664922(-)$1	235	63	85	16.6603
##cccuuuuuuuuuuuuccc22	chr5:137736972-137737209(-)$1	237	188	210	20.3068
!bbxxxxxxxxxxxxxxxbb22	chr11:41946818-41947090(-)$1	272	91	113	15.4950
e[cccuuuuuuuuuuuucccee	chr10:106256389-106256638(+)$1	249	30	52	20.1949
$ddddtttttttttttdddd55	chr8:41532325-41532562(+)$1	237	122	144	16.8694
#ddddwwwwwwwwwwwwwwddd	chr19:10058581-10058825(+)$1	244	120	142	20.2587
Dddddtttttttttttdddd::	chr2:34631511-34631748(+)$1	237	19	41	15.4109
ddcccwwwwwwwwwwwwwwccc	chr1:75212189-75212442(-)$1	253	177	199	20.2707
eeeeeuuuuuuuuuuuueeeee	chr2:181041975-181042222(-)$1	247	222	244	19.3102
ggggg^^^^^^^^^^^^^^^^^	chr12:4637380-4637615(+)$1	235	20	42	16.9413
ddd[axxxxxxxxxxxxxxxa]	chr19:7289793-7290030(-)$1	237	32	54	17.3575
[eeeeevvvvvvvvvvvvveee	chrX:148326258-148326496(+)$1	238	120	142	18.1891
ddddcccssssssssssccc]d	chr16:35299447-35299697(+)$1	250	79	101	12.7745
"""bbvvvvvvvvvvvvvbb55	chr8:47292820-47293064(-)$1	244	131	153	17.8686
===bbvvvvvvvvvvvvvbb]=	chr5:138398460-138398701(-)$1	241	139	161	18.7730
fffffyyyyyyyyyyyyyyyyf	chr5:34186114-34186353(+)$1	239	134	156	18.9310
[ddddxxxxxxxxxxxxxxxdd	chr10:41239320-41239558(+)$1	238	89	111	17.5028
ggggggtttttttttttggggg	chr19:10058959-10059195(+)$1	236	212	234	16.5646
ii[bb^^^^^^^^^^^^^^^^^	chr6:117123446-117123681(+)$1	235	67	89	16.5324
#ddddxxxxxxxxxxxxxxxdd	chr1:174210640-174210877(-)$1	237	203	225	17.4276
"dddd^^^^^^^^^^^^^^^^^	chr4:148761180-148761417(-)$1	237	60	82	17.4909
cccccvvvvvvvvvvvvvccc:	chr6:4591853-4592090(+)$1	237	70	92	19.3944

#otherMatches

#Seq PSSM
CUUACUGAUCCUAACCCCAGAA	chr2:6468061-6468303(-)$1	242	164	186	12.8036
AGGGCCAAAUAAAAAACCCCGA	chr4:126707015-126707250(+)$1	235	165	187	19.3922
AAGGUACAGACUCUCUCAUACU	chr12:21315974-21316209(+)$1	235	168	190	17.5998
GUUCAGACCUUACUCCCUCUAA	chr11:78335201-78335436(+)$1	235	51	73	12.8292
UCAGGGACAGCCCCCAACUCAC	chr19:47331845-47332080(+)$1	235	57	79	20.1699
AGAUAUAGGAAUGAAUUGUCUG	chr1:59927210-59927447(+)$1	237	94	116	16.4066
AUGCGCCCCCUACACUAUGCAG	chr11:115667985-115668222(-)$1	237	46	68	20.3233
GGCAGCGACGGUAUAAAGCCGG	chr16:11134462-11134700(-)$1	238	60	82	19.1473
ccggcuccuccaccccgcccGC	chr13:78336959-78337194(-)$1	235	25	47	15.2616
CCGCUUCGUUACCGCCAUCUUU	chr14:31989531-31989766(-)$1	235	92	114	17.4340
UCCAUCCCCUCAAACUAUAUAU	chr7:118217767-118218002(-)$1	235	56	78	16.9413
AGAACGUUUUCGGGUUUUGUUU	chr2:181041364-181041632(-)$1	268	188	210	16.9663
AUGUUCUCCUCCCUUUCAGCAU	chr15:31418450-31418687(-)$1	237	63	85	20.0558
AAGGAAGCCCUUUCCGUCCUUC	chr7:137872027-137872262(+)$1	235	69	91	17.0463
GGAGGUCUAACUCCACACCCCG	chr12:73675052-73675287(+)$1	235	106	128	12.7160
CCAGGCCUCUGACUAUUCCUGG	chr7:20150502-20150751(-)$1	249	163	185	18.3802
UCUUGUCUCUUUAUACUAAAAG	chr11:109528789-109529095(+)$1	306	224	246	17.4010
CUGCACCUUCUCCAUAUCCCCG	chr11:70483294-70483530(-)$1	236	86	108	17.5998
AGGACUUUUAUUAUUUCCCGUC	chr15:83666718-83666956(+)$1	238	71	93	20.0878
CCCUUUCCACAACAUCUGGGUA	chr7:148337524-148337759(+)$1	235	140	162	18.2795
AACUAGUUUGACAUCUGUAGUU	chr11:86602657-86602898(-)$1	241	170	192	19.3098
GGAACAGAGGAACAAAGGGAAG	chr11:31917577-31917812(+)$1	235	105	127	19.6184
ACUUCGAUGACUAUGAAGAAGA	chr3:146395453-146395688(-)$1	235	60	82	18.6495
CAGCAGGGAAAUGAAGAGCUGG	chr11:72025341-72025578(-)$1	237	178	200	18.4631
GAGGCAAAGAAUAUCAACAAGU	chr10:126680660-126680895(-)$1	235	123	145	17.3261
CCUCUACCCACCUACCCAGGCG	chr15:99351509-99351763(-)$1	254	41	63	18.6724
CCCAUUACCCCCUUGUUUAAAA	chr11:55208949-55209192(-)$1	243	159	181	17.4617
AGAACCUAUUUAUCAAUUUCUG	chr10:53063680-53063917(+)$1	237	74	96	18.4484
UGAACUUUCUCGAAUUUGUUCC	chr9:95945897-95946132(+)$1	235	113	135	20.3274
gauccacaucacccuccacauc	chr6:4706066-4706310(+)$1	244	181	203	16.3508
UCUUUCAAAAAAAAAAAAAAAA	chr8:63391717-63391957(-)$1	240	170	192	17.8279
GGAGAAUAUGACAUUCUUUCCG	chr8:46095312-46095551(+)$1	239	146	168	15.8632
UUUUUAACAGGGUGGAAGAAAG	chr16:14153931-14154176(-)$1	245	42	64	16.1667
CUGCACCUUCUCCAUAUCCCCG	chr11:70483254-70483493(-)$1	239	49	71	17.5998
UUGGGGAUUCCUUUUACCCACA	chr5:90646461-90646698(-)$1	237	214	236	14.9152
UCUCCACCAAUCUCAUGAGGAG	chr19:10058659-10058899(+)$1	240	64	86	17.1321
GCUGCUGUCAACUAUUUCACCA	chr5:72015103-72015349(-)$1	246	133	155	17.5330
CACCAUGUUCCUGCUUCUCUCU	chr7:65047791-65048042(+)$1	251	40	62	16.1579
UUGAUACAGCCCAUAAAUCAUA	chr18:46664687-46664922(-)$1	235	63	85	16.6603
CCGUGACCACUUUAUCCCAUCA	chr5:137736972-137737209(-)$1	237	188	210	20.3068
CCCCACACCCCAUCAAUAGGUU	chr11:41946818-41947090(-)$1	272	91	113	15.4950
CAGAUGACACCAGCCAAAUCGU	chr10:106256389-106256638(+)$1	249	30	52	20.1949
CUGGUCAUACUGGAAAACCAUU	chr8:41532325-41532562(+)$1	237	122	144	16.8694
UGAAGAACUUUGCCAAAUACUU	chr19:10058581-10058825(+)$1	244	120	142	20.2587
GGAACUAGAAGAAAUUGUUCAG	chr2:34631511-34631748(+)$1	237	19	41	15.4109
GCCCUGGAAAAAGAUUAUGAGG	chr1:75212189-75212442(-)$1	253	177	199	20.2707
AGCUCAACUACAAGAUGGAGCU	chr2:181041975-181042222(-)$1	247	222	244	19.3102
UAUUUUAUUUAGUAACAAAGUU	chr12:4637380-4637615(+)$1	235	20	42	16.9413
CCUUCUUUCUUGUACUCUGUGU	chr19:7289793-7290030(-)$1	237	32	54	17.3575
AUAUGGUGACUGUUCUAAUCCG	chrX:148326258-148326496(+)$1	238	120	142	18.1891
CCUUCUGUCUAGAUCAUCAGUG	chr16:35299447-35299697(+)$1	250	79	101	12.7745
AUUGCAAAAGAUGAAGGAGCCA	chr8:47292820-47293064(-)$1	244	131	153	17.8686
UUUUGGAGGAUAUACAAGCACA	chr5:138398460-138398701(-)$1	241	139	161	18.7730
UCAGAAGAAAACGAACAAAAAU	chr5:34186114-34186353(+)$1	239	134	156	18.9310
CAGCCCAACAUCACCACCCUGG	chr10:41239320-41239558(+)$1	238	89	111	17.5028
CCACGUGAGUAUCGGAAACGUG	chr19:10058959-10059195(+)$1	236	212	234	16.5646
CGGCUGAAGAACAACAACAGAC	chr6:117123446-117123681(+)$1	235	67	89	16.5324
GCUGGCCAACACAUCAUCUCCC	chr1:174210640-174210877(-)$1	237	203	225	17.4276
GUCCUUUCUCUCUUUUUGCCUU	chr4:148761180-148761417(-)$1	237	60	82	17.4909
CCGACACUCAACAUCAUCGUCA	chr6:4591853-4592090(+)$1	237	70	92	19.3944

#DB
(((.(((..........)))))	chr2:6468061-6468303(-)$1	1	164	186	12.8036
.(((.............)))..	chr4:126707015-126707250(+)$1	1	165	187	19.3922
..(((.................	chr12:21315974-21316209(+)$1	1	168	190	17.5998
(((.(((..........))).)	chr11:78335201-78335436(+)$1	1	51	73	12.8292
.((((................)	chr19:47331845-47332080(+)$1	1	57	79	20.1699
(((((...........))))).	chr1:59927210-59927447(+)$1	1	94	116	16.4066
.((((............)))))	chr11:115667985-115668222(-)$1	1	46	68	20.3233
(((..............))).)	chr16:11134462-11134700(-)$1	1	60	82	19.1473
..(((...........))).((	chr13:78336959-78337194(-)$1	1	25	47	15.2616
.(((..................	chr14:31989531-31989766(-)$1	1	92	114	17.4340
(((((.................	chr7:118217767-118218002(-)$1	1	56	78	16.9413
((((((...........)))))	chr2:181041364-181041632(-)$1	1	188	210	16.9663
(((((............)))).	chr15:31418450-31418687(-)$1	1	63	85	20.0558
(((((...........))))).	chr7:137872027-137872262(+)$1	1	69	91	17.0463
((.(((..........))))))	chr12:73675052-73675287(+)$1	1	106	128	12.7160
(((((............)))))	chr7:20150502-20150751(-)$1	1	163	185	18.3802
.(((...............)))	chr11:109528789-109529095(+)$1	1	224	246	17.4010
..(((.................	chr11:70483294-70483530(-)$1	1	86	108	17.5998
(((((..............)))	chr15:83666718-83666956(+)$1	1	71	93	20.0878
(((..............)))).	chr7:148337524-148337759(+)$1	1	140	162	18.2795
(((((............)))))	chr11:86602657-86602898(-)$1	1	170	192	19.3098
(((((................)	chr11:31917577-31917812(+)$1	1	105	127	19.6184
.((((............)))).	chr3:146395453-146395688(-)$1	1	60	82	18.6495
((((.............)))).	chr11:72025341-72025578(-)$1	1	178	200	18.4631
(((((.................	chr10:126680660-126680895(-)$1	1	123	145	17.3261
(((..............))))(	chr15:99351509-99351763(-)$1	1	41	63	18.6724
.(((..................	chr11:55208949-55209192(-)$1	1	159	181	17.4617
((((.............)))))	chr10:53063680-53063917(+)$1	1	74	96	18.4484
.((((............)))).	chr9:95945897-95946132(+)$1	1	113	135	20.3274
(((((.................	chr6:4706066-4706310(+)$1	1	181	203	16.3508
(.(((...........))).))	chr8:63391717-63391957(-)$1	1	170	192	17.8279
(((((...........))))))	chr8:46095312-46095551(+)$1	1	146	168	15.8632
(((((.................	chr16:14153931-14154176(-)$1	1	42	64	16.1667
..(((.................	chr11:70483254-70483493(-)$1	1	49	71	17.5998
.((((...........))))))	chr5:90646461-90646698(-)$1	1	214	236	14.9152
(((((.............))))	chr19:10058659-10058899(+)$1	1	64	86	17.1321
.((((.................	chr5:72015103-72015349(-)$1	1	133	155	17.5330
.((((.(...............	chr7:65047791-65048042(+)$1	1	40	62	16.1579
.((((...........))))..	chr18:46664687-46664922(-)$1	1	63	85	16.6603
..(((............)))..	chr5:137736972-137737209(-)$1	1	188	210	20.3068
.((...............))..	chr11:41946818-41947090(-)$1	1	91	113	15.4950
(.(((............)))))	chr10:106256389-106256638(+)$1	1	30	52	20.1949
.((((...........))))..	chr8:41532325-41532562(+)$1	1	122	144	16.8694
.((((..............)))	chr19:10058581-10058825(+)$1	1	120	142	20.2587
(((((...........))))..	chr2:34631511-34631748(+)$1	1	19	41	15.4109
(((((..............)))	chr1:75212189-75212442(-)$1	1	177	199	20.2707
(((((............)))))	chr2:181041975-181042222(-)$1	1	222	244	19.3102
(((((.................	chr12:4637380-4637615(+)$1	1	20	42	16.9413
(((.(...............).	chr19:7289793-7290030(-)$1	1	32	54	17.3575
.(((((.............)))	chrX:148326258-148326496(+)$1	1	120	142	18.1891
(((((((..........))).)	chr16:35299447-35299697(+)$1	1	79	101	12.7745
...((.............))..	chr8:47292820-47293064(-)$1	1	131	153	17.8686
(((((.............)).)	chr5:138398460-138398701(-)$1	1	139	161	18.7730
(((((................)	chr5:34186114-34186353(+)$1	1	134	156	18.9310
.((((...............))	chr10:41239320-41239558(+)$1	1	89	111	17.5028
((((((...........)))))	chr19:10058959-10059195(+)$1	1	212	234	16.5646
((.((.................	chr6:117123446-117123681(+)$1	1	67	89	16.5324
.((((...............))	chr1:174210640-174210877(-)$1	1	203	225	17.4276
.((((.................	chr4:148761180-148761417(-)$1	1	60	82	17.4909
))(((.............))).	chr6:4591853-4592090(+)$1	1	70	92	19.3944

#PSSM
! : 0.11	[ : 0.11	g : 0.11	c : 0.09	d : 0.09	e : 0.08	f : 0.08	" : 0.05	: : 0.05	# : 0.05	= : 0.03	h : 0.03	' : 0.01	$ : 0.01	D : 0.01	i : 0.01	
d : 0.36	c : 0.15	g : 0.09	e : 0.08	f : 0.06	! : 0.05	= : 0.03	[ : 0.03	h : 0.03	: : 0.01	# : 0.01	b : 0.01	" : 0.01	i : 0.01	
d : 0.35	c : 0.28	e : 0.08	g : 0.08	f : 0.06	= : 0.03	[ : 0.03	h : 0.03	b : 0.01	" : 0.01	
d : 0.30	c : 0.24	e : 0.08	g : 0.08	f : 0.06	[ : 0.05	w : 0.05	b : 0.05	h : 0.03	= : 0.01	x : 0.01	
d : 0.26	c : 0.23	g : 0.08	e : 0.06	f : 0.06	v : 0.05	w : 0.05	b : 0.05	^ : 0.03	x : 0.03	h : 0.03	= : 0.01	a : 0.01	
^ : 0.21	t : 0.15	u : 0.15	v : 0.11	w : 0.09	x : 0.08	c : 0.06	y : 0.05	= : 0.01	[ : 0.01	e : 0.01	g : 0.01	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.08	c : 0.05	y : 0.05	s : 0.01	a : 0.01	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.09	s : 0.06	y : 0.05	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.09	s : 0.06	y : 0.05	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.09	s : 0.06	y : 0.05	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.09	s : 0.06	y : 0.05	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.09	s : 0.06	y : 0.05	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.09	s : 0.06	y : 0.05	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.09	s : 0.06	y : 0.05	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.09	s : 0.06	y : 0.05	
^ : 0.21	t : 0.18	u : 0.15	v : 0.13	w : 0.09	x : 0.09	s : 0.06	y : 0.05	
^ : 0.21	u : 0.15	v : 0.13	w : 0.09	x : 0.09	d : 0.06	s : 0.05	y : 0.05	c : 0.05	e : 0.03	t : 0.03	f : 0.01	
^ : 0.21	d : 0.18	c : 0.16	x : 0.09	v : 0.08	e : 0.06	y : 0.05	w : 0.05	f : 0.03	g : 0.03	= : 0.01	
^ : 0.21	c : 0.18	d : 0.18	x : 0.08	e : 0.06	y : 0.05	w : 0.05	b : 0.05	f : 0.03	g : 0.03	= : 0.01	h : 0.01	v : 0.01	
^ : 0.21	d : 0.21	c : 0.16	e : 0.08	x : 0.06	y : 0.05	g : 0.05	b : 0.05	f : 0.03	: : 0.01	= : 0.01	] : 0.01	h : 0.01	
^ : 0.21	d : 0.18	e : 0.11	c : 0.06	] : 0.06	g : 0.06	y : 0.05	f : 0.03	2 : 0.03	5 : 0.03	8 : 0.01	= : 0.01	C : 0.01	h : 0.01	x : 0.01	9 : 0.01	: : 0.01	a : 0.01	
^ : 0.21	d : 0.09	: : 0.09	e : 0.09	g : 0.08	c : 0.06	= : 0.05	] : 0.05	f : 0.05	2 : 0.05	5 : 0.03	8 : 0.01	b : 0.01	C : 0.01	h : 0.01	x : 0.01	9 : 0.01	

#score	1055.1926385499737
#seq	60
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_UTR_m3_run1.txt

#BEAR
""cccqqqqqqqqccce	chr2:148522020-148522233(-)$1	213	135	152	13.6556
!!cccqqqqqqqqccc2	chr4:151645607-151645809(+)$1	202	117	134	13.5179
!!cccqqqqqqqqccc2	chr11:106363824-106364040(-)$1	216	192	209	13.5179
dd[bbqqqqqqqqbb]d	chr9:109905370-109905571(+)$1	201	16	33	12.3429
gggggqqqqqqqqgggg	chr1:157899592-157899814(-)$1	222	130	147	13.1092
:ddddqqqqqqqqdddd	chr4:108734184-108734397(+)$1	213	175	192	14.2050
:ddddqqqqqqqqdddd	chr19:46962819-46963019(+)$1	200	178	195	14.2050
:ddddqqqqqqqqdddd	chr17:25967512-25967726(-)$1	214	2	19	14.2050
gggggqqqqqqqqgggg	chr18:67384822-67385044(-)$1	222	168	185	13.1092
"ddddqqqqqqqqdddd	chr10:107935754-107935954(-)$1	200	52	69	14.8675
eeeeeqqqqqqqqeeee	chr13:54780752-54780964(-)$1	212	77	94	14.0538
:ddddqqqqqqqqdddd	chr4:75587960-75588176(-)$1	216	123	140	14.2050
:ddddqqqqqqqqdddd	chr19:44471777-44471978(-)$1	201	40	57	14.2050
"""bbqqqqqqqqbb44	chr15:96406676-96406878(-)$1	202	47	64	12.0567
:ddddqqqqqqqqdddd	chr1:163917737-163917946(-)$1	209	128	145	14.2050
a[cccqqqqqqqqccc]	chr7:67133476-67133682(-)$1	206	32	49	13.5494
#ddddqqqqqqqqdddd	chr3:95038641-95038847(+)$1	206	136	153	14.8539
:ddddqqqqqqqqdddd	chr9:54452171-54452379(+)$1	208	58	75	14.2050
[ddddqqqqqqqqdddd	chr6:13038928-13039136(-)$1	208	132	149	14.8664
eeeeeqqqqqqqqeeee	chr2:6468009-6468211(-)$1	202	11	28	14.0538
eeeeeqqqqqqqqeeee	chr9:36686079-36686288(+)$1	209	180	197	14.0538
eeeeeqqqqqqqqeeee	chr12:8992445-8992669(+)$1	224	151	168	14.0538
iiiiiqqqqqqqqiiii	chr8:96590825-96591032(+)$1	207	13	30	13.0315
eeeeeqqqqqqqqeeee	chr2:166928761-166928985(+)$1	224	49	66	14.0538
eeeeeqqqqqqqqeeee	chr15:30958131-30958331(-)$1	200	12	29	14.0538
##cccqqqqqqqqccc2	chr2:52283910-52284117(-)$1	207	114	131	13.2833
:ddddqqqqqqqqdddd	chr10:7433256-7433467(+)$1	211	49	66	14.2050
:ddddqqqqqqqqdddd	chr9:89921555-89921755(-)$1	200	2	19	14.2050
!!cccqqqqqqqqccc]	chr11:52059497-52059702(+)$1	205	87	104	13.7101
b[cccqqqqqqqqccc]	chr18:15550553-15550765(-)$1	212	105	122	13.3489
gggggqqqqqqqqgggg	chr19:46962211-46962423(-)$1	212	146	163	13.1092
cccbbqqqqqqqqbb]c	chr2:26775573-26775782(+)$1	209	123	140	12.1186
Gddddqqqqqqqqdddd	chrX:92246689-92246896(-)$1	207	183	200	14.4938
!ddddqqqqqqqqdddd	chr6:35459938-35460140(-)$1	202	164	181	14.9180
eeeeeqqqqqqqqeeee	chr1:81333225-81333439(+)$1	214	104	121	14.0538
fffffqqqqqqqqffff	chr19:41288869-41289075(-)$1	206	74	91	12.2360
$ddddqqqqqqqqdddd	chr13:99018263-99018475(-)$1	212	126	143	14.6832
cccccqqqqqqqqccc]	chr19:46386495-46386697(+)$1	202	48	65	13.4132
Jddddqqqqqqqqdddd	chr16:31872214-31872420(-)$1	206	158	175	13.5722
fffffqqqqqqqqffff	chr19:59979615-59979834(-)$1	219	18	35	12.2360
fff[aqqqqqqqqa]ff	chr11:87794087-87794292(-)$1	205	170	187	12.3654
fffffqqqqqqqqffff	chr2:150658292-150658495(-)$1	203	5	22	12.2360
:ddddqqqqqqqqdddd	chr15:4104282-4104488(+)$1	206	71	88	14.2050
=====qqqqqqqq====	chr10:111900717-111900918(+)$1	201	146	163	13.2414
eeeeeqqqqqqqqeeee	chr8:114060741-114060944(+)$1	203	129	146	14.0538
[ddddqqqqqqqqdddd	chr4:148554674-148554877(-)$1	203	40	57	14.8664
eeeeeqqqqqqqqeeee	chr16:5014103-5014313(+)$1	210	28	45	14.0538
eeeeeqqqqqqqqeeee	chr7:4744731-4744934(+)$1	203	79	96	14.0538
:ddddqqqqqqqqdddd	chr9:75421331-75421538(-)$1	207	144	161	14.2050
e[cccqqqqqqqqccc2	chrX:133371924-133372132(+)$1	208	105	122	13.3381
eeeeeqqqqqqqqeeee	chr7:31220056-31220259(-)$1	203	40	57	14.0538
:ddddqqqqqqqqdddd	chr16:49913322-49913525(+)$1	203	121	138	14.2050
eeeeeqqqqqqqqeeee	chr4:119299136-119299339(+)$1	203	87	104	14.0538
[ddddqqqqqqqqdddd	chr2:117107111-117107319(-)$1	208	181	198	14.8664
fffffqqqqqqqqffff	chr7:99595348-99595561(+)$1	213	48	65	12.2360
:ddddqqqqqqqqdddd	chr2:84442196-84442413(-)$1	217	99	116	14.2050
e!!bbqqqqqqqqbb44	chr7:150078652-150078873(+)$1	221	159	176	12.2217
eeeeeqqqqqqqqeeee	chr12:60059707-60059920(-)$1	213	155	172	14.0538
[ddddqqqqqqqqdddd	chr6:126589028-126589228(-)$1	200	91	108	14.8664
Fddddqqqqqqqqdddd	chr15:100651396-100651608(+)$1	212	10	27	14.5250
gggggqqqqqqqqgggg	chr6:119876185-119876392(+)$1	207	109	126	13.1092
dddddqqqqqqqqdddd	chr15:96406980-96407181(-)$1	201	107	124	14.6011
eeeeeqqqqqqqqeeee	chr15:93115032-93115235(-)$1	203	42	59	14.0538
[ddddqqqqqqqqdddd	chr11:76594172-76594383(-)$1	211	120	137	14.8664
:ddddqqqqqqqqdddd	chr1:136096988-136097194(-)$1	206	19	36	14.2050
eddddqqqqqqqqdddd	chr18:24049759-24049969(+)$1	210	192	209	14.7726
eee[aqqqqqqqqa22e	chr9:57290726-57290929(+)$1	203	81	98	12.7602
eeeeeqqqqqqqqeeee	chr9:108720269-108720474(+)$1	205	154	171	14.0538

#otherMatches

#Seq PSSM
UGCUCUGUUAUUUGAGA	chr2:148522020-148522233(-)$1	213	135	152	13.6556
CCAGUAUGCAGUCACUU	chr4:151645607-151645809(+)$1	202	117	134	13.5179
UUUGUUUAAAGCUGCAU	chr11:106363824-106364040(-)$1	216	192	209	13.5179
GCCUCUUUCUGCUGAUG	chr9:109905370-109905571(+)$1	201	16	33	12.3429
UAUGCUAAAAUAUGCAU	chr1:157899592-157899814(-)$1	222	130	147	13.1092
AGGUUAUAGGUGAAACC	chr4:108734184-108734397(+)$1	213	175	192	14.2050
UUCGUACAUCCAGAUGA	chr19:46962819-46963019(+)$1	200	178	195	14.2050
UGGGUUCUGAACUGCUC	chr17:25967512-25967726(-)$1	214	2	19	14.2050
GUGUUUCUGUGCUAAUG	chr18:67384822-67385044(-)$1	222	168	185	13.1092
CUGUGCACUAGUCCACA	chr10:107935754-107935954(-)$1	200	52	69	14.8675
CUUUUUUUAAAAUGAAA	chr13:54780752-54780964(-)$1	212	77	94	14.0538
AGUUUAAUUUCCCAGGC	chr4:75587960-75588176(-)$1	216	123	140	14.2050
CUUUCUGUUUUCUGAAA	chr19:44471777-44471978(-)$1	201	40	57	14.2050
UCUUCACUUGUUAGAUA	chr15:96406676-96406878(-)$1	202	47	64	12.0567
CUUCUCCCAAACCAGAA	chr1:163917737-163917946(-)$1	209	128	145	14.2050
UGUGUUUUCCUCUGCAG	chr7:67133476-67133682(-)$1	206	32	49	13.5494
uuuaauuaaaauuuuaa	chr3:95038641-95038847(+)$1	206	136	153	14.8539
AGCUGUCUUCCCUUAGC	chr9:54452171-54452379(+)$1	208	58	75	14.2050
UAUUCCACCAUCCGAAU	chr6:13038928-13039136(-)$1	208	132	149	14.8664
UUUCAGAUCGGCAUGAA	chr2:6468009-6468211(-)$1	202	11	28	14.0538
UGUAUUUAAACGUGUAU	chr9:36686079-36686288(+)$1	209	180	197	14.0538
CAAAGUAAGCAAUCUUU	chr12:8992445-8992669(+)$1	224	151	168	14.0538
AAAUAACUCAAAAUAUU	chr8:96590825-96591032(+)$1	207	13	30	13.0315
CUUGUUUUAAAGUGCGA	chr2:166928761-166928985(+)$1	224	49	66	14.0538
UGAAAAAAAUCUAUUUC	chr15:30958131-30958331(-)$1	200	12	29	14.0538
UUUGUGAACAAAGACAU	chr2:52283910-52284117(-)$1	207	114	131	13.2833
CUGUAAUCACAAAUACA	chr10:7433256-7433467(+)$1	211	49	66	14.2050
AGAGAUAAUAUAUUCUC	chr9:89921555-89921755(-)$1	200	2	19	14.2050
UUUAUAAUUGUUAAUAU	chr11:52059497-52059702(+)$1	205	87	104	13.7101
CCUUCCGCCCAUCGAAU	chr18:15550553-15550765(-)$1	212	105	122	13.3489
CUAUUGCUCUUCAAAUG	chr19:46962211-46962423(-)$1	212	146	163	13.1092
UGCCAAACCAAUAUGUG	chr2:26775573-26775782(+)$1	209	123	140	12.1186
GAGGAUUCCCGUCUCCU	chrX:92246689-92246896(-)$1	207	183	200	14.4938
AGUUUCuuuaaaaaaau	chr6:35459938-35460140(-)$1	202	164	181	14.9180
UGAGCUCCACAUUGCUU	chr1:81333225-81333439(+)$1	214	104	121	14.0538
uuuaaaaacaaaauuaa	chr19:41288869-41289075(-)$1	206	74	91	12.2360
AUAUGUAACCCUCCAUA	chr13:99018263-99018475(-)$1	212	126	143	14.6832
CCCUGAGCGAGAAUAGA	chr19:46386495-46386697(+)$1	202	48	65	13.4132
AAGCGUGCACAGUUGCU	chr16:31872214-31872420(-)$1	206	158	175	13.5722
AGUUGUAAUUUUCCAGC	chr19:59979615-59979834(-)$1	219	18	35	12.2360
AUUUCUGGUGACUGUAG	chr11:87794087-87794292(-)$1	205	170	187	12.3654
AGGAAAAUGGUUCUUUC	chr2:150658292-150658495(-)$1	203	5	22	12.2360
AAGACAACCAACCGUCU	chr15:4104282-4104488(+)$1	206	71	88	14.2050
CUGCAUGUUGAAUUGUG	chr10:111900717-111900918(+)$1	201	146	163	13.2414
UGAGGAUUCCCCCCCUC	chr8:114060741-114060944(+)$1	203	129	146	14.0538
AAGUGUUACCUCUCAUU	chr4:148554674-148554877(-)$1	203	40	57	14.8664
GUGAAAAUAAAAAUUCA	chr16:5014103-5014313(+)$1	210	28	45	14.0538
AAAGCUCUUGCUCGCUU	chr7:4744731-4744934(+)$1	203	79	96	14.0538
AGUGUCUCUACAUGCAC	chr9:75421331-75421538(-)$1	207	144	161	14.2050
AUAGAAGUUACUGUCUC	chrX:133371924-133372132(+)$1	208	105	122	13.3381
GACAAAUUCAUUCUUGU	chr7:31220056-31220259(-)$1	203	40	57	14.0538
UCAAUUUUUAUUUAUUG	chr16:49913322-49913525(+)$1	203	121	138	14.2050
CUGUUGUGAUUUGGACA	chr4:119299136-119299339(+)$1	203	87	104	14.0538
CUGCUCAUUAUAAGGCA	chr2:117107111-117107319(-)$1	208	181	198	14.8664
AACCACAAACCAUUGGU	chr7:99595348-99595561(+)$1	213	48	65	12.2360
UGCUAACUUGACCUGGC	chr2:84442196-84442413(-)$1	217	99	116	14.2050
CAAGAGCAGCCCAUCAA	chr7:150078652-150078873(+)$1	221	159	176	12.2217
UUUUAAAAUCUAGUAAA	chr12:60059707-60059920(-)$1	213	155	172	14.0538
GGGCACUCUACCCUGCU	chr6:126589028-126589228(-)$1	200	91	108	14.8664
cagagauuuuuagcucu	chr15:100651396-100651608(+)$1	212	10	27	14.5250
UAGUUAGUAUAUAGGCU	chr6:119876185-119876392(+)$1	207	109	126	13.1092
UUUUGCAAGUUUACAGA	chr15:96406980-96407181(-)$1	201	107	124	14.6011
UGCUUAUUUUUCAAAGC	chr15:93115032-93115235(-)$1	203	42	59	14.0538
ACUUGUACUAAAUCAGG	chr11:76594172-76594383(-)$1	211	120	137	14.8664
UGGUACCCAGAUCUGCC	chr1:136096988-136097194(-)$1	206	19	36	14.2050
UGACAGUAGCUUGUGUC	chr18:24049759-24049969(+)$1	210	192	209	14.7726
UUUAGGAAGACAACGAA	chr9:57290726-57290929(+)$1	203	81	98	12.7602
CUGAGUCUUGACCCUCA	chr9:108720269-108720474(+)$1	205	154	171	14.0538

#DB
..(((........))))	chr2:148522020-148522233(-)$1	1	135	152	13.6556
..(((........))).	chr4:151645607-151645809(+)$1	1	117	134	13.5179
..(((........))).	chr11:106363824-106364040(-)$1	1	192	209	13.5179
((.((........)).)	chr9:109905370-109905571(+)$1	1	16	33	12.3429
(((((........))))	chr1:157899592-157899814(-)$1	1	130	147	13.1092
.((((........))))	chr4:108734184-108734397(+)$1	1	175	192	14.2050
.((((........))))	chr19:46962819-46963019(+)$1	1	178	195	14.2050
.((((........))))	chr17:25967512-25967726(-)$1	1	2	19	14.2050
(((((........))))	chr18:67384822-67385044(-)$1	1	168	185	13.1092
.((((........))))	chr10:107935754-107935954(-)$1	1	52	69	14.8675
(((((........))))	chr13:54780752-54780964(-)$1	1	77	94	14.0538
.((((........))))	chr4:75587960-75588176(-)$1	1	123	140	14.2050
.((((........))))	chr19:44471777-44471978(-)$1	1	40	57	14.2050
...((........))..	chr15:96406676-96406878(-)$1	1	47	64	12.0567
.((((........))))	chr1:163917737-163917946(-)$1	1	128	145	14.2050
(.(((........))).	chr7:67133476-67133682(-)$1	1	32	49	13.5494
.((((........))))	chr3:95038641-95038847(+)$1	1	136	153	14.8539
.((((........))))	chr9:54452171-54452379(+)$1	1	58	75	14.2050
.((((........))))	chr6:13038928-13039136(-)$1	1	132	149	14.8664
(((((........))))	chr2:6468009-6468211(-)$1	1	11	28	14.0538
(((((........))))	chr9:36686079-36686288(+)$1	1	180	197	14.0538
(((((........))))	chr12:8992445-8992669(+)$1	1	151	168	14.0538
(((((........))))	chr8:96590825-96591032(+)$1	1	13	30	13.0315
(((((........))))	chr2:166928761-166928985(+)$1	1	49	66	14.0538
(((((........))))	chr15:30958131-30958331(-)$1	1	12	29	14.0538
..(((........))).	chr2:52283910-52284117(-)$1	1	114	131	13.2833
.((((........))))	chr10:7433256-7433467(+)$1	1	49	66	14.2050
.((((........))))	chr9:89921555-89921755(-)$1	1	2	19	14.2050
..(((........))).	chr11:52059497-52059702(+)$1	1	87	104	13.7101
(.(((........))).	chr18:15550553-15550765(-)$1	1	105	122	13.3489
(((((........))))	chr19:46962211-46962423(-)$1	1	146	163	13.1092
(((((........)).)	chr2:26775573-26775782(+)$1	1	123	140	12.1186
)((((........))))	chrX:92246689-92246896(-)$1	1	183	200	14.4938
.((((........))))	chr6:35459938-35460140(-)$1	1	164	181	14.9180
(((((........))))	chr1:81333225-81333439(+)$1	1	104	121	14.0538
(((((........))))	chr19:41288869-41289075(-)$1	1	74	91	12.2360
.((((........))))	chr13:99018263-99018475(-)$1	1	126	143	14.6832
(((((........))).	chr19:46386495-46386697(+)$1	1	48	65	13.4132
)((((........))))	chr16:31872214-31872420(-)$1	1	158	175	13.5722
(((((........))))	chr19:59979615-59979834(-)$1	1	18	35	12.2360
(((.(........).))	chr11:87794087-87794292(-)$1	1	170	187	12.3654
(((((........))))	chr2:150658292-150658495(-)$1	1	5	22	12.2360
.((((........))))	chr15:4104282-4104488(+)$1	1	71	88	14.2050
(((((........))))	chr10:111900717-111900918(+)$1	1	146	163	13.2414
(((((........))))	chr8:114060741-114060944(+)$1	1	129	146	14.0538
.((((........))))	chr4:148554674-148554877(-)$1	1	40	57	14.8664
(((((........))))	chr16:5014103-5014313(+)$1	1	28	45	14.0538
(((((........))))	chr7:4744731-4744934(+)$1	1	79	96	14.0538
.((((........))))	chr9:75421331-75421538(-)$1	1	144	161	14.2050
(.(((........))).	chrX:133371924-133372132(+)$1	1	105	122	13.3381
(((((........))))	chr7:31220056-31220259(-)$1	1	40	57	14.0538
.((((........))))	chr16:49913322-49913525(+)$1	1	121	138	14.2050
(((((........))))	chr4:119299136-119299339(+)$1	1	87	104	14.0538
.((((........))))	chr2:117107111-117107319(-)$1	1	181	198	14.8664
(((((........))))	chr7:99595348-99595561(+)$1	1	48	65	12.2360
.((((........))))	chr2:84442196-84442413(-)$1	1	99	116	14.2050
(..((........))..	chr7:150078652-150078873(+)$1	1	159	176	12.2217
(((((........))))	chr12:60059707-60059920(-)$1	1	155	172	14.0538
.((((........))))	chr6:126589028-126589228(-)$1	1	91	108	14.8664
(((((........))))	chr15:100651396-100651608(+)$1	1	10	27	14.5250
(((((........))))	chr6:119876185-119876392(+)$1	1	109	126	13.1092
(((((........))))	chr15:96406980-96407181(-)$1	1	107	124	14.6011
(((((........))))	chr15:93115032-93115235(-)$1	1	42	59	14.0538
.((((........))))	chr11:76594172-76594383(-)$1	1	120	137	14.8664
.((((........))))	chr1:136096988-136097194(-)$1	1	19	36	14.2050
)((((........))))	chr18:24049759-24049969(+)$1	1	192	209	14.7726
(((.(........)..)	chr9:57290726-57290929(+)$1	1	81	98	12.7602
(((((........))))	chr9:108720269-108720474(+)$1	1	154	171	14.0538

#PSSM
e : 0.27	: : 0.20	[ : 0.07	f : 0.07	! : 0.05	g : 0.05	" : 0.04	d : 0.02	# : 0.02	c : 0.02	a : 0.01	i : 0.01	b : 0.01	G : 0.01	$ : 0.01	J : 0.01	= : 0.01	F : 0.01	
d : 0.42	e : 0.23	f : 0.07	! : 0.05	g : 0.05	[ : 0.04	" : 0.02	c : 0.02	i : 0.01	# : 0.01	= : 0.01	
d : 0.41	e : 0.23	c : 0.14	f : 0.07	g : 0.05	[ : 0.01	" : 0.01	i : 0.01	= : 0.01	! : 0.01	
d : 0.41	e : 0.22	c : 0.13	b : 0.05	g : 0.05	f : 0.05	[ : 0.02	i : 0.01	= : 0.01	
d : 0.41	e : 0.22	c : 0.13	b : 0.05	g : 0.05	f : 0.05	a : 0.02	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 : 0.41	e : 0.22	c : 0.13	b : 0.05	g : 0.05	f : 0.05	a : 0.02	i : 0.01	= : 0.01	
d : 0.41	e : 0.22	c : 0.13	b : 0.05	g : 0.05	f : 0.05	i : 0.01	] : 0.01	= : 0.01	2 : 0.01	
d : 0.41	e : 0.22	c : 0.13	f : 0.07	g : 0.05	] : 0.02	4 : 0.02	i : 0.01	= : 0.01	2 : 0.01	
d : 0.42	e : 0.25	f : 0.07	2 : 0.05	g : 0.05	] : 0.05	4 : 0.02	i : 0.01	c : 0.01	= : 0.01	

#score	938.1541379865498
#seq	68
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_UTR_m3_run1.txt

#BEAR
iiiiiiiiimmmmiiiiiiiii	chr2:32162847-32163126(+)$1	279	172	194	10.5571
fffffddddmmmmdddd333ff	chr6:30079454-30079729(+)$1	275	41	63	8.2333
iiiiiiiiimmmmiiiiiiiii	chr2:32134292-32134590(-)$1	298	196	218	10.5571
eeeee[cccmmmmccc]eeeee	chr2:30302693-30302995(+)$1	302	235	257	10.2064
!eeeee[bbmmmmbb]eeeee2	chr4:151560200-151560489(+)$1	289	186	208	8.4619
iiiiiiiiiooooooiiiiiii	chr6:56728726-56729000(-)$1	274	164	186	7.9441
eeeee[cccmmmmccc]eeeee	chr4:33125089-33125364(+)$1	275	209	231	10.2064
fiiiiiiiiillliiiiiiiii	chr3:145309905-145310179(-)$1	274	17	39	8.2539
dd####cccmmmmccc333ddd	chr5:145942303-145942575(+)$1	272	152	174	10.7822
dd[ffffffmmmmffffff]dd	chr10:76508552-76508827(+)$1	275	17	39	8.9717
cc[bb!!ccclllccc]bb]cc	chr11:117828673-117828945(-)$1	272	223	245	8.0379
eeeee[cccmmmmccceeeee3	chr2:79512562-79512842(+)$1	280	243	265	10.1758
dd[bb[cccmmmmcccbb]ddd	chr4:63211330-63211606(+)$1	276	236	258	9.4299
ccccc!!bbmmmmbb22ccc]c	chr7:72016753-72017039(-)$1	286	89	111	9.6008
=========mmmm=========	chr9:30881655-30881942(+)$1	287	187	209	11.0699
iiiiiiiiiooooooiiiiiii	chr16:98170644-98170921(-)$1	277	117	139	7.9441
e[aa!!cccmmmmccc22a]a]	chr12:113887155-113887428(+)$1	273	25	47	11.3199
ggg"""cccmmmmccc22gggg	chr16:92084361-92084635(+)$1	274	149	171	11.3200
=========mmmm=========	chr18:34930930-34931222(+)$1	292	114	136	11.0699
!dddd!!bbmmmmbb]dddd22	chr15:101926263-101926530(+)$1	267	80	102	8.3105
dd[ffffffmmmmffffff]dd	chrX:11614220-11614489(-)$1	269	23	45	8.9717
dddffffffmmmmffffff]dd	chr11:87794777-87795061(-)$1	284	227	249	8.6191
ccc"""cccmmmmcccccc555	chr17:35119075-35119345(+)$1	270	139	161	8.7935
fffff[cccmmmmccc]fffff	chr3:95464619-95464908(+)$1	289	176	198	10.4120
ggggg[cccmmmmccc]ggggg	chr11:98015256-98015533(-)$1	277	198	220	11.4611
ccc[cccbbmmmmbb22ccc22	chr9:90098144-90098412(-)$1	268	73	95	9.4098
da[ffffffmmmmffffff]a]	chr15:80761843-80762129(+)$1	286	202	224	9.3937
h[gggggggmmmmggggggg]h	chr7:30106085-30106361(-)$1	276	91	113	9.9105
[ccc!!cccmmmmccc22ccc]	chr14:55505758-55506041(+)$1	283	114	136	11.2214
cc!!eeeeemmmmeeeee]ccc	chr11:79506341-79506633(+)$1	292	38	60	8.2706
eee"""cccmmmmccc333eee	chr11:53590397-53590671(+)$1	274	139	161	11.0957
!a[ffffffmmmmffffff]a2	chr2:31615419-31615714(+)$1	295	77	99	9.4432
ggg[a[cccmmmmccc]agggg	chr11:52221498-52221778(+)$1	280	194	216	11.4781
eeeffffffmmmmffffff333	chr19:8964904-8965185(+)$1	281	169	191	9.2705
e[dddd[bbmmmmbb]dddd22	chr10:20845089-20845386(-)$1	297	99	121	7.8829
cc####cccmmmmcccccc]dd	chr11:117828139-117828471(-)$1	332	183	205	10.9412
iiiiiiiiiooooooiiiiiii	chr16:98170671-98170948(-)$1	277	144	166	7.9441
a[ccc[cccmmmmcccccc]a2	chr4:126421180-126421460(-)$1	280	127	149	11.2149
cc[a[ddddmmmmddddaccc3	chr6:140543072-140543349(+)$1	277	144	166	8.8921
!!ccc[cccmmmmcccccc22g	chr17:37209972-37210240(+)$1	268	136	158	10.8672
!a[ccccccmmmmccc22ccc]	chr8:125096545-125096859(+)$1	314	188	210	10.8542
a[ggggggglllggggggg]af	chr3:122242260-122242557(-)$1	297	151	173	7.7613
ff[bb[cccmmmmccc]bbfff	chr3:108163839-108164128(+)$1	289	19	41	9.8849
ffff"""bbmmmmbb333ffff	chr3:90057072-90057343(+)$1	271	22	44	9.6066
""gggggggmmmmggggggg33	chr7:151775188-151775455(-)$1	267	27	49	10.3084
ddd"""cccmmmmccc4444dd	chr1:36501838-36502111(-)$1	273	97	119	10.6111
b[gggggggmmmmggggggg]b	chr7:25670028-25670303(+)$1	275	159	181	9.5622
ccc[cccbbmmmmbb]ccc]cc	chr17:57032824-57033135(-)$1	311	16	38	9.9185
H:ccc[cccmmmmccc4444cc	chr17:32498275-32498549(-)$1	274	19	41	9.2621
ffff!!cccmmmmccc22ffff	chr11:68635132-68635416(-)$1	284	6	28	10.4453
eeea[ddddmmmmdddd]a]ee	chr19:5456434-5456714(-)$1	280	2	24	8.3736
ccc[cccbbmmmmbb]cccccc	chr15:80761601-80761877(+)$1	276	199	221	9.6286
ggg[a[ccclllccc]aggggg	chr1:181447940-181448228(-)$1	288	251	273	8.8156

#otherMatches

#Seq PSSM
AGGCAGUUGGGGCUAACUGCCU	chr2:32162847-32163126(+)$1	279	172	194	10.5571
AAAGGGAGCCUUUGCUUCAGCC	chr6:30079454-30079729(+)$1	275	41	63	8.2333
ACAUACUUGUGAGUAGGUGUGU	chr2:32134292-32134590(-)$1	298	196	218	10.5571
CUGGGCCUAGGCAUAGACUCAG	chr2:30302693-30302995(+)$1	302	235	257	10.2064
GCCUGGCCAGGAGUGUUCGGGG	chr4:151560200-151560489(+)$1	289	186	208	8.4619
UAUCCUUUGCUAAACCAGAGGA	chr6:56728726-56729000(-)$1	274	164	186	7.9441
GCUAACAGUAAGAGCUCUUGGC	chr4:33125089-33125364(+)$1	275	209	231	10.2064
GGGGACACUCUGUGAGUGUCCU	chr3:145309905-145310179(-)$1	274	17	39	8.2539
CCAGCACCUAAAGAGGACGGGU	chr5:145942303-145942575(+)$1	272	152	174	10.7822
CUUUGGUUUCCCUGGGCCAUAG	chr10:76508552-76508827(+)$1	275	17	39	8.9717
CCCGCAGAGUAGAGCUGGCAGG	chr11:117828673-117828945(-)$1	272	223	245	8.0379
AACCAGUGAAAACUCGUGGUUU	chr2:79512562-79512842(+)$1	280	243	265	10.1758
AGCCUUAGAGUACUCUAGCCUG	chr4:63211330-63211606(+)$1	276	236	258	9.4299
GGUCUGAGGGACUCUGGAGAUC	chr7:72016753-72017039(-)$1	286	89	111	9.6008
UUAUUUUGUUUAUACAAAAUGA	chr9:30881655-30881942(+)$1	287	187	209	11.0699
UUCUGAGUAGUGGGAUGCUUGG	chr16:98170644-98170921(-)$1	277	117	139	7.9441
AACUGUGCAGCUAUGCCGACGA	chr12:113887155-113887428(+)$1	273	25	47	11.3199
CAGGAACGGAGCUCUGCGCUGG	chr16:92084361-92084635(+)$1	274	149	171	11.3200
uguguacuugugugagugugcg	chr18:34930930-34931222(+)$1	292	114	136	11.0699
GAGUGAGUCUACGGGGCACUAA	chr15:101926263-101926530(+)$1	267	80	102	8.3105
UUCUUUUCUAAGGAGaaaaaaa	chrX:11614220-11614489(-)$1	269	23	45	8.9717
UGGCUGUGCUACUGCAUGGACU	chr11:87794777-87795061(-)$1	284	227	249	8.6191
GGAAACCUUUAGCAAGUCCAAG	chr17:35119075-35119345(+)$1	270	139	161	8.7935
UGCAUCUGUGAAAACAUGUGUA	chr3:95464619-95464908(+)$1	289	176	198	10.4120
GACCUUUUUGGAGAAACAGGUC	chr11:98015256-98015533(-)$1	277	198	220	11.4611
GCCCCACCCCCUUGGAAGUGCC	chr9:90098144-90098412(-)$1	268	73	95	9.4098
GCAUGUAAGUGGCUUUGUAAGA	chr15:80761843-80762129(+)$1	286	202	224	9.3937
auauauauauauauauauauuu	chr7:30106085-30106361(-)$1	276	91	113	9.9105
UGUUUUAGUCCAGACUUUGGCU	chr14:55505758-55506041(+)$1	283	114	136	11.2214
CUAAGGGCAGGCCUGCCUGAGG	chr11:79506341-79506633(+)$1	292	38	60	8.2706
GCACUUUCUCUGUGGACUUUGC	chr11:53590397-53590671(+)$1	274	139	161	11.0957
GCGCGGCCUGGCGGGGCUGGGG	chr2:31615419-31615714(+)$1	295	77	99	9.4432
aggucagagguuucucaguuug	chr11:52221498-52221778(+)$1	280	194	216	11.4781
AAAAAAUAUUAGCAUAUUUCAC	chr19:8964904-8965185(+)$1	281	169	191	9.2705
UUUAGCCUGUAGUCAUGCUGCU	chr10:20845089-20845386(-)$1	297	99	121	7.8829
GCUAUACUGGUGCCAGGCUCCU	chr11:117828139-117828471(-)$1	332	183	205	10.9412
UUCUGAGUAGUGGGAUGCUUGG	chr16:98170671-98170948(-)$1	277	144	166	7.9441
GAGCAUCAGAUCCCUGUGCCCC	chr4:126421180-126421460(-)$1	280	127	149	11.2149
CUAGAGUUAGGAAUGACCAGUU	chr6:140543072-140543349(+)$1	277	144	166	8.8921
GGUCUUCAGUACUCUGGGAAAC	chr17:37209972-37210240(+)$1	268	136	158	10.8672
GUAUGUUGGAUGGCCAUUGCAC	chr8:125096545-125096859(+)$1	314	188	210	10.8542
AGAGAAUGUGAAACGUUCUGUG	chr3:122242260-122242557(-)$1	297	151	173	7.7613
acauguUAAUGAUUUAUCAGUA	chr3:108163839-108164128(+)$1	289	19	41	9.8849
ucagucugccucugccuccuga	chr3:90057072-90057343(+)$1	271	22	44	9.6066
UCCUUCUGGGAGCUCAGAAGUU	chr7:151775188-151775455(-)$1	267	27	49	10.3084
GGGCCAAGCUUUUGCUCUUUCU	chr1:36501838-36502111(-)$1	273	97	119	10.6111
CAGGAGUUCGUCAGAGCUCUGG	chr7:25670028-25670303(+)$1	275	159	181	9.5622
UCCUGGCCACAUGUGCGCCUGG	chr17:57032824-57033135(-)$1	311	16	38	9.9185
UCUGGCAGGAUCCCCUACACCC	chr17:32498275-32498549(-)$1	274	19	41	9.2621
UCCUCUGUCCUCAGACUCAGGA	chr11:68635132-68635416(-)$1	284	6	28	10.4453
GGUCGUAGCUUCGGCUGAGCAC	chr19:5456434-5456714(-)$1	280	2	24	8.3736
ACAUGAAGUGCCGACAUUCUGU	chr15:80761601-80761877(+)$1	276	199	221	9.6286
UUGGCUUACACUGUGUGCAAGG	chr1:181447940-181448228(-)$1	288	251	273	8.8156

#DB
(((((((((....)))))))))	chr2:32162847-32163126(+)$1	1	172	194	10.5571
(((((((((....))))...))	chr6:30079454-30079729(+)$1	1	41	63	8.2333
(((((((((....)))))))))	chr2:32134292-32134590(-)$1	1	196	218	10.5571
(((((.(((....))).)))))	chr2:30302693-30302995(+)$1	1	235	257	10.2064
.(((((.((....)).))))).	chr4:151560200-151560489(+)$1	1	186	208	8.4619
(((((((((......)))))))	chr6:56728726-56729000(-)$1	1	164	186	7.9441
(((((.(((....))).)))))	chr4:33125089-33125364(+)$1	1	209	231	10.2064
)(((((((((...)))))))))	chr3:145309905-145310179(-)$1	1	17	39	8.2539
((....(((....)))...)))	chr5:145942303-145942575(+)$1	1	152	174	10.7822
((.((((((....)))))).))	chr10:76508552-76508827(+)$1	1	17	39	8.9717
((.((..(((...))).)).))	chr11:117828673-117828945(-)$1	1	223	245	8.0379
(((((.(((....)))))))).	chr2:79512562-79512842(+)$1	1	243	265	10.1758
((.((.(((....))))).)))	chr4:63211330-63211606(+)$1	1	236	258	9.4299
(((((..((....))..))).)	chr7:72016753-72017039(-)$1	1	89	111	9.6008
(((((((((....)))))))))	chr9:30881655-30881942(+)$1	1	187	209	11.0699
(((((((((......)))))))	chr16:98170644-98170921(-)$1	1	117	139	7.9441
(.((..(((....)))..).).	chr12:113887155-113887428(+)$1	1	25	47	11.3199
(((...(((....)))..))))	chr16:92084361-92084635(+)$1	1	149	171	11.3200
(((((((((....)))))))))	chr18:34930930-34931222(+)$1	1	114	136	11.0699
.((((..((....)).))))..	chr15:101926263-101926530(+)$1	1	80	102	8.3105
((.((((((....)))))).))	chrX:11614220-11614489(-)$1	1	23	45	8.9717
(((((((((....)))))).))	chr11:87794777-87795061(-)$1	1	227	249	8.6191
(((...(((....))))))...	chr17:35119075-35119345(+)$1	1	139	161	8.7935
(((((.(((....))).)))))	chr3:95464619-95464908(+)$1	1	176	198	10.4120
(((((.(((....))).)))))	chr11:98015256-98015533(-)$1	1	198	220	11.4611
(((.(((((....))..)))..	chr9:90098144-90098412(-)$1	1	73	95	9.4098
((.((((((....)))))).).	chr15:80761843-80762129(+)$1	1	202	224	9.3937
(.(((((((....))))))).)	chr7:30106085-30106361(-)$1	1	91	113	9.9105
.(((..(((....)))..))).	chr14:55505758-55506041(+)$1	1	114	136	11.2214
((..(((((....))))).)))	chr11:79506341-79506633(+)$1	1	38	60	8.2706
(((...(((....)))...)))	chr11:53590397-53590671(+)$1	1	139	161	11.0957
.(.((((((....)))))).).	chr2:31615419-31615714(+)$1	1	77	99	9.4432
(((.(.(((....))).)))))	chr11:52221498-52221778(+)$1	1	194	216	11.4781
(((((((((....))))))...	chr19:8964904-8965185(+)$1	1	169	191	9.2705
(.((((.((....)).))))..	chr10:20845089-20845386(-)$1	1	99	121	7.8829
((....(((....)))))).))	chr11:117828139-117828471(-)$1	1	183	205	10.9412
(((((((((......)))))))	chr16:98170671-98170948(-)$1	1	144	166	7.9441
(.(((.(((....)))))).).	chr4:126421180-126421460(-)$1	1	127	149	11.2149
((.(.((((....)))))))).	chr6:140543072-140543349(+)$1	1	144	166	8.8921
..(((.(((....))))))..)	chr17:37209972-37210240(+)$1	1	136	158	10.8672
.(.((((((....)))..))).	chr8:125096545-125096859(+)$1	1	188	210	10.8542
(.(((((((...))))))).)(	chr3:122242260-122242557(-)$1	1	151	173	7.7613
((.((.(((....))).)))))	chr3:108163839-108164128(+)$1	1	19	41	9.8849
((((...((....))...))))	chr3:90057072-90057343(+)$1	1	22	44	9.6066
..(((((((....)))))))..	chr7:151775188-151775455(-)$1	1	27	49	10.3084
(((...(((....)))....))	chr1:36501838-36502111(-)$1	1	97	119	10.6111
(.(((((((....))))))).)	chr7:25670028-25670303(+)$1	1	159	181	9.5622
(((.(((((....)).))).))	chr17:57032824-57033135(-)$1	1	16	38	9.9185
(.(((.(((....)))....))	chr17:32498275-32498549(-)$1	1	19	41	9.2621
((((..(((....)))..))))	chr11:68635132-68635416(-)$1	1	6	28	10.4453
((((.((((....)))).).))	chr19:5456434-5456714(-)$1	1	2	24	8.3736
(((.(((((....)).))))))	chr15:80761601-80761877(+)$1	1	199	221	9.6286
(((.(.(((...))).))))))	chr1:181447940-181448228(-)$1	1	251	273	8.8156

#PSSM
c : 0.16	e : 0.15	d : 0.13	f : 0.11	i : 0.09	! : 0.09	g : 0.07	= : 0.03	a : 0.03	h : 0.01	[ : 0.01	" : 0.01	b : 0.01	H : 0.01	
c : 0.18	e : 0.13	d : 0.13	i : 0.11	[ : 0.11	f : 0.09	g : 0.07	a : 0.05	= : 0.03	! : 0.01	" : 0.01	: : 0.01	
[ : 0.16	c : 0.16	g : 0.15	e : 0.13	i : 0.11	f : 0.07	d : 0.07	# : 0.03	= : 0.03	a : 0.01	! : 0.01	
f : 0.18	i : 0.11	c : 0.11	g : 0.09	[ : 0.09	e : 0.07	" : 0.07	b : 0.05	a : 0.05	# : 0.03	= : 0.03	d : 0.03	! : 0.01	
f : 0.15	c : 0.15	i : 0.11	e : 0.09	" : 0.09	g : 0.09	b : 0.05	! : 0.05	# : 0.03	= : 0.03	d : 0.03	a : 0.03	[ : 0.03	
[ : 0.22	i : 0.11	f : 0.11	! : 0.11	" : 0.09	d : 0.07	c : 0.07	g : 0.07	e : 0.03	# : 0.03	= : 0.03	
c : 0.47	i : 0.11	f : 0.11	g : 0.07	d : 0.05	! : 0.05	[ : 0.03	= : 0.03	e : 0.01	" : 0.01	
c : 0.43	b : 0.15	i : 0.11	f : 0.11	g : 0.07	d : 0.05	= : 0.03	e : 0.01	
c : 0.43	b : 0.15	i : 0.11	f : 0.11	g : 0.07	d : 0.05	= : 0.03	e : 0.01	
m : 0.86	o : 0.05	l : 0.03	i : 0.01	c : 0.01	
m : 0.86	l : 0.07	o : 0.05	
m : 0.86	l : 0.07	o : 0.05	
m : 0.86	o : 0.05	l : 0.03	g : 0.01	c : 0.01	
c : 0.43	b : 0.15	f : 0.11	g : 0.07	i : 0.05	d : 0.05	o : 0.05	= : 0.03	e : 0.01	
c : 0.43	b : 0.15	f : 0.11	g : 0.07	i : 0.05	d : 0.05	o : 0.05	= : 0.03	e : 0.01	
c : 0.41	i : 0.11	] : 0.11	f : 0.11	g : 0.07	d : 0.05	2 : 0.03	= : 0.03	e : 0.01	3 : 0.01	
] : 0.13	2 : 0.13	i : 0.11	f : 0.11	c : 0.11	d : 0.09	g : 0.07	e : 0.05	3 : 0.05	= : 0.03	4 : 0.03	b : 0.01	a : 0.01	
c : 0.15	f : 0.13	i : 0.11	g : 0.11	e : 0.09	2 : 0.09	3 : 0.07	b : 0.05	= : 0.03	d : 0.03	a : 0.03	4 : 0.03	] : 0.01	
c : 0.20	f : 0.16	g : 0.15	i : 0.11	e : 0.07	3 : 0.05	b : 0.03	] : 0.03	= : 0.03	a : 0.03	d : 0.03	4 : 0.03	
] : 0.22	c : 0.13	g : 0.13	i : 0.11	e : 0.09	d : 0.07	f : 0.07	3 : 0.03	= : 0.03	4 : 0.03	5 : 0.01	2 : 0.01	
c : 0.15	d : 0.13	i : 0.11	e : 0.11	f : 0.09	a : 0.09	g : 0.07	2 : 0.07	] : 0.05	= : 0.03	3 : 0.03	5 : 0.01	
d : 0.13	i : 0.11	f : 0.11	2 : 0.11	c : 0.11	g : 0.09	e : 0.07	3 : 0.07	] : 0.07	= : 0.03	5 : 0.01	h : 0.01	b : 0.01	

#score	512.9811040988623
#seq	53
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_UTR_m1_run2.txt

#BEAR
!!bbbbtttttttttttbb]bb4	chr3:122242303-122242524(-)$1	221	54	77	20.9845
g!!ccctttttttttttcccggg	chr14:48356039-48356264(+)$1	225	195	218	23.3873
eeewwwwwwwwwwwwwweeeee3	chr11:109260929-109261149(+)$1	220	77	100	20.4724
bcccwwwwwwwwwwwwwwccc22	chr16:55966439-55966659(+)$1	220	182	205	20.4390
ffffwwwwwwwwwwwwwwfffff	chr19:41287791-41288011(-)$1	220	2	25	20.0706
======uuuuuuuuuuuu=====	chr12:56404734-56404954(+)$1	220	119	142	22.8076
eyyyyyyyyyyyyyyyyeeeee3	chr12:3249523-3249749(-)$1	226	31	54	20.2995
ggggguuuuuuuuuuuugggggg	chr19:40922904-40923124(+)$1	220	98	121	22.2851
ggggggvvvvvvvvvvvvvgggg	chr2:160547448-160547669(+)$1	221	71	94	21.7452
[ddddvvvvvvvvvvvvvdddd]	chr3:58394890-58395110(+)$1	220	64	87	22.1301
fffffftttttttttttffffff	chr7:125262952-125263172(-)$1	220	83	106	21.9544
cccyyyyyyyyyyyyyyyyccc]	chr14:8783052-8783273(+)$1	221	52	75	20.8126
cccccctttttttttttccc]cc	chr3:144259978-144260213(+)$1	235	75	98	22.9743
eeeeeuuuuuuuuuuuueeeee]	chr9:109795513-109795733(+)$1	220	62	85	22.8694
iyyyyyyyyyyyyyyyyiiiiii	chrX:17133847-17134067(-)$1	220	194	217	19.7952
[ddddvvvvvvvvvvvvvdddd]	chr8:47292628-47292852(-)$1	224	28	51	22.1301
eyyyyyyyyyyyyyyyyeeeee]	chr2:59192602-59192825(+)$1	223	183	206	20.2835
ddddwwwwwwwwwwwwwwdddd]	chr6:58615032-58615259(+)$1	227	169	192	20.4962
"""ccctttttttttttccc333	chr12:4248705-4248931(-)$1	226	51	74	23.4237
fffffftttttttttttffffff	chr11:106642210-106642431(-)$1	221	115	138	21.9544
hhhhhhuuuuuuuuuuuuhhhhh	chr10:36721416-36721636(+)$1	220	76	99	20.1116
ggggggtttttttttttgggggg	chr9:13596359-13596579(+)$1	220	82	105	22.6352
[eeeeettttttttttteeeee3	chr17:21955094-21955315(-)$1	221	144	167	23.4449
##ddddtttttttttttdddd44	chr1:95601873-95602093(-)$1	220	89	112	22.6147
======uuuuuuuuuuuu=====	chr18:34436118-34436339(+)$1	221	87	110	22.8076
dd[ccctttttttttttccc]dd	chr9:67407320-67407540(-)$1	220	6	29	22.7357
eeeeeuuuuuuuuuuuueeeee]	chr5:136384401-136384621(-)$1	220	47	70	22.8694
ffffffvvvvvvvvvvvvvffff	chr2:5218792-5219013(-)$1	221	45	68	21.0918
bb:ccctttttttttttcccccc	chr8:86246757-86246977(+)$1	220	148	171	21.7135
c!!cccuuuuuuuuuuuuccc]c	chr11:72997748-72997983(-)$1	235	122	145	22.9973
fffffftttttttttttffffff	chr19:7349432-7349659(+)$1	227	140	163	21.9544
ccccccvvvvvvvvvvvvvccc]	chr2:113671884-113672105(-)$1	221	85	108	22.1687
iiiiwwwwwwwwwwwwwwiiiii	chr5:135421582-135421802(-)$1	220	27	50	20.7378
fffffftttttttttttffffff	chr4:119300142-119300362(+)$1	220	61	84	21.9544
$$$ccctttttttttttccc555	chr19:4289241-4289461(-)$1	220	21	44	20.3795
c[ddddtttttttttttdddd]c	chrX:101477325-101477545(-)$1	220	87	110	22.4455
!!ddddtttttttttttdddd22	chr3:135187467-135187687(+)$1	220	96	119	22.4328
:eeeeettttttttttteeeeeD	chr3:95035853-95036073(+)$1	220	193	216	21.0651
gyyyyyyyyyyyyyyyygggggg	chr1:136499067-136499287(+)$1	220	194	217	19.8215
:eeeeettttttttttteeeee:	chrX:138755076-138755296(-)$1	220	2	25	21.4706
ddyyyyyyyyyyyyyyyydddd5	chr2:109739165-109739385(+)$1	220	33	56	19.6652
bb[cccvvvvvvvvvvvvvccc]	chr10:80725599-80725824(+)$1	225	109	132	21.9093
ddddwwwwwwwwwwwwwwdddd]	chr1:53405025-53405252(-)$1	227	112	135	20.4962
'eeeeettttttttttteeeee8	chr13:63921209-63921429(+)$1	220	134	157	22.4113
[eeeeevvvvvvvvvvvvveeee	chr13:73651296-73651516(+)$1	220	161	184	22.0391
feeeeettttttttttteeeee]	chr10:6380617-6380837(-)$1	220	121	144	23.2460
fffffftttttttttttffffff	chr5:117732811-117733031(-)$1	220	8	31	21.9544
ffffffvvvvvvvvvvvvvffff	chr4:128895741-128895961(+)$1	220	6	29	21.0918
eeeeeettttttttttteeeee9	chr7:116180856-116181076(-)$1	220	97	120	22.5423
eeeeeuuuuuuuuuuuueeeee9	chr12:112783191-112783415(+)$1	224	75	98	22.1699
[ddddyyyyyyyyyyyyyyyydd	chr4:106870063-106870283(+)$1	220	57	80	19.5901
a[ddddtttttttttttdddd]a	chr14:55261466-55261696(-)$1	230	126	149	22.4882
eeeeewwwwwwwwwwwwwweeee	chr11:101320160-101320380(-)$1	220	196	219	20.7497
:eeeeeuuuuuuuuuuuueeeee	chr11:52202333-52202562(+)$1	229	78	101	21.9175
bb[cccuuuuuuuuuuuuccc22	chr6:122266476-122266706(+)$1	230	58	81	22.3356
e"""bbtttttttttttbb333e	chr11:52059609-52059832(+)$1	223	102	125	21.3850
ff[ccctttttttttttcccfff	chr1:95715646-95715866(+)$1	220	71	94	22.9314
"eeeeettttttttttteeeee4	chr17:37095238-37095468(-)$1	230	95	118	23.3244
:eeeeettttttttttteeeee:	chr2:37428701-37428921(-)$1	220	69	92	21.4706
ddddwwwwwwwwwwwwwwddddf	chr16:20509168-20509403(+)$1	235	127	150	20.1893
"""ccctttttttttttccceee	chr11:49525763-49525983(-)$1	220	124	147	23.2222
:eeeeevvvvvvvvvvvvveeee	chr7:105863771-105863991(+)$1	220	20	43	21.1303
iiiiiitttttttttttiiiiii	chr5:143144771-143145008(+)$1	237	24	47	22.6091
&cccwwwwwwwwwwwwwwccc77	chr1:34248838-34249058(+)$1	220	127	150	19.3659
:dddduuuuuuuuuuuudddd:d	chr1:60387654-60387919(+)$1	265	60	83	20.0524
:::ccctttttttttttcccddd	chr12:117700398-117700618(+)$1	220	152	175	20.1881
iiii[avvvvvvvvvvvvva]ii	chr2:131879107-131879327(-)$1	220	141	164	21.8027
ggggggvvvvvvvvvvvvvgggg	chr2:103606129-103606349(-)$1	220	51	74	21.7452

#otherMatches

#Seq PSSM
GGGGGGGAUUGUUUGUACCACUG	chr3:122242303-122242524(-)$1	221	54	77	20.9845
CAUGACUCACUCUGAUUGUCGUU	chr14:48356039-48356264(+)$1	225	195	218	23.3873
UCUGAAACCUGACUCCGAGGUGC	chr11:109260929-109261149(+)$1	220	77	100	20.4724
CAGCGCACAUACUAACGAGCUUC	chr16:55966439-55966659(+)$1	220	182	205	20.4390
guuucaaGGGGAAAAAAAGAACA	chr19:41287791-41288011(-)$1	220	2	25	20.0706
GAAACUGUUUUAUUUUUAAGUUU	chr12:56404734-56404954(+)$1	220	119	142	22.8076
UCCAUUUUUAACUCUAAACAGAU	chr12:3249523-3249749(-)$1	226	31	54	20.2995
CAGCAGGGUUAGAUGAGUGCUGU	chr19:40922904-40923124(+)$1	220	98	121	22.2851
UUUGAAUUUUGUUUUUACUUUCA	chr2:160547448-160547669(+)$1	221	71	94	21.7452
AUGAAUUUUCAUUUUUUUUUUAA	chr3:58394890-58395110(+)$1	220	64	87	22.1301
AGUAGAAAACUAGAUUAUCUAUU	chr7:125262952-125263172(-)$1	220	83	106	21.9544
GCGUCCCCAUCCCAAACCUUGCC	chr14:8783052-8783273(+)$1	221	52	75	20.8126
CAGUCCAUAAUAUAUCAGGAUCU	chr3:144259978-144260213(+)$1	235	75	98	22.9743
UUCCAUCAGGCCAGUACUGGAAU	chr9:109795513-109795733(+)$1	220	62	85	22.8694
CUCCCAUUGUAUACUCUGUGUCU	chrX:17133847-17134067(-)$1	220	194	217	19.7952
AUGUGUAAUACCCAAGCUCACAA	chr8:47292628-47292852(-)$1	224	28	51	22.1301
GGGUGAGAUGAGAUGGGUAUGUG	chr2:59192602-59192825(+)$1	223	183	206	20.2835
UAACACAAUCAUUAAAGAGUUAG	chr6:58615032-58615259(+)$1	227	169	192	20.4962
AUGGGUGAAGGACAAGAACCAAG	chr12:4248705-4248931(-)$1	226	51	74	23.4237
GUCUCCACAUUAUUUCAGGGGAU	chr11:106642210-106642431(-)$1	221	115	138	21.9544
CUUGUUUUUGUUUUUCUUGGCAA	chr10:36721416-36721636(+)$1	220	76	99	20.1116
UUGCUCAUAAACCGGAGGGGCGA	chr9:13596359-13596579(+)$1	220	82	105	22.6352
cuuacaaauguagugaaugugac	chr17:21955094-21955315(-)$1	221	144	167	23.4449
AAGGCCUUUAUUUUUAUGGCUGA	chr1:95601873-95602093(-)$1	220	89	112	22.6147
UUGUGGUCUUAGUUUUCCUUACA	chr18:34436118-34436339(+)$1	221	87	110	22.8076
UGACAGUUGUGUUUCUUUUGCCA	chr9:67407320-67407540(-)$1	220	6	29	22.7357
UGUUAGCUUACUCUUAAUAAUGU	chr5:136384401-136384621(-)$1	220	47	70	22.8694
UCUCUCAUGAGCAUUACCCGAGA	chr2:5218792-5219013(-)$1	221	45	68	21.0918
CCAGAGGAAAUAGAUAUCUCCAC	chr8:86246757-86246977(+)$1	220	148	171	21.7135
GGUGGUGGAGGGGAGAGAACUGU	chr11:72997748-72997983(-)$1	235	122	145	22.9973
AUCUGGUGGGAAGAAUGUUGGGU	chr19:7349432-7349659(+)$1	227	140	163	21.9544
AGGGAUUUAUUUGGUCAGCAUCG	chr2:113671884-113672105(-)$1	221	85	108	22.1687
GUAAAAAUAUCUUGCUGCUUACA	chr5:135421582-135421802(-)$1	220	27	50	20.7378
CAGAGCUUUGAUCAGUUGCUUUG	chr4:119300142-119300362(+)$1	220	61	84	21.9544
GUUGACUCCUCCUCUUUGUCCUG	chr19:4289241-4289461(-)$1	220	21	44	20.3795
UUGAAUAAGUCAGGUCCGUUCUA	chrX:101477325-101477545(-)$1	220	87	110	22.4455
AGGCUUAAAAAUUGAGAAAGCAG	chr3:135187467-135187687(+)$1	220	96	119	22.4328
AUUCAUUACCAUGUGCUGUGAAG	chr3:95035853-95036073(+)$1	220	193	216	21.0651
ACUAAGAACAGCAGCCUUGAGGA	chr1:136499067-136499287(+)$1	220	194	217	19.8215
GCCUUCAAGCUGAAAAGGAAGGA	chrX:138755076-138755296(-)$1	220	2	25	21.4706
UAUAUUAAAGAAAAGCGUUGGUG	chr2:109739165-109739385(+)$1	220	33	56	19.6652
CAUUUGGAAGGAUUUUGUACAAC	chr10:80725599-80725824(+)$1	225	109	132	21.9093
AGGUGUUUUGACUAUCCAACCUG	chr1:53405025-53405252(-)$1	227	112	135	20.4962
GACUUGGAAAAACAAUACAGGUA	chr13:63921209-63921429(+)$1	220	134	157	22.4113
CAGGGGACAUGAAUGGAGCCCCC	chr13:73651296-73651516(+)$1	220	161	184	22.0391
GUGUGUUUCAUCGCUUUGCACAU	chr10:6380617-6380837(-)$1	220	121	144	23.2460
GUUGUUGAUAUAAAAAAAGCAAC	chr5:117732811-117733031(-)$1	220	8	31	21.9544
UCUCCUGUAAAUCACUAAAAGGG	chr4:128895741-128895961(+)$1	220	6	29	21.0918
CGAGUCAUGAAAUGGGAGACUCA	chr7:116180856-116181076(-)$1	220	97	120	22.5423
UAAUGAACUUACUCAGCCAUUAA	chr12:112783191-112783415(+)$1	224	75	98	22.1699
UGGAUUUUAACCACAACCCUUGU	chr4:106870063-106870283(+)$1	220	57	80	19.5901
CGCUAGCCAAGAAAACACUAGAG	chr14:55261466-55261696(-)$1	230	126	149	22.4882
GCCUCUCUGUUGUCAAAUUGAGG	chr11:101320160-101320380(-)$1	220	196	219	20.7497
AGGGAUGUUUUUAGACUGAUCCU	chr11:52202333-52202562(+)$1	229	78	101	21.9175
GCCGGUCUCCCAUCUCUCACCUU	chr6:122266476-122266706(+)$1	230	58	81	22.3356
UUACUCUGAAUAAAACCGAACUA	chr11:52059609-52059832(+)$1	223	102	125	21.3850
UGUGCUGCAUCCCACUAGGCCAG	chr1:95715646-95715866(+)$1	220	71	94	22.9314
CUAGCACUCCAAACUCUUGCUGU	chr17:37095238-37095468(-)$1	230	95	118	23.3244
CUCCUGGGUGUUAUGGACAGGAA	chr2:37428701-37428921(-)$1	220	69	92	21.4706
AGGGGAACUCUAGACAGACCCUG	chr16:20509168-20509403(+)$1	235	127	150	20.1893
AGAGGUGAGCGCGACGGGCCCGA	chr11:49525763-49525983(-)$1	220	124	147	23.2222
CAGCGGUCAACACAUUAUUCUGC	chr7:105863771-105863991(+)$1	220	20	43	21.1303
GGCCUCUCUAGGGAGCUGGGGUC	chr5:143144771-143145008(+)$1	237	24	47	22.6091
AACGAACAUACCCCAAGCUGUGC	chr1:34248838-34249058(+)$1	220	127	150	19.3659
CUCUGGAUUACCUUAAACAGAUG	chr1:60387654-60387919(+)$1	265	60	83	20.0524
AUAAUGGGAAGAAUUUACAUCAU	chr12:117700398-117700618(+)$1	220	152	175	20.1881
GGUGAGUUUAAUCUUCAGUCAUA	chr2:131879107-131879327(-)$1	220	141	164	21.8027
AAAGCCAAAUUGCAAAUCAGGCU	chr2:103606129-103606349(-)$1	220	51	74	21.7452

#DB
..((((...........)).)).	chr3:122242303-122242524(-)$1	1	54	77	20.9845
(..(((...........))))))	chr14:48356039-48356264(+)$1	1	195	218	23.3873
(((..............))))).	chr11:109260929-109261149(+)$1	1	77	100	20.4724
((((..............)))..	chr16:55966439-55966659(+)$1	1	182	205	20.4390
((((..............)))))	chr19:41287791-41288011(-)$1	1	2	25	20.0706
((((((............)))))	chr12:56404734-56404954(+)$1	1	119	142	22.8076
(................))))).	chr12:3249523-3249749(-)$1	1	31	54	20.2995
(((((............))))))	chr19:40922904-40923124(+)$1	1	98	121	22.2851
((((((.............))))	chr2:160547448-160547669(+)$1	1	71	94	21.7452
.((((.............)))).	chr3:58394890-58395110(+)$1	1	64	87	22.1301
((((((...........))))))	chr7:125262952-125263172(-)$1	1	83	106	21.9544
(((................))).	chr14:8783052-8783273(+)$1	1	52	75	20.8126
((((((...........))).))	chr3:144259978-144260213(+)$1	1	75	98	22.9743
(((((............))))).	chr9:109795513-109795733(+)$1	1	62	85	22.8694
(................))))))	chrX:17133847-17134067(-)$1	1	194	217	19.7952
.((((.............)))).	chr8:47292628-47292852(-)$1	1	28	51	22.1301
(................))))).	chr2:59192602-59192825(+)$1	1	183	206	20.2835
((((..............)))).	chr6:58615032-58615259(+)$1	1	169	192	20.4962
...(((...........)))...	chr12:4248705-4248931(-)$1	1	51	74	23.4237
((((((...........))))))	chr11:106642210-106642431(-)$1	1	115	138	21.9544
((((((............)))))	chr10:36721416-36721636(+)$1	1	76	99	20.1116
((((((...........))))))	chr9:13596359-13596579(+)$1	1	82	105	22.6352
.(((((...........))))).	chr17:21955094-21955315(-)$1	1	144	167	23.4449
..((((...........))))..	chr1:95601873-95602093(-)$1	1	89	112	22.6147
((((((............)))))	chr18:34436118-34436339(+)$1	1	87	110	22.8076
((.(((...........))).))	chr9:67407320-67407540(-)$1	1	6	29	22.7357
(((((............))))).	chr5:136384401-136384621(-)$1	1	47	70	22.8694
((((((.............))))	chr2:5218792-5219013(-)$1	1	45	68	21.0918
)).(((...........)))(((	chr8:86246757-86246977(+)$1	1	148	171	21.7135
(..(((............))).)	chr11:72997748-72997983(-)$1	1	122	145	22.9973
((((((...........))))))	chr19:7349432-7349659(+)$1	1	140	163	21.9544
((((((.............))).	chr2:113671884-113672105(-)$1	1	85	108	22.1687
((((..............)))))	chr5:135421582-135421802(-)$1	1	27	50	20.7378
((((((...........))))))	chr4:119300142-119300362(+)$1	1	61	84	21.9544
...(((...........)))...	chr19:4289241-4289461(-)$1	1	21	44	20.3795
(.((((...........)))).)	chrX:101477325-101477545(-)$1	1	87	110	22.4455
..((((...........))))..	chr3:135187467-135187687(+)$1	1	96	119	22.4328
.(((((...........))))))	chr3:95035853-95036073(+)$1	1	193	216	21.0651
(................))))))	chr1:136499067-136499287(+)$1	1	194	217	19.8215
.(((((...........))))).	chrX:138755076-138755296(-)$1	1	2	25	21.4706
((................)))).	chr2:109739165-109739385(+)$1	1	33	56	19.6652
((.(((.............))).	chr10:80725599-80725824(+)$1	1	109	132	21.9093
((((..............)))).	chr1:53405025-53405252(-)$1	1	112	135	20.4962
.(((((...........))))).	chr13:63921209-63921429(+)$1	1	134	157	22.4113
.(((((.............))))	chr13:73651296-73651516(+)$1	1	161	184	22.0391
((((((...........))))).	chr10:6380617-6380837(-)$1	1	121	144	23.2460
((((((...........))))))	chr5:117732811-117733031(-)$1	1	8	31	21.9544
((((((.............))))	chr4:128895741-128895961(+)$1	1	6	29	21.0918
((((((...........))))).	chr7:116180856-116181076(-)$1	1	97	120	22.5423
(((((............))))).	chr12:112783191-112783415(+)$1	1	75	98	22.1699
.((((................))	chr4:106870063-106870283(+)$1	1	57	80	19.5901
(.((((...........)))).)	chr14:55261466-55261696(-)$1	1	126	149	22.4882
(((((..............))))	chr11:101320160-101320380(-)$1	1	196	219	20.7497
.(((((............)))))	chr11:52202333-52202562(+)$1	1	78	101	21.9175
((.(((............)))..	chr6:122266476-122266706(+)$1	1	58	81	22.3356
(...((...........))...)	chr11:52059609-52059832(+)$1	1	102	125	21.3850
((.(((...........))))))	chr1:95715646-95715866(+)$1	1	71	94	22.9314
.(((((...........))))).	chr17:37095238-37095468(-)$1	1	95	118	23.3244
.(((((...........))))).	chr2:37428701-37428921(-)$1	1	69	92	21.4706
((((..............)))))	chr16:20509168-20509403(+)$1	1	127	150	20.1893
...(((...........))))))	chr11:49525763-49525983(-)$1	1	124	147	23.2222
.(((((.............))))	chr7:105863771-105863991(+)$1	1	20	43	21.1303
((((((...........))))))	chr5:143144771-143145008(+)$1	1	24	47	22.6091
.(((..............)))..	chr1:34248838-34249058(+)$1	1	127	150	19.3659
.((((............)))).(	chr1:60387654-60387919(+)$1	1	60	83	20.0524
...(((...........)))(((	chr12:117700398-117700618(+)$1	1	152	175	20.1881
((((.(.............).))	chr2:131879107-131879327(-)$1	1	141	164	21.8027
((((((.............))))	chr2:103606129-103606349(-)$1	1	51	74	21.7452

#PSSM
f : 0.14	e : 0.13	: : 0.10	g : 0.08	[ : 0.07	c : 0.07	d : 0.07	b : 0.05	i : 0.05	" : 0.04	! : 0.02	= : 0.02	h : 0.01	# : 0.01	$ : 0.01	' : 0.01	a : 0.01	& : 0.01	
e : 0.23	f : 0.13	d : 0.13	c : 0.07	! : 0.05	y : 0.05	g : 0.05	" : 0.04	b : 0.04	i : 0.04	= : 0.02	[ : 0.02	h : 0.01	# : 0.01	$ : 0.01	: : 0.01	
e : 0.23	d : 0.16	f : 0.11	c : 0.07	y : 0.07	g : 0.05	[ : 0.05	" : 0.04	i : 0.04	! : 0.02	= : 0.02	: : 0.02	b : 0.01	h : 0.01	$ : 0.01	
c : 0.22	e : 0.22	d : 0.16	f : 0.11	y : 0.08	g : 0.05	i : 0.04	= : 0.02	b : 0.01	w : 0.01	h : 0.01	" : 0.01	
e : 0.22	c : 0.19	w : 0.11	d : 0.11	f : 0.10	y : 0.08	g : 0.05	b : 0.02	= : 0.02	h : 0.01	i : 0.01	[ : 0.01	
c : 0.19	e : 0.16	w : 0.13	y : 0.10	f : 0.10	u : 0.07	d : 0.05	g : 0.04	b : 0.02	= : 0.02	v : 0.02	h : 0.01	i : 0.01	a : 0.01	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
t : 0.44	u : 0.16	v : 0.16	w : 0.13	y : 0.10	
e : 0.20	v : 0.16	c : 0.13	w : 0.11	u : 0.08	f : 0.07	d : 0.07	g : 0.04	y : 0.04	b : 0.02	i : 0.02	
e : 0.22	c : 0.19	d : 0.16	v : 0.13	f : 0.08	g : 0.04	i : 0.04	b : 0.02	= : 0.02	y : 0.02	h : 0.01	w : 0.01	
e : 0.26	c : 0.23	d : 0.16	f : 0.11	g : 0.07	i : 0.04	= : 0.02	] : 0.01	h : 0.01	y : 0.01	3 : 0.01	a : 0.01	
e : 0.27	d : 0.17	f : 0.13	c : 0.11	g : 0.08	] : 0.04	i : 0.04	= : 0.02	3 : 0.02	b : 0.01	h : 0.01	5 : 0.01	y : 0.01	
e : 0.27	f : 0.13	d : 0.13	g : 0.08	c : 0.07	i : 0.05	2 : 0.04	] : 0.04	= : 0.02	3 : 0.02	b : 0.01	h : 0.01	4 : 0.01	5 : 0.01	7 : 0.01	: : 0.01	
] : 0.16	f : 0.14	g : 0.08	e : 0.08	3 : 0.05	c : 0.05	i : 0.05	d : 0.05	4 : 0.04	2 : 0.04	= : 0.02	5 : 0.02	: : 0.02	9 : 0.02	h : 0.01	D : 0.01	8 : 0.01	a : 0.01	7 : 0.01	

#score	1472.7936717040907
#seq	68
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_CDS_m3_run1.txt

#BEAR
cc!!ccc^^^^^^^^^^^^^^^^^^^^^^ccc22ccc	chr10:81028331-81028570(+)$1	239	185	222	21.2610
dddbb[dddd[ccctttttttttttccc]dddd]bb]	chr1:89088986-89089221(+)$1	235	79	116	20.7219
b[eeeeeddddxxxxxxxxxxxxxxxdddd]eeeee]	chr5:52575932-52576167(-)$1	235	131	168	23.8362
bb!!a[cccddddrrrrrrrrrdddd]ccc]a22bb4	chr1:172771744-172771979(-)$1	235	138	175	14.8592
!ggggggg!!ayyyyyyyyyyyyyyyya22ggggggg	chr13:55422845-55423080(-)$1	235	99	136	27.3684
eeeeeeee[bbbbwwwwwwwwwwwwwwbb]bbeeeee	chr16:31104864-31105099(-)$1	235	120	157	22.5679
eeeee[eeeeeyyyyyyyyyyyyyyyyeeeee22eee	chr5:143533280-143533519(-)$1	239	81	118	28.7135
:dddd[gggggggtttttttttttggggggg]dddd:	chr5:122941662-122941901(-)$1	239	17	54	18.2348
eeeee[ccczzzzzzzzzzzzzzzzzccc]eeeee]a	chr2:113875924-113876162(-)$1	238	158	195	22.9400

#otherMatches

#Seq PSSM
AGCUCUGUCACUACCCAAGCUUACACCUCCAGUCCUG	chr10:81028331-81028570(+)$1	239	185	222	21.2610
AUGGCUCGUUCCAGAUUUCUUAUGCCUGCAAUGUGCU	chr1:89088986-89089221(+)$1	235	79	116	20.7219
GAAUUGAGAGCUUCCACCAAUGCUAUGCUUAUCAGUG	chr5:52575932-52576167(-)$1	235	131	168	23.8362
GUCACUGGUCCUGGAAACAAAACAGGUAUCUGCCGCU	chr1:172771744-172771979(-)$1	235	138	175	14.8592
UGCUGGGCAAGGAAUACGUGGGCAAGACGAGCCUGGU	chr13:55422845-55423080(-)$1	235	99	136	27.3684
UCCAAGGCCGGGGACCACUGCACCAUGCCACCGUCUU	chr16:31104864-31105099(-)$1	235	120	157	22.5679
UGAGGACAGUCUGCCCCAGCCAUCUUUGACUGAGCCU	chr5:143533280-143533519(-)$1	239	81	118	28.7135
AACUUACAUAAUGUUUUAUCCUUUUAUUAUGAAAGUA	chr5:122941662-122941901(-)$1	239	17	54	18.2348
GGUCACUGAUUACGUAUAUUCUCAACUCACUGACUUU	chr2:113875924-113876162(-)$1	238	158	195	22.9400

#DB
((..(((......................)))..)))	chr10:81028331-81028570(+)$1	1	185	222	21.2610
(((((.((((.(((...........))).)))).)).	chr1:89088986-89089221(+)$1	1	79	116	20.7219
(.(((((((((...............)))).))))).	chr5:52575932-52576167(-)$1	1	131	168	23.8362
((..(.(((((((.........)))).))).)..)).	chr1:172771744-172771979(-)$1	1	138	175	14.8592
.(((((((..(................)..)))))))	chr13:55422845-55423080(-)$1	1	99	136	27.3684
((((((((.((((..............)).)))))))	chr16:31104864-31105099(-)$1	1	120	157	22.5679
(((((.(((((................)))))..)))	chr5:143533280-143533519(-)$1	1	81	118	28.7135
.((((.(((((((...........))))))).)))).	chr5:122941662-122941901(-)$1	1	17	54	18.2348
(((((.(((.................))).))))).)	chr2:113875924-113876162(-)$1	1	158	195	22.9400

#PSSM
e : 0.33	b : 0.22	c : 0.11	d : 0.11	! : 0.11	: : 0.11	
e : 0.33	d : 0.22	c : 0.11	[ : 0.11	b : 0.11	g : 0.11	
e : 0.44	! : 0.22	d : 0.22	g : 0.11	
e : 0.44	! : 0.22	b : 0.11	g : 0.11	d : 0.11	
e : 0.44	c : 0.11	b : 0.11	a : 0.11	g : 0.11	d : 0.11	
[ : 0.55	e : 0.22	c : 0.11	g : 0.11	
c : 0.33	e : 0.33	g : 0.22	d : 0.11	
d : 0.22	c : 0.22	g : 0.22	e : 0.22	^ : 0.11	
d : 0.22	c : 0.22	^ : 0.11	! : 0.11	[ : 0.11	e : 0.11	g : 0.11	
d : 0.33	^ : 0.11	! : 0.11	b : 0.11	e : 0.11	g : 0.11	z : 0.11	
d : 0.22	^ : 0.11	[ : 0.11	a : 0.11	b : 0.11	e : 0.11	g : 0.11	z : 0.11	
y : 0.22	^ : 0.11	c : 0.11	x : 0.11	d : 0.11	b : 0.11	g : 0.11	z : 0.11	
y : 0.22	^ : 0.11	c : 0.11	x : 0.11	d : 0.11	b : 0.11	g : 0.11	z : 0.11	
y : 0.22	^ : 0.11	c : 0.11	x : 0.11	r : 0.11	w : 0.11	t : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	r : 0.11	w : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	r : 0.11	w : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	r : 0.11	w : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	r : 0.11	w : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	r : 0.11	w : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	r : 0.11	w : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	r : 0.11	w : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	r : 0.11	w : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	d : 0.11	w : 0.11	z : 0.11	
t : 0.22	y : 0.22	^ : 0.11	x : 0.11	d : 0.11	w : 0.11	z : 0.11	
y : 0.22	^ : 0.11	t : 0.11	x : 0.11	d : 0.11	w : 0.11	g : 0.11	z : 0.11	
y : 0.22	^ : 0.11	c : 0.11	x : 0.11	d : 0.11	w : 0.11	g : 0.11	z : 0.11	
c : 0.22	y : 0.22	^ : 0.11	d : 0.11	] : 0.11	w : 0.11	g : 0.11	
c : 0.33	^ : 0.11	d : 0.11	a : 0.11	b : 0.11	e : 0.11	g : 0.11	
c : 0.22	^ : 0.11	] : 0.11	d : 0.11	2 : 0.11	b : 0.11	e : 0.11	g : 0.11	
c : 0.22	d : 0.22	] : 0.22	2 : 0.11	e : 0.11	g : 0.11	
] : 0.22	g : 0.22	e : 0.22	c : 0.11	d : 0.11	b : 0.11	
e : 0.33	c : 0.11	d : 0.11	a : 0.11	g : 0.11	b : 0.11	] : 0.11	
2 : 0.33	e : 0.33	d : 0.22	g : 0.11	
2 : 0.33	e : 0.33	] : 0.11	g : 0.11	d : 0.11	
e : 0.44	b : 0.22	c : 0.11	g : 0.11	d : 0.11	
e : 0.33	b : 0.22	c : 0.11	g : 0.11	d : 0.11	] : 0.11	
] : 0.22	e : 0.22	c : 0.11	4 : 0.11	g : 0.11	: : 0.11	a : 0.11	

#score	200.5034372716999
#seq	9
#width	37
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_transcript_m3_run2.txt

#BEAR
[gggggggmmmmgggggggc	chr5:147072535-147072789(+)$1	254	64	84	10.6397
bb[a[cccmmmmccc]a]bb	chr1:34933815-34934074(+)$1	259	181	201	10.6819
cc"""cccmmmmccc]ccce	chr9:30957848-30958085(-)$1	237	61	81	11.6092
[gggggggmmmmggggggg]	chr15:58649129-58649364(-)$1	235	24	44	10.5817
iiiiiiiimmmmiiiiiiii	chr11:68635611-68635852(-)$1	241	32	52	10.9927
ccc!!cccmmmmccc22ccc	chr8:46912753-46912988(+)$1	235	139	159	12.0038
ggggggbbmmmmbb]ggggg	chr17:87398130-87398365(+)$1	235	206	226	9.9280
eeee[cccmmmmccc]eeee	chr19:24757738-24757973(-)$1	235	123	143	10.6990
ddd!!cccmmmmccc22ddd	chr2:72240354-72240607(+)$1	253	215	235	11.3209
:gggggggmmmmgggggggd	chr9:121364568-121364806(+)$1	238	90	110	9.4939
=========lll========	chr14:55565114-55565368(-)$1	254	195	215	9.3243
========mmmm========	chr3:51323788-51324027(-)$1	239	197	217	11.4489
!bb!!cccmmmmccc22bbe	chr1:129839793-129840031(+)$1	238	185	205	10.7702
iiiiiiiimmmmiiiiiiii	chr11:50108261-50108515(-)$1	254	51	71	10.9927
dddd[cccmmmmccc22ddd	chr11:109528792-109529029(+)$1	237	191	211	10.9535
gggggg[ammmma]gggggg	chr6:29402139-29402374(+)$1	235	201	221	10.2396
gggg[bbammmma]bbgggg	chr1:34178373-34178608(+)$1	235	75	95	9.4922
gggggcccmmmmccc333gg	chr6:119875219-119875455(-)$1	236	11	31	12.1483
ccc!!cccmmmmccc22ccc	chr1:60389515-60389763(+)$1	248	189	209	12.0038
gggg!!bbmmmmbb22gggg	chr9:121364093-121364352(+)$1	259	66	86	10.3248
[gggggggmmmmggggggg]	chr8:59070600-59070836(+)$1	236	57	77	10.5817
dddd[cccmmmmcccddddc	chr4:137797888-137798143(+)$1	255	186	206	10.1381
dddd[cccmmmmccc]dddd	chr6:124885829-124886072(+)$1	243	3	23	10.6852
Fccc[cccmmmmccc]ccci	chr18:78021187-78021422(+)$1	235	110	130	11.2734
========mmmm========	chr1:135552554-135552791(-)$1	237	124	144	11.4489
gggg!!bbmmmmbb22gggg	chr11:19964296-19964533(-)$1	237	76	96	10.3248
eee!!cccmmmmccc22eee	chr2:114019151-114019395(-)$1	244	39	59	11.2675
ddd!!cccmmmmccc333dd	chr10:82203496-82203737(+)$1	241	141	161	11.8844
======bbmmmmbb]=====	chr2:31923305-31923540(-)$1	235	9	29	10.5629
eeee[cccmmmmccceeeee	chr12:54249529-54249776(+)$1	247	40	60	10.1399
iiiiiiiimmmmiiiiiiii	chr19:61168172-61168427(+)$1	255	195	215	10.9927
gggg[cccmmmmccc]gggg	chr16:29651894-29652129(+)$1	235	212	232	12.2143
f[a!!cccmmmmccc22a]f	chr12:111820777-111821023(+)$1	246	95	115	11.5124
:ccc[cccmmmmccc333cc	chr11:109529413-109529649(+)$1	236	170	190	11.2903
:gggggggmmmmgggggggc	chr15:72936345-72936583(-)$1	238	129	149	9.5867
iiii[ccclllccciiiiii	chr10:117252017-117252253(-)$1	236	170	190	9.4255
:ccc[cccmmmmccccccgg	chr3:138218802-138219042(+)$1	240	79	99	10.3879
cc!!acccmmmmccc]a22c	chr8:71430247-71430482(+)$1	235	140	160	11.1949
!gggggggmmmmgggggggc	chr16:17044965-17045200(+)$1	235	115	135	10.6109
=========lll========	chr6:30404433-30404668(+)$1	235	36	56	9.3243
d!!a[cccmmmmccc]a22d	chr12:111819804-111820044(+)$1	240	91	111	11.3033
[a[cccbbmmmmbb]ccc]a	chr6:148181130-148181368(-)$1	238	158	178	9.1594
[ccc[cccmmmmcccccc33	chr17:44174403-44174641(+)$1	238	209	229	11.2739
ddd!!cccmmmmccc]dddd	chr15:4104924-4105174(+)$1	250	122	142	11.0526
ccc!!cccmmmmccc333cc	chr11:87897636-87897884(+)$1	248	169	189	12.4250
ccca!!bbmmmmbb22a]cc	chr11:54792867-54793114(-)$1	247	98	118	9.8890
[gggggggmmmmgggggggb	chr2:155214476-155214718(+)$1	242	181	201	10.3272
dddd[cccmmmmccc]dddd	chr11:29642544-29642783(+)$1	239	138	158	10.6852
[a"""cccmmmmccc333a]	chr7:146765008-146765298(+)$1	290	256	276	12.1416
d####cccmmmmccc333dd	chr11:60370461-60370714(+)$1	253	112	132	11.6695
=========lll========	chr5:122950679-122950926(-)$1	247	3	23	9.3243

#otherMatches

#Seq PSSM
uggggggcccaaguccuucu	chr5:147072535-147072789(+)$1	254	64	84	10.6397
UAGUUCUUUUGAAGGUGGUA	chr1:34933815-34934074(+)$1	259	181	201	10.6819
AUUAUUUGUUUUCAAUGUAU	chr9:30957848-30958085(-)$1	237	61	81	11.6092
AUUCUACCAGGUGGUAGAAC	chr15:58649129-58649364(-)$1	235	24	44	10.5817
GUGAUACAUACGUGUAUUAC	chr11:68635611-68635852(-)$1	241	32	52	10.9927
AAUACACAUAAAUGUCAGUU	chr8:46912753-46912988(+)$1	235	139	159	12.0038
UUUCCAAGUUGCCUGUGGAG	chr17:87398130-87398365(+)$1	235	206	226	9.9280
UCUGUCAAAAACUUGCUAGG	chr19:24757738-24757973(-)$1	235	123	143	10.6990
cgccugcgccugcgccugcg	chr2:72240354-72240607(+)$1	253	215	235	11.3209
ACACAGGUACAGACUUGUGC	chr9:121364568-121364806(+)$1	238	90	110	9.4939
CGGGUGCAGCUGCUGCACUC	chr14:55565114-55565368(-)$1	254	195	215	9.3243
AGUUGCUGAAGCCGGUAGCU	chr3:51323788-51324027(-)$1	239	197	217	11.4489
CAGAAUGCAUCAGUACGCUG	chr1:129839793-129840031(+)$1	238	185	205	10.7702
AAAAAAAAAAUUUUUUUUUU	chr11:50108261-50108515(-)$1	254	51	71	10.9927
GCAGCGCCCAGUGGCCACUG	chr11:109528792-109529029(+)$1	237	191	211	10.9535
UGGGGGCGAACACAUCCCCA	chr6:29402139-29402374(+)$1	235	201	221	10.2396
GUGGAGCCGUGAGUGCCCGU	chr1:34178373-34178608(+)$1	235	75	95	9.4922
GUGGAAAGAAAUCUUAGGUC	chr6:119875219-119875455(-)$1	236	11	31	12.1483
AACAUAGCUUCUGCUCCGUU	chr1:60389515-60389763(+)$1	248	189	209	12.0038
UGUGUGUGUGAUCAAUCACA	chr9:121364093-121364352(+)$1	259	66	86	10.3248
GUCUAACACAACUGUUAGAG	chr8:59070600-59070836(+)$1	236	57	77	10.5817
GCAGACUUGCUAGAGCUGUG	chr4:137797888-137798143(+)$1	255	186	206	10.1381
UAACUUGAGUUCUCAUGUUG	chr6:124885829-124886072(+)$1	243	3	23	10.6852
UGGUGGUCAGAGGACAGCCA	chr18:78021187-78021422(+)$1	235	110	130	11.2734
UGUUAGUGACUGCAUUAACA	chr1:135552554-135552791(-)$1	237	124	144	11.4489
GGCAAGGGGUUGCUGCUGCU	chr11:19964296-19964533(-)$1	237	76	96	10.3248
CAAGCUUCUUAUGGGAAUUG	chr2:114019151-114019395(-)$1	244	39	59	11.2675
UACCUCAUUAUUAUGUUUGU	chr10:82203496-82203737(+)$1	241	141	161	11.8844
AGGCCAUUGUGAAACUGGCU	chr2:31923305-31923540(-)$1	235	9	29	10.5629
UGCGUGAAUAAUUUCUGUAU	chr12:54249529-54249776(+)$1	247	40	60	10.1399
GGGUUACAAAAAUGUGACUC	chr19:61168172-61168427(+)$1	255	195	215	10.9927
GAGAUUAAGAAGUUGCUCUC	chr16:29651894-29652129(+)$1	235	212	232	12.2143
AGUUCAAGUGUCUUUCUAGU	chr12:111820777-111821023(+)$1	246	95	115	11.5124
UGGUUGUGACUUCACUGCAC	chr11:109529413-109529649(+)$1	236	170	190	11.2903
CCCUUUCGUUGACGAGGGGC	chr15:72936345-72936583(-)$1	238	129	149	9.5867
UUUAACAAUUUUUGUAAAUC	chr10:117252017-117252253(-)$1	236	170	190	9.4255
AGAGUCUGAGUACAGCUUUC	chr3:138218802-138219042(+)$1	240	79	99	10.3879
UUAGCCCUUGCUAGGAGAAA	chr8:71430247-71430482(+)$1	235	140	160	11.1949
AGGUUUCUGUGCAGAGACCA	chr16:17044965-17045200(+)$1	235	115	135	10.6109
CUGGGCCUGAAGCAGGCUCA	chr6:30404433-30404668(+)$1	235	36	56	9.3243
AUCCUGCUCAAAAGCUGCUU	chr12:111819804-111820044(+)$1	240	91	111	11.3033
GUGCUGAGGUGUCUCCAGAG	chr6:148181130-148181368(-)$1	238	158	178	9.1594
UUUGAGGGUAUGCCCCAACU	chr17:44174403-44174641(+)$1	238	209	229	11.2739
AGUGGAUGGCCACGUGGCUG	chr15:4104924-4105174(+)$1	250	122	142	11.0526
GAUAGGCCGUGUGGUGAAAU	chr11:87897636-87897884(+)$1	248	169	189	12.4250
CCUCUGGAGACUUCAUGAAG	chr11:54792867-54793114(-)$1	247	98	118	9.8890
AUAGAUGCUAUAGCAUUUGA	chr2:155214476-155214718(+)$1	242	181	201	10.3272
CUGUUUUCAAGAGAACAUAG	chr11:29642544-29642783(+)$1	239	138	158	10.6852
CGGAGCCUGCUGAGGAAACA	chr7:146765008-146765298(+)$1	290	256	276	12.1416
AAUCUCUGUAGUUAGUUGUU	chr11:60370461-60370714(+)$1	253	112	132	11.6695
UGUUAUUUUGGAGAGAUGAU	chr5:122950679-122950926(-)$1	247	3	23	9.3243

#DB
.(((((((....))))))))	chr5:147072535-147072789(+)$1	1	64	84	10.6397
((.(.(((....))).).))	chr1:34933815-34934074(+)$1	1	181	201	10.6819
((...(((....))).))))	chr9:30957848-30958085(-)$1	1	61	81	11.6092
.(((((((....))))))).	chr15:58649129-58649364(-)$1	1	24	44	10.5817
((((((((....))))))))	chr11:68635611-68635852(-)$1	1	32	52	10.9927
(((..(((....)))..)))	chr8:46912753-46912988(+)$1	1	139	159	12.0038
((((((((....)).)))))	chr17:87398130-87398365(+)$1	1	206	226	9.9280
((((.(((....))).))))	chr19:24757738-24757973(-)$1	1	123	143	10.6990
(((..(((....)))..)))	chr2:72240354-72240607(+)$1	1	215	235	11.3209
.(((((((....)))))))(	chr9:121364568-121364806(+)$1	1	90	110	9.4939
(((((((((...))))))))	chr14:55565114-55565368(-)$1	1	195	215	9.3243
((((((((....))))))))	chr3:51323788-51324027(-)$1	1	197	217	11.4489
.((..(((....)))..)))	chr1:129839793-129840031(+)$1	1	185	205	10.7702
((((((((....))))))))	chr11:50108261-50108515(-)$1	1	51	71	10.9927
((((.(((....)))..)))	chr11:109528792-109529029(+)$1	1	191	211	10.9535
((((((.(....).))))))	chr6:29402139-29402374(+)$1	1	201	221	10.2396
((((.(((....).))))))	chr1:34178373-34178608(+)$1	1	75	95	9.4922
((((((((....)))...))	chr6:119875219-119875455(-)$1	1	11	31	12.1483
(((..(((....)))..)))	chr1:60389515-60389763(+)$1	1	189	209	12.0038
((((..((....))..))))	chr9:121364093-121364352(+)$1	1	66	86	10.3248
.(((((((....))))))).	chr8:59070600-59070836(+)$1	1	57	77	10.5817
((((.(((....)))))))(	chr4:137797888-137798143(+)$1	1	186	206	10.1381
((((.(((....))).))))	chr6:124885829-124886072(+)$1	1	3	23	10.6852
((((.(((....))).)))(	chr18:78021187-78021422(+)$1	1	110	130	11.2734
((((((((....))))))))	chr1:135552554-135552791(-)$1	1	124	144	11.4489
((((..((....))..))))	chr11:19964296-19964533(-)$1	1	76	96	10.3248
(((..(((....)))..)))	chr2:114019151-114019395(-)$1	1	39	59	11.2675
(((..(((....)))...))	chr10:82203496-82203737(+)$1	1	141	161	11.8844
((((((((....)).)))))	chr2:31923305-31923540(-)$1	1	9	29	10.5629
((((.(((....))))))))	chr12:54249529-54249776(+)$1	1	40	60	10.1399
((((((((....))))))))	chr19:61168172-61168427(+)$1	1	195	215	10.9927
((((.(((....))).))))	chr16:29651894-29652129(+)$1	1	212	232	12.2143
(.(..(((....)))..).)	chr12:111820777-111821023(+)$1	1	95	115	11.5124
.(((.(((....)))...))	chr11:109529413-109529649(+)$1	1	170	190	11.2903
.(((((((....)))))))(	chr15:72936345-72936583(-)$1	1	129	149	9.5867
((((.(((...)))))))))	chr10:117252017-117252253(-)$1	1	170	190	9.4255
.(((.(((....))))))((	chr3:138218802-138219042(+)$1	1	79	99	10.3879
((..((((....))).)..)	chr8:71430247-71430482(+)$1	1	140	160	11.1949
.(((((((....))))))))	chr16:17044965-17045200(+)$1	1	115	135	10.6109
(((((((((...))))))))	chr6:30404433-30404668(+)$1	1	36	56	9.3243
(..(.(((....))).)..)	chr12:111819804-111820044(+)$1	1	91	111	11.3033
.(.(((((....)).))).)	chr6:148181130-148181368(-)$1	1	158	178	9.1594
.(((.(((....))))))..	chr17:44174403-44174641(+)$1	1	209	229	11.2739
(((..(((....))).))))	chr15:4104924-4105174(+)$1	1	122	142	11.0526
(((..(((....)))...))	chr11:87897636-87897884(+)$1	1	169	189	12.4250
((((..((....))..).))	chr11:54792867-54793114(-)$1	1	98	118	9.8890
.(((((((....))))))))	chr2:155214476-155214718(+)$1	1	181	201	10.3272
((((.(((....))).))))	chr11:29642544-29642783(+)$1	1	138	158	10.6852
.(...(((....)))...).	chr7:146765008-146765298(+)$1	1	256	276	12.1416
(....(((....)))...))	chr11:60370461-60370714(+)$1	1	112	132	11.6695
(((((((((...))))))))	chr5:122950679-122950926(-)$1	1	3	23	9.3243

#PSSM
d : 0.17	[ : 0.13	g : 0.13	c : 0.11	= : 0.11	i : 0.07	: : 0.07	e : 0.05	! : 0.03	b : 0.01	F : 0.01	f : 0.01	
g : 0.27	c : 0.19	d : 0.13	= : 0.11	i : 0.07	e : 0.05	b : 0.03	a : 0.03	[ : 0.01	! : 0.01	# : 0.01	
g : 0.27	c : 0.15	d : 0.13	= : 0.11	i : 0.07	e : 0.05	[ : 0.03	" : 0.03	! : 0.03	b : 0.01	a : 0.01	# : 0.01	
g : 0.27	! : 0.19	= : 0.11	c : 0.09	i : 0.07	d : 0.07	a : 0.05	" : 0.03	e : 0.03	# : 0.01	
[ : 0.29	! : 0.23	g : 0.19	= : 0.11	i : 0.05	" : 0.03	a : 0.01	c : 0.01	# : 0.01	
c : 0.56	g : 0.17	= : 0.11	i : 0.05	! : 0.05	b : 0.01	
c : 0.54	g : 0.13	b : 0.13	= : 0.09	i : 0.05	[ : 0.01	
c : 0.54	g : 0.13	b : 0.11	= : 0.09	i : 0.05	a : 0.03	
m : 0.92	= : 0.05	l : 0.01	
m : 0.92	l : 0.07	
m : 0.92	l : 0.07	
m : 0.92	l : 0.05	c : 0.01	
c : 0.54	g : 0.13	b : 0.11	= : 0.09	i : 0.05	a : 0.03	
c : 0.54	g : 0.13	b : 0.11	= : 0.09	i : 0.05	] : 0.03	
c : 0.52	g : 0.15	= : 0.09	i : 0.07	] : 0.05	2 : 0.05	b : 0.01	
] : 0.19	2 : 0.19	g : 0.17	= : 0.11	3 : 0.11	i : 0.07	c : 0.05	b : 0.01	d : 0.01	e : 0.01	
g : 0.25	2 : 0.13	= : 0.11	3 : 0.11	c : 0.09	a : 0.07	i : 0.07	d : 0.07	e : 0.03	
g : 0.25	c : 0.13	d : 0.11	= : 0.11	3 : 0.11	i : 0.07	e : 0.05	] : 0.03	2 : 0.03	b : 0.01	a : 0.01	
g : 0.29	d : 0.15	c : 0.13	= : 0.11	i : 0.07	e : 0.05	b : 0.03	] : 0.03	2 : 0.03	3 : 0.01	a : 0.01	
c : 0.19	d : 0.17	g : 0.15	= : 0.11	e : 0.09	i : 0.09	] : 0.05	b : 0.03	f : 0.01	a : 0.01	3 : 0.01	

#score	549.7498815381043
#seq	51
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_UTR_m1_run2.txt

#BEAR
a"""a[bbeeeee[aooooooaeeeee]bb]a333a]d	chr2:14999759-15000046(+)$1	287	142	180	14.6078
++++ggggggg[cccoooooocccggggggghhhhhhh	chr5:145942303-145942575(+)$1	272	45	83	12.5291
b####ccc"""ddddoooooodddd]ccc4444bb]dd	chr8:11834139-11834413(+)$1	274	108	146	14.8012
$$$iiiiiiiii!!aooooooa22iiiiiiiii22a]b	chr4:137798692-137798972(+)$1	280	102	140	16.1448
=======[a####cccmmmmccc22a]===========	chr18:34930930-34931222(+)$1	292	29	67	14.9453
C===========ccclllccc22===========gggg	chr15:79656085-79656364(-)$1	279	158	196	13.4316
bb####ccc"""cccnnnnnccc4444ccc333bb]ff	chr16:98014687-98014959(-)$1	272	146	184	13.9252
=======[gggggggpppppppggggggg333======	chr17:32498275-32498549(-)$1	274	210	248	12.4182
ff[bb[eeeee[cccooooooccc]eeeee]bbfffff	chr11:69813257-69813538(+)$1	281	182	220	13.8913
==========bbccclllccc22bb]============	chr5:137968786-137969068(+)$1	282	81	119	13.7335
[ccc!!a[iiiiiiiiimmmmiiiiiiiii]accc]a2	chr11:79506341-79506633(+)$1	292	157	195	12.8849
dddd===========nnnnn===========:dddd[a	chr3:90057072-90057343(+)$1	271	106	144	12.0853
iiii[cccccc[cccoooooocccccc22ccc22iiii	chr5:123807810-123808084(+)$1	274	193	231	15.8165
ccc!!ccc[gggggggooooooggggggg]ccc]ccc:	chr5:76641535-76641823(-)$1	288	57	95	13.7049
ee"""==========qqqqqqqq==========eeeee	chr4:99324900-99325179(+)$1	279	236	274	11.8657
""bb"""dddd[cccoooooocccdddd]bb]eeeee:	chr5:93697524-93697808(+)$1	284	75	113	13.3957
gggggg!!gggggggooooooggggggg]ggggggg::	chr11:117828139-117828471(-)$1	332	6	44	14.2700
"a[bb[dddd[bb[aooooooa]bb]ddddbb]a4444	chr1:133921794-133922065(+)$1	271	76	114	12.9640
ffffff"""bbddddoooooodddd4444bb333ffff	chr1:64840465-64840748(-)$1	283	94	132	13.1283
ddd"""iiiiiiiiiooooooiiiiiiiii4444dddd	chr19:5456434-5456714(-)$1	280	69	107	16.1653
[ccc"""ccc[ddddoooooodddd22ccc333ccc]e	chr15:79655896-79656195(-)$1	299	243	281	15.5002
ffff####gggggggooooooggggggg4444ffffff	chr17:6084557-6084835(+)$1	278	70	108	15.1666
##ffffff!!eeeeeooooooeeeee22ffffff4444	chr8:123178705-123178986(-)$1	281	209	247	13.0416
$$iiiiiiiiissssssssssiiiiiiiiiiiiiiiii	chr10:29066280-29066564(-)$1	284	146	184	11.5516
iiiiiii[ccc!!bboooooobb]ccciiiiiiiii33	chr5:137966884-137967196(+)$1	312	80	118	16.1889
=======$$$$$cccooooooccc]===========33	chr7:107985033-107985335(+)$1	302	54	92	18.4087
cc[ggggggg!!ddddllldddd333gggggggcccdd	chr8:74842841-74843113(+)$1	272	75	113	12.2703
ddd!!eeeee!!cccooooooccc22eeeee]dddd::	chr4:126421180-126421460(-)$1	280	38	76	12.2843
========!!ffffffnnnnnffffff==========h	chr3:145309905-145310179(-)$1	274	175	213	13.8493
!!gggggggffffffooooooffffff22ggggggg22	chr15:81535366-81535658(-)$1	292	247	285	14.2301
$$$$$dddd"""cccooooooccc333dddd55555ff	chr6:30079454-30079729(+)$1	275	145	183	11.8952
c[eeeee"""eeeeennnnneeeee333eeeee]ccc]	chr8:11834069-11834348(+)$1	279	73	111	10.7885
"ggggggg[bb[a[cccmmmmccc]abbgggggggbbc	chr5:75006662-75006928(-)$1	266	139	177	11.2679
""ggggggg####bbnnnnnbb4444ggggggg4444e	chr5:108863235-108863508(-)$1	273	62	100	13.1255
fff!!eeeee!!cccooooooccc22eeeeeffffff4	chr12:113887155-113887428(+)$1	273	75	113	14.5083
========####cccooooooccc333===========	chr15:44595258-44595531(-)$1	273	153	191	19.6615
ff####a[gggggggooooooggggggg]a333fffff	chr2:31071139-31071426(+)$1	287	225	263	16.4298
==####bb!!bb[bbnnnnnbb]bb22bb=========	chr15:80761843-80762129(+)$1	286	99	137	12.0934
==####bb[ffffffnnnnnffffff]bb4444=====	chr3:95464619-95464908(+)$1	289	9	47	12.6296
"""cccdddd!!ddddmmmmdddd]dddd333ccc444	chr16:91227830-91228116(+)$1	286	147	185	11.2019
!ggggggg[bb[cccooooooccc]bb]ggggggg22a	chr15:98734299-98734578(-)$1	279	106	144	15.7887
gggggg[eeeee[cccmmmmccc22eeeee]ggggggg	chr7:25670028-25670303(+)$1	275	56	94	11.3924
=====!!dddd[cccoooooocccdddd55555=====	chr12:8798856-8799128(+)$1	272	153	191	13.0972
!!iiiiiiiii[cccmmmmccciiiiiiiii333eeee	chr6:54767244-54767517(+)$1	273	159	197	14.2699
ggggg[ggggggg[cccmmmmccc]ggggggggggggg	chr15:81678793-81679067(-)$1	274	220	258	12.7923
b!!a[a[ffffff!!aooooooa22ffffff]a]a22b	chr4:138012732-138013003(+)$1	271	112	150	12.9723
"==========[a[aooooooa]a]==========333	chr19:5664675-5664943(-)$1	268	211	249	19.3469
iiii[a[a[eeeee[ccclllccc22eeeee]a]a]ii	chr14:55505758-55506041(+)$1	283	57	95	12.0692
!cccdddd"""cccrrrrrrrrrccc]dddd]ccc]gg	chr5:141098323-141098602(-)$1	279	50	88	11.0080
###ccc[hhhhhhhhoooooohhhhhhhhccc333ccc	chr5:31924703-31924994(+)$1	291	94	132	13.5514
eee[a!!ddddddddoooooodddd4444dddda]eee	chr13:69138016-69138287(-)$1	271	148	186	12.3764
ffffffccc[eeeeeooooooeeeee]ccc333fffff	chr19:45079711-45079992(-)$1	281	242	280	13.6121
========[ffffffnnnnnffffff]==========f	chr5:137967098-137967380(+)$1	282	187	225	14.2294

#otherMatches

#Seq PSSM
GGGAUGGGAACUGAGAAAAUACCAGUUACUGAAAGCAC	chr2:14999759-15000046(+)$1	287	142	180	14.6078
uGGACUCCCUGUACACUGUCCUGUUGGGGAGAGAGAAG	chr5:145942303-145942575(+)$1	272	45	83	12.5291
CCCCCGCCCACCCACCCACCUGUGGAGGUUUCUGCGUG	chr8:11834139-11834413(+)$1	274	108	146	14.8012
AUAUCCUCUGGCCCCUUACAUGCUGCCAGAGGAGAAGG	chr4:137798692-137798972(+)$1	280	102	140	16.1448
gugcauggguguguacuugugugagugugugugcgugc	chr18:34930930-34931222(+)$1	292	29	67	14.9453
GGACAGCGGUAGUGGGACCCAACUUACUGUUGUUGCCU	chr15:79656085-79656364(-)$1	279	158	196	13.4316
AGAGCAGUAGAGGUCCUCGUGACAGAAUACAAACUGGC	chr16:98014687-98014959(-)$1	272	146	184	13.9252
CCAGGGUAGAAAUGGAGACCUGCCGUUUCCGGAUCCUG	chr17:32498275-32498549(-)$1	274	210	248	12.4182
ACUGUUGGCCGGCUGCUCAGACAGACGGCCUGCGUGUU	chr11:69813257-69813538(+)$1	281	182	220	13.8913
AGAGGCCUUAACCCUGUGAGGAAGUGUGGGGCCUCUCC	chr5:137968786-137969068(+)$1	282	81	119	13.7335
GGGCCAUGGCUGUGGGUGACAACCCACGGUGAGCUGUG	chr11:79506341-79506633(+)$1	292	157	195	12.8849
UGCUGAGGUGCUGGGGCCUGCCUAGCACCUCAGUGGAG	chr3:90057072-90057343(+)$1	271	106	144	12.0853
aaguagguuccagggaucgaacucggaucaucaagcuu	chr5:123807810-123808084(+)$1	274	193	231	15.8165
UCAGGUCCAGUGAACCGUAGCAGGUUUAUGGGAAUGAU	chr5:76641535-76641823(-)$1	288	57	95	13.7049
AGCUUUGAACUUUCAUAUUUUUUUGAAGGUUCACUCUG	chr4:99324900-99325179(+)$1	279	236	274	11.8657
UACGUAUCCGGAUUAUAUUCUUAACCGGCCGCGGUGUA	chr5:93697524-93697808(+)$1	284	75	113	13.3957
GUUUGCGCUUUGAUUUGGUUUGAUCAAGAGCAGGCACC	chr11:117828139-117828471(-)$1	332	6	44	14.2700
AUGUGCAAUAGUAGUGUGAGAAGUAGUGUUCAGAGUGG	chr1:133921794-133922065(+)$1	271	76	114	12.9640
AUUCAGUCCGCGUAACUACUCUUGCUUUUGUAUCCUGG	chr1:64840465-64840748(-)$1	283	94	132	13.1283
UCCUUGCUCUUGCUGGCAGAGCAGCAGGGGAAAUGGAG	chr19:5456434-5456714(-)$1	280	69	107	16.1653
AAGAUGCGAGCCUGCCAAUGAGCAGCCCUCUUCUCUCU	chr15:79655896-79656195(-)$1	299	243	281	15.5002
UGCCUUUUCUCUUACCCAGAAGUGAGAGCGCUGGUGUU	chr17:6084557-6084835(+)$1	278	70	108	15.1666
AAGUCUGUACGGCCAGCAGGAUGGCCCAGCAGAUGAAG	chr8:123178705-123178986(-)$1	281	209	247	13.0416
UUGAGAGCUGUUCAGUAUAACACAGUUUUCUUGACAUC	chr10:29066280-29066564(-)$1	284	146	184	11.5516
ACUCGGGUGGUGGCAGCAGCAUGGACCCUUGGGUCUCC	chr5:137966884-137967196(+)$1	312	80	118	16.1889
CAGGCUCAGAACCUGGGAAAGCAGAGAGUUUGGGGAAG	chr7:107985033-107985335(+)$1	302	54	92	18.4087
UGUGCCUGCCGCGCCUAUAAGGCCUGGGUGGGCCGGGC	chr8:74842841-74843113(+)$1	272	75	113	12.2703
CUUGAGCUUUUGUGUCAUGUUGCAGCAGAGUGAAGAUG	chr4:126421180-126421460(-)$1	280	38	76	12.2843
AUUUUAUAUCAGUGAAGAGaauuuauuuauaaaauuaa	chr3:145309905-145310179(-)$1	274	175	213	13.8493
UCUCCCUGCUGGACUAACCCAAGUCCACUGUGGGGAAU	chr15:81535366-81535658(-)$1	292	247	285	14.2301
uuguuguuguuguuguuguuUUAAAUCUGGCCUUUUCU	chr6:30079454-30079729(+)$1	275	145	183	11.8952
GUCAGAGAUACUUUCCCUUAGAAAGGUGUUUUGUCUUU	chr8:11834069-11834348(+)$1	279	73	111	10.7885
GUCCAGCCCAGACAUCUUUCAAGAAGCUGGCUGGAUCA	chr5:75006662-75006928(-)$1	266	139	177	11.2679
AGGAGGCGGCUUUCAUUCUCUGUCUUCCGCCUCAGUUG	chr5:108863235-108863508(-)$1	273	62	100	13.1255
GCUAUGUUUGAAGCCUGAGGUGGCCACAGACAGCACAA	chr12:113887155-113887428(+)$1	273	75	113	14.5083
GUGUGAUGUUCAGAGAAAAAccuuagguaucaugcacg	chr15:44595258-44595531(-)$1	273	153	191	19.6615
AGCCACAGCCUGCCUCUCAGAGGGCAGGGUCUUUUUGG	chr2:31071139-31071426(+)$1	287	225	263	16.4298
AACAAUGCCUAAUGUAUUUAACUUUCAGCUUGUGUCUU	chr15:80761843-80762129(+)$1	286	99	137	12.0934
GGAUGGGUUUGUGGAGUUCUUCCACGUACAGGACCUAG	chr3:95464619-95464908(+)$1	289	9	47	12.6296
CUUAGACGAGACGCAGAGCACUGCACUUGACUUCUUUC	chr16:91227830-91228116(+)$1	286	147	185	11.2019
GCCGAAGCACUGUGCUAUCCUGUGGAGGGCUUUGGACC	chr15:98734299-98734578(-)$1	279	106	144	15.7887
UGGUGUUGACCUGGACCCACGUCAGGGGUUUGCACCAA	chr7:25670028-25670303(+)$1	275	56	94	11.3924
AGCACUUACCCAUAGAGACCGCUAGGGUUGGCCGUGCU	chr12:8798856-8799128(+)$1	272	153	191	13.0972
cuggcgggccgcgUCUGGUGAUCGGCUCGCUCCCGGCC	chr6:54767244-54767517(+)$1	273	159	197	14.2699
UUUGUAUUCAGAACAUUGUGCAAUAUUUUGGAAUGAGA	chr15:81678793-81679067(-)$1	274	220	258	12.7923
CAACUUGUGUCUCAAGUCAGGCCGGGAGACAGAUGAGG	chr4:138012732-138013003(+)$1	271	112	150	12.9723
UGUGGCAAGGGUGGGUUCAUUCGUUCUUUUGUCAUUUU	chr19:5664675-5664943(-)$1	268	211	249	19.3469
CCUAGAAUGUGGCAUCAUAUCGUGCUUGCUAGAAUGUG	chr14:55505758-55506041(+)$1	283	57	95	12.0692
ACUUUCCUCUCGGUUUCAUUCUCACCCAGGACAAGCGG	chr5:141098323-141098602(-)$1	279	50	88	11.0080
GAGUAGUGGAUUGAAAAUGAAUUUGAUUCCUAAAUGAG	chr5:31924703-31924994(+)$1	291	94	132	13.5514
UGCGGGACCGCGCCGAggcggcggcagcagcggcggcg	chr13:69138016-69138287(-)$1	271	148	186	12.3764
guuggcagaggcagaugaaucucugcguuuaaggccag	chr19:45079711-45079992(-)$1	281	242	280	13.6121
uuguuuuuauuuuuUAGaaaaaaaaaaaaagauaaaaa	chr5:137967098-137967380(+)$1	282	187	225	14.2294

#DB
(...(.(((((((.(......)))))).)).)...).)	chr2:14999759-15000046(+)$1	1	142	180	14.6078
....(((((((.(((......)))))))))))))))))	chr5:145942303-145942575(+)$1	1	45	83	12.5291
(....(((...((((......)))).)))....)).))	chr8:11834139-11834413(+)$1	1	108	146	14.8012
...(((((((((..(......)..)))))))))..).)	chr4:137798692-137798972(+)$1	1	102	140	16.1448
(((((((.(....(((....)))..).)))))))))))	chr18:34930930-34931222(+)$1	1	29	67	14.9453
(((((((((((((((...)))..)))))))))))((((	chr15:79656085-79656364(-)$1	1	158	196	13.4316
((....(((...(((.....)))....)))...)).))	chr16:98014687-98014959(-)$1	1	146	184	13.9252
(((((((.(((((((.......)))))))...))))))	chr17:32498275-32498549(-)$1	1	210	248	12.4182
((.((.(((((.(((......))).))))).)))))))	chr11:69813257-69813538(+)$1	1	182	220	13.8913
(((((((((((((((...)))..)).))))))))))))	chr5:137968786-137969068(+)$1	1	81	119	13.7335
.(((..(.(((((((((....))))))))).)))).).	chr11:79506341-79506633(+)$1	1	157	195	12.8849
))))(((((((((((.....))))))))))).((((.(	chr3:90057072-90057343(+)$1	1	106	144	12.0853
((((.((((((.(((......))))))..)))..))))	chr5:123807810-123808084(+)$1	1	193	231	15.8165
(((..(((.(((((((......))))))).))).))).	chr5:76641535-76641823(-)$1	1	57	95	13.7049
((...((((((((((........)))))))))))))))	chr4:99324900-99325179(+)$1	1	236	274	11.8657
..((...((((.(((......))))))).)).))))).	chr5:93697524-93697808(+)$1	1	75	113	13.3957
((((((..(((((((......))))))).)))))))..	chr11:117828139-117828471(-)$1	1	6	44	14.2700
.(.((.((((.((.(......).)).)))))).)....	chr1:133921794-133922065(+)$1	1	76	114	12.9640
((((((...((((((......))))....))...))))	chr1:64840465-64840748(-)$1	1	94	132	13.1283
(((...(((((((((......)))))))))....))))	chr19:5456434-5456714(-)$1	1	69	107	16.1653
.(((...(((.((((......))))..)))...))).)	chr15:79655896-79656195(-)$1	1	243	281	15.5002
((((....(((((((......)))))))....))))))	chr17:6084557-6084835(+)$1	1	70	108	15.1666
..((((((..(((((......)))))..))))))....	chr8:123178705-123178986(-)$1	1	209	247	13.0416
..(((((((((..........)))))))))))))))))	chr10:29066280-29066564(-)$1	1	146	184	11.5516
(((((((.(((..((......)).))))))))))))..	chr5:137966884-137967196(+)$1	1	80	118	16.1889
(((((((.....(((......))).)))))))))))..	chr7:107985033-107985335(+)$1	1	54	92	18.4087
((.(((((((..((((...))))...))))))))))((	chr8:74842841-74843113(+)$1	1	75	113	12.2703
(((..(((((..(((......)))..))))).))))..	chr4:126421180-126421460(-)$1	1	38	76	12.2843
((((((((..((((((.....)))))))))))))))))	chr3:145309905-145310179(-)$1	1	175	213	13.8493
..(((((((((((((......))))))..)))))))..	chr15:81535366-81535658(-)$1	1	247	285	14.2301
.....((((...(((......)))...)))).....))	chr6:30079454-30079729(+)$1	1	145	183	11.8952
(.(((((...(((((.....)))))...))))).))).	chr8:11834069-11834348(+)$1	1	73	111	10.7885
.(((((((.((.(.(((....))).)))))))))))))	chr5:75006662-75006928(-)$1	1	139	177	11.2679
..(((((((....((.....))....)))))))....)	chr5:108863235-108863508(-)$1	1	62	100	13.1255
(((..(((((..(((......)))..))))))))))).	chr12:113887155-113887428(+)$1	1	75	113	14.5083
((((((((....(((......)))...)))))))))))	chr15:44595258-44595531(-)$1	1	153	191	19.6615
((....(.(((((((......))))))).)...)))))	chr2:31071139-31071426(+)$1	1	225	263	16.4298
((....((..((.((.....)).))..)))))))))))	chr15:80761843-80762129(+)$1	1	99	137	12.0934
((....((.((((((.....)))))).))....)))))	chr3:95464619-95464908(+)$1	1	9	47	12.6296
...(((((((..((((....)))).))))...)))...	chr16:91227830-91228116(+)$1	1	147	185	11.2019
.(((((((.((.(((......))).)).)))))))..)	chr15:98734299-98734578(-)$1	1	106	144	15.7887
((((((.(((((.(((....)))..))))).)))))))	chr7:25670028-25670303(+)$1	1	56	94	11.3924
(((((..((((.(((......))))))).....)))))	chr12:8798856-8799128(+)$1	1	153	191	13.0972
..(((((((((.(((....))))))))))))...))))	chr6:54767244-54767517(+)$1	1	159	197	14.2699
(((((.(((((((.(((....))).)))))))))))))	chr15:81678793-81679067(-)$1	1	220	258	12.7923
(..(.(.((((((..(......)..)))))).).)..)	chr4:138012732-138013003(+)$1	1	112	150	12.9723
.((((((((((.(.(......).).))))))))))...	chr19:5664675-5664943(-)$1	1	211	249	19.3469
((((.(.(.(((((.(((...)))..))))).).).))	chr14:55505758-55506041(+)$1	1	57	95	12.0692
.(((((((...(((.........))).)))).))).))	chr5:141098323-141098602(-)$1	1	50	88	11.0080
...(((.((((((((......)))))))))))...)))	chr5:31924703-31924994(+)$1	1	94	132	13.5514
(((.(..((((((((......))))....))))).)))	chr13:69138016-69138287(-)$1	1	148	186	12.3764
(((((((((.(((((......))))).)))...)))))	chr19:45079711-45079992(-)$1	1	242	280	13.6121
((((((((.((((((.....)))))).)))))))))))	chr5:137967098-137967380(+)$1	1	187	225	14.2294

#PSSM
= : 0.18	f : 0.11	" : 0.11	! : 0.07	b : 0.05	$ : 0.05	d : 0.05	i : 0.05	c : 0.05	g : 0.05	[ : 0.03	e : 0.03	# : 0.03	a : 0.01	+ : 0.01	C : 0.01	
= : 0.22	f : 0.11	c : 0.09	g : 0.09	" : 0.07	# : 0.05	$ : 0.05	d : 0.05	i : 0.05	! : 0.05	e : 0.03	+ : 0.01	b : 0.01	a : 0.01	[ : 0.01	
= : 0.18	g : 0.13	# : 0.11	i : 0.09	f : 0.09	c : 0.07	" : 0.05	[ : 0.05	d : 0.05	$ : 0.03	e : 0.03	+ : 0.01	b : 0.01	! : 0.01	
= : 0.18	g : 0.15	i : 0.11	# : 0.09	c : 0.09	f : 0.07	" : 0.05	b : 0.05	! : 0.05	+ : 0.01	d : 0.01	$ : 0.01	e : 0.01	a : 0.01	[ : 0.01	
= : 0.20	g : 0.16	# : 0.11	i : 0.07	! : 0.07	" : 0.07	[ : 0.05	f : 0.05	a : 0.03	b : 0.03	c : 0.03	$ : 0.01	e : 0.01	d : 0.01	
= : 0.20	g : 0.15	c : 0.09	# : 0.09	[ : 0.07	i : 0.07	! : 0.05	" : 0.05	f : 0.05	e : 0.05	d : 0.03	a : 0.03	
= : 0.20	g : 0.13	c : 0.09	i : 0.09	e : 0.07	d : 0.07	[ : 0.07	b : 0.05	" : 0.05	! : 0.05	a : 0.03	# : 0.01	f : 0.01	
= : 0.15	g : 0.13	d : 0.13	c : 0.11	[ : 0.09	i : 0.07	e : 0.07	b : 0.05	" : 0.03	f : 0.03	! : 0.01	# : 0.01	$ : 0.01	a : 0.01	h : 0.01	
g : 0.16	[ : 0.11	d : 0.11	e : 0.09	i : 0.09	= : 0.09	c : 0.09	" : 0.07	! : 0.05	a : 0.01	$ : 0.01	# : 0.01	f : 0.01	h : 0.01	
g : 0.15	e : 0.11	" : 0.09	i : 0.09	= : 0.09	d : 0.09	f : 0.07	# : 0.05	c : 0.05	b : 0.05	! : 0.05	$ : 0.01	h : 0.01	[ : 0.01	
e : 0.13	g : 0.13	i : 0.09	b : 0.09	f : 0.09	" : 0.07	= : 0.07	! : 0.07	# : 0.05	d : 0.05	c : 0.03	[ : 0.03	$ : 0.01	h : 0.01	
[ : 0.16	e : 0.11	g : 0.11	! : 0.09	f : 0.09	d : 0.07	i : 0.05	# : 0.05	= : 0.05	b : 0.05	" : 0.03	s : 0.01	$ : 0.01	c : 0.01	h : 0.01	
c : 0.30	d : 0.11	g : 0.11	e : 0.09	f : 0.09	! : 0.03	# : 0.03	i : 0.03	= : 0.03	a : 0.03	[ : 0.03	b : 0.01	s : 0.01	h : 0.01	
c : 0.33	d : 0.11	[ : 0.09	g : 0.09	e : 0.07	f : 0.07	b : 0.05	! : 0.03	i : 0.03	= : 0.03	s : 0.01	h : 0.01	
c : 0.35	d : 0.11	g : 0.09	a : 0.07	f : 0.07	e : 0.05	b : 0.05	i : 0.03	= : 0.03	s : 0.01	! : 0.01	[ : 0.01	r : 0.01	h : 0.01	
o : 0.52	n : 0.13	c : 0.09	l : 0.03	d : 0.03	p : 0.01	i : 0.01	g : 0.01	q : 0.01	s : 0.01	f : 0.01	m : 0.01	a : 0.01	r : 0.01	
o : 0.56	n : 0.15	m : 0.07	l : 0.05	c : 0.05	p : 0.01	i : 0.01	q : 0.01	s : 0.01	r : 0.01	
o : 0.56	n : 0.15	m : 0.13	l : 0.05	p : 0.01	q : 0.01	s : 0.01	c : 0.01	r : 0.01	
o : 0.56	n : 0.15	m : 0.13	c : 0.03	l : 0.03	p : 0.01	q : 0.01	s : 0.01	r : 0.01	
o : 0.56	n : 0.15	m : 0.11	c : 0.05	p : 0.01	q : 0.01	s : 0.01	d : 0.01	l : 0.01	r : 0.01	
o : 0.56	c : 0.11	m : 0.05	d : 0.03	b : 0.03	f : 0.03	p : 0.01	= : 0.01	q : 0.01	s : 0.01	n : 0.01	e : 0.01	l : 0.01	r : 0.01	
c : 0.33	d : 0.11	a : 0.07	f : 0.07	i : 0.05	g : 0.05	e : 0.05	b : 0.05	2 : 0.03	o : 0.03	p : 0.01	= : 0.01	q : 0.01	r : 0.01	h : 0.01	
c : 0.32	d : 0.11	g : 0.09	e : 0.07	i : 0.07	f : 0.07	2 : 0.05	] : 0.05	= : 0.01	q : 0.01	b : 0.01	4 : 0.01	a : 0.01	r : 0.01	h : 0.01	
c : 0.28	d : 0.09	g : 0.09	e : 0.07	2 : 0.07	i : 0.07	f : 0.07	= : 0.05	b : 0.05	4 : 0.03	] : 0.01	3 : 0.01	a : 0.01	h : 0.01	
] : 0.13	g : 0.11	d : 0.11	2 : 0.11	i : 0.09	e : 0.07	f : 0.07	= : 0.05	b : 0.05	c : 0.05	3 : 0.05	4 : 0.03	h : 0.01	
g : 0.13	e : 0.09	i : 0.09	= : 0.09	2 : 0.09	f : 0.09	4 : 0.07	3 : 0.07	] : 0.05	c : 0.05	d : 0.05	a : 0.03	b : 0.01	h : 0.01	
g : 0.16	e : 0.11	= : 0.11	i : 0.09	] : 0.09	d : 0.07	c : 0.05	4 : 0.05	2 : 0.05	f : 0.05	3 : 0.05	b : 0.03	h : 0.01	
= : 0.18	g : 0.16	i : 0.11	d : 0.11	e : 0.09	c : 0.07	2 : 0.05	b : 0.05	] : 0.03	4 : 0.03	3 : 0.01	f : 0.01	h : 0.01	
= : 0.18	g : 0.15	i : 0.11	e : 0.11	c : 0.07	d : 0.07	b : 0.05	] : 0.05	4 : 0.05	2 : 0.03	f : 0.03	5 : 0.01	h : 0.01	
= : 0.20	g : 0.15	i : 0.11	e : 0.11	c : 0.09	d : 0.07	b : 0.05	4 : 0.05	3 : 0.03	f : 0.03	] : 0.01	a : 0.01	5 : 0.01	
= : 0.20	g : 0.15	3 : 0.11	] : 0.07	4 : 0.07	i : 0.07	e : 0.07	c : 0.05	b : 0.05	d : 0.05	f : 0.03	5 : 0.01	
= : 0.18	3 : 0.15	g : 0.15	] : 0.09	4 : 0.07	i : 0.05	c : 0.05	a : 0.03	b : 0.03	f : 0.03	5 : 0.03	h : 0.01	: : 0.01	e : 0.01	d : 0.01	
= : 0.20	3 : 0.15	g : 0.15	c : 0.07	4 : 0.05	i : 0.05	d : 0.05	f : 0.05	e : 0.03	5 : 0.03	a : 0.03	h : 0.01	b : 0.01	2 : 0.01	] : 0.01	
= : 0.22	f : 0.11	g : 0.11	c : 0.09	3 : 0.07	] : 0.07	b : 0.03	2 : 0.03	d : 0.03	e : 0.03	a : 0.03	4 : 0.03	i : 0.03	h : 0.01	5 : 0.01	
= : 0.20	g : 0.13	c : 0.13	f : 0.11	d : 0.05	i : 0.05	e : 0.05	4 : 0.05	3 : 0.03	b : 0.03	a : 0.03	h : 0.01	2 : 0.01	5 : 0.01	] : 0.01	
= : 0.18	f : 0.11	] : 0.09	g : 0.09	c : 0.09	e : 0.07	4 : 0.07	d : 0.05	i : 0.05	a : 0.03	2 : 0.03	h : 0.01	5 : 0.01	b : 0.01	3 : 0.01	
= : 0.16	f : 0.15	g : 0.07	e : 0.07	4 : 0.07	] : 0.05	d : 0.05	i : 0.05	c : 0.05	3 : 0.05	2 : 0.05	: : 0.03	h : 0.01	a : 0.01	[ : 0.01	b : 0.01	
f : 0.15	= : 0.13	e : 0.09	d : 0.07	g : 0.07	: : 0.07	4 : 0.07	i : 0.05	3 : 0.05	h : 0.03	b : 0.03	2 : 0.03	a : 0.03	c : 0.03	] : 0.01	

#score	729.3104445072054
#seq	53
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_CDS_m2_run1.txt

#BEAR
cceeeeewwwwwwwwwwwwwweeeee	chr6:73220861-73221104(+)$1	243	40	66	22.9425
d"""cccvvvvvvvvvvvvvccc333	chr11:117002667-117002927(+)$1	260	222	248	24.3530
gggggggvvvvvvvvvvvvvgggggg	chr5:3891496-3891716(-)$1	220	71	97	24.6457
iiiiiiiiuuuuuuuuuuuuiiiiii	chr13:12499725-12499945(+)$1	220	184	210	23.9282
[ccccccxxxxxxxxxxxxxxxccc]	chr4:86420209-86420429(+)$1	220	157	183	20.0237
:ffffffuuuuuuuuuuuuffffff:	chr1:9715236-9715456(-)$1	220	123	149	21.0594
[gggggggtttttttttttggggggg	chr5:138602596-138602816(+)$1	220	143	169	22.5147
ee!!cccuuuuuuuuuuuuccc333e	chr12:13490463-13490700(+)$1	237	121	147	24.1241
ccc!!ddddtttttttttttdddd22	chr19:9088885-9089115(+)$1	230	88	114	20.5210
[fffffftttttttttttffffff]h	chr10:87610940-87611160(+)$1	220	143	169	20.9924
a[ccc[bbtttttttttttbbccc]a	chr3:88439478-88439698(+)$1	220	105	131	21.9454
ffffffwwwwwwwwwwwwwwffffff	chr12:111723951-111724171(+)$1	220	33	59	22.7014
"""ddddtttttttttttdddd4444	chr12:72164054-72164275(+)$1	221	103	129	20.4228
gggg[bbwwwwwwwwwwwwwwbb]gg	chr9:7833738-7833970(-)$1	232	26	52	23.5821
=======vvvvvvvvvvvvv======	chr11:30709808-30710028(+)$1	220	40	66	24.8870
cffffffvvvvvvvvvvvvvffffff	chr8:109177706-109177926(+)$1	220	57	83	23.4253
iiiiiiiyyyyyyyyyyyyyyyyiii	chr1:58054915-58055135(+)$1	220	165	191	23.0154
========uuuuuuuuuuuu======	chr5:110665351-110665582(+)$1	231	146	172	24.3623
f!!bb[ccctttttttttttccc]bb	chr12:66200220-66200440(+)$1	220	7	33	21.1181
ggeeeeevvvvvvvvvvvvveeeee:	chr1:120226005-120226225(+)$1	220	106	132	22.4576
e!!dddduuuuuuuuuuuudddd333	chr13:13599918-13600138(+)$1	220	179	205	22.9903
bb[bbbbuuuuuuuuuuuubb]bbbb	chr5:3822067-3822287(+)$1	220	75	101	21.0292
!ffffffvvvvvvvvvvvvvffffff	chr17:29834886-29835106(+)$1	220	154	180	23.5618
fff!!awwwwwwwwwwwwwwa22fff	chr17:68159598-68159818(+)$1	220	149	175	22.9169
ggggggguuuuuuuuuuuuggggggg	chr5:104490633-104490853(+)$1	220	45	71	24.1059
ee[eeeeeuuuuuuuuuuuueeeee6	chr17:46873609-46873829(-)$1	220	119	145	22.2135
gggggggxxxxxxxxxxxxxxxgggg	chr9:118572938-118573158(+)$1	220	71	97	20.3887
c[eeeeewwwwwwwwwwwwwweeeee	chr12:4678208-4678428(+)$1	220	147	173	22.9901
=======vvvvvvvvvvvvv======	chr1:34249021-34249242(+)$1	221	159	185	24.8870
gggggggvvvvvvvvvvvvvgggggg	chr9:78053716-78053936(+)$1	220	191	217	24.6457
!ffffffwwwwwwwwwwwwwwfffff	chr17:35981287-35981508(+)$1	221	154	180	23.3245
fffddddwwwwwwwwwwwwwwdddd2	chr7:125322178-125322398(-)$1	220	183	209	22.3573
cc[dddduuuuuuuuuuuudddd]cc	chr8:82197426-82197646(+)$1	220	9	35	22.8641
ggeeeeeyyyyyyyyyyyyyyyyeee	chr10:57940005-57940225(+)$1	220	79	105	22.0061
hhhhhhhyyyyyyyyyyyyyyyyhhh	chr12:16964158-16964378(+)$1	220	101	127	21.0945
gggggggxxxxxxxxxxxxxxxgggg	chr16:20372116-20372336(-)$1	220	151	177	20.3887
eeeee[bbuuuuuuuuuuuubb]eee	chr11:95614112-95614333(+)$1	221	79	105	22.5018
hhh!!bbwwwwwwwwwwwwwwbb22h	chr3:89232252-89232472(+)$1	220	69	95	22.4459
ggggg[ccctttttttttttccc]gg	chr5:76005406-76005641(+)$1	235	135	161	22.7172
ccc!!bbuuuuuuuuuuuubb22ccc	chrX:156266310-156266530(+)$1	220	89	115	22.9175
$a!!cccuuuuuuuuuuuuccc22a3	chr4:3529207-3529432(+)$1	225	22	48	23.6805
ffffffwwwwwwwwwwwwwwffffff	chr3:30938223-30938462(+)$1	239	20	46	22.7014
[bb[cccvvvvvvvvvvvvvccc22b	chr14:56206260-56206480(-)$1	220	79	105	23.5629
dddd[bbuuuuuuuuuuuubb]dddd	chrX:45631590-45631810(+)$1	220	23	49	21.8845
iiiiiiivvvvvvvvvvvvviiiiii	chr1:166192141-166192361(+)$1	220	57	83	24.6019
[ccc[axxxxxxxxxxxxxxxaccc]	chr19:45017879-45018100(+)$1	221	69	95	19.8398
ggeeeeeyyyyyyyyyyyyyyyyeee	chr15:81466524-81466745(+)$1	221	103	129	22.0061
cc"""cccuuuuuuuuuuuuccc22c	chr1:136512695-136512915(+)$1	220	55	81	23.7259
dddd[ccctttttttttttccc]ddd	chr7:142890091-142890313(-)$1	222	156	182	21.4732
iiiiiiiyyyyyyyyyyyyyyyyiii	chr7:105014549-105014769(+)$1	220	75	101	23.0154
[a[cccwwwwwwwwwwwwwwccc]a]	chr9:44628028-44628253(-)$1	225	15	41	23.8466
ffff!!ccctttttttttttcccfff	chr10:127520849-127521069(+)$1	220	91	117	21.8197
!!ffffffuuuuuuuuuuuuffffff	chr17:35400348-35400582(+)$1	234	189	215	23.0716
ggg[cccwwwwwwwwwwwwwwcccgg	chr7:48905019-48905239(+)$1	220	9	35	24.3598
+ccccccvvvvvvvvvvvvvccc333	chr5:135632222-135632442(+)$1	220	131	157	23.9174
ggggggguuuuuuuuuuuuggggggg	chr3:33938354-33938574(+)$1	220	114	140	24.1059
[fffffftttttttttttffffff]c	chr2:158256206-158256426(+)$1	220	153	179	21.1368
[dddd!!auuuuuuuuuuuua22ddd	chr15:80714598-80714821(+)$1	223	68	94	22.8194
gggggggvvvvvvvvvvvvvgggggg	chr11:45761608-45761829(-)$1	221	153	179	24.6457
!dddd[bbuuuuuuuuuuuubb]ddd	chr6:113069426-113069646(+)$1	220	117	143	22.1849
gggggggwwwwwwwwwwwwwwggggg	chr15:9081192-9081418(+)$1	226	2	28	24.3668
:eeeeewwwwwwwwwwwwwweeeee:	chr4:40209854-40210074(-)$1	220	104	130	20.5642
bb!!cccwwwwwwwwwwwwwwccc22	chr8:87495164-87495385(+)$1	221	100	126	23.3503
iiiiiiiiitttttttttttiiiiii	chr15:35381794-35382040(+)$1	246	1	27	21.5657
ccc[bbyyyyyyyyyyyyyyyybb]c	chr5:65665148-65665415(-)$1	267	123	149	21.5794
ggggggguuuuuuuuuuuuggggggg	chr13:14279237-14279460(+)$1	223	99	125	24.1059
cc[dddduuuuuuuuuuuuddddccc	chr9:122834147-122834367(+)$1	220	36	62	22.7550

#otherMatches

#Seq PSSM
ACGUAAGUUCUACGCUUUCUCCUUAC	chr6:73220861-73221104(+)$1	243	40	66	22.9425
GGAAACUGUGGGGGUUUGUGGGUGAA	chr11:117002667-117002927(+)$1	260	222	248	24.3530
ACAGCCUGGAGUUUUUAACAAGGCUG	chr5:3891496-3891716(-)$1	220	71	97	24.6457
UACUUUAGAUUUUUUCCACCUUAGAG	chr13:12499725-12499945(+)$1	220	184	210	23.9282
CACUCCAAGCAAACUUGAAUUAUGGA	chr4:86420209-86420429(+)$1	220	157	183	20.0237
GCAGGACAUUUCCCCAUUGGUCCUGA	chr1:9715236-9715456(-)$1	220	123	149	21.0594
UAAAUCUCAAAAUCUCUUGGAGAUUU	chr5:138602596-138602816(+)$1	220	143	169	22.5147
GUCAGAAUAUCUUAUCUAUUUCCAAA	chr12:13490463-13490700(+)$1	237	121	147	24.1241
CCUGAACCUGAAAGGGCCAAAGGUGA	chr19:9088885-9089115(+)$1	230	88	114	20.5210
GCGGCAGUAAUUAUGUGGUUGUUGGC	chr10:87610940-87611160(+)$1	220	143	169	20.9924
CUCAGCGGAUCACCAAAUACCCUGUG	chr3:88439478-88439698(+)$1	220	105	131	21.9454
AGUUUGUCUUUUUUUUUUUUUAAACU	chr12:111723951-111724171(+)$1	220	33	59	22.7014
AAAAGAGGAAAAAAAAGACUUUGAAG	chr12:72164054-72164275(+)$1	221	103	129	20.4228
GCCAGAUUUCUUACUUACAGUAUGUG	chr9:7833738-7833970(-)$1	232	26	52	23.5821
AAUUAGUACAAAAACAUUUAGCUGGU	chr11:30709808-30710028(+)$1	220	40	66	24.8870
CAGGCUGGCUGAAAGUGACACAGCCU	chr8:109177706-109177926(+)$1	220	57	83	23.4253
AUUUUAGCAAAUAUAGAAAACUACUA	chr1:58054915-58055135(+)$1	220	165	191	23.0154
GGUAAGGAUUCUCUACCUCUUUCUUA	chr5:110665351-110665582(+)$1	231	146	172	24.3623
UUUGCAGACAUAUAAUCAGAGUCAGU	chr12:66200220-66200440(+)$1	220	7	33	21.1181
AAGGGGAUUGAUUAUAGUUUUCCCUC	chr1:120226005-120226225(+)$1	220	106	132	22.4576
GUUGGcaaaucucacccacugccucu	chr13:13599918-13600138(+)$1	220	179	205	22.9903
GCAUGGCAAUAAUACCACAGCACAGC	chr5:3822067-3822287(+)$1	220	75	101	21.0292
CGGCCCUGAGGCAGGAGGAUGGGGCC	chr17:29834886-29835106(+)$1	220	154	180	23.5618
CUGGCCACAUUCGCCACCAAGAACAG	chr17:68159598-68159818(+)$1	220	149	175	22.9169
CCUCUUGGAAGUAGAUAUAUAAGGGG	chr5:104490633-104490853(+)$1	220	45	71	24.1059
CCAACGCCGAGGAGGAGGAGGGUGUG	chr17:46873609-46873829(-)$1	220	119	145	22.2135
GAAGAUCAGGGACCUUAAUAAAGAUC	chr9:118572938-118573158(+)$1	220	71	97	20.3887
CAGACUCAUAAAAAAGAUGAAGAGUC	chr12:4678208-4678428(+)$1	220	147	173	22.9901
GUCACGCCUACCUCAUCAAAGUGUGG	chr1:34249021-34249242(+)$1	221	159	185	24.8870
GUUCAAAAAGAUAAACAAAGUUugga	chr9:78053716-78053936(+)$1	220	191	217	24.6457
UGGCUCCUUGGGGUAUAGUGUGGAGC	chr17:35981287-35981508(+)$1	221	154	180	23.3245
GAUGUACAGAAACCCCUAAAAGUAUA	chr7:125322178-125322398(-)$1	220	183	209	22.3573
AGAUUCUAAACAGAGAAAGAGAACCU	chr8:82197426-82197646(+)$1	220	9	35	22.8641
AAGAGGCCCAGAACAUUUUAAAAGCC	chr10:57940005-57940225(+)$1	220	79	105	22.0061
UCUUUAGAUCUAUUAAUACUCGCCUA	chr12:16964158-16964378(+)$1	220	101	127	21.0945
CAUUUUUGACAGGUUUAUCAGGAAAA	chr16:20372116-20372336(-)$1	220	151	177	20.3887
GUUUCCUGUAACAAAUCCUUCAAGAA	chr11:95614112-95614333(+)$1	221	79	105	22.5018
GGGCAGCGAACUGUGCCUACAGCAAC	chr3:89232252-89232472(+)$1	220	69	95	22.4459
GCAUUCUGACAAAUUCACCCUCAAAG	chr5:76005406-76005641(+)$1	235	135	161	22.7172
CCAGCCCAAGAAAGUUAAAGGAGUGG	chrX:156266310-156266530(+)$1	220	89	115	22.9175
UGUUUUCUUUUUCACGCUUGAAUUCU	chr4:3529207-3529432(+)$1	225	22	48	23.6805
AUGGUUAUUAUUCAUAGCAAGGCCAU	chr3:30938223-30938462(+)$1	239	20	46	22.7014
CUGAGCUUUAUCAUAUCAUCAGCAGC	chr14:56206260-56206480(-)$1	220	79	105	23.5629
AGUUCCUAAAAGAGAAGAGAGAAGCU	chrX:45631590-45631810(+)$1	220	23	49	21.8845
UUGGCUAUAUAAAGCUAUCUUGGUCA	chr1:166192141-166192361(+)$1	220	57	83	24.6019
AGAGCGGAACUUACACAAAUACCUUA	chr19:45017879-45018100(+)$1	221	69	95	19.8398
UUUCCAAGAGAAAAAAUGACACGUUG	chr15:81466524-81466745(+)$1	221	103	129	22.0061
CCCUUGUCUUUGUAGGUAUCGAUCUG	chr1:136512695-136512915(+)$1	220	55	81	23.7259
GGAUGUGACAGAAGAAAUUUCAGGUC	chr7:142890091-142890313(-)$1	222	156	182	21.4732
AGAACAGAAGAAAAACCCACAGGCUG	chr7:105014549-105014769(+)$1	220	75	101	23.0154
GAGUGACCAUCACAGAAAAAUCAGUA	chr9:44628028-44628253(-)$1	225	15	41	23.8466
CUGCUAGCCAGAGACUAUGCGGCGCA	chr10:127520849-127521069(+)$1	220	91	117	21.8197
GUGGUUCCGAGUGAGCCUGAGGAACC	chr17:35400348-35400582(+)$1	234	189	215	23.0716
cuuauguauguaaacacuguagcaaa	chr7:48905019-48905239(+)$1	220	9	35	24.3598
AAGCGCCCAUCAUCAACAUCGGCAUU	chr5:135632222-135632442(+)$1	220	131	157	23.9174
CGAAGACUCCCUCACAGUUGUUUUUG	chr3:33938354-33938574(+)$1	220	114	140	24.1059
AAUUUACAUUUAAACUUAGUGAAUGA	chr2:158256206-158256426(+)$1	220	153	179	21.1368
AGAGUGACGGACCAGUCACAGGAGCU	chr15:80714598-80714821(+)$1	223	68	94	22.8194
AGAACUGACCUCACGCUCUGCAGUUC	chr11:45761608-45761829(-)$1	221	153	179	24.6457
AGUUGGAGAAGAGACAAAAACUGCAG	chr6:113069426-113069646(+)$1	220	117	143	22.1849
GAAGUUAUUAUUUAGAUAAAUUGACU	chr15:9081192-9081418(+)$1	226	2	28	24.3668
UACUUAGAUCGUUGCCUACAUAAGUU	chr4:40209854-40210074(-)$1	220	104	130	20.5642
CAGAAUUACGGCGUGUUGAAAAAUGA	chr8:87495164-87495385(+)$1	221	100	126	23.3503
AAGAAGAUUAACUUAUUUAAAAUCUU	chr15:35381794-35382040(+)$1	246	1	27	21.5657
CUAGGUUUUACACAAUCUCAGUAUGU	chr5:65665148-65665415(-)$1	267	123	149	21.5794
UGAUUUUGAAGAGGAAGAUGAAAUCA	chr13:14279237-14279460(+)$1	223	99	125	24.1059
GGUAUCCCUCAGCUAUCAAGGAUCCU	chr9:122834147-122834367(+)$1	220	36	62	22.7550

#DB
))(((((..............)))))	chr6:73220861-73221104(+)$1	1	40	66	22.9425
(...(((.............)))...	chr11:117002667-117002927(+)$1	1	222	248	24.3530
(((((((.............))))))	chr5:3891496-3891716(-)$1	1	71	97	24.6457
((((((((............))))))	chr13:12499725-12499945(+)$1	1	184	210	23.9282
.((((((...............))).	chr4:86420209-86420429(+)$1	1	157	183	20.0237
.((((((............)))))).	chr1:9715236-9715456(-)$1	1	123	149	21.0594
.(((((((...........)))))))	chr5:138602596-138602816(+)$1	1	143	169	22.5147
((..(((............)))...)	chr12:13490463-13490700(+)$1	1	121	147	24.1241
(((..((((...........))))..	chr19:9088885-9089115(+)$1	1	88	114	20.5210
.((((((...........)))))).)	chr10:87610940-87611160(+)$1	1	143	169	20.9924
(.(((.((...........))))).)	chr3:88439478-88439698(+)$1	1	105	131	21.9454
((((((..............))))))	chr12:111723951-111724171(+)$1	1	33	59	22.7014
...((((...........))))....	chr12:72164054-72164275(+)$1	1	103	129	20.4228
((((.((..............)).))	chr9:7833738-7833970(-)$1	1	26	52	23.5821
(((((((.............))))))	chr11:30709808-30710028(+)$1	1	40	66	24.8870
)((((((.............))))))	chr8:109177706-109177926(+)$1	1	57	83	23.4253
(((((((................)))	chr1:58054915-58055135(+)$1	1	165	191	23.0154
((((((((............))))))	chr5:110665351-110665582(+)$1	1	146	172	24.3623
(..((.(((...........))).))	chr12:66200220-66200440(+)$1	1	7	33	21.1181
))(((((.............))))).	chr1:120226005-120226225(+)$1	1	106	132	22.4576
(..((((............))))...	chr13:13599918-13600138(+)$1	1	179	205	22.9903
((.((((............)).))))	chr5:3822067-3822287(+)$1	1	75	101	21.0292
.((((((.............))))))	chr17:29834886-29835106(+)$1	1	154	180	23.5618
(((..(..............)..)))	chr17:68159598-68159818(+)$1	1	149	175	22.9169
(((((((............)))))))	chr5:104490633-104490853(+)$1	1	45	71	24.1059
((.(((((............))))).	chr17:46873609-46873829(-)$1	1	119	145	22.2135
(((((((...............))))	chr9:118572938-118573158(+)$1	1	71	97	20.3887
(.(((((..............)))))	chr12:4678208-4678428(+)$1	1	147	173	22.9901
(((((((.............))))))	chr1:34249021-34249242(+)$1	1	159	185	24.8870
(((((((.............))))))	chr9:78053716-78053936(+)$1	1	191	217	24.6457
.((((((..............)))))	chr17:35981287-35981508(+)$1	1	154	180	23.3245
(((((((..............)))).	chr7:125322178-125322398(-)$1	1	183	209	22.3573
((.((((............)))).))	chr8:82197426-82197646(+)$1	1	9	35	22.8641
))(((((................)))	chr10:57940005-57940225(+)$1	1	79	105	22.0061
(((((((................)))	chr12:16964158-16964378(+)$1	1	101	127	21.0945
(((((((...............))))	chr16:20372116-20372336(-)$1	1	151	177	20.3887
(((((.((............)).)))	chr11:95614112-95614333(+)$1	1	79	105	22.5018
(((..((..............))..)	chr3:89232252-89232472(+)$1	1	69	95	22.4459
(((((.(((...........))).))	chr5:76005406-76005641(+)$1	1	135	161	22.7172
(((..((............))..)))	chrX:156266310-156266530(+)$1	1	89	115	22.9175
.(..(((............)))..).	chr4:3529207-3529432(+)$1	1	22	48	23.6805
((((((..............))))))	chr3:30938223-30938462(+)$1	1	20	46	22.7014
.((.(((.............)))..)	chr14:56206260-56206480(-)$1	1	79	105	23.5629
((((.((............)).))))	chrX:45631590-45631810(+)$1	1	23	49	21.8845
(((((((.............))))))	chr1:166192141-166192361(+)$1	1	57	83	24.6019
.(((.(...............)))).	chr19:45017879-45018100(+)$1	1	69	95	19.8398
(((((((................)))	chr15:81466524-81466745(+)$1	1	103	129	22.0061
((...(((............)))..)	chr1:136512695-136512915(+)$1	1	55	81	23.7259
((((.(((...........))).)))	chr7:142890091-142890313(-)$1	1	156	182	21.4732
(((((((................)))	chr7:105014549-105014769(+)$1	1	75	101	23.0154
.(.(((..............))).).	chr9:44628028-44628253(-)$1	1	15	41	23.8466
((((..(((...........))))))	chr10:127520849-127521069(+)$1	1	91	117	21.8197
..((((((............))))))	chr17:35400348-35400582(+)$1	1	189	215	23.0716
(((.(((..............)))))	chr7:48905019-48905239(+)$1	1	9	35	24.3598
.((((((.............)))...	chr5:135632222-135632442(+)$1	1	131	157	23.9174
(((((((............)))))))	chr3:33938354-33938574(+)$1	1	114	140	24.1059
.((((((...........)))))).)	chr2:158256206-158256426(+)$1	1	153	179	21.1368
.((((..(............)..)))	chr15:80714598-80714821(+)$1	1	68	94	22.8194
(((((((.............))))))	chr11:45761608-45761829(-)$1	1	153	179	24.6457
.((((.((............)).)))	chr6:113069426-113069646(+)$1	1	117	143	22.1849
(((((((..............)))))	chr15:9081192-9081418(+)$1	1	2	28	24.3668
.(((((..............))))).	chr4:40209854-40210074(-)$1	1	104	130	20.5642
((..(((..............)))..	chr8:87495164-87495385(+)$1	1	100	126	23.3503
(((((((((...........))))))	chr15:35381794-35382040(+)$1	1	1	27	21.5657
(((.((................)).)	chr5:65665148-65665415(-)$1	1	123	149	21.5794
(((((((............)))))))	chr13:14279237-14279460(+)$1	1	99	125	24.1059
((.((((............)))))))	chr9:122834147-122834367(+)$1	1	36	62	22.7550

#PSSM
g : 0.22	c : 0.13	[ : 0.11	f : 0.08	i : 0.07	e : 0.05	! : 0.05	d : 0.04	= : 0.04	: : 0.02	b : 0.02	h : 0.02	a : 0.01	" : 0.01	$ : 0.01	+ : 0.01	
g : 0.23	f : 0.16	c : 0.14	i : 0.07	e : 0.05	d : 0.05	= : 0.04	! : 0.04	b : 0.04	" : 0.02	[ : 0.02	h : 0.02	a : 0.02	
g : 0.19	f : 0.17	e : 0.10	c : 0.10	i : 0.07	! : 0.07	[ : 0.07	d : 0.05	" : 0.04	= : 0.04	h : 0.02	b : 0.01	
g : 0.17	f : 0.14	d : 0.13	e : 0.11	! : 0.10	i : 0.07	c : 0.07	= : 0.04	[ : 0.04	" : 0.02	b : 0.02	h : 0.01	
g : 0.16	c : 0.14	f : 0.13	e : 0.11	d : 0.10	i : 0.07	! : 0.07	[ : 0.05	= : 0.04	b : 0.04	h : 0.01	" : 0.01	
c : 0.16	g : 0.14	f : 0.13	e : 0.10	d : 0.08	b : 0.08	i : 0.07	[ : 0.07	= : 0.04	a : 0.02	! : 0.02	h : 0.01	
c : 0.19	g : 0.14	b : 0.11	f : 0.10	e : 0.08	d : 0.08	i : 0.07	w : 0.07	= : 0.04	h : 0.01	x : 0.01	! : 0.01	y : 0.01	
w : 0.20	v : 0.17	u : 0.17	y : 0.08	c : 0.07	x : 0.05	t : 0.04	b : 0.04	i : 0.02	g : 0.01	d : 0.01	= : 0.01	e : 0.01	f : 0.01	a : 0.01	
u : 0.29	w : 0.20	v : 0.17	t : 0.08	y : 0.08	x : 0.05	c : 0.04	d : 0.01	i : 0.01	
u : 0.29	w : 0.20	v : 0.17	t : 0.16	y : 0.08	x : 0.05	
u : 0.29	w : 0.20	v : 0.17	t : 0.16	y : 0.08	x : 0.05	
u : 0.29	w : 0.20	v : 0.17	t : 0.16	y : 0.08	x : 0.05	
u : 0.29	w : 0.20	v : 0.17	t : 0.16	y : 0.08	x : 0.05	
u : 0.29	w : 0.20	v : 0.17	t : 0.16	y : 0.08	x : 0.05	
u : 0.29	w : 0.20	v : 0.17	t : 0.16	y : 0.08	x : 0.05	
u : 0.29	w : 0.20	v : 0.17	t : 0.16	y : 0.08	x : 0.05	
u : 0.29	w : 0.20	v : 0.17	t : 0.16	y : 0.08	x : 0.05	
u : 0.29	w : 0.20	v : 0.17	t : 0.16	y : 0.08	x : 0.05	
u : 0.29	w : 0.20	v : 0.17	t : 0.11	y : 0.08	x : 0.05	f : 0.02	d : 0.01	
w : 0.20	v : 0.17	u : 0.11	y : 0.08	t : 0.07	x : 0.05	g : 0.05	b : 0.05	d : 0.05	f : 0.04	c : 0.04	
c : 0.16	w : 0.13	f : 0.11	g : 0.10	b : 0.08	y : 0.08	d : 0.07	x : 0.05	i : 0.04	= : 0.04	e : 0.04	a : 0.02	
c : 0.20	f : 0.13	g : 0.11	d : 0.08	y : 0.08	e : 0.07	b : 0.05	i : 0.04	x : 0.04	= : 0.04	2 : 0.04	] : 0.02	a : 0.01	
c : 0.19	g : 0.14	f : 0.13	d : 0.08	e : 0.07	y : 0.07	b : 0.05	2 : 0.05	i : 0.04	= : 0.04	] : 0.04	3 : 0.01	4 : 0.01	
f : 0.16	g : 0.14	e : 0.11	c : 0.10	d : 0.08	i : 0.07	] : 0.07	3 : 0.05	2 : 0.05	= : 0.04	b : 0.02	4 : 0.01	h : 0.01	
g : 0.19	f : 0.13	e : 0.11	i : 0.07	c : 0.07	2 : 0.07	d : 0.07	3 : 0.05	] : 0.05	= : 0.04	b : 0.02	a : 0.02	4 : 0.01	h : 0.01	
g : 0.19	f : 0.11	e : 0.08	c : 0.08	i : 0.07	3 : 0.05	d : 0.05	] : 0.04	: : 0.04	2 : 0.04	h : 0.04	= : 0.04	b : 0.04	a : 0.01	4 : 0.01	6 : 0.01	

#score	1522.0582382643831
#seq	67
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_UTR_m1_run1.txt

#BEAR
ddd!!eeeee!!ccc[aooooooa]ccc]eeeee22dddd	chrX:71479452-71479758(-)$1	306	73	113	15.4097
dddd"""ccc!!eeeeeooooooeeeee22ccc4444ddd	chr4:46507859-46508132(+)$1	273	177	217	15.3982
cccggggggg"""cccpppppppccc4444ggggggg22c	chr14:31996750-31997037(-)$1	287	132	172	13.7787
=========[eeeeeqqqqqqqqeeeee4444========	chr14:55260886-55261169(-)$1	283	105	145	12.1702
d[eeeee[bb"""cccooooooccc4444bb]eeeeeddd	chr1:121492135-121492426(-)$1	291	204	244	15.4738
::ccc[dddd"""ddddoooooodddd333dddd22cccd	chr4:138451253-138451535(-)$1	282	43	83	14.8269
ddddeeeee!!bb[cccooooooccc]bb22eeeeedddd	chr4:90918715-90919001(-)$1	286	140	180	14.0548
[eeeee[bb"""cccrrrrrrrrrccc22bb]eeeeeeee	chr11:94152352-94152620(-)$1	268	101	141	13.2670
cddddaccc####cccqqqqqqqqccc333ccc]a]dddd	chr4:118809523-118809875(+)$1	352	211	251	13.2284
e!!ggggggg"""ddddoooooodddd]gggggggeeeee	chr10:114822585-114822885(+)$1	300	24	64	16.6430
"ggggggg####ccc!!cccooooooccc22ccc4444gg	chr6:67235146-67235414(+)$1	268	86	126	14.0308
$$ggggggg####cccooooooccc55555ggggggg22b	chr14:24966258-24966567(-)$1	309	32	72	14.0040
b[cccccc[ccc[ddddoooooodddd]ccc]ccc22ccc	chr6:149283757-149284031(+)$1	274	59	99	14.8062
b[ggggggg"""ccc[aooooooaccc333ggggggg333	chr4:55540467-55540742(-)$1	275	66	106	20.2218
e"""ffffff[ffffffooooooffffff]ffffff]eee	chr17:28536484-28536771(-)$1	287	14	54	13.1900
diiiiiiiii!!cccrrrrrrrrrccc22iiiiiiiiiEE	chr11:97579879-97580153(-)$1	274	109	149	13.4875
ccc!!dddd[bb[bb[aooooooabb]bb]ddddccc]ff	chr3:95432949-95433235(+)$1	286	36	76	13.2071
!!ggggggg[cccfffffflllffffff333ccc]ggggg	chrX:98877594-98877862(+)$1	268	131	171	12.6770
ff!!ffffff[bb[cccooooooccc22bb]fffffffff	chr4:131888235-131888504(-)$1	269	75	115	13.6065
=====dddd!!gggggggooooooggggggg22dddd22=	chr6:71342053-71342327(-)$1	274	80	120	13.7250
bb"""eeeee!!ddddoooooodddd22eeeee333bb]g	chr5:92502103-92502411(-)$1	308	26	66	14.0106
e"""ggggggg[a[cccpppppppccc]a]ggggggg444	chr15:59370481-59370815(+)$1	334	110	150	12.3657
===####ccc!!cccooooooccc]ccc22==========	chr12:70297936-70298204(-)$1	268	43	83	16.3623
c"""eeeee[eeeee[arrrrrrrrraeeeeeeeeee333	chr18:35965641-35965909(+)$1	268	27	67	11.3252
:===============ddddllldddd]============	chr3:65185218-65185502(-)$1	284	85	125	13.0127
"ccc!!cccbb[eeeeeooooooeeeee]bb22ccc22cc	chr3:31018524-31018818(+)$1	294	216	256	13.9133
::===========[cccooooooccc]===========BB	chr1:157694957-157695226(-)$1	269	11	51	14.8029
hhhh"""ccc####cccooooooccc333ccc22hhhhhh	chr8:109709417-109709696(+)$1	279	165	205	16.0957
ccc"""ccc"""ccc"""bbmmmmbb333ccc22cccccc	chr13:23842876-23843153(+)$1	277	106	146	12.1598
b:iiiiiiiii!!ddddoooooodddd22iiiiiiiii::	chr18:9995301-9995580(-)$1	279	133	173	14.5097
!!iiiiiiiiiffffffooooooffffff4444iiiiiii	chr4:56891798-56892106(-)$1	308	113	153	15.8907
##dddd!!bb"""cccoooooocccbb22dddd22cccee	chr15:94409494-94409779(-)$1	285	217	257	14.8884
dddda[ggggggg####bboooooobb333ggggggg]ad	chr3:154242599-154242872(-)$1	273	125	165	13.3422
eee[bb[==========oooooo==========333bb]e	chr6:11957466-11957743(+)$1	277	139	179	15.8328
""ccc[ccc"""fffffflllffffff4444ccc]ccc33	chr7:16912530-16912821(-)$1	291	167	207	13.8856
gggggggggg[ccc!!ammmma22ccc4444ggggggg]g	chr1:93308281-93308567(-)$1	286	102	142	13.3630
c[iiiiiiiii[ddddoooooodddd>>>>>>>>>>>>ii	chr11:95135925-95136195(-)$1	270	84	124	14.0215
cc!!eeeeeaeeeee[aooooooa]eeeee]a>>>>>>>>	chr17:37185909-37186253(+)$1	344	286	326	12.8719
bb[dddd####ccc[bboooooobb]ccc4444dddd]bb	chr5:130759520-130759796(+)$1	276	158	198	13.9894
ccc!!eeeeeccc[cccooooooccc333ccc]eeeee22	chr2:33306977-33307251(-)$1	274	86	126	16.2469
gggg####a"""bb[ddddoooooodddd]bb333a333g	chr5:90658110-90658393(-)$1	283	153	193	13.9954
c####ccc!!bb"""cccooooooccc333bb]ccc22cc	chr6:13532341-13532629(-)$1	288	56	96	16.1599
"a[dddd####ddddcccooooooccc]dddd4444dddd	chr3:87719628-87719922(+)$1	294	190	230	14.1932
=======[bb!!ccc!!ccclllccc]ccc]bb]======	chr4:106728415-106728689(-)$1	274	25	65	13.4119
eeeeffffff[a[a!!aooooooa22a]a]ffffff]eee	chrX:160388826-160389119(-)$1	293	175	215	13.9984
eeeedddd"""ccc[bboooooobb]ccc333dddd4444	chr1:182828624-182828902(+)$1	278	132	172	14.8460
iii####bb"""eeeeeooooooeeeee22bb333iiiii	chr13:12278942-12279257(-)$1	315	14	54	16.5774
!dddddddda"""ddddoooooodddd333a]dddd]ddd	chr4:56883680-56883951(-)$1	271	52	92	16.3150
d[eeeee!!gggggggooooooggggggg333eeeeeddd	chr8:112252507-112252786(-)$1	279	188	228	14.0593
##ggggggg[bb!!cccooooooccc22bb]ggggggg55	chr19:56396294-56396563(-)$1	269	19	59	14.8725
!!eeeeeccc!!ccc[bblllbb]ccc4444ccc]eeeee	chr3:151899508-151899783(+)$1	275	227	267	13.2038
ggggg[ccc"""ddddpppppppdddd333ccc22ggggg	chr9:111181010-111181280(+)$1	270	147	187	13.2872
ccffffff$$$$$ddddoooooodddd4444ffffff]cc	chr17:26418510-26418849(+)$1	339	235	275	15.4627
:===========!!cccooooooccc]===========::	chr2:172295194-172295485(+)$1	291	167	207	15.9403
!ccc[dddd"""cccssssssssssccc]ddddccc]ccc	chr16:4544895-4545201(-)$1	306	77	117	11.8075
ff[bb[ccc"""ddddooooooddddccc]bb]ffffff4	chr18:42315880-42316153(+)$1	273	173	213	14.2683
==========ffffffnnnnnffffff333==========	chr17:45722405-45722684(-)$1	279	129	169	12.9764
========ccceeeeeooooooeeeee4444ccc22====	chr17:35970982-35971283(-)$1	301	156	196	16.0090

#otherMatches

#Seq PSSM
GGGAGUUGGGAGUGGGUACAAAGAGCCAACCUAAGGUUCU	chrX:71479452-71479758(-)$1	306	73	113	15.4097
UUGAGUUCAGUUCAGGGCAGCUUCCCUGUUCUGUUAAUUA	chr4:46507859-46508132(+)$1	273	177	217	15.3982
UGGGGACAGGGCAGUCGGUCCAGGACGAAGCCUGUUCUAC	chr14:31996750-31997037(-)$1	287	132	172	13.7787
uauuuuuuuuauuauuaaauGAUGUGGUCUAUGGAAAAAU	chr14:55260886-55261169(-)$1	283	105	145	12.1702
CAUAGCACUGUGUCCUCGGGAAGGGUUUUCAAUGUUAGCA	chr1:121492135-121492426(-)$1	291	204	244	15.4738
UCACCUCCUAGAACUCAAAACACUGAGCCAUAGGCUGGUC	chr4:138451253-138451535(-)$1	282	43	83	14.8269
AUCUGUUCUUCCUAAAGAAAUCCCUUCAGAUAGAGCUCAU	chr4:90918715-90919001(-)$1	286	140	180	14.0548
ACACUUGUGCUCUCCUUAGCCUUUGGAUUUAGAAGUGAAA	chr11:94152352-94152620(-)$1	268	101	141	13.2670
CGGAGGCUGAGAACUUAACUGCUGAAGACACGGACACUCC	chr4:118809523-118809875(+)$1	352	211	251	13.2284
GCCGUCGGGGUCCCUGUCGGAAAGCAGCCCCCGGCCGUCC	chr10:114822585-114822885(+)$1	300	24	64	16.6430
GUUUUCUAGGAUAUUUUUAUUCACAUAUAUUGAUUAAAUA	chr6:67235146-67235414(+)$1	268	86	126	14.0308
AGUCUCAGACCAGGCACCGUUCUGCAACCUUCUGAGAACC	chr14:24966258-24966567(-)$1	309	32	72	14.0040
gugagucuggugaagucagcuuaggcuacaugggagccuc	chr6:149283757-149284031(+)$1	274	59	99	14.8062
ACUUACAAAAUGCCAAGGGGUGACUGGAAGUUUGUGGAUA	chr4:55540467-55540742(-)$1	275	66	106	20.2218
UCAAGAUGUGUGGCUGUAGUAAGACAGUCUCAUGUCAGGC	chr17:28536484-28536771(-)$1	287	14	54	13.1900
UGCAGCCUGUGACCUGAAGGAAGAAGGGGACGGGCUGUUU	chr11:97579879-97580153(-)$1	274	109	149	13.4875
AGAAAGGUAGAGUGAAGGAGAUGCUCUCUGUGCUUCUAAG	chr3:95432949-95433235(+)$1	286	36	76	13.2071
AGGGAACUAGAUAACAUGCUUUGUGUGUAUCUGUGUAGUU	chrX:98877594-98877862(+)$1	268	131	171	12.6770
GCUUAAGACUACGUGCAACAUCCUGCCCCGGGGUUUUGCU	chr4:131888235-131888504(-)$1	269	75	115	13.6065
GUGUUAUGCAUGUGUAUAGAAGUGUGUGCACCAGCAUCAA	chr6:71342053-71342327(-)$1	274	80	120	13.7250
GUUAUAUAUCUAAGAAGAUUUAUUUUGUGGUAUUUUGCAA	chr5:92502103-92502411(-)$1	308	26	66	14.0106
UGGUAGGUUAGUAGCAAUUGUGGUUUGGUUCUGAUUUUUA	chr15:59370481-59370815(+)$1	334	110	150	12.3657
AGGAGACCGGAACUGACGACGUAGCCCGCACUUCCGCGGG	chr12:70297936-70298204(-)$1	268	43	83	16.3623
UUCAUUUCAUCCUGAAGGACCUACAACUUAGGUGAAAGUU	chr18:35965641-35965909(+)$1	268	27	67	11.3252
AUUUGUAAUUUAUAAUAACUCAAAGUUAAUUGUAAAUUAC	chr3:65185218-65185502(-)$1	284	85	125	13.0127
CCUCUUGCCUCUGCCCACAGUACUGGGUCGACAGGCCUGA	chr3:31018524-31018818(+)$1	294	216	256	13.9133
UUUAAAAUAGGCAAACGCAAGAUUGUCUGCCUAUUUUACA	chr1:157694957-157695226(-)$1	269	11	51	14.8029
GAGUGCAGGACAGGAGCGUCCCAGCUAACUCCAAACUUGA	chr8:109709417-109709696(+)$1	279	165	205	16.0957
CUGAUACUUAAACGCAUACAUGUCUGGACGCGGAAAGCAG	chr13:23842876-23843153(+)$1	277	106	146	12.1598
GGAAAAAGAGGGAUUAACAACUUUUGACAUUUCUUUUUAG	chr18:9995301-9995580(-)$1	279	133	173	14.5097
agcuguuguuccagcuguuguuccagcuguCCUGGGCAGC	chr4:56891798-56892106(-)$1	308	113	153	15.8907
AGGGCUGACGCCAGACGUUCAUGUUCGAAAGCCAAGGAUC	chr15:94409494-94409779(-)$1	285	217	257	14.8884
AUGCGAGUUGGAGCCAUGGGAACAACCUCACUCCAACCCU	chr3:154242599-154242872(-)$1	273	125	165	13.3422
AGAUGGCCUAGAUAGAGUUUAUUUUUUGUUUGGUUUCCUU	chr6:11957466-11957743(+)$1	277	139	179	15.8328
cuguaaauuucagggccaaguuggucuacauaauguacca	chr7:16912530-16912821(-)$1	291	167	207	13.8856
AGCACUAUUUUUUCGUGGACCCUAGAGCUCUGGAUGGUGG	chr1:93308281-93308567(-)$1	286	102	142	13.3630
UACGGUUUGCUUCGCUCUCAACAGUGCCUCCCUCCCCCAG	chr11:95135925-95136195(-)$1	270	84	124	14.0215
UGCUUGCCUCUUUGCUGUCUUUUCUGCAAACGUCUCCCUU	chr17:37185909-37186253(+)$1	344	286	326	12.8719
AUCGACCUCAUGUCUUGAAAUGCCAUGGCUCAUGGUCCAU	chr5:130759520-130759796(+)$1	276	158	198	13.9894
CCCAUUGAAGUCUAUUCAUAUAAGAGCUGAGACCUUUGCA	chr2:33306977-33307251(-)$1	274	86	126	16.2469
UUUUUAUGCUCCCAAAUCAUUCUACUGAUGUGCUUGACUG	chr5:90658110-90658393(-)$1	283	153	193	13.9954
CUGAAUGUAAAUGUGUAAGAGAUGUUAAAAGUAACAGUGC	chr6:13532341-13532629(-)$1	288	56	96	16.1599
AGAGUUGGUCUCUGGUGUUUUCUCACAUCCAGUUUGUAGC	chr3:87719628-87719922(+)$1	294	190	230	14.1932
UUUUUAGCUCUGUACUUGCAUGGUGUUGUGUGAACUAAGA	chr4:106728415-106728689(-)$1	274	25	65	13.4119
UCUGUUUUGUGAGUGAGGUAUAGCAGAGUGGUAAAAGUAG	chrX:160388826-160389119(-)$1	293	175	215	13.9984
GAGAGUGUUUCCUGGAUAAGCAAGUAUAGAAUACAUAAAA	chr1:182828624-182828902(+)$1	278	132	172	14.8460
CUGUUUUUCCUUUAAACUUUUAUGUUUGCUGACCUCAGGG	chr13:12278942-12279257(-)$1	315	14	54	16.5774
AUUAUAGCACUUAUUACUGAGUUGUAAAAUGUUGCUCAUG	chr4:56883680-56883951(-)$1	271	52	92	16.3150
AGCUAGACUGACCCUGUAAACUUAGGGUUCCAUUUGGUCU	chr8:112252507-112252786(-)$1	279	188	228	14.0593
UUUGCUUCUCUGAUUCGCAGUUCCGGUACAAAGAGGCAUU	chr19:56396294-56396563(-)$1	269	19	59	14.8725
AUUUUGUAUUCUUUAUGGUUUCCUUAAUUAAAAUAAUAAA	chr3:151899508-151899783(+)$1	275	227	267	13.2038
UUGGAAGAUAACACUACUGGUCCUAGUUACAUCACUCUAA	chr9:111181010-111181280(+)$1	270	147	187	13.2872
GUUCGGCACCGCCUAAAUUACCCUUUAUAUUUGCUGAUAC	chr17:26418510-26418849(+)$1	339	235	275	15.4627
CAUGACCUUUGUACUUAGAAAAUUGAAAUAAAGGUUGUAG	chr2:172295194-172295485(+)$1	291	167	207	15.9403
CUGUCGGGUUAUCUUUUUCUCUUUUAAGCACUUACAUGGG	chr16:4544895-4545201(-)$1	306	77	117	11.8075
cccugacuguccuagaacucacucuguagacgaggcuggu	chr18:42315880-42316153(+)$1	273	173	213	14.2683
GCAGGGGUCGAGAGGGGCUGUUCUUCUAGCUGACUUCUGC	chr17:45722405-45722684(-)$1	279	129	169	12.9764
UGGGGGUGCGGCAAGGUCUUGGUCUUGGUCUCUGAACACU	chr17:35970982-35971283(-)$1	301	156	196	16.0090

#DB
(((..(((((..(((.(......).))).)))))..))))	chrX:71479452-71479758(-)$1	1	73	113	15.4097
((((...(((..(((((......)))))..)))....)))	chr4:46507859-46508132(+)$1	1	177	217	15.3982
((((((((((...(((.......)))....)))))))..)	chr14:31996750-31997037(-)$1	1	132	172	13.7787
(((((((((.(((((........)))))....))))))))	chr14:55260886-55261169(-)$1	1	105	145	12.1702
(.(((((.((...(((......)))....)).))))))))	chr1:121492135-121492426(-)$1	1	204	244	15.4738
..(((.((((...((((......))))...))))..)))(	chr4:138451253-138451535(-)$1	1	43	83	14.8269
))))(((((..((.(((......))).))..)))))((((	chr4:90918715-90919001(-)$1	1	140	180	14.0548
.(((((.((...(((.........)))..)).))))))))	chr11:94152352-94152620(-)$1	1	101	141	13.2670
)((((((((....(((........)))...))).).))))	chr4:118809523-118809875(+)$1	1	211	251	13.2284
(..(((((((...((((......)))).))))))))))))	chr10:114822585-114822885(+)$1	1	24	64	16.6430
.(((((((....(((..(((......)))..)))....))	chr6:67235146-67235414(+)$1	1	86	126	14.0308
..(((((((....(((......))).....)))))))..)	chr14:24966258-24966567(-)$1	1	32	72	14.0040
(.((((((.(((.((((......)))).))).)))..)))	chr6:149283757-149284031(+)$1	1	59	99	14.8062
(.(((((((...(((.(......))))...)))))))...	chr4:55540467-55540742(-)$1	1	66	106	20.2218
(...((((((.((((((......)))))).)))))).)))	chr17:28536484-28536771(-)$1	1	14	54	13.1900
)(((((((((..(((.........)))..)))))))))))	chr11:97579879-97580153(-)$1	1	109	149	13.4875
(((..((((.((.((.(......))).)).))))))).))	chr3:95432949-95433235(+)$1	1	36	76	13.2071
..(((((((.(((((((((...))))))...))).)))))	chrX:98877594-98877862(+)$1	1	131	171	12.6770
((..((((((.((.(((......)))..)).)))))))))	chr4:131888235-131888504(-)$1	1	75	115	13.6065
(((((((((..(((((((......)))))))..))))..)	chr6:71342053-71342327(-)$1	1	80	120	13.7250
((...(((((..((((......))))..)))))...)).)	chr5:92502103-92502411(-)$1	1	26	66	14.0106
(...(((((((.(.(((.......))).).)))))))...	chr15:59370481-59370815(+)$1	1	110	150	12.3657
(((....(((..(((......))).)))..))))))))))	chr12:70297936-70298204(-)$1	1	43	83	16.3623
(...(((((.(((((.(.........)))))))))))...	chr18:35965641-35965909(+)$1	1	27	67	11.3252
.(((((((((((((((((((...)))).))))))))))))	chr3:65185218-65185502(-)$1	1	85	125	13.0127
.(((..(((((.(((((......))))).))..)))..))	chr3:31018524-31018818(+)$1	1	216	256	13.9133
..(((((((((((.(((......))).)))))))))))((	chr1:157694957-157695226(-)$1	1	11	51	14.8029
((((...(((....(((......)))...)))..))))))	chr8:109709417-109709696(+)$1	1	165	205	16.0957
(((...(((...(((...((....))...)))..))))))	chr13:23842876-23843153(+)$1	1	106	146	12.1598
).(((((((((..((((......))))..)))))))))..	chr18:9995301-9995580(-)$1	1	133	173	14.5097
..(((((((((((((((......))))))....)))))))	chr4:56891798-56892106(-)$1	1	113	153	15.8907
..((((..((...(((......)))))..))))..)))))	chr15:94409494-94409779(-)$1	1	217	257	14.8884
))))(.(((((((....((......))...))))))).)(	chr3:154242599-154242872(-)$1	1	125	165	13.3422
(((.((.((((((((((......))))))))))...)).)	chr6:11957466-11957743(+)$1	1	139	179	15.8328
..(((.(((...((((((...))))))....))).)))..	chr7:16912530-16912821(-)$1	1	167	207	13.8856
((((((((((.(((..(....)..)))....))))))).)	chr1:93308281-93308567(-)$1	1	102	142	13.3630
(.(((((((((.((((......))))............))	chr11:95135925-95136195(-)$1	1	84	124	14.0215
((..(((((((((((.(......).))))).)........	chr17:37185909-37186253(+)$1	1	286	326	12.8719
((.((((....(((.((......)).)))....)))).))	chr5:130759520-130759796(+)$1	1	158	198	13.9894
(((..((((((((.(((......)))...))).)))))..	chr2:33306977-33307251(-)$1	1	86	126	16.2469
((((....(...((.((((......)))).))...)...)	chr5:90658110-90658393(-)$1	1	153	193	13.9954
(....(((..((...(((......)))...)).)))..))	chr6:13532341-13532629(-)$1	1	56	96	16.1599
.(.((((....(((((((......))).))))....))))	chr3:87719628-87719922(+)$1	1	190	230	14.1932
(((((((.((..(((..(((...))).))).)).))))))	chr4:106728415-106728689(-)$1	1	25	65	13.4119
((((((((((.(.(..(......)..).).)))))).)))	chrX:160388826-160389119(-)$1	1	175	215	13.9984
((((((((...(((.((......)).)))...))))....	chr1:182828624-182828902(+)$1	1	132	172	14.8460
(((....((...(((((......)))))..))...)))))	chr13:12278942-12279257(-)$1	1	14	54	16.5774
.(((((((((...((((......))))...).)))).)))	chr4:56883680-56883951(-)$1	1	52	92	16.3150
(.(((((..(((((((......)))))))...))))))))	chr8:112252507-112252786(-)$1	1	188	228	14.0593
..(((((((.((..(((......)))..)).)))))))..	chr19:56396294-56396563(-)$1	1	19	59	14.8725
..((((((((..(((.((...)).)))....))).)))))	chr3:151899508-151899783(+)$1	1	227	267	13.2038
(((((.(((...((((.......))))...)))..)))))	chr9:111181010-111181280(+)$1	1	147	187	13.2872
((((((((.....((((......))))....)))))).))	chr17:26418510-26418849(+)$1	1	235	275	15.4627
.(((((((((((..(((......))).)))))))))))..	chr2:172295194-172295485(+)$1	1	167	207	15.9403
.(((.((((...(((..........))).))))))).)))	chr16:4544895-4545201(-)$1	1	77	117	11.8075
((.((.(((...((((......))))))).)).)))))).	chr18:42315880-42316153(+)$1	1	173	213	14.2683
((((((((((((((((.....))))))...))))))))))	chr17:45722405-45722684(-)$1	1	129	169	12.9764
((((((((((((((((......)))))....)))..))))	chr17:35970982-35971283(-)$1	1	156	196	16.0090

#PSSM
c : 0.17	d : 0.12	= : 0.10	e : 0.10	b : 0.08	! : 0.08	: : 0.06	" : 0.06	g : 0.05	f : 0.03	# : 0.03	[ : 0.01	$ : 0.01	h : 0.01	i : 0.01	
c : 0.13	= : 0.13	d : 0.10	[ : 0.08	e : 0.06	! : 0.06	g : 0.06	" : 0.06	: : 0.05	# : 0.05	i : 0.03	f : 0.03	b : 0.03	$ : 0.01	h : 0.01	a : 0.01	
c : 0.15	= : 0.15	g : 0.13	d : 0.12	e : 0.12	i : 0.08	" : 0.06	! : 0.05	[ : 0.05	h : 0.01	# : 0.01	f : 0.01	
g : 0.17	d : 0.13	= : 0.13	e : 0.10	! : 0.08	c : 0.08	" : 0.08	i : 0.06	# : 0.05	h : 0.01	[ : 0.01	f : 0.01	b : 0.01	
g : 0.17	= : 0.13	e : 0.12	d : 0.10	! : 0.06	" : 0.06	f : 0.06	i : 0.06	# : 0.06	c : 0.05	b : 0.03	a : 0.01	[ : 0.01	
e : 0.17	g : 0.15	d : 0.13	= : 0.12	[ : 0.08	f : 0.06	i : 0.06	" : 0.05	# : 0.05	c : 0.03	a : 0.01	! : 0.01	b : 0.01	
g : 0.17	e : 0.15	d : 0.13	c : 0.13	= : 0.12	f : 0.06	i : 0.06	# : 0.05	" : 0.03	[ : 0.03	! : 0.01	
c : 0.20	g : 0.17	= : 0.12	e : 0.10	d : 0.10	f : 0.06	i : 0.06	# : 0.05	[ : 0.03	b : 0.03	! : 0.03	
c : 0.18	g : 0.15	e : 0.10	= : 0.10	b : 0.08	d : 0.08	i : 0.06	# : 0.05	f : 0.05	! : 0.03	[ : 0.01	a : 0.01	" : 0.01	$ : 0.01	
" : 0.17	c : 0.10	g : 0.10	[ : 0.08	# : 0.08	= : 0.08	b : 0.06	i : 0.06	e : 0.05	! : 0.05	f : 0.05	a : 0.03	d : 0.01	$ : 0.01	
" : 0.27	! : 0.15	# : 0.10	c : 0.06	[ : 0.06	b : 0.06	= : 0.06	e : 0.05	g : 0.05	i : 0.05	$ : 0.01	f : 0.01	
" : 0.25	! : 0.13	c : 0.10	b : 0.08	e : 0.06	# : 0.06	= : 0.06	f : 0.05	g : 0.05	[ : 0.05	d : 0.01	a : 0.01	$ : 0.01	
c : 0.25	e : 0.12	" : 0.12	d : 0.08	f : 0.06	b : 0.05	# : 0.05	[ : 0.05	g : 0.05	= : 0.05	! : 0.05	a : 0.01	$ : 0.01	
c : 0.31	d : 0.18	e : 0.12	[ : 0.08	f : 0.08	b : 0.03	g : 0.03	= : 0.03	# : 0.03	! : 0.03	" : 0.01	a : 0.01	
c : 0.39	d : 0.18	e : 0.12	f : 0.08	[ : 0.05	g : 0.03	= : 0.03	! : 0.03	b : 0.01	# : 0.01	" : 0.01	
c : 0.25	d : 0.18	[ : 0.10	f : 0.08	e : 0.06	! : 0.06	r : 0.03	g : 0.03	= : 0.03	b : 0.03	q : 0.01	o : 0.01	" : 0.01	# : 0.01	s : 0.01	
c : 0.17	o : 0.15	d : 0.13	a : 0.12	f : 0.06	e : 0.05	b : 0.05	p : 0.03	q : 0.03	r : 0.03	! : 0.03	g : 0.01	" : 0.01	# : 0.01	= : 0.01	s : 0.01	n : 0.01	
o : 0.60	c : 0.06	p : 0.05	r : 0.05	q : 0.03	f : 0.03	d : 0.03	b : 0.03	g : 0.01	" : 0.01	m : 0.01	s : 0.01	n : 0.01	
o : 0.65	p : 0.05	r : 0.05	q : 0.03	c : 0.03	d : 0.03	b : 0.03	l : 0.03	f : 0.01	m : 0.01	s : 0.01	n : 0.01	
o : 0.68	p : 0.05	r : 0.05	l : 0.05	q : 0.03	c : 0.03	d : 0.01	b : 0.01	m : 0.01	s : 0.01	n : 0.01	
o : 0.70	l : 0.08	p : 0.05	r : 0.05	q : 0.03	m : 0.03	s : 0.01	n : 0.01	
o : 0.68	p : 0.05	r : 0.05	l : 0.05	q : 0.03	f : 0.03	c : 0.01	m : 0.01	a : 0.01	b : 0.01	s : 0.01	
o : 0.55	c : 0.06	p : 0.05	r : 0.05	f : 0.05	d : 0.05	q : 0.03	l : 0.03	m : 0.01	2 : 0.01	g : 0.01	b : 0.01	s : 0.01	e : 0.01	
c : 0.22	d : 0.18	o : 0.10	a : 0.08	e : 0.08	f : 0.08	r : 0.05	b : 0.03	q : 0.01	p : 0.01	m : 0.01	= : 0.01	2 : 0.01	g : 0.01	] : 0.01	s : 0.01	
c : 0.36	d : 0.18	e : 0.08	f : 0.08	b : 0.06	] : 0.05	o : 0.05	g : 0.03	r : 0.01	= : 0.01	2 : 0.01	s : 0.01	
c : 0.36	d : 0.20	e : 0.10	f : 0.08	b : 0.06	g : 0.03	] : 0.03	4 : 0.01	o : 0.01	5 : 0.01	r : 0.01	= : 0.01	2 : 0.01	
c : 0.27	d : 0.15	e : 0.10	] : 0.08	f : 0.08	2 : 0.05	3 : 0.05	4 : 0.03	g : 0.03	a : 0.03	b : 0.03	5 : 0.01	= : 0.01	> : 0.01	
3 : 0.18	c : 0.13	4 : 0.12	2 : 0.12	e : 0.10	] : 0.10	f : 0.05	= : 0.05	b : 0.03	g : 0.03	5 : 0.01	> : 0.01	d : 0.01	
3 : 0.20	4 : 0.13	2 : 0.12	c : 0.10	b : 0.06	= : 0.06	] : 0.05	g : 0.05	e : 0.05	f : 0.03	a : 0.03	d : 0.03	5 : 0.01	> : 0.01	
3 : 0.18	4 : 0.15	] : 0.10	2 : 0.08	b : 0.08	c : 0.08	e : 0.06	= : 0.06	d : 0.05	g : 0.03	i : 0.03	5 : 0.01	> : 0.01	
4 : 0.13	c : 0.12	g : 0.12	b : 0.12	= : 0.10	d : 0.08	] : 0.06	e : 0.05	3 : 0.05	2 : 0.03	f : 0.03	i : 0.03	> : 0.01	a : 0.01	
c : 0.18	g : 0.13	= : 0.10	d : 0.08	b : 0.08	e : 0.06	] : 0.06	f : 0.06	4 : 0.05	i : 0.03	2 : 0.03	3 : 0.03	> : 0.01	a : 0.01	
c : 0.15	g : 0.13	e : 0.12	= : 0.12	d : 0.10	f : 0.06	2 : 0.06	4 : 0.05	] : 0.05	i : 0.03	> : 0.03	3 : 0.03	b : 0.01	
c : 0.15	g : 0.13	e : 0.12	= : 0.10	d : 0.10	f : 0.08	3 : 0.06	2 : 0.06	i : 0.05	4 : 0.03	] : 0.03	> : 0.03	
g : 0.13	= : 0.12	e : 0.10	c : 0.10	2 : 0.08	f : 0.08	d : 0.06	3 : 0.06	4 : 0.05	i : 0.05	] : 0.05	> : 0.03	a : 0.01	h : 0.01	
g : 0.15	e : 0.13	= : 0.12	c : 0.12	f : 0.08	2 : 0.06	i : 0.06	d : 0.06	4 : 0.05	3 : 0.03	> : 0.03	] : 0.01	h : 0.01	a : 0.01	
g : 0.15	= : 0.13	e : 0.12	d : 0.10	c : 0.08	] : 0.06	i : 0.06	4 : 0.05	2 : 0.05	f : 0.05	b : 0.03	> : 0.03	h : 0.01	3 : 0.01	
d : 0.13	= : 0.13	c : 0.10	e : 0.10	2 : 0.08	i : 0.06	] : 0.06	g : 0.06	4 : 0.05	3 : 0.05	f : 0.03	b : 0.03	> : 0.03	h : 0.01	
d : 0.13	c : 0.12	= : 0.10	e : 0.10	2 : 0.06	3 : 0.06	g : 0.05	f : 0.05	] : 0.05	i : 0.05	4 : 0.03	: : 0.03	E : 0.01	B : 0.01	h : 0.01	a : 0.01	> : 0.01	b : 0.01	5 : 0.01	
d : 0.17	c : 0.12	= : 0.12	e : 0.12	g : 0.10	3 : 0.05	4 : 0.05	i : 0.05	b : 0.03	f : 0.03	: : 0.03	E : 0.01	B : 0.01	h : 0.01	> : 0.01	2 : 0.01	5 : 0.01	

#score	831.4842149109776
#seq	58
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_UTR_m3_run1.txt

#BEAR
fffffqqqqqqqqfffff	chr19:44378317-44378581(+)$1	264	207	225	12.4524
ee!!aqqqqqqqqa22ee	chr4:101315261-101315505(+)$1	244	190	208	13.0206
cc[bbqqqqqqqqbb]cc	chr17:29294824-29295061(-)$1	237	8	26	12.9702
[ddddqqqqqqqqddddc	chr17:88390678-88390933(-)$1	255	184	202	14.5139
dddddqqqqqqqqdddd:	chr12:101788826-101789076(-)$1	250	184	202	13.5305
eeeeeqqqqqqqqeeeee	chr11:42445183-42445421(+)$1	238	34	52	13.7470
eeeeeqqqqqqqqeeeee	chr4:137798140-137798391(+)$1	251	209	227	13.7470
eeeeeqqqqqqqqeeeee	chr12:11332579-11332822(-)$1	243	74	92	13.7470
d[cccqqqqqqqqcccdd	chrX:71273426-71273666(-)$1	240	70	88	13.8478
b[cccqqqqqqqqccc]b	chr4:81936504-81936742(-)$1	238	35	53	13.5103
:ddddqqqqqqqqdddd:	chr16:38245366-38245610(+)$1	244	8	26	12.8317
fffffqqqqqqqqfffff	chr1:183096476-183096714(+)$1	238	7	25	12.4524
eeeeeqqqqqqqqeeeee	chr9:75070815-75071053(+)$1	238	43	61	13.7470
hh[bbqqqqqqqqbb]hh	chr14:63761672-63761934(+)$1	262	75	93	12.2772
!ddddqqqqqqqqdddd4	chr2:73655880-73656141(-)$1	261	81	99	14.6540
""cccqqqqqqqqccc33	chr11:74488082-74488319(-)$1	237	170	188	14.2149
!ddddqqqqqqqqdddd3	chr12:71347000-71347238(-)$1	238	104	122	14.7499
[acccqqqqqqqqccc22	chr1:63639947-63640182(+)$1	235	26	44	13.8435
:ddddqqqqqqqqdddd:	chr15:36701296-36701535(-)$1	239	95	113	12.8317
###bbqqqqqqqqbb444	chr19:58871435-58871670(-)$1	235	143	161	13.0752
eeeeeqqqqqqqqeeeee	chr6:115224826-115225115(+)$1	289	59	77	13.7470
!ddddqqqqqqqqdddde	chr16:84954707-84954943(-)$1	236	129	147	14.5924
"""bbqqqqqqqqbb444	chr9:21820361-21820611(-)$1	250	103	121	13.1899
cc[bbqqqqqqqqbb]cc	chr4:6322045-6322294(+)$1	249	88	106	12.9702
[ddddqqqqqqqqdddd]	chr1:123202257-123202496(-)$1	239	180	198	14.7223
:ddddqqqqqqqqdddd:	chr17:85413769-85414025(+)$1	256	89	107	12.8317
h[cccqqqqqqqqccchh	chr2:30882241-30882476(-)$1	235	151	169	13.3133
:ddddqqqqqqqqdddd:	chr14:120829697-120829948(+)$1	251	167	185	12.8317
ddd[aqqqqqqqqa]ddd	chr13:8802337-8802585(-)$1	248	189	207	13.5734
:ddddqqqqqqqqdddd:	chr15:90059937-90060172(+)$1	235	21	39	12.8317
"""bbqqqqqqqqbb]hh	chr11:115883769-115884019(-)$1	250	148	166	12.8048
:ddddqqqqqqqqdddd:	chrX:71549857-71550109(+)$1	252	32	50	12.8317
gggbbqqqqqqqqbb]gg	chr17:9177335-9177581(+)$1	246	15	33	13.0250
=====qqqqqqqq=====	chr8:98238309-98238570(+)$1	261	34	52	13.7675
##cccqqqqqqqqccc22	chr11:106641661-106641916(-)$1	255	68	86	13.8374
"ddddqqqqqqqqdddd]	chr10:107935762-107936048(-)$1	286	146	164	14.7123
dd[bbqqqqqqqqbb]dd	chrX:133370696-133370935(+)$1	239	90	108	13.1018
eeeeeqqqqqqqqeeeee	chr13:57527483-57527738(-)$1	255	118	136	13.7470
fddddqqqqqqqqdddd8	chr4:122869796-122870058(+)$1	262	60	78	13.9158
ddd[aqqqqqqqqa]ddd	chr2:83646413-83646674(+)$1	261	25	43	13.5734
fffbbqqqqqqqqbb]ff	chr10:70718207-70718465(-)$1	258	174	192	12.4983
iiiiiqqqqqqqqiiiii	chr11:118163220-118163468(-)$1	248	39	57	13.5067
!!cccqqqqqqqqccc22	chr5:131913931-131914168(-)$1	237	34	52	14.0331
ee[bbqqqqqqqqbbeee	chr7:107789216-107789457(+)$1	241	97	115	13.2366
:ddddqqqqqqqqdddd:	chr9:79618401-79618644(-)$1	243	155	173	12.8317
eeeeeqqqqqqqqeeeee	chr11:31932899-31933135(+)$1	236	94	112	13.7470
=====qqqqqqqq=====	chr2:104269214-104269453(-)$1	239	153	171	13.7675
[ddddqqqqqqqqdddd]	chr9:107850725-107850974(+)$1	249	138	156	14.7223
bbcccqqqqqqqqccc]b	chr11:29999474-29999718(-)$1	244	184	202	13.0963
!!cccqqqqqqqqccc22	chr3:115953965-115954210(-)$1	245	201	219	14.0331
:ddddqqqqqqqqddddh	chr1:125229828-125230079(-)$1	251	106	124	13.3449
fffffqqqqqqqqfffff	chr6:113696891-113697177(-)$1	286	168	186	12.4524
e[cccqqqqqqqqccc]e	chr2:102628870-102629117(+)$1	247	60	78	13.9677
dddddqqqqqqqqdddd]	chr14:52524965-52525214(-)$1	249	109	127	14.4410
iiiiiqqqqqqqqiiiii	chr4:101314850-101315101(+)$1	251	120	138	13.5067
[ddddqqqqqqqqdddd]	chr18:24052159-24052395(+)$1	236	18	36	14.7223
iiiiiqqqqqqqqiiiii	chr13:34994550-34994812(+)$1	262	118	136	13.5067
eeeeeqqqqqqqqeeeee	chr9:103085374-103085609(+)$1	235	148	166	13.7470
eeeeeqqqqqqqqeeeee	chr4:122871777-122872029(+)$1	252	17	35	13.7470
"ddddqqqqqqqqdddde	chr2:134420525-134420770(-)$1	245	111	129	14.5513
f[a[aqqqqqqqqaa]ff	chr10:59764859-59765116(+)$1	257	210	228	13.1502
d[cccqqqqqqqqcccdd	chr2:60590243-60590486(-)$1	243	162	180	13.8478
[ddddqqqqqqqqdddd]	chr11:87794732-87794987(-)$1	255	215	233	14.7223
fffffqqqqqqqqfffff	chr11:41946818-41947090(-)$1	272	150	168	12.4524
eeeeeqqqqqqqqeeeee	chrX:92246474-92246715(-)$1	241	36	54	13.7470
""cccqqqqqqqqccc22	chr3:116334598-116334833(-)$1	235	122	140	13.9094
eeeeeqqqqqqqqeeeee	chr9:123371097-123371334(+)$1	237	70	88	13.7470
dddddqqqqqqqqdddd:	chr15:31385917-31386158(-)$1	241	172	190	13.5305
##cccqqqqqqqqccc22	chr4:90918261-90918497(-)$1	236	96	114	13.8374
fffffqqqqqqqqfffff	chr16:17044950-17045193(+)$1	243	205	223	12.4524
#ddddqqqqqqqqdddd3	chr18:46664348-46664588(-)$1	240	216	234	14.6787
gggggqqqqqqqqggggg	chr1:52222280-52222532(-)$1	252	89	107	13.3565
eeeeeqqqqqqqqeeeee	chr2:163879181-163879427(-)$1	246	209	227	13.7470

#otherMatches

#Seq PSSM
uugcaucuuaaauugcag	chr19:44378317-44378581(+)$1	264	207	225	12.4524
cagagagaugacgcagug	chr4:101315261-101315505(+)$1	244	190	208	13.0206
GGCCACCGUCCUUUGUCC	chr17:29294824-29295061(-)$1	237	8	26	12.9702
UCCAGCAAUGUUUCUGGU	chr17:88390678-88390933(-)$1	255	184	202	14.5139
AGGUACUGUAUUUUACCA	chr12:101788826-101789076(-)$1	250	184	202	13.5305
UUCAGAAGCUGCCCUGAG	chr11:42445183-42445421(+)$1	238	34	52	13.7470
UGGUGUUGCUUAUUACCA	chr4:137798140-137798391(+)$1	251	209	227	13.7470
UUGAUUAUAUAAUAUUAG	chr12:11332579-11332822(-)$1	243	74	92	13.7470
CUGGUCCUCUUUAACUGU	chrX:71273426-71273666(-)$1	240	70	88	13.8478
UGCUUCUGUCACUGAGAA	chr4:81936504-81936742(-)$1	238	35	53	13.5103
CUGAAUUUUUUUUUUCAU	chr16:38245366-38245610(+)$1	244	8	26	12.8317
AUUUUUACCACAUAAAGU	chr1:183096476-183096714(+)$1	238	7	25	12.4524
AAAGGUGAUUUCUCCUUU	chr9:75070815-75071053(+)$1	238	43	61	13.7470
UUUGUGUACCUCAACCAA	chr14:63761672-63761934(+)$1	262	75	93	12.2772
ugguugccagaaaagcCU	chr2:73655880-73656141(-)$1	261	81	99	14.6540
UUGUUUGuuuuuuaauuu	chr11:74488082-74488319(-)$1	237	170	188	14.2149
UGUUGUUUUUCUUUAAUU	chr12:71347000-71347238(-)$1	238	104	122	14.7499
GAGCUGGAACUUGAGCAA	chr1:63639947-63640182(+)$1	235	26	44	13.8435
CUACAGCUUUUCAUGUAA	chr15:36701296-36701535(-)$1	239	95	113	12.8317
UUUUGGUUAAUAACGCUG	chr19:58871435-58871670(-)$1	235	143	161	13.0752
AGUUCCACCCAGUGAACU	chr6:115224826-115225115(+)$1	289	59	77	13.7470
CUGGUCUCCAAUUACCAA	chr16:84954707-84954943(-)$1	236	129	147	14.5924
UUAACUUAUUGCUGUGUU	chr9:21820361-21820611(-)$1	250	103	121	13.1899
AUUGCCUUUGAUAGUUAU	chr4:6322045-6322294(+)$1	249	88	106	12.9702
UUACCAACCUUUCGGUAU	chr1:123202257-123202496(-)$1	239	180	198	14.7223
UUACACAUCACAAUGUAU	chr17:85413769-85414025(+)$1	256	89	107	12.8317
ACGUGACAUUUACCGCUU	chr2:30882241-30882476(-)$1	235	151	169	13.3133
UAUCUUACAUCAUAGAUC	chr14:120829697-120829948(+)$1	251	167	185	12.8317
AAAGguuuuauuuuguuu	chr13:8802337-8802585(-)$1	248	189	207	13.5734
UCAGUUCUGUGCUACUGU	chr15:90059937-90060172(+)$1	235	21	39	12.8317
UUCGGUUUCGUUUCUUUU	chr11:115883769-115884019(-)$1	250	148	166	12.8048
AUCACGAGGAUUGGUGAA	chrX:71549857-71550109(+)$1	252	32	50	12.8317
AGGCAGUUUGAUGUGACC	chr17:9177335-9177581(+)$1	246	15	33	13.0250
GUUCUGAGGCAAGAGGAC	chr8:98238309-98238570(+)$1	261	34	52	13.7675
UUACAUAUUUUACUGUUC	chr11:106641661-106641916(-)$1	255	68	86	13.8374
CUGUGCACUAGUCCACAU	chr10:107935762-107936048(-)$1	286	146	164	14.7123
AGUGAUUAAUCUCUCUCU	chrX:133370696-133370935(+)$1	239	90	108	13.1018
CUAUUGUAGGUGAAAUAG	chr13:57527483-57527738(-)$1	255	118	136	13.7470
GGCGGAGAUUGCCCUGCA	chr4:122869796-122870058(+)$1	262	60	78	13.9158
GGUCCUUUUAUUUGAACC	chr2:83646413-83646674(+)$1	261	25	43	13.5734
AAAGCAACCAGACGCUUU	chr10:70718207-70718465(-)$1	258	174	192	12.4983
UUUUAAGACAGACUGGGA	chr11:118163220-118163468(-)$1	248	39	57	13.5067
GUUGGAUACAUUGCCACA	chr5:131913931-131914168(-)$1	237	34	52	14.0331
UUUACUAGUUAUUGUGAG	chr7:107789216-107789457(+)$1	241	97	115	13.2366
AUAGAAAUUAAUAUCUAA	chr9:79618401-79618644(-)$1	243	155	173	12.8317
AGCAUUACUGUUUGUGCU	chr11:31932899-31933135(+)$1	236	94	112	13.7470
UUUUUCCUUAUUAAGAGG	chr2:104269214-104269453(-)$1	239	153	171	13.7675
AGGCCAGAGGCAGGGCCA	chr9:107850725-107850974(+)$1	249	138	156	14.7223
GGCAUCUAUAGUAAUGAC	chr11:29999474-29999718(-)$1	244	184	202	13.0963
UGUAGAUAGUAUCCUAAC	chr3:115953965-115954210(-)$1	245	201	219	14.0331
UCCUAUAAAUGUUUGGGU	chr1:125229828-125230079(-)$1	251	106	124	13.3449
UUACAAUAUAUACUGUAG	chr6:113696891-113697177(-)$1	286	168	186	12.4524
AAAUGAAAGACAACAUAU	chr2:102628870-102629117(+)$1	247	60	78	13.9677
CUAAGGGAAAGAGCUUAG	chr14:52524965-52525214(-)$1	249	109	127	14.4410
GUGUGAACUACAGUAUAU	chr4:101314850-101315101(+)$1	251	120	138	13.5067
AUUAUAAAUAUCGAUAAG	chr18:24052159-24052395(+)$1	236	18	36	14.7223
CAUGGGAAGUGGGCCGUG	chr13:34994550-34994812(+)$1	262	118	136	13.5067
ACUACAAGCAAAAGUAGU	chr9:103085374-103085609(+)$1	235	148	166	13.7470
UCCCAGUUCACUAUGGGA	chr4:122871777-122872029(+)$1	252	17	35	13.7470
UUUUAUUUGUCUUUGGAA	chr2:134420525-134420770(-)$1	245	111	129	14.5513
UGGUCUUUUGUGUGUGAG	chr10:59764859-59765116(+)$1	257	210	228	13.1502
GCAGCAGCCUAGGGCUUU	chr2:60590243-60590486(-)$1	243	162	180	13.8478
CAAACUCCUUUCUGUUUA	chr11:87794732-87794987(-)$1	255	215	233	14.7223
AGAAUUGCUUUCUGUUCU	chr11:41946818-41947090(-)$1	272	150	168	12.4524
CUGCAAAUGUUCCUGUAG	chrX:92246474-92246715(-)$1	241	36	54	13.7470
AAUUGUAGAAAACCAGAA	chr3:116334598-116334833(-)$1	235	122	140	13.9094
auucaccaagcguuggau	chr9:123371097-123371334(+)$1	237	70	88	13.7470
UCCAAUAAUAGCUUUGGC	chr15:31385917-31386158(-)$1	241	172	190	13.5305
UUCGUUUAUAAAUAUGUU	chr4:90918261-90918497(-)$1	236	96	114	13.8374
UAUUCCAUGAAGAGAAUG	chr16:17044950-17045193(+)$1	243	205	223	12.4524
CACUUCUGUCUUCAAGUU	chr18:46664348-46664588(-)$1	240	216	234	14.6787
CUGAUUAGAUUUUAUCAG	chr1:52222280-52222532(-)$1	252	89	107	13.3565
AUGGUAACAACUGACUAU	chr2:163879181-163879427(-)$1	246	209	227	13.7470

#DB
(((((........)))))	chr19:44378317-44378581(+)$1	1	207	225	12.4524
((..(........)..))	chr4:101315261-101315505(+)$1	1	190	208	13.0206
((.((........)).))	chr17:29294824-29295061(-)$1	1	8	26	12.9702
.((((........)))))	chr17:88390678-88390933(-)$1	1	184	202	14.5139
)((((........)))).	chr12:101788826-101789076(-)$1	1	184	202	13.5305
(((((........)))))	chr11:42445183-42445421(+)$1	1	34	52	13.7470
(((((........)))))	chr4:137798140-137798391(+)$1	1	209	227	13.7470
(((((........)))))	chr12:11332579-11332822(-)$1	1	74	92	13.7470
(.(((........)))))	chrX:71273426-71273666(-)$1	1	70	88	13.8478
(.(((........))).)	chr4:81936504-81936742(-)$1	1	35	53	13.5103
.((((........)))).	chr16:38245366-38245610(+)$1	1	8	26	12.8317
(((((........)))))	chr1:183096476-183096714(+)$1	1	7	25	12.4524
(((((........)))))	chr9:75070815-75071053(+)$1	1	43	61	13.7470
((.((........)).))	chr14:63761672-63761934(+)$1	1	75	93	12.2772
.((((........)))).	chr2:73655880-73656141(-)$1	1	81	99	14.6540
..(((........)))..	chr11:74488082-74488319(-)$1	1	170	188	14.2149
.((((........)))).	chr12:71347000-71347238(-)$1	1	104	122	14.7499
.((((........)))..	chr1:63639947-63640182(+)$1	1	26	44	13.8435
.((((........)))).	chr15:36701296-36701535(-)$1	1	95	113	12.8317
...((........))...	chr19:58871435-58871670(-)$1	1	143	161	13.0752
(((((........)))))	chr6:115224826-115225115(+)$1	1	59	77	13.7470
.((((........)))))	chr16:84954707-84954943(-)$1	1	129	147	14.5924
...((........))...	chr9:21820361-21820611(-)$1	1	103	121	13.1899
((.((........)).))	chr4:6322045-6322294(+)$1	1	88	106	12.9702
.((((........)))).	chr1:123202257-123202496(-)$1	1	180	198	14.7223
.((((........)))).	chr17:85413769-85414025(+)$1	1	89	107	12.8317
(.(((........)))))	chr2:30882241-30882476(-)$1	1	151	169	13.3133
.((((........)))).	chr14:120829697-120829948(+)$1	1	167	185	12.8317
(((.(........).)))	chr13:8802337-8802585(-)$1	1	189	207	13.5734
.((((........)))).	chr15:90059937-90060172(+)$1	1	21	39	12.8317
...((........)).))	chr11:115883769-115884019(-)$1	1	148	166	12.8048
.((((........)))).	chrX:71549857-71550109(+)$1	1	32	50	12.8317
(((((........)).))	chr17:9177335-9177581(+)$1	1	15	33	13.0250
(((((........)))))	chr8:98238309-98238570(+)$1	1	34	52	13.7675
..(((........)))..	chr11:106641661-106641916(-)$1	1	68	86	13.8374
.((((........)))).	chr10:107935762-107936048(-)$1	1	146	164	14.7123
((.((........)).))	chrX:133370696-133370935(+)$1	1	90	108	13.1018
(((((........)))))	chr13:57527483-57527738(-)$1	1	118	136	13.7470
(((((........)))).	chr4:122869796-122870058(+)$1	1	60	78	13.9158
(((.(........).)))	chr2:83646413-83646674(+)$1	1	25	43	13.5734
(((((........)).))	chr10:70718207-70718465(-)$1	1	174	192	12.4983
(((((........)))))	chr11:118163220-118163468(-)$1	1	39	57	13.5067
..(((........)))..	chr5:131913931-131914168(-)$1	1	34	52	14.0331
((.((........)))))	chr7:107789216-107789457(+)$1	1	97	115	13.2366
.((((........)))).	chr9:79618401-79618644(-)$1	1	155	173	12.8317
(((((........)))))	chr11:31932899-31933135(+)$1	1	94	112	13.7470
(((((........)))))	chr2:104269214-104269453(-)$1	1	153	171	13.7675
.((((........)))).	chr9:107850725-107850974(+)$1	1	138	156	14.7223
(((((........))).)	chr11:29999474-29999718(-)$1	1	184	202	13.0963
..(((........)))..	chr3:115953965-115954210(-)$1	1	201	219	14.0331
.((((........))))(	chr1:125229828-125230079(-)$1	1	106	124	13.3449
(((((........)))))	chr6:113696891-113697177(-)$1	1	168	186	12.4524
(.(((........))).)	chr2:102628870-102629117(+)$1	1	60	78	13.9677
(((((........)))).	chr14:52524965-52525214(-)$1	1	109	127	14.4410
(((((........)))))	chr4:101314850-101315101(+)$1	1	120	138	13.5067
.((((........)))).	chr18:24052159-24052395(+)$1	1	18	36	14.7223
(((((........)))))	chr13:34994550-34994812(+)$1	1	118	136	13.5067
(((((........)))))	chr9:103085374-103085609(+)$1	1	148	166	13.7470
(((((........)))))	chr4:122871777-122872029(+)$1	1	17	35	13.7470
.((((........)))))	chr2:134420525-134420770(-)$1	1	111	129	14.5513
(.(.(........)).))	chr10:59764859-59765116(+)$1	1	210	228	13.1502
(.(((........)))))	chr2:60590243-60590486(-)$1	1	162	180	13.8478
.((((........)))).	chr11:87794732-87794987(-)$1	1	215	233	14.7223
(((((........)))))	chr11:41946818-41947090(-)$1	1	150	168	12.4524
(((((........)))))	chrX:92246474-92246715(-)$1	1	36	54	13.7470
..(((........)))..	chr3:116334598-116334833(-)$1	1	122	140	13.9094
(((((........)))))	chr9:123371097-123371334(+)$1	1	70	88	13.7470
)((((........)))).	chr15:31385917-31386158(-)$1	1	172	190	13.5305
..(((........)))..	chr4:90918261-90918497(-)$1	1	96	114	13.8374
(((((........)))))	chr16:17044950-17045193(+)$1	1	205	223	12.4524
.((((........)))).	chr18:46664348-46664588(-)$1	1	216	234	14.6787
(((((........)))))	chr1:52222280-52222532(-)$1	1	89	107	13.3565
(((((........)))))	chr2:163879181-163879427(-)$1	1	209	227	13.7470

#PSSM
e : 0.20	f : 0.10	d : 0.10	: : 0.10	[ : 0.08	" : 0.08	! : 0.06	# : 0.05	i : 0.04	c : 0.02	b : 0.02	h : 0.02	g : 0.02	= : 0.02	
d : 0.35	e : 0.19	f : 0.08	[ : 0.08	" : 0.05	# : 0.04	i : 0.04	c : 0.02	g : 0.02	= : 0.02	! : 0.02	h : 0.01	a : 0.01	b : 0.01	
d : 0.34	c : 0.17	e : 0.16	f : 0.08	[ : 0.06	i : 0.04	" : 0.02	g : 0.02	= : 0.02	! : 0.01	# : 0.01	a : 0.01	
d : 0.31	c : 0.17	e : 0.16	b : 0.13	f : 0.06	[ : 0.04	i : 0.04	= : 0.02	! : 0.01	g : 0.01	
d : 0.31	c : 0.17	e : 0.16	b : 0.13	f : 0.06	a : 0.05	i : 0.04	= : 0.02	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	
d : 0.31	c : 0.17	e : 0.16	b : 0.13	f : 0.06	a : 0.05	i : 0.04	= : 0.02	g : 0.01	
d : 0.31	c : 0.17	e : 0.16	b : 0.13	f : 0.06	i : 0.04	] : 0.02	= : 0.02	2 : 0.01	a : 0.01	g : 0.01	
d : 0.34	e : 0.17	c : 0.17	] : 0.10	f : 0.06	i : 0.04	4 : 0.02	= : 0.02	2 : 0.01	g : 0.01	
d : 0.38	e : 0.19	f : 0.09	2 : 0.08	] : 0.04	h : 0.04	i : 0.04	c : 0.02	4 : 0.02	g : 0.02	= : 0.02	3 : 0.01	
e : 0.23	: : 0.12	f : 0.09	2 : 0.08	] : 0.08	d : 0.06	h : 0.05	c : 0.04	4 : 0.04	3 : 0.04	i : 0.04	b : 0.02	g : 0.02	= : 0.02	8 : 0.01	

#score	990.3271788912625
#seq	73
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_UTR_m2_run1.txt

#BEAR
dggggggguuuuuuuuuuuugggggg	chr12:71367074-71367313(-)$1	239	191	217	24.0722
ccc[dddduuuuuuuuuuuudddd33	chr18:34478851-34479088(+)$1	237	63	89	23.2862
a$$$$$ccctttttttttttccc444	chr11:31957933-31958193(+)$1	260	34	60	22.1745
ffffffwwwwwwwwwwwwwwffffff	chr14:66929370-66929632(+)$1	262	197	223	22.8316
ffffff[atttttttttttaffffff	chr5:137509001-137509236(+)$1	235	151	177	23.4164
ffff[ayyyyyyyyyyyyyyyya]ff	chr11:78140021-78140298(+)$1	277	202	228	21.7775
ggggggwwwwwwwwwwwwwwgggggg	chr6:125170615-125170893(+)$1	278	231	257	22.7986
:ccc[awwwwwwwwwwwwwwa]ccc:	chr12:12380094-12380336(+)$1	242	16	42	20.9027
a!!ddddwwwwwwwwwwwwwwdddd2	chr9:75069990-75070247(+)$1	257	206	232	21.9024
iiiiiiccctttttttttttccc]ii	chr14:37934879-37935169(-)$1	290	253	279	23.6700
iiiiiiiwwwwwwwwwwwwwwiiiii	chr10:110733431-110733666(+)$1	235	158	184	22.9081
g[ffffffuuuuuuuuuuuuffffff	chr3:31101926-31102161(-)$1	235	195	221	24.4147
gggeeeeeuuuuuuuuuuuueeeee]	chr5:136384479-136384794(-)$1	315	217	243	23.5449
====[a[attttttttttta]a====	chr11:77524382-77524622(+)$1	240	197	223	23.4062
eeee!!bbvvvvvvvvvvvvvbb22e	chr5:151612526-151612769(+)$1	243	49	75	22.5251
:bb[cccvvvvvvvvvvvvvccc]bb	chr9:79618583-79618902(-)$1	319	177	203	22.5656
hh"""ddddtttttttttttdddd33	chr12:8757528-8757775(+)$1	247	161	187	21.5177
b[ddddccctttttttttttccc]dd	chr12:4110460-4110698(+)$1	238	184	210	22.6683
:ffffffvvvvvvvvvvvvvffffff	chr16:31093849-31094091(-)$1	242	88	114	23.2752
eeee!!bbuuuuuuuuuuuubbeeee	chr9:58499808-58500092(+)$1	284	177	203	23.1915
ffffffccctttttttttttccc]ff	chr6:113696548-113696811(-)$1	263	87	113	23.7987
f[a"""ccctttttttttttccc444	chr5:67679172-67679423(+)$1	251	110	136	23.2896
ffff[cccvvvvvvvvvvvvvcccff	chr9:42772292-42772528(-)$1	236	76	102	24.4975
eggggggguuuuuuuuuuuugggggg	chr4:40680719-40680957(+)$1	238	57	83	24.1596
ddddyyyyyyyyyyyyyyyydddd]e	chr15:79358603-79358847(-)$1	244	151	177	19.6609
eeeeddddyyyyyyyyyyyyyyyydd	chr3:146395078-146395338(-)$1	260	57	83	19.6890
ddd[ddddyyyyyyyyyyyyyyyydd	chr7:67133472-67133731(-)$1	259	169	195	19.4438
%ffffffvvvvvvvvvvvvvffffff	chr17:10406203-10406508(-)$1	305	60	86	23.5185
Effffffvvvvvvvvvvvvvffffff	chr7:118214773-118215008(-)$1	235	206	232	23.1940
eeefffffftttttttttttffffff	chr5:93600345-93600582(+)$1	237	143	169	22.7536
""eeeeewwwwwwwwwwwwwweeeee	chr1:152209721-152209959(-)$1	238	14	40	22.5188
eeeee[ccctttttttttttccc]ee	chr3:116334598-116334833(-)$1	235	188	214	23.4941
g:ffffffuuuuuuuuuuuuffffff	chr7:25763264-25763503(-)$1	239	23	49	23.2790
HHffffffuuuuuuuuuuuuffffff	chr9:72595391-72595637(+)$1	246	41	67	23.0804
ff[eeeeeuuuuuuuuuuuueeeeef	chr5:122905949-122906267(-)$1	318	160	186	23.4877
!ccc[cccuuuuuuuuuuuuccc22c	chrX:69677955-69678230(-)$1	275	26	52	24.5938
ff[ddddvvvvvvvvvvvvvdddd]f	chr18:6788883-6789127(+)$1	244	146	172	22.9310
eeee[cccuuuuuuuuuuuuccc]ee	chr1:58582440-58582708(-)$1	268	74	100	24.9157
eeeeeyyyyyyyyyyyyyyyyeeeee	chr2:180716414-180716656(+)$1	242	169	195	20.8781
###eeeeeuuuuuuuuuuuueeeee2	chr1:52846191-52846426(-)$1	235	130	156	23.1355
!!bb[cccvvvvvvvvvvvvvccc]b	chr18:58105896-58106147(+)$1	251	45	71	23.7795
:ccc[ccctttttttttttccc]ccc	chrX:149046577-149046823(-)$1	246	90	116	22.2803
::ffffffuuuuuuuuuuuuffffff	chr8:48268656-48268894(-)$1	238	70	96	22.4676
+gggggggtttttttttttggggggg	chrX:162824607-162824878(+)$1	271	46	72	21.8538
!ffffffvvvvvvvvvvvvvffffff	chr11:109530403-109530714(+)$1	311	134	160	24.1820
""fffffftttttttttttffffff4	chr12:39358640-39358903(+)$1	263	56	82	22.5499
!!bb[cccwwwwwwwwwwwwwwccc]	chr13:20697656-20697893(+)$1	237	174	200	22.7178
ddeeeeewwwwwwwwwwwwwweeeee	chrX:154259971-154260219(-)$1	248	3	29	22.1908
ddd"""ccctttttttttttccc]dd	chr18:20845873-20846128(-)$1	255	146	172	22.8277
d[ccc[ccctttttttttttccc]cc	chr16:37886917-37887183(+)$1	266	3	29	23.5738
ff!!dddduuuuuuuuuuuuddddff	chr15:36407574-36407829(-)$1	255	223	249	23.3128
ffffffwwwwwwwwwwwwwwffffff	chr17:35971695-35971945(-)$1	250	190	216	22.8316
ccc!!cccxxxxxxxxxxxxxxxccc	chr11:109528789-109529095(+)$1	306	220	246	18.0624
ee"""cccwwwwwwwwwwwwwwccc2	chr2:66110180-66110416(-)$1	236	66	92	22.5229
hhhhhhhhvvvvvvvvvvvvvhhhhh	chr5:122906322-122906560(-)$1	238	182	208	20.9933
""ffffffuuuuuuuuuuuuffffff	chr16:59653243-59653500(-)$1	257	24	50	24.3280
eeeecccvvvvvvvvvvvvvccc]ee	chr6:24563982-24564219(-)$1	237	170	196	24.2588
cc!!cccvvvvvvvvvvvvvccc22c	chr13:54860178-54860450(-)$1	272	10	36	23.9812
hhhhhhhhvvvvvvvvvvvvvhhhhh	chr17:85462769-85463009(-)$1	240	152	178	20.9933

#otherMatches

#Seq PSSM
UCUAUUUGUUCUCCCUCAUUUAAGUA	chr12:71367074-71367313(-)$1	239	191	217	24.0722
AGUAGGUAGAAUUUUUGCUAUGCUGU	chr18:34478851-34479088(+)$1	237	63	89	23.2862
GAUAAAAUGAAUUUAAAAAGCAUGAA	chr11:31957933-31958193(+)$1	260	34	60	22.1745
AAAGUUUUUUCUUUCUUUUUAAUUUU	chr14:66929370-66929632(+)$1	262	197	223	22.8316
CUCUGUUGUAAAUACCCCUCACGGAG	chr5:137509001-137509236(+)$1	235	151	177	23.4164
CUCUGAGUACAUAGCAAAUAAAUGAG	chr11:78140021-78140298(+)$1	277	202	228	21.7775
UGCUUCUCUUCAUGUCACCUGAAGCA	chr6:125170615-125170893(+)$1	278	231	257	22.7986
AGCACGUCCCCCACCCUCUUCCUGCC	chr12:12380094-12380336(+)$1	242	16	42	20.9027
AGAGGUUAGAAUUUAUAAAGCAACCA	chr9:75069990-75070247(+)$1	257	206	232	21.9024
GUCAGUUUGAAUGCCCAGGACAACAC	chr14:37934879-37935169(-)$1	290	253	279	23.6700
UUAUUAAUAAGAUUAACAUAUUUAGU	chr10:110733431-110733666(+)$1	235	158	184	22.9081
AUAUGCACAUGUACUAUAAAGUGUGU	chr3:31101926-31102161(-)$1	235	195	221	24.4147
CAGUGUUAGCUUACUCUUAAUAAUGU	chr5:136384479-136384794(-)$1	315	217	243	23.5449
CGCgugucugugugucugugucugug	chr11:77524382-77524622(+)$1	240	197	223	23.4062
GAGCCUGUAAUUUUACAACCCGCCUG	chr5:151612526-151612769(+)$1	243	49	75	22.5251
UGUGCCUACUGUGUGAUGAAAGGGAU	chr9:79618583-79618902(-)$1	319	177	203	22.5656
UGGAAUCUGUUUUCUCUCUUCGGGAA	chr12:8757528-8757775(+)$1	247	161	187	21.5177
UCUUUGGUGUAAAACUAGACCACACA	chr12:4110460-4110698(+)$1	238	184	210	22.6683
ACAGUGUACCUAACUAAUUGACGCUG	chr16:31093849-31094091(-)$1	242	88	114	23.2752
GGCAAAGCUCUAAACGCACUGCUGCC	chr9:58499808-58500092(+)$1	284	177	203	23.1915
GACAUUUUGAAUACCAUGACCGAUGA	chr6:113696548-113696811(-)$1	263	87	113	23.7987
cucuuucauuugugucGUGUGUGCGC	chr5:67679172-67679423(+)$1	251	110	136	23.2896
GGCGUGCUCUUGUUCCCGUCUGGCUG	chr9:42772292-42772528(-)$1	236	76	102	24.4975
UCCAACGUAACUGCAAUUUAAUGUUG	chr4:40680719-40680957(+)$1	238	57	83	24.1596
CCCCUUCUAUUACUGCCUCCGGGGAU	chr15:79358603-79358847(-)$1	244	151	177	19.6609
CUGACCAGUGCUCCCUUUAUUUUCCU	chr3:146395078-146395338(-)$1	260	57	83	19.6890
UUAUAUCCCUUCCCCGAGUAUUAAGG	chr7:67133472-67133731(-)$1	259	169	195	19.4438
CUACAGUUGAUUUUAAAACUACUGUG	chr17:10406203-10406508(-)$1	305	60	86	23.5185
AGACCACAGAAAUAGACUGGGUGGUC	chr7:118214773-118215008(-)$1	235	206	232	23.1940
UAUCAGUAACUUAGCUCAUUUUACUG	chr5:93600345-93600582(+)$1	237	143	169	22.7536
CCUGAUCAUCCAGAAAUCACGGAUCA	chr1:152209721-152209959(-)$1	238	14	40	22.5188
GGCUGUUCUGAAGAAUGAAAAGAUCA	chr3:116334598-116334833(-)$1	235	188	214	23.4941
GAGGGGCCUUCUCUCCCCAUGGcccc	chr7:25763264-25763503(-)$1	239	23	49	23.2790
UGCGACAUACUUAGUACCACAUGUCG	chr9:72595391-72595637(+)$1	246	41	67	23.0804
GUAUGUUUUGUAAAAUCUGUAAAUAG	chr5:122905949-122906267(-)$1	318	160	186	23.4877
GUCUGUAGGUAAACUUAUGACUAGAA	chrX:69677955-69678230(-)$1	275	26	52	24.5938
GCUUAAUUACUGAAUUACUUGUUAUG	chr18:6788883-6789127(+)$1	244	146	172	22.9310
GCUGGUAGUCUCGAUUCCAUUUAGUA	chr1:58582440-58582708(-)$1	268	74	100	24.9157
UGUCCAGCCCUCAGUUAAAUGGGACA	chr2:180716414-180716656(+)$1	242	169	195	20.8781
GAACCCUUCAAUAAAAUACCAAGGGA	chr1:52846191-52846426(-)$1	235	130	156	23.1355
UAAAGUGAAAAUUCUCAACCAUUAGU	chr18:58105896-58106147(+)$1	251	45	71	23.7795
ACCCUUGUGAUUUAGCCAGACACGGG	chrX:149046577-149046823(-)$1	246	90	116	22.2803
AAAAAAGCAAUGUUUCAAACGCUUUU	chr8:48268656-48268894(-)$1	238	70	96	22.4676
UAACUUGGUCAUUUUAUUCCCAAGUU	chrX:162824607-162824878(+)$1	271	46	72	21.8538
UGAUGUAGAACGCCAUAAAAUGCAUU	chr11:109530403-109530714(+)$1	311	134	160	24.1820
UUAUCAGUUCUAUUUUUCUAUUGAUU	chr12:39358640-39358903(+)$1	263	56	82	22.5499
CAGGUCUCCCAAACUGUCCACAGAGU	chr13:20697656-20697893(+)$1	237	174	200	22.7178
GGAUAGAUCCUCCUUUACUAUUCUAU	chrX:154259971-154260219(-)$1	248	3	29	22.1908
GGAUCUUGUGCCUCAAAAAAACGUUC	chr18:20845873-20846128(-)$1	255	146	172	22.8277
CUGGUGGUUAUAAUACAGCAGGCGGC	chr16:37886917-37887183(+)$1	266	3	29	23.5738
UCAAGUUCAAAGCAUGUUCAGGACGA	chr15:36407574-36407829(-)$1	255	223	249	23.3128
GUGGAAUGUCUCCUUUCUCUUUCCAC	chr17:35971695-35971945(-)$1	250	190	216	22.8316
AGCUUCUUGUCUCUUUAUACUAAAAG	chr11:109528789-109529095(+)$1	306	220	246	18.0624
AAAAAGUCGAAAGGAAAGCAAAGACA	chr2:66110180-66110416(-)$1	236	66	92	22.5229
GUUUAAAAGAAAAAUAAAACAUUUUA	chr5:122906322-122906560(-)$1	238	182	208	20.9933
AAGAAGAAAAUAGCUGAUCAUUCUUC	chr16:59653243-59653500(-)$1	257	24	50	24.3280
CCUUUGCGUUUAACAAACUAGCAUGA	chr6:24563982-24564219(-)$1	237	170	196	24.2588
AAUUCGACCCCUAAAAuguuuuguuu	chr13:54860178-54860450(-)$1	272	10	36	23.9812
CCAAUUAUAAAGCAUUUAUAAAUAGU	chr17:85462769-85463009(-)$1	240	152	178	20.9933

#DB
((((((((............))))))	chr12:71367074-71367313(-)$1	1	191	217	24.0722
(((.((((............))))..	chr18:34478851-34479088(+)$1	1	63	89	23.2862
(.....(((...........)))...	chr11:31957933-31958193(+)$1	1	34	60	22.1745
((((((..............))))))	chr14:66929370-66929632(+)$1	1	197	223	22.8316
((((((.(...........)))))))	chr5:137509001-137509236(+)$1	1	151	177	23.4164
((((.(................).))	chr11:78140021-78140298(+)$1	1	202	228	21.7775
((((((..............))))))	chr6:125170615-125170893(+)$1	1	231	257	22.7986
.(((.(..............).))).	chr12:12380094-12380336(+)$1	1	16	42	20.9027
(..((((..............)))).	chr9:75069990-75070247(+)$1	1	206	232	21.9024
(((((((((...........))).))	chr14:37934879-37935169(-)$1	1	253	279	23.6700
(((((((..............)))))	chr10:110733431-110733666(+)$1	1	158	184	22.9081
(.((((((............))))))	chr3:31101926-31102161(-)$1	1	195	221	24.4147
((((((((............))))).	chr5:136384479-136384794(-)$1	1	217	243	23.5449
((((.(.(...........).)))))	chr11:77524382-77524622(+)$1	1	197	223	23.4062
((((..((.............))..)	chr5:151612526-151612769(+)$1	1	49	75	22.5251
.((.(((.............))).))	chr9:79618583-79618902(-)$1	1	177	203	22.5656
((...((((...........))))..	chr12:8757528-8757775(+)$1	1	161	187	21.5177
(.(((((((...........))).))	chr12:4110460-4110698(+)$1	1	184	210	22.6683
.((((((.............))))))	chr16:31093849-31094091(-)$1	1	88	114	23.2752
((((..((............))))))	chr9:58499808-58500092(+)$1	1	177	203	23.1915
(((((((((...........))).))	chr6:113696548-113696811(-)$1	1	87	113	23.7987
(.(...(((...........)))...	chr5:67679172-67679423(+)$1	1	110	136	23.2896
((((.(((.............)))))	chr9:42772292-42772528(-)$1	1	76	102	24.4975
)(((((((............))))))	chr4:40680719-40680957(+)$1	1	57	83	24.1596
((((................)))).)	chr15:79358603-79358847(-)$1	1	151	177	19.6609
((((((((................))	chr3:146395078-146395338(-)$1	1	57	83	19.6890
(((.((((................))	chr7:67133472-67133731(-)$1	1	169	195	19.4438
.((((((.............))))))	chr17:10406203-10406508(-)$1	1	60	86	23.5185
)((((((.............))))))	chr7:118214773-118215008(-)$1	1	206	232	23.1940
(((((((((...........))))))	chr5:93600345-93600582(+)$1	1	143	169	22.7536
..(((((..............)))))	chr1:152209721-152209959(-)$1	1	14	40	22.5188
(((((.(((...........))).))	chr3:116334598-116334833(-)$1	1	188	214	23.4941
).((((((............))))))	chr7:25763264-25763503(-)$1	1	23	49	23.2790
((((((((............))))))	chr9:72595391-72595637(+)$1	1	41	67	23.0804
((.(((((............))))))	chr5:122905949-122906267(-)$1	1	160	186	23.4877
.(((.(((............)))..)	chrX:69677955-69678230(-)$1	1	26	52	24.5938
((.((((.............)))).)	chr18:6788883-6789127(+)$1	1	146	172	22.9310
((((.(((............))).))	chr1:58582440-58582708(-)$1	1	74	100	24.9157
(((((................)))))	chr2:180716414-180716656(+)$1	1	169	195	20.8781
...(((((............))))).	chr1:52846191-52846426(-)$1	1	130	156	23.1355
..((.(((.............))).)	chr18:58105896-58106147(+)$1	1	45	71	23.7795
.(((.(((...........))).)))	chrX:149046577-149046823(-)$1	1	90	116	22.2803
..((((((............))))))	chr8:48268656-48268894(-)$1	1	70	96	22.4676
.(((((((...........)))))))	chrX:162824607-162824878(+)$1	1	46	72	21.8538
.((((((.............))))))	chr11:109530403-109530714(+)$1	1	134	160	24.1820
..((((((...........)))))).	chr12:39358640-39358903(+)$1	1	56	82	22.5499
..((.(((..............))).	chr13:20697656-20697893(+)$1	1	174	200	22.7178
(((((((..............)))))	chrX:154259971-154260219(-)$1	1	3	29	22.1908
(((...(((...........))).))	chr18:20845873-20846128(-)$1	1	146	172	22.8277
(.(((.(((...........))).))	chr16:37886917-37887183(+)$1	1	3	29	23.5738
((..((((............))))))	chr15:36407574-36407829(-)$1	1	223	249	23.3128
((((((..............))))))	chr17:35971695-35971945(-)$1	1	190	216	22.8316
(((..(((...............)))	chr11:109528789-109529095(+)$1	1	220	246	18.0624
((...(((..............))).	chr2:66110180-66110416(-)$1	1	66	92	22.5229
((((((((.............)))))	chr5:122906322-122906560(-)$1	1	182	208	20.9933
..((((((............))))))	chr16:59653243-59653500(-)$1	1	24	50	24.3280
(((((((.............))).))	chr6:24563982-24564219(-)$1	1	170	196	24.2588
((..(((.............)))..)	chr13:54860178-54860450(-)$1	1	10	36	23.9812
((((((((.............)))))	chr17:85462769-85463009(-)$1	1	152	178	20.9933

#PSSM
f : 0.16	e : 0.16	d : 0.10	: : 0.08	g : 0.06	! : 0.06	c : 0.05	h : 0.05	" : 0.05	a : 0.03	i : 0.03	= : 0.01	b : 0.01	% : 0.01	E : 0.01	H : 0.01	# : 0.01	+ : 0.01	
f : 0.22	e : 0.15	c : 0.10	g : 0.08	[ : 0.06	d : 0.06	! : 0.05	h : 0.05	" : 0.05	i : 0.03	: : 0.03	$ : 0.01	= : 0.01	b : 0.01	H : 0.01	# : 0.01	
f : 0.27	e : 0.16	c : 0.10	g : 0.08	d : 0.06	! : 0.05	b : 0.05	i : 0.03	" : 0.03	[ : 0.03	h : 0.03	$ : 0.01	= : 0.01	a : 0.01	# : 0.01	
f : 0.28	e : 0.20	g : 0.06	c : 0.06	d : 0.06	" : 0.06	[ : 0.05	! : 0.05	i : 0.03	b : 0.03	h : 0.03	$ : 0.01	= : 0.01	
f : 0.25	[ : 0.15	d : 0.11	e : 0.11	g : 0.06	c : 0.06	" : 0.06	! : 0.05	i : 0.03	h : 0.03	$ : 0.01	y : 0.01	
f : 0.25	c : 0.18	d : 0.13	e : 0.08	g : 0.06	a : 0.05	i : 0.03	! : 0.03	" : 0.03	y : 0.03	[ : 0.03	h : 0.03	$ : 0.01	
c : 0.32	f : 0.18	d : 0.11	e : 0.08	w : 0.06	g : 0.05	y : 0.05	[ : 0.03	b : 0.03	h : 0.03	i : 0.01	
c : 0.27	w : 0.13	v : 0.13	f : 0.11	d : 0.08	g : 0.05	y : 0.05	e : 0.05	a : 0.03	b : 0.03	h : 0.03	
u : 0.25	v : 0.22	w : 0.16	c : 0.13	t : 0.08	y : 0.08	d : 0.01	f : 0.01	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	t : 0.25	v : 0.22	w : 0.16	y : 0.08	x : 0.01	
u : 0.25	v : 0.22	t : 0.16	w : 0.16	y : 0.08	a : 0.03	c : 0.01	g : 0.01	f : 0.01	x : 0.01	
c : 0.23	f : 0.23	w : 0.10	d : 0.08	v : 0.08	g : 0.06	y : 0.06	e : 0.05	a : 0.01	] : 0.01	b : 0.01	x : 0.01	
c : 0.27	f : 0.23	d : 0.10	e : 0.10	g : 0.06	y : 0.05	b : 0.03	w : 0.03	h : 0.03	] : 0.01	i : 0.01	a : 0.01	x : 0.01	
c : 0.30	f : 0.23	e : 0.11	d : 0.10	g : 0.06	y : 0.03	h : 0.03	a : 0.01	i : 0.01	= : 0.01	b : 0.01	] : 0.01	x : 0.01	
f : 0.23	] : 0.16	c : 0.11	e : 0.11	d : 0.10	g : 0.06	2 : 0.05	4 : 0.03	y : 0.03	h : 0.03	i : 0.01	= : 0.01	
f : 0.30	e : 0.16	c : 0.10	d : 0.08	g : 0.06	2 : 0.05	] : 0.05	3 : 0.03	4 : 0.03	i : 0.03	h : 0.03	= : 0.01	b : 0.01	
f : 0.32	e : 0.15	c : 0.08	g : 0.06	d : 0.06	4 : 0.05	2 : 0.05	3 : 0.03	i : 0.03	] : 0.03	b : 0.03	h : 0.03	: : 0.01	= : 0.01	

#score	1342.878957279385
#seq	59
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_CDS_m3_run2.txt

#BEAR
dd[ddddnnnnndddddddd	chr2:24916943-24917186(+)$1	243	145	165	10.3709
"dddd[annnnna]dddd44	chr1:134533465-134533706(-)$1	241	100	120	10.6634
""eeeeennnnneeeee333	chr15:90772552-90772792(-)$1	240	116	136	11.1738
ggg[cccnnnnnccc]gggg	chr5:92493359-92493610(-)$1	251	200	220	12.4051
ddd!!bbnnnnnbb]dddd]	chr4:11154228-11154486(-)$1	258	168	188	12.1302
eeeddddnnnnndddd]eee	chr11:83931649-83931891(-)$1	242	176	196	10.4753
""eeeeennnnneeeee444	chr11:83154675-83154937(+)$1	262	41	61	10.9632
ccc[cccnnnnncccccc]c	chr4:100861622-100861901(-)$1	279	179	199	12.1431
ddd[cccnnnnnccc]dddd	chr3:103568284-103568526(-)$1	242	198	218	11.7019
cc"""bbnnnnnbb4444cc	chr3:107768906-107769165(-)$1	259	49	69	13.5002
fff[cccnnnnnccc]ffff	chr1:46868730-46868999(-)$1	269	228	248	11.8324
##a!!bbnnnnnbb22aeee	chr4:154374534-154374789(-)$1	255	23	43	13.0747
"""ddddnnnnndddd333c	chr10:13521556-13521808(-)$1	252	28	48	12.0665
h[eeeeennnnneeeee333	chr11:100749902-100750166(-)$1	264	11	31	10.6851
eee[cccnnnnnccc]eeee	chr2:59172684-59173014(+)$1	330	48	68	12.0152
[a"""bbnnnnnbb333add	chr11:60019794-60020049(-)$1	255	198	218	13.6949
###ddddnnnnndddd22ee	chr8:56140626-56140907(+)$1	281	86	106	11.2452
f####bbnnnnnbb333fff	chr17:13112158-13112416(+)$1	258	96	116	13.4890
eee[cccnnnnnccc]eeee	chr6:115187174-115187430(+)$1	256	233	253	12.0152
!!eeeeennnnneeeee22a	chrX:73050458-73050715(-)$1	257	31	51	10.5956
ffff[bbnnnnnbb]fffff	chr6:7821050-7821312(+)$1	262	66	86	11.5319
$$$$$bbnnnnnbb4444bb	chrX:67599614-67599851(-)$1	237	201	221	12.1678
$$$ddddnnnnndddd]ggg	chr3:32486437-32486710(-)$1	273	105	125	10.8780
ee[a!!annnnna22a]eee	chr3:62300623-62300884(-)$1	261	205	225	11.0823
[bb[cccnnnnnccc]bb]=	chr17:87846031-87846299(-)$1	268	13	33	11.7285
fffffbbnnnnnbb]fffff	chr2:119598162-119598407(-)$1	245	72	92	11.1782
gggg[bbnnnnnbb]ggggg	chr5:21565967-21566208(-)$1	241	173	193	12.3581
c[a[cccnnnnnccc]a]cc	chr17:56575332-56575595(-)$1	263	188	208	12.6789
eee[cccnnnnnccc22eee	chr11:80291493-80291784(+)$1	291	185	205	11.9513
ff"""bbnnnnnbb]fffff	chr10:87664465-87664730(+)$1	265	232	252	12.4907
[ccc[bbnnnnnbb]ccc22	chr9:62767095-62767342(-)$1	247	212	232	12.1337
==eeeeennnnneeeee22=	chr6:113698054-113698378(-)$1	324	275	295	10.3873
!!eeeeennnnneeeee]cc	chr17:57220703-57221028(-)$1	325	153	173	10.8496
"""ddddnnnnndddddddd	chrX:22797673-22797914(-)$1	241	170	190	11.1837
gg[bbbbnnnnnbb]bb]gg	chr15:81736235-81736476(+)$1	241	191	211	11.2038
e####bbnnnnnbb4444ee	chr6:135683287-135683532(-)$1	245	15	35	13.4127
$$$$cccnnnnnccc22ddd	chr16:32023073-32023325(-)$1	252	69	89	11.8610
dd"""bbnnnnnbbdddd33	chr19:57453497-57453734(+)$1	237	141	161	12.6412
bb"""bbnnnnnbb22bb]b	chr4:41152619-41152877(-)$1	258	122	142	11.9141
!!eeeeennnnneeeee]dd	chr5:134716646-134716900(-)$1	254	124	144	10.6833
iiii[bbnnnnnbb22iiii	chr13:34166370-34166611(-)$1	241	67	87	12.5468
[dddd[annnnna]dddd]b	chr10:90579687-90579941(-)$1	254	33	53	10.4184
!ccc[bbnnnnnbbccc22f	chr11:61359898-61360151(-)$1	253	157	177	12.1632
ddd!!bbnnnnnbb22dddd	chr8:15920996-15921247(-)$1	251	92	112	12.0888
ffffcccnnnnnccc]ffff	chr10:69460744-69461074(+)$1	330	40	60	11.3316
c"""cccnnnnnccc]ccc]	chr4:41686127-41686449(-)$1	322	91	111	12.9843
f"""cccnnnnncccfffff	chr9:49352655-49352921(-)$1	266	93	113	12.2729
gggg[bbnnnnnbb]ggggg	chr13:85341929-85342186(+)$1	257	46	66	12.3581
ff"""bbnnnnnbb333fff	chr5:23247591-23247847(-)$1	256	10	30	13.3156
!bb[cccnnnnnccc]bb44	chr7:26073616-26073891(+)$1	275	107	127	11.7229
iiiiiiinnnnniiiiiiii	chr15:97620343-97620603(+)$1	260	234	254	11.2398
cc[ddddnnnnndddd]ccc	chr14:13538209-13538459(-)$1	250	49	69	11.0516
ccc[cccnnnnnccccccdd	chr2:135886476-135886735(+)$1	259	174	194	11.8907
eeee[bbnnnnnbb4444ee	chr5:141236429-141236706(-)$1	277	77	97	12.4618
ddd[cccnnnnncccdddda	chr9:121403487-121403747(-)$1	260	53	73	11.4586
gggg[bbnnnnnbb]ggggg	chr5:114815653-114815903(-)$1	250	148	168	12.3581
###ddddnnnnndddd4444	chr2:32601495-32601757(+)$1	262	207	227	11.7069
ccc!!bbnnnnnbb333ccc	chr6:13786181-13786460(-)$1	279	118	138	13.3696
bb!!cccnnnnnccc22bb:	chr2:30268510-30268768(-)$1	258	229	249	10.6132
cc!!cccnnnnnccc]ccc:	chr6:40361515-40361757(-)$1	242	25	45	11.7574
i"""cccnnnnnccc22iii	chr11:93904816-93905080(+)$1	264	168	188	12.9417

#otherMatches

#Seq PSSM
GUGAGCUAUCCCGGCUGCCU	chr2:24916943-24917186(+)$1	243	145	165	10.3709
AACAUCCUGAUUGAAUGUGA	chr1:134533465-134533706(-)$1	241	100	120	10.6634
CCUGGGGGUUCACCCUAACA	chr15:90772552-90772792(-)$1	240	116	136	11.1738
GAGAAGUCGGCCACUCCUCC	chr5:92493359-92493610(-)$1	251	200	220	12.4051
AGAUUUGGUUUACAUUCUCA	chr4:11154228-11154486(-)$1	258	168	188	12.1302
UUAUUUAGUAUUUAGACUGA	chr11:83931649-83931891(-)$1	242	176	196	10.4753
CUACUGUUAAAUACAGUUCU	chr11:83154675-83154937(+)$1	262	41	61	10.9632
GGAUGACAAAACGUCUCUCC	chr4:100861622-100861901(-)$1	279	179	199	12.1431
GAUUUUAGUGAAUAAUGUCU	chr3:103568284-103568526(-)$1	242	198	218	11.7019
GGUCACCUAUGUGGAUUUCC	chr3:107768906-107769165(-)$1	259	49	69	13.5002
AAAAAUGGAAGACAUAUUUG	chr1:46868730-46868999(-)$1	269	228	248	11.8324
CCGCAGGCUUUACCAACUAC	chr4:154374534-154374789(-)$1	255	23	43	13.0747
ACAAAAGAUUUCCUUUCUCU	chr10:13521556-13521808(-)$1	252	28	48	12.0665
UGUCCUCGUACAGAGGGAUG	chr11:100749902-100750166(-)$1	264	11	31	10.6851
GGGCUCAUGUGUUGGUUCCU	chr2:59172684-59173014(+)$1	330	48	68	12.0152
UGGAUGCUGCUCGCUUACAG	chr11:60019794-60020049(-)$1	255	198	218	13.6949
AUUCUGUCUUCUGCAGCUGA	chr8:56140626-56140907(+)$1	281	86	106	11.2452
GCUAGUCAAACAGAAAAUUC	chr17:13112158-13112416(+)$1	258	96	116	13.4890
GAUGUGGUGGUUUCAAGUCA	chr6:115187174-115187430(+)$1	256	233	253	12.0152
AACAAGCGUAGGGCUUGGGG	chrX:73050458-73050715(-)$1	257	31	51	10.5956
GAAUUAGAAUACCUCGUUUA	chr6:7821050-7821312(+)$1	262	66	86	11.5319
UGAUCGCCUAUAGCCAGUAC	chrX:67599614-67599851(-)$1	237	201	221	12.1678
CUCAUGACAAUAUCAUCUGU	chr3:32486437-32486710(-)$1	273	105	125	10.8780
CUCAGCCGAGAAGAAUUAGU	chr3:62300623-62300884(-)$1	261	205	225	11.0823
GUUAUCUGGAUGAGGCGGAG	chr17:87846031-87846299(-)$1	268	13	33	11.7285
GUCCCCUAUAGGGGUGGGGC	chr2:119598162-119598407(-)$1	245	72	92	11.1782
AAUAUUAUUGCUUAUUAUUU	chr5:21565967-21566208(-)$1	241	173	193	12.3581
AGAUCUGGGUGUCAGCUGUC	chr17:56575332-56575595(-)$1	263	188	208	12.6789
GGCUGUCCUGCUGACCUGUC	chr11:80291493-80291784(+)$1	291	185	205	11.9513
CCUUCCGUCUUUCGUGGUGA	chr10:87664465-87664730(+)$1	265	232	252	12.4907
UCCUGUCAUAAAGAAGGGUU	chr9:62767095-62767342(-)$1	247	212	232	12.1337
GUUUCCUUAGGCGGGAACUG	chr6:113698054-113698378(-)$1	324	275	295	10.3873
GCUGGUGGAGAACACUGAUG	chr17:57220703-57221028(-)$1	325	153	173	10.8496
CCAUGUUAAGAGGGCAGAGU	chrX:22797673-22797914(-)$1	241	170	190	11.1837
UGGCACUAGGCAGGAUGGUA	chr15:81736235-81736476(+)$1	241	191	211	11.2038
GUCAAUCAGCAAGAAACCCC	chr6:135683287-135683532(-)$1	245	15	35	13.4127
AGUUGACAUAUGGUCUCUGG	chr16:32023073-32023325(-)$1	252	69	89	11.8610
UGAAACCGUGGAGGCAGUUA	chr19:57453497-57453734(+)$1	237	141	161	12.6412
CUCUUUCCCAAUGACCAGUG	chr4:41152619-41152877(-)$1	258	122	142	11.9141
GAUCAGAACGAGUCUGAAGG	chr5:134716646-134716900(-)$1	254	124	144	10.6833
GUUCAAGCGCAUCUCGGAGC	chr13:34166370-34166611(-)$1	241	67	87	12.5468
AGGUGGCGCUCGGGCACUCA	chr10:90579687-90579941(-)$1	254	33	53	10.4184
AUCAAGACAGGUUCUGAGCG	chr11:61359898-61360151(-)$1	253	157	177	12.1632
CACUUUCAACAAGACCGUGA	chr8:15920996-15921247(-)$1	251	92	112	12.0888
UUUGAUGAACUACAUGUAAA	chr10:69460744-69461074(+)$1	330	40	60	11.3316
ACCCUGUUCUUUGCACUAGC	chr4:41686127-41686449(-)$1	322	91	111	12.9843
CUCAAGUACAAGGCUGAGUG	chr9:49352655-49352921(-)$1	266	93	113	12.2729
GAAAACAGCUGAUGAUUUUC	chr13:85341929-85342186(+)$1	257	46	66	12.3581
UCUUUGGUCAGUCUUUUGGU	chr5:23247591-23247847(-)$1	256	10	30	13.3156
AUGACAUAGCAGGUGCCAGG	chr7:26073616-26073891(+)$1	275	107	127	11.7229
CCUUAUUGUUGAAAUAGGGA	chr15:97620343-97620603(+)$1	260	234	254	11.2398
GCAGUGGCACUUCCAUGGCU	chr14:13538209-13538459(-)$1	250	49	69	11.0516
CAGCAGACCAUUUCUCUGGC	chr2:135886476-135886735(+)$1	259	174	194	11.8907
GAACCGCAGCAAGCCCCUGU	chr5:141236429-141236706(-)$1	277	77	97	12.4618
GAGGCCAGUCUUUGGUUCAC	chr9:121403487-121403747(-)$1	260	53	73	11.4586
UCUCAUCACCUGGACGAGGA	chr5:114815653-114815903(-)$1	250	148	168	12.3581
GCCAGCCCCUCAGGCUCCAA	chr2:32601495-32601757(+)$1	262	207	227	11.7069
AUGCUGCUCCUUGCUCUCAU	chr6:13786181-13786460(-)$1	279	118	138	13.3696
GGGACUGGAGCGCAGGGCCA	chr2:30268510-30268768(-)$1	258	229	249	10.6132
UGCUGGCUGUAUGUCUCAGU	chr6:40361515-40361757(-)$1	242	25	45	11.7574
GCUUUGUUAUAUACACUUUU	chr11:93904816-93905080(+)$1	264	168	188	12.9417

#DB
((.((((.....))))))))	chr2:24916943-24917186(+)$1	1	145	165	10.3709
.((((.(.....).))))..	chr1:134533465-134533706(-)$1	1	100	120	10.6634
..(((((.....)))))...	chr15:90772552-90772792(-)$1	1	116	136	11.1738
(((.(((.....))).))))	chr5:92493359-92493610(-)$1	1	200	220	12.4051
(((..((.....)).)))).	chr4:11154228-11154486(-)$1	1	168	188	12.1302
(((((((.....)))).)))	chr11:83931649-83931891(-)$1	1	176	196	10.4753
..(((((.....)))))...	chr11:83154675-83154937(+)$1	1	41	61	10.9632
(((.(((.....)))))).)	chr4:100861622-100861901(-)$1	1	179	199	12.1431
(((.(((.....))).))))	chr3:103568284-103568526(-)$1	1	198	218	11.7019
((...((.....))....))	chr3:107768906-107769165(-)$1	1	49	69	13.5002
(((.(((.....))).))))	chr1:46868730-46868999(-)$1	1	228	248	11.8324
..(..((.....))..))))	chr4:154374534-154374789(-)$1	1	23	43	13.0747
...((((.....))))...)	chr10:13521556-13521808(-)$1	1	28	48	12.0665
(.(((((.....)))))...	chr11:100749902-100750166(-)$1	1	11	31	10.6851
(((.(((.....))).))))	chr2:59172684-59173014(+)$1	1	48	68	12.0152
.(...((.....))...)))	chr11:60019794-60020049(-)$1	1	198	218	13.6949
...((((.....))))..))	chr8:56140626-56140907(+)$1	1	86	106	11.2452
(....((.....))...)))	chr17:13112158-13112416(+)$1	1	96	116	13.4890
(((.(((.....))).))))	chr6:115187174-115187430(+)$1	1	233	253	12.0152
..(((((.....)))))..)	chrX:73050458-73050715(-)$1	1	31	51	10.5956
((((.((.....)).)))))	chr6:7821050-7821312(+)$1	1	66	86	11.5319
.....((.....))....))	chrX:67599614-67599851(-)$1	1	201	221	12.1678
...((((.....)))).)))	chr3:32486437-32486710(-)$1	1	105	125	10.8780
((.(..(.....)..).)))	chr3:62300623-62300884(-)$1	1	205	225	11.0823
.((.(((.....))).)).)	chr17:87846031-87846299(-)$1	1	13	33	11.7285
(((((((.....)).)))))	chr2:119598162-119598407(-)$1	1	72	92	11.1782
((((.((.....)).)))))	chr5:21565967-21566208(-)$1	1	173	193	12.3581
(.(.(((.....))).).))	chr17:56575332-56575595(-)$1	1	188	208	12.6789
(((.(((.....)))..)))	chr11:80291493-80291784(+)$1	1	185	205	11.9513
((...((.....)).)))))	chr10:87664465-87664730(+)$1	1	232	252	12.4907
.(((.((.....)).)))..	chr9:62767095-62767342(-)$1	1	212	232	12.1337
(((((((.....)))))..)	chr6:113698054-113698378(-)$1	1	275	295	10.3873
..(((((.....))))).))	chr17:57220703-57221028(-)$1	1	153	173	10.8496
...((((.....))))))))	chrX:22797673-22797914(-)$1	1	170	190	11.1837
((.((((.....)).)).))	chr15:81736235-81736476(+)$1	1	191	211	11.2038
(....((.....))....))	chr6:135683287-135683532(-)$1	1	15	35	13.4127
....(((.....)))..)))	chr16:32023073-32023325(-)$1	1	69	89	11.8610
((...((.....))))))..	chr19:57453497-57453734(+)$1	1	141	161	12.6412
((...((.....))..)).)	chr4:41152619-41152877(-)$1	1	122	142	11.9141
..(((((.....))))).))	chr5:134716646-134716900(-)$1	1	124	144	10.6833
((((.((.....))..))))	chr13:34166370-34166611(-)$1	1	67	87	12.5468
.((((.(.....).)))).)	chr10:90579687-90579941(-)$1	1	33	53	10.4184
.(((.((.....)))))..)	chr11:61359898-61360151(-)$1	1	157	177	12.1632
(((..((.....))..))))	chr8:15920996-15921247(-)$1	1	92	112	12.0888
(((((((.....))).))))	chr10:69460744-69461074(+)$1	1	40	60	11.3316
(...(((.....))).))).	chr4:41686127-41686449(-)$1	1	91	111	12.9843
(...(((.....))))))))	chr9:49352655-49352921(-)$1	1	93	113	12.2729
((((.((.....)).)))))	chr13:85341929-85342186(+)$1	1	46	66	12.3581
((...((.....))...)))	chr5:23247591-23247847(-)$1	1	10	30	13.3156
.((.(((.....))).))..	chr7:26073616-26073891(+)$1	1	107	127	11.7229
(((((((.....))))))))	chr15:97620343-97620603(+)$1	1	234	254	11.2398
((.((((.....)))).)))	chr14:13538209-13538459(-)$1	1	49	69	11.0516
(((.(((.....))))))))	chr2:135886476-135886735(+)$1	1	174	194	11.8907
((((.((.....))....))	chr5:141236429-141236706(-)$1	1	77	97	12.4618
(((.(((.....))))))))	chr9:121403487-121403747(-)$1	1	53	73	11.4586
((((.((.....)).)))))	chr5:114815653-114815903(-)$1	1	148	168	12.3581
...((((.....))))....	chr2:32601495-32601757(+)$1	1	207	227	11.7069
(((..((.....))...)))	chr6:13786181-13786460(-)$1	1	118	138	13.3696
((..(((.....)))..)).	chr2:30268510-30268768(-)$1	1	229	249	10.6132
((..(((.....))).))).	chr6:40361515-40361757(-)$1	1	25	45	11.7574
(...(((.....)))..)))	chr11:93904816-93905080(+)$1	1	168	188	12.9417

#PSSM
c : 0.13	f : 0.13	e : 0.11	d : 0.09	" : 0.08	g : 0.08	! : 0.08	[ : 0.06	# : 0.04	$ : 0.04	i : 0.04	b : 0.03	h : 0.01	= : 0.01	
d : 0.13	c : 0.13	" : 0.11	e : 0.09	f : 0.09	g : 0.08	# : 0.08	b : 0.06	! : 0.04	$ : 0.04	[ : 0.03	i : 0.03	a : 0.01	= : 0.01	
e : 0.19	" : 0.18	d : 0.09	c : 0.08	[ : 0.06	g : 0.06	f : 0.06	# : 0.06	$ : 0.04	a : 0.03	b : 0.03	i : 0.03	! : 0.03	
[ : 0.19	d : 0.16	" : 0.14	e : 0.13	! : 0.09	f : 0.04	g : 0.04	# : 0.03	$ : 0.03	c : 0.03	i : 0.03	a : 0.01	b : 0.01	
c : 0.31	d : 0.16	[ : 0.13	e : 0.11	" : 0.09	! : 0.08	# : 0.03	$ : 0.01	f : 0.01	b : 0.01	i : 0.01	
b : 0.37	c : 0.31	d : 0.13	e : 0.11	[ : 0.03	! : 0.01	i : 0.01	
b : 0.37	c : 0.31	d : 0.13	e : 0.11	a : 0.04	i : 0.01	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
b : 0.37	c : 0.31	d : 0.13	e : 0.11	a : 0.04	i : 0.01	
b : 0.37	c : 0.31	d : 0.13	e : 0.11	] : 0.03	2 : 0.01	i : 0.01	
c : 0.32	d : 0.18	] : 0.14	e : 0.11	2 : 0.08	4 : 0.06	3 : 0.06	i : 0.01	
d : 0.21	] : 0.18	2 : 0.13	e : 0.11	c : 0.06	4 : 0.06	3 : 0.06	f : 0.06	g : 0.04	a : 0.01	b : 0.01	i : 0.01	
d : 0.14	e : 0.14	c : 0.09	f : 0.09	4 : 0.08	3 : 0.08	2 : 0.08	g : 0.06	] : 0.06	b : 0.06	a : 0.03	i : 0.03	
d : 0.16	f : 0.13	c : 0.11	e : 0.09	4 : 0.09	g : 0.08	2 : 0.06	b : 0.06	] : 0.06	3 : 0.04	i : 0.04	a : 0.01	
d : 0.16	e : 0.14	f : 0.13	c : 0.11	g : 0.09	4 : 0.06	3 : 0.06	] : 0.06	2 : 0.06	i : 0.04	b : 0.03	
e : 0.14	f : 0.14	d : 0.13	c : 0.11	g : 0.09	4 : 0.06	3 : 0.04	b : 0.04	i : 0.04	] : 0.03	a : 0.03	= : 0.03	: : 0.03	2 : 0.01	

#score	722.611888453777
#seq	61
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_UTR_m1_run2.txt

#BEAR
fffff!!ccctttttttttttccc22fff	chr15:4105022-4105266(+)$1	244	207	236	21.0677
==========rrrrrrrrr==========	chrX:39460266-39460511(+)$1	245	56	85	13.5653
f[ccc[eeeeerrrrrrrrreeeee]ccc	chr1:180181907-180182144(+)$1	237	92	121	12.8422
FFFddddwwwwwwwwwwwwwwdddd::ee	chr16:36035202-36035440(+)$1	238	13	42	15.9504
chhhhhhhhuuuuuuuuuuuuhhhhhhhh	chr2:57220188-57220427(+)$1	239	195	224	18.8488
eehhhhhhhhxxxxxxxxxxxxxxxhhhh	chr14:21319545-21319780(-)$1	235	70	99	14.4090
fccc"""ccctttttttttttccc22ccc	chr2:6465641-6465886(-)$1	245	116	145	21.4878
eeee!!cccwwwwwwwwwwwwwwccc]ee	chr4:147247927-147248162(-)$1	235	21	50	21.6048
iiii^^^^^^^^^^^^^^^^^^^iiiiii	chr6:71758227-71758463(+)$1	236	78	107	14.9094
cc[ggggggguuuuuuuuuuuuggggggg	chr4:104704900-104705153(-)$1	253	215	244	22.5183
h"""ccc!!cccrrrrrrrrrccc22ccc	chr2:155214476-155214718(+)$1	242	29	58	13.3726
!!accc!!bbuuuuuuuuuuuubb22ccc	chr16:28827388-28827623(-)$1	235	77	106	21.6151
ggeeeee[bbtttttttttttbb]eeeee	chr5:92481805-92482063(-)$1	258	95	124	20.2751
ffffff[bbuuuuuuuuuuuubb]fffff	chr8:107740674-107740909(+)$1	235	138	167	20.0468
fffff[ddddtttttttttttdddd]fff	chr10:127514114-127514349(+)$1	235	176	205	20.0722
###gggggggvvvvvvvvvvvvvgggggg	chr5:107538225-107538463(-)$1	238	121	150	21.9024
""a[ffffffuuuuuuuuuuuuffffff]	chrX:98878669-98878906(+)$1	237	82	111	21.1793
eee::eeeeewwwwwwwwwwwwwweeeee	chr2:153594688-153594923(+)$1	235	77	106	18.1276
"""eeeee[bbssssssssssbbeeeeec	chr17:33855430-33855665(-)$1	235	194	223	15.0462
==========ssssssssss=========	chr2:134420525-134420761(-)$1	236	176	205	16.6053
ddd!!bb[bbuuuuuuuuuuuubbbb22d	chr19:12842903-12843138(-)$1	235	180	209	19.6918
hhhhhhhyyyyyyyyyyyyyyyyhhhhhh	chr4:33107028-33107268(+)$1	240	144	173	17.7604
##ccc[addddssssssssssdddd]a]c	chr3:51323609-51323852(-)$1	243	107	136	15.3481
==========ttttttttttt========	chr19:47809707-47809942(+)$1	235	71	100	22.4121
dddddddxxxxxxxxxxxxxxxdddd22d	chr7:122615150-122615411(-)$1	261	3	32	14.7162
!!ccc!!eeeeerrrrrrrrreeeeeccc	chr12:111819314-111819568(+)$1	254	104	133	13.0261
eeee[ddddvvvvvvvvvvvvvdddd]ee	chr10:39679454-39679689(-)$1	235	183	212	20.3716
gggggg[bbuuuuuuuuuuuubbgggggg	chr4:104704625-104704860(-)$1	235	152	181	21.6348
iiiiieeeeeuuuuuuuuuuuueeeee]i	chr5:136384359-136384619(-)$1	260	40	69	21.6918
ccc!!cccvvvvvvvvvvvvvccc22ccc	chr17:34406174-34406409(+)$1	235	115	144	20.9285
cc::ffffffuuuuuuuuuuuuffffff:	chr13:29999174-29999409(-)$1	235	137	166	17.8474
=========vvvvvvvvvvvvv=======	chr15:4104015-4104251(+)$1	236	143	172	22.5893
ff####ccc[assssssssssa]cccfff	chr1:134401574-134401813(+)$1	239	137	166	16.1414
iiiiii!!ddddrrrrrrrrrddddiiii	chr3:102824451-102824692(+)$1	241	127	156	13.1725
==========ttttttttttt========	chr11:60370509-60370744(+)$1	235	163	192	22.4121
cc[bb[axxxxxxxxxxxxxxxa]bb]cc	chr12:16992617-16992852(+)$1	235	6	35	16.1215
+++gggggggtttttttttttggggggg0	chr2:104266800-104267037(-)$1	237	136	165	19.0908
eeeeee[ccctttttttttttccceeeee	chr9:14348715-14348958(-)$1	243	5	34	21.0616
[ccc!!cccvvvvvvvvvvvvvccc22cc	chrX:99709798-99710042(-)$1	244	154	183	21.7883
"""gggggggtttttttttttggggggg4	chr2:14998809-14999056(+)$1	247	162	191	21.7471
dddd"""cccvvvvvvvvvvvvvccc]dd	chrX:54486260-54486495(-)$1	235	150	179	20.8683
d"""gggggggrrrrrrrrrgggggggdd	chr2:72240598-72240836(+)$1	238	124	153	12.6606
=========^^^^^^^^^^^^^^^^^^==	chr4:15210745-15211006(+)$1	261	20	49	15.0584
ggggg[bb[bbssssssssssbbbb]ggg	chr4:109126112-109126352(-)$1	240	124	153	15.1981
d"""ccc[bbvvvvvvvvvvvvvbb]ccc	chr5:68012977-68013215(-)$1	238	32	61	20.9182
eeee[eeeeettttttttttteeeee]ee	chr13:99612929-99613169(-)$1	240	8	37	20.5631
eeeee!!ccctttttttttttccc22eee	chr3:116445886-116446121(-)$1	235	44	73	21.2673
ggggg^^^^^^^^^^^^^^^^^^^ggggg	chr7:31339759-31340011(+)$1	252	201	230	14.8984
[cccddddxxxxxxxxxxxxxxxdddd]c	chr17:87535641-87535878(+)$1	237	41	70	15.8722
dd!!fffffftttttttttttffffff]d	chr3:97725293-97725538(+)$1	245	37	66	20.2947
ff!!bb!!cccsssssssssscccbb]ff	chr5:36944555-36944801(-)$1	246	122	151	15.4748
iiiggggggguuuuuuuuuuuuggggggg	chr19:12841729-12841976(-)$1	247	84	113	22.6057
:dddd[ddddtttttttttttdddddddd	chr9:14346543-14346793(-)$1	250	94	123	18.3683
eeeeffffffssssssssssffffff]ee	chr5:136386488-136386735(-)$1	247	140	169	14.4560
dd[ggggggguuuuuuuuuuuuggggggg	chr7:119254506-119254741(+)$1	235	66	95	22.3103
==!!ffffffvvvvvvvvvvvvvffffff	chr11:109530395-109530652(+)$1	257	139	168	20.8842

#otherMatches

#Seq PSSM
GGCUUCUAAGAAUGUCUUAAACUUCAAAG	chr15:4105022-4105266(+)$1	244	207	236	21.0677
UUCAUGAGUUGCGAAAUUGAAUUCAUGGA	chrX:39460266-39460511(+)$1	245	56	85	13.5653
UUGGUGGCAUUGGCUUUAGAAGUGUGACU	chr1:180181907-180182144(+)$1	237	92	121	12.8422
CCUAGGAAGAACAUGCCCACCUCCUGCUU	chr16:36035202-36035440(+)$1	238	13	42	15.9504
AUCUCUUGACCUGUUAAUAUUUUGGGAGA	chr2:57220188-57220427(+)$1	239	195	224	18.8488
GGCUUUGUAUCAUCUUUAUGUUUAAAUGC	chr14:21319545-21319780(-)$1	235	70	99	14.4090
UGUGUUGGCCUGAGAAGCAUUGGCGUCAC	chr2:6465641-6465886(-)$1	245	116	145	21.4878
UCUUGGCCAAGGUCAGCAUGUAAUGGAAA	chr4:147247927-147248162(-)$1	235	21	50	21.6048
UUUGGCUUAAUGUAAUGAACUCGCAAGGG	chr6:71758227-71758463(+)$1	236	78	107	14.9094
ACACAGAGCUAUCGUCCCUCUGAGCUCUG	chr4:104704900-104705153(-)$1	253	215	244	22.5183
CAUGAUCUUGCUGCUGUAGGAAGCUUGAU	chr2:155214476-155214718(+)$1	242	29	58	13.3726
CUCUUGCUUGCUUUCUGUCCCACACCCAG	chr16:28827388-28827623(-)$1	235	77	106	21.6151
UUGUGGACACAGAUUUUUGUAGUUUCCAU	chr5:92481805-92482063(-)$1	258	95	124	20.2751
GAUGAAGAUGAGUCUUAGAAAAUGUUCAU	chr8:107740674-107740909(+)$1	235	138	167	20.0468
GUGAAUGUGUUGUCCUCCUGUACAUUUUC	chr10:127514114-127514349(+)$1	235	176	205	20.0722
UGUCCAGGUGUCCAAACAUCCAUCAUUUG	chr5:107538225-107538463(-)$1	238	121	150	21.9024
ACAGGCAGUUAUUUUAUUUUUAGACUGUG	chrX:98878669-98878906(+)$1	237	82	111	21.1793
CAGAAAGCCUGACCUAGUUGCUUAAGGCU	chr2:153594688-153594923(+)$1	235	77	106	18.1276
UGGGCCUGACCCGAGUAUGUAGGCAGGUU	chr17:33855430-33855665(-)$1	235	194	223	15.0462
UAUUAUAAAAUGGUGUGUUUUUUUGUAAU	chr2:134420525-134420761(-)$1	236	176	205	16.6053
UUCCCUGUGUACUUCAGAAUCAGCCAUUG	chr19:12842903-12843138(-)$1	235	180	209	19.6918
UAGCCCUAUUUCAAACCAUUCUAAGGGUU	chr4:33107028-33107268(+)$1	240	144	173	17.7604
UAAAGGGCUCUGGGAAAGGGGAGAGAUGC	chr3:51323609-51323852(-)$1	243	107	136	15.3481
uuaaguauaaaaaaauuaaaauuGUGUUU	chr19:47809707-47809942(+)$1	235	71	100	22.4121
UACUGUAACCCUUUUCUUUGCCUACAUUG	chr7:122615150-122615411(-)$1	261	3	32	14.7162
GAGGGUUCUGAGAAGUGCUUCCUCAGCCC	chr12:111819314-111819568(+)$1	254	104	133	13.0261
AGUUCGAAAUUAAUCGCACUGUUUUCUAA	chr10:39679454-39679689(-)$1	235	183	212	20.3716
GGUGGGGCCCAUGCAUUUCCAGGUCUGCU	chr4:104704625-104704860(-)$1	235	152	181	21.6348
ACCAGUGUUAGCUUACUCUUAAUAAUGUC	chr5:136384359-136384619(-)$1	260	40	69	21.6918
GAUCuguaguaaaccaauguaugcuuauc	chr17:34406174-34406409(+)$1	235	115	144	20.9285
CCAUUGAGUUGCUGCUACUAAAAGCUCAC	chr13:29999174-29999409(-)$1	235	137	166	17.8474
UAUCUUUUACCUUCCUCUGUUUUGAGAGA	chr15:4104015-4104251(+)$1	236	143	172	22.5893
GUUUCUAGUUCUGUUGCUCCUGUGCUGCU	chr1:134401574-134401813(+)$1	239	137	166	16.1414
GCUGAGCUGUUGGGGUGAGUACGACCUCA	chr3:102824451-102824692(+)$1	241	127	156	13.1725
UGAGGGAGAUGCAUUUUACCAGUUUCUCu	chr11:60370509-60370744(+)$1	235	163	192	22.4121
GUGAUCCUAAAAAAAAAUCUGUGUGUGGC	chr12:16992617-16992852(+)$1	235	6	35	16.1215
CUAUGCUACACUAGUUUGCCAUGUAGCAA	chr2:104266800-104267037(-)$1	237	136	165	19.0908
UUCCACACCCAGCUUUCCUUAGGGGUGGA	chr9:14348715-14348958(-)$1	243	5	34	21.0616
UCUCCUGGUUUUCCUUGUUUCUACCCAGA	chrX:99709798-99710042(-)$1	244	154	183	21.7883
ACUGAAAGGCAUAAUAACAUGGUCUUUCC	chr2:14998809-14999056(+)$1	247	162	191	21.7471
GUGACCCAGUUGCACUUCCCUUUACUAUC	chrX:54486260-54486495(-)$1	235	150	179	20.8683
AAAUACGUGAUUACACACAUAUCAUGUUC	chr2:72240598-72240836(+)$1	238	124	153	12.6606
GAACAGAAAAAUAACCCAAAUAUUUUCUU	chr4:15210745-15211006(+)$1	261	20	49	15.0584
UAGGAAAUGCAGAAUUCACAGUGAUCUCC	chr4:109126112-109126352(-)$1	240	124	153	15.1981
CGUUUGCUACUAAAAUCUGUGAUGUUGCA	chr5:68012977-68013215(-)$1	238	32	61	20.9182
CCCUCUGUGCCCUAAGCAUAUGCACAUGG	chr13:99612929-99613169(-)$1	240	8	37	20.5631
AAUGAGCACCAUCACCUAAGCGGUAAUCA	chr3:116445886-116446121(-)$1	235	44	73	21.2673
GCAGGCCUCCUACCGCACUUGUAACCUGU	chr7:31339759-31340011(+)$1	252	201	230	14.8984
UGUUGGACUGUGUUCCCGGUUCUGUCCUA	chr17:87535641-87535878(+)$1	237	41	70	15.8722
CUGAAAAUGAAAGAUGGCGCCUCGUUUAA	chr3:97725293-97725538(+)$1	245	37	66	20.2947
CUGAAGAAGCCAAGGAUUUGAGGCCUGGG	chr5:36944555-36944801(-)$1	246	122	151	15.4748
AUUAGACCCUAACACAUUUUACAGGGUUU	chr19:12841729-12841976(-)$1	247	84	113	22.6057
UCCACUGCCUUGUGUGUGUAUAGGUGUGG	chr9:14346543-14346793(-)$1	250	94	123	18.3683
UGCCUUUAGUUUAACUUAUUGCUAGACGG	chr5:136386488-136386735(-)$1	247	140	169	14.4560
UUCUAGAAUGCUUGUAAAGUCCCGUUUUA	chr7:119254506-119254741(+)$1	235	66	95	22.3103
GAAUGAUGUAGAACGCCAUAAAAUGCAUU	chr11:109530395-109530652(+)$1	257	139	168	20.8842

#DB
(((((..(((...........)))..)))	chr15:4105022-4105266(+)$1	1	207	236	21.0677
((((((((((.........))))))))))	chrX:39460266-39460511(+)$1	1	56	85	13.5653
(.(((.(((((.........))))).)))	chr1:180181907-180182144(+)$1	1	92	121	12.8422
(((((((..............))))..((	chr16:36035202-36035440(+)$1	1	13	42	15.9504
(((((((((............))))))))	chr2:57220188-57220427(+)$1	1	195	224	18.8488
))((((((((...............))))	chr14:21319545-21319780(-)$1	1	70	99	14.4090
)(((...(((...........)))..)))	chr2:6465641-6465886(-)$1	1	116	145	21.4878
((((..(((..............))).))	chr4:147247927-147248162(-)$1	1	21	50	21.6048
((((...................))))))	chr6:71758227-71758463(+)$1	1	78	107	14.9094
((.(((((((............)))))))	chr4:104704900-104705153(-)$1	1	215	244	22.5183
(...(((..(((.........)))..)))	chr2:155214476-155214718(+)$1	1	29	58	13.3726
..((((..((............))..)))	chr16:28827388-28827623(-)$1	1	77	106	21.6151
))(((((.((...........)).)))))	chr5:92481805-92482063(-)$1	1	95	124	20.2751
((((((.((............)).)))))	chr8:107740674-107740909(+)$1	1	138	167	20.0468
(((((.((((...........)))).)))	chr10:127514114-127514349(+)$1	1	176	205	20.0722
...(((((((.............))))))	chr5:107538225-107538463(-)$1	1	121	150	21.9024
..(.((((((............)))))).	chrX:98878669-98878906(+)$1	1	82	111	21.1793
)))..(((((..............)))))	chr2:153594688-153594923(+)$1	1	77	106	18.1276
...(((((.((..........))))))))	chr17:33855430-33855665(-)$1	1	194	223	15.0462
((((((((((..........)))))))))	chr2:134420525-134420761(-)$1	1	176	205	16.6053
(((..((.((............))))..)	chr19:12842903-12843138(-)$1	1	180	209	19.6918
(((((((................))))))	chr4:33107028-33107268(+)$1	1	144	173	17.7604
..(((.(((((..........)))).).)	chr3:51323609-51323852(-)$1	1	107	136	15.3481
((((((((((...........))))))))	chr19:47809707-47809942(+)$1	1	71	100	22.4121
(((((((...............))))..)	chr7:122615150-122615411(-)$1	1	3	32	14.7162
..(((..(((((.........))))))))	chr12:111819314-111819568(+)$1	1	104	133	13.0261
((((.((((.............)))).))	chr10:39679454-39679689(-)$1	1	183	212	20.3716
((((((.((............))))))))	chr4:104704625-104704860(-)$1	1	152	181	21.6348
((((((((((............))))).)	chr5:136384359-136384619(-)$1	1	40	69	21.6918
(((..(((.............)))..)))	chr17:34406174-34406409(+)$1	1	115	144	20.9285
))..((((((............)))))).	chr13:29999174-29999409(-)$1	1	137	166	17.8474
(((((((((.............)))))))	chr15:4104015-4104251(+)$1	1	143	172	22.5893
((....(((.(..........).))))))	chr1:134401574-134401813(+)$1	1	137	166	16.1414
((((((..((((.........))))))))	chr3:102824451-102824692(+)$1	1	127	156	13.1725
((((((((((...........))))))))	chr11:60370509-60370744(+)$1	1	163	192	22.4121
((.((.(...............).)).))	chr12:16992617-16992852(+)$1	1	6	35	16.1215
...(((((((...........))))))).	chr2:104266800-104267037(-)$1	1	136	165	19.0908
((((((.(((...........))))))))	chr9:14348715-14348958(-)$1	1	5	34	21.0616
.(((..(((.............)))..))	chrX:99709798-99710042(-)$1	1	154	183	21.7883
...(((((((...........))))))).	chr2:14998809-14999056(+)$1	1	162	191	21.7471
((((...(((.............))).))	chrX:54486260-54486495(-)$1	1	150	179	20.8683
(...(((((((.........)))))))))	chr2:72240598-72240836(+)$1	1	124	153	12.6606
(((((((((..................))	chr4:15210745-15211006(+)$1	1	20	49	15.0584
(((((.((.((..........)))).)))	chr4:109126112-109126352(-)$1	1	124	153	15.1981
(...(((.((.............)).)))	chr5:68012977-68013215(-)$1	1	32	61	20.9182
((((.(((((...........))))).))	chr13:99612929-99613169(-)$1	1	8	37	20.5631
(((((..(((...........)))..)))	chr3:116445886-116446121(-)$1	1	44	73	21.2673
(((((...................)))))	chr7:31339759-31340011(+)$1	1	201	230	14.8984
.(((((((...............)))).)	chr17:87535641-87535878(+)$1	1	41	70	15.8722
((..((((((...........)))))).)	chr3:97725293-97725538(+)$1	1	37	66	20.2947
((..((..(((..........))))).))	chr5:36944555-36944801(-)$1	1	122	151	15.4748
)))(((((((............)))))))	chr19:12841729-12841976(-)$1	1	84	113	22.6057
.((((.((((...........))))))))	chr9:14346543-14346793(-)$1	1	94	123	18.3683
((((((((((..........)))))).))	chr5:136386488-136386735(-)$1	1	140	169	14.4560
((.(((((((............)))))))	chr7:119254506-119254741(+)$1	1	66	95	22.3103
((..((((((.............))))))	chr11:109530395-109530652(+)$1	1	139	168	20.8842

#PSSM
e : 0.14	f : 0.12	= : 0.12	d : 0.12	c : 0.08	i : 0.07	g : 0.07	" : 0.05	h : 0.03	! : 0.03	# : 0.03	[ : 0.03	F : 0.01	+ : 0.01	: : 0.01	
e : 0.14	= : 0.12	c : 0.12	" : 0.10	d : 0.10	f : 0.08	i : 0.07	g : 0.07	h : 0.03	! : 0.03	# : 0.03	[ : 0.01	F : 0.01	+ : 0.01	
e : 0.14	c : 0.12	= : 0.10	" : 0.08	i : 0.07	d : 0.07	f : 0.05	h : 0.05	[ : 0.05	g : 0.05	! : 0.05	a : 0.03	# : 0.03	F : 0.01	: : 0.01	+ : 0.01	
g : 0.16	e : 0.14	c : 0.12	= : 0.10	! : 0.08	d : 0.07	f : 0.05	h : 0.05	i : 0.05	" : 0.05	: : 0.03	[ : 0.01	# : 0.01	b : 0.01	
g : 0.17	f : 0.14	= : 0.10	c : 0.10	d : 0.07	! : 0.07	e : 0.07	h : 0.05	" : 0.03	[ : 0.03	i : 0.03	b : 0.03	^ : 0.01	: : 0.01	# : 0.01	
g : 0.14	= : 0.10	[ : 0.10	e : 0.10	f : 0.10	! : 0.08	d : 0.07	c : 0.07	h : 0.05	" : 0.03	^ : 0.03	b : 0.03	# : 0.01	i : 0.01	
g : 0.12	! : 0.10	= : 0.10	e : 0.10	d : 0.10	c : 0.10	f : 0.08	h : 0.05	[ : 0.05	" : 0.03	^ : 0.03	b : 0.03	a : 0.03	
c : 0.16	g : 0.12	= : 0.10	e : 0.10	d : 0.08	f : 0.08	! : 0.07	[ : 0.05	b : 0.05	h : 0.03	^ : 0.03	x : 0.03	w : 0.01	y : 0.01	
c : 0.16	g : 0.12	= : 0.10	b : 0.10	e : 0.08	d : 0.08	f : 0.08	x : 0.05	h : 0.03	^ : 0.03	[ : 0.03	w : 0.01	! : 0.01	y : 0.01	v : 0.01	
c : 0.12	g : 0.12	b : 0.10	e : 0.08	f : 0.08	= : 0.07	d : 0.07	v : 0.07	u : 0.05	^ : 0.05	x : 0.05	w : 0.03	h : 0.01	y : 0.01	[ : 0.01	
t : 0.23	u : 0.19	v : 0.14	x : 0.07	w : 0.05	^ : 0.05	e : 0.03	c : 0.03	b : 0.03	s : 0.03	d : 0.03	r : 0.01	y : 0.01	a : 0.01	g : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.12	x : 0.07	r : 0.05	w : 0.05	^ : 0.05	c : 0.01	y : 0.01	e : 0.01	d : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.12	r : 0.10	x : 0.07	w : 0.05	^ : 0.05	y : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.12	r : 0.10	x : 0.07	w : 0.05	^ : 0.05	y : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.12	r : 0.10	x : 0.07	w : 0.05	^ : 0.05	y : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.12	r : 0.10	x : 0.07	w : 0.05	^ : 0.05	y : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.12	r : 0.10	x : 0.07	w : 0.05	^ : 0.05	y : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.12	r : 0.10	x : 0.07	w : 0.05	^ : 0.05	y : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.12	r : 0.10	x : 0.07	w : 0.05	^ : 0.05	y : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.12	r : 0.08	x : 0.07	w : 0.05	^ : 0.05	= : 0.01	y : 0.01	
t : 0.23	u : 0.19	v : 0.14	s : 0.08	x : 0.07	w : 0.05	^ : 0.05	r : 0.05	= : 0.03	e : 0.01	y : 0.01	g : 0.01	f : 0.01	
u : 0.14	c : 0.12	v : 0.12	d : 0.08	b : 0.08	= : 0.07	x : 0.07	e : 0.05	^ : 0.05	g : 0.05	w : 0.03	f : 0.03	h : 0.01	y : 0.01	a : 0.01	
c : 0.14	d : 0.12	b : 0.12	g : 0.10	= : 0.08	e : 0.07	v : 0.07	f : 0.07	^ : 0.05	x : 0.03	w : 0.03	h : 0.01	y : 0.01	] : 0.01	a : 0.01	
c : 0.19	d : 0.14	g : 0.14	= : 0.08	e : 0.08	f : 0.08	b : 0.07	] : 0.05	h : 0.03	^ : 0.03	x : 0.01	i : 0.01	w : 0.01	
g : 0.16	e : 0.14	d : 0.14	2 : 0.10	f : 0.10	= : 0.08	b : 0.08	c : 0.07	h : 0.03	x : 0.01	i : 0.01	^ : 0.01	
g : 0.16	2 : 0.12	e : 0.12	f : 0.10	= : 0.08	] : 0.08	d : 0.07	h : 0.05	c : 0.05	b : 0.05	i : 0.03	: : 0.01	^ : 0.01	
g : 0.17	f : 0.14	c : 0.12	] : 0.12	e : 0.10	= : 0.08	h : 0.05	2 : 0.05	i : 0.03	d : 0.03	: : 0.01	a : 0.01	^ : 0.01	
e : 0.17	c : 0.16	g : 0.16	f : 0.14	= : 0.10	] : 0.07	h : 0.05	d : 0.05	i : 0.03	2 : 0.03	
c : 0.21	e : 0.16	g : 0.12	f : 0.10	= : 0.10	d : 0.10	h : 0.05	i : 0.05	] : 0.01	: : 0.01	0 : 0.01	4 : 0.01	

#score	1036.7010674556304
#seq	56
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_CDS_m1_run1.txt

#BEAR
e[ffffff^^^^^^^^^^^^^^^^^^^ffff	chrY:602060-602264(-)$1	204	70	101	23.7989
!!ddddcccvvvvvvvvvvvvvccc]dddd]	chr19:23061861-23062064(+)$1	203	135	166	20.6117
^^^^^^^^^^^^^^^^^^^^^^^^hhhhhhh	chr14:99701233-99701453(+)$1	220	120	151	21.7821
::ccc[cccwwwwwwwwwwwwwwccc]ccc:	chr12:86337893-86338096(+)$1	203	84	115	20.0983
dddd!!cccyyyyyyyyyyyyyyyyccc22d	chr5:14678185-14678398(+)$1	213	101	132	24.6838
ccca!!cccyyyyyyyyyyyyyyyyccc22a	chr1:164627728-164627934(-)$1	206	138	169	25.3552
%%eeeee^^^^^^^^^^^^^^^^^^^^^^^^	chrX:55287496-55287731(+)$1	235	127	158	24.4947
f!!bbcccyyyyyyyyyyyyyyyyccc]bb2	chr14:57309771-57309988(+)$1	217	162	193	24.3909
%%dddd[cccuuuuuuuuuuuuccc4444dd	chr3:97011187-97011391(-)$1	204	120	151	20.5638
:eeeee[bbuuuuuuuuuuuubb]eeeeegg	chr11:69660868-69661078(+)$1	210	104	135	18.2406
""bb[ddddyyyyyyyyyyyyyyyydddd]b	chr2:37656033-37656246(-)$1	213	35	66	24.3458
b[gggggggwwwwwwwwwwwwwwggggggg]	chr6:22951895-22952110(+)$1	215	8	39	21.6647
[ccc[eeeeevvvvvvvvvvvvveeeee]cc	chr9:78326849-78327069(-)$1	220	36	67	20.5023
:ccc!!cccxxxxxxxxxxxxxxxccc4444	chr5:131950837-131951042(-)$1	205	103	134	22.8096
[a[ddddcccvvvvvvvvvvvvvccc]dddd	chr2:25299843-25300048(+)$1	205	28	59	20.7022
^^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chr11:70483359-70483567(-)$1	208	169	200	23.5853
dddeeeeeyyyyyyyyyyyyyyyyeeeee]d	chr17:23957887-23958090(+)$1	203	17	48	24.0707
####ggggggguuuuuuuuuuuuggggggg4	chr4:80959340-80959557(-)$1	217	130	161	20.4913
[ggggggg^^^^^^^^^^^^^^^^^^ggggg	chr9:36683818-36684028(+)$1	210	50	81	24.4405
!!ccc[ddddwwwwwwwwwwwwwwdddd]cc	chr14:22659666-22659876(+)$1	210	171	202	22.4753
eeeee^^^^^^^^^^^^^^^^^^^eeeeeGG	chr11:69638636-69638840(-)$1	204	104	135	22.2379
^^^^^^^^^^^^^^^^^^^^^^^^^^dddd:	chr11:62143014-62143214(-)$1	200	110	141	23.4814
""gggggggxxxxxxxxxxxxxxxggggggg	chr2:180821409-180821611(-)$1	202	58	89	22.7513
gggggggbbvvvvvvvvvvvvvbb]gggggg	chr2:113935636-113935848(-)$1	212	63	94	19.4717
ffffff!!dddduuuuuuuuuuuuddddfff	chr2:122520075-122520296(-)$1	221	39	70	18.7726
ddddffffffwwwwwwwwwwwwwwffffff:	chr2:112192560-112192770(+)$1	210	117	148	19.4304
f[a[bb^^^^^^^^^^^^^^^^^^bb]a]ff	chr17:31983386-31983605(-)$1	219	88	119	23.4123
g[ddddcccxxxxxxxxxxxxxxxccc5555	chr15:96523368-96523585(-)$1	217	24	55	20.3189
""eeeeezzzzzzzzzzzzzzzzzeeeeeff	chr18:78018573-78018786(+)$1	213	56	87	20.2015
"""ccc^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:143535406-143535610(-)$1	204	67	98	26.1893
ggggg[ccc^^^^^^^^^^^^^^^^^^^^^c	chr17:57162692-57162907(-)$1	215	108	139	24.7201
####bb^^^^^^^^^^^^^^^^^^^^^^^^^	chr4:133276721-133276929(-)$1	208	118	149	25.5502
c!!addddyyyyyyyyyyyyyyyydddd]a2	chr11:76021501-76021704(+)$1	203	98	129	24.9316
a[dddd^^^^^^^^^^^^^^^^^^dddd]a]	chr9:61762112-61762333(-)$1	221	120	151	24.1374
$$ccc####bbvvvvvvvvvvvvvbb4444c	chr5:122252133-122252337(+)$1	204	80	111	21.2592
""bb!!ccc^^^^^^^^^^^^^^^^^^^^cc	chr2:130441595-130441817(-)$1	222	181	212	25.0593
[a[eeeeeyyyyyyyyyyyyyyyyeeeeea]	chr13:110728151-110728359(+)$1	208	106	137	25.0776
b!!eeeeeyyyyyyyyyyyyyyyyeeeee]b	chr3:87728904-87729122(-)$1	218	44	75	24.7658
ccc[ffffffvvvvvvvvvvvvvffffff]c	chr17:64632711-64632911(-)$1	200	4	35	19.2729
dd[eeeeeyyyyyyyyyyyyyyyyeeeee]d	chr9:86414389-86414607(+)$1	218	148	179	24.2845
^^^^^^^^^^^^^^^^^^^^^^^^ccc22cc	chr15:101947159-101947365(-)$1	206	71	102	23.8465
====!!ddddwwwwwwwwwwwwwwdddd22=	chr2:163456680-163456884(-)$1	204	146	177	21.8647
"""ccc!!ccctttttttttttccc22ccc5	chr8:96528993-96529193(-)$1	200	84	115	17.8653
cc[ccc[bbxxxxxxxxxxxxxxxbb]ccc]	chr11:59999500-59999704(+)$1	204	76	107	21.9731
ffff!!cccyyyyyyyyyyyyyyyyccc22f	chr3:94970860-94971077(-)$1	217	95	126	24.6661
dddd!!cccyyyyyyyyyyyyyyyycccddd	chr5:135858165-135858373(-)$1	208	112	143	24.5086
=========^^^^^^^^^^^^^^^^^^^^^^	chr6:22950193-22950403(+)$1	210	154	185	24.7782
b[ggggggg^^^^^^^^^^^^^^^^^^^^^^	chr17:32339021-32339239(-)$1	218	70	101	24.5572
""ccc^^^^^^^^^^^^^^^^^^^^^^^^cc	chr4:55383087-55383297(+)$1	210	13	44	26.0540
"""bb^^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:123895745-123895964(+)$1	219	156	187	25.7305
!!ffffff^^^^^^^^^^^^^^^^^^^^^^f	chr10:127925178-127925380(+)$1	202	47	78	24.9577
eeee[bb[ayyyyyyyyyyyyyyyyabb]ee	chrX:133366464-133366664(+)$1	200	136	167	23.6493
""ffffff^^^^^^^^^^^^^^^^^^^ffff	chr17:85471279-85471484(-)$1	205	169	200	24.3775
!!dddd[ddddvvvvvvvvvvvvvdddd]dd	chr2:25447784-25447986(-)$1	202	129	160	20.0682
[a[dddd^^^^^^^^^^^^^^^^^^^^dddd	chr13:69121214-69121420(-)$1	206	12	43	24.5200
hhhhhh!!cccvvvvvvvvvvvvvccc4444	chr2:91334145-91334368(+)$1	223	7	38	20.2980
b[ccc^^^^^^^^^^^^^^^^^^^ccc]bba	chr7:25850313-25850534(-)$1	221	18	49	23.8600
cc!!eeeeexxxxxxxxxxxxxxxeeeee]c	chr7:5049131-5049335(+)$1	204	152	183	22.1740
ccc[ccc[bbwwwwwwwwwwwwwwbbccccc	chr7:119480349-119480554(+)$1	205	150	181	21.7652
ccc:::ddddwwwwwwwwwwwwwwddddccc	chr12:88029108-88029339(+)$1	231	79	110	18.7126
b[ggggggg^^^^^^^^^^^^^^^^^^^^^^	chr17:32339100-32339301(-)$1	201	132	163	24.5572
[ggggggg^^^^^^^^^^^^^^^^^^^gggg	chr2:142035742-142035976(+)$1	234	77	108	24.7006
eee[bb^^^^^^^^^^^^^^^^^^^^^bb]e	chr7:30168174-30168388(-)$1	214	106	137	23.5660

#otherMatches

#Seq PSSM
UUUUUGGGUUUUAUUUUUCUUUUCAUUUUCA	chrY:602060-602264(-)$1	204	70	101	23.7989
AAGUAGUGCCUAUGCAACGCUCGCACCUACA	chr19:23061861-23062064(+)$1	203	135	166	20.6117
ACAACCCAAAUUUACCUGCCACUCUGCCAGU	chr14:99701233-99701453(+)$1	220	120	151	21.7821
CCGCUCAGCCCUACCUGCCUCCUGCUCAGCC	chr12:86337893-86338096(+)$1	203	84	115	20.0983
GGCCCAUGCUGAUGCUAUUCCUACUGUAGAG	chr5:14678185-14678398(+)$1	213	101	132	24.6838
gacccagacccagacccaCAAACCAGUCCAG	chr1:164627728-164627934(-)$1	206	138	169	25.3552
UUCUGCAAACAGUAAAGAUACCACUAAAACC	chrX:55287496-55287731(+)$1	235	127	158	24.4947
UCAGAGUGGGAAAAAUUUAUUGAACACAUCA	chr14:57309771-57309988(+)$1	217	162	193	24.3909
CCCUCUAGCACACCUUAUCCCAUGCCUCCAG	chr3:97011187-97011391(-)$1	204	120	151	20.5638
CGGCUUCGCUCUCUUCCCCUCGCCAGGCCCA	chr11:69660868-69661078(+)$1	210	104	135	18.2406
CAGGCAGCACCAUCCCAUCACAUCCUGCUAC	chr2:37656033-37656246(-)$1	213	35	66	24.3458
AAAAUACGCUUAUAAACAAGCUUGUGUAUUC	chr6:22951895-22952110(+)$1	215	8	39	21.6647
AAGGCAAGACUUAAAUACACGCUGUUUUUCU	chr9:78326849-78327069(-)$1	220	36	67	20.5023
UGCACAGCUUCACACCCACCCUCCAGCCCCC	chr5:131950837-131951042(-)$1	205	103	134	22.8096
UGCGUGAUCAUCCUCUUUGUCUUUGACUUAC	chr2:25299843-25300048(+)$1	205	28	59	20.7022
CUUCCUGACUUGCCUUAUUUAUUUGUUCGAG	chr11:70483359-70483567(-)$1	208	169	200	23.5853
ACCCCAGGCUCCAACCCCCGCAAACCUGGUG	chr17:23957887-23958090(+)$1	203	17	48	24.0707
UCUCUCCAGCUCACCACUGACCAGGUUGGAU	chr4:80959340-80959557(-)$1	217	130	161	20.4913
UCUCCUUCUCUAGUUCUCUUCGCCAUGAAGG	chr9:36683818-36684028(+)$1	210	50	81	24.4405
UACUCUGGGAUGAUGUAGAAACCUUCCCUGG	chr14:22659666-22659876(+)$1	210	171	202	22.4753
UACCCCAUCCCCACUCCACCACUCGGGUAUA	chr11:69638636-69638840(-)$1	204	104	135	22.2379
UACUUCUACAUUCCAAACUUCACCAUCUGCU	chr11:62143014-62143214(-)$1	200	110	141	23.4814
UUGGAGGUCUCUUCCCACCUUGUUGGCUUCU	chr2:180821409-180821611(-)$1	202	58	89	22.7513
UGGAGAGGCAGAGUAUGUAGUGGCGCUCUUC	chr2:113935636-113935848(-)$1	212	63	94	19.4717
UUAGCAAUUAUGACAGAUGCACUCCAUAUGC	chr2:122520075-122520296(-)$1	221	39	70	18.7726
AAGGACCUCCUCACACUAAAAACUGGAGGUA	chr2:112192560-112192770(+)$1	210	117	148	19.4304
CCCCGGUCCCCUAUGUGCUUGCUCCCUGUGA	chr17:31983386-31983605(-)$1	219	88	119	23.4123
UUGGUGGCCAACGAAACUGUGAACGGCACCU	chr15:96523368-96523585(-)$1	217	24	55	20.3189
GGCUCCCUACUCCGGCUGCUCCAUGGGAGAG	chr18:78018573-78018786(+)$1	213	56	87	20.2015
CUAAGCCUCCAGCCUAUACCUACCCCGCCAC	chr5:143535406-143535610(-)$1	204	67	98	26.1893
CUGGGCUGCCUACUACUCUCACUACUACCAG	chr17:57162692-57162907(-)$1	215	108	139	24.7201
CCCAGCAACCACCAUCCCAGACCCCUCAUGC	chr4:133276721-133276929(-)$1	208	118	149	25.5502
UCCCCAGCUCUACUGGUUCUCACUGCUGUGC	chr11:76021501-76021704(+)$1	203	98	129	24.9316
CUUGCAUCUACUCCGCCCUCAUCCUGCACGA	chr9:61762112-61762333(-)$1	221	120	151	24.1374
CAGCCCUCAGCAGUUUCCCAAUCAGCCUUUG	chr5:122252133-122252337(+)$1	204	80	111	21.2592
UUUGUUGACUUAAGAAUUCCCCCCUCCCUGU	chr2:130441595-130441817(-)$1	222	181	212	25.0593
UGACGUGGCCUAUCACAACAACAUCCAUGCU	chr13:110728151-110728359(+)$1	208	106	137	25.0776
GCUGCCUGGCCAUGAACUACCCUACAGGCUC	chr3:87728904-87729122(-)$1	218	44	75	24.7658
GGUUUGUUCCCUCUCUCCAGUCCGGAACAUG	chr17:64632711-64632911(-)$1	200	4	35	19.2729
GCUUUUGUAAACGCCAUUUCAACAACAAGUG	chr9:86414389-86414607(+)$1	218	148	179	24.2845
UCACCUACCCACCCCCCACCCUGUGCCCCAG	chr15:101947159-101947365(-)$1	206	71	102	23.8465
AAAACAAGGUCUUCAUCAGCCUCAACCUGAU	chr2:163456680-163456884(-)$1	204	146	177	21.8647
CUUGCUGUGUUUUGAUGUUGGUGGCUAAGCU	chr8:96528993-96529193(-)$1	200	84	115	17.8653
AGCCCGAGCUCCAGCCACUCCCCUGCACGGU	chr11:59999500-59999704(+)$1	204	76	107	21.9731
UCCGCAGCCACAGCAUCGUCCUCCAGGCCCC	chr3:94970860-94971077(-)$1	217	95	126	24.6661
UGCUUCGUCUAUAACCCCACUCACUGACAGC	chr5:135858165-135858373(-)$1	208	112	143	24.5086
UGUGUCAUUUGAAUCCAUCCUGUCUUCCUAU	chr6:22950193-22950403(+)$1	210	154	185	24.7782
AGCACAGCACUCCACCCCAUCUCAACCAGCA	chr17:32339021-32339239(-)$1	218	70	101	24.5572
CAGCUACAACCCAGCCAUCAAGUACUCCCAG	chr4:55383087-55383297(+)$1	210	13	44	26.0540
CCUUGUUAUCACAGCACACCAUCCAACCCCC	chr5:123895745-123895964(+)$1	219	156	187	25.7305
CCGGGCACUAUCCCCCCACCUAACCUGCCUG	chr10:127925178-127925380(+)$1	202	47	78	24.9577
UUUGGCGACUACAAGACCACCAUCUGCGGCA	chrX:133366464-133366664(+)$1	200	136	167	23.6493
AACUGGUCACGAAGAUCCGAUUACAAAGACC	chr17:85471279-85471484(-)$1	205	169	200	24.3775
CCUGCAUAAGUUCUUCAACAUCCCAUUUUUG	chr2:25447784-25447986(-)$1	202	129	160	20.0682
UGUGGCAUUUUUAAUAACCGUUCCCACUGCC	chr13:69121214-69121420(-)$1	206	12	43	24.5200
CACCUCCGCUCAAUCUCCUCCACAGAGAAUU	chr2:91334145-91334368(+)$1	223	7	38	20.2980
CUCUGGUUUCUUCUCUGCUCUUCACAGUGUG	chr7:25850313-25850534(-)$1	221	18	49	23.8600
CCACCCACCUACAUCUCUCCUCUUGGUGGAG	chr7:5049131-5049335(+)$1	204	152	183	22.1740
GAAUCAUCGCCUCCCCCCACCCCUGCAUGUU	chr7:119480349-119480554(+)$1	205	150	181	21.7652
CCAAAGAGGCUCUGCCAAUCAAAUGCCUGGA	chr12:88029108-88029339(+)$1	231	79	110	18.7126
AGCACAGCACUCCACCCCAUCUCAACCAGCA	chr17:32339100-32339301(-)$1	201	132	163	24.5572
UUUCCUUUUCCAACAGAUGAUAACAAUGAAG	chr2:142035742-142035976(+)$1	234	77	108	24.7006
UCGCACUUCCAGCACGUCUUCAUCAUCGUCC	chr7:30168174-30168388(-)$1	214	106	137	23.5660

#DB
(.((((((...................))))	chrY:602060-602264(-)$1	1	70	101	23.7989
..(((((((.............))).)))).	chr19:23061861-23062064(+)$1	1	135	166	20.6117
........................)))))))	chr14:99701233-99701453(+)$1	1	120	151	21.7821
..(((.(((..............))).))).	chr12:86337893-86338096(+)$1	1	84	115	20.0983
((((..(((................)))..)	chr5:14678185-14678398(+)$1	1	101	132	24.6838
((((..(((................)))..)	chr1:164627728-164627934(-)$1	1	138	169	25.3552
..(((((........................	chrX:55287496-55287731(+)$1	1	127	158	24.4947
(..(((((................))).)).	chr14:57309771-57309988(+)$1	1	162	193	24.3909
..((((.(((............)))....))	chr3:97011187-97011391(-)$1	1	120	151	20.5638
.(((((.((............)).)))))((	chr11:69660868-69661078(+)$1	1	104	135	18.2406
..((.((((................)))).)	chr2:37656033-37656246(-)$1	1	35	66	24.3458
(.(((((((..............))))))).	chr6:22951895-22952110(+)$1	1	8	39	21.6647
.(((.(((((.............))))).))	chr9:78326849-78327069(-)$1	1	36	67	20.5023
.(((..(((...............)))....	chr5:131950837-131951042(-)$1	1	103	134	22.8096
.(.(((((((.............))).))))	chr2:25299843-25300048(+)$1	1	28	59	20.7022
........................)))))))	chr11:70483359-70483567(-)$1	1	169	200	23.5853
((((((((................))))).)	chr17:23957887-23958090(+)$1	1	17	48	24.0707
....(((((((............))))))).	chr4:80959340-80959557(-)$1	1	130	161	20.4913
.(((((((..................)))))	chr9:36683818-36684028(+)$1	1	50	81	24.4405
..(((.((((..............)))).))	chr14:22659666-22659876(+)$1	1	171	202	22.4753
(((((...................)))))))	chr11:69638636-69638840(-)$1	1	104	135	22.2379
..........................)))).	chr11:62143014-62143214(-)$1	1	110	141	23.4814
..(((((((...............)))))))	chr2:180821409-180821611(-)$1	1	58	89	22.7513
(((((((((.............)).))))))	chr2:113935636-113935848(-)$1	1	63	94	19.4717
((((((..((((............)))))))	chr2:122520075-122520296(-)$1	1	39	70	18.7726
))))((((((..............)))))).	chr2:112192560-112192770(+)$1	1	117	148	19.4304
(.(.((..................)).).))	chr17:31983386-31983605(-)$1	1	88	119	23.4123
(.(((((((...............)))....	chr15:96523368-96523585(-)$1	1	24	55	20.3189
..(((((.................)))))))	chr18:78018573-78018786(+)$1	1	56	87	20.2015
...(((.........................	chr5:143535406-143535610(-)$1	1	67	98	26.1893
(((((.(((.....................)	chr17:57162692-57162907(-)$1	1	108	139	24.7201
....((.........................	chr4:133276721-133276929(-)$1	1	118	149	25.5502
(..(((((................)))).).	chr11:76021501-76021704(+)$1	1	98	129	24.9316
(.((((..................)))).).	chr9:61762112-61762333(-)$1	1	120	151	24.1374
..(((....((.............))....)	chr5:122252133-122252337(+)$1	1	80	111	21.2592
..((..(((....................))	chr2:130441595-130441817(-)$1	1	181	212	25.0593
.(.(((((................)))))).	chr13:110728151-110728359(+)$1	1	106	137	25.0776
(..(((((................))))).)	chr3:87728904-87729122(-)$1	1	44	75	24.7658
(((.((((((.............)))))).)	chr17:64632711-64632911(-)$1	1	4	35	19.2729
((.(((((................))))).)	chr9:86414389-86414607(+)$1	1	148	179	24.2845
........................)))..))	chr15:101947159-101947365(-)$1	1	71	102	23.8465
((((..((((..............))))..)	chr2:163456680-163456884(-)$1	1	146	177	21.8647
...(((..(((...........)))..))).	chr8:96528993-96529193(-)$1	1	84	115	17.8653
((.(((.((...............)).))).	chr11:59999500-59999704(+)$1	1	76	107	21.9731
((((..(((................)))..)	chr3:94970860-94971077(-)$1	1	95	126	24.6661
((((..(((................))))))	chr5:135858165-135858373(-)$1	1	112	143	24.5086
(((((((((......................	chr6:22950193-22950403(+)$1	1	154	185	24.7782
(.(((((((......................	chr17:32339021-32339239(-)$1	1	70	101	24.5572
..(((........................))	chr4:55383087-55383297(+)$1	1	13	44	26.0540
...((..........................	chr5:123895745-123895964(+)$1	1	156	187	25.7305
..((((((......................)	chr10:127925178-127925380(+)$1	1	47	78	24.9577
((((.((.(................))).))	chrX:133366464-133366664(+)$1	1	136	167	23.6493
..((((((...................))))	chr17:85471279-85471484(-)$1	1	169	200	24.3775
..((((.((((.............)))).))	chr2:25447784-25447986(-)$1	1	129	160	20.0682
.(.((((....................))))	chr13:69121214-69121420(-)$1	1	12	43	24.5200
((((((..(((.............)))....	chr2:91334145-91334368(+)$1	1	7	38	20.2980
(.(((...................))).))(	chr7:25850313-25850534(-)$1	1	18	49	23.8600
((..(((((...............))))).)	chr7:5049131-5049335(+)$1	1	152	183	22.1740
(((.(((.((..............)))))))	chr7:119480349-119480554(+)$1	1	150	181	21.7652
)))...((((..............))))(((	chr12:88029108-88029339(+)$1	1	79	110	18.7126
(.(((((((......................	chr17:32339100-32339301(-)$1	1	132	163	24.5572
.(((((((...................))))	chr2:142035742-142035976(+)$1	1	77	108	24.7006
(((.((.....................)).)	chr7:30168174-30168388(-)$1	1	106	137	23.5660

#PSSM
" : 0.14	c : 0.11	[ : 0.09	d : 0.07	b : 0.07	e : 0.06	! : 0.06	^ : 0.06	f : 0.06	: : 0.04	g : 0.04	% : 0.03	# : 0.03	= : 0.03	a : 0.01	$ : 0.01	h : 0.01	
" : 0.14	[ : 0.12	c : 0.12	! : 0.11	d : 0.07	^ : 0.06	e : 0.06	g : 0.06	a : 0.04	% : 0.03	# : 0.03	f : 0.03	= : 0.03	: : 0.01	$ : 0.01	h : 0.01	
c : 0.17	d : 0.14	g : 0.12	e : 0.09	f : 0.07	[ : 0.07	^ : 0.06	! : 0.06	" : 0.04	b : 0.03	# : 0.03	= : 0.03	a : 0.01	h : 0.01	
d : 0.15	c : 0.15	e : 0.14	g : 0.12	f : 0.07	^ : 0.06	b : 0.06	[ : 0.06	a : 0.03	# : 0.03	= : 0.03	h : 0.01	! : 0.01	: : 0.01	
c : 0.14	e : 0.14	g : 0.14	d : 0.12	! : 0.11	f : 0.09	b : 0.07	^ : 0.06	[ : 0.04	= : 0.01	h : 0.01	: : 0.01	
d : 0.14	e : 0.14	^ : 0.12	g : 0.12	! : 0.11	f : 0.09	c : 0.07	b : 0.06	[ : 0.04	# : 0.01	= : 0.01	h : 0.01	: : 0.01	
^ : 0.20	c : 0.19	e : 0.12	g : 0.12	d : 0.11	f : 0.07	[ : 0.06	! : 0.04	# : 0.01	= : 0.01	b : 0.01	
^ : 0.23	c : 0.20	g : 0.11	d : 0.09	e : 0.09	f : 0.07	b : 0.04	! : 0.04	[ : 0.03	z : 0.01	# : 0.01	= : 0.01	
^ : 0.31	c : 0.22	y : 0.09	d : 0.09	g : 0.07	b : 0.06	e : 0.03	f : 0.03	z : 0.01	# : 0.01	= : 0.01	a : 0.01	
^ : 0.39	y : 0.19	x : 0.07	d : 0.07	c : 0.06	v : 0.03	w : 0.03	f : 0.03	b : 0.03	u : 0.01	e : 0.01	g : 0.01	z : 0.01	
^ : 0.39	y : 0.19	w : 0.11	v : 0.07	x : 0.07	u : 0.03	d : 0.03	c : 0.03	g : 0.01	z : 0.01	b : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.04	d : 0.01	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.06	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.06	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.06	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.06	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.06	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.06	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.06	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.06	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.06	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	v : 0.12	w : 0.11	x : 0.07	u : 0.04	b : 0.01	z : 0.01	t : 0.01	
^ : 0.39	y : 0.19	w : 0.11	v : 0.09	x : 0.07	c : 0.04	b : 0.03	u : 0.03	z : 0.01	
^ : 0.39	y : 0.19	c : 0.07	x : 0.07	w : 0.07	v : 0.04	g : 0.03	] : 0.01	e : 0.01	b : 0.01	u : 0.01	z : 0.01	f : 0.01	
^ : 0.28	c : 0.17	e : 0.14	d : 0.11	y : 0.09	g : 0.06	b : 0.06	f : 0.03	h : 0.01	] : 0.01	
^ : 0.28	c : 0.19	e : 0.14	d : 0.12	g : 0.07	b : 0.06	f : 0.03	] : 0.01	h : 0.01	4 : 0.01	2 : 0.01	a : 0.01	
^ : 0.25	c : 0.17	d : 0.15	e : 0.14	g : 0.09	] : 0.06	4 : 0.03	f : 0.03	h : 0.01	2 : 0.01	b : 0.01	
d : 0.19	^ : 0.17	e : 0.14	c : 0.12	g : 0.11	f : 0.06	4 : 0.06	] : 0.03	b : 0.03	h : 0.01	a : 0.01	5 : 0.01	2 : 0.01	
^ : 0.17	e : 0.12	g : 0.11	] : 0.11	d : 0.09	f : 0.07	c : 0.07	2 : 0.07	4 : 0.06	b : 0.04	h : 0.01	5 : 0.01	
c : 0.15	^ : 0.14	g : 0.12	d : 0.11	] : 0.11	f : 0.09	2 : 0.06	4 : 0.04	a : 0.04	b : 0.03	h : 0.01	G : 0.01	5 : 0.01	e : 0.01	
c : 0.17	d : 0.12	f : 0.11	^ : 0.11	g : 0.09	] : 0.07	: : 0.04	4 : 0.04	a : 0.03	2 : 0.03	b : 0.03	5 : 0.03	e : 0.03	h : 0.01	G : 0.01	= : 0.01	

#score	1437.4873583095628
#seq	63
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_CDS_m3_run2.txt

#BEAR
ee####cccooooooccc8888888	chr17:34768733-34768947(+)$1	214	131	156	12.2056
dd[bb[cccooooooccc]bb333d	chr3:94970860-94971077(-)$1	217	167	192	14.5162
:ccc[ddddoooooodddd]ccccc	chr15:98427531-98427759(-)$1	228	127	152	11.3677
"""a[ddddoooooodddd]a333c	chr13:36818498-36818700(-)$1	202	158	183	13.2848
ccccc[cccoooooocccccc22cc	chr7:3637294-3637512(-)$1	218	105	130	14.8420
hhhh!!cccooooooccc22hhhhh	chr9:44656731-44656951(-)$1	220	108	133	12.5220
eeee!!cccooooooccc]eeeeec	chr4:58889857-58890065(-)$1	208	89	114	14.0833
eeebb[ddddoooooodddd333bb	chr18:37992868-37993085(+)$1	217	108	133	11.3163
""ccc"""ammmma333ccc333gg	chrX:148354606-148354806(+)$1	200	12	37	9.2089
ccc[ddddaooooooa]ddddccc:	chr2:163453596-163453806(-)$1	210	112	137	11.3138
[dddd[cccoooooocccdddd22d	chr4:94236341-94236545(-)$1	204	72	97	13.3320
ea[a"""bboooooobb333a]a]e	chr1:75471489-75471691(-)$1	202	132	157	13.1168
fff[eeeeeooooooeeeee4444f	chr3:95151871-95152105(-)$1	234	171	196	11.5121
ddd"""cccoooooocccdddd]cc	chr10:126723255-126723464(-)$1	209	28	53	14.0788
d[ccc[cccooooooccc22ccc]d	chr18:78018573-78018786(+)$1	213	114	139	14.2179
=========oooooo==========	chr15:76002565-76002779(-)$1	214	136	161	13.2068
ccc"""cccoooooocccccc::EE	chr1:148598850-148599084(+)$1	234	84	109	11.2597
ffff!!cccoooooocccffffff2	chr11:62143014-62143214(-)$1	200	60	85	13.2360
bbaccccccooooooccc]ccc]a]	chr19:41676515-41676726(-)$1	211	65	90	13.6021
dddccccccoooooocccbb!!bb[	chr6:22951413-22951619(+)$1	206	143	168	11.5675
c!!bb[cccooooooccc]bb]ccc	chr11:35392417-35392625(+)$1	208	146	171	14.3526
ccc"""cccooooooccc666666c	chr2:121131484-121131684(+)$1	200	159	184	12.8955
effffffbboooooobb333fffff	chr15:83686648-83686860(-)$1	212	5	30	10.9147
[dddd[a[aooooooa]addddeee	chrX:96661807-96662013(-)$1	206	116	141	11.8530
##ccc[cccmmmmccc]ccc4444b	chr9:103328976-103329195(-)$1	219	75	100	9.5828
cc####cccooooooccc4444ccc	chr14:55525842-55526042(-)$1	200	4	29	15.2491
=====[cccooooooccc]======	chr2:148221194-148221413(+)$1	219	40	65	15.0619
fff!!ddddooooooddddffffff	chr10:57242880-57243082(-)$1	202	174	199	11.4686
ggggg!!bboooooobb22gggggg	chr2:25299843-25300048(+)$1	205	178	203	11.8389
b[gggggggooooooggggggg]bb	chr5:102339864-102340067(-)$1	203	103	128	12.0288
g####ddddoooooodddd4444gg	chr2:80346278-80346487(-)$1	209	178	203	13.0301
bb[bb[cccooooooccc]bb]bb]	chr13:67034499-67034700(-)$1	201	146	171	13.2512
:dddd[cccooooooccc333dddd	chr1:39416495-39416712(+)$1	217	127	152	12.9519
ba[dddd[aooooooa]dddd]a]b	chr11:49961601-49961810(+)$1	209	93	118	11.8558
eeeee[cccooooooccc]eeeee:	chrX:71003850-71004080(+)$1	230	140	165	12.9988
ccc!!a[ccclllccc]accc22bb	chr15:76452595-76452807(-)$1	212	140	165	9.0382
cc[a!!cccrrrrrrrrrccc]acc	chr18:36807011-36807229(+)$1	218	109	134	9.6090
ggggg[cccooooooccc]gggggg	chr11:69638636-69638840(-)$1	204	148	173	14.4099
eeeee[cccooooooccc22eeeee	chr4:149019367-149019573(+)$1	206	147	172	13.4429
""eeeee[aooooooaeeeee333e	chr13:98016347-98016558(+)$1	211	156	181	12.3112
d[ccc!!ccclllccc22ccc22dd	chr10:17813589-17813790(+)$1	201	17	42	8.5415
cc"""eeeeeooooooeeeee22cc	chr3:69530236-69530439(+)$1	203	28	53	10.6868
eeeee[cccooooooccc]eeeee:	chr12:25608984-25609195(-)$1	211	173	198	12.9988
eeee!!cccooooooccc333eeee	chr9:40610849-40611059(+)$1	210	152	177	14.4647
iiiiiiiiiooooooiiiiiiiii]	chr11:6303762-6303962(+)$1	200	23	48	12.4723
!!ccc[cccmmmmccc]ccc333dd	chr4:149012378-149012596(+)$1	218	160	185	9.7856
###bb[cccooooooccc]bb22bb	chr3:117029519-117029731(-)$1	212	76	101	13.9854
ffff!!cccoooooocccffffff2	chr11:62142965-62143175(-)$1	210	21	46	13.2360
eeeee[bboooooobbeeeee4444	chr2:118616369-118616578(+)$1	209	95	120	10.3577
fffff[cccooooooccc333ffff	chr12:25563081-25563283(+)$1	202	94	119	13.9985
!!bb[ddddooooooddddbb22bb	chr14:58465693-58465900(-)$1	207	77	102	11.6422
ccc[a[cccooooooccc]a]ccci	chr9:103118137-103118352(-)$1	215	92	117	14.7139
dddd[a[cccoooooocccadddd:	chr7:109007089-109007310(-)$1	221	196	221	10.4135

#otherMatches

#Seq PSSM
CCCACAGGCAUCAUCGCCAUCUUCA	chr17:34768733-34768947(+)$1	214	131	156	12.2056
AUACUGAGCAUGGCAGCUGAGAUGA	chr3:94970860-94971077(-)$1	217	167	192	14.5162
UCACUGUGCUGAUCUGUGCCGUGUG	chr15:98427531-98427759(-)$1	228	127	152	11.3677
CCUGGUGUCUCUCUCGGCAGCUUUA	chr13:36818498-36818700(-)$1	202	158	183	13.2848
CCGCAUGCGCUUCUACGUUGCCUGG	chr7:3637294-3637512(-)$1	218	105	130	14.8420
UUCUGCUGCUCCCAUGCAAGGGAAG	chr9:44656731-44656951(-)$1	220	108	133	12.5220
UGAGCUGGCCCCUACGCUUCUUACU	chr4:58889857-58890065(-)$1	208	89	114	14.0833
CUGCAAGCCAUGAUCUUGGCCUCUG	chr18:37992868-37993085(+)$1	217	108	133	11.3163
cccugucacuucugcuccagcucug	chrX:148354606-148354806(+)$1	200	12	37	9.2089
UGCUCCGCCGUCACAGAGUGGGCAC	chr2:163453596-163453806(-)$1	210	112	137	11.3138
AAAGCCAGCAAACCAGCUGCUUGCU	chr4:94236341-94236545(-)$1	204	72	97	13.3320
GGGAACAGCACCUAAGCCCCUGCAC	chr1:75471489-75471691(-)$1	202	132	157	13.1168
UCAAGAUCUACAUAAAGGUUAGUGU	chr3:95151871-95152105(-)$1	234	171	196	11.5121
CUGAUCCAGUUCCCUCUGCAGGCAG	chr10:126723255-126723464(-)$1	209	28	53	14.0788
UUGAUCAUCUAUGACGAUCUAUCCA	chr18:78018573-78018786(+)$1	213	114	139	14.2179
GGCCUUCAGCCUCUCUUGGGGGCCC	chr15:76002565-76002779(-)$1	214	136	161	13.2068
GCACUGAGCUACAUUGCUUGCAAUU	chr1:148598850-148599084(+)$1	234	84	109	11.2597
CAAAUUAUCACACAAGAUUUUGCUA	chr11:62143014-62143214(-)$1	200	60	85	13.2360
CCCCAGGGCCUGUGUGCCACUGUGA	chr19:41676515-41676726(-)$1	211	65	90	13.6021
ACUGGCUGGAACCCCCCAGGUUGAA	chr6:22951413-22951619(+)$1	206	143	168	11.5675
GACUGACAGAGAUCCCUGCCAACCU	chr11:35392417-35392625(+)$1	208	146	171	14.3526
CCCUGUGGCUCUCUUGCCUUCUCUG	chr2:121131484-121131684(+)$1	200	159	184	12.8955
AGGCUCUUGGCCAGACAUACAGAGC	chr15:83686648-83686860(-)$1	212	5	30	10.9147
AGGCUCGUCGUAACAGUCAGCCUGG	chrX:96661807-96662013(-)$1	206	116	141	11.8530
CACUCUUUUGUAGAAACGAGGCCUG	chr9:103328976-103329195(-)$1	219	75	100	9.5828
CCAAGCGCAAGCUUCUGCCAGAGGU	chr14:55525842-55526042(-)$1	200	4	29	15.2491
GGGUCGAGGACACCACCUGGACCCC	chr2:148221194-148221413(+)$1	219	40	65	15.0619
UCAACAUGCUCCUCUGCAUUGGCGC	chr10:57242880-57243082(-)$1	202	174	199	11.4686
CCACCACUGUUUGUCCACAGGUGGU	chr2:25299843-25300048(+)$1	205	178	203	11.8389
CCUGCUUUGUGAUUUUGAAGUAAGU	chr5:102339864-102340067(-)$1	203	103	128	12.0288
UGACAUUUUACAAAGAAAACAAAAA	chr2:80346278-80346487(-)$1	209	178	203	13.0301
GAAGAAGUCUAUGGUGAUGUCCUCC	chr13:67034499-67034700(-)$1	201	146	171	13.2512
ACUGCAGCCAGCACAGGCACAGCAG	chr1:39416495-39416712(+)$1	217	127	152	12.9519
GAAGAUGCGUGCCGCCUCAUCAUAC	chr11:49961601-49961810(+)$1	209	93	118	11.8558
CCAGCUUCAACCACCUGGUGCUGGC	chrX:71003850-71004080(+)$1	230	140	165	12.9988
CCUAAGCCUCACCGAGACAGGAAUG	chr15:76452595-76452807(-)$1	212	140	165	9.0382
CUUGGCUGCUCAAACUAUGCAACAG	chr18:36807011-36807229(+)$1	218	109	134	9.6090
GGAGGUCUGCCUCCCUAGCCCUCCC	chr11:69638636-69638840(-)$1	204	148	173	14.4099
AGUUCAAGCUCAUUUGCUCAGAACU	chr4:149019367-149019573(+)$1	206	147	172	13.4429
AGAUGUGACAGCCAAGCGCAUGAGC	chr13:98016347-98016558(+)$1	211	156	181	12.3112
GUGGUCUGGACAGUCCCCGCCUCCA	chr10:17813589-17813790(+)$1	201	17	42	8.5415
AAUGUUAUCUUCUUUCAGAUAUUUU	chr3:69530236-69530439(+)$1	203	28	53	10.6868
UUCUUAACGGUACAUUGUCAAGAAA	chr12:25608984-25609195(-)$1	211	173	198	12.9988
UGUUAGGGUUAACUUGCCAGAAACA	chr9:40610849-40611059(+)$1	210	152	177	14.4647
UAGGUUCCAACUUCAUGGGGCCUGG	chr11:6303762-6303962(+)$1	200	23	48	12.4723
CUUACCGUGUCCUCACUGUGUCAGA	chr4:149012378-149012596(+)$1	218	160	185	9.7856
CAUUCCCAUCCCAACAUGCGACCCU	chr3:117029519-117029731(-)$1	212	76	101	13.9854
CAAAUUAUCACACAAGAUUUUGCUA	chr11:62142965-62143175(-)$1	210	21	46	13.2360
GCGCCUGCUGCCCUGUGGUGUCAUU	chr2:118616369-118616578(+)$1	209	95	120	10.3577
UAUCUUGCAUUUUUUUGCUUUGGAU	chr12:25563081-25563283(+)$1	202	94	119	13.9985
UCGUCAGUGUGCUCUCACUAUUUAG	chr14:58465693-58465900(-)$1	207	77	102	11.6422
UCAAGGCUGCGCUCCCGGGUAUGAG	chr9:103118137-103118352(-)$1	215	92	117	14.7139
GGUUCGACCCAGCCCAGGGCAACCC	chr7:109007089-109007310(-)$1	221	196	221	10.4135

#DB
((....(((......))).......	chr17:34768733-34768947(+)$1	1	131	156	12.2056
((.((.(((......))).))...)	chr3:94970860-94971077(-)$1	1	167	192	14.5162
.(((.((((......)))).)))((	chr15:98427531-98427759(-)$1	1	127	152	11.3677
...(.((((......)))).)...)	chr13:36818498-36818700(-)$1	1	158	183	13.2848
(((((.(((......))))))..))	chr7:3637294-3637512(-)$1	1	105	130	14.8420
((((..(((......)))..)))))	chr9:44656731-44656951(-)$1	1	108	133	12.5220
((((..(((......))).)))))(	chr4:58889857-58890065(-)$1	1	89	114	14.0833
(((((.((((......))))...))	chr18:37992868-37993085(+)$1	1	108	133	11.3163
..(((...(....)...)))...))	chrX:148354606-148354806(+)$1	1	12	37	9.2089
(((.(((((......).))))))).	chr2:163453596-163453806(-)$1	1	112	137	11.3138
.((((.(((......)))))))..)	chr4:94236341-94236545(-)$1	1	72	97	13.3320
((.(...((......))...).).)	chr1:75471489-75471691(-)$1	1	132	157	13.1168
(((.(((((......)))))....)	chr3:95151871-95152105(-)$1	1	171	196	11.5121
(((...(((......))))))).))	chr10:126723255-126723464(-)$1	1	28	53	14.0788
(.(((.(((......)))..))).)	chr18:78018573-78018786(+)$1	1	114	139	14.2179
(((((((((......))))))))))	chr15:76002565-76002779(-)$1	1	136	161	13.2068
(((...(((......))))))..((	chr1:148598850-148599084(+)$1	1	84	109	11.2597
((((..(((......))))))))).	chr11:62143014-62143214(-)$1	1	60	85	13.2360
(((((((((......))).))).).	chr19:41676515-41676726(-)$1	1	65	90	13.6021
))))))(((......)))((..((.	chr6:22951413-22951619(+)$1	1	143	168	11.5675
(..((.(((......))).)).)))	chr11:35392417-35392625(+)$1	1	146	171	14.3526
(((...(((......)))......)	chr2:121131484-121131684(+)$1	1	159	184	12.8955
(((((((((......))...)))))	chr15:83686648-83686860(-)$1	1	5	30	10.9147
.((((.(.(......).))))))))	chrX:96661807-96662013(-)$1	1	116	141	11.8530
..(((.(((....))).)))....)	chr9:103328976-103329195(-)$1	1	75	100	9.5828
((....(((......)))....)))	chr14:55525842-55526042(-)$1	1	4	29	15.2491
(((((.(((......))).))))))	chr2:148221194-148221413(+)$1	1	40	65	15.0619
(((..((((......))))))))))	chr10:57242880-57243082(-)$1	1	174	199	11.4686
(((((..((......))..))))))	chr2:25299843-25300048(+)$1	1	178	203	11.8389
(.(((((((......))))))).))	chr5:102339864-102340067(-)$1	1	103	128	12.0288
(....((((......))))....))	chr2:80346278-80346487(-)$1	1	178	203	13.0301
((.((.(((......))).)).)).	chr13:67034499-67034700(-)$1	1	146	171	13.2512
.((((.(((......)))...))))	chr1:39416495-39416712(+)$1	1	127	152	12.9519
((.((((.(......).)))).).)	chr11:49961601-49961810(+)$1	1	93	118	11.8558
(((((.(((......))).))))).	chrX:71003850-71004080(+)$1	1	140	165	12.9988
(((..(.(((...))).))))..))	chr15:76452595-76452807(-)$1	1	140	165	9.0382
((.(..(((.........))).)))	chr18:36807011-36807229(+)$1	1	109	134	9.6090
(((((.(((......))).))))))	chr11:69638636-69638840(-)$1	1	148	173	14.4099
(((((.(((......)))..)))))	chr4:149019367-149019573(+)$1	1	147	172	13.4429
..(((((.(......))))))...)	chr13:98016347-98016558(+)$1	1	156	181	12.3112
(.(((..(((...)))..)))..))	chr10:17813589-17813790(+)$1	1	17	42	8.5415
((...(((((......)))))..))	chr3:69530236-69530439(+)$1	1	28	53	10.6868
(((((.(((......))).))))).	chr12:25608984-25609195(-)$1	1	173	198	12.9988
((((..(((......)))...))))	chr9:40610849-40611059(+)$1	1	152	177	14.4647
(((((((((......))))))))).	chr11:6303762-6303962(+)$1	1	23	48	12.4723
..(((.(((....))).)))...))	chr4:149012378-149012596(+)$1	1	160	185	9.7856
...((.(((......))).))..))	chr3:117029519-117029731(-)$1	1	76	101	13.9854
((((..(((......))))))))).	chr11:62142965-62143175(-)$1	1	21	46	13.2360
(((((.((......)))))))....	chr2:118616369-118616578(+)$1	1	95	120	10.3577
(((((.(((......)))...))))	chr12:25563081-25563283(+)$1	1	94	119	13.9985
..((.((((......))))))..))	chr14:58465693-58465900(-)$1	1	77	102	11.6422
(((.(.(((......))).).))))	chr9:103118137-103118352(-)$1	1	92	117	14.7139
((((.(.(((......)))))))).	chr7:109007089-109007310(-)$1	1	196	221	10.4135

#PSSM
e : 0.18	c : 0.18	d : 0.11	f : 0.09	b : 0.07	" : 0.05	g : 0.05	: : 0.03	[ : 0.03	= : 0.03	# : 0.03	! : 0.03	h : 0.01	i : 0.01	
c : 0.18	e : 0.15	d : 0.13	f : 0.11	" : 0.05	[ : 0.05	! : 0.05	# : 0.05	a : 0.03	= : 0.03	b : 0.03	g : 0.03	h : 0.01	i : 0.01	
c : 0.22	e : 0.15	d : 0.11	f : 0.11	[ : 0.09	# : 0.07	g : 0.05	" : 0.03	= : 0.03	h : 0.01	a : 0.01	! : 0.01	i : 0.01	b : 0.01	
c : 0.16	e : 0.13	b : 0.11	d : 0.09	" : 0.07	f : 0.07	# : 0.05	a : 0.05	[ : 0.05	g : 0.05	= : 0.03	! : 0.03	h : 0.01	i : 0.01	
c : 0.15	! : 0.15	e : 0.11	b : 0.09	d : 0.09	" : 0.09	[ : 0.07	# : 0.05	g : 0.05	= : 0.03	f : 0.03	i : 0.01	a : 0.01	
[ : 0.37	! : 0.15	d : 0.13	" : 0.09	e : 0.05	# : 0.03	c : 0.03	a : 0.03	= : 0.01	f : 0.01	g : 0.01	i : 0.01	
c : 0.56	d : 0.15	e : 0.05	" : 0.03	! : 0.03	[ : 0.03	= : 0.01	f : 0.01	a : 0.01	g : 0.01	i : 0.01	b : 0.01	
c : 0.62	d : 0.13	b : 0.07	[ : 0.05	e : 0.03	" : 0.01	= : 0.01	g : 0.01	i : 0.01	
c : 0.62	d : 0.11	a : 0.09	b : 0.05	e : 0.03	= : 0.01	g : 0.01	i : 0.01	o : 0.01	
o : 0.83	m : 0.05	c : 0.05	d : 0.01	r : 0.01	e : 0.01	
o : 0.88	m : 0.05	l : 0.03	r : 0.01	
o : 0.88	m : 0.05	l : 0.03	r : 0.01	
o : 0.88	m : 0.05	l : 0.03	r : 0.01	
o : 0.88	c : 0.07	a : 0.01	r : 0.01	
o : 0.86	c : 0.07	3 : 0.01	r : 0.01	b : 0.01	
c : 0.58	d : 0.09	a : 0.07	b : 0.07	o : 0.05	3 : 0.01	e : 0.01	= : 0.01	g : 0.01	r : 0.01	i : 0.01	
c : 0.52	d : 0.11	] : 0.11	e : 0.07	b : 0.05	3 : 0.01	= : 0.01	g : 0.01	r : 0.01	2 : 0.01	i : 0.01	
c : 0.58	d : 0.15	e : 0.07	3 : 0.03	a : 0.03	2 : 0.03	= : 0.01	g : 0.01	r : 0.01	i : 0.01	
] : 0.20	d : 0.20	c : 0.16	3 : 0.09	2 : 0.07	e : 0.07	f : 0.03	8 : 0.01	= : 0.01	b : 0.01	6 : 0.01	4 : 0.01	g : 0.01	i : 0.01	
c : 0.16	e : 0.13	b : 0.11	d : 0.11	3 : 0.09	2 : 0.05	f : 0.05	g : 0.05	] : 0.03	= : 0.03	4 : 0.03	a : 0.03	8 : 0.01	6 : 0.01	i : 0.01	
c : 0.15	e : 0.13	3 : 0.11	d : 0.11	b : 0.09	4 : 0.07	f : 0.07	g : 0.05	a : 0.03	= : 0.03	8 : 0.01	h : 0.01	! : 0.01	6 : 0.01	i : 0.01	] : 0.01	
3 : 0.11	2 : 0.11	c : 0.09	e : 0.09	d : 0.09	] : 0.09	4 : 0.09	f : 0.09	g : 0.05	= : 0.03	8 : 0.01	h : 0.01	: : 0.01	! : 0.01	6 : 0.01	i : 0.01	
2 : 0.13	3 : 0.11	c : 0.11	e : 0.11	f : 0.09	4 : 0.07	a : 0.05	] : 0.05	= : 0.03	b : 0.03	g : 0.03	d : 0.03	8 : 0.01	h : 0.01	: : 0.01	6 : 0.01	i : 0.01	
c : 0.16	b : 0.13	e : 0.11	f : 0.09	g : 0.07	d : 0.07	3 : 0.05	] : 0.05	4 : 0.05	= : 0.03	8 : 0.01	h : 0.01	2 : 0.01	E : 0.01	a : 0.01	6 : 0.01	i : 0.01	
c : 0.18	b : 0.13	d : 0.11	e : 0.09	g : 0.07	: : 0.07	f : 0.07	] : 0.05	= : 0.03	2 : 0.03	8 : 0.01	h : 0.01	E : 0.01	[ : 0.01	4 : 0.01	i : 0.01	

#score	659.2350525644791
#seq	53
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_CDS_m3_run2.txt

#BEAR
[bbcccqqqqqqqqccc]bbb	chr1:137728407-137728635(+)$1	228	102	123	14.0071
e[ddddqqqqqqqqdddd]ee	chr18:31948725-31948945(+)$1	220	196	217	14.0927
iiiiiiqqqqqqqqiiiiiii	chr6:125072398-125072618(+)$1	220	29	50	15.0996
cc!!bbqqqqqqqqbb22ccc	chr3:88132081-88132301(+)$1	220	1	22	15.4161
[eeeeeqqqqqqqqeeeee]e	chr14:59829305-59829532(+)$1	227	187	208	14.4081
e[ddddqqqqqqqqdddd]ee	chr3:95988862-95989082(+)$1	220	181	202	14.0927
hhhhbbqqqqqqqqbb]hhhh	chr3:101243552-101243774(+)$1	222	195	216	14.2387
eee[bbqqqqqqqqbb]eeee	chr17:56743470-56743718(+)$1	248	139	160	15.5916
=!!abbqqqqqqqqbb]a22=	chr11:78080547-78080767(+)$1	220	137	158	15.4762
!!ddddqqqqqqqqdddd22a	chr12:60173579-60173799(+)$1	220	151	172	13.9441
###cccqqqqqqqqccc22bb	chr17:56860685-56860905(+)$1	220	113	134	14.5451
ee[cccqqqqqqqqccceeee	chr2:180396288-180396522(-)$1	234	164	185	15.4478
!bb!!aqqqqqqqqa22bb]c	chr4:137112458-137112683(+)$1	225	97	118	13.9209
bb[cccqqqqqqqqccc]bb]	chr10:5892565-5892785(-)$1	220	16	37	14.3211
f[ddddqqqqqqqqdddd>>>	chr10:66681683-66681903(+)$1	220	86	107	13.3084
iii[bbqqqqqqqqbbiiiii	chr16:17130594-17130814(-)$1	220	13	34	15.6127
bb[cccqqqqqqqqccc]bbf	chr5:88984102-88984341(+)$1	239	176	197	14.2880
iiiiiiqqqqqqqqiiiiiii	chr13:98016332-98016552(+)$1	220	99	120	15.0996
ggggggqqqqqqqqggggggg	chr8:47615715-47615935(+)$1	220	146	167	14.9155
ggggbbqqqqqqqqbb]gggg	chr15:8100689-8100909(+)$1	220	141	162	15.5231
f!!cccqqqqqqqqccc]fff	chr1:58454460-58454680(+)$1	220	43	64	15.2402
b[ddddqqqqqqqqddddbbb	chr15:25926870-25927104(+)$1	234	191	212	12.9890
ee[cccqqqqqqqqccceeee	chr11:78068507-78068727(+)$1	220	125	146	15.4478
ggggggqqqqqqqqggggggg	chr9:61223263-61223483(+)$1	220	8	29	14.9155
ffffffqqqqqqqqffffff]	chr19:53715167-53715398(+)$1	231	127	148	13.4075
cc!!bbqqqqqqqqbb22ccc	chr11:79908594-79908814(+)$1	220	92	113	15.4161
"""cccqqqqqqqqccc4444	chr4:146987712-146987932(-)$1	220	166	187	15.3505
dd[cccqqqqqqqqcccdddd	chr5:135686644-135686864(+)$1	220	192	213	14.8744
ddd[bbqqqqqqqqbb]dddd	chr8:46110154-46110414(+)$1	260	42	63	14.9439
ddd!!aqqqqqqqqa22dddd	chr5:37771556-37771776(+)$1	220	178	199	14.3440
ccccccqqqqqqqqccc]ccc	chr2:164664042-164664262(+)$1	220	107	128	15.2320
c[cccaqqqqqqqqa]ccc]c	chr3:131270197-131270417(+)$1	220	178	199	15.3027
[eeeeeqqqqqqqqeeeee]c	chr17:79240481-79240709(+)$1	228	189	210	14.4160
cc!!bbqqqqqqqqbbcccff	chr13:24895143-24895380(+)$1	237	164	185	15.3495
ggggggqqqqqqqqggggggg	chr10:98485371-98485597(+)$1	226	89	110	14.9155
e!!cccqqqqqqqqccc22ee	chr9:108846707-108846928(+)$1	221	78	99	15.3644
ceeeeeqqqqqqqqeeeee]c	chr7:148340483-148340712(+)$1	229	47	68	14.2816
eeee[aqqqqqqqqa]eeeee	chr10:62779353-62779574(+)$1	221	14	35	14.9472
[eeeeeqqqqqqqqeeeee]c	chr9:21445398-21445618(+)$1	220	183	204	14.4160
ggg[bbqqqqqqqqbbggggg	chr9:110504622-110504842(+)$1	220	75	96	15.5331
ggggggqqqqqqqqggggggg	chr15:38969673-38969896(+)$1	223	17	38	14.9155
!!ddddqqqqqqqqdddd444	chr13:41104505-41104725(+)$1	220	14	35	14.1973
dd[cccqqqqqqqqccc]ddd	chr13:5864481-5864701(+)$1	220	173	194	15.0388
eeeebbqqqqqqqqbb]eeee	chr4:108533890-108534110(+)$1	220	15	36	15.3393
!cccbbqqqqqqqqbb]cccc	chr18:50121928-50122148(+)$1	220	192	213	15.4448
eeee[aqqqqqqqqa]eeeee	chr6:55002073-55002293(+)$1	220	9	30	14.9472
!eeeeeqqqqqqqqeeeee22	chr15:102316285-102316505(+)$1	220	33	54	13.9304
#eeeeeqqqqqqqqeeeeegg	chr11:11701562-11701784(-)$1	222	56	77	14.2311
ddd[bbqqqqqqqqbb]dddd	chr8:46110132-46110352(+)$1	220	64	85	14.9439
dd"""aqqqqqqqqa333ddd	chr15:25294483-25294729(-)$1	246	77	98	15.0368
cc[cccqqqqqqqqccc333c	chr10:66688844-66689064(+)$1	220	33	54	15.7100
[ccc[aqqqqqqqqa]ccc]e	chr11:77993344-77993564(+)$1	220	194	215	15.2364
ffffffqqqqqqqqffffffh	chr3:88727663-88727883(-)$1	220	126	147	13.3396
cc[cccqqqqqqqqccc22cc	chr10:93683407-93683627(+)$1	220	138	159	15.2250
ggggggqqqqqqqqggggggg	chr9:53303836-53304073(-)$1	237	74	95	14.9155
======qqqqqqqq=======	chr10:102855981-102856208(+)$1	227	146	167	15.5614
c!!cccqqqqqqqqccc22cc	chr2:129033881-129034102(+)$1	221	17	38	15.3661
ddd[bbqqqqqqqqbb]dddd	chr12:88301263-88301483(+)$1	220	95	116	14.9439
"ccc[aqqqqqqqqa]ccc22	chr1:88148794-88149014(+)$1	220	76	97	14.6700
eeee[aqqqqqqqqa]eeeee	chr8:87824944-87825165(+)$1	221	1	22	14.9472
eee[bbqqqqqqqqbb]eeee	chr9:56948882-56949102(+)$1	220	20	41	15.5916
eee[bbqqqqqqqqbb]eeee	chr3:90161713-90161935(+)$1	222	160	181	15.5916
ccc[bbqqqqqqqqbb]cccd	chr9:53198572-53198792(+)$1	220	188	209	15.3357
ee[cccqqqqqqqqccc]eee	chr5:124358080-124358330(+)$1	250	121	142	15.5309
ff!!bbqqqqqqqqbb4444f	chr2:167924162-167924382(+)$1	220	136	157	15.3851
$$$$bbqqqqqqqqbb4444b	chr10:114848199-114848419(+)$1	220	157	178	14.3375
======qqqqqqqq=======	chr9:106117183-106117468(+)$1	285	243	264	15.5614
!!a!!aqqqqqqqqa22a]cc	chr3:151883605-151883825(+)$1	220	68	89	15.1228
eee[bbqqqqqqqqbbeeeee	chr12:112780379-112780599(+)$1	220	156	177	15.3663

#otherMatches

#Seq PSSM
AUCCCUGGAUGCAGAGGUGAG	chr1:137728407-137728635(+)$1	228	102	123	14.0071
CUGAGGUGACAUAGUCUUUGA	chr18:31948725-31948945(+)$1	220	196	217	14.0927
GUGGAGCUGUGGAACUCUGUU	chr6:125072398-125072618(+)$1	220	29	50	15.0996
GCCUGCCUUCCUAAGCUUGCU	chr3:88132081-88132301(+)$1	220	1	22	15.4161
AUCAAAUAACUAACUUUGGAU	chr14:59829305-59829532(+)$1	227	187	208	14.4081
UACUCCCGCUUUGAGGAGGAG	chr3:95988862-95989082(+)$1	220	181	202	14.0927
GUCUGCACAGCAUAGUAAGGC	chr3:101243552-101243774(+)$1	222	195	216	14.2387
UGGAUGACCGUUACCACUCAG	chr17:56743470-56743718(+)$1	248	139	160	15.5916
UAUGCUAGCACUGGAGACCCA	chr11:78080547-78080767(+)$1	220	137	158	15.4762
UCGAUCAGGCAAAAGAUCUUC	chr12:60173579-60173799(+)$1	220	151	172	13.9441
AGCCAGAUGACCCCCUGAACU	chr17:56860685-56860905(+)$1	220	113	134	14.5451
AGGAGCAAGAAGAAGCUCUCC	chr2:180396288-180396522(-)$1	234	164	185	15.4478
AUCCAGAACUUAGACCAGAGC	chr4:137112458-137112683(+)$1	225	97	118	13.9209
UUUGUGUCUGACGUUACUGAG	chr10:5892565-5892785(-)$1	220	16	37	14.3211
CUGAGCAUGAAAAGGCUCCGG	chr10:66681683-66681903(+)$1	220	86	107	13.3084
GCGAGAGGCCAGUGUCCGCUU	chr16:17130594-17130814(-)$1	220	13	34	15.6127
UGUUGAAGAAAGAAUCACCAG	chr5:88984102-88984341(+)$1	239	176	197	14.2880
UGGAGAUACAGAGUUCUCUGC	chr13:98016332-98016552(+)$1	220	99	120	15.0996
GCAGCUCCUGUAAUAGCUGCU	chr8:47615715-47615935(+)$1	220	146	167	14.9155
AUCUCAUCCAUAGCUGCAGAU	chr15:8100689-8100909(+)$1	220	141	162	15.5231
CUCUCUCCCUAUCCAGAUGAA	chr1:58454460-58454680(+)$1	220	43	64	15.2402
GAUGCAUCUCCCGCUGCACUU	chr15:25926870-25927104(+)$1	234	191	212	12.9890
AGCUGUGACUCUAAAUACUCU	chr11:78068507-78068727(+)$1	220	125	146	15.4478
GGGUUGCCUGUUAAUGACCCu	chr9:61223263-61223483(+)$1	220	8	29	14.9155
GCUCCAGAAAAGUAUGGAGCG	chr19:53715167-53715398(+)$1	231	127	148	13.4075
CUAAUGUUGUGAUCCAGGAGG	chr11:79908594-79908814(+)$1	220	92	113	15.4161
GAACAcuuacacuugugguga	chr4:146987712-146987932(-)$1	220	166	187	15.3505
GGAUAAAUAAAGCCUUACUAG	chr5:135686644-135686864(+)$1	220	192	213	14.8744
GUGCAGCCAUCUUACUCCACA	chr8:46110154-46110414(+)$1	260	42	63	14.9439
CCAGAGACUGCAGGCCAUGGA	chr5:37771556-37771776(+)$1	220	178	199	14.3440
AUCCUGCUCUACAACGGAGAU	chr2:164664042-164664262(+)$1	220	107	128	15.2320
UACCGCCUUACCCCGACGGAG	chr3:131270197-131270417(+)$1	220	178	199	15.3027
GUCCAGUAGUGUACCUGGAAU	chr17:79240481-79240709(+)$1	228	189	210	14.4160
GAAAGAAAAAAGAAUCUCUAG	chr13:24895143-24895380(+)$1	237	164	185	15.3495
UUCGUAGUUCUUUAUACGAAG	chr10:98485371-98485597(+)$1	226	89	110	14.9155
AGAUCGAGAAGGAACGAGAUG	chr9:108846707-108846928(+)$1	221	78	99	15.3644
CUGAGGCUGGUCUUCUUCGUG	chr7:148340483-148340712(+)$1	229	47	68	14.2816
GGGUUGUAAUAUUCCUACUCU	chr10:62779353-62779574(+)$1	221	14	35	14.9472
GCUGGGCUGUUCACCCCAGGA	chr9:21445398-21445618(+)$1	220	183	204	14.4160
UUUACCUCCCAACUGGAAGAC	chr9:110504622-110504842(+)$1	220	75	96	15.5331
UCUGCAGUACUUGAUGUGGAC	chr15:38969673-38969896(+)$1	223	17	38	14.9155
ugcugggaauggagccagguu	chr13:41104505-41104725(+)$1	220	14	35	14.1973
GGAGGGAGCCAGGACCCCCCC	chr13:5864481-5864701(+)$1	220	173	194	15.0388
UCUGUGUUGUCACCCAUCAGA	chr4:108533890-108534110(+)$1	220	15	36	15.3393
AUCACCUGCACCAUGGAUGAA	chr18:50121928-50122148(+)$1	220	192	213	15.4448
acauccuuucacuuguguguc	chr6:55002073-55002293(+)$1	220	9	30	14.9472
gcuggugacaaggugccggau	chr15:102316285-102316505(+)$1	220	33	54	13.9304
UAAAGGAAUUCUGCUCUUUGG	chr11:11701562-11701784(-)$1	222	56	77	14.2311
GUGCAGCCAUCUUACUCCACA	chr8:46110132-46110352(+)$1	220	64	85	14.9439
CUGAGCAAGAAGAAGAAGGGC	chr15:25294483-25294729(-)$1	246	77	98	15.0368
UUCGAAUGUACUUCUUCAAAA	chr10:66688844-66689064(+)$1	220	33	54	15.7100
CUCACCUUAAGGAUGAUGAUG	chr11:77993344-77993564(+)$1	220	194	215	15.2364
CGCUGUAAGCACGGACAGCGG	chr3:88727663-88727883(-)$1	220	126	147	13.3396
UUAUUCCACCACUAGAAAGAA	chr10:93683407-93683627(+)$1	220	138	159	15.2250
GUCUGUGAAGGAAAACAGACU	chr9:53303836-53304073(-)$1	237	74	95	14.9155
GGUUUGGAAUUACAUAAGCCC	chr10:102855981-102856208(+)$1	227	146	167	15.5614
CCCUUGAGACGCAACAACAGC	chr2:129033881-129034102(+)$1	221	17	38	15.3661
AUGGUCGUCAUGAAGAGCGUG	chr12:88301263-88301483(+)$1	220	95	116	14.9439
AGGCACGGAGGAAAGGGCCGG	chr1:88148794-88149014(+)$1	220	76	97	14.6700
UUUGCCUAAGUGUUGACAAAG	chr8:87824944-87825165(+)$1	221	1	22	14.9472
GGUUUUUCUUUAUUAAUGCCA	chr9:56948882-56949102(+)$1	220	20	41	15.5916
GACAUGAUCCCUCCCAGGUCU	chr3:90161713-90161935(+)$1	222	160	181	15.5916
UCUUUGGGGAAAUACACAGAC	chr9:53198572-53198792(+)$1	220	188	209	15.3357
CUUCGAGUCCUUUAUUGUGGA	chr5:124358080-124358330(+)$1	250	121	142	15.5309
GAUAGCCAACAGCCGCAACCU	chr2:167924162-167924382(+)$1	220	136	157	15.3851
AAACGCAAACUGGAGCAGGAC	chr10:114848199-114848419(+)$1	220	157	178	14.3375
UUUCCUGUGGGACAAGGAGGG	chr9:106117183-106117468(+)$1	285	243	264	15.5614
UAGCACAGAUAACAGGACCUC	chr3:151883605-151883825(+)$1	220	68	89	15.1228
AUAACUUUUUCUCUGGUAUCU	chr12:112780379-112780599(+)$1	220	156	177	15.3663

#DB
.(((((........))).)))	chr1:137728407-137728635(+)$1	1	102	123	14.0071
(.((((........)))).))	chr18:31948725-31948945(+)$1	1	196	217	14.0927
((((((........)))))))	chr6:125072398-125072618(+)$1	1	29	50	15.0996
((..((........))..)))	chr3:88132081-88132301(+)$1	1	1	22	15.4161
.(((((........))))).)	chr14:59829305-59829532(+)$1	1	187	208	14.4081
(.((((........)))).))	chr3:95988862-95989082(+)$1	1	181	202	14.0927
((((((........)).))))	chr3:101243552-101243774(+)$1	1	195	216	14.2387
(((.((........)).))))	chr17:56743470-56743718(+)$1	1	139	160	15.5916
(..(((........)).)..)	chr11:78080547-78080767(+)$1	1	137	158	15.4762
..((((........))))..)	chr12:60173579-60173799(+)$1	1	151	172	13.9441
...(((........)))..))	chr17:56860685-56860905(+)$1	1	113	134	14.5451
((.(((........)))))))	chr2:180396288-180396522(-)$1	1	164	185	15.4478
.((..(........)..)).)	chr4:137112458-137112683(+)$1	1	97	118	13.9209
((.(((........))).)).	chr10:5892565-5892785(-)$1	1	16	37	14.3211
(.((((........))))...	chr10:66681683-66681903(+)$1	1	86	107	13.3084
(((.((........)))))))	chr16:17130594-17130814(-)$1	1	13	34	15.6127
((.(((........))).))(	chr5:88984102-88984341(+)$1	1	176	197	14.2880
((((((........)))))))	chr13:98016332-98016552(+)$1	1	99	120	15.0996
((((((........)))))))	chr8:47615715-47615935(+)$1	1	146	167	14.9155
((((((........)).))))	chr15:8100689-8100909(+)$1	1	141	162	15.5231
(..(((........))).)))	chr1:58454460-58454680(+)$1	1	43	64	15.2402
(.((((........)))))))	chr15:25926870-25927104(+)$1	1	191	212	12.9890
((.(((........)))))))	chr11:78068507-78068727(+)$1	1	125	146	15.4478
((((((........)))))))	chr9:61223263-61223483(+)$1	1	8	29	14.9155
((((((........)))))).	chr19:53715167-53715398(+)$1	1	127	148	13.4075
((..((........))..)))	chr11:79908594-79908814(+)$1	1	92	113	15.4161
...(((........)))....	chr4:146987712-146987932(-)$1	1	166	187	15.3505
((.(((........)))))))	chr5:135686644-135686864(+)$1	1	192	213	14.8744
(((.((........)).))))	chr8:46110154-46110414(+)$1	1	42	63	14.9439
(((..(........)..))))	chr5:37771556-37771776(+)$1	1	178	199	14.3440
((((((........))).)))	chr2:164664042-164664262(+)$1	1	107	128	15.2320
(.((((........).))).)	chr3:131270197-131270417(+)$1	1	178	199	15.3027
.(((((........))))).)	chr17:79240481-79240709(+)$1	1	189	210	14.4160
((..((........)))))))	chr13:24895143-24895380(+)$1	1	164	185	15.3495
((((((........)))))))	chr10:98485371-98485597(+)$1	1	89	110	14.9155
(..(((........)))..))	chr9:108846707-108846928(+)$1	1	78	99	15.3644
((((((........))))).)	chr7:148340483-148340712(+)$1	1	47	68	14.2816
((((.(........).)))))	chr10:62779353-62779574(+)$1	1	14	35	14.9472
.(((((........))))).)	chr9:21445398-21445618(+)$1	1	183	204	14.4160
(((.((........)))))))	chr9:110504622-110504842(+)$1	1	75	96	15.5331
((((((........)))))))	chr15:38969673-38969896(+)$1	1	17	38	14.9155
..((((........))))...	chr13:41104505-41104725(+)$1	1	14	35	14.1973
((.(((........))).)))	chr13:5864481-5864701(+)$1	1	173	194	15.0388
((((((........)).))))	chr4:108533890-108534110(+)$1	1	15	36	15.3393
.(((((........)).))))	chr18:50121928-50122148(+)$1	1	192	213	15.4448
((((.(........).)))))	chr6:55002073-55002293(+)$1	1	9	30	14.9472
.(((((........)))))..	chr15:102316285-102316505(+)$1	1	33	54	13.9304
.(((((........)))))))	chr11:11701562-11701784(-)$1	1	56	77	14.2311
(((.((........)).))))	chr8:46110132-46110352(+)$1	1	64	85	14.9439
((...(........)...)))	chr15:25294483-25294729(-)$1	1	77	98	15.0368
((.(((........)))...)	chr10:66688844-66689064(+)$1	1	33	54	15.7100
.(((.(........).))).)	chr11:77993344-77993564(+)$1	1	194	215	15.2364
((((((........))))))(	chr3:88727663-88727883(-)$1	1	126	147	13.3396
((.(((........)))..))	chr10:93683407-93683627(+)$1	1	138	159	15.2250
((((((........)))))))	chr9:53303836-53304073(-)$1	1	74	95	14.9155
((((((........)))))))	chr10:102855981-102856208(+)$1	1	146	167	15.5614
(..(((........)))..))	chr2:129033881-129034102(+)$1	1	17	38	15.3661
(((.((........)).))))	chr12:88301263-88301483(+)$1	1	95	116	14.9439
.(((.(........).)))..	chr1:88148794-88149014(+)$1	1	76	97	14.6700
((((.(........).)))))	chr8:87824944-87825165(+)$1	1	1	22	14.9472
(((.((........)).))))	chr9:56948882-56949102(+)$1	1	20	41	15.5916
(((.((........)).))))	chr3:90161713-90161935(+)$1	1	160	181	15.5916
(((.((........)).))))	chr9:53198572-53198792(+)$1	1	188	209	15.3357
((.(((........))).)))	chr5:124358080-124358330(+)$1	1	121	142	15.5309
((..((........))....)	chr2:167924162-167924382(+)$1	1	136	157	15.3851
....((........))....)	chr10:114848199-114848419(+)$1	1	157	178	14.3375
((((((........)))))))	chr9:106117183-106117468(+)$1	1	243	264	15.5614
..(..(........)..).))	chr3:151883605-151883825(+)$1	1	68	89	15.1228
(((.((........)))))))	chr12:112780379-112780599(+)$1	1	156	177	15.3663

#PSSM
e : 0.20	c : 0.14	g : 0.10	d : 0.10	! : 0.08	[ : 0.07	f : 0.07	i : 0.04	= : 0.04	b : 0.04	# : 0.02	" : 0.02	h : 0.01	$ : 0.01	
e : 0.24	c : 0.14	! : 0.10	g : 0.10	d : 0.10	[ : 0.07	b : 0.05	i : 0.04	f : 0.04	= : 0.02	h : 0.01	# : 0.01	" : 0.01	$ : 0.01	
e : 0.20	d : 0.14	[ : 0.13	! : 0.11	g : 0.10	c : 0.08	i : 0.04	b : 0.02	f : 0.02	" : 0.02	= : 0.02	h : 0.01	# : 0.01	$ : 0.01	a : 0.01	
c : 0.28	e : 0.14	[ : 0.14	! : 0.10	d : 0.08	g : 0.08	i : 0.02	f : 0.02	= : 0.02	h : 0.01	a : 0.01	" : 0.01	$ : 0.01	
b : 0.28	c : 0.24	d : 0.08	e : 0.08	g : 0.07	[ : 0.07	! : 0.04	i : 0.02	f : 0.02	= : 0.02	" : 0.01	
b : 0.28	c : 0.23	a : 0.14	d : 0.08	e : 0.08	g : 0.07	i : 0.02	f : 0.02	= : 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	
b : 0.28	c : 0.23	a : 0.14	d : 0.08	e : 0.08	g : 0.07	i : 0.02	f : 0.02	= : 0.02	
b : 0.28	c : 0.23	d : 0.08	e : 0.08	] : 0.08	g : 0.07	2 : 0.04	i : 0.02	f : 0.02	= : 0.02	3 : 0.01	
c : 0.28	] : 0.17	e : 0.14	d : 0.08	g : 0.08	2 : 0.07	i : 0.04	f : 0.02	= : 0.02	4 : 0.02	3 : 0.01	
e : 0.23	d : 0.15	] : 0.10	g : 0.10	2 : 0.08	c : 0.08	i : 0.04	4 : 0.04	a : 0.02	f : 0.02	3 : 0.02	= : 0.02	h : 0.01	b : 0.01	
e : 0.24	c : 0.13	g : 0.10	d : 0.10	2 : 0.08	b : 0.07	4 : 0.05	] : 0.04	i : 0.04	f : 0.04	= : 0.02	h : 0.01	> : 0.01	3 : 0.01	
e : 0.20	c : 0.11	g : 0.11	] : 0.10	d : 0.10	b : 0.07	2 : 0.05	f : 0.05	4 : 0.05	i : 0.04	= : 0.02	h : 0.01	> : 0.01	3 : 0.01	
e : 0.23	c : 0.18	g : 0.11	d : 0.11	b : 0.05	f : 0.05	i : 0.04	= : 0.04	h : 0.02	] : 0.02	4 : 0.02	2 : 0.02	a : 0.01	> : 0.01	

#score	1025.802338169837
#seq	69
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_UTR_m3_run1.txt

#BEAR
:GGGGGGG~~~~EEEEE}A	chr18:34930961-34931234(+)$1	273	236	255	7.1988
FFFFFYYBB}CCC}BB:::	chr15:79658142-79658416(-)$1	274	190	209	10.1441
DD}FFFFFF}CCC}EEEEE	chr2:34678076-34678352(-)$1	276	235	254	10.3739
EIIIIIIIIIYYBBEEEEE	chr2:152654266-152654557(-)$1	291	196	215	8.4522
FFFFFZZZBB?????A}DD	chr7:134911688-134911984(+)$1	296	265	284	8.3329
GGGGGGCCC}ADDDDDDDD	chr9:119147934-119148213(-)$1	279	237	256	7.5745
:CCC}CCCYYCCC}DDDDY	chr7:117008957-117009223(-)$1	266	169	188	8.4044
:FFFFFFZZZCCC}A}DDD	chr14:65431215-65431492(-)$1	277	203	222	9.6175
EEEEEYYA}DDDD}EEEEE	chr2:30882339-30882614(-)$1	275	247	266	10.7698
EEEEEYYEEEEEYYHHHHH	chr11:79506359-79506633(+)$1	274	246	265	7.8794
EEEEE}DDDDCCC}BBFFF	chr11:117828172-117828460(-)$1	288	218	237	9.2514
GGGGG}EEEEE}FFFFFF:	chr2:168780770-168781049(-)$1	279	258	277	7.7712
HHHHHYYEEEEEYYEEEEE	chr2:31615419-31615714(+)$1	295	255	274	10.7110
eeEEEEE}EEEEE}EEEEE	chr14:55505758-55506035(+)$1	277	170	189	8.3998
FFFFF?????EEEEEEEEE	chr12:114059359-114059639(-)$1	280	236	255	9.9358
FFFFF}CCC~~~~EEEEEY	chr15:81535417-81535702(-)$1	285	255	274	12.4764
CCCZZZCCC}CCC~~~~AY	chr1:184398225-184398498(-)$1	273	239	258	8.2889
}IIIIIIIII}BB}EEEEE	chr3:95464614-95464908(+)$1	294	255	274	8.8430
FFFF}DDDD}CCCYYAYYD	chr11:87794725-87795014(-)$1	289	265	284	10.3859
?DDDDYYDDDD}A}EEEEE	chr5:108863240-108863508(-)$1	268	243	262	8.5365
FFFFFF}AYYCCC}EEEEE	chr10:127827760-127828042(+)$1	282	131	150	12.6649
GGGGYYCCCYYEEEEEYYD	chr15:80761609-80761882(+)$1	273	227	246	10.2998
DGGGGGGGYYCCCEEEEEZ	chr8:86621057-86621344(-)$1	287	223	242	7.5485
ZZFFFFFF}DDDD}EEEEE	chr15:79655068-79655353(-)$1	285	142	161	8.7585
JJJJJJ~~~~CCC}FFFFF	chr15:81678793-81679086(-)$1	293	176	195	9.8969
FFFFFZZZEEEEE}A:::c	chr6:124863939-124864209(-)$1	270	229	248	8.0253
GGGGGG}CCCCCC}CCC::	chr19:5456434-5456714(-)$1	280	260	279	7.1258
}DDDD}CCCYYA}DDDD}C	chr17:34791800-34792094(+)$1	294	107	126	8.6230
EEEEE~~~~CCCYYDDDDY	chr4:135560418-135560706(-)$1	288	174	193	10.0892
EEEEE~~~~DDDD}EEEEE	chr5:37138907-37139205(-)$1	298	239	258	10.8180
HHHBBYYBB}CCCZZZDDD	chr2:32134292-32134577(-)$1	285	262	281	9.4068
EEEEE}BB}CCCBBYYBB}	chr10:116509619-116509901(-)$1	282	225	244	9.8738
JJJJJJCCC}CCCYYHHHH	chr19:24758574-24758848(-)$1	274	245	264	8.0746
DDD}EEEEE}CCC}EEEEE	chr16:37882822-37883102(+)$1	280	206	225	10.4992
EEEEE}BBZZZDDDD}EEE	chr11:32327052-32327325(+)$1	273	252	271	10.0010
FFFFYYCCC}BB}FFFFFF	chr15:79656085-79656364(-)$1	279	236	255	10.3841
JJJJYYCCCYYBB}EEEEE	chr8:74842841-74843113(+)$1	272	238	257	11.2448
FFFFF}DDDD}FFFFFF}C	chr15:81535368-81535654(-)$1	286	195	214	8.9067
C~~~~DDDD}CCCYYEEEE	chr2:157383278-157383551(-)$1	273	247	266	8.3947
EEEEE~~~~DDDD}BBYYD	chr1:62843167-62843435(+)$1	268	216	235	9.7908
GGGGGG}BB}CCCZZZDDD	chr7:25670028-25670303(+)$1	275	241	260	8.4427
IIIII}CCC~~~~EEEEE:	chr5:138223490-138223786(-)$1	296	159	178	10.9396
JJJJJ}CCCYYEEEEE}EE	chr2:157382615-157382901(-)$1	286	252	271	10.6179
FFFFF}CCC?????FFFFF	chr10:86297866-86298144(+)$1	278	242	261	9.3680
EEE~~~~BB}CCC}FFFFF	chr2:157383364-157383639(-)$1	275	220	239	10.0057
FFFFF}CCC}BB?????EE	chr7:107985018-107985335(+)$1	317	269	288	9.7794
FFFFFYYEEEEECCC::::	chr4:147320746-147321041(+)$1	295	222	241	8.1436
FFFFFF::CCCKKEEEEE{	chr5:138223116-138223399(-)$1	283	193	212	7.6443
FFFFFF~~~~FFFFFFYYD	chr8:11834139-11834413(+)$1	274	153	172	10.2844
IIIII______BB}FFFFF	chr3:133126987-133127268(-)$1	281	117	136	9.5346
FFFFFF~~~~BBEEEEE::	chr8:74844691-74844960(+)$1	269	228	247	10.7912
FFFFF}BBZZZBB}A}DDD	chr8:125096552-125096860(+)$1	308	219	238	11.1538
JJJJJJJ}A?????EEEEE	chr16:37882880-37883165(+)$1	285	218	237	7.7467
FFFFFFCCC~~~~FFFFFF	chr11:105142915-105143222(+)$1	307	242	261	10.7014
FFFFF}CCC}CCC}EEEEE	chr3:154259844-154260110(-)$1	266	142	161	12.9667
GGGGGGCCCBBYYDDDD}A	chr15:75900547-75900820(-)$1	273	86	105	7.5651
DDYYBBBBYYCCC}AZZZJ	chr19:8964904-8965185(+)$1	281	133	152	8.2719
FFFFF}CCCZZZDDDD:::	chr5:123809705-123809984(+)$1	279	192	211	8.6059
EEEEE}CCC}CCC}DDDD:	chr17:46305889-46306171(+)$1	282	130	149	10.2137
FFFFFFEEEEEKKFFFFFF	chr16:98170652-98170921(-)$1	269	30	49	7.9805
JJJJJZZZDDDDBBYYCCC	chr11:97574608-97574878(+)$1	270	200	219	7.6774
fFFFFFFEEEEEYYEEEEE	chr4:140884838-140885115(+)$1	277	207	226	10.1336
EEEEEYYDDDDDDDDYYDD	chr17:57032824-57033135(-)$1	311	239	258	8.6751
DDD}A}CCC}EEEEE}AYY	chr7:107985091-107985371(+)$1	280	168	187	9.6712
FFFFFYYDDDD}DDDDYYF	chr7:24891391-24891687(+)$1	296	142	161	9.6342
FFFFF}AZZZDDDDYYBBY	chr8:109599437-109599706(-)$1	269	186	205	10.1366

#otherMatches

#Seq PSSM
UUCCUUAAUAUAACAUUGG	chr18:34930961-34931234(+)$1	273	236	255	7.1988
GGAAGAUCUGCUCCCUAGU	chr15:79658142-79658416(-)$1	274	190	209	10.1441
GUGUAUGCACUUUACUACA	chr2:34678076-34678352(-)$1	276	235	254	10.3739
ugaguccuggcccugucac	chr2:152654266-152654557(-)$1	291	196	215	8.4522
UGUCAAGACAGGGGGCGCU	chr7:134911688-134911984(+)$1	296	265	284	8.3329
AGGUGGGACAGCUGGGAGC	chr9:119147934-119148213(-)$1	279	237	256	7.5745
ugcugcugcugcugcugcu	chr7:117008957-117009223(-)$1	266	169	188	8.4044
UCUUCUCUGUGUGACACUG	chr14:65431215-65431492(-)$1	277	203	222	9.6175
AGAACCUGCCCUGCAGAUG	chr2:30882339-30882614(-)$1	275	247	266	10.7698
ACAGCAAGGCCUGGAAGCU	chr11:79506359-79506633(+)$1	274	246	265	7.8794
UCGCAGAUCCCUUGCACCC	chr11:117828172-117828460(-)$1	288	218	237	9.2514
ACAUCCGUCCCCGCCUCAC	chr2:168780770-168781049(-)$1	279	258	277	7.7712
CUGCCCGCCCGUGCCCUGU	chr2:31615419-31615714(+)$1	295	255	274	10.7110
UGGGGGAUGUGGGAGGCUG	chr14:55505758-55506035(+)$1	277	170	189	8.3998
UUUCUAAAAUUAAGUUUUA	chr12:114059359-114059639(-)$1	280	236	255	9.9358
UGGGUAUGUACUUCCUGUC	chr15:81535417-81535702(-)$1	285	255	274	12.4764
GGAACAUUGACUUCAUCGG	chr1:184398225-184398498(-)$1	273	239	258	8.2889
GUAGCAACAUAGCAAAAAG	chr3:95464614-95464908(+)$1	294	255	274	8.8430
CUGGGGAAGAAGGCUGCUU	chr11:87794725-87795014(-)$1	289	265	284	10.3859
UUGCCCACCCUUGGGACUG	chr5:108863240-108863508(-)$1	268	243	262	8.5365
GAGGGGAGGAUGCACUGGG	chr10:127827760-127828042(+)$1	282	131	150	12.6649
GCCCAUUCCAACCCCUGAC	chr15:80761609-80761882(+)$1	273	227	246	10.2998
AGUCCUGCUUCCUGCGCUC	chr8:86621057-86621344(-)$1	287	223	242	7.5485
CUGGUCAGUUCUACCCUUG	chr15:79655068-79655353(-)$1	285	142	161	8.7585
AGAGGAGCCCGGGAGCGGG	chr15:81678793-81679086(-)$1	293	176	195	9.8969
CCCCAGCCAGCCCUCACUU	chr6:124863939-124864209(-)$1	270	229	248	8.0253
ACUGCAGAGCUAGGGCUGA	chr19:5456434-5456714(-)$1	280	260	279	7.1258
UAGGUCCCCAGGUGGGACA	chr17:34791800-34792094(+)$1	294	107	126	8.6230
AGAGGAACGGUAUUGUGCU	chr4:135560418-135560706(-)$1	288	174	193	10.0892
UUACAGUGAACAGUGUUUC	chr5:37138907-37139205(-)$1	298	239	258	10.8180
CUACUAGCCCGUCACACCU	chr2:32134292-32134577(-)$1	285	262	281	9.4068
AGUGAAGAAAGGCCACUCA	chr10:116509619-116509901(-)$1	282	225	244	9.8738
gggaggagagagagagaga	chr19:24758574-24758848(-)$1	274	245	264	8.0746
UCUGGUCGUACCACUGGCA	chr16:37882822-37883102(+)$1	280	206	225	10.4992
GCUGUACAGUUAAGACAAU	chr11:32327052-32327325(+)$1	273	252	271	10.0010
CUUCAGCUCUCUGGGUCAC	chr15:79656085-79656364(-)$1	279	236	255	10.3841
GUAGCAAGGUACCAGGCUA	chr8:74842841-74843113(+)$1	272	238	257	11.2448
GGUGUGUGUGUGUGGGUAU	chr15:81535368-81535654(-)$1	286	195	214	8.9067
GUCUCAAUGUCACCUCCAU	chr2:157383278-157383551(-)$1	273	247	266	8.3947
CCCCAUCCCAAGCCACCCA	chr1:62843167-62843435(+)$1	268	216	235	9.7908
CCCCAAUGUGUCAUUAAUC	chr7:25670028-25670303(+)$1	275	241	260	8.4427
CUUGCUGCUCCUGAGGACC	chr5:138223490-138223786(-)$1	296	159	178	10.9396
UGAAGAAGCUUUAUUGAAU	chr2:157382615-157382901(-)$1	286	252	271	10.6179
GCGAGCGCUUGCGCUCUGG	chr10:86297866-86298144(+)$1	278	242	261	9.3680
CUUAUGGUUGUGUGUUCUG	chr2:157383364-157383639(-)$1	275	220	239	10.0057
CUCAGACCUGCCAAACAGC	chr7:107985018-107985335(+)$1	317	269	288	9.7794
CCUCCACUUCCCCCAUUUC	chr4:147320746-147321041(+)$1	295	222	241	8.1436
GGUGGGAGGGAGCUGGGUU	chr5:138223116-138223399(-)$1	283	193	212	7.6443
AGAGGCCGUUUGUGCUCUC	chr8:11834139-11834413(+)$1	274	153	172	10.2844
AGUGUGGUUUGAGAGGAUG	chr3:133126987-133127268(-)$1	281	117	136	9.5346
AGCCGGACAAGUGUGGCCA	chr8:74844691-74844960(+)$1	269	228	247	10.7912
AGGUAUGGUCAAGACCCAA	chr8:125096552-125096860(+)$1	308	219	238	11.1538
GCUAUGCUCUCUCCCUCAC	chr16:37882880-37883165(+)$1	285	218	237	7.7467
UCCUUCACCCCUUUUUUAU	chr11:105142915-105143222(+)$1	307	242	261	10.7014
GCCGGUGGAAGGCGCAGAG	chr3:154259844-154260110(-)$1	266	142	161	12.9667
GCACUUGCCCCUUCCUUCC	chr15:75900547-75900820(-)$1	273	86	105	7.5651
GUCAACAGCACUGAGAAAG	chr19:8964904-8965185(+)$1	281	133	152	8.2719
AGUAUAGUCAACCGAGAUC	chr5:123809705-123809984(+)$1	279	192	211	8.6059
CUGACCCAGUUUGUGCCUC	chr17:46305889-46306171(+)$1	282	130	149	10.2137
ACCUCACAGCUUUCUGGAC	chr16:98170652-98170921(-)$1	269	30	49	7.9805
UCUUUCAUGCCUGCCUGCC	chr11:97574608-97574878(+)$1	270	200	219	7.6774
CAGGGCUGGAGACAGAGGA	chr4:140884838-140885115(+)$1	277	207	226	10.1336
GGAGGCCUGGCCUCCCAGC	chr17:57032824-57033135(-)$1	311	239	258	8.6751
CUGGCACUUCCUUCAGAGA	chr7:107985091-107985371(+)$1	280	168	187	9.6712
GUUUGAGUUCUGGCCUGGU	chr7:24891391-24891687(+)$1	296	142	161	9.6342
UGUCCUGACCUGCACUGUG	chr8:109599437-109599706(-)$1	269	186	205	10.1366

#DB
.)))))))....))))).)	chr18:34930961-34931234(+)$1	1	236	255	7.1988
)))))..)).))).))...	chr15:79658142-79658416(-)$1	1	190	209	10.1441
)).)))))).))).)))))	chr2:34678076-34678352(-)$1	1	235	254	10.3739
))))))))))..))(((((	chr2:152654266-152654557(-)$1	1	196	215	8.4522
)))))...)).....).))	chr7:134911688-134911984(+)$1	1	265	284	8.3329
))))))))).)))))))))	chr9:119147934-119148213(-)$1	1	237	256	7.5745
.))).)))..))).)))).	chr7:117008957-117009223(-)$1	1	169	188	8.4044
.))))))...))).).)))	chr14:65431215-65431492(-)$1	1	203	222	9.6175
)))))..).)))).)))))	chr2:30882339-30882614(-)$1	1	247	266	10.7698
)))))..)))))..)))))	chr11:79506359-79506633(+)$1	1	246	265	7.8794
))))).))))))).)))))	chr11:117828172-117828460(-)$1	1	218	237	9.2514
))))).))))).)))))).	chr2:168780770-168781049(-)$1	1	258	277	7.7712
)))))..)))))..)))))	chr2:31615419-31615714(+)$1	1	255	274	10.7110
))))))).))))).)))))	chr14:55505758-55506035(+)$1	1	170	189	8.3998
))))).....)))))))))	chr12:114059359-114059639(-)$1	1	236	255	9.9358
))))).)))....))))).	chr15:81535417-81535702(-)$1	1	255	274	12.4764
)))...))).)))....).	chr1:184398225-184398498(-)$1	1	239	258	8.2889
.))))))))).)).)))))	chr3:95464614-95464908(+)$1	1	255	274	8.8430
)))).)))).)))..)..)	chr11:87794725-87795014(-)$1	1	265	284	10.3859
.))))..)))).).)))))	chr5:108863240-108863508(-)$1	1	243	262	8.5365
)))))).)..))).)))))	chr10:127827760-127828042(+)$1	1	131	150	12.6649
))))..)))..)))))..)	chr15:80761609-80761882(+)$1	1	227	246	10.2998
))))))))..)))))))).	chr8:86621057-86621344(-)$1	1	223	242	7.5485
..)))))).)))).)))))	chr15:79655068-79655353(-)$1	1	142	161	8.7585
))))))....))).)))))	chr15:81678793-81679086(-)$1	1	176	195	9.8969
)))))...))))).)...(	chr6:124863939-124864209(-)$1	1	229	248	8.0253
)))))).)))))).)))..	chr19:5456434-5456714(-)$1	1	260	279	7.1258
.)))).)))..).)))).)	chr17:34791800-34792094(+)$1	1	107	126	8.6230
)))))....)))..)))).	chr4:135560418-135560706(-)$1	1	174	193	10.0892
)))))....)))).)))))	chr5:37138907-37139205(-)$1	1	239	258	10.8180
)))))..)).)))...)))	chr2:32134292-32134577(-)$1	1	262	281	9.4068
))))).)).)))))..)).	chr10:116509619-116509901(-)$1	1	225	244	9.8738
))))))))).)))..))))	chr19:24758574-24758848(-)$1	1	245	264	8.0746
))).))))).))).)))))	chr16:37882822-37883102(+)$1	1	206	225	10.4992
))))).))...)))).)))	chr11:32327052-32327325(+)$1	1	252	271	10.0010
))))..))).)).))))))	chr15:79656085-79656364(-)$1	1	236	255	10.3841
))))..)))..)).)))))	chr8:74842841-74843113(+)$1	1	238	257	11.2448
))))).)))).)))))).)	chr15:81535368-81535654(-)$1	1	195	214	8.9067
)....)))).)))..))))	chr2:157383278-157383551(-)$1	1	247	266	8.3947
)))))....)))).))..)	chr1:62843167-62843435(+)$1	1	216	235	9.7908
)))))).)).)))...)))	chr7:25670028-25670303(+)$1	1	241	260	8.4427
))))).)))....))))).	chr5:138223490-138223786(-)$1	1	159	178	10.9396
))))).)))..))))).))	chr2:157382615-157382901(-)$1	1	252	271	10.6179
))))).))).....)))))	chr10:86297866-86298144(+)$1	1	242	261	9.3680
)))....)).))).)))))	chr2:157383364-157383639(-)$1	1	220	239	10.0057
))))).))).)).....))	chr7:107985018-107985335(+)$1	1	269	288	9.7794
)))))..))))))))....	chr4:147320746-147321041(+)$1	1	222	241	8.1436
))))))..(((..(((((.	chr5:138223116-138223399(-)$1	1	193	212	7.6443
))))))....))))))..)	chr8:11834139-11834413(+)$1	1	153	172	10.2844
)))))......)).)))))	chr3:133126987-133127268(-)$1	1	117	136	9.5346
))))))....)))))))..	chr8:74844691-74844960(+)$1	1	228	247	10.7912
))))).))...)).).)))	chr8:125096552-125096860(+)$1	1	219	238	11.1538
))))))).).....)))))	chr16:37882880-37883165(+)$1	1	218	237	7.7467
)))))))))....))))))	chr11:105142915-105143222(+)$1	1	242	261	10.7014
))))).))).))).)))))	chr3:154259844-154260110(-)$1	1	142	161	12.9667
)))))))))))..)))).)	chr15:75900547-75900820(-)$1	1	86	105	7.5651
))..))))..))).)...)	chr19:8964904-8965185(+)$1	1	133	152	8.2719
))))).)))...))))...	chr5:123809705-123809984(+)$1	1	192	211	8.6059
))))).))).))).)))).	chr17:46305889-46306171(+)$1	1	130	149	10.2137
(((((((((((..((((((	chr16:98170652-98170921(-)$1	1	30	49	7.9805
)))))...))))))..)))	chr11:97574608-97574878(+)$1	1	200	219	7.6774
))))))))))))..)))))	chr4:140884838-140885115(+)$1	1	207	226	10.1336
)))))..))))))))..))	chr17:57032824-57033135(-)$1	1	239	258	8.6751
))).).))).))))).)..	chr7:107985091-107985371(+)$1	1	168	187	9.6712
)))))..)))).))))..)	chr7:24891391-24891687(+)$1	1	142	161	9.6342
))))).)...))))..)).	chr8:109599437-109599706(-)$1	1	186	205	10.1366

#PSSM
F : 0.33	E : 0.18	G : 0.09	J : 0.09	D : 0.07	: : 0.04	H : 0.03	C : 0.03	} : 0.03	I : 0.03	e : 0.01	? : 0.01	Z : 0.01	f : 0.01	
F : 0.36	E : 0.16	G : 0.12	D : 0.09	J : 0.09	I : 0.06	C : 0.03	H : 0.03	e : 0.01	Z : 0.01	~ : 0.01	
F : 0.37	E : 0.18	G : 0.12	J : 0.09	I : 0.06	D : 0.06	C : 0.03	H : 0.03	} : 0.01	~ : 0.01	Y : 0.01	
F : 0.39	E : 0.16	G : 0.12	J : 0.09	I : 0.06	D : 0.03	} : 0.03	~ : 0.03	C : 0.01	H : 0.01	Z : 0.01	B : 0.01	Y : 0.01	
F : 0.36	E : 0.18	G : 0.10	J : 0.07	I : 0.06	Y : 0.04	} : 0.03	D : 0.03	B : 0.03	~ : 0.03	H : 0.01	Z : 0.01	A : 0.01	
} : 0.25	Y : 0.18	F : 0.15	G : 0.09	Z : 0.06	~ : 0.06	J : 0.04	I : 0.03	E : 0.03	D : 0.03	C : 0.01	? : 0.01	_ : 0.01	B : 0.01	
C : 0.28	Y : 0.13	~ : 0.10	F : 0.06	D : 0.06	E : 0.06	B : 0.06	Z : 0.04	} : 0.04	G : 0.03	I : 0.03	? : 0.01	: : 0.01	_ : 0.01	J : 0.01	A : 0.01	
C : 0.30	B : 0.12	E : 0.10	D : 0.10	~ : 0.09	Z : 0.07	G : 0.03	F : 0.03	I : 0.03	A : 0.03	} : 0.03	? : 0.01	: : 0.01	_ : 0.01	
C : 0.30	E : 0.13	D : 0.12	~ : 0.10	B : 0.07	Y : 0.06	Z : 0.06	} : 0.04	I : 0.03	F : 0.01	? : 0.01	_ : 0.01	A : 0.01	
} : 0.24	D : 0.15	Y : 0.12	E : 0.12	~ : 0.10	Z : 0.07	C : 0.06	? : 0.04	I : 0.03	B : 0.03	_ : 0.01	
C : 0.34	E : 0.15	D : 0.13	Y : 0.07	~ : 0.06	B : 0.06	? : 0.04	Z : 0.04	} : 0.03	A : 0.01	F : 0.01	_ : 0.01	
C : 0.33	E : 0.15	D : 0.13	B : 0.10	~ : 0.06	? : 0.04	} : 0.04	Y : 0.03	F : 0.03	K : 0.03	A : 0.01	Z : 0.01	
C : 0.31	D : 0.15	E : 0.12	B : 0.10	Y : 0.07	? : 0.06	F : 0.04	~ : 0.04	} : 0.03	K : 0.03	A : 0.01	
} : 0.36	E : 0.15	D : 0.12	Y : 0.10	F : 0.09	? : 0.06	B : 0.04	Z : 0.03	~ : 0.01	C : 0.01	
E : 0.37	D : 0.15	F : 0.15	Y : 0.09	A : 0.06	B : 0.04	? : 0.03	C : 0.03	Z : 0.03	H : 0.01	~ : 0.01	
E : 0.37	F : 0.15	D : 0.12	} : 0.06	Y : 0.06	B : 0.04	Z : 0.04	A : 0.03	H : 0.03	: : 0.03	~ : 0.01	C : 0.01	? : 0.01	
E : 0.36	D : 0.15	F : 0.15	Y : 0.09	: : 0.06	} : 0.03	H : 0.03	C : 0.03	B : 0.03	~ : 0.01	? : 0.01	Z : 0.01	A : 0.01	
E : 0.36	D : 0.15	F : 0.13	: : 0.09	Y : 0.09	} : 0.06	H : 0.03	B : 0.03	A : 0.01	Z : 0.01	C : 0.01	
E : 0.30	D : 0.16	F : 0.13	: : 0.12	Y : 0.09	C : 0.04	A : 0.03	H : 0.03	Z : 0.01	c : 0.01	} : 0.01	{ : 0.01	J : 0.01	

#score	620.4620801193298
#seq	66
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_UTR_m3_run2.txt

#BEAR
d[bb[ddddnnnnndddd]bb]	chr14:51544803-51545017(+)$1	214	86	108	12.0453
:ccc!!cccnnnnnccc22ccc	chr10:90628594-90628877(-)$1	283	159	181	12.6825
ee[a[ddddnnnnndddda]ee	chr1:59277133-59277369(-)$1	236	107	129	12.6055
eeee"""bbnnnnnbb4444ee	chr3:126513483-126513692(+)$1	209	126	148	12.0376
fbb!!ddddnnnnndddd22bb	chr4:133147339-133147558(+)$1	219	127	149	11.7983
ffffffcccnnnnncccfffff	chr7:123683863-123684081(+)$1	218	108	130	11.7202
iiiii!!bbnnnnnbb]iiiii	chr11:97256958-97257170(+)$1	212	78	100	12.2387
!!cccddddnnnnndddd]ccc	chr6:8209348-8209567(+)$1	219	59	81	12.9246
fffff!!bbnnnnnbb]fffff	chr10:90628678-90628893(-)$1	215	68	90	11.4584
eeeee[cccnnnnnccc]eeee	chr4:24430084-24430302(+)$1	218	77	99	12.4550
gggggg[bbnnnnnbb]ggggg	chr12:3309444-3309672(-)$1	228	184	206	12.0283
d####ddddnnnnndddddddd	chr2:30159706-30159934(+)$1	228	10	32	12.0770
hhhh[ddddnnnnndddd]hhh	chr16:18407810-18408016(-)$1	206	29	51	11.8289
ee"""ddddnnnnndddd22ee	chr2:102654178-102654399(-)$1	221	8	30	12.5660
fffff[cccnnnnncccfffff	chr19:5364892-5365109(-)$1	217	72	94	12.0881
:eeeee[bbnnnnnbb]eeeee	chr10:17775715-17775924(+)$1	209	77	99	10.5289
:ccc!!cccnnnnnccc22ccc	chr13:23830591-23830813(+)$1	222	81	103	12.6825
dddd[ddddnnnnndddddddd	chr15:76024292-76024505(-)$1	213	120	142	12.0771
dccc[ddddnnnnndddd]ccc	chr16:94605403-94605628(+)$1	225	100	122	13.1638
""ddddcccnnnnnccc22ddd	chr14:21513632-21513841(+)$1	209	162	184	12.2879
:eeeeecccnnnnnccc4444e	chr10:39332927-39333145(-)$1	218	125	147	11.4864
b!!ccc[bbnnnnnbb333ccc	chr1:75387531-75387752(+)$1	221	157	179	12.4449
ddd"""cccnnnnnccc]dddd	chrX:17739675-17739892(+)$1	217	149	171	12.5419
ddddeeeeennnnneeeee]dd	chr12:107043083-107043314(+)$1	231	103	125	10.7631
c[bb[ddddnnnnnddddbbcc	chr9:80094143-80094367(+)$1	224	187	209	11.9388
ccc!!ddddnnnnndddd]ccc	chr16:45802818-45803039(-)$1	221	138	160	13.3288
dddd[a[bbnnnnnbb]a]ddd	chr10:76180452-76180677(-)$1	225	163	185	11.8811
ffff[ddddnnnnnddddffff	chr7:120469352-120469562(-)$1	210	87	109	12.2999
cc!!eeeeennnnneeeeeccc	chr14:63761736-63761945(+)$1	209	69	91	11.5366
ggggg[cccnnnnnccc]gggg	chr9:123500068-123500289(+)$1	221	96	118	13.0971
ccc!!ddddnnnnndddd]ccc	chr19:5476054-5476264(+)$1	210	49	71	13.3288
ccc[eeeeennnnneeeee]cc	chr2:155984838-155985047(-)$1	209	85	107	11.4718
cc[ffffffnnnnnffffff]c	chr6:115568835-115569058(-)$1	223	14	36	10.5260
[dddd[cccnnnnnccc]dddd	chr5:124203769-124203985(+)$1	216	4	26	12.1812
eeeee[cccnnnnnccc]eeee	chr9:44627530-44627762(-)$1	232	180	202	12.4550
e!!bb[cccnnnnnccc]bbee	chr15:79517708-79517922(-)$1	214	177	199	11.7958
ggggggg[annnnna]gggggg	chr13:59596838-59597067(-)$1	229	136	158	11.6901
#ccc[bb[annnnna]bb22cc	chr19:5897814-5898021(-)$1	207	66	88	10.7462
cdddd!!bbnnnnnbb]dddd4	chr13:37985730-37985950(+)$1	220	89	111	11.4332
ddd!!ddddnnnnndddd22dd	chr5:96559984-96560193(-)$1	209	152	174	12.5655
b"""eeeeennnnneeeee333	chr15:55441016-55441227(+)$1	211	136	158	10.9839
=:gggggggnnnnnggggggg:	chr6:140582120-140582341(+)$1	221	28	50	9.7341
ff[ccccccnnnnnccc333cc	chr12:85196345-85196566(-)$1	221	54	76	13.1395
ffff[ddddnnnnndddd]fff	chr8:108167353-108167563(+)$1	210	15	37	12.6604
b[bb[ddddnnnnndddd]bb3	chr14:120674941-120675164(+)$1	223	100	122	11.9810
ffff!!cccnnnnnccc22fff	chr17:51164396-51164626(-)$1	230	201	223	12.9752
ccdddd[bbnnnnnbb]dddd]	chr7:111613521-111613743(-)$1	222	76	98	11.3962
iiiiii[bbnnnnnbb]iiiii	chr4:144745085-144745297(-)$1	212	134	156	12.0099
eeee"""bbnnnnnbb333eee	chr8:109848450-109848702(+)$1	252	24	46	12.2489
ffff!!cccnnnnnccc22fff	chr2:165708722-165708945(-)$1	223	16	38	12.9752
""ccc[cccnnnnnccc]cccf	chr16:48993980-48994193(-)$1	213	171	193	12.8505
ggggg[cccnnnnnccc]gggg	chr11:108333246-108333502(+)$1	256	170	192	13.0971
b[gggggggnnnnngggggggb	chr16:45094365-45094590(+)$1	225	96	118	11.4206

#otherMatches

#Seq PSSM
AGCGCAGUAAACACUGCUUCGG	chr14:51544803-51545017(+)$1	214	86	108	12.0453
AGAUAUGGAGUGAAUCCUGGUC	chr10:90628594-90628877(-)$1	283	159	181	12.6825
GUGAUGGAGUACUCCUCCUGAC	chr1:59277133-59277369(-)$1	236	107	129	12.6055
GCUUGAGGCAAAGAGUGGGAAA	chr3:126513483-126513692(+)$1	209	126	148	12.0376
AAGCCCCAGGAGGACUGGCUCU	chr4:133147339-133147558(+)$1	219	127	149	11.7983
UGUCUGCCAGAACUUGGAAGAA	chr7:123683863-123684081(+)$1	218	108	130	11.7202
GGAACUUGUGUUGUGCUGUUCU	chr11:97256958-97257170(+)$1	212	78	100	12.2387
UGGAGCGGCCGAACGUCGACUU	chr6:8209348-8209567(+)$1	219	59	81	12.9246
UUUGUUUGCAGAAAGCCACAAA	chr10:90628678-90628893(-)$1	215	68	90	11.4584
UGGUCGAUGAGCUCCGUGGAUU	chr4:24430084-24430302(+)$1	218	77	99	12.4550
GAGUUGGUUGUAGUGAGCAGUU	chr12:3309444-3309672(-)$1	228	184	206	12.0283
AAUUUCAUGUCACUCAUGUUCA	chr2:30159706-30159934(+)$1	228	10	32	12.0770
GGACGGCUUGGAGAAGGCAGUC	chr16:18407810-18408016(-)$1	206	29	51	11.8289
GUGCAUUUGGUGAACAAGGAAC	chr2:102654178-102654399(-)$1	221	8	30	12.5660
GAGAAUGGUGUGAUGCCUUCUU	chr19:5364892-5365109(-)$1	217	72	94	12.0881
GCCGAGCAGAAAUACUACUCGG	chr10:17775715-17775924(+)$1	209	77	99	10.5289
UCUAUCGGCGUACUGCCACUAG	chr13:23830591-23830813(+)$1	222	81	103	12.6825
GUGCCUGCCGACAUGGCAGCAC	chr15:76024292-76024505(-)$1	213	120	142	12.0771
UCACUGUCUCCUUAGGACUGUG	chr16:94605403-94605628(+)$1	225	100	122	13.1638
CUCAGCUUCCACCAGAAACGUU	chr14:21513632-21513841(+)$1	209	162	184	12.2879
AGUGGAUGCUGUAUGCAAAUCU	chr10:39332927-39333145(-)$1	218	125	147	11.4864
CACCCCAAGGUGAGCUACAGGG	chr1:75387531-75387752(+)$1	221	157	179	12.4449
AGCUCCCGCUCCUCGCGCGCUC	chrX:17739675-17739892(+)$1	217	149	171	12.5419
UGGAUCUUACAGACUAGGAGUC	chr12:107043083-107043314(+)$1	231	103	125	10.7631
GAGAAGCUUCACUUGAGCUCCC	chr9:80094143-80094367(+)$1	224	187	209	11.9388
GAAGACGCCCGGAUGGUGAUUC	chr16:45802818-45803039(-)$1	221	138	160	13.3288
UCCUGAGACCCACAGUGUGAGG	chr10:76180452-76180677(-)$1	225	163	185	11.8811
GAGUUAUCAAAUGAUGGUGCUC	chr7:120469352-120469562(-)$1	210	87	109	12.2999
GUAUGGCUUAAAACAAGCUACA	chr14:63761736-63761945(+)$1	209	69	91	11.5366
CAAAAGUACCUCCUGUGGUUUU	chr9:123500068-123500289(+)$1	221	96	118	13.0971
GGUGAGAUGAAAUGCAUCAACC	chr19:5476054-5476264(+)$1	210	49	71	13.3288
UGUGCCAAAAAGGCUUUGGAAC	chr2:155984838-155985047(-)$1	209	85	107	11.4718
UUGUAGGGCAAGUGGCCUUGGA	chr6:115568835-115569058(-)$1	223	14	36	10.5260
CUUUAUUUCCCAAAGAACUAAG	chr5:124203769-124203985(+)$1	216	4	26	12.1812
AGCAGUCCUCCUUCAGGCCUGC	chr9:44627530-44627762(-)$1	232	180	202	12.4550
AUUGAGGCCUAGUUGGCAUCUG	chr15:79517708-79517922(-)$1	214	177	199	11.7958
AUUAGAAAGUAAGCCAUUUUAA	chr13:59596838-59597067(-)$1	229	136	158	11.6901
AACCUGUCCUCCCUGUGCUUGG	chr19:5897814-5898021(-)$1	207	66	88	10.7462
UCCAGGACCAAAUCGGAUUGGC	chr13:37985730-37985950(+)$1	220	89	111	11.4332
AUCAAAUAAAAAACUUAUGGGA	chr5:96559984-96560193(-)$1	209	152	174	12.5655
CUUUGCUGGGUUUACUGGCCUU	chr15:55441016-55441227(+)$1	211	136	158	10.9839
UAUAAGAUCGUAAUGGUUUUGG	chr6:140582120-140582341(+)$1	221	28	50	9.7341
aacaauuguauaagacauuuau	chr12:85196345-85196566(-)$1	221	54	76	13.1395
UAUGUGAAUUUGCUGUUUUCAU	chr8:108167353-108167563(+)$1	210	15	37	12.6604
AUGCGGUGGAGAAGCCACGGCC	chr14:120674941-120675164(+)$1	223	100	122	11.9810
UGUUCAGUUAUUCAAAUAAAAC	chr17:51164396-51164626(-)$1	230	201	223	12.9752
GGCUGAAUCAUCAAGACUUAGA	chr7:111613521-111613743(-)$1	222	76	98	11.3962
UUUUGAAAGUGUGUUUGUCAGA	chr4:144745085-144745297(-)$1	212	134	156	12.0099
ACAUACUCAUUUCUUGUACAUG	chr8:109848450-109848702(+)$1	252	24	46	12.2489
AAAAAAAAAAAAAAUUUCCUUU	chr2:165708722-165708945(-)$1	223	16	38	12.9752
CUCCGUGCCGCGCGGGCUCGGU	chr16:48993980-48994193(-)$1	213	171	193	12.8505
AGUAUUUAUUUUAUAUGCAUAU	chr11:108333246-108333502(+)$1	256	170	192	13.0971
CACCUAGGAAACUGUCCUGGGG	chr16:45094365-45094590(+)$1	225	96	118	11.4206

#DB
(.((.((((.....)))).)).	chr14:51544803-51545017(+)$1	1	86	108	12.0453
.(((..(((.....)))..)))	chr10:90628594-90628877(-)$1	1	159	181	12.6825
((.(.((((.....))))).))	chr1:59277133-59277369(-)$1	1	107	129	12.6055
((((...((.....))....))	chr3:126513483-126513692(+)$1	1	126	148	12.0376
(((..((((.....))))..))	chr4:133147339-133147558(+)$1	1	127	149	11.7983
))))))(((.....)))(((((	chr7:123683863-123684081(+)$1	1	108	130	11.7202
(((((..((.....)).)))))	chr11:97256958-97257170(+)$1	1	78	100	12.2387
..(((((((.....)))).)))	chr6:8209348-8209567(+)$1	1	59	81	12.9246
(((((..((.....)).)))))	chr10:90628678-90628893(-)$1	1	68	90	11.4584
(((((.(((.....))).))))	chr4:24430084-24430302(+)$1	1	77	99	12.4550
((((((.((.....)).)))))	chr12:3309444-3309672(-)$1	1	184	206	12.0283
(....((((.....))))))))	chr2:30159706-30159934(+)$1	1	10	32	12.0770
((((.((((.....)))).)))	chr16:18407810-18408016(-)$1	1	29	51	11.8289
((...((((.....))))..))	chr2:102654178-102654399(-)$1	1	8	30	12.5660
(((((.(((.....))))))))	chr19:5364892-5365109(-)$1	1	72	94	12.0881
.(((((.((.....)).)))))	chr10:17775715-17775924(+)$1	1	77	99	10.5289
.(((..(((.....)))..)))	chr13:23830591-23830813(+)$1	1	81	103	12.6825
((((.((((.....))))))))	chr15:76024292-76024505(-)$1	1	120	142	12.0771
((((.((((.....)))).)))	chr16:94605403-94605628(+)$1	1	100	122	13.1638
..(((((((.....)))..)))	chr14:21513632-21513841(+)$1	1	162	184	12.2879
.((((((((.....)))....)	chr10:39332927-39333145(-)$1	1	125	147	11.4864
(..(((.((.....))...)))	chr1:75387531-75387752(+)$1	1	157	179	12.4449
(((...(((.....))).))))	chrX:17739675-17739892(+)$1	1	149	171	12.5419
(((((((((.....))))).))	chr12:107043083-107043314(+)$1	1	103	125	10.7631
(.((.((((.....))))))))	chr9:80094143-80094367(+)$1	1	187	209	11.9388
(((..((((.....)))).)))	chr16:45802818-45803039(-)$1	1	138	160	13.3288
((((.(.((.....)).).)))	chr10:76180452-76180677(-)$1	1	163	185	11.8811
((((.((((.....))))))))	chr7:120469352-120469562(-)$1	1	87	109	12.2999
((..(((((.....))))))))	chr14:63761736-63761945(+)$1	1	69	91	11.5366
(((((.(((.....))).))))	chr9:123500068-123500289(+)$1	1	96	118	13.0971
(((..((((.....)))).)))	chr19:5476054-5476264(+)$1	1	49	71	13.3288
(((.(((((.....))))).))	chr2:155984838-155985047(-)$1	1	85	107	11.4718
((.((((((.....)))))).)	chr6:115568835-115569058(-)$1	1	14	36	10.5260
.((((.(((.....))).))))	chr5:124203769-124203985(+)$1	1	4	26	12.1812
(((((.(((.....))).))))	chr9:44627530-44627762(-)$1	1	180	202	12.4550
(..((.(((.....))).))))	chr15:79517708-79517922(-)$1	1	177	199	11.7958
(((((((.(.....).))))))	chr13:59596838-59597067(-)$1	1	136	158	11.6901
.(((.((.(.....).))..))	chr19:5897814-5898021(-)$1	1	66	88	10.7462
(((((..((.....)).)))).	chr13:37985730-37985950(+)$1	1	89	111	11.4332
(((..((((.....))))..))	chr5:96559984-96560193(-)$1	1	152	174	12.5655
(...(((((.....)))))...	chr15:55441016-55441227(+)$1	1	136	158	10.9839
).(((((((.....))))))).	chr6:140582120-140582341(+)$1	1	28	50	9.7341
((.((((((.....)))...))	chr12:85196345-85196566(-)$1	1	54	76	13.1395
((((.((((.....)))).)))	chr8:108167353-108167563(+)$1	1	15	37	12.6604
(.((.((((.....)))).)).	chr14:120674941-120675164(+)$1	1	100	122	11.9810
((((..(((.....)))..)))	chr17:51164396-51164626(-)$1	1	201	223	12.9752
((((((.((.....)).)))).	chr7:111613521-111613743(-)$1	1	76	98	11.3962
((((((.((.....)).)))))	chr4:144745085-144745297(-)$1	1	134	156	12.0099
((((...((.....))...)))	chr8:109848450-109848702(+)$1	1	24	46	12.2489
((((..(((.....)))..)))	chr2:165708722-165708945(-)$1	1	16	38	12.9752
..(((.(((.....))).))))	chr16:48993980-48994193(-)$1	1	171	193	12.8505
(((((.(((.....))).))))	chr11:108333246-108333502(+)$1	1	170	192	13.0971
(.(((((((.....))))))))	chr16:45094365-45094590(+)$1	1	96	118	11.4206

#PSSM
f : 0.16	d : 0.15	c : 0.15	e : 0.13	: : 0.07	g : 0.07	b : 0.07	i : 0.03	" : 0.03	! : 0.01	h : 0.01	[ : 0.01	# : 0.01	= : 0.01	
c : 0.18	e : 0.15	f : 0.15	d : 0.13	[ : 0.07	g : 0.07	! : 0.05	" : 0.05	i : 0.03	b : 0.01	# : 0.01	h : 0.01	: : 0.01	
c : 0.16	d : 0.16	f : 0.13	e : 0.11	g : 0.11	b : 0.07	[ : 0.05	! : 0.05	i : 0.03	" : 0.03	# : 0.01	h : 0.01	
c : 0.15	f : 0.15	d : 0.13	e : 0.11	g : 0.11	! : 0.09	b : 0.07	" : 0.05	i : 0.03	a : 0.01	# : 0.01	h : 0.01	[ : 0.01	
[ : 0.20	! : 0.15	e : 0.15	g : 0.11	" : 0.07	f : 0.07	c : 0.07	d : 0.07	i : 0.03	# : 0.01	b : 0.01	
d : 0.33	[ : 0.15	! : 0.13	e : 0.11	g : 0.07	" : 0.05	f : 0.03	c : 0.03	a : 0.01	b : 0.01	i : 0.01	
c : 0.32	d : 0.30	[ : 0.11	e : 0.07	! : 0.05	g : 0.05	" : 0.03	f : 0.01	b : 0.01	
c : 0.32	d : 0.30	b : 0.20	e : 0.07	[ : 0.03	g : 0.03	f : 0.01	
c : 0.32	d : 0.30	b : 0.20	e : 0.07	a : 0.03	g : 0.03	f : 0.01	
n : 0.99	
n : 0.99	
n : 0.99	
n : 0.99	
n : 0.99	
c : 0.32	d : 0.30	b : 0.20	e : 0.07	a : 0.03	g : 0.03	f : 0.01	
c : 0.32	d : 0.30	b : 0.20	e : 0.07	] : 0.03	g : 0.03	f : 0.01	
c : 0.32	d : 0.30	] : 0.15	e : 0.07	g : 0.05	3 : 0.03	4 : 0.01	f : 0.01	b : 0.01	
d : 0.33	] : 0.15	2 : 0.09	e : 0.09	f : 0.07	g : 0.07	3 : 0.05	4 : 0.03	i : 0.03	a : 0.01	b : 0.01	
] : 0.16	2 : 0.16	e : 0.13	g : 0.11	d : 0.11	f : 0.09	3 : 0.05	4 : 0.03	i : 0.03	b : 0.03	a : 0.01	c : 0.01	
c : 0.16	f : 0.15	d : 0.15	g : 0.11	b : 0.07	2 : 0.07	e : 0.07	] : 0.05	4 : 0.03	i : 0.03	3 : 0.03	h : 0.01	
c : 0.24	d : 0.18	e : 0.15	f : 0.13	g : 0.11	b : 0.05	i : 0.03	h : 0.01	4 : 0.01	] : 0.01	3 : 0.01	
c : 0.24	e : 0.16	f : 0.15	d : 0.15	g : 0.07	] : 0.03	b : 0.03	i : 0.03	3 : 0.03	h : 0.01	4 : 0.01	: : 0.01	

#score	640.2817167661472
#seq	53
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_UTR_m2_run1.txt

#BEAR
++ggggggg$$$$$ccclllccc4444ggggggg]eeee	chr1:87746789-87747024(+)$1	235	181	220	11.4427
[hhhhhhhh"""ddddoooooodddd]hhhhhhhh4444	chr3:57646018-57646264(-)$1	246	103	142	10.6796
[ccciiiiiiiii!!bbnnnnnbb]iiiiiiiii]ccc]	chr4:8073081-8073325(-)$1	244	184	223	15.6402
ggg::::==========nnnnn==========ggggggg	chr7:67133472-67133731(-)$1	259	31	70	12.2940
:ggggggg####eeeeennnnneeeee22ggggggg:FF	chr2:70439477-70439769(+)$1	292	57	96	11.1473
d"""iiiiiiiii[ddddmmmmddddiiiiiiiiidddd	chr11:77345323-77345558(-)$1	235	70	109	12.6256
gg::ccc!!==========mmmm==========4444cc	chr16:17046775-17047017(+)$1	242	200	239	11.4379
[bb[ccc==========oooooo==========22ccc]	chr15:82121507-82121747(+)$1	240	38	77	15.6535
::===============mmmm===============:dd	chr18:82753463-82753764(+)$1	301	18	57	12.1577
eeeee!!bb[gggggggnnnnnggggggg]bb22eeeee	chr1:75243514-75243753(-)$1	239	65	104	12.4523
ddeeeee[a[eeeee[annnnna]eeeee]a22eeeee]	chr15:37298249-37298509(-)$1	260	107	146	12.1006
!!iiiiiiiii$$$$$ccc"""dddd===========^^	chr3:31101926-31102161(-)$1	235	24	63	10.9213
========"""a[ddddnnnnndddd]a==========2	chr17:37210548-37210814(+)$1	266	48	87	15.6917
b"""dddd[ccc!!cccooooooccc]cccdddd]bbaf	chrX:35552112-35552349(-)$1	237	42	81	11.7512
eeeee!!ccc[dddd[ammmma]dddd]ccc333eeeee	chr19:58870931-58871176(-)$1	245	3	42	10.9664
[bb!!eeeee####cccrrrrrrrrrccc4444eeeee2	chrX:50945835-50946079(-)$1	244	64	103	10.3337
::cccccc[a[ffffffnnnnnffffff]a]ccc]cccd	chr15:76910056-76910325(-)$1	269	156	195	10.5781
[iiiiiiiiieeeee[bbmmmmbb]eeeee333iiiiii	chrX:102318827-102319101(+)$1	274	113	152	11.7630
eee!!===========ppppppp===========333ee	chr1:66487120-66487367(+)$1	247	104	143	12.1498
cc####ddddccc[cccnnnnnccc333ccc]ddddccc	chr11:105789566-105789820(+)$1	254	108	147	12.7941
:a[bb[============mmmm============22bb]	chr4:150435600-150435837(-)$1	237	55	94	12.7980
fffff!!ccc####cccooooooccccccffffffffff	chr7:6659323-6659572(-)$1	249	32	71	12.6757
iiiiiiiii$$$$$cccnnnnnccc333iiiiiiiiiGG	chr11:16182584-16182855(+)$1	271	84	123	14.3100
gggg[ccc!!ccc[ddddlllddddccc]ccc]gggggg	chr5:17771193-17771449(-)$1	256	135	174	12.2995
$$eeeeebb[gggggggnnnnnggggggg333bb22eee	chr2:115688855-115689106(-)$1	251	33	72	11.9895
eeee[a[ccc[ddddbbnnnnnbb333dddd]ccca]ee	chr2:148521935-148522196(-)$1	261	59	98	11.9049
ggggggggggg"""eeeeellleeeee4444gggggggd	chr11:90139073-90139323(+)$1	250	48	87	12.2295
e!!gggggggeeeee[aooooooa]eeeee]ggggggg2	chr2:73450531-73450829(-)$1	298	92	131	13.5058
eee[eeeee!!ffffffnnnnnffffff22eeeee]eee	chr4:15210855-15211098(+)$1	243	4	43	10.9921
[bb!!eeeee"""ddddllldddd333eeeeebb22ccc	chr6:115226410-115226651(+)$1	241	172	211	10.3425
ff[iiiiiiiii[ddddnnnnnddddiiiiiiiiiffff	chr13:97408234-97408484(+)$1	250	87	126	14.8123
cc"""===========ppppppp===========]cccc	chr12:109151060-109151322(-)$1	262	34	73	12.1287
ee[ccc[eeeee[ddddllldddd]eeeee]ccceeeee	chr3:103546005-103546268(-)$1	263	195	234	10.6934
feeeeeggggggg[cccooooooccc]gggggggFFFFF	chr4:65276427-65276671(+)$1	244	111	150	11.8828
hh]ccc===========nnnnn===========:::ddd	chr9:79618792-79619037(-)$1	245	31	70	12.5690
bb$$$$$==========nnnnn==========4444bb7	chr6:30403189-30403426(+)$1	237	110	149	13.9893
!!ccc[ggggggg####===========[eeeeeeeeee	chr15:90764099-90764382(-)$1	283	84	123	10.4669
FFFF=============mmmm=============::ddd	chr5:113672263-113672498(-)$1	235	132	171	10.8837
dddd"""ffffff[cccnnnnnccc22ffffff22dddd	chr3:80648540-80648847(-)$1	307	129	168	11.6011
eeee[ccca[ccc[cccmmmmccc]ccc333a]ccceee	chr17:87535638-87535876(+)$1	238	85	124	11.7141
ggggggg####eeeeeooooooeeeee22gggggggccc	chr8:98238456-98238694(+)$1	238	3	42	13.0975
iiiiiiiii!!ffffff[ammmma]ffffffiiiiiiii	chr6:47974257-47974517(-)$1	260	93	132	11.1497
iiiiiiiiiccc[cccrrrrrrrrrccc]ccc]iiiiii	chr6:67237489-67237732(+)$1	243	134	173	12.0702
ffffff"""bb[bbcccnnnnnccc]bb]bb333fffff	chr3:22112044-22112297(+)$1	253	177	216	11.4701
eeee!!eeeee"""bboooooobbeeeeeeeeee]dddd	chr6:115226082-115226321(+)$1	239	87	126	11.3785
gg####ffffff!!cccnnnnnccc]ffffffggggggg	chr1:66487173-66487420(+)$1	247	94	133	13.4639
dd[ddddccc!!eeeeeooooooeeeee22ccc]dddd]	chr12:109152528-109152775(-)$1	247	107	146	11.3075
ffffff!!ccc[eeeeennnnneeeeecccfffffffff	chr4:6321939-6322229(+)$1	290	44	83	11.7600
[ccc[dddd"""ddddoooooodddddddd]ccc]bb22	chr1:99718162-99718399(-)$1	237	84	123	11.0199
ggggggg"""bb[cccooooooccc]bbggggggg:eee	chr5:136384198-136384458(-)$1	260	51	90	12.3335
ggggg"""eeeee[ddddmmmmdddd]eeeee333gggg	chr5:125940134-125940374(+)$1	240	92	131	11.4253
ffffffggggggg[cccooooooccc]ggggggg4444f	chr2:134420897-134421154(-)$1	257	84	123	13.8988
ccccccggggggg!!ccclllccc]ggggggg333ccc]	chr7:6658952-6659214(-)$1	262	127	166	13.9116
===####eeeee[ddddnnnnnddddeeeee]=======	chr11:100888528-100888792(+)$1	264	214	253	13.6045
=========[gggggggooooooggggggg22=======	chr17:85462769-85463009(-)$1	240	37	76	15.0643
###hhhhhhhh"""cccooooooccc22hhhhhhhh444	chr15:92170923-92171174(+)$1	251	42	81	11.1150
d[ccc[ffffffbb[ccclllccc]bb]ffffff]ccc]	chr10:52158705-52158968(+)$1	263	171	210	10.1133
==========a[eeeeellleeeee]a]==========:	chr1:179379339-179379646(+)$1	307	184	223	12.7522
e[dddd!!eeeee!!bbnnnnnbb22eeeee333dddd]	chr1:166367605-166367872(-)$1	267	132	171	11.7718
ccc[ccc[bb[a"""bbnnnnnbb333a]bb22cccccc	chr5:136385166-136385427(-)$1	261	216	255	12.5772
dffffff[cccaeeeeennnnneeeee]a]cccffffff	chr10:107935762-107936048(-)$1	286	174	213	11.6155
dd[a####ggggggg[bbmmmmbbggggggg4444a333	chr6:125170615-125170893(+)$1	278	168	207	11.3760

#otherMatches

#Seq PSSM
GUAGCCGAGUAACUGAAUAAUUCUAACUUUGGCUUCUCU	chr1:87746789-87747024(+)$1	235	181	220	11.4427
UUGCAUUAUUGUGGACUUGGCUGUCUUGUGAUGUAUUUU	chr3:57646018-57646264(-)$1	246	103	142	10.6796
ACUUUUGCACAUACUGCUUGUUGCUUAUGUGUAGAAAGA	chr4:8073081-8073325(-)$1	244	184	223	15.6402
AUAUACUGUUUGAAAAUGGUUGAUUUUUAAGCCAUGGAU	chr7:67133472-67133731(-)$1	259	31	70	12.2940
CAAAUAUAUACCAUGUUAAAGAGACAUCUUGUAUUUUCU	chr2:70439477-70439769(+)$1	292	57	96	11.1473
UAUGUAAAUUAUGCAGGUGAUAACUUUAUGGUUUGGGAC	chr11:77345323-77345558(-)$1	235	70	109	12.6256
UACAAGUUUUUUUAAAGCAUUUGUGCUUUAAAAUUGUGC	chr16:17046775-17047017(+)$1	242	200	239	11.4379
guguguguguaugcauguguguguauguaugcguguACU	chr15:82121507-82121747(+)$1	240	38	77	15.6535
UCCUGUCUUUUCUUUUUCCCAGGGAGGAAGAGACAGCCG	chr18:82753463-82753764(+)$1	301	18	57	12.1577
ACAUUUCUAGAAAAGUAAAAUCUACUUUUGUAUCAGUGU	chr1:75243514-75243753(-)$1	239	65	104	12.4523
GCCCACGUGCUUGUGGAGAGCAUGCACAGACUUCGUGGU	chr15:37298249-37298509(-)$1	260	107	146	12.1006
UUAACGAGUAUAACUUGCAUUUGCAGAUGGUGAUUUCUG	chr3:31101926-31102161(-)$1	235	24	63	10.9213
UGUGCUUGGGUAGGCGUGCAUGAUGUGUUGAGCACACCA	chr17:37210548-37210814(+)$1	266	48	87	15.6917
UAUGAUAGCACCUUGGUUGAAUCACCUGGUCUAUAGGCU	chrX:35552112-35552349(-)$1	237	42	81	11.7512
UACUCCAUGGGCCAAGGUUUCCGUUGGGUCGAAUGAGUG	chr19:58870931-58871176(-)$1	245	3	42	10.9664
AGGCCUGUGCUGACGCUGCCAUUUCAAGCCCCUGCACAA	chrX:50945835-50946079(-)$1	244	64	103	10.3337
GUGCUUGUUGGGCAGCCCGUUUGGCUGCGUUAUAUAGCG	chr15:76910056-76910325(-)$1	269	156	195	10.5781
UGUACUUUGUGCUGUGAGCAUUUUGAUAGUGUUAUAAAG	chrX:102318827-102319101(+)$1	274	113	152	11.7630
UGUUCUUUUGCUUGCUCGGGAUUGGUGGGUGGAAUAUGC	chr1:66487120-66487367(+)$1	247	104	143	12.1498
AGCACUUGAUGGCUGGAUUUUUUCCUUUGCUAAUCACUA	chr11:105789566-105789820(+)$1	254	108	147	12.7941
AUGGCAAGAUGAAAUUAUUUGUAUAGUUUUGUCUGAGCG	chr4:150435600-150435837(-)$1	237	55	94	12.7980
GCUGUGUGGAAACAGGCAUUUUAGCUUCUACAGCCAUUU	chr7:6659323-6659572(-)$1	249	32	71	12.6757
UAUAGGCAAACCUGGCAAAUUCUGUAAAUUGCUUAUAGU	chr11:16182584-16182855(+)$1	271	84	123	14.3100
AGCGUGUGGAGAACUGUAAACUACAUUCACACCUGUUUA	chr5:17771193-17771449(-)$1	256	135	174	12.2995
UGUUUCAUGUUAGAUAUUCUAUGUGUUUACCUCAAUUGA	chr2:115688855-115689106(-)$1	251	33	72	11.9895
UAUGAGCUCUGAUGUCCUAUUUGGUUUACAUAAGACGUA	chr2:148521935-148522196(-)$1	261	59	98	11.9049
UGGCGAAUUGUAUUUGCCACUUUGGUGCCCAACGGUUCA	chr11:90139073-90139323(+)$1	250	48	87	12.2295
GCUUCCCAGAGUAAACUGUCAUGACUUUGCUUUUGGGGU	chr2:73450531-73450829(-)$1	298	92	131	13.5058
GUAUAGAGUUCGCAAUGGCUCUUGUUGUAUGCUCUUUGC	chr4:15210855-15211098(+)$1	243	4	43	10.9921
UGUUAAGUUGUAAAGUUUCUGGCUGUUCGAUUACCUCUG	chr6:115226410-115226651(+)$1	241	172	211	10.3425
GAUGUAUUUAUGUAAAUCAGGCAUUUCGUAGAUGCUUUG	chr13:97408234-97408484(+)$1	250	87	126	14.8123
AAAAUGAGAAGAAAAAAAAGUCCUUUUUCUUUUCCUUGA	chr12:109151060-109151322(-)$1	262	34	73	12.1287
CUUGCUACCUGGCUUCUGUGAGAGUUCAGGAAGCAGGCG	chr3:103546005-103546268(-)$1	263	195	234	10.6934
CCCUUGUGUUUGAAAUUUGUAUUGGUAUUGAAUAGUCAU	chr4:65276427-65276671(+)$1	244	111	150	11.8828
AUGUCAUUUUGAAGUUGGCACAUAACUUUAAAAAAACAA	chr9:79618792-79619037(-)$1	245	31	70	12.5690
GGUCUGUUCCUCAGUUUGCUAGGAGCUGAGGGUUUCCCA	chr6:30403189-30403426(+)$1	237	110	149	13.9893
UUUCAGUUGUUCUUCAUUCUGUGCUCAGGAUUGAAAUGC	chr15:90764099-90764382(-)$1	283	84	123	10.4669
GGCAUGGGCGGGAGGGGGGUAUUCCUCCUGCCCAAGGCG	chr5:113672263-113672498(-)$1	235	132	171	10.8837
CUGUAAAGUCUGUGCACCGACUGUGAGAUAGAUAGAUAG	chr3:80648540-80648847(-)$1	307	129	168	11.6011
ACAGUAGCCAAAUCCAUUCCUGUGUGUUGCCGUGCUCUG	chr17:87535638-87535876(+)$1	238	85	124	11.7141
GUUCAGUUCACUCACGUGCUUCCGUGAAUACUGAAUGUG	chr8:98238456-98238694(+)$1	238	3	42	13.0975
UUCCCCAGGGCCCCAGGGGGGAGUGCUUGGGCCUGGGGA	chr6:47974257-47974517(-)$1	260	93	132	11.1497
AUGGAGCUCUUAGUAAUUCAGUAAUUUAGUAAUGAGUUC	chr6:67237489-67237732(+)$1	243	134	173	12.0702
GACGUGCCAUGAUGCUGCUCCACAGACACCACACCAUGU	chr3:22112044-22112297(+)$1	253	177	216	11.4701
GUGUAUUACAUCCAGGUGCUUUUCAUGUGACAUUUGUGA	chr6:115226082-115226321(+)$1	239	87	126	11.3785
AUAAAUGUGAAAAAGCUGUCUGGGUGUUUUAUGUCUCUG	chr1:66487173-66487420(+)$1	247	94	133	13.4639
UCUGCCCUUUGCUGUAGAUUUGGCUGCAUAAAAUGGGCC	chr12:109152528-109152775(-)$1	247	107	146	11.3075
UAAGCCAUUGUGAUUAGGAUGACUGGUAUAGGCUUAGCU	chr4:6321939-6322229(+)$1	290	44	83	11.7600
UGUAAAGUUCUGUGCAUUUGAUUGUAAACUGUACUCGUC	chr1:99718162-99718399(-)$1	237	84	123	11.0199
UCCGUGUUUCGCUAAGGAAUUAUUUCGCACACGGACCAU	chr5:136384198-136384458(-)$1	260	51	90	12.3335
CGGAUUUCAAGCUUAUGCUGUUGUGUCAGUUUCCUGUCU	chr5:125940134-125940374(+)$1	240	92	131	11.4253
GAGAAUGGAGCUUUUGCUGGUGUGUACAGGUUUUCUGUG	chr2:134420897-134421154(-)$1	257	84	123	13.8988
CACCUGUGUGGUGUUGUAUUGUGCUUGCCACAAGUCAGU	chr7:6658952-6659214(-)$1	262	127	166	13.9116
UAGCCCAGAGCAGUCGCACAGCGUGGUGUUUCCUAGAUC	chr11:100888528-100888792(+)$1	264	214	253	13.6045
UUUUUAAAAAGAAUAUUGACAUAAAUGUUUGAUUUUAAG	chr17:85462769-85463009(-)$1	240	37	76	15.0643
AGUAUCAGAAUCUCUGAAUGUUCUCAUUGUUCUGGUUUU	chr15:92170923-92171174(+)$1	251	42	81	11.1150
UUUGGCAACUUGUAAAUAAUGUGUAUACCAAGUUUUUAU	chr10:52158705-52158968(+)$1	263	171	210	10.1133
GGGGUGUCAAAGAACUUGACAGGUUGUGUUGAUGCUCUU	chr1:179379339-179379646(+)$1	307	184	223	12.7522
GAUGGGUUGUGUUGUGCUCCGUGCUGAAUGCUGUCUCGC	chr1:166367605-166367872(-)$1	267	132	171	11.7718
GUGUGCCAGCACCCCCUAACCGAGACCGCGCAAGGCCGC	chr5:136385166-136385427(-)$1	261	216	255	12.5772
GAGGUAGACAGCCACUUCAGGAAGGUGAGCCUGCUACCU	chr10:107935762-107936048(-)$1	286	174	213	11.6155
GGCGUACUUUCUGGUUGUAAAAACACCAGGACACUCUUA	chr6:125170615-125170893(+)$1	278	168	207	11.3760

#DB
..(((((((.....(((...)))....))))))).))))	chr1:87746789-87747024(+)$1	1	181	220	11.4427
.((((((((...((((......)))).))))))))....	chr3:57646018-57646264(-)$1	1	103	142	10.6796
.((((((((((((..((.....)).))))))))).))).	chr4:8073081-8073325(-)$1	1	184	223	15.6402
)))....((((((((((.....))))))))))(((((((	chr7:67133472-67133731(-)$1	1	31	70	12.2940
.(((((((....(((((.....)))))..))))))).))	chr2:70439477-70439769(+)$1	1	57	96	11.1473
(...(((((((((.((((....)))))))))))))))))	chr11:77345323-77345558(-)$1	1	70	109	12.6256
))..(((..((((((((((....))))))))))....))	chr16:17046775-17047017(+)$1	1	200	239	11.4379
.((.(((((((((((((......))))))))))..))).	chr15:82121507-82121747(+)$1	1	38	77	15.6535
..(((((((((((((((....))))))))))))))).((	chr18:82753463-82753764(+)$1	1	18	57	12.1577
(((((..((.(((((((.....))))))).))..)))))	chr1:75243514-75243753(-)$1	1	65	104	12.4523
(((((((.(.(((((.(.....).))))).)..))))).	chr15:37298249-37298509(-)$1	1	107	146	12.1006
..(((((((((.....(((...(((((((((((((((..	chr3:31101926-31102161(-)$1	1	24	63	10.9213
((((((((...(.((((.....)))).))))))))))).	chr17:37210548-37210814(+)$1	1	48	87	15.6917
(...((((.(((..(((......))).))))))).))))	chrX:35552112-35552349(-)$1	1	42	81	11.7512
(((((..(((.((((.(....).)))).)))...)))))	chr19:58870931-58871176(-)$1	1	3	42	10.9664
.((..(((((....(((.........)))....))))).	chrX:50945835-50946079(-)$1	1	64	103	10.3337
..((((((.(.((((((.....)))))).).))).)))(	chr15:76910056-76910325(-)$1	1	156	195	10.5781
.((((((((((((((.((....)).)))))...))))))	chrX:102318827-102319101(+)$1	1	113	152	11.7630
(((..(((((((((((.......)))))))))))...))	chr1:66487120-66487367(+)$1	1	104	143	12.1498
((....(((((((.(((.....)))...))).)))))))	chr11:105789566-105789820(+)$1	1	108	147	12.7941
.(.((.((((((((((((....))))))))))))..)).	chr4:150435600-150435837(-)$1	1	55	94	12.7980
(((((..(((....(((......))))))))))))((((	chr7:6659323-6659572(-)$1	1	32	71	12.6757
(((((((((.....(((.....)))...)))))))))))	chr11:16182584-16182855(+)$1	1	84	123	14.3100
((((.(((..(((.((((...))))))).))).))))))	chr5:17771193-17771449(-)$1	1	135	174	12.2995
..(((((((.(((((((.....)))))))...))..)))	chr2:115688855-115689106(-)$1	1	33	72	11.9895
((((.(.(((.((((((.....))...)))).)))).))	chr2:148521935-148522196(-)$1	1	59	98	11.9049
))))(((((((...(((((...)))))....)))))))(	chr11:90139073-90139323(+)$1	1	48	87	12.2295
(..((((((((((((.(......).))))).))))))).	chr2:73450531-73450829(-)$1	1	92	131	13.5058
(((.(((((..((((((.....))))))..))))).)))	chr4:15210855-15211098(+)$1	1	4	43	10.9921
.((..(((((...((((...))))...)))))))..)))	chr6:115226410-115226651(+)$1	1	172	211	10.3425
((.(((((((((.((((.....)))))))))))))))))	chr13:97408234-97408484(+)$1	1	87	126	14.8123
((...(((((((((((.......))))))))))).))))	chr12:109151060-109151322(-)$1	1	34	73	12.1287
((.(((.(((((.((((...)))).))))).))))))))	chr3:103546005-103546268(-)$1	1	195	234	10.6934
))))))(((((((.(((......))).))))))))))))	chr4:65276427-65276671(+)$1	1	111	150	11.8828
)).)))(((((((((((.....)))))))))))...(((	chr9:79618792-79619037(-)$1	1	31	70	12.5690
((.....((((((((((.....))))))))))....)).	chr6:30403189-30403426(+)$1	1	110	149	13.9893
..(((.(((((((....(((((((((((.((((((((((	chr15:90764099-90764382(-)$1	1	84	123	10.4669
(((((((((((((((((....)))))))))))))..(((	chr5:113672263-113672498(-)$1	1	132	171	10.8837
((((...((((((.(((.....)))..))))))..))))	chr3:80648540-80648847(-)$1	1	129	168	11.6011
((((.((((.(((.(((....))).)))...).))))))	chr17:87535638-87535876(+)$1	1	85	124	11.7141
(((((((....(((((......)))))..)))))))(((	chr8:98238456-98238694(+)$1	1	3	42	13.0975
(((((((((..((((((.(....).))))))))))))))	chr6:47974257-47974517(-)$1	1	93	132	11.1497
((((((((((((.(((.........))).))).))))))	chr6:67237489-67237732(+)$1	1	134	173	12.0702
((((((...((.(((((.....))).)).))...)))))	chr3:22112044-22112297(+)$1	1	177	216	11.4701
((((..(((((...((......)))))))))))).))))	chr6:115226082-115226321(+)$1	1	87	126	11.3785
((....((((((..(((.....))).)))))))))))))	chr1:66487173-66487420(+)$1	1	94	133	13.4639
((.(((((((..(((((......)))))..))).)))).	chr12:109152528-109152775(-)$1	1	107	146	11.3075
((((((..(((.(((((.....))))))))))))))(((	chr4:6321939-6322229(+)$1	1	44	83	11.7600
.(((.((((...((((......)))))))).))).))..	chr1:99718162-99718399(-)$1	1	84	123	11.0199
(((((((...((.(((......))).))))))))).(((	chr5:136384198-136384458(-)$1	1	51	90	12.3335
(((((...(((((.((((....)))).)))))...))))	chr5:125940134-125940374(+)$1	1	92	131	11.4253
(((((((((((((.(((......))).)))))))....)	chr2:134420897-134421154(-)$1	1	84	123	13.8988
(((((((((((((..(((...))).)))))))...))).	chr7:6658952-6659214(-)$1	1	127	166	13.9116
(((....(((((.((((.....))))))))).)))))))	chr11:100888528-100888792(+)$1	1	214	253	13.6045
(((((((((.(((((((......)))))))..)))))))	chr17:85462769-85463009(-)$1	1	37	76	15.0643
...((((((((...(((......)))..))))))))...	chr15:92170923-92171174(+)$1	1	42	81	11.1150
(.(((.((((((((.(((...))).)).)))))).))).	chr10:52158705-52158968(+)$1	1	171	210	10.1133
(((((((((((.(((((...))))).).)))))))))).	chr1:179379339-179379646(+)$1	1	184	223	12.7522
(.((((..(((((..((.....))..)))))...)))).	chr1:166367605-166367872(-)$1	1	132	171	11.7718
(((.(((.((.(...((.....))...).))..))))))	chr5:136385166-136385427(-)$1	1	216	255	12.5772
)((((((.(((((((((.....))))).).)))))))))	chr10:107935762-107936048(-)$1	1	174	213	11.6155
((.(....(((((((.((....)))))))))....)...	chr6:125170615-125170893(+)$1	1	168	207	11.3760

#PSSM
e : 0.16	g : 0.12	[ : 0.11	d : 0.11	f : 0.09	: : 0.06	= : 0.06	c : 0.06	i : 0.04	! : 0.03	b : 0.03	+ : 0.01	$ : 0.01	h : 0.01	F : 0.01	# : 0.01	
g : 0.14	e : 0.14	c : 0.09	f : 0.09	b : 0.06	d : 0.06	= : 0.06	i : 0.06	! : 0.04	h : 0.03	" : 0.03	: : 0.03	[ : 0.03	+ : 0.01	a : 0.01	$ : 0.01	F : 0.01	# : 0.01	
e : 0.16	g : 0.12	c : 0.11	= : 0.08	i : 0.08	[ : 0.08	f : 0.08	" : 0.04	b : 0.04	# : 0.04	d : 0.03	h : 0.01	: : 0.01	! : 0.01	] : 0.01	$ : 0.01	F : 0.01	
g : 0.12	c : 0.12	e : 0.12	i : 0.09	f : 0.08	= : 0.06	" : 0.04	[ : 0.04	! : 0.04	# : 0.04	d : 0.04	h : 0.03	: : 0.03	b : 0.01	$ : 0.01	F : 0.01	a : 0.01	
c : 0.14	i : 0.12	g : 0.11	e : 0.09	= : 0.08	f : 0.08	! : 0.06	# : 0.06	[ : 0.06	d : 0.04	h : 0.03	" : 0.03	: : 0.01	b : 0.01	$ : 0.01	
c : 0.14	i : 0.12	= : 0.11	g : 0.09	e : 0.09	! : 0.06	d : 0.06	# : 0.06	f : 0.06	[ : 0.04	h : 0.03	" : 0.03	: : 0.01	a : 0.01	$ : 0.01	
g : 0.16	= : 0.14	i : 0.12	c : 0.09	e : 0.09	! : 0.08	d : 0.06	" : 0.04	f : 0.04	h : 0.03	[ : 0.03	# : 0.03	: : 0.01	$ : 0.01	
= : 0.19	g : 0.12	i : 0.12	c : 0.11	e : 0.09	! : 0.04	[ : 0.04	d : 0.04	f : 0.04	" : 0.04	h : 0.03	b : 0.03	# : 0.03	
= : 0.17	g : 0.12	i : 0.12	e : 0.12	c : 0.09	b : 0.04	" : 0.04	f : 0.04	h : 0.03	# : 0.03	! : 0.03	a : 0.03	[ : 0.03	d : 0.03	
= : 0.17	c : 0.12	e : 0.11	g : 0.11	i : 0.08	[ : 0.08	" : 0.06	! : 0.04	f : 0.04	$ : 0.03	# : 0.03	b : 0.03	a : 0.01	d : 0.01	h : 0.01	
= : 0.16	g : 0.14	e : 0.12	c : 0.11	" : 0.06	i : 0.06	# : 0.06	[ : 0.06	! : 0.04	f : 0.04	$ : 0.03	b : 0.03	h : 0.01	a : 0.01	
= : 0.16	g : 0.12	e : 0.12	" : 0.09	f : 0.09	c : 0.08	$ : 0.04	i : 0.04	# : 0.04	a : 0.04	[ : 0.04	d : 0.03	! : 0.01	b : 0.01	
e : 0.17	= : 0.16	g : 0.12	[ : 0.09	" : 0.08	d : 0.06	f : 0.06	$ : 0.04	c : 0.04	i : 0.03	! : 0.03	# : 0.03	b : 0.03	
= : 0.16	d : 0.14	e : 0.14	[ : 0.12	! : 0.08	g : 0.06	" : 0.06	$ : 0.04	# : 0.04	f : 0.04	c : 0.03	b : 0.03	
c : 0.24	d : 0.19	= : 0.16	e : 0.16	g : 0.06	! : 0.04	f : 0.04	$ : 0.01	# : 0.01	b : 0.01	[ : 0.01	" : 0.01	
c : 0.27	d : 0.16	= : 0.16	e : 0.11	b : 0.08	[ : 0.08	g : 0.04	f : 0.04	$ : 0.01	# : 0.01	
c : 0.25	= : 0.12	d : 0.12	b : 0.09	e : 0.09	o : 0.08	g : 0.04	a : 0.04	f : 0.04	p : 0.03	# : 0.01	r : 0.01	
n : 0.37	o : 0.22	l : 0.06	m : 0.06	d : 0.04	= : 0.04	c : 0.04	r : 0.03	b : 0.03	p : 0.03	e : 0.01	[ : 0.01	
n : 0.37	o : 0.22	m : 0.14	l : 0.11	= : 0.03	r : 0.03	p : 0.03	c : 0.01	e : 0.01	a : 0.01	
n : 0.37	o : 0.22	m : 0.17	l : 0.12	r : 0.03	p : 0.03	" : 0.01	= : 0.01	
n : 0.37	o : 0.22	m : 0.17	l : 0.06	r : 0.03	p : 0.03	d : 0.03	c : 0.01	" : 0.01	= : 0.01	e : 0.01	
n : 0.37	o : 0.22	m : 0.11	c : 0.06	= : 0.04	d : 0.04	r : 0.03	p : 0.03	" : 0.01	a : 0.01	l : 0.01	e : 0.01	
d : 0.17	c : 0.16	o : 0.14	b : 0.11	= : 0.11	e : 0.09	m : 0.03	g : 0.03	r : 0.03	f : 0.03	p : 0.03	a : 0.01	] : 0.01	
c : 0.22	d : 0.19	= : 0.17	b : 0.11	e : 0.11	g : 0.04	r : 0.03	f : 0.03	a : 0.03	4 : 0.01	] : 0.01	
= : 0.17	c : 0.17	d : 0.16	e : 0.14	] : 0.12	g : 0.06	3 : 0.04	r : 0.03	f : 0.03	4 : 0.01	2 : 0.01	
= : 0.17	e : 0.17	d : 0.14	c : 0.12	g : 0.08	3 : 0.08	] : 0.06	f : 0.04	2 : 0.03	4 : 0.01	i : 0.01	r : 0.01	b : 0.01	
e : 0.20	= : 0.19	] : 0.09	g : 0.08	c : 0.08	3 : 0.08	f : 0.06	i : 0.04	b : 0.04	d : 0.03	2 : 0.03	4 : 0.01	a : 0.01	
= : 0.19	e : 0.16	g : 0.12	c : 0.11	f : 0.08	] : 0.06	i : 0.04	2 : 0.04	a : 0.03	3 : 0.03	d : 0.03	b : 0.03	h : 0.01	4 : 0.01	
= : 0.20	g : 0.14	e : 0.14	c : 0.09	] : 0.08	i : 0.06	2 : 0.06	f : 0.06	h : 0.03	d : 0.03	4 : 0.01	[ : 0.01	3 : 0.01	a : 0.01	
= : 0.20	g : 0.14	e : 0.14	c : 0.09	f : 0.08	i : 0.06	] : 0.04	h : 0.03	4 : 0.03	3 : 0.03	d : 0.03	2 : 0.03	b : 0.03	a : 0.01	
= : 0.20	g : 0.12	e : 0.11	c : 0.09	f : 0.09	i : 0.06	] : 0.06	b : 0.04	3 : 0.04	h : 0.03	d : 0.03	4 : 0.03	a : 0.01	2 : 0.01	
= : 0.20	g : 0.14	c : 0.11	i : 0.08	3 : 0.08	f : 0.08	e : 0.08	2 : 0.04	] : 0.04	h : 0.03	4 : 0.03	b : 0.01	d : 0.01	a : 0.01	
= : 0.20	g : 0.16	3 : 0.09	c : 0.09	i : 0.08	f : 0.06	2 : 0.04	4 : 0.04	] : 0.04	e : 0.04	h : 0.03	d : 0.03	b : 0.03	
g : 0.17	= : 0.16	i : 0.11	c : 0.09	e : 0.08	3 : 0.08	f : 0.06	4 : 0.04	2 : 0.04	h : 0.03	d : 0.03	b : 0.03	: : 0.01	] : 0.01	
] : 0.12	g : 0.12	e : 0.11	i : 0.09	= : 0.09	2 : 0.08	4 : 0.06	f : 0.06	3 : 0.04	d : 0.04	c : 0.04	h : 0.03	: : 0.03	F : 0.01	
c : 0.12	g : 0.12	e : 0.11	d : 0.09	= : 0.09	f : 0.08	4 : 0.06	i : 0.06	2 : 0.04	: : 0.04	b : 0.03	a : 0.03	3 : 0.01	] : 0.01	F : 0.01	h : 0.01	
e : 0.17	c : 0.16	d : 0.11	g : 0.09	= : 0.08	f : 0.08	4 : 0.06	b : 0.06	i : 0.06	: : 0.03	3 : 0.03	] : 0.01	F : 0.01	
e : 0.20	c : 0.17	d : 0.12	g : 0.09	f : 0.08	= : 0.06	4 : 0.04	i : 0.04	F : 0.03	b : 0.03	^ : 0.01	a : 0.01	G : 0.01	2 : 0.01	3 : 0.01	
e : 0.17	] : 0.12	d : 0.12	f : 0.11	c : 0.09	g : 0.06	2 : 0.06	i : 0.04	4 : 0.03	F : 0.03	= : 0.03	^ : 0.01	G : 0.01	7 : 0.01	: : 0.01	3 : 0.01	

#score	756.6489080159015
#seq	62
#width	39
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000